Multiple sequence alignment - TraesCS7A01G444400

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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 TraesCS7A01G444400 chr7A 100.000 2944 0 0 1 2944 638713254 638710311 0.000000e+00 5437.0
1 TraesCS7A01G444400 chr7B 85.048 1759 159 53 727 2411 599418345 599416617 0.000000e+00 1696.0
2 TraesCS7A01G444400 chr7B 86.387 1528 116 33 852 2322 599394294 599392802 0.000000e+00 1585.0
3 TraesCS7A01G444400 chr7B 82.577 1808 185 60 530 2250 599361065 599359301 0.000000e+00 1474.0
4 TraesCS7A01G444400 chr7B 96.364 880 30 2 2067 2944 598479068 598478189 0.000000e+00 1447.0
5 TraesCS7A01G444400 chr7B 96.136 880 31 3 2067 2944 644555481 644554603 0.000000e+00 1434.0
6 TraesCS7A01G444400 chr7B 91.592 999 62 11 568 1562 598480749 598479769 0.000000e+00 1360.0
7 TraesCS7A01G444400 chr7B 95.387 542 22 1 2403 2944 599416325 599415787 0.000000e+00 859.0
8 TraesCS7A01G444400 chr7B 86.727 550 32 18 1543 2064 598479749 598479213 9.150000e-160 573.0
9 TraesCS7A01G444400 chr7B 89.610 385 27 3 1543 1926 644556194 644555822 7.380000e-131 477.0
10 TraesCS7A01G444400 chr7B 95.652 138 5 1 1927 2064 644555762 644555626 1.370000e-53 220.0
11 TraesCS7A01G444400 chr7B 94.737 133 6 1 723 855 599394784 599394653 3.850000e-49 206.0
12 TraesCS7A01G444400 chr7B 85.542 166 14 5 567 724 599395267 599395104 6.530000e-37 165.0
13 TraesCS7A01G444400 chr7D 93.918 1003 42 7 568 1561 552968009 552967017 0.000000e+00 1496.0
14 TraesCS7A01G444400 chr7D 82.960 1743 190 49 572 2259 552989316 552987626 0.000000e+00 1474.0
15 TraesCS7A01G444400 chr7D 95.333 857 29 4 2089 2944 552966472 552965626 0.000000e+00 1351.0
16 TraesCS7A01G444400 chr7D 94.000 400 20 2 1528 1926 552967017 552966621 1.170000e-168 603.0
17 TraesCS7A01G444400 chr7D 93.237 414 17 4 1696 2102 553064621 553064212 1.510000e-167 599.0
18 TraesCS7A01G444400 chr7D 94.815 135 7 0 2389 2523 552987233 552987099 8.270000e-51 211.0
19 TraesCS7A01G444400 chr7D 93.056 144 9 1 2389 2532 553071460 553071318 2.970000e-50 209.0
20 TraesCS7A01G444400 chr7D 94.215 121 5 1 1927 2045 552966593 552966473 1.800000e-42 183.0
21 TraesCS7A01G444400 chr7D 93.137 102 6 1 530 631 553066140 553066040 6.570000e-32 148.0
22 TraesCS7A01G444400 chr7D 94.937 79 4 0 2132 2210 553062829 553062751 1.110000e-24 124.0
23 TraesCS7A01G444400 chr7D 91.026 78 3 2 614 689 553064692 553064617 5.190000e-18 102.0
24 TraesCS7A01G444400 chr6B 90.872 493 32 9 2 491 659810960 659810478 0.000000e+00 649.0
25 TraesCS7A01G444400 chr4A 87.010 485 32 7 4 485 618280859 618280403 4.350000e-143 518.0
26 TraesCS7A01G444400 chr2B 84.667 450 54 11 33 475 159880510 159880951 4.510000e-118 435.0
27 TraesCS7A01G444400 chr5D 96.335 191 5 2 297 485 447639671 447639481 2.200000e-81 313.0
28 TraesCS7A01G444400 chr1A 84.360 211 30 1 1716 1926 85318161 85318368 1.380000e-48 204.0
29 TraesCS7A01G444400 chr2D 73.884 448 62 28 34 466 333509862 333510269 8.560000e-26 128.0
30 TraesCS7A01G444400 chr6A 86.747 83 11 0 2862 2944 104514341 104514259 3.120000e-15 93.5


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 TraesCS7A01G444400 chr7A 638710311 638713254 2943 True 5437.000000 5437 100.000000 1 2944 1 chr7A.!!$R1 2943
1 TraesCS7A01G444400 chr7B 599359301 599361065 1764 True 1474.000000 1474 82.577000 530 2250 1 chr7B.!!$R1 1720
2 TraesCS7A01G444400 chr7B 599415787 599418345 2558 True 1277.500000 1696 90.217500 727 2944 2 chr7B.!!$R4 2217
3 TraesCS7A01G444400 chr7B 598478189 598480749 2560 True 1126.666667 1447 91.561000 568 2944 3 chr7B.!!$R2 2376
4 TraesCS7A01G444400 chr7B 644554603 644556194 1591 True 710.333333 1434 93.799333 1543 2944 3 chr7B.!!$R5 1401
5 TraesCS7A01G444400 chr7B 599392802 599395267 2465 True 652.000000 1585 88.888667 567 2322 3 chr7B.!!$R3 1755
6 TraesCS7A01G444400 chr7D 552965626 552968009 2383 True 908.250000 1496 94.366500 568 2944 4 chr7D.!!$R2 2376
7 TraesCS7A01G444400 chr7D 552987099 552989316 2217 True 842.500000 1474 88.887500 572 2523 2 chr7D.!!$R3 1951
8 TraesCS7A01G444400 chr7D 553062751 553066140 3389 True 243.250000 599 93.084250 530 2210 4 chr7D.!!$R4 1680

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
441 442 0.033504 AGAAACAGATCGTGCGGTGT 59.966 50.0 0.00 0.00 0.0 4.16 F
442 443 0.163788 GAAACAGATCGTGCGGTGTG 59.836 55.0 0.37 0.37 0.0 3.82 F
511 512 0.178068 CCTAGCGCTGCCCTTCTTAA 59.822 55.0 22.90 0.00 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 3856 0.315059 GTGTTTATCATGGTCGCGCG 60.315 55.0 26.76 26.76 0.00 6.86 R
1767 3978 0.337428 AAGCAGATGGGGCAATCCTT 59.663 50.0 0.00 0.00 35.33 3.36 R
2351 6551 0.824109 CGCACTATGACCTCTGGGAA 59.176 55.0 0.00 0.00 36.25 3.97 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
29 30 2.287393 GGCAACACCAACGAGTTTTT 57.713 45.000 0.00 0.00 38.86 1.94
55 56 4.399004 TTTTTGCTACAACCTGCATGTT 57.601 36.364 1.04 1.04 39.07 2.71
56 57 4.399004 TTTTGCTACAACCTGCATGTTT 57.601 36.364 4.46 0.61 39.07 2.83
57 58 4.399004 TTTGCTACAACCTGCATGTTTT 57.601 36.364 4.46 1.68 39.07 2.43
