Multiple sequence alignment - TraesCS6D01G137700

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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 TraesCS6D01G137700 chr6D 100.000 5500 0 0 1 5500 106089596 106084097 0.000000e+00 10157.0
1 TraesCS6D01G137700 chr6D 100.000 243 0 0 6155 6397 106083442 106083200 3.520000e-122 449.0
2 TraesCS6D01G137700 chr6D 84.109 258 25 8 1663 1906 106086726 106086471 1.070000e-57 235.0
3 TraesCS6D01G137700 chr6D 84.109 258 25 8 2871 3126 106087934 106087691 1.070000e-57 235.0
4 TraesCS6D01G137700 chr6D 87.113 194 20 2 5111 5304 354152 354340 1.400000e-51 215.0
5 TraesCS6D01G137700 chr6D 96.000 50 1 1 4030 4079 354105 354153 5.320000e-11 80.5
6 TraesCS6D01G137700 chr6D 100.000 31 0 0 2540 2570 106086985 106086955 2.490000e-04 58.4
7 TraesCS6D01G137700 chr6D 100.000 31 0 0 2612 2642 106087057 106087027 2.490000e-04 58.4
8 TraesCS6D01G137700 chr6B 93.788 2286 83 22 589 2836 192939804 192937540 0.000000e+00 3380.0
9 TraesCS6D01G137700 chr6B 93.885 1668 58 13 3706 5355 192936335 192934694 0.000000e+00 2475.0
10 TraesCS6D01G137700 chr6B 95.338 665 27 4 2183 2846 27706060 27706721 0.000000e+00 1053.0
11 TraesCS6D01G137700 chr6B 95.377 584 18 1 2831 3414 192937308 192936734 0.000000e+00 920.0
12 TraesCS6D01G137700 chr6B 95.318 299 14 0 2183 2481 81724607 81724309 5.800000e-130 475.0
13 TraesCS6D01G137700 chr6B 90.258 349 33 1 1 348 192940289 192939941 7.560000e-124 455.0
14 TraesCS6D01G137700 chr6B 97.484 159 4 0 3451 3609 192936730 192936572 8.170000e-69 272.0
15 TraesCS6D01G137700 chr6B 86.017 236 24 5 2894 3126 192938702 192938473 1.780000e-60 244.0
16 TraesCS6D01G137700 chr6B 83.721 258 26 8 1663 1906 192937268 192937013 4.990000e-56 230.0
17 TraesCS6D01G137700 chr6B 90.164 122 8 2 484 605 192939937 192939820 8.590000e-34 156.0
18 TraesCS6D01G137700 chr6B 97.727 44 1 0 3629 3672 192936572 192936529 6.880000e-10 76.8
19 TraesCS6D01G137700 chr6B 100.000 31 0 0 2540 2570 27706487 27706517 2.490000e-04 58.4
20 TraesCS6D01G137700 chr6B 100.000 31 0 0 2612 2642 192937835 192937805 2.490000e-04 58.4
21 TraesCS6D01G137700 chr6A 92.593 2241 110 33 627 2836 129356859 129354644 0.000000e+00 3168.0
22 TraesCS6D01G137700 chr6A 95.913 783 23 3 4189 4971 129352667 129351894 0.000000e+00 1260.0
23 TraesCS6D01G137700 chr6A 94.915 649 20 10 2853 3499 129354408 129353771 0.000000e+00 1003.0
24 TraesCS6D01G137700 chr6A 94.038 520 14 3 3689 4191 129353498 129352979 0.000000e+00 773.0
25 TraesCS6D01G137700 chr6A 96.678 301 8 2 4989 5288 129351646 129351347 3.440000e-137 499.0
26 TraesCS6D01G137700 chr6A 95.473 243 11 0 6155 6397 129344621 129344379 7.780000e-104 388.0
27 TraesCS6D01G137700 chr6A 89.540 239 11 5 5275 5500 129345450 129345213 2.260000e-74 291.0
28 TraesCS6D01G137700 chr6A 97.037 135 4 0 3534 3668 129353774 129353640 1.790000e-55 228.0
29 TraesCS6D01G137700 chr6A 81.858 226 26 6 1663 1875 129354390 129354167 6.590000e-40 176.0
30 TraesCS6D01G137700 chr6A 100.000 31 0 0 2540 2570 129354866 129354836 2.490000e-04 58.4
31 TraesCS6D01G137700 chr6A 100.000 31 0 0 2612 2642 129354937 129354907 2.490000e-04 58.4
32 TraesCS6D01G137700 chr3B 96.284 296 11 0 2183 2478 830286121 830286416 2.680000e-133 486.0
33 TraesCS6D01G137700 chr3B 96.284 296 11 0 2183 2478 830560079 830560374 2.680000e-133 486.0
34 TraesCS6D01G137700 chr1B 95.946 296 12 0 2183 2478 24002817 24003112 1.250000e-131 481.0
35 TraesCS6D01G137700 chr1B 95.652 299 13 0 2183 2481 593219857 593219559 1.250000e-131 481.0
36 TraesCS6D01G137700 chr5B 95.318 299 14 0 2183 2481 535287354 535287056 5.800000e-130 475.0
37 TraesCS6D01G137700 chr5D 87.113 194 20 2 5111 5304 545187803 545187615 1.400000e-51 215.0
38 TraesCS6D01G137700 chr5D 96.000 50 1 1 4030 4079 545187850 545187802 5.320000e-11 80.5
39 TraesCS6D01G137700 chr4D 86.979 192 20 2 5113 5304 400119816 400119630 1.810000e-50 211.0
40 TraesCS6D01G137700 chr4D 94.545 55 2 1 4030 4084 400119865 400119812 4.110000e-12 84.2
41 TraesCS6D01G137700 chr1A 86.458 192 21 2 5113 5304 45386702 45386516 8.410000e-49 206.0
42 TraesCS6D01G137700 chr1A 92.727 55 3 1 4030 4084 45386751 45386698 1.910000e-10 78.7
