Multiple sequence alignment - TraesCS3D01G201800

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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 TraesCS3D01G201800 chr3D 100.000 6018 0 0 1 6018 241670453 241664436 0.000000e+00 11114.0
1 TraesCS3D01G201800 chr3D 94.048 84 3 2 3932 4015 241666442 241666361 6.330000e-25 126.0
2 TraesCS3D01G201800 chr3D 94.048 84 3 2 4012 4093 241666522 241666439 6.330000e-25 126.0
3 TraesCS3D01G201800 chr3D 89.062 64 4 3 4401 4462 131489157 131489219 6.470000e-10 76.8
4 TraesCS3D01G201800 chr3D 97.500 40 1 0 2715 2754 401175201 401175240 1.080000e-07 69.4
5 TraesCS3D01G201800 chr3D 95.349 43 0 2 2713 2754 138890663 138890622 3.890000e-07 67.6
6 TraesCS3D01G201800 chr3A 96.748 2706 49 11 2752 5455 260068834 260066166 0.000000e+00 4473.0
7 TraesCS3D01G201800 chr3A 98.791 1820 22 0 900 2719 260070639 260068820 0.000000e+00 3240.0
8 TraesCS3D01G201800 chr3A 92.500 560 35 4 5459 6018 260032084 260031532 0.000000e+00 795.0
9 TraesCS3D01G201800 chr3A 92.079 202 14 1 3095 3296 375018263 375018064 3.550000e-72 283.0
10 TraesCS3D01G201800 chr3A 95.238 84 2 2 3932 4015 260067603 260067522 1.360000e-26 132.0
11 TraesCS3D01G201800 chr3A 93.902 82 5 0 4012 4093 260067681 260067600 2.280000e-24 124.0
12 TraesCS3D01G201800 chr3B 98.032 1829 27 1 900 2719 376635766 376633938 0.000000e+00 3169.0
13 TraesCS3D01G201800 chr3B 96.074 1452 41 5 4180 5624 376632773 376631331 0.000000e+00 2351.0
14 TraesCS3D01G201800 chr3B 91.579 1235 49 26 2752 3985 376633952 376632772 0.000000e+00 1653.0
15 TraesCS3D01G201800 chr3B 91.605 405 16 8 5620 6018 376627801 376627409 1.480000e-150 544.0
16 TraesCS3D01G201800 chr3B 90.741 54 3 2 4012 4063 376632825 376632772 3.010000e-08 71.3
17 TraesCS3D01G201800 chr3B 100.000 38 0 0 2717 2754 784595697 784595660 3.010000e-08 71.3
18 TraesCS3D01G201800 chr2D 87.875 899 79 19 1 880 96682065 96681178 0.000000e+00 1029.0
19 TraesCS3D01G201800 chr2D 93.684 190 11 1 3107 3296 380416532 380416720 3.550000e-72 283.0
20 TraesCS3D01G201800 chr2D 97.561 41 0 1 2715 2754 8667833 8667873 1.080000e-07 69.4
21 TraesCS3D01G201800 chr7D 87.360 894 82 15 1 870 495295773 495294887 0.000000e+00 996.0
22 TraesCS3D01G201800 chr7D 86.874 899 83 17 1 873 430935343 430934454 0.000000e+00 974.0
23 TraesCS3D01G201800 chr7D 80.093 864 119 32 43 872 248458933 248458089 1.440000e-165 593.0
24 TraesCS3D01G201800 chr7D 91.089 202 16 1 3095 3296 425729471 425729272 7.690000e-69 272.0
25 TraesCS3D01G201800 chr1D 86.277 889 89 17 1 870 439098373 439099247 0.000000e+00 935.0
26 TraesCS3D01G201800 chr1D 85.314 892 108 17 1 873 342118695 342117808 0.000000e+00 900.0
27 TraesCS3D01G201800 chr1D 79.661 177 28 6 715 888 458348345 458348174 2.950000e-23 121.0
28 TraesCS3D01G201800 chr1D 100.000 37 0 0 2718 2754 277361136 277361172 1.080000e-07 69.4
29 TraesCS3D01G201800 chr1D 95.238 42 1 1 2713 2754 10263816 10263776 1.400000e-06 65.8
30 TraesCS3D01G201800 chr6D 87.515 825 79 11 1 809 408697401 408698217 0.000000e+00 931.0
31 TraesCS3D01G201800 chr6D 90.426 94 9 0 5535 5628 459045397 459045490 2.280000e-24 124.0
32 TraesCS3D01G201800 chr6D 95.238 42 1 1 2715 2755 403063984 403063943 1.400000e-06 65.8
33 TraesCS3D01G201800 chr6A 85.714 896 97 19 1 872 200243184 200244072 0.000000e+00 917.0
34 TraesCS3D01G201800 chr6A 91.919 198 14 1 3099 3296 381088703 381088898 5.940000e-70 276.0
35 TraesCS3D01G201800 chr2A 85.682 894 92 25 1 873 634110481 634111359 0.000000e+00 909.0
36 TraesCS3D01G201800 chr2A 78.182 165 27 8 707 865 77187459 77187298 4.960000e-16 97.1
37 TraesCS3D01G201800 chr2A 87.500 64 3 4 2713 2772 67977279 67977217 1.080000e-07 69.4
38 TraesCS3D01G201800 chr5D 87.390 793 83 13 1 777 205124528 205125319 0.000000e+00 894.0
39 TraesCS3D01G201800 chr5D 91.584 202 15 1 3095 3296 480372507 480372706 1.650000e-70 278.0
40 TraesCS3D01G201800 chr5D 100.000 37 0 0 2718 2754 563758959 563758995 1.080000e-07 69.4
41 TraesCS3D01G201800 chr5A 84.139 889 116 19 4 872 345228514 345227631 0.000000e+00 837.0
42 TraesCS3D01G201800 chr5A 91.667 60 4 1 4403 4462 429512898 429512956 1.390000e-11 82.4
