Multiple sequence alignment - TraesCS4B01G372200

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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 TraesCS4B01G372200 chr4B 100.000 4545 0 0 1 4545 657269914 657274458 0.000000e+00 8394.0
1 TraesCS4B01G372200 chr4B 85.482 2032 264 23 1457 3462 657254240 657252214 0.000000e+00 2089.0
2 TraesCS4B01G372200 chr4B 87.020 1302 158 9 1448 2742 657243918 657245215 0.000000e+00 1458.0
3 TraesCS4B01G372200 chr4B 87.225 728 76 8 2804 3529 657245235 657245947 0.000000e+00 813.0
4 TraesCS4B01G372200 chr4B 85.079 630 75 12 704 1318 657255586 657254961 3.860000e-175 625.0
5 TraesCS4B01G372200 chr4B 75.768 293 40 9 4224 4495 657255968 657256250 7.990000e-23 119.0
6 TraesCS4B01G372200 chr4D 94.612 1856 84 8 1907 3760 509483363 509481522 0.000000e+00 2859.0
7 TraesCS4B01G372200 chr4D 86.762 1541 190 11 1862 3389 509517347 509518886 0.000000e+00 1703.0
8 TraesCS4B01G372200 chr4D 97.355 794 13 4 3755 4545 509481480 509480692 0.000000e+00 1343.0
9 TraesCS4B01G372200 chr4D 86.264 728 84 11 2810 3532 509535102 509534386 0.000000e+00 776.0
10 TraesCS4B01G372200 chr4D 85.437 618 71 11 701 1309 509538035 509537428 3.860000e-175 625.0
11 TraesCS4B01G372200 chr4D 83.307 629 88 14 695 1309 509510778 509511403 8.540000e-157 564.0
12 TraesCS4B01G372200 chr4D 89.189 74 6 2 445 516 262387919 262387846 1.740000e-14 91.6
13 TraesCS4B01G372200 chr5A 93.901 1492 75 5 2064 3554 698361417 698359941 0.000000e+00 2237.0
14 TraesCS4B01G372200 chr5A 88.467 1292 137 7 1447 2729 698484092 698482804 0.000000e+00 1550.0
15 TraesCS4B01G372200 chr5A 86.899 1290 164 4 1457 2742 698372533 698371245 0.000000e+00 1441.0
16 TraesCS4B01G372200 chr5A 85.670 1284 182 2 1447 2729 698450201 698448919 0.000000e+00 1351.0
17 TraesCS4B01G372200 chr5A 95.849 795 22 7 3754 4545 698359671 698358885 0.000000e+00 1275.0
18 TraesCS4B01G372200 chr5A 87.782 974 113 5 1447 2416 698388917 698389888 0.000000e+00 1134.0
19 TraesCS4B01G372200 chr5A 86.373 998 125 9 1446 2436 698455512 698454519 0.000000e+00 1079.0
20 TraesCS4B01G372200 chr5A 82.028 996 160 11 2483 3462 698389886 698390878 0.000000e+00 830.0
21 TraesCS4B01G372200 chr5A 86.676 728 80 8 2807 3532 698448886 698448174 0.000000e+00 791.0
22 TraesCS4B01G372200 chr5A 85.577 728 88 8 2807 3532 698482771 698482059 0.000000e+00 747.0
23 TraesCS4B01G372200 chr5A 85.205 730 84 9 2807 3532 698454076 698453367 0.000000e+00 728.0
24 TraesCS4B01G372200 chr5A 84.026 626 92 6 695 1318 698451531 698450912 3.030000e-166 595.0
25 TraesCS4B01G372200 chr5A 83.070 632 82 14 705 1318 698456846 698456222 6.650000e-153 551.0
26 TraesCS4B01G372200 chr5A 83.771 419 54 10 704 1109 698490420 698490003 7.130000e-103 385.0
27 TraesCS4B01G372200 chr5A 85.276 163 24 0 1293 1455 698450862 698450700 7.820000e-38 169.0
28 TraesCS4B01G372200 chr5A 96.774 93 3 0 3568 3660 698359828 698359736 6.090000e-34 156.0
29 TraesCS4B01G372200 chr5A 92.308 78 6 0 4467 4544 698482060 698481983 1.340000e-20 111.0
30 TraesCS4B01G372200 chr7B 98.047 512 10 0 1 512 99802682 99803193 0.000000e+00 891.0
31 TraesCS4B01G372200 chr3A 89.266 531 24 4 1 512 693442162 693442678 6.410000e-178 634.0
32 TraesCS4B01G372200 chr6A 78.632 950 193 8 1429 2370 12056693 12057640 4.990000e-174 621.0
33 TraesCS4B01G372200 chr6A 80.300 533 86 15 789 1309 12055466 12055991 7.130000e-103 385.0
34 TraesCS4B01G372200 chr6A 94.118 51 3 0 462 512 552175002 552175052 1.360000e-10 78.7
35 TraesCS4B01G372200 chr1D 82.931 621 86 16 703 1309 203268382 203268996 4.000000e-150 542.0
36 TraesCS4B01G372200 chr1D 82.482 411 72 0 1447 1857 203269716 203270126 1.200000e-95 361.0
37 TraesCS4B01G372200 chr1B 81.804 621 93 16 703 1309 297056978 297057592 1.890000e-138 503.0
38 TraesCS4B01G372200 chr5D 81.322 605 106 5 707 1308 33679461 33678861 6.840000e-133 484.0
39 TraesCS4B01G372200 chr5D 84.286 70 9 2 445 514 517371785 517371718 2.930000e-07 67.6
40 TraesCS4B01G372200 chr5D 87.719 57 5 2 466 521 61647762 61647707 1.060000e-06 65.8
41 TraesCS4B01G372200 chr1A 82.778 540 83 8 785 1318 257415565 257416100 1.480000e-129 473.0
42 TraesCS4B01G372200 chr1A 81.707 410 75 0 1448 1857 257416812 257417221 4.350000e-90 342.0
43 TraesCS4B01G372200 chr6B 78.664 614 117 12 704 1309 19233002 19233609 3.300000e-106 396.0
44 TraesCS4B01G372200 chr2B 94.760 229 11 1 4 232 232279516 232279289 5.590000e-94 355.0