43 TraesCS6D01G137700 chr7D 94.545 55 2 1 4030 4084 69358219 69358272 4.110000e-12 84.2
44 TraesCS6D01G137700 chr5A 94.545 55 2 1 4030 4084 491402692 491402639 4.110000e-12 84.2
45 TraesCS6D01G137700 chr3A 92.727 55 3 1 4030 4084 40984362 40984415 1.910000e-10 78.7


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 TraesCS6D01G137700 chr6D 106083200 106089596 6396 True 1865.466667 10157 94.703000 1 6397 6 chr6D.!!$R1 6396
1 TraesCS6D01G137700 chr6B 192934694 192940289 5595 True 826.720000 3380 92.842100 1 5355 10 chr6B.!!$R2 5354
2 TraesCS6D01G137700 chr6B 27706060 27706721 661 False 555.700000 1053 97.669000 2183 2846 2 chr6B.!!$F1 663
3 TraesCS6D01G137700 chr6A 129351347 129356859 5512 True 802.644444 3168 94.781333 627 5288 9 chr6A.!!$R2 4661
4 TraesCS6D01G137700 chr6A 129344379 129345450 1071 True 339.500000 388 92.506500 5275 6397 2 chr6A.!!$R1 1122

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
931 974 0.247460 CGTGCATCAGTCAGGGAAGA 59.753 55.000 0.00 0.0 0.00 2.87 F
1641 1702 0.321564 TGTCATTTCTGTCTGCCCCG 60.322 55.000 0.00 0.0 0.00 5.73 F
1942 2018 1.276421 AGGAAACCGAGGAGTCACATG 59.724 52.381 0.00 0.0 0.00 3.21 F
2154 2239 1.805945 CTCGGTGAACACTAGCGCC 60.806 63.158 2.29 0.0 38.76 6.53 F
3703 4151 1.005924 CCCCCTCTGCCAAGTGTTAAT 59.994 52.381 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2445 0.310543 TGTCGCTGAAACATGTTGGC 59.689 50.0 12.82 15.16 0.00 4.52 R
3296 3623 1.404477 CTTTTGTTTAACCGCCTGCG 58.596 50.0 4.20 4.20 39.44 5.18 R
3684 4011 2.514458 ATTAACACTTGGCAGAGGGG 57.486 50.0 4.41 0.00 0.00 4.79 R
3979 4484 2.695147 GCAAACATGAAATCCTAGGGGG 59.305 50.0 9.46 0.00 0.00 5.40 R
5420 6489 0.251077 CATAGGAGGGGGCAGCATTC 60.251 60.0 0.00 0.00 0.00 2.67 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
42 43 2.508891 CGTGCGACCTCGATTGAGC 61.509 63.158 4.21 0.00 41.13 4.26
46 47 1.743855 GCGACCTCGATTGAGCGAAC 61.744 60.000 12.58 0.73 41.13 3.95
47 48 0.456142 CGACCTCGATTGAGCGAACA 60.456 55.000 4.21 0.00 41.13 3.18
64 65 1.024579 ACAATCGATGGGTGGCGAAC 61.025 55.000 4.46 0.00 40.20 3.95
116 117 3.326578 ATGGGTGTGGTAGCGGCA 61.327 61.111 1.45 0.00 0.00 5.69
148 149 1.146774 TCAAGGCCAACATGGGAAAGA 59.853 47.619 5.01 0.00 38.19 2.52
151 152 0.608035 GGCCAACATGGGAAAGACGA 60.608 55.000 0.00 0.00 38.19 4.20
154 155 2.436417 CCAACATGGGAAAGACGACAT 58.564 47.619 0.00 0.00 32.67 3.06
155 156 2.162208 CCAACATGGGAAAGACGACATG 59.838 50.000 0.00 0.00 44.61 3.21
159 160 1.452110 TGGGAAAGACGACATGCATG 58.548 50.000 25.09 25.09 0.00 4.06
181 182 2.031465 GGGACGCCAACGGAGAAA 59.969 61.111 0.00 0.00 46.04 2.52
183 184 1.574702 GGGACGCCAACGGAGAAAAG 61.575 60.000 0.00 0.00 46.04 2.27
260 262 5.512082 AGAAAACGACATATATATCGCGCTC 59.488 40.000 13.18 7.11 42.12 5.03
262 264 4.553756 ACGACATATATATCGCGCTCAT 57.446 40.909 13.18 0.00 42.12 2.90
273 275 0.925267 CGCGCTCATGTATTTTGGCG 60.925 55.000 5.56 0.00 44.40 5.69
310 312 3.193903 TCGACGAATTAGTGGTGGATCAA 59.806 43.478 0.00 0.00 0.00 2.57
312 314 4.025730 CGACGAATTAGTGGTGGATCAATG 60.026 45.833 0.00 0.00 0.00 2.82
313 315 4.843728 ACGAATTAGTGGTGGATCAATGT 58.156 39.130 0.00 0.00 0.00 2.71
325 327 5.829924 GGTGGATCAATGTGATTAGTGGATT 59.170 40.000 0.00 0.00 37.20 3.01
330 332 5.953183 TCAATGTGATTAGTGGATTGTTGC 58.047 37.500 0.00 0.00 0.00 4.17
339 341 1.068748 GTGGATTGTTGCTGTGCTCAG 60.069 52.381 11.44 11.44 43.87 3.35
361 363 4.508662 GCTAGTGCTCAACATCTTAAGGT 58.491 43.478 1.85 0.00 36.03 3.50
362 364 4.938226 GCTAGTGCTCAACATCTTAAGGTT 59.062 41.667 1.85 0.00 36.03 3.50
363 365 5.412904 GCTAGTGCTCAACATCTTAAGGTTT 59.587 40.000 1.85 0.00 36.03 3.27
364 366 6.072452 GCTAGTGCTCAACATCTTAAGGTTTT 60.072 38.462 1.85 0.00 36.03 2.43
365 367 6.076981 AGTGCTCAACATCTTAAGGTTTTG 57.923 37.500 8.11 8.11 0.00 2.44
366 368 5.010012 AGTGCTCAACATCTTAAGGTTTTGG 59.990 40.000 13.35 6.72 0.00 3.28
367 369 5.009610 GTGCTCAACATCTTAAGGTTTTGGA 59.990 40.000 13.35 2.04 0.00 3.53
368 370 5.009610 TGCTCAACATCTTAAGGTTTTGGAC 59.990 40.000 13.35 7.52 0.00 4.02
408 410 9.729023 GATTATGATTAGATGGTCTAGATGACG 57.271 37.037 0.00 0.00 46.24 4.35
409 411 8.863872 TTATGATTAGATGGTCTAGATGACGA 57.136 34.615 0.00 0.00 46.24 4.20
410 412 7.953005 ATGATTAGATGGTCTAGATGACGAT 57.047 36.000 0.00 0.00 46.24 3.73
