Multiple sequence alignment - TraesCS5A01G022400

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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 TraesCS5A01G022400 chr5A 100.000 2344 0 0 1 2344 18394014 18396357 0.000000e+00 4329.0
1 TraesCS5A01G022400 chr5A 100.000 1326 0 0 2617 3942 18396630 18397955 0.000000e+00 2449.0
2 TraesCS5A01G022400 chr5A 82.700 711 95 19 981 1677 18576086 18576782 1.210000e-169 606.0
3 TraesCS5A01G022400 chr5A 85.714 581 67 11 3149 3720 18530999 18531572 2.030000e-167 599.0
4 TraesCS5A01G022400 chr5A 88.699 469 49 3 2660 3124 18530470 18530938 1.590000e-158 569.0
5 TraesCS5A01G022400 chr5A 81.702 705 89 18 990 1680 18572651 18571973 5.760000e-153 551.0
6 TraesCS5A01G022400 chr5B 92.331 1330 68 6 2617 3942 18666270 18667569 0.000000e+00 1860.0
7 TraesCS5A01G022400 chr5B 91.472 1114 73 12 818 1916 18664468 18665574 0.000000e+00 1511.0
8 TraesCS5A01G022400 chr5B 80.993 705 95 18 994 1682 18775845 18776526 1.260000e-144 523.0
9 TraesCS5A01G022400 chr5B 90.592 287 23 2 466 752 325096760 325096478 1.030000e-100 377.0
10 TraesCS5A01G022400 chr5B 93.923 181 9 1 187 367 18664127 18664305 5.020000e-69 272.0
11 TraesCS5A01G022400 chr5B 86.782 174 20 3 3 174 631487047 631486875 1.450000e-44 191.0
12 TraesCS5A01G022400 chr5B 81.675 191 35 0 2804 2994 18589713 18589903 4.080000e-35 159.0
13 TraesCS5A01G022400 chr5B 84.713 157 23 1 2103 2259 589236977 589237132 5.270000e-34 156.0
14 TraesCS5A01G022400 chr5B 90.722 97 6 2 2248 2344 18666088 18666181 4.140000e-25 126.0
15 TraesCS5A01G022400 chr5B 80.374 107 16 5 1790 1893 18777354 18777458 4.220000e-10 76.8
16 TraesCS5A01G022400 chr5D 92.559 1223 75 6 2732 3942 26520989 26519771 0.000000e+00 1742.0
17 TraesCS5A01G022400 chr5D 93.068 1154 74 5 2792 3942 26475703 26474553 0.000000e+00 1683.0
18 TraesCS5A01G022400 chr5D 91.217 1093 84 8 1007 2098 26507944 26506863 0.000000e+00 1476.0
19 TraesCS5A01G022400 chr5D 89.112 1194 78 19 786 1960 26523538 26522378 0.000000e+00 1437.0
20 TraesCS5A01G022400 chr5D 93.095 782 49 3 1244 2025 26474492 26473716 0.000000e+00 1140.0
21 TraesCS5A01G022400 chr5D 87.973 582 52 13 3149 3720 26471247 26470674 0.000000e+00 671.0
22 TraesCS5A01G022400 chr5D 89.689 514 50 2 2631 3142 26471802 26471290 0.000000e+00 652.0
23 TraesCS5A01G022400 chr5D 83.404 711 90 19 981 1677 26785257 26785953 5.560000e-178 634.0
24 TraesCS5A01G022400 chr5D 94.278 367 19 1 1 367 26525696 26525332 9.570000e-156 560.0
25 TraesCS5A01G022400 chr5D 81.151 695 84 26 990 1680 26682536 26681885 7.550000e-142 514.0
26 TraesCS5A01G022400 chr5D 91.633 251 19 1 2094 2344 26506215 26505967 2.920000e-91 346.0
27 TraesCS5A01G022400 chr5D 96.648 179 6 0 2617 2795 26505496 26505318 8.280000e-77 298.0
28 TraesCS5A01G022400 chr5D 91.935 186 15 0 2094 2279 26521856 26521671 1.090000e-65 261.0
29 TraesCS5A01G022400 chr5D 76.215 391 72 14 2617 2994 26549930 26549548 1.870000e-43 187.0
30 TraesCS5A01G022400 chr5D 79.439 107 17 5 1790 1893 26680843 26680739 1.970000e-08 71.3
31 TraesCS5A01G022400 chr1D 85.870 644 85 4 3304 3942 276775984 276775342 0.000000e+00 680.0
32 TraesCS5A01G022400 chr1D 82.249 169 25 5 2094 2260 204222236 204222401 1.480000e-29 141.0
33 TraesCS5A01G022400 chr3D 83.463 641 91 6 3304 3939 310648899 310649529 2.040000e-162 582.0
34 TraesCS5A01G022400 chr3D 83.854 192 27 4 3 192 15242837 15242648 3.130000e-41 180.0
35 TraesCS5A01G022400 chr7B 83.412 639 93 8 3304 3935 662462951 662462319 7.340000e-162 580.0
36 TraesCS5A01G022400 chr7B 85.311 177 24 2 3 178 530021694 530021869 8.700000e-42 182.0
37 TraesCS5A01G022400 chr3A 83.369 469 74 3 3304 3771 57772287 57771822 7.830000e-117 431.0
38 TraesCS5A01G022400 chr4D 87.719 171 20 1 9 178 309508302 309508472 8.640000e-47 198.0
39 TraesCS5A01G022400 chr4B 85.635 181 24 2 3 182 590021059 590020880 5.200000e-44 189.0
40 TraesCS5A01G022400 chr6A 84.574 188 27 2 3 189 105639338 105639152 6.730000e-43 185.0
41 TraesCS5A01G022400 chr6A 84.865 185 25 3 3 186 572024657 572024475 2.420000e-42 183.0
42 TraesCS5A01G022400 chr6A 73.214 336 84 6 3489 3820 606982390 606982057 2.490000e-22 117.0
43 TraesCS5A01G022400 chr2B 87.261 157 20 0 2094 2250 401266664 401266820 3.130000e-41 180.0
44 TraesCS5A01G022400 chr2A 84.127 189 23 7 7 192 385236175 385235991 4.050000e-40 176.0
45 TraesCS5A01G022400 chr3B 82.424 165 27 2 2094 2257 536072680 536072517 4.110000e-30 143.0
46 TraesCS5A01G022400 chr7D 94.444 36 2 0 2029 2064 13454715 13454680 5.500000e-04 56.5


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 TraesCS5A01G022400 chr5A 18394014 18397955 3941 False 3389.000000 4329 100.00000 1 3942 2 chr5A.!!$F2 3941
