Multiple sequence alignment - TraesCS5B01G078800

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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 TraesCS5B01G078800 chr5B 100.000 5448 0 0 1 5448 95511280 95516727 0.000000e+00 10061.0
1 TraesCS5B01G078800 chr5B 83.546 626 49 23 2623 3209 53664967 53665577 2.230000e-148 536.0
2 TraesCS5B01G078800 chr5D 96.242 3193 61 10 1891 5049 88878459 88875292 0.000000e+00 5177.0
3 TraesCS5B01G078800 chr5D 96.580 1199 31 2 701 1899 88879565 88878377 0.000000e+00 1978.0
4 TraesCS5B01G078800 chr5D 90.557 413 23 10 5047 5448 88875265 88874858 2.890000e-147 532.0
5 TraesCS5B01G078800 chr5D 92.523 321 19 3 1 319 88881131 88880814 6.430000e-124 455.0
6 TraesCS5B01G078800 chr5D 98.077 52 1 0 662 713 88880504 88880453 2.090000e-14 91.6
7 TraesCS5B01G078800 chr5A 93.274 3360 120 26 1891 5175 82871337 82868009 0.000000e+00 4855.0
8 TraesCS5B01G078800 chr5A 96.284 1238 30 5 671 1899 82872485 82871255 0.000000e+00 2017.0
9 TraesCS5B01G078800 chr5A 88.509 322 22 10 1 319 82873068 82872759 5.150000e-100 375.0
10 TraesCS5B01G078800 chr5A 93.220 59 2 1 5220 5278 82868011 82867955 9.720000e-13 86.1
11 TraesCS5B01G078800 chr4A 82.895 532 51 16 2676 3180 58720871 58720353 5.010000e-120 442.0
12 TraesCS5B01G078800 chr4A 92.157 51 3 1 2623 2672 58786705 58786655 2.720000e-08 71.3
13 TraesCS5B01G078800 chr2B 83.704 405 28 12 2626 2993 10728516 10728919 1.120000e-91 348.0
14 TraesCS5B01G078800 chr2B 93.220 118 7 1 1664 1781 574708122 574708238 7.260000e-39 172.0
15 TraesCS5B01G078800 chr3A 93.491 169 10 1 3248 3415 34532615 34532447 3.260000e-62 250.0
16 TraesCS5B01G078800 chr3A 81.006 179 28 6 5275 5448 568537134 568537311 2.650000e-28 137.0
17 TraesCS5B01G078800 chr3A 81.325 166 26 5 5287 5448 606867760 606867924 4.430000e-26 130.0
18 TraesCS5B01G078800 chr3D 92.398 171 13 0 3246 3416 426452027 426451857 1.520000e-60 244.0
19 TraesCS5B01G078800 chr3D 92.771 166 12 0 3248 3413 71517844 71517679 1.960000e-59 241.0
20 TraesCS5B01G078800 chr3B 92.899 169 11 1 3248 3415 42630984 42630816 1.520000e-60 244.0
21 TraesCS5B01G078800 chr3B 93.252 163 10 1 3248 3410 117589430 117589269 7.050000e-59 239.0
22 TraesCS5B01G078800 chr1D 92.308 169 12 1 3248 3415 175820002 175819834 7.050000e-59 239.0
23 TraesCS5B01G078800 chr7B 91.765 170 13 1 3247 3415 522721480 522721311 9.120000e-58 235.0
24 TraesCS5B01G078800 chr2A 84.916 179 22 5 5274 5448 458734569 458734392 5.610000e-40 176.0
25 TraesCS5B01G078800 chr2A 90.678 118 10 1 1664 1781 634598169 634598285 7.310000e-34 156.0
26 TraesCS5B01G078800 chr7D 85.380 171 20 5 5282 5448 367991462 367991631 7.260000e-39 172.0
27 TraesCS5B01G078800 chr1B 84.884 172 19 7 5282 5448 470102999 470103168 3.380000e-37 167.0
28 TraesCS5B01G078800 chr4B 84.940 166 19 6 5288 5448 147722722 147722558 4.370000e-36 163.0
29 TraesCS5B01G078800 chr1A 84.393 173 19 6 5282 5448 47828440 47828610 4.370000e-36 163.0
30 TraesCS5B01G078800 chr2D 83.140 172 23 6 5282 5448 474174321 474174491 9.450000e-33 152.0


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 TraesCS5B01G078800 chr5B 95511280 95516727 5447 False 10061.000 10061 100.00000 1 5448 1 chr5B.!!$F2 5447
1 TraesCS5B01G078800 chr5B 53664967 53665577 610 False 536.000 536 83.54600 2623 3209 1 chr5B.!!$F1 586
2 TraesCS5B01G078800 chr5D 88874858 88881131 6273 True 1646.720 5177 94.79580 1 5448 5 chr5D.!!$R1 5447
3 TraesCS5B01G078800 chr5A 82867955 82873068 5113 True 1833.275 4855 92.82175 1 5278 4 chr5A.!!$R1 5277
4 TraesCS5B01G078800 chr4A 58720353 58720871 518 True 442.000 442 82.89500 2676 3180 1 chr4A.!!$R1 504

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
533 638 0.040067 GCACTGGCTCAGTTTTTCGG 60.040 55.0 5.24 0.00 42.59 4.30 F
1305 2347 0.113190 AGGAAACTCTGCCCCTTTGG 59.887 55.0 0.00 0.00 32.90 3.28 F
3077 4167 0.110104 CGGTATCTCCTACCTCGGGT 59.890 60.0 1.14 1.14 46.81 5.28 F
3736 4849 1.117994 TCCTGCAGGAGCTACATGAG 58.882 55.0 32.00 1.23 39.78 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2968 2.912956 TCAGGAGAAAAGCATACCCTGT 59.087 45.455 0.0 0.0 41.29 4.00 R
3256 4352 1.149174 CTTCACCACTGCACCAGGT 59.851 57.895 0.0 0.0 35.51 4.00 R
