Multiple sequence alignment - TraesCS7A01G389900

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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 TraesCS7A01G389900 chr7A 100.000 5225 0 0 1 5225 566127064 566132288 0.000000e+00 9649.0
1 TraesCS7A01G389900 chr7A 92.100 1000 50 9 3479 4467 566294753 566295734 0.000000e+00 1382.0
2 TraesCS7A01G389900 chr7A 92.100 1000 50 9 3479 4467 566305881 566306862 0.000000e+00 1382.0
3 TraesCS7A01G389900 chr7A 92.000 1000 51 9 3479 4467 566265417 566266398 0.000000e+00 1376.0
4 TraesCS7A01G389900 chr7A 89.474 988 54 17 2405 3370 566304924 566305883 0.000000e+00 1203.0
5 TraesCS7A01G389900 chr7A 89.463 987 55 17 2405 3370 566264461 566265419 0.000000e+00 1201.0
6 TraesCS7A01G389900 chr7A 91.939 856 41 9 3479 4322 566330549 566331388 0.000000e+00 1173.0
7 TraesCS7A01G389900 chr7A 91.981 848 41 8 3479 4315 566282172 566283003 0.000000e+00 1164.0
8 TraesCS7A01G389900 chr7A 91.981 848 41 8 3479 4315 566317913 566318744 0.000000e+00 1164.0
9 TraesCS7A01G389900 chr7A 92.716 659 25 8 3517 4165 566341499 566342144 0.000000e+00 929.0
10 TraesCS7A01G389900 chr7A 87.766 752 47 12 2543 3285 566204454 566205169 0.000000e+00 837.0
11 TraesCS7A01G389900 chr7A 89.065 631 54 10 4607 5225 566209037 566209664 0.000000e+00 769.0
12 TraesCS7A01G389900 chr7A 94.179 481 22 4 2891 3370 566281699 566282174 0.000000e+00 728.0
13 TraesCS7A01G389900 chr7A 94.179 481 22 4 2891 3370 566294280 566294755 0.000000e+00 728.0
14 TraesCS7A01G389900 chr7A 94.179 481 22 4 2891 3370 566317440 566317915 0.000000e+00 728.0
15 TraesCS7A01G389900 chr7A 94.179 481 22 4 2891 3370 566330076 566330551 0.000000e+00 728.0
16 TraesCS7A01G389900 chr7A 86.616 523 33 15 2372 2868 566340664 566341175 1.280000e-150 544.0
17 TraesCS7A01G389900 chr7A 85.851 523 34 18 4024 4536 566208542 566209034 2.160000e-143 520.0
18 TraesCS7A01G389900 chr7A 81.975 638 65 22 4614 5217 566273395 566274016 3.630000e-136 496.0
19 TraesCS7A01G389900 chr7A 81.947 637 66 22 4614 5217 566298031 566298651 1.310000e-135 494.0
20 TraesCS7A01G389900 chr7A 81.918 636 68 21 4614 5217 566321640 566322260 1.310000e-135 494.0
21 TraesCS7A01G389900 chr7A 85.516 504 31 13 2405 2890 566281125 566281604 6.080000e-134 488.0
22 TraesCS7A01G389900 chr7A 85.516 504 31 13 2405 2890 566293422 566293901 6.080000e-134 488.0
23 TraesCS7A01G389900 chr7A 81.790 637 67 27 4614 5217 566309159 566309779 6.080000e-134 488.0
24 TraesCS7A01G389900 chr7A 85.516 504 31 13 2405 2890 566328527 566329006 6.080000e-134 488.0
25 TraesCS7A01G389900 chr7A 81.633 637 68 21 4614 5217 566286530 566287150 2.830000e-132 483.0
26 TraesCS7A01G389900 chr7A 81.476 637 70 21 4614 5217 566333619 566334240 3.660000e-131 479.0
27 TraesCS7A01G389900 chr7A 92.446 278 16 5 2085 2360 566264176 566264450 4.910000e-105 392.0
28 TraesCS7A01G389900 chr7A 92.446 278 16 5 2085 2360 566280840 566281114 4.910000e-105 392.0
29 TraesCS7A01G389900 chr7A 92.446 278 16 5 2085 2360 566293137 566293411 4.910000e-105 392.0
30 TraesCS7A01G389900 chr7A 92.446 278 16 5 2085 2360 566304639 566304913 4.910000e-105 392.0
31 TraesCS7A01G389900 chr7A 92.446 278 16 5 2085 2360 566328242 566328516 4.910000e-105 392.0
32 TraesCS7A01G389900 chr7A 94.667 150 7 1 2085 2234 566204073 566204221 1.130000e-56 231.0
33 TraesCS7A01G389900 chr7A 88.028 142 9 8 4463 4601 566285508 566285644 1.510000e-35 161.0
34 TraesCS7A01G389900 chr7A 88.028 142 9 8 4463 4601 566296997 566297133 1.510000e-35 161.0
35 TraesCS7A01G389900 chr7A 88.028 142 9 8 4463 4601 566332586 566332722 1.510000e-35 161.0
36 TraesCS7A01G389900 chr7A 87.324 142 10 8 4463 4601 566320606 566320742 7.010000e-34 156.0
37 TraesCS7A01G389900 chr7A 86.806 144 11 8 4461 4601 566272359 566272497 2.520000e-33 154.0
38 TraesCS7A01G389900 chr7A 86.620 142 11 8 4463 4601 566308125 566308261 3.260000e-32 150.0
39 TraesCS7A01G389900 chr7A 93.750 80 5 0 3380 3459 686137816 686137737 2.560000e-23 121.0
40 TraesCS7A01G389900 chr7D 96.121 2475 59 20 922 3370 500243827 500246290 0.000000e+00 4004.0
41 TraesCS7A01G389900 chr7D 89.340 1726 90 28 3519 5225 500246309 500247959 0.000000e+00 2082.0
42 TraesCS7A01G389900 chr7D 90.898 835 59 8 1 822 575166044 575166874 0.000000e+00 1105.0
43 TraesCS7A01G389900 chr7D 92.150 293 15 6 3947 4239 500252852 500253136 1.750000e-109 407.0
44 TraesCS7A01G389900 chr7D 87.698 252 19 6 2621 2862 500251922 500252171 3.080000e-72 283.0
45 TraesCS7A01G389900 chr7D 82.918 281 23 14 4260 4536 500253189 500253448 4.070000e-56 230.0
46 TraesCS7A01G389900 chr7D 95.122 82 4 0 3375 3456 226697752 226697833 4.250000e-26 130.0
47 TraesCS7A01G389900 chr7B 93.948 2495 100 26 922 3379 528403317 528405797 0.000000e+00 3723.0
48 TraesCS7A01G389900 chr7B 91.710 1146 55 20 3479 4606 528405794 528406917 0.000000e+00 1554.0
49 TraesCS7A01G389900 chr7B 86.747 581 41 18 4041 4606 528733727 528734286 9.620000e-172 614.0
50 TraesCS7A01G389900 chr7B 89.414 444 33 6 4788 5225 528684980 528685415 9.890000e-152 547.0
51 TraesCS7A01G389900 chr7B 88.514 444 37 8 4788 5225 528705650 528706085 4.640000e-145 525.0
52 TraesCS7A01G389900 chr7B 87.886 421 32 9 4607 5012 528734259 528734675 1.320000e-130 477.0
53 TraesCS7A01G389900 chr7B 93.750 176 8 2 4607 4782 528406890 528407062 1.440000e-65 261.0