43 TraesCS3D01G201800 chr4A 82.781 906 102 26 1 872 495125935 495126820 0.000000e+00 760.0
44 TraesCS3D01G201800 chr4A 81.986 433 54 11 450 872 669241825 669241407 4.460000e-91 346.0
45 TraesCS3D01G201800 chr7A 91.960 199 14 1 3098 3296 559395816 559395620 1.650000e-70 278.0
46 TraesCS3D01G201800 chr6B 90.141 213 17 3 3084 3296 199069125 199068917 2.140000e-69 274.0
47 TraesCS3D01G201800 chr6B 91.935 62 3 2 4402 4462 530560471 530560411 1.070000e-12 86.1
48 TraesCS3D01G201800 chr6B 100.000 37 0 0 2718 2754 17498724 17498760 1.080000e-07 69.4
49 TraesCS3D01G201800 chr6B 97.561 41 0 1 2714 2754 240045512 240045473 1.080000e-07 69.4
50 TraesCS3D01G201800 chr6B 89.286 56 0 4 2705 2754 95494743 95494798 1.400000e-06 65.8
51 TraesCS3D01G201800 chr4B 88.983 118 13 0 5571 5688 520914557 520914440 4.860000e-31 147.0
52 TraesCS3D01G201800 chr4B 97.500 40 1 0 2715 2754 577051717 577051756 1.080000e-07 69.4
53 TraesCS3D01G201800 chr4B 100.000 36 0 0 2720 2755 107660460 107660425 3.890000e-07 67.6
54 TraesCS3D01G201800 chr1B 85.938 128 15 2 3440 3564 60451477 60451604 3.780000e-27 134.0
55 TraesCS3D01G201800 chr1B 85.039 127 19 0 3440 3566 632208831 632208705 4.890000e-26 130.0
56 TraesCS3D01G201800 chr1B 90.000 60 5 1 4403 4462 439444720 439444778 6.470000e-10 76.8
57 TraesCS3D01G201800 chr1B 94.000 50 1 2 2712 2760 157274666 157274618 2.330000e-09 75.0
58 TraesCS3D01G201800 chr1B 100.000 37 0 0 2718 2754 269039096 269039060 1.080000e-07 69.4
59 TraesCS3D01G201800 chr5B 87.037 108 14 0 3444 3551 493936240 493936133 8.190000e-24 122.0
60 TraesCS3D01G201800 chr5B 91.667 60 4 1 4403 4462 379815699 379815641 1.390000e-11 82.4
61 TraesCS3D01G201800 chr5B 100.000 40 0 0 2715 2754 253197013 253196974 2.330000e-09 75.0
62 TraesCS3D01G201800 chr5B 97.500 40 0 1 2715 2754 180042667 180042705 3.890000e-07 67.6
63 TraesCS3D01G201800 chr5B 91.667 48 2 2 2708 2754 174867640 174867686 1.400000e-06 65.8
64 TraesCS3D01G201800 chr5B 93.478 46 0 3 2710 2754 703803315 703803358 1.400000e-06 65.8
65 TraesCS3D01G201800 chr5B 91.667 48 0 3 2710 2754 506666415 506666461 5.040000e-06 63.9
66 TraesCS3D01G201800 chr2B 91.525 59 4 1 4401 4459 622914114 622914057 5.000000e-11 80.5
67 TraesCS3D01G201800 chr1A 87.324 71 5 4 4407 4475 71070793 71070861 1.800000e-10 78.7
68 TraesCS3D01G201800 chr1A 100.000 37 0 0 2718 2754 82526067 82526031 1.080000e-07 69.4
69 TraesCS3D01G201800 chr1A 100.000 37 0 0 2718 2754 350015717 350015753 1.080000e-07 69.4
70 TraesCS3D01G201800 chr1A 100.000 36 0 0 2720 2755 25707961 25707926 3.890000e-07 67.6
71 TraesCS3D01G201800 chr7B 100.000 40 0 0 2715 2754 657226685 657226646 2.330000e-09 75.0
72 TraesCS3D01G201800 chr7B 100.000 35 0 0 2720 2754 506378157 506378123 1.400000e-06 65.8
73 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 15977965 15977999 1.400000e-06 65.8
74 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 37328491 37328457 1.400000e-06 65.8
75 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 119877654 119877688 1.400000e-06 65.8
76 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 222916202 222916236 1.400000e-06 65.8
77 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 277315450 277315484 1.400000e-06 65.8
78 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 283384491 283384457 1.400000e-06 65.8
79 TraesCS3D01G201800 chrUn 97.368 38 1 0 2717 2754 348740511 348740548 1.400000e-06 65.8
80 TraesCS3D01G201800 chrUn 97.368 38 1 0 2717 2754 364369463 364369500 1.400000e-06 65.8
81 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 374196421 374196387 1.400000e-06 65.8
82 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 374198279 374198245 1.400000e-06 65.8
83 TraesCS3D01G201800 chrUn 100.000 35 0 0 2720 2754 374285582 374285548 1.400000e-06 65.8


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 TraesCS3D01G201800 chr3D 241664436 241670453 6017 True 11114.00 11114 100.00000 1 6018 1 chr3D.!!$R2 6017
1 TraesCS3D01G201800 chr3A 260066166 260070639 4473 True 1992.25 4473 96.16975 900 5455 4 chr3A.!!$R3 4555
2 TraesCS3D01G201800 chr3A 260031532 260032084 552 True 795.00 795 92.50000 5459 6018 1 chr3A.!!$R1 559
