Multiple sequence alignment - TraesCS7D01G114500

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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 TraesCS7D01G114500 chr7D 100.000 3530 0 0 1 3530 70047411 70050940 0.000000e+00 6519.0
1 TraesCS7D01G114500 chr7D 98.807 3352 29 2 1 3341 70154906 70151555 0.000000e+00 5958.0
2 TraesCS7D01G114500 chr7D 91.606 2061 118 20 633 2662 69953931 69955967 0.000000e+00 2796.0
3 TraesCS7D01G114500 chr7D 93.144 1269 50 10 890 2152 70736793 70735556 0.000000e+00 1827.0
4 TraesCS7D01G114500 chr7D 92.776 969 38 14 2181 3117 70735561 70734593 0.000000e+00 1373.0
5 TraesCS7D01G114500 chr7D 97.125 313 8 1 3090 3401 70729530 70729218 8.680000e-146 527.0
6 TraesCS7D01G114500 chr7D 89.008 373 23 7 719 1085 70361728 70362088 2.500000e-121 446.0
7 TraesCS7D01G114500 chr7D 83.260 454 64 3 1 445 70737558 70737108 1.180000e-109 407.0
8 TraesCS7D01G114500 chr7D 83.249 394 52 7 1 387 69952263 69952649 2.020000e-92 350.0
9 TraesCS7D01G114500 chr7D 96.791 187 5 1 3026 3212 70362324 70362509 9.520000e-81 311.0
10 TraesCS7D01G114500 chr7D 93.567 171 11 0 1850 2020 70362284 70362114 4.520000e-64 255.0
11 TraesCS7D01G114500 chr7D 84.746 236 13 13 591 813 70737047 70736822 7.670000e-52 215.0
12 TraesCS7D01G114500 chr7D 93.893 131 6 2 3401 3530 70729187 70729058 2.780000e-46 196.0
13 TraesCS7D01G114500 chr7D 84.466 103 8 5 40 135 42551664 42551563 1.040000e-15 95.3
14 TraesCS7D01G114500 chr7D 100.000 37 0 0 3365 3401 70096487 70096451 6.320000e-08 69.4
15 TraesCS7D01G114500 chr7B 93.453 2673 125 15 2 2662 12720277 12717643 0.000000e+00 3921.0
16 TraesCS7D01G114500 chr7B 91.395 1964 129 17 722 2662 12951767 12953713 0.000000e+00 2654.0
17 TraesCS7D01G114500 chr7B 81.664 769 36 37 550 1251 12716053 12716783 3.100000e-150 542.0
18 TraesCS7D01G114500 chr7B 84.848 264 26 4 1 257 12715638 12715894 1.630000e-63 254.0
19 TraesCS7D01G114500 chr7B 88.333 180 21 0 286 465 634772088 634772267 2.130000e-52 217.0
20 TraesCS7D01G114500 chr7B 96.825 63 2 0 3468 3530 142862716 142862654 4.820000e-19 106.0
21 TraesCS7D01G114500 chr7A 93.222 1077 52 5 2155 3212 76550199 76551273 0.000000e+00 1565.0
22 TraesCS7D01G114500 chr7A 83.926 647 80 11 1 635 76818453 76819087 6.520000e-167 597.0
23 TraesCS7D01G114500 chr7A 82.331 266 33 4 1 259 76549301 76549559 5.930000e-53 219.0
24 TraesCS7D01G114500 chr7A 88.387 155 15 2 484 636 617915757 617915910 2.160000e-42 183.0
25 TraesCS7D01G114500 chr7A 89.844 128 8 4 491 616 76549679 76549803 3.650000e-35 159.0
26 TraesCS7D01G114500 chr7A 89.796 98 4 1 678 775 76819166 76819257 1.720000e-23 121.0
27 TraesCS7D01G114500 chr4A 88.462 182 21 0 284 465 304782102 304782283 1.650000e-53 220.0
28 TraesCS7D01G114500 chr4A 87.097 93 11 1 40 131 649434314 649434222 1.730000e-18 104.0
29 TraesCS7D01G114500 chr6A 87.912 182 22 0 284 465 201453009 201453190 7.670000e-52 215.0
30 TraesCS7D01G114500 chr6A 87.500 64 5 3 37 98 496018473 496018535 1.760000e-08 71.3
31 TraesCS7D01G114500 chr4B 87.302 189 22 2 284 470 455976795 455976607 7.670000e-52 215.0
32 TraesCS7D01G114500 chr4B 87.912 182 22 0 284 465 529837134 529837315 7.670000e-52 215.0
33 TraesCS7D01G114500 chr1B 85.577 208 27 3 266 470 408109537 408109330 7.670000e-52 215.0
34 TraesCS7D01G114500 chr1B 87.912 182 22 0 284 465 524162274 524162455 7.670000e-52 215.0
35 TraesCS7D01G114500 chr1B 87.395 119 11 3 9 123 616595122 616595240 2.210000e-27 134.0
