Multiple sequence alignment - TraesCS5A01G334300

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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 TraesCS5A01G334300 chr5A 100.000 2749 0 0 1 2749 543933269 543930521 0.000000e+00 5077.0
1 TraesCS5A01G334300 chr5A 87.013 308 28 4 217 517 678195902 678196204 1.220000e-88 337.0
2 TraesCS5A01G334300 chr5A 93.401 197 11 2 5 199 678193622 678193818 9.630000e-75 291.0
3 TraesCS5A01G334300 chr5A 88.235 136 6 8 520 649 119008064 119007933 1.320000e-33 154.0
4 TraesCS5A01G334300 chr5A 82.635 167 17 12 532 687 122640100 122640265 1.330000e-28 137.0
5 TraesCS5A01G334300 chr5A 80.583 206 13 22 542 741 60752977 60752793 1.720000e-27 134.0
6 TraesCS5A01G334300 chr5D 92.067 1311 56 26 737 2032 428390717 428389440 0.000000e+00 1801.0
7 TraesCS5A01G334300 chr5D 96.491 57 2 0 2693 2749 428388817 428388761 8.100000e-16 95.3
8 TraesCS5A01G334300 chr5B 92.043 1307 65 23 736 2032 517579705 517578428 0.000000e+00 1801.0
9 TraesCS5A01G334300 chr5B 84.713 157 14 10 521 675 660864630 660864778 6.130000e-32 148.0
10 TraesCS5A01G334300 chr5B 90.541 74 7 0 2676 2749 517577700 517577627 6.270000e-17 99.0
11 TraesCS5A01G334300 chr3B 89.803 304 26 2 205 507 51762071 51761772 4.290000e-103 385.0
12 TraesCS5A01G334300 chr3B 93.171 205 14 0 1 205 51763714 51763510 4.450000e-78 302.0
13 TraesCS5A01G334300 chr3B 92.308 78 6 0 2562 2639 767559167 767559244 8.050000e-21 111.0
14 TraesCS5A01G334300 chr3D 88.599 307 27 4 205 508 313813528 313813227 1.560000e-97 366.0
15 TraesCS5A01G334300 chr4D 87.987 308 31 2 205 511 12199912 12200214 2.600000e-95 359.0
16 TraesCS5A01G334300 chr4D 82.249 169 13 16 533 690 20236448 20236286 2.220000e-26 130.0
17 TraesCS5A01G334300 chr3A 87.908 306 34 3 205 507 165096809 165096504 9.360000e-95 357.0
18 TraesCS5A01G334300 chr3A 91.542 201 17 0 5 205 165098498 165098298 7.500000e-71 278.0
19 TraesCS5A01G334300 chr7D 86.943 314 30 4 205 517 607218676 607218979 2.620000e-90 342.0
20 TraesCS5A01G334300 chr7D 95.506 89 3 1 122 210 412668154 412668241 1.030000e-29 141.0
21 TraesCS5A01G334300 chr2A 93.467 199 13 0 7 205 2930147 2929949 2.070000e-76 296.0
22 TraesCS5A01G334300 chr2A 87.356 174 17 3 356 528 2928504 2928335 7.770000e-46 195.0
23 TraesCS5A01G334300 chr2A 83.537 164 18 8 530 687 457919487 457919327 7.930000e-31 145.0
24 TraesCS5A01G334300 chr4A 93.035 201 14 0 5 205 42041977 42041777 7.440000e-76 294.0
25 TraesCS5A01G334300 chr4A 89.385 179 17 2 339 516 42040224 42040047 9.910000e-55 224.0
26 TraesCS5A01G334300 chr4A 84.324 185 18 9 536 720 58836968 58837141 1.310000e-38 171.0
27 TraesCS5A01G334300 chr4A 85.000 140 12 8 536 669 58837812 58837948 1.720000e-27 134.0
28 TraesCS5A01G334300 chr1D 91.707 205 8 4 1 205 495226439 495226634 2.700000e-70 276.0
29 TraesCS5A01G334300 chr4B 88.083 193 17 2 205 397 223403000 223402814 9.910000e-55 224.0
30 TraesCS5A01G334300 chr4B 94.595 37 1 1 2591 2627 363309560 363309595 3.820000e-04 56.5
31 TraesCS5A01G334300 chr7B 94.262 122 7 0 1 122 698485932 698486053 1.300000e-43 187.0
32 TraesCS5A01G334300 chr6D 84.343 198 16 14 536 725 291699198 291699008 2.180000e-41 180.0
33 TraesCS5A01G334300 chr7A 92.623 122 9 0 1 122 655908130 655908251 2.810000e-40 176.0
34 TraesCS5A01G334300 chr7A 96.552 87 2 1 122 208 172230710 172230795 2.850000e-30 143.0
35 TraesCS5A01G334300 chr1B 92.373 118 9 0 5 122 323660722 323660839 4.710000e-38 169.0
36 TraesCS5A01G334300 chr2D 98.810 84 1 0 122 205 349602639 349602722 1.710000e-32 150.0


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 TraesCS5A01G334300 chr5A 543930521 543933269 2748 True 5077.00 5077 100.0000 1 2749 1 chr5A.!!$R3 2748
1 TraesCS5A01G334300 chr5A 678193622 678196204 2582 False 314.00 337 90.2070 5 517 2 chr5A.!!$F2 512
2 TraesCS5A01G334300 chr5D 428388761 428390717 1956 True 948.15 1801 94.2790 737 2749 2 chr5D.!!$R1 2012
3 TraesCS5A01G334300 chr5B 517577627 517579705 2078 True 950.00 1801 91.2920 736 2749 2 chr5B.!!$R1 2013
4 TraesCS5A01G334300 chr3B 51761772 51763714 1942 True 343.50 385 91.4870 1 507 2 chr3B.!!$R1 506
5 TraesCS5A01G334300 chr3A 165096504 165098498 1994 True 317.50 357 89.7250 5 507 2 chr3A.!!$R1 502
6 TraesCS5A01G334300 chr2A 2928335 2930147 1812 True 245.50 296 90.4115 7 528 2 chr2A.!!$R2 521
7 TraesCS5A01G334300 chr4A 42040047 42041977 1930 True 259.00 294 91.2100 5 516 2 chr4A.!!$R1 511

