Multiple sequence alignment - TraesCS2D01G246900

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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 TraesCS2D01G246900 chr2D 100.000 5989 0 0 1 5989 290734420 290740408 0.000000e+00 11060.0
1 TraesCS2D01G246900 chr2D 91.347 809 60 3 1 800 590029301 590028494 0.000000e+00 1098.0
2 TraesCS2D01G246900 chr2D 91.100 809 63 2 1 800 600313789 600312981 0.000000e+00 1086.0
3 TraesCS2D01G246900 chr2D 89.344 244 20 6 5552 5794 290747020 290747258 9.750000e-78 302.0
4 TraesCS2D01G246900 chr2D 93.878 98 6 0 4525 4622 2476584 2476681 1.340000e-31 148.0
5 TraesCS2D01G246900 chr2D 90.291 103 10 0 5552 5654 48314304 48314406 1.050000e-27 135.0
6 TraesCS2D01G246900 chr2D 80.952 105 10 9 5827 5926 34359439 34359538 2.310000e-09 75.0
7 TraesCS2D01G246900 chr2D 91.489 47 4 0 3167 3213 579190785 579190739 1.390000e-06 65.8
8 TraesCS2D01G246900 chr2A 96.596 4700 110 22 753 5421 315041845 315037165 0.000000e+00 7747.0
9 TraesCS2D01G246900 chr2A 90.864 810 64 3 1 800 765216377 765215568 0.000000e+00 1077.0
10 TraesCS2D01G246900 chr2A 90.741 810 65 3 1 800 765245206 765244397 0.000000e+00 1072.0
11 TraesCS2D01G246900 chr2A 89.791 382 31 4 5402 5780 315037136 315036760 3.250000e-132 483.0
12 TraesCS2D01G246900 chr2A 89.216 102 10 1 5196 5296 314669542 314669441 6.300000e-25 126.0
13 TraesCS2D01G246900 chr2B 93.534 4779 183 53 836 5554 340590359 340595071 0.000000e+00 6998.0
14 TraesCS2D01G246900 chr2B 90.786 369 31 2 836 1203 340552641 340553007 1.940000e-134 490.0
15 TraesCS2D01G246900 chr2B 90.291 103 10 0 5550 5652 300252835 300252733 1.050000e-27 135.0
16 TraesCS2D01G246900 chr2B 88.785 107 12 0 5552 5658 40937755 40937649 1.350000e-26 132.0
17 TraesCS2D01G246900 chr2B 93.023 43 3 0 3171 3213 696355719 696355677 5.010000e-06 63.9
18 TraesCS2D01G246900 chr2B 96.970 33 1 0 5954 5986 361643370 361643402 8.390000e-04 56.5
19 TraesCS2D01G246900 chr1D 90.943 806 62 5 1 797 461900307 461901110 0.000000e+00 1074.0
20 TraesCS2D01G246900 chr1D 90.729 809 64 3 1 800 486402007 486402813 0.000000e+00 1068.0
21 TraesCS2D01G246900 chr3B 90.741 810 65 3 1 800 2343075 2342266 0.000000e+00 1072.0
22 TraesCS2D01G246900 chr4D 90.718 808 65 3 1 799 28487864 28488670 0.000000e+00 1068.0
23 TraesCS2D01G246900 chr3D 90.170 824 71 3 1 815 341474236 341473414 0.000000e+00 1064.0
24 TraesCS2D01G246900 chr3D 93.069 101 6 1 4522 4622 601221752 601221851 4.840000e-31 147.0
25 TraesCS2D01G246900 chr5D 90.710 366 34 0 1084 1449 491439676 491440041 6.980000e-134 488.0
26 TraesCS2D01G246900 chr5D 74.079 760 173 19 3322 4065 491440872 491441623 2.110000e-74 291.0
27 TraesCS2D01G246900 chr5D 91.089 101 7 1 5552 5652 556863008 556863106 1.050000e-27 135.0
28 TraesCS2D01G246900 chr5D 85.938 64 8 1 5858 5921 547838816 547838754 3.870000e-07 67.6
29 TraesCS2D01G246900 chr5A 89.617 366 38 0 1084 1449 613589180 613589545 3.270000e-127 466.0
30 TraesCS2D01G246900 chr5A 74.737 760 171 18 3322 4065 613590490 613591244 2.690000e-83 320.0
31 TraesCS2D01G246900 chr5A 92.929 99 7 0 5198 5296 27110710 27110808 1.740000e-30 145.0
32 TraesCS2D01G246900 chr5A 80.645 93 11 6 5833 5922 692537844 692537932 1.390000e-06 65.8
33 TraesCS2D01G246900 chr5A 84.286 70 6 5 5837 5902 589758430 589758498 5.010000e-06 63.9
34 TraesCS2D01G246900 chrUn 94.898 98 5 0 4525 4622 15904018 15903921 2.890000e-33 154.0
35 TraesCS2D01G246900 chrUn 82.278 79 8 4 5827 5902 1651416 1651491 5.010000e-06 63.9
36 TraesCS2D01G246900 chr1A 93.269 104 4 3 4522 4624 460934471 460934572 3.740000e-32 150.0
37 TraesCS2D01G246900 chr1A 82.278 79 8 4 5827 5902 570096684 570096759 5.010000e-06 63.9
38 TraesCS2D01G246900 chr4A 93.814 97 5 1 4526 4622 37060207 37060112 1.740000e-30 145.0
39 TraesCS2D01G246900 chr3A 92.929 99 7 0 4524 4622 12778804 12778902 1.740000e-30 145.0
40 TraesCS2D01G246900 chr5B 92.857 98 7 0 4526 4623 539467724 539467821 6.260000e-30 143.0
41 TraesCS2D01G246900 chr5B 91.089 101 9 0 5552 5652 319316132 319316232 2.910000e-28 137.0
42 TraesCS2D01G246900 chr7B 91.089 101 9 0 5552 5652 418864031 418863931 2.910000e-28 137.0
43 TraesCS2D01G246900 chr7B 89.524 105 9 2 5552 5656 657535659 657535557 1.350000e-26 132.0
44 TraesCS2D01G246900 chr7A 93.258 89 6 0 5208 5296 710467689 710467601 1.350000e-26 132.0
45 TraesCS2D01G246900 chr7A 90.698 43 2 2 3172 3213 92881518 92881477 8.390000e-04 56.5
46 TraesCS2D01G246900 chr7A 90.698 43 2 2 3172 3213 92883220 92883179 8.390000e-04 56.5
47 TraesCS2D01G246900 chr7A 90.698 43 2 2 3172 3213 92885101 92885060 8.390000e-04 56.5
48 TraesCS2D01G246900 chr7A 96.970 33 1 0 5858 5890 676068479 676068447 8.390000e-04 56.5
49 TraesCS2D01G246900 chr7D 85.294 68 5 5 5839 5902 201159887 201159953 1.390000e-06 65.8
50 TraesCS2D01G246900 chr7D 88.000 50 4 2 3228 3276 515820160 515820208 2.330000e-04 58.4
51 TraesCS2D01G246900 chr7D 94.444 36 2 0 5954 5989 10636108 10636143 8.390000e-04 56.5
52 TraesCS2D01G246900 chr6D 100.000 31 0 0 3168 3198 42547739 42547709 2.330000e-04 58.4
53 TraesCS2D01G246900 chr6A 96.970 33 1 0 5858 5890 590135629 590135661 8.390000e-04 56.5


