Multiple sequence alignment - TraesCS1A01G319300

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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 TraesCS1A01G319300 chr1A 100.000 3425 0 0 1 3425 510355295 510351871 0.000000e+00 6325.0
1 TraesCS1A01G319300 chr1A 86.009 1408 179 13 1013 2408 510343194 510341793 0.000000e+00 1493.0
2 TraesCS1A01G319300 chr1B 86.243 1730 196 24 983 2696 557464432 557462729 0.000000e+00 1838.0
3 TraesCS1A01G319300 chr1B 87.872 1410 153 12 1013 2411 557412413 557411011 0.000000e+00 1640.0
4 TraesCS1A01G319300 chr1B 86.159 289 15 8 3137 3425 557462375 557462112 4.320000e-74 289.0
5 TraesCS1A01G319300 chr1B 81.818 121 22 0 3305 3425 557916930 557916810 6.050000e-18 102.0
6 TraesCS1A01G319300 chr1D 87.527 1411 168 6 1013 2419 413234473 413233067 0.000000e+00 1624.0
7 TraesCS1A01G319300 chr1D 85.880 1381 176 16 1000 2372 413224947 413226316 0.000000e+00 1452.0
8 TraesCS1A01G319300 chr1D 88.499 826 52 19 1696 2493 413298076 413297266 0.000000e+00 959.0
9 TraesCS1A01G319300 chr1D 93.568 653 25 4 1390 2040 413319371 413318734 0.000000e+00 957.0
10 TraesCS1A01G319300 chr1D 86.874 838 90 16 1465 2298 413359803 413358982 0.000000e+00 920.0
11 TraesCS1A01G319300 chr1D 89.560 546 44 5 1756 2289 413348641 413348097 0.000000e+00 680.0
12 TraesCS1A01G319300 chr1D 94.976 418 21 0 2033 2450 413315820 413315403 0.000000e+00 656.0
13 TraesCS1A01G319300 chr1D 92.388 289 19 1 3137 3425 413296053 413295768 3.180000e-110 409.0
14 TraesCS1A01G319300 chr1D 89.151 212 15 6 2491 2696 413315400 413315191 1.220000e-64 257.0
15 TraesCS1A01G319300 chr1D 85.714 245 24 8 999 1243 413319645 413319412 7.340000e-62 248.0
16 TraesCS1A01G319300 chr1D 87.952 166 14 2 2532 2692 413297264 413297100 1.250000e-44 191.0
17 TraesCS1A01G319300 chr1D 79.681 251 39 10 2450 2692 413411934 413411688 1.630000e-38 171.0
18 TraesCS1A01G319300 chr4B 97.436 780 20 0 1 780 573504034 573503255 0.000000e+00 1330.0
19 TraesCS1A01G319300 chr4B 96.923 780 23 1 1 780 671054129 671053351 0.000000e+00 1306.0
20 TraesCS1A01G319300 chr4B 90.183 438 28 8 2263 2696 559852468 559852042 1.070000e-154 556.0
21 TraesCS1A01G319300 chr4B 93.772 289 16 1 3137 3425 559851686 559851400 1.890000e-117 433.0
22 TraesCS1A01G319300 chr3B 97.436 780 19 1 1 780 146317548 146318326 0.000000e+00 1328.0
23 TraesCS1A01G319300 chr3B 87.531 401 40 10 2693 3087 565729692 565729296 4.030000e-124 455.0
24 TraesCS1A01G319300 chr7A 97.308 780 21 0 1 780 571354250 571353471 0.000000e+00 1325.0
25 TraesCS1A01G319300 chr7A 83.634 1387 202 19 1001 2384 62279361 62277997 0.000000e+00 1280.0
26 TraesCS1A01G319300 chr6B 96.927 781 22 1 2 780 353090927 353090147 0.000000e+00 1308.0
27 TraesCS1A01G319300 chr4A 96.292 782 20 4 3 780 433889089 433889865 0.000000e+00 1275.0
28 TraesCS1A01G319300 chr4A 97.297 703 16 2 1 703 591567577 591566878 0.000000e+00 1190.0
29 TraesCS1A01G319300 chr4A 96.552 87 2 1 783 868 478069139 478069225 3.560000e-30 143.0
30 TraesCS1A01G319300 chr7B 96.950 754 18 4 2 751 54785228 54784476 0.000000e+00 1260.0
31 TraesCS1A01G319300 chr7B 86.053 337 33 7 2693 3029 223716300 223716622 1.960000e-92 350.0
32 TraesCS1A01G319300 chr7B 98.824 85 1 0 783 867 132144667 132144751 5.920000e-33 152.0
33 TraesCS1A01G319300 chr7B 96.512 86 2 1 783 867 685277547 685277632 1.280000e-29 141.0
34 TraesCS1A01G319300 chrUn 97.013 703 18 2 1 703 416770878 416771577 0.000000e+00 1179.0
35 TraesCS1A01G319300 chrUn 87.826 230 21 7 2698 2925 55137328 55137104 2.620000e-66 263.0
36 TraesCS1A01G319300 chr5A 94.785 441 21 2 2696 3136 340145858 340146296 0.000000e+00 686.0
37 TraesCS1A01G319300 chr5A 96.667 90 1 2 783 871 338226030 338226118 7.660000e-32 148.0
38 TraesCS1A01G319300 chr5D 93.833 454 20 5 2693 3138 526763778 526764231 0.000000e+00 676.0
39 TraesCS1A01G319300 chr3D 89.474 380 34 6 2693 3068 433319057 433318680 3.090000e-130 475.0
40 TraesCS1A01G319300 chr3A 87.500 400 43 6 2693 3087 571411886 571411489 4.030000e-124 455.0
41 TraesCS1A01G319300 chr3A 95.699 93 2 2 783 874 344148762 344148853 7.660000e-32 148.0
42 TraesCS1A01G319300 chr2D 92.800 250 18 0 2875 3124 118743595 118743844 2.510000e-96 363.0
43 TraesCS1A01G319300 chr2D 91.979 187 15 0 2689 2875 118743126 118743312 2.620000e-66 263.0
44 TraesCS1A01G319300 chr5B 98.824 85 1 0 783 867 254152327 254152411 5.920000e-33 152.0
45 TraesCS1A01G319300 chr5B 100.000 28 0 0 2690 2717 429441474 429441447 6.000000e-03 52.8
46 TraesCS1A01G319300 chr2B 97.674 86 1 1 783 867 89528646 89528731 2.750000e-31 147.0
47 TraesCS1A01G319300 chr2B 97.674 86 1 1 783 867 250057267 250057182 2.750000e-31 147.0
48 TraesCS1A01G319300 chr2A 94.737 95 4 1 783 876 716907878 716907784 2.750000e-31 147.0


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 TraesCS1A01G319300 chr1A 510351871 510355295 3424 True 6325.000000 6325 100.00000 1 3425 1 chr1A.!!$R2 3424
