Multiple sequence alignment - TraesCS3D01G447500

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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 TraesCS3D01G447500 chr3D 100.000 2418 0 0 1 2418 555913504 555911087 0.000000e+00 4466.0
1 TraesCS3D01G447500 chr3D 91.981 424 19 3 2008 2418 555904174 555903753 4.480000e-162 580.0
2 TraesCS3D01G447500 chr3D 81.506 757 73 37 950 1672 555801419 555800696 5.840000e-156 560.0
3 TraesCS3D01G447500 chr3D 87.602 492 47 9 2 480 555799319 555798829 2.100000e-155 558.0
4 TraesCS3D01G447500 chr3D 92.105 342 26 1 1711 2052 382115231 382114891 4.680000e-132 481.0
5 TraesCS3D01G447500 chr3A 95.728 1615 57 6 1 1604 692946232 692944619 0.000000e+00 2590.0
6 TraesCS3D01G447500 chr3A 80.000 1215 128 67 517 1672 692724325 692723167 0.000000e+00 791.0
7 TraesCS3D01G447500 chr3A 84.211 456 49 11 46 480 692721489 692721036 2.870000e-114 422.0
8 TraesCS3D01G447500 chr3A 85.979 378 48 3 2042 2418 65825017 65824644 1.350000e-107 399.0
9 TraesCS3D01G447500 chr3A 94.488 127 6 1 1643 1768 692944195 692944069 6.820000e-46 195.0
10 TraesCS3D01G447500 chr3A 98.630 73 1 0 1577 1649 692944425 692944353 1.950000e-26 130.0
11 TraesCS3D01G447500 chr3A 79.861 144 12 6 512 639 692954562 692954420 3.310000e-14 89.8
12 TraesCS3D01G447500 chr3B 91.800 1122 61 14 324 1433 738911382 738910280 0.000000e+00 1533.0
13 TraesCS3D01G447500 chr3B 89.309 1057 77 14 512 1548 738993297 738992257 0.000000e+00 1293.0
14 TraesCS3D01G447500 chr3B 89.637 965 64 7 1476 2418 738910119 738909169 0.000000e+00 1195.0
15 TraesCS3D01G447500 chr3B 81.267 726 71 31 977 1672 738757576 738756886 5.920000e-146 527.0
16 TraesCS3D01G447500 chr3B 86.611 478 49 6 6 468 738755635 738755158 4.610000e-142 514.0
17 TraesCS3D01G447500 chr3B 87.003 377 41 6 2042 2416 670153151 670153521 3.720000e-113 418.0
18 TraesCS3D01G447500 chr3B 91.304 276 18 5 650 923 738758702 738758431 2.940000e-99 372.0
19 TraesCS3D01G447500 chr3B 85.591 347 39 4 1 336 738912610 738912264 1.060000e-93 353.0
20 TraesCS3D01G447500 chr3B 89.313 131 9 2 1546 1673 738918309 738918181 2.490000e-35 159.0
21 TraesCS3D01G447500 chr1A 93.343 661 32 5 747 1405 510456968 510457618 0.000000e+00 966.0
22 TraesCS3D01G447500 chr2D 92.283 311 24 0 1742 2052 70945658 70945968 2.210000e-120 442.0
23 TraesCS3D01G447500 chr2D 84.615 455 50 6 1724 2158 535583815 535583361 3.690000e-118 435.0
24 TraesCS3D01G447500 chr2D 84.901 404 43 12 537 938 378165739 378166126 2.250000e-105 392.0
25 TraesCS3D01G447500 chr2D 80.567 494 86 7 940 1429 378166220 378166707 2.940000e-99 372.0
26 TraesCS3D01G447500 chr7D 89.504 343 33 2 1717 2056 209788425 209788083 4.780000e-117 431.0
27 TraesCS3D01G447500 chr7D 78.541 699 117 21 940 1635 175443544 175444212 1.720000e-116 429.0
28 TraesCS3D01G447500 chr7D 84.211 380 54 6 2043 2418 603661702 603662079 4.910000e-97 364.0
29 TraesCS3D01G447500 chr1D 90.149 335 27 5 1720 2052 387054679 387055009 4.780000e-117 431.0
30 TraesCS3D01G447500 chr7B 88.427 337 39 0 1716 2052 719054093 719053757 8.050000e-110 407.0
31 TraesCS3D01G447500 chr6D 88.270 341 39 1 1713 2052 56836231 56836571 8.050000e-110 407.0
32 TraesCS3D01G447500 chr6D 83.594 384 46 10 2043 2418 44286952 44287326 6.400000e-91 344.0
33 TraesCS3D01G447500 chr7A 86.162 383 40 9 2047 2418 173430950 173430570 3.740000e-108 401.0
34 TraesCS3D01G447500 chr7A 88.166 338 39 1 1715 2052 612587163 612587499 3.740000e-108 401.0
35 TraesCS3D01G447500 chr7A 84.697 379 51 5 2042 2418 129083118 129082745 2.940000e-99 372.0
36 TraesCS3D01G447500 chr5D 85.602 382 47 5 2044 2418 538019751 538019371 6.270000e-106 394.0
37 TraesCS3D01G447500 chr2A 77.483 715 124 23 940 1648 512442286 512442969 6.270000e-106 394.0
38 TraesCS3D01G447500 chr2B 84.514 381 54 4 2042 2418 713787716 713788095 2.940000e-99 372.0
39 TraesCS3D01G447500 chr6A 80.241 415 62 13 1173 1584 14098682 14099079 6.540000e-76 294.0


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 TraesCS3D01G447500 chr3D 555911087 555913504 2417 True 4466.000000 4466 100.000000 1 2418 1 chr3D.!!$R3 2417
1 TraesCS3D01G447500 chr3D 555798829 555801419 2590 True 559.000000 560 84.554000 2 1672 2 chr3D.!!$R4 1670
2 TraesCS3D01G447500 chr3A 692944069 692946232 2163 True 971.666667 2590 96.282000 1 1768 3 chr3A.!!$R4 1767
3 TraesCS3D01G447500 chr3A 692721036 692724325 3289 True 606.500000 791 82.105500 46 1672 2 chr3A.!!$R3 1626
4 TraesCS3D01G447500 chr3B 738992257 738993297 1040 True 1293.000000 1293 89.309000 512 1548 1 chr3B.!!$R2 1036
5 TraesCS3D01G447500 chr3B 738909169 738912610 3441 True 1027.000000 1533 89.009333 1 2418 3 chr3B.!!$R4 2417
6 TraesCS3D01G447500 chr3B 738755158 738758702 3544 True 471.000000 527 86.394000 6 1672 3 chr3B.!!$R3 1666
7 TraesCS3D01G447500 chr1A 510456968 510457618 650 False 966.000000 966 93.343000 747 1405 1 chr1A.!!$F1 658
8 TraesCS3D01G447500 chr2D 378165739 378166707 968 False 382.000000 392 82.734000 537 1429 2 chr2D.!!$F2 892
9 TraesCS3D01G447500 chr7D 175443544 175444212 668 False 429.000000 429 78.541000 940 1635 1 chr7D.!!$F1 695
10 TraesCS3D01G447500 chr2A 512442286 512442969 683 False 394.000000 394 77.483000 940 1648 1 chr2A.!!$F1 708

