Multiple sequence alignment - TraesCS4B01G145400

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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 TraesCS4B01G145400 chr4B 100.000 6942 0 0 1 6942 203853832 203846891 0.000000e+00 12820.0
1 TraesCS4B01G145400 chr4D 97.406 6553 99 16 1 6511 172019992 172026515 0.000000e+00 11093.0
2 TraesCS4B01G145400 chr4D 85.981 107 9 4 6538 6639 14609594 14609699 7.360000e-20 110.0
3 TraesCS4B01G145400 chr4A 95.782 6922 178 48 1 6856 415677387 415684260 0.000000e+00 11060.0
4 TraesCS4B01G145400 chr1A 86.712 2506 305 23 3449 5943 208212431 208209943 0.000000e+00 2758.0
5 TraesCS4B01G145400 chr1A 86.931 857 108 3 4359 5213 207986861 207986007 0.000000e+00 959.0
6 TraesCS4B01G145400 chr1A 80.233 688 115 19 2071 2752 208213873 208213201 1.340000e-136 497.0
7 TraesCS4B01G145400 chr1A 84.127 441 63 7 5212 5647 207957766 207957328 2.990000e-113 420.0
8 TraesCS4B01G145400 chr1D 86.669 2513 303 27 3444 5943 153773314 153775807 0.000000e+00 2756.0
9 TraesCS4B01G145400 chr1D 79.798 693 114 22 2071 2752 153771932 153772609 1.350000e-131 481.0
10 TraesCS4B01G145400 chr1D 88.780 205 19 2 2460 2664 70540903 70540703 1.500000e-61 248.0
11 TraesCS4B01G145400 chr1B 86.027 2512 321 24 3444 5943 230946414 230948907 0.000000e+00 2667.0
12 TraesCS4B01G145400 chr1B 78.792 712 121 24 2071 2774 230945066 230945755 1.060000e-122 451.0
13 TraesCS4B01G145400 chr5D 81.109 1551 188 52 1038 2527 55546089 55544583 0.000000e+00 1144.0
14 TraesCS4B01G145400 chr5D 81.101 1090 132 52 1506 2541 55549413 55548344 0.000000e+00 804.0
15 TraesCS4B01G145400 chr5D 83.360 625 68 18 3088 3693 55543965 55543358 4.730000e-151 545.0
16 TraesCS4B01G145400 chr5D 87.560 418 38 7 3753 4169 55548071 55547667 8.150000e-129 472.0
17 TraesCS4B01G145400 chr5D 86.757 370 40 7 1038 1405 55549836 55549474 3.020000e-108 403.0
18 TraesCS4B01G145400 chr5D 89.268 205 18 2 2460 2664 388420538 388420338 3.210000e-63 254.0
19 TraesCS4B01G145400 chr5D 89.000 100 8 3 6540 6638 491004601 491004698 3.400000e-23 121.0
20 TraesCS4B01G145400 chr5D 87.000 100 9 4 6534 6632 423232379 423232475 7.360000e-20 110.0
21 TraesCS4B01G145400 chr5B 81.661 1096 123 43 1506 2541 57977874 57976797 0.000000e+00 839.0
22 TraesCS4B01G145400 chr5B 86.170 282 24 10 1126 1405 57978257 57977989 2.450000e-74 291.0
23 TraesCS4B01G145400 chr5B 86.641 262 27 6 3293 3548 57975868 57975609 4.100000e-72 283.0
24 TraesCS4B01G145400 chr5B 91.176 204 16 2 2551 2753 57976707 57976505 6.860000e-70 276.0
25 TraesCS4B01G145400 chr5B 94.737 38 2 0 3769 3806 57975603 57975566 7.520000e-05 60.2
26 TraesCS4B01G145400 chr5A 81.171 1025 123 40 1572 2541 44287779 44286770 0.000000e+00 760.0
27 TraesCS4B01G145400 chr5A 82.240 625 71 24 3088 3693 44286159 44285556 2.890000e-138 503.0
28 TraesCS4B01G145400 chr5A 84.792 480 55 8 2551 3015 44286681 44286205 3.790000e-127 466.0
29 TraesCS4B01G145400 chr3B 87.317 205 21 3 2460 2664 545855431 545855630 5.420000e-56 230.0
30 TraesCS4B01G145400 chr7B 92.174 115 7 1 2550 2664 742259029 742259141 2.000000e-35 161.0
31 TraesCS4B01G145400 chr7B 87.000 100 10 2 6540 6639 64413104 64413008 7.360000e-20 110.0
32 TraesCS4B01G145400 chr7B 89.130 92 3 4 6541 6632 115197 115281 2.650000e-19 108.0
33 TraesCS4B01G145400 chr2D 90.816 98 7 2 6544 6640 83966687 83966783 5.650000e-26 130.0
34 TraesCS4B01G145400 chr2D 89.130 92 6 3 6541 6632 376700734 376700821 2.050000e-20 111.0
35 TraesCS4B01G145400 chr7D 86.607 112 9 4 6534 6643 604292587 604292694 1.220000e-22 119.0
