Multiple sequence alignment - TraesCS6A01G400200

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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 TraesCS6A01G400200 chr6A 100.000 3984 0 0 1 3984 609550301 609554284 0.000000e+00 7358.0
1 TraesCS6A01G400200 chr6A 82.755 1038 159 15 1583 2607 609480485 609479455 0.000000e+00 907.0
2 TraesCS6A01G400200 chr6A 86.875 160 19 2 1310 1468 609480647 609480489 1.140000e-40 178.0
3 TraesCS6A01G400200 chr6B 90.967 3299 173 62 1 3238 705489664 705492898 0.000000e+00 4325.0
4 TraesCS6A01G400200 chr6B 82.588 1051 160 18 1579 2614 705473752 705474794 0.000000e+00 905.0
5 TraesCS6A01G400200 chr6B 88.298 376 34 8 3270 3639 705492962 705493333 3.650000e-120 442.0
6 TraesCS6A01G400200 chr6B 92.308 273 20 1 3712 3984 705493331 705493602 1.740000e-103 387.0
7 TraesCS6A01G400200 chr6B 88.679 159 16 2 1310 1467 705473594 705473751 4.060000e-45 193.0
8 TraesCS6A01G400200 chr6D 94.193 2738 112 20 801 3520 462689331 462692039 0.000000e+00 4132.0
9 TraesCS6A01G400200 chr6D 83.061 1039 154 17 1583 2607 462635747 462634717 0.000000e+00 924.0
10 TraesCS6A01G400200 chr6D 88.125 160 17 2 1310 1468 462635909 462635751 5.260000e-44 189.0
11 TraesCS6A01G400200 chr6D 97.297 37 1 0 3238 3274 462691507 462691543 3.320000e-06 63.9
12 TraesCS6A01G400200 chr7D 83.902 528 61 19 115 629 593637239 593637755 2.150000e-132 483.0
13 TraesCS6A01G400200 chr7D 75.174 576 123 17 1569 2134 83063533 83064098 1.840000e-63 254.0
14 TraesCS6A01G400200 chr2B 83.633 501 64 14 139 629 39809277 39809769 4.690000e-124 455.0
15 TraesCS6A01G400200 chr7B 82.674 531 64 19 109 629 484276391 484275879 2.820000e-121 446.0
16 TraesCS6A01G400200 chr7B 75.087 578 120 21 1569 2134 32344790 32345355 8.550000e-62 248.0
17 TraesCS6A01G400200 chr7B 74.870 577 123 19 1569 2134 32408639 32409204 3.980000e-60 243.0
18 TraesCS6A01G400200 chr7B 75.490 306 65 10 2205 2505 650129034 650128734 1.490000e-29 141.0
19 TraesCS6A01G400200 chr2A 81.955 532 68 19 109 629 10487755 10487241 3.680000e-115 425.0
20 TraesCS6A01G400200 chr5A 82.270 423 51 18 216 629 573763487 573763080 1.060000e-90 344.0
21 TraesCS6A01G400200 chr4D 78.912 294 52 10 1575 1863 44422855 44423143 1.460000e-44 191.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G400200 chr6A 609550301 609554284 3983 False 7358.00 7358 100.000000 1 3984 1 chr6A.!!$F1 3983
1 TraesCS6A01G400200 chr6A 609479455 609480647 1192 True 542.50 907 84.815000 1310 2607 2 chr6A.!!$R1 1297
2 TraesCS6A01G400200 chr6B 705489664 705493602 3938 False 1718.00 4325 90.524333 1 3984 3 chr6B.!!$F2 3983
3 TraesCS6A01G400200 chr6B 705473594 705474794 1200 False 549.00 905 85.633500 1310 2614 2 chr6B.!!$F1 1304
4 TraesCS6A01G400200 chr6D 462689331 462692039 2708 False 2097.95 4132 95.745000 801 3520 2 chr6D.!!$F1 2719
5 TraesCS6A01G400200 chr6D 462634717 462635909 1192 True 556.50 924 85.593000 1310 2607 2 chr6D.!!$R1 1297
6 TraesCS6A01G400200 chr7D 593637239 593637755 516 False 483.00 483 83.902000 115 629 1 chr7D.!!$F2 514
7 TraesCS6A01G400200 chr7D 83063533 83064098 565 False 254.00 254 75.174000 1569 2134 1 chr7D.!!$F1 565
8 TraesCS6A01G400200 chr7B 484275879 484276391 512 True 446.00 446 82.674000 109 629 1 chr7B.!!$R1 520
9 TraesCS6A01G400200 chr7B 32344790 32345355 565 False 248.00 248 75.087000 1569 2134 1 chr7B.!!$F1 565
