Multiple sequence alignment - TraesCS6A01G214000

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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 TraesCS6A01G214000 chr6A 100.000 7312 0 0 1 7312 389960402 389953091 0.000000e+00 13503.0
1 TraesCS6A01G214000 chr6A 96.887 514 14 2 1 514 116580355 116580866 0.000000e+00 859.0
2 TraesCS6A01G214000 chr6A 96.311 515 19 0 1 515 501165085 501165599 0.000000e+00 846.0
3 TraesCS6A01G214000 chr6B 96.068 6078 165 38 514 6564 434303874 434297844 0.000000e+00 9832.0
4 TraesCS6A01G214000 chr6B 87.654 648 60 8 6673 7312 434296625 434295990 0.000000e+00 736.0
5 TraesCS6A01G214000 chr6D 95.460 4581 145 24 514 5082 272863894 272859365 0.000000e+00 7249.0
6 TraesCS6A01G214000 chr6D 94.423 789 25 10 5087 5868 272859231 272858455 0.000000e+00 1195.0
7 TraesCS6A01G214000 chr6D 91.206 398 14 10 5790 6180 272858485 272858102 8.410000e-144 521.0
8 TraesCS6A01G214000 chr6D 86.468 436 30 12 3528 3938 301725714 301726145 1.120000e-122 451.0
9 TraesCS6A01G214000 chr6D 100.000 38 0 0 5783 5820 272858443 272858406 3.660000e-08 71.3
10 TraesCS6A01G214000 chr3A 84.685 2749 318 56 1532 4227 96250124 96247426 0.000000e+00 2649.0
11 TraesCS6A01G214000 chr3A 86.630 1623 156 24 1957 3567 56668613 56670186 0.000000e+00 1738.0
12 TraesCS6A01G214000 chr3A 88.484 1207 90 18 4628 5815 56675056 56676232 0.000000e+00 1413.0
13 TraesCS6A01G214000 chr3A 88.674 1139 89 18 4609 5735 96243129 96242019 0.000000e+00 1352.0
14 TraesCS6A01G214000 chr3A 81.818 539 75 18 604 1129 96251200 96250672 1.460000e-116 431.0
15 TraesCS6A01G214000 chr3A 80.754 504 62 19 4228 4715 56670820 56671304 1.940000e-95 361.0
16 TraesCS6A01G214000 chr3A 81.407 398 34 24 5840 6223 96241971 96241600 9.280000e-74 289.0
17 TraesCS6A01G214000 chr3A 75.815 368 43 23 4235 4598 96247507 96247182 2.130000e-30 145.0
18 TraesCS6A01G214000 chr3D 84.366 2744 318 55 1532 4227 81720947 81718267 0.000000e+00 2588.0
19 TraesCS6A01G214000 chr3D 84.490 2708 295 68 1537 4177 44882109 44884758 0.000000e+00 2558.0
20 TraesCS6A01G214000 chr3D 88.640 1206 81 13 4628 5817 44887852 44889017 0.000000e+00 1417.0
21 TraesCS6A01G214000 chr3D 88.489 1138 95 20 4609 5734 81715527 81714414 0.000000e+00 1343.0
22 TraesCS6A01G214000 chr3D 80.754 504 62 14 4228 4715 44884723 44885207 1.940000e-95 361.0
23 TraesCS6A01G214000 chr3D 83.292 401 35 18 5838 6223 81714364 81713981 2.530000e-89 340.0
24 TraesCS6A01G214000 chr3D 74.932 367 48 21 4235 4598 81718348 81718023 2.140000e-25 128.0
25 TraesCS6A01G214000 chr3B 84.356 2755 308 64 1532 4227 127936112 127933422 0.000000e+00 2586.0
26 TraesCS6A01G214000 chr3B 86.660 1919 195 32 1537 3433 69811377 69813256 0.000000e+00 2069.0
27 TraesCS6A01G214000 chr3B 88.687 1211 83 24 4628 5817 69817202 69818379 0.000000e+00 1428.0
28 TraesCS6A01G214000 chr3B 88.179 1142 90 25 4609 5734 127930586 127929474 0.000000e+00 1319.0
29 TraesCS6A01G214000 chr3B 82.114 492 50 15 4242 4715 69814022 69814493 3.200000e-103 387.0
30 TraesCS6A01G214000 chr3B 83.081 396 35 12 5837 6220 127929418 127929043 1.520000e-86 331.0
31 TraesCS6A01G214000 chr5A 97.485 517 13 0 1 517 563006973 563006457 0.000000e+00 883.0
32 TraesCS6A01G214000 chr2A 96.893 515 16 0 1 515 448495693 448495179 0.000000e+00 863.0
33 TraesCS6A01G214000 chr2A 95.573 384 17 0 132 515 543316830 543317213 3.750000e-172 616.0
