Multiple sequence alignment - TraesCS4D01G297000

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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 TraesCS4D01G297000 chr4D 100.000 4283 0 0 1 4283 466128357 466132639 0.000000e+00 7910.0
1 TraesCS4D01G297000 chr4A 93.406 3488 152 32 835 4283 4529277 4525829 0.000000e+00 5096.0
2 TraesCS4D01G297000 chr4A 95.668 554 23 1 121 673 4530086 4529533 0.000000e+00 889.0
3 TraesCS4D01G297000 chr4A 93.846 65 4 0 3685 3749 30189653 30189717 9.800000e-17 99.0
4 TraesCS4D01G297000 chr4B 94.352 2939 115 18 753 3671 583592511 583595418 0.000000e+00 4460.0
5 TraesCS4D01G297000 chr4B 90.856 689 56 4 1 688 583591585 583592267 0.000000e+00 917.0
6 TraesCS4D01G297000 chr6D 83.636 165 26 1 4119 4283 106699712 106699549 2.060000e-33 154.0
7 TraesCS4D01G297000 chr2D 93.151 73 4 1 3685 3756 349588098 349588026 5.860000e-19 106.0
8 TraesCS4D01G297000 chr2D 93.939 66 4 0 3685 3750 383863274 383863209 2.730000e-17 100.0
9 TraesCS4D01G297000 chr2B 91.667 72 6 0 4212 4283 583417420 583417349 2.730000e-17 100.0
10 TraesCS4D01G297000 chr2B 92.537 67 4 1 3685 3750 416184605 416184671 1.270000e-15 95.3
11 TraesCS4D01G297000 chr6B 92.537 67 5 0 3682 3748 681080389 681080455 3.530000e-16 97.1
12 TraesCS4D01G297000 chr2A 92.424 66 5 0 3685 3750 465346021 465345956 1.270000e-15 95.3
13 TraesCS4D01G297000 chr5D 90.141 71 3 2 3681 3750 13787931 13787998 5.900000e-14 89.8
14 TraesCS4D01G297000 chr1A 91.045 67 5 1 3686 3751 375114881 375114947 5.900000e-14 89.8


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 TraesCS4D01G297000 chr4D 466128357 466132639 4282 False 7910.0 7910 100.000 1 4283 1 chr4D.!!$F1 4282
1 TraesCS4D01G297000 chr4A 4525829 4530086 4257 True 2992.5 5096 94.537 121 4283 2 chr4A.!!$R1 4162
2 TraesCS4D01G297000 chr4B 583591585 583595418 3833 False 2688.5 4460 92.604 1 3671 2 chr4B.!!$F1 3670

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
692 695 0.108520 GACGACCCCTTGTATCGCAA 60.109 55.000 0.00 0.00 39.47 4.85 F
719 722 0.108945 GCCAGCATTCAAGTTGGAGC 60.109 55.000 2.34 5.11 41.87 4.70 F
731 734 0.394899 GTTGGAGCCATTCCTCTGGG 60.395 60.000 0.00 0.00 46.92 4.45 F
2150 2332 1.338200 ACTTCACCACCGAGAATCAGC 60.338 52.381 0.00 0.00 33.17 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2307 0.966920 TCTCGGTGGTGAAGTTCTCC 59.033 55.000 15.67 15.67 0.00 3.71 R
2370 2553 3.731089 ACGGTTCGAAGTAATGGTTTGA 58.269 40.909 0.00 0.00 0.00 2.69 R
2384 2567 4.735662 TTGGACATAAAAGAACGGTTCG 57.264 40.909 14.70 2.83 34.02 3.95 R
3850 4083 1.334960 GCAGTGGAATCACAAACACCG 60.335 52.381 0.00 0.00 45.91 4.94 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
22 23 4.431416 AGTTGTAGTTCCACATGGTTCA 57.569 40.909 0.00 0.00 36.34 3.18
552 554 4.680407 TGGTAGGAGCTAAGTCAGGTAAA 58.320 43.478 0.00 0.00 34.30 2.01
567 569 4.700213 TCAGGTAAATTTGCTGGAGCTTAC 59.300 41.667 6.23 0.78 42.66 2.34
587 589 7.872993 AGCTTACGTATATGTTGCATGAACTAT 59.127 33.333 18.59 2.24 35.37 2.12
644 647 6.823182 TGGACCATCATAATTTCACTACACAG 59.177 38.462 0.00 0.00 0.00 3.66