36 TraesCS7D01G114500 chr1B 95.238 63 3 0 3468 3530 329380713 329380775 2.240000e-17 100.0
37 TraesCS7D01G114500 chr3B 88.816 152 11 2 485 636 243767563 243767708 7.780000e-42 182.0
38 TraesCS7D01G114500 chr3A 87.261 157 16 4 485 639 199149601 199149447 3.620000e-40 176.0
39 TraesCS7D01G114500 chr3D 87.500 152 18 1 485 636 168492505 168492655 1.300000e-39 174.0
40 TraesCS7D01G114500 chr3D 86.806 144 19 0 284 427 508380040 508380183 1.010000e-35 161.0
41 TraesCS7D01G114500 chr3D 95.238 63 3 0 3468 3530 320633982 320633920 2.240000e-17 100.0
42 TraesCS7D01G114500 chr3D 95.238 63 3 0 3468 3530 320634187 320634125 2.240000e-17 100.0
43 TraesCS7D01G114500 chr5A 84.348 115 13 2 3417 3526 632761303 632761417 1.340000e-19 108.0
44 TraesCS7D01G114500 chr5A 83.908 87 2 6 594 669 16416025 16415940 4.890000e-09 73.1
45 TraesCS7D01G114500 chr1D 96.825 63 2 0 3468 3530 249135516 249135454 4.820000e-19 106.0
46 TraesCS7D01G114500 chr6B 91.892 74 6 0 3457 3530 4550240 4550167 1.730000e-18 104.0
47 TraesCS7D01G114500 chr5B 95.238 63 3 0 3468 3530 441526082 441526020 2.240000e-17 100.0


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 TraesCS7D01G114500 chr7D 70047411 70050940 3529 False 6519.000000 6519 100.000000 1 3530 1 chr7D.!!$F1 3529
1 TraesCS7D01G114500 chr7D 70151555 70154906 3351 True 5958.000000 5958 98.807000 1 3341 1 chr7D.!!$R3 3340
2 TraesCS7D01G114500 chr7D 69952263 69955967 3704 False 1573.000000 2796 87.427500 1 2662 2 chr7D.!!$F2 2661
3 TraesCS7D01G114500 chr7D 70734593 70737558 2965 True 955.500000 1827 88.481500 1 3117 4 chr7D.!!$R6 3116
4 TraesCS7D01G114500 chr7D 70361728 70362509 781 False 378.500000 446 92.899500 719 3212 2 chr7D.!!$F3 2493
5 TraesCS7D01G114500 chr7B 12717643 12720277 2634 True 3921.000000 3921 93.453000 2 2662 1 chr7B.!!$R1 2660
6 TraesCS7D01G114500 chr7B 12951767 12953713 1946 False 2654.000000 2654 91.395000 722 2662 1 chr7B.!!$F1 1940
7 TraesCS7D01G114500 chr7B 12715638 12716783 1145 False 398.000000 542 83.256000 1 1251 2 chr7B.!!$F3 1250
8 TraesCS7D01G114500 chr7A 76549301 76551273 1972 False 647.666667 1565 88.465667 1 3212 3 chr7A.!!$F2 3211
9 TraesCS7D01G114500 chr7A 76818453 76819257 804 False 359.000000 597 86.861000 1 775 2 chr7A.!!$F3 774

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
427 439 3.650950 GTCCTGGAGGCTGGGCAA 61.651 66.667 0.0 0.0 34.44 4.52 F
1368 2691 0.867753 CGAGATCGGCTTCTTCCACG 60.868 60.000 0.0 0.0 35.37 4.94 F
1759 3088 2.741092 GACAGTCGCCAAGGGTGA 59.259 61.111 0.0 0.0 40.17 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 3022 1.004745 TGCTCCTAAGGAAAAGCCCTG 59.995 52.381 0.00 0.0 36.49 4.45 R
2202 3531 1.607178 CAGCAATGGTGAAGGGGCA 60.607 57.895 6.59 0.0 32.22 5.36 R
3407 4792 0.264359 AGGGGTCTGCTAGAGATGCT 59.736 55.000 0.00 0.0 31.63 3.79 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
181 193 6.547880 TGAGGGTTTAAATTTAAGCAGTGTGA 59.452 34.615 21.60 0.00 0.00 3.58
279 291 7.626084 TGAGTTACTTTTTCATCCCCTCCTATA 59.374 37.037 0.00 0.00 0.00 1.31
427 439 3.650950 GTCCTGGAGGCTGGGCAA 61.651 66.667 0.00 0.00 34.44 4.52
1368 2691 0.867753 CGAGATCGGCTTCTTCCACG 60.868 60.000 0.00 0.00 35.37 4.94
1527 2850 3.654143 TCGACCTCCCGTCCCTCA 61.654 66.667 0.00 0.00 38.36 3.86
1759 3088 2.741092 GACAGTCGCCAAGGGTGA 59.259 61.111 0.00 0.00 40.17 4.02
2202 3531 1.929860 TAGGATCCGACCCTCCGTGT 61.930 60.000 5.98 0.00 36.62 4.49