34 TraesCS6A01G214000 chr2A 95.420 131 5 1 2 131 768991165 768991295 2.670000e-49 207.0
35 TraesCS6A01G214000 chr4A 94.027 519 27 1 2 520 713971922 713971408 0.000000e+00 784.0
36 TraesCS6A01G214000 chr4A 89.556 383 32 4 4597 4977 706471903 706471527 5.130000e-131 479.0
37 TraesCS6A01G214000 chr4A 85.748 428 36 9 5103 5527 706471532 706471127 5.240000e-116 429.0
38 TraesCS6A01G214000 chr4A 80.064 627 68 25 3510 4107 706494079 706493481 5.280000e-111 412.0
39 TraesCS6A01G214000 chr4A 89.286 168 13 3 4370 4534 706478335 706478170 9.620000e-49 206.0
40 TraesCS6A01G214000 chr4A 92.000 75 6 0 6181 6255 706471125 706471051 1.000000e-18 106.0
41 TraesCS6A01G214000 chr4A 86.842 76 7 3 6614 6686 693531810 693531735 1.690000e-11 82.4
42 TraesCS6A01G214000 chr5B 92.115 520 31 7 2 515 23357084 23356569 0.000000e+00 725.0
43 TraesCS6A01G214000 chr7B 89.266 531 34 4 2 512 334311820 334312347 1.720000e-180 643.0
44 TraesCS6A01G214000 chr7B 84.988 433 46 14 3528 3946 18958580 18958153 8.770000e-114 422.0
45 TraesCS6A01G214000 chr2B 87.184 515 51 9 9 516 12170662 12171168 8.230000e-159 571.0
46 TraesCS6A01G214000 chr7D 83.591 518 57 23 1534 2049 46890971 46891462 1.860000e-125 460.0
47 TraesCS6A01G214000 chr7D 85.430 302 34 2 2056 2357 46893215 46893506 9.220000e-79 305.0
48 TraesCS6A01G214000 chr7D 89.655 58 6 0 6640 6697 168789618 168789561 2.830000e-09 75.0
49 TraesCS6A01G214000 chr7A 86.463 229 15 6 2521 2749 23791393 23791605 3.410000e-58 237.0
50 TraesCS6A01G214000 chr7A 87.931 58 7 0 6640 6697 222779811 222779754 1.320000e-07 69.4


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 TraesCS6A01G214000 chr6A 389953091 389960402 7311 True 13503.000000 13503 100.000000 1 7312 1 chr6A.!!$R1 7311
1 TraesCS6A01G214000 chr6A 116580355 116580866 511 False 859.000000 859 96.887000 1 514 1 chr6A.!!$F1 513
2 TraesCS6A01G214000 chr6A 501165085 501165599 514 False 846.000000 846 96.311000 1 515 1 chr6A.!!$F2 514
3 TraesCS6A01G214000 chr6B 434295990 434303874 7884 True 5284.000000 9832 91.861000 514 7312 2 chr6B.!!$R1 6798
4 TraesCS6A01G214000 chr6D 272858102 272863894 5792 True 2259.075000 7249 95.272250 514 6180 4 chr6D.!!$R1 5666
5 TraesCS6A01G214000 chr3A 56668613 56676232 7619 False 1170.666667 1738 85.289333 1957 5815 3 chr3A.!!$F1 3858
6 TraesCS6A01G214000 chr3A 96247182 96251200 4018 True 1075.000000 2649 80.772667 604 4598 3 chr3A.!!$R2 3994
7 TraesCS6A01G214000 chr3A 96241600 96243129 1529 True 820.500000 1352 85.040500 4609 6223 2 chr3A.!!$R1 1614
8 TraesCS6A01G214000 chr3D 44882109 44889017 6908 False 1445.333333 2558 84.628000 1537 5817 3 chr3D.!!$F1 4280
9 TraesCS6A01G214000 chr3D 81713981 81720947 6966 True 1099.750000 2588 82.769750 1532 6223 4 chr3D.!!$R1 4691
10 TraesCS6A01G214000 chr3B 127929043 127936112 7069 True 1412.000000 2586 85.205333 1532 6220 3 chr3B.!!$R1 4688
11 TraesCS6A01G214000 chr3B 69811377 69818379 7002 False 1294.666667 2069 85.820333 1537 5817 3 chr3B.!!$F1 4280
12 TraesCS6A01G214000 chr5A 563006457 563006973 516 True 883.000000 883 97.485000 1 517 1 chr5A.!!$R1 516
13 TraesCS6A01G214000 chr2A 448495179 448495693 514 True 863.000000 863 96.893000 1 515 1 chr2A.!!$R1 514
14 TraesCS6A01G214000 chr4A 713971408 713971922 514 True 784.000000 784 94.027000 2 520 1 chr4A.!!$R4 518