54 TraesCS7A01G389900 chr7B 93.750 176 8 1 4607 4782 528407433 528407605 1.440000e-65 261.0
55 TraesCS7A01G389900 chr7B 93.750 80 5 0 3380 3459 708467900 708467821 2.560000e-23 121.0
56 TraesCS7A01G389900 chr3D 92.252 826 60 4 1 823 506059576 506060400 0.000000e+00 1168.0
57 TraesCS7A01G389900 chr3D 87.143 350 30 7 1 347 585940081 585939744 2.950000e-102 383.0
58 TraesCS7A01G389900 chr3D 82.759 116 14 4 824 936 278073700 278073812 1.200000e-16 99.0
59 TraesCS7A01G389900 chr5D 90.571 806 60 9 1 793 41127799 41128601 0.000000e+00 1053.0
60 TraesCS7A01G389900 chr5D 89.808 834 58 13 2 822 50861433 50860614 0.000000e+00 1044.0
61 TraesCS7A01G389900 chr5D 95.294 85 4 0 3375 3459 491658854 491658770 9.130000e-28 135.0
62 TraesCS7A01G389900 chr5D 82.114 123 14 5 828 945 42933233 42933352 1.200000e-16 99.0
63 TraesCS7A01G389900 chr1D 89.831 826 76 8 1 822 468338115 468337294 0.000000e+00 1053.0
64 TraesCS7A01G389900 chr1D 95.062 81 4 0 3379 3459 356929218 356929138 1.530000e-25 128.0
65 TraesCS7A01G389900 chr1D 91.667 84 7 0 3376 3459 478229495 478229412 3.310000e-22 117.0
66 TraesCS7A01G389900 chr4B 89.461 835 73 9 1 822 43231450 43232282 0.000000e+00 1040.0
67 TraesCS7A01G389900 chr1A 88.313 830 79 12 7 823 592162421 592161597 0.000000e+00 979.0
68 TraesCS7A01G389900 chr2D 88.557 804 88 4 10 812 249876932 249877732 0.000000e+00 972.0
69 TraesCS7A01G389900 chr2D 81.746 126 15 6 819 940 39820983 39821104 1.200000e-16 99.0
70 TraesCS7A01G389900 chr3B 84.110 837 111 13 1 823 780712170 780711342 0.000000e+00 789.0
71 TraesCS7A01G389900 chr2A 84.337 830 84 10 1 816 203273517 203272720 0.000000e+00 771.0
72 TraesCS7A01G389900 chrUn 81.947 637 66 22 4614 5217 374373795 374374415 1.310000e-135 494.0
73 TraesCS7A01G389900 chrUn 88.889 72 6 2 4840 4911 45538235 45538304 2.590000e-13 87.9
74 TraesCS7A01G389900 chr3A 94.805 77 4 0 3380 3456 647367268 647367344 2.560000e-23 121.0
75 TraesCS7A01G389900 chr3A 82.400 125 12 8 822 943 564940072 564939955 3.330000e-17 100.0
76 TraesCS7A01G389900 chr6A 85.246 122 11 7 819 936 27786263 27786381 9.190000e-23 119.0
77 TraesCS7A01G389900 chr4A 84.375 128 13 6 819 942 450788396 450788272 9.190000e-23 119.0
78 TraesCS7A01G389900 chr4A 82.787 122 14 6 827 944 675933930 675934048 9.260000e-18 102.0
79 TraesCS7A01G389900 chr4A 82.114 123 15 5 828 946 620927122 620927003 1.200000e-16 99.0
80 TraesCS7A01G389900 chr5B 92.500 80 6 0 3377 3456 445765202 445765281 1.190000e-21 115.0
81 TraesCS7A01G389900 chr5A 92.208 77 6 0 3380 3456 511980222 511980298 5.530000e-20 110.0
82 TraesCS7A01G389900 chr2B 82.500 120 15 6 828 944 585712608 585712492 3.330000e-17 100.0


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 TraesCS7A01G389900 chr7A 566127064 566132288 5224 False 9649.000000 9649 100.000000 1 5225 1 chr7A.!!$F1 5224
1 TraesCS7A01G389900 chr7A 566264176 566266398 2222 False 989.666667 1376 91.303000 2085 4467 3 chr7A.!!$F3 2382
2 TraesCS7A01G389900 chr7A 566340664 566342144 1480 False 736.500000 929 89.666000 2372 4165 2 chr7A.!!$F10 1793
3 TraesCS7A01G389900 chr7A 566304639 566309779 5140 False 723.000000 1382 88.486000 2085 5217 5 chr7A.!!$F7 3132
4 TraesCS7A01G389900 chr7A 566317440 566322260 4820 False 635.500000 1164 88.850500 2891 5217 4 chr7A.!!$F8 2326
5 TraesCS7A01G389900 chr7A 566293137 566298651 5514 False 607.500000 1382 89.036000 2085 5217 6 chr7A.!!$F6 3132
6 TraesCS7A01G389900 chr7A 566204073 566209664 5591 False 589.250000 837 89.337250 2085 5225 4 chr7A.!!$F2 3140
7 TraesCS7A01G389900 chr7A 566328242 566334240 5998 False 570.166667 1173 88.930667 2085 5217 6 chr7A.!!$F9 3132
8 TraesCS7A01G389900 chr7A 566280840 566287150 6310 False 569.333333 1164 88.963833 2085 5217 6 chr7A.!!$F5 3132
9 TraesCS7A01G389900 chr7A 566272359 566274016 1657 False 325.000000 496 84.390500 4461 5217 2 chr7A.!!$F4 756
10 TraesCS7A01G389900 chr7D 500243827 500253448 9621 False 1401.200000 4004 89.645400 922 5225 5 chr7D.!!$F3 4303
11 TraesCS7A01G389900 chr7D 575166044 575166874 830 False 1105.000000 1105 90.898000 1 822 1 chr7D.!!$F2 821
12 TraesCS7A01G389900 chr7B 528403317 528407605 4288 False 1449.750000 3723 93.289500 922 4782 4 chr7B.!!$F3 3860
13 TraesCS7A01G389900 chr7B 528733727 528734675 948 False 545.500000 614 87.316500 4041 5012 2 chr7B.!!$F4 971
14 TraesCS7A01G389900 chr3D 506059576 506060400 824 False 1168.000000 1168 92.252000 1 823 1 chr3D.!!$F2 822
15 TraesCS7A01G389900 chr5D 41127799 41128601 802 False 1053.000000 1053 90.571000 1 793 1 chr5D.!!$F1 792
16 TraesCS7A01G389900 chr5D 50860614 50861433 819 True 1044.000000 1044 89.808000 2 822 1 chr5D.!!$R1 820
17 TraesCS7A01G389900 chr1D 468337294 468338115 821 True 1053.000000 1053 89.831000 1 822 1 chr1D.!!$R2 821
18 TraesCS7A01G389900 chr4B 43231450 43232282 832 False 1040.000000 1040 89.461000 1 822 1 chr4B.!!$F1 821
19 TraesCS7A01G389900 chr1A 592161597 592162421 824 True 979.000000 979 88.313000 7 823 1 chr1A.!!$R1 816
20 TraesCS7A01G389900 chr2D 249876932 249877732 800 False 972.000000 972 88.557000 10 812 1 chr2D.!!$F2 802
21 TraesCS7A01G389900 chr3B 780711342 780712170 828 True 789.000000 789 84.110000 1 823 1 chr3B.!!$R1 822
22 TraesCS7A01G389900 chr2A 203272720 203273517 797 True 771.000000 771 84.337000 1 816 1 chr2A.!!$R1 815
