Multiple sequence alignment - TraesCS5D01G479600

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 TraesCS5D01G479600 chr5D 100.000 5318 0 0 1 5318 517665658 517670975 0.000000e+00 9821.0
1 TraesCS5D01G479600 chr5D 84.898 245 29 5 3090 3331 517667945 517668184 1.910000e-59 241.0
2 TraesCS5D01G479600 chr5D 84.898 245 29 5 2288 2527 517668747 517668988 1.910000e-59 241.0
3 TraesCS5D01G479600 chr5B 91.496 2246 132 29 397 2610 650159810 650162028 0.000000e+00 3035.0
4 TraesCS5D01G479600 chr5B 92.695 1369 57 19 3731 5082 650163240 650164582 0.000000e+00 1934.0
5 TraesCS5D01G479600 chr5B 85.702 1161 100 27 2610 3734 650162080 650163210 0.000000e+00 1164.0
6 TraesCS5D01G479600 chr5B 81.855 496 54 21 1025 1512 650161158 650161625 8.350000e-103 385.0
7 TraesCS5D01G479600 chr5B 82.198 455 50 15 1771 2200 650160489 650160937 3.910000e-96 363.0
8 TraesCS5D01G479600 chr5B 90.171 234 19 4 166 398 650159420 650159650 8.660000e-78 302.0
9 TraesCS5D01G479600 chr5B 91.878 197 10 3 5123 5317 650164584 650164776 2.440000e-68 270.0
10 TraesCS5D01G479600 chr5B 84.586 266 29 10 2032 2291 650162283 650162542 2.460000e-63 254.0
11 TraesCS5D01G479600 chr5B 100.000 31 0 0 1542 1572 650162133 650162163 2.070000e-04 58.4
12 TraesCS5D01G479600 chr5A 88.345 1613 100 41 3731 5317 645123304 645124854 0.000000e+00 1857.0
13 TraesCS5D01G479600 chr5A 85.911 1015 86 22 357 1358 645120464 645121434 0.000000e+00 1029.0
14 TraesCS5D01G479600 chr5A 89.516 372 34 5 1665 2034 645121791 645122159 2.900000e-127 466.0
15 TraesCS5D01G479600 chr5A 91.450 269 17 5 2345 2610 645122262 645122527 1.090000e-96 364.0
16 TraesCS5D01G479600 chr5A 84.459 296 24 10 1738 2011 645121105 645121400 6.790000e-69 272.0
17 TraesCS5D01G479600 chr5A 86.111 180 18 4 1397 1569 645121434 645121613 2.530000e-43 187.0
18 TraesCS5D01G479600 chr5A 90.265 113 7 3 2087 2199 645122152 645122260 1.540000e-30 145.0
19 TraesCS5D01G479600 chr5A 94.915 59 2 1 1609 1666 645121609 645121667 2.040000e-14 91.6
20 TraesCS5D01G479600 chr4D 88.154 363 27 10 4540 4901 446988442 446988095 8.240000e-113 418.0
21 TraesCS5D01G479600 chr4D 94.767 172 5 1 1 168 220226146 220226317 1.140000e-66 265.0
22 TraesCS5D01G479600 chr4D 93.258 178 7 3 1 173 219954723 219954546 1.900000e-64 257.0
23 TraesCS5D01G479600 chr4D 93.678 174 7 1 1 170 301343189 301343016 1.900000e-64 257.0
24 TraesCS5D01G479600 chr4A 87.772 368 29 9 4540 4906 17269188 17268836 2.960000e-112 416.0
25 TraesCS5D01G479600 chr2A 87.945 365 28 9 4540 4903 654734457 654734806 2.960000e-112 416.0
26 TraesCS5D01G479600 chr3A 87.534 369 28 10 4540 4906 157989876 157989524 1.380000e-110 411.0
27 TraesCS5D01G479600 chr7A 87.228 368 31 9 4540 4906 643996073 643995721 6.410000e-109 405.0
28 TraesCS5D01G479600 chr2B 86.538 364 35 10 4540 4902 225356357 225356707 6.460000e-104 388.0
29 TraesCS5D01G479600 chr3B 85.870 368 36 10 4540 4906 755565349 755564997 1.400000e-100 377.0
30 TraesCS5D01G479600 chr6A 94.737 171 8 1 1 170 421644587 421644757 1.140000e-66 265.0
31 TraesCS5D01G479600 chr1D 94.253 174 5 2 1 170 297298490 297298662 1.470000e-65 261.0
32 TraesCS5D01G479600 chr1D 93.220 177 8 1 1 173 191405841 191405665 1.900000e-64 257.0
33 TraesCS5D01G479600 chr6D 94.118 170 9 1 1 170 199397161 199397329 1.900000e-64 257.0
34 TraesCS5D01G479600 chr2D 93.642 173 8 1 1 170 448103877 448104049 6.830000e-64 255.0
35 TraesCS5D01G479600 chr2D 92.655 177 9 1 1 173 611537952 611537776 8.840000e-63 252.0


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 TraesCS5D01G479600 chr5D 517665658 517670975 5317 False 3434.333333 9821 89.932000 1 5318 3 chr5D.!!$F1 5317
1 TraesCS5D01G479600 chr5B 650159420 650164776 5356 False 862.822222 3035 88.953444 166 5317 9 chr5B.!!$F1 5151
2 TraesCS5D01G479600 chr5A 645120464 645124854 4390 False 551.450000 1857 88.871500 357 5317 8 chr5A.!!$F1 4960

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
99 100 0.028770 CTTTTGCAAGTGACCGCGAA 59.971 50.0 8.23 0.00 0.0 4.70 F
129 130 0.035739 ACCCCTTTATCGCGTTGTGT 59.964 50.0 5.77 0.00 0.0 3.72 F
1340 1531 0.108615 ATGCCCTTCTTGACGAGTCG 60.109 55.0 11.85 11.85 0.0 4.18 F
1800 2121 0.316204 CAACGACGAGTGGGGTAACT 59.684 55.0 0.00 0.00 0.0 2.24 F
2034 2362 0.319405 GCATGCCCTTTTTGAGCAGT 59.681 50.0 6.36 0.00 40.4 4.40 F
3331 3751 0.322277 ACAGGAGGCAATGCAGACAG 60.322 55.0 7.79 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2410 0.944386 CACCAGGTCTGTTCAAACCG 59.056 55.000 0.00 0.00 40.63 4.44 R
2134 2462 3.803082 CAGTCCGCGGGCATTGTG 61.803 66.667 34.17 18.06 0.00 3.33 R
3111 3514 0.325272 TGGGTTGGTACTTATGCGCA 59.675 50.000 14.96 14.96 0.00 6.09 R
3722 4167 1.336440 GTTGGCACATGTACAACAGCA 59.664 47.619 27.47 4.75 42.88 4.41 R
3769 4251 4.634883 AGCATCAACATTGTAAGAGCTCAG 59.365 41.667 17.77 0.00 0.00 3.35 R
4716 5232 0.108756 GGAGTCACCGGTTGCTCTAC 60.109 60.000 25.46 11.66 32.20 2.59 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
89 90 8.939201 TCTCTATTAGATCTCACTTTTGCAAG 57.061 34.615 0.00 0.00 35.92 4.01
90 91 8.535335 TCTCTATTAGATCTCACTTTTGCAAGT 58.465 33.333 0.00 0.00 44.72 3.16
97 98 1.355210 ACTTTTGCAAGTGACCGCG 59.645 52.632 0.00 0.00 42.05 6.46
98 99 1.092921 ACTTTTGCAAGTGACCGCGA 61.093 50.000 8.23 0.00 42.05 5.87
99 100 0.028770 CTTTTGCAAGTGACCGCGAA 59.971 50.000 8.23 0.00 0.00 4.70
100 101 0.028770 TTTTGCAAGTGACCGCGAAG 59.971 50.000 8.23 0.00 33.19 3.79
