Multiple sequence alignment - TraesCS5A01G255600

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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 TraesCS5A01G255600 chr5A 100.000 3543 0 0 1 3543 471468689 471465147 0.000000e+00 6543.0
1 TraesCS5A01G255600 chr5A 72.378 677 152 30 2877 3530 616347984 616348648 7.810000e-42 182.0
2 TraesCS5A01G255600 chr5A 77.344 256 44 11 3045 3294 42115533 42115780 4.770000e-29 139.0
3 TraesCS5A01G255600 chr5D 86.495 2673 216 67 930 3541 369066285 369063697 0.000000e+00 2802.0
4 TraesCS5A01G255600 chr5D 90.028 361 30 3 60 415 369066874 369066515 2.490000e-126 462.0
5 TraesCS5A01G255600 chr5D 87.603 121 13 1 779 899 369066529 369066411 4.770000e-29 139.0
6 TraesCS5A01G255600 chr5D 88.333 60 5 2 2511 2568 359472407 359472348 1.760000e-08 71.3
7 TraesCS5A01G255600 chr5B 87.629 1835 125 47 779 2562 437563993 437562210 0.000000e+00 2037.0
8 TraesCS5A01G255600 chr5B 82.413 887 97 31 2358 3214 437555532 437554675 0.000000e+00 719.0
9 TraesCS5A01G255600 chr5B 89.130 414 38 5 7 415 437564390 437563979 3.160000e-140 508.0
10 TraesCS5A01G255600 chr5B 85.356 239 35 0 3303 3541 437554383 437554145 7.600000e-62 248.0
11 TraesCS5A01G255600 chr5B 72.381 630 153 18 2877 3494 608540142 608540762 2.810000e-41 180.0
12 TraesCS5A01G255600 chr5B 88.333 60 5 2 2511 2568 367076371 367076312 1.760000e-08 71.3
13 TraesCS5A01G255600 chr6D 84.590 305 28 12 1967 2265 441894979 441895270 5.790000e-73 285.0
14 TraesCS5A01G255600 chr6B 82.036 334 32 16 1973 2296 667895403 667895718 3.510000e-65 259.0
15 TraesCS5A01G255600 chr6A 91.176 170 15 0 1973 2142 591263103 591263272 7.650000e-57 231.0
16 TraesCS5A01G255600 chr6A 78.635 337 61 9 2875 3206 445609915 445610245 2.770000e-51 213.0
17 TraesCS5A01G255600 chr6A 85.827 127 8 5 2184 2302 591263561 591263685 3.710000e-25 126.0
18 TraesCS5A01G255600 chr3D 77.744 328 62 8 2894 3212 531432058 531431733 1.300000e-44 191.0
19 TraesCS5A01G255600 chr3D 80.894 246 36 8 3057 3293 37764988 37765231 2.170000e-42 183.0
20 TraesCS5A01G255600 chr3D 100.000 35 0 0 2528 2562 21365356 21365390 8.210000e-07 65.8
21 TraesCS5A01G255600 chr3B 76.829 328 65 9 2894 3212 703029573 703029248 1.310000e-39 174.0
22 TraesCS5A01G255600 chr3A 77.090 323 60 10 2883 3197 635122871 635122555 1.310000e-39 174.0
23 TraesCS5A01G255600 chr7A 75.862 319 71 6 2980 3294 128403443 128403759 1.320000e-34 158.0
24 TraesCS5A01G255600 chr7A 89.655 58 4 2 2511 2568 209155544 209155599 4.910000e-09 73.1
25 TraesCS5A01G255600 chr2D 77.632 228 48 2 3069 3294 13480963 13481189 6.170000e-28 135.0
26 TraesCS5A01G255600 chr7D 100.000 40 0 0 2529 2568 199355658 199355697 1.360000e-09 75.0
27 TraesCS5A01G255600 chr7B 89.091 55 5 1 2514 2568 522816797 522816850 2.280000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G255600 chr5A 471465147 471468689 3542 True 6543.000000 6543 100.0000 1 3543 1 chr5A.!!$R1 3542
1 TraesCS5A01G255600 chr5D 369063697 369066874 3177 True 1134.333333 2802 88.0420 60 3541 3 chr5D.!!$R2 3481
2 TraesCS5A01G255600 chr5B 437562210 437564390 2180 True 1272.500000 2037 88.3795 7 2562 2 chr5B.!!$R3 2555
3 TraesCS5A01G255600 chr5B 437554145 437555532 1387 True 483.500000 719 83.8845 2358 3541 2 chr5B.!!$R2 1183

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
30 31 1.170919 GCGCATGAGCAATCATCCCT 61.171 55.0 17.16 0.0 42.27 4.20 F
1029 1144 0.109179 TGTGAAGCCAAATGCATCGC 60.109 50.0 0.00 2.1 45.81 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1708 0.459237 CATGTCTCCGGAGCTGTGTC 60.459 60.0 27.39 12.05 0.0 3.67 R
2812 2991 0.178992 TTGGGCAGGAAGTTGGTCAG 60.179 55.0 0.00 0.00 0.0 3.51 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
22 23 2.993220 CCTAATATACGCGCATGAGCAA 59.007 45.455 21.59 9.02 42.27 3.91
26 27 1.516161 ATACGCGCATGAGCAATCAT 58.484 45.000 21.59 5.37 42.27 2.45
29 30 1.285023 GCGCATGAGCAATCATCCC 59.715 57.895 17.16 0.00 42.27 3.85
30 31 1.170919 GCGCATGAGCAATCATCCCT 61.171 55.000 17.16 0.00 42.27 4.20
33 34 2.418976 CGCATGAGCAATCATCCCTATG 59.581 50.000 0.00 0.00 42.27 2.23
43 44 5.335740 GCAATCATCCCTATGAGCATTTCAG 60.336 44.000 0.00 0.00 45.17 3.02
56 57 5.653330 TGAGCATTTCAGCCTCATAATTGAA 59.347 36.000 0.00 0.00 34.23 2.69
57 58 6.145338 AGCATTTCAGCCTCATAATTGAAG 57.855 37.500 0.00 0.00 31.85 3.02
58 59 5.889853 AGCATTTCAGCCTCATAATTGAAGA 59.110 36.000 0.00 0.00 31.85 2.87
81 82 7.588512 AGAGAACATTGTCAAACATAGAAAGC 58.411 34.615 0.00 0.00 0.00 3.51
185 190 2.264005 TTGGTTGCGGTAATGACACT 57.736 45.000 0.00 0.00 0.00 3.55
187 192 2.967362 TGGTTGCGGTAATGACACTAG 58.033 47.619 0.00 0.00 0.00 2.57
191 196 5.360429 TGGTTGCGGTAATGACACTAGTATA 59.640 40.000 0.00 0.00 0.00 1.47
332 337 8.254508 ACCATCTATGACTAAGTCAGACTTTTC 58.745 37.037 21.05 16.88 46.04 2.29
408 414 3.906660 GGAGACGACACCATGAACA 57.093 52.632 0.00 0.00 0.00 3.18
409 415 2.386661 GGAGACGACACCATGAACAT 57.613 50.000 0.00 0.00 0.00 2.71
410 416 2.002586 GGAGACGACACCATGAACATG 58.997 52.381 7.70 7.70 38.51 3.21
425 431 7.578310 CATGAACATGGAGAAAATATCAGGT 57.422 36.000 6.87 0.00 35.24 4.00
426 432 7.423199 CATGAACATGGAGAAAATATCAGGTG 58.577 38.462 6.87 0.00 35.24 4.00
427 433 5.357878 TGAACATGGAGAAAATATCAGGTGC 59.642 40.000 0.00 0.00 0.00 5.01
428 434 5.121380 ACATGGAGAAAATATCAGGTGCT 57.879 39.130 0.00 0.00 0.00 4.40
429 435 6.252599 ACATGGAGAAAATATCAGGTGCTA 57.747 37.500 0.00 0.00 0.00 3.49