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
58 59 0.31812 TGACTTGCTCGACTGCATCA 59.682 50.0 0.0 0.01 42.96 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 4370 1.464997 GCAAAGTAGGCTTGAGAACGG 59.535 52.381 0.0 0.0 34.71 4.44 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
58 59 0.318120 TGACTTGCTCGACTGCATCA 59.682 50.000 0.00 0.01 42.96 3.07
73 74 1.655484 CATCACGTTGCATGAGCCTA 58.345 50.000 0.00 0.00 41.13 3.93
177 180 1.271217 CGCCATCACCTCCATCATCAT 60.271 52.381 0.00 0.00 0.00 2.45
210 2477 1.416401 GATGGCTCTCCGGATTGGTTA 59.584 52.381 3.57 0.00 39.52 2.85
245 2512 1.070758 GAACAGCAGGTCCTGTCTTCA 59.929 52.381 20.24 0.00 44.86 3.02
251 2518 2.553028 GCAGGTCCTGTCTTCAAATCCA 60.553 50.000 20.24 0.00 33.43 3.41
263 2530 2.170166 TCAAATCCAACATGAGCACCC 58.830 47.619 0.00 0.00 0.00 4.61
276 2549 2.031870 GAGCACCCACTTTTCACCTTT 58.968 47.619 0.00 0.00 0.00 3.11
277 2550 2.430694 GAGCACCCACTTTTCACCTTTT 59.569 45.455 0.00 0.00 0.00 2.27
278 2551 2.837591 AGCACCCACTTTTCACCTTTTT 59.162 40.909 0.00 0.00 0.00 1.94
391 2664 3.676172 CGAGGCACAAATTGTACTAACGA 59.324 43.478 0.00 0.00 0.00 3.85
416 2695 5.771165 GGGTTTGAAATTAGTACCACCTTGA 59.229 40.000 0.00 0.00 0.00 3.02
434 2713 9.353999 CCACCTTGAATAGCAAAGTAAAATAAC 57.646 33.333 0.00 0.00 35.74 1.89
435 2714 9.061610 CACCTTGAATAGCAAAGTAAAATAACG 57.938 33.333 0.00 0.00 35.74 3.18
436 2715 9.005777 ACCTTGAATAGCAAAGTAAAATAACGA 57.994 29.630 0.00 0.00 35.74 3.85
437 2716 9.834628 CCTTGAATAGCAAAGTAAAATAACGAA 57.165 29.630 0.00 0.00 35.74 3.85
440 2719 9.337091 TGAATAGCAAAGTAAAATAACGAAAGC 57.663 29.630 0.00 0.00 0.00 3.51
441 2720 7.948513 ATAGCAAAGTAAAATAACGAAAGCG 57.051 32.000 0.00 0.00 44.79 4.68
457 2736 6.683090 CGAAAGCGTAAATTCATGGAAAAA 57.317 33.333 0.00 0.00 0.00 1.94
479 2758 5.560966 AAACATATTGTGACGGTGAATCC 57.439 39.130 0.00 0.00 0.00 3.01
480 2759 4.214986 ACATATTGTGACGGTGAATCCA 57.785 40.909 0.00 0.00 35.57 3.41
481 2760 4.780815 ACATATTGTGACGGTGAATCCAT 58.219 39.130 0.00 0.00 35.57 3.41
482 2761 4.576053 ACATATTGTGACGGTGAATCCATG 59.424 41.667 0.00 0.00 35.57 3.66
483 2762 2.849294 TTGTGACGGTGAATCCATGA 57.151 45.000 0.00 0.00 35.57 3.07
484 2763 2.849294 TGTGACGGTGAATCCATGAA 57.151 45.000 0.00 0.00 35.57 2.57
485 2764 2.698803 TGTGACGGTGAATCCATGAAG 58.301 47.619 0.00 0.00 35.57 3.02
486 2765 2.038426 TGTGACGGTGAATCCATGAAGT 59.962 45.455 0.00 0.00 35.57 3.01
487 2766 2.673368 GTGACGGTGAATCCATGAAGTC 59.327 50.000 0.00 0.00 35.57 3.01
488 2767 2.301583 TGACGGTGAATCCATGAAGTCA 59.698 45.455 0.00 0.00 35.38 3.41
489 2768 2.673368 GACGGTGAATCCATGAAGTCAC 59.327 50.000 3.69 3.69 39.73 3.67
490 2769 2.303022 ACGGTGAATCCATGAAGTCACT 59.697 45.455 12.31 0.00 40.20 3.41
491 2770 2.932614 CGGTGAATCCATGAAGTCACTC 59.067 50.000 12.31 2.20 40.20 3.51
492 2771 3.274288 GGTGAATCCATGAAGTCACTCC 58.726 50.000 12.31 0.00 40.20 3.85
493 2772 2.932614 GTGAATCCATGAAGTCACTCCG 59.067 50.000 5.19 0.00 37.88 4.63
494 2773 2.567169 TGAATCCATGAAGTCACTCCGT 59.433 45.455 0.00 0.00 0.00 4.69
495 2774 2.680312 ATCCATGAAGTCACTCCGTG 57.320 50.000 0.00 0.00 34.45 4.94
496 2775 0.608130 TCCATGAAGTCACTCCGTGG 59.392 55.000 0.00 0.00 33.87 4.94
497 2776 0.321671 CCATGAAGTCACTCCGTGGT 59.678 55.000 0.00 0.00 33.87 4.16
498 2777 1.270839 CCATGAAGTCACTCCGTGGTT 60.271 52.381 0.00 0.00 33.87 3.67
499 2778 2.494059 CATGAAGTCACTCCGTGGTTT 58.506 47.619 0.00 0.00 33.87 3.27
500 2779 3.556213 CCATGAAGTCACTCCGTGGTTTA 60.556 47.826 0.00 0.00 33.87 2.01
501 2780 4.253685 CATGAAGTCACTCCGTGGTTTAT 58.746 43.478 0.00 0.00 33.87 1.40
502 2781 4.345859 TGAAGTCACTCCGTGGTTTATT 57.654 40.909 0.00 0.00 33.87 1.40
503 2782 5.471556 TGAAGTCACTCCGTGGTTTATTA 57.528 39.130 0.00 0.00 33.87 0.98
504 2783 6.045072 TGAAGTCACTCCGTGGTTTATTAT 57.955 37.500 0.00 0.00 33.87 1.28
505 2784 6.469410 TGAAGTCACTCCGTGGTTTATTATT 58.531 36.000 0.00 0.00 33.87 1.40
506 2785 7.613585 TGAAGTCACTCCGTGGTTTATTATTA 58.386 34.615 0.00 0.00 33.87 0.98
507 2786 8.095792 TGAAGTCACTCCGTGGTTTATTATTAA 58.904 33.333 0.00 0.00 33.87 1.40
508 2787 8.488651 AAGTCACTCCGTGGTTTATTATTAAG 57.511 34.615 0.00 0.00 33.87 1.85
509 2788 7.046033 AGTCACTCCGTGGTTTATTATTAAGG 58.954 38.462 0.00 0.00 33.87 2.69
510 2789 7.043565 GTCACTCCGTGGTTTATTATTAAGGA 58.956 38.462 0.00 0.00 33.87 3.36
511 2790 7.713942 GTCACTCCGTGGTTTATTATTAAGGAT 59.286 37.037 0.00 0.00 33.87 3.24
512 2791 8.926374 TCACTCCGTGGTTTATTATTAAGGATA 58.074 33.333 0.00 0.00 33.87 2.59
