Multiple sequence alignment - TraesCS6D01G219300

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 TraesCS6D01G219300 chr6D 100.000 4592 0 0 1 4592 309340366 309344957 0.000000e+00 8480.0
1 TraesCS6D01G219300 chr6D 94.755 877 35 10 3726 4592 449815434 449814559 0.000000e+00 1354.0
2 TraesCS6D01G219300 chr6B 92.981 2892 113 30 849 3722 476840889 476843708 0.000000e+00 4133.0
3 TraesCS6D01G219300 chr6B 90.667 675 35 8 3 655 476840105 476840773 0.000000e+00 872.0
4 TraesCS6D01G219300 chr6B 89.655 87 9 0 2820 2906 32333634 32333548 1.350000e-20 111.0
5 TraesCS6D01G219300 chr6A 90.132 2959 119 49 849 3722 446091612 446094482 0.000000e+00 3687.0
6 TraesCS6D01G219300 chr6A 90.469 640 30 5 23 633 446090839 446091476 0.000000e+00 815.0
7 TraesCS6D01G219300 chr6A 89.655 87 9 0 2820 2906 18703454 18703540 1.350000e-20 111.0
8 TraesCS6D01G219300 chr6A 95.000 40 2 0 750 789 446091545 446091584 3.840000e-06 63.9
9 TraesCS6D01G219300 chr1D 95.558 878 27 10 3726 4592 463250902 463250026 0.000000e+00 1395.0
10 TraesCS6D01G219300 chr4D 95.216 878 29 8 3726 4592 35123713 35124588 0.000000e+00 1376.0
11 TraesCS6D01G219300 chr4D 94.863 876 33 9 3726 4592 364025901 364026773 0.000000e+00 1358.0
12 TraesCS6D01G219300 chrUn 94.983 877 34 5 3725 4592 45208432 45207557 0.000000e+00 1367.0
13 TraesCS6D01G219300 chr5D 94.875 878 32 10 3725 4592 510946251 510945377 0.000000e+00 1360.0
14 TraesCS6D01G219300 chr7D 95.052 869 34 7 3732 4592 104758732 104757865 0.000000e+00 1358.0
15 TraesCS6D01G219300 chr2D 94.622 874 36 9 3727 4592 503850643 503849773 0.000000e+00 1343.0
16 TraesCS6D01G219300 chr2D 90.196 153 13 2 1539 1690 471896666 471896515 1.010000e-46 198.0
17 TraesCS6D01G219300 chr2D 89.610 154 15 1 1546 1698 471373148 471372995 1.300000e-45 195.0
18 TraesCS6D01G219300 chr2D 92.366 131 10 0 1556 1686 471450868 471450738 2.180000e-43 187.0
19 TraesCS6D01G219300 chr2D 85.211 142 19 2 1136 1276 471373628 471373488 1.330000e-30 145.0
20 TraesCS6D01G219300 chr2D 83.803 142 21 2 1136 1276 471451329 471451189 2.880000e-27 134.0
21 TraesCS6D01G219300 chr2D 84.536 97 15 0 2818 2914 471372056 471371960 3.780000e-16 97.1
22 TraesCS6D01G219300 chr3D 94.400 875 38 7 3727 4592 597182190 597183062 0.000000e+00 1334.0
23 TraesCS6D01G219300 chr2B 90.260 154 14 1 1546 1698 550997445 550997292 2.800000e-47 200.0
24 TraesCS6D01G219300 chr2B 89.610 154 15 1 1546 1698 550720281 550720128 1.300000e-45 195.0
25 TraesCS6D01G219300 chr2B 89.796 147 14 1 1546 1692 550512068 550511923 2.180000e-43 187.0
26 TraesCS6D01G219300 chr2B 85.211 142 19 2 1136 1276 550512562 550512422 1.330000e-30 145.0
27 TraesCS6D01G219300 chr2B 83.803 142 21 2 1136 1276 550720730 550720590 2.880000e-27 134.0
28 TraesCS6D01G219300 chr2B 83.803 142 21 2 1136 1276 550859182 550859042 2.880000e-27 134.0
29 TraesCS6D01G219300 chr2B 84.536 97 15 0 2818 2914 550510859 550510763 3.780000e-16 97.1
30 TraesCS6D01G219300 chr2B 84.536 97 15 0 2818 2914 550719331 550719235 3.780000e-16 97.1
31 TraesCS6D01G219300 chr2A 90.260 154 14 1 1546 1698 613274643 613274490 2.800000e-47 200.0
32 TraesCS6D01G219300 chr2A 85.211 142 19 2 1136 1276 613038794 613038654 1.330000e-30 145.0
33 TraesCS6D01G219300 chr2A 84.507 142 20 2 1136 1276 613175773 613175633 6.200000e-29 139.0
34 TraesCS6D01G219300 chr2A 73.641 368 54 30 2818 3174 613037363 613037028 8.130000e-18 102.0
