Multiple sequence alignment - TraesCS1D01G336600

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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 TraesCS1D01G336600 chr1D 100.000 2910 0 0 1 2910 426651011 426653920 0.000000e+00 5374
1 TraesCS1D01G336600 chr1D 97.031 1044 29 2 1868 2910 69481763 69482805 0.000000e+00 1755
2 TraesCS1D01G336600 chr1D 85.841 113 16 0 1284 1396 17169027 17168915 1.420000e-23 121
3 TraesCS1D01G336600 chr6D 97.318 1044 26 2 1868 2910 119451058 119452100 0.000000e+00 1772
4 TraesCS1D01G336600 chr6D 96.839 1044 30 3 1869 2910 144546072 144547114 0.000000e+00 1742
5 TraesCS1D01G336600 chr2D 97.124 1043 29 1 1869 2910 512897759 512896717 0.000000e+00 1759
6 TraesCS1D01G336600 chr4D 97.031 1044 28 3 1867 2910 66479949 66478909 0.000000e+00 1753
7 TraesCS1D01G336600 chr4D 96.272 1046 34 5 1868 2910 277622030 277620987 0.000000e+00 1711
8 TraesCS1D01G336600 chr5D 96.842 1045 29 4 1868 2910 532000527 532001569 0.000000e+00 1744
9 TraesCS1D01G336600 chr5D 96.364 1045 33 5 1869 2910 329850839 329851881 0.000000e+00 1714
10 TraesCS1D01G336600 chr5D 83.333 126 19 2 1284 1408 103175916 103175792 6.590000e-22 115
11 TraesCS1D01G336600 chr5D 78.916 166 31 3 1245 1408 525957952 525958115 3.070000e-20 110
12 TraesCS1D01G336600 chr1A 95.338 1094 38 4 771 1851 521738495 521739588 0.000000e+00 1725
13 TraesCS1D01G336600 chr1A 92.336 548 22 12 1 547 521737838 521738366 0.000000e+00 761
14 TraesCS1D01G336600 chr1A 84.000 125 20 0 1284 1408 18461681 18461557 1.420000e-23 121
15 TraesCS1D01G336600 chr3D 96.077 1045 35 3 1869 2910 558587892 558586851 0.000000e+00 1698
16 TraesCS1D01G336600 chr3D 88.318 214 19 3 1207 1420 406772760 406772553 4.810000e-63 252
17 TraesCS1D01G336600 chr3D 81.726 197 27 8 1221 1409 376169979 376169784 3.880000e-34 156
18 TraesCS1D01G336600 chr3D 87.611 113 14 0 1284 1396 610544129 610544241 6.540000e-27 132
19 TraesCS1D01G336600 chr1B 93.447 1053 48 7 737 1774 576521198 576522244 0.000000e+00 1543
20 TraesCS1D01G336600 chr1B 94.073 523 24 5 27 549 576520604 576521119 0.000000e+00 787
21 TraesCS1D01G336600 chr3A 88.785 214 18 3 1207 1420 544969600 544969807 1.030000e-64 257
22 TraesCS1D01G336600 chr3A 82.682 179 25 5 1237 1409 500978816 500978638 1.400000e-33 154
23 TraesCS1D01G336600 chr3B 88.318 214 19 3 1207 1420 532667438 532667231 4.810000e-63 252
24 TraesCS1D01G336600 chr7B 90.503 179 16 1 1238 1415 712841444 712841622 4.850000e-58 235
25 TraesCS1D01G336600 chr7B 89.071 183 18 2 1233 1415 712841873 712842053 2.920000e-55 226
26 TraesCS1D01G336600 chr5B 89.071 183 18 2 1233 1415 488559779 488559959 2.920000e-55 226
27 TraesCS1D01G336600 chr5B 85.714 126 16 2 1284 1408 112194674 112194550 6.540000e-27 132
28 TraesCS1D01G336600 chr5B 78.916 166 31 3 1245 1408 660589522 660589685 3.070000e-20 110
29 TraesCS1D01G336600 chr5A 84.921 126 17 2 1284 1408 95869266 95869390 3.040000e-25 126


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 TraesCS1D01G336600 chr1D 426651011 426653920 2909 False 5374.0 5374 100.000 1 2910 1 chr1D.!!$F2 2909
1 TraesCS1D01G336600 chr1D 69481763 69482805 1042 False 1755.0 1755 97.031 1868 2910 1 chr1D.!!$F1 1042
2 TraesCS1D01G336600 chr6D 119451058 119452100 1042 False 1772.0 1772 97.318 1868 2910 1 chr6D.!!$F1 1042
3 TraesCS1D01G336600 chr6D 144546072 144547114 1042 False 1742.0 1742 96.839 1869 2910 1 chr6D.!!$F2 1041