15 TraesCS6A01G214000 chr4A 706493481 706494079 598 True 412.000000 412 80.064000 3510 4107 1 chr4A.!!$R3 597
16 TraesCS6A01G214000 chr4A 706471051 706471903 852 True 338.000000 479 89.101333 4597 6255 3 chr4A.!!$R5 1658
17 TraesCS6A01G214000 chr5B 23356569 23357084 515 True 725.000000 725 92.115000 2 515 1 chr5B.!!$R1 513
18 TraesCS6A01G214000 chr7B 334311820 334312347 527 False 643.000000 643 89.266000 2 512 1 chr7B.!!$F1 510
19 TraesCS6A01G214000 chr2B 12170662 12171168 506 False 571.000000 571 87.184000 9 516 1 chr2B.!!$F1 507
20 TraesCS6A01G214000 chr7D 46890971 46893506 2535 False 382.500000 460 84.510500 1534 2357 2 chr7D.!!$F1 823

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
489 514 0.039437 GAAGCCTCGACAACTCGACA 60.039 55.000 0.00 0.00 44.14 4.35 F
1594 1788 0.030101 TTTCGGCTTTTGTGCTTCCG 59.970 50.000 0.00 0.00 41.30 4.30 F
2902 4871 0.249868 TGAGGCTGTGAACGTTCCTG 60.250 55.000 24.78 18.83 0.00 3.86 F
3641 5700 0.106708 TCCTGCAACTGTCTCACACC 59.893 55.000 0.00 0.00 0.00 4.16 F
4094 6217 1.028330 TACCGCCTCTGTAGTCACCG 61.028 60.000 0.00 0.00 0.00 4.94 F
4119 6252 1.352083 TCTGTTCCCTCCTTGTCCAG 58.648 55.000 0.00 0.00 0.00 3.86 F
5571 15555 1.340405 CCATGCAGTTTCCCTAGCAGT 60.340 52.381 0.00 0.00 40.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 4373 0.178068 TGCCCTCGAGGATTGTAAGC 59.822 55.000 33.39 24.01 38.24 3.09 R
2905 4874 0.689623 AAGTGACTGAGGCCAGGAAG 59.310 55.000 5.01 0.00 44.60 3.46 R
4170 6303 0.176680 AGCGAGTCAGCCATACAAGG 59.823 55.000 3.79 0.00 38.01 3.61 R
4961 14799 0.469494 TGTCAGAAAGAGGTGCAGCA 59.531 50.000 19.63 0.00 0.00 4.41 R
5204 15174 1.375523 AAGGTCCCGCTTACGCTTG 60.376 57.895 0.00 0.00 38.22 4.01 R
5626 15612 4.320494 GGCAATTGTTCTGTCTTTGACGAT 60.320 41.667 7.40 0.00 34.95 3.73 R
6860 18053 0.601841 AACTTGTAACTCCCGCCACG 60.602 55.000 0.00 0.00 0.00 4.94 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
378 402 2.949644 CAAAACCGTTCAGGAACCTTCT 59.050 45.455 6.59 0.00 45.00 2.85
489 514 0.039437 GAAGCCTCGACAACTCGACA 60.039 55.000 0.00 0.00 44.14 4.35
496 521 0.933047 CGACAACTCGACACAGCGAA 60.933 55.000 0.00 0.00 43.06 4.70
724 754 2.287915 CCCAGAAATTATCGAACCGCAG 59.712 50.000 0.00 0.00 0.00 5.18
790 820 2.902705 GCCCCACGATACATAGTCAA 57.097 50.000 0.00 0.00 0.00 3.18
1051 1084 1.099879 GCTCCGTCCCGCTCTACTTA 61.100 60.000 0.00 0.00 0.00 2.24
1102 1143 0.744771 GATCCAACTCCACTTCGGGC 60.745 60.000 0.00 0.00 34.36 6.13
1168 1216 3.575351 GACAACTGGAGGCGCGAGT 62.575 63.158 12.10 0.00 37.12 4.18
1172 1220 2.507992 CTGGAGGCGCGAGTGAAG 60.508 66.667 12.10 0.00 0.00 3.02
1188 1236 3.831911 AGTGAAGGGAGAACAAGAGAGAG 59.168 47.826 0.00 0.00 0.00 3.20
1189 1237 3.829601 GTGAAGGGAGAACAAGAGAGAGA 59.170 47.826 0.00 0.00 0.00 3.10
1192 1240 5.011533 TGAAGGGAGAACAAGAGAGAGAAAG 59.988 44.000 0.00 0.00 0.00 2.62
1198 1246 5.151454 AGAACAAGAGAGAGAAAGGAGGAA 58.849 41.667 0.00 0.00 0.00 3.36
1209 1257 6.980577 AGAGAAAGGAGGAAGAGAGAAGATA 58.019 40.000 0.00 0.00 0.00 1.98
1395 1444 4.100084 CCGTGGCCTGCATCCTCA 62.100 66.667 3.32 0.00 0.00 3.86
1492 1542 4.324402 GCCAATTACAAGATTTGAGCGTTG 59.676 41.667 0.00 0.00 0.00 4.10
1581 1775 6.019881 GCATTTGAATACCTGTAAATTTCGGC 60.020 38.462 0.00 0.00 0.00 5.54
1584 1778 6.827586 TGAATACCTGTAAATTTCGGCTTT 57.172 33.333 0.00 0.00 0.00 3.51
1594 1788 0.030101 TTTCGGCTTTTGTGCTTCCG 59.970 50.000 0.00 0.00 41.30 4.30
1686 1906 3.632643 TTATTCAGCAGATCTGTGCCA 57.367 42.857 23.38 10.70 45.20 4.92
