Multiple sequence alignment - TraesCS4B01G057700

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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 TraesCS4B01G057700 chr4B 100.000 4236 0 0 1 4236 47625866 47621631 0.000000e+00 7823.0
1 TraesCS4B01G057700 chr4B 86.207 87 11 1 2389 2475 14016276 14016191 4.510000e-15 93.5
2 TraesCS4B01G057700 chr4A 94.004 2485 108 25 1366 3831 569866858 569869320 0.000000e+00 3725.0
3 TraesCS4B01G057700 chr4A 91.176 442 20 2 940 1362 569866373 569866814 2.200000e-162 582.0
4 TraesCS4B01G057700 chr4A 80.838 668 90 28 1 649 637734902 637735550 1.370000e-134 490.0
5 TraesCS4B01G057700 chr4A 83.901 323 10 17 3934 4236 569869595 569869895 1.940000e-68 270.0
6 TraesCS4B01G057700 chr4A 87.640 89 10 1 2389 2477 569867971 569867884 7.490000e-18 102.0
7 TraesCS4B01G057700 chr4A 88.235 85 9 1 2389 2473 662286502 662286419 2.700000e-17 100.0
8 TraesCS4B01G057700 chr4D 94.301 2439 101 14 1366 3790 32769508 32767094 0.000000e+00 3699.0
9 TraesCS4B01G057700 chr4D 92.461 451 18 6 935 1369 32769995 32769545 7.730000e-177 630.0
10 TraesCS4B01G057700 chr4D 84.053 301 16 11 3829 4112 32766733 32766448 1.170000e-65 261.0
11 TraesCS4B01G057700 chr4D 90.000 100 6 1 4133 4232 32766380 32766285 4.450000e-25 126.0
12 TraesCS4B01G057700 chr4D 85.882 85 10 2 2384 2468 509646352 509646434 5.830000e-14 89.8
13 TraesCS4B01G057700 chr4D 85.366 82 11 1 2376 2457 20114843 20114923 2.710000e-12 84.2
14 TraesCS4B01G057700 chr4D 84.507 71 11 0 2389 2459 163563103 163563173 2.110000e-08 71.3
15 TraesCS4B01G057700 chr4D 93.333 45 3 0 2389 2433 25648767 25648811 2.730000e-07 67.6
16 TraesCS4B01G057700 chr4D 100.000 36 0 0 4107 4142 32766440 32766405 2.730000e-07 67.6
17 TraesCS4B01G057700 chr4D 93.182 44 3 0 2387 2430 438145623 438145666 9.830000e-07 65.8
18 TraesCS4B01G057700 chr4D 87.719 57 4 1 2402 2455 56740882 56740938 3.540000e-06 63.9
19 TraesCS4B01G057700 chr3D 82.593 856 89 33 1 839 580608141 580608953 0.000000e+00 701.0
20 TraesCS4B01G057700 chr3D 83.714 657 76 14 1 634 471392775 471393423 3.650000e-165 592.0
21 TraesCS4B01G057700 chr3D 84.783 92 10 4 2389 2479 126949045 126949133 5.830000e-14 89.8
22 TraesCS4B01G057700 chr3D 88.732 71 8 0 2389 2459 582882084 582882154 2.100000e-13 87.9
23 TraesCS4B01G057700 chr7D 85.236 657 70 19 6 649 134525134 134524492 0.000000e+00 651.0
24 TraesCS4B01G057700 chr7D 86.525 564 50 18 1 552 589282304 589281755 7.840000e-167 597.0
25 TraesCS4B01G057700 chr6D 82.910 708 83 29 1 692 422634089 422634774 1.680000e-168 603.0
26 TraesCS4B01G057700 chr6D 82.491 554 69 17 111 649 422067190 422067730 1.070000e-125 460.0
27 TraesCS4B01G057700 chr6D 91.304 69 6 0 2389 2457 343295805 343295737 1.250000e-15 95.3
28 TraesCS4B01G057700 chr6D 93.333 45 3 0 2389 2433 121540587 121540631 2.730000e-07 67.6
29 TraesCS4B01G057700 chr6D 92.683 41 3 0 2390 2430 363033206 363033166 4.570000e-05 60.2
30 TraesCS4B01G057700 chr6D 100.000 28 0 0 2403 2430 84214218 84214191 8.000000e-03 52.8
31 TraesCS4B01G057700 chr5B 83.556 675 66 19 1 649 596886135 596886790 1.310000e-164 590.0
32 TraesCS4B01G057700 chr5B 85.393 89 12 1 2389 2477 582392059 582391972 1.620000e-14 91.6
33 TraesCS4B01G057700 chr5D 83.333 666 81 24 1 649 28027352 28026700 4.720000e-164 588.0
34 TraesCS4B01G057700 chr5D 92.941 85 5 1 2389 2473 456063698 456063615 5.750000e-24 122.0
35 TraesCS4B01G057700 chr5D 91.111 90 6 2 2390 2479 456063615 456063702 2.070000e-23 121.0
36 TraesCS4B01G057700 chr5D 86.813 91 7 4 2389 2476 410399114 410399202 3.490000e-16 97.1
37 TraesCS4B01G057700 chr5D 84.783 92 9 3 2389 2480 546857278 546857364 2.100000e-13 87.9
38 TraesCS4B01G057700 chr7B 81.659 687 79 28 1 655 586655427 586654756 1.040000e-145 527.0
39 TraesCS4B01G057700 chr7B 81.433 684 84 26 1 649 77801907 77801232 1.750000e-143 520.0
40 TraesCS4B01G057700 chr7B 84.906 106 14 2 2372 2476 454616852 454616748 5.790000e-19 106.0
41 TraesCS4B01G057700 chr3A 81.979 677 70 24 1 644 535229035 535228378 1.040000e-145 527.0
42 TraesCS4B01G057700 chr1A 81.493 670 91 21 1 649 30495518 30494861 1.750000e-143 520.0
43 TraesCS4B01G057700 chr1A 90.909 66 4 2 2390 2455 78548523 78548460 2.100000e-13 87.9
44 TraesCS4B01G057700 chr1A 87.500 72 5 2 2389 2457 331272281 331272211 3.510000e-11 80.5
45 TraesCS4B01G057700 chr3B 84.906 106 14 2 2372 2476 503721588 503721692 5.790000e-19 106.0
46 TraesCS4B01G057700 chr2B 91.139 79 4 3 2389 2466 232785730 232785806 2.080000e-18 104.0
47 TraesCS4B01G057700 chr2B 77.397 146 18 9 607 746 82101714 82101578 5.880000e-09 73.1
48 TraesCS4B01G057700 chr1B 84.906 106 13 3 2372 2476 380693284 380693387 2.080000e-18 104.0
49 TraesCS4B01G057700 chr1B 84.375 96 13 2 2389 2484 402110448 402110355 4.510000e-15 93.5
50 TraesCS4B01G057700 chr2D 86.517 89 11 1 2390 2478 75504894 75504981 3.490000e-16 97.1
51 TraesCS4B01G057700 chr6B 81.452 124 15 6 724 839 583266126 583266249 1.250000e-15 95.3