36 TraesCS4B01G145400 chr2A 87.755 98 8 3 6538 6632 746253393 746253489 2.050000e-20 111.0


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 TraesCS4B01G145400 chr4B 203846891 203853832 6941 True 12820.000000 12820 100.000000 1 6942 1 chr4B.!!$R1 6941
1 TraesCS4B01G145400 chr4D 172019992 172026515 6523 False 11093.000000 11093 97.406000 1 6511 1 chr4D.!!$F2 6510
2 TraesCS4B01G145400 chr4A 415677387 415684260 6873 False 11060.000000 11060 95.782000 1 6856 1 chr4A.!!$F1 6855
3 TraesCS4B01G145400 chr1A 208209943 208213873 3930 True 1627.500000 2758 83.472500 2071 5943 2 chr1A.!!$R3 3872
4 TraesCS4B01G145400 chr1A 207986007 207986861 854 True 959.000000 959 86.931000 4359 5213 1 chr1A.!!$R2 854
5 TraesCS4B01G145400 chr1D 153771932 153775807 3875 False 1618.500000 2756 83.233500 2071 5943 2 chr1D.!!$F1 3872
6 TraesCS4B01G145400 chr1B 230945066 230948907 3841 False 1559.000000 2667 82.409500 2071 5943 2 chr1B.!!$F1 3872
7 TraesCS4B01G145400 chr5D 55543358 55549836 6478 True 673.600000 1144 83.977400 1038 4169 5 chr5D.!!$R2 3131
8 TraesCS4B01G145400 chr5B 57975566 57978257 2691 True 349.840000 839 88.077000 1126 3806 5 chr5B.!!$R1 2680
9 TraesCS4B01G145400 chr5A 44285556 44287779 2223 True 576.333333 760 82.734333 1572 3693 3 chr5A.!!$R1 2121


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
962 998 2.773487 TGTTAAATCTGGTGTCGTGGG 58.227 47.619 0.00 0.00 0.00 4.61 F
1413 4157 1.005924 AGTAATTCTGCCACCCCAAGG 59.994 52.381 0.00 0.00 40.04 3.61 F
1633 4378 1.092345 GGCAGATCAGAAACGAGCCC 61.092 60.000 0.00 0.00 34.71 5.19 F
2950 5906 2.143122 TCTCCGATGTTGTTTGCTCAC 58.857 47.619 0.00 0.00 0.00 3.51 F
3135 6287 3.002038 TGGACATGCATGCAACATCTA 57.998 42.857 26.68 16.75 0.00 1.98 F
4817 8122 2.092158 TGTCTTGGTTGGTGATCCACAA 60.092 45.455 0.00 0.00 44.22 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 4864 0.605589 AGTTCCGACTCCTCTGCTTG 59.394 55.000 0.00 0.00 0.00 4.01 R
2541 5447 2.361789 TGGGTAAATAAGCGGAGTTGC 58.638 47.619 0.00 0.00 0.00 4.17 R
2960 5916 2.392821 CATGTATGACGAGAGCAGAGC 58.607 52.381 0.00 0.00 0.00 4.09 R
4817 8122 1.127567 TAACAGTGGCAGGGAGCTGT 61.128 55.000 0.00 2.18 44.79 4.40 R
5017 8322 4.710423 TCTCTATAGAATGCCTCATCGC 57.290 45.455 3.57 0.00 0.00 4.58 R
6519 9834 1.043816 TTGTTTACGGACGGGGTACA 58.956 50.000 0.00 0.00 0.00 2.90 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
58 69 3.370978 GTCGCTGATAGCTTTGCTACAAA 59.629 43.478 0.00 0.00 44.24 2.83
91 102 6.395629 CAAACTAACGACCTCTTCCAGATAA 58.604 40.000 0.00 0.00 0.00 1.75
274 285 4.578105 GGGAAATCAAGAGTCAGCTATTGG 59.422 45.833 0.00 0.00 42.43 3.16
445 456 4.871993 CGCAGCTTCTCAGTTATTGATT 57.128 40.909 0.00 0.00 34.68 2.57
446 457 5.227238 CGCAGCTTCTCAGTTATTGATTT 57.773 39.130 0.00 0.00 34.68 2.17
447 458 5.634896 CGCAGCTTCTCAGTTATTGATTTT 58.365 37.500 0.00 0.00 34.68 1.82
600 611 3.983044 AGGAAAGAGGCGAACTGTTAT 57.017 42.857 0.00 0.00 31.52 1.89
962 998 2.773487 TGTTAAATCTGGTGTCGTGGG 58.227 47.619 0.00 0.00 0.00 4.61
1034 1070 2.328819 AGAGATCCAGTGCTTCATGC 57.671 50.000 0.00 0.00 43.25 4.06
1413 4157 1.005924 AGTAATTCTGCCACCCCAAGG 59.994 52.381 0.00 0.00 40.04 3.61
1633 4378 1.092345 GGCAGATCAGAAACGAGCCC 61.092 60.000 0.00 0.00 34.71 5.19
1832 4583 7.119699 CAGTTGAATACAGTTGCTTAATCTGGA 59.880 37.037 0.00 0.00 34.02 3.86
2021 4806 8.227791 TCTTTTGCGTCTTCACTATTTCATTAC 58.772 33.333 0.00 0.00 0.00 1.89
2541 5447 6.598753 TTTACTCTCGAGAAAGTGTTTTGG 57.401 37.500 17.36 3.02 0.00 3.28