102 103 3.423154 GCAAGTGACCGCGAAGGG 61.423 66.667 8.23 0.00 46.96 3.95
103 104 2.342279 CAAGTGACCGCGAAGGGA 59.658 61.111 8.23 0.00 46.37 4.20
104 105 1.079127 CAAGTGACCGCGAAGGGAT 60.079 57.895 8.23 0.00 46.37 3.85
105 106 0.673644 CAAGTGACCGCGAAGGGATT 60.674 55.000 8.23 0.00 46.37 3.01
106 107 0.673644 AAGTGACCGCGAAGGGATTG 60.674 55.000 8.23 0.00 46.37 2.67
107 108 1.079405 GTGACCGCGAAGGGATTGA 60.079 57.895 8.23 0.00 46.37 2.57
108 109 1.079405 TGACCGCGAAGGGATTGAC 60.079 57.895 8.23 0.00 46.37 3.18
109 110 1.079405 GACCGCGAAGGGATTGACA 60.079 57.895 8.23 0.00 46.37 3.58
110 111 0.672401 GACCGCGAAGGGATTGACAA 60.672 55.000 8.23 0.00 46.37 3.18
111 112 0.953960 ACCGCGAAGGGATTGACAAC 60.954 55.000 8.23 0.00 46.37 3.32
112 113 1.644786 CCGCGAAGGGATTGACAACC 61.645 60.000 8.23 0.00 46.37 3.77
113 114 1.644786 CGCGAAGGGATTGACAACCC 61.645 60.000 0.00 14.59 46.37 4.11
114 115 1.313091 GCGAAGGGATTGACAACCCC 61.313 60.000 10.02 10.02 46.64 4.95
121 122 2.949644 GGGATTGACAACCCCTTTATCG 59.050 50.000 10.82 0.00 40.19 2.92
122 123 2.357952 GGATTGACAACCCCTTTATCGC 59.642 50.000 0.00 0.00 0.00 4.58
123 124 1.444836 TTGACAACCCCTTTATCGCG 58.555 50.000 0.00 0.00 0.00 5.87
124 125 0.322322 TGACAACCCCTTTATCGCGT 59.678 50.000 5.77 0.00 0.00 6.01
125 126 1.270947 TGACAACCCCTTTATCGCGTT 60.271 47.619 5.77 0.00 0.00 4.84
126 127 1.129811 GACAACCCCTTTATCGCGTTG 59.870 52.381 5.77 2.01 39.70 4.10
127 128 1.161843 CAACCCCTTTATCGCGTTGT 58.838 50.000 5.77 0.00 31.36 3.32
128 129 1.135803 CAACCCCTTTATCGCGTTGTG 60.136 52.381 5.77 0.00 31.36 3.33
129 130 0.035739 ACCCCTTTATCGCGTTGTGT 59.964 50.000 5.77 0.00 0.00 3.72
130 131 0.446222 CCCCTTTATCGCGTTGTGTG 59.554 55.000 5.77 0.00 0.00 3.82
131 132 0.179200 CCCTTTATCGCGTTGTGTGC 60.179 55.000 5.77 0.00 0.00 4.57
132 133 0.515127 CCTTTATCGCGTTGTGTGCA 59.485 50.000 5.77 0.00 0.00 4.57
133 134 1.069568 CCTTTATCGCGTTGTGTGCAA 60.070 47.619 5.77 0.00 0.00 4.08
134 135 2.233355 CTTTATCGCGTTGTGTGCAAG 58.767 47.619 5.77 0.00 34.94 4.01
135 136 1.222300 TTATCGCGTTGTGTGCAAGT 58.778 45.000 5.77 0.00 34.94 3.16
136 137 1.222300 TATCGCGTTGTGTGCAAGTT 58.778 45.000 5.77 0.00 34.94 2.66
137 138 0.316937 ATCGCGTTGTGTGCAAGTTG 60.317 50.000 5.77 0.00 34.94 3.16
138 139 1.226267 CGCGTTGTGTGCAAGTTGT 60.226 52.632 4.48 0.00 34.94 3.32
139 140 0.796491 CGCGTTGTGTGCAAGTTGTT 60.796 50.000 4.48 0.00 34.94 2.83
140 141 1.345410 GCGTTGTGTGCAAGTTGTTT 58.655 45.000 4.48 0.00 34.94 2.83
141 142 1.058979 GCGTTGTGTGCAAGTTGTTTG 59.941 47.619 4.48 0.00 39.88 2.93
142 143 2.590073 CGTTGTGTGCAAGTTGTTTGA 58.410 42.857 4.48 0.00 39.21 2.69
143 144 2.341168 CGTTGTGTGCAAGTTGTTTGAC 59.659 45.455 4.48 0.00 39.21 3.18
144 145 3.574614 GTTGTGTGCAAGTTGTTTGACT 58.425 40.909 4.48 0.00 39.21 3.41
145 146 3.214697 TGTGTGCAAGTTGTTTGACTG 57.785 42.857 4.48 0.00 39.21 3.51
146 147 2.556189 TGTGTGCAAGTTGTTTGACTGT 59.444 40.909 4.48 0.00 39.21 3.55
147 148 3.005261 TGTGTGCAAGTTGTTTGACTGTT 59.995 39.130 4.48 0.00 39.21 3.16
148 149 3.987220 GTGTGCAAGTTGTTTGACTGTTT 59.013 39.130 4.48 0.00 39.21 2.83
149 150 3.986572 TGTGCAAGTTGTTTGACTGTTTG 59.013 39.130 4.48 0.00 39.21 2.93
150 151 3.987220 GTGCAAGTTGTTTGACTGTTTGT 59.013 39.130 4.48 0.00 39.21 2.83
151 152 3.986572 TGCAAGTTGTTTGACTGTTTGTG 59.013 39.130 4.48 0.00 39.21 3.33
152 153 3.181531 GCAAGTTGTTTGACTGTTTGTGC 60.182 43.478 4.48 0.00 39.21 4.57
153 154 3.932545 AGTTGTTTGACTGTTTGTGCA 57.067 38.095 0.00 0.00 0.00 4.57
154 155 3.836949 AGTTGTTTGACTGTTTGTGCAG 58.163 40.909 0.00 0.00 41.92 4.41
155 156 2.923020 GTTGTTTGACTGTTTGTGCAGG 59.077 45.455 0.00 0.00 40.59 4.85
156 157 2.166829 TGTTTGACTGTTTGTGCAGGT 58.833 42.857 0.00 0.00 40.59 4.00
157 158 3.348119 TGTTTGACTGTTTGTGCAGGTA 58.652 40.909 0.00 0.00 40.59 3.08
158 159 3.951037 TGTTTGACTGTTTGTGCAGGTAT 59.049 39.130 0.00 0.00 40.59 2.73
159 160 4.400884 TGTTTGACTGTTTGTGCAGGTATT 59.599 37.500 0.00 0.00 40.59 1.89
160 161 4.566545 TTGACTGTTTGTGCAGGTATTG 57.433 40.909 0.00 0.00 40.59 1.90
161 162 2.884012 TGACTGTTTGTGCAGGTATTGG 59.116 45.455 0.00 0.00 40.59 3.16
162 163 2.884639 GACTGTTTGTGCAGGTATTGGT 59.115 45.455 0.00 0.00 40.59 3.67
163 164 2.622942 ACTGTTTGTGCAGGTATTGGTG 59.377 45.455 0.00 0.00 40.59 4.17
164 165 2.884012 CTGTTTGTGCAGGTATTGGTGA 59.116 45.455 0.00 0.00 33.11 4.02
184 185 8.187913 TGGTGATTTGTTCAGATATTTTTCCA 57.812 30.769 0.00 0.00 34.17 3.53
186 187 9.657419 GGTGATTTGTTCAGATATTTTTCCAAT 57.343 29.630 0.00 0.00 34.17 3.16
238 239 2.877866 TCCTCAAAAGAGAGAGACGGT 58.122 47.619 0.00 0.00 37.87 4.83
252 253 5.045724 AGAGAGACGGTTTTCTCCTACTCTA 60.046 44.000 15.64 0.00 42.81 2.43
256 257 2.790468 CGGTTTTCTCCTACTCTACGCG 60.790 54.545 3.53 3.53 0.00 6.01
326 327 6.719370 GGGTTGGCCTAATATCATCATGTTAA 59.281 38.462 3.32 0.00 34.45 2.01
510 672 6.422333 TCCATATACTTGGAGCAAATGTTCA 58.578 36.000 0.00 0.00 40.90 3.18
554 716 6.743627 TCGTATATTTTCAAAAATCACGTGCC 59.256 34.615 21.73 3.54 41.99 5.01
556 718 7.906010 CGTATATTTTCAAAAATCACGTGCCTA 59.094 33.333 11.67 0.00 39.50 3.93
567 730 1.398390 CACGTGCCTAGAAAATGCTCC 59.602 52.381 0.82 0.00 0.00 4.70
673 839 3.529634 TTCTAATTGTGCCGTCAAACG 57.470 42.857 0.00 0.00 42.11 3.60
681 847 0.865111 TGCCGTCAAACGACTTGATG 59.135 50.000 13.75 13.75 46.05 3.07
693 859 5.264060 ACGACTTGATGTTTATGTTCACG 57.736 39.130 0.00 0.00 0.00 4.35
888 1057 2.931325 GGTCGGTGTGCGTTATTAATCA 59.069 45.455 0.00 0.00 0.00 2.57
