Multiple sequence alignment - TraesCS5B01G439500

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 TraesCS5B01G439500 chr5B 100.000 2462 0 0 1 2462 611676758 611679219 0.000000e+00 4547.0
1 TraesCS5B01G439500 chr5B 89.358 1043 69 26 816 1821 649498368 649499405 0.000000e+00 1273.0
2 TraesCS5B01G439500 chr5B 87.487 999 91 22 817 1804 629926478 629925503 0.000000e+00 1122.0
3 TraesCS5B01G439500 chr5B 86.660 1027 88 23 825 1821 628724530 628723523 0.000000e+00 1092.0
4 TraesCS5B01G439500 chr5B 88.143 894 77 18 939 1821 633171388 633172263 0.000000e+00 1037.0
5 TraesCS5B01G439500 chr5B 91.587 630 17 15 816 1435 649694250 649694853 0.000000e+00 837.0
6 TraesCS5B01G439500 chr5B 87.311 331 32 8 825 1147 625133876 625133548 1.080000e-98 370.0
7 TraesCS5B01G439500 chr5B 84.167 120 12 3 1835 1953 633172046 633172159 2.590000e-20 110.0
8 TraesCS5B01G439500 chr5B 88.889 54 4 1 1916 1967 629951863 629951810 5.680000e-07 65.8
9 TraesCS5B01G439500 chr5B 94.872 39 2 0 1992 2030 629925540 629925502 7.350000e-06 62.1
10 TraesCS5B01G439500 chr5D 90.509 1296 79 18 725 1984 495199689 495200976 0.000000e+00 1672.0
11 TraesCS5B01G439500 chr5D 90.842 950 52 20 725 1653 495142262 495143197 0.000000e+00 1240.0
12 TraesCS5B01G439500 chr5D 89.123 901 80 12 816 1705 501450196 501449303 0.000000e+00 1105.0
13 TraesCS5B01G439500 chr5D 90.703 839 50 14 817 1634 517213268 517214099 0.000000e+00 1092.0
14 TraesCS5B01G439500 chr5D 89.895 475 29 4 1992 2462 495201022 495201481 5.860000e-166 593.0
15 TraesCS5B01G439500 chr5D 86.010 386 48 6 232 612 388771582 388771966 2.280000e-110 409.0
16 TraesCS5B01G439500 chr5D 91.093 247 17 3 1835 2076 495143290 495143536 1.830000e-86 329.0
17 TraesCS5B01G439500 chr5D 95.425 153 7 0 735 887 495138827 495138979 6.800000e-61 244.0
18 TraesCS5B01G439500 chr5A 90.123 1306 67 19 722 1984 619343979 619345265 0.000000e+00 1640.0
19 TraesCS5B01G439500 chr5A 88.207 1043 76 18 816 1817 644310265 644311301 0.000000e+00 1201.0
20 TraesCS5B01G439500 chr5A 86.277 940 81 27 919 1821 625715365 625716293 0.000000e+00 977.0
21 TraesCS5B01G439500 chr5A 89.679 436 29 2 1992 2425 619345576 619345997 2.150000e-150 542.0
22 TraesCS5B01G439500 chr5A 81.055 417 38 25 1603 1984 619345120 619345530 6.660000e-76 294.0
23 TraesCS5B01G439500 chr5A 89.216 102 11 0 606 707 477539898 477539999 7.150000e-26 128.0
24 TraesCS5B01G439500 chr5A 94.595 37 2 0 1994 2030 625716240 625716276 9.510000e-05 58.4
25 TraesCS5B01G439500 chr5A 92.105 38 3 0 1992 2029 619345047 619345084 1.000000e-03 54.7
26 TraesCS5B01G439500 chr7B 86.872 617 62 14 2 605 643163497 643164107 0.000000e+00 673.0
27 TraesCS5B01G439500 chr7B 85.481 613 71 18 1 604 9636332 9635729 7.480000e-175 623.0
28 TraesCS5B01G439500 chr7B 97.030 101 3 0 607 707 727438196 727438296 1.170000e-38 171.0
29 TraesCS5B01G439500 chr2A 85.622 619 71 17 1 612 603859730 603859123 3.450000e-178 634.0
30 TraesCS5B01G439500 chr2A 91.899 358 22 4 2104 2458 60618844 60618491 6.120000e-136 494.0
31 TraesCS5B01G439500 chr2A 80.315 635 77 19 1 605 693439557 693438941 1.050000e-118 436.0
32 TraesCS5B01G439500 chr2A 88.462 156 13 4 1 152 762573727 762573881 1.500000e-42 183.0
33 TraesCS5B01G439500 chr2B 86.496 585 57 14 36 605 642448194 642447617 7.480000e-175 623.0
34 TraesCS5B01G439500 chr2B 84.591 623 60 28 2 611 585716854 585716255 9.810000e-164 586.0
35 TraesCS5B01G439500 chr2B 83.877 583 70 15 36 604 32066473 32067045 3.600000e-148 534.0
36 TraesCS5B01G439500 chr2B 86.413 368 42 7 252 615 765059800 765060163 1.770000e-106 396.0
37 TraesCS5B01G439500 chr7D 85.089 617 72 18 1 604 506162482 506161873 1.620000e-171 612.0
38 TraesCS5B01G439500 chr4A 88.430 484 48 7 128 606 695793833 695794313 5.900000e-161 577.0
39 TraesCS5B01G439500 chr6B 87.226 501 50 12 113 609 49968626 49969116 2.140000e-155 558.0
40 TraesCS5B01G439500 chr6B 85.513 497 59 12 128 618 678288615 678288126 7.860000e-140 507.0
41 TraesCS5B01G439500 chr6B 91.620 358 23 4 2104 2458 667435715 667436068 2.850000e-134 488.0
42 TraesCS5B01G439500 chr7A 82.353 629 89 15 2 616 158671643 158672263 6.030000e-146 527.0
43 TraesCS5B01G439500 chr7A 91.086 359 24 5 2104 2458 2148737 2148383 1.710000e-131 479.0
44 TraesCS5B01G439500 chr7A 91.086 359 24 5 2104 2458 2168663 2168309 1.710000e-131 479.0
45 TraesCS5B01G439500 chr1D 85.657 502 60 10 119 616 301250848 301250355 3.630000e-143 518.0
46 TraesCS5B01G439500 chr1D 82.188 393 50 11 227 613 375256724 375257102 1.100000e-83 320.0
47 TraesCS5B01G439500 chr1D 93.137 102 7 0 606 707 357159987 357159886 1.530000e-32 150.0
48 TraesCS5B01G439500 chr1A 91.643 359 22 5 2104 2458 558712381 558712735 7.910000e-135 490.0
49 TraesCS5B01G439500 chrUn 91.086 359 24 5 2104 2458 330079190 330078836 1.710000e-131 479.0
