Multiple sequence alignment - TraesCS7A01G424000

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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 TraesCS7A01G424000 chr7A 100.000 5491 0 0 1 5491 617009072 617003582 0.000000e+00 10141.0
1 TraesCS7A01G424000 chr7A 92.420 686 39 8 3971 4652 104462260 104461584 0.000000e+00 966.0
2 TraesCS7A01G424000 chr7A 85.664 844 77 18 4652 5490 684994550 684995354 0.000000e+00 848.0
3 TraesCS7A01G424000 chr7A 77.895 855 106 45 750 1543 108111139 108110307 6.480000e-124 455.0
4 TraesCS7A01G424000 chr5A 98.825 3914 39 7 742 4652 607949327 607953236 0.000000e+00 6966.0
5 TraesCS7A01G424000 chr5A 92.790 957 61 7 3143 4097 560600088 560599138 0.000000e+00 1378.0
6 TraesCS7A01G424000 chr5A 85.900 844 75 16 4652 5490 4626116 4626920 0.000000e+00 859.0
7 TraesCS7A01G424000 chr5A 89.041 365 26 7 4289 4651 560598498 560598146 1.820000e-119 440.0
8 TraesCS7A01G424000 chr5A 94.118 289 16 1 2861 3149 560600561 560600274 6.530000e-119 438.0
9 TraesCS7A01G424000 chr5A 77.532 770 96 39 748 1454 560602083 560601328 5.160000e-105 392.0
10 TraesCS7A01G424000 chr5A 83.654 104 17 0 544 647 4625883 4625986 1.260000e-16 99.0
11 TraesCS7A01G424000 chr6D 97.284 3903 80 11 750 4650 38776223 38772345 0.000000e+00 6597.0
12 TraesCS7A01G424000 chr3A 99.134 1385 12 0 3269 4653 694982242 694983626 0.000000e+00 2492.0
13 TraesCS7A01G424000 chr3A 90.354 1524 110 12 3143 4652 690721517 690723017 0.000000e+00 1965.0
14 TraesCS7A01G424000 chr3A 92.390 657 38 7 3971 4623 23890309 23890957 0.000000e+00 926.0
15 TraesCS7A01G424000 chr3A 86.951 751 73 9 1477 2214 485686830 485687568 0.000000e+00 821.0
16 TraesCS7A01G424000 chr3A 94.810 289 15 0 2861 3149 690720831 690721119 8.390000e-123 451.0
17 TraesCS7A01G424000 chr3A 79.350 615 78 26 751 1331 690719287 690719886 2.400000e-103 387.0
18 TraesCS7A01G424000 chr3A 87.766 188 21 1 1356 1543 690719949 690720134 9.260000e-53 219.0
19 TraesCS7A01G424000 chr3A 86.111 72 10 0 4694 4765 76632696 76632625 1.640000e-10 78.7
20 TraesCS7A01G424000 chr3B 91.432 1529 99 14 3143 4657 277024980 277026490 0.000000e+00 2069.0
21 TraesCS7A01G424000 chr3B 90.873 1523 111 11 3143 4652 221134417 221132910 0.000000e+00 2017.0
22 TraesCS7A01G424000 chr3B 87.450 749 69 9 1477 2214 474408881 474409615 0.000000e+00 839.0
23 TraesCS7A01G424000 chr3B 88.437 467 33 15 2183 2631 277021758 277022221 1.350000e-150 544.0
24 TraesCS7A01G424000 chr3B 88.816 456 31 14 2183 2620 277019710 277020163 4.840000e-150 542.0