652 655 3.469008 TTTCACTACACAGTCCACAGG 57.531 47.619 0.00 0.00 30.46 4.00
676 679 6.063272 GTCACTTTTTCTTTACTTAGCGACG 58.937 40.000 0.00 0.00 0.00 5.12
688 691 1.027357 TAGCGACGACCCCTTGTATC 58.973 55.000 0.00 0.00 0.00 2.24
689 692 1.588139 GCGACGACCCCTTGTATCG 60.588 63.158 0.00 0.00 41.60 2.92
690 693 1.588139 CGACGACCCCTTGTATCGC 60.588 63.158 0.00 0.00 39.47 4.58
691 694 1.514087 GACGACCCCTTGTATCGCA 59.486 57.895 0.00 0.00 39.47 5.10
692 695 0.108520 GACGACCCCTTGTATCGCAA 60.109 55.000 0.00 0.00 39.47 4.85
693 696 0.322322 ACGACCCCTTGTATCGCAAA 59.678 50.000 0.00 0.00 39.47 3.68
694 697 0.725117 CGACCCCTTGTATCGCAAAC 59.275 55.000 0.00 0.00 36.53 2.93
695 698 1.092348 GACCCCTTGTATCGCAAACC 58.908 55.000 0.00 0.00 36.53 3.27
696 699 0.402504 ACCCCTTGTATCGCAAACCA 59.597 50.000 0.00 0.00 36.53 3.67
697 700 1.005450 ACCCCTTGTATCGCAAACCAT 59.995 47.619 0.00 0.00 36.53 3.55
698 701 1.405105 CCCCTTGTATCGCAAACCATG 59.595 52.381 0.00 0.00 36.53 3.66
699 702 2.364632 CCCTTGTATCGCAAACCATGA 58.635 47.619 0.00 0.00 36.53 3.07
700 703 2.355756 CCCTTGTATCGCAAACCATGAG 59.644 50.000 0.00 0.00 36.53 2.90
701 704 2.223340 CCTTGTATCGCAAACCATGAGC 60.223 50.000 0.00 0.00 36.53 4.26
702 705 1.378531 TGTATCGCAAACCATGAGCC 58.621 50.000 0.00 0.00 0.00 4.70
703 706 1.339535 TGTATCGCAAACCATGAGCCA 60.340 47.619 0.00 0.00 0.00 4.75
704 707 1.331756 GTATCGCAAACCATGAGCCAG 59.668 52.381 0.00 0.00 0.00 4.85
705 708 1.660560 ATCGCAAACCATGAGCCAGC 61.661 55.000 0.00 0.00 0.00 4.85
706 709 2.628696 CGCAAACCATGAGCCAGCA 61.629 57.895 0.00 0.00 0.00 4.41
707 710 1.895238 GCAAACCATGAGCCAGCAT 59.105 52.632 0.00 0.00 0.00 3.79
708 711 0.248289 GCAAACCATGAGCCAGCATT 59.752 50.000 0.00 0.00 0.00 3.56
709 712 1.738030 GCAAACCATGAGCCAGCATTC 60.738 52.381 0.00 0.00 0.00 2.67
710 713 1.546923 CAAACCATGAGCCAGCATTCA 59.453 47.619 0.00 0.00 0.00 2.57
711 714 1.927487 AACCATGAGCCAGCATTCAA 58.073 45.000 0.00 0.00 0.00 2.69
712 715 1.471119 ACCATGAGCCAGCATTCAAG 58.529 50.000 0.00 0.00 0.00 3.02
713 716 1.272313 ACCATGAGCCAGCATTCAAGT 60.272 47.619 0.00 0.00 0.00 3.16
714 717 1.822990 CCATGAGCCAGCATTCAAGTT 59.177 47.619 0.00 0.00 0.00 2.66
715 718 2.416836 CCATGAGCCAGCATTCAAGTTG 60.417 50.000 0.00 0.00 0.00 3.16
716 719 1.250328 TGAGCCAGCATTCAAGTTGG 58.750 50.000 2.34 0.00 42.17 3.77
717 720 1.202915 TGAGCCAGCATTCAAGTTGGA 60.203 47.619 2.34 0.00 41.87 3.53
718 721 1.471684 GAGCCAGCATTCAAGTTGGAG 59.528 52.381 2.34 0.00 41.87 3.86
719 722 0.108945 GCCAGCATTCAAGTTGGAGC 60.109 55.000 2.34 5.11 41.87 4.70
720 723 0.529378 CCAGCATTCAAGTTGGAGCC 59.471 55.000 2.34 0.00 41.87 4.70
721 724 1.250328 CAGCATTCAAGTTGGAGCCA 58.750 50.000 2.34 0.00 0.00 4.75
722 725 1.822990 CAGCATTCAAGTTGGAGCCAT 59.177 47.619 2.34 0.00 0.00 4.40
723 726 2.232941 CAGCATTCAAGTTGGAGCCATT 59.767 45.455 2.34 0.00 0.00 3.16
724 727 2.494870 AGCATTCAAGTTGGAGCCATTC 59.505 45.455 2.34 0.00 0.00 2.67
725 728 2.417787 GCATTCAAGTTGGAGCCATTCC 60.418 50.000 2.34 0.00 46.98 3.01
726 729 2.978156 TTCAAGTTGGAGCCATTCCT 57.022 45.000 2.34 0.00 46.92 3.36
