Multiple sequence alignment - TraesCS2A01G248000

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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 TraesCS2A01G248000 chr2A 100.000 4699 0 0 1 4699 369205424 369200726 0.000000e+00 8678.0
1 TraesCS2A01G248000 chr2A 99.414 1024 6 0 1820 2843 187960405 187959382 0.000000e+00 1858.0
2 TraesCS2A01G248000 chr2A 82.188 1033 107 40 1524 2517 754350249 754351243 0.000000e+00 817.0
3 TraesCS2A01G248000 chr2A 99.628 269 0 1 1524 1792 187960672 187960405 1.520000e-134 490.0
4 TraesCS2A01G248000 chr2A 88.670 203 12 6 687 878 65173882 65173680 2.190000e-58 237.0
5 TraesCS2A01G248000 chr2A 87.879 198 13 5 3863 4050 65173478 65173674 6.120000e-54 222.0
6 TraesCS2A01G248000 chr2A 95.122 123 6 0 3486 3608 65092671 65092793 1.330000e-45 195.0
7 TraesCS2A01G248000 chr6B 95.188 1330 32 8 1524 2839 559406767 559408078 0.000000e+00 2073.0
8 TraesCS2A01G248000 chr6B 92.537 134 9 1 2413 2545 37065448 37065315 1.730000e-44 191.0
9 TraesCS2A01G248000 chr4A 87.407 1342 111 29 1525 2843 105027347 105026041 0.000000e+00 1489.0
10 TraesCS2A01G248000 chr7A 88.702 1071 79 21 1794 2843 26168681 26169730 0.000000e+00 1269.0
11 TraesCS2A01G248000 chr7A 82.779 842 91 32 1778 2582 722522600 722523424 0.000000e+00 702.0
12 TraesCS2A01G248000 chr7A 88.312 231 15 6 1525 1747 722522383 722522609 2.790000e-67 267.0
13 TraesCS2A01G248000 chr7A 85.659 258 29 6 2591 2843 722523471 722523725 1.000000e-66 265.0
14 TraesCS2A01G248000 chr7D 87.605 831 67 16 1524 2344 378895854 378895050 0.000000e+00 931.0
15 TraesCS2A01G248000 chr7D 86.272 692 90 3 1 687 61143047 61143738 0.000000e+00 747.0
16 TraesCS2A01G248000 chr7D 90.397 479 33 3 2379 2845 378893208 378892731 6.680000e-173 617.0
17 TraesCS2A01G248000 chr7B 96.462 537 16 3 2301 2834 538426821 538427357 0.000000e+00 883.0
18 TraesCS2A01G248000 chr7B 82.280 1044 109 40 1526 2531 667200893 667199888 0.000000e+00 833.0
19 TraesCS2A01G248000 chr7B 96.552 406 13 1 1905 2310 538421344 538421748 0.000000e+00 671.0
20 TraesCS2A01G248000 chr7B 84.081 691 102 8 3 687 417555035 417555723 0.000000e+00 660.0
21 TraesCS2A01G248000 chr7B 96.401 389 9 4 1525 1912 538420031 538420415 1.840000e-178 636.0
22 TraesCS2A01G248000 chr7B 86.444 509 59 9 181 682 201436758 201436253 2.470000e-152 549.0
23 TraesCS2A01G248000 chr2D 90.909 649 53 4 4051 4698 296697450 296696807 0.000000e+00 867.0
24 TraesCS2A01G248000 chr2D 90.798 652 21 3 2844 3456 296704737 296705388 0.000000e+00 835.0
25 TraesCS2A01G248000 chr2D 87.848 683 79 2 3 681 25073672 25074354 0.000000e+00 798.0
26 TraesCS2A01G248000 chr2D 89.610 616 62 2 3 616 19388268 19388883 0.000000e+00 782.0
27 TraesCS2A01G248000 chr2D 87.858 593 69 3 3 593 625461055 625461646 0.000000e+00 693.0
28 TraesCS2A01G248000 chr2D 81.042 691 122 9 4 687 343719295 343718607 4.140000e-150 542.0
29 TraesCS2A01G248000 chr2D 94.576 295 11 3 3469 3761 296705366 296705657 7.170000e-123 451.0
30 TraesCS2A01G248000 chr2D 92.701 274 15 2 3781 4050 296708775 296709047 1.590000e-104 390.0
31 TraesCS2A01G248000 chr2D 97.674 215 5 0 1219 1433 296699401 296699615 2.070000e-98 370.0
32 TraesCS2A01G248000 chr2D 93.333 195 10 1 687 878 296709247 296709053 7.700000e-73 285.0
33 TraesCS2A01G248000 chr2D 96.970 132 4 0 875 1006 296697438 296697569 6.120000e-54 222.0
34 TraesCS2A01G248000 chr2D 86.339 183 13 7 687 857 63554550 63554368 6.210000e-44 189.0
35 TraesCS2A01G248000 chr2D 93.913 115 7 0 3932 4046 63554210 63554324 1.740000e-39 174.0
36 TraesCS2A01G248000 chr2D 96.774 93 3 0 1432 1524 296704652 296704744 6.300000e-34 156.0
37 TraesCS2A01G248000 chr2D 94.048 84 4 1 1137 1220 296697566 296697648 4.940000e-25 126.0
38 TraesCS2A01G248000 chr5D 91.479 622 37 8 916 1524 371634451 371633833 0.000000e+00 841.0
39 TraesCS2A01G248000 chr5D 88.496 565 41 11 2843 3399 371633841 371633293 0.000000e+00 662.0
40 TraesCS2A01G248000 chr5B 90.214 654 44 10 890 1524 441528045 441527393 0.000000e+00 835.0
41 TraesCS2A01G248000 chr5B 87.084 511 36 10 2885 3395 441527377 441526897 6.870000e-153 551.0
42 TraesCS2A01G248000 chr5B 77.105 974 152 49 1523 2467 224572810 224573741 9.080000e-137 497.0
43 TraesCS2A01G248000 chr5B 83.448 145 20 2 547 687 701514435 701514579 1.060000e-26 132.0
44 TraesCS2A01G248000 chr5B 78.512 121 24 2 3029 3148 604290364 604290245 1.400000e-10 78.7
45 TraesCS2A01G248000 chr1B 81.155 1056 135 38 1525 2544 479074363 479075390 0.000000e+00 789.0
46 TraesCS2A01G248000 chr1B 86.183 579 79 1 3 580 174785102 174784524 3.990000e-175 625.0
47 TraesCS2A01G248000 chr6D 89.159 535 50 6 1869 2400 284081918 284082447 0.000000e+00 660.0
48 TraesCS2A01G248000 chr6D 88.493 365 31 8 1522 1881 284074419 284074777 9.340000e-117 431.0
49 TraesCS2A01G248000 chr3A 83.196 607 89 12 86 685 16112115 16111515 1.150000e-150 544.0
50 TraesCS2A01G248000 chr1A 78.261 690 131 14 4 690 497749167 497748494 4.350000e-115 425.0
51 TraesCS2A01G248000 chr2B 91.667 264 14 2 3791 4050 364949926 364949667 4.470000e-95 359.0
52 TraesCS2A01G248000 chr2B 92.672 232 12 3 3469 3698 364954951 364954723 3.510000e-86 329.0
53 TraesCS2A01G248000 chr2B 93.069 202 13 1 2975 3176 364961906 364961706 1.280000e-75 294.0
54 TraesCS2A01G248000 chr2B 86.905 252 27 5 2610 2856 113759791 113759541 1.290000e-70 278.0
55 TraesCS2A01G248000 chr2B 85.603 257 33 3 2589 2842 66960847 66961102 2.790000e-67 267.0