35 TraesCS6D01G219300 chr2A 85.567 97 14 0 2818 2914 613174190 613174094 8.130000e-18 102.0


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 TraesCS6D01G219300 chr6D 309340366 309344957 4591 False 8480.000000 8480 100.000 1 4592 1 chr6D.!!$F1 4591
1 TraesCS6D01G219300 chr6D 449814559 449815434 875 True 1354.000000 1354 94.755 3726 4592 1 chr6D.!!$R1 866
2 TraesCS6D01G219300 chr6B 476840105 476843708 3603 False 2502.500000 4133 91.824 3 3722 2 chr6B.!!$F1 3719
3 TraesCS6D01G219300 chr6A 446090839 446094482 3643 False 1521.966667 3687 91.867 23 3722 3 chr6A.!!$F2 3699
4 TraesCS6D01G219300 chr1D 463250026 463250902 876 True 1395.000000 1395 95.558 3726 4592 1 chr1D.!!$R1 866
5 TraesCS6D01G219300 chr4D 35123713 35124588 875 False 1376.000000 1376 95.216 3726 4592 1 chr4D.!!$F1 866
6 TraesCS6D01G219300 chr4D 364025901 364026773 872 False 1358.000000 1358 94.863 3726 4592 1 chr4D.!!$F2 866
7 TraesCS6D01G219300 chrUn 45207557 45208432 875 True 1367.000000 1367 94.983 3725 4592 1 chrUn.!!$R1 867
8 TraesCS6D01G219300 chr5D 510945377 510946251 874 True 1360.000000 1360 94.875 3725 4592 1 chr5D.!!$R1 867
9 TraesCS6D01G219300 chr7D 104757865 104758732 867 True 1358.000000 1358 95.052 3732 4592 1 chr7D.!!$R1 860
10 TraesCS6D01G219300 chr2D 503849773 503850643 870 True 1343.000000 1343 94.622 3727 4592 1 chr2D.!!$R2 865
11 TraesCS6D01G219300 chr3D 597182190 597183062 872 False 1334.000000 1334 94.400 3727 4592 1 chr3D.!!$F1 865

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
655 708 0.658897 CGCACCACAAACGTAAACCT 59.341 50.0 0.0 0.0 0.00 3.50 F
1700 1784 0.816825 AAGCAGTCCAGCACACACTG 60.817 55.0 0.0 0.0 40.53 3.66 F
2730 2871 0.106149 ACCGACAGAAACCGAAGCTT 59.894 50.0 0.0 0.0 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1884 0.394216 AAACATGGCAGCGGCATCTA 60.394 50.000 11.88 0.0 45.69 1.98 R
3136 3299 0.109532 TGCGAACATCACCTTGGGAA 59.890 50.000 0.00 0.0 0.00 3.97 R
3722 3907 1.067582 CACTTATCGGGCGTCCTCC 59.932 63.158 3.66 0.0 0.00 4.30 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
58 62 6.599244 TCAAGTTTGACACTTTCAACTCTCAT 59.401 34.615 0.00 0.00 43.89 2.90
59 63 6.610741 AGTTTGACACTTTCAACTCTCATC 57.389 37.500 0.00 0.00 44.28 2.92
60 64 6.115446 AGTTTGACACTTTCAACTCTCATCA 58.885 36.000 0.00 0.00 44.28 3.07
163 192 4.952957 TGATAGATAGATAGTGCCTGCTCC 59.047 45.833 0.00 0.00 0.00 4.70
209 238 5.165961 TGGCTTCTATTACAAGCAAGTCT 57.834 39.130 6.74 0.00 46.94 3.24
272 304 2.200373 TTGCTTTCTAGACCCTTGCC 57.800 50.000 0.00 0.00 0.00 4.52
375 426 3.270877 ACCGTTTGATATCTGCCACTTC 58.729 45.455 3.98 0.00 0.00 3.01
381 432 0.759346 ATATCTGCCACTTCCGACCC 59.241 55.000 0.00 0.00 0.00 4.46
559 612 6.036735 CAGCTGGCCTTGATTTTGATTAATTG 59.963 38.462 5.57 0.00 0.00 2.32
607 660 6.479972 TCTTTAAAACCTCACTCTCTCACA 57.520 37.500 0.00 0.00 0.00 3.58
613 666 2.824936 ACCTCACTCTCTCACACTCATG 59.175 50.000 0.00 0.00 0.00 3.07
619 672 6.625362 TCACTCTCTCACACTCATGTATTTC 58.375 40.000 0.00 0.00 36.72 2.17
647 700 8.850454 ATTTCAATAATATACGCACCACAAAC 57.150 30.769 0.00 0.00 0.00 2.93
655 708 0.658897 CGCACCACAAACGTAAACCT 59.341 50.000 0.00 0.00 0.00 3.50
658 711 2.796735 GCACCACAAACGTAAACCTTGG 60.797 50.000 0.00 0.00 0.00 3.61
659 712 2.025898 ACCACAAACGTAAACCTTGGG 58.974 47.619 0.00 0.00 0.00 4.12
660 713 1.338655 CCACAAACGTAAACCTTGGGG 59.661 52.381 3.90 3.90 37.29 4.96
