Multiple sequence alignment - TraesCS4B01G100100

Loading Multiple Alignment...

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 TraesCS4B01G100100 chr4B 100.000 5661 0 0 1 5661 105955707 105961367 0.000000e+00 10455.0
1 TraesCS4B01G100100 chr4B 92.208 77 2 2 2425 2500 667623469 667623396 7.760000e-19 106.0
2 TraesCS4B01G100100 chr4D 95.208 2525 90 9 2497 5001 72909751 72912264 0.000000e+00 3964.0
3 TraesCS4B01G100100 chr4D 94.341 1767 62 23 679 2426 72908005 72909752 0.000000e+00 2675.0
4 TraesCS4B01G100100 chr4D 92.368 642 34 8 1 632 72816592 72817228 0.000000e+00 900.0
5 TraesCS4B01G100100 chr4D 89.159 618 49 13 5055 5661 72912438 72913048 0.000000e+00 754.0
6 TraesCS4B01G100100 chr4D 78.352 522 87 26 35 541 443685283 443684773 1.180000e-81 315.0
7 TraesCS4B01G100100 chr4D 77.778 522 92 22 34 541 34327767 34327256 3.320000e-77 300.0
8 TraesCS4B01G100100 chr4D 96.552 58 2 0 633 690 72861972 72862029 4.670000e-16 97.1
9 TraesCS4B01G100100 chr4A 92.926 1767 91 10 2497 4230 514431831 514430066 0.000000e+00 2540.0
10 TraesCS4B01G100100 chr4A 93.162 1755 75 24 697 2425 514433568 514431833 0.000000e+00 2534.0
11 TraesCS4B01G100100 chr4A 91.366 776 48 9 4228 5001 514430013 514429255 0.000000e+00 1044.0
12 TraesCS4B01G100100 chr4A 87.987 616 50 13 5055 5661 514429110 514428510 0.000000e+00 706.0
13 TraesCS4B01G100100 chr2D 76.565 751 122 35 10 735 478092864 478092143 4.170000e-96 363.0
14 TraesCS4B01G100100 chr2D 74.865 370 57 28 380 735 630363107 630362760 9.890000e-28 135.0
15 TraesCS4B01G100100 chr6B 78.443 501 85 23 34 518 158055249 158054756 7.130000e-79 305.0
16 TraesCS4B01G100100 chrUn 77.996 509 90 22 34 529 21914998 21915497 3.320000e-77 300.0
17 TraesCS4B01G100100 chrUn 78.737 475 80 20 34 496 15499431 15499896 1.190000e-76 298.0
18 TraesCS4B01G100100 chr5D 77.692 520 96 20 34 541 315143475 315142964 3.320000e-77 300.0
19 TraesCS4B01G100100 chr5D 89.873 79 7 1 2422 2499 106658785 106658707 3.610000e-17 100.0
20 TraesCS4B01G100100 chr5B 77.886 511 92 19 34 529 54238493 54237989 1.190000e-76 298.0
21 TraesCS4B01G100100 chr5B 90.909 77 2 2 2423 2499 62043058 62042987 1.300000e-16 99.0
22 TraesCS4B01G100100 chr1D 78.526 475 82 20 34 496 24661312 24661778 1.540000e-75 294.0
23 TraesCS4B01G100100 chr7D 93.421 76 3 1 2425 2500 13036222 13036149 1.670000e-20 111.0
24 TraesCS4B01G100100 chr7D 90.667 75 5 1 2425 2499 612444382 612444454 1.300000e-16 99.0
25 TraesCS4B01G100100 chr6A 91.139 79 7 0 2420 2498 146551634 146551712 2.160000e-19 108.0
26 TraesCS4B01G100100 chr3D 89.024 82 5 2 2421 2498 525726522 525726603 1.300000e-16 99.0
27 TraesCS4B01G100100 chr3B 89.744 78 5 1 2425 2502 707043932 707043858 4.670000e-16 97.1
28 TraesCS4B01G100100 chr3A 86.813 91 5 4 2409 2498 699284168 699284084 1.680000e-15 95.3


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 TraesCS4B01G100100 chr4B 105955707 105961367 5660 False 10455.000000 10455 100.000000 1 5661 1 chr4B.!!$F1 5660
1 TraesCS4B01G100100 chr4D 72908005 72913048 5043 False 2464.333333 3964 92.902667 679 5661 3 chr4D.!!$F3 4982
2 TraesCS4B01G100100 chr4D 72816592 72817228 636 False 900.000000 900 92.368000 1 632 1 chr4D.!!$F1 631
3 TraesCS4B01G100100 chr4D 443684773 443685283 510 True 315.000000 315 78.352000 35 541 1 chr4D.!!$R2 506
4 TraesCS4B01G100100 chr4D 34327256 34327767 511 True 300.000000 300 77.778000 34 541 1 chr4D.!!$R1 507
5 TraesCS4B01G100100 chr4A 514428510 514433568 5058 True 1706.000000 2540 91.360250 697 5661 4 chr4A.!!$R1 4964
6 TraesCS4B01G100100 chr2D 478092143 478092864 721 True 363.000000 363 76.565000 10 735 1 chr2D.!!$R1 725
7 TraesCS4B01G100100 chr5D 315142964 315143475 511 True 300.000000 300 77.692000 34 541 1 chr5D.!!$R2 507
8 TraesCS4B01G100100 chr5B 54237989 54238493 504 True 298.000000 298 77.886000 34 529 1 chr5B.!!$R1 495

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
953 983 0.252927 CCCTCTCCACCCCTTCTCTT 60.253 60.0 0.0 0.0 0.00 2.85 F
2437 2493 0.103755 GGGAATTACTCCGTCCGTCC 59.896 60.0 0.0 0.0 46.51 4.79 F
2438 2494 0.103755 GGAATTACTCCGTCCGTCCC 59.896 60.0 0.0 0.0 33.37 4.46 F
3411 3500 0.321210 TTCGTGTTGTGGATGCCGAT 60.321 50.0 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 2614 0.108138 CCCTCATCCAGAACACGGAC 60.108 60.000 0.00 0.0 34.69 4.79 R
4335 4480 0.035458 GGTGCTAGTGCCACTGAAGT 59.965 55.000 7.83 0.0 38.71 3.01 R
4381 4526 1.376037 GCCAGCGTACTTGCTCCTT 60.376 57.895 0.00 0.0 45.23 3.36 R
5186 5466 0.318275 GTAGCGGCTGAGAGATTCCG 60.318 60.000 13.86 0.0 44.29 4.30 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
91 93 5.665812 TGTTAGGGTTTGATGCCTAGTATCT 59.334 40.000 5.99 0.00 0.00 1.98
150 152 4.551702 TGCTTAATGCTTGTCACTAGGA 57.448 40.909 0.00 0.00 43.37 2.94