4 TraesCS1D01G336600 chr2D 512896717 512897759 1042 True 1759.0 1759 97.124 1869 2910 1 chr2D.!!$R1 1041
5 TraesCS1D01G336600 chr4D 66478909 66479949 1040 True 1753.0 1753 97.031 1867 2910 1 chr4D.!!$R1 1043
6 TraesCS1D01G336600 chr4D 277620987 277622030 1043 True 1711.0 1711 96.272 1868 2910 1 chr4D.!!$R2 1042
7 TraesCS1D01G336600 chr5D 532000527 532001569 1042 False 1744.0 1744 96.842 1868 2910 1 chr5D.!!$F3 1042
8 TraesCS1D01G336600 chr5D 329850839 329851881 1042 False 1714.0 1714 96.364 1869 2910 1 chr5D.!!$F1 1041
9 TraesCS1D01G336600 chr1A 521737838 521739588 1750 False 1243.0 1725 93.837 1 1851 2 chr1A.!!$F1 1850
10 TraesCS1D01G336600 chr3D 558586851 558587892 1041 True 1698.0 1698 96.077 1869 2910 1 chr3D.!!$R3 1041
11 TraesCS1D01G336600 chr1B 576520604 576522244 1640 False 1165.0 1543 93.760 27 1774 2 chr1B.!!$F1 1747
12 TraesCS1D01G336600 chr7B 712841444 712842053 609 False 230.5 235 89.787 1233 1415 2 chr7B.!!$F1 182

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
299 300 0.095417 GCCAAAGCGAGTAAAGCGAG 59.905 55.0 0.00 0.0 40.04 5.03 F
550 552 0.188342 AGGCCATGTTTGGAACACCT 59.812 50.0 5.01 0.0 46.92 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1453 1.148310 CAACACTCATGACCGTGGAC 58.852 55.0 16.80 0.0 35.51 4.02 R
1938 1961 2.545532 CGGGCCGACGGTGTATTATTTA 60.546 50.0 24.41 0.0 0.00 1.40 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
24 25 7.088589 TCAACAGAAAGAAAGGAAGAAGTTG 57.911 36.000 0.00 0.00 35.30 3.16
32 33 9.723447 GAAAGAAAGGAAGAAGTTGTAAAGAAG 57.277 33.333 0.00 0.00 0.00 2.85
87 88 7.835634 AAATCTAAGTCTAGCTACAAAGTGC 57.164 36.000 0.00 0.00 0.00 4.40
88 89 6.783708 ATCTAAGTCTAGCTACAAAGTGCT 57.216 37.500 0.00 0.00 42.67 4.40
91 92 5.723672 AAGTCTAGCTACAAAGTGCTACA 57.276 39.130 0.00 0.00 40.35 2.74
226 227 1.069049 CCCTTTGGAAAGCCACTGTTG 59.931 52.381 0.00 0.00 45.94 3.33
299 300 0.095417 GCCAAAGCGAGTAAAGCGAG 59.905 55.000 0.00 0.00 40.04 5.03
362 363 4.057432 CCACGAAAAAGCCATCAAATGTT 58.943 39.130 0.00 0.00 0.00 2.71
521 523 0.307760 CGTTTCTTGGCGCTGAAACT 59.692 50.000 30.41 0.00 45.59 2.66
536 538 4.881850 GCTGAAACTAGCTTAATTAGGCCA 59.118 41.667 15.33 1.72 40.52 5.36
549 551 1.917872 TAGGCCATGTTTGGAACACC 58.082 50.000 5.01 0.00 46.92 4.16
550 552 0.188342 AGGCCATGTTTGGAACACCT 59.812 50.000 5.01 0.00 46.92 4.00
552 554 0.319813 GCCATGTTTGGAACACCTGC 60.320 55.000 0.00 0.00 46.92 4.85
553 555 1.331214 CCATGTTTGGAACACCTGCT 58.669 50.000 0.00 0.00 46.92 4.24
554 556 1.688197 CCATGTTTGGAACACCTGCTT 59.312 47.619 0.00 0.00 46.92 3.91
555 557 2.288395 CCATGTTTGGAACACCTGCTTC 60.288 50.000 0.00 0.00 46.92 3.86
557 559 1.748493 TGTTTGGAACACCTGCTTCAC 59.252 47.619 0.00 0.00 39.29 3.18
560 562 1.679139 TGGAACACCTGCTTCACTTG 58.321 50.000 0.00 0.00 0.00 3.16
561 563 1.211703 TGGAACACCTGCTTCACTTGA 59.788 47.619 0.00 0.00 0.00 3.02
562 564 2.297701 GGAACACCTGCTTCACTTGAA 58.702 47.619 0.00 0.00 0.00 2.69
563 565 2.033424 GGAACACCTGCTTCACTTGAAC 59.967 50.000 0.00 0.00 0.00 3.18
564 566 1.680338 ACACCTGCTTCACTTGAACC 58.320 50.000 0.00 0.00 0.00 3.62
566 568 2.301346 CACCTGCTTCACTTGAACCTT 58.699 47.619 0.00 0.00 0.00 3.50
567 569 2.689983 CACCTGCTTCACTTGAACCTTT 59.310 45.455 0.00 0.00 0.00 3.11
568 570 3.131046 CACCTGCTTCACTTGAACCTTTT 59.869 43.478 0.00 0.00 0.00 2.27
570 572 4.142160 ACCTGCTTCACTTGAACCTTTTTC 60.142 41.667 0.00 0.00 0.00 2.29
571 573 4.142182 CCTGCTTCACTTGAACCTTTTTCA 60.142 41.667 0.00 0.00 0.00 2.69
573 575 4.112634 GCTTCACTTGAACCTTTTTCACC 58.887 43.478 0.00 0.00 0.00 4.02