430 436 6.058183 ACATGGAGAAAATATCAGGTGCTAC 58.942 40.000 0.00 0.00 0.00 3.58
431 437 5.036117 TGGAGAAAATATCAGGTGCTACC 57.964 43.478 0.00 0.00 38.99 3.18
432 438 4.473196 TGGAGAAAATATCAGGTGCTACCA 59.527 41.667 7.86 0.00 41.95 3.25
433 439 5.059833 GGAGAAAATATCAGGTGCTACCAG 58.940 45.833 7.86 0.67 41.95 4.00
434 440 4.455606 AGAAAATATCAGGTGCTACCAGC 58.544 43.478 7.86 0.00 41.95 4.85
436 442 3.760580 AATATCAGGTGCTACCAGCTC 57.239 47.619 7.86 0.00 46.22 4.09
437 443 2.461300 TATCAGGTGCTACCAGCTCT 57.539 50.000 7.86 0.00 46.22 4.09
438 444 1.577736 ATCAGGTGCTACCAGCTCTT 58.422 50.000 7.86 0.00 46.22 2.85
439 445 2.231716 TCAGGTGCTACCAGCTCTTA 57.768 50.000 7.86 0.00 46.22 2.10
440 446 2.752030 TCAGGTGCTACCAGCTCTTAT 58.248 47.619 7.86 0.00 46.22 1.73
441 447 3.910989 TCAGGTGCTACCAGCTCTTATA 58.089 45.455 7.86 0.00 46.22 0.98
442 448 4.483950 TCAGGTGCTACCAGCTCTTATAT 58.516 43.478 7.86 0.00 46.22 0.86
443 449 4.281941 TCAGGTGCTACCAGCTCTTATATG 59.718 45.833 7.86 0.00 46.22 1.78
444 450 3.007398 AGGTGCTACCAGCTCTTATATGC 59.993 47.826 7.86 0.00 46.22 3.14
445 451 3.007398 GGTGCTACCAGCTCTTATATGCT 59.993 47.826 0.00 0.00 42.97 3.79
446 452 4.220821 GGTGCTACCAGCTCTTATATGCTA 59.779 45.833 0.00 0.00 42.97 3.49
447 453 5.164954 GTGCTACCAGCTCTTATATGCTAC 58.835 45.833 0.00 0.00 42.97 3.58
448 454 4.220821 TGCTACCAGCTCTTATATGCTACC 59.779 45.833 0.00 0.00 42.97 3.18
449 455 4.220821 GCTACCAGCTCTTATATGCTACCA 59.779 45.833 0.00 0.00 38.45 3.25
450 456 5.105146 GCTACCAGCTCTTATATGCTACCAT 60.105 44.000 0.00 0.00 38.45 3.55
451 457 5.157940 ACCAGCTCTTATATGCTACCATG 57.842 43.478 0.00 0.00 37.81 3.66
452 458 4.840680 ACCAGCTCTTATATGCTACCATGA 59.159 41.667 0.00 0.00 37.81 3.07
453 459 5.486775 ACCAGCTCTTATATGCTACCATGAT 59.513 40.000 0.00 0.00 37.81 2.45
454 460 6.669591 ACCAGCTCTTATATGCTACCATGATA 59.330 38.462 0.00 0.00 37.81 2.15
455 461 6.983307 CCAGCTCTTATATGCTACCATGATAC 59.017 42.308 0.00 0.00 37.81 2.24
456 462 6.983307 CAGCTCTTATATGCTACCATGATACC 59.017 42.308 0.00 0.00 37.81 2.73
457 463 6.669591 AGCTCTTATATGCTACCATGATACCA 59.330 38.462 0.00 0.00 37.81 3.25
458 464 7.180946 AGCTCTTATATGCTACCATGATACCAA 59.819 37.037 0.00 0.00 37.81 3.67
459 465 7.824289 GCTCTTATATGCTACCATGATACCAAA 59.176 37.037 0.00 0.00 32.85 3.28
460 466 9.896645 CTCTTATATGCTACCATGATACCAAAT 57.103 33.333 0.00 0.00 32.85 2.32
464 470 8.938801 ATATGCTACCATGATACCAAATTCAA 57.061 30.769 0.00 0.00 32.85 2.69
465 471 7.658525 ATGCTACCATGATACCAAATTCAAA 57.341 32.000 0.00 0.00 0.00 2.69
466 472 7.473735 TGCTACCATGATACCAAATTCAAAA 57.526 32.000 0.00 0.00 0.00 2.44
467 473 7.901029 TGCTACCATGATACCAAATTCAAAAA 58.099 30.769 0.00 0.00 0.00 1.94
468 474 8.538701 TGCTACCATGATACCAAATTCAAAAAT 58.461 29.630 0.00 0.00 0.00 1.82
469 475 9.382275 GCTACCATGATACCAAATTCAAAAATT 57.618 29.630 0.00 0.00 36.64 1.82
472 478 9.790344 ACCATGATACCAAATTCAAAAATTCAA 57.210 25.926 0.00 0.00 33.93 2.69
531 537 4.508662 TGTTCACAACATATATGGCGACA 58.491 39.130 16.96 0.00 40.21 4.35
532 538 4.938226 TGTTCACAACATATATGGCGACAA 59.062 37.500 16.96 1.80 39.57 3.18
533 539 5.588246 TGTTCACAACATATATGGCGACAAT 59.412 36.000 16.96 0.00 39.57 2.71
534 540 6.238347 TGTTCACAACATATATGGCGACAATC 60.238 38.462 16.96 2.56 39.57 2.67
535 541 9.063031 TGTTCACAACATATATGGCGACAATCC 62.063 40.741 16.96 0.00 39.57 3.01
543 549 2.588464 TGGCGACAATCCCCTAAAAA 57.412 45.000 0.00 0.00 37.44 1.94
578 584 8.771920 AAAATCGACATACACATAGAGAAACA 57.228 30.769 0.00 0.00 0.00 2.83
579 585 8.771920 AAATCGACATACACATAGAGAAACAA 57.228 30.769 0.00 0.00 0.00 2.83
580 586 8.771920 AATCGACATACACATAGAGAAACAAA 57.228 30.769 0.00 0.00 0.00 2.83
581 587 8.771920 ATCGACATACACATAGAGAAACAAAA 57.228 30.769 0.00 0.00 0.00 2.44
582 588 8.596271 TCGACATACACATAGAGAAACAAAAA 57.404 30.769 0.00 0.00 0.00 1.94
620 626 9.280174 TGATTAATAGTCTTTTTGTTTCTCCGT 57.720 29.630 0.00 0.00 0.00 4.69
621 627 9.543018 GATTAATAGTCTTTTTGTTTCTCCGTG 57.457 33.333 0.00 0.00 0.00 4.94
622 628 6.937436 AATAGTCTTTTTGTTTCTCCGTGT 57.063 33.333 0.00 0.00 0.00 4.49
623 629 9.545105 TTAATAGTCTTTTTGTTTCTCCGTGTA 57.455 29.630 0.00 0.00 0.00 2.90
624 630 8.617290 AATAGTCTTTTTGTTTCTCCGTGTAT 57.383 30.769 0.00 0.00 0.00 2.29
625 631 9.715121 AATAGTCTTTTTGTTTCTCCGTGTATA 57.285 29.630 0.00 0.00 0.00 1.47
626 632 9.886132 ATAGTCTTTTTGTTTCTCCGTGTATAT 57.114 29.630 0.00 0.00 0.00 0.86
627 633 8.617290 AGTCTTTTTGTTTCTCCGTGTATATT 57.383 30.769 0.00 0.00 0.00 1.28
628 634 9.063615 AGTCTTTTTGTTTCTCCGTGTATATTT 57.936 29.630 0.00 0.00 0.00 1.40
629 635 9.673454 GTCTTTTTGTTTCTCCGTGTATATTTT 57.327 29.630 0.00 0.00 0.00 1.82
630 636 9.672086 TCTTTTTGTTTCTCCGTGTATATTTTG 57.328 29.630 0.00 0.00 0.00 2.44
631 637 9.672086 CTTTTTGTTTCTCCGTGTATATTTTGA 57.328 29.630 0.00 0.00 0.00 2.69
673 679 8.989653 TTTAGTCGTTGTCAACATATATGTCA 57.010 30.769 18.52 9.87 40.80 3.58
674 680 9.594478 TTTAGTCGTTGTCAACATATATGTCAT 57.406 29.630 18.52 1.42 40.80 3.06
675 681 7.468922 AGTCGTTGTCAACATATATGTCATG 57.531 36.000 18.52 13.89 40.80 3.07
676 682 7.264947 AGTCGTTGTCAACATATATGTCATGA 58.735 34.615 18.52 15.86 40.80 3.07
677 683 7.763985 AGTCGTTGTCAACATATATGTCATGAA 59.236 33.333 18.52 7.37 40.80 2.57
678 684 7.846107 GTCGTTGTCAACATATATGTCATGAAC 59.154 37.037 18.52 16.14 40.80 3.18
679 685 7.547370 TCGTTGTCAACATATATGTCATGAACA 59.453 33.333 18.52 15.13 40.80 3.18