56 TraesCS2A01G248000 chr2B 91.795 195 11 2 687 878 364949469 364949661 2.790000e-67 267.0
57 TraesCS2A01G248000 chr2B 82.979 235 33 7 2134 2364 792125261 792125030 6.160000e-49 206.0
58 TraesCS2A01G248000 chr2B 92.958 71 5 0 3691 3761 364954706 364954636 2.310000e-18 104.0
59 TraesCS2A01G248000 chr4B 75.098 510 79 27 2102 2590 253656093 253655611 1.330000e-45 195.0
60 TraesCS2A01G248000 chr5A 87.421 159 15 3 2413 2566 577826047 577825889 1.340000e-40 178.0
61 TraesCS2A01G248000 chr5A 78.571 126 25 2 3024 3148 611834012 611833888 1.080000e-11 82.4


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 TraesCS2A01G248000 chr2A 369200726 369205424 4698 True 8678.000000 8678 100.000000 1 4699 1 chr2A.!!$R2 4698
1 TraesCS2A01G248000 chr2A 187959382 187960672 1290 True 1174.000000 1858 99.521000 1524 2843 2 chr2A.!!$R3 1319
2 TraesCS2A01G248000 chr2A 754350249 754351243 994 False 817.000000 817 82.188000 1524 2517 1 chr2A.!!$F3 993
3 TraesCS2A01G248000 chr6B 559406767 559408078 1311 False 2073.000000 2073 95.188000 1524 2839 1 chr6B.!!$F1 1315
4 TraesCS2A01G248000 chr4A 105026041 105027347 1306 True 1489.000000 1489 87.407000 1525 2843 1 chr4A.!!$R1 1318
5 TraesCS2A01G248000 chr7A 26168681 26169730 1049 False 1269.000000 1269 88.702000 1794 2843 1 chr7A.!!$F1 1049
6 TraesCS2A01G248000 chr7A 722522383 722523725 1342 False 411.333333 702 85.583333 1525 2843 3 chr7A.!!$F2 1318
7 TraesCS2A01G248000 chr7D 378892731 378895854 3123 True 774.000000 931 89.001000 1524 2845 2 chr7D.!!$R1 1321
8 TraesCS2A01G248000 chr7D 61143047 61143738 691 False 747.000000 747 86.272000 1 687 1 chr7D.!!$F1 686
9 TraesCS2A01G248000 chr7B 538426821 538427357 536 False 883.000000 883 96.462000 2301 2834 1 chr7B.!!$F2 533
10 TraesCS2A01G248000 chr7B 667199888 667200893 1005 True 833.000000 833 82.280000 1526 2531 1 chr7B.!!$R2 1005
11 TraesCS2A01G248000 chr7B 417555035 417555723 688 False 660.000000 660 84.081000 3 687 1 chr7B.!!$F1 684
12 TraesCS2A01G248000 chr7B 538420031 538421748 1717 False 653.500000 671 96.476500 1525 2310 2 chr7B.!!$F3 785
13 TraesCS2A01G248000 chr7B 201436253 201436758 505 True 549.000000 549 86.444000 181 682 1 chr7B.!!$R1 501
14 TraesCS2A01G248000 chr2D 296696807 296697450 643 True 867.000000 867 90.909000 4051 4698 1 chr2D.!!$R2 647
15 TraesCS2A01G248000 chr2D 25073672 25074354 682 False 798.000000 798 87.848000 3 681 1 chr2D.!!$F2 678
16 TraesCS2A01G248000 chr2D 19388268 19388883 615 False 782.000000 782 89.610000 3 616 1 chr2D.!!$F1 613
17 TraesCS2A01G248000 chr2D 625461055 625461646 591 False 693.000000 693 87.858000 3 593 1 chr2D.!!$F4 590
18 TraesCS2A01G248000 chr2D 343718607 343719295 688 True 542.000000 542 81.042000 4 687 1 chr2D.!!$R4 683
19 TraesCS2A01G248000 chr2D 296704652 296709047 4395 False 458.000000 835 93.712250 1432 4050 4 chr2D.!!$F6 2618
20 TraesCS2A01G248000 chr2D 296697438 296699615 2177 False 239.333333 370 96.230667 875 1433 3 chr2D.!!$F5 558
21 TraesCS2A01G248000 chr5D 371633293 371634451 1158 True 751.500000 841 89.987500 916 3399 2 chr5D.!!$R1 2483
22 TraesCS2A01G248000 chr5B 441526897 441528045 1148 True 693.000000 835 88.649000 890 3395 2 chr5B.!!$R2 2505
23 TraesCS2A01G248000 chr5B 224572810 224573741 931 False 497.000000 497 77.105000 1523 2467 1 chr5B.!!$F1 944
24 TraesCS2A01G248000 chr1B 479074363 479075390 1027 False 789.000000 789 81.155000 1525 2544 1 chr1B.!!$F1 1019
25 TraesCS2A01G248000 chr1B 174784524 174785102 578 True 625.000000 625 86.183000 3 580 1 chr1B.!!$R1 577
26 TraesCS2A01G248000 chr6D 284081918 284082447 529 False 660.000000 660 89.159000 1869 2400 1 chr6D.!!$F2 531
27 TraesCS2A01G248000 chr3A 16111515 16112115 600 True 544.000000 544 83.196000 86 685 1 chr3A.!!$R1 599
28 TraesCS2A01G248000 chr1A 497748494 497749167 673 True 425.000000 425 78.261000 4 690 1 chr1A.!!$R1 686

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
873 881 0.031449 GGAGCTAGCACTGGATCGAC 59.969 60.000 18.83 0.0 0.00 4.20 F
1027 1036 0.475906 GGAGGCCCACATATGCTCTT 59.524 55.000 0.00 0.0 0.00 2.85 F
1050 1065 0.801872 TCATCAATTCGCAACCACCG 59.198 50.000 0.00 0.0 0.00 4.94 F
1874 3712 1.364721 TGGATTTATGTGGACGCGTG 58.635 50.000 20.70 0.0 0.00 5.34 F
3269 7966 6.151312 ACTCAGTCTTTCTCTGACGCTATTAA 59.849 38.462 0.00 0.0 39.24 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 3712 1.599797 GGGGCGTATGGTGTATGGC 60.600 63.158 0.00 0.0 0.00 4.40 R
2893 7569 1.218316 GCGGGACCGACTTCTTGAT 59.782 57.895 15.99 0.0 42.83 2.57 R
2973 7649 1.365999 CGTGTACTCCACAGCCACA 59.634 57.895 0.00 0.0 44.78 4.17 R
3218 7894 0.107993 ACAGATACATGCACGCTGCT 60.108 50.000 10.54 0.0 45.31 4.24 R
4307 12130 0.183731 TCATCGGAGCTCTCAGGCTA 59.816 55.000 14.64 0.0 43.20 3.93 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
69 70 0.967887 CTCGGGCTCCTCTGAAGTGA 60.968 60.000 0.00 0.00 0.00 3.41
99 100 3.266772 TCACCTGGTTGGCTATGAGAAAT 59.733 43.478 0.00 0.00 40.22 2.17
102 103 4.141390 ACCTGGTTGGCTATGAGAAATAGG 60.141 45.833 0.00 0.00 40.22 2.57
145 146 3.450115 GTCGCAGCCTCCCGTACT 61.450 66.667 0.00 0.00 0.00 2.73
152 153 0.178958 AGCCTCCCGTACTAGGATGG 60.179 60.000 6.18 6.18 34.58 3.51
176 177 0.393077 CCGTTCTGTGACCAGGAAGT 59.607 55.000 0.00 0.00 39.31 3.01
196 197 8.105829 AGGAAGTTGAAACTATTGATCACATCT 58.894 33.333 0.00 0.00 38.57 2.90
203 204 9.676861 TGAAACTATTGATCACATCTTTCTGAT 57.323 29.630 0.00 0.00 35.40 2.90
