Multiple sequence alignment - TraesCS5D01G274500

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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 TraesCS5D01G274500 chr5D 100.000 3555 0 0 1 3555 377489894 377486340 0.000000e+00 6565
1 TraesCS5D01G274500 chr5A 90.583 2846 155 62 753 3555 478020021 478017246 0.000000e+00 3666
2 TraesCS5D01G274500 chr5B 95.215 2299 77 17 764 3044 450775355 450773072 0.000000e+00 3605
3 TraesCS5D01G274500 chr5B 85.178 533 35 27 3052 3555 450772951 450772434 1.140000e-139 507
4 TraesCS5D01G274500 chr4D 95.402 609 26 1 142 750 483619172 483619778 0.000000e+00 968
5 TraesCS5D01G274500 chr2D 95.058 607 26 3 144 750 546412159 546411557 0.000000e+00 952
6 TraesCS5D01G274500 chr3A 93.904 607 33 3 144 750 703806885 703807487 0.000000e+00 913
7 TraesCS5D01G274500 chr3A 92.633 638 36 7 114 750 100863661 100864288 0.000000e+00 907
8 TraesCS5D01G274500 chr3A 92.163 638 39 6 114 750 127190846 127190219 0.000000e+00 891
9 TraesCS5D01G274500 chr1B 91.862 639 40 8 114 750 651903072 651902444 0.000000e+00 881
10 TraesCS5D01G274500 chr2B 91.706 639 41 8 114 750 669239049 669239677 0.000000e+00 876
11 TraesCS5D01G274500 chr6B 91.460 644 42 8 109 750 682643302 682643934 0.000000e+00 872
12 TraesCS5D01G274500 chr4B 91.536 638 40 8 114 750 573397859 573398483 0.000000e+00 867
13 TraesCS5D01G274500 chr7B 77.047 684 127 24 1198 1869 185390962 185390297 2.020000e-97 366
14 TraesCS5D01G274500 chr7A 76.075 744 139 29 1216 1947 227958978 227958262 5.650000e-93 351


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 TraesCS5D01G274500 chr5D 377486340 377489894 3554 True 6565 6565 100.0000 1 3555 1 chr5D.!!$R1 3554
1 TraesCS5D01G274500 chr5A 478017246 478020021 2775 True 3666 3666 90.5830 753 3555 1 chr5A.!!$R1 2802
2 TraesCS5D01G274500 chr5B 450772434 450775355 2921 True 2056 3605 90.1965 764 3555 2 chr5B.!!$R1 2791
3 TraesCS5D01G274500 chr4D 483619172 483619778 606 False 968 968 95.4020 142 750 1 chr4D.!!$F1 608
4 TraesCS5D01G274500 chr2D 546411557 546412159 602 True 952 952 95.0580 144 750 1 chr2D.!!$R1 606
5 TraesCS5D01G274500 chr3A 703806885 703807487 602 False 913 913 93.9040 144 750 1 chr3A.!!$F2 606
6 TraesCS5D01G274500 chr3A 100863661 100864288 627 False 907 907 92.6330 114 750 1 chr3A.!!$F1 636
7 TraesCS5D01G274500 chr3A 127190219 127190846 627 True 891 891 92.1630 114 750 1 chr3A.!!$R1 636
8 TraesCS5D01G274500 chr1B 651902444 651903072 628 True 881 881 91.8620 114 750 1 chr1B.!!$R1 636
9 TraesCS5D01G274500 chr2B 669239049 669239677 628 False 876 876 91.7060 114 750 1 chr2B.!!$F1 636
10 TraesCS5D01G274500 chr6B 682643302 682643934 632 False 872 872 91.4600 109 750 1 chr6B.!!$F1 641
11 TraesCS5D01G274500 chr4B 573397859 573398483 624 False 867 867 91.5360 114 750 1 chr4B.!!$F1 636
12 TraesCS5D01G274500 chr7B 185390297 185390962 665 True 366 366 77.0470 1198 1869 1 chr7B.!!$R1 671
13 TraesCS5D01G274500 chr7A 227958262 227958978 716 True 351 351 76.0750 1216 1947 1 chr7A.!!$R1 731

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
136 137 0.109532 TTTGATCGAAGGGCCACACA 59.890 50.000 6.18 0.0 0.0 3.72 F
137 138 0.321564 TTGATCGAAGGGCCACACAG 60.322 55.000 6.18 0.0 0.0 3.66 F
847 855 1.069227 CGCAAAGACAAAGTACTGGCC 60.069 52.381 0.00 0.0 0.0 5.36 F
1089 1099 1.153168 CCGAAATGGCGTGATCCCT 60.153 57.895 0.00 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1233 2.616458 GGAGGCCTTCATGGTGGGT 61.616 63.158 6.77 0.0 38.35 4.51 R