727 730 2.496899 TCAAGTTGGAGCCATTCCTC 57.503 50.000 2.34 0.00 46.92 3.71
728 731 1.988107 TCAAGTTGGAGCCATTCCTCT 59.012 47.619 2.34 0.00 46.92 3.69
729 732 2.089980 CAAGTTGGAGCCATTCCTCTG 58.910 52.381 0.00 0.00 46.92 3.35
730 733 0.622665 AGTTGGAGCCATTCCTCTGG 59.377 55.000 0.00 0.00 46.92 3.86
731 734 0.394899 GTTGGAGCCATTCCTCTGGG 60.395 60.000 0.00 0.00 46.92 4.45
732 735 1.574526 TTGGAGCCATTCCTCTGGGG 61.575 60.000 0.00 0.00 46.92 4.96
733 736 2.761465 GGAGCCATTCCTCTGGGGG 61.761 68.421 0.00 0.00 43.16 5.40
752 755 4.855340 GGGGGAAATCTTCAGTACATTGA 58.145 43.478 0.00 0.00 0.00 2.57
753 756 5.261216 GGGGGAAATCTTCAGTACATTGAA 58.739 41.667 0.00 0.00 35.83 2.69
754 757 5.125578 GGGGGAAATCTTCAGTACATTGAAC 59.874 44.000 0.00 0.00 33.71 3.18
755 758 5.710099 GGGGAAATCTTCAGTACATTGAACA 59.290 40.000 0.00 0.00 33.71 3.18
756 759 6.127897 GGGGAAATCTTCAGTACATTGAACAG 60.128 42.308 0.00 0.00 33.71 3.16
757 760 6.655003 GGGAAATCTTCAGTACATTGAACAGA 59.345 38.462 0.00 0.00 33.71 3.41
758 761 7.148340 GGGAAATCTTCAGTACATTGAACAGAG 60.148 40.741 0.00 0.00 33.71 3.35
759 762 6.734104 AATCTTCAGTACATTGAACAGAGC 57.266 37.500 0.00 0.00 33.71 4.09
760 763 5.213891 TCTTCAGTACATTGAACAGAGCA 57.786 39.130 0.00 0.00 33.71 4.26
761 764 5.798132 TCTTCAGTACATTGAACAGAGCAT 58.202 37.500 0.00 0.00 33.71 3.79
762 765 6.233434 TCTTCAGTACATTGAACAGAGCATT 58.767 36.000 0.00 0.00 33.71 3.56
766 945 8.565896 TCAGTACATTGAACAGAGCATTATTT 57.434 30.769 0.00 0.00 0.00 1.40
821 1000 6.294731 GGCTTATGTTTCCAACTCAATCTGTT 60.295 38.462 0.00 0.00 0.00 3.16
842 1021 7.502226 TCTGTTTTTCAACCTCTGATACAACAT 59.498 33.333 0.00 0.00 32.78 2.71
993 1175 2.304180 AGAGAGCTAAGCTGGCTTCAAA 59.696 45.455 11.28 0.00 39.88 2.69
1195 1377 6.101997 TCATCACACTCAACATATGTGTCTC 58.898 40.000 9.63 0.00 43.42 3.36
1287 1469 2.367567 GGTTCAGTCCAGTGTTCCTGTA 59.632 50.000 0.00 0.00 39.74 2.74
1671 1853 2.229062 ACCTCAGGTATGCGTATGATCG 59.771 50.000 0.00 0.00 32.11 3.69
1686 1868 7.439955 TGCGTATGATCGTAGGTTTAATTGAAT 59.560 33.333 14.42 0.00 0.00 2.57
1687 1869 7.740346 GCGTATGATCGTAGGTTTAATTGAATG 59.260 37.037 14.42 0.00 0.00 2.67
1688 1870 8.974408 CGTATGATCGTAGGTTTAATTGAATGA 58.026 33.333 6.50 0.00 0.00 2.57
1718 1900 6.356190 CGATCAACAACGGAACTTTAAACTTC 59.644 38.462 0.00 0.40 0.00 3.01
1841 2023 3.737559 AAATGCACCTAGGATGGTTGA 57.262 42.857 17.98 0.00 38.45 3.18
2030 2212 5.185828 AGACATAAAAAGGGAATCAGCAACC 59.814 40.000 0.00 0.00 0.00 3.77
2075 2257 5.880332 GCTTTATAGGAGTTCACCATCAACA 59.120 40.000 0.00 0.00 0.00 3.33
2125 2307 2.203280 TTCACCACCAACGCCAGG 60.203 61.111 0.00 0.00 0.00 4.45
2150 2332 1.338200 ACTTCACCACCGAGAATCAGC 60.338 52.381 0.00 0.00 33.17 4.26
2256 2438 2.214376 TACCCTTCCAACATGCTTGG 57.786 50.000 16.49 16.49 40.87 3.61
2361 2544 4.273480 GTCATGTGTGTATACTTGGGCATC 59.727 45.833 4.17 0.00 0.00 3.91
2370 2553 6.992715 GTGTATACTTGGGCATCTATGAACTT 59.007 38.462 4.17 0.00 0.00 2.66
2384 2567 9.994432 CATCTATGAACTTCAAACCATTACTTC 57.006 33.333 0.00 0.00 0.00 3.01
2389 2572 5.684550 ACTTCAAACCATTACTTCGAACC 57.315 39.130 0.00 0.00 0.00 3.62
