Multiple sequence alignment - TraesCS5A01G266900

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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 TraesCS5A01G266900 chr5A 100.000 4065 0 0 1 4065 478323165 478319101 0.000000e+00 7507
1 TraesCS5A01G266900 chr5B 84.738 1697 163 45 1665 3334 450841419 450839792 0.000000e+00 1611
2 TraesCS5A01G266900 chr5B 90.288 1040 64 19 635 1665 450842475 450841464 0.000000e+00 1327
3 TraesCS5A01G266900 chr5B 89.432 757 40 15 3330 4064 450839614 450838876 0.000000e+00 918
4 TraesCS5A01G266900 chr5B 86.874 739 78 12 933 1665 516605667 516604942 0.000000e+00 809
5 TraesCS5A01G266900 chr5B 89.574 470 19 10 1 459 450843073 450842623 1.640000e-158 569
6 TraesCS5A01G266900 chr5D 87.158 1207 101 36 481 1665 377535101 377533927 0.000000e+00 1321
7 TraesCS5A01G266900 chr5D 84.783 828 77 18 1668 2481 377533880 377533088 0.000000e+00 785
8 TraesCS5A01G266900 chr5D 87.730 652 68 7 2594 3240 377532657 377532013 0.000000e+00 750
9 TraesCS5A01G266900 chr5D 92.505 507 27 6 3563 4064 377531623 377531123 0.000000e+00 715
10 TraesCS5A01G266900 chr5D 90.870 460 17 8 1 449 377535527 377535082 9.730000e-166 593
11 TraesCS5A01G266900 chr5D 91.045 201 15 1 3297 3497 377531996 377531799 6.700000e-68 268
12 TraesCS5A01G266900 chr5D 98.387 62 1 0 3494 3555 377531762 377531701 4.300000e-20 110
13 TraesCS5A01G266900 chr6B 87.640 534 56 8 1136 1665 575575932 575575405 2.690000e-171 612
14 TraesCS5A01G266900 chr4B 84.848 297 34 9 1007 1297 149735484 149735775 5.140000e-74 289
15 TraesCS5A01G266900 chr7A 94.595 185 10 0 999 1183 229143261 229143077 1.850000e-73 287
16 TraesCS5A01G266900 chr7B 92.857 196 12 2 990 1183 184299349 184299544 2.390000e-72 283
17 TraesCS5A01G266900 chr7B 84.300 293 33 8 1007 1292 683245404 683245690 1.440000e-69 274
18 TraesCS5A01G266900 chr7D 93.122 189 13 0 995 1183 216082336 216082148 1.110000e-70 278
19 TraesCS5A01G266900 chr6D 80.161 373 53 15 1102 1469 427527775 427528131 4.030000e-65 259
20 TraesCS5A01G266900 chr4A 83.165 297 35 9 1007 1294 707060512 707060802 1.450000e-64 257
21 TraesCS5A01G266900 chr1B 85.043 234 24 6 1678 1910 212226278 212226501 1.140000e-55 228


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 TraesCS5A01G266900 chr5A 478319101 478323165 4064 True 7507.000000 7507 100.000 1 4065 1 chr5A.!!$R1 4064
1 TraesCS5A01G266900 chr5B 450838876 450843073 4197 True 1106.250000 1611 88.508 1 4064 4 chr5B.!!$R2 4063
2 TraesCS5A01G266900 chr5B 516604942 516605667 725 True 809.000000 809 86.874 933 1665 1 chr5B.!!$R1 732
3 TraesCS5A01G266900 chr5D 377531123 377535527 4404 True 648.857143 1321 90.354 1 4064 7 chr5D.!!$R1 4063
4 TraesCS5A01G266900 chr6B 575575405 575575932 527 True 612.000000 612 87.640 1136 1665 1 chr6B.!!$R1 529

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
605 634 0.106769 TTTCCTGCTGCTGGTGTTGA 60.107 50.0 22.62 2.87 0.00 3.18 F
611 640 0.391130 GCTGCTGGTGTTGATCCGTA 60.391 55.0 0.00 0.00 0.00 4.02 F
778 811 0.604780 CTCTTCCACACAGCACAGGG 60.605 60.0 0.00 0.00 0.00 4.45 F
2078 2178 0.740868 TTGCATGACTAGCACGAGGC 60.741 55.0 0.00 0.00 42.54 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2177 0.034089 AGGTATCTTTGGCTGGTGGC 60.034 55.0 0.00 0.0 40.90 5.01 R
2385 2494 0.179113 CCAACCACACAAGCCACAAC 60.179 55.0 0.00 0.0 0.00 3.32 R
2386 2495 1.954362 GCCAACCACACAAGCCACAA 61.954 55.0 0.00 0.0 0.00 3.33 R
3656 4395 0.466124 GAGTAGCCGGGAAGATTGCT 59.534 55.0 2.18 0.0 37.84 3.91 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
26 27 4.200283 CTGAGCGAGTCCTCCGGC 62.200 72.222 0.00 0.00 0.00 6.13
160 171 4.856487 CGTAGAACTCTGAAGCAGAAGAAG 59.144 45.833 0.00 0.00 40.18 2.85
161 172 5.335269 CGTAGAACTCTGAAGCAGAAGAAGA 60.335 44.000 0.00 0.00 40.18 2.87
162 173 5.543507 AGAACTCTGAAGCAGAAGAAGAA 57.456 39.130 0.00 0.00 40.18 2.52
193 204 2.492484 ACCTGAACTAGATGTCACCGTC 59.508 50.000 0.00 0.00 0.00 4.79
195 206 2.156917 TGAACTAGATGTCACCGTCGT 58.843 47.619 0.00 0.00 0.00 4.34
253 264 3.728718 GGCGTTGAACTGTTTAATGTGTG 59.271 43.478 15.77 1.45 0.00 3.82
254 265 4.347813 GCGTTGAACTGTTTAATGTGTGT 58.652 39.130 15.77 0.00 0.00 3.72
255 266 4.436523 GCGTTGAACTGTTTAATGTGTGTC 59.563 41.667 15.77 0.00 0.00 3.67
256 267 5.564768 CGTTGAACTGTTTAATGTGTGTCA 58.435 37.500 8.60 0.00 0.00 3.58
267 278 3.953712 ATGTGTGTCAGTCGTGGATTA 57.046 42.857 0.00 0.00 0.00 1.75
282 293 3.502211 GTGGATTATTGTTAGCCCGGATG 59.498 47.826 0.73 0.00 0.00 3.51
283 294 3.081804 GGATTATTGTTAGCCCGGATGG 58.918 50.000 0.73 0.00 37.09 3.51
284 295 3.244770 GGATTATTGTTAGCCCGGATGGA 60.245 47.826 0.73 0.00 37.49 3.41
285 296 4.567747 GGATTATTGTTAGCCCGGATGGAT 60.568 45.833 0.73 0.00 37.49 3.41
327 338 1.344226 TATCGTCGTGTCGTCGTCGT 61.344 55.000 1.33 6.94 41.28 4.34