411 413 7.767250 TGATTAGATGGTCTAGATGACGATT 57.233 36.000 0.00 0.00 46.24 3.34
412 414 8.183104 TGATTAGATGGTCTAGATGACGATTT 57.817 34.615 0.00 0.00 46.24 2.17
413 415 8.084684 TGATTAGATGGTCTAGATGACGATTTG 58.915 37.037 0.00 0.00 46.24 2.32
414 416 5.207110 AGATGGTCTAGATGACGATTTGG 57.793 43.478 0.00 0.00 46.24 3.28
415 417 4.895889 AGATGGTCTAGATGACGATTTGGA 59.104 41.667 0.00 0.00 46.24 3.53
416 418 5.541868 AGATGGTCTAGATGACGATTTGGAT 59.458 40.000 0.00 0.00 46.24 3.41
417 419 5.201713 TGGTCTAGATGACGATTTGGATC 57.798 43.478 0.00 0.00 46.24 3.36
418 420 4.895889 TGGTCTAGATGACGATTTGGATCT 59.104 41.667 0.00 0.00 46.24 2.75
419 421 5.221322 TGGTCTAGATGACGATTTGGATCTG 60.221 44.000 0.00 0.00 46.24 2.90
420 422 5.221342 GGTCTAGATGACGATTTGGATCTGT 60.221 44.000 0.00 0.00 46.24 3.41
421 423 5.918011 GTCTAGATGACGATTTGGATCTGTC 59.082 44.000 0.00 0.00 36.86 3.51
422 424 4.065321 AGATGACGATTTGGATCTGTCC 57.935 45.455 0.00 0.00 45.31 4.02
423 425 3.708631 AGATGACGATTTGGATCTGTCCT 59.291 43.478 0.00 0.00 45.32 3.85
424 426 3.526931 TGACGATTTGGATCTGTCCTC 57.473 47.619 0.00 0.00 45.32 3.71
425 427 3.099905 TGACGATTTGGATCTGTCCTCT 58.900 45.455 0.00 0.00 45.32 3.69
426 428 3.131223 TGACGATTTGGATCTGTCCTCTC 59.869 47.826 0.00 0.00 45.32 3.20
427 429 3.099905 ACGATTTGGATCTGTCCTCTCA 58.900 45.455 0.00 0.00 45.32 3.27
428 430 3.708631 ACGATTTGGATCTGTCCTCTCAT 59.291 43.478 0.00 0.00 45.32 2.90
429 431 4.895889 ACGATTTGGATCTGTCCTCTCATA 59.104 41.667 0.00 0.00 45.32 2.15
430 432 5.541868 ACGATTTGGATCTGTCCTCTCATAT 59.458 40.000 0.00 0.00 45.32 1.78
431 433 6.042552 ACGATTTGGATCTGTCCTCTCATATT 59.957 38.462 0.00 0.00 45.32 1.28
432 434 6.933521 CGATTTGGATCTGTCCTCTCATATTT 59.066 38.462 0.00 0.00 45.32 1.40
433 435 7.443575 CGATTTGGATCTGTCCTCTCATATTTT 59.556 37.037 0.00 0.00 45.32 1.82
434 436 9.129532 GATTTGGATCTGTCCTCTCATATTTTT 57.870 33.333 0.00 0.00 45.32 1.94
439 441 9.883142 GGATCTGTCCTCTCATATTTTTATAGG 57.117 37.037 0.00 0.00 41.60 2.57
440 442 9.883142 GATCTGTCCTCTCATATTTTTATAGGG 57.117 37.037 0.00 0.00 0.00 3.53
441 443 9.621239 ATCTGTCCTCTCATATTTTTATAGGGA 57.379 33.333 0.00 0.00 0.00 4.20
442 444 9.621239 TCTGTCCTCTCATATTTTTATAGGGAT 57.379 33.333 0.00 0.00 0.00 3.85
445 447 9.825109 GTCCTCTCATATTTTTATAGGGATAGC 57.175 37.037 0.00 0.00 0.00 2.97
446 448 9.560860 TCCTCTCATATTTTTATAGGGATAGCA 57.439 33.333 0.00 0.00 0.00 3.49
447 449 9.829507 CCTCTCATATTTTTATAGGGATAGCAG 57.170 37.037 0.00 0.00 0.00 4.24
456 458 9.693739 TTTTTATAGGGATAGCAGATGAAAACA 57.306 29.630 0.00 0.00 0.00 2.83
457 459 9.866655 TTTTATAGGGATAGCAGATGAAAACAT 57.133 29.630 0.00 0.00 0.00 2.71
462 464 8.773033 AGGGATAGCAGATGAAAACATAATTT 57.227 30.769 0.00 0.00 0.00 1.82
463 465 8.854117 AGGGATAGCAGATGAAAACATAATTTC 58.146 33.333 0.00 0.00 39.28 2.17
464 466 8.854117 GGGATAGCAGATGAAAACATAATTTCT 58.146 33.333 1.99 0.00 39.51 2.52
468 470 8.284945 AGCAGATGAAAACATAATTTCTAGCA 57.715 30.769 1.99 0.00 39.51 3.49
469 471 8.910944 AGCAGATGAAAACATAATTTCTAGCAT 58.089 29.630 1.99 0.00 39.51 3.79
470 472 9.178427 GCAGATGAAAACATAATTTCTAGCATC 57.822 33.333 0.00 0.00 39.51 3.91
475 477 9.671279 TGAAAACATAATTTCTAGCATCTGAGA 57.329 29.630 0.00 0.00 39.51 3.27
477 479 8.674263 AAACATAATTTCTAGCATCTGAGAGG 57.326 34.615 0.00 0.00 0.00 3.69
478 480 6.767456 ACATAATTTCTAGCATCTGAGAGGG 58.233 40.000 0.00 0.00 0.00 4.30
479 481 4.703379 AATTTCTAGCATCTGAGAGGGG 57.297 45.455 0.00 0.00 0.00 4.79
480 482 2.094100 TTCTAGCATCTGAGAGGGGG 57.906 55.000 0.00 0.00 0.00 5.40
481 483 0.937441 TCTAGCATCTGAGAGGGGGT 59.063 55.000 0.00 0.00 0.00 4.95
482 484 1.047002 CTAGCATCTGAGAGGGGGTG 58.953 60.000 0.00 0.00 0.00 4.61
495 497 4.162690 GGGTGCTAGCGGGAGTGG 62.163 72.222 10.77 0.00 0.00 4.00
527 529 4.507710 TGAGTGGTGCTCTATGTTTGATC 58.492 43.478 0.00 0.00 44.41 2.92
528 530 4.223700 TGAGTGGTGCTCTATGTTTGATCT 59.776 41.667 0.00 0.00 44.41 2.75
529 531 5.171339 AGTGGTGCTCTATGTTTGATCTT 57.829 39.130 0.00 0.00 0.00 2.40
530 532 5.181748 AGTGGTGCTCTATGTTTGATCTTC 58.818 41.667 0.00 0.00 0.00 2.87
531 533 4.937620 GTGGTGCTCTATGTTTGATCTTCA 59.062 41.667 0.00 0.00 0.00 3.02
563 565 5.288015 TGTCATGTTTGATTTTGAATGCGT 58.712 33.333 0.00 0.00 33.56 5.24
