Multiple sequence alignment - TraesCS7B01G056000

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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 TraesCS7B01G056000 chr7B 100.000 3455 0 0 1 3455 59077731 59081185 0.000000e+00 6381
1 TraesCS7B01G056000 chr7D 94.122 1412 61 13 1410 2808 101780857 101779455 0.000000e+00 2128
2 TraesCS7B01G056000 chr7D 92.815 682 29 6 2794 3455 101778762 101778081 0.000000e+00 970
3 TraesCS7B01G056000 chr7D 91.935 558 27 3 851 1390 101781400 101780843 0.000000e+00 765
4 TraesCS7B01G056000 chr7D 82.392 744 80 32 2491 3198 37973635 37974363 4.930000e-168 601
5 TraesCS7B01G056000 chr7D 84.225 374 36 9 350 702 101742685 101743056 3.300000e-90 342
6 TraesCS7B01G056000 chr5B 84.729 1015 93 29 2488 3455 488827699 488828698 0.000000e+00 959
7 TraesCS7B01G056000 chr5B 77.119 354 72 8 1963 2310 65525371 65525021 2.720000e-46 196
8 TraesCS7B01G056000 chr7A 84.028 1008 110 31 2491 3455 39663130 39664129 0.000000e+00 922
9 TraesCS7B01G056000 chr7A 87.537 682 71 9 68 742 105619329 105620003 0.000000e+00 776
10 TraesCS7B01G056000 chr5D 86.124 872 75 25 2621 3455 529843799 529842937 0.000000e+00 898
11 TraesCS7B01G056000 chr5D 76.524 328 68 8 1963 2284 65009898 65010222 1.650000e-38 171
12 TraesCS7B01G056000 chr6D 78.397 1435 247 44 1003 2401 417775857 417777264 0.000000e+00 874
13 TraesCS7B01G056000 chr6D 78.378 1443 238 42 1005 2401 417752071 417750657 0.000000e+00 869
14 TraesCS7B01G056000 chr6D 81.928 747 86 27 2491 3198 308942759 308942023 1.380000e-163 586
15 TraesCS7B01G056000 chr6D 88.558 437 43 6 3023 3455 87489178 87488745 1.100000e-144 523
16 TraesCS7B01G056000 chr6D 82.162 555 68 23 2655 3198 426481267 426480733 6.800000e-122 448
17 TraesCS7B01G056000 chr6A 78.478 1445 233 47 1005 2401 560192872 560191458 0.000000e+00 874
18 TraesCS7B01G056000 chr1A 78.243 1457 246 46 1001 2426 533409286 533410702 0.000000e+00 869
19 TraesCS7B01G056000 chr1A 78.125 1440 255 39 997 2414 533323406 533324807 0.000000e+00 859
20 TraesCS7B01G056000 chr1A 83.201 1006 84 37 2493 3454 496124002 496124966 0.000000e+00 843
21 TraesCS7B01G056000 chr6B 82.742 1014 109 39 2488 3453 76198870 76199865 0.000000e+00 843
22 TraesCS7B01G056000 chr6B 80.086 934 149 16 1497 2401 626489170 626488245 0.000000e+00 660
23 TraesCS7B01G056000 chr1D 77.847 1449 255 47 997 2414 436112819 436114232 0.000000e+00 837
24 TraesCS7B01G056000 chr1D 78.214 1198 209 38 1247 2425 436120185 436121349 0.000000e+00 719
25 TraesCS7B01G056000 chr1D 83.533 753 74 22 2491 3198 329674005 329673258 0.000000e+00 658
26 TraesCS7B01G056000 chr1B 77.694 1466 257 45 1001 2425 590091037 590092473 0.000000e+00 832
27 TraesCS7B01G056000 chr1B 77.809 1442 250 47 997 2414 589976580 589977975 0.000000e+00 826
28 TraesCS7B01G056000 chr3B 82.881 958 119 32 2533 3453 813791172 813792121 0.000000e+00 819
29 TraesCS7B01G056000 chr2B 85.306 769 77 16 2714 3454 795590521 795589761 0.000000e+00 761
30 TraesCS7B01G056000 chr2B 81.568 727 88 27 2494 3198 697712339 697711637 3.010000e-155 558
31 TraesCS7B01G056000 chr3D 76.875 1440 260 48 998 2396 17698279 17699686 0.000000e+00 747
32 TraesCS7B01G056000 chr3D 84.532 737 74 24 2491 3198 481517098 481517823 0.000000e+00 693
33 TraesCS7B01G056000 chr3D 77.216 970 173 30 1001 1946 17343130 17342185 1.100000e-144 523
34 TraesCS7B01G056000 chr3D 81.026 585 65 28 2491 3052 385435302 385435863 1.150000e-114 424
35 TraesCS7B01G056000 chr4D 81.586 744 84 33 2487 3198 43674869 43674147 1.800000e-157 566


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 TraesCS7B01G056000 chr7B 59077731 59081185 3454 False 6381.000000 6381 100.000000 1 3455 1 chr7B.!!$F1 3454
1 TraesCS7B01G056000 chr7D 101778081 101781400 3319 True 1287.666667 2128 92.957333 851 3455 3 chr7D.!!$R1 2604
2 TraesCS7B01G056000 chr7D 37973635 37974363 728 False 601.000000 601 82.392000 2491 3198 1 chr7D.!!$F1 707
3 TraesCS7B01G056000 chr5B 488827699 488828698 999 False 959.000000 959 84.729000 2488 3455 1 chr5B.!!$F1 967
4 TraesCS7B01G056000 chr7A 39663130 39664129 999 False 922.000000 922 84.028000 2491 3455 1 chr7A.!!$F1 964
5 TraesCS7B01G056000 chr7A 105619329 105620003 674 False 776.000000 776 87.537000 68 742 1 chr7A.!!$F2 674
6 TraesCS7B01G056000 chr5D 529842937 529843799 862 True 898.000000 898 86.124000 2621 3455 1 chr5D.!!$R1 834
7 TraesCS7B01G056000 chr6D 417775857 417777264 1407 False 874.000000 874 78.397000 1003 2401 1 chr6D.!!$F1 1398
8 TraesCS7B01G056000 chr6D 417750657 417752071 1414 True 869.000000 869 78.378000 1005 2401 1 chr6D.!!$R3 1396
9 TraesCS7B01G056000 chr6D 308942023 308942759 736 True 586.000000 586 81.928000 2491 3198 1 chr6D.!!$R2 707
10 TraesCS7B01G056000 chr6D 426480733 426481267 534 True 448.000000 448 82.162000 2655 3198 1 chr6D.!!$R4 543