52 TraesCS4B01G057700 chr5A 83.333 102 15 2 2374 2474 382114842 382114942 4.510000e-15 93.5
53 TraesCS4B01G057700 chr1D 92.424 66 3 2 2384 2449 422838287 422838350 4.510000e-15 93.5
54 TraesCS4B01G057700 chr1D 90.909 66 6 0 2394 2459 410795983 410795918 5.830000e-14 89.8
55 TraesCS4B01G057700 chr1D 84.507 71 11 0 2389 2459 122974481 122974411 2.110000e-08 71.3
56 TraesCS4B01G057700 chr6A 87.324 71 7 2 2409 2478 483734855 483734786 3.510000e-11 80.5
57 TraesCS4B01G057700 chr7A 88.000 50 4 2 770 817 631260004 631259955 1.650000e-04 58.4


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 TraesCS4B01G057700 chr4B 47621631 47625866 4235 True 7823.000000 7823 100.000000 1 4236 1 chr4B.!!$R2 4235
1 TraesCS4B01G057700 chr4A 569866373 569869895 3522 False 1525.666667 3725 89.693667 940 4236 3 chr4A.!!$F2 3296
2 TraesCS4B01G057700 chr4A 637734902 637735550 648 False 490.000000 490 80.838000 1 649 1 chr4A.!!$F1 648
3 TraesCS4B01G057700 chr4D 32766285 32769995 3710 True 956.720000 3699 92.163000 935 4232 5 chr4D.!!$R1 3297
4 TraesCS4B01G057700 chr3D 580608141 580608953 812 False 701.000000 701 82.593000 1 839 1 chr3D.!!$F3 838
5 TraesCS4B01G057700 chr3D 471392775 471393423 648 False 592.000000 592 83.714000 1 634 1 chr3D.!!$F2 633
6 TraesCS4B01G057700 chr7D 134524492 134525134 642 True 651.000000 651 85.236000 6 649 1 chr7D.!!$R1 643
7 TraesCS4B01G057700 chr7D 589281755 589282304 549 True 597.000000 597 86.525000 1 552 1 chr7D.!!$R2 551
8 TraesCS4B01G057700 chr6D 422634089 422634774 685 False 603.000000 603 82.910000 1 692 1 chr6D.!!$F3 691
9 TraesCS4B01G057700 chr6D 422067190 422067730 540 False 460.000000 460 82.491000 111 649 1 chr6D.!!$F2 538
10 TraesCS4B01G057700 chr5B 596886135 596886790 655 False 590.000000 590 83.556000 1 649 1 chr5B.!!$F1 648
11 TraesCS4B01G057700 chr5D 28026700 28027352 652 True 588.000000 588 83.333000 1 649 1 chr5D.!!$R1 648
12 TraesCS4B01G057700 chr7B 586654756 586655427 671 True 527.000000 527 81.659000 1 655 1 chr7B.!!$R3 654
13 TraesCS4B01G057700 chr7B 77801232 77801907 675 True 520.000000 520 81.433000 1 649 1 chr7B.!!$R1 648
14 TraesCS4B01G057700 chr3A 535228378 535229035 657 True 527.000000 527 81.979000 1 644 1 chr3A.!!$R1 643
15 TraesCS4B01G057700 chr1A 30494861 30495518 657 True 520.000000 520 81.493000 1 649 1 chr1A.!!$R1 648

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
764 1076 0.028374 CGTTTCAAAAGCCGAACCGT 59.972 50.0 0.00 0.0 0.00 4.83 F
892 1206 0.039180 TCTCTGTCCGGTTCTAGCCA 59.961 55.0 0.00 0.0 0.00 4.75 F
913 1227 0.305313 GCCGTGCGTGTTACTCAAAA 59.695 50.0 0.00 0.0 0.00 2.44 F
2085 2472 0.034863 GGCCCTTTGGGTTGTCGATA 60.035 55.0 4.42 0.0 46.51 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 2041 0.392193 GGGCAGTGTGATCTCCAGTG 60.392 60.0 13.37 13.37 36.53 3.66 R
1945 2332 0.880278 TGCAGCTCGTCAAGTGGAAC 60.880 55.0 0.00 0.00 0.00 3.62 R
2530 2917 1.291132 GAGCGGAGTTATGCAGAACC 58.709 55.0 20.09 11.61 0.00 3.62 R
3599 3997 0.320771 GAAGGGTGCGTGACAGACAT 60.321 55.0 0.00 0.00 0.00 3.06 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 2.546368 CTCGAACCGTTTTCACCATTGA 59.454 45.455 0.00 0.00 0.00 2.57
97 98 2.408704 CGCGTCGAGATCTTCAAAACTT 59.591 45.455 0.00 0.00 0.00 2.66
98 99 3.120991 CGCGTCGAGATCTTCAAAACTTT 60.121 43.478 0.00 0.00 0.00 2.66
266 306 1.743252 GTGCCTCTTGCGGAAGGAG 60.743 63.158 17.16 12.06 45.60 3.69
438 589 3.325870 CTCTCATGAAAGCACAACCGTA 58.674 45.455 0.00 0.00 0.00 4.02
451 602 2.101249 ACAACCGTACCTCTCACGAAAA 59.899 45.455 0.00 0.00 41.91 2.29
507 817 3.100658 TCGTTTCCGAAAGTCATGACA 57.899 42.857 27.02 2.75 40.86 3.58
509 819 2.411547 CGTTTCCGAAAGTCATGACAGC 60.412 50.000 27.02 14.28 35.63 4.40
547 857 2.202676 CGTGCCTCTCTCGGAAGC 60.203 66.667 0.00 0.00 32.35 3.86
550 860 0.320771 GTGCCTCTCTCGGAAGCAAA 60.321 55.000 0.00 0.00 42.24 3.68
551 861 0.396435 TGCCTCTCTCGGAAGCAAAA 59.604 50.000 0.00 0.00 38.32 2.44
552 862 0.799393 GCCTCTCTCGGAAGCAAAAC 59.201 55.000 0.00 0.00 32.03 2.43
553 863 1.443802 CCTCTCTCGGAAGCAAAACC 58.556 55.000 0.00 0.00 0.00 3.27
554 864 1.002544 CCTCTCTCGGAAGCAAAACCT 59.997 52.381 0.00 0.00 0.00 3.50
555 865 2.072298 CTCTCTCGGAAGCAAAACCTG 58.928 52.381 0.00 0.00 0.00 4.00
563 873 3.936653 GCAAAACCTGCCTTTCGC 58.063 55.556 0.00 0.00 46.13 4.70
564 874 2.016165 GCAAAACCTGCCTTTCGCG 61.016 57.895 0.00 0.00 46.13 5.87
565 875 1.652012 CAAAACCTGCCTTTCGCGA 59.348 52.632 3.71 3.71 42.08 5.87
566 876 0.030101 CAAAACCTGCCTTTCGCGAA 59.970 50.000 19.38 19.38 42.08 4.70
567 877 0.741915 AAAACCTGCCTTTCGCGAAA 59.258 45.000 30.47 30.47 42.08 3.46
568 878 0.310854 AAACCTGCCTTTCGCGAAAG 59.689 50.000 41.12 41.12 45.47 2.62
607 917 5.942325 AACACGTTTCTTTTTCATTTCCG 57.058 34.783 0.00 0.00 0.00 4.30
608 918 5.238006 ACACGTTTCTTTTTCATTTCCGA 57.762 34.783 0.00 0.00 0.00 4.55
609 919 5.270853 ACACGTTTCTTTTTCATTTCCGAG 58.729 37.500 0.00 0.00 0.00 4.63