582 584 6.820470 TGCGTCTTTAAATTTTGAACTTGG 57.180 33.333 0.00 0.00 0.00 3.61
583 585 6.565234 TGCGTCTTTAAATTTTGAACTTGGA 58.435 32.000 0.00 0.00 0.00 3.53
587 589 7.167468 CGTCTTTAAATTTTGAACTTGGACAGG 59.833 37.037 0.00 0.00 0.00 4.00
605 639 5.888161 GGACAGGATGGATGTTTGACTTATT 59.112 40.000 0.00 0.00 43.62 1.40
609 643 7.554118 ACAGGATGGATGTTTGACTTATTACAG 59.446 37.037 0.00 0.00 43.62 2.74
644 680 7.549839 AGTATTCATAAGGTTAGTACACGCAA 58.450 34.615 0.00 0.00 0.00 4.85
655 691 8.789762 AGGTTAGTACACGCAAAGAAAAATAAT 58.210 29.630 0.00 0.00 0.00 1.28
740 776 8.832735 ACTATTATTGAGGTGGGAGAGTTTTAA 58.167 33.333 0.00 0.00 0.00 1.52
794 830 4.762251 GCACCAGAAACTCTTGGATAAAGT 59.238 41.667 0.00 0.00 37.18 2.66
926 969 3.857854 GCGCGTGCATCAGTCAGG 61.858 66.667 17.66 0.00 42.15 3.86
927 970 3.190849 CGCGTGCATCAGTCAGGG 61.191 66.667 0.00 0.00 0.00 4.45
928 971 2.265739 GCGTGCATCAGTCAGGGA 59.734 61.111 0.00 0.00 0.00 4.20
929 972 1.375908 GCGTGCATCAGTCAGGGAA 60.376 57.895 0.00 0.00 0.00 3.97
930 973 1.364626 GCGTGCATCAGTCAGGGAAG 61.365 60.000 0.00 0.00 0.00 3.46
931 974 0.247460 CGTGCATCAGTCAGGGAAGA 59.753 55.000 0.00 0.00 0.00 2.87
932 975 1.738365 CGTGCATCAGTCAGGGAAGAG 60.738 57.143 0.00 0.00 0.00 2.85
942 985 2.764547 GGGAAGAGGAGGGGACGG 60.765 72.222 0.00 0.00 0.00 4.79
1177 1220 2.663188 GCCGATCCATCCGTCTGC 60.663 66.667 0.00 0.00 0.00 4.26
1488 1539 3.126831 GCCTGTCGAATTCATCTAGGTG 58.873 50.000 6.22 0.00 0.00 4.00
1506 1557 2.227194 GTGGTTTTCGACAAGGATGGT 58.773 47.619 0.00 0.00 0.00 3.55
1599 1650 6.074034 GCAAGATAAGCGAGGTATTCTTCTTC 60.074 42.308 0.00 0.00 0.00 2.87
1602 1653 4.394439 AAGCGAGGTATTCTTCTTCCTC 57.606 45.455 0.00 0.00 41.91 3.71
1617 1678 3.582647 TCTTCCTCATGGCTTGTAACAGA 59.417 43.478 0.00 0.00 0.00 3.41
1641 1702 0.321564 TGTCATTTCTGTCTGCCCCG 60.322 55.000 0.00 0.00 0.00 5.73
1740 1808 3.520721 TCAATCCTGAGCTCCTGAATTGA 59.479 43.478 18.98 18.98 31.29 2.57
1775 1843 5.629435 GGTTAAGTTGATTAAGTTGCTGTGC 59.371 40.000 0.72 0.00 34.01 4.57
1783 1851 4.870123 TTAAGTTGCTGTGCATCCATTT 57.130 36.364 0.00 0.00 38.76 2.32
1798 1866 1.747355 CCATTTCTCGCCTTCTGCATT 59.253 47.619 0.00 0.00 41.33 3.56
1833 1901 7.504924 TGTTCAGAGGGTTAAGTTATGTTTG 57.495 36.000 0.00 0.00 0.00 2.93
1836 1904 7.074653 TCAGAGGGTTAAGTTATGTTTGAGT 57.925 36.000 0.00 0.00 0.00 3.41
1839 1908 8.718734 CAGAGGGTTAAGTTATGTTTGAGTTAC 58.281 37.037 0.00 0.00 0.00 2.50
1840 1909 8.434392 AGAGGGTTAAGTTATGTTTGAGTTACA 58.566 33.333 0.00 0.00 0.00 2.41
1842 1911 9.582648 AGGGTTAAGTTATGTTTGAGTTACATT 57.417 29.630 0.00 0.00 37.42 2.71
1885 1961 9.958180 TGAATAGAGTTCACCAAGATGAAAATA 57.042 29.630 0.00 0.00 40.22 1.40
1894 1970 6.818644 TCACCAAGATGAAAATACTGTAGCTC 59.181 38.462 0.00 0.00 0.00 4.09
1895 1971 6.820656 CACCAAGATGAAAATACTGTAGCTCT 59.179 38.462 0.00 0.00 0.00 4.09
1929 2005 6.822170 AGGTCGACATATTAAAAGAGGAAACC 59.178 38.462 18.91 0.00 0.00 3.27
1942 2018 1.276421 AGGAAACCGAGGAGTCACATG 59.724 52.381 0.00 0.00 0.00 3.21
2132 2217 2.304180 CCTGGATGTTGAGACTGGAACT 59.696 50.000 0.00 0.00 0.00 3.01
2154 2239 1.805945 CTCGGTGAACACTAGCGCC 60.806 63.158 2.29 0.00 38.76 6.53
2320 2405 7.359595 TGTTGTCTCAATAAACAATGTACAGC 58.640 34.615 0.33 0.00 37.67 4.40
2339 2424 2.158914 AGCATGCGAGTGGATGATGTAA 60.159 45.455 13.01 0.00 45.96 2.41
2340 2425 2.810274 GCATGCGAGTGGATGATGTAAT 59.190 45.455 0.00 0.00 45.96 1.89
2450 2535 3.991773 TGACGTTCTTATTTGGAAGACCG 59.008 43.478 2.15 2.15 44.26 4.79
2524 2609 2.791849 GCTTAAGGAGTACGACAGCGAG 60.792 54.545 4.29 0.00 41.64 5.03
2597 2682 5.814783 AGTGAAGCGCAAATAGATGAATTC 58.185 37.500 11.47 0.00 0.00 2.17
2600 2685 3.554934 AGCGCAAATAGATGAATTCCCA 58.445 40.909 11.47 0.00 0.00 4.37
2682 2767 5.867716 GTGGGCTTGATATAACGAATCGTAT 59.132 40.000 9.30 0.00 39.99 3.06
2687 2772 6.237595 GCTTGATATAACGAATCGTATGCTCC 60.238 42.308 9.30 0.00 39.99 4.70
2848 3173 5.801350 TGAGTTTATTTTCGCCATCTCAG 57.199 39.130 0.00 0.00 0.00 3.35
2926 3251 4.173256 GTGAGGTTGTGTTCTTTTGGTTG 58.827 43.478 0.00 0.00 0.00 3.77
3115 3441 7.543868 CACCAGAGATAAATATACTGTAGCTGC 59.456 40.741 0.00 0.00 0.00 5.25
3186 3513 5.634859 GTCGACGTATTTAAAGAGGAAACCA 59.365 40.000 9.34 0.00 0.00 3.67