1687 1907 1.747709 ATTCAGCAGATCTGTGCCAC 58.252 50.000 23.38 6.87 45.20 5.01
1688 1908 0.321919 TTCAGCAGATCTGTGCCACC 60.322 55.000 23.38 6.14 45.20 4.61
1689 1909 1.196766 TCAGCAGATCTGTGCCACCT 61.197 55.000 23.38 8.40 45.20 4.00
2016 2236 3.456277 GGGATCTCCTTAAGAAGCCAGAA 59.544 47.826 3.36 0.00 37.61 3.02
2070 4036 0.743688 CGTACTCATCCTCTGCTGCT 59.256 55.000 0.00 0.00 0.00 4.24
2232 4198 3.940221 AGAAGCTCATGACTCAGAAATGC 59.060 43.478 0.00 0.00 0.00 3.56
2261 4227 8.928733 TCATATTTTTAATATTCCGGTAGACGC 58.071 33.333 0.00 0.00 42.52 5.19
2322 4288 2.297895 CCCGATGGACCTTGGGACA 61.298 63.158 9.72 0.00 41.92 4.02
2407 4373 3.059325 GCTGACCTTTAGCAATGCGATAG 60.059 47.826 0.00 0.00 40.81 2.08
2513 4479 1.271656 GAAGTTGGCTTCTGCTGCAAT 59.728 47.619 3.02 0.00 45.68 3.56
2576 4542 0.401395 AAGACCCCTCCTGTTGACCA 60.401 55.000 0.00 0.00 0.00 4.02
2897 4866 1.344438 TGAGAATGAGGCTGTGAACGT 59.656 47.619 0.00 0.00 0.00 3.99
2898 4867 2.224281 TGAGAATGAGGCTGTGAACGTT 60.224 45.455 0.00 0.00 0.00 3.99
2899 4868 2.413453 GAGAATGAGGCTGTGAACGTTC 59.587 50.000 21.42 21.42 0.00 3.95
2900 4869 1.464997 GAATGAGGCTGTGAACGTTCC 59.535 52.381 24.78 16.21 0.00 3.62
2901 4870 0.687354 ATGAGGCTGTGAACGTTCCT 59.313 50.000 24.78 15.12 0.00 3.36
2902 4871 0.249868 TGAGGCTGTGAACGTTCCTG 60.250 55.000 24.78 18.83 0.00 3.86
2903 4872 0.951040 GAGGCTGTGAACGTTCCTGG 60.951 60.000 24.78 14.81 0.00 4.45
2904 4873 2.617274 GGCTGTGAACGTTCCTGGC 61.617 63.158 24.78 23.63 0.00 4.85
2905 4874 2.617274 GCTGTGAACGTTCCTGGCC 61.617 63.158 24.78 0.00 0.00 5.36
3016 4988 5.521735 CACCATCAATGCACTTACTAGAGAC 59.478 44.000 0.00 0.00 0.00 3.36
3023 4995 5.630661 TGCACTTACTAGAGACTGACTTC 57.369 43.478 0.00 0.00 0.00 3.01
3025 4997 5.182190 TGCACTTACTAGAGACTGACTTCTG 59.818 44.000 0.00 0.00 0.00 3.02
3383 5381 8.918961 AAACGTTGTTGAAATCTGATTTTACA 57.081 26.923 16.14 18.10 31.47 2.41
3567 5576 7.768120 AGAAGTAGCAGAATCCATAGAAACTTG 59.232 37.037 0.00 0.00 0.00 3.16
3630 5689 2.072298 GACAGAGTGTCATCCTGCAAC 58.928 52.381 2.12 0.00 46.22 4.17
3641 5700 0.106708 TCCTGCAACTGTCTCACACC 59.893 55.000 0.00 0.00 0.00 4.16
3649 5708 3.032017 ACTGTCTCACACCGATTCTTG 57.968 47.619 0.00 0.00 0.00 3.02
4056 6175 6.528321 TCCTTAGCTCTACATTCATCCATTG 58.472 40.000 0.00 0.00 0.00 2.82
4064 6183 4.361451 ACATTCATCCATTGTTCGCTTC 57.639 40.909 0.00 0.00 0.00 3.86
4094 6217 1.028330 TACCGCCTCTGTAGTCACCG 61.028 60.000 0.00 0.00 0.00 4.94
4119 6252 1.352083 TCTGTTCCCTCCTTGTCCAG 58.648 55.000 0.00 0.00 0.00 3.86
4170 6303 4.627467 CAGTGTCCACAGTTAGCTTCATAC 59.373 45.833 0.00 0.00 0.00 2.39
4180 6313 5.237344 CAGTTAGCTTCATACCTTGTATGGC 59.763 44.000 12.82 9.77 0.00 4.40
4246 6379 3.036084 GTGTCAGTGTCCGCGGTG 61.036 66.667 27.15 16.50 0.00 4.94
4345 6479 6.525578 TGTGTGGATCTTTACGATACTCTT 57.474 37.500 0.00 0.00 33.81 2.85
4652 10649 6.249035 ACCATTGGTTAAATAACAGACACG 57.751 37.500 1.37 0.00 37.92 4.49
4717 14553 1.379642 GCACCTGAGGGTAAGCATGC 61.380 60.000 10.51 10.51 45.41 4.06
4901 14738 7.165812 CGTTATGCTGATGTTATTGTTAAAGCC 59.834 37.037 0.00 0.00 0.00 4.35
4930 14768 2.677875 CAGCCAGGTTTGGGAGCC 60.678 66.667 0.00 0.00 45.16 4.70
5571 15555 1.340405 CCATGCAGTTTCCCTAGCAGT 60.340 52.381 0.00 0.00 40.71 4.40
5626 15612 3.072330 TCTGTTGACATGTTGGAGCCTTA 59.928 43.478 0.00 0.00 0.00 2.69
6274 16356 4.036262 TCAAAAATGTTGTGAACTCCCTCG 59.964 41.667 0.00 0.00 0.00 4.63