50 TraesCS5B01G439500 chrUn 91.086 359 24 5 2104 2458 340823487 340823841 1.710000e-131 479.0
51 TraesCS5B01G439500 chr1B 86.650 397 43 9 227 616 387382581 387382188 4.860000e-117 431.0
52 TraesCS5B01G439500 chr4B 84.742 426 50 11 227 642 533740645 533740225 1.760000e-111 412.0
53 TraesCS5B01G439500 chr3B 84.080 402 35 14 233 629 530615044 530615421 6.470000e-96 361.0
54 TraesCS5B01G439500 chr3B 84.651 215 17 12 2 209 803457969 803457764 1.490000e-47 200.0
55 TraesCS5B01G439500 chr6D 92.593 162 12 0 1067 1228 29381258 29381097 1.470000e-57 233.0
56 TraesCS5B01G439500 chr6D 91.975 162 13 0 1067 1228 24001596 24001757 6.850000e-56 228.0
57 TraesCS5B01G439500 chr6D 91.358 162 14 0 1067 1228 16502931 16503092 3.190000e-54 222.0
58 TraesCS5B01G439500 chr6D 91.358 162 14 0 1067 1228 29089724 29089885 3.190000e-54 222.0
59 TraesCS5B01G439500 chr6D 91.346 104 9 0 606 709 82197366 82197263 2.550000e-30 143.0
60 TraesCS5B01G439500 chr3D 86.275 102 5 1 606 707 526999792 526999884 4.330000e-18 102.0


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 TraesCS5B01G439500 chr5B 611676758 611679219 2461 False 4547.000000 4547 100.000000 1 2462 1 chr5B.!!$F1 2461
1 TraesCS5B01G439500 chr5B 649498368 649499405 1037 False 1273.000000 1273 89.358000 816 1821 1 chr5B.!!$F2 1005
2 TraesCS5B01G439500 chr5B 628723523 628724530 1007 True 1092.000000 1092 86.660000 825 1821 1 chr5B.!!$R2 996
3 TraesCS5B01G439500 chr5B 649694250 649694853 603 False 837.000000 837 91.587000 816 1435 1 chr5B.!!$F3 619
4 TraesCS5B01G439500 chr5B 629925502 629926478 976 True 592.050000 1122 91.179500 817 2030 2 chr5B.!!$R4 1213
5 TraesCS5B01G439500 chr5B 633171388 633172263 875 False 573.500000 1037 86.155000 939 1953 2 chr5B.!!$F4 1014
6 TraesCS5B01G439500 chr5D 495199689 495201481 1792 False 1132.500000 1672 90.202000 725 2462 2 chr5D.!!$F4 1737
7 TraesCS5B01G439500 chr5D 501449303 501450196 893 True 1105.000000 1105 89.123000 816 1705 1 chr5D.!!$R1 889
8 TraesCS5B01G439500 chr5D 517213268 517214099 831 False 1092.000000 1092 90.703000 817 1634 1 chr5D.!!$F2 817
9 TraesCS5B01G439500 chr5D 495138827 495143536 4709 False 604.333333 1240 92.453333 725 2076 3 chr5D.!!$F3 1351
10 TraesCS5B01G439500 chr5A 644310265 644311301 1036 False 1201.000000 1201 88.207000 816 1817 1 chr5A.!!$F2 1001
11 TraesCS5B01G439500 chr5A 619343979 619345997 2018 False 632.675000 1640 88.240500 722 2425 4 chr5A.!!$F3 1703
12 TraesCS5B01G439500 chr5A 625715365 625716293 928 False 517.700000 977 90.436000 919 2030 2 chr5A.!!$F4 1111
13 TraesCS5B01G439500 chr7B 643163497 643164107 610 False 673.000000 673 86.872000 2 605 1 chr7B.!!$F1 603
14 TraesCS5B01G439500 chr7B 9635729 9636332 603 True 623.000000 623 85.481000 1 604 1 chr7B.!!$R1 603
15 TraesCS5B01G439500 chr2A 603859123 603859730 607 True 634.000000 634 85.622000 1 612 1 chr2A.!!$R2 611
16 TraesCS5B01G439500 chr2A 693438941 693439557 616 True 436.000000 436 80.315000 1 605 1 chr2A.!!$R3 604
17 TraesCS5B01G439500 chr2B 642447617 642448194 577 True 623.000000 623 86.496000 36 605 1 chr2B.!!$R2 569
18 TraesCS5B01G439500 chr2B 585716255 585716854 599 True 586.000000 586 84.591000 2 611 1 chr2B.!!$R1 609
19 TraesCS5B01G439500 chr2B 32066473 32067045 572 False 534.000000 534 83.877000 36 604 1 chr2B.!!$F1 568
20 TraesCS5B01G439500 chr7D 506161873 506162482 609 True 612.000000 612 85.089000 1 604 1 chr7D.!!$R1 603
21 TraesCS5B01G439500 chr7A 158671643 158672263 620 False 527.000000 527 82.353000 2 616 1 chr7A.!!$F1 614

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
704 756 0.030638 CGGGCGGCAAATAGGATTTG 59.969 55.0 12.47 7.43 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 5338 0.68792 TCCCACCACGCAGATGTAAA 59.312 50.0 0.0 0.0 0.0 2.01 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
97 101 1.807226 GGCCGTGCCTATTGGAAAC 59.193 57.895 7.58 0.00 46.69 2.78
99 103 1.022451 GCCGTGCCTATTGGAAACGA 61.022 55.000 18.55 0.00 43.27 3.85
177 212 2.162716 CGTGCCTCCTCGGAAAAAG 58.837 57.895 0.00 0.00 33.16 2.27
222 257 4.452890 TTCTTTTCTTTTGCGAGAGTCG 57.547 40.909 0.00 0.00 43.89 4.18
261 298 1.812571 AGGCATGGTTGTGATTTCGTC 59.187 47.619 0.00 0.00 0.00 4.20
285 322 3.936203 ACGGGCGTGCCTCTTTCA 61.936 61.111 11.25 0.00 36.10 2.69
298 335 4.099419 TGCCTCTTTCAGAAAGGGAAAAAC 59.901 41.667 22.65 8.15 41.66 2.43
310 348 1.598685 GAAAAACCCGTGCTCCCGA 60.599 57.895 0.00 0.00 0.00 5.14
313 351 0.538746 AAAACCCGTGCTCCCGATTT 60.539 50.000 0.00 0.00 0.00 2.17
398 449 9.177608 CTATCAACATGGGATCTAGTTTTGAAA 57.822 33.333 5.52 0.00 0.00 2.69
420 471 2.733127 TCGACGCGAGAAATCCAAC 58.267 52.632 15.93 0.00 0.00 3.77
437 488 1.427592 AACGGCGAAAACGGTTCGAA 61.428 50.000 22.75 0.00 43.97 3.71