1965 2001 4.314121 CCTTCTTGTCCTCTTCAGACTTG 58.686 47.826 0.00 0.0 35.21 3.16 R
2387 2425 1.264288 CGTTTGCTTCCACTCAAGGAC 59.736 52.381 0.00 0.0 37.42 3.85 R
2713 2753 3.009363 TCCATGATTCCTGCACTTTCTGA 59.991 43.478 0.00 0.0 0.00 3.27 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
40 41 8.885494 TTCATCACGATCATAATGTATCAACA 57.115 30.769 0.00 0.00 40.69 3.33
41 42 8.885494 TCATCACGATCATAATGTATCAACAA 57.115 30.769 0.00 0.00 39.58 2.83
42 43 8.981647 TCATCACGATCATAATGTATCAACAAG 58.018 33.333 0.00 0.00 39.58 3.16
43 44 8.981647 CATCACGATCATAATGTATCAACAAGA 58.018 33.333 0.00 0.00 39.58 3.02
44 45 8.940768 TCACGATCATAATGTATCAACAAGAA 57.059 30.769 0.00 0.00 39.58 2.52
45 46 8.817100 TCACGATCATAATGTATCAACAAGAAC 58.183 33.333 0.00 0.00 39.58 3.01
46 47 8.064222 CACGATCATAATGTATCAACAAGAACC 58.936 37.037 0.00 0.00 39.58 3.62
47 48 7.042725 ACGATCATAATGTATCAACAAGAACCG 60.043 37.037 0.00 0.00 39.58 4.44
48 49 7.042725 CGATCATAATGTATCAACAAGAACCGT 60.043 37.037 0.00 0.00 39.58 4.83
49 50 7.915293 TCATAATGTATCAACAAGAACCGTT 57.085 32.000 0.00 0.00 39.58 4.44
50 51 8.330466 TCATAATGTATCAACAAGAACCGTTT 57.670 30.769 0.00 0.00 39.58 3.60
51 52 8.233868 TCATAATGTATCAACAAGAACCGTTTG 58.766 33.333 0.00 0.00 39.58 2.93
52 53 4.822036 TGTATCAACAAGAACCGTTTGG 57.178 40.909 0.00 0.00 35.05 3.28
53 54 3.566322 TGTATCAACAAGAACCGTTTGGG 59.434 43.478 0.00 0.00 33.72 4.12
54 55 4.928167 TGTATCAACAAGAACCGTTTGGGT 60.928 41.667 0.00 0.00 41.61 4.51
56 57 8.334966 TGTATCAACAAGAACCGTTTGGGTTG 62.335 42.308 2.33 12.81 45.65 3.77
62 63 3.650369 CCGTTTGGGTTGGTCGAG 58.350 61.111 0.00 0.00 0.00 4.04
63 64 2.613506 CCGTTTGGGTTGGTCGAGC 61.614 63.158 7.89 7.89 0.00 5.03
64 65 1.597027 CGTTTGGGTTGGTCGAGCT 60.597 57.895 16.64 0.00 0.00 4.09
65 66 0.320073 CGTTTGGGTTGGTCGAGCTA 60.320 55.000 16.64 5.25 0.00 3.32
66 67 1.439679 GTTTGGGTTGGTCGAGCTAG 58.560 55.000 16.64 0.00 0.00 3.42
67 68 1.053424 TTTGGGTTGGTCGAGCTAGT 58.947 50.000 16.64 0.00 0.00 2.57
68 69 0.320374 TTGGGTTGGTCGAGCTAGTG 59.680 55.000 16.64 0.00 0.00 2.74
69 70 0.541063 TGGGTTGGTCGAGCTAGTGA 60.541 55.000 16.64 0.00 0.00 3.41
70 71 0.606604 GGGTTGGTCGAGCTAGTGAA 59.393 55.000 16.64 0.00 0.00 3.18
71 72 1.207329 GGGTTGGTCGAGCTAGTGAAT 59.793 52.381 16.64 0.00 0.00 2.57
72 73 2.271800 GGTTGGTCGAGCTAGTGAATG 58.728 52.381 16.64 0.00 0.00 2.67
73 74 2.353803 GGTTGGTCGAGCTAGTGAATGT 60.354 50.000 16.64 0.00 0.00 2.71
74 75 3.326747 GTTGGTCGAGCTAGTGAATGTT 58.673 45.455 16.64 0.00 0.00 2.71
75 76 4.491676 GTTGGTCGAGCTAGTGAATGTTA 58.508 43.478 16.64 0.00 0.00 2.41
76 77 4.371855 TGGTCGAGCTAGTGAATGTTAG 57.628 45.455 16.64 0.00 0.00 2.34
77 78 3.130516 TGGTCGAGCTAGTGAATGTTAGG 59.869 47.826 16.64 0.00 0.00 2.69
78 79 3.130693 GGTCGAGCTAGTGAATGTTAGGT 59.869 47.826 7.51 0.00 0.00 3.08
79 80 4.352887 GTCGAGCTAGTGAATGTTAGGTC 58.647 47.826 0.00 1.70 39.70 3.85
80 81 4.014406 TCGAGCTAGTGAATGTTAGGTCA 58.986 43.478 10.24 0.00 41.93 4.02
81 82 4.461431 TCGAGCTAGTGAATGTTAGGTCAA 59.539 41.667 10.24 0.00 41.93 3.18
82 83 5.127194 TCGAGCTAGTGAATGTTAGGTCAAT 59.873 40.000 10.24 0.00 41.93 2.57
83 84 5.812642 CGAGCTAGTGAATGTTAGGTCAATT 59.187 40.000 10.24 0.00 41.93 2.32
84 85 6.237942 CGAGCTAGTGAATGTTAGGTCAATTG 60.238 42.308 0.00 0.00 41.93 2.32
85 86 5.355350 AGCTAGTGAATGTTAGGTCAATTGC 59.645 40.000 0.00 0.00 39.65 3.56
86 87 5.123820 GCTAGTGAATGTTAGGTCAATTGCA 59.876 40.000 0.00 0.00 39.33 4.08