45 TraesCS4B01G372200 chr2B 84.058 69 9 2 445 513 276270471 276270537 1.060000e-06 65.8
46 TraesCS4B01G372200 chr2A 94.397 232 12 1 1 232 187317621 187317851 5.590000e-94 355.0
47 TraesCS4B01G372200 chr2D 90.385 52 5 0 461 512 622343232 622343181 8.160000e-08 69.4
48 TraesCS4B01G372200 chr6D 84.058 69 7 4 445 512 197300988 197301053 3.800000e-06 63.9


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 TraesCS4B01G372200 chr4B 657269914 657274458 4544 False 8394.000000 8394 100.000000 1 4545 1 chr4B.!!$F2 4544
1 TraesCS4B01G372200 chr4B 657252214 657255586 3372 True 1357.000000 2089 85.280500 704 3462 2 chr4B.!!$R1 2758
2 TraesCS4B01G372200 chr4B 657243918 657245947 2029 False 1135.500000 1458 87.122500 1448 3529 2 chr4B.!!$F3 2081
3 TraesCS4B01G372200 chr4D 509480692 509483363 2671 True 2101.000000 2859 95.983500 1907 4545 2 chr4D.!!$R2 2638
4 TraesCS4B01G372200 chr4D 509517347 509518886 1539 False 1703.000000 1703 86.762000 1862 3389 1 chr4D.!!$F2 1527
5 TraesCS4B01G372200 chr4D 509534386 509538035 3649 True 700.500000 776 85.850500 701 3532 2 chr4D.!!$R3 2831
6 TraesCS4B01G372200 chr4D 509510778 509511403 625 False 564.000000 564 83.307000 695 1309 1 chr4D.!!$F1 614
7 TraesCS4B01G372200 chr5A 698371245 698372533 1288 True 1441.000000 1441 86.899000 1457 2742 1 chr5A.!!$R1 1285
8 TraesCS4B01G372200 chr5A 698358885 698361417 2532 True 1222.666667 2237 95.508000 2064 4545 3 chr5A.!!$R3 2481
9 TraesCS4B01G372200 chr5A 698388917 698390878 1961 False 982.000000 1134 84.905000 1447 3462 2 chr5A.!!$F1 2015
10 TraesCS4B01G372200 chr5A 698481983 698484092 2109 True 802.666667 1550 88.784000 1447 4544 3 chr5A.!!$R5 3097
11 TraesCS4B01G372200 chr5A 698448174 698456846 8672 True 752.000000 1351 85.185143 695 3532 7 chr5A.!!$R4 2837
12 TraesCS4B01G372200 chr7B 99802682 99803193 511 False 891.000000 891 98.047000 1 512 1 chr7B.!!$F1 511
13 TraesCS4B01G372200 chr3A 693442162 693442678 516 False 634.000000 634 89.266000 1 512 1 chr3A.!!$F1 511
14 TraesCS4B01G372200 chr6A 12055466 12057640 2174 False 503.000000 621 79.466000 789 2370 2 chr6A.!!$F2 1581
15 TraesCS4B01G372200 chr1D 203268382 203270126 1744 False 451.500000 542 82.706500 703 1857 2 chr1D.!!$F1 1154
16 TraesCS4B01G372200 chr1B 297056978 297057592 614 False 503.000000 503 81.804000 703 1309 1 chr1B.!!$F1 606
17 TraesCS4B01G372200 chr5D 33678861 33679461 600 True 484.000000 484 81.322000 707 1308 1 chr5D.!!$R1 601
18 TraesCS4B01G372200 chr1A 257415565 257417221 1656 False 407.500000 473 82.242500 785 1857 2 chr1A.!!$F1 1072
19 TraesCS4B01G372200 chr6B 19233002 19233609 607 False 396.000000 396 78.664000 704 1309 1 chr6B.!!$F1 605

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
989 1030 0.107800 CCCTCGTCAGACTCGACCTA 60.108 60.0 0.0 0.0 33.71 3.08 F
1084 1125 0.104487 TAACAACAACCTCGCCGACA 59.896 50.0 0.0 0.0 0.00 4.35 F
2619 3667 0.039035 CCGGACAAATTCCCCCAGAA 59.961 55.0 0.0 0.0 42.27 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2500 0.250513 ATCAGACGGCAACTTCCCTC 59.749 55.000 0.0 0.0 34.88 4.30 R
2718 8959 1.075374 TGGACCAACTGGGGAAGATTG 59.925 52.381 0.0 0.0 42.91 2.67 R
4438 10868 1.071699 AGGAGCAAGTTTGGCGAAGTA 59.928 47.619 0.0 0.0 36.08 2.24 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
264 265 5.196695 AGGATTATGCCTTCTCCTTTCAAC 58.803 41.667 0.00 0.00 34.42 3.18
462 482 7.509141 TGTGCCCTACAATATTCACATAATG 57.491 36.000 2.26 0.00 36.06 1.90
512 532 1.421410 GCGCAACGGGTCATCTAGTG 61.421 60.000 0.30 0.00 0.00 2.74
513 533 0.172578 CGCAACGGGTCATCTAGTGA 59.827 55.000 0.00 0.00 0.00 3.41
514 534 1.403647 CGCAACGGGTCATCTAGTGAA 60.404 52.381 0.00 0.00 38.90 3.18
515 535 2.695359 GCAACGGGTCATCTAGTGAAA 58.305 47.619 0.00 0.00 38.90 2.69
516 536 3.071479 GCAACGGGTCATCTAGTGAAAA 58.929 45.455 0.00 0.00 38.90 2.29
517 537 3.125316 GCAACGGGTCATCTAGTGAAAAG 59.875 47.826 0.00 0.00 38.90 2.27
518 538 4.566004 CAACGGGTCATCTAGTGAAAAGA 58.434 43.478 0.00 0.00 38.90 2.52
519 539 4.884668 ACGGGTCATCTAGTGAAAAGAA 57.115 40.909 0.00 0.00 38.90 2.52
520 540 4.566987 ACGGGTCATCTAGTGAAAAGAAC 58.433 43.478 0.00 0.00 38.90 3.01
521 541 3.612860 CGGGTCATCTAGTGAAAAGAACG 59.387 47.826 0.00 0.00 38.90 3.95
522 542 3.933332 GGGTCATCTAGTGAAAAGAACGG 59.067 47.826 0.00 0.00 38.90 4.44
523 543 3.371285 GGTCATCTAGTGAAAAGAACGGC 59.629 47.826 0.00 0.00 38.90 5.68
524 544 3.060895 GTCATCTAGTGAAAAGAACGGCG 59.939 47.826 4.80 4.80 38.90 6.46
