Multiple sequence alignment - TraesCS2D01G473400

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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 TraesCS2D01G473400 chr2D 100.000 5970 0 0 1 5970 577108173 577114142 0.000000e+00 11025.0
1 TraesCS2D01G473400 chr2D 82.412 1484 252 7 444 1924 577098828 577100305 0.000000e+00 1286.0
2 TraesCS2D01G473400 chr2D 73.326 1912 448 53 1343 3218 2735536 2733651 0.000000e+00 649.0
3 TraesCS2D01G473400 chr2D 72.394 355 90 7 471 821 2681275 2680925 8.180000e-19 106.0
4 TraesCS2D01G473400 chr2D 72.523 222 55 6 1300 1518 2358943 2359161 3.860000e-07 67.6
5 TraesCS2D01G473400 chr2D 100.000 28 0 0 3542 3569 22568359 22568332 1.100000e-02 52.8
6 TraesCS2D01G473400 chr2B 90.718 5268 393 54 66 5293 693723522 693728733 0.000000e+00 6931.0
7 TraesCS2D01G473400 chr2B 85.077 5287 688 53 444 5682 693321635 693326868 0.000000e+00 5299.0
8 TraesCS2D01G473400 chr2B 80.903 4697 774 75 1048 5682 693365706 693370341 0.000000e+00 3591.0
9 TraesCS2D01G473400 chr2B 80.665 3941 605 83 1465 5332 693738599 693742455 0.000000e+00 2911.0
10 TraesCS2D01G473400 chr2B 76.926 3155 641 66 1050 4168 693892719 693895822 0.000000e+00 1712.0
11 TraesCS2D01G473400 chr2B 82.964 1262 130 51 4476 5682 693849007 693850238 0.000000e+00 1061.0
12 TraesCS2D01G473400 chr2B 88.414 561 58 6 3554 4109 693345369 693345927 0.000000e+00 669.0
13 TraesCS2D01G473400 chr2B 83.648 477 51 11 4090 4547 693345989 693346457 1.990000e-114 424.0
14 TraesCS2D01G473400 chr2B 75.000 972 209 17 2810 3773 9896525 9895580 9.250000e-113 418.0
15 TraesCS2D01G473400 chr2B 79.932 588 88 17 4669 5246 693346531 693347098 7.200000e-109 405.0
16 TraesCS2D01G473400 chr2B 91.362 301 12 5 5679 5970 693370383 693370678 3.350000e-107 399.0
17 TraesCS2D01G473400 chr2B 93.536 263 11 3 5684 5944 693326908 693327166 2.610000e-103 387.0
18 TraesCS2D01G473400 chr2B 90.000 300 17 4 5679 5970 693850281 693850575 5.650000e-100 375.0
19 TraesCS2D01G473400 chr2B 93.117 247 15 2 3864 4109 693848172 693848417 1.580000e-95 361.0
20 TraesCS2D01G473400 chr2B 81.557 244 34 6 5679 5914 693729263 693729503 2.200000e-44 191.0
21 TraesCS2D01G473400 chr2A 84.737 3361 475 22 444 3795 715274385 715277716 0.000000e+00 3330.0
22 TraesCS2D01G473400 chr2A 73.241 2160 508 59 1300 3421 2881728 2883855 0.000000e+00 723.0
23 TraesCS2D01G473400 chr2A 87.580 628 59 9 3919 4544 715290230 715290840 0.000000e+00 710.0
24 TraesCS2D01G473400 chr2A 91.324 219 19 0 3705 3923 715277703 715277921 3.500000e-77 300.0
25 TraesCS2D01G473400 chr4A 73.814 2509 565 64 1300 3774 658967599 658965149 0.000000e+00 909.0


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 TraesCS2D01G473400 chr2D 577108173 577114142 5969 False 11025.000000 11025 100.000000 1 5970 1 chr2D.!!$F3 5969
1 TraesCS2D01G473400 chr2D 577098828 577100305 1477 False 1286.000000 1286 82.412000 444 1924 1 chr2D.!!$F2 1480
2 TraesCS2D01G473400 chr2D 2733651 2735536 1885 True 649.000000 649 73.326000 1343 3218 1 chr2D.!!$R2 1875
3 TraesCS2D01G473400 chr2B 693723522 693729503 5981 False 3561.000000 6931 86.137500 66 5914 2 chr2B.!!$F6 5848
4 TraesCS2D01G473400 chr2B 693738599 693742455 3856 False 2911.000000 2911 80.665000 1465 5332 1 chr2B.!!$F1 3867
5 TraesCS2D01G473400 chr2B 693321635 693327166 5531 False 2843.000000 5299 89.306500 444 5944 2 chr2B.!!$F3 5500
6 TraesCS2D01G473400 chr2B 693365706 693370678 4972 False 1995.000000 3591 86.132500 1048 5970 2 chr2B.!!$F5 4922
7 TraesCS2D01G473400 chr2B 693892719 693895822 3103 False 1712.000000 1712 76.926000 1050 4168 1 chr2B.!!$F2 3118
8 TraesCS2D01G473400 chr2B 693848172 693850575 2403 False 599.000000 1061 88.693667 3864 5970 3 chr2B.!!$F7 2106
9 TraesCS2D01G473400 chr2B 693345369 693347098 1729 False 499.333333 669 83.998000 3554 5246 3 chr2B.!!$F4 1692
10 TraesCS2D01G473400 chr2B 9895580 9896525 945 True 418.000000 418 75.000000 2810 3773 1 chr2B.!!$R1 963
11 TraesCS2D01G473400 chr2A 715274385 715277921 3536 False 1815.000000 3330 88.030500 444 3923 2 chr2A.!!$F3 3479