153 155 5.104776 TGCTTAATGCTTGTCACTAGGATCT 60.105 40.000 0.00 0.00 43.37 2.75
170 172 5.394738 AGGATCTGAATGCCATGATTTCAT 58.605 37.500 0.00 0.00 36.96 2.57
182 184 7.738847 TGCCATGATTTCATATCTGAACTCTA 58.261 34.615 10.99 1.48 41.05 2.43
184 186 8.666573 GCCATGATTTCATATCTGAACTCTATG 58.333 37.037 10.99 11.44 41.05 2.23
253 258 3.785486 TGCACCTGATATCGTTCTGAAG 58.215 45.455 0.00 0.00 0.00 3.02
324 332 6.957631 ACCTTGAGGATTACATGTATTCACA 58.042 36.000 22.69 19.00 37.62 3.58
364 372 6.013984 TGTTCCGGTTCTCTATTAAAAGGAGT 60.014 38.462 0.00 0.00 0.00 3.85
403 422 4.704833 CTGGTGCCACGGAGGGTG 62.705 72.222 0.00 0.00 46.57 4.61
437 457 2.619013 ATGCAAGTTCTTAGCGCAAC 57.381 45.000 11.47 5.00 35.98 4.17
438 458 1.304254 TGCAAGTTCTTAGCGCAACA 58.696 45.000 11.47 0.00 0.00 3.33
439 459 1.673400 TGCAAGTTCTTAGCGCAACAA 59.327 42.857 11.47 0.00 0.00 2.83
509 529 9.142515 TGAATTGAAGCTAATTTATTGTTGCTG 57.857 29.630 0.00 0.00 30.78 4.41
576 596 5.068723 CCACAATCTACTTCCATACCTACGT 59.931 44.000 0.00 0.00 0.00 3.57
593 613 6.671190 ACCTACGTTTTATTTTACTGTTGCC 58.329 36.000 0.00 0.00 0.00 4.52
607 627 1.351683 TGTTGCCCCCGTTACAACTAT 59.648 47.619 6.65 0.00 43.19 2.12
617 637 6.268566 CCCCGTTACAACTATTACTACTGTC 58.731 44.000 0.00 0.00 0.00 3.51
621 641 6.021939 CGTTACAACTATTACTACTGTCGCAC 60.022 42.308 0.00 0.00 0.00 5.34
622 642 5.640189 ACAACTATTACTACTGTCGCACT 57.360 39.130 0.00 0.00 0.00 4.40
623 643 5.399858 ACAACTATTACTACTGTCGCACTG 58.600 41.667 0.00 0.00 0.00 3.66
634 654 5.578005 ACTGTCGCACTGTGTTACTATAT 57.422 39.130 9.86 0.00 0.00 0.86
635 655 5.962433 ACTGTCGCACTGTGTTACTATATT 58.038 37.500 9.86 0.00 0.00 1.28
637 657 7.713750 ACTGTCGCACTGTGTTACTATATTAT 58.286 34.615 9.86 0.00 0.00 1.28
638 658 7.648112 ACTGTCGCACTGTGTTACTATATTATG 59.352 37.037 9.86 0.00 0.00 1.90
639 659 6.419710 TGTCGCACTGTGTTACTATATTATGC 59.580 38.462 9.86 0.00 0.00 3.14
640 660 6.419710 GTCGCACTGTGTTACTATATTATGCA 59.580 38.462 9.86 0.00 0.00 3.96
643 663 7.952101 CGCACTGTGTTACTATATTATGCAATC 59.048 37.037 9.86 0.00 0.00 2.67
644 664 8.993121 GCACTGTGTTACTATATTATGCAATCT 58.007 33.333 9.86 0.00 0.00 2.40
660 681 7.602517 ATGCAATCTTGTTACTCTTACTGTC 57.397 36.000 0.00 0.00 0.00 3.51
664 685 7.813148 GCAATCTTGTTACTCTTACTGTCACTA 59.187 37.037 0.00 0.00 0.00 2.74
676 697 9.619316 CTCTTACTGTCACTATATCATTACTGC 57.381 37.037 0.00 0.00 0.00 4.40
740 761 6.457528 GCAAGTTATCTATTCAGGTGCAAGTC 60.458 42.308 0.00 0.00 0.00 3.01
752 773 2.299867 GGTGCAAGTCATCCACCATTTT 59.700 45.455 4.29 0.00 46.38 1.82
753 774 3.578688 GTGCAAGTCATCCACCATTTTC 58.421 45.455 0.00 0.00 0.00 2.29
756 777 4.344679 TGCAAGTCATCCACCATTTTCTTT 59.655 37.500 0.00 0.00 0.00 2.52
757 778 5.538053 TGCAAGTCATCCACCATTTTCTTTA 59.462 36.000 0.00 0.00 0.00 1.85
758 779 6.211184 TGCAAGTCATCCACCATTTTCTTTAT 59.789 34.615 0.00 0.00 0.00 1.40
759 780 7.395772 TGCAAGTCATCCACCATTTTCTTTATA 59.604 33.333 0.00 0.00 0.00 0.98
786 809 4.526970 ACATTGCATTTTCCCTACGAGAT 58.473 39.130 0.00 0.00 0.00 2.75
787 810 5.680619 ACATTGCATTTTCCCTACGAGATA 58.319 37.500 0.00 0.00 0.00 1.98
794 822 7.065803 TGCATTTTCCCTACGAGATAGAAAAAG 59.934 37.037 0.00 0.00 39.21 2.27
819 847 3.505386 TCTGGGCCTTTAAATGCAAAGA 58.495 40.909 15.94 13.90 37.66 2.52
943 973 1.288335 TCCTCTCCTAACCCTCTCCAC 59.712 57.143 0.00 0.00 0.00 4.02
953 983 0.252927 CCCTCTCCACCCCTTCTCTT 60.253 60.000 0.00 0.00 0.00 2.85
1054 1084 5.429681 TCCTCCGATTTTCTTCCATAACA 57.570 39.130 0.00 0.00 0.00 2.41
1066 1096 5.907207 TCTTCCATAACATTTCTCTCCTCG 58.093 41.667 0.00 0.00 0.00 4.63
1154 1186 0.963355 GCGCCCTGATTTGGTGGTAA 60.963 55.000 0.00 0.00 33.89 2.85
1617 1651 9.125026 CCAGGTAAATTAGTCAATCAATTAGCT 57.875 33.333 0.00 0.00 29.22 3.32
1649 1683 6.290605 TCTCATCAATCAGCATTTAATCGGA 58.709 36.000 0.00 0.00 0.00 4.55
1685 1719 7.705325 CCTGGATTTCTCAGCTTAATCATTTTG 59.295 37.037 0.00 0.00 31.47 2.44
1828 1865 5.798125 AAGACTTCAGACTTCAGACATCA 57.202 39.130 0.00 0.00 0.00 3.07
1829 1866 5.389859 AGACTTCAGACTTCAGACATCAG 57.610 43.478 0.00 0.00 0.00 2.90
1830 1867 4.832266 AGACTTCAGACTTCAGACATCAGT 59.168 41.667 0.00 0.00 0.00 3.41
1891 1934 8.944029 CAGTGTCAATTATTTGAGATCTCACTT 58.056 33.333 25.07 16.79 42.41 3.16
2006 2049 6.340962 AGTAAACCAAATCTAAAGGTTGCC 57.659 37.500 0.00 0.00 44.44 4.52
2008 2051 7.235804 AGTAAACCAAATCTAAAGGTTGCCTA 58.764 34.615 0.00 0.00 44.44 3.93
2013 2056 5.888161 CCAAATCTAAAGGTTGCCTATGAGT 59.112 40.000 0.00 0.00 31.13 3.41
2045 2091 9.161684 CGTTGACTTAACCTTTGTTTATTGTAC 57.838 33.333 0.00 0.00 35.84 2.90
2067 2113 3.316283 TGCCGTCTGAAATTGATTTTGC 58.684 40.909 0.00 0.00 0.00 3.68
2138 2184 5.659440 TTTTAGGATCAATTTGGTGCCTC 57.341 39.130 0.00 0.00 0.00 4.70
2175 2222 7.129109 TGTAAGTTCATCGAAAAGATCCAAC 57.871 36.000 0.00 0.00 37.52 3.77