10 TraesCS6A01G400200 chr7B 32408639 32409204 565 False 243.00 243 74.870000 1569 2134 1 chr7B.!!$F2 565
11 TraesCS6A01G400200 chr2A 10487241 10487755 514 True 425.00 425 81.955000 109 629 1 chr2A.!!$R1 520

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
193 198 0.321653 AATTGAGAGGACCGTGGTGC 60.322 55.000 1.81 1.81 36.69 5.01 F
550 569 0.390124 AAGCTGTTACGGGTCAACGA 59.610 50.000 0.00 0.00 37.61 3.85 F
718 739 1.004918 ACAGTTGCTAGTGGCCGAC 60.005 57.895 7.88 0.00 40.92 4.79 F
1140 1166 1.074752 AAGACTACGACGACGAGGAC 58.925 55.000 15.32 6.47 42.66 3.85 F
1851 1898 1.376466 GCAGAAGTTCCTCCAGGCA 59.624 57.895 0.00 0.00 34.44 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1393 1.078848 AAGATCTGCGTGGTGGAGC 60.079 57.895 0.00 0.0 35.70 4.70 R
2127 2180 1.486310 ACGAGCACCATCATGTACCAT 59.514 47.619 0.00 0.0 0.00 3.55 R
2660 2720 0.033796 ATGGTGGATGCTGGAACTGG 60.034 55.000 0.00 0.0 0.00 4.00 R
2718 2778 0.040058 ATCCCCTGCAGCAACAATCA 59.960 50.000 8.66 0.0 0.00 2.57 R
3307 3441 0.463620 ACCAAAATGCCAACAAGCGT 59.536 45.000 0.00 0.0 34.65 5.07 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
74 79 1.209128 CATCGTCGGGTGAATGCTAC 58.791 55.000 0.00 0.00 0.00 3.58
105 110 3.950395 ACTTAAGAAGCTTCATCCATGGC 59.050 43.478 27.57 0.00 0.00 4.40
107 112 0.465097 AGAAGCTTCATCCATGGCCG 60.465 55.000 27.57 0.00 0.00 6.13
141 146 1.197949 GCTGGAACCGCTTCTCTTTTC 59.802 52.381 0.00 0.00 0.00 2.29
142 147 2.772287 CTGGAACCGCTTCTCTTTTCT 58.228 47.619 0.00 0.00 0.00 2.52
143 148 3.142174 CTGGAACCGCTTCTCTTTTCTT 58.858 45.455 0.00 0.00 0.00 2.52
144 149 3.551846 TGGAACCGCTTCTCTTTTCTTT 58.448 40.909 0.00 0.00 0.00 2.52
193 198 0.321653 AATTGAGAGGACCGTGGTGC 60.322 55.000 1.81 1.81 36.69 5.01
275 287 4.642885 TGCTACTACCAGCTTTGTGTTTTT 59.357 37.500 0.00 0.00 42.30 1.94
346 360 5.735070 GCTGGGACAACGAATTTTTGTTACT 60.735 40.000 7.57 0.00 38.70 2.24
440 457 2.364647 TGCATGAATGTTGCAACTGGAA 59.635 40.909 28.61 10.42 46.48 3.53
510 529 0.963856 AGCACACATGGATGCACCTG 60.964 55.000 21.33 0.75 44.59 4.00
515 534 0.915872 ACATGGATGCACCTGGGAGA 60.916 55.000 0.00 0.00 39.86 3.71
542 561 0.521735 GGGCAGAAAAGCTGTTACGG 59.478 55.000 0.00 0.00 46.62 4.02
550 569 0.390124 AAGCTGTTACGGGTCAACGA 59.610 50.000 0.00 0.00 37.61 3.85
567 586 7.376530 GTCAACGACCTATTTTTCTTTTGTG 57.623 36.000 0.00 0.00 0.00 3.33
568 587 6.970613 GTCAACGACCTATTTTTCTTTTGTGT 59.029 34.615 0.00 0.00 0.00 3.72
646 667 3.037686 ATGGTTACGCCCGCCATGA 62.038 57.895 0.00 0.00 41.05 3.07
677 698 2.989840 GTGTTGACCAGATCGAAGACTG 59.010 50.000 9.60 9.60 42.51 3.51
678 699 2.890945 TGTTGACCAGATCGAAGACTGA 59.109 45.455 15.69 0.00 42.51 3.41
679 700 3.057245 TGTTGACCAGATCGAAGACTGAG 60.057 47.826 15.69 10.05 42.51 3.35
688 709 1.203137 TCGAAGACTGAGGGGGAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
715 736 3.267974 GCACAGTTGCTAGTGGCC 58.732 61.111 7.88 0.00 46.17 5.36
716 737 2.680913 GCACAGTTGCTAGTGGCCG 61.681 63.158 7.88 0.00 46.17 6.13
717 738 1.005037 CACAGTTGCTAGTGGCCGA 60.005 57.895 7.88 0.00 40.92 5.54
718 739 1.004918 ACAGTTGCTAGTGGCCGAC 60.005 57.895 7.88 0.00 40.92 4.79
719 740 1.741770 CAGTTGCTAGTGGCCGACC 60.742 63.158 0.00 0.00 40.92 4.79
720 741 2.813908 GTTGCTAGTGGCCGACCG 60.814 66.667 0.00 0.00 40.92 4.79
721 742 4.077184 TTGCTAGTGGCCGACCGG 62.077 66.667 0.00 0.00 40.92 5.28
739 760 1.531739 GGCTCAAATTTGGGTCGGCA 61.532 55.000 19.08 0.00 0.00 5.69
770 796 3.060895 CCTAGCGCTGTCTCGTTTTAAAG 59.939 47.826 22.90 3.85 0.00 1.85
