Multiple sequence alignment - TraesCS7D01G393100

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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 TraesCS7D01G393100 chr7D 100.000 3605 0 0 1 3605 508334745 508331141 0.000000e+00 6658.0
1 TraesCS7D01G393100 chr7B 93.801 2081 77 18 585 2629 536638804 536640868 0.000000e+00 3081.0
2 TraesCS7D01G393100 chr7B 91.626 812 43 10 2818 3605 612601921 612602731 0.000000e+00 1099.0
3 TraesCS7D01G393100 chr2B 93.268 2050 105 11 598 2629 157372338 157374372 0.000000e+00 2990.0
4 TraesCS7D01G393100 chr2D 93.695 1919 90 11 713 2611 107027337 107029244 0.000000e+00 2844.0
5 TraesCS7D01G393100 chr2D 92.857 210 12 1 2422 2631 107133596 107133802 5.850000e-78 302.0
6 TraesCS7D01G393100 chr2D 93.077 130 9 0 713 842 107136682 107136811 1.320000e-44 191.0
7 TraesCS7D01G393100 chr2D 85.714 91 11 1 585 673 107136594 107136684 1.070000e-15 95.3
8 TraesCS7D01G393100 chr7A 91.739 2070 100 25 585 2629 578716980 578719003 0.000000e+00 2809.0
9 TraesCS7D01G393100 chr7A 84.358 179 11 9 88 254 725683947 725683774 3.730000e-35 159.0
10 TraesCS7D01G393100 chr3D 97.697 912 16 4 2696 3605 611570897 611571805 0.000000e+00 1563.0
11 TraesCS7D01G393100 chr3D 79.236 602 103 15 1202 1792 448497005 448496415 2.020000e-107 399.0
12 TraesCS7D01G393100 chr3D 88.599 307 20 9 267 571 298577496 298577789 3.420000e-95 359.0
13 TraesCS7D01G393100 chr3D 84.211 152 13 5 128 269 298576649 298576799 1.750000e-28 137.0
14 TraesCS7D01G393100 chr6D 96.112 926 14 7 2696 3602 32071902 32070980 0.000000e+00 1491.0
15 TraesCS7D01G393100 chr2A 91.290 930 72 3 1703 2629 103380998 103381921 0.000000e+00 1260.0
16 TraesCS7D01G393100 chr2A 86.957 943 79 26 2696 3605 710127767 710126836 0.000000e+00 1020.0
17 TraesCS7D01G393100 chr2A 87.772 597 40 11 2804 3371 51968603 51969195 0.000000e+00 667.0
18 TraesCS7D01G393100 chr2A 92.929 297 15 2 2333 2629 103366020 103366310 9.250000e-116 427.0
19 TraesCS7D01G393100 chr2A 87.948 307 23 9 268 571 142340125 142340420 2.060000e-92 350.0
20 TraesCS7D01G393100 chr2A 87.129 303 23 10 267 564 738802120 738802411 2.680000e-86 329.0
21 TraesCS7D01G393100 chr2A 95.238 42 2 0 134 175 738801539 738801580 2.320000e-07 67.6
22 TraesCS7D01G393100 chr2A 84.507 71 3 2 209 272 142330319 142330388 3.000000e-06 63.9
23 TraesCS7D01G393100 chr2A 100.000 34 0 0 238 271 738801630 738801663 3.000000e-06 63.9
24 TraesCS7D01G393100 chr1B 91.971 822 39 11 2807 3605 658458790 658457973 0.000000e+00 1127.0
25 TraesCS7D01G393100 chr1B 83.895 267 20 11 267 531 486350932 486350687 2.160000e-57 233.0
26 TraesCS7D01G393100 chr1B 80.255 157 14 5 128 268 486351572 486351417 6.370000e-18 102.0
27 TraesCS7D01G393100 chr6A 91.768 826 36 10 2804 3605 133812432 133813249 0.000000e+00 1120.0
28 TraesCS7D01G393100 chr6A 83.172 309 20 17 267 571 79405836 79405556 1.660000e-63 254.0
29 TraesCS7D01G393100 chr6A 95.556 45 2 0 134 178 79406402 79406358 4.990000e-09 73.1
30 TraesCS7D01G393100 chr4B 91.415 827 42 10 2804 3605 665212083 665212905 0.000000e+00 1107.0
31 TraesCS7D01G393100 chr4B 91.592 785 41 6 2807 3568 604538749 604537967 0.000000e+00 1061.0
32 TraesCS7D01G393100 chr4B 86.039 308 19 12 267 571 12612491 12612777 3.500000e-80 309.0
33 TraesCS7D01G393100 chr4B 74.603 378 87 8 1421 1795 653210351 653210722 1.340000e-34 158.0
34 TraesCS7D01G393100 chr5A 90.756 833 42 13 2804 3605 606183281 606184109 0.000000e+00 1079.0
35 TraesCS7D01G393100 chr5A 87.900 281 21 8 263 541 113585735 113585466 5.810000e-83 318.0
36 TraesCS7D01G393100 chr5A 94.167 120 6 1 2696 2814 606183120 606183239 7.950000e-42 182.0
37 TraesCS7D01G393100 chr5A 83.696 92 6 2 191 273 113586237 113586146 1.070000e-10 78.7
38 TraesCS7D01G393100 chr1A 89.442 824 46 14 2807 3605 521868205 521867398 0.000000e+00 1002.0
39 TraesCS7D01G393100 chr1A 83.226 310 23 16 267 571 494389603 494389888 1.280000e-64 257.0
40 TraesCS7D01G393100 chr1A 90.647 139 8 5 2696 2832 521868366 521868231 2.860000e-41 180.0
41 TraesCS7D01G393100 chr1A 92.683 41 3 0 128 168 494388736 494388776 3.890000e-05 60.2
42 TraesCS7D01G393100 chr4A 97.426 272 6 1 1 271 698195102 698195373 2.540000e-126 462.0
43 TraesCS7D01G393100 chr4A 94.079 304 11 2 267 570 698202545 698202841 4.240000e-124 455.0
44 TraesCS7D01G393100 chr3A 79.236 602 103 15 1202 1792 589826413 589825823 2.020000e-107 399.0
45 TraesCS7D01G393100 chr3B 78.738 602 108 15 1202 1793 588696522 588695931 5.650000e-103 385.0
46 TraesCS7D01G393100 chr3B 95.122 41 0 1 128 166 384329299 384329339 3.000000e-06 63.9
47 TraesCS7D01G393100 chr6B 85.390 308 32 10 267 571 189221691 189221394 1.260000e-79 307.0
48 TraesCS7D01G393100 chr6B 82.468 154 17 5 128 272 189235063 189234911 3.780000e-25 126.0
49 TraesCS7D01G393100 chr5B 85.065 154 13 4 128 272 679047731 679047579 8.060000e-32 148.0
50 TraesCS7D01G393100 chrUn 73.684 380 87 11 1421 1795 126798420 126798791 6.280000e-28 135.0


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 TraesCS7D01G393100 chr7D 508331141 508334745 3604 True 6658.0 6658 100.0000 1 3605 1 chr7D.!!$R1 3604
1 TraesCS7D01G393100 chr7B 536638804 536640868 2064 False 3081.0 3081 93.8010 585 2629 1 chr7B.!!$F1 2044
2 TraesCS7D01G393100 chr7B 612601921 612602731 810 False 1099.0 1099 91.6260 2818 3605 1 chr7B.!!$F2 787