2176 2223 6.934645 TGTAAGTTCATCGAAAAGATCCAACT 59.065 34.615 0.00 0.00 39.47 3.16
2177 2224 6.487689 AAGTTCATCGAAAAGATCCAACTC 57.512 37.500 0.00 0.00 38.01 3.01
2178 2225 5.799213 AGTTCATCGAAAAGATCCAACTCT 58.201 37.500 0.00 0.00 35.87 3.24
2179 2226 6.936279 AGTTCATCGAAAAGATCCAACTCTA 58.064 36.000 0.00 0.00 35.87 2.43
2180 2227 7.560368 AGTTCATCGAAAAGATCCAACTCTAT 58.440 34.615 0.00 0.00 35.87 1.98
2181 2228 7.708752 AGTTCATCGAAAAGATCCAACTCTATC 59.291 37.037 0.00 0.00 35.87 2.08
2182 2229 7.112452 TCATCGAAAAGATCCAACTCTATCA 57.888 36.000 0.00 0.00 37.52 2.15
2265 2315 1.375853 GGCACAGATGGCGCATTACA 61.376 55.000 10.83 0.00 42.22 2.41
2285 2335 1.774254 ACATCACCCAACCAAGTCTGA 59.226 47.619 0.00 0.00 0.00 3.27
2290 2340 1.145738 ACCCAACCAAGTCTGAATGCT 59.854 47.619 0.00 0.00 0.00 3.79
2291 2341 2.375174 ACCCAACCAAGTCTGAATGCTA 59.625 45.455 0.00 0.00 0.00 3.49
2292 2342 3.012518 CCCAACCAAGTCTGAATGCTAG 58.987 50.000 0.00 0.00 0.00 3.42
2368 2418 5.064558 GCAACAGATGAGGATGATTGAGAT 58.935 41.667 0.00 0.00 0.00 2.75
2392 2446 6.451309 TCAGCATGGAAGTATACCATACGGT 61.451 44.000 0.00 0.00 45.00 4.83
2426 2482 3.798337 CGCATGAATTTGCTGGGAATTAC 59.202 43.478 0.00 0.00 40.54 1.89
2427 2483 4.440525 CGCATGAATTTGCTGGGAATTACT 60.441 41.667 0.00 0.00 40.54 2.24
2428 2484 5.045872 GCATGAATTTGCTGGGAATTACTC 58.954 41.667 0.00 0.00 39.57 2.59
2429 2485 5.594926 CATGAATTTGCTGGGAATTACTCC 58.405 41.667 0.00 0.00 44.54 3.85
2430 2486 3.694072 TGAATTTGCTGGGAATTACTCCG 59.306 43.478 0.00 0.00 46.51 4.63
2431 2487 2.871096 TTTGCTGGGAATTACTCCGT 57.129 45.000 0.00 0.00 46.51 4.69
2432 2488 2.396590 TTGCTGGGAATTACTCCGTC 57.603 50.000 0.00 0.00 46.51 4.79
2433 2489 0.539986 TGCTGGGAATTACTCCGTCC 59.460 55.000 0.00 0.00 46.51 4.79
2434 2490 0.529992 GCTGGGAATTACTCCGTCCG 60.530 60.000 0.00 0.00 46.51 4.79
2435 2491 0.822164 CTGGGAATTACTCCGTCCGT 59.178 55.000 0.00 0.00 46.51 4.69
2436 2492 0.819582 TGGGAATTACTCCGTCCGTC 59.180 55.000 0.00 0.00 46.51 4.79
2437 2493 0.103755 GGGAATTACTCCGTCCGTCC 59.896 60.000 0.00 0.00 46.51 4.79
2438 2494 0.103755 GGAATTACTCCGTCCGTCCC 59.896 60.000 0.00 0.00 33.37 4.46
2439 2495 0.819582 GAATTACTCCGTCCGTCCCA 59.180 55.000 0.00 0.00 0.00 4.37
2440 2496 1.411612 GAATTACTCCGTCCGTCCCAT 59.588 52.381 0.00 0.00 0.00 4.00
2441 2497 2.369983 ATTACTCCGTCCGTCCCATA 57.630 50.000 0.00 0.00 0.00 2.74
2442 2498 2.142356 TTACTCCGTCCGTCCCATAA 57.858 50.000 0.00 0.00 0.00 1.90
2443 2499 2.369983 TACTCCGTCCGTCCCATAAT 57.630 50.000 0.00 0.00 0.00 1.28
2444 2500 2.369983 ACTCCGTCCGTCCCATAATA 57.630 50.000 0.00 0.00 0.00 0.98
2445 2501 2.885616 ACTCCGTCCGTCCCATAATAT 58.114 47.619 0.00 0.00 0.00 1.28
2446 2502 4.038271 ACTCCGTCCGTCCCATAATATA 57.962 45.455 0.00 0.00 0.00 0.86
2447 2503 4.410099 ACTCCGTCCGTCCCATAATATAA 58.590 43.478 0.00 0.00 0.00 0.98
2448 2504 4.461781 ACTCCGTCCGTCCCATAATATAAG 59.538 45.833 0.00 0.00 0.00 1.73
2449 2505 4.665451 TCCGTCCGTCCCATAATATAAGA 58.335 43.478 0.00 0.00 0.00 2.10
2450 2506 4.703575 TCCGTCCGTCCCATAATATAAGAG 59.296 45.833 0.00 0.00 0.00 2.85
2451 2507 4.461781 CCGTCCGTCCCATAATATAAGAGT 59.538 45.833 0.00 0.00 0.00 3.24
2452 2508 5.399858 CGTCCGTCCCATAATATAAGAGTG 58.600 45.833 0.00 0.00 0.00 3.51
2453 2509 5.048224 CGTCCGTCCCATAATATAAGAGTGT 60.048 44.000 0.00 0.00 0.00 3.55
2454 2510 6.516194 CGTCCGTCCCATAATATAAGAGTGTT 60.516 42.308 0.00 0.00 0.00 3.32
2455 2511 7.215085 GTCCGTCCCATAATATAAGAGTGTTT 58.785 38.462 0.00 0.00 0.00 2.83
2456 2512 7.713942 GTCCGTCCCATAATATAAGAGTGTTTT 59.286 37.037 0.00 0.00 0.00 2.43
2457 2513 8.269317 TCCGTCCCATAATATAAGAGTGTTTTT 58.731 33.333 0.00 0.00 0.00 1.94
2485 2541 8.861086 ACACTAGTGACACTCTTATATTATGGG 58.139 37.037 29.30 0.00 0.00 4.00
2486 2542 9.078990 CACTAGTGACACTCTTATATTATGGGA 57.921 37.037 18.45 0.00 0.00 4.37
2487 2543 9.080097 ACTAGTGACACTCTTATATTATGGGAC 57.920 37.037 12.39 0.00 0.00 4.46
2488 2544 6.982852 AGTGACACTCTTATATTATGGGACG 58.017 40.000 1.07 0.00 0.00 4.79
2489 2545 6.015350 AGTGACACTCTTATATTATGGGACGG 60.015 42.308 1.07 0.00 0.00 4.79
2490 2546 6.015688 GTGACACTCTTATATTATGGGACGGA 60.016 42.308 0.00 0.00 0.00 4.69
2491 2547 6.208797 TGACACTCTTATATTATGGGACGGAG 59.791 42.308 0.00 0.00 0.00 4.63
2492 2548 5.480772 ACACTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
2493 2549 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
2494 2550 5.222484 ACTCTTATATTATGGGACGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
2495 2551 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2496 2552 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2497 2553 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2558 2614 3.964031 TCCCATTAAAATCGGGGGAAATG 59.036 43.478 0.00 0.00 44.59 2.32