58 59 4.399004 TTGCTACAACCTGCATGTTTTT 57.601 36.364 4.46 0.00 39.07 1.94
78 79 2.048127 GCTCGACCAGCGGACTTT 60.048 61.111 1.50 0.00 38.76 2.66
79 80 1.668151 GCTCGACCAGCGGACTTTT 60.668 57.895 1.50 0.00 38.76 2.27
80 81 1.228657 GCTCGACCAGCGGACTTTTT 61.229 55.000 1.50 0.00 38.76 1.94
96 97 2.785713 TTTTTGCTACTTCCGGCAAC 57.214 45.000 0.00 0.00 46.14 4.17
97 98 0.955905 TTTTGCTACTTCCGGCAACC 59.044 50.000 0.00 0.00 46.14 3.77
98 99 0.891904 TTTGCTACTTCCGGCAACCC 60.892 55.000 0.00 0.00 46.14 4.11
110 111 1.180029 GGCAACCCGAGTAGAGTACA 58.820 55.000 0.00 0.00 0.00 2.90
111 112 1.134560 GGCAACCCGAGTAGAGTACAG 59.865 57.143 0.00 0.00 0.00 2.74
112 113 1.817447 GCAACCCGAGTAGAGTACAGT 59.183 52.381 0.00 0.00 0.00 3.55
113 114 2.230750 GCAACCCGAGTAGAGTACAGTT 59.769 50.000 0.00 0.00 0.00 3.16
114 115 3.305881 GCAACCCGAGTAGAGTACAGTTT 60.306 47.826 0.00 0.00 0.00 2.66
115 116 4.235360 CAACCCGAGTAGAGTACAGTTTG 58.765 47.826 0.00 0.00 0.00 2.93
116 117 2.230750 ACCCGAGTAGAGTACAGTTTGC 59.769 50.000 0.00 0.00 0.00 3.68
117 118 2.516923 CCGAGTAGAGTACAGTTTGCG 58.483 52.381 0.00 0.00 0.00 4.85
118 119 2.161012 CCGAGTAGAGTACAGTTTGCGA 59.839 50.000 0.00 0.00 0.00 5.10
119 120 3.418094 CGAGTAGAGTACAGTTTGCGAG 58.582 50.000 0.00 0.00 0.00 5.03
120 121 3.172824 GAGTAGAGTACAGTTTGCGAGC 58.827 50.000 0.00 0.00 0.00 5.03
121 122 2.820787 AGTAGAGTACAGTTTGCGAGCT 59.179 45.455 0.00 0.00 0.00 4.09
122 123 2.355717 AGAGTACAGTTTGCGAGCTC 57.644 50.000 2.73 2.73 0.00 4.09
123 124 0.985549 GAGTACAGTTTGCGAGCTCG 59.014 55.000 31.37 31.37 43.27 5.03
124 125 0.314302 AGTACAGTTTGCGAGCTCGT 59.686 50.000 34.46 17.21 42.22 4.18
125 126 0.708918 GTACAGTTTGCGAGCTCGTC 59.291 55.000 34.46 26.25 42.22 4.20
137 138 2.645567 CTCGTCGTGAGTGTGCCT 59.354 61.111 0.00 0.00 40.03 4.75
138 139 1.442857 CTCGTCGTGAGTGTGCCTC 60.443 63.158 0.00 0.00 40.03 4.70
139 140 2.430921 CGTCGTGAGTGTGCCTCC 60.431 66.667 0.00 0.00 39.65 4.30
140 141 2.734591 GTCGTGAGTGTGCCTCCA 59.265 61.111 0.00 0.00 39.65 3.86
141 142 1.664965 GTCGTGAGTGTGCCTCCAC 60.665 63.158 0.00 0.00 39.65 4.02
142 143 2.357517 CGTGAGTGTGCCTCCACC 60.358 66.667 0.00 0.00 41.35 4.61
143 144 2.357517 GTGAGTGTGCCTCCACCG 60.358 66.667 0.00 0.00 41.35 4.94
144 145 3.625897 TGAGTGTGCCTCCACCGG 61.626 66.667 0.00 0.00 41.35 5.28
145 146 4.394712 GAGTGTGCCTCCACCGGG 62.395 72.222 6.32 0.00 41.35 5.73
166 167 4.657824 CGTCGGCACCGGAGTTGT 62.658 66.667 9.46 0.00 40.25 3.32
167 168 3.041940 GTCGGCACCGGAGTTGTG 61.042 66.667 9.46 0.00 40.25 3.33
168 169 4.308458 TCGGCACCGGAGTTGTGG 62.308 66.667 9.46 0.00 40.25 4.17
172 173 3.041940 CACCGGAGTTGTGGCGTC 61.042 66.667 9.46 0.00 0.00 5.19
173 174 4.657824 ACCGGAGTTGTGGCGTCG 62.658 66.667 9.46 0.00 0.00 5.12
176 177 2.742372 GGAGTTGTGGCGTCGCAT 60.742 61.111 20.50 0.00 32.95 4.73
177 178 2.740714 GGAGTTGTGGCGTCGCATC 61.741 63.158 20.50 3.31 32.95 3.91
178 179 3.071459 GAGTTGTGGCGTCGCATCG 62.071 63.158 20.50 0.00 32.95 3.84
186 187 3.976375 CGTCGCATCGCATCGGTG 61.976 66.667 0.00 0.00 41.32 4.94
210 211 3.449227 CGTCGCCACAGGGAGCTA 61.449 66.667 0.00 0.00 35.29 3.32
211 212 2.184579 GTCGCCACAGGGAGCTAC 59.815 66.667 0.00 0.00 35.29 3.58
212 213 2.283604 TCGCCACAGGGAGCTACA 60.284 61.111 0.00 0.00 35.59 2.74
213 214 1.911269 TCGCCACAGGGAGCTACAA 60.911 57.895 0.00 0.00 35.59 2.41
214 215 1.741770 CGCCACAGGGAGCTACAAC 60.742 63.158 0.00 0.00 35.59 3.32
215 216 1.377333 GCCACAGGGAGCTACAACC 60.377 63.158 0.00 0.00 35.59 3.77
216 217 2.066340 CCACAGGGAGCTACAACCA 58.934 57.895 0.00 0.00 35.59 3.67
217 218 0.321653 CCACAGGGAGCTACAACCAC 60.322 60.000 0.00 0.00 35.59 4.16
218 219 0.670546 CACAGGGAGCTACAACCACG 60.671 60.000 0.00 0.00 0.00 4.94
219 220 1.079127 CAGGGAGCTACAACCACGG 60.079 63.158 0.00 0.00 0.00 4.94
220 221 2.267961 GGGAGCTACAACCACGGG 59.732 66.667 0.00 0.00 0.00 5.28
221 222 2.436115 GGAGCTACAACCACGGGC 60.436 66.667 0.00 0.00 0.00 6.13
222 223 2.345991 GAGCTACAACCACGGGCA 59.654 61.111 0.00 0.00 0.00 5.36
223 224 2.032071 AGCTACAACCACGGGCAC 59.968 61.111 0.00 0.00 0.00 5.01
224 225 2.281208 GCTACAACCACGGGCACA 60.281 61.111 0.00 0.00 0.00 4.57
225 226 2.613506 GCTACAACCACGGGCACAC 61.614 63.158 0.00 0.00 0.00 3.82
226 227 1.227704 CTACAACCACGGGCACACA 60.228 57.895 0.00 0.00 0.00 3.72
227 228 0.605319 CTACAACCACGGGCACACAT 60.605 55.000 0.00 0.00 0.00 3.21
228 229 0.179015 TACAACCACGGGCACACATT 60.179 50.000 0.00 0.00 0.00 2.71
229 230 1.007502 CAACCACGGGCACACATTG 60.008 57.895 0.00 0.00 0.00 2.82
230 231 1.152860 AACCACGGGCACACATTGA 60.153 52.632 0.00 0.00 0.00 2.57
231 232 0.539438 AACCACGGGCACACATTGAT 60.539 50.000 0.00 0.00 0.00 2.57
232 233 1.243342 ACCACGGGCACACATTGATG 61.243 55.000 0.00 0.00 0.00 3.07
233 234 1.153978 CACGGGCACACATTGATGC 60.154 57.895 8.54 8.54 41.29 3.91
234 235 1.603171 ACGGGCACACATTGATGCA 60.603 52.632 15.93 0.00 43.93 3.96
235 236 1.153978 CGGGCACACATTGATGCAC 60.154 57.895 15.93 12.68 43.93 4.57
236 237 1.588824 CGGGCACACATTGATGCACT 61.589 55.000 14.82 0.00 43.37 4.40
237 238 0.108992 GGGCACACATTGATGCACTG 60.109 55.000 15.93 0.00 42.22 3.66
238 239 0.108992 GGCACACATTGATGCACTGG 60.109 55.000 15.93 0.00 43.93 4.00
