Multiple sequence alignment - TraesCS5D01G377500

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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 TraesCS5D01G377500 chr5D 100.000 3176 0 0 1 3176 449292110 449288935 0.000000e+00 5866.0
1 TraesCS5D01G377500 chr5D 90.642 716 57 7 2462 3176 558037047 558036341 0.000000e+00 942.0
2 TraesCS5D01G377500 chr5D 77.116 638 117 22 12 642 458762815 458763430 3.030000e-90 342.0
3 TraesCS5D01G377500 chr5D 85.149 101 13 2 1021 1120 495892751 495892652 5.600000e-18 102.0
4 TraesCS5D01G377500 chr5B 95.432 810 37 0 859 1668 548693581 548694390 0.000000e+00 1291.0
5 TraesCS5D01G377500 chr5B 89.966 887 37 19 1 867 548691679 548692533 0.000000e+00 1098.0
6 TraesCS5D01G377500 chr5B 91.213 717 49 6 2461 3176 425113300 425112597 0.000000e+00 963.0
7 TraesCS5D01G377500 chr5B 93.062 663 39 2 1667 2329 548694494 548695149 0.000000e+00 963.0
8 TraesCS5D01G377500 chr5B 91.213 717 49 6 2461 3176 658178892 658179595 0.000000e+00 963.0
9 TraesCS5D01G377500 chr5B 78.843 605 102 17 24 621 6577317 6576732 4.970000e-103 385.0
10 TraesCS5D01G377500 chr5B 78.620 594 96 23 28 611 639157561 639158133 6.470000e-97 364.0
11 TraesCS5D01G377500 chr5B 86.139 101 12 2 1021 1120 613168156 613168057 1.200000e-19 108.0
12 TraesCS5D01G377500 chr6B 91.353 717 47 10 2461 3176 561640662 561641364 0.000000e+00 966.0
13 TraesCS5D01G377500 chr6B 90.656 717 53 6 2461 3176 114411706 114411003 0.000000e+00 941.0
14 TraesCS5D01G377500 chr6B 74.387 652 123 33 13 654 116748415 116749032 4.090000e-59 239.0
15 TraesCS5D01G377500 chr5A 91.213 717 49 6 2461 3176 99023232 99022529 0.000000e+00 963.0
16 TraesCS5D01G377500 chr5A 78.840 293 46 14 371 654 343601390 343601105 1.950000e-42 183.0
17 TraesCS5D01G377500 chr5A 77.500 240 42 9 13 242 687951237 687951000 1.990000e-27 134.0
18 TraesCS5D01G377500 chr5A 86.139 101 12 2 1021 1120 619849597 619849498 1.200000e-19 108.0
19 TraesCS5D01G377500 chr7A 91.074 717 50 7 2461 3176 679315742 679315039 0.000000e+00 957.0
20 TraesCS5D01G377500 chr7A 79.851 134 23 3 1011 1142 733079545 733079676 9.380000e-16 95.3
21 TraesCS5D01G377500 chrUn 90.795 717 52 9 2461 3176 53927995 53928698 0.000000e+00 946.0
22 TraesCS5D01G377500 chr3A 90.795 717 52 8 2461 3176 743535849 743535146 0.000000e+00 946.0
23 TraesCS5D01G377500 chr7D 77.727 651 106 29 33 665 139193987 139193358 2.330000e-96 363.0
24 TraesCS5D01G377500 chr7D 77.364 645 115 23 22 658 149710193 149709572 1.400000e-93 353.0
25 TraesCS5D01G377500 chr7D 75.097 514 87 29 84 587 24823197 24822715 5.370000e-48 202.0
26 TraesCS5D01G377500 chr7D 79.104 134 24 3 1011 1142 633616951 633616820 4.360000e-14 89.8
27 TraesCS5D01G377500 chr7D 100.000 30 0 0 2386 2415 175443023 175442994 4.430000e-04 56.5
28 TraesCS5D01G377500 chr2D 76.190 630 109 25 23 640 304226767 304226167 8.620000e-76 294.0
29 TraesCS5D01G377500 chr2D 77.636 313 61 7 13 321 310715590 310715897 7.000000e-42 182.0
30 TraesCS5D01G377500 chr2D 85.593 118 15 2 1014 1130 5116368 5116484 4.300000e-24 122.0
31 TraesCS5D01G377500 chr2D 100.000 28 0 0 2388 2415 6901874 6901901 6.000000e-03 52.8
32 TraesCS5D01G377500 chr2A 76.248 581 103 25 13 584 171608172 171608726 3.120000e-70 276.0
33 TraesCS5D01G377500 chr4A 83.077 260 33 9 371 621 625326471 625326728 3.190000e-55 226.0
34 TraesCS5D01G377500 chr7B 78.070 342 68 7 13 351 748714312 748714649 3.210000e-50 209.0
35 TraesCS5D01G377500 chr1D 77.524 307 55 12 5 299 7481472 7481168 4.210000e-39 172.0
36 TraesCS5D01G377500 chr3D 74.353 464 86 23 5 459 508163186 508162747 1.960000e-37 167.0
37 TraesCS5D01G377500 chr1B 76.426 263 52 8 93 351 595509473 595509217 1.990000e-27 134.0
38 TraesCS5D01G377500 chr1B 83.036 112 17 2 1019 1129 635854547 635854657 2.020000e-17 100.0
39 TraesCS5D01G377500 chr1B 81.905 105 17 1 23 125 9800881 9800985 1.570000e-13 87.9
40 TraesCS5D01G377500 chr3B 79.710 138 19 6 994 1129 818241929 818241799 1.210000e-14 91.6


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 TraesCS5D01G377500 chr5D 449288935 449292110 3175 True 5866.000000 5866 100.000 1 3176 1 chr5D.!!$R1 3175
1 TraesCS5D01G377500 chr5D 558036341 558037047 706 True 942.000000 942 90.642 2462 3176 1 chr5D.!!$R3 714