1 TraesCS1A01G319300 chr1A 510341793 510343194 1401 True 1493.000000 1493 86.00900 1013 2408 1 chr1A.!!$R1 1395
2 TraesCS1A01G319300 chr1B 557411011 557412413 1402 True 1640.000000 1640 87.87200 1013 2411 1 chr1B.!!$R1 1398
3 TraesCS1A01G319300 chr1B 557462112 557464432 2320 True 1063.500000 1838 86.20100 983 3425 2 chr1B.!!$R3 2442
4 TraesCS1A01G319300 chr1D 413233067 413234473 1406 True 1624.000000 1624 87.52700 1013 2419 1 chr1D.!!$R1 1406
5 TraesCS1A01G319300 chr1D 413224947 413226316 1369 False 1452.000000 1452 85.88000 1000 2372 1 chr1D.!!$F1 1372
6 TraesCS1A01G319300 chr1D 413358982 413359803 821 True 920.000000 920 86.87400 1465 2298 1 chr1D.!!$R3 833
7 TraesCS1A01G319300 chr1D 413348097 413348641 544 True 680.000000 680 89.56000 1756 2289 1 chr1D.!!$R2 533
8 TraesCS1A01G319300 chr1D 413315191 413319645 4454 True 529.500000 957 90.85225 999 2696 4 chr1D.!!$R6 1697
9 TraesCS1A01G319300 chr1D 413295768 413298076 2308 True 519.666667 959 89.61300 1696 3425 3 chr1D.!!$R5 1729
10 TraesCS1A01G319300 chr4B 573503255 573504034 779 True 1330.000000 1330 97.43600 1 780 1 chr4B.!!$R1 779
11 TraesCS1A01G319300 chr4B 671053351 671054129 778 True 1306.000000 1306 96.92300 1 780 1 chr4B.!!$R2 779
12 TraesCS1A01G319300 chr4B 559851400 559852468 1068 True 494.500000 556 91.97750 2263 3425 2 chr4B.!!$R3 1162
13 TraesCS1A01G319300 chr3B 146317548 146318326 778 False 1328.000000 1328 97.43600 1 780 1 chr3B.!!$F1 779
14 TraesCS1A01G319300 chr7A 571353471 571354250 779 True 1325.000000 1325 97.30800 1 780 1 chr7A.!!$R2 779
15 TraesCS1A01G319300 chr7A 62277997 62279361 1364 True 1280.000000 1280 83.63400 1001 2384 1 chr7A.!!$R1 1383
16 TraesCS1A01G319300 chr6B 353090147 353090927 780 True 1308.000000 1308 96.92700 2 780 1 chr6B.!!$R1 778
17 TraesCS1A01G319300 chr4A 433889089 433889865 776 False 1275.000000 1275 96.29200 3 780 1 chr4A.!!$F1 777
18 TraesCS1A01G319300 chr4A 591566878 591567577 699 True 1190.000000 1190 97.29700 1 703 1 chr4A.!!$R1 702
19 TraesCS1A01G319300 chr7B 54784476 54785228 752 True 1260.000000 1260 96.95000 2 751 1 chr7B.!!$R1 749
20 TraesCS1A01G319300 chrUn 416770878 416771577 699 False 1179.000000 1179 97.01300 1 703 1 chrUn.!!$F1 702
21 TraesCS1A01G319300 chr2D 118743126 118743844 718 False 313.000000 363 92.38950 2689 3124 2 chr2D.!!$F1 435

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
807 818 0.097325 CGGCAGTGACTAGACGTCTC 59.903 60.0 23.89 8.99 43.25 3.36 F
808 819 0.097325 GGCAGTGACTAGACGTCTCG 59.903 60.0 23.89 18.96 43.25 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1720 0.107831 CCGTTCCAGGTCCAAGAACA 59.892 55.0 18.81 0.0 39.89 3.18 R
2687 5713 0.249657 CTAGATCCGCCACTGCCTTC 60.250 60.0 0.00 0.0 0.00 3.46 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
103 105 7.625828 ATTTAGTTGGCTTGTAATGTAGTCC 57.374 36.000 0.00 0.00 0.00 3.85
135 137 4.826733 ACACATTGATGTTTAGTTGGCAGA 59.173 37.500 0.00 0.00 39.39 4.26
146 148 8.911918 TGTTTAGTTGGCAGAAAGACTAATTA 57.088 30.769 8.98 1.02 35.31 1.40
250 254 1.066215 ACATATGCTCAGTTGGCGTGA 60.066 47.619 1.58 0.00 0.00 4.35
320 325 1.908344 TGGCACACACACATATGCTT 58.092 45.000 1.58 0.00 38.18 3.91
693 704 5.950758 AGCGGACAAAAATTACACACATA 57.049 34.783 0.00 0.00 0.00 2.29
751 762 2.202878 GCCACTCCATCGCGCTAA 60.203 61.111 5.56 0.00 0.00 3.09
780 791 2.112815 GCCGCCCATTAAACGCTCT 61.113 57.895 0.00 0.00 0.00 4.09
781 792 0.812412 GCCGCCCATTAAACGCTCTA 60.812 55.000 0.00 0.00 0.00 2.43
782 793 1.658994 CCGCCCATTAAACGCTCTAA 58.341 50.000 0.00 0.00 0.00 2.10
783 794 2.011222 CCGCCCATTAAACGCTCTAAA 58.989 47.619 0.00 0.00 0.00 1.85
784 795 2.616842 CCGCCCATTAAACGCTCTAAAT 59.383 45.455 0.00 0.00 0.00 1.40
785 796 3.810941 CCGCCCATTAAACGCTCTAAATA 59.189 43.478 0.00 0.00 0.00 1.40
786 797 4.454504 CCGCCCATTAAACGCTCTAAATAT 59.545 41.667 0.00 0.00 0.00 1.28
787 798 5.382303 CGCCCATTAAACGCTCTAAATATG 58.618 41.667 0.00 0.00 0.00 1.78
788 799 5.154222 GCCCATTAAACGCTCTAAATATGC 58.846 41.667 0.00 0.00 0.00 3.14
794 805 1.502231 CGCTCTAAATATGCGGCAGT 58.498 50.000 9.25 0.00 45.07 4.40
795 806 1.193203 CGCTCTAAATATGCGGCAGTG 59.807 52.381 9.25 0.00 45.07 3.66
796 807 2.483876 GCTCTAAATATGCGGCAGTGA 58.516 47.619 9.25 0.00 0.00 3.41
797 808 2.221981 GCTCTAAATATGCGGCAGTGAC 59.778 50.000 9.25 0.00 0.00 3.67
798 809 3.722147 CTCTAAATATGCGGCAGTGACT 58.278 45.455 9.25 0.00 0.00 3.41
799 810 4.796290 GCTCTAAATATGCGGCAGTGACTA 60.796 45.833 9.25 0.00 0.00 2.59
800 811 4.871513 TCTAAATATGCGGCAGTGACTAG 58.128 43.478 9.25 5.79 0.00 2.57
801 812 3.819564 AAATATGCGGCAGTGACTAGA 57.180 42.857 9.25 0.00 0.00 2.43
802 813 2.802787 ATATGCGGCAGTGACTAGAC 57.197 50.000 9.25 0.00 0.00 2.59
803 814 0.380733 TATGCGGCAGTGACTAGACG 59.619 55.000 9.25 6.02 0.00 4.18
804 815 1.595993 ATGCGGCAGTGACTAGACGT 61.596 55.000 9.25 0.00 0.00 4.34
805 816 1.514443 GCGGCAGTGACTAGACGTC 60.514 63.158 7.70 7.70 43.14 4.34
