Multiple sequence alignment - TraesCS5A01G365300

Loading Multiple Alignment...

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 TraesCS5A01G365300 chr5A 100.000 4386 0 0 1 4386 565487362 565491747 0.000000e+00 8100.0
1 TraesCS5A01G365300 chr5A 80.977 2150 323 39 1339 3452 565416052 565418151 0.000000e+00 1626.0
2 TraesCS5A01G365300 chr5D 96.503 2202 72 4 2188 4385 447142100 447139900 0.000000e+00 3635.0
3 TraesCS5A01G365300 chr5D 81.686 2681 373 71 847 3452 447194231 447191594 0.000000e+00 2122.0
4 TraesCS5A01G365300 chr5D 94.884 1251 59 4 891 2137 447143442 447142193 0.000000e+00 1951.0
5 TraesCS5A01G365300 chr5D 78.053 606 92 31 353 932 447144039 447143449 1.170000e-90 344.0
6 TraesCS5A01G365300 chr5B 92.015 1603 97 19 2173 3755 545576303 545577894 0.000000e+00 2222.0
7 TraesCS5A01G365300 chr5B 92.206 1360 94 7 803 2160 545574907 545576256 0.000000e+00 1914.0
8 TraesCS5A01G365300 chr5B 89.615 260 22 5 3780 4037 545578249 545578505 4.230000e-85 326.0
9 TraesCS5A01G365300 chr5B 85.897 156 19 2 207 362 545573321 545573473 3.510000e-36 163.0
10 TraesCS5A01G365300 chr5B 93.396 106 7 0 712 817 545574641 545574746 1.630000e-34 158.0
11 TraesCS5A01G365300 chr5B 80.000 130 19 7 3714 3839 529963638 529963764 6.040000e-14 89.8
12 TraesCS5A01G365300 chr6D 80.000 2365 376 70 1085 3402 24377790 24375476 0.000000e+00 1657.0
13 TraesCS5A01G365300 chr6D 83.114 1214 198 7 2196 3406 24293687 24292478 0.000000e+00 1099.0
14 TraesCS5A01G365300 chr6D 81.624 1219 205 16 2183 3391 27058046 27059255 0.000000e+00 992.0
15 TraesCS5A01G365300 chr6D 86.087 115 16 0 1375 1489 24383389 24383275 1.660000e-24 124.0
16 TraesCS5A01G365300 chr6D 83.784 74 10 2 3712 3784 20106806 20106734 7.870000e-08 69.4
17 TraesCS5A01G365300 chr6A 79.898 2358 370 76 1085 3393 22953141 22955443 0.000000e+00 1633.0
18 TraesCS5A01G365300 chr6A 78.065 310 54 5 1787 2095 28411281 28411577 2.690000e-42 183.0
19 TraesCS5A01G365300 chr6B 84.063 1211 182 10 2188 3392 39368323 39369528 0.000000e+00 1157.0
20 TraesCS5A01G365300 chr6B 80.952 1218 214 15 2183 3391 49735194 49736402 0.000000e+00 948.0
21 TraesCS5A01G365300 chr6B 81.888 1049 179 10 2194 3236 49306668 49307711 0.000000e+00 874.0
22 TraesCS5A01G365300 chr6B 79.299 913 128 35 1086 1969 39367240 39368120 2.270000e-162 582.0
23 TraesCS5A01G365300 chrUn 81.194 1223 223 6 2189 3406 35133926 35135146 0.000000e+00 977.0
24 TraesCS5A01G365300 chrUn 76.895 541 107 14 1086 1621 35132793 35133320 1.540000e-74 291.0
25 TraesCS5A01G365300 chrUn 81.609 87 14 1 3780 3866 108877885 108877801 2.190000e-08 71.3
26 TraesCS5A01G365300 chr2A 79.000 200 38 1 4187 4386 162017378 162017183 2.750000e-27 134.0
27 TraesCS5A01G365300 chr3B 81.250 160 28 2 4219 4377 789160172 789160014 1.280000e-25 128.0
28 TraesCS5A01G365300 chr3B 100.000 28 0 0 4179 4206 411290091 411290118 8.000000e-03 52.8
29 TraesCS5A01G365300 chr4B 80.606 165 22 10 3705 3865 658592197 658592039 7.710000e-23 119.0
30 TraesCS5A01G365300 chr4B 82.270 141 19 6 3705 3842 658622862 658622725 2.770000e-22 117.0
31 TraesCS5A01G365300 chr4B 87.302 63 7 1 4323 4385 15415076 15415137 2.190000e-08 71.3
32 TraesCS5A01G365300 chr1A 79.545 132 22 5 3712 3839 31952956 31953086 6.040000e-14 89.8
33 TraesCS5A01G365300 chr7D 85.714 77 8 2 3788 3864 618771915 618771988 1.310000e-10 78.7
34 TraesCS5A01G365300 chr7D 91.892 37 3 0 431 467 522978493 522978529 8.000000e-03 52.8
35 TraesCS5A01G365300 chr1B 80.899 89 9 8 3741 3825 108837643 108837727 3.660000e-06 63.9
36 TraesCS5A01G365300 chr3D 94.872 39 2 0 3713 3751 380483380 380483342 1.320000e-05 62.1
37 TraesCS5A01G365300 chr3A 95.000 40 1 1 3712 3751 262017640 262017678 1.320000e-05 62.1
38 TraesCS5A01G365300 chr1D 93.023 43 2 1 426 467 211691868 211691910 1.320000e-05 62.1


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 TraesCS5A01G365300 chr5A 565487362 565491747 4385 False 8100.000000 8100 100.000000 1 4386 1 chr5A.!!$F2 4385
1 TraesCS5A01G365300 chr5A 565416052 565418151 2099 False 1626.000000 1626 80.977000 1339 3452 1 chr5A.!!$F1 2113
2 TraesCS5A01G365300 chr5D 447191594 447194231 2637 True 2122.000000 2122 81.686000 847 3452 1 chr5D.!!$R1 2605
3 TraesCS5A01G365300 chr5D 447139900 447144039 4139 True 1976.666667 3635 89.813333 353 4385 3 chr5D.!!$R2 4032
4 TraesCS5A01G365300 chr5B 545573321 545578505 5184 False 956.600000 2222 90.625800 207 4037 5 chr5B.!!$F2 3830
5 TraesCS5A01G365300 chr6D 24375476 24377790 2314 True 1657.000000 1657 80.000000 1085 3402 1 chr6D.!!$R3 2317
6 TraesCS5A01G365300 chr6D 24292478 24293687 1209 True 1099.000000 1099 83.114000 2196 3406 1 chr6D.!!$R2 1210