889 1058 3.558418 GGTCGGTGTGCGTTATTAATCAT 59.442 43.478 0.00 0.00 0.00 2.45
890 1059 4.514506 GTCGGTGTGCGTTATTAATCATG 58.485 43.478 0.00 0.00 0.00 3.07
891 1060 3.001838 TCGGTGTGCGTTATTAATCATGC 59.998 43.478 6.85 6.85 0.00 4.06
892 1061 3.628017 GGTGTGCGTTATTAATCATGCC 58.372 45.455 10.57 4.14 0.00 4.40
893 1062 3.066064 GGTGTGCGTTATTAATCATGCCA 59.934 43.478 10.57 6.26 0.00 4.92
894 1063 4.282068 GTGTGCGTTATTAATCATGCCAG 58.718 43.478 10.57 0.00 0.00 4.85
895 1064 4.035091 GTGTGCGTTATTAATCATGCCAGA 59.965 41.667 10.57 0.00 0.00 3.86
896 1065 4.035091 TGTGCGTTATTAATCATGCCAGAC 59.965 41.667 10.57 4.27 0.00 3.51
897 1066 3.247411 TGCGTTATTAATCATGCCAGACG 59.753 43.478 10.57 0.00 0.00 4.18
898 1067 3.363970 GCGTTATTAATCATGCCAGACGG 60.364 47.826 2.89 0.00 0.00 4.79
899 1068 3.186409 CGTTATTAATCATGCCAGACGGG 59.814 47.826 0.00 0.00 40.85 5.28
1147 1325 1.880027 CCTTGTTTCTTACTGCGCCTT 59.120 47.619 4.18 0.00 0.00 4.35
1175 1356 2.481449 GCTGAAGTACCCCACTGTATCG 60.481 54.545 0.00 0.00 37.63 2.92
1211 1395 2.364002 TGTCGTGATTGTGTTGAGGAGA 59.636 45.455 0.00 0.00 0.00 3.71
1212 1396 3.181470 TGTCGTGATTGTGTTGAGGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
1213 1397 3.430218 GTCGTGATTGTGTTGAGGAGAAG 59.570 47.826 0.00 0.00 0.00 2.85
1225 1409 5.124138 TGTTGAGGAGAAGTTCGATCTAGAC 59.876 44.000 0.00 0.00 0.00 2.59
1239 1423 1.472878 TCTAGACGCGTGATGCTTTCT 59.527 47.619 20.70 7.36 43.27 2.52
1246 1430 2.723010 CGCGTGATGCTTTCTTTGACTC 60.723 50.000 0.00 0.00 43.27 3.36
1247 1431 2.723010 GCGTGATGCTTTCTTTGACTCG 60.723 50.000 0.00 0.00 41.73 4.18
1249 1433 3.059597 CGTGATGCTTTCTTTGACTCGTT 60.060 43.478 0.00 0.00 0.00 3.85
1251 1435 5.273944 GTGATGCTTTCTTTGACTCGTTTT 58.726 37.500 0.00 0.00 0.00 2.43
1340 1531 0.108615 ATGCCCTTCTTGACGAGTCG 60.109 55.000 11.85 11.85 0.00 4.18
1361 1552 2.222596 GCAGCAGTCGTGTTAATTCGAG 60.223 50.000 5.45 0.00 36.76 4.04
1524 1715 2.821969 AGGTGGAATTGCTTACTGCTTG 59.178 45.455 0.00 0.00 43.37 4.01
1540 1735 6.500684 ACTGCTTGTAGGTTATGAAATGTG 57.499 37.500 0.00 0.00 0.00 3.21
1577 1772 5.828630 GTTTGAAGAAAACAACGTGTGAAC 58.171 37.500 0.00 0.00 46.30 3.18
1580 1775 5.387279 TGAAGAAAACAACGTGTGAACTTC 58.613 37.500 0.00 1.89 35.75 3.01
1585 1780 2.218603 ACAACGTGTGAACTTCATCCC 58.781 47.619 0.00 0.00 0.00 3.85
1595 1790 5.009911 TGTGAACTTCATCCCTGTTTTGATG 59.990 40.000 0.00 0.00 39.75 3.07
1637 1833 2.336554 ATGACTGCATTTTCGCACAC 57.663 45.000 0.00 0.00 36.86 3.82
1684 2005 1.520787 GTATTGAGCCACCGGACGG 60.521 63.158 9.46 9.78 42.03 4.79
1741 2062 1.541379 ACCCAATACCAAACCTTCGC 58.459 50.000 0.00 0.00 0.00 4.70
1750 2071 4.629523 AACCTTCGCCGGCGGAAA 62.630 61.111 44.95 32.13 40.25 3.13
1800 2121 0.316204 CAACGACGAGTGGGGTAACT 59.684 55.000 0.00 0.00 0.00 2.24
1942 2270 2.163010 AGATGCGTGATGCTTTCTTTGG 59.837 45.455 0.00 0.00 46.63 3.28
1996 2324 1.379044 GGGAGTTGCCTGGGACATG 60.379 63.158 0.00 0.00 38.20 3.21
2034 2362 0.319405 GCATGCCCTTTTTGAGCAGT 59.681 50.000 6.36 0.00 40.40 4.40
2070 2398 5.440610 AGAAAAGTATGCATTACCTGGGAG 58.559 41.667 3.54 0.00 0.00 4.30
2073 2401 6.763715 AAAGTATGCATTACCTGGGAGATA 57.236 37.500 3.54 0.00 0.00 1.98
2082 2410 7.044798 GCATTACCTGGGAGATAATCATACTC 58.955 42.308 0.00 0.00 0.00 2.59
2123 2451 5.233689 GTGTGTTGAAGTTATACGCCTATCC 59.766 44.000 0.00 0.00 0.00 2.59
2124 2452 5.128171 TGTGTTGAAGTTATACGCCTATCCT 59.872 40.000 0.00 0.00 0.00 3.24
2125 2453 6.047231 GTGTTGAAGTTATACGCCTATCCTT 58.953 40.000 0.00 0.00 0.00 3.36
2126 2454 6.537660 GTGTTGAAGTTATACGCCTATCCTTT 59.462 38.462 0.00 0.00 0.00 3.11
2127 2455 7.707893 GTGTTGAAGTTATACGCCTATCCTTTA 59.292 37.037 0.00 0.00 0.00 1.85
2134 2462 7.985752 AGTTATACGCCTATCCTTTATTATGGC 59.014 37.037 0.00 0.00 35.94 4.40
2229 2557 4.576993 GCCTTGGGCGATGTTTTG 57.423 55.556 0.00 0.00 39.62 2.44
2276 2604 7.648142 TGTAAAAACATCTGCTAGTTTGAAGG 58.352 34.615 0.00 0.00 37.94 3.46
2301 2629 9.698617 GGAAACAACGTGTAAAATATATGTCTC 57.301 33.333 0.00 0.00 0.00 3.36
2310 2638 9.864034 GTGTAAAATATATGTCTCCATTTGTCG 57.136 33.333 0.00 0.00 32.29 4.35
2374 2702 5.604231 AGCCATCAGTCTTGATATCTTGGTA 59.396 40.000 3.98 0.00 42.12 3.25
2375 2703 6.271857 AGCCATCAGTCTTGATATCTTGGTAT 59.728 38.462 3.98 0.00 42.12 2.73
2452 2782 1.557099 TATGAGTGACGCCCTGAAGT 58.443 50.000 0.00 0.00 0.00 3.01
2469 2799 5.388475 CCTGAAGTGTACGATTTGTTTCTCG 60.388 44.000 0.00 0.00 40.62 4.04
2493 2823 8.715088 TCGTGATGATTCATGCTTAAATATGAG 58.285 33.333 3.32 0.00 38.53 2.90
2627 3010 3.089284 GTTGCCTACTATTGCTTTGGGT 58.911 45.455 0.00 0.00 0.00 4.51
2636 3019 8.695456 CCTACTATTGCTTTGGGTGATATTTTT 58.305 33.333 0.00 0.00 0.00 1.94
2637 3020 9.520204 CTACTATTGCTTTGGGTGATATTTTTG 57.480 33.333 0.00 0.00 0.00 2.44
2638 3021 6.818142 ACTATTGCTTTGGGTGATATTTTTGC 59.182 34.615 0.00 0.00 0.00 3.68
2639 3022 3.936564 TGCTTTGGGTGATATTTTTGCC 58.063 40.909 0.00 0.00 0.00 4.52
2784 3177 0.538057 TTCCTGGGAGCAGCAAACAG 60.538 55.000 0.00 0.00 0.00 3.16
2805 3198 1.673920 GCCCTTTTTGACGAGTCACAA 59.326 47.619 5.30 3.05 39.66 3.33
2833 3235 8.491134 AGTTGTATTAAGTATGCATTACCTGGA 58.509 33.333 3.54 0.00 0.00 3.86
2835 3237 8.671384 TGTATTAAGTATGCATTACCTGGAAC 57.329 34.615 3.54 0.00 0.00 3.62
2842 3244 5.947228 ATGCATTACCTGGAACATAATCG 57.053 39.130 0.00 0.00 38.20 3.34
2843 3245 4.776349 TGCATTACCTGGAACATAATCGT 58.224 39.130 0.00 0.00 38.20 3.73
2848 3250 7.654520 GCATTACCTGGAACATAATCGTTACTA 59.345 37.037 0.00 0.00 38.20 1.82
