Multiple sequence alignment - TraesCS1D01G153300

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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 TraesCS1D01G153300 chr1D 100.000 5898 0 0 1 5898 212528706 212534603 0.000000e+00 10892.0
1 TraesCS1D01G153300 chr1D 81.915 188 21 6 5222 5403 212720873 212721053 4.760000e-31 147.0
2 TraesCS1D01G153300 chr1D 98.765 81 1 0 657 737 194467358 194467278 1.710000e-30 145.0
3 TraesCS1D01G153300 chr1D 94.444 90 4 1 657 746 312515430 312515518 2.870000e-28 137.0
4 TraesCS1D01G153300 chr1B 97.438 3786 81 5 735 4509 302763851 302760071 0.000000e+00 6440.0
5 TraesCS1D01G153300 chr1B 95.599 1227 36 10 4508 5724 302759813 302758595 0.000000e+00 1951.0
6 TraesCS1D01G153300 chr1B 93.481 675 26 4 1 659 302764510 302763838 0.000000e+00 987.0
7 TraesCS1D01G153300 chr1B 87.821 156 13 4 5726 5881 302758342 302758193 1.690000e-40 178.0
8 TraesCS1D01G153300 chr1A 96.517 2613 70 11 3291 5890 268935030 268937634 0.000000e+00 4301.0
9 TraesCS1D01G153300 chr1A 97.283 2540 41 7 735 3263 268932509 268935031 0.000000e+00 4283.0
10 TraesCS1D01G153300 chr1A 94.241 573 21 6 86 657 268931959 268932520 0.000000e+00 865.0
11 TraesCS1D01G153300 chr1A 84.416 77 12 0 5454 5530 268937296 268937372 6.340000e-10 76.8
12 TraesCS1D01G153300 chr7A 86.106 511 66 5 1224 1734 145454387 145453882 4.020000e-151 545.0
13 TraesCS1D01G153300 chr2B 86.083 503 64 6 1232 1734 648923497 648923001 2.420000e-148 536.0
14 TraesCS1D01G153300 chr2B 96.552 87 2 1 651 737 79014308 79014393 6.160000e-30 143.0
15 TraesCS1D01G153300 chr5A 84.932 511 72 5 1224 1734 452443302 452442797 4.080000e-141 512.0
16 TraesCS1D01G153300 chr6B 85.019 514 57 9 1221 1734 539001782 539002275 6.820000e-139 505.0
17 TraesCS1D01G153300 chr6B 81.389 360 38 10 1623 1974 551926752 551926414 3.500000e-67 267.0
18 TraesCS1D01G153300 chr3B 80.563 355 40 11 1623 1968 795220270 795219936 4.560000e-61 246.0
19 TraesCS1D01G153300 chr3B 92.784 97 6 1 657 753 224957159 224957064 7.970000e-29 139.0
20 TraesCS1D01G153300 chr3D 91.608 143 10 2 1833 1974 550507049 550506908 4.660000e-46 196.0
21 TraesCS1D01G153300 chr3D 93.333 105 7 0 3621 3725 87392411 87392307 7.910000e-34 156.0
22 TraesCS1D01G153300 chr5B 90.909 143 11 2 1833 1974 508813904 508813763 2.170000e-44 191.0
23 TraesCS1D01G153300 chr5B 94.444 90 5 0 657 746 40788515 40788426 7.970000e-29 139.0
24 TraesCS1D01G153300 chr5B 94.505 91 4 1 657 746 662522339 662522429 7.970000e-29 139.0
25 TraesCS1D01G153300 chr4A 90.909 143 11 2 1833 1974 648470054 648469913 2.170000e-44 191.0
26 TraesCS1D01G153300 chr4A 94.505 91 4 1 657 746 205657651 205657561 7.970000e-29 139.0
27 TraesCS1D01G153300 chr5D 97.590 83 2 0 657 739 434383453 434383371 6.160000e-30 143.0
28 TraesCS1D01G153300 chr2A 96.552 87 2 1 657 742 177014398 177014484 6.160000e-30 143.0
29 TraesCS1D01G153300 chr6D 93.103 58 4 0 3669 3726 446545331 446545388 1.050000e-12 86.1


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 TraesCS1D01G153300 chr1D 212528706 212534603 5897 False 10892.00 10892 100.00000 1 5898 1 chr1D.!!$F1 5897
1 TraesCS1D01G153300 chr1B 302758193 302764510 6317 True 2389.00 6440 93.58475 1 5881 4 chr1B.!!$R1 5880
2 TraesCS1D01G153300 chr1A 268931959 268937634 5675 False 2381.45 4301 93.11425 86 5890 4 chr1A.!!$F1 5804