806 817 1.924320 GCGGCAGTGACTAGACGTCT 61.924 60.000 23.66 23.66 43.25 4.18
807 818 0.097325 CGGCAGTGACTAGACGTCTC 59.903 60.000 23.89 8.99 43.25 3.36
808 819 0.097325 GGCAGTGACTAGACGTCTCG 59.903 60.000 23.89 18.96 43.25 4.04
809 820 0.097325 GCAGTGACTAGACGTCTCGG 59.903 60.000 23.89 18.10 43.25 4.63
810 821 1.723220 CAGTGACTAGACGTCTCGGA 58.277 55.000 23.89 3.45 43.25 4.55
811 822 1.394227 CAGTGACTAGACGTCTCGGAC 59.606 57.143 23.89 16.08 43.25 4.79
812 823 1.001746 AGTGACTAGACGTCTCGGACA 59.998 52.381 23.89 18.40 43.25 4.02
813 824 1.394227 GTGACTAGACGTCTCGGACAG 59.606 57.143 23.89 15.91 43.25 3.51
814 825 1.008329 GACTAGACGTCTCGGACAGG 58.992 60.000 23.89 7.21 39.61 4.00
815 826 0.392729 ACTAGACGTCTCGGACAGGG 60.393 60.000 23.89 5.86 32.09 4.45
816 827 1.716826 CTAGACGTCTCGGACAGGGC 61.717 65.000 23.89 0.00 32.09 5.19
817 828 4.131088 GACGTCTCGGACAGGGCC 62.131 72.222 8.70 0.00 32.09 5.80
839 850 3.741860 GCTAGCGAGCGGTACCTA 58.258 61.111 10.90 0.00 39.39 3.08
840 851 1.575423 GCTAGCGAGCGGTACCTAG 59.425 63.158 10.90 13.69 39.39 3.02
841 852 1.575423 CTAGCGAGCGGTACCTAGC 59.425 63.158 10.90 7.03 34.22 3.42
861 872 4.241555 CCGGCCGCCAGCTAGATT 62.242 66.667 22.85 0.00 43.05 2.40
862 873 2.969238 CGGCCGCCAGCTAGATTG 60.969 66.667 14.67 0.00 43.05 2.67
863 874 2.592861 GGCCGCCAGCTAGATTGG 60.593 66.667 3.91 8.87 43.05 3.16
864 875 2.190578 GCCGCCAGCTAGATTGGT 59.809 61.111 13.38 0.00 38.02 3.67
865 876 1.889573 GCCGCCAGCTAGATTGGTC 60.890 63.158 13.38 6.76 38.02 4.02
866 877 1.227674 CCGCCAGCTAGATTGGTCC 60.228 63.158 13.38 0.00 38.02 4.46
867 878 1.227674 CGCCAGCTAGATTGGTCCC 60.228 63.158 13.38 0.00 38.02 4.46
868 879 1.915228 GCCAGCTAGATTGGTCCCA 59.085 57.895 13.38 0.00 38.02 4.37
869 880 0.475906 GCCAGCTAGATTGGTCCCAT 59.524 55.000 13.38 0.00 38.02 4.00
870 881 1.544314 GCCAGCTAGATTGGTCCCATC 60.544 57.143 13.38 0.00 38.02 3.51
871 882 1.770658 CCAGCTAGATTGGTCCCATCA 59.229 52.381 5.77 0.00 0.00 3.07
872 883 2.173356 CCAGCTAGATTGGTCCCATCAA 59.827 50.000 5.77 0.00 0.00 2.57
873 884 3.181436 CCAGCTAGATTGGTCCCATCAAT 60.181 47.826 5.77 0.00 37.52 2.57
874 885 4.042062 CCAGCTAGATTGGTCCCATCAATA 59.958 45.833 5.77 0.00 35.26 1.90
875 886 5.456619 CCAGCTAGATTGGTCCCATCAATAA 60.457 44.000 5.77 0.00 35.26 1.40
876 887 6.243900 CAGCTAGATTGGTCCCATCAATAAT 58.756 40.000 5.77 0.00 35.26 1.28
877 888 6.718454 CAGCTAGATTGGTCCCATCAATAATT 59.282 38.462 5.77 0.00 35.26 1.40
878 889 6.718454 AGCTAGATTGGTCCCATCAATAATTG 59.282 38.462 5.77 0.00 35.26 2.32
879 890 6.491403 GCTAGATTGGTCCCATCAATAATTGT 59.509 38.462 5.77 0.00 35.26 2.71
880 891 7.665559 GCTAGATTGGTCCCATCAATAATTGTA 59.334 37.037 5.77 0.00 35.26 2.41
881 892 7.823745 AGATTGGTCCCATCAATAATTGTAC 57.176 36.000 5.77 0.00 35.26 2.90
882 893 6.777580 AGATTGGTCCCATCAATAATTGTACC 59.222 38.462 5.77 0.00 35.26 3.34
883 894 5.725551 TGGTCCCATCAATAATTGTACCT 57.274 39.130 0.00 0.00 0.00 3.08
884 895 5.690865 TGGTCCCATCAATAATTGTACCTC 58.309 41.667 0.00 0.00 0.00 3.85
885 896 5.070685 GGTCCCATCAATAATTGTACCTCC 58.929 45.833 0.00 0.00 0.00 4.30
886 897 5.398581 GGTCCCATCAATAATTGTACCTCCA 60.399 44.000 0.00 0.00 0.00 3.86
887 898 5.765182 GTCCCATCAATAATTGTACCTCCAG 59.235 44.000 0.00 0.00 0.00 3.86
888 899 5.072741 CCCATCAATAATTGTACCTCCAGG 58.927 45.833 0.00 0.00 42.17 4.45
889 900 4.520492 CCATCAATAATTGTACCTCCAGGC 59.480 45.833 0.00 0.00 39.32 4.85
890 901 4.164843 TCAATAATTGTACCTCCAGGCC 57.835 45.455 0.00 0.00 39.32 5.19
891 902 3.525609 TCAATAATTGTACCTCCAGGCCA 59.474 43.478 5.01 0.00 39.32 5.36
892 903 4.167892 TCAATAATTGTACCTCCAGGCCAT 59.832 41.667 5.01 0.00 39.32 4.40
893 904 5.371176 TCAATAATTGTACCTCCAGGCCATA 59.629 40.000 5.01 0.00 39.32 2.74
894 905 6.045459 TCAATAATTGTACCTCCAGGCCATAT 59.955 38.462 5.01 0.00 39.32 1.78
895 906 4.814224 AATTGTACCTCCAGGCCATATT 57.186 40.909 5.01 0.00 39.32 1.28
896 907 3.576078 TTGTACCTCCAGGCCATATTG 57.424 47.619 5.01 0.00 39.32 1.90
897 908 2.770447 TGTACCTCCAGGCCATATTGA 58.230 47.619 5.01 0.00 39.32 2.57
898 909 2.438021 TGTACCTCCAGGCCATATTGAC 59.562 50.000 5.01 0.00 39.32 3.18
899 910 1.595311 ACCTCCAGGCCATATTGACA 58.405 50.000 5.01 0.00 39.32 3.58
900 911 2.138542 ACCTCCAGGCCATATTGACAT 58.861 47.619 5.01 0.00 39.32 3.06
901 912 2.107204 ACCTCCAGGCCATATTGACATC 59.893 50.000 5.01 0.00 39.32 3.06
902 913 2.420642 CTCCAGGCCATATTGACATCG 58.579 52.381 5.01 0.00 0.00 3.84
903 914 2.037641 CTCCAGGCCATATTGACATCGA 59.962 50.000 5.01 0.00 0.00 3.59
904 915 2.146342 CCAGGCCATATTGACATCGAC 58.854 52.381 5.01 0.00 0.00 4.20
905 916 1.794701 CAGGCCATATTGACATCGACG 59.205 52.381 5.01 0.00 0.00 5.12
906 917 1.412710 AGGCCATATTGACATCGACGT 59.587 47.619 5.01 0.00 0.00 4.34
907 918 1.792949 GGCCATATTGACATCGACGTC 59.207 52.381 4.33 4.33 36.40 4.34
908 919 1.452025 GCCATATTGACATCGACGTCG 59.548 52.381 31.30 31.30 38.84 5.12
909 920 1.452025 CCATATTGACATCGACGTCGC 59.548 52.381 32.19 18.72 38.84 5.19
