Multiple sequence alignment - TraesCS3A01G140100

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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 TraesCS3A01G140100 chr3A 100.000 3374 0 0 1 3374 119140497 119137124 0.000000e+00 6231.0
1 TraesCS3A01G140100 chr3A 83.756 197 29 2 1223 1416 524756976 524757172 2.070000e-42 183.0
2 TraesCS3A01G140100 chr3A 100.000 31 0 0 831 861 397142977 397142947 1.310000e-04 58.4
3 TraesCS3A01G140100 chr3D 89.495 2970 145 70 1 2907 111205666 111208531 0.000000e+00 3602.0
4 TraesCS3A01G140100 chr3D 86.866 434 31 14 2958 3374 111208529 111208953 2.370000e-126 462.0
5 TraesCS3A01G140100 chr3D 83.756 197 29 2 1223 1416 403111176 403111372 2.070000e-42 183.0
6 TraesCS3A01G140100 chr3B 88.040 2985 126 89 1 2907 162221984 162224815 0.000000e+00 3321.0
7 TraesCS3A01G140100 chr3B 91.885 419 26 6 2958 3374 162224813 162225225 2.260000e-161 579.0
8 TraesCS3A01G140100 chr3B 84.264 197 28 2 1223 1416 529404956 529405152 4.440000e-44 189.0


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 TraesCS3A01G140100 chr3A 119137124 119140497 3373 True 6231 6231 100.0000 1 3374 1 chr3A.!!$R1 3373
1 TraesCS3A01G140100 chr3D 111205666 111208953 3287 False 2032 3602 88.1805 1 3374 2 chr3D.!!$F2 3373
2 TraesCS3A01G140100 chr3B 162221984 162225225 3241 False 1950 3321 89.9625 1 3374 2 chr3B.!!$F2 3373

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
250 281 0.042708 CGCATACGCAGATTGACAGC 60.043 55.0 0.0 0.0 38.40 4.40 F
380 411 0.108585 TCTCCAAAGCTCCCACACAC 59.891 55.0 0.0 0.0 0.00 3.82 F
381 412 0.179020 CTCCAAAGCTCCCACACACA 60.179 55.0 0.0 0.0 0.00 3.72 F
906 946 0.250640 AAGTGCAGCAGGACCAAGAG 60.251 55.0 0.0 0.0 36.65 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1300 1.079336 GACCTTACTGTGCCGGTCC 60.079 63.158 1.9 0.00 39.96 4.46 R
1929 1978 1.153369 GAATGAGTAGCTGGCCGCA 60.153 57.895 19.3 5.31 42.61 5.69 R
1938 1987 1.883084 GCCACCGCCGAATGAGTAG 60.883 63.158 0.0 0.00 0.00 2.57 R
2404 2453 0.106719 CACTGTGGAGGTTGGTTGGT 60.107 55.000 0.0 0.00 0.00 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.110036 TGAACACATCATGTCTCTACCG 57.890 45.455 0.00 0.00 42.31 4.02
30 31 3.509967 TGAACACATCATGTCTCTACCGT 59.490 43.478 0.00 0.00 42.31 4.83
37 40 4.610605 TCATGTCTCTACCGTTTTTCCA 57.389 40.909 0.00 0.00 0.00 3.53
41 44 5.488645 TGTCTCTACCGTTTTTCCAAAAC 57.511 39.130 2.55 2.55 0.00 2.43
55 58 8.800972 GTTTTTCCAAAACTAGAAAAGTAACCG 58.199 33.333 0.00 0.00 41.55 4.44
120 123 2.681848 CCATGTTGGCTCTCAATCACTC 59.318 50.000 0.00 0.00 37.73 3.51
131 141 0.329261 CAATCACTCCTTGGGCTCCA 59.671 55.000 0.00 0.00 0.00 3.86
158 168 4.140599 CCTCGCTCGGCTCAGCTT 62.141 66.667 0.00 0.00 37.25 3.74
162 172 4.087892 GCTCGGCTCAGCTTGGGA 62.088 66.667 0.00 0.00 36.38 4.37
183 208 1.372623 GCAAGCAAGCAAGCAGTCC 60.373 57.895 3.19 0.00 36.85 3.85
192 222 1.904032 CAAGCAGTCCCTCTCCTCC 59.096 63.158 0.00 0.00 0.00 4.30
195 225 2.063378 GCAGTCCCTCTCCTCCCTG 61.063 68.421 0.00 0.00 0.00 4.45
241 272 2.576893 CGCCTACACGCATACGCAG 61.577 63.158 0.00 0.00 45.53 5.18
250 281 0.042708 CGCATACGCAGATTGACAGC 60.043 55.000 0.00 0.00 38.40 4.40
279 310 1.805345 CAGCAGCAAGGAGAGAAACAG 59.195 52.381 0.00 0.00 0.00 3.16
341 372 1.539157 CTGTTTTCCTGCCTCCCTTC 58.461 55.000 0.00 0.00 0.00 3.46
342 373 1.074566 CTGTTTTCCTGCCTCCCTTCT 59.925 52.381 0.00 0.00 0.00 2.85
343 374 1.202927 TGTTTTCCTGCCTCCCTTCTG 60.203 52.381 0.00 0.00 0.00 3.02
379 410 0.397941 CTCTCCAAAGCTCCCACACA 59.602 55.000 0.00 0.00 0.00 3.72
380 411 0.108585 TCTCCAAAGCTCCCACACAC 59.891 55.000 0.00 0.00 0.00 3.82
381 412 0.179020 CTCCAAAGCTCCCACACACA 60.179 55.000 0.00 0.00 0.00 3.72
382 413 0.478072 TCCAAAGCTCCCACACACAT 59.522 50.000 0.00 0.00 0.00 3.21
383 414 1.702401 TCCAAAGCTCCCACACACATA 59.298 47.619 0.00 0.00 0.00 2.29
384 415 1.812571 CCAAAGCTCCCACACACATAC 59.187 52.381 0.00 0.00 0.00 2.39
385 416 2.503331 CAAAGCTCCCACACACATACA 58.497 47.619 0.00 0.00 0.00 2.29
386 417 2.185004 AAGCTCCCACACACATACAC 57.815 50.000 0.00 0.00 0.00 2.90
387 418 0.324943 AGCTCCCACACACATACACC 59.675 55.000 0.00 0.00 0.00 4.16
388 419 0.676782 GCTCCCACACACATACACCC 60.677 60.000 0.00 0.00 0.00 4.61
389 420 0.690192 CTCCCACACACATACACCCA 59.310 55.000 0.00 0.00 0.00 4.51
390 421 0.690192 TCCCACACACATACACCCAG 59.310 55.000 0.00 0.00 0.00 4.45
406 437 0.325110 CCAGCCCAAGAGGAGAGAGA 60.325 60.000 0.00 0.00 38.24 3.10
407 438 1.113788 CAGCCCAAGAGGAGAGAGAG 58.886 60.000 0.00 0.00 38.24 3.20