489 541 9.719279 AACGTTTTGAATAAACAGATTTACGAA 57.281 25.926 0.00 0.00 33.09 3.85
527 579 2.904866 TTGGGACAAGTGGCGCAC 60.905 61.111 10.83 5.73 46.21 5.34
528 580 3.705934 TTGGGACAAGTGGCGCACA 62.706 57.895 10.83 1.22 46.21 4.57
529 581 2.672996 GGGACAAGTGGCGCACAT 60.673 61.111 10.83 0.00 36.74 3.21
530 582 1.376683 GGGACAAGTGGCGCACATA 60.377 57.895 10.83 0.00 36.74 2.29
531 583 1.644786 GGGACAAGTGGCGCACATAC 61.645 60.000 10.83 2.11 36.74 2.39
532 584 0.953471 GGACAAGTGGCGCACATACA 60.953 55.000 10.83 0.00 36.74 2.29
533 585 0.443869 GACAAGTGGCGCACATACAG 59.556 55.000 10.83 2.38 36.74 2.74
534 586 1.135315 CAAGTGGCGCACATACAGC 59.865 57.895 10.83 0.00 36.74 4.40
541 593 2.480555 GCACATACAGCGCACCAC 59.519 61.111 11.47 0.00 0.00 4.16
542 594 2.034879 GCACATACAGCGCACCACT 61.035 57.895 11.47 0.00 0.00 4.00
543 595 1.577328 GCACATACAGCGCACCACTT 61.577 55.000 11.47 0.00 0.00 3.16
544 596 0.166597 CACATACAGCGCACCACTTG 59.833 55.000 11.47 0.00 0.00 3.16
545 597 0.250295 ACATACAGCGCACCACTTGT 60.250 50.000 11.47 6.56 0.00 3.16
546 598 1.001520 ACATACAGCGCACCACTTGTA 59.998 47.619 11.47 8.93 0.00 2.41
547 599 1.660607 CATACAGCGCACCACTTGTAG 59.339 52.381 11.47 0.00 30.39 2.74
548 600 0.677288 TACAGCGCACCACTTGTAGT 59.323 50.000 11.47 0.00 0.00 2.73
549 601 0.677288 ACAGCGCACCACTTGTAGTA 59.323 50.000 11.47 0.00 0.00 1.82
550 602 1.069513 ACAGCGCACCACTTGTAGTAA 59.930 47.619 11.47 0.00 0.00 2.24
551 603 1.459592 CAGCGCACCACTTGTAGTAAC 59.540 52.381 11.47 0.00 0.00 2.50
552 604 0.794473 GCGCACCACTTGTAGTAACC 59.206 55.000 0.30 0.00 0.00 2.85
553 605 1.607251 GCGCACCACTTGTAGTAACCT 60.607 52.381 0.30 0.00 0.00 3.50
554 606 2.066262 CGCACCACTTGTAGTAACCTG 58.934 52.381 0.00 0.00 0.00 4.00
555 607 2.288579 CGCACCACTTGTAGTAACCTGA 60.289 50.000 0.00 0.00 0.00 3.86
556 608 3.326747 GCACCACTTGTAGTAACCTGAG 58.673 50.000 0.00 0.00 0.00 3.35
557 609 3.864921 GCACCACTTGTAGTAACCTGAGG 60.865 52.174 0.00 0.00 0.00 3.86
558 610 3.576982 CACCACTTGTAGTAACCTGAGGA 59.423 47.826 4.99 0.00 0.00 3.71
559 611 4.039973 CACCACTTGTAGTAACCTGAGGAA 59.960 45.833 4.99 0.00 0.00 3.36
560 612 4.844655 ACCACTTGTAGTAACCTGAGGAAT 59.155 41.667 4.99 0.00 0.00 3.01
561 613 5.309806 ACCACTTGTAGTAACCTGAGGAATT 59.690 40.000 4.99 0.00 0.00 2.17
562 614 5.643777 CCACTTGTAGTAACCTGAGGAATTG 59.356 44.000 4.99 0.00 0.00 2.32
563 615 5.643777 CACTTGTAGTAACCTGAGGAATTGG 59.356 44.000 4.99 0.00 0.00 3.16
564 616 5.546499 ACTTGTAGTAACCTGAGGAATTGGA 59.454 40.000 4.99 0.00 0.00 3.53
565 617 6.043938 ACTTGTAGTAACCTGAGGAATTGGAA 59.956 38.462 4.99 0.00 0.00 3.53
566 618 6.636454 TGTAGTAACCTGAGGAATTGGAAT 57.364 37.500 4.99 0.00 0.00 3.01
567 619 7.743116 TGTAGTAACCTGAGGAATTGGAATA 57.257 36.000 4.99 0.00 0.00 1.75
568 620 8.153221 TGTAGTAACCTGAGGAATTGGAATAA 57.847 34.615 4.99 0.00 0.00 1.40
569 621 8.778059 TGTAGTAACCTGAGGAATTGGAATAAT 58.222 33.333 4.99 0.00 0.00 1.28
570 622 9.274206 GTAGTAACCTGAGGAATTGGAATAATC 57.726 37.037 4.99 0.00 0.00 1.75
571 623 8.107196 AGTAACCTGAGGAATTGGAATAATCT 57.893 34.615 4.99 0.00 0.00 2.40
572 624 8.560903 AGTAACCTGAGGAATTGGAATAATCTT 58.439 33.333 4.99 0.00 0.00 2.40
573 625 7.888250 AACCTGAGGAATTGGAATAATCTTC 57.112 36.000 4.99 0.00 0.00 2.87
574 626 6.058183 ACCTGAGGAATTGGAATAATCTTCG 58.942 40.000 4.99 0.00 0.00 3.79
575 627 5.049129 CCTGAGGAATTGGAATAATCTTCGC 60.049 44.000 0.00 0.00 0.00 4.70
576 628 5.436175 TGAGGAATTGGAATAATCTTCGCA 58.564 37.500 0.00 0.00 0.00 5.10
577 629 5.885352 TGAGGAATTGGAATAATCTTCGCAA 59.115 36.000 0.00 0.00 0.00 4.85
578 630 6.136541 AGGAATTGGAATAATCTTCGCAAC 57.863 37.500 0.00 0.00 0.00 4.17
579 631 5.652014 AGGAATTGGAATAATCTTCGCAACA 59.348 36.000 0.00 0.00 0.00 3.33
580 632 6.152661 AGGAATTGGAATAATCTTCGCAACAA 59.847 34.615 0.00 0.00 0.00 2.83
581 633 6.473455 GGAATTGGAATAATCTTCGCAACAAG 59.527 38.462 0.00 0.00 0.00 3.16
582 634 5.957842 TTGGAATAATCTTCGCAACAAGT 57.042 34.783 0.00 0.00 0.00 3.16
583 635 7.624360 ATTGGAATAATCTTCGCAACAAGTA 57.376 32.000 0.00 0.00 0.00 2.24
584 636 6.417191 TGGAATAATCTTCGCAACAAGTAC 57.583 37.500 0.00 0.00 0.00 2.73
585 637 6.170506 TGGAATAATCTTCGCAACAAGTACT 58.829 36.000 0.00 0.00 0.00 2.73
586 638 6.312918 TGGAATAATCTTCGCAACAAGTACTC 59.687 38.462 0.00 0.00 0.00 2.59
587 639 6.238130 GGAATAATCTTCGCAACAAGTACTCC 60.238 42.308 0.00 0.00 0.00 3.85
588 640 3.963428 ATCTTCGCAACAAGTACTCCT 57.037 42.857 0.00 0.00 0.00 3.69
589 641 3.746045 TCTTCGCAACAAGTACTCCTT 57.254 42.857 0.00 0.00 0.00 3.36
590 642 4.859304 TCTTCGCAACAAGTACTCCTTA 57.141 40.909 0.00 0.00 0.00 2.69
591 643 5.204409 TCTTCGCAACAAGTACTCCTTAA 57.796 39.130 0.00 0.00 0.00 1.85
592 644 4.986659 TCTTCGCAACAAGTACTCCTTAAC 59.013 41.667 0.00 0.00 0.00 2.01
593 645 4.595762 TCGCAACAAGTACTCCTTAACT 57.404 40.909 0.00 0.00 0.00 2.24