4310 5424 0.033504 TCAGAGTTCACCTCCAACGC 59.966 55.000 0.0 0.0 41.47 4.84 R
4853 5982 0.868406 GACAGCAGAAACACCCTTCG 59.132 55.000 0.0 0.0 0.00 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
54 56 0.179150 GACGGCAGCTCACTAGTCAG 60.179 60.000 0.00 0.00 0.00 3.51
55 57 0.896019 ACGGCAGCTCACTAGTCAGT 60.896 55.000 0.00 0.00 34.42 3.41
56 58 1.095600 CGGCAGCTCACTAGTCAGTA 58.904 55.000 0.00 0.00 32.21 2.74
57 59 1.064803 CGGCAGCTCACTAGTCAGTAG 59.935 57.143 0.00 0.00 32.21 2.57
67 69 9.021807 AGCTCACTAGTCAGTAGTAAACAAATA 57.978 33.333 0.00 0.00 40.27 1.40
117 121 2.703798 CCGCCCTGCATCCAACAAG 61.704 63.158 0.00 0.00 0.00 3.16
143 147 7.622672 GCATGTGATTTTTGTGAATTGTGATCC 60.623 37.037 0.00 0.00 0.00 3.36
163 167 0.817634 CCTGGTCACGGCAGACAAAA 60.818 55.000 8.99 0.00 40.29 2.44
168 173 1.798813 GTCACGGCAGACAAAACCTAG 59.201 52.381 2.55 0.00 38.40 3.02
176 181 3.848554 GCAGACAAAACCTAGACGTTTGC 60.849 47.826 10.74 0.00 36.12 3.68
237 242 0.941542 GCGTGCTAAACCAACACAGA 59.058 50.000 0.00 0.00 33.89 3.41
303 308 3.229293 TGTGATGATGTTTTTCCCTGCA 58.771 40.909 0.00 0.00 0.00 4.41
328 333 5.520376 CCAATTTATGGTTCCAGTCCATC 57.480 43.478 0.53 0.00 44.85 3.51
330 335 5.068198 CCAATTTATGGTTCCAGTCCATCAG 59.932 44.000 0.53 0.00 44.85 2.90
331 336 5.715439 ATTTATGGTTCCAGTCCATCAGA 57.285 39.130 0.53 0.00 43.58 3.27
332 337 4.487714 TTATGGTTCCAGTCCATCAGAC 57.512 45.455 0.53 0.00 43.58 3.51
384 389 7.903995 TTCAATTAATGAAAAGGGATTGTGC 57.096 32.000 0.00 0.00 44.94 4.57
385 390 6.405538 TCAATTAATGAAAAGGGATTGTGCC 58.594 36.000 0.00 0.00 34.30 5.01
386 391 6.576045 TCAATTAATGAAAAGGGATTGTGCCC 60.576 38.462 0.00 0.00 41.05 5.36
387 392 9.666668 TCAATTAATGAAAAGGGATTGTGCCCG 62.667 40.741 0.00 0.00 43.63 6.13
392 397 2.034999 GGGATTGTGCCCGGTTCA 59.965 61.111 0.00 0.00 38.58 3.18
393 398 1.605165 GGGATTGTGCCCGGTTCAA 60.605 57.895 0.00 3.05 38.58 2.69
394 399 1.182385 GGGATTGTGCCCGGTTCAAA 61.182 55.000 0.00 0.00 38.58 2.69
395 400 0.243636 GGATTGTGCCCGGTTCAAAG 59.756 55.000 0.00 0.00 0.00 2.77
401 406 0.400213 TGCCCGGTTCAAAGATCAGT 59.600 50.000 0.00 0.00 0.00 3.41
416 421 9.337396 TCAAAGATCAGTGTTTAAGTTGTACAT 57.663 29.630 0.00 0.00 0.00 2.29
417 422 9.385902 CAAAGATCAGTGTTTAAGTTGTACATG 57.614 33.333 0.00 0.00 0.00 3.21
425 430 7.994334 AGTGTTTAAGTTGTACATGGGAGTTTA 59.006 33.333 0.00 0.00 0.00 2.01
427 432 8.788806 TGTTTAAGTTGTACATGGGAGTTTATG 58.211 33.333 0.00 0.00 0.00 1.90
429 434 8.556213 TTAAGTTGTACATGGGAGTTTATGTC 57.444 34.615 0.00 0.00 38.41 3.06
430 435 6.374417 AGTTGTACATGGGAGTTTATGTCT 57.626 37.500 0.00 0.00 38.41 3.41
432 437 6.655003 AGTTGTACATGGGAGTTTATGTCTTG 59.345 38.462 0.00 0.00 38.41 3.02
433 438 6.121776 TGTACATGGGAGTTTATGTCTTGT 57.878 37.500 0.00 0.00 38.41 3.16
434 439 5.937540 TGTACATGGGAGTTTATGTCTTGTG 59.062 40.000 0.00 0.00 38.41 3.33
435 440 4.335416 ACATGGGAGTTTATGTCTTGTGG 58.665 43.478 0.00 0.00 32.32 4.17
436 441 2.790433 TGGGAGTTTATGTCTTGTGGC 58.210 47.619 0.00 0.00 0.00 5.01
437 442 1.737793 GGGAGTTTATGTCTTGTGGCG 59.262 52.381 0.00 0.00 0.00 5.69
438 443 2.614481 GGGAGTTTATGTCTTGTGGCGA 60.614 50.000 0.00 0.00 0.00 5.54
439 444 3.270877 GGAGTTTATGTCTTGTGGCGAT 58.729 45.455 0.00 0.00 0.00 4.58
440 445 4.439057 GGAGTTTATGTCTTGTGGCGATA 58.561 43.478 0.00 0.00 0.00 2.92
441 446 5.057149 GGAGTTTATGTCTTGTGGCGATAT 58.943 41.667 0.00 0.00 0.00 1.63
442 447 5.050091 GGAGTTTATGTCTTGTGGCGATATG 60.050 44.000 0.00 0.00 0.00 1.78
443 448 4.273480 AGTTTATGTCTTGTGGCGATATGC 59.727 41.667 0.00 0.00 45.38 3.14
461 466 3.071874 TGCGTTCATTGGAAGGAGATT 57.928 42.857 1.72 0.00 40.47 2.40
465 470 4.156739 GCGTTCATTGGAAGGAGATTTTCT 59.843 41.667 1.72 0.00 40.47 2.52
479 484 5.286558 GGAGATTTTCTCGTCGACTACAAAG 59.713 44.000 14.70 3.49 44.28 2.77
484 489 4.825546 TCTCGTCGACTACAAAGACTTT 57.174 40.909 14.70 0.00 33.10 2.66
497 602 1.429463 AGACTTTTGTAGCGGCTTCG 58.571 50.000 8.26 0.00 0.00 3.79
515 620 4.552378 GCTTCGTCAATCTCAAGATGATGC 60.552 45.833 0.00 0.00 40.97 3.91
517 622 3.867493 TCGTCAATCTCAAGATGATGCAC 59.133 43.478 0.00 0.00 34.49 4.57
518 623 3.869832 CGTCAATCTCAAGATGATGCACT 59.130 43.478 0.00 0.00 34.49 4.40
520 625 4.035324 GTCAATCTCAAGATGATGCACTGG 59.965 45.833 0.00 0.00 34.49 4.00
