Multiple sequence alignment - TraesCS7B01G465600

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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 TraesCS7B01G465600 chr7B 100.000 2150 0 0 1 2150 722090815 722088666 0.000000e+00 3971.0
1 TraesCS7B01G465600 chr7B 100.000 2028 0 0 2318 4345 722088498 722086471 0.000000e+00 3746.0
2 TraesCS7B01G465600 chr7B 87.909 1894 174 28 1 1868 656300538 656302402 0.000000e+00 2178.0
3 TraesCS7B01G465600 chr7B 85.728 1044 105 14 2857 3864 656303936 656304971 0.000000e+00 1062.0
4 TraesCS7B01G465600 chr7B 86.874 838 82 8 2856 3672 651872400 651871570 0.000000e+00 913.0
5 TraesCS7B01G465600 chr7B 90.188 693 60 6 2 692 708677183 708676497 0.000000e+00 896.0
6 TraesCS7B01G465600 chr7B 87.469 798 72 9 3564 4345 708671866 708671081 0.000000e+00 894.0
7 TraesCS7B01G465600 chr7B 89.527 697 64 6 1 692 652402596 652401904 0.000000e+00 874.0
8 TraesCS7B01G465600 chr7B 88.800 625 55 13 849 1462 652174977 652174357 0.000000e+00 752.0
9 TraesCS7B01G465600 chr7B 85.759 646 70 4 2869 3497 652167183 652166543 0.000000e+00 664.0
10 TraesCS7B01G465600 chr7B 90.717 474 44 0 3863 4336 656314943 656315416 2.200000e-177 632.0
11 TraesCS7B01G465600 chr7B 91.753 388 32 0 3958 4345 652166169 652165782 1.370000e-149 540.0
12 TraesCS7B01G465600 chr7B 84.221 526 73 6 2318 2841 717954047 717954564 1.800000e-138 503.0
13 TraesCS7B01G465600 chr7B 84.197 386 47 7 3564 3943 652166526 652166149 3.190000e-96 363.0
14 TraesCS7B01G465600 chr7B 96.209 211 8 0 2318 2528 201904556 201904346 3.220000e-91 346.0
15 TraesCS7B01G465600 chr7B 92.735 234 17 0 1917 2150 652057889 652057656 5.380000e-89 339.0
16 TraesCS7B01G465600 chr7B 93.013 229 16 0 1922 2150 652439014 652438786 6.960000e-88 335.0
17 TraesCS7B01G465600 chr7B 81.227 277 38 11 2856 3121 652053352 652053079 1.220000e-50 211.0
18 TraesCS7B01G465600 chr7B 93.204 103 7 0 4243 4345 651662956 651662854 7.530000e-33 152.0
19 TraesCS7B01G465600 chr7D 88.168 2096 208 22 76 2150 586118117 586120193 0.000000e+00 2460.0
20 TraesCS7B01G465600 chr7D 93.354 1610 67 5 2773 4345 584214348 584212742 0.000000e+00 2344.0
21 TraesCS7B01G465600 chr7D 88.508 1810 173 18 76 1866 586111892 586113685 0.000000e+00 2158.0
22 TraesCS7B01G465600 chr7D 88.434 1807 173 18 76 1863 586105160 586106949 0.000000e+00 2146.0
23 TraesCS7B01G465600 chr7D 87.574 1521 136 24 368 1866 586023064 586024553 0.000000e+00 1712.0
24 TraesCS7B01G465600 chr7D 90.188 693 63 4 1 692 584218361 584217673 0.000000e+00 898.0
25 TraesCS7B01G465600 chr7D 89.799 696 63 6 1 692 584604338 584603647 0.000000e+00 885.0
26 TraesCS7B01G465600 chr7D 88.269 699 52 10 1 692 584276506 584277181 0.000000e+00 809.0
27 TraesCS7B01G465600 chr7D 85.642 787 87 9 3022 3783 586115438 586116223 0.000000e+00 804.0
28 TraesCS7B01G465600 chr7D 85.242 786 90 9 3022 3782 586109213 586109997 0.000000e+00 785.0
29 TraesCS7B01G465600 chr7D 86.339 732 71 10 3458 4168 584589850 584589127 0.000000e+00 771.0
30 TraesCS7B01G465600 chr7D 89.280 625 50 8 850 1459 584277189 584277811 0.000000e+00 767.0
31 TraesCS7B01G465600 chr7D 88.995 627 54 7 849 1462 582679788 582679164 0.000000e+00 761.0
32 TraesCS7B01G465600 chr7D 85.151 761 81 16 3022 3756 586121712 586122466 0.000000e+00 750.0
33 TraesCS7B01G465600 chr7D 88.640 625 58 6 849 1462 582603017 582602395 0.000000e+00 749.0
34 TraesCS7B01G465600 chr7D 88.018 651 51 12 849 1475 584217666 584217019 0.000000e+00 745.0
35 TraesCS7B01G465600 chr7D 87.025 632 60 8 849 1462 584603640 584603013 0.000000e+00 693.0
36 TraesCS7B01G465600 chr7D 85.289 537 59 13 2856 3380 583032677 583032149 1.780000e-148 536.0
37 TraesCS7B01G465600 chr7D 87.859 453 35 6 849 1286 583035042 583034595 8.330000e-142 514.0