7 TraesCS5A01G365300 chr6D 27058046 27059255 1209 False 992.000000 992 81.624000 2183 3391 1 chr6D.!!$F1 1208
8 TraesCS5A01G365300 chr6A 22953141 22955443 2302 False 1633.000000 1633 79.898000 1085 3393 1 chr6A.!!$F1 2308
9 TraesCS5A01G365300 chr6B 49735194 49736402 1208 False 948.000000 948 80.952000 2183 3391 1 chr6B.!!$F2 1208
10 TraesCS5A01G365300 chr6B 49306668 49307711 1043 False 874.000000 874 81.888000 2194 3236 1 chr6B.!!$F1 1042
11 TraesCS5A01G365300 chr6B 39367240 39369528 2288 False 869.500000 1157 81.681000 1086 3392 2 chr6B.!!$F3 2306
12 TraesCS5A01G365300 chrUn 35132793 35135146 2353 False 634.000000 977 79.044500 1086 3406 2 chrUn.!!$F1 2320

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
24 25 0.033642 TATGTGTCGTGTTTGGCCGA 59.966 50.0 0.00 0.0 0.00 5.54 F
279 280 0.036732 TCACGCTTGGAAGATGGCTT 59.963 50.0 0.00 0.0 36.96 4.35 F
349 350 0.323087 ATTACCGACCAACCTTGCCC 60.323 55.0 0.00 0.0 0.00 5.36 F
2079 3187 1.039068 CTCGGATCAGAGATGGCTGT 58.961 55.0 16.95 0.0 40.57 4.40 F
2377 3574 0.894835 TGTCGCAGAAGGCAGACATA 59.105 50.0 8.92 0.0 44.78 2.29 F
2914 4112 0.684153 CAGGGGATGAAACCGCCATT 60.684 55.0 0.00 0.0 42.68 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 2083 0.032540 GCAACAGAAAGGGCAACAGG 59.967 55.000 0.00 0.00 39.74 4.00 R
1863 2971 0.178301 TGCGGTAGTTGTTGGTGACA 59.822 50.000 0.00 0.00 39.83 3.58 R
2293 3490 2.827921 CTGCTTGGATACTTTTGCCCTT 59.172 45.455 0.00 0.00 37.61 3.95 R
2881 4079 0.179045 CCCCTGTTTGATCTAGCGGG 60.179 60.000 11.13 11.13 0.00 6.13 R
3209 4407 1.211212 CATCTCCACTTGCCTCATGGA 59.789 52.381 0.00 0.00 40.27 3.41 R
3898 5448 1.345112 ACTCCCCTCATCCGGGTTTAT 60.345 52.381 0.00 0.00 43.06 1.40 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
21 22 4.153958 TGAATTATGTGTCGTGTTTGGC 57.846 40.909 0.00 0.00 0.00 4.52
22 23 3.057876 TGAATTATGTGTCGTGTTTGGCC 60.058 43.478 0.00 0.00 0.00 5.36
23 24 0.869068 TTATGTGTCGTGTTTGGCCG 59.131 50.000 0.00 0.00 0.00 6.13
24 25 0.033642 TATGTGTCGTGTTTGGCCGA 59.966 50.000 0.00 0.00 0.00 5.54
25 26 0.816018 ATGTGTCGTGTTTGGCCGAA 60.816 50.000 0.00 0.00 34.47 4.30
26 27 0.816018 TGTGTCGTGTTTGGCCGAAT 60.816 50.000 9.15 0.00 34.47 3.34
27 28 0.309612 GTGTCGTGTTTGGCCGAATT 59.690 50.000 9.15 0.00 34.47 2.17
28 29 1.025812 TGTCGTGTTTGGCCGAATTT 58.974 45.000 9.15 0.00 34.47 1.82
29 30 1.405821 TGTCGTGTTTGGCCGAATTTT 59.594 42.857 9.15 0.00 34.47 1.82
30 31 1.784283 GTCGTGTTTGGCCGAATTTTG 59.216 47.619 9.15 0.00 34.47 2.44
31 32 1.135867 CGTGTTTGGCCGAATTTTGG 58.864 50.000 9.15 0.00 0.00 3.28
32 33 1.507562 GTGTTTGGCCGAATTTTGGG 58.492 50.000 9.15 0.00 0.00 4.12
37 38 3.274067 GCCGAATTTTGGGCGAGT 58.726 55.556 4.81 0.00 42.16 4.18
38 39 2.473457 GCCGAATTTTGGGCGAGTA 58.527 52.632 4.81 0.00 42.16 2.59
39 40 1.021968 GCCGAATTTTGGGCGAGTAT 58.978 50.000 4.81 0.00 42.16 2.12
40 41 1.268539 GCCGAATTTTGGGCGAGTATG 60.269 52.381 4.81 0.00 42.16 2.39
41 42 2.285083 CCGAATTTTGGGCGAGTATGA 58.715 47.619 0.00 0.00 0.00 2.15
42 43 2.878406 CCGAATTTTGGGCGAGTATGAT 59.122 45.455 0.00 0.00 0.00 2.45
43 44 3.315191 CCGAATTTTGGGCGAGTATGATT 59.685 43.478 0.00 0.00 0.00 2.57
44 45 4.202010 CCGAATTTTGGGCGAGTATGATTT 60.202 41.667 0.00 0.00 0.00 2.17
45 46 5.339990 CGAATTTTGGGCGAGTATGATTTT 58.660 37.500 0.00 0.00 0.00 1.82
46 47 6.459024 CCGAATTTTGGGCGAGTATGATTTTA 60.459 38.462 0.00 0.00 0.00 1.52
47 48 6.970043 CGAATTTTGGGCGAGTATGATTTTAA 59.030 34.615 0.00 0.00 0.00 1.52
48 49 7.486551 CGAATTTTGGGCGAGTATGATTTTAAA 59.513 33.333 0.00 0.00 0.00 1.52
49 50 9.145865 GAATTTTGGGCGAGTATGATTTTAAAA 57.854 29.630 2.51 2.51 0.00 1.52
50 51 7.876896 TTTTGGGCGAGTATGATTTTAAAAC 57.123 32.000 1.97 0.00 0.00 2.43
51 52 6.576662 TTGGGCGAGTATGATTTTAAAACA 57.423 33.333 1.97 4.43 0.00 2.83
52 53 6.576662 TGGGCGAGTATGATTTTAAAACAA 57.423 33.333 1.97 0.00 0.00 2.83
53 54 6.383415 TGGGCGAGTATGATTTTAAAACAAC 58.617 36.000 1.97 0.00 0.00 3.32
54 55 6.207810 TGGGCGAGTATGATTTTAAAACAACT 59.792 34.615 1.97 4.63 0.00 3.16
55 56 6.526674 GGGCGAGTATGATTTTAAAACAACTG 59.473 38.462 1.97 2.34 0.00 3.16
56 57 6.033513 GGCGAGTATGATTTTAAAACAACTGC 59.966 38.462 1.97 9.80 0.00 4.40
57 58 6.236941 GCGAGTATGATTTTAAAACAACTGCG 60.237 38.462 1.97 10.30 0.00 5.18
58 59 6.795114 CGAGTATGATTTTAAAACAACTGCGT 59.205 34.615 1.97 0.00 0.00 5.24
59 60 7.201149 CGAGTATGATTTTAAAACAACTGCGTG 60.201 37.037 1.97 0.00 0.00 5.34
60 61 7.422399 AGTATGATTTTAAAACAACTGCGTGT 58.578 30.769 1.97 0.00 0.00 4.49
61 62 5.940603 TGATTTTAAAACAACTGCGTGTG 57.059 34.783 1.97 0.00 0.00 3.82
62 63 4.800993 TGATTTTAAAACAACTGCGTGTGG 59.199 37.500 1.97 0.00 0.00 4.17