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 TraesCS2D01G246900 chr2D 290734420 290740408 5988 False 11060.0 11060 100.0000 1 5989 1 chr2D.!!$F4 5988
1 TraesCS2D01G246900 chr2D 590028494 590029301 807 True 1098.0 1098 91.3470 1 800 1 chr2D.!!$R2 799
2 TraesCS2D01G246900 chr2D 600312981 600313789 808 True 1086.0 1086 91.1000 1 800 1 chr2D.!!$R3 799
3 TraesCS2D01G246900 chr2A 315036760 315041845 5085 True 4115.0 7747 93.1935 753 5780 2 chr2A.!!$R4 5027
4 TraesCS2D01G246900 chr2A 765215568 765216377 809 True 1077.0 1077 90.8640 1 800 1 chr2A.!!$R2 799
5 TraesCS2D01G246900 chr2A 765244397 765245206 809 True 1072.0 1072 90.7410 1 800 1 chr2A.!!$R3 799
6 TraesCS2D01G246900 chr2B 340590359 340595071 4712 False 6998.0 6998 93.5340 836 5554 1 chr2B.!!$F2 4718
7 TraesCS2D01G246900 chr1D 461900307 461901110 803 False 1074.0 1074 90.9430 1 797 1 chr1D.!!$F1 796
8 TraesCS2D01G246900 chr1D 486402007 486402813 806 False 1068.0 1068 90.7290 1 800 1 chr1D.!!$F2 799
9 TraesCS2D01G246900 chr3B 2342266 2343075 809 True 1072.0 1072 90.7410 1 800 1 chr3B.!!$R1 799
10 TraesCS2D01G246900 chr4D 28487864 28488670 806 False 1068.0 1068 90.7180 1 799 1 chr4D.!!$F1 798
11 TraesCS2D01G246900 chr3D 341473414 341474236 822 True 1064.0 1064 90.1700 1 815 1 chr3D.!!$R1 814
12 TraesCS2D01G246900 chr5D 491439676 491441623 1947 False 389.5 488 82.3945 1084 4065 2 chr5D.!!$F2 2981
13 TraesCS2D01G246900 chr5A 613589180 613591244 2064 False 393.0 466 82.1770 1084 4065 2 chr5A.!!$F4 2981

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
644 656 0.613777 GGGTGAGGAGGTGATTCGTT 59.386 55.0 0.00 0.0 0.00 3.85 F
1852 2362 1.619654 TATGTTGCTTTGCTGTGGCT 58.380 45.0 0.00 0.0 39.59 4.75 F
2263 2812 3.209410 GCTGACTGGATATTCTTGGGTG 58.791 50.0 0.00 0.0 0.00 4.61 F
4163 4754 0.687427 AAAACTTGCCTGGCAGTGGT 60.687 50.0 22.17 17.9 40.61 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2818 1.508632 ACCAAACGATCTGTCAACGG 58.491 50.000 0.0 0.0 0.00 4.44 R
2901 3454 2.203788 ACCTGAGCCTCCCAACGA 60.204 61.111 0.0 0.0 0.00 3.85 R
4210 4802 1.371467 AATCCCCATCAGTGACCACA 58.629 50.000 0.0 0.0 0.00 4.17 R
5943 6640 0.043053 CACAACGCACTTGACAGACG 60.043 55.000 0.0 0.0 33.59 4.18 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
29 31 1.764054 CAGGGGAGGCCGATCTTCT 60.764 63.158 0.00 0.00 0.00 2.85
84 86 2.838693 TCGGTGGTCGGTGGTGAA 60.839 61.111 0.00 0.00 39.77 3.18
124 126 1.659098 CGTGTGGATCGCTTTTACTCC 59.341 52.381 0.00 0.00 0.00 3.85
139 141 5.957771 TTTACTCCCTCGTAGTCTAGGTA 57.042 43.478 0.00 0.00 0.00 3.08
166 168 3.003275 GGTTGTTCATCGTCTTTGCTTCA 59.997 43.478 0.00 0.00 0.00 3.02
213 215 8.689788 GAATAAAGATTCTTCGGATCCTTCCCG 61.690 44.444 10.75 0.00 41.84 5.14
316 328 2.997315 CTGTGTCCTCGGGCTCCA 60.997 66.667 0.00 0.00 0.00 3.86
341 353 2.357034 GACGGCGTTTGCTCCTGA 60.357 61.111 16.19 0.00 42.25 3.86
367 379 1.861982 GTGGAGCTTGGGAGGTAGTA 58.138 55.000 0.00 0.00 32.79 1.82
388 400 1.123077 AGGAGCGGATGCAGATTGTA 58.877 50.000 0.00 0.00 46.23 2.41
403 415 0.800631 TTGTAGTCTGCGTCGACGAT 59.199 50.000 39.74 20.83 43.02 3.73
451 463 1.014044 CGTGGTTCGTGGATGACAGG 61.014 60.000 0.00 0.00 36.32 4.00
458 470 3.021177 TCGTGGATGACAGGTATGGTA 57.979 47.619 0.00 0.00 36.39 3.25
466 478 3.845860 TGACAGGTATGGTATCCTCCTC 58.154 50.000 0.00 0.00 30.91 3.71
529 541 4.265056 GTGTCCGGGGTGTTGCCT 62.265 66.667 0.00 0.00 37.43 4.75
550 562 1.126846 CAGTCTGATTCGTTCAACGGC 59.873 52.381 10.69 0.72 42.81 5.68
567 579 1.039856 GGCAAGGGCTTCACTTTTGA 58.960 50.000 0.00 0.00 40.87 2.69
595 607 0.890996 CTTGGAGGTCCGCAAAGCTT 60.891 55.000 0.00 0.00 39.43 3.74
605 617 1.672363 CCGCAAAGCTTCATATCAGCA 59.328 47.619 0.00 0.00 39.99 4.41
607 619 3.427909 CCGCAAAGCTTCATATCAGCAAA 60.428 43.478 0.00 0.00 39.99 3.68
644 656 0.613777 GGGTGAGGAGGTGATTCGTT 59.386 55.000 0.00 0.00 0.00 3.85
657 669 7.119262 GGAGGTGATTCGTTATTCTTTTCTTCA 59.881 37.037 0.00 0.00 0.00 3.02
681 693 4.947147 GCTGTGGTGGTGCCGGAA 62.947 66.667 5.05 0.00 41.21 4.30
692 704 4.373116 GCCGGAAGCAGGTGACGA 62.373 66.667 5.05 0.00 42.97 4.20
700 712 2.935955 CAGGTGACGAACGTTGGC 59.064 61.111 5.00 0.35 0.00 4.52
747 759 9.935682 GCTATCTTTTCAATTTTGTCATATCGA 57.064 29.630 0.00 0.00 0.00 3.59
755 767 9.914923 TTCAATTTTGTCATATCGATCTTTACG 57.085 29.630 0.00 0.00 0.00 3.18
756 768 9.093970 TCAATTTTGTCATATCGATCTTTACGT 57.906 29.630 0.00 0.00 0.00 3.57
757 769 9.147364 CAATTTTGTCATATCGATCTTTACGTG 57.853 33.333 0.00 0.00 0.00 4.49
761 773 6.427974 TGTCATATCGATCTTTACGTGACTC 58.572 40.000 0.00 0.00 36.23 3.36
762 774 6.260271 TGTCATATCGATCTTTACGTGACTCT 59.740 38.462 0.00 0.00 36.23 3.24
765 777 8.281194 TCATATCGATCTTTACGTGACTCTTAC 58.719 37.037 0.00 0.00 0.00 2.34
769 781 6.800408 TCGATCTTTACGTGACTCTTACTTTG 59.200 38.462 0.00 0.00 0.00 2.77
772 784 7.689953 TCTTTACGTGACTCTTACTTTGTTC 57.310 36.000 0.00 0.00 0.00 3.18
793 805 8.352752 TGTTCGTTATGATATGAATGAGACAC 57.647 34.615 0.00 0.00 0.00 3.67
794 806 7.167468 TGTTCGTTATGATATGAATGAGACACG 59.833 37.037 0.00 0.00 0.00 4.49
795 807 6.735130 TCGTTATGATATGAATGAGACACGT 58.265 36.000 0.00 0.00 0.00 4.49