12 TraesCS2D01G473400 chr2A 2881728 2883855 2127 False 723.000000 723 73.241000 1300 3421 1 chr2A.!!$F1 2121
13 TraesCS2D01G473400 chr2A 715290230 715290840 610 False 710.000000 710 87.580000 3919 4544 1 chr2A.!!$F2 625
14 TraesCS2D01G473400 chr4A 658965149 658967599 2450 True 909.000000 909 73.814000 1300 3774 1 chr4A.!!$R1 2474

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
868 871 0.105039 CTGCTAACCCTCGTCATCCC 59.895 60.0 0.00 0.00 0.00 3.85 F
1972 1989 0.033920 CCCCTCTTGCAGCAAAAACC 59.966 55.0 9.65 0.00 0.00 3.27 F
2440 2475 0.109919 TCCGTCACTTGTCGATCGTG 60.110 55.0 15.94 5.63 0.00 4.35 F
2664 2708 0.457035 CCCTTGGAATCCATGTTGCG 59.543 55.0 1.39 0.00 31.53 4.85 F
4343 4601 0.103823 TTACCACCCTTTCCCTCCCA 60.104 55.0 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2851 2902 3.618351 ACCTGAAAGAAGCTCATCATGG 58.382 45.455 0.00 0.0 34.07 3.66 R
3718 3848 0.179076 TATGCAGACCATCCTGTGCG 60.179 55.000 0.00 0.0 38.84 5.34 R
4278 4518 0.034089 AGTTATGGCTTGGAGGGCAC 60.034 55.000 0.00 0.0 44.25 5.01 R
4591 5022 1.198713 AGCCCTCGATGTCATCTGTT 58.801 50.000 11.04 0.0 0.00 3.16 R
5246 5738 0.239879 TTTTCAGACAATTCGCGGGC 59.760 50.000 6.13 0.0 0.00 6.13 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 3.470888 CGAGGGACCCCAGCGATT 61.471 66.667 7.00 0.00 38.03 3.34
26 27 2.131709 CGAGGGACCCCAGCGATTA 61.132 63.158 7.00 0.00 38.03 1.75
27 28 1.749033 GAGGGACCCCAGCGATTAG 59.251 63.158 7.00 0.00 38.92 1.73
28 29 1.003051 AGGGACCCCAGCGATTAGT 59.997 57.895 7.00 0.00 38.92 2.24
29 30 0.620700 AGGGACCCCAGCGATTAGTT 60.621 55.000 7.00 0.00 38.92 2.24
30 31 1.125633 GGGACCCCAGCGATTAGTTA 58.874 55.000 0.00 0.00 35.81 2.24
31 32 1.202615 GGGACCCCAGCGATTAGTTAC 60.203 57.143 0.00 0.00 35.81 2.50
32 33 1.761198 GGACCCCAGCGATTAGTTACT 59.239 52.381 0.00 0.00 0.00 2.24
33 34 2.169978 GGACCCCAGCGATTAGTTACTT 59.830 50.000 0.00 0.00 0.00 2.24
34 35 3.455327 GACCCCAGCGATTAGTTACTTC 58.545 50.000 0.00 0.00 0.00 3.01
35 36 2.169978 ACCCCAGCGATTAGTTACTTCC 59.830 50.000 0.00 0.00 0.00 3.46
36 37 2.484947 CCCCAGCGATTAGTTACTTCCC 60.485 54.545 0.00 0.00 0.00 3.97
37 38 2.169769 CCCAGCGATTAGTTACTTCCCA 59.830 50.000 0.00 0.00 0.00 4.37
38 39 3.181454 CCCAGCGATTAGTTACTTCCCAT 60.181 47.826 0.00 0.00 0.00 4.00
39 40 3.809832 CCAGCGATTAGTTACTTCCCATG 59.190 47.826 0.00 0.00 0.00 3.66
40 41 4.442893 CCAGCGATTAGTTACTTCCCATGA 60.443 45.833 0.00 0.00 0.00 3.07
41 42 5.300752 CAGCGATTAGTTACTTCCCATGAT 58.699 41.667 0.00 0.00 0.00 2.45
42 43 5.406780 CAGCGATTAGTTACTTCCCATGATC 59.593 44.000 0.00 0.00 0.00 2.92
43 44 4.691216 GCGATTAGTTACTTCCCATGATCC 59.309 45.833 0.00 0.00 0.00 3.36
44 45 5.238583 CGATTAGTTACTTCCCATGATCCC 58.761 45.833 0.00 0.00 0.00 3.85
45 46 5.561679 GATTAGTTACTTCCCATGATCCCC 58.438 45.833 0.00 0.00 0.00 4.81
46 47 2.858644 AGTTACTTCCCATGATCCCCA 58.141 47.619 0.00 0.00 0.00 4.96
47 48 2.509964 AGTTACTTCCCATGATCCCCAC 59.490 50.000 0.00 0.00 0.00 4.61
48 49 2.509964 GTTACTTCCCATGATCCCCACT 59.490 50.000 0.00 0.00 0.00 4.00
49 50 0.921896 ACTTCCCATGATCCCCACTG 59.078 55.000 0.00 0.00 0.00 3.66
50 51 0.184451 CTTCCCATGATCCCCACTGG 59.816 60.000 0.00 0.00 0.00 4.00
51 52 1.936767 TTCCCATGATCCCCACTGGC 61.937 60.000 0.00 0.00 0.00 4.85
52 53 2.692824 CCCATGATCCCCACTGGCA 61.693 63.158 0.00 0.00 0.00 4.92
53 54 1.454479 CCATGATCCCCACTGGCAC 60.454 63.158 0.00 0.00 0.00 5.01
54 55 1.303948 CATGATCCCCACTGGCACA 59.696 57.895 0.00 0.00 0.00 4.57
55 56 0.323633 CATGATCCCCACTGGCACAA 60.324 55.000 0.00 0.00 38.70 3.33
56 57 0.409092 ATGATCCCCACTGGCACAAA 59.591 50.000 0.00 0.00 38.70 2.83
57 58 0.187117 TGATCCCCACTGGCACAAAA 59.813 50.000 0.00 0.00 38.70 2.44
58 59 1.337118 GATCCCCACTGGCACAAAAA 58.663 50.000 0.00 0.00 38.70 1.94
59 60 1.901833 GATCCCCACTGGCACAAAAAT 59.098 47.619 0.00 0.00 38.70 1.82
60 61 1.799933 TCCCCACTGGCACAAAAATT 58.200 45.000 0.00 0.00 38.70 1.82
61 62 2.964209 TCCCCACTGGCACAAAAATTA 58.036 42.857 0.00 0.00 38.70 1.40