3282 4667 5.875224 TGGAAAAATGTGATGTGAGGAGTA 58.125 37.500 0.00 0.00 0.00 2.59
3300 4685 8.160765 TGAGGAGTACATATCTTTTGTTGGAAA 58.839 33.333 0.00 0.00 0.00 3.13
3345 4730 6.558771 GCAAAAATATGCCCTTGTTCTTTT 57.441 33.333 0.00 0.00 40.49 2.27
3346 4731 6.969366 GCAAAAATATGCCCTTGTTCTTTTT 58.031 32.000 0.00 0.00 40.49 1.94
3368 4753 7.595819 TTTTTAGGAATGAACATGTTCCAGT 57.404 32.000 30.66 19.62 45.03 4.00
3369 4754 7.595819 TTTTAGGAATGAACATGTTCCAGTT 57.404 32.000 30.66 22.80 45.03 3.16
3370 4755 8.698973 TTTTAGGAATGAACATGTTCCAGTTA 57.301 30.769 30.66 15.64 45.03 2.24
3371 4756 7.921786 TTAGGAATGAACATGTTCCAGTTAG 57.078 36.000 30.66 0.00 45.03 2.34
3372 4757 6.126863 AGGAATGAACATGTTCCAGTTAGA 57.873 37.500 30.66 14.29 45.03 2.10
3373 4758 5.940470 AGGAATGAACATGTTCCAGTTAGAC 59.060 40.000 30.66 17.03 45.03 2.59
3374 4759 5.940470 GGAATGAACATGTTCCAGTTAGACT 59.060 40.000 30.66 4.91 42.72 3.24
3375 4760 6.431234 GGAATGAACATGTTCCAGTTAGACTT 59.569 38.462 30.66 12.82 42.72 3.01
3376 4761 6.808008 ATGAACATGTTCCAGTTAGACTTG 57.192 37.500 30.66 0.00 38.77 3.16
3377 4762 5.063204 TGAACATGTTCCAGTTAGACTTGG 58.937 41.667 30.66 0.00 38.77 3.61
3378 4763 4.706842 ACATGTTCCAGTTAGACTTGGT 57.293 40.909 0.00 0.00 0.00 3.67
3379 4764 4.389374 ACATGTTCCAGTTAGACTTGGTG 58.611 43.478 0.00 0.00 0.00 4.17
3380 4765 2.846193 TGTTCCAGTTAGACTTGGTGC 58.154 47.619 0.00 0.00 0.00 5.01
3381 4766 2.152016 GTTCCAGTTAGACTTGGTGCC 58.848 52.381 0.00 0.00 0.00 5.01
3382 4767 0.690762 TCCAGTTAGACTTGGTGCCC 59.309 55.000 0.00 0.00 0.00 5.36
3383 4768 0.400213 CCAGTTAGACTTGGTGCCCA 59.600 55.000 0.00 0.00 0.00 5.36
3384 4769 1.611673 CCAGTTAGACTTGGTGCCCAG 60.612 57.143 0.00 0.00 33.81 4.45
3385 4770 0.036875 AGTTAGACTTGGTGCCCAGC 59.963 55.000 0.00 0.00 33.81 4.85
3386 4771 0.250727 GTTAGACTTGGTGCCCAGCA 60.251 55.000 0.00 0.00 33.81 4.41
3387 4772 0.476338 TTAGACTTGGTGCCCAGCAA 59.524 50.000 11.79 11.79 45.29 3.91
3388 4773 0.698238 TAGACTTGGTGCCCAGCAAT 59.302 50.000 12.61 4.60 46.12 3.56
3389 4774 0.698238 AGACTTGGTGCCCAGCAATA 59.302 50.000 12.61 0.00 46.12 1.90
3390 4775 1.285962 AGACTTGGTGCCCAGCAATAT 59.714 47.619 12.61 5.34 46.12 1.28
3391 4776 1.406539 GACTTGGTGCCCAGCAATATG 59.593 52.381 12.61 5.18 46.12 1.78
3392 4777 0.748450 CTTGGTGCCCAGCAATATGG 59.252 55.000 12.61 0.00 46.12 2.74
3393 4778 1.329171 TTGGTGCCCAGCAATATGGC 61.329 55.000 8.66 0.00 43.00 4.40
3395 4780 0.178992 GGTGCCCAGCAATATGGCTA 60.179 55.000 3.70 0.00 43.68 3.93
3396 4781 1.242076 GTGCCCAGCAATATGGCTAG 58.758 55.000 3.70 0.00 43.68 3.42
3397 4782 0.846015 TGCCCAGCAATATGGCTAGT 59.154 50.000 3.70 0.00 43.68 2.57
3398 4783 2.054021 TGCCCAGCAATATGGCTAGTA 58.946 47.619 3.70 0.00 43.68 1.82
3399 4784 2.224523 TGCCCAGCAATATGGCTAGTAC 60.225 50.000 3.70 0.00 43.68 2.73
3400 4785 2.876079 GCCCAGCAATATGGCTAGTACC 60.876 54.545 3.70 0.00 43.68 3.34
3401 4786 2.290323 CCCAGCAATATGGCTAGTACCC 60.290 54.545 3.70 0.00 43.68 3.69
3402 4787 2.290323 CCAGCAATATGGCTAGTACCCC 60.290 54.545 3.70 0.00 43.68 4.95
3403 4788 2.639839 CAGCAATATGGCTAGTACCCCT 59.360 50.000 3.70 0.00 43.68 4.79
3404 4789 2.907042 AGCAATATGGCTAGTACCCCTC 59.093 50.000 1.59 0.00 43.70 4.30
3405 4790 2.637872 GCAATATGGCTAGTACCCCTCA 59.362 50.000 0.00 0.00 0.00 3.86
3406 4791 3.557264 GCAATATGGCTAGTACCCCTCAC 60.557 52.174 0.00 0.00 0.00 3.51
3407 4792 3.630625 ATATGGCTAGTACCCCTCACA 57.369 47.619 0.00 0.00 0.00 3.58
3408 4793 1.794714 ATGGCTAGTACCCCTCACAG 58.205 55.000 0.00 0.00 0.00 3.66