796 808 7.867752 TCGTTATGATATGAATGAGACACGTA 58.132 34.615 0.00 0.00 0.00 3.57
797 809 8.512138 TCGTTATGATATGAATGAGACACGTAT 58.488 33.333 0.00 0.00 0.00 3.06
873 885 2.607187 ACGAATTCTTAGCTCCACGTG 58.393 47.619 9.08 9.08 0.00 4.49
1557 1613 4.195225 GCTTTAGCTAGGACAGTTGAGT 57.805 45.455 0.00 0.00 38.21 3.41
1791 2301 5.118286 TGTTGAGTATGGTATGCATCAGTG 58.882 41.667 0.19 0.00 0.00 3.66
1852 2362 1.619654 TATGTTGCTTTGCTGTGGCT 58.380 45.000 0.00 0.00 39.59 4.75
2041 2551 8.810041 AGTTCATCTTTTTGCCTAATCTCAATT 58.190 29.630 0.00 0.00 0.00 2.32
2177 2726 4.092091 GTCACTGCAATGCTGTAGTCTAAC 59.908 45.833 17.06 6.03 44.26 2.34
2263 2812 3.209410 GCTGACTGGATATTCTTGGGTG 58.791 50.000 0.00 0.00 0.00 4.61
2269 2818 5.930135 ACTGGATATTCTTGGGTGTACATC 58.070 41.667 0.00 0.00 0.00 3.06
2409 2958 3.233507 AGGCAATGTGTTTGGAATGACT 58.766 40.909 0.00 0.00 35.75 3.41
2901 3454 3.173151 TCTCATGGTGGTATGTCACTGT 58.827 45.455 0.00 0.00 37.75 3.55
3257 3822 2.510382 TCAACCCCCTTGTAAAGTGTGA 59.490 45.455 0.00 0.00 44.25 3.58
3475 4055 4.440880 CATTCAGGTTCCAGACTCTGATC 58.559 47.826 7.69 0.00 36.28 2.92
3774 4362 7.760340 GGGAGCAAGTATACTTACTATATGTGC 59.240 40.741 17.62 13.81 37.70 4.57
4163 4754 0.687427 AAAACTTGCCTGGCAGTGGT 60.687 50.000 22.17 17.90 40.61 4.16
4237 4829 5.893824 GGTCACTGATGGGGATTTTTCTTAT 59.106 40.000 0.00 0.00 0.00 1.73
4318 4910 9.219603 CTATAAACAATTTCAGTGAGAGGTGAA 57.780 33.333 0.00 0.00 0.00 3.18
4471 5063 1.268488 TGTTTGTGCTGCTTAGTTGCG 60.268 47.619 0.00 0.00 35.36 4.85
4518 5110 7.205297 AGAATTGCTGTTAAATATGATGCACC 58.795 34.615 0.00 0.00 0.00 5.01
4655 5260 8.630054 TGTAGTTTGCTAACCAAGAATAATGT 57.370 30.769 7.43 0.00 34.71 2.71
4747 5366 1.708341 ACATGGTTGCTTTCTTGGCT 58.292 45.000 0.00 0.00 0.00 4.75
4748 5367 2.041701 ACATGGTTGCTTTCTTGGCTT 58.958 42.857 0.00 0.00 0.00 4.35
4997 5616 0.622665 CAAGAATCTGAGGCCACCCT 59.377 55.000 5.01 0.00 46.74 4.34
5035 5654 1.666189 GGAGGCTCTTGTGTAAATCGC 59.334 52.381 15.23 0.00 0.00 4.58
5219 5838 0.832135 ATATGGGCACGACCTCGGAT 60.832 55.000 0.00 0.00 44.95 4.18
5262 5881 6.206634 TGATCTTTTACGATGCAAAACTCCTT 59.793 34.615 0.00 0.00 0.00 3.36
5290 5909 7.621796 AGATCCACCGATAAAATAATACTCCC 58.378 38.462 0.00 0.00 0.00 4.30
5367 6013 1.933247 AACAACATGCAAACAACGGG 58.067 45.000 0.00 0.00 0.00 5.28
5371 6017 0.951558 ACATGCAAACAACGGGTCTC 59.048 50.000 0.00 0.00 0.00 3.36
5381 6027 1.538512 CAACGGGTCTCGAGTCAAGTA 59.461 52.381 13.13 0.00 42.43 2.24
5474 6168 4.389077 GCTACACATGTTGTCTAACCTGTC 59.611 45.833 0.00 0.00 41.66 3.51
5512 6206 8.687292 TCCACTCATAATACTCACGTATACTT 57.313 34.615 0.56 0.00 35.32 2.24
5529 6223 9.350357 ACGTATACTTCATATATAAAGGCAACG 57.650 33.333 13.21 13.21 46.39 4.10
5545 6239 2.159572 GCAACGATACAAAACGCCATCT 60.160 45.455 0.00 0.00 0.00 2.90
5550 6244 4.214545 ACGATACAAAACGCCATCTGAAAA 59.785 37.500 0.00 0.00 0.00 2.29
5670 6364 0.877071 ACAAAGAATCAGGCACGCAG 59.123 50.000 0.00 0.00 0.00 5.18
5693 6387 2.201732 CCACCTCATGTACATGTACGC 58.798 52.381 30.03 8.77 39.72 4.42
5696 6390 2.684374 ACCTCATGTACATGTACGCGTA 59.316 45.455 30.03 16.41 39.72 4.42
5725 6422 7.032598 TCTCCTATTTCCTTCAAATCCAACT 57.967 36.000 0.00 0.00 36.09 3.16
5764 6461 6.269307 GTCATCTCTCTCCTAGTCCTAGTACT 59.731 46.154 0.00 0.00 0.00 2.73
5769 6466 9.895507 TCTCTCTCCTAGTCCTAGTACTATTTA 57.104 37.037 2.33 0.00 31.70 1.40
5798 6495 7.340122 AGGAAAGCTAATTAATCTCTTTGGC 57.660 36.000 11.73 1.46 0.00 4.52
5799 6496 6.322456 AGGAAAGCTAATTAATCTCTTTGGCC 59.678 38.462 0.00 0.00 0.00 5.36
5800 6497 6.096846 GGAAAGCTAATTAATCTCTTTGGCCA 59.903 38.462 0.00 0.00 0.00 5.36
5801 6498 6.456795 AAGCTAATTAATCTCTTTGGCCAC 57.543 37.500 3.88 0.00 0.00 5.01
5802 6499 4.576463 AGCTAATTAATCTCTTTGGCCACG 59.424 41.667 3.88 0.00 0.00 4.94
5803 6500 4.335594 GCTAATTAATCTCTTTGGCCACGT 59.664 41.667 3.88 0.00 0.00 4.49
5804 6501 5.163652 GCTAATTAATCTCTTTGGCCACGTT 60.164 40.000 3.88 0.00 0.00 3.99
5805 6502 4.701956 ATTAATCTCTTTGGCCACGTTG 57.298 40.909 3.88 0.00 0.00 4.10
5806 6503 2.270352 AATCTCTTTGGCCACGTTGA 57.730 45.000 3.88 1.99 0.00 3.18
5807 6504 2.496899 ATCTCTTTGGCCACGTTGAT 57.503 45.000 3.88 4.68 0.00 2.57
5808 6505 1.808411 TCTCTTTGGCCACGTTGATC 58.192 50.000 3.88 0.00 0.00 2.92
5809 6506 1.071542 TCTCTTTGGCCACGTTGATCA 59.928 47.619 3.88 0.00 0.00 2.92
5810 6507 1.197721 CTCTTTGGCCACGTTGATCAC 59.802 52.381 3.88 0.00 0.00 3.06
5811 6508 0.950836 CTTTGGCCACGTTGATCACA 59.049 50.000 3.88 0.00 0.00 3.58
5812 6509 0.950836 TTTGGCCACGTTGATCACAG 59.049 50.000 3.88 0.00 0.00 3.66
5813 6510 0.888736 TTGGCCACGTTGATCACAGG 60.889 55.000 3.88 0.00 0.00 4.00
5814 6511 1.003839 GGCCACGTTGATCACAGGA 60.004 57.895 0.00 0.00 0.00 3.86
5815 6512 1.298859 GGCCACGTTGATCACAGGAC 61.299 60.000 0.00 0.00 0.00 3.85
5816 6513 0.320771 GCCACGTTGATCACAGGACT 60.321 55.000 0.00 0.00 0.00 3.85
5817 6514 1.878102 GCCACGTTGATCACAGGACTT 60.878 52.381 0.00 0.00 0.00 3.01
5818 6515 2.611971 GCCACGTTGATCACAGGACTTA 60.612 50.000 0.00 0.00 0.00 2.24
5819 6516 3.861840 CCACGTTGATCACAGGACTTAT 58.138 45.455 0.00 0.00 0.00 1.73
5820 6517 3.865745 CCACGTTGATCACAGGACTTATC 59.134 47.826 0.00 0.00 0.00 1.75
5821 6518 4.382040 CCACGTTGATCACAGGACTTATCT 60.382 45.833 0.00 0.00 0.00 1.98