2950 5906 2.143122 TCTCCGATGTTGTTTGCTCAC 58.857 47.619 0.00 0.00 0.00 3.51
2960 5916 4.270084 TGTTGTTTGCTCACTAAGACTTCG 59.730 41.667 0.00 0.00 0.00 3.79
3135 6287 3.002038 TGGACATGCATGCAACATCTA 57.998 42.857 26.68 16.75 0.00 1.98
3309 6594 5.190677 GGGTTTTAGCTGCTAGGTTGATAA 58.809 41.667 9.62 0.00 0.00 1.75
3866 7171 5.130477 TGGAGTAGTGAAGAAACAAGAACCT 59.870 40.000 0.00 0.00 0.00 3.50
4088 7393 4.859304 AGTTTTGCAGAGCATGAATCAA 57.141 36.364 0.00 0.00 38.76 2.57
4817 8122 2.092158 TGTCTTGGTTGGTGATCCACAA 60.092 45.455 0.00 0.00 44.22 3.33
5375 8680 1.077357 TGCCTCAAACCACGGTGTT 60.077 52.632 7.45 0.00 0.00 3.32
5472 8777 7.296856 TCCATCCTCCTTCAAAAATATGCATA 58.703 34.615 9.27 9.27 0.00 3.14
6395 9708 4.456911 CCTGCATAAATTCTGTCTGTGTGT 59.543 41.667 0.00 0.00 0.00 3.72
6396 9709 5.643348 CCTGCATAAATTCTGTCTGTGTGTA 59.357 40.000 0.00 0.00 0.00 2.90
6397 9710 6.317140 CCTGCATAAATTCTGTCTGTGTGTAT 59.683 38.462 0.00 0.00 0.00 2.29
6398 9711 7.075674 TGCATAAATTCTGTCTGTGTGTATG 57.924 36.000 0.00 0.00 0.00 2.39
6444 9757 4.819105 ACAAGTCCATAATCTGGTTCGA 57.181 40.909 0.00 0.00 46.08 3.71
6445 9758 5.359194 ACAAGTCCATAATCTGGTTCGAT 57.641 39.130 0.00 0.00 46.08 3.59
6473 9786 4.424711 GGCATGGCCGACCTTGGA 62.425 66.667 8.35 0.00 39.62 3.53
6474 9787 2.124151 GCATGGCCGACCTTGGAT 60.124 61.111 5.80 0.00 40.63 3.41
6519 9834 6.016360 TGTGCTTGCACTGTCTTAATATTGTT 60.016 34.615 23.53 0.00 0.00 2.83
6520 9835 6.306356 GTGCTTGCACTGTCTTAATATTGTTG 59.694 38.462 17.36 0.00 0.00 3.33
6521 9836 6.016360 TGCTTGCACTGTCTTAATATTGTTGT 60.016 34.615 0.00 0.00 0.00 3.32
6522 9837 7.174080 TGCTTGCACTGTCTTAATATTGTTGTA 59.826 33.333 0.00 0.00 0.00 2.41
6523 9838 7.481798 GCTTGCACTGTCTTAATATTGTTGTAC 59.518 37.037 0.00 0.00 0.00 2.90
6530 9860 5.525012 GTCTTAATATTGTTGTACCCCGTCC 59.475 44.000 0.00 0.00 0.00 4.79
6542 9872 3.632643 ACCCCGTCCGTAAACAAATAT 57.367 42.857 0.00 0.00 0.00 1.28
6544 9874 3.940852 ACCCCGTCCGTAAACAAATATTC 59.059 43.478 0.00 0.00 0.00 1.75
6545 9875 3.313249 CCCCGTCCGTAAACAAATATTCC 59.687 47.826 0.00 0.00 0.00 3.01
6546 9876 3.313249 CCCGTCCGTAAACAAATATTCCC 59.687 47.826 0.00 0.00 0.00 3.97
6548 9878 4.271776 CCGTCCGTAAACAAATATTCCCTC 59.728 45.833 0.00 0.00 0.00 4.30
6549 9879 4.271776 CGTCCGTAAACAAATATTCCCTCC 59.728 45.833 0.00 0.00 0.00 4.30
6550 9880 4.271776 GTCCGTAAACAAATATTCCCTCCG 59.728 45.833 0.00 0.00 0.00 4.63
6551 9881 4.080975 TCCGTAAACAAATATTCCCTCCGT 60.081 41.667 0.00 0.00 0.00 4.69
6586 9916 4.270834 AGAGCGTTTAGATCACTACTCCA 58.729 43.478 0.00 0.00 37.82 3.86
6587 9917 4.336993 AGAGCGTTTAGATCACTACTCCAG 59.663 45.833 0.00 0.00 37.82 3.86
6588 9918 4.017808 AGCGTTTAGATCACTACTCCAGT 58.982 43.478 0.00 0.00 38.32 4.00
6600 9930 5.444744 ACTACTCCAGTGATCTGAGTAGT 57.555 43.478 25.40 25.40 46.01 2.73
6610 9940 6.909895 CAGTGATCTGAGTAGTGATCTAAACG 59.090 42.308 0.00 0.00 43.76 3.60
6633 9963 9.804758 AACGGTCTTATATTTCTTTACAGAGAG 57.195 33.333 0.00 0.00 0.00 3.20
6634 9964 8.414778 ACGGTCTTATATTTCTTTACAGAGAGG 58.585 37.037 0.00 0.00 0.00 3.69
6635 9965 7.868415 CGGTCTTATATTTCTTTACAGAGAGGG 59.132 40.741 0.00 0.00 0.00 4.30
6636 9966 8.706521 GGTCTTATATTTCTTTACAGAGAGGGT 58.293 37.037 0.00 0.00 0.00 4.34
6713 10046 4.312443 AGTACCAGTGTGTTTATCAACGG 58.688 43.478 0.00 0.00 35.40 4.44
6740 10073 1.967779 TCACAAGTGTACCTAGCTGCA 59.032 47.619 1.02 0.00 0.00 4.41
6745 10078 0.460987 GTGTACCTAGCTGCAGGCAG 60.461 60.000 17.12 16.68 46.15 4.85
6746 10079 1.144936 GTACCTAGCTGCAGGCAGG 59.855 63.158 21.63 16.97 43.77 4.85
6747 10080 1.001631 TACCTAGCTGCAGGCAGGA 59.998 57.895 21.63 5.64 43.77 3.86