87 88 6.183360 GCTAGTGAATGTTAGGTCAATTGCAT 60.183 38.462 0.00 0.00 39.33 3.96
88 89 6.199937 AGTGAATGTTAGGTCAATTGCATC 57.800 37.500 0.00 0.00 0.00 3.91
89 90 5.126061 AGTGAATGTTAGGTCAATTGCATCC 59.874 40.000 0.00 3.47 0.00 3.51
90 91 4.402155 TGAATGTTAGGTCAATTGCATCCC 59.598 41.667 0.00 0.00 0.00 3.85
91 92 3.448093 TGTTAGGTCAATTGCATCCCA 57.552 42.857 0.00 0.00 0.00 4.37
92 93 3.355378 TGTTAGGTCAATTGCATCCCAG 58.645 45.455 0.00 0.00 0.00 4.45
93 94 3.010027 TGTTAGGTCAATTGCATCCCAGA 59.990 43.478 0.00 0.00 0.00 3.86
94 95 2.905415 AGGTCAATTGCATCCCAGAA 57.095 45.000 0.00 0.00 0.00 3.02
95 96 2.731572 AGGTCAATTGCATCCCAGAAG 58.268 47.619 0.00 0.00 0.00 2.85
96 97 1.753073 GGTCAATTGCATCCCAGAAGG 59.247 52.381 0.00 0.00 0.00 3.46
97 98 2.450476 GTCAATTGCATCCCAGAAGGT 58.550 47.619 0.00 0.00 36.75 3.50
98 99 2.827921 GTCAATTGCATCCCAGAAGGTT 59.172 45.455 0.00 0.00 36.75 3.50
99 100 2.827322 TCAATTGCATCCCAGAAGGTTG 59.173 45.455 0.00 0.00 38.25 3.77
100 101 1.856629 ATTGCATCCCAGAAGGTTGG 58.143 50.000 0.00 0.00 36.05 3.77
101 102 0.776810 TTGCATCCCAGAAGGTTGGA 59.223 50.000 0.00 0.00 40.87 3.53
102 103 1.002069 TGCATCCCAGAAGGTTGGAT 58.998 50.000 0.00 0.00 40.87 3.41
103 104 1.358787 TGCATCCCAGAAGGTTGGATT 59.641 47.619 0.00 0.00 40.87 3.01
104 105 2.027385 GCATCCCAGAAGGTTGGATTC 58.973 52.381 0.00 0.00 40.87 2.52
105 106 2.621407 GCATCCCAGAAGGTTGGATTCA 60.621 50.000 0.00 0.00 40.87 2.57
106 107 3.700538 CATCCCAGAAGGTTGGATTCAA 58.299 45.455 0.00 0.00 40.87 2.69
107 108 3.439857 TCCCAGAAGGTTGGATTCAAG 57.560 47.619 0.00 0.00 40.87 3.02
108 109 2.041620 TCCCAGAAGGTTGGATTCAAGG 59.958 50.000 0.00 0.00 40.87 3.61
109 110 2.041620 CCCAGAAGGTTGGATTCAAGGA 59.958 50.000 0.00 0.00 40.87 3.36
110 111 3.350833 CCAGAAGGTTGGATTCAAGGAG 58.649 50.000 0.00 0.00 40.87 3.69
111 112 3.009473 CCAGAAGGTTGGATTCAAGGAGA 59.991 47.826 0.00 0.00 40.87 3.71
112 113 4.507335 CCAGAAGGTTGGATTCAAGGAGAA 60.507 45.833 0.00 0.00 40.87 2.87
114 115 5.713861 CAGAAGGTTGGATTCAAGGAGAATT 59.286 40.000 0.00 0.00 46.76 2.17
115 116 6.210185 CAGAAGGTTGGATTCAAGGAGAATTT 59.790 38.462 0.00 0.00 46.76 1.82
116 117 6.784473 AGAAGGTTGGATTCAAGGAGAATTTT 59.216 34.615 0.00 0.00 46.76 1.82
117 118 7.290948 AGAAGGTTGGATTCAAGGAGAATTTTT 59.709 33.333 0.00 0.00 46.76 1.94
134 135 1.988293 TTTTTGATCGAAGGGCCACA 58.012 45.000 6.18 0.00 0.00 4.17
135 136 1.243902 TTTTGATCGAAGGGCCACAC 58.756 50.000 6.18 0.00 0.00 3.82
136 137 0.109532 TTTGATCGAAGGGCCACACA 59.890 50.000 6.18 0.00 0.00 3.72
137 138 0.321564 TTGATCGAAGGGCCACACAG 60.322 55.000 6.18 0.00 0.00 3.66
138 139 2.045926 ATCGAAGGGCCACACAGC 60.046 61.111 6.18 0.00 0.00 4.40
251 254 2.808567 GCTCCAGCCTATCAAGCCTAAC 60.809 54.545 0.00 0.00 34.31 2.34
368 371 2.712057 TCAACGGACTAAAGGACGAC 57.288 50.000 0.00 0.00 0.00 4.34
585 588 6.691508 AGGGAACAAACAAGAAAGATAATGC 58.308 36.000 0.00 0.00 0.00 3.56
588 591 6.928492 GGAACAAACAAGAAAGATAATGCCAA 59.072 34.615 0.00 0.00 0.00 4.52
682 685 6.127730 GCAGCAGTACCCAATAAAACAACTAT 60.128 38.462 0.00 0.00 0.00 2.12
683 686 7.472543 CAGCAGTACCCAATAAAACAACTATC 58.527 38.462 0.00 0.00 0.00 2.08
716 719 4.708421 TCGGTATAGCTAGACAACCAGTTT 59.292 41.667 19.55 0.00 0.00 2.66
719 722 6.403878 GGTATAGCTAGACAACCAGTTTTGA 58.596 40.000 19.55 0.00 0.00 2.69
753 756 5.893897 AAAAGACATTGGAGCTCTCATTC 57.106 39.130 14.64 4.39 0.00 2.67
754 757 3.557228 AGACATTGGAGCTCTCATTCC 57.443 47.619 14.64 0.00 0.00 3.01