5822 6519 5.163550 CCACGTTGATCACAGGACTTATCTA 60.164 44.000 0.00 0.00 0.00 1.98
5823 6520 5.744345 CACGTTGATCACAGGACTTATCTAC 59.256 44.000 0.00 0.00 0.00 2.59
5824 6521 5.163540 ACGTTGATCACAGGACTTATCTACC 60.164 44.000 0.00 0.00 0.00 3.18
5825 6522 5.602628 GTTGATCACAGGACTTATCTACCC 58.397 45.833 0.00 0.00 0.00 3.69
5826 6523 4.223953 TGATCACAGGACTTATCTACCCC 58.776 47.826 0.00 0.00 0.00 4.95
5827 6524 4.078571 TGATCACAGGACTTATCTACCCCT 60.079 45.833 0.00 0.00 0.00 4.79
5828 6525 5.135533 TGATCACAGGACTTATCTACCCCTA 59.864 44.000 0.00 0.00 0.00 3.53
5829 6526 5.476950 TCACAGGACTTATCTACCCCTAA 57.523 43.478 0.00 0.00 0.00 2.69
5830 6527 6.039415 TCACAGGACTTATCTACCCCTAAT 57.961 41.667 0.00 0.00 0.00 1.73
5831 6528 6.075984 TCACAGGACTTATCTACCCCTAATC 58.924 44.000 0.00 0.00 0.00 1.75
5832 6529 6.078664 CACAGGACTTATCTACCCCTAATCT 58.921 44.000 0.00 0.00 0.00 2.40
5833 6530 7.074623 TCACAGGACTTATCTACCCCTAATCTA 59.925 40.741 0.00 0.00 0.00 1.98
5834 6531 7.896496 CACAGGACTTATCTACCCCTAATCTAT 59.104 40.741 0.00 0.00 0.00 1.98
5835 6532 8.117312 ACAGGACTTATCTACCCCTAATCTATC 58.883 40.741 0.00 0.00 0.00 2.08
5836 6533 8.340757 CAGGACTTATCTACCCCTAATCTATCT 58.659 40.741 0.00 0.00 0.00 1.98
5837 6534 9.591220 AGGACTTATCTACCCCTAATCTATCTA 57.409 37.037 0.00 0.00 0.00 1.98
5877 6574 9.987272 ATTCATTAATAAAAGGGCTATTGCTTC 57.013 29.630 0.00 0.00 39.59 3.86
5878 6575 8.766994 TCATTAATAAAAGGGCTATTGCTTCT 57.233 30.769 0.00 0.00 39.59 2.85
5879 6576 9.200817 TCATTAATAAAAGGGCTATTGCTTCTT 57.799 29.630 0.00 1.30 39.59 2.52
5882 6579 6.961360 ATAAAAGGGCTATTGCTTCTTACC 57.039 37.500 0.00 0.00 39.59 2.85
5883 6580 4.316025 AAAGGGCTATTGCTTCTTACCA 57.684 40.909 0.00 0.00 39.59 3.25
5884 6581 4.526438 AAGGGCTATTGCTTCTTACCAT 57.474 40.909 0.00 0.00 39.59 3.55
5885 6582 4.526438 AGGGCTATTGCTTCTTACCATT 57.474 40.909 0.00 0.00 39.59 3.16
5886 6583 4.210331 AGGGCTATTGCTTCTTACCATTG 58.790 43.478 0.00 0.00 39.59 2.82
5887 6584 3.954258 GGGCTATTGCTTCTTACCATTGT 59.046 43.478 0.00 0.00 39.59 2.71
5888 6585 5.104109 AGGGCTATTGCTTCTTACCATTGTA 60.104 40.000 0.00 0.00 39.59 2.41
5889 6586 5.592688 GGGCTATTGCTTCTTACCATTGTAA 59.407 40.000 0.00 0.00 39.59 2.41
5890 6587 6.096282 GGGCTATTGCTTCTTACCATTGTAAA 59.904 38.462 0.00 0.00 36.62 2.01
5891 6588 6.972901 GGCTATTGCTTCTTACCATTGTAAAC 59.027 38.462 0.00 0.00 36.62 2.01
5892 6589 7.148069 GGCTATTGCTTCTTACCATTGTAAACT 60.148 37.037 0.00 0.00 36.62 2.66
5893 6590 8.244113 GCTATTGCTTCTTACCATTGTAAACTT 58.756 33.333 0.00 0.00 34.97 2.66
5894 6591 9.774742 CTATTGCTTCTTACCATTGTAAACTTC 57.225 33.333 0.00 0.00 36.54 3.01
5895 6592 6.236017 TGCTTCTTACCATTGTAAACTTCG 57.764 37.500 0.00 0.00 36.54 3.79
5896 6593 5.761234 TGCTTCTTACCATTGTAAACTTCGT 59.239 36.000 0.00 0.00 36.54 3.85
5897 6594 6.261381 TGCTTCTTACCATTGTAAACTTCGTT 59.739 34.615 0.00 0.00 36.54 3.85
5898 6595 6.795593 GCTTCTTACCATTGTAAACTTCGTTC 59.204 38.462 0.00 0.00 36.54 3.95
5899 6596 6.456447 TCTTACCATTGTAAACTTCGTTCG 57.544 37.500 0.00 0.00 36.54 3.95
5900 6597 5.984926 TCTTACCATTGTAAACTTCGTTCGT 59.015 36.000 0.00 0.00 36.54 3.85
5901 6598 6.479660 TCTTACCATTGTAAACTTCGTTCGTT 59.520 34.615 0.00 0.00 36.54 3.85
5902 6599 7.651304 TCTTACCATTGTAAACTTCGTTCGTTA 59.349 33.333 0.00 0.00 36.54 3.18
5903 6600 6.790285 ACCATTGTAAACTTCGTTCGTTAT 57.210 33.333 0.00 0.00 0.00 1.89
5904 6601 7.193377 ACCATTGTAAACTTCGTTCGTTATT 57.807 32.000 0.00 0.00 0.00 1.40
5905 6602 8.309163 ACCATTGTAAACTTCGTTCGTTATTA 57.691 30.769 0.00 0.00 0.00 0.98
5906 6603 8.437742 ACCATTGTAAACTTCGTTCGTTATTAG 58.562 33.333 0.00 0.00 0.00 1.73
5907 6604 8.437742 CCATTGTAAACTTCGTTCGTTATTAGT 58.562 33.333 0.00 0.00 0.00 2.24
5908 6605 9.801714 CATTGTAAACTTCGTTCGTTATTAGTT 57.198 29.630 0.00 0.00 0.00 2.24
5911 6608 9.635632 TGTAAACTTCGTTCGTTATTAGTTTTG 57.364 29.630 0.00 0.00 37.16 2.44
5912 6609 9.636965 GTAAACTTCGTTCGTTATTAGTTTTGT 57.363 29.630 0.00 0.00 37.16 2.83
5914 6611 8.757817 AACTTCGTTCGTTATTAGTTTTGTTC 57.242 30.769 0.00 0.00 0.00 3.18
5915 6612 7.059212 ACTTCGTTCGTTATTAGTTTTGTTCG 58.941 34.615 0.00 0.00 0.00 3.95
5916 6613 6.509317 TCGTTCGTTATTAGTTTTGTTCGT 57.491 33.333 0.00 0.00 0.00 3.85
5917 6614 6.571588 TCGTTCGTTATTAGTTTTGTTCGTC 58.428 36.000 0.00 0.00 0.00 4.20
5918 6615 5.780269 CGTTCGTTATTAGTTTTGTTCGTCC 59.220 40.000 0.00 0.00 0.00 4.79
5919 6616 5.499268 TCGTTATTAGTTTTGTTCGTCCG 57.501 39.130 0.00 0.00 0.00 4.79
5920 6617 4.981674 TCGTTATTAGTTTTGTTCGTCCGT 59.018 37.500 0.00 0.00 0.00 4.69
5921 6618 5.461737 TCGTTATTAGTTTTGTTCGTCCGTT 59.538 36.000 0.00 0.00 0.00 4.44
5922 6619 5.557405 CGTTATTAGTTTTGTTCGTCCGTTG 59.443 40.000 0.00 0.00 0.00 4.10
5923 6620 6.421405 GTTATTAGTTTTGTTCGTCCGTTGT 58.579 36.000 0.00 0.00 0.00 3.32
5924 6621 4.519191 TTAGTTTTGTTCGTCCGTTGTC 57.481 40.909 0.00 0.00 0.00 3.18
5925 6622 1.667212 AGTTTTGTTCGTCCGTTGTCC 59.333 47.619 0.00 0.00 0.00 4.02
5926 6623 1.397692 GTTTTGTTCGTCCGTTGTCCA 59.602 47.619 0.00 0.00 0.00 4.02
5927 6624 1.956297 TTTGTTCGTCCGTTGTCCAT 58.044 45.000 0.00 0.00 0.00 3.41
5928 6625 1.504359 TTGTTCGTCCGTTGTCCATC 58.496 50.000 0.00 0.00 0.00 3.51