6748 10081 1.045350 TACCTAGCTGCAGGCAGGAG 61.045 60.000 21.63 6.77 43.77 3.69
6749 10082 2.062777 CCTAGCTGCAGGCAGGAGA 61.063 63.158 21.63 0.00 43.77 3.71
6750 10083 1.442567 CTAGCTGCAGGCAGGAGAG 59.557 63.158 21.63 0.00 43.77 3.20
6751 10084 1.305633 TAGCTGCAGGCAGGAGAGT 60.306 57.895 21.63 0.00 43.77 3.24
6752 10085 1.326213 TAGCTGCAGGCAGGAGAGTC 61.326 60.000 21.63 4.98 43.77 3.36
6753 10086 2.583520 CTGCAGGCAGGAGAGTCC 59.416 66.667 13.39 0.00 38.04 3.85
6754 10087 3.368190 CTGCAGGCAGGAGAGTCCG 62.368 68.421 13.39 0.00 42.75 4.79
6755 10088 3.386237 GCAGGCAGGAGAGTCCGT 61.386 66.667 0.00 0.00 42.75 4.69
6756 10089 2.888863 CAGGCAGGAGAGTCCGTC 59.111 66.667 0.00 0.00 42.75 4.79
6784 10117 1.001503 CCTCTGGTGGCTCTCCTCT 59.998 63.158 0.00 0.00 0.00 3.69
6786 10119 1.958902 CTCTGGTGGCTCTCCTCTGC 61.959 65.000 0.00 0.00 0.00 4.26
6793 10126 4.200283 CTCTCCTCTGCCGGCGAC 62.200 72.222 23.90 0.00 0.00 5.19
6808 10141 2.987547 GACCCTGGTCGTCGGTGA 60.988 66.667 0.00 0.00 35.30 4.02
6809 10142 2.283676 ACCCTGGTCGTCGGTGAT 60.284 61.111 0.00 0.00 0.00 3.06
6814 10147 1.303806 TGGTCGTCGGTGATGAGGA 60.304 57.895 0.00 0.00 0.00 3.71
6821 10154 1.141881 CGGTGATGAGGAGGGTTCG 59.858 63.158 0.00 0.00 0.00 3.95
6822 10155 1.153349 GGTGATGAGGAGGGTTCGC 60.153 63.158 0.00 0.00 0.00 4.70
6825 10158 3.447025 GATGAGGAGGGTTCGCCGG 62.447 68.421 0.00 0.00 37.94 6.13
6831 10164 1.186267 GGAGGGTTCGCCGGATCTAT 61.186 60.000 5.05 0.00 38.45 1.98
6835 10168 0.731855 GGTTCGCCGGATCTATACGC 60.732 60.000 5.05 0.00 31.29 4.42
6856 10189 3.674138 GCGTGGATCGTGTAGTTTTAGGA 60.674 47.826 0.00 0.00 42.13 2.94
6857 10190 4.679662 CGTGGATCGTGTAGTTTTAGGAT 58.320 43.478 0.00 0.00 34.52 3.24
6858 10191 5.107133 CGTGGATCGTGTAGTTTTAGGATT 58.893 41.667 0.00 0.00 34.52 3.01
6859 10192 5.005394 CGTGGATCGTGTAGTTTTAGGATTG 59.995 44.000 0.00 0.00 34.52 2.67
6860 10193 5.873164 GTGGATCGTGTAGTTTTAGGATTGT 59.127 40.000 0.00 0.00 0.00 2.71
6861 10194 6.035758 GTGGATCGTGTAGTTTTAGGATTGTC 59.964 42.308 0.00 0.00 0.00 3.18
6862 10195 6.070995 TGGATCGTGTAGTTTTAGGATTGTCT 60.071 38.462 0.00 0.00 0.00 3.41
6863 10196 6.817140 GGATCGTGTAGTTTTAGGATTGTCTT 59.183 38.462 0.00 0.00 0.00 3.01
6864 10197 7.201530 GGATCGTGTAGTTTTAGGATTGTCTTG 60.202 40.741 0.00 0.00 0.00 3.02
6865 10198 5.929992 TCGTGTAGTTTTAGGATTGTCTTGG 59.070 40.000 0.00 0.00 0.00 3.61
6866 10199 5.390567 CGTGTAGTTTTAGGATTGTCTTGGC 60.391 44.000 0.00 0.00 0.00 4.52
6867 10200 5.705905 GTGTAGTTTTAGGATTGTCTTGGCT 59.294 40.000 0.00 0.00 0.00 4.75
6868 10201 6.206829 GTGTAGTTTTAGGATTGTCTTGGCTT 59.793 38.462 0.00 0.00 0.00 4.35
6869 10202 5.966742 AGTTTTAGGATTGTCTTGGCTTC 57.033 39.130 0.00 0.00 0.00 3.86
6870 10203 5.385198 AGTTTTAGGATTGTCTTGGCTTCA 58.615 37.500 0.00 0.00 0.00 3.02
6871 10204 5.833131 AGTTTTAGGATTGTCTTGGCTTCAA 59.167 36.000 0.00 0.00 0.00 2.69
6872 10205 6.323739 AGTTTTAGGATTGTCTTGGCTTCAAA 59.676 34.615 0.00 0.00 0.00 2.69
6873 10206 6.723298 TTTAGGATTGTCTTGGCTTCAAAA 57.277 33.333 0.00 0.00 0.00 2.44
6874 10207 4.861102 AGGATTGTCTTGGCTTCAAAAG 57.139 40.909 0.00 0.00 0.00 2.27
6875 10208 4.218312 AGGATTGTCTTGGCTTCAAAAGT 58.782 39.130 0.00 0.00 0.00 2.66
6876 10209 4.038402 AGGATTGTCTTGGCTTCAAAAGTG 59.962 41.667 0.00 0.00 0.00 3.16
6877 10210 3.799281 TTGTCTTGGCTTCAAAAGTGG 57.201 42.857 0.00 0.00 0.00 4.00
6878 10211 1.408702 TGTCTTGGCTTCAAAAGTGGC 59.591 47.619 0.00 0.00 0.00 5.01
6879 10212 0.667993 TCTTGGCTTCAAAAGTGGCG 59.332 50.000 0.00 0.00 0.00 5.69
