Multiple sequence alignment - TraesCS3B01G184600

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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 TraesCS3B01G184600 chr3B 100.000 3227 0 0 1 3227 200478069 200481295 0.000000e+00 5960
1 TraesCS3B01G184600 chr3B 79.070 215 33 10 1348 1553 200479338 200479549 1.560000e-28 137
2 TraesCS3B01G184600 chr3B 79.070 215 33 10 1270 1481 200479416 200479621 1.560000e-28 137
3 TraesCS3B01G184600 chr3B 82.353 119 15 2 1440 1552 200479355 200479473 7.370000e-17 99
4 TraesCS3B01G184600 chr3B 82.353 119 15 2 1287 1405 200479508 200479620 7.370000e-17 99
5 TraesCS3B01G184600 chr3D 92.082 3170 120 61 121 3227 137008736 137005635 0.000000e+00 4342
6 TraesCS3B01G184600 chr3D 81.364 220 32 7 1341 1556 137007602 137007388 1.540000e-38 171
7 TraesCS3B01G184600 chr3D 87.719 114 12 2 1440 1552 137007579 137007467 7.260000e-27 132
8 TraesCS3B01G184600 chr3D 84.874 119 12 2 1287 1405 137007432 137007320 7.320000e-22 115
9 TraesCS3B01G184600 chr3A 92.035 2988 113 55 84 3014 155056601 155059520 0.000000e+00 4084
10 TraesCS3B01G184600 chr3A 84.874 119 12 2 1287 1405 155057925 155058037 7.320000e-22 115
11 TraesCS3B01G184600 chr5A 95.789 95 3 1 88 182 644821028 644821121 5.580000e-33 152
12 TraesCS3B01G184600 chr5A 89.381 113 7 4 69 179 650138213 650138104 1.560000e-28 137
13 TraesCS3B01G184600 chr5D 97.701 87 2 0 82 168 446400810 446400724 2.010000e-32 150
14 TraesCS3B01G184600 chr5D 95.604 91 2 2 88 177 521846310 521846221 9.330000e-31 145
15 TraesCS3B01G184600 chr5D 93.069 101 4 3 88 186 522112144 522112045 9.330000e-31 145
16 TraesCS3B01G184600 chr5B 94.565 92 5 0 84 175 544329729 544329638 3.360000e-30 143
17 TraesCS3B01G184600 chr5B 92.929 99 5 2 82 178 650023824 650023922 3.360000e-30 143
18 TraesCS3B01G184600 chr5B 94.565 92 5 0 88 179 658381120 658381029 3.360000e-30 143


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 TraesCS3B01G184600 chr3B 200478069 200481295 3226 False 1286.4 5960 84.56920 1 3227 5 chr3B.!!$F1 3226
1 TraesCS3B01G184600 chr3D 137005635 137008736 3101 True 1190.0 4342 86.50975 121 3227 4 chr3D.!!$R1 3106
2 TraesCS3B01G184600 chr3A 155056601 155059520 2919 False 2099.5 4084 88.45450 84 3014 2 chr3A.!!$F1 2930

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
794 835 0.110486 GAAAAGCACCTCCACCTCCA 59.890 55.0 0.0 0.0 0.0 3.86 F
829 870 0.171231 CGCAGCAGCTCACTACACTA 59.829 55.0 0.0 0.0 39.1 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2140 1.152881 GTCCACCTCCATCATGGCC 60.153 63.158 0.0 0.0 37.47 5.36 R
2245 2311 1.345415 TCTTACAGTTCAACCCCCGAC 59.655 52.381 0.0 0.0 0.00 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
19 20 4.056125 CGTGCGCACTCCTCCAGA 62.056 66.667 35.27 0.00 0.00 3.86
31 32 3.233355 CTCCAGAGGAAACCGTTGG 57.767 57.895 0.00 0.00 34.66 3.77
32 33 0.955919 CTCCAGAGGAAACCGTTGGC 60.956 60.000 0.00 0.00 33.83 4.52
33 34 1.971695 CCAGAGGAAACCGTTGGCC 60.972 63.158 0.00 0.00 0.00 5.36
34 35 2.032071 AGAGGAAACCGTTGGCCG 59.968 61.111 0.00 0.00 0.00 6.13
35 36 2.031465 GAGGAAACCGTTGGCCGA 59.969 61.111 0.00 0.00 39.56 5.54
36 37 2.281276 AGGAAACCGTTGGCCGAC 60.281 61.111 13.74 13.74 39.56 4.79
37 38 2.592287 GGAAACCGTTGGCCGACA 60.592 61.111 23.21 0.00 39.56 4.35
38 39 1.969589 GGAAACCGTTGGCCGACAT 60.970 57.895 23.21 7.51 39.56 3.06
39 40 1.209127 GAAACCGTTGGCCGACATG 59.791 57.895 23.21 15.12 39.56 3.21
40 41 1.228003 AAACCGTTGGCCGACATGA 60.228 52.632 23.21 0.00 39.56 3.07
