Multiple sequence alignment - TraesCS4A01G397200

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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 TraesCS4A01G397200 chr4A 100.000 2810 0 0 1 2810 672408546 672411355 0.000000e+00 5190.0
1 TraesCS4A01G397200 chr4A 79.371 1939 341 42 354 2266 672516826 672518731 0.000000e+00 1310.0
2 TraesCS4A01G397200 chr4A 79.202 1404 259 25 435 1831 669921697 669920320 0.000000e+00 944.0
3 TraesCS4A01G397200 chr4A 78.233 1539 246 56 354 1831 672319078 672320588 0.000000e+00 904.0
4 TraesCS4A01G397200 chr4A 78.252 1407 256 31 433 1831 672000655 672002019 0.000000e+00 857.0
5 TraesCS4A01G397200 chr4A 85.294 442 56 4 535 973 672178087 672178522 5.520000e-122 448.0
6 TraesCS4A01G397200 chr4A 87.537 337 42 0 1495 1831 672197350 672197686 9.440000e-105 390.0
7 TraesCS4A01G397200 chr4A 77.147 652 137 7 355 1003 670980805 670980163 4.420000e-98 368.0
8 TraesCS4A01G397200 chr4A 77.472 617 118 12 1211 1825 672212764 672213361 1.600000e-92 350.0
9 TraesCS4A01G397200 chr4A 81.295 417 72 5 586 999 673088231 673088644 1.610000e-87 333.0
10 TraesCS4A01G397200 chr4A 83.128 243 27 10 1850 2082 672197754 672197992 2.840000e-50 209.0
11 TraesCS4A01G397200 chr4A 80.080 251 31 11 1842 2078 669920273 669920028 4.810000e-38 169.0
12 TraesCS4A01G397200 chr4A 78.605 215 43 3 354 567 669994115 669993903 3.770000e-29 139.0
13 TraesCS4A01G397200 chr7D 93.401 1485 75 9 362 1832 55784951 55786426 0.000000e+00 2178.0
14 TraesCS4A01G397200 chr7D 78.328 1675 283 46 354 1985 54373302 54371665 0.000000e+00 1009.0
15 TraesCS4A01G397200 chr7D 76.850 1689 276 72 194 1832 55555540 55557163 0.000000e+00 846.0
16 TraesCS4A01G397200 chr7D 79.294 1246 227 27 587 1825 55487216 55488437 0.000000e+00 843.0
17 TraesCS4A01G397200 chr7D 92.179 537 31 6 2272 2806 55786950 55787477 0.000000e+00 749.0
18 TraesCS4A01G397200 chr7D 88.642 405 36 6 1843 2245 55786562 55786958 4.210000e-133 484.0
19 TraesCS4A01G397200 chr7D 75.225 888 200 15 355 1233 55014534 55015410 1.210000e-108 403.0
20 TraesCS4A01G397200 chr7D 79.381 582 109 5 1211 1791 55529978 55530549 1.570000e-107 399.0
21 TraesCS4A01G397200 chr7D 86.350 337 44 1 1495 1831 55648889 55649223 1.590000e-97 366.0
22 TraesCS4A01G397200 chr7D 80.576 417 74 6 586 999 56419385 56419797 5.840000e-82 315.0
23 TraesCS4A01G397200 chr7D 82.720 353 60 1 1458 1810 55610864 55611215 2.100000e-81 313.0
24 TraesCS4A01G397200 chr7D 83.721 258 35 6 1842 2096 55649283 55649536 1.300000e-58 237.0
25 TraesCS4A01G397200 chr7D 93.284 134 9 0 195 328 55784826 55784959 6.140000e-47 198.0
26 TraesCS4A01G397200 chr7D 90.071 141 12 2 1844 1984 55585024 55584886 6.180000e-42 182.0
27 TraesCS4A01G397200 chr7D 94.545 55 2 1 1843 1896 55786509 55786563 1.790000e-12 84.2
28 TraesCS4A01G397200 chrUn 77.472 617 118 12 1211 1825 284725219 284725816 1.600000e-92 350.0
29 TraesCS4A01G397200 chr7A 75.839 149 25 9 194 341 59432601 59432739 6.500000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G397200 chr4A 672408546 672411355 2809 False 5190.00 5190 100.0000 1 2810 1 chr4A.!!$F5 2809
1 TraesCS4A01G397200 chr4A 672516826 672518731 1905 False 1310.00 1310 79.3710 354 2266 1 chr4A.!!$F6 1912
2 TraesCS4A01G397200 chr4A 672319078 672320588 1510 False 904.00 904 78.2330 354 1831 1 chr4A.!!$F4 1477
3 TraesCS4A01G397200 chr4A 672000655 672002019 1364 False 857.00 857 78.2520 433 1831 1 chr4A.!!$F1 1398
4 TraesCS4A01G397200 chr4A 669920028 669921697 1669 True 556.50 944 79.6410 435 2078 2 chr4A.!!$R3 1643
5 TraesCS4A01G397200 chr4A 670980163 670980805 642 True 368.00 368 77.1470 355 1003 1 chr4A.!!$R2 648
6 TraesCS4A01G397200 chr4A 672212764 672213361 597 False 350.00 350 77.4720 1211 1825 1 chr4A.!!$F3 614
7 TraesCS4A01G397200 chr4A 672197350 672197992 642 False 299.50 390 85.3325 1495 2082 2 chr4A.!!$F8 587
8 TraesCS4A01G397200 chr7D 54371665 54373302 1637 True 1009.00 1009 78.3280 354 1985 1 chr7D.!!$R1 1631
9 TraesCS4A01G397200 chr7D 55555540 55557163 1623 False 846.00 846 76.8500 194 1832 1 chr7D.!!$F4 1638
10 TraesCS4A01G397200 chr7D 55487216 55488437 1221 False 843.00 843 79.2940 587 1825 1 chr7D.!!$F2 1238
11 TraesCS4A01G397200 chr7D 55784826 55787477 2651 False 738.64 2178 92.4102 195 2806 5 chr7D.!!$F8 2611
12 TraesCS4A01G397200 chr7D 55014534 55015410 876 False 403.00 403 75.2250 355 1233 1 chr7D.!!$F1 878
13 TraesCS4A01G397200 chr7D 55529978 55530549 571 False 399.00 399 79.3810 1211 1791 1 chr7D.!!$F3 580
14 TraesCS4A01G397200 chr7D 55648889 55649536 647 False 301.50 366 85.0355 1495 2096 2 chr7D.!!$F7 601
15 TraesCS4A01G397200 chrUn 284725219 284725816 597 False 350.00 350 77.4720 1211 1825 1 chrUn.!!$F1 614

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
171 172 0.035317 ATGGAGTGTGTGTGCGATGT 59.965 50.0 0.0 0.0 0.0 3.06 F