3 TraesCS1D01G153300 chr7A 145453882 145454387 505 True 545.00 545 86.10600 1224 1734 1 chr7A.!!$R1 510
4 TraesCS1D01G153300 chr5A 452442797 452443302 505 True 512.00 512 84.93200 1224 1734 1 chr5A.!!$R1 510

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
680 697 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.0 0.00 4.96 F
681 698 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.0 0.00 4.12 F
683 700 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.0 0.00 3.16 F
684 701 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.0 0.00 2.66 F
1722 1748 1.135721 GATCTGGCCACAGGAAAATGC 59.864 52.381 0.00 0.0 44.99 3.56 F
2914 2944 1.050204 ATGGGTGTTGTTTGCTGCAT 58.950 45.000 1.84 0.0 0.00 3.96 F
3055 3085 1.603802 GCACACATAAGCACACACACT 59.396 47.619 0.00 0.0 0.00 3.55 F
3063 3095 2.113860 AGCACACACACTCACTTGTT 57.886 45.000 0.00 0.0 0.00 2.83 F
3283 3315 4.435137 TCCTTCTGATTTCCACTCCCTAA 58.565 43.478 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1562 2.575805 AAGGCAAGGAGAAGACAAGG 57.424 50.000 0.00 0.00 0.00 3.61 R
2269 2295 4.571984 CCAAAGACATCGCTATGACATTCA 59.428 41.667 5.05 0.00 36.54 2.57 R
2750 2776 7.659186 AGGATAAATACTCACGTTCTGGATAC 58.341 38.462 0.00 0.00 0.00 2.24 R
2801 2831 6.933521 AGTATTCAGCCAGTAGATAAGCAATG 59.066 38.462 0.00 0.00 0.00 2.82 R
3034 3064 1.333308 GTGTGTGTGCTTATGTGTGCA 59.667 47.619 0.00 0.00 36.79 4.57 R
4053 4085 0.461135 CACAATGCAATACCAGGGGC 59.539 55.000 0.00 0.00 0.00 5.80 R
4321 4372 0.902984 TTCCGGCTTCCAGCTCTACA 60.903 55.000 0.00 0.00 41.99 2.74 R
4715 5025 1.470632 GGCCTTGTCTCTCACGATGAG 60.471 57.143 0.00 8.24 45.59 2.90 R
5070 5386 1.593787 CTTGAGCTCAGCCTTCCGA 59.406 57.895 17.43 0.00 0.00 4.55 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
34 35 2.434185 GGTGCGATCTGGTTGCGA 60.434 61.111 0.00 0.00 40.35 5.10
42 43 2.288642 ATCTGGTTGCGATGCCCCAT 62.289 55.000 0.00 0.00 30.33 4.00
116 132 2.315386 GCGTGGGTTTCTCGTGTCC 61.315 63.158 0.00 0.00 35.12 4.02
242 258 1.228124 TCCTCGTTGCCAAACCCTG 60.228 57.895 0.00 0.00 32.23 4.45
337 353 1.367840 GCCCGTCACTGTCTCAGTT 59.632 57.895 0.00 0.00 42.59 3.16
343 359 2.292016 CGTCACTGTCTCAGTTGTCTCT 59.708 50.000 0.00 0.00 42.59 3.10
367 383 1.157585 GGTCAAACCGAAGCTCTTCC 58.842 55.000 4.23 0.00 36.27 3.46
625 642 2.652941 TATACGGGTTTCGGTGTGAC 57.347 50.000 0.00 0.00 44.45 3.67
657 674 1.623811 TCCCGAGGGTTTCTCTTCTTG 59.376 52.381 8.20 0.00 40.30 3.02
658 675 1.339151 CCCGAGGGTTTCTCTTCTTGG 60.339 57.143 0.00 0.00 40.30 3.61
659 676 1.339151 CCGAGGGTTTCTCTTCTTGGG 60.339 57.143 0.00 0.00 40.30 4.12
660 677 1.348036 CGAGGGTTTCTCTTCTTGGGT 59.652 52.381 0.00 0.00 40.30 4.51
661 678 2.224548 CGAGGGTTTCTCTTCTTGGGTT 60.225 50.000 0.00 0.00 40.30 4.11
662 679 3.747708 CGAGGGTTTCTCTTCTTGGGTTT 60.748 47.826 0.00 0.00 40.30 3.27
663 680 3.821600 GAGGGTTTCTCTTCTTGGGTTTC 59.178 47.826 0.00 0.00 39.38 2.78
664 681 3.204382 AGGGTTTCTCTTCTTGGGTTTCA 59.796 43.478 0.00 0.00 0.00 2.69
665 682 3.318275 GGGTTTCTCTTCTTGGGTTTCAC 59.682 47.826 0.00 0.00 0.00 3.18
666 683 3.318275 GGTTTCTCTTCTTGGGTTTCACC 59.682 47.826 0.00 0.00 37.60 4.02
667 684 4.207955 GTTTCTCTTCTTGGGTTTCACCT 58.792 43.478 0.00 0.00 38.64 4.00
668 685 3.771577 TCTCTTCTTGGGTTTCACCTC 57.228 47.619 0.00 0.00 38.64 3.85
669 686 3.318313 TCTCTTCTTGGGTTTCACCTCT 58.682 45.455 0.00 0.00 38.64 3.69