3 TraesCS7D01G393100 chr2B 157372338 157374372 2034 False 2990.0 2990 93.2680 598 2629 1 chr2B.!!$F1 2031
4 TraesCS7D01G393100 chr2D 107027337 107029244 1907 False 2844.0 2844 93.6950 713 2611 1 chr2D.!!$F1 1898
5 TraesCS7D01G393100 chr7A 578716980 578719003 2023 False 2809.0 2809 91.7390 585 2629 1 chr7A.!!$F1 2044
6 TraesCS7D01G393100 chr3D 611570897 611571805 908 False 1563.0 1563 97.6970 2696 3605 1 chr3D.!!$F1 909
7 TraesCS7D01G393100 chr3D 448496415 448497005 590 True 399.0 399 79.2360 1202 1792 1 chr3D.!!$R1 590
8 TraesCS7D01G393100 chr3D 298576649 298577789 1140 False 248.0 359 86.4050 128 571 2 chr3D.!!$F2 443
9 TraesCS7D01G393100 chr6D 32070980 32071902 922 True 1491.0 1491 96.1120 2696 3602 1 chr6D.!!$R1 906
10 TraesCS7D01G393100 chr2A 103380998 103381921 923 False 1260.0 1260 91.2900 1703 2629 1 chr2A.!!$F3 926
11 TraesCS7D01G393100 chr2A 710126836 710127767 931 True 1020.0 1020 86.9570 2696 3605 1 chr2A.!!$R1 909
12 TraesCS7D01G393100 chr2A 51968603 51969195 592 False 667.0 667 87.7720 2804 3371 1 chr2A.!!$F1 567
13 TraesCS7D01G393100 chr1B 658457973 658458790 817 True 1127.0 1127 91.9710 2807 3605 1 chr1B.!!$R1 798
14 TraesCS7D01G393100 chr6A 133812432 133813249 817 False 1120.0 1120 91.7680 2804 3605 1 chr6A.!!$F1 801
15 TraesCS7D01G393100 chr4B 665212083 665212905 822 False 1107.0 1107 91.4150 2804 3605 1 chr4B.!!$F3 801
16 TraesCS7D01G393100 chr4B 604537967 604538749 782 True 1061.0 1061 91.5920 2807 3568 1 chr4B.!!$R1 761
17 TraesCS7D01G393100 chr5A 606183120 606184109 989 False 630.5 1079 92.4615 2696 3605 2 chr5A.!!$F1 909
18 TraesCS7D01G393100 chr1A 521867398 521868366 968 True 591.0 1002 90.0445 2696 3605 2 chr1A.!!$R1 909
19 TraesCS7D01G393100 chr3A 589825823 589826413 590 True 399.0 399 79.2360 1202 1792 1 chr3A.!!$R1 590
20 TraesCS7D01G393100 chr3B 588695931 588696522 591 True 385.0 385 78.7380 1202 1793 1 chr3B.!!$R1 591

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
353 1063 0.034477 AGGGATTTCGTGCGGGATTT 60.034 50.0 0.00 0.0 0.0 2.17 F
2019 2786 0.030235 CGACGCTATGGTCCATCGAA 59.970 55.0 17.35 0.0 33.3 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 3083 0.618968 AGAACCTCTCCGGCCTGAAT 60.619 55.0 0.0 0.0 35.61 2.57 R
3365 4297 1.831652 AACTGAGAGACAAGCGGGGG 61.832 60.0 0.0 0.0 0.00 5.40 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
25 26 6.395426 AGAAAAAGATGTTGCTCATGAACA 57.605 33.333 1.34 1.34 36.83 3.18
26 27 6.211515 AGAAAAAGATGTTGCTCATGAACAC 58.788 36.000 0.00 0.00 36.18 3.32
27 28 5.518848 AAAAGATGTTGCTCATGAACACA 57.481 34.783 0.00 1.12 36.18 3.72
28 29 5.518848 AAAGATGTTGCTCATGAACACAA 57.481 34.783 0.00 0.00 36.18 3.33
29 30 5.518848 AAGATGTTGCTCATGAACACAAA 57.481 34.783 0.00 0.00 36.18 2.83
30 31 5.717078 AGATGTTGCTCATGAACACAAAT 57.283 34.783 0.00 0.00 36.18 2.32
31 32 5.466819 AGATGTTGCTCATGAACACAAATG 58.533 37.500 0.00 0.00 36.18 2.32
32 33 3.382855 TGTTGCTCATGAACACAAATGC 58.617 40.909 0.00 0.00 0.00 3.56
33 34 3.068448 TGTTGCTCATGAACACAAATGCT 59.932 39.130 0.00 0.00 0.00 3.79
34 35 3.291809 TGCTCATGAACACAAATGCTG 57.708 42.857 0.00 0.00 0.00 4.41
35 36 2.885894 TGCTCATGAACACAAATGCTGA 59.114 40.909 0.00 0.00 0.00 4.26
36 37 3.318557 TGCTCATGAACACAAATGCTGAA 59.681 39.130 0.00 0.00 0.00 3.02
37 38 3.671928 GCTCATGAACACAAATGCTGAAC 59.328 43.478 0.00 0.00 0.00 3.18
38 39 4.793678 GCTCATGAACACAAATGCTGAACA 60.794 41.667 0.00 0.00 0.00 3.18
39 40 4.609947 TCATGAACACAAATGCTGAACAC 58.390 39.130 0.00 0.00 0.00 3.32
40 41 4.097589 TCATGAACACAAATGCTGAACACA 59.902 37.500 0.00 0.00 0.00 3.72
41 42 4.031418 TGAACACAAATGCTGAACACAG 57.969 40.909 0.00 0.00 35.06 3.66
42 43 3.693578 TGAACACAAATGCTGAACACAGA 59.306 39.130 0.00 0.00 33.94 3.41
43 44 4.338964 TGAACACAAATGCTGAACACAGAT 59.661 37.500 0.00 0.00 33.94 2.90
44 45 4.233123 ACACAAATGCTGAACACAGATG 57.767 40.909 0.00 0.00 33.94 2.90
45 46 3.633525 ACACAAATGCTGAACACAGATGT 59.366 39.130 0.00 0.00 42.46 3.06
59 60 6.119144 ACACAGATGTTACAGTGTTTTCAC 57.881 37.500 0.00 0.00 42.06 3.18
71 72 4.840401 GTGTTTTCACTGCTGGAAAAAC 57.160 40.909 19.63 19.63 43.52 2.43
72 73 4.241681 GTGTTTTCACTGCTGGAAAAACA 58.758 39.130 22.66 22.66 43.52 2.83
73 74 4.869861 GTGTTTTCACTGCTGGAAAAACAT 59.130 37.500 26.02 0.00 43.52 2.71
74 75 4.869297 TGTTTTCACTGCTGGAAAAACATG 59.131 37.500 22.66 0.00 43.52 3.21
75 76 2.798976 TCACTGCTGGAAAAACATGC 57.201 45.000 0.00 0.00 0.00 4.06
76 77 2.309613 TCACTGCTGGAAAAACATGCT 58.690 42.857 0.00 0.00 0.00 3.79
77 78 2.034939 TCACTGCTGGAAAAACATGCTG 59.965 45.455 0.00 0.00 0.00 4.41
78 79 2.034939 CACTGCTGGAAAAACATGCTGA 59.965 45.455 0.00 0.00 0.00 4.26
79 80 2.035066 ACTGCTGGAAAAACATGCTGAC 59.965 45.455 0.00 0.00 0.00 3.51
80 81 1.340889 TGCTGGAAAAACATGCTGACC 59.659 47.619 0.00 0.00 0.00 4.02
81 82 1.340889 GCTGGAAAAACATGCTGACCA 59.659 47.619 0.00 0.00 0.00 4.02
82 83 2.863704 GCTGGAAAAACATGCTGACCAC 60.864 50.000 0.00 0.00 0.00 4.16
83 84 2.361757 CTGGAAAAACATGCTGACCACA 59.638 45.455 0.00 0.00 0.00 4.17
84 85 2.762887 TGGAAAAACATGCTGACCACAA 59.237 40.909 0.00 0.00 0.00 3.33
85 86 3.196469 TGGAAAAACATGCTGACCACAAA 59.804 39.130 0.00 0.00 0.00 2.83
86 87 3.555547 GGAAAAACATGCTGACCACAAAC 59.444 43.478 0.00 0.00 0.00 2.93