2686 2743 6.867799 GATGAGATATACTCTTCATGTGCG 57.132 41.667 0.00 0.00 44.24 5.34
2687 2744 5.774498 TGAGATATACTCTTCATGTGCGT 57.226 39.130 0.00 0.00 45.13 5.24
3087 3173 3.041940 GTGTTCACCGGCCACTCG 61.042 66.667 0.00 0.00 0.00 4.18
3132 3218 1.966451 GGCGCTGCACTACCTTTGT 60.966 57.895 7.64 0.00 0.00 2.83
3150 3236 6.042777 CCTTTGTATCTCATCGTTAAGCTCA 58.957 40.000 0.00 0.00 0.00 4.26
3336 3425 2.108514 CCCAGTGCGCGTCATCATT 61.109 57.895 8.43 0.00 0.00 2.57
3348 3437 3.392882 CGTCATCATTGGTATGCAGCTA 58.607 45.455 0.00 0.00 0.00 3.32
3392 3481 2.224670 ACAACACGGGTGTAATGACCAT 60.225 45.455 4.68 0.00 44.13 3.55
3405 3494 2.559698 TGACCATTCGTGTTGTGGAT 57.440 45.000 0.00 0.00 36.82 3.41
3411 3500 0.321210 TTCGTGTTGTGGATGCCGAT 60.321 50.000 0.00 0.00 0.00 4.18
3432 3521 2.032681 GAGGGGCTGCGTCAACTT 59.967 61.111 0.00 0.00 0.00 2.66
3495 3584 3.063084 GACCCAGAGTCGCGAGGT 61.063 66.667 15.98 15.98 35.30 3.85
3498 3587 3.374402 CCAGAGTCGCGAGGTGGT 61.374 66.667 10.24 0.00 0.00 4.16
3529 3618 4.060038 CGTTCGGGGCCTACGTGT 62.060 66.667 17.51 0.00 0.00 4.49
3642 3731 0.622738 ACACATCATCCCTGGAGGCT 60.623 55.000 0.00 0.00 34.51 4.58
3837 3926 1.144936 GCGATACTGGCTGAAGGCT 59.855 57.895 5.41 0.00 41.69 4.58
3842 3931 3.551863 CGATACTGGCTGAAGGCTTCTAG 60.552 52.174 26.26 21.06 41.69 2.43
3957 4046 1.766069 CATCATTCGACGCCGACATA 58.234 50.000 0.00 0.00 45.50 2.29
4050 4139 1.989508 GGGCCAGTTTTGGGATGGG 60.990 63.158 4.39 0.00 45.16 4.00
4065 4154 0.706433 ATGGGGTCCTCACAATGCTT 59.294 50.000 0.00 0.00 0.00 3.91
4158 4247 0.678684 TCGTCGAGCCACTGGACATA 60.679 55.000 9.85 0.00 38.76 2.29
4258 4403 3.573538 AGCTGCAAACACCATTGTTCATA 59.426 39.130 1.02 0.00 45.69 2.15
4262 4407 6.641169 TGCAAACACCATTGTTCATACTTA 57.359 33.333 0.00 0.00 45.69 2.24
4335 4480 2.291043 GGTGGAAGGAGAAGGGCGA 61.291 63.158 0.00 0.00 0.00 5.54
4399 4544 1.376037 AAGGAGCAAGTACGCTGGC 60.376 57.895 0.00 0.00 44.01 4.85
4472 4617 3.553095 GAAAGTGCCCAGGCCGAGT 62.553 63.158 6.14 0.00 41.09 4.18
4683 4828 6.656902 AGTTCTGATGATGAATTAGCTGGAA 58.343 36.000 0.00 0.00 0.00 3.53
4685 4830 5.052481 TCTGATGATGAATTAGCTGGAACG 58.948 41.667 0.00 0.00 0.00 3.95
4706 4851 9.366216 GGAACGGCTCAAGAATTTTATTTTTAT 57.634 29.630 0.00 0.00 0.00 1.40
4817 4962 7.391554 ACTGCATTATGTTGTTGTATCAGTTCT 59.608 33.333 0.00 0.00 0.00 3.01
4819 4964 8.022550 TGCATTATGTTGTTGTATCAGTTCTTG 58.977 33.333 0.00 0.00 0.00 3.02
4876 5021 3.135994 TCTTCTTCAAGGCCAACGTTAC 58.864 45.455 5.01 0.00 0.00 2.50
4908 5053 3.384168 TGAGCATCAGGGTGGTATAGTT 58.616 45.455 0.00 0.00 42.56 2.24
4962 5107 1.335597 ACATGATACCGTGATACCGCG 60.336 52.381 0.00 0.00 45.12 6.46
4989 5135 9.771915 TCTCAAAATTCAAATTTGCAAGTTTTC 57.228 25.926 16.38 0.00 38.53 2.29
5001 5147 9.702494 AATTTGCAAGTTTTCAAAAATTCCAAA 57.298 22.222 13.04 13.04 36.02 3.28
5002 5148 8.739649 TTTGCAAGTTTTCAAAAATTCCAAAG 57.260 26.923 7.83 0.00 30.19 2.77
5003 5149 7.678947 TGCAAGTTTTCAAAAATTCCAAAGA 57.321 28.000 0.00 0.00 0.00 2.52
5005 5151 8.571336 TGCAAGTTTTCAAAAATTCCAAAGAAA 58.429 25.926 0.00 0.00 35.09 2.52
5006 5152 9.404348 GCAAGTTTTCAAAAATTCCAAAGAAAA 57.596 25.926 0.00 0.00 35.09 2.29
5041 5261 4.350346 CAACATGCGTCAACTTTTCAGAA 58.650 39.130 0.00 0.00 0.00 3.02
5047 5267 7.704472 ACATGCGTCAACTTTTCAGAATTTTTA 59.296 29.630 0.00 0.00 0.00 1.52
5048 5268 8.538856 CATGCGTCAACTTTTCAGAATTTTTAA 58.461 29.630 0.00 0.00 0.00 1.52
5051 5271 8.803799 GCGTCAACTTTTCAGAATTTTTAAGAA 58.196 29.630 0.00 0.00 0.00 2.52
5060 5339 8.801715 TTCAGAATTTTTAAGAACTGACATGC 57.198 30.769 0.00 0.00 34.79 4.06
5088 5367 3.812053 AGATCAAGCAAACTGTGTGAGAC 59.188 43.478 1.19 0.00 0.00 3.36
5157 5437 8.186709 TGATGCTTCAGTATTCTAGATCATCA 57.813 34.615 0.00 0.00 35.62 3.07
5186 5466 2.032681 GCCACCCACTCCACTGAC 59.967 66.667 0.00 0.00 0.00 3.51
5199 5479 1.470632 CCACTGACGGAATCTCTCAGC 60.471 57.143 7.37 0.00 35.75 4.26
5203 5483 2.811101 CGGAATCTCTCAGCCGCT 59.189 61.111 0.00 0.00 37.08 5.52
5210 5490 1.769026 TCTCTCAGCCGCTACTGAAT 58.231 50.000 6.94 0.00 45.72 2.57
5252 5532 7.114849 AGGATATCTACTCAGGAAGAAGGAT 57.885 40.000 2.05 0.00 0.00 3.24
5253 5533 7.543755 AGGATATCTACTCAGGAAGAAGGATT 58.456 38.462 2.05 0.00 0.00 3.01
5254 5534 8.016054 AGGATATCTACTCAGGAAGAAGGATTT 58.984 37.037 2.05 0.00 0.00 2.17
5290 5572 5.233476 CGCTGTCAAAACTTACAGACTACAA 59.767 40.000 6.65 0.00 44.79 2.41
5305 5587 8.627208 ACAGACTACAACATTCTGAATCAAAT 57.373 30.769 0.00 0.00 39.36 2.32
5306 5588 8.509690 ACAGACTACAACATTCTGAATCAAATG 58.490 33.333 0.00 12.95 39.36 2.32
5307 5589 8.724229 CAGACTACAACATTCTGAATCAAATGA 58.276 33.333 18.14 0.00 39.36 2.57
5308 5590 8.725148 AGACTACAACATTCTGAATCAAATGAC 58.275 33.333 18.14 0.00 36.57 3.06
5309 5591 8.394971 ACTACAACATTCTGAATCAAATGACA 57.605 30.769 18.14 0.00 36.57 3.58