272 273 4.740822 GCCGCAGTGGTCCCCAAT 62.741 66.667 0.89 0.00 41.21 3.16
350 351 1.895020 ATGGAGTTACGGGCGCTTCA 61.895 55.000 7.64 0.00 0.00 3.02
502 504 1.510480 GGCGAAGTGGATAGCATGCC 61.510 60.000 15.66 0.00 0.00 4.40
541 543 3.272818 TGGGTAGGTAGTGAGTAATCCCA 59.727 47.826 0.00 0.00 39.81 4.37
620 624 6.702723 TGTAGCGTTTAACACTCTGTAACATT 59.297 34.615 0.00 0.00 0.00 2.71
626 630 7.480542 CGTTTAACACTCTGTAACATTAATGGC 59.519 37.037 19.37 9.61 0.00 4.40
632 636 4.580868 TCTGTAACATTAATGGCGGTTGA 58.419 39.130 19.37 7.59 0.00 3.18
690 698 2.512885 TCGTGCGTATTCGAGAAGAAC 58.487 47.619 0.00 0.00 42.39 3.01
691 699 2.161012 TCGTGCGTATTCGAGAAGAACT 59.839 45.455 0.00 0.00 42.39 3.01
692 700 2.915463 CGTGCGTATTCGAGAAGAACTT 59.085 45.455 0.00 0.00 42.39 2.66
693 701 3.241364 CGTGCGTATTCGAGAAGAACTTG 60.241 47.826 0.00 0.00 42.39 3.16
694 702 3.060895 GTGCGTATTCGAGAAGAACTTGG 59.939 47.826 0.00 0.00 42.39 3.61
695 703 3.057104 TGCGTATTCGAGAAGAACTTGGA 60.057 43.478 0.00 0.00 42.39 3.53
696 704 3.548268 GCGTATTCGAGAAGAACTTGGAG 59.452 47.826 0.00 0.00 42.39 3.86
697 705 4.734917 CGTATTCGAGAAGAACTTGGAGT 58.265 43.478 0.00 0.00 42.39 3.85
698 706 5.675575 GCGTATTCGAGAAGAACTTGGAGTA 60.676 44.000 0.00 0.00 42.39 2.59
699 707 5.966503 CGTATTCGAGAAGAACTTGGAGTAG 59.033 44.000 0.00 0.00 42.39 2.57
700 708 4.785511 TTCGAGAAGAACTTGGAGTAGG 57.214 45.455 0.00 0.00 33.14 3.18
701 709 2.492484 TCGAGAAGAACTTGGAGTAGGC 59.508 50.000 0.00 0.00 0.00 3.93
702 710 2.417515 CGAGAAGAACTTGGAGTAGGCC 60.418 54.545 0.00 0.00 0.00 5.19
703 711 2.567615 GAGAAGAACTTGGAGTAGGCCA 59.432 50.000 5.01 0.00 35.78 5.36
704 712 3.185455 AGAAGAACTTGGAGTAGGCCAT 58.815 45.455 5.01 0.00 37.86 4.40
705 713 3.054802 AGAAGAACTTGGAGTAGGCCATG 60.055 47.826 5.01 0.00 37.86 3.66
706 714 2.269940 AGAACTTGGAGTAGGCCATGT 58.730 47.619 5.01 0.00 45.15 3.21
707 715 2.026822 AGAACTTGGAGTAGGCCATGTG 60.027 50.000 5.01 0.00 43.21 3.21
708 716 0.035056 ACTTGGAGTAGGCCATGTGC 60.035 55.000 5.01 0.00 42.63 4.57
709 717 0.254178 CTTGGAGTAGGCCATGTGCT 59.746 55.000 5.01 0.00 40.92 4.40
710 718 0.035152 TTGGAGTAGGCCATGTGCTG 60.035 55.000 5.01 0.00 40.92 4.41
756 764 3.764049 GCCAGTGACGCGAACGAC 61.764 66.667 15.93 3.02 43.93 4.34
757 765 2.354188 CCAGTGACGCGAACGACA 60.354 61.111 15.93 1.60 43.93 4.35
761 769 2.656007 TGACGCGAACGACACCAC 60.656 61.111 15.93 0.00 43.93 4.16
762 770 3.400590 GACGCGAACGACACCACC 61.401 66.667 15.93 0.00 43.93 4.61
764 772 4.986587 CGCGAACGACACCACCGA 62.987 66.667 0.00 0.00 43.93 4.69
765 773 3.400590 GCGAACGACACCACCGAC 61.401 66.667 0.00 0.00 0.00 4.79
766 774 2.026445 CGAACGACACCACCGACA 59.974 61.111 0.00 0.00 0.00 4.35
767 775 1.372499 CGAACGACACCACCGACAT 60.372 57.895 0.00 0.00 0.00 3.06
768 776 1.342082 CGAACGACACCACCGACATC 61.342 60.000 0.00 0.00 0.00 3.06
769 777 1.342082 GAACGACACCACCGACATCG 61.342 60.000 0.00 0.00 38.71 3.84
770 778 3.179265 CGACACCACCGACATCGC 61.179 66.667 0.00 0.00 38.18 4.58
771 779 2.813908 GACACCACCGACATCGCC 60.814 66.667 0.00 0.00 38.18 5.54
772 780 4.735132 ACACCACCGACATCGCCG 62.735 66.667 0.00 0.00 38.18 6.46
773 781 4.735132 CACCACCGACATCGCCGT 62.735 66.667 0.00 0.00 38.18 5.68
774 782 4.430765 ACCACCGACATCGCCGTC 62.431 66.667 0.00 0.00 38.18 4.79
775 783 4.429212 CCACCGACATCGCCGTCA 62.429 66.667 0.00 0.00 35.54 4.35
776 784 3.179265 CACCGACATCGCCGTCAC 61.179 66.667 0.00 0.00 35.54 3.67
777 785 4.771356 ACCGACATCGCCGTCACG 62.771 66.667 0.00 0.00 35.54 4.35
815 823 4.735132 GTACAGCAGCGACGGCCA 62.735 66.667 2.24 0.00 41.24 5.36
816 824 4.735132 TACAGCAGCGACGGCCAC 62.735 66.667 2.24 0.00 41.24 5.01
821 829 2.887568 CAGCGACGGCCACATCTC 60.888 66.667 2.24 0.00 41.24 2.75
822 830 3.071206 AGCGACGGCCACATCTCT 61.071 61.111 2.24 0.00 41.24 3.10
823 831 2.583593 GCGACGGCCACATCTCTC 60.584 66.667 2.24 0.00 0.00 3.20
824 832 3.069980 GCGACGGCCACATCTCTCT 62.070 63.158 2.24 0.00 0.00 3.10
825 833 1.064946 CGACGGCCACATCTCTCTC 59.935 63.158 2.24 0.00 0.00 3.20
826 834 1.380403 CGACGGCCACATCTCTCTCT 61.380 60.000 2.24 0.00 0.00 3.10
827 835 0.383949 GACGGCCACATCTCTCTCTC 59.616 60.000 2.24 0.00 0.00 3.20
828 836 0.033601 ACGGCCACATCTCTCTCTCT 60.034 55.000 2.24 0.00 0.00 3.10
829 837 0.667993 CGGCCACATCTCTCTCTCTC 59.332 60.000 2.24 0.00 0.00 3.20
830 838 1.750332 CGGCCACATCTCTCTCTCTCT 60.750 57.143 2.24 0.00 0.00 3.10
831 839 1.956477 GGCCACATCTCTCTCTCTCTC 59.044 57.143 0.00 0.00 0.00 3.20
832 840 2.423373 GGCCACATCTCTCTCTCTCTCT 60.423 54.545 0.00 0.00 0.00 3.10
833 841 3.290710 GCCACATCTCTCTCTCTCTCTT 58.709 50.000 0.00 0.00 0.00 2.85
834 842 3.067180 GCCACATCTCTCTCTCTCTCTTG 59.933 52.174 0.00 0.00 0.00 3.02
835 843 4.272489 CCACATCTCTCTCTCTCTCTTGT 58.728 47.826 0.00 0.00 0.00 3.16
836 844 4.336433 CCACATCTCTCTCTCTCTCTTGTC 59.664 50.000 0.00 0.00 0.00 3.18
837 845 4.336433 CACATCTCTCTCTCTCTCTTGTCC 59.664 50.000 0.00 0.00 0.00 4.02
838 846 4.018506 ACATCTCTCTCTCTCTCTTGTCCA 60.019 45.833 0.00 0.00 0.00 4.02
839 847 3.950397 TCTCTCTCTCTCTCTTGTCCAC 58.050 50.000 0.00 0.00 0.00 4.02
840 848 3.587061 TCTCTCTCTCTCTCTTGTCCACT 59.413 47.826 0.00 0.00 0.00 4.00
841 849 4.042809 TCTCTCTCTCTCTCTTGTCCACTT 59.957 45.833 0.00 0.00 0.00 3.16
842 850 4.078537 TCTCTCTCTCTCTTGTCCACTTG 58.921 47.826 0.00 0.00 0.00 3.16
843 851 3.161067 TCTCTCTCTCTTGTCCACTTGG 58.839 50.000 0.00 0.00 0.00 3.61
844 852 1.620819 TCTCTCTCTTGTCCACTTGGC 59.379 52.381 0.00 0.00 34.44 4.52