610 920 5.065474 ACACGTTTCTTTTTCATTTCCGAGA 59.935 36.000 0.00 0.00 0.00 4.04
611 921 5.621228 CACGTTTCTTTTTCATTTCCGAGAG 59.379 40.000 0.00 0.00 0.00 3.20
629 939 3.728474 GCATGGCCATGACTCTCG 58.272 61.111 43.18 20.02 41.20 4.04
630 940 2.541120 GCATGGCCATGACTCTCGC 61.541 63.158 43.18 25.43 41.20 5.03
631 941 2.107750 ATGGCCATGACTCTCGCG 59.892 61.111 20.04 0.00 0.00 5.87
632 942 2.426406 ATGGCCATGACTCTCGCGA 61.426 57.895 20.04 9.26 0.00 5.87
633 943 1.960040 ATGGCCATGACTCTCGCGAA 61.960 55.000 20.04 0.00 0.00 4.70
634 944 1.880340 GGCCATGACTCTCGCGAAG 60.880 63.158 11.33 13.12 0.00 3.79
648 958 3.729004 CGAAGCAAAACCGTGACTC 57.271 52.632 0.00 0.00 0.00 3.36
649 959 0.111266 CGAAGCAAAACCGTGACTCG 60.111 55.000 0.00 0.00 39.52 4.18
650 960 0.384353 GAAGCAAAACCGTGACTCGC 60.384 55.000 0.00 0.00 38.35 5.03
651 961 1.092921 AAGCAAAACCGTGACTCGCA 61.093 50.000 0.00 0.00 38.35 5.10
652 962 1.368850 GCAAAACCGTGACTCGCAC 60.369 57.895 0.00 0.00 44.21 5.34
659 969 2.643272 GTGACTCGCACGACAGGA 59.357 61.111 0.00 0.00 37.83 3.86
660 970 1.442857 GTGACTCGCACGACAGGAG 60.443 63.158 0.00 0.00 37.83 3.69
661 971 2.179517 GACTCGCACGACAGGAGG 59.820 66.667 0.00 0.00 32.11 4.30
667 977 0.234884 CGCACGACAGGAGGAAAAAC 59.765 55.000 0.00 0.00 0.00 2.43
714 1024 7.994425 AATTTGGTCCAAAAGTTTTGAAAGT 57.006 28.000 26.36 15.77 36.90 2.66
716 1026 5.730296 TGGTCCAAAAGTTTTGAAAGTCA 57.270 34.783 26.36 14.72 0.00 3.41
761 1073 2.197792 AACCGTTTCAAAAGCCGAAC 57.802 45.000 0.00 0.00 0.00 3.95
762 1074 0.382873 ACCGTTTCAAAAGCCGAACC 59.617 50.000 0.00 0.00 0.00 3.62
763 1075 0.659123 CCGTTTCAAAAGCCGAACCG 60.659 55.000 0.00 0.00 0.00 4.44
764 1076 0.028374 CGTTTCAAAAGCCGAACCGT 59.972 50.000 0.00 0.00 0.00 4.83
765 1077 1.472990 GTTTCAAAAGCCGAACCGTG 58.527 50.000 0.00 0.00 0.00 4.94
766 1078 1.096416 TTTCAAAAGCCGAACCGTGT 58.904 45.000 0.00 0.00 0.00 4.49
767 1079 0.378962 TTCAAAAGCCGAACCGTGTG 59.621 50.000 0.00 0.00 0.00 3.82
768 1080 0.745128 TCAAAAGCCGAACCGTGTGT 60.745 50.000 0.00 0.00 0.00 3.72
769 1081 0.938713 CAAAAGCCGAACCGTGTGTA 59.061 50.000 0.00 0.00 0.00 2.90
803 1117 1.293498 TGGAAGAAGCGTCCAGAGC 59.707 57.895 0.00 0.00 40.33 4.09
813 1127 4.700365 TCCAGAGCGCGACACGTG 62.700 66.667 15.48 15.48 46.11 4.49
839 1153 4.451150 CTGGGAGCGCGCCAAGTA 62.451 66.667 31.51 13.30 0.00 2.24
840 1154 4.451150 TGGGAGCGCGCCAAGTAG 62.451 66.667 31.51 0.00 0.00 2.57
842 1156 4.821589 GGAGCGCGCCAAGTAGCT 62.822 66.667 30.33 6.10 43.33 3.32
843 1157 3.558411 GAGCGCGCCAAGTAGCTG 61.558 66.667 30.33 0.00 40.39 4.24
849 1163 4.096003 GCCAAGTAGCTGGGCCGA 62.096 66.667 3.18 0.00 44.48 5.54
850 1164 2.125106 CCAAGTAGCTGGGCCGAC 60.125 66.667 0.00 0.00 32.32 4.79
851 1165 2.509336 CAAGTAGCTGGGCCGACG 60.509 66.667 0.00 0.00 0.00 5.12
852 1166 4.452733 AAGTAGCTGGGCCGACGC 62.453 66.667 0.00 0.94 0.00 5.19
878 1192 4.200283 GACGCCGGAGCCTCTCTG 62.200 72.222 5.05 0.00 36.69 3.35
880 1194 4.200283 CGCCGGAGCCTCTCTGTC 62.200 72.222 5.05 0.00 35.27 3.51
881 1195 3.844090 GCCGGAGCCTCTCTGTCC 61.844 72.222 5.05 0.00 35.27 4.02
884 1198 2.363147 GGAGCCTCTCTGTCCGGT 60.363 66.667 0.00 0.00 0.00 5.28
885 1199 1.985116 GGAGCCTCTCTGTCCGGTT 60.985 63.158 0.00 0.00 0.00 4.44
886 1200 1.513622 GAGCCTCTCTGTCCGGTTC 59.486 63.158 0.00 0.00 0.00 3.62
887 1201 0.968393 GAGCCTCTCTGTCCGGTTCT 60.968 60.000 0.00 0.00 0.00 3.01
888 1202 0.331954 AGCCTCTCTGTCCGGTTCTA 59.668 55.000 0.00 0.00 0.00 2.10
889 1203 0.741915 GCCTCTCTGTCCGGTTCTAG 59.258 60.000 0.00 0.00 0.00 2.43
890 1204 0.741915 CCTCTCTGTCCGGTTCTAGC 59.258 60.000 0.00 0.00 0.00 3.42
891 1205 0.741915 CTCTCTGTCCGGTTCTAGCC 59.258 60.000 0.00 0.00 0.00 3.93
892 1206 0.039180 TCTCTGTCCGGTTCTAGCCA 59.961 55.000 0.00 0.00 0.00 4.75
893 1207 0.895530 CTCTGTCCGGTTCTAGCCAA 59.104 55.000 0.00 0.00 0.00 4.52
894 1208 0.895530 TCTGTCCGGTTCTAGCCAAG 59.104 55.000 0.00 0.00 0.00 3.61
895 1209 0.741221 CTGTCCGGTTCTAGCCAAGC 60.741 60.000 0.00 0.00 0.00 4.01
896 1210 1.449778 GTCCGGTTCTAGCCAAGCC 60.450 63.158 0.00 0.00 0.00 4.35
897 1211 2.511600 CCGGTTCTAGCCAAGCCG 60.512 66.667 0.00 0.00 41.82 5.52
898 1212 2.264794 CGGTTCTAGCCAAGCCGT 59.735 61.111 0.00 0.00 37.87 5.68
899 1213 2.100631 CGGTTCTAGCCAAGCCGTG 61.101 63.158 0.00 0.00 37.87 4.94
900 1214 2.399356 GGTTCTAGCCAAGCCGTGC 61.399 63.158 0.00 0.00 0.00 5.34
901 1215 2.434185 TTCTAGCCAAGCCGTGCG 60.434 61.111 0.00 0.00 0.00 5.34
902 1216 3.234630 TTCTAGCCAAGCCGTGCGT 62.235 57.895 0.00 0.00 0.00 5.24
903 1217 3.490759 CTAGCCAAGCCGTGCGTG 61.491 66.667 5.17 5.17 37.74 5.34
904 1218 4.308458 TAGCCAAGCCGTGCGTGT 62.308 61.111 9.92 0.00 36.37 4.49
905 1219 3.818121 TAGCCAAGCCGTGCGTGTT 62.818 57.895 9.92 2.76 36.37 3.32
906 1220 2.437518 TAGCCAAGCCGTGCGTGTTA 62.438 55.000 9.92 2.04 36.37 2.41
907 1221 2.554272 CCAAGCCGTGCGTGTTAC 59.446 61.111 9.92 0.00 36.37 2.50
908 1222 1.959226 CCAAGCCGTGCGTGTTACT 60.959 57.895 9.92 0.00 36.37 2.24
909 1223 1.491563 CAAGCCGTGCGTGTTACTC 59.508 57.895 4.22 0.00 33.67 2.59