11 TraesCS7B01G056000 chr6A 560191458 560192872 1414 True 874.000000 874 78.478000 1005 2401 1 chr6A.!!$R1 1396
12 TraesCS7B01G056000 chr1A 533409286 533410702 1416 False 869.000000 869 78.243000 1001 2426 1 chr1A.!!$F3 1425
13 TraesCS7B01G056000 chr1A 533323406 533324807 1401 False 859.000000 859 78.125000 997 2414 1 chr1A.!!$F2 1417
14 TraesCS7B01G056000 chr1A 496124002 496124966 964 False 843.000000 843 83.201000 2493 3454 1 chr1A.!!$F1 961
15 TraesCS7B01G056000 chr6B 76198870 76199865 995 False 843.000000 843 82.742000 2488 3453 1 chr6B.!!$F1 965
16 TraesCS7B01G056000 chr6B 626488245 626489170 925 True 660.000000 660 80.086000 1497 2401 1 chr6B.!!$R1 904
17 TraesCS7B01G056000 chr1D 436112819 436114232 1413 False 837.000000 837 77.847000 997 2414 1 chr1D.!!$F1 1417
18 TraesCS7B01G056000 chr1D 436120185 436121349 1164 False 719.000000 719 78.214000 1247 2425 1 chr1D.!!$F2 1178
19 TraesCS7B01G056000 chr1D 329673258 329674005 747 True 658.000000 658 83.533000 2491 3198 1 chr1D.!!$R1 707
20 TraesCS7B01G056000 chr1B 590091037 590092473 1436 False 832.000000 832 77.694000 1001 2425 1 chr1B.!!$F2 1424
21 TraesCS7B01G056000 chr1B 589976580 589977975 1395 False 826.000000 826 77.809000 997 2414 1 chr1B.!!$F1 1417
22 TraesCS7B01G056000 chr3B 813791172 813792121 949 False 819.000000 819 82.881000 2533 3453 1 chr3B.!!$F1 920
23 TraesCS7B01G056000 chr2B 795589761 795590521 760 True 761.000000 761 85.306000 2714 3454 1 chr2B.!!$R2 740
24 TraesCS7B01G056000 chr2B 697711637 697712339 702 True 558.000000 558 81.568000 2494 3198 1 chr2B.!!$R1 704
25 TraesCS7B01G056000 chr3D 17698279 17699686 1407 False 747.000000 747 76.875000 998 2396 1 chr3D.!!$F1 1398
26 TraesCS7B01G056000 chr3D 481517098 481517823 725 False 693.000000 693 84.532000 2491 3198 1 chr3D.!!$F3 707
27 TraesCS7B01G056000 chr3D 17342185 17343130 945 True 523.000000 523 77.216000 1001 1946 1 chr3D.!!$R1 945
28 TraesCS7B01G056000 chr3D 385435302 385435863 561 False 424.000000 424 81.026000 2491 3052 1 chr3D.!!$F2 561
29 TraesCS7B01G056000 chr4D 43674147 43674869 722 True 566.000000 566 81.586000 2487 3198 1 chr4D.!!$R1 711

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
752 760 0.034059 ACTGAAGCGAAGTGGTGGAG 59.966 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 2801 0.451135 GTACGAGCAGCAAAAGCGTG 60.451 55.0 0.0 0.0 36.51 5.34 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
61 62 9.768215 TTTAGGGAAATAAATGTTCAGATTCCT 57.232 29.630 0.00 0.00 36.10 3.36
81 82 4.456222 TCCTATAGAAATCTTCCTCTCGCG 59.544 45.833 0.00 0.00 0.00 5.87
82 83 4.216687 CCTATAGAAATCTTCCTCTCGCGT 59.783 45.833 5.77 0.00 0.00 6.01
83 84 2.570442 AGAAATCTTCCTCTCGCGTC 57.430 50.000 5.77 0.00 0.00 5.19
113 114 3.634397 TTCCTGAAGTTCATGGGCTAG 57.366 47.619 5.91 0.00 0.00 3.42
146 147 2.425668 CCTTTCGTTGGTGTCCTTTTGT 59.574 45.455 0.00 0.00 0.00 2.83
148 149 4.096682 CCTTTCGTTGGTGTCCTTTTGTAA 59.903 41.667 0.00 0.00 0.00 2.41
154 155 5.910723 CGTTGGTGTCCTTTTGTAATTGTAC 59.089 40.000 0.00 0.00 0.00 2.90
162 163 9.053840 TGTCCTTTTGTAATTGTACGAATTACA 57.946 29.630 24.30 24.30 45.82 2.41
193 194 6.549912 AACGAAATTGTTACAGGTCCTTAC 57.450 37.500 0.00 0.00 0.00 2.34
195 196 4.092383 CGAAATTGTTACAGGTCCTTACGG 59.908 45.833 0.00 0.00 0.00 4.02
210 211 4.468007 CGGACCCGTTTCCTGTTT 57.532 55.556 0.00 0.00 32.88 2.83
211 212 3.610637 CGGACCCGTTTCCTGTTTA 57.389 52.632 0.00 0.00 32.88 2.01
224 225 7.921745 CCGTTTCCTGTTTAAAAACCTAAATGA 59.078 33.333 3.27 0.00 38.11 2.57
253 254 7.040494 CGATCAGATGTCATATTTCTAGCCAT 58.960 38.462 0.00 0.00 0.00 4.40
265 269 6.770286 ATTTCTAGCCATTCAATCCCTAGA 57.230 37.500 0.00 1.13 34.36 2.43
268 272 3.567478 AGCCATTCAATCCCTAGACAC 57.433 47.619 0.00 0.00 0.00 3.67
269 273 2.846206 AGCCATTCAATCCCTAGACACA 59.154 45.455 0.00 0.00 0.00 3.72
272 276 4.686944 GCCATTCAATCCCTAGACACATCA 60.687 45.833 0.00 0.00 0.00 3.07
279 283 1.974236 CCCTAGACACATCAGATCCCC 59.026 57.143 0.00 0.00 0.00 4.81
283 287 0.911769 GACACATCAGATCCCCCACA 59.088 55.000 0.00 0.00 0.00 4.17
299 303 3.382546 CCCCACAAGAATCCTAAAGCATG 59.617 47.826 0.00 0.00 0.00 4.06
343 347 1.993370 GAACAGCGAGCTAACGACATT 59.007 47.619 0.00 0.00 35.09 2.71
347 351 4.181578 ACAGCGAGCTAACGACATTAAAT 58.818 39.130 0.00 0.00 35.09 1.40
353 357 5.062934 CGAGCTAACGACATTAAATGGACAA 59.937 40.000 0.00 0.00 35.09 3.18
363 367 8.977505 CGACATTAAATGGACAATTTCTGTTTT 58.022 29.630 0.00 0.00 38.84 2.43
373 377 6.587608 GGACAATTTCTGTTTTTAGAGCATGG 59.412 38.462 0.00 0.00 38.84 3.66
381 385 9.691362 TTCTGTTTTTAGAGCATGGTAATTTTC 57.309 29.630 0.00 0.00 0.00 2.29
382 386 8.855110 TCTGTTTTTAGAGCATGGTAATTTTCA 58.145 29.630 0.00 0.00 0.00 2.69
384 388 7.870445 TGTTTTTAGAGCATGGTAATTTTCACC 59.130 33.333 0.00 0.00 36.54 4.02
385 389 7.775053 TTTTAGAGCATGGTAATTTTCACCT 57.225 32.000 0.00 0.00 36.96 4.00
417 421 8.070171 CGTTGATATAACATGTCAATTCCCTTC 58.930 37.037 0.00 0.00 41.40 3.46