62 63 2.896685 TCCCCACTGGCACAAAAATTAG 59.103 45.455 0.00 0.00 38.70 1.73
63 64 2.612721 CCCCACTGGCACAAAAATTAGC 60.613 50.000 0.00 0.00 38.70 3.09
64 65 2.299867 CCCACTGGCACAAAAATTAGCT 59.700 45.455 0.00 0.00 38.70 3.32
71 72 4.943705 TGGCACAAAAATTAGCTAGGAGAG 59.056 41.667 0.00 0.00 31.92 3.20
104 105 6.650427 GGTCTGAACCCAAGTCTTAATTTT 57.350 37.500 0.00 0.00 39.93 1.82
115 116 7.968405 CCCAAGTCTTAATTTTATTTGAGACCG 59.032 37.037 5.74 0.00 40.97 4.79
116 117 7.484959 CCAAGTCTTAATTTTATTTGAGACCGC 59.515 37.037 5.74 0.00 40.97 5.68
117 118 7.681939 AGTCTTAATTTTATTTGAGACCGCA 57.318 32.000 5.74 0.00 40.97 5.69
119 120 8.398665 AGTCTTAATTTTATTTGAGACCGCATC 58.601 33.333 5.74 0.00 40.97 3.91
120 121 8.181573 GTCTTAATTTTATTTGAGACCGCATCA 58.818 33.333 0.00 0.00 36.65 3.07
121 122 8.181573 TCTTAATTTTATTTGAGACCGCATCAC 58.818 33.333 0.00 0.00 0.00 3.06
122 123 6.515272 AATTTTATTTGAGACCGCATCACT 57.485 33.333 0.00 0.00 0.00 3.41
123 124 4.944962 TTTATTTGAGACCGCATCACTG 57.055 40.909 0.00 0.00 0.00 3.66
124 125 2.768253 ATTTGAGACCGCATCACTGA 57.232 45.000 0.00 0.00 0.00 3.41
125 126 2.084610 TTTGAGACCGCATCACTGAG 57.915 50.000 0.00 0.00 0.00 3.35
126 127 0.969149 TTGAGACCGCATCACTGAGT 59.031 50.000 0.00 0.00 0.00 3.41
127 128 0.244721 TGAGACCGCATCACTGAGTG 59.755 55.000 6.18 6.18 34.45 3.51
128 129 1.079543 AGACCGCATCACTGAGTGC 60.080 57.895 7.93 0.00 37.97 4.40
132 133 1.284657 CCGCATCACTGAGTGCTTAG 58.715 55.000 7.93 0.00 39.16 2.18
144 145 4.009675 TGAGTGCTTAGTTAATTGGCAGG 58.990 43.478 0.00 0.00 33.47 4.85
173 175 6.985653 TTTTATTGATCCCAACCACTCAAA 57.014 33.333 0.00 0.00 34.72 2.69
177 179 4.111255 TGATCCCAACCACTCAAATGAA 57.889 40.909 0.00 0.00 0.00 2.57
180 182 5.185635 TGATCCCAACCACTCAAATGAATTC 59.814 40.000 0.00 0.00 0.00 2.17
184 187 5.464168 CCAACCACTCAAATGAATTCACTC 58.536 41.667 11.07 0.00 0.00 3.51
191 194 4.490743 TCAAATGAATTCACTCGACGCTA 58.509 39.130 11.07 0.00 0.00 4.26
201 204 2.085320 ACTCGACGCTACTCACATCTT 58.915 47.619 0.00 0.00 0.00 2.40
203 206 3.688185 ACTCGACGCTACTCACATCTTTA 59.312 43.478 0.00 0.00 0.00 1.85
207 210 6.600350 TCGACGCTACTCACATCTTTATATC 58.400 40.000 0.00 0.00 0.00 1.63
208 211 5.795939 CGACGCTACTCACATCTTTATATCC 59.204 44.000 0.00 0.00 0.00 2.59
209 212 6.026947 ACGCTACTCACATCTTTATATCCC 57.973 41.667 0.00 0.00 0.00 3.85
210 213 5.047235 ACGCTACTCACATCTTTATATCCCC 60.047 44.000 0.00 0.00 0.00 4.81
212 215 5.485708 GCTACTCACATCTTTATATCCCCCT 59.514 44.000 0.00 0.00 0.00 4.79
213 216 6.351456 GCTACTCACATCTTTATATCCCCCTC 60.351 46.154 0.00 0.00 0.00 4.30
214 217 4.528596 ACTCACATCTTTATATCCCCCTCG 59.471 45.833 0.00 0.00 0.00 4.63
229 232 1.649664 CCTCGTCCTGCATTTCTCTG 58.350 55.000 0.00 0.00 0.00 3.35
241 244 3.929610 GCATTTCTCTGTCACTCCTACAC 59.070 47.826 0.00 0.00 0.00 2.90
253 256 3.023119 ACTCCTACACATCTCTCTGCAG 58.977 50.000 7.63 7.63 0.00 4.41
277 280 1.071471 ACAGCAAACACCCTCTCCG 59.929 57.895 0.00 0.00 0.00 4.63
283 286 0.609131 AAACACCCTCTCCGGCATTG 60.609 55.000 0.00 0.00 0.00 2.82
291 294 3.764160 CTCCGGCATTGCTCCCTCC 62.764 68.421 8.82 0.00 0.00 4.30
295 298 2.586792 GCATTGCTCCCTCCGTCT 59.413 61.111 0.16 0.00 0.00 4.18
379 382 6.197364 TCTTTCTAGTTACTCTAGCAGCAC 57.803 41.667 0.00 0.00 44.10 4.40
382 385 3.695060 TCTAGTTACTCTAGCAGCACCAC 59.305 47.826 0.00 0.00 44.10 4.16
383 386 1.202582 AGTTACTCTAGCAGCACCACG 59.797 52.381 0.00 0.00 0.00 4.94
390 393 2.034685 TCTAGCAGCACCACGTGATATC 59.965 50.000 19.30 2.99 35.23 1.63
411 414 4.832248 TCAGCATAACTTGGGACTAACTG 58.168 43.478 0.00 0.00 0.00 3.16
413 416 3.264450 AGCATAACTTGGGACTAACTGCT 59.736 43.478 0.00 0.00 32.92 4.24
435 438 0.240678 TGCTAATGGTTTGCAGCGTG 59.759 50.000 0.00 0.00 36.81 5.34
437 440 1.466360 GCTAATGGTTTGCAGCGTGAG 60.466 52.381 0.00 0.00 0.00 3.51
438 441 1.131126 CTAATGGTTTGCAGCGTGAGG 59.869 52.381 0.00 0.00 0.00 3.86
439 442 1.526575 AATGGTTTGCAGCGTGAGGG 61.527 55.000 0.00 0.00 0.00 4.30
451 454 3.000819 TGAGGGCCGATGGACGTT 61.001 61.111 0.00 0.00 40.78 3.99
628 631 1.141881 CAGGGAGATCGACAACCCG 59.858 63.158 14.24 7.94 46.13 5.28