2 TraesCS5D01G377500 chr5D 458762815 458763430 615 False 342.000000 342 77.116 12 642 1 chr5D.!!$F1 630
3 TraesCS5D01G377500 chr5B 548691679 548695149 3470 False 1117.333333 1291 92.820 1 2329 3 chr5B.!!$F3 2328
4 TraesCS5D01G377500 chr5B 425112597 425113300 703 True 963.000000 963 91.213 2461 3176 1 chr5B.!!$R2 715
5 TraesCS5D01G377500 chr5B 658178892 658179595 703 False 963.000000 963 91.213 2461 3176 1 chr5B.!!$F2 715
6 TraesCS5D01G377500 chr5B 6576732 6577317 585 True 385.000000 385 78.843 24 621 1 chr5B.!!$R1 597
7 TraesCS5D01G377500 chr5B 639157561 639158133 572 False 364.000000 364 78.620 28 611 1 chr5B.!!$F1 583
8 TraesCS5D01G377500 chr6B 561640662 561641364 702 False 966.000000 966 91.353 2461 3176 1 chr6B.!!$F2 715
9 TraesCS5D01G377500 chr6B 114411003 114411706 703 True 941.000000 941 90.656 2461 3176 1 chr6B.!!$R1 715
10 TraesCS5D01G377500 chr6B 116748415 116749032 617 False 239.000000 239 74.387 13 654 1 chr6B.!!$F1 641
11 TraesCS5D01G377500 chr5A 99022529 99023232 703 True 963.000000 963 91.213 2461 3176 1 chr5A.!!$R1 715
12 TraesCS5D01G377500 chr7A 679315039 679315742 703 True 957.000000 957 91.074 2461 3176 1 chr7A.!!$R1 715
13 TraesCS5D01G377500 chrUn 53927995 53928698 703 False 946.000000 946 90.795 2461 3176 1 chrUn.!!$F1 715
14 TraesCS5D01G377500 chr3A 743535146 743535849 703 True 946.000000 946 90.795 2461 3176 1 chr3A.!!$R1 715
15 TraesCS5D01G377500 chr7D 139193358 139193987 629 True 363.000000 363 77.727 33 665 1 chr7D.!!$R2 632
16 TraesCS5D01G377500 chr7D 149709572 149710193 621 True 353.000000 353 77.364 22 658 1 chr7D.!!$R3 636
17 TraesCS5D01G377500 chr2D 304226167 304226767 600 True 294.000000 294 76.190 23 640 1 chr2D.!!$R1 617
18 TraesCS5D01G377500 chr2A 171608172 171608726 554 False 276.000000 276 76.248 13 584 1 chr2A.!!$F1 571

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
658 701 1.410882 GCGCTCATCCTTTCTACTCCT 59.589 52.381 0.00 0.00 0.00 3.69 F
1668 2783 0.520404 GCATGAGCTCTTGGTGTGTG 59.480 55.000 25.89 9.23 37.91 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 2979 0.032813 ACCCATAGCAGCTTGCCATT 60.033 50.0 0.0 0.0 46.52 3.16 R
2653 3873 0.103390 TGACAAGGTCTTTGCGTCGA 59.897 50.0 0.0 0.0 40.59 4.20 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
277 303 5.511545 GCCCACCAAAACACCACATTATAAA 60.512 40.000 0.00 0.00 0.00 1.40
344 374 7.937649 ACCAAATACTCACTTAGTTCCAAAAC 58.062 34.615 0.00 0.00 39.80 2.43
437 475 6.275335 CCAAAAATATCGAGCATCCACAATT 58.725 36.000 0.00 0.00 0.00 2.32
546 585 5.864628 AACTTGATCGAACTTAAAGAGGC 57.135 39.130 0.00 0.00 0.00 4.70
597 639 7.839680 ACATTTTGAAACAGAGGGAGTAAAT 57.160 32.000 0.00 0.00 0.00 1.40
629 672 7.111247 TGAAAATCCAACAACATCAAGAAGT 57.889 32.000 0.00 0.00 0.00 3.01
658 701 1.410882 GCGCTCATCCTTTCTACTCCT 59.589 52.381 0.00 0.00 0.00 3.69
659 702 2.159028 GCGCTCATCCTTTCTACTCCTT 60.159 50.000 0.00 0.00 0.00 3.36
660 703 3.068307 GCGCTCATCCTTTCTACTCCTTA 59.932 47.826 0.00 0.00 0.00 2.69
813 872 1.801765 GCTTTGACTCGTATCCGACCC 60.802 57.143 0.00 0.00 38.40 4.46
830 889 4.038080 CGGTTTGGTTCTGGGCGC 62.038 66.667 0.00 0.00 0.00 6.53
894 2009 3.589495 ACACGGTAAGGTTTAGAGCTC 57.411 47.619 5.27 5.27 32.03 4.09
910 2025 3.259930 TCGTGCACGATCGAGACA 58.740 55.556 36.40 13.53 44.22 3.41
927 2042 2.623889 AGACACGCCTAGATCCATGTAC 59.376 50.000 0.00 0.00 0.00 2.90
959 2074 4.749099 CCTAGCTTGATTGATCTCTTTCCG 59.251 45.833 0.00 0.00 0.00 4.30
986 2101 2.630592 GATTCGACGCCTGAGTCCCC 62.631 65.000 0.00 0.00 37.85 4.81
1060 2175 1.144093 ACCTCCTCCTAGACATCTCCG 59.856 57.143 0.00 0.00 0.00 4.63
1198 2313 1.002257 AACCGCATCATCCACTGCA 60.002 52.632 0.00 0.00 38.30 4.41
1242 2357 1.337110 GCAAAACATTGAGCGACCGC 61.337 55.000 6.25 6.25 42.33 5.68
1262 2377 2.339100 GACTTCGACCTAGAGGCGCC 62.339 65.000 21.89 21.89 39.32 6.53
1284 2399 2.106332 CCGGGCACATCGTCCTAC 59.894 66.667 0.00 0.00 37.17 3.18
1321 2436 2.283173 GGAACTGGGTTGGCAGGG 60.283 66.667 0.00 0.00 0.00 4.45
1340 2455 2.809601 AGACGGCATGAACGCGTC 60.810 61.111 14.44 7.01 36.41 5.19
1425 2540 2.770048 CCCCTCCCGGAGCTTGAT 60.770 66.667 9.17 0.00 0.00 2.57
1465 2580 1.811965 CAATGGAGAATGTTCACGGCA 59.188 47.619 0.00 0.00 0.00 5.69
1492 2607 2.750888 GGCGATGGCACCGTCTTTC 61.751 63.158 1.89 0.00 42.47 2.62