38 TraesCS7B01G465600 chr7D 93.293 328 19 3 2516 2841 110161682 110162008 8.450000e-132 481.0
39 TraesCS7B01G465600 chr7D 88.472 373 24 11 1460 1819 583034334 583033968 2.400000e-117 433.0
40 TraesCS7B01G465600 chr7D 88.525 366 23 12 1457 1808 582602371 582602011 4.020000e-115 425.0
41 TraesCS7B01G465600 chr7D 88.166 338 33 4 356 692 582603355 582603024 3.150000e-106 396.0
42 TraesCS7B01G465600 chr7D 88.166 338 33 4 356 692 582680126 582679795 3.150000e-106 396.0
43 TraesCS7B01G465600 chr7D 87.324 355 25 11 1460 1800 584277842 584278190 5.270000e-104 388.0
44 TraesCS7B01G465600 chr7D 86.089 381 30 13 1500 1866 584593169 584592798 5.270000e-104 388.0
45 TraesCS7B01G465600 chr7D 87.988 333 21 12 1457 1775 582679140 582678813 4.100000e-100 375.0
46 TraesCS7B01G465600 chr7D 93.534 232 15 0 1919 2150 586107463 586107694 3.220000e-91 346.0
47 TraesCS7B01G465600 chr7D 93.534 232 15 0 1919 2150 586113688 586113919 3.220000e-91 346.0
48 TraesCS7B01G465600 chr7D 94.009 217 13 0 1917 2133 582678803 582678587 3.240000e-86 329.0
49 TraesCS7B01G465600 chr7D 92.444 225 17 0 1922 2146 584592792 584592568 5.420000e-84 322.0
50 TraesCS7B01G465600 chr7D 92.760 221 16 0 1930 2150 586024575 586024795 1.950000e-83 320.0
51 TraesCS7B01G465600 chr7D 93.088 217 15 0 1917 2133 582601588 582601372 7.010000e-83 318.0
52 TraesCS7B01G465600 chr7D 93.103 203 14 0 1933 2135 583033969 583033767 9.140000e-77 298.0
53 TraesCS7B01G465600 chr7D 91.469 211 6 5 1562 1761 584216929 584216720 3.310000e-71 279.0
54 TraesCS7B01G465600 chr7D 90.000 160 16 0 1991 2150 584278194 584278353 1.580000e-49 207.0
55 TraesCS7B01G465600 chr7D 91.538 130 11 0 4216 4345 584589134 584589005 3.450000e-41 180.0
56 TraesCS7B01G465600 chr7D 82.558 172 21 7 2853 3021 586118958 586119123 4.530000e-30 143.0
57 TraesCS7B01G465600 chr7D 94.186 86 4 1 1465 1550 584216928 584217012 3.530000e-26 130.0
58 TraesCS7B01G465600 chr7A 85.877 1848 189 29 17 1843 677439403 677441199 0.000000e+00 1901.0
59 TraesCS7B01G465600 chr7A 88.243 1514 145 13 1 1506 677611335 677612823 0.000000e+00 1779.0
60 TraesCS7B01G465600 chr7A 86.625 1271 128 17 2878 4109 677446646 677447913 0.000000e+00 1367.0
61 TraesCS7B01G465600 chr7A 87.425 994 93 17 1174 2150 676992829 676993807 0.000000e+00 1114.0
62 TraesCS7B01G465600 chr7A 85.244 1064 120 16 2878 3907 677616604 677617664 0.000000e+00 1061.0
63 TraesCS7B01G465600 chr7A 87.455 837 81 10 2856 3672 676995108 676995940 0.000000e+00 942.0
64 TraesCS7B01G465600 chr7A 89.714 700 59 6 1 692 675870656 675871350 0.000000e+00 881.0
65 TraesCS7B01G465600 chr7A 89.353 695 61 9 1 692 708496139 708495455 0.000000e+00 861.0
66 TraesCS7B01G465600 chr7A 87.482 703 60 14 1460 2150 674682484 674681798 0.000000e+00 785.0
67 TraesCS7B01G465600 chr7A 91.103 562 50 0 3775 4336 677001274 677001835 0.000000e+00 761.0
68 TraesCS7B01G465600 chr7A 88.387 620 62 3 849 1458 674683135 674682516 0.000000e+00 737.0
69 TraesCS7B01G465600 chr7A 85.962 691 82 9 2856 3532 675875374 675876063 0.000000e+00 725.0
70 TraesCS7B01G465600 chr7A 85.962 691 82 9 2856 3532 675913249 675913938 0.000000e+00 725.0
71 TraesCS7B01G465600 chr7A 84.416 539 65 13 2856 3382 674680140 674679609 3.000000e-141 512.0
72 TraesCS7B01G465600 chr7A 92.582 337 22 3 2516 2850 296798652 296798317 8.450000e-132 481.0
73 TraesCS7B01G465600 chr7A 86.508 378 27 11 1506 1870 677614172 677614538 1.130000e-105 394.0
74 TraesCS7B01G465600 chr7A 93.103 232 16 0 1919 2150 677614541 677614772 1.500000e-89 340.0
75 TraesCS7B01G465600 chr7A 92.672 232 17 0 1919 2150 677441221 677441452 6.960000e-88 335.0
76 TraesCS7B01G465600 chr7A 91.703 229 18 1 1922 2150 675908680 675908907 2.520000e-82 316.0