63 64 2.853731 TTAAAACAACTGCGTGTGGG 57.146 45.000 0.00 0.00 0.00 4.61
64 65 1.025812 TAAAACAACTGCGTGTGGGG 58.974 50.000 0.00 0.00 0.00 4.96
65 66 2.291457 AAAACAACTGCGTGTGGGGC 62.291 55.000 0.00 0.00 0.00 5.80
70 71 4.988598 CTGCGTGTGGGGCGACTT 62.989 66.667 0.00 0.00 0.00 3.01
85 86 4.864334 CTTGGGGCTGGCGGCTAG 62.864 72.222 19.30 9.22 41.46 3.42
98 99 4.365505 GCTAGGAGCCCGATCGCC 62.366 72.222 10.32 5.40 34.48 5.54
99 100 3.686045 CTAGGAGCCCGATCGCCC 61.686 72.222 10.32 7.72 0.00 6.13
108 109 4.908687 CGATCGCCCCGATGCCAA 62.909 66.667 0.26 0.00 47.00 4.52
109 110 2.515991 GATCGCCCCGATGCCAAA 60.516 61.111 4.70 0.00 47.00 3.28
110 111 1.898574 GATCGCCCCGATGCCAAAT 60.899 57.895 4.70 0.00 47.00 2.32
111 112 1.455383 GATCGCCCCGATGCCAAATT 61.455 55.000 4.70 0.00 47.00 1.82
112 113 1.042559 ATCGCCCCGATGCCAAATTT 61.043 50.000 0.00 0.00 45.24 1.82
113 114 0.394488 TCGCCCCGATGCCAAATTTA 60.394 50.000 0.00 0.00 0.00 1.40
114 115 0.673437 CGCCCCGATGCCAAATTTAT 59.327 50.000 0.00 0.00 0.00 1.40
115 116 1.883275 CGCCCCGATGCCAAATTTATA 59.117 47.619 0.00 0.00 0.00 0.98
116 117 2.095263 CGCCCCGATGCCAAATTTATAG 60.095 50.000 0.00 0.00 0.00 1.31
117 118 2.352715 GCCCCGATGCCAAATTTATAGC 60.353 50.000 0.00 0.00 0.00 2.97
118 119 2.231235 CCCCGATGCCAAATTTATAGCC 59.769 50.000 0.00 0.00 0.00 3.93
119 120 2.095263 CCCGATGCCAAATTTATAGCCG 60.095 50.000 0.00 0.00 0.00 5.52
120 121 2.095263 CCGATGCCAAATTTATAGCCGG 60.095 50.000 0.00 0.00 0.00 6.13
121 122 2.668279 CGATGCCAAATTTATAGCCGGC 60.668 50.000 21.89 21.89 40.02 6.13
122 123 0.665835 TGCCAAATTTATAGCCGGCG 59.334 50.000 23.20 0.00 42.57 6.46
123 124 0.663269 GCCAAATTTATAGCCGGCGC 60.663 55.000 23.20 10.58 0.00 6.53
124 125 0.385473 CCAAATTTATAGCCGGCGCG 60.385 55.000 23.20 0.00 41.18 6.86
125 126 0.306533 CAAATTTATAGCCGGCGCGT 59.693 50.000 23.20 13.71 41.18 6.01
126 127 0.584876 AAATTTATAGCCGGCGCGTC 59.415 50.000 23.20 3.30 41.18 5.19
127 128 0.249741 AATTTATAGCCGGCGCGTCT 60.250 50.000 23.20 5.39 41.18 4.18
128 129 0.666577 ATTTATAGCCGGCGCGTCTC 60.667 55.000 23.20 0.00 41.18 3.36
129 130 2.688526 TTTATAGCCGGCGCGTCTCC 62.689 60.000 23.20 0.00 41.18 3.71
140 141 4.147449 CGTCTCCAGGCGGCATGA 62.147 66.667 17.22 5.97 0.00 3.07
141 142 2.507944 GTCTCCAGGCGGCATGAT 59.492 61.111 17.22 0.00 0.00 2.45
142 143 1.153086 GTCTCCAGGCGGCATGATT 60.153 57.895 17.22 0.00 0.00 2.57
143 144 0.749454 GTCTCCAGGCGGCATGATTT 60.749 55.000 17.22 0.00 0.00 2.17
144 145 0.464373 TCTCCAGGCGGCATGATTTC 60.464 55.000 17.22 0.00 0.00 2.17
145 146 0.749091 CTCCAGGCGGCATGATTTCA 60.749 55.000 17.22 0.00 0.00 2.69
146 147 0.749091 TCCAGGCGGCATGATTTCAG 60.749 55.000 17.22 0.00 0.00 3.02
147 148 1.731433 CCAGGCGGCATGATTTCAGG 61.731 60.000 17.22 0.00 0.00 3.86
148 149 0.749091 CAGGCGGCATGATTTCAGGA 60.749 55.000 9.35 0.00 0.00 3.86
149 150 0.465097 AGGCGGCATGATTTCAGGAG 60.465 55.000 13.08 0.00 0.00 3.69
150 151 0.464373 GGCGGCATGATTTCAGGAGA 60.464 55.000 3.07 0.00 0.00 3.71
151 152 1.602311 GCGGCATGATTTCAGGAGAT 58.398 50.000 0.00 0.00 0.00 2.75
152 153 1.266175 GCGGCATGATTTCAGGAGATG 59.734 52.381 0.00 0.00 0.00 2.90
153 154 1.266175 CGGCATGATTTCAGGAGATGC 59.734 52.381 0.00 0.00 38.96 3.91
154 155 2.584236 GGCATGATTTCAGGAGATGCT 58.416 47.619 0.00 0.00 39.51 3.79
155 156 2.553172 GGCATGATTTCAGGAGATGCTC 59.447 50.000 0.00 0.00 39.51 4.26
156 157 3.478509 GCATGATTTCAGGAGATGCTCT 58.521 45.455 0.00 0.00 37.13 4.09
157 158 4.504514 GGCATGATTTCAGGAGATGCTCTA 60.505 45.833 0.00 0.00 39.51 2.43
158 159 5.061853 GCATGATTTCAGGAGATGCTCTAA 58.938 41.667 0.00 0.00 37.13 2.10
159 160 5.049543 GCATGATTTCAGGAGATGCTCTAAC 60.050 44.000 0.00 0.00 37.13 2.34
160 161 5.028549 TGATTTCAGGAGATGCTCTAACC 57.971 43.478 0.00 0.00 0.00 2.85
161 162 4.718774 TGATTTCAGGAGATGCTCTAACCT 59.281 41.667 0.00 0.00 0.00 3.50
162 163 4.744795 TTTCAGGAGATGCTCTAACCTC 57.255 45.455 0.00 0.00 0.00 3.85
163 164 3.388552 TCAGGAGATGCTCTAACCTCA 57.611 47.619 0.00 0.00 0.00 3.86
164 165 3.921104 TCAGGAGATGCTCTAACCTCAT 58.079 45.455 0.00 0.00 0.00 2.90
165 166 5.066913 TCAGGAGATGCTCTAACCTCATA 57.933 43.478 0.00 0.00 0.00 2.15
166 167 5.458595 TCAGGAGATGCTCTAACCTCATAA 58.541 41.667 0.00 0.00 0.00 1.90
167 168 5.538053 TCAGGAGATGCTCTAACCTCATAAG 59.462 44.000 0.00 0.00 0.00 1.73
168 169 4.283212 AGGAGATGCTCTAACCTCATAAGC 59.717 45.833 0.00 0.00 0.00 3.09
169 170 4.283212 GGAGATGCTCTAACCTCATAAGCT 59.717 45.833 0.00 0.00 34.11 3.74
170 171 5.212532 AGATGCTCTAACCTCATAAGCTG 57.787 43.478 0.00 0.00 34.11 4.24
171 172 4.653341 AGATGCTCTAACCTCATAAGCTGT 59.347 41.667 0.00 0.00 34.11 4.40
172 173 4.128925 TGCTCTAACCTCATAAGCTGTG 57.871 45.455 0.00 0.00 34.11 3.66