1 TraesCS5A01G022400 chr5A 18576086 18576782 696 False 606.000000 606 82.70000 981 1677 1 chr5A.!!$F1 696
2 TraesCS5A01G022400 chr5A 18530470 18531572 1102 False 584.000000 599 87.20650 2660 3720 2 chr5A.!!$F3 1060
3 TraesCS5A01G022400 chr5A 18571973 18572651 678 True 551.000000 551 81.70200 990 1680 1 chr5A.!!$R1 690
4 TraesCS5A01G022400 chr5B 18664127 18667569 3442 False 942.250000 1860 92.11200 187 3942 4 chr5B.!!$F3 3755
5 TraesCS5A01G022400 chr5B 18775845 18777458 1613 False 299.900000 523 80.68350 994 1893 2 chr5B.!!$F4 899
6 TraesCS5A01G022400 chr5D 26470674 26475703 5029 True 1036.500000 1683 90.95625 1244 3942 4 chr5D.!!$R2 2698
7 TraesCS5A01G022400 chr5D 26519771 26525696 5925 True 1000.000000 1742 91.97100 1 3942 4 chr5D.!!$R4 3941
8 TraesCS5A01G022400 chr5D 26505318 26507944 2626 True 706.666667 1476 93.16600 1007 2795 3 chr5D.!!$R3 1788
9 TraesCS5A01G022400 chr5D 26785257 26785953 696 False 634.000000 634 83.40400 981 1677 1 chr5D.!!$F1 696
10 TraesCS5A01G022400 chr5D 26680739 26682536 1797 True 292.650000 514 80.29500 990 1893 2 chr5D.!!$R5 903
11 TraesCS5A01G022400 chr1D 276775342 276775984 642 True 680.000000 680 85.87000 3304 3942 1 chr1D.!!$R1 638
12 TraesCS5A01G022400 chr3D 310648899 310649529 630 False 582.000000 582 83.46300 3304 3939 1 chr3D.!!$F1 635
13 TraesCS5A01G022400 chr7B 662462319 662462951 632 True 580.000000 580 83.41200 3304 3935 1 chr7B.!!$R1 631

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
435 436 0.108804 CTTCTATGTGTGACGCGGGT 60.109 55.0 12.47 4.12 0.00 5.28 F
455 456 0.320771 ATGCGTGTCCCTTGTGTCTC 60.321 55.0 0.00 0.00 0.00 3.36 F
589 590 0.463620 TTTTTCCTGCAACAGCACCC 59.536 50.0 0.00 0.00 33.99 4.61 F
591 592 0.469705 TTTCCTGCAACAGCACCCAT 60.470 50.0 0.00 0.00 33.99 4.00 F
2730 7333 0.610232 GCTGCTGGTTTCCATCCACT 60.610 55.0 0.00 0.00 30.82 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 4672 1.065199 GGATTGGCCACAGATCAGTCA 60.065 52.381 3.88 0.00 36.34 3.41 R
1989 4675 2.022195 CAAGGATTGGCCACAGATCAG 58.978 52.381 3.88 0.00 43.94 2.90 R
2188 6267 5.918011 GCGTTTGACCATTGACAAGATTAAA 59.082 36.000 0.00 0.00 0.00 1.52 R
2767 7375 6.629128 TCTCCGTAGAGTATAATCTCCTACG 58.371 44.000 14.11 14.11 41.26 3.51 R
3536 8193 0.607217 TCCACATGTTCAGCCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24 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 5.340803 CGTTCATGTGCTAGCCGTATATAT 58.659 41.667 13.29 0.00 0.00 0.86
185 186 4.413495 TGCTAAATTTTCCAGCACGTAC 57.587 40.909 9.55 0.00 40.26 3.67
229 230 6.517914 TTGAAATTTTGGAAATTTCGTCCG 57.482 33.333 23.19 0.00 45.06 4.79
246 247 2.483106 GTCCGTTTTCTTCCCTTGTAGC 59.517 50.000 0.00 0.00 0.00 3.58
264 265 2.310309 CAGTGCTGCGTTTCTGTCA 58.690 52.632 0.00 0.00 0.00 3.58
271 272 2.223249 GCTGCGTTTCTGTCAGAAAACA 60.223 45.455 25.87 23.59 44.84 2.83
347 348 3.949754 TCGACCACTATTTGATACGACCT 59.050 43.478 0.00 0.00 0.00 3.85
384 385 9.838339 TTTTTATTTGGAAAATGCTTACCTTCA 57.162 25.926 0.00 0.00 0.00 3.02
385 386 9.487790 TTTTATTTGGAAAATGCTTACCTTCAG 57.512 29.630 0.00 0.00 0.00 3.02
386 387 4.519540 TTGGAAAATGCTTACCTTCAGC 57.480 40.909 0.00 0.00 37.82 4.26
387 388 2.825532 TGGAAAATGCTTACCTTCAGCC 59.174 45.455 0.00 0.00 36.33 4.85
389 390 1.463674 AAATGCTTACCTTCAGCCGG 58.536 50.000 0.00 0.00 36.33 6.13
391 392 0.392998 ATGCTTACCTTCAGCCGGTG 60.393 55.000 1.90 0.00 36.33 4.94
395 396 0.539986 TTACCTTCAGCCGGTGGATC 59.460 55.000 1.90 0.00 35.98 3.36
398 399 3.664025 CTTCAGCCGGTGGATCGCA 62.664 63.158 1.90 0.00 0.00 5.10
399 400 2.930385 CTTCAGCCGGTGGATCGCAT 62.930 60.000 1.90 0.00 0.00 4.73
400 401 3.274586 CAGCCGGTGGATCGCATG 61.275 66.667 1.90 0.00 0.00 4.06
420 421 1.153745 GAGTGATGCGCCGTCTTCT 60.154 57.895 4.18 6.43 0.00 2.85
423 424 0.855349 GTGATGCGCCGTCTTCTATG 59.145 55.000 4.18 0.00 0.00 2.23
425 426 0.855349 GATGCGCCGTCTTCTATGTG 59.145 55.000 4.18 0.00 0.00 3.21
426 427 0.175760 ATGCGCCGTCTTCTATGTGT 59.824 50.000 4.18 0.00 0.00 3.72
427 428 0.735978 TGCGCCGTCTTCTATGTGTG 60.736 55.000 4.18 0.00 0.00 3.82
428 429 0.457853 GCGCCGTCTTCTATGTGTGA 60.458 55.000 0.00 0.00 0.00 3.58
432 433 0.907837 CGTCTTCTATGTGTGACGCG 59.092 55.000 3.53 3.53 44.00 6.01
433 434 1.269166 GTCTTCTATGTGTGACGCGG 58.731 55.000 12.47 0.00 0.00 6.46
434 435 0.172578 TCTTCTATGTGTGACGCGGG 59.827 55.000 12.47 0.00 0.00 6.13
435 436 0.108804 CTTCTATGTGTGACGCGGGT 60.109 55.000 12.47 4.12 0.00 5.28
437 438 1.395635 TCTATGTGTGACGCGGGTAT 58.604 50.000 12.47 0.00 0.00 2.73
438 439 1.066454 TCTATGTGTGACGCGGGTATG 59.934 52.381 12.47 0.00 0.00 2.39
448 449 2.582436 CGGGTATGCGTGTCCCTT 59.418 61.111 15.75 0.00 39.10 3.95
449 450 1.813753 CGGGTATGCGTGTCCCTTG 60.814 63.158 15.75 2.01 39.10 3.61