681 687 9.655769 GTTGTCAACATATATGTCATGAACATC 57.344 33.333 18.52 13.44 45.78 3.06
682 688 8.382030 TGTCAACATATATGTCATGAACATCC 57.618 34.615 18.52 8.07 45.78 3.51
683 689 7.992033 TGTCAACATATATGTCATGAACATCCA 59.008 33.333 18.52 10.20 45.78 3.41
684 690 9.006839 GTCAACATATATGTCATGAACATCCAT 57.993 33.333 18.52 7.34 45.78 3.41
685 691 9.005777 TCAACATATATGTCATGAACATCCATG 57.994 33.333 18.52 15.84 45.78 3.66
686 692 9.005777 CAACATATATGTCATGAACATCCATGA 57.994 33.333 18.52 0.00 45.78 3.07
760 766 9.935241 GGTATCATGGTAGCATATAAGATATGG 57.065 37.037 10.32 0.00 0.00 2.74
811 817 4.497507 GGTGACTTGTTTCAAGCTTGTACC 60.498 45.833 25.19 9.98 0.00 3.34
821 827 4.638304 TCAAGCTTGTACCTACCTTTGTC 58.362 43.478 25.19 0.00 0.00 3.18
827 833 5.742255 GCTTGTACCTACCTTTGTCTCAAGT 60.742 44.000 0.00 0.00 33.33 3.16
829 835 6.243216 TGTACCTACCTTTGTCTCAAGTTT 57.757 37.500 0.00 0.00 0.00 2.66
885 892 4.600692 ACGTACCTATTGATGCATAGCA 57.399 40.909 0.00 0.00 44.86 3.49
920 1031 1.633561 CGTCTCGTCATCATGCAAGT 58.366 50.000 0.00 0.00 0.00 3.16
921 1032 1.995484 CGTCTCGTCATCATGCAAGTT 59.005 47.619 0.00 0.00 0.00 2.66
922 1033 2.413112 CGTCTCGTCATCATGCAAGTTT 59.587 45.455 0.00 0.00 0.00 2.66
923 1034 3.120546 CGTCTCGTCATCATGCAAGTTTT 60.121 43.478 0.00 0.00 0.00 2.43
924 1035 4.398247 GTCTCGTCATCATGCAAGTTTTC 58.602 43.478 0.00 0.00 0.00 2.29
925 1036 4.153117 GTCTCGTCATCATGCAAGTTTTCT 59.847 41.667 0.00 0.00 0.00 2.52
926 1037 4.389992 TCTCGTCATCATGCAAGTTTTCTC 59.610 41.667 0.00 0.00 0.00 2.87
927 1038 4.318332 TCGTCATCATGCAAGTTTTCTCT 58.682 39.130 0.00 0.00 0.00 3.10
928 1039 4.389992 TCGTCATCATGCAAGTTTTCTCTC 59.610 41.667 0.00 0.00 0.00 3.20
943 1054 8.298729 AGTTTTCTCTCTTTTCCTTTTGACAT 57.701 30.769 0.00 0.00 0.00 3.06
962 1073 4.940463 ACATATTTCATTGGCATGACAGC 58.060 39.130 0.00 0.00 39.28 4.40
1029 1144 0.109179 TGTGAAGCCAAATGCATCGC 60.109 50.000 0.00 2.10 45.81 4.58
1096 1215 0.174845 TCGGAGTTAATGGACAGCCG 59.825 55.000 0.00 0.00 39.52 5.52
1107 1226 4.322385 ACAGCCGCCGCGAAAAAC 62.322 61.111 15.93 0.00 41.18 2.43
1154 1276 6.088824 CAGATCACTTATTTCACAAGCAACC 58.911 40.000 0.00 0.00 0.00 3.77
1196 1318 3.186909 CGTCCACGAAGCAATTCTATCA 58.813 45.455 0.00 0.00 43.02 2.15
1200 1322 3.689161 CCACGAAGCAATTCTATCAACCA 59.311 43.478 0.00 0.00 0.00 3.67
1207 1329 4.082245 AGCAATTCTATCAACCAAAACCCG 60.082 41.667 0.00 0.00 0.00 5.28
1225 1347 2.416547 CCCGCGATTATTCCTTAGCATG 59.583 50.000 8.23 0.00 0.00 4.06
1226 1348 3.067106 CCGCGATTATTCCTTAGCATGT 58.933 45.455 8.23 0.00 0.00 3.21
1244 1366 2.561569 TGTCGCGAGAGATATCACTCA 58.438 47.619 24.20 7.54 43.49 3.41
1253 1375 4.885413 AGAGATATCACTCAGATGCAAGC 58.115 43.478 5.32 0.00 39.14 4.01
1281 1404 8.421784 AGAAAAAGAAGATTGTTAAACCTTCCC 58.578 33.333 0.00 0.00 36.57 3.97
1301 1424 2.433436 CTCCTTTTACTTCCCAACCCG 58.567 52.381 0.00 0.00 0.00 5.28
1351 1475 2.099098 GCCACCCATGATAAAGAAACCG 59.901 50.000 0.00 0.00 0.00 4.44
1376 1500 3.055591 CACATTAGCAGGAGCAGTATCG 58.944 50.000 0.00 0.00 45.49 2.92
1390 1514 2.609459 CAGTATCGAACAAGCACATCCC 59.391 50.000 0.00 0.00 0.00 3.85
1402 1526 1.607509 GCACATCCCGATCCATCTGAG 60.608 57.143 0.00 0.00 0.00 3.35
1408 1532 0.317799 CCGATCCATCTGAGCTCCTG 59.682 60.000 12.15 6.17 0.00 3.86
1411 1535 2.299582 CGATCCATCTGAGCTCCTGATT 59.700 50.000 12.15 0.58 32.03 2.57
1413 1537 1.685517 TCCATCTGAGCTCCTGATTCG 59.314 52.381 12.15 7.58 32.03 3.34
1421 1545 1.410882 AGCTCCTGATTCGAAGCTACC 59.589 52.381 15.31 0.00 43.04 3.18
1422 1546 1.866063 GCTCCTGATTCGAAGCTACCG 60.866 57.143 15.31 2.33 0.00 4.02
1525 1649 2.014554 GCGCTGTTCGTCGTCAGAA 61.015 57.895 18.61 0.00 41.07 3.02
1584 1708 4.436998 GTGCAGGACTCCGGTCGG 62.437 72.222 0.00 2.52 42.97 4.79
1607 1731 2.512515 GCTCCGGAGACATGGCAC 60.513 66.667 35.69 10.76 0.00 5.01
1608 1732 3.023949 GCTCCGGAGACATGGCACT 62.024 63.158 35.69 0.00 0.00 4.40
1609 1733 1.153489 CTCCGGAGACATGGCACTG 60.153 63.158 28.21 0.00 0.00 3.66
1610 1734 2.124983 CCGGAGACATGGCACTGG 60.125 66.667 9.70 9.70 0.00 4.00
1611 1735 2.821366 CGGAGACATGGCACTGGC 60.821 66.667 0.00 0.00 40.13 4.85
1612 1736 2.352422 GGAGACATGGCACTGGCA 59.648 61.111 7.88 7.88 43.71 4.92
1680 1807 0.463204 CGCTGGACAGGATGATCACT 59.537 55.000 0.00 0.00 39.69 3.41
1763 1890 4.702826 GTTGCGCACGCGTCAGAC 62.703 66.667 11.12 0.00 45.51 3.51
2296 2436 1.638529 CACAACTCTCAGGGACCTCT 58.361 55.000 0.00 0.00 0.00 3.69
2408 2562 7.742525 CGAGTATATCAATGTTCTAGTGTCGAG 59.257 40.741 0.00 0.00 0.00 4.04
2423 2577 2.552315 TGTCGAGAAATTGTTTGGAGGC 59.448 45.455 0.00 0.00 0.00 4.70
2445 2599 4.499696 GCCTTCACTGTAACATTGCAACTT 60.500 41.667 0.00 0.00 0.00 2.66
2446 2600 5.278266 GCCTTCACTGTAACATTGCAACTTA 60.278 40.000 0.00 0.00 0.00 2.24
2447 2601 6.142817 CCTTCACTGTAACATTGCAACTTAC 58.857 40.000 16.77 16.77 0.00 2.34
2483 2637 2.430921 GATGATAGGGCGCGGACG 60.431 66.667 8.83 0.00 44.07 4.79
2513 2685 6.263168 CCATGTCCCCTAATTGTCTGTATTTC 59.737 42.308 0.00 0.00 0.00 2.17
2543 2718 9.168451 TCTAATTCCGCAACACTCAAAATAATA 57.832 29.630 0.00 0.00 0.00 0.98
2569 2744 8.757982 ATAGAAAATAGCACAATTCATCCACT 57.242 30.769 0.00 0.00 0.00 4.00
2570 2745 7.472334 AGAAAATAGCACAATTCATCCACTT 57.528 32.000 0.00 0.00 0.00 3.16
2571 2746 7.899973 AGAAAATAGCACAATTCATCCACTTT 58.100 30.769 0.00 0.00 0.00 2.66
2572 2747 8.370182 AGAAAATAGCACAATTCATCCACTTTT 58.630 29.630 0.00 0.00 0.00 2.27
2573 2748 8.907222 AAAATAGCACAATTCATCCACTTTTT 57.093 26.923 0.00 0.00 0.00 1.94