239 240 0.734942 GCACACATTGATGCACTGGC 60.735 55.000 11.21 0.00 41.65 4.85
240 241 0.455464 CACACATTGATGCACTGGCG 60.455 55.000 0.00 0.00 45.35 5.69
241 242 0.890542 ACACATTGATGCACTGGCGT 60.891 50.000 0.00 0.00 45.35 5.68
242 243 1.085893 CACATTGATGCACTGGCGTA 58.914 50.000 0.00 0.00 45.35 4.42
243 244 1.063027 CACATTGATGCACTGGCGTAG 59.937 52.381 0.00 0.00 45.35 3.51
261 262 4.910956 CGGATGAGAAACGCAGGA 57.089 55.556 0.00 0.00 0.00 3.86
262 263 2.670635 CGGATGAGAAACGCAGGAG 58.329 57.895 0.00 0.00 0.00 3.69
263 264 0.173481 CGGATGAGAAACGCAGGAGA 59.827 55.000 0.00 0.00 0.00 3.71
264 265 1.646189 GGATGAGAAACGCAGGAGAC 58.354 55.000 0.00 0.00 0.00 3.36
265 266 1.272781 GATGAGAAACGCAGGAGACG 58.727 55.000 0.00 0.00 0.00 4.18
266 267 0.888619 ATGAGAAACGCAGGAGACGA 59.111 50.000 0.00 0.00 0.00 4.20
267 268 0.039437 TGAGAAACGCAGGAGACGAC 60.039 55.000 0.00 0.00 0.00 4.34
268 269 1.066114 GAGAAACGCAGGAGACGACG 61.066 60.000 0.00 0.00 39.09 5.12
269 270 2.049433 AAACGCAGGAGACGACGG 60.049 61.111 0.00 0.00 37.76 4.79
270 271 2.744307 GAAACGCAGGAGACGACGGT 62.744 60.000 0.00 0.00 37.76 4.83
271 272 3.553437 AACGCAGGAGACGACGGTG 62.553 63.158 0.00 0.00 37.76 4.94
272 273 4.778415 CGCAGGAGACGACGGTGG 62.778 72.222 0.00 0.00 0.00 4.61
274 275 4.778415 CAGGAGACGACGGTGGCG 62.778 72.222 0.00 0.00 0.00 5.69
326 327 3.818787 GGCGAGGGCAGCAACATG 61.819 66.667 0.00 0.00 42.47 3.21
327 328 4.487412 GCGAGGGCAGCAACATGC 62.487 66.667 0.00 0.00 45.46 4.06
337 338 3.498840 GCAACATGCGAGACGAATC 57.501 52.632 0.00 0.00 31.71 2.52
338 339 0.721154 GCAACATGCGAGACGAATCA 59.279 50.000 0.00 0.00 31.71 2.57
339 340 1.267235 GCAACATGCGAGACGAATCAG 60.267 52.381 0.00 0.00 31.71 2.90
340 341 1.325640 CAACATGCGAGACGAATCAGG 59.674 52.381 0.00 0.00 0.00 3.86
341 342 0.179100 ACATGCGAGACGAATCAGGG 60.179 55.000 0.00 0.00 0.00 4.45
342 343 0.877649 CATGCGAGACGAATCAGGGG 60.878 60.000 0.00 0.00 0.00 4.79
343 344 2.032860 ATGCGAGACGAATCAGGGGG 62.033 60.000 0.00 0.00 0.00 5.40
344 345 2.107141 CGAGACGAATCAGGGGGC 59.893 66.667 0.00 0.00 0.00 5.80
345 346 2.107141 GAGACGAATCAGGGGGCG 59.893 66.667 0.00 0.00 0.00 6.13
346 347 3.447025 GAGACGAATCAGGGGGCGG 62.447 68.421 0.00 0.00 0.00 6.13
347 348 3.782443 GACGAATCAGGGGGCGGT 61.782 66.667 0.00 0.00 0.00 5.68
348 349 4.096003 ACGAATCAGGGGGCGGTG 62.096 66.667 0.00 0.00 0.00 4.94
350 351 4.115199 GAATCAGGGGGCGGTGCT 62.115 66.667 0.00 0.00 0.00 4.40
351 352 3.645268 GAATCAGGGGGCGGTGCTT 62.645 63.158 0.00 0.00 0.00 3.91
352 353 3.645268 AATCAGGGGGCGGTGCTTC 62.645 63.158 0.00 0.00 0.00 3.86
366 367 4.473520 CTTCGAGGCGGGGCATGT 62.474 66.667 0.00 0.00 0.00 3.21
367 368 4.467084 TTCGAGGCGGGGCATGTC 62.467 66.667 0.00 0.00 0.00 3.06
375 376 4.077184 GGGGCATGTCGGTCGTCA 62.077 66.667 0.00 0.00 0.00 4.35
376 377 2.047655 GGGCATGTCGGTCGTCAA 60.048 61.111 0.00 0.00 0.00 3.18
377 378 1.449601 GGGCATGTCGGTCGTCAAT 60.450 57.895 0.00 0.00 0.00 2.57
378 379 1.705337 GGGCATGTCGGTCGTCAATG 61.705 60.000 0.00 0.00 0.00 2.82
379 380 1.705337 GGCATGTCGGTCGTCAATGG 61.705 60.000 0.00 0.00 0.00 3.16
380 381 1.715585 CATGTCGGTCGTCAATGGC 59.284 57.895 0.00 0.00 0.00 4.40
381 382 1.018752 CATGTCGGTCGTCAATGGCA 61.019 55.000 0.00 0.00 0.00 4.92
382 383 0.740868 ATGTCGGTCGTCAATGGCAG 60.741 55.000 0.00 0.00 0.00 4.85
383 384 1.374252 GTCGGTCGTCAATGGCAGT 60.374 57.895 0.00 0.00 0.00 4.40
384 385 0.949105 GTCGGTCGTCAATGGCAGTT 60.949 55.000 0.00 0.00 0.00 3.16
385 386 0.948623 TCGGTCGTCAATGGCAGTTG 60.949 55.000 0.00 0.00 0.00 3.16
386 387 1.875963 GGTCGTCAATGGCAGTTGG 59.124 57.895 0.00 0.00 0.00 3.77
387 388 0.605319 GGTCGTCAATGGCAGTTGGA 60.605 55.000 0.00 0.00 0.00 3.53
388 389 0.798776 GTCGTCAATGGCAGTTGGAG 59.201 55.000 0.00 0.00 0.00 3.86
389 390 0.396435 TCGTCAATGGCAGTTGGAGT 59.604 50.000 0.00 0.00 0.00 3.85
390 391 1.202758 TCGTCAATGGCAGTTGGAGTT 60.203 47.619 0.00 0.00 0.00 3.01
391 392 1.608590 CGTCAATGGCAGTTGGAGTTT 59.391 47.619 0.00 0.00 0.00 2.66
392 393 2.034558 CGTCAATGGCAGTTGGAGTTTT 59.965 45.455 0.00 0.00 0.00 2.43
393 394 3.490761 CGTCAATGGCAGTTGGAGTTTTT 60.491 43.478 0.00 0.00 0.00 1.94
394 395 4.051237 GTCAATGGCAGTTGGAGTTTTTC 58.949 43.478 0.00 0.00 0.00 2.29
395 396 3.960102 TCAATGGCAGTTGGAGTTTTTCT 59.040 39.130 0.00 0.00 0.00 2.52
396 397 4.037923 TCAATGGCAGTTGGAGTTTTTCTC 59.962 41.667 0.00 0.00 42.07 2.87
411 412 3.915437 TTTCTCCAAGAAAATGGCGTC 57.085 42.857 0.00 0.00 40.89 5.19
412 413 1.438651 TCTCCAAGAAAATGGCGTCG 58.561 50.000 0.00 0.00 40.46 5.12
413 414 0.447801 CTCCAAGAAAATGGCGTCGG 59.552 55.000 0.00 0.00 40.46 4.79
414 415 0.958382 TCCAAGAAAATGGCGTCGGG 60.958 55.000 0.00 0.00 40.46 5.14
415 416 1.506262 CAAGAAAATGGCGTCGGGG 59.494 57.895 0.00 0.00 0.00 5.73
416 417 0.958382 CAAGAAAATGGCGTCGGGGA 60.958 55.000 0.00 0.00 0.00 4.81
417 418 0.676782 AAGAAAATGGCGTCGGGGAG 60.677 55.000 0.00 0.00 0.00 4.30
418 419 2.045340 AAAATGGCGTCGGGGAGG 60.045 61.111 0.00 0.00 0.00 4.30
419 420 2.530958 GAAAATGGCGTCGGGGAGGA 62.531 60.000 0.00 0.00 0.00 3.71
420 421 2.132089 AAAATGGCGTCGGGGAGGAA 62.132 55.000 0.00 0.00 0.00 3.36