670 687 4.489737 TCTCTTCTTGGGTTTCACCTCTA 58.510 43.478 0.00 0.00 38.64 2.43
671 688 4.528596 TCTCTTCTTGGGTTTCACCTCTAG 59.471 45.833 0.00 0.00 38.64 2.43
672 689 3.008049 TCTTCTTGGGTTTCACCTCTAGC 59.992 47.826 0.00 0.00 38.64 3.42
673 690 1.628846 TCTTGGGTTTCACCTCTAGCC 59.371 52.381 0.00 0.00 38.64 3.93
674 691 1.630878 CTTGGGTTTCACCTCTAGCCT 59.369 52.381 0.00 0.00 38.64 4.58
675 692 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
676 693 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
677 694 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
678 695 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
679 696 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
680 697 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
681 698 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
682 699 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
683 700 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
684 701 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
685 702 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
686 703 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
687 704 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
688 705 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
689 706 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
699 716 3.715628 CAACTTGTTTGGGACTGAAGG 57.284 47.619 0.00 0.00 0.00 3.46
700 717 1.692411 ACTTGTTTGGGACTGAAGGC 58.308 50.000 0.00 0.00 0.00 4.35
701 718 1.215423 ACTTGTTTGGGACTGAAGGCT 59.785 47.619 0.00 0.00 0.00 4.58
702 719 2.310538 CTTGTTTGGGACTGAAGGCTT 58.689 47.619 0.00 0.00 0.00 4.35
703 720 2.452600 TGTTTGGGACTGAAGGCTTT 57.547 45.000 0.00 0.00 0.00 3.51
704 721 3.586470 TGTTTGGGACTGAAGGCTTTA 57.414 42.857 0.00 0.00 0.00 1.85
705 722 4.112634 TGTTTGGGACTGAAGGCTTTAT 57.887 40.909 0.00 0.00 0.00 1.40
706 723 4.479158 TGTTTGGGACTGAAGGCTTTATT 58.521 39.130 0.00 0.00 0.00 1.40
707 724 4.280677 TGTTTGGGACTGAAGGCTTTATTG 59.719 41.667 0.00 0.00 0.00 1.90
708 725 3.806949 TGGGACTGAAGGCTTTATTGT 57.193 42.857 0.00 0.00 0.00 2.71
709 726 4.112634 TGGGACTGAAGGCTTTATTGTT 57.887 40.909 0.00 0.00 0.00 2.83
710 727 3.826157 TGGGACTGAAGGCTTTATTGTTG 59.174 43.478 0.00 0.00 0.00 3.33
711 728 3.826729 GGGACTGAAGGCTTTATTGTTGT 59.173 43.478 0.00 0.00 0.00 3.32
712 729 4.280929 GGGACTGAAGGCTTTATTGTTGTT 59.719 41.667 0.00 0.00 0.00 2.83
713 730 5.222631 GGACTGAAGGCTTTATTGTTGTTG 58.777 41.667 0.00 0.00 0.00 3.33
714 731 5.221244 GGACTGAAGGCTTTATTGTTGTTGT 60.221 40.000 0.00 0.00 0.00 3.32
715 732 6.220726 ACTGAAGGCTTTATTGTTGTTGTT 57.779 33.333 0.00 0.00 0.00 2.83
716 733 6.042143 ACTGAAGGCTTTATTGTTGTTGTTG 58.958 36.000 0.00 0.00 0.00 3.33
717 734 5.971763 TGAAGGCTTTATTGTTGTTGTTGT 58.028 33.333 0.00 0.00 0.00 3.32
718 735 6.402222 TGAAGGCTTTATTGTTGTTGTTGTT 58.598 32.000 0.00 0.00 0.00 2.83
719 736 6.312426 TGAAGGCTTTATTGTTGTTGTTGTTG 59.688 34.615 0.00 0.00 0.00 3.33
720 737 5.729510 AGGCTTTATTGTTGTTGTTGTTGT 58.270 33.333 0.00 0.00 0.00 3.32
721 738 6.169800 AGGCTTTATTGTTGTTGTTGTTGTT 58.830 32.000 0.00 0.00 0.00 2.83
722 739 6.091986 AGGCTTTATTGTTGTTGTTGTTGTTG 59.908 34.615 0.00 0.00 0.00 3.33
723 740 6.128418 GGCTTTATTGTTGTTGTTGTTGTTGT 60.128 34.615 0.00 0.00 0.00 3.32
724 741 7.294473 GCTTTATTGTTGTTGTTGTTGTTGTT 58.706 30.769 0.00 0.00 0.00 2.83
725 742 7.268023 GCTTTATTGTTGTTGTTGTTGTTGTTG 59.732 33.333 0.00 0.00 0.00 3.33
