Multiple sequence alignment - TraesCS7A01G519000

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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 TraesCS7A01G519000 chr7A 100.000 3199 0 0 1 3199 703532722 703535920 0.000000e+00 5908
1 TraesCS7A01G519000 chr7A 97.333 975 23 3 2226 3199 703541760 703542732 0.000000e+00 1653
2 TraesCS7A01G519000 chr7A 96.821 975 28 3 2226 3199 29923869 29922897 0.000000e+00 1626
3 TraesCS7A01G519000 chr7A 86.548 617 54 23 1 600 106674479 106673875 0.000000e+00 652
4 TraesCS7A01G519000 chr7A 95.238 84 4 0 2145 2228 703543493 703543576 2.000000e-27 134
5 TraesCS7A01G519000 chr5A 95.376 1449 66 1 781 2228 477828053 477829501 0.000000e+00 2303
6 TraesCS7A01G519000 chr5A 97.533 973 23 1 2227 3199 658922535 658921564 0.000000e+00 1663
7 TraesCS7A01G519000 chr5A 97.328 973 25 1 2227 3199 658915549 658914578 0.000000e+00 1652
8 TraesCS7A01G519000 chr5A 96.633 980 28 2 2224 3199 54513426 54512448 0.000000e+00 1622
9 TraesCS7A01G519000 chr5A 95.683 139 5 1 742 880 477833199 477833062 4.150000e-54 222
10 TraesCS7A01G519000 chr5A 96.970 99 3 0 2130 2228 477829480 477829578 1.970000e-37 167
11 TraesCS7A01G519000 chr3A 93.061 1470 88 13 742 2206 697017807 697019267 0.000000e+00 2137
12 TraesCS7A01G519000 chr3A 96.830 978 26 4 2227 3199 630775987 630776964 0.000000e+00 1629
13 TraesCS7A01G519000 chr3A 96.817 974 28 3 2227 3199 25779813 25778842 0.000000e+00 1624
14 TraesCS7A01G519000 chr3A 96.821 975 26 5 2227 3199 542336386 542335415 0.000000e+00 1624
15 TraesCS7A01G519000 chr3A 94.406 143 8 0 742 884 697023952 697023810 1.490000e-53 220
16 TraesCS7A01G519000 chr1A 97.026 975 26 3 2227 3199 556075579 556074606 0.000000e+00 1637
17 TraesCS7A01G519000 chr2B 87.712 1359 129 21 875 2206 151459865 151458518 0.000000e+00 1550
18 TraesCS7A01G519000 chr2B 91.263 950 58 10 1280 2206 106839067 106840014 0.000000e+00 1271
19 TraesCS7A01G519000 chr2B 91.193 545 44 3 742 1285 106829873 106830414 0.000000e+00 737
20 TraesCS7A01G519000 chr2B 94.964 139 7 0 742 880 106859961 106859823 5.370000e-53 219
21 TraesCS7A01G519000 chr2B 91.367 139 12 0 742 880 151460041 151459903 1.170000e-44 191
22 TraesCS7A01G519000 chr6D 93.410 607 38 2 1 606 22109224 22108619 0.000000e+00 898
23 TraesCS7A01G519000 chr6B 93.311 598 39 1 3 599 245047288 245047885 0.000000e+00 881
24 TraesCS7A01G519000 chr6B 94.681 188 10 0 1 188 76745436 76745623 3.120000e-75 292
25 TraesCS7A01G519000 chr4A 91.681 601 48 2 1 600 637128531 637129130 0.000000e+00 832
26 TraesCS7A01G519000 chr4A 86.623 613 53 22 1 596 609314194 609313594 0.000000e+00 651
27 TraesCS7A01G519000 chr2A 90.566 530 45 4 8 534 605389896 605389369 0.000000e+00 697
28 TraesCS7A01G519000 chr2A 95.105 143 7 0 742 884 773233647 773233789 3.210000e-55 226
29 TraesCS7A01G519000 chr2A 95.105 143 7 0 742 884 773263214 773263072 3.210000e-55 226
30 TraesCS7A01G519000 chr3B 86.872 617 51 23 1 599 46031116 46031720 0.000000e+00 664
31 TraesCS7A01G519000 chr3B 86.179 615 57 22 1 599 68202142 68201540 9.680000e-180 640
32 TraesCS7A01G519000 chr7B 86.710 617 52 23 1 599 733044965 733045569 0.000000e+00 658
33 TraesCS7A01G519000 chr6A 88.445 476 41 7 1 474 8799320 8799783 2.150000e-156 562
34 TraesCS7A01G519000 chrUn 94.650 243 12 1 1 242 79943707 79943949 3.010000e-100 375
35 TraesCS7A01G519000 chrUn 93.416 243 15 1 1 242 108796743 108796985 3.030000e-95 359
36 TraesCS7A01G519000 chr1D 93.416 243 15 1 1 242 4248383 4248141 3.030000e-95 359
