Multiple sequence alignment - TraesCS5A01G092100

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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 TraesCS5A01G092100 chr5A 100.000 3365 0 0 1 3365 127531936 127535300 0.000000e+00 6215.0
1 TraesCS5A01G092100 chr5A 96.651 209 7 0 1 209 127523047 127523255 6.910000e-92 348.0
2 TraesCS5A01G092100 chr5A 88.106 227 21 3 11 236 176975941 176975720 7.160000e-67 265.0
3 TraesCS5A01G092100 chr5A 85.950 242 25 6 2 238 169999304 169999541 2.000000e-62 250.0
4 TraesCS5A01G092100 chr5A 81.279 219 34 6 2956 3168 175390860 175390643 1.610000e-38 171.0
5 TraesCS5A01G092100 chr5A 83.523 176 26 3 1094 1266 127519778 127519953 9.660000e-36 161.0
6 TraesCS5A01G092100 chr5A 83.099 71 11 1 2514 2584 600354456 600354525 2.800000e-06 63.9
7 TraesCS5A01G092100 chr5D 92.046 1471 91 9 1910 3363 118010630 118012091 0.000000e+00 2045.0
8 TraesCS5A01G092100 chr5D 89.865 1559 90 27 264 1785 118009016 118010543 0.000000e+00 1941.0
9 TraesCS5A01G092100 chr5D 77.753 445 62 23 2942 3362 300961586 300962017 4.340000e-59 239.0
10 TraesCS5A01G092100 chr5D 84.118 170 25 2 1098 1266 118007904 118008072 2.690000e-36 163.0
11 TraesCS5A01G092100 chr5D 80.095 211 23 13 2944 3137 176098173 176098381 4.530000e-29 139.0
12 TraesCS5A01G092100 chr5D 88.710 62 7 0 2526 2587 317328370 317328309 3.600000e-10 76.8
13 TraesCS5A01G092100 chr5B 89.692 1591 92 30 267 1823 128854683 128853131 0.000000e+00 1964.0
14 TraesCS5A01G092100 chr5B 93.491 1183 69 6 1822 3001 128853017 128851840 0.000000e+00 1751.0
15 TraesCS5A01G092100 chr5B 84.118 170 25 2 1098 1266 128855785 128855617 2.690000e-36 163.0
16 TraesCS5A01G092100 chr5B 89.091 110 11 1 2959 3068 644596548 644596440 5.860000e-28 135.0
17 TraesCS5A01G092100 chr7D 87.083 240 25 3 2 239 612884500 612884735 1.990000e-67 267.0
18 TraesCS5A01G092100 chr7D 77.958 431 71 15 2953 3365 462141747 462142171 7.210000e-62 248.0
19 TraesCS5A01G092100 chr7D 77.778 441 65 18 2943 3362 610688533 610688961 1.210000e-59 241.0
20 TraesCS5A01G092100 chr7D 78.539 219 21 17 2940 3138 585372971 585373183 1.640000e-23 121.0
21 TraesCS5A01G092100 chr7D 86.667 60 3 4 2942 3000 563664883 563664828 1.010000e-05 62.1
22 TraesCS5A01G092100 chr3B 87.083 240 23 7 2 238 128939105 128938871 7.160000e-67 265.0
23 TraesCS5A01G092100 chr3B 82.000 100 17 1 2485 2584 780055992 780056090 2.150000e-12 84.2
24 TraesCS5A01G092100 chr2B 78.886 431 60 18 2953 3362 195375150 195375570 2.570000e-66 263.0
25 TraesCS5A01G092100 chr2B 78.353 425 59 21 2960 3362 130722297 130721884 9.330000e-61 244.0
26 TraesCS5A01G092100 chr3D 78.704 432 63 14 2952 3363 348132777 348133199 9.260000e-66 261.0
27 TraesCS5A01G092100 chr3D 82.403 233 24 12 2956 3171 110171035 110170803 1.590000e-43 187.0
28 TraesCS5A01G092100 chr3D 83.621 116 18 1 2469 2584 583011219 583011333 1.280000e-19 108.0
29 TraesCS5A01G092100 chr3D 80.488 82 16 0 2527 2608 104031522 104031441 2.800000e-06 63.9
30 TraesCS5A01G092100 chr1D 78.404 426 65 16 2953 3359 119356665 119357082 5.570000e-63 252.0
31 TraesCS5A01G092100 chr1D 100.000 31 0 0 2640 2670 254628045 254628075 1.300000e-04 58.4
32 TraesCS5A01G092100 chr3A 85.833 240 27 4 2 238 594576143 594576378 7.210000e-62 248.0
33 TraesCS5A01G092100 chr3A 78.037 428 63 19 2956 3362 418909936 418909519 1.210000e-59 241.0
34 TraesCS5A01G092100 chr3A 79.741 232 30 6 2954 3168 497618693 497618462 5.820000e-33 152.0
35 TraesCS5A01G092100 chr3A 88.393 112 12 1 2956 3066 510000529 510000418 2.110000e-27 134.0
36 TraesCS5A01G092100 chrUn 85.417 240 28 6 2 239 81662385 81662151 3.350000e-60 243.0
37 TraesCS5A01G092100 chr4A 85.356 239 29 3 2 238 247797632 247797866 3.350000e-60 243.0
38 TraesCS5A01G092100 chr1A 85.062 241 28 7 2 240 36624305 36624071 4.340000e-59 239.0
39 TraesCS5A01G092100 chr1A 78.293 410 60 18 2973 3362 347009960 347010360 1.560000e-58 237.0
40 TraesCS5A01G092100 chr1A 85.484 62 5 3 2939 3000 76546245 76546302 1.010000e-05 62.1
41 TraesCS5A01G092100 chr7B 76.112 427 56 23 2952 3361 220876082 220875685 7.420000e-42 182.0
42 TraesCS5A01G092100 chr4B 87.000 100 13 0 2485 2584 529917274 529917373 2.740000e-21 113.0
43 TraesCS5A01G092100 chr4D 84.337 83 13 0 2526 2608 391710015 391709933 7.740000e-12 82.4
44 TraesCS5A01G092100 chr7A 75.385 195 31 12 2518 2697 612031210 612031018 1.000000e-10 78.7


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 TraesCS5A01G092100 chr5A 127531936 127535300 3364 False 6215.000000 6215 100.000000 1 3365 1 chr5A.!!$F1 3364
1 TraesCS5A01G092100 chr5A 127519778 127523255 3477 False 254.500000 348 90.087000 1 1266 2 chr5A.!!$F4 1265
2 TraesCS5A01G092100 chr5D 118007904 118012091 4187 False 1383.000000 2045 88.676333 264 3363 3 chr5D.!!$F3 3099
3 TraesCS5A01G092100 chr5B 128851840 128855785 3945 True 1292.666667 1964 89.100333 267 3001 3 chr5B.!!$R2 2734

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
57 58 0.106149 CGGCGGCTAGGGTTTAGAAT 59.894 55.0 7.61 0.0 0.00 2.40 F
140 141 0.107703 TATTGCTTGAGCCTCGTGGG 60.108 55.0 5.54 0.0 41.18 4.61 F
