Multiple sequence alignment - TraesCS3B01G120500

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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 TraesCS3B01G120500 chr3B 100.000 3129 0 0 1 3129 90207961 90211089 0.000000e+00 5779.0
1 TraesCS3B01G120500 chr3B 93.088 1606 58 25 605 2180 90159848 90158266 0.000000e+00 2302.0
2 TraesCS3B01G120500 chr3B 87.660 470 30 21 2172 2638 90157716 90157272 3.580000e-144 521.0
3 TraesCS3B01G120500 chr3B 83.186 113 15 1 2907 3015 89627697 89627585 1.990000e-17 100.0
4 TraesCS3B01G120500 chr3B 94.118 51 1 2 2754 2803 534172387 534172338 3.350000e-10 76.8
5 TraesCS3B01G120500 chr3B 89.831 59 4 2 2751 2809 71403704 71403648 1.200000e-09 75.0
6 TraesCS3B01G120500 chr3B 100.000 33 0 0 2983 3015 89611572 89611540 9.370000e-06 62.1
7 TraesCS3B01G120500 chr3D 89.347 1793 123 38 972 2729 57335325 57337084 0.000000e+00 2191.0
8 TraesCS3B01G120500 chr3D 91.149 1480 65 27 1 1439 57327520 57328974 0.000000e+00 1947.0
9 TraesCS3B01G120500 chr3D 85.116 2029 154 67 401 2355 57179718 57177764 0.000000e+00 1938.0
10 TraesCS3B01G120500 chr3D 86.640 988 76 29 5 943 57334349 57335329 0.000000e+00 1042.0
11 TraesCS3B01G120500 chr3D 90.438 753 45 14 1131 1867 57325125 57325866 0.000000e+00 966.0
12 TraesCS3B01G120500 chr3D 97.131 244 7 0 2797 3040 57337087 57337330 2.250000e-111 412.0
13 TraesCS3B01G120500 chr3D 90.038 261 19 3 488 745 57319954 57320210 6.470000e-87 331.0
14 TraesCS3B01G120500 chr3D 84.831 356 19 15 753 1079 57324780 57325129 3.010000e-85 326.0
15 TraesCS3B01G120500 chr3D 90.688 247 15 4 97 339 57180043 57179801 3.890000e-84 322.0
16 TraesCS3B01G120500 chr3D 88.933 253 20 4 1518 1769 57330838 57331083 3.920000e-79 305.0
17 TraesCS3B01G120500 chr3D 88.716 257 16 6 1319 1571 57330383 57330630 5.070000e-78 302.0
18 TraesCS3B01G120500 chr3D 89.862 217 21 1 5 221 57194950 57195165 8.550000e-71 278.0
19 TraesCS3B01G120500 chr3D 84.466 206 20 3 2864 3065 57177282 57177085 3.180000e-45 193.0
20 TraesCS3B01G120500 chr3D 96.703 91 3 0 3039 3129 57354674 57354764 5.400000e-33 152.0
21 TraesCS3B01G120500 chr3D 92.208 77 4 2 1689 1764 57331083 57331158 1.190000e-19 108.0
22 TraesCS3B01G120500 chr3D 84.906 106 14 2 2912 3015 56846333 56846438 4.270000e-19 106.0
23 TraesCS3B01G120500 chr3D 96.491 57 2 0 1 57 57319814 57319870 9.240000e-16 95.3
24 TraesCS3B01G120500 chr3A 83.786 2208 168 96 491 2638 66273275 66271198 0.000000e+00 1919.0
25 TraesCS3B01G120500 chr3A 83.829 1478 112 66 1283 2725 66363075 66364460 0.000000e+00 1288.0
26 TraesCS3B01G120500 chr3A 88.686 601 33 9 1 594 66361708 66362280 0.000000e+00 701.0
27 TraesCS3B01G120500 chr3A 82.603 730 56 34 592 1293 66362361 66363047 2.090000e-161 579.0
28 TraesCS3B01G120500 chr3A 79.669 423 42 21 2220 2638 66367703 66368085 6.650000e-67 265.0
29 TraesCS3B01G120500 chr3A 83.420 193 19 4 2900 3080 66270966 66270775 1.930000e-37 167.0
30 TraesCS3B01G120500 chr3A 86.709 158 11 5 2900 3049 66368318 66368473 1.930000e-37 167.0
31 TraesCS3B01G120500 chr3A 95.238 63 2 1 10 72 66273333 66273272 7.140000e-17 99.0
32 TraesCS3B01G120500 chr4A 84.071 113 14 1 2907 3015 609326265 609326153 4.270000e-19 106.0