173 174 3.515502 TGCTCTAACCTCATAAGCTGTGT 59.484 43.478 0.00 0.00 34.11 3.72
174 175 3.868077 GCTCTAACCTCATAAGCTGTGTG 59.132 47.826 0.00 0.00 0.00 3.82
175 176 4.382040 GCTCTAACCTCATAAGCTGTGTGA 60.382 45.833 0.00 0.00 0.00 3.58
176 177 5.330455 TCTAACCTCATAAGCTGTGTGAG 57.670 43.478 13.52 13.52 43.33 3.51
186 187 2.099141 GCTGTGTGAGCCATAGAACA 57.901 50.000 0.00 0.00 42.54 3.18
187 188 1.734465 GCTGTGTGAGCCATAGAACAC 59.266 52.381 0.00 0.00 42.54 3.32
188 189 2.350522 CTGTGTGAGCCATAGAACACC 58.649 52.381 2.64 0.00 41.75 4.16
189 190 1.696884 TGTGTGAGCCATAGAACACCA 59.303 47.619 2.64 0.00 41.75 4.17
190 191 2.305635 TGTGTGAGCCATAGAACACCAT 59.694 45.455 2.64 0.00 41.75 3.55
191 192 3.244875 TGTGTGAGCCATAGAACACCATT 60.245 43.478 2.64 0.00 41.75 3.16
192 193 3.758554 GTGTGAGCCATAGAACACCATTT 59.241 43.478 0.00 0.00 37.53 2.32
193 194 3.758023 TGTGAGCCATAGAACACCATTTG 59.242 43.478 0.00 0.00 33.08 2.32
194 195 2.754552 TGAGCCATAGAACACCATTTGC 59.245 45.455 0.00 0.00 0.00 3.68
195 196 2.099756 GAGCCATAGAACACCATTTGCC 59.900 50.000 0.00 0.00 0.00 4.52
196 197 2.102578 GCCATAGAACACCATTTGCCT 58.897 47.619 0.00 0.00 0.00 4.75
197 198 2.099756 GCCATAGAACACCATTTGCCTC 59.900 50.000 0.00 0.00 0.00 4.70
198 199 2.689983 CCATAGAACACCATTTGCCTCC 59.310 50.000 0.00 0.00 0.00 4.30
199 200 3.624777 CATAGAACACCATTTGCCTCCT 58.375 45.455 0.00 0.00 0.00 3.69
200 201 2.206576 AGAACACCATTTGCCTCCTC 57.793 50.000 0.00 0.00 0.00 3.71
201 202 1.177401 GAACACCATTTGCCTCCTCC 58.823 55.000 0.00 0.00 0.00 4.30
202 203 0.779997 AACACCATTTGCCTCCTCCT 59.220 50.000 0.00 0.00 0.00 3.69
203 204 0.779997 ACACCATTTGCCTCCTCCTT 59.220 50.000 0.00 0.00 0.00 3.36
204 205 1.147817 ACACCATTTGCCTCCTCCTTT 59.852 47.619 0.00 0.00 0.00 3.11
205 206 1.547372 CACCATTTGCCTCCTCCTTTG 59.453 52.381 0.00 0.00 0.00 2.77
209 210 3.445096 CCATTTGCCTCCTCCTTTGTAAG 59.555 47.826 0.00 0.00 0.00 2.34
223 224 5.009610 TCCTTTGTAAGAGTTGTGCCAAATC 59.990 40.000 7.12 7.12 0.00 2.17
226 227 6.403866 TTGTAAGAGTTGTGCCAAATCATT 57.596 33.333 14.72 9.79 0.00 2.57
227 228 6.403866 TGTAAGAGTTGTGCCAAATCATTT 57.596 33.333 14.72 6.62 0.00 2.32
279 280 0.036732 TCACGCTTGGAAGATGGCTT 59.963 50.000 0.00 0.00 36.96 4.35
287 288 3.168035 TGGAAGATGGCTTGCCTAAAA 57.832 42.857 13.18 0.00 41.28 1.52
288 289 3.505386 TGGAAGATGGCTTGCCTAAAAA 58.495 40.909 13.18 0.00 41.28 1.94
289 290 4.095946 TGGAAGATGGCTTGCCTAAAAAT 58.904 39.130 13.18 0.00 41.28 1.82
290 291 4.081531 TGGAAGATGGCTTGCCTAAAAATG 60.082 41.667 13.18 0.00 41.28 2.32
291 292 4.436332 GAAGATGGCTTGCCTAAAAATGG 58.564 43.478 13.18 0.00 33.61 3.16
292 293 2.767960 AGATGGCTTGCCTAAAAATGGG 59.232 45.455 13.18 0.00 0.00 4.00
293 294 1.274712 TGGCTTGCCTAAAAATGGGG 58.725 50.000 13.18 0.00 0.00 4.96
303 304 3.258622 CCTAAAAATGGGGGCAACGTTTA 59.741 43.478 0.00 0.00 37.60 2.01
304 305 4.081365 CCTAAAAATGGGGGCAACGTTTAT 60.081 41.667 0.00 0.00 37.60 1.40
314 315 5.885912 GGGGGCAACGTTTATATGATCATAT 59.114 40.000 27.06 27.06 36.16 1.78
323 324 9.803315 ACGTTTATATGATCATATATTGACGCT 57.197 29.630 33.65 26.31 38.77 5.07
335 336 1.930567 TTGACGCTTCGCCTATTACC 58.069 50.000 0.00 0.00 0.00 2.85
349 350 0.323087 ATTACCGACCAACCTTGCCC 60.323 55.000 0.00 0.00 0.00 5.36
395 398 1.375396 CGAGGACCGATTGGCAACA 60.375 57.895 0.00 0.00 44.01 3.33
448 486 2.341846 TTTGCTGGAGAACTTTCGGT 57.658 45.000 0.00 0.00 0.00 4.69
451 489 2.244695 TGCTGGAGAACTTTCGGTCTA 58.755 47.619 0.00 0.00 0.00 2.59
453 491 3.260884 TGCTGGAGAACTTTCGGTCTATT 59.739 43.478 0.00 0.00 0.00 1.73
454 492 3.866327 GCTGGAGAACTTTCGGTCTATTC 59.134 47.826 0.00 0.00 0.00 1.75
455 493 4.620803 GCTGGAGAACTTTCGGTCTATTCA 60.621 45.833 0.00 0.00 0.00 2.57
456 494 5.665459 CTGGAGAACTTTCGGTCTATTCAT 58.335 41.667 0.00 0.00 0.00 2.57
459 497 6.070767 TGGAGAACTTTCGGTCTATTCATCTT 60.071 38.462 0.00 0.00 0.00 2.40
460 498 6.819146 GGAGAACTTTCGGTCTATTCATCTTT 59.181 38.462 0.00 0.00 0.00 2.52
461 499 7.980099 GGAGAACTTTCGGTCTATTCATCTTTA 59.020 37.037 0.00 0.00 0.00 1.85
465 503 9.667107 AACTTTCGGTCTATTCATCTTTAATCA 57.333 29.630 0.00 0.00 0.00 2.57
466 504 9.838339 ACTTTCGGTCTATTCATCTTTAATCAT 57.162 29.630 0.00 0.00 0.00 2.45
513 557 7.326789 CAGAAAATAGTACAATGCTGGTGTTTG 59.673 37.037 0.00 0.00 0.00 2.93
516 560 2.548057 AGTACAATGCTGGTGTTTGTCG 59.452 45.455 0.00 0.00 35.37 4.35
518 562 2.566913 ACAATGCTGGTGTTTGTCGTA 58.433 42.857 0.00 0.00 0.00 3.43
537 581 4.084507 CGTAAGAAAAAGCAAGAGCATCG 58.915 43.478 0.00 0.00 42.26 3.84
541 585 4.319177 AGAAAAAGCAAGAGCATCGTAGT 58.681 39.130 0.00 0.00 45.49 2.73
543 587 2.751166 AAGCAAGAGCATCGTAGTGT 57.249 45.000 0.00 0.00 45.49 3.55