23 TraesCS7A01G389900 chrUn 374373795 374374415 620 False 494.000000 494 81.947000 4614 5217 1 chrUn.!!$F2 603

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
769 843 0.178981 AATGAGCCAAGCCCGCATAT 60.179 50.0 0.00 0.0 0.00 1.78 F
820 894 0.615850 GGGGTCTGCTAGAGTGCTTT 59.384 55.0 0.00 0.0 0.00 3.51 F
2046 2145 1.191489 TCAAGGTCATCAGCCACCGA 61.191 55.0 0.00 0.0 37.79 4.69 F
2654 2793 0.947960 GCGATCGATCTGTCTCTGGA 59.052 55.0 21.57 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2145 0.806102 CGACGATGAACCTGCGGAAT 60.806 55.00 0.0 0.0 0.00 3.01 R
2654 2793 4.739793 TGAATGAAGTCCCATTTTCAGGT 58.260 39.13 0.0 0.0 36.93 4.00 R
3423 4729 0.401738 TTTGAGGAGTGGCTGGAAGG 59.598 55.00 0.0 0.0 0.00 3.46 R
4271 8610 0.320073 CAAATGGGGCACAACAGCAG 60.320 55.00 0.0 0.0 35.83 4.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 57 4.697756 CCTTGGCGGCGAGGTTGA 62.698 66.667 32.29 0.00 0.00 3.18
157 183 4.405173 GCAACGGCGTCGACGAAC 62.405 66.667 39.74 28.38 43.02 3.95
421 492 1.890510 GTCGCGGTTGGTCCACTTT 60.891 57.895 6.13 0.00 35.57 2.66
507 578 3.842923 CGGATCTGCTGCCGGAGT 61.843 66.667 5.05 0.00 43.67 3.85
583 655 1.813753 GCCAGCGGCGAGAAATGTA 60.814 57.895 12.98 0.00 39.62 2.29
595 667 3.643792 CGAGAAATGTAGAGAGGGGGAAT 59.356 47.826 0.00 0.00 0.00 3.01
603 675 1.011293 AGAGAGGGGGAATGGGAATCA 59.989 52.381 0.00 0.00 0.00 2.57
612 684 0.327924 AATGGGAATCACGTGGCTCA 59.672 50.000 17.00 12.08 0.00 4.26
629 701 3.792736 AGCGGCGGCAAGGGATAA 61.793 61.111 19.21 0.00 43.41 1.75
660 732 1.952133 CAAACGAGTCGCGGAACCA 60.952 57.895 13.59 0.00 46.49 3.67
753 826 1.470098 CTCTGTTCTGGCCGGAAAATG 59.530 52.381 28.65 19.67 0.00 2.32
769 843 0.178981 AATGAGCCAAGCCCGCATAT 60.179 50.000 0.00 0.00 0.00 1.78
785 859 2.797792 GCATATTCGCCGGAATTTTGCA 60.798 45.455 5.05 0.00 43.22 4.08
800 874 3.308660 GCAGGTTTGCGTGTTTGC 58.691 55.556 0.00 0.00 41.13 3.68
801 875 2.576002 GCAGGTTTGCGTGTTTGCG 61.576 57.895 0.00 0.00 41.13 4.85
802 876 1.943693 CAGGTTTGCGTGTTTGCGG 60.944 57.895 0.00 0.00 37.81 5.69
803 877 2.656973 GGTTTGCGTGTTTGCGGG 60.657 61.111 0.00 0.00 37.81 6.13
804 878 2.656973 GTTTGCGTGTTTGCGGGG 60.657 61.111 0.00 0.00 37.81 5.73
805 879 3.141488 TTTGCGTGTTTGCGGGGT 61.141 55.556 0.00 0.00 37.81 4.95
806 880 3.127352 TTTGCGTGTTTGCGGGGTC 62.127 57.895 0.00 0.00 37.81 4.46
807 881 4.555709 TGCGTGTTTGCGGGGTCT 62.556 61.111 0.00 0.00 37.81 3.85
808 882 4.025401 GCGTGTTTGCGGGGTCTG 62.025 66.667 0.00 0.00 0.00 3.51
809 883 4.025401 CGTGTTTGCGGGGTCTGC 62.025 66.667 0.00 0.00 0.00 4.26
810 884 2.594592 GTGTTTGCGGGGTCTGCT 60.595 61.111 0.30 0.00 0.00 4.24
811 885 1.302192 GTGTTTGCGGGGTCTGCTA 60.302 57.895 0.30 0.00 0.00 3.49
812 886 1.003839 TGTTTGCGGGGTCTGCTAG 60.004 57.895 0.30 0.00 0.00 3.42
813 887 1.295423 GTTTGCGGGGTCTGCTAGA 59.705 57.895 0.00 0.00 0.00 2.43
814 888 0.741221 GTTTGCGGGGTCTGCTAGAG 60.741 60.000 0.00 0.00 0.00 2.43
815 889 1.192146 TTTGCGGGGTCTGCTAGAGT 61.192 55.000 0.00 0.00 0.00 3.24
816 890 1.888436 TTGCGGGGTCTGCTAGAGTG 61.888 60.000 0.00 0.00 0.00 3.51
817 891 2.496817 CGGGGTCTGCTAGAGTGC 59.503 66.667 0.00 0.00 0.00 4.40
818 892 2.055042 CGGGGTCTGCTAGAGTGCT 61.055 63.158 0.00 0.00 0.00 4.40
819 893 1.608717 CGGGGTCTGCTAGAGTGCTT 61.609 60.000 0.00 0.00 0.00 3.91
820 894 0.615850 GGGGTCTGCTAGAGTGCTTT 59.384 55.000 0.00 0.00 0.00 3.51
821 895 1.831736 GGGGTCTGCTAGAGTGCTTTA 59.168 52.381 0.00 0.00 0.00 1.85
822 896 2.236395 GGGGTCTGCTAGAGTGCTTTAA 59.764 50.000 0.00 0.00 0.00 1.52
823 897 3.118223 GGGGTCTGCTAGAGTGCTTTAAT 60.118 47.826 0.00 0.00 0.00 1.40
824 898 4.101119 GGGGTCTGCTAGAGTGCTTTAATA 59.899 45.833 0.00 0.00 0.00 0.98
825 899 5.221742 GGGGTCTGCTAGAGTGCTTTAATAT 60.222 44.000 0.00 0.00 0.00 1.28
826 900 5.698545 GGGTCTGCTAGAGTGCTTTAATATG 59.301 44.000 0.00 0.00 0.00 1.78
827 901 5.698545 GGTCTGCTAGAGTGCTTTAATATGG 59.301 44.000 0.00 0.00 0.00 2.74
828 902 6.463049 GGTCTGCTAGAGTGCTTTAATATGGA 60.463 42.308 0.00 0.00 0.00 3.41
829 903 6.422400 GTCTGCTAGAGTGCTTTAATATGGAC 59.578 42.308 0.00 0.00 0.00 4.02
830 904 6.325028 TCTGCTAGAGTGCTTTAATATGGACT 59.675 38.462 0.00 0.00 37.56 3.85
831 905 7.505923 TCTGCTAGAGTGCTTTAATATGGACTA 59.494 37.037 0.00 0.00 35.07 2.59
832 906 7.434492 TGCTAGAGTGCTTTAATATGGACTAC 58.566 38.462 0.00 0.00 35.07 2.73
833 907 7.069455 TGCTAGAGTGCTTTAATATGGACTACA 59.931 37.037 0.00 0.00 35.07 2.74
834 908 8.091449 GCTAGAGTGCTTTAATATGGACTACAT 58.909 37.037 0.00 0.00 43.68 2.29
837 911 8.924303 AGAGTGCTTTAATATGGACTACATACA 58.076 33.333 0.00 0.00 44.41 2.29
838 912 9.197694 GAGTGCTTTAATATGGACTACATACAG 57.802 37.037 0.00 0.00 44.41 2.74
839 913 8.924303 AGTGCTTTAATATGGACTACATACAGA 58.076 33.333 0.00 0.00 44.41 3.41
840 914 9.197694 GTGCTTTAATATGGACTACATACAGAG 57.802 37.037 0.00 0.00 44.41 3.35
841 915 8.924303 TGCTTTAATATGGACTACATACAGAGT 58.076 33.333 0.00 0.00 44.41 3.24
842 916 9.197694 GCTTTAATATGGACTACATACAGAGTG 57.802 37.037 0.00 0.00 44.41 3.51
843 917 9.197694 CTTTAATATGGACTACATACAGAGTGC 57.802 37.037 0.00 0.00 44.41 4.40
844 918 6.731292 AATATGGACTACATACAGAGTGCA 57.269 37.500 0.00 0.00 46.27 4.57
845 919 6.731292 ATATGGACTACATACAGAGTGCAA 57.269 37.500 0.31 0.00 45.50 4.08
846 920 4.882842 TGGACTACATACAGAGTGCAAA 57.117 40.909 0.00 0.00 40.54 3.68
847 921 5.222079 TGGACTACATACAGAGTGCAAAA 57.778 39.130 0.00 0.00 40.54 2.44
848 922 5.804639 TGGACTACATACAGAGTGCAAAAT 58.195 37.500 0.00 0.00 40.54 1.82