3296 3623 9.710900 AATGAACTTTCCTTGATAAAATGTTCC 57.289 29.630 0.00 0.00 32.82 3.62
3407 3734 1.912371 GCTGCAGGCGACAAGGTAAC 61.912 60.000 17.12 0.00 0.00 2.50
3470 3797 7.680442 AACCAAATTGTGCTTAAAACAAAGT 57.320 28.000 7.30 2.26 40.69 2.66
3669 3996 4.998788 GTGAAACTCTTGGCAATATTCCC 58.001 43.478 0.00 0.00 0.00 3.97
3703 4151 1.005924 CCCCCTCTGCCAAGTGTTAAT 59.994 52.381 0.00 0.00 0.00 1.40
3740 4228 6.096036 CAGTATCAGTGACTCTTTGTAGGTG 58.904 44.000 0.00 0.00 0.00 4.00
3979 4484 4.429108 ACCACGCATAATGCAATTAAACC 58.571 39.130 0.00 0.00 45.36 3.27
4200 5020 4.641396 TCAAGTGTAGTAACTGCAAGCAT 58.359 39.130 0.00 0.00 37.60 3.79
4413 5233 6.602803 TGCAGAATGGCAAATCTACTGATAAA 59.397 34.615 5.93 0.00 41.65 1.40
4443 5263 4.963318 TCATAGCCAGCAAGCTTAGTAT 57.037 40.909 0.00 0.00 41.41 2.12
4524 5344 6.975772 AGCTTTTCATTTTTGCTACGTTTGTA 59.024 30.769 0.00 0.00 31.71 2.41
4551 5371 6.289834 ACATCCAGAAATCTATGAGCTCTTG 58.710 40.000 16.19 5.11 0.00 3.02
4590 5410 2.592993 CCTCTGCCTTTCGGGGACA 61.593 63.158 0.00 0.00 35.12 4.02
4600 5420 3.275999 CTTTCGGGGACATAAATCCGTT 58.724 45.455 0.00 0.00 42.71 4.44
4879 5706 2.182842 GGGCAGCTACAATCCAGCG 61.183 63.158 0.00 0.00 43.97 5.18
5038 6094 6.017770 ACAAAGCTAATAAACACGCAACTACA 60.018 34.615 0.00 0.00 0.00 2.74
5101 6157 1.202879 TGGCGACCTGGATTTTTCTGT 60.203 47.619 0.00 0.00 0.00 3.41
5266 6327 8.791327 TGATATGTACATTCAACAGTTGATGT 57.209 30.769 23.37 23.37 46.97 3.06
5323 6385 6.073369 CGAATTATCGCTTGTACATGAATGG 58.927 40.000 12.65 0.00 42.96 3.16
5405 6474 2.493675 GGGCCAGTTCTTCCTTGATTTC 59.506 50.000 4.39 0.00 0.00 2.17
5419 6488 3.385193 TGATTTCACGACAGCTTCTCA 57.615 42.857 0.00 0.00 0.00 3.27
5420 6489 3.320626 TGATTTCACGACAGCTTCTCAG 58.679 45.455 0.00 0.00 0.00 3.35
5422 6491 3.452755 TTTCACGACAGCTTCTCAGAA 57.547 42.857 0.00 0.00 0.00 3.02
5423 6492 3.667497 TTCACGACAGCTTCTCAGAAT 57.333 42.857 0.00 0.00 0.00 2.40
5424 6493 2.951726 TCACGACAGCTTCTCAGAATG 58.048 47.619 0.00 0.00 37.54 2.67
5425 6494 1.392853 CACGACAGCTTCTCAGAATGC 59.607 52.381 0.00 0.00 34.76 3.56
5426 6495 1.274728 ACGACAGCTTCTCAGAATGCT 59.725 47.619 5.75 5.75 34.76 3.79
5430 6503 0.394080 AGCTTCTCAGAATGCTGCCC 60.394 55.000 9.72 0.00 42.01 5.36
5445 6518 1.849823 GCCCCCTCCTATGGCTCAT 60.850 63.158 0.00 0.00 42.01 2.90
5465 6538 3.365265 CTCGTTTGGCACCCAGGC 61.365 66.667 0.00 0.00 44.50 4.85
5474 6547 2.574018 GCACCCAGGCCCAAGTTTC 61.574 63.158 0.00 0.00 0.00 2.78
5475 6548 1.153756 CACCCAGGCCCAAGTTTCT 59.846 57.895 0.00 0.00 0.00 2.52
5488 6561 3.108144 CAAGTTTCTTGTTTGGCTGTCG 58.892 45.455 1.84 0.00 0.00 4.35
5489 6562 1.065551 AGTTTCTTGTTTGGCTGTCGC 59.934 47.619 0.00 0.00 0.00 5.19
6329 7402 2.466846 TCCACGAATGATCCAGAGGAA 58.533 47.619 0.00 0.00 34.34 3.36
6356 7429 9.146984 CATTGAGTAATTGTTGATGCATTTCTT 57.853 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.710013 TTGTTCGCTCAATCGAGGTC 58.290 50.000 0.00 0.00 39.88 3.85
42 43 1.721487 GCCACCCATCGATTGTTCG 59.279 57.895 0.00 0.00 46.87 3.95
46 47 1.714899 GGTTCGCCACCCATCGATTG 61.715 60.000 0.00 0.00 40.19 2.67
47 48 1.451387 GGTTCGCCACCCATCGATT 60.451 57.895 0.00 0.00 40.19 3.34
64 65 0.250553 TCCCTAAGCGTGGTTTGTGG 60.251 55.000 0.00 0.00 0.00 4.17
73 74 0.971447 GTCCACCTCTCCCTAAGCGT 60.971 60.000 0.00 0.00 0.00 5.07
116 117 2.035626 CCTTGAACACCGCCCCAT 59.964 61.111 0.00 0.00 0.00 4.00
124 125 0.318120 CCCATGTTGGCCTTGAACAC 59.682 55.000 9.15 0.00 36.18 3.32
148 149 3.126879 CCACGCCATGCATGTCGT 61.127 61.111 28.29 28.29 35.35 4.34
151 152 2.751436 GTCCCACGCCATGCATGT 60.751 61.111 24.58 4.09 0.00 3.21
175 176 0.883370 ACCGACCAACGCTTTTCTCC 60.883 55.000 0.00 0.00 41.07 3.71
216 217 1.743623 CCTATTGCCGCCGTCAACA 60.744 57.895 0.00 0.00 0.00 3.33
227 228 7.907214 ATATATGTCGTTTTCTCCCTATTGC 57.093 36.000 0.00 0.00 0.00 3.56
260 262 3.942539 TCGTCATCGCCAAAATACATG 57.057 42.857 0.00 0.00 36.96 3.21
262 264 3.124466 CACTTCGTCATCGCCAAAATACA 59.876 43.478 0.00 0.00 36.96 2.29
273 275 2.031314 TCGTCGATACCACTTCGTCATC 59.969 50.000 0.00 0.00 37.82 2.92
288 290 2.756207 TGATCCACCACTAATTCGTCGA 59.244 45.455 0.00 0.00 0.00 4.20
290 292 4.876107 ACATTGATCCACCACTAATTCGTC 59.124 41.667 0.00 0.00 0.00 4.20
293 295 6.949352 ATCACATTGATCCACCACTAATTC 57.051 37.500 0.00 0.00 29.59 2.17