419 423 9.473007 TTGATATAACATGTCAATTCCCTTCAA 57.527 29.630 0.00 0.00 35.80 2.69
421 425 9.125026 GATATAACATGTCAATTCCCTTCAAGT 57.875 33.333 0.00 0.00 0.00 3.16
428 432 4.096984 GTCAATTCCCTTCAAGTAGCATGG 59.903 45.833 0.00 0.00 0.00 3.66
432 436 2.025037 TCCCTTCAAGTAGCATGGCAAT 60.025 45.455 0.00 0.00 0.00 3.56
440 444 5.419788 TCAAGTAGCATGGCAATTTTCATCT 59.580 36.000 0.00 0.00 0.00 2.90
474 478 3.806380 AGGCTGTCAATTCTCTATGCTG 58.194 45.455 0.00 0.00 0.00 4.41
475 479 2.290093 GGCTGTCAATTCTCTATGCTGC 59.710 50.000 0.00 0.00 0.00 5.25
497 501 7.654520 GCTGCAATCATGGTAAATATGTGAAAT 59.345 33.333 0.00 0.00 0.00 2.17
498 502 9.537192 CTGCAATCATGGTAAATATGTGAAATT 57.463 29.630 0.00 0.00 0.00 1.82
518 525 6.615264 AATTACATGATTACTCTGCTGCAG 57.385 37.500 23.31 23.31 0.00 4.41
538 545 4.561606 GCAGCATGACAATTTTCAGACATC 59.438 41.667 0.00 0.00 39.69 3.06
540 547 6.387465 CAGCATGACAATTTTCAGACATCTT 58.613 36.000 0.00 0.00 39.69 2.40
546 553 9.683069 ATGACAATTTTCAGACATCTTTACAAC 57.317 29.630 0.23 0.00 0.00 3.32
553 560 7.800155 TTCAGACATCTTTACAACATGACAA 57.200 32.000 0.00 0.00 0.00 3.18
619 626 7.964011 TGAAAAATTTATCCGTTTCCGTATGAC 59.036 33.333 0.00 0.00 0.00 3.06
626 633 4.316645 TCCGTTTCCGTATGACAATTCAA 58.683 39.130 0.00 0.00 34.61 2.69
675 683 2.719739 ACAGCATGAATGACCTTCCTG 58.280 47.619 0.00 0.00 39.69 3.86
685 693 1.534235 ACCTTCCTGCGACCTGAGT 60.534 57.895 0.00 0.00 0.00 3.41
690 698 1.734477 CCTGCGACCTGAGTGAACG 60.734 63.158 0.00 0.00 0.00 3.95
691 699 1.007271 CTGCGACCTGAGTGAACGT 60.007 57.895 0.00 0.00 0.00 3.99
697 705 0.249489 ACCTGAGTGAACGTCAGTGC 60.249 55.000 0.00 0.00 39.98 4.40
704 712 3.179830 AGTGAACGTCAGTGCGATATTC 58.820 45.455 12.77 7.55 35.59 1.75
726 734 1.621814 GGTAAAAAGGAAACCCTGCCC 59.378 52.381 0.00 0.00 33.44 5.36
738 746 0.251916 CCCTGCCCGTATGAACTGAA 59.748 55.000 0.00 0.00 0.00 3.02
739 747 1.656652 CCTGCCCGTATGAACTGAAG 58.343 55.000 0.00 0.00 0.00 3.02
740 748 1.009829 CTGCCCGTATGAACTGAAGC 58.990 55.000 0.00 0.00 0.00 3.86
741 749 0.739462 TGCCCGTATGAACTGAAGCG 60.739 55.000 0.00 0.00 0.00 4.68
742 750 0.459585 GCCCGTATGAACTGAAGCGA 60.460 55.000 0.00 0.00 0.00 4.93
743 751 2.004583 CCCGTATGAACTGAAGCGAA 57.995 50.000 0.00 0.00 0.00 4.70
744 752 1.927174 CCCGTATGAACTGAAGCGAAG 59.073 52.381 0.00 0.00 0.00 3.79
745 753 2.607187 CCGTATGAACTGAAGCGAAGT 58.393 47.619 0.00 0.00 0.00 3.01
746 754 2.345641 CCGTATGAACTGAAGCGAAGTG 59.654 50.000 0.00 0.00 0.00 3.16
747 755 2.345641 CGTATGAACTGAAGCGAAGTGG 59.654 50.000 0.00 0.00 0.00 4.00
748 756 2.550830 ATGAACTGAAGCGAAGTGGT 57.449 45.000 0.00 0.00 0.00 4.16
749 757 1.581934 TGAACTGAAGCGAAGTGGTG 58.418 50.000 0.00 0.00 0.00 4.17
750 758 0.868406 GAACTGAAGCGAAGTGGTGG 59.132 55.000 0.00 0.00 0.00 4.61
751 759 0.468226 AACTGAAGCGAAGTGGTGGA 59.532 50.000 0.00 0.00 0.00 4.02
752 760 0.034059 ACTGAAGCGAAGTGGTGGAG 59.966 55.000 0.00 0.00 0.00 3.86
753 761 1.294659 CTGAAGCGAAGTGGTGGAGC 61.295 60.000 0.00 0.00 0.00 4.70
754 762 2.032681 AAGCGAAGTGGTGGAGCC 59.967 61.111 0.00 0.00 37.90 4.70
755 763 3.883744 AAGCGAAGTGGTGGAGCCG 62.884 63.158 0.00 0.00 41.21 5.52
756 764 4.681978 GCGAAGTGGTGGAGCCGT 62.682 66.667 0.00 0.00 41.21 5.68
757 765 2.432628 CGAAGTGGTGGAGCCGTC 60.433 66.667 0.00 0.00 41.21 4.79
758 766 2.932234 CGAAGTGGTGGAGCCGTCT 61.932 63.158 0.00 0.00 41.21 4.18
759 767 1.374758 GAAGTGGTGGAGCCGTCTG 60.375 63.158 0.00 0.00 41.21 3.51
760 768 2.100879 GAAGTGGTGGAGCCGTCTGT 62.101 60.000 0.00 0.00 41.21 3.41
761 769 2.357517 GTGGTGGAGCCGTCTGTG 60.358 66.667 0.00 0.00 41.21 3.66
762 770 4.314440 TGGTGGAGCCGTCTGTGC 62.314 66.667 0.00 0.00 41.21 4.57
770 778 3.966215 CCGTCTGTGCGGTGAAAT 58.034 55.556 0.00 0.00 46.11 2.17
771 779 1.497278 CCGTCTGTGCGGTGAAATG 59.503 57.895 0.00 0.00 46.11 2.32
772 780 0.948623 CCGTCTGTGCGGTGAAATGA 60.949 55.000 0.00 0.00 46.11 2.57
773 781 1.078709 CGTCTGTGCGGTGAAATGAT 58.921 50.000 0.00 0.00 0.00 2.45
774 782 1.464608 CGTCTGTGCGGTGAAATGATT 59.535 47.619 0.00 0.00 0.00 2.57
775 783 2.095768 CGTCTGTGCGGTGAAATGATTT 60.096 45.455 0.00 0.00 0.00 2.17
776 784 3.236816 GTCTGTGCGGTGAAATGATTTG 58.763 45.455 0.00 0.00 0.00 2.32
777 785 3.058293 GTCTGTGCGGTGAAATGATTTGA 60.058 43.478 0.00 0.00 0.00 2.69
778 786 3.567585 TCTGTGCGGTGAAATGATTTGAA 59.432 39.130 0.00 0.00 0.00 2.69
779 787 4.218200 TCTGTGCGGTGAAATGATTTGAAT 59.782 37.500 0.00 0.00 0.00 2.57
780 788 4.484236 TGTGCGGTGAAATGATTTGAATC 58.516 39.130 0.00 0.00 35.97 2.52
781 789 4.218200 TGTGCGGTGAAATGATTTGAATCT 59.782 37.500 0.00 0.00 36.39 2.40
782 790 4.560035 GTGCGGTGAAATGATTTGAATCTG 59.440 41.667 0.00 0.00 36.39 2.90
783 791 4.458642 TGCGGTGAAATGATTTGAATCTGA 59.541 37.500 0.00 0.00 36.39 3.27
784 792 4.795278 GCGGTGAAATGATTTGAATCTGAC 59.205 41.667 0.00 0.00 36.39 3.51
785 793 5.335127 CGGTGAAATGATTTGAATCTGACC 58.665 41.667 0.00 0.00 36.39 4.02