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
465 466 0.108329 AAGACAGGTCGCCCAATACG 60.108 55.0 0.0 0.0 34.09 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 5056 0.31716 AGTCATTCAGCGACACCGAA 59.683 50.0 0.0 0.0 38.22 4.3 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
79 80 7.287950 TCAGAAATGTTAGAATTTGACGTTCG 58.712 34.615 0.00 0.00 29.89 3.95
81 82 5.607119 AATGTTAGAATTTGACGTTCGCT 57.393 34.783 0.00 0.00 0.00 4.93
82 83 4.383774 TGTTAGAATTTGACGTTCGCTG 57.616 40.909 0.00 0.00 0.00 5.18
83 84 3.185594 TGTTAGAATTTGACGTTCGCTGG 59.814 43.478 0.00 0.00 0.00 4.85
84 85 1.878953 AGAATTTGACGTTCGCTGGT 58.121 45.000 0.00 0.00 0.00 4.00
85 86 2.218603 AGAATTTGACGTTCGCTGGTT 58.781 42.857 0.00 0.00 0.00 3.67
86 87 3.395639 AGAATTTGACGTTCGCTGGTTA 58.604 40.909 0.00 0.00 0.00 2.85
87 88 3.810941 AGAATTTGACGTTCGCTGGTTAA 59.189 39.130 0.00 0.00 0.00 2.01
88 89 3.806316 ATTTGACGTTCGCTGGTTAAG 57.194 42.857 0.00 0.00 0.00 1.85
100 101 3.872511 CTGGTTAAGCATGGCAAATCA 57.127 42.857 7.98 0.00 0.00 2.57
101 102 4.191033 CTGGTTAAGCATGGCAAATCAA 57.809 40.909 7.98 0.00 0.00 2.57
103 104 5.163281 TGGTTAAGCATGGCAAATCAAAT 57.837 34.783 2.54 0.00 0.00 2.32
104 105 4.936411 TGGTTAAGCATGGCAAATCAAATG 59.064 37.500 2.54 0.00 0.00 2.32
106 107 5.412286 GGTTAAGCATGGCAAATCAAATGTT 59.588 36.000 0.00 0.00 0.00 2.71
108 109 7.118971 GGTTAAGCATGGCAAATCAAATGTTTA 59.881 33.333 0.00 0.00 0.00 2.01
112 113 8.373048 AGCATGGCAAATCAAATGTTTATATG 57.627 30.769 0.00 0.00 0.00 1.78
113 114 7.442969 AGCATGGCAAATCAAATGTTTATATGG 59.557 33.333 0.00 0.00 0.00 2.74
114 115 7.577979 CATGGCAAATCAAATGTTTATATGGC 58.422 34.615 0.00 0.00 0.00 4.40
115 116 6.647229 TGGCAAATCAAATGTTTATATGGCA 58.353 32.000 0.00 0.00 38.30 4.92
117 118 6.292274 GGCAAATCAAATGTTTATATGGCACG 60.292 38.462 0.00 0.00 0.00 5.34
118 119 6.292274 GCAAATCAAATGTTTATATGGCACGG 60.292 38.462 0.00 0.00 0.00 4.94
119 120 4.300189 TCAAATGTTTATATGGCACGGC 57.700 40.909 0.00 0.00 0.00 5.68
121 122 4.158579 TCAAATGTTTATATGGCACGGCAA 59.841 37.500 0.00 0.00 0.00 4.52
123 124 4.935352 ATGTTTATATGGCACGGCAAAT 57.065 36.364 0.00 0.00 0.00 2.32
124 125 4.300189 TGTTTATATGGCACGGCAAATC 57.700 40.909 0.00 0.00 0.00 2.17
125 126 3.067461 TGTTTATATGGCACGGCAAATCC 59.933 43.478 0.00 0.00 0.00 3.01
126 127 2.949177 TATATGGCACGGCAAATCCT 57.051 45.000 0.00 0.00 0.00 3.24
127 128 1.321474 ATATGGCACGGCAAATCCTG 58.679 50.000 0.00 0.00 0.00 3.86
128 129 0.751277 TATGGCACGGCAAATCCTGG 60.751 55.000 0.00 0.00 0.00 4.45
129 130 2.676471 GGCACGGCAAATCCTGGT 60.676 61.111 0.00 0.00 0.00 4.00
130 131 1.377987 GGCACGGCAAATCCTGGTA 60.378 57.895 0.00 0.00 0.00 3.25
131 132 0.963355 GGCACGGCAAATCCTGGTAA 60.963 55.000 0.00 0.00 0.00 2.85
133 134 1.135402 GCACGGCAAATCCTGGTAAAG 60.135 52.381 0.00 0.00 0.00 1.85
136 137 1.401905 CGGCAAATCCTGGTAAAGAGC 59.598 52.381 0.00 0.00 0.00 4.09
137 138 2.728007 GGCAAATCCTGGTAAAGAGCT 58.272 47.619 0.00 0.00 0.00 4.09
138 139 2.424956 GGCAAATCCTGGTAAAGAGCTG 59.575 50.000 0.00 0.00 0.00 4.24
139 140 2.424956 GCAAATCCTGGTAAAGAGCTGG 59.575 50.000 0.00 0.00 42.05 4.85
143 144 2.551270 TCCTGGTAAAGAGCTGGACAT 58.449 47.619 0.00 0.00 43.80 3.06
144 145 2.237143 TCCTGGTAAAGAGCTGGACATG 59.763 50.000 0.00 0.00 43.80 3.21
145 146 2.237143 CCTGGTAAAGAGCTGGACATGA 59.763 50.000 0.00 0.00 43.03 3.07
146 147 3.307691 CCTGGTAAAGAGCTGGACATGAA 60.308 47.826 0.00 0.00 43.03 2.57
147 148 3.937706 CTGGTAAAGAGCTGGACATGAAG 59.062 47.826 0.00 0.00 0.00 3.02
148 149 3.274288 GGTAAAGAGCTGGACATGAAGG 58.726 50.000 0.00 0.00 0.00 3.46
150 151 4.384647 GGTAAAGAGCTGGACATGAAGGAT 60.385 45.833 0.00 0.00 0.00 3.24
151 152 3.557228 AAGAGCTGGACATGAAGGATC 57.443 47.619 0.00 0.00 0.00 3.36
153 154 3.921104 AGAGCTGGACATGAAGGATCTA 58.079 45.455 0.00 0.00 0.00 1.98
155 156 2.703007 AGCTGGACATGAAGGATCTACC 59.297 50.000 0.00 0.00 39.35 3.18
156 157 2.435805 GCTGGACATGAAGGATCTACCA 59.564 50.000 0.00 0.00 42.04 3.25
157 158 3.072184 GCTGGACATGAAGGATCTACCAT 59.928 47.826 0.00 0.00 42.04 3.55
158 159 4.445448 GCTGGACATGAAGGATCTACCATT 60.445 45.833 0.00 0.00 42.04 3.16
160 161 6.688922 GCTGGACATGAAGGATCTACCATTTA 60.689 42.308 0.00 0.00 42.04 1.40
161 162 7.206789 TGGACATGAAGGATCTACCATTTAA 57.793 36.000 0.00 0.00 42.04 1.52
163 164 8.112822 TGGACATGAAGGATCTACCATTTAAAA 58.887 33.333 0.00 0.00 42.04 1.52
165 166 8.525290 ACATGAAGGATCTACCATTTAAAAGG 57.475 34.615 7.92 7.92 42.04 3.11
166 167 8.336235 ACATGAAGGATCTACCATTTAAAAGGA 58.664 33.333 16.12 0.00 42.04 3.36
167 168 9.189156 CATGAAGGATCTACCATTTAAAAGGAA 57.811 33.333 16.12 2.07 42.04 3.36
168 169 9.768215 ATGAAGGATCTACCATTTAAAAGGAAA 57.232 29.630 16.12 3.28 42.04 3.13
169 170 9.768215 TGAAGGATCTACCATTTAAAAGGAAAT 57.232 29.630 16.12 6.17 42.04 2.17
188 189 8.985315 AGGAAATTGATATCTTCATGCTAACA 57.015 30.769 3.98 0.00 33.34 2.41
189 190 9.584008 AGGAAATTGATATCTTCATGCTAACAT 57.416 29.630 3.98 0.00 36.79 2.71
202 203 9.531942 CTTCATGCTAACATAATTTGCCATAAA 57.468 29.630 0.00 0.00 33.67 1.40
203 204 9.881649 TTCATGCTAACATAATTTGCCATAAAA 57.118 25.926 0.00 0.00 33.67 1.52
212 213 9.474920 ACATAATTTGCCATAAAATATGTTCGG 57.525 29.630 7.08 0.00 29.42 4.30
213 214 9.474920 CATAATTTGCCATAAAATATGTTCGGT 57.525 29.630 0.00 0.00 0.00 4.69