910 921 2.116366 CATATTGACATCGACGTCGCA 58.884 47.619 32.19 21.12 38.84 5.10
911 922 2.265647 TATTGACATCGACGTCGCAA 57.734 45.000 32.19 27.48 38.84 4.85
912 923 0.713883 ATTGACATCGACGTCGCAAC 59.286 50.000 32.19 21.38 38.84 4.17
913 924 1.279527 TTGACATCGACGTCGCAACC 61.280 55.000 32.19 20.19 38.84 3.77
914 925 2.774951 GACATCGACGTCGCAACCG 61.775 63.158 32.19 19.09 39.60 4.44
915 926 4.191485 CATCGACGTCGCAACCGC 62.191 66.667 32.19 0.00 39.60 5.68
921 932 4.368808 CGTCGCAACCGCCACAAG 62.369 66.667 0.00 0.00 33.11 3.16
922 933 4.683334 GTCGCAACCGCCACAAGC 62.683 66.667 0.00 0.00 38.52 4.01
923 934 4.927782 TCGCAACCGCCACAAGCT 62.928 61.111 0.00 0.00 40.39 3.74
924 935 3.964875 CGCAACCGCCACAAGCTT 61.965 61.111 0.00 0.00 40.39 3.74
925 936 2.050077 GCAACCGCCACAAGCTTC 60.050 61.111 0.00 0.00 40.39 3.86
926 937 2.844451 GCAACCGCCACAAGCTTCA 61.844 57.895 0.00 0.00 40.39 3.02
927 938 1.283793 CAACCGCCACAAGCTTCAG 59.716 57.895 0.00 0.00 40.39 3.02
928 939 2.555547 AACCGCCACAAGCTTCAGC 61.556 57.895 0.00 0.00 40.39 4.26
929 940 3.741476 CCGCCACAAGCTTCAGCC 61.741 66.667 0.00 0.00 43.38 4.85
930 941 2.670934 CGCCACAAGCTTCAGCCT 60.671 61.111 0.00 0.00 43.38 4.58
931 942 2.263741 CGCCACAAGCTTCAGCCTT 61.264 57.895 0.00 0.00 43.38 4.35
932 943 1.583477 GCCACAAGCTTCAGCCTTC 59.417 57.895 0.00 0.00 43.38 3.46
933 944 1.174712 GCCACAAGCTTCAGCCTTCA 61.175 55.000 0.00 0.00 43.38 3.02
934 945 0.879765 CCACAAGCTTCAGCCTTCAG 59.120 55.000 0.00 0.00 43.38 3.02
935 946 1.602311 CACAAGCTTCAGCCTTCAGT 58.398 50.000 0.00 0.00 43.38 3.41
936 947 1.952296 CACAAGCTTCAGCCTTCAGTT 59.048 47.619 0.00 0.00 43.38 3.16
937 948 2.031333 CACAAGCTTCAGCCTTCAGTTC 60.031 50.000 0.00 0.00 43.38 3.01
938 949 2.224606 CAAGCTTCAGCCTTCAGTTCA 58.775 47.619 0.00 0.00 43.38 3.18
939 950 2.181954 AGCTTCAGCCTTCAGTTCAG 57.818 50.000 0.00 0.00 43.38 3.02
940 951 1.419387 AGCTTCAGCCTTCAGTTCAGT 59.581 47.619 0.00 0.00 43.38 3.41
941 952 1.534595 GCTTCAGCCTTCAGTTCAGTG 59.465 52.381 0.00 0.00 34.31 3.66
942 953 1.534595 CTTCAGCCTTCAGTTCAGTGC 59.465 52.381 0.00 0.00 0.00 4.40
943 954 0.761187 TCAGCCTTCAGTTCAGTGCT 59.239 50.000 0.00 0.00 0.00 4.40
944 955 0.873054 CAGCCTTCAGTTCAGTGCTG 59.127 55.000 0.00 0.00 40.05 4.41
945 956 0.888285 AGCCTTCAGTTCAGTGCTGC 60.888 55.000 0.00 0.00 34.21 5.25
946 957 0.888285 GCCTTCAGTTCAGTGCTGCT 60.888 55.000 0.00 0.00 34.21 4.24
947 958 0.873054 CCTTCAGTTCAGTGCTGCTG 59.127 55.000 0.00 3.02 46.34 4.41
948 959 0.237761 CTTCAGTTCAGTGCTGCTGC 59.762 55.000 8.89 8.89 44.66 5.25
949 960 0.179037 TTCAGTTCAGTGCTGCTGCT 60.179 50.000 17.00 0.00 44.66 4.24
950 961 0.681175 TCAGTTCAGTGCTGCTGCTA 59.319 50.000 17.00 0.47 44.66 3.49
951 962 0.795085 CAGTTCAGTGCTGCTGCTAC 59.205 55.000 17.00 12.50 44.66 3.58
952 963 0.321122 AGTTCAGTGCTGCTGCTACC 60.321 55.000 17.00 4.92 44.66 3.18
953 964 1.003355 TTCAGTGCTGCTGCTACCC 60.003 57.895 17.00 2.52 44.66 3.69
954 965 1.767654 TTCAGTGCTGCTGCTACCCA 61.768 55.000 17.00 0.00 44.66 4.51
955 966 2.037136 CAGTGCTGCTGCTACCCAC 61.037 63.158 17.00 6.04 38.52 4.61
956 967 2.219875 AGTGCTGCTGCTACCCACT 61.220 57.895 17.00 8.29 40.48 4.00
957 968 1.743252 GTGCTGCTGCTACCCACTC 60.743 63.158 17.00 0.00 40.48 3.51
958 969 2.510238 GCTGCTGCTACCCACTCG 60.510 66.667 8.53 0.00 36.03 4.18
959 970 3.006756 GCTGCTGCTACCCACTCGA 62.007 63.158 8.53 0.00 36.03 4.04
960 971 1.153745 CTGCTGCTACCCACTCGAC 60.154 63.158 0.00 0.00 0.00 4.20
961 972 1.599606 CTGCTGCTACCCACTCGACT 61.600 60.000 0.00 0.00 0.00 4.18
962 973 1.139947 GCTGCTACCCACTCGACTC 59.860 63.158 0.00 0.00 0.00 3.36
963 974 1.810532 CTGCTACCCACTCGACTCC 59.189 63.158 0.00 0.00 0.00 3.85
964 975 0.965866 CTGCTACCCACTCGACTCCA 60.966 60.000 0.00 0.00 0.00 3.86
965 976 0.324368 TGCTACCCACTCGACTCCAT 60.324 55.000 0.00 0.00 0.00 3.41
966 977 0.824759 GCTACCCACTCGACTCCATT 59.175 55.000 0.00 0.00 0.00 3.16
967 978 2.029623 GCTACCCACTCGACTCCATTA 58.970 52.381 0.00 0.00 0.00 1.90
968 979 2.628657 GCTACCCACTCGACTCCATTAT 59.371 50.000 0.00 0.00 0.00 1.28
969 980 3.069729 GCTACCCACTCGACTCCATTATT 59.930 47.826 0.00 0.00 0.00 1.40
970 981 4.443034 GCTACCCACTCGACTCCATTATTT 60.443 45.833 0.00 0.00 0.00 1.40
971 982 4.138487 ACCCACTCGACTCCATTATTTC 57.862 45.455 0.00 0.00 0.00 2.17
972 983 3.517901 ACCCACTCGACTCCATTATTTCA 59.482 43.478 0.00 0.00 0.00 2.69
973 984 4.122776 CCCACTCGACTCCATTATTTCAG 58.877 47.826 0.00 0.00 0.00 3.02
974 985 3.557595 CCACTCGACTCCATTATTTCAGC 59.442 47.826 0.00 0.00 0.00 4.26
975 986 4.183865 CACTCGACTCCATTATTTCAGCA 58.816 43.478 0.00 0.00 0.00 4.41
976 987 4.631377 CACTCGACTCCATTATTTCAGCAA 59.369 41.667 0.00 0.00 0.00 3.91
977 988 5.122239 CACTCGACTCCATTATTTCAGCAAA 59.878 40.000 0.00 0.00 0.00 3.68
978 989 5.122396 ACTCGACTCCATTATTTCAGCAAAC 59.878 40.000 0.00 0.00 0.00 2.93
979 990 5.000591 TCGACTCCATTATTTCAGCAAACA 58.999 37.500 0.00 0.00 0.00 2.83