3 TraesCS3D01G201800 chr3B 376627409 376635766 8357 True 1557.66 3169 93.60620 900 6018 5 chr3B.!!$R2 5118
4 TraesCS3D01G201800 chr2D 96681178 96682065 887 True 1029.00 1029 87.87500 1 880 1 chr2D.!!$R1 879
5 TraesCS3D01G201800 chr7D 495294887 495295773 886 True 996.00 996 87.36000 1 870 1 chr7D.!!$R4 869
6 TraesCS3D01G201800 chr7D 430934454 430935343 889 True 974.00 974 86.87400 1 873 1 chr7D.!!$R3 872
7 TraesCS3D01G201800 chr7D 248458089 248458933 844 True 593.00 593 80.09300 43 872 1 chr7D.!!$R1 829
8 TraesCS3D01G201800 chr1D 439098373 439099247 874 False 935.00 935 86.27700 1 870 1 chr1D.!!$F2 869
9 TraesCS3D01G201800 chr1D 342117808 342118695 887 True 900.00 900 85.31400 1 873 1 chr1D.!!$R2 872
10 TraesCS3D01G201800 chr6D 408697401 408698217 816 False 931.00 931 87.51500 1 809 1 chr6D.!!$F1 808
11 TraesCS3D01G201800 chr6A 200243184 200244072 888 False 917.00 917 85.71400 1 872 1 chr6A.!!$F1 871
12 TraesCS3D01G201800 chr2A 634110481 634111359 878 False 909.00 909 85.68200 1 873 1 chr2A.!!$F1 872
13 TraesCS3D01G201800 chr5D 205124528 205125319 791 False 894.00 894 87.39000 1 777 1 chr5D.!!$F1 776
14 TraesCS3D01G201800 chr5A 345227631 345228514 883 True 837.00 837 84.13900 4 872 1 chr5A.!!$R1 868
15 TraesCS3D01G201800 chr4A 495125935 495126820 885 False 760.00 760 82.78100 1 872 1 chr4A.!!$F1 871

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
886 978 0.037590 TCTTATGCAGGTGGGCGTTT 59.962 50.0 0.00 0.00 36.28 3.60 F
1023 1124 0.315706 CGTCGATCCCGTCTAACGAC 60.316 60.0 0.00 0.00 46.05 4.34 F
2873 2974 0.616371 TACTATGGCGCCCAAAGTGT 59.384 50.0 26.77 15.87 36.95 3.55 F
3498 3627 0.672342 AGTACAGGGACACGTGACAC 59.328 55.0 25.01 18.49 36.39 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2885 2986 0.033366 AATTTGACACTTTGGGCGCC 59.967 50.000 21.18 21.18 0.0 6.53 R
2886 2987 2.030274 AGTAATTTGACACTTTGGGCGC 60.030 45.455 0.00 0.00 0.0 6.53 R
3821 3950 0.976641 ACTGTCATCTCCGCTTTCCA 59.023 50.000 0.00 0.00 0.0 3.53 R
5312 5450 1.160137 GAGTGACACCAGCATTGTCC 58.840 55.000 0.84 2.76 42.4 4.02 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
107 110 1.797713 CGCGAAGTACATCGTCCACAT 60.798 52.381 20.28 0.00 44.49 3.21
114 117 0.317160 ACATCGTCCACATCGTGTGT 59.683 50.000 14.25 4.34 46.45 3.72
390 394 4.515404 GCCATTTACTCGTCGGCT 57.485 55.556 0.00 0.00 39.73 5.52
395 401 2.343101 CATTTACTCGTCGGCTGGAAA 58.657 47.619 0.00 0.00 0.00 3.13
404 413 2.361737 GGCTGGAAAGGGGAGTGC 60.362 66.667 0.00 0.00 0.00 4.40
430 451 1.135939 CGTGTGACGATGCGAGGTA 59.864 57.895 0.00 0.00 46.05 3.08
436 457 1.278238 GACGATGCGAGGTAAAGTGG 58.722 55.000 0.00 0.00 0.00 4.00
437 458 0.606604 ACGATGCGAGGTAAAGTGGT 59.393 50.000 0.00 0.00 0.00 4.16
438 459 1.001633 ACGATGCGAGGTAAAGTGGTT 59.998 47.619 0.00 0.00 0.00 3.67
439 460 1.393539 CGATGCGAGGTAAAGTGGTTG 59.606 52.381 0.00 0.00 0.00 3.77
712 769 2.516695 AAAAACGCGTTCCCCGGT 60.517 55.556 26.77 5.18 36.94 5.28
797 885 0.966370 AGGCTCCTGGTACACGACTC 60.966 60.000 0.00 0.00 0.00 3.36
798 886 1.248785 GGCTCCTGGTACACGACTCA 61.249 60.000 0.00 0.00 0.00 3.41
874 966 2.610727 GCGGGTGGAGATACTCTTATGC 60.611 54.545 0.00 0.00 0.00 3.14
876 968 3.305676 CGGGTGGAGATACTCTTATGCAG 60.306 52.174 0.00 0.00 0.00 4.41
880 972 3.643320 TGGAGATACTCTTATGCAGGTGG 59.357 47.826 0.00 0.00 0.00 4.61
881 973 3.007398 GGAGATACTCTTATGCAGGTGGG 59.993 52.174 0.00 0.00 0.00 4.61
882 974 2.370189 AGATACTCTTATGCAGGTGGGC 59.630 50.000 0.00 0.00 0.00 5.36
883 975 0.464036 TACTCTTATGCAGGTGGGCG 59.536 55.000 0.00 0.00 36.28 6.13
884 976 1.221840 CTCTTATGCAGGTGGGCGT 59.778 57.895 0.00 0.00 36.28 5.68
885 977 0.392998 CTCTTATGCAGGTGGGCGTT 60.393 55.000 0.00 0.00 36.28 4.84
886 978 0.037590 TCTTATGCAGGTGGGCGTTT 59.962 50.000 0.00 0.00 36.28 3.60
887 979 0.887933 CTTATGCAGGTGGGCGTTTT 59.112 50.000 0.00 0.00 36.28 2.43
888 980 2.088423 CTTATGCAGGTGGGCGTTTTA 58.912 47.619 0.00 0.00 36.28 1.52
889 981 1.455248 TATGCAGGTGGGCGTTTTAC 58.545 50.000 0.00 0.00 36.28 2.01
890 982 1.248101 ATGCAGGTGGGCGTTTTACC 61.248 55.000 0.00 0.00 36.28 2.85
891 983 2.973316 GCAGGTGGGCGTTTTACCG 61.973 63.158 0.00 0.00 39.46 4.02