410 441 1.341976 GCCCAAGAGGAGAGAGAGAGT 60.342 57.143 0.00 0.00 38.24 3.24
411 442 2.378038 CCCAAGAGGAGAGAGAGAGTG 58.622 57.143 0.00 0.00 38.24 3.51
412 443 2.025416 CCCAAGAGGAGAGAGAGAGTGA 60.025 54.545 0.00 0.00 38.24 3.41
413 444 3.282021 CCAAGAGGAGAGAGAGAGTGAG 58.718 54.545 0.00 0.00 36.89 3.51
414 445 3.308402 CCAAGAGGAGAGAGAGAGTGAGT 60.308 52.174 0.00 0.00 36.89 3.41
415 446 3.634397 AGAGGAGAGAGAGAGTGAGTG 57.366 52.381 0.00 0.00 0.00 3.51
416 447 3.181329 AGAGGAGAGAGAGAGTGAGTGA 58.819 50.000 0.00 0.00 0.00 3.41
417 448 3.198635 AGAGGAGAGAGAGAGTGAGTGAG 59.801 52.174 0.00 0.00 0.00 3.51
418 449 3.181329 AGGAGAGAGAGAGTGAGTGAGA 58.819 50.000 0.00 0.00 0.00 3.27
419 450 3.198635 AGGAGAGAGAGAGTGAGTGAGAG 59.801 52.174 0.00 0.00 0.00 3.20
420 451 3.197766 GGAGAGAGAGAGTGAGTGAGAGA 59.802 52.174 0.00 0.00 0.00 3.10
421 452 4.437239 GAGAGAGAGAGTGAGTGAGAGAG 58.563 52.174 0.00 0.00 0.00 3.20
422 453 4.096681 AGAGAGAGAGTGAGTGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
423 454 4.161189 AGAGAGAGAGTGAGTGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
424 455 4.096681 AGAGAGAGTGAGTGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
425 456 4.532126 AGAGAGAGTGAGTGAGAGAGAGAA 59.468 45.833 0.00 0.00 0.00 2.87
426 457 4.836825 AGAGAGTGAGTGAGAGAGAGAAG 58.163 47.826 0.00 0.00 0.00 2.85
427 458 3.347216 AGAGTGAGTGAGAGAGAGAAGC 58.653 50.000 0.00 0.00 0.00 3.86
428 459 2.423538 GAGTGAGTGAGAGAGAGAAGCC 59.576 54.545 0.00 0.00 0.00 4.35
429 460 2.166829 GTGAGTGAGAGAGAGAAGCCA 58.833 52.381 0.00 0.00 0.00 4.75
430 461 2.164219 GTGAGTGAGAGAGAGAAGCCAG 59.836 54.545 0.00 0.00 0.00 4.85
582 622 2.693864 CCCCTCATGCACCCTCCT 60.694 66.667 0.00 0.00 0.00 3.69
584 624 2.750657 CCCTCATGCACCCTCCTCC 61.751 68.421 0.00 0.00 0.00 4.30
585 625 2.503061 CTCATGCACCCTCCTCCG 59.497 66.667 0.00 0.00 0.00 4.63
586 626 3.746949 CTCATGCACCCTCCTCCGC 62.747 68.421 0.00 0.00 0.00 5.54
587 627 4.864334 CATGCACCCTCCTCCGCC 62.864 72.222 0.00 0.00 0.00 6.13
590 630 4.475135 GCACCCTCCTCCGCCTTC 62.475 72.222 0.00 0.00 0.00 3.46
591 631 2.685380 CACCCTCCTCCGCCTTCT 60.685 66.667 0.00 0.00 0.00 2.85
592 632 2.122954 ACCCTCCTCCGCCTTCTT 59.877 61.111 0.00 0.00 0.00 2.52
593 633 1.990614 ACCCTCCTCCGCCTTCTTC 60.991 63.158 0.00 0.00 0.00 2.87
594 634 2.736826 CCCTCCTCCGCCTTCTTCC 61.737 68.421 0.00 0.00 0.00 3.46
595 635 1.687493 CCTCCTCCGCCTTCTTCCT 60.687 63.158 0.00 0.00 0.00 3.36
596 636 1.681486 CCTCCTCCGCCTTCTTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
597 637 1.681486 CTCCTCCGCCTTCTTCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
598 638 1.687493 CCTCCGCCTTCTTCCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
599 639 1.681486 CCTCCGCCTTCTTCCTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
600 640 0.686112 CTCCGCCTTCTTCCTCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
601 641 0.252284 TCCGCCTTCTTCCTCCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
688 728 4.824166 CGCGCATTGGAGCAGCAC 62.824 66.667 8.75 0.00 40.14 4.40
906 946 0.250640 AAGTGCAGCAGGACCAAGAG 60.251 55.000 0.00 0.00 36.65 2.85
1035 1075 4.028490 TCCCACCATCACCACGGC 62.028 66.667 0.00 0.00 0.00 5.68
1041 1081 2.436646 CATCACCACGGCCTCCAC 60.437 66.667 0.00 0.00 0.00 4.02
1242 1291 2.562912 CACATTGTGCGCTCCACC 59.437 61.111 9.73 0.00 44.01 4.61
1503 1552 2.606519 CCGTCCTCCTCCACCCAA 60.607 66.667 0.00 0.00 0.00 4.12
1650 1699 2.413765 GACTCGGACTCCATCGCC 59.586 66.667 0.00 0.00 0.00 5.54
1665 1714 2.158959 CGCCGACACGATCAAGTCC 61.159 63.158 8.47 0.00 34.06 3.85
1722 1771 4.314440 TCGTCCACTGTGGCTGCC 62.314 66.667 22.02 12.87 37.47 4.85
1765 1814 1.982938 GGCTACACACCGGACCTCT 60.983 63.158 9.46 0.00 0.00 3.69
1806 1855 1.371183 CCAAGAACTCCGGCTGTCA 59.629 57.895 0.00 0.00 0.00 3.58
1847 1896 0.260230 ATGTTTCACCACCACCACCA 59.740 50.000 0.00 0.00 0.00 4.17
1848 1897 0.681564 TGTTTCACCACCACCACCAC 60.682 55.000 0.00 0.00 0.00 4.16
1849 1898 1.076632 TTTCACCACCACCACCACC 60.077 57.895 0.00 0.00 0.00 4.61
1850 1899 1.864263 TTTCACCACCACCACCACCA 61.864 55.000 0.00 0.00 0.00 4.17
1851 1900 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
1852 1901 4.204028 ACCACCACCACCACCAGC 62.204 66.667 0.00 0.00 0.00 4.85
1853 1902 4.202574 CCACCACCACCACCAGCA 62.203 66.667 0.00 0.00 0.00 4.41
1854 1903 2.595463 CACCACCACCACCAGCAG 60.595 66.667 0.00 0.00 0.00 4.24
1855 1904 4.586235 ACCACCACCACCAGCAGC 62.586 66.667 0.00 0.00 0.00 5.25
1856 1905 4.584518 CCACCACCACCAGCAGCA 62.585 66.667 0.00 0.00 0.00 4.41
1857 1906 2.981909 CACCACCACCAGCAGCAG 60.982 66.667 0.00 0.00 0.00 4.24