2885 3287 7.260603 ACCTGGTATGTTGAAGTTATACGTAC 58.739 38.462 0.00 9.28 34.86 3.67
2886 3288 6.415867 CCTGGTATGTTGAAGTTATACGTACG 59.584 42.308 15.01 15.01 35.90 3.67
2896 3298 8.153479 TGAAGTTATACGTACGCCTATCTTTA 57.847 34.615 16.72 10.94 0.00 1.85
2897 3299 8.786898 TGAAGTTATACGTACGCCTATCTTTAT 58.213 33.333 16.72 5.63 0.00 1.40
2900 3302 7.391554 AGTTATACGTACGCCTATCTTTATGGA 59.608 37.037 16.72 0.00 0.00 3.41
2930 3333 3.181491 GCACAAACTGGTTGAAACTAGCA 60.181 43.478 13.22 0.00 40.73 3.49
2968 3371 5.368145 TGAAGATATTTGAGGTGGAATCGG 58.632 41.667 0.00 0.00 0.00 4.18
2999 3402 2.159254 TGCTTTGGGCGATATTTTGCTC 60.159 45.455 0.00 0.00 45.43 4.26
3063 3466 9.299963 TGAAGAAAACAATGTGTAAACTTCATG 57.700 29.630 12.91 0.00 37.53 3.07
3073 3476 6.567959 TGTGTAAACTTCATGCATGTTTTGA 58.432 32.000 25.43 4.57 34.85 2.69
3133 3536 1.208535 CGCATAAGTACCAACCCAGGA 59.791 52.381 0.00 0.00 0.00 3.86
3176 3579 7.083062 AGCCATTGGTCTTGATATATCTTGA 57.917 36.000 13.79 8.76 0.00 3.02
3220 3623 8.924511 TCTTGATTCACCTTCATAACTCTTTT 57.075 30.769 0.00 0.00 0.00 2.27
3221 3624 9.003658 TCTTGATTCACCTTCATAACTCTTTTC 57.996 33.333 0.00 0.00 0.00 2.29
3222 3625 8.924511 TTGATTCACCTTCATAACTCTTTTCT 57.075 30.769 0.00 0.00 0.00 2.52
3223 3626 8.327941 TGATTCACCTTCATAACTCTTTTCTG 57.672 34.615 0.00 0.00 0.00 3.02
3224 3627 8.156820 TGATTCACCTTCATAACTCTTTTCTGA 58.843 33.333 0.00 0.00 0.00 3.27
3265 3677 1.648467 GCCAACTGAAGGGTGCGATC 61.648 60.000 0.00 0.00 0.00 3.69
3274 3686 1.270907 AGGGTGCGATCTGTTTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
3331 3751 0.322277 ACAGGAGGCAATGCAGACAG 60.322 55.000 7.79 0.00 0.00 3.51
3339 3759 1.400846 GCAATGCAGACAGTCCTCATG 59.599 52.381 0.00 0.00 0.00 3.07
3341 3761 1.283347 ATGCAGACAGTCCTCATGGT 58.717 50.000 0.00 0.00 34.23 3.55
3505 3942 9.974980 ATGTTTATTGTTTCTTAAACCGTTGAT 57.025 25.926 0.41 0.00 40.67 2.57
3512 3949 9.672086 TTGTTTCTTAAACCGTTGATATGAAAG 57.328 29.630 0.41 0.00 40.67 2.62
3513 3950 8.842280 TGTTTCTTAAACCGTTGATATGAAAGT 58.158 29.630 0.41 0.00 40.67 2.66
3514 3951 9.673454 GTTTCTTAAACCGTTGATATGAAAGTT 57.327 29.630 5.11 0.00 35.35 2.66
3516 3953 9.672086 TTCTTAAACCGTTGATATGAAAGTTTG 57.328 29.630 11.92 1.30 0.00 2.93
3517 3954 9.058174 TCTTAAACCGTTGATATGAAAGTTTGA 57.942 29.630 11.92 5.76 0.00 2.69
3518 3955 9.113876 CTTAAACCGTTGATATGAAAGTTTGAC 57.886 33.333 11.92 0.00 0.00 3.18
3519 3956 5.277601 ACCGTTGATATGAAAGTTTGACG 57.722 39.130 0.00 0.00 0.00 4.35
3520 3957 4.753107 ACCGTTGATATGAAAGTTTGACGT 59.247 37.500 0.00 0.00 0.00 4.34
3521 3958 5.079406 CCGTTGATATGAAAGTTTGACGTG 58.921 41.667 0.00 0.00 0.00 4.49
3522 3959 4.549599 CGTTGATATGAAAGTTTGACGTGC 59.450 41.667 0.00 0.00 0.00 5.34
3523 3960 5.614668 CGTTGATATGAAAGTTTGACGTGCT 60.615 40.000 0.00 0.00 0.00 4.40
3575 4012 8.123639 TCAAGAGAGTTATGTGCTACTAACTT 57.876 34.615 6.78 0.00 38.09 2.66
3584 4024 3.578716 TGTGCTACTAACTTCCTTCTGCT 59.421 43.478 0.00 0.00 0.00 4.24
3613 4053 0.519077 GCTAGTGACTTGCTTGCACC 59.481 55.000 11.67 0.00 35.41 5.01
3642 4085 6.813293 TCTCATGAAACTTGATATCAGGGA 57.187 37.500 18.11 1.69 0.00 4.20
3643 4086 6.824553 TCTCATGAAACTTGATATCAGGGAG 58.175 40.000 18.11 13.00 33.34 4.30
3644 4087 6.385176 TCTCATGAAACTTGATATCAGGGAGT 59.615 38.462 18.11 10.68 33.58 3.85
3645 4088 6.962182 TCATGAAACTTGATATCAGGGAGTT 58.038 36.000 18.11 15.51 32.33 3.01
3646 4089 7.050377 TCATGAAACTTGATATCAGGGAGTTC 58.950 38.462 18.11 16.50 30.77 3.01
3647 4090 6.627087 TGAAACTTGATATCAGGGAGTTCT 57.373 37.500 18.11 10.10 30.77 3.01
3648 4091 7.733773 TGAAACTTGATATCAGGGAGTTCTA 57.266 36.000 18.11 9.32 30.77 2.10
3684 4127 7.620880 AGTAGTTGTGGCTCATTACTTGAATA 58.379 34.615 0.00 0.00 32.78 1.75
3686 4129 5.648092 AGTTGTGGCTCATTACTTGAATACC 59.352 40.000 0.00 0.00 32.78 2.73
3716 4161 2.334977 TGTGGAAGGTGGTACTGATGT 58.665 47.619 0.00 0.00 0.00 3.06
3722 4167 3.708236 AGGTGGTACTGATGTAGGGAT 57.292 47.619 0.00 0.00 0.00 3.85
3729 4174 3.272574 ACTGATGTAGGGATGCTGTTG 57.727 47.619 0.00 0.00 0.00 3.33
3747 4226 3.066064 TGTTGTACATGTGCCAACTGTTC 59.934 43.478 28.45 13.54 39.30 3.18
3748 4227 3.207265 TGTACATGTGCCAACTGTTCT 57.793 42.857 9.11 0.00 0.00 3.01
4101 4592 0.885879 CATCAGGAGCAAAGCAGCAA 59.114 50.000 0.00 0.00 36.85 3.91
4132 4623 0.320771 AGTTGGCCGTAAGCAGAGTG 60.321 55.000 0.00 0.00 46.50 3.51
4287 4778 2.607892 GCTTGACCCACACTGTCGC 61.608 63.158 0.00 0.00 35.46 5.19
4293 4784 2.801162 CCACACTGTCGCGAGTCG 60.801 66.667 10.24 8.54 40.15 4.18
4344 4835 1.202855 GGCTGCCATATGATGTGTCCT 60.203 52.381 15.17 0.00 0.00 3.85
4356 4847 2.593346 TGTGTCCTTTTGCGCAAAAT 57.407 40.000 39.49 0.00 39.29 1.82
4390 4881 0.982852 TGCTGTGGGCTACTGGCTAT 60.983 55.000 16.55 0.00 42.39 2.97
4433 4924 7.615582 TGTTATCTGCAAGTTTATGAGAAGG 57.384 36.000 0.00 0.00 33.76 3.46
4443 4934 7.475840 CAAGTTTATGAGAAGGAATAGCCAAC 58.524 38.462 0.00 0.00 40.02 3.77
4464 4955 5.135508 ACGGTATTCTATGGTATGCAGAC 57.864 43.478 1.94 1.94 0.00 3.51
4538 5047 3.066621 GTGGCATGTGGTATTGTATGTGG 59.933 47.826 0.00 0.00 0.00 4.17
4572 5081 3.157087 TCTTGCCTCCTTGGTTGAAATC 58.843 45.455 0.00 0.00 38.35 2.17
4578 5087 3.691609 CCTCCTTGGTTGAAATCTGTAGC 59.308 47.826 0.00 0.00 0.00 3.58
4590 5099 0.611062 TCTGTAGCTGCTGGTACCGT 60.611 55.000 24.46 0.00 44.08 4.83
4593 5102 0.037605 GTAGCTGCTGGTACCGTTGT 60.038 55.000 18.95 0.00 40.24 3.32
4598 5107 2.933492 GCTGCTGGTACCGTTGTCATTA 60.933 50.000 7.57 0.00 0.00 1.90