328 339 2.539972 ATCGTCGTGTCGTCGTCGTC 62.540 60.000 1.33 0.00 41.28 4.20
329 340 2.857992 GTCGTGTCGTCGTCGTCG 60.858 66.667 5.50 5.50 38.33 5.12
417 429 0.454600 GGCTGTGATGCTGATGGTTG 59.545 55.000 0.00 0.00 0.00 3.77
432 444 6.128035 GCTGATGGTTGTTCTTTTTGGTTTTT 60.128 34.615 0.00 0.00 0.00 1.94
440 452 7.685532 TGTTCTTTTTGGTTTTTGTTTTTGC 57.314 28.000 0.00 0.00 0.00 3.68
441 453 7.257722 TGTTCTTTTTGGTTTTTGTTTTTGCA 58.742 26.923 0.00 0.00 0.00 4.08
442 454 7.759433 TGTTCTTTTTGGTTTTTGTTTTTGCAA 59.241 25.926 0.00 0.00 0.00 4.08
443 455 7.920908 TCTTTTTGGTTTTTGTTTTTGCAAG 57.079 28.000 0.00 0.00 0.00 4.01
444 456 6.419116 TCTTTTTGGTTTTTGTTTTTGCAAGC 59.581 30.769 0.00 0.00 0.00 4.01
445 457 5.444663 TTTGGTTTTTGTTTTTGCAAGCT 57.555 30.435 0.00 0.00 0.00 3.74
446 458 5.444663 TTGGTTTTTGTTTTTGCAAGCTT 57.555 30.435 0.00 0.00 0.00 3.74
447 459 5.444663 TGGTTTTTGTTTTTGCAAGCTTT 57.555 30.435 0.00 0.00 0.00 3.51
448 460 5.836347 TGGTTTTTGTTTTTGCAAGCTTTT 58.164 29.167 0.00 0.00 0.00 2.27
449 461 6.276091 TGGTTTTTGTTTTTGCAAGCTTTTT 58.724 28.000 0.00 0.00 0.00 1.94
450 462 6.199719 TGGTTTTTGTTTTTGCAAGCTTTTTG 59.800 30.769 0.00 0.00 0.00 2.44
451 463 5.819270 TTTTGTTTTTGCAAGCTTTTTGC 57.181 30.435 0.00 0.00 45.11 3.68
460 472 3.428163 GCAAGCTTTTTGCAAGTTTTGG 58.572 40.909 0.00 0.00 45.94 3.28
461 473 3.119884 GCAAGCTTTTTGCAAGTTTTGGT 60.120 39.130 0.00 0.00 45.94 3.67
462 474 4.405196 CAAGCTTTTTGCAAGTTTTGGTG 58.595 39.130 0.00 0.00 45.94 4.17
463 475 3.673902 AGCTTTTTGCAAGTTTTGGTGT 58.326 36.364 0.00 0.00 45.94 4.16
464 476 4.071423 AGCTTTTTGCAAGTTTTGGTGTT 58.929 34.783 0.00 0.00 45.94 3.32
465 477 4.154015 AGCTTTTTGCAAGTTTTGGTGTTC 59.846 37.500 0.00 0.00 45.94 3.18
466 478 4.154015 GCTTTTTGCAAGTTTTGGTGTTCT 59.846 37.500 0.00 0.00 42.31 3.01
467 479 5.334802 GCTTTTTGCAAGTTTTGGTGTTCTT 60.335 36.000 0.00 0.00 42.31 2.52
468 480 6.625873 TTTTTGCAAGTTTTGGTGTTCTTT 57.374 29.167 0.00 0.00 0.00 2.52
469 481 5.604010 TTTGCAAGTTTTGGTGTTCTTTG 57.396 34.783 0.00 0.00 0.00 2.77
470 482 4.264460 TGCAAGTTTTGGTGTTCTTTGT 57.736 36.364 0.00 0.00 0.00 2.83
471 483 3.993081 TGCAAGTTTTGGTGTTCTTTGTG 59.007 39.130 0.00 0.00 0.00 3.33
472 484 3.370672 GCAAGTTTTGGTGTTCTTTGTGG 59.629 43.478 0.00 0.00 0.00 4.17
473 485 4.815269 CAAGTTTTGGTGTTCTTTGTGGA 58.185 39.130 0.00 0.00 0.00 4.02
474 486 5.418676 CAAGTTTTGGTGTTCTTTGTGGAT 58.581 37.500 0.00 0.00 0.00 3.41
475 487 5.675684 AGTTTTGGTGTTCTTTGTGGATT 57.324 34.783 0.00 0.00 0.00 3.01
476 488 6.048732 AGTTTTGGTGTTCTTTGTGGATTT 57.951 33.333 0.00 0.00 0.00 2.17
477 489 6.472016 AGTTTTGGTGTTCTTTGTGGATTTT 58.528 32.000 0.00 0.00 0.00 1.82
478 490 6.939730 AGTTTTGGTGTTCTTTGTGGATTTTT 59.060 30.769 0.00 0.00 0.00 1.94
479 491 6.976636 TTTGGTGTTCTTTGTGGATTTTTC 57.023 33.333 0.00 0.00 0.00 2.29
480 492 5.930837 TGGTGTTCTTTGTGGATTTTTCT 57.069 34.783 0.00 0.00 0.00 2.52
481 493 6.293004 TGGTGTTCTTTGTGGATTTTTCTT 57.707 33.333 0.00 0.00 0.00 2.52
482 494 6.706295 TGGTGTTCTTTGTGGATTTTTCTTT 58.294 32.000 0.00 0.00 0.00 2.52
483 495 7.841956 TGGTGTTCTTTGTGGATTTTTCTTTA 58.158 30.769 0.00 0.00 0.00 1.85
484 496 8.482128 TGGTGTTCTTTGTGGATTTTTCTTTAT 58.518 29.630 0.00 0.00 0.00 1.40
485 497 9.325198 GGTGTTCTTTGTGGATTTTTCTTTATT 57.675 29.630 0.00 0.00 0.00 1.40
510 522 5.421212 TTTTGCAAATTTTCCTGTGATGC 57.579 34.783 13.65 0.00 0.00 3.91
518 530 4.707030 TTTTCCTGTGATGCTGCTAATG 57.293 40.909 0.00 0.00 0.00 1.90
527 539 3.376234 TGATGCTGCTAATGTTTCTGCTC 59.624 43.478 0.00 0.00 0.00 4.26
528 540 2.086869 TGCTGCTAATGTTTCTGCTCC 58.913 47.619 0.00 0.00 0.00 4.70
529 541 2.290514 TGCTGCTAATGTTTCTGCTCCT 60.291 45.455 0.00 0.00 0.00 3.69
530 542 3.055167 TGCTGCTAATGTTTCTGCTCCTA 60.055 43.478 0.00 0.00 0.00 2.94
531 543 3.559242 GCTGCTAATGTTTCTGCTCCTAG 59.441 47.826 0.00 0.00 0.00 3.02
532 544 3.535561 TGCTAATGTTTCTGCTCCTAGC 58.464 45.455 0.00 0.00 42.82 3.42
533 545 3.198635 TGCTAATGTTTCTGCTCCTAGCT 59.801 43.478 0.00 0.00 42.97 3.32
534 546 3.807071 GCTAATGTTTCTGCTCCTAGCTC 59.193 47.826 0.00 0.00 42.97 4.09
540 552 2.759973 TGCTCCTAGCTCCCGTGG 60.760 66.667 0.00 0.00 42.97 4.94
565 589 4.687483 GCTGATGGTTTTTCTGTTTGGATG 59.313 41.667 0.00 0.00 0.00 3.51
595 624 1.500108 TTGCGCAATTTTTCCTGCTG 58.500 45.000 21.02 0.00 0.00 4.41
598 627 1.065358 CGCAATTTTTCCTGCTGCTG 58.935 50.000 0.00 0.00 0.00 4.41
601 630 2.409975 CAATTTTTCCTGCTGCTGGTG 58.590 47.619 22.62 10.56 0.00 4.17
604 633 0.746063 TTTTCCTGCTGCTGGTGTTG 59.254 50.000 22.62 0.00 0.00 3.33
605 634 0.106769 TTTCCTGCTGCTGGTGTTGA 60.107 50.000 22.62 2.87 0.00 3.18
608 637 1.310933 CCTGCTGCTGGTGTTGATCC 61.311 60.000 16.56 0.00 0.00 3.36
609 638 1.642037 CTGCTGCTGGTGTTGATCCG 61.642 60.000 0.00 0.00 0.00 4.18
611 640 0.391130 GCTGCTGGTGTTGATCCGTA 60.391 55.000 0.00 0.00 0.00 4.02