892 984 2.032987 AGGTGGGCGTTTTACCGG 59.967 61.111 0.00 0.00 39.46 5.28
893 985 3.057548 GGTGGGCGTTTTACCGGG 61.058 66.667 6.32 0.00 0.00 5.73
894 986 3.057548 GTGGGCGTTTTACCGGGG 61.058 66.667 6.32 0.00 0.00 5.73
895 987 3.568208 TGGGCGTTTTACCGGGGT 61.568 61.111 6.32 0.00 0.00 4.95
896 988 3.057548 GGGCGTTTTACCGGGGTG 61.058 66.667 6.32 0.00 0.00 4.61
897 989 3.740397 GGCGTTTTACCGGGGTGC 61.740 66.667 6.32 0.02 0.00 5.01
898 990 2.979120 GCGTTTTACCGGGGTGCA 60.979 61.111 6.32 0.00 0.00 4.57
1018 1119 1.512996 GATGGCGTCGATCCCGTCTA 61.513 60.000 15.45 0.05 34.89 2.59
1023 1124 0.315706 CGTCGATCCCGTCTAACGAC 60.316 60.000 0.00 0.00 46.05 4.34
1549 1650 0.758734 CTCCCCTGACGCCATTATCA 59.241 55.000 0.00 0.00 0.00 2.15
2116 2217 1.068121 GGCTATGGTAGGGATGCCTT 58.932 55.000 12.53 0.00 37.58 4.35
2368 2469 2.776526 AGGGGTTCACCAGTGCCA 60.777 61.111 0.00 0.00 42.91 4.92
2407 2508 3.906720 AGGTACTGTTGTCAACACTGT 57.093 42.857 14.48 13.82 37.18 3.55
2586 2687 4.511636 TGCATCTACGCATTCGCA 57.488 50.000 0.00 0.00 36.86 5.10
2706 2807 9.554724 TGTTGAACTTCGAAAATATTTATCTGC 57.445 29.630 0.01 0.00 0.00 4.26
2707 2808 9.554724 GTTGAACTTCGAAAATATTTATCTGCA 57.445 29.630 0.01 0.00 0.00 4.41
2712 2813 9.520204 ACTTCGAAAATATTTATCTGCAAATGG 57.480 29.630 0.01 0.00 30.84 3.16
2713 2814 7.928908 TCGAAAATATTTATCTGCAAATGGC 57.071 32.000 0.01 0.00 45.13 4.40
2714 2815 7.715657 TCGAAAATATTTATCTGCAAATGGCT 58.284 30.769 0.01 0.00 45.15 4.75
2715 2816 7.648908 TCGAAAATATTTATCTGCAAATGGCTG 59.351 33.333 0.01 0.00 45.15 4.85
2716 2817 7.436080 CGAAAATATTTATCTGCAAATGGCTGT 59.564 33.333 0.01 0.00 45.15 4.40
2717 2818 9.748708 GAAAATATTTATCTGCAAATGGCTGTA 57.251 29.630 0.01 0.00 45.15 2.74
2723 2824 9.754382 ATTTATCTGCAAATGGCTGTATAAAAG 57.246 29.630 0.00 0.00 45.15 2.27
2724 2825 5.581126 TCTGCAAATGGCTGTATAAAAGG 57.419 39.130 0.00 0.00 45.15 3.11
2725 2826 4.402155 TCTGCAAATGGCTGTATAAAAGGG 59.598 41.667 0.00 0.00 45.15 3.95
2726 2827 3.118811 TGCAAATGGCTGTATAAAAGGGC 60.119 43.478 0.00 0.00 45.15 5.19
2727 2828 3.118811 GCAAATGGCTGTATAAAAGGGCA 60.119 43.478 0.00 0.00 40.25 5.36
2728 2829 4.685924 CAAATGGCTGTATAAAAGGGCAG 58.314 43.478 0.00 0.00 37.64 4.85
2731 2832 1.032794 GCTGTATAAAAGGGCAGCCC 58.967 55.000 24.90 24.90 45.96 5.19
2741 2842 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
2742 2843 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
2743 2844 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
2744 2845 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
2745 2846 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
2844 2945 5.640357 TCATAAACTAAACGGCGACAAAGAT 59.360 36.000 16.62 0.00 0.00 2.40
2867 2968 3.703921 TGATATACTACTATGGCGCCCA 58.296 45.455 26.77 12.96 38.19 5.36
2868 2969 4.090819 TGATATACTACTATGGCGCCCAA 58.909 43.478 26.77 11.23 36.95 4.12
2869 2970 4.528987 TGATATACTACTATGGCGCCCAAA 59.471 41.667 26.77 5.45 36.95 3.28
2870 2971 2.902705 TACTACTATGGCGCCCAAAG 57.097 50.000 26.77 20.31 36.95 2.77
2871 2972 0.909623 ACTACTATGGCGCCCAAAGT 59.090 50.000 26.77 24.79 36.95 2.66
2872 2973 1.299541 CTACTATGGCGCCCAAAGTG 58.700 55.000 26.77 14.18 36.95 3.16
2873 2974 0.616371 TACTATGGCGCCCAAAGTGT 59.384 50.000 26.77 15.87 36.95 3.55
2874 2975 0.676782 ACTATGGCGCCCAAAGTGTC 60.677 55.000 26.77 0.00 36.95 3.67
2875 2976 0.676466 CTATGGCGCCCAAAGTGTCA 60.676 55.000 26.77 0.73 46.45 3.58
2876 2977 1.304381 ATGGCGCCCAAAGTGTCAT 60.304 52.632 26.77 3.74 46.04 3.06
2877 2978 1.376848 TGGCGCCCAAAGTGTCATA 59.623 52.632 26.77 0.00 35.12 2.15
2878 2979 0.958382 TGGCGCCCAAAGTGTCATAC 60.958 55.000 26.77 0.00 35.12 2.39
2879 2980 0.676782 GGCGCCCAAAGTGTCATACT 60.677 55.000 18.11 0.00 42.89 2.12
2880 2981 1.406341 GGCGCCCAAAGTGTCATACTA 60.406 52.381 18.11 0.00 39.18 1.82
2881 2982 1.664151 GCGCCCAAAGTGTCATACTAC 59.336 52.381 0.00 0.00 39.18 2.73
2882 2983 2.677037 GCGCCCAAAGTGTCATACTACT 60.677 50.000 0.00 0.00 39.18 2.57
2883 2984 3.429822 GCGCCCAAAGTGTCATACTACTA 60.430 47.826 0.00 0.00 39.18 1.82
2884 2985 4.739735 GCGCCCAAAGTGTCATACTACTAT 60.740 45.833 0.00 0.00 39.18 2.12
2885 2986 4.745125 CGCCCAAAGTGTCATACTACTATG 59.255 45.833 0.00 0.00 39.18 2.23