661 714 2.299521 CACAAACGTAAACCTTGGGGA 58.700 47.619 0.00 0.00 36.25 4.81
662 715 2.688958 CACAAACGTAAACCTTGGGGAA 59.311 45.455 0.00 0.00 36.25 3.97
663 716 3.130693 CACAAACGTAAACCTTGGGGAAA 59.869 43.478 0.00 0.00 36.25 3.13
664 717 3.768215 ACAAACGTAAACCTTGGGGAAAA 59.232 39.130 0.00 0.00 36.25 2.29
665 718 4.406326 ACAAACGTAAACCTTGGGGAAAAT 59.594 37.500 0.00 0.00 36.25 1.82
666 719 5.597594 ACAAACGTAAACCTTGGGGAAAATA 59.402 36.000 0.00 0.00 36.25 1.40
667 720 6.268158 ACAAACGTAAACCTTGGGGAAAATAT 59.732 34.615 0.00 0.00 36.25 1.28
668 721 6.519679 AACGTAAACCTTGGGGAAAATATC 57.480 37.500 0.00 0.00 36.25 1.63
669 722 5.572252 ACGTAAACCTTGGGGAAAATATCA 58.428 37.500 0.00 0.00 36.25 2.15
670 723 5.650703 ACGTAAACCTTGGGGAAAATATCAG 59.349 40.000 0.00 0.00 36.25 2.90
671 724 5.883673 CGTAAACCTTGGGGAAAATATCAGA 59.116 40.000 0.00 0.00 36.25 3.27
672 725 6.038271 CGTAAACCTTGGGGAAAATATCAGAG 59.962 42.308 0.00 0.00 36.25 3.35
673 726 5.536497 AACCTTGGGGAAAATATCAGAGT 57.464 39.130 0.00 0.00 36.25 3.24
674 727 6.652205 AACCTTGGGGAAAATATCAGAGTA 57.348 37.500 0.00 0.00 36.25 2.59
675 728 6.848562 ACCTTGGGGAAAATATCAGAGTAT 57.151 37.500 0.00 0.00 36.25 2.12
676 729 7.947782 ACCTTGGGGAAAATATCAGAGTATA 57.052 36.000 0.00 0.00 36.25 1.47
677 730 7.978925 ACCTTGGGGAAAATATCAGAGTATAG 58.021 38.462 0.00 0.00 36.25 1.31
678 731 7.794683 ACCTTGGGGAAAATATCAGAGTATAGA 59.205 37.037 0.00 0.00 36.25 1.98
679 732 8.660435 CCTTGGGGAAAATATCAGAGTATAGAA 58.340 37.037 0.00 0.00 33.58 2.10
719 772 7.964604 AGAACGCATTAGACTTAACTTTTCT 57.035 32.000 0.00 0.00 0.00 2.52
720 773 8.379457 AGAACGCATTAGACTTAACTTTTCTT 57.621 30.769 0.00 0.00 0.00 2.52
738 791 4.994907 TCTTAGTAGAACGCATTAGCCA 57.005 40.909 0.00 0.00 37.52 4.75
739 792 5.531122 TCTTAGTAGAACGCATTAGCCAT 57.469 39.130 0.00 0.00 37.52 4.40
741 794 2.743938 AGTAGAACGCATTAGCCATCG 58.256 47.619 0.00 0.00 37.52 3.84
743 796 1.290203 AGAACGCATTAGCCATCGTG 58.710 50.000 0.00 0.00 37.52 4.35
748 801 0.947244 GCATTAGCCATCGTGAAGGG 59.053 55.000 0.00 0.00 33.58 3.95
755 816 2.158900 AGCCATCGTGAAGGGATTACAG 60.159 50.000 0.00 0.00 0.00 2.74
758 819 4.621991 CCATCGTGAAGGGATTACAGTAG 58.378 47.826 0.00 0.00 0.00 2.57
791 852 3.558505 CGGCAATTGCAGTAGATTATGC 58.441 45.455 30.32 8.60 44.36 3.14
794 855 5.615544 CGGCAATTGCAGTAGATTATGCTAC 60.616 44.000 30.32 7.36 42.98 3.58
797 861 7.119699 GGCAATTGCAGTAGATTATGCTACATA 59.880 37.037 30.32 0.00 42.98 2.29
814 878 8.800370 TGCTACATAATTCCTATTGTTCACAA 57.200 30.769 0.00 0.00 40.51 3.33
823 887 9.590451 AATTCCTATTGTTCACAATTATTGCTG 57.410 29.630 10.38 3.44 43.48 4.41
824 888 7.099266 TCCTATTGTTCACAATTATTGCTGG 57.901 36.000 10.38 0.00 43.48 4.85
825 889 6.663093 TCCTATTGTTCACAATTATTGCTGGT 59.337 34.615 10.38 0.00 43.48 4.00
826 890 7.178274 TCCTATTGTTCACAATTATTGCTGGTT 59.822 33.333 10.38 0.00 43.48 3.67
827 891 7.818930 CCTATTGTTCACAATTATTGCTGGTTT 59.181 33.333 10.38 0.00 43.48 3.27
828 892 7.656707 ATTGTTCACAATTATTGCTGGTTTC 57.343 32.000 4.68 0.00 43.48 2.78
829 893 6.154203 TGTTCACAATTATTGCTGGTTTCA 57.846 33.333 4.68 0.00 0.00 2.69
830 894 5.982516 TGTTCACAATTATTGCTGGTTTCAC 59.017 36.000 4.68 0.00 0.00 3.18
831 895 6.183360 TGTTCACAATTATTGCTGGTTTCACT 60.183 34.615 4.68 0.00 0.00 3.41
832 896 7.013750 TGTTCACAATTATTGCTGGTTTCACTA 59.986 33.333 4.68 0.00 0.00 2.74
833 897 7.701539 TCACAATTATTGCTGGTTTCACTAT 57.298 32.000 4.68 0.00 0.00 2.12
834 898 8.121305 TCACAATTATTGCTGGTTTCACTATT 57.879 30.769 4.68 0.00 0.00 1.73