775 801 3.432252 CGCTGTCTCGTTTTAAAGATGGT 59.568 43.478 0.00 0.00 0.00 3.55
776 802 4.624024 CGCTGTCTCGTTTTAAAGATGGTA 59.376 41.667 0.00 0.00 0.00 3.25
825 851 5.199024 TGTAGATTGCAGCAACAAAACAT 57.801 34.783 10.85 0.00 32.27 2.71
827 853 6.923012 TGTAGATTGCAGCAACAAAACATAT 58.077 32.000 10.85 0.00 32.27 1.78
1053 1079 2.912025 CACAACACCCACAGCCCC 60.912 66.667 0.00 0.00 0.00 5.80
1126 1152 1.846712 GAGGAAGCCTGGCCAAGACT 61.847 60.000 16.57 6.87 31.76 3.24
1140 1166 1.074752 AAGACTACGACGACGAGGAC 58.925 55.000 15.32 6.47 42.66 3.85
1398 1424 1.819632 GATCTTCGCCGGCCACATT 60.820 57.895 23.46 2.65 0.00 2.71
1488 1514 2.478292 GTGAGTCCCCATCCTCCTTTA 58.522 52.381 0.00 0.00 0.00 1.85
1491 1519 3.716872 TGAGTCCCCATCCTCCTTTAATC 59.283 47.826 0.00 0.00 0.00 1.75
1851 1898 1.376466 GCAGAAGTTCCTCCAGGCA 59.624 57.895 0.00 0.00 34.44 4.75
2127 2180 1.611006 GTGATGCTCTGCCTCGAGATA 59.389 52.381 15.71 0.76 32.74 1.98
2457 2510 3.781307 AACATCGCCGGCCTGCTA 61.781 61.111 23.46 6.72 0.00 3.49
2660 2720 1.466025 TACACACCACCACCTCCGAC 61.466 60.000 0.00 0.00 0.00 4.79
2709 2769 2.887337 CATTGCTGCAATGCTGATTGA 58.113 42.857 34.26 4.15 43.38 2.57
2710 2770 3.457234 CATTGCTGCAATGCTGATTGAT 58.543 40.909 34.26 7.16 43.38 2.57
2711 2771 2.863401 TGCTGCAATGCTGATTGATC 57.137 45.000 16.29 0.00 41.49 2.92
2712 2772 2.375146 TGCTGCAATGCTGATTGATCT 58.625 42.857 16.29 0.00 41.49 2.75
2713 2773 2.758423 TGCTGCAATGCTGATTGATCTT 59.242 40.909 16.29 0.00 41.49 2.40
2714 2774 3.116300 GCTGCAATGCTGATTGATCTTG 58.884 45.455 16.29 0.00 41.49 3.02
2715 2775 3.181490 GCTGCAATGCTGATTGATCTTGA 60.181 43.478 16.29 0.00 41.49 3.02
2716 2776 4.499865 GCTGCAATGCTGATTGATCTTGAT 60.500 41.667 16.29 0.00 41.49 2.57
2717 2777 5.183014 TGCAATGCTGATTGATCTTGATC 57.817 39.130 6.82 3.82 41.49 2.92
2718 2778 4.887655 TGCAATGCTGATTGATCTTGATCT 59.112 37.500 6.82 0.00 41.49 2.75
2719 2779 5.215903 GCAATGCTGATTGATCTTGATCTG 58.784 41.667 11.31 1.28 41.49 2.90
2720 2780 5.008712 GCAATGCTGATTGATCTTGATCTGA 59.991 40.000 11.31 2.00 41.49 3.27
2721 2781 6.294231 GCAATGCTGATTGATCTTGATCTGAT 60.294 38.462 11.31 0.00 41.49 2.90
2722 2782 7.652727 CAATGCTGATTGATCTTGATCTGATT 58.347 34.615 11.31 8.02 41.49 2.57
2723 2783 6.619801 TGCTGATTGATCTTGATCTGATTG 57.380 37.500 11.31 2.14 0.00 2.67
2727 2787 6.792326 TGATTGATCTTGATCTGATTGTTGC 58.208 36.000 11.31 0.00 0.00 4.17
2816 2876 0.034896 TCAAGACCGACTGGAAAGCC 59.965 55.000 0.00 0.00 39.21 4.35
2834 2898 2.880890 AGCCGAGGTAATTTGATGATGC 59.119 45.455 0.00 0.00 0.00 3.91
2838 2902 5.008613 GCCGAGGTAATTTGATGATGCTTAA 59.991 40.000 0.00 0.00 0.00 1.85
3023 3101 5.106237 CCGAAACTGTGTACTAGAGCTTAGT 60.106 44.000 0.00 11.59 0.00 2.24
3031 3109 7.368833 TGTGTACTAGAGCTTAGTTTCAGTTC 58.631 38.462 11.97 0.00 0.00 3.01
3109 3189 7.069986 TCAATGAGTTAGATACTTAGGCTCCT 58.930 38.462 0.00 0.00 37.17 3.69
3129 3225 3.749609 CCTTTTGTAGAAACACCTACGGG 59.250 47.826 0.00 0.00 41.34 5.28
3307 3441 1.284785 GGGGAACACCATGGATCTTCA 59.715 52.381 21.47 0.00 42.91 3.02
3332 3466 2.114616 TGTTGGCATTTTGGTGTCCTT 58.885 42.857 0.00 0.00 0.00 3.36
3338 3472 2.858260 GCATTTTGGTGTCCTTGTGTCG 60.858 50.000 0.00 0.00 0.00 4.35
3492 3631 7.533426 AGCAAAGTGAAGATCATCAAACATAC 58.467 34.615 1.48 0.00 0.00 2.39
3520 3659 7.649306 ACAAAGTGATCTAAAATGCTCAAACAC 59.351 33.333 0.00 0.00 0.00 3.32
3545 3684 1.343789 CATCAAACACCACCATTGCCA 59.656 47.619 0.00 0.00 0.00 4.92