4602 5111 5.294356 TGCTGGTACCGTTGTCATTATATC 58.706 41.667 7.57 0.00 0.00 1.63
4614 5130 8.247562 CGTTGTCATTATATCTTTTTCCCCAAA 58.752 33.333 0.00 0.00 0.00 3.28
4659 5175 2.682856 TGTGGAAAGTGTTCACAAGCTC 59.317 45.455 0.00 0.00 35.25 4.09
4667 5183 4.675510 AGTGTTCACAAGCTCAACAAATG 58.324 39.130 5.74 0.00 31.95 2.32
4692 5208 3.251972 GGGCTTTTCACTCTATATGCAGC 59.748 47.826 0.00 0.00 0.00 5.25
4713 5229 3.014623 CACCAGATGCAGTCATGAATGT 58.985 45.455 22.89 5.51 31.96 2.71
4715 5231 4.820173 CACCAGATGCAGTCATGAATGTAT 59.180 41.667 23.73 23.73 34.62 2.29
4716 5232 4.820173 ACCAGATGCAGTCATGAATGTATG 59.180 41.667 27.51 17.11 32.25 2.39
4717 5233 4.820173 CCAGATGCAGTCATGAATGTATGT 59.180 41.667 27.51 21.80 32.25 2.29
4718 5234 5.993441 CCAGATGCAGTCATGAATGTATGTA 59.007 40.000 27.51 9.39 32.25 2.29
4719 5235 6.147328 CCAGATGCAGTCATGAATGTATGTAG 59.853 42.308 27.51 15.25 32.25 2.74
4720 5236 6.927381 CAGATGCAGTCATGAATGTATGTAGA 59.073 38.462 27.51 4.16 32.25 2.59
4721 5237 7.116519 CAGATGCAGTCATGAATGTATGTAGAG 59.883 40.741 27.51 11.06 32.25 2.43
4722 5238 5.052481 TGCAGTCATGAATGTATGTAGAGC 58.948 41.667 22.89 7.14 0.00 4.09
4723 5239 5.052481 GCAGTCATGAATGTATGTAGAGCA 58.948 41.667 22.89 0.00 0.00 4.26
4724 5240 5.525012 GCAGTCATGAATGTATGTAGAGCAA 59.475 40.000 22.89 0.00 0.00 3.91
4808 5324 8.584157 ACAGTAATCTCTATAGAATGGAAGCAG 58.416 37.037 3.57 0.00 34.73 4.24
4815 5331 2.322355 AGAATGGAAGCAGGTCATCG 57.678 50.000 0.00 0.00 0.00 3.84
4888 5404 2.192979 GGCGCCTTGATCCATCCA 59.807 61.111 22.15 0.00 0.00 3.41
5058 5575 2.037511 ACCATTTGGCAATTGACCACAG 59.962 45.455 20.47 11.73 36.76 3.66
5060 5577 3.319755 CATTTGGCAATTGACCACAGAC 58.680 45.455 17.69 0.00 36.76 3.51
5105 5623 5.720041 TGATATGATGATGAGAGCTGATGGA 59.280 40.000 0.00 0.00 0.00 3.41
5110 5628 2.144730 GATGAGAGCTGATGGATGCAC 58.855 52.381 0.00 0.00 0.00 4.57
5111 5629 0.906775 TGAGAGCTGATGGATGCACA 59.093 50.000 0.00 0.00 0.00 4.57
5112 5630 1.489230 TGAGAGCTGATGGATGCACAT 59.511 47.619 0.00 0.00 0.00 3.21
5113 5631 1.874231 GAGAGCTGATGGATGCACATG 59.126 52.381 0.00 0.00 0.00 3.21
5114 5632 0.311165 GAGCTGATGGATGCACATGC 59.689 55.000 0.00 0.00 42.50 4.06
5257 5782 9.033481 TCAAAACAAAATGCAACATAAGAGAAG 57.967 29.630 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.535335 ACTTGCAAAAGTGAGATCTAATAGAGA 58.465 33.333 0.00 0.00 39.01 3.10
65 66 8.715191 ACTTGCAAAAGTGAGATCTAATAGAG 57.285 34.615 0.00 0.00 0.00 2.43
79 80 1.092921 TCGCGGTCACTTGCAAAAGT 61.093 50.000 6.13 0.00 0.00 2.66
80 81 0.028770 TTCGCGGTCACTTGCAAAAG 59.971 50.000 6.13 0.00 0.00 2.27
81 82 0.028770 CTTCGCGGTCACTTGCAAAA 59.971 50.000 6.13 0.00 0.00 2.44
82 83 1.646540 CTTCGCGGTCACTTGCAAA 59.353 52.632 6.13 0.00 0.00 3.68
83 84 2.250939 CCTTCGCGGTCACTTGCAA 61.251 57.895 6.13 0.00 0.00 4.08
84 85 2.664851 CCTTCGCGGTCACTTGCA 60.665 61.111 6.13 0.00 0.00 4.08
85 86 3.423154 CCCTTCGCGGTCACTTGC 61.423 66.667 6.13 0.00 0.00 4.01
86 87 0.673644 AATCCCTTCGCGGTCACTTG 60.674 55.000 6.13 0.00 0.00 3.16
87 88 0.673644 CAATCCCTTCGCGGTCACTT 60.674 55.000 6.13 0.00 0.00 3.16
88 89 1.079127 CAATCCCTTCGCGGTCACT 60.079 57.895 6.13 0.00 0.00 3.41
89 90 1.079405 TCAATCCCTTCGCGGTCAC 60.079 57.895 6.13 0.00 0.00 3.67
90 91 1.079405 GTCAATCCCTTCGCGGTCA 60.079 57.895 6.13 0.00 0.00 4.02
91 92 0.672401 TTGTCAATCCCTTCGCGGTC 60.672 55.000 6.13 0.00 0.00 4.79
92 93 0.953960 GTTGTCAATCCCTTCGCGGT 60.954 55.000 6.13 0.00 0.00 5.68
93 94 1.644786 GGTTGTCAATCCCTTCGCGG 61.645 60.000 6.13 0.00 0.00 6.46
94 95 1.644786 GGGTTGTCAATCCCTTCGCG 61.645 60.000 3.15 0.00 40.48 5.87
95 96 1.313091 GGGGTTGTCAATCCCTTCGC 61.313 60.000 24.72 0.00 43.00 4.70
96 97 2.868253 GGGGTTGTCAATCCCTTCG 58.132 57.895 24.72 0.00 43.00 3.79
100 101 2.949644 CGATAAAGGGGTTGTCAATCCC 59.050 50.000 24.64 24.64 42.73 3.85
101 102 2.357952 GCGATAAAGGGGTTGTCAATCC 59.642 50.000 6.29 6.29 0.00 3.01
102 103 2.031683 CGCGATAAAGGGGTTGTCAATC 59.968 50.000 0.00 0.00 0.00 2.67
103 104 2.014128 CGCGATAAAGGGGTTGTCAAT 58.986 47.619 0.00 0.00 0.00 2.57
104 105 1.270947 ACGCGATAAAGGGGTTGTCAA 60.271 47.619 15.93 0.00 0.00 3.18
105 106 0.322322 ACGCGATAAAGGGGTTGTCA 59.678 50.000 15.93 0.00 0.00 3.58
106 107 1.129811 CAACGCGATAAAGGGGTTGTC 59.870 52.381 15.93 0.00 46.81 3.18
107 108 1.161843 CAACGCGATAAAGGGGTTGT 58.838 50.000 15.93 0.00 46.81 3.32
108 109 3.988459 CAACGCGATAAAGGGGTTG 57.012 52.632 15.93 0.00 46.85 3.77
109 110 1.161843 CACAACGCGATAAAGGGGTT 58.838 50.000 15.93 0.00 40.63 4.11
110 111 0.035739 ACACAACGCGATAAAGGGGT 59.964 50.000 15.93 0.00 0.00 4.95
111 112 0.446222 CACACAACGCGATAAAGGGG 59.554 55.000 15.93 0.00 0.00 4.79
112 113 0.179200 GCACACAACGCGATAAAGGG 60.179 55.000 15.93 0.00 0.00 3.95
113 114 0.515127 TGCACACAACGCGATAAAGG 59.485 50.000 15.93 0.00 0.00 3.11
114 115 2.233355 CTTGCACACAACGCGATAAAG 58.767 47.619 15.93 0.29 0.00 1.85
115 116 1.600013 ACTTGCACACAACGCGATAAA 59.400 42.857 15.93 0.00 0.00 1.40
116 117 1.222300 ACTTGCACACAACGCGATAA 58.778 45.000 15.93 0.00 0.00 1.75
117 118 1.070242 CAACTTGCACACAACGCGATA 60.070 47.619 15.93 0.00 0.00 2.92
118 119 0.316937 CAACTTGCACACAACGCGAT 60.317 50.000 15.93 0.00 0.00 4.58
119 120 1.061729 CAACTTGCACACAACGCGA 59.938 52.632 15.93 0.00 0.00 5.87
120 121 0.796491 AACAACTTGCACACAACGCG 60.796 50.000 3.53 3.53 0.00 6.01
121 122 1.058979 CAAACAACTTGCACACAACGC 59.941 47.619 0.00 0.00 0.00 4.84