487 1380 0.465460 TTTGAGCTTTCGTGTGCCCT 60.465 50.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 2312 0.179062 GCAATGCCTCCTCGATCTGT 60.179 55.000 0.00 0.0 0.0 3.41 R
1861 2915 1.202891 GCAGAGGCCGGGGTAATAAAT 60.203 52.381 2.18 0.0 0.0 1.40 R
2406 3461 0.170339 GAACACGCATGCCTAAACCC 59.830 55.000 13.15 0.0 0.0 4.11 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
40 41 4.389576 GCAAGTGTGAAGCGGCGG 62.390 66.667 9.78 0.00 0.00 6.13
41 42 4.389576 CAAGTGTGAAGCGGCGGC 62.390 66.667 9.78 8.43 40.37 6.53
53 54 4.165486 GGCGGCGGCTAGGGTTTA 62.165 66.667 27.22 0.00 39.81 2.01
54 55 2.588034 GCGGCGGCTAGGGTTTAG 60.588 66.667 9.78 0.00 35.83 1.85
56 57 1.518774 CGGCGGCTAGGGTTTAGAA 59.481 57.895 7.61 0.00 0.00 2.10
57 58 0.106149 CGGCGGCTAGGGTTTAGAAT 59.894 55.000 7.61 0.00 0.00 2.40
58 59 1.872653 CGGCGGCTAGGGTTTAGAATC 60.873 57.143 7.61 0.00 0.00 2.52
59 60 1.499049 GCGGCTAGGGTTTAGAATCG 58.501 55.000 0.00 0.00 0.00 3.34
60 61 1.068127 GCGGCTAGGGTTTAGAATCGA 59.932 52.381 0.00 0.00 0.00 3.59
61 62 2.740452 CGGCTAGGGTTTAGAATCGAC 58.260 52.381 0.00 0.00 0.00 4.20
62 63 2.361438 CGGCTAGGGTTTAGAATCGACT 59.639 50.000 0.00 0.00 0.00 4.18
64 65 4.120589 GGCTAGGGTTTAGAATCGACTTG 58.879 47.826 0.00 0.00 0.00 3.16
65 66 4.382793 GGCTAGGGTTTAGAATCGACTTGT 60.383 45.833 0.00 0.00 0.00 3.16
67 68 4.884668 AGGGTTTAGAATCGACTTGTGA 57.115 40.909 0.00 0.00 0.00 3.58
68 69 5.422214 AGGGTTTAGAATCGACTTGTGAT 57.578 39.130 0.00 0.00 0.00 3.06
69 70 6.540438 AGGGTTTAGAATCGACTTGTGATA 57.460 37.500 0.00 0.00 0.00 2.15
70 71 6.574350 AGGGTTTAGAATCGACTTGTGATAG 58.426 40.000 0.00 0.00 0.00 2.08
71 72 6.380274 AGGGTTTAGAATCGACTTGTGATAGA 59.620 38.462 0.00 0.00 0.00 1.98
72 73 7.070074 AGGGTTTAGAATCGACTTGTGATAGAT 59.930 37.037 0.00 0.00 0.00 1.98
74 75 9.182933 GGTTTAGAATCGACTTGTGATAGATAC 57.817 37.037 0.00 0.00 0.00 2.24
75 76 9.182933 GTTTAGAATCGACTTGTGATAGATACC 57.817 37.037 0.00 0.00 0.00 2.73
76 77 6.961360 AGAATCGACTTGTGATAGATACCA 57.039 37.500 0.00 0.00 0.00 3.25
77 78 7.531857 AGAATCGACTTGTGATAGATACCAT 57.468 36.000 0.00 0.00 0.00 3.55
78 79 7.374272 AGAATCGACTTGTGATAGATACCATG 58.626 38.462 0.00 0.00 0.00 3.66
79 80 6.656632 ATCGACTTGTGATAGATACCATGT 57.343 37.500 0.00 0.00 0.00 3.21
80 81 6.465439 TCGACTTGTGATAGATACCATGTT 57.535 37.500 0.00 0.00 0.00 2.71
81 82 7.576861 TCGACTTGTGATAGATACCATGTTA 57.423 36.000 0.00 0.00 0.00 2.41
82 83 7.649057 TCGACTTGTGATAGATACCATGTTAG 58.351 38.462 0.00 0.00 0.00 2.34
83 84 7.501225 TCGACTTGTGATAGATACCATGTTAGA 59.499 37.037 0.00 0.00 0.00 2.10
84 85 8.135529 CGACTTGTGATAGATACCATGTTAGAA 58.864 37.037 0.00 0.00 0.00 2.10
85 86 9.469807 GACTTGTGATAGATACCATGTTAGAAG 57.530 37.037 0.00 0.00 0.00 2.85
86 87 8.424918 ACTTGTGATAGATACCATGTTAGAAGG 58.575 37.037 0.00 0.00 0.00 3.46
87 88 7.303182 TGTGATAGATACCATGTTAGAAGGG 57.697 40.000 0.00 0.00 0.00 3.95
89 90 7.233553 TGTGATAGATACCATGTTAGAAGGGAG 59.766 40.741 0.00 0.00 0.00 4.30
90 91 7.451877 GTGATAGATACCATGTTAGAAGGGAGA 59.548 40.741 0.00 0.00 0.00 3.71
91 92 7.671819 TGATAGATACCATGTTAGAAGGGAGAG 59.328 40.741 0.00 0.00 0.00 3.20
92 93 6.031964 AGATACCATGTTAGAAGGGAGAGA 57.968 41.667 0.00 0.00 0.00 3.10
93 94 6.444704 AGATACCATGTTAGAAGGGAGAGAA 58.555 40.000 0.00 0.00 0.00 2.87
94 95 6.903534 AGATACCATGTTAGAAGGGAGAGAAA 59.096 38.462 0.00 0.00 0.00 2.52
95 96 5.428184 ACCATGTTAGAAGGGAGAGAAAG 57.572 43.478 0.00 0.00 0.00 2.62
96 97 5.094387 ACCATGTTAGAAGGGAGAGAAAGA 58.906 41.667 0.00 0.00 0.00 2.52
97 98 5.548056 ACCATGTTAGAAGGGAGAGAAAGAA 59.452 40.000 0.00 0.00 0.00 2.52
98 99 6.216456 ACCATGTTAGAAGGGAGAGAAAGAAT 59.784 38.462 0.00 0.00 0.00 2.40
99 100 7.115414 CCATGTTAGAAGGGAGAGAAAGAATT 58.885 38.462 0.00 0.00 0.00 2.17
100 101 7.066766 CCATGTTAGAAGGGAGAGAAAGAATTG 59.933 40.741 0.00 0.00 0.00 2.32
101 102 7.316393 TGTTAGAAGGGAGAGAAAGAATTGA 57.684 36.000 0.00 0.00 0.00 2.57
102 103 7.922382 TGTTAGAAGGGAGAGAAAGAATTGAT 58.078 34.615 0.00 0.00 0.00 2.57
104 105 5.753716 AGAAGGGAGAGAAAGAATTGATGG 58.246 41.667 0.00 0.00 0.00 3.51
105 106 5.490357 AGAAGGGAGAGAAAGAATTGATGGA 59.510 40.000 0.00 0.00 0.00 3.41
107 108 6.338591 AGGGAGAGAAAGAATTGATGGAAT 57.661 37.500 0.00 0.00 0.00 3.01
108 109 7.457380 AGGGAGAGAAAGAATTGATGGAATA 57.543 36.000 0.00 0.00 0.00 1.75
109 110 8.054931 AGGGAGAGAAAGAATTGATGGAATAT 57.945 34.615 0.00 0.00 0.00 1.28
110 111 9.175577 AGGGAGAGAAAGAATTGATGGAATATA 57.824 33.333 0.00 0.00 0.00 0.86
111 112 9.799106 GGGAGAGAAAGAATTGATGGAATATAA 57.201 33.333 0.00 0.00 0.00 0.98
126 127 9.708222 GATGGAATATAATGATCGTTGTATTGC 57.292 33.333 27.21 27.21 35.55 3.56
128 129 9.283768 TGGAATATAATGATCGTTGTATTGCTT 57.716 29.630 30.43 14.68 35.79 3.91
132 133 4.542662 ATGATCGTTGTATTGCTTGAGC 57.457 40.909 0.00 0.00 42.50 4.26
133 134 2.677836 TGATCGTTGTATTGCTTGAGCC 59.322 45.455 0.00 0.00 41.18 4.70
134 135 2.472695 TCGTTGTATTGCTTGAGCCT 57.527 45.000 0.00 0.00 41.18 4.58
135 136 2.346803 TCGTTGTATTGCTTGAGCCTC 58.653 47.619 0.00 0.00 41.18 4.70
136 137 1.061131 CGTTGTATTGCTTGAGCCTCG 59.939 52.381 0.00 0.00 41.18 4.63
137 138 2.076863 GTTGTATTGCTTGAGCCTCGT 58.923 47.619 0.00 0.00 41.18 4.18