87 88 2.888834 AAACATGCTGACCACAAACC 57.111 45.000 0.00 0.00 0.00 3.27
88 89 1.039856 AACATGCTGACCACAAACCC 58.960 50.000 0.00 0.00 0.00 4.11
89 90 0.827507 ACATGCTGACCACAAACCCC 60.828 55.000 0.00 0.00 0.00 4.95
90 91 0.540365 CATGCTGACCACAAACCCCT 60.540 55.000 0.00 0.00 0.00 4.79
91 92 1.072266 ATGCTGACCACAAACCCCTA 58.928 50.000 0.00 0.00 0.00 3.53
92 93 0.109723 TGCTGACCACAAACCCCTAC 59.890 55.000 0.00 0.00 0.00 3.18
93 94 0.400594 GCTGACCACAAACCCCTACT 59.599 55.000 0.00 0.00 0.00 2.57
94 95 1.202891 GCTGACCACAAACCCCTACTT 60.203 52.381 0.00 0.00 0.00 2.24
95 96 2.779506 CTGACCACAAACCCCTACTTC 58.220 52.381 0.00 0.00 0.00 3.01
96 97 2.372172 CTGACCACAAACCCCTACTTCT 59.628 50.000 0.00 0.00 0.00 2.85
97 98 2.105821 TGACCACAAACCCCTACTTCTG 59.894 50.000 0.00 0.00 0.00 3.02
98 99 2.105993 GACCACAAACCCCTACTTCTGT 59.894 50.000 0.00 0.00 0.00 3.41
99 100 2.512476 ACCACAAACCCCTACTTCTGTT 59.488 45.455 0.00 0.00 0.00 3.16
100 101 3.146847 CCACAAACCCCTACTTCTGTTC 58.853 50.000 0.00 0.00 0.00 3.18
101 102 3.146847 CACAAACCCCTACTTCTGTTCC 58.853 50.000 0.00 0.00 0.00 3.62
102 103 2.107726 ACAAACCCCTACTTCTGTTCCC 59.892 50.000 0.00 0.00 0.00 3.97
103 104 2.107552 CAAACCCCTACTTCTGTTCCCA 59.892 50.000 0.00 0.00 0.00 4.37
104 105 2.127651 ACCCCTACTTCTGTTCCCAA 57.872 50.000 0.00 0.00 0.00 4.12
105 106 2.424793 ACCCCTACTTCTGTTCCCAAA 58.575 47.619 0.00 0.00 0.00 3.28
106 107 2.107726 ACCCCTACTTCTGTTCCCAAAC 59.892 50.000 0.00 0.00 35.85 2.93
107 108 2.375509 CCCCTACTTCTGTTCCCAAACT 59.624 50.000 0.00 0.00 36.30 2.66
108 109 3.585732 CCCCTACTTCTGTTCCCAAACTA 59.414 47.826 0.00 0.00 36.30 2.24
109 110 4.323562 CCCCTACTTCTGTTCCCAAACTAG 60.324 50.000 0.00 0.00 36.30 2.57
110 111 4.530946 CCCTACTTCTGTTCCCAAACTAGA 59.469 45.833 0.00 0.00 36.30 2.43
111 112 5.480205 CCTACTTCTGTTCCCAAACTAGAC 58.520 45.833 0.00 0.00 36.30 2.59
112 113 5.011738 CCTACTTCTGTTCCCAAACTAGACA 59.988 44.000 0.00 0.00 36.30 3.41
113 114 4.704965 ACTTCTGTTCCCAAACTAGACAC 58.295 43.478 0.00 0.00 36.30 3.67
114 115 4.163458 ACTTCTGTTCCCAAACTAGACACA 59.837 41.667 0.00 0.00 36.30 3.72
115 116 4.764050 TCTGTTCCCAAACTAGACACAA 57.236 40.909 0.00 0.00 36.30 3.33
116 117 5.105567 TCTGTTCCCAAACTAGACACAAA 57.894 39.130 0.00 0.00 36.30 2.83
117 118 5.690865 TCTGTTCCCAAACTAGACACAAAT 58.309 37.500 0.00 0.00 36.30 2.32
118 119 5.530915 TCTGTTCCCAAACTAGACACAAATG 59.469 40.000 0.00 0.00 36.30 2.32
119 120 4.037446 TGTTCCCAAACTAGACACAAATGC 59.963 41.667 0.00 0.00 36.30 3.56
120 121 4.098914 TCCCAAACTAGACACAAATGCT 57.901 40.909 0.00 0.00 0.00 3.79
121 122 3.820467 TCCCAAACTAGACACAAATGCTG 59.180 43.478 0.00 0.00 0.00 4.41
122 123 3.820467 CCCAAACTAGACACAAATGCTGA 59.180 43.478 0.00 0.00 0.00 4.26
123 124 4.278170 CCCAAACTAGACACAAATGCTGAA 59.722 41.667 0.00 0.00 0.00 3.02
124 125 5.221224 CCCAAACTAGACACAAATGCTGAAA 60.221 40.000 0.00 0.00 0.00 2.69
125 126 6.272318 CCAAACTAGACACAAATGCTGAAAA 58.728 36.000 0.00 0.00 0.00 2.29
126 127 6.756074 CCAAACTAGACACAAATGCTGAAAAA 59.244 34.615 0.00 0.00 0.00 1.94
178 179 7.928167 TGAAACACAGATATATTGCCTACAGAG 59.072 37.037 0.00 0.00 0.00 3.35
180 181 5.541868 ACACAGATATATTGCCTACAGAGCT 59.458 40.000 0.00 0.00 0.00 4.09
181 182 6.042552 ACACAGATATATTGCCTACAGAGCTT 59.957 38.462 0.00 0.00 0.00 3.74
182 183 7.233553 ACACAGATATATTGCCTACAGAGCTTA 59.766 37.037 0.00 0.00 0.00 3.09
183 184 7.543868 CACAGATATATTGCCTACAGAGCTTAC 59.456 40.741 0.00 0.00 0.00 2.34
185 186 7.758980 CAGATATATTGCCTACAGAGCTTACAG 59.241 40.741 0.00 0.00 0.00 2.74
189 190 4.617253 TGCCTACAGAGCTTACAGAAAA 57.383 40.909 0.00 0.00 0.00 2.29
196 197 7.443575 CCTACAGAGCTTACAGAAAATGCATAT 59.556 37.037 0.00 0.00 0.00 1.78
206 209 6.392354 ACAGAAAATGCATATTGAACCACAG 58.608 36.000 0.00 0.00 0.00 3.66
282 991 1.079681 ACCCGCGCTCGTTGAATTA 60.080 52.632 5.56 0.00 0.00 1.40
283 992 1.082117 ACCCGCGCTCGTTGAATTAG 61.082 55.000 5.56 0.00 0.00 1.73
291 1000 2.526688 GCTCGTTGAATTAGACTCGTCG 59.473 50.000 0.00 0.00 34.09 5.12
297 1006 1.664321 AATTAGACTCGTCGCCGGCT 61.664 55.000 26.68 3.45 33.95 5.52
298 1007 2.061182 ATTAGACTCGTCGCCGGCTC 62.061 60.000 26.68 14.27 33.95 4.70
299 1008 3.677284 TAGACTCGTCGCCGGCTCT 62.677 63.158 26.68 20.98 33.95 4.09
300 1009 4.539881 GACTCGTCGCCGGCTCTC 62.540 72.222 26.68 13.30 33.95 3.20
302 1011 4.244802 CTCGTCGCCGGCTCTCTC 62.245 72.222 26.68 8.86 33.95 3.20
346 1055 0.931005 CGAAGCTAGGGATTTCGTGC 59.069 55.000 0.00 0.00 38.96 5.34
348 1057 0.462047 AAGCTAGGGATTTCGTGCGG 60.462 55.000 0.00 0.00 0.00 5.69
353 1063 0.034477 AGGGATTTCGTGCGGGATTT 60.034 50.000 0.00 0.00 0.00 2.17
378 1088 3.775654 GCCGGGAGAGGGTGTGAG 61.776 72.222 2.18 0.00 0.00 3.51
379 1089 3.077556 CCGGGAGAGGGTGTGAGG 61.078 72.222 0.00 0.00 0.00 3.86
380 1090 3.077556 CGGGAGAGGGTGTGAGGG 61.078 72.222 0.00 0.00 0.00 4.30
381 1091 2.122954 GGGAGAGGGTGTGAGGGT 59.877 66.667 0.00 0.00 0.00 4.34
382 1092 2.294078 GGGAGAGGGTGTGAGGGTG 61.294 68.421 0.00 0.00 0.00 4.61
386 1096 3.864983 GAGGGTGTGAGGGTGGGGA 62.865 68.421 0.00 0.00 0.00 4.81
388 1098 2.434774 GGTGTGAGGGTGGGGAAC 59.565 66.667 0.00 0.00 0.00 3.62
412 1122 2.365617 GGAAACGGCAGGATAGATGAGA 59.634 50.000 0.00 0.00 0.00 3.27
413 1123 3.181465 GGAAACGGCAGGATAGATGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
425 1135 2.010582 GATGAGAAGGCGCGTCTCCT 62.011 60.000 27.36 21.21 40.77 3.69