77 TraesCS7B01G465600 chr7A 90.558 233 20 1 4106 4336 677449557 677449789 1.520000e-79 307.0
78 TraesCS7B01G465600 chr2D 87.817 788 80 7 3564 4345 107820839 107820062 0.000000e+00 909.0
79 TraesCS7B01G465600 chr2D 91.549 639 47 5 8 646 107838931 107838300 0.000000e+00 874.0
80 TraesCS7B01G465600 chr2D 86.914 619 61 12 849 1451 107838261 107837647 0.000000e+00 676.0
81 TraesCS7B01G465600 chr2D 92.576 229 17 0 1922 2150 107837237 107837009 3.240000e-86 329.0
82 TraesCS7B01G465600 chr2D 87.171 304 20 10 1460 1750 107837610 107837313 1.170000e-85 327.0
83 TraesCS7B01G465600 chr2D 87.121 132 17 0 706 837 579823801 579823670 2.710000e-32 150.0
84 TraesCS7B01G465600 chr2D 83.117 154 24 2 692 843 508239115 508239268 5.860000e-29 139.0
85 TraesCS7B01G465600 chr2D 87.755 98 10 2 2 97 367812448 367812545 3.550000e-21 113.0
86 TraesCS7B01G465600 chr4D 85.213 541 65 10 2318 2850 249161187 249160654 3.820000e-150 542.0
87 TraesCS7B01G465600 chr4D 90.270 370 29 7 2475 2841 178673751 178674116 1.090000e-130 477.0
88 TraesCS7B01G465600 chr4D 80.855 538 79 18 2318 2841 215445380 215445907 6.770000e-108 401.0
89 TraesCS7B01G465600 chr4D 91.045 67 6 0 693 759 386752465 386752399 1.660000e-14 91.6
90 TraesCS7B01G465600 chr1D 85.448 536 60 12 2318 2850 80885881 80885361 3.820000e-150 542.0
91 TraesCS7B01G465600 chr4A 92.582 337 22 3 2516 2850 452251444 452251779 8.450000e-132 481.0
92 TraesCS7B01G465600 chr4A 97.630 211 5 0 2318 2528 709855496 709855286 3.190000e-96 363.0
93 TraesCS7B01G465600 chr4A 83.871 155 20 5 692 843 715440726 715440878 4.530000e-30 143.0
94 TraesCS7B01G465600 chr6A 92.082 341 24 3 2512 2850 200746984 200747323 1.090000e-130 477.0
95 TraesCS7B01G465600 chr4B 96.682 211 7 0 2318 2528 33313502 33313292 6.910000e-93 351.0
96 TraesCS7B01G465600 chr6B 96.209 211 8 0 2318 2528 19441625 19441415 3.220000e-91 346.0
97 TraesCS7B01G465600 chr6B 95.755 212 8 1 2318 2528 136907487 136907698 1.500000e-89 340.0
98 TraesCS7B01G465600 chr1A 89.881 168 15 2 683 849 584507968 584507802 9.460000e-52 215.0
99 TraesCS7B01G465600 chr2A 94.215 121 7 0 729 849 452592935 452592815 7.420000e-43 185.0
100 TraesCS7B01G465600 chr1B 87.333 150 19 0 694 843 73033026 73033175 5.780000e-39 172.0
101 TraesCS7B01G465600 chr3A 90.909 121 11 0 692 812 629049438 629049318 3.480000e-36 163.0
102 TraesCS7B01G465600 chr3D 89.381 113 12 0 692 804 560322647 560322759 4.530000e-30 143.0
103 TraesCS7B01G465600 chr3D 77.372 137 23 8 717 849 418376312 418376444 1.680000e-09 75.0


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 TraesCS7B01G465600 chr7B 722086471 722090815 4344 True 3858.500000 3971 100.000000 1 4345 2 chr7B.!!$R12 4344
1 TraesCS7B01G465600 chr7B 656300538 656304971 4433 False 1620.000000 2178 86.818500 1 3864 2 chr7B.!!$F3 3863
2 TraesCS7B01G465600 chr7B 651871570 651872400 830 True 913.000000 913 86.874000 2856 3672 1 chr7B.!!$R3 816
3 TraesCS7B01G465600 chr7B 708676497 708677183 686 True 896.000000 896 90.188000 2 692 1 chr7B.!!$R10 690
4 TraesCS7B01G465600 chr7B 708671081 708671866 785 True 894.000000 894 87.469000 3564 4345 1 chr7B.!!$R9 781
5 TraesCS7B01G465600 chr7B 652401904 652402596 692 True 874.000000 874 89.527000 1 692 1 chr7B.!!$R7 691
6 TraesCS7B01G465600 chr7B 652174357 652174977 620 True 752.000000 752 88.800000 849 1462 1 chr7B.!!$R6 613
7 TraesCS7B01G465600 chr7B 652165782 652167183 1401 True 522.333333 664 87.236333 2869 4345 3 chr7B.!!$R11 1476
8 TraesCS7B01G465600 chr7B 717954047 717954564 517 False 503.000000 503 84.221000 2318 2841 1 chr7B.!!$F2 523
9 TraesCS7B01G465600 chr7D 586105160 586122466 17306 False 1104.222222 2460 87.863444 76 3783 9 chr7D.!!$F5 3707
10 TraesCS7B01G465600 chr7D 584212742 584218361 5619 True 1066.500000 2344 90.757250 1 4345 4 chr7D.!!$R4 4344