3558 3697 2.129607 CATTGCCACACTCAAACTTGC 58.870 47.619 0.00 0.00 0.00 4.01
3566 3705 3.068590 CACACTCAAACTTGCCCATCTTT 59.931 43.478 0.00 0.00 0.00 2.52
3577 3716 2.168936 TGCCCATCTTTGAATTGGATGC 59.831 45.455 0.00 0.00 36.49 3.91
3592 3731 7.224753 TGAATTGGATGCGACTAATAAGACTTC 59.775 37.037 0.00 0.00 0.00 3.01
3609 3748 1.339610 CTTCGAGCCATAGTGGAGAGG 59.660 57.143 0.00 0.00 40.96 3.69
3619 3758 4.956700 CCATAGTGGAGAGGTTCTGAGTTA 59.043 45.833 0.00 0.00 40.96 2.24
3629 3768 5.179555 AGAGGTTCTGAGTTAAATTGCGTTC 59.820 40.000 0.00 0.00 0.00 3.95
3635 3774 4.052608 TGAGTTAAATTGCGTTCGAGACA 58.947 39.130 0.00 0.00 0.00 3.41
3636 3775 4.688879 TGAGTTAAATTGCGTTCGAGACAT 59.311 37.500 0.00 0.00 0.00 3.06
3637 3776 5.178623 TGAGTTAAATTGCGTTCGAGACATT 59.821 36.000 0.00 0.00 0.00 2.71
3638 3777 5.382303 AGTTAAATTGCGTTCGAGACATTG 58.618 37.500 0.00 0.00 0.00 2.82
3639 3778 2.247311 AATTGCGTTCGAGACATTGC 57.753 45.000 0.00 0.00 0.00 3.56
3640 3779 0.447801 ATTGCGTTCGAGACATTGCC 59.552 50.000 0.00 0.00 0.00 4.52
3641 3780 0.602638 TTGCGTTCGAGACATTGCCT 60.603 50.000 0.00 0.00 0.00 4.75
3642 3781 0.602638 TGCGTTCGAGACATTGCCTT 60.603 50.000 0.00 0.00 0.00 4.35
3643 3782 1.337354 TGCGTTCGAGACATTGCCTTA 60.337 47.619 0.00 0.00 0.00 2.69
3644 3783 1.060698 GCGTTCGAGACATTGCCTTAC 59.939 52.381 0.00 0.00 0.00 2.34
3645 3784 1.659098 CGTTCGAGACATTGCCTTACC 59.341 52.381 0.00 0.00 0.00 2.85
3646 3785 1.659098 GTTCGAGACATTGCCTTACCG 59.341 52.381 0.00 0.00 0.00 4.02
3647 3786 0.892755 TCGAGACATTGCCTTACCGT 59.107 50.000 0.00 0.00 0.00 4.83
3648 3787 0.999406 CGAGACATTGCCTTACCGTG 59.001 55.000 0.00 0.00 0.00 4.94
3649 3788 1.671850 CGAGACATTGCCTTACCGTGT 60.672 52.381 0.00 0.00 0.00 4.49
3650 3789 2.416296 CGAGACATTGCCTTACCGTGTA 60.416 50.000 0.00 0.00 0.00 2.90
3651 3790 3.737047 CGAGACATTGCCTTACCGTGTAT 60.737 47.826 0.00 0.00 0.00 2.29
3652 3791 3.531538 AGACATTGCCTTACCGTGTATG 58.468 45.455 0.00 0.00 0.00 2.39
3653 3792 2.014128 ACATTGCCTTACCGTGTATGC 58.986 47.619 0.00 0.00 0.00 3.14
3654 3793 2.288666 CATTGCCTTACCGTGTATGCT 58.711 47.619 0.00 0.00 0.00 3.79
3655 3794 3.118555 ACATTGCCTTACCGTGTATGCTA 60.119 43.478 0.00 0.00 0.00 3.49
3656 3795 3.613494 TTGCCTTACCGTGTATGCTAA 57.387 42.857 0.00 0.00 0.00 3.09
3657 3796 3.830744 TGCCTTACCGTGTATGCTAAT 57.169 42.857 0.00 0.00 0.00 1.73
3658 3797 3.462982 TGCCTTACCGTGTATGCTAATG 58.537 45.455 0.00 0.00 0.00 1.90
3659 3798 2.806244 GCCTTACCGTGTATGCTAATGG 59.194 50.000 0.00 0.00 0.00 3.16
3660 3799 3.399330 CCTTACCGTGTATGCTAATGGG 58.601 50.000 0.00 0.00 0.00 4.00
3661 3800 3.070446 CCTTACCGTGTATGCTAATGGGA 59.930 47.826 0.00 0.00 0.00 4.37
3662 3801 4.262894 CCTTACCGTGTATGCTAATGGGAT 60.263 45.833 0.00 0.00 0.00 3.85
3663 3802 3.857157 ACCGTGTATGCTAATGGGATT 57.143 42.857 0.00 0.00 0.00 3.01
3664 3803 4.164843 ACCGTGTATGCTAATGGGATTT 57.835 40.909 0.00 0.00 0.00 2.17
3665 3804 5.298989 ACCGTGTATGCTAATGGGATTTA 57.701 39.130 0.00 0.00 0.00 1.40
3666 3805 5.686753 ACCGTGTATGCTAATGGGATTTAA 58.313 37.500 0.00 0.00 0.00 1.52
3667 3806 6.303839 ACCGTGTATGCTAATGGGATTTAAT 58.696 36.000 0.00 0.00 0.00 1.40
3668 3807 7.455058 ACCGTGTATGCTAATGGGATTTAATA 58.545 34.615 0.00 0.00 0.00 0.98
3669 3808 7.389607 ACCGTGTATGCTAATGGGATTTAATAC 59.610 37.037 0.00 0.00 0.00 1.89
3670 3809 7.606456 CCGTGTATGCTAATGGGATTTAATACT 59.394 37.037 0.00 0.00 0.00 2.12