513 2792 9.204570 CACTCCGTGGTTTATTATTAAGGATAG 57.795 37.037 0.00 0.00 0.00 2.08
514 2793 9.151177 ACTCCGTGGTTTATTATTAAGGATAGA 57.849 33.333 0.00 0.00 0.00 1.98
558 2837 2.482721 ACTGAAAGCGTAAATTCACGGG 59.517 45.455 2.77 0.00 42.18 5.28
577 2856 3.071479 GGGAAGAAAGCGTATTGTGACA 58.929 45.455 0.00 0.00 0.00 3.58
613 2892 8.149973 GGAGTCAATCCGTGCTTTATTATTAA 57.850 34.615 0.00 0.00 38.67 1.40
614 2893 8.617809 GGAGTCAATCCGTGCTTTATTATTAAA 58.382 33.333 0.00 0.00 38.67 1.52
754 3033 4.766891 GGGAGAGATTGGAAAACATGTTCA 59.233 41.667 12.39 2.72 0.00 3.18
822 3101 2.808315 CCGTGTCCGAGCATAGCT 59.192 61.111 0.00 0.00 43.88 3.32
935 3215 0.613777 CCGACCAGAAAACCCTAGCT 59.386 55.000 0.00 0.00 0.00 3.32
1132 3415 0.249155 CCGGTATGTACGTCGCCATT 60.249 55.000 0.00 0.00 0.00 3.16
1613 3896 5.773680 CCCGTCTTCTATCCTAACTATTGGA 59.226 44.000 0.00 0.00 36.72 3.53
1615 3898 7.146648 CCGTCTTCTATCCTAACTATTGGAAC 58.853 42.308 0.00 0.00 35.81 3.62
1658 3941 4.398319 TGGTAGCTTCCTTTCTTTTCTGG 58.602 43.478 11.05 0.00 0.00 3.86
1660 3943 4.697828 GGTAGCTTCCTTTCTTTTCTGGAG 59.302 45.833 1.39 0.00 0.00 3.86
1661 3944 4.445557 AGCTTCCTTTCTTTTCTGGAGT 57.554 40.909 0.00 0.00 0.00 3.85
1662 3945 5.568620 AGCTTCCTTTCTTTTCTGGAGTA 57.431 39.130 0.00 0.00 0.00 2.59
1663 3946 5.309638 AGCTTCCTTTCTTTTCTGGAGTAC 58.690 41.667 0.00 0.00 0.00 2.73
1664 3947 5.072464 AGCTTCCTTTCTTTTCTGGAGTACT 59.928 40.000 0.00 0.00 0.00 2.73
1665 3948 5.410132 GCTTCCTTTCTTTTCTGGAGTACTC 59.590 44.000 14.87 14.87 0.00 2.59
1677 3960 4.936411 TCTGGAGTACTCTACTGTTCTTCG 59.064 45.833 21.88 1.77 39.59 3.79
1691 3974 3.181469 TGTTCTTCGTTTGTACTGCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
1704 3987 2.832733 ACTGCTCCTTACCTAGTTGTCC 59.167 50.000 0.00 0.00 0.00 4.02
1732 4015 7.675962 ACGGCTTTGAACAAGTTACAATATA 57.324 32.000 0.00 0.00 0.00 0.86
1801 4088 3.221771 TGGATTCAGTTCCAACAACCTG 58.778 45.455 0.00 0.00 42.82 4.00
1885 4181 8.621286 AGTTTTAATTCTTAACACCAGTGTCAG 58.379 33.333 3.49 4.06 44.13 3.51
1899 4195 4.473199 CAGTGTCAGTGCATCAGAAATTG 58.527 43.478 0.00 0.00 0.00 2.32
1906 4202 4.015084 AGTGCATCAGAAATTGGAAGAGG 58.985 43.478 0.00 0.00 0.00 3.69
1931 4227 8.940952 GGATTGTAATAGAATCATAACTGCCTC 58.059 37.037 11.48 0.00 32.34 4.70
1941 4237 4.005650 TCATAACTGCCTCTTTGAGCAAG 58.994 43.478 0.00 0.00 38.82 4.01
1949 4245 3.006217 GCCTCTTTGAGCAAGACCATTTT 59.994 43.478 0.00 0.00 36.51 1.82
2016 4312 2.282745 GCATATCAGGGGCAGCCC 60.283 66.667 24.23 24.23 44.51 5.19
2040 4370 6.818644 CCAACATATATGTCCCTACTGCATAC 59.181 42.308 18.52 0.00 40.80 2.39
2041 4371 6.546428 ACATATATGTCCCTACTGCATACC 57.454 41.667 12.75 0.00 35.87 2.73
2058 4388 4.504858 CATACCGTTCTCAAGCCTACTTT 58.495 43.478 0.00 0.00 32.29 2.66
2061 4391 2.143122 CGTTCTCAAGCCTACTTTGCA 58.857 47.619 0.00 0.00 32.29 4.08
2086 4416 9.577110 CATTGTGCAATAACTATCATTTCAAGT 57.423 29.630 0.00 0.00 0.00 3.16
2096 4426 7.736447 ACTATCATTTCAAGTTAGGCATAGC 57.264 36.000 0.00 0.00 0.00 2.97
2111 4441 0.247460 ATAGCGTGCTCACTGCTCAA 59.753 50.000 17.56 7.02 43.37 3.02
2118 4448 3.676049 CGTGCTCACTGCTCAATAACCTA 60.676 47.826 0.00 0.00 43.37 3.08
2119 4449 4.446371 GTGCTCACTGCTCAATAACCTAT 58.554 43.478 0.00 0.00 43.37 2.57
2125 4455 7.543868 GCTCACTGCTCAATAACCTATAGTATG 59.456 40.741 0.00 0.00 38.95 2.39
2190 4527 3.084786 GCTCTGTGCTCCCAAAGTTTAT 58.915 45.455 0.00 0.00 38.95 1.40
2200 4537 6.015772 TGCTCCCAAAGTTTATTACTGAAACC 60.016 38.462 0.00 0.00 37.48 3.27
2201 4538 6.015772 GCTCCCAAAGTTTATTACTGAAACCA 60.016 38.462 0.00 0.00 37.48 3.67
2208 4545 5.408604 AGTTTATTACTGAAACCAGAGCACG 59.591 40.000 0.00 0.00 37.48 5.34
2231 4568 5.277154 CGTACAGAAACTCAACGGAAATGTT 60.277 40.000 0.00 0.00 0.00 2.71
2246 4583 6.029607 CGGAAATGTTATCATGTTTGTGAGG 58.970 40.000 0.00 0.00 34.19 3.86
2283 4630 4.142138 ACAGTCTTAGATCCGGACATTGTC 60.142 45.833 6.12 8.34 32.98 3.18
2297 4644 1.935873 CATTGTCCATACGCCTGACAG 59.064 52.381 0.00 0.00 39.89 3.51
2303 4650 2.134287 ATACGCCTGACAGCCGGAT 61.134 57.895 5.05 4.00 0.00 4.18
2306 4653 4.554036 GCCTGACAGCCGGATCCC 62.554 72.222 5.05 0.00 0.00 3.85
2318 4665 0.110295 CGGATCCCAACCATGGCATA 59.890 55.000 13.04 0.00 46.09 3.14
2337 4704 7.946207 TGGCATAGAACAAACACTGAAAATAA 58.054 30.769 0.00 0.00 0.00 1.40
2389 4917 7.441836 AGACGAATTATAAGGTCATGCACATA 58.558 34.615 13.40 0.00 31.93 2.29
2393 4921 6.785488 ATTATAAGGTCATGCACATACACG 57.215 37.500 0.00 0.00 0.00 4.49
2428 4956 0.172578 TCTATTCCACGCGGACTGTG 59.827 55.000 12.47 0.00 42.67 3.66