786 794 5.124457 CGGTGAAATGATTTGAATCTGACCT 59.876 40.000 0.00 0.00 36.39 3.85
787 795 6.349611 CGGTGAAATGATTTGAATCTGACCTT 60.350 38.462 0.00 0.00 36.39 3.50
788 796 7.031975 GGTGAAATGATTTGAATCTGACCTTC 58.968 38.462 0.00 2.71 36.39 3.46
789 797 7.309377 GGTGAAATGATTTGAATCTGACCTTCA 60.309 37.037 0.00 4.68 36.39 3.02
790 798 7.540055 GTGAAATGATTTGAATCTGACCTTCAC 59.460 37.037 0.00 10.87 36.39 3.18
791 799 6.521151 AATGATTTGAATCTGACCTTCACC 57.479 37.500 5.42 0.00 36.39 4.02
792 800 4.002982 TGATTTGAATCTGACCTTCACCG 58.997 43.478 5.42 0.00 36.39 4.94
793 801 2.472695 TTGAATCTGACCTTCACCGG 57.527 50.000 0.00 0.00 32.57 5.28
794 802 1.348064 TGAATCTGACCTTCACCGGT 58.652 50.000 0.00 0.00 40.80 5.28
795 803 1.001974 TGAATCTGACCTTCACCGGTG 59.998 52.381 29.26 29.26 37.42 4.94
796 804 0.324943 AATCTGACCTTCACCGGTGG 59.675 55.000 33.40 20.85 37.42 4.61
797 805 0.544357 ATCTGACCTTCACCGGTGGA 60.544 55.000 33.40 25.77 37.42 4.02
798 806 0.544357 TCTGACCTTCACCGGTGGAT 60.544 55.000 33.40 12.29 37.42 3.41
799 807 0.391661 CTGACCTTCACCGGTGGATG 60.392 60.000 33.40 24.63 37.42 3.51
800 808 1.078426 GACCTTCACCGGTGGATGG 60.078 63.158 33.40 29.93 37.42 3.51
801 809 1.537889 ACCTTCACCGGTGGATGGA 60.538 57.895 33.40 12.08 35.52 3.41
802 810 0.914417 ACCTTCACCGGTGGATGGAT 60.914 55.000 33.40 18.39 35.52 3.41
803 811 0.464373 CCTTCACCGGTGGATGGATG 60.464 60.000 33.40 13.35 32.77 3.51
804 812 1.077787 TTCACCGGTGGATGGATGC 60.078 57.895 33.40 0.00 0.00 3.91
805 813 1.561769 TTCACCGGTGGATGGATGCT 61.562 55.000 33.40 0.00 0.00 3.79
806 814 0.689412 TCACCGGTGGATGGATGCTA 60.689 55.000 33.40 8.03 0.00 3.49
807 815 0.397941 CACCGGTGGATGGATGCTAT 59.602 55.000 27.57 0.00 0.00 2.97
808 816 1.140312 ACCGGTGGATGGATGCTATT 58.860 50.000 6.12 0.00 0.00 1.73
809 817 1.072331 ACCGGTGGATGGATGCTATTC 59.928 52.381 6.12 0.00 0.00 1.75
810 818 1.072173 CCGGTGGATGGATGCTATTCA 59.928 52.381 0.00 0.00 0.00 2.57
811 819 2.420642 CGGTGGATGGATGCTATTCAG 58.579 52.381 0.00 0.00 0.00 3.02
812 820 2.224378 CGGTGGATGGATGCTATTCAGT 60.224 50.000 0.00 0.00 0.00 3.41
813 821 3.406764 GGTGGATGGATGCTATTCAGTC 58.593 50.000 0.00 0.00 0.00 3.51
814 822 3.181451 GGTGGATGGATGCTATTCAGTCA 60.181 47.826 0.00 0.00 0.00 3.41
815 823 3.812053 GTGGATGGATGCTATTCAGTCAC 59.188 47.826 0.00 0.00 0.00 3.67
816 824 3.455543 TGGATGGATGCTATTCAGTCACA 59.544 43.478 0.00 0.00 0.00 3.58
817 825 4.080413 TGGATGGATGCTATTCAGTCACAA 60.080 41.667 0.00 0.00 0.00 3.33
818 826 5.068636 GGATGGATGCTATTCAGTCACAAT 58.931 41.667 0.00 0.00 0.00 2.71
819 827 5.180868 GGATGGATGCTATTCAGTCACAATC 59.819 44.000 0.00 0.00 0.00 2.67
820 828 4.122046 TGGATGCTATTCAGTCACAATCG 58.878 43.478 0.00 0.00 0.00 3.34
821 829 3.496130 GGATGCTATTCAGTCACAATCGG 59.504 47.826 0.00 0.00 0.00 4.18
822 830 3.610040 TGCTATTCAGTCACAATCGGT 57.390 42.857 0.00 0.00 0.00 4.69
830 838 2.126888 CACAATCGGTGCCGTTGC 60.127 61.111 18.50 0.00 41.36 4.17
831 839 2.281484 ACAATCGGTGCCGTTGCT 60.281 55.556 18.50 8.96 40.74 3.91
832 840 2.325082 ACAATCGGTGCCGTTGCTC 61.325 57.895 18.50 0.00 40.74 4.26
833 841 2.034879 CAATCGGTGCCGTTGCTCT 61.035 57.895 10.60 0.00 40.74 4.09
834 842 1.741770 AATCGGTGCCGTTGCTCTC 60.742 57.895 10.60 0.00 40.74 3.20
835 843 2.172483 AATCGGTGCCGTTGCTCTCT 62.172 55.000 10.60 0.00 40.74 3.10
836 844 2.842394 ATCGGTGCCGTTGCTCTCTG 62.842 60.000 10.60 0.00 40.74 3.35
837 845 2.743928 GGTGCCGTTGCTCTCTGG 60.744 66.667 0.00 0.00 38.71 3.86
840 848 3.426568 GCCGTTGCTCTCTGGCAC 61.427 66.667 0.00 0.00 46.76 5.01
841 849 2.743928 CCGTTGCTCTCTGGCACC 60.744 66.667 0.00 0.00 42.27 5.01
842 850 2.031012 CGTTGCTCTCTGGCACCA 59.969 61.111 0.00 0.00 42.27 4.17
843 851 1.597854 CGTTGCTCTCTGGCACCAA 60.598 57.895 0.00 0.00 42.27 3.67
844 852 1.165907 CGTTGCTCTCTGGCACCAAA 61.166 55.000 0.00 0.00 42.27 3.28
845 853 0.595095 GTTGCTCTCTGGCACCAAAG 59.405 55.000 0.00 0.00 42.27 2.77
846 854 0.473755 TTGCTCTCTGGCACCAAAGA 59.526 50.000 0.00 0.00 42.27 2.52
847 855 0.473755 TGCTCTCTGGCACCAAAGAA 59.526 50.000 0.00 0.00 37.29 2.52
848 856 1.074405 TGCTCTCTGGCACCAAAGAAT 59.926 47.619 0.00 0.00 37.29 2.40
849 857 2.165998 GCTCTCTGGCACCAAAGAATT 58.834 47.619 0.00 0.00 0.00 2.17
850 858 2.094854 GCTCTCTGGCACCAAAGAATTG 60.095 50.000 0.00 0.00 36.25 2.32
878 886 2.556287 CTCCGCACCGAACTTTGC 59.444 61.111 0.00 0.00 35.26 3.68
919 927 0.250124 TGTCGACCACGGCTTCAAAT 60.250 50.000 14.12 0.00 44.93 2.32
941 952 4.840005 GCTAGGCTCCGGTGGTGC 62.840 72.222 0.00 1.94 40.94 5.01
967 989 0.618458 TGGTGAGGCATCAGTAACCC 59.382 55.000 0.00 0.00 35.66 4.11
999 1025 1.303806 TCGGTGTCCACGATCTCCA 60.304 57.895 0.00 0.00 35.12 3.86
1300 1371 3.753434 ACGACCTGCTCTGCTCCG 61.753 66.667 0.00 0.00 0.00 4.63
1335 1427 0.656259 CCGTGATCTTCGACTCGCTA 59.344 55.000 11.24 0.00 0.00 4.26
1391 1534 0.184451 ATCCCCGCCTACGTCTTCTA 59.816 55.000 0.00 0.00 37.70 2.10