3671 3810 8.656849 CGTGTATGCTAATGGGATTTAATACTC 58.343 37.037 0.00 0.00 0.00 2.59
3672 3811 9.726438 GTGTATGCTAATGGGATTTAATACTCT 57.274 33.333 0.00 0.00 0.00 3.24
3673 3812 9.944376 TGTATGCTAATGGGATTTAATACTCTC 57.056 33.333 0.00 0.00 0.00 3.20
3674 3813 9.944376 GTATGCTAATGGGATTTAATACTCTCA 57.056 33.333 0.00 0.00 0.00 3.27
3703 3842 9.567776 TTTTGTTTAATCTGTTAGTGAGATGGA 57.432 29.630 0.00 0.00 30.30 3.41
3704 3843 9.567776 TTTGTTTAATCTGTTAGTGAGATGGAA 57.432 29.630 0.00 0.00 30.30 3.53
3705 3844 8.547967 TGTTTAATCTGTTAGTGAGATGGAAC 57.452 34.615 0.00 0.00 32.00 3.62
3706 3845 7.330946 TGTTTAATCTGTTAGTGAGATGGAACG 59.669 37.037 0.00 0.00 32.98 3.95
3707 3846 5.661056 AATCTGTTAGTGAGATGGAACGA 57.339 39.130 0.00 0.00 30.30 3.85
3708 3847 5.860941 ATCTGTTAGTGAGATGGAACGAT 57.139 39.130 0.00 0.00 0.00 3.73
3709 3848 5.250235 TCTGTTAGTGAGATGGAACGATC 57.750 43.478 0.00 0.00 0.00 3.69
3710 3849 4.705023 TCTGTTAGTGAGATGGAACGATCA 59.295 41.667 0.00 0.00 0.00 2.92
3714 3853 3.801698 AGTGAGATGGAACGATCATTGG 58.198 45.455 0.00 0.00 0.00 3.16
3726 3865 8.949177 TGGAACGATCATTGGATATAAATCATG 58.051 33.333 0.00 0.00 32.67 3.07
3794 3933 1.486726 CTTCGAGAAAGCCTATGGGGT 59.513 52.381 0.00 0.00 46.45 4.95
3828 3967 5.387113 TTGCCACCTATCCTATTCAACAT 57.613 39.130 0.00 0.00 0.00 2.71
3835 3974 6.428159 CACCTATCCTATTCAACATAGTTGCC 59.572 42.308 5.06 0.00 0.00 4.52
3836 3975 5.639506 CCTATCCTATTCAACATAGTTGCCG 59.360 44.000 5.06 0.00 0.00 5.69
3844 3983 6.751514 TTCAACATAGTTGCCGATATGTTT 57.248 33.333 12.33 0.78 45.70 2.83
3853 3992 1.476488 GCCGATATGTTTGTTGCCCTT 59.524 47.619 0.00 0.00 0.00 3.95
3855 3994 3.317993 GCCGATATGTTTGTTGCCCTTAT 59.682 43.478 0.00 0.00 0.00 1.73
3906 4045 2.553028 GGTGGACTCATTCCTTGCTTGA 60.553 50.000 0.00 0.00 46.10 3.02
3915 4054 1.926561 TCCTTGCTTGATCGATGTCG 58.073 50.000 0.54 0.00 41.45 4.35
3916 4055 1.204704 TCCTTGCTTGATCGATGTCGT 59.795 47.619 0.54 0.00 40.80 4.34
3943 4082 9.171877 TGTGTTAGTATTGCATTATGTTGATGA 57.828 29.630 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.438564 TCTTAAGTACACTGTTGTAGCATTCA 58.561 34.615 1.63 0.00 38.95 2.57
74 79 6.844696 TGAAGCTTCTTAAGTACACTGTTG 57.155 37.500 26.09 0.00 0.00 3.33
141 146 6.391227 TCTAAAGAAGGTTCCAGCAAAAAG 57.609 37.500 0.00 0.00 0.00 2.27
142 147 6.976934 ATCTAAAGAAGGTTCCAGCAAAAA 57.023 33.333 0.00 0.00 0.00 1.94
143 148 6.976934 AATCTAAAGAAGGTTCCAGCAAAA 57.023 33.333 0.00 0.00 0.00 2.44
144 149 6.976934 AAATCTAAAGAAGGTTCCAGCAAA 57.023 33.333 0.00 0.00 0.00 3.68
314 328 1.745890 GTTGTCCCAGCAAAACCCC 59.254 57.895 0.00 0.00 0.00 4.95
440 457 4.988598 CGCCAGTGTTGCCGTCCT 62.989 66.667 0.00 0.00 0.00 3.85
479 498 1.367840 GTGTGCTCCTTCTCGGTGT 59.632 57.895 0.00 0.00 0.00 4.16
550 569 8.652463 CGTCAAAAACACAAAAGAAAAATAGGT 58.348 29.630 0.00 0.00 0.00 3.08
555 574 7.171678 ACCATCGTCAAAAACACAAAAGAAAAA 59.828 29.630 0.00 0.00 0.00 1.94
560 579 5.098893 TCACCATCGTCAAAAACACAAAAG 58.901 37.500 0.00 0.00 0.00 2.27
563 582 3.488384 GCTCACCATCGTCAAAAACACAA 60.488 43.478 0.00 0.00 0.00 3.33
565 584 2.650608 GCTCACCATCGTCAAAAACAC 58.349 47.619 0.00 0.00 0.00 3.32
567 586 1.399727 CCGCTCACCATCGTCAAAAAC 60.400 52.381 0.00 0.00 0.00 2.43
568 587 0.871722 CCGCTCACCATCGTCAAAAA 59.128 50.000 0.00 0.00 0.00 1.94
594 615 1.225745 CGATGCTCGCCGTTGAAAC 60.226 57.895 0.00 0.00 31.14 2.78
646 667 0.186386 TGGTCAACACGGGGGAAATT 59.814 50.000 0.00 0.00 0.00 1.82