2454 5066 2.665519 GCTGTTTATCAGTGTGGTTGCG 60.666 50.000 0.00 0.00 45.23 4.85
2480 5092 6.049149 GCTAAATGCAGTAGTAGGATGTGAA 58.951 40.000 8.55 0.00 42.31 3.18
2506 5118 6.633500 ATTTGTAGCTTTACTTGCTGTCAA 57.367 33.333 0.00 0.00 41.32 3.18
2537 5152 9.982291 GTCAATTATCAAAAGCTTCATTACGTA 57.018 29.630 0.00 0.00 0.00 3.57
2539 5154 9.438291 CAATTATCAAAAGCTTCATTACGTAGG 57.562 33.333 0.00 0.00 0.00 3.18
2540 5155 8.958119 ATTATCAAAAGCTTCATTACGTAGGA 57.042 30.769 0.00 0.00 0.00 2.94
2541 5156 8.780846 TTATCAAAAGCTTCATTACGTAGGAA 57.219 30.769 0.00 10.24 0.00 3.36
2542 5157 7.865706 ATCAAAAGCTTCATTACGTAGGAAT 57.134 32.000 0.00 0.00 0.00 3.01
2543 5158 8.958119 ATCAAAAGCTTCATTACGTAGGAATA 57.042 30.769 0.00 0.00 0.00 1.75
2544 5159 8.420374 TCAAAAGCTTCATTACGTAGGAATAG 57.580 34.615 0.00 3.90 0.00 1.73
2545 5160 7.494625 TCAAAAGCTTCATTACGTAGGAATAGG 59.505 37.037 0.00 3.53 0.00 2.57
2546 5161 6.726490 AAGCTTCATTACGTAGGAATAGGA 57.274 37.500 10.87 0.00 0.00 2.94
2547 5162 6.086785 AGCTTCATTACGTAGGAATAGGAC 57.913 41.667 10.87 2.29 0.00 3.85
2548 5163 5.834204 AGCTTCATTACGTAGGAATAGGACT 59.166 40.000 10.87 3.93 0.00 3.85
2549 5164 6.324254 AGCTTCATTACGTAGGAATAGGACTT 59.676 38.462 10.87 0.00 0.00 3.01
2550 5165 6.985059 GCTTCATTACGTAGGAATAGGACTTT 59.015 38.462 10.87 0.00 0.00 2.66
2551 5166 7.494952 GCTTCATTACGTAGGAATAGGACTTTT 59.505 37.037 10.87 0.00 0.00 2.27
2552 5167 9.379791 CTTCATTACGTAGGAATAGGACTTTTT 57.620 33.333 10.87 0.00 0.00 1.94
2555 5170 8.762426 CATTACGTAGGAATAGGACTTTTTAGC 58.238 37.037 0.00 0.00 0.00 3.09
2556 5171 5.668471 ACGTAGGAATAGGACTTTTTAGCC 58.332 41.667 0.00 0.00 0.00 3.93
2557 5172 4.743644 CGTAGGAATAGGACTTTTTAGCCG 59.256 45.833 0.00 0.00 0.00 5.52
2558 5173 4.152284 AGGAATAGGACTTTTTAGCCGG 57.848 45.455 0.00 0.00 0.00 6.13
2559 5174 3.118000 AGGAATAGGACTTTTTAGCCGGG 60.118 47.826 2.18 0.00 0.00 5.73
2560 5175 3.211865 GAATAGGACTTTTTAGCCGGGG 58.788 50.000 2.18 0.00 0.00 5.73
2561 5176 0.913924 TAGGACTTTTTAGCCGGGGG 59.086 55.000 2.18 0.00 0.00 5.40
2579 5194 3.160872 GGCTTACTTGAGGCCTGTC 57.839 57.895 12.00 0.00 42.31 3.51
2580 5195 0.615850 GGCTTACTTGAGGCCTGTCT 59.384 55.000 12.00 0.00 42.31 3.41
2581 5196 1.003696 GGCTTACTTGAGGCCTGTCTT 59.996 52.381 12.00 0.00 42.31 3.01
2582 5197 2.351455 GCTTACTTGAGGCCTGTCTTC 58.649 52.381 12.00 0.00 0.00 2.87
2583 5198 2.027653 GCTTACTTGAGGCCTGTCTTCT 60.028 50.000 12.00 0.00 0.00 2.85
2584 5199 3.558109 GCTTACTTGAGGCCTGTCTTCTT 60.558 47.826 12.00 0.00 0.00 2.52
2585 5200 2.849294 ACTTGAGGCCTGTCTTCTTC 57.151 50.000 12.00 0.00 0.00 2.87
2586 5201 2.050144 ACTTGAGGCCTGTCTTCTTCA 58.950 47.619 12.00 0.00 0.00 3.02
2587 5202 2.439507 ACTTGAGGCCTGTCTTCTTCAA 59.560 45.455 12.00 4.58 0.00 2.69
2588 5203 3.117888 ACTTGAGGCCTGTCTTCTTCAAA 60.118 43.478 12.00 0.00 0.00 2.69
2589 5204 3.576078 TGAGGCCTGTCTTCTTCAAAA 57.424 42.857 12.00 0.00 0.00 2.44
2590 5205 3.214328 TGAGGCCTGTCTTCTTCAAAAC 58.786 45.455 12.00 0.00 0.00 2.43
2591 5206 3.117888 TGAGGCCTGTCTTCTTCAAAACT 60.118 43.478 12.00 0.00 0.00 2.66
2592 5207 3.481453 AGGCCTGTCTTCTTCAAAACTC 58.519 45.455 3.11 0.00 0.00 3.01
2593 5208 2.224314 GGCCTGTCTTCTTCAAAACTCG 59.776 50.000 0.00 0.00 0.00 4.18
2594 5209 3.131396 GCCTGTCTTCTTCAAAACTCGA 58.869 45.455 0.00 0.00 0.00 4.04
2595 5210 3.560068 GCCTGTCTTCTTCAAAACTCGAA 59.440 43.478 0.00 0.00 0.00 3.71
2596 5211 4.035208 GCCTGTCTTCTTCAAAACTCGAAA 59.965 41.667 0.00 0.00 0.00 3.46
2597 5212 5.278022 GCCTGTCTTCTTCAAAACTCGAAAT 60.278 40.000 0.00 0.00 0.00 2.17
2598 5213 6.729187 CCTGTCTTCTTCAAAACTCGAAATT 58.271 36.000 0.00 0.00 0.00 1.82
2599 5214 6.853362 CCTGTCTTCTTCAAAACTCGAAATTC 59.147 38.462 0.00 0.00 0.00 2.17
2600 5215 6.418956 TGTCTTCTTCAAAACTCGAAATTCG 58.581 36.000 9.38 9.38 42.10 3.34
2601 5216 6.036735 TGTCTTCTTCAAAACTCGAAATTCGT 59.963 34.615 15.34 0.00 41.35 3.85
2602 5217 6.905609 GTCTTCTTCAAAACTCGAAATTCGTT 59.094 34.615 15.34 0.17 41.35 3.85
2603 5218 7.428472 GTCTTCTTCAAAACTCGAAATTCGTTT 59.572 33.333 15.34 6.71 41.35 3.60
2604 5219 7.966204 TCTTCTTCAAAACTCGAAATTCGTTTT 59.034 29.630 15.34 12.17 41.35 2.43
2605 5220 8.455598 TTCTTCAAAACTCGAAATTCGTTTTT 57.544 26.923 15.34 16.88 41.35 1.94
2628 5243 7.448748 TTTCAAAAGAAACAGGACTATAGCC 57.551 36.000 0.00 2.38 0.00 3.93
2629 5244 6.374417 TCAAAAGAAACAGGACTATAGCCT 57.626 37.500 9.23 9.23 35.75 4.58
2630 5245 6.779860 TCAAAAGAAACAGGACTATAGCCTT 58.220 36.000 11.64 0.79 32.12 4.35