421 422 2.536997 AAATGGCGTCGGGGAGGAAG 62.537 60.000 0.00 0.00 0.00 3.46
422 423 3.976490 ATGGCGTCGGGGAGGAAGA 62.976 63.158 0.00 0.00 0.00 2.87
423 424 3.839432 GGCGTCGGGGAGGAAGAG 61.839 72.222 0.00 0.00 0.00 2.85
424 425 2.754658 GCGTCGGGGAGGAAGAGA 60.755 66.667 0.00 0.00 0.00 3.10
425 426 2.348888 GCGTCGGGGAGGAAGAGAA 61.349 63.158 0.00 0.00 0.00 2.87
426 427 1.885163 GCGTCGGGGAGGAAGAGAAA 61.885 60.000 0.00 0.00 0.00 2.52
427 428 0.108756 CGTCGGGGAGGAAGAGAAAC 60.109 60.000 0.00 0.00 0.00 2.78
428 429 0.974383 GTCGGGGAGGAAGAGAAACA 59.026 55.000 0.00 0.00 0.00 2.83
429 430 1.066787 GTCGGGGAGGAAGAGAAACAG 60.067 57.143 0.00 0.00 0.00 3.16
430 431 1.203137 TCGGGGAGGAAGAGAAACAGA 60.203 52.381 0.00 0.00 0.00 3.41
431 432 1.834263 CGGGGAGGAAGAGAAACAGAT 59.166 52.381 0.00 0.00 0.00 2.90
432 433 2.159028 CGGGGAGGAAGAGAAACAGATC 60.159 54.545 0.00 0.00 0.00 2.75
433 434 2.159028 GGGGAGGAAGAGAAACAGATCG 60.159 54.545 0.00 0.00 0.00 3.69
434 435 2.498078 GGGAGGAAGAGAAACAGATCGT 59.502 50.000 0.00 0.00 0.00 3.73
435 436 3.516615 GGAGGAAGAGAAACAGATCGTG 58.483 50.000 0.00 0.00 0.00 4.35
436 437 2.926838 GAGGAAGAGAAACAGATCGTGC 59.073 50.000 0.00 0.00 0.00 5.34
437 438 1.656095 GGAAGAGAAACAGATCGTGCG 59.344 52.381 0.00 0.00 0.00 5.34
438 439 1.656095 GAAGAGAAACAGATCGTGCGG 59.344 52.381 0.00 0.00 0.00 5.69
439 440 0.603569 AGAGAAACAGATCGTGCGGT 59.396 50.000 0.00 0.00 0.00 5.68
440 441 0.716108 GAGAAACAGATCGTGCGGTG 59.284 55.000 0.00 0.00 0.00 4.94
441 442 0.033504 AGAAACAGATCGTGCGGTGT 59.966 50.000 0.00 0.00 0.00 4.16
442 443 0.163788 GAAACAGATCGTGCGGTGTG 59.836 55.000 0.37 0.37 0.00 3.82
443 444 0.531974 AAACAGATCGTGCGGTGTGT 60.532 50.000 1.72 1.72 0.00 3.72
444 445 0.315886 AACAGATCGTGCGGTGTGTA 59.684 50.000 8.02 0.00 0.00 2.90
445 446 0.388134 ACAGATCGTGCGGTGTGTAC 60.388 55.000 5.84 0.00 0.00 2.90
453 454 3.408020 CGGTGTGTACGGGCGTTG 61.408 66.667 0.00 0.00 0.00 4.10
454 455 2.029369 GGTGTGTACGGGCGTTGA 59.971 61.111 0.00 0.00 0.00 3.18
455 456 2.312436 GGTGTGTACGGGCGTTGAC 61.312 63.158 0.00 0.00 0.00 3.18
456 457 2.029369 TGTGTACGGGCGTTGACC 59.971 61.111 0.00 0.00 0.00 4.02
465 466 3.855159 GGCGTTGACCCTACTGAAT 57.145 52.632 0.00 0.00 0.00 2.57
466 467 2.109425 GGCGTTGACCCTACTGAATT 57.891 50.000 0.00 0.00 0.00 2.17
467 468 1.737793 GGCGTTGACCCTACTGAATTG 59.262 52.381 0.00 0.00 0.00 2.32
468 469 1.737793 GCGTTGACCCTACTGAATTGG 59.262 52.381 0.00 0.00 0.00 3.16
473 474 3.191182 CCCTACTGAATTGGGTGGC 57.809 57.895 0.00 0.00 38.50 5.01
474 475 0.625849 CCCTACTGAATTGGGTGGCT 59.374 55.000 0.00 0.00 38.50 4.75
475 476 1.683011 CCCTACTGAATTGGGTGGCTG 60.683 57.143 0.00 0.00 38.50 4.85
476 477 1.683011 CCTACTGAATTGGGTGGCTGG 60.683 57.143 0.00 0.00 0.00 4.85
477 478 0.323360 TACTGAATTGGGTGGCTGGC 60.323 55.000 0.00 0.00 0.00 4.85
478 479 1.607178 CTGAATTGGGTGGCTGGCA 60.607 57.895 0.00 0.00 0.00 4.92
479 480 0.974010 CTGAATTGGGTGGCTGGCAT 60.974 55.000 7.33 0.00 0.00 4.40
480 481 1.259142 TGAATTGGGTGGCTGGCATG 61.259 55.000 7.33 0.00 0.00 4.06
481 482 2.582734 GAATTGGGTGGCTGGCATGC 62.583 60.000 9.90 9.90 0.00 4.06
486 487 3.136123 GTGGCTGGCATGCGACAT 61.136 61.111 12.44 0.00 40.56 3.06
487 488 2.825387 TGGCTGGCATGCGACATC 60.825 61.111 12.44 0.17 0.00 3.06
488 489 3.945434 GGCTGGCATGCGACATCG 61.945 66.667 12.44 0.00 43.27 3.84
489 490 3.945434 GCTGGCATGCGACATCGG 61.945 66.667 12.44 3.35 40.23 4.18
490 491 3.945434 CTGGCATGCGACATCGGC 61.945 66.667 12.44 0.00 40.23 5.54
508 509 4.168291 GCCTAGCGCTGCCCTTCT 62.168 66.667 22.90 0.00 0.00 2.85
509 510 2.586792 CCTAGCGCTGCCCTTCTT 59.413 61.111 22.90 0.00 0.00 2.52
510 511 1.823295 CCTAGCGCTGCCCTTCTTA 59.177 57.895 22.90 0.00 0.00 2.10
511 512 0.178068 CCTAGCGCTGCCCTTCTTAA 59.822 55.000 22.90 0.00 0.00 1.85
512 513 1.406887 CCTAGCGCTGCCCTTCTTAAA 60.407 52.381 22.90 0.00 0.00 1.52
513 514 2.356135 CTAGCGCTGCCCTTCTTAAAA 58.644 47.619 22.90 0.00 0.00 1.52
514 515 1.616159 AGCGCTGCCCTTCTTAAAAA 58.384 45.000 10.39 0.00 0.00 1.94
579 593 0.385473 GTGCGTTGTGTCCGAATTGG 60.385 55.000 0.00 0.00 40.09 3.16
604 620 4.778143 ATCGGCGGGTTGTCAGGC 62.778 66.667 7.21 0.00 0.00 4.85
612 1992 3.522553 GCGGGTTGTCAGGCTATATATC 58.477 50.000 0.00 0.00 0.00 1.63
670 2054 3.494626 AGAAATATAATCACAGCACGGCG 59.505 43.478 4.80 4.80 0.00 6.46
721 2435 3.027449 GCGCGCGAGATTCTCTCC 61.027 66.667 37.18 7.60 40.34 3.71
1272 3384 4.640364 ACCAAGAAGAAGAAGAAGCAGAG 58.360 43.478 0.00 0.00 0.00 3.35
1273 3385 4.102367 ACCAAGAAGAAGAAGAAGCAGAGT 59.898 41.667 0.00 0.00 0.00 3.24
1689 3873 1.275657 CCGCGCGACCATGATAAAC 59.724 57.895 34.63 0.00 0.00 2.01
1862 4073 3.499737 GTCTTCCATGGCGCGTGG 61.500 66.667 20.80 20.80 41.56 4.94
1942 4222 4.539152 GTCGACGTTCGGCAAGTA 57.461 55.556 0.00 0.00 45.01 2.24
1971 4256 4.023707 ACAAATGTGCAACTAGCTGTTCTC 60.024 41.667 0.00 0.00 45.94 2.87
1999 4288 9.783081 AGAAATTATTTGTTTTGCTGAAGGATT 57.217 25.926 0.00 0.00 0.00 3.01
2115 5938 7.632721 AGTGAAAATTGTTTGTTCAATCATGC 58.367 30.769 0.00 0.00 37.09 4.06
2173 6051 4.952262 TGCATCAGCTGAACTTTCATAC 57.048 40.909 22.50 0.00 42.74 2.39