835 899 8.584157 TCACAATTATTGCTGGTTTCACTATTT 58.416 29.630 4.68 0.00 0.00 1.40
836 900 8.649841 CACAATTATTGCTGGTTTCACTATTTG 58.350 33.333 4.68 0.00 0.00 2.32
837 901 7.331687 ACAATTATTGCTGGTTTCACTATTTGC 59.668 33.333 4.68 0.00 0.00 3.68
838 902 6.588719 TTATTGCTGGTTTCACTATTTGCT 57.411 33.333 0.00 0.00 0.00 3.91
839 903 4.935352 TTGCTGGTTTCACTATTTGCTT 57.065 36.364 0.00 0.00 0.00 3.91
840 904 6.588719 ATTGCTGGTTTCACTATTTGCTTA 57.411 33.333 0.00 0.00 0.00 3.09
841 905 6.398234 TTGCTGGTTTCACTATTTGCTTAA 57.602 33.333 0.00 0.00 0.00 1.85
842 906 5.768317 TGCTGGTTTCACTATTTGCTTAAC 58.232 37.500 0.00 0.00 0.00 2.01
843 907 5.161358 GCTGGTTTCACTATTTGCTTAACC 58.839 41.667 0.00 0.00 34.21 2.85
844 908 5.278758 GCTGGTTTCACTATTTGCTTAACCA 60.279 40.000 0.00 0.00 37.97 3.67
845 909 6.716934 TGGTTTCACTATTTGCTTAACCAA 57.283 33.333 0.00 0.00 37.65 3.67
846 910 7.113658 TGGTTTCACTATTTGCTTAACCAAA 57.886 32.000 0.00 0.00 37.65 3.28
847 911 7.556844 TGGTTTCACTATTTGCTTAACCAAAA 58.443 30.769 0.00 0.00 37.65 2.44
1075 1149 4.880537 CGCCGCTGCCTCCTGTAG 62.881 72.222 0.00 0.00 0.00 2.74
1083 1157 1.003646 TGCCTCCTGTAGACCTCTCT 58.996 55.000 0.00 0.00 0.00 3.10
1297 1375 1.078848 GACCACCGCTCTTGCATCT 60.079 57.895 0.00 0.00 39.64 2.90
1343 1421 4.389374 GGGCATAATTGAGGAGAATTCGA 58.611 43.478 0.00 0.00 0.00 3.71
1358 1437 2.036958 TTCGATGCATTGGGTCGAAT 57.963 45.000 15.94 0.00 45.90 3.34
1362 1441 3.066380 CGATGCATTGGGTCGAATATCA 58.934 45.455 5.98 0.00 37.55 2.15
1370 1449 1.412710 GGGTCGAATATCAGGTGCTCA 59.587 52.381 0.00 0.00 0.00 4.26
1390 1469 2.186903 CACCTGTAATCGGCGCCT 59.813 61.111 26.68 8.66 0.00 5.52
1405 1484 1.281899 CGCCTCTCGACTGAATTTCC 58.718 55.000 0.00 0.00 41.67 3.13
1428 1507 4.742649 TCTCCGGCCAGCTCGTCT 62.743 66.667 2.24 0.00 0.00 4.18
1433 1512 1.880340 CGGCCAGCTCGTCTGAATC 60.880 63.158 2.24 0.00 45.72 2.52
1525 1604 4.394300 GGTTCTGACTTCTGACCATGATTG 59.606 45.833 0.00 0.00 0.00 2.67
1526 1605 5.240891 GTTCTGACTTCTGACCATGATTGA 58.759 41.667 0.00 0.00 0.00 2.57
1527 1606 5.488262 TCTGACTTCTGACCATGATTGAA 57.512 39.130 0.00 0.00 0.00 2.69
1528 1607 5.868454 TCTGACTTCTGACCATGATTGAAA 58.132 37.500 0.00 0.00 0.00 2.69
1529 1608 6.479006 TCTGACTTCTGACCATGATTGAAAT 58.521 36.000 0.00 0.00 0.00 2.17
1530 1609 6.944290 TCTGACTTCTGACCATGATTGAAATT 59.056 34.615 0.00 0.00 0.00 1.82
1531 1610 7.120285 TCTGACTTCTGACCATGATTGAAATTC 59.880 37.037 0.00 0.00 0.00 2.17
1532 1611 6.944290 TGACTTCTGACCATGATTGAAATTCT 59.056 34.615 0.00 0.00 0.00 2.40
1533 1612 7.094506 TGACTTCTGACCATGATTGAAATTCTG 60.095 37.037 0.00 0.00 0.00 3.02
1534 1613 5.571784 TCTGACCATGATTGAAATTCTGC 57.428 39.130 0.00 0.00 0.00 4.26
1535 1614 4.095334 TCTGACCATGATTGAAATTCTGCG 59.905 41.667 0.00 0.00 0.00 5.18
1536 1615 3.129113 TGACCATGATTGAAATTCTGCGG 59.871 43.478 0.00 0.00 0.00 5.69
1537 1616 3.091545 ACCATGATTGAAATTCTGCGGT 58.908 40.909 0.00 0.00 0.00 5.68
1538 1617 3.119388 ACCATGATTGAAATTCTGCGGTG 60.119 43.478 0.00 0.00 0.00 4.94
1539 1618 2.634982 TGATTGAAATTCTGCGGTGC 57.365 45.000 0.00 0.00 0.00 5.01
1540 1619 1.135717 TGATTGAAATTCTGCGGTGCG 60.136 47.619 0.00 0.00 0.00 5.34
1649 1728 1.000612 GGAGGAGGAGGAGACGGTT 59.999 63.158 0.00 0.00 0.00 4.44
1687 1766 1.512926 CTCGGCAACAAGTAAGCAGT 58.487 50.000 0.00 0.00 0.00 4.40
1700 1784 0.816825 AAGCAGTCCAGCACACACTG 60.817 55.000 0.00 0.00 40.53 3.66