1593 2708 2.087857 AAATGAACCCCAAGGCCGGA 62.088 55.000 5.05 0.00 36.11 5.14
1605 2720 2.027605 GCCGGAGATGATCGCGAA 59.972 61.111 15.24 0.00 0.00 4.70
1642 2757 2.045536 GAGGCAAGGTCCTGCTGG 60.046 66.667 2.58 2.58 42.25 4.85
1668 2783 0.520404 GCATGAGCTCTTGGTGTGTG 59.480 55.000 25.89 9.23 37.91 3.82
1669 2784 1.162698 CATGAGCTCTTGGTGTGTGG 58.837 55.000 19.36 0.00 0.00 4.17
1671 2786 1.419381 TGAGCTCTTGGTGTGTGGTA 58.581 50.000 16.19 0.00 0.00 3.25
1672 2787 1.765904 TGAGCTCTTGGTGTGTGGTAA 59.234 47.619 16.19 0.00 0.00 2.85
1674 2789 0.865769 GCTCTTGGTGTGTGGTAACG 59.134 55.000 0.00 0.00 42.51 3.18
1684 2799 3.384348 TGGTAACGCAGGAGGGAC 58.616 61.111 0.00 0.00 42.51 4.46
1721 2941 1.144057 GTGACCCGATCGCCAGATT 59.856 57.895 10.32 0.00 37.19 2.40
1758 2978 2.483106 TGAGAACTACGTCCTTCAGTCG 59.517 50.000 0.00 0.00 0.00 4.18
1759 2979 2.740981 GAGAACTACGTCCTTCAGTCGA 59.259 50.000 0.00 0.00 0.00 4.20
1760 2980 3.144506 AGAACTACGTCCTTCAGTCGAA 58.855 45.455 0.00 0.00 0.00 3.71
1836 3056 1.456892 TGGTGGCTCGTATCCGGAT 60.457 57.895 22.95 22.95 33.95 4.18
1854 3074 2.653726 GATATGTGGGTGATGGTGCAA 58.346 47.619 0.00 0.00 0.00 4.08
1885 3105 1.568504 AGAAGCCGGTGGTGAGAATA 58.431 50.000 1.90 0.00 0.00 1.75
1899 3119 1.593006 GAGAATATGCGTTGGGTGACG 59.407 52.381 0.00 0.00 45.40 4.35
1932 3152 0.798776 GCTTGGGTGATCGTGTCTTG 59.201 55.000 0.00 0.00 0.00 3.02
2055 3275 2.024871 GACGATGGCGAGACCGAG 59.975 66.667 0.00 0.00 43.94 4.63
2081 3301 4.360563 GTGATGTACCATCCTCTTACACG 58.639 47.826 2.02 0.00 0.00 4.49
2082 3302 3.383505 TGATGTACCATCCTCTTACACGG 59.616 47.826 2.02 0.00 0.00 4.94
2127 3347 2.350458 CCAACCTCCAATTGCCCCG 61.350 63.158 0.00 0.00 0.00 5.73
2143 3363 2.088423 CCCCGATGACCGAAATTCAAA 58.912 47.619 0.00 0.00 41.76 2.69
2160 3380 2.628178 TCAAAAGAGACTGGAAGCTCGA 59.372 45.455 0.00 0.00 40.48 4.04
2161 3381 3.259374 TCAAAAGAGACTGGAAGCTCGAT 59.741 43.478 0.00 0.00 40.48 3.59
2162 3382 3.971245 AAAGAGACTGGAAGCTCGATT 57.029 42.857 0.00 0.00 40.48 3.34
2164 3384 2.451490 AGAGACTGGAAGCTCGATTCA 58.549 47.619 1.49 0.00 40.48 2.57
2165 3385 2.828520 AGAGACTGGAAGCTCGATTCAA 59.171 45.455 1.49 0.00 40.48 2.69
2166 3386 3.259374 AGAGACTGGAAGCTCGATTCAAA 59.741 43.478 1.49 0.00 40.48 2.69
2167 3387 4.081198 AGAGACTGGAAGCTCGATTCAAAT 60.081 41.667 1.49 0.00 40.48 2.32
2168 3388 4.583871 AGACTGGAAGCTCGATTCAAATT 58.416 39.130 1.49 0.00 37.60 1.82
2169 3389 5.734720 AGACTGGAAGCTCGATTCAAATTA 58.265 37.500 1.49 0.00 37.60 1.40
2178 3398 8.634475 AAGCTCGATTCAAATTAAAATAAGGC 57.366 30.769 0.00 0.00 0.00 4.35
2200 3420 3.560068 CGAAGCAAGAAGTTTGGTGTAGT 59.440 43.478 0.00 0.00 0.00 2.73
2219 3439 1.829222 GTCCCTCACCGGATTTGAGTA 59.171 52.381 9.46 0.00 39.15 2.59
2231 3451 9.716507 CACCGGATTTGAGTATAAAATTTACAG 57.283 33.333 9.46 0.00 0.00 2.74
2232 3452 9.457436 ACCGGATTTGAGTATAAAATTTACAGT 57.543 29.630 9.46 0.00 0.00 3.55
2263 3483 1.879380 TGGATGCCGTTTTCAAGTGAG 59.121 47.619 0.00 0.00 0.00 3.51
2271 3491 6.744112 TGCCGTTTTCAAGTGAGATTATTTT 58.256 32.000 0.00 0.00 0.00 1.82
2282 3502 7.275888 AGTGAGATTATTTTGAAGCACAACA 57.724 32.000 0.00 0.00 38.29 3.33
2285 3505 8.025445 GTGAGATTATTTTGAAGCACAACATCT 58.975 33.333 0.00 0.00 38.29 2.90
2356 3576 6.844097 TTGTTACAAAATGAGGATTACCCC 57.156 37.500 0.00 0.00 36.73 4.95
2357 3577 5.265989 TGTTACAAAATGAGGATTACCCCC 58.734 41.667 0.00 0.00 36.73 5.40
2358 3578 3.012934 ACAAAATGAGGATTACCCCCG 57.987 47.619 0.00 0.00 36.73 5.73
2359 3579 2.306847 CAAAATGAGGATTACCCCCGG 58.693 52.381 0.00 0.00 36.73 5.73
2360 3580 0.185175 AAATGAGGATTACCCCCGGC 59.815 55.000 0.00 0.00 36.73 6.13
2361 3581 1.716028 AATGAGGATTACCCCCGGCC 61.716 60.000 0.00 0.00 36.73 6.13
2362 3582 2.447959 GAGGATTACCCCCGGCCT 60.448 66.667 0.00 0.00 36.73 5.19
2363 3583 2.043941 AGGATTACCCCCGGCCTT 59.956 61.111 0.00 0.00 36.73 4.35
2364 3584 1.621514 AGGATTACCCCCGGCCTTT 60.622 57.895 0.00 0.00 36.73 3.11
2365 3585 1.455032 GGATTACCCCCGGCCTTTG 60.455 63.158 0.00 0.00 0.00 2.77
2366 3586 2.043349 ATTACCCCCGGCCTTTGC 60.043 61.111 0.00 0.00 0.00 3.68
2367 3587 2.847366 GATTACCCCCGGCCTTTGCA 62.847 60.000 0.00 0.00 40.13 4.08
2368 3588 2.236959 ATTACCCCCGGCCTTTGCAT 62.237 55.000 0.00 0.00 40.13 3.96
2369 3589 3.653664 TACCCCCGGCCTTTGCATG 62.654 63.158 0.00 0.00 40.13 4.06