450 451 1.298667 GGGTATGCGTGTCCCTTGT 59.701 57.895 12.09 0.00 38.29 3.16
451 452 1.024579 GGGTATGCGTGTCCCTTGTG 61.025 60.000 12.09 0.00 38.29 3.33
452 453 0.321298 GGTATGCGTGTCCCTTGTGT 60.321 55.000 0.00 0.00 0.00 3.72
453 454 1.076332 GTATGCGTGTCCCTTGTGTC 58.924 55.000 0.00 0.00 0.00 3.67
454 455 0.973632 TATGCGTGTCCCTTGTGTCT 59.026 50.000 0.00 0.00 0.00 3.41
455 456 0.320771 ATGCGTGTCCCTTGTGTCTC 60.321 55.000 0.00 0.00 0.00 3.36
456 457 1.367840 GCGTGTCCCTTGTGTCTCT 59.632 57.895 0.00 0.00 0.00 3.10
457 458 0.667792 GCGTGTCCCTTGTGTCTCTC 60.668 60.000 0.00 0.00 0.00 3.20
458 459 0.962489 CGTGTCCCTTGTGTCTCTCT 59.038 55.000 0.00 0.00 0.00 3.10
459 460 1.341531 CGTGTCCCTTGTGTCTCTCTT 59.658 52.381 0.00 0.00 0.00 2.85
461 462 2.630580 GTGTCCCTTGTGTCTCTCTTCT 59.369 50.000 0.00 0.00 0.00 2.85
463 464 2.630580 GTCCCTTGTGTCTCTCTTCTGT 59.369 50.000 0.00 0.00 0.00 3.41
465 466 4.281182 GTCCCTTGTGTCTCTCTTCTGTAA 59.719 45.833 0.00 0.00 0.00 2.41
466 467 4.281182 TCCCTTGTGTCTCTCTTCTGTAAC 59.719 45.833 0.00 0.00 0.00 2.50
469 470 6.226787 CCTTGTGTCTCTCTTCTGTAACATT 58.773 40.000 0.00 0.00 0.00 2.71
470 471 7.378966 CCTTGTGTCTCTCTTCTGTAACATTA 58.621 38.462 0.00 0.00 0.00 1.90
471 472 8.037758 CCTTGTGTCTCTCTTCTGTAACATTAT 58.962 37.037 0.00 0.00 0.00 1.28
472 473 8.763049 TTGTGTCTCTCTTCTGTAACATTATG 57.237 34.615 0.00 0.00 0.00 1.90
473 474 7.896811 TGTGTCTCTCTTCTGTAACATTATGT 58.103 34.615 0.00 0.00 0.00 2.29
474 475 7.814587 TGTGTCTCTCTTCTGTAACATTATGTG 59.185 37.037 0.00 0.00 0.00 3.21
475 476 7.815068 GTGTCTCTCTTCTGTAACATTATGTGT 59.185 37.037 0.00 0.00 44.84 3.72
476 477 7.814587 TGTCTCTCTTCTGTAACATTATGTGTG 59.185 37.037 0.00 0.00 41.14 3.82
477 478 7.815068 GTCTCTCTTCTGTAACATTATGTGTGT 59.185 37.037 0.00 0.00 41.14 3.72
478 479 8.367911 TCTCTCTTCTGTAACATTATGTGTGTT 58.632 33.333 0.00 0.00 41.14 3.32
480 481 6.898041 TCTTCTGTAACATTATGTGTGTTGC 58.102 36.000 0.00 1.52 41.14 4.17
481 482 6.484977 TCTTCTGTAACATTATGTGTGTTGCA 59.515 34.615 0.00 8.92 45.51 4.08
483 484 7.032377 TCTGTAACATTATGTGTGTTGCAAA 57.968 32.000 0.00 0.00 46.40 3.68
484 485 7.484140 TCTGTAACATTATGTGTGTTGCAAAA 58.516 30.769 0.00 0.00 46.40 2.44
485 486 7.976175 TCTGTAACATTATGTGTGTTGCAAAAA 59.024 29.630 0.00 0.00 46.40 1.94
486 487 8.654230 TGTAACATTATGTGTGTTGCAAAAAT 57.346 26.923 0.00 0.00 45.00 1.82
487 488 9.102757 TGTAACATTATGTGTGTTGCAAAAATT 57.897 25.926 0.00 0.00 45.00 1.82
488 489 9.928236 GTAACATTATGTGTGTTGCAAAAATTT 57.072 25.926 0.00 0.00 41.14 1.82
491 492 8.891720 ACATTATGTGTGTTGCAAAAATTTCTT 58.108 25.926 0.00 0.00 40.28 2.52
492 493 9.372541 CATTATGTGTGTTGCAAAAATTTCTTC 57.627 29.630 0.00 0.00 0.00 2.87
493 494 5.793026 TGTGTGTTGCAAAAATTTCTTCC 57.207 34.783 0.00 0.00 0.00 3.46
495 496 3.308323 TGTGTTGCAAAAATTTCTTCCGC 59.692 39.130 0.00 0.00 0.00 5.54
496 497 3.308323 GTGTTGCAAAAATTTCTTCCGCA 59.692 39.130 0.00 0.00 0.00 5.69
497 498 3.935203 TGTTGCAAAAATTTCTTCCGCAA 59.065 34.783 0.00 0.25 35.68 4.85
498 499 4.528531 TTGCAAAAATTTCTTCCGCAAC 57.471 36.364 0.00 0.00 33.31 4.17
499 500 3.525537 TGCAAAAATTTCTTCCGCAACA 58.474 36.364 0.00 0.00 0.00 3.33
500 501 3.935203 TGCAAAAATTTCTTCCGCAACAA 59.065 34.783 0.00 0.00 0.00 2.83
501 502 4.201763 TGCAAAAATTTCTTCCGCAACAAC 60.202 37.500 0.00 0.00 0.00 3.32
503 504 5.491973 CAAAAATTTCTTCCGCAACAACAG 58.508 37.500 0.00 0.00 0.00 3.16
504 505 4.385358 AAATTTCTTCCGCAACAACAGT 57.615 36.364 0.00 0.00 0.00 3.55
506 507 2.031258 TTCTTCCGCAACAACAGTCA 57.969 45.000 0.00 0.00 0.00 3.41
507 508 2.254546 TCTTCCGCAACAACAGTCAT 57.745 45.000 0.00 0.00 0.00 3.06
508 509 1.872952 TCTTCCGCAACAACAGTCATG 59.127 47.619 0.00 0.00 0.00 3.07
509 510 1.603802 CTTCCGCAACAACAGTCATGT 59.396 47.619 0.00 0.00 43.15 3.21
526 527 7.811236 ACAGTCATGTTGCAAAAGATAAAGATG 59.189 33.333 0.00 0.00 35.63 2.90
527 528 8.024865 CAGTCATGTTGCAAAAGATAAAGATGA 58.975 33.333 0.00 0.00 31.97 2.92
528 529 8.579006 AGTCATGTTGCAAAAGATAAAGATGAA 58.421 29.630 0.00 0.00 35.06 2.57
529 530 9.195411 GTCATGTTGCAAAAGATAAAGATGAAA 57.805 29.630 0.00 0.00 35.06 2.69
556 557 8.752766 AAACTCAAATATTCTCTGCAACATTG 57.247 30.769 0.00 0.00 0.00 2.82
558 559 7.889469 ACTCAAATATTCTCTGCAACATTGTT 58.111 30.769 0.00 0.00 0.00 2.83
560 561 8.523523 TCAAATATTCTCTGCAACATTGTTTG 57.476 30.769 0.00 0.00 0.00 2.93
561 562 8.143193 TCAAATATTCTCTGCAACATTGTTTGT 58.857 29.630 0.00 0.00 41.53 2.83
563 564 4.717233 TTCTCTGCAACATTGTTTGTGT 57.283 36.364 0.00 0.00 38.99 3.72
564 565 4.717233 TCTCTGCAACATTGTTTGTGTT 57.283 36.364 0.00 0.00 38.99 3.32
573 574 7.564044 CAACATTGTTTGTGTTGCAAATTTT 57.436 28.000 0.00 0.00 46.64 1.82
574 575 8.004585 CAACATTGTTTGTGTTGCAAATTTTT 57.995 26.923 0.00 0.00 46.64 1.94
