Multiple sequence alignment - TraesCS7A01G057700

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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 TraesCS7A01G057700 chr7A 100.000 1743 0 0 936 2678 27901271 27903013 0.000000e+00 3219
1 TraesCS7A01G057700 chr7A 100.000 313 0 0 1 313 27900336 27900648 1.790000e-161 579
2 TraesCS7A01G057700 chr7A 82.390 636 74 23 1052 1683 27905351 27904750 1.100000e-143 520
3 TraesCS7A01G057700 chr7D 88.379 1024 78 22 962 1973 27453104 27454098 0.000000e+00 1194
4 TraesCS7A01G057700 chr7D 83.566 645 64 22 1046 1681 27468174 27467563 1.390000e-157 566
5 TraesCS7A01G057700 chr7D 81.195 686 85 28 1047 1724 27471405 27470756 1.840000e-141 512
6 TraesCS7A01G057700 chr7D 78.336 697 55 43 2032 2658 27454284 27454954 1.960000e-96 363
7 TraesCS7A01G057700 chr4A 86.517 979 73 24 1012 1966 703932147 703933090 0.000000e+00 1022
8 TraesCS7A01G057700 chr4A 81.674 693 84 30 1046 1724 703941964 703941301 1.090000e-148 536
9 TraesCS7A01G057700 chr4A 82.527 641 74 20 1048 1681 704153966 704153357 1.830000e-146 529
10 TraesCS7A01G057700 chr4A 87.083 240 16 11 2260 2491 703933722 703933954 9.510000e-65 257
11 TraesCS7A01G057700 chr4B 82.963 540 52 17 1437 1973 603047935 603048437 4.070000e-123 451
12 TraesCS7A01G057700 chr2D 89.014 355 32 4 1049 1402 7228077 7227729 1.470000e-117 433
13 TraesCS7A01G057700 chr2B 84.507 355 39 5 1049 1402 1706433 1706772 1.190000e-88 337
14 TraesCS7A01G057700 chr3B 88.318 214 16 3 1421 1631 743337926 743338133 5.720000e-62 248


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 TraesCS7A01G057700 chr7A 27900336 27903013 2677 False 1899.0 3219 100.0000 1 2678 2 chr7A.!!$F1 2677
1 TraesCS7A01G057700 chr7A 27904750 27905351 601 True 520.0 520 82.3900 1052 1683 1 chr7A.!!$R1 631
2 TraesCS7A01G057700 chr7D 27453104 27454954 1850 False 778.5 1194 83.3575 962 2658 2 chr7D.!!$F1 1696
3 TraesCS7A01G057700 chr7D 27467563 27471405 3842 True 539.0 566 82.3805 1046 1724 2 chr7D.!!$R1 678
4 TraesCS7A01G057700 chr4A 703932147 703933954 1807 False 639.5 1022 86.8000 1012 2491 2 chr4A.!!$F1 1479
5 TraesCS7A01G057700 chr4A 703941301 703941964 663 True 536.0 536 81.6740 1046 1724 1 chr4A.!!$R1 678
6 TraesCS7A01G057700 chr4A 704153357 704153966 609 True 529.0 529 82.5270 1048 1681 1 chr4A.!!$R2 633
7 TraesCS7A01G057700 chr4B 603047935 603048437 502 False 451.0 451 82.9630 1437 1973 1 chr4B.!!$F1 536