33 TraesCS3B01G120500 chr4A 83.186 113 15 1 2907 3015 609344871 609344759 1.990000e-17 100.0
34 TraesCS3B01G120500 chr5A 92.727 55 2 2 2753 2807 363922442 363922494 9.300000e-11 78.7
35 TraesCS3B01G120500 chr4D 92.453 53 2 2 2753 2805 455312006 455312056 1.200000e-09 75.0
36 TraesCS3B01G120500 chr4D 92.308 52 3 1 2753 2804 341923483 341923533 4.330000e-09 73.1
37 TraesCS3B01G120500 chrUn 90.741 54 3 2 2750 2802 165277584 165277636 1.560000e-08 71.3
38 TraesCS3B01G120500 chrUn 90.741 54 3 2 2750 2802 165308792 165308844 1.560000e-08 71.3
39 TraesCS3B01G120500 chr7B 88.136 59 5 2 2753 2811 361147126 361147070 5.600000e-08 69.4
40 TraesCS3B01G120500 chr1A 95.000 40 2 0 2753 2792 361441677 361441716 2.610000e-06 63.9


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 TraesCS3B01G120500 chr3B 90207961 90211089 3128 False 5779.000000 5779 100.000000 1 3129 1 chr3B.!!$F1 3128
1 TraesCS3B01G120500 chr3B 90157272 90159848 2576 True 1411.500000 2302 90.374000 605 2638 2 chr3B.!!$R5 2033
2 TraesCS3B01G120500 chr3D 57324780 57337330 12550 False 844.333333 2191 89.932556 1 3040 9 chr3D.!!$F5 3039
3 TraesCS3B01G120500 chr3D 57177085 57180043 2958 True 817.666667 1938 86.756667 97 3065 3 chr3D.!!$R1 2968
4 TraesCS3B01G120500 chr3A 66270775 66273333 2558 True 728.333333 1919 87.481333 10 3080 3 chr3A.!!$R1 3070
5 TraesCS3B01G120500 chr3A 66361708 66368473 6765 False 600.000000 1288 84.299200 1 3049 5 chr3A.!!$F1 3048

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
429 3225 0.318955 GAAATGTTTGCAGCGCCACT 60.319 50.0 2.29 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 12792 0.392998 AATCATGTGACCCTGCGTCC 60.393 55.0 0.0 0.0 41.18 4.79 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
73 2814 6.345298 TCTATTGTCGAGTGATTATGGCAAA 58.655 36.000 0.00 0.00 0.00 3.68
140 2881 6.818142 AGTCAAAGGGAAAACTGTTTCATTTG 59.182 34.615 18.24 18.24 44.29 2.32
176 2920 1.400846 CATGTTCTGATCACAGGCAGC 59.599 52.381 0.00 0.00 43.60 5.25
182 2926 1.227205 GATCACAGGCAGCCGAGAG 60.227 63.158 5.55 1.71 0.00 3.20
197 2941 0.884514 GAGAGATGGCATCGATCGGA 59.115 55.000 21.01 2.25 0.00 4.55
258 3003 0.615331 TGGTCAGATGTGGAAGGAGC 59.385 55.000 0.00 0.00 0.00 4.70
346 3142 1.787155 CAGCAGGCGTCGTGATTATAC 59.213 52.381 0.00 0.00 0.00 1.47
372 3168 2.158449 GTCAACGAATCTTGTGAGCAGG 59.842 50.000 0.00 0.00 0.00 4.85
398 3194 2.030562 ACTCGTGCCGGTTTCAGG 59.969 61.111 1.90 0.00 0.00 3.86
429 3225 0.318955 GAAATGTTTGCAGCGCCACT 60.319 50.000 2.29 0.00 0.00 4.00
508 3304 5.715434 TTTTGGCACCTACTGAAATAACC 57.285 39.130 0.00 0.00 0.00 2.85
571 3367 6.066690 CAGAACCATCCCATCATGTCTTATT 58.933 40.000 0.00 0.00 0.00 1.40
637 3528 4.352009 ACATTCATAAGGGTTTGGCATGA 58.648 39.130 0.00 0.00 0.00 3.07
703 3606 2.751436 CCACCTCACCCATTGGCG 60.751 66.667 0.00 0.00 33.59 5.69
810 3733 1.272769 GTATGTAGGGCGGTCATCTCC 59.727 57.143 0.00 0.00 0.00 3.71
841 3764 1.271934 CTCATCATCTGCCTCCTACCG 59.728 57.143 0.00 0.00 0.00 4.02
842 3765 1.043816 CATCATCTGCCTCCTACCGT 58.956 55.000 0.00 0.00 0.00 4.83
844 3767 0.755698 TCATCTGCCTCCTACCGTCC 60.756 60.000 0.00 0.00 0.00 4.79
970 3937 5.550232 TCATCACCAGAAATTCACATTCG 57.450 39.130 0.00 0.00 32.04 3.34