1392 1535 0.184451 TCCCCGCCTACGTCTTCTAT 59.816 55.000 0.00 0.00 37.70 1.98
1393 1536 1.421268 TCCCCGCCTACGTCTTCTATA 59.579 52.381 0.00 0.00 37.70 1.31
1394 1537 1.538950 CCCCGCCTACGTCTTCTATAC 59.461 57.143 0.00 0.00 37.70 1.47
1395 1538 1.538950 CCCGCCTACGTCTTCTATACC 59.461 57.143 0.00 0.00 37.70 2.73
1396 1539 2.502295 CCGCCTACGTCTTCTATACCT 58.498 52.381 0.00 0.00 37.70 3.08
1397 1540 2.483491 CCGCCTACGTCTTCTATACCTC 59.517 54.545 0.00 0.00 37.70 3.85
1398 1541 2.483491 CGCCTACGTCTTCTATACCTCC 59.517 54.545 0.00 0.00 33.53 4.30
1399 1542 3.753815 GCCTACGTCTTCTATACCTCCT 58.246 50.000 0.00 0.00 0.00 3.69
1400 1543 3.502979 GCCTACGTCTTCTATACCTCCTG 59.497 52.174 0.00 0.00 0.00 3.86
1401 1544 3.502979 CCTACGTCTTCTATACCTCCTGC 59.497 52.174 0.00 0.00 0.00 4.85
1402 1545 1.948145 ACGTCTTCTATACCTCCTGCG 59.052 52.381 0.00 0.00 0.00 5.18
1403 1546 1.335142 CGTCTTCTATACCTCCTGCGC 60.335 57.143 0.00 0.00 0.00 6.09
1404 1547 0.952280 TCTTCTATACCTCCTGCGCG 59.048 55.000 0.00 0.00 0.00 6.86
1405 1548 0.669077 CTTCTATACCTCCTGCGCGT 59.331 55.000 8.43 0.00 0.00 6.01
1406 1549 0.666913 TTCTATACCTCCTGCGCGTC 59.333 55.000 8.43 0.00 0.00 5.19
1407 1550 1.170919 TCTATACCTCCTGCGCGTCC 61.171 60.000 8.43 0.00 0.00 4.79
1408 1551 1.452953 CTATACCTCCTGCGCGTCCA 61.453 60.000 8.43 0.00 0.00 4.02
1409 1552 1.731433 TATACCTCCTGCGCGTCCAC 61.731 60.000 8.43 0.00 0.00 4.02
1421 1564 3.462678 GTCCACCCTCCTCGCCTC 61.463 72.222 0.00 0.00 0.00 4.70
1422 1565 4.779733 TCCACCCTCCTCGCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
1480 1623 1.553704 GTCGGAAAGGCTTTAGGGAGA 59.446 52.381 13.37 5.47 0.00 3.71
1488 1631 4.776059 AGGCTTTAGGGAGATAGGAGAT 57.224 45.455 0.00 0.00 0.00 2.75
1494 1637 1.649100 AGGGAGATAGGAGATAGCCCC 59.351 57.143 0.00 0.00 34.62 5.80
1742 1897 2.107953 GCCTCTCATCGGGAGCAC 59.892 66.667 0.75 0.00 43.70 4.40
1743 1898 2.415010 CCTCTCATCGGGAGCACG 59.585 66.667 0.75 0.00 43.70 5.34
1829 1987 2.089349 GCGTCGTGTTCCTCTGCTC 61.089 63.158 0.00 0.00 0.00 4.26
1844 2002 2.415010 CTCCGGGAGCATGACGAG 59.585 66.667 11.83 0.00 0.00 4.18
2133 2336 3.737172 GGCGTGCCGATGCTTTGT 61.737 61.111 0.00 0.00 38.71 2.83
2208 2411 2.509336 GTCGCCGTGGAGATGGTG 60.509 66.667 0.00 0.00 39.80 4.17
2272 2475 4.649692 CAAGGTAAGGATGATCATGGAGG 58.350 47.826 14.30 0.00 0.00 4.30
2320 2523 4.335584 CGGCGGCGCAAAAGGAAA 62.336 61.111 34.36 0.00 0.00 3.13
2485 2691 2.189521 GGATGCGGTTCCGGTGAT 59.810 61.111 13.16 0.00 0.00 3.06
2578 2786 6.384258 TTGTGCTTTAAGATTTGTGCAGTA 57.616 33.333 0.00 0.00 0.00 2.74
2618 2840 0.606096 TTTGCTGCTCGTACTAGGCA 59.394 50.000 0.00 0.92 34.66 4.75
2619 2841 0.824109 TTGCTGCTCGTACTAGGCAT 59.176 50.000 0.00 0.00 35.37 4.40
2622 2844 1.880675 GCTGCTCGTACTAGGCATCTA 59.119 52.381 0.00 0.00 35.37 1.98
2787 3069 7.276878 CGGATGTTGAGTGTGTGTAAATGTATA 59.723 37.037 0.00 0.00 0.00 1.47
3052 4095 7.502561 AGACCCCTAAAGTTGCATTGTTATATC 59.497 37.037 0.00 0.00 0.00 1.63
3062 4105 6.480524 TGCATTGTTATATCTGTATTCGCC 57.519 37.500 0.00 0.00 0.00 5.54
3277 4329 9.740239 AAATTGCACTGTATATGCTTATTTCTG 57.260 29.630 0.00 0.36 43.77 3.02
3280 4333 6.318396 TGCACTGTATATGCTTATTTCTGCAA 59.682 34.615 0.00 0.00 43.77 4.08
3293 4348 8.764287 GCTTATTTCTGCAAATTACAAAAGTGT 58.236 29.630 0.00 0.00 36.35 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.768215 AGGAATCTGAACATTTATTTCCCTAAA 57.232 29.630 0.00 0.00 0.00 1.85
49 50 9.218525 AGGAAGATTTCTATAGGAATCTGAACA 57.781 33.333 29.34 0.00 33.53 3.18
50 51 9.705290 GAGGAAGATTTCTATAGGAATCTGAAC 57.295 37.037 29.34 22.50 33.53 3.18
51 52 9.667607 AGAGGAAGATTTCTATAGGAATCTGAA 57.332 33.333 29.34 1.10 33.53 3.02
52 53 9.308000 GAGAGGAAGATTTCTATAGGAATCTGA 57.692 37.037 29.34 0.00 33.53 3.27
53 54 8.243426 CGAGAGGAAGATTTCTATAGGAATCTG 58.757 40.741 29.34 15.54 33.53 2.90
54 55 7.093945 GCGAGAGGAAGATTTCTATAGGAATCT 60.094 40.741 25.10 25.10 33.53 2.40
55 56 7.033185 GCGAGAGGAAGATTTCTATAGGAATC 58.967 42.308 21.85 21.85 33.53 2.52
56 57 6.349777 CGCGAGAGGAAGATTTCTATAGGAAT 60.350 42.308 5.92 5.92 33.53 3.01
57 58 5.048643 CGCGAGAGGAAGATTTCTATAGGAA 60.049 44.000 0.00 0.00 0.00 3.36
58 59 4.456222 CGCGAGAGGAAGATTTCTATAGGA 59.544 45.833 0.00 0.00 0.00 2.94
59 60 4.216687 ACGCGAGAGGAAGATTTCTATAGG 59.783 45.833 15.93 0.00 0.00 2.57
60 61 5.365403 ACGCGAGAGGAAGATTTCTATAG 57.635 43.478 15.93 0.00 0.00 1.31
61 62 4.215827 GGACGCGAGAGGAAGATTTCTATA 59.784 45.833 15.93 0.00 0.00 1.31
62 63 3.004944 GGACGCGAGAGGAAGATTTCTAT 59.995 47.826 15.93 0.00 0.00 1.98
63 64 2.358267 GGACGCGAGAGGAAGATTTCTA 59.642 50.000 15.93 0.00 0.00 2.10
64 65 1.135333 GGACGCGAGAGGAAGATTTCT 59.865 52.381 15.93 0.00 0.00 2.52
65 66 1.135083 TGGACGCGAGAGGAAGATTTC 60.135 52.381 15.93 0.00 0.00 2.17
66 67 0.895530 TGGACGCGAGAGGAAGATTT 59.104 50.000 15.93 0.00 0.00 2.17
92 93 2.978156 AGCCCATGAACTTCAGGAAA 57.022 45.000 4.98 0.00 27.97 3.13
93 94 2.239654 CCTAGCCCATGAACTTCAGGAA 59.760 50.000 4.98 0.00 27.97 3.36