6277 16359 0.391597 TGTTGTGAACTCCCTCGACC 59.608 55.000 0.00 0.00 0.00 4.79
6286 16368 1.978580 ACTCCCTCGACCTTCATGTTT 59.021 47.619 0.00 0.00 0.00 2.83
6293 16375 5.878116 CCCTCGACCTTCATGTTTGTATTAA 59.122 40.000 0.00 0.00 0.00 1.40
6294 16376 6.542370 CCCTCGACCTTCATGTTTGTATTAAT 59.458 38.462 0.00 0.00 0.00 1.40
6295 16377 7.067008 CCCTCGACCTTCATGTTTGTATTAATT 59.933 37.037 0.00 0.00 0.00 1.40
6336 16418 3.444034 AGTTCACGTAAGCAGAGATGCTA 59.556 43.478 2.72 0.00 45.54 3.49
6359 16441 1.038130 GCGGAGGCTGGAGAGACTAA 61.038 60.000 0.00 0.00 37.88 2.24
6361 16443 1.339610 CGGAGGCTGGAGAGACTAATG 59.660 57.143 0.00 0.00 37.88 1.90
6368 16450 3.603532 CTGGAGAGACTAATGCAAAGCA 58.396 45.455 0.00 0.00 44.86 3.91
6404 16486 1.437573 CTGAGCGAGGCGTATGGAA 59.562 57.895 0.00 0.00 0.00 3.53
6420 16502 3.191078 TGGAACCCGTCGTTTTCTAAA 57.809 42.857 0.00 0.00 33.74 1.85
6458 16540 4.222810 GGACATTTAAACCTGGGCATCTTT 59.777 41.667 0.00 0.00 0.00 2.52
6491 16573 1.659098 CAGATCCGCTAAAACCACGTC 59.341 52.381 0.00 0.00 0.00 4.34
6501 16583 5.106830 CGCTAAAACCACGTCCTCTAAAAAT 60.107 40.000 0.00 0.00 0.00 1.82
6511 16593 6.686253 CACGTCCTCTAAAAATAGTAGACGAC 59.314 42.308 23.55 12.17 41.46 4.34
6564 16646 4.632327 TTGTATGTCACCAACAGATCCA 57.368 40.909 0.00 0.00 42.37 3.41
6565 16647 4.842531 TGTATGTCACCAACAGATCCAT 57.157 40.909 0.00 0.00 42.37 3.41
6569 16856 6.767423 TGTATGTCACCAACAGATCCATTATG 59.233 38.462 0.00 0.00 42.37 1.90
6573 16860 5.066505 GTCACCAACAGATCCATTATGAACC 59.933 44.000 0.00 0.00 0.00 3.62
6582 16869 8.418662 ACAGATCCATTATGAACCAATTGAATG 58.581 33.333 7.12 7.58 0.00 2.67
6654 16944 8.970859 AAACTTCCTCAAATGGATGTATCTAG 57.029 34.615 0.00 0.00 41.67 2.43
6661 16951 6.899089 TCAAATGGATGTATCTAGCTCCAAA 58.101 36.000 0.00 0.00 40.94 3.28
6665 16955 9.866655 AAATGGATGTATCTAGCTCCAAATTAA 57.133 29.630 0.00 0.00 40.94 1.40
6668 16958 8.659527 TGGATGTATCTAGCTCCAAATTAATGA 58.340 33.333 0.00 0.00 34.91 2.57
6762 17955 6.907212 CACACATAAAAAGCAATCGGATACTC 59.093 38.462 0.00 0.00 0.00 2.59
6767 17960 1.949133 GCAATCGGATACTCGCGCA 60.949 57.895 8.75 0.00 0.00 6.09
6807 18000 3.314331 AGCAGGGTCTGGTGGTCG 61.314 66.667 0.00 0.00 40.87 4.79
6833 18026 2.333225 GCTCGAGGATGATCGCGT 59.667 61.111 15.58 0.00 42.43 6.01
6848 18041 3.227276 CGTAGAGGCGGCAGGGAT 61.227 66.667 13.08 0.00 0.00 3.85
6880 18073 1.601166 GTGGCGGGAGTTACAAGTTT 58.399 50.000 0.00 0.00 0.00 2.66
6887 18080 2.289506 GGGAGTTACAAGTTTCCTCGCT 60.290 50.000 0.00 0.00 33.70 4.93
6896 18089 2.024414 AGTTTCCTCGCTGCAAAAACT 58.976 42.857 0.00 6.65 35.82 2.66
6908 18101 3.110447 GCAAAAACTGCCTCCAATTCA 57.890 42.857 0.00 0.00 46.13 2.57
6909 18102 3.062042 GCAAAAACTGCCTCCAATTCAG 58.938 45.455 0.00 0.00 46.13 3.02
6916 18109 3.073650 ACTGCCTCCAATTCAGGATATCC 59.926 47.826 14.41 14.41 36.99 2.59
6920 18113 3.557898 CCTCCAATTCAGGATATCCACGG 60.558 52.174 23.81 12.43 36.99 4.94
6950 18143 6.725364 AGCCCATATTTTAGAGGGATATGTG 58.275 40.000 0.00 0.00 44.30 3.21
7009 18202 6.073447 TGTGGTACCAGATATGGACATTTT 57.927 37.500 16.93 0.00 0.00 1.82
7032 18225 5.783100 TTTTGCCTCGTACTATAAAACGG 57.217 39.130 6.67 0.00 39.52 4.44
7034 18227 2.428171 TGCCTCGTACTATAAAACGGCT 59.572 45.455 0.00 0.00 39.52 5.52
7035 18228 3.631686 TGCCTCGTACTATAAAACGGCTA 59.368 43.478 0.00 0.00 39.52 3.93
7041 18234 9.415544 CCTCGTACTATAAAACGGCTATTATTT 57.584 33.333 6.67 0.00 39.52 1.40