215 216 8.785329 AATTTGCCATAAAATATGTTCGGTTT 57.215 26.923 0.00 0.00 0.00 3.27
216 217 7.588143 TTTGCCATAAAATATGTTCGGTTTG 57.412 32.000 0.00 0.00 0.00 2.93
217 218 5.105752 TGCCATAAAATATGTTCGGTTTGC 58.894 37.500 0.00 0.00 0.00 3.68
235 236 7.786305 GGTTTGCCGTACTTAAAAATCTAAC 57.214 36.000 0.00 0.00 0.00 2.34
236 237 6.520790 GGTTTGCCGTACTTAAAAATCTAACG 59.479 38.462 0.00 0.00 0.00 3.18
237 238 6.783892 TTGCCGTACTTAAAAATCTAACGT 57.216 33.333 0.00 0.00 0.00 3.99
238 239 6.783892 TGCCGTACTTAAAAATCTAACGTT 57.216 33.333 5.88 5.88 0.00 3.99
239 240 6.820459 TGCCGTACTTAAAAATCTAACGTTC 58.180 36.000 2.82 0.00 0.00 3.95
240 241 5.948085 GCCGTACTTAAAAATCTAACGTTCG 59.052 40.000 2.82 0.00 0.00 3.95
244 245 5.923665 ACTTAAAAATCTAACGTTCGCTGG 58.076 37.500 2.82 0.00 0.00 4.85
245 246 5.467735 ACTTAAAAATCTAACGTTCGCTGGT 59.532 36.000 2.82 0.00 0.00 4.00
246 247 4.823790 AAAAATCTAACGTTCGCTGGTT 57.176 36.364 2.82 0.00 0.00 3.67
247 248 5.927954 AAAAATCTAACGTTCGCTGGTTA 57.072 34.783 2.82 0.00 0.00 2.85
250 251 3.853831 TCTAACGTTCGCTGGTTATCA 57.146 42.857 2.82 0.00 0.00 2.15
251 252 4.177165 TCTAACGTTCGCTGGTTATCAA 57.823 40.909 2.82 0.00 0.00 2.57
253 254 5.172934 TCTAACGTTCGCTGGTTATCAAAT 58.827 37.500 2.82 0.00 0.00 2.32
254 255 6.331845 TCTAACGTTCGCTGGTTATCAAATA 58.668 36.000 2.82 0.00 0.00 1.40
256 257 5.652744 ACGTTCGCTGGTTATCAAATATC 57.347 39.130 0.00 0.00 0.00 1.63
257 258 4.510340 ACGTTCGCTGGTTATCAAATATCC 59.490 41.667 0.00 0.00 0.00 2.59
259 260 5.236478 CGTTCGCTGGTTATCAAATATCCTT 59.764 40.000 0.00 0.00 0.00 3.36
260 261 6.238374 CGTTCGCTGGTTATCAAATATCCTTT 60.238 38.462 0.00 0.00 0.00 3.11
261 262 7.480810 GTTCGCTGGTTATCAAATATCCTTTT 58.519 34.615 0.00 0.00 0.00 2.27
262 263 7.639113 TCGCTGGTTATCAAATATCCTTTTT 57.361 32.000 0.00 0.00 0.00 1.94
263 264 7.703328 TCGCTGGTTATCAAATATCCTTTTTC 58.297 34.615 0.00 0.00 0.00 2.29
280 281 8.361169 TCCTTTTTCTATTCCTATGTTTTGGG 57.639 34.615 0.00 0.00 0.00 4.12
281 282 8.174085 TCCTTTTTCTATTCCTATGTTTTGGGA 58.826 33.333 0.00 0.00 0.00 4.37
287 288 8.220755 TCTATTCCTATGTTTTGGGAATTTCG 57.779 34.615 10.97 2.85 44.49 3.46
288 289 8.050325 TCTATTCCTATGTTTTGGGAATTTCGA 58.950 33.333 10.97 4.70 44.49 3.71
290 291 6.902771 TCCTATGTTTTGGGAATTTCGAAA 57.097 33.333 13.91 13.91 0.00 3.46
291 292 7.475137 TCCTATGTTTTGGGAATTTCGAAAT 57.525 32.000 17.60 17.60 0.00 2.17
294 295 9.646427 CCTATGTTTTGGGAATTTCGAAATAAA 57.354 29.630 22.99 16.17 0.00 1.40
297 298 8.718102 TGTTTTGGGAATTTCGAAATAAAACA 57.282 26.923 33.16 33.16 38.94 2.83
298 299 8.604890 TGTTTTGGGAATTTCGAAATAAAACAC 58.395 29.630 33.16 23.19 37.74 3.32
301 302 7.701809 TGGGAATTTCGAAATAAAACACAAC 57.298 32.000 22.99 7.54 0.00 3.32
302 303 7.265673 TGGGAATTTCGAAATAAAACACAACA 58.734 30.769 22.99 9.67 0.00 3.33
303 304 7.436673 TGGGAATTTCGAAATAAAACACAACAG 59.563 33.333 22.99 0.00 0.00 3.16
304 305 7.436970 GGGAATTTCGAAATAAAACACAACAGT 59.563 33.333 22.99 3.31 0.00 3.55
305 306 8.476925 GGAATTTCGAAATAAAACACAACAGTC 58.523 33.333 22.99 11.77 0.00 3.51
307 308 8.918961 ATTTCGAAATAAAACACAACAGTCAA 57.081 26.923 21.55 0.00 0.00 3.18
309 310 8.744008 TTCGAAATAAAACACAACAGTCAAAA 57.256 26.923 0.00 0.00 0.00 2.44
315 316 9.736023 AATAAAACACAACAGTCAAAAGATCTC 57.264 29.630 0.00 0.00 0.00 2.75
316 317 7.396540 AAAACACAACAGTCAAAAGATCTCT 57.603 32.000 0.00 0.00 0.00 3.10
320 321 7.920738 ACACAACAGTCAAAAGATCTCTAAAC 58.079 34.615 0.00 0.00 0.00 2.01
322 323 6.761714 ACAACAGTCAAAAGATCTCTAAACGT 59.238 34.615 0.00 0.00 0.00 3.99
323 324 7.042658 ACAACAGTCAAAAGATCTCTAAACGTC 60.043 37.037 0.00 0.00 0.00 4.34
324 325 6.513180 ACAGTCAAAAGATCTCTAAACGTCA 58.487 36.000 0.00 0.00 0.00 4.35
325 326 6.984474 ACAGTCAAAAGATCTCTAAACGTCAA 59.016 34.615 0.00 0.00 0.00 3.18
327 328 6.146347 AGTCAAAAGATCTCTAAACGTCAAGC 59.854 38.462 0.00 0.00 0.00 4.01
329 330 6.650807 TCAAAAGATCTCTAAACGTCAAGCAT 59.349 34.615 0.00 0.00 0.00 3.79
330 331 6.654793 AAAGATCTCTAAACGTCAAGCATC 57.345 37.500 0.00 0.00 0.00 3.91
331 332 5.590530 AGATCTCTAAACGTCAAGCATCT 57.409 39.130 0.00 0.00 0.00 2.90
332 333 6.701145 AGATCTCTAAACGTCAAGCATCTA 57.299 37.500 0.00 0.00 0.00 1.98
333 334 7.101652 AGATCTCTAAACGTCAAGCATCTAA 57.898 36.000 0.00 0.00 0.00 2.10
334 335 7.721402 AGATCTCTAAACGTCAAGCATCTAAT 58.279 34.615 0.00 0.00 0.00 1.73
335 336 8.200792 AGATCTCTAAACGTCAAGCATCTAATT 58.799 33.333 0.00 0.00 0.00 1.40
336 337 7.525688 TCTCTAAACGTCAAGCATCTAATTG 57.474 36.000 0.00 0.00 0.00 2.32
337 338 7.320399 TCTCTAAACGTCAAGCATCTAATTGA 58.680 34.615 0.00 0.00 33.16 2.57
338 339 7.981789 TCTCTAAACGTCAAGCATCTAATTGAT 59.018 33.333 0.00 0.00 37.72 2.57
339 340 8.492673 TCTAAACGTCAAGCATCTAATTGATT 57.507 30.769 0.00 0.00 37.72 2.57
340 341 8.390354 TCTAAACGTCAAGCATCTAATTGATTG 58.610 33.333 0.00 0.00 42.78 2.67
341 342 6.741992 AACGTCAAGCATCTAATTGATTGA 57.258 33.333 1.37 1.37 46.47 2.57
346 347 6.951643 TCAAGCATCTAATTGATTGACGATG 58.048 36.000 1.37 0.00 44.52 3.84
347 348 6.512253 TCAAGCATCTAATTGATTGACGATGC 60.512 38.462 18.90 18.90 44.52 3.91
348 349 4.146719 GCATCTAATTGATTGACGATGCG 58.853 43.478 15.16 0.00 42.60 4.73
349 350 4.084380 GCATCTAATTGATTGACGATGCGA 60.084 41.667 15.16 0.00 42.60 5.10
350 351 5.558844 GCATCTAATTGATTGACGATGCGAA 60.559 40.000 15.16 0.00 42.60 4.70