755 758 2.842496 AGACATTGGAGCTCTCATTCCA 59.158 45.455 14.64 0.00 41.59 3.53
756 759 3.118334 AGACATTGGAGCTCTCATTCCAG 60.118 47.826 14.64 0.00 43.89 3.86
787 790 5.734720 AGGACGATCAGTTACACATTCAAT 58.265 37.500 0.00 0.00 0.00 2.57
788 791 6.173339 AGGACGATCAGTTACACATTCAATT 58.827 36.000 0.00 0.00 0.00 2.32
789 792 6.655003 AGGACGATCAGTTACACATTCAATTT 59.345 34.615 0.00 0.00 0.00 1.82
790 793 6.961554 GGACGATCAGTTACACATTCAATTTC 59.038 38.462 0.00 0.00 0.00 2.17
791 794 7.360861 GGACGATCAGTTACACATTCAATTTCA 60.361 37.037 0.00 0.00 0.00 2.69
792 795 7.870826 ACGATCAGTTACACATTCAATTTCAA 58.129 30.769 0.00 0.00 0.00 2.69
793 796 8.017373 ACGATCAGTTACACATTCAATTTCAAG 58.983 33.333 0.00 0.00 0.00 3.02
814 817 2.915349 CCATGCTGAGCAGTACTGATT 58.085 47.619 27.08 13.31 43.65 2.57
816 819 3.311871 CCATGCTGAGCAGTACTGATTTC 59.688 47.826 27.08 18.62 43.65 2.17
825 828 6.310467 TGAGCAGTACTGATTTCGTACATTTC 59.690 38.462 27.08 4.16 39.66 2.17
833 836 5.617609 TGATTTCGTACATTTCTCGCAAAG 58.382 37.500 0.00 0.00 0.00 2.77
847 855 1.069227 CGCAAAGACAAAGTACTGGCC 60.069 52.381 0.00 0.00 0.00 5.36
885 894 7.650903 CCTGACTGAGAAAGGAAAAGAAAAATG 59.349 37.037 0.00 0.00 32.43 2.32
991 1001 1.812571 CCTCCACCCATTTCGTTTCAG 59.187 52.381 0.00 0.00 0.00 3.02
1089 1099 1.153168 CCGAAATGGCGTGATCCCT 60.153 57.895 0.00 0.00 0.00 4.20
1212 1233 2.933287 CCCTAGCCACCACCACCA 60.933 66.667 0.00 0.00 0.00 4.17
1308 1329 4.821589 GGGCTGCCGTTCCTCTCG 62.822 72.222 13.40 0.00 0.00 4.04
1639 1666 4.379243 ACAAGCTGGCCGACCTCG 62.379 66.667 0.00 0.00 36.63 4.63
2193 2229 1.827344 CCTCTGCAAAATCCTTTCCCC 59.173 52.381 0.00 0.00 0.00 4.81
2352 2390 8.557869 CAAGCTCTGCAATTTTACATCTATTC 57.442 34.615 0.00 0.00 0.00 1.75
2387 2425 0.889186 AGGTTGGTAGGCAGTTTGCG 60.889 55.000 0.00 0.00 46.21 4.85
2508 2547 1.775208 CTGCGTTTTCGTCTTTGCAAG 59.225 47.619 0.00 0.00 46.03 4.01
2713 2753 1.596603 GCCAACTTTTGCATTTGCCT 58.403 45.000 0.00 0.00 41.18 4.75
2779 2819 3.766068 ATGAATGATCTGACTCCGCAT 57.234 42.857 0.00 0.00 0.00 4.73
2794 2834 7.604549 TGACTCCGCATATATTAAATTCCGTA 58.395 34.615 0.00 0.00 0.00 4.02
2856 2904 9.571816 AGGTACAGTAGAAGGTAGAATATGTAC 57.428 37.037 0.00 0.00 39.63 2.90
2864 2912 8.611051 AGAAGGTAGAATATGTACCAGTCTTT 57.389 34.615 14.26 2.89 42.28 2.52
2910 2958 2.421073 TGTGTGCTGCTATGCTTTGATC 59.579 45.455 0.00 0.00 0.00 2.92
2912 2960 3.083293 TGTGCTGCTATGCTTTGATCAA 58.917 40.909 3.38 3.38 0.00 2.57
2913 2961 3.506844 TGTGCTGCTATGCTTTGATCAAA 59.493 39.130 19.45 19.45 0.00 2.69
2920 2968 7.019774 TGCTATGCTTTGATCAAATACTCAC 57.980 36.000 20.76 10.47 0.00 3.51
2923 2971 8.494347 GCTATGCTTTGATCAAATACTCACTAG 58.506 37.037 20.76 14.25 0.00 2.57
2928 2976 8.983724 GCTTTGATCAAATACTCACTAGATACC 58.016 37.037 20.76 0.00 0.00 2.73
3030 3079 5.749462 CATCCAAAGAGTTCCTCCAGTAAT 58.251 41.667 0.00 0.00 0.00 1.89
3087 3249 2.821366 GTCTGACATGGGCGGCTG 60.821 66.667 9.56 2.20 0.00 4.85
3097 3259 0.468400 TGGGCGGCTGGTTTAAAACT 60.468 50.000 9.56 0.00 0.00 2.66
3101 3263 2.542178 GGCGGCTGGTTTAAAACTTTTG 59.458 45.455 4.60 0.00 0.00 2.44
3128 3291 9.811995 ATTTTAGGAACAGTTGGTTTAAAACTC 57.188 29.630 4.60 0.00 40.63 3.01
3148 3312 5.202004 ACTCGGTGTACTAGAATCCTGAAT 58.798 41.667 0.00 0.00 0.00 2.57
3160 3324 8.407064 ACTAGAATCCTGAATTCACTACTTACG 58.593 37.037 3.38 0.00 45.34 3.18
3192 3356 4.511826 ACAATTTCGTCTTCACTCCTTCAC 59.488 41.667 0.00 0.00 0.00 3.18