122 123 2.341168 GTCAAACAACTTGCACACAACG 59.659 45.455 0.00 0.00 34.76 4.10
123 124 3.364621 CAGTCAAACAACTTGCACACAAC 59.635 43.478 0.00 0.00 34.76 3.32
124 125 3.005261 ACAGTCAAACAACTTGCACACAA 59.995 39.130 0.00 0.00 34.76 3.33
125 126 2.556189 ACAGTCAAACAACTTGCACACA 59.444 40.909 0.00 0.00 34.76 3.72
126 127 3.216147 ACAGTCAAACAACTTGCACAC 57.784 42.857 0.00 0.00 34.76 3.82
127 128 3.932545 AACAGTCAAACAACTTGCACA 57.067 38.095 0.00 0.00 34.76 4.57
128 129 3.987220 ACAAACAGTCAAACAACTTGCAC 59.013 39.130 0.00 0.00 34.76 4.57
129 130 3.986572 CACAAACAGTCAAACAACTTGCA 59.013 39.130 0.00 0.00 34.76 4.08
130 131 3.181531 GCACAAACAGTCAAACAACTTGC 60.182 43.478 0.00 0.00 34.76 4.01
131 132 3.986572 TGCACAAACAGTCAAACAACTTG 59.013 39.130 0.00 0.00 36.25 3.16
132 133 4.236935 CTGCACAAACAGTCAAACAACTT 58.763 39.130 0.00 0.00 32.78 2.66
133 134 3.367292 CCTGCACAAACAGTCAAACAACT 60.367 43.478 0.00 0.00 35.83 3.16
134 135 2.923020 CCTGCACAAACAGTCAAACAAC 59.077 45.455 0.00 0.00 35.83 3.32
135 136 2.560542 ACCTGCACAAACAGTCAAACAA 59.439 40.909 0.00 0.00 35.83 2.83
136 137 2.166829 ACCTGCACAAACAGTCAAACA 58.833 42.857 0.00 0.00 35.83 2.83
137 138 2.939460 ACCTGCACAAACAGTCAAAC 57.061 45.000 0.00 0.00 35.83 2.93
138 139 4.202101 CCAATACCTGCACAAACAGTCAAA 60.202 41.667 0.00 0.00 35.83 2.69
139 140 3.317711 CCAATACCTGCACAAACAGTCAA 59.682 43.478 0.00 0.00 35.83 3.18
140 141 2.884012 CCAATACCTGCACAAACAGTCA 59.116 45.455 0.00 0.00 35.83 3.41
141 142 2.884639 ACCAATACCTGCACAAACAGTC 59.115 45.455 0.00 0.00 35.83 3.51
142 143 2.622942 CACCAATACCTGCACAAACAGT 59.377 45.455 0.00 0.00 35.83 3.55
143 144 2.884012 TCACCAATACCTGCACAAACAG 59.116 45.455 0.00 0.00 37.42 3.16
144 145 2.937519 TCACCAATACCTGCACAAACA 58.062 42.857 0.00 0.00 0.00 2.83
145 146 4.519540 AATCACCAATACCTGCACAAAC 57.480 40.909 0.00 0.00 0.00 2.93
146 147 4.343526 ACAAATCACCAATACCTGCACAAA 59.656 37.500 0.00 0.00 0.00 2.83
147 148 3.894427 ACAAATCACCAATACCTGCACAA 59.106 39.130 0.00 0.00 0.00 3.33
148 149 3.495331 ACAAATCACCAATACCTGCACA 58.505 40.909 0.00 0.00 0.00 4.57
149 150 4.022416 TGAACAAATCACCAATACCTGCAC 60.022 41.667 0.00 0.00 31.50 4.57
150 151 4.148079 TGAACAAATCACCAATACCTGCA 58.852 39.130 0.00 0.00 31.50 4.41
151 152 4.458989 TCTGAACAAATCACCAATACCTGC 59.541 41.667 0.00 0.00 33.47 4.85
152 153 6.764308 ATCTGAACAAATCACCAATACCTG 57.236 37.500 0.00 0.00 33.47 4.00
153 154 9.479549 AAATATCTGAACAAATCACCAATACCT 57.520 29.630 0.00 0.00 33.47 3.08
157 158 9.657419 GGAAAAATATCTGAACAAATCACCAAT 57.343 29.630 0.00 0.00 33.47 3.16
158 159 8.646004 TGGAAAAATATCTGAACAAATCACCAA 58.354 29.630 0.00 0.00 33.47 3.67
159 160 8.187913 TGGAAAAATATCTGAACAAATCACCA 57.812 30.769 0.00 0.00 33.47 4.17
160 161 9.657419 ATTGGAAAAATATCTGAACAAATCACC 57.343 29.630 0.00 0.00 33.47 4.02
189 190 9.473007 AATTCCCTTTTTCTGGATTTTCAAAAA 57.527 25.926 0.00 0.00 0.00 1.94
191 192 8.270744 TCAATTCCCTTTTTCTGGATTTTCAAA 58.729 29.630 0.00 0.00 0.00 2.69
238 239 5.575957 CATAACGCGTAGAGTAGGAGAAAA 58.424 41.667 14.46 0.00 41.76 2.29
252 253 3.425404 GTCAATTTCATGCATAACGCGT 58.575 40.909 5.58 5.58 46.97 6.01
256 257 8.757789 CATTGTATGGTCAATTTCATGCATAAC 58.242 33.333 0.00 0.00 36.27 1.89
533 695 8.050778 TCTAGGCACGTGATTTTTGAAAATAT 57.949 30.769 22.23 0.00 38.64 1.28
540 702 5.164061 GCATTTTCTAGGCACGTGATTTTTG 60.164 40.000 22.23 5.40 0.00 2.44
547 709 1.398390 GGAGCATTTTCTAGGCACGTG 59.602 52.381 12.28 12.28 0.00 4.49
657 823 3.837669 GTCGTTTGACGGCACAATT 57.162 47.368 0.00 0.00 46.84 2.32
673 839 4.846137 GCACGTGAACATAAACATCAAGTC 59.154 41.667 22.23 0.00 0.00 3.01
681 847 4.203950 TCAAGTGCACGTGAACATAAAC 57.796 40.909 29.43 9.25 31.70 2.01
727 893 5.137551 TGTTCTAGGGTTTCCTCTTTTTGG 58.862 41.667 0.00 0.00 43.66 3.28
784 953 2.095567 CGTGTTCTGCTCTCCCATTTTG 60.096 50.000 0.00 0.00 0.00 2.44
825 994 2.872557 CGGTGTCTTGCTGGCATG 59.127 61.111 0.00 0.00 30.58 4.06
900 1069 3.114616 CAGTGCTCCTTGTCGCCG 61.115 66.667 0.00 0.00 0.00 6.46
1175 1356 4.856664 TCACGACAGAAGAACAAGAGTAC 58.143 43.478 0.00 0.00 0.00 2.73
1211 1395 1.736126 TCACGCGTCTAGATCGAACTT 59.264 47.619 9.86 0.05 0.00 2.66
1212 1396 1.366679 TCACGCGTCTAGATCGAACT 58.633 50.000 9.86 0.00 0.00 3.01
1213 1397 2.037649 CATCACGCGTCTAGATCGAAC 58.962 52.381 9.86 0.00 0.00 3.95
1239 1423 3.245284 CGAGCAAGAGAAAACGAGTCAAA 59.755 43.478 0.00 0.00 0.00 2.69
1246 1430 1.725164 GGGTACGAGCAAGAGAAAACG 59.275 52.381 0.00 0.00 0.00 3.60
1247 1431 2.762745 TGGGTACGAGCAAGAGAAAAC 58.237 47.619 0.00 0.00 0.00 2.43
1249 1433 2.093658 GGATGGGTACGAGCAAGAGAAA 60.094 50.000 0.00 0.00 0.00 2.52
1251 1435 1.112113 GGATGGGTACGAGCAAGAGA 58.888 55.000 0.00 0.00 0.00 3.10
1340 1531 1.724623 TCGAATTAACACGACTGCTGC 59.275 47.619 0.00 0.00 33.62 5.25
1361 1552 7.817418 TTCCCAGGTATAATGCATACTTTTC 57.183 36.000 0.00 0.00 39.67 2.29
1421 1612 9.740710 GTCCCATAAAGATAGCCATATAACTTT 57.259 33.333 0.00 0.00 0.00 2.66
1502 1693 2.927553 GCAGTAAGCAATTCCACCTG 57.072 50.000 0.00 0.00 44.79 4.00
1524 1715 9.559958 CAGATGTTTTCACATTTCATAACCTAC 57.440 33.333 0.00 0.00 44.22 3.18
1540 1735 8.746751 GTTTTCTTCAAACTAGCAGATGTTTTC 58.253 33.333 0.00 0.00 41.58 2.29
1567 1762 2.158813 ACAGGGATGAAGTTCACACGTT 60.159 45.455 7.96 0.00 0.00 3.99
1568 1763 1.416401 ACAGGGATGAAGTTCACACGT 59.584 47.619 7.96 2.96 0.00 4.49
1577 1772 9.793252 CTATTTAACATCAAAACAGGGATGAAG 57.207 33.333 8.47 0.00 42.73 3.02
1580 1775 8.960591 AGTCTATTTAACATCAAAACAGGGATG 58.039 33.333 0.00 0.00 44.97 3.51