11 TraesCS7B01G465600 chr7D 586023064 586024795 1731 False 1016.000000 1712 90.167000 368 2150 2 chr7D.!!$F4 1782
12 TraesCS7B01G465600 chr7D 584603013 584604338 1325 True 789.000000 885 88.412000 1 1462 2 chr7D.!!$R6 1461
13 TraesCS7B01G465600 chr7D 584276506 584278353 1847 False 542.750000 809 88.718250 1 2150 4 chr7D.!!$F3 2149
14 TraesCS7B01G465600 chr7D 582601372 582603355 1983 True 472.000000 749 89.604750 356 2133 4 chr7D.!!$R1 1777
15 TraesCS7B01G465600 chr7D 582678587 582680126 1539 True 465.250000 761 89.789500 356 2133 4 chr7D.!!$R2 1777
16 TraesCS7B01G465600 chr7D 583032149 583035042 2893 True 445.250000 536 88.680750 849 3380 4 chr7D.!!$R3 2531
17 TraesCS7B01G465600 chr7D 584589005 584593169 4164 True 415.250000 771 89.102500 1500 4345 4 chr7D.!!$R5 2845
18 TraesCS7B01G465600 chr7A 677439403 677441452 2049 False 1118.000000 1901 89.274500 17 2150 2 chr7A.!!$F7 2133
19 TraesCS7B01G465600 chr7A 676992829 676995940 3111 False 1028.000000 1114 87.440000 1174 3672 2 chr7A.!!$F6 2498
20 TraesCS7B01G465600 chr7A 677611335 677617664 6329 False 893.500000 1779 88.274500 1 3907 4 chr7A.!!$F9 3906
21 TraesCS7B01G465600 chr7A 675870656 675871350 694 False 881.000000 881 89.714000 1 692 1 chr7A.!!$F1 691
22 TraesCS7B01G465600 chr7A 708495455 708496139 684 True 861.000000 861 89.353000 1 692 1 chr7A.!!$R2 691
23 TraesCS7B01G465600 chr7A 677446646 677449789 3143 False 837.000000 1367 88.591500 2878 4336 2 chr7A.!!$F8 1458
24 TraesCS7B01G465600 chr7A 677001274 677001835 561 False 761.000000 761 91.103000 3775 4336 1 chr7A.!!$F5 561
25 TraesCS7B01G465600 chr7A 675875374 675876063 689 False 725.000000 725 85.962000 2856 3532 1 chr7A.!!$F2 676
26 TraesCS7B01G465600 chr7A 675913249 675913938 689 False 725.000000 725 85.962000 2856 3532 1 chr7A.!!$F4 676
27 TraesCS7B01G465600 chr7A 674679609 674683135 3526 True 678.000000 785 86.761667 849 3382 3 chr7A.!!$R3 2533
28 TraesCS7B01G465600 chr2D 107820062 107820839 777 True 909.000000 909 87.817000 3564 4345 1 chr2D.!!$R1 781
29 TraesCS7B01G465600 chr2D 107837009 107838931 1922 True 551.500000 874 89.552500 8 2150 4 chr2D.!!$R3 2142
30 TraesCS7B01G465600 chr4D 249160654 249161187 533 True 542.000000 542 85.213000 2318 2850 1 chr4D.!!$R1 532
31 TraesCS7B01G465600 chr4D 215445380 215445907 527 False 401.000000 401 80.855000 2318 2841 1 chr4D.!!$F2 523
32 TraesCS7B01G465600 chr1D 80885361 80885881 520 True 542.000000 542 85.448000 2318 2850 1 chr1D.!!$R1 532

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
122 133 1.130938 CACGCATGTTGCATTCTAGCA 59.869 47.619 0.00 0.0 45.36 3.49 F
320 335 1.188863 GTAGGTTGAGAGCCCGGTTA 58.811 55.000 0.00 0.0 0.00 2.85 F
1555 9856 0.441145 GTTACAACCCTTGCGCTACG 59.559 55.000 9.73 0.0 0.00 3.51 F
1866 10561 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1447 0.333993 AGCCATTGACTCCAAGGCAT 59.666 50.000 15.53 0.0 43.13 4.40 R
1861 10556 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 R
2960 15011 0.323302 TGACAATTAGGAGCACGGCA 59.677 50.000 0.00 0.0 0.00 5.69 R
3757 16459 1.476891 GTATGCCTTGACAGACTCCGA 59.523 52.381 0.00 0.0 0.00 4.55 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
116 127 1.814394 ACTGATCACGCATGTTGCATT 59.186 42.857 0.00 0.00 45.36 3.56
122 133 1.130938 CACGCATGTTGCATTCTAGCA 59.869 47.619 0.00 0.00 45.36 3.49
153 168 4.745125 CCAAATACTCGACGCATGTAAGAT 59.255 41.667 0.00 0.00 0.00 2.40
163 178 3.389983 ACGCATGTAAGATAGGGCCTAAA 59.610 43.478 18.91 0.00 0.00 1.85
219 234 1.304381 GCTCATCCAAACAGGGCCA 60.304 57.895 6.18 0.00 38.24 5.36
320 335 1.188863 GTAGGTTGAGAGCCCGGTTA 58.811 55.000 0.00 0.00 0.00 2.85
344 359 3.272574 AGATCCATACAACCAGCAGTG 57.727 47.619 0.00 0.00 0.00 3.66