37 TraesCS7A01G519000 chr7D 94.483 145 8 0 600 744 612707816 612707960 1.150000e-54 224


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 TraesCS7A01G519000 chr7A 703532722 703535920 3198 False 5908.0 5908 100.0000 1 3199 1 chr7A.!!$F1 3198
1 TraesCS7A01G519000 chr7A 29922897 29923869 972 True 1626.0 1626 96.8210 2226 3199 1 chr7A.!!$R1 973
2 TraesCS7A01G519000 chr7A 703541760 703543576 1816 False 893.5 1653 96.2855 2145 3199 2 chr7A.!!$F2 1054
3 TraesCS7A01G519000 chr7A 106673875 106674479 604 True 652.0 652 86.5480 1 600 1 chr7A.!!$R2 599
4 TraesCS7A01G519000 chr5A 658921564 658922535 971 True 1663.0 1663 97.5330 2227 3199 1 chr5A.!!$R4 972
5 TraesCS7A01G519000 chr5A 658914578 658915549 971 True 1652.0 1652 97.3280 2227 3199 1 chr5A.!!$R3 972
6 TraesCS7A01G519000 chr5A 54512448 54513426 978 True 1622.0 1622 96.6330 2224 3199 1 chr5A.!!$R1 975
7 TraesCS7A01G519000 chr5A 477828053 477829578 1525 False 1235.0 2303 96.1730 781 2228 2 chr5A.!!$F1 1447
8 TraesCS7A01G519000 chr3A 697017807 697019267 1460 False 2137.0 2137 93.0610 742 2206 1 chr3A.!!$F2 1464
9 TraesCS7A01G519000 chr3A 630775987 630776964 977 False 1629.0 1629 96.8300 2227 3199 1 chr3A.!!$F1 972
10 TraesCS7A01G519000 chr3A 25778842 25779813 971 True 1624.0 1624 96.8170 2227 3199 1 chr3A.!!$R1 972
11 TraesCS7A01G519000 chr3A 542335415 542336386 971 True 1624.0 1624 96.8210 2227 3199 1 chr3A.!!$R2 972
12 TraesCS7A01G519000 chr1A 556074606 556075579 973 True 1637.0 1637 97.0260 2227 3199 1 chr1A.!!$R1 972
13 TraesCS7A01G519000 chr2B 106839067 106840014 947 False 1271.0 1271 91.2630 1280 2206 1 chr2B.!!$F2 926
14 TraesCS7A01G519000 chr2B 151458518 151460041 1523 True 870.5 1550 89.5395 742 2206 2 chr2B.!!$R2 1464
15 TraesCS7A01G519000 chr2B 106829873 106830414 541 False 737.0 737 91.1930 742 1285 1 chr2B.!!$F1 543
16 TraesCS7A01G519000 chr6D 22108619 22109224 605 True 898.0 898 93.4100 1 606 1 chr6D.!!$R1 605
17 TraesCS7A01G519000 chr6B 245047288 245047885 597 False 881.0 881 93.3110 3 599 1 chr6B.!!$F2 596
18 TraesCS7A01G519000 chr4A 637128531 637129130 599 False 832.0 832 91.6810 1 600 1 chr4A.!!$F1 599
19 TraesCS7A01G519000 chr4A 609313594 609314194 600 True 651.0 651 86.6230 1 596 1 chr4A.!!$R1 595
20 TraesCS7A01G519000 chr2A 605389369 605389896 527 True 697.0 697 90.5660 8 534 1 chr2A.!!$R1 526
21 TraesCS7A01G519000 chr3B 46031116 46031720 604 False 664.0 664 86.8720 1 599 1 chr3B.!!$F1 598
22 TraesCS7A01G519000 chr3B 68201540 68202142 602 True 640.0 640 86.1790 1 599 1 chr3B.!!$R1 598
23 TraesCS7A01G519000 chr7B 733044965 733045569 604 False 658.0 658 86.7100 1 599 1 chr7B.!!$F1 598

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
617 653 0.112606 AGTGGAGAAGGTCTCGTGGA 59.887 55.0 0.0 0.0 44.28 4.02 F
689 725 0.171455 GCAGGTGACTCTACAGACGG 59.829 60.0 0.0 0.0 40.21 4.79 F
690 726 0.171455 CAGGTGACTCTACAGACGGC 59.829 60.0 0.0 0.0 40.21 5.68 F
692 728 0.171455 GGTGACTCTACAGACGGCAG 59.829 60.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1637 0.320771 ACCACACGAGTGCAATCCTC 60.321 55.000 8.83 0.26 44.53 3.71 R
1778 1862 0.825010 CAAGGCAGCACCCTCTTGTT 60.825 55.000 0.00 0.00 40.58 2.83 R
2006 2090 2.683211 AACTCATCAGGCAACCCTTT 57.317 45.000 0.00 0.00 40.33 3.11 R
2318 2427 2.874780 CGTAGTCGGTCTGCGTGC 60.875 66.667 4.78 0.00 44.80 5.34 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