437 1147 3.781280 GCGCGTCTCCTAAAATTTCGAAG 60.781 47.826 8.43 0.00 0.00 3.79
438 1148 3.671256 GCGTCTCCTAAAATTTCGAAGC 58.329 45.455 0.00 0.00 0.00 3.86
441 1151 4.490479 CGTCTCCTAAAATTTCGAAGCGAC 60.490 45.833 0.00 0.00 34.89 5.19
443 1153 3.004862 TCCTAAAATTTCGAAGCGACCC 58.995 45.455 0.00 0.00 34.89 4.46
444 1154 2.222953 CCTAAAATTTCGAAGCGACCCG 60.223 50.000 0.00 0.00 34.89 5.28
446 1156 0.794473 AAATTTCGAAGCGACCCGAC 59.206 50.000 0.00 0.00 34.89 4.79
447 1157 0.320073 AATTTCGAAGCGACCCGACA 60.320 50.000 0.00 0.00 34.89 4.35
449 1159 0.530211 TTTCGAAGCGACCCGACAAA 60.530 50.000 0.00 0.00 34.89 2.83
450 1160 0.530211 TTCGAAGCGACCCGACAAAA 60.530 50.000 0.00 0.00 34.89 2.44
451 1161 0.530211 TCGAAGCGACCCGACAAAAA 60.530 50.000 0.00 0.00 0.00 1.94
465 1175 2.280753 AAAAACCACCGCCCACCT 59.719 55.556 0.00 0.00 0.00 4.00
466 1176 2.131067 AAAAACCACCGCCCACCTG 61.131 57.895 0.00 0.00 0.00 4.00
467 1177 4.596585 AAACCACCGCCCACCTGG 62.597 66.667 0.00 0.00 37.09 4.45
476 1186 4.016706 CCCACCTGGTCGGTCCAC 62.017 72.222 1.83 0.00 44.93 4.02
477 1187 4.016706 CCACCTGGTCGGTCCACC 62.017 72.222 0.00 4.09 44.93 4.61
478 1188 3.238497 CACCTGGTCGGTCCACCA 61.238 66.667 11.34 11.34 44.93 4.17
484 1194 4.699522 GTCGGTCCACCAGGCCAC 62.700 72.222 5.01 0.00 35.14 5.01
488 1198 4.250305 GTCCACCAGGCCACGTGT 62.250 66.667 15.65 1.57 33.74 4.49
489 1199 3.936203 TCCACCAGGCCACGTGTC 61.936 66.667 15.65 0.00 33.74 3.67
490 1200 3.941188 CCACCAGGCCACGTGTCT 61.941 66.667 15.65 8.80 0.00 3.41
491 1201 2.666190 CACCAGGCCACGTGTCTG 60.666 66.667 21.86 21.86 0.00 3.51
492 1202 3.161450 ACCAGGCCACGTGTCTGT 61.161 61.111 24.71 15.21 0.00 3.41
493 1203 2.666190 CCAGGCCACGTGTCTGTG 60.666 66.667 24.71 16.60 39.60 3.66
494 1204 2.421314 CAGGCCACGTGTCTGTGA 59.579 61.111 21.02 0.00 42.55 3.58
495 1205 1.665916 CAGGCCACGTGTCTGTGAG 60.666 63.158 21.02 4.99 42.55 3.51
496 1206 2.357517 GGCCACGTGTCTGTGAGG 60.358 66.667 15.65 0.00 42.55 3.86
497 1207 2.357517 GCCACGTGTCTGTGAGGG 60.358 66.667 15.65 0.00 42.55 4.30
498 1208 3.138625 CCACGTGTCTGTGAGGGT 58.861 61.111 15.65 0.00 42.55 4.34
499 1209 1.006102 CCACGTGTCTGTGAGGGTC 60.006 63.158 15.65 0.00 42.55 4.46
500 1210 1.371758 CACGTGTCTGTGAGGGTCG 60.372 63.158 7.58 0.00 42.55 4.79
501 1211 2.430921 CGTGTCTGTGAGGGTCGC 60.431 66.667 0.00 0.00 0.00 5.19
502 1212 2.430921 GTGTCTGTGAGGGTCGCG 60.431 66.667 0.00 0.00 0.00 5.87
503 1213 4.357947 TGTCTGTGAGGGTCGCGC 62.358 66.667 0.00 0.00 0.00 6.86
508 1218 4.194720 GTGAGGGTCGCGCGAGAT 62.195 66.667 35.75 22.04 0.00 2.75
509 1219 3.889044 TGAGGGTCGCGCGAGATC 61.889 66.667 35.75 28.62 0.00 2.75
510 1220 4.965858 GAGGGTCGCGCGAGATCG 62.966 72.222 35.75 6.68 43.27 3.69
518 1228 4.219846 CGCGAGATCGACGGTCGT 62.220 66.667 27.53 16.27 41.35 4.34
519 1229 2.648102 GCGAGATCGACGGTCGTG 60.648 66.667 27.53 15.18 41.35 4.35
520 1230 2.022902 CGAGATCGACGGTCGTGG 59.977 66.667 27.53 8.63 41.35 4.94
521 1231 2.747822 CGAGATCGACGGTCGTGGT 61.748 63.158 27.53 16.06 41.35 4.16
522 1232 1.226323 GAGATCGACGGTCGTGGTG 60.226 63.158 27.53 2.09 41.35 4.17
523 1233 2.879462 GATCGACGGTCGTGGTGC 60.879 66.667 27.53 11.53 41.35 5.01
524 1234 4.771356 ATCGACGGTCGTGGTGCG 62.771 66.667 27.53 3.65 41.35 5.34
545 1255 4.326153 GCTGCATCGCGTCTGATA 57.674 55.556 5.77 0.00 0.00 2.15
546 1256 2.140066 GCTGCATCGCGTCTGATAG 58.860 57.895 5.77 8.54 0.00 2.08
547 1257 1.884769 GCTGCATCGCGTCTGATAGC 61.885 60.000 5.77 14.00 0.00 2.97
571 1281 2.434185 GCACCGGACAGCGATTGA 60.434 61.111 9.46 0.00 0.00 2.57
572 1282 2.032634 GCACCGGACAGCGATTGAA 61.033 57.895 9.46 0.00 0.00 2.69
573 1283 1.573829 GCACCGGACAGCGATTGAAA 61.574 55.000 9.46 0.00 0.00 2.69
574 1284 0.871722 CACCGGACAGCGATTGAAAA 59.128 50.000 9.46 0.00 0.00 2.29
575 1285 1.265635 CACCGGACAGCGATTGAAAAA 59.734 47.619 9.46 0.00 0.00 1.94
676 1395 1.267806 CAACCAGCGCAGTCTCAATTT 59.732 47.619 11.47 0.00 0.00 1.82
693 1412 1.444119 TTTTGACCACACAGGAGCGC 61.444 55.000 0.00 0.00 41.22 5.92
722 1441 3.825014 GGTGCATCTATCTCATGGCAAAT 59.175 43.478 0.00 0.00 0.00 2.32
809 1536 1.261989 CATCAACTTTTGCCGCATCG 58.738 50.000 0.00 0.00 0.00 3.84
931 1675 0.732571 ACGTTCACAGCAACCAACAG 59.267 50.000 0.00 0.00 0.00 3.16
949 1696 0.545171 AGCATAGCATCAGCACCAGT 59.455 50.000 0.00 0.00 45.49 4.00
991 1755 2.811317 AAGCTAGCACTCGCGCAC 60.811 61.111 18.83 0.00 45.49 5.34
1067 1831 3.735181 CCGTGTACTGGCTCCTTAC 57.265 57.895 0.00 0.00 0.00 2.34
1248 2012 0.834687 ACCTCAACCACCGCTTCCTA 60.835 55.000 0.00 0.00 0.00 2.94
1326 2090 2.147387 GGTGGTGGTGTCAGACCCT 61.147 63.158 0.00 0.00 45.45 4.34
1328 2092 1.074850 TGGTGGTGTCAGACCCTCA 60.075 57.895 0.00 0.47 45.45 3.86
1971 2738 3.364062 GGAGAACGTGATCTACATCGTG 58.636 50.000 0.00 0.00 36.77 4.35
1989 2756 1.069227 GTGGAGAACATCAACGTTGCC 60.069 52.381 23.47 16.31 0.00 4.52
2019 2786 0.030235 CGACGCTATGGTCCATCGAA 59.970 55.000 17.35 0.00 33.30 3.71
2121 2888 1.224592 GCCCATCACCGAGTCCAAT 59.775 57.895 0.00 0.00 0.00 3.16
2259 3026 2.036256 CCCAAGGGCTCCAAGGTG 59.964 66.667 0.00 0.00 0.00 4.00
2262 3029 1.604593 CAAGGGCTCCAAGGTGGTG 60.605 63.158 0.00 0.00 39.03 4.17
2359 3126 1.666011 GAGGAGAGCAACGTGGACA 59.334 57.895 0.00 0.00 0.00 4.02
2620 3393 3.756434 ACCATGACCAATTACTTCAACCG 59.244 43.478 0.00 0.00 0.00 4.44