1146 1227 0.178995 TTTGTGTGAGCCAGCCATCA 60.179 50.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 1525 0.753111 GGATTGTCCCTGGCCATGAC 60.753 60.0 22.5 22.5 0.0 3.06 R
2386 2644 0.039180 TAGGGGTGCGAGAGAGAACA 59.961 55.0 0.0 0.0 0.0 3.18 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
35 36 9.948964 AATATGCAGTAATATACATTGCTCTGA 57.051 29.630 0.00 0.00 35.19 3.27
37 38 7.662604 TGCAGTAATATACATTGCTCTGATG 57.337 36.000 6.37 0.00 35.19 3.07
38 39 7.219322 TGCAGTAATATACATTGCTCTGATGT 58.781 34.615 6.37 0.00 35.19 3.06
39 40 7.172019 TGCAGTAATATACATTGCTCTGATGTG 59.828 37.037 0.31 0.00 38.17 3.21
40 41 7.386025 GCAGTAATATACATTGCTCTGATGTGA 59.614 37.037 0.31 0.00 38.17 3.58
41 42 9.264719 CAGTAATATACATTGCTCTGATGTGAA 57.735 33.333 0.31 0.00 38.17 3.18
42 43 9.486497 AGTAATATACATTGCTCTGATGTGAAG 57.514 33.333 0.31 0.00 38.17 3.02
43 44 6.798315 ATATACATTGCTCTGATGTGAAGC 57.202 37.500 0.31 0.00 38.17 3.86
44 45 2.089980 ACATTGCTCTGATGTGAAGCC 58.910 47.619 0.00 0.00 36.43 4.35
45 46 2.089201 CATTGCTCTGATGTGAAGCCA 58.911 47.619 0.00 0.00 0.00 4.75
46 47 2.502142 TTGCTCTGATGTGAAGCCAT 57.498 45.000 0.00 0.00 0.00 4.40
47 48 2.502142 TGCTCTGATGTGAAGCCATT 57.498 45.000 0.00 0.00 0.00 3.16
48 49 2.362736 TGCTCTGATGTGAAGCCATTC 58.637 47.619 0.00 0.00 35.87 2.67
49 50 1.329906 GCTCTGATGTGAAGCCATTCG 59.670 52.381 0.00 0.00 38.34 3.34
50 51 2.625737 CTCTGATGTGAAGCCATTCGT 58.374 47.619 0.00 0.00 38.34 3.85
51 52 3.005554 CTCTGATGTGAAGCCATTCGTT 58.994 45.455 0.00 0.00 38.34 3.85
52 53 3.002791 TCTGATGTGAAGCCATTCGTTC 58.997 45.455 0.00 0.00 38.34 3.95
53 54 2.743664 CTGATGTGAAGCCATTCGTTCA 59.256 45.455 0.00 0.00 38.34 3.18
54 55 2.743664 TGATGTGAAGCCATTCGTTCAG 59.256 45.455 0.00 0.00 38.34 3.02
55 56 2.254546 TGTGAAGCCATTCGTTCAGT 57.745 45.000 0.00 0.00 38.34 3.41
56 57 3.394674 TGTGAAGCCATTCGTTCAGTA 57.605 42.857 0.00 0.00 38.34 2.74
57 58 3.937814 TGTGAAGCCATTCGTTCAGTAT 58.062 40.909 0.00 0.00 38.34 2.12
58 59 3.684305 TGTGAAGCCATTCGTTCAGTATG 59.316 43.478 0.00 0.00 38.34 2.39
59 60 2.677836 TGAAGCCATTCGTTCAGTATGC 59.322 45.455 0.00 0.00 38.34 3.14
60 61 2.401583 AGCCATTCGTTCAGTATGCA 57.598 45.000 0.00 0.00 34.76 3.96
61 62 2.009774 AGCCATTCGTTCAGTATGCAC 58.990 47.619 0.00 0.00 34.76 4.57
62 63 2.009774 GCCATTCGTTCAGTATGCACT 58.990 47.619 0.00 0.00 34.76 4.40
63 64 2.420022 GCCATTCGTTCAGTATGCACTT 59.580 45.455 0.00 0.00 34.76 3.16
64 65 3.621268 GCCATTCGTTCAGTATGCACTTA 59.379 43.478 0.00 0.00 34.76 2.24
65 66 4.094294 GCCATTCGTTCAGTATGCACTTAA 59.906 41.667 0.00 0.00 34.76 1.85
66 67 5.220854 GCCATTCGTTCAGTATGCACTTAAT 60.221 40.000 0.00 0.00 34.76 1.40
67 68 6.018262 GCCATTCGTTCAGTATGCACTTAATA 60.018 38.462 0.00 0.00 34.76 0.98
68 69 7.466725 GCCATTCGTTCAGTATGCACTTAATAA 60.467 37.037 0.00 0.00 34.76 1.40
69 70 8.064222 CCATTCGTTCAGTATGCACTTAATAAG 58.936 37.037 0.00 0.00 34.76 1.73
70 71 8.817100 CATTCGTTCAGTATGCACTTAATAAGA 58.183 33.333 7.06 0.00 34.76 2.10
71 72 8.942338 TTCGTTCAGTATGCACTTAATAAGAT 57.058 30.769 7.06 0.00 34.76 2.40
72 73 8.352752 TCGTTCAGTATGCACTTAATAAGATG 57.647 34.615 7.06 3.08 34.76 2.90
73 74 7.042725 TCGTTCAGTATGCACTTAATAAGATGC 60.043 37.037 7.06 12.46 36.63 3.91
74 75 7.355778 GTTCAGTATGCACTTAATAAGATGCC 58.644 38.462 18.01 8.49 35.84 4.40
75 76 6.591001 TCAGTATGCACTTAATAAGATGCCA 58.409 36.000 18.01 10.77 35.84 4.92
76 77 6.483307 TCAGTATGCACTTAATAAGATGCCAC 59.517 38.462 18.01 15.92 35.84 5.01
77 78 6.260714 CAGTATGCACTTAATAAGATGCCACA 59.739 38.462 18.01 6.76 35.84 4.17
78 79 7.000472 AGTATGCACTTAATAAGATGCCACAT 59.000 34.615 18.01 11.34 35.84 3.21
79 80 5.756195 TGCACTTAATAAGATGCCACATC 57.244 39.130 18.01 0.00 35.84 3.06
80 81 5.439721 TGCACTTAATAAGATGCCACATCT 58.560 37.500 18.01 4.26 35.84 2.90
81 82 5.887598 TGCACTTAATAAGATGCCACATCTT 59.112 36.000 22.39 22.39 40.95 2.40
82 83 6.377996 TGCACTTAATAAGATGCCACATCTTT 59.622 34.615 23.55 12.26 39.01 2.52
83 84 7.093814 TGCACTTAATAAGATGCCACATCTTTT 60.094 33.333 23.55 18.73 39.01 2.27
84 85 7.761249 GCACTTAATAAGATGCCACATCTTTTT 59.239 33.333 23.55 22.35 39.01 1.94
85 86 9.294030 CACTTAATAAGATGCCACATCTTTTTC 57.706 33.333 23.55 0.00 39.01 2.29
86 87 9.247861 ACTTAATAAGATGCCACATCTTTTTCT 57.752 29.630 23.55 11.22 39.01 2.52
87 88 9.512435 CTTAATAAGATGCCACATCTTTTTCTG 57.488 33.333 23.55 15.00 39.01 3.02
88 89 3.863142 AGATGCCACATCTTTTTCTGC 57.137 42.857 4.26 0.00 0.00 4.26
89 90 3.159472 AGATGCCACATCTTTTTCTGCA 58.841 40.909 4.26 0.00 0.00 4.41
90 91 3.767673 AGATGCCACATCTTTTTCTGCAT 59.232 39.130 4.26 0.00 40.37 3.96
91 92 4.951715 AGATGCCACATCTTTTTCTGCATA 59.048 37.500 4.26 0.00 38.02 3.14
92 93 5.419788 AGATGCCACATCTTTTTCTGCATAA 59.580 36.000 4.26 0.00 38.02 1.90
93 94 5.664294 TGCCACATCTTTTTCTGCATAAT 57.336 34.783 0.00 0.00 0.00 1.28
94 95 6.040209 TGCCACATCTTTTTCTGCATAATT 57.960 33.333 0.00 0.00 0.00 1.40