1720 1804 7.002879 ACACTGTTTACCTACTTACTCTCTGA 58.997 38.462 0.00 0.00 0.00 3.27
1785 1883 3.004524 ACTTCTCCACGTTGTCTGTCTAC 59.995 47.826 0.00 0.00 0.00 2.59
1786 1884 2.860009 TCTCCACGTTGTCTGTCTACT 58.140 47.619 0.00 0.00 0.00 2.57
1787 1885 4.011966 TCTCCACGTTGTCTGTCTACTA 57.988 45.455 0.00 0.00 0.00 1.82
1887 1988 2.596346 TGGACGTGAAAGGTACCAGTA 58.404 47.619 15.94 0.00 33.73 2.74
1927 2038 3.905249 GGCAATCCCGTTCTGGAC 58.095 61.111 0.00 0.00 42.00 4.02
1946 2057 3.367025 GGACCACGTTAATTCGAGTGAAG 59.633 47.826 2.09 0.00 37.57 3.02
1947 2058 3.323243 ACCACGTTAATTCGAGTGAAGG 58.677 45.455 2.09 0.00 37.57 3.46
1948 2059 3.006110 ACCACGTTAATTCGAGTGAAGGA 59.994 43.478 4.86 0.00 37.57 3.36
1949 2060 3.991773 CCACGTTAATTCGAGTGAAGGAA 59.008 43.478 4.86 0.00 37.57 3.36
1950 2061 4.091509 CCACGTTAATTCGAGTGAAGGAAG 59.908 45.833 4.86 0.00 37.57 3.46
2091 2202 1.734655 TTTTCTCCTCTGTCTGCCCT 58.265 50.000 0.00 0.00 0.00 5.19
2126 2237 3.146066 TGATTACACCTGCTTTTCGCTT 58.854 40.909 0.00 0.00 40.11 4.68
2297 2412 9.357161 GAGTTTCTTTCTAGTATATCCTCTGGA 57.643 37.037 0.00 0.00 35.55 3.86
2443 2571 1.078426 ATCCCAACTGGCACGTAGC 60.078 57.895 0.00 0.00 44.65 3.58
2724 2865 3.110178 GCCGACCGACAGAAACCG 61.110 66.667 0.00 0.00 0.00 4.44
2725 2866 2.646719 CCGACCGACAGAAACCGA 59.353 61.111 0.00 0.00 0.00 4.69
2726 2867 1.007038 CCGACCGACAGAAACCGAA 60.007 57.895 0.00 0.00 0.00 4.30
2727 2868 1.007336 CCGACCGACAGAAACCGAAG 61.007 60.000 0.00 0.00 0.00 3.79
2728 2869 1.615107 CGACCGACAGAAACCGAAGC 61.615 60.000 0.00 0.00 0.00 3.86
2729 2870 0.319641 GACCGACAGAAACCGAAGCT 60.320 55.000 0.00 0.00 0.00 3.74
2730 2871 0.106149 ACCGACAGAAACCGAAGCTT 59.894 50.000 0.00 0.00 0.00 3.74
2731 2872 1.226746 CCGACAGAAACCGAAGCTTT 58.773 50.000 0.00 0.00 0.00 3.51
2732 2873 1.602377 CCGACAGAAACCGAAGCTTTT 59.398 47.619 0.00 0.00 0.00 2.27
2733 2874 2.032924 CCGACAGAAACCGAAGCTTTTT 59.967 45.455 0.00 0.00 0.00 1.94
2782 2943 3.470645 AAGTGAACCGCAAGTAACTCT 57.529 42.857 0.00 0.00 0.00 3.24
2783 2944 3.027974 AGTGAACCGCAAGTAACTCTC 57.972 47.619 0.00 0.00 0.00 3.20
2784 2945 2.628657 AGTGAACCGCAAGTAACTCTCT 59.371 45.455 0.00 0.00 0.00 3.10
2785 2946 2.731976 GTGAACCGCAAGTAACTCTCTG 59.268 50.000 0.00 0.00 0.00 3.35
3006 3169 1.276622 GAGCCAAGGGGAAGTCAGTA 58.723 55.000 0.00 0.00 35.59 2.74
3296 3459 3.402681 CAGGTCGATGGGCCACCT 61.403 66.667 9.28 8.25 41.52 4.00
3459 3625 0.683973 CTAGAGCATCGCCAAGGGAT 59.316 55.000 0.00 0.00 42.67 3.85
3463 3629 0.109342 AGCATCGCCAAGGGATAAGG 59.891 55.000 0.00 0.00 33.49 2.69
3595 3766 7.283807 AGCAATCAATTTGAGAGCATGTATACA 59.716 33.333 20.92 8.27 37.53 2.29
3729 3914 7.960262 AGTTAAGGGTTAATATTAGGAGGACG 58.040 38.462 0.00 0.00 0.00 4.79
3730 3915 4.886496 AGGGTTAATATTAGGAGGACGC 57.114 45.455 0.00 0.03 0.00 5.19
3764 3950 2.529643 TTGTGGGCGTTAGGGGGA 60.530 61.111 0.00 0.00 0.00 4.81
4050 4245 0.953471 CTTCGGTTGCCATGTCGGAA 60.953 55.000 0.00 0.00 36.56 4.30
4072 4267 2.504367 ACTACAGTTGTCATGGTTGCC 58.496 47.619 0.00 0.00 0.00 4.52
4132 4327 7.254727 GCAGTTGCCATGATTTCAAAACTTTAA 60.255 33.333 0.00 0.00 34.31 1.52
4225 4420 2.347731 GGGTAAAAGAGAGAGTTGCCG 58.652 52.381 0.00 0.00 0.00 5.69
4278 4473 6.350110 GCCATGTAAAAGAAAGAGTTGCCATA 60.350 38.462 0.00 0.00 0.00 2.74
4295 4490 0.930310 ATATGCTTACGTGCACGCTG 59.070 50.000 37.35 26.59 46.33 5.18
4410 4609 1.274167 CCTGCAGAAACACATGGCAAT 59.726 47.619 17.39 0.00 33.58 3.56