2178 6056 6.037500 GCATCAGCTGAACTTTCATACACATA 59.962 38.462 22.50 0.00 36.46 2.29
2351 6551 1.075601 TGCAATGGGAGAGAGGGTTT 58.924 50.000 0.00 0.00 0.00 3.27
2429 6929 3.548745 GTGATCATCACATCCTCCACA 57.451 47.619 13.26 0.00 46.22 4.17
2642 7142 5.565439 GCTGGTTACATGCTTCTTGAAATGT 60.565 40.000 0.00 6.12 37.11 2.71
2878 7378 3.195396 CACCTACCAAATTGGGGAACATG 59.805 47.826 17.27 3.23 43.37 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.287393 AAAAACTCGTTGGTGTTGCC 57.713 45.000 0.00 0.00 37.90 4.52
34 35 4.399004 AACATGCAGGTTGTAGCAAAAA 57.601 36.364 17.13 0.00 44.88 1.94
35 36 4.399004 AAACATGCAGGTTGTAGCAAAA 57.601 36.364 18.64 0.00 44.88 2.44
36 37 4.399004 AAAACATGCAGGTTGTAGCAAA 57.601 36.364 18.64 0.00 44.88 3.68
37 38 4.399004 AAAAACATGCAGGTTGTAGCAA 57.601 36.364 18.64 0.00 44.88 3.91
61 62 1.228657 AAAAAGTCCGCTGGTCGAGC 61.229 55.000 7.89 7.89 45.20 5.03
62 63 2.914379 AAAAAGTCCGCTGGTCGAG 58.086 52.632 0.00 0.00 41.67 4.04
80 81 1.302993 GGGTTGCCGGAAGTAGCAA 60.303 57.895 5.05 0.00 46.26 3.91
81 82 2.349755 GGGTTGCCGGAAGTAGCA 59.650 61.111 5.05 0.00 37.18 3.49
82 83 2.818274 CGGGTTGCCGGAAGTAGC 60.818 66.667 5.05 0.00 0.00 3.58
83 84 1.153628 CTCGGGTTGCCGGAAGTAG 60.154 63.158 5.05 0.00 32.59 2.57
84 85 0.611618 TACTCGGGTTGCCGGAAGTA 60.612 55.000 5.05 0.00 32.59 2.24
85 86 1.885163 CTACTCGGGTTGCCGGAAGT 61.885 60.000 5.05 0.00 32.59 3.01
86 87 1.153628 CTACTCGGGTTGCCGGAAG 60.154 63.158 5.05 0.00 32.59 3.46
87 88 1.601419 CTCTACTCGGGTTGCCGGAA 61.601 60.000 5.05 0.00 32.59 4.30
88 89 2.036098 TCTACTCGGGTTGCCGGA 59.964 61.111 5.05 0.00 0.00 5.14
89 90 1.033746 TACTCTACTCGGGTTGCCGG 61.034 60.000 0.00 0.00 0.00 6.13
90 91 0.100146 GTACTCTACTCGGGTTGCCG 59.900 60.000 0.00 0.00 0.00 5.69
91 92 1.134560 CTGTACTCTACTCGGGTTGCC 59.865 57.143 0.00 0.00 0.00 4.52
92 93 1.817447 ACTGTACTCTACTCGGGTTGC 59.183 52.381 0.00 0.00 0.00 4.17
93 94 4.235360 CAAACTGTACTCTACTCGGGTTG 58.765 47.826 0.00 0.00 0.00 3.77
94 95 3.305881 GCAAACTGTACTCTACTCGGGTT 60.306 47.826 0.00 0.00 0.00 4.11
95 96 2.230750 GCAAACTGTACTCTACTCGGGT 59.769 50.000 0.00 0.00 0.00 5.28
96 97 2.731341 CGCAAACTGTACTCTACTCGGG 60.731 54.545 0.00 0.00 0.00 5.14
97 98 2.161012 TCGCAAACTGTACTCTACTCGG 59.839 50.000 0.00 0.00 0.00 4.63
98 99 3.418094 CTCGCAAACTGTACTCTACTCG 58.582 50.000 0.00 0.00 0.00 4.18
99 100 3.119779 AGCTCGCAAACTGTACTCTACTC 60.120 47.826 0.00 0.00 0.00 2.59
100 101 2.820787 AGCTCGCAAACTGTACTCTACT 59.179 45.455 0.00 0.00 0.00 2.57
101 102 3.172824 GAGCTCGCAAACTGTACTCTAC 58.827 50.000 0.00 0.00 0.00 2.59
102 103 2.159558 CGAGCTCGCAAACTGTACTCTA 60.160 50.000 25.07 0.00 0.00 2.43
103 104 1.401670 CGAGCTCGCAAACTGTACTCT 60.402 52.381 25.07 0.00 0.00 3.24
104 105 0.985549 CGAGCTCGCAAACTGTACTC 59.014 55.000 25.07 0.00 0.00 2.59
105 106 0.314302 ACGAGCTCGCAAACTGTACT 59.686 50.000 34.83 9.46 44.43 2.73
106 107 0.708918 GACGAGCTCGCAAACTGTAC 59.291 55.000 34.83 11.59 44.43 2.90
107 108 0.728129 CGACGAGCTCGCAAACTGTA 60.728 55.000 34.83 0.00 44.43 2.74
108 109 2.016704 CGACGAGCTCGCAAACTGT 61.017 57.895 34.83 14.67 44.43 3.55
109 110 2.765785 CGACGAGCTCGCAAACTG 59.234 61.111 34.83 14.75 44.43 3.16
116 117 1.794003 CACACTCACGACGAGCTCG 60.794 63.158 33.45 33.45 46.63 5.03
117 118 2.083522 GCACACTCACGACGAGCTC 61.084 63.158 2.73 2.73 46.63 4.09
118 119 2.049985 GCACACTCACGACGAGCT 60.050 61.111 0.00 0.00 46.63 4.09
119 120 3.106407 GGCACACTCACGACGAGC 61.106 66.667 0.00 0.00 46.63 5.03
120 121 1.442857 GAGGCACACTCACGACGAG 60.443 63.158 0.00 0.00 45.85 4.18
121 122 2.643272 GAGGCACACTCACGACGA 59.357 61.111 0.00 0.00 45.85 4.20
128 129 4.394712 CCCGGTGGAGGCACACTC 62.395 72.222 0.00 0.00 45.84 3.51
149 150 4.657824 ACAACTCCGGTGCCGACG 62.658 66.667 12.71 5.00 42.83 5.12
150 151 3.041940 CACAACTCCGGTGCCGAC 61.042 66.667 12.71 0.00 42.83 4.79
151 152 4.308458 CCACAACTCCGGTGCCGA 62.308 66.667 12.71 0.00 42.83 5.54
155 156 3.041940 GACGCCACAACTCCGGTG 61.042 66.667 0.00 0.00 38.79 4.94
156 157 4.657824 CGACGCCACAACTCCGGT 62.658 66.667 0.00 0.00 0.00 5.28
159 160 2.740714 GATGCGACGCCACAACTCC 61.741 63.158 18.69 0.00 0.00 3.85
160 161 2.778679 GATGCGACGCCACAACTC 59.221 61.111 18.69 0.88 0.00 3.01
161 162 3.112075 CGATGCGACGCCACAACT 61.112 61.111 18.69 0.00 0.00 3.16
169 170 3.976375 CACCGATGCGATGCGACG 61.976 66.667 0.00 0.00 0.00 5.12
170 171 4.285149 GCACCGATGCGATGCGAC 62.285 66.667 0.00 0.00 43.33 5.19
193 194 3.449227 TAGCTCCCTGTGGCGACG 61.449 66.667 0.00 0.00 0.00 5.12
194 195 2.167398 TTGTAGCTCCCTGTGGCGAC 62.167 60.000 0.00 0.00 35.29 5.19
195 196 1.911269 TTGTAGCTCCCTGTGGCGA 60.911 57.895 0.00 0.00 0.00 5.54
196 197 1.741770 GTTGTAGCTCCCTGTGGCG 60.742 63.158 0.00 0.00 0.00 5.69
197 198 1.377333 GGTTGTAGCTCCCTGTGGC 60.377 63.158 0.00 0.00 0.00 5.01
198 199 0.321653 GTGGTTGTAGCTCCCTGTGG 60.322 60.000 0.00 0.00 0.00 4.17
199 200 0.670546 CGTGGTTGTAGCTCCCTGTG 60.671 60.000 0.00 0.00 0.00 3.66
200 201 1.671742 CGTGGTTGTAGCTCCCTGT 59.328 57.895 0.00 0.00 0.00 4.00
201 202 1.079127 CCGTGGTTGTAGCTCCCTG 60.079 63.158 0.00 0.00 0.00 4.45