845 853 0.687354 TCTCTCTTGTCCACTTGGCC 59.313 55.000 0.00 0.00 34.44 5.36
846 854 0.689623 CTCTCTTGTCCACTTGGCCT 59.310 55.000 3.32 0.00 34.44 5.19
847 855 1.072965 CTCTCTTGTCCACTTGGCCTT 59.927 52.381 3.32 0.00 34.44 4.35
848 856 1.202806 TCTCTTGTCCACTTGGCCTTG 60.203 52.381 3.32 0.00 34.44 3.61
849 857 0.178992 TCTTGTCCACTTGGCCTTGG 60.179 55.000 3.32 8.38 34.44 3.61
850 858 0.468029 CTTGTCCACTTGGCCTTGGT 60.468 55.000 15.68 4.59 34.19 3.67
851 859 0.754957 TTGTCCACTTGGCCTTGGTG 60.755 55.000 15.68 14.64 34.19 4.17
852 860 1.152756 GTCCACTTGGCCTTGGTGT 60.153 57.895 15.68 0.71 34.19 4.16
853 861 0.109723 GTCCACTTGGCCTTGGTGTA 59.890 55.000 15.68 2.38 34.19 2.90
854 862 0.400213 TCCACTTGGCCTTGGTGTAG 59.600 55.000 15.68 6.07 34.19 2.74
855 863 0.609131 CCACTTGGCCTTGGTGTAGG 60.609 60.000 3.32 0.00 38.40 3.18
856 864 0.400213 CACTTGGCCTTGGTGTAGGA 59.600 55.000 3.32 0.00 37.50 2.94
857 865 0.693049 ACTTGGCCTTGGTGTAGGAG 59.307 55.000 3.32 0.00 37.50 3.69
858 866 0.678048 CTTGGCCTTGGTGTAGGAGC 60.678 60.000 3.32 0.00 37.50 4.70
859 867 1.133809 TTGGCCTTGGTGTAGGAGCT 61.134 55.000 3.32 0.00 37.50 4.09
860 868 0.252513 TGGCCTTGGTGTAGGAGCTA 60.253 55.000 3.32 0.00 37.50 3.32
861 869 0.466124 GGCCTTGGTGTAGGAGCTAG 59.534 60.000 0.00 0.00 37.50 3.42
862 870 0.179070 GCCTTGGTGTAGGAGCTAGC 60.179 60.000 6.62 6.62 37.50 3.42
863 871 1.195115 CCTTGGTGTAGGAGCTAGCA 58.805 55.000 18.83 0.00 37.50 3.49
864 872 1.134670 CCTTGGTGTAGGAGCTAGCAC 60.135 57.143 18.83 11.05 37.50 4.40
865 873 1.827969 CTTGGTGTAGGAGCTAGCACT 59.172 52.381 18.83 16.64 32.90 4.40
866 874 1.186200 TGGTGTAGGAGCTAGCACTG 58.814 55.000 18.83 0.00 32.90 3.66
867 875 0.461961 GGTGTAGGAGCTAGCACTGG 59.538 60.000 18.83 0.00 32.90 4.00
868 876 1.475403 GTGTAGGAGCTAGCACTGGA 58.525 55.000 18.83 3.14 0.00 3.86
869 877 2.035632 GTGTAGGAGCTAGCACTGGAT 58.964 52.381 18.83 0.00 0.00 3.41
870 878 2.035321 GTGTAGGAGCTAGCACTGGATC 59.965 54.545 18.83 4.03 0.00 3.36
871 879 1.268352 GTAGGAGCTAGCACTGGATCG 59.732 57.143 18.83 0.00 0.00 3.69
872 880 0.106469 AGGAGCTAGCACTGGATCGA 60.106 55.000 18.83 0.00 0.00 3.59
873 881 0.031449 GGAGCTAGCACTGGATCGAC 59.969 60.000 18.83 0.00 0.00 4.20
874 882 0.031449 GAGCTAGCACTGGATCGACC 59.969 60.000 18.83 0.00 39.54 4.79
875 883 1.068250 GCTAGCACTGGATCGACCC 59.932 63.158 10.63 0.00 38.00 4.46
876 884 1.395826 GCTAGCACTGGATCGACCCT 61.396 60.000 10.63 0.00 38.00 4.34
877 885 1.115467 CTAGCACTGGATCGACCCTT 58.885 55.000 0.00 0.00 38.00 3.95
1027 1036 0.475906 GGAGGCCCACATATGCTCTT 59.524 55.000 0.00 0.00 0.00 2.85
1028 1037 1.602311 GAGGCCCACATATGCTCTTG 58.398 55.000 0.00 0.00 0.00 3.02
1029 1038 1.141657 GAGGCCCACATATGCTCTTGA 59.858 52.381 0.00 0.00 0.00 3.02
1030 1039 1.133976 AGGCCCACATATGCTCTTGAC 60.134 52.381 0.00 0.00 0.00 3.18
1031 1040 1.133976 GGCCCACATATGCTCTTGACT 60.134 52.381 1.58 0.00 0.00 3.41
1032 1041 2.216898 GCCCACATATGCTCTTGACTC 58.783 52.381 1.58 0.00 0.00 3.36
1033 1042 2.420547 GCCCACATATGCTCTTGACTCA 60.421 50.000 1.58 0.00 0.00 3.41
1034 1043 3.746751 GCCCACATATGCTCTTGACTCAT 60.747 47.826 1.58 0.00 0.00 2.90
1050 1065 0.801872 TCATCAATTCGCAACCACCG 59.198 50.000 0.00 0.00 0.00 4.94
1061 1076 3.236003 AACCACCGCTTCGACCTCC 62.236 63.158 0.00 0.00 0.00 4.30
1208 1223 2.125512 AATGCGGCGGAGACAGAC 60.126 61.111 9.78 0.00 27.25 3.51
1331 3100 4.443266 GCTCTCCTGGAAGCGCGT 62.443 66.667 8.43 0.00 0.00 6.01
1433 3202 2.356780 CGGTTACCTCGCCCTCCTT 61.357 63.158 0.00 0.00 0.00 3.36
1874 3712 1.364721 TGGATTTATGTGGACGCGTG 58.635 50.000 20.70 0.00 0.00 5.34
3269 7966 6.151312 ACTCAGTCTTTCTCTGACGCTATTAA 59.849 38.462 0.00 0.00 39.24 1.40
3420 8139 2.872245 TCTTTGAGTGGCAGTTTTCTCG 59.128 45.455 0.00 0.00 0.00 4.04
3456 8175 2.164624 CGAACGTTCCCTGAATCTCTCT 59.835 50.000 22.07 0.00 0.00 3.10
3457 8176 3.732471 CGAACGTTCCCTGAATCTCTCTC 60.732 52.174 22.07 0.00 0.00 3.20
3458 8177 3.094484 ACGTTCCCTGAATCTCTCTCT 57.906 47.619 0.00 0.00 0.00 3.10
3459 8178 3.020984 ACGTTCCCTGAATCTCTCTCTC 58.979 50.000 0.00 0.00 0.00 3.20
3460 8179 3.287222 CGTTCCCTGAATCTCTCTCTCT 58.713 50.000 0.00 0.00 0.00 3.10
3461 8180 3.699038 CGTTCCCTGAATCTCTCTCTCTT 59.301 47.826 0.00 0.00 0.00 2.85
3462 8181 4.159506 CGTTCCCTGAATCTCTCTCTCTTT 59.840 45.833 0.00 0.00 0.00 2.52
3463 8182 5.337169 CGTTCCCTGAATCTCTCTCTCTTTT 60.337 44.000 0.00 0.00 0.00 2.27
3464 8183 6.472016 GTTCCCTGAATCTCTCTCTCTTTTT 58.528 40.000 0.00 0.00 0.00 1.94
3482 8201 3.312736 TTTTCTGGCAGAAAGTTCCCT 57.687 42.857 33.73 0.00 44.14 4.20
3483 8202 2.276732 TTCTGGCAGAAAGTTCCCTG 57.723 50.000 26.78 0.00 29.99 4.45
3484 8203 1.140312 TCTGGCAGAAAGTTCCCTGT 58.860 50.000 16.28 0.00 33.19 4.00
3485 8204 2.334977 TCTGGCAGAAAGTTCCCTGTA 58.665 47.619 16.28 0.00 33.19 2.74
3486 8205 2.912956 TCTGGCAGAAAGTTCCCTGTAT 59.087 45.455 16.28 0.00 33.19 2.29
3487 8206 3.055094 TCTGGCAGAAAGTTCCCTGTATC 60.055 47.826 16.28 0.00 33.19 2.24
3488 8207 2.642311 TGGCAGAAAGTTCCCTGTATCA 59.358 45.455 6.97 2.54 33.19 2.15
3489 8208 3.010420 GGCAGAAAGTTCCCTGTATCAC 58.990 50.000 6.97 0.00 33.19 3.06
3490 8209 3.307762 GGCAGAAAGTTCCCTGTATCACT 60.308 47.826 6.97 0.00 33.19 3.41
3491 8210 3.935828 GCAGAAAGTTCCCTGTATCACTC 59.064 47.826 6.97 0.00 33.19 3.51
3663 8382 4.437682 TTTCCTTCAGAACATCAGGTGT 57.562 40.909 0.00 0.00 44.84 4.16
3681 8402 0.249911 GTCCACTGACCAGACCACAC 60.250 60.000 3.76 0.00 35.34 3.82
3705 8426 4.150098 GCTCTTTTCATGACGTAACGAACT 59.850 41.667 0.00 0.00 0.00 3.01