574 576 4.142160 GCTTCACTTGAACCTTTTTCACCT 60.142 41.667 0.00 0.00 0.00 4.00
575 577 4.981806 TCACTTGAACCTTTTTCACCTG 57.018 40.909 0.00 0.00 0.00 4.00
577 579 3.131046 CACTTGAACCTTTTTCACCTGCT 59.869 43.478 0.00 0.00 0.00 4.24
578 580 3.769300 ACTTGAACCTTTTTCACCTGCTT 59.231 39.130 0.00 0.00 0.00 3.91
581 583 3.130340 TGAACCTTTTTCACCTGCTTCAC 59.870 43.478 0.00 0.00 0.00 3.18
583 585 2.952310 ACCTTTTTCACCTGCTTCACTC 59.048 45.455 0.00 0.00 0.00 3.51
584 586 2.951642 CCTTTTTCACCTGCTTCACTCA 59.048 45.455 0.00 0.00 0.00 3.41
587 589 0.761187 TTCACCTGCTTCACTCAGCT 59.239 50.000 0.00 0.00 40.79 4.24
588 590 1.632589 TCACCTGCTTCACTCAGCTA 58.367 50.000 0.00 0.00 40.79 3.32
589 591 1.970640 TCACCTGCTTCACTCAGCTAA 59.029 47.619 0.00 0.00 40.79 3.09
590 592 2.568956 TCACCTGCTTCACTCAGCTAAT 59.431 45.455 0.00 0.00 40.79 1.73
591 593 3.008375 TCACCTGCTTCACTCAGCTAATT 59.992 43.478 0.00 0.00 40.79 1.40
592 594 4.222810 TCACCTGCTTCACTCAGCTAATTA 59.777 41.667 0.00 0.00 40.79 1.40
593 595 4.331168 CACCTGCTTCACTCAGCTAATTAC 59.669 45.833 0.00 0.00 40.79 1.89
594 596 3.553511 CCTGCTTCACTCAGCTAATTACG 59.446 47.826 0.00 0.00 40.79 3.18
595 597 3.521560 TGCTTCACTCAGCTAATTACGG 58.478 45.455 0.00 0.00 40.79 4.02
596 598 3.194755 TGCTTCACTCAGCTAATTACGGA 59.805 43.478 0.00 0.00 40.79 4.69
597 599 4.181578 GCTTCACTCAGCTAATTACGGAA 58.818 43.478 0.00 0.00 36.79 4.30
598 600 4.630069 GCTTCACTCAGCTAATTACGGAAA 59.370 41.667 0.00 0.00 36.79 3.13
599 601 5.121768 GCTTCACTCAGCTAATTACGGAAAA 59.878 40.000 0.00 0.00 36.79 2.29
600 602 6.183360 GCTTCACTCAGCTAATTACGGAAAAT 60.183 38.462 0.00 0.00 36.79 1.82
601 603 7.626452 GCTTCACTCAGCTAATTACGGAAAATT 60.626 37.037 0.00 0.00 36.79 1.82
602 604 8.780846 TTCACTCAGCTAATTACGGAAAATTA 57.219 30.769 0.00 0.00 31.63 1.40
603 605 8.420374 TCACTCAGCTAATTACGGAAAATTAG 57.580 34.615 16.61 16.61 45.84 1.73
604 606 7.494625 TCACTCAGCTAATTACGGAAAATTAGG 59.505 37.037 19.85 11.16 44.36 2.69
613 615 8.969121 AATTACGGAAAATTAGGTAAAAACCG 57.031 30.769 0.00 0.00 42.78 4.44
614 616 7.736447 TTACGGAAAATTAGGTAAAAACCGA 57.264 32.000 0.00 0.00 40.78 4.69
615 617 6.822667 ACGGAAAATTAGGTAAAAACCGAT 57.177 33.333 0.00 0.00 40.78 4.18
616 618 7.920160 ACGGAAAATTAGGTAAAAACCGATA 57.080 32.000 0.00 0.00 40.78 2.92
617 619 7.751732 ACGGAAAATTAGGTAAAAACCGATAC 58.248 34.615 0.00 0.00 40.78 2.24
618 620 7.390162 ACGGAAAATTAGGTAAAAACCGATACA 59.610 33.333 0.00 0.00 40.78 2.29
619 621 8.235905 CGGAAAATTAGGTAAAAACCGATACAA 58.764 33.333 0.00 0.00 40.16 2.41
620 622 9.911138 GGAAAATTAGGTAAAAACCGATACAAA 57.089 29.630 0.00 0.00 34.28 2.83
625 627 9.681692 ATTAGGTAAAAACCGATACAAACAAAC 57.318 29.630 0.00 0.00 34.28 2.93
626 628 7.098074 AGGTAAAAACCGATACAAACAAACA 57.902 32.000 0.00 0.00 34.28 2.83
627 629 7.197703 AGGTAAAAACCGATACAAACAAACAG 58.802 34.615 0.00 0.00 34.28 3.16
628 630 6.418523 GGTAAAAACCGATACAAACAAACAGG 59.581 38.462 0.00 0.00 0.00 4.00
629 631 4.577834 AAACCGATACAAACAAACAGGG 57.422 40.909 0.00 0.00 0.00 4.45
630 632 3.217681 ACCGATACAAACAAACAGGGT 57.782 42.857 0.00 0.00 0.00 4.34
631 633 3.558033 ACCGATACAAACAAACAGGGTT 58.442 40.909 0.00 0.00 0.00 4.11
632 634 4.716794 ACCGATACAAACAAACAGGGTTA 58.283 39.130 0.00 0.00 0.00 2.85
633 635 4.758165 ACCGATACAAACAAACAGGGTTAG 59.242 41.667 0.00 0.00 0.00 2.34
634 636 4.155280 CCGATACAAACAAACAGGGTTAGG 59.845 45.833 0.00 0.00 0.00 2.69
635 637 4.379082 CGATACAAACAAACAGGGTTAGGC 60.379 45.833 0.00 0.00 0.00 3.93