5929 6626 0.389757 TGTTCGTCCGTTGTCCATCA 59.610 50.000 0.00 0.00 0.00 3.07
5930 6627 1.068474 GTTCGTCCGTTGTCCATCAG 58.932 55.000 0.00 0.00 0.00 2.90
5931 6628 0.677288 TTCGTCCGTTGTCCATCAGT 59.323 50.000 0.00 0.00 0.00 3.41
5932 6629 1.536940 TCGTCCGTTGTCCATCAGTA 58.463 50.000 0.00 0.00 0.00 2.74
5933 6630 2.097036 TCGTCCGTTGTCCATCAGTAT 58.903 47.619 0.00 0.00 0.00 2.12
5934 6631 2.494471 TCGTCCGTTGTCCATCAGTATT 59.506 45.455 0.00 0.00 0.00 1.89
5935 6632 2.603110 CGTCCGTTGTCCATCAGTATTG 59.397 50.000 0.00 0.00 0.00 1.90
5936 6633 3.596214 GTCCGTTGTCCATCAGTATTGT 58.404 45.455 0.00 0.00 0.00 2.71
5937 6634 4.000988 GTCCGTTGTCCATCAGTATTGTT 58.999 43.478 0.00 0.00 0.00 2.83
5938 6635 4.092968 GTCCGTTGTCCATCAGTATTGTTC 59.907 45.833 0.00 0.00 0.00 3.18
5939 6636 3.062099 CCGTTGTCCATCAGTATTGTTCG 59.938 47.826 0.00 0.00 0.00 3.95
5940 6637 3.678072 CGTTGTCCATCAGTATTGTTCGT 59.322 43.478 0.00 0.00 0.00 3.85
5941 6638 4.151689 CGTTGTCCATCAGTATTGTTCGTT 59.848 41.667 0.00 0.00 0.00 3.85
5942 6639 5.333798 CGTTGTCCATCAGTATTGTTCGTTT 60.334 40.000 0.00 0.00 0.00 3.60
5943 6640 5.856126 TGTCCATCAGTATTGTTCGTTTC 57.144 39.130 0.00 0.00 0.00 2.78
5944 6641 4.387559 TGTCCATCAGTATTGTTCGTTTCG 59.612 41.667 0.00 0.00 0.00 3.46
5945 6642 4.387862 GTCCATCAGTATTGTTCGTTTCGT 59.612 41.667 0.00 0.00 0.00 3.85
5946 6643 4.624024 TCCATCAGTATTGTTCGTTTCGTC 59.376 41.667 0.00 0.00 0.00 4.20
5947 6644 4.625742 CCATCAGTATTGTTCGTTTCGTCT 59.374 41.667 0.00 0.00 0.00 4.18
5948 6645 5.444613 CCATCAGTATTGTTCGTTTCGTCTG 60.445 44.000 0.00 0.00 0.00 3.51
5949 6646 4.613944 TCAGTATTGTTCGTTTCGTCTGT 58.386 39.130 0.00 0.00 0.00 3.41
5950 6647 4.678287 TCAGTATTGTTCGTTTCGTCTGTC 59.322 41.667 0.00 0.00 0.00 3.51
5951 6648 4.443063 CAGTATTGTTCGTTTCGTCTGTCA 59.557 41.667 0.00 0.00 0.00 3.58
5952 6649 5.045215 AGTATTGTTCGTTTCGTCTGTCAA 58.955 37.500 0.00 0.00 0.00 3.18
5953 6650 3.918258 TTGTTCGTTTCGTCTGTCAAG 57.082 42.857 0.00 0.00 0.00 3.02
5954 6651 2.883574 TGTTCGTTTCGTCTGTCAAGT 58.116 42.857 0.00 0.00 0.00 3.16
5955 6652 2.601314 TGTTCGTTTCGTCTGTCAAGTG 59.399 45.455 0.00 0.00 0.00 3.16
5956 6653 1.205657 TCGTTTCGTCTGTCAAGTGC 58.794 50.000 0.00 0.00 0.00 4.40
5957 6654 0.111704 CGTTTCGTCTGTCAAGTGCG 60.112 55.000 0.00 0.00 0.00 5.34
5958 6655 0.928229 GTTTCGTCTGTCAAGTGCGT 59.072 50.000 0.00 0.00 0.00 5.24
5959 6656 1.326548 GTTTCGTCTGTCAAGTGCGTT 59.673 47.619 0.00 0.00 0.00 4.84
5960 6657 0.927537 TTCGTCTGTCAAGTGCGTTG 59.072 50.000 0.00 0.00 37.52 4.10
5961 6658 0.179121 TCGTCTGTCAAGTGCGTTGT 60.179 50.000 0.00 0.00 37.43 3.32
5962 6659 0.043053 CGTCTGTCAAGTGCGTTGTG 60.043 55.000 0.00 0.00 37.43 3.33
5963 6660 0.304705 GTCTGTCAAGTGCGTTGTGG 59.695 55.000 0.00 0.00 37.43 4.17
5964 6661 1.009675 CTGTCAAGTGCGTTGTGGC 60.010 57.895 0.00 0.00 37.43 5.01
5965 6662 2.331451 GTCAAGTGCGTTGTGGCC 59.669 61.111 0.00 0.00 37.43 5.36
5966 6663 2.904866 TCAAGTGCGTTGTGGCCC 60.905 61.111 0.00 0.00 37.43 5.80
5967 6664 3.215568 CAAGTGCGTTGTGGCCCA 61.216 61.111 0.00 0.00 0.00 5.36
5968 6665 2.441164 AAGTGCGTTGTGGCCCAA 60.441 55.556 0.00 0.55 0.00 4.12
5969 6666 1.832167 AAGTGCGTTGTGGCCCAAT 60.832 52.632 0.00 0.00 35.02 3.16
5970 6667 0.538516 AAGTGCGTTGTGGCCCAATA 60.539 50.000 0.00 0.00 35.02 1.90
5971 6668 0.538516 AGTGCGTTGTGGCCCAATAA 60.539 50.000 0.00 0.00 35.02 1.40
5972 6669 0.315568 GTGCGTTGTGGCCCAATAAA 59.684 50.000 0.00 0.00 35.02 1.40
5973 6670 1.067213 GTGCGTTGTGGCCCAATAAAT 60.067 47.619 0.00 0.00 35.02 1.40
5974 6671 1.203523 TGCGTTGTGGCCCAATAAATC 59.796 47.619 0.00 0.00 35.02 2.17
5975 6672 1.470805 GCGTTGTGGCCCAATAAATCC 60.471 52.381 0.00 0.00 35.02 3.01
5976 6673 1.202245 CGTTGTGGCCCAATAAATCCG 60.202 52.381 0.00 0.00 35.02 4.18
5977 6674 1.136110 GTTGTGGCCCAATAAATCCGG 59.864 52.381 0.00 0.00 35.02 5.14
5978 6675 1.040339 TGTGGCCCAATAAATCCGGC 61.040 55.000 0.00 0.00 40.85 6.13
5980 6677 3.455152 GCCCAATAAATCCGGCCC 58.545 61.111 0.00 0.00 35.23 5.80
5981 6678 2.561037 GCCCAATAAATCCGGCCCG 61.561 63.158 0.00 0.00 35.23 6.13
5982 6679 1.149627 CCCAATAAATCCGGCCCGA 59.850 57.895 3.71 0.00 0.00 5.14
5983 6680 1.170290 CCCAATAAATCCGGCCCGAC 61.170 60.000 3.71 0.00 0.00 4.79
5984 6681 1.170290 CCAATAAATCCGGCCCGACC 61.170 60.000 3.71 0.00 0.00 4.79
5985 6682 1.149854 AATAAATCCGGCCCGACCC 59.850 57.895 3.71 0.00 33.26 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 4.029809 CCCCCTTCACCACCGACC 62.030 72.222 0.00 0.00 0.00 4.79
124 126 6.545298 ACAACCTAAATACCTAGACTACGAGG 59.455 42.308 0.00 0.00 43.10 4.63
139 141 5.473504 AGCAAAGACGATGAACAACCTAAAT 59.526 36.000 0.00 0.00 0.00 1.40
182 184 3.555956 TCCGAAGAATCTTTATTCAGCGC 59.444 43.478 0.00 0.00 43.44 5.92
213 215 1.335132 TAGGACCGATGGCCTTGTCC 61.335 60.000 19.52 19.52 46.12 4.02
339 351 3.303135 AAGCTCCACGCCGACTCA 61.303 61.111 0.00 0.00 40.39 3.41
341 353 4.379243 CCAAGCTCCACGCCGACT 62.379 66.667 0.00 0.00 40.39 4.18
367 379 0.463295 CAATCTGCATCCGCTCCTGT 60.463 55.000 0.00 0.00 39.64 4.00
388 400 1.261885 CAGATATCGTCGACGCAGACT 59.738 52.381 32.19 23.10 38.90 3.24
403 415 2.101415 CACATGCTCCGTCTTCCAGATA 59.899 50.000 0.00 0.00 0.00 1.98