614 643 1.277842 TGCTGGTGTTGATCCGTATGT 59.722 47.619 0.00 0.00 0.00 2.29
617 646 3.595173 CTGGTGTTGATCCGTATGTTGA 58.405 45.455 0.00 0.00 0.00 3.18
618 647 4.191544 CTGGTGTTGATCCGTATGTTGAT 58.808 43.478 0.00 0.00 0.00 2.57
622 651 5.583061 GGTGTTGATCCGTATGTTGATGTTA 59.417 40.000 0.00 0.00 0.00 2.41
625 654 6.312672 TGTTGATCCGTATGTTGATGTTACTG 59.687 38.462 0.00 0.00 0.00 2.74
630 659 4.094294 CCGTATGTTGATGTTACTGGGTTG 59.906 45.833 0.00 0.00 0.00 3.77
631 660 4.436852 CGTATGTTGATGTTACTGGGTTGC 60.437 45.833 0.00 0.00 0.00 4.17
632 661 3.222173 TGTTGATGTTACTGGGTTGCT 57.778 42.857 0.00 0.00 0.00 3.91
633 662 2.884012 TGTTGATGTTACTGGGTTGCTG 59.116 45.455 0.00 0.00 0.00 4.41
638 671 2.331166 TGTTACTGGGTTGCTGGAGTA 58.669 47.619 0.00 0.00 0.00 2.59
650 683 2.270275 CTGGAGTACGTCTTCAGCTG 57.730 55.000 7.63 7.63 42.13 4.24
652 685 2.229062 CTGGAGTACGTCTTCAGCTGAA 59.771 50.000 26.87 26.87 42.13 3.02
671 704 2.262423 AGTTGACTGGCTTTGGAGAC 57.738 50.000 0.00 0.00 0.00 3.36
673 706 2.147150 GTTGACTGGCTTTGGAGACTC 58.853 52.381 0.00 0.00 0.00 3.36
698 731 1.446272 CAGGAGAAGGCGACGGTTC 60.446 63.158 0.00 0.00 0.00 3.62
708 741 1.134530 GCGACGGTTCAGAGATCACG 61.135 60.000 0.00 0.00 0.00 4.35
778 811 0.604780 CTCTTCCACACAGCACAGGG 60.605 60.000 0.00 0.00 0.00 4.45
815 848 1.548269 AGAAGACGGCCAAGAGAAGAG 59.452 52.381 2.24 0.00 0.00 2.85
816 849 1.546476 GAAGACGGCCAAGAGAAGAGA 59.454 52.381 2.24 0.00 0.00 3.10
817 850 1.633774 AGACGGCCAAGAGAAGAGAA 58.366 50.000 2.24 0.00 0.00 2.87
818 851 1.548269 AGACGGCCAAGAGAAGAGAAG 59.452 52.381 2.24 0.00 0.00 2.85
819 852 1.546476 GACGGCCAAGAGAAGAGAAGA 59.454 52.381 2.24 0.00 0.00 2.87
890 923 4.871910 CTAGCCAGCCAGCCAGCC 62.872 72.222 0.00 0.00 0.00 4.85
943 987 2.691779 GGGAGACGAGAGGGGGAGA 61.692 68.421 0.00 0.00 0.00 3.71
1201 1250 5.095809 AGGTAGTAATCCAACACCCAGTAA 58.904 41.667 0.00 0.00 0.00 2.24
1215 1265 4.027437 ACCCAGTAATCTCTGTCTCCTTC 58.973 47.826 0.00 0.00 34.02 3.46
1255 1305 1.595382 CCTGCGTATGCCCTAGTGC 60.595 63.158 4.05 0.00 41.78 4.40
1287 1337 1.001020 GGTGGTGTCCATGGCATGA 60.001 57.895 28.43 11.86 35.28 3.07
1357 1409 7.228108 TGCATTTCAGATTTATCAGTGATCTCC 59.772 37.037 9.42 0.00 0.00 3.71
1381 1433 2.032620 AGTTGCTCGATATCCGGAAGT 58.967 47.619 9.01 0.00 39.14 3.01
1400 1452 7.360946 CCGGAAGTAATTCTGAAGTTTAAGTGG 60.361 40.741 13.22 0.00 0.00 4.00
1404 1456 4.749245 ATTCTGAAGTTTAAGTGGCGTG 57.251 40.909 0.00 0.00 0.00 5.34
1407 1459 2.215196 TGAAGTTTAAGTGGCGTGGTC 58.785 47.619 0.00 0.00 0.00 4.02
1429 1481 4.023536 TCGAATTTGGTAGAAGGTGTTTGC 60.024 41.667 0.00 0.00 0.00 3.68
1516 1570 2.775911 TGAGCATCTTTGAGGTCTGG 57.224 50.000 0.00 0.00 34.92 3.86
1540 1594 1.301716 AGGTGCACTGGTTACGCTG 60.302 57.895 17.98 0.00 0.00 5.18
1541 1595 1.597027 GGTGCACTGGTTACGCTGT 60.597 57.895 17.98 0.00 0.00 4.40
1640 1694 2.309162 TGAGTGGGACTACTACTGCTCT 59.691 50.000 0.00 0.00 0.00 4.09
1651 1705 9.504708 GGACTACTACTGCTCTTATCATAGTTA 57.495 37.037 0.00 0.00 0.00 2.24
1720 1819 3.928375 GCACATGGATGAAAATTGGTGTC 59.072 43.478 0.00 0.00 0.00 3.67
1730 1829 6.907853 TGAAAATTGGTGTCATGATTACCA 57.092 33.333 23.37 23.37 42.40 3.25
1731 1830 7.479352 TGAAAATTGGTGTCATGATTACCAT 57.521 32.000 26.05 16.22 43.45 3.55
1732 1831 8.586879 TGAAAATTGGTGTCATGATTACCATA 57.413 30.769 26.05 19.30 43.45 2.74
1736 1835 8.677148 AATTGGTGTCATGATTACCATAGTAC 57.323 34.615 26.05 1.57 43.45 2.73
1761 1860 1.757118 CCGTAGTGATGTGAGTGGGAT 59.243 52.381 0.00 0.00 0.00 3.85
1773 1872 2.111384 GAGTGGGATTACTCCTGCTCA 58.889 52.381 14.06 0.00 40.92 4.26
1845 1945 7.893824 TGTTCGAAAAATGTCATGTTTTTCTG 58.106 30.769 21.12 16.68 46.05 3.02
1851 1951 6.592798 AAATGTCATGTTTTTCTGTTGCTG 57.407 33.333 0.00 0.00 0.00 4.41
1855 1955 5.101628 GTCATGTTTTTCTGTTGCTGAACA 58.898 37.500 0.00 0.00 39.88 3.18
2053 2153 4.825422 TCTGACCAAAGTGCTCTTATCTG 58.175 43.478 0.66 5.07 33.09 2.90
2059 2159 4.699257 CCAAAGTGCTCTTATCTGCTTTCT 59.301 41.667 0.66 0.00 33.09 2.52
2074 2174 2.475187 GCTTTCTTGCATGACTAGCACG 60.475 50.000 21.55 0.00 42.54 5.34
2077 2177 1.134995 TCTTGCATGACTAGCACGAGG 60.135 52.381 0.00 0.00 42.54 4.63
2078 2178 0.740868 TTGCATGACTAGCACGAGGC 60.741 55.000 0.00 0.00 42.54 4.70
2079 2179 1.884926 GCATGACTAGCACGAGGCC 60.885 63.158 0.00 0.00 46.50 5.19
2099 2199 0.995024 ACCAGCCAAAGATACCTGCT 59.005 50.000 0.00 0.00 0.00 4.24
2106 2206 4.471386 AGCCAAAGATACCTGCTTCTCTTA 59.529 41.667 0.00 0.00 0.00 2.10
2114 2214 7.800092 AGATACCTGCTTCTCTTATTGATTGT 58.200 34.615 0.00 0.00 0.00 2.71
2120 2220 5.942236 TGCTTCTCTTATTGATTGTCTGCTT 59.058 36.000 0.00 0.00 0.00 3.91
2157 2257 3.334691 TGCGGGAAATTGACTACTGAAG 58.665 45.455 0.00 0.00 0.00 3.02
2186 2286 3.737972 GCACCCTTTGACTTGTTTTCCTG 60.738 47.826 0.00 0.00 0.00 3.86
2196 2296 5.580297 TGACTTGTTTTCCTGCATGTTTTTC 59.420 36.000 0.00 0.00 0.00 2.29