139 140 1.009829 GTATTGCTTGAGCCTCGTGG 58.990 55.000 0.00 0.00 41.18 4.94
140 141 0.107703 TATTGCTTGAGCCTCGTGGG 60.108 55.000 5.54 0.00 41.18 4.61
143 144 1.264749 TGCTTGAGCCTCGTGGGTAT 61.265 55.000 8.42 0.00 45.24 2.73
144 145 0.750850 GCTTGAGCCTCGTGGGTATA 59.249 55.000 8.42 0.00 45.24 1.47
145 146 1.344763 GCTTGAGCCTCGTGGGTATAT 59.655 52.381 8.42 0.00 45.24 0.86
146 147 2.561419 GCTTGAGCCTCGTGGGTATATA 59.439 50.000 8.42 0.00 45.24 0.86
147 148 3.195825 GCTTGAGCCTCGTGGGTATATAT 59.804 47.826 8.42 0.00 45.24 0.86
148 149 4.401519 GCTTGAGCCTCGTGGGTATATATA 59.598 45.833 8.42 0.00 45.24 0.86
149 150 5.069251 GCTTGAGCCTCGTGGGTATATATAT 59.931 44.000 8.42 0.00 45.24 0.86
150 151 6.264744 GCTTGAGCCTCGTGGGTATATATATA 59.735 42.308 8.42 0.00 45.24 0.86
151 152 7.522399 GCTTGAGCCTCGTGGGTATATATATAG 60.522 44.444 8.42 0.00 45.24 1.31
152 153 6.304624 TGAGCCTCGTGGGTATATATATAGG 58.695 44.000 8.42 2.39 45.24 2.57
153 154 6.102174 TGAGCCTCGTGGGTATATATATAGGA 59.898 42.308 8.42 0.00 45.24 2.94
154 155 6.919158 AGCCTCGTGGGTATATATATAGGAA 58.081 40.000 6.40 0.00 43.12 3.36
155 156 7.536625 AGCCTCGTGGGTATATATATAGGAAT 58.463 38.462 6.40 0.00 43.12 3.01
156 157 8.676020 AGCCTCGTGGGTATATATATAGGAATA 58.324 37.037 6.40 0.00 43.12 1.75
158 159 9.803507 CCTCGTGGGTATATATATAGGAATACA 57.196 37.037 2.53 0.00 0.00 2.29
174 175 6.711277 AGGAATACATGTTCTACTTGAAGCA 58.289 36.000 2.30 0.00 35.01 3.91
175 176 6.595716 AGGAATACATGTTCTACTTGAAGCAC 59.404 38.462 2.30 0.00 35.01 4.40
177 178 7.094805 GGAATACATGTTCTACTTGAAGCACAA 60.095 37.037 2.30 0.00 35.01 3.33
186 187 1.761449 TTGAAGCACAAGACAAGCCA 58.239 45.000 0.00 0.00 34.20 4.75
188 189 1.134128 TGAAGCACAAGACAAGCCAGA 60.134 47.619 0.00 0.00 0.00 3.86
189 190 1.949525 GAAGCACAAGACAAGCCAGAA 59.050 47.619 0.00 0.00 0.00 3.02
190 191 2.283145 AGCACAAGACAAGCCAGAAT 57.717 45.000 0.00 0.00 0.00 2.40
191 192 3.423539 AGCACAAGACAAGCCAGAATA 57.576 42.857 0.00 0.00 0.00 1.75
192 193 3.960571 AGCACAAGACAAGCCAGAATAT 58.039 40.909 0.00 0.00 0.00 1.28
197 198 6.094048 GCACAAGACAAGCCAGAATATTTCTA 59.906 38.462 0.00 0.00 38.11 2.10
198 199 7.467623 CACAAGACAAGCCAGAATATTTCTAC 58.532 38.462 0.00 0.00 38.11 2.59
200 201 7.885399 ACAAGACAAGCCAGAATATTTCTACTT 59.115 33.333 0.00 0.00 38.11 2.24
201 202 8.734386 CAAGACAAGCCAGAATATTTCTACTTT 58.266 33.333 0.00 0.00 38.11 2.66
202 203 9.959721 AAGACAAGCCAGAATATTTCTACTTTA 57.040 29.630 0.00 0.00 38.11 1.85
206 207 9.566432 CAAGCCAGAATATTTCTACTTTATCCT 57.434 33.333 0.00 0.00 38.11 3.24
236 237 9.444600 TTTCCTAATACAATCAGGTTACTCAAC 57.555 33.333 0.00 0.00 0.00 3.18
238 239 8.038944 TCCTAATACAATCAGGTTACTCAACAC 58.961 37.037 0.00 0.00 36.29 3.32
240 241 4.431416 ACAATCAGGTTACTCAACACCA 57.569 40.909 0.00 0.00 36.29 4.17
241 242 4.134563 ACAATCAGGTTACTCAACACCAC 58.865 43.478 0.00 0.00 36.29 4.16
242 243 4.141482 ACAATCAGGTTACTCAACACCACT 60.141 41.667 0.00 0.00 36.29 4.00
246 247 3.322254 CAGGTTACTCAACACCACTCTCT 59.678 47.826 0.00 0.00 36.29 3.10
247 248 3.574826 AGGTTACTCAACACCACTCTCTC 59.425 47.826 0.00 0.00 36.29 3.20
248 249 3.574826 GGTTACTCAACACCACTCTCTCT 59.425 47.826 0.00 0.00 36.29 3.10
249 250 4.765856 GGTTACTCAACACCACTCTCTCTA 59.234 45.833 0.00 0.00 36.29 2.43
250 251 5.243283 GGTTACTCAACACCACTCTCTCTAA 59.757 44.000 0.00 0.00 36.29 2.10
252 253 3.257127 ACTCAACACCACTCTCTCTAAGC 59.743 47.826 0.00 0.00 0.00 3.09
253 254 2.563179 TCAACACCACTCTCTCTAAGCC 59.437 50.000 0.00 0.00 0.00 4.35
254 255 2.564947 CAACACCACTCTCTCTAAGCCT 59.435 50.000 0.00 0.00 0.00 4.58
255 256 3.741245 ACACCACTCTCTCTAAGCCTA 57.259 47.619 0.00 0.00 0.00 3.93
256 257 4.048970 ACACCACTCTCTCTAAGCCTAA 57.951 45.455 0.00 0.00 0.00 2.69
257 258 4.417437 ACACCACTCTCTCTAAGCCTAAA 58.583 43.478 0.00 0.00 0.00 1.85
260 261 4.838986 ACCACTCTCTCTAAGCCTAAAACA 59.161 41.667 0.00 0.00 0.00 2.83
261 262 5.172205 CCACTCTCTCTAAGCCTAAAACAC 58.828 45.833 0.00 0.00 0.00 3.32
264 265 5.709164 ACTCTCTCTAAGCCTAAAACACGTA 59.291 40.000 0.00 0.00 0.00 3.57
265 266 5.947443 TCTCTCTAAGCCTAAAACACGTAC 58.053 41.667 0.00 0.00 0.00 3.67
266 267 5.064441 TCTCTAAGCCTAAAACACGTACC 57.936 43.478 0.00 0.00 0.00 3.34
269 270 5.473039 TCTAAGCCTAAAACACGTACCTTC 58.527 41.667 0.00 0.00 0.00 3.46
270 271 3.049708 AGCCTAAAACACGTACCTTCC 57.950 47.619 0.00 0.00 0.00 3.46
289 1182 5.696270 CCTTCCCTGTTTTACTTTGAATTGC 59.304 40.000 0.00 0.00 0.00 3.56
395 1288 3.792047 CGCACTGCACCGTGATGG 61.792 66.667 10.09 0.00 46.41 3.51
484 1377 2.225491 TGGTATTTGAGCTTTCGTGTGC 59.775 45.455 0.00 0.00 0.00 4.57
485 1378 2.414161 GGTATTTGAGCTTTCGTGTGCC 60.414 50.000 0.00 0.00 0.00 5.01
486 1379 0.598065 ATTTGAGCTTTCGTGTGCCC 59.402 50.000 0.00 0.00 0.00 5.36
487 1380 0.465460 TTTGAGCTTTCGTGTGCCCT 60.465 50.000 0.00 0.00 0.00 5.19
492 1385 2.594303 TTTCGTGTGCCCTGCCAG 60.594 61.111 0.00 0.00 0.00 4.85
497 1390 3.225798 TGTGCCCTGCCAGTTTGC 61.226 61.111 0.00 0.00 0.00 3.68
520 1413 5.750067 GCGCATCTTTGTGAATAAATGGATT 59.250 36.000 0.30 0.00 35.26 3.01
522 1415 6.753279 CGCATCTTTGTGAATAAATGGATTGT 59.247 34.615 0.00 0.00 35.26 2.71