2623 2801 5.947228 TCAGGATGTTCACAAGAATTCAC 57.053 39.130 8.44 0.00 35.92 3.18
2646 2824 5.122396 ACTGATTTTGAATTCAGCGGTACTC 59.878 40.000 8.41 1.68 42.51 2.59
2683 2861 5.693104 ACACATGTCGTTTCGTACATAGTTT 59.307 36.000 0.00 0.00 34.61 2.66
2691 2869 7.113965 GTCGTTTCGTACATAGTTTCTCTTGAA 59.886 37.037 0.00 0.00 0.00 2.69
2700 2878 7.963532 ACATAGTTTCTCTTGAACTTCACCTA 58.036 34.615 0.00 0.00 31.02 3.08
2705 2883 7.775561 AGTTTCTCTTGAACTTCACCTAACAAT 59.224 33.333 0.00 0.00 31.02 2.71
2730 2908 2.987752 GCGTAAATAGCTCGCCCTT 58.012 52.632 5.49 0.00 43.41 3.95
2731 2909 0.582005 GCGTAAATAGCTCGCCCTTG 59.418 55.000 5.49 0.00 43.41 3.61
2733 2911 1.472728 CGTAAATAGCTCGCCCTTGGT 60.473 52.381 0.00 0.00 0.00 3.67
2748 2926 2.904434 CCTTGGTCTTGTAGTACAGGGT 59.096 50.000 12.06 0.00 0.00 4.34
2760 2939 1.116536 TACAGGGTGACAAGCGTCCA 61.117 55.000 0.00 0.00 41.85 4.02
2795 2974 5.634859 CCTGATGGTTATCAAGTTGCAAAAC 59.365 40.000 0.00 0.13 42.48 2.43
2812 2991 7.928908 TGCAAAACTGAGTGAATCAATAAAC 57.071 32.000 0.00 0.00 37.52 2.01
2814 2993 7.648908 TGCAAAACTGAGTGAATCAATAAACTG 59.351 33.333 0.00 0.00 37.52 3.16
2815 2994 7.862372 GCAAAACTGAGTGAATCAATAAACTGA 59.138 33.333 0.00 0.00 37.52 3.41
2816 2995 9.173939 CAAAACTGAGTGAATCAATAAACTGAC 57.826 33.333 0.00 0.00 37.52 3.51
2818 2997 6.533730 ACTGAGTGAATCAATAAACTGACCA 58.466 36.000 0.00 0.00 37.52 4.02
2820 2999 7.041098 ACTGAGTGAATCAATAAACTGACCAAC 60.041 37.037 0.00 0.00 37.52 3.77
2821 3000 6.998074 TGAGTGAATCAATAAACTGACCAACT 59.002 34.615 0.00 0.00 34.02 3.16
2822 3001 7.502226 TGAGTGAATCAATAAACTGACCAACTT 59.498 33.333 0.00 0.00 34.02 2.66
2823 3002 7.875971 AGTGAATCAATAAACTGACCAACTTC 58.124 34.615 0.00 0.00 0.00 3.01
2826 3005 6.824305 ATCAATAAACTGACCAACTTCCTG 57.176 37.500 0.00 0.00 0.00 3.86
2827 3006 4.518970 TCAATAAACTGACCAACTTCCTGC 59.481 41.667 0.00 0.00 0.00 4.85
2828 3007 1.692411 AAACTGACCAACTTCCTGCC 58.308 50.000 0.00 0.00 0.00 4.85
2829 3008 0.178990 AACTGACCAACTTCCTGCCC 60.179 55.000 0.00 0.00 0.00 5.36
2830 3009 1.352622 ACTGACCAACTTCCTGCCCA 61.353 55.000 0.00 0.00 0.00 5.36
2833 3012 1.342474 TGACCAACTTCCTGCCCAAAA 60.342 47.619 0.00 0.00 0.00 2.44
2905 3084 1.208052 CCGATGGTCACATTGTCTCCT 59.792 52.381 7.86 0.00 37.47 3.69
2920 3099 1.067565 TCTCCTCTCGTGCAATCACAC 60.068 52.381 0.00 0.00 43.28 3.82
2922 3101 0.320683 CCTCTCGTGCAATCACACCA 60.321 55.000 0.00 0.00 43.28 4.17
2938 3117 4.644234 TCACACCACAAAACTTCATGACAT 59.356 37.500 0.00 0.00 0.00 3.06
2960 3139 3.513912 TCGTTGGAGATGATGTACAACCT 59.486 43.478 11.56 0.00 38.46 3.50
2961 3140 3.618594 CGTTGGAGATGATGTACAACCTG 59.381 47.826 11.56 0.00 38.46 4.00
2983 3162 6.164408 TGATACGTTAGTGACTTTGCATTG 57.836 37.500 0.00 0.00 0.00 2.82
2988 3167 2.869233 AGTGACTTTGCATTGCGTTT 57.131 40.000 3.84 0.00 0.00 3.60
2991 3170 5.621197 AGTGACTTTGCATTGCGTTTATA 57.379 34.783 3.84 0.00 0.00 0.98
2997 3176 7.031226 ACTTTGCATTGCGTTTATAGATGAT 57.969 32.000 3.84 0.00 0.00 2.45
3009 3188 6.292328 CGTTTATAGATGATGTGCATGTCGTT 60.292 38.462 0.00 0.00 37.34 3.85
3013 3192 0.250684 TGATGTGCATGTCGTTGGGT 60.251 50.000 0.00 0.00 0.00 4.51
3092 3272 4.273480 CCTTGTTCATGCCTATAAAGTCCG 59.727 45.833 0.00 0.00 0.00 4.79
3095 3275 3.111853 TCATGCCTATAAAGTCCGCAG 57.888 47.619 0.00 0.00 32.06 5.18
3100 3280 3.243336 GCCTATAAAGTCCGCAGATACG 58.757 50.000 0.00 0.00 0.00 3.06
3130 3310 2.223845 CGCATCACACAACAACTCATCA 59.776 45.455 0.00 0.00 0.00 3.07
3136 3316 7.626876 GCATCACACAACAACTCATCATCAATA 60.627 37.037 0.00 0.00 0.00 1.90
3142 3322 6.092670 ACAACAACTCATCATCAATAACCGAG 59.907 38.462 0.00 0.00 0.00 4.63
3146 3326 6.465439 ACTCATCATCAATAACCGAGTACA 57.535 37.500 0.00 0.00 30.79 2.90
3155 3335 2.278596 CCGAGTACACCGCCATCG 60.279 66.667 0.00 0.00 0.00 3.84
3182 3365 6.404293 GCTTACTCCAGAAAACAACAAGTTCA 60.404 38.462 0.00 0.00 40.26 3.18
3217 3402 7.965107 GCTCAATAACATTTGACTAAAGACCTG 59.035 37.037 0.00 0.00 32.39 4.00
3218 3403 8.918202 TCAATAACATTTGACTAAAGACCTGT 57.082 30.769 0.00 0.00 30.82 4.00
3219 3404 8.999431 TCAATAACATTTGACTAAAGACCTGTC 58.001 33.333 0.00 0.00 30.82 3.51
3222 3407 3.396260 TTTGACTAAAGACCTGTCGGG 57.604 47.619 0.00 0.00 41.89 5.14
3223 3408 0.606604 TGACTAAAGACCTGTCGGGC 59.393 55.000 0.00 0.00 39.31 6.13
3238 3423 4.367023 GGCGTGGTGTCTGCCGTA 62.367 66.667 0.00 0.00 39.30 4.02
3263 3449 4.137615 TCGAGAGGGGGCGGATGA 62.138 66.667 0.00 0.00 0.00 2.92
3275 3461 1.447217 CGGATGATACCTGGCTGCA 59.553 57.895 0.50 0.00 0.00 4.41
3283 3469 1.050988 TACCTGGCTGCAGAGGGATC 61.051 60.000 20.43 0.00 33.16 3.36
3288 3474 3.117452 GCTGCAGAGGGATCCTGGG 62.117 68.421 20.43 0.25 31.76 4.45
3300 3486 4.033776 CCTGGGTGGACCGCATGT 62.034 66.667 7.48 0.00 44.64 3.21
3323 3711 3.642503 CGTGGGTGGGGGCTGTAA 61.643 66.667 0.00 0.00 0.00 2.41
3325 3713 1.605451 GTGGGTGGGGGCTGTAAAC 60.605 63.158 0.00 0.00 0.00 2.01
3328 3716 1.673337 GGTGGGGGCTGTAAACGTC 60.673 63.158 0.00 0.00 0.00 4.34
3329 3717 1.373812 GTGGGGGCTGTAAACGTCT 59.626 57.895 0.00 0.00 0.00 4.18
3330 3718 0.953960 GTGGGGGCTGTAAACGTCTG 60.954 60.000 0.00 0.00 0.00 3.51
3344 3732 3.473647 TCTGAGGATGCCTGGGCG 61.474 66.667 7.14 0.00 45.51 6.13
3370 3758 1.673808 GGAGAGGTACAACGGCGGAT 61.674 60.000 13.24 0.00 0.00 4.18
3372 3760 1.520787 GAGGTACAACGGCGGATGG 60.521 63.158 13.24 0.00 0.00 3.51
3397 3785 0.114954 ATGAAAGCAAGGGGGAGCAA 59.885 50.000 0.00 0.00 0.00 3.91