575 576 8.154666 CAACATTGTTTGTGTTGCAAATTTTTC 58.845 29.630 0.00 0.00 46.64 2.29
579 580 4.612932 TTGTGTTGCAAATTTTTCCTGC 57.387 36.364 0.00 0.00 33.53 4.85
580 581 3.603532 TGTGTTGCAAATTTTTCCTGCA 58.396 36.364 0.00 0.00 44.04 4.41
586 587 2.613133 GCAAATTTTTCCTGCAACAGCA 59.387 40.909 0.00 0.00 36.09 4.41
587 588 3.546616 GCAAATTTTTCCTGCAACAGCAC 60.547 43.478 0.00 0.00 36.09 4.40
588 589 2.531522 ATTTTTCCTGCAACAGCACC 57.468 45.000 0.00 0.00 33.99 5.01
589 590 0.463620 TTTTTCCTGCAACAGCACCC 59.536 50.000 0.00 0.00 33.99 4.61
590 591 0.685785 TTTTCCTGCAACAGCACCCA 60.686 50.000 0.00 0.00 33.99 4.51
591 592 0.469705 TTTCCTGCAACAGCACCCAT 60.470 50.000 0.00 0.00 33.99 4.00
592 593 1.180456 TTCCTGCAACAGCACCCATG 61.180 55.000 0.00 0.00 33.99 3.66
593 594 1.904865 CCTGCAACAGCACCCATGT 60.905 57.895 0.00 0.00 33.99 3.21
594 595 1.466025 CCTGCAACAGCACCCATGTT 61.466 55.000 0.00 0.00 41.47 2.71
597 598 4.274012 AACAGCACCCATGTTGCA 57.726 50.000 16.53 0.00 40.52 4.08
598 599 2.514129 AACAGCACCCATGTTGCAA 58.486 47.368 16.53 0.00 40.52 4.08
599 600 0.829333 AACAGCACCCATGTTGCAAA 59.171 45.000 16.53 0.00 40.52 3.68
600 601 0.829333 ACAGCACCCATGTTGCAAAA 59.171 45.000 16.53 0.00 40.52 2.44
652 653 8.968242 CATCATCTATGTTGCAAATGATTTCTG 58.032 33.333 17.10 7.55 35.45 3.02
653 654 6.976349 TCATCTATGTTGCAAATGATTTCTGC 59.024 34.615 0.00 0.00 36.60 4.26
654 655 6.270156 TCTATGTTGCAAATGATTTCTGCA 57.730 33.333 0.00 0.67 44.04 4.41
662 663 7.155655 TGCAAATGATTTCTGCAACATAGTA 57.844 32.000 2.28 0.00 42.84 1.82
663 664 7.774134 TGCAAATGATTTCTGCAACATAGTAT 58.226 30.769 2.28 0.00 42.84 2.12
664 665 8.252417 TGCAAATGATTTCTGCAACATAGTATT 58.748 29.630 2.28 0.00 42.84 1.89
689 1781 8.630054 TTATGGTAAAGTATTTCTGCAACACT 57.370 30.769 0.00 0.00 40.09 3.55
690 1782 9.727859 TTATGGTAAAGTATTTCTGCAACACTA 57.272 29.630 0.00 0.00 40.09 2.74
691 1783 8.807948 ATGGTAAAGTATTTCTGCAACACTAT 57.192 30.769 0.00 0.00 40.09 2.12
692 1784 8.263940 TGGTAAAGTATTTCTGCAACACTATC 57.736 34.615 0.00 0.00 40.09 2.08
693 1785 7.880713 TGGTAAAGTATTTCTGCAACACTATCA 59.119 33.333 0.00 0.00 40.09 2.15
694 1786 8.893727 GGTAAAGTATTTCTGCAACACTATCAT 58.106 33.333 0.00 0.00 40.09 2.45
697 1789 7.928307 AGTATTTCTGCAACACTATCATTGT 57.072 32.000 0.00 0.00 0.00 2.71
698 1790 8.340618 AGTATTTCTGCAACACTATCATTGTT 57.659 30.769 0.00 0.00 37.69 2.83
705 1797 5.220557 CAACACTATCATTGTTGCGATGA 57.779 39.130 2.50 1.99 45.36 2.92
706 1798 4.864916 ACACTATCATTGTTGCGATGAC 57.135 40.909 1.56 0.00 37.13 3.06
707 1799 3.306973 ACACTATCATTGTTGCGATGACG 59.693 43.478 1.56 0.00 37.13 4.35
712 2206 2.411748 TCATTGTTGCGATGACGAGAAC 59.588 45.455 0.00 0.00 42.66 3.01
713 2207 1.859383 TTGTTGCGATGACGAGAACA 58.141 45.000 0.00 0.00 42.66 3.18
715 2209 1.525197 TGTTGCGATGACGAGAACAAC 59.475 47.619 0.00 0.00 39.01 3.32
726 2220 2.186076 CGAGAACAACGTCTGGATAGC 58.814 52.381 0.00 0.00 0.00 2.97
727 2221 2.159366 CGAGAACAACGTCTGGATAGCT 60.159 50.000 0.00 0.00 0.00 3.32
729 2223 4.261238 CGAGAACAACGTCTGGATAGCTAT 60.261 45.833 5.76 5.76 0.00 2.97
730 2224 5.049612 CGAGAACAACGTCTGGATAGCTATA 60.050 44.000 6.13 0.00 0.00 1.31
731 2225 6.074544 AGAACAACGTCTGGATAGCTATAC 57.925 41.667 9.21 9.21 0.00 1.47
742 2236 5.077564 TGGATAGCTATACATCTGACGGTT 58.922 41.667 15.02 0.00 0.00 4.44
743 2237 5.048013 TGGATAGCTATACATCTGACGGTTG 60.048 44.000 15.02 0.00 0.00 3.77
744 2238 3.099267 AGCTATACATCTGACGGTTGC 57.901 47.619 0.00 0.00 0.00 4.17
745 2239 2.135933 GCTATACATCTGACGGTTGCC 58.864 52.381 0.00 0.00 0.00 4.52
805 2390 4.131088 GGGCAGTCCGACTCGTCC 62.131 72.222 0.00 2.16 0.00 4.79
807 2392 2.179517 GCAGTCCGACTCGTCCAG 59.820 66.667 0.00 0.00 0.00 3.86
816 2401 4.394712 CTCGTCCAGCCACCCACC 62.395 72.222 0.00 0.00 0.00 4.61
869 2472 8.954350 ACACCGTTAGCCTGTTATATATAGTAG 58.046 37.037 0.00 0.00 0.00 2.57
870 2473 8.954350 CACCGTTAGCCTGTTATATATAGTAGT 58.046 37.037 0.00 0.00 0.00 2.73
898 2501 7.769272 ATATAAGTACGTAGCTAGGATCGAC 57.231 40.000 19.82 11.15 0.00 4.20
901 2504 1.595466 ACGTAGCTAGGATCGACCAG 58.405 55.000 19.82 3.98 42.04 4.00
906 2509 3.579534 AGCTAGGATCGACCAGACTAA 57.420 47.619 6.78 0.00 42.04 2.24
907 2510 3.899726 AGCTAGGATCGACCAGACTAAA 58.100 45.455 6.78 0.00 42.04 1.85
908 2511 3.633065 AGCTAGGATCGACCAGACTAAAC 59.367 47.826 6.78 0.00 42.04 2.01
909 2512 3.633065 GCTAGGATCGACCAGACTAAACT 59.367 47.826 6.78 0.00 42.04 2.66
910 2513 4.820716 GCTAGGATCGACCAGACTAAACTA 59.179 45.833 6.78 0.00 42.04 2.24
924 2535 7.010738 CCAGACTAAACTACTTTCAAACACGAA 59.989 37.037 0.00 0.00 0.00 3.85
979 2593 3.734902 CGCCTGCAAATTCCCATAAGAAC 60.735 47.826 0.00 0.00 0.00 3.01
1018 2632 2.616330 ATGAGCCGTTTGTGGTGCG 61.616 57.895 0.00 0.00 0.00 5.34