41 42 1.234615 AAACCGTTGGCCGACATGAG 61.235 55.000 23.21 10.47 39.56 2.90
42 43 2.819595 CCGTTGGCCGACATGAGG 60.820 66.667 23.21 11.86 39.56 3.86
43 44 2.047274 CGTTGGCCGACATGAGGT 60.047 61.111 23.21 0.00 39.56 3.85
44 45 1.671054 CGTTGGCCGACATGAGGTT 60.671 57.895 23.21 0.00 39.56 3.50
45 46 1.875963 GTTGGCCGACATGAGGTTG 59.124 57.895 18.96 0.00 0.00 3.77
51 52 1.586422 CCGACATGAGGTTGGCTATG 58.414 55.000 0.00 0.00 44.11 2.23
52 53 1.138859 CCGACATGAGGTTGGCTATGA 59.861 52.381 0.00 0.00 44.11 2.15
53 54 2.477825 CGACATGAGGTTGGCTATGAG 58.522 52.381 0.00 0.00 0.00 2.90
54 55 2.159043 CGACATGAGGTTGGCTATGAGT 60.159 50.000 0.00 0.00 0.00 3.41
55 56 3.679917 CGACATGAGGTTGGCTATGAGTT 60.680 47.826 0.00 0.00 0.00 3.01
56 57 3.873952 GACATGAGGTTGGCTATGAGTTC 59.126 47.826 0.00 0.00 0.00 3.01
57 58 3.521126 ACATGAGGTTGGCTATGAGTTCT 59.479 43.478 0.00 0.00 0.00 3.01
58 59 4.716784 ACATGAGGTTGGCTATGAGTTCTA 59.283 41.667 0.00 0.00 0.00 2.10
59 60 5.367937 ACATGAGGTTGGCTATGAGTTCTAT 59.632 40.000 0.00 0.00 0.00 1.98
60 61 6.554982 ACATGAGGTTGGCTATGAGTTCTATA 59.445 38.462 0.00 0.00 0.00 1.31
61 62 6.656632 TGAGGTTGGCTATGAGTTCTATAG 57.343 41.667 0.00 0.00 0.00 1.31
62 63 5.540337 TGAGGTTGGCTATGAGTTCTATAGG 59.460 44.000 0.00 0.00 0.00 2.57
64 65 4.563786 GGTTGGCTATGAGTTCTATAGGCC 60.564 50.000 13.68 0.00 47.00 5.19
65 66 3.173965 TGGCTATGAGTTCTATAGGCCC 58.826 50.000 0.00 0.72 47.00 5.80
66 67 3.181406 TGGCTATGAGTTCTATAGGCCCT 60.181 47.826 0.00 0.00 47.00 5.19
67 68 3.196685 GGCTATGAGTTCTATAGGCCCTG 59.803 52.174 0.00 0.00 43.82 4.45
68 69 3.196685 GCTATGAGTTCTATAGGCCCTGG 59.803 52.174 0.00 0.00 0.00 4.45
69 70 2.868964 TGAGTTCTATAGGCCCTGGT 57.131 50.000 0.00 0.00 0.00 4.00
70 71 3.130734 TGAGTTCTATAGGCCCTGGTT 57.869 47.619 0.00 0.00 0.00 3.67
71 72 2.771943 TGAGTTCTATAGGCCCTGGTTG 59.228 50.000 0.00 0.00 0.00 3.77
72 73 3.039011 GAGTTCTATAGGCCCTGGTTGA 58.961 50.000 0.00 0.00 0.00 3.18
73 74 3.454812 GAGTTCTATAGGCCCTGGTTGAA 59.545 47.826 0.00 0.00 0.00 2.69
74 75 3.850173 AGTTCTATAGGCCCTGGTTGAAA 59.150 43.478 0.00 0.00 0.00 2.69
75 76 3.926058 TCTATAGGCCCTGGTTGAAAC 57.074 47.619 0.00 0.00 0.00 2.78
76 77 3.460825 TCTATAGGCCCTGGTTGAAACT 58.539 45.455 0.00 0.00 0.00 2.66
77 78 3.850173 TCTATAGGCCCTGGTTGAAACTT 59.150 43.478 0.00 0.00 0.00 2.66
78 79 3.542969 ATAGGCCCTGGTTGAAACTTT 57.457 42.857 0.00 0.00 0.00 2.66
79 80 1.413118 AGGCCCTGGTTGAAACTTTG 58.587 50.000 0.00 0.00 0.00 2.77
80 81 1.119684 GGCCCTGGTTGAAACTTTGT 58.880 50.000 0.00 0.00 0.00 2.83
81 82 2.091555 AGGCCCTGGTTGAAACTTTGTA 60.092 45.455 0.00 0.00 0.00 2.41
82 83 2.035449 GGCCCTGGTTGAAACTTTGTAC 59.965 50.000 0.00 0.00 0.00 2.90
89 90 4.097286 TGGTTGAAACTTTGTACAAGCTCC 59.903 41.667 8.56 5.35 40.07 4.70
93 94 1.779569 ACTTTGTACAAGCTCCGTCG 58.220 50.000 8.56 0.00 0.00 5.12
149 150 1.152096 AGACCCGGGTTCAAGTCCT 60.152 57.895 30.89 15.82 0.00 3.85
242 253 0.758734 GGATGATCATCACCCCGTCA 59.241 55.000 31.49 0.00 39.54 4.35
363 380 4.745620 GCTAAGATCTTGTAGCTTTACCCG 59.254 45.833 18.47 0.00 39.73 5.28
442 460 5.175856 CCGAGAGCAACTAGAAAATAATCGG 59.824 44.000 0.00 3.77 38.85 4.18
443 461 5.977725 CGAGAGCAACTAGAAAATAATCGGA 59.022 40.000 0.00 0.00 0.00 4.55
470 488 4.288626 TCAAATTAACCTACTCCTGCTGGT 59.711 41.667 9.73 0.00 34.23 4.00
505 530 3.004106 CAGCAGCAGCCAATAGATAAACC 59.996 47.826 0.00 0.00 43.56 3.27
508 533 4.147321 CAGCAGCCAATAGATAAACCCAT 58.853 43.478 0.00 0.00 0.00 4.00
509 534 4.217118 CAGCAGCCAATAGATAAACCCATC 59.783 45.833 0.00 0.00 0.00 3.51