2631 5246 7.231467 TCAAAAGAAACAGGACTATAGCCTTT 58.769 34.615 11.64 6.47 32.12 3.11
2632 5247 8.380099 TCAAAAGAAACAGGACTATAGCCTTTA 58.620 33.333 11.64 0.00 32.12 1.85
2633 5248 8.669243 CAAAAGAAACAGGACTATAGCCTTTAG 58.331 37.037 11.64 5.62 32.12 1.85
2634 5249 7.735326 AAGAAACAGGACTATAGCCTTTAGA 57.265 36.000 11.64 0.00 32.12 2.10
2635 5250 7.735326 AGAAACAGGACTATAGCCTTTAGAA 57.265 36.000 11.64 0.00 32.12 2.10
2636 5251 7.787028 AGAAACAGGACTATAGCCTTTAGAAG 58.213 38.462 11.64 4.52 32.12 2.85
2649 5264 5.665916 CCTTTAGAAGGCCAATTGACATT 57.334 39.130 5.01 0.00 42.78 2.71
2650 5265 5.413499 CCTTTAGAAGGCCAATTGACATTG 58.587 41.667 5.01 0.00 42.78 2.82
2651 5266 5.185635 CCTTTAGAAGGCCAATTGACATTGA 59.814 40.000 5.01 0.00 41.14 2.57
2652 5267 5.643379 TTAGAAGGCCAATTGACATTGAC 57.357 39.130 5.01 0.00 42.35 3.18
2653 5268 3.771216 AGAAGGCCAATTGACATTGACT 58.229 40.909 5.01 0.00 42.35 3.41
2654 5269 4.154942 AGAAGGCCAATTGACATTGACTT 58.845 39.130 5.01 3.00 42.35 3.01
2655 5270 4.590222 AGAAGGCCAATTGACATTGACTTT 59.410 37.500 5.01 0.00 42.35 2.66
2656 5271 4.961438 AGGCCAATTGACATTGACTTTT 57.039 36.364 5.01 0.00 42.35 2.27
2657 5272 4.634199 AGGCCAATTGACATTGACTTTTG 58.366 39.130 5.01 0.00 42.35 2.44
2658 5273 4.344679 AGGCCAATTGACATTGACTTTTGA 59.655 37.500 5.01 0.00 42.35 2.69
2659 5274 5.012354 AGGCCAATTGACATTGACTTTTGAT 59.988 36.000 5.01 0.00 42.35 2.57
2660 5275 6.211184 AGGCCAATTGACATTGACTTTTGATA 59.789 34.615 5.01 0.00 42.35 2.15
2661 5276 6.532657 GGCCAATTGACATTGACTTTTGATAG 59.467 38.462 7.12 0.00 42.35 2.08
2662 5277 7.092716 GCCAATTGACATTGACTTTTGATAGT 58.907 34.615 7.12 0.00 42.35 2.12
2663 5278 7.599998 GCCAATTGACATTGACTTTTGATAGTT 59.400 33.333 7.12 0.00 42.35 2.24
2664 5279 9.132521 CCAATTGACATTGACTTTTGATAGTTC 57.867 33.333 7.12 0.00 42.35 3.01
2665 5280 9.132521 CAATTGACATTGACTTTTGATAGTTCC 57.867 33.333 0.00 0.00 42.35 3.62
2666 5281 7.815840 TTGACATTGACTTTTGATAGTTCCA 57.184 32.000 0.00 0.00 0.00 3.53
2667 5282 7.439157 TGACATTGACTTTTGATAGTTCCAG 57.561 36.000 0.00 0.00 0.00 3.86
2668 5283 6.072508 TGACATTGACTTTTGATAGTTCCAGC 60.073 38.462 0.00 0.00 0.00 4.85
2669 5284 6.006449 ACATTGACTTTTGATAGTTCCAGCT 58.994 36.000 0.00 0.00 0.00 4.24
2670 5285 5.947228 TTGACTTTTGATAGTTCCAGCTG 57.053 39.130 6.78 6.78 0.00 4.24
2671 5286 3.753272 TGACTTTTGATAGTTCCAGCTGC 59.247 43.478 8.66 0.00 0.00 5.25
2672 5287 3.084786 ACTTTTGATAGTTCCAGCTGCC 58.915 45.455 8.66 0.00 0.00 4.85
2673 5288 2.128771 TTTGATAGTTCCAGCTGCCC 57.871 50.000 8.66 0.00 0.00 5.36
2674 5289 0.255890 TTGATAGTTCCAGCTGCCCC 59.744 55.000 8.66 0.00 0.00 5.80
2684 5299 0.033228 CAGCTGCCCCGAGAAGATAG 59.967 60.000 0.00 0.00 0.00 2.08
2687 5302 0.683973 CTGCCCCGAGAAGATAGCAT 59.316 55.000 0.00 0.00 0.00 3.79
2688 5303 1.071385 CTGCCCCGAGAAGATAGCATT 59.929 52.381 0.00 0.00 0.00 3.56
2691 5306 2.952310 GCCCCGAGAAGATAGCATTTTT 59.048 45.455 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.000896 ATCTGGGCCAAAAGGACGG 60.001 57.895 8.04 0.00 0.00 4.79
58 59 2.471255 GCTTAGGCTCATGCAACGT 58.529 52.632 0.00 0.00 41.91 3.99
73 74 3.875727 CGATCATCTTCCACATCAAGCTT 59.124 43.478 0.00 0.00 0.00 3.74
210 2477 4.401022 TGCTGTTCCATCAAGAAGAACAT 58.599 39.130 15.16 0.00 46.31 2.71
231 2498 3.423539 TGGATTTGAAGACAGGACCTG 57.576 47.619 20.45 20.45 37.52 4.00
245 2512 1.895131 GTGGGTGCTCATGTTGGATTT 59.105 47.619 0.00 0.00 0.00 2.17
251 2518 2.362077 GTGAAAAGTGGGTGCTCATGTT 59.638 45.455 0.00 0.00 0.00 2.71
280 2553 9.719279 CACGGTCCGCTTAATAAAAATAAAATA 57.281 29.630 12.28 0.00 0.00 1.40
367 2640 1.165270 AGTACAATTTGTGCCTCGCC 58.835 50.000 12.30 0.00 33.24 5.54
391 2664 5.594199 AGGTGGTACTAATTTCAAACCCT 57.406 39.130 0.00 0.00 0.00 4.34
416 2695 8.376972 CGCTTTCGTTATTTTACTTTGCTATT 57.623 30.769 0.00 0.00 0.00 1.73
434 2713 6.683090 TTTTTCCATGAATTTACGCTTTCG 57.317 33.333 0.00 0.00 42.43 3.46
455 2734 6.015856 TGGATTCACCGTCACAATATGTTTTT 60.016 34.615 0.00 0.00 42.61 1.94
456 2735 5.475220 TGGATTCACCGTCACAATATGTTTT 59.525 36.000 0.00 0.00 42.61 2.43
457 2736 5.007034 TGGATTCACCGTCACAATATGTTT 58.993 37.500 0.00 0.00 42.61 2.83
458 2737 4.584874 TGGATTCACCGTCACAATATGTT 58.415 39.130 0.00 0.00 42.61 2.71
459 2738 4.214986 TGGATTCACCGTCACAATATGT 57.785 40.909 0.00 0.00 42.61 2.29
460 2739 4.815846 TCATGGATTCACCGTCACAATATG 59.184 41.667 0.00 0.00 42.61 1.78
461 2740 5.034852 TCATGGATTCACCGTCACAATAT 57.965 39.130 0.00 0.00 42.61 1.28
462 2741 4.479786 TCATGGATTCACCGTCACAATA 57.520 40.909 0.00 0.00 42.61 1.90