7076 18269 2.093764 GCGGGATATGCTAGAGATGCTT 60.094 50.000 0.00 0.00 0.00 3.91
7083 18276 6.091441 GGATATGCTAGAGATGCTTTTAACGG 59.909 42.308 0.00 0.00 0.00 4.44
7088 18281 3.809905 AGAGATGCTTTTAACGGATCCC 58.190 45.455 6.06 0.00 30.52 3.85
7097 18290 5.593010 CTTTTAACGGATCCCACAAAAACA 58.407 37.500 6.06 0.00 0.00 2.83
7111 18304 5.808030 CCACAAAAACACGTCCTGTAAAAAT 59.192 36.000 0.00 0.00 30.51 1.82
7139 18332 1.075536 AGGCCCCTCAAACGAATTTCT 59.924 47.619 0.00 0.00 0.00 2.52
7145 18338 5.236695 GCCCCTCAAACGAATTTCTAGTATC 59.763 44.000 0.00 0.00 0.00 2.24
7158 18351 3.078837 TCTAGTATCGTGCGGCATATGA 58.921 45.455 5.72 5.43 0.00 2.15
7214 18413 4.457466 TCTACTTTTTCCCGTGCTTCTTT 58.543 39.130 0.00 0.00 0.00 2.52
7277 18476 3.502455 CGCACAGCCATGACGCAT 61.502 61.111 0.00 0.00 0.00 4.73
7307 18506 3.771491 CAGAGCGCACGACTGCAC 61.771 66.667 11.47 0.00 44.50 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
489 514 1.080974 CCTAACGGACGTTCGCTGT 60.081 57.895 18.04 4.37 39.31 4.40
496 521 1.404583 CGGGAATTTCCTAACGGACGT 60.405 52.381 14.95 0.00 39.60 4.34
558 583 4.044439 CTCCTGGCCTGCCTTGCT 62.044 66.667 9.97 0.00 36.94 3.91
613 639 1.069090 TGAAGGCTGGTGACACGTC 59.931 57.895 0.00 0.00 35.60 4.34
724 754 4.775253 TCATTGGATTTGGGTAGTTTTCCC 59.225 41.667 0.00 0.00 44.81 3.97
730 760 3.701040 GCATGTCATTGGATTTGGGTAGT 59.299 43.478 0.00 0.00 0.00 2.73
785 815 2.730672 GATCGCGCGCTGTTTGACT 61.731 57.895 30.48 8.36 0.00 3.41
790 820 3.490759 CAAGGATCGCGCGCTGTT 61.491 61.111 30.48 17.03 0.00 3.16
1102 1143 4.856607 GAAGCGACCGAGCCCGAG 62.857 72.222 0.00 0.00 38.22 4.63
1145 1193 1.079543 CGCCTCCAGTTGTCTCCTG 60.080 63.158 0.00 0.00 0.00 3.86
1147 1195 2.435059 GCGCCTCCAGTTGTCTCC 60.435 66.667 0.00 0.00 0.00 3.71
1153 1201 2.771763 CTTCACTCGCGCCTCCAGTT 62.772 60.000 0.00 0.00 0.00 3.16
1168 1216 4.119556 TCTCTCTCTTGTTCTCCCTTCA 57.880 45.455 0.00 0.00 0.00 3.02
1172 1220 3.835395 TCCTTTCTCTCTCTTGTTCTCCC 59.165 47.826 0.00 0.00 0.00 4.30
1188 1236 7.768582 CCTTTTATCTTCTCTCTTCCTCCTTTC 59.231 40.741 0.00 0.00 0.00 2.62
1189 1237 7.459444 TCCTTTTATCTTCTCTCTTCCTCCTTT 59.541 37.037 0.00 0.00 0.00 3.11
1192 1240 6.800072 TCCTTTTATCTTCTCTCTTCCTCC 57.200 41.667 0.00 0.00 0.00 4.30
1198 1246 8.622572 ATCCTCTTTCCTTTTATCTTCTCTCT 57.377 34.615 0.00 0.00 0.00 3.10
1209 1257 4.191963 TCCCCCTTATCCTCTTTCCTTTT 58.808 43.478 0.00 0.00 0.00 2.27
1471 1521 4.858692 CCCAACGCTCAAATCTTGTAATTG 59.141 41.667 0.00 0.00 0.00 2.32
1492 1542 1.648467 GAGCACAAATCCGACAGCCC 61.648 60.000 0.00 0.00 0.00 5.19
1581 1775 4.684242 GGGATTTAAACGGAAGCACAAAAG 59.316 41.667 0.00 0.00 0.00 2.27
1584 1778 3.254657 CAGGGATTTAAACGGAAGCACAA 59.745 43.478 0.00 0.00 0.00 3.33
1594 1788 5.208463 TGAAACCTTGCAGGGATTTAAAC 57.792 39.130 23.57 4.64 40.58 2.01
1688 1908 3.950794 TTACCAGGCGCCAGCGAAG 62.951 63.158 31.54 10.43 46.35 3.79
1689 1909 4.010224 TTACCAGGCGCCAGCGAA 62.010 61.111 31.54 14.25 46.35 4.70
2261 4227 2.813754 TCTGGAATGTTCAGCTTTTCCG 59.186 45.455 0.00 0.00 32.63 4.30
2322 4288 6.956497 ACCAGAATCTAGCTTCTTCTTGATT 58.044 36.000 6.10 0.00 39.81 2.57
2407 4373 0.178068 TGCCCTCGAGGATTGTAAGC 59.822 55.000 33.39 24.01 38.24 3.09
2513 4479 1.955778 CAACCTCAACATGTGGCTTCA 59.044 47.619 0.00 0.00 34.53 3.02
2576 4542 2.093973 CGCTCTATTGACAAGTCCCTGT 60.094 50.000 0.00 0.00 0.00 4.00