594 646 5.710513 TCGCAACAAGTACTCCTTAACTA 57.289 39.130 0.00 0.00 0.00 2.24
595 647 5.706916 TCGCAACAAGTACTCCTTAACTAG 58.293 41.667 0.00 0.00 0.00 2.57
596 648 5.242393 TCGCAACAAGTACTCCTTAACTAGT 59.758 40.000 0.00 0.00 0.00 2.57
597 649 5.345202 CGCAACAAGTACTCCTTAACTAGTG 59.655 44.000 0.00 0.00 0.00 2.74
598 650 6.453092 GCAACAAGTACTCCTTAACTAGTGA 58.547 40.000 0.00 0.00 0.00 3.41
599 651 7.097834 GCAACAAGTACTCCTTAACTAGTGAT 58.902 38.462 0.00 0.00 0.00 3.06
600 652 7.603024 GCAACAAGTACTCCTTAACTAGTGATT 59.397 37.037 0.00 0.00 0.00 2.57
601 653 9.490379 CAACAAGTACTCCTTAACTAGTGATTT 57.510 33.333 0.00 0.00 0.00 2.17
602 654 9.708092 AACAAGTACTCCTTAACTAGTGATTTC 57.292 33.333 0.00 0.00 0.00 2.17
603 655 8.027771 ACAAGTACTCCTTAACTAGTGATTTCG 58.972 37.037 0.00 0.00 0.00 3.46
604 656 7.098074 AGTACTCCTTAACTAGTGATTTCGG 57.902 40.000 0.00 0.00 0.00 4.30
605 657 6.888632 AGTACTCCTTAACTAGTGATTTCGGA 59.111 38.462 0.00 0.00 0.00 4.55
606 658 6.600882 ACTCCTTAACTAGTGATTTCGGAA 57.399 37.500 0.00 0.00 0.00 4.30
607 659 7.001099 ACTCCTTAACTAGTGATTTCGGAAA 57.999 36.000 5.52 5.52 0.00 3.13
608 660 7.447594 ACTCCTTAACTAGTGATTTCGGAAAA 58.552 34.615 7.33 0.00 0.00 2.29
609 661 7.935210 ACTCCTTAACTAGTGATTTCGGAAAAA 59.065 33.333 7.33 0.00 0.00 1.94
610 662 8.091385 TCCTTAACTAGTGATTTCGGAAAAAC 57.909 34.615 7.33 9.05 0.00 2.43
611 663 7.716123 TCCTTAACTAGTGATTTCGGAAAAACA 59.284 33.333 7.33 8.21 0.00 2.83
612 664 8.015658 CCTTAACTAGTGATTTCGGAAAAACAG 58.984 37.037 7.33 10.69 29.01 3.16
613 665 5.358298 ACTAGTGATTTCGGAAAAACAGC 57.642 39.130 7.33 6.44 29.01 4.40
614 666 4.819630 ACTAGTGATTTCGGAAAAACAGCA 59.180 37.500 7.33 0.00 29.01 4.41
615 667 3.964909 AGTGATTTCGGAAAAACAGCAC 58.035 40.909 7.33 3.97 29.01 4.40
616 668 2.719046 GTGATTTCGGAAAAACAGCACG 59.281 45.455 7.33 0.00 29.01 5.34
617 669 1.713932 GATTTCGGAAAAACAGCACGC 59.286 47.619 7.33 0.00 0.00 5.34
618 670 0.590230 TTTCGGAAAAACAGCACGCG 60.590 50.000 3.53 3.53 0.00 6.01
619 671 1.707239 TTCGGAAAAACAGCACGCGT 61.707 50.000 5.58 5.58 0.00 6.01
620 672 0.875040 TCGGAAAAACAGCACGCGTA 60.875 50.000 13.44 0.00 0.00 4.42
621 673 0.042013 CGGAAAAACAGCACGCGTAA 60.042 50.000 13.44 0.00 0.00 3.18
622 674 1.399215 CGGAAAAACAGCACGCGTAAT 60.399 47.619 13.44 0.00 0.00 1.89
623 675 2.239201 GGAAAAACAGCACGCGTAATC 58.761 47.619 13.44 4.06 0.00 1.75
624 676 2.239201 GAAAAACAGCACGCGTAATCC 58.761 47.619 13.44 0.16 0.00 3.01
625 677 0.165079 AAAACAGCACGCGTAATCCG 59.835 50.000 13.44 0.00 40.40 4.18
626 678 0.947180 AAACAGCACGCGTAATCCGT 60.947 50.000 13.44 1.84 39.91 4.69
627 679 0.109179 AACAGCACGCGTAATCCGTA 60.109 50.000 13.44 0.00 37.12 4.02
628 680 0.799534 ACAGCACGCGTAATCCGTAC 60.800 55.000 13.44 0.00 37.12 3.67
635 687 4.425578 GTAATCCGTACGTGGGCC 57.574 61.111 15.21 0.00 0.00 5.80
636 688 1.589727 GTAATCCGTACGTGGGCCG 60.590 63.158 15.21 0.00 44.03 6.13
637 689 2.784356 TAATCCGTACGTGGGCCGG 61.784 63.158 15.21 0.00 42.24 6.13
656 708 3.801997 CCATGCGGAGGCTCCCTT 61.802 66.667 27.36 14.84 40.82 3.95
657 709 2.515523 CATGCGGAGGCTCCCTTG 60.516 66.667 27.36 21.28 40.82 3.61
658 710 2.688666 ATGCGGAGGCTCCCTTGA 60.689 61.111 27.36 9.29 40.82 3.02
659 711 2.739996 ATGCGGAGGCTCCCTTGAG 61.740 63.158 27.36 14.08 41.84 3.02
678 730 3.406682 CGAAGCCTTGACCATTTGC 57.593 52.632 0.00 0.00 0.00 3.68
679 731 0.883833 CGAAGCCTTGACCATTTGCT 59.116 50.000 0.00 0.00 0.00 3.91
680 732 1.401931 CGAAGCCTTGACCATTTGCTG 60.402 52.381 0.00 0.00 31.55 4.41
681 733 0.319405 AAGCCTTGACCATTTGCTGC 59.681 50.000 0.00 0.00 31.55 5.25
682 734 1.079612 GCCTTGACCATTTGCTGCC 60.080 57.895 0.00 0.00 0.00 4.85
683 735 1.593265 CCTTGACCATTTGCTGCCC 59.407 57.895 0.00 0.00 0.00 5.36
684 736 1.213537 CTTGACCATTTGCTGCCCG 59.786 57.895 0.00 0.00 0.00 6.13
685 737 2.824071 CTTGACCATTTGCTGCCCGC 62.824 60.000 0.00 0.00 39.77 6.13
686 738 4.481112 GACCATTTGCTGCCCGCG 62.481 66.667 0.00 0.00 43.27 6.46
701 753 2.594592 GCGGGCGGCAAATAGGAT 60.595 61.111 12.47 0.00 42.87 3.24
702 754 2.193536 GCGGGCGGCAAATAGGATT 61.194 57.895 12.47 0.00 42.87 3.01
703 755 1.734388 GCGGGCGGCAAATAGGATTT 61.734 55.000 12.47 0.00 42.87 2.17
704 756 0.030638 CGGGCGGCAAATAGGATTTG 59.969 55.000 12.47 7.43 0.00 2.32
713 765 4.290155 GCAAATAGGATTTGCCACATACG 58.710 43.478 21.04 0.00 46.51 3.06
714 766 4.792704 GCAAATAGGATTTGCCACATACGG 60.793 45.833 21.04 0.00 46.51 4.02
715 767 4.431416 AATAGGATTTGCCACATACGGA 57.569 40.909 0.00 0.00 40.02 4.69
716 768 4.640771 ATAGGATTTGCCACATACGGAT 57.359 40.909 0.00 0.00 40.02 4.18
717 769 3.297134 AGGATTTGCCACATACGGATT 57.703 42.857 0.00 0.00 40.02 3.01
718 770 3.631250 AGGATTTGCCACATACGGATTT 58.369 40.909 0.00 0.00 40.02 2.17
719 771 3.381272 AGGATTTGCCACATACGGATTTG 59.619 43.478 0.00 0.00 40.02 2.32
720 772 3.130340 GGATTTGCCACATACGGATTTGT 59.870 43.478 0.00 0.00 36.34 2.83