910 1224 1.068417 AAGCCGTGCGTGTTACTCA 59.932 52.632 0.00 0.00 0.00 3.41
911 1225 0.531090 AAGCCGTGCGTGTTACTCAA 60.531 50.000 0.00 0.00 0.00 3.02
912 1226 0.531090 AGCCGTGCGTGTTACTCAAA 60.531 50.000 0.00 0.00 0.00 2.69
913 1227 0.305313 GCCGTGCGTGTTACTCAAAA 59.695 50.000 0.00 0.00 0.00 2.44
914 1228 1.268133 GCCGTGCGTGTTACTCAAAAA 60.268 47.619 0.00 0.00 0.00 1.94
937 1251 3.979101 AAGAGAGAGAGAAAGCCAAGG 57.021 47.619 0.00 0.00 0.00 3.61
1048 1368 2.673341 TCGGAGCTCACTCGTGCT 60.673 61.111 17.19 0.00 44.48 4.40
1125 1445 1.080772 CTACAGCTCCGTGTTCGCA 60.081 57.895 0.00 0.00 35.54 5.10
1338 1671 1.763545 AGGGATTTCTCGCCTTACCTC 59.236 52.381 0.00 0.00 34.99 3.85
1351 1684 0.963962 TTACCTCGCTGACGTTTCCT 59.036 50.000 0.00 0.00 41.18 3.36
1382 1755 3.530265 TGTTTGTTCGGTGACACTACT 57.470 42.857 5.39 0.00 0.00 2.57
1479 1866 4.156008 AGTTTCATGCGTTGTTCCTTATCC 59.844 41.667 0.00 0.00 0.00 2.59
1654 2041 2.202349 GCAGCGACGGCAACATTC 60.202 61.111 0.00 0.00 43.41 2.67
1706 2093 0.462789 CATGCCCTCCTTCAATTGCC 59.537 55.000 0.00 0.00 0.00 4.52
1780 2167 7.148086 ACCGTATTGTGCAATGTCAGATATTTT 60.148 33.333 7.60 0.00 32.50 1.82
1860 2247 5.163353 CCCCAAATTACAGTGGTCAAAAAGT 60.163 40.000 0.00 0.00 32.60 2.66
1887 2274 2.373169 ACTGAAGGATGTTCTCTGCCAA 59.627 45.455 0.00 0.00 0.00 4.52
1900 2287 2.751806 CTCTGCCAATTCCAAGAGGTTC 59.248 50.000 0.00 0.00 35.89 3.62
1915 2302 6.998673 CCAAGAGGTTCGGGAGATATTATTTT 59.001 38.462 0.00 0.00 39.57 1.82
1921 2308 6.940298 GGTTCGGGAGATATTATTTTCCATCA 59.060 38.462 9.21 0.00 39.57 3.07
1938 2325 4.641541 TCCATCATTTCATTAGTGCCACTG 59.358 41.667 7.83 0.00 0.00 3.66
1939 2326 4.202080 CCATCATTTCATTAGTGCCACTGG 60.202 45.833 7.83 0.00 0.00 4.00
1975 2362 2.154462 ACGAGCTGCATATTTATGGGC 58.846 47.619 1.02 0.00 34.32 5.36
2085 2472 0.034863 GGCCCTTTGGGTTGTCGATA 60.035 55.000 4.42 0.00 46.51 2.92
2361 2748 3.820467 CAGGTTTCCTGCATTAAGTGACA 59.180 43.478 2.77 0.00 45.13 3.58
2364 2751 5.648092 AGGTTTCCTGCATTAAGTGACATAC 59.352 40.000 0.00 0.00 29.57 2.39
2366 2753 6.821665 GGTTTCCTGCATTAAGTGACATACTA 59.178 38.462 0.00 0.00 39.18 1.82
2371 2758 7.509318 TCCTGCATTAAGTGACATACTATACCT 59.491 37.037 0.00 0.00 39.18 3.08
2530 2917 9.941664 CAGATATTTTATAGCCTGTTGAAGTTG 57.058 33.333 0.00 0.00 0.00 3.16
2545 2932 4.072131 TGAAGTTGGTTCTGCATAACTCC 58.928 43.478 13.89 0.31 35.99 3.85
2549 2936 1.291132 GGTTCTGCATAACTCCGCTC 58.709 55.000 13.89 0.00 0.00 5.03
2563 2950 3.117436 ACTCCGCTCCTCCTAGTATCTTT 60.117 47.826 0.00 0.00 0.00 2.52
2595 2982 7.397221 TGAAATCCTCATGAGTATGTTCTTGT 58.603 34.615 21.11 0.00 35.73 3.16
2708 3096 3.454371 TTTTCTGATACTAGGAGCGCC 57.546 47.619 2.29 0.00 0.00 6.53
2709 3097 1.329256 TTCTGATACTAGGAGCGCCC 58.671 55.000 2.29 5.07 33.31 6.13
2738 3126 2.365293 GTTCCATGAAAACCTGGCAACT 59.635 45.455 0.00 0.00 32.30 3.16
2741 3129 2.546373 CCATGAAAACCTGGCAACTGTG 60.546 50.000 0.00 0.00 37.61 3.66
2777 3165 1.973812 GCAACCCCCTTCTGTGAGC 60.974 63.158 0.00 0.00 0.00 4.26
2841 3229 2.680352 ATCTGCCCGTCGGTGAGT 60.680 61.111 11.06 0.00 0.00 3.41
2904 3292 5.116882 GTCATGTAGTTCCCTGACCATAAC 58.883 45.833 0.00 0.00 33.51 1.89
2942 3330 5.152623 TCCTGAATGAAGATGACGAACTT 57.847 39.130 0.00 0.00 0.00 2.66
3083 3472 4.839174 GTCGAAACGATGAAACACTTAAGC 59.161 41.667 1.29 0.00 38.42 3.09
3085 3474 5.006844 TCGAAACGATGAAACACTTAAGCAA 59.993 36.000 1.29 0.00 0.00 3.91
3157 3547 4.448732 TGATCGTTCTTGTCATGTGTTCTG 59.551 41.667 0.00 0.00 0.00 3.02
3221 3611 4.379243 AGCCTGTCGCCGTGAAGG 62.379 66.667 6.05 6.05 44.97 3.46
3239 3629 3.050275 GCACCGACAGCTGAACCC 61.050 66.667 23.35 5.44 0.00 4.11
3278 3668 2.322355 ATCGAGATGCTGAAGTTGGG 57.678 50.000 0.00 0.00 0.00 4.12
3332 3722 7.394816 ACTAAGTTATGGAAACTGTGTATGCT 58.605 34.615 0.00 0.00 0.00 3.79
3446 3836 4.325119 GACCAGTAAAAAGGAAGAGGGAC 58.675 47.826 0.00 0.00 0.00 4.46
3451 3841 5.705905 CAGTAAAAAGGAAGAGGGACGAAAT 59.294 40.000 0.00 0.00 0.00 2.17
3452 3842 6.877322 CAGTAAAAAGGAAGAGGGACGAAATA 59.123 38.462 0.00 0.00 0.00 1.40
3528 3926 1.347062 GCAAGGGGTCAAAATTCCCA 58.653 50.000 2.58 0.00 45.06 4.37
3529 3927 1.696884 GCAAGGGGTCAAAATTCCCAA 59.303 47.619 2.58 0.00 45.06 4.12
3557 3955 0.591170 ACGAAATTGGCGTCCACTTG 59.409 50.000 0.00 0.00 37.42 3.16
3599 3997 5.714333 TGCCAGCCTAATTACTGAAAATTGA 59.286 36.000 4.98 0.00 35.90 2.57
3605 4003 8.680903 AGCCTAATTACTGAAAATTGATGTCTG 58.319 33.333 0.00 0.00 31.63 3.51
3607 4005 9.994432 CCTAATTACTGAAAATTGATGTCTGTC 57.006 33.333 0.00 0.00 31.63 3.51
3625 4023 2.094182 TGTCACGCACCCTTCTAGATTC 60.094 50.000 0.00 0.00 0.00 2.52
3656 4054 3.114065 GCGTAGTTGCTGACTGGTATAC 58.886 50.000 0.00 0.00 39.48 1.47
3657 4055 3.428452 GCGTAGTTGCTGACTGGTATACA 60.428 47.826 5.01 0.00 39.48 2.29
3659 4057 5.506815 GCGTAGTTGCTGACTGGTATACATA 60.507 44.000 5.01 0.00 39.48 2.29
3722 4120 0.605319 CCTTGGTTGCTCGCCTAACA 60.605 55.000 0.00 0.00 0.00 2.41