3409 4794 0.976073 TGGCTAGTACCCCTCACAGC 60.976 60.000 0.00 0.00 0.00 4.40
3410 4795 0.976073 GGCTAGTACCCCTCACAGCA 60.976 60.000 0.00 0.00 0.00 4.41
3411 4796 1.123928 GCTAGTACCCCTCACAGCAT 58.876 55.000 0.00 0.00 0.00 3.79
3412 4797 1.069358 GCTAGTACCCCTCACAGCATC 59.931 57.143 0.00 0.00 0.00 3.91
3413 4798 2.672098 CTAGTACCCCTCACAGCATCT 58.328 52.381 0.00 0.00 0.00 2.90
3414 4799 1.490574 AGTACCCCTCACAGCATCTC 58.509 55.000 0.00 0.00 0.00 2.75
3415 4800 1.007721 AGTACCCCTCACAGCATCTCT 59.992 52.381 0.00 0.00 0.00 3.10
3416 4801 2.245028 AGTACCCCTCACAGCATCTCTA 59.755 50.000 0.00 0.00 0.00 2.43
3417 4802 1.786937 ACCCCTCACAGCATCTCTAG 58.213 55.000 0.00 0.00 0.00 2.43
3418 4803 0.392336 CCCCTCACAGCATCTCTAGC 59.608 60.000 0.00 0.00 0.00 3.42
3419 4804 1.117994 CCCTCACAGCATCTCTAGCA 58.882 55.000 0.00 0.00 0.00 3.49
3420 4805 1.068895 CCCTCACAGCATCTCTAGCAG 59.931 57.143 0.00 0.00 0.00 4.24
3421 4806 2.030371 CCTCACAGCATCTCTAGCAGA 58.970 52.381 0.00 0.00 34.78 4.26
3422 4807 2.223782 CCTCACAGCATCTCTAGCAGAC 60.224 54.545 0.00 0.00 32.26 3.51
3423 4808 1.753649 TCACAGCATCTCTAGCAGACC 59.246 52.381 0.00 0.00 32.26 3.85
3424 4809 1.118838 ACAGCATCTCTAGCAGACCC 58.881 55.000 0.00 0.00 32.26 4.46
3425 4810 0.392336 CAGCATCTCTAGCAGACCCC 59.608 60.000 0.00 0.00 32.26 4.95
3426 4811 0.264359 AGCATCTCTAGCAGACCCCT 59.736 55.000 0.00 0.00 32.26 4.79
3427 4812 0.678950 GCATCTCTAGCAGACCCCTC 59.321 60.000 0.00 0.00 32.26 4.30
3428 4813 2.031624 GCATCTCTAGCAGACCCCTCA 61.032 57.143 0.00 0.00 32.26 3.86
3429 4814 2.607499 CATCTCTAGCAGACCCCTCAT 58.393 52.381 0.00 0.00 32.26 2.90
3430 4815 3.772387 CATCTCTAGCAGACCCCTCATA 58.228 50.000 0.00 0.00 32.26 2.15
3431 4816 3.517296 TCTCTAGCAGACCCCTCATAG 57.483 52.381 0.00 0.00 0.00 2.23
3432 4817 1.892474 CTCTAGCAGACCCCTCATAGC 59.108 57.143 0.00 0.00 0.00 2.97
3433 4818 0.972883 CTAGCAGACCCCTCATAGCC 59.027 60.000 0.00 0.00 0.00 3.93
3434 4819 0.827925 TAGCAGACCCCTCATAGCCG 60.828 60.000 0.00 0.00 0.00 5.52
3435 4820 2.134287 GCAGACCCCTCATAGCCGA 61.134 63.158 0.00 0.00 0.00 5.54
3436 4821 1.686325 GCAGACCCCTCATAGCCGAA 61.686 60.000 0.00 0.00 0.00 4.30
3437 4822 0.830648 CAGACCCCTCATAGCCGAAA 59.169 55.000 0.00 0.00 0.00 3.46
3438 4823 1.417890 CAGACCCCTCATAGCCGAAAT 59.582 52.381 0.00 0.00 0.00 2.17
3439 4824 1.417890 AGACCCCTCATAGCCGAAATG 59.582 52.381 0.00 0.00 0.00 2.32
3440 4825 1.141053 GACCCCTCATAGCCGAAATGT 59.859 52.381 0.00 0.00 0.00 2.71
3441 4826 2.367567 GACCCCTCATAGCCGAAATGTA 59.632 50.000 0.00 0.00 0.00 2.29
3442 4827 2.775384 ACCCCTCATAGCCGAAATGTAA 59.225 45.455 0.00 0.00 0.00 2.41
3443 4828 3.201266 ACCCCTCATAGCCGAAATGTAAA 59.799 43.478 0.00 0.00 0.00 2.01
3444 4829 4.204012 CCCCTCATAGCCGAAATGTAAAA 58.796 43.478 0.00 0.00 0.00 1.52
3445 4830 4.036380 CCCCTCATAGCCGAAATGTAAAAC 59.964 45.833 0.00 0.00 0.00 2.43
3446 4831 4.638421 CCCTCATAGCCGAAATGTAAAACA 59.362 41.667 0.00 0.00 0.00 2.83
3447 4832 5.220854 CCCTCATAGCCGAAATGTAAAACAG 60.221 44.000 0.00 0.00 0.00 3.16
3448 4833 5.584649 CCTCATAGCCGAAATGTAAAACAGA 59.415 40.000 0.00 0.00 0.00 3.41
3449 4834 6.093495 CCTCATAGCCGAAATGTAAAACAGAA 59.907 38.462 0.00 0.00 0.00 3.02
3450 4835 7.201732 CCTCATAGCCGAAATGTAAAACAGAAT 60.202 37.037 0.00 0.00 0.00 2.40
3451 4836 7.471721 TCATAGCCGAAATGTAAAACAGAATG 58.528 34.615 0.00 0.00 46.00 2.67
3452 4837 4.485163 AGCCGAAATGTAAAACAGAATGC 58.515 39.130 0.00 0.00 42.53 3.56