721 773 3.567576 TTTGCCACATACGGATTTGTG 57.432 42.857 0.00 0.00 42.25 3.33
722 774 2.192664 TGCCACATACGGATTTGTGT 57.807 45.000 0.88 0.00 41.27 3.72
723 775 2.509569 TGCCACATACGGATTTGTGTT 58.490 42.857 0.88 0.00 41.27 3.32
1468 5018 2.939103 CCCAAGAAGGCTTAGTCGATTG 59.061 50.000 0.00 0.00 35.39 2.67
1541 5095 4.058124 TCGATGTAATGCTATGTTCTGCC 58.942 43.478 0.00 0.00 0.00 4.85
1595 5157 9.952188 ACTTTTAGTAAATTCTTTGCTCTGTTC 57.048 29.630 0.00 0.00 36.90 3.18
1600 5304 7.220030 AGTAAATTCTTTGCTCTGTTCTCTGA 58.780 34.615 0.00 0.00 29.11 3.27
1601 5305 7.882271 AGTAAATTCTTTGCTCTGTTCTCTGAT 59.118 33.333 0.00 0.00 29.11 2.90
1606 5310 5.468072 TCTTTGCTCTGTTCTCTGATTGTTC 59.532 40.000 0.00 0.00 0.00 3.18
1607 5311 4.341366 TGCTCTGTTCTCTGATTGTTCA 57.659 40.909 0.00 0.00 0.00 3.18
1619 5326 7.435305 TCTCTGATTGTTCATTGATTTTGCAA 58.565 30.769 0.00 0.00 0.00 4.08
1627 5334 4.765281 CATTGATTTTGCAATGCTACGG 57.235 40.909 6.82 0.00 45.80 4.02
1628 5335 4.422840 CATTGATTTTGCAATGCTACGGA 58.577 39.130 6.82 0.00 45.80 4.69
1631 5338 3.947196 TGATTTTGCAATGCTACGGAGAT 59.053 39.130 6.82 0.00 0.00 2.75
1634 5341 5.888691 TTTTGCAATGCTACGGAGATTTA 57.111 34.783 6.82 0.00 0.00 1.40
1651 5360 0.908910 TTACATCTGCGTGGTGGGAT 59.091 50.000 0.00 0.00 0.00 3.85
1698 5408 5.596268 TGAATCTGAATTCACTTCGTGTG 57.404 39.130 3.38 5.26 44.94 3.82
1702 5412 4.951254 TCTGAATTCACTTCGTGTGGTTA 58.049 39.130 3.38 0.21 46.20 2.85
1703 5413 4.748102 TCTGAATTCACTTCGTGTGGTTAC 59.252 41.667 3.38 0.00 46.20 2.50
1704 5414 4.699637 TGAATTCACTTCGTGTGGTTACT 58.300 39.130 3.38 0.00 46.20 2.24
1706 5416 5.924254 TGAATTCACTTCGTGTGGTTACTAG 59.076 40.000 3.38 0.00 46.20 2.57
1707 5417 5.717078 ATTCACTTCGTGTGGTTACTAGA 57.283 39.130 0.00 0.00 46.20 2.43
1708 5418 5.518848 TTCACTTCGTGTGGTTACTAGAA 57.481 39.130 0.00 0.00 46.20 2.10
1711 5421 6.339730 TCACTTCGTGTGGTTACTAGAAAAA 58.660 36.000 0.00 0.00 46.20 1.94
1712 5422 6.256321 TCACTTCGTGTGGTTACTAGAAAAAC 59.744 38.462 0.00 0.00 46.20 2.43
1713 5423 6.036300 CACTTCGTGTGGTTACTAGAAAAACA 59.964 38.462 0.00 0.00 42.68 2.83
1714 5424 6.257193 ACTTCGTGTGGTTACTAGAAAAACAG 59.743 38.462 0.00 0.00 0.00 3.16
1763 5479 4.153475 CCAACCTGTATTTTACCTGTCACG 59.847 45.833 0.00 0.00 0.00 4.35
1766 5482 6.100404 ACCTGTATTTTACCTGTCACGTAA 57.900 37.500 0.00 0.00 0.00 3.18
1785 5501 7.706607 TCACGTAATATGATTTCAGGTTCAGAG 59.293 37.037 0.00 0.00 0.00 3.35
1829 5546 4.175516 CCAAATCCCACGTTCATGATTTG 58.824 43.478 20.83 20.83 46.89 2.32
1833 5550 2.551887 TCCCACGTTCATGATTTGTGTG 59.448 45.455 16.54 11.61 0.00 3.82
1867 5584 7.916977 TCATGATTTTGCAATGCTATGTAGTTC 59.083 33.333 6.82 0.00 0.00 3.01
1895 5878 1.561542 GTGTGGTGGGATGAATCCTCT 59.438 52.381 9.18 0.00 46.35 3.69
1938 5922 5.125100 TGAATCTGACAAATTCACTTGGC 57.875 39.130 0.00 0.00 38.02 4.52
1953 5937 4.288626 TCACTTGGCCTGGTTACTAGAAAT 59.711 41.667 3.32 0.00 0.00 2.17
1984 5974 3.124976 GTCAGAGTTGCAAGATGAGAAGC 59.875 47.826 0.00 0.00 0.00 3.86
2032 6062 6.801539 ACATTTGTGTATGTCAAGTACCAG 57.198 37.500 0.00 0.00 33.58 4.00
2033 6063 6.296026 ACATTTGTGTATGTCAAGTACCAGT 58.704 36.000 0.00 0.00 33.58 4.00
2057 6087 8.739972 AGTAAACCAAATTTCCAGCTTATGTAG 58.260 33.333 0.00 0.00 0.00 2.74
2106 6137 5.957771 ATTCCTCTAGTGGCTTATGTCAA 57.042 39.130 5.93 0.00 0.00 3.18
2209 6242 7.037586 ACAAATACAGAGAAAGAGGACCCATTA 60.038 37.037 0.00 0.00 0.00 1.90
2210 6243 7.698163 AATACAGAGAAAGAGGACCCATTAT 57.302 36.000 0.00 0.00 0.00 1.28
2253 6286 4.325109 GGGTTATGGGAACTTAGAAAGGCT 60.325 45.833 0.00 0.00 0.00 4.58
2267 6300 3.774216 AGAAAGGCTTCTAGCTGATGAGT 59.226 43.478 0.00 0.00 40.26 3.41
2269 6302 3.540314 AGGCTTCTAGCTGATGAGTTG 57.460 47.619 0.00 0.00 41.99 3.16
2271 6304 2.935201 GGCTTCTAGCTGATGAGTTGTG 59.065 50.000 0.00 0.00 41.99 3.33
2288 6321 8.142994 TGAGTTGTGAGTGACTAATTTTCTTC 57.857 34.615 0.00 0.00 0.00 2.87
2337 6370 2.612212 ACACATTTGCTCGTCGTTTTCT 59.388 40.909 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 1.087501 GCCTCTCGCGAAAGGAAAAT 58.912 50.000 32.19 0.00 34.35 1.82
122 155 2.300066 GCAAAACCGTGCCTTTCGC 61.300 57.895 0.00 0.00 38.66 4.70
126 159 1.739667 GGAAGCAAAACCGTGCCTT 59.260 52.632 0.00 0.00 46.14 4.35
222 257 1.441016 CTCGCAGAAGCAAAACCGC 60.441 57.895 0.00 0.00 42.27 5.68
246 282 2.766313 CCTCTGACGAAATCACAACCA 58.234 47.619 0.00 0.00 32.37 3.67
298 335 2.824041 CCAAATCGGGAGCACGGG 60.824 66.667 0.00 0.00 0.00 5.28
412 463 0.039888 CCGTTTTCGCCGTTGGATTT 60.040 50.000 0.00 0.00 42.58 2.17
420 471 0.110554 ATTTCGAACCGTTTTCGCCG 60.111 50.000 10.66 0.00 41.30 6.46
437 488 4.394729 TCTCTTAAACCTGCGTCCAAATT 58.605 39.130 0.00 0.00 0.00 1.82
508 560 3.670377 GCGCCACTTGTCCCAACC 61.670 66.667 0.00 0.00 0.00 3.77
513 565 0.953471 TGTATGTGCGCCACTTGTCC 60.953 55.000 4.18 0.00 35.11 4.02