728 731 1.033574 CATCCAGGACGGTCTCTACC 58.966 60.000 8.23 0.00 42.95 3.18
736 739 2.799371 GGTCTCTACCGCACCTCG 59.201 66.667 0.00 0.00 35.62 4.63
748 751 2.364842 ACCTCGGAGGCTGCTGAT 60.365 61.111 23.84 0.00 39.63 2.90
766 769 1.895131 GATGAACATGCCAAGGGTTGT 59.105 47.619 0.00 0.00 0.00 3.32
793 796 1.216710 CCTCTTCCTCCACGCTCAC 59.783 63.158 0.00 0.00 0.00 3.51
863 866 1.811679 GCTGCTGCTAACCCTCGTC 60.812 63.158 8.53 0.00 36.03 4.20
868 871 0.105039 CTGCTAACCCTCGTCATCCC 59.895 60.000 0.00 0.00 0.00 3.85
869 872 1.067582 GCTAACCCTCGTCATCCCG 59.932 63.158 0.00 0.00 0.00 5.14
876 879 4.458829 TCGTCATCCCGGGGAGCT 62.459 66.667 23.50 2.02 34.05 4.09
877 880 4.227134 CGTCATCCCGGGGAGCTG 62.227 72.222 23.50 15.76 34.05 4.24
910 913 3.341823 AGATACAAGGCAGCAAGTTCAG 58.658 45.455 0.00 0.00 0.00 3.02
985 991 2.233271 CCAAACACAGACCAAGCTGAT 58.767 47.619 0.00 0.00 39.20 2.90
997 1003 4.891037 GCTGATGGGGAGGCCAGC 62.891 72.222 5.01 0.00 44.00 4.85
1167 1176 0.877071 AAGCATGTGAAGGAAGCACG 59.123 50.000 0.00 0.00 39.07 5.34
1200 1209 8.652290 AGAGTTTGATAGGGTGGATTTATCTAC 58.348 37.037 0.00 0.00 37.53 2.59
1284 1293 8.215050 TCTTAATCTTGAGTTGTTGGGTTCTAA 58.785 33.333 0.00 0.00 0.00 2.10
1392 1401 7.363705 CCCTGCGAAGAAGAGAATCATAGATAT 60.364 40.741 0.00 0.00 37.82 1.63
1567 1576 9.693739 TCCCAGAATTTCATTGTTAATAAGCTA 57.306 29.630 0.00 0.00 0.00 3.32
1701 1716 7.823310 AGATGATATATGGAAGTGTGAATCTGC 59.177 37.037 0.00 0.00 0.00 4.26
1702 1717 6.829849 TGATATATGGAAGTGTGAATCTGCA 58.170 36.000 0.00 0.00 0.00 4.41
1879 1896 2.636647 TCCGAGCATGCATATTTGGA 57.363 45.000 21.98 14.71 0.00 3.53
1972 1989 0.033920 CCCCTCTTGCAGCAAAAACC 59.966 55.000 9.65 0.00 0.00 3.27
2440 2475 0.109919 TCCGTCACTTGTCGATCGTG 60.110 55.000 15.94 5.63 0.00 4.35
2464 2508 8.247562 GTGATAGATGGTCCAGATGATAGTAAC 58.752 40.741 0.00 0.00 0.00 2.50
2527 2571 7.321745 ACTTAAGACAAAACTGAAGGTTGAG 57.678 36.000 10.09 0.00 38.29 3.02
2664 2708 0.457035 CCCTTGGAATCCATGTTGCG 59.543 55.000 1.39 0.00 31.53 4.85
2790 2837 5.596836 TTGGATCTACAAAAATGGGATGC 57.403 39.130 0.00 0.00 0.00 3.91
2851 2902 3.608316 TTATGCCATTTTCTTGCCCAC 57.392 42.857 0.00 0.00 0.00 4.61
2869 2923 3.349927 CCACCATGATGAGCTTCTTTCA 58.650 45.455 0.00 0.00 0.00 2.69
3442 3506 2.375174 ACCACAGCCCACTCATTTCTTA 59.625 45.455 0.00 0.00 0.00 2.10
3491 3555 2.770164 TTGCCCTAAACTCTCAGAGC 57.230 50.000 0.00 0.00 32.04 4.09
3592 3656 4.583871 AGATAGAAAACTGCCCTGAAGTG 58.416 43.478 0.00 0.00 0.00 3.16
3610 3674 2.840651 AGTGTTGCTACTGCCTCCTATT 59.159 45.455 0.00 0.00 38.71 1.73
3718 3848 8.095169 TCTTCTGGAGTAGAATTGGAAGTTAAC 58.905 37.037 0.00 0.00 44.12 2.01
3722 3852 5.163884 GGAGTAGAATTGGAAGTTAACGCAC 60.164 44.000 0.00 0.00 0.00 5.34
3769 3899 7.062749 TCAGGTGTTACTATTCAGTCAACTT 57.937 36.000 0.00 0.00 36.14 2.66
3827 3957 6.817765 CACCTTTGGAGCTGAAGTATTTTA 57.182 37.500 0.00 0.00 0.00 1.52
4251 4488 2.884012 TGCAGACGTTGGTCATCAAAAT 59.116 40.909 0.00 0.00 45.92 1.82
4252 4489 4.068599 TGCAGACGTTGGTCATCAAAATA 58.931 39.130 0.00 0.00 45.92 1.40
4264 4504 2.279935 TCAAAATAGGTGGTGCGGTT 57.720 45.000 0.00 0.00 0.00 4.44
4278 4518 0.804989 GCGGTTGTTCATTCCCTCAG 59.195 55.000 0.00 0.00 0.00 3.35
4292 4532 2.853542 TCAGTGCCCTCCAAGCCA 60.854 61.111 0.00 0.00 0.00 4.75
4339 4597 4.220724 GTTCTTTTTACCACCCTTTCCCT 58.779 43.478 0.00 0.00 0.00 4.20
4340 4598 4.108501 TCTTTTTACCACCCTTTCCCTC 57.891 45.455 0.00 0.00 0.00 4.30
4343 4601 0.103823 TTACCACCCTTTCCCTCCCA 60.104 55.000 0.00 0.00 0.00 4.37
4345 4603 2.351276 CACCCTTTCCCTCCCACG 59.649 66.667 0.00 0.00 0.00 4.94
4386 4654 3.414700 CGTGAAGGGCGTGCAGAC 61.415 66.667 0.00 0.00 0.00 3.51
4417 4685 3.181439 CCCTTTCAAACCTCACCTCTCTT 60.181 47.826 0.00 0.00 0.00 2.85
4511 4918 4.559300 GCCAGCTCAGCAATTTAAAAGTCA 60.559 41.667 0.00 0.00 0.00 3.41
4591 5022 3.401033 TCCAAACTGCAGAATCTCGAA 57.599 42.857 23.35 0.00 0.00 3.71
4612 5043 2.388735 ACAGATGACATCGAGGGCTTA 58.611 47.619 3.82 0.00 0.00 3.09
4626 5057 2.104331 CTTACTCGATGCGCCCGT 59.896 61.111 16.81 4.64 0.00 5.28