3453 4838 4.218417 AGCCGAAATGTAAAACAGAATGCT 59.782 37.500 0.00 0.00 42.53 3.79
3454 4839 5.414454 AGCCGAAATGTAAAACAGAATGCTA 59.586 36.000 0.00 0.00 42.53 3.49
3455 4840 5.739161 GCCGAAATGTAAAACAGAATGCTAG 59.261 40.000 0.00 0.00 42.53 3.42
3456 4841 6.258160 CCGAAATGTAAAACAGAATGCTAGG 58.742 40.000 0.00 0.00 42.53 3.02
3457 4842 5.739161 CGAAATGTAAAACAGAATGCTAGGC 59.261 40.000 0.00 0.00 42.53 3.93
3458 4843 5.582689 AATGTAAAACAGAATGCTAGGCC 57.417 39.130 0.00 0.00 42.53 5.19
3459 4844 3.006940 TGTAAAACAGAATGCTAGGCCG 58.993 45.455 0.00 0.00 42.53 6.13
3460 4845 1.463674 AAAACAGAATGCTAGGCCGG 58.536 50.000 0.00 0.00 42.53 6.13
3461 4846 1.032114 AAACAGAATGCTAGGCCGGC 61.032 55.000 21.18 21.18 42.53 6.13
3462 4847 2.969238 CAGAATGCTAGGCCGGCG 60.969 66.667 22.54 8.08 0.00 6.46
3463 4848 4.918201 AGAATGCTAGGCCGGCGC 62.918 66.667 22.54 19.33 0.00 6.53
3469 4854 4.241555 CTAGGCCGGCGCAGGAAT 62.242 66.667 31.49 19.06 36.38 3.01
3470 4855 4.235762 TAGGCCGGCGCAGGAATC 62.236 66.667 31.49 17.60 36.38 2.52
3473 4858 4.838152 GCCGGCGCAGGAATCAGA 62.838 66.667 31.49 0.00 34.03 3.27
3474 4859 2.109799 CCGGCGCAGGAATCAGAT 59.890 61.111 23.19 0.00 0.00 2.90
3475 4860 2.249535 CCGGCGCAGGAATCAGATG 61.250 63.158 23.19 0.00 0.00 2.90
3476 4861 2.249535 CGGCGCAGGAATCAGATGG 61.250 63.158 10.83 0.00 0.00 3.51
3477 4862 1.895707 GGCGCAGGAATCAGATGGG 60.896 63.158 10.83 0.00 0.00 4.00
3478 4863 1.153086 GCGCAGGAATCAGATGGGT 60.153 57.895 0.30 0.00 0.00 4.51
3479 4864 0.749454 GCGCAGGAATCAGATGGGTT 60.749 55.000 0.30 0.00 0.00 4.11
3480 4865 1.755179 CGCAGGAATCAGATGGGTTT 58.245 50.000 0.00 0.00 0.00 3.27
3481 4866 2.094675 CGCAGGAATCAGATGGGTTTT 58.905 47.619 0.00 0.00 0.00 2.43
3482 4867 2.493278 CGCAGGAATCAGATGGGTTTTT 59.507 45.455 0.00 0.00 0.00 1.94
3483 4868 3.694072 CGCAGGAATCAGATGGGTTTTTA 59.306 43.478 0.00 0.00 0.00 1.52
3484 4869 4.339247 CGCAGGAATCAGATGGGTTTTTAT 59.661 41.667 0.00 0.00 0.00 1.40
3485 4870 5.506317 CGCAGGAATCAGATGGGTTTTTATC 60.506 44.000 0.00 0.00 0.00 1.75
3486 4871 5.595952 GCAGGAATCAGATGGGTTTTTATCT 59.404 40.000 0.00 0.00 34.09 1.98
3496 4881 8.421249 AGATGGGTTTTTATCTGAATTTGACA 57.579 30.769 0.00 0.00 32.65 3.58
3497 4882 8.306761 AGATGGGTTTTTATCTGAATTTGACAC 58.693 33.333 0.00 0.00 32.65 3.67
3498 4883 7.353414 TGGGTTTTTATCTGAATTTGACACA 57.647 32.000 0.00 0.00 0.00 3.72
3499 4884 7.961351 TGGGTTTTTATCTGAATTTGACACAT 58.039 30.769 0.00 0.00 0.00 3.21
3500 4885 9.083422 TGGGTTTTTATCTGAATTTGACACATA 57.917 29.630 0.00 0.00 0.00 2.29
3504 4889 9.585099 TTTTTATCTGAATTTGACACATATGCC 57.415 29.630 1.58 0.00 0.00 4.40
3505 4890 7.878547 TTATCTGAATTTGACACATATGCCA 57.121 32.000 1.58 0.00 0.00 4.92
3506 4891 5.565592 TCTGAATTTGACACATATGCCAC 57.434 39.130 1.58 0.00 0.00 5.01
3507 4892 5.008980 TCTGAATTTGACACATATGCCACA 58.991 37.500 1.58 0.00 0.00 4.17
3508 4893 5.653330 TCTGAATTTGACACATATGCCACAT 59.347 36.000 1.58 0.00 0.00 3.21
3509 4894 6.827762 TCTGAATTTGACACATATGCCACATA 59.172 34.615 1.58 0.00 0.00 2.29
3510 4895 7.503230 TCTGAATTTGACACATATGCCACATAT 59.497 33.333 1.58 0.00 0.00 1.78
3511 4896 8.009622 TGAATTTGACACATATGCCACATATT 57.990 30.769 1.58 7.18 0.00 1.28
3512 4897 8.136800 TGAATTTGACACATATGCCACATATTC 58.863 33.333 19.63 19.63 32.63 1.75
3513 4898 7.585579 ATTTGACACATATGCCACATATTCA 57.414 32.000 1.58 0.00 0.00 2.57
3514 4899 6.622833 TTGACACATATGCCACATATTCAG 57.377 37.500 1.58 0.00 0.00 3.02
3515 4900 5.927819 TGACACATATGCCACATATTCAGA 58.072 37.500 1.58 0.00 0.00 3.27