526 578 0.250295 ACAAGTGGTGCGCTGTATGT 60.250 50.000 9.73 3.57 0.00 2.29
527 579 1.660607 CTACAAGTGGTGCGCTGTATG 59.339 52.381 9.73 2.89 0.00 2.39
528 580 1.275291 ACTACAAGTGGTGCGCTGTAT 59.725 47.619 9.73 0.00 0.00 2.29
529 581 0.677288 ACTACAAGTGGTGCGCTGTA 59.323 50.000 9.73 6.87 0.00 2.74
530 582 0.677288 TACTACAAGTGGTGCGCTGT 59.323 50.000 9.73 5.88 0.00 4.40
531 583 1.459592 GTTACTACAAGTGGTGCGCTG 59.540 52.381 9.73 0.00 0.00 5.18
532 584 1.607251 GGTTACTACAAGTGGTGCGCT 60.607 52.381 9.73 0.00 0.00 5.92
533 585 0.794473 GGTTACTACAAGTGGTGCGC 59.206 55.000 0.00 0.00 0.00 6.09
534 586 2.066262 CAGGTTACTACAAGTGGTGCG 58.934 52.381 0.00 0.00 0.00 5.34
535 587 3.326747 CTCAGGTTACTACAAGTGGTGC 58.673 50.000 0.00 0.00 0.00 5.01
536 588 3.576982 TCCTCAGGTTACTACAAGTGGTG 59.423 47.826 0.00 0.00 0.00 4.17
537 589 3.853207 TCCTCAGGTTACTACAAGTGGT 58.147 45.455 0.00 0.00 0.00 4.16
538 590 4.884668 TTCCTCAGGTTACTACAAGTGG 57.115 45.455 0.00 0.00 0.00 4.00
539 591 5.643777 CCAATTCCTCAGGTTACTACAAGTG 59.356 44.000 0.00 0.00 0.00 3.16
540 592 5.546499 TCCAATTCCTCAGGTTACTACAAGT 59.454 40.000 0.00 0.00 0.00 3.16
541 593 6.049955 TCCAATTCCTCAGGTTACTACAAG 57.950 41.667 0.00 0.00 0.00 3.16
542 594 6.442541 TTCCAATTCCTCAGGTTACTACAA 57.557 37.500 0.00 0.00 0.00 2.41
543 595 6.636454 ATTCCAATTCCTCAGGTTACTACA 57.364 37.500 0.00 0.00 0.00 2.74
544 596 9.274206 GATTATTCCAATTCCTCAGGTTACTAC 57.726 37.037 0.00 0.00 0.00 2.73
545 597 9.225682 AGATTATTCCAATTCCTCAGGTTACTA 57.774 33.333 0.00 0.00 0.00 1.82
546 598 8.107196 AGATTATTCCAATTCCTCAGGTTACT 57.893 34.615 0.00 0.00 0.00 2.24
547 599 8.753497 AAGATTATTCCAATTCCTCAGGTTAC 57.247 34.615 0.00 0.00 0.00 2.50
548 600 7.715249 CGAAGATTATTCCAATTCCTCAGGTTA 59.285 37.037 0.00 0.00 0.00 2.85
549 601 6.543831 CGAAGATTATTCCAATTCCTCAGGTT 59.456 38.462 0.00 0.00 0.00 3.50
550 602 6.058183 CGAAGATTATTCCAATTCCTCAGGT 58.942 40.000 0.00 0.00 0.00 4.00
551 603 5.049129 GCGAAGATTATTCCAATTCCTCAGG 60.049 44.000 0.00 0.00 0.00 3.86
552 604 5.528690 TGCGAAGATTATTCCAATTCCTCAG 59.471 40.000 0.00 0.00 0.00 3.35
553 605 5.436175 TGCGAAGATTATTCCAATTCCTCA 58.564 37.500 0.00 0.00 0.00 3.86
554 606 6.183360 TGTTGCGAAGATTATTCCAATTCCTC 60.183 38.462 0.00 0.00 0.00 3.71
555 607 5.652014 TGTTGCGAAGATTATTCCAATTCCT 59.348 36.000 0.00 0.00 0.00 3.36
556 608 5.890334 TGTTGCGAAGATTATTCCAATTCC 58.110 37.500 0.00 0.00 0.00 3.01
557 609 7.029563 ACTTGTTGCGAAGATTATTCCAATTC 58.970 34.615 0.00 0.00 0.00 2.17
558 610 6.924111 ACTTGTTGCGAAGATTATTCCAATT 58.076 32.000 0.00 0.00 0.00 2.32
559 611 6.515272 ACTTGTTGCGAAGATTATTCCAAT 57.485 33.333 0.00 0.00 0.00 3.16
560 612 5.957842 ACTTGTTGCGAAGATTATTCCAA 57.042 34.783 0.00 0.00 0.00 3.53
561 613 6.170506 AGTACTTGTTGCGAAGATTATTCCA 58.829 36.000 0.00 0.00 0.00 3.53
562 614 6.238130 GGAGTACTTGTTGCGAAGATTATTCC 60.238 42.308 0.00 0.00 0.00 3.01
563 615 6.535508 AGGAGTACTTGTTGCGAAGATTATTC 59.464 38.462 0.00 0.00 0.00 1.75
564 616 6.407202 AGGAGTACTTGTTGCGAAGATTATT 58.593 36.000 0.00 0.00 0.00 1.40
565 617 5.978814 AGGAGTACTTGTTGCGAAGATTAT 58.021 37.500 0.00 0.00 0.00 1.28
566 618 5.401531 AGGAGTACTTGTTGCGAAGATTA 57.598 39.130 0.00 0.00 0.00 1.75
567 619 4.273148 AGGAGTACTTGTTGCGAAGATT 57.727 40.909 0.00 0.00 0.00 2.40
568 620 3.963428 AGGAGTACTTGTTGCGAAGAT 57.037 42.857 0.00 0.00 0.00 2.40
569 621 3.746045 AAGGAGTACTTGTTGCGAAGA 57.254 42.857 0.00 0.00 38.21 2.87
570 622 4.989168 AGTTAAGGAGTACTTGTTGCGAAG 59.011 41.667 0.00 0.00 40.37 3.79
571 623 4.952460 AGTTAAGGAGTACTTGTTGCGAA 58.048 39.130 0.00 0.00 40.37 4.70
572 624 4.595762 AGTTAAGGAGTACTTGTTGCGA 57.404 40.909 0.00 0.00 40.37 5.10
573 625 5.345202 CACTAGTTAAGGAGTACTTGTTGCG 59.655 44.000 0.00 0.00 40.37 4.85
574 626 6.453092 TCACTAGTTAAGGAGTACTTGTTGC 58.547 40.000 0.00 0.00 40.37 4.17
575 627 9.490379 AAATCACTAGTTAAGGAGTACTTGTTG 57.510 33.333 0.00 0.00 40.37 3.33
576 628 9.708092 GAAATCACTAGTTAAGGAGTACTTGTT 57.292 33.333 0.00 0.00 40.37 2.83
577 629 8.027771 CGAAATCACTAGTTAAGGAGTACTTGT 58.972 37.037 0.00 0.00 40.37 3.16
578 630 7.488471 CCGAAATCACTAGTTAAGGAGTACTTG 59.512 40.741 0.00 0.00 40.37 3.16
579 631 7.395489 TCCGAAATCACTAGTTAAGGAGTACTT 59.605 37.037 0.00 0.00 43.28 2.24
580 632 6.888632 TCCGAAATCACTAGTTAAGGAGTACT 59.111 38.462 0.00 0.00 0.00 2.73
581 633 7.093322 TCCGAAATCACTAGTTAAGGAGTAC 57.907 40.000 0.00 0.00 0.00 2.73
582 634 7.707624 TTCCGAAATCACTAGTTAAGGAGTA 57.292 36.000 0.00 0.00 0.00 2.59
583 635 6.600882 TTCCGAAATCACTAGTTAAGGAGT 57.399 37.500 0.00 0.00 0.00 3.85
584 636 7.900782 TTTTCCGAAATCACTAGTTAAGGAG 57.099 36.000 0.00 0.00 0.00 3.69
585 637 7.716123 TGTTTTTCCGAAATCACTAGTTAAGGA 59.284 33.333 0.00 0.00 0.00 3.36
586 638 7.867752 TGTTTTTCCGAAATCACTAGTTAAGG 58.132 34.615 0.00 0.00 0.00 2.69