463 2742 3.348647 TCATGGATTCACCGTCACAAT 57.651 42.857 0.00 0.00 42.61 2.71
464 2743 2.849294 TCATGGATTCACCGTCACAA 57.151 45.000 0.00 0.00 42.61 3.33
465 2744 2.038426 ACTTCATGGATTCACCGTCACA 59.962 45.455 0.00 0.00 42.61 3.58
466 2745 2.673368 GACTTCATGGATTCACCGTCAC 59.327 50.000 0.00 0.00 42.61 3.67
467 2746 2.301583 TGACTTCATGGATTCACCGTCA 59.698 45.455 0.00 0.00 42.61 4.35
468 2747 2.673368 GTGACTTCATGGATTCACCGTC 59.327 50.000 12.44 0.00 42.61 4.79
469 2748 2.303022 AGTGACTTCATGGATTCACCGT 59.697 45.455 18.31 1.32 39.39 4.83
470 2749 2.932614 GAGTGACTTCATGGATTCACCG 59.067 50.000 18.31 0.00 39.39 4.94
471 2750 3.274288 GGAGTGACTTCATGGATTCACC 58.726 50.000 18.31 11.14 39.39 4.02
472 2751 2.932614 CGGAGTGACTTCATGGATTCAC 59.067 50.000 15.06 15.06 38.95 3.18
473 2752 2.567169 ACGGAGTGACTTCATGGATTCA 59.433 45.455 0.00 0.00 42.51 2.57
474 2753 3.252974 ACGGAGTGACTTCATGGATTC 57.747 47.619 0.00 0.00 42.51 2.52
523 2802 9.959749 TTACGCTTTCAGTTTAAATTTGAATCT 57.040 25.926 14.86 0.00 31.54 2.40
530 2809 8.687301 CGTGAATTTACGCTTTCAGTTTAAATT 58.313 29.630 9.97 0.00 37.24 1.82
531 2810 7.325097 CCGTGAATTTACGCTTTCAGTTTAAAT 59.675 33.333 16.60 0.00 42.44 1.40
532 2811 6.633634 CCGTGAATTTACGCTTTCAGTTTAAA 59.366 34.615 16.60 0.00 42.44 1.52
533 2812 6.137415 CCGTGAATTTACGCTTTCAGTTTAA 58.863 36.000 16.60 0.00 42.44 1.52
534 2813 5.334260 CCCGTGAATTTACGCTTTCAGTTTA 60.334 40.000 16.60 0.00 42.44 2.01
535 2814 4.533222 CCGTGAATTTACGCTTTCAGTTT 58.467 39.130 16.60 0.00 42.44 2.66
536 2815 3.058501 CCCGTGAATTTACGCTTTCAGTT 60.059 43.478 16.60 0.00 42.44 3.16
537 2816 2.482721 CCCGTGAATTTACGCTTTCAGT 59.517 45.455 16.60 0.00 42.44 3.41
538 2817 2.739913 TCCCGTGAATTTACGCTTTCAG 59.260 45.455 16.60 2.79 42.44 3.02
558 2837 4.447724 TCACTGTCACAATACGCTTTCTTC 59.552 41.667 0.00 0.00 0.00 2.87
577 2856 1.002087 GATTGACTCCGTGGGTTCACT 59.998 52.381 0.00 0.00 41.53 3.41
722 3001 9.053472 TGTTTTCCAATCTCTCCCTAGTAATAA 57.947 33.333 0.00 0.00 0.00 1.40
723 3002 8.618240 TGTTTTCCAATCTCTCCCTAGTAATA 57.382 34.615 0.00 0.00 0.00 0.98
724 3003 7.510675 TGTTTTCCAATCTCTCCCTAGTAAT 57.489 36.000 0.00 0.00 0.00 1.89
725 3004 6.945636 TGTTTTCCAATCTCTCCCTAGTAA 57.054 37.500 0.00 0.00 0.00 2.24
726 3005 6.443849 ACATGTTTTCCAATCTCTCCCTAGTA 59.556 38.462 0.00 0.00 0.00 1.82
727 3006 5.251700 ACATGTTTTCCAATCTCTCCCTAGT 59.748 40.000 0.00 0.00 0.00 2.57
728 3007 5.749462 ACATGTTTTCCAATCTCTCCCTAG 58.251 41.667 0.00 0.00 0.00 3.02
729 3008 5.779241 ACATGTTTTCCAATCTCTCCCTA 57.221 39.130 0.00 0.00 0.00 3.53
730 3009 4.664688 ACATGTTTTCCAATCTCTCCCT 57.335 40.909 0.00 0.00 0.00 4.20
731 3010 4.766891 TGAACATGTTTTCCAATCTCTCCC 59.233 41.667 13.36 0.00 0.00 4.30
732 3011 5.964958 TGAACATGTTTTCCAATCTCTCC 57.035 39.130 13.36 0.00 0.00 3.71
733 3012 5.860716 GCTTGAACATGTTTTCCAATCTCTC 59.139 40.000 13.36 0.00 0.00 3.20
734 3013 5.302568 TGCTTGAACATGTTTTCCAATCTCT 59.697 36.000 13.36 0.00 0.00 3.10
735 3014 5.403466 GTGCTTGAACATGTTTTCCAATCTC 59.597 40.000 13.36 5.76 0.00 2.75
1613 3896 6.928492 CCAATTACATTGCAAAGTTACCAGTT 59.072 34.615 13.15 0.00 38.92 3.16
1615 3898 6.454795 ACCAATTACATTGCAAAGTTACCAG 58.545 36.000 13.15 2.89 38.92 4.00
1646 3929 7.662897 ACAGTAGAGTACTCCAGAAAAGAAAG 58.337 38.462 19.38 0.64 36.76 2.62
1658 3941 6.437094 ACAAACGAAGAACAGTAGAGTACTC 58.563 40.000 15.41 15.41 36.76 2.59
1660 3943 7.323177 CAGTACAAACGAAGAACAGTAGAGTAC 59.677 40.741 0.00 0.00 0.00 2.73
1661 3944 7.358066 CAGTACAAACGAAGAACAGTAGAGTA 58.642 38.462 0.00 0.00 0.00 2.59
1662 3945 6.207213 CAGTACAAACGAAGAACAGTAGAGT 58.793 40.000 0.00 0.00 0.00 3.24
1663 3946 5.117287 GCAGTACAAACGAAGAACAGTAGAG 59.883 44.000 0.00 0.00 0.00 2.43
1664 3947 4.980434 GCAGTACAAACGAAGAACAGTAGA 59.020 41.667 0.00 0.00 0.00 2.59
1665 3948 4.982916 AGCAGTACAAACGAAGAACAGTAG 59.017 41.667 0.00 0.00 0.00 2.57
1677 3960 5.402997 ACTAGGTAAGGAGCAGTACAAAC 57.597 43.478 0.00 0.00 0.00 2.93
1691 3974 2.493278 GCCGTACTGGACAACTAGGTAA 59.507 50.000 7.77 0.00 42.00 2.85
1704 3987 3.963383 AACTTGTTCAAAGCCGTACTG 57.037 42.857 0.00 0.00 0.00 2.74
1732 4015 7.985184 TGGCTAGATATTCGAAACAGTGTATTT 59.015 33.333 0.00 0.00 0.00 1.40
1801 4088 7.811117 AGAGATACAGATAACTACACTGTCC 57.189 40.000 0.00 0.00 42.65 4.02
1829 4116 7.907214 AAACAGAGTATTTTAGCCTGTACAG 57.093 36.000 16.34 16.34 37.12 2.74
1864 4151 5.468746 GCACTGACACTGGTGTTAAGAATTA 59.531 40.000 18.00 0.00 45.05 1.40