1637 1833 4.403734 ACTTGGTACTGGGTTGGTATTTG 58.596 43.478 0.00 0.00 0.00 2.32
1699 2020 2.230660 GTATTTATGTCCAGGGGCAGC 58.769 52.381 0.00 0.00 0.00 5.25
1701 2022 2.209758 TGGTATTTATGTCCAGGGGCA 58.790 47.619 0.00 0.00 0.00 5.36
1782 2103 1.909700 TAGTTACCCCACTCGTCGTT 58.090 50.000 0.00 0.00 0.00 3.85
1800 2121 1.610554 GCAGAGGCGGGTGGTAGTTA 61.611 60.000 0.00 0.00 0.00 2.24
1869 2190 5.279206 CGGCAGAAGAACATGAGTAGGATAT 60.279 44.000 0.00 0.00 0.00 1.63
1942 2270 3.552294 GGTACGAGCAAGAGAATAACAGC 59.448 47.826 0.00 0.00 0.00 4.40
1996 2324 5.755813 CATGCTTGCTACAGTAATTGATCC 58.244 41.667 0.00 0.00 0.00 3.36
2070 2398 7.042658 GGTCTGTTCAAACCGAGTATGATTATC 60.043 40.741 0.00 0.00 0.00 1.75
2073 2401 4.935808 GGTCTGTTCAAACCGAGTATGATT 59.064 41.667 0.00 0.00 0.00 2.57
2082 2410 0.944386 CACCAGGTCTGTTCAAACCG 59.056 55.000 0.00 0.00 40.63 4.44
2134 2462 3.803082 CAGTCCGCGGGCATTGTG 61.803 66.667 34.17 18.06 0.00 3.33
2146 2474 2.808543 CACAGCTAGTTTCAACCAGTCC 59.191 50.000 0.00 0.00 0.00 3.85
2147 2475 3.467803 ACACAGCTAGTTTCAACCAGTC 58.532 45.455 0.00 0.00 0.00 3.51
2227 2555 9.696974 ACATTCTATGGCCTAAGCAGTAAGCAA 62.697 40.741 3.32 0.00 42.56 3.91
2228 2556 8.324085 ACATTCTATGGCCTAAGCAGTAAGCA 62.324 42.308 3.32 0.00 42.56 3.91
2229 2557 3.753294 TCTATGGCCTAAGCAGTAAGC 57.247 47.619 3.32 0.00 42.56 3.09
2276 2604 9.698617 GGAGACATATATTTTACACGTTGTTTC 57.301 33.333 0.00 0.00 0.00 2.78
2298 2626 2.288579 ACTTACGTGCGACAAATGGAGA 60.289 45.455 0.00 0.00 0.00 3.71
2301 2629 2.226262 CACTTACGTGCGACAAATGG 57.774 50.000 0.00 0.00 33.82 3.16
2327 2655 7.189512 GCTCAATGCTAGTAAACTTGGTATTG 58.810 38.462 14.26 14.26 38.95 1.90
2394 2722 4.346418 AGAGAGTTGTGAAGGTGAATCAGT 59.654 41.667 0.00 0.00 0.00 3.41
2395 2723 4.892433 AGAGAGTTGTGAAGGTGAATCAG 58.108 43.478 0.00 0.00 0.00 2.90
2442 2770 1.393539 CAAATCGTACACTTCAGGGCG 59.606 52.381 0.00 0.00 0.00 6.13
2469 2799 7.754027 GGCTCATATTTAAGCATGAATCATCAC 59.246 37.037 0.00 0.00 40.36 3.06
2493 2823 2.103941 CTCCTGTCATAGAGGAAAGGGC 59.896 54.545 0.66 0.00 41.83 5.19
2721 3104 8.296713 GCAAACTCCTCTATTTAATTGTGTTGA 58.703 33.333 0.00 0.00 0.00 3.18
2723 3106 7.451566 AGGCAAACTCCTCTATTTAATTGTGTT 59.548 33.333 0.00 0.00 0.00 3.32
2724 3107 6.948309 AGGCAAACTCCTCTATTTAATTGTGT 59.052 34.615 0.00 0.00 0.00 3.72
2725 3108 7.253422 CAGGCAAACTCCTCTATTTAATTGTG 58.747 38.462 0.00 0.00 33.25 3.33
2726 3109 6.378280 CCAGGCAAACTCCTCTATTTAATTGT 59.622 38.462 0.00 0.00 33.25 2.71
2728 3111 5.893824 CCCAGGCAAACTCCTCTATTTAATT 59.106 40.000 0.00 0.00 33.25 1.40
2729 3112 5.193728 TCCCAGGCAAACTCCTCTATTTAAT 59.806 40.000 0.00 0.00 33.25 1.40
2730 3113 4.538490 TCCCAGGCAAACTCCTCTATTTAA 59.462 41.667 0.00 0.00 33.25 1.52
2731 3114 4.080526 GTCCCAGGCAAACTCCTCTATTTA 60.081 45.833 0.00 0.00 33.25 1.40
2732 3115 2.919602 TCCCAGGCAAACTCCTCTATTT 59.080 45.455 0.00 0.00 33.25 1.40
2733 3116 2.239907 GTCCCAGGCAAACTCCTCTATT 59.760 50.000 0.00 0.00 33.25 1.73
2734 3117 1.840635 GTCCCAGGCAAACTCCTCTAT 59.159 52.381 0.00 0.00 33.25 1.98
2736 3119 0.768221 TGTCCCAGGCAAACTCCTCT 60.768 55.000 0.00 0.00 33.25 3.69
2737 3120 0.329596 ATGTCCCAGGCAAACTCCTC 59.670 55.000 0.00 0.00 33.25 3.71
2738 3121 1.668826 TATGTCCCAGGCAAACTCCT 58.331 50.000 0.00 0.00 36.78 3.69
2746 3139 5.416952 CAGGAAATTGATATATGTCCCAGGC 59.583 44.000 0.00 0.00 0.00 4.85
2784 3177 0.591659 GTGACTCGTCAAAAAGGGCC 59.408 55.000 0.00 0.00 41.85 5.80
2805 3198 9.109393 CAGGTAATGCATACTTAATACAACTGT 57.891 33.333 0.00 0.00 34.74 3.55
2833 3235 8.836268 TGTTCAAACCTAGTAACGATTATGTT 57.164 30.769 0.00 0.00 35.86 2.71
2835 3237 8.592998 GTCTGTTCAAACCTAGTAACGATTATG 58.407 37.037 0.00 0.00 0.00 1.90
2842 3244 4.995487 CCAGGTCTGTTCAAACCTAGTAAC 59.005 45.833 0.00 0.00 44.13 2.50
2843 3245 4.657039 ACCAGGTCTGTTCAAACCTAGTAA 59.343 41.667 0.00 0.00 44.13 2.24
2848 3250 3.394606 ACATACCAGGTCTGTTCAAACCT 59.605 43.478 4.74 0.00 46.94 3.50
2885 3287 6.149308 TGCATATTGTTCCATAAAGATAGGCG 59.851 38.462 0.00 0.00 31.53 5.52
2886 3288 7.040478 TGTGCATATTGTTCCATAAAGATAGGC 60.040 37.037 0.00 0.00 30.47 3.93
2896 3298 4.527816 ACCAGTTTGTGCATATTGTTCCAT 59.472 37.500 0.00 0.00 0.00 3.41
2897 3299 3.894427 ACCAGTTTGTGCATATTGTTCCA 59.106 39.130 0.00 0.00 0.00 3.53
2900 3302 5.528043 TCAACCAGTTTGTGCATATTGTT 57.472 34.783 0.00 0.00 36.49 2.83
2946 3349 5.611374 TCCGATTCCACCTCAAATATCTTC 58.389 41.667 0.00 0.00 0.00 2.87
2947 3350 5.630415 TCCGATTCCACCTCAAATATCTT 57.370 39.130 0.00 0.00 0.00 2.40
2988 3391 9.774742 CTTGTAACCTTAAGTGAGCAAAATATC 57.225 33.333 0.97 0.00 0.00 1.63
3024 3427 6.899393 TGTTTTCTTCAAACCAGCAGATAT 57.101 33.333 0.00 0.00 43.87 1.63
3111 3514 0.325272 TGGGTTGGTACTTATGCGCA 59.675 50.000 14.96 14.96 0.00 6.09
3133 3536 4.010349 GGCTCAATGCTAGTAAACTTGGT 58.990 43.478 0.00 0.00 42.39 3.67
3190 3593 6.159398 AGTTATGAAGGTGAATCAAGAGGGAT 59.841 38.462 0.00 0.00 0.00 3.85
3234 3637 4.275196 CCTTCAGTTGGCATCACTCATATG 59.725 45.833 0.00 0.00 0.00 1.78
3265 3677 6.438259 AAGCATGATCATCAAGAGAAACAG 57.562 37.500 4.86 0.00 0.00 3.16
3274 3686 6.073058 GGCTCGTATTTAAGCATGATCATCAA 60.073 38.462 4.86 0.00 40.36 2.57
3331 3751 5.825593 TCCTATTTCCATACCATGAGGAC 57.174 43.478 0.00 0.00 38.69 3.85
3498 3919 5.079406 CACGTCAAACTTTCATATCAACGG 58.921 41.667 0.00 0.00 32.30 4.44
3500 3921 5.689819 AGCACGTCAAACTTTCATATCAAC 58.310 37.500 0.00 0.00 0.00 3.18