30 31 0.245813 GTCCGGTTAAAGCTCGGTCT 59.754 55.000 10.26 0.00 43.75 3.85
31 32 1.474077 GTCCGGTTAAAGCTCGGTCTA 59.526 52.381 10.26 0.00 43.75 2.59
179 214 4.408821 TGCGCCGCCATCTTCCTT 62.409 61.111 6.63 0.00 0.00 3.36
199 234 2.685380 CTTCCTCTCCCCGGCACT 60.685 66.667 0.00 0.00 0.00 4.40
200 235 3.003173 TTCCTCTCCCCGGCACTG 61.003 66.667 0.00 0.00 0.00 3.66
228 263 2.829003 CCGCGCCTCTACCTCTCA 60.829 66.667 0.00 0.00 0.00 3.27
335 370 4.803426 CCTTTCTCTCGCGCCGCT 62.803 66.667 7.78 0.00 0.00 5.52
428 463 0.250424 CACATGGCAGTGACTGGACA 60.250 55.000 15.24 3.83 42.05 4.02
430 465 1.908619 ACATGGCAGTGACTGGACATA 59.091 47.619 15.24 0.00 31.21 2.29
490 525 2.044650 CAGTCGGTCCGGTCCCTA 60.045 66.667 12.29 0.00 0.00 3.53
523 558 2.936912 GCACAGCTCGGTCTGGTCT 61.937 63.158 9.11 0.00 38.36 3.85
577 613 2.283676 GGACAGGGACCAGACCGA 60.284 66.667 0.00 0.00 0.00 4.69
609 645 2.765352 CACCCTGAGTGGAGAAGGT 58.235 57.895 0.00 0.00 43.26 3.50
610 646 0.610687 CACCCTGAGTGGAGAAGGTC 59.389 60.000 0.00 0.00 43.26 3.85
611 647 0.489567 ACCCTGAGTGGAGAAGGTCT 59.510 55.000 0.00 0.00 38.35 3.85
612 648 1.190643 CCCTGAGTGGAGAAGGTCTC 58.809 60.000 0.00 0.00 42.66 3.36
613 649 0.814457 CCTGAGTGGAGAAGGTCTCG 59.186 60.000 0.00 0.00 44.28 4.04
614 650 1.540267 CTGAGTGGAGAAGGTCTCGT 58.460 55.000 0.00 0.00 44.28 4.18
615 651 1.201181 CTGAGTGGAGAAGGTCTCGTG 59.799 57.143 0.00 0.00 44.28 4.35
616 652 0.528470 GAGTGGAGAAGGTCTCGTGG 59.472 60.000 0.00 0.00 44.28 4.94
617 653 0.112606 AGTGGAGAAGGTCTCGTGGA 59.887 55.000 0.00 0.00 44.28 4.02
618 654 0.966920 GTGGAGAAGGTCTCGTGGAA 59.033 55.000 0.00 0.00 44.28 3.53
619 655 1.343465 GTGGAGAAGGTCTCGTGGAAA 59.657 52.381 0.00 0.00 44.28 3.13
620 656 2.028020 GTGGAGAAGGTCTCGTGGAAAT 60.028 50.000 0.00 0.00 44.28 2.17
621 657 2.028112 TGGAGAAGGTCTCGTGGAAATG 60.028 50.000 0.00 0.00 44.28 2.32
622 658 2.003301 GAGAAGGTCTCGTGGAAATGC 58.997 52.381 0.00 0.00 33.35 3.56
623 659 1.625818 AGAAGGTCTCGTGGAAATGCT 59.374 47.619 0.00 0.00 0.00 3.79
624 660 1.734465 GAAGGTCTCGTGGAAATGCTG 59.266 52.381 0.00 0.00 0.00 4.41
625 661 0.674895 AGGTCTCGTGGAAATGCTGC 60.675 55.000 0.00 0.00 0.00 5.25
626 662 0.674895 GGTCTCGTGGAAATGCTGCT 60.675 55.000 0.00 0.00 0.00 4.24
627 663 1.405526 GGTCTCGTGGAAATGCTGCTA 60.406 52.381 0.00 0.00 0.00 3.49
628 664 2.555199 GTCTCGTGGAAATGCTGCTAT 58.445 47.619 0.00 0.00 0.00 2.97
629 665 2.939103 GTCTCGTGGAAATGCTGCTATT 59.061 45.455 0.00 0.00 0.00 1.73
630 666 3.001736 GTCTCGTGGAAATGCTGCTATTC 59.998 47.826 0.00 5.38 0.00 1.75
631 667 2.288666 TCGTGGAAATGCTGCTATTCC 58.711 47.619 22.06 22.06 42.39 3.01
632 668 2.092968 TCGTGGAAATGCTGCTATTCCT 60.093 45.455 26.04 4.47 42.50 3.36
633 669 3.133901 TCGTGGAAATGCTGCTATTCCTA 59.866 43.478 26.04 15.84 42.50 2.94
634 670 4.067896 CGTGGAAATGCTGCTATTCCTAT 58.932 43.478 26.04 0.59 42.50 2.57
635 671 4.083643 CGTGGAAATGCTGCTATTCCTATG 60.084 45.833 26.04 17.84 42.50 2.23
636 672 4.217118 GTGGAAATGCTGCTATTCCTATGG 59.783 45.833 26.04 0.00 42.50 2.74
637 673 3.760684 GGAAATGCTGCTATTCCTATGGG 59.239 47.826 21.76 0.00 39.60 4.00
638 674 4.507335 GGAAATGCTGCTATTCCTATGGGA 60.507 45.833 21.76 0.00 39.60 4.37
639 675 4.942363 AATGCTGCTATTCCTATGGGAT 57.058 40.909 0.00 0.00 41.87 3.85
640 676 3.708403 TGCTGCTATTCCTATGGGATG 57.292 47.619 0.00 0.00 41.87 3.51
641 677 2.290514 TGCTGCTATTCCTATGGGATGC 60.291 50.000 0.00 5.05 41.87 3.91
642 678 2.290514 GCTGCTATTCCTATGGGATGCA 60.291 50.000 16.04 16.04 41.87 3.96
643 679 3.624205 GCTGCTATTCCTATGGGATGCAT 60.624 47.826 16.85 0.00 41.87 3.96