95 96 6.465948 TGCCACATCTTTTTCTGCATAATTT 58.534 32.000 0.00 0.00 0.00 1.82
96 97 6.935771 TGCCACATCTTTTTCTGCATAATTTT 59.064 30.769 0.00 0.00 0.00 1.82
97 98 8.093307 TGCCACATCTTTTTCTGCATAATTTTA 58.907 29.630 0.00 0.00 0.00 1.52
98 99 8.934825 GCCACATCTTTTTCTGCATAATTTTAA 58.065 29.630 0.00 0.00 0.00 1.52
121 122 9.998106 TTAATACTTAATAGAATGCCCTCAGAC 57.002 33.333 0.00 0.00 0.00 3.51
122 123 5.297569 ACTTAATAGAATGCCCTCAGACC 57.702 43.478 0.00 0.00 0.00 3.85
123 124 4.971924 ACTTAATAGAATGCCCTCAGACCT 59.028 41.667 0.00 0.00 0.00 3.85
124 125 5.430089 ACTTAATAGAATGCCCTCAGACCTT 59.570 40.000 0.00 0.00 0.00 3.50
125 126 6.615726 ACTTAATAGAATGCCCTCAGACCTTA 59.384 38.462 0.00 0.00 0.00 2.69
126 127 5.975988 AATAGAATGCCCTCAGACCTTAA 57.024 39.130 0.00 0.00 0.00 1.85
127 128 6.521527 AATAGAATGCCCTCAGACCTTAAT 57.478 37.500 0.00 0.00 0.00 1.40
128 129 4.429854 AGAATGCCCTCAGACCTTAATC 57.570 45.455 0.00 0.00 0.00 1.75
129 130 4.043596 AGAATGCCCTCAGACCTTAATCT 58.956 43.478 0.00 0.00 0.00 2.40
130 131 5.219739 AGAATGCCCTCAGACCTTAATCTA 58.780 41.667 0.00 0.00 0.00 1.98
131 132 5.848921 AGAATGCCCTCAGACCTTAATCTAT 59.151 40.000 0.00 0.00 0.00 1.98
132 133 7.019388 AGAATGCCCTCAGACCTTAATCTATA 58.981 38.462 0.00 0.00 0.00 1.31
133 134 7.682028 AGAATGCCCTCAGACCTTAATCTATAT 59.318 37.037 0.00 0.00 0.00 0.86
134 135 7.821134 ATGCCCTCAGACCTTAATCTATATT 57.179 36.000 0.00 0.00 0.00 1.28
135 136 8.917414 ATGCCCTCAGACCTTAATCTATATTA 57.083 34.615 0.00 0.00 0.00 0.98
136 137 8.736097 TGCCCTCAGACCTTAATCTATATTAA 57.264 34.615 0.00 0.00 36.39 1.40
137 138 9.338968 TGCCCTCAGACCTTAATCTATATTAAT 57.661 33.333 0.00 0.00 37.04 1.40
165 166 6.907206 AAAAATGAAAATGGAGTGTGTGTG 57.093 33.333 0.00 0.00 0.00 3.82
166 167 3.648339 ATGAAAATGGAGTGTGTGTGC 57.352 42.857 0.00 0.00 0.00 4.57
167 168 1.333308 TGAAAATGGAGTGTGTGTGCG 59.667 47.619 0.00 0.00 0.00 5.34
168 169 1.601903 GAAAATGGAGTGTGTGTGCGA 59.398 47.619 0.00 0.00 0.00 5.10
169 170 1.896220 AAATGGAGTGTGTGTGCGAT 58.104 45.000 0.00 0.00 0.00 4.58
170 171 1.159285 AATGGAGTGTGTGTGCGATG 58.841 50.000 0.00 0.00 0.00 3.84
171 172 0.035317 ATGGAGTGTGTGTGCGATGT 59.965 50.000 0.00 0.00 0.00 3.06
172 173 0.179059 TGGAGTGTGTGTGCGATGTT 60.179 50.000 0.00 0.00 0.00 2.71
173 174 0.235665 GGAGTGTGTGTGCGATGTTG 59.764 55.000 0.00 0.00 0.00 3.33
174 175 1.217001 GAGTGTGTGTGCGATGTTGA 58.783 50.000 0.00 0.00 0.00 3.18
175 176 0.937304 AGTGTGTGTGCGATGTTGAC 59.063 50.000 0.00 0.00 0.00 3.18
176 177 0.383002 GTGTGTGTGCGATGTTGACG 60.383 55.000 0.00 0.00 0.00 4.35
177 178 1.204062 GTGTGTGCGATGTTGACGG 59.796 57.895 0.00 0.00 0.00 4.79
178 179 1.958715 TGTGTGCGATGTTGACGGG 60.959 57.895 0.00 0.00 0.00 5.28
179 180 2.358125 TGTGCGATGTTGACGGGG 60.358 61.111 0.00 0.00 0.00 5.73
180 181 2.358247 GTGCGATGTTGACGGGGT 60.358 61.111 0.00 0.00 0.00 4.95
181 182 2.047655 TGCGATGTTGACGGGGTC 60.048 61.111 0.00 0.00 0.00 4.46
182 183 2.047655 GCGATGTTGACGGGGTCA 60.048 61.111 0.00 0.00 41.09 4.02
183 184 2.388232 GCGATGTTGACGGGGTCAC 61.388 63.158 0.00 0.00 42.60 3.67
184 185 1.292223 CGATGTTGACGGGGTCACT 59.708 57.895 0.00 0.00 42.60 3.41
185 186 0.320421 CGATGTTGACGGGGTCACTT 60.320 55.000 0.00 0.00 42.60 3.16
186 187 1.067425 CGATGTTGACGGGGTCACTTA 60.067 52.381 0.00 0.00 42.60 2.24
187 188 2.418197 CGATGTTGACGGGGTCACTTAT 60.418 50.000 0.00 0.00 42.60 1.73
188 189 2.465860 TGTTGACGGGGTCACTTATG 57.534 50.000 0.00 0.00 42.60 1.90
189 190 1.695242 TGTTGACGGGGTCACTTATGT 59.305 47.619 0.00 0.00 42.60 2.29
190 191 2.105134 TGTTGACGGGGTCACTTATGTT 59.895 45.455 0.00 0.00 42.60 2.71
191 192 2.465860 TGACGGGGTCACTTATGTTG 57.534 50.000 0.00 0.00 37.67 3.33
192 193 1.002659 TGACGGGGTCACTTATGTTGG 59.997 52.381 0.00 0.00 37.67 3.77
205 206 4.158394 ACTTATGTTGGGCAGCTTGTTATG 59.842 41.667 0.00 0.00 0.00 1.90
286 288 1.995484 CTGTTGTAGTCATGCACCTCG 59.005 52.381 0.00 0.00 0.00 4.63
287 289 1.337728 TGTTGTAGTCATGCACCTCGG 60.338 52.381 0.00 0.00 0.00 4.63
338 340 7.088905 TGTCTAAGCTTAGTTGCAGTTACTAC 58.911 38.462 28.31 16.72 34.99 2.73
339 341 7.039923 TGTCTAAGCTTAGTTGCAGTTACTACT 60.040 37.037 28.31 0.00 34.99 2.57
340 342 7.813627 GTCTAAGCTTAGTTGCAGTTACTACTT 59.186 37.037 28.31 1.90 34.99 2.24
341 343 6.787085 AAGCTTAGTTGCAGTTACTACTTG 57.213 37.500 0.00 0.00 34.99 3.16
342 344 5.238583 AGCTTAGTTGCAGTTACTACTTGG 58.761 41.667 0.00 0.00 34.99 3.61
343 345 4.995487 GCTTAGTTGCAGTTACTACTTGGT 59.005 41.667 0.00 0.00 30.26 3.67
344 346 5.120363 GCTTAGTTGCAGTTACTACTTGGTC 59.880 44.000 0.00 0.00 30.26 4.02
345 347 4.004196 AGTTGCAGTTACTACTTGGTCC 57.996 45.455 0.00 0.00 30.26 4.46
346 348 3.646637 AGTTGCAGTTACTACTTGGTCCT 59.353 43.478 0.00 0.00 30.26 3.85
347 349 4.102681 AGTTGCAGTTACTACTTGGTCCTT 59.897 41.667 0.00 0.00 30.26 3.36
348 350 5.306160 AGTTGCAGTTACTACTTGGTCCTTA 59.694 40.000 0.00 0.00 30.26 2.69