636 638 2.036387 ACAAACAAACAGGGTTAGGCC 58.964 47.619 0.00 0.00 0.00 5.19
637 639 2.035632 CAAACAAACAGGGTTAGGCCA 58.964 47.619 5.01 0.00 39.65 5.36
638 640 1.995376 AACAAACAGGGTTAGGCCAG 58.005 50.000 5.01 0.00 39.65 4.85
639 641 1.145571 ACAAACAGGGTTAGGCCAGA 58.854 50.000 5.01 0.00 39.65 3.86
640 642 1.202891 ACAAACAGGGTTAGGCCAGAC 60.203 52.381 5.01 2.07 39.65 3.51
641 643 1.145571 AAACAGGGTTAGGCCAGACA 58.854 50.000 5.01 0.00 39.65 3.41
642 644 1.372501 AACAGGGTTAGGCCAGACAT 58.627 50.000 5.01 0.00 39.65 3.06
643 645 0.912486 ACAGGGTTAGGCCAGACATC 59.088 55.000 5.01 0.00 39.65 3.06
644 646 0.911769 CAGGGTTAGGCCAGACATCA 59.088 55.000 5.01 0.00 39.65 3.07
645 647 0.912486 AGGGTTAGGCCAGACATCAC 59.088 55.000 5.01 0.00 39.65 3.06
646 648 0.462047 GGGTTAGGCCAGACATCACG 60.462 60.000 5.01 0.00 39.65 4.35
647 649 0.249398 GGTTAGGCCAGACATCACGT 59.751 55.000 5.01 0.00 37.17 4.49
648 650 1.479323 GGTTAGGCCAGACATCACGTA 59.521 52.381 5.01 0.00 37.17 3.57
649 651 2.537401 GTTAGGCCAGACATCACGTAC 58.463 52.381 5.01 0.00 0.00 3.67
650 652 0.736636 TAGGCCAGACATCACGTACG 59.263 55.000 15.01 15.01 0.00 3.67
651 653 1.518572 GGCCAGACATCACGTACGG 60.519 63.158 21.06 8.79 0.00 4.02
652 654 1.518572 GCCAGACATCACGTACGGG 60.519 63.158 21.06 17.09 0.00 5.28
653 655 1.141019 CCAGACATCACGTACGGGG 59.859 63.158 19.08 10.34 0.00 5.73
654 656 1.518572 CAGACATCACGTACGGGGC 60.519 63.158 19.08 6.96 0.00 5.80
655 657 2.202837 GACATCACGTACGGGGCC 60.203 66.667 19.08 0.00 0.00 5.80
656 658 4.137872 ACATCACGTACGGGGCCG 62.138 66.667 19.08 8.89 46.03 6.13
675 677 1.823828 GCGCATGAGCTTGATCTTTG 58.176 50.000 14.75 0.00 39.10 2.77
676 678 1.823828 CGCATGAGCTTGATCTTTGC 58.176 50.000 0.00 0.00 39.10 3.68
677 679 1.533338 CGCATGAGCTTGATCTTTGCC 60.533 52.381 0.00 0.00 39.10 4.52
678 680 1.475280 GCATGAGCTTGATCTTTGCCA 59.525 47.619 0.00 0.00 37.91 4.92
679 681 2.094390 GCATGAGCTTGATCTTTGCCAA 60.094 45.455 0.00 0.00 37.91 4.52
680 682 3.770666 CATGAGCTTGATCTTTGCCAAG 58.229 45.455 0.00 0.00 41.84 3.61
681 683 2.867624 TGAGCTTGATCTTTGCCAAGT 58.132 42.857 0.00 0.00 41.21 3.16
682 684 2.816087 TGAGCTTGATCTTTGCCAAGTC 59.184 45.455 0.00 0.00 41.21 3.01
683 685 1.808945 AGCTTGATCTTTGCCAAGTCG 59.191 47.619 0.00 0.00 41.21 4.18
684 686 1.135575 GCTTGATCTTTGCCAAGTCGG 60.136 52.381 0.00 0.00 41.21 4.79
694 696 2.779282 CCAAGTCGGCATGCATACA 58.221 52.632 21.36 0.00 0.00 2.29
695 697 1.311859 CCAAGTCGGCATGCATACAT 58.688 50.000 21.36 6.80 36.79 2.29
700 702 1.800586 GTCGGCATGCATACATCGAAT 59.199 47.619 21.36 0.00 35.19 3.34
702 704 3.431912 GTCGGCATGCATACATCGAATTA 59.568 43.478 21.36 0.00 35.19 1.40
705 707 4.667415 CGGCATGCATACATCGAATTACAG 60.667 45.833 21.36 0.00 32.87 2.74
706 708 4.153986 GCATGCATACATCGAATTACAGC 58.846 43.478 14.21 0.00 32.87 4.40
707 709 4.388790 CATGCATACATCGAATTACAGCG 58.611 43.478 0.00 0.00 32.87 5.18
708 710 3.453424 TGCATACATCGAATTACAGCGT 58.547 40.909 0.00 0.00 0.00 5.07
709 711 3.868661 TGCATACATCGAATTACAGCGTT 59.131 39.130 0.00 0.00 0.00 4.84
728 730 3.701664 GTTCCAAATGGGTCCTTGATCT 58.298 45.455 0.00 0.00 38.11 2.75
729 731 4.625324 CGTTCCAAATGGGTCCTTGATCTA 60.625 45.833 0.00 0.00 38.11 1.98
730 732 4.503714 TCCAAATGGGTCCTTGATCTAC 57.496 45.455 0.00 0.00 38.11 2.59
731 733 4.111577 TCCAAATGGGTCCTTGATCTACT 58.888 43.478 0.00 0.00 38.11 2.57
732 734 5.285401 TCCAAATGGGTCCTTGATCTACTA 58.715 41.667 0.00 0.00 38.11 1.82
733 735 5.729229 TCCAAATGGGTCCTTGATCTACTAA 59.271 40.000 0.00 0.00 38.11 2.24