2390 2573 4.212636 ACTTCAAACCATTACTTCGAACCG 59.787 41.667 0.00 0.00 0.00 4.44
2402 2585 5.587033 ACTTCGAACCGTTCTTTTATGTC 57.413 39.130 9.55 0.00 0.00 3.06
2584 2768 8.434733 AAGTAGTACACCTCTGTTTCTTTTTC 57.565 34.615 2.52 0.00 0.00 2.29
2863 3052 1.142870 ACAAAGCTGCTGGAAGTGGTA 59.857 47.619 1.35 0.00 35.30 3.25
2865 3054 0.036875 AAGCTGCTGGAAGTGGTACC 59.963 55.000 4.43 4.43 35.30 3.34
2889 3078 1.227176 GAACCCCGACGATGCCTAC 60.227 63.158 0.00 0.00 0.00 3.18
2893 3082 2.278596 CCGACGATGCCTACACCG 60.279 66.667 0.00 0.00 0.00 4.94
2994 3183 5.071788 ACAGTCATGGTTTCTGAACTTCCTA 59.928 40.000 12.37 0.00 36.03 2.94
3003 3192 3.422796 TCTGAACTTCCTAGAAGACGCT 58.577 45.455 11.17 0.00 0.00 5.07
3035 3224 3.065925 GGATTCAAATTTGAGAGCCGAGG 59.934 47.826 19.64 0.00 38.61 4.63
3060 3249 1.071471 CAGCACCAGAGAACGGGTT 59.929 57.895 0.00 0.00 42.28 4.11
3171 3360 2.998949 GAGGGGGCGAAACCTGAT 59.001 61.111 0.00 0.00 37.18 2.90
3174 3363 1.227383 GGGGGCGAAACCTGATGAT 59.773 57.895 0.00 0.00 39.10 2.45
3234 3423 3.288308 CTCGTGCCTGCTCGGAACT 62.288 63.158 12.86 0.00 39.45 3.01
3237 3426 1.598130 GTGCCTGCTCGGAACTGTT 60.598 57.895 0.00 0.00 38.44 3.16
3249 3438 3.454587 AACTGTTGAGACCGCGGCA 62.455 57.895 28.58 13.23 0.00 5.69
3386 3583 2.103941 GGAGCGAAGGAGAATGGAGATT 59.896 50.000 0.00 0.00 0.00 2.40
3387 3584 3.129871 GAGCGAAGGAGAATGGAGATTG 58.870 50.000 0.00 0.00 0.00 2.67
3389 3586 3.198635 AGCGAAGGAGAATGGAGATTGAA 59.801 43.478 0.00 0.00 0.00 2.69
3390 3587 4.133078 GCGAAGGAGAATGGAGATTGAAT 58.867 43.478 0.00 0.00 0.00 2.57
3450 3653 5.570973 CGAGGATTGAGAGATGTAAATAGCG 59.429 44.000 0.00 0.00 0.00 4.26
3491 3694 8.857216 GTTAAGTTATTCGTTCGATCTTCTTCA 58.143 33.333 0.00 0.00 0.00 3.02
3531 3735 2.624838 CCTTGTGAAATGGCAGTCTGTT 59.375 45.455 0.93 0.00 0.00 3.16
3543 3747 3.378427 GGCAGTCTGTTTGTTCTTCAGTT 59.622 43.478 0.93 0.00 0.00 3.16
3546 3750 5.619981 GCAGTCTGTTTGTTCTTCAGTTGTT 60.620 40.000 0.93 0.00 0.00 2.83
3560 3767 6.650807 TCTTCAGTTGTTTCTGGCTAATACAG 59.349 38.462 0.00 0.00 36.25 2.74
3581 3788 5.011329 ACAGATGGATGAATGTTTGCACTTT 59.989 36.000 0.00 0.00 0.00 2.66
3594 3801 5.106908 TGTTTGCACTTTGCCTAAAACAAAC 60.107 36.000 10.95 0.00 40.99 2.93
3648 3858 2.286713 TGCGGCGCAAAACATATCATAC 60.287 45.455 34.58 0.00 34.76 2.39
3666 3876 5.118990 TCATACCAGCTCTCATTTGTAAGC 58.881 41.667 0.00 0.00 34.95 3.09
3673 3883 3.669023 GCTCTCATTTGTAAGCTGTGTGC 60.669 47.826 0.00 0.00 43.29 4.57
3784 4017 8.568676 TGTATAGCTGTGCTGGTATTTTTAAA 57.431 30.769 0.00 0.00 40.10 1.52
3788 4021 5.069781 AGCTGTGCTGGTATTTTTAAAACCA 59.930 36.000 9.37 9.37 40.94 3.67
3792 4025 3.362534 GCTGGTATTTTTAAAACCACGCG 59.637 43.478 3.53 3.53 38.36 6.01
3797 4030 2.088338 TTTTAAAACCACGCGTGTCG 57.912 45.000 34.81 23.86 45.38 4.35
3802 4035 2.625973 AAACCACGCGTGTCGGTGTA 62.626 55.000 34.81 0.00 43.86 2.90
3807 4040 2.505498 CGCGTGTCGGTGTATGCTC 61.505 63.158 0.00 0.00 33.78 4.26
3812 4045 2.470821 GTGTCGGTGTATGCTCCATAC 58.529 52.381 8.11 8.11 44.74 2.39
3850 4083 5.112686 AGAAAGTTCAGTGTGAAGACTGTC 58.887 41.667 7.40 0.00 43.38 3.51