991 3971 1.490490 TCCTTGTTCTTGCACTGTCCT 59.510 47.619 0.00 0.00 0.00 3.85
1041 4048 1.094073 CGCAAGGAGGGAATGAGCTG 61.094 60.000 0.00 0.00 0.00 4.24
1042 4049 0.254178 GCAAGGAGGGAATGAGCTGA 59.746 55.000 0.00 0.00 0.00 4.26
1043 4050 1.133853 GCAAGGAGGGAATGAGCTGAT 60.134 52.381 0.00 0.00 0.00 2.90
1044 4051 2.573369 CAAGGAGGGAATGAGCTGATG 58.427 52.381 0.00 0.00 0.00 3.07
1045 4052 1.138568 AGGAGGGAATGAGCTGATGG 58.861 55.000 0.00 0.00 0.00 3.51
1046 4053 0.536915 GGAGGGAATGAGCTGATGGC 60.537 60.000 0.00 0.00 42.19 4.40
1047 4054 0.182061 GAGGGAATGAGCTGATGGCA 59.818 55.000 0.00 0.00 44.79 4.92
1401 11250 4.450053 AGCTGATCATCTTTTCTGGTAGC 58.550 43.478 0.00 0.00 0.00 3.58
1402 11251 4.080695 AGCTGATCATCTTTTCTGGTAGCA 60.081 41.667 0.00 0.00 0.00 3.49
1403 11252 4.034975 GCTGATCATCTTTTCTGGTAGCAC 59.965 45.833 0.00 0.00 0.00 4.40
1430 11279 7.674471 ACTAACTTTGCATTAAGAAGTCTCC 57.326 36.000 5.15 0.00 32.79 3.71
1433 11282 5.006386 ACTTTGCATTAAGAAGTCTCCCTG 58.994 41.667 5.15 0.00 0.00 4.45
1769 11640 2.611292 GAGGTCTCCATTGAATTCTGCG 59.389 50.000 7.05 0.00 0.00 5.18
1778 11661 1.447838 GAATTCTGCGCCGGAGACA 60.448 57.895 8.15 5.72 0.00 3.41
2055 11944 1.831736 AGAGCTGGTATGTGGTGGTAC 59.168 52.381 0.00 0.00 0.00 3.34
2056 11945 1.831736 GAGCTGGTATGTGGTGGTACT 59.168 52.381 0.00 0.00 0.00 2.73
2057 11946 1.555075 AGCTGGTATGTGGTGGTACTG 59.445 52.381 0.00 0.00 0.00 2.74
2059 11948 1.906574 CTGGTATGTGGTGGTACTGGT 59.093 52.381 0.00 0.00 0.00 4.00
2204 12667 6.697395 TGCTGTTAGTGCTGTAAGATAAGAA 58.303 36.000 0.00 0.00 34.07 2.52
2228 12695 1.876849 AGATGCAGTCACTCCAGGAT 58.123 50.000 0.00 0.00 0.00 3.24
2229 12696 3.037851 AGATGCAGTCACTCCAGGATA 57.962 47.619 0.00 0.00 0.00 2.59
2230 12697 2.964464 AGATGCAGTCACTCCAGGATAG 59.036 50.000 0.00 0.00 0.00 2.08
2313 12792 4.760715 CAGATTGCAGAAATCCTAGATGGG 59.239 45.833 0.00 0.00 45.10 4.00
2500 12984 1.581447 CAAGTTTTCCTGCTCGCCC 59.419 57.895 0.00 0.00 0.00 6.13
2538 13022 0.716108 CGTGGCGTTCAGACATCTTC 59.284 55.000 0.00 0.00 41.88 2.87
2544 13028 1.429463 GTTCAGACATCTTCGGCGTT 58.571 50.000 6.85 0.00 0.00 4.84
2546 13030 2.163818 TCAGACATCTTCGGCGTTTT 57.836 45.000 6.85 0.00 0.00 2.43
2547 13031 2.066262 TCAGACATCTTCGGCGTTTTC 58.934 47.619 6.85 0.00 0.00 2.29
2550 13034 2.875933 AGACATCTTCGGCGTTTTCAAA 59.124 40.909 6.85 0.00 0.00 2.69
2551 13035 3.502211 AGACATCTTCGGCGTTTTCAAAT 59.498 39.130 6.85 0.00 0.00 2.32
2730 16930 6.729187 AGAGCACAAAACAGACTATTGAAAC 58.271 36.000 0.00 0.00 0.00 2.78
2731 16931 6.543831 AGAGCACAAAACAGACTATTGAAACT 59.456 34.615 0.00 0.00 0.00 2.66
2732 16932 6.498304 AGCACAAAACAGACTATTGAAACTG 58.502 36.000 0.00 0.00 36.58 3.16
2733 16933 6.318648 AGCACAAAACAGACTATTGAAACTGA 59.681 34.615 0.00 0.00 34.88 3.41
2734 16934 6.634436 GCACAAAACAGACTATTGAAACTGAG 59.366 38.462 0.00 0.00 34.88 3.35
2735 16935 7.134815 CACAAAACAGACTATTGAAACTGAGG 58.865 38.462 0.00 0.00 34.88 3.86
2736 16936 6.263168 ACAAAACAGACTATTGAAACTGAGGG 59.737 38.462 0.00 0.00 34.88 4.30
2737 16937 5.825593 AACAGACTATTGAAACTGAGGGA 57.174 39.130 0.00 0.00 34.88 4.20
2738 16938 5.413309 ACAGACTATTGAAACTGAGGGAG 57.587 43.478 0.00 0.00 34.88 4.30