703 724 2.813908 CGGTCGGCCACTAGCAAC 60.814 66.667 6.96 0.00 46.50 4.17
704 725 4.077184 CCGGTCGGCCACTAGCAA 62.077 66.667 6.96 0.00 46.50 3.91
714 735 1.506262 CCAAATTTGAGCCGGTCGG 59.494 57.895 19.86 4.85 38.57 4.79
715 736 1.241315 ACCCAAATTTGAGCCGGTCG 61.241 55.000 19.86 0.00 0.00 4.79
716 737 0.526211 GACCCAAATTTGAGCCGGTC 59.474 55.000 21.18 21.18 31.77 4.79
717 738 1.241315 CGACCCAAATTTGAGCCGGT 61.241 55.000 19.86 16.82 0.00 5.28
718 739 1.506262 CGACCCAAATTTGAGCCGG 59.494 57.895 19.86 13.78 0.00 6.13
719 740 1.506262 CCGACCCAAATTTGAGCCG 59.494 57.895 19.86 10.60 0.00 5.52
720 741 1.215382 GCCGACCCAAATTTGAGCC 59.785 57.895 19.86 0.00 0.00 4.70
721 742 0.388520 GTGCCGACCCAAATTTGAGC 60.389 55.000 19.86 13.29 0.00 4.26
722 743 0.958091 TGTGCCGACCCAAATTTGAG 59.042 50.000 19.86 9.10 0.00 3.02
723 744 0.671251 GTGTGCCGACCCAAATTTGA 59.329 50.000 19.86 0.00 0.00 2.69
747 768 1.014564 AAAACGAGACAGCGCTAGGC 61.015 55.000 10.99 7.16 44.05 3.93
754 775 6.476243 TTACCATCTTTAAAACGAGACAGC 57.524 37.500 0.00 0.00 0.00 4.40
758 779 8.842358 ACAAGATTACCATCTTTAAAACGAGA 57.158 30.769 0.00 0.00 46.07 4.04
799 825 6.183360 TGTTTTGTTGCTGCAATCTACAGTAA 60.183 34.615 19.11 7.79 37.40 2.24
997 1023 0.107017 GGCTCTGTGTATGCCATGGT 60.107 55.000 14.67 0.00 45.46 3.55
1011 1037 1.349357 GTGGTGAAAAGGAGAGGCTCT 59.651 52.381 18.80 18.80 0.00 4.09
1116 1142 1.582968 GTCGTCGTAGTCTTGGCCA 59.417 57.895 0.00 0.00 0.00 5.36
1126 1152 2.436646 GGGGTCCTCGTCGTCGTA 60.437 66.667 1.33 0.00 38.33 3.43
1332 1358 1.590238 CAGAGGATGTTGAACGCGATC 59.410 52.381 15.93 12.43 0.00 3.69
1367 1393 1.078848 AAGATCTGCGTGGTGGAGC 60.079 57.895 0.00 0.00 35.70 4.70
1398 1424 2.707849 GGAGAGCTCGCGGTTACCA 61.708 63.158 11.54 0.00 0.00 3.25
1488 1514 3.519510 TCGGAGGAGGAAGAACAATGATT 59.480 43.478 0.00 0.00 0.00 2.57
1491 1519 3.462021 GATCGGAGGAGGAAGAACAATG 58.538 50.000 0.00 0.00 0.00 2.82
1538 1566 3.301906 CGTCACATTGTCAGTTCGATCTC 59.698 47.826 0.00 0.00 0.00 2.75
1851 1898 2.113986 GCCACCACCTTGCTCTGT 59.886 61.111 0.00 0.00 0.00 3.41
2127 2180 1.486310 ACGAGCACCATCATGTACCAT 59.514 47.619 0.00 0.00 0.00 3.55
2175 2228 2.415608 GGAGTCCACGGCGATCTCA 61.416 63.158 16.62 0.00 0.00 3.27
2583 2636 3.070302 GGAAGAGGTAGCCGAAGATGAAT 59.930 47.826 0.00 0.00 0.00 2.57
2660 2720 0.033796 ATGGTGGATGCTGGAACTGG 60.034 55.000 0.00 0.00 0.00 4.00
2707 2767 4.095932 GCAGCAACAATCAGATCAAGATCA 59.904 41.667 12.21 0.00 40.22 2.92
2708 2768 4.095932 TGCAGCAACAATCAGATCAAGATC 59.904 41.667 0.00 1.81 38.09 2.75
2709 2769 4.014406 TGCAGCAACAATCAGATCAAGAT 58.986 39.130 0.00 0.00 0.00 2.40
2710 2770 3.414269 TGCAGCAACAATCAGATCAAGA 58.586 40.909 0.00 0.00 0.00 3.02
2711 2771 3.427638 CCTGCAGCAACAATCAGATCAAG 60.428 47.826 8.66 0.00 0.00 3.02
2712 2772 2.490509 CCTGCAGCAACAATCAGATCAA 59.509 45.455 8.66 0.00 0.00 2.57
2713 2773 2.089201 CCTGCAGCAACAATCAGATCA 58.911 47.619 8.66 0.00 0.00 2.92
2714 2774 1.404391 CCCTGCAGCAACAATCAGATC 59.596 52.381 8.66 0.00 0.00 2.75
2715 2775 1.471119 CCCTGCAGCAACAATCAGAT 58.529 50.000 8.66 0.00 0.00 2.90
2716 2776 0.609957 CCCCTGCAGCAACAATCAGA 60.610 55.000 8.66 0.00 0.00 3.27
2717 2777 0.609957 TCCCCTGCAGCAACAATCAG 60.610 55.000 8.66 0.00 0.00 2.90
2718 2778 0.040058 ATCCCCTGCAGCAACAATCA 59.960 50.000 8.66 0.00 0.00 2.57
2719 2779 1.188863 AATCCCCTGCAGCAACAATC 58.811 50.000 8.66 0.00 0.00 2.67
2720 2780 1.276989 CAAATCCCCTGCAGCAACAAT 59.723 47.619 8.66 0.00 0.00 2.71