3210 3374 3.486383 TCACCCAGAACAAAGATTGACC 58.514 45.455 0.00 0.00 0.00 4.02
3221 3385 5.670485 ACAAAGATTGACCGTAGATATGCA 58.330 37.500 0.00 0.00 0.00 3.96
3222 3386 5.523916 ACAAAGATTGACCGTAGATATGCAC 59.476 40.000 0.00 0.00 0.00 4.57
3224 3388 5.474578 AGATTGACCGTAGATATGCACAT 57.525 39.130 0.00 0.00 0.00 3.21
3238 3402 8.026341 AGATATGCACATTCGTAGATTCATTG 57.974 34.615 0.00 0.00 35.04 2.82
3241 3405 3.548818 GCACATTCGTAGATTCATTGGCC 60.549 47.826 0.00 0.00 35.04 5.36
3242 3406 3.627123 CACATTCGTAGATTCATTGGCCA 59.373 43.478 0.00 0.00 35.04 5.36
3289 3454 2.219875 CCCCACCTGTCAGTCAGCT 61.220 63.158 0.00 0.00 42.38 4.24
3297 3462 3.070018 CCTGTCAGTCAGCTAACCAAAG 58.930 50.000 0.00 0.00 42.38 2.77
3313 3482 0.465460 AAAGAGACACCGCTTGCCAA 60.465 50.000 0.00 0.00 32.69 4.52
3323 3492 3.613737 CACCGCTTGCCAAATTCAAATAG 59.386 43.478 0.00 0.00 0.00 1.73
3340 3531 6.349300 TCAAATAGTTTCCATACTCTGAGCC 58.651 40.000 4.19 0.00 0.00 4.70
3395 3589 2.483714 GGATCTAGCCATGACGCTGAAA 60.484 50.000 6.71 0.00 40.08 2.69
3400 3594 3.665745 AGCCATGACGCTGAAATTTTT 57.334 38.095 0.00 0.00 37.82 1.94
3401 3595 4.782019 AGCCATGACGCTGAAATTTTTA 57.218 36.364 0.00 0.00 37.82 1.52
3403 3597 4.458989 AGCCATGACGCTGAAATTTTTAGA 59.541 37.500 5.19 0.00 37.82 2.10
3487 3681 0.801067 CGTCAGGCTAACGGTAGTGC 60.801 60.000 9.69 0.00 36.51 4.40
3544 3740 4.344865 ACGCAGGAATTGGCCCGT 62.345 61.111 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.492973 TGTTGATACATTATGATCGTGATGAAT 57.507 29.630 22.61 7.22 0.00 2.57
15 16 8.885494 TGTTGATACATTATGATCGTGATGAA 57.115 30.769 22.61 6.97 0.00 2.57
16 17 8.885494 TTGTTGATACATTATGATCGTGATGA 57.115 30.769 22.61 9.55 33.44 2.92
17 18 8.981647 TCTTGTTGATACATTATGATCGTGATG 58.018 33.333 16.05 16.05 33.44 3.07
18 19 9.546428 TTCTTGTTGATACATTATGATCGTGAT 57.454 29.630 0.00 0.00 33.44 3.06
19 20 8.817100 GTTCTTGTTGATACATTATGATCGTGA 58.183 33.333 0.00 0.00 33.44 4.35
20 21 8.064222 GGTTCTTGTTGATACATTATGATCGTG 58.936 37.037 0.00 0.00 33.44 4.35
21 22 7.042725 CGGTTCTTGTTGATACATTATGATCGT 60.043 37.037 0.00 0.00 33.44 3.73
22 23 7.042725 ACGGTTCTTGTTGATACATTATGATCG 60.043 37.037 0.00 0.00 33.44 3.69
23 24 8.142994 ACGGTTCTTGTTGATACATTATGATC 57.857 34.615 0.00 0.00 33.44 2.92
24 25 8.506168 AACGGTTCTTGTTGATACATTATGAT 57.494 30.769 0.00 0.00 33.44 2.45
25 26 7.915293 AACGGTTCTTGTTGATACATTATGA 57.085 32.000 0.00 0.00 33.44 2.15
26 27 7.484641 CCAAACGGTTCTTGTTGATACATTATG 59.515 37.037 0.00 0.00 33.44 1.90
27 28 7.362574 CCCAAACGGTTCTTGTTGATACATTAT 60.363 37.037 0.00 0.00 33.44 1.28
28 29 6.072397 CCCAAACGGTTCTTGTTGATACATTA 60.072 38.462 0.00 0.00 33.44 1.90
29 30 5.278758 CCCAAACGGTTCTTGTTGATACATT 60.279 40.000 0.00 0.00 33.44 2.71
30 31 4.217550 CCCAAACGGTTCTTGTTGATACAT 59.782 41.667 0.00 0.00 33.44 2.29
31 32 3.566322 CCCAAACGGTTCTTGTTGATACA 59.434 43.478 0.00 0.00 0.00 2.29
32 33 3.566742 ACCCAAACGGTTCTTGTTGATAC 59.433 43.478 0.00 0.00 45.36 2.24
33 34 3.822940 ACCCAAACGGTTCTTGTTGATA 58.177 40.909 0.00 0.00 45.36 2.15
34 35 2.661718 ACCCAAACGGTTCTTGTTGAT 58.338 42.857 0.00 0.00 45.36 2.57
35 36 2.131776 ACCCAAACGGTTCTTGTTGA 57.868 45.000 0.00 0.00 45.36 3.18
45 46 2.613506 GCTCGACCAACCCAAACGG 61.614 63.158 0.00 0.00 37.81 4.44
46 47 0.320073 TAGCTCGACCAACCCAAACG 60.320 55.000 0.00 0.00 0.00 3.60
47 48 1.270678 ACTAGCTCGACCAACCCAAAC 60.271 52.381 0.00 0.00 0.00 2.93
48 49 1.053424 ACTAGCTCGACCAACCCAAA 58.947 50.000 0.00 0.00 0.00 3.28