2629 3402 5.182380 CCAATTACTTCAACCGAAAAGCCTA 59.818 40.000 0.00 0.00 0.00 3.93
2630 3403 5.874895 ATTACTTCAACCGAAAAGCCTAC 57.125 39.130 0.00 0.00 0.00 3.18
2631 3404 3.202829 ACTTCAACCGAAAAGCCTACA 57.797 42.857 0.00 0.00 0.00 2.74
2632 3405 2.876550 ACTTCAACCGAAAAGCCTACAC 59.123 45.455 0.00 0.00 0.00 2.90
2633 3406 1.504359 TCAACCGAAAAGCCTACACG 58.496 50.000 0.00 0.00 0.00 4.49
2643 3416 2.202703 CCTACACGGCTACACGGC 60.203 66.667 0.00 0.00 38.39 5.68
2644 3417 2.707849 CCTACACGGCTACACGGCT 61.708 63.158 0.00 0.00 38.39 5.52
2645 3418 1.378882 CCTACACGGCTACACGGCTA 61.379 60.000 0.00 0.00 38.39 3.93
2646 3419 0.248377 CTACACGGCTACACGGCTAC 60.248 60.000 0.00 0.00 38.39 3.58
2647 3420 0.959867 TACACGGCTACACGGCTACA 60.960 55.000 0.00 0.00 38.39 2.74
2648 3421 1.804326 CACGGCTACACGGCTACAC 60.804 63.158 0.00 0.00 38.39 2.90
2649 3422 2.578713 CGGCTACACGGCTACACG 60.579 66.667 0.00 0.00 40.31 4.49
2650 3423 2.884207 GGCTACACGGCTACACGC 60.884 66.667 0.00 0.00 37.37 5.34
2651 3424 2.126228 GCTACACGGCTACACGCA 60.126 61.111 0.00 0.00 41.67 5.24
2652 3425 2.442188 GCTACACGGCTACACGCAC 61.442 63.158 0.00 0.00 41.67 5.34
2653 3426 1.081041 CTACACGGCTACACGCACA 60.081 57.895 0.00 0.00 41.67 4.57
2654 3427 0.665068 CTACACGGCTACACGCACAA 60.665 55.000 0.00 0.00 41.67 3.33
2655 3428 0.038067 TACACGGCTACACGCACAAT 60.038 50.000 0.00 0.00 41.67 2.71
2656 3429 0.882927 ACACGGCTACACGCACAATT 60.883 50.000 0.00 0.00 41.67 2.32
2657 3430 1.072391 CACGGCTACACGCACAATTA 58.928 50.000 0.00 0.00 41.67 1.40
2658 3431 1.073177 ACGGCTACACGCACAATTAC 58.927 50.000 0.00 0.00 41.67 1.89
2659 3432 1.337447 ACGGCTACACGCACAATTACT 60.337 47.619 0.00 0.00 41.67 2.24
2660 3433 1.323534 CGGCTACACGCACAATTACTC 59.676 52.381 0.00 0.00 41.67 2.59
2661 3434 2.618053 GGCTACACGCACAATTACTCT 58.382 47.619 0.00 0.00 41.67 3.24
2662 3435 3.000727 GGCTACACGCACAATTACTCTT 58.999 45.455 0.00 0.00 41.67 2.85
2663 3436 3.062234 GGCTACACGCACAATTACTCTTC 59.938 47.826 0.00 0.00 41.67 2.87
2664 3437 3.927142 GCTACACGCACAATTACTCTTCT 59.073 43.478 0.00 0.00 38.92 2.85
2665 3438 4.031878 GCTACACGCACAATTACTCTTCTC 59.968 45.833 0.00 0.00 38.92 2.87
2666 3439 2.987149 ACACGCACAATTACTCTTCTCG 59.013 45.455 0.00 0.00 0.00 4.04
2667 3440 2.345641 CACGCACAATTACTCTTCTCGG 59.654 50.000 0.00 0.00 0.00 4.63
2668 3441 1.927174 CGCACAATTACTCTTCTCGGG 59.073 52.381 0.00 0.00 0.00 5.14
2669 3442 2.674177 CGCACAATTACTCTTCTCGGGT 60.674 50.000 0.00 0.00 0.00 5.28
2670 3443 3.335579 GCACAATTACTCTTCTCGGGTT 58.664 45.455 0.00 0.00 0.00 4.11
2671 3444 4.501071 GCACAATTACTCTTCTCGGGTTA 58.499 43.478 0.00 0.00 0.00 2.85
2672 3445 4.329256 GCACAATTACTCTTCTCGGGTTAC 59.671 45.833 0.00 0.00 0.00 2.50
2673 3446 5.475719 CACAATTACTCTTCTCGGGTTACA 58.524 41.667 0.00 0.00 0.00 2.41
2674 3447 5.929992 CACAATTACTCTTCTCGGGTTACAA 59.070 40.000 0.00 0.00 0.00 2.41
2675 3448 6.425721 CACAATTACTCTTCTCGGGTTACAAA 59.574 38.462 0.00 0.00 0.00 2.83
2676 3449 7.119262 CACAATTACTCTTCTCGGGTTACAAAT 59.881 37.037 0.00 0.00 0.00 2.32
2677 3450 8.316214 ACAATTACTCTTCTCGGGTTACAAATA 58.684 33.333 0.00 0.00 0.00 1.40
2678 3451 9.326413 CAATTACTCTTCTCGGGTTACAAATAT 57.674 33.333 0.00 0.00 0.00 1.28
2679 3452 8.888579 ATTACTCTTCTCGGGTTACAAATATG 57.111 34.615 0.00 0.00 0.00 1.78
2680 3453 6.295719 ACTCTTCTCGGGTTACAAATATGT 57.704 37.500 0.00 0.00 43.74 2.29
2681 3454 6.338937 ACTCTTCTCGGGTTACAAATATGTC 58.661 40.000 0.00 0.00 41.05 3.06
2682 3455 6.154706 ACTCTTCTCGGGTTACAAATATGTCT 59.845 38.462 0.00 0.00 41.05 3.41
2683 3456 7.341256 ACTCTTCTCGGGTTACAAATATGTCTA 59.659 37.037 0.00 0.00 41.05 2.59
2684 3457 7.713750 TCTTCTCGGGTTACAAATATGTCTAG 58.286 38.462 0.00 0.00 41.05 2.43
2685 3458 7.558807 TCTTCTCGGGTTACAAATATGTCTAGA 59.441 37.037 0.00 0.00 41.05 2.43
2686 3459 7.649533 TCTCGGGTTACAAATATGTCTAGAA 57.350 36.000 0.00 0.00 41.05 2.10
2687 3460 7.486647 TCTCGGGTTACAAATATGTCTAGAAC 58.513 38.462 0.00 0.00 41.05 3.01
2688 3461 7.341256 TCTCGGGTTACAAATATGTCTAGAACT 59.659 37.037 0.00 0.00 41.05 3.01
2689 3462 7.486647 TCGGGTTACAAATATGTCTAGAACTC 58.513 38.462 0.00 0.00 41.05 3.01
2690 3463 7.123098 TCGGGTTACAAATATGTCTAGAACTCA 59.877 37.037 0.00 0.00 41.05 3.41
2691 3464 7.435488 CGGGTTACAAATATGTCTAGAACTCAG 59.565 40.741 0.00 0.00 41.05 3.35
2692 3465 8.258708 GGGTTACAAATATGTCTAGAACTCAGT 58.741 37.037 0.00 0.00 41.05 3.41
2693 3466 9.303537 GGTTACAAATATGTCTAGAACTCAGTC 57.696 37.037 0.00 0.00 41.05 3.51
2694 3467 9.011407 GTTACAAATATGTCTAGAACTCAGTCG 57.989 37.037 0.00 0.00 41.05 4.18
3178 4096 9.823647 ACACAATAACACAAATCCAAAATGTAA 57.176 25.926 0.00 0.00 0.00 2.41
3364 4296 1.720694 CCTCGCCCGTTCTCTCTCTC 61.721 65.000 0.00 0.00 0.00 3.20
3365 4297 1.720694 CTCGCCCGTTCTCTCTCTCC 61.721 65.000 0.00 0.00 0.00 3.71
3428 4360 4.100189 GCCTCTAGAAAGATGTTGAGCCTA 59.900 45.833 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.536622 GTGTTCATGAGCAACATCTTTTTCTAG 59.463 37.037 14.30 0.00 36.19 2.43
1 2 7.013178 TGTGTTCATGAGCAACATCTTTTTCTA 59.987 33.333 14.30 0.00 36.19 2.10
3 4 5.978919 TGTGTTCATGAGCAACATCTTTTTC 59.021 36.000 14.30 0.00 36.19 2.29
4 5 5.904941 TGTGTTCATGAGCAACATCTTTTT 58.095 33.333 14.30 0.00 36.19 1.94
5 6 5.518848 TGTGTTCATGAGCAACATCTTTT 57.481 34.783 14.30 0.00 36.19 2.27
6 7 5.518848 TTGTGTTCATGAGCAACATCTTT 57.481 34.783 14.30 0.00 36.19 2.52