2721 2781 0.680618 CAAATCCCCTGCAGCAACAA 59.319 50.000 8.66 0.00 0.00 2.83
2722 2782 1.186917 CCAAATCCCCTGCAGCAACA 61.187 55.000 8.66 0.00 0.00 3.33
2723 2783 1.593265 CCAAATCCCCTGCAGCAAC 59.407 57.895 8.66 0.00 0.00 4.17
2727 2787 3.142838 CGCCCAAATCCCCTGCAG 61.143 66.667 6.78 6.78 0.00 4.41
2816 2876 8.013947 CAGATTAAGCATCATCAAATTACCTCG 58.986 37.037 0.00 0.00 33.75 4.63
3000 3078 5.940595 ACTAAGCTCTAGTACACAGTTTCG 58.059 41.667 6.75 0.00 0.00 3.46
3023 3101 9.261180 CACACTATCTGTAAAAGAGAACTGAAA 57.739 33.333 0.00 0.00 38.67 2.69
3031 3109 7.008719 CGATGTCACACACTATCTGTAAAAGAG 59.991 40.741 0.00 0.00 38.67 2.85
3129 3225 6.309712 TCCAGCATGTAGTTCTACGTATAC 57.690 41.667 0.00 0.00 0.00 1.47
3307 3441 0.463620 ACCAAAATGCCAACAAGCGT 59.536 45.000 0.00 0.00 34.65 5.07
3332 3466 7.643579 TCAAATTGTTTGATATGAACGACACA 58.356 30.769 1.24 0.00 44.21 3.72
3393 3532 9.545105 AACAATGTTGAATGTATGTGTGAAATT 57.455 25.926 0.00 0.00 0.00 1.82
3430 3569 6.458888 GCCCGAAATTTGGAATTTCACAAAAA 60.459 34.615 20.01 3.88 39.69 1.94
3435 3574 3.658709 TGCCCGAAATTTGGAATTTCAC 58.341 40.909 20.01 12.21 37.76 3.18
3437 3576 5.872070 TGTTATGCCCGAAATTTGGAATTTC 59.128 36.000 13.47 13.47 35.34 2.17
3492 3631 8.482429 GTTTGAGCATTTTAGATCACTTTGTTG 58.518 33.333 0.00 0.00 33.03 3.33
3520 3659 0.888736 TGGTGGTGTTTGATGCTCCG 60.889 55.000 0.00 0.00 0.00 4.63
3545 3684 2.664402 AGATGGGCAAGTTTGAGTGT 57.336 45.000 0.00 0.00 0.00 3.55
3558 3697 2.689471 TCGCATCCAATTCAAAGATGGG 59.311 45.455 9.30 9.30 46.58 4.00
3566 3705 6.582636 AGTCTTATTAGTCGCATCCAATTCA 58.417 36.000 0.00 0.00 0.00 2.57
3577 3716 4.288670 TGGCTCGAAGTCTTATTAGTCG 57.711 45.455 0.00 0.00 0.00 4.18
3592 3731 1.067821 GAACCTCTCCACTATGGCTCG 59.932 57.143 0.00 0.00 37.47 5.03
3609 3748 5.013861 TCGAACGCAATTTAACTCAGAAC 57.986 39.130 0.00 0.00 0.00 3.01
3619 3758 2.584791 GCAATGTCTCGAACGCAATTT 58.415 42.857 0.00 0.00 0.00 1.82
3629 3768 0.999406 CACGGTAAGGCAATGTCTCG 59.001 55.000 0.00 0.00 0.00 4.04
3635 3774 2.710096 AGCATACACGGTAAGGCAAT 57.290 45.000 2.80 0.00 0.00 3.56
3636 3775 3.613494 TTAGCATACACGGTAAGGCAA 57.387 42.857 2.80 0.00 0.00 4.52
3637 3776 3.462982 CATTAGCATACACGGTAAGGCA 58.537 45.455 2.80 0.00 32.76 4.75
3638 3777 2.806244 CCATTAGCATACACGGTAAGGC 59.194 50.000 0.00 0.00 32.76 4.35
3639 3778 3.070446 TCCCATTAGCATACACGGTAAGG 59.930 47.826 0.00 0.00 32.76 2.69
3640 3779 4.330944 TCCCATTAGCATACACGGTAAG 57.669 45.455 0.00 0.00 32.76 2.34
3641 3780 4.967084 ATCCCATTAGCATACACGGTAA 57.033 40.909 0.00 0.00 33.70 2.85
3642 3781 4.967084 AATCCCATTAGCATACACGGTA 57.033 40.909 0.00 0.00 0.00 4.02
3643 3782 3.857157 AATCCCATTAGCATACACGGT 57.143 42.857 0.00 0.00 0.00 4.83
3644 3783 6.817765 ATTAAATCCCATTAGCATACACGG 57.182 37.500 0.00 0.00 0.00 4.94
3645 3784 8.547967 AGTATTAAATCCCATTAGCATACACG 57.452 34.615 0.00 0.00 0.00 4.49
3646 3785 9.726438 AGAGTATTAAATCCCATTAGCATACAC 57.274 33.333 0.00 0.00 0.00 2.90
3647 3786 9.944376 GAGAGTATTAAATCCCATTAGCATACA 57.056 33.333 0.00 0.00 0.00 2.29
3648 3787 9.944376 TGAGAGTATTAAATCCCATTAGCATAC 57.056 33.333 0.00 0.00 0.00 2.39
3677 3816 9.567776 TCCATCTCACTAACAGATTAAACAAAA 57.432 29.630 0.00 0.00 0.00 2.44
3678 3817 9.567776 TTCCATCTCACTAACAGATTAAACAAA 57.432 29.630 0.00 0.00 0.00 2.83
3679 3818 8.999431 GTTCCATCTCACTAACAGATTAAACAA 58.001 33.333 0.00 0.00 29.91 2.83
3680 3819 7.330946 CGTTCCATCTCACTAACAGATTAAACA 59.669 37.037 0.00 0.00 29.91 2.83