2198 2298 6.172630 ACTTGTTTTCCTGCATGTTTTTCTT 58.827 32.000 0.00 0.00 0.00 2.52
2201 2301 7.446001 TGTTTTCCTGCATGTTTTTCTTTTT 57.554 28.000 0.00 0.00 0.00 1.94
2257 2357 2.546795 GCTCGTGTCTATGGATTCTGGG 60.547 54.545 0.00 0.00 0.00 4.45
2289 2390 5.460419 GCACTCGAGGAAATACTGAATAGTG 59.540 44.000 18.41 1.64 37.78 2.74
2385 2494 9.301153 GCACTATTCAGTTAATTGGGTAAAATG 57.699 33.333 0.00 0.00 30.46 2.32
2405 2514 1.954362 TTGTGGCTTGTGTGGTTGGC 61.954 55.000 0.00 0.00 0.00 4.52
2408 2517 2.026014 GCTTGTGTGGTTGGCACG 59.974 61.111 0.00 0.00 39.53 5.34
2430 2539 4.493708 CGCATGATTTCAGAGTGTCATGTC 60.494 45.833 16.71 11.25 45.95 3.06
2446 2558 8.474025 AGTGTCATGTCCATCTTAAAACAAAAA 58.526 29.630 0.00 0.00 0.00 1.94
2482 2602 3.715628 ATCTGAACCTGCACACAAAAC 57.284 42.857 0.00 0.00 0.00 2.43
2502 2622 5.520748 AACTTGTCCAGGGAGAATGTAAT 57.479 39.130 0.00 0.00 0.00 1.89
2577 2711 7.645402 TGATGTGCTTTATCATTTATGCTCTG 58.355 34.615 0.00 0.00 30.03 3.35
2579 2713 7.395190 TGTGCTTTATCATTTATGCTCTGTT 57.605 32.000 0.00 0.00 0.00 3.16
2591 2725 6.647212 TTATGCTCTGTTGTTCATTACGAG 57.353 37.500 0.00 0.00 0.00 4.18
2599 2733 7.351981 TCTGTTGTTCATTACGAGTGATTTTG 58.648 34.615 0.00 0.00 0.00 2.44
2605 3035 4.764823 TCATTACGAGTGATTTTGGGCTTT 59.235 37.500 0.00 0.00 0.00 3.51
2613 3043 7.773690 ACGAGTGATTTTGGGCTTTATATTAGT 59.226 33.333 0.00 0.00 0.00 2.24
2618 3048 8.846211 TGATTTTGGGCTTTATATTAGTGTAGC 58.154 33.333 0.00 0.00 0.00 3.58
2627 3057 0.105039 ATTAGTGTAGCGAGCCCTGC 59.895 55.000 0.00 0.00 0.00 4.85
2640 3070 1.226686 GCCCTGCTGCGATGACTATG 61.227 60.000 0.00 0.00 0.00 2.23
2645 3075 3.486375 CCTGCTGCGATGACTATGTTTTG 60.486 47.826 0.00 0.00 0.00 2.44
2681 3111 6.209391 AGCAGGATAAGTTAAGTGCACATTTT 59.791 34.615 21.04 7.37 33.24 1.82
2691 3121 4.825546 AGTGCACATTTTGTTCTCTCAG 57.174 40.909 21.04 0.00 0.00 3.35
2693 3123 4.274459 AGTGCACATTTTGTTCTCTCAGAC 59.726 41.667 21.04 0.00 0.00 3.51
2695 3125 3.817647 GCACATTTTGTTCTCTCAGACCT 59.182 43.478 0.00 0.00 0.00 3.85
2733 3167 8.974060 TTGAACTTAGAACCAGACTTAAACAT 57.026 30.769 0.00 0.00 0.00 2.71
2734 3168 8.603242 TGAACTTAGAACCAGACTTAAACATC 57.397 34.615 0.00 0.00 0.00 3.06
2736 3170 8.608844 AACTTAGAACCAGACTTAAACATCAG 57.391 34.615 0.00 0.00 0.00 2.90
2787 3222 6.982852 TCGATAGACAAAAGTGAAGAGTTCT 58.017 36.000 0.00 0.00 42.67 3.01
2789 3224 7.382488 TCGATAGACAAAAGTGAAGAGTTCTTG 59.618 37.037 0.00 0.00 42.67 3.02
2799 3234 7.164230 AGTGAAGAGTTCTTGATCGATAACT 57.836 36.000 12.34 12.34 36.11 2.24
2806 3242 7.972623 AGTTCTTGATCGATAACTCTAAACG 57.027 36.000 7.71 0.00 0.00 3.60
2820 3256 5.915175 ACTCTAAACGTATCCATTCCTTCC 58.085 41.667 0.00 0.00 0.00 3.46
2821 3257 5.163332 ACTCTAAACGTATCCATTCCTTCCC 60.163 44.000 0.00 0.00 0.00 3.97
2830 3266 5.682234 ATCCATTCCTTCCCAAATGAAAC 57.318 39.130 0.00 0.00 35.35 2.78
2834 3270 5.359576 CCATTCCTTCCCAAATGAAACGATA 59.640 40.000 0.00 0.00 35.35 2.92
2841 3277 4.457603 TCCCAAATGAAACGATAACACCAG 59.542 41.667 0.00 0.00 0.00 4.00
2845 3281 1.804151 TGAAACGATAACACCAGCAGC 59.196 47.619 0.00 0.00 0.00 5.25
2848 3284 0.736325 ACGATAACACCAGCAGCGTC 60.736 55.000 0.00 0.00 0.00 5.19
2850 3286 1.726853 GATAACACCAGCAGCGTCTT 58.273 50.000 0.00 0.00 0.00 3.01
2851 3287 1.661112 GATAACACCAGCAGCGTCTTC 59.339 52.381 0.00 0.00 0.00 2.87
2873 3309 5.128205 TCTTATCATGGCTTGATTGACAGG 58.872 41.667 19.42 4.36 42.62 4.00
2899 3335 4.121317 CTCATCTTTGACAGGCTGAGATC 58.879 47.826 23.66 9.19 35.93 2.75
2929 3365 1.227497 GGCGAGGCTGAAGATGGAG 60.227 63.158 0.00 0.00 0.00 3.86
2932 3368 1.805871 GCGAGGCTGAAGATGGAGAAG 60.806 57.143 0.00 0.00 0.00 2.85
2992 3428 2.238521 GCCTCCAATCAAGACAACCAA 58.761 47.619 0.00 0.00 0.00 3.67
3055 3491 3.322514 CCTTCGTTTCTCCAAGGCA 57.677 52.632 0.00 0.00 30.57 4.75
3065 3501 3.795688 TCTCCAAGGCAAAGAAGTGAT 57.204 42.857 0.00 0.00 0.00 3.06
3073 3510 2.749621 GGCAAAGAAGTGATGGACGAAT 59.250 45.455 0.00 0.00 0.00 3.34
3081 3518 1.227380 GATGGACGAATGAGGCGCT 60.227 57.895 7.64 0.00 0.00 5.92
3240 3684 3.206150 TCATGCCGAGCTAAGGATTTTC 58.794 45.455 11.57 0.00 0.00 2.29
3242 3686 2.632377 TGCCGAGCTAAGGATTTTCAG 58.368 47.619 11.57 0.00 0.00 3.02
3244 3688 3.010420 GCCGAGCTAAGGATTTTCAGTT 58.990 45.455 11.57 0.00 0.00 3.16
3246 3690 4.082733 GCCGAGCTAAGGATTTTCAGTTTT 60.083 41.667 11.57 0.00 0.00 2.43
3248 3692 6.086871 CCGAGCTAAGGATTTTCAGTTTTTC 58.913 40.000 1.60 0.00 0.00 2.29
3249 3693 6.293955 CCGAGCTAAGGATTTTCAGTTTTTCA 60.294 38.462 1.60 0.00 0.00 2.69
3250 3694 7.308435 CGAGCTAAGGATTTTCAGTTTTTCAT 58.692 34.615 0.00 0.00 0.00 2.57
3252 3696 8.822652 AGCTAAGGATTTTCAGTTTTTCATTG 57.177 30.769 0.00 0.00 0.00 2.82
3254 3698 8.490355 GCTAAGGATTTTCAGTTTTTCATTGTG 58.510 33.333 0.00 0.00 0.00 3.33
3255 3699 9.533253 CTAAGGATTTTCAGTTTTTCATTGTGT 57.467 29.630 0.00 0.00 0.00 3.72