734 736 6.389869 TCCAAATGGGTCCTTGATCTACTAAT 59.610 38.462 0.00 0.00 38.11 1.73
735 737 7.062957 CCAAATGGGTCCTTGATCTACTAATT 58.937 38.462 0.00 0.00 0.00 1.40
756 758 9.208022 CTAATTAATTAGTCATCGAGGCAATGA 57.792 33.333 22.14 0.00 36.01 2.57
759 761 1.661341 AGTCATCGAGGCAATGAAGC 58.339 50.000 0.00 0.00 35.04 3.86
763 765 0.391661 ATCGAGGCAATGAAGCGTGT 60.392 50.000 0.00 0.00 34.64 4.49
764 766 1.133253 CGAGGCAATGAAGCGTGTG 59.867 57.895 0.00 0.00 34.64 3.82
765 767 1.503542 GAGGCAATGAAGCGTGTGG 59.496 57.895 0.00 0.00 34.64 4.17
766 768 2.126346 GGCAATGAAGCGTGTGGC 60.126 61.111 0.00 0.00 44.05 5.01
768 770 2.918345 GCAATGAAGCGTGTGGCCA 61.918 57.895 0.00 0.00 45.17 5.36
769 771 1.885157 CAATGAAGCGTGTGGCCAT 59.115 52.632 9.72 0.00 45.17 4.40
799 804 2.522436 AGACGGGGACACGAACCA 60.522 61.111 0.00 0.00 37.61 3.67
803 808 1.524165 CGGGGACACGAACCAAACA 60.524 57.895 0.00 0.00 35.47 2.83
943 948 2.628657 ACAGAGCACGTATCCTATTCCC 59.371 50.000 0.00 0.00 0.00 3.97
945 950 0.966920 AGCACGTATCCTATTCCCGG 59.033 55.000 0.00 0.00 0.00 5.73
1011 1018 2.894387 GTGGCATCAGAGAGCGCC 60.894 66.667 2.29 0.00 45.11 6.53
1014 1021 4.212913 GCATCAGAGAGCGCCGGA 62.213 66.667 5.05 0.00 0.00 5.14
1434 1453 3.803082 CCGGTGCTTCATGGTGCG 61.803 66.667 0.00 0.00 0.00 5.34
1499 1518 2.766229 TCCGGGGATGCCGAATGA 60.766 61.111 0.00 0.00 0.00 2.57
1669 1688 2.766263 TCTCTGCGGATCAACCAATACT 59.234 45.455 0.00 0.00 38.90 2.12
1784 1804 5.234329 GGTTTGCTATTTCTCAATCGATCGA 59.766 40.000 21.86 21.86 0.00 3.59
1792 1812 6.635030 TTTCTCAATCGATCGAGGAATAGA 57.365 37.500 23.84 16.75 0.00 1.98
1804 1824 7.802720 CGATCGAGGAATAGATATAGCTCAATG 59.197 40.741 10.26 0.00 0.00 2.82
1820 1840 4.240888 CTCAATGGATGCTATAGTGGTCG 58.759 47.826 0.84 0.00 0.00 4.79
1842 1862 3.617263 GGATTGTACGCAGAGATTCGTTT 59.383 43.478 0.00 0.00 39.79 3.60
1844 1864 5.390567 GGATTGTACGCAGAGATTCGTTTTT 60.391 40.000 0.00 0.00 39.79 1.94
2064 2087 3.419580 TCGGATTGGGCTGGCCAT 61.420 61.111 24.56 13.77 37.98 4.40
2225 2336 2.355615 CCTTCCTCCCTTCTTCTTCTGC 60.356 54.545 0.00 0.00 0.00 4.26
2250 2361 5.246429 TCTTCTTCTGTTCTTACCTTCTCCC 59.754 44.000 0.00 0.00 0.00 4.30
2477 2589 0.318445 CGTCGTTCTTCGTTGGAGGT 60.318 55.000 0.00 0.00 40.80 3.85
2625 2738 5.303747 TGTGAAATAAATTAGGTGTGCGG 57.696 39.130 0.00 0.00 0.00 5.69
2645 2758 2.482316 GGTTATTGTTATTTGCCCCGGC 60.482 50.000 0.00 0.00 42.35 6.13
2805 2918 4.982916 CGTAATATAGGCAGTCCAGTCAAC 59.017 45.833 0.00 0.00 33.74 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 4.686091 GCTTTGCTTTAGGGCTTTTTGTAG 59.314 41.667 0.00 0.00 0.00 2.74
88 89 4.343814 AGCTTTGCTTTAGGGCTTTTTGTA 59.656 37.500 0.00 0.00 33.89 2.41
299 300 1.339727 ACTATCCGAAACCAAGGTGCC 60.340 52.381 0.00 0.00 0.00 5.01
362 363 5.278463 GCTTCCTTGCTTTACAATCAACTGA 60.278 40.000 0.00 0.00 37.72 3.41
521 523 5.761205 TCCAAACATGGCCTAATTAAGCTA 58.239 37.500 3.32 0.22 0.00 3.32
536 538 2.362077 GTGAAGCAGGTGTTCCAAACAT 59.638 45.455 0.00 0.00 44.35 2.71
552 554 5.343249 CAGGTGAAAAAGGTTCAAGTGAAG 58.657 41.667 0.00 0.00 34.27 3.02
553 555 4.381505 GCAGGTGAAAAAGGTTCAAGTGAA 60.382 41.667 0.00 0.00 0.00 3.18
554 556 3.130340 GCAGGTGAAAAAGGTTCAAGTGA 59.870 43.478 0.00 0.00 0.00 3.41
555 557 3.131046 AGCAGGTGAAAAAGGTTCAAGTG 59.869 43.478 0.00 0.00 0.00 3.16
557 559 4.142182 TGAAGCAGGTGAAAAAGGTTCAAG 60.142 41.667 0.00 0.00 43.07 3.02
560 562 3.381590 AGTGAAGCAGGTGAAAAAGGTTC 59.618 43.478 0.00 0.00 38.55 3.62