644 680 3.945921 CTGCTATTCCTATGGGATGCATG 59.054 47.826 16.85 10.22 41.87 4.06
645 681 2.686915 GCTATTCCTATGGGATGCATGC 59.313 50.000 11.82 11.82 41.87 4.06
646 682 3.624205 GCTATTCCTATGGGATGCATGCT 60.624 47.826 20.33 4.11 41.87 3.79
647 683 2.281539 TTCCTATGGGATGCATGCTG 57.718 50.000 20.33 6.18 41.87 4.41
648 684 1.142936 TCCTATGGGATGCATGCTGT 58.857 50.000 20.33 7.62 36.57 4.40
649 685 1.496001 TCCTATGGGATGCATGCTGTT 59.504 47.619 20.33 3.46 36.57 3.16
650 686 2.091720 TCCTATGGGATGCATGCTGTTT 60.092 45.455 20.33 0.66 36.57 2.83
651 687 2.696707 CCTATGGGATGCATGCTGTTTT 59.303 45.455 20.33 2.18 33.58 2.43
652 688 3.133362 CCTATGGGATGCATGCTGTTTTT 59.867 43.478 20.33 2.71 33.58 1.94
653 689 2.459060 TGGGATGCATGCTGTTTTTG 57.541 45.000 20.33 0.00 0.00 2.44
654 690 1.002201 TGGGATGCATGCTGTTTTTGG 59.998 47.619 20.33 0.00 0.00 3.28
655 691 1.002315 GGGATGCATGCTGTTTTTGGT 59.998 47.619 20.33 0.00 0.00 3.67
656 692 2.233431 GGGATGCATGCTGTTTTTGGTA 59.767 45.455 20.33 0.00 0.00 3.25
657 693 3.118665 GGGATGCATGCTGTTTTTGGTAT 60.119 43.478 20.33 0.00 0.00 2.73
658 694 4.506758 GGATGCATGCTGTTTTTGGTATT 58.493 39.130 20.33 0.00 0.00 1.89
659 695 4.937015 GGATGCATGCTGTTTTTGGTATTT 59.063 37.500 20.33 0.00 0.00 1.40
660 696 5.163834 GGATGCATGCTGTTTTTGGTATTTG 60.164 40.000 20.33 0.00 0.00 2.32
661 697 4.063689 TGCATGCTGTTTTTGGTATTTGG 58.936 39.130 20.33 0.00 0.00 3.28
662 698 4.202295 TGCATGCTGTTTTTGGTATTTGGA 60.202 37.500 20.33 0.00 0.00 3.53
663 699 4.389687 GCATGCTGTTTTTGGTATTTGGAG 59.610 41.667 11.37 0.00 0.00 3.86
664 700 3.988819 TGCTGTTTTTGGTATTTGGAGC 58.011 40.909 0.00 0.00 0.00 4.70
665 701 3.244044 TGCTGTTTTTGGTATTTGGAGCC 60.244 43.478 0.00 0.00 0.00 4.70
666 702 3.006859 GCTGTTTTTGGTATTTGGAGCCT 59.993 43.478 0.00 0.00 0.00 4.58
667 703 4.809673 CTGTTTTTGGTATTTGGAGCCTC 58.190 43.478 0.00 0.00 0.00 4.70
668 704 3.576550 TGTTTTTGGTATTTGGAGCCTCC 59.423 43.478 2.98 2.98 36.96 4.30
669 705 3.534357 TTTTGGTATTTGGAGCCTCCA 57.466 42.857 10.05 10.05 46.61 3.86
676 712 3.324930 TGGAGCCTCCAGCAGGTG 61.325 66.667 10.05 0.00 42.67 4.00
677 713 3.005539 GGAGCCTCCAGCAGGTGA 61.006 66.667 5.69 0.00 45.61 4.02
678 714 2.267324 GAGCCTCCAGCAGGTGAC 59.733 66.667 0.00 0.00 45.61 3.67
679 715 2.203907 AGCCTCCAGCAGGTGACT 60.204 61.111 0.00 0.00 45.61 3.41
680 716 2.237534 GAGCCTCCAGCAGGTGACTC 62.238 65.000 0.00 0.00 45.61 3.36
681 717 2.289532 GCCTCCAGCAGGTGACTCT 61.290 63.158 0.00 0.00 45.61 3.24
682 718 0.972983 GCCTCCAGCAGGTGACTCTA 60.973 60.000 0.00 0.00 45.61 2.43
683 719 0.820871 CCTCCAGCAGGTGACTCTAC 59.179 60.000 0.00 0.00 40.21 2.59
684 720 1.550327 CTCCAGCAGGTGACTCTACA 58.450 55.000 0.00 0.00 40.21 2.74
685 721 1.476085 CTCCAGCAGGTGACTCTACAG 59.524 57.143 0.00 0.00 40.21 2.74
686 722 1.075536 TCCAGCAGGTGACTCTACAGA 59.924 52.381 0.00 0.00 40.21 3.41
687 723 1.203523 CCAGCAGGTGACTCTACAGAC 59.796 57.143 0.00 0.00 40.21 3.51
688 724 1.135546 CAGCAGGTGACTCTACAGACG 60.136 57.143 0.00 0.00 40.21 4.18
689 725 0.171455 GCAGGTGACTCTACAGACGG 59.829 60.000 0.00 0.00 40.21 4.79
690 726 0.171455 CAGGTGACTCTACAGACGGC 59.829 60.000 0.00 0.00 40.21 5.68
691 727 0.251209 AGGTGACTCTACAGACGGCA 60.251 55.000 0.00 0.00 32.90 5.69
692 728 0.171455 GGTGACTCTACAGACGGCAG 59.829 60.000 0.00 0.00 0.00 4.85
693 729 1.166129 GTGACTCTACAGACGGCAGA 58.834 55.000 0.00 0.00 0.00 4.26
694 730 1.131504 GTGACTCTACAGACGGCAGAG 59.868 57.143 2.64 2.64 41.32 3.35