4481 4682 2.282462 CACACACCAGCCCCTTCC 60.282 66.667 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.293399 GGAACGGAACCATCATATTGGC 59.707 50.000 0.00 0.00 40.68 4.52
17 18 2.135933 CTTGACTGTTGGTCTCGGAAC 58.864 52.381 0.00 0.00 44.74 3.62
58 62 2.989909 ACAATCAACGCTCCATGATGA 58.010 42.857 0.00 0.00 36.44 2.92
59 63 6.732531 ATATACAATCAACGCTCCATGATG 57.267 37.500 0.00 0.00 36.44 3.07
60 64 6.536582 GCTATATACAATCAACGCTCCATGAT 59.463 38.462 0.00 0.00 37.88 2.45
209 238 5.630415 TTCCTTTGAACCAGAAAGAGAGA 57.370 39.130 0.00 0.00 33.01 3.10
272 304 1.234821 TGGCTTGGTTCTAAAGTGCG 58.765 50.000 0.00 0.00 0.00 5.34
366 417 3.691342 TCGGGTCGGAAGTGGCAG 61.691 66.667 0.00 0.00 0.00 4.85
403 454 6.762187 TCGTCTGGTGTATGTTTTTCAAACTA 59.238 34.615 1.33 0.00 0.00 2.24
477 528 5.770417 AGAGTACAAGTAGTGGAGAAAACG 58.230 41.667 0.00 0.00 0.00 3.60
633 686 2.223845 GGTTTACGTTTGTGGTGCGTAT 59.776 45.455 0.00 0.00 40.15 3.06
635 688 0.377905 GGTTTACGTTTGTGGTGCGT 59.622 50.000 0.00 0.00 41.86 5.24
638 691 2.223618 CCCAAGGTTTACGTTTGTGGTG 60.224 50.000 0.00 0.00 0.00 4.17
640 693 1.338655 CCCCAAGGTTTACGTTTGTGG 59.661 52.381 0.00 0.00 0.00 4.17
641 694 2.299521 TCCCCAAGGTTTACGTTTGTG 58.700 47.619 0.00 0.00 0.00 3.33
647 700 5.883673 TCTGATATTTTCCCCAAGGTTTACG 59.116 40.000 0.00 0.00 0.00 3.18
688 741 9.918630 AGTTAAGTCTAATGCGTTCTACTAAAA 57.081 29.630 0.00 0.00 0.00 1.52
689 742 9.918630 AAGTTAAGTCTAATGCGTTCTACTAAA 57.081 29.630 0.00 0.00 0.00 1.85
690 743 9.918630 AAAGTTAAGTCTAATGCGTTCTACTAA 57.081 29.630 0.00 0.00 0.00 2.24
691 744 9.918630 AAAAGTTAAGTCTAATGCGTTCTACTA 57.081 29.630 0.00 0.00 0.00 1.82
692 745 8.828688 AAAAGTTAAGTCTAATGCGTTCTACT 57.171 30.769 0.00 0.00 0.00 2.57
693 746 8.923683 AGAAAAGTTAAGTCTAATGCGTTCTAC 58.076 33.333 0.00 0.00 0.00 2.59
694 747 9.485206 AAGAAAAGTTAAGTCTAATGCGTTCTA 57.515 29.630 0.00 0.00 0.00 2.10
695 748 7.964604 AGAAAAGTTAAGTCTAATGCGTTCT 57.035 32.000 0.00 0.00 0.00 3.01
696 749 9.742552 CTAAGAAAAGTTAAGTCTAATGCGTTC 57.257 33.333 0.00 0.00 0.00 3.95
697 750 9.269453 ACTAAGAAAAGTTAAGTCTAATGCGTT 57.731 29.630 0.00 0.00 0.00 4.84
698 751 8.828688 ACTAAGAAAAGTTAAGTCTAATGCGT 57.171 30.769 0.00 0.00 0.00 5.24
704 757 9.617975 GCGTTCTACTAAGAAAAGTTAAGTCTA 57.382 33.333 0.00 0.00 43.30 2.59
705 758 8.139989 TGCGTTCTACTAAGAAAAGTTAAGTCT 58.860 33.333 0.00 0.00 43.30 3.24
706 759 8.290663 TGCGTTCTACTAAGAAAAGTTAAGTC 57.709 34.615 0.00 0.00 43.30 3.01
707 760 8.828688 ATGCGTTCTACTAAGAAAAGTTAAGT 57.171 30.769 0.00 0.00 43.30 2.24
710 763 8.866956 GCTAATGCGTTCTACTAAGAAAAGTTA 58.133 33.333 0.00 0.00 43.30 2.24
711 764 7.148457 GGCTAATGCGTTCTACTAAGAAAAGTT 60.148 37.037 0.00 0.00 38.48 2.66
713 766 6.312918 TGGCTAATGCGTTCTACTAAGAAAAG 59.687 38.462 0.00 0.00 38.48 2.27
719 772 4.202080 ACGATGGCTAATGCGTTCTACTAA 60.202 41.667 0.00 0.00 40.82 2.24
720 773 3.317149 ACGATGGCTAATGCGTTCTACTA 59.683 43.478 0.00 0.00 40.82 1.82
728 781 0.583438 CCTTCACGATGGCTAATGCG 59.417 55.000 0.00 0.00 40.82 4.73
738 791 5.934402 AACTACTGTAATCCCTTCACGAT 57.066 39.130 0.00 0.00 0.00 3.73
739 792 5.733620 AAACTACTGTAATCCCTTCACGA 57.266 39.130 0.00 0.00 0.00 4.35
741 794 7.981102 AGAAAAACTACTGTAATCCCTTCAC 57.019 36.000 0.00 0.00 0.00 3.18
743 796 9.163899 CCTAAGAAAAACTACTGTAATCCCTTC 57.836 37.037 0.00 0.00 0.00 3.46
748 801 6.456584 GCCGCCTAAGAAAAACTACTGTAATC 60.457 42.308 0.00 0.00 0.00 1.75