352 353 7.622048 GCATCTAATTGATTGACGATGCGAATA 60.622 37.037 15.16 0.00 42.60 1.75
353 354 7.707774 TCTAATTGATTGACGATGCGAATAA 57.292 32.000 0.00 0.00 0.00 1.40
355 356 8.275632 TCTAATTGATTGACGATGCGAATAAAG 58.724 33.333 0.00 0.00 0.00 1.85
356 357 6.603237 ATTGATTGACGATGCGAATAAAGA 57.397 33.333 0.00 0.00 0.00 2.52
358 359 5.795766 TGATTGACGATGCGAATAAAGAAC 58.204 37.500 0.00 0.00 0.00 3.01
360 361 5.599359 TTGACGATGCGAATAAAGAACAA 57.401 34.783 0.00 0.00 0.00 2.83
362 363 4.092821 TGACGATGCGAATAAAGAACAAGG 59.907 41.667 0.00 0.00 0.00 3.61
363 364 4.000988 ACGATGCGAATAAAGAACAAGGT 58.999 39.130 0.00 0.00 0.00 3.50
364 365 5.172934 ACGATGCGAATAAAGAACAAGGTA 58.827 37.500 0.00 0.00 0.00 3.08
365 366 5.063060 ACGATGCGAATAAAGAACAAGGTAC 59.937 40.000 0.00 0.00 0.00 3.34
379 380 2.808906 AGGTACTTTTCCTGGATGCC 57.191 50.000 0.00 0.00 27.25 4.40
381 382 2.092323 GGTACTTTTCCTGGATGCCAC 58.908 52.381 0.00 0.00 0.00 5.01
382 383 1.737793 GTACTTTTCCTGGATGCCACG 59.262 52.381 0.00 0.00 0.00 4.94
383 384 1.244019 ACTTTTCCTGGATGCCACGC 61.244 55.000 0.00 0.00 0.00 5.34
384 385 2.257286 CTTTTCCTGGATGCCACGCG 62.257 60.000 3.53 3.53 0.00 6.01
387 388 4.529219 CCTGGATGCCACGCGCTA 62.529 66.667 5.73 0.00 38.78 4.26
388 389 2.280389 CTGGATGCCACGCGCTAT 60.280 61.111 5.73 0.00 38.78 2.97
389 390 2.280119 TGGATGCCACGCGCTATC 60.280 61.111 5.73 4.93 38.78 2.08
390 391 2.029666 GGATGCCACGCGCTATCT 59.970 61.111 5.73 0.00 38.78 1.98
391 392 2.024319 GGATGCCACGCGCTATCTC 61.024 63.158 5.73 0.00 38.78 2.75
392 393 1.006805 GATGCCACGCGCTATCTCT 60.007 57.895 5.73 0.00 38.78 3.10
393 394 0.598680 GATGCCACGCGCTATCTCTT 60.599 55.000 5.73 0.00 38.78 2.85
394 395 0.179073 ATGCCACGCGCTATCTCTTT 60.179 50.000 5.73 0.00 38.78 2.52
396 397 0.301987 GCCACGCGCTATCTCTTTTC 59.698 55.000 5.73 0.00 0.00 2.29
397 398 1.927895 CCACGCGCTATCTCTTTTCT 58.072 50.000 5.73 0.00 0.00 2.52
399 400 2.673368 CCACGCGCTATCTCTTTTCTTT 59.327 45.455 5.73 0.00 0.00 2.52
400 401 3.242123 CCACGCGCTATCTCTTTTCTTTC 60.242 47.826 5.73 0.00 0.00 2.62
401 402 2.930682 ACGCGCTATCTCTTTTCTTTCC 59.069 45.455 5.73 0.00 0.00 3.13
402 403 2.285488 CGCGCTATCTCTTTTCTTTCCC 59.715 50.000 5.56 0.00 0.00 3.97
403 404 2.614520 GCGCTATCTCTTTTCTTTCCCC 59.385 50.000 0.00 0.00 0.00 4.81
404 405 3.682999 GCGCTATCTCTTTTCTTTCCCCT 60.683 47.826 0.00 0.00 0.00 4.79
405 406 4.123506 CGCTATCTCTTTTCTTTCCCCTC 58.876 47.826 0.00 0.00 0.00 4.30
406 407 4.456535 GCTATCTCTTTTCTTTCCCCTCC 58.543 47.826 0.00 0.00 0.00 4.30
408 409 3.005529 TCTCTTTTCTTTCCCCTCCCT 57.994 47.619 0.00 0.00 0.00 4.20
409 410 3.336676 TCTCTTTTCTTTCCCCTCCCTT 58.663 45.455 0.00 0.00 0.00 3.95
410 411 3.727391 TCTCTTTTCTTTCCCCTCCCTTT 59.273 43.478 0.00 0.00 0.00 3.11
411 412 3.829026 CTCTTTTCTTTCCCCTCCCTTTG 59.171 47.826 0.00 0.00 0.00 2.77
412 413 2.009681 TTTCTTTCCCCTCCCTTTGC 57.990 50.000 0.00 0.00 0.00 3.68
413 414 0.856982 TTCTTTCCCCTCCCTTTGCA 59.143 50.000 0.00 0.00 0.00 4.08
414 415 0.405585 TCTTTCCCCTCCCTTTGCAG 59.594 55.000 0.00 0.00 0.00 4.41
420 421 1.529010 CCTCCCTTTGCAGCACACA 60.529 57.895 0.00 0.00 0.00 3.72
423 424 0.682532 TCCCTTTGCAGCACACACAA 60.683 50.000 0.00 0.00 0.00 3.33
424 425 0.175302 CCCTTTGCAGCACACACAAA 59.825 50.000 0.00 0.00 0.00 2.83
425 426 1.405256 CCCTTTGCAGCACACACAAAA 60.405 47.619 0.00 0.00 33.24 2.44
427 428 2.285756 CCTTTGCAGCACACACAAAATG 59.714 45.455 0.00 0.00 33.24 2.32
428 429 2.955477 TTGCAGCACACACAAAATGA 57.045 40.000 0.00 0.00 0.00 2.57
429 430 2.495409 TGCAGCACACACAAAATGAG 57.505 45.000 0.00 0.00 0.00 2.90
432 433 2.811855 CAGCACACACAAAATGAGCAA 58.188 42.857 0.00 0.00 0.00 3.91
433 434 2.792674 CAGCACACACAAAATGAGCAAG 59.207 45.455 0.00 0.00 0.00 4.01
436 437 3.038017 CACACACAAAATGAGCAAGACG 58.962 45.455 0.00 0.00 0.00 4.18
437 438 2.046313 CACACAAAATGAGCAAGACGC 58.954 47.619 0.00 0.00 42.91 5.19
438 439 1.001378 ACACAAAATGAGCAAGACGCC 60.001 47.619 0.00 0.00 44.04 5.68
441 442 2.100584 ACAAAATGAGCAAGACGCCAAA 59.899 40.909 0.00 0.00 44.04 3.28
443 444 1.896220 AATGAGCAAGACGCCAAAGA 58.104 45.000 0.00 0.00 44.04 2.52
444 445 2.119801 ATGAGCAAGACGCCAAAGAT 57.880 45.000 0.00 0.00 44.04 2.40
445 446 1.159285 TGAGCAAGACGCCAAAGATG 58.841 50.000 0.00 0.00 44.04 2.90
447 448 1.806542 GAGCAAGACGCCAAAGATGAA 59.193 47.619 0.00 0.00 44.04 2.57
448 449 1.808945 AGCAAGACGCCAAAGATGAAG 59.191 47.619 0.00 0.00 44.04 3.02
451 452 2.807967 CAAGACGCCAAAGATGAAGACA 59.192 45.455 0.00 0.00 0.00 3.41
452 453 2.693069 AGACGCCAAAGATGAAGACAG 58.307 47.619 0.00 0.00 0.00 3.51
453 454 1.734465 GACGCCAAAGATGAAGACAGG 59.266 52.381 0.00 0.00 0.00 4.00
454 455 1.072331 ACGCCAAAGATGAAGACAGGT 59.928 47.619 0.00 0.00 0.00 4.00
455 456 1.734465 CGCCAAAGATGAAGACAGGTC 59.266 52.381 0.00 0.00 0.00 3.85
456 457 1.734465 GCCAAAGATGAAGACAGGTCG 59.266 52.381 0.00 0.00 34.09 4.79
458 459 1.734465 CAAAGATGAAGACAGGTCGCC 59.266 52.381 0.00 0.00 34.09 5.54
459 460 0.250513 AAGATGAAGACAGGTCGCCC 59.749 55.000 0.00 0.00 34.09 6.13
460 461 0.904865 AGATGAAGACAGGTCGCCCA 60.905 55.000 0.00 0.00 34.09 5.36
462 463 0.620556 ATGAAGACAGGTCGCCCAAT 59.379 50.000 0.00 0.00 34.09 3.16
464 465 1.066430 TGAAGACAGGTCGCCCAATAC 60.066 52.381 0.00 0.00 34.09 1.89