1858 1907 4.962836 ACCACCACCAGCAGCAGC 62.963 66.667 0.00 0.00 42.56 5.25
1929 1978 3.043999 GCAGGCACTATTCCCCGGT 62.044 63.158 0.00 0.00 36.02 5.28
1947 1996 3.724494 GCGGCCAGCTACTCATTC 58.276 61.111 2.24 0.00 44.04 2.67
2188 2237 4.647654 TCGAAGCTGACGACAACC 57.352 55.556 11.32 0.00 34.85 3.77
2387 2436 1.070445 ACTGACAGCAGCAGTGGAC 59.930 57.895 1.25 0.00 46.26 4.02
2404 2453 1.272490 GGACGACAGATGACTTCACCA 59.728 52.381 0.00 0.00 0.00 4.17
2405 2454 2.329379 GACGACAGATGACTTCACCAC 58.671 52.381 0.00 0.00 0.00 4.16
2406 2455 1.000955 ACGACAGATGACTTCACCACC 59.999 52.381 0.00 0.00 0.00 4.61
2407 2456 1.000843 CGACAGATGACTTCACCACCA 59.999 52.381 0.00 0.00 0.00 4.17
2439 2488 3.673338 CACAGTGTACCAGTAACGACATG 59.327 47.826 0.00 0.00 0.00 3.21
2440 2489 3.570975 ACAGTGTACCAGTAACGACATGA 59.429 43.478 0.00 0.00 0.00 3.07
2441 2490 4.166523 CAGTGTACCAGTAACGACATGAG 58.833 47.826 0.00 0.00 0.00 2.90
2442 2491 2.921754 GTGTACCAGTAACGACATGAGC 59.078 50.000 0.00 0.00 0.00 4.26
2443 2492 2.094390 TGTACCAGTAACGACATGAGCC 60.094 50.000 0.00 0.00 0.00 4.70
2444 2493 0.973632 ACCAGTAACGACATGAGCCA 59.026 50.000 0.00 0.00 0.00 4.75
2480 2529 3.126514 CCACTTGCATCACTGTGAGAATC 59.873 47.826 16.46 5.69 32.72 2.52
2483 2536 4.223700 ACTTGCATCACTGTGAGAATCCTA 59.776 41.667 16.46 0.00 0.00 2.94
2487 2540 4.514441 GCATCACTGTGAGAATCCTAATGG 59.486 45.833 16.46 0.00 0.00 3.16
2491 2544 3.118112 ACTGTGAGAATCCTAATGGCCTG 60.118 47.826 3.32 0.00 0.00 4.85
2504 2557 1.419381 TGGCCTGACTGACTTGTACA 58.581 50.000 3.32 0.00 0.00 2.90
2559 2612 2.332654 GCATTGCCGTCGACCCTTT 61.333 57.895 10.58 0.00 0.00 3.11
2567 2620 1.270147 CCGTCGACCCTTTCTTGAACT 60.270 52.381 10.58 0.00 0.00 3.01
2568 2621 1.792949 CGTCGACCCTTTCTTGAACTG 59.207 52.381 10.58 0.00 0.00 3.16
2569 2622 1.531578 GTCGACCCTTTCTTGAACTGC 59.468 52.381 3.51 0.00 0.00 4.40
2586 2660 0.750546 TGCATCATCCTCTTGCAGGC 60.751 55.000 0.00 0.00 43.08 4.85
2587 2661 1.453762 GCATCATCCTCTTGCAGGCC 61.454 60.000 0.00 0.00 43.08 5.19
2588 2662 1.147824 ATCATCCTCTTGCAGGCCG 59.852 57.895 0.00 0.00 43.08 6.13
2590 2664 4.496336 ATCCTCTTGCAGGCCGGC 62.496 66.667 22.10 22.10 43.08 6.13
2605 2679 0.742990 CCGGCGCTAGTTTGATTCCA 60.743 55.000 7.64 0.00 0.00 3.53
2610 2684 3.003480 GCGCTAGTTTGATTCCACTTCT 58.997 45.455 0.00 0.00 0.00 2.85
2614 2688 5.389935 CGCTAGTTTGATTCCACTTCTTCAC 60.390 44.000 0.00 0.00 0.00 3.18
2615 2689 5.470098 GCTAGTTTGATTCCACTTCTTCACA 59.530 40.000 0.00 0.00 0.00 3.58
2618 2692 5.297776 AGTTTGATTCCACTTCTTCACACAG 59.702 40.000 0.00 0.00 0.00 3.66
2626 2700 2.029828 ACTTCTTCACACAGTAGGAGCG 60.030 50.000 0.00 0.00 0.00 5.03
2637 2711 3.025189 TAGGAGCGGGCGATTGCAA 62.025 57.895 7.38 0.00 45.35 4.08
2638 2712 2.923426 TAGGAGCGGGCGATTGCAAG 62.923 60.000 4.94 0.67 45.35 4.01
2639 2713 3.127533 GAGCGGGCGATTGCAAGT 61.128 61.111 4.94 0.00 45.35 3.16
2641 2716 1.766143 GAGCGGGCGATTGCAAGTAG 61.766 60.000 4.94 0.00 45.35 2.57
2659 2734 4.294347 AGTAGCTAGGAGGAGCAAAATCT 58.706 43.478 0.00 0.00 45.43 2.40
2660 2735 4.719273 AGTAGCTAGGAGGAGCAAAATCTT 59.281 41.667 0.00 0.00 45.43 2.40
2661 2736 4.149511 AGCTAGGAGGAGCAAAATCTTC 57.850 45.455 0.00 0.00 45.43 2.87
2663 2738 3.625313 GCTAGGAGGAGCAAAATCTTCAC 59.375 47.826 0.00 0.00 42.36 3.18
2664 2739 3.795688 AGGAGGAGCAAAATCTTCACA 57.204 42.857 0.00 0.00 0.00 3.58
2665 2740 3.416156 AGGAGGAGCAAAATCTTCACAC 58.584 45.455 0.00 0.00 0.00 3.82
2667 2742 3.067106 GAGGAGCAAAATCTTCACACGA 58.933 45.455 0.00 0.00 0.00 4.35
2668 2743 3.070018 AGGAGCAAAATCTTCACACGAG 58.930 45.455 0.00 0.00 0.00 4.18
2669 2744 2.808543 GGAGCAAAATCTTCACACGAGT 59.191 45.455 0.00 0.00 0.00 4.18
2670 2745 3.120511 GGAGCAAAATCTTCACACGAGTC 60.121 47.826 0.00 0.00 0.00 3.36
2671 2746 2.476619 AGCAAAATCTTCACACGAGTCG 59.523 45.455 11.85 11.85 0.00 4.18
2672 2747 2.411547 GCAAAATCTTCACACGAGTCGG 60.412 50.000 18.30 8.43 0.00 4.79
2673 2748 1.429463 AAATCTTCACACGAGTCGGC 58.571 50.000 18.30 0.00 0.00 5.54
2674 2749 0.732880 AATCTTCACACGAGTCGGCG 60.733 55.000 18.30 10.06 37.29 6.46
2675 2750 1.583495 ATCTTCACACGAGTCGGCGA 61.583 55.000 18.30 4.99 34.83 5.54
2676 2751 1.154016 CTTCACACGAGTCGGCGAT 60.154 57.895 14.79 1.58 34.83 4.58
2677 2752 0.732880 CTTCACACGAGTCGGCGATT 60.733 55.000 14.79 9.40 34.83 3.34
2678 2753 1.006825 TTCACACGAGTCGGCGATTG 61.007 55.000 14.79 10.87 34.83 2.67
2679 2754 2.809601 ACACGAGTCGGCGATTGC 60.810 61.111 14.79 4.61 41.71 3.56
2680 2755 2.809174 CACGAGTCGGCGATTGCA 60.809 61.111 14.79 0.00 45.35 4.08