525 545 3.057104 TCATCTAGTGAAAAGAACGGCGA 60.057 43.478 16.62 0.00 32.78 5.54
526 546 2.669364 TCTAGTGAAAAGAACGGCGAC 58.331 47.619 16.62 7.38 0.00 5.19
527 547 2.295349 TCTAGTGAAAAGAACGGCGACT 59.705 45.455 16.62 9.91 0.00 4.18
528 548 1.217882 AGTGAAAAGAACGGCGACTG 58.782 50.000 16.62 0.00 0.00 3.51
529 549 0.234884 GTGAAAAGAACGGCGACTGG 59.765 55.000 16.62 0.00 0.00 4.00
530 550 1.206831 GAAAAGAACGGCGACTGGC 59.793 57.895 16.62 2.44 42.51 4.85
541 561 3.371063 GACTGGCGAGGTCGGTCA 61.371 66.667 4.41 0.00 40.23 4.02
542 562 3.628280 GACTGGCGAGGTCGGTCAC 62.628 68.421 4.41 0.00 40.23 3.67
543 563 3.374402 CTGGCGAGGTCGGTCACT 61.374 66.667 0.89 0.00 40.23 3.41
544 564 3.633094 CTGGCGAGGTCGGTCACTG 62.633 68.421 0.89 0.00 40.23 3.66
545 565 4.436998 GGCGAGGTCGGTCACTGG 62.437 72.222 0.89 0.00 40.23 4.00
546 566 3.681835 GCGAGGTCGGTCACTGGT 61.682 66.667 0.89 0.00 40.23 4.00
547 567 2.258591 CGAGGTCGGTCACTGGTG 59.741 66.667 0.00 0.00 35.37 4.17
548 568 2.657237 GAGGTCGGTCACTGGTGG 59.343 66.667 0.70 0.00 0.00 4.61
549 569 1.906824 GAGGTCGGTCACTGGTGGA 60.907 63.158 0.70 0.00 0.00 4.02
550 570 1.458777 AGGTCGGTCACTGGTGGAA 60.459 57.895 0.70 0.00 0.00 3.53
551 571 1.004918 GGTCGGTCACTGGTGGAAG 60.005 63.158 0.70 0.00 0.00 3.46
552 572 1.746517 GTCGGTCACTGGTGGAAGT 59.253 57.895 0.70 0.00 0.00 3.01
553 573 0.319641 GTCGGTCACTGGTGGAAGTC 60.320 60.000 0.70 0.00 0.00 3.01
554 574 0.757561 TCGGTCACTGGTGGAAGTCA 60.758 55.000 0.70 0.00 0.00 3.41
555 575 0.600255 CGGTCACTGGTGGAAGTCAC 60.600 60.000 0.70 0.00 45.34 3.67
564 584 1.230324 GTGGAAGTCACAAGTCAGGC 58.770 55.000 0.00 0.00 45.39 4.85
565 585 0.108585 TGGAAGTCACAAGTCAGGCC 59.891 55.000 0.00 0.00 0.00 5.19
566 586 0.108585 GGAAGTCACAAGTCAGGCCA 59.891 55.000 5.01 0.00 0.00 5.36
567 587 1.230324 GAAGTCACAAGTCAGGCCAC 58.770 55.000 5.01 0.00 0.00 5.01
568 588 0.546122 AAGTCACAAGTCAGGCCACA 59.454 50.000 5.01 0.00 0.00 4.17
569 589 0.179045 AGTCACAAGTCAGGCCACAC 60.179 55.000 5.01 0.00 0.00 3.82
570 590 0.463654 GTCACAAGTCAGGCCACACA 60.464 55.000 5.01 0.00 0.00 3.72
571 591 0.254462 TCACAAGTCAGGCCACACAA 59.746 50.000 5.01 0.00 0.00 3.33
572 592 1.102154 CACAAGTCAGGCCACACAAA 58.898 50.000 5.01 0.00 0.00 2.83
573 593 1.102978 ACAAGTCAGGCCACACAAAC 58.897 50.000 5.01 0.00 0.00 2.93
574 594 0.385390 CAAGTCAGGCCACACAAACC 59.615 55.000 5.01 0.00 0.00 3.27
575 595 1.101049 AAGTCAGGCCACACAAACCG 61.101 55.000 5.01 0.00 0.00 4.44
576 596 2.203280 TCAGGCCACACAAACCGG 60.203 61.111 5.01 0.00 0.00 5.28
577 597 3.294493 CAGGCCACACAAACCGGG 61.294 66.667 6.32 0.00 0.00 5.73
578 598 4.596585 AGGCCACACAAACCGGGG 62.597 66.667 6.32 0.00 0.00 5.73
579 599 4.589675 GGCCACACAAACCGGGGA 62.590 66.667 6.32 0.00 0.00 4.81
580 600 2.519780 GCCACACAAACCGGGGAA 60.520 61.111 6.32 0.00 0.00 3.97
581 601 2.852180 GCCACACAAACCGGGGAAC 61.852 63.158 6.32 0.00 0.00 3.62
582 602 1.152839 CCACACAAACCGGGGAACT 60.153 57.895 6.32 0.00 0.00 3.01
583 603 1.170290 CCACACAAACCGGGGAACTC 61.170 60.000 6.32 0.00 0.00 3.01
584 604 1.227734 ACACAAACCGGGGAACTCG 60.228 57.895 6.32 0.00 0.00 4.18
585 605 2.281276 ACAAACCGGGGAACTCGC 60.281 61.111 6.32 0.00 0.00 5.03
586 606 2.032071 CAAACCGGGGAACTCGCT 59.968 61.111 6.32 0.00 0.00 4.93
587 607 2.033194 CAAACCGGGGAACTCGCTC 61.033 63.158 6.32 0.00 0.00 5.03
588 608 2.214920 AAACCGGGGAACTCGCTCT 61.215 57.895 6.32 0.00 0.00 4.09
589 609 2.168666 AAACCGGGGAACTCGCTCTC 62.169 60.000 6.32 0.00 0.00 3.20
590 610 2.756283 CCGGGGAACTCGCTCTCT 60.756 66.667 0.00 0.00 0.00 3.10
591 611 2.492090 CGGGGAACTCGCTCTCTG 59.508 66.667 0.00 0.00 0.00 3.35
592 612 2.185608 GGGGAACTCGCTCTCTGC 59.814 66.667 0.00 0.00 38.57 4.26
593 613 2.355193 GGGGAACTCGCTCTCTGCT 61.355 63.158 0.00 0.00 40.11 4.24
594 614 1.038130 GGGGAACTCGCTCTCTGCTA 61.038 60.000 0.00 0.00 40.11 3.49
595 615 0.383949 GGGAACTCGCTCTCTGCTAG 59.616 60.000 0.00 0.00 39.96 3.42
596 616 0.248866 GGAACTCGCTCTCTGCTAGC 60.249 60.000 8.10 8.10 37.93 3.42
601 621 4.085302 GCTCTCTGCTAGCGTGTG 57.915 61.111 10.77 6.74 38.95 3.82
602 622 2.164026 GCTCTCTGCTAGCGTGTGC 61.164 63.158 10.77 13.34 39.17 4.57
603 623 1.518133 CTCTCTGCTAGCGTGTGCC 60.518 63.158 10.77 0.00 44.31 5.01
604 624 2.882777 CTCTGCTAGCGTGTGCCG 60.883 66.667 10.77 0.00 44.31 5.69
605 625 3.633094 CTCTGCTAGCGTGTGCCGT 62.633 63.158 10.77 0.00 44.31 5.68
606 626 3.181967 CTGCTAGCGTGTGCCGTC 61.182 66.667 10.77 0.00 44.31 4.79