349 351 5.401531 TGCAGTTACTACTTGGTCCTTAG 57.598 43.478 0.00 0.00 30.26 2.18
350 352 4.836736 TGCAGTTACTACTTGGTCCTTAGT 59.163 41.667 3.25 3.25 30.26 2.24
351 353 5.306160 TGCAGTTACTACTTGGTCCTTAGTT 59.694 40.000 3.06 0.00 30.26 2.24
352 354 5.868258 GCAGTTACTACTTGGTCCTTAGTTC 59.132 44.000 3.06 0.30 30.26 3.01
414 425 1.378911 TAGTGCGAGGTTAGGCGGA 60.379 57.895 0.00 0.00 0.00 5.54
418 429 1.153429 GCGAGGTTAGGCGGATTGT 60.153 57.895 0.00 0.00 0.00 2.71
491 506 6.072064 CCCCTGCATCTTCATATTCTCATTTC 60.072 42.308 0.00 0.00 0.00 2.17
581 609 4.291540 CACATGTGCTGTTAGTTGTTGT 57.708 40.909 13.94 0.00 35.29 3.32
582 610 5.416862 CACATGTGCTGTTAGTTGTTGTA 57.583 39.130 13.94 0.00 35.29 2.41
584 612 6.079763 CACATGTGCTGTTAGTTGTTGTATC 58.920 40.000 13.94 0.00 35.29 2.24
585 613 5.997746 ACATGTGCTGTTAGTTGTTGTATCT 59.002 36.000 0.00 0.00 32.90 1.98
588 616 7.328277 TGTGCTGTTAGTTGTTGTATCTTTT 57.672 32.000 0.00 0.00 0.00 2.27
618 685 4.710324 TGTTTAACCACGAATCCTCTGTT 58.290 39.130 0.00 0.00 0.00 3.16
702 771 0.474660 ACTCTTGGGCCTTGTCCTCT 60.475 55.000 4.53 0.00 0.00 3.69
908 980 3.282021 TGGCTCAATTGATAACTGGCTC 58.718 45.455 8.96 3.22 0.00 4.70
934 1006 5.658190 TCCTCATTCACAGTGATGATGAGTA 59.342 40.000 28.35 18.79 35.12 2.59
1009 1081 2.041701 AGTTTGGCAGCATGAGGTTTT 58.958 42.857 0.00 0.00 39.69 2.43
1062 1137 2.925706 TTGGTAGCACCCTCGCCA 60.926 61.111 0.00 0.00 37.50 5.69
1124 1205 7.350744 TCATTGGTGATGGGAATATGAAAAG 57.649 36.000 0.00 0.00 36.37 2.27
1146 1227 0.178995 TTTGTGTGAGCCAGCCATCA 60.179 50.000 0.00 0.00 0.00 3.07
1350 1431 0.813184 ATGTGCCAGAATGCTTTCCG 59.187 50.000 8.62 0.00 31.84 4.30
1366 1447 4.558496 GCTTTCCGAGAGAGGAGATGTATG 60.558 50.000 0.00 0.00 41.98 2.39
1444 1525 0.893270 TCGTGTCATGGGCCCTTTTG 60.893 55.000 25.70 17.82 0.00 2.44
1445 1526 1.178534 CGTGTCATGGGCCCTTTTGT 61.179 55.000 25.70 0.33 0.00 2.83
1446 1527 0.603065 GTGTCATGGGCCCTTTTGTC 59.397 55.000 25.70 15.50 0.00 3.18
1447 1528 0.187117 TGTCATGGGCCCTTTTGTCA 59.813 50.000 25.70 17.81 0.00 3.58
1448 1529 1.203162 TGTCATGGGCCCTTTTGTCAT 60.203 47.619 25.70 2.32 0.00 3.06
1449 1530 1.205417 GTCATGGGCCCTTTTGTCATG 59.795 52.381 25.70 16.38 37.23 3.07
1450 1531 0.538118 CATGGGCCCTTTTGTCATGG 59.462 55.000 25.70 0.00 33.60 3.66
1642 1729 3.806521 CCAAGAGGATTGCATCTACTTCG 59.193 47.826 0.00 0.00 33.31 3.79
1656 1743 6.508088 GCATCTACTTCGTTTTTGACTATCCG 60.508 42.308 0.00 0.00 0.00 4.18
1663 1750 3.241552 CGTTTTTGACTATCCGCGTACAG 60.242 47.826 4.92 0.42 0.00 2.74
1719 1807 1.315257 ACAACATGCGGAATGGGAGC 61.315 55.000 0.12 0.00 40.94 4.70
1738 1827 1.781555 GTCACGCCGTTGATGTCTG 59.218 57.895 0.00 0.00 0.00 3.51
1915 2149 8.743714 CCTAGTGATATGTTATCATGCAGACTA 58.256 37.037 0.00 0.00 35.70 2.59
1997 2239 8.870116 AGTGATATGTTATGCATGGTCTAGTTA 58.130 33.333 10.16 0.00 38.47 2.24
2045 2287 8.956426 GGTGTCCACTTCAAATCTTATGAATTA 58.044 33.333 0.00 0.00 36.30 1.40
2082 2332 6.781138 TGTATTTCGATGTGCAACTTTATCC 58.219 36.000 0.00 0.00 38.04 2.59
2118 2370 8.150296 TGATGTGTGTTAAGCTATAGCATATGT 58.850 33.333 26.07 2.34 45.16 2.29
2126 2378 9.155975 GTTAAGCTATAGCATATGTACTTGCAT 57.844 33.333 26.07 0.00 45.16 3.96
2139 2393 5.171476 TGTACTTGCATAAACTCTCTCTGC 58.829 41.667 0.00 0.00 0.00 4.26
2144 2398 3.769300 TGCATAAACTCTCTCTGCAGGTA 59.231 43.478 15.13 0.91 37.88 3.08
2147 2401 5.064071 GCATAAACTCTCTCTGCAGGTAAAC 59.936 44.000 15.13 0.00 33.13 2.01
2183 2437 4.408921 CCCACTAACCACTGAATCCTGATA 59.591 45.833 0.00 0.00 0.00 2.15
2185 2439 5.129485 CCACTAACCACTGAATCCTGATAGT 59.871 44.000 0.00 0.00 0.00 2.12
2190 2444 2.868583 CACTGAATCCTGATAGTTGCCG 59.131 50.000 0.00 0.00 0.00 5.69
2197 2452 2.203209 GATAGTTGCCGCTGGGGG 60.203 66.667 13.07 2.93 35.78 5.40
2227 2482 2.320745 TGCTCACAGCTATGGTCATG 57.679 50.000 0.00 0.00 42.97 3.07
2240 2496 3.940209 TGGTCATGTTTGGATTGCTTC 57.060 42.857 0.00 0.00 0.00 3.86
2248 2504 2.814336 GTTTGGATTGCTTCGAACTCCT 59.186 45.455 0.00 0.00 0.00 3.69
2252 2508 2.545946 GGATTGCTTCGAACTCCTATGC 59.454 50.000 0.00 0.00 0.00 3.14
2253 2509 2.760634 TTGCTTCGAACTCCTATGCA 57.239 45.000 0.00 0.00 0.00 3.96
2277 2533 4.900635 GGCAACTTTCAAGTCTCTTTGA 57.099 40.909 0.00 0.00 38.57 2.69
2278 2534 5.248870 GGCAACTTTCAAGTCTCTTTGAA 57.751 39.130 0.00 0.00 43.32 2.69
2279 2535 5.836347 GGCAACTTTCAAGTCTCTTTGAAT 58.164 37.500 2.43 0.00 44.12 2.57
2318 2574 1.761449 TGCCATTGGTGCGTATGATT 58.239 45.000 4.26 0.00 0.00 2.57
2341 2597 1.271325 TGTCAATGACCGCCATCACTT 60.271 47.619 11.24 0.00 33.53 3.16
2362 2620 3.146066 TGGACATCAACCTTTAGCACAC 58.854 45.455 0.00 0.00 0.00 3.82
2369 2627 5.437289 TCAACCTTTAGCACACAGAAATG 57.563 39.130 0.00 0.00 0.00 2.32
2371 2629 6.058833 TCAACCTTTAGCACACAGAAATGTA 58.941 36.000 0.00 0.00 0.00 2.29
2428 2686 3.499048 CTGTTGTCAAGCAAGATGATGC 58.501 45.455 0.00 0.00 46.78 3.91
2535 2793 5.087323 ACTCATCAACCTCTTCTGGAACTA 58.913 41.667 0.00 0.00 0.00 2.24