25 TraesCS7A01G424000 chr3B 88.009 467 35 15 2183 2631 277023802 277024265 2.910000e-147 532.0
26 TraesCS7A01G424000 chr3B 89.269 438 30 10 2183 2605 817346636 817346201 2.910000e-147 532.0
27 TraesCS7A01G424000 chr3B 93.772 289 18 0 2861 3149 277020424 277020712 8.450000e-118 435.0
28 TraesCS7A01G424000 chr3B 93.772 289 18 0 2861 3149 277024506 277024794 8.450000e-118 435.0
29 TraesCS7A01G424000 chr3B 87.234 188 23 1 1356 1543 817346824 817346638 4.310000e-51 213.0
30 TraesCS7A01G424000 chr3B 80.180 222 42 2 744 963 543843163 543843384 1.220000e-36 165.0
31 TraesCS7A01G424000 chr2B 91.339 1524 101 13 3143 4652 75906884 75908390 0.000000e+00 2054.0
32 TraesCS7A01G424000 chr2B 88.437 467 33 15 2183 2631 75905710 75906173 1.350000e-150 544.0
33 TraesCS7A01G424000 chr2B 93.772 289 18 0 2861 3149 75906410 75906698 8.450000e-118 435.0
34 TraesCS7A01G424000 chr1B 91.148 1525 103 14 3143 4654 123484350 123485855 0.000000e+00 2039.0
35 TraesCS7A01G424000 chr1B 86.938 467 40 11 2183 2631 123483171 123483634 6.350000e-139 505.0
36 TraesCS7A01G424000 chr1B 82.420 438 71 6 4937 5371 37041022 37040588 1.440000e-100 377.0
37 TraesCS7A01G424000 chr1B 83.186 226 35 1 1318 1543 123482947 123483169 2.590000e-48 204.0
38 TraesCS7A01G424000 chr2A 90.879 1524 102 12 3143 4652 721615690 721614190 0.000000e+00 2010.0
39 TraesCS7A01G424000 chr2A 93.013 687 35 8 3971 4653 543681104 543681781 0.000000e+00 990.0
40 TraesCS7A01G424000 chr2A 85.409 843 82 19 4652 5490 462370342 462371147 0.000000e+00 837.0
41 TraesCS7A01G424000 chr2A 87.152 467 26 17 2183 2631 721616866 721616416 2.950000e-137 499.0
42 TraesCS7A01G424000 chr2A 94.464 289 16 0 2861 3149 721616172 721615884 3.900000e-121 446.0
43 TraesCS7A01G424000 chr2A 79.417 617 76 35 750 1331 721617716 721617116 6.670000e-104 388.0
44 TraesCS7A01G424000 chr2A 84.615 104 16 0 544 647 462370109 462370212 2.710000e-18 104.0
45 TraesCS7A01G424000 chr6A 90.218 1421 98 16 3248 4653 457042684 457041290 0.000000e+00 1816.0
46 TraesCS7A01G424000 chr6A 92.581 957 64 4 3143 4097 41601175 41602126 0.000000e+00 1367.0
47 TraesCS7A01G424000 chr6A 77.910 842 111 42 763 1543 41599175 41600002 6.480000e-124 455.0
48 TraesCS7A01G424000 chr6A 87.705 366 31 6 4289 4652 41602753 41603106 1.100000e-111 414.0
49 TraesCS7A01G424000 chr1D 91.409 1292 75 7 3143 4421 416150175 416151443 0.000000e+00 1738.0
50 TraesCS7A01G424000 chr1D 87.794 467 34 13 2183 2631 416149004 416149465 4.870000e-145 525.0
51 TraesCS7A01G424000 chr1D 94.118 289 17 0 2861 3149 416149701 416149989 1.820000e-119 440.0