4858 5292 4.473520 CTCCGGTCGCTGCCCAAT 62.474 66.667 0.00 0.00 0.00 3.16
4898 5332 4.627035 CACTGCGAGAATTAGATGTCAACA 59.373 41.667 0.00 0.00 0.00 3.33
4939 5373 2.848858 AAAGCAGTGCAGGCGGTTG 61.849 57.895 19.20 0.00 36.08 3.77
5006 5448 2.029828 CAGACACTTCCTTGCTCGTACT 60.030 50.000 0.00 0.00 0.00 2.73
5048 5499 2.158325 ACCCTTGCTTTTTCCTGATCCA 60.158 45.455 0.00 0.00 0.00 3.41
5054 5505 4.410099 TGCTTTTTCCTGATCCAACAGAT 58.590 39.130 0.00 0.00 39.94 2.90
5055 5506 4.219070 TGCTTTTTCCTGATCCAACAGATG 59.781 41.667 0.00 0.00 39.94 2.90
5062 5514 3.370846 CCTGATCCAACAGATGCCAACTA 60.371 47.826 0.00 0.00 39.94 2.24
5064 5516 4.858850 TGATCCAACAGATGCCAACTAAT 58.141 39.130 0.00 0.00 34.42 1.73
5065 5517 5.263599 TGATCCAACAGATGCCAACTAATT 58.736 37.500 0.00 0.00 34.42 1.40
5207 5677 2.360350 CAGTGGCGCATGAGGGTT 60.360 61.111 10.83 0.00 0.00 4.11
5249 5741 7.165485 TCATGTACATAATATGGTAAGTGCCC 58.835 38.462 8.32 0.00 33.60 5.36
5252 5744 2.157834 TAATATGGTAAGTGCCCGCG 57.842 50.000 0.00 0.00 0.00 6.46
5270 5762 4.334443 CCGCGAATTGTCTGAAAAGTATG 58.666 43.478 8.23 0.00 0.00 2.39
5305 5849 4.686972 TCTGTCTGATAGAAATTGCTCCG 58.313 43.478 1.26 0.00 0.00 4.63
5346 5893 0.953727 TGCTCTTGAGCGCATGTTTT 59.046 45.000 11.47 0.00 37.69 2.43
5440 5993 9.674068 TTATGCTTATGTAAATTGGTCAGTACA 57.326 29.630 0.00 0.00 0.00 2.90
5459 6013 3.403038 ACACCAAATACTGAGAGTGTGC 58.597 45.455 0.00 0.00 37.10 4.57
5489 6046 8.621532 AGCAGAATAATACACAAAAGTGAGAA 57.378 30.769 2.22 0.00 0.00 2.87
5491 6048 9.282247 GCAGAATAATACACAAAAGTGAGAATG 57.718 33.333 2.22 0.00 0.00 2.67
5539 6127 5.510520 CCTTGTTAGCCTGATCTGAGGATAC 60.511 48.000 3.27 0.00 33.65 2.24
5621 6209 4.588528 TCTTGTTTCCTTTTTGGCATAGCT 59.411 37.500 0.00 0.00 35.26 3.32
5627 6215 3.091545 CCTTTTTGGCATAGCTCAGGAA 58.908 45.455 0.00 0.00 0.00 3.36
5726 6500 5.472148 TCATGCAAGGTTGAACATGAAATC 58.528 37.500 0.00 0.00 44.29 2.17
5797 6582 0.940126 AGCAGCAGTTTCAGAACACG 59.060 50.000 0.00 0.00 38.26 4.49
5801 6586 0.593128 GCAGTTTCAGAACACGGCAT 59.407 50.000 12.34 0.00 38.26 4.40
5945 6730 0.964700 TGCATCATCGAGGAGCTAGG 59.035 55.000 17.76 3.15 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.088674 CTAATCGCTGGGGTCCCTCG 62.089 65.000 8.15 9.45 36.94 4.63
9 10 1.049289 ACTAATCGCTGGGGTCCCTC 61.049 60.000 8.15 0.00 36.94 4.30
10 11 0.620700 AACTAATCGCTGGGGTCCCT 60.621 55.000 8.15 0.00 36.94 4.20
11 12 1.125633 TAACTAATCGCTGGGGTCCC 58.874 55.000 0.00 0.00 0.00 4.46
12 13 1.761198 AGTAACTAATCGCTGGGGTCC 59.239 52.381 0.00 0.00 0.00 4.46
13 14 3.455327 GAAGTAACTAATCGCTGGGGTC 58.545 50.000 0.00 0.00 0.00 4.46
14 15 2.169978 GGAAGTAACTAATCGCTGGGGT 59.830 50.000 0.00 0.00 0.00 4.95
15 16 2.484947 GGGAAGTAACTAATCGCTGGGG 60.485 54.545 0.00 0.00 0.00 4.96
16 17 2.169769 TGGGAAGTAACTAATCGCTGGG 59.830 50.000 0.00 0.00 0.00 4.45
17 18 3.536956 TGGGAAGTAACTAATCGCTGG 57.463 47.619 0.00 0.00 0.00 4.85
18 19 4.693283 TCATGGGAAGTAACTAATCGCTG 58.307 43.478 0.00 0.00 0.00 5.18
19 20 5.511545 GGATCATGGGAAGTAACTAATCGCT 60.512 44.000 0.00 0.00 0.00 4.93
20 21 4.691216 GGATCATGGGAAGTAACTAATCGC 59.309 45.833 0.00 0.00 0.00 4.58
21 22 5.238583 GGGATCATGGGAAGTAACTAATCG 58.761 45.833 0.00 0.00 0.00 3.34
22 23 5.073144 TGGGGATCATGGGAAGTAACTAATC 59.927 44.000 0.00 0.00 0.00 1.75
23 24 4.981647 TGGGGATCATGGGAAGTAACTAAT 59.018 41.667 0.00 0.00 0.00 1.73
24 25 4.165372 GTGGGGATCATGGGAAGTAACTAA 59.835 45.833 0.00 0.00 0.00 2.24
25 26 3.714798 GTGGGGATCATGGGAAGTAACTA 59.285 47.826 0.00 0.00 0.00 2.24
26 27 2.509964 GTGGGGATCATGGGAAGTAACT 59.490 50.000 0.00 0.00 0.00 2.24
27 28 2.509964 AGTGGGGATCATGGGAAGTAAC 59.490 50.000 0.00 0.00 0.00 2.50
28 29 2.509548 CAGTGGGGATCATGGGAAGTAA 59.490 50.000 0.00 0.00 0.00 2.24
29 30 2.126882 CAGTGGGGATCATGGGAAGTA 58.873 52.381 0.00 0.00 0.00 2.24
30 31 0.921896 CAGTGGGGATCATGGGAAGT 59.078 55.000 0.00 0.00 0.00 3.01
31 32 0.184451 CCAGTGGGGATCATGGGAAG 59.816 60.000 0.00 0.00 40.01 3.46
32 33 1.936767 GCCAGTGGGGATCATGGGAA 61.937 60.000 12.15 0.00 40.01 3.97