849 923 5.643348 TGGACTACATACAGAGTGCAAAATG 59.357 40.000 0.00 0.00 40.54 2.32
850 924 5.874810 GGACTACATACAGAGTGCAAAATGA 59.125 40.000 0.00 0.00 34.44 2.57
851 925 6.036517 GGACTACATACAGAGTGCAAAATGAG 59.963 42.308 0.00 0.00 34.44 2.90
852 926 6.467677 ACTACATACAGAGTGCAAAATGAGT 58.532 36.000 0.00 0.00 0.00 3.41
853 927 5.618056 ACATACAGAGTGCAAAATGAGTG 57.382 39.130 0.00 0.00 0.00 3.51
854 928 5.308014 ACATACAGAGTGCAAAATGAGTGA 58.692 37.500 0.00 0.00 0.00 3.41
855 929 5.764686 ACATACAGAGTGCAAAATGAGTGAA 59.235 36.000 0.00 0.00 0.00 3.18
856 930 6.432162 ACATACAGAGTGCAAAATGAGTGAAT 59.568 34.615 0.00 0.00 0.00 2.57
857 931 5.368256 ACAGAGTGCAAAATGAGTGAATC 57.632 39.130 0.00 0.00 0.00 2.52
858 932 5.068636 ACAGAGTGCAAAATGAGTGAATCT 58.931 37.500 0.00 0.00 0.00 2.40
859 933 5.048921 ACAGAGTGCAAAATGAGTGAATCTG 60.049 40.000 0.00 0.00 37.16 2.90
860 934 4.082895 AGAGTGCAAAATGAGTGAATCTGC 60.083 41.667 0.00 0.00 0.00 4.26
861 935 3.570975 AGTGCAAAATGAGTGAATCTGCA 59.429 39.130 0.00 0.00 36.06 4.41
862 936 3.904571 TGCAAAATGAGTGAATCTGCAC 58.095 40.909 0.00 0.00 39.05 4.57
873 947 6.492007 AGTGAATCTGCACTCTAAAATGTG 57.508 37.500 0.00 0.00 45.54 3.21
874 948 6.000219 AGTGAATCTGCACTCTAAAATGTGT 59.000 36.000 0.00 0.00 45.54 3.72
875 949 6.148480 AGTGAATCTGCACTCTAAAATGTGTC 59.852 38.462 0.00 0.00 45.54 3.67
876 950 6.148480 GTGAATCTGCACTCTAAAATGTGTCT 59.852 38.462 0.00 0.00 36.63 3.41
877 951 7.331934 GTGAATCTGCACTCTAAAATGTGTCTA 59.668 37.037 0.00 0.00 36.63 2.59
878 952 8.043113 TGAATCTGCACTCTAAAATGTGTCTAT 58.957 33.333 0.00 0.00 36.63 1.98
879 953 9.534565 GAATCTGCACTCTAAAATGTGTCTATA 57.465 33.333 0.00 0.00 36.63 1.31
882 956 9.967346 TCTGCACTCTAAAATGTGTCTATATAC 57.033 33.333 0.00 0.00 36.63 1.47
883 957 9.750125 CTGCACTCTAAAATGTGTCTATATACA 57.250 33.333 0.00 0.00 36.63 2.29
891 965 8.818141 AAAATGTGTCTATATACATCTGGACG 57.182 34.615 0.00 0.00 36.52 4.79
892 966 7.526142 AATGTGTCTATATACATCTGGACGT 57.474 36.000 0.00 0.00 36.52 4.34
893 967 8.631480 AATGTGTCTATATACATCTGGACGTA 57.369 34.615 0.00 0.00 36.52 3.57
894 968 7.430992 TGTGTCTATATACATCTGGACGTAC 57.569 40.000 0.00 0.00 0.00 3.67
895 969 7.222161 TGTGTCTATATACATCTGGACGTACT 58.778 38.462 0.00 0.00 0.00 2.73
896 970 7.387122 TGTGTCTATATACATCTGGACGTACTC 59.613 40.741 0.00 0.00 0.00 2.59
897 971 7.603404 GTGTCTATATACATCTGGACGTACTCT 59.397 40.741 0.00 0.00 0.00 3.24
898 972 8.155510 TGTCTATATACATCTGGACGTACTCTT 58.844 37.037 0.00 0.00 0.00 2.85
899 973 9.001542 GTCTATATACATCTGGACGTACTCTTT 57.998 37.037 0.00 0.00 0.00 2.52
900 974 9.000486 TCTATATACATCTGGACGTACTCTTTG 58.000 37.037 0.00 0.00 0.00 2.77
901 975 7.818997 ATATACATCTGGACGTACTCTTTGA 57.181 36.000 0.00 0.00 0.00 2.69
902 976 4.866508 ACATCTGGACGTACTCTTTGAA 57.133 40.909 0.00 0.00 0.00 2.69
903 977 5.209818 ACATCTGGACGTACTCTTTGAAA 57.790 39.130 0.00 0.00 0.00 2.69
904 978 5.794894 ACATCTGGACGTACTCTTTGAAAT 58.205 37.500 0.00 0.00 0.00 2.17
905 979 6.931838 ACATCTGGACGTACTCTTTGAAATA 58.068 36.000 0.00 0.00 0.00 1.40
906 980 7.556844 ACATCTGGACGTACTCTTTGAAATAT 58.443 34.615 0.00 0.00 0.00 1.28
907 981 7.492669 ACATCTGGACGTACTCTTTGAAATATG 59.507 37.037 0.00 0.00 0.00 1.78
908 982 6.931838 TCTGGACGTACTCTTTGAAATATGT 58.068 36.000 0.00 0.00 0.00 2.29
909 983 8.058667 TCTGGACGTACTCTTTGAAATATGTA 57.941 34.615 0.00 0.00 0.00 2.29
910 984 8.525316 TCTGGACGTACTCTTTGAAATATGTAA 58.475 33.333 0.00 0.00 0.00 2.41
911 985 9.146984 CTGGACGTACTCTTTGAAATATGTAAA 57.853 33.333 0.00 0.00 0.00 2.01
912 986 9.491675 TGGACGTACTCTTTGAAATATGTAAAA 57.508 29.630 0.00 0.00 0.00 1.52
968 1042 1.512926 TTCTTTCTGTTCGGCTCTGC 58.487 50.000 0.00 0.00 0.00 4.26
1217 1311 1.803555 GAGCTCCTCTGAAGCAAACAC 59.196 52.381 0.87 0.00 0.00 3.32
1249 1343 3.195698 GACGAATCCCAGCCGTGC 61.196 66.667 0.00 0.00 36.60 5.34
1252 1346 4.778143 GAATCCCAGCCGTGCGGT 62.778 66.667 12.46 0.00 37.65 5.68
1254 1348 4.778143 ATCCCAGCCGTGCGGTTC 62.778 66.667 12.46 0.00 37.65 3.62
1431 1530 2.034879 GGTGTGCATGGACCACTCG 61.035 63.158 15.34 0.00 34.38 4.18
1482 1581 3.708220 CTTCCTGCTCCTCGCCGTC 62.708 68.421 0.00 0.00 38.05 4.79
2046 2145 1.191489 TCAAGGTCATCAGCCACCGA 61.191 55.000 0.00 0.00 37.79 4.69
2207 2306 2.955660 CTCCACTCTCTTAGGCTCGATT 59.044 50.000 0.00 0.00 0.00 3.34
2654 2793 0.947960 GCGATCGATCTGTCTCTGGA 59.052 55.000 21.57 0.00 0.00 3.86
2820 2959 7.001073 AGAGCTCCTGTAGTTTTCAGATTTTT 58.999 34.615 10.93 0.00 35.20 1.94
2855 2994 5.692613 ACAGCGACCTCTATACTGTATTC 57.307 43.478 5.52 0.00 39.69 1.75
2991 4206 9.676861 TGATATTCAGAAGAATCACACTTCATT 57.323 29.630 0.00 0.00 43.26 2.57
3084 4304 2.810274 TGAGAAACAGCAAAGCTAGCAG 59.190 45.455 18.83 7.50 36.40 4.24
3219 4460 6.044754 AGGGCCATGAATCAGTGATCTTATTA 59.955 38.462 6.18 0.00 0.00 0.98
3380 4686 9.978044 AGTTTCAGTGTTACTTAGTTACTTAGG 57.022 33.333 3.42 0.00 0.00 2.69
3381 4687 8.706936 GTTTCAGTGTTACTTAGTTACTTAGGC 58.293 37.037 3.42 0.00 0.00 3.93
3382 4688 6.928520 TCAGTGTTACTTAGTTACTTAGGCC 58.071 40.000 0.00 0.00 0.00 5.19
3383 4689 6.071165 TCAGTGTTACTTAGTTACTTAGGCCC 60.071 42.308 0.00 0.00 0.00 5.80
3384 4690 6.021672 AGTGTTACTTAGTTACTTAGGCCCT 58.978 40.000 0.00 0.00 0.00 5.19
3385 4691 6.070938 AGTGTTACTTAGTTACTTAGGCCCTG 60.071 42.308 0.00 0.00 0.00 4.45
3386 4692 5.781818 TGTTACTTAGTTACTTAGGCCCTGT 59.218 40.000 0.00 0.00 0.00 4.00