2744 16944 4.618920 ATTGAAACTGAGGGAGTACGTT 57.381 40.909 0.00 0.00 33.09 3.99
2750 16950 2.036862 ACTGAGGGAGTACGTTTGTTCC 59.963 50.000 0.00 0.00 30.86 3.62
2754 16954 3.683365 GGGAGTACGTTTGTTCCCTTA 57.317 47.619 15.22 0.00 40.62 2.69
2756 16956 4.582869 GGGAGTACGTTTGTTCCCTTAAT 58.417 43.478 15.22 0.00 40.62 1.40
2757 16957 5.733676 GGGAGTACGTTTGTTCCCTTAATA 58.266 41.667 15.22 0.00 40.62 0.98
2758 16958 5.582269 GGGAGTACGTTTGTTCCCTTAATAC 59.418 44.000 15.22 0.00 40.62 1.89
2759 16959 6.165577 GGAGTACGTTTGTTCCCTTAATACA 58.834 40.000 0.00 0.00 0.00 2.29
2760 16960 6.650390 GGAGTACGTTTGTTCCCTTAATACAA 59.350 38.462 0.00 0.00 0.00 2.41
2761 16961 7.173047 GGAGTACGTTTGTTCCCTTAATACAAA 59.827 37.037 0.00 0.00 38.90 2.83
2762 16962 8.091385 AGTACGTTTGTTCCCTTAATACAAAG 57.909 34.615 0.00 0.00 41.04 2.77
2763 16963 6.947644 ACGTTTGTTCCCTTAATACAAAGT 57.052 33.333 0.00 0.00 41.04 2.66
2764 16964 7.337480 ACGTTTGTTCCCTTAATACAAAGTT 57.663 32.000 0.00 0.00 41.04 2.66
2765 16965 7.197703 ACGTTTGTTCCCTTAATACAAAGTTG 58.802 34.615 0.00 0.00 41.04 3.16
2766 16966 6.639279 CGTTTGTTCCCTTAATACAAAGTTGG 59.361 38.462 0.00 0.00 41.04 3.77
2767 16967 6.658188 TTGTTCCCTTAATACAAAGTTGGG 57.342 37.500 0.00 0.00 34.76 4.12
2768 16968 5.707495 TGTTCCCTTAATACAAAGTTGGGT 58.293 37.500 0.00 0.00 35.00 4.51
2769 16969 5.771165 TGTTCCCTTAATACAAAGTTGGGTC 59.229 40.000 0.00 0.00 35.00 4.46
2770 16970 5.586155 TCCCTTAATACAAAGTTGGGTCA 57.414 39.130 0.00 0.00 35.00 4.02
2771 16971 6.147437 TCCCTTAATACAAAGTTGGGTCAT 57.853 37.500 0.00 0.00 35.00 3.06
2772 16972 6.184789 TCCCTTAATACAAAGTTGGGTCATC 58.815 40.000 0.00 0.00 35.00 2.92
2773 16973 6.011981 TCCCTTAATACAAAGTTGGGTCATCT 60.012 38.462 0.00 0.00 35.00 2.90
2774 16974 7.183112 TCCCTTAATACAAAGTTGGGTCATCTA 59.817 37.037 0.00 0.00 35.00 1.98
2775 16975 7.998964 CCCTTAATACAAAGTTGGGTCATCTAT 59.001 37.037 0.00 0.00 0.00 1.98
2776 16976 9.408648 CCTTAATACAAAGTTGGGTCATCTATT 57.591 33.333 0.00 0.00 0.00 1.73
2780 16980 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2781 16981 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2782 16982 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2783 16983 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2784 16984 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2785 16985 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2786 16986 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2787 16987 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2788 16988 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2789 16989 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2790 16990 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2791 16991 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2792 16992 2.504175 TCTATTTTGGAACGGAGGGAGG 59.496 50.000 0.00 0.00 0.00 4.30
2793 16993 0.331616 ATTTTGGAACGGAGGGAGGG 59.668 55.000 0.00 0.00 0.00 4.30
2794 16994 0.768997 TTTTGGAACGGAGGGAGGGA 60.769 55.000 0.00 0.00 0.00 4.20
2795 16995 1.198759 TTTGGAACGGAGGGAGGGAG 61.199 60.000 0.00 0.00 0.00 4.30
2808 17008 2.827921 GGGAGGGAGTACGTTTGTTCTA 59.172 50.000 0.00 0.00 0.00 2.10
2896 17135 3.452627 ACTCAGTTACTCCCTTATGCCTG 59.547 47.826 0.00 0.00 0.00 4.85