726 743 7.715265 TTATTGTTGTTGTTGTTGTTGTTGT 57.285 28.000 0.00 0.00 0.00 3.32
727 744 6.610741 ATTGTTGTTGTTGTTGTTGTTGTT 57.389 29.167 0.00 0.00 0.00 2.83
728 745 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
729 746 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
730 747 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
731 748 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
732 749 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
733 750 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
734 751 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
735 752 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
736 753 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
737 754 6.128282 TGTTGTTGTTGTTGTTGTTGTTGTTT 60.128 30.769 0.00 0.00 0.00 2.83
738 755 6.037423 TGTTGTTGTTGTTGTTGTTGTTTC 57.963 33.333 0.00 0.00 0.00 2.78
739 756 5.812642 TGTTGTTGTTGTTGTTGTTGTTTCT 59.187 32.000 0.00 0.00 0.00 2.52
740 757 6.019479 TGTTGTTGTTGTTGTTGTTGTTTCTC 60.019 34.615 0.00 0.00 0.00 2.87
741 758 5.837437 TGTTGTTGTTGTTGTTGTTTCTCT 58.163 33.333 0.00 0.00 0.00 3.10
742 759 6.276847 TGTTGTTGTTGTTGTTGTTTCTCTT 58.723 32.000 0.00 0.00 0.00 2.85
743 760 6.419413 TGTTGTTGTTGTTGTTGTTTCTCTTC 59.581 34.615 0.00 0.00 0.00 2.87
744 761 6.325919 TGTTGTTGTTGTTGTTTCTCTTCT 57.674 33.333 0.00 0.00 0.00 2.85
745 762 6.744112 TGTTGTTGTTGTTGTTTCTCTTCTT 58.256 32.000 0.00 0.00 0.00 2.52
856 874 8.972458 TGCTGCTTTGTTATACCATCTTATTA 57.028 30.769 0.00 0.00 0.00 0.98
989 1010 4.602732 AGGGTACTAGTACTAGGATCTGGG 59.397 50.000 29.05 7.31 37.49 4.45
1714 1740 2.787473 TAGGTTTGATCTGGCCACAG 57.213 50.000 0.00 0.00 46.30 3.66
1722 1748 1.135721 GATCTGGCCACAGGAAAATGC 59.864 52.381 0.00 0.00 44.99 3.56
1997 2023 3.367292 GCGGAACACATTTTCATCATGGT 60.367 43.478 0.00 0.00 0.00 3.55
2240 2266 2.045926 GATGTGGGCTGCGGAGTT 60.046 61.111 5.62 0.00 0.00 3.01
2735 2761 2.774234 AGTATGGGGAGTGACAATGGAG 59.226 50.000 0.00 0.00 0.00 3.86
2750 2776 2.695314 GGAGGCTTGCATTACTCCG 58.305 57.895 13.26 0.00 40.01 4.63
2914 2944 1.050204 ATGGGTGTTGTTTGCTGCAT 58.950 45.000 1.84 0.00 0.00 3.96
2922 2952 4.618489 GTGTTGTTTGCTGCATGTTAGATC 59.382 41.667 1.84 0.00 0.00 2.75
3017 3047 6.128929 GGATGCATCTTTCCGTTTTGTTTTAC 60.129 38.462 25.28 0.00 0.00 2.01
3055 3085 1.603802 GCACACATAAGCACACACACT 59.396 47.619 0.00 0.00 0.00 3.55
3056 3086 2.349817 GCACACATAAGCACACACACTC 60.350 50.000 0.00 0.00 0.00 3.51
3063 3095 2.113860 AGCACACACACTCACTTGTT 57.886 45.000 0.00 0.00 0.00 2.83
3091 3123 5.765182 ACTGGTAAACAAAGGATCTTCAGTG 59.235 40.000 0.00 0.00 31.63 3.66
3195 3227 6.259829 AGCATTTGTGTTAATTTGTGGTTTCC 59.740 34.615 0.00 0.00 0.00 3.13
3231 3263 5.968676 ATGCTAACAGGTAGGATGGTTTA 57.031 39.130 0.00 0.00 39.27 2.01
3232 3264 5.968676 TGCTAACAGGTAGGATGGTTTAT 57.031 39.130 0.00 0.00 0.00 1.40
3233 3265 6.321821 TGCTAACAGGTAGGATGGTTTATT 57.678 37.500 0.00 0.00 0.00 1.40
3283 3315 4.435137 TCCTTCTGATTTCCACTCCCTAA 58.565 43.478 0.00 0.00 0.00 2.69
3302 3334 5.932303 CCCTAATAATTGTCATCCCTGTACG 59.068 44.000 0.00 0.00 0.00 3.67
3513 3545 5.725042 GCAGATTTGTATGTTACAGCTGACG 60.725 44.000 23.35 0.00 40.24 4.35
4226 4277 5.299782 TGCCTTTTTCCTTTAGCGTCTTAAA 59.700 36.000 0.00 0.00 0.00 1.52
4321 4372 7.308435 GCTTACAGTGAAATGACAATAAAGCT 58.692 34.615 0.00 0.00 35.37 3.74