3401 3789 3.984732 GCAAGGGGGAGCAAGGGT 61.985 66.667 0.00 0.00 0.00 4.34
3402 3790 2.036256 CAAGGGGGAGCAAGGGTG 59.964 66.667 0.00 0.00 0.00 4.61
3440 3828 3.375699 GACTGGGAGGGAGATTTGAGTA 58.624 50.000 0.00 0.00 0.00 2.59
3451 3839 2.025887 AGATTTGAGTAGGCTGGGGTTG 60.026 50.000 0.00 0.00 0.00 3.77
3454 3842 0.472925 TGAGTAGGCTGGGGTTGTCA 60.473 55.000 0.00 0.00 0.00 3.58
3460 3848 1.754745 GCTGGGGTTGTCAGAGTCA 59.245 57.895 0.00 0.00 34.36 3.41
3463 3851 2.171448 GCTGGGGTTGTCAGAGTCATAT 59.829 50.000 0.00 0.00 34.36 1.78
3469 3857 2.584492 TGTCAGAGTCATATGTGGCG 57.416 50.000 1.90 0.00 34.36 5.69
3473 3861 1.134699 CAGAGTCATATGTGGCGGTGT 60.135 52.381 1.90 0.00 34.36 4.16
3476 3864 1.014352 GTCATATGTGGCGGTGTTCC 58.986 55.000 1.90 0.00 0.00 3.62
3496 3884 4.394712 ACTCTCGCAAAGCCCCCG 62.395 66.667 0.00 0.00 0.00 5.73
3510 3898 1.757949 CCCCGCCCCAATTTGTTTT 59.242 52.632 0.00 0.00 0.00 2.43
3519 3907 3.181482 CCCCAATTTGTTTTTGGTTTGCC 60.181 43.478 2.12 0.00 41.74 4.52
3526 3914 2.742589 TGTTTTTGGTTTGCCGGAAAAC 59.257 40.909 27.49 27.49 44.59 2.43
3527 3915 2.742589 GTTTTTGGTTTGCCGGAAAACA 59.257 40.909 33.93 22.46 44.21 2.83
3541 3929 0.463654 AAAACAGACAGCTGGACGCA 60.464 50.000 19.93 0.00 46.60 5.24
3542 3930 0.250467 AAACAGACAGCTGGACGCAT 60.250 50.000 19.93 0.00 46.60 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.324736 GCTCATGCGCGTATATTAGGC 59.675 52.381 10.00 6.35 36.30 3.93
1 2 2.606108 TGCTCATGCGCGTATATTAGG 58.394 47.619 10.00 0.00 43.34 2.69
2 3 4.327087 TGATTGCTCATGCGCGTATATTAG 59.673 41.667 10.00 9.00 43.34 1.73
3 4 4.241681 TGATTGCTCATGCGCGTATATTA 58.758 39.130 10.00 0.00 43.34 0.98
4 5 3.066380 TGATTGCTCATGCGCGTATATT 58.934 40.909 10.00 0.00 43.34 1.28
5 6 2.687370 TGATTGCTCATGCGCGTATAT 58.313 42.857 10.00 0.00 43.34 0.86
11 12 4.937781 GGATGATTGCTCATGCGC 57.062 55.556 0.00 0.00 42.27 6.09
22 23 4.333690 GCTGAAATGCTCATAGGGATGAT 58.666 43.478 0.00 0.00 41.33 2.45
26 27 2.105477 GAGGCTGAAATGCTCATAGGGA 59.895 50.000 0.00 0.00 32.14 4.20
29 30 7.174426 TCAATTATGAGGCTGAAATGCTCATAG 59.826 37.037 0.00 0.00 36.04 2.23
30 31 6.999871 TCAATTATGAGGCTGAAATGCTCATA 59.000 34.615 0.00 0.00 34.84 2.15
33 34 5.762825 TCAATTATGAGGCTGAAATGCTC 57.237 39.130 0.00 0.00 0.00 4.26
43 44 7.093322 ACAATGTTCTCTTCAATTATGAGGC 57.907 36.000 0.00 0.00 36.78 4.70
56 57 7.229306 TGCTTTCTATGTTTGACAATGTTCTCT 59.771 33.333 0.00 0.00 0.00 3.10
57 58 7.362662 TGCTTTCTATGTTTGACAATGTTCTC 58.637 34.615 0.00 0.00 0.00 2.87
58 59 7.013655 ACTGCTTTCTATGTTTGACAATGTTCT 59.986 33.333 0.00 0.00 0.00 3.01
81 82 1.686355 TTGGTGCCCAGTAAACACTG 58.314 50.000 0.00 0.00 33.81 3.66
104 105 7.849804 ACTTGGTTGTATTTCTAGTGCTATG 57.150 36.000 0.00 0.00 0.00 2.23
203 208 8.097662 AGATCGGGATTTCAATATCCTTTCTAC 58.902 37.037 0.00 0.00 43.08 2.59
213 218 4.594123 TGCGTAGATCGGGATTTCAATA 57.406 40.909 0.00 0.00 40.26 1.90
221 226 1.686587 ACATTGATGCGTAGATCGGGA 59.313 47.619 0.00 0.00 40.26 5.14
282 287 9.035607 GGTATATTCATATCTTGTAATCGGCTG 57.964 37.037 0.00 0.00 0.00 4.85
332 337 1.234615 ATTGTCGTCCTTGTTGCGGG 61.235 55.000 0.00 0.00 0.00 6.13
384 390 2.048503 GGTGTCGTCTCCGGGTTG 60.049 66.667 0.00 0.00 33.95 3.77
404 410 5.591877 AGCACCTGATATTTTCTCCATGTTC 59.408 40.000 0.00 0.00 0.00 3.18
405 411 5.513233 AGCACCTGATATTTTCTCCATGTT 58.487 37.500 0.00 0.00 0.00 2.71
406 412 5.121380 AGCACCTGATATTTTCTCCATGT 57.879 39.130 0.00 0.00 0.00 3.21
407 413 5.471456 GGTAGCACCTGATATTTTCTCCATG 59.529 44.000 0.00 0.00 34.73 3.66
408 414 5.132648 TGGTAGCACCTGATATTTTCTCCAT 59.867 40.000 6.83 0.00 39.58 3.41
409 415 4.473196 TGGTAGCACCTGATATTTTCTCCA 59.527 41.667 6.83 0.00 39.58 3.86
410 416 5.036117 TGGTAGCACCTGATATTTTCTCC 57.964 43.478 6.83 0.00 39.58 3.71
411 417 4.513318 GCTGGTAGCACCTGATATTTTCTC 59.487 45.833 13.67 0.00 41.89 2.87
412 418 4.164988 AGCTGGTAGCACCTGATATTTTCT 59.835 41.667 13.67 0.86 45.56 2.52
413 419 4.455606 AGCTGGTAGCACCTGATATTTTC 58.544 43.478 13.67 0.00 45.56 2.29
414 420 4.164988 AGAGCTGGTAGCACCTGATATTTT 59.835 41.667 13.67 0.00 45.56 1.82
415 421 3.713764 AGAGCTGGTAGCACCTGATATTT 59.286 43.478 13.67 0.00 45.56 1.40
416 422 3.312890 AGAGCTGGTAGCACCTGATATT 58.687 45.455 13.67 1.02 45.56 1.28
417 423 2.969628 AGAGCTGGTAGCACCTGATAT 58.030 47.619 13.67 4.68 45.56 1.63
418 424 2.461300 AGAGCTGGTAGCACCTGATA 57.539 50.000 13.67 0.00 45.56 2.15
419 425 1.577736 AAGAGCTGGTAGCACCTGAT 58.422 50.000 13.67 8.85 45.56 2.90
420 426 2.231716 TAAGAGCTGGTAGCACCTGA 57.768 50.000 13.67 0.00 45.56 3.86
421 427 4.564041 CATATAAGAGCTGGTAGCACCTG 58.436 47.826 0.00 7.20 45.56 4.00
422 428 3.007398 GCATATAAGAGCTGGTAGCACCT 59.993 47.826 0.00 0.00 45.56 4.00
423 429 3.007398 AGCATATAAGAGCTGGTAGCACC 59.993 47.826 0.00 0.00 45.56 5.01
424 430 4.264460 AGCATATAAGAGCTGGTAGCAC 57.736 45.455 0.00 0.00 45.56 4.40
425 431 4.220821 GGTAGCATATAAGAGCTGGTAGCA 59.779 45.833 0.00 0.00 45.56 3.49
426 432 4.220821 TGGTAGCATATAAGAGCTGGTAGC 59.779 45.833 0.00 0.00 41.97 3.58
427 433 5.984695 TGGTAGCATATAAGAGCTGGTAG 57.015 43.478 0.00 0.00 41.97 3.18
428 434 6.016555 TCATGGTAGCATATAAGAGCTGGTA 58.983 40.000 7.18 0.00 41.97 3.25
429 435 4.840680 TCATGGTAGCATATAAGAGCTGGT 59.159 41.667 7.18 0.00 41.97 4.00
430 436 5.411831 TCATGGTAGCATATAAGAGCTGG 57.588 43.478 7.18 0.00 41.97 4.85
431 437 6.983307 GGTATCATGGTAGCATATAAGAGCTG 59.017 42.308 10.32 0.00 41.97 4.24