6880 10213 0.667993 CTTGGCTTCAAAAGTGGCGA 59.332 50.000 0.00 0.00 0.00 5.54
6881 10214 1.270550 CTTGGCTTCAAAAGTGGCGAT 59.729 47.619 0.00 0.00 0.00 4.58
6882 10215 0.881118 TGGCTTCAAAAGTGGCGATC 59.119 50.000 0.00 0.00 0.00 3.69
6883 10216 0.179189 GGCTTCAAAAGTGGCGATCG 60.179 55.000 11.69 11.69 0.00 3.69
6884 10217 0.794605 GCTTCAAAAGTGGCGATCGC 60.795 55.000 31.52 31.52 41.06 4.58
6885 10218 0.519175 CTTCAAAAGTGGCGATCGCG 60.519 55.000 31.76 17.24 43.06 5.87
6895 10228 3.608041 CGATCGCGCCGTTGAATA 58.392 55.556 0.26 0.00 0.00 1.75
6896 10229 1.198397 CGATCGCGCCGTTGAATAC 59.802 57.895 0.26 0.00 0.00 1.89
6897 10230 1.476235 CGATCGCGCCGTTGAATACA 61.476 55.000 0.26 0.00 0.00 2.29
6898 10231 0.229753 GATCGCGCCGTTGAATACAG 59.770 55.000 0.00 0.00 0.00 2.74
6899 10232 0.179121 ATCGCGCCGTTGAATACAGA 60.179 50.000 0.00 0.00 0.00 3.41
6900 10233 0.388778 TCGCGCCGTTGAATACAGAA 60.389 50.000 0.00 0.00 0.00 3.02
6901 10234 0.025001 CGCGCCGTTGAATACAGAAG 59.975 55.000 0.00 0.00 0.00 2.85
6902 10235 1.076332 GCGCCGTTGAATACAGAAGT 58.924 50.000 0.00 0.00 0.00 3.01
6903 10236 1.463444 GCGCCGTTGAATACAGAAGTT 59.537 47.619 0.00 0.00 0.00 2.66
6904 10237 2.095919 GCGCCGTTGAATACAGAAGTTT 60.096 45.455 0.00 0.00 0.00 2.66
6905 10238 3.732943 CGCCGTTGAATACAGAAGTTTC 58.267 45.455 0.00 0.00 0.00 2.78
6906 10239 3.185594 CGCCGTTGAATACAGAAGTTTCA 59.814 43.478 0.00 0.00 0.00 2.69
6907 10240 4.666655 CGCCGTTGAATACAGAAGTTTCAG 60.667 45.833 0.00 0.00 31.40 3.02
6908 10241 4.451096 GCCGTTGAATACAGAAGTTTCAGA 59.549 41.667 0.00 0.00 31.40 3.27
6909 10242 5.122396 GCCGTTGAATACAGAAGTTTCAGAT 59.878 40.000 0.00 0.00 31.40 2.90
6910 10243 6.673316 GCCGTTGAATACAGAAGTTTCAGATC 60.673 42.308 0.00 0.00 31.40 2.75
6911 10244 6.591834 CCGTTGAATACAGAAGTTTCAGATCT 59.408 38.462 0.00 0.00 31.40 2.75
6912 10245 7.201478 CCGTTGAATACAGAAGTTTCAGATCTC 60.201 40.741 0.00 0.00 31.40 2.75
6913 10246 7.543868 CGTTGAATACAGAAGTTTCAGATCTCT 59.456 37.037 0.00 0.00 31.40 3.10
6914 10247 9.213799 GTTGAATACAGAAGTTTCAGATCTCTT 57.786 33.333 0.00 0.00 31.40 2.85
6915 10248 8.994429 TGAATACAGAAGTTTCAGATCTCTTC 57.006 34.615 11.99 11.99 37.24 2.87
6916 10249 8.037758 TGAATACAGAAGTTTCAGATCTCTTCC 58.962 37.037 14.96 3.71 37.56 3.46
6917 10250 5.159273 ACAGAAGTTTCAGATCTCTTCCC 57.841 43.478 14.96 0.00 37.56 3.97
6918 10251 4.180057 CAGAAGTTTCAGATCTCTTCCCG 58.820 47.826 14.96 6.46 37.56 5.14
6919 10252 4.081972 CAGAAGTTTCAGATCTCTTCCCGA 60.082 45.833 14.96 0.00 37.56 5.14
6920 10253 3.878160 AGTTTCAGATCTCTTCCCGAC 57.122 47.619 0.00 0.00 0.00 4.79
6921 10254 2.164624 AGTTTCAGATCTCTTCCCGACG 59.835 50.000 0.00 0.00 0.00 5.12
6922 10255 2.124277 TTCAGATCTCTTCCCGACGA 57.876 50.000 0.00 0.00 0.00 4.20
6923 10256 1.669604 TCAGATCTCTTCCCGACGAG 58.330 55.000 0.00 0.00 0.00 4.18
6924 10257 0.665835 CAGATCTCTTCCCGACGAGG 59.334 60.000 0.00 0.00 40.63 4.63
6925 10258 1.104577 AGATCTCTTCCCGACGAGGC 61.105 60.000 0.00 0.00 39.21 4.70
6926 10259 1.379977 ATCTCTTCCCGACGAGGCA 60.380 57.895 0.00 0.00 39.21 4.75
6927 10260 0.970937 ATCTCTTCCCGACGAGGCAA 60.971 55.000 0.00 0.00 39.21 4.52
6928 10261 0.970937 TCTCTTCCCGACGAGGCAAT 60.971 55.000 0.00 0.00 39.21 3.56
6929 10262 0.108138 CTCTTCCCGACGAGGCAATT 60.108 55.000 0.00 0.00 39.21 2.32
6930 10263 0.391130 TCTTCCCGACGAGGCAATTG 60.391 55.000 0.00 0.00 39.21 2.32
6931 10264 1.369091 CTTCCCGACGAGGCAATTGG 61.369 60.000 7.72 0.00 39.21 3.16
6932 10265 2.046314 CCCGACGAGGCAATTGGT 60.046 61.111 7.72 0.00 39.21 3.67
6933 10266 1.674322 CCCGACGAGGCAATTGGTT 60.674 57.895 7.72 0.00 39.21 3.67