4441 4492 6.581171 AAACCATTTTTCTGGATCAGAGTC 57.419 37.500 0.00 0.00 41.75 3.36
4983 5293 2.108075 TCAGTTGCTCCCTCCAAATTCA 59.892 45.455 0.00 0.00 0.00 2.57
5070 5386 6.662755 TGTTTCTCAGGATATGGCAAGTATT 58.337 36.000 0.00 0.00 0.00 1.89
5095 5411 1.449956 GCTGAGCTCAAGCCCTCTG 60.450 63.158 18.85 4.37 43.38 3.35
5221 5538 1.608590 CGTCCATTTGTTGAAGTGGCT 59.391 47.619 0.00 0.00 0.00 4.75
5310 5627 0.540830 AGCTAGGGATAGTGGCCTCG 60.541 60.000 3.32 0.00 0.00 4.63
5413 5730 5.980116 CGATAGAGCTAGCAAATACAACACT 59.020 40.000 18.83 3.00 39.76 3.55
5442 5759 6.260050 AGACGCTGAAGAGAGAATAGTAGAAG 59.740 42.308 0.00 0.00 0.00 2.85
5461 5778 3.340814 AGATCAGGAAACGCTTGTGAT 57.659 42.857 0.00 0.00 0.00 3.06
5481 5798 6.059484 GTGATAGAAATTACCCCCAAATCGA 58.941 40.000 0.00 0.00 0.00 3.59
5551 5869 1.244019 ACCCCAAGATTGACGCTTGC 61.244 55.000 0.00 0.00 41.00 4.01
5554 5872 0.169672 CCAAGATTGACGCTTGCCAG 59.830 55.000 0.00 0.00 41.00 4.85
5569 5887 3.197927 TGCCAGAAAAATTACCCCCAT 57.802 42.857 0.00 0.00 0.00 4.00
5628 5946 2.906691 TTGTTCCACATTTTGCCCTG 57.093 45.000 0.00 0.00 0.00 4.45
5637 5955 4.834496 CCACATTTTGCCCTGGTATGATAT 59.166 41.667 0.00 0.00 0.00 1.63
5692 6011 0.177141 GCTGATTTGGCATGCCATGT 59.823 50.000 38.78 28.94 46.64 3.21
5779 6349 4.308458 CAACGGGGCCTCGTGTCA 62.308 66.667 35.29 0.00 43.07 3.58
5793 6363 2.426023 GTCAGTGCCCACGAGGTT 59.574 61.111 0.00 0.00 38.26 3.50
5847 6417 4.717629 CGCGCCCTCTTCGTGTGA 62.718 66.667 0.00 0.00 33.31 3.58
5853 6423 1.213013 CCTCTTCGTGTGACGGAGG 59.787 63.158 4.64 5.93 46.83 4.30
5854 6424 1.241990 CCTCTTCGTGTGACGGAGGA 61.242 60.000 13.19 0.07 46.83 3.71
5855 6425 0.596577 CTCTTCGTGTGACGGAGGAA 59.403 55.000 4.64 0.00 46.83 3.36
5856 6426 0.596577 TCTTCGTGTGACGGAGGAAG 59.403 55.000 4.64 0.00 46.83 3.46
5857 6427 0.596577 CTTCGTGTGACGGAGGAAGA 59.403 55.000 0.00 0.00 43.30 2.87
5858 6428 0.596577 TTCGTGTGACGGAGGAAGAG 59.403 55.000 0.00 0.00 42.81 2.85
5863 6433 2.296471 GTGTGACGGAGGAAGAGAAAGA 59.704 50.000 0.00 0.00 0.00 2.52
5866 6436 1.822371 GACGGAGGAAGAGAAAGAGCT 59.178 52.381 0.00 0.00 0.00 4.09
5883 6453 1.589716 GCTGCGCCTGGTCATTCTTT 61.590 55.000 4.18 0.00 0.00 2.52
5884 6454 0.169672 CTGCGCCTGGTCATTCTTTG 59.830 55.000 4.18 0.00 0.00 2.77
5886 6456 0.169009 GCGCCTGGTCATTCTTTGTC 59.831 55.000 0.00 0.00 0.00 3.18
5887 6457 0.443869 CGCCTGGTCATTCTTTGTCG 59.556 55.000 0.00 0.00 0.00 4.35
5889 6459 1.882352 GCCTGGTCATTCTTTGTCGGT 60.882 52.381 0.00 0.00 0.00 4.69
5890 6460 1.806542 CCTGGTCATTCTTTGTCGGTG 59.193 52.381 0.00 0.00 0.00 4.94
5891 6461 1.197721 CTGGTCATTCTTTGTCGGTGC 59.802 52.381 0.00 0.00 0.00 5.01
5892 6462 1.234821 GGTCATTCTTTGTCGGTGCA 58.765 50.000 0.00 0.00 0.00 4.57
5893 6463 1.606668 GGTCATTCTTTGTCGGTGCAA 59.393 47.619 0.00 0.00 0.00 4.08
5894 6464 2.604614 GGTCATTCTTTGTCGGTGCAAC 60.605 50.000 0.00 0.00 0.00 4.17
5895 6465 2.032799 GTCATTCTTTGTCGGTGCAACA 59.967 45.455 0.98 0.00 39.98 3.33
5896 6466 2.685388 TCATTCTTTGTCGGTGCAACAA 59.315 40.909 0.98 0.00 39.98 2.83
5897 6467 3.129462 TCATTCTTTGTCGGTGCAACAAA 59.871 39.130 13.13 13.13 42.63 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.195334 GGAGGACGCATGGGGCAT 62.195 66.667 18.51 10.92 45.17 4.40
112 128 4.444838 CGCGAATCCCACCGGACA 62.445 66.667 9.46 0.00 42.48 4.02
242 258 2.031870 AGCAGCGGATTAAAAATCCCC 58.968 47.619 12.03 4.49 34.76 4.81