7 8 5.518848 TTTGTGTTCATGAGCAACATCTT 57.481 34.783 14.30 0.00 36.19 2.40
8 9 5.466819 CATTTGTGTTCATGAGCAACATCT 58.533 37.500 14.30 3.37 36.19 2.90
9 10 4.090930 GCATTTGTGTTCATGAGCAACATC 59.909 41.667 14.30 2.48 36.19 3.06
10 11 3.991773 GCATTTGTGTTCATGAGCAACAT 59.008 39.130 14.30 3.94 36.19 2.71
11 12 3.068448 AGCATTTGTGTTCATGAGCAACA 59.932 39.130 14.30 11.45 0.00 3.33
12 13 3.427528 CAGCATTTGTGTTCATGAGCAAC 59.572 43.478 14.30 9.11 0.00 4.17
13 14 3.318557 TCAGCATTTGTGTTCATGAGCAA 59.681 39.130 14.30 9.24 0.00 3.91
14 15 2.885894 TCAGCATTTGTGTTCATGAGCA 59.114 40.909 8.32 8.32 0.00 4.26
15 16 3.564235 TCAGCATTTGTGTTCATGAGC 57.436 42.857 2.05 2.05 0.00 4.26
16 17 4.678287 GTGTTCAGCATTTGTGTTCATGAG 59.322 41.667 0.00 0.00 0.00 2.90
17 18 4.097589 TGTGTTCAGCATTTGTGTTCATGA 59.902 37.500 0.00 0.00 0.00 3.07
18 19 4.361420 TGTGTTCAGCATTTGTGTTCATG 58.639 39.130 0.00 0.00 0.00 3.07
19 20 4.338964 TCTGTGTTCAGCATTTGTGTTCAT 59.661 37.500 0.00 0.00 41.10 2.57
20 21 3.693578 TCTGTGTTCAGCATTTGTGTTCA 59.306 39.130 0.00 0.00 41.10 3.18
21 22 4.291540 TCTGTGTTCAGCATTTGTGTTC 57.708 40.909 0.00 0.00 41.10 3.18
22 23 4.098349 ACATCTGTGTTCAGCATTTGTGTT 59.902 37.500 0.00 0.00 41.10 3.32
23 24 3.633525 ACATCTGTGTTCAGCATTTGTGT 59.366 39.130 0.00 0.00 41.10 3.72
24 25 4.233123 ACATCTGTGTTCAGCATTTGTG 57.767 40.909 0.00 0.00 41.10 3.33
25 26 4.924305 AACATCTGTGTTCAGCATTTGT 57.076 36.364 0.00 0.00 45.14 2.83
26 27 5.761003 TGTAACATCTGTGTTCAGCATTTG 58.239 37.500 0.00 0.00 45.14 2.32
27 28 5.532406 ACTGTAACATCTGTGTTCAGCATTT 59.468 36.000 14.67 0.00 45.14 2.32
28 29 5.049198 CACTGTAACATCTGTGTTCAGCATT 60.049 40.000 14.67 1.84 45.14 3.56
29 30 4.453478 CACTGTAACATCTGTGTTCAGCAT 59.547 41.667 14.67 2.22 45.14 3.79
30 31 3.809279 CACTGTAACATCTGTGTTCAGCA 59.191 43.478 14.67 6.73 45.14 4.41
31 32 3.809832 ACACTGTAACATCTGTGTTCAGC 59.190 43.478 14.67 0.00 45.14 4.26
36 37 5.880332 AGTGAAAACACTGTAACATCTGTGT 59.120 36.000 0.00 0.00 46.72 3.72
37 38 6.194463 CAGTGAAAACACTGTAACATCTGTG 58.806 40.000 18.40 0.00 45.40 3.66
38 39 6.363577 CAGTGAAAACACTGTAACATCTGT 57.636 37.500 18.40 0.00 45.40 3.41
49 50 4.021544 TGTTTTTCCAGCAGTGAAAACACT 60.022 37.500 13.06 0.00 43.21 3.55
50 51 4.241681 TGTTTTTCCAGCAGTGAAAACAC 58.758 39.130 13.06 11.69 43.21 3.32
51 52 4.527509 TGTTTTTCCAGCAGTGAAAACA 57.472 36.364 13.06 13.06 44.81 2.83
52 53 4.260334 GCATGTTTTTCCAGCAGTGAAAAC 60.260 41.667 9.17 9.17 40.39 2.43
53 54 3.870419 GCATGTTTTTCCAGCAGTGAAAA 59.130 39.130 0.00 4.54 39.30 2.29
54 55 3.132646 AGCATGTTTTTCCAGCAGTGAAA 59.867 39.130 0.00 0.00 0.00 2.69
55 56 2.694628 AGCATGTTTTTCCAGCAGTGAA 59.305 40.909 0.00 0.00 0.00 3.18
56 57 2.034939 CAGCATGTTTTTCCAGCAGTGA 59.965 45.455 0.00 0.00 0.00 3.41
57 58 2.034939 TCAGCATGTTTTTCCAGCAGTG 59.965 45.455 0.00 0.00 37.40 3.66
58 59 2.035066 GTCAGCATGTTTTTCCAGCAGT 59.965 45.455 0.00 0.00 37.40 4.40
59 60 2.608752 GGTCAGCATGTTTTTCCAGCAG 60.609 50.000 0.00 0.00 37.40 4.24
60 61 1.340889 GGTCAGCATGTTTTTCCAGCA 59.659 47.619 0.00 0.00 37.40 4.41
61 62 1.340889 TGGTCAGCATGTTTTTCCAGC 59.659 47.619 0.00 0.00 37.40 4.85
62 63 2.361757 TGTGGTCAGCATGTTTTTCCAG 59.638 45.455 0.00 0.00 37.40 3.86
63 64 2.382882 TGTGGTCAGCATGTTTTTCCA 58.617 42.857 0.00 0.00 37.40 3.53
64 65 3.451141 TTGTGGTCAGCATGTTTTTCC 57.549 42.857 0.00 0.00 37.40 3.13
65 66 3.555547 GGTTTGTGGTCAGCATGTTTTTC 59.444 43.478 0.00 0.00 37.40 2.29
66 67 3.530535 GGTTTGTGGTCAGCATGTTTTT 58.469 40.909 0.00 0.00 37.40 1.94
67 68 2.158971 GGGTTTGTGGTCAGCATGTTTT 60.159 45.455 0.00 0.00 37.40 2.43
68 69 1.412343 GGGTTTGTGGTCAGCATGTTT 59.588 47.619 0.00 0.00 37.40 2.83
69 70 1.039856 GGGTTTGTGGTCAGCATGTT 58.960 50.000 0.00 0.00 37.40 2.71
70 71 0.827507 GGGGTTTGTGGTCAGCATGT 60.828 55.000 0.00 0.00 37.40 3.21
71 72 0.540365 AGGGGTTTGTGGTCAGCATG 60.540 55.000 0.00 0.00 37.54 4.06
72 73 1.072266 TAGGGGTTTGTGGTCAGCAT 58.928 50.000 0.00 0.00 0.00 3.79
73 74 0.109723 GTAGGGGTTTGTGGTCAGCA 59.890 55.000 0.00 0.00 0.00 4.41
74 75 0.400594 AGTAGGGGTTTGTGGTCAGC 59.599 55.000 0.00 0.00 0.00 4.26
75 76 2.372172 AGAAGTAGGGGTTTGTGGTCAG 59.628 50.000 0.00 0.00 0.00 3.51
76 77 2.105821 CAGAAGTAGGGGTTTGTGGTCA 59.894 50.000 0.00 0.00 0.00 4.02
77 78 2.105993 ACAGAAGTAGGGGTTTGTGGTC 59.894 50.000 0.00 0.00 0.00 4.02
78 79 2.132686 ACAGAAGTAGGGGTTTGTGGT 58.867 47.619 0.00 0.00 0.00 4.16
79 80 2.951229 ACAGAAGTAGGGGTTTGTGG 57.049 50.000 0.00 0.00 0.00 4.17
80 81 3.146847 GGAACAGAAGTAGGGGTTTGTG 58.853 50.000 0.00 0.00 0.00 3.33
81 82 2.107726 GGGAACAGAAGTAGGGGTTTGT 59.892 50.000 0.00 0.00 0.00 2.83
82 83 2.107552 TGGGAACAGAAGTAGGGGTTTG 59.892 50.000 0.00 0.00 35.01 2.93
83 84 2.424793 TGGGAACAGAAGTAGGGGTTT 58.575 47.619 0.00 0.00 35.01 3.27
84 85 2.127651 TGGGAACAGAAGTAGGGGTT 57.872 50.000 0.00 0.00 35.01 4.11
85 86 2.107726 GTTTGGGAACAGAAGTAGGGGT 59.892 50.000 0.00 0.00 44.54 4.95
86 87 2.375509 AGTTTGGGAACAGAAGTAGGGG 59.624 50.000 0.00 0.00 44.54 4.79
87 88 3.790089 AGTTTGGGAACAGAAGTAGGG 57.210 47.619 0.00 0.00 44.54 3.53
88 89 5.011738 TGTCTAGTTTGGGAACAGAAGTAGG 59.988 44.000 0.00 0.00 44.54 3.18
89 90 5.927115 GTGTCTAGTTTGGGAACAGAAGTAG 59.073 44.000 0.00 0.00 44.54 2.57
90 91 5.364446 TGTGTCTAGTTTGGGAACAGAAGTA 59.636 40.000 0.00 0.00 44.54 2.24