52 TraesCS7A01G424000 chr1D 79.495 634 73 29 954 1543 416148382 416149002 1.110000e-106 398.0
53 TraesCS7A01G424000 chr4A 93.950 843 41 4 4652 5491 650520069 650519234 0.000000e+00 1266.0
54 TraesCS7A01G424000 chr4A 97.115 104 2 1 643 745 650520172 650520069 2.030000e-39 174.0
55 TraesCS7A01G424000 chr4A 90.909 110 10 0 543 652 650520305 650520196 1.230000e-31 148.0
56 TraesCS7A01G424000 chr7D 93.824 842 48 2 4653 5491 325487506 325486666 0.000000e+00 1264.0
57 TraesCS7A01G424000 chr7D 87.517 745 64 11 4652 5393 597432865 597433583 0.000000e+00 833.0
58 TraesCS7A01G424000 chr7D 90.792 467 42 1 76 541 536456614 536457080 1.680000e-174 623.0
59 TraesCS7A01G424000 chr7D 82.751 429 59 10 4925 5342 29479028 29479452 8.690000e-98 368.0
60 TraesCS7A01G424000 chr7D 95.327 107 3 2 643 747 325487610 325487504 9.460000e-38 169.0
61 TraesCS7A01G424000 chr7D 93.043 115 7 1 5377 5490 597435588 597435702 3.400000e-37 167.0
62 TraesCS7A01G424000 chr7D 91.892 111 9 0 540 650 325487742 325487632 7.360000e-34 156.0
63 TraesCS7A01G424000 chr7D 87.037 108 10 4 641 745 29478566 29478672 9.660000e-23 119.0
64 TraesCS7A01G424000 chr7D 83.036 112 16 3 533 643 586225939 586226048 1.260000e-16 99.0
65 TraesCS7A01G424000 chr7D 90.000 70 5 2 4 73 536454400 536454467 7.580000e-14 89.8
66 TraesCS7A01G424000 chr7D 91.489 47 3 1 532 578 603087692 603087647 4.590000e-06 63.9
67 TraesCS7A01G424000 chr2D 88.493 843 67 13 4652 5490 184364727 184365543 0.000000e+00 992.0
68 TraesCS7A01G424000 chr2D 82.114 369 49 7 1810 2165 315108303 315108667 3.220000e-77 300.0
69 TraesCS7A01G424000 chr2D 80.096 417 55 14 1810 2214 612483385 612483785 9.000000e-73 285.0
70 TraesCS7A01G424000 chr2D 86.345 249 34 0 1477 1725 612483140 612483388 7.010000e-69 272.0
71 TraesCS7A01G424000 chr2D 80.833 240 34 10 740 972 286742616 286742850 1.570000e-40 178.0
72 TraesCS7A01G424000 chr2D 79.730 222 39 5 744 962 588720670 588720452 7.360000e-34 156.0
73 TraesCS7A01G424000 chr2D 85.437 103 15 0 545 647 184364495 184364597 2.090000e-19 108.0
74 TraesCS7A01G424000 chr3D 88.016 751 66 8 1477 2214 364263292 364264031 0.000000e+00 867.0
75 TraesCS7A01G424000 chrUn 100.000 389 0 0 2303 2691 480104604 480104992 0.000000e+00 719.0
76 TraesCS7A01G424000 chrUn 88.732 213 20 4 4652 4863 477216552 477216343 1.960000e-64 257.0
77 TraesCS7A01G424000 chrUn 84.231 260 22 13 1078 1331 476699348 476699594 9.200000e-58 235.0
78 TraesCS7A01G424000 chrUn 87.255 102 10 2 641 740 49772820 49772920 4.500000e-21 113.0
79 TraesCS7A01G424000 chr7B 88.425 527 49 4 16 541 579672523 579673038 4.670000e-175 625.0