2372 3592 4.137872 CCCGGCCTTTGCATGCAG 62.138 66.667 21.50 10.86 40.13 4.41
2373 3593 4.807039 CCGGCCTTTGCATGCAGC 62.807 66.667 21.50 20.20 45.96 5.25
2374 3594 4.807039 CGGCCTTTGCATGCAGCC 62.807 66.667 30.11 30.11 44.83 4.85
2375 3595 3.697747 GGCCTTTGCATGCAGCCA 61.698 61.111 33.09 14.62 44.83 4.75
2376 3596 2.582436 GCCTTTGCATGCAGCCAT 59.418 55.556 21.50 0.00 44.83 4.40
2377 3597 1.078708 GCCTTTGCATGCAGCCATT 60.079 52.632 21.50 0.00 44.83 3.16
2378 3598 0.675522 GCCTTTGCATGCAGCCATTT 60.676 50.000 21.50 0.00 44.83 2.32
2379 3599 1.816074 CCTTTGCATGCAGCCATTTT 58.184 45.000 21.50 0.00 44.83 1.82
2380 3600 1.466950 CCTTTGCATGCAGCCATTTTG 59.533 47.619 21.50 6.01 44.83 2.44
2381 3601 2.147958 CTTTGCATGCAGCCATTTTGT 58.852 42.857 21.50 0.00 44.83 2.83
2382 3602 2.257691 TTGCATGCAGCCATTTTGTT 57.742 40.000 21.50 0.00 44.83 2.83
2383 3603 3.397849 TTGCATGCAGCCATTTTGTTA 57.602 38.095 21.50 0.00 44.83 2.41
2384 3604 2.686235 TGCATGCAGCCATTTTGTTAC 58.314 42.857 18.46 0.00 44.83 2.50
2385 3605 2.036862 TGCATGCAGCCATTTTGTTACA 59.963 40.909 18.46 0.00 44.83 2.41
2386 3606 3.065655 GCATGCAGCCATTTTGTTACAA 58.934 40.909 14.21 0.00 37.23 2.41
2387 3607 3.497640 GCATGCAGCCATTTTGTTACAAA 59.502 39.130 14.21 6.41 37.23 2.83
2388 3608 4.024218 GCATGCAGCCATTTTGTTACAAAA 60.024 37.500 22.90 22.90 37.23 2.44
2389 3609 5.335035 GCATGCAGCCATTTTGTTACAAAAT 60.335 36.000 24.96 24.96 37.23 1.82
2390 3610 5.670149 TGCAGCCATTTTGTTACAAAATG 57.330 34.783 36.87 36.87 43.57 2.32
2391 3611 5.363101 TGCAGCCATTTTGTTACAAAATGA 58.637 33.333 41.36 28.34 45.59 2.57
2392 3612 5.466058 TGCAGCCATTTTGTTACAAAATGAG 59.534 36.000 41.36 34.04 45.59 2.90
2393 3613 5.106987 GCAGCCATTTTGTTACAAAATGAGG 60.107 40.000 41.36 32.72 45.59 3.86
2394 3614 6.222389 CAGCCATTTTGTTACAAAATGAGGA 58.778 36.000 41.36 18.69 45.59 3.71
2395 3615 6.875195 CAGCCATTTTGTTACAAAATGAGGAT 59.125 34.615 41.36 30.55 45.59 3.24
2396 3616 7.388500 CAGCCATTTTGTTACAAAATGAGGATT 59.612 33.333 41.36 26.89 45.59 3.01
2397 3617 8.592809 AGCCATTTTGTTACAAAATGAGGATTA 58.407 29.630 41.36 16.90 45.59 1.75
2398 3618 8.655970 GCCATTTTGTTACAAAATGAGGATTAC 58.344 33.333 41.36 25.82 45.59 1.89
2399 3619 9.150348 CCATTTTGTTACAAAATGAGGATTACC 57.850 33.333 41.36 0.00 45.59 2.85
2400 3620 9.150348 CATTTTGTTACAAAATGAGGATTACCC 57.850 33.333 39.01 0.00 45.59 3.69
2401 3621 6.844097 TTGTTACAAAATGAGGATTACCCC 57.156 37.500 0.00 0.00 36.73 4.95
2402 3622 4.944930 TGTTACAAAATGAGGATTACCCCG 59.055 41.667 0.00 0.00 36.73 5.73
2403 3623 3.012934 ACAAAATGAGGATTACCCCGG 57.987 47.619 0.00 0.00 36.73 5.73
2404 3624 1.681264 CAAAATGAGGATTACCCCGGC 59.319 52.381 0.00 0.00 36.73 6.13
2405 3625 0.185175 AAATGAGGATTACCCCGGCC 59.815 55.000 0.00 0.00 36.73 6.13
2406 3626 0.697854 AATGAGGATTACCCCGGCCT 60.698 55.000 0.00 0.00 36.73 5.19
2407 3627 1.128188 ATGAGGATTACCCCGGCCTC 61.128 60.000 14.67 14.67 45.59 4.70
2408 3628 1.459730 GAGGATTACCCCGGCCTCT 60.460 63.158 14.36 0.00 42.81 3.69
2409 3629 1.759459 GAGGATTACCCCGGCCTCTG 61.759 65.000 14.36 0.00 42.81 3.35
2410 3630 2.111251 GATTACCCCGGCCTCTGC 59.889 66.667 0.00 0.00 0.00 4.26
2411 3631 2.690881 ATTACCCCGGCCTCTGCA 60.691 61.111 0.00 0.00 40.13 4.41
2412 3632 2.056906 GATTACCCCGGCCTCTGCAT 62.057 60.000 0.00 0.00 40.13 3.96
2413 3633 2.056906 ATTACCCCGGCCTCTGCATC 62.057 60.000 0.00 0.00 40.13 3.91
2414 3634 3.993865 TACCCCGGCCTCTGCATCA 62.994 63.158 0.00 0.00 40.13 3.07
2415 3635 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
2416 3636 2.194056 CCCGGCCTCTGCATCATT 59.806 61.111 0.00 0.00 40.13 2.57
2417 3637 1.454479 CCCGGCCTCTGCATCATTT 60.454 57.895 0.00 0.00 40.13 2.32
2418 3638 1.039233 CCCGGCCTCTGCATCATTTT 61.039 55.000 0.00 0.00 40.13 1.82
2419 3639 0.819582 CCGGCCTCTGCATCATTTTT 59.180 50.000 0.00 0.00 40.13 1.94
2441 3661 7.489574 TTTTTGTTACAAAATGAGGATTGCC 57.510 32.000 21.63 0.00 0.00 4.52
2442 3662 4.799564 TGTTACAAAATGAGGATTGCCC 57.200 40.909 0.00 0.00 33.31 5.36
2443 3663 3.513515 TGTTACAAAATGAGGATTGCCCC 59.486 43.478 0.00 0.00 34.66 5.80
2444 3664 1.571955 ACAAAATGAGGATTGCCCCC 58.428 50.000 0.00 0.00 34.66 5.40
2445 3665 0.461135 CAAAATGAGGATTGCCCCCG 59.539 55.000 0.00 0.00 34.66 5.73