6934 10267 1.241315 CCCGACGAGGCAATTGGTTT 61.241 55.000 7.72 0.00 39.21 3.27
6935 10268 0.596082 CCGACGAGGCAATTGGTTTT 59.404 50.000 7.72 0.00 0.00 2.43
6936 10269 1.807742 CCGACGAGGCAATTGGTTTTA 59.192 47.619 7.72 0.00 0.00 1.52
6937 10270 2.422127 CCGACGAGGCAATTGGTTTTAT 59.578 45.455 7.72 0.00 0.00 1.40
6938 10271 3.425404 CGACGAGGCAATTGGTTTTATG 58.575 45.455 7.72 0.00 0.00 1.90
6939 10272 3.126171 CGACGAGGCAATTGGTTTTATGA 59.874 43.478 7.72 0.00 0.00 2.15
6940 10273 4.201910 CGACGAGGCAATTGGTTTTATGAT 60.202 41.667 7.72 0.00 0.00 2.45
6941 10274 5.650543 GACGAGGCAATTGGTTTTATGATT 58.349 37.500 7.72 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 69 5.419471 AGAGGTCGTTAGTTTGCTATCTTCT 59.581 40.000 0.00 0.00 0.00 2.85
91 102 2.695147 GCATGTGCTAAGGGCCTTTAAT 59.305 45.455 26.29 8.42 40.92 1.40
274 285 0.034670 AGGAAGCTGAATGTGCTCCC 60.035 55.000 0.00 0.00 40.22 4.30
397 408 9.014297 CAAATTTTCCCTTATATAGCCTACTGG 57.986 37.037 0.00 0.00 0.00 4.00
600 611 6.122277 AGAGACACCAAAGACAAATCTTCAA 58.878 36.000 0.00 0.00 44.82 2.69
775 786 3.096489 TGAATTGCTTGTGAAACCTGC 57.904 42.857 0.00 0.00 34.36 4.85
962 998 3.002348 GTCAGCAGCAATCCCGTATTTAC 59.998 47.826 0.00 0.00 0.00 2.01
1034 1070 1.340114 GGTTTTCTAGCTCTGTGGGGG 60.340 57.143 0.00 0.00 0.00 5.40
1413 4157 5.128919 ACACTGGAATCTGCATTTCTATCC 58.871 41.667 8.83 2.85 0.00 2.59
1504 4249 2.890945 GCCTTGGTACAGATTGTTGGTT 59.109 45.455 0.00 0.00 42.39 3.67
1832 4583 9.961265 CATTCTCATCACACAGCATATAATTTT 57.039 29.630 0.00 0.00 0.00 1.82
2021 4806 5.615544 CGTGCAAAAGTAGTCTTTCCATCAG 60.616 44.000 0.00 0.00 42.26 2.90
2078 4864 0.605589 AGTTCCGACTCCTCTGCTTG 59.394 55.000 0.00 0.00 0.00 4.01
2541 5447 2.361789 TGGGTAAATAAGCGGAGTTGC 58.638 47.619 0.00 0.00 0.00 4.17
2950 5906 2.538737 CGAGAGCAGAGCGAAGTCTTAG 60.539 54.545 0.00 0.00 0.00 2.18
2960 5916 2.392821 CATGTATGACGAGAGCAGAGC 58.607 52.381 0.00 0.00 0.00 4.09
3866 7171 2.950781 TGTACCAATGTGAAAGGCCAA 58.049 42.857 5.01 0.00 0.00 4.52
4088 7393 1.947456 GGAAGAGTGCGAAACAGGTTT 59.053 47.619 0.00 0.00 35.14 3.27
4817 8122 1.127567 TAACAGTGGCAGGGAGCTGT 61.128 55.000 0.00 2.18 44.79 4.40
5017 8322 4.710423 TCTCTATAGAATGCCTCATCGC 57.290 45.455 3.57 0.00 0.00 4.58
5375 8680 3.127895 GGCGTATATCTGCAACAAAACCA 59.872 43.478 0.00 0.00 0.00 3.67
5472 8777 7.568199 AAACAACACTAGTACATTGCTCTTT 57.432 32.000 11.65 5.05 0.00 2.52
6138 9446 6.767524 TGTTCAAATATGGTCCATGTAACC 57.232 37.500 15.10 7.42 37.31 2.85
6396 9709 5.929697 CATGCGGATTTCTGTATGTACAT 57.070 39.130 13.93 13.93 39.50 2.29
6467 9780 1.519455 GACCGACGCAGATCCAAGG 60.519 63.158 0.00 0.00 0.00 3.61
6468 9781 1.874019 CGACCGACGCAGATCCAAG 60.874 63.158 0.00 0.00 34.51 3.61
6469 9782 1.663379 ATCGACCGACGCAGATCCAA 61.663 55.000 0.00 0.00 42.26 3.53
6471 9784 1.658717 CATCGACCGACGCAGATCC 60.659 63.158 0.00 0.00 42.26 3.36
6473 9786 2.278857 GCATCGACCGACGCAGAT 60.279 61.111 5.57 0.00 42.26 2.90
6474 9787 2.867333 GAAGCATCGACCGACGCAGA 62.867 60.000 12.85 0.00 42.26 4.26
6519 9834 1.043816 TTGTTTACGGACGGGGTACA 58.956 50.000 0.00 0.00 0.00 2.90
6520 9835 2.162319 TTTGTTTACGGACGGGGTAC 57.838 50.000 0.00 0.00 0.00 3.34
6521 9836 4.751767 ATATTTGTTTACGGACGGGGTA 57.248 40.909 0.00 0.00 0.00 3.69
6522 9837 3.632643 ATATTTGTTTACGGACGGGGT 57.367 42.857 0.00 0.00 0.00 4.95
6523 9838 3.313249 GGAATATTTGTTTACGGACGGGG 59.687 47.826 0.00 0.00 0.00 5.73
6530 9860 8.592105 TTATACGGAGGGAATATTTGTTTACG 57.408 34.615 0.00 0.00 0.00 3.18
6542 9872 8.529476 GCTCTTATATTTCTTATACGGAGGGAA 58.471 37.037 0.00 0.00 30.88 3.97