607 627 4.735132 TGCTAGCGTGTGCCGTCC 62.735 66.667 10.77 0.00 44.31 4.79
619 639 2.874751 CCGTCCGGCATTTCCAAC 59.125 61.111 0.00 0.00 34.01 3.77
620 640 2.696759 CCGTCCGGCATTTCCAACC 61.697 63.158 0.00 0.00 34.01 3.77
621 641 2.696759 CGTCCGGCATTTCCAACCC 61.697 63.158 0.00 0.00 34.01 4.11
622 642 1.605165 GTCCGGCATTTCCAACCCA 60.605 57.895 0.00 0.00 34.01 4.51
623 643 1.304052 TCCGGCATTTCCAACCCAG 60.304 57.895 0.00 0.00 34.01 4.45
624 644 1.606313 CCGGCATTTCCAACCCAGT 60.606 57.895 0.00 0.00 34.01 4.00
625 645 0.322997 CCGGCATTTCCAACCCAGTA 60.323 55.000 0.00 0.00 34.01 2.74
626 646 1.094785 CGGCATTTCCAACCCAGTAG 58.905 55.000 0.00 0.00 34.01 2.57
627 647 0.817654 GGCATTTCCAACCCAGTAGC 59.182 55.000 0.00 0.00 34.01 3.58
628 648 1.544724 GCATTTCCAACCCAGTAGCA 58.455 50.000 0.00 0.00 0.00 3.49
629 649 1.202348 GCATTTCCAACCCAGTAGCAC 59.798 52.381 0.00 0.00 0.00 4.40
630 650 1.818674 CATTTCCAACCCAGTAGCACC 59.181 52.381 0.00 0.00 0.00 5.01
631 651 1.145571 TTTCCAACCCAGTAGCACCT 58.854 50.000 0.00 0.00 0.00 4.00
632 652 0.690762 TTCCAACCCAGTAGCACCTC 59.309 55.000 0.00 0.00 0.00 3.85
633 653 1.079127 CCAACCCAGTAGCACCTCG 60.079 63.158 0.00 0.00 0.00 4.63
634 654 1.079127 CAACCCAGTAGCACCTCGG 60.079 63.158 0.00 0.00 0.00 4.63
635 655 2.291043 AACCCAGTAGCACCTCGGG 61.291 63.158 0.00 0.00 43.02 5.14
636 656 4.162690 CCCAGTAGCACCTCGGGC 62.163 72.222 0.00 0.00 0.00 6.13
637 657 3.390521 CCAGTAGCACCTCGGGCA 61.391 66.667 0.00 0.00 0.00 5.36
638 658 2.185350 CAGTAGCACCTCGGGCAG 59.815 66.667 0.00 0.00 0.00 4.85
646 666 4.181010 CCTCGGGCAGGGACATGG 62.181 72.222 0.00 0.00 38.91 3.66
647 667 4.864334 CTCGGGCAGGGACATGGC 62.864 72.222 1.65 1.65 44.61 4.40
650 670 4.864334 GGGCAGGGACATGGCGAG 62.864 72.222 4.49 0.00 46.20 5.03
651 671 3.785859 GGCAGGGACATGGCGAGA 61.786 66.667 0.00 0.00 35.90 4.04
652 672 2.512515 GCAGGGACATGGCGAGAC 60.513 66.667 0.00 0.00 0.00 3.36
653 673 2.187946 CAGGGACATGGCGAGACC 59.812 66.667 0.00 0.00 39.84 3.85
654 674 3.461773 AGGGACATGGCGAGACCG 61.462 66.667 0.00 0.00 43.94 4.79
655 675 4.530857 GGGACATGGCGAGACCGG 62.531 72.222 0.00 0.00 43.94 5.28
673 693 3.479269 CGTTCGCGCACCTCCTTC 61.479 66.667 8.75 0.00 0.00 3.46
674 694 3.479269 GTTCGCGCACCTCCTTCG 61.479 66.667 8.75 0.00 0.00 3.79
680 700 4.681978 GCACCTCCTTCGCACCGT 62.682 66.667 0.00 0.00 0.00 4.83
681 701 2.432628 CACCTCCTTCGCACCGTC 60.433 66.667 0.00 0.00 0.00 4.79
682 702 4.052229 ACCTCCTTCGCACCGTCG 62.052 66.667 0.00 0.00 0.00 5.12
919 960 4.838486 GACCGCGCTCGACCTCAG 62.838 72.222 5.56 0.00 38.10 3.35
927 968 4.373116 TCGACCTCAGCGCCAACC 62.373 66.667 2.29 0.00 0.00 3.77
935 976 2.281761 AGCGCCAACCAACTCAGG 60.282 61.111 2.29 0.00 0.00 3.86
980 1021 2.640302 GCTGCAGTCCCTCGTCAGA 61.640 63.158 16.64 0.00 0.00 3.27
989 1030 0.107800 CCCTCGTCAGACTCGACCTA 60.108 60.000 0.00 0.00 33.71 3.08
994 1035 1.174783 GTCAGACTCGACCTAGGCAA 58.825 55.000 9.30 0.00 0.00 4.52
999 1040 1.272769 GACTCGACCTAGGCAACAACT 59.727 52.381 9.30 0.00 41.41 3.16
1065 1106 0.534427 TCGTCGACCTCCGCATCTAT 60.534 55.000 10.58 0.00 38.37 1.98
1084 1125 0.104487 TAACAACAACCTCGCCGACA 59.896 50.000 0.00 0.00 0.00 4.35
1085 1126 1.157870 AACAACAACCTCGCCGACAG 61.158 55.000 0.00 0.00 0.00 3.51
1152 1193 0.768221 TGGGCTCCAACTTCCTCACT 60.768 55.000 0.00 0.00 0.00 3.41
1158 1199 0.764890 CCAACTTCCTCACTGACCCA 59.235 55.000 0.00 0.00 0.00 4.51
1185 1229 2.436646 AAGTTCTCGCCCATGCCG 60.437 61.111 0.00 0.00 0.00 5.69
1221 1265 3.054875 TGTCGCTCTACCTCAACTACCTA 60.055 47.826 0.00 0.00 0.00 3.08
1291 1335 1.990799 CGACCTGTCGCAGAACAATA 58.009 50.000 6.77 0.00 46.50 1.90
1309 1353 3.715638 ATATCTCTGGACCGATACCGA 57.284 47.619 0.00 0.00 38.22 4.69
1319 1438 1.432251 CGATACCGAGGTCGCTGTT 59.568 57.895 0.00 0.00 38.22 3.16
1367 1486 3.214328 GGGTTGGCGATAACAATCTGAT 58.786 45.455 4.90 0.00 32.22 2.90
1377 1496 5.532406 CGATAACAATCTGATGGGTGGAATT 59.468 40.000 0.00 0.00 0.00 2.17
1401 1520 1.747444 AGTTCCTTGGGTCCATGTCT 58.253 50.000 0.00 0.00 0.00 3.41
1402 1521 2.915869 AGTTCCTTGGGTCCATGTCTA 58.084 47.619 0.00 0.00 0.00 2.59
1407 1526 2.025887 CCTTGGGTCCATGTCTAAGCTT 60.026 50.000 3.48 3.48 0.00 3.74
1561 2187 4.406972 CACTCAGGAATCTCCAATACCTCA 59.593 45.833 0.00 0.00 39.61 3.86
1570 2196 4.906618 TCTCCAATACCTCAACCTGTTTC 58.093 43.478 0.00 0.00 0.00 2.78
1584 2210 3.119990 ACCTGTTTCACAACAACTTCACG 60.120 43.478 0.00 0.00 42.53 4.35