98 99 3.073274 ACAACCTAGCCCATGAACTTC 57.927 47.619 0.00 0.00 0.00 3.01
113 114 3.738791 CCAACGAAAGGCAAATTACAACC 59.261 43.478 0.00 0.00 0.00 3.77
154 155 8.687301 ACAATTTCGTTAAGCTTTTGTAATTCG 58.313 29.630 3.20 0.00 0.00 3.34
162 163 7.485810 ACCTGTAACAATTTCGTTAAGCTTTT 58.514 30.769 3.20 0.00 33.31 2.27
193 194 1.881591 TTAAACAGGAAACGGGTCCG 58.118 50.000 7.97 7.97 43.03 4.79
195 196 4.098349 AGGTTTTTAAACAGGAAACGGGTC 59.902 41.667 7.57 0.00 40.63 4.46
224 225 9.579768 GCTAGAAATATGACATCTGATCGTTAT 57.420 33.333 0.00 0.00 0.00 1.89
228 229 6.393171 TGGCTAGAAATATGACATCTGATCG 58.607 40.000 0.00 0.00 0.00 3.69
233 234 9.228949 GATTGAATGGCTAGAAATATGACATCT 57.771 33.333 0.00 0.00 0.00 2.90
234 235 8.457261 GGATTGAATGGCTAGAAATATGACATC 58.543 37.037 0.00 0.00 0.00 3.06
246 247 4.101585 TGTGTCTAGGGATTGAATGGCTAG 59.898 45.833 0.00 0.00 0.00 3.42
253 254 5.070981 GGATCTGATGTGTCTAGGGATTGAA 59.929 44.000 0.00 0.00 0.00 2.69
265 269 1.283029 CTTGTGGGGGATCTGATGTGT 59.717 52.381 0.00 0.00 0.00 3.72
268 272 3.484407 GATTCTTGTGGGGGATCTGATG 58.516 50.000 0.00 0.00 0.00 3.07
269 273 2.444766 GGATTCTTGTGGGGGATCTGAT 59.555 50.000 0.00 0.00 0.00 2.90
272 276 2.293598 AGGATTCTTGTGGGGGATCT 57.706 50.000 0.00 0.00 0.00 2.75
279 283 3.488047 CGCATGCTTTAGGATTCTTGTGG 60.488 47.826 17.13 0.00 0.00 4.17
304 308 2.171635 GCTTAGAGGCGTTTGTGGG 58.828 57.895 0.00 0.00 0.00 4.61
316 320 1.092348 TAGCTCGCTGTTCGCTTAGA 58.908 50.000 0.85 0.00 38.27 2.10
330 334 6.417191 TTGTCCATTTAATGTCGTTAGCTC 57.583 37.500 4.15 0.00 0.00 4.09
335 339 7.657336 ACAGAAATTGTCCATTTAATGTCGTT 58.343 30.769 4.15 0.00 35.02 3.85
343 347 9.691362 GCTCTAAAAACAGAAATTGTCCATTTA 57.309 29.630 0.00 0.00 39.73 1.40
347 351 6.707440 TGCTCTAAAAACAGAAATTGTCCA 57.293 33.333 0.00 0.00 39.73 4.02
363 367 7.775053 AAAGGTGAAAATTACCATGCTCTAA 57.225 32.000 0.00 0.00 40.74 2.10
373 377 7.940178 ATCAACGGAAAAAGGTGAAAATTAC 57.060 32.000 0.00 0.00 38.95 1.89
380 384 7.392113 ACATGTTATATCAACGGAAAAAGGTGA 59.608 33.333 0.00 0.00 39.89 4.02
381 385 7.535139 ACATGTTATATCAACGGAAAAAGGTG 58.465 34.615 0.00 0.00 0.00 4.00
382 386 7.392113 TGACATGTTATATCAACGGAAAAAGGT 59.608 33.333 0.00 0.00 0.00 3.50
384 388 9.787532 ATTGACATGTTATATCAACGGAAAAAG 57.212 29.630 0.00 0.00 35.28 2.27
401 405 4.702131 GCTACTTGAAGGGAATTGACATGT 59.298 41.667 0.00 0.00 0.00 3.21
417 421 5.657474 AGATGAAAATTGCCATGCTACTTG 58.343 37.500 0.00 0.00 0.00 3.16
419 423 5.927281 AAGATGAAAATTGCCATGCTACT 57.073 34.783 0.00 0.00 0.00 2.57
421 425 6.594937 GGAAAAAGATGAAAATTGCCATGCTA 59.405 34.615 0.00 0.00 0.00 3.49
497 501 3.873361 GCTGCAGCAGAGTAATCATGTAA 59.127 43.478 33.36 0.00 41.59 2.41
498 502 3.461061 GCTGCAGCAGAGTAATCATGTA 58.539 45.455 33.36 0.00 41.59 2.29
512 519 2.666508 CTGAAAATTGTCATGCTGCAGC 59.333 45.455 31.89 31.89 42.50 5.25
518 525 7.809331 TGTAAAGATGTCTGAAAATTGTCATGC 59.191 33.333 0.00 0.00 0.00 4.06
531 538 9.467258 AAAATTGTCATGTTGTAAAGATGTCTG 57.533 29.630 0.00 0.00 46.63 3.51
611 618 5.227805 CGAATGCTTTTGAATTGTCATACGG 59.772 40.000 0.00 0.00 32.48 4.02
614 621 6.585702 CCAACGAATGCTTTTGAATTGTCATA 59.414 34.615 6.58 0.00 32.48 2.15
619 626 4.305769 TCCCAACGAATGCTTTTGAATTG 58.694 39.130 6.58 2.19 0.00 2.32
626 633 2.270352 TCACTCCCAACGAATGCTTT 57.730 45.000 0.00 0.00 0.00 3.51
663 671 0.036010 CAGGTCGCAGGAAGGTCATT 60.036 55.000 0.00 0.00 0.00 2.57
675 683 1.004277 CTGACGTTCACTCAGGTCGC 61.004 60.000 0.00 0.00 34.83 5.19
676 684 0.311165 ACTGACGTTCACTCAGGTCG 59.689 55.000 6.21 0.00 39.69 4.79
685 693 2.182014 CGAATATCGCACTGACGTTCA 58.818 47.619 0.00 0.00 31.14 3.18
690 698 2.787601 TACCCGAATATCGCACTGAC 57.212 50.000 0.00 0.00 38.82 3.51
691 699 3.804786 TTTACCCGAATATCGCACTGA 57.195 42.857 0.00 0.00 38.82 3.41
697 705 5.220912 GGGTTTCCTTTTTACCCGAATATCG 60.221 44.000 0.00 0.00 41.93 2.92
722 730 0.739462 CGCTTCAGTTCATACGGGCA 60.739 55.000 0.00 0.00 0.00 5.36
726 734 2.345641 CCACTTCGCTTCAGTTCATACG 59.654 50.000 0.00 0.00 0.00 3.06
738 746 4.379243 CGGCTCCACCACTTCGCT 62.379 66.667 0.00 0.00 39.03 4.93
739 747 4.681978 ACGGCTCCACCACTTCGC 62.682 66.667 0.00 0.00 39.03 4.70
740 748 2.432628 GACGGCTCCACCACTTCG 60.433 66.667 0.00 0.00 39.03 3.79
741 749 1.374758 CAGACGGCTCCACCACTTC 60.375 63.158 0.00 0.00 39.03 3.01
742 750 2.140792 ACAGACGGCTCCACCACTT 61.141 57.895 0.00 0.00 39.03 3.16
743 751 2.524394 ACAGACGGCTCCACCACT 60.524 61.111 0.00 0.00 39.03 4.00
744 752 2.357517 CACAGACGGCTCCACCAC 60.358 66.667 0.00 0.00 39.03 4.16
745 753 4.314440 GCACAGACGGCTCCACCA 62.314 66.667 0.00 0.00 39.03 4.17
754 762 1.078709 ATCATTTCACCGCACAGACG 58.921 50.000 0.00 0.00 0.00 4.18
755 763 3.058293 TCAAATCATTTCACCGCACAGAC 60.058 43.478 0.00 0.00 0.00 3.51
756 764 3.145286 TCAAATCATTTCACCGCACAGA 58.855 40.909 0.00 0.00 0.00 3.41
757 765 3.557577 TCAAATCATTTCACCGCACAG 57.442 42.857 0.00 0.00 0.00 3.66