49 50 0.320374 CACTAGCTCGACCAACCCAA 59.680 55.000 0.00 0.00 0.00 4.12
50 51 0.541063 TCACTAGCTCGACCAACCCA 60.541 55.000 0.00 0.00 0.00 4.51
51 52 0.606604 TTCACTAGCTCGACCAACCC 59.393 55.000 0.00 0.00 0.00 4.11
52 53 2.271800 CATTCACTAGCTCGACCAACC 58.728 52.381 0.00 0.00 0.00 3.77
53 54 2.960819 ACATTCACTAGCTCGACCAAC 58.039 47.619 0.00 0.00 0.00 3.77
54 55 3.678056 AACATTCACTAGCTCGACCAA 57.322 42.857 0.00 0.00 0.00 3.67
55 56 3.130516 CCTAACATTCACTAGCTCGACCA 59.869 47.826 0.00 0.00 0.00 4.02
56 57 3.130693 ACCTAACATTCACTAGCTCGACC 59.869 47.826 0.00 0.00 0.00 4.79
57 58 4.142447 TGACCTAACATTCACTAGCTCGAC 60.142 45.833 0.00 0.00 0.00 4.20
58 59 4.014406 TGACCTAACATTCACTAGCTCGA 58.986 43.478 0.00 0.00 0.00 4.04
59 60 4.371855 TGACCTAACATTCACTAGCTCG 57.628 45.455 0.00 0.00 0.00 5.03
60 61 6.457528 GCAATTGACCTAACATTCACTAGCTC 60.458 42.308 10.34 0.00 0.00 4.09
61 62 5.355350 GCAATTGACCTAACATTCACTAGCT 59.645 40.000 10.34 0.00 0.00 3.32
62 63 5.123820 TGCAATTGACCTAACATTCACTAGC 59.876 40.000 10.34 0.00 0.00 3.42
63 64 6.741992 TGCAATTGACCTAACATTCACTAG 57.258 37.500 10.34 0.00 0.00 2.57
64 65 6.318648 GGATGCAATTGACCTAACATTCACTA 59.681 38.462 10.34 0.00 0.00 2.74
65 66 5.126061 GGATGCAATTGACCTAACATTCACT 59.874 40.000 10.34 0.00 0.00 3.41
66 67 5.343249 GGATGCAATTGACCTAACATTCAC 58.657 41.667 10.34 0.00 0.00 3.18
67 68 4.402155 GGGATGCAATTGACCTAACATTCA 59.598 41.667 10.34 0.00 0.00 2.57
68 69 4.402155 TGGGATGCAATTGACCTAACATTC 59.598 41.667 10.34 0.42 0.00 2.67
69 70 4.352009 TGGGATGCAATTGACCTAACATT 58.648 39.130 10.34 0.00 0.00 2.71
70 71 3.956199 CTGGGATGCAATTGACCTAACAT 59.044 43.478 10.34 1.40 0.00 2.71
71 72 3.010027 TCTGGGATGCAATTGACCTAACA 59.990 43.478 10.34 0.00 0.00 2.41
72 73 3.620488 TCTGGGATGCAATTGACCTAAC 58.380 45.455 10.34 0.00 0.00 2.34
73 74 4.272489 CTTCTGGGATGCAATTGACCTAA 58.728 43.478 10.34 4.03 0.00 2.69
74 75 3.371917 CCTTCTGGGATGCAATTGACCTA 60.372 47.826 10.34 6.18 37.23 3.08
75 76 2.622452 CCTTCTGGGATGCAATTGACCT 60.622 50.000 10.34 0.00 37.23 3.85
76 77 1.753073 CCTTCTGGGATGCAATTGACC 59.247 52.381 10.34 8.77 37.23 4.02
77 78 2.450476 ACCTTCTGGGATGCAATTGAC 58.550 47.619 10.34 1.02 38.76 3.18
78 79 2.827322 CAACCTTCTGGGATGCAATTGA 59.173 45.455 10.34 0.00 38.76 2.57
79 80 2.093869 CCAACCTTCTGGGATGCAATTG 60.094 50.000 0.00 0.00 36.66 2.32
80 81 2.181975 CCAACCTTCTGGGATGCAATT 58.818 47.619 0.00 0.00 36.66 2.32
81 82 1.358787 TCCAACCTTCTGGGATGCAAT 59.641 47.619 0.00 0.00 36.66 3.56
82 83 0.776810 TCCAACCTTCTGGGATGCAA 59.223 50.000 0.00 0.00 36.66 4.08
83 84 1.002069 ATCCAACCTTCTGGGATGCA 58.998 50.000 0.00 0.00 39.87 3.96
84 85 2.027385 GAATCCAACCTTCTGGGATGC 58.973 52.381 0.00 0.00 40.46 3.91
85 86 3.370840 TGAATCCAACCTTCTGGGATG 57.629 47.619 0.00 0.00 40.46 3.51
86 87 3.309410 CCTTGAATCCAACCTTCTGGGAT 60.309 47.826 0.00 0.00 43.12 3.85
87 88 2.041620 CCTTGAATCCAACCTTCTGGGA 59.958 50.000 0.00 0.00 37.06 4.37
88 89 2.041620 TCCTTGAATCCAACCTTCTGGG 59.958 50.000 0.00 0.00 37.06 4.45
89 90 3.009473 TCTCCTTGAATCCAACCTTCTGG 59.991 47.826 0.00 0.00 37.87 3.86
90 91 4.292186 TCTCCTTGAATCCAACCTTCTG 57.708 45.455 0.00 0.00 0.00 3.02
91 92 5.527026 ATTCTCCTTGAATCCAACCTTCT 57.473 39.130 0.00 0.00 41.17 2.85
92 93 6.596309 AAATTCTCCTTGAATCCAACCTTC 57.404 37.500 0.00 0.00 43.99 3.46
93 94 7.379059 AAAAATTCTCCTTGAATCCAACCTT 57.621 32.000 0.00 0.00 43.99 3.50
115 116 1.611491 GTGTGGCCCTTCGATCAAAAA 59.389 47.619 0.00 0.00 0.00 1.94