2916 17155 2.564062 TGGTTGCCTACGCTAGTTTACT 59.436 45.455 0.00 0.00 35.36 2.24
2959 17205 7.642669 TCAGATTCTAGAAGCACAACTTTTTG 58.357 34.615 21.97 8.66 39.29 2.44
3000 17253 2.931969 GCTTTTGAAAAGCACAGCAAGT 59.068 40.909 31.21 0.00 42.56 3.16
3050 17308 9.654663 CTATTTGCCTAGATGTATAAAGGTACC 57.345 37.037 2.73 2.73 0.00 3.34
3051 17309 5.717078 TGCCTAGATGTATAAAGGTACCG 57.283 43.478 6.18 0.00 0.00 4.02
3065 17323 0.250166 GTACCGAGTTGCCAGTTGGT 60.250 55.000 9.44 9.44 42.31 3.67
3075 17333 1.944024 TGCCAGTTGGTTTAACTCACG 59.056 47.619 0.00 0.00 46.55 4.35
3078 17336 3.065648 GCCAGTTGGTTTAACTCACGAAA 59.934 43.478 0.00 0.00 46.55 3.46
3079 17337 4.788521 GCCAGTTGGTTTAACTCACGAAAG 60.789 45.833 0.00 0.00 46.55 2.62
3080 17338 4.261031 CCAGTTGGTTTAACTCACGAAAGG 60.261 45.833 0.00 0.00 46.55 3.11
3081 17339 4.334481 CAGTTGGTTTAACTCACGAAAGGT 59.666 41.667 0.00 0.00 46.55 3.50
3082 17340 4.334481 AGTTGGTTTAACTCACGAAAGGTG 59.666 41.667 0.00 0.00 46.55 4.00
3083 17341 5.858947 AGTTGGTTTAACTCACGAAAGGTGA 60.859 40.000 0.00 0.00 46.55 4.02
3094 17352 4.568152 ACGAAAGGTGACAAAATCAAGG 57.432 40.909 0.00 0.00 39.72 3.61
3095 17353 3.317993 ACGAAAGGTGACAAAATCAAGGG 59.682 43.478 0.00 0.00 39.72 3.95
3096 17354 3.317993 CGAAAGGTGACAAAATCAAGGGT 59.682 43.478 0.00 0.00 39.72 4.34
3097 17355 4.517453 CGAAAGGTGACAAAATCAAGGGTA 59.483 41.667 0.00 0.00 39.72 3.69
3098 17356 5.183140 CGAAAGGTGACAAAATCAAGGGTAT 59.817 40.000 0.00 0.00 39.72 2.73
3099 17357 6.590234 AAAGGTGACAAAATCAAGGGTATC 57.410 37.500 0.00 0.00 39.72 2.24
3100 17358 5.520748 AGGTGACAAAATCAAGGGTATCT 57.479 39.130 0.00 0.00 39.72 1.98
3101 17359 5.892348 AGGTGACAAAATCAAGGGTATCTT 58.108 37.500 0.00 0.00 39.72 2.40
3102 17360 6.314917 AGGTGACAAAATCAAGGGTATCTTT 58.685 36.000 0.00 0.00 39.72 2.52
3103 17361 7.466804 AGGTGACAAAATCAAGGGTATCTTTA 58.533 34.615 0.00 0.00 39.72 1.85
3104 17362 7.611855 AGGTGACAAAATCAAGGGTATCTTTAG 59.388 37.037 0.00 0.00 39.72 1.85
3105 17363 7.251281 GTGACAAAATCAAGGGTATCTTTAGC 58.749 38.462 0.00 0.00 39.72 3.09
3106 17364 7.121315 GTGACAAAATCAAGGGTATCTTTAGCT 59.879 37.037 0.00 0.00 39.72 3.32
3107 17365 7.336931 TGACAAAATCAAGGGTATCTTTAGCTC 59.663 37.037 0.00 0.00 33.02 4.09
3108 17366 6.316390 ACAAAATCAAGGGTATCTTTAGCTCG 59.684 38.462 0.00 0.00 32.41 5.03
3109 17367 3.454371 TCAAGGGTATCTTTAGCTCGC 57.546 47.619 0.00 0.00 32.41 5.03
3110 17368 3.031736 TCAAGGGTATCTTTAGCTCGCT 58.968 45.455 0.00 0.00 32.41 4.93
3111 17369 4.212716 TCAAGGGTATCTTTAGCTCGCTA 58.787 43.478 0.00 0.00 32.41 4.26
3112 17370 4.647853 TCAAGGGTATCTTTAGCTCGCTAA 59.352 41.667 7.25 7.25 36.81 3.09
3113 17371 5.304614 TCAAGGGTATCTTTAGCTCGCTAAT 59.695 40.000 11.73 1.09 38.20 1.73
3114 17372 5.810080 AGGGTATCTTTAGCTCGCTAATT 57.190 39.130 11.73 4.04 38.20 1.40
3115 17373 6.176014 AGGGTATCTTTAGCTCGCTAATTT 57.824 37.500 11.73 3.74 38.20 1.82
3116 17374 6.224584 AGGGTATCTTTAGCTCGCTAATTTC 58.775 40.000 11.73 2.97 38.20 2.17
3117 17375 5.989777 GGGTATCTTTAGCTCGCTAATTTCA 59.010 40.000 11.73 0.00 38.20 2.69
3118 17376 6.146347 GGGTATCTTTAGCTCGCTAATTTCAG 59.854 42.308 11.73 6.91 38.20 3.02
3119 17377 6.924060 GGTATCTTTAGCTCGCTAATTTCAGA 59.076 38.462 11.73 11.41 38.20 3.27