337 353 0.108585 GGTTTGACCCAGCAGAGACA 59.891 55.000 0.00 0.00 30.04 3.41
343 359 1.896660 GCTTCGGTTTGACCCAGCA 60.897 57.895 9.84 0.00 39.63 4.41
569 586 2.417719 GCAGTGGTAAAGAGTGGAGTG 58.582 52.381 0.00 0.00 0.00 3.51
573 590 1.298859 GCGGCAGTGGTAAAGAGTGG 61.299 60.000 0.00 0.00 0.00 4.00
601 618 3.859386 CACACCGAAACCCGTATAAGTAC 59.141 47.826 0.00 0.00 36.31 2.73
614 631 6.150396 ACAAATTAAATGGTCACACCGAAA 57.850 33.333 0.00 0.00 42.58 3.46
625 642 3.361786 ACCCTCGGGACAAATTAAATGG 58.638 45.455 9.43 0.00 38.96 3.16
659 676 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
660 677 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
661 678 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
662 679 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
663 680 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
664 681 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
665 682 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
666 683 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
667 684 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
668 685 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
669 686 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
670 687 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
679 696 2.223805 GCCTTCAGTCCCAAACAAGTTG 60.224 50.000 0.00 0.00 36.94 3.16
680 697 2.031870 GCCTTCAGTCCCAAACAAGTT 58.968 47.619 0.00 0.00 0.00 2.66
681 698 1.215423 AGCCTTCAGTCCCAAACAAGT 59.785 47.619 0.00 0.00 0.00 3.16
682 699 1.986882 AGCCTTCAGTCCCAAACAAG 58.013 50.000 0.00 0.00 0.00 3.16
683 700 2.452600 AAGCCTTCAGTCCCAAACAA 57.547 45.000 0.00 0.00 0.00 2.83
684 701 2.452600 AAAGCCTTCAGTCCCAAACA 57.547 45.000 0.00 0.00 0.00 2.83
685 702 4.280929 ACAATAAAGCCTTCAGTCCCAAAC 59.719 41.667 0.00 0.00 0.00 2.93
686 703 4.479158 ACAATAAAGCCTTCAGTCCCAAA 58.521 39.130 0.00 0.00 0.00 3.28
687 704 4.112634 ACAATAAAGCCTTCAGTCCCAA 57.887 40.909 0.00 0.00 0.00 4.12
688 705 3.806949 ACAATAAAGCCTTCAGTCCCA 57.193 42.857 0.00 0.00 0.00 4.37
689 706 3.826729 ACAACAATAAAGCCTTCAGTCCC 59.173 43.478 0.00 0.00 0.00 4.46
690 707 5.221244 ACAACAACAATAAAGCCTTCAGTCC 60.221 40.000 0.00 0.00 0.00 3.85
691 708 5.831997 ACAACAACAATAAAGCCTTCAGTC 58.168 37.500 0.00 0.00 0.00 3.51
692 709 5.852282 ACAACAACAATAAAGCCTTCAGT 57.148 34.783 0.00 0.00 0.00 3.41
693 710 6.042143 ACAACAACAACAATAAAGCCTTCAG 58.958 36.000 0.00 0.00 0.00 3.02
694 711 5.971763 ACAACAACAACAATAAAGCCTTCA 58.028 33.333 0.00 0.00 0.00 3.02
695 712 6.312672 ACAACAACAACAACAATAAAGCCTTC 59.687 34.615 0.00 0.00 0.00 3.46
696 713 6.169800 ACAACAACAACAACAATAAAGCCTT 58.830 32.000 0.00 0.00 0.00 4.35
697 714 5.729510 ACAACAACAACAACAATAAAGCCT 58.270 33.333 0.00 0.00 0.00 4.58
698 715 6.128418 ACAACAACAACAACAACAATAAAGCC 60.128 34.615 0.00 0.00 0.00 4.35
699 716 6.826612 ACAACAACAACAACAACAATAAAGC 58.173 32.000 0.00 0.00 0.00 3.51
700 717 8.279103 ACAACAACAACAACAACAACAATAAAG 58.721 29.630 0.00 0.00 0.00 1.85
701 718 8.142994 ACAACAACAACAACAACAACAATAAA 57.857 26.923 0.00 0.00 0.00 1.40
702 719 7.715265 ACAACAACAACAACAACAACAATAA 57.285 28.000 0.00 0.00 0.00 1.40
703 720 7.224753 ACAACAACAACAACAACAACAACAATA 59.775 29.630 0.00 0.00 0.00 1.90
704 721 6.037610 ACAACAACAACAACAACAACAACAAT 59.962 30.769 0.00 0.00 0.00 2.71
705 722 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