533 638 0.040067 GCACTGGCTCAGTTTTTCGG 60.040 55.000 5.24 0.00 42.59 4.30
536 641 1.160137 CTGGCTCAGTTTTTCGGAGG 58.840 55.000 0.00 0.00 38.48 4.30
538 643 1.695242 TGGCTCAGTTTTTCGGAGGTA 59.305 47.619 0.00 0.00 38.48 3.08
558 664 5.652891 AGGTAGTCATAAGATAGGGTATGCG 59.347 44.000 0.00 0.00 0.00 4.73
574 681 5.092781 GGTATGCGTGTGTTTAAGAAATGG 58.907 41.667 0.00 0.00 0.00 3.16
584 691 7.174253 GTGTGTTTAAGAAATGGGTGTATGAGA 59.826 37.037 0.00 0.00 0.00 3.27
587 694 8.598916 TGTTTAAGAAATGGGTGTATGAGAGTA 58.401 33.333 0.00 0.00 0.00 2.59
588 695 9.614792 GTTTAAGAAATGGGTGTATGAGAGTAT 57.385 33.333 0.00 0.00 0.00 2.12
589 696 9.613428 TTTAAGAAATGGGTGTATGAGAGTATG 57.387 33.333 0.00 0.00 0.00 2.39
591 698 7.200434 AGAAATGGGTGTATGAGAGTATGTT 57.800 36.000 0.00 0.00 0.00 2.71
593 700 8.768397 AGAAATGGGTGTATGAGAGTATGTTTA 58.232 33.333 0.00 0.00 0.00 2.01
594 701 9.391006 GAAATGGGTGTATGAGAGTATGTTTAA 57.609 33.333 0.00 0.00 0.00 1.52
596 703 6.346096 TGGGTGTATGAGAGTATGTTTAAGC 58.654 40.000 0.00 0.00 0.00 3.09
597 704 5.462398 GGGTGTATGAGAGTATGTTTAAGCG 59.538 44.000 0.00 0.00 0.00 4.68
598 705 6.270815 GGTGTATGAGAGTATGTTTAAGCGA 58.729 40.000 0.00 0.00 0.00 4.93
599 706 6.418226 GGTGTATGAGAGTATGTTTAAGCGAG 59.582 42.308 0.00 0.00 0.00 5.03
601 708 7.166142 GTGTATGAGAGTATGTTTAAGCGAGAC 59.834 40.741 0.00 0.00 0.00 3.36
618 725 4.957971 CGAGACGCATTGTGTATCTTTTT 58.042 39.130 19.39 0.00 32.94 1.94
652 759 1.227527 CGTGAGGTTGGACTGCACA 60.228 57.895 0.00 0.00 0.00 4.57
656 763 2.484264 GTGAGGTTGGACTGCACATTAC 59.516 50.000 0.00 0.00 0.00 1.89
669 776 4.062293 TGCACATTACAGTGTACAACTCC 58.938 43.478 1.43 0.00 41.52 3.85
716 1754 3.124921 ATTACAGTGTGCCGCGGC 61.125 61.111 42.35 42.35 42.35 6.53
755 1793 4.334118 TGCTGGCGCAGATGTGGT 62.334 61.111 10.83 0.00 42.25 4.16
1056 2094 3.741476 GCGTCGGTGTACGTCCCT 61.741 66.667 0.00 0.00 44.64 4.20
1212 2250 2.046217 GGTTTCCCCGAGGTGAGC 60.046 66.667 0.00 0.00 0.00 4.26
1213 2251 2.434359 GTTTCCCCGAGGTGAGCG 60.434 66.667 0.00 0.00 0.00 5.03
1214 2252 4.388499 TTTCCCCGAGGTGAGCGC 62.388 66.667 0.00 0.00 0.00 5.92
1305 2347 0.113190 AGGAAACTCTGCCCCTTTGG 59.887 55.000 0.00 0.00 32.90 3.28
1319 2361 2.899256 CCCTTTGGTGGGGCAATATATG 59.101 50.000 0.00 0.00 43.45 1.78
1373 2415 5.220491 GCAACTCCGCAACACAAATTTTTAA 60.220 36.000 0.00 0.00 0.00 1.52
1435 2480 6.692486 CAGCATAGAATAGGTTACCTGTAGG 58.308 44.000 15.13 3.54 42.17 3.18
1448 2493 1.202582 CCTGTAGGTTGAGGTGTCTCG 59.797 57.143 0.00 0.00 42.79 4.04
1519 2570 1.743252 GTGAGCTTCCAGCCTTCCG 60.743 63.158 0.00 0.00 43.77 4.30
1570 2621 8.451748 TCGAATCGATGTACTAGAATAGGATTG 58.548 37.037 0.00 0.00 44.97 2.67
1578 2629 7.445121 TGTACTAGAATAGGATTGGCATCTTG 58.555 38.462 0.00 0.00 44.97 3.02
1884 2935 9.814899 CTCCTGAATCATACCATTCATATAGAC 57.185 37.037 0.00 0.00 41.06 2.59
1885 2936 9.552695 TCCTGAATCATACCATTCATATAGACT 57.447 33.333 0.00 0.00 41.06 3.24
1907 2958 9.427821 AGACTATAGTTCAAGTTGGTGATATCT 57.572 33.333 6.88 0.00 0.00 1.98
1912 2963 9.911788 ATAGTTCAAGTTGGTGATATCTTCAAT 57.088 29.630 2.34 0.00 35.70 2.57
1914 2965 9.739276 AGTTCAAGTTGGTGATATCTTCAATAA 57.261 29.630 2.34 1.30 35.70 1.40
1921 2972 9.573133 GTTGGTGATATCTTCAATAAAAACAGG 57.427 33.333 3.98 0.00 35.70 4.00
1922 2973 8.292444 TGGTGATATCTTCAATAAAAACAGGG 57.708 34.615 3.98 0.00 35.70 4.45
1923 2974 7.893302 TGGTGATATCTTCAATAAAAACAGGGT 59.107 33.333 3.98 0.00 35.70 4.34
1924 2975 9.403583 GGTGATATCTTCAATAAAAACAGGGTA 57.596 33.333 3.98 0.00 35.70 3.69
1927 2978 9.899226 GATATCTTCAATAAAAACAGGGTATGC 57.101 33.333 0.00 0.00 0.00 3.14
1928 2979 7.961326 ATCTTCAATAAAAACAGGGTATGCT 57.039 32.000 0.00 0.00 0.00 3.79
1929 2980 7.775053 TCTTCAATAAAAACAGGGTATGCTT 57.225 32.000 0.00 0.00 0.00 3.91
1930 2981 8.189119 TCTTCAATAAAAACAGGGTATGCTTT 57.811 30.769 0.00 0.00 0.00 3.51
1931 2982 8.646900 TCTTCAATAAAAACAGGGTATGCTTTT 58.353 29.630 0.00 0.00 39.76 2.27
1932 2983 8.825667 TTCAATAAAAACAGGGTATGCTTTTC 57.174 30.769 0.00 0.00 38.04 2.29
1933 2984 8.189119 TCAATAAAAACAGGGTATGCTTTTCT 57.811 30.769 0.00 0.00 38.04 2.52
1934 2985 8.303876 TCAATAAAAACAGGGTATGCTTTTCTC 58.696 33.333 0.00 0.00 38.04 2.87