33 34 2.386100 GCCAGTGGGGATCATGGGA 61.386 63.158 12.15 0.00 40.01 4.37
34 35 2.196776 GCCAGTGGGGATCATGGG 59.803 66.667 12.15 0.00 40.01 4.00
35 36 1.454479 GTGCCAGTGGGGATCATGG 60.454 63.158 12.15 0.00 40.01 3.66
36 37 0.323633 TTGTGCCAGTGGGGATCATG 60.324 55.000 12.15 0.00 40.01 3.07
37 38 0.409092 TTTGTGCCAGTGGGGATCAT 59.591 50.000 12.15 0.00 40.01 2.45
38 39 0.187117 TTTTGTGCCAGTGGGGATCA 59.813 50.000 12.15 0.00 40.01 2.92
39 40 1.337118 TTTTTGTGCCAGTGGGGATC 58.663 50.000 12.15 0.00 40.01 3.36
40 41 2.028561 ATTTTTGTGCCAGTGGGGAT 57.971 45.000 12.15 0.00 40.01 3.85
41 42 1.799933 AATTTTTGTGCCAGTGGGGA 58.200 45.000 12.15 0.00 40.01 4.81
42 43 2.612721 GCTAATTTTTGTGCCAGTGGGG 60.613 50.000 12.15 0.00 40.85 4.96
43 44 2.299867 AGCTAATTTTTGTGCCAGTGGG 59.700 45.455 12.15 0.00 37.18 4.61
44 45 3.665745 AGCTAATTTTTGTGCCAGTGG 57.334 42.857 4.20 4.20 0.00 4.00
45 46 4.458989 TCCTAGCTAATTTTTGTGCCAGTG 59.541 41.667 0.00 0.00 0.00 3.66
46 47 4.662278 TCCTAGCTAATTTTTGTGCCAGT 58.338 39.130 0.00 0.00 0.00 4.00
47 48 4.943705 TCTCCTAGCTAATTTTTGTGCCAG 59.056 41.667 0.00 0.00 0.00 4.85
48 49 4.917385 TCTCCTAGCTAATTTTTGTGCCA 58.083 39.130 0.00 0.00 0.00 4.92
49 50 5.491635 CTCTCCTAGCTAATTTTTGTGCC 57.508 43.478 0.00 0.00 0.00 5.01
63 64 1.732917 CTCGCACTGGCTCTCCTAG 59.267 63.158 0.00 0.00 38.10 3.02
64 65 1.754621 CCTCGCACTGGCTCTCCTA 60.755 63.158 0.00 0.00 38.10 2.94
71 72 2.029844 GTTCAGACCTCGCACTGGC 61.030 63.158 0.00 0.00 35.20 4.85
76 77 1.371183 CTTGGGTTCAGACCTCGCA 59.629 57.895 0.00 0.00 45.75 5.10
78 79 0.969894 AGACTTGGGTTCAGACCTCG 59.030 55.000 0.00 0.00 45.75 4.63
98 99 7.335673 TCAGTGATGCGGTCTCAAATAAAATTA 59.664 33.333 0.00 0.00 0.00 1.40
104 105 3.195610 ACTCAGTGATGCGGTCTCAAATA 59.804 43.478 0.00 0.00 0.00 1.40
109 110 1.080995 GCACTCAGTGATGCGGTCTC 61.081 60.000 9.70 0.00 35.23 3.36
110 111 1.079543 GCACTCAGTGATGCGGTCT 60.080 57.895 9.70 0.00 35.23 3.85
111 112 0.671781 AAGCACTCAGTGATGCGGTC 60.672 55.000 9.70 0.00 46.74 4.79
115 116 6.253746 CAATTAACTAAGCACTCAGTGATGC 58.746 40.000 9.70 15.55 42.39 3.91
116 117 6.676456 GCCAATTAACTAAGCACTCAGTGATG 60.676 42.308 9.70 0.00 35.23 3.07
117 118 5.355350 GCCAATTAACTAAGCACTCAGTGAT 59.645 40.000 9.70 0.00 35.23 3.06
119 120 4.455533 TGCCAATTAACTAAGCACTCAGTG 59.544 41.667 0.00 0.00 36.51 3.66
120 121 4.651778 TGCCAATTAACTAAGCACTCAGT 58.348 39.130 0.00 0.00 0.00 3.41
121 122 4.095483 CCTGCCAATTAACTAAGCACTCAG 59.905 45.833 0.00 0.00 0.00 3.35
122 123 4.009675 CCTGCCAATTAACTAAGCACTCA 58.990 43.478 0.00 0.00 0.00 3.41
123 124 3.378427 CCCTGCCAATTAACTAAGCACTC 59.622 47.826 0.00 0.00 0.00 3.51
124 125 3.010138 TCCCTGCCAATTAACTAAGCACT 59.990 43.478 0.00 0.00 0.00 4.40
125 126 3.352648 TCCCTGCCAATTAACTAAGCAC 58.647 45.455 0.00 0.00 0.00 4.40
126 127 3.730215 TCCCTGCCAATTAACTAAGCA 57.270 42.857 0.00 0.00 0.00 3.91
127 128 6.901081 ATAATCCCTGCCAATTAACTAAGC 57.099 37.500 0.00 0.00 0.00 3.09
144 145 8.250143 AGTGGTTGGGATCAATAAAATAATCC 57.750 34.615 0.00 0.00 37.53 3.01
160 162 4.281688 AGTGAATTCATTTGAGTGGTTGGG 59.718 41.667 12.12 0.00 0.00 4.12
164 166 4.452455 GTCGAGTGAATTCATTTGAGTGGT 59.548 41.667 18.49 0.00 28.30 4.16
168 170 3.369147 AGCGTCGAGTGAATTCATTTGAG 59.631 43.478 18.49 13.92 28.30 3.02
173 175 3.128764 TGAGTAGCGTCGAGTGAATTCAT 59.871 43.478 12.12 0.66 0.00 2.57
177 179 1.810755 TGTGAGTAGCGTCGAGTGAAT 59.189 47.619 0.00 0.00 0.00 2.57
180 182 1.398739 AGATGTGAGTAGCGTCGAGTG 59.601 52.381 0.00 0.00 0.00 3.51
184 187 5.795939 GGATATAAAGATGTGAGTAGCGTCG 59.204 44.000 0.00 0.00 0.00 5.12
191 194 4.528596 CGAGGGGGATATAAAGATGTGAGT 59.471 45.833 0.00 0.00 0.00 3.41
201 204 1.132977 TGCAGGACGAGGGGGATATAA 60.133 52.381 0.00 0.00 0.00 0.98
203 206 0.178891 ATGCAGGACGAGGGGGATAT 60.179 55.000 0.00 0.00 0.00 1.63
207 210 1.452108 GAAATGCAGGACGAGGGGG 60.452 63.158 0.00 0.00 0.00 5.40
208 211 0.462759 GAGAAATGCAGGACGAGGGG 60.463 60.000 0.00 0.00 0.00 4.79
209 212 0.539051 AGAGAAATGCAGGACGAGGG 59.461 55.000 0.00 0.00 0.00 4.30