2446 3666 0.687427 AAAATGAGGATTGCCCCCGG 60.687 55.000 0.00 0.00 34.66 5.73
2459 3679 4.757355 CCCGGCCTTTGCATCCCA 62.757 66.667 0.00 0.00 40.13 4.37
2525 3745 4.816385 CCTAATACCAAACAGACATCGCAT 59.184 41.667 0.00 0.00 0.00 4.73
2615 3835 1.964448 CACACTCACCGAGGCTACA 59.036 57.895 0.00 0.00 33.35 2.74
2644 3864 4.192317 GTCATCCACCTAACCATCTTCAC 58.808 47.826 0.00 0.00 0.00 3.18
2653 3873 4.141620 CCTAACCATCTTCACAGCAGGTAT 60.142 45.833 0.00 0.00 0.00 2.73
2670 3890 2.334838 GTATCGACGCAAAGACCTTGT 58.665 47.619 0.00 0.00 37.36 3.16
2707 3928 1.004560 CACCATGACGCCAGACAGT 60.005 57.895 0.00 0.00 0.00 3.55
2714 3935 4.624364 CGCCAGACAGTGCCACCA 62.624 66.667 0.00 0.00 0.00 4.17
2742 3963 2.581354 GTGCTCGTCCATCCAGCT 59.419 61.111 0.00 0.00 34.03 4.24
2841 4063 2.110213 GGCAACTCCACACCGTCA 59.890 61.111 0.00 0.00 34.01 4.35
2858 4080 4.135153 ACCGCTGCTGGAGCTACG 62.135 66.667 19.01 8.64 46.64 3.51
2883 4105 0.253894 TCCATCACCCACAGCATCTG 59.746 55.000 0.00 0.00 37.52 2.90
2895 4117 2.032634 GCATCTGTCCGCCGAACAA 61.033 57.895 0.00 0.00 0.00 2.83
2901 4123 0.250124 TGTCCGCCGAACAACAGAAT 60.250 50.000 0.00 0.00 0.00 2.40
2935 4157 2.789842 CTCGATGGAGGGTACGACA 58.210 57.895 0.00 0.00 36.61 4.35
2942 4164 1.192428 GGAGGGTACGACATGAAGGT 58.808 55.000 0.00 0.00 0.00 3.50
2943 4165 1.134788 GGAGGGTACGACATGAAGGTG 60.135 57.143 0.00 0.00 0.00 4.00
2948 4170 1.537814 TACGACATGAAGGTGGCCGT 61.538 55.000 0.00 0.00 36.78 5.68
2949 4171 1.671054 CGACATGAAGGTGGCCGTT 60.671 57.895 0.00 0.00 0.00 4.44
2981 4203 6.983906 ATCCAGACTGAATTTTGGACTTTT 57.016 33.333 3.32 0.00 42.12 2.27
3046 4268 2.503920 CTCCACGGAGGGTAATAACG 57.496 55.000 5.08 0.00 38.51 3.18
3047 4269 1.753073 CTCCACGGAGGGTAATAACGT 59.247 52.381 5.08 0.00 38.51 3.99
3048 4270 2.951642 CTCCACGGAGGGTAATAACGTA 59.048 50.000 5.08 0.00 38.51 3.57
3068 4290 3.485431 TCGAGAGACGTCGCCGAC 61.485 66.667 21.74 7.29 43.13 4.79
3093 4315 1.533731 GACCGAACAAGCCGATCAAAA 59.466 47.619 0.00 0.00 0.00 2.44
3132 4354 3.520317 TCATATACCACCAAACCTCCGTT 59.480 43.478 0.00 0.00 0.00 4.44
3133 4355 4.715792 TCATATACCACCAAACCTCCGTTA 59.284 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 319 2.103153 GGGGGAGATGATGGAGTGTA 57.897 55.000 0.00 0.00 0.00 2.90
310 339 2.161609 GTGAGTATTTGGTTTGGCGAGG 59.838 50.000 0.00 0.00 0.00 4.63
574 616 9.546428 AAAATTTACTCCCTCTGTTTCAAAATG 57.454 29.630 0.00 0.00 0.00 2.32
629 672 2.173669 GGATGAGCGCGCTTTGCTA 61.174 57.895 36.87 19.04 44.18 3.49
733 776 7.493743 TTTGAGCGGGCGTTTATATTTAATA 57.506 32.000 0.00 0.00 0.00 0.98
762 805 2.841881 TCTGTTTTATCTACCCCGCCTT 59.158 45.455 0.00 0.00 0.00 4.35
763 806 2.434702 CTCTGTTTTATCTACCCCGCCT 59.565 50.000 0.00 0.00 0.00 5.52
764 807 2.484947 CCTCTGTTTTATCTACCCCGCC 60.485 54.545 0.00 0.00 0.00 6.13
767 810 5.431179 TGTTCCTCTGTTTTATCTACCCC 57.569 43.478 0.00 0.00 0.00 4.95
773 816 8.730680 TCAAAGCTTATGTTCCTCTGTTTTATC 58.269 33.333 0.00 0.00 0.00 1.75
813 872 4.038080 GCGCCCAGAACCAAACCG 62.038 66.667 0.00 0.00 0.00 4.44
875 1990 2.094854 ACGAGCTCTAAACCTTACCGTG 60.095 50.000 12.85 0.00 0.00 4.94
894 2009 2.488792 CGTGTCTCGATCGTGCACG 61.489 63.158 31.44 31.44 44.88 5.34
910 2025 0.314302 GCGTACATGGATCTAGGCGT 59.686 55.000 0.00 0.00 0.00 5.68
1033 2148 4.790962 TAGGAGGAGGTCGCGCGT 62.791 66.667 30.98 11.13 0.00 6.01
1034 2149 3.955101 CTAGGAGGAGGTCGCGCG 61.955 72.222 26.76 26.76 0.00 6.86
1048 2163 0.820074 AGACGGCCGGAGATGTCTAG 60.820 60.000 31.76 0.00 39.76 2.43
1167 2282 0.179124 TGCGGTTGTTGTTGGAAAGC 60.179 50.000 0.00 0.00 0.00 3.51
1217 2332 2.030893 TCGCTCAATGTTTTGCAAGGAG 60.031 45.455 0.00 3.01 35.63 3.69
1242 2357 1.352404 CGCCTCTAGGTCGAAGTCG 59.648 63.158 6.93 0.00 37.05 4.18
1281 2396 0.465097 TCTTCCTCCTACCGCCGTAG 60.465 60.000 5.35 5.35 41.55 3.51
1284 2399 3.121019 CTCTTCCTCCTACCGCCG 58.879 66.667 0.00 0.00 0.00 6.46
1321 2436 4.505217 CGCGTTCATGCCGTCTGC 62.505 66.667 0.00 0.00 41.77 4.26
1340 2455 2.159014 TCGGGACCCATGACGAAAATAG 60.159 50.000 12.15 0.00 31.79 1.73
1425 2540 0.911769 ACCGCCTGATTTCCTCATCA 59.088 50.000 0.00 0.00 32.10 3.07
1476 2591 0.670546 ACAGAAAGACGGTGCCATCG 60.671 55.000 0.00 0.00 0.00 3.84
1561 2676 2.159572 GGTTCATTTTCATGACCGTCCG 60.160 50.000 0.00 0.00 39.28 4.79
1605 2720 1.482621 CGTGATACGCTGCGCAAGAT 61.483 55.000 23.51 10.42 34.61 2.40