3516 4901 6.355747 TGACACATATGCCACATATTCAGAA 58.644 36.000 1.58 0.00 0.00 3.02
3517 4902 6.999871 TGACACATATGCCACATATTCAGAAT 59.000 34.615 1.58 0.20 0.00 2.40
3518 4903 7.503230 TGACACATATGCCACATATTCAGAATT 59.497 33.333 1.58 0.00 0.00 2.17
3519 4904 8.922931 ACACATATGCCACATATTCAGAATTA 57.077 30.769 1.58 0.00 0.00 1.40
3520 4905 8.786898 ACACATATGCCACATATTCAGAATTAC 58.213 33.333 1.58 0.00 0.00 1.89
3521 4906 9.006839 CACATATGCCACATATTCAGAATTACT 57.993 33.333 1.58 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 291 1.400494 GTCACGTTTGACCAGCTTTGT 59.600 47.619 0.00 0.00 45.77 2.83
1411 2734 4.794439 CGACGATCCTGTGGCGCA 62.794 66.667 10.83 0.00 0.00 6.09
1693 3022 1.004745 TGCTCCTAAGGAAAAGCCCTG 59.995 52.381 0.00 0.00 36.49 4.45
1759 3088 2.239150 AGCTGCATGATCTTCCTTGAGT 59.761 45.455 1.02 0.00 0.00 3.41
2202 3531 1.607178 CAGCAATGGTGAAGGGGCA 60.607 57.895 6.59 0.00 32.22 5.36
3344 4729 7.595819 ACTGGAACATGTTCATTCCTAAAAA 57.404 32.000 33.42 6.10 44.13 1.94
3345 4730 7.595819 AACTGGAACATGTTCATTCCTAAAA 57.404 32.000 33.42 6.43 44.13 1.52
3346 4731 8.160765 TCTAACTGGAACATGTTCATTCCTAAA 58.839 33.333 33.42 13.95 44.13 1.85
3347 4732 7.606456 GTCTAACTGGAACATGTTCATTCCTAA 59.394 37.037 33.42 15.18 44.13 2.69
3348 4733 7.038302 AGTCTAACTGGAACATGTTCATTCCTA 60.038 37.037 33.42 18.69 44.13 2.94
3349 4734 5.940470 GTCTAACTGGAACATGTTCATTCCT 59.060 40.000 33.42 18.59 44.13 3.36
3350 4735 5.940470 AGTCTAACTGGAACATGTTCATTCC 59.060 40.000 33.42 21.21 44.08 3.01
3351 4736 7.301054 CAAGTCTAACTGGAACATGTTCATTC 58.699 38.462 33.42 20.05 41.20 2.67
3352 4737 6.207417 CCAAGTCTAACTGGAACATGTTCATT 59.793 38.462 33.42 25.77 41.20 2.57
3353 4738 5.707298 CCAAGTCTAACTGGAACATGTTCAT 59.293 40.000 33.42 20.68 41.20 2.57
3354 4739 5.063204 CCAAGTCTAACTGGAACATGTTCA 58.937 41.667 33.42 20.85 41.20 3.18
3355 4740 5.049405 CACCAAGTCTAACTGGAACATGTTC 60.049 44.000 27.16 27.16 38.20 3.18
3356 4741 4.821805 CACCAAGTCTAACTGGAACATGTT 59.178 41.667 11.78 11.78 38.20 2.71
3357 4742 4.389374 CACCAAGTCTAACTGGAACATGT 58.611 43.478 0.00 0.00 38.20 3.21
3358 4743 3.189287 GCACCAAGTCTAACTGGAACATG 59.811 47.826 0.00 0.00 38.20 3.21
3359 4744 3.412386 GCACCAAGTCTAACTGGAACAT 58.588 45.455 0.00 0.00 38.20 2.71
3360 4745 2.486548 GGCACCAAGTCTAACTGGAACA 60.487 50.000 0.00 0.00 0.00 3.18
3361 4746 2.152016 GGCACCAAGTCTAACTGGAAC 58.848 52.381 0.00 0.00 0.00 3.62
3362 4747 2.561478 GGCACCAAGTCTAACTGGAA 57.439 50.000 0.00 0.00 0.00 3.53
3380 4765 2.290323 GGGTACTAGCCATATTGCTGGG 60.290 54.545 15.28 8.90 43.45 4.45
3381 4766 2.290323 GGGGTACTAGCCATATTGCTGG 60.290 54.545 11.44 10.79 44.57 4.85
3382 4767 2.639839 AGGGGTACTAGCCATATTGCTG 59.360 50.000 11.44 4.50 42.77 4.41
3383 4768 2.907042 GAGGGGTACTAGCCATATTGCT 59.093 50.000 6.53 6.53 45.38 3.91
3384 4769 2.637872 TGAGGGGTACTAGCCATATTGC 59.362 50.000 6.63 0.00 37.54 3.56
3385 4770 3.646162 TGTGAGGGGTACTAGCCATATTG 59.354 47.826 6.63 0.00 37.54 1.90
3386 4771 3.904339 CTGTGAGGGGTACTAGCCATATT 59.096 47.826 6.63 0.00 37.54 1.28
3387 4772 3.511477 CTGTGAGGGGTACTAGCCATAT 58.489 50.000 6.63 0.00 37.54 1.78
3388 4773 2.958818 CTGTGAGGGGTACTAGCCATA 58.041 52.381 6.63 0.00 37.54 2.74
3389 4774 1.794714 CTGTGAGGGGTACTAGCCAT 58.205 55.000 6.63 0.00 37.54 4.40
3390 4775 0.976073 GCTGTGAGGGGTACTAGCCA 60.976 60.000 6.63 0.00 37.54 4.75
3391 4776 0.976073 TGCTGTGAGGGGTACTAGCC 60.976 60.000 0.00 0.00 34.31 3.93