2540 2798 6.282199 TCAACCTCTTCTGGAACTATGTAC 57.718 41.667 0.00 0.00 0.00 2.90
2541 2799 6.017192 TCAACCTCTTCTGGAACTATGTACT 58.983 40.000 0.00 0.00 0.00 2.73
2554 2812 9.647918 TGGAACTATGTACTCTCTGAAGATATT 57.352 33.333 0.00 0.00 0.00 1.28
2579 2837 9.953565 TTAGTAACCATGAGTATAAAGTGCTTT 57.046 29.630 0.00 2.60 36.63 3.51
2598 2856 4.021981 GCTTTTTATCAGCCTTCCAGTTGT 60.022 41.667 0.00 0.00 0.00 3.32
2636 2894 6.674694 ACAATCTGCACATTCTGTATTCTC 57.325 37.500 0.00 0.00 0.00 2.87
2644 2902 6.127083 TGCACATTCTGTATTCTCACCTCATA 60.127 38.462 0.00 0.00 0.00 2.15
2645 2903 6.933521 GCACATTCTGTATTCTCACCTCATAT 59.066 38.462 0.00 0.00 0.00 1.78
2646 2904 8.090831 GCACATTCTGTATTCTCACCTCATATA 58.909 37.037 0.00 0.00 0.00 0.86
2664 2922 8.877779 CCTCATATATACTGCAGTAAGAAATGC 58.122 37.037 29.26 0.00 42.86 3.56
2671 2929 4.459390 TGCAGTAAGAAATGCATGCATT 57.541 36.364 34.78 34.78 46.97 3.56
2717 2975 5.176223 GCATGATGCAAGAATATTTTTCGGG 59.824 40.000 13.36 0.00 44.26 5.14
2744 3002 3.307691 CCAGTCTTCCAGCCATCAGTTTA 60.308 47.826 0.00 0.00 0.00 2.01
2759 3017 8.673711 GCCATCAGTTTATACACTAAAATCACA 58.326 33.333 0.00 0.00 0.00 3.58
2788 3046 9.906660 ACGAGAAAAGATAGAAGAATATGCTAG 57.093 33.333 0.00 0.00 0.00 3.42
2806 3064 9.836864 ATATGCTAGACATTATGAGAAAACACA 57.163 29.630 0.00 0.00 40.38 3.72
2807 3065 7.977789 TGCTAGACATTATGAGAAAACACAA 57.022 32.000 0.00 0.00 0.00 3.33
2808 3066 8.565896 TGCTAGACATTATGAGAAAACACAAT 57.434 30.769 0.00 0.00 0.00 2.71
2809 3067 8.453320 TGCTAGACATTATGAGAAAACACAATG 58.547 33.333 0.00 0.00 39.58 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.948964 TCAGAGCAATGTATATTACTGCATATT 57.051 29.630 0.00 0.00 33.70 1.28
11 12 9.374838 CATCAGAGCAATGTATATTACTGCATA 57.625 33.333 0.00 0.00 33.70 3.14
12 13 7.881751 ACATCAGAGCAATGTATATTACTGCAT 59.118 33.333 0.00 0.00 35.62 3.96
13 14 7.172019 CACATCAGAGCAATGTATATTACTGCA 59.828 37.037 0.00 0.00 35.62 4.41
14 15 7.386025 TCACATCAGAGCAATGTATATTACTGC 59.614 37.037 0.00 0.00 35.62 4.40
15 16 8.822652 TCACATCAGAGCAATGTATATTACTG 57.177 34.615 0.00 0.00 35.62 2.74
16 17 9.486497 CTTCACATCAGAGCAATGTATATTACT 57.514 33.333 0.00 0.00 35.62 2.24
17 18 8.226448 GCTTCACATCAGAGCAATGTATATTAC 58.774 37.037 0.00 0.00 35.62 1.89
18 19 7.388776 GGCTTCACATCAGAGCAATGTATATTA 59.611 37.037 0.00 0.00 35.62 0.98
19 20 6.206243 GGCTTCACATCAGAGCAATGTATATT 59.794 38.462 0.00 0.00 35.62 1.28
20 21 5.704515 GGCTTCACATCAGAGCAATGTATAT 59.295 40.000 0.00 0.00 35.62 0.86
21 22 5.059161 GGCTTCACATCAGAGCAATGTATA 58.941 41.667 0.00 0.00 35.62 1.47
22 23 3.881688 GGCTTCACATCAGAGCAATGTAT 59.118 43.478 0.00 0.00 35.62 2.29
23 24 3.273434 GGCTTCACATCAGAGCAATGTA 58.727 45.455 0.00 0.00 35.62 2.29
24 25 2.089980 GGCTTCACATCAGAGCAATGT 58.910 47.619 0.00 0.00 37.85 2.71
25 26 2.089201 TGGCTTCACATCAGAGCAATG 58.911 47.619 0.00 0.00 0.00 2.82
26 27 2.502142 TGGCTTCACATCAGAGCAAT 57.498 45.000 0.00 0.00 0.00 3.56
27 28 2.502142 ATGGCTTCACATCAGAGCAA 57.498 45.000 0.00 0.00 0.00 3.91
28 29 2.362736 GAATGGCTTCACATCAGAGCA 58.637 47.619 0.00 0.00 0.00 4.26
29 30 1.329906 CGAATGGCTTCACATCAGAGC 59.670 52.381 0.00 0.00 0.00 4.09
30 31 2.625737 ACGAATGGCTTCACATCAGAG 58.374 47.619 0.00 0.00 0.00 3.35
31 32 2.768253 ACGAATGGCTTCACATCAGA 57.232 45.000 0.00 0.00 0.00 3.27
32 33 2.743664 TGAACGAATGGCTTCACATCAG 59.256 45.455 0.00 0.00 0.00 2.90
33 34 2.743664 CTGAACGAATGGCTTCACATCA 59.256 45.455 0.00 0.00 0.00 3.07
34 35 2.744202 ACTGAACGAATGGCTTCACATC 59.256 45.455 0.00 0.00 0.00 3.06
35 36 2.783135 ACTGAACGAATGGCTTCACAT 58.217 42.857 0.00 0.00 0.00 3.21
36 37 2.254546 ACTGAACGAATGGCTTCACA 57.745 45.000 0.00 0.00 0.00 3.58
37 38 3.485877 GCATACTGAACGAATGGCTTCAC 60.486 47.826 0.00 0.00 0.00 3.18
38 39 2.677836 GCATACTGAACGAATGGCTTCA 59.322 45.455 0.00 0.00 0.00 3.02
39 40 2.677836 TGCATACTGAACGAATGGCTTC 59.322 45.455 0.00 0.00 0.00 3.86
40 41 2.420022 GTGCATACTGAACGAATGGCTT 59.580 45.455 0.00 0.00 0.00 4.35
41 42 2.009774 GTGCATACTGAACGAATGGCT 58.990 47.619 0.00 0.00 0.00 4.75
42 43 2.009774 AGTGCATACTGAACGAATGGC 58.990 47.619 0.00 0.00 35.34 4.40
43 44 5.794687 TTAAGTGCATACTGAACGAATGG 57.205 39.130 0.00 0.00 37.19 3.16
44 45 8.817100 TCTTATTAAGTGCATACTGAACGAATG 58.183 33.333 3.45 0.00 37.19 2.67
45 46 8.942338 TCTTATTAAGTGCATACTGAACGAAT 57.058 30.769 3.45 0.00 37.19 3.34
46 47 8.817100 CATCTTATTAAGTGCATACTGAACGAA 58.183 33.333 3.45 0.00 37.19 3.85
47 48 7.042725 GCATCTTATTAAGTGCATACTGAACGA 60.043 37.037 18.15 0.00 37.19 3.85
48 49 7.065894 GCATCTTATTAAGTGCATACTGAACG 58.934 38.462 18.15 0.00 37.19 3.95
49 50 7.012327 TGGCATCTTATTAAGTGCATACTGAAC 59.988 37.037 21.60 10.20 37.19 3.18
50 51 7.012327 GTGGCATCTTATTAAGTGCATACTGAA 59.988 37.037 21.60 0.00 37.19 3.02
51 52 6.483307 GTGGCATCTTATTAAGTGCATACTGA 59.517 38.462 21.60 0.00 37.19 3.41
52 53 6.260714 TGTGGCATCTTATTAAGTGCATACTG 59.739 38.462 21.60 6.85 37.19 2.74