5310 5592 9.017509 ACTACAACATTCTGAATCAAATGACAT 57.982 29.630 18.14 9.46 36.57 3.06
5312 5594 8.752766 ACAACATTCTGAATCAAATGACATTC 57.247 30.769 18.14 0.00 36.57 2.67
5314 5596 8.860128 CAACATTCTGAATCAAATGACATTCTG 58.140 33.333 18.14 3.04 36.57 3.02
5315 5597 8.344446 ACATTCTGAATCAAATGACATTCTGA 57.656 30.769 18.14 8.06 36.57 3.27
5316 5598 8.799367 ACATTCTGAATCAAATGACATTCTGAA 58.201 29.630 18.14 15.34 44.37 3.02
5317 5599 9.290483 CATTCTGAATCAAATGACATTCTGAAG 57.710 33.333 16.83 3.59 43.92 3.02
5319 5601 8.625786 TCTGAATCAAATGACATTCTGAAGAA 57.374 30.769 0.05 0.00 35.33 2.52
5320 5602 8.509690 TCTGAATCAAATGACATTCTGAAGAAC 58.490 33.333 0.05 3.28 35.33 3.01
5338 5628 6.313658 TGAAGAACATATCTGATTGACAACGG 59.686 38.462 0.00 0.00 38.79 4.44
5365 5655 1.523258 AGCGATCATCAGCCACTGC 60.523 57.895 0.00 0.00 37.95 4.40
5367 5657 2.879070 CGATCATCAGCCACTGCGC 61.879 63.158 0.00 0.00 44.33 6.09
5376 5666 3.031964 GCCACTGCGCTGCTTGTAG 62.032 63.158 14.80 0.03 0.00 2.74
5378 5668 0.389817 CCACTGCGCTGCTTGTAGTA 60.390 55.000 14.80 0.00 0.00 1.82
5382 5672 0.037326 TGCGCTGCTTGTAGTAAGCT 60.037 50.000 9.73 0.00 43.38 3.74
5383 5673 1.203758 TGCGCTGCTTGTAGTAAGCTA 59.796 47.619 9.73 0.00 43.38 3.32
5384 5674 1.855360 GCGCTGCTTGTAGTAAGCTAG 59.145 52.381 12.24 9.09 43.38 3.42
5385 5675 1.855360 CGCTGCTTGTAGTAAGCTAGC 59.145 52.381 6.62 6.62 43.38 3.42
5387 5677 2.605366 GCTGCTTGTAGTAAGCTAGCAC 59.395 50.000 18.83 7.34 41.99 4.40
5388 5678 3.677424 GCTGCTTGTAGTAAGCTAGCACT 60.677 47.826 18.83 14.91 41.99 4.40
5389 5679 3.849911 TGCTTGTAGTAAGCTAGCACTG 58.150 45.455 18.83 1.97 43.38 3.66
5390 5680 3.509967 TGCTTGTAGTAAGCTAGCACTGA 59.490 43.478 18.83 1.38 43.38 3.41
5391 5681 4.160439 TGCTTGTAGTAAGCTAGCACTGAT 59.840 41.667 18.83 0.98 43.38 2.90
5392 5682 4.742659 GCTTGTAGTAAGCTAGCACTGATC 59.257 45.833 18.83 8.31 40.01 2.92
5393 5683 5.451242 GCTTGTAGTAAGCTAGCACTGATCT 60.451 44.000 18.83 8.53 40.01 2.75
5394 5684 5.506686 TGTAGTAAGCTAGCACTGATCTG 57.493 43.478 18.83 0.00 0.00 2.90
5395 5685 3.451141 AGTAAGCTAGCACTGATCTGC 57.549 47.619 18.83 0.00 37.44 4.26
5396 5686 2.762887 AGTAAGCTAGCACTGATCTGCA 59.237 45.455 18.83 0.00 39.86 4.41
5397 5687 3.387374 AGTAAGCTAGCACTGATCTGCAT 59.613 43.478 18.83 0.00 39.86 3.96
5410 5702 5.101648 TGATCTGCATATGTCAGGAACAA 57.898 39.130 20.07 7.30 42.37 2.83
5412 5704 6.124340 TGATCTGCATATGTCAGGAACAAAT 58.876 36.000 20.07 10.05 42.37 2.32
5414 5706 6.441093 TCTGCATATGTCAGGAACAAATTC 57.559 37.500 20.07 0.00 42.37 2.17
5569 5861 2.183409 CAGTACCACTGGCAATGGC 58.817 57.895 16.10 0.00 42.35 4.40
5615 5907 1.212935 CCCCTTCAGATTGTACTGGGG 59.787 57.143 0.00 0.00 38.34 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 152 7.888546 TCAGATATGAAATCATGGCATTCAGAT 59.111 33.333 8.06 8.06 37.62 2.90
153 155 7.504574 AGTTCAGATATGAAATCATGGCATTCA 59.495 33.333 3.95 0.00 37.15 2.57
170 172 9.942850 TTCATGAAAACACATAGAGTTCAGATA 57.057 29.630 5.45 0.00 32.13 1.98
220 222 6.478673 CGATATCAGGTGCATACAACTTACAA 59.521 38.462 3.12 0.00 42.91 2.41
253 258 6.079424 TGTATTGTCACTTTGGGTTTAAGC 57.921 37.500 0.00 0.00 0.00 3.09
324 332 7.664318 AGAACCGGAACAAAATCTTAACATACT 59.336 33.333 9.46 0.00 0.00 2.12
334 342 9.556030 CTTTTAATAGAGAACCGGAACAAAATC 57.444 33.333 9.46 0.00 0.00 2.17
364 372 6.414732 CAGGATCCTAGTGGAAATTGTAACA 58.585 40.000 15.67 0.00 46.80 2.41
403 422 8.443953 AGAACTTGCATAACATCTATTCTTCC 57.556 34.615 0.00 0.00 0.00 3.46
431 450 0.835120 GTTGTACGTGTTTGTTGCGC 59.165 50.000 0.00 0.00 0.00 6.09
437 457 9.272901 CATTCCATAAATAGTTGTACGTGTTTG 57.727 33.333 0.00 0.00 0.00 2.93
438 458 7.966204 GCATTCCATAAATAGTTGTACGTGTTT 59.034 33.333 0.00 0.00 0.00 2.83
439 459 7.119992 TGCATTCCATAAATAGTTGTACGTGTT 59.880 33.333 0.00 0.00 0.00 3.32
509 529 7.184800 TCAATATGCAACGGTCATAACATAC 57.815 36.000 0.00 0.00 31.08 2.39
576 596 3.896272 ACGGGGGCAACAGTAAAATAAAA 59.104 39.130 0.00 0.00 39.74 1.52
593 613 6.212888 ACAGTAGTAATAGTTGTAACGGGG 57.787 41.667 0.00 0.00 0.00 5.73
607 627 3.720949 AACACAGTGCGACAGTAGTAA 57.279 42.857 0.00 0.00 0.00 2.24
617 637 6.763303 TGCATAATATAGTAACACAGTGCG 57.237 37.500 0.00 0.00 0.00 5.34
634 654 9.151471 GACAGTAAGAGTAACAAGATTGCATAA 57.849 33.333 0.00 0.00 0.00 1.90
635 655 8.311109 TGACAGTAAGAGTAACAAGATTGCATA 58.689 33.333 0.00 0.00 0.00 3.14
637 657 6.423905 GTGACAGTAAGAGTAACAAGATTGCA 59.576 38.462 0.00 0.00 0.00 4.08
638 658 6.647067 AGTGACAGTAAGAGTAACAAGATTGC 59.353 38.462 0.00 0.00 0.00 3.56
639 659 9.862371 ATAGTGACAGTAAGAGTAACAAGATTG 57.138 33.333 0.00 0.00 0.00 2.67
650 670 9.619316 GCAGTAATGATATAGTGACAGTAAGAG 57.381 37.037 0.00 0.00 0.00 2.85
651 671 9.355916 AGCAGTAATGATATAGTGACAGTAAGA 57.644 33.333 0.00 0.00 0.00 2.10