80 TraesCS7A01G424000 chr7B 86.465 495 51 8 5002 5490 692308822 692309306 3.770000e-146 529.0
81 TraesCS7A01G424000 chr7B 86.938 467 31 13 76 541 579569240 579569677 1.060000e-136 497.0
82 TraesCS7A01G424000 chr7B 89.254 335 36 0 16 350 579683816 579684150 2.370000e-113 420.0
83 TraesCS7A01G424000 chr7B 88.144 194 12 5 16 209 579773988 579774170 2.570000e-53 220.0
84 TraesCS7A01G424000 chr6B 81.105 561 87 16 4819 5370 147252384 147251834 1.090000e-116 431.0
85 TraesCS7A01G424000 chr6B 79.372 223 43 3 744 963 657072316 657072094 2.650000e-33 154.0
86 TraesCS7A01G424000 chr1A 81.384 419 47 11 1810 2214 97188182 97188583 4.130000e-81 313.0
87 TraesCS7A01G424000 chr1A 85.542 249 34 1 1477 1725 97187939 97188185 5.460000e-65 259.0
88 TraesCS7A01G424000 chr1A 81.735 219 35 4 743 960 144563730 144563516 1.570000e-40 178.0
89 TraesCS7A01G424000 chr1A 83.158 190 27 5 744 930 518023068 518023255 9.460000e-38 169.0
90 TraesCS7A01G424000 chr1A 80.093 216 38 5 749 962 584839374 584839162 7.360000e-34 156.0
91 TraesCS7A01G424000 chr1A 95.652 46 1 1 533 578 326026277 326026233 7.630000e-09 73.1
92 TraesCS7A01G424000 chr1A 89.796 49 2 2 533 579 71235410 71235457 5.940000e-05 60.2


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 TraesCS7A01G424000 chr7A 617003582 617009072 5490 True 10141.000000 10141 100.000000 1 5491 1 chr7A.!!$R3 5490
1 TraesCS7A01G424000 chr7A 104461584 104462260 676 True 966.000000 966 92.420000 3971 4652 1 chr7A.!!$R1 681
2 TraesCS7A01G424000 chr7A 684994550 684995354 804 False 848.000000 848 85.664000 4652 5490 1 chr7A.!!$F1 838
3 TraesCS7A01G424000 chr7A 108110307 108111139 832 True 455.000000 455 77.895000 750 1543 1 chr7A.!!$R2 793
4 TraesCS7A01G424000 chr5A 607949327 607953236 3909 False 6966.000000 6966 98.825000 742 4652 1 chr5A.!!$F1 3910
5 TraesCS7A01G424000 chr5A 560598146 560602083 3937 True 662.000000 1378 88.370250 748 4651 4 chr5A.!!$R1 3903
6 TraesCS7A01G424000 chr5A 4625883 4626920 1037 False 479.000000 859 84.777000 544 5490 2 chr5A.!!$F2 4946
7 TraesCS7A01G424000 chr6D 38772345 38776223 3878 True 6597.000000 6597 97.284000 750 4650 1 chr6D.!!$R1 3900
8 TraesCS7A01G424000 chr3A 694982242 694983626 1384 False 2492.000000 2492 99.134000 3269 4653 1 chr3A.!!$F3 1384
9 TraesCS7A01G424000 chr3A 23890309 23890957 648 False 926.000000 926 92.390000 3971 4623 1 chr3A.!!$F1 652
10 TraesCS7A01G424000 chr3A 485686830 485687568 738 False 821.000000 821 86.951000 1477 2214 1 chr3A.!!$F2 737