202 203 2.291043 CCCGTGGTTGTAGCTCCCT 61.291 63.158 0.00 0.00 0.00 4.20
203 204 2.267961 CCCGTGGTTGTAGCTCCC 59.732 66.667 0.00 0.00 0.00 4.30
204 205 2.436115 GCCCGTGGTTGTAGCTCC 60.436 66.667 0.00 0.00 0.00 4.70
205 206 2.033194 GTGCCCGTGGTTGTAGCTC 61.033 63.158 0.00 0.00 0.00 4.09
206 207 2.032071 GTGCCCGTGGTTGTAGCT 59.968 61.111 0.00 0.00 0.00 3.32
207 208 2.281208 TGTGCCCGTGGTTGTAGC 60.281 61.111 0.00 0.00 0.00 3.58
208 209 0.605319 ATGTGTGCCCGTGGTTGTAG 60.605 55.000 0.00 0.00 0.00 2.74
209 210 0.179015 AATGTGTGCCCGTGGTTGTA 60.179 50.000 0.00 0.00 0.00 2.41
210 211 1.454847 AATGTGTGCCCGTGGTTGT 60.455 52.632 0.00 0.00 0.00 3.32
211 212 1.007502 CAATGTGTGCCCGTGGTTG 60.008 57.895 0.00 0.00 0.00 3.77
212 213 0.539438 ATCAATGTGTGCCCGTGGTT 60.539 50.000 0.00 0.00 0.00 3.67
213 214 1.074775 ATCAATGTGTGCCCGTGGT 59.925 52.632 0.00 0.00 0.00 4.16
214 215 1.507630 CATCAATGTGTGCCCGTGG 59.492 57.895 0.00 0.00 0.00 4.94
215 216 1.153978 GCATCAATGTGTGCCCGTG 60.154 57.895 2.85 0.00 35.35 4.94
216 217 1.603171 TGCATCAATGTGTGCCCGT 60.603 52.632 9.89 0.00 40.56 5.28
217 218 1.153978 GTGCATCAATGTGTGCCCG 60.154 57.895 9.89 0.00 40.56 6.13
218 219 0.108992 CAGTGCATCAATGTGTGCCC 60.109 55.000 9.89 0.70 40.56 5.36
219 220 0.108992 CCAGTGCATCAATGTGTGCC 60.109 55.000 9.89 3.57 40.56 5.01
220 221 0.734942 GCCAGTGCATCAATGTGTGC 60.735 55.000 0.00 6.46 41.61 4.57
221 222 0.455464 CGCCAGTGCATCAATGTGTG 60.455 55.000 0.00 0.00 37.32 3.82
222 223 0.890542 ACGCCAGTGCATCAATGTGT 60.891 50.000 0.00 0.00 37.32 3.72
223 224 1.063027 CTACGCCAGTGCATCAATGTG 59.937 52.381 0.00 0.00 37.32 3.21
224 225 1.372582 CTACGCCAGTGCATCAATGT 58.627 50.000 0.00 0.00 37.32 2.71
225 226 0.028505 GCTACGCCAGTGCATCAATG 59.971 55.000 0.00 0.00 37.32 2.82
226 227 1.431488 CGCTACGCCAGTGCATCAAT 61.431 55.000 0.00 0.00 37.32 2.57
227 228 2.100031 CGCTACGCCAGTGCATCAA 61.100 57.895 0.00 0.00 37.32 2.57
228 229 2.509111 CGCTACGCCAGTGCATCA 60.509 61.111 0.00 0.00 37.32 3.07
229 230 2.978452 ATCCGCTACGCCAGTGCATC 62.978 60.000 0.00 0.00 37.32 3.91
230 231 3.094062 ATCCGCTACGCCAGTGCAT 62.094 57.895 0.00 0.00 37.32 3.96
231 232 3.770040 ATCCGCTACGCCAGTGCA 61.770 61.111 0.00 0.00 37.32 4.57
232 233 3.264897 CATCCGCTACGCCAGTGC 61.265 66.667 0.00 0.00 33.09 4.40
233 234 1.589993 CTCATCCGCTACGCCAGTG 60.590 63.158 0.00 0.00 34.31 3.66
234 235 1.320344 TTCTCATCCGCTACGCCAGT 61.320 55.000 0.00 0.00 0.00 4.00
235 236 0.179111 TTTCTCATCCGCTACGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
236 237 0.459585 GTTTCTCATCCGCTACGCCA 60.460 55.000 0.00 0.00 0.00 5.69
237 238 1.480219 CGTTTCTCATCCGCTACGCC 61.480 60.000 0.00 0.00 0.00 5.68
238 239 1.917921 CGTTTCTCATCCGCTACGC 59.082 57.895 0.00 0.00 0.00 4.42
239 240 1.917921 GCGTTTCTCATCCGCTACG 59.082 57.895 0.00 0.00 43.81 3.51
244 245 0.173481 TCTCCTGCGTTTCTCATCCG 59.827 55.000 0.00 0.00 0.00 4.18
245 246 1.646189 GTCTCCTGCGTTTCTCATCC 58.354 55.000 0.00 0.00 0.00 3.51
246 247 1.135373 TCGTCTCCTGCGTTTCTCATC 60.135 52.381 0.00 0.00 0.00 2.92
247 248 0.888619 TCGTCTCCTGCGTTTCTCAT 59.111 50.000 0.00 0.00 0.00 2.90
248 249 0.039437 GTCGTCTCCTGCGTTTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
249 250 1.066114 CGTCGTCTCCTGCGTTTCTC 61.066 60.000 0.00 0.00 0.00 2.87
250 251 1.081376 CGTCGTCTCCTGCGTTTCT 60.081 57.895 0.00 0.00 0.00 2.52
251 252 2.087009 CCGTCGTCTCCTGCGTTTC 61.087 63.158 0.00 0.00 0.00 2.78
252 253 2.049433 CCGTCGTCTCCTGCGTTT 60.049 61.111 0.00 0.00 0.00 3.60
253 254 3.292936 ACCGTCGTCTCCTGCGTT 61.293 61.111 0.00 0.00 0.00 4.84
254 255 4.039357 CACCGTCGTCTCCTGCGT 62.039 66.667 0.00 0.00 0.00 5.24
255 256 4.778415 CCACCGTCGTCTCCTGCG 62.778 72.222 0.00 0.00 0.00 5.18
257 258 4.778415 CGCCACCGTCGTCTCCTG 62.778 72.222 0.00 0.00 0.00 3.86
309 310 3.818787 CATGTTGCTGCCCTCGCC 61.819 66.667 0.00 0.00 0.00 5.54
310 311 4.487412 GCATGTTGCTGCCCTCGC 62.487 66.667 0.00 0.00 40.96 5.03
311 312 4.170062 CGCATGTTGCTGCCCTCG 62.170 66.667 0.00 0.00 42.25 4.63
312 313 2.747460 TCGCATGTTGCTGCCCTC 60.747 61.111 0.00 0.00 42.25 4.30
313 314 2.749044 CTCGCATGTTGCTGCCCT 60.749 61.111 0.00 0.00 42.25 5.19
314 315 2.747460 TCTCGCATGTTGCTGCCC 60.747 61.111 0.00 0.00 42.25 5.36
315 316 2.482374 GTCTCGCATGTTGCTGCC 59.518 61.111 0.00 0.00 42.25 4.85
316 317 1.900585 TTCGTCTCGCATGTTGCTGC 61.901 55.000 0.00 0.00 42.25 5.25
317 318 0.723414 ATTCGTCTCGCATGTTGCTG 59.277 50.000 0.00 0.00 42.25 4.41
318 319 1.002366 GATTCGTCTCGCATGTTGCT 58.998 50.000 0.00 0.00 42.25 3.91
319 320 0.721154 TGATTCGTCTCGCATGTTGC 59.279 50.000 0.00 0.00 40.69 4.17
320 321 1.325640 CCTGATTCGTCTCGCATGTTG 59.674 52.381 0.00 0.00 0.00 3.33
321 322 1.645034 CCTGATTCGTCTCGCATGTT 58.355 50.000 0.00 0.00 0.00 2.71
322 323 0.179100 CCCTGATTCGTCTCGCATGT 60.179 55.000 0.00 0.00 0.00 3.21
323 324 0.877649 CCCCTGATTCGTCTCGCATG 60.878 60.000 0.00 0.00 0.00 4.06
324 325 1.443407 CCCCTGATTCGTCTCGCAT 59.557 57.895 0.00 0.00 0.00 4.73
325 326 2.721167 CCCCCTGATTCGTCTCGCA 61.721 63.158 0.00 0.00 0.00 5.10
326 327 2.107141 CCCCCTGATTCGTCTCGC 59.893 66.667 0.00 0.00 0.00 5.03