310 312 5.012239 ACAGCAACAATCCACTAATCACAT 58.988 37.500 0.00 0.00 0.00 3.21
312 314 4.726416 CACAGCAACAATCCACTAATCAC 58.274 43.478 0.00 0.00 0.00 3.06
313 315 3.191162 GCACAGCAACAATCCACTAATCA 59.809 43.478 0.00 0.00 0.00 2.57
339 341 4.508662 ACCTTAAGATGTTGAGCACTAGC 58.491 43.478 3.36 0.00 42.56 3.42
382 384 9.729023 CGTCATCTAGACCATCTAATCATAATC 57.271 37.037 0.00 0.00 44.66 1.75
383 385 9.467796 TCGTCATCTAGACCATCTAATCATAAT 57.532 33.333 0.00 0.00 44.66 1.28
384 386 8.863872 TCGTCATCTAGACCATCTAATCATAA 57.136 34.615 0.00 0.00 44.66 1.90
385 387 9.467796 AATCGTCATCTAGACCATCTAATCATA 57.532 33.333 0.00 0.00 44.66 2.15
386 388 7.953005 ATCGTCATCTAGACCATCTAATCAT 57.047 36.000 0.00 0.00 44.66 2.45
387 389 7.767250 AATCGTCATCTAGACCATCTAATCA 57.233 36.000 0.00 0.00 44.66 2.57
388 390 7.543868 CCAAATCGTCATCTAGACCATCTAATC 59.456 40.741 0.00 0.00 44.66 1.75
389 391 7.233553 TCCAAATCGTCATCTAGACCATCTAAT 59.766 37.037 0.00 0.00 44.66 1.73
390 392 6.549736 TCCAAATCGTCATCTAGACCATCTAA 59.450 38.462 0.00 0.00 44.66 2.10
391 393 6.068670 TCCAAATCGTCATCTAGACCATCTA 58.931 40.000 0.00 0.00 44.66 1.98
392 394 4.895889 TCCAAATCGTCATCTAGACCATCT 59.104 41.667 0.00 0.00 44.66 2.90
393 395 5.201713 TCCAAATCGTCATCTAGACCATC 57.798 43.478 0.00 0.00 44.66 3.51
394 396 5.541868 AGATCCAAATCGTCATCTAGACCAT 59.458 40.000 0.00 0.00 44.66 3.55
395 397 4.895889 AGATCCAAATCGTCATCTAGACCA 59.104 41.667 0.00 0.00 44.66 4.02
396 398 5.221342 ACAGATCCAAATCGTCATCTAGACC 60.221 44.000 0.00 0.00 44.66 3.85
397 399 5.837437 ACAGATCCAAATCGTCATCTAGAC 58.163 41.667 0.00 0.00 44.02 2.59
398 400 5.010112 GGACAGATCCAAATCGTCATCTAGA 59.990 44.000 0.00 0.00 45.47 2.43
399 401 5.226396 GGACAGATCCAAATCGTCATCTAG 58.774 45.833 0.00 0.00 45.47 2.43
400 402 5.201713 GGACAGATCCAAATCGTCATCTA 57.798 43.478 0.00 0.00 45.47 1.98
401 403 4.065321 GGACAGATCCAAATCGTCATCT 57.935 45.455 0.00 0.00 45.47 2.90
413 415 9.883142 CCTATAAAAATATGAGAGGACAGATCC 57.117 37.037 0.00 0.00 46.69 3.36
414 416 9.883142 CCCTATAAAAATATGAGAGGACAGATC 57.117 37.037 0.00 0.00 0.00 2.75
415 417 9.621239 TCCCTATAAAAATATGAGAGGACAGAT 57.379 33.333 0.00 0.00 0.00 2.90
416 418 9.621239 ATCCCTATAAAAATATGAGAGGACAGA 57.379 33.333 0.00 0.00 0.00 3.41
419 421 9.825109 GCTATCCCTATAAAAATATGAGAGGAC 57.175 37.037 0.00 0.00 0.00 3.85
420 422 9.560860 TGCTATCCCTATAAAAATATGAGAGGA 57.439 33.333 0.00 0.00 0.00 3.71
421 423 9.829507 CTGCTATCCCTATAAAAATATGAGAGG 57.170 37.037 0.00 0.00 0.00 3.69
430 432 9.693739 TGTTTTCATCTGCTATCCCTATAAAAA 57.306 29.630 0.00 0.00 0.00 1.94
431 433 9.866655 ATGTTTTCATCTGCTATCCCTATAAAA 57.133 29.630 0.00 0.00 35.32 1.52
436 438 9.866655 AAATTATGTTTTCATCTGCTATCCCTA 57.133 29.630 0.00 0.00 41.25 3.53
437 439 8.773033 AAATTATGTTTTCATCTGCTATCCCT 57.227 30.769 0.00 0.00 41.25 4.20
438 440 8.854117 AGAAATTATGTTTTCATCTGCTATCCC 58.146 33.333 5.36 0.00 41.25 3.85
442 444 9.394767 TGCTAGAAATTATGTTTTCATCTGCTA 57.605 29.630 0.00 0.00 41.25 3.49
443 445 8.284945 TGCTAGAAATTATGTTTTCATCTGCT 57.715 30.769 0.00 0.00 41.25 4.24
444 446 9.178427 GATGCTAGAAATTATGTTTTCATCTGC 57.822 33.333 0.00 0.00 41.25 4.26
449 451 9.671279 TCTCAGATGCTAGAAATTATGTTTTCA 57.329 29.630 0.00 0.00 37.93 2.69
451 453 9.118300 CCTCTCAGATGCTAGAAATTATGTTTT 57.882 33.333 0.00 0.00 0.00 2.43
452 454 7.718753 CCCTCTCAGATGCTAGAAATTATGTTT 59.281 37.037 0.00 0.00 0.00 2.83
453 455 7.222872 CCCTCTCAGATGCTAGAAATTATGTT 58.777 38.462 0.00 0.00 0.00 2.71
454 456 6.239829 CCCCTCTCAGATGCTAGAAATTATGT 60.240 42.308 0.00 0.00 0.00 2.29
455 457 6.171921 CCCCTCTCAGATGCTAGAAATTATG 58.828 44.000 0.00 0.00 0.00 1.90
456 458 5.250313 CCCCCTCTCAGATGCTAGAAATTAT 59.750 44.000 0.00 0.00 0.00 1.28
457 459 4.594920 CCCCCTCTCAGATGCTAGAAATTA 59.405 45.833 0.00 0.00 0.00 1.40
458 460 3.393941 CCCCCTCTCAGATGCTAGAAATT 59.606 47.826 0.00 0.00 0.00 1.82
459 461 2.978278 CCCCCTCTCAGATGCTAGAAAT 59.022 50.000 0.00 0.00 0.00 2.17
460 462 2.293184 ACCCCCTCTCAGATGCTAGAAA 60.293 50.000 0.00 0.00 0.00 2.52
461 463 1.292242 ACCCCCTCTCAGATGCTAGAA 59.708 52.381 0.00 0.00 0.00 2.10
462 464 0.937441 ACCCCCTCTCAGATGCTAGA 59.063 55.000 0.00 0.00 0.00 2.43
463 465 1.047002 CACCCCCTCTCAGATGCTAG 58.953 60.000 0.00 0.00 0.00 3.42