1138 2782 2.279517 GCCCAGCGTCGACTATGG 60.280 66.667 22.47 22.47 0.00 2.74
1139 2783 2.279517 CCCAGCGTCGACTATGGC 60.280 66.667 23.49 15.56 0.00 4.40
1145 2789 4.865761 GTCGACTATGGCGCGGCA 62.866 66.667 37.91 37.91 0.00 5.69
1147 2800 4.873129 CGACTATGGCGCGGCAGT 62.873 66.667 38.11 31.02 0.00 4.40
1150 2803 2.309764 GACTATGGCGCGGCAGTTTG 62.310 60.000 38.11 27.44 0.00 2.93
1158 2811 3.283684 CGGCAGTTTGGTCGGCAA 61.284 61.111 0.00 0.00 30.96 4.52
1359 3015 2.105006 AGCACAGGCATAAGACAGTG 57.895 50.000 0.00 0.00 44.61 3.66
1444 3100 3.702048 GTGGCCTGGGCGTCTACA 61.702 66.667 16.08 0.00 43.06 2.74
1452 3108 3.488090 GGCGTCTACAACAGCCGC 61.488 66.667 0.00 0.00 43.35 6.53
1629 3296 0.965866 TCTTCACCGGACTGCTCGAT 60.966 55.000 9.46 0.00 0.00 3.59
1651 3318 1.336125 GGTATAAGACCGACGGTGAGG 59.664 57.143 27.26 0.00 38.87 3.86
1774 4445 5.579718 AGTGGATTCAATCTAACGACGTAG 58.420 41.667 0.00 0.00 0.00 3.51
1875 4561 1.067582 GGCAATCCTACGTCGGAGG 59.932 63.158 18.21 18.21 36.31 4.30
2009 4695 2.022195 CTGATCTGTGGCCAATCCTTG 58.978 52.381 7.24 0.00 35.26 3.61
2068 5402 8.488651 ACTTTGTATATTACTTTTGTCTCGGG 57.511 34.615 0.00 0.00 0.00 5.14
2069 5403 8.098912 ACTTTGTATATTACTTTTGTCTCGGGT 58.901 33.333 0.00 0.00 0.00 5.28
2070 5404 8.483307 TTTGTATATTACTTTTGTCTCGGGTC 57.517 34.615 0.00 0.00 0.00 4.46
2073 5407 8.095792 TGTATATTACTTTTGTCTCGGGTCAAA 58.904 33.333 3.46 3.46 32.75 2.69
2081 5415 7.704899 ACTTTTGTCTCGGGTCAAATTTTTAAG 59.295 33.333 8.51 4.85 34.30 1.85
2110 6189 7.616313 TGACCAAGTATATGACATGTGTGTTA 58.384 34.615 1.15 0.00 39.09 2.41
2324 6703 2.125106 GCCGACCCTCACCACATC 60.125 66.667 0.00 0.00 0.00 3.06
2331 6710 1.002087 ACCCTCACCACATCGAACTTC 59.998 52.381 0.00 0.00 0.00 3.01
2730 7333 0.610232 GCTGCTGGTTTCCATCCACT 60.610 55.000 0.00 0.00 30.82 4.00
2767 7375 0.035439 TTGGGAAGGCAACCGAGATC 60.035 55.000 0.00 0.00 37.17 2.75
2777 7385 2.034812 GCAACCGAGATCGTAGGAGATT 59.965 50.000 10.41 0.00 37.74 2.40
2790 7398 6.629128 TCGTAGGAGATTATACTCTACGGAG 58.371 44.000 17.25 0.00 44.62 4.63
2846 7454 7.363181 CCAAGAGAAGATTGTGGCATTTATCAA 60.363 37.037 0.00 0.00 0.00 2.57
3040 7651 9.938280 ACGGTGCATTATATATAGTACACAAAT 57.062 29.630 16.28 3.31 0.00 2.32
3044 7655 9.173021 TGCATTATATATAGTACACAAATGGGC 57.827 33.333 0.00 0.00 0.00 5.36
3085 7698 1.890041 CGGTTGAAGCGTTGGGTCA 60.890 57.895 8.81 0.00 33.95 4.02
3136 7750 1.671166 AAAAATCCGGCCCAACTGC 59.329 52.632 0.00 0.00 0.00 4.40
3145 7795 1.336755 CGGCCCAACTGCAATTATACC 59.663 52.381 0.00 0.00 0.00 2.73
3191 7841 0.958876 GTTTGGGTTAGCGGTCCCTG 60.959 60.000 12.19 0.00 43.74 4.45
3220 7870 2.663196 CCGGGTTGACCTCACTCC 59.337 66.667 0.00 0.00 36.97 3.85
3233 7886 2.200370 ACTCCCCGTCACACTCCA 59.800 61.111 0.00 0.00 0.00 3.86
3241 7894 0.972983 CGTCACACTCCATCCTCCCT 60.973 60.000 0.00 0.00 0.00 4.20
3242 7895 0.539051 GTCACACTCCATCCTCCCTG 59.461 60.000 0.00 0.00 0.00 4.45
3322 7979 2.103094 TCACATACTCCACATAGGCAGC 59.897 50.000 0.00 0.00 37.29 5.25
3380 8037 2.235402 TCCAACTCTTTCCATACCGGAC 59.765 50.000 9.46 0.00 46.36 4.79
3396 8053 1.078143 GACGCCAAAGCCCATCTCT 60.078 57.895 0.00 0.00 34.57 3.10
3409 8066 5.675538 AGCCCATCTCTCAGTTGTATTAAC 58.324 41.667 0.00 0.00 0.00 2.01
3500 8157 0.719465 GTCCGTGTTGAATAGGCGTG 59.281 55.000 0.00 0.00 0.00 5.34
3536 8193 3.748568 AGAGCACAAAACCGAGAATTCTC 59.251 43.478 23.20 23.20 39.55 2.87
3651 8317 5.010282 ACAGCAAATTTGTAGGAAGGTAGG 58.990 41.667 19.03 0.00 0.00 3.18
3739 8407 6.630443 GCATAGAAGATGACAAGCGTTAATTG 59.370 38.462 0.00 0.00 0.00 2.32
3869 8541 5.845985 TCAAGTGAATCAAATGAGACGTC 57.154 39.130 7.70 7.70 0.00 4.34
3917 8589 7.420800 CATCTGAAATAATGTTAACAGAGGGC 58.579 38.462 14.65 2.79 37.70 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.034863 TGAACGGGCAAATAGGGGAC 60.035 55.000 0.00 0.00 0.00 4.46
42 43 5.995282 AGAACCGAAACATCTATGAACACAA 59.005 36.000 0.00 0.00 0.00 3.33
185 186 6.442952 TCAAAGGTGAACGAAATATTTGTGG 58.557 36.000 5.17 0.00 0.00 4.17
229 230 3.304726 GCACTGCTACAAGGGAAGAAAAC 60.305 47.826 0.00 0.00 0.00 2.43
246 247 0.234106 CTGACAGAAACGCAGCACTG 59.766 55.000 0.00 0.00 36.58 3.66
261 262 5.215239 GCTCTTGCTCTATGTTTTCTGAC 57.785 43.478 0.00 0.00 36.03 3.51
329 330 8.740906 ACATCTATAGGTCGTATCAAATAGTGG 58.259 37.037 0.00 0.00 0.00 4.00
367 368 2.159379 CGGCTGAAGGTAAGCATTTTCC 60.159 50.000 0.00 0.00 42.69 3.13
369 370 1.818674 CCGGCTGAAGGTAAGCATTTT 59.181 47.619 0.00 0.00 42.69 1.82
371 372 0.328258 ACCGGCTGAAGGTAAGCATT 59.672 50.000 0.00 0.00 42.69 3.56
378 379 2.990479 GATCCACCGGCTGAAGGT 59.010 61.111 0.00 0.00 43.97 3.50
379 380 2.202932 CGATCCACCGGCTGAAGG 60.203 66.667 0.00 0.00 0.00 3.46