561 563 3.365472 AGTGAAGCAGGTGAAAAAGGTT 58.635 40.909 0.00 0.00 0.00 3.50
562 564 2.952310 GAGTGAAGCAGGTGAAAAAGGT 59.048 45.455 0.00 0.00 0.00 3.50
563 565 2.951642 TGAGTGAAGCAGGTGAAAAAGG 59.048 45.455 0.00 0.00 0.00 3.11
564 566 3.549625 GCTGAGTGAAGCAGGTGAAAAAG 60.550 47.826 0.00 0.00 43.01 2.27
566 568 1.949525 GCTGAGTGAAGCAGGTGAAAA 59.050 47.619 0.00 0.00 43.01 2.29
567 569 1.141657 AGCTGAGTGAAGCAGGTGAAA 59.858 47.619 0.00 0.00 46.08 2.69
568 570 0.761187 AGCTGAGTGAAGCAGGTGAA 59.239 50.000 0.00 0.00 46.08 3.18
570 572 2.462456 TTAGCTGAGTGAAGCAGGTG 57.538 50.000 0.00 0.00 46.08 4.00
571 573 3.710209 AATTAGCTGAGTGAAGCAGGT 57.290 42.857 0.00 0.00 46.08 4.00
573 575 3.553511 CCGTAATTAGCTGAGTGAAGCAG 59.446 47.826 0.00 0.00 46.08 4.24
574 576 3.194755 TCCGTAATTAGCTGAGTGAAGCA 59.805 43.478 0.00 0.00 46.08 3.91
575 577 3.782046 TCCGTAATTAGCTGAGTGAAGC 58.218 45.455 0.00 0.00 43.88 3.86
577 579 7.681939 AATTTTCCGTAATTAGCTGAGTGAA 57.318 32.000 0.00 0.00 0.00 3.18
578 580 7.494625 CCTAATTTTCCGTAATTAGCTGAGTGA 59.505 37.037 0.00 0.00 42.64 3.41
581 583 7.787725 ACCTAATTTTCCGTAATTAGCTGAG 57.212 36.000 0.00 5.87 42.64 3.35
588 590 8.791675 TCGGTTTTTACCTAATTTTCCGTAATT 58.208 29.630 0.00 0.00 37.26 1.40
589 591 8.334263 TCGGTTTTTACCTAATTTTCCGTAAT 57.666 30.769 0.00 0.00 37.26 1.89
590 592 7.736447 TCGGTTTTTACCTAATTTTCCGTAA 57.264 32.000 0.00 0.00 37.26 3.18
591 593 7.920160 ATCGGTTTTTACCTAATTTTCCGTA 57.080 32.000 0.00 0.00 37.26 4.02
592 594 6.822667 ATCGGTTTTTACCTAATTTTCCGT 57.177 33.333 0.00 0.00 37.26 4.69
593 595 7.750769 TGTATCGGTTTTTACCTAATTTTCCG 58.249 34.615 0.00 0.00 37.29 4.30
594 596 9.911138 TTTGTATCGGTTTTTACCTAATTTTCC 57.089 29.630 0.00 0.00 0.00 3.13
599 601 9.681692 GTTTGTTTGTATCGGTTTTTACCTAAT 57.318 29.630 0.00 0.00 0.00 1.73
600 602 8.680903 TGTTTGTTTGTATCGGTTTTTACCTAA 58.319 29.630 0.00 0.00 0.00 2.69
601 603 8.218338 TGTTTGTTTGTATCGGTTTTTACCTA 57.782 30.769 0.00 0.00 0.00 3.08
602 604 7.098074 TGTTTGTTTGTATCGGTTTTTACCT 57.902 32.000 0.00 0.00 0.00 3.08
603 605 6.418523 CCTGTTTGTTTGTATCGGTTTTTACC 59.581 38.462 0.00 0.00 0.00 2.85
604 606 6.418523 CCCTGTTTGTTTGTATCGGTTTTTAC 59.581 38.462 0.00 0.00 0.00 2.01
605 607 6.096564 ACCCTGTTTGTTTGTATCGGTTTTTA 59.903 34.615 0.00 0.00 0.00 1.52
606 608 5.105269 ACCCTGTTTGTTTGTATCGGTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
607 609 4.403113 ACCCTGTTTGTTTGTATCGGTTTT 59.597 37.500 0.00 0.00 0.00 2.43
608 610 3.955551 ACCCTGTTTGTTTGTATCGGTTT 59.044 39.130 0.00 0.00 0.00 3.27
609 611 3.558033 ACCCTGTTTGTTTGTATCGGTT 58.442 40.909 0.00 0.00 0.00 4.44
610 612 3.217681 ACCCTGTTTGTTTGTATCGGT 57.782 42.857 0.00 0.00 0.00 4.69
611 613 4.155280 CCTAACCCTGTTTGTTTGTATCGG 59.845 45.833 0.00 0.00 0.00 4.18
612 614 4.379082 GCCTAACCCTGTTTGTTTGTATCG 60.379 45.833 0.00 0.00 0.00 2.92
613 615 4.082408 GGCCTAACCCTGTTTGTTTGTATC 60.082 45.833 0.00 0.00 0.00 2.24
614 616 3.830178 GGCCTAACCCTGTTTGTTTGTAT 59.170 43.478 0.00 0.00 0.00 2.29
615 617 3.224269 GGCCTAACCCTGTTTGTTTGTA 58.776 45.455 0.00 0.00 0.00 2.41
616 618 2.036387 GGCCTAACCCTGTTTGTTTGT 58.964 47.619 0.00 0.00 0.00 2.83
617 619 2.035632 TGGCCTAACCCTGTTTGTTTG 58.964 47.619 3.32 0.00 37.83 2.93
618 620 2.091555 TCTGGCCTAACCCTGTTTGTTT 60.092 45.455 3.32 0.00 37.83 2.83
619 621 1.497286 TCTGGCCTAACCCTGTTTGTT 59.503 47.619 3.32 0.00 37.83 2.83
620 622 1.145571 TCTGGCCTAACCCTGTTTGT 58.854 50.000 3.32 0.00 37.83 2.83
621 623 1.202879 TGTCTGGCCTAACCCTGTTTG 60.203 52.381 3.32 0.00 37.83 2.93