3120 17378 7.600752 GGTATCTTTAGCTCGCTAATTTCAGAT 59.399 37.037 19.39 19.39 38.20 2.90
3121 17379 8.983724 GTATCTTTAGCTCGCTAATTTCAGATT 58.016 33.333 20.12 10.60 38.20 2.40
3122 17380 7.849804 TCTTTAGCTCGCTAATTTCAGATTT 57.150 32.000 11.73 0.00 38.20 2.17
3123 17381 8.942338 TCTTTAGCTCGCTAATTTCAGATTTA 57.058 30.769 11.73 0.00 38.20 1.40
3124 17382 9.547753 TCTTTAGCTCGCTAATTTCAGATTTAT 57.452 29.630 11.73 0.00 38.20 1.40
3126 17384 9.935682 TTTAGCTCGCTAATTTCAGATTTATTG 57.064 29.630 11.73 0.00 38.20 1.90
3127 17385 7.792374 AGCTCGCTAATTTCAGATTTATTGA 57.208 32.000 0.00 0.00 0.00 2.57
3128 17386 8.213518 AGCTCGCTAATTTCAGATTTATTGAA 57.786 30.769 0.00 0.00 33.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 2814 2.120718 ACCAGAACGGGCTCTCCT 59.879 61.111 0.00 0.00 40.22 3.69
140 2881 4.214971 AGAACATGTGATGTGAAAGTCAGC 59.785 41.667 0.00 0.00 44.07 4.26
176 2920 0.455802 CGATCGATGCCATCTCTCGG 60.456 60.000 10.26 0.00 33.38 4.63
182 2926 3.904136 ATTTTTCCGATCGATGCCATC 57.096 42.857 18.66 0.00 0.00 3.51
188 2932 8.673711 TCAAACTTGATAATTTTTCCGATCGAT 58.326 29.630 18.66 0.00 31.01 3.59
197 2941 9.252962 CTGTTCAGCTCAAACTTGATAATTTTT 57.747 29.630 9.32 0.00 36.46 1.94
291 3040 3.771479 AGTCATTATGAGGAGCAGTGTCA 59.229 43.478 0.00 0.00 0.00 3.58
346 3142 4.560819 GCTCACAAGATTCGTTGACTAGAG 59.439 45.833 0.00 0.00 0.00 2.43
372 3168 3.044305 GGCACGAGTGACCACTGC 61.044 66.667 7.47 5.92 42.66 4.40
398 3194 4.633565 TGCAAACATTTCTGGAACCAAAAC 59.366 37.500 0.00 0.00 0.00 2.43
450 3246 9.654663 ACTTTCAGAAGGTACACATAGATAAAC 57.345 33.333 0.00 0.00 37.19 2.01
571 3367 1.764723 AGTATCTATGCACAGCAGCCA 59.235 47.619 0.00 0.00 43.65 4.75
703 3606 1.478105 GTTTGGATTGGCATGGACTCC 59.522 52.381 0.00 0.00 0.00 3.85
782 3695 0.388649 CGCCCTACATACGCATCTCC 60.389 60.000 0.00 0.00 0.00 3.71
810 3733 0.935898 GATGATGAGCTTGTCTGCGG 59.064 55.000 0.00 0.00 38.13 5.69
970 3937 1.604278 GGACAGTGCAAGAACAAGGAC 59.396 52.381 0.00 0.00 0.00 3.85
1046 4053 5.686771 CGTAGGATAACATGCATCGTATG 57.313 43.478 0.00 11.72 0.00 2.39
1340 11186 2.739609 GCAGCTGAGCTTTGTTTGGTTT 60.740 45.455 20.43 0.00 36.40 3.27
1401 11250 8.856490 ACTTCTTAATGCAAAGTTAGTTTGTG 57.144 30.769 13.23 0.00 46.44 3.33
1402 11251 8.903820 AGACTTCTTAATGCAAAGTTAGTTTGT 58.096 29.630 13.23 0.00 46.44 2.83
1430 11279 4.021719 AGGTCAATCAGAATTGTTTGCAGG 60.022 41.667 0.00 0.00 42.46 4.85
1433 11282 7.599998 ACATAAAGGTCAATCAGAATTGTTTGC 59.400 33.333 0.00 0.00 42.46 3.68
1769 11640 4.522971 GGAGTCATTGTCTCCGGC 57.477 61.111 13.10 0.00 41.36 6.13
1778 11661 5.745312 TTCATGTACAGTCTGGAGTCATT 57.255 39.130 4.53 0.00 0.00 2.57
2056 11945 1.675219 GAACTGGAACGGGCTACCA 59.325 57.895 0.00 0.00 40.47 3.25
2057 11946 1.078637 GGAACTGGAACGGGCTACC 60.079 63.158 0.00 0.00 40.47 3.18
2059 11948 0.543410 TCTGGAACTGGAACGGGCTA 60.543 55.000 0.00 0.00 40.47 3.93
2204 12667 3.387374 CCTGGAGTGACTGCATCTATCTT 59.613 47.826 7.39 0.00 30.16 2.40
2228 12695 5.155161 ACCCTGTTGCCATGATATCTACTA 58.845 41.667 3.98 0.00 0.00 1.82
2229 12696 3.976654 ACCCTGTTGCCATGATATCTACT 59.023 43.478 3.98 0.00 0.00 2.57
2230 12697 4.357918 ACCCTGTTGCCATGATATCTAC 57.642 45.455 3.98 0.00 0.00 2.59