695 731 1.003233 TGACTCTACAGACGGCAGAGA 59.997 52.381 10.88 0.00 38.46 3.10
696 732 2.085320 GACTCTACAGACGGCAGAGAA 58.915 52.381 10.88 0.00 38.46 2.87
697 733 2.488545 GACTCTACAGACGGCAGAGAAA 59.511 50.000 10.88 0.00 38.46 2.52
698 734 2.229302 ACTCTACAGACGGCAGAGAAAC 59.771 50.000 10.88 0.00 38.46 2.78
699 735 2.229062 CTCTACAGACGGCAGAGAAACA 59.771 50.000 0.00 0.00 38.46 2.83
700 736 2.626266 TCTACAGACGGCAGAGAAACAA 59.374 45.455 0.00 0.00 0.00 2.83
701 737 1.871080 ACAGACGGCAGAGAAACAAG 58.129 50.000 0.00 0.00 0.00 3.16
702 738 1.151668 CAGACGGCAGAGAAACAAGG 58.848 55.000 0.00 0.00 0.00 3.61
703 739 1.048601 AGACGGCAGAGAAACAAGGA 58.951 50.000 0.00 0.00 0.00 3.36
704 740 1.149148 GACGGCAGAGAAACAAGGAC 58.851 55.000 0.00 0.00 0.00 3.85
705 741 0.468226 ACGGCAGAGAAACAAGGACA 59.532 50.000 0.00 0.00 0.00 4.02
706 742 1.151668 CGGCAGAGAAACAAGGACAG 58.848 55.000 0.00 0.00 0.00 3.51
707 743 0.877743 GGCAGAGAAACAAGGACAGC 59.122 55.000 0.00 0.00 0.00 4.40
708 744 1.544314 GGCAGAGAAACAAGGACAGCT 60.544 52.381 0.00 0.00 0.00 4.24
709 745 1.534595 GCAGAGAAACAAGGACAGCTG 59.465 52.381 13.48 13.48 0.00 4.24
710 746 1.534595 CAGAGAAACAAGGACAGCTGC 59.465 52.381 15.27 6.61 0.00 5.25
711 747 0.877743 GAGAAACAAGGACAGCTGCC 59.122 55.000 15.27 16.08 0.00 4.85
712 748 0.475906 AGAAACAAGGACAGCTGCCT 59.524 50.000 20.03 20.03 37.35 4.75
713 749 1.133668 AGAAACAAGGACAGCTGCCTT 60.134 47.619 26.88 26.88 46.36 4.35
714 750 1.268079 GAAACAAGGACAGCTGCCTTC 59.732 52.381 28.64 18.95 43.68 3.46
715 751 0.886490 AACAAGGACAGCTGCCTTCG 60.886 55.000 28.64 25.01 43.68 3.79
716 752 2.359230 AAGGACAGCTGCCTTCGC 60.359 61.111 26.88 9.01 41.85 4.70
717 753 2.888447 AAGGACAGCTGCCTTCGCT 61.888 57.895 26.88 12.69 41.85 4.93
726 762 1.302366 CTGCCTTCGCTGCATATTCA 58.698 50.000 0.00 0.00 38.22 2.57
727 763 1.878088 CTGCCTTCGCTGCATATTCAT 59.122 47.619 0.00 0.00 38.22 2.57
728 764 1.605232 TGCCTTCGCTGCATATTCATG 59.395 47.619 0.00 0.00 32.85 3.07
740 776 3.365832 CATATTCATGCCTTTGTCGTGC 58.634 45.455 0.00 0.00 0.00 5.34
778 814 1.346395 TCGGGTGCACTTAAGTCACAT 59.654 47.619 25.75 0.00 31.98 3.21
791 827 7.700234 CACTTAAGTCACATTACTTGCAAAACA 59.300 33.333 4.77 0.00 39.95 2.83
849 885 0.682209 AGGTCACATTGGCCATCTGC 60.682 55.000 6.09 0.00 46.77 4.26
981 1060 3.501349 TCCCCTTCTCGATCCAGAATAG 58.499 50.000 3.07 0.00 31.84 1.73
1078 1160 4.572571 TTGTGGCGGCGTCCCTTT 62.573 61.111 9.84 0.00 0.00 3.11
1197 1279 3.478724 CTATGTAGCCGCGCCGTCA 62.479 63.158 0.00 0.00 0.00 4.35
1221 1303 2.332159 GAGGTAGTAGCGGCGCTC 59.668 66.667 39.97 27.66 40.44 5.03
1289 1372 1.310933 GGACTCGCGTGTCTTCCCTA 61.311 60.000 32.49 0.00 37.16 3.53
1397 1480 1.528824 CAGGCATTCCACGGGAGAT 59.471 57.895 0.00 0.00 31.21 2.75
1400 1483 1.441729 GCATTCCACGGGAGATCGA 59.558 57.895 0.00 0.00 31.21 3.59
1427 1510 0.677731 CACCATCATTGGACAGCCGT 60.678 55.000 0.00 0.00 46.92 5.68
1429 1512 0.392863 CCATCATTGGACAGCCGTGA 60.393 55.000 0.00 0.00 46.92 4.35
1770 1854 0.388659 GAGCTCATCGACATGCTCCT 59.611 55.000 18.74 0.17 44.16 3.69
1778 1862 1.032794 CGACATGCTCCTGGCTACTA 58.967 55.000 0.00 0.00 42.39 1.82
1784 1868 2.536066 TGCTCCTGGCTACTAACAAGA 58.464 47.619 0.00 0.00 42.39 3.02
1830 1914 1.210478 ACGCAATCCTAGTGCCATTCT 59.790 47.619 0.00 0.00 38.86 2.40
1867 1951 0.395862 CTGTTCCGGCTCCTCCTCTA 60.396 60.000 0.00 0.00 0.00 2.43
1978 2062 3.935203 CAGTGACCATACATGTCAAGGAC 59.065 47.826 15.62 10.95 0.00 3.85
1995 2079 4.429212 CGTCATCGACCGTGGCCA 62.429 66.667 0.00 0.00 39.71 5.36