210 213 1.066573 ACAGAGAAATGCAGGACGAGG 60.067 52.381 0.00 0.00 0.00 4.63
212 215 1.618343 TGACAGAGAAATGCAGGACGA 59.382 47.619 0.00 0.00 0.00 4.20
213 216 1.728971 GTGACAGAGAAATGCAGGACG 59.271 52.381 0.00 0.00 0.00 4.79
214 217 2.999355 GAGTGACAGAGAAATGCAGGAC 59.001 50.000 0.00 0.00 0.00 3.85
229 232 3.181491 GCAGAGAGATGTGTAGGAGTGAC 60.181 52.174 0.00 0.00 0.00 3.67
262 265 3.056328 GCCGGAGAGGGTGTTTGC 61.056 66.667 5.05 0.00 41.48 3.68
277 280 2.514824 GACGGAGGGAGCAATGCC 60.515 66.667 0.00 0.00 0.00 4.40
283 286 1.323271 TGTGATGAGACGGAGGGAGC 61.323 60.000 0.00 0.00 0.00 4.70
291 294 1.485838 GCAGGCGATGTGATGAGACG 61.486 60.000 0.00 0.00 0.00 4.18
295 298 0.462581 GAAGGCAGGCGATGTGATGA 60.463 55.000 0.00 0.00 0.00 2.92
320 323 4.262079 CCGGTATGAAGTATGAACTCCCTC 60.262 50.000 0.00 0.00 33.75 4.30
379 382 4.212004 CCAAGTTATGCTGATATCACGTGG 59.788 45.833 17.00 5.42 0.00 4.94
382 385 4.449068 GTCCCAAGTTATGCTGATATCACG 59.551 45.833 0.00 0.00 0.00 4.35
383 386 5.615289 AGTCCCAAGTTATGCTGATATCAC 58.385 41.667 0.00 0.00 0.00 3.06
390 393 3.375299 GCAGTTAGTCCCAAGTTATGCTG 59.625 47.826 0.00 0.00 0.00 4.41
435 438 2.511600 CAACGTCCATCGGCCCTC 60.512 66.667 0.00 0.00 44.69 4.30
595 598 2.551912 CCTGCCACGGGTGTTGTTC 61.552 63.158 0.00 0.00 0.00 3.18
735 738 0.463295 ATGTTCATCAGCAGCCTCCG 60.463 55.000 0.00 0.00 0.00 4.63
736 739 1.022735 CATGTTCATCAGCAGCCTCC 58.977 55.000 0.00 0.00 0.00 4.30
745 748 1.894466 CAACCCTTGGCATGTTCATCA 59.106 47.619 0.00 0.00 0.00 3.07
748 751 1.039068 CACAACCCTTGGCATGTTCA 58.961 50.000 0.00 0.00 34.12 3.18
766 769 2.027192 GTGGAGGAAGAGGTTGCATACA 60.027 50.000 0.00 0.00 0.00 2.29
793 796 2.489275 AACAGCTTTGGCGGTGTGG 61.489 57.895 0.00 0.00 45.39 4.17
863 866 1.825281 GATCTCAGCTCCCCGGGATG 61.825 65.000 26.32 15.60 0.00 3.51
868 871 2.081425 CTTCCGATCTCAGCTCCCCG 62.081 65.000 0.00 0.00 0.00 5.73
869 872 0.757188 TCTTCCGATCTCAGCTCCCC 60.757 60.000 0.00 0.00 0.00 4.81
876 879 4.202161 GCCTTGTATCTTCTTCCGATCTCA 60.202 45.833 0.00 0.00 0.00 3.27
877 880 4.202161 TGCCTTGTATCTTCTTCCGATCTC 60.202 45.833 0.00 0.00 0.00 2.75
910 913 2.260434 CATGGCCAAGTGCAGCAC 59.740 61.111 18.55 18.55 43.89 4.40
932 935 3.673599 GCCACTTGCAGTTCTCCC 58.326 61.111 0.00 0.00 40.77 4.30
1167 1176 8.753497 ATCCACCCTATCAAACTCTAATTTTC 57.247 34.615 0.00 0.00 0.00 2.29
1200 1209 7.255491 TGCTCTACAATATGCTTCATTCTTG 57.745 36.000 0.00 0.00 0.00 3.02
1284 1293 5.163301 GGAATGTCTGTGGTGGTAGTATGAT 60.163 44.000 0.00 0.00 0.00 2.45
1418 1427 6.599638 ACAATTGGCAAGATAGTTAGGTTCTC 59.400 38.462 10.83 0.00 0.00 2.87
1701 1716 3.756117 ACTAAAAGCCTTTCCCAGTCTG 58.244 45.455 0.00 0.00 0.00 3.51
1702 1717 4.263374 GGTACTAAAAGCCTTTCCCAGTCT 60.263 45.833 0.00 0.00 0.00 3.24
1879 1896 6.829229 TGATCTTTTTGTGATTGCTCATCT 57.171 33.333 0.00 0.00 32.98 2.90
1972 1989 6.214399 GTGGTTCCTCAATAATCTACCTACG 58.786 44.000 0.00 0.00 0.00 3.51
2329 2364 7.039784 ACCTTTAAAGCTAAATCATGCAACAGA 60.040 33.333 9.86 0.00 0.00 3.41
2440 2475 7.415765 CCGTTACTATCATCTGGACCATCTATC 60.416 44.444 0.00 0.00 0.00 2.08
2464 2508 9.722056 CTCTTAAATTTTTCATCAGTTATCCCG 57.278 33.333 0.00 0.00 0.00 5.14
2516 2560 4.142403 TGTTTGCAAGTTCTCAACCTTCAG 60.142 41.667 0.00 0.00 0.00 3.02
2664 2708 5.239525 AGGTGCAGAAGTGATGAAAAGTTAC 59.760 40.000 0.00 0.00 0.00 2.50
2790 2837 8.307483 TCATGTCTCTAGGTAACAGAAAAGAAG 58.693 37.037 0.00 0.00 41.41 2.85
2851 2902 3.618351 ACCTGAAAGAAGCTCATCATGG 58.382 45.455 0.00 0.00 34.07 3.66
2913 2967 1.135112 CCTTATTGACGGCAAAAGCCC 60.135 52.381 8.31 0.00 37.59 5.19
2923 2977 3.749609 ACCCTTCGTTTTCCTTATTGACG 59.250 43.478 0.00 0.00 35.24 4.35
2951 3005 6.040955 TCGGTCAGATGCTCTAGTTGATTTAT 59.959 38.462 0.00 0.00 0.00 1.40
3348 3403 4.522022 ACTTGCAAAAGCTTTGCTCTAGAT 59.478 37.500 24.26 3.24 45.13 1.98
3378 3433 7.113658 TCTAATCCAGTGAGTGTAATCTTCC 57.886 40.000 0.00 0.00 0.00 3.46
3379 3434 9.436957 TTTTCTAATCCAGTGAGTGTAATCTTC 57.563 33.333 0.00 0.00 0.00 2.87
3380 3435 9.965902 ATTTTCTAATCCAGTGAGTGTAATCTT 57.034 29.630 0.00 0.00 0.00 2.40