706 723 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
707 724 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
708 725 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
709 726 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
710 727 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
711 728 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
712 729 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
713 730 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
714 731 6.313905 AGAAACAACAACAACAACAACAACAA 59.686 30.769 0.00 0.00 0.00 2.83
715 732 5.812642 AGAAACAACAACAACAACAACAACA 59.187 32.000 0.00 0.00 0.00 3.33
716 733 6.200097 AGAGAAACAACAACAACAACAACAAC 59.800 34.615 0.00 0.00 0.00 3.32
717 734 6.276847 AGAGAAACAACAACAACAACAACAA 58.723 32.000 0.00 0.00 0.00 2.83
718 735 5.837437 AGAGAAACAACAACAACAACAACA 58.163 33.333 0.00 0.00 0.00 3.33
719 736 6.640907 AGAAGAGAAACAACAACAACAACAAC 59.359 34.615 0.00 0.00 0.00 3.32
720 737 6.744112 AGAAGAGAAACAACAACAACAACAA 58.256 32.000 0.00 0.00 0.00 2.83
721 738 6.325919 AGAAGAGAAACAACAACAACAACA 57.674 33.333 0.00 0.00 0.00 3.33
722 739 6.089417 CCAAGAAGAGAAACAACAACAACAAC 59.911 38.462 0.00 0.00 0.00 3.32
723 740 6.155827 CCAAGAAGAGAAACAACAACAACAA 58.844 36.000 0.00 0.00 0.00 2.83
724 741 5.708948 CCAAGAAGAGAAACAACAACAACA 58.291 37.500 0.00 0.00 0.00 3.33
725 742 4.562789 GCCAAGAAGAGAAACAACAACAAC 59.437 41.667 0.00 0.00 0.00 3.32
726 743 4.219507 TGCCAAGAAGAGAAACAACAACAA 59.780 37.500 0.00 0.00 0.00 2.83
727 744 3.761218 TGCCAAGAAGAGAAACAACAACA 59.239 39.130 0.00 0.00 0.00 3.33
728 745 4.354587 CTGCCAAGAAGAGAAACAACAAC 58.645 43.478 0.00 0.00 0.00 3.32
729 746 3.381272 CCTGCCAAGAAGAGAAACAACAA 59.619 43.478 0.00 0.00 0.00 2.83
730 747 2.951642 CCTGCCAAGAAGAGAAACAACA 59.048 45.455 0.00 0.00 0.00 3.33
731 748 2.287849 GCCTGCCAAGAAGAGAAACAAC 60.288 50.000 0.00 0.00 0.00 3.32
732 749 1.956477 GCCTGCCAAGAAGAGAAACAA 59.044 47.619 0.00 0.00 0.00 2.83
733 750 1.143684 AGCCTGCCAAGAAGAGAAACA 59.856 47.619 0.00 0.00 0.00 2.83
734 751 1.902938 AGCCTGCCAAGAAGAGAAAC 58.097 50.000 0.00 0.00 0.00 2.78
735 752 2.508526 GAAGCCTGCCAAGAAGAGAAA 58.491 47.619 0.00 0.00 0.00 2.52
736 753 1.271597 GGAAGCCTGCCAAGAAGAGAA 60.272 52.381 0.00 0.00 0.00 2.87
737 754 0.326264 GGAAGCCTGCCAAGAAGAGA 59.674 55.000 0.00 0.00 0.00 3.10
738 755 0.037303 TGGAAGCCTGCCAAGAAGAG 59.963 55.000 0.00 0.00 31.13 2.85
739 756 0.037303 CTGGAAGCCTGCCAAGAAGA 59.963 55.000 0.00 0.00 34.44 2.87
740 757 2.564471 CTGGAAGCCTGCCAAGAAG 58.436 57.895 0.00 0.00 34.44 2.85
741 758 4.828409 CTGGAAGCCTGCCAAGAA 57.172 55.556 0.00 0.00 34.44 2.52
790 807 4.057432 CAAGCAACCGAACCAAAATTGAT 58.943 39.130 0.00 0.00 0.00 2.57
856 874 4.634199 CAAAAACAAGCCATGAGACCAAT 58.366 39.130 0.00 0.00 0.00 3.16
924 942 4.197750 CTGTCCTCAAGATTCATGAAGGG 58.802 47.826 14.54 8.67 0.00 3.95
962 980 7.677745 CCAGATCCTAGTACTAGTACCCTACTA 59.322 44.444 25.97 14.24 40.14 1.82
1536 1562 2.575805 AAGGCAAGGAGAAGACAAGG 57.424 50.000 0.00 0.00 0.00 3.61
1714 1740 5.163824 GCAGGCAAAATTCTAAGCATTTTCC 60.164 40.000 0.00 0.00 32.57 3.13
1722 1748 6.116680 CTACAGAGCAGGCAAAATTCTAAG 57.883 41.667 0.00 0.00 0.00 2.18
1997 2023 8.024865 GCAATGCTTGATATATATTTGTCAGCA 58.975 33.333 13.98 13.98 33.07 4.41
2240 2266 6.814954 AGAAGATATCCTCCAAAACTAGCA 57.185 37.500 0.00 0.00 0.00 3.49