3723 4121 0.517316 CTTGGTTGCTCGCCTAACAC 59.483 55.000 0.00 0.00 0.00 3.32
3724 4122 0.107831 TTGGTTGCTCGCCTAACACT 59.892 50.000 0.00 0.00 0.00 3.55
3725 4123 0.970640 TGGTTGCTCGCCTAACACTA 59.029 50.000 0.00 0.00 0.00 2.74
3726 4124 1.345089 TGGTTGCTCGCCTAACACTAA 59.655 47.619 0.00 0.00 0.00 2.24
3727 4125 1.730612 GGTTGCTCGCCTAACACTAAC 59.269 52.381 0.00 0.00 0.00 2.34
3728 4126 2.409975 GTTGCTCGCCTAACACTAACA 58.590 47.619 0.00 0.00 0.00 2.41
3745 4143 5.246307 ACTAACAGTGACCCTTGAATTAGC 58.754 41.667 0.00 0.00 0.00 3.09
3758 4156 9.930158 ACCCTTGAATTAGCTTACCAATTATTA 57.070 29.630 0.00 0.00 0.00 0.98
3769 4167 7.888546 AGCTTACCAATTATTACTCCAACAAGT 59.111 33.333 0.00 0.00 0.00 3.16
3785 4183 2.808543 ACAAGTCGCCTGATGAGAAAAC 59.191 45.455 0.00 0.00 0.00 2.43
3839 4685 1.467920 GGCACAAATCCCCTCTCTTG 58.532 55.000 0.00 0.00 0.00 3.02
3842 4688 2.943199 GCACAAATCCCCTCTCTTGGAG 60.943 54.545 0.00 0.00 41.51 3.86
3887 4733 2.473609 GCGAACGTATATCGGATTGCAA 59.526 45.455 0.00 0.00 44.69 4.08
3904 4750 2.158971 TGCAAAGACAGGAGCGCATATA 60.159 45.455 11.47 0.00 0.00 0.86
3905 4751 3.070018 GCAAAGACAGGAGCGCATATAT 58.930 45.455 11.47 0.00 0.00 0.86
3906 4752 4.245660 GCAAAGACAGGAGCGCATATATA 58.754 43.478 11.47 0.00 0.00 0.86
3907 4753 4.872691 GCAAAGACAGGAGCGCATATATAT 59.127 41.667 11.47 0.00 0.00 0.86
3908 4754 5.006165 GCAAAGACAGGAGCGCATATATATC 59.994 44.000 11.47 0.00 0.00 1.63
3909 4755 4.560136 AGACAGGAGCGCATATATATCG 57.440 45.455 11.47 9.06 0.00 2.92
3910 4756 3.948473 AGACAGGAGCGCATATATATCGT 59.052 43.478 11.47 0.00 0.00 3.73
3911 4757 4.033990 ACAGGAGCGCATATATATCGTG 57.966 45.455 11.47 10.85 33.29 4.35
3912 4758 3.694566 ACAGGAGCGCATATATATCGTGA 59.305 43.478 11.47 0.00 31.91 4.35
3913 4759 4.038361 CAGGAGCGCATATATATCGTGAC 58.962 47.826 11.47 6.50 0.00 3.67
3914 4760 3.948473 AGGAGCGCATATATATCGTGACT 59.052 43.478 11.47 8.27 0.00 3.41
3915 4761 4.038361 GGAGCGCATATATATCGTGACTG 58.962 47.826 11.47 0.00 0.00 3.51
3916 4762 4.033990 AGCGCATATATATCGTGACTGG 57.966 45.455 11.47 0.00 0.00 4.00
3918 4764 3.116300 CGCATATATATCGTGACTGGGC 58.884 50.000 0.00 0.00 0.00 5.36
3919 4765 3.428862 CGCATATATATCGTGACTGGGCA 60.429 47.826 0.00 0.00 0.00 5.36
3920 4766 4.115516 GCATATATATCGTGACTGGGCAG 58.884 47.826 0.00 0.00 0.00 4.85
3921 4767 4.686972 CATATATATCGTGACTGGGCAGG 58.313 47.826 0.00 0.00 0.00 4.85
3922 4768 0.679505 TATATCGTGACTGGGCAGGC 59.320 55.000 0.00 0.00 36.85 4.85
3923 4769 2.044806 ATATCGTGACTGGGCAGGCC 62.045 60.000 5.91 5.91 34.90 5.19
3924 4770 6.897290 TATATATCGTGACTGGGCAGGCCT 62.897 50.000 15.38 0.00 34.90 5.19
3925 4771 4.767255 CGTGACTGGGCAGGCCTC 62.767 72.222 15.38 4.86 34.90 4.70
3926 4772 4.767255 GTGACTGGGCAGGCCTCG 62.767 72.222 15.38 7.92 34.90 4.63
3955 4801 2.552743 GGTTCTCGTGGAAGAAAAAGGG 59.447 50.000 0.00 0.00 37.04 3.95
3967 4813 4.955693 AGAAAAAGGGGAGCTTTAGGAT 57.044 40.909 0.00 0.00 0.00 3.24
3968 4814 4.861196 AGAAAAAGGGGAGCTTTAGGATC 58.139 43.478 0.00 0.00 0.00 3.36
3969 4815 4.542119 AGAAAAAGGGGAGCTTTAGGATCT 59.458 41.667 0.00 0.00 0.00 2.75
3970 4816 4.511786 AAAAGGGGAGCTTTAGGATCTC 57.488 45.455 0.00 0.00 0.00 2.75
3971 4817 1.710816 AGGGGAGCTTTAGGATCTCG 58.289 55.000 0.00 0.00 30.27 4.04
3972 4818 1.218196 AGGGGAGCTTTAGGATCTCGA 59.782 52.381 0.00 0.00 30.27 4.04
3980 4838 6.222038 AGCTTTAGGATCTCGAATGTTACA 57.778 37.500 0.00 0.00 0.00 2.41
4001 4859 3.716195 CGCACCAGATCCACCCCA 61.716 66.667 0.00 0.00 0.00 4.96
4015 4873 2.104132 CCCATGCGATGTCGACGA 59.896 61.111 11.62 0.00 43.02 4.20
4016 4874 2.230940 CCCATGCGATGTCGACGAC 61.231 63.158 20.97 20.97 43.02 4.34
4017 4875 2.568031 CCATGCGATGTCGACGACG 61.568 63.158 22.06 23.08 43.02 5.12
4071 4932 3.393970 CGGAGGGCAGGAGAAGCA 61.394 66.667 0.00 0.00 0.00 3.91
4074 4935 1.077858 GAGGGCAGGAGAAGCAAGG 60.078 63.158 0.00 0.00 0.00 3.61
4080 4941 2.029560 GGCAGGAGAAGCAAGGAAAAAG 60.030 50.000 0.00 0.00 0.00 2.27
4081 4942 2.887152 GCAGGAGAAGCAAGGAAAAAGA 59.113 45.455 0.00 0.00 0.00 2.52
4082 4943 3.057666 GCAGGAGAAGCAAGGAAAAAGAG 60.058 47.826 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 6.317642 CGTCAAAACCTATCAACATGGGATAA 59.682 38.462 9.69 0.00 34.16 1.75
98 99 5.820423 CGTCAAAACCTATCAACATGGGATA 59.180 40.000 0.00 3.51 34.16 2.59
180 220 1.230324 GCGTGCCTCTTTCAGAAAGT 58.770 50.000 20.28 0.00 39.52 2.66
288 336 0.790814 GTGCCTCCTCGAAAACGAAG 59.209 55.000 0.00 0.00 0.00 3.79
317 366 1.577328 ATGGTTGTGCTTTCGCGAGG 61.577 55.000 9.59 7.89 39.65 4.63
438 589 3.875134 ACGATTTTGTTTTCGTGAGAGGT 59.125 39.130 0.00 0.00 46.03 3.85
462 613 2.271821 ACGCGTTTTCTGCTGTTTTT 57.728 40.000 5.58 0.00 0.00 1.94
509 819 1.275471 TTGTGCTTTCGCGAGAGTCG 61.275 55.000 25.34 4.35 43.69 4.18
547 857 0.030101 TTCGCGAAAGGCAGGTTTTG 59.970 50.000 21.14 0.00 43.84 2.44
550 860 1.949257 CTTTCGCGAAAGGCAGGTT 59.051 52.632 40.75 0.00 42.96 3.50
551 861 3.655481 CTTTCGCGAAAGGCAGGT 58.345 55.556 40.75 0.00 42.96 4.00
582 892 7.116519 TCGGAAATGAAAAAGAAACGTGTTTTT 59.883 29.630 13.27 13.27 41.49 1.94