622 624 1.145571 TGTCTGGCCTAACCCTGTTT 58.854 50.000 3.32 0.00 37.83 2.83
623 625 1.282157 GATGTCTGGCCTAACCCTGTT 59.718 52.381 3.32 0.00 37.83 3.16
624 626 0.912486 GATGTCTGGCCTAACCCTGT 59.088 55.000 3.32 0.00 37.83 4.00
625 627 0.911769 TGATGTCTGGCCTAACCCTG 59.088 55.000 3.32 0.00 37.83 4.45
626 628 0.912486 GTGATGTCTGGCCTAACCCT 59.088 55.000 3.32 0.00 37.83 4.34
627 629 0.462047 CGTGATGTCTGGCCTAACCC 60.462 60.000 3.32 0.00 37.83 4.11
628 630 0.249398 ACGTGATGTCTGGCCTAACC 59.751 55.000 3.32 0.00 39.84 2.85
629 631 2.537401 GTACGTGATGTCTGGCCTAAC 58.463 52.381 3.32 2.23 0.00 2.34
630 632 1.133598 CGTACGTGATGTCTGGCCTAA 59.866 52.381 7.22 0.00 0.00 2.69
631 633 0.736636 CGTACGTGATGTCTGGCCTA 59.263 55.000 7.22 0.00 0.00 3.93
632 634 1.511305 CGTACGTGATGTCTGGCCT 59.489 57.895 7.22 0.00 0.00 5.19
633 635 1.518572 CCGTACGTGATGTCTGGCC 60.519 63.158 15.21 0.00 0.00 5.36
634 636 1.518572 CCCGTACGTGATGTCTGGC 60.519 63.158 15.21 0.00 0.00 4.85
635 637 1.141019 CCCCGTACGTGATGTCTGG 59.859 63.158 15.21 5.24 0.00 3.86
636 638 1.518572 GCCCCGTACGTGATGTCTG 60.519 63.158 15.21 0.00 0.00 3.51
637 639 2.718073 GGCCCCGTACGTGATGTCT 61.718 63.158 15.21 0.00 0.00 3.41
638 640 2.202837 GGCCCCGTACGTGATGTC 60.203 66.667 15.21 0.00 0.00 3.06
639 641 4.137872 CGGCCCCGTACGTGATGT 62.138 66.667 15.21 0.00 34.35 3.06
653 655 3.518293 GATCAAGCTCATGCGCGGC 62.518 63.158 8.83 1.27 45.42 6.53
654 656 1.434622 AAGATCAAGCTCATGCGCGG 61.435 55.000 8.83 0.00 45.42 6.46
655 657 0.376152 AAAGATCAAGCTCATGCGCG 59.624 50.000 0.00 0.00 45.42 6.86
656 658 1.823828 CAAAGATCAAGCTCATGCGC 58.176 50.000 0.00 0.00 45.42 6.09
657 659 1.533338 GGCAAAGATCAAGCTCATGCG 60.533 52.381 0.00 0.00 45.42 4.73
658 660 1.475280 TGGCAAAGATCAAGCTCATGC 59.525 47.619 0.00 0.00 40.05 4.06
659 661 3.192844 ACTTGGCAAAGATCAAGCTCATG 59.807 43.478 8.15 0.00 42.82 3.07
660 662 3.428532 ACTTGGCAAAGATCAAGCTCAT 58.571 40.909 8.15 0.00 42.82 2.90
664 666 1.135575 CCGACTTGGCAAAGATCAAGC 60.136 52.381 8.15 0.00 42.82 4.01
676 678 1.265095 GATGTATGCATGCCGACTTGG 59.735 52.381 16.68 0.00 36.67 3.61
677 679 1.070376 CGATGTATGCATGCCGACTTG 60.070 52.381 16.68 3.72 35.07 3.16
678 680 1.202521 TCGATGTATGCATGCCGACTT 60.203 47.619 16.68 10.93 35.07 3.01
679 681 0.389025 TCGATGTATGCATGCCGACT 59.611 50.000 16.68 3.30 35.07 4.18
680 682 1.217001 TTCGATGTATGCATGCCGAC 58.783 50.000 16.68 13.48 33.18 4.79
681 683 2.168326 ATTCGATGTATGCATGCCGA 57.832 45.000 16.68 12.78 35.07 5.54
682 684 2.975410 AATTCGATGTATGCATGCCG 57.025 45.000 16.68 10.40 35.07 5.69
683 685 4.715896 CTGTAATTCGATGTATGCATGCC 58.284 43.478 16.68 0.00 35.07 4.40
684 686 4.153986 GCTGTAATTCGATGTATGCATGC 58.846 43.478 11.82 11.82 35.07 4.06
685 687 4.084380 ACGCTGTAATTCGATGTATGCATG 60.084 41.667 10.16 0.00 35.07 4.06
686 688 4.058124 ACGCTGTAATTCGATGTATGCAT 58.942 39.130 3.79 3.79 38.18 3.96
687 689 3.453424 ACGCTGTAATTCGATGTATGCA 58.547 40.909 0.00 0.00 0.00 3.96
688 690 4.446234 GAACGCTGTAATTCGATGTATGC 58.554 43.478 0.00 0.00 0.00 3.14
689 691 4.506288 TGGAACGCTGTAATTCGATGTATG 59.494 41.667 0.00 0.00 0.00 2.39
690 692 4.689071 TGGAACGCTGTAATTCGATGTAT 58.311 39.130 0.00 0.00 0.00 2.29
691 693 4.112716 TGGAACGCTGTAATTCGATGTA 57.887 40.909 0.00 0.00 0.00 2.29
692 694 2.967362 TGGAACGCTGTAATTCGATGT 58.033 42.857 0.00 0.00 0.00 3.06
693 695 4.335082 TTTGGAACGCTGTAATTCGATG 57.665 40.909 0.00 0.00 0.00 3.84
694 696 4.201910 CCATTTGGAACGCTGTAATTCGAT 60.202 41.667 0.00 0.00 37.39 3.59