3442 3506 7.066284 GTGATAATCAGTACTTGCAAATGAGGT 59.934 37.037 0.00 0.00 0.00 3.85
3491 3555 2.739913 CAATGTGGCTTGAAAATGGCAG 59.260 45.455 0.00 0.00 39.38 4.85
3592 3656 2.436173 AGGAATAGGAGGCAGTAGCAAC 59.564 50.000 0.00 0.00 44.61 4.17
3610 3674 2.875296 CACAAAGATTGGGTCCAAGGA 58.125 47.619 8.49 0.00 39.47 3.36
3718 3848 0.179076 TATGCAGACCATCCTGTGCG 60.179 55.000 0.00 0.00 38.84 5.34
3722 3852 5.282055 TCTAAGTTATGCAGACCATCCTG 57.718 43.478 0.00 0.00 35.34 3.86
4251 4488 0.398696 ATGAACAACCGCACCACCTA 59.601 50.000 0.00 0.00 0.00 3.08
4252 4489 0.467290 AATGAACAACCGCACCACCT 60.467 50.000 0.00 0.00 0.00 4.00
4264 4504 0.038166 GGGCACTGAGGGAATGAACA 59.962 55.000 0.00 0.00 0.00 3.18
4278 4518 0.034089 AGTTATGGCTTGGAGGGCAC 60.034 55.000 0.00 0.00 44.25 5.01
4326 4584 2.160853 GTGGGAGGGAAAGGGTGGT 61.161 63.158 0.00 0.00 0.00 4.16
4339 4597 2.037367 AGGTCTAGCAGCGTGGGA 59.963 61.111 0.00 0.00 0.00 4.37
4340 4598 2.185350 CAGGTCTAGCAGCGTGGG 59.815 66.667 0.00 0.00 0.00 4.61
4343 4601 1.374758 GTTGCAGGTCTAGCAGCGT 60.375 57.895 0.00 0.00 43.75 5.07
4345 4603 1.466558 GAAAGTTGCAGGTCTAGCAGC 59.533 52.381 0.00 0.00 43.75 5.25
4386 4654 2.084546 GGTTTGAAAGGGACTCCATCG 58.915 52.381 0.00 0.00 38.49 3.84
4387 4655 3.244911 TGAGGTTTGAAAGGGACTCCATC 60.245 47.826 0.00 0.00 38.49 3.51
4388 4656 2.716424 TGAGGTTTGAAAGGGACTCCAT 59.284 45.455 0.00 0.00 38.49 3.41
4389 4657 2.131854 TGAGGTTTGAAAGGGACTCCA 58.868 47.619 0.00 0.00 38.49 3.86
4390 4658 2.505405 GTGAGGTTTGAAAGGGACTCC 58.495 52.381 0.00 0.00 38.49 3.85
4391 4659 2.106684 AGGTGAGGTTTGAAAGGGACTC 59.893 50.000 0.00 0.00 38.49 3.36
4393 4661 2.106684 AGAGGTGAGGTTTGAAAGGGAC 59.893 50.000 0.00 0.00 0.00 4.46
4394 4662 2.372172 GAGAGGTGAGGTTTGAAAGGGA 59.628 50.000 0.00 0.00 0.00 4.20
4417 4685 6.748658 CGCAACGATATATTTCTAATCGGGTA 59.251 38.462 9.09 0.00 45.13 3.69
4511 4918 4.356405 CAAAGAAATTGGGGCTTCCTTT 57.644 40.909 0.00 0.00 35.27 3.11
4591 5022 1.198713 AGCCCTCGATGTCATCTGTT 58.801 50.000 11.04 0.00 0.00 3.16
4626 5057 1.602440 AGAGAGGAGGCTACAGAGGA 58.398 55.000 0.00 0.00 0.00 3.71
4686 5117 2.170985 CCTTTGTGAAGCGCGTCG 59.829 61.111 18.34 3.65 0.00 5.12
4771 5202 4.463879 CCTGCAGGGAGGTGCTCG 62.464 72.222 26.14 0.00 44.32 5.03
4898 5332 2.651361 CTCCTCGTTGTCGCACCT 59.349 61.111 0.00 0.00 36.96 4.00
4939 5373 3.699038 TGATTTTCGGAATGGTTCCCATC 59.301 43.478 3.30 1.95 44.40 3.51
4951 5385 8.311836 GGATTGGTCTATAGTATGATTTTCGGA 58.688 37.037 0.00 0.00 0.00 4.55
5006 5448 5.134661 GGTAATGGTGGAAATCGGGAATAA 58.865 41.667 0.00 0.00 0.00 1.40
5207 5677 4.647611 ACATGAAGAAAATACCACACGGA 58.352 39.130 0.00 0.00 35.59 4.69
5246 5738 0.239879 TTTTCAGACAATTCGCGGGC 59.760 50.000 6.13 0.00 0.00 6.13
5249 5741 4.783036 CACATACTTTTCAGACAATTCGCG 59.217 41.667 0.00 0.00 0.00 5.87
5252 5744 8.289618 TGTAAGCACATACTTTTCAGACAATTC 58.710 33.333 0.00 0.00 0.00 2.17
5294 5838 7.541122 AACTAATAGAACTCGGAGCAATTTC 57.459 36.000 4.58 1.52 0.00 2.17
5360 5907 6.180472 CCCTCCAATTGTTAGTCACATACTT 58.820 40.000 4.43 0.00 39.80 2.24
5440 5993 3.307059 GGAGCACACTCTCAGTATTTGGT 60.307 47.826 0.00 0.00 42.98 3.67
5459 6013 8.607459 CACTTTTGTGTATTATTCTGCTAGGAG 58.393 37.037 4.60 4.60 44.94 3.69
5598 6186 4.588528 AGCTATGCCAAAAAGGAAACAAGA 59.411 37.500 0.00 0.00 41.22 3.02
5621 6209 5.309543 TGAGGGAACAAAGAACTATTCCTGA 59.690 40.000 2.15 0.00 40.47 3.86
5627 6215 6.881602 GTGAATCTGAGGGAACAAAGAACTAT 59.118 38.462 0.00 0.00 0.00 2.12
5706 6480 4.341806 ACAGATTTCATGTTCAACCTTGCA 59.658 37.500 0.00 0.00 0.00 4.08
5797 6582 3.467374 TGGTCCTTTGTCAAAAATGCC 57.533 42.857 0.00 1.11 0.00 4.40
5801 6586 5.115480 GCTCAAATGGTCCTTTGTCAAAAA 58.885 37.500 0.00 0.00 37.39 1.94
5851 6636 4.391830 CGCTGTTGTACAACCTATCAATGT 59.608 41.667 30.68 0.00 40.46 2.71
5852 6637 4.629634 TCGCTGTTGTACAACCTATCAATG 59.370 41.667 30.68 14.56 40.46 2.82
5853 6638 4.827692 TCGCTGTTGTACAACCTATCAAT 58.172 39.130 30.68 0.00 40.46 2.57
5945 6730 4.553330 TGGTTCCTGATTAACTCCTGTC 57.447 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.