3256 3700 7.775397 AGGATTTTCAGTTTTTCATTGTGTG 57.225 32.000 0.00 0.00 0.00 3.82
3265 3709 6.645827 CAGTTTTTCATTGTGTGCATTATGGA 59.354 34.615 0.00 0.00 0.00 3.41
3266 3710 7.332430 CAGTTTTTCATTGTGTGCATTATGGAT 59.668 33.333 0.00 0.00 0.00 3.41
3335 3961 0.886563 GCTGCAAATGGAACTCAGCT 59.113 50.000 5.40 0.00 44.71 4.24
3340 3966 2.490903 GCAAATGGAACTCAGCTGATGT 59.509 45.455 18.63 14.38 0.00 3.06
3342 3968 4.156556 GCAAATGGAACTCAGCTGATGTAA 59.843 41.667 18.63 2.73 0.00 2.41
3401 4032 1.983119 TACCAGGCCCAGCTATGCAC 61.983 60.000 0.00 0.00 0.00 4.57
3477 4108 9.280174 GAATGTTCCGGTATTAATTCTCCAATA 57.720 33.333 0.00 0.00 0.00 1.90
3492 4123 9.997172 AATTCTCCAATATTTCTTTCCCTTACT 57.003 29.630 0.00 0.00 0.00 2.24
3610 4348 7.786030 TCCTGCCAACTTATATATATCTCAGC 58.214 38.462 0.00 0.00 0.00 4.26
3611 4349 7.621285 TCCTGCCAACTTATATATATCTCAGCT 59.379 37.037 0.00 0.00 0.00 4.24
3612 4350 7.925483 CCTGCCAACTTATATATATCTCAGCTC 59.075 40.741 0.00 0.00 0.00 4.09
3613 4351 8.366359 TGCCAACTTATATATATCTCAGCTCA 57.634 34.615 0.00 0.00 0.00 4.26
3615 4353 9.829507 GCCAACTTATATATATCTCAGCTCAAT 57.170 33.333 0.00 0.00 0.00 2.57
3656 4395 5.630680 CCGTTCTTAACAGCTACGAAAACTA 59.369 40.000 4.57 0.00 32.56 2.24
3666 4406 4.870991 AGCTACGAAAACTAGCAATCTTCC 59.129 41.667 4.99 0.00 39.36 3.46
3732 4472 2.224426 ACATTGCTCGGTTTAGTCCACA 60.224 45.455 0.00 0.00 0.00 4.17
3769 4514 3.326747 CCTGTGTACCAGAGCACTTTAC 58.673 50.000 11.58 0.00 44.49 2.01
3839 4587 3.385193 AAAATTCCAGCTTTGGGAACG 57.615 42.857 6.17 0.00 46.53 3.95
3853 4601 1.203758 GGGAACGGCCATTTGTTTAGG 59.796 52.381 2.24 0.00 38.95 2.69
3861 4609 2.675032 GCCATTTGTTTAGGCTTGGAGC 60.675 50.000 3.36 0.00 44.92 4.70
3882 4630 2.124151 ATCAACGGCTGGCCCATC 60.124 61.111 0.00 0.00 0.00 3.51
3932 4680 3.782443 GTCGTCCTCCGGGCCAAT 61.782 66.667 4.39 0.00 37.11 3.16
3979 4727 0.598065 AAAGCACCATGGAAACGCTC 59.402 50.000 21.47 0.00 31.17 5.03
3980 4728 1.244019 AAGCACCATGGAAACGCTCC 61.244 55.000 21.47 0.00 45.64 4.70
4052 4806 0.925466 CCGCCACGTCTATAAAACCG 59.075 55.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.043652 CCCTGGTTCATGGGGCTG 60.044 66.667 0.00 0.00 39.76 4.85
32 33 1.221840 CGGGACTCCCTGGTTCATG 59.778 63.158 12.62 0.00 42.67 3.07
187 198 2.184385 ATTACGCTAAGACGACGGTG 57.816 50.000 0.00 0.00 36.70 4.94
193 204 2.919229 ACCACGAAATTACGCTAAGACG 59.081 45.455 0.00 0.00 36.70 4.18
195 206 3.119884 TCGACCACGAAATTACGCTAAGA 60.120 43.478 0.00 0.00 45.74 2.10
253 264 4.270325 GGCTAACAATAATCCACGACTGAC 59.730 45.833 0.00 0.00 0.00 3.51
254 265 4.439057 GGCTAACAATAATCCACGACTGA 58.561 43.478 0.00 0.00 0.00 3.41
255 266 3.560068 GGGCTAACAATAATCCACGACTG 59.440 47.826 0.00 0.00 0.00 3.51
256 267 3.740141 CGGGCTAACAATAATCCACGACT 60.740 47.826 0.00 0.00 0.00 4.18
267 278 1.494721 ACATCCATCCGGGCTAACAAT 59.505 47.619 0.00 0.00 36.21 2.71
282 293 3.245284 CGACACATTAATCCACGACATCC 59.755 47.826 0.00 0.00 0.00 3.51
283 294 3.245284 CCGACACATTAATCCACGACATC 59.755 47.826 0.00 0.00 0.00 3.06
284 295 3.118920 TCCGACACATTAATCCACGACAT 60.119 43.478 0.00 0.00 0.00 3.06
285 296 2.231721 TCCGACACATTAATCCACGACA 59.768 45.455 0.00 0.00 0.00 4.35
327 338 0.039256 CCACCGGTTAAACTCGACGA 60.039 55.000 2.97 0.00 0.00 4.20
328 339 0.318955 ACCACCGGTTAAACTCGACG 60.319 55.000 2.97 0.00 27.29 5.12
329 340 1.869774 AACCACCGGTTAAACTCGAC 58.130 50.000 2.97 0.00 44.94 4.20
417 429 7.685532 TGCAAAAACAAAAACCAAAAAGAAC 57.314 28.000 0.00 0.00 0.00 3.01
440 452 4.083377 ACACCAAAACTTGCAAAAAGCTTG 60.083 37.500 0.00 0.42 45.94 4.01
441 453 4.071423 ACACCAAAACTTGCAAAAAGCTT 58.929 34.783 0.00 0.00 45.94 3.74
442 454 3.673902 ACACCAAAACTTGCAAAAAGCT 58.326 36.364 0.00 0.00 45.94 3.74
443 455 4.154015 AGAACACCAAAACTTGCAAAAAGC 59.846 37.500 0.00 0.00 45.96 3.51
444 456 5.861222 AGAACACCAAAACTTGCAAAAAG 57.139 34.783 0.00 0.00 0.00 2.27
445 457 6.038714 ACAAAGAACACCAAAACTTGCAAAAA 59.961 30.769 0.00 0.00 0.00 1.94
446 458 5.529060 ACAAAGAACACCAAAACTTGCAAAA 59.471 32.000 0.00 0.00 0.00 2.44
447 459 5.049818 CACAAAGAACACCAAAACTTGCAAA 60.050 36.000 0.00 0.00 0.00 3.68
448 460 4.450419 CACAAAGAACACCAAAACTTGCAA 59.550 37.500 0.00 0.00 0.00 4.08
449 461 3.993081 CACAAAGAACACCAAAACTTGCA 59.007 39.130 0.00 0.00 0.00 4.08
450 462 3.370672 CCACAAAGAACACCAAAACTTGC 59.629 43.478 0.00 0.00 0.00 4.01
451 463 4.815269 TCCACAAAGAACACCAAAACTTG 58.185 39.130 0.00 0.00 0.00 3.16
452 464 5.675684 ATCCACAAAGAACACCAAAACTT 57.324 34.783 0.00 0.00 0.00 2.66
453 465 5.675684 AATCCACAAAGAACACCAAAACT 57.324 34.783 0.00 0.00 0.00 2.66
454 466 6.735678 AAAATCCACAAAGAACACCAAAAC 57.264 33.333 0.00 0.00 0.00 2.43
455 467 7.164803 AGAAAAATCCACAAAGAACACCAAAA 58.835 30.769 0.00 0.00 0.00 2.44
456 468 6.706295 AGAAAAATCCACAAAGAACACCAAA 58.294 32.000 0.00 0.00 0.00 3.28