2681 2756 2.048597 ACGAGTCGGCGATTGCAA 60.049 55.556 14.79 0.00 45.35 4.08
2682 2757 2.380410 ACGAGTCGGCGATTGCAAC 61.380 57.895 14.79 4.44 45.35 4.17
2690 2765 1.076332 GGCGATTGCAACTCTACGTT 58.924 50.000 0.00 0.00 45.35 3.99
2703 2778 2.546789 CTCTACGTTTGGTTGGTTGGTC 59.453 50.000 0.00 0.00 0.00 4.02
2705 2780 0.392729 ACGTTTGGTTGGTTGGTCGA 60.393 50.000 0.00 0.00 0.00 4.20
2710 2785 0.538516 TGGTTGGTTGGTCGATTGGG 60.539 55.000 0.00 0.00 0.00 4.12
2723 2798 3.375299 GTCGATTGGGTTTCCATCTCTTG 59.625 47.826 0.00 0.00 43.63 3.02
2728 2803 1.815003 GGGTTTCCATCTCTTGTGCTG 59.185 52.381 0.00 0.00 0.00 4.41
2731 2806 1.300971 TTCCATCTCTTGTGCTGCGC 61.301 55.000 6.19 6.19 0.00 6.09
2742 2817 3.726517 GCTGCGCGTGTCATTGGT 61.727 61.111 8.43 0.00 0.00 3.67
2774 2849 2.955660 AGATCACTCGGAGCTTCTTAGG 59.044 50.000 4.58 0.00 39.85 2.69
2775 2850 0.818296 TCACTCGGAGCTTCTTAGGC 59.182 55.000 4.58 0.00 0.00 3.93
2808 2888 3.669354 GCGACATAGCTAGCTGGTT 57.331 52.632 27.68 10.45 0.00 3.67
2821 2905 3.256178 TGGTTAGCCAGCCAGCCA 61.256 61.111 0.00 0.00 40.46 4.75
2822 2906 2.439156 GGTTAGCCAGCCAGCCAG 60.439 66.667 0.00 0.00 34.09 4.85
2823 2907 3.136791 GTTAGCCAGCCAGCCAGC 61.137 66.667 0.00 0.00 0.00 4.85
2824 2908 4.431131 TTAGCCAGCCAGCCAGCC 62.431 66.667 0.00 0.00 0.00 4.85
2828 2912 4.798344 CCAGCCAGCCAGCCTCTG 62.798 72.222 0.00 0.00 0.00 3.35
2832 2916 2.433446 CCAGCCAGCCTCTGTGTT 59.567 61.111 0.00 0.00 0.00 3.32
2835 2919 3.730761 GCCAGCCTCTGTGTTGCG 61.731 66.667 0.00 0.00 0.00 4.85
2863 2947 3.895232 AGGTGTAGTTGATGCTGTAGG 57.105 47.619 0.00 0.00 0.00 3.18
2865 2949 3.195825 AGGTGTAGTTGATGCTGTAGGTC 59.804 47.826 0.00 0.00 0.00 3.85
2866 2950 3.056107 GGTGTAGTTGATGCTGTAGGTCA 60.056 47.826 0.00 0.00 0.00 4.02
2868 2952 2.370281 AGTTGATGCTGTAGGTCACG 57.630 50.000 0.00 0.00 0.00 4.35
2869 2953 0.721718 GTTGATGCTGTAGGTCACGC 59.278 55.000 0.00 0.00 0.00 5.34
2871 2955 0.608130 TGATGCTGTAGGTCACGCTT 59.392 50.000 0.00 0.00 0.00 4.68
2872 2956 1.822371 TGATGCTGTAGGTCACGCTTA 59.178 47.619 0.00 0.00 0.00 3.09
2873 2957 2.232696 TGATGCTGTAGGTCACGCTTAA 59.767 45.455 0.00 0.00 0.00 1.85
2899 2992 6.266168 TGCTTTCTTTCTTTCACTTGTTGA 57.734 33.333 0.00 0.00 0.00 3.18
2907 3000 6.631971 TTCTTTCACTTGTTGATGTATGCA 57.368 33.333 0.00 0.00 32.84 3.96
2908 3001 6.822667 TCTTTCACTTGTTGATGTATGCAT 57.177 33.333 3.79 3.79 38.18 3.96
2909 3002 6.614160 TCTTTCACTTGTTGATGTATGCATG 58.386 36.000 10.16 0.00 35.07 4.06
2910 3003 4.968812 TCACTTGTTGATGTATGCATGG 57.031 40.909 10.16 0.00 35.07 3.66
2912 3005 5.195185 TCACTTGTTGATGTATGCATGGAT 58.805 37.500 10.16 4.68 35.07 3.41
2913 3006 5.066764 TCACTTGTTGATGTATGCATGGATG 59.933 40.000 10.16 0.00 35.07 3.51
2914 3007 9.701229 TTCACTTGTTGATGTATGCATGGATGC 62.701 40.741 10.16 9.31 43.47 3.91
2924 3017 2.953669 CATGGATGCTTTGCTTCGC 58.046 52.632 0.00 0.00 34.22 4.70
2925 3018 0.526954 CATGGATGCTTTGCTTCGCC 60.527 55.000 0.00 0.00 34.22 5.54
2926 3019 1.669999 ATGGATGCTTTGCTTCGCCC 61.670 55.000 0.00 0.00 34.22 6.13
2927 3020 2.048603 GGATGCTTTGCTTCGCCCT 61.049 57.895 0.00 0.00 34.22 5.19
2928 3021 1.138247 GATGCTTTGCTTCGCCCTG 59.862 57.895 0.00 0.00 0.00 4.45
2929 3022 1.589716 GATGCTTTGCTTCGCCCTGT 61.590 55.000 0.00 0.00 0.00 4.00
2930 3023 1.870055 ATGCTTTGCTTCGCCCTGTG 61.870 55.000 0.00 0.00 0.00 3.66
2931 3024 2.956987 CTTTGCTTCGCCCTGTGG 59.043 61.111 0.00 0.00 0.00 4.17
2933 3026 3.429372 TTTGCTTCGCCCTGTGGGT 62.429 57.895 4.42 0.00 46.51 4.51
2934 3027 2.920076 TTTGCTTCGCCCTGTGGGTT 62.920 55.000 4.42 0.00 46.51 4.11
2935 3028 3.056328 GCTTCGCCCTGTGGGTTC 61.056 66.667 4.42 0.00 46.51 3.62
2936 3029 2.429930 CTTCGCCCTGTGGGTTCA 59.570 61.111 4.42 0.00 46.51 3.18
2937 3030 1.672356 CTTCGCCCTGTGGGTTCAG 60.672 63.158 4.42 0.00 46.51 3.02
2948 3041 2.284405 GGTTCAGGACCCGGGAGA 60.284 66.667 32.02 16.44 43.06 3.71
2949 3042 1.916777 GGTTCAGGACCCGGGAGAA 60.917 63.158 32.02 21.33 43.06 2.87
2950 3043 1.597461 GTTCAGGACCCGGGAGAAG 59.403 63.158 32.02 14.55 0.00 2.85
2951 3044 2.291043 TTCAGGACCCGGGAGAAGC 61.291 63.158 32.02 10.50 0.00 3.86
2952 3045 3.003173 CAGGACCCGGGAGAAGCA 61.003 66.667 32.02 0.00 0.00 3.91
2953 3046 2.203938 AGGACCCGGGAGAAGCAA 60.204 61.111 32.02 0.00 0.00 3.91
2954 3047 2.046217 GGACCCGGGAGAAGCAAC 60.046 66.667 32.02 7.28 0.00 4.17
2955 3048 2.434359 GACCCGGGAGAAGCAACG 60.434 66.667 32.02 0.00 0.00 4.10
2956 3049 3.952628 GACCCGGGAGAAGCAACGG 62.953 68.421 32.02 0.00 45.57 4.44
2957 3050 4.016706 CCCGGGAGAAGCAACGGT 62.017 66.667 18.48 0.00 44.57 4.83