53 54 6.356556 TGTGGCATCTTATTAAGTGCATACT 58.643 36.000 21.60 0.00 37.31 2.12
54 55 6.618287 TGTGGCATCTTATTAAGTGCATAC 57.382 37.500 21.60 19.58 37.31 2.39
55 56 7.226441 AGATGTGGCATCTTATTAAGTGCATA 58.774 34.615 21.60 13.15 37.31 3.14
56 57 6.066690 AGATGTGGCATCTTATTAAGTGCAT 58.933 36.000 21.60 12.93 37.31 3.96
57 58 5.439721 AGATGTGGCATCTTATTAAGTGCA 58.560 37.500 21.60 11.95 37.31 4.57
58 59 6.382869 AAGATGTGGCATCTTATTAAGTGC 57.617 37.500 19.16 16.25 36.68 4.40
59 60 9.294030 GAAAAAGATGTGGCATCTTATTAAGTG 57.706 33.333 20.40 3.30 37.38 3.16
60 61 9.247861 AGAAAAAGATGTGGCATCTTATTAAGT 57.752 29.630 20.40 5.53 37.38 2.24
61 62 9.512435 CAGAAAAAGATGTGGCATCTTATTAAG 57.488 33.333 20.40 10.27 37.38 1.85
62 63 7.975616 GCAGAAAAAGATGTGGCATCTTATTAA 59.024 33.333 20.40 0.00 37.38 1.40
63 64 7.122501 TGCAGAAAAAGATGTGGCATCTTATTA 59.877 33.333 20.40 5.35 37.38 0.98
64 65 6.071221 TGCAGAAAAAGATGTGGCATCTTATT 60.071 34.615 20.40 14.74 37.38 1.40
65 66 5.419788 TGCAGAAAAAGATGTGGCATCTTAT 59.580 36.000 20.40 14.19 37.38 1.73
66 67 4.766373 TGCAGAAAAAGATGTGGCATCTTA 59.234 37.500 20.40 4.95 37.38 2.10
67 68 3.575256 TGCAGAAAAAGATGTGGCATCTT 59.425 39.130 16.04 16.04 39.82 2.40
68 69 3.159472 TGCAGAAAAAGATGTGGCATCT 58.841 40.909 5.86 5.86 0.00 2.90
69 70 3.581024 TGCAGAAAAAGATGTGGCATC 57.419 42.857 0.00 1.18 0.00 3.91
70 71 5.664294 TTATGCAGAAAAAGATGTGGCAT 57.336 34.783 0.00 0.00 42.50 4.40
71 72 5.664294 ATTATGCAGAAAAAGATGTGGCA 57.336 34.783 0.00 0.00 0.00 4.92
72 73 6.973229 AAATTATGCAGAAAAAGATGTGGC 57.027 33.333 0.00 0.00 0.00 5.01
95 96 9.998106 GTCTGAGGGCATTCTATTAAGTATTAA 57.002 33.333 0.00 0.00 45.80 1.40
96 97 8.594550 GGTCTGAGGGCATTCTATTAAGTATTA 58.405 37.037 0.00 0.00 0.00 0.98
97 98 7.293535 AGGTCTGAGGGCATTCTATTAAGTATT 59.706 37.037 0.00 0.00 0.00 1.89
98 99 6.789959 AGGTCTGAGGGCATTCTATTAAGTAT 59.210 38.462 0.00 0.00 0.00 2.12
99 100 6.143915 AGGTCTGAGGGCATTCTATTAAGTA 58.856 40.000 0.00 0.00 0.00 2.24
100 101 4.971924 AGGTCTGAGGGCATTCTATTAAGT 59.028 41.667 0.00 0.00 0.00 2.24
101 102 5.559148 AGGTCTGAGGGCATTCTATTAAG 57.441 43.478 0.00 0.00 0.00 1.85
102 103 5.975988 AAGGTCTGAGGGCATTCTATTAA 57.024 39.130 0.00 0.00 0.00 1.40
103 104 7.514127 AGATTAAGGTCTGAGGGCATTCTATTA 59.486 37.037 0.00 0.00 0.00 0.98
104 105 5.975988 TTAAGGTCTGAGGGCATTCTATT 57.024 39.130 0.00 0.00 0.00 1.73
105 106 5.848921 AGATTAAGGTCTGAGGGCATTCTAT 59.151 40.000 0.00 0.00 0.00 1.98
106 107 5.219739 AGATTAAGGTCTGAGGGCATTCTA 58.780 41.667 0.00 0.00 0.00 2.10
107 108 4.043596 AGATTAAGGTCTGAGGGCATTCT 58.956 43.478 0.00 0.00 0.00 2.40
108 109 4.429854 AGATTAAGGTCTGAGGGCATTC 57.570 45.455 0.00 0.00 0.00 2.67
109 110 7.821134 ATATAGATTAAGGTCTGAGGGCATT 57.179 36.000 0.00 0.00 0.00 3.56
110 111 7.821134 AATATAGATTAAGGTCTGAGGGCAT 57.179 36.000 0.00 0.00 0.00 4.40
111 112 8.736097 TTAATATAGATTAAGGTCTGAGGGCA 57.264 34.615 0.00 0.00 33.46 5.36
142 143 5.294060 GCACACACACTCCATTTTCATTTTT 59.706 36.000 0.00 0.00 0.00 1.94
143 144 4.810491 GCACACACACTCCATTTTCATTTT 59.190 37.500 0.00 0.00 0.00 1.82
144 145 4.370917 GCACACACACTCCATTTTCATTT 58.629 39.130 0.00 0.00 0.00 2.32
145 146 3.550639 CGCACACACACTCCATTTTCATT 60.551 43.478 0.00 0.00 0.00 2.57
146 147 2.030893 CGCACACACACTCCATTTTCAT 60.031 45.455 0.00 0.00 0.00 2.57
147 148 1.333308 CGCACACACACTCCATTTTCA 59.667 47.619 0.00 0.00 0.00 2.69
148 149 1.601903 TCGCACACACACTCCATTTTC 59.398 47.619 0.00 0.00 0.00 2.29
149 150 1.674359 TCGCACACACACTCCATTTT 58.326 45.000 0.00 0.00 0.00 1.82
150 151 1.536766 CATCGCACACACACTCCATTT 59.463 47.619 0.00 0.00 0.00 2.32
151 152 1.159285 CATCGCACACACACTCCATT 58.841 50.000 0.00 0.00 0.00 3.16
152 153 0.035317 ACATCGCACACACACTCCAT 59.965 50.000 0.00 0.00 0.00 3.41
153 154 0.179059 AACATCGCACACACACTCCA 60.179 50.000 0.00 0.00 0.00 3.86
154 155 0.235665 CAACATCGCACACACACTCC 59.764 55.000 0.00 0.00 0.00 3.85
155 156 1.070577 GTCAACATCGCACACACACTC 60.071 52.381 0.00 0.00 0.00 3.51
156 157 0.937304 GTCAACATCGCACACACACT 59.063 50.000 0.00 0.00 0.00 3.55
157 158 0.383002 CGTCAACATCGCACACACAC 60.383 55.000 0.00 0.00 0.00 3.82
158 159 1.494766 CCGTCAACATCGCACACACA 61.495 55.000 0.00 0.00 0.00 3.72
159 160 1.204062 CCGTCAACATCGCACACAC 59.796 57.895 0.00 0.00 0.00 3.82
160 161 1.958715 CCCGTCAACATCGCACACA 60.959 57.895 0.00 0.00 0.00 3.72
161 162 2.677003 CCCCGTCAACATCGCACAC 61.677 63.158 0.00 0.00 0.00 3.82
162 163 2.358125 CCCCGTCAACATCGCACA 60.358 61.111 0.00 0.00 0.00 4.57
163 164 2.358247 ACCCCGTCAACATCGCAC 60.358 61.111 0.00 0.00 0.00 5.34
164 165 2.047655 GACCCCGTCAACATCGCA 60.048 61.111 0.00 0.00 32.09 5.10
165 166 2.047655 TGACCCCGTCAACATCGC 60.048 61.111 0.00 0.00 39.78 4.58
166 167 0.320421 AAGTGACCCCGTCAACATCG 60.320 55.000 0.00 0.00 44.49 3.84
167 168 2.754946 TAAGTGACCCCGTCAACATC 57.245 50.000 0.00 0.00 44.49 3.06