3681 3820 7.544566 TCGTTCCATCTCACTAACAGATTAAAC 59.455 37.037 0.00 0.00 0.00 2.01
3682 3821 7.608153 TCGTTCCATCTCACTAACAGATTAAA 58.392 34.615 0.00 0.00 0.00 1.52
3683 3822 7.165460 TCGTTCCATCTCACTAACAGATTAA 57.835 36.000 0.00 0.00 0.00 1.40
3684 3823 6.769134 TCGTTCCATCTCACTAACAGATTA 57.231 37.500 0.00 0.00 0.00 1.75
3685 3824 5.661056 TCGTTCCATCTCACTAACAGATT 57.339 39.130 0.00 0.00 0.00 2.40
3686 3825 5.360999 TGATCGTTCCATCTCACTAACAGAT 59.639 40.000 0.00 0.00 0.00 2.90
3687 3826 4.705023 TGATCGTTCCATCTCACTAACAGA 59.295 41.667 0.00 0.00 0.00 3.41
3688 3827 4.998788 TGATCGTTCCATCTCACTAACAG 58.001 43.478 0.00 0.00 0.00 3.16
3689 3828 5.598416 ATGATCGTTCCATCTCACTAACA 57.402 39.130 0.00 0.00 0.00 2.41
3690 3829 5.235186 CCAATGATCGTTCCATCTCACTAAC 59.765 44.000 0.00 0.00 0.00 2.34
3691 3830 5.128663 TCCAATGATCGTTCCATCTCACTAA 59.871 40.000 0.00 0.00 0.00 2.24
3692 3831 4.649218 TCCAATGATCGTTCCATCTCACTA 59.351 41.667 0.00 0.00 0.00 2.74
3693 3832 3.452264 TCCAATGATCGTTCCATCTCACT 59.548 43.478 0.00 0.00 0.00 3.41
3694 3833 3.797039 TCCAATGATCGTTCCATCTCAC 58.203 45.455 0.00 0.00 0.00 3.51
3695 3834 4.694760 ATCCAATGATCGTTCCATCTCA 57.305 40.909 0.00 0.00 0.00 3.27
3696 3835 8.777865 TTTATATCCAATGATCGTTCCATCTC 57.222 34.615 0.00 0.00 32.18 2.75
3697 3836 9.388506 GATTTATATCCAATGATCGTTCCATCT 57.611 33.333 0.00 0.00 32.18 2.90
3698 3837 9.166173 TGATTTATATCCAATGATCGTTCCATC 57.834 33.333 0.00 0.00 32.18 3.51
3699 3838 9.690913 ATGATTTATATCCAATGATCGTTCCAT 57.309 29.630 0.00 0.00 32.18 3.41
3700 3839 8.949177 CATGATTTATATCCAATGATCGTTCCA 58.051 33.333 0.00 0.00 32.18 3.53
3701 3840 9.166173 TCATGATTTATATCCAATGATCGTTCC 57.834 33.333 0.00 0.00 32.18 3.62
3746 3885 2.092323 TGATGATCACCTCGTCGAGTT 58.908 47.619 20.37 3.67 42.00 3.01
3747 3886 1.751437 TGATGATCACCTCGTCGAGT 58.249 50.000 20.37 6.52 42.00 4.18
3749 3888 1.405463 CCTTGATGATCACCTCGTCGA 59.595 52.381 0.00 0.00 42.00 4.20
3750 3889 1.135139 ACCTTGATGATCACCTCGTCG 59.865 52.381 0.00 0.00 42.00 5.12
3751 3890 2.969628 ACCTTGATGATCACCTCGTC 57.030 50.000 0.00 0.00 39.90 4.20
3752 3891 3.381908 GTCTACCTTGATGATCACCTCGT 59.618 47.826 0.00 0.00 0.00 4.18
3753 3892 3.634448 AGTCTACCTTGATGATCACCTCG 59.366 47.826 0.00 0.00 0.00 4.63
3755 3894 4.098654 CGAAGTCTACCTTGATGATCACCT 59.901 45.833 0.00 0.00 32.03 4.00
3794 3933 2.507407 GGTGGCAAAGAATCACCCTA 57.493 50.000 0.00 0.00 43.65 3.53
3799 3938 5.912149 ATAGGATAGGTGGCAAAGAATCA 57.088 39.130 0.00 0.00 0.00 2.57
3828 3967 3.127895 GGCAACAAACATATCGGCAACTA 59.872 43.478 0.00 0.00 0.00 2.24
3835 3974 4.739716 GCAATAAGGGCAACAAACATATCG 59.260 41.667 0.00 0.00 39.74 2.92
3836 3975 5.659463 TGCAATAAGGGCAACAAACATATC 58.341 37.500 0.00 0.00 38.54 1.63
3853 3992 7.601856 ACCATTTTCTTTCTCGATTTGCAATA 58.398 30.769 0.00 0.00 0.00 1.90
3855 3994 5.841810 ACCATTTTCTTTCTCGATTTGCAA 58.158 33.333 0.00 0.00 0.00 4.08
3906 4045 5.005394 GCAATACTAACACAACGACATCGAT 59.995 40.000 8.54 0.00 43.02 3.59
3915 4054 9.787532 ATCAACATAATGCAATACTAACACAAC 57.212 29.630 0.00 0.00 0.00 3.32
3916 4055 9.786105 CATCAACATAATGCAATACTAACACAA 57.214 29.630 0.00 0.00 0.00 3.33
3943 4082 6.484364 AATGTTCCAAGAAAAAGATGGTGT 57.516 33.333 0.00 0.00 35.66 4.16
3951 4090 9.762933 CTTTTCCAGATAATGTTCCAAGAAAAA 57.237 29.630 0.00 0.00 32.24 1.94


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

AutoCloner maintained by Alex Coulton.