464 466 1.050988 GCACCCCCTCTCAGATGCTA 61.051 60.000 0.00 0.00 0.00 3.49
465 467 2.373707 GCACCCCCTCTCAGATGCT 61.374 63.158 0.00 0.00 0.00 3.79
466 468 1.050988 TAGCACCCCCTCTCAGATGC 61.051 60.000 0.00 0.00 0.00 3.91
467 469 1.047002 CTAGCACCCCCTCTCAGATG 58.953 60.000 0.00 0.00 0.00 2.90
468 470 0.762461 GCTAGCACCCCCTCTCAGAT 60.762 60.000 10.63 0.00 0.00 2.90
469 471 1.381872 GCTAGCACCCCCTCTCAGA 60.382 63.158 10.63 0.00 0.00 3.27
470 472 2.790791 CGCTAGCACCCCCTCTCAG 61.791 68.421 16.45 0.00 0.00 3.35
471 473 2.759973 CGCTAGCACCCCCTCTCA 60.760 66.667 16.45 0.00 0.00 3.27
472 474 3.541713 CCGCTAGCACCCCCTCTC 61.542 72.222 16.45 0.00 0.00 3.20
477 479 4.162690 CACTCCCGCTAGCACCCC 62.163 72.222 16.45 0.00 0.00 4.95
478 480 4.162690 CCACTCCCGCTAGCACCC 62.163 72.222 16.45 0.00 0.00 4.61
479 481 2.180159 TTTCCACTCCCGCTAGCACC 62.180 60.000 16.45 0.00 0.00 5.01
480 482 0.107654 ATTTCCACTCCCGCTAGCAC 60.108 55.000 16.45 0.00 0.00 4.40
481 483 0.107703 CATTTCCACTCCCGCTAGCA 60.108 55.000 16.45 0.00 0.00 3.49
482 484 0.178068 TCATTTCCACTCCCGCTAGC 59.822 55.000 4.06 4.06 0.00 3.42
493 495 3.084039 GCACCACTCATTCTCATTTCCA 58.916 45.455 0.00 0.00 0.00 3.53
495 497 4.612932 GAGCACCACTCATTCTCATTTC 57.387 45.455 0.00 0.00 45.49 2.17
560 562 6.474102 TGTCCAAGTTCAAAATTTAAAGACGC 59.526 34.615 0.00 0.00 0.00 5.19
561 563 7.167468 CCTGTCCAAGTTCAAAATTTAAAGACG 59.833 37.037 0.00 0.00 0.00 4.18
563 565 8.299990 TCCTGTCCAAGTTCAAAATTTAAAGA 57.700 30.769 0.00 0.00 0.00 2.52
582 584 7.552687 TGTAATAAGTCAAACATCCATCCTGTC 59.447 37.037 0.00 0.00 0.00 3.51
583 585 7.402054 TGTAATAAGTCAAACATCCATCCTGT 58.598 34.615 0.00 0.00 0.00 4.00
587 589 8.492673 TCACTGTAATAAGTCAAACATCCATC 57.507 34.615 0.00 0.00 0.00 3.51
668 704 6.432403 TCTTTTGCAGGTCCCAAATAAAAT 57.568 33.333 0.00 0.00 32.76 1.82
740 776 5.901413 TCTCCATCCAGCAGATTTCTTAT 57.099 39.130 0.00 0.00 30.59 1.73
918 961 0.041833 CCCTCCTCTTCCCTGACTGA 59.958 60.000 0.00 0.00 0.00 3.41
919 962 0.980231 CCCCTCCTCTTCCCTGACTG 60.980 65.000 0.00 0.00 0.00 3.51
921 964 0.978667 GTCCCCTCCTCTTCCCTGAC 60.979 65.000 0.00 0.00 0.00 3.51
922 965 1.392534 GTCCCCTCCTCTTCCCTGA 59.607 63.158 0.00 0.00 0.00 3.86
923 966 2.060980 CGTCCCCTCCTCTTCCCTG 61.061 68.421 0.00 0.00 0.00 4.45
924 967 2.364961 CGTCCCCTCCTCTTCCCT 59.635 66.667 0.00 0.00 0.00 4.20
925 968 2.764547 CCGTCCCCTCCTCTTCCC 60.765 72.222 0.00 0.00 0.00 3.97
926 969 2.764547 CCCGTCCCCTCCTCTTCC 60.765 72.222 0.00 0.00 0.00 3.46
927 970 1.758906 CTCCCGTCCCCTCCTCTTC 60.759 68.421 0.00 0.00 0.00 2.87
928 971 2.231540 CTCTCCCGTCCCCTCCTCTT 62.232 65.000 0.00 0.00 0.00 2.85
929 972 2.617538 TCTCCCGTCCCCTCCTCT 60.618 66.667 0.00 0.00 0.00 3.69
930 973 2.123640 CTCTCCCGTCCCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
931 974 2.617538 TCTCTCCCGTCCCCTCCT 60.618 66.667 0.00 0.00 0.00 3.69
932 975 2.123640 CTCTCTCCCGTCCCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
942 985 1.064017 TGGCTCCTCTTCTCTCTCTCC 60.064 57.143 0.00 0.00 0.00 3.71
1154 1197 2.088763 CGGATGGATCGGCGAATCG 61.089 63.158 15.93 8.02 0.00 3.34
1177 1220 1.490693 CGATCGATCTGCCCAAACCG 61.491 60.000 22.43 2.74 0.00 4.44
1380 1430 2.287668 CCGGCGTCTCTTAACAGATAGG 60.288 54.545 6.01 0.00 0.00 2.57
1488 1539 2.031157 CACACCATCCTTGTCGAAAACC 60.031 50.000 0.00 0.00 0.00 3.27
1599 1650 3.005554 CTGTCTGTTACAAGCCATGAGG 58.994 50.000 0.00 0.00 37.74 3.86
1602 1653 2.485426 CACCTGTCTGTTACAAGCCATG 59.515 50.000 0.00 0.00 37.74 3.66
1617 1678 2.498167 GCAGACAGAAATGACACCTGT 58.502 47.619 6.67 6.67 43.11 4.00
1641 1702 2.683968 TCGAACTTATGACAGTGCACC 58.316 47.619 14.63 0.00 0.00 5.01
1652 1713 4.706842 ATACCCAGCCAATCGAACTTAT 57.293 40.909 0.00 0.00 0.00 1.73
1740 1808 2.972713 TCAACTTAACCCTCTGAGCACT 59.027 45.455 0.00 0.00 0.00 4.40
1775 1843 1.332997 GCAGAAGGCGAGAAATGGATG 59.667 52.381 0.00 0.00 0.00 3.51
1798 1866 3.202818 ACCCTCTGAACATGCCATCAATA 59.797 43.478 0.00 0.00 0.00 1.90
1885 1961 3.010361 ACCTACCTGTGTAGAGCTACAGT 59.990 47.826 10.42 8.08 46.18 3.55
1894 1970 5.769484 AATATGTCGACCTACCTGTGTAG 57.231 43.478 14.12 0.00 43.46 2.74
1895 1971 7.643569 TTTAATATGTCGACCTACCTGTGTA 57.356 36.000 14.12 0.00 0.00 2.90