1935 2986 5.468540 AAAAACAGGGTATGCTTTTCTCC 57.531 39.130 0.00 0.00 32.97 3.71
1936 2987 4.388577 AAACAGGGTATGCTTTTCTCCT 57.611 40.909 0.00 0.00 0.00 3.69
1937 2988 3.356529 ACAGGGTATGCTTTTCTCCTG 57.643 47.619 0.00 0.00 45.13 3.86
1938 2989 2.912956 ACAGGGTATGCTTTTCTCCTGA 59.087 45.455 13.29 0.00 43.05 3.86
1939 2990 3.330701 ACAGGGTATGCTTTTCTCCTGAA 59.669 43.478 13.29 0.00 43.05 3.02
1940 2991 4.018050 ACAGGGTATGCTTTTCTCCTGAAT 60.018 41.667 13.29 0.00 43.05 2.57
1941 2992 4.578105 CAGGGTATGCTTTTCTCCTGAATC 59.422 45.833 0.00 0.00 43.05 2.52
1942 2993 3.561725 GGGTATGCTTTTCTCCTGAATCG 59.438 47.826 0.00 0.00 31.56 3.34
1943 2994 4.192317 GGTATGCTTTTCTCCTGAATCGT 58.808 43.478 0.00 0.00 31.56 3.73
1944 2995 5.357257 GGTATGCTTTTCTCCTGAATCGTA 58.643 41.667 0.00 0.00 31.56 3.43
1945 2996 5.234543 GGTATGCTTTTCTCCTGAATCGTAC 59.765 44.000 0.00 0.00 31.56 3.67
1946 2997 3.596214 TGCTTTTCTCCTGAATCGTACC 58.404 45.455 0.00 0.00 31.56 3.34
1947 2998 2.603560 GCTTTTCTCCTGAATCGTACCG 59.396 50.000 0.00 0.00 31.56 4.02
1948 2999 3.846360 CTTTTCTCCTGAATCGTACCGT 58.154 45.455 0.00 0.00 31.56 4.83
1949 3000 3.947910 TTTCTCCTGAATCGTACCGTT 57.052 42.857 0.00 0.00 31.56 4.44
1950 3001 3.498927 TTCTCCTGAATCGTACCGTTC 57.501 47.619 0.00 0.00 0.00 3.95
1951 3002 1.399440 TCTCCTGAATCGTACCGTTCG 59.601 52.381 0.00 0.00 0.00 3.95
1952 3003 1.131883 CTCCTGAATCGTACCGTTCGT 59.868 52.381 0.00 0.00 0.00 3.85
1953 3004 2.352651 CTCCTGAATCGTACCGTTCGTA 59.647 50.000 0.00 0.00 0.00 3.43
1954 3005 2.945008 TCCTGAATCGTACCGTTCGTAT 59.055 45.455 0.00 0.00 0.00 3.06
1955 3006 4.126437 TCCTGAATCGTACCGTTCGTATA 58.874 43.478 0.00 0.00 0.00 1.47
1956 3007 4.212004 TCCTGAATCGTACCGTTCGTATAG 59.788 45.833 0.00 0.00 0.00 1.31
1957 3008 4.212004 CCTGAATCGTACCGTTCGTATAGA 59.788 45.833 0.00 0.00 0.00 1.98
1958 3009 5.083136 TGAATCGTACCGTTCGTATAGAC 57.917 43.478 0.00 0.00 0.00 2.59
2106 3159 2.161609 GGACTGGAAAAGTACGCCATTG 59.838 50.000 0.00 0.00 40.07 2.82
2109 3162 2.156098 TGGAAAAGTACGCCATTGGTC 58.844 47.619 4.26 0.00 0.00 4.02
2152 3205 7.150640 TGTAGCATGCTCTTATTATCTCTGTG 58.849 38.462 26.57 0.00 0.00 3.66
2219 3275 4.214971 AGTTATCAGAACAGTTTGCTGCAG 59.785 41.667 10.11 10.11 46.30 4.41
2542 3598 8.623030 TGTGGTAATGGTTGTTAGTAAGAAAAC 58.377 33.333 0.00 0.00 0.00 2.43
2632 3688 8.244113 CCCTTGGTACTTTTTGCTTTCTTATAG 58.756 37.037 0.00 0.00 0.00 1.31
2702 3765 8.784043 GCCAGGTATAATTATCACCTAAAGTTG 58.216 37.037 18.43 10.86 40.77 3.16
2750 3813 5.102953 TGTCTAATGCTGAATACAGGCTT 57.897 39.130 0.00 0.00 43.62 4.35
2862 3952 2.215907 ATCAGAAGACGATGAAGCGG 57.784 50.000 0.00 0.00 35.12 5.52
2887 3977 6.016443 GCTAATGAATCAGAAAAGAGGGATGG 60.016 42.308 0.00 0.00 0.00 3.51
3062 4152 4.008330 CTGTTTCACTACCTCTCTCGGTA 58.992 47.826 0.00 0.00 38.49 4.02
3077 4167 0.110104 CGGTATCTCCTACCTCGGGT 59.890 60.000 1.14 1.14 46.81 5.28
3088 4178 3.199289 CCTACCTCGGGTTACTCCATTTT 59.801 47.826 0.72 0.00 37.09 1.82
3155 4245 3.202818 TGACTCCGTTCTATACCCCTGTA 59.797 47.826 0.00 0.00 0.00 2.74
3410 4506 1.620819 CTTGTAGCACTGGGTCTGTCT 59.379 52.381 0.00 0.00 0.00 3.41
3675 4775 9.220767 TCTTTCTAATCTTCTTGCCTTAAGTTC 57.779 33.333 0.97 0.00 37.65 3.01
3736 4849 1.117994 TCCTGCAGGAGCTACATGAG 58.882 55.000 32.00 1.23 39.78 2.90
3860 4973 7.265647 TGTTCTATCTCCTACTTCTTCATCG 57.734 40.000 0.00 0.00 0.00 3.84
3922 5035 4.579869 TCCAGTGCTTCTTATTGTCCTTC 58.420 43.478 0.00 0.00 0.00 3.46
4229 5343 4.146245 TCAGCCCCTCATATCTATTCCA 57.854 45.455 0.00 0.00 0.00 3.53
4296 5410 7.079451 TGGATTTATAGCCCTCTTTTCCTAG 57.921 40.000 0.00 0.00 0.00 3.02
4310 5424 3.644966 TTCCTAGGTTGCCTATTGGTG 57.355 47.619 9.08 0.00 35.36 4.17
4430 5544 1.760192 GCAGCTCCTGGAAATGTCAT 58.240 50.000 0.00 0.00 31.21 3.06
4583 5712 2.836360 TCCGCGGACCAGGGTATC 60.836 66.667 27.28 0.00 0.00 2.24
4716 5845 0.998669 TCGTGCTGTGCATATGTTCG 59.001 50.000 4.29 0.00 41.91 3.95
4837 5966 6.919775 TGATCTAACTATCTAAGGCCCTTC 57.080 41.667 0.00 0.00 0.00 3.46
4853 5982 4.082733 GGCCCTTCTTATTTGTGTCAACTC 60.083 45.833 0.00 0.00 0.00 3.01
4874 6003 0.178990 AAGGGTGTTTCTGCTGTCCC 60.179 55.000 0.00 0.00 35.56 4.46
4922 6051 5.139727 TGGTCTGGAAATGAGATGTTTTGT 58.860 37.500 0.00 0.00 0.00 2.83