548 593 5.178797 AGCAAGAGCATCGTAGTGTAAAAT 58.821 37.500 0.00 0.00 45.49 1.82
588 634 7.802117 TCTTTAGGTAAAATAGGGGACATCAG 58.198 38.462 0.00 0.00 0.00 2.90
599 645 2.638363 GGGGACATCAGTCTATTACCCC 59.362 54.545 0.00 0.00 46.94 4.95
636 1289 3.222603 GTTGTTGGTCATCTTGGAACCT 58.777 45.455 0.00 0.00 0.00 3.50
639 1292 5.255397 TGTTGGTCATCTTGGAACCTTAT 57.745 39.130 0.00 0.00 0.00 1.73
641 1294 5.476599 TGTTGGTCATCTTGGAACCTTATTG 59.523 40.000 0.00 0.00 0.00 1.90
643 1296 6.381498 TGGTCATCTTGGAACCTTATTGTA 57.619 37.500 0.00 0.00 0.00 2.41
646 1299 6.657541 GGTCATCTTGGAACCTTATTGTAACA 59.342 38.462 0.00 0.00 0.00 2.41
647 1300 7.339466 GGTCATCTTGGAACCTTATTGTAACAT 59.661 37.037 0.00 0.00 0.00 2.71
650 1303 8.739039 CATCTTGGAACCTTATTGTAACATTGA 58.261 33.333 0.00 0.00 0.00 2.57
651 1304 8.877864 TCTTGGAACCTTATTGTAACATTGAT 57.122 30.769 0.00 0.00 0.00 2.57
653 1306 9.927668 CTTGGAACCTTATTGTAACATTGATTT 57.072 29.630 0.00 0.00 0.00 2.17
882 1883 9.973450 TGAGATATTTCTTGCAAGTAGATAGAC 57.027 33.333 25.19 16.77 30.30 2.59
883 1884 9.973450 GAGATATTTCTTGCAAGTAGATAGACA 57.027 33.333 25.19 0.22 30.30 3.41
886 1887 6.727824 TTTCTTGCAAGTAGATAGACAAGC 57.272 37.500 25.19 0.00 35.60 4.01
1397 2469 2.963320 GTTCGTGGTGTCGGCGTT 60.963 61.111 6.85 0.00 0.00 4.84
1685 2766 2.178521 CGAGACGGACTGGTTCGG 59.821 66.667 6.38 0.00 0.00 4.30
2001 3109 1.447140 GTTCATGTGCTCCGGCGTA 60.447 57.895 6.01 0.00 42.25 4.42
2069 3177 1.450312 GTGGCAACCCTCGGATCAG 60.450 63.158 0.00 0.00 0.00 2.90
2079 3187 1.039068 CTCGGATCAGAGATGGCTGT 58.961 55.000 16.95 0.00 40.57 4.40
2138 3286 8.486210 ACAACACCATTGATGATACATAGTACT 58.514 33.333 0.00 0.00 30.22 2.73
2162 3319 1.379044 GAGATTGCACACCAGGGGG 60.379 63.158 0.00 0.00 41.29 5.40
2179 3336 5.955355 CCAGGGGGTTTTATTTCTGACATTA 59.045 40.000 0.00 0.00 0.00 1.90
2183 3340 9.111519 AGGGGGTTTTATTTCTGACATTATTTT 57.888 29.630 0.00 0.00 0.00 1.82
2377 3574 0.894835 TGTCGCAGAAGGCAGACATA 59.105 50.000 8.92 0.00 44.78 2.29
2410 3607 1.225704 CATCCCCTTGGTGGAGCTC 59.774 63.158 4.71 4.71 38.35 4.09
2666 3864 6.238676 GCTAGTATACGAGTTCATCTCCAACA 60.239 42.308 13.64 0.00 39.84 3.33
2683 3881 3.502211 CCAACAGGACACTTTACCATCAC 59.498 47.826 0.00 0.00 0.00 3.06
2779 3977 1.064296 CGCGTATCTTCACTCGGCT 59.936 57.895 0.00 0.00 0.00 5.52
2881 4079 1.538047 TTGGAGCTTCAAGGTGCATC 58.462 50.000 11.94 0.00 43.33 3.91
2914 4112 0.684153 CAGGGGATGAAACCGCCATT 60.684 55.000 0.00 0.00 42.68 3.16
3145 4343 2.170166 GTCATGATGGAAGGTGGCAAA 58.830 47.619 0.00 0.00 0.00 3.68
3310 4511 6.974622 CACAAGGTTATACAATGATTGAAGGC 59.025 38.462 12.80 0.00 0.00 4.35
3364 4565 4.640647 AGCCGGGAAGAAGAATATTTGTTC 59.359 41.667 2.18 0.00 33.48 3.18
3430 4631 1.551430 ACATGGACCAAATGGCATGTG 59.449 47.619 18.84 10.85 42.95 3.21
3504 4713 7.905604 TCATATATACCAAAGCGGAAGAATG 57.094 36.000 0.00 0.00 38.63 2.67
3531 4740 5.538053 TGCCTTCACATAAATCAAAGAACCA 59.462 36.000 0.00 0.00 0.00 3.67
3694 4907 2.675844 CAAAATGCCATGCTCAATGTGG 59.324 45.455 0.00 0.00 34.11 4.17
3898 5448 5.445964 GCCCAAAATATGAGGGAGACTAAA 58.554 41.667 10.70 0.00 45.80 1.85
3997 5547 5.030295 GCATGAATACGAATGACAAGGTTG 58.970 41.667 0.00 0.00 0.00 3.77
4195 5745 2.369394 CCAACTAAGGGCATCTCCAAC 58.631 52.381 0.00 0.00 36.21 3.77
4215 5765 2.584608 CAACCCGCGGATTCCTCT 59.415 61.111 30.73 0.00 0.00 3.69
4229 5779 5.336055 CGGATTCCTCTGGTATATGTCTGTC 60.336 48.000 0.30 0.00 0.00 3.51
4261 5811 2.821969 GACATGGTCCATGGGCATAATC 59.178 50.000 30.96 16.36 45.16 1.75
4297 5847 7.308589 GCCATCCATCGCTAATTACAAAGTATT 60.309 37.037 0.00 0.00 0.00 1.89
4363 5913 7.558444 GGTGGGATATTTGTTATTTAGTGTCCA 59.442 37.037 0.00 0.00 0.00 4.02
4385 5935 4.711355 CAGTTGGGAGAAGAGAGAGAAGAT 59.289 45.833 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.498082 GGCCAAACACGACACATAATTC 58.502 45.455 0.00 0.00 0.00 2.17
3 4 1.466950 CGGCCAAACACGACACATAAT 59.533 47.619 2.24 0.00 0.00 1.28
6 7 0.816018 TTCGGCCAAACACGACACAT 60.816 50.000 2.24 0.00 39.04 3.21
9 10 1.025812 AAATTCGGCCAAACACGACA 58.974 45.000 2.24 0.00 39.04 4.35
10 11 1.784283 CAAAATTCGGCCAAACACGAC 59.216 47.619 2.24 0.00 39.04 4.34
11 12 1.269309 CCAAAATTCGGCCAAACACGA 60.269 47.619 2.24 0.00 37.33 4.35
12 13 1.135867 CCAAAATTCGGCCAAACACG 58.864 50.000 2.24 0.00 0.00 4.49
13 14 1.507562 CCCAAAATTCGGCCAAACAC 58.492 50.000 2.24 0.00 0.00 3.32
14 15 0.250081 GCCCAAAATTCGGCCAAACA 60.250 50.000 2.24 0.00 39.39 2.83
15 16 1.288419 CGCCCAAAATTCGGCCAAAC 61.288 55.000 2.24 0.00 42.53 2.93
16 17 1.005630 CGCCCAAAATTCGGCCAAA 60.006 52.632 2.24 0.00 42.53 3.28
17 18 1.872197 CTCGCCCAAAATTCGGCCAA 61.872 55.000 2.24 0.00 42.53 4.52