2006 2090 1.003812 ACCGTGGCCAATTGCTAACTA 59.996 47.619 7.24 0.00 40.92 2.24
2100 2184 2.035961 GCGGCAAGATAGATGGTACTGA 59.964 50.000 0.00 0.00 0.00 3.41
2164 2271 7.203255 AGTTGGAGTTGAGTATGTTTTTAGC 57.797 36.000 0.00 0.00 0.00 3.09
2318 2427 2.159599 GGGAGAGTGTTGTCTACGTACG 60.160 54.545 15.01 15.01 0.00 3.67
2333 2442 2.034317 TACGCACGCAGACCGACTA 61.034 57.895 0.00 0.00 41.02 2.59
2378 2487 4.260170 AGGAAGTAGTCGTACGTCTTCAT 58.740 43.478 27.06 22.82 37.67 2.57
2386 2495 4.098044 AGTCGTACGTCTTCATGATCCAAT 59.902 41.667 16.05 0.00 0.00 3.16
2391 2500 4.697514 ACGTCTTCATGATCCAATCGATT 58.302 39.130 4.39 4.39 0.00 3.34
2475 2584 0.684535 TCCGATCCAGCAAAGTGTCA 59.315 50.000 0.00 0.00 0.00 3.58
2938 3057 0.394899 CGGTAACCTCCCGGTACTCT 60.395 60.000 0.00 0.00 44.73 3.24
3022 3141 7.921786 TCAATCTTTATGTCTCGACCATTTT 57.078 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.594317 TCTTCTGATTAGCTTTAATTGGGCC 59.406 40.000 0.00 0.00 0.00 5.80
59 60 5.435686 TGGGCTCTTCTGATTAGCTTTAA 57.564 39.130 0.00 0.00 36.48 1.52
102 113 0.108138 GTGGCAGTTCGCTAGGTCAT 60.108 55.000 0.00 0.00 41.91 3.06
146 180 2.456840 CAGGGGAGGAAGAGGGGT 59.543 66.667 0.00 0.00 0.00 4.95
428 463 3.227276 CCTCGCGGTCCTGGCTAT 61.227 66.667 6.13 0.00 0.00 2.97
465 500 1.153369 CGGACCGACTGGCATGAAT 60.153 57.895 8.64 0.00 39.70 2.57
490 525 0.537143 TGTGCAGCGGTCCTGATTTT 60.537 50.000 0.00 0.00 44.64 1.82
558 594 4.083862 GGTCTGGTCCCTGTCCGC 62.084 72.222 0.00 0.00 0.00 5.54
603 639 1.625818 AGCATTTCCACGAGACCTTCT 59.374 47.619 0.00 0.00 0.00 2.85
606 642 0.674895 GCAGCATTTCCACGAGACCT 60.675 55.000 0.00 0.00 0.00 3.85
607 643 0.674895 AGCAGCATTTCCACGAGACC 60.675 55.000 0.00 0.00 0.00 3.85
608 644 2.010145 TAGCAGCATTTCCACGAGAC 57.990 50.000 0.00 0.00 0.00 3.36
609 645 2.988010 ATAGCAGCATTTCCACGAGA 57.012 45.000 0.00 0.00 0.00 4.04
610 646 2.289002 GGAATAGCAGCATTTCCACGAG 59.711 50.000 17.40 0.00 39.00 4.18
611 647 2.092968 AGGAATAGCAGCATTTCCACGA 60.093 45.455 22.00 0.00 41.15 4.35
612 648 2.292267 AGGAATAGCAGCATTTCCACG 58.708 47.619 22.00 0.00 41.15 4.94
613 649 4.217118 CCATAGGAATAGCAGCATTTCCAC 59.783 45.833 22.00 3.43 41.15 4.02
614 650 4.401022 CCATAGGAATAGCAGCATTTCCA 58.599 43.478 22.00 12.21 41.15 3.53
615 651 3.760684 CCCATAGGAATAGCAGCATTTCC 59.239 47.826 15.41 15.41 39.38 3.13
616 652 4.655963 TCCCATAGGAATAGCAGCATTTC 58.344 43.478 0.00 0.00 40.08 2.17
617 653 4.729552 TCCCATAGGAATAGCAGCATTT 57.270 40.909 0.00 0.00 40.08 2.32
625 661 4.567116 ACAGCATGCATCCCATAGGAATAG 60.567 45.833 21.98 0.00 43.97 1.73
626 662 3.331591 ACAGCATGCATCCCATAGGAATA 59.668 43.478 21.98 0.00 43.97 1.75
627 663 2.109480 ACAGCATGCATCCCATAGGAAT 59.891 45.455 21.98 0.00 43.97 3.01
628 664 1.496001 ACAGCATGCATCCCATAGGAA 59.504 47.619 21.98 0.00 43.97 3.36
629 665 1.142936 ACAGCATGCATCCCATAGGA 58.857 50.000 21.98 0.00 44.75 2.94
630 666 1.991121 AACAGCATGCATCCCATAGG 58.009 50.000 21.98 0.00 42.53 2.57
631 667 4.116961 CAAAAACAGCATGCATCCCATAG 58.883 43.478 21.98 0.00 42.53 2.23
632 668 3.118702 CCAAAAACAGCATGCATCCCATA 60.119 43.478 21.98 0.00 42.53 2.74
633 669 2.355310 CCAAAAACAGCATGCATCCCAT 60.355 45.455 21.98 0.00 42.53 4.00
634 670 1.002201 CCAAAAACAGCATGCATCCCA 59.998 47.619 21.98 0.00 42.53 4.37
635 671 1.002315 ACCAAAAACAGCATGCATCCC 59.998 47.619 21.98 0.00 42.53 3.85
636 672 2.460757 ACCAAAAACAGCATGCATCC 57.539 45.000 21.98 0.00 42.53 3.51
637 673 5.163834 CCAAATACCAAAAACAGCATGCATC 60.164 40.000 21.98 0.00 42.53 3.91