11 TraesCS7A01G424000 chr3A 690719287 690723017 3730 False 755.500000 1965 88.070000 751 4652 4 chr3A.!!$F4 3901
12 TraesCS7A01G424000 chr3B 221132910 221134417 1507 True 2017.000000 2017 90.873000 3143 4652 1 chr3B.!!$R1 1509
13 TraesCS7A01G424000 chr3B 474408881 474409615 734 False 839.000000 839 87.450000 1477 2214 1 chr3B.!!$F1 737
14 TraesCS7A01G424000 chr3B 277019710 277026490 6780 False 759.500000 2069 90.706333 2183 4657 6 chr3B.!!$F3 2474
15 TraesCS7A01G424000 chr3B 817346201 817346824 623 True 372.500000 532 88.251500 1356 2605 2 chr3B.!!$R2 1249
16 TraesCS7A01G424000 chr2B 75905710 75908390 2680 False 1011.000000 2054 91.182667 2183 4652 3 chr2B.!!$F1 2469
17 TraesCS7A01G424000 chr1B 123482947 123485855 2908 False 916.000000 2039 87.090667 1318 4654 3 chr1B.!!$F1 3336
18 TraesCS7A01G424000 chr2A 543681104 543681781 677 False 990.000000 990 93.013000 3971 4653 1 chr2A.!!$F1 682
19 TraesCS7A01G424000 chr2A 721614190 721617716 3526 True 835.750000 2010 87.978000 750 4652 4 chr2A.!!$R1 3902
20 TraesCS7A01G424000 chr2A 462370109 462371147 1038 False 470.500000 837 85.012000 544 5490 2 chr2A.!!$F2 4946
21 TraesCS7A01G424000 chr6A 457041290 457042684 1394 True 1816.000000 1816 90.218000 3248 4653 1 chr6A.!!$R1 1405
22 TraesCS7A01G424000 chr6A 41599175 41603106 3931 False 745.333333 1367 86.065333 763 4652 3 chr6A.!!$F1 3889
23 TraesCS7A01G424000 chr1D 416148382 416151443 3061 False 775.250000 1738 88.204000 954 4421 4 chr1D.!!$F1 3467
24 TraesCS7A01G424000 chr4A 650519234 650520305 1071 True 529.333333 1266 93.991333 543 5491 3 chr4A.!!$R1 4948
25 TraesCS7A01G424000 chr7D 325486666 325487742 1076 True 529.666667 1264 93.681000 540 5491 3 chr7D.!!$R2 4951
26 TraesCS7A01G424000 chr7D 597432865 597435702 2837 False 500.000000 833 90.280000 4652 5490 2 chr7D.!!$F4 838
27 TraesCS7A01G424000 chr7D 536454400 536457080 2680 False 356.400000 623 90.396000 4 541 2 chr7D.!!$F3 537
28 TraesCS7A01G424000 chr7D 29478566 29479452 886 False 243.500000 368 84.894000 641 5342 2 chr7D.!!$F2 4701
29 TraesCS7A01G424000 chr2D 184364495 184365543 1048 False 550.000000 992 86.965000 545 5490 2 chr2D.!!$F3 4945
30 TraesCS7A01G424000 chr2D 612483140 612483785 645 False 278.500000 285 83.220500 1477 2214 2 chr2D.!!$F4 737
31 TraesCS7A01G424000 chr3D 364263292 364264031 739 False 867.000000 867 88.016000 1477 2214 1 chr3D.!!$F1 737
32 TraesCS7A01G424000 chr7B 579672523 579673038 515 False 625.000000 625 88.425000 16 541 1 chr7B.!!$F2 525
33 TraesCS7A01G424000 chr6B 147251834 147252384 550 True 431.000000 431 81.105000 4819 5370 1 chr6B.!!$R1 551