5026 6155 5.785243 AGTTTTTGTTTTCGTTTTCCAGGA 58.215 33.333 0.00 0.00 0.00 3.86
5190 6349 8.538409 AGGATTGTGAGCAATTTGAATTTTAC 57.462 30.769 0.00 0.00 44.61 2.01
5199 6358 6.934083 AGCAATTTGAATTTTACGGAATTGGT 59.066 30.769 0.00 5.73 39.16 3.67
5211 6370 3.807071 ACGGAATTGGTTGTTTGATTTGC 59.193 39.130 0.00 0.00 0.00 3.68
5217 6376 3.791245 TGGTTGTTTGATTTGCAGGAAC 58.209 40.909 0.00 0.00 0.00 3.62
5278 6437 9.535878 GTTAACTCCTGAGAAGGTAAGATTATG 57.464 37.037 0.22 0.00 0.00 1.90
5290 6449 3.382083 AAGATTATGCCCCCTTCGTTT 57.618 42.857 0.00 0.00 0.00 3.60
5301 6460 6.059484 TGCCCCCTTCGTTTCTTTATATAAG 58.941 40.000 0.00 0.00 0.00 1.73
5380 6539 8.598041 TCCTCATAATTCTCTTATTAGCCCTTC 58.402 37.037 0.00 0.00 0.00 3.46
5381 6540 8.378565 CCTCATAATTCTCTTATTAGCCCTTCA 58.621 37.037 0.00 0.00 0.00 3.02
5382 6541 9.434420 CTCATAATTCTCTTATTAGCCCTTCAG 57.566 37.037 0.00 0.00 0.00 3.02
5383 6542 9.159254 TCATAATTCTCTTATTAGCCCTTCAGA 57.841 33.333 0.00 0.00 0.00 3.27
5414 6581 8.469200 AGAAACATCTCTCTTCTGATTGTCTAG 58.531 37.037 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 7.735500 TGTCAACGATGCTATTTGTTTACTAC 58.264 34.615 0.00 0.00 0.00 2.73
55 57 7.892778 TGTCAACGATGCTATTTGTTTACTA 57.107 32.000 0.00 0.00 0.00 1.82
56 58 6.795098 TGTCAACGATGCTATTTGTTTACT 57.205 33.333 0.00 0.00 0.00 2.24
57 59 7.845617 TTTGTCAACGATGCTATTTGTTTAC 57.154 32.000 0.00 0.00 0.00 2.01
67 69 3.130340 AGTTTGGTTTTGTCAACGATGCT 59.870 39.130 0.00 0.00 0.00 3.79
117 121 6.528014 TCACAATTCACAAAAATCACATGC 57.472 33.333 0.00 0.00 0.00 4.06
143 147 2.674563 TTTGTCTGCCGTGACCAGGG 62.675 60.000 4.49 4.49 39.26 4.45
163 167 1.677552 CTGGGGCAAACGTCTAGGT 59.322 57.895 0.00 0.00 0.00 3.08
176 181 0.251297 TGGTCAGTTGATTGCTGGGG 60.251 55.000 0.00 0.00 34.89 4.96
183 188 2.421073 CGTGATGCATGGTCAGTTGATT 59.579 45.455 2.46 0.00 0.00 2.57
237 242 7.675962 TGGAATAACAAAACACGTAAGCTAT 57.324 32.000 0.00 0.00 45.62 2.97
358 363 9.598517 GCACAATCCCTTTTCATTAATTGAATA 57.401 29.630 0.00 0.00 43.73 1.75
359 364 7.553760 GGCACAATCCCTTTTCATTAATTGAAT 59.446 33.333 0.00 0.00 43.73 2.57
360 365 6.878389 GGCACAATCCCTTTTCATTAATTGAA 59.122 34.615 0.00 0.00 42.62 2.69
361 366 6.405538 GGCACAATCCCTTTTCATTAATTGA 58.594 36.000 0.00 0.00 0.00 2.57
362 367 5.585844 GGGCACAATCCCTTTTCATTAATTG 59.414 40.000 0.00 0.00 43.13 2.32
363 368 5.626578 CGGGCACAATCCCTTTTCATTAATT 60.627 40.000 0.00 0.00 44.30 1.40
364 369 4.141959 CGGGCACAATCCCTTTTCATTAAT 60.142 41.667 0.00 0.00 44.30 1.40
365 370 3.194542 CGGGCACAATCCCTTTTCATTAA 59.805 43.478 0.00 0.00 44.30 1.40
366 371 2.757868 CGGGCACAATCCCTTTTCATTA 59.242 45.455 0.00 0.00 44.30 1.90
367 372 1.550072 CGGGCACAATCCCTTTTCATT 59.450 47.619 0.00 0.00 44.30 2.57
368 373 1.185315 CGGGCACAATCCCTTTTCAT 58.815 50.000 0.00 0.00 44.30 2.57
369 374 0.897863 CCGGGCACAATCCCTTTTCA 60.898 55.000 0.00 0.00 44.30 2.69
370 375 0.898326 ACCGGGCACAATCCCTTTTC 60.898 55.000 6.32 0.00 44.30 2.29
371 376 0.471022 AACCGGGCACAATCCCTTTT 60.471 50.000 6.32 0.00 44.30 2.27
372 377 0.898326 GAACCGGGCACAATCCCTTT 60.898 55.000 6.32 0.00 44.30 3.11
373 378 1.304134 GAACCGGGCACAATCCCTT 60.304 57.895 6.32 0.00 44.30 3.95
374 379 2.075355 TTGAACCGGGCACAATCCCT 62.075 55.000 6.32 0.00 44.30 4.20
375 380 1.182385 TTTGAACCGGGCACAATCCC 61.182 55.000 6.32 0.00 43.02 3.85
376 381 0.243636 CTTTGAACCGGGCACAATCC 59.756 55.000 6.32 0.00 0.00 3.01
377 382 1.243902 TCTTTGAACCGGGCACAATC 58.756 50.000 6.32 0.00 0.00 2.67
378 383 1.818674 GATCTTTGAACCGGGCACAAT 59.181 47.619 6.32 0.00 0.00 2.71
379 384 1.243902 GATCTTTGAACCGGGCACAA 58.756 50.000 6.32 6.25 0.00 3.33
380 385 0.109532 TGATCTTTGAACCGGGCACA 59.890 50.000 6.32 0.00 0.00 4.57
381 386 0.804989 CTGATCTTTGAACCGGGCAC 59.195 55.000 6.32 0.00 0.00 5.01
382 387 0.400213 ACTGATCTTTGAACCGGGCA 59.600 50.000 6.32 0.00 0.00 5.36
383 388 0.804989 CACTGATCTTTGAACCGGGC 59.195 55.000 6.32 0.00 0.00 6.13
384 389 2.185004 ACACTGATCTTTGAACCGGG 57.815 50.000 6.32 0.00 0.00 5.73
385 390 5.238650 ACTTAAACACTGATCTTTGAACCGG 59.761 40.000 0.00 0.00 0.00 5.28
386 391 6.300354 ACTTAAACACTGATCTTTGAACCG 57.700 37.500 0.00 0.00 0.00 4.44
387 392 7.480810 ACAACTTAAACACTGATCTTTGAACC 58.519 34.615 0.00 0.00 0.00 3.62