2886 2987 5.057149 GCCCAAAGTGTCATACTACTATGG 58.943 45.833 0.00 0.00 39.18 2.74
2887 2988 5.057149 CCCAAAGTGTCATACTACTATGGC 58.943 45.833 0.00 0.00 39.18 4.40
2888 2989 4.745125 CCAAAGTGTCATACTACTATGGCG 59.255 45.833 0.00 0.00 37.74 5.69
2889 2990 3.644884 AGTGTCATACTACTATGGCGC 57.355 47.619 0.00 0.00 43.21 6.53
2890 2991 2.296471 AGTGTCATACTACTATGGCGCC 59.704 50.000 22.73 22.73 43.70 6.53
2891 2992 1.616865 TGTCATACTACTATGGCGCCC 59.383 52.381 26.77 6.44 37.74 6.13
3130 3231 4.278310 ACAACAACAAAGCCTTTAGTCCT 58.722 39.130 0.00 0.00 0.00 3.85
3283 3384 5.932303 TCAAATCTTTCTTTACGGACTCCTG 59.068 40.000 0.00 0.00 0.00 3.86
3302 3403 6.719370 ACTCCTGCCATGTCAAGTTAAAAATA 59.281 34.615 0.00 0.00 0.00 1.40
3404 3505 5.104259 AGATTGGAATTGTCTCCCACTAC 57.896 43.478 0.00 0.00 34.22 2.73
3405 3506 4.785376 AGATTGGAATTGTCTCCCACTACT 59.215 41.667 0.00 0.00 34.22 2.57
3406 3507 4.553330 TTGGAATTGTCTCCCACTACTC 57.447 45.455 0.00 0.00 34.22 2.59
3407 3508 3.516586 TGGAATTGTCTCCCACTACTCA 58.483 45.455 0.00 0.00 34.22 3.41
3408 3509 3.515502 TGGAATTGTCTCCCACTACTCAG 59.484 47.826 0.00 0.00 34.22 3.35
3409 3510 3.769844 GGAATTGTCTCCCACTACTCAGA 59.230 47.826 0.00 0.00 0.00 3.27
3410 3511 4.407296 GGAATTGTCTCCCACTACTCAGAT 59.593 45.833 0.00 0.00 0.00 2.90
3411 3512 5.104735 GGAATTGTCTCCCACTACTCAGATT 60.105 44.000 0.00 0.00 0.00 2.40
3412 3513 4.808414 TTGTCTCCCACTACTCAGATTG 57.192 45.455 0.00 0.00 0.00 2.67
3413 3514 3.099905 TGTCTCCCACTACTCAGATTGG 58.900 50.000 0.00 0.00 0.00 3.16
3419 3520 4.760530 CCACTACTCAGATTGGGATTGA 57.239 45.455 0.00 0.00 0.00 2.57
3420 3521 4.701765 CCACTACTCAGATTGGGATTGAG 58.298 47.826 0.00 0.00 43.04 3.02
3421 3522 4.406972 CCACTACTCAGATTGGGATTGAGA 59.593 45.833 7.64 0.00 40.54 3.27
3422 3523 5.104776 CCACTACTCAGATTGGGATTGAGAA 60.105 44.000 7.64 0.00 40.54 2.87
3423 3524 6.047870 CACTACTCAGATTGGGATTGAGAAG 58.952 44.000 7.64 0.00 40.54 2.85
3424 3525 3.883669 ACTCAGATTGGGATTGAGAAGC 58.116 45.455 7.64 0.00 40.54 3.86
3425 3526 3.265221 ACTCAGATTGGGATTGAGAAGCA 59.735 43.478 7.64 0.00 40.54 3.91
3426 3527 4.263639 ACTCAGATTGGGATTGAGAAGCAA 60.264 41.667 7.64 0.00 40.54 3.91
3427 3528 4.665451 TCAGATTGGGATTGAGAAGCAAA 58.335 39.130 0.00 0.00 40.48 3.68
3428 3529 4.460382 TCAGATTGGGATTGAGAAGCAAAC 59.540 41.667 0.00 0.00 40.48 2.93
3429 3530 4.461781 CAGATTGGGATTGAGAAGCAAACT 59.538 41.667 0.00 0.00 40.48 2.66
3430 3531 5.649395 CAGATTGGGATTGAGAAGCAAACTA 59.351 40.000 0.00 0.00 40.48 2.24
3493 3622 2.012673 GATACGAGTACAGGGACACGT 58.987 52.381 11.63 11.63 46.18 4.49
3498 3627 0.672342 AGTACAGGGACACGTGACAC 59.328 55.000 25.01 18.49 36.39 3.67
3522 3651 6.375455 ACGACAATTTCTGGAAAGAGCAATAT 59.625 34.615 0.00 0.00 33.32 1.28
3674 3803 1.351350 GGGCAGAAGTCAGGGTTAGTT 59.649 52.381 0.00 0.00 0.00 2.24
3700 3829 2.360350 CAACTGGGCTCGCCATGT 60.360 61.111 10.51 4.85 37.98 3.21
3951 4082 5.117135 CGTCGTGTGGATTATATTAGCTGTG 59.883 44.000 0.00 0.00 0.00 3.66
3952 4083 5.983720 GTCGTGTGGATTATATTAGCTGTGT 59.016 40.000 0.00 0.00 0.00 3.72
4170 4301 5.709164 CCAGAGTTGTTGAGGATCTGAAAAT 59.291 40.000 2.20 0.00 39.80 1.82
4284 4415 4.685169 AATGCTGTTACATGTGCTACAC 57.315 40.909 9.11 6.06 34.56 2.90
4365 4496 0.180406 GGACCGTGGCATCTACCATT 59.820 55.000 0.00 0.00 43.01 3.16
4559 4690 3.551846 TGGTTTCCTTTGAAGTCCAGAC 58.448 45.455 0.00 0.00 34.04 3.51
4703 4835 1.262151 CTGCAATTGCTGTTTGGTTGC 59.738 47.619 29.37 2.00 43.93 4.17
4772 4904 5.472148 GCACAAATCCTGTCATTTCATTCA 58.528 37.500 0.00 0.00 35.47 2.57
4814 4946 2.334006 AGATGTCCCAAGTCTGAGGT 57.666 50.000 0.00 0.00 0.00 3.85
4849 4981 0.730494 GCGCTGTTGTCATTGCCTTC 60.730 55.000 0.00 0.00 0.00 3.46
5061 5193 1.522355 ATCCGAAGATGCTGTGGCG 60.522 57.895 0.00 0.00 42.25 5.69
5127 5259 4.139038 GAGATCTAGTTCTTCGGTAGCCT 58.861 47.826 4.82 0.00 0.00 4.58
5156 5288 2.821546 GCATCGCCAGTTGATGTAGTA 58.178 47.619 5.03 0.00 44.02 1.82
5312 5450 7.068341 GCTTTCTAGATTGATTGCTGATTACG 58.932 38.462 0.00 0.00 0.00 3.18
5483 5621 6.314917 AGGAAAACTGGTTGGAAAGTGATAT 58.685 36.000 0.00 0.00 0.00 1.63
5506 5644 5.604010 AAGCGAGAACAAGATTCAGAAAG 57.396 39.130 0.00 0.00 0.00 2.62