980 991 5.471797 TCGACTCCATTATTTCAGCAAACAA 59.528 36.000 0.00 0.00 0.00 2.83
981 992 5.796935 CGACTCCATTATTTCAGCAAACAAG 59.203 40.000 0.00 0.00 0.00 3.16
982 993 6.348458 CGACTCCATTATTTCAGCAAACAAGA 60.348 38.462 0.00 0.00 0.00 3.02
983 994 7.288810 ACTCCATTATTTCAGCAAACAAGAA 57.711 32.000 0.00 0.00 0.00 2.52
984 995 7.147976 ACTCCATTATTTCAGCAAACAAGAAC 58.852 34.615 0.00 0.00 0.00 3.01
985 996 7.048629 TCCATTATTTCAGCAAACAAGAACA 57.951 32.000 0.00 0.00 0.00 3.18
986 997 7.495901 TCCATTATTTCAGCAAACAAGAACAA 58.504 30.769 0.00 0.00 0.00 2.83
987 998 7.984050 TCCATTATTTCAGCAAACAAGAACAAA 59.016 29.630 0.00 0.00 0.00 2.83
988 999 8.063630 CCATTATTTCAGCAAACAAGAACAAAC 58.936 33.333 0.00 0.00 0.00 2.93
989 1000 8.602328 CATTATTTCAGCAAACAAGAACAAACA 58.398 29.630 0.00 0.00 0.00 2.83
990 1001 8.715191 TTATTTCAGCAAACAAGAACAAACAT 57.285 26.923 0.00 0.00 0.00 2.71
991 1002 9.809096 TTATTTCAGCAAACAAGAACAAACATA 57.191 25.926 0.00 0.00 0.00 2.29
992 1003 8.891671 ATTTCAGCAAACAAGAACAAACATAT 57.108 26.923 0.00 0.00 0.00 1.78
993 1004 7.928908 TTCAGCAAACAAGAACAAACATATC 57.071 32.000 0.00 0.00 0.00 1.63
994 1005 6.142139 TCAGCAAACAAGAACAAACATATCG 58.858 36.000 0.00 0.00 0.00 2.92
995 1006 6.017523 TCAGCAAACAAGAACAAACATATCGA 60.018 34.615 0.00 0.00 0.00 3.59
996 1007 6.303970 CAGCAAACAAGAACAAACATATCGAG 59.696 38.462 0.00 0.00 0.00 4.04
997 1008 5.569059 GCAAACAAGAACAAACATATCGAGG 59.431 40.000 0.00 0.00 0.00 4.63
1041 1052 0.254178 ACAAGCTGCGGATCCTGATT 59.746 50.000 10.75 2.11 0.00 2.57
1359 1390 1.390383 CGCAGGAGGCTCTCATCAGA 61.390 60.000 15.23 0.00 41.67 3.27
1360 1391 0.829333 GCAGGAGGCTCTCATCAGAA 59.171 55.000 15.23 0.00 40.25 3.02
1414 1445 1.344763 ACTTCTTCTGGAACTCCACCG 59.655 52.381 0.00 0.00 42.01 4.94
1485 1516 2.282391 TCAAGGCTTGCCATGCGT 60.282 55.556 22.31 0.00 0.00 5.24
2019 2113 2.681778 CTCGTCAGAGGGTGGGCT 60.682 66.667 0.00 0.00 40.75 5.19
2337 5354 2.811317 CAGGAGCTCGCCGTGAAC 60.811 66.667 7.83 0.00 0.00 3.18
2397 5414 2.502947 TGATCTGCACAGGCTTATCAGT 59.497 45.455 0.00 0.00 41.91 3.41
2426 5443 2.565391 TGGAAACACGGAAGATCTAGCA 59.435 45.455 0.00 0.00 33.40 3.49
2447 5464 1.480212 AACCCATCGAGCAGGTGACA 61.480 55.000 4.71 0.00 33.05 3.58
2448 5465 1.296392 CCCATCGAGCAGGTGACAA 59.704 57.895 0.00 0.00 30.86 3.18
2464 5481 0.182775 ACAAAAGTCGGCCAGGTTCT 59.817 50.000 2.24 0.00 0.00 3.01
2527 5544 2.821969 CAGTGAGATTGGTTTCCTTGGG 59.178 50.000 0.00 0.00 0.00 4.12
2571 5592 6.738114 TCCTGAATTTGTTTCATTCTGTCAC 58.262 36.000 0.00 0.00 43.30 3.67
2584 5605 2.184020 CTGTCACCCCGATTGCCTGA 62.184 60.000 0.00 0.00 0.00 3.86
2597 5618 4.380233 CGATTGCCTGAAAAGCTCTGAAAT 60.380 41.667 0.00 0.00 0.00 2.17
2598 5619 5.163723 CGATTGCCTGAAAAGCTCTGAAATA 60.164 40.000 0.00 0.00 0.00 1.40
2600 5621 4.910195 TGCCTGAAAAGCTCTGAAATAGA 58.090 39.130 0.00 0.00 0.00 1.98
2630 5656 6.145371 ACGGTGCAACATTTGATTTTGTAATC 59.855 34.615 0.98 0.00 39.98 1.75
2653 5679 1.339711 GCGACATTTGCACAACATCC 58.660 50.000 0.00 0.00 0.00 3.51
2677 5703 5.230936 CGCAGATTATGATAGGCGATGTTAG 59.769 44.000 8.90 0.00 46.65 2.34
2687 5713 2.693797 GCGATGTTAGCCAATGGATG 57.306 50.000 2.05 0.00 0.00 3.51
2706 5732 0.249657 GAAGGCAGTGGCGGATCTAG 60.250 60.000 11.51 0.00 42.47 2.43
2723 5749 5.602978 GGATCTAGGATTTGAAGTCAGGGTA 59.397 44.000 0.00 0.00 0.00 3.69
2732 5957 2.111972 TGAAGTCAGGGTAGTCCTTCCT 59.888 50.000 0.00 0.00 45.47 3.36
2863 6229 6.830324 CCATGGTCCTCTTCATTCTTCAATAA 59.170 38.462 2.57 0.00 0.00 1.40
2870 6236 8.805175 TCCTCTTCATTCTTCAATAATTTTGCA 58.195 29.630 0.00 0.00 0.00 4.08
2963 6959 4.952262 ATGGTTGTCGATTCATGTTCTG 57.048 40.909 0.00 0.00 0.00 3.02
2975 6971 4.743057 TCATGTTCTGGACAGTGGATAG 57.257 45.455 0.00 0.00 42.62 2.08
3000 6996 7.702348 AGCACAACAAAGAACAAACTCTAAATC 59.298 33.333 0.00 0.00 0.00 2.17
3017 7013 7.178983 ACTCTAAATCAATTGGAGATTTGGCAA 59.821 33.333 13.52 0.00 46.52 4.52
3022 7018 0.903942 TTGGAGATTTGGCAATGGGC 59.096 50.000 0.00 0.00 43.74 5.36
3025 7021 0.101219 GAGATTTGGCAATGGGCGAC 59.899 55.000 0.00 0.00 46.16 5.19
3068 7064 2.103373 GTGCTGGAGACCTGAGATGTA 58.897 52.381 0.00 0.00 0.00 2.29
3080 7076 2.353607 GATGTACTCCGAGCGCCG 60.354 66.667 2.29 7.65 38.18 6.46
3140 7136 1.623542 GGGAGGCTCGTGGGTGTAAT 61.624 60.000 8.69 0.00 0.00 1.89
3174 7170 1.731709 TCGCGTCCATTTGTCATTCTG 59.268 47.619 5.77 0.00 0.00 3.02
3200 7196 4.196971 GGCGGTTTTTATGGTCATAGTCT 58.803 43.478 0.00 0.00 0.00 3.24
3226 7222 0.250467 TGCACTGCTTGAAGAGGTCC 60.250 55.000 1.98 0.00 0.00 4.46
3317 7313 7.855784 TCTATTTGGACCATAGCTCTAATGA 57.144 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 3.358707 ACATCAATGTGTGTGCAACTG 57.641 42.857 0.00 0.00 40.03 3.16
135 137 6.715464 GCATATGCGTGTGTAATTAGTCTTT 58.285 36.000 12.82 0.00 0.00 2.52
250 254 5.820423 TGTGTGTGCAACTAGACTAAATTGT 59.180 36.000 0.00 0.00 38.04 2.71
320 325 0.529773 CTAGATTGCCGCGCCAACTA 60.530 55.000 3.97 8.13 0.00 2.24
587 598 6.823182 ACAGATCACATATCCATTTGTTTCGA 59.177 34.615 0.00 0.00 0.00 3.71