3392 4777 1.069358 GATGCTGTGAGGGGTACTAGC 59.931 57.143 0.00 0.00 0.00 3.42
3393 4778 2.625790 GAGATGCTGTGAGGGGTACTAG 59.374 54.545 0.00 0.00 0.00 2.57
3394 4779 2.245028 AGAGATGCTGTGAGGGGTACTA 59.755 50.000 0.00 0.00 0.00 1.82
3395 4780 1.007721 AGAGATGCTGTGAGGGGTACT 59.992 52.381 0.00 0.00 0.00 2.73
3396 4781 1.490574 AGAGATGCTGTGAGGGGTAC 58.509 55.000 0.00 0.00 0.00 3.34
3397 4782 2.950781 CTAGAGATGCTGTGAGGGGTA 58.049 52.381 0.00 0.00 0.00 3.69
3398 4783 1.786937 CTAGAGATGCTGTGAGGGGT 58.213 55.000 0.00 0.00 0.00 4.95
3399 4784 0.392336 GCTAGAGATGCTGTGAGGGG 59.608 60.000 0.00 0.00 0.00 4.79
3400 4785 1.068895 CTGCTAGAGATGCTGTGAGGG 59.931 57.143 0.00 0.00 0.00 4.30
3401 4786 2.030371 TCTGCTAGAGATGCTGTGAGG 58.970 52.381 0.00 0.00 0.00 3.86
3402 4787 2.223782 GGTCTGCTAGAGATGCTGTGAG 60.224 54.545 0.00 0.00 31.63 3.51
3403 4788 1.753649 GGTCTGCTAGAGATGCTGTGA 59.246 52.381 0.00 0.00 31.63 3.58
3404 4789 1.202510 GGGTCTGCTAGAGATGCTGTG 60.203 57.143 0.00 0.00 31.63 3.66
3405 4790 1.118838 GGGTCTGCTAGAGATGCTGT 58.881 55.000 0.00 0.00 31.63 4.40
3406 4791 0.392336 GGGGTCTGCTAGAGATGCTG 59.608 60.000 0.00 0.00 31.63 4.41
3407 4792 0.264359 AGGGGTCTGCTAGAGATGCT 59.736 55.000 0.00 0.00 31.63 3.79
3408 4793 0.678950 GAGGGGTCTGCTAGAGATGC 59.321 60.000 0.00 0.00 31.63 3.91
3409 4794 2.079170 TGAGGGGTCTGCTAGAGATG 57.921 55.000 0.00 0.00 31.63 2.90
3410 4795 3.817567 GCTATGAGGGGTCTGCTAGAGAT 60.818 52.174 0.00 0.00 31.63 2.75
3411 4796 2.489985 GCTATGAGGGGTCTGCTAGAGA 60.490 54.545 0.00 0.00 0.00 3.10
3412 4797 1.892474 GCTATGAGGGGTCTGCTAGAG 59.108 57.143 0.00 0.00 0.00 2.43
3413 4798 1.481428 GGCTATGAGGGGTCTGCTAGA 60.481 57.143 0.00 0.00 0.00 2.43
3414 4799 0.972883 GGCTATGAGGGGTCTGCTAG 59.027 60.000 0.00 0.00 0.00 3.42
3415 4800 0.827925 CGGCTATGAGGGGTCTGCTA 60.828 60.000 0.00 0.00 0.00 3.49
3416 4801 2.136878 CGGCTATGAGGGGTCTGCT 61.137 63.158 0.00 0.00 0.00 4.24
3417 4802 1.686325 TTCGGCTATGAGGGGTCTGC 61.686 60.000 0.00 0.00 0.00 4.26
3418 4803 0.830648 TTTCGGCTATGAGGGGTCTG 59.169 55.000 0.00 0.00 0.00 3.51
3419 4804 1.417890 CATTTCGGCTATGAGGGGTCT 59.582 52.381 0.00 0.00 0.00 3.85
3420 4805 1.141053 ACATTTCGGCTATGAGGGGTC 59.859 52.381 0.00 0.00 0.00 4.46
3421 4806 1.213296 ACATTTCGGCTATGAGGGGT 58.787 50.000 0.00 0.00 0.00 4.95
3422 4807 3.485463 TTACATTTCGGCTATGAGGGG 57.515 47.619 0.00 0.00 0.00 4.79
3423 4808 4.638421 TGTTTTACATTTCGGCTATGAGGG 59.362 41.667 0.00 0.00 0.00 4.30
3424 4809 5.584649 TCTGTTTTACATTTCGGCTATGAGG 59.415 40.000 0.00 0.00 0.00 3.86
3425 4810 6.662414 TCTGTTTTACATTTCGGCTATGAG 57.338 37.500 0.00 0.00 0.00 2.90
3426 4811 7.471721 CATTCTGTTTTACATTTCGGCTATGA 58.528 34.615 0.00 0.00 0.00 2.15
3427 4812 6.197096 GCATTCTGTTTTACATTTCGGCTATG 59.803 38.462 0.00 0.00 0.00 2.23
3428 4813 6.095440 AGCATTCTGTTTTACATTTCGGCTAT 59.905 34.615 0.00 0.00 0.00 2.97
3429 4814 5.414454 AGCATTCTGTTTTACATTTCGGCTA 59.586 36.000 0.00 0.00 0.00 3.93
3430 4815 4.218417 AGCATTCTGTTTTACATTTCGGCT 59.782 37.500 0.00 0.00 0.00 5.52
3431 4816 4.485163 AGCATTCTGTTTTACATTTCGGC 58.515 39.130 0.00 0.00 0.00 5.54
3432 4817 6.258160 CCTAGCATTCTGTTTTACATTTCGG 58.742 40.000 0.00 0.00 0.00 4.30
3433 4818 5.739161 GCCTAGCATTCTGTTTTACATTTCG 59.261 40.000 0.00 0.00 0.00 3.46
3434 4819 6.036470 GGCCTAGCATTCTGTTTTACATTTC 58.964 40.000 0.00 0.00 0.00 2.17
3435 4820 5.393027 CGGCCTAGCATTCTGTTTTACATTT 60.393 40.000 0.00 0.00 0.00 2.32