34 TraesCS7A01G424000 chr1A 97187939 97188583 644 False 286.000000 313 83.463000 1477 2214 2 chr1A.!!$F3 737

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
586 2732 0.462047 CACGGGGCTAGCCTACAAAG 60.462 60.000 32.18 18.43 36.10 2.77 F
923 3105 1.702182 TCAAATGTTCTGCCTGGCAA 58.298 45.000 23.51 8.16 38.41 4.52 F
1349 3596 3.063704 CATGTGCCACGCCCATGT 61.064 61.111 1.49 0.00 33.06 3.21 F
1717 3967 3.871594 ACACTTTCAGTCACTACACTTGC 59.128 43.478 0.00 0.00 0.00 4.01 F
3013 9481 0.263172 AGATCTCCATCTGGACCGGT 59.737 55.000 6.92 6.92 38.03 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 3664 1.845809 GCAAGGAACCACGACTGCAG 61.846 60.000 13.48 13.48 0.00 4.41 R
1950 4201 1.906574 ACAGGCTTCCGGTATCAAAGA 59.093 47.619 0.00 0.00 28.50 2.52 R
3013 9481 3.307269 CCTTGAGATTCTGGAAGCTGTCA 60.307 47.826 5.82 0.00 37.15 3.58 R
3017 9485 5.707066 ATTACCTTGAGATTCTGGAAGCT 57.293 39.130 0.49 0.49 40.10 3.74 R
4749 12093 5.349543 GGAGCAGCAAAAATGATTTGGTAAG 59.650 40.000 5.43 0.00 37.96 2.34 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
53 54 1.112916 TCGGACACCAGCTCTTGACA 61.113 55.000 0.00 0.00 0.00 3.58
58 59 1.202580 ACACCAGCTCTTGACACTGTC 60.203 52.381 1.86 1.86 0.00 3.51
88 2233 3.387947 ACCGGCCCTAACTCCACG 61.388 66.667 0.00 0.00 0.00 4.94
97 2242 1.139058 CCTAACTCCACGGATCCAAGG 59.861 57.143 13.41 12.78 0.00 3.61
129 2274 1.685224 CCCTTGCCTTCTAGCACCA 59.315 57.895 0.00 0.00 43.97 4.17
134 2279 0.617535 TGCCTTCTAGCACCAGCCTA 60.618 55.000 0.00 0.00 43.56 3.93
143 2288 1.196012 GCACCAGCCTAACTAGGTCT 58.804 55.000 4.72 0.21 45.42 3.85
146 2291 3.034635 CACCAGCCTAACTAGGTCTGAT 58.965 50.000 20.05 7.95 43.80 2.90
209 2354 2.766828 GCTATCCACTAGAACACCCACT 59.233 50.000 0.00 0.00 0.00 4.00
219 2364 3.939066 AGAACACCCACTAGAAAATCGG 58.061 45.455 0.00 0.00 0.00 4.18
246 2391 2.698855 ATAATGCGAACCAGAGCTGT 57.301 45.000 0.00 0.00 0.00 4.40
257 2402 2.193248 GAGCTGTGTATGGGCCCC 59.807 66.667 22.27 3.99 0.00 5.80
268 2413 3.797353 GGGCCCCGCTCAATGAGA 61.797 66.667 12.23 0.00 0.00 3.27
299 2444 1.270893 GGTGTGGGTCAAGAAGAGGAC 60.271 57.143 0.00 0.00 0.00 3.85
306 2451 3.008485 GGGTCAAGAAGAGGACAGTCAAT 59.992 47.826 2.17 0.00 35.74 2.57
331 2476 3.653344 GATGTCGATCGGAATGAATGGA 58.347 45.455 16.41 0.00 0.00 3.41
376 2522 2.430921 GGAGTGGCGTGACTCGTG 60.431 66.667 9.10 0.00 42.97 4.35
508 2654 7.707464 TCATTTTTCAACTCGAACTACTACACA 59.293 33.333 0.00 0.00 31.73 3.72
529 2675 6.481976 ACACAGACACAGACATAAATTTTCGA 59.518 34.615 0.00 0.00 0.00 3.71
532 2678 7.387673 ACAGACACAGACATAAATTTTCGATGA 59.612 33.333 6.46 0.00 0.00 2.92