388 393 9.434559 GTACAACTTAAACACTGATCTTTGAAC 57.565 33.333 0.00 0.00 0.00 3.18
389 394 9.168451 TGTACAACTTAAACACTGATCTTTGAA 57.832 29.630 0.00 0.00 0.00 2.69
390 395 8.725405 TGTACAACTTAAACACTGATCTTTGA 57.275 30.769 0.00 0.00 0.00 2.69
391 396 9.385902 CATGTACAACTTAAACACTGATCTTTG 57.614 33.333 0.00 0.00 0.00 2.77
392 397 8.567948 CCATGTACAACTTAAACACTGATCTTT 58.432 33.333 0.00 0.00 0.00 2.52
393 398 7.174946 CCCATGTACAACTTAAACACTGATCTT 59.825 37.037 0.00 0.00 0.00 2.40
394 399 6.655003 CCCATGTACAACTTAAACACTGATCT 59.345 38.462 0.00 0.00 0.00 2.75
395 400 6.653320 TCCCATGTACAACTTAAACACTGATC 59.347 38.462 0.00 0.00 0.00 2.92
401 406 8.788806 CATAAACTCCCATGTACAACTTAAACA 58.211 33.333 0.00 0.00 0.00 2.83
416 421 2.790433 GCCACAAGACATAAACTCCCA 58.210 47.619 0.00 0.00 0.00 4.37
417 422 1.737793 CGCCACAAGACATAAACTCCC 59.262 52.381 0.00 0.00 0.00 4.30
425 430 1.220529 CGCATATCGCCACAAGACAT 58.779 50.000 0.00 0.00 37.30 3.06
427 432 1.004927 GAACGCATATCGCCACAAGAC 60.005 52.381 0.00 0.00 43.23 3.01
429 434 1.006086 TGAACGCATATCGCCACAAG 58.994 50.000 0.00 0.00 43.23 3.16
430 435 1.662517 ATGAACGCATATCGCCACAA 58.337 45.000 0.00 0.00 43.23 3.33
432 437 1.334059 CCAATGAACGCATATCGCCAC 60.334 52.381 0.00 0.00 43.23 5.01
433 438 0.943673 CCAATGAACGCATATCGCCA 59.056 50.000 0.00 0.00 43.23 5.69
434 439 1.225855 TCCAATGAACGCATATCGCC 58.774 50.000 0.00 0.00 43.23 5.54
435 440 2.349817 CCTTCCAATGAACGCATATCGC 60.350 50.000 0.00 0.00 43.23 4.58
436 441 3.130633 TCCTTCCAATGAACGCATATCG 58.869 45.455 0.00 0.00 45.38 2.92
437 442 4.380531 TCTCCTTCCAATGAACGCATATC 58.619 43.478 0.00 0.00 33.44 1.63
438 443 4.422073 TCTCCTTCCAATGAACGCATAT 57.578 40.909 0.00 0.00 33.44 1.78
439 444 3.904800 TCTCCTTCCAATGAACGCATA 57.095 42.857 0.00 0.00 33.44 3.14
440 445 2.787473 TCTCCTTCCAATGAACGCAT 57.213 45.000 0.00 0.00 35.92 4.73
441 446 2.787473 ATCTCCTTCCAATGAACGCA 57.213 45.000 0.00 0.00 0.00 5.24
442 447 4.156739 AGAAAATCTCCTTCCAATGAACGC 59.843 41.667 0.00 0.00 0.00 4.84
443 448 5.446473 CGAGAAAATCTCCTTCCAATGAACG 60.446 44.000 1.98 0.00 40.34 3.95
444 449 5.412904 ACGAGAAAATCTCCTTCCAATGAAC 59.587 40.000 1.98 0.00 40.34 3.18
445 450 5.560724 ACGAGAAAATCTCCTTCCAATGAA 58.439 37.500 1.98 0.00 40.34 2.57
461 466 4.825546 AGTCTTTGTAGTCGACGAGAAA 57.174 40.909 17.61 17.61 33.10 2.52
479 484 1.126296 GACGAAGCCGCTACAAAAGTC 59.874 52.381 0.00 0.00 39.95 3.01
484 489 1.067142 AGATTGACGAAGCCGCTACAA 60.067 47.619 0.00 0.00 39.95 2.41
488 493 0.037326 TTGAGATTGACGAAGCCGCT 60.037 50.000 0.00 0.00 39.95 5.52
489 494 0.371645 CTTGAGATTGACGAAGCCGC 59.628 55.000 0.00 0.00 39.95 6.53
491 496 3.525537 TCATCTTGAGATTGACGAAGCC 58.474 45.455 0.00 0.00 31.21 4.35
497 602 4.035324 CCAGTGCATCATCTTGAGATTGAC 59.965 45.833 0.00 0.00 31.21 3.18
515 620 1.532868 CTCCGAAAAACTGAGCCAGTG 59.467 52.381 8.37 0.00 44.62 3.66
517 622 1.160137 CCTCCGAAAAACTGAGCCAG 58.840 55.000 1.16 1.16 37.52 4.85
518 623 0.472471 ACCTCCGAAAAACTGAGCCA 59.528 50.000 0.00 0.00 0.00 4.75
520 625 2.994578 GACTACCTCCGAAAAACTGAGC 59.005 50.000 0.00 0.00 0.00 4.26
533 638 6.183360 CGCATACCCTATCTTATGACTACCTC 60.183 46.154 0.00 0.00 0.00 3.85
536 641 6.072064 ACACGCATACCCTATCTTATGACTAC 60.072 42.308 0.00 0.00 0.00 2.73
538 643 4.833380 ACACGCATACCCTATCTTATGACT 59.167 41.667 0.00 0.00 0.00 3.41
558 664 7.174253 TCTCATACACCCATTTCTTAAACACAC 59.826 37.037 0.00 0.00 0.00 3.82
574 681 6.270815 TCGCTTAAACATACTCTCATACACC 58.729 40.000 0.00 0.00 0.00 4.16
596 703 4.584029 AAAAGATACACAATGCGTCTCG 57.416 40.909 0.00 0.00 0.00 4.04
624 731 1.616159 CAACCTCACGGGGAAAACAT 58.384 50.000 0.00 0.00 40.03 2.71
625 732 0.466555 CCAACCTCACGGGGAAAACA 60.467 55.000 0.00 0.00 40.03 2.83
626 733 0.179012 TCCAACCTCACGGGGAAAAC 60.179 55.000 0.00 0.00 40.03 2.43
627 734 0.179012 GTCCAACCTCACGGGGAAAA 60.179 55.000 0.00 0.00 40.03 2.29
628 735 1.057851 AGTCCAACCTCACGGGGAAA 61.058 55.000 0.00 0.00 40.03 3.13
629 736 1.460689 AGTCCAACCTCACGGGGAA 60.461 57.895 0.00 0.00 40.03 3.97
630 737 2.203182 AGTCCAACCTCACGGGGA 59.797 61.111 0.00 0.00 40.03 4.81
631 738 2.347490 CAGTCCAACCTCACGGGG 59.653 66.667 0.00 0.00 40.03 5.73
632 739 2.358737 GCAGTCCAACCTCACGGG 60.359 66.667 0.00 0.00 41.89 5.28