465 466 0.108329 AAGACAGGTCGCCCAATACG 60.108 55.000 0.00 0.00 34.09 3.06
466 467 1.520787 GACAGGTCGCCCAATACGG 60.521 63.158 0.00 0.00 0.00 4.02
467 468 2.895372 CAGGTCGCCCAATACGGC 60.895 66.667 0.00 0.00 46.13 5.68
489 490 2.372690 CGCGCGCGCCTAAATAGAT 61.373 57.895 44.64 0.00 37.98 1.98
491 492 1.278238 GCGCGCGCCTAAATAGATAT 58.722 50.000 42.83 0.00 34.56 1.63
494 495 3.791122 GCGCGCGCCTAAATAGATATAGA 60.791 47.826 42.83 0.00 34.56 1.98
495 496 4.537965 CGCGCGCCTAAATAGATATAGAT 58.462 43.478 27.72 0.00 0.00 1.98
497 498 6.315551 CGCGCGCCTAAATAGATATAGATAT 58.684 40.000 27.72 0.00 0.00 1.63
499 500 7.636745 CGCGCGCCTAAATAGATATAGATATAG 59.363 40.741 27.72 0.00 0.00 1.31
645 659 4.324669 CCGCAAACATATATCTCGTAGCTG 59.675 45.833 0.00 0.00 0.00 4.24
648 662 6.249471 CGCAAACATATATCTCGTAGCTGTAG 59.751 42.308 0.00 0.00 0.00 2.74
1219 3094 3.120086 ATGGGGTGCAGCCGTATCC 62.120 63.158 27.67 14.45 38.44 2.59
1220 3095 4.910585 GGGGTGCAGCCGTATCCG 62.911 72.222 27.67 0.00 38.44 4.18
1768 4357 3.047877 CCTCAAACGCCCGTGGAC 61.048 66.667 0.00 0.00 0.00 4.02
1819 4408 1.268743 GGCATGCCTCAAATTAGCGAC 60.269 52.381 29.98 0.00 0.00 5.19
1876 4465 7.966246 AAATTCATACAAAGCATGCAAAAGA 57.034 28.000 21.98 5.31 0.00 2.52
1881 4470 6.591062 TCATACAAAGCATGCAAAAGAAATCC 59.409 34.615 21.98 0.00 0.00 3.01
1907 4496 2.205074 ACTACATCGACGTACTACCCG 58.795 52.381 0.00 0.00 0.00 5.28
1909 4498 1.009829 ACATCGACGTACTACCCGAC 58.990 55.000 0.00 0.00 33.69 4.79
1919 4554 2.035530 ACTACCCGACCTACTCTTCG 57.964 55.000 0.00 0.00 34.93 3.79
1944 4610 1.226323 GAGATGTCCACGACGACGG 60.226 63.158 12.58 1.22 44.46 4.79
2038 4704 1.066587 CGAACATCTCCGCCTCCTC 59.933 63.158 0.00 0.00 0.00 3.71
2091 4757 1.697284 GGAGGGAATTGAGAATGGCC 58.303 55.000 0.00 0.00 0.00 5.36
2092 4758 1.697284 GAGGGAATTGAGAATGGCCC 58.303 55.000 0.00 0.00 36.85 5.80
2094 4760 1.735973 GGAATTGAGAATGGCCCGC 59.264 57.895 0.00 0.00 0.00 6.13
2238 4925 2.103934 CTCAAGGAGCTCGAGCCG 59.896 66.667 32.94 16.58 43.38 5.52
2301 4988 2.499685 GGGTGTGGCTACTAGGCG 59.500 66.667 0.64 0.00 44.78 5.52
2305 4992 1.325355 GTGTGGCTACTAGGCGGATA 58.675 55.000 0.64 0.00 44.78 2.59
2324 5011 1.150536 GGTGGAGTGGAAAGTGGCA 59.849 57.895 0.00 0.00 0.00 4.92
2331 5018 3.294493 GGAAAGTGGCAGCGGCAA 61.294 61.111 11.88 0.00 43.71 4.52
2368 5056 1.874129 TGTGGATCGATGGTAGGGTT 58.126 50.000 0.54 0.00 0.00 4.11
2394 5082 5.234329 CGGTGTCGCTGAATGACTTAAATAT 59.766 40.000 0.00 0.00 37.26 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 7.957484 CGAACGTCAAATTCTAACATTTCTGAT 59.043 33.333 0.00 0.00 0.00 2.90
54 55 7.287950 CGAACGTCAAATTCTAACATTTCTGA 58.712 34.615 0.00 0.00 0.00 3.27
56 57 6.073222 AGCGAACGTCAAATTCTAACATTTCT 60.073 34.615 0.00 0.00 0.00 2.52
57 58 6.031417 CAGCGAACGTCAAATTCTAACATTTC 59.969 38.462 0.00 0.00 0.00 2.17
58 59 5.851177 CAGCGAACGTCAAATTCTAACATTT 59.149 36.000 0.00 0.00 0.00 2.32
62 63 3.185797 ACCAGCGAACGTCAAATTCTAAC 59.814 43.478 0.00 0.00 0.00 2.34
63 64 3.395639 ACCAGCGAACGTCAAATTCTAA 58.604 40.909 0.00 0.00 0.00 2.10
65 66 1.878953 ACCAGCGAACGTCAAATTCT 58.121 45.000 0.00 0.00 0.00 2.40
66 67 2.681152 AACCAGCGAACGTCAAATTC 57.319 45.000 0.00 0.00 0.00 2.17
68 69 2.095919 GCTTAACCAGCGAACGTCAAAT 60.096 45.455 0.00 0.00 39.29 2.32
69 70 1.262151 GCTTAACCAGCGAACGTCAAA 59.738 47.619 0.00 0.00 39.29 2.69
70 71 0.863144 GCTTAACCAGCGAACGTCAA 59.137 50.000 0.00 0.00 39.29 3.18
81 82 4.613925 TTTGATTTGCCATGCTTAACCA 57.386 36.364 0.00 0.00 0.00 3.67
82 83 4.937015 ACATTTGATTTGCCATGCTTAACC 59.063 37.500 0.00 0.00 0.00 2.85
83 84 6.484818 AACATTTGATTTGCCATGCTTAAC 57.515 33.333 0.00 0.00 0.00 2.01
84 85 8.789825 ATAAACATTTGATTTGCCATGCTTAA 57.210 26.923 0.00 0.00 0.00 1.85
86 87 8.832521 CATATAAACATTTGATTTGCCATGCTT 58.167 29.630 0.00 0.00 0.00 3.91
87 88 7.442969 CCATATAAACATTTGATTTGCCATGCT 59.557 33.333 0.00 0.00 0.00 3.79
88 89 7.577979 CCATATAAACATTTGATTTGCCATGC 58.422 34.615 0.00 0.00 0.00 4.06
89 90 7.226918 TGCCATATAAACATTTGATTTGCCATG 59.773 33.333 0.00 0.00 0.00 3.66
90 91 7.227116 GTGCCATATAAACATTTGATTTGCCAT 59.773 33.333 0.00 0.00 0.00 4.40
91 92 6.538021 GTGCCATATAAACATTTGATTTGCCA 59.462 34.615 0.00 0.00 0.00 4.92
92 93 6.292274 CGTGCCATATAAACATTTGATTTGCC 60.292 38.462 0.00 0.00 0.00 4.52
93 94 6.292274 CCGTGCCATATAAACATTTGATTTGC 60.292 38.462 0.00 0.00 0.00 3.68
94 95 6.292274 GCCGTGCCATATAAACATTTGATTTG 60.292 38.462 0.00 0.00 0.00 2.32
95 96 5.752955 GCCGTGCCATATAAACATTTGATTT 59.247 36.000 0.00 0.00 0.00 2.17
96 97 5.163468 TGCCGTGCCATATAAACATTTGATT 60.163 36.000 0.00 0.00 0.00 2.57
98 99 3.696548 TGCCGTGCCATATAAACATTTGA 59.303 39.130 0.00 0.00 0.00 2.69
99 100 4.039151 TGCCGTGCCATATAAACATTTG 57.961 40.909 0.00 0.00 0.00 2.32
100 101 4.727507 TTGCCGTGCCATATAAACATTT 57.272 36.364 0.00 0.00 0.00 2.32
101 102 4.727507 TTTGCCGTGCCATATAAACATT 57.272 36.364 0.00 0.00 0.00 2.71
103 104 3.067461 GGATTTGCCGTGCCATATAAACA 59.933 43.478 0.00 0.00 0.00 2.83
104 105 3.317993 AGGATTTGCCGTGCCATATAAAC 59.682 43.478 0.00 0.00 43.43 2.01
106 107 2.884012 CAGGATTTGCCGTGCCATATAA 59.116 45.455 0.00 0.00 43.43 0.98
108 109 1.321474 CAGGATTTGCCGTGCCATAT 58.679 50.000 0.00 0.00 43.43 1.78
112 113 0.963355 TTACCAGGATTTGCCGTGCC 60.963 55.000 0.00 0.00 43.43 5.01