2313 12792 0.392998 AATCATGTGACCCTGCGTCC 60.393 55.000 0.00 0.00 41.18 4.79
2519 13003 0.716108 GAAGATGTCTGAACGCCACG 59.284 55.000 0.00 0.00 0.00 4.94
2612 16803 4.711846 TCTTCTGAAGGTGCTAAGATGCTA 59.288 41.667 16.83 0.00 0.00 3.49
2730 16930 2.612221 GGGAACAAACGTACTCCCTCAG 60.612 54.545 14.03 0.00 43.74 3.35
2731 16931 1.345415 GGGAACAAACGTACTCCCTCA 59.655 52.381 14.03 0.00 43.74 3.86
2732 16932 2.090400 GGGAACAAACGTACTCCCTC 57.910 55.000 14.03 0.00 43.74 4.30
2734 16934 2.556144 AAGGGAACAAACGTACTCCC 57.444 50.000 13.63 13.63 46.94 4.30
2735 16935 6.165577 TGTATTAAGGGAACAAACGTACTCC 58.834 40.000 0.00 0.00 0.00 3.85
2736 16936 7.656707 TTGTATTAAGGGAACAAACGTACTC 57.343 36.000 0.00 0.00 30.54 2.59
2737 16937 7.716560 ACTTTGTATTAAGGGAACAAACGTACT 59.283 33.333 0.00 0.00 37.99 2.73
2738 16938 7.864686 ACTTTGTATTAAGGGAACAAACGTAC 58.135 34.615 0.00 0.00 37.99 3.67
2744 16944 6.137559 ACCCAACTTTGTATTAAGGGAACAA 58.862 36.000 0.00 0.00 38.21 2.83
2750 16950 8.980481 ATAGATGACCCAACTTTGTATTAAGG 57.020 34.615 0.00 0.00 0.00 2.69
2754 16954 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
2756 16956 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2757 16957 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2758 16958 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2759 16959 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2760 16960 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2761 16961 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2762 16962 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2763 16963 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2764 16964 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2765 16965 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2766 16966 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2767 16967 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2768 16968 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2769 16969 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2770 16970 3.136626 CCTCCCTCCGTTCCAAAATAGAT 59.863 47.826 0.00 0.00 0.00 1.98
2771 16971 2.504175 CCTCCCTCCGTTCCAAAATAGA 59.496 50.000 0.00 0.00 0.00 1.98
2772 16972 2.421529 CCCTCCCTCCGTTCCAAAATAG 60.422 54.545 0.00 0.00 0.00 1.73
2773 16973 1.562475 CCCTCCCTCCGTTCCAAAATA 59.438 52.381 0.00 0.00 0.00 1.40
2774 16974 0.331616 CCCTCCCTCCGTTCCAAAAT 59.668 55.000 0.00 0.00 0.00 1.82
2775 16975 0.768997 TCCCTCCCTCCGTTCCAAAA 60.769 55.000 0.00 0.00 0.00 2.44
2776 16976 1.151987 TCCCTCCCTCCGTTCCAAA 60.152 57.895 0.00 0.00 0.00 3.28
2777 16977 1.612442 CTCCCTCCCTCCGTTCCAA 60.612 63.158 0.00 0.00 0.00 3.53
2778 16978 1.512201 TACTCCCTCCCTCCGTTCCA 61.512 60.000 0.00 0.00 0.00 3.53
2779 16979 1.042003 GTACTCCCTCCCTCCGTTCC 61.042 65.000 0.00 0.00 0.00 3.62
2780 16980 1.382692 CGTACTCCCTCCCTCCGTTC 61.383 65.000 0.00 0.00 0.00 3.95
2781 16981 1.379576 CGTACTCCCTCCCTCCGTT 60.380 63.158 0.00 0.00 0.00 4.44
2782 16982 2.147433 AACGTACTCCCTCCCTCCGT 62.147 60.000 0.00 0.00 0.00 4.69
2783 16983 0.969409 AAACGTACTCCCTCCCTCCG 60.969 60.000 0.00 0.00 0.00 4.63
2784 16984 0.535797 CAAACGTACTCCCTCCCTCC 59.464 60.000 0.00 0.00 0.00 4.30