1885 4181 4.012374 TCCTCTTCCAATTTCTGATGCAC 58.988 43.478 0.00 0.00 0.00 4.57
1906 4202 9.717942 AGAGGCAGTTATGATTCTATTACAATC 57.282 33.333 0.00 0.00 0.00 2.67
1918 4214 4.226427 TGCTCAAAGAGGCAGTTATGAT 57.774 40.909 0.00 0.00 34.22 2.45
1931 4227 6.145048 GTCATTCAAAATGGTCTTGCTCAAAG 59.855 38.462 0.19 0.00 37.22 2.77
2016 4312 6.818644 GGTATGCAGTAGGGACATATATGTTG 59.181 42.308 19.19 13.01 41.95 3.33
2017 4313 6.351033 CGGTATGCAGTAGGGACATATATGTT 60.351 42.308 19.19 6.78 41.95 2.71
2040 4370 1.464997 GCAAAGTAGGCTTGAGAACGG 59.535 52.381 0.00 0.00 34.71 4.44
2041 4371 2.143122 TGCAAAGTAGGCTTGAGAACG 58.857 47.619 0.00 0.00 34.71 3.95
2075 4405 5.008019 CACGCTATGCCTAACTTGAAATGAT 59.992 40.000 0.00 0.00 0.00 2.45
2078 4408 4.882671 CACGCTATGCCTAACTTGAAAT 57.117 40.909 0.00 0.00 0.00 2.17
2150 4480 6.820656 ACAGAGCTTCTTCAACAGGTATATTG 59.179 38.462 0.00 0.00 0.00 1.90
2185 4522 5.178809 ACGTGCTCTGGTTTCAGTAATAAAC 59.821 40.000 0.00 0.00 41.59 2.01
2190 4527 2.902705 ACGTGCTCTGGTTTCAGTAA 57.097 45.000 0.00 0.00 41.59 2.24
2200 4537 3.013276 TGAGTTTCTGTACGTGCTCTG 57.987 47.619 4.97 0.00 0.00 3.35
2201 4538 3.381949 GTTGAGTTTCTGTACGTGCTCT 58.618 45.455 4.97 0.00 0.00 4.09
2208 4545 5.668558 ACATTTCCGTTGAGTTTCTGTAC 57.331 39.130 0.00 0.00 0.00 2.90
2231 4568 2.025981 AGCCTGCCTCACAAACATGATA 60.026 45.455 0.00 0.00 0.00 2.15
2246 4583 2.003196 GACTGTGAGTCTAAGCCTGC 57.997 55.000 0.00 0.00 41.88 4.85
2297 4644 2.519302 CCATGGTTGGGATCCGGC 60.519 66.667 5.45 0.00 39.56 6.13
2306 4653 4.022068 AGTGTTTGTTCTATGCCATGGTTG 60.022 41.667 14.67 1.40 0.00 3.77
2472 5084 9.476202 AAGTAAAGCTACAAATTTTTCACATCC 57.524 29.630 0.00 0.00 0.00 3.51
2474 5086 8.764287 GCAAGTAAAGCTACAAATTTTTCACAT 58.236 29.630 0.00 0.00 0.00 3.21
2475 5087 7.978975 AGCAAGTAAAGCTACAAATTTTTCACA 59.021 29.630 0.00 0.00 41.32 3.58
2476 5088 8.268738 CAGCAAGTAAAGCTACAAATTTTTCAC 58.731 33.333 0.00 0.00 41.14 3.18
2480 5092 7.488322 TGACAGCAAGTAAAGCTACAAATTTT 58.512 30.769 0.00 0.00 41.14 1.82
2535 5150 5.055144 CCGGCTAAAAAGTCCTATTCCTAC 58.945 45.833 0.00 0.00 0.00 3.18
2537 5152 3.118000 CCCGGCTAAAAAGTCCTATTCCT 60.118 47.826 0.00 0.00 0.00 3.36
2538 5153 3.211865 CCCGGCTAAAAAGTCCTATTCC 58.788 50.000 0.00 0.00 0.00 3.01
2539 5154 3.211865 CCCCGGCTAAAAAGTCCTATTC 58.788 50.000 0.00 0.00 0.00 1.75
2540 5155 2.092049 CCCCCGGCTAAAAAGTCCTATT 60.092 50.000 0.00 0.00 0.00 1.73
2541 5156 1.493446 CCCCCGGCTAAAAAGTCCTAT 59.507 52.381 0.00 0.00 0.00 2.57
2542 5157 0.913924 CCCCCGGCTAAAAAGTCCTA 59.086 55.000 0.00 0.00 0.00 2.94
2543 5158 1.689412 CCCCCGGCTAAAAAGTCCT 59.311 57.895 0.00 0.00 0.00 3.85
2544 5159 4.331622 CCCCCGGCTAAAAAGTCC 57.668 61.111 0.00 0.00 0.00 3.85
2558 5173 2.275748 GGCCTCAAGTAAGCCCCC 59.724 66.667 0.00 0.00 41.00 5.40
2562 5177 2.027653 AGAAGACAGGCCTCAAGTAAGC 60.028 50.000 0.00 0.00 0.00 3.09
2563 5178 3.971245 AGAAGACAGGCCTCAAGTAAG 57.029 47.619 0.00 0.00 0.00 2.34
2564 5179 3.646162 TGAAGAAGACAGGCCTCAAGTAA 59.354 43.478 0.00 0.00 0.00 2.24
2565 5180 3.239449 TGAAGAAGACAGGCCTCAAGTA 58.761 45.455 0.00 0.00 0.00 2.24
2566 5181 2.050144 TGAAGAAGACAGGCCTCAAGT 58.950 47.619 0.00 0.00 0.00 3.16
2567 5182 2.847327 TGAAGAAGACAGGCCTCAAG 57.153 50.000 0.00 0.00 0.00 3.02
2568 5183 3.576078 TTTGAAGAAGACAGGCCTCAA 57.424 42.857 0.00 0.00 0.00 3.02
2569 5184 3.117888 AGTTTTGAAGAAGACAGGCCTCA 60.118 43.478 0.00 0.00 0.00 3.86
2570 5185 3.481453 AGTTTTGAAGAAGACAGGCCTC 58.519 45.455 0.00 0.00 0.00 4.70
2571 5186 3.481453 GAGTTTTGAAGAAGACAGGCCT 58.519 45.455 0.00 0.00 0.00 5.19
2572 5187 2.224314 CGAGTTTTGAAGAAGACAGGCC 59.776 50.000 0.00 0.00 0.00 5.19
2573 5188 3.131396 TCGAGTTTTGAAGAAGACAGGC 58.869 45.455 0.00 0.00 0.00 4.85
2574 5189 5.734855 TTTCGAGTTTTGAAGAAGACAGG 57.265 39.130 0.00 0.00 0.00 4.00
2575 5190 6.571520 CGAATTTCGAGTTTTGAAGAAGACAG 59.428 38.462 13.45 0.00 43.74 3.51
2576 5191 6.036735 ACGAATTTCGAGTTTTGAAGAAGACA 59.963 34.615 24.50 0.00 43.74 3.41
2577 5192 6.419771 ACGAATTTCGAGTTTTGAAGAAGAC 58.580 36.000 24.50 0.00 43.74 3.01
2578 5193 6.598753 ACGAATTTCGAGTTTTGAAGAAGA 57.401 33.333 24.50 0.00 43.74 2.87
2579 5194 7.665080 AAACGAATTTCGAGTTTTGAAGAAG 57.335 32.000 24.50 0.00 43.74 2.85
2580 5195 8.455598 AAAAACGAATTTCGAGTTTTGAAGAA 57.544 26.923 24.50 0.00 44.29 2.52
2604 5219 7.231467 AGGCTATAGTCCTGTTTCTTTTGAAA 58.769 34.615 13.07 0.00 38.05 2.69
2605 5220 6.779860 AGGCTATAGTCCTGTTTCTTTTGAA 58.220 36.000 13.07 0.00 32.51 2.69