2958 3051 2.742372 CCGGGAGAAGCAACGGTG 60.742 66.667 0.00 0.00 41.34 4.94
2972 3065 4.650754 CAACGGTGCTACTACCTTAGAT 57.349 45.455 0.00 0.00 38.62 1.98
2973 3066 4.360563 CAACGGTGCTACTACCTTAGATG 58.639 47.826 0.00 0.00 38.62 2.90
2974 3067 3.629087 ACGGTGCTACTACCTTAGATGT 58.371 45.455 0.00 0.00 38.62 3.06
2982 3075 6.649141 TGCTACTACCTTAGATGTTGTTGTTG 59.351 38.462 0.00 0.00 0.00 3.33
3143 3245 2.496070 TGTCGTGGAGTATCTTCCCTTG 59.504 50.000 0.00 0.00 36.35 3.61
3154 3256 8.047310 GGAGTATCTTCCCTTGACATCTTTTTA 58.953 37.037 0.00 0.00 33.73 1.52
3156 3258 9.401058 AGTATCTTCCCTTGACATCTTTTTATG 57.599 33.333 0.00 0.00 0.00 1.90
3180 3287 7.580600 TGTTTATATTATATGCTGTGCAACCG 58.419 34.615 0.00 0.00 43.62 4.44
3207 3314 5.885912 TCCAACCTTGTTATTTCTATCCAGC 59.114 40.000 0.00 0.00 0.00 4.85
3227 3334 5.278512 CCAGCCTCTCTTGTTTTTAAAGACC 60.279 44.000 6.43 0.00 30.61 3.85
3236 3343 7.317390 TCTTGTTTTTAAAGACCTGTTTGGAC 58.683 34.615 6.43 0.00 39.71 4.02
3240 3347 2.364972 AAAGACCTGTTTGGACCTGG 57.635 50.000 0.00 0.00 39.71 4.45
3265 3372 4.376340 AGAACTTGCTCAAAACAACCAG 57.624 40.909 0.00 0.00 0.00 4.00
3307 3414 9.155975 TGCAAACTTTTAAGCTTCAAAAATACA 57.844 25.926 0.00 0.00 0.00 2.29
3329 3441 4.809496 CCGCAAGCTCCCATGGCT 62.809 66.667 6.09 0.00 42.31 4.75
3330 3442 3.515286 CGCAAGCTCCCATGGCTG 61.515 66.667 6.09 1.64 40.19 4.85
3334 3446 3.951769 AAGCTCCCATGGCTGTGGC 62.952 63.158 6.09 5.42 40.19 5.01
3336 3448 2.357836 CTCCCATGGCTGTGGCTT 59.642 61.111 6.09 0.00 37.96 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.746307 AGTTTTGGAAAAACGGTAGAGAC 57.254 39.130 9.31 0.00 35.42 3.36
21 22 6.819284 TCTAGTTTTGGAAAAACGGTAGAGA 58.181 36.000 9.31 6.56 35.42 3.10
22 23 7.486802 TTCTAGTTTTGGAAAAACGGTAGAG 57.513 36.000 9.31 4.86 35.42 2.43
23 24 7.862512 TTTCTAGTTTTGGAAAAACGGTAGA 57.137 32.000 9.31 9.15 31.76 2.59
24 25 8.186163 ACTTTTCTAGTTTTGGAAAAACGGTAG 58.814 33.333 9.31 7.43 41.38 3.18
25 26 8.054152 ACTTTTCTAGTTTTGGAAAAACGGTA 57.946 30.769 9.31 0.00 41.38 4.02
26 27 6.927416 ACTTTTCTAGTTTTGGAAAAACGGT 58.073 32.000 9.31 0.00 41.38 4.83
27 28 8.800972 GTTACTTTTCTAGTTTTGGAAAAACGG 58.199 33.333 9.31 7.33 41.38 4.44
28 29 8.800972 GGTTACTTTTCTAGTTTTGGAAAAACG 58.199 33.333 9.31 0.00 41.38 3.60
29 30 8.800972 CGGTTACTTTTCTAGTTTTGGAAAAAC 58.199 33.333 7.38 7.38 41.38 2.43
30 31 7.975058 CCGGTTACTTTTCTAGTTTTGGAAAAA 59.025 33.333 0.00 0.00 41.38 1.94
37 40 6.203530 GTGTAGCCGGTTACTTTTCTAGTTTT 59.796 38.462 26.16 0.00 38.33 2.43
41 44 4.813027 TGTGTAGCCGGTTACTTTTCTAG 58.187 43.478 26.16 0.00 0.00 2.43
55 58 2.352503 CAGGTTTTGCATGTGTAGCC 57.647 50.000 0.00 0.00 0.00 3.93
102 105 1.980765 AGGAGTGATTGAGAGCCAACA 59.019 47.619 0.00 0.00 37.63 3.33
103 106 2.746362 CAAGGAGTGATTGAGAGCCAAC 59.254 50.000 0.00 0.00 37.63 3.77
110 113 1.407989 GGAGCCCAAGGAGTGATTGAG 60.408 57.143 0.00 0.00 0.00 3.02
158 168 0.892358 CTTGCTTGCTTGCTCTCCCA 60.892 55.000 3.47 0.00 0.00 4.37
161 171 0.109689 CTGCTTGCTTGCTTGCTCTC 60.110 55.000 10.35 0.00 0.00 3.20
162 172 0.822532 ACTGCTTGCTTGCTTGCTCT 60.823 50.000 10.35 0.00 0.00 4.09
206 237 1.916697 GCGCAGGGCAGAAAAGAGAC 61.917 60.000 0.30 0.00 42.87 3.36
241 272 3.869272 CCGCTGCCGCTGTCAATC 61.869 66.667 0.00 0.00 0.00 2.67
272 303 4.079253 GTGAGGAGAGAGAGTCTGTTTCT 58.921 47.826 0.00 0.00 34.71 2.52
279 310 4.583073 GGGATTTAGTGAGGAGAGAGAGTC 59.417 50.000 0.00 0.00 0.00 3.36
341 372 4.411981 AGGAGGCAGCAGCAGCAG 62.412 66.667 12.41 0.00 45.49 4.24
342 373 4.717313 CAGGAGGCAGCAGCAGCA 62.717 66.667 12.41 0.00 45.49 4.41
379 410 0.620556 CTCTTGGGCTGGGTGTATGT 59.379 55.000 0.00 0.00 0.00 2.29
380 411 0.107017 CCTCTTGGGCTGGGTGTATG 60.107 60.000 0.00 0.00 0.00 2.39
381 412 0.253160 TCCTCTTGGGCTGGGTGTAT 60.253 55.000 0.00 0.00 34.39 2.29
382 413 0.909610 CTCCTCTTGGGCTGGGTGTA 60.910 60.000 0.00 0.00 34.39 2.90
383 414 2.121963 TCCTCTTGGGCTGGGTGT 60.122 61.111 0.00 0.00 34.39 4.16
384 415 1.908340 CTCTCCTCTTGGGCTGGGTG 61.908 65.000 0.00 0.00 34.39 4.61
385 416 1.614824 CTCTCCTCTTGGGCTGGGT 60.615 63.158 0.00 0.00 34.39 4.51
386 417 1.306482 TCTCTCCTCTTGGGCTGGG 60.306 63.158 0.00 0.00 34.39 4.45
387 418 0.325110 TCTCTCTCCTCTTGGGCTGG 60.325 60.000 0.00 0.00 34.39 4.85
388 419 1.113788 CTCTCTCTCCTCTTGGGCTG 58.886 60.000 0.00 0.00 34.39 4.85
389 420 1.006813 TCTCTCTCTCCTCTTGGGCT 58.993 55.000 0.00 0.00 34.39 5.19
390 421 1.341976 ACTCTCTCTCTCCTCTTGGGC 60.342 57.143 0.00 0.00 34.39 5.36
406 437 3.347216 GCTTCTCTCTCTCACTCACTCT 58.653 50.000 0.00 0.00 0.00 3.24