386 401 6.425735 TGCTTTGATGGAGGATCAGAAAATA 58.574 36.000 0.00 0.00 42.24 1.40
543 567 5.671493 AGTCAGGCGTATTAAGCTATGTTT 58.329 37.500 1.69 0.00 34.52 2.83
546 572 3.247648 AGGCGTATTAAGCTATGTTTGCG 59.752 43.478 1.69 0.00 35.28 4.85
555 581 2.076863 GCTATGTTTGCGTGTCCTTCT 58.923 47.619 0.00 0.00 0.00 2.85
576 602 1.971149 TCCACATCCAATGGAGGACT 58.029 50.000 21.63 0.00 41.47 3.85
626 652 2.494073 GTGGTTGGTGTGAAACTTTGGA 59.506 45.455 0.00 0.00 38.04 3.53
758 785 4.563140 ACAGGTGTAAATTACCGGTCAT 57.437 40.909 12.40 1.43 41.76 3.06
763 790 5.895534 AGGTGTAAATTACCGGTCATCTCTA 59.104 40.000 12.40 0.00 43.06 2.43
776 803 1.415659 CATCTCTAGGTTCCTGCCTGG 59.584 57.143 1.12 0.00 39.60 4.45
796 823 3.009033 TGGAATGAAAACGACAGGAGGAT 59.991 43.478 0.00 0.00 0.00 3.24
797 824 4.224147 TGGAATGAAAACGACAGGAGGATA 59.776 41.667 0.00 0.00 0.00 2.59
823 850 6.439375 TCTGTATCCTAAACTAGCCAGAAACA 59.561 38.462 0.00 0.00 0.00 2.83
827 854 4.041691 TCCTAAACTAGCCAGAAACAAGCT 59.958 41.667 0.00 0.00 40.66 3.74
854 881 1.623811 CTAATCCAATCGGGGGATCGT 59.376 52.381 4.30 0.00 44.30 3.73
918 961 9.770097 ACACTAGGCATGTGATATATATATTGC 57.230 33.333 14.73 14.73 38.65 3.56
967 1010 2.740981 ACTGCTCGCTCATTCTTTTCTG 59.259 45.455 0.00 0.00 0.00 3.02
1022 1074 1.202076 GGCGCCTTCAGAAAAGAATCG 60.202 52.381 22.15 0.00 0.00 3.34
1023 1075 1.464997 GCGCCTTCAGAAAAGAATCGT 59.535 47.619 0.00 0.00 0.00 3.73
1050 1102 4.201950 GCGATTGTGCTCCTAATTGTCATT 60.202 41.667 0.00 0.00 0.00 2.57
1116 1176 2.573369 TGTCCGTATCTCTCCTAGCAC 58.427 52.381 0.00 0.00 0.00 4.40
1117 1177 1.532007 GTCCGTATCTCTCCTAGCACG 59.468 57.143 0.00 0.00 34.80 5.34
1132 1197 2.282407 AGCACGTTAAGTCGTTTTGGT 58.718 42.857 0.00 0.00 42.27 3.67
1151 1216 3.320541 TGGTGTTAAATTGGCTGGTTCAG 59.679 43.478 0.00 0.00 34.12 3.02
1239 1306 2.935849 TGTGCTAGTATGTTCAATGCCG 59.064 45.455 0.00 0.00 0.00 5.69
1262 1329 3.188786 GCACGCAGTCGACATCCC 61.189 66.667 19.50 1.56 41.61 3.85
1269 1349 1.407437 GCAGTCGACATCCCTTGGATT 60.407 52.381 19.50 0.00 39.79 3.01
1309 1447 5.822519 CCTAAGCAGCAATTATTACAGACCA 59.177 40.000 0.00 0.00 0.00 4.02
1336 1474 1.369625 GAGTCAATGGCTACGGTTGG 58.630 55.000 0.00 0.00 0.00 3.77
1360 1498 1.468520 CGTGTATGCCAAGGTGAAAGG 59.531 52.381 0.00 0.00 0.00 3.11
1383 1522 1.372128 CACCTTTTCTGGCGCTTGC 60.372 57.895 7.64 0.00 38.11 4.01
1455 1595 1.300542 GCTAGCACTCCGATCCAGC 60.301 63.158 10.63 0.00 0.00 4.85
1497 8443 0.546598 CCCTTCCGGGCTCTTATGTT 59.453 55.000 0.00 0.00 45.33 2.71
1553 9854 3.236604 GGTTACAACCCTTGCGCTA 57.763 52.632 9.73 0.00 43.43 4.26
1555 9856 0.441145 GTTACAACCCTTGCGCTACG 59.559 55.000 9.73 0.00 0.00 3.51
1800 10123 8.413229 AGCTTAGTTGTGTTGTTACAAATGAAT 58.587 29.630 0.00 0.00 41.75 2.57
1845 10540 9.528018 AAAATAAATTTGACTTTTCTCGAGCAA 57.472 25.926 7.81 0.00 0.00 3.91
1860 10555 1.198867 GAGCAAACACACACACACACA 59.801 47.619 0.00 0.00 0.00 3.72
1861 10556 1.068610 AGCAAACACACACACACACAC 60.069 47.619 0.00 0.00 0.00 3.82
1862 10557 1.335415 GCAAACACACACACACACACA 60.335 47.619 0.00 0.00 0.00 3.72
1863 10558 2.315011 CAAACACACACACACACACAC 58.685 47.619 0.00 0.00 0.00 3.82
1864 10559 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1865 10560 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1866 10561 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1867 10562 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1868 10563 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1869 10564 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1870 10565 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1871 10566 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1872 10567 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1873 10568 