5563 5701 3.282885 GGGCAAAATCAGGAGTTCTAGG 58.717 50.000 0.00 0.00 0.00 3.02
5577 5715 1.329256 TCTAGGGCGATACAAGAGGC 58.671 55.000 0.00 0.00 0.00 4.70
5750 9422 4.016444 AGCCTTTTGTCTGAAAGTGAACA 58.984 39.130 0.00 0.00 35.37 3.18
5751 9423 4.096984 AGCCTTTTGTCTGAAAGTGAACAG 59.903 41.667 0.00 0.00 35.37 3.16
5752 9424 4.354587 CCTTTTGTCTGAAAGTGAACAGC 58.645 43.478 0.00 0.00 35.37 4.40
5753 9425 3.673746 TTTGTCTGAAAGTGAACAGCG 57.326 42.857 0.00 0.00 34.57 5.18
5754 9426 2.309528 TGTCTGAAAGTGAACAGCGT 57.690 45.000 0.00 0.00 34.57 5.07
5755 9427 2.201732 TGTCTGAAAGTGAACAGCGTC 58.798 47.619 0.00 0.00 34.57 5.19
5774 9446 4.838152 GCGATGCCTGGGAAGCGA 62.838 66.667 9.65 0.00 0.00 4.93
5902 9574 5.972935 TGAATTAACTGAAGGTGATCGCTA 58.027 37.500 6.18 0.00 0.00 4.26
5911 9583 4.020928 TGAAGGTGATCGCTAGGTGTTAAA 60.021 41.667 6.18 0.00 0.00 1.52
5938 9610 3.588569 AGATATAGTCTGGTTGGGTCCC 58.411 50.000 0.00 0.00 35.31 4.46
5955 9627 0.754217 CCCGACAACTCCCCTCGATA 60.754 60.000 0.00 0.00 0.00 2.92
5956 9628 1.329256 CCGACAACTCCCCTCGATAT 58.671 55.000 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 91 1.852895 GATGTGGACGATGTACTTCGC 59.147 52.381 25.83 19.01 42.82 4.70
107 110 4.337060 CCGCCGACAGACACACGA 62.337 66.667 0.00 0.00 0.00 4.35
148 152 2.167861 GCTCGTCGTTGATGGAGGC 61.168 63.158 0.00 0.00 0.00 4.70
380 384 2.657237 CCTTTCCAGCCGACGAGT 59.343 61.111 0.00 0.00 0.00 4.18
390 394 3.249189 AGCGCACTCCCCTTTCCA 61.249 61.111 11.47 0.00 0.00 3.53
395 401 4.400961 GAAGCAGCGCACTCCCCT 62.401 66.667 11.47 0.00 0.00 4.79
430 451 1.077357 TGGACGCCACAACCACTTT 60.077 52.632 0.00 0.00 0.00 2.66
639 686 0.179187 CGCTGTTCTCATCGTCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
644 691 0.179187 CGAGACGCTGTTCTCATCGT 60.179 55.000 7.41 0.00 46.57 3.73
676 733 2.361567 GGTACGAACGGGGATGGGT 61.362 63.158 0.00 0.00 0.00 4.51
788 875 2.602878 GAAAATCGGCTGAGTCGTGTA 58.397 47.619 6.28 0.00 30.45 2.90
831 919 1.078426 CCCAACAAGGCCCTAGACG 60.078 63.158 0.00 0.00 35.39 4.18
832 920 1.303282 CCCCAACAAGGCCCTAGAC 59.697 63.158 0.00 0.00 35.39 2.59
833 921 1.928567 CCCCCAACAAGGCCCTAGA 60.929 63.158 0.00 0.00 35.39 2.43
865 957 1.221840 CGCCCACCTGCATAAGAGT 59.778 57.895 0.00 0.00 0.00 3.24
874 966 2.329614 CCGGTAAAACGCCCACCTG 61.330 63.158 0.00 0.00 0.00 4.00
876 968 3.057548 CCCGGTAAAACGCCCACC 61.058 66.667 0.00 0.00 0.00 4.61
880 972 3.740397 GCACCCCGGTAAAACGCC 61.740 66.667 0.00 0.00 0.00 5.68
881 973 2.466520 CTTGCACCCCGGTAAAACGC 62.467 60.000 0.00 0.00 0.00 4.84
882 974 1.167781 ACTTGCACCCCGGTAAAACG 61.168 55.000 0.00 0.00 0.00 3.60
883 975 0.594602 GACTTGCACCCCGGTAAAAC 59.405 55.000 0.00 0.00 0.00 2.43
884 976 0.885596 CGACTTGCACCCCGGTAAAA 60.886 55.000 0.00 0.00 0.00 1.52
885 977 1.301874 CGACTTGCACCCCGGTAAA 60.302 57.895 0.00 0.00 0.00 2.01
886 978 2.162338 CTCGACTTGCACCCCGGTAA 62.162 60.000 0.00 0.00 0.00 2.85
887 979 2.601067 TCGACTTGCACCCCGGTA 60.601 61.111 0.00 0.00 0.00 4.02
888 980 4.003788 CTCGACTTGCACCCCGGT 62.004 66.667 0.00 0.00 0.00 5.28
889 981 3.934391 GACTCGACTTGCACCCCGG 62.934 68.421 0.00 0.00 0.00 5.73
890 982 2.432628 GACTCGACTTGCACCCCG 60.433 66.667 0.00 0.00 0.00 5.73
891 983 2.047179 GGACTCGACTTGCACCCC 60.047 66.667 0.00 0.00 0.00 4.95
892 984 2.047179 GGGACTCGACTTGCACCC 60.047 66.667 0.00 0.00 0.00 4.61
893 985 2.432628 CGGGACTCGACTTGCACC 60.433 66.667 0.00 0.00 42.43 5.01
894 986 2.649034 TCGGGACTCGACTTGCAC 59.351 61.111 0.00 0.00 43.74 4.57
1549 1650 2.434884 CGCAGCATGGAACTCCGT 60.435 61.111 0.00 0.00 39.43 4.69
1734 1835 0.295763 CAATGTCTCGCACATCGACG 59.704 55.000 0.00 0.00 45.77 5.12
1809 1910 1.225376 TGCGGGTGTGTAAGAAAGCG 61.225 55.000 0.00 0.00 0.00 4.68
2116 2217 4.035558 GTCACTCTCAATGCAAAGACAACA 59.964 41.667 0.00 0.00 0.00 3.33
2368 2469 2.444421 CTTCTCAGCTGGCCTCAATTT 58.556 47.619 15.13 0.00 0.00 1.82
2704 2805 3.118811 GCCCTTTTATACAGCCATTTGCA 60.119 43.478 0.00 0.00 44.83 4.08
2705 2806 3.118811 TGCCCTTTTATACAGCCATTTGC 60.119 43.478 0.00 0.00 41.71 3.68
2706 2807 4.685924 CTGCCCTTTTATACAGCCATTTG 58.314 43.478 0.00 0.00 0.00 2.32
2713 2814 1.308998 CGGGCTGCCCTTTTATACAG 58.691 55.000 33.39 12.34 42.67 2.74