407 438 2.423538 GGCTTCTCTCTCTCACTCACTC 59.576 54.545 0.00 0.00 0.00 3.51
410 441 2.445427 CTGGCTTCTCTCTCTCACTCA 58.555 52.381 0.00 0.00 0.00 3.41
411 442 1.134946 GCTGGCTTCTCTCTCTCACTC 59.865 57.143 0.00 0.00 0.00 3.51
412 443 1.185315 GCTGGCTTCTCTCTCTCACT 58.815 55.000 0.00 0.00 0.00 3.41
413 444 0.894141 TGCTGGCTTCTCTCTCTCAC 59.106 55.000 0.00 0.00 0.00 3.51
414 445 1.184431 CTGCTGGCTTCTCTCTCTCA 58.816 55.000 0.00 0.00 0.00 3.27
415 446 0.179103 GCTGCTGGCTTCTCTCTCTC 60.179 60.000 0.00 0.00 38.06 3.20
416 447 0.903924 TGCTGCTGGCTTCTCTCTCT 60.904 55.000 0.00 0.00 42.39 3.10
417 448 0.460635 CTGCTGCTGGCTTCTCTCTC 60.461 60.000 0.00 0.00 42.39 3.20
418 449 1.597989 CTGCTGCTGGCTTCTCTCT 59.402 57.895 0.00 0.00 42.39 3.10
419 450 2.107903 GCTGCTGCTGGCTTCTCTC 61.108 63.158 8.53 0.00 42.39 3.20
420 451 2.046120 GCTGCTGCTGGCTTCTCT 60.046 61.111 8.53 0.00 42.39 3.10
421 452 3.497932 CGCTGCTGCTGGCTTCTC 61.498 66.667 14.03 0.00 42.39 2.87
422 453 3.541950 TTCGCTGCTGCTGGCTTCT 62.542 57.895 14.03 0.00 42.39 2.85
423 454 3.036783 CTTCGCTGCTGCTGGCTTC 62.037 63.158 14.03 0.00 42.39 3.86
424 455 3.054503 CTTCGCTGCTGCTGGCTT 61.055 61.111 14.03 0.00 42.39 4.35
438 469 0.967887 GGAGGGAGGCAAAAGCCTTC 60.968 60.000 10.76 8.46 40.79 3.46
441 472 2.363018 GGGAGGGAGGCAAAAGCC 60.363 66.667 0.00 0.00 0.00 4.35
582 622 0.252284 AAGAGGAGGAAGAAGGCGGA 60.252 55.000 0.00 0.00 0.00 5.54
584 624 1.190643 AGAAGAGGAGGAAGAAGGCG 58.809 55.000 0.00 0.00 0.00 5.52
585 625 2.569404 TCAAGAAGAGGAGGAAGAAGGC 59.431 50.000 0.00 0.00 0.00 4.35
586 626 5.189539 AGAATCAAGAAGAGGAGGAAGAAGG 59.810 44.000 0.00 0.00 0.00 3.46
587 627 6.298441 AGAATCAAGAAGAGGAGGAAGAAG 57.702 41.667 0.00 0.00 0.00 2.85
588 628 6.500049 AGAAGAATCAAGAAGAGGAGGAAGAA 59.500 38.462 0.00 0.00 0.00 2.52
589 629 6.022315 AGAAGAATCAAGAAGAGGAGGAAGA 58.978 40.000 0.00 0.00 0.00 2.87
590 630 6.070881 TGAGAAGAATCAAGAAGAGGAGGAAG 60.071 42.308 0.00 0.00 0.00 3.46
591 631 5.782331 TGAGAAGAATCAAGAAGAGGAGGAA 59.218 40.000 0.00 0.00 0.00 3.36
592 632 5.336945 TGAGAAGAATCAAGAAGAGGAGGA 58.663 41.667 0.00 0.00 0.00 3.71
593 633 5.674052 TGAGAAGAATCAAGAAGAGGAGG 57.326 43.478 0.00 0.00 0.00 4.30
594 634 6.050432 CCATGAGAAGAATCAAGAAGAGGAG 58.950 44.000 0.00 0.00 31.76 3.69
595 635 5.486775 ACCATGAGAAGAATCAAGAAGAGGA 59.513 40.000 0.00 0.00 31.76 3.71
596 636 5.743117 ACCATGAGAAGAATCAAGAAGAGG 58.257 41.667 0.00 0.00 31.76 3.69
597 637 7.684937 AAACCATGAGAAGAATCAAGAAGAG 57.315 36.000 0.00 0.00 31.76 2.85
598 638 8.469309 AAAAACCATGAGAAGAATCAAGAAGA 57.531 30.769 0.00 0.00 31.76 2.87
599 639 7.811713 GGAAAAACCATGAGAAGAATCAAGAAG 59.188 37.037 0.00 0.00 38.79 2.85
600 640 7.506938 AGGAAAAACCATGAGAAGAATCAAGAA 59.493 33.333 0.00 0.00 42.04 2.52
601 641 7.006509 AGGAAAAACCATGAGAAGAATCAAGA 58.993 34.615 0.00 0.00 42.04 3.02
688 728 4.530857 CTTCGCCCCCGCTACTGG 62.531 72.222 0.00 0.00 0.00 4.00
823 863 1.749638 GCTGCTGCTGCTCCTCATT 60.750 57.895 22.10 0.00 40.48 2.57
846 886 0.179029 GGTAGTGGTGGTGCTGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
1023 1063 3.716195 TGGAGGCCGTGGTGATGG 61.716 66.667 0.00 0.00 0.00 3.51
1035 1075 3.699894 AGGAGCTGCGTGTGGAGG 61.700 66.667 0.00 0.00 33.49 4.30
1041 1081 1.621301 CGAAAGACAGGAGCTGCGTG 61.621 60.000 7.37 5.47 34.37 5.34
1251 1300 1.079336 GACCTTACTGTGCCGGTCC 60.079 63.158 1.90 0.00 39.96 4.46
1497 1546 2.358737 GCGGAGTCAGGTTGGGTG 60.359 66.667 0.00 0.00 0.00 4.61
1503 1552 2.915659 TTGTCGGCGGAGTCAGGT 60.916 61.111 7.21 0.00 0.00 4.00
1650 1699 2.638556 AGAAGGACTTGATCGTGTCG 57.361 50.000 10.46 0.00 34.31 4.35
1722 1771 4.838152 CCCATGGCCGACGAGTGG 62.838 72.222 6.09 0.00 0.00 4.00
1806 1855 1.261238 GGTCTGGTAGAGGCTGCAGT 61.261 60.000 16.64 0.00 0.00 4.40
1816 1865 3.517901 TGGTGAAACATAGGGTCTGGTAG 59.482 47.826 0.00 0.00 39.98 3.18
1852 1901 3.128188 CTCCTGCTGCTGCTGCTG 61.128 66.667 27.67 25.97 40.48 4.41
1855 1904 3.128188 CTGCTCCTGCTGCTGCTG 61.128 66.667 17.00 15.58 40.48 4.41
1929 1978 1.153369 GAATGAGTAGCTGGCCGCA 60.153 57.895 19.30 5.31 42.61 5.69
1938 1987 1.883084 GCCACCGCCGAATGAGTAG 60.883 63.158 0.00 0.00 0.00 2.57
2034 2083 2.047655 TTGAACAGGTAGCCGCCG 60.048 61.111 0.00 0.00 0.00 6.46
2259 2308 4.821589 GAGAAGCTGACGCCGGGG 62.822 72.222 18.33 18.33 36.60 5.73
2387 2436 1.000843 TGGTGGTGAAGTCATCTGTCG 59.999 52.381 0.00 0.00 0.00 4.35
2404 2453 0.106719 CACTGTGGAGGTTGGTTGGT 60.107 55.000 0.00 0.00 0.00 3.67
2405 2454 0.106719 ACACTGTGGAGGTTGGTTGG 60.107 55.000 13.09 0.00 0.00 3.77