2606 5221 6.374417 AGGCTATAGTCCTGTTTCTTTTGA 57.626 37.500 13.07 0.00 31.53 2.69
2607 5222 7.454260 AAAGGCTATAGTCCTGTTTCTTTTG 57.546 36.000 14.17 0.00 33.43 2.44
2608 5223 8.603304 TCTAAAGGCTATAGTCCTGTTTCTTTT 58.397 33.333 14.17 3.61 33.43 2.27
2609 5224 8.147244 TCTAAAGGCTATAGTCCTGTTTCTTT 57.853 34.615 14.17 4.22 33.43 2.52
2610 5225 7.735326 TCTAAAGGCTATAGTCCTGTTTCTT 57.265 36.000 14.17 8.54 33.43 2.52
2611 5226 7.147637 CCTTCTAAAGGCTATAGTCCTGTTTCT 60.148 40.741 14.17 0.00 42.78 2.52
2612 5227 6.987404 CCTTCTAAAGGCTATAGTCCTGTTTC 59.013 42.308 14.17 0.00 42.78 2.78
2613 5228 6.890293 CCTTCTAAAGGCTATAGTCCTGTTT 58.110 40.000 14.17 6.03 42.78 2.83
2614 5229 6.487299 CCTTCTAAAGGCTATAGTCCTGTT 57.513 41.667 14.17 12.54 42.78 3.16
2627 5242 5.185635 TCAATGTCAATTGGCCTTCTAAAGG 59.814 40.000 7.75 1.20 45.10 3.11
2628 5243 6.095377 GTCAATGTCAATTGGCCTTCTAAAG 58.905 40.000 7.75 0.00 41.66 1.85
2629 5244 6.024552 GTCAATGTCAATTGGCCTTCTAAA 57.975 37.500 7.75 0.00 41.66 1.85
2630 5245 5.643379 GTCAATGTCAATTGGCCTTCTAA 57.357 39.130 7.75 0.00 41.66 2.10
2637 5252 7.092716 ACTATCAAAAGTCAATGTCAATTGGC 58.907 34.615 2.20 2.20 46.76 4.52
2638 5253 9.132521 GAACTATCAAAAGTCAATGTCAATTGG 57.867 33.333 5.42 0.00 42.97 3.16
2639 5254 9.132521 GGAACTATCAAAAGTCAATGTCAATTG 57.867 33.333 0.00 0.00 43.94 2.32
2640 5255 8.859090 TGGAACTATCAAAAGTCAATGTCAATT 58.141 29.630 0.00 0.00 0.00 2.32
2641 5256 8.408043 TGGAACTATCAAAAGTCAATGTCAAT 57.592 30.769 0.00 0.00 0.00 2.57
2642 5257 7.522073 GCTGGAACTATCAAAAGTCAATGTCAA 60.522 37.037 0.00 0.00 0.00 3.18
2643 5258 6.072508 GCTGGAACTATCAAAAGTCAATGTCA 60.073 38.462 0.00 0.00 0.00 3.58
2644 5259 6.150140 AGCTGGAACTATCAAAAGTCAATGTC 59.850 38.462 0.00 0.00 0.00 3.06
2645 5260 6.006449 AGCTGGAACTATCAAAAGTCAATGT 58.994 36.000 0.00 0.00 0.00 2.71
2646 5261 6.320171 CAGCTGGAACTATCAAAAGTCAATG 58.680 40.000 5.57 0.00 0.00 2.82
2647 5262 5.105997 GCAGCTGGAACTATCAAAAGTCAAT 60.106 40.000 17.12 0.00 0.00 2.57
2648 5263 4.216257 GCAGCTGGAACTATCAAAAGTCAA 59.784 41.667 17.12 0.00 0.00 3.18
2649 5264 3.753272 GCAGCTGGAACTATCAAAAGTCA 59.247 43.478 17.12 0.00 0.00 3.41
2650 5265 3.127721 GGCAGCTGGAACTATCAAAAGTC 59.872 47.826 17.12 0.00 0.00 3.01
2651 5266 3.084786 GGCAGCTGGAACTATCAAAAGT 58.915 45.455 17.12 0.00 0.00 2.66
2652 5267 2.424956 GGGCAGCTGGAACTATCAAAAG 59.575 50.000 17.12 0.00 0.00 2.27
2653 5268 2.446435 GGGCAGCTGGAACTATCAAAA 58.554 47.619 17.12 0.00 0.00 2.44
2654 5269 1.340991 GGGGCAGCTGGAACTATCAAA 60.341 52.381 17.12 0.00 0.00 2.69
2655 5270 0.255890 GGGGCAGCTGGAACTATCAA 59.744 55.000 17.12 0.00 0.00 2.57
2656 5271 1.915228 GGGGCAGCTGGAACTATCA 59.085 57.895 17.12 0.00 0.00 2.15
2657 5272 1.227674 CGGGGCAGCTGGAACTATC 60.228 63.158 17.12 0.00 0.00 2.08
2658 5273 1.689233 TCGGGGCAGCTGGAACTAT 60.689 57.895 17.12 0.00 0.00 2.12
2659 5274 2.284331 TCGGGGCAGCTGGAACTA 60.284 61.111 17.12 0.00 0.00 2.24
2660 5275 3.710722 CTCGGGGCAGCTGGAACT 61.711 66.667 17.12 0.00 0.00 3.01
2661 5276 3.254024 TTCTCGGGGCAGCTGGAAC 62.254 63.158 17.12 0.00 0.00 3.62
2662 5277 2.927856 TTCTCGGGGCAGCTGGAA 60.928 61.111 17.12 6.29 0.00 3.53
2663 5278 3.393970 CTTCTCGGGGCAGCTGGA 61.394 66.667 17.12 2.81 0.00 3.86
2664 5279 1.402896 TATCTTCTCGGGGCAGCTGG 61.403 60.000 17.12 0.00 0.00 4.85
2665 5280 0.033228 CTATCTTCTCGGGGCAGCTG 59.967 60.000 10.11 10.11 0.00 4.24
2666 5281 1.753368 GCTATCTTCTCGGGGCAGCT 61.753 60.000 0.00 0.00 0.00 4.24
2667 5282 1.301322 GCTATCTTCTCGGGGCAGC 60.301 63.158 0.00 0.00 0.00 5.25
2668 5283 0.683973 ATGCTATCTTCTCGGGGCAG 59.316 55.000 0.00 0.00 33.23 4.85
2669 5284 1.131638 AATGCTATCTTCTCGGGGCA 58.868 50.000 0.00 0.00 0.00 5.36
2670 5285 2.262423 AAATGCTATCTTCTCGGGGC 57.738 50.000 0.00 0.00 0.00 5.80
2671 5286 4.199310 TGAAAAATGCTATCTTCTCGGGG 58.801 43.478 0.00 0.00 0.00 5.73
2672 5287 5.123820 TGTTGAAAAATGCTATCTTCTCGGG 59.876 40.000 0.00 0.00 0.00 5.14
2673 5288 6.092670 TCTGTTGAAAAATGCTATCTTCTCGG 59.907 38.462 0.00 0.00 0.00 4.63
2674 5289 7.065216 TCTGTTGAAAAATGCTATCTTCTCG 57.935 36.000 0.00 0.00 0.00 4.04
2684 5299 8.749499 GCATATACTCAATCTGTTGAAAAATGC 58.251 33.333 9.54 9.54 43.39 3.56
2687 5302 7.970061 GCAGCATATACTCAATCTGTTGAAAAA 59.030 33.333 0.00 0.00 43.39 1.94
2688 5303 7.415541 GGCAGCATATACTCAATCTGTTGAAAA 60.416 37.037 0.00 0.00 43.39 2.29
2691 5306 5.059161 GGCAGCATATACTCAATCTGTTGA 58.941 41.667 0.00 0.00 41.89 3.18


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

AutoCloner maintained by Alex Coulton.