113 114 0.885196 TTTACCAGGATTTGCCGTGC 59.115 50.000 0.00 0.00 43.43 5.34
114 115 2.420022 CTCTTTACCAGGATTTGCCGTG 59.580 50.000 0.00 0.00 43.43 4.94
115 116 2.711542 CTCTTTACCAGGATTTGCCGT 58.288 47.619 0.00 0.00 43.43 5.68
117 118 2.424956 CAGCTCTTTACCAGGATTTGCC 59.575 50.000 0.00 0.00 0.00 4.52
118 119 2.424956 CCAGCTCTTTACCAGGATTTGC 59.575 50.000 0.00 0.00 0.00 3.68
119 120 3.691609 GTCCAGCTCTTTACCAGGATTTG 59.308 47.826 0.00 0.00 0.00 2.32
121 122 2.912956 TGTCCAGCTCTTTACCAGGATT 59.087 45.455 0.00 0.00 0.00 3.01
123 124 2.024176 TGTCCAGCTCTTTACCAGGA 57.976 50.000 0.00 0.00 0.00 3.86
124 125 2.237143 TCATGTCCAGCTCTTTACCAGG 59.763 50.000 0.00 0.00 0.00 4.45
125 126 3.616956 TCATGTCCAGCTCTTTACCAG 57.383 47.619 0.00 0.00 0.00 4.00
126 127 3.307691 CCTTCATGTCCAGCTCTTTACCA 60.308 47.826 0.00 0.00 0.00 3.25
127 128 3.055094 TCCTTCATGTCCAGCTCTTTACC 60.055 47.826 0.00 0.00 0.00 2.85
128 129 4.207891 TCCTTCATGTCCAGCTCTTTAC 57.792 45.455 0.00 0.00 0.00 2.01
129 130 4.718774 AGATCCTTCATGTCCAGCTCTTTA 59.281 41.667 0.00 0.00 0.00 1.85
130 131 3.522750 AGATCCTTCATGTCCAGCTCTTT 59.477 43.478 0.00 0.00 0.00 2.52
131 132 3.113824 AGATCCTTCATGTCCAGCTCTT 58.886 45.455 0.00 0.00 0.00 2.85
133 134 3.244044 GGTAGATCCTTCATGTCCAGCTC 60.244 52.174 0.00 0.00 0.00 4.09
136 137 4.970860 ATGGTAGATCCTTCATGTCCAG 57.029 45.455 0.00 0.00 37.07 3.86
137 138 5.715439 AAATGGTAGATCCTTCATGTCCA 57.285 39.130 0.00 0.00 37.07 4.02
138 139 8.519799 TTTTAAATGGTAGATCCTTCATGTCC 57.480 34.615 0.00 0.00 37.07 4.02
139 140 8.624776 CCTTTTAAATGGTAGATCCTTCATGTC 58.375 37.037 11.17 0.00 37.07 3.06
140 141 8.336235 TCCTTTTAAATGGTAGATCCTTCATGT 58.664 33.333 17.20 0.00 37.07 3.21
141 142 8.752005 TCCTTTTAAATGGTAGATCCTTCATG 57.248 34.615 17.20 0.00 37.07 3.07
143 144 9.768215 ATTTCCTTTTAAATGGTAGATCCTTCA 57.232 29.630 17.20 0.00 37.07 3.02
146 147 9.768215 TCAATTTCCTTTTAAATGGTAGATCCT 57.232 29.630 17.20 0.00 37.07 3.24
163 164 8.985315 TGTTAGCATGAAGATATCAATTTCCT 57.015 30.769 5.32 0.00 42.54 3.36
171 172 9.565213 GGCAAATTATGTTAGCATGAAGATATC 57.435 33.333 1.80 0.00 36.58 1.63
173 174 8.462589 TGGCAAATTATGTTAGCATGAAGATA 57.537 30.769 1.80 0.00 36.58 1.98
174 175 7.350744 TGGCAAATTATGTTAGCATGAAGAT 57.649 32.000 1.80 0.00 36.58 2.40
175 176 6.772360 TGGCAAATTATGTTAGCATGAAGA 57.228 33.333 1.80 0.00 36.58 2.87
176 177 9.531942 TTTATGGCAAATTATGTTAGCATGAAG 57.468 29.630 1.80 0.00 36.58 3.02
177 178 9.881649 TTTTATGGCAAATTATGTTAGCATGAA 57.118 25.926 1.80 0.00 36.58 2.57
186 187 9.474920 CCGAACATATTTTATGGCAAATTATGT 57.525 29.630 11.11 11.11 37.85 2.29
187 188 9.474920 ACCGAACATATTTTATGGCAAATTATG 57.525 29.630 0.00 2.00 33.30 1.90
189 190 9.877178 AAACCGAACATATTTTATGGCAAATTA 57.123 25.926 0.00 0.00 0.00 1.40
191 192 7.201600 GCAAACCGAACATATTTTATGGCAAAT 60.202 33.333 0.00 0.00 0.00 2.32
192 193 6.091441 GCAAACCGAACATATTTTATGGCAAA 59.909 34.615 0.00 0.00 0.00 3.68
193 194 5.578727 GCAAACCGAACATATTTTATGGCAA 59.421 36.000 0.00 0.00 0.00 4.52
195 196 4.506288 GGCAAACCGAACATATTTTATGGC 59.494 41.667 0.10 0.00 0.00 4.40
211 212 6.520790 CGTTAGATTTTTAAGTACGGCAAACC 59.479 38.462 0.00 0.00 0.00 3.27
212 213 7.071414 ACGTTAGATTTTTAAGTACGGCAAAC 58.929 34.615 0.00 0.00 32.33 2.93
213 214 7.188468 ACGTTAGATTTTTAAGTACGGCAAA 57.812 32.000 0.00 0.00 32.33 3.68
215 216 6.399880 CGAACGTTAGATTTTTAAGTACGGCA 60.400 38.462 0.00 0.00 32.33 5.69
216 217 5.948085 CGAACGTTAGATTTTTAAGTACGGC 59.052 40.000 0.00 0.00 32.33 5.68
217 218 5.948085 GCGAACGTTAGATTTTTAAGTACGG 59.052 40.000 12.92 0.00 32.33 4.02
219 220 6.952083 CCAGCGAACGTTAGATTTTTAAGTAC 59.048 38.462 12.92 0.00 0.00 2.73
220 221 6.646240 ACCAGCGAACGTTAGATTTTTAAGTA 59.354 34.615 12.92 0.00 0.00 2.24
221 222 5.467735 ACCAGCGAACGTTAGATTTTTAAGT 59.532 36.000 12.92 0.00 0.00 2.24
222 223 5.923665 ACCAGCGAACGTTAGATTTTTAAG 58.076 37.500 12.92 0.00 0.00 1.85
225 226 4.823790 AACCAGCGAACGTTAGATTTTT 57.176 36.364 12.92 0.00 0.00 1.94
226 227 5.640357 TGATAACCAGCGAACGTTAGATTTT 59.360 36.000 12.92 4.29 0.00 1.82
227 228 5.172934 TGATAACCAGCGAACGTTAGATTT 58.827 37.500 12.92 0.85 0.00 2.17
228 229 4.751060 TGATAACCAGCGAACGTTAGATT 58.249 39.130 12.92 3.26 0.00 2.40
231 232 4.914312 TTTGATAACCAGCGAACGTTAG 57.086 40.909 0.00 1.30 0.00 2.34
232 233 6.201425 GGATATTTGATAACCAGCGAACGTTA 59.799 38.462 0.00 0.00 0.00 3.18
233 234 5.007332 GGATATTTGATAACCAGCGAACGTT 59.993 40.000 0.00 0.00 0.00 3.99
234 235 4.510340 GGATATTTGATAACCAGCGAACGT 59.490 41.667 0.00 0.00 0.00 3.99
235 236 4.750098 AGGATATTTGATAACCAGCGAACG 59.250 41.667 0.00 0.00 30.66 3.95
236 237 6.619801 AAGGATATTTGATAACCAGCGAAC 57.380 37.500 0.00 0.00 30.66 3.95
237 238 7.639113 AAAAGGATATTTGATAACCAGCGAA 57.361 32.000 0.00 0.00 30.66 4.70
238 239 7.556275 AGAAAAAGGATATTTGATAACCAGCGA 59.444 33.333 0.00 0.00 30.66 4.93
239 240 7.707104 AGAAAAAGGATATTTGATAACCAGCG 58.293 34.615 0.00 0.00 30.66 5.18
254 255 8.981659 CCCAAAACATAGGAATAGAAAAAGGAT 58.018 33.333 0.00 0.00 0.00 3.24
256 257 8.361169 TCCCAAAACATAGGAATAGAAAAAGG 57.639 34.615 0.00 0.00 0.00 3.11
267 268 6.902771 TTTCGAAATTCCCAAAACATAGGA 57.097 33.333 6.47 0.00 0.00 2.94
271 272 9.331282 TGTTTTATTTCGAAATTCCCAAAACAT 57.669 25.926 33.16 14.27 37.74 2.71