2406 2455 2.218603 GTACACTGTGGAGGTTGGTTG 58.781 52.381 13.09 0.00 0.00 3.77
2407 2456 1.142262 GGTACACTGTGGAGGTTGGTT 59.858 52.381 13.09 0.00 0.00 3.67
2480 2529 2.026822 ACAAGTCAGTCAGGCCATTAGG 60.027 50.000 5.01 0.00 38.23 2.69
2483 2536 2.371841 TGTACAAGTCAGTCAGGCCATT 59.628 45.455 5.01 0.00 0.00 3.16
2487 2540 2.821991 ACTGTACAAGTCAGTCAGGC 57.178 50.000 0.00 0.00 41.52 4.85
2509 2562 6.926272 GGAGAACAGGCAGAATTATAGTACTG 59.074 42.308 5.39 0.00 0.00 2.74
2510 2563 6.611642 TGGAGAACAGGCAGAATTATAGTACT 59.388 38.462 0.00 0.00 0.00 2.73
2559 2612 4.259356 CAAGAGGATGATGCAGTTCAAGA 58.741 43.478 0.00 0.00 0.00 3.02
2567 2620 0.750546 GCCTGCAAGAGGATGATGCA 60.751 55.000 0.00 0.00 46.33 3.96
2568 2621 1.453762 GGCCTGCAAGAGGATGATGC 61.454 60.000 0.00 0.00 46.33 3.91
2569 2622 1.164662 CGGCCTGCAAGAGGATGATG 61.165 60.000 0.00 0.00 46.33 3.07
2586 2660 0.742990 TGGAATCAAACTAGCGCCGG 60.743 55.000 2.29 0.00 0.00 6.13
2587 2661 0.373716 GTGGAATCAAACTAGCGCCG 59.626 55.000 2.29 0.00 0.00 6.46
2588 2662 1.739067 AGTGGAATCAAACTAGCGCC 58.261 50.000 2.29 0.00 0.00 6.53
2590 2664 4.690748 TGAAGAAGTGGAATCAAACTAGCG 59.309 41.667 0.00 0.00 0.00 4.26
2595 2669 5.066505 ACTGTGTGAAGAAGTGGAATCAAAC 59.933 40.000 0.00 0.00 31.94 2.93
2605 2679 2.029828 CGCTCCTACTGTGTGAAGAAGT 60.030 50.000 0.00 0.00 0.00 3.01
2610 2684 1.972198 CCCGCTCCTACTGTGTGAA 59.028 57.895 0.00 0.00 0.00 3.18
2614 2688 2.298158 AATCGCCCGCTCCTACTGTG 62.298 60.000 0.00 0.00 0.00 3.66
2615 2689 2.058595 AATCGCCCGCTCCTACTGT 61.059 57.895 0.00 0.00 0.00 3.55
2618 2692 2.967615 GCAATCGCCCGCTCCTAC 60.968 66.667 0.00 0.00 0.00 3.18
2626 2700 1.221414 CTAGCTACTTGCAATCGCCC 58.779 55.000 0.00 0.00 45.94 6.13
2637 2711 4.294347 AGATTTTGCTCCTCCTAGCTACT 58.706 43.478 0.00 0.00 43.19 2.57
2638 2712 4.681074 AGATTTTGCTCCTCCTAGCTAC 57.319 45.455 0.00 0.00 43.19 3.58
2639 2713 4.716784 TGAAGATTTTGCTCCTCCTAGCTA 59.283 41.667 0.00 0.00 43.19 3.32
2641 2716 3.625313 GTGAAGATTTTGCTCCTCCTAGC 59.375 47.826 0.00 0.00 43.08 3.42
2659 2734 1.006825 CAATCGCCGACTCGTGTGAA 61.007 55.000 0.00 0.00 0.00 3.18
2660 2735 1.443702 CAATCGCCGACTCGTGTGA 60.444 57.895 0.00 2.12 0.00 3.58
2661 2736 3.071459 GCAATCGCCGACTCGTGTG 62.071 63.158 0.00 0.00 0.00 3.82
2663 2738 2.379634 TTGCAATCGCCGACTCGTG 61.380 57.895 0.00 0.00 37.32 4.35
2664 2739 2.048597 TTGCAATCGCCGACTCGT 60.049 55.556 0.00 0.00 37.32 4.18
2665 2740 2.014093 GAGTTGCAATCGCCGACTCG 62.014 60.000 0.59 0.00 39.20 4.18
2667 2742 0.530744 TAGAGTTGCAATCGCCGACT 59.469 50.000 0.59 0.00 36.54 4.18
2668 2743 0.645868 GTAGAGTTGCAATCGCCGAC 59.354 55.000 0.59 0.00 37.32 4.79
2669 2744 0.800683 CGTAGAGTTGCAATCGCCGA 60.801 55.000 0.59 0.00 37.32 5.54
2670 2745 1.076533 ACGTAGAGTTGCAATCGCCG 61.077 55.000 0.59 10.90 37.32 6.46
2671 2746 1.076332 AACGTAGAGTTGCAATCGCC 58.924 50.000 0.59 0.00 42.39 5.54
2672 2747 2.495939 CAAACGTAGAGTTGCAATCGC 58.504 47.619 0.59 0.00 43.37 4.58
2673 2748 2.478894 ACCAAACGTAGAGTTGCAATCG 59.521 45.455 0.59 5.96 43.37 3.34
2674 2749 4.219033 CAACCAAACGTAGAGTTGCAATC 58.781 43.478 0.59 1.43 43.37 2.67
2675 2750 3.004315 CCAACCAAACGTAGAGTTGCAAT 59.996 43.478 0.59 0.00 43.37 3.56
2676 2751 2.356382 CCAACCAAACGTAGAGTTGCAA 59.644 45.455 15.35 0.00 43.37 4.08
2677 2752 1.944024 CCAACCAAACGTAGAGTTGCA 59.056 47.619 15.35 0.00 43.37 4.08
2678 2753 1.944709 ACCAACCAAACGTAGAGTTGC 59.055 47.619 15.35 0.00 43.37 4.17
2679 2754 3.242936 CCAACCAACCAAACGTAGAGTTG 60.243 47.826 14.32 14.32 43.37 3.16
2680 2755 2.946990 CCAACCAACCAAACGTAGAGTT 59.053 45.455 0.00 0.00 46.76 3.01
2681 2756 2.092807 ACCAACCAACCAAACGTAGAGT 60.093 45.455 0.00 0.00 0.00 3.24
2682 2757 2.546789 GACCAACCAACCAAACGTAGAG 59.453 50.000 0.00 0.00 0.00 2.43
2690 2765 1.323412 CCAATCGACCAACCAACCAA 58.677 50.000 0.00 0.00 0.00 3.67
2703 2778 3.127548 CACAAGAGATGGAAACCCAATCG 59.872 47.826 0.00 0.00 37.24 3.34
2705 2780 2.827921 GCACAAGAGATGGAAACCCAAT 59.172 45.455 0.00 0.00 37.24 3.16
2710 2785 1.135859 CGCAGCACAAGAGATGGAAAC 60.136 52.381 0.00 0.00 0.00 2.78
2728 2803 0.502275 CAAAAACCAATGACACGCGC 59.498 50.000 5.73 0.00 0.00 6.86
2731 2806 3.443037 TGAAGCAAAAACCAATGACACG 58.557 40.909 0.00 0.00 0.00 4.49
2742 2817 4.133820 TCCGAGTGATCTTGAAGCAAAAA 58.866 39.130 0.00 0.00 0.00 1.94
2774 2849 1.206072 CGCTGCACTCTCACAAAGC 59.794 57.895 0.00 0.00 0.00 3.51
2775 2850 0.510359 GTCGCTGCACTCTCACAAAG 59.490 55.000 0.00 0.00 0.00 2.77
2817 2901 2.282040 GCAACACAGAGGCTGGCT 60.282 61.111 2.24 2.24 35.51 4.75