3861 4094 2.093921 TGAAGACTGTCGGTGTTTGTGA 60.094 45.455 1.52 0.00 31.28 3.58
3894 4127 1.376037 CCTCGAGGCAGTTCCAACC 60.376 63.158 20.67 0.00 37.29 3.77
3895 4128 1.371183 CTCGAGGCAGTTCCAACCA 59.629 57.895 3.91 0.00 37.29 3.67
3896 4129 0.250295 CTCGAGGCAGTTCCAACCAA 60.250 55.000 3.91 0.00 37.29 3.67
3916 4149 2.664436 GGCCAAACGGACGTTCTCG 61.664 63.158 10.76 0.00 37.35 4.04
3920 4153 0.598158 CAAACGGACGTTCTCGGGAA 60.598 55.000 10.76 0.00 41.85 3.97
3924 4157 0.319297 CGGACGTTCTCGGGAAGTTT 60.319 55.000 0.00 0.00 41.85 2.66
3933 4166 6.071728 ACGTTCTCGGGAAGTTTCTCTTTATA 60.072 38.462 0.00 0.00 41.85 0.98
3934 4167 6.979238 CGTTCTCGGGAAGTTTCTCTTTATAT 59.021 38.462 0.00 0.00 36.40 0.86
3935 4168 7.167801 CGTTCTCGGGAAGTTTCTCTTTATATC 59.832 40.741 0.00 0.00 36.40 1.63
3936 4169 7.899648 TCTCGGGAAGTTTCTCTTTATATCT 57.100 36.000 0.00 0.00 36.40 1.98
3951 4184 9.118300 CTCTTTATATCTGCTGGAGAAACAATT 57.882 33.333 2.14 0.00 33.12 2.32
3998 4231 3.197664 AGCTTATTTGCTGCTCCCC 57.802 52.632 0.00 0.00 42.33 4.81
4000 4233 1.728490 GCTTATTTGCTGCTCCCCGG 61.728 60.000 0.00 0.00 0.00 5.73
4001 4234 0.394352 CTTATTTGCTGCTCCCCGGT 60.394 55.000 0.00 0.00 0.00 5.28
4002 4235 0.913205 TTATTTGCTGCTCCCCGGTA 59.087 50.000 0.00 0.00 0.00 4.02
4003 4236 1.136828 TATTTGCTGCTCCCCGGTAT 58.863 50.000 0.00 0.00 0.00 2.73
4012 4245 2.174639 TGCTCCCCGGTATCATGAAATT 59.825 45.455 0.00 0.00 0.00 1.82
4050 4283 2.227388 GCTCCCATGCTCCAATTTATCG 59.773 50.000 0.00 0.00 0.00 2.92
4055 4288 6.303054 TCCCATGCTCCAATTTATCGAAATA 58.697 36.000 0.00 0.00 34.01 1.40
4100 4333 7.561237 AATTCCGAAACAAATTGTACAATCG 57.439 32.000 21.02 18.36 0.00 3.34
4106 4339 7.201232 CCGAAACAAATTGTACAATCGCTAAAG 60.201 37.037 21.02 10.91 0.00 1.85
4107 4340 7.322699 CGAAACAAATTGTACAATCGCTAAAGT 59.677 33.333 21.02 9.36 0.00 2.66
4111 4344 9.769093 ACAAATTGTACAATCGCTAAAGTATTC 57.231 29.630 21.02 0.00 0.00 1.75
4124 4357 9.567848 TCGCTAAAGTATTCAAATCAAAATTCC 57.432 29.630 0.00 0.00 0.00 3.01
4189 4422 8.911247 AATAGTGTCACAAAAAGACAAAAGTC 57.089 30.769 5.62 0.00 46.50 3.01
4199 4432 3.145212 AGACAAAAGTCAAAACGCCAC 57.855 42.857 0.00 0.00 0.00 5.01
4200 4433 2.490115 AGACAAAAGTCAAAACGCCACA 59.510 40.909 0.00 0.00 0.00 4.17
4216 4449 3.440173 CGCCACAATTTACATCAGGACTT 59.560 43.478 0.00 0.00 0.00 3.01
4245 4478 7.922505 TTTTTGTTTCTCCATGTATGTTTCG 57.077 32.000 0.00 0.00 0.00 3.46
4253 4486 6.851609 TCTCCATGTATGTTTCGAATTTTGG 58.148 36.000 0.00 0.40 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.821846 TGGACAAAGCTTAGAAACAACAAAAAT 59.178 29.630 0.00 0.00 0.00 1.82
70 71 3.935828 GCACAGGTTTGGCAACTTAAAAA 59.064 39.130 0.00 0.00 32.90 1.94
71 72 3.196685 AGCACAGGTTTGGCAACTTAAAA 59.803 39.130 0.00 0.00 32.90 1.52
84 85 2.567615 CTCCTACCTAACAGCACAGGTT 59.432 50.000 0.00 0.00 42.68 3.50
151 153 3.515901 AGTTGGTAGCTCCCTAGAAACAG 59.484 47.826 0.00 0.00 34.77 3.16
345 347 3.876156 GCCTAAATTTGGCCACCTGTCTA 60.876 47.826 3.88 0.00 44.32 2.59
425 427 7.272731 GGAGGAATTCTAACGCACAAAAATAAC 59.727 37.037 5.23 0.00 0.00 1.89