519 544 3.654806 AGATAAACCCATCCTCATCCCTG 59.345 47.826 0.00 0.00 0.00 4.45
566 592 2.461110 CCGTACTGTCCATTGGCGC 61.461 63.158 0.00 0.00 0.00 6.53
790 831 0.250338 AGTCGAAAAGCACCTCCACC 60.250 55.000 0.00 0.00 0.00 4.61
794 835 0.110486 GAAAAGCACCTCCACCTCCA 59.890 55.000 0.00 0.00 0.00 3.86
795 836 0.178990 AAAAGCACCTCCACCTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
796 837 1.062488 AAAGCACCTCCACCTCCACT 61.062 55.000 0.00 0.00 0.00 4.00
797 838 1.484444 AAGCACCTCCACCTCCACTC 61.484 60.000 0.00 0.00 0.00 3.51
798 839 2.960688 GCACCTCCACCTCCACTCC 61.961 68.421 0.00 0.00 0.00 3.85
800 841 2.122729 CCTCCACCTCCACTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
801 842 2.294078 CCTCCACCTCCACTCCCAC 61.294 68.421 0.00 0.00 0.00 4.61
802 843 1.229336 CTCCACCTCCACTCCCACT 60.229 63.158 0.00 0.00 0.00 4.00
803 844 0.838122 CTCCACCTCCACTCCCACTT 60.838 60.000 0.00 0.00 0.00 3.16
827 868 3.468007 CGCAGCAGCTCACTACAC 58.532 61.111 0.00 0.00 39.10 2.90
828 869 1.080230 CGCAGCAGCTCACTACACT 60.080 57.895 0.00 0.00 39.10 3.55
829 870 0.171231 CGCAGCAGCTCACTACACTA 59.829 55.000 0.00 0.00 39.10 2.74
830 871 1.634702 GCAGCAGCTCACTACACTAC 58.365 55.000 0.00 0.00 37.91 2.73
831 872 1.737363 GCAGCAGCTCACTACACTACC 60.737 57.143 0.00 0.00 37.91 3.18
832 873 1.134965 CAGCAGCTCACTACACTACCC 60.135 57.143 0.00 0.00 0.00 3.69
833 874 0.175989 GCAGCTCACTACACTACCCC 59.824 60.000 0.00 0.00 0.00 4.95
834 875 0.824759 CAGCTCACTACACTACCCCC 59.175 60.000 0.00 0.00 0.00 5.40
835 876 0.412244 AGCTCACTACACTACCCCCA 59.588 55.000 0.00 0.00 0.00 4.96
836 877 1.203262 AGCTCACTACACTACCCCCAA 60.203 52.381 0.00 0.00 0.00 4.12
837 878 1.207329 GCTCACTACACTACCCCCAAG 59.793 57.143 0.00 0.00 0.00 3.61
838 879 2.537143 CTCACTACACTACCCCCAAGT 58.463 52.381 0.00 0.00 0.00 3.16
839 880 3.705051 CTCACTACACTACCCCCAAGTA 58.295 50.000 0.00 0.00 0.00 2.24
840 881 3.434309 TCACTACACTACCCCCAAGTAC 58.566 50.000 0.00 0.00 0.00 2.73
841 882 2.498885 CACTACACTACCCCCAAGTACC 59.501 54.545 0.00 0.00 0.00 3.34
842 883 2.113807 CTACACTACCCCCAAGTACCC 58.886 57.143 0.00 0.00 0.00 3.69
843 884 0.194080 ACACTACCCCCAAGTACCCA 59.806 55.000 0.00 0.00 0.00 4.51
844 885 0.909623 CACTACCCCCAAGTACCCAG 59.090 60.000 0.00 0.00 0.00 4.45
896 943 2.854401 CGCACATGCCACCCAACAA 61.854 57.895 0.00 0.00 37.91 2.83
1337 1392 3.865830 GCCGGAGCAGCTTTACGC 61.866 66.667 5.05 0.00 39.53 4.42
1338 1393 2.434185 CCGGAGCAGCTTTACGCA 60.434 61.111 0.00 0.00 42.61 5.24
1339 1394 2.456119 CCGGAGCAGCTTTACGCAG 61.456 63.158 0.00 0.00 42.61 5.18
2220 2278 3.570212 AGGGTGCTTGGCTTCCGT 61.570 61.111 0.00 0.00 0.00 4.69
2227 2285 1.871772 CTTGGCTTCCGTTGCTGAG 59.128 57.895 0.00 0.00 0.00 3.35
2240 2300 2.670934 CTGAGCCGCAGCCAAGTT 60.671 61.111 0.00 0.00 41.25 2.66
2241 2301 2.669569 TGAGCCGCAGCCAAGTTC 60.670 61.111 0.00 0.00 41.25 3.01
2247 2313 3.056328 GCAGCCAAGTTCGGGGTC 61.056 66.667 0.00 0.00 32.88 4.46
2255 2321 4.710167 GTTCGGGGTCGGGGGTTG 62.710 72.222 0.00 0.00 36.95 3.77
2271 2337 5.474189 CGGGGGTTGAACTGTAAGAAATTAA 59.526 40.000 0.00 0.00 37.43 1.40
2273 2339 7.544622 GGGGGTTGAACTGTAAGAAATTAATC 58.455 38.462 0.00 0.00 37.43 1.75
2291 2357 7.961326 ATTAATCAAGGCAGGATTTTACAGT 57.039 32.000 8.61 0.00 36.45 3.55
2330 2412 2.871182 AGAATCGTGCGCTAGAATCA 57.129 45.000 9.73 0.00 0.00 2.57
2335 2417 0.578683 CGTGCGCTAGAATCATGTGG 59.421 55.000 9.73 0.00 0.00 4.17
2340 2422 3.561310 TGCGCTAGAATCATGTGGATTTC 59.439 43.478 9.73 0.00 46.17 2.17