430 442 0.389757 TGTCATCCACGAACCACGAA 59.610 50.000 0.00 0.00 45.77 3.85
466 478 1.665599 ACCACGACTAAAACGCCGG 60.666 57.895 0.00 0.00 34.36 6.13
510 522 4.922026 GCAACACCCCGGACACGT 62.922 66.667 0.73 0.00 38.78 4.49
529 541 2.672714 CCGTTGAACGAATCAGACTGA 58.327 47.619 20.47 7.80 46.05 3.41
550 562 3.613432 GCTCATCAAAAGTGAAGCCCTTG 60.613 47.826 0.00 0.00 37.30 3.61
595 607 1.811558 GCGGCTCCTTTGCTGATATGA 60.812 52.381 0.00 0.00 41.56 2.15
644 656 4.456911 CAGCAGCCACTGAAGAAAAGAATA 59.543 41.667 0.00 0.00 40.25 1.75
657 669 3.492353 ACCACCACAGCAGCCACT 61.492 61.111 0.00 0.00 0.00 4.00
681 693 1.594293 CCAACGTTCGTCACCTGCT 60.594 57.895 0.00 0.00 0.00 4.24
747 759 7.114529 CGAACAAAGTAAGAGTCACGTAAAGAT 59.885 37.037 0.00 0.00 0.00 2.40
748 760 6.415867 CGAACAAAGTAAGAGTCACGTAAAGA 59.584 38.462 0.00 0.00 0.00 2.52
749 761 6.197842 ACGAACAAAGTAAGAGTCACGTAAAG 59.802 38.462 0.00 0.00 0.00 1.85
750 762 6.035843 ACGAACAAAGTAAGAGTCACGTAAA 58.964 36.000 0.00 0.00 0.00 2.01
751 763 5.581605 ACGAACAAAGTAAGAGTCACGTAA 58.418 37.500 0.00 0.00 0.00 3.18
752 764 5.173774 ACGAACAAAGTAAGAGTCACGTA 57.826 39.130 0.00 0.00 0.00 3.57
753 765 4.037858 ACGAACAAAGTAAGAGTCACGT 57.962 40.909 0.00 0.00 0.00 4.49
754 766 6.361481 TCATAACGAACAAAGTAAGAGTCACG 59.639 38.462 0.00 0.00 0.00 4.35
755 767 7.633361 TCATAACGAACAAAGTAAGAGTCAC 57.367 36.000 0.00 0.00 0.00 3.67
765 777 9.855361 GTCTCATTCATATCATAACGAACAAAG 57.145 33.333 0.00 0.00 0.00 2.77
769 781 7.167635 ACGTGTCTCATTCATATCATAACGAAC 59.832 37.037 0.00 0.00 0.00 3.95
772 784 6.993175 ACGTGTCTCATTCATATCATAACG 57.007 37.500 0.00 0.00 0.00 3.18
814 826 4.769688 TGTGCATTCTTGGTCTTATCGAT 58.230 39.130 2.16 2.16 0.00 3.59
822 834 1.606668 TCGGTTTGTGCATTCTTGGTC 59.393 47.619 0.00 0.00 0.00 4.02
828 840 0.165944 CTCGGTCGGTTTGTGCATTC 59.834 55.000 0.00 0.00 0.00 2.67
854 866 2.599082 GACACGTGGAGCTAAGAATTCG 59.401 50.000 21.57 0.00 0.00 3.34
873 885 2.746277 GTGCCATCCACGGGTGAC 60.746 66.667 0.00 0.00 34.22 3.67
1557 1613 5.291858 GCACTAACATCAATCGAATCACAGA 59.708 40.000 0.00 0.00 0.00 3.41
1791 2301 9.611284 GGAATGAAAAATCAAAATTGTAAAGCC 57.389 29.630 0.00 0.00 0.00 4.35
1852 2362 3.008923 TGTGATCAACAGTTGGGCATAGA 59.991 43.478 13.52 0.00 33.78 1.98
2041 2551 3.769739 AAAGAGGATGTGTGTGCTACA 57.230 42.857 0.00 0.00 36.82 2.74
2263 2812 3.146618 ACGATCTGTCAACGGATGTAC 57.853 47.619 9.16 0.00 41.75 2.90
2269 2818 1.508632 ACCAAACGATCTGTCAACGG 58.491 50.000 0.00 0.00 0.00 4.44
2409 2958 5.943349 TCGGTTCCATGGTATAAAGAAGA 57.057 39.130 12.58 0.00 0.00 2.87
2901 3454 2.203788 ACCTGAGCCTCCCAACGA 60.204 61.111 0.00 0.00 0.00 3.85
2949 3502 9.129209 GGAATGAAAATAACTGAAAAGCTACAC 57.871 33.333 0.00 0.00 0.00 2.90
3257 3822 7.698163 AAAGACTGGGGATCTAGATATTTGT 57.302 36.000 4.89 1.68 0.00 2.83
4210 4802 1.371467 AATCCCCATCAGTGACCACA 58.629 50.000 0.00 0.00 0.00 4.17
4237 4829 6.621316 TTTGTTCATACTTTAAACGCTCCA 57.379 33.333 0.00 0.00 0.00 3.86
4318 4910 4.304110 CAGAAACTCAAAGCATGCACATT 58.696 39.130 21.98 9.03 0.00 2.71
4471 5063 8.575565 TTCTACTAATCATGAAACGTGATAGC 57.424 34.615 0.00 0.00 35.35 2.97
4518 5110 3.963374 TGGATCAGAGGGAGTACATTCAG 59.037 47.826 0.00 0.00 0.00 3.02
4786 5405 0.179936 AGCTGCAGAGACATAAGGGC 59.820 55.000 20.43 0.00 0.00 5.19
4997 5616 1.371183 CGAACCAGGGCAGAGTTCA 59.629 57.895 11.60 0.00 39.89 3.18
5035 5654 5.458452 ACAACATACAGAACAAATTGTTGCG 59.542 36.000 16.78 9.08 44.71 4.85
5219 5838 0.592637 CAGGACAAAACATCAGCGCA 59.407 50.000 11.47 0.00 0.00 6.09
5262 5881 9.706691 GAGTATTATTTTATCGGTGGATCTTGA 57.293 33.333 0.00 0.00 34.00 3.02
5290 5909 1.135527 TGGTCGTCGTAGCCCTAATTG 59.864 52.381 0.00 0.00 0.00 2.32
5300 5935 1.647346 GATTGCCATTGGTCGTCGTA 58.353 50.000 4.26 0.00 0.00 3.43
5362 6008 1.538950 GTACTTGACTCGAGACCCGTT 59.461 52.381 21.68 0.00 39.75 4.44
5364 6010 1.162698 TGTACTTGACTCGAGACCCG 58.837 55.000 21.68 9.08 40.25 5.28
5367 6013 7.689953 TTAAAAGTTGTACTTGACTCGAGAC 57.310 36.000 21.68 14.43 38.66 3.36
5371 6017 6.655062 TGCATTAAAAGTTGTACTTGACTCG 58.345 36.000 0.00 0.00 38.66 4.18
5381 6027 8.715191 TGTGAATTTTCTGCATTAAAAGTTGT 57.285 26.923 11.40 0.42 29.93 3.32
5529 6223 6.378582 TCTTTTTCAGATGGCGTTTTGTATC 58.621 36.000 0.00 0.00 0.00 2.24
5652 6346 0.169672 CCTGCGTGCCTGATTCTTTG 59.830 55.000 0.00 0.00 0.00 2.77
5653 6347 1.589716 GCCTGCGTGCCTGATTCTTT 61.590 55.000 0.00 0.00 0.00 2.52
5654 6348 2.042831 GCCTGCGTGCCTGATTCTT 61.043 57.895 0.00 0.00 0.00 2.52
5670 6364 0.255890 ACATGTACATGAGGTGGGCC 59.744 55.000 36.36 0.00 41.20 5.80
5678 6372 4.984205 TCTTTACGCGTACATGTACATGA 58.016 39.130 36.36 20.00 41.20 3.07
5693 6387 8.718102 TTTGAAGGAAATAGGAGATCTTTACG 57.282 34.615 0.00 0.00 0.00 3.18
5696 6390 8.339247 TGGATTTGAAGGAAATAGGAGATCTTT 58.661 33.333 0.00 0.00 34.18 2.52
5725 6422 3.572682 AGAGATGACGTGTTGGACAAGTA 59.427 43.478 0.00 0.00 40.74 2.24
5774 6471 6.322456 GGCCAAAGAGATTAATTAGCTTTCCT 59.678 38.462 0.00 0.00 0.00 3.36
5776 6473 6.975197 GTGGCCAAAGAGATTAATTAGCTTTC 59.025 38.462 7.24 0.00 0.00 2.62
5779 6476 4.576463 CGTGGCCAAAGAGATTAATTAGCT 59.424 41.667 7.24 0.00 0.00 3.32
5780 6477 4.335594 ACGTGGCCAAAGAGATTAATTAGC 59.664 41.667 7.24 0.00 0.00 3.09