18 19 2.282532 TCGCCCAAAATTCGGCCA 60.283 55.556 2.24 0.00 42.53 5.36
19 20 1.027792 TACTCGCCCAAAATTCGGCC 61.028 55.000 0.00 0.00 42.53 6.13
20 21 1.021968 ATACTCGCCCAAAATTCGGC 58.978 50.000 1.89 1.89 42.05 5.54
21 22 2.285083 TCATACTCGCCCAAAATTCGG 58.715 47.619 0.00 0.00 0.00 4.30
22 23 4.552166 AATCATACTCGCCCAAAATTCG 57.448 40.909 0.00 0.00 0.00 3.34
23 24 8.696410 TTTAAAATCATACTCGCCCAAAATTC 57.304 30.769 0.00 0.00 0.00 2.17
24 25 8.931775 GTTTTAAAATCATACTCGCCCAAAATT 58.068 29.630 3.52 0.00 0.00 1.82
25 26 8.091449 TGTTTTAAAATCATACTCGCCCAAAAT 58.909 29.630 3.52 0.00 0.00 1.82
26 27 7.434492 TGTTTTAAAATCATACTCGCCCAAAA 58.566 30.769 3.52 0.00 0.00 2.44
27 28 6.982852 TGTTTTAAAATCATACTCGCCCAAA 58.017 32.000 3.52 0.00 0.00 3.28
28 29 6.576662 TGTTTTAAAATCATACTCGCCCAA 57.423 33.333 3.52 0.00 0.00 4.12
29 30 6.207810 AGTTGTTTTAAAATCATACTCGCCCA 59.792 34.615 3.52 0.00 0.00 5.36
30 31 6.526674 CAGTTGTTTTAAAATCATACTCGCCC 59.473 38.462 3.52 0.00 0.00 6.13
31 32 6.033513 GCAGTTGTTTTAAAATCATACTCGCC 59.966 38.462 3.52 0.00 0.00 5.54
32 33 6.236941 CGCAGTTGTTTTAAAATCATACTCGC 60.237 38.462 3.52 9.84 0.00 5.03
33 34 6.795114 ACGCAGTTGTTTTAAAATCATACTCG 59.205 34.615 3.52 11.70 37.78 4.18
34 35 7.589954 ACACGCAGTTGTTTTAAAATCATACTC 59.410 33.333 3.52 0.00 41.61 2.59
35 36 7.378461 CACACGCAGTTGTTTTAAAATCATACT 59.622 33.333 3.52 3.23 41.61 2.12
36 37 7.358023 CCACACGCAGTTGTTTTAAAATCATAC 60.358 37.037 3.52 1.08 41.61 2.39
37 38 6.638873 CCACACGCAGTTGTTTTAAAATCATA 59.361 34.615 3.52 0.00 41.61 2.15
38 39 5.461737 CCACACGCAGTTGTTTTAAAATCAT 59.538 36.000 3.52 0.00 41.61 2.45
39 40 4.800993 CCACACGCAGTTGTTTTAAAATCA 59.199 37.500 3.52 1.91 41.61 2.57
40 41 4.208253 CCCACACGCAGTTGTTTTAAAATC 59.792 41.667 3.52 0.00 41.61 2.17
41 42 4.116238 CCCACACGCAGTTGTTTTAAAAT 58.884 39.130 3.52 0.00 41.61 1.82
42 43 3.512680 CCCACACGCAGTTGTTTTAAAA 58.487 40.909 0.00 0.00 41.61 1.52
43 44 2.159226 CCCCACACGCAGTTGTTTTAAA 60.159 45.455 0.00 0.00 41.61 1.52
44 45 1.405821 CCCCACACGCAGTTGTTTTAA 59.594 47.619 0.00 0.00 41.61 1.52
45 46 1.025812 CCCCACACGCAGTTGTTTTA 58.974 50.000 0.00 0.00 41.61 1.52
46 47 1.813192 CCCCACACGCAGTTGTTTT 59.187 52.632 0.00 0.00 41.61 2.43
47 48 2.781158 GCCCCACACGCAGTTGTTT 61.781 57.895 0.00 0.00 41.61 2.83
48 49 3.216292 GCCCCACACGCAGTTGTT 61.216 61.111 0.00 0.00 41.61 2.83
53 54 4.988598 AAGTCGCCCCACACGCAG 62.989 66.667 0.00 0.00 0.00 5.18
68 69 4.864334 CTAGCCGCCAGCCCCAAG 62.864 72.222 0.00 0.00 45.47 3.61
81 82 4.365505 GGCGATCGGGCTCCTAGC 62.366 72.222 18.30 0.00 41.46 3.42
82 83 3.686045 GGGCGATCGGGCTCCTAG 61.686 72.222 18.30 0.00 41.87 3.02
91 92 4.908687 TTGGCATCGGGGCGATCG 62.909 66.667 11.69 11.69 45.19 3.69
92 93 1.455383 AATTTGGCATCGGGGCGATC 61.455 55.000 0.00 0.00 45.19 3.69
96 97 2.352715 GCTATAAATTTGGCATCGGGGC 60.353 50.000 0.00 0.00 43.73 5.80
97 98 2.231235 GGCTATAAATTTGGCATCGGGG 59.769 50.000 0.00 0.00 0.00 5.73
98 99 2.095263 CGGCTATAAATTTGGCATCGGG 60.095 50.000 0.00 0.00 0.00 5.14
99 100 2.095263 CCGGCTATAAATTTGGCATCGG 60.095 50.000 0.00 8.05 0.00 4.18
100 101 2.668279 GCCGGCTATAAATTTGGCATCG 60.668 50.000 22.15 7.01 42.03 3.84
101 102 2.668279 CGCCGGCTATAAATTTGGCATC 60.668 50.000 26.68 0.00 42.57 3.91
102 103 1.269448 CGCCGGCTATAAATTTGGCAT 59.731 47.619 26.68 0.00 42.57 4.40
103 104 0.665835 CGCCGGCTATAAATTTGGCA 59.334 50.000 26.68 0.00 42.57 4.92
104 105 0.663269 GCGCCGGCTATAAATTTGGC 60.663 55.000 26.68 12.59 39.10 4.52
105 106 0.385473 CGCGCCGGCTATAAATTTGG 60.385 55.000 26.68 5.48 36.88 3.28
106 107 0.306533 ACGCGCCGGCTATAAATTTG 59.693 50.000 26.68 6.32 36.88 2.32
107 108 0.584876 GACGCGCCGGCTATAAATTT 59.415 50.000 26.68 0.00 36.88 1.82
108 109 0.249741 AGACGCGCCGGCTATAAATT 60.250 50.000 26.68 0.53 46.54 1.82
109 110 1.366366 AGACGCGCCGGCTATAAAT 59.634 52.632 26.68 3.26 46.54 1.40
110 111 2.809706 AGACGCGCCGGCTATAAA 59.190 55.556 26.68 0.00 46.54 1.40
123 124 2.930385 AATCATGCCGCCTGGAGACG 62.930 60.000 0.00 0.00 37.49 4.18
124 125 0.749454 AAATCATGCCGCCTGGAGAC 60.749 55.000 0.00 0.00 37.49 3.36
125 126 0.464373 GAAATCATGCCGCCTGGAGA 60.464 55.000 0.00 0.00 37.49 3.71
126 127 0.749091 TGAAATCATGCCGCCTGGAG 60.749 55.000 0.00 0.00 37.49 3.86
127 128 0.749091 CTGAAATCATGCCGCCTGGA 60.749 55.000 0.00 0.00 37.49 3.86
128 129 1.731433 CCTGAAATCATGCCGCCTGG 61.731 60.000 0.00 0.00 38.77 4.45
129 130 0.749091 TCCTGAAATCATGCCGCCTG 60.749 55.000 0.00 0.00 0.00 4.85
130 131 0.465097 CTCCTGAAATCATGCCGCCT 60.465 55.000 0.00 0.00 0.00 5.52
131 132 0.464373 TCTCCTGAAATCATGCCGCC 60.464 55.000 0.00 0.00 0.00 6.13
132 133 1.266175 CATCTCCTGAAATCATGCCGC 59.734 52.381 0.00 0.00 0.00 6.53