116 117 1.243902 GTGTGGCCCTTCGATCAAAA 58.756 50.000 0.00 0.00 0.00 2.44
117 118 0.109532 TGTGTGGCCCTTCGATCAAA 59.890 50.000 0.00 0.00 0.00 2.69
138 139 3.074369 GAAAATGGGGGCCACGGG 61.074 66.667 4.39 0.00 35.80 5.28
139 140 1.264045 AATGAAAATGGGGGCCACGG 61.264 55.000 4.39 0.00 35.80 4.94
140 141 0.612744 AAATGAAAATGGGGGCCACG 59.387 50.000 4.39 0.00 35.80 4.94
251 254 9.755804 GTGATATATATATCAGTGGTGTGATGG 57.244 37.037 28.19 0.00 46.94 3.51
273 276 2.240414 TGAAGCATCCTGATGTGGTGAT 59.760 45.455 8.79 0.00 40.80 3.06
274 277 1.629861 TGAAGCATCCTGATGTGGTGA 59.370 47.619 8.79 0.00 40.80 4.02
368 371 7.087639 TCGAAGCCTTTATGTTAATTTGGTTG 58.912 34.615 0.00 0.00 0.00 3.77
548 551 6.891388 TGTTTGTTCCCTACTTGACTCTTAA 58.109 36.000 0.00 0.00 0.00 1.85
549 552 6.488769 TGTTTGTTCCCTACTTGACTCTTA 57.511 37.500 0.00 0.00 0.00 2.10
585 588 6.212388 AGTGTTATGCCTAGAGATCCTATTGG 59.788 42.308 0.00 0.00 0.00 3.16
588 591 7.863901 AAAGTGTTATGCCTAGAGATCCTAT 57.136 36.000 0.00 0.00 0.00 2.57
633 636 8.049117 TGCTCTCTTGTGGTCTATATGAAAAAT 58.951 33.333 0.00 0.00 0.00 1.82
638 641 4.038522 GCTGCTCTCTTGTGGTCTATATGA 59.961 45.833 0.00 0.00 0.00 2.15
682 685 6.654161 GTCTAGCTATACCGACAAAGATAGGA 59.346 42.308 6.09 0.00 30.73 2.94
683 686 6.430308 TGTCTAGCTATACCGACAAAGATAGG 59.570 42.308 10.26 0.00 33.84 2.57
693 696 3.894759 ACTGGTTGTCTAGCTATACCGA 58.105 45.455 6.79 0.00 0.00 4.69
750 753 1.133761 TCGTCCTCGATCTCCTGGAAT 60.134 52.381 0.00 0.00 41.35 3.01
751 754 0.255033 TCGTCCTCGATCTCCTGGAA 59.745 55.000 0.00 0.00 41.35 3.53
752 755 1.912971 TCGTCCTCGATCTCCTGGA 59.087 57.895 0.00 0.00 41.35 3.86
753 756 4.561452 TCGTCCTCGATCTCCTGG 57.439 61.111 0.00 0.00 41.35 4.45
787 790 0.885879 CTGCTCAGCATGGCTTGAAA 59.114 50.000 0.00 0.00 38.13 2.69
788 791 0.251033 ACTGCTCAGCATGGCTTGAA 60.251 50.000 0.00 0.00 38.13 2.69
789 792 0.614812 TACTGCTCAGCATGGCTTGA 59.385 50.000 0.00 0.00 38.13 3.02
790 793 0.731417 GTACTGCTCAGCATGGCTTG 59.269 55.000 0.00 0.00 38.13 4.01
791 794 0.617413 AGTACTGCTCAGCATGGCTT 59.383 50.000 0.00 0.00 38.13 4.35
792 795 0.107800 CAGTACTGCTCAGCATGGCT 60.108 55.000 10.54 0.00 38.13 4.75
793 796 0.107993 TCAGTACTGCTCAGCATGGC 60.108 55.000 18.45 0.00 38.13 4.40
814 817 4.052608 TGTCTTTGCGAGAAATGTACGAA 58.947 39.130 0.00 0.00 35.79 3.85
816 819 4.383774 TTGTCTTTGCGAGAAATGTACG 57.616 40.909 0.00 0.00 35.79 3.67
825 828 2.096218 GCCAGTACTTTGTCTTTGCGAG 60.096 50.000 0.00 0.00 0.00 5.03
833 836 0.608308 GGTGGGGCCAGTACTTTGTC 60.608 60.000 4.39 0.00 37.17 3.18
847 855 1.553248 TCAGTCAGGTAAATCGGTGGG 59.447 52.381 0.00 0.00 0.00 4.61
885 894 3.482436 CGTTTTTACCGCTGATTACGTCC 60.482 47.826 0.00 0.00 0.00 4.79
991 1001 2.246719 CGGAGGAGGATGAATGGAAC 57.753 55.000 0.00 0.00 0.00 3.62
1212 1233 2.616458 GGAGGCCTTCATGGTGGGT 61.616 63.158 6.77 0.00 38.35 4.51
1965 2001 4.314121 CCTTCTTGTCCTCTTCAGACTTG 58.686 47.826 0.00 0.00 35.21 3.16
2193 2229 1.579698 CATGGAGATCAGGCTTCACG 58.420 55.000 0.00 0.00 0.00 4.35
2352 2390 9.436957 CCTACCAACCTATATTATTAAGCACAG 57.563 37.037 0.00 0.00 0.00 3.66
2387 2425 1.264288 CGTTTGCTTCCACTCAAGGAC 59.736 52.381 0.00 0.00 37.42 3.85
2454 2492 5.707242 ATGACATATCCTAACACGACGAT 57.293 39.130 0.00 0.00 0.00 3.73
2508 2547 8.976471 GTTGAAACTTCTACTACTAACAGGAAC 58.024 37.037 0.00 0.00 31.64 3.62
2713 2753 3.009363 TCCATGATTCCTGCACTTTCTGA 59.991 43.478 0.00 0.00 0.00 3.27