3725 8446 1.955778 TCTCCTTGCATGTTGGTTGTG 59.044 47.619 0.00 0.00 0.00 3.33
3734 8455 3.491447 GCATGTTGGTTGTGAAGCTTTCT 60.491 43.478 0.00 0.00 0.00 2.52
3761 8482 6.070995 TCACGGAAGGATGTACTAACAAGAAT 60.071 38.462 0.00 0.00 39.58 2.40
3762 8483 6.036083 CACGGAAGGATGTACTAACAAGAATG 59.964 42.308 0.00 0.00 39.58 2.67
3766 8487 7.492994 GGAAGGATGTACTAACAAGAATGAGAC 59.507 40.741 0.00 0.00 39.58 3.36
3768 8489 6.153000 AGGATGTACTAACAAGAATGAGACGT 59.847 38.462 0.00 0.00 39.58 4.34
3769 8490 6.472808 GGATGTACTAACAAGAATGAGACGTC 59.527 42.308 7.70 7.70 39.58 4.34
3770 8491 6.570672 TGTACTAACAAGAATGAGACGTCT 57.429 37.500 20.18 20.18 30.91 4.18
3771 8492 6.379386 TGTACTAACAAGAATGAGACGTCTG 58.621 40.000 25.58 10.11 30.91 3.51
3772 8493 5.707242 ACTAACAAGAATGAGACGTCTGA 57.293 39.130 25.58 16.64 0.00 3.27
3773 8494 6.085555 ACTAACAAGAATGAGACGTCTGAA 57.914 37.500 25.58 11.65 0.00 3.02
3774 8495 6.513180 ACTAACAAGAATGAGACGTCTGAAA 58.487 36.000 25.58 8.82 0.00 2.69
3778 11597 5.235186 ACAAGAATGAGACGTCTGAAACAAG 59.765 40.000 25.58 10.41 0.00 3.16
3779 11598 3.743396 AGAATGAGACGTCTGAAACAAGC 59.257 43.478 25.58 10.48 0.00 4.01
3796 11615 4.363990 CGTGGGCTCAGCACGTCT 62.364 66.667 0.00 0.00 32.76 4.18
3837 11656 1.270465 ACCAAAGTAGTAAGCCGCGTT 60.270 47.619 4.92 0.00 0.00 4.84
3896 11715 3.252400 CTGCCTGCAAAATTAATTCGCA 58.748 40.909 18.85 18.85 0.00 5.10
3902 11721 4.051922 TGCAAAATTAATTCGCACCGTTT 58.948 34.783 17.00 0.00 0.00 3.60
3907 11726 6.591313 AAATTAATTCGCACCGTTTGTTTT 57.409 29.167 0.10 0.00 0.00 2.43
3921 11744 1.490574 TGTTTTGGGTGGGTCAAAGG 58.509 50.000 0.00 0.00 35.81 3.11
3970 11793 3.062763 GCATCCTCCATCATAACTCACG 58.937 50.000 0.00 0.00 0.00 4.35
3973 11796 1.138859 CCTCCATCATAACTCACGCCA 59.861 52.381 0.00 0.00 0.00 5.69
3988 11811 1.302033 GCCATAGGCTCCCATGACG 60.302 63.158 0.00 0.00 46.69 4.35
4063 11886 5.940470 AGGAGATGCGCTTTAAATAATAGGG 59.060 40.000 9.73 0.00 0.00 3.53
4197 12020 7.133891 ACTATGTTCGAAAAGACATCAAAGG 57.866 36.000 0.00 0.00 0.00 3.11
4204 12027 5.466728 TCGAAAAGACATCAAAGGAGACAAG 59.533 40.000 0.00 0.00 0.00 3.16
4205 12028 5.466728 CGAAAAGACATCAAAGGAGACAAGA 59.533 40.000 0.00 0.00 0.00 3.02
4217 12040 1.694696 GAGACAAGAGAGGTGGGTTGT 59.305 52.381 0.00 0.00 35.84 3.32
4256 12079 1.202879 GGTGGAAGTGGTCATGGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
4268 12091 3.678289 TCATGGTTGACATTCCTGAGTG 58.322 45.455 0.00 0.00 37.84 3.51
4282 12105 5.921360 TCCTGAGTGGTTTGCTACAGCAC 62.921 52.174 2.75 4.99 43.39 4.40
4307 12130 0.760567 TGTGACCCACTGTCTGAGCT 60.761 55.000 0.00 0.00 44.75 4.09
4310 12133 0.174617 GACCCACTGTCTGAGCTAGC 59.825 60.000 6.62 6.62 41.03 3.42
4317 12140 1.677576 CTGTCTGAGCTAGCCTGAGAG 59.322 57.143 12.13 15.01 34.33 3.20
4323 12146 1.826054 GCTAGCCTGAGAGCTCCGA 60.826 63.158 10.93 0.00 43.67 4.55
4368 12191 3.074412 AGTGTTATCACCCTTTTCAGCG 58.926 45.455 0.18 0.00 44.83 5.18
4370 12193 3.252458 GTGTTATCACCCTTTTCAGCGTT 59.748 43.478 0.00 0.00 38.51 4.84
4410 12233 1.205966 CGGGTGGGATTGTAGGGTTA 58.794 55.000 0.00 0.00 0.00 2.85
4416 12239 4.165372 GGTGGGATTGTAGGGTTAGAATCA 59.835 45.833 6.73 0.00 39.88 2.57
4420 12243 6.159575 TGGGATTGTAGGGTTAGAATCATCAA 59.840 38.462 6.73 0.00 39.88 2.57
4426 12249 6.670464 TGTAGGGTTAGAATCATCAACTGGTA 59.330 38.462 0.00 0.00 0.00 3.25
4461 12284 7.889873 TCAACTTTAACTTGGATCCTGAAAA 57.110 32.000 14.23 10.53 0.00 2.29
4480 12303 2.925966 AGCTTCCCATCAATCCCAAA 57.074 45.000 0.00 0.00 0.00 3.28
4482 12305 3.519667 AGCTTCCCATCAATCCCAAAAA 58.480 40.909 0.00 0.00 0.00 1.94
4508 12331 4.098960 GTGTCCTCGGATATCTTGGTGTAA 59.901 45.833 2.05 0.00 0.00 2.41
4516 12340 7.220740 TCGGATATCTTGGTGTAATATTGCAA 58.779 34.615 7.88 0.00 0.00 4.08
4575 12399 7.765695 ATTAGAAGTTGTGTTGTCAATCCAT 57.234 32.000 0.00 0.00 0.00 3.41
4582 12406 7.851228 AGTTGTGTTGTCAATCCATATCTAGA 58.149 34.615 0.00 0.00 0.00 2.43
4614 12438 3.312890 AGGTGGAGATAATCTGGTCCAG 58.687 50.000 13.21 13.21 39.80 3.86
4615 12439 2.370189 GGTGGAGATAATCTGGTCCAGG 59.630 54.545 19.11 0.53 39.80 4.45
4621 12445 4.302067 AGATAATCTGGTCCAGGATGTGT 58.698 43.478 19.11 2.61 31.51 3.72
4645 12469 1.677576 TCGCATCATTTGGGATTGAGC 59.322 47.619 0.00 0.00 41.91 4.26
4648 12472 3.429822 CGCATCATTTGGGATTGAGCTTT 60.430 43.478 0.00 0.00 40.62 3.51
4668 12492 6.769341 AGCTTTCTCAATTTCAGCCAAATTTT 59.231 30.769 1.97 0.00 41.19 1.82
4669 12493 6.854381 GCTTTCTCAATTTCAGCCAAATTTTG 59.146 34.615 1.99 1.99 41.19 2.44
4685 12509 0.749818 TTTGTGCGACTTGGCCTCAA 60.750 50.000 3.32 0.00 0.00 3.02
4698 12522 6.485171 ACTTGGCCTCAACTTCAATATTACT 58.515 36.000 3.32 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.754957 CAGAGGAGCCCGAGATCACT 60.755 60.000 0.00 0.00 0.00 3.41
69 70 0.535102 CCAACCAGGTGAAGAAGCGT 60.535 55.000 0.00 0.00 0.00 5.07
99 100 1.347707 CTGTCCAAAGTCCAGCACCTA 59.652 52.381 0.00 0.00 0.00 3.08
102 103 1.202698 AGTCTGTCCAAAGTCCAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
133 134 0.178958 CCATCCTAGTACGGGAGGCT 60.179 60.000 14.20 0.00 36.21 4.58
142 143 0.689745 AACGGGCAGCCATCCTAGTA 60.690 55.000 15.19 0.00 0.00 1.82
145 146 1.689233 AGAACGGGCAGCCATCCTA 60.689 57.895 15.19 0.00 0.00 2.94
152 153 3.050275 GGTCACAGAACGGGCAGC 61.050 66.667 0.00 0.00 0.00 5.25
176 177 9.506018 TCAGAAAGATGTGATCAATAGTTTCAA 57.494 29.630 17.49 7.92 0.00 2.69
222 223 2.147150 GAGCACAGAGTTCTCCAAACC 58.853 52.381 0.00 0.00 0.00 3.27
272 273 0.404040 CTTTAGGGTGTCTTGGGCCA 59.596 55.000 0.00 0.00 0.00 5.36