3387 4693 6.270695 TGTTACTTAGTTACTTAGGCCCTGTT 59.729 38.462 0.00 0.00 0.00 3.16
3388 4694 5.837770 ACTTAGTTACTTAGGCCCTGTTT 57.162 39.130 0.00 0.00 0.00 2.83
3389 4695 5.557866 ACTTAGTTACTTAGGCCCTGTTTG 58.442 41.667 0.00 0.00 0.00 2.93
3390 4696 3.434940 AGTTACTTAGGCCCTGTTTGG 57.565 47.619 0.00 0.00 0.00 3.28
3398 4704 4.576993 CCCTGTTTGGCAAATCGC 57.423 55.556 16.74 3.99 41.28 4.58
3407 4713 3.430862 GCAAATCGCCACGGAGCA 61.431 61.111 0.00 0.00 32.94 4.26
3408 4714 2.787249 CAAATCGCCACGGAGCAG 59.213 61.111 0.00 0.00 0.00 4.24
3409 4715 1.741401 CAAATCGCCACGGAGCAGA 60.741 57.895 0.00 0.00 0.00 4.26
3410 4716 1.448540 AAATCGCCACGGAGCAGAG 60.449 57.895 0.00 0.00 0.00 3.35
3411 4717 4.521062 ATCGCCACGGAGCAGAGC 62.521 66.667 0.00 0.00 0.00 4.09
3439 4745 2.270527 GCCTTCCAGCCACTCCTC 59.729 66.667 0.00 0.00 0.00 3.71
3440 4746 2.596851 GCCTTCCAGCCACTCCTCA 61.597 63.158 0.00 0.00 0.00 3.86
3441 4747 2.069776 CCTTCCAGCCACTCCTCAA 58.930 57.895 0.00 0.00 0.00 3.02
3442 4748 0.401738 CCTTCCAGCCACTCCTCAAA 59.598 55.000 0.00 0.00 0.00 2.69
3443 4749 1.005215 CCTTCCAGCCACTCCTCAAAT 59.995 52.381 0.00 0.00 0.00 2.32
3444 4750 2.556114 CCTTCCAGCCACTCCTCAAATT 60.556 50.000 0.00 0.00 0.00 1.82
3445 4751 3.308402 CCTTCCAGCCACTCCTCAAATTA 60.308 47.826 0.00 0.00 0.00 1.40
3446 4752 3.634397 TCCAGCCACTCCTCAAATTAG 57.366 47.619 0.00 0.00 0.00 1.73
3447 4753 3.181329 TCCAGCCACTCCTCAAATTAGA 58.819 45.455 0.00 0.00 0.00 2.10
3448 4754 3.587061 TCCAGCCACTCCTCAAATTAGAA 59.413 43.478 0.00 0.00 0.00 2.10
3449 4755 3.691609 CCAGCCACTCCTCAAATTAGAAC 59.308 47.826 0.00 0.00 0.00 3.01
3450 4756 4.566488 CCAGCCACTCCTCAAATTAGAACT 60.566 45.833 0.00 0.00 0.00 3.01
3451 4757 5.338381 CCAGCCACTCCTCAAATTAGAACTA 60.338 44.000 0.00 0.00 0.00 2.24
3452 4758 5.814705 CAGCCACTCCTCAAATTAGAACTAG 59.185 44.000 0.00 0.00 0.00 2.57
3453 4759 5.721960 AGCCACTCCTCAAATTAGAACTAGA 59.278 40.000 0.00 0.00 0.00 2.43
3454 4760 6.385467 AGCCACTCCTCAAATTAGAACTAGAT 59.615 38.462 0.00 0.00 0.00 1.98
3455 4761 6.704050 GCCACTCCTCAAATTAGAACTAGATC 59.296 42.308 0.00 0.00 0.00 2.75
3456 4762 6.920758 CCACTCCTCAAATTAGAACTAGATCG 59.079 42.308 0.00 0.00 0.00 3.69
3457 4763 7.416890 CCACTCCTCAAATTAGAACTAGATCGT 60.417 40.741 0.00 0.00 0.00 3.73
3458 4764 7.433719 CACTCCTCAAATTAGAACTAGATCGTG 59.566 40.741 0.00 0.00 0.00 4.35
3459 4765 6.806751 TCCTCAAATTAGAACTAGATCGTGG 58.193 40.000 0.00 0.00 0.00 4.94
3460 4766 6.605995 TCCTCAAATTAGAACTAGATCGTGGA 59.394 38.462 0.00 0.00 0.00 4.02
3461 4767 6.920758 CCTCAAATTAGAACTAGATCGTGGAG 59.079 42.308 0.00 0.00 0.00 3.86
3462 4768 7.201830 CCTCAAATTAGAACTAGATCGTGGAGA 60.202 40.741 0.00 0.00 0.00 3.71
3463 4769 7.708051 TCAAATTAGAACTAGATCGTGGAGAG 58.292 38.462 0.00 0.00 0.00 3.20
3464 4770 7.556635 TCAAATTAGAACTAGATCGTGGAGAGA 59.443 37.037 0.00 0.00 0.00 3.10
3465 4771 7.504924 AATTAGAACTAGATCGTGGAGAGAG 57.495 40.000 0.00 0.00 0.00 3.20
3466 4772 4.497291 AGAACTAGATCGTGGAGAGAGT 57.503 45.455 0.00 0.00 0.00 3.24
3467 4773 4.448210 AGAACTAGATCGTGGAGAGAGTC 58.552 47.826 0.00 0.00 0.00 3.36
3475 4781 3.202467 GGAGAGAGTCCGACCAGC 58.798 66.667 0.00 0.00 34.84 4.85
3476 4782 2.419739 GGAGAGAGTCCGACCAGCC 61.420 68.421 0.00 0.00 34.84 4.85
3477 4783 2.363147 AGAGAGTCCGACCAGCCC 60.363 66.667 0.00 0.00 0.00 5.19
3478 4784 3.462678 GAGAGTCCGACCAGCCCC 61.463 72.222 0.00 0.00 0.00 5.80
3574 5110 8.809066 AGATATATGTGGTAACTTACGGCATTA 58.191 33.333 10.29 5.94 37.61 1.90
3824 5375 2.747460 GCCTGCTGCACCATCGAA 60.747 61.111 0.00 0.00 40.77 3.71
4092 8418 3.876914 TGAAAAACGATCTTGCAGTGACT 59.123 39.130 0.00 0.00 0.00 3.41
4253 8592 2.744202 GGACTGTATGCACAAGGTTCTG 59.256 50.000 0.00 0.00 33.22 3.02
4258 8597 4.065088 TGTATGCACAAGGTTCTGTTCTC 58.935 43.478 0.00 0.00 0.00 2.87
4271 8610 6.039829 AGGTTCTGTTCTCTTCCATGTTTTTC 59.960 38.462 0.00 0.00 0.00 2.29
4286 8625 0.685785 TTTTCTGCTGTTGTGCCCCA 60.686 50.000 0.00 0.00 0.00 4.96
4409 8753 2.565046 TTGGTGTGTGCTGATGATCA 57.435 45.000 0.00 0.00 0.00 2.92
4461 8805 6.757010 GTGGATGTAAGGTCTATGTACAGTTG 59.243 42.308 0.33 0.00 31.61 3.16
4485 11198 1.068434 GATGAGTGCTGTAGAGCCTCC 59.932 57.143 20.24 6.56 45.57 4.30
4486 11199 1.315981 TGAGTGCTGTAGAGCCTCCG 61.316 60.000 20.24 0.00 45.57 4.63
4488 11201 2.679996 TGCTGTAGAGCCTCCGCA 60.680 61.111 9.72 0.00 45.57 5.69
4621 12764 4.893424 TGGTTCAAGAAAACTCTTTCCG 57.107 40.909 0.00 0.00 41.72 4.30
4817 12976 3.955650 TTCCTGTGTGCTCCTAACTAC 57.044 47.619 0.00 0.00 0.00 2.73
4828 12987 2.753452 CTCCTAACTACGCAGAGGTCAA 59.247 50.000 0.00 0.00 0.00 3.18
4833 12992 5.067413 CCTAACTACGCAGAGGTCAAATCTA 59.933 44.000 0.00 0.00 0.00 1.98
4867 13043 8.673711 GCTTATTGTGTTTGTATCCACTTGATA 58.326 33.333 0.00 0.00 34.76 2.15
4975 13151 7.201938 CCATTTTCCAGTATCTGCATATGGTTT 60.202 37.037 4.56 0.00 32.68 3.27
5004 13180 0.460284 AATGTGTCCTCGTGGCGATC 60.460 55.000 0.00 0.00 34.61 3.69
5005 13181 1.604147 ATGTGTCCTCGTGGCGATCA 61.604 55.000 0.00 0.00 34.61 2.92
5038 13237 3.497879 GCGCTTTAGGTGCCGAAT 58.502 55.556 0.00 0.00 44.87 3.34
5043 13247 2.545113 CGCTTTAGGTGCCGAATAGCTA 60.545 50.000 0.00 0.00 0.00 3.32
5068 13272 2.603110 CTCGTTATAGCTTTGCTCGCAA 59.397 45.455 0.00 0.00 40.44 4.85
5125 13330 1.393539 GCTCGCTTTATCAAGTTCGCA 59.606 47.619 0.00 0.00 31.86 5.10
5126 13331 2.784665 GCTCGCTTTATCAAGTTCGCAC 60.785 50.000 0.00 0.00 31.86 5.34