457 469 6.293004 AGAAAAATCCACAAAGAACACCAA 57.707 33.333 0.00 0.00 0.00 3.67
458 470 5.930837 AGAAAAATCCACAAAGAACACCA 57.069 34.783 0.00 0.00 0.00 4.17
459 471 8.887036 ATAAAGAAAAATCCACAAAGAACACC 57.113 30.769 0.00 0.00 0.00 4.16
496 508 4.708421 ACATTAGCAGCATCACAGGAAAAT 59.292 37.500 0.00 0.00 0.00 1.82
507 519 2.686915 GGAGCAGAAACATTAGCAGCAT 59.313 45.455 0.00 0.00 0.00 3.79
509 521 2.363683 AGGAGCAGAAACATTAGCAGC 58.636 47.619 0.00 0.00 0.00 5.25
510 522 3.559242 GCTAGGAGCAGAAACATTAGCAG 59.441 47.826 0.00 0.00 41.89 4.24
518 530 0.179097 CGGGAGCTAGGAGCAGAAAC 60.179 60.000 0.64 0.00 45.56 2.78
531 543 2.821366 CATCAGCACCACGGGAGC 60.821 66.667 4.59 4.59 39.54 4.70
532 544 2.124983 CCATCAGCACCACGGGAG 60.125 66.667 0.00 0.00 0.00 4.30
533 545 2.063015 AAACCATCAGCACCACGGGA 62.063 55.000 0.00 0.00 0.00 5.14
534 546 1.178534 AAAACCATCAGCACCACGGG 61.179 55.000 0.00 0.00 0.00 5.28
540 552 3.803778 CCAAACAGAAAAACCATCAGCAC 59.196 43.478 0.00 0.00 0.00 4.40
578 602 0.668401 AGCAGCAGGAAAAATTGCGC 60.668 50.000 0.00 0.00 44.80 6.09
579 603 1.065358 CAGCAGCAGGAAAAATTGCG 58.935 50.000 0.00 0.00 44.80 4.85
595 624 2.024176 ACATACGGATCAACACCAGC 57.976 50.000 0.00 0.00 0.00 4.85
598 627 3.938963 ACATCAACATACGGATCAACACC 59.061 43.478 0.00 0.00 0.00 4.16
601 630 6.238103 CCAGTAACATCAACATACGGATCAAC 60.238 42.308 0.00 0.00 0.00 3.18
604 633 4.750098 CCCAGTAACATCAACATACGGATC 59.250 45.833 0.00 0.00 0.00 3.36
605 634 4.163458 ACCCAGTAACATCAACATACGGAT 59.837 41.667 0.00 0.00 0.00 4.18
608 637 4.436852 GCAACCCAGTAACATCAACATACG 60.437 45.833 0.00 0.00 0.00 3.06
609 638 4.700213 AGCAACCCAGTAACATCAACATAC 59.300 41.667 0.00 0.00 0.00 2.39
611 640 3.507233 CAGCAACCCAGTAACATCAACAT 59.493 43.478 0.00 0.00 0.00 2.71
614 643 2.107378 TCCAGCAACCCAGTAACATCAA 59.893 45.455 0.00 0.00 0.00 2.57
617 646 1.705186 ACTCCAGCAACCCAGTAACAT 59.295 47.619 0.00 0.00 0.00 2.71
618 647 1.136828 ACTCCAGCAACCCAGTAACA 58.863 50.000 0.00 0.00 0.00 2.41
622 651 1.119574 ACGTACTCCAGCAACCCAGT 61.120 55.000 0.00 0.00 0.00 4.00
625 654 0.320697 AAGACGTACTCCAGCAACCC 59.679 55.000 0.00 0.00 0.00 4.11
630 659 3.037485 GCTGAAGACGTACTCCAGC 57.963 57.895 9.62 9.62 42.52 4.85
631 660 1.813178 TCAGCTGAAGACGTACTCCAG 59.187 52.381 15.67 0.00 0.00 3.86
632 661 1.905637 TCAGCTGAAGACGTACTCCA 58.094 50.000 15.67 0.00 0.00 3.86
650 683 2.550180 GTCTCCAAAGCCAGTCAACTTC 59.450 50.000 0.00 0.00 0.00 3.01
652 685 1.771255 AGTCTCCAAAGCCAGTCAACT 59.229 47.619 0.00 0.00 0.00 3.16
656 689 0.390472 CGGAGTCTCCAAAGCCAGTC 60.390 60.000 19.15 0.00 35.91 3.51
659 692 3.885814 ACGGAGTCTCCAAAGCCA 58.114 55.556 19.15 0.00 29.74 4.75
698 731 2.415010 CGCCTCCCGTGATCTCTG 59.585 66.667 0.00 0.00 0.00 3.35
740 773 0.393537 GAAGATGTGGGACCCAGCAG 60.394 60.000 15.52 0.00 32.34 4.24
815 848 2.434185 TGCGCCGATGGTGTCTTC 60.434 61.111 4.18 0.00 35.34 2.87
816 849 2.742372 GTGCGCCGATGGTGTCTT 60.742 61.111 4.18 0.00 35.34 3.01
887 920 3.866582 GCGATACCCAGGCTGGCT 61.867 66.667 28.51 17.72 35.79 4.75
890 923 4.609018 CCGGCGATACCCAGGCTG 62.609 72.222 9.30 7.75 33.26 4.85
938 982 1.819905 CTTCCGCTCTCCTTCTCCC 59.180 63.158 0.00 0.00 0.00 4.30
943 987 2.283529 TTCCGCTTCCGCTCTCCTT 61.284 57.895 0.00 0.00 0.00 3.36
1201 1250 1.623834 GGTGGGGAAGGAGACAGAGAT 60.624 57.143 0.00 0.00 0.00 2.75
1215 1265 3.220110 CAGATGAATCAGAATGGTGGGG 58.780 50.000 0.00 0.00 36.16 4.96
1255 1305 0.469917 ACCACCACCAACTGACTCAG 59.530 55.000 4.36 4.36 37.52 3.35
1287 1337 6.294453 CGATATCTGAACTACTCTGAAGGCAT 60.294 42.308 0.34 0.00 35.82 4.40
1357 1409 2.552743 TCCGGATATCGAGCAACTACAG 59.447 50.000 0.00 0.00 42.43 2.74
1381 1433 5.180492 CCACGCCACTTAAACTTCAGAATTA 59.820 40.000 0.00 0.00 0.00 1.40
1400 1452 1.717194 TCTACCAAATTCGACCACGC 58.283 50.000 0.00 0.00 39.58 5.34
1404 1456 3.671716 ACACCTTCTACCAAATTCGACC 58.328 45.455 0.00 0.00 0.00 4.79
1407 1459 4.023193 AGCAAACACCTTCTACCAAATTCG 60.023 41.667 0.00 0.00 0.00 3.34
1481 1533 5.770663 AGATGCTCATAGTAACCGTAGATGT 59.229 40.000 0.00 0.00 0.00 3.06
1516 1570 0.109723 TAACCAGTGCACCTGAACCC 59.890 55.000 14.63 0.00 44.49 4.11
1540 1594 2.563179 ACATCCAGTCACTGACTACCAC 59.437 50.000 11.47 0.00 41.37 4.16
1541 1595 2.889512 ACATCCAGTCACTGACTACCA 58.110 47.619 11.47 0.00 41.37 3.25
1610 1664 4.274147 AGTAGTCCCACTCACATCACTAG 58.726 47.826 0.00 0.00 0.00 2.57
1675 1774 3.855668 AGAACCTGGCTAGCTCATATCT 58.144 45.455 15.72 10.42 0.00 1.98
1683 1782 0.606401 TGTGCAAGAACCTGGCTAGC 60.606 55.000 6.04 6.04 30.50 3.42
1705 1804 7.546358 TGGTAATCATGACACCAATTTTCATC 58.454 34.615 22.74 0.25 39.36 2.92
1730 1829 8.373981 ACTCACATCACTACGGTATAGTACTAT 58.626 37.037 19.07 19.07 0.00 2.12
1731 1830 7.654923 CACTCACATCACTACGGTATAGTACTA 59.345 40.741 4.77 4.77 0.00 1.82
1732 1831 6.482641 CACTCACATCACTACGGTATAGTACT 59.517 42.308 0.00 0.00 0.00 2.73