6544 9874 6.973474 CGCTCTTATATTTCTTATACGGAGGG 59.027 42.308 0.00 0.00 34.04 4.30
6545 9875 7.536855 ACGCTCTTATATTTCTTATACGGAGG 58.463 38.462 0.00 0.00 30.88 4.30
6546 9876 8.967552 AACGCTCTTATATTTCTTATACGGAG 57.032 34.615 0.00 0.00 32.05 4.63
6579 9909 5.432645 TCACTACTCAGATCACTGGAGTAG 58.567 45.833 25.83 25.83 45.95 2.57
6582 9912 5.132502 AGATCACTACTCAGATCACTGGAG 58.867 45.833 0.00 0.00 42.36 3.86
6586 9916 6.038825 CCGTTTAGATCACTACTCAGATCACT 59.961 42.308 0.00 0.00 42.36 3.41
6587 9917 6.183360 ACCGTTTAGATCACTACTCAGATCAC 60.183 42.308 0.00 0.00 42.36 3.06
6588 9918 5.886474 ACCGTTTAGATCACTACTCAGATCA 59.114 40.000 0.00 0.00 42.36 2.92
6589 9919 6.261381 AGACCGTTTAGATCACTACTCAGATC 59.739 42.308 0.00 0.00 40.68 2.75
6590 9920 6.123651 AGACCGTTTAGATCACTACTCAGAT 58.876 40.000 0.00 0.00 0.00 2.90
6592 9922 5.821516 AGACCGTTTAGATCACTACTCAG 57.178 43.478 0.00 0.00 0.00 3.35
6593 9923 7.876936 ATAAGACCGTTTAGATCACTACTCA 57.123 36.000 0.00 0.00 0.00 3.41
6610 9940 8.706521 ACCCTCTCTGTAAAGAAATATAAGACC 58.293 37.037 0.00 0.00 0.00 3.85
6713 10046 5.070580 AGCTAGGTACACTTGTGATTATCCC 59.929 44.000 7.83 0.00 0.00 3.85
6740 10073 2.363147 GGACGGACTCTCCTGCCT 60.363 66.667 0.00 0.00 33.30 4.75
6745 10078 4.500116 GCTGCGGACGGACTCTCC 62.500 72.222 0.00 0.00 0.00 3.71
6746 10079 4.500116 GGCTGCGGACGGACTCTC 62.500 72.222 0.00 0.00 0.00 3.20
6748 10081 3.991536 GAAGGCTGCGGACGGACTC 62.992 68.421 0.00 0.00 40.88 3.36
6749 10082 4.070552 GAAGGCTGCGGACGGACT 62.071 66.667 0.00 0.00 45.14 3.85
6752 10085 4.821589 GAGGAAGGCTGCGGACGG 62.822 72.222 0.00 0.00 0.00 4.79
6753 10086 3.764466 AGAGGAAGGCTGCGGACG 61.764 66.667 0.00 0.00 0.00 4.79
6754 10087 2.125350 CAGAGGAAGGCTGCGGAC 60.125 66.667 0.00 0.00 0.00 4.79
6755 10088 3.393970 CCAGAGGAAGGCTGCGGA 61.394 66.667 0.00 0.00 32.06 5.54
6756 10089 3.710722 ACCAGAGGAAGGCTGCGG 61.711 66.667 0.00 0.00 32.06 5.69
6793 10126 2.184322 CATCACCGACGACCAGGG 59.816 66.667 0.00 0.00 0.00 4.45
6800 10133 1.605058 AACCCTCCTCATCACCGACG 61.605 60.000 0.00 0.00 0.00 5.12
6804 10137 1.153349 GCGAACCCTCCTCATCACC 60.153 63.158 0.00 0.00 0.00 4.02
6808 10141 3.470888 CCGGCGAACCCTCCTCAT 61.471 66.667 9.30 0.00 0.00 2.90
6809 10142 3.976490 ATCCGGCGAACCCTCCTCA 62.976 63.158 9.30 0.00 0.00 3.86
6814 10147 1.254954 GTATAGATCCGGCGAACCCT 58.745 55.000 9.30 2.18 0.00 4.34
6821 10154 1.443872 CCACGCGTATAGATCCGGC 60.444 63.158 13.44 0.00 0.00 6.13
6822 10155 0.809385 ATCCACGCGTATAGATCCGG 59.191 55.000 13.44 6.53 0.00 5.14
6825 10158 2.095869 ACACGATCCACGCGTATAGATC 60.096 50.000 24.96 24.96 46.94 2.75
6831 10164 0.804364 AACTACACGATCCACGCGTA 59.196 50.000 13.44 0.00 46.94 4.42
6856 10189 3.493176 GCCACTTTTGAAGCCAAGACAAT 60.493 43.478 0.00 0.00 33.23 2.71
6857 10190 2.159114 GCCACTTTTGAAGCCAAGACAA 60.159 45.455 0.00 0.00 33.23 3.18
6858 10191 1.408702 GCCACTTTTGAAGCCAAGACA 59.591 47.619 0.00 0.00 33.23 3.41
6859 10192 1.600413 CGCCACTTTTGAAGCCAAGAC 60.600 52.381 0.00 0.00 33.23 3.01
6860 10193 0.667993 CGCCACTTTTGAAGCCAAGA 59.332 50.000 0.00 0.00 33.23 3.02
6861 10194 0.667993 TCGCCACTTTTGAAGCCAAG 59.332 50.000 0.00 0.00 33.23 3.61
6862 10195 1.269448 GATCGCCACTTTTGAAGCCAA 59.731 47.619 0.00 0.00 0.00 4.52
6863 10196 0.881118 GATCGCCACTTTTGAAGCCA 59.119 50.000 0.00 0.00 0.00 4.75
6864 10197 0.179189 CGATCGCCACTTTTGAAGCC 60.179 55.000 0.26 0.00 0.00 4.35
6865 10198 0.794605 GCGATCGCCACTTTTGAAGC 60.795 55.000 29.48 0.00 34.56 3.86
6866 10199 0.519175 CGCGATCGCCACTTTTGAAG 60.519 55.000 32.63 11.93 37.98 3.02