168 169 2.304761 ACATAAGTGACCCCGTCAACAT 59.695 45.455 0.00 0.00 44.49 2.71
169 170 1.695242 ACATAAGTGACCCCGTCAACA 59.305 47.619 0.00 0.00 44.49 3.33
170 171 2.467566 ACATAAGTGACCCCGTCAAC 57.532 50.000 0.00 0.00 44.49 3.18
171 172 2.551287 CCAACATAAGTGACCCCGTCAA 60.551 50.000 0.00 0.00 44.49 3.18
172 173 1.002659 CCAACATAAGTGACCCCGTCA 59.997 52.381 0.00 0.00 40.50 4.35
173 174 1.677820 CCCAACATAAGTGACCCCGTC 60.678 57.143 0.00 0.00 0.00 4.79
174 175 0.326927 CCCAACATAAGTGACCCCGT 59.673 55.000 0.00 0.00 0.00 5.28
175 176 1.029947 GCCCAACATAAGTGACCCCG 61.030 60.000 0.00 0.00 0.00 5.73
176 177 0.039035 TGCCCAACATAAGTGACCCC 59.961 55.000 0.00 0.00 0.00 4.95
177 178 1.463674 CTGCCCAACATAAGTGACCC 58.536 55.000 0.00 0.00 0.00 4.46
178 179 0.811281 GCTGCCCAACATAAGTGACC 59.189 55.000 0.00 0.00 0.00 4.02
179 180 1.826385 AGCTGCCCAACATAAGTGAC 58.174 50.000 0.00 0.00 0.00 3.67
180 181 2.161855 CAAGCTGCCCAACATAAGTGA 58.838 47.619 0.00 0.00 0.00 3.41
181 182 1.888512 ACAAGCTGCCCAACATAAGTG 59.111 47.619 0.00 0.00 0.00 3.16
182 183 2.292828 ACAAGCTGCCCAACATAAGT 57.707 45.000 0.00 0.00 0.00 2.24
183 184 4.675510 CATAACAAGCTGCCCAACATAAG 58.324 43.478 0.00 0.00 0.00 1.73
184 185 3.119173 GCATAACAAGCTGCCCAACATAA 60.119 43.478 0.00 0.00 0.00 1.90
185 186 2.426738 GCATAACAAGCTGCCCAACATA 59.573 45.455 0.00 0.00 0.00 2.29
186 187 1.205417 GCATAACAAGCTGCCCAACAT 59.795 47.619 0.00 0.00 0.00 2.71
187 188 0.602562 GCATAACAAGCTGCCCAACA 59.397 50.000 0.00 0.00 0.00 3.33
188 189 0.890683 AGCATAACAAGCTGCCCAAC 59.109 50.000 0.00 0.00 41.61 3.77
189 190 1.176527 GAGCATAACAAGCTGCCCAA 58.823 50.000 0.00 0.00 43.58 4.12
190 191 0.329261 AGAGCATAACAAGCTGCCCA 59.671 50.000 0.00 0.00 43.58 5.36
191 192 0.737219 CAGAGCATAACAAGCTGCCC 59.263 55.000 0.00 0.00 43.58 5.36
192 193 0.100146 GCAGAGCATAACAAGCTGCC 59.900 55.000 0.00 0.00 44.50 4.85
205 206 1.517242 AACACTAACAGCAGCAGAGC 58.483 50.000 0.00 0.00 0.00 4.09
251 252 9.436957 TGACTACAACAGAAAAGAATATCCTTC 57.563 33.333 0.00 0.00 0.00 3.46
258 260 6.294176 GGTGCATGACTACAACAGAAAAGAAT 60.294 38.462 0.00 0.00 0.00 2.40
271 273 0.391130 TTGCCGAGGTGCATGACTAC 60.391 55.000 0.00 0.00 41.70 2.73
309 311 6.287589 ACTGCAACTAAGCTTAGACAGTAT 57.712 37.500 34.21 22.87 39.12 2.12
338 340 4.254492 GCAGTAAGGAACTAAGGACCAAG 58.746 47.826 0.00 0.00 38.49 3.61
339 341 3.649023 TGCAGTAAGGAACTAAGGACCAA 59.351 43.478 0.00 0.00 38.49 3.67
340 342 3.244582 TGCAGTAAGGAACTAAGGACCA 58.755 45.455 0.00 0.00 38.49 4.02
341 343 3.863041 CTGCAGTAAGGAACTAAGGACC 58.137 50.000 5.25 0.00 38.49 4.46
342 344 3.055747 AGCTGCAGTAAGGAACTAAGGAC 60.056 47.826 16.64 0.00 38.49 3.85
343 345 3.055819 CAGCTGCAGTAAGGAACTAAGGA 60.056 47.826 16.64 0.00 38.49 3.36
344 346 3.265791 CAGCTGCAGTAAGGAACTAAGG 58.734 50.000 16.64 0.00 38.49 2.69
345 347 3.931578 ACAGCTGCAGTAAGGAACTAAG 58.068 45.455 15.27 0.00 38.49 2.18
346 348 4.065088 CAACAGCTGCAGTAAGGAACTAA 58.935 43.478 15.27 0.00 38.49 2.24
347 349 3.071023 ACAACAGCTGCAGTAAGGAACTA 59.929 43.478 15.27 0.00 38.49 2.24
349 351 2.222027 ACAACAGCTGCAGTAAGGAAC 58.778 47.619 15.27 0.00 0.00 3.62
350 352 2.638480 ACAACAGCTGCAGTAAGGAA 57.362 45.000 15.27 0.00 0.00 3.36
351 353 2.638480 AACAACAGCTGCAGTAAGGA 57.362 45.000 15.27 0.00 0.00 3.36
352 354 2.484264 GGTAACAACAGCTGCAGTAAGG 59.516 50.000 15.27 5.09 0.00 2.69
399 407 1.153449 CAATCCGCCTAACCTCGCA 60.153 57.895 0.00 0.00 0.00 5.10
440 451 2.341846 TCAACCCACCAGACAGAAAC 57.658 50.000 0.00 0.00 0.00 2.78
514 531 4.460948 AGGCCATCAGCTAAATTTTGTG 57.539 40.909 5.01 0.00 43.05 3.33
588 616 6.993902 AGGATTCGTGGTTAAACAGAGTTAAA 59.006 34.615 0.00 0.00 0.00 1.52
590 618 6.014840 AGAGGATTCGTGGTTAAACAGAGTTA 60.015 38.462 0.00 0.00 0.00 2.24
591 619 4.969484 AGGATTCGTGGTTAAACAGAGTT 58.031 39.130 0.00 0.00 0.00 3.01
604 671 4.273480 ACAAGACAAAACAGAGGATTCGTG 59.727 41.667 0.00 0.00 0.00 4.35
876 948 2.756760 CAATTGAGCCATGGCAACTACT 59.243 45.455 37.18 16.94 44.88 2.57
877 949 2.754552 TCAATTGAGCCATGGCAACTAC 59.245 45.455 37.18 21.59 44.88 2.73
908 980 5.425630 TCATCATCACTGTGAATGAGGAAG 58.574 41.667 22.71 14.75 40.02 3.46
934 1006 3.074412 GAGAACGGGTTCATCAATGTGT 58.926 45.455 13.52 0.00 41.84 3.72
1062 1137 6.805016 AGTGAATCTGGTGATGAATCTAGT 57.195 37.500 0.00 0.00 32.44 2.57
1124 1205 0.819259 TGGCTGGCTCACACAAAGTC 60.819 55.000 2.00 0.00 0.00 3.01
1146 1227 3.466836 TCTGAACGAGCAAGTGACAATT 58.533 40.909 0.00 0.00 0.00 2.32
1280 1361 9.806203 TTATGGATTTGATGTTTGAATTGCTAG 57.194 29.630 0.00 0.00 0.00 3.42
1319 1400 5.787953 TTCTGGCACATGAAGAAAATCAA 57.212 34.783 0.00 0.00 38.20 2.57
1330 1411 1.468565 CGGAAAGCATTCTGGCACATG 60.469 52.381 2.47 0.00 38.13 3.21
1350 1431 3.888323 TGAGCACATACATCTCCTCTCTC 59.112 47.826 0.00 0.00 0.00 3.20
1366 1447 7.547370 ACATTCAACTAGATAGAACTTGAGCAC 59.453 37.037 0.00 0.00 0.00 4.40