480 482 3.311486 ACAAACAAATACGGCATTGGG 57.689 42.857 0.00 0.00 0.00 4.12
552 554 5.611374 ACATATACGTAAGCTCCAGCAAAT 58.389 37.500 0.00 0.00 45.16 2.32
587 589 8.846943 TTGATAGCTCAACAGAAACATAGAAA 57.153 30.769 0.00 0.00 36.46 2.52
609 612 7.901283 AATTATGATGGTCCATTGATGTTGA 57.099 32.000 5.65 0.00 0.00 3.18
614 617 9.071276 GTAGTGAAATTATGATGGTCCATTGAT 57.929 33.333 5.65 4.33 0.00 2.57
644 647 4.983671 AAAGAAAAAGTGACCTGTGGAC 57.016 40.909 0.00 0.00 0.00 4.02
652 655 6.063272 CGTCGCTAAGTAAAGAAAAAGTGAC 58.937 40.000 0.00 0.00 39.75 3.67
676 679 1.092348 GGTTTGCGATACAAGGGGTC 58.908 55.000 0.00 0.00 40.06 4.46
688 691 1.940883 ATGCTGGCTCATGGTTTGCG 61.941 55.000 0.00 0.00 0.00 4.85
689 692 0.248289 AATGCTGGCTCATGGTTTGC 59.752 50.000 0.00 0.00 0.00 3.68
690 693 1.546923 TGAATGCTGGCTCATGGTTTG 59.453 47.619 0.00 0.00 0.00 2.93
691 694 1.927487 TGAATGCTGGCTCATGGTTT 58.073 45.000 0.00 0.00 0.00 3.27
692 695 1.822990 CTTGAATGCTGGCTCATGGTT 59.177 47.619 0.00 0.00 0.00 3.67
693 696 1.272313 ACTTGAATGCTGGCTCATGGT 60.272 47.619 0.00 0.00 0.00 3.55
694 697 1.471119 ACTTGAATGCTGGCTCATGG 58.529 50.000 0.00 0.00 0.00 3.66
695 698 2.416836 CCAACTTGAATGCTGGCTCATG 60.417 50.000 0.00 0.00 0.00 3.07
696 699 1.822990 CCAACTTGAATGCTGGCTCAT 59.177 47.619 0.00 0.00 0.00 2.90
697 700 1.202915 TCCAACTTGAATGCTGGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
698 701 1.471684 CTCCAACTTGAATGCTGGCTC 59.528 52.381 0.00 0.00 0.00 4.70
699 702 1.542492 CTCCAACTTGAATGCTGGCT 58.458 50.000 0.00 0.00 0.00 4.75
700 703 0.108945 GCTCCAACTTGAATGCTGGC 60.109 55.000 0.00 0.00 0.00 4.85
701 704 0.529378 GGCTCCAACTTGAATGCTGG 59.471 55.000 0.00 0.00 0.00 4.85
702 705 1.250328 TGGCTCCAACTTGAATGCTG 58.750 50.000 0.00 0.00 0.00 4.41
703 706 2.226962 ATGGCTCCAACTTGAATGCT 57.773 45.000 0.00 0.00 0.00 3.79
704 707 2.417787 GGAATGGCTCCAACTTGAATGC 60.418 50.000 0.00 0.00 44.67 3.56
705 708 3.515330 GGAATGGCTCCAACTTGAATG 57.485 47.619 0.00 0.00 44.67 2.67
715 718 2.761465 CCCCCAGAGGAATGGCTCC 61.761 68.421 0.00 0.00 45.81 4.70
716 719 2.922234 CCCCCAGAGGAATGGCTC 59.078 66.667 0.00 0.00 39.17 4.70
730 733 4.855340 TCAATGTACTGAAGATTTCCCCC 58.145 43.478 0.00 0.00 0.00 5.40
731 734 5.710099 TGTTCAATGTACTGAAGATTTCCCC 59.290 40.000 0.00 0.00 36.01 4.81
732 735 6.655003 TCTGTTCAATGTACTGAAGATTTCCC 59.345 38.462 0.00 0.00 36.01 3.97
733 736 7.625185 GCTCTGTTCAATGTACTGAAGATTTCC 60.625 40.741 0.00 0.00 36.01 3.13
734 737 7.095060 TGCTCTGTTCAATGTACTGAAGATTTC 60.095 37.037 0.00 0.00 36.01 2.17
735 738 6.712095 TGCTCTGTTCAATGTACTGAAGATTT 59.288 34.615 0.00 0.00 36.01 2.17
736 739 6.233434 TGCTCTGTTCAATGTACTGAAGATT 58.767 36.000 0.00 0.00 36.01 2.40
737 740 5.798132 TGCTCTGTTCAATGTACTGAAGAT 58.202 37.500 0.00 0.00 36.01 2.40
738 741 5.213891 TGCTCTGTTCAATGTACTGAAGA 57.786 39.130 0.00 0.00 36.01 2.87
739 742 6.492007 AATGCTCTGTTCAATGTACTGAAG 57.508 37.500 0.00 0.00 36.01 3.02
740 743 8.565896 AATAATGCTCTGTTCAATGTACTGAA 57.434 30.769 0.00 0.00 32.89 3.02
741 744 8.565896 AAATAATGCTCTGTTCAATGTACTGA 57.434 30.769 0.00 0.45 0.00 3.41