638 674 4.696402 CCAAATACCAAAAACAGCATGCAT 59.304 37.500 21.98 4.26 42.53 3.96
639 675 4.063689 CCAAATACCAAAAACAGCATGCA 58.936 39.130 21.98 0.00 42.53 3.96
640 676 4.314121 TCCAAATACCAAAAACAGCATGC 58.686 39.130 10.51 10.51 42.53 4.06
641 677 4.389687 GCTCCAAATACCAAAAACAGCATG 59.610 41.667 0.00 0.00 46.00 4.06
642 678 4.563374 GGCTCCAAATACCAAAAACAGCAT 60.563 41.667 0.00 0.00 0.00 3.79
643 679 3.244044 GGCTCCAAATACCAAAAACAGCA 60.244 43.478 0.00 0.00 0.00 4.41
644 680 3.006859 AGGCTCCAAATACCAAAAACAGC 59.993 43.478 0.00 0.00 0.00 4.40
645 681 4.321974 GGAGGCTCCAAATACCAAAAACAG 60.322 45.833 28.55 0.00 36.28 3.16
646 682 3.576550 GGAGGCTCCAAATACCAAAAACA 59.423 43.478 28.55 0.00 36.28 2.83
647 683 3.576550 TGGAGGCTCCAAATACCAAAAAC 59.423 43.478 33.38 2.13 45.00 2.43
648 684 3.850752 TGGAGGCTCCAAATACCAAAAA 58.149 40.909 33.38 5.68 45.00 1.94
649 685 3.534357 TGGAGGCTCCAAATACCAAAA 57.466 42.857 33.38 6.26 45.00 2.44
665 701 1.476085 CTGTAGAGTCACCTGCTGGAG 59.524 57.143 17.64 8.84 37.04 3.86
666 702 1.075536 TCTGTAGAGTCACCTGCTGGA 59.924 52.381 17.64 0.00 37.04 3.86
667 703 1.203523 GTCTGTAGAGTCACCTGCTGG 59.796 57.143 8.29 8.29 39.83 4.85
668 704 1.135546 CGTCTGTAGAGTCACCTGCTG 60.136 57.143 0.00 0.00 0.00 4.41
669 705 1.169577 CGTCTGTAGAGTCACCTGCT 58.830 55.000 0.00 0.00 0.00 4.24
670 706 0.171455 CCGTCTGTAGAGTCACCTGC 59.829 60.000 0.00 0.00 0.00 4.85
671 707 0.171455 GCCGTCTGTAGAGTCACCTG 59.829 60.000 0.00 0.00 0.00 4.00
672 708 0.251209 TGCCGTCTGTAGAGTCACCT 60.251 55.000 0.00 0.00 0.00 4.00
673 709 0.171455 CTGCCGTCTGTAGAGTCACC 59.829 60.000 0.00 0.00 0.00 4.02
674 710 1.131504 CTCTGCCGTCTGTAGAGTCAC 59.868 57.143 1.88 0.00 45.67 3.67
675 711 1.454201 CTCTGCCGTCTGTAGAGTCA 58.546 55.000 1.88 0.00 45.67 3.41
679 715 2.235891 TGTTTCTCTGCCGTCTGTAGA 58.764 47.619 0.00 0.00 34.28 2.59
680 716 2.724977 TGTTTCTCTGCCGTCTGTAG 57.275 50.000 0.00 0.00 0.00 2.74
681 717 2.288825 CCTTGTTTCTCTGCCGTCTGTA 60.289 50.000 0.00 0.00 0.00 2.74
682 718 1.541233 CCTTGTTTCTCTGCCGTCTGT 60.541 52.381 0.00 0.00 0.00 3.41
683 719 1.151668 CCTTGTTTCTCTGCCGTCTG 58.848 55.000 0.00 0.00 0.00 3.51
684 720 1.048601 TCCTTGTTTCTCTGCCGTCT 58.951 50.000 0.00 0.00 0.00 4.18
685 721 1.149148 GTCCTTGTTTCTCTGCCGTC 58.851 55.000 0.00 0.00 0.00 4.79
686 722 0.468226 TGTCCTTGTTTCTCTGCCGT 59.532 50.000 0.00 0.00 0.00 5.68
687 723 1.151668 CTGTCCTTGTTTCTCTGCCG 58.848 55.000 0.00 0.00 0.00 5.69
688 724 0.877743 GCTGTCCTTGTTTCTCTGCC 59.122 55.000 0.00 0.00 0.00 4.85
689 725 1.534595 CAGCTGTCCTTGTTTCTCTGC 59.465 52.381 5.25 0.00 0.00 4.26
690 726 1.534595 GCAGCTGTCCTTGTTTCTCTG 59.465 52.381 16.64 0.00 0.00 3.35
691 727 1.544314 GGCAGCTGTCCTTGTTTCTCT 60.544 52.381 16.64 0.00 0.00 3.10
692 728 0.877743 GGCAGCTGTCCTTGTTTCTC 59.122 55.000 16.64 0.00 0.00 2.87
693 729 0.475906 AGGCAGCTGTCCTTGTTTCT 59.524 50.000 16.31 0.00 0.00 2.52
694 730 1.268079 GAAGGCAGCTGTCCTTGTTTC 59.732 52.381 33.22 20.05 43.54 2.78
695 731 1.322442 GAAGGCAGCTGTCCTTGTTT 58.678 50.000 33.22 16.37 43.54 2.83
696 732 0.886490 CGAAGGCAGCTGTCCTTGTT 60.886 55.000 33.22 16.71 43.54 2.83
697 733 1.302033 CGAAGGCAGCTGTCCTTGT 60.302 57.895 33.22 19.16 43.54 3.16
698 734 2.684843 GCGAAGGCAGCTGTCCTTG 61.685 63.158 33.22 26.38 43.54 3.61
699 735 2.359230 GCGAAGGCAGCTGTCCTT 60.359 61.111 30.40 30.40 45.98 3.36
700 736 3.317571 AGCGAAGGCAGCTGTCCT 61.318 61.111 16.31 18.57 44.22 3.85