2406 2489 6.690194 ATGAATTTGACATAGCCTGTTCTC 57.310 37.500 0.00 0.00 38.54 2.87
2424 2507 4.350368 TCTCCAGTAGCATGTTGAACAA 57.650 40.909 0.62 0.00 0.00 2.83
2433 2516 6.803320 AGTAGCATGTTGAACAAATTTCATCG 59.197 34.615 0.62 0.00 0.00 3.84
2437 2525 7.385752 AGCATGTTGAACAAATTTCATCGAAAT 59.614 29.630 0.62 0.00 43.07 2.17
2444 2532 8.924691 TGAACAAATTTCATCGAAATCATTTCC 58.075 29.630 4.47 0.00 40.77 3.13
2445 2533 8.830201 AACAAATTTCATCGAAATCATTTCCA 57.170 26.923 4.47 0.00 40.77 3.53
2446 2534 9.439500 AACAAATTTCATCGAAATCATTTCCAT 57.561 25.926 4.47 0.00 40.77 3.41
2447 2535 9.439500 ACAAATTTCATCGAAATCATTTCCATT 57.561 25.926 4.47 0.00 40.77 3.16
2451 2539 8.613613 TTTCATCGAAATCATTTCCATTTACG 57.386 30.769 4.47 0.00 36.30 3.18
2452 2540 6.724263 TCATCGAAATCATTTCCATTTACGG 58.276 36.000 4.47 0.00 36.30 4.02
2460 2548 5.885881 TCATTTCCATTTACGGTATGTTGC 58.114 37.500 0.00 0.00 0.00 4.17
2464 2552 3.013921 CCATTTACGGTATGTTGCCACT 58.986 45.455 0.00 0.00 0.00 4.00
2482 2570 5.046663 TGCCACTACAGATCTTACATGTTGA 60.047 40.000 2.30 3.47 0.00 3.18
2849 2937 1.141053 ACAGGGGCATACTTCCGAATC 59.859 52.381 0.00 0.00 0.00 2.52
2909 2997 8.914011 AGATTAATAAGAAAAAGTATGGTGGCC 58.086 33.333 0.00 0.00 0.00 5.36
2926 3014 2.497675 TGGCCAGTGTTGACTAGAGATC 59.502 50.000 0.00 0.00 0.00 2.75
3043 3131 1.985473 TGAGCAGTTTGTGGCAGATT 58.015 45.000 0.00 0.00 0.00 2.40
3055 3143 0.035820 GGCAGATTACAACGGGACCA 60.036 55.000 0.00 0.00 0.00 4.02
3057 3145 2.156098 GCAGATTACAACGGGACCAAA 58.844 47.619 0.00 0.00 0.00 3.28
3058 3146 2.161609 GCAGATTACAACGGGACCAAAG 59.838 50.000 0.00 0.00 0.00 2.77
3060 3148 3.818773 CAGATTACAACGGGACCAAAGTT 59.181 43.478 0.00 0.00 0.00 2.66
3061 3149 4.998672 CAGATTACAACGGGACCAAAGTTA 59.001 41.667 0.00 0.00 0.00 2.24
3062 3150 4.999311 AGATTACAACGGGACCAAAGTTAC 59.001 41.667 0.00 0.00 0.00 2.50
3066 3154 4.018490 ACAACGGGACCAAAGTTACTTTT 58.982 39.130 7.71 0.00 30.60 2.27
3067 3155 4.463539 ACAACGGGACCAAAGTTACTTTTT 59.536 37.500 7.71 0.00 30.60 1.94
3091 3179 9.979270 TTTTACTGCACATTGTTTATTTGTTTG 57.021 25.926 0.00 0.00 0.00 2.93
3092 3180 6.601741 ACTGCACATTGTTTATTTGTTTGG 57.398 33.333 0.00 0.00 0.00 3.28
3096 3184 6.478344 TGCACATTGTTTATTTGTTTGGAGTC 59.522 34.615 0.00 0.00 0.00 3.36
3106 3194 6.824305 ATTTGTTTGGAGTCAGGATTACAG 57.176 37.500 0.00 0.00 0.00 2.74
3107 3195 5.560722 TTGTTTGGAGTCAGGATTACAGA 57.439 39.130 0.00 0.00 0.00 3.41
3108 3196 4.894784 TGTTTGGAGTCAGGATTACAGAC 58.105 43.478 0.00 0.00 0.00 3.51
3109 3197 4.346709 TGTTTGGAGTCAGGATTACAGACA 59.653 41.667 0.00 0.00 34.80 3.41
3110 3198 5.163248 TGTTTGGAGTCAGGATTACAGACAA 60.163 40.000 0.00 0.00 34.80 3.18
3111 3199 4.537135 TGGAGTCAGGATTACAGACAAC 57.463 45.455 0.00 0.00 34.80 3.32
3112 3200 3.901222 TGGAGTCAGGATTACAGACAACA 59.099 43.478 0.00 0.00 34.80 3.33
3113 3201 4.346709 TGGAGTCAGGATTACAGACAACAA 59.653 41.667 0.00 0.00 34.80 2.83
3114 3202 5.163248 TGGAGTCAGGATTACAGACAACAAA 60.163 40.000 0.00 0.00 34.80 2.83
3115 3203 5.763204 GGAGTCAGGATTACAGACAACAAAA 59.237 40.000 0.00 0.00 34.80 2.44
3116 3204 6.431234 GGAGTCAGGATTACAGACAACAAAAT 59.569 38.462 0.00 0.00 34.80 1.82
3117 3205 7.040409 GGAGTCAGGATTACAGACAACAAAATT 60.040 37.037 0.00 0.00 34.80 1.82
3118 3206 8.237811 AGTCAGGATTACAGACAACAAAATTT 57.762 30.769 0.00 0.00 34.80 1.82
3119 3207 8.137437 AGTCAGGATTACAGACAACAAAATTTG 58.863 33.333 3.89 3.89 34.80 2.32
3155 3243 6.183359 CCAATCAAACTAAAATCGAAAGCACG 60.183 38.462 0.00 0.00 0.00 5.34
3163 3251 1.726853 ATCGAAAGCACGAGGGAAAG 58.273 50.000 0.00 0.00 45.22 2.62