1608 2234 0.981277 CCATACCTCCGGACCTTGGT 60.981 60.000 16.57 16.57 36.66 3.67
1625 2251 4.386424 CCTTGGTAAGGGGCTAAGCTTAAT 60.386 45.833 7.74 0.00 45.27 1.40
1641 2267 0.524816 TAATCGACGTGAGCTTCGCC 60.525 55.000 11.19 1.14 36.49 5.54
1647 2273 0.884704 ACGTGAGCTTCGCCAACAAT 60.885 50.000 11.19 0.00 0.00 2.71
1649 2275 1.463056 CGTGAGCTTCGCCAACAATAA 59.537 47.619 0.00 0.00 0.00 1.40
1652 2278 2.742053 TGAGCTTCGCCAACAATAACTC 59.258 45.455 0.00 0.00 0.00 3.01
1707 2333 0.104855 TCGTGCTGCAGAACTTCACT 59.895 50.000 22.63 0.00 0.00 3.41
1749 2375 1.305623 CAGGCTGCCATCCTTCCTT 59.694 57.895 22.65 0.00 0.00 3.36
1750 2376 1.035932 CAGGCTGCCATCCTTCCTTG 61.036 60.000 22.65 2.69 0.00 3.61
1762 2388 2.154462 CCTTCCTTGAGAATTGCACGT 58.846 47.619 0.00 0.00 32.82 4.49
1770 2396 3.124560 TGAGAATTGCACGTCGTTGTTA 58.875 40.909 0.00 0.00 0.00 2.41
1859 2488 3.779444 TGGACTACTTGGATGTCTCAGT 58.221 45.455 0.00 0.00 0.00 3.41
1871 2500 1.140852 TGTCTCAGTGAACCAGTTGGG 59.859 52.381 2.79 0.00 44.81 4.12
2189 3113 6.658188 TTTTCCATCCGTAATTGAAACCTT 57.342 33.333 0.00 0.00 30.88 3.50
2217 3144 4.171878 TCTCGTCATCCTAGATCTTGGT 57.828 45.455 20.66 7.59 0.00 3.67
2290 3217 4.152647 TCTTCTAACAGTTCTGAGCCTCA 58.847 43.478 6.83 0.00 0.00 3.86
2306 3233 3.896888 AGCCTCACATCCAACAATTTCAA 59.103 39.130 0.00 0.00 0.00 2.69
2619 3667 0.039035 CCGGACAAATTCCCCCAGAA 59.961 55.000 0.00 0.00 42.27 3.02
2679 3727 3.310774 CCAACAATAGCTTGACAGGATCG 59.689 47.826 0.00 0.00 36.20 3.69
2700 8941 5.860611 TCGATTCCTGTAACCTTCAGAAAA 58.139 37.500 0.00 0.00 35.20 2.29
2770 9017 6.072452 GGATTCCGCTCCTTTAAAGATTATGG 60.072 42.308 16.98 11.01 32.18 2.74
3233 9489 0.474184 CCTACATTGGGCGAGGGAAT 59.526 55.000 0.00 0.00 0.00 3.01
3337 9596 2.175202 GAGCTCTGTTCTTCCTGGAGA 58.825 52.381 6.43 0.00 0.00 3.71
3409 9668 0.321298 TGTCACCCGCTAAGGCTTTC 60.321 55.000 4.45 0.00 39.21 2.62
3433 9700 8.837788 TCTATAATCACATGTAAATCAGCAGG 57.162 34.615 0.00 0.00 0.00 4.85
3466 9734 5.356426 AGCGTCAATTATGTACTGTATGCA 58.644 37.500 0.00 0.00 0.00 3.96
3469 9737 5.234116 CGTCAATTATGTACTGTATGCAGCA 59.766 40.000 11.09 0.00 46.30 4.41
3471 9739 7.073883 GTCAATTATGTACTGTATGCAGCATG 58.926 38.462 18.81 3.80 46.30 4.06
3756 10138 4.806247 CCATAAACAAAAACAACTGGCGAA 59.194 37.500 0.00 0.00 0.00 4.70
3757 10139 5.051106 CCATAAACAAAAACAACTGGCGAAG 60.051 40.000 0.00 0.00 0.00 3.79
3773 10200 1.931172 CGAAGCCCTGTATTACAACGG 59.069 52.381 0.00 2.13 0.00 4.44
3859 10289 0.550914 AACAAGAACCCAGCCAGTGA 59.449 50.000 0.00 0.00 0.00 3.41
3897 10327 2.108157 GTCTCCACGGCACACACA 59.892 61.111 0.00 0.00 0.00 3.72
3898 10328 2.108157 TCTCCACGGCACACACAC 59.892 61.111 0.00 0.00 0.00 3.82
3899 10329 2.972505 CTCCACGGCACACACACC 60.973 66.667 0.00 0.00 0.00 4.16
3900 10330 3.460672 CTCCACGGCACACACACCT 62.461 63.158 0.00 0.00 0.00 4.00
3902 10332 1.667830 CCACGGCACACACACCTAG 60.668 63.158 0.00 0.00 0.00 3.02
3903 10333 2.030562 ACGGCACACACACCTAGC 59.969 61.111 0.00 0.00 0.00 3.42
3904 10334 2.030412 CGGCACACACACCTAGCA 59.970 61.111 0.00 0.00 0.00 3.49
3905 10335 1.596752 CGGCACACACACCTAGCAA 60.597 57.895 0.00 0.00 0.00 3.91
3906 10336 1.568612 CGGCACACACACCTAGCAAG 61.569 60.000 0.00 0.00 0.00 4.01
3907 10337 0.535102 GGCACACACACCTAGCAAGT 60.535 55.000 0.00 0.00 0.00 3.16
3908 10338 0.868406 GCACACACACCTAGCAAGTC 59.132 55.000 0.00 0.00 0.00 3.01
3909 10339 1.541233 GCACACACACCTAGCAAGTCT 60.541 52.381 0.00 0.00 0.00 3.24
4020 10450 7.195352 GTGAAGATCACAGAAGCATTAGCGG 62.195 48.000 5.65 0.00 46.22 5.52
4058 10488 4.916983 AGCAACACATGTAAAGCTCAAA 57.083 36.364 11.09 0.00 0.00 2.69
4267 10697 2.039418 CCCCCTATTGTCGTCAGATCA 58.961 52.381 0.00 0.00 0.00 2.92
4268 10698 2.224066 CCCCCTATTGTCGTCAGATCAC 60.224 54.545 0.00 0.00 0.00 3.06
4438 10868 2.145397 TCCAGTCGCCTCTGTATCTT 57.855 50.000 2.84 0.00 34.02 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 8.860780 AGAAGGCATAATCCTCTCATAATTTC 57.139 34.615 0.00 0.00 34.82 2.17
264 265 5.461078 GCAATAGCATGCAAGTAAATTCCTG 59.539 40.000 21.98 2.05 45.70 3.86
462 482 4.538917 CAAAAAGCCAATTCAAACCATGC 58.461 39.130 0.00 0.00 0.00 4.06
512 532 1.206831 GCCAGTCGCCGTTCTTTTC 59.793 57.895 0.00 0.00 0.00 2.29
513 533 2.604174 CGCCAGTCGCCGTTCTTTT 61.604 57.895 0.00 0.00 0.00 2.27
514 534 3.041940 CGCCAGTCGCCGTTCTTT 61.042 61.111 0.00 0.00 0.00 2.52
515 535 3.916392 CTCGCCAGTCGCCGTTCTT 62.916 63.158 0.00 0.00 38.27 2.52
516 536 4.421479 CTCGCCAGTCGCCGTTCT 62.421 66.667 0.00 0.00 38.27 3.01