133 134 1.266175 GCATCTCCTGAAATCATGCCG 59.734 52.381 0.00 0.00 0.00 5.69
134 135 2.553172 GAGCATCTCCTGAAATCATGCC 59.447 50.000 0.00 0.00 34.43 4.40
135 136 3.900388 GAGCATCTCCTGAAATCATGC 57.100 47.619 0.00 0.00 0.00 4.06
149 150 4.749099 CACAGCTTATGAGGTTAGAGCATC 59.251 45.833 0.00 0.00 35.86 3.91
150 151 4.163078 ACACAGCTTATGAGGTTAGAGCAT 59.837 41.667 1.67 0.00 35.86 3.79
151 152 3.515502 ACACAGCTTATGAGGTTAGAGCA 59.484 43.478 1.67 0.00 35.86 4.26
152 153 3.868077 CACACAGCTTATGAGGTTAGAGC 59.132 47.826 1.67 0.00 0.00 4.09
153 154 5.330455 TCACACAGCTTATGAGGTTAGAG 57.670 43.478 1.67 0.00 0.00 2.43
154 155 4.382040 GCTCACACAGCTTATGAGGTTAGA 60.382 45.833 16.57 0.00 45.83 2.10
155 156 3.868077 GCTCACACAGCTTATGAGGTTAG 59.132 47.826 16.57 0.11 45.83 2.34
156 157 3.861840 GCTCACACAGCTTATGAGGTTA 58.138 45.455 16.57 0.00 45.83 2.85
157 158 2.704572 GCTCACACAGCTTATGAGGTT 58.295 47.619 16.57 0.00 45.83 3.50
158 159 2.393271 GCTCACACAGCTTATGAGGT 57.607 50.000 16.57 0.00 45.83 3.85
168 169 2.289631 TGGTGTTCTATGGCTCACACAG 60.290 50.000 3.87 0.00 41.17 3.66
169 170 1.696884 TGGTGTTCTATGGCTCACACA 59.303 47.619 3.87 0.00 41.17 3.72
170 171 2.472695 TGGTGTTCTATGGCTCACAC 57.527 50.000 0.00 0.00 39.08 3.82
171 172 3.719268 AATGGTGTTCTATGGCTCACA 57.281 42.857 0.00 0.00 33.17 3.58
172 173 3.428045 GCAAATGGTGTTCTATGGCTCAC 60.428 47.826 0.00 0.00 0.00 3.51
173 174 2.754552 GCAAATGGTGTTCTATGGCTCA 59.245 45.455 0.00 0.00 0.00 4.26
174 175 2.099756 GGCAAATGGTGTTCTATGGCTC 59.900 50.000 0.00 0.00 0.00 4.70
175 176 2.102578 GGCAAATGGTGTTCTATGGCT 58.897 47.619 0.00 0.00 0.00 4.75
176 177 2.099756 GAGGCAAATGGTGTTCTATGGC 59.900 50.000 0.00 0.00 0.00 4.40
177 178 2.689983 GGAGGCAAATGGTGTTCTATGG 59.310 50.000 0.00 0.00 0.00 2.74
178 179 3.624777 AGGAGGCAAATGGTGTTCTATG 58.375 45.455 0.00 0.00 0.00 2.23
179 180 3.372025 GGAGGAGGCAAATGGTGTTCTAT 60.372 47.826 0.00 0.00 0.00 1.98
180 181 2.026262 GGAGGAGGCAAATGGTGTTCTA 60.026 50.000 0.00 0.00 0.00 2.10
181 182 1.272147 GGAGGAGGCAAATGGTGTTCT 60.272 52.381 0.00 0.00 0.00 3.01
182 183 1.177401 GGAGGAGGCAAATGGTGTTC 58.823 55.000 0.00 0.00 0.00 3.18
183 184 0.779997 AGGAGGAGGCAAATGGTGTT 59.220 50.000 0.00 0.00 0.00 3.32
184 185 0.779997 AAGGAGGAGGCAAATGGTGT 59.220 50.000 0.00 0.00 0.00 4.16
185 186 1.547372 CAAAGGAGGAGGCAAATGGTG 59.453 52.381 0.00 0.00 0.00 4.17
186 187 1.147817 ACAAAGGAGGAGGCAAATGGT 59.852 47.619 0.00 0.00 0.00 3.55
187 188 1.928868 ACAAAGGAGGAGGCAAATGG 58.071 50.000 0.00 0.00 0.00 3.16
188 189 4.335416 TCTTACAAAGGAGGAGGCAAATG 58.665 43.478 0.00 0.00 0.00 2.32
189 190 4.043435 ACTCTTACAAAGGAGGAGGCAAAT 59.957 41.667 0.00 0.00 34.22 2.32
190 191 3.394606 ACTCTTACAAAGGAGGAGGCAAA 59.605 43.478 0.00 0.00 34.22 3.68
191 192 2.979678 ACTCTTACAAAGGAGGAGGCAA 59.020 45.455 0.00 0.00 34.22 4.52
192 193 2.621070 ACTCTTACAAAGGAGGAGGCA 58.379 47.619 0.00 0.00 34.22 4.75
193 194 3.244596 ACAACTCTTACAAAGGAGGAGGC 60.245 47.826 0.00 0.00 34.22 4.70
194 195 4.319177 CACAACTCTTACAAAGGAGGAGG 58.681 47.826 0.00 0.00 34.22 4.30
195 196 3.748568 GCACAACTCTTACAAAGGAGGAG 59.251 47.826 0.00 0.00 34.22 3.69
196 197 3.496160 GGCACAACTCTTACAAAGGAGGA 60.496 47.826 0.00 0.00 34.22 3.71
197 198 2.814336 GGCACAACTCTTACAAAGGAGG 59.186 50.000 0.00 0.00 34.22 4.30
198 199 3.476552 TGGCACAACTCTTACAAAGGAG 58.523 45.455 0.00 0.00 31.92 3.69
199 200 3.569194 TGGCACAACTCTTACAAAGGA 57.431 42.857 0.00 0.00 31.92 3.36
236 237 8.959548 TGAATCTCATTGATAGCAAGCTAAAAA 58.040 29.630 5.81 4.34 37.45 1.94
287 288 3.904717 TCATATAAACGTTGCCCCCATT 58.095 40.909 0.00 0.00 0.00 3.16
288 289 3.586470 TCATATAAACGTTGCCCCCAT 57.414 42.857 0.00 0.00 0.00 4.00
289 290 3.117851 TGATCATATAAACGTTGCCCCCA 60.118 43.478 0.00 0.00 0.00 4.96
290 291 3.482436 TGATCATATAAACGTTGCCCCC 58.518 45.455 0.00 0.00 0.00 5.40
291 292 8.677148 ATATATGATCATATAAACGTTGCCCC 57.323 34.615 30.07 0.00 39.07 5.80
292 293 9.935682 CAATATATGATCATATAAACGTTGCCC 57.064 33.333 30.07 0.00 39.07 5.36
323 324 1.134729 GGTTGGTCGGTAATAGGCGAA 60.135 52.381 0.00 0.00 0.00 4.70
335 336 4.278513 TGGGGGCAAGGTTGGTCG 62.279 66.667 0.00 0.00 0.00 4.79
349 350 4.911390 AGGAAGTTTACAACTCATCTGGG 58.089 43.478 0.00 0.00 41.91 4.45
351 352 4.627467 CCGAGGAAGTTTACAACTCATCTG 59.373 45.833 0.00 0.00 41.91 2.90
427 465 3.020984 ACCGAAAGTTCTCCAGCAAAAA 58.979 40.909 0.00 0.00 0.00 1.94
430 468 1.416401 AGACCGAAAGTTCTCCAGCAA 59.584 47.619 0.00 0.00 0.00 3.91
431 469 1.048601 AGACCGAAAGTTCTCCAGCA 58.951 50.000 0.00 0.00 0.00 4.41
433 471 5.073311 TGAATAGACCGAAAGTTCTCCAG 57.927 43.478 0.00 0.00 0.00 3.86