586 2732 0.462047 CACGGGGCTAGCCTACAAAG 60.462 60.000 32.18 18.43 36.10 2.77
842 3024 8.655935 AATCAGAACCCTCAAATTAAGTCAAT 57.344 30.769 0.00 0.00 0.00 2.57
923 3105 1.702182 TCAAATGTTCTGCCTGGCAA 58.298 45.000 23.51 8.16 38.41 4.52
1349 3596 3.063704 CATGTGCCACGCCCATGT 61.064 61.111 1.49 0.00 33.06 3.21
1417 3664 4.509600 CCGTCTCTGCATAGGAATCTTTTC 59.490 45.833 0.00 0.00 0.00 2.29
1717 3967 3.871594 ACACTTTCAGTCACTACACTTGC 59.128 43.478 0.00 0.00 0.00 4.01
1950 4201 5.317733 TGAAACTGACACATTTTTCGGTT 57.682 34.783 0.00 0.00 42.06 4.44
2691 7027 5.446143 AGCAGACTCGATCGAATCTAATT 57.554 39.130 26.72 13.43 28.98 1.40
3013 9481 0.263172 AGATCTCCATCTGGACCGGT 59.737 55.000 6.92 6.92 38.03 5.28
3017 9485 1.229051 TCCATCTGGACCGGTGACA 60.229 57.895 14.63 10.53 39.78 3.58
3292 10164 8.405531 GTTGAATATAGTGCATTGTTATGTGGT 58.594 33.333 0.00 0.00 34.12 4.16
3442 10314 4.765339 GGTCTAAACCAAATGTTAGGCACT 59.235 41.667 0.00 0.00 45.68 4.40
3715 10593 4.322725 CCTTTTTATGCCACCCTTCTTTCC 60.323 45.833 0.00 0.00 0.00 3.13
4782 12126 4.503741 TTTTTGCTGCTCCAACACTATC 57.496 40.909 0.00 0.00 0.00 2.08
4865 12314 9.500785 TGTGATAACATCTTCATCAGTTTGTTA 57.499 29.630 0.00 0.00 36.98 2.41
4933 12382 7.321153 ACAGTAAAAGTCGTCAGCAACTATAT 58.679 34.615 0.00 0.00 0.00 0.86
4981 12430 1.892474 CACCCGATTGACAACCCAATT 59.108 47.619 0.00 0.00 36.93 2.32
5287 12750 6.528321 TCATTCTAGGATCTGTGGCATAAAG 58.472 40.000 0.00 0.00 0.00 1.85
5351 12819 0.961857 TCTTGCGACAGCCATGCAAT 60.962 50.000 0.00 0.00 46.39 3.56
5443 14933 4.582701 TTTTCTCAAAACCATGTGCGAT 57.417 36.364 0.00 0.00 0.00 4.58
5453 14943 2.964740 CCATGTGCGATGGTATCCTAG 58.035 52.381 6.43 0.00 34.56 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.914131 CGAGATCAATACTTGGTGATATCTTTA 57.086 33.333 3.98 0.00 39.33 1.85
11 12 7.875041 CCGAGATCAATACTTGGTGATATCTTT 59.125 37.037 3.98 0.00 39.33 2.52
12 13 7.233553 TCCGAGATCAATACTTGGTGATATCTT 59.766 37.037 3.98 0.00 39.33 2.40
13 14 6.721668 TCCGAGATCAATACTTGGTGATATCT 59.278 38.462 3.98 0.00 39.33 1.98
14 15 6.809196 GTCCGAGATCAATACTTGGTGATATC 59.191 42.308 0.00 0.00 38.52 1.63
53 54 0.317938 GTGTTCGCAGAGTCGACAGT 60.318 55.000 19.50 0.30 38.43 3.55
58 59 2.805353 CCGGTGTTCGCAGAGTCG 60.805 66.667 0.00 0.00 38.43 4.18
88 2233 1.087501 GCTTTCGTGACCTTGGATCC 58.912 55.000 4.20 4.20 0.00 3.36
97 2242 1.668151 AAGGGCGAGCTTTCGTGAC 60.668 57.895 0.00 0.00 35.26 3.67
143 2288 0.413434 TCCTGGAGTCCTGGTCATCA 59.587 55.000 28.78 11.36 42.31 3.07
146 2291 1.079256 CCTCCTGGAGTCCTGGTCA 59.921 63.158 28.78 14.04 42.31 4.02