2828 2868 8.504409 ACATATTCTACCTTCTACTGTACCTCT 58.496 37.037 0.00 0.00 0.00 3.69
2833 2873 9.570468 CTGGTACATATTCTACCTTCTACTGTA 57.430 37.037 0.00 0.00 38.20 2.74
2834 2874 8.060075 ACTGGTACATATTCTACCTTCTACTGT 58.940 37.037 0.00 0.00 38.20 3.55
2835 2875 8.466617 ACTGGTACATATTCTACCTTCTACTG 57.533 38.462 0.00 0.00 38.20 2.74
2856 2904 7.962964 TCTTACTGTGTTGATTAAAGACTGG 57.037 36.000 0.00 0.00 35.90 4.00
2864 2912 8.506437 CAAAGAAGCATCTTACTGTGTTGATTA 58.494 33.333 4.34 0.00 45.19 1.75
2910 2958 6.810911 ACTGCAGGTATCTAGTGAGTATTTG 58.189 40.000 19.93 0.00 0.00 2.32
2912 2960 8.713708 AATACTGCAGGTATCTAGTGAGTATT 57.286 34.615 19.93 6.04 39.94 1.89
2913 2961 8.713708 AAATACTGCAGGTATCTAGTGAGTAT 57.286 34.615 19.93 0.00 39.94 2.12
2920 2968 8.184304 ACTCCTTAAATACTGCAGGTATCTAG 57.816 38.462 19.93 8.25 39.94 2.43
2923 2971 5.921408 CGACTCCTTAAATACTGCAGGTATC 59.079 44.000 19.93 0.31 39.94 2.24
2928 2976 4.210120 GCATCGACTCCTTAAATACTGCAG 59.790 45.833 13.48 13.48 0.00 4.41
3050 3212 9.585099 GTCAGACCAATATTTGCATCAATTTTA 57.415 29.630 0.00 0.00 0.00 1.52
3101 3263 9.811995 AGTTTTAAACCAACTGTTCCTAAAATC 57.188 29.630 4.01 0.00 34.29 2.17
3128 3291 5.749109 GTGAATTCAGGATTCTAGTACACCG 59.251 44.000 8.80 0.00 43.74 4.94
3168 3332 5.694910 GTGAAGGAGTGAAGACGAAATTGTA 59.305 40.000 0.00 0.00 0.00 2.41
3169 3333 4.511826 GTGAAGGAGTGAAGACGAAATTGT 59.488 41.667 0.00 0.00 0.00 2.71
3170 3334 4.083802 GGTGAAGGAGTGAAGACGAAATTG 60.084 45.833 0.00 0.00 0.00 2.32
3171 3335 4.065789 GGTGAAGGAGTGAAGACGAAATT 58.934 43.478 0.00 0.00 0.00 1.82
3172 3336 3.557264 GGGTGAAGGAGTGAAGACGAAAT 60.557 47.826 0.00 0.00 0.00 2.17
3174 3338 1.343465 GGGTGAAGGAGTGAAGACGAA 59.657 52.381 0.00 0.00 0.00 3.85
3175 3339 0.966920 GGGTGAAGGAGTGAAGACGA 59.033 55.000 0.00 0.00 0.00 4.20
3176 3340 0.679505 TGGGTGAAGGAGTGAAGACG 59.320 55.000 0.00 0.00 0.00 4.18
3177 3341 1.971357 TCTGGGTGAAGGAGTGAAGAC 59.029 52.381 0.00 0.00 0.00 3.01
3187 3351 4.022849 GGTCAATCTTTGTTCTGGGTGAAG 60.023 45.833 0.00 0.00 35.01 3.02
3192 3356 2.504367 ACGGTCAATCTTTGTTCTGGG 58.496 47.619 0.00 0.00 0.00 4.45
3210 3374 6.801862 TGAATCTACGAATGTGCATATCTACG 59.198 38.462 12.92 12.92 0.00 3.51
3221 3385 3.884895 TGGCCAATGAATCTACGAATGT 58.115 40.909 0.61 0.00 0.00 2.71
3222 3386 6.558771 TTATGGCCAATGAATCTACGAATG 57.441 37.500 10.96 0.00 0.00 2.67
3224 3388 6.375736 TGTTTTATGGCCAATGAATCTACGAA 59.624 34.615 10.96 0.00 0.00 3.85
3238 3402 1.204704 GCAACCTCCTGTTTTATGGCC 59.795 52.381 0.00 0.00 34.00 5.36
3241 3405 3.913089 GGTTGCAACCTCCTGTTTTATG 58.087 45.455 36.26 0.00 45.75 1.90
3289 3454 2.489971 CAAGCGGTGTCTCTTTGGTTA 58.510 47.619 0.00 0.00 0.00 2.85
3297 3462 0.598065 AATTTGGCAAGCGGTGTCTC 59.402 50.000 0.00 0.00 30.97 3.36
3313 3482 8.897752 GCTCAGAGTATGGAAACTATTTGAATT 58.102 33.333 0.00 0.00 0.00 2.17
3323 3492 3.895232 TGAGGCTCAGAGTATGGAAAC 57.105 47.619 14.43 0.00 0.00 2.78
3395 3589 7.095607 CGTCACTGAGCTAAACTGTCTAAAAAT 60.096 37.037 0.00 0.00 0.00 1.82
3400 3594 3.366070 GCGTCACTGAGCTAAACTGTCTA 60.366 47.826 0.00 0.00 0.00 2.59
3401 3595 2.608261 GCGTCACTGAGCTAAACTGTCT 60.608 50.000 0.00 0.00 0.00 3.41
3403 3597 1.784525 GCGTCACTGAGCTAAACTGT 58.215 50.000 0.00 0.00 0.00 3.55
3487 3681 0.039074 GATCACTGATCGGCCTACGG 60.039 60.000 0.00 0.00 44.45 4.02
3491 3685 1.406065 CCCTGATCACTGATCGGCCT 61.406 60.000 19.07 0.00 42.32 5.19


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

AutoCloner maintained by Alex Coulton.