435 473 5.908341 AGATGAATAGACCGAAAGTTCTCC 58.092 41.667 0.00 0.00 0.00 3.71
436 474 7.835634 AAAGATGAATAGACCGAAAGTTCTC 57.164 36.000 0.00 0.00 0.00 2.87
437 475 9.892130 ATTAAAGATGAATAGACCGAAAGTTCT 57.108 29.630 0.00 0.00 0.00 3.01
467 505 9.871175 TTTTCTGGGGTTATTAAGAAAACTACT 57.129 29.630 5.56 0.00 41.37 2.57
486 530 5.415701 ACACCAGCATTGTACTATTTTCTGG 59.584 40.000 19.15 19.15 43.90 3.86
487 531 6.500684 ACACCAGCATTGTACTATTTTCTG 57.499 37.500 0.00 0.00 0.00 3.02
497 541 2.566913 ACGACAAACACCAGCATTGTA 58.433 42.857 0.00 0.00 37.41 2.41
498 542 1.388547 ACGACAAACACCAGCATTGT 58.611 45.000 0.00 0.00 39.82 2.71
502 546 2.605837 TCTTACGACAAACACCAGCA 57.394 45.000 0.00 0.00 0.00 4.41
513 557 4.468095 TGCTCTTGCTTTTTCTTACGAC 57.532 40.909 0.00 0.00 40.48 4.34
516 560 5.035784 ACGATGCTCTTGCTTTTTCTTAC 57.964 39.130 0.00 0.00 40.48 2.34
518 562 4.757149 ACTACGATGCTCTTGCTTTTTCTT 59.243 37.500 0.00 0.00 40.48 2.52
526 570 4.921470 TTTTACACTACGATGCTCTTGC 57.079 40.909 0.00 0.00 40.20 4.01
528 572 5.470845 GCATTTTACACTACGATGCTCTT 57.529 39.130 0.00 0.00 39.84 2.85
548 593 5.570320 ACCTAAAGAATTTCTGCCTTAGCA 58.430 37.500 0.00 0.00 43.18 3.49
570 615 9.708092 GTAATAGACTGATGTCCCCTATTTTAC 57.292 37.037 0.00 0.00 43.91 2.01
578 624 2.638363 GGGGTAATAGACTGATGTCCCC 59.362 54.545 0.00 0.00 43.91 4.81
717 1536 6.613755 ACAAGTGTATGTGAGTTTACCAAC 57.386 37.500 0.00 0.00 30.82 3.77
719 1538 8.911918 AATTACAAGTGTATGTGAGTTTACCA 57.088 30.769 0.00 0.00 34.75 3.25
726 1545 8.322906 TCTCCAAAATTACAAGTGTATGTGAG 57.677 34.615 0.00 0.00 34.75 3.51
731 1550 8.877864 TGGATTCTCCAAAATTACAAGTGTAT 57.122 30.769 0.00 0.00 45.00 2.29
828 1823 5.010282 AGGACAAGGACACCAAAATATGAC 58.990 41.667 0.00 0.00 0.00 3.06
838 1833 3.260884 TCTCATACAAGGACAAGGACACC 59.739 47.826 0.00 0.00 0.00 4.16
880 1881 1.711206 GTTGACCGACTAGGCTTGTC 58.289 55.000 17.50 17.50 46.52 3.18
882 1883 1.352156 GCGTTGACCGACTAGGCTTG 61.352 60.000 0.00 0.00 46.52 4.01
883 1884 1.080025 GCGTTGACCGACTAGGCTT 60.080 57.895 0.00 0.00 46.52 4.35
884 1885 1.533469 AAGCGTTGACCGACTAGGCT 61.533 55.000 0.00 0.00 46.52 4.58
885 1886 1.080025 AAGCGTTGACCGACTAGGC 60.080 57.895 0.00 0.00 46.52 3.93
1020 2083 0.032540 GCAACAGAAAGGGCAACAGG 59.967 55.000 0.00 0.00 39.74 4.00
1397 2469 0.880278 GAGCACGAACCTGTTGAGCA 60.880 55.000 0.00 0.00 0.00 4.26
1400 2472 0.531974 GGTGAGCACGAACCTGTTGA 60.532 55.000 0.00 0.00 33.40 3.18
1863 2971 0.178301 TGCGGTAGTTGTTGGTGACA 59.822 50.000 0.00 0.00 39.83 3.58
1973 3081 4.679106 CGGAGCACATGAACTTATCAGTCT 60.679 45.833 0.00 0.00 42.53 3.24
1975 3083 3.525537 CGGAGCACATGAACTTATCAGT 58.474 45.455 0.00 0.00 42.53 3.41
2069 3177 4.197750 AGATGATTTGACACAGCCATCTC 58.802 43.478 0.00 0.00 36.90 2.75
2079 3187 7.615757 TCACCTAGACTTAGAGATGATTTGACA 59.384 37.037 0.00 0.00 0.00 3.58
2189 3346 7.574217 GCCGATACTTAAACCTGAAAAATGTCA 60.574 37.037 0.00 0.00 0.00 3.58
2293 3490 2.827921 CTGCTTGGATACTTTTGCCCTT 59.172 45.455 0.00 0.00 37.61 3.95
2410 3607 0.535102 AGTTGTTGGTGGCCTTCTCG 60.535 55.000 3.32 0.00 0.00 4.04
2666 3864 3.650942 TGAAGGTGATGGTAAAGTGTCCT 59.349 43.478 0.00 0.00 0.00 3.85
2779 3977 4.358214 TGTGGACTATAGGGAATGACACA 58.642 43.478 4.43 5.68 34.37 3.72
2881 4079 0.179045 CCCCTGTTTGATCTAGCGGG 60.179 60.000 11.13 11.13 0.00 6.13
2914 4112 2.354328 AGGTACCCAAATGTCCCTTGA 58.646 47.619 8.74 0.00 0.00 3.02
3145 4343 9.860898 GCCAACATAATTACTTCTTCAATCTTT 57.139 29.630 0.00 0.00 0.00 2.52
3209 4407 1.211212 CATCTCCACTTGCCTCATGGA 59.789 52.381 0.00 0.00 40.27 3.41
3310 4511 1.601419 TAACCTCCTCCGTGCTTCCG 61.601 60.000 0.00 0.00 0.00 4.30
3478 4687 9.599866 CATTCTTCCGCTTTGGTATATATGATA 57.400 33.333 0.00 0.00 39.52 2.15
3504 4713 5.653507 TCTTTGATTTATGTGAAGGCATGC 58.346 37.500 9.90 9.90 0.00 4.06
3531 4740 9.028284 CCTTTGGTTTAGATATGCATATCCATT 57.972 33.333 33.32 22.03 39.94 3.16
3717 4936 3.470645 CCCAAAATACGAGGGGACTAG 57.529 52.381 0.00 0.00 44.43 2.57
3875 5424 3.584733 AGTCTCCCTCATATTTTGGGC 57.415 47.619 0.00 0.00 40.69 5.36
3898 5448 1.345112 ACTCCCCTCATCCGGGTTTAT 60.345 52.381 0.00 0.00 43.06 1.40
3972 5522 4.699735 ACCTTGTCATTCGTATTCATGCAA 59.300 37.500 0.00 0.00 0.00 4.08
3974 5524 4.882671 ACCTTGTCATTCGTATTCATGC 57.117 40.909 0.00 0.00 0.00 4.06
3997 5547 2.774234 TCAAGGTGATGAGAGAATCCCC 59.226 50.000 0.00 0.00 33.66 4.81
4206 5756 5.777732 AGACAGACATATACCAGAGGAATCC 59.222 44.000 0.00 0.00 0.00 3.01
4215 5765 6.239204 CCGGACATAAAGACAGACATATACCA 60.239 42.308 0.00 0.00 0.00 3.25
4297 5847 2.266279 ACCTTTTCTCCTTCCATCCGA 58.734 47.619 0.00 0.00 0.00 4.55
4363 5913 4.396357 TCTTCTCTCTCTTCTCCCAACT 57.604 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.