91 92 4.163458 TGTGTCTAGTTTGGGAACAGAAGT 59.837 41.667 0.00 0.00 44.54 3.01
92 93 4.703897 TGTGTCTAGTTTGGGAACAGAAG 58.296 43.478 0.00 0.00 44.54 2.85
93 94 4.764050 TGTGTCTAGTTTGGGAACAGAA 57.236 40.909 0.00 0.00 44.54 3.02
94 95 4.764050 TTGTGTCTAGTTTGGGAACAGA 57.236 40.909 0.00 0.00 44.54 3.41
95 96 5.762045 CATTTGTGTCTAGTTTGGGAACAG 58.238 41.667 0.00 0.00 44.54 3.16
96 97 4.037446 GCATTTGTGTCTAGTTTGGGAACA 59.963 41.667 0.00 0.00 38.26 3.18
97 98 4.278419 AGCATTTGTGTCTAGTTTGGGAAC 59.722 41.667 0.00 0.00 35.97 3.62
98 99 4.278170 CAGCATTTGTGTCTAGTTTGGGAA 59.722 41.667 0.00 0.00 0.00 3.97
99 100 3.820467 CAGCATTTGTGTCTAGTTTGGGA 59.180 43.478 0.00 0.00 0.00 4.37
100 101 3.820467 TCAGCATTTGTGTCTAGTTTGGG 59.180 43.478 0.00 0.00 0.00 4.12
101 102 5.437289 TTCAGCATTTGTGTCTAGTTTGG 57.563 39.130 0.00 0.00 0.00 3.28
102 103 7.754069 TTTTTCAGCATTTGTGTCTAGTTTG 57.246 32.000 0.00 0.00 0.00 2.93
103 104 9.463443 GTATTTTTCAGCATTTGTGTCTAGTTT 57.537 29.630 0.00 0.00 0.00 2.66
104 105 8.082242 GGTATTTTTCAGCATTTGTGTCTAGTT 58.918 33.333 0.00 0.00 0.00 2.24
105 106 7.448469 AGGTATTTTTCAGCATTTGTGTCTAGT 59.552 33.333 0.00 0.00 0.00 2.57
106 107 7.820648 AGGTATTTTTCAGCATTTGTGTCTAG 58.179 34.615 0.00 0.00 0.00 2.43
107 108 7.759489 AGGTATTTTTCAGCATTTGTGTCTA 57.241 32.000 0.00 0.00 0.00 2.59
108 109 6.655078 AGGTATTTTTCAGCATTTGTGTCT 57.345 33.333 0.00 0.00 0.00 3.41
109 110 8.986477 ATAAGGTATTTTTCAGCATTTGTGTC 57.014 30.769 0.00 0.00 0.00 3.67
110 111 9.855021 GTATAAGGTATTTTTCAGCATTTGTGT 57.145 29.630 0.00 0.00 0.00 3.72
144 145 7.012327 GCAATATATCTGTGTTTCAGTAGGCAA 59.988 37.037 0.00 0.00 43.97 4.52
157 158 6.035368 AGCTCTGTAGGCAATATATCTGTG 57.965 41.667 0.00 0.00 0.00 3.66
171 172 6.674694 ATGCATTTTCTGTAAGCTCTGTAG 57.325 37.500 0.00 0.00 0.00 2.74
174 175 7.700505 TCAATATGCATTTTCTGTAAGCTCTG 58.299 34.615 3.54 0.00 0.00 3.35
175 176 7.870509 TCAATATGCATTTTCTGTAAGCTCT 57.129 32.000 3.54 0.00 0.00 4.09
178 179 7.009540 GTGGTTCAATATGCATTTTCTGTAAGC 59.990 37.037 3.54 5.49 0.00 3.09
180 181 7.890515 TGTGGTTCAATATGCATTTTCTGTAA 58.109 30.769 3.54 0.00 0.00 2.41
181 182 7.362834 CCTGTGGTTCAATATGCATTTTCTGTA 60.363 37.037 3.54 0.00 0.00 2.74
182 183 6.343716 TGTGGTTCAATATGCATTTTCTGT 57.656 33.333 3.54 0.00 0.00 3.41
183 184 5.808540 CCTGTGGTTCAATATGCATTTTCTG 59.191 40.000 3.54 0.00 0.00 3.02
185 186 4.567959 GCCTGTGGTTCAATATGCATTTTC 59.432 41.667 3.54 0.00 0.00 2.29
189 190 1.677576 CGCCTGTGGTTCAATATGCAT 59.322 47.619 3.79 3.79 0.00 3.96
196 197 3.286751 GCAGCGCCTGTGGTTCAA 61.287 61.111 2.29 0.00 33.43 2.69
206 209 3.793144 CAACTTCTCGGCAGCGCC 61.793 66.667 2.29 9.20 46.75 6.53
215 218 4.214332 CCTGTTTTCAGTAGGCAACTTCTC 59.786 45.833 0.00 0.00 46.26 2.87
217 220 3.883489 ACCTGTTTTCAGTAGGCAACTTC 59.117 43.478 0.00 0.00 46.26 3.01
220 223 3.630312 TCAACCTGTTTTCAGTAGGCAAC 59.370 43.478 0.00 0.00 45.68 4.17
291 1000 2.826738 AGAGTCGAGAGAGCCGGC 60.827 66.667 21.89 21.89 43.49 6.13
324 1033 1.066430 ACGAAATCCCTAGCTTCGCAA 60.066 47.619 0.00 0.00 44.40 4.85
325 1034 0.535335 ACGAAATCCCTAGCTTCGCA 59.465 50.000 0.00 0.00 44.40 5.10
371 1081 2.434774 GTTCCCCACCCTCACACC 59.565 66.667 0.00 0.00 0.00 4.16
377 1087 4.603097 TTCCCCGTTCCCCACCCT 62.603 66.667 0.00 0.00 0.00 4.34
378 1088 3.582358 TTTCCCCGTTCCCCACCC 61.582 66.667 0.00 0.00 0.00 4.61
379 1089 2.282674 GTTTCCCCGTTCCCCACC 60.283 66.667 0.00 0.00 0.00 4.61
380 1090 2.670592 CGTTTCCCCGTTCCCCAC 60.671 66.667 0.00 0.00 0.00 4.61
381 1091 3.956314 CCGTTTCCCCGTTCCCCA 61.956 66.667 0.00 0.00 0.00 4.96
386 1096 1.555477 TATCCTGCCGTTTCCCCGTT 61.555 55.000 0.00 0.00 0.00 4.44
388 1098 1.227556 CTATCCTGCCGTTTCCCCG 60.228 63.158 0.00 0.00 0.00 5.73
412 1122 2.109425 AATTTTAGGAGACGCGCCTT 57.891 45.000 5.73 0.00 34.91 4.35
413 1123 2.007608 GAAATTTTAGGAGACGCGCCT 58.992 47.619 5.73 7.64 37.45 5.52
425 1135 2.412770 GTCGGGTCGCTTCGAAATTTTA 59.587 45.455 0.00 0.00 37.72 1.52
449 1159 2.520741 CAGGTGGGCGGTGGTTTT 60.521 61.111 0.00 0.00 0.00 2.43
450 1160 4.596585 CCAGGTGGGCGGTGGTTT 62.597 66.667 0.00 0.00 0.00 3.27
467 1177 4.699522 GTGGCCTGGTGGACCGAC 62.700 72.222 3.32 0.00 42.00 4.79
471 1181 4.250305 ACACGTGGCCTGGTGGAC 62.250 66.667 21.57 5.28 43.36 4.02
472 1182 3.936203 GACACGTGGCCTGGTGGA 61.936 66.667 21.57 0.00 38.46 4.02
473 1183 3.941188 AGACACGTGGCCTGGTGG 61.941 66.667 20.18 11.21 38.46 4.61
474 1184 2.666190 CAGACACGTGGCCTGGTG 60.666 66.667 20.18 20.65 39.98 4.17
475 1185 3.161450 ACAGACACGTGGCCTGGT 61.161 61.111 30.34 20.40 32.52 4.00
476 1186 2.666190 CACAGACACGTGGCCTGG 60.666 66.667 30.34 19.85 33.05 4.45
477 1187 1.665916 CTCACAGACACGTGGCCTG 60.666 63.158 27.57 27.57 37.50 4.85
478 1188 2.737180 CTCACAGACACGTGGCCT 59.263 61.111 20.18 12.48 37.50 5.19
479 1189 2.357517 CCTCACAGACACGTGGCC 60.358 66.667 20.18 10.10 37.50 5.36
480 1190 2.357517 CCCTCACAGACACGTGGC 60.358 66.667 21.57 18.79 37.50 5.01
481 1191 1.006102 GACCCTCACAGACACGTGG 60.006 63.158 21.57 4.47 37.50 4.94
482 1192 1.371758 CGACCCTCACAGACACGTG 60.372 63.158 15.48 15.48 38.29 4.49
483 1193 3.039988 CGACCCTCACAGACACGT 58.960 61.111 0.00 0.00 0.00 4.49
484 1194 2.430921 GCGACCCTCACAGACACG 60.431 66.667 0.00 0.00 0.00 4.49
485 1195 2.430921 CGCGACCCTCACAGACAC 60.431 66.667 0.00 0.00 0.00 3.67
486 1196 4.357947 GCGCGACCCTCACAGACA 62.358 66.667 12.10 0.00 0.00 3.41