2580 4546 2.924290 GACACGCTCTATTGACAAGTCC 59.076 50.000 0.00 0.00 0.00 3.85
2613 4579 8.533657 TCAAATGTCATCTTTGGCTTCATAATT 58.466 29.630 0.27 0.00 34.95 1.40
2904 4873 1.197430 AGTGACTGAGGCCAGGAAGG 61.197 60.000 5.01 0.00 44.60 3.46
2905 4874 0.689623 AAGTGACTGAGGCCAGGAAG 59.310 55.000 5.01 0.00 44.60 3.46
3016 4988 2.133553 CTGAGTGCACACAGAAGTCAG 58.866 52.381 32.79 22.84 36.82 3.51
3023 4995 1.146930 ACCACCTGAGTGCACACAG 59.853 57.895 30.41 30.41 43.09 3.66
3025 4997 0.882042 CTCACCACCTGAGTGCACAC 60.882 60.000 21.04 14.15 43.09 3.82
3383 5381 8.685838 TTTGCTTCACTACCTTATGTAAACTT 57.314 30.769 0.00 0.00 0.00 2.66
3441 5444 5.183530 TGAATTTCAGATGGTCAGATGGT 57.816 39.130 0.00 0.00 0.00 3.55
3544 5553 7.187824 TCAAGTTTCTATGGATTCTGCTACT 57.812 36.000 0.00 0.00 0.00 2.57
3630 5689 2.289072 ACCAAGAATCGGTGTGAGACAG 60.289 50.000 0.00 0.00 34.69 3.51
3641 5700 5.007039 CCACATATCAGTTCACCAAGAATCG 59.993 44.000 0.00 0.00 38.76 3.34
3649 5708 2.710377 TGCACCACATATCAGTTCACC 58.290 47.619 0.00 0.00 0.00 4.02
3866 5979 4.079253 GGCTACCAACCTTTTCTGATTCA 58.921 43.478 0.00 0.00 0.00 2.57
4056 6175 5.080068 CGGTAAAGAAAATGAGAAGCGAAC 58.920 41.667 0.00 0.00 0.00 3.95
4064 6183 4.003648 ACAGAGGCGGTAAAGAAAATGAG 58.996 43.478 0.00 0.00 0.00 2.90
4094 6217 1.501654 AAGGAGGGAACAGAAGGGCC 61.502 60.000 0.00 0.00 0.00 5.80
4119 6252 6.047231 AGGCGTGGTACTATCAGAAATAAAC 58.953 40.000 0.00 0.00 0.00 2.01
4170 6303 0.176680 AGCGAGTCAGCCATACAAGG 59.823 55.000 3.79 0.00 38.01 3.61
4377 6511 4.890088 TCTTGCCACAACGTTAGTAGAAT 58.110 39.130 0.00 0.00 0.00 2.40
4387 6521 4.223320 ACAATAAACTCTTGCCACAACG 57.777 40.909 0.00 0.00 0.00 4.10
4643 10638 2.879233 ATCACCGGCCGTGTCTGTT 61.879 57.895 26.12 5.80 43.51 3.16
4644 10639 3.311110 ATCACCGGCCGTGTCTGT 61.311 61.111 26.12 11.69 43.51 3.41
4652 10649 1.745489 GAGTTCCACATCACCGGCC 60.745 63.158 0.00 0.00 0.00 6.13
4717 14553 7.386299 GGTCTCATATGAACCTGCTTACATAAG 59.614 40.741 20.76 0.00 36.40 1.73
4901 14738 1.153289 CTGGCTGAGAATCCCACGG 60.153 63.158 0.00 0.00 0.00 4.94
4930 14768 8.553459 TGAAGGAAAGAAAGCTAGATGTAAAG 57.447 34.615 0.00 0.00 0.00 1.85
4961 14799 0.469494 TGTCAGAAAGAGGTGCAGCA 59.531 50.000 19.63 0.00 0.00 4.41
4998 14836 1.880941 ATCTCCACCCTCACCCTAAC 58.119 55.000 0.00 0.00 0.00 2.34
5000 14838 3.246203 TGTTTATCTCCACCCTCACCCTA 60.246 47.826 0.00 0.00 0.00 3.53
5204 15174 1.375523 AAGGTCCCGCTTACGCTTG 60.376 57.895 0.00 0.00 38.22 4.01
5571 15555 8.146053 TGATTTCTACTTCCTCCACATCTTTA 57.854 34.615 0.00 0.00 0.00 1.85
5626 15612 4.320494 GGCAATTGTTCTGTCTTTGACGAT 60.320 41.667 7.40 0.00 34.95 3.73
6293 16375 9.709495 TGAACTCTTTGCAGCAAAATTAATAAT 57.291 25.926 20.95 3.24 32.75 1.28
6294 16376 8.977505 GTGAACTCTTTGCAGCAAAATTAATAA 58.022 29.630 20.95 2.83 32.75 1.40
6295 16377 7.325821 CGTGAACTCTTTGCAGCAAAATTAATA 59.674 33.333 20.95 4.96 32.75 0.98
6335 16417 0.179015 CTCTCCAGCCTCCGCTACTA 60.179 60.000 0.00 0.00 46.25 1.82
6336 16418 1.454847 CTCTCCAGCCTCCGCTACT 60.455 63.158 0.00 0.00 46.25 2.57
6361 16443 1.465354 CGAGTCTGCTTCATGCTTTGC 60.465 52.381 0.00 0.00 43.37 3.68
6368 16450 2.300152 TCAGGAAACGAGTCTGCTTCAT 59.700 45.455 0.00 0.00 0.00 2.57
6404 16486 8.953368 ATTAATATCTTTAGAAAACGACGGGT 57.047 30.769 0.00 0.00 0.00 5.28
6485 16567 5.970023 CGTCTACTATTTTTAGAGGACGTGG 59.030 44.000 0.00 0.00 38.82 4.94
6491 16573 6.129053 ACCGTCGTCTACTATTTTTAGAGG 57.871 41.667 0.00 0.00 34.25 3.69