5217 13423 1.533033 TTCCTCTGTCCCGACTGCA 60.533 57.895 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 72 0.318441 CTCGAAGACCTTCAGTGGCA 59.682 55.000 10.03 0.00 39.46 4.92
155 181 1.987855 TCATCGGGCCGGAAGAGTT 60.988 57.895 27.98 0.00 0.00 3.01
156 182 2.363795 TCATCGGGCCGGAAGAGT 60.364 61.111 27.98 2.49 0.00 3.24
157 183 2.107141 GTCATCGGGCCGGAAGAG 59.893 66.667 27.98 11.60 0.00 2.85
477 548 3.081409 ATCCGACGGTGGAAGGGG 61.081 66.667 14.79 0.00 42.46 4.79
568 640 1.066303 CTCTCTACATTTCTCGCCGCT 59.934 52.381 0.00 0.00 0.00 5.52
583 655 1.011293 TGATTCCCATTCCCCCTCTCT 59.989 52.381 0.00 0.00 0.00 3.10
595 667 1.296392 CTGAGCCACGTGATTCCCA 59.704 57.895 19.30 6.52 0.00 4.37
612 684 3.757248 CTTATCCCTTGCCGCCGCT 62.757 63.158 0.00 0.00 35.36 5.52
629 701 3.850508 GTTTGCGGGTCCAAACCT 58.149 55.556 6.52 0.00 45.41 3.50
660 732 2.024590 GCCCCGACCGCTATAACTGT 62.025 60.000 0.00 0.00 0.00 3.55
712 784 4.175337 GCATACTCGCCTGGCCCA 62.175 66.667 14.12 0.00 0.00 5.36
718 790 3.917760 GAGCCCGCATACTCGCCT 61.918 66.667 0.00 0.00 0.00 5.52
753 826 1.845809 CGAATATGCGGGCTTGGCTC 61.846 60.000 0.00 0.00 0.00 4.70
758 832 2.972505 CGGCGAATATGCGGGCTT 60.973 61.111 0.00 0.00 35.06 4.35
769 843 1.175983 ACCTGCAAAATTCCGGCGAA 61.176 50.000 9.30 0.58 0.00 4.70
785 859 2.411290 CCGCAAACACGCAAACCT 59.589 55.556 0.00 0.00 0.00 3.50
799 873 2.496817 CACTCTAGCAGACCCCGC 59.503 66.667 0.00 0.00 0.00 6.13
800 874 1.608717 AAGCACTCTAGCAGACCCCG 61.609 60.000 0.00 0.00 36.85 5.73
801 875 0.615850 AAAGCACTCTAGCAGACCCC 59.384 55.000 0.00 0.00 36.85 4.95
802 876 3.611766 TTAAAGCACTCTAGCAGACCC 57.388 47.619 0.00 0.00 36.85 4.46
803 877 5.698545 CCATATTAAAGCACTCTAGCAGACC 59.301 44.000 0.00 0.00 36.85 3.85
804 878 6.422400 GTCCATATTAAAGCACTCTAGCAGAC 59.578 42.308 0.00 0.00 36.85 3.51
805 879 6.325028 AGTCCATATTAAAGCACTCTAGCAGA 59.675 38.462 0.00 0.00 36.85 4.26
806 880 6.520272 AGTCCATATTAAAGCACTCTAGCAG 58.480 40.000 0.00 0.00 36.85 4.24
807 881 6.485830 AGTCCATATTAAAGCACTCTAGCA 57.514 37.500 0.00 0.00 36.85 3.49
808 882 7.434492 TGTAGTCCATATTAAAGCACTCTAGC 58.566 38.462 0.00 0.00 0.00 3.42
811 885 8.924303 TGTATGTAGTCCATATTAAAGCACTCT 58.076 33.333 0.00 0.00 38.29 3.24
812 886 9.197694 CTGTATGTAGTCCATATTAAAGCACTC 57.802 37.037 0.00 0.00 38.29 3.51
813 887 8.924303 TCTGTATGTAGTCCATATTAAAGCACT 58.076 33.333 0.00 0.00 38.29 4.40
814 888 9.197694 CTCTGTATGTAGTCCATATTAAAGCAC 57.802 37.037 0.00 0.00 38.29 4.40
815 889 8.924303 ACTCTGTATGTAGTCCATATTAAAGCA 58.076 33.333 0.00 0.00 38.29 3.91
816 890 9.197694 CACTCTGTATGTAGTCCATATTAAAGC 57.802 37.037 0.00 0.00 38.29 3.51
817 891 9.197694 GCACTCTGTATGTAGTCCATATTAAAG 57.802 37.037 0.00 0.00 38.29 1.85
818 892 8.700973 TGCACTCTGTATGTAGTCCATATTAAA 58.299 33.333 0.00 0.00 38.29 1.52
819 893 8.245195 TGCACTCTGTATGTAGTCCATATTAA 57.755 34.615 0.00 0.00 38.29 1.40
820 894 7.833285 TGCACTCTGTATGTAGTCCATATTA 57.167 36.000 0.00 0.00 38.29 0.98
821 895 6.731292 TGCACTCTGTATGTAGTCCATATT 57.269 37.500 0.00 0.00 38.29 1.28
822 896 6.731292 TTGCACTCTGTATGTAGTCCATAT 57.269 37.500 0.00 0.00 38.29 1.78
823 897 6.538945 TTTGCACTCTGTATGTAGTCCATA 57.461 37.500 0.00 0.00 34.86 2.74
824 898 5.420725 TTTGCACTCTGTATGTAGTCCAT 57.579 39.130 0.00 0.00 37.58 3.41
825 899 4.882842 TTTGCACTCTGTATGTAGTCCA 57.117 40.909 0.00 0.00 0.00 4.02
826 900 5.874810 TCATTTTGCACTCTGTATGTAGTCC 59.125 40.000 0.00 0.00 0.00 3.85
827 901 6.591834 ACTCATTTTGCACTCTGTATGTAGTC 59.408 38.462 0.00 0.00 0.00 2.59
828 902 6.369890 CACTCATTTTGCACTCTGTATGTAGT 59.630 38.462 0.00 0.00 0.00 2.73
829 903 6.591448 TCACTCATTTTGCACTCTGTATGTAG 59.409 38.462 0.00 0.00 0.00 2.74
830 904 6.463360 TCACTCATTTTGCACTCTGTATGTA 58.537 36.000 0.00 0.00 0.00 2.29
831 905 5.308014 TCACTCATTTTGCACTCTGTATGT 58.692 37.500 0.00 0.00 0.00 2.29
832 906 5.868043 TCACTCATTTTGCACTCTGTATG 57.132 39.130 0.00 0.00 0.00 2.39
833 907 6.883217 AGATTCACTCATTTTGCACTCTGTAT 59.117 34.615 0.00 0.00 0.00 2.29
834 908 6.148315 CAGATTCACTCATTTTGCACTCTGTA 59.852 38.462 0.00 0.00 0.00 2.74
835 909 5.048921 CAGATTCACTCATTTTGCACTCTGT 60.049 40.000 0.00 0.00 0.00 3.41
836 910 5.391449 CAGATTCACTCATTTTGCACTCTG 58.609 41.667 0.00 0.00 0.00 3.35
837 911 4.082895 GCAGATTCACTCATTTTGCACTCT 60.083 41.667 0.00 0.00 0.00 3.24
838 912 4.164294 GCAGATTCACTCATTTTGCACTC 58.836 43.478 0.00 0.00 0.00 3.51
839 913 3.570975 TGCAGATTCACTCATTTTGCACT 59.429 39.130 0.00 0.00 35.41 4.40
840 914 3.904571 TGCAGATTCACTCATTTTGCAC 58.095 40.909 0.00 0.00 35.41 4.57
841 915 3.570975 AGTGCAGATTCACTCATTTTGCA 59.429 39.130 0.00 0.00 43.28 4.08
842 916 4.170292 AGTGCAGATTCACTCATTTTGC 57.830 40.909 0.00 0.00 43.28 3.68
851 925 6.148480 AGACACATTTTAGAGTGCAGATTCAC 59.852 38.462 0.00 0.00 39.30 3.18
852 926 6.233434 AGACACATTTTAGAGTGCAGATTCA 58.767 36.000 0.00 0.00 39.30 2.57
853 927 6.734104 AGACACATTTTAGAGTGCAGATTC 57.266 37.500 0.00 0.00 39.30 2.52
856 930 9.967346 GTATATAGACACATTTTAGAGTGCAGA 57.033 33.333 0.00 0.00 39.30 4.26
857 931 9.750125 TGTATATAGACACATTTTAGAGTGCAG 57.250 33.333 0.00 0.00 39.30 4.41
865 939 9.908152 CGTCCAGATGTATATAGACACATTTTA 57.092 33.333 1.52 0.00 35.55 1.52
866 940 8.421784 ACGTCCAGATGTATATAGACACATTTT 58.578 33.333 1.52 0.00 35.55 1.82
867 941 7.952671 ACGTCCAGATGTATATAGACACATTT 58.047 34.615 1.52 0.00 35.55 2.32
868 942 7.526142 ACGTCCAGATGTATATAGACACATT 57.474 36.000 1.52 0.00 35.55 2.71