3164 3252 0.391597 TCGAAAGCACGAGGGAAAGT 59.608 50.000 0.00 0.00 37.37 2.66
3165 3253 1.202604 TCGAAAGCACGAGGGAAAGTT 60.203 47.619 0.00 0.00 37.37 2.66
3166 3254 1.602377 CGAAAGCACGAGGGAAAGTTT 59.398 47.619 0.00 0.00 35.09 2.66
3167 3255 2.602217 CGAAAGCACGAGGGAAAGTTTG 60.602 50.000 0.00 0.00 35.09 2.93
3168 3256 2.052782 AAGCACGAGGGAAAGTTTGT 57.947 45.000 0.00 0.00 0.00 2.83
3169 3257 1.308998 AGCACGAGGGAAAGTTTGTG 58.691 50.000 0.00 0.00 32.88 3.33
3170 3258 0.310854 GCACGAGGGAAAGTTTGTGG 59.689 55.000 0.00 0.00 30.85 4.17
3172 3260 2.294074 CACGAGGGAAAGTTTGTGGAA 58.706 47.619 0.00 0.00 0.00 3.53
3173 3261 2.290641 CACGAGGGAAAGTTTGTGGAAG 59.709 50.000 0.00 0.00 0.00 3.46
3174 3262 2.092592 ACGAGGGAAAGTTTGTGGAAGT 60.093 45.455 0.00 0.00 0.00 3.01
3175 3263 3.135167 ACGAGGGAAAGTTTGTGGAAGTA 59.865 43.478 0.00 0.00 0.00 2.24
3176 3264 4.202430 ACGAGGGAAAGTTTGTGGAAGTAT 60.202 41.667 0.00 0.00 0.00 2.12
3177 3265 4.154195 CGAGGGAAAGTTTGTGGAAGTATG 59.846 45.833 0.00 0.00 0.00 2.39
3178 3266 3.826729 AGGGAAAGTTTGTGGAAGTATGC 59.173 43.478 0.00 0.00 0.00 3.14
3208 3296 2.691927 CTGCTCAACTGTCATGTGCTA 58.308 47.619 7.71 0.00 37.96 3.49
3216 3304 6.643388 TCAACTGTCATGTGCTATTCTACAT 58.357 36.000 0.00 0.00 37.99 2.29
3221 3309 8.883731 ACTGTCATGTGCTATTCTACATAAAAC 58.116 33.333 0.00 0.00 35.86 2.43
3222 3310 9.102757 CTGTCATGTGCTATTCTACATAAAACT 57.897 33.333 0.00 0.00 35.86 2.66
3223 3311 8.882736 TGTCATGTGCTATTCTACATAAAACTG 58.117 33.333 0.00 0.00 35.86 3.16
3224 3312 8.883731 GTCATGTGCTATTCTACATAAAACTGT 58.116 33.333 0.00 0.00 35.86 3.55
3225 3313 8.882736 TCATGTGCTATTCTACATAAAACTGTG 58.117 33.333 0.00 0.00 35.86 3.66
3226 3314 8.882736 CATGTGCTATTCTACATAAAACTGTGA 58.117 33.333 0.00 0.00 35.86 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.978723 CTCTGGAGGAGTGCGCACG 62.979 68.421 32.94 17.96 37.30 5.34
3 4 2.125753 CTCTGGAGGAGTGCGCAC 60.126 66.667 32.79 32.79 37.30 5.34
13 14 0.955919 GCCAACGGTTTCCTCTGGAG 60.956 60.000 0.00 0.00 31.21 3.86
14 15 1.072505 GCCAACGGTTTCCTCTGGA 59.927 57.895 0.00 0.00 0.00 3.86
15 16 1.971695 GGCCAACGGTTTCCTCTGG 60.972 63.158 0.00 0.00 0.00 3.86
16 17 2.325082 CGGCCAACGGTTTCCTCTG 61.325 63.158 2.24 0.00 39.42 3.35
17 18 2.032071 CGGCCAACGGTTTCCTCT 59.968 61.111 2.24 0.00 39.42 3.69
18 19 2.031465 TCGGCCAACGGTTTCCTC 59.969 61.111 2.24 0.00 44.45 3.71
19 20 2.281276 GTCGGCCAACGGTTTCCT 60.281 61.111 2.24 0.00 44.45 3.36
20 21 1.969589 ATGTCGGCCAACGGTTTCC 60.970 57.895 2.24 0.00 44.45 3.13
21 22 1.209127 CATGTCGGCCAACGGTTTC 59.791 57.895 2.24 0.00 44.45 2.78
22 23 1.228003 TCATGTCGGCCAACGGTTT 60.228 52.632 2.24 0.00 44.45 3.27
23 24 1.671054 CTCATGTCGGCCAACGGTT 60.671 57.895 2.24 0.00 44.45 4.44
24 25 2.047274 CTCATGTCGGCCAACGGT 60.047 61.111 2.24 0.00 44.45 4.83
25 26 2.819595 CCTCATGTCGGCCAACGG 60.820 66.667 2.24 0.00 44.45 4.44
26 27 1.671054 AACCTCATGTCGGCCAACG 60.671 57.895 2.24 0.00 46.11 4.10
27 28 1.586154 CCAACCTCATGTCGGCCAAC 61.586 60.000 2.24 0.00 0.00 3.77
28 29 1.303236 CCAACCTCATGTCGGCCAA 60.303 57.895 2.24 0.00 0.00 4.52
29 30 2.350895 CCAACCTCATGTCGGCCA 59.649 61.111 2.24 0.00 0.00 5.36
30 31 2.252072 TAGCCAACCTCATGTCGGCC 62.252 60.000 0.00 0.00 44.06 6.13
31 32 0.179045 ATAGCCAACCTCATGTCGGC 60.179 55.000 0.00 0.00 43.31 5.54
32 33 1.138859 TCATAGCCAACCTCATGTCGG 59.861 52.381 0.00 0.00 0.00 4.79
33 34 2.159043 ACTCATAGCCAACCTCATGTCG 60.159 50.000 0.00 0.00 0.00 4.35
34 35 3.550437 ACTCATAGCCAACCTCATGTC 57.450 47.619 0.00 0.00 0.00 3.06