2714 2815 0.106918 CCGGGCTGCCCTTTTATACA 60.107 55.000 33.39 0.00 42.67 2.29
2715 2816 0.106868 ACCGGGCTGCCCTTTTATAC 60.107 55.000 33.39 6.69 42.67 1.47
2716 2817 0.106918 CACCGGGCTGCCCTTTTATA 60.107 55.000 33.39 0.00 42.67 0.98
2717 2818 1.379843 CACCGGGCTGCCCTTTTAT 60.380 57.895 33.39 12.60 42.67 1.40
2718 2819 2.034999 CACCGGGCTGCCCTTTTA 59.965 61.111 33.39 0.00 42.67 1.52
2724 2825 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
2725 2826 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
2726 2827 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
2727 2828 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
2728 2829 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
2729 2830 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
2743 2844 2.182537 GCCATTTGCAAGCGGGAG 59.817 61.111 15.70 0.00 40.77 4.30
2744 2845 2.283101 AGCCATTTGCAAGCGGGA 60.283 55.556 15.70 0.00 44.83 5.14
2745 2846 1.594194 TACAGCCATTTGCAAGCGGG 61.594 55.000 15.70 12.08 44.83 6.13
2746 2847 0.457035 ATACAGCCATTTGCAAGCGG 59.543 50.000 10.99 10.99 44.83 5.52
2747 2848 1.552226 CATACAGCCATTTGCAAGCG 58.448 50.000 0.00 0.00 44.83 4.68
2748 2849 1.283736 GCATACAGCCATTTGCAAGC 58.716 50.000 0.00 0.00 44.83 4.01
2749 2850 2.658373 TGCATACAGCCATTTGCAAG 57.342 45.000 0.00 0.00 41.76 4.01
2750 2851 4.732672 TTATGCATACAGCCATTTGCAA 57.267 36.364 5.74 0.00 46.97 4.08
2844 2945 5.451354 TGGGCGCCATAGTAGTATATCATA 58.549 41.667 30.85 0.00 0.00 2.15
2867 2968 4.369182 GCGCCATAGTAGTATGACACTTT 58.631 43.478 17.61 0.00 38.76 2.66
2868 2969 3.243771 GGCGCCATAGTAGTATGACACTT 60.244 47.826 24.80 0.00 38.76 3.16
2869 2970 2.296471 GGCGCCATAGTAGTATGACACT 59.704 50.000 24.80 0.00 38.76 3.55
2870 2971 2.609737 GGGCGCCATAGTAGTATGACAC 60.610 54.545 30.85 0.00 38.76 3.67
2871 2972 1.616865 GGGCGCCATAGTAGTATGACA 59.383 52.381 30.85 0.00 38.76 3.58
2872 2973 1.616865 TGGGCGCCATAGTAGTATGAC 59.383 52.381 30.85 6.12 38.76 3.06
2873 2974 2.003937 TGGGCGCCATAGTAGTATGA 57.996 50.000 30.85 0.00 38.76 2.15
2874 2975 2.831685 TTGGGCGCCATAGTAGTATG 57.168 50.000 30.85 10.21 36.52 2.39
2875 2976 2.704065 ACTTTGGGCGCCATAGTAGTAT 59.296 45.455 30.85 2.43 42.37 2.12
2876 2977 2.112998 ACTTTGGGCGCCATAGTAGTA 58.887 47.619 30.85 2.89 42.37 1.82
2877 2978 0.909623 ACTTTGGGCGCCATAGTAGT 59.090 50.000 30.85 19.48 42.37 2.73
2878 2979 1.299541 CACTTTGGGCGCCATAGTAG 58.700 55.000 30.85 18.82 42.31 2.57
2879 2980 0.616371 ACACTTTGGGCGCCATAGTA 59.384 50.000 30.85 7.30 42.31 1.82
2880 2981 0.676782 GACACTTTGGGCGCCATAGT 60.677 55.000 30.85 23.48 44.36 2.12
2881 2982 0.676466 TGACACTTTGGGCGCCATAG 60.676 55.000 30.85 22.80 38.30 2.23
2882 2983 0.250945 TTGACACTTTGGGCGCCATA 60.251 50.000 30.85 14.39 31.53 2.74
2883 2984 1.112315 TTTGACACTTTGGGCGCCAT 61.112 50.000 30.85 4.46 31.53 4.40
2884 2985 1.112315 ATTTGACACTTTGGGCGCCA 61.112 50.000 30.85 12.04 0.00 5.69
2885 2986 0.033366 AATTTGACACTTTGGGCGCC 59.967 50.000 21.18 21.18 0.00 6.53
2886 2987 2.030274 AGTAATTTGACACTTTGGGCGC 60.030 45.455 0.00 0.00 0.00 6.53
2887 2988 3.915437 AGTAATTTGACACTTTGGGCG 57.085 42.857 0.00 0.00 0.00 6.13
2888 2989 6.509418 TCATAGTAATTTGACACTTTGGGC 57.491 37.500 0.00 0.00 0.00 5.36
2889 2990 8.511604 AGATCATAGTAATTTGACACTTTGGG 57.488 34.615 0.00 0.00 0.00 4.12
2890 2991 9.388506 AGAGATCATAGTAATTTGACACTTTGG 57.611 33.333 0.00 0.00 0.00 3.28
3130 3231 5.751586 CTCTAGCCTACCCCAAATTGTTTA 58.248 41.667 0.00 0.00 0.00 2.01
3188 3289 2.612471 GCTAGCTATCCATGTGCCAGAG 60.612 54.545 7.70 0.00 0.00 3.35
3283 3384 9.685828 TTGTAACTATTTTTAACTTGACATGGC 57.314 29.630 0.00 0.00 0.00 4.40
3313 3414 7.226325 CAGGCAATTCAAACCATTTTTAACTCA 59.774 33.333 0.00 0.00 0.00 3.41
3404 3505 3.882444 TGCTTCTCAATCCCAATCTGAG 58.118 45.455 0.00 0.00 38.34 3.35
3405 3506 4.305539 TTGCTTCTCAATCCCAATCTGA 57.694 40.909 0.00 0.00 0.00 3.27
3406 3507 4.461781 AGTTTGCTTCTCAATCCCAATCTG 59.538 41.667 0.00 0.00 34.12 2.90
3407 3508 4.670765 AGTTTGCTTCTCAATCCCAATCT 58.329 39.130 0.00 0.00 34.12 2.40
3408 3509 5.649831 AGTAGTTTGCTTCTCAATCCCAATC 59.350 40.000 0.00 0.00 34.12 2.67
3409 3510 5.574188 AGTAGTTTGCTTCTCAATCCCAAT 58.426 37.500 0.00 0.00 34.12 3.16