583 893 6.586844 TCGGAAATGAAAAAGAAACGTGTTTT 59.413 30.769 0.00 0.00 31.87 2.43
584 894 6.094061 TCGGAAATGAAAAAGAAACGTGTTT 58.906 32.000 0.00 0.00 35.14 2.83
585 895 5.642686 TCGGAAATGAAAAAGAAACGTGTT 58.357 33.333 0.00 0.00 0.00 3.32
586 896 5.065474 TCTCGGAAATGAAAAAGAAACGTGT 59.935 36.000 0.00 0.00 0.00 4.49
587 897 5.507077 TCTCGGAAATGAAAAAGAAACGTG 58.493 37.500 0.00 0.00 0.00 4.49
588 898 5.277828 CCTCTCGGAAATGAAAAAGAAACGT 60.278 40.000 0.00 0.00 0.00 3.99
589 899 5.147162 CCTCTCGGAAATGAAAAAGAAACG 58.853 41.667 0.00 0.00 0.00 3.60
590 900 4.917998 GCCTCTCGGAAATGAAAAAGAAAC 59.082 41.667 0.00 0.00 0.00 2.78
591 901 4.582656 TGCCTCTCGGAAATGAAAAAGAAA 59.417 37.500 0.00 0.00 0.00 2.52
592 902 4.141287 TGCCTCTCGGAAATGAAAAAGAA 58.859 39.130 0.00 0.00 0.00 2.52
593 903 3.750371 TGCCTCTCGGAAATGAAAAAGA 58.250 40.909 0.00 0.00 0.00 2.52
594 904 4.418392 CATGCCTCTCGGAAATGAAAAAG 58.582 43.478 0.00 0.00 31.15 2.27
595 905 3.193267 CCATGCCTCTCGGAAATGAAAAA 59.807 43.478 0.00 0.00 31.15 1.94
596 906 2.754552 CCATGCCTCTCGGAAATGAAAA 59.245 45.455 0.00 0.00 31.15 2.29
597 907 2.368439 CCATGCCTCTCGGAAATGAAA 58.632 47.619 0.00 0.00 31.15 2.69
598 908 2.018644 GCCATGCCTCTCGGAAATGAA 61.019 52.381 0.00 0.00 31.15 2.57
599 909 0.464373 GCCATGCCTCTCGGAAATGA 60.464 55.000 0.00 0.00 31.15 2.57
600 910 1.450531 GGCCATGCCTCTCGGAAATG 61.451 60.000 0.00 0.00 46.69 2.32
601 911 1.152881 GGCCATGCCTCTCGGAAAT 60.153 57.895 0.00 0.00 46.69 2.17
602 912 2.272146 GGCCATGCCTCTCGGAAA 59.728 61.111 0.00 0.00 46.69 3.13
612 922 2.541120 GCGAGAGTCATGGCCATGC 61.541 63.158 36.47 29.69 38.65 4.06
613 923 2.242572 CGCGAGAGTCATGGCCATG 61.243 63.158 35.76 35.76 40.09 3.66
614 924 1.960040 TTCGCGAGAGTCATGGCCAT 61.960 55.000 14.09 14.09 43.69 4.40
615 925 2.563050 CTTCGCGAGAGTCATGGCCA 62.563 60.000 8.56 8.56 43.69 5.36
616 926 1.880340 CTTCGCGAGAGTCATGGCC 60.880 63.158 9.59 0.00 43.69 5.36
617 927 2.520904 GCTTCGCGAGAGTCATGGC 61.521 63.158 9.59 0.00 43.69 4.40
618 928 0.737367 TTGCTTCGCGAGAGTCATGG 60.737 55.000 9.59 0.00 43.69 3.66
619 929 1.070821 TTTGCTTCGCGAGAGTCATG 58.929 50.000 9.59 0.00 43.69 3.07
620 930 1.461127 GTTTTGCTTCGCGAGAGTCAT 59.539 47.619 9.59 0.00 43.69 3.06
621 931 0.859232 GTTTTGCTTCGCGAGAGTCA 59.141 50.000 9.59 9.49 43.69 3.41
622 932 0.164002 GGTTTTGCTTCGCGAGAGTC 59.836 55.000 9.59 7.22 43.69 3.36
623 933 1.557443 CGGTTTTGCTTCGCGAGAGT 61.557 55.000 9.59 0.00 43.69 3.24
624 934 1.130613 CGGTTTTGCTTCGCGAGAG 59.869 57.895 9.59 11.22 43.69 3.20
625 935 1.593209 ACGGTTTTGCTTCGCGAGA 60.593 52.632 9.59 0.00 39.20 4.04
626 936 1.438710 CACGGTTTTGCTTCGCGAG 60.439 57.895 9.59 4.97 0.00 5.03
627 937 1.883544 TCACGGTTTTGCTTCGCGA 60.884 52.632 3.71 3.71 0.00 5.87
628 938 1.721133 GTCACGGTTTTGCTTCGCG 60.721 57.895 0.00 0.00 0.00 5.87
629 939 0.384353 GAGTCACGGTTTTGCTTCGC 60.384 55.000 0.00 0.00 0.00 4.70
630 940 0.111266 CGAGTCACGGTTTTGCTTCG 60.111 55.000 0.00 0.00 38.46 3.79
631 941 0.384353 GCGAGTCACGGTTTTGCTTC 60.384 55.000 0.00 0.00 42.83 3.86
632 942 1.092921 TGCGAGTCACGGTTTTGCTT 61.093 50.000 0.00 0.00 42.83 3.91
633 943 1.522806 TGCGAGTCACGGTTTTGCT 60.523 52.632 0.00 0.00 42.83 3.91
634 944 1.368850 GTGCGAGTCACGGTTTTGC 60.369 57.895 0.00 0.00 42.83 3.68
635 945 4.893241 GTGCGAGTCACGGTTTTG 57.107 55.556 0.00 0.00 42.83 2.44
642 952 1.442857 CTCCTGTCGTGCGAGTCAC 60.443 63.158 0.00 0.00 42.23 3.67
643 953 2.626780 CCTCCTGTCGTGCGAGTCA 61.627 63.158 0.00 0.00 0.00 3.41
644 954 1.863662 TTCCTCCTGTCGTGCGAGTC 61.864 60.000 0.00 0.00 0.00 3.36
645 955 1.461091 TTTCCTCCTGTCGTGCGAGT 61.461 55.000 0.00 0.00 0.00 4.18
646 956 0.319555 TTTTCCTCCTGTCGTGCGAG 60.320 55.000 0.00 0.00 0.00 5.03
647 957 0.105224 TTTTTCCTCCTGTCGTGCGA 59.895 50.000 0.00 0.00 0.00 5.10
648 958 0.234884 GTTTTTCCTCCTGTCGTGCG 59.765 55.000 0.00 0.00 0.00 5.34
649 959 0.234884 CGTTTTTCCTCCTGTCGTGC 59.765 55.000 0.00 0.00 0.00 5.34
650 960 1.260561 CACGTTTTTCCTCCTGTCGTG 59.739 52.381 0.00 0.00 40.33 4.35
651 961 1.134610 ACACGTTTTTCCTCCTGTCGT 60.135 47.619 0.00 0.00 0.00 4.34
652 962 1.578583 ACACGTTTTTCCTCCTGTCG 58.421 50.000 0.00 0.00 0.00 4.35
653 963 4.365899 AAAACACGTTTTTCCTCCTGTC 57.634 40.909 0.00 0.00 39.52 3.51
654 964 4.794278 AAAAACACGTTTTTCCTCCTGT 57.206 36.364 13.49 0.00 46.30 4.00
742 1054 1.202325 GGTTCGGCTTTTGAAACGGTT 60.202 47.619 0.00 0.00 0.00 4.44
744 1056 3.173247 GGTTCGGCTTTTGAAACGG 57.827 52.632 0.00 0.00 0.00 4.44
748 1060 0.378962 CACACGGTTCGGCTTTTGAA 59.621 50.000 0.00 0.00 0.00 2.69
750 1062 0.938713 TACACACGGTTCGGCTTTTG 59.061 50.000 0.00 0.00 0.00 2.44
785 1099 1.293498 GCTCTGGACGCTTCTTCCA 59.707 57.895 0.00 0.00 41.06 3.53
863 1177 4.200283 GACAGAGAGGCTCCGGCG 62.200 72.222 11.71 0.00 39.81 6.46
864 1178 3.844090 GGACAGAGAGGCTCCGGC 61.844 72.222 11.71 1.78 37.82 6.13
865 1179 3.522731 CGGACAGAGAGGCTCCGG 61.523 72.222 11.71 0.00 42.76 5.14