324 325 0.748450 CCCGTAACTCCATCGGCTTA 59.252 55.000 0.00 0.00 42.48 3.09
332 333 1.895020 ATGAAGCGCCCGTAACTCCA 61.895 55.000 2.29 0.00 0.00 3.86
350 351 1.010917 ACTCCCAAAGCCCTAGGGTAT 59.989 52.381 28.96 15.48 43.31 2.73
502 504 0.249398 CCACCCTACCAGAAGTTCGG 59.751 60.000 10.87 10.87 0.00 4.30
541 543 1.632046 CGCCTACAAACGCGGTGATT 61.632 55.000 17.62 1.21 44.57 2.57
576 580 7.011669 ACGCTACAGTAACAACAACACTAAATT 59.988 33.333 0.00 0.00 0.00 1.82
581 585 3.788937 ACGCTACAGTAACAACAACACT 58.211 40.909 0.00 0.00 0.00 3.55
620 624 1.223487 GGAGCCTCAACCGCCATTA 59.777 57.895 0.00 0.00 0.00 1.90
626 630 3.787001 GAGGGGGAGCCTCAACCG 61.787 72.222 0.00 0.00 34.72 4.44
632 636 2.596411 ATAAAAGAGAGGGGGAGCCT 57.404 50.000 0.00 0.00 0.00 4.58
648 656 6.976349 ACGAGTGTGCGTATCATCTTTTATAA 59.024 34.615 0.00 0.00 43.61 0.98
687 695 2.359900 CACATGGCCTACTCCAAGTTC 58.640 52.381 3.32 0.00 39.96 3.01
690 698 0.254178 AGCACATGGCCTACTCCAAG 59.746 55.000 3.32 0.00 46.50 3.61
691 699 0.035152 CAGCACATGGCCTACTCCAA 60.035 55.000 3.32 0.00 46.50 3.53
692 700 1.603842 CAGCACATGGCCTACTCCA 59.396 57.895 3.32 0.00 46.50 3.86
693 701 1.153086 CCAGCACATGGCCTACTCC 60.153 63.158 3.32 0.00 43.83 3.85
694 702 4.547859 CCAGCACATGGCCTACTC 57.452 61.111 3.32 0.00 43.83 2.59
717 725 3.844090 GTGGGCCTCTCCGAGCTC 61.844 72.222 4.53 2.73 34.94 4.09
739 747 3.764049 GTCGTTCGCGTCACTGGC 61.764 66.667 5.77 0.00 42.11 4.85
740 748 2.354188 TGTCGTTCGCGTCACTGG 60.354 61.111 5.77 0.00 42.11 4.00
744 752 2.656007 GTGGTGTCGTTCGCGTCA 60.656 61.111 5.77 0.00 42.11 4.35
745 753 3.400590 GGTGGTGTCGTTCGCGTC 61.401 66.667 5.77 0.00 42.11 5.19
747 755 4.986587 TCGGTGGTGTCGTTCGCG 62.987 66.667 0.00 0.00 42.98 5.87
748 756 3.400590 GTCGGTGGTGTCGTTCGC 61.401 66.667 0.00 0.00 0.00 4.70
749 757 1.342082 GATGTCGGTGGTGTCGTTCG 61.342 60.000 0.00 0.00 0.00 3.95
750 758 1.342082 CGATGTCGGTGGTGTCGTTC 61.342 60.000 0.00 0.00 35.37 3.95
751 759 1.372499 CGATGTCGGTGGTGTCGTT 60.372 57.895 0.00 0.00 35.37 3.85
752 760 2.257371 CGATGTCGGTGGTGTCGT 59.743 61.111 0.00 0.00 35.37 4.34
753 761 3.179265 GCGATGTCGGTGGTGTCG 61.179 66.667 4.44 0.00 40.23 4.35
754 762 2.813908 GGCGATGTCGGTGGTGTC 60.814 66.667 4.44 0.00 40.23 3.67
755 763 4.735132 CGGCGATGTCGGTGGTGT 62.735 66.667 0.00 0.00 40.23 4.16
756 764 4.735132 ACGGCGATGTCGGTGGTG 62.735 66.667 16.62 0.00 40.23 4.17
757 765 4.430765 GACGGCGATGTCGGTGGT 62.431 66.667 16.62 0.00 40.23 4.16
758 766 4.429212 TGACGGCGATGTCGGTGG 62.429 66.667 16.62 0.00 41.87 4.61
759 767 3.179265 GTGACGGCGATGTCGGTG 61.179 66.667 16.62 0.00 41.87 4.94
760 768 4.771356 CGTGACGGCGATGTCGGT 62.771 66.667 16.62 0.00 41.87 4.69
761 769 4.470170 TCGTGACGGCGATGTCGG 62.470 66.667 16.62 0.00 41.87 4.79
798 806 4.735132 TGGCCGTCGCTGCTGTAC 62.735 66.667 0.00 0.00 34.44 2.90
799 807 4.735132 GTGGCCGTCGCTGCTGTA 62.735 66.667 0.00 0.00 34.44 2.74
804 812 2.887568 GAGATGTGGCCGTCGCTG 60.888 66.667 0.00 0.00 34.44 5.18
805 813 3.069980 GAGAGATGTGGCCGTCGCT 62.070 63.158 8.25 8.25 39.16 4.93
806 814 2.583593 GAGAGATGTGGCCGTCGC 60.584 66.667 0.00 0.00 0.00 5.19
807 815 1.064946 GAGAGAGATGTGGCCGTCG 59.935 63.158 0.00 0.00 0.00 5.12
808 816 0.383949 GAGAGAGAGATGTGGCCGTC 59.616 60.000 0.00 0.00 0.00 4.79
809 817 0.033601 AGAGAGAGAGATGTGGCCGT 60.034 55.000 0.00 0.00 0.00 5.68
810 818 0.667993 GAGAGAGAGAGATGTGGCCG 59.332 60.000 0.00 0.00 0.00 6.13
811 819 1.956477 GAGAGAGAGAGAGATGTGGCC 59.044 57.143 0.00 0.00 0.00 5.36
812 820 2.936202 AGAGAGAGAGAGAGATGTGGC 58.064 52.381 0.00 0.00 0.00 5.01
813 821 4.272489 ACAAGAGAGAGAGAGAGATGTGG 58.728 47.826 0.00 0.00 0.00 4.17
814 822 4.336433 GGACAAGAGAGAGAGAGAGATGTG 59.664 50.000 0.00 0.00 0.00 3.21
815 823 4.018506 TGGACAAGAGAGAGAGAGAGATGT 60.019 45.833 0.00 0.00 0.00 3.06
816 824 4.336433 GTGGACAAGAGAGAGAGAGAGATG 59.664 50.000 0.00 0.00 0.00 2.90
817 825 4.228210 AGTGGACAAGAGAGAGAGAGAGAT 59.772 45.833 0.00 0.00 0.00 2.75
818 826 3.587061 AGTGGACAAGAGAGAGAGAGAGA 59.413 47.826 0.00 0.00 0.00 3.10
819 827 3.955471 AGTGGACAAGAGAGAGAGAGAG 58.045 50.000 0.00 0.00 0.00 3.20
820 828 4.078537 CAAGTGGACAAGAGAGAGAGAGA 58.921 47.826 0.00 0.00 0.00 3.10
821 829 3.193267 CCAAGTGGACAAGAGAGAGAGAG 59.807 52.174 0.00 0.00 37.39 3.20
822 830 3.161067 CCAAGTGGACAAGAGAGAGAGA 58.839 50.000 0.00 0.00 37.39 3.10
823 831 2.353605 GCCAAGTGGACAAGAGAGAGAG 60.354 54.545 0.18 0.00 37.39 3.20
824 832 1.620819 GCCAAGTGGACAAGAGAGAGA 59.379 52.381 0.18 0.00 37.39 3.10
825 833 1.338579 GGCCAAGTGGACAAGAGAGAG 60.339 57.143 0.00 0.00 44.76 3.20
826 834 0.687354 GGCCAAGTGGACAAGAGAGA 59.313 55.000 0.00 0.00 44.76 3.10
827 835 3.239861 GGCCAAGTGGACAAGAGAG 57.760 57.895 0.00 0.00 44.76 3.20
834 842 0.109723 TACACCAAGGCCAAGTGGAC 59.890 55.000 22.95 0.00 46.16 4.02
835 843 0.400213 CTACACCAAGGCCAAGTGGA 59.600 55.000 22.95 14.32 38.36 4.02
836 844 0.609131 CCTACACCAAGGCCAAGTGG 60.609 60.000 20.00 18.30 41.00 4.00
837 845 0.400213 TCCTACACCAAGGCCAAGTG 59.600 55.000 15.86 15.86 36.51 3.16
838 846 0.693049 CTCCTACACCAAGGCCAAGT 59.307 55.000 5.01 0.00 36.51 3.16
839 847 0.678048 GCTCCTACACCAAGGCCAAG 60.678 60.000 5.01 0.00 36.51 3.61
840 848 1.133809 AGCTCCTACACCAAGGCCAA 61.134 55.000 5.01 0.00 36.51 4.52
841 849 0.252513 TAGCTCCTACACCAAGGCCA 60.253 55.000 5.01 0.00 36.51 5.36
842 850 0.466124 CTAGCTCCTACACCAAGGCC 59.534 60.000 0.00 0.00 36.51 5.19