1736 1835 4.023107 CCCACTCACATCACTACGGTATAG 60.023 50.000 0.00 0.00 0.00 1.31
1742 1841 3.526931 AATCCCACTCACATCACTACG 57.473 47.619 0.00 0.00 0.00 3.51
1761 1860 5.939764 AACTATGACATGAGCAGGAGTAA 57.060 39.130 0.00 0.00 0.00 2.24
1773 1872 8.918202 TTACTTGGAACTGAAAACTATGACAT 57.082 30.769 0.00 0.00 0.00 3.06
1845 1945 6.478344 CACTAAGGATCTATCTGTTCAGCAAC 59.522 42.308 0.00 0.00 0.00 4.17
1851 1951 7.151308 CCACATCACTAAGGATCTATCTGTTC 58.849 42.308 0.00 0.00 0.00 3.18
1855 1955 5.011533 GCACCACATCACTAAGGATCTATCT 59.988 44.000 0.00 0.00 0.00 1.98
1913 2013 8.015185 AGCGTGGTTTTACTCCTATATTAAGA 57.985 34.615 0.00 0.00 0.00 2.10
2053 2153 2.475187 CGTGCTAGTCATGCAAGAAAGC 60.475 50.000 16.55 16.55 42.41 3.51
2059 2159 0.740868 GCCTCGTGCTAGTCATGCAA 60.741 55.000 0.00 0.00 42.41 4.08
2077 2177 0.034089 AGGTATCTTTGGCTGGTGGC 60.034 55.000 0.00 0.00 40.90 5.01
2078 2178 1.755179 CAGGTATCTTTGGCTGGTGG 58.245 55.000 0.00 0.00 0.00 4.61
2079 2179 1.098050 GCAGGTATCTTTGGCTGGTG 58.902 55.000 0.00 0.00 0.00 4.17
2099 2199 9.507329 AACTTAAGCAGACAATCAATAAGAGAA 57.493 29.630 1.29 0.00 0.00 2.87
2138 2238 4.994852 TCAACTTCAGTAGTCAATTTCCCG 59.005 41.667 0.00 0.00 35.54 5.14
2145 2245 4.515191 GGTGCATTCAACTTCAGTAGTCAA 59.485 41.667 0.00 0.00 35.54 3.18
2157 2257 3.181476 ACAAGTCAAAGGGTGCATTCAAC 60.181 43.478 0.00 0.00 0.00 3.18
2201 2301 8.402472 CCGAGATATAACCAAATTAGCAACAAA 58.598 33.333 0.00 0.00 0.00 2.83
2213 2313 3.191669 CAACGTGCCGAGATATAACCAA 58.808 45.455 0.00 0.00 0.00 3.67
2215 2315 2.538449 CACAACGTGCCGAGATATAACC 59.462 50.000 0.00 0.00 0.00 2.85
2240 2340 2.486191 CCAGCCCAGAATCCATAGACAC 60.486 54.545 0.00 0.00 0.00 3.67
2268 2368 7.545965 ACAAACACTATTCAGTATTTCCTCGAG 59.454 37.037 5.13 5.13 28.80 4.04
2269 2369 7.383687 ACAAACACTATTCAGTATTTCCTCGA 58.616 34.615 0.00 0.00 28.80 4.04
2270 2370 7.596749 ACAAACACTATTCAGTATTTCCTCG 57.403 36.000 0.00 0.00 28.80 4.63
2271 2371 9.871238 TCTACAAACACTATTCAGTATTTCCTC 57.129 33.333 0.00 0.00 28.80 3.71
2289 2390 8.164153 CACAAAATATGCTTGCAATCTACAAAC 58.836 33.333 0.00 0.00 0.00 2.93
2385 2494 0.179113 CCAACCACACAAGCCACAAC 60.179 55.000 0.00 0.00 0.00 3.32
2386 2495 1.954362 GCCAACCACACAAGCCACAA 61.954 55.000 0.00 0.00 0.00 3.33
2388 2497 2.417097 GCCAACCACACAAGCCAC 59.583 61.111 0.00 0.00 0.00 5.01
2405 2514 2.738314 TGACACTCTGAAATCATGCGTG 59.262 45.455 0.00 0.00 0.00 5.34
2430 2539 9.054922 ACATCCACAATTTTTGTTTTAAGATGG 57.945 29.630 0.00 0.00 43.23 3.51
2446 2558 5.431765 GTTCAGATACTGGACATCCACAAT 58.568 41.667 5.44 0.00 39.61 2.71
2460 2572 4.275936 AGTTTTGTGTGCAGGTTCAGATAC 59.724 41.667 0.00 0.00 0.00 2.24
2461 2573 4.460263 AGTTTTGTGTGCAGGTTCAGATA 58.540 39.130 0.00 0.00 0.00 1.98
2464 2576 3.181397 CAAGTTTTGTGTGCAGGTTCAG 58.819 45.455 0.00 0.00 0.00 3.02
2482 2602 4.572389 CGAATTACATTCTCCCTGGACAAG 59.428 45.833 0.00 0.00 37.13 3.16
2554 2688 7.578310 ACAGAGCATAAATGATAAAGCACAT 57.422 32.000 0.00 0.00 0.00 3.21
2577 2711 5.856455 CCCAAAATCACTCGTAATGAACAAC 59.144 40.000 0.00 0.00 0.00 3.32
2579 2713 4.083003 GCCCAAAATCACTCGTAATGAACA 60.083 41.667 0.00 0.00 0.00 3.18
2588 2722 8.070171 CACTAATATAAAGCCCAAAATCACTCG 58.930 37.037 0.00 0.00 0.00 4.18
2599 2733 4.626172 GCTCGCTACACTAATATAAAGCCC 59.374 45.833 0.00 0.00 0.00 5.19
2605 3035 3.192844 GCAGGGCTCGCTACACTAATATA 59.807 47.826 0.00 0.00 0.00 0.86
2613 3043 4.457496 GCAGCAGGGCTCGCTACA 62.457 66.667 2.62 0.00 37.72 2.74
2618 3048 4.519437 TCATCGCAGCAGGGCTCG 62.519 66.667 0.00 0.00 36.40 5.03
2627 3057 4.926860 TGACAAAACATAGTCATCGCAG 57.073 40.909 0.00 0.00 39.65 5.18
2640 3070 8.677148 TTATCCTGCTCCTAATATGACAAAAC 57.323 34.615 0.00 0.00 0.00 2.43
2645 3075 9.646427 CTTAACTTATCCTGCTCCTAATATGAC 57.354 37.037 0.00 0.00 0.00 3.06
2681 3111 6.672266 AATGTCTTAAGGTCTGAGAGAACA 57.328 37.500 1.85 0.00 33.37 3.18
2720 3154 7.856145 ATAAGAAGCTGATGTTTAAGTCTGG 57.144 36.000 0.00 0.00 0.00 3.86
2764 3198 7.382488 TCAAGAACTCTTCACTTTTGTCTATCG 59.618 37.037 0.00 0.00 33.11 2.92
2767 3201 7.382488 CGATCAAGAACTCTTCACTTTTGTCTA 59.618 37.037 0.00 0.00 33.11 2.59
2771 3205 6.530913 TCGATCAAGAACTCTTCACTTTTG 57.469 37.500 0.00 0.00 33.11 2.44
2782 3217 7.536855 ACGTTTAGAGTTATCGATCAAGAACT 58.463 34.615 10.36 10.36 34.88 3.01
2785 3220 8.288208 GGATACGTTTAGAGTTATCGATCAAGA 58.712 37.037 0.00 0.00 0.00 3.02
2787 3222 7.933396 TGGATACGTTTAGAGTTATCGATCAA 58.067 34.615 0.00 0.00 42.51 2.57
2789 3224 8.967552 AATGGATACGTTTAGAGTTATCGATC 57.032 34.615 0.00 0.00 45.79 3.69
2806 3242 6.573434 GTTTCATTTGGGAAGGAATGGATAC 58.427 40.000 0.00 0.00 35.71 2.24
2820 3256 4.165779 GCTGGTGTTATCGTTTCATTTGG 58.834 43.478 0.00 0.00 0.00 3.28
2821 3257 4.793071 TGCTGGTGTTATCGTTTCATTTG 58.207 39.130 0.00 0.00 0.00 2.32