866 1180 3.522731 CCGGACAGAGAGGCTCCG 61.523 72.222 11.71 7.29 45.49 4.63
867 1181 1.950973 GAACCGGACAGAGAGGCTCC 61.951 65.000 9.46 2.69 0.00 4.70
868 1182 0.968393 AGAACCGGACAGAGAGGCTC 60.968 60.000 9.46 6.34 0.00 4.70
869 1183 0.331954 TAGAACCGGACAGAGAGGCT 59.668 55.000 9.46 0.00 0.00 4.58
870 1184 0.741915 CTAGAACCGGACAGAGAGGC 59.258 60.000 9.46 0.00 0.00 4.70
871 1185 0.741915 GCTAGAACCGGACAGAGAGG 59.258 60.000 9.46 0.00 0.00 3.69
872 1186 0.741915 GGCTAGAACCGGACAGAGAG 59.258 60.000 9.46 0.00 0.00 3.20
873 1187 0.039180 TGGCTAGAACCGGACAGAGA 59.961 55.000 9.46 0.00 0.00 3.10
874 1188 0.895530 TTGGCTAGAACCGGACAGAG 59.104 55.000 9.46 0.49 0.00 3.35
875 1189 0.895530 CTTGGCTAGAACCGGACAGA 59.104 55.000 9.46 0.00 0.00 3.41
876 1190 0.741221 GCTTGGCTAGAACCGGACAG 60.741 60.000 9.46 0.00 0.00 3.51
877 1191 1.295423 GCTTGGCTAGAACCGGACA 59.705 57.895 9.46 0.00 0.00 4.02
878 1192 1.449778 GGCTTGGCTAGAACCGGAC 60.450 63.158 9.46 0.99 0.00 4.79
879 1193 2.987125 GGCTTGGCTAGAACCGGA 59.013 61.111 9.46 0.00 0.00 5.14
880 1194 2.511600 CGGCTTGGCTAGAACCGG 60.512 66.667 0.00 0.00 40.18 5.28
882 1196 2.399356 GCACGGCTTGGCTAGAACC 61.399 63.158 0.00 0.00 0.00 3.62
883 1197 2.740714 CGCACGGCTTGGCTAGAAC 61.741 63.158 0.00 0.00 0.00 3.01
884 1198 2.434185 CGCACGGCTTGGCTAGAA 60.434 61.111 0.00 0.00 0.00 2.10
885 1199 3.691342 ACGCACGGCTTGGCTAGA 61.691 61.111 0.00 0.00 0.00 2.43
886 1200 3.490759 CACGCACGGCTTGGCTAG 61.491 66.667 0.00 0.00 0.00 3.42
887 1201 2.437518 TAACACGCACGGCTTGGCTA 62.438 55.000 7.16 0.00 31.96 3.93
888 1202 3.818121 TAACACGCACGGCTTGGCT 62.818 57.895 7.16 0.00 31.96 4.75
889 1203 3.350612 TAACACGCACGGCTTGGC 61.351 61.111 7.16 0.00 31.96 4.52
890 1204 1.897398 GAGTAACACGCACGGCTTGG 61.897 60.000 7.16 0.00 31.96 3.61
891 1205 1.218875 TGAGTAACACGCACGGCTTG 61.219 55.000 0.00 1.75 33.94 4.01
892 1206 0.531090 TTGAGTAACACGCACGGCTT 60.531 50.000 0.00 0.00 0.00 4.35
893 1207 0.531090 TTTGAGTAACACGCACGGCT 60.531 50.000 0.00 0.00 0.00 5.52
894 1208 0.305313 TTTTGAGTAACACGCACGGC 59.695 50.000 0.00 0.00 0.00 5.68
895 1209 2.741122 TTTTTGAGTAACACGCACGG 57.259 45.000 0.00 0.00 0.00 4.94
914 1228 5.069318 CCTTGGCTTTCTCTCTCTCTTTTT 58.931 41.667 0.00 0.00 0.00 1.94
915 1229 4.650734 CCTTGGCTTTCTCTCTCTCTTTT 58.349 43.478 0.00 0.00 0.00 2.27
916 1230 3.558958 GCCTTGGCTTTCTCTCTCTCTTT 60.559 47.826 4.11 0.00 0.00 2.52
917 1231 2.027285 GCCTTGGCTTTCTCTCTCTCTT 60.027 50.000 4.11 0.00 0.00 2.85
918 1232 1.554617 GCCTTGGCTTTCTCTCTCTCT 59.445 52.381 4.11 0.00 0.00 3.10
919 1233 1.277557 TGCCTTGGCTTTCTCTCTCTC 59.722 52.381 13.18 0.00 0.00 3.20
920 1234 1.356124 TGCCTTGGCTTTCTCTCTCT 58.644 50.000 13.18 0.00 0.00 3.10
921 1235 2.083002 CTTGCCTTGGCTTTCTCTCTC 58.917 52.381 13.18 0.00 0.00 3.20
922 1236 1.885790 GCTTGCCTTGGCTTTCTCTCT 60.886 52.381 13.18 0.00 0.00 3.10
923 1237 0.525311 GCTTGCCTTGGCTTTCTCTC 59.475 55.000 13.18 0.00 0.00 3.20
924 1238 0.897401 GGCTTGCCTTGGCTTTCTCT 60.897 55.000 13.18 0.00 0.00 3.10
925 1239 1.588597 GGCTTGCCTTGGCTTTCTC 59.411 57.895 13.18 0.00 0.00 2.87
926 1240 2.270986 CGGCTTGCCTTGGCTTTCT 61.271 57.895 13.18 0.00 0.00 2.52
927 1241 2.259511 CGGCTTGCCTTGGCTTTC 59.740 61.111 13.18 1.71 0.00 2.62
928 1242 3.994853 GCGGCTTGCCTTGGCTTT 61.995 61.111 13.18 0.00 37.76 3.51
1031 1351 2.673341 AGCACGAGTGAGCTCCGA 60.673 61.111 16.27 0.00 37.49 4.55
1338 1671 0.179215 GCATCAAGGAAACGTCAGCG 60.179 55.000 0.00 0.00 44.93 5.18
1351 1684 2.228582 CCGAACAAACATCAGGCATCAA 59.771 45.455 0.00 0.00 0.00 2.57
1382 1755 2.959030 AGGTGCGCTAAGTCTGATGATA 59.041 45.455 9.73 0.00 0.00 2.15
1654 2041 0.392193 GGGCAGTGTGATCTCCAGTG 60.392 60.000 13.37 13.37 36.53 3.66
1706 2093 6.482835 TGAAAATTAGATGAAATGTACCGCG 58.517 36.000 0.00 0.00 0.00 6.46
1780 2167 5.455183 CCATATAGCTTGTGTGATCCTTCCA 60.455 44.000 0.00 0.00 0.00 3.53
1860 2247 5.545588 CAGAGAACATCCTTCAGTCTTGAA 58.454 41.667 0.00 0.00 40.92 2.69
1887 2274 1.952621 TCTCCCGAACCTCTTGGAAT 58.047 50.000 0.00 0.00 37.04 3.01
1900 2287 9.013229 TGAAATGATGGAAAATAATATCTCCCG 57.987 33.333 0.54 0.00 0.00 5.14
1915 2302 4.641541 CAGTGGCACTAATGAAATGATGGA 59.358 41.667 21.59 0.00 0.00 3.41
1921 2308 5.321102 TGTAACCAGTGGCACTAATGAAAT 58.679 37.500 21.59 5.27 0.00 2.17
1945 2332 0.880278 TGCAGCTCGTCAAGTGGAAC 60.880 55.000 0.00 0.00 0.00 3.62
1952 2339 3.814842 CCCATAAATATGCAGCTCGTCAA 59.185 43.478 0.00 0.00 32.40 3.18
1954 2341 2.160417 GCCCATAAATATGCAGCTCGTC 59.840 50.000 0.00 0.00 32.22 4.20
1956 2343 2.153645 TGCCCATAAATATGCAGCTCG 58.846 47.619 12.15 0.00 34.50 5.03
2085 2472 3.543680 AGCATATGTCGGCTTTGTAGT 57.456 42.857 4.29 0.00 36.92 2.73
2458 2845 4.101645 TCATAGTACTAGCTCTGTCCCC 57.898 50.000 8.85 0.00 0.00 4.81
2530 2917 1.291132 GAGCGGAGTTATGCAGAACC 58.709 55.000 20.09 11.61 0.00 3.62
2568 2955 7.429374 AGAACATACTCATGAGGATTTCAGA 57.571 36.000 27.06 9.10 39.68 3.27
2708 3096 4.342092 AGGTTTTCATGGAACTTTCTGTGG 59.658 41.667 11.08 0.00 0.00 4.17