638 745 2.106511 ACTGTAATGTGCAGTCCAACCT 59.893 45.455 0.00 0.00 42.90 3.50
640 747 2.878406 ACACTGTAATGTGCAGTCCAAC 59.122 45.455 0.00 0.00 44.43 3.77
650 757 4.280174 ACTCGGAGTTGTACACTGTAATGT 59.720 41.667 4.45 0.00 35.01 2.71
652 759 5.464030 AACTCGGAGTTGTACACTGTAAT 57.536 39.130 21.86 0.00 37.00 1.89
656 763 3.245284 CACAAACTCGGAGTTGTACACTG 59.755 47.826 23.05 17.69 38.66 3.66
669 776 4.776743 CTCCAAAAGTCATCACAAACTCG 58.223 43.478 0.00 0.00 0.00 4.18
716 1754 1.671054 CAGGCCCAGTTACCGTGTG 60.671 63.158 0.00 0.00 0.00 3.82
723 1761 0.036732 CAGCAGAACAGGCCCAGTTA 59.963 55.000 10.86 0.00 0.00 2.24
752 1790 1.810755 CGTACTGAGTGAGCACTACCA 59.189 52.381 2.65 0.00 42.66 3.25
755 1793 2.774687 TCACGTACTGAGTGAGCACTA 58.225 47.619 2.65 0.00 42.91 2.74
1044 2082 3.015312 GCTCCCAGGGACGTACACC 62.015 68.421 3.01 0.00 0.00 4.16
1214 2252 3.461982 GTATCGGCATCGCGCTCG 61.462 66.667 5.56 2.28 41.91 5.03
1230 2268 3.461773 CCACGGAGGAGCATCGGT 61.462 66.667 0.00 0.00 41.22 4.69
1255 2297 1.068885 CGGACAGACAGACAGACAGAC 60.069 57.143 0.00 0.00 0.00 3.51
1256 2298 1.239347 CGGACAGACAGACAGACAGA 58.761 55.000 0.00 0.00 0.00 3.41
1257 2299 0.955178 ACGGACAGACAGACAGACAG 59.045 55.000 0.00 0.00 0.00 3.51
1258 2300 0.668535 CACGGACAGACAGACAGACA 59.331 55.000 0.00 0.00 0.00 3.41
1373 2415 4.242475 TCTGTCTGCACGATCGTATTTTT 58.758 39.130 22.26 0.00 0.00 1.94
1448 2493 7.064728 GGTAAATAACTTCATCACACCTGTCTC 59.935 40.741 0.00 0.00 0.00 3.36
1519 2570 5.746284 AGGATAGGAGTAACTTTTTCCAGC 58.254 41.667 0.00 0.00 33.32 4.85
1570 2621 5.140747 ACTCGATAGGATTACAAGATGCC 57.859 43.478 0.00 0.00 0.00 4.40
1578 2629 6.368243 TCAGTACATCGACTCGATAGGATTAC 59.632 42.308 13.54 9.78 45.19 1.89
1886 2937 9.911788 ATTGAAGATATCACCAACTTGAACTAT 57.088 29.630 5.32 0.00 37.92 2.12
1888 2939 9.739276 TTATTGAAGATATCACCAACTTGAACT 57.261 29.630 5.32 0.00 37.92 3.01
1895 2946 9.573133 CCTGTTTTTATTGAAGATATCACCAAC 57.427 33.333 5.32 0.00 37.92 3.77
1896 2947 8.748412 CCCTGTTTTTATTGAAGATATCACCAA 58.252 33.333 5.32 8.65 37.92 3.67
1897 2948 7.893302 ACCCTGTTTTTATTGAAGATATCACCA 59.107 33.333 5.32 0.00 37.92 4.17
1898 2949 8.293699 ACCCTGTTTTTATTGAAGATATCACC 57.706 34.615 5.32 0.00 37.92 4.02
1901 2952 9.899226 GCATACCCTGTTTTTATTGAAGATATC 57.101 33.333 0.00 0.00 0.00 1.63
1902 2953 9.646522 AGCATACCCTGTTTTTATTGAAGATAT 57.353 29.630 0.00 0.00 0.00 1.63
1903 2954 9.474313 AAGCATACCCTGTTTTTATTGAAGATA 57.526 29.630 0.00 0.00 0.00 1.98
1904 2955 7.961326 AGCATACCCTGTTTTTATTGAAGAT 57.039 32.000 0.00 0.00 0.00 2.40
1905 2956 7.775053 AAGCATACCCTGTTTTTATTGAAGA 57.225 32.000 0.00 0.00 0.00 2.87
1906 2957 8.831715 AAAAGCATACCCTGTTTTTATTGAAG 57.168 30.769 0.00 0.00 43.73 3.02
1907 2958 8.646900 AGAAAAGCATACCCTGTTTTTATTGAA 58.353 29.630 0.73 0.00 45.00 2.69
1908 2959 8.189119 AGAAAAGCATACCCTGTTTTTATTGA 57.811 30.769 0.73 0.00 45.00 2.57
1909 2960 7.545615 GGAGAAAAGCATACCCTGTTTTTATTG 59.454 37.037 0.73 0.00 45.00 1.90
1910 2961 7.454694 AGGAGAAAAGCATACCCTGTTTTTATT 59.545 33.333 0.73 0.00 45.00 1.40
1911 2962 6.954102 AGGAGAAAAGCATACCCTGTTTTTAT 59.046 34.615 0.73 0.00 45.00 1.40
1912 2963 6.208599 CAGGAGAAAAGCATACCCTGTTTTTA 59.791 38.462 0.00 0.00 45.00 1.52
1913 2964 5.011023 CAGGAGAAAAGCATACCCTGTTTTT 59.989 40.000 0.00 0.35 46.84 1.94
1914 2965 4.524328 CAGGAGAAAAGCATACCCTGTTTT 59.476 41.667 0.00 0.00 39.64 2.43
1915 2966 4.082125 CAGGAGAAAAGCATACCCTGTTT 58.918 43.478 0.00 0.00 37.11 2.83
1916 2967 3.330701 TCAGGAGAAAAGCATACCCTGTT 59.669 43.478 0.00 0.00 41.29 3.16
1917 2968 2.912956 TCAGGAGAAAAGCATACCCTGT 59.087 45.455 0.00 0.00 41.29 4.00
1918 2969 3.634397 TCAGGAGAAAAGCATACCCTG 57.366 47.619 0.00 0.00 41.74 4.45
1919 2970 4.684485 CGATTCAGGAGAAAAGCATACCCT 60.684 45.833 0.00 0.00 37.29 4.34
1920 2971 3.561725 CGATTCAGGAGAAAAGCATACCC 59.438 47.826 0.00 0.00 37.29 3.69
1921 2972 4.192317 ACGATTCAGGAGAAAAGCATACC 58.808 43.478 0.00 0.00 37.29 2.73
1922 2973 5.234543 GGTACGATTCAGGAGAAAAGCATAC 59.765 44.000 0.00 0.00 37.29 2.39
1923 2974 5.357257 GGTACGATTCAGGAGAAAAGCATA 58.643 41.667 0.00 0.00 37.29 3.14
1924 2975 4.192317 GGTACGATTCAGGAGAAAAGCAT 58.808 43.478 0.00 0.00 37.29 3.79