6867 10200 1.495509 CGCGATCGCCACTTTTGAA 59.504 52.632 32.63 0.00 37.98 2.69
6868 10201 3.164576 CGCGATCGCCACTTTTGA 58.835 55.556 32.63 0.00 37.98 2.69
6878 10211 1.198397 GTATTCAACGGCGCGATCG 59.802 57.895 12.10 15.98 39.07 3.69
6879 10212 0.229753 CTGTATTCAACGGCGCGATC 59.770 55.000 12.10 0.00 0.00 3.69
6880 10213 0.179121 TCTGTATTCAACGGCGCGAT 60.179 50.000 12.10 0.00 34.14 4.58
6881 10214 0.388778 TTCTGTATTCAACGGCGCGA 60.389 50.000 12.10 0.00 34.14 5.87
6882 10215 0.025001 CTTCTGTATTCAACGGCGCG 59.975 55.000 6.90 0.00 34.14 6.86
6883 10216 1.076332 ACTTCTGTATTCAACGGCGC 58.924 50.000 6.90 0.00 34.14 6.53
6884 10217 3.185594 TGAAACTTCTGTATTCAACGGCG 59.814 43.478 4.80 4.80 34.14 6.46
6885 10218 4.451096 TCTGAAACTTCTGTATTCAACGGC 59.549 41.667 0.00 0.00 33.08 5.68
6886 10219 6.591834 AGATCTGAAACTTCTGTATTCAACGG 59.408 38.462 0.00 0.00 33.08 4.44
6887 10220 7.543868 AGAGATCTGAAACTTCTGTATTCAACG 59.456 37.037 0.00 0.00 33.08 4.10
6888 10221 8.770438 AGAGATCTGAAACTTCTGTATTCAAC 57.230 34.615 0.00 0.00 33.08 3.18
6889 10222 9.429359 GAAGAGATCTGAAACTTCTGTATTCAA 57.571 33.333 0.00 0.00 36.72 2.69
6890 10223 8.037758 GGAAGAGATCTGAAACTTCTGTATTCA 58.962 37.037 16.98 0.00 38.78 2.57
6891 10224 7.494298 GGGAAGAGATCTGAAACTTCTGTATTC 59.506 40.741 16.98 4.43 38.78 1.75
6892 10225 7.334858 GGGAAGAGATCTGAAACTTCTGTATT 58.665 38.462 16.98 0.00 38.78 1.89
6893 10226 6.406400 CGGGAAGAGATCTGAAACTTCTGTAT 60.406 42.308 16.98 0.00 38.78 2.29
6894 10227 5.105716 CGGGAAGAGATCTGAAACTTCTGTA 60.106 44.000 16.98 0.00 38.78 2.74
6895 10228 4.322349 CGGGAAGAGATCTGAAACTTCTGT 60.322 45.833 16.98 0.00 38.78 3.41
6896 10229 4.081972 TCGGGAAGAGATCTGAAACTTCTG 60.082 45.833 16.98 12.00 38.78 3.02
6897 10230 4.081917 GTCGGGAAGAGATCTGAAACTTCT 60.082 45.833 16.98 0.00 38.78 2.85
6898 10231 4.177783 GTCGGGAAGAGATCTGAAACTTC 58.822 47.826 0.00 6.65 38.26 3.01
6899 10232 3.367498 CGTCGGGAAGAGATCTGAAACTT 60.367 47.826 0.00 0.00 0.00 2.66
6900 10233 2.164624 CGTCGGGAAGAGATCTGAAACT 59.835 50.000 0.00 0.00 0.00 2.66
6901 10234 2.163815 TCGTCGGGAAGAGATCTGAAAC 59.836 50.000 0.00 0.00 0.00 2.78
6902 10235 2.423892 CTCGTCGGGAAGAGATCTGAAA 59.576 50.000 0.00 0.00 38.88 2.69
6903 10236 2.017782 CTCGTCGGGAAGAGATCTGAA 58.982 52.381 0.00 0.00 38.88 3.02
6904 10237 1.669604 CTCGTCGGGAAGAGATCTGA 58.330 55.000 0.00 0.00 38.88 3.27
6905 10238 0.665835 CCTCGTCGGGAAGAGATCTG 59.334 60.000 12.30 0.00 38.88 2.90
6906 10239 1.104577 GCCTCGTCGGGAAGAGATCT 61.105 60.000 12.30 0.00 38.88 2.75
6907 10240 1.360911 GCCTCGTCGGGAAGAGATC 59.639 63.158 12.30 1.85 38.88 2.75
6908 10241 0.970937 TTGCCTCGTCGGGAAGAGAT 60.971 55.000 12.30 0.00 38.30 2.75
6909 10242 0.970937 ATTGCCTCGTCGGGAAGAGA 60.971 55.000 12.30 0.00 46.96 3.10
6910 10243 0.108138 AATTGCCTCGTCGGGAAGAG 60.108 55.000 0.00 4.87 46.96 2.85
6911 10244 0.391130 CAATTGCCTCGTCGGGAAGA 60.391 55.000 0.00 0.00 46.96 2.87
6912 10245 1.369091 CCAATTGCCTCGTCGGGAAG 61.369 60.000 0.00 0.00 46.96 3.46
6914 10247 2.119484 AACCAATTGCCTCGTCGGGA 62.119 55.000 0.00 0.00 0.00 5.14
6915 10248 1.241315 AAACCAATTGCCTCGTCGGG 61.241 55.000 0.00 0.00 0.00 5.14
6916 10249 0.596082 AAAACCAATTGCCTCGTCGG 59.404 50.000 0.00 0.00 0.00 4.79
6917 10250 3.126171 TCATAAAACCAATTGCCTCGTCG 59.874 43.478 0.00 0.00 0.00 5.12
6918 10251 4.695217 TCATAAAACCAATTGCCTCGTC 57.305 40.909 0.00 0.00 0.00 4.20
6919 10252 5.659440 AATCATAAAACCAATTGCCTCGT 57.341 34.783 0.00 0.00 0.00 4.18



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

AutoCloner maintained by Alex Coulton.