758 766 3.998099 TTCAAATCATTTCACCGCACA 57.002 38.095 0.00 0.00 0.00 4.57
759 767 4.560035 CAGATTCAAATCATTTCACCGCAC 59.440 41.667 5.59 0.00 37.89 5.34
760 768 4.458642 TCAGATTCAAATCATTTCACCGCA 59.541 37.500 5.59 0.00 37.89 5.69
761 769 4.795278 GTCAGATTCAAATCATTTCACCGC 59.205 41.667 5.59 0.00 37.89 5.68
762 770 5.124457 AGGTCAGATTCAAATCATTTCACCG 59.876 40.000 5.59 0.00 37.89 4.94
763 771 6.521151 AGGTCAGATTCAAATCATTTCACC 57.479 37.500 5.59 3.87 37.89 4.02
764 772 7.540055 GTGAAGGTCAGATTCAAATCATTTCAC 59.460 37.037 5.59 11.34 38.34 3.18
765 773 7.309377 GGTGAAGGTCAGATTCAAATCATTTCA 60.309 37.037 5.59 5.02 38.34 2.69
766 774 7.031975 GGTGAAGGTCAGATTCAAATCATTTC 58.968 38.462 5.59 3.00 38.34 2.17
767 775 6.349611 CGGTGAAGGTCAGATTCAAATCATTT 60.350 38.462 5.59 0.00 38.34 2.32
768 776 5.124457 CGGTGAAGGTCAGATTCAAATCATT 59.876 40.000 5.59 0.00 38.34 2.57
769 777 4.637534 CGGTGAAGGTCAGATTCAAATCAT 59.362 41.667 5.59 0.00 38.34 2.45
770 778 4.002982 CGGTGAAGGTCAGATTCAAATCA 58.997 43.478 5.59 0.00 38.34 2.57
771 779 3.375299 CCGGTGAAGGTCAGATTCAAATC 59.625 47.826 0.00 0.00 38.34 2.17
772 780 3.244911 ACCGGTGAAGGTCAGATTCAAAT 60.245 43.478 6.12 0.00 41.46 2.32
773 781 2.105821 ACCGGTGAAGGTCAGATTCAAA 59.894 45.455 6.12 0.00 41.46 2.69
774 782 1.697432 ACCGGTGAAGGTCAGATTCAA 59.303 47.619 6.12 0.00 41.46 2.69
775 783 1.001974 CACCGGTGAAGGTCAGATTCA 59.998 52.381 31.31 0.00 43.89 2.57
776 784 1.676014 CCACCGGTGAAGGTCAGATTC 60.676 57.143 36.07 0.00 43.89 2.52
777 785 0.324943 CCACCGGTGAAGGTCAGATT 59.675 55.000 36.07 0.00 43.89 2.40
778 786 0.544357 TCCACCGGTGAAGGTCAGAT 60.544 55.000 36.07 0.00 43.89 2.90
779 787 0.544357 ATCCACCGGTGAAGGTCAGA 60.544 55.000 36.07 21.73 43.89 3.27
780 788 0.391661 CATCCACCGGTGAAGGTCAG 60.392 60.000 36.07 16.95 43.89 3.51
781 789 1.676968 CATCCACCGGTGAAGGTCA 59.323 57.895 36.07 12.00 43.89 4.02
782 790 1.078426 CCATCCACCGGTGAAGGTC 60.078 63.158 36.07 0.00 43.89 3.85
784 792 0.464373 CATCCATCCACCGGTGAAGG 60.464 60.000 36.07 29.56 37.30 3.46
785 793 1.097547 GCATCCATCCACCGGTGAAG 61.098 60.000 36.07 22.61 0.00 3.02
786 794 1.077787 GCATCCATCCACCGGTGAA 60.078 57.895 36.07 18.54 0.00 3.18
787 795 0.689412 TAGCATCCATCCACCGGTGA 60.689 55.000 36.07 21.38 0.00 4.02
788 796 0.397941 ATAGCATCCATCCACCGGTG 59.602 55.000 28.26 28.26 0.00 4.94
789 797 1.072331 GAATAGCATCCATCCACCGGT 59.928 52.381 0.00 0.00 0.00 5.28
790 798 1.072173 TGAATAGCATCCATCCACCGG 59.928 52.381 0.00 0.00 0.00 5.28
791 799 2.224378 ACTGAATAGCATCCATCCACCG 60.224 50.000 0.00 0.00 0.00 4.94
792 800 3.181451 TGACTGAATAGCATCCATCCACC 60.181 47.826 0.00 0.00 0.00 4.61
793 801 3.812053 GTGACTGAATAGCATCCATCCAC 59.188 47.826 0.00 0.00 0.00 4.02
794 802 3.455543 TGTGACTGAATAGCATCCATCCA 59.544 43.478 0.00 0.00 0.00 3.41
795 803 4.077300 TGTGACTGAATAGCATCCATCC 57.923 45.455 0.00 0.00 0.00 3.51
796 804 5.107182 CGATTGTGACTGAATAGCATCCATC 60.107 44.000 0.00 0.00 0.00 3.51
797 805 4.753610 CGATTGTGACTGAATAGCATCCAT 59.246 41.667 0.00 0.00 0.00 3.41
798 806 4.122046 CGATTGTGACTGAATAGCATCCA 58.878 43.478 0.00 0.00 0.00 3.41
799 807 3.496130 CCGATTGTGACTGAATAGCATCC 59.504 47.826 0.00 0.00 0.00 3.51
800 808 4.122776 ACCGATTGTGACTGAATAGCATC 58.877 43.478 0.00 0.00 0.00 3.91
801 809 4.142609 ACCGATTGTGACTGAATAGCAT 57.857 40.909 0.00 0.00 0.00 3.79
802 810 3.610040 ACCGATTGTGACTGAATAGCA 57.390 42.857 0.00 0.00 0.00 3.49
814 822 2.281484 AGCAACGGCACCGATTGT 60.281 55.556 17.40 5.23 44.61 2.71
815 823 1.970917 GAGAGCAACGGCACCGATTG 61.971 60.000 17.40 16.18 44.61 2.67
816 824 1.741770 GAGAGCAACGGCACCGATT 60.742 57.895 17.40 3.61 44.61 3.34
817 825 2.125512 GAGAGCAACGGCACCGAT 60.126 61.111 17.40 0.00 44.61 4.18
818 826 3.303135 AGAGAGCAACGGCACCGA 61.303 61.111 17.40 0.00 44.61 4.69
819 827 3.114616 CAGAGAGCAACGGCACCG 61.115 66.667 7.71 7.71 44.61 4.94
820 828 2.743928 CCAGAGAGCAACGGCACC 60.744 66.667 0.00 0.00 44.61 5.01
821 829 3.426568 GCCAGAGAGCAACGGCAC 61.427 66.667 0.00 0.00 44.25 5.01
823 831 3.426568 GTGCCAGAGAGCAACGGC 61.427 66.667 0.00 0.00 46.19 5.68
824 832 2.743928 GGTGCCAGAGAGCAACGG 60.744 66.667 0.00 0.00 46.19 4.44
827 835 0.473755 TCTTTGGTGCCAGAGAGCAA 59.526 50.000 7.30 0.00 46.19 3.91
828 836 0.473755 TTCTTTGGTGCCAGAGAGCA 59.526 50.000 10.69 0.00 38.21 4.26
829 837 1.831580 ATTCTTTGGTGCCAGAGAGC 58.168 50.000 10.69 0.00 38.21 4.09
830 838 2.490903 CCAATTCTTTGGTGCCAGAGAG 59.509 50.000 10.69 1.78 46.27 3.20
831 839 2.517959 CCAATTCTTTGGTGCCAGAGA 58.482 47.619 7.30 7.30 46.27 3.10
841 849 3.082725 AGGTGGTGCCTCCAATTCTTTG 61.083 50.000 11.38 0.00 46.96 2.77
842 850 1.147817 AGGTGGTGCCTCCAATTCTTT 59.852 47.619 11.38 0.00 46.96 2.52
843 851 0.779997 AGGTGGTGCCTCCAATTCTT 59.220 50.000 11.38 0.00 46.96 2.52
844 852 2.479562 AGGTGGTGCCTCCAATTCT 58.520 52.632 11.38 0.00 46.96 2.40
855 863 4.308458 TTCGGTGCGGAGGTGGTG 62.308 66.667 0.00 0.00 0.00 4.17