755 816 4.696899 ATTGCCGCCTAAGAAAAACTAC 57.303 40.909 0.00 0.00 0.00 2.73
758 819 2.411748 GCAATTGCCGCCTAAGAAAAAC 59.588 45.455 20.06 0.00 34.31 2.43
797 861 9.590451 CAGCAATAATTGTGAACAATAGGAATT 57.410 29.630 9.01 5.11 45.06 2.17
810 874 8.649841 CAAATAGTGAAACCAGCAATAATTGTG 58.350 33.333 0.00 0.00 37.80 3.33
814 878 7.174107 AGCAAATAGTGAAACCAGCAATAAT 57.826 32.000 0.00 0.00 37.80 1.28
817 881 5.473066 AAGCAAATAGTGAAACCAGCAAT 57.527 34.783 0.00 0.00 37.80 3.56
820 884 5.161358 GGTTAAGCAAATAGTGAAACCAGC 58.839 41.667 0.00 0.00 37.80 4.85
822 886 6.716934 TTGGTTAAGCAAATAGTGAAACCA 57.283 33.333 17.34 0.00 40.98 3.67
823 887 8.601845 ATTTTGGTTAAGCAAATAGTGAAACC 57.398 30.769 27.97 0.62 37.80 3.27
827 891 9.267084 GGAAAATTTTGGTTAAGCAAATAGTGA 57.733 29.630 27.97 16.27 0.00 3.41
828 892 9.271828 AGGAAAATTTTGGTTAAGCAAATAGTG 57.728 29.630 27.97 0.00 0.00 2.74
829 893 9.845740 AAGGAAAATTTTGGTTAAGCAAATAGT 57.154 25.926 27.97 17.19 0.00 2.12
832 896 9.407380 AGAAAGGAAAATTTTGGTTAAGCAAAT 57.593 25.926 27.97 16.38 0.00 2.32
833 897 8.800370 AGAAAGGAAAATTTTGGTTAAGCAAA 57.200 26.923 24.87 24.87 0.00 3.68
834 898 9.892130 TTAGAAAGGAAAATTTTGGTTAAGCAA 57.108 25.926 15.83 15.83 0.00 3.91
835 899 9.892130 TTTAGAAAGGAAAATTTTGGTTAAGCA 57.108 25.926 8.47 2.54 0.00 3.91
1061 1128 2.010582 GAGGTCTACAGGAGGCAGCG 62.011 65.000 0.00 0.00 0.00 5.18
1067 1134 2.930950 CCTCAGAGAGGTCTACAGGAG 58.069 57.143 0.00 0.00 44.25 3.69
1297 1375 0.320858 TTCGTGCCCGTAGAAATGCA 60.321 50.000 0.00 0.00 35.01 3.96
1309 1387 0.968393 TTATGCCCCCTTTTCGTGCC 60.968 55.000 0.00 0.00 0.00 5.01
1343 1421 3.181440 ACCTGATATTCGACCCAATGCAT 60.181 43.478 0.00 0.00 0.00 3.96
1370 1449 2.186903 CGCCGATTACAGGTGCCT 59.813 61.111 0.00 0.00 32.08 4.75
1377 1456 2.116533 TCGAGAGGCGCCGATTACA 61.117 57.895 23.20 1.25 40.61 2.41
1390 1469 5.013547 AGAGAGAAGGAAATTCAGTCGAGA 58.986 41.667 0.00 0.00 40.67 4.04
1405 1484 2.015227 GAGCTGGCCGGAGAGAGAAG 62.015 65.000 18.31 0.00 0.00 2.85
1525 1604 2.202479 GCCGCACCGCAGAATTTC 60.202 61.111 0.00 0.00 0.00 2.17
1526 1605 4.101790 CGCCGCACCGCAGAATTT 62.102 61.111 0.00 0.00 0.00 1.82
1649 1728 4.221422 GCGGCGTGGAGGCTCATA 62.221 66.667 17.69 1.26 44.22 2.15
1687 1766 1.488812 AGGTAAACAGTGTGTGCTGGA 59.511 47.619 0.00 0.00 40.59 3.86
1700 1784 7.884257 ACAGTTCAGAGAGTAAGTAGGTAAAC 58.116 38.462 0.00 0.00 0.00 2.01
1720 1804 5.699001 TCAATCATTTGCGTACAGTACAGTT 59.301 36.000 11.37 0.00 32.61 3.16
1785 1883 0.816825 AACATGGCAGCGGCATCTAG 60.817 55.000 11.88 5.45 45.69 2.43
1786 1884 0.394216 AAACATGGCAGCGGCATCTA 60.394 50.000 11.88 0.00 45.69 1.98
1787 1885 1.252904 AAAACATGGCAGCGGCATCT 61.253 50.000 11.88 0.00 45.69 2.90
1887 1988 0.839946 AGCCGAGCAGGGACAATTAT 59.160 50.000 0.00 0.00 41.48 1.28
1924 2035 2.950433 TCACTCGAATTAACGTGGTCC 58.050 47.619 0.00 0.00 34.70 4.46
1927 2038 3.581755 TCCTTCACTCGAATTAACGTGG 58.418 45.455 0.00 0.00 34.70 4.94
1946 2057 5.386060 TCTTTTCTTTCCTTCCTTCCTTCC 58.614 41.667 0.00 0.00 0.00 3.46
1947 2058 5.475220 CCTCTTTTCTTTCCTTCCTTCCTTC 59.525 44.000 0.00 0.00 0.00 3.46
1948 2059 5.389520 CCTCTTTTCTTTCCTTCCTTCCTT 58.610 41.667 0.00 0.00 0.00 3.36
1949 2060 4.202620 CCCTCTTTTCTTTCCTTCCTTCCT 60.203 45.833 0.00 0.00 0.00 3.36
1950 2061 4.082845 CCCTCTTTTCTTTCCTTCCTTCC 58.917 47.826 0.00 0.00 0.00 3.46
2077 2188 2.587247 GCACAGGGCAGACAGAGGA 61.587 63.158 0.00 0.00 43.97 3.71
2091 2202 4.082841 GGTGTAATCATCACAATGTGCACA 60.083 41.667 24.08 24.08 37.52 4.57