869 943 7.883833 AGTACGTCCAGATGTATATAGACACAT 59.116 37.037 1.52 0.00 38.08 3.21
870 944 7.222161 AGTACGTCCAGATGTATATAGACACA 58.778 38.462 1.52 0.00 35.50 3.72
871 945 7.603404 AGAGTACGTCCAGATGTATATAGACAC 59.397 40.741 1.52 0.00 35.50 3.67
872 946 7.677892 AGAGTACGTCCAGATGTATATAGACA 58.322 38.462 2.07 2.07 35.50 3.41
873 947 8.550710 AAGAGTACGTCCAGATGTATATAGAC 57.449 38.462 0.00 0.00 35.50 2.59
874 948 9.000486 CAAAGAGTACGTCCAGATGTATATAGA 58.000 37.037 0.00 0.00 35.50 1.98
875 949 9.000486 TCAAAGAGTACGTCCAGATGTATATAG 58.000 37.037 0.00 0.00 35.50 1.31
876 950 8.913487 TCAAAGAGTACGTCCAGATGTATATA 57.087 34.615 0.00 0.00 35.50 0.86
877 951 7.818997 TCAAAGAGTACGTCCAGATGTATAT 57.181 36.000 0.00 0.00 35.50 0.86
878 952 7.634671 TTCAAAGAGTACGTCCAGATGTATA 57.365 36.000 0.00 0.00 35.50 1.47
879 953 6.525578 TTCAAAGAGTACGTCCAGATGTAT 57.474 37.500 0.00 0.00 35.50 2.29
880 954 5.970317 TTCAAAGAGTACGTCCAGATGTA 57.030 39.130 0.00 0.00 0.00 2.29
881 955 4.866508 TTCAAAGAGTACGTCCAGATGT 57.133 40.909 0.00 0.00 0.00 3.06
882 956 7.492669 ACATATTTCAAAGAGTACGTCCAGATG 59.507 37.037 0.00 0.00 0.00 2.90
883 957 7.556844 ACATATTTCAAAGAGTACGTCCAGAT 58.443 34.615 0.00 0.00 0.00 2.90
884 958 6.931838 ACATATTTCAAAGAGTACGTCCAGA 58.068 36.000 0.00 0.00 0.00 3.86
885 959 8.697846 TTACATATTTCAAAGAGTACGTCCAG 57.302 34.615 0.00 0.00 0.00 3.86
886 960 9.491675 TTTTACATATTTCAAAGAGTACGTCCA 57.508 29.630 0.00 0.00 0.00 4.02
910 984 9.569122 ACTCCGTTTGTAAATATATGCCTATTT 57.431 29.630 0.00 0.00 35.85 1.40
911 985 8.999431 CACTCCGTTTGTAAATATATGCCTATT 58.001 33.333 0.00 0.00 0.00 1.73
912 986 8.372459 TCACTCCGTTTGTAAATATATGCCTAT 58.628 33.333 0.00 0.00 0.00 2.57
913 987 7.728148 TCACTCCGTTTGTAAATATATGCCTA 58.272 34.615 0.00 0.00 0.00 3.93
914 988 6.588204 TCACTCCGTTTGTAAATATATGCCT 58.412 36.000 0.00 0.00 0.00 4.75
915 989 6.854496 TCACTCCGTTTGTAAATATATGCC 57.146 37.500 0.00 0.00 0.00 4.40
916 990 9.807386 GTATTCACTCCGTTTGTAAATATATGC 57.193 33.333 0.00 0.00 0.00 3.14
927 1001 6.649557 AGAAAGGTAAGTATTCACTCCGTTTG 59.350 38.462 0.00 0.00 32.29 2.93
1051 1126 3.649986 GTGTCGCAGGTGTGTGGC 61.650 66.667 0.00 0.00 39.39 5.01
1066 1145 0.950836 ATCTCGGCATCTCTCTCGTG 59.049 55.000 0.00 0.00 0.00 4.35
1217 1311 2.358737 GTCCCCGCTTGTGTCTGG 60.359 66.667 0.00 0.00 0.00 3.86
1247 1341 2.717044 ATCGGATCCACGAACCGCA 61.717 57.895 13.41 0.00 45.42 5.69
1249 1343 1.591594 CCATCGGATCCACGAACCG 60.592 63.158 13.41 4.14 46.80 4.44
1250 1344 1.227556 CCCATCGGATCCACGAACC 60.228 63.158 13.41 0.00 46.92 3.62
1252 1346 3.101796 GCCCCATCGGATCCACGAA 62.102 63.158 13.41 0.00 46.92 3.85
1254 1348 4.969196 CGCCCCATCGGATCCACG 62.969 72.222 13.41 0.00 0.00 4.94
1813 1912 2.795297 GAGGACGTCGCTGAGGAG 59.205 66.667 9.92 0.00 0.00 3.69
2046 2145 0.806102 CGACGATGAACCTGCGGAAT 60.806 55.000 0.00 0.00 0.00 3.01
2207 2306 4.880696 TGAACACACACATCACATTCAGAA 59.119 37.500 0.00 0.00 0.00 3.02
2319 2421 5.076873 AGGCAGTTCCAACTTGCTTATAAA 58.923 37.500 11.27 0.00 37.08 1.40
2509 2625 8.786826 ATAATCTCTCATCTACTTAGAGGACG 57.213 38.462 0.00 0.00 38.11 4.79
2654 2793 4.739793 TGAATGAAGTCCCATTTTCAGGT 58.260 39.130 0.00 0.00 36.93 4.00
2895 4109 3.807622 CGCTGAAACTGGAACTTCTAACA 59.192 43.478 0.00 0.00 0.00 2.41
3219 4460 1.282157 CCCCCTTCGGTTTGAGATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3311 4554 7.134815 GCTAGATTTGTTAATGCCACATACAG 58.865 38.462 0.00 0.00 0.00 2.74
3312 4555 6.601217 TGCTAGATTTGTTAATGCCACATACA 59.399 34.615 0.00 0.00 0.00 2.29
3313 4556 7.012327 TCTGCTAGATTTGTTAATGCCACATAC 59.988 37.037 0.00 0.00 0.00 2.39
3314 4557 7.053498 TCTGCTAGATTTGTTAATGCCACATA 58.947 34.615 0.00 0.00 0.00 2.29
3315 4558 5.887598 TCTGCTAGATTTGTTAATGCCACAT 59.112 36.000 0.00 0.00 0.00 3.21
3364 4670 6.940430 AACAGGGCCTAAGTAACTAAGTAA 57.060 37.500 5.28 0.00 0.00 2.24
3365 4671 6.296030 CCAAACAGGGCCTAAGTAACTAAGTA 60.296 42.308 5.28 0.00 0.00 2.24
3366 4672 5.514310 CCAAACAGGGCCTAAGTAACTAAGT 60.514 44.000 5.28 0.00 0.00 2.24
3367 4673 4.941873 CCAAACAGGGCCTAAGTAACTAAG 59.058 45.833 5.28 0.00 0.00 2.18
3368 4674 4.913784 CCAAACAGGGCCTAAGTAACTAA 58.086 43.478 5.28 0.00 0.00 2.24
3369 4675 4.563140 CCAAACAGGGCCTAAGTAACTA 57.437 45.455 5.28 0.00 0.00 2.24
3370 4676 3.434940 CCAAACAGGGCCTAAGTAACT 57.565 47.619 5.28 0.00 0.00 2.24
3381 4687 4.576993 GCGATTTGCCAAACAGGG 57.423 55.556 0.00 0.00 38.09 4.45
3390 4696 3.386867 CTGCTCCGTGGCGATTTGC 62.387 63.158 0.00 0.00 45.38 3.68
3391 4697 1.699656 CTCTGCTCCGTGGCGATTTG 61.700 60.000 0.00 0.00 34.52 2.32
3392 4698 1.448540 CTCTGCTCCGTGGCGATTT 60.449 57.895 0.00 0.00 34.52 2.17
3393 4699 2.185350 CTCTGCTCCGTGGCGATT 59.815 61.111 0.00 0.00 34.52 3.34
3394 4700 4.521062 GCTCTGCTCCGTGGCGAT 62.521 66.667 0.00 0.00 34.52 4.58
3423 4729 0.401738 TTTGAGGAGTGGCTGGAAGG 59.598 55.000 0.00 0.00 0.00 3.46
3424 4730 2.503895 ATTTGAGGAGTGGCTGGAAG 57.496 50.000 0.00 0.00 0.00 3.46
3425 4731 2.978156 AATTTGAGGAGTGGCTGGAA 57.022 45.000 0.00 0.00 0.00 3.53
3426 4732 3.181329 TCTAATTTGAGGAGTGGCTGGA 58.819 45.455 0.00 0.00 0.00 3.86
3427 4733 3.634397 TCTAATTTGAGGAGTGGCTGG 57.366 47.619 0.00 0.00 0.00 4.85
3428 4734 4.583871 AGTTCTAATTTGAGGAGTGGCTG 58.416 43.478 0.00 0.00 0.00 4.85
3429 4735 4.917906 AGTTCTAATTTGAGGAGTGGCT 57.082 40.909 0.00 0.00 0.00 4.75
3430 4736 5.978814 TCTAGTTCTAATTTGAGGAGTGGC 58.021 41.667 0.00 0.00 0.00 5.01