523 1416 7.043854 CGCATCTTTGTGAATAAATGGATTGTC 60.044 37.037 0.00 0.00 35.26 3.18
525 1418 6.321717 TCTTTGTGAATAAATGGATTGTCGC 58.678 36.000 0.00 0.00 0.00 5.19
526 1419 5.635417 TTGTGAATAAATGGATTGTCGCA 57.365 34.783 0.00 0.00 0.00 5.10
542 1449 2.033662 GTCGCAGTTCACAACTTCAGAC 60.034 50.000 0.00 0.00 40.46 3.51
557 1464 1.813178 TCAGACTAGTGAACTCCTGCG 59.187 52.381 0.00 0.00 0.00 5.18
595 1504 6.686484 ATCCTACATGCTACATGTGGATTA 57.314 37.500 23.89 13.18 36.99 1.75
606 1515 7.774625 TGCTACATGTGGATTATTGATTGAGAA 59.225 33.333 14.15 0.00 0.00 2.87
607 1516 8.790718 GCTACATGTGGATTATTGATTGAGAAT 58.209 33.333 14.15 0.00 0.00 2.40
719 1640 1.087202 TGCAGTGGACACGTGTGTTC 61.087 55.000 28.82 15.47 45.05 3.18
720 1641 1.087202 GCAGTGGACACGTGTGTTCA 61.087 55.000 28.82 17.93 46.19 3.18
727 1648 2.030457 GGACACGTGTGTTCAGTTCTTG 59.970 50.000 28.82 0.00 45.05 3.02
729 1650 2.415168 ACACGTGTGTTCAGTTCTTGTG 59.585 45.455 22.71 0.00 41.83 3.33
748 1669 7.870826 TCTTGTGGAACTGTATGTAATTTGTG 58.129 34.615 0.00 0.00 38.04 3.33
777 1698 8.292448 TGTATGCTTCTTCTGTTCAGATTTTTC 58.708 33.333 3.28 0.00 0.00 2.29
778 1699 6.949352 TGCTTCTTCTGTTCAGATTTTTCT 57.051 33.333 3.28 0.00 0.00 2.52
789 1714 7.102346 TGTTCAGATTTTTCTCCTTGCAAAAA 58.898 30.769 0.00 0.00 36.25 1.94
791 1716 6.282930 TCAGATTTTTCTCCTTGCAAAAAGG 58.717 36.000 0.00 0.00 35.50 3.11
793 1718 3.836365 TTTTCTCCTTGCAAAAAGGGG 57.164 42.857 0.00 0.00 39.30 4.79
794 1719 2.765689 TTCTCCTTGCAAAAAGGGGA 57.234 45.000 1.03 1.03 44.84 4.81
795 1720 1.995376 TCTCCTTGCAAAAAGGGGAC 58.005 50.000 1.03 0.00 41.81 4.46
796 1721 1.499007 TCTCCTTGCAAAAAGGGGACT 59.501 47.619 1.03 0.00 41.81 3.85
797 1722 1.889170 CTCCTTGCAAAAAGGGGACTC 59.111 52.381 0.00 0.00 40.41 3.36
798 1723 1.216678 TCCTTGCAAAAAGGGGACTCA 59.783 47.619 0.00 0.00 42.68 3.41
799 1724 2.158325 TCCTTGCAAAAAGGGGACTCAT 60.158 45.455 0.00 0.00 42.68 2.90
894 1821 2.193248 GCCGCTAGCCCCATTTCT 59.807 61.111 9.66 0.00 34.35 2.52
903 1830 2.781667 AGCCCCATTTCTCAGAGGTAT 58.218 47.619 0.00 0.00 0.00 2.73
938 1865 3.264193 TCATCAGCTGCTTCCCTTCTTTA 59.736 43.478 9.47 0.00 0.00 1.85
955 1885 8.359642 CCCTTCTTTACTTGTTCATCATCAAAA 58.640 33.333 0.00 0.00 0.00 2.44
959 1889 8.690884 TCTTTACTTGTTCATCATCAAAACCAA 58.309 29.630 0.00 0.00 0.00 3.67
971 1901 3.436243 TCAAAACCAACCAAGTTCAGGT 58.564 40.909 0.00 0.00 42.34 4.00
979 1909 2.690840 ACCAAGTTCAGGTCACTAGGT 58.309 47.619 0.00 0.00 32.90 3.08
980 1910 3.853207 ACCAAGTTCAGGTCACTAGGTA 58.147 45.455 0.00 0.00 32.90 3.08
981 1911 4.228824 ACCAAGTTCAGGTCACTAGGTAA 58.771 43.478 0.00 0.00 32.90 2.85
1093 2028 0.955919 GTCAGGAGCCAACGGGAAAG 60.956 60.000 0.00 0.00 35.59 2.62
1377 2312 1.024046 ATGTATGCGGCGTGCTTTGA 61.024 50.000 9.37 0.00 46.63 2.69
1393 2328 1.489481 TTGACAGATCGAGGAGGCAT 58.511 50.000 0.00 0.00 0.00 4.40
1395 2330 1.137675 TGACAGATCGAGGAGGCATTG 59.862 52.381 0.00 0.00 0.00 2.82
1399 2334 1.202627 AGATCGAGGAGGCATTGCTTC 60.203 52.381 12.03 12.03 33.80 3.86
1455 2390 8.788409 ATTGATACATCGTCGCTATATGTATG 57.212 34.615 17.29 4.04 43.45 2.39
1462 2399 4.393990 TCGTCGCTATATGTATGTAGGTGG 59.606 45.833 0.00 0.00 0.00 4.61
1606 2543 4.142049 TGGTTTGCCTTTCTAACTTTGGTG 60.142 41.667 0.00 0.00 35.27 4.17
1621 2558 2.029844 GGTGCTCACGCTTCTGTCC 61.030 63.158 0.00 0.00 36.97 4.02
1690 2627 8.260818 TGGTTGAATTTGACCAAATCTGTAAAA 58.739 29.630 10.45 0.00 42.68 1.52
1691 2628 8.764287 GGTTGAATTTGACCAAATCTGTAAAAG 58.236 33.333 8.26 0.00 39.88 2.27
1727 2665 6.417635 ACATCTACAACACAAAATTTGCTTCG 59.582 34.615 5.52 0.00 0.00 3.79
1730 2668 7.473366 TCTACAACACAAAATTTGCTTCGTTA 58.527 30.769 5.52 0.00 0.00 3.18
1746 2684 8.050778 TGCTTCGTTAGATTCATAACCATTTT 57.949 30.769 0.00 0.00 32.99 1.82
1757 2695 6.334378 TCATAACCATTTTCCTATCACCCA 57.666 37.500 0.00 0.00 0.00 4.51
1758 2696 6.736581 TCATAACCATTTTCCTATCACCCAA 58.263 36.000 0.00 0.00 0.00 4.12
1788 2727 8.593945 AAGATACTTCATGCCATTTTTCCTAA 57.406 30.769 0.00 0.00 0.00 2.69
1797 2736 6.227298 TGCCATTTTTCCTAAAGTTTGACA 57.773 33.333 0.00 0.00 0.00 3.58
1876 2930 3.503800 AGAAGATTTATTACCCCGGCC 57.496 47.619 0.00 0.00 0.00 6.13
1878 2932 3.072622 AGAAGATTTATTACCCCGGCCTC 59.927 47.826 0.00 0.00 0.00 4.70
2102 3157 6.186957 ACCATTGACCATGCTTGTAATAAGA 58.813 36.000 0.00 0.00 0.00 2.10
2110 3165 9.807649 GACCATGCTTGTAATAAGAATGAAAAT 57.192 29.630 8.80 0.00 35.71 1.82
2169 3224 3.684788 ACAACGATCAAGTAGCAACCATC 59.315 43.478 0.00 0.00 0.00 3.51
2170 3225 3.610040 ACGATCAAGTAGCAACCATCA 57.390 42.857 0.00 0.00 0.00 3.07
2286 3341 2.958204 CTGCACTCACAACGCGCAT 61.958 57.895 5.73 0.00 31.10 4.73
2349 3404 2.236893 GCATGAACAATTGGGGTTCCAT 59.763 45.455 10.83 1.22 43.63 3.41
2377 3432 8.856153 AAAGGAGGCTTGAAAAAGTTTTTAAA 57.144 26.923 13.45 11.55 0.00 1.52
2402 3457 7.129425 AGCCCTTAGGTTAGAGATAGATATGG 58.871 42.308 0.00 0.00 34.57 2.74
2406 3461 9.196139 CCTTAGGTTAGAGATAGATATGGAAGG 57.804 40.741 0.00 0.00 0.00 3.46
2436 3491 4.142687 GGCATGCGTGTTCAAGTATTAACT 60.143 41.667 12.44 0.00 37.65 2.24
2456 3511 6.446781 AACTGATTGCCTTGTAGATCAATG 57.553 37.500 0.00 0.00 35.35 2.82