327 328 2.107141 GCCCCCTGATTCGTCTCG 59.893 66.667 0.00 0.00 0.00 4.04
328 329 2.107141 CGCCCCCTGATTCGTCTC 59.893 66.667 0.00 0.00 0.00 3.36
329 330 3.470888 CCGCCCCCTGATTCGTCT 61.471 66.667 0.00 0.00 0.00 4.18
330 331 3.782443 ACCGCCCCCTGATTCGTC 61.782 66.667 0.00 0.00 0.00 4.20
331 332 4.096003 CACCGCCCCCTGATTCGT 62.096 66.667 0.00 0.00 0.00 3.85
333 334 3.645268 AAGCACCGCCCCCTGATTC 62.645 63.158 0.00 0.00 0.00 2.52
334 335 3.645268 GAAGCACCGCCCCCTGATT 62.645 63.158 0.00 0.00 0.00 2.57
335 336 4.115199 GAAGCACCGCCCCCTGAT 62.115 66.667 0.00 0.00 0.00 2.90
349 350 4.473520 ACATGCCCCGCCTCGAAG 62.474 66.667 0.00 0.00 0.00 3.79
350 351 4.467084 GACATGCCCCGCCTCGAA 62.467 66.667 0.00 0.00 0.00 3.71
358 359 2.869503 ATTGACGACCGACATGCCCC 62.870 60.000 0.00 0.00 0.00 5.80
359 360 1.449601 ATTGACGACCGACATGCCC 60.450 57.895 0.00 0.00 0.00 5.36
360 361 1.705337 CCATTGACGACCGACATGCC 61.705 60.000 0.00 0.00 0.00 4.40
361 362 1.715585 CCATTGACGACCGACATGC 59.284 57.895 0.00 0.00 0.00 4.06
362 363 1.018752 TGCCATTGACGACCGACATG 61.019 55.000 0.00 0.00 0.00 3.21
363 364 0.740868 CTGCCATTGACGACCGACAT 60.741 55.000 0.00 0.00 0.00 3.06
364 365 1.374125 CTGCCATTGACGACCGACA 60.374 57.895 0.00 0.00 0.00 4.35
365 366 0.949105 AACTGCCATTGACGACCGAC 60.949 55.000 0.00 0.00 0.00 4.79
366 367 0.948623 CAACTGCCATTGACGACCGA 60.949 55.000 0.00 0.00 0.00 4.69
367 368 1.497278 CAACTGCCATTGACGACCG 59.503 57.895 0.00 0.00 0.00 4.79
368 369 0.605319 TCCAACTGCCATTGACGACC 60.605 55.000 0.00 0.00 0.00 4.79
369 370 0.798776 CTCCAACTGCCATTGACGAC 59.201 55.000 0.00 0.00 0.00 4.34
370 371 0.396435 ACTCCAACTGCCATTGACGA 59.604 50.000 0.00 0.00 0.00 4.20
371 372 1.238439 AACTCCAACTGCCATTGACG 58.762 50.000 0.00 0.00 0.00 4.35
372 373 3.733443 AAAACTCCAACTGCCATTGAC 57.267 42.857 0.00 0.00 0.00 3.18
373 374 3.960102 AGAAAAACTCCAACTGCCATTGA 59.040 39.130 0.00 0.00 0.00 2.57
374 375 4.301628 GAGAAAAACTCCAACTGCCATTG 58.698 43.478 0.00 0.00 39.53 2.82
375 376 4.590850 GAGAAAAACTCCAACTGCCATT 57.409 40.909 0.00 0.00 39.53 3.16
391 392 2.225491 CGACGCCATTTTCTTGGAGAAA 59.775 45.455 1.13 0.00 42.00 2.52
392 393 1.804151 CGACGCCATTTTCTTGGAGAA 59.196 47.619 1.13 0.00 38.71 2.87
393 394 1.438651 CGACGCCATTTTCTTGGAGA 58.561 50.000 1.13 0.00 38.71 3.71
394 395 0.447801 CCGACGCCATTTTCTTGGAG 59.552 55.000 0.00 0.00 41.79 3.86
395 396 0.958382 CCCGACGCCATTTTCTTGGA 60.958 55.000 0.00 0.00 39.25 3.53
396 397 1.506262 CCCGACGCCATTTTCTTGG 59.494 57.895 0.00 0.00 39.94 3.61
397 398 0.958382 TCCCCGACGCCATTTTCTTG 60.958 55.000 0.00 0.00 0.00 3.02
398 399 0.676782 CTCCCCGACGCCATTTTCTT 60.677 55.000 0.00 0.00 0.00 2.52
399 400 1.078426 CTCCCCGACGCCATTTTCT 60.078 57.895 0.00 0.00 0.00 2.52
400 401 2.112815 CCTCCCCGACGCCATTTTC 61.113 63.158 0.00 0.00 0.00 2.29
401 402 2.045340 CCTCCCCGACGCCATTTT 60.045 61.111 0.00 0.00 0.00 1.82
402 403 2.536997 CTTCCTCCCCGACGCCATTT 62.537 60.000 0.00 0.00 0.00 2.32
403 404 3.006728 TTCCTCCCCGACGCCATT 61.007 61.111 0.00 0.00 0.00 3.16
404 405 3.470888 CTTCCTCCCCGACGCCAT 61.471 66.667 0.00 0.00 0.00 4.40
405 406 4.689549 TCTTCCTCCCCGACGCCA 62.690 66.667 0.00 0.00 0.00 5.69
406 407 3.839432 CTCTTCCTCCCCGACGCC 61.839 72.222 0.00 0.00 0.00 5.68
407 408 1.885163 TTTCTCTTCCTCCCCGACGC 61.885 60.000 0.00 0.00 0.00 5.19
408 409 0.108756 GTTTCTCTTCCTCCCCGACG 60.109 60.000 0.00 0.00 0.00 5.12
409 410 0.974383 TGTTTCTCTTCCTCCCCGAC 59.026 55.000 0.00 0.00 0.00 4.79
410 411 1.203137 TCTGTTTCTCTTCCTCCCCGA 60.203 52.381 0.00 0.00 0.00 5.14
411 412 1.267121 TCTGTTTCTCTTCCTCCCCG 58.733 55.000 0.00 0.00 0.00 5.73
412 413 2.159028 CGATCTGTTTCTCTTCCTCCCC 60.159 54.545 0.00 0.00 0.00 4.81
413 414 2.498078 ACGATCTGTTTCTCTTCCTCCC 59.502 50.000 0.00 0.00 0.00 4.30
414 415 3.516615 CACGATCTGTTTCTCTTCCTCC 58.483 50.000 0.00 0.00 0.00 4.30
415 416 2.926838 GCACGATCTGTTTCTCTTCCTC 59.073 50.000 0.00 0.00 0.00 3.71
416 417 2.672478 CGCACGATCTGTTTCTCTTCCT 60.672 50.000 0.00 0.00 0.00 3.36
417 418 1.656095 CGCACGATCTGTTTCTCTTCC 59.344 52.381 0.00 0.00 0.00 3.46
418 419 1.656095 CCGCACGATCTGTTTCTCTTC 59.344 52.381 0.00 0.00 0.00 2.87
419 420 1.000955 ACCGCACGATCTGTTTCTCTT 59.999 47.619 0.00 0.00 0.00 2.85
420 421 0.603569 ACCGCACGATCTGTTTCTCT 59.396 50.000 0.00 0.00 0.00 3.10
421 422 0.716108 CACCGCACGATCTGTTTCTC 59.284 55.000 0.00 0.00 0.00 2.87
422 423 0.033504 ACACCGCACGATCTGTTTCT 59.966 50.000 0.00 0.00 0.00 2.52
423 424 0.163788 CACACCGCACGATCTGTTTC 59.836 55.000 0.00 0.00 0.00 2.78
424 425 0.531974 ACACACCGCACGATCTGTTT 60.532 50.000 0.00 0.00 0.00 2.83
425 426 0.315886 TACACACCGCACGATCTGTT 59.684 50.000 0.00 0.00 0.00 3.16
426 427 0.388134 GTACACACCGCACGATCTGT 60.388 55.000 0.00 0.00 0.00 3.41
427 428 1.403225 CGTACACACCGCACGATCTG 61.403 60.000 0.00 0.00 37.89 2.90
428 429 1.154093 CGTACACACCGCACGATCT 60.154 57.895 0.00 0.00 37.89 2.75
429 430 2.156446 CCGTACACACCGCACGATC 61.156 63.158 0.00 0.00 37.89 3.69
430 431 2.126228 CCGTACACACCGCACGAT 60.126 61.111 0.00 0.00 37.89 3.73
431 432 4.345962 CCCGTACACACCGCACGA 62.346 66.667 0.00 0.00 37.89 4.35