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1874 10569 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1875 10570 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1876 10571 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1877 10572 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1878 10573 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1879 10574 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1880 10575 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1881 10576 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1882 10577 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1883 10578 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1884 10579 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1885 10580 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1886 10581 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2113 10932 7.177184 TGGCTTGAGGCATCAATATAATACAT 58.823 34.615 15.02 0.00 44.32 2.29
2135 10954 8.142994 ACATATTTTAGAAGCAGAACCATACG 57.857 34.615 0.00 0.00 0.00 3.06
2350 11782 9.758651 ATATTTGTACGTGAAATAGAGTATGCA 57.241 29.630 15.59 0.00 30.69 3.96
2356 11788 7.377766 ACGTGAAATAGAGTATGCACAAAAT 57.622 32.000 0.00 0.00 0.00 1.82
2435 11877 4.840911 ACATACTACGCGTACATACACTG 58.159 43.478 16.41 5.58 0.00 3.66
2436 11878 2.184385 ACTACGCGTACATACACTGC 57.816 50.000 16.41 0.00 0.00 4.40
2438 11880 2.095110 ACTACGCGTACATACACTGCAA 60.095 45.455 16.41 0.00 0.00 4.08
2440 11882 3.153676 ACGCGTACATACACTGCAATA 57.846 42.857 11.67 0.00 0.00 1.90
2461 11903 9.938670 GCAATATGATAGATACTACCTAGAACG 57.061 37.037 0.00 0.00 0.00 3.95
2471 11913 9.182214 AGATACTACCTAGAACGTATCAAACAA 57.818 33.333 18.75 0.00 40.22 2.83
2478 11920 5.432885 AGAACGTATCAAACAAAAGTGGG 57.567 39.130 0.00 0.00 0.00 4.61
2489 11931 6.316890 TCAAACAAAAGTGGGAGTAACTACAC 59.683 38.462 0.00 0.00 0.00 2.90
2495 11937 2.143876 GGGAGTAACTACACCCGGTA 57.856 55.000 0.00 0.00 45.03 4.02
2507 13005 3.946606 ACACCCGGTAGTAGGAAAAATG 58.053 45.455 0.00 0.00 0.00 2.32
2515 13013 5.337330 CGGTAGTAGGAAAAATGTGTCCTCT 60.337 44.000 0.00 0.00 43.44 3.69
2588 14241 6.749036 ATTCTTCACCCGAGGTAATCTTAT 57.251 37.500 0.00 0.00 32.11 1.73
2867 14909 0.879765 TTCCGGACTTCTCACTCGAC 59.120 55.000 1.83 0.00 0.00 4.20
2888 14930 2.987547 CCACCAACCTGCCTGCTG 60.988 66.667 0.00 0.00 0.00 4.41
2910 14952 9.985730 TGCTGATTCTTTTCTTCAACATAAAAT 57.014 25.926 0.00 0.00 0.00 1.82
2960 15011 6.596621 GCCTTTAGGAAAGAATATCTCTGGT 58.403 40.000 0.00 0.00 41.02 4.00
3050 15127 4.379652 AGCAACTAAAGTTTTGGCATTGG 58.620 39.130 0.00 0.00 35.83 3.16
3087 15196 9.072294 GTATGCAACTTAATATGTTGTTTGGAC 57.928 33.333 16.82 7.78 44.54 4.02
3128 15237 9.492973 AGATGTTGTTTTGATTAATCTTTTGGG 57.507 29.630 16.24 0.00 0.00 4.12
3164 15274 2.223537 TGCATGTGCTAGTATGTCCG 57.776 50.000 6.55 0.00 42.66 4.79
3408 15794 0.824109 CAGTTATCCCAGCCTGACGA 59.176 55.000 0.00 0.00 0.00 4.20
3426 15812 8.798153 GCCTGACGATTCTTAAAAATAAATGTG 58.202 33.333 0.00 0.00 0.00 3.21
3504 16150 6.526566 AATAAAGTCGTTTGAGTGTGAGAC 57.473 37.500 0.00 0.00 0.00 3.36
3757 16459 0.762418 TGTCTCACCAAACCCATCGT 59.238 50.000 0.00 0.00 0.00 3.73
3769 16471 1.313091 CCCATCGTCGGAGTCTGTCA 61.313 60.000 0.00 0.00 0.00 3.58
3795 22707 1.545841 ACTCCATCGCGCCATAGATA 58.454 50.000 0.00 0.00 0.00 1.98
3837 22749 0.108138 CTTCCTCCTCGCCGATGTTT 60.108 55.000 0.00 0.00 0.00 2.83
3876 22788 0.247736 GCTACAGCTACAGCACAGGT 59.752 55.000 12.61 0.00 45.16 4.00
3974 22921 3.008049 ACGGGAAGCTAAGTCACTGAATT 59.992 43.478 0.00 0.00 0.00 2.17
4013 22960 4.494199 CGATCAAGATTAACGGGCTGTTTC 60.494 45.833 18.19 9.87 42.09 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 2.270275 TCCGCGCATAAAATTTGGTG 57.730 45.000 8.75 0.00 0.00 4.17