2504 3559 6.697641 AAACTCAGATGGTTAGGTTCCTTA 57.302 37.500 0.00 0.00 0.00 2.69
2556 3611 1.717032 AGACTTGGCACTAGTGGTCA 58.283 50.000 23.95 9.96 0.00 4.02
2595 3650 3.737172 GGCCTTGCGACAATGCGT 61.737 61.111 0.00 0.00 37.81 5.24
2596 3651 2.395360 GGCCTTGCGACAATGCGTA 61.395 57.895 0.00 0.00 37.81 4.42
2628 3683 1.520564 ATTACGAAGGCGCATGCGA 60.521 52.632 41.98 20.04 44.10 5.10
2636 3691 1.137404 GGCGCATGCGATGACTTTT 59.863 52.632 41.98 0.00 44.10 2.27
2642 3697 3.609373 CGCATGCGATGACTTTTTCAATT 59.391 39.130 35.82 0.00 42.83 2.32
2663 3718 1.069978 TCAAGATGTTGTGCCGACTCA 59.930 47.619 2.11 0.00 34.98 3.41
2685 3740 6.004574 TCAATATCTCGTAGGTGCTCATAGT 58.995 40.000 0.00 0.00 0.00 2.12
2819 3874 1.270907 GAGCCTTTGGTCTCTCTGGA 58.729 55.000 0.00 0.00 36.07 3.86
2830 3885 7.510675 TTGGTCTCTCTGGATTTATTACCTT 57.489 36.000 0.00 0.00 0.00 3.50
2833 3888 7.037586 TGGTCTCTCTGGATTTATTACCTTGTT 60.038 37.037 0.00 0.00 0.00 2.83
2841 3896 9.853177 CTGGATTTATTACCTTGTTTCCTAGAT 57.147 33.333 0.00 0.00 0.00 1.98
2954 4009 4.571369 AGAGTAGAGTGGTAGCACTGTA 57.429 45.455 31.01 26.98 35.23 2.74
2961 4016 2.428890 AGTGGTAGCACTGTATGAGAGC 59.571 50.000 26.01 0.00 38.49 4.09
2963 4018 1.069358 GGTAGCACTGTATGAGAGCCC 59.931 57.143 0.00 0.00 38.97 5.19
2966 4021 1.443407 CACTGTATGAGAGCCCGGG 59.557 63.158 19.09 19.09 0.00 5.73
3003 4058 9.593565 TGATAGACTACTCATATCAACAAGGAT 57.406 33.333 0.00 0.00 33.99 3.24
3038 4094 3.689346 GGAGCTCATTCGCAAAGAAATC 58.311 45.455 17.19 0.00 42.91 2.17
3127 4206 2.071688 AAGTGCGCAGACAAGACTAG 57.928 50.000 12.22 0.00 0.00 2.57
3139 4218 6.127703 GCAGACAAGACTAGTATTGGTCTGTA 60.128 42.308 33.38 0.00 41.28 2.74
3140 4219 7.577046 GCAGACAAGACTAGTATTGGTCTGTAA 60.577 40.741 33.38 0.00 41.28 2.41
3148 4227 8.466617 ACTAGTATTGGTCTGTAAGGATAGTG 57.533 38.462 0.00 0.00 0.00 2.74
3214 5100 5.584649 ACCACGATGTTACAATTGGTATCAG 59.415 40.000 10.83 6.96 35.55 2.90
3217 5103 5.523916 ACGATGTTACAATTGGTATCAGAGC 59.476 40.000 10.83 0.00 35.68 4.09
3291 5507 2.435234 GGCGCGTGTGTCCCATTA 60.435 61.111 8.43 0.00 0.00 1.90
3354 5570 0.759959 TACGTGTGCCAAGAGGGAAA 59.240 50.000 0.00 0.00 36.80 3.13
3363 5579 2.784347 CCAAGAGGGAAAGTTCCTGAC 58.216 52.381 9.88 2.67 46.72 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.389576 GCCGCCGCTTCACACTTG 62.390 66.667 0.00 0.00 0.00 3.16
38 39 0.106149 ATTCTAAACCCTAGCCGCCG 59.894 55.000 0.00 0.00 0.00 6.46
40 41 1.068127 TCGATTCTAAACCCTAGCCGC 59.932 52.381 0.00 0.00 0.00 6.53
41 42 2.361438 AGTCGATTCTAAACCCTAGCCG 59.639 50.000 0.00 0.00 0.00 5.52
43 44 4.567159 CACAAGTCGATTCTAAACCCTAGC 59.433 45.833 0.00 0.00 0.00 3.42
45 46 5.988310 TCACAAGTCGATTCTAAACCCTA 57.012 39.130 0.00 0.00 0.00 3.53
48 49 9.182933 GTATCTATCACAAGTCGATTCTAAACC 57.817 37.037 0.00 0.00 0.00 3.27
50 51 8.909923 TGGTATCTATCACAAGTCGATTCTAAA 58.090 33.333 0.00 0.00 0.00 1.85
51 52 8.459911 TGGTATCTATCACAAGTCGATTCTAA 57.540 34.615 0.00 0.00 0.00 2.10
52 53 8.515414 CATGGTATCTATCACAAGTCGATTCTA 58.485 37.037 0.00 0.00 0.00 2.10
53 54 6.961360 TGGTATCTATCACAAGTCGATTCT 57.039 37.500 0.00 0.00 0.00 2.40
54 55 7.148641 ACATGGTATCTATCACAAGTCGATTC 58.851 38.462 0.00 0.00 0.00 2.52
56 57 6.656632 ACATGGTATCTATCACAAGTCGAT 57.343 37.500 0.00 0.00 0.00 3.59
57 58 6.465439 AACATGGTATCTATCACAAGTCGA 57.535 37.500 0.00 0.00 0.00 4.20
58 59 7.649057 TCTAACATGGTATCTATCACAAGTCG 58.351 38.462 0.00 0.00 0.00 4.18
59 60 9.469807 CTTCTAACATGGTATCTATCACAAGTC 57.530 37.037 0.00 0.00 0.00 3.01
60 61 8.424918 CCTTCTAACATGGTATCTATCACAAGT 58.575 37.037 0.00 0.00 0.00 3.16
61 62 7.875041 CCCTTCTAACATGGTATCTATCACAAG 59.125 40.741 0.00 0.00 0.00 3.16
62 63 7.567250 TCCCTTCTAACATGGTATCTATCACAA 59.433 37.037 0.00 0.00 0.00 3.33
64 65 7.451877 TCTCCCTTCTAACATGGTATCTATCAC 59.548 40.741 0.00 0.00 0.00 3.06
65 66 7.535738 TCTCCCTTCTAACATGGTATCTATCA 58.464 38.462 0.00 0.00 0.00 2.15
67 68 7.770662 TCTCTCCCTTCTAACATGGTATCTAT 58.229 38.462 0.00 0.00 0.00 1.98
68 69 7.162973 TCTCTCCCTTCTAACATGGTATCTA 57.837 40.000 0.00 0.00 0.00 1.98
69 70 6.031964 TCTCTCCCTTCTAACATGGTATCT 57.968 41.667 0.00 0.00 0.00 1.98
70 71 6.732896 TTCTCTCCCTTCTAACATGGTATC 57.267 41.667 0.00 0.00 0.00 2.24
71 72 6.903534 TCTTTCTCTCCCTTCTAACATGGTAT 59.096 38.462 0.00 0.00 0.00 2.73
72 73 6.261435 TCTTTCTCTCCCTTCTAACATGGTA 58.739 40.000 0.00 0.00 0.00 3.25
74 75 5.683876 TCTTTCTCTCCCTTCTAACATGG 57.316 43.478 0.00 0.00 0.00 3.66
75 76 7.826252 TCAATTCTTTCTCTCCCTTCTAACATG 59.174 37.037 0.00 0.00 0.00 3.21
76 77 7.922382 TCAATTCTTTCTCTCCCTTCTAACAT 58.078 34.615 0.00 0.00 0.00 2.71
77 78 7.316393 TCAATTCTTTCTCTCCCTTCTAACA 57.684 36.000 0.00 0.00 0.00 2.41
78 79 7.281999 CCATCAATTCTTTCTCTCCCTTCTAAC 59.718 40.741 0.00 0.00 0.00 2.34
79 80 7.182749 TCCATCAATTCTTTCTCTCCCTTCTAA 59.817 37.037 0.00 0.00 0.00 2.10
80 81 6.673978 TCCATCAATTCTTTCTCTCCCTTCTA 59.326 38.462 0.00 0.00 0.00 2.10
81 82 5.490357 TCCATCAATTCTTTCTCTCCCTTCT 59.510 40.000 0.00 0.00 0.00 2.85
82 83 5.749462 TCCATCAATTCTTTCTCTCCCTTC 58.251 41.667 0.00 0.00 0.00 3.46
83 84 5.786121 TCCATCAATTCTTTCTCTCCCTT 57.214 39.130 0.00 0.00 0.00 3.95