2818 2902 3.730761 CGCAACACAGAGGCTGGC 61.731 66.667 0.00 0.00 35.51 4.85
2819 2903 1.893808 AACGCAACACAGAGGCTGG 60.894 57.895 0.00 0.00 35.51 4.85
2820 2904 1.280746 CAACGCAACACAGAGGCTG 59.719 57.895 0.00 0.00 37.52 4.85
2821 2905 2.546494 GCAACGCAACACAGAGGCT 61.546 57.895 0.00 0.00 0.00 4.58
2822 2906 2.050985 GCAACGCAACACAGAGGC 60.051 61.111 0.00 0.00 0.00 4.70
2823 2907 0.311790 AATGCAACGCAACACAGAGG 59.688 50.000 0.00 0.00 43.62 3.69
2824 2908 2.413239 CCTAATGCAACGCAACACAGAG 60.413 50.000 0.00 0.00 43.62 3.35
2828 2912 1.001815 ACACCTAATGCAACGCAACAC 60.002 47.619 0.00 0.00 43.62 3.32
2832 2916 2.465860 ACTACACCTAATGCAACGCA 57.534 45.000 0.00 0.00 44.86 5.24
2835 2919 4.396166 AGCATCAACTACACCTAATGCAAC 59.604 41.667 7.75 0.00 41.42 4.17
2863 2947 5.915196 AGAAAGAAAGCAAATTAAGCGTGAC 59.085 36.000 0.00 0.00 37.01 3.67
2865 2949 6.753897 AAGAAAGAAAGCAAATTAAGCGTG 57.246 33.333 0.00 0.00 37.01 5.34
2866 2950 6.978080 TGAAAGAAAGAAAGCAAATTAAGCGT 59.022 30.769 0.00 0.00 37.01 5.07
2868 2952 8.357796 AGTGAAAGAAAGAAAGCAAATTAAGC 57.642 30.769 0.00 0.00 0.00 3.09
2871 2955 9.651913 AACAAGTGAAAGAAAGAAAGCAAATTA 57.348 25.926 0.00 0.00 0.00 1.40
2872 2956 8.445493 CAACAAGTGAAAGAAAGAAAGCAAATT 58.555 29.630 0.00 0.00 0.00 1.82
2873 2957 7.818930 TCAACAAGTGAAAGAAAGAAAGCAAAT 59.181 29.630 0.00 0.00 31.51 2.32
2932 3025 1.597461 CTTCTCCCGGGTCCTGAAC 59.403 63.158 22.86 0.00 0.00 3.18
2933 3026 2.291043 GCTTCTCCCGGGTCCTGAA 61.291 63.158 22.86 18.30 0.00 3.02
2934 3027 2.683933 GCTTCTCCCGGGTCCTGA 60.684 66.667 22.86 12.03 0.00 3.86
2935 3028 2.592993 TTGCTTCTCCCGGGTCCTG 61.593 63.158 22.86 11.01 0.00 3.86
2936 3029 2.203938 TTGCTTCTCCCGGGTCCT 60.204 61.111 22.86 0.00 0.00 3.85
2937 3030 2.046217 GTTGCTTCTCCCGGGTCC 60.046 66.667 22.86 6.03 0.00 4.46
2938 3031 2.434359 CGTTGCTTCTCCCGGGTC 60.434 66.667 22.86 6.45 0.00 4.46
2939 3032 4.016706 CCGTTGCTTCTCCCGGGT 62.017 66.667 22.86 0.00 36.84 5.28
2940 3033 4.016706 ACCGTTGCTTCTCCCGGG 62.017 66.667 16.85 16.85 44.57 5.73
2941 3034 2.742372 CACCGTTGCTTCTCCCGG 60.742 66.667 0.00 0.00 45.72 5.73
2942 3035 3.423154 GCACCGTTGCTTCTCCCG 61.423 66.667 0.00 0.00 46.17 5.14
2951 3044 4.142227 ACATCTAAGGTAGTAGCACCGTTG 60.142 45.833 1.58 0.00 43.84 4.10
2952 3045 4.021916 ACATCTAAGGTAGTAGCACCGTT 58.978 43.478 1.58 0.00 43.84 4.44
2953 3046 3.629087 ACATCTAAGGTAGTAGCACCGT 58.371 45.455 1.58 0.00 43.84 4.83
2954 3047 4.142227 ACAACATCTAAGGTAGTAGCACCG 60.142 45.833 1.58 0.00 43.84 4.94
2955 3048 5.340439 ACAACATCTAAGGTAGTAGCACC 57.660 43.478 1.58 0.00 39.02 5.01
2956 3049 6.164176 ACAACAACATCTAAGGTAGTAGCAC 58.836 40.000 1.58 0.00 0.00 4.40
2957 3050 6.354794 ACAACAACATCTAAGGTAGTAGCA 57.645 37.500 1.58 0.00 0.00 3.49
2958 3051 6.649557 ACAACAACAACATCTAAGGTAGTAGC 59.350 38.462 0.00 0.00 0.00 3.58
2959 3052 7.870954 TGACAACAACAACATCTAAGGTAGTAG 59.129 37.037 0.00 0.00 0.00 2.57
2960 3053 7.728148 TGACAACAACAACATCTAAGGTAGTA 58.272 34.615 0.00 0.00 0.00 1.82
2961 3054 6.588204 TGACAACAACAACATCTAAGGTAGT 58.412 36.000 0.00 0.00 0.00 2.73
2962 3055 7.490962 TTGACAACAACAACATCTAAGGTAG 57.509 36.000 0.00 0.00 0.00 3.18
2963 3056 7.554835 AGTTTGACAACAACAACATCTAAGGTA 59.445 33.333 0.00 0.00 35.63 3.08
2964 3057 6.377146 AGTTTGACAACAACAACATCTAAGGT 59.623 34.615 0.00 0.00 35.63 3.50
2965 3058 6.795399 AGTTTGACAACAACAACATCTAAGG 58.205 36.000 0.00 0.00 35.63 2.69
2966 3059 9.950680 ATAAGTTTGACAACAACAACATCTAAG 57.049 29.630 0.00 0.00 35.63 2.18
2972 3065 9.307121 CCATTTATAAGTTTGACAACAACAACA 57.693 29.630 0.00 0.00 35.63 3.33
2973 3066 9.522804 TCCATTTATAAGTTTGACAACAACAAC 57.477 29.630 0.00 0.00 35.63 3.32
2982 3075 9.903682 CATCCATCATCCATTTATAAGTTTGAC 57.096 33.333 0.00 0.00 0.00 3.18
3034 3127 4.527816 TGACCAAAAAGGATGGAAAGATGG 59.472 41.667 0.00 0.00 40.56 3.51
3154 3256 8.236586 CGGTTGCACAGCATATAATATAAACAT 58.763 33.333 0.00 0.00 38.76 2.71
3156 3258 7.802738 TCGGTTGCACAGCATATAATATAAAC 58.197 34.615 0.00 0.00 38.76 2.01
3180 3287 8.519799 TGGATAGAAATAACAAGGTTGGATTC 57.480 34.615 0.00 0.00 0.00 2.52
3207 3314 6.944234 ACAGGTCTTTAAAAACAAGAGAGG 57.056 37.500 0.00 0.00 30.72 3.69
3227 3334 2.623416 GTTCTTTCCCAGGTCCAAACAG 59.377 50.000 0.00 0.00 0.00 3.16
3236 3343 2.276732 TGAGCAAGTTCTTTCCCAGG 57.723 50.000 0.00 0.00 0.00 4.45
3240 3347 4.566759 GGTTGTTTTGAGCAAGTTCTTTCC 59.433 41.667 0.00 0.00 0.00 3.13
3265 3372 6.225981 AGTTTGCATTAAATCCATCCCTTC 57.774 37.500 0.00 0.00 0.00 3.46
3307 3414 1.228552 ATGGGAGCTTGCGGTTGTT 60.229 52.632 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.