172 2317 1.370609 TAGCGGTCAGAGTCGAGAAG 58.629 55.000 0.00 0.00 0.00 2.85
209 2354 6.039616 GCATTATTTGGTTGCCGATTTTCTA 58.960 36.000 0.00 0.00 0.00 2.10
219 2364 2.923020 CTGGTTCGCATTATTTGGTTGC 59.077 45.455 0.00 0.00 0.00 4.17
246 2391 2.382770 ATTGAGCGGGGCCCATACA 61.383 57.895 26.86 15.60 0.00 2.29
257 2402 1.900351 TGAGGGGTCTCATTGAGCG 59.100 57.895 8.89 0.00 44.39 5.03
275 2420 1.780309 TCTTCTTGACCCACACCCATT 59.220 47.619 0.00 0.00 0.00 3.16
328 2473 1.133809 CACCCACCTCCCTTCTTCCA 61.134 60.000 0.00 0.00 0.00 3.53
331 2476 2.069165 GCACACCCACCTCCCTTCTT 62.069 60.000 0.00 0.00 0.00 2.52
376 2522 0.972134 TCCATCATCTCTCGGCCATC 59.028 55.000 2.24 0.00 0.00 3.51
456 2602 6.726490 AGCCCTATTAGAATACAAGTCGAA 57.274 37.500 0.00 0.00 0.00 3.71
475 2621 5.560966 TCGAGTTGAAAAATGATTAGCCC 57.439 39.130 0.00 0.00 0.00 5.19
508 2654 7.905604 TCATCGAAAATTTATGTCTGTGTCT 57.094 32.000 0.00 0.00 0.00 3.41
550 2696 3.187058 GCGAATGCACGGGTTGAT 58.813 55.556 0.00 0.00 42.15 2.57
1349 3596 4.314961 CAGCATATTATTCACCGTGGCTA 58.685 43.478 0.00 0.00 0.00 3.93
1417 3664 1.845809 GCAAGGAACCACGACTGCAG 61.846 60.000 13.48 13.48 0.00 4.41
1717 3967 4.747108 CAGAAGGATTTGCCGTAGATAGTG 59.253 45.833 0.00 0.00 43.43 2.74
1859 4109 9.558396 AGATGAAGAGCAAAATAGGAGAAATAG 57.442 33.333 0.00 0.00 0.00 1.73
1950 4201 1.906574 ACAGGCTTCCGGTATCAAAGA 59.093 47.619 0.00 0.00 28.50 2.52
2691 7027 3.815962 ACGCAACAAACACACCATATACA 59.184 39.130 0.00 0.00 0.00 2.29
3013 9481 3.307269 CCTTGAGATTCTGGAAGCTGTCA 60.307 47.826 5.82 0.00 37.15 3.58
3017 9485 5.707066 ATTACCTTGAGATTCTGGAAGCT 57.293 39.130 0.49 0.49 40.10 3.74
3292 10164 5.883115 TGCATCAATTCATAAGGTTCCGTAA 59.117 36.000 0.00 0.00 0.00 3.18
3442 10314 6.095300 CCAACTGTGCACATAATCCTCATTTA 59.905 38.462 22.00 0.00 0.00 1.40
3715 10593 8.442632 TCAGAGCAAATAAGTTGGAATATGAG 57.557 34.615 0.00 0.00 37.73 2.90
4749 12093 5.349543 GGAGCAGCAAAAATGATTTGGTAAG 59.650 40.000 5.43 0.00 37.96 2.34
4855 12304 9.698309 CAGAGAAGATTAGACTTAACAAACTGA 57.302 33.333 0.00 0.00 0.00 3.41
4865 12314 8.734593 ATATAAGGCCAGAGAAGATTAGACTT 57.265 34.615 5.01 0.00 0.00 3.01
5016 12465 0.963962 TGTAGGACAGGTCAACGGAC 59.036 55.000 1.41 0.00 43.55 4.79
5287 12750 6.039781 TGTAAAAAGCACAAAGTAGACGAC 57.960 37.500 0.00 0.00 0.00 4.34
5351 12819 9.639563 TGCCAAGAAATATATATTCTCAAACCA 57.360 29.630 8.42 0.00 36.14 3.67
5443 14933 7.206789 TCACCATGATTTTTCTAGGATACCA 57.793 36.000 0.00 0.00 37.17 3.25


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

AutoCloner maintained by Alex Coulton.