1617 2732 0.179081 GGACCTTGCCTCCGTGATAC 60.179 60.000 0.00 0.00 0.00 2.24
1624 2739 2.045536 CAGCAGGACCTTGCCTCC 60.046 66.667 11.03 0.00 45.18 4.30
1642 2757 1.022735 CAAGAGCTCATGCCCATGTC 58.977 55.000 17.77 0.00 40.80 3.06
1668 2783 1.516423 GAGTCCCTCCTGCGTTACC 59.484 63.158 0.00 0.00 0.00 2.85
1669 2784 1.139095 CGAGTCCCTCCTGCGTTAC 59.861 63.158 0.00 0.00 0.00 2.50
1671 2786 3.382832 CCGAGTCCCTCCTGCGTT 61.383 66.667 0.00 0.00 0.00 4.84
1674 2789 4.154347 CAGCCGAGTCCCTCCTGC 62.154 72.222 0.00 0.00 0.00 4.85
1676 2791 4.390556 AGCAGCCGAGTCCCTCCT 62.391 66.667 0.00 0.00 0.00 3.69
1678 2793 3.844090 GGAGCAGCCGAGTCCCTC 61.844 72.222 0.00 0.00 0.00 4.30
1753 2973 1.136147 GCAGCTTGCCATTCGACTG 59.864 57.895 0.00 0.00 37.42 3.51
1758 2978 0.672342 CCCATAGCAGCTTGCCATTC 59.328 55.000 0.00 0.00 46.52 2.67
1759 2979 0.032813 ACCCATAGCAGCTTGCCATT 60.033 50.000 0.00 0.00 46.52 3.16
1760 2980 0.846015 TACCCATAGCAGCTTGCCAT 59.154 50.000 0.00 0.00 46.52 4.40
1836 3056 1.954733 GCTTGCACCATCACCCACATA 60.955 52.381 0.00 0.00 0.00 2.29
1854 3074 1.376553 GGCTTCTTCTTCCAGCGCT 60.377 57.895 2.64 2.64 34.09 5.92
1885 3105 1.745115 CCATCGTCACCCAACGCAT 60.745 57.895 0.00 0.00 42.31 4.73
1899 3119 0.462047 CCAAGCTACGGGTGTCCATC 60.462 60.000 0.00 0.00 0.00 3.51
1932 3152 0.111639 TGGTTGGGTAGCCAAGGAAC 59.888 55.000 26.32 15.19 33.89 3.62
2034 3254 1.872679 GGTCTCGCCATCGTCGAAC 60.873 63.158 0.00 0.00 35.38 3.95
2081 3301 2.357034 ACACATGTGCGTCGGTCC 60.357 61.111 25.68 0.00 0.00 4.46
2082 3302 2.667318 CCACACATGTGCGTCGGTC 61.667 63.158 25.68 0.00 44.34 4.79
2127 3347 6.310197 CAGTCTCTTTTGAATTTCGGTCATC 58.690 40.000 0.00 0.00 0.00 2.92
2143 3363 2.828520 TGAATCGAGCTTCCAGTCTCTT 59.171 45.455 0.00 0.00 0.00 2.85
2160 3380 8.770438 TTGCTTCGCCTTATTTTAATTTGAAT 57.230 26.923 0.00 0.00 0.00 2.57
2161 3381 8.085296 TCTTGCTTCGCCTTATTTTAATTTGAA 58.915 29.630 0.00 0.00 0.00 2.69
2162 3382 7.598278 TCTTGCTTCGCCTTATTTTAATTTGA 58.402 30.769 0.00 0.00 0.00 2.69
2164 3384 8.088365 ACTTCTTGCTTCGCCTTATTTTAATTT 58.912 29.630 0.00 0.00 0.00 1.82
2165 3385 7.602753 ACTTCTTGCTTCGCCTTATTTTAATT 58.397 30.769 0.00 0.00 0.00 1.40
2166 3386 7.158099 ACTTCTTGCTTCGCCTTATTTTAAT 57.842 32.000 0.00 0.00 0.00 1.40
2167 3387 6.569179 ACTTCTTGCTTCGCCTTATTTTAA 57.431 33.333 0.00 0.00 0.00 1.52
2168 3388 6.569179 AACTTCTTGCTTCGCCTTATTTTA 57.431 33.333 0.00 0.00 0.00 1.52
2169 3389 5.453567 AACTTCTTGCTTCGCCTTATTTT 57.546 34.783 0.00 0.00 0.00 1.82
2178 3398 3.560068 ACTACACCAAACTTCTTGCTTCG 59.440 43.478 0.00 0.00 0.00 3.79
2184 3404 3.714798 TGAGGGACTACACCAAACTTCTT 59.285 43.478 0.00 0.00 41.55 2.52
2193 3413 0.686769 ATCCGGTGAGGGACTACACC 60.687 60.000 0.00 0.00 46.04 4.16
2194 3414 1.192428 AATCCGGTGAGGGACTACAC 58.808 55.000 0.00 0.00 41.55 2.90
2200 3420 2.241281 TACTCAAATCCGGTGAGGGA 57.759 50.000 20.96 8.79 45.66 4.20
2238 3458 3.886505 ACTTGAAAACGGCATCCAACTAA 59.113 39.130 0.00 0.00 0.00 2.24
2239 3459 3.252215 CACTTGAAAACGGCATCCAACTA 59.748 43.478 0.00 0.00 0.00 2.24
2240 3460 2.034558 CACTTGAAAACGGCATCCAACT 59.965 45.455 0.00 0.00 0.00 3.16
2241 3461 2.034053 TCACTTGAAAACGGCATCCAAC 59.966 45.455 0.00 0.00 0.00 3.77
2271 3491 4.734398 ACCAAAAAGATGTTGTGCTTCA 57.266 36.364 0.00 0.00 0.00 3.02
2330 3550 8.151596 GGGGTAATCCTCATTTTGTAACAAAAA 58.848 33.333 0.00 3.21 33.58 1.94
2331 3551 7.256368 GGGGGTAATCCTCATTTTGTAACAAAA 60.256 37.037 0.00 0.00 35.50 2.44
2332 3552 6.211785 GGGGGTAATCCTCATTTTGTAACAAA 59.788 38.462 0.00 0.00 35.50 2.83
2333 3553 5.717654 GGGGGTAATCCTCATTTTGTAACAA 59.282 40.000 0.00 0.00 35.50 2.83
2334 3554 5.265989 GGGGGTAATCCTCATTTTGTAACA 58.734 41.667 0.00 0.00 35.50 2.41
2335 3555 4.337274 CGGGGGTAATCCTCATTTTGTAAC 59.663 45.833 0.00 0.00 35.01 2.50
2336 3556 4.528920 CGGGGGTAATCCTCATTTTGTAA 58.471 43.478 0.00 0.00 35.01 2.41
2337 3557 3.117813 CCGGGGGTAATCCTCATTTTGTA 60.118 47.826 0.00 0.00 35.01 2.41
2338 3558 2.357777 CCGGGGGTAATCCTCATTTTGT 60.358 50.000 0.00 0.00 35.01 2.83
2339 3559 2.306847 CCGGGGGTAATCCTCATTTTG 58.693 52.381 0.00 0.00 35.01 2.44
2340 3560 1.411074 GCCGGGGGTAATCCTCATTTT 60.411 52.381 2.18 0.00 35.01 1.82
2341 3561 0.185175 GCCGGGGGTAATCCTCATTT 59.815 55.000 2.18 0.00 35.01 2.32