380 381 2.892425 GCGATCCACCGGCTGAAG 60.892 66.667 0.00 0.00 0.00 3.02
381 382 3.030168 ATGCGATCCACCGGCTGAA 62.030 57.895 0.00 0.00 0.00 3.02
382 383 3.469970 ATGCGATCCACCGGCTGA 61.470 61.111 0.00 0.00 0.00 4.26
383 384 3.274586 CATGCGATCCACCGGCTG 61.275 66.667 0.00 0.00 0.00 4.85
386 387 4.889856 TCGCATGCGATCCACCGG 62.890 66.667 37.21 7.94 44.01 5.28
406 407 0.855349 CACATAGAAGACGGCGCATC 59.145 55.000 10.83 6.21 0.00 3.91
407 408 0.175760 ACACATAGAAGACGGCGCAT 59.824 50.000 10.83 0.00 0.00 4.73
408 409 0.735978 CACACATAGAAGACGGCGCA 60.736 55.000 10.83 0.00 0.00 6.09
409 410 0.457853 TCACACATAGAAGACGGCGC 60.458 55.000 6.90 0.00 0.00 6.53
410 411 1.269166 GTCACACATAGAAGACGGCG 58.731 55.000 4.80 4.80 0.00 6.46
414 415 1.269166 CCGCGTCACACATAGAAGAC 58.731 55.000 4.92 0.00 0.00 3.01
420 421 0.528901 GCATACCCGCGTCACACATA 60.529 55.000 4.92 0.00 0.00 2.29
432 433 1.024579 CACAAGGGACACGCATACCC 61.025 60.000 0.00 0.00 43.55 3.69
433 434 0.321298 ACACAAGGGACACGCATACC 60.321 55.000 0.00 0.00 0.00 2.73
434 435 1.076332 GACACAAGGGACACGCATAC 58.924 55.000 0.00 0.00 0.00 2.39
435 436 0.973632 AGACACAAGGGACACGCATA 59.026 50.000 0.00 0.00 0.00 3.14
437 438 1.069090 GAGACACAAGGGACACGCA 59.931 57.895 0.00 0.00 0.00 5.24
438 439 0.667792 GAGAGACACAAGGGACACGC 60.668 60.000 0.00 0.00 0.00 5.34
440 441 2.630580 AGAAGAGAGACACAAGGGACAC 59.369 50.000 0.00 0.00 0.00 3.67
441 442 2.630098 CAGAAGAGAGACACAAGGGACA 59.370 50.000 0.00 0.00 0.00 4.02
442 443 2.630580 ACAGAAGAGAGACACAAGGGAC 59.369 50.000 0.00 0.00 0.00 4.46
443 444 2.964209 ACAGAAGAGAGACACAAGGGA 58.036 47.619 0.00 0.00 0.00 4.20
444 445 4.039245 TGTTACAGAAGAGAGACACAAGGG 59.961 45.833 0.00 0.00 0.00 3.95
446 447 8.867935 CATAATGTTACAGAAGAGAGACACAAG 58.132 37.037 0.00 0.00 0.00 3.16
448 449 7.814587 CACATAATGTTACAGAAGAGAGACACA 59.185 37.037 0.00 0.00 0.00 3.72
449 450 7.815068 ACACATAATGTTACAGAAGAGAGACAC 59.185 37.037 0.00 0.00 38.98 3.67
450 451 7.814587 CACACATAATGTTACAGAAGAGAGACA 59.185 37.037 0.00 0.00 40.64 3.41
451 452 7.815068 ACACACATAATGTTACAGAAGAGAGAC 59.185 37.037 0.00 0.00 40.64 3.36
452 453 7.896811 ACACACATAATGTTACAGAAGAGAGA 58.103 34.615 0.00 0.00 40.64 3.10
453 454 8.438513 CAACACACATAATGTTACAGAAGAGAG 58.561 37.037 0.00 0.00 40.64 3.20
454 455 7.095229 GCAACACACATAATGTTACAGAAGAGA 60.095 37.037 0.00 0.00 40.64 3.10
455 456 7.017645 GCAACACACATAATGTTACAGAAGAG 58.982 38.462 0.00 0.00 40.64 2.85
456 457 6.484977 TGCAACACACATAATGTTACAGAAGA 59.515 34.615 0.00 0.00 40.64 2.87
457 458 6.667370 TGCAACACACATAATGTTACAGAAG 58.333 36.000 0.00 0.00 40.64 2.85
458 459 6.625873 TGCAACACACATAATGTTACAGAA 57.374 33.333 0.00 0.00 40.64 3.02
459 460 6.625873 TTGCAACACACATAATGTTACAGA 57.374 33.333 0.00 0.00 40.64 3.41
461 462 8.654230 ATTTTTGCAACACACATAATGTTACA 57.346 26.923 0.00 0.00 40.64 2.41
465 466 8.436046 AGAAATTTTTGCAACACACATAATGT 57.564 26.923 0.00 0.00 44.81 2.71
466 467 9.372541 GAAGAAATTTTTGCAACACACATAATG 57.627 29.630 0.00 0.00 0.00 1.90
469 470 6.199908 CGGAAGAAATTTTTGCAACACACATA 59.800 34.615 0.00 0.00 0.00 2.29
470 471 5.006552 CGGAAGAAATTTTTGCAACACACAT 59.993 36.000 0.00 0.00 0.00 3.21
471 472 4.328440 CGGAAGAAATTTTTGCAACACACA 59.672 37.500 0.00 0.00 0.00 3.72
472 473 4.781883 GCGGAAGAAATTTTTGCAACACAC 60.782 41.667 0.00 0.00 0.00 3.82
473 474 3.308323 GCGGAAGAAATTTTTGCAACACA 59.692 39.130 0.00 0.00 0.00 3.72
474 475 3.308323 TGCGGAAGAAATTTTTGCAACAC 59.692 39.130 0.00 0.00 0.00 3.32
475 476 3.525537 TGCGGAAGAAATTTTTGCAACA 58.474 36.364 0.00 0.00 0.00 3.33
476 477 4.528531 TTGCGGAAGAAATTTTTGCAAC 57.471 36.364 0.00 0.00 36.09 4.17
477 478 3.935203 TGTTGCGGAAGAAATTTTTGCAA 59.065 34.783 0.00 0.00 38.40 4.08
478 479 3.525537 TGTTGCGGAAGAAATTTTTGCA 58.474 36.364 0.00 0.00 0.00 4.08
480 481 5.063312 ACTGTTGTTGCGGAAGAAATTTTTG 59.937 36.000 0.00 0.00 0.00 2.44
481 482 5.175127 ACTGTTGTTGCGGAAGAAATTTTT 58.825 33.333 0.00 0.00 0.00 1.94
483 484 4.142271 TGACTGTTGTTGCGGAAGAAATTT 60.142 37.500 0.00 0.00 0.00 1.82
484 485 3.380004 TGACTGTTGTTGCGGAAGAAATT 59.620 39.130 0.00 0.00 0.00 1.82
485 486 2.948979 TGACTGTTGTTGCGGAAGAAAT 59.051 40.909 0.00 0.00 0.00 2.17
486 487 2.360844 TGACTGTTGTTGCGGAAGAAA 58.639 42.857 0.00 0.00 0.00 2.52
487 488 2.031258 TGACTGTTGTTGCGGAAGAA 57.969 45.000 0.00 0.00 0.00 2.52
488 489 1.872952 CATGACTGTTGTTGCGGAAGA 59.127 47.619 0.00 0.00 0.00 2.87
491 492 1.674359 AACATGACTGTTGTTGCGGA 58.326 45.000 0.00 0.00 43.92 5.54
499 500 7.715657 TCTTTATCTTTTGCAACATGACTGTT 58.284 30.769 0.00 0.00 46.54 3.16
500 501 7.275888 TCTTTATCTTTTGCAACATGACTGT 57.724 32.000 0.00 0.00 37.12 3.55
501 502 8.024865 TCATCTTTATCTTTTGCAACATGACTG 58.975 33.333 0.00 0.00 0.00 3.51