116 127 3.515502 AGTATTTGGTGAGCACTGCTAGA 59.484 43.478 2.71 0.00 39.88 2.43
122 133 2.671351 CGTCGAGTATTTGGTGAGCACT 60.671 50.000 0.16 0.00 0.00 4.40
153 168 4.719773 TGATTAGCTGACTTTTAGGCCCTA 59.280 41.667 0.00 0.00 0.00 3.53
163 178 3.618507 GCTGACCAGTGATTAGCTGACTT 60.619 47.826 0.00 0.00 36.12 3.01
219 234 5.585047 GGAGTTTCCTATTTCTTGTGCGTAT 59.415 40.000 0.00 0.00 32.53 3.06
244 259 1.691976 TGACCCGCTTTCTTCTCTCAA 59.308 47.619 0.00 0.00 0.00 3.02
320 335 4.012374 CTGCTGGTTGTATGGATCTTTGT 58.988 43.478 0.00 0.00 0.00 2.83
496 520 6.709018 AAGTAAACATAACACCAAGTTGCT 57.291 33.333 0.00 0.00 41.50 3.91
509 533 9.740239 CTTAATACGCCTGACTAAGTAAACATA 57.260 33.333 0.00 0.00 0.00 2.29
543 567 1.069090 GTGGACAGAAGGACACGCA 59.931 57.895 0.00 0.00 0.00 5.24
546 572 1.347707 TGGATGTGGACAGAAGGACAC 59.652 52.381 0.00 0.00 0.00 3.67
555 581 1.281867 GTCCTCCATTGGATGTGGACA 59.718 52.381 26.40 3.23 44.35 4.02
665 691 4.336993 AGTGTTTTCCGACATAAGCACAAA 59.663 37.500 0.00 0.00 37.76 2.83
758 785 0.710588 TCCAGGCAGGAACCTAGAGA 59.289 55.000 0.00 0.00 45.65 3.10
776 803 6.201806 CAGATATCCTCCTGTCGTTTTCATTC 59.798 42.308 0.00 0.00 0.00 2.67
796 823 8.639761 GTTTCTGGCTAGTTTAGGATACAGATA 58.360 37.037 0.00 0.00 41.41 1.98
797 824 7.125811 TGTTTCTGGCTAGTTTAGGATACAGAT 59.874 37.037 0.00 0.00 41.41 2.90
812 839 2.548057 CGTTTCAGCTTGTTTCTGGCTA 59.452 45.455 0.00 0.00 34.71 3.93
823 850 3.063997 CGATTGGATTAGCGTTTCAGCTT 59.936 43.478 0.00 0.00 46.80 3.74
827 854 2.285083 CCCGATTGGATTAGCGTTTCA 58.715 47.619 0.00 0.00 37.49 2.69
887 914 3.701205 ATCACATGCCTAGTGTGTTCA 57.299 42.857 10.71 0.00 45.45 3.18
918 961 0.028242 CGATCGAGTGAGAAGTCCGG 59.972 60.000 10.26 0.00 0.00 5.14
967 1010 2.815478 TGGGATGTTTTTGAACGTTGC 58.185 42.857 5.00 0.00 0.00 4.17
1022 1074 1.438651 TAGGAGCACAATCGCACAAC 58.561 50.000 0.00 0.00 0.00 3.32
1023 1075 2.177394 TTAGGAGCACAATCGCACAA 57.823 45.000 0.00 0.00 0.00 3.33
1032 1084 3.758023 CCACAATGACAATTAGGAGCACA 59.242 43.478 0.00 0.00 0.00 4.57
1116 1176 7.305533 CCAATTTAACACCAAAACGACTTAACG 60.306 37.037 0.00 0.00 39.31 3.18
1117 1177 7.515528 GCCAATTTAACACCAAAACGACTTAAC 60.516 37.037 0.00 0.00 0.00 2.01
1132 1197 2.298729 GCCTGAACCAGCCAATTTAACA 59.701 45.455 0.00 0.00 0.00 2.41
1184 1250 6.594937 AGAACGTGGTTATAATTAGCCGAAAA 59.405 34.615 0.00 0.00 31.60 2.29
1239 1306 3.413861 TCGACTGCGTGCATGCAC 61.414 61.111 35.76 35.76 40.62 4.57
1262 1329 3.316029 TGTGTGTGCAAAGAGAATCCAAG 59.684 43.478 0.00 0.00 33.66 3.61
1269 1349 3.466836 CTTAGGTGTGTGTGCAAAGAGA 58.533 45.455 0.00 0.00 0.00 3.10
1309 1447 0.333993 AGCCATTGACTCCAAGGCAT 59.666 50.000 15.53 0.00 43.13 4.40
1318 1456 0.981183 TCCAACCGTAGCCATTGACT 59.019 50.000 0.00 0.00 0.00 3.41
1320 1458 2.639065 GATTCCAACCGTAGCCATTGA 58.361 47.619 0.00 0.00 0.00 2.57
1336 1474 2.627945 TCACCTTGGCATACACGATTC 58.372 47.619 0.00 0.00 0.00 2.52
1383 1522 3.502920 AGAGTAGCATTTGAAGTCGTCG 58.497 45.455 0.00 0.00 0.00 5.12
1800 10123 5.667539 TTTTGATCCACAAGTCCAACAAA 57.332 34.783 0.00 0.00 39.77 2.83
1845 10540 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
1860 10555 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1861 10556 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1862 10557 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1863 10558 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1864 10559 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1865 10560 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1866 10561 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1867 10562 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1868 10563 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
1869 10564 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