587 639 7.534239 GCTGTTTTTCCGAAATCACTAGTTAAG 59.466 37.037 0.00 0.00 0.00 1.85
588 640 7.012515 TGCTGTTTTTCCGAAATCACTAGTTAA 59.987 33.333 0.00 0.00 0.00 2.01
589 641 6.483974 TGCTGTTTTTCCGAAATCACTAGTTA 59.516 34.615 0.00 0.00 0.00 2.24
590 642 5.298276 TGCTGTTTTTCCGAAATCACTAGTT 59.702 36.000 0.00 0.00 0.00 2.24
591 643 4.819630 TGCTGTTTTTCCGAAATCACTAGT 59.180 37.500 0.00 0.00 0.00 2.57
592 644 5.147162 GTGCTGTTTTTCCGAAATCACTAG 58.853 41.667 0.00 0.00 0.00 2.57
593 645 4.319190 CGTGCTGTTTTTCCGAAATCACTA 60.319 41.667 0.00 0.00 0.00 2.74
594 646 3.548014 CGTGCTGTTTTTCCGAAATCACT 60.548 43.478 0.00 0.00 0.00 3.41
595 647 2.719046 CGTGCTGTTTTTCCGAAATCAC 59.281 45.455 0.00 0.00 0.00 3.06
596 648 2.856720 GCGTGCTGTTTTTCCGAAATCA 60.857 45.455 0.00 0.00 0.00 2.57
597 649 1.713932 GCGTGCTGTTTTTCCGAAATC 59.286 47.619 0.00 0.00 0.00 2.17
598 650 1.766069 GCGTGCTGTTTTTCCGAAAT 58.234 45.000 0.00 0.00 0.00 2.17
599 651 0.590230 CGCGTGCTGTTTTTCCGAAA 60.590 50.000 0.00 0.00 0.00 3.46
600 652 1.010574 CGCGTGCTGTTTTTCCGAA 60.011 52.632 0.00 0.00 0.00 4.30
601 653 0.875040 TACGCGTGCTGTTTTTCCGA 60.875 50.000 24.59 0.00 0.00 4.55
602 654 0.042013 TTACGCGTGCTGTTTTTCCG 60.042 50.000 24.59 0.00 0.00 4.30
603 655 2.239201 GATTACGCGTGCTGTTTTTCC 58.761 47.619 24.59 0.00 0.00 3.13
604 656 2.239201 GGATTACGCGTGCTGTTTTTC 58.761 47.619 24.59 6.52 0.00 2.29
605 657 1.399215 CGGATTACGCGTGCTGTTTTT 60.399 47.619 24.59 0.00 34.82 1.94
606 658 0.165079 CGGATTACGCGTGCTGTTTT 59.835 50.000 24.59 0.00 34.82 2.43
607 659 1.785321 CGGATTACGCGTGCTGTTT 59.215 52.632 24.59 0.00 34.82 2.83
608 660 3.470267 CGGATTACGCGTGCTGTT 58.530 55.556 24.59 0.98 34.82 3.16
610 662 1.794455 CGTACGGATTACGCGTGCTG 61.794 60.000 24.59 17.86 46.76 4.41
611 663 1.584483 CGTACGGATTACGCGTGCT 60.584 57.895 24.59 8.80 46.76 4.40
612 664 2.908363 CGTACGGATTACGCGTGC 59.092 61.111 24.59 11.10 46.76 5.34
618 670 1.589727 CGGCCCACGTACGGATTAC 60.590 63.158 21.06 5.87 37.93 1.89
619 671 2.806929 CGGCCCACGTACGGATTA 59.193 61.111 21.06 0.00 37.93 1.75
639 691 3.801997 AAGGGAGCCTCCGCATGG 61.802 66.667 4.29 0.00 37.43 3.66
640 692 2.515523 CAAGGGAGCCTCCGCATG 60.516 66.667 4.29 0.00 37.43 4.06
641 693 2.688666 TCAAGGGAGCCTCCGCAT 60.689 61.111 4.29 0.00 37.43 4.73
642 694 3.393970 CTCAAGGGAGCCTCCGCA 61.394 66.667 4.29 0.00 37.43 5.69
650 702 1.023513 CAAGGCTTCGCTCAAGGGAG 61.024 60.000 0.00 0.00 44.33 4.30
651 703 1.003355 CAAGGCTTCGCTCAAGGGA 60.003 57.895 0.00 0.00 35.07 4.20
652 704 1.003355 TCAAGGCTTCGCTCAAGGG 60.003 57.895 0.00 0.00 31.94 3.95
653 705 1.301677 GGTCAAGGCTTCGCTCAAGG 61.302 60.000 0.00 0.00 31.94 3.61
654 706 0.603707 TGGTCAAGGCTTCGCTCAAG 60.604 55.000 0.00 0.00 34.85 3.02
655 707 0.036732 ATGGTCAAGGCTTCGCTCAA 59.963 50.000 0.00 0.00 0.00 3.02
656 708 0.036732 AATGGTCAAGGCTTCGCTCA 59.963 50.000 0.00 0.00 0.00 4.26
657 709 1.135575 CAAATGGTCAAGGCTTCGCTC 60.136 52.381 0.00 0.00 0.00 5.03
658 710 0.883833 CAAATGGTCAAGGCTTCGCT 59.116 50.000 0.00 0.00 0.00 4.93
659 711 0.733909 GCAAATGGTCAAGGCTTCGC 60.734 55.000 0.00 0.00 0.00 4.70
660 712 0.883833 AGCAAATGGTCAAGGCTTCG 59.116 50.000 0.00 0.00 0.00 3.79
661 713 1.670967 GCAGCAAATGGTCAAGGCTTC 60.671 52.381 0.00 0.00 31.30 3.86
662 714 0.319405 GCAGCAAATGGTCAAGGCTT 59.681 50.000 0.00 0.00 31.30 4.35
663 715 1.538687 GGCAGCAAATGGTCAAGGCT 61.539 55.000 0.00 0.00 34.64 4.58
664 716 1.079612 GGCAGCAAATGGTCAAGGC 60.080 57.895 0.00 0.00 0.00 4.35
665 717 1.593265 GGGCAGCAAATGGTCAAGG 59.407 57.895 0.00 0.00 0.00 3.61
666 718 1.213537 CGGGCAGCAAATGGTCAAG 59.786 57.895 0.00 0.00 0.00 3.02
667 719 3.364442 CGGGCAGCAAATGGTCAA 58.636 55.556 0.00 0.00 0.00 3.18
684 736 1.734388 AAATCCTATTTGCCGCCCGC 61.734 55.000 0.00 0.00 38.31 6.13
685 737 0.030638 CAAATCCTATTTGCCGCCCG 59.969 55.000 0.00 0.00 0.00 6.13
686 738 0.249447 GCAAATCCTATTTGCCGCCC 60.249 55.000 21.23 0.19 46.51 6.13
687 739 3.272766 GCAAATCCTATTTGCCGCC 57.727 52.632 21.23 0.50 46.51 6.13
692 744 4.578516 TCCGTATGTGGCAAATCCTATTTG 59.421 41.667 0.00 7.80 35.26 2.32
693 745 4.787551 TCCGTATGTGGCAAATCCTATTT 58.212 39.130 0.00 0.00 35.26 1.40
694 746 4.431416 TCCGTATGTGGCAAATCCTATT 57.569 40.909 0.00 0.00 35.26 1.73
695 747 4.640771 ATCCGTATGTGGCAAATCCTAT 57.359 40.909 0.00 0.00 35.26 2.57
696 748 4.431416 AATCCGTATGTGGCAAATCCTA 57.569 40.909 0.00 0.00 35.26 2.94
697 749 3.297134 AATCCGTATGTGGCAAATCCT 57.703 42.857 0.00 0.00 35.26 3.24
698 750 3.130340 ACAAATCCGTATGTGGCAAATCC 59.870 43.478 0.00 0.00 0.00 3.01
699 751 4.104776 CACAAATCCGTATGTGGCAAATC 58.895 43.478 0.00 0.00 42.46 2.17
700 752 4.108699 CACAAATCCGTATGTGGCAAAT 57.891 40.909 0.00 0.00 42.46 2.32
701 753 3.567576 CACAAATCCGTATGTGGCAAA 57.432 42.857 0.00 0.00 42.46 3.68