491 1201 4.194720 ATCTCGCGCGACCCTCAC 62.195 66.667 31.40 0.00 0.00 3.51
492 1202 3.889044 GATCTCGCGCGACCCTCA 61.889 66.667 31.40 7.56 0.00 3.86
493 1203 4.965858 CGATCTCGCGCGACCCTC 62.966 72.222 31.40 22.59 0.00 4.30
501 1211 4.219846 ACGACCGTCGATCTCGCG 62.220 66.667 27.03 0.00 43.74 5.87
502 1212 2.648102 CACGACCGTCGATCTCGC 60.648 66.667 27.03 0.00 43.74 5.03
503 1213 2.022902 CCACGACCGTCGATCTCG 59.977 66.667 27.03 9.42 43.74 4.04
504 1214 1.226323 CACCACGACCGTCGATCTC 60.226 63.158 27.03 0.00 43.74 2.75
505 1215 2.875485 CACCACGACCGTCGATCT 59.125 61.111 27.03 2.06 43.74 2.75
506 1216 2.879462 GCACCACGACCGTCGATC 60.879 66.667 27.03 7.29 43.74 3.69
528 1238 1.884769 GCTATCAGACGCGATGCAGC 61.885 60.000 15.93 17.63 0.00 5.25
529 1239 2.140066 GCTATCAGACGCGATGCAG 58.860 57.895 15.93 12.22 0.00 4.41
530 1240 4.326153 GCTATCAGACGCGATGCA 57.674 55.556 15.93 0.00 0.00 3.96
554 1264 1.573829 TTTCAATCGCTGTCCGGTGC 61.574 55.000 0.00 3.93 37.59 5.01
555 1265 0.871722 TTTTCAATCGCTGTCCGGTG 59.128 50.000 0.00 0.00 37.59 4.94
556 1266 1.600023 TTTTTCAATCGCTGTCCGGT 58.400 45.000 0.00 0.00 37.59 5.28
617 1327 1.142748 GCTCTGATGGACCTGGTCG 59.857 63.158 19.98 6.55 32.65 4.79
628 1338 2.386661 ATTCGTTTGACCGCTCTGAT 57.613 45.000 0.00 0.00 0.00 2.90
676 1395 2.280797 GCGCTCCTGTGTGGTCAA 60.281 61.111 0.00 0.00 37.07 3.18
693 1412 1.543802 GAGATAGATGCACCCTCTCGG 59.456 57.143 0.00 0.00 37.81 4.63
931 1675 1.332997 GAACTGGTGCTGATGCTATGC 59.667 52.381 0.00 0.00 40.48 3.14
949 1696 4.286101 CGTGCAATGTATGTGTGTTTGAA 58.714 39.130 0.00 0.00 0.00 2.69
1065 1829 0.108992 GTGCGTGGAGGAACGATGTA 60.109 55.000 0.17 0.00 46.49 2.29
1067 1831 2.100631 GGTGCGTGGAGGAACGATG 61.101 63.158 0.17 0.00 46.49 3.84
1320 2084 3.325753 GTGGCCAGCTGAGGGTCT 61.326 66.667 17.39 0.00 0.00 3.85
1677 2441 4.397348 GTGGCCTCCACGAACATT 57.603 55.556 3.32 0.00 44.95 2.71
1722 2486 1.874466 GTAGTCGAAGCTCTGCGCC 60.874 63.158 4.18 0.00 40.39 6.53
1959 2726 5.188327 TGATGTTCTCCACGATGTAGATC 57.812 43.478 0.00 0.00 0.00 2.75
2259 3026 2.978010 CACCAGGCGTTGACCACC 60.978 66.667 0.00 0.00 0.00 4.61
2316 3083 0.618968 AGAACCTCTCCGGCCTGAAT 60.619 55.000 0.00 0.00 35.61 2.57
2559 3326 2.736682 GACGACGGAATGGTTGGCG 61.737 63.158 0.00 0.00 0.00 5.69
2629 3402 2.270257 TGTAGCCGTGTAGCCGTGT 61.270 57.895 0.00 0.00 0.00 4.49
2630 3403 1.804326 GTGTAGCCGTGTAGCCGTG 60.804 63.158 0.00 0.00 0.00 4.94
2631 3404 2.570181 GTGTAGCCGTGTAGCCGT 59.430 61.111 0.00 0.00 0.00 5.68
2632 3405 2.578713 CGTGTAGCCGTGTAGCCG 60.579 66.667 0.00 0.00 0.00 5.52
2633 3406 2.884207 GCGTGTAGCCGTGTAGCC 60.884 66.667 0.00 0.00 40.81 3.93
2643 3416 4.263209 CGAGAAGAGTAATTGTGCGTGTAG 59.737 45.833 0.00 0.00 0.00 2.74
2644 3417 4.163552 CGAGAAGAGTAATTGTGCGTGTA 58.836 43.478 0.00 0.00 0.00 2.90
2645 3418 2.987149 CGAGAAGAGTAATTGTGCGTGT 59.013 45.455 0.00 0.00 0.00 4.49
2646 3419 2.345641 CCGAGAAGAGTAATTGTGCGTG 59.654 50.000 0.00 0.00 0.00 5.34
2647 3420 2.607187 CCGAGAAGAGTAATTGTGCGT 58.393 47.619 0.00 0.00 0.00 5.24
2648 3421 1.927174 CCCGAGAAGAGTAATTGTGCG 59.073 52.381 0.00 0.00 0.00 5.34
2649 3422 2.973945 ACCCGAGAAGAGTAATTGTGC 58.026 47.619 0.00 0.00 0.00 4.57
2650 3423 5.475719 TGTAACCCGAGAAGAGTAATTGTG 58.524 41.667 0.00 0.00 0.00 3.33
2651 3424 5.733620 TGTAACCCGAGAAGAGTAATTGT 57.266 39.130 0.00 0.00 0.00 2.71
2652 3425 7.611213 ATTTGTAACCCGAGAAGAGTAATTG 57.389 36.000 0.00 0.00 0.00 2.32
2653 3426 9.326413 CATATTTGTAACCCGAGAAGAGTAATT 57.674 33.333 0.00 0.00 0.00 1.40
2654 3427 8.483758 ACATATTTGTAACCCGAGAAGAGTAAT 58.516 33.333 0.00 0.00 33.16 1.89
2655 3428 7.844009 ACATATTTGTAACCCGAGAAGAGTAA 58.156 34.615 0.00 0.00 33.16 2.24
2656 3429 7.341256 AGACATATTTGTAACCCGAGAAGAGTA 59.659 37.037 0.00 0.00 35.79 2.59
2657 3430 6.154706 AGACATATTTGTAACCCGAGAAGAGT 59.845 38.462 0.00 0.00 35.79 3.24
2658 3431 6.574350 AGACATATTTGTAACCCGAGAAGAG 58.426 40.000 0.00 0.00 35.79 2.85
2659 3432 6.540438 AGACATATTTGTAACCCGAGAAGA 57.460 37.500 0.00 0.00 35.79 2.87
2660 3433 7.713750 TCTAGACATATTTGTAACCCGAGAAG 58.286 38.462 0.00 0.00 35.79 2.85
2661 3434 7.649533 TCTAGACATATTTGTAACCCGAGAA 57.350 36.000 0.00 0.00 35.79 2.87
2662 3435 7.341256 AGTTCTAGACATATTTGTAACCCGAGA 59.659 37.037 0.00 0.00 35.79 4.04
2663 3436 7.490000 AGTTCTAGACATATTTGTAACCCGAG 58.510 38.462 0.00 0.00 35.79 4.63
2664 3437 7.123098 TGAGTTCTAGACATATTTGTAACCCGA 59.877 37.037 0.00 0.00 35.79 5.14
2665 3438 7.262772 TGAGTTCTAGACATATTTGTAACCCG 58.737 38.462 0.00 0.00 35.79 5.28
2666 3439 8.258708 ACTGAGTTCTAGACATATTTGTAACCC 58.741 37.037 0.00 0.00 35.79 4.11
2667 3440 9.303537 GACTGAGTTCTAGACATATTTGTAACC 57.696 37.037 0.00 0.00 35.79 2.85
2668 3441 9.011407 CGACTGAGTTCTAGACATATTTGTAAC 57.989 37.037 0.00 0.00 35.79 2.50
2669 3442 8.953313 TCGACTGAGTTCTAGACATATTTGTAA 58.047 33.333 0.00 0.00 35.79 2.41
2670 3443 8.502105 TCGACTGAGTTCTAGACATATTTGTA 57.498 34.615 0.00 0.00 35.79 2.41
2671 3444 7.392494 TCGACTGAGTTCTAGACATATTTGT 57.608 36.000 0.00 0.00 39.32 2.83
2672 3445 7.906611 CTCGACTGAGTTCTAGACATATTTG 57.093 40.000 0.00 0.00 37.46 2.32
3365 4297 1.831652 AACTGAGAGACAAGCGGGGG 61.832 60.000 0.00 0.00 0.00 5.40
3428 4360 2.334006 AGTCTCTGGAATGTGGACCT 57.666 50.000 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.