693 704 3.627577 CGGCTGGCTTAAAATAGACATGT 59.372 43.478 0.00 0.00 31.39 3.21
737 748 1.069765 CCCATTAGCGCGATGGAGT 59.930 57.895 33.56 7.75 45.59 3.85
780 791 4.617959 GTCTAGTCACTGCCGCATATTTA 58.382 43.478 0.00 0.00 0.00 1.40
781 792 3.458189 GTCTAGTCACTGCCGCATATTT 58.542 45.455 0.00 0.00 0.00 1.40
782 793 2.543861 CGTCTAGTCACTGCCGCATATT 60.544 50.000 0.00 0.00 0.00 1.28
783 794 1.001268 CGTCTAGTCACTGCCGCATAT 60.001 52.381 0.00 0.00 0.00 1.78
784 795 0.380733 CGTCTAGTCACTGCCGCATA 59.619 55.000 0.00 0.00 0.00 3.14
785 796 1.139734 CGTCTAGTCACTGCCGCAT 59.860 57.895 0.00 0.00 0.00 4.73
786 797 2.265904 ACGTCTAGTCACTGCCGCA 61.266 57.895 0.00 0.00 0.00 5.69
787 798 2.567049 ACGTCTAGTCACTGCCGC 59.433 61.111 0.00 0.00 0.00 6.53
796 807 0.392729 CCCTGTCCGAGACGTCTAGT 60.393 60.000 20.09 0.00 34.95 2.57
797 808 1.716826 GCCCTGTCCGAGACGTCTAG 61.717 65.000 20.09 18.77 34.95 2.43
798 809 1.748122 GCCCTGTCCGAGACGTCTA 60.748 63.158 20.09 0.00 34.95 2.59
799 810 3.063084 GCCCTGTCCGAGACGTCT 61.063 66.667 20.18 20.18 34.95 4.18
800 811 4.131088 GGCCCTGTCCGAGACGTC 62.131 72.222 7.70 7.70 34.95 4.34
822 833 1.575423 CTAGGTACCGCTCGCTAGC 59.425 63.158 6.18 4.06 45.86 3.42
823 834 1.575423 GCTAGGTACCGCTCGCTAG 59.425 63.158 6.18 2.72 0.00 3.42
824 835 2.249535 CGCTAGGTACCGCTCGCTA 61.250 63.158 6.18 0.00 0.00 4.26
825 836 3.584052 CGCTAGGTACCGCTCGCT 61.584 66.667 6.18 0.00 0.00 4.93
844 855 4.241555 AATCTAGCTGGCGGCCGG 62.242 66.667 29.38 23.69 43.05 6.13
845 856 2.969238 CAATCTAGCTGGCGGCCG 60.969 66.667 24.05 24.05 43.05 6.13
846 857 2.592861 CCAATCTAGCTGGCGGCC 60.593 66.667 16.15 13.32 43.05 6.13
847 858 1.889573 GACCAATCTAGCTGGCGGC 60.890 63.158 11.19 11.19 37.48 6.53
848 859 1.227674 GGACCAATCTAGCTGGCGG 60.228 63.158 9.88 0.00 37.48 6.13
849 860 1.227674 GGGACCAATCTAGCTGGCG 60.228 63.158 9.88 0.00 37.48 5.69
850 861 0.475906 ATGGGACCAATCTAGCTGGC 59.524 55.000 9.88 4.38 37.48 4.85
851 862 1.770658 TGATGGGACCAATCTAGCTGG 59.229 52.381 10.36 8.69 40.05 4.85
852 863 3.565764 TTGATGGGACCAATCTAGCTG 57.434 47.619 10.36 0.00 0.00 4.24
853 864 5.912149 TTATTGATGGGACCAATCTAGCT 57.088 39.130 10.36 0.00 35.94 3.32
854 865 6.491403 ACAATTATTGATGGGACCAATCTAGC 59.509 38.462 12.28 0.00 35.94 3.42
855 866 9.003658 GTACAATTATTGATGGGACCAATCTAG 57.996 37.037 12.28 0.00 35.94 2.43
856 867 7.942341 GGTACAATTATTGATGGGACCAATCTA 59.058 37.037 12.28 2.84 35.94 1.98
857 868 6.777580 GGTACAATTATTGATGGGACCAATCT 59.222 38.462 12.28 0.00 35.94 2.40
858 869 6.777580 AGGTACAATTATTGATGGGACCAATC 59.222 38.462 12.28 1.33 35.94 2.67
859 870 6.682537 AGGTACAATTATTGATGGGACCAAT 58.317 36.000 12.28 0.00 37.86 3.16
860 871 6.086011 AGGTACAATTATTGATGGGACCAA 57.914 37.500 12.28 0.00 0.00 3.67
861 872 5.398581 GGAGGTACAATTATTGATGGGACCA 60.399 44.000 12.28 0.00 0.00 4.02
862 873 5.070685 GGAGGTACAATTATTGATGGGACC 58.929 45.833 12.28 9.89 0.00 4.46
863 874 5.690865 TGGAGGTACAATTATTGATGGGAC 58.309 41.667 12.28 1.94 0.00 4.46
864 875 5.163099 CCTGGAGGTACAATTATTGATGGGA 60.163 44.000 12.28 0.00 0.00 4.37
865 876 5.072741 CCTGGAGGTACAATTATTGATGGG 58.927 45.833 12.28 0.00 0.00 4.00
866 877 4.520492 GCCTGGAGGTACAATTATTGATGG 59.480 45.833 12.28 3.29 37.57 3.51
867 878 4.520492 GGCCTGGAGGTACAATTATTGATG 59.480 45.833 12.28 0.00 37.57 3.07
868 879 4.167892 TGGCCTGGAGGTACAATTATTGAT 59.832 41.667 12.28 0.00 37.57 2.57
869 880 3.525609 TGGCCTGGAGGTACAATTATTGA 59.474 43.478 12.28 0.00 37.57 2.57
870 881 3.897239 TGGCCTGGAGGTACAATTATTG 58.103 45.455 3.32 3.07 37.57 1.90
871 882 4.814224 ATGGCCTGGAGGTACAATTATT 57.186 40.909 3.32 0.00 37.57 1.40
872 883 6.045459 TCAATATGGCCTGGAGGTACAATTAT 59.955 38.462 3.32 0.00 37.57 1.28
873 884 5.371176 TCAATATGGCCTGGAGGTACAATTA 59.629 40.000 3.32 0.00 37.57 1.40
874 885 4.167892 TCAATATGGCCTGGAGGTACAATT 59.832 41.667 3.32 0.00 37.57 2.32
875 886 3.721575 TCAATATGGCCTGGAGGTACAAT 59.278 43.478 3.32 0.00 37.57 2.71
876 887 3.118038 GTCAATATGGCCTGGAGGTACAA 60.118 47.826 3.32 0.00 37.57 2.41
877 888 2.438021 GTCAATATGGCCTGGAGGTACA 59.562 50.000 3.32 0.00 37.57 2.90
878 889 2.438021 TGTCAATATGGCCTGGAGGTAC 59.562 50.000 3.32 0.00 37.57 3.34
879 890 2.770447 TGTCAATATGGCCTGGAGGTA 58.230 47.619 3.32 0.00 37.57 3.08
880 891 1.595311 TGTCAATATGGCCTGGAGGT 58.405 50.000 3.32 0.00 37.57 3.85
881 892 2.787994 GATGTCAATATGGCCTGGAGG 58.212 52.381 3.32 0.00 38.53 4.30
882 893 2.037641 TCGATGTCAATATGGCCTGGAG 59.962 50.000 3.32 0.00 0.00 3.86
883 894 2.046292 TCGATGTCAATATGGCCTGGA 58.954 47.619 3.32 0.00 0.00 3.86
884 895 2.146342 GTCGATGTCAATATGGCCTGG 58.854 52.381 3.32 0.00 0.00 4.45
885 896 1.794701 CGTCGATGTCAATATGGCCTG 59.205 52.381 3.32 0.00 0.00 4.85
886 897 1.412710 ACGTCGATGTCAATATGGCCT 59.587 47.619 3.92 0.00 0.00 5.19
887 898 1.792949 GACGTCGATGTCAATATGGCC 59.207 52.381 28.64 0.00 38.75 5.36
888 899 1.452025 CGACGTCGATGTCAATATGGC 59.548 52.381 33.35 8.40 43.02 4.40