524 544 3.371063 TGACCGACCTCGCCAGTC 61.371 66.667 0.00 0.00 38.18 3.51
525 545 3.681835 GTGACCGACCTCGCCAGT 61.682 66.667 0.00 0.00 38.18 4.00
526 546 3.374402 AGTGACCGACCTCGCCAG 61.374 66.667 0.00 0.00 38.18 4.85
527 547 3.680786 CAGTGACCGACCTCGCCA 61.681 66.667 0.00 0.00 38.18 5.69
528 548 4.436998 CCAGTGACCGACCTCGCC 62.437 72.222 0.00 0.00 38.18 5.54
529 549 3.681835 ACCAGTGACCGACCTCGC 61.682 66.667 0.00 0.00 38.18 5.03
530 550 2.258591 CACCAGTGACCGACCTCG 59.741 66.667 0.00 0.00 39.44 4.63
531 551 1.469335 TTCCACCAGTGACCGACCTC 61.469 60.000 0.00 0.00 0.00 3.85
532 552 1.458777 TTCCACCAGTGACCGACCT 60.459 57.895 0.00 0.00 0.00 3.85
533 553 1.004918 CTTCCACCAGTGACCGACC 60.005 63.158 0.00 0.00 0.00 4.79
534 554 0.319641 GACTTCCACCAGTGACCGAC 60.320 60.000 0.00 0.00 0.00 4.79
535 555 0.757561 TGACTTCCACCAGTGACCGA 60.758 55.000 0.00 0.00 0.00 4.69
536 556 0.600255 GTGACTTCCACCAGTGACCG 60.600 60.000 0.00 0.00 39.86 4.79
537 557 0.468226 TGTGACTTCCACCAGTGACC 59.532 55.000 0.00 0.00 45.09 4.02
538 558 2.213499 CTTGTGACTTCCACCAGTGAC 58.787 52.381 0.00 0.00 45.09 3.67
539 559 1.837439 ACTTGTGACTTCCACCAGTGA 59.163 47.619 0.00 0.00 46.29 3.41
540 560 2.332063 ACTTGTGACTTCCACCAGTG 57.668 50.000 0.00 0.00 46.29 3.66
542 562 2.487934 CTGACTTGTGACTTCCACCAG 58.512 52.381 0.00 0.00 45.09 4.00
543 563 1.140852 CCTGACTTGTGACTTCCACCA 59.859 52.381 0.00 0.00 45.09 4.17
544 564 1.884235 CCTGACTTGTGACTTCCACC 58.116 55.000 0.00 0.00 45.09 4.61
545 565 1.230324 GCCTGACTTGTGACTTCCAC 58.770 55.000 0.00 0.00 45.88 4.02
546 566 0.108585 GGCCTGACTTGTGACTTCCA 59.891 55.000 0.00 0.00 0.00 3.53
547 567 0.108585 TGGCCTGACTTGTGACTTCC 59.891 55.000 3.32 0.00 0.00 3.46
548 568 1.230324 GTGGCCTGACTTGTGACTTC 58.770 55.000 3.32 0.00 0.00 3.01
549 569 0.546122 TGTGGCCTGACTTGTGACTT 59.454 50.000 3.32 0.00 0.00 3.01
550 570 0.179045 GTGTGGCCTGACTTGTGACT 60.179 55.000 3.32 0.00 0.00 3.41
551 571 0.463654 TGTGTGGCCTGACTTGTGAC 60.464 55.000 3.32 0.00 0.00 3.67
552 572 0.254462 TTGTGTGGCCTGACTTGTGA 59.746 50.000 3.32 0.00 0.00 3.58
553 573 1.102154 TTTGTGTGGCCTGACTTGTG 58.898 50.000 3.32 0.00 0.00 3.33
554 574 1.102978 GTTTGTGTGGCCTGACTTGT 58.897 50.000 3.32 0.00 0.00 3.16
555 575 0.385390 GGTTTGTGTGGCCTGACTTG 59.615 55.000 3.32 0.00 0.00 3.16
556 576 1.101049 CGGTTTGTGTGGCCTGACTT 61.101 55.000 3.32 0.00 0.00 3.01
557 577 1.525995 CGGTTTGTGTGGCCTGACT 60.526 57.895 3.32 0.00 0.00 3.41
558 578 2.551912 CCGGTTTGTGTGGCCTGAC 61.552 63.158 3.32 0.21 0.00 3.51
559 579 2.203280 CCGGTTTGTGTGGCCTGA 60.203 61.111 3.32 0.00 0.00 3.86
560 580 3.294493 CCCGGTTTGTGTGGCCTG 61.294 66.667 3.32 0.00 0.00 4.85
561 581 4.596585 CCCCGGTTTGTGTGGCCT 62.597 66.667 3.32 0.00 0.00 5.19
562 582 4.589675 TCCCCGGTTTGTGTGGCC 62.590 66.667 0.00 0.00 0.00 5.36
563 583 2.519780 TTCCCCGGTTTGTGTGGC 60.520 61.111 0.00 0.00 0.00 5.01
564 584 1.152839 AGTTCCCCGGTTTGTGTGG 60.153 57.895 0.00 0.00 0.00 4.17
565 585 1.503818 CGAGTTCCCCGGTTTGTGTG 61.504 60.000 0.00 0.00 0.00 3.82
566 586 1.227734 CGAGTTCCCCGGTTTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
567 587 2.613506 GCGAGTTCCCCGGTTTGTG 61.614 63.158 0.00 0.00 0.00 3.33
568 588 2.281276 GCGAGTTCCCCGGTTTGT 60.281 61.111 0.00 0.00 0.00 2.83
569 589 2.032071 AGCGAGTTCCCCGGTTTG 59.968 61.111 0.00 0.00 33.72 2.93
570 590 2.168666 GAGAGCGAGTTCCCCGGTTT 62.169 60.000 0.00 0.00 37.90 3.27
571 591 2.603776 AGAGCGAGTTCCCCGGTT 60.604 61.111 0.00 0.00 37.90 4.44
572 592 3.069318 GAGAGCGAGTTCCCCGGT 61.069 66.667 0.00 0.00 40.66 5.28
573 593 2.756283 AGAGAGCGAGTTCCCCGG 60.756 66.667 0.00 0.00 0.00 5.73
574 594 2.492090 CAGAGAGCGAGTTCCCCG 59.508 66.667 0.00 0.00 0.00 5.73
575 595 2.185608 GCAGAGAGCGAGTTCCCC 59.814 66.667 0.00 0.00 0.00 4.81
584 604 2.164026 GCACACGCTAGCAGAGAGC 61.164 63.158 16.45 12.06 38.33 4.09
585 605 1.518133 GGCACACGCTAGCAGAGAG 60.518 63.158 16.45 6.34 38.60 3.20
586 606 2.573869 GGCACACGCTAGCAGAGA 59.426 61.111 16.45 0.00 38.60 3.10
587 607 2.882777 CGGCACACGCTAGCAGAG 60.883 66.667 16.45 8.79 38.60 3.35
602 622 2.696759 GGTTGGAAATGCCGGACGG 61.697 63.158 5.05 6.35 40.66 4.79
603 623 2.696759 GGGTTGGAAATGCCGGACG 61.697 63.158 5.05 0.00 40.66 4.79
604 624 1.595093 CTGGGTTGGAAATGCCGGAC 61.595 60.000 5.05 0.00 40.66 4.79
605 625 1.304052 CTGGGTTGGAAATGCCGGA 60.304 57.895 5.05 0.00 40.66 5.14
606 626 0.322997 TACTGGGTTGGAAATGCCGG 60.323 55.000 0.00 0.00 40.66 6.13