742 745 9.630098 AAAAATAATGCTCTGTTCAATGTACTG 57.370 29.630 0.00 0.00 0.00 2.74
770 949 7.316544 AGTGAAGTTCAACGAAAAATGTACT 57.683 32.000 7.25 0.00 0.00 2.73
782 961 6.803154 AACATAAGCCTAGTGAAGTTCAAC 57.197 37.500 7.25 2.37 0.00 3.18
821 1000 8.154203 TCACTATGTTGTATCAGAGGTTGAAAA 58.846 33.333 0.00 0.00 39.77 2.29
993 1175 7.141758 TGGAGTAAGAGATGCCATATTCTTT 57.858 36.000 8.65 0.00 32.54 2.52
1195 1377 6.409704 TGAGTTCATTGTCCTCCTTTGATAG 58.590 40.000 0.00 0.00 0.00 2.08
1287 1469 1.149854 GACCCCAACAAGAACCGGT 59.850 57.895 0.00 0.00 0.00 5.28
1485 1667 0.180642 TGTAACGGGAAGCAACACCA 59.819 50.000 0.00 0.00 0.00 4.17
1686 1868 4.992319 AGTTCCGTTGTTGATCGTATTTCA 59.008 37.500 0.00 0.00 0.00 2.69
1687 1869 5.526010 AGTTCCGTTGTTGATCGTATTTC 57.474 39.130 0.00 0.00 0.00 2.17
1688 1870 5.934935 AAGTTCCGTTGTTGATCGTATTT 57.065 34.783 0.00 0.00 0.00 1.40
1689 1871 5.934935 AAAGTTCCGTTGTTGATCGTATT 57.065 34.783 0.00 0.00 0.00 1.89
1693 1875 5.744490 AGTTTAAAGTTCCGTTGTTGATCG 58.256 37.500 0.00 0.00 0.00 3.69
1718 1900 3.650070 TCTCAGAGCCACAATATAGCG 57.350 47.619 0.00 0.00 0.00 4.26
1828 2010 5.215252 ACGTAATCATCAACCATCCTAGG 57.785 43.478 0.82 0.82 0.00 3.02
1841 2023 6.307800 GCAATAACAGCAACAAACGTAATCAT 59.692 34.615 0.00 0.00 0.00 2.45
2075 2257 1.006102 CGGTGAAGTTCTCGCTGGT 60.006 57.895 4.17 0.00 37.29 4.00
2125 2307 0.966920 TCTCGGTGGTGAAGTTCTCC 59.033 55.000 15.67 15.67 0.00 3.71
2298 2480 7.503521 AGAAGACCTGAAATTCAGTCTTTTC 57.496 36.000 26.05 20.16 42.80 2.29
2302 2484 9.041354 ACTAATAGAAGACCTGAAATTCAGTCT 57.959 33.333 20.18 18.15 42.80 3.24
2361 2544 8.251750 TCGAAGTAATGGTTTGAAGTTCATAG 57.748 34.615 6.36 0.00 0.00 2.23
2370 2553 3.731089 ACGGTTCGAAGTAATGGTTTGA 58.269 40.909 0.00 0.00 0.00 2.69
2384 2567 4.735662 TTGGACATAAAAGAACGGTTCG 57.264 40.909 14.70 2.83 34.02 3.95
2415 2598 7.324935 ACAGCATGATTCAGAATAATTTTGCA 58.675 30.769 0.00 0.00 39.69 4.08
2432 2615 7.085746 CACAAAGAAATGAATGTACAGCATGA 58.914 34.615 13.00 0.00 39.69 3.07
2584 2768 9.577110 ACAATTCATATCAAAACTACAATGCTG 57.423 29.630 0.00 0.00 0.00 4.41
2863 3052 4.368543 GTCGGGGTTCTTCGCGGT 62.369 66.667 6.13 0.00 42.22 5.68
2865 3054 3.695022 ATCGTCGGGGTTCTTCGCG 62.695 63.158 0.00 0.00 43.10 5.87
2889 3078 4.735132 TCGAGCTTTCCGCCGGTG 62.735 66.667 8.42 8.42 40.39 4.94
2893 3082 2.472909 CCCATTCGAGCTTTCCGCC 61.473 63.158 0.00 0.00 40.39 6.13
2895 3084 2.472909 GGCCCATTCGAGCTTTCCG 61.473 63.158 0.00 0.00 0.00 4.30
2925 3114 2.796383 CGACCTGCGTATCTCCTTGAAG 60.796 54.545 0.00 0.00 34.64 3.02
3003 3192 2.107950 ATTTGAATCCGGACGCAAGA 57.892 45.000 6.12 5.95 43.62 3.02
3035 3224 2.147150 GTTCTCTGGTGCTGTTCTTCC 58.853 52.381 0.00 0.00 0.00 3.46
3060 3249 3.003173 CCCTTGGACTGCCCTCGA 61.003 66.667 0.00 0.00 35.38 4.04
3234 3423 2.434185 GATGCCGCGGTCTCAACA 60.434 61.111 28.70 15.52 0.00 3.33
3249 3438 2.479566 TTCTGCTTTCAAGAGCCGAT 57.520 45.000 0.00 0.00 42.01 4.18
3367 3564 2.768527 TCAATCTCCATTCTCCTTCGCT 59.231 45.455 0.00 0.00 0.00 4.93
3405 3606 5.468592 TCGCTCCTACGTTATTTTGTACAA 58.531 37.500 3.59 3.59 0.00 2.41