889 900 1.452025 GCGACGTCGATGTCAATATGG 59.548 52.381 39.74 17.94 43.02 2.74
890 901 2.116366 TGCGACGTCGATGTCAATATG 58.884 47.619 39.74 18.56 43.02 1.78
891 902 2.485266 TGCGACGTCGATGTCAATAT 57.515 45.000 39.74 0.60 43.02 1.28
892 903 1.915350 GTTGCGACGTCGATGTCAATA 59.085 47.619 39.74 17.14 43.02 1.90
893 904 0.713883 GTTGCGACGTCGATGTCAAT 59.286 50.000 39.74 1.76 43.02 2.57
894 905 1.279527 GGTTGCGACGTCGATGTCAA 61.280 55.000 39.74 28.75 43.02 3.18
895 906 1.731613 GGTTGCGACGTCGATGTCA 60.732 57.895 39.74 24.95 43.02 3.58
896 907 2.774951 CGGTTGCGACGTCGATGTC 61.775 63.158 39.74 24.88 43.02 3.06
897 908 2.803670 CGGTTGCGACGTCGATGT 60.804 61.111 39.74 10.75 43.02 3.06
898 909 4.191485 GCGGTTGCGACGTCGATG 62.191 66.667 39.74 22.97 43.02 3.84
914 925 1.174712 TGAAGGCTGAAGCTTGTGGC 61.175 55.000 2.10 8.78 41.70 5.01
915 926 0.879765 CTGAAGGCTGAAGCTTGTGG 59.120 55.000 2.10 0.00 41.70 4.17
916 927 1.602311 ACTGAAGGCTGAAGCTTGTG 58.398 50.000 2.10 0.00 41.70 3.33
917 928 2.225467 GAACTGAAGGCTGAAGCTTGT 58.775 47.619 2.10 0.00 41.70 3.16
918 929 2.224606 TGAACTGAAGGCTGAAGCTTG 58.775 47.619 2.10 0.00 41.70 4.01
919 930 2.158696 ACTGAACTGAAGGCTGAAGCTT 60.159 45.455 0.00 0.00 41.70 3.74
920 931 1.419387 ACTGAACTGAAGGCTGAAGCT 59.581 47.619 1.74 0.00 41.70 3.74
921 932 1.534595 CACTGAACTGAAGGCTGAAGC 59.465 52.381 0.00 0.00 41.14 3.86
922 933 1.534595 GCACTGAACTGAAGGCTGAAG 59.465 52.381 0.00 0.00 0.00 3.02
923 934 1.141657 AGCACTGAACTGAAGGCTGAA 59.858 47.619 0.00 0.00 0.00 3.02
924 935 0.761187 AGCACTGAACTGAAGGCTGA 59.239 50.000 0.00 0.00 0.00 4.26
925 936 0.873054 CAGCACTGAACTGAAGGCTG 59.127 55.000 0.00 0.00 42.14 4.85
926 937 0.888285 GCAGCACTGAACTGAAGGCT 60.888 55.000 0.81 0.00 37.32 4.58
927 938 0.888285 AGCAGCACTGAACTGAAGGC 60.888 55.000 0.81 0.00 37.32 4.35
928 939 3.319135 AGCAGCACTGAACTGAAGG 57.681 52.632 0.81 0.00 37.32 3.46
938 949 2.177594 GAGTGGGTAGCAGCAGCACT 62.178 60.000 3.17 0.00 45.49 4.40
939 950 1.743252 GAGTGGGTAGCAGCAGCAC 60.743 63.158 3.17 0.00 45.49 4.40
940 951 2.665000 GAGTGGGTAGCAGCAGCA 59.335 61.111 3.17 0.00 45.49 4.41
941 952 2.510238 CGAGTGGGTAGCAGCAGC 60.510 66.667 0.00 0.00 42.56 5.25
942 953 1.153745 GTCGAGTGGGTAGCAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
943 954 1.595993 GAGTCGAGTGGGTAGCAGCA 61.596 60.000 0.00 0.00 0.00 4.41
944 955 1.139947 GAGTCGAGTGGGTAGCAGC 59.860 63.158 0.00 0.00 0.00 5.25
945 956 0.965866 TGGAGTCGAGTGGGTAGCAG 60.966 60.000 0.00 0.00 0.00 4.24
946 957 0.324368 ATGGAGTCGAGTGGGTAGCA 60.324 55.000 0.00 0.00 0.00 3.49
947 958 0.824759 AATGGAGTCGAGTGGGTAGC 59.175 55.000 0.00 0.00 0.00 3.58
948 959 4.939052 AATAATGGAGTCGAGTGGGTAG 57.061 45.455 0.00 0.00 0.00 3.18
949 960 4.712829 TGAAATAATGGAGTCGAGTGGGTA 59.287 41.667 0.00 0.00 0.00 3.69
950 961 3.517901 TGAAATAATGGAGTCGAGTGGGT 59.482 43.478 0.00 0.00 0.00 4.51
951 962 4.122776 CTGAAATAATGGAGTCGAGTGGG 58.877 47.826 0.00 0.00 0.00 4.61
952 963 3.557595 GCTGAAATAATGGAGTCGAGTGG 59.442 47.826 0.00 0.00 0.00 4.00
953 964 4.183865 TGCTGAAATAATGGAGTCGAGTG 58.816 43.478 0.00 0.00 0.00 3.51
954 965 4.471904 TGCTGAAATAATGGAGTCGAGT 57.528 40.909 0.00 0.00 0.00 4.18
955 966 5.122239 TGTTTGCTGAAATAATGGAGTCGAG 59.878 40.000 0.00 0.00 0.00 4.04
956 967 5.000591 TGTTTGCTGAAATAATGGAGTCGA 58.999 37.500 0.00 0.00 0.00 4.20
957 968 5.295431 TGTTTGCTGAAATAATGGAGTCG 57.705 39.130 0.00 0.00 0.00 4.18
958 969 6.913170 TCTTGTTTGCTGAAATAATGGAGTC 58.087 36.000 0.00 0.00 0.00 3.36
959 970 6.899393 TCTTGTTTGCTGAAATAATGGAGT 57.101 33.333 0.00 0.00 0.00 3.85
960 971 7.147312 TGTTCTTGTTTGCTGAAATAATGGAG 58.853 34.615 0.00 0.00 0.00 3.86
961 972 7.048629 TGTTCTTGTTTGCTGAAATAATGGA 57.951 32.000 0.00 0.00 0.00 3.41
962 973 7.712264 TTGTTCTTGTTTGCTGAAATAATGG 57.288 32.000 0.00 0.00 0.00 3.16
963 974 8.602328 TGTTTGTTCTTGTTTGCTGAAATAATG 58.398 29.630 0.00 0.00 0.00 1.90
964 975 8.715191 TGTTTGTTCTTGTTTGCTGAAATAAT 57.285 26.923 0.00 0.00 0.00 1.28
965 976 8.715191 ATGTTTGTTCTTGTTTGCTGAAATAA 57.285 26.923 0.00 0.00 0.00 1.40
966 977 9.979578 ATATGTTTGTTCTTGTTTGCTGAAATA 57.020 25.926 0.00 0.00 0.00 1.40
967 978 8.891671 ATATGTTTGTTCTTGTTTGCTGAAAT 57.108 26.923 0.00 0.00 0.00 2.17
968 979 7.167302 CGATATGTTTGTTCTTGTTTGCTGAAA 59.833 33.333 0.00 0.00 0.00 2.69
969 980 6.636447 CGATATGTTTGTTCTTGTTTGCTGAA 59.364 34.615 0.00 0.00 0.00 3.02
970 981 6.017523 TCGATATGTTTGTTCTTGTTTGCTGA 60.018 34.615 0.00 0.00 0.00 4.26
971 982 6.142139 TCGATATGTTTGTTCTTGTTTGCTG 58.858 36.000 0.00 0.00 0.00 4.41
972 983 6.312399 TCGATATGTTTGTTCTTGTTTGCT 57.688 33.333 0.00 0.00 0.00 3.91
973 984 5.569059 CCTCGATATGTTTGTTCTTGTTTGC 59.431 40.000 0.00 0.00 0.00 3.68
974 985 6.898041 TCCTCGATATGTTTGTTCTTGTTTG 58.102 36.000 0.00 0.00 0.00 2.93
975 986 7.504924 TTCCTCGATATGTTTGTTCTTGTTT 57.495 32.000 0.00 0.00 0.00 2.83
976 987 7.504924 TTTCCTCGATATGTTTGTTCTTGTT 57.495 32.000 0.00 0.00 0.00 2.83