1929 2005 1.683385 TGCCTATCATGTGACTCCTCG 59.317 52.381 0.00 0.00 0.00 4.63
1958 2034 3.228453 CCTCCCTGCCTCGTTTAGTATA 58.772 50.000 0.00 0.00 0.00 1.47
2132 2217 1.335597 CGCTAGTGTTCACCGAGTTCA 60.336 52.381 0.00 0.00 0.00 3.18
2320 2405 4.083643 GGAATTACATCATCCACTCGCATG 60.084 45.833 0.00 0.00 33.30 4.06
2360 2445 0.310543 TGTCGCTGAAACATGTTGGC 59.689 50.000 12.82 15.16 0.00 4.52
2450 2535 4.142730 GCTTGGGCGATGATATCATTTCTC 60.143 45.833 19.11 13.71 36.57 2.87
2515 2600 3.257561 CGATTGGGCTCGCTGTCG 61.258 66.667 0.00 0.00 0.00 4.35
2597 2682 6.599244 TCTCACTTATGCTTCACTATTTTGGG 59.401 38.462 0.00 0.00 0.00 4.12
2600 2685 9.160496 CTCTTCTCACTTATGCTTCACTATTTT 57.840 33.333 0.00 0.00 0.00 1.82
2839 2927 3.133721 ACCAATCTAGTCACTGAGATGGC 59.866 47.826 0.00 0.00 32.66 4.40
2845 3170 7.540474 AGAAAGTAACCAATCTAGTCACTGA 57.460 36.000 0.00 0.00 0.00 3.41
2848 3173 7.573283 GCCAAAGAAAGTAACCAATCTAGTCAC 60.573 40.741 0.00 0.00 0.00 3.67
2926 3251 2.762535 TTCAGGAACTCGGGATTGAC 57.237 50.000 0.00 0.00 34.60 3.18
3115 3441 2.705658 TCCAGCATATTCTACCTGTGGG 59.294 50.000 0.00 0.00 38.88 4.61
3186 3513 8.749354 TGATATATGCCTATTATGTGACTCGTT 58.251 33.333 0.00 0.00 0.00 3.85
3223 3550 7.203910 ACTAATGAAAGTAGCCAATCTAGTCG 58.796 38.462 0.00 0.00 38.23 4.18
3296 3623 1.404477 CTTTTGTTTAACCGCCTGCG 58.596 50.000 4.20 4.20 39.44 5.18
3436 3763 5.121811 AGCACAATTTGGTTTGCAATAACA 58.878 33.333 0.00 0.00 37.44 2.41
3523 3850 4.906664 AGAGCTGGAGATATTGAACCATCT 59.093 41.667 0.00 0.00 34.19 2.90
3617 3944 5.705609 TGCTACAAGAAAATGAGTTTCCC 57.294 39.130 1.35 0.00 45.91 3.97
3684 4011 2.514458 ATTAACACTTGGCAGAGGGG 57.486 50.000 4.41 0.00 0.00 4.79
3685 4012 8.157476 ACTATTATATTAACACTTGGCAGAGGG 58.843 37.037 0.00 0.00 0.00 4.30
3720 4208 3.904339 ACCACCTACAAAGAGTCACTGAT 59.096 43.478 0.00 0.00 0.00 2.90
3740 4228 4.134563 TCTCTGGCAAGTACTTCAAAACC 58.865 43.478 4.77 3.43 0.00 3.27
3979 4484 2.695147 GCAAACATGAAATCCTAGGGGG 59.305 50.000 9.46 0.00 0.00 5.40
4413 5233 6.302269 AGCTTGCTGGCTATGAATATAAAGT 58.698 36.000 2.35 0.00 41.16 2.66
4524 5344 5.999044 AGCTCATAGATTTCTGGATGTTGT 58.001 37.500 0.00 0.00 0.00 3.32
4551 5371 2.611292 GAGATGATGTGGCAGCAACTAC 59.389 50.000 0.43 0.00 33.37 2.73
4879 5706 2.229784 CTGCTGATGTTTGAGGGGAAAC 59.770 50.000 0.00 0.00 36.53 2.78
4994 6050 7.704899 AGCTTTGTTGTAATGTTTTGAAGGTAC 59.295 33.333 0.00 0.00 0.00 3.34
5029 6085 2.263077 GAGATCCAGTGTGTAGTTGCG 58.737 52.381 0.00 0.00 0.00 4.85
5038 6094 1.911357 TGAATGCCTGAGATCCAGTGT 59.089 47.619 9.47 0.00 41.33 3.55
5187 6248 7.066284 GGACAAACTACAAGAATGTCTGCATAT 59.934 37.037 12.81 0.00 41.05 1.78
5188 6249 6.371548 GGACAAACTACAAGAATGTCTGCATA 59.628 38.462 12.81 0.00 41.05 3.14
5189 6250 5.182001 GGACAAACTACAAGAATGTCTGCAT 59.818 40.000 12.81 0.00 41.05 3.96
5190 6251 4.515191 GGACAAACTACAAGAATGTCTGCA 59.485 41.667 12.81 0.00 41.05 4.41
5266 6327 1.203758 ACATCGTACAGCACAATCCGA 59.796 47.619 0.00 0.00 0.00 4.55
5323 6385 2.497273 CAAGTCCCAAATCCCAATGGTC 59.503 50.000 0.00 0.00 34.79 4.02
5405 6474 1.392853 GCATTCTGAGAAGCTGTCGTG 59.607 52.381 0.00 0.00 0.00 4.35
5419 6488 0.402566 ATAGGAGGGGGCAGCATTCT 60.403 55.000 0.00 0.00 0.00 2.40
5420 6489 0.251077 CATAGGAGGGGGCAGCATTC 60.251 60.000 0.00 0.00 0.00 2.67
5422 6491 2.158810 CCATAGGAGGGGGCAGCAT 61.159 63.158 0.00 0.00 0.00 3.79
5423 6492 2.773918 CCATAGGAGGGGGCAGCA 60.774 66.667 0.00 0.00 0.00 4.41
5424 6493 4.277009 GCCATAGGAGGGGGCAGC 62.277 72.222 0.00 0.00 46.92 5.25
5430 6503 1.830477 GAGCTATGAGCCATAGGAGGG 59.170 57.143 18.22 0.00 43.77 4.30
5445 6518 1.003839 CTGGGTGCCAAACGAGCTA 60.004 57.895 0.00 0.00 30.80 3.32
5465 6538 2.168313 ACAGCCAAACAAGAAACTTGGG 59.832 45.455 14.51 8.18 40.05 4.12
5470 6543 1.477105 GCGACAGCCAAACAAGAAAC 58.523 50.000 0.00 0.00 37.42 2.78
5474 6547 1.369209 CACGCGACAGCCAAACAAG 60.369 57.895 15.93 0.00 41.18 3.16
5475 6548 2.712539 CACGCGACAGCCAAACAA 59.287 55.556 15.93 0.00 41.18 2.83
6329 7402 8.308931 AGAAATGCATCAACAATTACTCAATGT 58.691 29.630 0.00 0.00 0.00 2.71
6356 7429 1.603236 GCACCGGCAAATTGGGATCA 61.603 55.000 0.00 0.00 40.72 2.92


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

AutoCloner maintained by Alex Coulton.