607 627 1.094785 CTACTGGGTTGGAAATGCCG 58.905 55.000 0.00 0.00 40.66 5.69
608 628 0.817654 GCTACTGGGTTGGAAATGCC 59.182 55.000 0.00 0.00 37.10 4.40
609 629 1.202348 GTGCTACTGGGTTGGAAATGC 59.798 52.381 0.00 0.00 0.00 3.56
610 630 1.818674 GGTGCTACTGGGTTGGAAATG 59.181 52.381 0.00 0.00 0.00 2.32
611 631 1.710809 AGGTGCTACTGGGTTGGAAAT 59.289 47.619 0.00 0.00 0.00 2.17
612 632 1.073284 GAGGTGCTACTGGGTTGGAAA 59.927 52.381 0.00 0.00 0.00 3.13
613 633 0.690762 GAGGTGCTACTGGGTTGGAA 59.309 55.000 0.00 0.00 0.00 3.53
614 634 1.541310 CGAGGTGCTACTGGGTTGGA 61.541 60.000 0.00 0.00 0.00 3.53
615 635 1.079127 CGAGGTGCTACTGGGTTGG 60.079 63.158 0.00 0.00 0.00 3.77
616 636 1.079127 CCGAGGTGCTACTGGGTTG 60.079 63.158 2.03 0.00 32.33 3.77
617 637 2.291043 CCCGAGGTGCTACTGGGTT 61.291 63.158 8.07 0.00 34.85 4.11
618 638 2.683933 CCCGAGGTGCTACTGGGT 60.684 66.667 8.07 0.00 34.85 4.51
619 639 4.162690 GCCCGAGGTGCTACTGGG 62.163 72.222 3.00 3.00 43.02 4.45
620 640 3.376935 CTGCCCGAGGTGCTACTGG 62.377 68.421 0.00 0.00 0.00 4.00
621 641 2.185350 CTGCCCGAGGTGCTACTG 59.815 66.667 0.00 0.00 0.00 2.74
622 642 3.077556 CCTGCCCGAGGTGCTACT 61.078 66.667 0.00 0.00 37.02 2.57
623 643 4.162690 CCCTGCCCGAGGTGCTAC 62.163 72.222 0.00 0.00 40.87 3.58
624 644 4.392166 TCCCTGCCCGAGGTGCTA 62.392 66.667 0.00 0.00 40.87 3.49
627 647 3.402681 ATGTCCCTGCCCGAGGTG 61.403 66.667 0.00 0.00 40.87 4.00
628 648 3.402681 CATGTCCCTGCCCGAGGT 61.403 66.667 0.00 0.00 40.87 3.85
629 649 4.181010 CCATGTCCCTGCCCGAGG 62.181 72.222 0.00 0.00 42.38 4.63
630 650 4.864334 GCCATGTCCCTGCCCGAG 62.864 72.222 0.00 0.00 0.00 4.63
633 653 4.864334 CTCGCCATGTCCCTGCCC 62.864 72.222 0.00 0.00 0.00 5.36
634 654 3.785859 TCTCGCCATGTCCCTGCC 61.786 66.667 0.00 0.00 0.00 4.85
635 655 2.512515 GTCTCGCCATGTCCCTGC 60.513 66.667 0.00 0.00 0.00 4.85
636 656 2.187946 GGTCTCGCCATGTCCCTG 59.812 66.667 0.00 0.00 37.17 4.45
637 657 3.461773 CGGTCTCGCCATGTCCCT 61.462 66.667 0.00 0.00 36.97 4.20
638 658 4.530857 CCGGTCTCGCCATGTCCC 62.531 72.222 0.00 0.00 36.97 4.46
643 663 4.814294 GAACGCCGGTCTCGCCAT 62.814 66.667 1.90 0.00 36.97 4.40
656 676 3.479269 GAAGGAGGTGCGCGAACG 61.479 66.667 12.10 0.00 44.07 3.95
657 677 3.479269 CGAAGGAGGTGCGCGAAC 61.479 66.667 12.10 10.63 0.00 3.95
663 683 4.681978 ACGGTGCGAAGGAGGTGC 62.682 66.667 0.00 0.00 0.00 5.01
664 684 2.432628 GACGGTGCGAAGGAGGTG 60.433 66.667 0.00 0.00 0.00 4.00
665 685 4.052229 CGACGGTGCGAAGGAGGT 62.052 66.667 0.00 0.00 0.00 3.85
725 745 2.266055 CCGAGTCTGGCCTTCCAC 59.734 66.667 3.32 0.00 37.47 4.02
887 928 3.005539 GTCAGAGCTGGGAGGGCA 61.006 66.667 0.00 0.00 0.00 5.36
890 931 4.154347 GCGGTCAGAGCTGGGAGG 62.154 72.222 0.00 0.00 0.00 4.30
919 960 3.365265 CCCTGAGTTGGTTGGCGC 61.365 66.667 0.00 0.00 0.00 6.53
922 963 2.672996 CGCCCCTGAGTTGGTTGG 60.673 66.667 0.00 0.00 0.00 3.77
927 968 2.825836 GATGGCGCCCCTGAGTTG 60.826 66.667 26.77 0.00 0.00 3.16
968 1009 1.646624 GGTCGAGTCTGACGAGGGAC 61.647 65.000 1.52 8.25 40.37 4.46
976 1017 1.174783 GTTGCCTAGGTCGAGTCTGA 58.825 55.000 11.31 0.00 0.00 3.27
980 1021 1.339097 AGTTGTTGCCTAGGTCGAGT 58.661 50.000 11.31 1.99 0.00 4.18
989 1030 2.552315 CCGTTGAACATAGTTGTTGCCT 59.448 45.455 0.00 0.00 46.01 4.75
994 1035 2.224426 TGGAGCCGTTGAACATAGTTGT 60.224 45.455 0.00 0.00 37.82 3.32
999 1040 1.134220 GGGATGGAGCCGTTGAACATA 60.134 52.381 0.00 0.00 0.00 2.29
1033 1074 3.069318 GACGAGGCCGGAGAGGTT 61.069 66.667 5.05 0.00 43.70 3.50
1060 1101 3.131577 TCGGCGAGGTTGTTGTTATAGAT 59.868 43.478 4.99 0.00 0.00 1.98
1065 1106 0.104487 TGTCGGCGAGGTTGTTGTTA 59.896 50.000 11.20 0.00 0.00 2.41
1084 1125 4.479993 GAGCTGGTGCGGGATGCT 62.480 66.667 0.00 0.00 46.63 3.79
1085 1126 4.783621 TGAGCTGGTGCGGGATGC 62.784 66.667 0.00 0.00 45.42 3.91
1152 1193 0.830444 ACTTGCGGTAGTCTGGGTCA 60.830 55.000 0.00 0.00 0.00 4.02
1158 1199 0.109226 GCGAGAACTTGCGGTAGTCT 60.109 55.000 0.00 0.00 0.00 3.24
1185 1229 1.079503 GCGACAAGAAGGTGATGGTC 58.920 55.000 0.00 0.00 0.00 4.02
1189 1233 2.166664 GGTAGAGCGACAAGAAGGTGAT 59.833 50.000 0.00 0.00 0.00 3.06
1291 1335 1.545875 CCTCGGTATCGGTCCAGAGAT 60.546 57.143 0.00 0.00 36.95 2.75
1407 1526 1.429927 CGCCGAGTTCGAGAGCTCTA 61.430 60.000 18.25 0.00 43.02 2.43
1528 2154 2.408271 TTCCTGAGTGATGTGATGGC 57.592 50.000 0.00 0.00 0.00 4.40
1570 2196 0.248458 GTGCCCGTGAAGTTGTTGTG 60.248 55.000 0.00 0.00 0.00 3.33
1608 2234 3.243636 CGTCGATTAAGCTTAGCCCCTTA 60.244 47.826 6.24 0.00 0.00 2.69