2830 3266 0.458543 AGACGCTGCTGGTGTTATCG 60.459 55.000 0.00 0.00 38.95 2.92
2834 3270 0.179045 AAGAAGACGCTGCTGGTGTT 60.179 50.000 0.00 0.00 38.95 3.32
2841 3277 1.262683 GCCATGATAAGAAGACGCTGC 59.737 52.381 0.00 0.00 0.00 5.25
2873 3309 2.935201 CAGCCTGTCAAAGATGAGTAGC 59.065 50.000 0.00 0.00 35.88 3.58
2929 3365 2.541466 TCCTTCTCCAGGTTCTCCTTC 58.459 52.381 0.00 0.00 44.37 3.46
2932 3368 3.328050 TCTTTTCCTTCTCCAGGTTCTCC 59.672 47.826 0.00 0.00 44.37 3.71
2992 3428 1.527380 GATCTCGAGGGCTCCGTCT 60.527 63.158 13.56 0.00 0.00 4.18
3055 3491 4.256920 CCTCATTCGTCCATCACTTCTTT 58.743 43.478 0.00 0.00 0.00 2.52
3065 3501 2.125552 CAGCGCCTCATTCGTCCA 60.126 61.111 2.29 0.00 0.00 4.02
3091 3528 1.913778 TGCCTAGTTCAGTACACGGA 58.086 50.000 0.00 0.00 0.00 4.69
3240 3684 6.645827 TCCATAATGCACACAATGAAAAACTG 59.354 34.615 0.00 0.00 0.00 3.16
3242 3686 7.118101 ACATCCATAATGCACACAATGAAAAAC 59.882 33.333 0.00 0.00 39.12 2.43
3244 3688 6.699366 ACATCCATAATGCACACAATGAAAA 58.301 32.000 0.00 0.00 39.12 2.29
3246 3690 5.918426 ACATCCATAATGCACACAATGAA 57.082 34.783 0.00 0.00 39.12 2.57
3248 3692 5.289917 CACAACATCCATAATGCACACAATG 59.710 40.000 0.00 0.00 39.12 2.82
3249 3693 5.412640 CACAACATCCATAATGCACACAAT 58.587 37.500 0.00 0.00 39.12 2.71
3250 3694 4.807443 CACAACATCCATAATGCACACAA 58.193 39.130 0.00 0.00 39.12 3.33
3252 3696 3.181397 GCACAACATCCATAATGCACAC 58.819 45.455 0.00 0.00 39.12 3.82
3254 3698 3.507103 TGCACAACATCCATAATGCAC 57.493 42.857 0.00 0.00 38.11 4.57
3255 3699 3.510753 ACTTGCACAACATCCATAATGCA 59.489 39.130 0.00 0.00 41.08 3.96
3256 3700 4.114058 ACTTGCACAACATCCATAATGC 57.886 40.909 0.00 0.00 39.12 3.56
3283 3727 1.074248 ACCACCCGCCACCTAAAAG 59.926 57.895 0.00 0.00 0.00 2.27
3284 3728 1.228306 CACCACCCGCCACCTAAAA 60.228 57.895 0.00 0.00 0.00 1.52
3285 3729 2.432563 CACCACCCGCCACCTAAA 59.567 61.111 0.00 0.00 0.00 1.85
3286 3730 2.850130 ACACCACCCGCCACCTAA 60.850 61.111 0.00 0.00 0.00 2.69
3313 3757 0.599558 TGAGTTCCATTTGCAGCTGC 59.400 50.000 31.89 31.89 42.50 5.25
3315 3759 0.886563 GCTGAGTTCCATTTGCAGCT 59.113 50.000 0.00 0.00 46.17 4.24
3335 3961 0.894835 TGACAGGCGAGCTTACATCA 59.105 50.000 0.00 0.00 0.00 3.07
3340 3966 0.679505 ACAACTGACAGGCGAGCTTA 59.320 50.000 7.51 0.00 0.00 3.09
3342 3968 1.005630 GACAACTGACAGGCGAGCT 60.006 57.895 7.51 0.00 0.00 4.09
3401 4032 3.802685 GGTTAACGACTTGCTAGCATAGG 59.197 47.826 20.13 14.02 39.70 2.57
3477 4108 7.985589 TGGTCTAGAAAGTAAGGGAAAGAAAT 58.014 34.615 0.00 0.00 0.00 2.17
3482 4113 4.595781 TGCTGGTCTAGAAAGTAAGGGAAA 59.404 41.667 0.00 0.00 0.00 3.13
3483 4114 4.164981 TGCTGGTCTAGAAAGTAAGGGAA 58.835 43.478 0.00 0.00 0.00 3.97
3484 4115 3.786553 TGCTGGTCTAGAAAGTAAGGGA 58.213 45.455 0.00 0.00 0.00 4.20
3485 4116 4.762289 ATGCTGGTCTAGAAAGTAAGGG 57.238 45.455 0.00 0.00 0.00 3.95
3486 4117 5.755861 GCTAATGCTGGTCTAGAAAGTAAGG 59.244 44.000 0.00 0.00 36.03 2.69
3487 4118 6.341316 TGCTAATGCTGGTCTAGAAAGTAAG 58.659 40.000 0.00 0.00 40.48 2.34
3488 4119 6.294361 TGCTAATGCTGGTCTAGAAAGTAA 57.706 37.500 0.00 0.00 40.48 2.24
3490 4121 4.826274 TGCTAATGCTGGTCTAGAAAGT 57.174 40.909 0.00 0.00 40.48 2.66
3491 4122 7.157347 TGATATGCTAATGCTGGTCTAGAAAG 58.843 38.462 0.00 0.00 40.48 2.62
3492 4123 7.066307 TGATATGCTAATGCTGGTCTAGAAA 57.934 36.000 0.00 0.00 40.48 2.52
3499 4167 2.374504 AGCCTGATATGCTAATGCTGGT 59.625 45.455 0.00 0.00 37.28 4.00
3606 4344 6.540189 GGAGCTTAGTTAATTGATTGAGCTGA 59.460 38.462 14.89 0.00 39.15 4.26
3607 4345 6.238593 GGGAGCTTAGTTAATTGATTGAGCTG 60.239 42.308 14.89 0.00 39.15 4.24
3608 4346 5.825151 GGGAGCTTAGTTAATTGATTGAGCT 59.175 40.000 10.89 10.89 41.50 4.09
3609 4347 5.009110 GGGGAGCTTAGTTAATTGATTGAGC 59.991 44.000 2.03 2.03 0.00 4.26
3610 4348 5.237344 CGGGGAGCTTAGTTAATTGATTGAG 59.763 44.000 0.00 0.00 0.00 3.02
3611 4349 5.123227 CGGGGAGCTTAGTTAATTGATTGA 58.877 41.667 0.00 0.00 0.00 2.57
3612 4350 4.881850 ACGGGGAGCTTAGTTAATTGATTG 59.118 41.667 0.00 0.00 0.00 2.67
3613 4351 5.112129 ACGGGGAGCTTAGTTAATTGATT 57.888 39.130 0.00 0.00 0.00 2.57
3615 4353 4.224370 AGAACGGGGAGCTTAGTTAATTGA 59.776 41.667 0.00 0.00 0.00 2.57
3616 4354 4.514401 AGAACGGGGAGCTTAGTTAATTG 58.486 43.478 0.00 0.00 0.00 2.32
3656 4395 0.466124 GAGTAGCCGGGAAGATTGCT 59.534 55.000 2.18 0.00 37.84 3.91
3666 4406 2.289565 GAAATTTCCAGGAGTAGCCGG 58.710 52.381 6.95 0.00 43.43 6.13
3732 4472 1.143684 ACAGGCTGTTGGTCACATTCT 59.856 47.619 15.88 0.00 33.76 2.40
3769 4514 7.423314 GTGTACGTTTGTATAAATAAAGTGGCG 59.577 37.037 0.00 0.00 32.11 5.69
3867 4615 3.136123 CAGATGGGCCAGCCGTTG 61.136 66.667 19.93 6.64 36.85 4.10
3894 4642 2.730672 CCGTTTCTCCGCTCGCTTG 61.731 63.158 0.00 0.00 0.00 4.01
3979 4727 2.048503 GGGTGTGTCGTTCGAGGG 60.049 66.667 0.00 0.00 0.00 4.30
3980 4728 2.048503 GGGGTGTGTCGTTCGAGG 60.049 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.