2785 16985 1.264295 ACAAACGTACTCCCTCCCTC 58.736 55.000 0.00 0.00 0.00 4.30
2786 16986 1.622312 GAACAAACGTACTCCCTCCCT 59.378 52.381 0.00 0.00 0.00 4.20
2787 16987 1.622312 AGAACAAACGTACTCCCTCCC 59.378 52.381 0.00 0.00 0.00 4.30
2788 16988 4.401837 AGATAGAACAAACGTACTCCCTCC 59.598 45.833 0.00 0.00 0.00 4.30
2789 16989 5.105837 ACAGATAGAACAAACGTACTCCCTC 60.106 44.000 0.00 0.00 0.00 4.30
2790 16990 4.771054 ACAGATAGAACAAACGTACTCCCT 59.229 41.667 0.00 0.00 0.00 4.20
2791 16991 5.069501 ACAGATAGAACAAACGTACTCCC 57.930 43.478 0.00 0.00 0.00 4.30
2792 16992 9.962783 ATATTACAGATAGAACAAACGTACTCC 57.037 33.333 0.00 0.00 0.00 3.85
2896 17135 3.242549 AGTAAACTAGCGTAGGCAACC 57.757 47.619 10.48 0.00 43.41 3.77
2959 17205 8.699749 CAAAAGCAAAAGTTAGGCATTAGTAAC 58.300 33.333 2.04 0.00 0.00 2.50
3000 17253 2.037772 GCTCCCAGACAGAAGTTTCAGA 59.962 50.000 0.00 0.00 0.00 3.27
3050 17308 2.616842 AGTTAAACCAACTGGCAACTCG 59.383 45.455 0.00 0.00 46.01 4.18
3075 17333 4.937201 ACCCTTGATTTTGTCACCTTTC 57.063 40.909 0.00 0.00 36.32 2.62
3078 17336 5.520748 AGATACCCTTGATTTTGTCACCT 57.479 39.130 0.00 0.00 36.32 4.00
3079 17337 6.590234 AAAGATACCCTTGATTTTGTCACC 57.410 37.500 0.00 0.00 36.32 4.02
3080 17338 7.121315 AGCTAAAGATACCCTTGATTTTGTCAC 59.879 37.037 0.00 0.00 36.32 3.67
3081 17339 7.175104 AGCTAAAGATACCCTTGATTTTGTCA 58.825 34.615 0.00 0.00 34.79 3.58
3082 17340 7.466050 CGAGCTAAAGATACCCTTGATTTTGTC 60.466 40.741 0.00 0.00 34.79 3.18
3083 17341 6.316390 CGAGCTAAAGATACCCTTGATTTTGT 59.684 38.462 0.00 0.00 34.79 2.83
3084 17342 6.719365 CGAGCTAAAGATACCCTTGATTTTG 58.281 40.000 0.00 0.00 34.79 2.44
3085 17343 5.297029 GCGAGCTAAAGATACCCTTGATTTT 59.703 40.000 0.00 0.00 34.79 1.82
3086 17344 4.816925 GCGAGCTAAAGATACCCTTGATTT 59.183 41.667 0.00 0.00 34.79 2.17
3087 17345 4.101741 AGCGAGCTAAAGATACCCTTGATT 59.898 41.667 0.00 0.00 34.79 2.57
3088 17346 3.643792 AGCGAGCTAAAGATACCCTTGAT 59.356 43.478 0.00 0.00 34.79 2.57
3089 17347 3.031736 AGCGAGCTAAAGATACCCTTGA 58.968 45.455 0.00 0.00 34.79 3.02
3090 17348 3.460857 AGCGAGCTAAAGATACCCTTG 57.539 47.619 0.00 0.00 34.79 3.61
3091 17349 5.810080 ATTAGCGAGCTAAAGATACCCTT 57.190 39.130 19.66 0.00 41.21 3.95
3092 17350 5.810080 AATTAGCGAGCTAAAGATACCCT 57.190 39.130 19.66 0.28 41.21 4.34
3093 17351 5.989777 TGAAATTAGCGAGCTAAAGATACCC 59.010 40.000 19.66 7.41 41.21 3.69
3094 17352 6.924060 TCTGAAATTAGCGAGCTAAAGATACC 59.076 38.462 19.66 8.24 41.21 2.73
3095 17353 7.932120 TCTGAAATTAGCGAGCTAAAGATAC 57.068 36.000 19.66 11.00 41.21 2.24
3096 17354 9.547753 AAATCTGAAATTAGCGAGCTAAAGATA 57.452 29.630 20.79 10.44 41.21 1.98
3097 17355 8.443953 AAATCTGAAATTAGCGAGCTAAAGAT 57.556 30.769 19.66 18.33 41.21 2.40
3098 17356 7.849804 AAATCTGAAATTAGCGAGCTAAAGA 57.150 32.000 19.66 17.13 41.21 2.52
3100 17358 9.935682 CAATAAATCTGAAATTAGCGAGCTAAA 57.064 29.630 19.66 4.65 41.21 1.85
3101 17359 9.325198 TCAATAAATCTGAAATTAGCGAGCTAA 57.675 29.630 18.34 18.34 41.95 3.09
3102 17360 8.887036 TCAATAAATCTGAAATTAGCGAGCTA 57.113 30.769 0.00 0.00 0.00 3.32
3103 17361 7.792374 TCAATAAATCTGAAATTAGCGAGCT 57.208 32.000 2.25 2.25 0.00 4.09


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

AutoCloner maintained by Alex Coulton.