977 988 7.362056 CCATTTCCTCGATATGTTTGTTCTTGT 60.362 37.037 0.00 0.00 0.00 3.16
978 989 6.968904 CCATTTCCTCGATATGTTTGTTCTTG 59.031 38.462 0.00 0.00 0.00 3.02
979 990 6.404734 GCCATTTCCTCGATATGTTTGTTCTT 60.405 38.462 0.00 0.00 0.00 2.52
980 991 5.066505 GCCATTTCCTCGATATGTTTGTTCT 59.933 40.000 0.00 0.00 0.00 3.01
981 992 5.273944 GCCATTTCCTCGATATGTTTGTTC 58.726 41.667 0.00 0.00 0.00 3.18
982 993 4.097892 GGCCATTTCCTCGATATGTTTGTT 59.902 41.667 0.00 0.00 0.00 2.83
983 994 3.632145 GGCCATTTCCTCGATATGTTTGT 59.368 43.478 0.00 0.00 0.00 2.83
984 995 3.885297 AGGCCATTTCCTCGATATGTTTG 59.115 43.478 5.01 0.00 0.00 2.93
985 996 4.137543 GAGGCCATTTCCTCGATATGTTT 58.862 43.478 5.01 0.00 42.74 2.83
986 997 3.744660 GAGGCCATTTCCTCGATATGTT 58.255 45.455 5.01 0.00 42.74 2.71
987 998 3.409026 GAGGCCATTTCCTCGATATGT 57.591 47.619 5.01 0.00 42.74 2.29
995 1006 1.961180 CTCCGTCGAGGCCATTTCCT 61.961 60.000 5.01 0.00 40.77 3.36
996 1007 1.521681 CTCCGTCGAGGCCATTTCC 60.522 63.158 5.01 0.00 40.77 3.13
997 1008 2.174319 GCTCCGTCGAGGCCATTTC 61.174 63.158 5.01 0.00 40.77 2.17
1023 1034 0.661552 CAATCAGGATCCGCAGCTTG 59.338 55.000 5.98 5.22 0.00 4.01
1205 1233 2.758327 TGGCTATCCTGACGGCGT 60.758 61.111 14.65 14.65 0.00 5.68
1257 1285 3.377656 GAGAGGTTCTCCACGCCA 58.622 61.111 0.00 0.00 37.55 5.69
1315 1346 4.477975 CGTCAGCCCCTCGTCGAC 62.478 72.222 5.18 5.18 0.00 4.20
1350 1381 1.556911 GGGGACAGCTTTCTGATGAGA 59.443 52.381 0.00 0.00 42.95 3.27
1359 1390 2.032681 GCGTCAGGGGACAGCTTT 59.967 61.111 0.00 0.00 44.54 3.51
1360 1391 4.021925 GGCGTCAGGGGACAGCTT 62.022 66.667 0.00 0.00 44.54 3.74
1378 1409 2.230025 AGAAGTGGACATCTGTGACGAG 59.770 50.000 0.00 0.00 0.00 4.18
1386 1417 3.906846 AGTTCCAGAAGAAGTGGACATCT 59.093 43.478 0.00 0.00 44.06 2.90
1513 1556 4.087892 CACCTCCTGGCAGTCCGG 62.088 72.222 14.43 12.48 38.52 5.14
1593 1637 1.733526 GTGTTTCGCTTGGCACCTT 59.266 52.632 0.00 0.00 0.00 3.50
1673 1720 0.107831 CCGTTCCAGGTCCAAGAACA 59.892 55.000 18.81 0.00 39.89 3.18
1707 1754 2.357034 ACGTGGCCTTGCGTGTAG 60.357 61.111 17.05 0.00 40.03 2.74
2019 2113 2.362503 AGGATCGCGGTCTGTGGA 60.363 61.111 20.42 0.00 0.00 4.02
2215 5232 2.409651 CTGCTCCTCGTACCTCGC 59.590 66.667 0.00 0.00 39.67 5.03
2397 5414 3.260632 TCTTCCGTGTTTCCATCAGATCA 59.739 43.478 0.00 0.00 0.00 2.92
2426 5443 0.904865 TCACCTGCTCGATGGGTTCT 60.905 55.000 2.03 0.00 0.00 3.01
2447 5464 1.133915 TGAAGAACCTGGCCGACTTTT 60.134 47.619 0.00 0.00 0.00 2.27
2448 5465 0.472471 TGAAGAACCTGGCCGACTTT 59.528 50.000 0.00 0.00 0.00 2.66
2464 5481 1.118965 TTGGACACGAGCTCCCTGAA 61.119 55.000 8.47 0.00 0.00 3.02
2527 5544 2.227968 GACGCCATGAACACACGAGC 62.228 60.000 0.00 0.00 0.00 5.03
2571 5592 0.967380 AGCTTTTCAGGCAATCGGGG 60.967 55.000 0.00 0.00 0.00 5.73
2584 5605 5.392380 CCGTTGCATCTATTTCAGAGCTTTT 60.392 40.000 0.00 0.00 36.48 2.27
2630 5656 1.535028 TGTTGTGCAAATGTCGCCTAG 59.465 47.619 0.00 0.00 0.00 3.02
2653 5679 3.515630 ACATCGCCTATCATAATCTGCG 58.484 45.455 0.00 0.00 43.05 5.18
2677 5703 0.458669 CACTGCCTTCATCCATTGGC 59.541 55.000 0.00 0.00 45.10 4.52
2687 5713 0.249657 CTAGATCCGCCACTGCCTTC 60.250 60.000 0.00 0.00 0.00 3.46
2706 5732 3.519913 AGGACTACCCTGACTTCAAATCC 59.480 47.826 0.00 0.00 45.61 3.01
2777 6002 9.182214 GCATACATGATTTCTATGTGGGATTAT 57.818 33.333 0.00 0.00 39.03 1.28
2827 6052 1.168714 GGACCATGGACACTGCTTTC 58.831 55.000 21.47 1.16 0.00 2.62
2942 6774 3.691118 CCAGAACATGAATCGACAACCAT 59.309 43.478 0.00 0.00 0.00 3.55
2951 6783 3.942829 TCCACTGTCCAGAACATGAATC 58.057 45.455 0.00 0.00 37.23 2.52
2956 6788 2.840038 TGCTATCCACTGTCCAGAACAT 59.160 45.455 0.40 0.00 37.23 2.71
2963 6959 2.472695 TGTTGTGCTATCCACTGTCC 57.527 50.000 0.00 0.00 44.92 4.02
2975 6971 7.487829 TGATTTAGAGTTTGTTCTTTGTTGTGC 59.512 33.333 0.00 0.00 0.00 4.57
3000 6996 3.537580 CCCATTGCCAAATCTCCAATTG 58.462 45.455 0.00 0.00 0.00 2.32
3017 7013 0.911769 TCAGATTTGAGGTCGCCCAT 59.088 50.000 0.00 0.00 0.00 4.00
3022 7018 1.067846 TGGTCGTCAGATTTGAGGTCG 60.068 52.381 5.92 0.00 39.58 4.79
3025 7021 1.001974 TGGTGGTCGTCAGATTTGAGG 59.998 52.381 0.00 0.00 39.87 3.86
3124 7120 1.905512 GGATTACACCCACGAGCCT 59.094 57.895 0.00 0.00 0.00 4.58
3125 7121 4.534401 GGATTACACCCACGAGCC 57.466 61.111 0.00 0.00 0.00 4.70
3133 7129 4.438744 CGAAAATGCTTCAGGGATTACACC 60.439 45.833 0.00 0.00 34.89 4.16
3134 7130 4.662145 CGAAAATGCTTCAGGGATTACAC 58.338 43.478 0.00 0.00 34.89 2.90
3135 7131 3.128589 GCGAAAATGCTTCAGGGATTACA 59.871 43.478 0.00 0.00 34.89 2.41
3140 7136 0.605319 ACGCGAAAATGCTTCAGGGA 60.605 50.000 15.93 0.00 0.00 4.20
3174 7170 0.455464 GACCATAAAAACCGCCGTGC 60.455 55.000 0.00 0.00 0.00 5.34
3200 7196 0.469494 TTCAAGCAGTGCACTCTCCA 59.531 50.000 18.64 4.95 0.00 3.86
3226 7222 2.902065 GCTTCAAAGAGCTTTACCCG 57.098 50.000 0.00 0.00 39.57 5.28
3317 7313 1.940613 GAACAACTGTGCTTCCTTCGT 59.059 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.