843 851 0.179070 GCTAGCTCCTACACCAAGGC 60.179 60.000 7.70 0.00 36.51 4.35
844 852 1.134670 GTGCTAGCTCCTACACCAAGG 60.135 57.143 17.23 0.00 38.06 3.61
845 853 1.827969 AGTGCTAGCTCCTACACCAAG 59.172 52.381 17.23 0.00 33.46 3.61
846 854 1.550524 CAGTGCTAGCTCCTACACCAA 59.449 52.381 17.23 0.00 33.46 3.67
847 855 1.186200 CAGTGCTAGCTCCTACACCA 58.814 55.000 17.23 0.00 33.46 4.17
848 856 0.461961 CCAGTGCTAGCTCCTACACC 59.538 60.000 17.23 0.00 33.46 4.16
849 857 1.475403 TCCAGTGCTAGCTCCTACAC 58.525 55.000 17.23 4.28 0.00 2.90
850 858 2.311463 GATCCAGTGCTAGCTCCTACA 58.689 52.381 17.23 2.40 0.00 2.74
851 859 1.268352 CGATCCAGTGCTAGCTCCTAC 59.732 57.143 17.23 5.48 0.00 3.18
852 860 1.143073 TCGATCCAGTGCTAGCTCCTA 59.857 52.381 17.23 1.09 0.00 2.94
853 861 0.106469 TCGATCCAGTGCTAGCTCCT 60.106 55.000 17.23 8.96 0.00 3.69
854 862 0.031449 GTCGATCCAGTGCTAGCTCC 59.969 60.000 17.23 6.57 0.00 4.70
855 863 0.031449 GGTCGATCCAGTGCTAGCTC 59.969 60.000 17.23 12.88 35.97 4.09
856 864 1.395826 GGGTCGATCCAGTGCTAGCT 61.396 60.000 17.23 0.00 38.11 3.32
857 865 1.068250 GGGTCGATCCAGTGCTAGC 59.932 63.158 10.69 8.10 38.11 3.42
858 866 1.115467 AAGGGTCGATCCAGTGCTAG 58.885 55.000 19.03 0.00 38.11 3.42
859 867 1.568504 AAAGGGTCGATCCAGTGCTA 58.431 50.000 19.03 0.00 38.11 3.49
860 868 0.693049 AAAAGGGTCGATCCAGTGCT 59.307 50.000 19.03 0.00 38.11 4.40
861 869 2.396590 TAAAAGGGTCGATCCAGTGC 57.603 50.000 19.03 0.00 38.11 4.40
862 870 6.995511 TTAAATAAAAGGGTCGATCCAGTG 57.004 37.500 19.03 0.00 38.11 3.66
863 871 8.411991 TTTTTAAATAAAAGGGTCGATCCAGT 57.588 30.769 19.03 0.35 36.62 4.00
898 906 4.976116 CCGAAAAGAAAATCTGAACACACC 59.024 41.667 0.00 0.00 0.00 4.16
1027 1036 2.483877 GTGGTTGCGAATTGATGAGTCA 59.516 45.455 0.00 0.00 0.00 3.41
1028 1037 2.159517 GGTGGTTGCGAATTGATGAGTC 60.160 50.000 0.00 0.00 0.00 3.36
1029 1038 1.812571 GGTGGTTGCGAATTGATGAGT 59.187 47.619 0.00 0.00 0.00 3.41
1030 1039 1.202065 CGGTGGTTGCGAATTGATGAG 60.202 52.381 0.00 0.00 0.00 2.90
1031 1040 0.801872 CGGTGGTTGCGAATTGATGA 59.198 50.000 0.00 0.00 0.00 2.92
1032 1041 0.798009 GCGGTGGTTGCGAATTGATG 60.798 55.000 0.00 0.00 0.00 3.07
1033 1042 0.960364 AGCGGTGGTTGCGAATTGAT 60.960 50.000 0.00 0.00 37.44 2.57
1034 1043 1.169661 AAGCGGTGGTTGCGAATTGA 61.170 50.000 0.00 0.00 37.44 2.57
1061 1076 3.842126 CGCCACGCTGACGACATG 61.842 66.667 0.00 0.00 43.93 3.21
1139 1154 1.379977 CAGCTCCTCCACCCTACGA 60.380 63.158 0.00 0.00 0.00 3.43
1493 3274 0.739813 CCTCCGGTTCGATGTGTTCC 60.740 60.000 0.00 0.00 0.00 3.62
1795 3613 4.502604 GGTGGATCTATTAGGCTTGCGTAA 60.503 45.833 9.65 9.65 0.00 3.18
1874 3712 1.599797 GGGGCGTATGGTGTATGGC 60.600 63.158 0.00 0.00 0.00 4.40
2893 7569 1.218316 GCGGGACCGACTTCTTGAT 59.782 57.895 15.99 0.00 42.83 2.57
2973 7649 1.365999 CGTGTACTCCACAGCCACA 59.634 57.895 0.00 0.00 44.78 4.17
3015 7691 2.407428 CCTCGCGTACAGCTCCAGA 61.407 63.158 5.77 0.00 45.59 3.86
3107 7783 0.543277 CATCTCCCTTGCTAGCACCA 59.457 55.000 19.17 2.28 0.00 4.17
3213 7889 2.951457 TACATGCACGCTGCTAGTAA 57.049 45.000 10.54 0.00 45.31 2.24
3215 7891 1.410517 AGATACATGCACGCTGCTAGT 59.589 47.619 10.54 10.54 45.31 2.57
3216 7892 1.791204 CAGATACATGCACGCTGCTAG 59.209 52.381 10.54 6.25 45.31 3.42
3217 7893 1.136891 ACAGATACATGCACGCTGCTA 59.863 47.619 10.54 0.00 45.31 3.49
3218 7894 0.107993 ACAGATACATGCACGCTGCT 60.108 50.000 10.54 0.00 45.31 4.24
3273 7970 8.695456 ACAAAATAAACTTTGTGAACTGGAGAT 58.305 29.630 1.12 0.00 45.52 2.75
3332 8033 6.070021 TGCTCTTTAGGATCATGGAGAAGAAA 60.070 38.462 9.75 0.00 0.00 2.52
3387 8088 2.094894 CACTCAAAGACATAAGCGCCAG 59.905 50.000 2.29 0.00 0.00 4.85
3420 8139 3.936772 TTCGCCCAGGTTCCATGGC 62.937 63.158 6.96 10.34 40.54 4.40
3461 8180 3.384467 CAGGGAACTTTCTGCCAGAAAAA 59.616 43.478 19.66 0.07 42.95 1.94
3462 8181 2.958355 CAGGGAACTTTCTGCCAGAAAA 59.042 45.455 19.66 5.45 42.95 2.29
3463 8182 2.091885 ACAGGGAACTTTCTGCCAGAAA 60.092 45.455 18.31 18.31 41.51 2.52
3464 8183 1.494721 ACAGGGAACTTTCTGCCAGAA 59.505 47.619 2.24 2.24 40.21 3.02
3465 8184 1.140312 ACAGGGAACTTTCTGCCAGA 58.860 50.000 0.00 0.00 40.21 3.86
3466 8185 2.859165 TACAGGGAACTTTCTGCCAG 57.141 50.000 0.00 0.00 40.21 4.85
3467 8186 2.642311 TGATACAGGGAACTTTCTGCCA 59.358 45.455 0.00 0.00 40.21 4.92
3468 8187 3.010420 GTGATACAGGGAACTTTCTGCC 58.990 50.000 0.00 0.00 40.21 4.85
3469 8188 3.935828 GAGTGATACAGGGAACTTTCTGC 59.064 47.826 0.00 0.00 40.21 4.26
3470 8189 5.152623 TGAGTGATACAGGGAACTTTCTG 57.847 43.478 0.00 0.00 40.21 3.02
3471 8190 5.413309 CTGAGTGATACAGGGAACTTTCT 57.587 43.478 0.00 0.00 40.21 2.52
3481 8200 1.474478 ACGTCAGCCTGAGTGATACAG 59.526 52.381 0.00 0.00 35.43 2.74
3482 8201 1.545841 ACGTCAGCCTGAGTGATACA 58.454 50.000 0.00 0.00 0.00 2.29
3483 8202 2.656560 AACGTCAGCCTGAGTGATAC 57.343 50.000 0.00 0.00 0.00 2.24
3484 8203 2.353704 CCAAACGTCAGCCTGAGTGATA 60.354 50.000 0.00 0.00 0.00 2.15
3485 8204 1.609061 CCAAACGTCAGCCTGAGTGAT 60.609 52.381 0.00 0.00 0.00 3.06
3486 8205 0.249868 CCAAACGTCAGCCTGAGTGA 60.250 55.000 0.00 0.00 0.00 3.41
3487 8206 1.845809 GCCAAACGTCAGCCTGAGTG 61.846 60.000 0.00 0.00 0.00 3.51
3488 8207 1.598130 GCCAAACGTCAGCCTGAGT 60.598 57.895 0.00 0.00 0.00 3.41
3489 8208 2.328099 GGCCAAACGTCAGCCTGAG 61.328 63.158 14.36 0.00 43.62 3.35
3490 8209 2.281484 GGCCAAACGTCAGCCTGA 60.281 61.111 14.36 0.00 43.62 3.86
3579 8298 2.277969 CAGCTGCTATGAGTCCAACAG 58.722 52.381 0.00 0.00 0.00 3.16
3644 8363 2.303022 GGACACCTGATGTTCTGAAGGA 59.697 50.000 0.00 0.00 43.56 3.36