1925 2976 3.596214 GGTACGATTCAGGAGAAAAGCA 58.404 45.455 0.00 0.00 37.29 3.91
1942 2993 8.299262 TCAACTATAGTCTATACGAACGGTAC 57.701 38.462 5.70 0.00 32.95 3.34
1943 2994 8.887036 TTCAACTATAGTCTATACGAACGGTA 57.113 34.615 5.70 0.00 35.11 4.02
1944 2995 7.792374 TTCAACTATAGTCTATACGAACGGT 57.208 36.000 5.70 0.00 0.00 4.83
1945 2996 9.674824 AAATTCAACTATAGTCTATACGAACGG 57.325 33.333 5.70 0.00 0.00 4.44
1957 3008 9.388506 CCAGAGACAATCAAATTCAACTATAGT 57.611 33.333 0.00 0.00 0.00 2.12
1958 3009 9.388506 ACCAGAGACAATCAAATTCAACTATAG 57.611 33.333 0.00 0.00 0.00 1.31
2152 3205 6.013689 GTGACGTTGAATTTCGATTTCCTAC 58.986 40.000 0.00 4.48 0.00 3.18
2219 3275 3.332761 TTTGACATGTGCGACTCAAAC 57.667 42.857 1.15 0.00 29.66 2.93
2253 3309 8.830580 CATGAATCGGATTTTATAGTTCACACT 58.169 33.333 4.47 0.00 36.99 3.55
2542 3598 6.797033 AGTGAATAAAGCAAAGTTTTCGATCG 59.203 34.615 9.36 9.36 0.00 3.69
2750 3813 6.044404 ACAACTCTAGGATTCTTTCAAGGGAA 59.956 38.462 0.00 0.00 0.00 3.97
2862 3952 6.016443 CCATCCCTCTTTTCTGATTCATTAGC 60.016 42.308 0.00 0.00 0.00 3.09
2887 3977 9.139174 CACCCATATTTTCCGATAATAAATTGC 57.861 33.333 0.00 0.00 0.00 3.56
3062 4152 2.158490 GGAGTAACCCGAGGTAGGAGAT 60.158 54.545 0.00 0.00 33.12 2.75
3088 4178 9.513906 TGATTTCCTCAATACACAGACATTTTA 57.486 29.630 0.00 0.00 0.00 1.52
3115 4205 5.938125 GGAGTCAACACAATAACCACACTAT 59.062 40.000 0.00 0.00 0.00 2.12
3256 4352 1.149174 CTTCACCACTGCACCAGGT 59.851 57.895 0.00 0.00 35.51 4.00
3410 4506 4.202567 ACAGCCCACTAATCCTGAGAAAAA 60.203 41.667 0.00 0.00 0.00 1.94
3675 4775 3.569701 CCCAATAAAATCCGATGAGTGGG 59.430 47.826 8.53 8.53 37.43 4.61
3860 4973 7.617041 AACAAGAGGAAACATATTACTGCTC 57.383 36.000 0.00 0.00 0.00 4.26
3939 5052 2.763448 AGCGAACCTGAGAAGCTTATCT 59.237 45.455 20.95 5.05 34.05 1.98
4229 5343 2.586079 CGCGCAAGATGATCCCGT 60.586 61.111 8.75 0.00 43.02 5.28
4296 5410 0.109319 CAACGCACCAATAGGCAACC 60.109 55.000 0.00 0.00 39.06 3.77
4310 5424 0.033504 TCAGAGTTCACCTCCAACGC 59.966 55.000 0.00 0.00 41.47 4.84
4448 5562 2.158249 TGTCACCATGGGAAATTGGGAA 60.158 45.455 18.09 0.00 37.32 3.97
4449 5563 1.430853 TGTCACCATGGGAAATTGGGA 59.569 47.619 18.09 0.00 37.32 4.37
4450 5564 1.935799 TGTCACCATGGGAAATTGGG 58.064 50.000 18.09 0.00 37.32 4.12
4451 5565 4.441913 GCTATTGTCACCATGGGAAATTGG 60.442 45.833 18.09 5.66 39.02 3.16
4452 5566 4.441913 GGCTATTGTCACCATGGGAAATTG 60.442 45.833 18.09 11.31 0.00 2.32
4453 5567 3.706086 GGCTATTGTCACCATGGGAAATT 59.294 43.478 18.09 5.06 0.00 1.82
4454 5568 3.299503 GGCTATTGTCACCATGGGAAAT 58.700 45.455 18.09 11.93 0.00 2.17
4455 5569 2.042297 TGGCTATTGTCACCATGGGAAA 59.958 45.455 18.09 2.65 0.00 3.13
4583 5712 1.268794 CGACAGCGAATAGGAGACCAG 60.269 57.143 0.00 0.00 40.82 4.00
4716 5845 5.353400 GCAAAGGTTGATTACTACACTACCC 59.647 44.000 0.00 0.00 31.83 3.69
4837 5966 4.755123 ACCCTTCGAGTTGACACAAATAAG 59.245 41.667 0.00 0.00 0.00 1.73
4853 5982 0.868406 GACAGCAGAAACACCCTTCG 59.132 55.000 0.00 0.00 0.00 3.79
4874 6003 2.126888 AAAATGCGCGTTGGCTCG 60.127 55.556 17.00 0.00 36.88 5.03
4922 6051 1.518367 CCATAACCCCTCCAGGCTAA 58.482 55.000 0.00 0.00 0.00 3.09
5026 6155 5.529289 TGGTACTAAAGGATGGTCTCTGAT 58.471 41.667 0.00 0.00 0.00 2.90
5139 6298 9.685828 TTTGTTTTGCATGTAAAATCCTACTAC 57.314 29.630 22.03 9.95 32.71 2.73
5140 6299 9.906660 CTTTGTTTTGCATGTAAAATCCTACTA 57.093 29.630 22.03 6.55 32.71 1.82
5141 6300 7.872483 CCTTTGTTTTGCATGTAAAATCCTACT 59.128 33.333 22.03 0.00 32.71 2.57
5179 6338 8.391106 CAAACAACCAATTCCGTAAAATTCAAA 58.609 29.630 0.00 0.00 0.00 2.69
5190 6349 3.806521 TGCAAATCAAACAACCAATTCCG 59.193 39.130 0.00 0.00 0.00 4.30
5199 6358 5.273674 TCATGTTCCTGCAAATCAAACAA 57.726 34.783 0.00 0.00 31.45 2.83
5238 6397 6.831353 TCAGGAGTTAACCTTTTGATTTCACA 59.169 34.615 0.88 0.00 38.32 3.58
5278 6437 6.293698 TCTTATATAAAGAAACGAAGGGGGC 58.706 40.000 0.00 0.00 0.00 5.80
5333 6492 9.886132 TGAGGAATTAGAAGAAATACACCTTAC 57.114 33.333 0.00 0.00 0.00 2.34
5390 6549 8.359875 TCTAGACAATCAGAAGAGAGATGTTT 57.640 34.615 0.00 0.00 0.00 2.83
5398 6565 6.483307 ACGAGAGATCTAGACAATCAGAAGAG 59.517 42.308 0.00 0.00 0.00 2.85
5414 6581 4.564769 CCTTCTTTGCTACAACGAGAGATC 59.435 45.833 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.