432 438 6.669591 TGGTATCATGGTAGCATATAAGAGCT 59.330 38.462 13.80 0.00 44.55 4.09
433 439 6.878317 TGGTATCATGGTAGCATATAAGAGC 58.122 40.000 13.80 4.39 0.00 4.09
434 440 9.896645 ATTTGGTATCATGGTAGCATATAAGAG 57.103 33.333 18.10 0.00 32.69 2.85
439 445 8.938801 TTGAATTTGGTATCATGGTAGCATAT 57.061 30.769 18.10 15.50 32.69 1.78
440 446 8.759481 TTTGAATTTGGTATCATGGTAGCATA 57.241 30.769 18.10 13.92 32.69 3.14
441 447 7.658525 TTTGAATTTGGTATCATGGTAGCAT 57.341 32.000 18.10 4.14 32.69 3.79
442 448 7.473735 TTTTGAATTTGGTATCATGGTAGCA 57.526 32.000 13.80 13.80 0.00 3.49
443 449 8.947055 ATTTTTGAATTTGGTATCATGGTAGC 57.053 30.769 8.28 8.28 0.00 3.58
446 452 9.790344 TTGAATTTTTGAATTTGGTATCATGGT 57.210 25.926 0.00 0.00 0.00 3.55
509 515 4.508662 TGTCGCCATATATGTTGTGAACA 58.491 39.130 11.73 7.49 46.94 3.18
510 516 5.478233 TTGTCGCCATATATGTTGTGAAC 57.522 39.130 11.73 5.50 0.00 3.18
511 517 5.238432 GGATTGTCGCCATATATGTTGTGAA 59.762 40.000 11.73 0.07 0.00 3.18
512 518 4.754618 GGATTGTCGCCATATATGTTGTGA 59.245 41.667 11.73 6.56 0.00 3.58
513 519 4.083324 GGGATTGTCGCCATATATGTTGTG 60.083 45.833 11.73 4.37 0.00 3.33
514 520 4.072131 GGGATTGTCGCCATATATGTTGT 58.928 43.478 11.73 0.00 0.00 3.32
515 521 4.685169 GGGATTGTCGCCATATATGTTG 57.315 45.455 11.73 3.83 0.00 3.33
552 558 9.214957 TGTTTCTCTATGTGTATGTCGATTTTT 57.785 29.630 0.00 0.00 0.00 1.94
553 559 8.771920 TGTTTCTCTATGTGTATGTCGATTTT 57.228 30.769 0.00 0.00 0.00 1.82
554 560 8.771920 TTGTTTCTCTATGTGTATGTCGATTT 57.228 30.769 0.00 0.00 0.00 2.17
555 561 8.771920 TTTGTTTCTCTATGTGTATGTCGATT 57.228 30.769 0.00 0.00 0.00 3.34
556 562 8.771920 TTTTGTTTCTCTATGTGTATGTCGAT 57.228 30.769 0.00 0.00 0.00 3.59
557 563 8.596271 TTTTTGTTTCTCTATGTGTATGTCGA 57.404 30.769 0.00 0.00 0.00 4.20
594 600 9.280174 ACGGAGAAACAAAAAGACTATTAATCA 57.720 29.630 0.00 0.00 0.00 2.57
595 601 9.543018 CACGGAGAAACAAAAAGACTATTAATC 57.457 33.333 0.00 0.00 0.00 1.75
596 602 9.063615 ACACGGAGAAACAAAAAGACTATTAAT 57.936 29.630 0.00 0.00 0.00 1.40
597 603 8.441312 ACACGGAGAAACAAAAAGACTATTAA 57.559 30.769 0.00 0.00 0.00 1.40
598 604 9.715121 ATACACGGAGAAACAAAAAGACTATTA 57.285 29.630 0.00 0.00 0.00 0.98
599 605 6.937436 ACACGGAGAAACAAAAAGACTATT 57.063 33.333 0.00 0.00 0.00 1.73
600 606 9.886132 ATATACACGGAGAAACAAAAAGACTAT 57.114 29.630 0.00 0.00 0.00 2.12
601 607 9.715121 AATATACACGGAGAAACAAAAAGACTA 57.285 29.630 0.00 0.00 0.00 2.59
602 608 8.617290 AATATACACGGAGAAACAAAAAGACT 57.383 30.769 0.00 0.00 0.00 3.24
603 609 9.673454 AAAATATACACGGAGAAACAAAAAGAC 57.327 29.630 0.00 0.00 0.00 3.01
604 610 9.672086 CAAAATATACACGGAGAAACAAAAAGA 57.328 29.630 0.00 0.00 0.00 2.52
605 611 9.672086 TCAAAATATACACGGAGAAACAAAAAG 57.328 29.630 0.00 0.00 0.00 2.27
647 653 9.425577 TGACATATATGTTGACAACGACTAAAA 57.574 29.630 19.19 0.00 41.95 1.52
648 654 8.989653 TGACATATATGTTGACAACGACTAAA 57.010 30.769 19.19 0.00 41.95 1.85
649 655 9.030301 CATGACATATATGTTGACAACGACTAA 57.970 33.333 19.19 0.00 41.95 2.24
650 656 8.410141 TCATGACATATATGTTGACAACGACTA 58.590 33.333 19.19 5.82 41.95 2.59
651 657 7.264947 TCATGACATATATGTTGACAACGACT 58.735 34.615 19.19 3.84 41.95 4.18
652 658 7.463469 TCATGACATATATGTTGACAACGAC 57.537 36.000 19.19 4.41 41.95 4.34
653 659 7.547370 TGTTCATGACATATATGTTGACAACGA 59.453 33.333 19.19 10.76 41.95 3.85
654 660 7.683746 TGTTCATGACATATATGTTGACAACG 58.316 34.615 19.19 8.94 41.95 4.10
734 740 9.935241 CCATATCTTATATGCTACCATGATACC 57.065 37.037 0.00 0.00 32.85 2.73
756 762 9.910267 CATGGGAAAATATCAGATGATACCATA 57.090 33.333 15.89 4.78 37.06 2.74
757 763 8.617491 TCATGGGAAAATATCAGATGATACCAT 58.383 33.333 12.67 12.67 38.42 3.55
758 764 7.987820 TCATGGGAAAATATCAGATGATACCA 58.012 34.615 4.71 7.85 39.57 3.25
759 765 8.734386 GTTCATGGGAAAATATCAGATGATACC 58.266 37.037 4.71 2.41 35.97 2.73
760 766 9.288576 TGTTCATGGGAAAATATCAGATGATAC 57.711 33.333 4.71 0.00 35.97 2.24
762 768 8.803235 CATGTTCATGGGAAAATATCAGATGAT 58.197 33.333 5.02 0.31 35.22 2.45
763 769 7.231925 CCATGTTCATGGGAAAATATCAGATGA 59.768 37.037 20.44 0.00 38.04 2.92
764 770 7.014905 ACCATGTTCATGGGAAAATATCAGATG 59.985 37.037 28.20 5.31 45.84 2.90
765 771 7.014905 CACCATGTTCATGGGAAAATATCAGAT 59.985 37.037 28.20 6.79 45.84 2.90
766 772 6.321945 CACCATGTTCATGGGAAAATATCAGA 59.678 38.462 28.20 0.00 45.84 3.27
767 773 6.321945 TCACCATGTTCATGGGAAAATATCAG 59.678 38.462 28.20 10.32 45.84 2.90
768 774 6.096705 GTCACCATGTTCATGGGAAAATATCA 59.903 38.462 28.20 5.66 45.84 2.15
769 775 6.322201 AGTCACCATGTTCATGGGAAAATATC 59.678 38.462 28.20 13.51 45.84 1.63
770 776 6.197168 AGTCACCATGTTCATGGGAAAATAT 58.803 36.000 28.20 9.20 45.84 1.28
771 777 5.579047 AGTCACCATGTTCATGGGAAAATA 58.421 37.500 28.20 9.98 45.84 1.40
772 778 4.419282 AGTCACCATGTTCATGGGAAAAT 58.581 39.130 28.20 14.07 45.84 1.82
773 779 3.843422 AGTCACCATGTTCATGGGAAAA 58.157 40.909 28.20 12.75 45.84 2.29
774 780 3.524095 AGTCACCATGTTCATGGGAAA 57.476 42.857 28.20 14.72 45.84 3.13
775 781 3.156293 CAAGTCACCATGTTCATGGGAA 58.844 45.455 28.20 16.72 45.84 3.97
776 782 2.108075 ACAAGTCACCATGTTCATGGGA 59.892 45.455 28.20 20.89 45.84 4.37
777 783 2.517959 ACAAGTCACCATGTTCATGGG 58.482 47.619 28.20 19.41 45.84 4.00
778 784 4.037803 TGAAACAAGTCACCATGTTCATGG 59.962 41.667 24.78 24.78 46.92 3.66
779 785 5.185668 TGAAACAAGTCACCATGTTCATG 57.814 39.130 5.88 5.88 38.75 3.07
780 786 5.737063 GCTTGAAACAAGTCACCATGTTCAT 60.737 40.000 12.07 0.00 38.75 2.57