1444 1525 0.753111 GGATTGTCCCTGGCCATGAC 60.753 60.000 22.50 22.50 0.00 3.06
1445 1526 1.614711 GGATTGTCCCTGGCCATGA 59.385 57.895 5.51 2.82 0.00 3.07
1446 1527 4.265206 GGATTGTCCCTGGCCATG 57.735 61.111 5.51 2.45 0.00 3.66
1473 1560 2.862541 TCAAATCCAACAGTCTGGGTG 58.137 47.619 4.53 1.91 37.06 4.61
1642 1729 3.922240 TCTGTACGCGGATAGTCAAAAAC 59.078 43.478 15.24 0.00 0.00 2.43
1656 1743 2.342910 TCGGAGAAAACTCTGTACGC 57.657 50.000 0.00 0.00 0.00 4.42
1663 1750 4.093556 GTGACATGGATTCGGAGAAAACTC 59.906 45.833 0.00 0.00 45.90 3.01
1682 1770 1.202325 TGTACACACCACAGTCGTGAC 60.202 52.381 5.18 0.00 46.80 3.67
1719 1807 1.733041 AGACATCAACGGCGTGACG 60.733 57.895 15.70 8.68 40.31 4.35
1728 1817 1.731160 GCTGCAGTCTCAGACATCAAC 59.269 52.381 16.64 0.00 36.19 3.18
1799 1888 1.162698 CTGGATTGGTCACACAGCTG 58.837 55.000 13.48 13.48 0.00 4.24
2045 2287 7.000472 ACATCGAAATACATCCCATTGAGATT 59.000 34.615 0.00 0.00 0.00 2.40
2065 2315 4.393062 AGACAAGGATAAAGTTGCACATCG 59.607 41.667 0.00 0.00 0.00 3.84
2082 2332 5.333645 GCTTAACACACATCACTCAGACAAG 60.334 44.000 0.00 0.00 0.00 3.16
2118 2370 5.405935 TGCAGAGAGAGTTTATGCAAGTA 57.594 39.130 0.00 0.00 43.41 2.24
2126 2378 5.801531 TGTTTACCTGCAGAGAGAGTTTA 57.198 39.130 17.39 0.00 0.00 2.01
2139 2393 3.067601 GGACACCCAAGTTTGTTTACCTG 59.932 47.826 0.00 0.00 0.00 4.00
2164 2418 5.525378 GCAACTATCAGGATTCAGTGGTTAG 59.475 44.000 0.00 0.00 0.00 2.34
2167 2421 3.370953 GGCAACTATCAGGATTCAGTGGT 60.371 47.826 0.00 0.00 0.00 4.16
2183 2437 4.029809 GTACCCCCAGCGGCAACT 62.030 66.667 1.45 0.00 0.00 3.16
2185 2439 4.028490 CAGTACCCCCAGCGGCAA 62.028 66.667 1.45 0.00 0.00 4.52
2190 2444 1.534729 CAAAACTCAGTACCCCCAGC 58.465 55.000 0.00 0.00 0.00 4.85
2227 2482 2.814336 AGGAGTTCGAAGCAATCCAAAC 59.186 45.455 16.59 0.00 32.21 2.93
2240 2496 1.737838 TGCCTTTGCATAGGAGTTCG 58.262 50.000 25.48 0.00 44.23 3.95
2252 2508 4.907879 AGAGACTTGAAAGTTGCCTTTG 57.092 40.909 0.00 0.00 40.98 2.77
2253 2509 5.418840 TCAAAGAGACTTGAAAGTTGCCTTT 59.581 36.000 0.00 5.25 43.58 3.11
2261 2517 6.148264 GCAAGGATTCAAAGAGACTTGAAAG 58.852 40.000 0.00 0.00 45.75 2.62
2266 2522 4.978099 TCTGCAAGGATTCAAAGAGACTT 58.022 39.130 0.00 0.00 0.00 3.01
2267 2523 4.285517 TCTCTGCAAGGATTCAAAGAGACT 59.714 41.667 0.00 0.00 36.22 3.24
2268 2524 4.573900 TCTCTGCAAGGATTCAAAGAGAC 58.426 43.478 0.00 0.00 36.22 3.36
2269 2525 4.897509 TCTCTGCAAGGATTCAAAGAGA 57.102 40.909 0.00 0.00 38.21 3.10
2270 2526 4.335874 CCATCTCTGCAAGGATTCAAAGAG 59.664 45.833 0.00 0.00 33.91 2.85
2271 2527 4.019051 TCCATCTCTGCAAGGATTCAAAGA 60.019 41.667 0.00 0.00 0.00 2.52
2272 2528 4.267536 TCCATCTCTGCAAGGATTCAAAG 58.732 43.478 0.00 0.00 0.00 2.77
2273 2529 4.305539 TCCATCTCTGCAAGGATTCAAA 57.694 40.909 0.00 0.00 0.00 2.69
2274 2530 4.305539 TTCCATCTCTGCAAGGATTCAA 57.694 40.909 0.00 0.00 0.00 2.69
2275 2531 4.080186 TGATTCCATCTCTGCAAGGATTCA 60.080 41.667 0.00 0.00 37.88 2.57
2276 2532 4.458397 TGATTCCATCTCTGCAAGGATTC 58.542 43.478 0.00 0.00 33.39 2.52
2277 2533 4.515028 TGATTCCATCTCTGCAAGGATT 57.485 40.909 0.00 0.00 0.00 3.01
2278 2534 4.399219 CATGATTCCATCTCTGCAAGGAT 58.601 43.478 0.00 0.00 0.00 3.24
2279 2535 3.816994 CATGATTCCATCTCTGCAAGGA 58.183 45.455 0.00 0.00 0.00 3.36
2318 2574 1.065564 TGATGGCGGTCATTGACATGA 60.066 47.619 18.09 0.00 34.48 3.07
2341 2597 3.146066 GTGTGCTAAAGGTTGATGTCCA 58.854 45.455 0.00 0.00 0.00 4.02
2345 2601 5.437289 TTTCTGTGTGCTAAAGGTTGATG 57.563 39.130 0.00 0.00 0.00 3.07
2369 2627 8.841300 AGAGAGAACAGAAGAAAAATGGTTTAC 58.159 33.333 0.00 0.00 0.00 2.01
2371 2629 7.254932 CGAGAGAGAACAGAAGAAAAATGGTTT 60.255 37.037 0.00 0.00 0.00 3.27
2386 2644 0.039180 TAGGGGTGCGAGAGAGAACA 59.961 55.000 0.00 0.00 0.00 3.18
2428 2686 3.300857 CAGGATGTAGCGATACAGTTCG 58.699 50.000 19.35 4.38 41.99 3.95
2475 2733 2.738846 GCAATGGCATCGAGTCGATTAT 59.261 45.455 25.03 16.10 44.59 1.28
2518 2776 6.153680 AGAGTACATAGTTCCAGAAGAGGTTG 59.846 42.308 0.00 0.00 0.00 3.77
2541 2799 9.647918 ACTCATGGTTACTAATATCTTCAGAGA 57.352 33.333 0.00 0.00 36.09 3.10
2554 2812 9.953565 AAAAGCACTTTATACTCATGGTTACTA 57.046 29.630 0.00 0.00 31.19 1.82
2573 2831 3.507622 ACTGGAAGGCTGATAAAAAGCAC 59.492 43.478 0.00 0.00 42.69 4.40
2579 2837 4.640771 AGACAACTGGAAGGCTGATAAA 57.359 40.909 0.00 0.00 39.30 1.40
2598 2856 4.864806 GCAGATTGTTCGATACAGTCAAGA 59.135 41.667 18.21 0.57 43.76 3.02
2636 2894 9.935241 ATTTCTTACTGCAGTATATATGAGGTG 57.065 33.333 26.54 7.69 0.00 4.00
2664 2922 7.012704 ACAGTTACCTAGCTGAATAAATGCATG 59.987 37.037 0.00 0.00 37.85 4.06
2671 2929 5.183228 GCCAACAGTTACCTAGCTGAATAA 58.817 41.667 0.00 0.00 37.85 1.40
2688 2946 5.601583 AATATTCTTGCATCATGCCAACA 57.398 34.783 7.30 0.00 44.23 3.33
2693 2951 5.176223 CCCGAAAAATATTCTTGCATCATGC 59.824 40.000 1.35 1.35 45.29 4.06


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

AutoCloner maintained by Alex Coulton.