273 274 8.604890 TGTGTTTTATTTCGAAATTCCCAAAAC 58.395 29.630 30.59 30.59 35.61 2.43
274 275 8.718102 TGTGTTTTATTTCGAAATTCCCAAAA 57.282 26.923 27.10 22.06 0.00 2.44
276 277 7.764443 TGTTGTGTTTTATTTCGAAATTCCCAA 59.236 29.630 27.10 17.24 0.00 4.12
278 279 7.436970 ACTGTTGTGTTTTATTTCGAAATTCCC 59.563 33.333 27.10 13.74 0.00 3.97
279 280 8.347729 ACTGTTGTGTTTTATTTCGAAATTCC 57.652 30.769 27.10 13.44 0.00 3.01
280 281 9.015577 TGACTGTTGTGTTTTATTTCGAAATTC 57.984 29.630 27.10 14.31 0.00 2.17
281 282 8.918961 TGACTGTTGTGTTTTATTTCGAAATT 57.081 26.923 27.10 12.37 0.00 1.82
284 285 8.744008 TTTTGACTGTTGTGTTTTATTTCGAA 57.256 26.923 0.00 0.00 0.00 3.71
286 287 8.388319 TCTTTTGACTGTTGTGTTTTATTTCG 57.612 30.769 0.00 0.00 0.00 3.46
290 291 9.125026 AGAGATCTTTTGACTGTTGTGTTTTAT 57.875 29.630 0.00 0.00 0.00 1.40
291 292 8.506168 AGAGATCTTTTGACTGTTGTGTTTTA 57.494 30.769 0.00 0.00 0.00 1.52
294 295 8.398665 GTTTAGAGATCTTTTGACTGTTGTGTT 58.601 33.333 0.00 0.00 0.00 3.32
295 296 7.254455 CGTTTAGAGATCTTTTGACTGTTGTGT 60.254 37.037 0.00 0.00 0.00 3.72
296 297 7.065894 CGTTTAGAGATCTTTTGACTGTTGTG 58.934 38.462 0.00 0.00 0.00 3.33
297 298 6.761714 ACGTTTAGAGATCTTTTGACTGTTGT 59.238 34.615 0.00 0.00 0.00 3.32
298 299 7.042725 TGACGTTTAGAGATCTTTTGACTGTTG 60.043 37.037 0.00 0.00 0.00 3.33
301 302 7.408132 TTGACGTTTAGAGATCTTTTGACTG 57.592 36.000 0.00 0.00 0.00 3.51
302 303 6.146347 GCTTGACGTTTAGAGATCTTTTGACT 59.854 38.462 0.00 0.00 0.00 3.41
303 304 6.073765 TGCTTGACGTTTAGAGATCTTTTGAC 60.074 38.462 0.00 0.00 0.00 3.18
304 305 5.989168 TGCTTGACGTTTAGAGATCTTTTGA 59.011 36.000 0.00 0.00 0.00 2.69
305 306 6.228273 TGCTTGACGTTTAGAGATCTTTTG 57.772 37.500 0.00 0.00 0.00 2.44
307 308 6.402222 AGATGCTTGACGTTTAGAGATCTTT 58.598 36.000 0.00 0.00 0.00 2.52
309 310 5.590530 AGATGCTTGACGTTTAGAGATCT 57.409 39.130 0.00 0.00 0.00 2.75
313 314 7.525688 TCAATTAGATGCTTGACGTTTAGAG 57.474 36.000 0.00 0.00 0.00 2.43
314 315 8.390354 CAATCAATTAGATGCTTGACGTTTAGA 58.610 33.333 0.00 0.00 36.96 2.10
315 316 8.390354 TCAATCAATTAGATGCTTGACGTTTAG 58.610 33.333 0.00 0.00 36.96 1.85
316 317 8.175069 GTCAATCAATTAGATGCTTGACGTTTA 58.825 33.333 7.87 0.00 42.79 2.01
322 323 6.951643 CATCGTCAATCAATTAGATGCTTGA 58.048 36.000 0.00 0.00 36.96 3.02
327 328 5.580911 TCGCATCGTCAATCAATTAGATG 57.419 39.130 0.00 0.00 36.96 2.90
329 330 7.707774 TTATTCGCATCGTCAATCAATTAGA 57.292 32.000 0.00 0.00 0.00 2.10
330 331 8.275632 TCTTTATTCGCATCGTCAATCAATTAG 58.724 33.333 0.00 0.00 0.00 1.73
331 332 8.137210 TCTTTATTCGCATCGTCAATCAATTA 57.863 30.769 0.00 0.00 0.00 1.40
332 333 7.015226 TCTTTATTCGCATCGTCAATCAATT 57.985 32.000 0.00 0.00 0.00 2.32
333 334 6.603237 TCTTTATTCGCATCGTCAATCAAT 57.397 33.333 0.00 0.00 0.00 2.57
334 335 6.128418 TGTTCTTTATTCGCATCGTCAATCAA 60.128 34.615 0.00 0.00 0.00 2.57
335 336 5.350091 TGTTCTTTATTCGCATCGTCAATCA 59.650 36.000 0.00 0.00 0.00 2.57
336 337 5.795766 TGTTCTTTATTCGCATCGTCAATC 58.204 37.500 0.00 0.00 0.00 2.67
337 338 5.794687 TGTTCTTTATTCGCATCGTCAAT 57.205 34.783 0.00 0.00 0.00 2.57
338 339 5.390461 CCTTGTTCTTTATTCGCATCGTCAA 60.390 40.000 0.00 0.00 0.00 3.18
339 340 4.092821 CCTTGTTCTTTATTCGCATCGTCA 59.907 41.667 0.00 0.00 0.00 4.35
340 341 4.092968 ACCTTGTTCTTTATTCGCATCGTC 59.907 41.667 0.00 0.00 0.00 4.20
341 342 4.000988 ACCTTGTTCTTTATTCGCATCGT 58.999 39.130 0.00 0.00 0.00 3.73
342 343 4.600012 ACCTTGTTCTTTATTCGCATCG 57.400 40.909 0.00 0.00 0.00 3.84
343 344 6.663944 AGTACCTTGTTCTTTATTCGCATC 57.336 37.500 0.00 0.00 0.00 3.91
346 347 6.800408 GGAAAAGTACCTTGTTCTTTATTCGC 59.200 38.462 0.28 0.00 33.32 4.70
347 348 8.015658 CAGGAAAAGTACCTTGTTCTTTATTCG 58.984 37.037 0.28 0.00 33.32 3.34
348 349 8.297426 CCAGGAAAAGTACCTTGTTCTTTATTC 58.703 37.037 0.28 0.00 33.32 1.75
349 350 8.002459 TCCAGGAAAAGTACCTTGTTCTTTATT 58.998 33.333 0.00 0.00 33.32 1.40
350 351 7.523415 TCCAGGAAAAGTACCTTGTTCTTTAT 58.477 34.615 0.00 0.00 33.32 1.40
352 353 5.762279 TCCAGGAAAAGTACCTTGTTCTTT 58.238 37.500 0.00 0.00 35.32 2.52
353 354 5.382664 TCCAGGAAAAGTACCTTGTTCTT 57.617 39.130 0.00 0.00 35.35 2.52
355 356 4.082733 GCATCCAGGAAAAGTACCTTGTTC 60.083 45.833 0.00 0.00 35.35 3.18
356 357 3.826729 GCATCCAGGAAAAGTACCTTGTT 59.173 43.478 0.00 0.00 35.35 2.83
358 359 2.755103 GGCATCCAGGAAAAGTACCTTG 59.245 50.000 0.00 0.00 35.35 3.61
360 361 1.992557 TGGCATCCAGGAAAAGTACCT 59.007 47.619 0.00 0.00 38.40 3.08
362 363 1.737793 CGTGGCATCCAGGAAAAGTAC 59.262 52.381 0.00 0.00 41.36 2.73
363 364 1.948611 GCGTGGCATCCAGGAAAAGTA 60.949 52.381 9.47 0.00 41.36 2.24
364 365 1.244019 GCGTGGCATCCAGGAAAAGT 61.244 55.000 9.47 0.00 41.36 2.66
365 366 1.508088 GCGTGGCATCCAGGAAAAG 59.492 57.895 9.47 0.00 41.36 2.27
377 378 0.301987 GAAAAGAGATAGCGCGTGGC 59.698 55.000 8.43 0.00 44.05 5.01
378 379 1.927895 AGAAAAGAGATAGCGCGTGG 58.072 50.000 8.43 0.00 0.00 4.94
379 380 3.242123 GGAAAGAAAAGAGATAGCGCGTG 60.242 47.826 8.43 0.00 0.00 5.34
381 382 2.285488 GGGAAAGAAAAGAGATAGCGCG 59.715 50.000 0.00 0.00 0.00 6.86
382 383 2.614520 GGGGAAAGAAAAGAGATAGCGC 59.385 50.000 0.00 0.00 0.00 5.92
383 384 4.123506 GAGGGGAAAGAAAAGAGATAGCG 58.876 47.826 0.00 0.00 0.00 4.26
384 385 4.456535 GGAGGGGAAAGAAAAGAGATAGC 58.543 47.826 0.00 0.00 0.00 2.97
385 386 4.724293 AGGGAGGGGAAAGAAAAGAGATAG 59.276 45.833 0.00 0.00 0.00 2.08