707 759 2.230266 GGGCAAACACAAATCCGTATGT 59.770 45.455 0.00 0.00 0.00 2.29
708 760 2.416701 GGGGCAAACACAAATCCGTATG 60.417 50.000 0.00 0.00 0.00 2.39
709 761 1.822371 GGGGCAAACACAAATCCGTAT 59.178 47.619 0.00 0.00 0.00 3.06
710 762 1.202952 AGGGGCAAACACAAATCCGTA 60.203 47.619 0.00 0.00 0.00 4.02
711 763 0.469144 AGGGGCAAACACAAATCCGT 60.469 50.000 0.00 0.00 0.00 4.69
712 764 0.243636 GAGGGGCAAACACAAATCCG 59.756 55.000 0.00 0.00 0.00 4.18
713 765 1.632589 AGAGGGGCAAACACAAATCC 58.367 50.000 0.00 0.00 0.00 3.01
714 766 2.161609 CGTAGAGGGGCAAACACAAATC 59.838 50.000 0.00 0.00 0.00 2.17
715 767 2.159382 CGTAGAGGGGCAAACACAAAT 58.841 47.619 0.00 0.00 0.00 2.32
716 768 1.134037 ACGTAGAGGGGCAAACACAAA 60.134 47.619 0.00 0.00 0.00 2.83
717 769 0.470766 ACGTAGAGGGGCAAACACAA 59.529 50.000 0.00 0.00 0.00 3.33
718 770 0.034337 GACGTAGAGGGGCAAACACA 59.966 55.000 0.00 0.00 0.00 3.72
719 771 0.672711 GGACGTAGAGGGGCAAACAC 60.673 60.000 0.00 0.00 0.00 3.32
720 772 1.675219 GGACGTAGAGGGGCAAACA 59.325 57.895 0.00 0.00 0.00 2.83
721 773 1.447314 CGGACGTAGAGGGGCAAAC 60.447 63.158 0.00 0.00 0.00 2.93
722 774 0.611618 TACGGACGTAGAGGGGCAAA 60.612 55.000 0.00 0.00 0.00 3.68
723 775 0.611618 TTACGGACGTAGAGGGGCAA 60.612 55.000 4.67 0.00 31.71 4.52
1230 4763 4.033776 TTCCCGGCCAGCTCAAGG 62.034 66.667 2.24 0.00 0.00 3.61
1468 5018 0.038159 ACTACGAAGCACTGGACAGC 60.038 55.000 0.00 0.00 0.00 4.40
1595 5157 7.646446 TTGCAAAATCAATGAACAATCAGAG 57.354 32.000 0.00 0.00 39.39 3.35
1607 5311 4.398988 TCTCCGTAGCATTGCAAAATCAAT 59.601 37.500 11.91 0.00 37.16 2.57
1619 5326 4.310769 GCAGATGTAAATCTCCGTAGCAT 58.689 43.478 0.00 0.00 0.00 3.79
1622 5329 3.731216 CACGCAGATGTAAATCTCCGTAG 59.269 47.826 11.54 3.49 42.51 3.51
1625 5332 1.860950 CCACGCAGATGTAAATCTCCG 59.139 52.381 4.61 4.61 37.81 4.63
1626 5333 2.609459 CACCACGCAGATGTAAATCTCC 59.391 50.000 0.00 0.00 0.00 3.71
1627 5334 2.609459 CCACCACGCAGATGTAAATCTC 59.391 50.000 0.00 0.00 0.00 2.75
1628 5335 2.632377 CCACCACGCAGATGTAAATCT 58.368 47.619 0.00 0.00 0.00 2.40
1631 5338 0.687920 TCCCACCACGCAGATGTAAA 59.312 50.000 0.00 0.00 0.00 2.01
1634 5341 1.078214 CATCCCACCACGCAGATGT 60.078 57.895 0.00 0.00 33.09 3.06
1643 5352 6.153680 GGTAAATACAACAATTCATCCCACCA 59.846 38.462 0.00 0.00 0.00 4.17
1693 5403 5.751990 ACTCTGTTTTTCTAGTAACCACACG 59.248 40.000 0.00 0.00 0.00 4.49
1695 5405 6.037830 GCAACTCTGTTTTTCTAGTAACCACA 59.962 38.462 0.00 0.00 0.00 4.17
1698 5408 6.613755 TGCAACTCTGTTTTTCTAGTAACC 57.386 37.500 0.00 0.00 0.00 2.85
1702 5412 4.884164 AGCTTGCAACTCTGTTTTTCTAGT 59.116 37.500 0.00 0.00 0.00 2.57
1703 5413 5.008019 TCAGCTTGCAACTCTGTTTTTCTAG 59.992 40.000 18.26 0.00 0.00 2.43
1704 5414 4.881273 TCAGCTTGCAACTCTGTTTTTCTA 59.119 37.500 18.26 1.44 0.00 2.10
1706 5416 4.032703 TCAGCTTGCAACTCTGTTTTTC 57.967 40.909 18.26 0.00 0.00 2.29
1707 5417 4.158394 TCTTCAGCTTGCAACTCTGTTTTT 59.842 37.500 18.26 0.00 0.00 1.94
1708 5418 3.696051 TCTTCAGCTTGCAACTCTGTTTT 59.304 39.130 18.26 0.00 0.00 2.43
1711 5421 2.627515 TCTTCAGCTTGCAACTCTGT 57.372 45.000 18.26 0.00 0.00 3.41
1712 5422 2.350580 GCTTCTTCAGCTTGCAACTCTG 60.351 50.000 14.65 14.65 46.27 3.35
1713 5423 1.878734 GCTTCTTCAGCTTGCAACTCT 59.121 47.619 0.00 0.00 46.27 3.24
1714 5424 2.328655 GCTTCTTCAGCTTGCAACTC 57.671 50.000 0.00 0.00 46.27 3.01
1766 5482 8.900781 CACAAATCTCTGAACCTGAAATCATAT 58.099 33.333 0.00 0.00 0.00 1.78
1829 5546 3.542712 AAATCATGAACAGACGCACAC 57.457 42.857 0.00 0.00 0.00 3.82
1833 5550 2.932498 TGCAAAATCATGAACAGACGC 58.068 42.857 0.00 0.00 0.00 5.19
1867 5584 2.501316 TCATCCCACCACACAGATGTAG 59.499 50.000 0.00 0.00 36.72 2.74
1953 5937 7.498900 TCATCTTGCAACTCTGACTTTTAAGAA 59.501 33.333 0.00 0.00 0.00 2.52
1999 6029 4.761739 ACATACACAAATGTCTGAACCTGG 59.238 41.667 0.00 0.00 40.48 4.45
2032 6062 7.973944 CCTACATAAGCTGGAAATTTGGTTTAC 59.026 37.037 0.00 0.00 0.00 2.01
2033 6063 7.891183 TCCTACATAAGCTGGAAATTTGGTTTA 59.109 33.333 0.00 0.00 0.00 2.01
2097 6128 5.891451 TGTAGTGATCTCGGTTGACATAAG 58.109 41.667 0.00 0.00 0.00 1.73
2106 6137 5.886474 TGTTCTAGAATGTAGTGATCTCGGT 59.114 40.000 8.75 0.00 0.00 4.69
2209 6242 3.434167 CCCAGCAACTGTAGGCTATCAAT 60.434 47.826 0.00 0.00 38.56 2.57
2210 6243 2.092968 CCCAGCAACTGTAGGCTATCAA 60.093 50.000 0.00 0.00 38.56 2.57
2253 6286 4.524328 TCACTCACAACTCATCAGCTAGAA 59.476 41.667 0.00 0.00 0.00 2.10
2288 6321 8.964420 AAATCGTAAAAGTGGATGTTGTTATG 57.036 30.769 0.00 0.00 0.00 1.90
2293 6326 5.856455 GTGGAAATCGTAAAAGTGGATGTTG 59.144 40.000 0.00 0.00 0.00 3.33
2299 6332 4.822036 TGTGTGGAAATCGTAAAAGTGG 57.178 40.909 0.00 0.00 0.00 4.00
2337 6370 5.466058 CACACAAGCAGCCAATATTTTTCAA 59.534 36.000 0.00 0.00 0.00 2.69
2375 6573 3.762288 AGATCGCGGGCACTAGAATATAA 59.238 43.478 6.13 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.