2270 2385 9.362151 CCAGAGGATATACTAGAAAGAAACTCT 57.638 37.037 0.00 0.00 0.00 3.24
2279 2394 7.014711 CAGCAACTTCCAGAGGATATACTAGAA 59.985 40.741 0.00 0.00 0.00 2.10
2297 2412 1.312815 GGTGTTCTCTGCAGCAACTT 58.687 50.000 21.90 0.00 34.80 2.66
2600 2735 4.908601 TTCTCCTTTTGTGGCTCAGATA 57.091 40.909 0.00 0.00 0.00 1.98
2601 2736 3.795688 TTCTCCTTTTGTGGCTCAGAT 57.204 42.857 0.00 0.00 0.00 2.90
2604 2739 3.897239 TCTTTTCTCCTTTTGTGGCTCA 58.103 40.909 0.00 0.00 0.00 4.26
2741 2882 7.012327 TCACTTAACTTTGGTTTCTGTCATCAG 59.988 37.037 0.00 0.00 38.54 2.90
2742 2883 6.826231 TCACTTAACTTTGGTTTCTGTCATCA 59.174 34.615 0.00 0.00 36.92 3.07
2743 2884 7.259290 TCACTTAACTTTGGTTTCTGTCATC 57.741 36.000 0.00 0.00 36.92 2.92
2744 2885 7.416326 GGTTCACTTAACTTTGGTTTCTGTCAT 60.416 37.037 0.00 0.00 38.23 3.06
2745 2886 6.127842 GGTTCACTTAACTTTGGTTTCTGTCA 60.128 38.462 0.00 0.00 38.23 3.58
2746 2887 6.263344 GGTTCACTTAACTTTGGTTTCTGTC 58.737 40.000 0.00 0.00 38.23 3.51
2747 2888 5.163693 CGGTTCACTTAACTTTGGTTTCTGT 60.164 40.000 0.00 0.00 38.23 3.41
2748 2889 5.270853 CGGTTCACTTAACTTTGGTTTCTG 58.729 41.667 0.00 0.00 38.23 3.02
2749 2890 4.201980 GCGGTTCACTTAACTTTGGTTTCT 60.202 41.667 0.00 0.00 38.23 2.52
2750 2891 4.039703 GCGGTTCACTTAACTTTGGTTTC 58.960 43.478 0.00 0.00 38.23 2.78
2782 2943 3.876914 CGTCAATAATTAAGCCAGCCAGA 59.123 43.478 0.00 0.00 0.00 3.86
2783 2944 3.548818 GCGTCAATAATTAAGCCAGCCAG 60.549 47.826 0.00 0.00 0.00 4.85
2784 2945 2.357637 GCGTCAATAATTAAGCCAGCCA 59.642 45.455 0.00 0.00 0.00 4.75
2785 2946 2.602217 CGCGTCAATAATTAAGCCAGCC 60.602 50.000 0.00 0.00 0.00 4.85
2992 3155 1.885163 CGCCGTACTGACTTCCCCTT 61.885 60.000 0.00 0.00 0.00 3.95
3135 3298 1.271871 TGCGAACATCACCTTGGGAAT 60.272 47.619 0.00 0.00 0.00 3.01
3136 3299 0.109532 TGCGAACATCACCTTGGGAA 59.890 50.000 0.00 0.00 0.00 3.97
3511 3677 0.596082 AGCATTACAAACGCGCCTTT 59.404 45.000 5.73 0.00 0.00 3.11
3583 3754 3.249320 CACATGCACCTGTATACATGCTC 59.751 47.826 24.59 11.27 42.88 4.26
3722 3907 1.067582 CACTTATCGGGCGTCCTCC 59.932 63.158 3.66 0.00 0.00 4.30
3723 3908 1.591863 GCACTTATCGGGCGTCCTC 60.592 63.158 3.66 0.00 0.00 3.71
3724 3909 2.499685 GCACTTATCGGGCGTCCT 59.500 61.111 3.66 0.00 0.00 3.85
3725 3910 2.588034 GGCACTTATCGGGCGTCC 60.588 66.667 0.00 0.00 0.00 4.79
3726 3911 2.171725 GTGGCACTTATCGGGCGTC 61.172 63.158 11.13 0.00 0.00 5.19
3727 3912 2.125269 GTGGCACTTATCGGGCGT 60.125 61.111 11.13 0.00 0.00 5.68
3728 3913 2.125310 TGTGGCACTTATCGGGCG 60.125 61.111 19.83 0.00 0.00 6.13
3729 3914 1.078426 AGTGTGGCACTTATCGGGC 60.078 57.895 19.83 0.00 42.59 6.13
3747 3932 2.529643 TCCCCCTAACGCCCACAA 60.530 61.111 0.00 0.00 0.00 3.33
3851 4046 1.812686 CGTGTGAGAGGGGTCGGAAA 61.813 60.000 0.00 0.00 0.00 3.13
3853 4048 2.675423 CGTGTGAGAGGGGTCGGA 60.675 66.667 0.00 0.00 0.00 4.55
3912 4107 1.749638 CGAGGTACGAGGCCTGACT 60.750 63.158 12.00 0.00 45.77 3.41
4050 4245 3.317993 GGCAACCATGACAACTGTAGTTT 59.682 43.478 0.00 0.00 35.83 2.66
4132 4327 1.493022 TGTTTAGTGGGTGGCAACTCT 59.507 47.619 0.97 4.22 37.61 3.24
4410 4609 2.523902 CCCACCCAAAGCTGGCAA 60.524 61.111 0.00 0.00 41.99 4.52
4478 4679 1.279527 CTAGTTTCACGCACGCGGAA 61.280 55.000 16.70 12.85 44.69 4.30
4481 4682 1.127817 CACTAGTTTCACGCACGCG 59.872 57.895 10.36 10.36 46.03 6.01


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

AutoCloner maintained by Alex Coulton.