1707 2333 1.396648 CTGAAGTTGTTGTGTGACGCA 59.603 47.619 0.00 0.00 0.00 5.24
1711 2337 1.013596 CCGCTGAAGTTGTTGTGTGA 58.986 50.000 0.00 0.00 0.00 3.58
1712 2338 0.592247 GCCGCTGAAGTTGTTGTGTG 60.592 55.000 0.00 0.00 0.00 3.82
1713 2339 1.029408 TGCCGCTGAAGTTGTTGTGT 61.029 50.000 0.00 0.00 0.00 3.72
1745 2371 1.270094 ACGACGTGCAATTCTCAAGGA 60.270 47.619 0.00 0.00 0.00 3.36
1749 2375 1.577468 ACAACGACGTGCAATTCTCA 58.423 45.000 0.00 0.00 0.00 3.27
1750 2376 2.663279 AACAACGACGTGCAATTCTC 57.337 45.000 0.00 0.00 0.00 2.87
1762 2388 1.957186 GCCGCACCTGTAACAACGA 60.957 57.895 0.00 0.00 0.00 3.85
1770 2396 4.335647 CCTTCCAGCCGCACCTGT 62.336 66.667 0.00 0.00 0.00 4.00
1791 2420 2.083774 GAGATGTTGCCGGTGAATTGA 58.916 47.619 1.90 0.00 0.00 2.57
1815 2444 0.762418 TGGGATTGACACCGAACACT 59.238 50.000 0.00 0.00 0.00 3.55
1828 2457 3.655777 TCCAAGTAGTCCAAGTTGGGATT 59.344 43.478 21.85 10.03 46.05 3.01
1859 2488 0.771127 CTTCCCTCCCAACTGGTTCA 59.229 55.000 0.00 0.00 34.77 3.18
1871 2500 0.250513 ATCAGACGGCAACTTCCCTC 59.749 55.000 0.00 0.00 34.88 4.30
2189 3113 4.965200 TCTAGGATGACGAGATCTCTGA 57.035 45.455 20.26 4.56 0.00 3.27
2217 3144 6.592607 GGATATCACCGAAGAACTTGTTGTTA 59.407 38.462 4.83 0.00 39.30 2.41
2290 3217 5.549742 ACACCATTGAAATTGTTGGATGT 57.450 34.783 0.00 0.00 33.36 3.06
2679 3727 8.023706 GTCAATTTTCTGAAGGTTACAGGAATC 58.976 37.037 0.00 0.00 33.60 2.52
2689 3737 4.453480 TGGAGGTCAATTTTCTGAAGGT 57.547 40.909 0.00 0.00 0.00 3.50
2718 8959 1.075374 TGGACCAACTGGGGAAGATTG 59.925 52.381 0.00 0.00 42.91 2.67
2856 9109 3.133362 GGTCGATACCTGTGATTAACCCA 59.867 47.826 0.00 0.00 43.08 4.51
3233 9489 6.260050 GTCTATGAGTTTTGTGTGGTCTTCAA 59.740 38.462 0.00 0.00 0.00 2.69
3409 9668 8.837788 TCCTGCTGATTTACATGTGATTATAG 57.162 34.615 9.11 1.29 0.00 1.31
3433 9700 6.032722 ACATAATTGACGCTAATGTCGTTC 57.967 37.500 0.00 0.00 41.87 3.95
3469 9737 7.264947 ACAACTGTAAAAAGTAAAAGCAGCAT 58.735 30.769 0.00 0.00 0.00 3.79
3471 9739 8.529102 GTTACAACTGTAAAAAGTAAAAGCAGC 58.471 33.333 3.92 0.00 41.58 5.25
3472 9740 9.562583 TGTTACAACTGTAAAAAGTAAAAGCAG 57.437 29.630 3.92 0.00 41.58 4.24
3473 9741 9.344309 GTGTTACAACTGTAAAAAGTAAAAGCA 57.656 29.630 3.92 0.00 41.58 3.91
3474 9742 9.563898 AGTGTTACAACTGTAAAAAGTAAAAGC 57.436 29.630 3.92 0.00 41.58 3.51
3565 9947 7.993183 AGGTAACAAAGCTGCATATGTATTAGT 59.007 33.333 4.29 0.00 41.41 2.24
3566 9948 8.383318 AGGTAACAAAGCTGCATATGTATTAG 57.617 34.615 4.29 0.00 41.41 1.73
3567 9949 9.268268 GTAGGTAACAAAGCTGCATATGTATTA 57.732 33.333 4.29 0.00 38.12 0.98
3568 9950 7.228706 GGTAGGTAACAAAGCTGCATATGTATT 59.771 37.037 4.29 0.00 39.78 1.89
3569 9951 6.710744 GGTAGGTAACAAAGCTGCATATGTAT 59.289 38.462 4.29 0.00 39.78 2.29
3570 9952 6.053005 GGTAGGTAACAAAGCTGCATATGTA 58.947 40.000 4.29 0.00 39.78 2.29
3574 9956 4.561500 TGGTAGGTAACAAAGCTGCATA 57.438 40.909 1.02 0.00 39.78 3.14
3756 10138 2.570302 ACTTCCGTTGTAATACAGGGCT 59.430 45.455 7.46 0.00 0.00 5.19
3757 10139 2.981898 ACTTCCGTTGTAATACAGGGC 58.018 47.619 7.46 0.00 0.00 5.19
3897 10327 2.559381 AGGGATCAGACTTGCTAGGT 57.441 50.000 0.00 0.00 0.00 3.08
3898 10328 3.054802 ACAAAGGGATCAGACTTGCTAGG 60.055 47.826 0.00 0.00 0.00 3.02
3899 10329 3.937706 CACAAAGGGATCAGACTTGCTAG 59.062 47.826 0.00 0.00 0.00 3.42
3900 10330 3.582647 TCACAAAGGGATCAGACTTGCTA 59.417 43.478 0.00 0.00 0.00 3.49
3902 10332 2.746362 CTCACAAAGGGATCAGACTTGC 59.254 50.000 0.00 0.00 0.00 4.01
3903 10333 4.013267 ACTCACAAAGGGATCAGACTTG 57.987 45.455 0.00 0.00 0.00 3.16
3904 10334 4.713792 AACTCACAAAGGGATCAGACTT 57.286 40.909 0.00 0.00 0.00 3.01
3905 10335 4.505742 GGAAACTCACAAAGGGATCAGACT 60.506 45.833 0.00 0.00 0.00 3.24
3906 10336 3.753797 GGAAACTCACAAAGGGATCAGAC 59.246 47.826 0.00 0.00 0.00 3.51
3907 10337 3.394274 TGGAAACTCACAAAGGGATCAGA 59.606 43.478 0.00 0.00 0.00 3.27
3908 10338 3.754965 TGGAAACTCACAAAGGGATCAG 58.245 45.455 0.00 0.00 0.00 2.90
3909 10339 3.874383 TGGAAACTCACAAAGGGATCA 57.126 42.857 0.00 0.00 0.00 2.92
4020 10450 2.280797 TTCCAGCACTGACACCGC 60.281 61.111 0.00 0.00 0.00 5.68
4267 10697 4.202223 ACGTACATCAAGTTTGACAGGAGT 60.202 41.667 0.00 0.00 40.49 3.85
4268 10698 4.307432 ACGTACATCAAGTTTGACAGGAG 58.693 43.478 0.00 0.00 40.49 3.69
4438 10868 1.071699 AGGAGCAAGTTTGGCGAAGTA 59.928 47.619 0.00 0.00 36.08 2.24


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

AutoCloner maintained by Alex Coulton.