3645 8364 2.038952 TGGACACCTGATGTTCTGAAGG 59.961 50.000 0.00 0.00 43.56 3.46
3654 8373 0.686789 TGGTCAGTGGACACCTGATG 59.313 55.000 0.00 0.00 46.17 3.07
3663 8382 1.744320 CGTGTGGTCTGGTCAGTGGA 61.744 60.000 0.00 0.00 0.00 4.02
3681 8402 2.659757 TCGTTACGTCATGAAAAGAGCG 59.340 45.455 4.24 0.00 0.00 5.03
3705 8426 1.955778 CACAACCAACATGCAAGGAGA 59.044 47.619 5.75 0.00 0.00 3.71
3725 8446 4.124851 TCCTTCCGTGATAGAAAGCTTC 57.875 45.455 0.00 0.00 0.00 3.86
3734 8455 6.604396 TCTTGTTAGTACATCCTTCCGTGATA 59.396 38.462 0.00 0.00 33.44 2.15
3761 8482 1.202371 ACGCTTGTTTCAGACGTCTCA 60.202 47.619 16.96 7.93 29.64 3.27
3762 8483 1.190323 CACGCTTGTTTCAGACGTCTC 59.810 52.381 16.96 4.94 34.19 3.36
3766 8487 1.569493 CCCACGCTTGTTTCAGACG 59.431 57.895 0.00 0.00 0.00 4.18
3768 8489 1.148273 AGCCCACGCTTGTTTCAGA 59.852 52.632 0.00 0.00 45.55 3.27
3769 8490 3.749981 AGCCCACGCTTGTTTCAG 58.250 55.556 0.00 0.00 45.55 3.02
3808 11627 4.436986 GCTTACTACTTTGGTCATTTCCGC 60.437 45.833 0.00 0.00 0.00 5.54
3811 11630 4.436986 GCGGCTTACTACTTTGGTCATTTC 60.437 45.833 0.00 0.00 0.00 2.17
3837 11656 2.483877 CGTACGGCCGTCCTATACATAA 59.516 50.000 38.01 10.59 0.00 1.90
3884 11703 6.414890 CAAAACAAACGGTGCGAATTAATTT 58.585 32.000 1.43 0.00 0.00 1.82
3896 11715 0.615261 ACCCACCCAAAACAAACGGT 60.615 50.000 0.00 0.00 0.00 4.83
3902 11721 1.273324 ACCTTTGACCCACCCAAAACA 60.273 47.619 0.00 0.00 33.68 2.83
3907 11726 1.756024 CGTACCTTTGACCCACCCA 59.244 57.895 0.00 0.00 0.00 4.51
3973 11796 3.151906 GGCGTCATGGGAGCCTAT 58.848 61.111 16.22 0.00 46.83 2.57
4011 11834 0.328258 AGGCCGTTGGTTTATGCTCT 59.672 50.000 0.00 0.00 0.00 4.09
4063 11886 2.910688 TTATGAATGGAGCCGGAGTC 57.089 50.000 5.05 0.00 0.00 3.36
4090 11913 6.368791 GTGAGCTGATGTGTAAACTATTGTGA 59.631 38.462 0.00 0.00 0.00 3.58
4143 11966 9.516314 GCGAGACCTGCTATTATTTTTATTTTT 57.484 29.630 0.00 0.00 0.00 1.94
4150 11973 6.992715 AGTTATGCGAGACCTGCTATTATTTT 59.007 34.615 0.00 0.00 0.00 1.82
4197 12020 1.694696 ACAACCCACCTCTCTTGTCTC 59.305 52.381 0.00 0.00 0.00 3.36
4204 12027 1.600916 GCCACACAACCCACCTCTC 60.601 63.158 0.00 0.00 0.00 3.20
4205 12028 2.056906 GAGCCACACAACCCACCTCT 62.057 60.000 0.00 0.00 0.00 3.69
4217 12040 1.164411 CGGTATGCTTTTGAGCCACA 58.836 50.000 0.00 0.00 0.00 4.17
4235 12058 0.250727 AACCATGACCACTTCCACCG 60.251 55.000 0.00 0.00 0.00 4.94
4256 12079 2.664402 AGCAAACCACTCAGGAATGT 57.336 45.000 0.00 0.00 41.22 2.71
4259 12082 2.810400 GCTGTAGCAAACCACTCAGGAA 60.810 50.000 0.00 0.00 39.63 3.36
4300 12123 0.258484 AGCTCTCAGGCTAGCTCAGA 59.742 55.000 15.72 11.93 45.92 3.27
4307 12130 0.183731 TCATCGGAGCTCTCAGGCTA 59.816 55.000 14.64 0.00 43.20 3.93
4310 12133 1.541147 GATCTCATCGGAGCTCTCAGG 59.459 57.143 14.64 2.12 41.13 3.86
4317 12140 3.450457 AGGATAATGGATCTCATCGGAGC 59.550 47.826 0.00 0.00 41.13 4.70
4320 12143 5.654209 TGTAGAGGATAATGGATCTCATCGG 59.346 44.000 0.00 0.00 34.44 4.18
4323 12146 8.943085 ACTTTTGTAGAGGATAATGGATCTCAT 58.057 33.333 0.00 0.00 37.79 2.90
4368 12191 4.331168 GCTGACAATCAGGTGTCTATGAAC 59.669 45.833 7.89 0.00 46.70 3.18
4370 12193 3.429410 CGCTGACAATCAGGTGTCTATGA 60.429 47.826 7.89 0.00 46.70 2.15
4390 12213 2.192175 CCCTACAATCCCACCCGC 59.808 66.667 0.00 0.00 0.00 6.13
4410 12233 4.458397 CAGGCATACCAGTTGATGATTCT 58.542 43.478 0.00 0.00 39.06 2.40
4416 12239 0.552848 CCCCAGGCATACCAGTTGAT 59.447 55.000 0.00 0.00 39.06 2.57
4420 12243 0.844661 TGAACCCCAGGCATACCAGT 60.845 55.000 0.00 0.00 39.06 4.00
4426 12249 2.897326 GTTAAAGTTGAACCCCAGGCAT 59.103 45.455 0.00 0.00 0.00 4.40
4461 12284 2.925966 TTTGGGATTGATGGGAAGCT 57.074 45.000 0.00 0.00 0.00 3.74
4480 12303 5.126067 CCAAGATATCCGAGGACACATTTT 58.874 41.667 0.00 0.00 0.00 1.82
4482 12305 3.711704 ACCAAGATATCCGAGGACACATT 59.288 43.478 11.44 0.00 0.00 2.71
4483 12306 3.070159 CACCAAGATATCCGAGGACACAT 59.930 47.826 11.44 0.00 0.00 3.21
4485 12308 2.431057 ACACCAAGATATCCGAGGACAC 59.569 50.000 11.44 0.00 0.00 3.67
4487 12310 4.931661 TTACACCAAGATATCCGAGGAC 57.068 45.455 11.44 0.00 0.00 3.85
4488 12311 7.611770 CAATATTACACCAAGATATCCGAGGA 58.388 38.462 11.44 0.00 0.00 3.71
4495 12318 9.745018 ATAGCTTGCAATATTACACCAAGATAT 57.255 29.630 0.00 15.14 39.12 1.63
4508 12331 3.654806 AGGGTCAGGATAGCTTGCAATAT 59.345 43.478 0.00 0.00 0.00 1.28
4516 12340 6.143915 TGAAACTATTAGGGTCAGGATAGCT 58.856 40.000 0.00 0.00 0.00 3.32
4549 12373 8.006298 TGGATTGACAACACAACTTCTAATTT 57.994 30.769 0.00 0.00 32.50 1.82
4550 12374 7.581213 TGGATTGACAACACAACTTCTAATT 57.419 32.000 0.00 0.00 32.50 1.40
4551 12375 7.765695 ATGGATTGACAACACAACTTCTAAT 57.234 32.000 0.00 0.00 32.50 1.73
4603 12427 2.238144 CTGACACATCCTGGACCAGATT 59.762 50.000 23.77 6.70 32.44 2.40
4614 12438 1.945387 ATGATGCGACTGACACATCC 58.055 50.000 5.86 0.00 39.55 3.51
4615 12439 3.486375 CCAAATGATGCGACTGACACATC 60.486 47.826 2.01 2.01 40.48 3.06
4621 12445 2.684374 CAATCCCAAATGATGCGACTGA 59.316 45.455 0.00 0.00 0.00 3.41
4645 12469 7.853929 CACAAAATTTGGCTGAAATTGAGAAAG 59.146 33.333 10.71 0.00 42.41 2.62
4648 12472 5.236911 GCACAAAATTTGGCTGAAATTGAGA 59.763 36.000 10.71 0.00 42.41 3.27
4660 12484 1.526464 GCCAAGTCGCACAAAATTTGG 59.474 47.619 10.71 0.00 38.42 3.28
4668 12492 1.891919 GTTGAGGCCAAGTCGCACA 60.892 57.895 5.01 0.00 32.06 4.57
4669 12493 1.166531 AAGTTGAGGCCAAGTCGCAC 61.167 55.000 5.01 0.00 35.01 5.34


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

AutoCloner maintained by Alex Coulton.