6501 16583 3.340814 AAGAGGAACCGTCGTCTACTA 57.659 47.619 0.00 0.00 45.95 1.82
6511 16593 4.615541 GCAAATTCGTTTTAAGAGGAACCG 59.384 41.667 3.54 0.00 0.00 4.44
6569 16856 9.101655 CCTTCCATAAATTCATTCAATTGGTTC 57.898 33.333 5.42 0.00 34.69 3.62
6573 16860 9.485206 GGATCCTTCCATAAATTCATTCAATTG 57.515 33.333 3.84 0.00 42.12 2.32
6654 16944 9.453572 TGGATGTATCTATCATTAATTTGGAGC 57.546 33.333 0.00 0.00 0.00 4.70
6787 17980 3.957586 CCACCAGACCCTGCTGCA 61.958 66.667 0.88 0.88 34.56 4.41
6833 18026 2.844362 CCATCCCTGCCGCCTCTA 60.844 66.667 0.00 0.00 0.00 2.43
6854 18047 1.880819 TAACTCCCGCCACGGTCTTC 61.881 60.000 5.17 0.00 46.80 2.87
6860 18053 0.601841 AACTTGTAACTCCCGCCACG 60.602 55.000 0.00 0.00 0.00 4.94
6867 18060 2.737252 CAGCGAGGAAACTTGTAACTCC 59.263 50.000 0.00 0.00 44.43 3.85
6874 18067 2.490328 TTTTGCAGCGAGGAAACTTG 57.510 45.000 0.00 0.00 44.43 3.16
6896 18089 3.055328 TGGATATCCTGAATTGGAGGCA 58.945 45.455 22.35 0.00 39.78 4.75
6908 18101 1.625818 GCTTCATCCCGTGGATATCCT 59.374 52.381 22.35 0.00 40.98 3.24
6909 18102 1.339151 GGCTTCATCCCGTGGATATCC 60.339 57.143 15.39 15.39 40.98 2.59
6920 18113 5.012893 CCCTCTAAAATATGGGCTTCATCC 58.987 45.833 0.00 0.00 37.30 3.51
6972 18165 0.722848 ACCACAAAACGTCACGTGAC 59.277 50.000 33.76 33.76 39.99 3.67
6973 18166 1.925847 GTACCACAAAACGTCACGTGA 59.074 47.619 15.76 15.76 39.99 4.35
6974 18167 1.004715 GGTACCACAAAACGTCACGTG 60.005 52.381 9.94 9.94 39.99 4.49
6975 18168 1.289276 GGTACCACAAAACGTCACGT 58.711 50.000 7.15 0.00 43.97 4.49
6976 18169 1.259507 CTGGTACCACAAAACGTCACG 59.740 52.381 11.60 0.00 0.00 4.35
6977 18170 2.553086 TCTGGTACCACAAAACGTCAC 58.447 47.619 11.60 0.00 0.00 3.67
7009 18202 5.390779 GCCGTTTTATAGTACGAGGCAAAAA 60.391 40.000 9.48 0.00 40.03 1.94
7025 18218 9.841295 AGATCCTGTAAAATAATAGCCGTTTTA 57.159 29.630 0.00 0.00 0.00 1.52
7032 18225 7.591426 CCGCAAAAGATCCTGTAAAATAATAGC 59.409 37.037 0.00 0.00 0.00 2.97
7034 18227 7.776030 TCCCGCAAAAGATCCTGTAAAATAATA 59.224 33.333 0.00 0.00 0.00 0.98
7035 18228 6.605594 TCCCGCAAAAGATCCTGTAAAATAAT 59.394 34.615 0.00 0.00 0.00 1.28
7041 18234 3.644966 ATCCCGCAAAAGATCCTGTAA 57.355 42.857 0.00 0.00 0.00 2.41
7045 18238 2.107204 AGCATATCCCGCAAAAGATCCT 59.893 45.455 0.00 0.00 0.00 3.24
7048 18241 4.284490 TCTCTAGCATATCCCGCAAAAGAT 59.716 41.667 0.00 0.00 0.00 2.40
7076 18269 4.497674 CGTGTTTTTGTGGGATCCGTTAAA 60.498 41.667 5.45 3.85 0.00 1.52
7083 18276 2.031157 CAGGACGTGTTTTTGTGGGATC 60.031 50.000 0.00 0.00 0.00 3.36
7088 18281 6.879188 ATTTTTACAGGACGTGTTTTTGTG 57.121 33.333 6.05 0.00 40.94 3.33
7097 18290 9.662947 GGCCTATATATTATTTTTACAGGACGT 57.337 33.333 0.00 0.00 0.00 4.34
7111 18304 6.938698 TTCGTTTGAGGGGCCTATATATTA 57.061 37.500 0.84 0.00 0.00 0.98
7139 18332 2.413634 CGTCATATGCCGCACGATACTA 60.414 50.000 8.55 0.00 34.06 1.82
7158 18351 1.435577 GTTTACGGGATCTGTTGCGT 58.564 50.000 0.00 0.00 0.00 5.24
7214 18413 1.742831 GTCCATGCATGCGTCCTAAAA 59.257 47.619 21.69 0.00 0.00 1.52
7223 18422 0.804364 TCAAGTTCGTCCATGCATGC 59.196 50.000 21.69 11.82 0.00 4.06
7229 18428 2.356135 CCGGAATTCAAGTTCGTCCAT 58.644 47.619 7.93 0.00 0.00 3.41
7265 18464 3.116463 CATGCATGCGTCATGGCT 58.884 55.556 14.93 0.00 41.64 4.75
7277 18476 4.478371 CTCTGGCCGGAGCATGCA 62.478 66.667 28.46 0.00 42.56 3.96


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

AutoCloner maintained by Alex Coulton.