84 85 5.786121 TTCCATCAATTCTTTCTCTCCCT 57.214 39.130 0.00 0.00 0.00 4.20
85 86 9.799106 TTATATTCCATCAATTCTTTCTCTCCC 57.201 33.333 0.00 0.00 0.00 4.30
100 101 9.708222 GCAATACAACGATCATTATATTCCATC 57.292 33.333 0.00 0.00 0.00 3.51
101 102 9.453572 AGCAATACAACGATCATTATATTCCAT 57.546 29.630 0.00 0.00 0.00 3.41
102 103 8.846943 AGCAATACAACGATCATTATATTCCA 57.153 30.769 0.00 0.00 0.00 3.53
107 108 7.095229 GGCTCAAGCAATACAACGATCATTATA 60.095 37.037 4.13 0.00 44.36 0.98
108 109 6.293626 GGCTCAAGCAATACAACGATCATTAT 60.294 38.462 4.13 0.00 44.36 1.28
109 110 5.007626 GGCTCAAGCAATACAACGATCATTA 59.992 40.000 4.13 0.00 44.36 1.90
110 111 4.201950 GGCTCAAGCAATACAACGATCATT 60.202 41.667 4.13 0.00 44.36 2.57
111 112 3.313526 GGCTCAAGCAATACAACGATCAT 59.686 43.478 4.13 0.00 44.36 2.45
112 113 2.677836 GGCTCAAGCAATACAACGATCA 59.322 45.455 4.13 0.00 44.36 2.92
114 115 2.939103 GAGGCTCAAGCAATACAACGAT 59.061 45.455 10.25 0.00 44.36 3.73
115 116 2.346803 GAGGCTCAAGCAATACAACGA 58.653 47.619 10.25 0.00 44.36 3.85
116 117 1.061131 CGAGGCTCAAGCAATACAACG 59.939 52.381 15.95 0.00 44.36 4.10
117 118 2.076863 ACGAGGCTCAAGCAATACAAC 58.923 47.619 15.95 0.00 44.36 3.32
118 119 2.076100 CACGAGGCTCAAGCAATACAA 58.924 47.619 15.95 0.00 44.36 2.41
119 120 1.675714 CCACGAGGCTCAAGCAATACA 60.676 52.381 15.95 0.00 44.36 2.29
120 121 1.009829 CCACGAGGCTCAAGCAATAC 58.990 55.000 15.95 0.00 44.36 1.89
121 122 0.107703 CCCACGAGGCTCAAGCAATA 60.108 55.000 15.95 0.00 44.36 1.90
122 123 1.377725 CCCACGAGGCTCAAGCAAT 60.378 57.895 15.95 0.00 44.36 3.56
123 124 1.476845 TACCCACGAGGCTCAAGCAA 61.477 55.000 15.95 0.00 44.36 3.91
125 126 0.750850 TATACCCACGAGGCTCAAGC 59.249 55.000 15.95 0.00 40.58 4.01
126 127 6.716934 ATATATATACCCACGAGGCTCAAG 57.283 41.667 15.95 5.75 40.58 3.02
128 129 6.102174 TCCTATATATATACCCACGAGGCTCA 59.898 42.308 15.95 0.00 40.58 4.26
130 131 6.526056 TCCTATATATATACCCACGAGGCT 57.474 41.667 0.00 0.00 40.58 4.58
131 132 7.778185 ATTCCTATATATATACCCACGAGGC 57.222 40.000 0.00 0.00 40.58 4.70
132 133 9.803507 TGTATTCCTATATATATACCCACGAGG 57.196 37.037 0.00 0.00 43.78 4.63
147 148 9.982651 GCTTCAAGTAGAACATGTATTCCTATA 57.017 33.333 0.00 0.00 31.61 1.31
148 149 8.486210 TGCTTCAAGTAGAACATGTATTCCTAT 58.514 33.333 0.00 0.00 31.61 2.57
149 150 7.764443 GTGCTTCAAGTAGAACATGTATTCCTA 59.236 37.037 0.00 0.00 31.61 2.94
150 151 6.595716 GTGCTTCAAGTAGAACATGTATTCCT 59.404 38.462 0.00 0.00 31.61 3.36
151 152 6.371548 TGTGCTTCAAGTAGAACATGTATTCC 59.628 38.462 0.00 0.00 28.46 3.01
152 153 7.364522 TGTGCTTCAAGTAGAACATGTATTC 57.635 36.000 0.00 0.00 28.46 1.75
153 154 7.744087 TTGTGCTTCAAGTAGAACATGTATT 57.256 32.000 0.00 0.00 33.71 1.89
154 155 7.369803 CTTGTGCTTCAAGTAGAACATGTAT 57.630 36.000 0.00 0.00 45.89 2.29
155 156 6.785488 CTTGTGCTTCAAGTAGAACATGTA 57.215 37.500 0.00 0.00 45.89 2.29
156 157 5.679734 CTTGTGCTTCAAGTAGAACATGT 57.320 39.130 11.95 0.00 45.89 3.21
167 168 1.677576 CTGGCTTGTCTTGTGCTTCAA 59.322 47.619 0.00 0.00 34.61 2.69
168 169 1.134128 TCTGGCTTGTCTTGTGCTTCA 60.134 47.619 0.00 0.00 0.00 3.02
169 170 1.597742 TCTGGCTTGTCTTGTGCTTC 58.402 50.000 0.00 0.00 0.00 3.86
170 171 2.057137 TTCTGGCTTGTCTTGTGCTT 57.943 45.000 0.00 0.00 0.00 3.91
171 172 2.283145 ATTCTGGCTTGTCTTGTGCT 57.717 45.000 0.00 0.00 0.00 4.40
172 173 4.708726 AATATTCTGGCTTGTCTTGTGC 57.291 40.909 0.00 0.00 0.00 4.57
174 175 7.398024 AGTAGAAATATTCTGGCTTGTCTTGT 58.602 34.615 2.94 0.00 40.94 3.16
175 176 7.856145 AGTAGAAATATTCTGGCTTGTCTTG 57.144 36.000 2.94 0.00 40.94 3.02
180 181 9.566432 AGGATAAAGTAGAAATATTCTGGCTTG 57.434 33.333 2.94 0.00 40.94 4.01
210 211 9.444600 GTTGAGTAACCTGATTGTATTAGGAAA 57.555 33.333 4.68 0.00 38.24 3.13
211 212 8.598916 TGTTGAGTAACCTGATTGTATTAGGAA 58.401 33.333 4.68 0.00 38.24 3.36
213 214 7.280205 GGTGTTGAGTAACCTGATTGTATTAGG 59.720 40.741 0.00 0.00 41.52 2.69
215 216 7.604927 GTGGTGTTGAGTAACCTGATTGTATTA 59.395 37.037 0.00 0.00 37.36 0.98
216 217 6.430000 GTGGTGTTGAGTAACCTGATTGTATT 59.570 38.462 0.00 0.00 37.36 1.89
218 219 5.071250 AGTGGTGTTGAGTAACCTGATTGTA 59.929 40.000 0.00 0.00 37.36 2.41
220 221 4.389374 AGTGGTGTTGAGTAACCTGATTG 58.611 43.478 0.00 0.00 37.36 2.67
221 222 4.348168 AGAGTGGTGTTGAGTAACCTGATT 59.652 41.667 0.00 0.00 37.36 2.57
222 223 3.904339 AGAGTGGTGTTGAGTAACCTGAT 59.096 43.478 0.00 0.00 37.36 2.90
223 224 3.305720 AGAGTGGTGTTGAGTAACCTGA 58.694 45.455 0.00 0.00 37.36 3.86
224 225 3.322254 AGAGAGTGGTGTTGAGTAACCTG 59.678 47.826 0.00 0.00 37.36 4.00
225 226 3.574826 GAGAGAGTGGTGTTGAGTAACCT 59.425 47.826 0.00 0.00 37.36 3.50
227 228 4.857509 AGAGAGAGTGGTGTTGAGTAAC 57.142 45.455 0.00 0.00 37.32 2.50
230 231 3.257127 GCTTAGAGAGAGTGGTGTTGAGT 59.743 47.826 0.00 0.00 0.00 3.41
232 233 2.563179 GGCTTAGAGAGAGTGGTGTTGA 59.437 50.000 0.00 0.00 0.00 3.18
234 235 2.896039 AGGCTTAGAGAGAGTGGTGTT 58.104 47.619 0.00 0.00 0.00 3.32
235 236 2.614134 AGGCTTAGAGAGAGTGGTGT 57.386 50.000 0.00 0.00 0.00 4.16
236 237 5.172205 GTTTTAGGCTTAGAGAGAGTGGTG 58.828 45.833 0.00 0.00 0.00 4.17
238 239 5.172205 GTGTTTTAGGCTTAGAGAGAGTGG 58.828 45.833 0.00 0.00 0.00 4.00