3436 4821 4.096382 CGGCCTAGCATTCTGTTTTACATT 59.904 41.667 0.00 0.00 0.00 2.71
3437 4822 3.627577 CGGCCTAGCATTCTGTTTTACAT 59.372 43.478 0.00 0.00 0.00 2.29
3438 4823 3.006940 CGGCCTAGCATTCTGTTTTACA 58.993 45.455 0.00 0.00 0.00 2.41
3439 4824 2.354821 CCGGCCTAGCATTCTGTTTTAC 59.645 50.000 0.00 0.00 0.00 2.01
3440 4825 2.639065 CCGGCCTAGCATTCTGTTTTA 58.361 47.619 0.00 0.00 0.00 1.52
3441 4826 1.463674 CCGGCCTAGCATTCTGTTTT 58.536 50.000 0.00 0.00 0.00 2.43
3442 4827 1.032114 GCCGGCCTAGCATTCTGTTT 61.032 55.000 18.11 0.00 0.00 2.83
3443 4828 1.452108 GCCGGCCTAGCATTCTGTT 60.452 57.895 18.11 0.00 0.00 3.16
3444 4829 2.190578 GCCGGCCTAGCATTCTGT 59.809 61.111 18.11 0.00 0.00 3.41
3445 4830 2.969238 CGCCGGCCTAGCATTCTG 60.969 66.667 23.46 0.00 0.00 3.02
3446 4831 4.918201 GCGCCGGCCTAGCATTCT 62.918 66.667 23.46 0.00 0.00 2.40
3452 4837 4.241555 ATTCCTGCGCCGGCCTAG 62.242 66.667 23.46 18.90 38.85 3.02
3453 4838 4.235762 GATTCCTGCGCCGGCCTA 62.236 66.667 23.46 9.22 38.85 3.93
3456 4841 4.838152 TCTGATTCCTGCGCCGGC 62.838 66.667 19.07 19.07 40.52 6.13
3457 4842 2.109799 ATCTGATTCCTGCGCCGG 59.890 61.111 12.26 12.26 0.00 6.13
3458 4843 2.249535 CCATCTGATTCCTGCGCCG 61.250 63.158 4.18 0.00 0.00 6.46
3459 4844 1.895707 CCCATCTGATTCCTGCGCC 60.896 63.158 4.18 0.00 0.00 6.53
3460 4845 0.749454 AACCCATCTGATTCCTGCGC 60.749 55.000 0.00 0.00 0.00 6.09
3461 4846 1.755179 AAACCCATCTGATTCCTGCG 58.245 50.000 0.00 0.00 0.00 5.18
3462 4847 5.595952 AGATAAAAACCCATCTGATTCCTGC 59.404 40.000 0.00 0.00 30.30 4.85
3470 4855 8.306038 TGTCAAATTCAGATAAAAACCCATCTG 58.694 33.333 5.42 5.42 46.29 2.90
3471 4856 8.306761 GTGTCAAATTCAGATAAAAACCCATCT 58.693 33.333 0.00 0.00 31.58 2.90
3472 4857 8.087750 TGTGTCAAATTCAGATAAAAACCCATC 58.912 33.333 0.00 0.00 0.00 3.51
3473 4858 7.961351 TGTGTCAAATTCAGATAAAAACCCAT 58.039 30.769 0.00 0.00 0.00 4.00
3474 4859 7.353414 TGTGTCAAATTCAGATAAAAACCCA 57.647 32.000 0.00 0.00 0.00 4.51
3478 4863 9.585099 GGCATATGTGTCAAATTCAGATAAAAA 57.415 29.630 4.29 0.00 0.00 1.94
3479 4864 8.747471 TGGCATATGTGTCAAATTCAGATAAAA 58.253 29.630 4.29 0.00 36.93 1.52
3480 4865 8.190122 GTGGCATATGTGTCAAATTCAGATAAA 58.810 33.333 0.00 0.00 42.51 1.40
3481 4866 7.338957 TGTGGCATATGTGTCAAATTCAGATAA 59.661 33.333 0.00 0.00 42.51 1.75
3482 4867 6.827762 TGTGGCATATGTGTCAAATTCAGATA 59.172 34.615 0.00 0.00 42.51 1.98
3483 4868 5.653330 TGTGGCATATGTGTCAAATTCAGAT 59.347 36.000 0.00 0.00 42.51 2.90
3484 4869 5.008980 TGTGGCATATGTGTCAAATTCAGA 58.991 37.500 0.00 0.00 42.51 3.27
3485 4870 5.313520 TGTGGCATATGTGTCAAATTCAG 57.686 39.130 0.00 0.00 42.51 3.02
3486 4871 5.918426 ATGTGGCATATGTGTCAAATTCA 57.082 34.783 0.00 0.00 42.51 2.57
3487 4872 8.136800 TGAATATGTGGCATATGTGTCAAATTC 58.863 33.333 4.93 11.56 42.51 2.17
3488 4873 8.009622 TGAATATGTGGCATATGTGTCAAATT 57.990 30.769 4.93 3.08 42.51 1.82
3489 4874 7.503230 TCTGAATATGTGGCATATGTGTCAAAT 59.497 33.333 5.00 5.00 42.51 2.32
3490 4875 6.827762 TCTGAATATGTGGCATATGTGTCAAA 59.172 34.615 7.02 0.00 42.51 2.69
3491 4876 6.355747 TCTGAATATGTGGCATATGTGTCAA 58.644 36.000 7.02 0.00 42.51 3.18
3492 4877 5.927819 TCTGAATATGTGGCATATGTGTCA 58.072 37.500 7.02 6.58 37.69 3.58
3493 4878 6.866010 TTCTGAATATGTGGCATATGTGTC 57.134 37.500 7.02 2.39 0.00 3.67
3494 4879 7.828508 AATTCTGAATATGTGGCATATGTGT 57.171 32.000 7.02 0.00 0.00 3.72
3495 4880 9.006839 AGTAATTCTGAATATGTGGCATATGTG 57.993 33.333 7.02 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.