5781 6478 6.093495 TCAACGTGGCCAAAGAGATTAATTAG 59.907 38.462 7.24 0.00 0.00 1.73
5782 6479 5.941058 TCAACGTGGCCAAAGAGATTAATTA 59.059 36.000 7.24 0.00 0.00 1.40
5783 6480 4.764823 TCAACGTGGCCAAAGAGATTAATT 59.235 37.500 7.24 0.00 0.00 1.40
5784 6481 4.331968 TCAACGTGGCCAAAGAGATTAAT 58.668 39.130 7.24 0.00 0.00 1.40
5785 6482 3.745799 TCAACGTGGCCAAAGAGATTAA 58.254 40.909 7.24 0.00 0.00 1.40
5786 6483 3.410631 TCAACGTGGCCAAAGAGATTA 57.589 42.857 7.24 0.00 0.00 1.75
5787 6484 2.270352 TCAACGTGGCCAAAGAGATT 57.730 45.000 7.24 0.00 0.00 2.40
5788 6485 2.290260 TGATCAACGTGGCCAAAGAGAT 60.290 45.455 7.24 13.52 0.00 2.75
5789 6486 1.071542 TGATCAACGTGGCCAAAGAGA 59.928 47.619 7.24 9.24 0.00 3.10
5790 6487 1.197721 GTGATCAACGTGGCCAAAGAG 59.802 52.381 7.24 1.46 0.00 2.85
5791 6488 1.234821 GTGATCAACGTGGCCAAAGA 58.765 50.000 7.24 3.16 0.00 2.52
5792 6489 0.950836 TGTGATCAACGTGGCCAAAG 59.049 50.000 7.24 7.62 0.00 2.77
5793 6490 0.950836 CTGTGATCAACGTGGCCAAA 59.049 50.000 7.24 0.00 0.00 3.28
5794 6491 0.888736 CCTGTGATCAACGTGGCCAA 60.889 55.000 7.24 0.00 0.00 4.52
5795 6492 1.302431 CCTGTGATCAACGTGGCCA 60.302 57.895 0.00 0.00 0.00 5.36
5796 6493 1.003839 TCCTGTGATCAACGTGGCC 60.004 57.895 0.00 0.00 0.00 5.36
5797 6494 0.320771 AGTCCTGTGATCAACGTGGC 60.321 55.000 0.00 0.00 0.00 5.01
5798 6495 2.169832 AAGTCCTGTGATCAACGTGG 57.830 50.000 0.00 0.00 0.00 4.94
5799 6496 4.748892 AGATAAGTCCTGTGATCAACGTG 58.251 43.478 0.00 0.00 0.00 4.49
5800 6497 5.163540 GGTAGATAAGTCCTGTGATCAACGT 60.164 44.000 0.00 0.00 0.00 3.99
5801 6498 5.282510 GGTAGATAAGTCCTGTGATCAACG 58.717 45.833 0.00 0.00 0.00 4.10
5802 6499 5.453480 GGGGTAGATAAGTCCTGTGATCAAC 60.453 48.000 0.00 0.00 0.00 3.18
5803 6500 4.654262 GGGGTAGATAAGTCCTGTGATCAA 59.346 45.833 0.00 0.00 0.00 2.57
5804 6501 4.078571 AGGGGTAGATAAGTCCTGTGATCA 60.079 45.833 0.00 0.00 0.00 2.92
5805 6502 4.484912 AGGGGTAGATAAGTCCTGTGATC 58.515 47.826 0.00 0.00 0.00 2.92
5806 6503 4.561254 AGGGGTAGATAAGTCCTGTGAT 57.439 45.455 0.00 0.00 0.00 3.06
5807 6504 5.476950 TTAGGGGTAGATAAGTCCTGTGA 57.523 43.478 0.00 0.00 0.00 3.58
5808 6505 6.078664 AGATTAGGGGTAGATAAGTCCTGTG 58.921 44.000 0.00 0.00 0.00 3.66
5809 6506 6.296435 AGATTAGGGGTAGATAAGTCCTGT 57.704 41.667 0.00 0.00 0.00 4.00
5810 6507 8.340757 AGATAGATTAGGGGTAGATAAGTCCTG 58.659 40.741 0.00 0.00 0.00 3.86
5811 6508 8.485162 AGATAGATTAGGGGTAGATAAGTCCT 57.515 38.462 0.00 0.00 0.00 3.85
5851 6548 9.987272 GAAGCAATAGCCCTTTTATTAATGAAT 57.013 29.630 0.00 0.00 43.56 2.57
5852 6549 9.200817 AGAAGCAATAGCCCTTTTATTAATGAA 57.799 29.630 0.00 0.00 43.56 2.57
5853 6550 8.766994 AGAAGCAATAGCCCTTTTATTAATGA 57.233 30.769 0.00 0.00 43.56 2.57
5856 6553 8.909923 GGTAAGAAGCAATAGCCCTTTTATTAA 58.090 33.333 0.00 0.00 43.56 1.40
5857 6554 8.056400 TGGTAAGAAGCAATAGCCCTTTTATTA 58.944 33.333 0.00 0.00 43.56 0.98
5858 6555 6.895204 TGGTAAGAAGCAATAGCCCTTTTATT 59.105 34.615 0.00 0.00 43.56 1.40
5859 6556 6.431722 TGGTAAGAAGCAATAGCCCTTTTAT 58.568 36.000 0.00 0.00 43.56 1.40
5860 6557 5.822204 TGGTAAGAAGCAATAGCCCTTTTA 58.178 37.500 0.00 0.00 43.56 1.52
5861 6558 4.672899 TGGTAAGAAGCAATAGCCCTTTT 58.327 39.130 0.00 0.00 43.56 2.27
5862 6559 4.316025 TGGTAAGAAGCAATAGCCCTTT 57.684 40.909 0.00 0.00 43.56 3.11
5863 6560 4.526438 ATGGTAAGAAGCAATAGCCCTT 57.474 40.909 0.00 0.00 43.56 3.95
5864 6561 4.210331 CAATGGTAAGAAGCAATAGCCCT 58.790 43.478 0.00 0.00 43.56 5.19
5865 6562 3.954258 ACAATGGTAAGAAGCAATAGCCC 59.046 43.478 0.00 0.00 43.56 5.19
5866 6563 6.693315 TTACAATGGTAAGAAGCAATAGCC 57.307 37.500 0.00 0.00 36.61 3.93
5867 6564 7.762382 AGTTTACAATGGTAAGAAGCAATAGC 58.238 34.615 0.00 0.00 40.40 2.97
5868 6565 9.774742 GAAGTTTACAATGGTAAGAAGCAATAG 57.225 33.333 0.00 0.00 40.40 1.73
5869 6566 8.447833 CGAAGTTTACAATGGTAAGAAGCAATA 58.552 33.333 0.00 0.00 40.40 1.90
5870 6567 7.040686 ACGAAGTTTACAATGGTAAGAAGCAAT 60.041 33.333 0.00 0.00 37.78 3.56
5871 6568 6.261381 ACGAAGTTTACAATGGTAAGAAGCAA 59.739 34.615 0.00 0.00 37.78 3.91
5872 6569 5.761234 ACGAAGTTTACAATGGTAAGAAGCA 59.239 36.000 0.00 0.00 37.78 3.91
5873 6570 6.237313 ACGAAGTTTACAATGGTAAGAAGC 57.763 37.500 0.00 0.00 37.78 3.86
5891 6588 7.059212 ACGAACAAAACTAATAACGAACGAAG 58.941 34.615 0.14 0.00 0.00 3.79
5892 6589 6.932051 ACGAACAAAACTAATAACGAACGAA 58.068 32.000 0.14 0.00 0.00 3.85
5893 6590 6.345723 GGACGAACAAAACTAATAACGAACGA 60.346 38.462 0.14 0.00 0.00 3.85
5894 6591 5.780269 GGACGAACAAAACTAATAACGAACG 59.220 40.000 0.00 0.00 0.00 3.95
5895 6592 5.780269 CGGACGAACAAAACTAATAACGAAC 59.220 40.000 0.00 0.00 0.00 3.95
5896 6593 5.461737 ACGGACGAACAAAACTAATAACGAA 59.538 36.000 0.00 0.00 0.00 3.85
5897 6594 4.981674 ACGGACGAACAAAACTAATAACGA 59.018 37.500 0.00 0.00 0.00 3.85
5898 6595 5.254669 ACGGACGAACAAAACTAATAACG 57.745 39.130 0.00 0.00 0.00 3.18
5899 6596 6.421405 ACAACGGACGAACAAAACTAATAAC 58.579 36.000 0.00 0.00 0.00 1.89
5900 6597 6.292811 GGACAACGGACGAACAAAACTAATAA 60.293 38.462 0.00 0.00 0.00 1.40
5901 6598 5.177327 GGACAACGGACGAACAAAACTAATA 59.823 40.000 0.00 0.00 0.00 0.98
5902 6599 4.024641 GGACAACGGACGAACAAAACTAAT 60.025 41.667 0.00 0.00 0.00 1.73
5903 6600 3.309410 GGACAACGGACGAACAAAACTAA 59.691 43.478 0.00 0.00 0.00 2.24