786 809 4.724279 AAGGCCCAGAGTTCTTTTTCTA 57.276 40.909 0.00 0.00 0.00 2.10
787 810 3.602205 AAGGCCCAGAGTTCTTTTTCT 57.398 42.857 0.00 0.00 0.00 2.52
794 822 2.825532 TGCATTTAAAGGCCCAGAGTTC 59.174 45.455 21.02 0.00 34.24 3.01
819 847 4.625742 CACTCTGGTCAAATATTTCGTCGT 59.374 41.667 0.00 0.00 0.00 4.34
943 973 0.829990 GGAGAGAGCAAGAGAAGGGG 59.170 60.000 0.00 0.00 0.00 4.79
994 1024 3.067985 TGCGTCTTCCATGGCAGA 58.932 55.556 10.33 10.33 0.00 4.26
1054 1084 5.674052 ATATATGCTGCGAGGAGAGAAAT 57.326 39.130 0.00 0.00 0.00 2.17
1066 1096 5.109903 CCGGGAAGTACTTATATATGCTGC 58.890 45.833 8.42 0.00 0.00 5.25
1154 1186 5.075067 TCTCTCCCAAATTCCTCTCCTTTTT 59.925 40.000 0.00 0.00 0.00 1.94
1358 1392 3.116531 GAAGGCCACGTACACCGC 61.117 66.667 5.01 0.00 41.42 5.68
1649 1683 6.060788 GCTGAGAAATCCAGGAGATAAACAT 58.939 40.000 0.00 0.00 33.66 2.71
1685 1719 1.804151 TCACGCTAACAATCACAAGGC 59.196 47.619 0.00 0.00 0.00 4.35
1727 1764 0.759060 AACTTGGCCCAAAGGACCAC 60.759 55.000 0.00 0.00 42.80 4.16
1891 1934 9.391006 CCCAGTTAAGCTGTTAAGTTATTATCA 57.609 33.333 0.00 0.00 43.55 2.15
1936 1979 5.163513 GTTTCATTATTCCACAAGCCACAG 58.836 41.667 0.00 0.00 0.00 3.66
1985 2028 7.891183 TCATAGGCAACCTTTAGATTTGGTTTA 59.109 33.333 0.00 0.00 41.57 2.01
2006 2049 6.018994 GGTTAAGTCAACGGCAATACTCATAG 60.019 42.308 0.00 0.00 38.09 2.23
2008 2051 4.634443 GGTTAAGTCAACGGCAATACTCAT 59.366 41.667 0.00 0.00 38.09 2.90
2013 2056 4.822896 ACAAAGGTTAAGTCAACGGCAATA 59.177 37.500 0.00 0.00 38.09 1.90
2045 2091 3.365820 GCAAAATCAATTTCAGACGGCAG 59.634 43.478 0.00 0.00 0.00 4.85
2067 2113 1.125021 CTGAACTAGTCTTGCGCAACG 59.875 52.381 21.02 15.44 0.00 4.10
2074 2120 7.264221 AGAAGATATGCACTGAACTAGTCTTG 58.736 38.462 0.00 0.00 37.60 3.02
2078 2124 7.416964 AGAAGAAGATATGCACTGAACTAGT 57.583 36.000 0.00 0.00 41.36 2.57
2121 2167 2.424956 GTCAGAGGCACCAAATTGATCC 59.575 50.000 0.00 0.00 0.00 3.36
2138 2184 7.755373 TCGATGAACTTACAAACTCTATGTCAG 59.245 37.037 0.00 0.00 32.27 3.51
2175 2222 1.233019 CTGGCCGCCAATTGATAGAG 58.767 55.000 14.45 0.00 30.80 2.43
2176 2223 0.819259 GCTGGCCGCCAATTGATAGA 60.819 55.000 14.45 0.00 30.80 1.98
2177 2224 0.820891 AGCTGGCCGCCAATTGATAG 60.821 55.000 14.45 0.51 40.39 2.08
2178 2225 0.395586 AAGCTGGCCGCCAATTGATA 60.396 50.000 14.45 0.00 40.39 2.15
2179 2226 0.395586 TAAGCTGGCCGCCAATTGAT 60.396 50.000 14.45 0.00 40.39 2.57
2180 2227 0.610509 TTAAGCTGGCCGCCAATTGA 60.611 50.000 14.45 5.53 40.39 2.57
2181 2228 0.179129 CTTAAGCTGGCCGCCAATTG 60.179 55.000 14.45 2.91 40.39 2.32
2182 2229 0.323360 TCTTAAGCTGGCCGCCAATT 60.323 50.000 14.45 13.47 40.39 2.32
2265 2315 1.774254 TCAGACTTGGTTGGGTGATGT 59.226 47.619 0.00 0.00 0.00 3.06
2285 2335 8.739039 TGACAACAAAATAGCAATACTAGCATT 58.261 29.630 0.00 0.00 33.29 3.56
2290 2340 8.020819 GCAAGTGACAACAAAATAGCAATACTA 58.979 33.333 0.00 0.00 34.64 1.82
2291 2341 6.863126 GCAAGTGACAACAAAATAGCAATACT 59.137 34.615 0.00 0.00 0.00 2.12
2292 2342 6.640499 TGCAAGTGACAACAAAATAGCAATAC 59.360 34.615 0.00 0.00 0.00 1.89
2368 2418 4.021456 CCGTATGGTATACTTCCATGCTGA 60.021 45.833 2.25 0.00 44.26 4.26
2392 2446 6.597614 GCAAATTCATGCGTTCCAAATAAAA 58.402 32.000 0.00 0.00 36.45 1.52
2426 2482 4.703575 TCTTATATTATGGGACGGACGGAG 59.296 45.833 0.00 0.00 0.00 4.63
2427 2483 4.665451 TCTTATATTATGGGACGGACGGA 58.335 43.478 0.00 0.00 0.00 4.69
2428 2484 4.461781 ACTCTTATATTATGGGACGGACGG 59.538 45.833 0.00 0.00 0.00 4.79
2429 2485 5.048224 ACACTCTTATATTATGGGACGGACG 60.048 44.000 0.00 0.00 0.00 4.79
2430 2486 6.342338 ACACTCTTATATTATGGGACGGAC 57.658 41.667 0.00 0.00 0.00 4.79
2431 2487 6.989155 AACACTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
2432 2488 8.446599 AAAAACACTCTTATATTATGGGACGG 57.553 34.615 0.00 0.00 0.00 4.79
2459 2515 8.861086 CCCATAATATAAGAGTGTCACTAGTGT 58.139 37.037 21.99 2.89 0.00 3.55
2460 2516 9.078990 TCCCATAATATAAGAGTGTCACTAGTG 57.921 37.037 17.17 17.17 0.00 2.74
2461 2517 9.080097 GTCCCATAATATAAGAGTGTCACTAGT 57.920 37.037 5.21 0.00 0.00 2.57
2462 2518 8.237949 CGTCCCATAATATAAGAGTGTCACTAG 58.762 40.741 5.21 0.00 0.00 2.57
2463 2519 7.176165 CCGTCCCATAATATAAGAGTGTCACTA 59.824 40.741 5.21 0.00 0.00 2.74
2464 2520 6.015350 CCGTCCCATAATATAAGAGTGTCACT 60.015 42.308 4.81 4.81 0.00 3.41
2465 2521 6.015688 TCCGTCCCATAATATAAGAGTGTCAC 60.016 42.308 0.00 0.00 0.00 3.67
2466 2522 6.072649 TCCGTCCCATAATATAAGAGTGTCA 58.927 40.000 0.00 0.00 0.00 3.58
2467 2523 6.350277 CCTCCGTCCCATAATATAAGAGTGTC 60.350 46.154 0.00 0.00 0.00 3.67
2468 2524 5.480772 CCTCCGTCCCATAATATAAGAGTGT 59.519 44.000 0.00 0.00 0.00 3.55
2469 2525 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
2470 2526 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