781 787 4.439974 GCTTGAAACAAGTCACCATGTTCA 60.440 41.667 12.07 0.00 38.75 3.18
885 892 3.063997 CGAGACGGAATTTAGCATTGCTT 59.936 43.478 17.71 0.00 40.44 3.91
902 909 4.153117 AGAAAACTTGCATGATGACGAGAC 59.847 41.667 6.60 0.00 0.00 3.36
923 1034 9.573166 TGAAATATGTCAAAAGGAAAAGAGAGA 57.427 29.630 0.00 0.00 0.00 3.10
927 1038 9.709495 CCAATGAAATATGTCAAAAGGAAAAGA 57.291 29.630 0.00 0.00 0.00 2.52
928 1039 8.445493 GCCAATGAAATATGTCAAAAGGAAAAG 58.555 33.333 13.14 0.00 0.00 2.27
943 1054 4.271661 TGAGCTGTCATGCCAATGAAATA 58.728 39.130 0.00 0.00 44.40 1.40
996 1111 5.057819 TGGCTTCACATTGACGTACTAAAA 58.942 37.500 0.00 0.00 0.00 1.52
997 1112 4.633175 TGGCTTCACATTGACGTACTAAA 58.367 39.130 0.00 0.00 0.00 1.85
998 1113 4.260139 TGGCTTCACATTGACGTACTAA 57.740 40.909 0.00 0.00 0.00 2.24
1029 1144 3.996825 GCCACAAGCAATAGGTTCG 57.003 52.632 0.00 0.00 42.97 3.95
1096 1215 3.652000 TCGGGTGTTTTTCGCGGC 61.652 61.111 6.13 0.00 40.62 6.53
1196 1318 2.164827 GGAATAATCGCGGGTTTTGGTT 59.835 45.455 6.13 0.00 0.00 3.67
1200 1322 3.314357 GCTAAGGAATAATCGCGGGTTTT 59.686 43.478 6.13 0.00 0.00 2.43
1207 1329 3.423645 GCGACATGCTAAGGAATAATCGC 60.424 47.826 0.00 0.00 44.50 4.58
1225 1347 2.803386 TCTGAGTGATATCTCTCGCGAC 59.197 50.000 23.12 4.98 38.83 5.19
1226 1348 3.113260 TCTGAGTGATATCTCTCGCGA 57.887 47.619 23.12 19.51 38.83 5.87
1231 1353 4.344390 TGCTTGCATCTGAGTGATATCTCT 59.656 41.667 7.01 7.01 35.68 3.10
1244 1366 5.779529 TCTTCTTTTTCTTGCTTGCATCT 57.220 34.783 0.00 0.00 0.00 2.90
1281 1404 2.433436 CGGGTTGGGAAGTAAAAGGAG 58.567 52.381 0.00 0.00 0.00 3.69
1301 1424 3.453070 GAGCGGGATGGAGTGAGCC 62.453 68.421 0.00 0.00 0.00 4.70
1351 1475 1.602851 CTGCTCCTGCTAATGTGCATC 59.397 52.381 0.00 0.00 42.48 3.91
1376 1500 1.017387 GGATCGGGATGTGCTTGTTC 58.983 55.000 0.00 0.00 0.00 3.18
1390 1514 1.326328 TCAGGAGCTCAGATGGATCG 58.674 55.000 17.19 0.00 0.00 3.69
1402 1526 1.859383 GGTAGCTTCGAATCAGGAGC 58.141 55.000 0.00 0.00 0.00 4.70
1408 1532 1.949631 CGGGCGGTAGCTTCGAATC 60.950 63.158 12.38 0.00 44.37 2.52
1411 1535 3.515286 CTCGGGCGGTAGCTTCGA 61.515 66.667 12.38 8.45 44.37 3.71
1413 1537 4.893601 GCCTCGGGCGGTAGCTTC 62.894 72.222 0.00 0.00 44.37 3.86
1584 1708 0.459237 CATGTCTCCGGAGCTGTGTC 60.459 60.000 27.39 12.05 0.00 3.67
1607 1731 4.463879 CACTCTCCGCCCTGCCAG 62.464 72.222 0.00 0.00 0.00 4.85
1610 1734 4.154347 CTCCACTCTCCGCCCTGC 62.154 72.222 0.00 0.00 0.00 4.85
1611 1735 3.465403 CCTCCACTCTCCGCCCTG 61.465 72.222 0.00 0.00 0.00 4.45
1612 1736 3.673597 TCCTCCACTCTCCGCCCT 61.674 66.667 0.00 0.00 0.00 5.19
1616 1740 4.180946 CGCGTCCTCCACTCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
1656 1783 4.148825 ATCCTGTCCAGCGCGTCC 62.149 66.667 8.43 0.00 0.00 4.79
1669 1796 1.361993 GAGCGCGAGTGATCATCCT 59.638 57.895 12.10 0.00 0.00 3.24
1767 1894 4.702826 GTCTGACGCGTGCGCAAC 62.703 66.667 20.70 6.64 44.19 4.17
2121 2257 2.433664 CGTACCTGGCGGTGGTTC 60.434 66.667 10.60 1.89 45.18 3.62
2158 2294 3.628487 ACTACCTGTCGAGCTAAGCTTAG 59.372 47.826 26.20 26.20 39.88 2.18
2313 2457 4.785658 GCATTCTCTGTCAATGAATCGCAG 60.786 45.833 5.78 0.00 33.69 5.18
2408 2562 3.321968 AGTGAAGGCCTCCAAACAATTTC 59.678 43.478 5.23 0.00 0.00 2.17
2423 2577 4.836125 AGTTGCAATGTTACAGTGAAGG 57.164 40.909 17.19 0.00 30.53 3.46
2483 2637 2.301346 CAATTAGGGGACATGGTCAGC 58.699 52.381 0.00 0.00 33.68 4.26
2486 2658 3.054361 ACAGACAATTAGGGGACATGGTC 60.054 47.826 0.00 0.00 0.00 4.02
2493 2665 8.390921 AGAAAAGAAATACAGACAATTAGGGGA 58.609 33.333 0.00 0.00 0.00 4.81
2513 2685 5.356882 TGAGTGTTGCGGAATTAGAAAAG 57.643 39.130 0.00 0.00 0.00 2.27
2543 2718 9.193806 AGTGGATGAATTGTGCTATTTTCTATT 57.806 29.630 0.00 0.00 0.00 1.73
2594 2771 9.739276 AATTCTTGTGAACATCCTGAACTATTA 57.261 29.630 0.00 0.00 34.71 0.98
2623 2801 5.551760 AGTACCGCTGAATTCAAAATCAG 57.448 39.130 9.88 3.87 44.66 2.90
2668 2846 8.295569 AGTTCAAGAGAAACTATGTACGAAAC 57.704 34.615 0.00 0.00 35.08 2.78
2671 2849 7.594015 GTGAAGTTCAAGAGAAACTATGTACGA 59.406 37.037 7.25 0.00 35.08 3.43
2673 2851 7.873505 AGGTGAAGTTCAAGAGAAACTATGTAC 59.126 37.037 7.25 0.00 35.08 2.90
2674 2852 7.963532 AGGTGAAGTTCAAGAGAAACTATGTA 58.036 34.615 7.25 0.00 35.08 2.29
2675 2853 6.831976 AGGTGAAGTTCAAGAGAAACTATGT 58.168 36.000 7.25 0.00 35.08 2.29
2683 2861 6.591935 ACATTGTTAGGTGAAGTTCAAGAGA 58.408 36.000 7.25 0.00 0.00 3.10
2691 2869 4.870426 CGCTCATACATTGTTAGGTGAAGT 59.130 41.667 0.00 0.00 0.00 3.01
2724 2902 1.274167 TGTACTACAAGACCAAGGGCG 59.726 52.381 0.00 0.00 0.00 6.13
2728 2906 3.576982 TCACCCTGTACTACAAGACCAAG 59.423 47.826 0.00 0.00 0.00 3.61
2730 2908 2.895404 GTCACCCTGTACTACAAGACCA 59.105 50.000 0.00 0.00 0.00 4.02
2731 2909 2.895404 TGTCACCCTGTACTACAAGACC 59.105 50.000 0.00 0.00 0.00 3.85
2733 2911 3.006537 GCTTGTCACCCTGTACTACAAGA 59.993 47.826 15.56 1.69 46.29 3.02
2748 2926 1.136305 GTATAGCCTGGACGCTTGTCA 59.864 52.381 0.00 0.00 44.74 3.58
2778 2957 6.494842 TCACTCAGTTTTGCAACTTGATAAC 58.505 36.000 0.00 0.00 40.66 1.89
2784 2963 5.581126 TGATTCACTCAGTTTTGCAACTT 57.419 34.783 0.00 0.00 40.66 2.66
2795 2974 7.173907 AGTTGGTCAGTTTATTGATTCACTCAG 59.826 37.037 0.00 0.00 34.68 3.35
2812 2991 0.178992 TTGGGCAGGAAGTTGGTCAG 60.179 55.000 0.00 0.00 0.00 3.51
2814 2993 1.408969 TTTTGGGCAGGAAGTTGGTC 58.591 50.000 0.00 0.00 0.00 4.02
2815 2994 1.872773 TTTTTGGGCAGGAAGTTGGT 58.127 45.000 0.00 0.00 0.00 3.67
2848 3027 8.234546 CCGTAAGTTTTGCTTGTTATTCTACAT 58.765 33.333 0.00 0.00 38.05 2.29