5904 6601 2.865551 GGACAACGGACGAACAAAACTA 59.134 45.455 0.00 0.00 0.00 2.24
5905 6602 1.667212 GGACAACGGACGAACAAAACT 59.333 47.619 0.00 0.00 0.00 2.66
5906 6603 1.397692 TGGACAACGGACGAACAAAAC 59.602 47.619 0.00 0.00 0.00 2.43
5907 6604 1.735386 TGGACAACGGACGAACAAAA 58.265 45.000 0.00 0.00 0.00 2.44
5908 6605 1.868498 GATGGACAACGGACGAACAAA 59.132 47.619 0.00 0.00 0.00 2.83
5909 6606 1.202545 TGATGGACAACGGACGAACAA 60.203 47.619 0.00 0.00 0.00 2.83
5910 6607 0.389757 TGATGGACAACGGACGAACA 59.610 50.000 0.00 0.00 0.00 3.18
5911 6608 1.068474 CTGATGGACAACGGACGAAC 58.932 55.000 0.00 0.00 0.00 3.95
5912 6609 0.677288 ACTGATGGACAACGGACGAA 59.323 50.000 0.00 0.00 0.00 3.85
5913 6610 1.536940 TACTGATGGACAACGGACGA 58.463 50.000 0.00 0.00 0.00 4.20
5914 6611 2.579207 ATACTGATGGACAACGGACG 57.421 50.000 0.00 0.00 0.00 4.79
5915 6612 3.596214 ACAATACTGATGGACAACGGAC 58.404 45.455 0.00 0.00 0.00 4.79
5916 6613 3.973206 ACAATACTGATGGACAACGGA 57.027 42.857 0.00 0.00 0.00 4.69
5917 6614 3.062099 CGAACAATACTGATGGACAACGG 59.938 47.826 0.00 0.00 0.00 4.44
5918 6615 3.678072 ACGAACAATACTGATGGACAACG 59.322 43.478 0.00 0.00 0.00 4.10
5919 6616 5.607119 AACGAACAATACTGATGGACAAC 57.393 39.130 0.00 0.00 0.00 3.32
5920 6617 5.107259 CGAAACGAACAATACTGATGGACAA 60.107 40.000 0.00 0.00 0.00 3.18
5921 6618 4.387559 CGAAACGAACAATACTGATGGACA 59.612 41.667 0.00 0.00 0.00 4.02
5922 6619 4.387862 ACGAAACGAACAATACTGATGGAC 59.612 41.667 0.00 0.00 0.00 4.02
5923 6620 4.562082 ACGAAACGAACAATACTGATGGA 58.438 39.130 0.00 0.00 0.00 3.41
5924 6621 4.625742 AGACGAAACGAACAATACTGATGG 59.374 41.667 0.00 0.00 0.00 3.51
5925 6622 5.118664 ACAGACGAAACGAACAATACTGATG 59.881 40.000 0.00 0.00 0.00 3.07
5926 6623 5.227908 ACAGACGAAACGAACAATACTGAT 58.772 37.500 0.00 0.00 0.00 2.90
5927 6624 4.613944 ACAGACGAAACGAACAATACTGA 58.386 39.130 0.00 0.00 0.00 3.41
5928 6625 4.443063 TGACAGACGAAACGAACAATACTG 59.557 41.667 0.00 0.00 0.00 2.74
5929 6626 4.613944 TGACAGACGAAACGAACAATACT 58.386 39.130 0.00 0.00 0.00 2.12
5930 6627 4.959631 TGACAGACGAAACGAACAATAC 57.040 40.909 0.00 0.00 0.00 1.89
5931 6628 5.045215 ACTTGACAGACGAAACGAACAATA 58.955 37.500 0.00 0.00 0.00 1.90
5932 6629 3.869246 ACTTGACAGACGAAACGAACAAT 59.131 39.130 0.00 0.00 0.00 2.71
5933 6630 3.061563 CACTTGACAGACGAAACGAACAA 59.938 43.478 0.00 0.00 0.00 2.83
5934 6631 2.601314 CACTTGACAGACGAAACGAACA 59.399 45.455 0.00 0.00 0.00 3.18
5935 6632 2.596807 GCACTTGACAGACGAAACGAAC 60.597 50.000 0.00 0.00 0.00 3.95
5936 6633 1.591158 GCACTTGACAGACGAAACGAA 59.409 47.619 0.00 0.00 0.00 3.85
5937 6634 1.205657 GCACTTGACAGACGAAACGA 58.794 50.000 0.00 0.00 0.00 3.85
5938 6635 0.111704 CGCACTTGACAGACGAAACG 60.112 55.000 0.00 0.00 0.00 3.60
5939 6636 0.928229 ACGCACTTGACAGACGAAAC 59.072 50.000 0.00 0.00 0.00 2.78
5940 6637 1.326245 CAACGCACTTGACAGACGAAA 59.674 47.619 0.00 0.00 30.42 3.46
5941 6638 0.927537 CAACGCACTTGACAGACGAA 59.072 50.000 0.00 0.00 30.42 3.85
5942 6639 0.179121 ACAACGCACTTGACAGACGA 60.179 50.000 0.00 0.00 33.59 4.20
5943 6640 0.043053 CACAACGCACTTGACAGACG 60.043 55.000 0.00 0.00 33.59 4.18
5944 6641 0.304705 CCACAACGCACTTGACAGAC 59.695 55.000 0.00 0.00 33.59 3.51
5945 6642 1.436195 GCCACAACGCACTTGACAGA 61.436 55.000 0.00 0.00 33.59 3.41
5946 6643 1.009675 GCCACAACGCACTTGACAG 60.010 57.895 0.00 0.00 33.59 3.51
5947 6644 2.477176 GGCCACAACGCACTTGACA 61.477 57.895 0.00 0.00 33.59 3.58
5948 6645 2.331451 GGCCACAACGCACTTGAC 59.669 61.111 0.00 0.00 33.59 3.18
5949 6646 2.904866 GGGCCACAACGCACTTGA 60.905 61.111 4.39 0.00 33.59 3.02
5950 6647 2.086251 ATTGGGCCACAACGCACTTG 62.086 55.000 5.23 0.00 42.94 3.16
5951 6648 0.538516 TATTGGGCCACAACGCACTT 60.539 50.000 5.23 0.00 42.94 3.16
5952 6649 0.538516 TTATTGGGCCACAACGCACT 60.539 50.000 5.23 0.00 42.94 4.40
5953 6650 0.315568 TTTATTGGGCCACAACGCAC 59.684 50.000 5.23 0.00 42.94 5.34
5954 6651 1.203523 GATTTATTGGGCCACAACGCA 59.796 47.619 5.23 0.00 42.94 5.24
5955 6652 1.470805 GGATTTATTGGGCCACAACGC 60.471 52.381 5.23 0.00 42.94 4.84
5956 6653 1.202245 CGGATTTATTGGGCCACAACG 60.202 52.381 5.23 0.14 42.94 4.10
5957 6654 1.136110 CCGGATTTATTGGGCCACAAC 59.864 52.381 5.23 0.00 42.94 3.32
5958 6655 1.479709 CCGGATTTATTGGGCCACAA 58.520 50.000 5.23 7.14 44.54 3.33
5959 6656 1.040339 GCCGGATTTATTGGGCCACA 61.040 55.000 5.23 0.00 39.67 4.17
5960 6657 1.739667 GCCGGATTTATTGGGCCAC 59.260 57.895 5.23 0.00 39.67 5.01
5961 6658 4.268720 GCCGGATTTATTGGGCCA 57.731 55.556 5.05 0.00 39.67 5.36
5963 6660 2.561037 CGGGCCGGATTTATTGGGC 61.561 63.158 20.56 0.00 46.84 5.36
5964 6661 1.149627 TCGGGCCGGATTTATTGGG 59.850 57.895 27.98 0.00 0.00 4.12
5965 6662 1.170290 GGTCGGGCCGGATTTATTGG 61.170 60.000 27.98 0.00 0.00 3.16
5966 6663 1.170290 GGGTCGGGCCGGATTTATTG 61.170 60.000 27.98 0.00 38.44 1.90
5967 6664 1.149854 GGGTCGGGCCGGATTTATT 59.850 57.895 27.98 0.00 38.44 1.40
5968 6665 2.833957 GGGTCGGGCCGGATTTAT 59.166 61.111 27.98 0.00 38.44 1.40
5969 6666 3.852307 CGGGTCGGGCCGGATTTA 61.852 66.667 27.98 2.30 39.69 1.40


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

AutoCloner maintained by Alex Coulton.