2471 2527 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2472 2528 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2473 2529 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2474 2530 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2475 2531 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2476 2532 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2477 2533 4.350245 CATACTCCCTCCGTCCCATAATA 58.650 47.826 0.00 0.00 0.00 0.98
2478 2534 3.173965 CATACTCCCTCCGTCCCATAAT 58.826 50.000 0.00 0.00 0.00 1.28
2479 2535 2.605257 CATACTCCCTCCGTCCCATAA 58.395 52.381 0.00 0.00 0.00 1.90
2480 2536 1.826042 GCATACTCCCTCCGTCCCATA 60.826 57.143 0.00 0.00 0.00 2.74
2481 2537 1.122019 GCATACTCCCTCCGTCCCAT 61.122 60.000 0.00 0.00 0.00 4.00
2482 2538 1.760875 GCATACTCCCTCCGTCCCA 60.761 63.158 0.00 0.00 0.00 4.37
2483 2539 1.749334 CTGCATACTCCCTCCGTCCC 61.749 65.000 0.00 0.00 0.00 4.46
2484 2540 1.043673 ACTGCATACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
2485 2541 1.688772 TACTGCATACTCCCTCCGTC 58.311 55.000 0.00 0.00 0.00 4.79
2486 2542 2.154567 TTACTGCATACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
2487 2543 3.753294 AATTACTGCATACTCCCTCCG 57.247 47.619 0.00 0.00 0.00 4.63
2488 2544 4.816925 GTGAAATTACTGCATACTCCCTCC 59.183 45.833 0.00 0.00 0.00 4.30
2489 2545 5.428253 TGTGAAATTACTGCATACTCCCTC 58.572 41.667 0.00 0.00 0.00 4.30
2490 2546 5.435686 TGTGAAATTACTGCATACTCCCT 57.564 39.130 0.00 0.00 0.00 4.20
2491 2547 5.822519 TCATGTGAAATTACTGCATACTCCC 59.177 40.000 0.00 0.00 0.00 4.30
2492 2548 6.925610 TCATGTGAAATTACTGCATACTCC 57.074 37.500 0.00 0.00 0.00 3.85
2493 2549 7.978982 ACTTCATGTGAAATTACTGCATACTC 58.021 34.615 0.00 0.00 33.07 2.59
2494 2550 7.928307 ACTTCATGTGAAATTACTGCATACT 57.072 32.000 0.00 0.00 33.07 2.12
2544 2600 0.330267 ACGGACATTTCCCCCGATTT 59.670 50.000 7.06 0.00 45.58 2.17
2558 2614 0.108138 CCCTCATCCAGAACACGGAC 60.108 60.000 0.00 0.00 34.69 4.79
2722 2780 6.200475 GCTGACCGAGTAAAATGATACTAACC 59.800 42.308 0.00 0.00 36.28 2.85
2723 2781 6.755141 TGCTGACCGAGTAAAATGATACTAAC 59.245 38.462 0.00 0.00 36.28 2.34
3132 3218 5.866092 GCATGATGAGCTTAACGATGAGATA 59.134 40.000 0.00 0.00 0.00 1.98
3150 3236 0.463204 CAGGAGACGGACTGCATGAT 59.537 55.000 0.00 0.00 39.46 2.45
3336 3425 2.291365 CATTGCTGTAGCTGCATACCA 58.709 47.619 4.51 0.33 42.66 3.25
3348 3437 1.604593 GTGTCCTGGCCATTGCTGT 60.605 57.895 5.51 0.00 37.74 4.40
3392 3481 0.321210 ATCGGCATCCACAACACGAA 60.321 50.000 0.00 0.00 33.86 3.85
3405 3494 4.804420 AGCCCCTCCTGATCGGCA 62.804 66.667 9.35 0.00 44.18 5.69
3432 3521 1.300620 GCGGACATGCGCCTGTATA 60.301 57.895 18.56 0.00 0.00 1.47
3495 3584 0.396139 ACGGACGATAAGGGCTACCA 60.396 55.000 0.00 0.00 40.13 3.25
3498 3587 0.664761 CGAACGGACGATAAGGGCTA 59.335 55.000 0.00 0.00 35.09 3.93
3529 3618 3.936203 ACCTTCCGGCGAGCACAA 61.936 61.111 9.30 0.00 0.00 3.33
3616 3705 2.746375 GGGATGATGTGTCGCCCCT 61.746 63.158 0.00 0.00 36.23 4.79
3713 3802 1.137404 GATGCCAACACGTCCATGC 59.863 57.895 0.00 0.00 0.00 4.06
3957 4046 1.466856 TGAATGCGTCGTAGTACCCT 58.533 50.000 0.00 0.00 0.00 4.34
4065 4154 2.595463 GGCAGCTGGCTGTTGTCA 60.595 61.111 31.40 0.00 45.24 3.58
4158 4247 0.608130 TGTTGCGGTGATAGTCTGCT 59.392 50.000 0.00 0.00 37.96 4.24
4258 4403 3.491342 TCTGTGAGCTCACTGACTAAGT 58.509 45.455 37.87 0.00 45.59 2.24
4309 4454 1.801242 TCTCCTTCCACCACTTGTCA 58.199 50.000 0.00 0.00 0.00 3.58
4335 4480 0.035458 GGTGCTAGTGCCACTGAAGT 59.965 55.000 7.83 0.00 38.71 3.01
4381 4526 1.376037 GCCAGCGTACTTGCTCCTT 60.376 57.895 0.00 0.00 45.23 3.36
4472 4617 2.202557 CAGCATCGCCACGTCGTA 60.203 61.111 0.00 0.00 0.00 3.43
4492 4637 0.969409 GCAGCCTCCCAAGCTTCATT 60.969 55.000 0.00 0.00 38.95 2.57
4582 4727 2.786495 CCAGCGGGTGTAGCTCGAT 61.786 63.158 6.43 0.00 45.67 3.59
4706 4851 5.069518 ACCTAAAACTAGGGGCAAGAAAA 57.930 39.130 3.35 0.00 41.51 2.29
4710 4855 5.175388 AGTTACCTAAAACTAGGGGCAAG 57.825 43.478 3.35 0.00 41.51 4.01
4740 4885 0.685458 ACAACCGCCTATACGAGGGT 60.685 55.000 0.00 0.00 46.81 4.34
4876 5021 3.502595 CCCTGATGCTCAATAATGCAGAG 59.497 47.826 0.00 0.00 42.74 3.35
4908 5053 5.477496 ATCAGACGCTGATCATACAGGGAA 61.477 45.833 16.96 3.31 46.83 3.97
4962 5107 9.558648 AAAACTTGCAAATTTGAATTTTGAGAC 57.441 25.926 22.31 0.55 36.52 3.36
5013 5159 2.217750 AGTTGACGCATGTTGCTAACA 58.782 42.857 0.00 4.56 46.94 2.41
5014 5160 2.969443 AGTTGACGCATGTTGCTAAC 57.031 45.000 0.00 1.52 42.25 2.34
5015 5161 3.980646 AAAGTTGACGCATGTTGCTAA 57.019 38.095 0.00 0.00 42.25 3.09
5016 5162 3.313803 TGAAAAGTTGACGCATGTTGCTA 59.686 39.130 0.00 0.00 42.25 3.49
5017 5163 2.098934 TGAAAAGTTGACGCATGTTGCT 59.901 40.909 0.00 0.00 42.25 3.91
5018 5164 2.458951 TGAAAAGTTGACGCATGTTGC 58.541 42.857 0.00 0.00 40.69 4.17
5019 5165 3.951306 TCTGAAAAGTTGACGCATGTTG 58.049 40.909 0.00 0.00 0.00 3.33