386 387 4.711055 AGGGAGGGGAAAGAAAAGAGATA 58.289 43.478 0.00 0.00 0.00 1.98
387 388 3.546840 AGGGAGGGGAAAGAAAAGAGAT 58.453 45.455 0.00 0.00 0.00 2.75
388 389 3.005529 AGGGAGGGGAAAGAAAAGAGA 57.994 47.619 0.00 0.00 0.00 3.10
389 390 3.816398 AAGGGAGGGGAAAGAAAAGAG 57.184 47.619 0.00 0.00 0.00 2.85
390 391 3.844640 CAAAGGGAGGGGAAAGAAAAGA 58.155 45.455 0.00 0.00 0.00 2.52
391 392 2.300152 GCAAAGGGAGGGGAAAGAAAAG 59.700 50.000 0.00 0.00 0.00 2.27
392 393 2.325484 GCAAAGGGAGGGGAAAGAAAA 58.675 47.619 0.00 0.00 0.00 2.29
393 394 1.219213 TGCAAAGGGAGGGGAAAGAAA 59.781 47.619 0.00 0.00 0.00 2.52
394 395 0.856982 TGCAAAGGGAGGGGAAAGAA 59.143 50.000 0.00 0.00 0.00 2.52
396 397 1.253593 GCTGCAAAGGGAGGGGAAAG 61.254 60.000 0.00 0.00 32.28 2.62
397 398 1.228862 GCTGCAAAGGGAGGGGAAA 60.229 57.895 0.00 0.00 32.28 3.13
399 400 2.858476 TGCTGCAAAGGGAGGGGA 60.858 61.111 0.00 0.00 32.28 4.81
400 401 2.677875 GTGCTGCAAAGGGAGGGG 60.678 66.667 2.77 0.00 32.28 4.79
401 402 2.115910 TGTGCTGCAAAGGGAGGG 59.884 61.111 2.77 0.00 32.28 4.30
402 403 1.529010 TGTGTGCTGCAAAGGGAGG 60.529 57.895 2.77 0.00 32.28 4.30
403 404 1.102809 TGTGTGTGCTGCAAAGGGAG 61.103 55.000 2.77 0.00 35.23 4.30
404 405 0.682532 TTGTGTGTGCTGCAAAGGGA 60.683 50.000 2.77 0.00 0.00 4.20
405 406 0.175302 TTTGTGTGTGCTGCAAAGGG 59.825 50.000 2.77 0.00 0.00 3.95
406 407 2.007360 TTTTGTGTGTGCTGCAAAGG 57.993 45.000 2.77 0.00 34.25 3.11
408 409 3.188492 CTCATTTTGTGTGTGCTGCAAA 58.812 40.909 2.77 0.00 0.00 3.68
409 410 2.811855 CTCATTTTGTGTGTGCTGCAA 58.188 42.857 2.77 0.00 0.00 4.08
410 411 1.536496 GCTCATTTTGTGTGTGCTGCA 60.536 47.619 0.00 0.00 34.30 4.41
411 412 1.134226 GCTCATTTTGTGTGTGCTGC 58.866 50.000 0.00 0.00 34.30 5.25
412 413 2.495409 TGCTCATTTTGTGTGTGCTG 57.505 45.000 0.00 0.00 37.09 4.41
413 414 2.689471 TCTTGCTCATTTTGTGTGTGCT 59.311 40.909 0.00 0.00 37.09 4.40
414 415 2.791004 GTCTTGCTCATTTTGTGTGTGC 59.209 45.455 0.00 0.00 36.80 4.57
420 421 1.317613 TGGCGTCTTGCTCATTTTGT 58.682 45.000 0.00 0.00 45.43 2.83
423 424 2.229792 TCTTTGGCGTCTTGCTCATTT 58.770 42.857 0.00 0.00 45.43 2.32
424 425 1.896220 TCTTTGGCGTCTTGCTCATT 58.104 45.000 0.00 0.00 45.43 2.57
425 426 1.741706 CATCTTTGGCGTCTTGCTCAT 59.258 47.619 0.00 0.00 45.43 2.90
427 428 1.442769 TCATCTTTGGCGTCTTGCTC 58.557 50.000 0.00 0.00 45.43 4.26
428 429 1.808945 CTTCATCTTTGGCGTCTTGCT 59.191 47.619 0.00 0.00 45.43 3.91
429 430 1.806542 TCTTCATCTTTGGCGTCTTGC 59.193 47.619 0.00 0.00 45.38 4.01
432 433 2.613977 CCTGTCTTCATCTTTGGCGTCT 60.614 50.000 0.00 0.00 0.00 4.18
433 434 1.734465 CCTGTCTTCATCTTTGGCGTC 59.266 52.381 0.00 0.00 0.00 5.19
436 437 1.734465 CGACCTGTCTTCATCTTTGGC 59.266 52.381 0.00 0.00 0.00 4.52
437 438 1.734465 GCGACCTGTCTTCATCTTTGG 59.266 52.381 0.00 0.00 0.00 3.28
438 439 1.734465 GGCGACCTGTCTTCATCTTTG 59.266 52.381 0.00 0.00 0.00 2.77
458 459 3.925238 GCGCGTCTGCCGTATTGG 61.925 66.667 8.43 0.00 39.32 3.16
459 460 4.265630 CGCGCGTCTGCCGTATTG 62.266 66.667 24.19 0.00 39.32 1.90
469 470 3.264487 CTATTTAGGCGCGCGCGTC 62.264 63.158 46.93 46.97 45.28 5.19
471 472 1.068832 TATCTATTTAGGCGCGCGCG 61.069 55.000 45.73 45.73 43.06 6.86
472 473 1.278238 ATATCTATTTAGGCGCGCGC 58.722 50.000 44.40 44.40 41.06 6.86
473 474 3.948851 TCTATATCTATTTAGGCGCGCG 58.051 45.455 28.44 28.44 0.00 6.86
474 475 8.666573 TCTATATCTATATCTATTTAGGCGCGC 58.333 37.037 25.94 25.94 0.00 6.86
562 563 5.198207 TCCGTCTGTCCATTTGACTATCTA 58.802 41.667 0.00 0.00 44.75 1.98
566 567 3.118775 CCATCCGTCTGTCCATTTGACTA 60.119 47.826 0.00 0.00 44.75 2.59
569 570 1.905894 TCCATCCGTCTGTCCATTTGA 59.094 47.619 0.00 0.00 0.00 2.69
574 575 1.275291 GTCTTTCCATCCGTCTGTCCA 59.725 52.381 0.00 0.00 0.00 4.02
587 588 5.275067 AGCATCTATCTGTCTGTCTTTCC 57.725 43.478 0.00 0.00 0.00 3.13
645 659 3.258372 TGTATCCCGAGCATTCATCCTAC 59.742 47.826 0.00 0.00 0.00 3.18
648 662 2.839486 TGTATCCCGAGCATTCATCC 57.161 50.000 0.00 0.00 0.00 3.51
1219 3094 0.097499 TGTCGTCGCAGGTGTATACG 59.903 55.000 0.00 0.00 34.99 3.06
1220 3095 2.486951 ATGTCGTCGCAGGTGTATAC 57.513 50.000 0.00 0.00 0.00 1.47
1819 4408 2.084610 TGAGTGAGACGGATGCAAAG 57.915 50.000 0.00 0.00 0.00 2.77
1864 4453 3.758554 ACGTAGGATTTCTTTTGCATGCT 59.241 39.130 20.33 0.00 0.00 3.79
1876 4465 5.088141 CGTCGATGTAGTACGTAGGATTT 57.912 43.478 0.00 0.00 32.16 2.17
1907 4496 0.373024 CCGACGACGAAGAGTAGGTC 59.627 60.000 9.28 0.00 42.66 3.85
1909 4498 0.651551 CTCCGACGACGAAGAGTAGG 59.348 60.000 9.28 0.00 42.66 3.18
1919 4554 1.226323 CGTGGACATCTCCGACGAC 60.226 63.158 0.00 0.00 40.59 4.34
1982 4648 3.136750 CAGGAGGAGGATGAGCCG 58.863 66.667 0.00 0.00 43.43 5.52
2051 4717 4.796231 CGGAGTCGGTTGCGGAGG 62.796 72.222 0.00 0.00 0.00 4.30
2288 4975 0.889306 CCTATCCGCCTAGTAGCCAC 59.111 60.000 0.00 0.00 0.00 5.01
2301 4988 2.092914 CCACTTTCCACTCCACCTATCC 60.093 54.545 0.00 0.00 0.00 2.59
2305 4992 1.352622 TGCCACTTTCCACTCCACCT 61.353 55.000 0.00 0.00 0.00 4.00
2324 5011 2.797278 CCTCCTATCCGTTGCCGCT 61.797 63.158 0.00 0.00 0.00 5.52
2368 5056 0.317160 AGTCATTCAGCGACACCGAA 59.683 50.000 0.00 0.00 38.22 4.30
2394 5082 2.477176 GCGTAATGCATTGCCCGGA 61.477 57.895 22.27 0.00 45.45 5.14


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

AutoCloner maintained by Alex Coulton.