856 864 4.309950 GTTCGGTGCGGAGGTGGT 62.310 66.667 0.00 0.00 0.00 4.16
857 865 3.530910 AAGTTCGGTGCGGAGGTGG 62.531 63.158 0.00 0.00 0.00 4.61
858 866 1.597027 AAAGTTCGGTGCGGAGGTG 60.597 57.895 0.00 0.00 0.00 4.00
862 870 0.947180 GTAGCAAAGTTCGGTGCGGA 60.947 55.000 0.00 0.00 45.62 5.54
905 913 1.241315 CGGGAATTTGAAGCCGTGGT 61.241 55.000 0.00 0.00 0.00 4.16
908 916 0.035820 TAGCGGGAATTTGAAGCCGT 60.036 50.000 0.00 0.00 0.00 5.68
919 927 4.772231 ACCGGAGCCTAGCGGGAA 62.772 66.667 9.46 0.00 37.23 3.97
944 955 4.220413 CTGATGCCTCACCAGCAG 57.780 61.111 0.00 0.00 44.90 4.24
999 1025 2.169352 CAGGACGATGGTCTTCTCCATT 59.831 50.000 7.84 0.00 46.72 3.16
1278 1349 2.125753 CAGAGCAGGTCGTGGAGC 60.126 66.667 0.00 0.00 0.00 4.70
1371 1469 0.184451 AGAAGACGTAGGCGGGGATA 59.816 55.000 0.00 0.00 43.45 2.59
1385 1528 0.952280 CGCGCAGGAGGTATAGAAGA 59.048 55.000 8.75 0.00 0.00 2.87
1391 1534 2.758327 TGGACGCGCAGGAGGTAT 60.758 61.111 5.73 0.00 0.00 2.73
1392 1535 3.755628 GTGGACGCGCAGGAGGTA 61.756 66.667 5.73 0.00 0.00 3.08
1404 1547 3.462678 GAGGCGAGGAGGGTGGAC 61.463 72.222 0.00 0.00 0.00 4.02
1405 1548 4.779733 GGAGGCGAGGAGGGTGGA 62.780 72.222 0.00 0.00 0.00 4.02
1406 1549 2.946988 TATGGAGGCGAGGAGGGTGG 62.947 65.000 0.00 0.00 0.00 4.61
1407 1550 1.457643 TATGGAGGCGAGGAGGGTG 60.458 63.158 0.00 0.00 0.00 4.61
1408 1551 1.457831 GTATGGAGGCGAGGAGGGT 60.458 63.158 0.00 0.00 0.00 4.34
1409 1552 1.457643 TGTATGGAGGCGAGGAGGG 60.458 63.158 0.00 0.00 0.00 4.30
1410 1553 2.045280 CTGTATGGAGGCGAGGAGG 58.955 63.158 0.00 0.00 0.00 4.30
1411 1554 1.112315 AGCTGTATGGAGGCGAGGAG 61.112 60.000 0.00 0.00 0.00 3.69
1412 1555 0.687757 AAGCTGTATGGAGGCGAGGA 60.688 55.000 0.00 0.00 0.00 3.71
1413 1556 0.249657 GAAGCTGTATGGAGGCGAGG 60.250 60.000 0.00 0.00 0.00 4.63
1414 1557 0.461548 TGAAGCTGTATGGAGGCGAG 59.538 55.000 0.00 0.00 0.00 5.03
1415 1558 0.175760 GTGAAGCTGTATGGAGGCGA 59.824 55.000 0.00 0.00 0.00 5.54
1416 1559 0.176680 AGTGAAGCTGTATGGAGGCG 59.823 55.000 0.00 0.00 0.00 5.52
1417 1560 1.474143 GGAGTGAAGCTGTATGGAGGC 60.474 57.143 0.00 0.00 0.00 4.70
1418 1561 1.202463 CGGAGTGAAGCTGTATGGAGG 60.202 57.143 0.00 0.00 0.00 4.30
1419 1562 1.478510 ACGGAGTGAAGCTGTATGGAG 59.521 52.381 0.00 0.00 42.51 3.86
1420 1563 1.557099 ACGGAGTGAAGCTGTATGGA 58.443 50.000 0.00 0.00 42.51 3.41
1461 1604 1.946984 TCTCCCTAAAGCCTTTCCGA 58.053 50.000 0.00 0.00 0.00 4.55
1473 1616 2.860041 GGGGCTATCTCCTATCTCCCTA 59.140 54.545 0.00 0.00 32.98 3.53
1480 1623 0.697079 TCGACGGGGCTATCTCCTAT 59.303 55.000 0.00 0.00 0.00 2.57
1488 1631 2.187073 GAAGAACTCGACGGGGCTA 58.813 57.895 0.00 0.00 0.00 3.93
1829 1987 3.842923 AGCTCGTCATGCTCCCGG 61.843 66.667 0.00 0.00 35.67 5.73
2133 2336 1.092921 GTTCCGCATACATCGGCCAA 61.093 55.000 2.24 0.00 46.05 4.52
2272 2475 3.011517 TTCCCTGCCCTCCTCAGC 61.012 66.667 0.00 0.00 0.00 4.26
2313 2516 2.594592 ACAGCGGCGCTTTCCTTT 60.595 55.556 34.51 6.71 36.40 3.11
2470 2676 2.202878 CGATCACCGGAACCGCAT 60.203 61.111 9.46 0.00 38.24 4.73
2481 2687 3.232213 TCAGCTAAAGTGGTCGATCAC 57.768 47.619 21.37 21.37 37.89 3.06
2482 2688 4.471904 AATCAGCTAAAGTGGTCGATCA 57.528 40.909 0.00 0.00 0.00 2.92
2483 2689 4.870426 TGAAATCAGCTAAAGTGGTCGATC 59.130 41.667 0.00 0.00 0.00 3.69
2484 2690 4.832248 TGAAATCAGCTAAAGTGGTCGAT 58.168 39.130 0.00 0.00 0.00 3.59
2485 2691 4.245660 CTGAAATCAGCTAAAGTGGTCGA 58.754 43.478 0.00 0.00 37.15 4.20
2590 2798 3.198236 GAGCAGCAAAAGCGTGGCA 62.198 57.895 0.00 0.00 37.01 4.92
2591 2799 2.429739 GAGCAGCAAAAGCGTGGC 60.430 61.111 0.00 0.00 37.01 5.01
2593 2801 0.451135 GTACGAGCAGCAAAAGCGTG 60.451 55.000 0.00 0.00 36.51 5.34
2594 2802 0.600255 AGTACGAGCAGCAAAAGCGT 60.600 50.000 0.00 0.00 38.81 5.07
2595 2803 1.321743 CTAGTACGAGCAGCAAAAGCG 59.678 52.381 0.00 0.00 37.01 4.68
2596 2804 1.661112 CCTAGTACGAGCAGCAAAAGC 59.339 52.381 0.00 0.00 0.00 3.51
2597 2805 1.661112 GCCTAGTACGAGCAGCAAAAG 59.339 52.381 0.00 0.00 0.00 2.27
2618 2840 6.653989 AGAAAATCGACTGACCCAAATAGAT 58.346 36.000 0.00 0.00 0.00 1.98
2619 2841 6.049955 AGAAAATCGACTGACCCAAATAGA 57.950 37.500 0.00 0.00 0.00 1.98
2622 2844 5.316987 AGAAGAAAATCGACTGACCCAAAT 58.683 37.500 0.00 0.00 0.00 2.32
2985 4023 8.978539 ACATATTGTATAGTACTTTCGTGCATG 58.021 33.333 0.00 0.00 0.00 4.06
3208 4259 5.437289 CACACATGGTGTATCAAAGTTGT 57.563 39.130 1.15 0.00 45.65 3.32
3277 4329 7.307337 CCCTGAATTCACACTTTTGTAATTTGC 60.307 37.037 3.38 0.00 33.30 3.68
3280 4333 6.183360 TGCCCTGAATTCACACTTTTGTAATT 60.183 34.615 3.38 0.00 33.30 1.40
3293 4348 3.758023 CACACAAGTATGCCCTGAATTCA 59.242 43.478 8.12 8.12 0.00 2.57
3294 4349 3.428045 GCACACAAGTATGCCCTGAATTC 60.428 47.826 0.00 0.00 35.73 2.17
3336 4393 9.261180 GGAAAAATGAAACCCTTTAAGAAGAAG 57.739 33.333 0.00 0.00 34.71 2.85


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

AutoCloner maintained by Alex Coulton.