436 437 3.408020 CAACGCCCGTACACACCG 61.408 66.667 0.00 0.00 0.00 4.94
437 438 2.029369 TCAACGCCCGTACACACC 59.971 61.111 0.00 0.00 0.00 4.16
438 439 2.312436 GGTCAACGCCCGTACACAC 61.312 63.158 0.00 0.00 0.00 3.82
439 440 2.029369 GGTCAACGCCCGTACACA 59.971 61.111 0.00 0.00 0.00 3.72
440 441 2.739671 GGGTCAACGCCCGTACAC 60.740 66.667 0.00 0.00 39.17 2.90
447 448 1.737793 CAATTCAGTAGGGTCAACGCC 59.262 52.381 0.00 0.00 0.00 5.68
448 449 1.737793 CCAATTCAGTAGGGTCAACGC 59.262 52.381 0.00 0.00 0.00 4.84
449 450 2.356135 CCCAATTCAGTAGGGTCAACG 58.644 52.381 0.00 0.00 37.81 4.10
456 457 1.683011 CCAGCCACCCAATTCAGTAGG 60.683 57.143 0.00 0.00 0.00 3.18
457 458 1.755179 CCAGCCACCCAATTCAGTAG 58.245 55.000 0.00 0.00 0.00 2.57
458 459 0.323360 GCCAGCCACCCAATTCAGTA 60.323 55.000 0.00 0.00 0.00 2.74
459 460 1.607467 GCCAGCCACCCAATTCAGT 60.607 57.895 0.00 0.00 0.00 3.41
460 461 0.974010 ATGCCAGCCACCCAATTCAG 60.974 55.000 0.00 0.00 0.00 3.02
461 462 1.078891 ATGCCAGCCACCCAATTCA 59.921 52.632 0.00 0.00 0.00 2.57
462 463 1.518774 CATGCCAGCCACCCAATTC 59.481 57.895 0.00 0.00 0.00 2.17
463 464 2.662070 GCATGCCAGCCACCCAATT 61.662 57.895 6.36 0.00 0.00 2.32
464 465 3.078836 GCATGCCAGCCACCCAAT 61.079 61.111 6.36 0.00 0.00 3.16
469 470 3.117175 GATGTCGCATGCCAGCCAC 62.117 63.158 13.15 1.87 0.00 5.01
470 471 2.825387 GATGTCGCATGCCAGCCA 60.825 61.111 13.15 3.87 0.00 4.75
471 472 3.945434 CGATGTCGCATGCCAGCC 61.945 66.667 13.15 1.05 0.00 4.85
472 473 3.945434 CCGATGTCGCATGCCAGC 61.945 66.667 13.15 7.14 38.18 4.85
473 474 3.945434 GCCGATGTCGCATGCCAG 61.945 66.667 13.15 0.00 38.18 4.85
491 492 2.311688 TAAGAAGGGCAGCGCTAGGC 62.312 60.000 10.99 16.98 44.05 3.93
492 493 0.178068 TTAAGAAGGGCAGCGCTAGG 59.822 55.000 10.99 0.00 0.00 3.02
493 494 2.024176 TTTAAGAAGGGCAGCGCTAG 57.976 50.000 10.99 5.98 0.00 3.42
494 495 2.483014 TTTTAAGAAGGGCAGCGCTA 57.517 45.000 10.99 0.00 0.00 4.26
495 496 1.616159 TTTTTAAGAAGGGCAGCGCT 58.384 45.000 2.64 2.64 0.00 5.92
519 520 8.606040 TCAATTCAAAATGGACAGGAAAATTC 57.394 30.769 0.00 0.00 0.00 2.17
520 521 8.839343 GTTCAATTCAAAATGGACAGGAAAATT 58.161 29.630 0.00 0.00 0.00 1.82
521 522 8.212995 AGTTCAATTCAAAATGGACAGGAAAAT 58.787 29.630 0.00 0.00 0.00 1.82
522 523 7.495279 CAGTTCAATTCAAAATGGACAGGAAAA 59.505 33.333 0.00 0.00 0.00 2.29
523 524 6.985645 CAGTTCAATTCAAAATGGACAGGAAA 59.014 34.615 0.00 0.00 0.00 3.13
524 525 6.323482 TCAGTTCAATTCAAAATGGACAGGAA 59.677 34.615 0.00 0.00 0.00 3.36
525 526 5.832595 TCAGTTCAATTCAAAATGGACAGGA 59.167 36.000 0.00 0.00 0.00 3.86
526 527 6.016024 TCTCAGTTCAATTCAAAATGGACAGG 60.016 38.462 0.00 0.00 0.00 4.00
527 528 6.973843 TCTCAGTTCAATTCAAAATGGACAG 58.026 36.000 0.00 0.00 0.00 3.51
528 529 6.957920 TCTCAGTTCAATTCAAAATGGACA 57.042 33.333 0.00 0.00 0.00 4.02
579 593 3.325201 AACCCGCCGATCCCAAGTC 62.325 63.158 0.00 0.00 0.00 3.01
604 620 3.945921 TGAGTTCCGGGAGCGATATATAG 59.054 47.826 0.00 0.00 0.00 1.31
612 1992 0.447801 CAAAATGAGTTCCGGGAGCG 59.552 55.000 0.00 0.00 0.00 5.03
721 2435 6.062258 TCAGGGATTAGGGTTTAGACTTTG 57.938 41.667 0.00 0.00 0.00 2.77
966 3051 1.153289 CACCAAGATGGGGCTCTCG 60.153 63.158 0.87 0.00 43.37 4.04
1134 3237 1.067295 ACTCCATTTCCACCAGCTCA 58.933 50.000 0.00 0.00 0.00 4.26
1171 3277 1.819632 CCGGGCCTCCAAGAAATCG 60.820 63.158 0.84 0.00 0.00 3.34
1172 3278 2.121538 GCCGGGCCTCCAAGAAATC 61.122 63.158 8.12 0.00 0.00 2.17
1173 3279 2.043953 GCCGGGCCTCCAAGAAAT 60.044 61.111 8.12 0.00 0.00 2.17
1256 3368 3.482156 TGCACTCTGCTTCTTCTTCTT 57.518 42.857 0.00 0.00 45.31 2.52
1257 3369 3.401182 CTTGCACTCTGCTTCTTCTTCT 58.599 45.455 0.00 0.00 45.31 2.85
1258 3370 2.483491 CCTTGCACTCTGCTTCTTCTTC 59.517 50.000 0.00 0.00 45.31 2.87
1272 3384 1.028868 GCACCAGGATCTCCTTGCAC 61.029 60.000 15.06 0.00 46.09 4.57
1273 3385 1.203441 AGCACCAGGATCTCCTTGCA 61.203 55.000 19.88 0.00 46.96 4.08
1426 3538 0.976073 CCGGGGTATATCAGCCGGAT 60.976 60.000 12.97 0.00 46.54 4.18
1635 3816 1.452651 CAGCTCCATGCCGGTGAAT 60.453 57.895 1.90 0.00 44.23 2.57
1672 3856 0.315059 GTGTTTATCATGGTCGCGCG 60.315 55.000 26.76 26.76 0.00 6.86
1736 3947 4.083862 ACCCTCCTTCGCTTCGCC 62.084 66.667 0.00 0.00 0.00 5.54
1767 3978 0.337428 AAGCAGATGGGGCAATCCTT 59.663 50.000 0.00 0.00 35.33 3.36
1862 4073 1.444553 CACGAGGACGCTCTCCAAC 60.445 63.158 0.00 0.00 42.46 3.77
1942 4222 5.639506 CAGCTAGTTGCACATTTGTACTACT 59.360 40.000 0.00 4.01 45.94 2.57
1971 4256 7.656948 TCCTTCAGCAAAACAAATAATTTCTGG 59.343 33.333 0.00 0.00 0.00 3.86
1999 4288 4.016444 GACCATGAAACCCAAGAATGCTA 58.984 43.478 0.00 0.00 0.00 3.49
2115 5938 8.649841 CCAAAACTAGTTTGTGCATAATGATTG 58.350 33.333 21.22 10.50 44.46 2.67
2135 6013 6.018507 GCTGATGCATATGAATTTCCCAAAAC 60.019 38.462 6.97 0.00 39.41 2.43
2351 6551 0.824109 CGCACTATGACCTCTGGGAA 59.176 55.000 0.00 0.00 36.25 3.97
2642 7142 2.159043 CGCAAGCAAGGAGGAGATAGAA 60.159 50.000 0.00 0.00 0.00 2.10
2781 7281 4.206609 GGACATAACGCGAAACTACAGATC 59.793 45.833 15.93 0.00 0.00 2.75
2878 7378 1.648467 GAATGGCACCGCTGAGGAAC 61.648 60.000 3.87 0.00 45.00 3.62


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

AutoCloner maintained by Alex Coulton.