2709 3097 5.284079 CAGGTTTTCATGGAACTTTCTGTG 58.716 41.667 11.08 0.00 0.00 3.66
2738 3126 2.483877 CGGCAGAGCAAAATCTAACACA 59.516 45.455 0.00 0.00 0.00 3.72
2741 3129 1.468520 TGCGGCAGAGCAAAATCTAAC 59.531 47.619 0.00 0.00 45.06 2.34
2777 3165 2.753452 AGCTTGCTGGTCATCTTTGATG 59.247 45.455 0.00 1.45 33.56 3.07
2942 3330 2.997315 CACCCGCTCTGAGTCCCA 60.997 66.667 6.53 0.00 0.00 4.37
3106 3496 3.002656 GGAGTACATTGCACATCAATCCG 59.997 47.826 0.00 0.00 43.21 4.18
3157 3547 0.438830 GAACATCGAACGACCTGCAC 59.561 55.000 0.00 0.00 0.00 4.57
3221 3611 3.050275 GGTTCAGCTGTCGGTGCC 61.050 66.667 14.67 4.61 38.50 5.01
3239 3629 2.892373 TTGTAAATGCGAAGAAGGCG 57.108 45.000 0.00 0.00 0.00 5.52
3278 3668 3.364964 CCAGACAAACCGCTCACATTAAC 60.365 47.826 0.00 0.00 0.00 2.01
3446 3836 2.731976 GCAGGCGACCTAGATTATTTCG 59.268 50.000 0.00 0.00 29.64 3.46
3451 3841 2.067365 TCAGCAGGCGACCTAGATTA 57.933 50.000 0.00 0.00 29.64 1.75
3452 3842 1.137872 CTTCAGCAGGCGACCTAGATT 59.862 52.381 0.00 0.00 29.64 2.40
3528 3926 5.116069 ACGCCAATTTCGTAGAAACAATT 57.884 34.783 1.09 0.00 45.90 2.32
3529 3927 4.379082 GGACGCCAATTTCGTAGAAACAAT 60.379 41.667 2.86 0.00 45.90 2.71
3557 3955 4.569943 TGGCACACTTCTTTCATCTCTAC 58.430 43.478 0.00 0.00 0.00 2.59
3599 3997 0.320771 GAAGGGTGCGTGACAGACAT 60.321 55.000 0.00 0.00 0.00 3.06
3605 4003 2.541556 GAATCTAGAAGGGTGCGTGAC 58.458 52.381 0.00 0.00 0.00 3.67
3607 4005 1.560923 CGAATCTAGAAGGGTGCGTG 58.439 55.000 0.00 0.00 0.00 5.34
3636 4034 4.365899 TGTATACCAGTCAGCAACTACG 57.634 45.455 0.00 0.00 36.07 3.51
3638 4036 7.123697 ACTGTTATGTATACCAGTCAGCAACTA 59.876 37.037 6.67 0.00 36.07 2.24
3640 4038 6.036083 CACTGTTATGTATACCAGTCAGCAAC 59.964 42.308 8.91 0.15 36.06 4.17
3656 4054 5.491070 TCAGAGATCCAAACCACTGTTATG 58.509 41.667 0.00 0.00 33.30 1.90
3657 4055 5.762179 TCAGAGATCCAAACCACTGTTAT 57.238 39.130 0.00 0.00 33.30 1.89
3659 4057 4.437682 TTCAGAGATCCAAACCACTGTT 57.562 40.909 0.00 0.00 35.82 3.16
3722 4120 5.013183 AGCTAATTCAAGGGTCACTGTTAGT 59.987 40.000 0.00 0.00 0.00 2.24
3723 4121 5.491982 AGCTAATTCAAGGGTCACTGTTAG 58.508 41.667 0.00 0.00 0.00 2.34
3724 4122 5.499004 AGCTAATTCAAGGGTCACTGTTA 57.501 39.130 0.00 0.00 0.00 2.41
3725 4123 4.373156 AGCTAATTCAAGGGTCACTGTT 57.627 40.909 0.00 0.00 0.00 3.16
3726 4124 4.373156 AAGCTAATTCAAGGGTCACTGT 57.627 40.909 0.00 0.00 0.00 3.55
3727 4125 4.636206 GGTAAGCTAATTCAAGGGTCACTG 59.364 45.833 0.00 0.00 0.00 3.66
3728 4126 4.288626 TGGTAAGCTAATTCAAGGGTCACT 59.711 41.667 0.00 0.00 0.00 3.41
3745 4143 8.388103 CGACTTGTTGGAGTAATAATTGGTAAG 58.612 37.037 0.00 0.00 0.00 2.34
3758 4156 0.687354 ATCAGGCGACTTGTTGGAGT 59.313 50.000 0.00 0.00 40.21 3.85
3763 4161 2.839486 TTCTCATCAGGCGACTTGTT 57.161 45.000 0.00 0.00 40.21 2.83
3764 4162 2.808543 GTTTTCTCATCAGGCGACTTGT 59.191 45.455 0.00 0.00 40.21 3.16
3769 4167 4.832248 ACTATTGTTTTCTCATCAGGCGA 58.168 39.130 0.00 0.00 0.00 5.54
3839 4685 2.135933 CGGATAAAATCGGACTGCTCC 58.864 52.381 0.00 0.00 0.00 4.70
3877 4723 1.945819 GCTCCTGTCTTTGCAATCCGA 60.946 52.381 0.00 0.00 0.00 4.55
3887 4733 4.399618 ACGATATATATGCGCTCCTGTCTT 59.600 41.667 9.73 0.00 0.00 3.01
3904 4750 1.447643 GCCTGCCCAGTCACGATAT 59.552 57.895 0.00 0.00 0.00 1.63
3905 4751 2.731571 GGCCTGCCCAGTCACGATA 61.732 63.158 0.00 0.00 0.00 2.92
3906 4752 4.101448 GGCCTGCCCAGTCACGAT 62.101 66.667 0.00 0.00 0.00 3.73
3908 4754 4.767255 GAGGCCTGCCCAGTCACG 62.767 72.222 12.00 0.00 36.58 4.35
3909 4755 4.767255 CGAGGCCTGCCCAGTCAC 62.767 72.222 12.00 0.00 36.58 3.67
3955 4801 4.329462 ACATTCGAGATCCTAAAGCTCC 57.671 45.455 0.00 0.00 0.00 4.70
3967 4813 3.435566 GTGCGATCTGTAACATTCGAGA 58.564 45.455 5.51 0.00 33.59 4.04
3968 4814 2.535984 GGTGCGATCTGTAACATTCGAG 59.464 50.000 5.51 0.00 33.59 4.04
3969 4815 2.094442 TGGTGCGATCTGTAACATTCGA 60.094 45.455 5.51 0.00 33.59 3.71
3970 4816 2.267426 TGGTGCGATCTGTAACATTCG 58.733 47.619 0.00 0.00 34.83 3.34
3971 4817 3.521560 TCTGGTGCGATCTGTAACATTC 58.478 45.455 0.00 0.00 0.00 2.67
3972 4818 3.610040 TCTGGTGCGATCTGTAACATT 57.390 42.857 0.00 0.00 0.00 2.71
3980 4838 1.690219 GGGTGGATCTGGTGCGATCT 61.690 60.000 0.00 0.00 39.73 2.75
4001 4859 2.789249 TCGTCGTCGACATCGCAT 59.211 55.556 24.13 0.00 41.35 4.73
4015 4873 2.501222 GTGATGCGTCGTCGTCGT 60.501 61.111 13.09 0.00 39.49 4.34
4016 4874 3.238241 GGTGATGCGTCGTCGTCG 61.238 66.667 7.53 7.53 39.49 5.12
4017 4875 2.879462 GGGTGATGCGTCGTCGTC 60.879 66.667 3.66 0.00 39.49 4.20
4070 4931 6.770303 ACCTTTTCTCTCTCTCTTTTTCCTTG 59.230 38.462 0.00 0.00 0.00 3.61
4071 4932 6.905736 ACCTTTTCTCTCTCTCTTTTTCCTT 58.094 36.000 0.00 0.00 0.00 3.36
4074 4935 8.779303 CCTTTACCTTTTCTCTCTCTCTTTTTC 58.221 37.037 0.00 0.00 0.00 2.29
4080 4941 5.175127 CAGCCTTTACCTTTTCTCTCTCTC 58.825 45.833 0.00 0.00 0.00 3.20
4081 4942 4.564613 GCAGCCTTTACCTTTTCTCTCTCT 60.565 45.833 0.00 0.00 0.00 3.10
4082 4943 3.687212 GCAGCCTTTACCTTTTCTCTCTC 59.313 47.826 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.