35 36 3.521126 AGAACTCATAGCCAACCTCATGT 59.479 43.478 0.00 0.00 0.00 3.21
36 37 4.148128 AGAACTCATAGCCAACCTCATG 57.852 45.455 0.00 0.00 0.00 3.07
37 38 6.212388 CCTATAGAACTCATAGCCAACCTCAT 59.788 42.308 0.00 0.00 0.00 2.90
38 39 5.540337 CCTATAGAACTCATAGCCAACCTCA 59.460 44.000 0.00 0.00 0.00 3.86
39 40 5.567823 GCCTATAGAACTCATAGCCAACCTC 60.568 48.000 0.00 0.00 0.00 3.85
40 41 4.284746 GCCTATAGAACTCATAGCCAACCT 59.715 45.833 0.00 0.00 0.00 3.50
41 42 4.563786 GGCCTATAGAACTCATAGCCAACC 60.564 50.000 0.00 0.00 0.00 3.77
42 43 4.563786 GGGCCTATAGAACTCATAGCCAAC 60.564 50.000 0.84 0.00 30.28 3.77
43 44 3.583086 GGGCCTATAGAACTCATAGCCAA 59.417 47.826 0.84 0.00 30.28 4.52
44 45 3.173965 GGGCCTATAGAACTCATAGCCA 58.826 50.000 0.84 0.00 30.28 4.75
45 46 3.196685 CAGGGCCTATAGAACTCATAGCC 59.803 52.174 5.28 2.59 0.00 3.93
46 47 3.196685 CCAGGGCCTATAGAACTCATAGC 59.803 52.174 5.28 0.00 0.00 2.97
47 48 4.421131 ACCAGGGCCTATAGAACTCATAG 58.579 47.826 5.28 0.00 0.00 2.23
48 49 4.487282 ACCAGGGCCTATAGAACTCATA 57.513 45.455 5.28 0.00 0.00 2.15
49 50 3.352611 ACCAGGGCCTATAGAACTCAT 57.647 47.619 5.28 0.00 0.00 2.90
50 51 2.771943 CAACCAGGGCCTATAGAACTCA 59.228 50.000 5.28 0.00 0.00 3.41
51 52 3.039011 TCAACCAGGGCCTATAGAACTC 58.961 50.000 5.28 0.00 0.00 3.01
52 53 3.130734 TCAACCAGGGCCTATAGAACT 57.869 47.619 5.28 0.00 0.00 3.01
53 54 3.926058 TTCAACCAGGGCCTATAGAAC 57.074 47.619 5.28 0.00 0.00 3.01
54 55 3.850173 AGTTTCAACCAGGGCCTATAGAA 59.150 43.478 5.28 5.74 0.00 2.10
55 56 3.460825 AGTTTCAACCAGGGCCTATAGA 58.539 45.455 5.28 0.00 0.00 1.98
56 57 3.933861 AGTTTCAACCAGGGCCTATAG 57.066 47.619 5.28 0.00 0.00 1.31
57 58 4.202631 ACAAAGTTTCAACCAGGGCCTATA 60.203 41.667 5.28 0.00 0.00 1.31
58 59 3.165071 CAAAGTTTCAACCAGGGCCTAT 58.835 45.455 5.28 0.00 0.00 2.57
59 60 2.091555 ACAAAGTTTCAACCAGGGCCTA 60.092 45.455 5.28 0.00 0.00 3.93
60 61 1.342975 ACAAAGTTTCAACCAGGGCCT 60.343 47.619 0.00 0.00 0.00 5.19
61 62 1.119684 ACAAAGTTTCAACCAGGGCC 58.880 50.000 0.00 0.00 0.00 5.80
62 63 2.691011 TGTACAAAGTTTCAACCAGGGC 59.309 45.455 0.00 0.00 0.00 5.19
63 64 4.736464 GCTTGTACAAAGTTTCAACCAGGG 60.736 45.833 10.03 0.00 0.00 4.45
64 65 4.097892 AGCTTGTACAAAGTTTCAACCAGG 59.902 41.667 10.03 0.00 0.00 4.45
65 66 5.248870 AGCTTGTACAAAGTTTCAACCAG 57.751 39.130 10.03 0.00 0.00 4.00
66 67 4.097286 GGAGCTTGTACAAAGTTTCAACCA 59.903 41.667 10.03 0.00 0.00 3.67
67 68 4.607955 GGAGCTTGTACAAAGTTTCAACC 58.392 43.478 10.03 1.94 0.00 3.77
68 69 4.201881 ACGGAGCTTGTACAAAGTTTCAAC 60.202 41.667 10.03 0.00 0.00 3.18
69 70 3.942748 ACGGAGCTTGTACAAAGTTTCAA 59.057 39.130 10.03 0.00 0.00 2.69
70 71 3.537580 ACGGAGCTTGTACAAAGTTTCA 58.462 40.909 10.03 0.00 0.00 2.69
71 72 3.362693 CGACGGAGCTTGTACAAAGTTTC 60.363 47.826 10.03 5.01 0.00 2.78
72 73 2.542595 CGACGGAGCTTGTACAAAGTTT 59.457 45.455 10.03 0.00 0.00 2.66
73 74 2.132762 CGACGGAGCTTGTACAAAGTT 58.867 47.619 10.03 2.21 0.00 2.66
74 75 1.068127 ACGACGGAGCTTGTACAAAGT 59.932 47.619 10.03 5.09 0.00 2.66
75 76 1.779569 ACGACGGAGCTTGTACAAAG 58.220 50.000 10.03 5.34 0.00 2.77
76 77 2.294233 ACTACGACGGAGCTTGTACAAA 59.706 45.455 7.09 0.00 0.00 2.83
77 78 1.881973 ACTACGACGGAGCTTGTACAA 59.118 47.619 7.09 8.28 0.00 2.41
78 79 1.466167 GACTACGACGGAGCTTGTACA 59.534 52.381 7.09 0.00 0.00 2.90
79 80 1.736681 AGACTACGACGGAGCTTGTAC 59.263 52.381 7.09 0.00 0.00 2.90
80 81 2.105006 AGACTACGACGGAGCTTGTA 57.895 50.000 7.09 0.00 0.00 2.41
81 82 2.008329 CTAGACTACGACGGAGCTTGT 58.992 52.381 7.09 0.00 0.00 3.16