2269 2295 4.571984 CCAAAGACATCGCTATGACATTCA 59.428 41.667 5.05 0.00 36.54 2.57
2750 2776 7.659186 AGGATAAATACTCACGTTCTGGATAC 58.341 38.462 0.00 0.00 0.00 2.24
2801 2831 6.933521 AGTATTCAGCCAGTAGATAAGCAATG 59.066 38.462 0.00 0.00 0.00 2.82
2914 2944 6.826231 TCTTTTCCAACAACAGTGATCTAACA 59.174 34.615 0.00 0.00 0.00 2.41
2922 2952 6.813152 ACTCAAATTCTTTTCCAACAACAGTG 59.187 34.615 0.00 0.00 0.00 3.66
3034 3064 1.333308 GTGTGTGTGCTTATGTGTGCA 59.667 47.619 0.00 0.00 36.79 4.57
3035 3065 1.603802 AGTGTGTGTGCTTATGTGTGC 59.396 47.619 0.00 0.00 0.00 4.57
3055 3085 7.496591 CCTTTGTTTACCAGTACTAACAAGTGA 59.503 37.037 16.98 6.69 40.38 3.41
3056 3086 7.496591 TCCTTTGTTTACCAGTACTAACAAGTG 59.503 37.037 16.98 14.39 40.38 3.16
3063 3095 8.197592 TGAAGATCCTTTGTTTACCAGTACTA 57.802 34.615 0.00 0.00 0.00 1.82
3091 3123 2.361119 GGACAAAGAGGAAACAACCCAC 59.639 50.000 0.00 0.00 0.00 4.61
3195 3227 4.331968 TGTTAGCATAACCAAACCTCCAG 58.668 43.478 0.00 0.00 0.00 3.86
3231 3263 7.915293 TCGTTTCAACACTAATGACCATAAT 57.085 32.000 0.00 0.00 0.00 1.28
3232 3264 7.201487 CGATCGTTTCAACACTAATGACCATAA 60.201 37.037 7.03 0.00 0.00 1.90
3233 3265 6.254804 CGATCGTTTCAACACTAATGACCATA 59.745 38.462 7.03 0.00 0.00 2.74
3283 3315 4.141711 ACAGCGTACAGGGATGACAATTAT 60.142 41.667 0.00 0.00 0.00 1.28
3348 3380 4.942852 TGCAAAATGTCGTGAGGAAAAAT 58.057 34.783 0.00 0.00 0.00 1.82
3513 3545 7.806014 TCAACTTACCGTATCTTTTTCAAATGC 59.194 33.333 0.00 0.00 0.00 3.56
3603 3635 1.522668 CACATTTCCTGCACGGAGAA 58.477 50.000 5.26 4.52 44.28 2.87
4053 4085 0.461135 CACAATGCAATACCAGGGGC 59.539 55.000 0.00 0.00 0.00 5.80
4239 4290 4.552355 CGACATACAAAGTGTACTGGTGA 58.448 43.478 0.00 0.00 35.42 4.02
4251 4302 2.480037 CTGCTGAACTGCGACATACAAA 59.520 45.455 0.00 0.00 35.36 2.83
4321 4372 0.902984 TTCCGGCTTCCAGCTCTACA 60.903 55.000 0.00 0.00 41.99 2.74
4330 4381 2.438614 GAAGGGCTTCCGGCTTCC 60.439 66.667 0.00 0.00 41.46 3.46
4441 4492 4.873817 TGCAAAGAAATCATGGACACTTG 58.126 39.130 0.00 0.00 0.00 3.16
4715 5025 1.470632 GGCCTTGTCTCTCACGATGAG 60.471 57.143 0.00 8.24 45.59 2.90
5070 5386 1.593787 CTTGAGCTCAGCCTTCCGA 59.406 57.895 17.43 0.00 0.00 4.55
5095 5411 3.541632 TCTGTGGAGACAACAAAAGGAC 58.458 45.455 0.00 0.00 46.06 3.85
5221 5538 9.906660 CAATAAGCACCAAATCTGTTTACTAAA 57.093 29.630 0.00 0.00 0.00 1.85
5266 5583 6.544928 AACCTCATTTCCCCAAAATATGTC 57.455 37.500 0.00 0.00 35.77 3.06
5310 5627 4.881850 CAGGTATACATTCCTTGGTGGTTC 59.118 45.833 5.01 0.00 37.07 3.62
5413 5730 6.058833 ACTATTCTCTCTTCAGCGTCTATCA 58.941 40.000 0.00 0.00 0.00 2.15
5442 5759 4.433615 TCTATCACAAGCGTTTCCTGATC 58.566 43.478 5.31 0.00 0.00 2.92
5461 5778 5.438698 TGTCGATTTGGGGGTAATTTCTA 57.561 39.130 0.00 0.00 0.00 2.10
5481 5798 3.644265 GGGGTAAAAAGGTGACCAAATGT 59.356 43.478 3.63 0.00 34.73 2.71
5545 5863 2.606108 GGGTAATTTTTCTGGCAAGCG 58.394 47.619 0.00 0.00 0.00 4.68
5551 5869 5.240844 GTCGATATGGGGGTAATTTTTCTGG 59.759 44.000 0.00 0.00 0.00 3.86
5554 5872 6.894339 ATGTCGATATGGGGGTAATTTTTC 57.106 37.500 0.00 0.00 0.00 2.29
5779 6349 2.113139 CCAAACCTCGTGGGCACT 59.887 61.111 8.63 0.00 39.10 4.40
5804 6374 2.506957 GGTGGGGCCAAACCAGTTG 61.507 63.158 19.74 0.00 42.05 3.16
5847 6417 1.548269 CAGCTCTTTCTCTTCCTCCGT 59.452 52.381 0.00 0.00 0.00 4.69
5866 6436 0.537143 ACAAAGAATGACCAGGCGCA 60.537 50.000 10.83 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.