503 504 8.746922 TTCATCTTTATCTTTTGCAACATGAC 57.253 30.769 0.00 0.00 0.00 3.06
504 505 9.761504 TTTTCATCTTTATCTTTTGCAACATGA 57.238 25.926 0.00 0.00 0.00 3.07
529 530 9.768662 AATGTTGCAGAGAATATTTGAGTTTTT 57.231 25.926 0.00 0.00 0.00 1.94
531 532 8.362639 ACAATGTTGCAGAGAATATTTGAGTTT 58.637 29.630 0.00 0.00 0.00 2.66
532 533 7.889469 ACAATGTTGCAGAGAATATTTGAGTT 58.111 30.769 0.00 0.00 0.00 3.01
533 534 7.458409 ACAATGTTGCAGAGAATATTTGAGT 57.542 32.000 0.00 0.00 0.00 3.41
534 535 8.644619 CAAACAATGTTGCAGAGAATATTTGAG 58.355 33.333 0.00 0.00 0.00 3.02
535 536 8.143193 ACAAACAATGTTGCAGAGAATATTTGA 58.857 29.630 0.00 0.00 40.06 2.69
536 537 8.218441 CACAAACAATGTTGCAGAGAATATTTG 58.782 33.333 0.00 0.00 41.46 2.32
537 538 7.927629 ACACAAACAATGTTGCAGAGAATATTT 59.072 29.630 0.00 0.00 41.46 1.40
538 539 7.436118 ACACAAACAATGTTGCAGAGAATATT 58.564 30.769 0.00 0.00 41.46 1.28
539 540 6.985117 ACACAAACAATGTTGCAGAGAATAT 58.015 32.000 0.00 0.00 41.46 1.28
541 542 5.266733 ACACAAACAATGTTGCAGAGAAT 57.733 34.783 0.00 0.00 41.46 2.40
542 543 4.717233 ACACAAACAATGTTGCAGAGAA 57.283 36.364 0.00 0.00 41.46 2.87
543 544 4.717233 AACACAAACAATGTTGCAGAGA 57.283 36.364 0.00 0.00 41.46 3.10
558 559 4.005650 TGCAGGAAAAATTTGCAACACAA 58.994 34.783 0.00 0.00 44.13 3.33
564 565 2.613133 GCTGTTGCAGGAAAAATTTGCA 59.387 40.909 0.00 0.00 45.28 4.08
565 566 2.613133 TGCTGTTGCAGGAAAAATTTGC 59.387 40.909 0.00 0.00 45.31 3.68
578 579 4.659480 CAACATGGGTGCTGTTGC 57.341 55.556 0.00 0.00 44.78 4.17
580 581 0.829333 TTTGCAACATGGGTGCTGTT 59.171 45.000 20.33 0.00 37.31 3.16
581 582 0.829333 TTTTGCAACATGGGTGCTGT 59.171 45.000 20.33 0.00 0.00 4.40
582 583 1.950828 TTTTTGCAACATGGGTGCTG 58.049 45.000 20.33 1.92 0.00 4.41
626 627 8.968242 CAGAAATCATTTGCAACATAGATGATG 58.032 33.333 19.32 9.86 37.48 3.07
629 630 6.754675 TGCAGAAATCATTTGCAACATAGATG 59.245 34.615 0.00 0.00 44.13 2.90
638 639 6.028146 ACTATGTTGCAGAAATCATTTGCA 57.972 33.333 0.00 0.00 45.28 4.08
662 663 9.855021 GTGTTGCAGAAATACTTTACCATAAAT 57.145 29.630 0.00 0.00 0.00 1.40
663 664 9.073475 AGTGTTGCAGAAATACTTTACCATAAA 57.927 29.630 0.00 0.00 36.92 1.40
664 665 8.630054 AGTGTTGCAGAAATACTTTACCATAA 57.370 30.769 0.00 0.00 36.92 1.90
667 1759 7.880713 TGATAGTGTTGCAGAAATACTTTACCA 59.119 33.333 0.00 0.00 40.39 3.25
668 1760 8.263940 TGATAGTGTTGCAGAAATACTTTACC 57.736 34.615 0.00 0.00 40.39 2.85
671 1763 8.796475 ACAATGATAGTGTTGCAGAAATACTTT 58.204 29.630 0.00 0.00 40.39 2.66
673 1765 7.928307 ACAATGATAGTGTTGCAGAAATACT 57.072 32.000 0.00 0.00 42.33 2.12
689 1781 4.040445 TCTCGTCATCGCAACAATGATA 57.960 40.909 0.00 0.00 35.69 2.15
690 1782 2.892374 TCTCGTCATCGCAACAATGAT 58.108 42.857 0.00 0.00 35.69 2.45
691 1783 2.362169 TCTCGTCATCGCAACAATGA 57.638 45.000 0.00 0.00 36.96 2.57
692 1784 2.157474 TGTTCTCGTCATCGCAACAATG 59.843 45.455 0.00 0.00 36.97 2.82
693 1785 2.412870 TGTTCTCGTCATCGCAACAAT 58.587 42.857 0.00 0.00 36.97 2.71
694 1786 1.859383 TGTTCTCGTCATCGCAACAA 58.141 45.000 0.00 0.00 36.97 2.83
695 1787 1.525197 GTTGTTCTCGTCATCGCAACA 59.475 47.619 0.00 0.00 36.81 3.33
697 1789 0.781787 CGTTGTTCTCGTCATCGCAA 59.218 50.000 0.00 0.00 36.96 4.85
698 1790 0.318360 ACGTTGTTCTCGTCATCGCA 60.318 50.000 0.00 0.00 36.85 5.10
699 1791 2.431539 ACGTTGTTCTCGTCATCGC 58.568 52.632 0.00 0.00 36.85 4.58
705 1797 2.415625 GCTATCCAGACGTTGTTCTCGT 60.416 50.000 0.00 0.00 44.27 4.18
706 1798 2.159366 AGCTATCCAGACGTTGTTCTCG 60.159 50.000 0.00 0.00 0.00 4.04
707 1799 3.512033 AGCTATCCAGACGTTGTTCTC 57.488 47.619 0.00 0.00 0.00 2.87
712 2206 6.072452 TCAGATGTATAGCTATCCAGACGTTG 60.072 42.308 10.16 6.11 0.00 4.10
713 2207 6.004574 TCAGATGTATAGCTATCCAGACGTT 58.995 40.000 10.16 0.00 0.00 3.99
715 2209 5.446607 CGTCAGATGTATAGCTATCCAGACG 60.447 48.000 18.42 18.42 41.43 4.18
718 2212 4.702612 ACCGTCAGATGTATAGCTATCCAG 59.297 45.833 10.16 0.00 0.00 3.86
719 2213 4.663334 ACCGTCAGATGTATAGCTATCCA 58.337 43.478 10.16 5.31 0.00 3.41
722 2216 4.322049 GGCAACCGTCAGATGTATAGCTAT 60.322 45.833 11.77 11.77 0.00 2.97
723 2217 3.005472 GGCAACCGTCAGATGTATAGCTA 59.995 47.826 0.00 0.00 0.00 3.32
726 2220 2.394708 CGGCAACCGTCAGATGTATAG 58.605 52.381 0.00 0.00 42.73 1.31
727 2221 2.502213 CGGCAACCGTCAGATGTATA 57.498 50.000 0.00 0.00 42.73 1.47
729 2223 4.902308 CGGCAACCGTCAGATGTA 57.098 55.556 0.00 0.00 42.73 2.29
742 2236 3.109547 CAAAGCTACGCGTCGGCA 61.110 61.111 29.33 9.30 39.92 5.69
743 2237 4.500568 GCAAAGCTACGCGTCGGC 62.501 66.667 18.63 21.83 0.00 5.54
744 2238 3.849953 GGCAAAGCTACGCGTCGG 61.850 66.667 18.63 11.80 0.00 4.79
745 2239 3.849953 GGGCAAAGCTACGCGTCG 61.850 66.667 18.63 11.79 0.00 5.12
751 2245 4.426313 AGGCGGGGGCAAAGCTAC 62.426 66.667 0.00 0.00 0.00 3.58