707 743 1.302366 TGAATATGCAGCGAAGGCAG 58.698 50.000 0.00 0.00 45.68 4.85
708 744 1.605232 CATGAATATGCAGCGAAGGCA 59.395 47.619 0.00 0.00 46.66 4.75
709 745 2.327081 CATGAATATGCAGCGAAGGC 57.673 50.000 0.00 0.00 40.37 4.35
719 755 3.365832 GCACGACAAAGGCATGAATATG 58.634 45.455 0.00 0.00 37.36 1.78
720 756 2.032054 CGCACGACAAAGGCATGAATAT 59.968 45.455 0.00 0.00 0.00 1.28
721 757 1.396648 CGCACGACAAAGGCATGAATA 59.603 47.619 0.00 0.00 0.00 1.75
722 758 0.168788 CGCACGACAAAGGCATGAAT 59.831 50.000 0.00 0.00 0.00 2.57
723 759 1.163420 ACGCACGACAAAGGCATGAA 61.163 50.000 0.00 0.00 0.00 2.57
724 760 1.565156 GACGCACGACAAAGGCATGA 61.565 55.000 0.00 0.00 0.00 3.07
725 761 1.154413 GACGCACGACAAAGGCATG 60.154 57.895 0.00 0.00 0.00 4.06
726 762 1.568612 CTGACGCACGACAAAGGCAT 61.569 55.000 0.00 0.00 0.00 4.40
727 763 2.202946 TGACGCACGACAAAGGCA 60.203 55.556 0.00 0.00 0.00 4.75
728 764 1.891060 CTCTGACGCACGACAAAGGC 61.891 60.000 0.00 0.00 0.00 4.35
729 765 0.318699 TCTCTGACGCACGACAAAGG 60.319 55.000 0.00 0.00 0.00 3.11
730 766 1.190323 GTTCTCTGACGCACGACAAAG 59.810 52.381 0.00 0.00 0.00 2.77
731 767 1.202371 AGTTCTCTGACGCACGACAAA 60.202 47.619 0.00 0.00 0.00 2.83
732 768 0.384309 AGTTCTCTGACGCACGACAA 59.616 50.000 0.00 0.00 0.00 3.18
733 769 0.384309 AAGTTCTCTGACGCACGACA 59.616 50.000 0.00 0.00 0.00 4.35
734 770 0.778815 CAAGTTCTCTGACGCACGAC 59.221 55.000 0.00 0.00 0.00 4.34
735 771 0.384309 ACAAGTTCTCTGACGCACGA 59.616 50.000 0.00 0.00 0.00 4.35
736 772 0.778815 GACAAGTTCTCTGACGCACG 59.221 55.000 0.00 0.00 0.00 5.34
737 773 1.852942 TGACAAGTTCTCTGACGCAC 58.147 50.000 0.00 0.00 0.00 5.34
738 774 2.820059 ATGACAAGTTCTCTGACGCA 57.180 45.000 0.00 0.00 0.00 5.24
739 775 2.091277 CGAATGACAAGTTCTCTGACGC 59.909 50.000 0.00 0.00 0.00 5.19
740 776 2.663602 CCGAATGACAAGTTCTCTGACG 59.336 50.000 0.00 0.00 0.00 4.35
778 814 4.865365 CGGGTTTTTCTGTTTTGCAAGTAA 59.135 37.500 0.00 0.00 0.00 2.24
791 827 3.277142 AGTTCTGTGACGGGTTTTTCT 57.723 42.857 0.00 0.00 0.00 2.52
938 1017 1.896465 CGGGGAAAGGGCATGTTTTAA 59.104 47.619 0.00 0.00 0.00 1.52
1034 1116 4.393155 TCGCTGCCATCAACGCCT 62.393 61.111 0.00 0.00 32.30 5.52
1078 1160 0.321671 GCTACCTCTGCTCCACACAA 59.678 55.000 0.00 0.00 0.00 3.33
1125 1207 4.025858 ACTGCCTGCCACAGCGAT 62.026 61.111 0.00 0.00 44.31 4.58
1164 1246 0.176680 CATAGTGCCACGCTCTCCTT 59.823 55.000 0.00 0.00 34.22 3.36
1197 1279 3.760917 GCTACTACCTCCGGCGAT 58.239 61.111 9.30 0.00 0.00 4.58
1397 1480 3.140623 CAATGATGGTGGCATACATCGA 58.859 45.455 21.97 15.00 44.90 3.59
1553 1637 0.320771 ACCACACGAGTGCAATCCTC 60.321 55.000 8.83 0.26 44.53 3.71
1770 1854 1.278127 GCACCCTCTTGTTAGTAGCCA 59.722 52.381 0.00 0.00 0.00 4.75
1778 1862 0.825010 CAAGGCAGCACCCTCTTGTT 60.825 55.000 0.00 0.00 40.58 2.83
1830 1914 3.435275 ACAGAGATAGTGAGCACCTTCA 58.565 45.455 0.00 0.00 0.00 3.02
1867 1951 3.542676 TCTGGCGTCCACGGTTGT 61.543 61.111 0.55 0.00 40.23 3.32
1978 2062 3.925362 TTGGCCACGGTCGATGACG 62.925 63.158 3.88 5.73 41.26 4.35
1995 2079 4.220602 CAGGCAACCCTTTAGTTAGCAATT 59.779 41.667 0.00 0.00 40.33 2.32
2006 2090 2.683211 AACTCATCAGGCAACCCTTT 57.317 45.000 0.00 0.00 40.33 3.11
2318 2427 2.874780 CGTAGTCGGTCTGCGTGC 60.875 66.667 4.78 0.00 44.80 5.34
2378 2487 3.130633 CGGTGCTTAATCGATTGGATCA 58.869 45.455 20.87 9.93 32.59 2.92
2386 2495 3.173599 CGTAGTTTCGGTGCTTAATCGA 58.826 45.455 0.00 0.00 40.46 3.59
3113 3232 1.431496 GTCCGCACGCTTAAGGTTAA 58.569 50.000 4.29 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.