2342 3562 1.716028 GGCCGGGGGTAATCCTCATT 61.716 60.000 2.18 0.00 35.01 2.57
2343 3563 2.154074 GGCCGGGGGTAATCCTCAT 61.154 63.158 2.18 0.00 35.01 2.90
2344 3564 2.770904 GGCCGGGGGTAATCCTCA 60.771 66.667 2.18 0.00 35.01 3.86
2345 3565 1.642513 AAAGGCCGGGGGTAATCCTC 61.643 60.000 2.18 0.00 35.33 3.71
2346 3566 1.621514 AAAGGCCGGGGGTAATCCT 60.622 57.895 2.18 0.00 35.33 3.24
2347 3567 1.455032 CAAAGGCCGGGGGTAATCC 60.455 63.158 2.18 0.00 0.00 3.01
2348 3568 2.125326 GCAAAGGCCGGGGGTAATC 61.125 63.158 2.18 0.00 0.00 1.75
2349 3569 2.043349 GCAAAGGCCGGGGGTAAT 60.043 61.111 2.18 0.00 0.00 1.89
2350 3570 2.925117 ATGCAAAGGCCGGGGGTAA 61.925 57.895 2.18 0.00 40.13 2.85
2351 3571 3.343326 ATGCAAAGGCCGGGGGTA 61.343 61.111 2.18 0.00 40.13 3.69
2355 3575 4.137872 CTGCATGCAAAGGCCGGG 62.138 66.667 22.88 3.14 40.13 5.73
2356 3576 4.807039 GCTGCATGCAAAGGCCGG 62.807 66.667 22.88 9.19 42.31 6.13
2357 3577 4.807039 GGCTGCATGCAAAGGCCG 62.807 66.667 27.54 14.53 45.15 6.13
2358 3578 2.530958 AATGGCTGCATGCAAAGGCC 62.531 55.000 32.05 32.05 45.15 5.19
2359 3579 0.675522 AAATGGCTGCATGCAAAGGC 60.676 50.000 22.88 22.40 45.15 4.35
2360 3580 1.466950 CAAAATGGCTGCATGCAAAGG 59.533 47.619 22.88 11.54 45.15 3.11
2361 3581 2.147958 ACAAAATGGCTGCATGCAAAG 58.852 42.857 22.88 12.33 45.15 2.77
2362 3582 2.257691 ACAAAATGGCTGCATGCAAA 57.742 40.000 22.88 10.80 45.15 3.68
2363 3583 2.257691 AACAAAATGGCTGCATGCAA 57.742 40.000 22.88 7.52 45.15 4.08
2364 3584 2.036862 TGTAACAAAATGGCTGCATGCA 59.963 40.909 21.29 21.29 45.15 3.96
2365 3585 2.686235 TGTAACAAAATGGCTGCATGC 58.314 42.857 11.82 11.82 41.94 4.06
2366 3586 5.670149 TTTTGTAACAAAATGGCTGCATG 57.330 34.783 0.50 0.00 0.00 4.06
2367 3587 5.996513 TCATTTTGTAACAAAATGGCTGCAT 59.003 32.000 25.93 0.00 43.90 3.96
2368 3588 5.363101 TCATTTTGTAACAAAATGGCTGCA 58.637 33.333 25.93 14.38 43.90 4.41
2369 3589 5.106987 CCTCATTTTGTAACAAAATGGCTGC 60.107 40.000 25.93 0.00 43.90 5.25
2370 3590 6.222389 TCCTCATTTTGTAACAAAATGGCTG 58.778 36.000 25.93 19.98 43.90 4.85
2371 3591 6.418057 TCCTCATTTTGTAACAAAATGGCT 57.582 33.333 25.93 0.00 43.90 4.75
2372 3592 7.671495 AATCCTCATTTTGTAACAAAATGGC 57.329 32.000 25.93 0.00 43.90 4.40
2373 3593 9.150348 GGTAATCCTCATTTTGTAACAAAATGG 57.850 33.333 25.93 20.34 43.90 3.16
2374 3594 9.150348 GGGTAATCCTCATTTTGTAACAAAATG 57.850 33.333 23.37 23.37 44.65 2.32
2375 3595 8.318412 GGGGTAATCCTCATTTTGTAACAAAAT 58.682 33.333 0.00 0.00 33.58 1.82
2376 3596 7.524038 CGGGGTAATCCTCATTTTGTAACAAAA 60.524 37.037 0.00 0.00 32.73 2.44
2377 3597 6.071840 CGGGGTAATCCTCATTTTGTAACAAA 60.072 38.462 0.00 0.00 32.73 2.83
2378 3598 5.416326 CGGGGTAATCCTCATTTTGTAACAA 59.584 40.000 0.00 0.00 32.73 2.83
2379 3599 4.944930 CGGGGTAATCCTCATTTTGTAACA 59.055 41.667 0.00 0.00 32.73 2.41
2380 3600 4.337274 CCGGGGTAATCCTCATTTTGTAAC 59.663 45.833 0.00 0.00 32.73 2.50
2381 3601 4.528920 CCGGGGTAATCCTCATTTTGTAA 58.471 43.478 0.00 0.00 32.73 2.41
2382 3602 3.686120 GCCGGGGTAATCCTCATTTTGTA 60.686 47.826 2.18 0.00 32.73 2.41
2383 3603 2.948600 GCCGGGGTAATCCTCATTTTGT 60.949 50.000 2.18 0.00 32.73 2.83
2384 3604 1.681264 GCCGGGGTAATCCTCATTTTG 59.319 52.381 2.18 0.00 32.73 2.44
2385 3605 1.411074 GGCCGGGGTAATCCTCATTTT 60.411 52.381 2.18 0.00 32.73 1.82
2386 3606 0.185175 GGCCGGGGTAATCCTCATTT 59.815 55.000 2.18 0.00 32.73 2.32
2387 3607 0.697854 AGGCCGGGGTAATCCTCATT 60.698 55.000 2.18 0.00 32.73 2.57
2388 3608 1.073706 AGGCCGGGGTAATCCTCAT 60.074 57.895 2.18 0.00 32.73 2.90
2389 3609 1.764854 GAGGCCGGGGTAATCCTCA 60.765 63.158 16.17 0.00 43.42 3.86
2390 3610 1.459730 AGAGGCCGGGGTAATCCTC 60.460 63.158 13.92 13.92 44.09 3.71
2391 3611 1.766461 CAGAGGCCGGGGTAATCCT 60.766 63.158 2.18 0.00 35.33 3.24
2392 3612 2.829592 CAGAGGCCGGGGTAATCC 59.170 66.667 2.18 0.00 0.00 3.01
2393 3613 2.056906 ATGCAGAGGCCGGGGTAATC 62.057 60.000 2.18 0.00 40.13 1.75
2394 3614 2.056906 GATGCAGAGGCCGGGGTAAT 62.057 60.000 2.18 0.00 40.13 1.89
2395 3615 2.690881 ATGCAGAGGCCGGGGTAA 60.691 61.111 2.18 0.00 40.13 2.85
2396 3616 3.161450 GATGCAGAGGCCGGGGTA 61.161 66.667 2.18 0.00 40.13 3.69
2398 3618 2.916527 AAATGATGCAGAGGCCGGGG 62.917 60.000 2.18 0.00 40.13 5.73
2399 3619 1.039233 AAAATGATGCAGAGGCCGGG 61.039 55.000 2.18 0.00 40.13 5.73