3505 3942 7.921787 TCTTAAAAGCACGTCAAACTTTCATA 58.078 30.769 0.00 0.00 32.63 2.15
3509 3946 6.560711 ACATCTTAAAAGCACGTCAAACTTT 58.439 32.000 0.00 0.00 35.20 2.66
3510 3947 6.131544 ACATCTTAAAAGCACGTCAAACTT 57.868 33.333 0.00 0.00 0.00 2.66
3511 3948 5.751243 ACATCTTAAAAGCACGTCAAACT 57.249 34.783 0.00 0.00 0.00 2.66
3512 3949 5.968848 TGAACATCTTAAAAGCACGTCAAAC 59.031 36.000 0.00 0.00 0.00 2.93
3513 3950 6.125327 TGAACATCTTAAAAGCACGTCAAA 57.875 33.333 0.00 0.00 0.00 2.69
3514 3951 5.743026 TGAACATCTTAAAAGCACGTCAA 57.257 34.783 0.00 0.00 0.00 3.18
3515 3952 5.940192 ATGAACATCTTAAAAGCACGTCA 57.060 34.783 0.00 0.00 0.00 4.35
3516 3953 8.788813 CATTAATGAACATCTTAAAAGCACGTC 58.211 33.333 10.04 0.00 0.00 4.34
3517 3954 8.511321 TCATTAATGAACATCTTAAAAGCACGT 58.489 29.630 15.82 0.00 33.08 4.49
3518 3955 8.894409 TCATTAATGAACATCTTAAAAGCACG 57.106 30.769 15.82 0.00 33.08 5.34
3558 3995 6.036191 GCAGAAGGAAGTTAGTAGCACATAAC 59.964 42.308 0.00 0.00 33.06 1.89
3563 4000 3.929610 CAGCAGAAGGAAGTTAGTAGCAC 59.070 47.826 0.00 0.00 0.00 4.40
3575 4012 1.679944 GCATAACAGCCAGCAGAAGGA 60.680 52.381 0.00 0.00 0.00 3.36
3584 4024 3.599343 CAAGTCACTAGCATAACAGCCA 58.401 45.455 0.00 0.00 34.23 4.75
3648 4091 9.632638 ATGAGCCACAACTACTATTCAATAAAT 57.367 29.630 0.00 0.00 0.00 1.40
3708 4153 3.774766 ACAACAGCATCCCTACATCAGTA 59.225 43.478 0.00 0.00 0.00 2.74
3716 4161 3.872696 CACATGTACAACAGCATCCCTA 58.127 45.455 0.00 0.00 0.00 3.53
3722 4167 1.336440 GTTGGCACATGTACAACAGCA 59.664 47.619 27.47 4.75 42.88 4.41
3729 4174 5.411361 TGAATAGAACAGTTGGCACATGTAC 59.589 40.000 0.00 0.00 39.30 2.90
3748 4227 8.677300 GCTCAGATAAACCTCATGTTTTGAATA 58.323 33.333 0.00 0.00 44.80 1.75
3769 4251 4.634883 AGCATCAACATTGTAAGAGCTCAG 59.365 41.667 17.77 0.00 0.00 3.35
3774 4256 9.708222 GTAATTGTAGCATCAACATTGTAAGAG 57.292 33.333 0.00 0.00 0.00 2.85
4132 4623 3.304324 GCTTCCTTCAGCTTGTTTCTGAC 60.304 47.826 0.00 0.00 39.99 3.51
4234 4725 2.203209 CTTCGCCATGCCCCTACC 60.203 66.667 0.00 0.00 0.00 3.18
4287 4778 3.777465 TTCCTATCAAACTCCGACTCG 57.223 47.619 0.00 0.00 0.00 4.18
4293 4784 1.664151 CGCGGTTTCCTATCAAACTCC 59.336 52.381 0.00 0.00 36.62 3.85
4344 4835 7.938563 ATACAGTTAAAGATTTTGCGCAAAA 57.061 28.000 40.76 40.76 43.48 2.44
4356 4847 5.730550 CCCACAGCAGTATACAGTTAAAGA 58.269 41.667 5.50 0.00 0.00 2.52
4390 4881 2.503356 ACAAAGACATGTTTTTGGGGCA 59.497 40.909 32.91 0.00 38.51 5.36
4433 4924 5.548406 ACCATAGAATACCGTTGGCTATTC 58.452 41.667 8.73 8.73 31.86 1.75
4443 4934 5.184096 AGAGTCTGCATACCATAGAATACCG 59.816 44.000 0.00 0.00 0.00 4.02
4464 4955 8.927721 CATACATTCTAGCAAGATTCATGAGAG 58.072 37.037 0.00 0.00 0.00 3.20
4538 5047 5.675538 AGGAGGCAAGAATCTACACATAAC 58.324 41.667 0.00 0.00 0.00 1.89
4572 5081 0.246635 AACGGTACCAGCAGCTACAG 59.753 55.000 13.54 0.00 0.00 2.74
4578 5087 1.808411 AATGACAACGGTACCAGCAG 58.192 50.000 13.54 0.74 0.00 4.24
4598 5107 8.416329 CGATCAAGAATTTGGGGAAAAAGATAT 58.584 33.333 0.00 0.00 34.97 1.63
4602 5111 6.024552 TCGATCAAGAATTTGGGGAAAAAG 57.975 37.500 0.00 0.00 34.97 2.27
4659 5175 2.545106 GTGAAAAGCCCTGCATTTGTTG 59.455 45.455 0.00 0.00 29.57 3.33
4667 5183 3.251972 GCATATAGAGTGAAAAGCCCTGC 59.748 47.826 0.00 0.00 0.00 4.85
4692 5208 3.014623 ACATTCATGACTGCATCTGGTG 58.985 45.455 12.62 0.00 30.68 4.17
4713 5229 2.426024 GAGTCACCGGTTGCTCTACATA 59.574 50.000 21.61 0.00 0.00 2.29
4715 5231 0.601558 GAGTCACCGGTTGCTCTACA 59.398 55.000 21.61 0.00 0.00 2.74
4716 5232 0.108756 GGAGTCACCGGTTGCTCTAC 60.109 60.000 25.46 11.66 32.20 2.59
4717 5233 0.541063 TGGAGTCACCGGTTGCTCTA 60.541 55.000 25.46 20.38 42.61 2.43
4718 5234 1.837051 TGGAGTCACCGGTTGCTCT 60.837 57.895 25.46 13.86 42.61 4.09
4719 5235 1.668151 GTGGAGTCACCGGTTGCTC 60.668 63.158 21.05 21.05 42.61 4.26
4720 5236 0.830444 TAGTGGAGTCACCGGTTGCT 60.830 55.000 2.97 5.72 44.64 3.91
4721 5237 0.249398 ATAGTGGAGTCACCGGTTGC 59.751 55.000 2.97 0.00 44.64 4.17
4722 5238 5.524971 TTATATAGTGGAGTCACCGGTTG 57.475 43.478 2.97 0.00 44.64 3.77
4723 5239 5.895534 TCTTTATATAGTGGAGTCACCGGTT 59.104 40.000 2.97 0.00 44.64 4.44
4724 5240 5.452255 TCTTTATATAGTGGAGTCACCGGT 58.548 41.667 0.00 0.00 44.64 5.28
4766 5282 9.751542 GAGATTACTGTAAAGCTGTATGTATGT 57.248 33.333 4.11 0.00 32.73 2.29
4767 5283 9.973450 AGAGATTACTGTAAAGCTGTATGTATG 57.027 33.333 4.11 0.00 32.73 2.39
4808 5324 1.357334 GGCGAGAGAGACGATGACC 59.643 63.158 0.00 0.00 0.00 4.02
4815 5331 2.776913 CCCTTCCGGCGAGAGAGAC 61.777 68.421 9.30 0.00 0.00 3.36
4888 5404 3.211963 GCCATCGCCTTCGCCAAT 61.212 61.111 0.00 0.00 35.26 3.16
5058 5575 4.314961 TGAGTTCATGTATGTGTGTGGTC 58.685 43.478 0.00 0.00 0.00 4.02
5060 5577 5.225899 CATGAGTTCATGTATGTGTGTGG 57.774 43.478 12.82 0.00 46.40 4.17
5082 5599 6.223351 TCCATCAGCTCTCATCATCATATC 57.777 41.667 0.00 0.00 0.00 1.63
5090 5608 2.144730 GTGCATCCATCAGCTCTCATC 58.855 52.381 0.00 0.00 0.00 2.92
5114 5632 1.195448 CCAGAACAGTAAGCAAGCGTG 59.805 52.381 0.00 0.00 0.00 5.34
5115 5633 1.202651 ACCAGAACAGTAAGCAAGCGT 60.203 47.619 0.00 0.00 0.00 5.07
5116 5634 1.512926 ACCAGAACAGTAAGCAAGCG 58.487 50.000 0.00 0.00 0.00 4.68
5129 5647 2.104792 CACCAGAGAACAGGAACCAGAA 59.895 50.000 0.00 0.00 0.00 3.02
5223 5744 7.044181 TGTTGCATTTTGTTTTGAGTCCATAA 58.956 30.769 0.00 0.00 0.00 1.90
5236 5761 7.715657 TCAACTTCTCTTATGTTGCATTTTGT 58.284 30.769 0.00 0.00 41.02 2.83
5257 5782 0.613777 ACCCACGATTCCTCCTCAAC 59.386 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.