1900 10595 9.100197 TGTATGTATGTCTCTCTCTCTCTCTAT 57.900 37.037 0.00 0.00 0.00 1.98
1901 10596 8.364894 GTGTATGTATGTCTCTCTCTCTCTCTA 58.635 40.741 0.00 0.00 0.00 2.43
1903 10598 6.426937 GGTGTATGTATGTCTCTCTCTCTCTC 59.573 46.154 0.00 0.00 0.00 3.20
1904 10599 6.101150 AGGTGTATGTATGTCTCTCTCTCTCT 59.899 42.308 0.00 0.00 0.00 3.10
1905 10600 6.296026 AGGTGTATGTATGTCTCTCTCTCTC 58.704 44.000 0.00 0.00 0.00 3.20
1906 10601 6.260700 AGGTGTATGTATGTCTCTCTCTCT 57.739 41.667 0.00 0.00 0.00 3.10
1907 10602 8.630054 AATAGGTGTATGTATGTCTCTCTCTC 57.370 38.462 0.00 0.00 0.00 3.20
1908 10603 7.389330 CGAATAGGTGTATGTATGTCTCTCTCT 59.611 40.741 0.00 0.00 0.00 3.10
1910 10605 7.225011 TCGAATAGGTGTATGTATGTCTCTCT 58.775 38.462 0.00 0.00 0.00 3.10
1911 10606 7.436430 TCGAATAGGTGTATGTATGTCTCTC 57.564 40.000 0.00 0.00 0.00 3.20
1912 10607 8.410673 AATCGAATAGGTGTATGTATGTCTCT 57.589 34.615 0.00 0.00 0.00 3.10
1913 10608 8.916654 CAAATCGAATAGGTGTATGTATGTCTC 58.083 37.037 0.00 0.00 0.00 3.36
1914 10609 8.421784 ACAAATCGAATAGGTGTATGTATGTCT 58.578 33.333 0.00 0.00 0.00 3.41
1915 10610 8.589335 ACAAATCGAATAGGTGTATGTATGTC 57.411 34.615 0.00 0.00 0.00 3.06
1920 10615 5.104693 TGGGACAAATCGAATAGGTGTATGT 60.105 40.000 0.00 0.00 31.92 2.29
2001 10820 5.048713 GGTTCAGATTTATTTATGGCTCCGG 60.049 44.000 0.00 0.00 0.00 5.14
2113 10932 7.441157 CCATCGTATGGTTCTGCTTCTAAAATA 59.559 37.037 5.90 0.00 45.54 1.40
2422 11864 5.845985 ATCATATTGCAGTGTATGTACGC 57.154 39.130 12.60 0.00 36.98 4.42
2435 11877 9.938670 CGTTCTAGGTAGTATCTATCATATTGC 57.061 37.037 0.00 0.00 0.00 3.56
2454 11896 6.425721 TCCCACTTTTGTTTGATACGTTCTAG 59.574 38.462 0.00 0.00 0.00 2.43
2457 11899 5.008316 ACTCCCACTTTTGTTTGATACGTTC 59.992 40.000 0.00 0.00 0.00 3.95
2461 11903 7.506328 AGTTACTCCCACTTTTGTTTGATAC 57.494 36.000 0.00 0.00 0.00 2.24
2464 11906 6.316890 GTGTAGTTACTCCCACTTTTGTTTGA 59.683 38.462 7.55 0.00 0.00 2.69
2465 11907 6.459161 GGTGTAGTTACTCCCACTTTTGTTTG 60.459 42.308 12.62 0.00 34.61 2.93
2489 11931 3.937079 GACACATTTTTCCTACTACCGGG 59.063 47.826 6.32 0.00 0.00 5.73
2558 13457 5.340439 ACCTCGGGTGAAGAATAACTTAG 57.660 43.478 0.00 0.00 39.13 2.18
2786 14827 4.606961 ACGACGTAAAAAGAGACCGTAAA 58.393 39.130 0.00 0.00 0.00 2.01
2841 14883 2.232941 GTGAGAAGTCCGGAATACACCA 59.767 50.000 5.23 0.00 0.00 4.17
2867 14909 3.953775 AGGCAGGTTGGTGGACGG 61.954 66.667 0.00 0.00 0.00 4.79
2960 15011 0.323302 TGACAATTAGGAGCACGGCA 59.677 50.000 0.00 0.00 0.00 5.69
3050 15127 2.094675 AGTTGCATACACCAGCCAATC 58.905 47.619 0.00 0.00 0.00 2.67
3128 15237 6.473455 GCACATGCAAGAATCAGGTTAATTAC 59.527 38.462 0.00 0.00 41.59 1.89
3138 15248 5.430886 ACATACTAGCACATGCAAGAATCA 58.569 37.500 6.64 0.00 45.16 2.57
3139 15249 5.049818 GGACATACTAGCACATGCAAGAATC 60.050 44.000 6.64 0.00 45.16 2.52
3164 15274 2.079925 GGAGACTCCATTGAACACAGC 58.920 52.381 17.10 0.00 36.28 4.40
3426 15812 6.995091 ACATATGAGCCAAGAAGAGGTAATTC 59.005 38.462 10.38 0.00 0.00 2.17
3497 16143 7.445121 ACTTCACATTTGAATAGAGTCTCACA 58.555 34.615 0.00 0.00 41.05 3.58
3516 16162 6.364976 AGTTTGTGCAAGTAAAACAACTTCAC 59.635 34.615 14.35 10.02 37.61 3.18
3757 16459 1.476891 GTATGCCTTGACAGACTCCGA 59.523 52.381 0.00 0.00 0.00 4.55
3769 16471 1.595382 GCGCGATGGAGTATGCCTT 60.595 57.895 12.10 0.00 0.00 4.35
3795 22707 1.827399 ATGGGTTTGGCGAGACGACT 61.827 55.000 0.00 0.00 35.04 4.18
3837 22749 4.994201 GCACGCACGAGACGGACA 62.994 66.667 0.00 0.00 34.00 4.02
4013 22960 5.107133 AGTTAGGTTACAATCATCCGAACG 58.893 41.667 0.00 0.00 39.37 3.95
4058 23005 7.081976 GCTTAAAACAAACACTATCCAACGAT 58.918 34.615 0.00 0.00 0.00 3.73
4208 24808 1.518572 GTGCAGGCATGAGCATTGC 60.519 57.895 0.62 0.00 46.61 3.56


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

AutoCloner maintained by Alex Coulton.