3410 3511 4.985538 AGTAGTTTGCTTCTCAATCCCAA 58.014 39.130 0.00 0.00 34.12 4.12
3411 3512 4.640771 AGTAGTTTGCTTCTCAATCCCA 57.359 40.909 0.00 0.00 34.12 4.37
3412 3513 5.123027 CAGAAGTAGTTTGCTTCTCAATCCC 59.877 44.000 6.47 0.00 46.76 3.85
3413 3514 5.934625 TCAGAAGTAGTTTGCTTCTCAATCC 59.065 40.000 6.47 0.00 46.76 3.01
3414 3515 6.128418 GGTCAGAAGTAGTTTGCTTCTCAATC 60.128 42.308 6.47 0.00 46.76 2.67
3415 3516 5.703130 GGTCAGAAGTAGTTTGCTTCTCAAT 59.297 40.000 6.47 0.00 46.76 2.57
3416 3517 5.057149 GGTCAGAAGTAGTTTGCTTCTCAA 58.943 41.667 6.47 0.00 46.76 3.02
3417 3518 4.345257 AGGTCAGAAGTAGTTTGCTTCTCA 59.655 41.667 6.47 0.00 46.76 3.27
3418 3519 4.888917 AGGTCAGAAGTAGTTTGCTTCTC 58.111 43.478 6.47 0.00 46.76 2.87
3420 3521 4.621886 CGTAGGTCAGAAGTAGTTTGCTTC 59.378 45.833 0.00 0.00 41.78 3.86
3421 3522 4.280174 TCGTAGGTCAGAAGTAGTTTGCTT 59.720 41.667 0.00 0.00 0.00 3.91
3422 3523 3.825014 TCGTAGGTCAGAAGTAGTTTGCT 59.175 43.478 0.00 0.00 0.00 3.91
3423 3524 4.170292 TCGTAGGTCAGAAGTAGTTTGC 57.830 45.455 0.00 0.00 0.00 3.68
3424 3525 4.621886 GCTTCGTAGGTCAGAAGTAGTTTG 59.378 45.833 6.99 0.00 44.07 2.93
3425 3526 4.280174 TGCTTCGTAGGTCAGAAGTAGTTT 59.720 41.667 6.99 0.00 44.07 2.66
3426 3527 3.825014 TGCTTCGTAGGTCAGAAGTAGTT 59.175 43.478 6.99 0.00 44.07 2.24
3427 3528 3.190953 GTGCTTCGTAGGTCAGAAGTAGT 59.809 47.826 6.99 0.00 44.07 2.73
3428 3529 3.427773 GGTGCTTCGTAGGTCAGAAGTAG 60.428 52.174 6.99 0.00 44.07 2.57
3429 3530 2.490903 GGTGCTTCGTAGGTCAGAAGTA 59.509 50.000 6.99 0.16 44.07 2.24
3430 3531 1.272769 GGTGCTTCGTAGGTCAGAAGT 59.727 52.381 6.99 0.00 44.07 3.01
3493 3622 4.447290 TCTTTCCAGAAATTGTCGTGTCA 58.553 39.130 0.00 0.00 0.00 3.58
3498 3627 4.488126 TTGCTCTTTCCAGAAATTGTCG 57.512 40.909 0.00 0.00 0.00 4.35
3627 3756 0.833287 GGCATAGGTGAAGAGGCTGA 59.167 55.000 0.00 0.00 0.00 4.26
3674 3803 2.203480 GCCCAGTTGAAGCCCACA 60.203 61.111 0.00 0.00 0.00 4.17
3821 3950 0.976641 ACTGTCATCTCCGCTTTCCA 59.023 50.000 0.00 0.00 0.00 3.53
3951 4082 2.622064 ACACAAGTTCCCAGTGAGAC 57.378 50.000 0.00 0.00 37.05 3.36
3952 4083 3.194005 GAACACAAGTTCCCAGTGAGA 57.806 47.619 0.00 0.00 46.68 3.27
4069 4200 6.645827 TCACATAAACAAATGAATGCTTGGTG 59.354 34.615 0.00 0.00 0.00 4.17
4284 4415 6.360329 AGATAAACTTTTAAAGCGTGACACG 58.640 36.000 23.43 23.43 45.88 4.49
4365 4496 3.747529 GGCTAGTACAAGCACCGTAAAAA 59.252 43.478 0.00 0.00 44.64 1.94
4703 4835 9.613428 TGGTCAAATCTATAATAAACTGGAGTG 57.387 33.333 0.00 0.00 0.00 3.51
4814 4946 1.209504 AGCGCCAAACATTCCTAGCTA 59.790 47.619 2.29 0.00 31.38 3.32
4849 4981 1.878088 AGCATAATCGCCAAGCATGAG 59.122 47.619 0.00 0.00 0.00 2.90
5061 5193 6.238759 GGCACAGATCCACAACTAATTAATCC 60.239 42.308 0.00 0.00 0.00 3.01
5156 5288 9.066892 ACAACATTTGTCAGTATGTGAAAGTAT 57.933 29.630 4.09 0.00 40.56 2.12
5312 5450 1.160137 GAGTGACACCAGCATTGTCC 58.840 55.000 0.84 2.76 42.40 4.02
5483 5621 5.120830 GCTTTCTGAATCTTGTTCTCGCTTA 59.879 40.000 0.00 0.00 0.00 3.09
5506 5644 2.222908 GCTCGAGTAAATTCAGCACTGC 60.223 50.000 15.13 0.00 0.00 4.40
5563 5701 2.596904 TAGTTGCCTCTTGTATCGCC 57.403 50.000 0.00 0.00 0.00 5.54
5577 5715 1.886542 GTTCCTGGTTGGCCTTAGTTG 59.113 52.381 3.32 0.00 35.26 3.16
5678 9350 5.510671 TGCTTTACTTTTGCTTTTCTCTCG 58.489 37.500 0.00 0.00 0.00 4.04
5750 9422 4.827087 CCAGGCATCGCTGACGCT 62.827 66.667 0.00 0.00 39.84 5.07
5752 9424 3.664025 TTCCCAGGCATCGCTGACG 62.664 63.158 0.00 0.00 34.62 4.35
5753 9425 1.817099 CTTCCCAGGCATCGCTGAC 60.817 63.158 0.00 0.00 0.00 3.51
5754 9426 2.586245 CTTCCCAGGCATCGCTGA 59.414 61.111 0.00 0.00 0.00 4.26
5755 9427 3.207669 GCTTCCCAGGCATCGCTG 61.208 66.667 0.00 0.00 0.00 5.18
5774 9446 0.815734 ATCTTCATCGGACGGTCGTT 59.184 50.000 1.43 0.00 0.00 3.85
5867 9539 6.748333 TCAGTTAATTCAAAGCTCTGATGG 57.252 37.500 0.00 0.00 0.00 3.51
5911 9583 7.235812 GGACCCAACCAGACTATATCTAAAGAT 59.764 40.741 0.00 0.00 35.15 2.40
5938 9610 3.188873 GTCTATATCGAGGGGAGTTGTCG 59.811 52.174 0.00 0.00 34.98 4.35
5955 9627 3.025322 CTGAGGACAGGTCTGGTCTAT 57.975 52.381 2.87 0.00 40.14 1.98
5956 9628 2.516227 CTGAGGACAGGTCTGGTCTA 57.484 55.000 2.87 0.00 40.14 2.59


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

AutoCloner maintained by Alex Coulton.