3431 4737 6.920758 CGATCTAGTTCTAATTTGAGGAGTGG 59.079 42.308 0.00 0.00 0.00 4.00
3432 4738 7.433719 CACGATCTAGTTCTAATTTGAGGAGTG 59.566 40.741 0.00 0.00 0.00 3.51
3433 4739 7.416890 CCACGATCTAGTTCTAATTTGAGGAGT 60.417 40.741 0.00 0.00 0.00 3.85
3434 4740 6.920758 CCACGATCTAGTTCTAATTTGAGGAG 59.079 42.308 0.00 0.00 0.00 3.69
3435 4741 6.605995 TCCACGATCTAGTTCTAATTTGAGGA 59.394 38.462 0.00 0.00 0.00 3.71
3436 4742 6.806751 TCCACGATCTAGTTCTAATTTGAGG 58.193 40.000 0.00 0.00 0.00 3.86
3437 4743 7.708051 TCTCCACGATCTAGTTCTAATTTGAG 58.292 38.462 0.00 0.00 0.00 3.02
3438 4744 7.556635 TCTCTCCACGATCTAGTTCTAATTTGA 59.443 37.037 0.00 0.00 0.00 2.69
3439 4745 7.708051 TCTCTCCACGATCTAGTTCTAATTTG 58.292 38.462 0.00 0.00 0.00 2.32
3440 4746 7.558444 ACTCTCTCCACGATCTAGTTCTAATTT 59.442 37.037 0.00 0.00 0.00 1.82
3441 4747 7.057894 ACTCTCTCCACGATCTAGTTCTAATT 58.942 38.462 0.00 0.00 0.00 1.40
3442 4748 6.597562 ACTCTCTCCACGATCTAGTTCTAAT 58.402 40.000 0.00 0.00 0.00 1.73
3443 4749 5.991861 ACTCTCTCCACGATCTAGTTCTAA 58.008 41.667 0.00 0.00 0.00 2.10
3444 4750 5.453621 GGACTCTCTCCACGATCTAGTTCTA 60.454 48.000 0.00 0.00 39.21 2.10
3445 4751 4.448210 GACTCTCTCCACGATCTAGTTCT 58.552 47.826 0.00 0.00 0.00 3.01
3446 4752 3.562557 GGACTCTCTCCACGATCTAGTTC 59.437 52.174 0.00 0.00 39.21 3.01
3447 4753 3.547746 GGACTCTCTCCACGATCTAGTT 58.452 50.000 0.00 0.00 39.21 2.24
3448 4754 2.484065 CGGACTCTCTCCACGATCTAGT 60.484 54.545 0.00 0.00 39.39 2.57
3449 4755 2.139917 CGGACTCTCTCCACGATCTAG 58.860 57.143 0.00 0.00 39.39 2.43
3450 4756 1.761198 TCGGACTCTCTCCACGATCTA 59.239 52.381 0.00 0.00 39.39 1.98
3451 4757 0.542333 TCGGACTCTCTCCACGATCT 59.458 55.000 0.00 0.00 39.39 2.75
3452 4758 0.658897 GTCGGACTCTCTCCACGATC 59.341 60.000 0.00 0.00 39.39 3.69
3453 4759 0.748729 GGTCGGACTCTCTCCACGAT 60.749 60.000 8.23 0.00 39.39 3.73
3454 4760 1.376942 GGTCGGACTCTCTCCACGA 60.377 63.158 8.23 0.00 39.39 4.35
3455 4761 1.649390 CTGGTCGGACTCTCTCCACG 61.649 65.000 8.23 0.00 39.39 4.94
3456 4762 1.939769 GCTGGTCGGACTCTCTCCAC 61.940 65.000 8.23 0.00 39.39 4.02
3457 4763 1.679305 GCTGGTCGGACTCTCTCCA 60.679 63.158 8.23 0.00 39.39 3.86
3458 4764 2.419739 GGCTGGTCGGACTCTCTCC 61.420 68.421 8.23 0.00 35.33 3.71
3459 4765 2.419739 GGGCTGGTCGGACTCTCTC 61.420 68.421 8.23 0.00 0.00 3.20
3460 4766 2.363147 GGGCTGGTCGGACTCTCT 60.363 66.667 8.23 0.00 0.00 3.10
3461 4767 3.462678 GGGGCTGGTCGGACTCTC 61.463 72.222 8.23 0.00 0.00 3.20
3462 4768 2.164332 TAAGGGGCTGGTCGGACTCT 62.164 60.000 8.23 0.00 0.00 3.24
3463 4769 1.684734 TAAGGGGCTGGTCGGACTC 60.685 63.158 8.23 0.00 0.00 3.36
3464 4770 1.988406 GTAAGGGGCTGGTCGGACT 60.988 63.158 8.23 0.00 0.00 3.85
3465 4771 1.551019 AAGTAAGGGGCTGGTCGGAC 61.551 60.000 0.00 0.00 0.00 4.79
3466 4772 1.229400 AAGTAAGGGGCTGGTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
3467 4773 1.221021 GAAGTAAGGGGCTGGTCGG 59.779 63.158 0.00 0.00 0.00 4.79
3468 4774 1.153628 CGAAGTAAGGGGCTGGTCG 60.154 63.158 0.00 0.00 0.00 4.79
3469 4775 1.221021 CCGAAGTAAGGGGCTGGTC 59.779 63.158 0.00 0.00 0.00 4.02
3470 4776 2.967946 GCCGAAGTAAGGGGCTGGT 61.968 63.158 0.00 0.00 43.52 4.00
3471 4777 2.124695 GCCGAAGTAAGGGGCTGG 60.125 66.667 0.00 0.00 43.52 4.85
3475 4781 2.572290 CCAAATAGCCGAAGTAAGGGG 58.428 52.381 0.00 0.00 0.00 4.79
3476 4782 1.947456 GCCAAATAGCCGAAGTAAGGG 59.053 52.381 0.00 0.00 0.00 3.95
3477 4783 2.614057 CTGCCAAATAGCCGAAGTAAGG 59.386 50.000 0.00 0.00 0.00 2.69
3478 4784 2.032178 GCTGCCAAATAGCCGAAGTAAG 59.968 50.000 0.00 0.00 35.15 2.34
4092 8418 2.488347 GGCCTTGTTGTTCTCCAGGTAA 60.488 50.000 0.00 0.00 0.00 2.85
4253 8592 5.218139 CAGCAGAAAAACATGGAAGAGAAC 58.782 41.667 0.00 0.00 0.00 3.01
4258 8597 4.505191 CACAACAGCAGAAAAACATGGAAG 59.495 41.667 0.00 0.00 0.00 3.46
4271 8610 0.320073 CAAATGGGGCACAACAGCAG 60.320 55.000 0.00 0.00 35.83 4.24
4286 8625 7.255730 CCTTCTCTTTTCACACAAGGATCAAAT 60.256 37.037 0.00 0.00 33.50 2.32
4488 11201 4.394078 CAAGCAGCACGCACGCAT 62.394 61.111 0.00 0.00 46.13 4.73
4500 11213 1.336131 TAAACCTGCAATGCCAAGCA 58.664 45.000 1.53 0.00 44.86 3.91
4602 11858 8.851960 AAATAACGGAAAGAGTTTTCTTGAAC 57.148 30.769 0.69 0.00 42.80 3.18
4605 11861 7.704899 ACCAAAATAACGGAAAGAGTTTTCTTG 59.295 33.333 0.69 0.00 42.80 3.02
4621 12764 3.754850 ACAGCCGGTAGAACCAAAATAAC 59.245 43.478 1.90 0.00 38.47 1.89
4790 12948 0.947244 GAGCACACAGGAAACACCAG 59.053 55.000 0.00 0.00 42.04 4.00
4817 12976 2.799412 GAGCATAGATTTGACCTCTGCG 59.201 50.000 0.00 0.00 38.35 5.18
4828 12987 5.118990 ACACAATAAGCACGAGCATAGATT 58.881 37.500 7.77 0.00 45.49 2.40
4833 12992 3.253188 ACAAACACAATAAGCACGAGCAT 59.747 39.130 7.77 0.00 45.49 3.79
4952 13128 7.716799 AAAACCATATGCAGATACTGGAAAA 57.283 32.000 6.46 0.00 35.08 2.29
4975 13151 5.872617 CCACGAGGACACATTATACAGAAAA 59.127 40.000 0.00 0.00 36.89 2.29
5004 13180 2.263741 GCCGCATAGGAGCCCATTG 61.264 63.158 0.00 0.00 45.00 2.82
5005 13181 2.113986 GCCGCATAGGAGCCCATT 59.886 61.111 0.00 0.00 45.00 3.16
5038 13237 8.600810 AGCAAAGCTATAACGAGCGTTAGCTA 62.601 42.308 24.62 12.32 46.42 3.32
5068 13272 2.203070 CCTTATTCGGCTGCGGCT 60.203 61.111 18.85 0.00 38.73 5.52
5125 13330 8.364129 TGTAGGTAATAACGAAAGAAAAACGT 57.636 30.769 0.00 0.00 41.97 3.99
5126 13331 8.490355 ACTGTAGGTAATAACGAAAGAAAAACG 58.510 33.333 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.