752 2246 4.109675 GAGGCGGGGGCAAAGCTA 62.110 66.667 0.00 0.00 0.00 3.32
835 2429 2.033194 GCTAACGGTGTGGCCTGTC 61.033 63.158 3.32 0.00 34.25 3.51
842 2436 7.600065 ACTATATATAACAGGCTAACGGTGTG 58.400 38.462 0.00 0.00 0.00 3.82
843 2437 7.771927 ACTATATATAACAGGCTAACGGTGT 57.228 36.000 0.00 0.00 0.00 4.16
872 2475 9.307121 GTCGATCCTAGCTACGTACTTATATTA 57.693 37.037 0.00 0.00 0.00 0.98
873 2476 7.279758 GGTCGATCCTAGCTACGTACTTATATT 59.720 40.741 0.00 0.00 0.00 1.28
874 2477 6.760770 GGTCGATCCTAGCTACGTACTTATAT 59.239 42.308 0.00 0.00 0.00 0.86
875 2478 6.102663 GGTCGATCCTAGCTACGTACTTATA 58.897 44.000 0.00 0.00 0.00 0.98
876 2479 4.934602 GGTCGATCCTAGCTACGTACTTAT 59.065 45.833 0.00 0.00 0.00 1.73
898 2501 6.477688 TCGTGTTTGAAAGTAGTTTAGTCTGG 59.522 38.462 0.00 0.00 0.00 3.86
901 2504 8.749192 CTTTCGTGTTTGAAAGTAGTTTAGTC 57.251 34.615 7.82 0.00 46.20 2.59
979 2593 1.665161 GGTCGGTCGATAATACGCTGG 60.665 57.143 0.00 0.00 0.00 4.85
1018 2632 2.280052 GAGCATCTGGGAGAGCGC 60.280 66.667 0.00 0.00 0.00 5.92
1222 2875 1.825191 GGTCGCATGTGGCCATCAT 60.825 57.895 24.85 11.97 40.31 2.45
1359 3015 3.488569 TCCGGATGGCATGGGTCC 61.489 66.667 3.81 0.00 34.14 4.46
1647 3314 2.276116 AAGAGCGAAGGCGACCTCA 61.276 57.895 0.00 0.00 46.35 3.86
1651 3318 2.738521 TGCAAGAGCGAAGGCGAC 60.739 61.111 0.00 0.00 46.23 5.19
1981 4667 4.299586 TGGCCACAGATCAGTCATTTTA 57.700 40.909 0.00 0.00 0.00 1.52
1986 4672 1.065199 GGATTGGCCACAGATCAGTCA 60.065 52.381 3.88 0.00 36.34 3.41
1989 4675 2.022195 CAAGGATTGGCCACAGATCAG 58.978 52.381 3.88 0.00 43.94 2.90
1998 4684 5.972256 TTTCACATGAAAACAAGGATTGGCC 60.972 40.000 0.00 0.00 43.81 5.36
2009 4695 8.316640 ACAGAGAGAGTATTTCACATGAAAAC 57.683 34.615 10.90 10.15 45.81 2.43
2047 5380 7.172868 TGACCCGAGACAAAAGTAATATACA 57.827 36.000 0.00 0.00 0.00 2.29
2049 5382 9.675464 AATTTGACCCGAGACAAAAGTAATATA 57.325 29.630 0.00 0.00 40.21 0.86
2062 5396 5.975693 ATGCTTAAAAATTTGACCCGAGA 57.024 34.783 0.00 0.00 0.00 4.04
2063 5397 6.089417 GTCAATGCTTAAAAATTTGACCCGAG 59.911 38.462 0.00 0.00 39.99 4.63
2065 5399 6.151975 GTCAATGCTTAAAAATTTGACCCG 57.848 37.500 0.00 0.00 39.99 5.28
2068 5402 8.141835 ACTTGGTCAATGCTTAAAAATTTGAC 57.858 30.769 5.72 5.72 43.31 3.18
2069 5403 9.995003 ATACTTGGTCAATGCTTAAAAATTTGA 57.005 25.926 0.00 0.00 0.00 2.69
2081 5415 6.038603 ACACATGTCATATACTTGGTCAATGC 59.961 38.462 0.00 0.00 37.52 3.56
2110 6189 9.817809 ATACGAATCTAACTGTATGATTTGTGT 57.182 29.630 23.91 19.08 41.88 3.72
2188 6267 5.918011 GCGTTTGACCATTGACAAGATTAAA 59.082 36.000 0.00 0.00 0.00 1.52
2767 7375 6.629128 TCTCCGTAGAGTATAATCTCCTACG 58.371 44.000 14.11 14.11 41.26 3.51
2790 7398 2.964464 TGATCAGCTTCCAGGATCTCTC 59.036 50.000 11.12 0.00 38.55 3.20
2800 7408 1.202746 GGGTGAGGATGATCAGCTTCC 60.203 57.143 19.00 12.54 45.03 3.46
2846 7454 2.799126 TCCTCCATTGTATTGGCGTT 57.201 45.000 0.00 0.00 36.66 4.84
3040 7651 1.140052 CACCCAGATAATACACGCCCA 59.860 52.381 0.00 0.00 0.00 5.36
3044 7655 4.600692 TGGATCACCCAGATAATACACG 57.399 45.455 0.00 0.00 40.82 4.49
3085 7698 6.608808 ACAATTATGCTCTTGGGCTTTAAGAT 59.391 34.615 0.00 0.00 33.99 2.40
3124 7738 1.336755 GTATAATTGCAGTTGGGCCGG 59.663 52.381 4.47 0.00 0.00 6.13
3168 7818 1.339727 GGACCGCTAACCCAAACTCAT 60.340 52.381 0.00 0.00 0.00 2.90
3172 7822 3.991999 GGGACCGCTAACCCAAAC 58.008 61.111 0.00 0.00 44.96 2.93
3191 7841 2.728435 AACCCGGCGTATGGAGACC 61.728 63.158 6.01 0.00 0.00 3.85
3220 7870 1.517832 GAGGATGGAGTGTGACGGG 59.482 63.158 0.00 0.00 0.00 5.28
3233 7886 0.972983 CGGTGTGAGACAGGGAGGAT 60.973 60.000 0.00 0.00 0.00 3.24
3241 7894 1.552792 TGGATTATGCGGTGTGAGACA 59.447 47.619 0.00 0.00 0.00 3.41
3242 7895 1.933853 GTGGATTATGCGGTGTGAGAC 59.066 52.381 0.00 0.00 0.00 3.36
3293 7950 2.571202 TGTGGAGTATGTGAATCTGGCA 59.429 45.455 0.00 0.00 0.00 4.92
3298 7955 4.960938 TGCCTATGTGGAGTATGTGAATC 58.039 43.478 0.00 0.00 38.35 2.52
3380 8037 1.078214 TGAGAGATGGGCTTTGGCG 60.078 57.895 0.00 0.00 39.81 5.69
3409 8066 5.768662 TCACCGAGGGATATAACTTCTACAG 59.231 44.000 0.00 0.00 0.00 2.74
3500 8157 7.095649 GGTTTTGTGCTCTCCAAAAATCATTAC 60.096 37.037 0.00 0.00 41.82 1.89
3536 8193 0.607217 TCCACATGTTCAGCCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3622 8288 3.496884 TCCTACAAATTTGCTGTCACGAC 59.503 43.478 18.12 0.00 0.00 4.34
3651 8317 5.009010 CACTGGCAACTCATATGTAAATCCC 59.991 44.000 1.90 0.00 37.61 3.85
3739 8407 4.934602 GCTTCAGATGATTCCACTATAGGC 59.065 45.833 4.43 0.00 0.00 3.93
3820 8488 1.452108 CCGATGTTCCTCCCTTGGC 60.452 63.158 0.00 0.00 0.00 4.52
3869 8541 3.553511 GCACATCAGTCTTCATTCTACCG 59.446 47.826 0.00 0.00 0.00 4.02
3917 8589 6.456447 TGACGGTTCTTTCTGTTATTTACG 57.544 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.