240 241 4.523558 ACGTGTTTTAGGCTTAGAGAGAGT 59.476 41.667 0.00 0.00 0.00 3.24
241 242 5.061920 ACGTGTTTTAGGCTTAGAGAGAG 57.938 43.478 0.00 0.00 0.00 3.20
242 243 5.105997 GGTACGTGTTTTAGGCTTAGAGAGA 60.106 44.000 0.00 0.00 0.00 3.10
246 247 5.473039 GAAGGTACGTGTTTTAGGCTTAGA 58.527 41.667 0.00 0.00 0.00 2.10
247 248 4.628766 GGAAGGTACGTGTTTTAGGCTTAG 59.371 45.833 0.00 0.00 0.00 2.18
248 249 4.563374 GGGAAGGTACGTGTTTTAGGCTTA 60.563 45.833 0.00 0.00 0.00 3.09
249 250 3.405831 GGAAGGTACGTGTTTTAGGCTT 58.594 45.455 0.00 0.00 0.00 4.35
250 251 2.289882 GGGAAGGTACGTGTTTTAGGCT 60.290 50.000 0.00 0.00 0.00 4.58
252 253 3.244318 ACAGGGAAGGTACGTGTTTTAGG 60.244 47.826 0.00 0.00 33.63 2.69
253 254 3.999046 ACAGGGAAGGTACGTGTTTTAG 58.001 45.455 0.00 0.00 33.63 1.85
254 255 4.420522 AACAGGGAAGGTACGTGTTTTA 57.579 40.909 0.00 0.00 42.27 1.52
255 256 3.286329 AACAGGGAAGGTACGTGTTTT 57.714 42.857 0.00 0.00 42.27 2.43
256 257 3.286329 AAACAGGGAAGGTACGTGTTT 57.714 42.857 0.00 9.56 46.10 2.83
257 258 3.286329 AAAACAGGGAAGGTACGTGTT 57.714 42.857 0.00 0.00 45.50 3.32
260 261 4.694760 AAGTAAAACAGGGAAGGTACGT 57.305 40.909 0.00 0.00 0.00 3.57
261 262 5.058490 TCAAAGTAAAACAGGGAAGGTACG 58.942 41.667 0.00 0.00 0.00 3.67
264 265 6.685368 GCAATTCAAAGTAAAACAGGGAAGGT 60.685 38.462 0.00 0.00 0.00 3.50
265 266 5.696270 GCAATTCAAAGTAAAACAGGGAAGG 59.304 40.000 0.00 0.00 0.00 3.46
266 267 5.696270 GGCAATTCAAAGTAAAACAGGGAAG 59.304 40.000 0.00 0.00 0.00 3.46
269 270 4.202305 TGGGCAATTCAAAGTAAAACAGGG 60.202 41.667 0.00 0.00 0.00 4.45
270 271 4.954875 TGGGCAATTCAAAGTAAAACAGG 58.045 39.130 0.00 0.00 0.00 4.00
289 1182 1.100510 CACAGGTGAGCAATGATGGG 58.899 55.000 0.00 0.00 0.00 4.00
388 1281 3.268013 GGTTTCTTCACAACCATCACG 57.732 47.619 0.00 0.00 43.00 4.35
395 1288 3.843999 TGTGCTTTGGTTTCTTCACAAC 58.156 40.909 0.00 0.00 32.35 3.32
484 1377 3.346631 GATGCGCAAACTGGCAGGG 62.347 63.158 17.11 9.03 43.27 4.45
485 1378 1.870055 AAGATGCGCAAACTGGCAGG 61.870 55.000 17.11 1.78 43.27 4.85
486 1379 0.038892 AAAGATGCGCAAACTGGCAG 60.039 50.000 17.11 14.16 43.27 4.85
487 1380 0.318869 CAAAGATGCGCAAACTGGCA 60.319 50.000 17.11 0.00 44.29 4.92
492 1385 5.820926 TTTATTCACAAAGATGCGCAAAC 57.179 34.783 17.11 12.39 0.00 2.93
497 1390 6.753279 ACAATCCATTTATTCACAAAGATGCG 59.247 34.615 0.00 0.00 0.00 4.73
520 1413 1.933181 CTGAAGTTGTGAACTGCGACA 59.067 47.619 0.00 0.00 41.91 4.35
522 1415 2.159099 AGTCTGAAGTTGTGAACTGCGA 60.159 45.455 0.00 0.00 41.91 5.10
523 1416 2.205074 AGTCTGAAGTTGTGAACTGCG 58.795 47.619 0.00 0.00 41.91 5.18
525 1418 5.592054 TCACTAGTCTGAAGTTGTGAACTG 58.408 41.667 0.00 0.00 41.91 3.16
526 1419 5.854010 TCACTAGTCTGAAGTTGTGAACT 57.146 39.130 0.00 0.00 45.46 3.01
557 1464 6.763610 GCATGTAGGATTATTATGGGCTACTC 59.236 42.308 0.00 0.00 0.00 2.59
567 1474 8.201242 TCCACATGTAGCATGTAGGATTATTA 57.799 34.615 19.49 6.48 30.22 0.98
572 1479 5.573380 AATCCACATGTAGCATGTAGGAT 57.427 39.130 24.01 24.01 39.39 3.24
573 1480 6.686484 ATAATCCACATGTAGCATGTAGGA 57.314 37.500 22.63 22.63 35.41 2.94
575 1482 7.967890 TCAATAATCCACATGTAGCATGTAG 57.032 36.000 13.49 7.71 0.00 2.74
606 1515 4.847198 TGAGGCACATCAGTTATTCACAT 58.153 39.130 0.00 0.00 0.00 3.21
607 1516 4.284829 TGAGGCACATCAGTTATTCACA 57.715 40.909 0.00 0.00 0.00 3.58
664 1585 8.854312 CAGTCTTGATTACATATACATACAGCG 58.146 37.037 0.00 0.00 0.00 5.18
727 1648 8.296713 ACATTCACAAATTACATACAGTTCCAC 58.703 33.333 0.00 0.00 0.00 4.02
737 1658 9.793252 GAAGAAGCATACATTCACAAATTACAT 57.207 29.630 0.00 0.00 0.00 2.29
741 1662 7.889469 ACAGAAGAAGCATACATTCACAAATT 58.111 30.769 0.00 0.00 0.00 1.82
748 1669 6.974932 TCTGAACAGAAGAAGCATACATTC 57.025 37.500 1.79 0.00 33.91 2.67
777 1698 1.889170 GAGTCCCCTTTTTGCAAGGAG 59.111 52.381 4.39 4.52 39.81 3.69
778 1699 1.216678 TGAGTCCCCTTTTTGCAAGGA 59.783 47.619 4.39 2.33 39.81 3.36
894 1821 1.406539 GCGGACGGTTTATACCTCTGA 59.593 52.381 11.87 0.00 42.66 3.27
903 1830 2.004583 CTGATGAAGCGGACGGTTTA 57.995 50.000 10.60 7.08 35.84 2.01
938 1865 5.128499 TGGTTGGTTTTGATGATGAACAAGT 59.872 36.000 0.00 0.00 0.00 3.16
955 1885 1.564348 AGTGACCTGAACTTGGTTGGT 59.436 47.619 0.00 0.00 38.03 3.67
959 1889 2.690840 ACCTAGTGACCTGAACTTGGT 58.309 47.619 4.22 4.22 45.22 3.67
971 1901 4.529897 TCGAGCCAGTTATTACCTAGTGA 58.470 43.478 0.00 0.00 0.00 3.41
979 1909 3.101437 TGTTCCCTCGAGCCAGTTATTA 58.899 45.455 6.99 0.00 0.00 0.98
980 1910 1.906574 TGTTCCCTCGAGCCAGTTATT 59.093 47.619 6.99 0.00 0.00 1.40
981 1911 1.568504 TGTTCCCTCGAGCCAGTTAT 58.431 50.000 6.99 0.00 0.00 1.89
1023 1958 3.521796 GCCCTTTCCGCTGCCATC 61.522 66.667 0.00 0.00 0.00 3.51
1035 1970 1.604023 AGTCGACGTCTCTGCCCTT 60.604 57.895 14.70 0.00 0.00 3.95
1074 2009 0.955919 CTTTCCCGTTGGCTCCTGAC 60.956 60.000 0.00 0.00 0.00 3.51
1377 2312 0.179062 GCAATGCCTCCTCGATCTGT 60.179 55.000 0.00 0.00 0.00 3.41
1393 2328 4.154737 GCTATATGGCGATCAATGAAGCAA 59.845 41.667 14.14 5.24 0.00 3.91
1395 2330 3.686241 TGCTATATGGCGATCAATGAAGC 59.314 43.478 6.57 5.67 34.52 3.86
1399 2334 5.745514 GCTTATGCTATATGGCGATCAATG 58.254 41.667 6.57 0.00 36.03 2.82
1425 2360 9.931210 CATATAGCGACGATGTATCAATACTTA 57.069 33.333 0.00 0.00 34.41 2.24