2849 3028 7.308109 CCCGTAAGTTTTGCTTGTTATTCTACA 60.308 37.037 0.00 0.00 38.05 2.74
2850 3029 7.019418 CCCGTAAGTTTTGCTTGTTATTCTAC 58.981 38.462 0.00 0.00 38.05 2.59
2851 3030 6.711645 ACCCGTAAGTTTTGCTTGTTATTCTA 59.288 34.615 0.00 0.00 38.05 2.10
2852 3031 5.533528 ACCCGTAAGTTTTGCTTGTTATTCT 59.466 36.000 0.00 0.00 38.05 2.40
2853 3032 5.765176 ACCCGTAAGTTTTGCTTGTTATTC 58.235 37.500 0.00 0.00 38.05 1.75
2854 3033 5.777850 ACCCGTAAGTTTTGCTTGTTATT 57.222 34.783 0.00 0.00 38.05 1.40
2855 3034 5.299782 TCAACCCGTAAGTTTTGCTTGTTAT 59.700 36.000 0.00 0.00 38.05 1.89
2856 3035 4.639310 TCAACCCGTAAGTTTTGCTTGTTA 59.361 37.500 0.00 0.00 38.05 2.41
2857 3036 3.444388 TCAACCCGTAAGTTTTGCTTGTT 59.556 39.130 0.00 0.00 38.05 2.83
2858 3037 3.018149 TCAACCCGTAAGTTTTGCTTGT 58.982 40.909 0.00 0.00 38.05 3.16
2859 3038 3.368495 GTCAACCCGTAAGTTTTGCTTG 58.632 45.455 0.00 0.00 38.05 4.01
2888 3067 2.167281 CGAGAGGAGACAATGTGACCAT 59.833 50.000 0.00 0.00 0.00 3.55
2920 3099 4.488126 ACGATGTCATGAAGTTTTGTGG 57.512 40.909 0.00 0.00 0.00 4.17
2922 3101 4.578516 TCCAACGATGTCATGAAGTTTTGT 59.421 37.500 0.00 0.00 0.00 2.83
2938 3117 3.513912 AGGTTGTACATCATCTCCAACGA 59.486 43.478 0.00 0.00 37.00 3.85
2950 3129 6.152323 AGTCACTAACGTATCAGGTTGTACAT 59.848 38.462 0.00 0.00 0.00 2.29
2956 3135 4.689345 GCAAAGTCACTAACGTATCAGGTT 59.311 41.667 0.00 0.00 0.00 3.50
2960 3139 5.390461 GCAATGCAAAGTCACTAACGTATCA 60.390 40.000 0.00 0.00 0.00 2.15
2961 3140 5.022021 GCAATGCAAAGTCACTAACGTATC 58.978 41.667 0.00 0.00 0.00 2.24
2983 3162 5.348418 ACATGCACATCATCTATAAACGC 57.652 39.130 0.00 0.00 31.79 4.84
2988 3167 4.990426 CCAACGACATGCACATCATCTATA 59.010 41.667 0.00 0.00 31.79 1.31
2991 3170 2.011947 CCAACGACATGCACATCATCT 58.988 47.619 0.00 0.00 31.79 2.90
2997 3176 2.551006 GCACCCAACGACATGCACA 61.551 57.895 0.00 0.00 38.00 4.57
3027 3207 1.475280 TGCAGGCTTCATTTCATGAGC 59.525 47.619 0.00 0.00 40.94 4.26
3061 3241 0.955428 GCATGAACAAGGGCTCGACA 60.955 55.000 0.00 0.00 0.00 4.35
3063 3243 1.377202 GGCATGAACAAGGGCTCGA 60.377 57.895 0.00 0.00 0.00 4.04
3092 3272 0.094730 GCGTGGTTTGTCGTATCTGC 59.905 55.000 0.00 0.00 0.00 4.26
3095 3275 1.996898 TGATGCGTGGTTTGTCGTATC 59.003 47.619 8.23 8.23 44.69 2.24
3100 3280 0.660488 TGTGTGATGCGTGGTTTGTC 59.340 50.000 0.00 0.00 0.00 3.18
3130 3310 2.482490 GGCGGTGTACTCGGTTATTGAT 60.482 50.000 10.25 0.00 0.00 2.57
3136 3316 1.217244 GATGGCGGTGTACTCGGTT 59.783 57.895 10.25 0.00 0.00 4.44
3142 3322 0.458889 TAAGCACGATGGCGGTGTAC 60.459 55.000 0.00 0.00 43.17 2.90
3146 3326 1.153628 GAGTAAGCACGATGGCGGT 60.154 57.895 0.00 0.00 43.17 5.68
3155 3335 4.893424 TGTTGTTTTCTGGAGTAAGCAC 57.107 40.909 0.00 0.00 0.00 4.40
3198 3382 4.755123 CCGACAGGTCTTTAGTCAAATGTT 59.245 41.667 0.00 0.00 32.68 2.71
3208 3393 1.290955 CACGCCCGACAGGTCTTTA 59.709 57.895 0.00 0.00 38.26 1.85
3222 3407 2.809601 CTACGGCAGACACCACGC 60.810 66.667 0.00 0.00 0.00 5.34
3223 3408 2.959372 TCTACGGCAGACACCACG 59.041 61.111 0.00 0.00 0.00 4.94
3236 3421 2.708255 CCTCTCGACGCCGTCTAC 59.292 66.667 16.07 0.00 37.05 2.59
3245 3430 3.917760 CATCCGCCCCCTCTCGAC 61.918 72.222 0.00 0.00 0.00 4.20
3249 3434 1.536662 GGTATCATCCGCCCCCTCT 60.537 63.158 0.00 0.00 0.00 3.69
3257 3442 0.602106 CTGCAGCCAGGTATCATCCG 60.602 60.000 0.00 0.00 35.38 4.18
3258 3443 0.761187 TCTGCAGCCAGGTATCATCC 59.239 55.000 9.47 0.00 39.61 3.51
3263 3449 0.401105 ATCCCTCTGCAGCCAGGTAT 60.401 55.000 17.74 7.13 39.61 2.73
3275 3461 3.551322 TCCACCCAGGATCCCTCT 58.449 61.111 8.55 0.00 43.07 3.69
3283 3469 2.593468 CTACATGCGGTCCACCCAGG 62.593 65.000 0.00 0.00 39.47 4.45
3297 3483 4.467084 CCACCCACGCGCCTACAT 62.467 66.667 5.73 0.00 0.00 2.29
3323 3711 1.599047 CCAGGCATCCTCAGACGTT 59.401 57.895 0.00 0.00 0.00 3.99
3325 3713 2.503061 CCCAGGCATCCTCAGACG 59.497 66.667 0.00 0.00 0.00 4.18
3328 3716 4.559063 CCGCCCAGGCATCCTCAG 62.559 72.222 9.78 0.00 42.06 3.35
3344 3732 2.345760 TTGTACCTCTCCGGTCGCC 61.346 63.158 0.00 0.00 44.93 5.54
3351 3739 1.673808 ATCCGCCGTTGTACCTCTCC 61.674 60.000 0.00 0.00 0.00 3.71
3365 3753 0.379669 CTTTCATCTGCACCATCCGC 59.620 55.000 0.00 0.00 0.00 5.54
3370 3758 1.250328 CCTTGCTTTCATCTGCACCA 58.750 50.000 0.00 0.00 39.05 4.17
3372 3760 0.529378 CCCCTTGCTTTCATCTGCAC 59.471 55.000 0.00 0.00 39.05 4.57
3397 3785 2.136026 ACTTTTCTTCCACTCCACCCT 58.864 47.619 0.00 0.00 0.00 4.34
3401 3789 2.777692 AGTCCACTTTTCTTCCACTCCA 59.222 45.455 0.00 0.00 0.00 3.86
3402 3790 3.142174 CAGTCCACTTTTCTTCCACTCC 58.858 50.000 0.00 0.00 0.00 3.85
3440 3828 1.462238 ACTCTGACAACCCCAGCCT 60.462 57.895 0.00 0.00 0.00 4.58
3451 3839 1.137086 ACCGCCACATATGACTCTGAC 59.863 52.381 10.38 0.00 0.00 3.51
3454 3842 1.195115 ACACCGCCACATATGACTCT 58.805 50.000 10.38 0.00 0.00 3.24
3460 3848 1.153249 CCGGAACACCGCCACATAT 60.153 57.895 0.00 0.00 44.70 1.78
3463 3851 4.612412 GTCCGGAACACCGCCACA 62.612 66.667 5.23 0.00 44.70 4.17
3469 3857 2.126031 GCGAGAGTCCGGAACACC 60.126 66.667 5.23 0.00 0.00 4.16
3473 3861 1.374252 GCTTTGCGAGAGTCCGGAA 60.374 57.895 5.23 4.35 38.07 4.30
3476 3864 2.815647 GGGCTTTGCGAGAGTCCG 60.816 66.667 0.00 0.00 0.00 4.79
3510 3898 1.135333 GTCTGTTTTCCGGCAAACCAA 59.865 47.619 24.01 11.28 36.03 3.67
3519 3907 0.868406 GTCCAGCTGTCTGTTTTCCG 59.132 55.000 13.81 0.00 38.66 4.30


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

AutoCloner maintained by Alex Coulton.