82 83 1.331138 CCTAGACTACGACGGAGCTTG 59.669 57.143 7.09 6.50 0.00 4.01
89 90 2.611292 CCTAACCACCTAGACTACGACG 59.389 54.545 0.00 0.00 0.00 5.12
93 94 5.700373 CGAGTATCCTAACCACCTAGACTAC 59.300 48.000 0.00 0.00 0.00 2.73
171 172 3.751175 TGCCTGTTAATCGAGGAACAAAG 59.249 43.478 13.94 10.29 35.24 2.77
175 176 2.673368 CTGTGCCTGTTAATCGAGGAAC 59.327 50.000 5.49 5.49 38.31 3.62
176 177 2.354704 CCTGTGCCTGTTAATCGAGGAA 60.355 50.000 0.00 0.00 0.00 3.36
258 269 1.548132 CGGCGTTTTGGCTTGCTTTC 61.548 55.000 0.00 0.00 42.02 2.62
302 317 2.956987 CTGGTTCCGCTTTGGCTG 59.043 61.111 0.00 0.00 37.80 4.85
386 403 9.683069 GAGATACACTTTGTTGTTTCATTCATT 57.317 29.630 0.00 0.00 31.82 2.57
442 460 7.011857 CAGCAGGAGTAGGTTAATTTGATCTTC 59.988 40.741 0.00 0.00 0.00 2.87
443 461 6.825721 CAGCAGGAGTAGGTTAATTTGATCTT 59.174 38.462 0.00 0.00 0.00 2.40
470 488 3.300934 CTGCTGCGCTGGTAGGTGA 62.301 63.158 16.47 0.00 0.00 4.02
479 497 3.982316 TATTGGCTGCTGCTGCGCT 62.982 57.895 22.39 13.04 43.34 5.92
493 518 6.012157 AGGGATGAGGATGGGTTTATCTATTG 60.012 42.308 0.00 0.00 0.00 1.90
494 519 6.012157 CAGGGATGAGGATGGGTTTATCTATT 60.012 42.308 0.00 0.00 0.00 1.73
505 530 0.179026 CAGCACAGGGATGAGGATGG 60.179 60.000 0.00 0.00 33.82 3.51
508 533 1.614525 AGCAGCACAGGGATGAGGA 60.615 57.895 0.00 0.00 33.82 3.71
509 534 1.451567 CAGCAGCACAGGGATGAGG 60.452 63.158 0.00 0.00 33.82 3.86
790 831 0.108615 CGCAGTAAGTGGGAGTGGAG 60.109 60.000 0.00 0.00 41.74 3.86
794 835 2.261671 CGCGCAGTAAGTGGGAGT 59.738 61.111 8.75 0.00 42.75 3.85
795 836 3.188786 GCGCGCAGTAAGTGGGAG 61.189 66.667 29.10 0.00 42.75 4.30
796 837 3.932580 CTGCGCGCAGTAAGTGGGA 62.933 63.158 44.44 16.25 42.75 4.37
797 838 3.490759 CTGCGCGCAGTAAGTGGG 61.491 66.667 44.44 23.83 42.97 4.61
816 857 0.412244 TGGGGGTAGTGTAGTGAGCT 59.588 55.000 0.00 0.00 0.00 4.09
817 858 1.207329 CTTGGGGGTAGTGTAGTGAGC 59.793 57.143 0.00 0.00 0.00 4.26
818 859 2.537143 ACTTGGGGGTAGTGTAGTGAG 58.463 52.381 0.00 0.00 0.00 3.51
819 860 2.708037 ACTTGGGGGTAGTGTAGTGA 57.292 50.000 0.00 0.00 0.00 3.41
820 861 2.498885 GGTACTTGGGGGTAGTGTAGTG 59.501 54.545 0.00 0.00 0.00 2.74
822 863 2.113807 GGGTACTTGGGGGTAGTGTAG 58.886 57.143 0.00 0.00 0.00 2.74
823 864 1.436355 TGGGTACTTGGGGGTAGTGTA 59.564 52.381 0.00 0.00 0.00 2.90
824 865 0.194080 TGGGTACTTGGGGGTAGTGT 59.806 55.000 0.00 0.00 0.00 3.55
825 866 0.909623 CTGGGTACTTGGGGGTAGTG 59.090 60.000 0.00 0.00 0.00 2.74
826 867 0.912968 GCTGGGTACTTGGGGGTAGT 60.913 60.000 0.00 0.00 0.00 2.73
827 868 1.632965 GGCTGGGTACTTGGGGGTAG 61.633 65.000 0.00 0.00 0.00 3.18
828 869 1.617233 GGCTGGGTACTTGGGGGTA 60.617 63.158 0.00 0.00 0.00 3.69
829 870 2.939353 GGCTGGGTACTTGGGGGT 60.939 66.667 0.00 0.00 0.00 4.95
830 871 3.739613 GGGCTGGGTACTTGGGGG 61.740 72.222 0.00 0.00 0.00 5.40
831 872 2.938798 TGGGCTGGGTACTTGGGG 60.939 66.667 0.00 0.00 0.00 4.96
832 873 2.198304 GACTGGGCTGGGTACTTGGG 62.198 65.000 0.00 0.00 0.00 4.12
833 874 1.299976 GACTGGGCTGGGTACTTGG 59.700 63.158 0.00 0.00 0.00 3.61
834 875 1.299976 GGACTGGGCTGGGTACTTG 59.700 63.158 0.00 0.00 0.00 3.16
835 876 1.923909 GGGACTGGGCTGGGTACTT 60.924 63.158 0.00 0.00 0.00 2.24
836 877 2.285442 GGGACTGGGCTGGGTACT 60.285 66.667 0.00 0.00 0.00 2.73
837 878 3.408853 GGGGACTGGGCTGGGTAC 61.409 72.222 0.00 0.00 0.00 3.34
838 879 3.948360 TGGGGACTGGGCTGGGTA 61.948 66.667 0.00 0.00 0.00 3.69
896 943 4.497300 GGCACAATAATGCTGAACAATGT 58.503 39.130 0.00 0.00 45.38 2.71
1851 1909 2.125350 GAGGCCACCTGCTCGAAG 60.125 66.667 5.01 0.00 40.92 3.79