2400 3620 0.819582 AAAAATGATGCAGAGGCCGG 59.180 50.000 0.00 0.00 40.13 6.13
2417 3637 6.484977 GGGCAATCCTCATTTTGTAACAAAAA 59.515 34.615 0.00 3.21 33.76 1.94
2418 3638 5.994668 GGGCAATCCTCATTTTGTAACAAAA 59.005 36.000 0.00 0.00 0.00 2.44
2419 3639 5.512232 GGGGCAATCCTCATTTTGTAACAAA 60.512 40.000 0.00 0.00 35.33 2.83
2420 3640 4.020662 GGGGCAATCCTCATTTTGTAACAA 60.021 41.667 0.00 0.00 35.33 2.83
2421 3641 3.513515 GGGGCAATCCTCATTTTGTAACA 59.486 43.478 0.00 0.00 35.33 2.41
2422 3642 3.118775 GGGGGCAATCCTCATTTTGTAAC 60.119 47.826 0.00 0.00 35.56 2.50
2423 3643 3.103742 GGGGGCAATCCTCATTTTGTAA 58.896 45.455 0.00 0.00 35.56 2.41
2424 3644 2.745968 GGGGGCAATCCTCATTTTGTA 58.254 47.619 0.00 0.00 35.56 2.41
2425 3645 1.571955 GGGGGCAATCCTCATTTTGT 58.428 50.000 0.00 0.00 35.56 2.83
2426 3646 0.461135 CGGGGGCAATCCTCATTTTG 59.539 55.000 0.00 0.00 35.01 2.44
2427 3647 0.687427 CCGGGGGCAATCCTCATTTT 60.687 55.000 0.00 0.00 35.01 1.82
2428 3648 1.076044 CCGGGGGCAATCCTCATTT 60.076 57.895 0.00 0.00 35.01 2.32
2429 3649 2.603008 CCGGGGGCAATCCTCATT 59.397 61.111 0.00 0.00 35.01 2.57
2442 3662 4.757355 TGGGATGCAAAGGCCGGG 62.757 66.667 2.18 0.00 40.13 5.73
2443 3663 3.142838 CTGGGATGCAAAGGCCGG 61.143 66.667 0.00 0.00 40.13 6.13
2444 3664 2.891941 TAGCTGGGATGCAAAGGCCG 62.892 60.000 0.00 0.00 40.13 6.13
2445 3665 1.076777 TAGCTGGGATGCAAAGGCC 60.077 57.895 0.00 0.00 40.13 5.19
2446 3666 0.394899 AGTAGCTGGGATGCAAAGGC 60.395 55.000 0.00 0.00 41.68 4.35
2447 3667 1.673168 GAGTAGCTGGGATGCAAAGG 58.327 55.000 0.00 0.00 34.99 3.11
2448 3668 1.211457 AGGAGTAGCTGGGATGCAAAG 59.789 52.381 0.00 0.00 34.99 2.77
2449 3669 1.289160 AGGAGTAGCTGGGATGCAAA 58.711 50.000 0.00 0.00 34.99 3.68
2450 3670 2.174685 TAGGAGTAGCTGGGATGCAA 57.825 50.000 0.00 0.00 34.99 4.08
2451 3671 2.251818 GATAGGAGTAGCTGGGATGCA 58.748 52.381 0.00 0.00 34.99 3.96
2452 3672 1.552792 GGATAGGAGTAGCTGGGATGC 59.447 57.143 0.00 0.00 0.00 3.91
2453 3673 2.183679 GGGATAGGAGTAGCTGGGATG 58.816 57.143 0.00 0.00 0.00 3.51
2454 3674 1.079658 GGGGATAGGAGTAGCTGGGAT 59.920 57.143 0.00 0.00 0.00 3.85
2455 3675 0.487772 GGGGATAGGAGTAGCTGGGA 59.512 60.000 0.00 0.00 0.00 4.37
2456 3676 0.489567 AGGGGATAGGAGTAGCTGGG 59.510 60.000 0.00 0.00 0.00 4.45
2457 3677 1.974236 CAAGGGGATAGGAGTAGCTGG 59.026 57.143 0.00 0.00 0.00 4.85
2458 3678 2.964209 TCAAGGGGATAGGAGTAGCTG 58.036 52.381 0.00 0.00 0.00 4.24
2459 3679 3.515562 CATCAAGGGGATAGGAGTAGCT 58.484 50.000 0.00 0.00 33.95 3.32
2525 3745 4.638421 CCGGCATTAGATGTTAGGTTTTGA 59.362 41.667 0.00 0.00 0.00 2.69
2574 3794 1.228124 ACCGGTGTGTGACCCATTG 60.228 57.895 6.12 0.00 42.62 2.82
2598 3818 1.878656 GCTGTAGCCTCGGTGAGTGT 61.879 60.000 0.00 0.00 34.31 3.55
2621 3841 3.843619 TGAAGATGGTTAGGTGGATGACA 59.156 43.478 0.00 0.00 0.00 3.58
2644 3864 0.647410 CTTTGCGTCGATACCTGCTG 59.353 55.000 0.00 0.00 0.00 4.41
2653 3873 0.103390 TGACAAGGTCTTTGCGTCGA 59.897 50.000 0.00 0.00 40.59 4.20
2670 3890 2.954611 CGTCGACAGCTGACCTGA 59.045 61.111 23.35 9.22 44.64 3.86
2728 3949 0.879400 GATGCAGCTGGATGGACGAG 60.879 60.000 26.69 0.00 0.00 4.18
2729 3950 1.144716 GATGCAGCTGGATGGACGA 59.855 57.895 26.69 0.00 0.00 4.20
2730 3951 1.145598 AGATGCAGCTGGATGGACG 59.854 57.895 26.69 0.00 0.00 4.79
2731 3952 0.107312 ACAGATGCAGCTGGATGGAC 60.107 55.000 33.28 11.35 40.20 4.02
2732 3953 0.179702 GACAGATGCAGCTGGATGGA 59.820 55.000 33.28 0.00 40.20 3.41
2742 3963 3.615834 GCTGGATATCGATGACAGATGCA 60.616 47.826 22.11 12.52 0.00 3.96
2858 4080 2.125106 GTGGGTGATGGACTCCGC 60.125 66.667 0.00 0.00 33.42 5.54
2883 4105 0.442699 GATTCTGTTGTTCGGCGGAC 59.557 55.000 12.39 12.39 0.00 4.79
2895 4117 0.250513 GCCGTCTTGGGAGATTCTGT 59.749 55.000 0.00 0.00 38.63 3.41
2920 4142 2.224066 CCTTCATGTCGTACCCTCCATC 60.224 54.545 0.00 0.00 0.00 3.51
2948 4170 2.361104 GTCTGGATTGGGCGGCAA 60.361 61.111 12.47 0.00 0.00 4.52
2949 4171 3.329889 AGTCTGGATTGGGCGGCA 61.330 61.111 12.47 0.00 0.00 5.69
3019 4241 2.579201 CTCCGTGGAGGCGATGTT 59.421 61.111 8.09 0.00 40.77 2.71
3132 4354 0.394192 CATTGCCAGATCCGGAGCTA 59.606 55.000 24.15 11.09 0.00 3.32
3133 4355 1.147824 CATTGCCAGATCCGGAGCT 59.852 57.895 18.52 18.52 0.00 4.09
3144 4366 1.511318 CGGTTCGTGGTTCATTGCCA 61.511 55.000 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.