1431 2366 7.758495 ACATACATATAGCGACGATGTATCAA 58.242 34.615 13.87 1.52 42.26 2.57
1437 2372 5.965918 CACCTACATACATATAGCGACGATG 59.034 44.000 0.00 0.00 0.00 3.84
1455 2390 1.521681 GCTGACATCGGCCACCTAC 60.522 63.158 2.24 0.00 42.27 3.18
1621 2558 7.716612 ACCCAGAACTTCAGTTATTTTGAAAG 58.283 34.615 0.00 0.00 38.56 2.62
1690 2627 8.846943 TGTGTTGTAGATGTTGACATATTTCT 57.153 30.769 0.00 0.00 36.57 2.52
1691 2628 9.891828 TTTGTGTTGTAGATGTTGACATATTTC 57.108 29.630 0.00 0.00 36.57 2.17
1697 2634 7.009999 GCAAATTTTGTGTTGTAGATGTTGACA 59.990 33.333 10.65 0.00 0.00 3.58
1698 2635 7.222611 AGCAAATTTTGTGTTGTAGATGTTGAC 59.777 33.333 10.65 0.00 0.00 3.18
1730 2668 7.725844 GGGTGATAGGAAAATGGTTATGAATCT 59.274 37.037 0.00 0.00 0.00 2.40
1765 2704 8.470002 ACTTTAGGAAAAATGGCATGAAGTATC 58.530 33.333 0.00 0.00 0.00 2.24
1766 2705 8.366359 ACTTTAGGAAAAATGGCATGAAGTAT 57.634 30.769 0.00 0.00 0.00 2.12
1767 2706 7.775053 ACTTTAGGAAAAATGGCATGAAGTA 57.225 32.000 0.00 0.00 0.00 2.24
1769 2708 7.656948 TCAAACTTTAGGAAAAATGGCATGAAG 59.343 33.333 0.00 0.00 0.00 3.02
1770 2709 7.440856 GTCAAACTTTAGGAAAAATGGCATGAA 59.559 33.333 0.00 0.00 0.00 2.57
1771 2710 6.928492 GTCAAACTTTAGGAAAAATGGCATGA 59.072 34.615 0.00 0.00 0.00 3.07
1861 2915 1.202891 GCAGAGGCCGGGGTAATAAAT 60.203 52.381 2.18 0.00 0.00 1.40
1876 2930 7.741027 AGGTATATGAATTGTTGATGCAGAG 57.259 36.000 0.00 0.00 0.00 3.35
1878 2932 9.060347 AGTTAGGTATATGAATTGTTGATGCAG 57.940 33.333 0.00 0.00 0.00 4.41
1908 2962 3.543494 GCACGTTGACATATTGCATTGTC 59.457 43.478 14.66 14.66 42.05 3.18
1954 3009 6.483307 GCTGGTCATGCACAGTTATTAGATTA 59.517 38.462 15.04 0.00 37.07 1.75
1965 3020 3.129502 CCCGCTGGTCATGCACAG 61.130 66.667 10.91 10.91 37.76 3.66
2030 3085 2.711009 ACCAAACTCTCCATGTCTCCAA 59.289 45.455 0.00 0.00 0.00 3.53
2131 3186 2.159626 CGTTGTTTCGGTTAATCGCCAT 60.160 45.455 2.43 0.00 0.00 4.40
2214 3269 9.994432 CTGCAAGAAATCAGTTTAATTAGGTAG 57.006 33.333 0.00 0.00 34.07 3.18
2286 3341 3.056179 TCTTCACTATCATCACGGTGCAA 60.056 43.478 2.51 0.00 0.00 4.08
2349 3404 7.418337 AAAACTTTTTCAAGCCTCCTTTCTA 57.582 32.000 0.00 0.00 32.57 2.10
2377 3432 7.035764 TCCATATCTATCTCTAACCTAAGGGCT 60.036 40.741 0.00 0.00 35.63 5.19
2402 3457 0.679960 ACGCATGCCTAAACCCCTTC 60.680 55.000 13.15 0.00 0.00 3.46
2406 3461 0.170339 GAACACGCATGCCTAAACCC 59.830 55.000 13.15 0.00 0.00 4.11
2436 3491 5.124297 CACACATTGATCTACAAGGCAATCA 59.876 40.000 0.00 0.00 42.97 2.57
2456 3511 0.388649 AGTTCGCGATGAGACCACAC 60.389 55.000 10.88 0.80 0.00 3.82
2504 3559 3.440127 CCTATTGGGTTGGTTCCAACAT 58.560 45.455 28.31 18.73 45.74 2.71
2556 3611 7.038088 AGGCCTGAAATAAATCCAGAAAAATGT 60.038 33.333 3.11 0.00 0.00 2.71
2595 3650 6.680625 GCCTTCGTAATGACTCTCACTGAATA 60.681 42.308 0.00 0.00 0.00 1.75
2596 3651 5.655488 CCTTCGTAATGACTCTCACTGAAT 58.345 41.667 0.00 0.00 0.00 2.57
2628 3683 9.603921 ACAACATCTTGAAATTGAAAAAGTCAT 57.396 25.926 0.00 0.00 35.70 3.06
2636 3691 4.037327 TCGGCACAACATCTTGAAATTGAA 59.963 37.500 0.00 0.00 0.00 2.69
2642 3697 2.143122 GAGTCGGCACAACATCTTGAA 58.857 47.619 0.00 0.00 0.00 2.69
2663 3718 6.004574 TCACTATGAGCACCTACGAGATATT 58.995 40.000 0.00 0.00 0.00 1.28
2685 3740 3.118775 GCACACCCACATACACTCTATCA 60.119 47.826 0.00 0.00 0.00 2.15
2830 3885 8.335532 ACGATGAAAAATGAATCTAGGAAACA 57.664 30.769 0.00 0.00 0.00 2.83
2833 3888 8.792633 ACAAACGATGAAAAATGAATCTAGGAA 58.207 29.630 0.00 0.00 0.00 3.36
2862 3917 3.620488 TGTTTAGAAGGACATCCATGCC 58.380 45.455 0.00 0.00 38.89 4.40
2954 4009 1.978580 CCTATTAACCCGGGCTCTCAT 59.021 52.381 24.08 8.49 0.00 2.90
2961 4016 5.484290 AGTCTATCATTCCTATTAACCCGGG 59.516 44.000 22.25 22.25 0.00 5.73
2963 4018 8.350852 AGTAGTCTATCATTCCTATTAACCCG 57.649 38.462 0.00 0.00 0.00 5.28
3003 4058 4.819105 TGAGCTCCGAAAAAGAAGGATA 57.181 40.909 12.15 0.00 33.04 2.59
3004 4059 3.703001 TGAGCTCCGAAAAAGAAGGAT 57.297 42.857 12.15 0.00 33.04 3.24
3015 4070 0.246360 TCTTTGCGAATGAGCTCCGA 59.754 50.000 12.15 0.00 38.13 4.55
3038 4094 6.705381 TCCAAATCAAACATGCTTAACTTTGG 59.295 34.615 15.85 15.85 40.76 3.28
3089 4168 0.942410 TTGTCCTTACTCGTGCGCAC 60.942 55.000 30.42 30.42 0.00 5.34
3101 4180 0.463654 TGTCTGCGCACTTTGTCCTT 60.464 50.000 5.66 0.00 0.00 3.36
3127 4206 8.461249 TCTACACTATCCTTACAGACCAATAC 57.539 38.462 0.00 0.00 0.00 1.89
3139 4218 2.249139 GGCGGGATCTACACTATCCTT 58.751 52.381 0.00 0.00 42.27 3.36
3140 4219 1.147191 TGGCGGGATCTACACTATCCT 59.853 52.381 0.00 0.00 42.27 3.24
3196 5082 4.816385 CGGCTCTGATACCAATTGTAACAT 59.184 41.667 4.43 0.00 32.51 2.71
3197 5083 4.081365 TCGGCTCTGATACCAATTGTAACA 60.081 41.667 4.43 2.06 31.94 2.41
3214 5100 1.547372 TGTAACTACAAGGGTCGGCTC 59.453 52.381 0.00 0.00 32.40 4.70
3217 5103 2.498481 TCCATGTAACTACAAGGGTCGG 59.502 50.000 10.42 0.00 43.32 4.79
3288 5504 2.363038 GTGACATGCCATGTGCCATAAT 59.637 45.455 16.43 0.00 45.03 1.28
3291 5507 0.612453 TGTGACATGCCATGTGCCAT 60.612 50.000 16.43 0.00 45.03 4.40
3306 5522 3.307108 TCCGACCGGCACATGTGA 61.307 61.111 29.80 2.48 34.68 3.58


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

AutoCloner maintained by Alex Coulton.