2040 2098 4.760047 GTCATGTCCAGCGGCGGT 62.760 66.667 5.44 5.44 0.00 5.68
2082 2140 1.152881 GTCCACCTCCATCATGGCC 60.153 63.158 0.00 0.00 37.47 5.36
2237 2297 4.968311 AACCCCCGACCCCGAACT 62.968 66.667 0.00 0.00 38.22 3.01
2238 2298 4.710167 CAACCCCCGACCCCGAAC 62.710 72.222 0.00 0.00 38.22 3.95
2239 2299 4.958158 TCAACCCCCGACCCCGAA 62.958 66.667 0.00 0.00 38.22 4.30
2240 2300 4.958158 TTCAACCCCCGACCCCGA 62.958 66.667 0.00 0.00 38.22 5.14
2241 2301 4.710167 GTTCAACCCCCGACCCCG 62.710 72.222 0.00 0.00 0.00 5.73
2245 2311 1.345415 TCTTACAGTTCAACCCCCGAC 59.655 52.381 0.00 0.00 0.00 4.79
2247 2313 2.554370 TTCTTACAGTTCAACCCCCG 57.446 50.000 0.00 0.00 0.00 5.73
2255 2321 7.970614 CCTGCCTTGATTAATTTCTTACAGTTC 59.029 37.037 0.00 0.00 0.00 3.01
2271 2337 6.719370 TGTTTACTGTAAAATCCTGCCTTGAT 59.281 34.615 14.10 0.00 0.00 2.57
2273 2339 6.325919 TGTTTACTGTAAAATCCTGCCTTG 57.674 37.500 14.10 0.00 0.00 3.61
2291 2357 8.020819 CGATTCTAGTTGAAATTGCCTTGTTTA 58.979 33.333 0.00 0.00 38.29 2.01
2330 2412 2.577606 TTGACACGGGAAATCCACAT 57.422 45.000 0.00 0.00 37.91 3.21
2335 2417 5.174943 GTGAAATGTTTTGACACGGGAAATC 59.825 40.000 0.00 0.00 0.00 2.17
2340 2422 2.738135 GGTGAAATGTTTTGACACGGG 58.262 47.619 0.00 0.00 33.08 5.28
2388 2471 3.942829 CTGGAGAACAGGCTATGTCAAA 58.057 45.455 0.00 0.00 43.00 2.69
2406 2489 6.215121 TGAAATTTGTTCAACATGCTACTGG 58.785 36.000 0.00 0.00 0.00 4.00
2433 2516 9.019764 CAACATACCGTAAATGGAAATGATTTC 57.980 33.333 9.36 9.36 38.94 2.17
2437 2525 5.163602 GGCAACATACCGTAAATGGAAATGA 60.164 40.000 12.30 0.00 33.25 2.57
2460 2548 5.521735 GCTCAACATGTAAGATCTGTAGTGG 59.478 44.000 11.36 0.00 0.00 4.00
2464 2552 6.071391 TGTGAGCTCAACATGTAAGATCTGTA 60.071 38.462 20.19 9.34 0.00 2.74
2482 2570 5.859205 AATTGGTCTTCTTTTTGTGAGCT 57.141 34.783 0.00 0.00 0.00 4.09
2608 2696 4.620982 ACAGTAAACCCGTTGTGTAGTAC 58.379 43.478 0.00 0.00 0.00 2.73
2849 2937 2.168313 ACTTGTGGTTTTTCAGGCCTTG 59.832 45.455 0.00 0.00 0.00 3.61
2909 2997 3.099905 TGGGGATCTCTAGTCAACACTG 58.900 50.000 0.00 0.00 33.62 3.66
2926 3014 3.055963 TGCATTAACAAAGCAGAATGGGG 60.056 43.478 0.00 0.00 35.86 4.96
3043 3131 4.420522 AAGTAACTTTGGTCCCGTTGTA 57.579 40.909 0.00 0.00 0.00 2.41
3066 3154 8.607459 CCAAACAAATAAACAATGTGCAGTAAA 58.393 29.630 0.00 0.00 0.00 2.01
3067 3155 7.981789 TCCAAACAAATAAACAATGTGCAGTAA 59.018 29.630 0.00 0.00 0.00 2.24
3070 3158 6.479660 ACTCCAAACAAATAAACAATGTGCAG 59.520 34.615 0.00 0.00 0.00 4.41
3079 3167 8.573035 TGTAATCCTGACTCCAAACAAATAAAC 58.427 33.333 0.00 0.00 0.00 2.01
3091 3179 4.537135 TGTTGTCTGTAATCCTGACTCC 57.463 45.455 0.00 0.00 41.29 3.85
3092 3180 6.861065 TTTTGTTGTCTGTAATCCTGACTC 57.139 37.500 0.00 0.00 41.29 3.36
3121 3209 7.361713 CGATTTTAGTTTGATTGGCTACTTCCA 60.362 37.037 0.00 0.00 0.00 3.53
3137 3225 3.435671 CCCTCGTGCTTTCGATTTTAGTT 59.564 43.478 0.00 0.00 39.12 2.24
3155 3243 4.082733 GCATACTTCCACAAACTTTCCCTC 60.083 45.833 0.00 0.00 0.00 4.30
3163 3251 1.165270 AGCGGCATACTTCCACAAAC 58.835 50.000 1.45 0.00 0.00 2.93
3164 3252 1.539388 CAAGCGGCATACTTCCACAAA 59.461 47.619 1.45 0.00 0.00 2.83
3165 3253 1.164411 CAAGCGGCATACTTCCACAA 58.836 50.000 1.45 0.00 0.00 3.33
3166 3254 1.305219 GCAAGCGGCATACTTCCACA 61.305 55.000 1.45 0.00 43.97 4.17
3167 3255 1.429423 GCAAGCGGCATACTTCCAC 59.571 57.895 1.45 0.00 43.97 4.02
3168 3256 3.903783 GCAAGCGGCATACTTCCA 58.096 55.556 1.45 0.00 43.97 3.53


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

AutoCloner maintained by Alex Coulton.