695 697 3.126171 CCATTTGGAACGCTGTAATTCGA 59.874 43.478 0.00 0.00 37.39 3.71
700 702 2.156098 GACCCATTTGGAACGCTGTAA 58.844 47.619 0.00 0.00 37.39 2.41
702 704 0.893727 GGACCCATTTGGAACGCTGT 60.894 55.000 0.00 0.00 37.39 4.40
705 707 0.243636 CAAGGACCCATTTGGAACGC 59.756 55.000 0.00 0.00 37.39 4.84
706 708 1.904287 TCAAGGACCCATTTGGAACG 58.096 50.000 0.00 0.00 37.39 3.95
707 709 3.701664 AGATCAAGGACCCATTTGGAAC 58.298 45.455 0.00 0.00 37.39 3.62
708 710 4.540099 AGTAGATCAAGGACCCATTTGGAA 59.460 41.667 0.00 0.00 37.39 3.53
709 711 4.111577 AGTAGATCAAGGACCCATTTGGA 58.888 43.478 0.00 0.00 37.39 3.53
730 732 9.208022 TCATTGCCTCGATGACTAATTAATTAG 57.792 33.333 26.65 26.65 44.07 1.73
731 733 9.554395 TTCATTGCCTCGATGACTAATTAATTA 57.446 29.630 7.66 7.66 34.40 1.40
732 734 8.450578 TTCATTGCCTCGATGACTAATTAATT 57.549 30.769 5.89 5.89 34.40 1.40
733 735 7.308229 GCTTCATTGCCTCGATGACTAATTAAT 60.308 37.037 0.00 0.00 34.40 1.40
734 736 6.017934 GCTTCATTGCCTCGATGACTAATTAA 60.018 38.462 0.00 0.00 34.40 1.40
735 737 5.466728 GCTTCATTGCCTCGATGACTAATTA 59.533 40.000 0.00 0.00 34.40 1.40
738 740 3.198068 GCTTCATTGCCTCGATGACTAA 58.802 45.455 0.00 0.00 34.40 2.24
744 746 0.391661 ACACGCTTCATTGCCTCGAT 60.392 50.000 0.00 0.00 0.00 3.59
746 748 1.133253 CACACGCTTCATTGCCTCG 59.867 57.895 0.00 0.00 0.00 4.63
765 767 4.746309 TCAGCACCTGGCCATGGC 62.746 66.667 29.47 29.47 46.50 4.40
766 768 2.439701 CTCAGCACCTGGCCATGG 60.440 66.667 5.51 13.05 46.50 3.66
768 770 2.673523 GTCTCAGCACCTGGCCAT 59.326 61.111 5.51 0.00 46.50 4.40
769 771 4.007644 CGTCTCAGCACCTGGCCA 62.008 66.667 4.71 4.71 46.50 5.36
779 784 1.080705 GTTCGTGTCCCCGTCTCAG 60.081 63.158 0.00 0.00 0.00 3.35
799 804 1.569493 GTGACGTGCGATGCTGTTT 59.431 52.632 0.00 0.00 0.00 2.83
955 962 2.349627 CGGCCGTATATATAGCTCGCTC 60.350 54.545 19.50 0.00 0.00 5.03
1014 1021 1.664649 CATGTCGGTCAGTGCGTGT 60.665 57.895 0.00 0.00 0.00 4.49
1434 1453 1.148310 CAACACTCATGACCGTGGAC 58.852 55.000 16.80 0.00 35.51 4.02
1697 1716 6.257411 TGCAACTTTTTACATTGTTGGACATG 59.743 34.615 0.00 0.00 39.82 3.21
1784 1804 7.347748 AGCATCCATTGAGCTATATCTATTCCT 59.652 37.037 0.00 0.00 36.73 3.36
1792 1812 7.346698 ACCACTATAGCATCCATTGAGCTATAT 59.653 37.037 17.70 10.53 46.67 0.86
1804 1824 3.006967 ACAATCCGACCACTATAGCATCC 59.993 47.826 0.00 0.00 0.00 3.51
1820 1840 2.810650 ACGAATCTCTGCGTACAATCC 58.189 47.619 0.00 0.00 39.21 3.01
1845 1865 5.221048 GCTTAACTCTGAGCCAGTTCAAAAA 60.221 40.000 4.19 0.00 35.63 1.94
1850 1870 3.326836 AGCTTAACTCTGAGCCAGTTC 57.673 47.619 4.19 0.00 39.71 3.01
1851 1871 4.891992 TTAGCTTAACTCTGAGCCAGTT 57.108 40.909 4.19 0.00 39.71 3.16
1852 1872 5.428184 AATTAGCTTAACTCTGAGCCAGT 57.572 39.130 4.19 0.00 39.71 4.00
1853 1873 6.749923 AAAATTAGCTTAACTCTGAGCCAG 57.250 37.500 4.19 0.00 39.71 4.85
1938 1961 2.545532 CGGGCCGACGGTGTATTATTTA 60.546 50.000 24.41 0.00 0.00 1.40
2225 2336 6.394809 GGAGAAGGTAAGAACAGAAGAAGAG 58.605 44.000 0.00 0.00 0.00 2.85
2250 2361 3.191371 GGTGGCATTTTTGTGTAGAGAGG 59.809 47.826 0.00 0.00 0.00 3.69
2301 2412 3.732892 ACGGTGCCAAAATCGCGG 61.733 61.111 6.13 0.00 0.00 6.46
2477 2589 2.594303 CAAACTGCCGGTGCTCCA 60.594 61.111 1.90 0.00 38.71 3.86
2625 2738 2.816689 GCCGGGGCAAATAACAATAAC 58.183 47.619 2.18 0.00 41.49 1.89
2778 2891 3.827302 CTGGACTGCCTATATTACGGACT 59.173 47.826 0.00 0.00 34.31 3.85


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

AutoCloner maintained by Alex Coulton.