3491 3694 1.537202 GGAACAGAGACAGCGCAAAAT 59.463 47.619 11.47 0.00 0.00 1.82
3531 3735 4.016444 AGCCAGAAACAACTGAAGAACAA 58.984 39.130 0.00 0.00 39.94 2.83
3543 3747 5.692115 TCCATCTGTATTAGCCAGAAACA 57.308 39.130 0.00 0.00 41.93 2.83
3546 3750 6.499106 TTCATCCATCTGTATTAGCCAGAA 57.501 37.500 0.00 0.00 41.93 3.02
3560 3767 4.092383 GCAAAGTGCAAACATTCATCCATC 59.908 41.667 0.00 0.00 44.26 3.51
3581 3788 7.921214 TCGAATAATTGTTGTTTGTTTTAGGCA 59.079 29.630 0.00 0.00 0.00 4.75
3594 3801 3.374988 TGCAGAGGCTCGAATAATTGTTG 59.625 43.478 9.22 0.00 41.91 3.33
3666 3876 1.398041 CAATATCCACCACGCACACAG 59.602 52.381 0.00 0.00 0.00 3.66
3673 3883 5.601662 ACAAGAGTATCAATATCCACCACG 58.398 41.667 0.00 0.00 37.82 4.94
3755 3988 8.746052 AAAATACCAGCACAGCTATACAAATA 57.254 30.769 0.00 0.00 36.40 1.40
3784 4017 2.424705 ATACACCGACACGCGTGGTT 62.425 55.000 39.21 22.75 38.67 3.67
3788 4021 2.807895 GCATACACCGACACGCGT 60.808 61.111 5.58 5.58 38.67 6.01
3792 4025 2.470821 GTATGGAGCATACACCGACAC 58.529 52.381 0.00 0.00 44.14 3.67
3812 4045 3.834610 ACTTTCTCAGTTACGTCCATCG 58.165 45.455 0.00 0.00 37.85 3.84
3850 4083 1.334960 GCAGTGGAATCACAAACACCG 60.335 52.381 0.00 0.00 45.91 4.94
3861 4094 3.628646 GAGGTGCCCGCAGTGGAAT 62.629 63.158 0.00 0.00 42.00 3.01
3894 4127 2.125202 GAACGTCCGTTTGGCCCTTG 62.125 60.000 6.52 0.00 38.60 3.61
3895 4128 1.895231 GAACGTCCGTTTGGCCCTT 60.895 57.895 6.52 0.00 38.60 3.95
3896 4129 2.281276 GAACGTCCGTTTGGCCCT 60.281 61.111 6.52 0.00 38.60 5.19
3916 4149 6.484977 CCAGCAGATATAAAGAGAAACTTCCC 59.515 42.308 0.00 0.00 37.93 3.97
3920 4153 7.667575 TCTCCAGCAGATATAAAGAGAAACT 57.332 36.000 0.00 0.00 0.00 2.66
3924 4157 7.423844 TGTTTCTCCAGCAGATATAAAGAGA 57.576 36.000 0.00 0.00 0.00 3.10
3933 4166 4.038271 TCCAATTGTTTCTCCAGCAGAT 57.962 40.909 4.43 0.00 0.00 2.90
3934 4167 3.507162 TCCAATTGTTTCTCCAGCAGA 57.493 42.857 4.43 0.00 0.00 4.26
3935 4168 4.589216 TTTCCAATTGTTTCTCCAGCAG 57.411 40.909 4.43 0.00 0.00 4.24
3936 4169 5.070180 TGAATTTCCAATTGTTTCTCCAGCA 59.930 36.000 4.43 0.00 0.00 4.41
3998 4231 4.085357 TCTCCCCAATTTCATGATACCG 57.915 45.455 0.00 0.00 0.00 4.02
4000 4233 8.868522 TGATATTCTCCCCAATTTCATGATAC 57.131 34.615 0.00 0.00 0.00 2.24
4001 4234 8.111545 CCTGATATTCTCCCCAATTTCATGATA 58.888 37.037 0.00 0.00 0.00 2.15
4002 4235 6.952358 CCTGATATTCTCCCCAATTTCATGAT 59.048 38.462 0.00 0.00 0.00 2.45
4003 4236 6.126097 ACCTGATATTCTCCCCAATTTCATGA 60.126 38.462 0.00 0.00 0.00 3.07
4012 4245 2.050144 GAGCACCTGATATTCTCCCCA 58.950 52.381 0.00 0.00 0.00 4.96
4076 4309 6.088883 GCGATTGTACAATTTGTTTCGGAATT 59.911 34.615 21.63 0.00 0.00 2.17
4151 4384 9.562408 TTTGTGACACTATTCATACTGGTTTTA 57.438 29.630 7.20 0.00 0.00 1.52
4155 4388 7.936847 TCTTTTTGTGACACTATTCATACTGGT 59.063 33.333 7.20 0.00 0.00 4.00
4189 4422 4.385447 CCTGATGTAAATTGTGGCGTTTTG 59.615 41.667 0.00 0.00 0.00 2.44
4232 4465 7.383572 TCAAACCAAAATTCGAAACATACATGG 59.616 33.333 0.00 6.91 0.00 3.66
4253 4486 9.758651 AGTGTACAATCCCTAAAAATTTCAAAC 57.241 29.630 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.