5022 5168 6.515043 AAAATTCTGAAAAGTTGACGCATG 57.485 33.333 0.00 0.00 0.00 4.06
5025 5171 8.335256 TCTTAAAAATTCTGAAAAGTTGACGC 57.665 30.769 0.00 0.00 0.00 5.19
5047 5267 6.647229 TGATCTAGAATGCATGTCAGTTCTT 58.353 36.000 0.00 0.00 33.36 2.52
5048 5268 6.231258 TGATCTAGAATGCATGTCAGTTCT 57.769 37.500 0.00 1.03 35.32 3.01
5051 5271 4.815308 GCTTGATCTAGAATGCATGTCAGT 59.185 41.667 8.45 0.00 0.00 3.41
5052 5272 4.814771 TGCTTGATCTAGAATGCATGTCAG 59.185 41.667 8.45 0.00 0.00 3.51
5053 5273 4.773013 TGCTTGATCTAGAATGCATGTCA 58.227 39.130 8.45 0.00 0.00 3.58
5060 5339 6.148315 TCACACAGTTTGCTTGATCTAGAATG 59.852 38.462 8.45 0.00 0.00 2.67
5088 5367 5.785599 GTCACATTTCAATTCGAAAGACTCG 59.214 40.000 0.00 0.00 46.57 4.18
5119 5398 3.190953 TGAAGCATCATGAATTCGTTGCA 59.809 39.130 20.92 0.93 32.66 4.08
5122 5401 6.932356 ATACTGAAGCATCATGAATTCGTT 57.068 33.333 0.00 0.00 34.37 3.85
5124 5403 7.187244 AGAATACTGAAGCATCATGAATTCG 57.813 36.000 0.00 4.67 35.32 3.34
5131 5410 8.813951 TGATGATCTAGAATACTGAAGCATCAT 58.186 33.333 0.00 0.00 38.52 2.45
5157 5437 1.339929 GTGGGTGGCGTTGAAGATTTT 59.660 47.619 0.00 0.00 0.00 1.82
5186 5466 0.318275 GTAGCGGCTGAGAGATTCCG 60.318 60.000 13.86 0.00 44.29 4.30
5227 5507 7.649702 TCCTTCTTCCTGAGTAGATATCCTA 57.350 40.000 0.00 0.00 0.00 2.94
5260 5541 5.813672 TCTGTAAGTTTTGACAGCGTTTACT 59.186 36.000 0.16 0.00 42.35 2.24
5290 5572 8.344446 TCAGAATGTCATTTGATTCAGAATGT 57.656 30.769 0.00 0.00 35.30 2.71
5305 5587 9.106070 CAATCAGATATGTTCTTCAGAATGTCA 57.894 33.333 0.00 0.00 36.33 3.58
5306 5588 9.322773 TCAATCAGATATGTTCTTCAGAATGTC 57.677 33.333 0.00 0.00 36.33 3.06
5307 5589 9.107177 GTCAATCAGATATGTTCTTCAGAATGT 57.893 33.333 0.00 0.00 36.33 2.71
5308 5590 9.106070 TGTCAATCAGATATGTTCTTCAGAATG 57.894 33.333 0.00 0.00 36.33 2.67
5309 5591 9.676861 TTGTCAATCAGATATGTTCTTCAGAAT 57.323 29.630 0.00 0.00 36.33 2.40
5310 5592 8.939929 GTTGTCAATCAGATATGTTCTTCAGAA 58.060 33.333 0.00 0.00 29.93 3.02
5312 5594 7.397194 CGTTGTCAATCAGATATGTTCTTCAG 58.603 38.462 0.00 0.00 29.93 3.02
5314 5596 6.535150 TCCGTTGTCAATCAGATATGTTCTTC 59.465 38.462 0.00 0.00 29.93 2.87
5315 5597 6.406370 TCCGTTGTCAATCAGATATGTTCTT 58.594 36.000 0.00 0.00 29.93 2.52
5316 5598 5.977635 TCCGTTGTCAATCAGATATGTTCT 58.022 37.500 0.00 0.00 33.90 3.01
5317 5599 5.277058 GCTCCGTTGTCAATCAGATATGTTC 60.277 44.000 0.00 0.00 0.00 3.18
5319 5601 4.122776 GCTCCGTTGTCAATCAGATATGT 58.877 43.478 0.00 0.00 0.00 2.29
5320 5602 3.183172 CGCTCCGTTGTCAATCAGATATG 59.817 47.826 0.00 0.00 0.00 1.78
5338 5628 1.720316 CTGATGATCGCTGAATCGCTC 59.280 52.381 0.00 0.00 0.00 5.03
5365 5655 1.855360 GCTAGCTTACTACAAGCAGCG 59.145 52.381 7.70 0.98 45.30 5.18
5367 5657 3.862267 CAGTGCTAGCTTACTACAAGCAG 59.138 47.826 17.23 7.61 45.30 4.24
5376 5666 3.170791 TGCAGATCAGTGCTAGCTTAC 57.829 47.619 17.23 6.69 44.32 2.34
5378 5668 4.202336 ACATATGCAGATCAGTGCTAGCTT 60.202 41.667 17.23 0.92 44.32 3.74
5382 5672 4.262335 CCTGACATATGCAGATCAGTGCTA 60.262 45.833 21.45 0.21 44.32 3.49
5383 5673 3.494573 CCTGACATATGCAGATCAGTGCT 60.495 47.826 21.45 0.00 44.32 4.40
5384 5674 2.806818 CCTGACATATGCAGATCAGTGC 59.193 50.000 21.45 0.00 44.27 4.40
5385 5675 4.332428 TCCTGACATATGCAGATCAGTG 57.668 45.455 21.45 12.60 37.47 3.66
5387 5677 4.700700 TGTTCCTGACATATGCAGATCAG 58.299 43.478 21.45 16.98 38.65 2.90
5388 5678 4.758773 TGTTCCTGACATATGCAGATCA 57.241 40.909 21.45 15.52 35.39 2.92
5389 5679 6.630444 ATTTGTTCCTGACATATGCAGATC 57.370 37.500 21.45 13.94 38.26 2.75
5390 5680 6.604396 TGAATTTGTTCCTGACATATGCAGAT 59.396 34.615 21.45 0.00 38.26 2.90
5391 5681 5.945191 TGAATTTGTTCCTGACATATGCAGA 59.055 36.000 21.45 10.08 38.26 4.26
5392 5682 6.198650 TGAATTTGTTCCTGACATATGCAG 57.801 37.500 15.92 15.92 38.26 4.41
5393 5683 6.778834 ATGAATTTGTTCCTGACATATGCA 57.221 33.333 1.58 1.17 38.91 3.96
5394 5684 8.570488 TGATATGAATTTGTTCCTGACATATGC 58.430 33.333 1.58 0.00 38.26 3.14
5396 5686 8.790718 GCTGATATGAATTTGTTCCTGACATAT 58.209 33.333 0.00 0.00 38.26 1.78
5397 5687 7.229306 GGCTGATATGAATTTGTTCCTGACATA 59.771 37.037 0.00 0.00 38.26 2.29
5410 5702 1.352352 CCCTCGGGGCTGATATGAATT 59.648 52.381 0.00 0.00 35.35 2.17
5412 5704 0.105194 TCCCTCGGGGCTGATATGAA 60.105 55.000 0.00 0.00 43.94 2.57
5414 5706 0.764890 TTTCCCTCGGGGCTGATATG 59.235 55.000 0.00 0.00 43.94 1.78
5460 5752 2.418746 GCTTCCTAGAGGATCGTGCAAA 60.419 50.000 0.00 0.00 44.98 3.68
5484 5776 1.378646 TGATGAGTCGGTCCGCTCT 60.379 57.895 25.72 18.24 33.64 4.09
5566 5858 1.198094 TTCTTCCTGGATGACGGCCA 61.198 55.000 11.48 0.00 0.00 5.36
5569 5861 2.831333 CATCTTCTTCCTGGATGACGG 58.169 52.381 11.48 8.18 39.12 4.79
5615 5907 1.287730 CTCCAAGTCTGTCTGTGCGC 61.288 60.000 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.