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
309 310 0.322546 ACAGGACCGGAAAAGGCATC 60.323 55.0 9.46 0.00 33.69 3.91 F
310 311 1.032114 CAGGACCGGAAAAGGCATCC 61.032 60.0 9.46 0.82 33.69 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1528 0.041488 GCATCGGGTAGTCGTCGTAG 60.041 60.0 0.0 0.0 0.00 3.51 R
2168 5794 0.098376 CCGTGGAGTAGCAGTACGTC 59.902 60.0 0.0 0.0 33.97 4.34 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
27 28 8.779354 AGAGACCTCAATGTAACTTTTATGAC 57.221 34.615 0.00 0.00 0.00 3.06
28 29 8.375506 AGAGACCTCAATGTAACTTTTATGACA 58.624 33.333 0.00 0.00 0.00 3.58
29 30 9.167311 GAGACCTCAATGTAACTTTTATGACAT 57.833 33.333 0.00 0.00 34.00 3.06
30 31 9.520515 AGACCTCAATGTAACTTTTATGACATT 57.479 29.630 0.00 0.00 41.92 2.71
38 39 8.755696 TGTAACTTTTATGACATTTTGGATGC 57.244 30.769 0.00 0.00 0.00 3.91
39 40 8.584157 TGTAACTTTTATGACATTTTGGATGCT 58.416 29.630 0.00 0.00 0.00 3.79
40 41 9.423061 GTAACTTTTATGACATTTTGGATGCTT 57.577 29.630 0.00 0.00 0.00 3.91
41 42 8.907222 AACTTTTATGACATTTTGGATGCTTT 57.093 26.923 0.00 0.00 0.00 3.51
42 43 9.995003 AACTTTTATGACATTTTGGATGCTTTA 57.005 25.926 0.00 0.00 0.00 1.85
49 50 8.984891 TGACATTTTGGATGCTTTATTTACTG 57.015 30.769 0.00 0.00 0.00 2.74
50 51 7.545265 TGACATTTTGGATGCTTTATTTACTGC 59.455 33.333 0.00 0.00 0.00 4.40
51 52 7.614494 ACATTTTGGATGCTTTATTTACTGCT 58.386 30.769 0.00 0.00 0.00 4.24
52 53 8.748412 ACATTTTGGATGCTTTATTTACTGCTA 58.252 29.630 0.00 0.00 0.00 3.49
53 54 9.754382 CATTTTGGATGCTTTATTTACTGCTAT 57.246 29.630 0.00 0.00 0.00 2.97
54 55 9.754382 ATTTTGGATGCTTTATTTACTGCTATG 57.246 29.630 0.00 0.00 0.00 2.23
55 56 8.518430 TTTGGATGCTTTATTTACTGCTATGA 57.482 30.769 0.00 0.00 0.00 2.15
56 57 8.696043 TTGGATGCTTTATTTACTGCTATGAT 57.304 30.769 0.00 0.00 0.00 2.45
57 58 8.102800 TGGATGCTTTATTTACTGCTATGATG 57.897 34.615 0.00 0.00 0.00 3.07
58 59 7.938490 TGGATGCTTTATTTACTGCTATGATGA 59.062 33.333 0.00 0.00 0.00 2.92
59 60 8.786898 GGATGCTTTATTTACTGCTATGATGAA 58.213 33.333 0.00 0.00 0.00 2.57
62 63 9.565090 TGCTTTATTTACTGCTATGATGAATCT 57.435 29.630 0.00 0.00 0.00 2.40
69 70 9.453572 TTTACTGCTATGATGAATCTTCTTTGT 57.546 29.630 0.00 0.00 0.00 2.83
72 73 9.624373 ACTGCTATGATGAATCTTCTTTGTATT 57.376 29.630 0.00 0.00 0.00 1.89
89 90 9.702253 TCTTTGTATTAGTAGATCCAAGTCTCT 57.298 33.333 0.00 0.00 0.00 3.10
92 93 8.155821 TGTATTAGTAGATCCAAGTCTCTTCG 57.844 38.462 0.00 0.00 0.00 3.79
93 94 5.502153 TTAGTAGATCCAAGTCTCTTCGC 57.498 43.478 0.00 0.00 0.00 4.70
94 95 3.357203 AGTAGATCCAAGTCTCTTCGCA 58.643 45.455 0.00 0.00 0.00 5.10
95 96 3.957497 AGTAGATCCAAGTCTCTTCGCAT 59.043 43.478 0.00 0.00 0.00 4.73
96 97 3.451141 AGATCCAAGTCTCTTCGCATC 57.549 47.619 0.00 0.00 0.00 3.91
97 98 3.030291 AGATCCAAGTCTCTTCGCATCT 58.970 45.455 0.00 0.00 0.00 2.90
98 99 4.211125 AGATCCAAGTCTCTTCGCATCTA 58.789 43.478 0.00 0.00 0.00 1.98
99 100 4.832266 AGATCCAAGTCTCTTCGCATCTAT 59.168 41.667 0.00 0.00 0.00 1.98
100 101 6.007076 AGATCCAAGTCTCTTCGCATCTATA 58.993 40.000 0.00 0.00 0.00 1.31
101 102 6.491745 AGATCCAAGTCTCTTCGCATCTATAA 59.508 38.462 0.00 0.00 0.00 0.98
102 103 5.833082 TCCAAGTCTCTTCGCATCTATAAC 58.167 41.667 0.00 0.00 0.00 1.89
103 104 5.359860 TCCAAGTCTCTTCGCATCTATAACA 59.640 40.000 0.00 0.00 0.00 2.41
104 105 6.042777 CCAAGTCTCTTCGCATCTATAACAA 58.957 40.000 0.00 0.00 0.00 2.83
105 106 6.703607 CCAAGTCTCTTCGCATCTATAACAAT 59.296 38.462 0.00 0.00 0.00 2.71
106 107 7.225538 CCAAGTCTCTTCGCATCTATAACAATT 59.774 37.037 0.00 0.00 0.00 2.32
107 108 9.249457 CAAGTCTCTTCGCATCTATAACAATTA 57.751 33.333 0.00 0.00 0.00 1.40
108 109 8.804688 AGTCTCTTCGCATCTATAACAATTAC 57.195 34.615 0.00 0.00 0.00 1.89
109 110 7.591795 AGTCTCTTCGCATCTATAACAATTACG 59.408 37.037 0.00 0.00 0.00 3.18
110 111 7.590322 GTCTCTTCGCATCTATAACAATTACGA 59.410 37.037 0.00 0.00 0.00 3.43
111 112 7.590322 TCTCTTCGCATCTATAACAATTACGAC 59.410 37.037 0.00 0.00 0.00 4.34
112 113 7.423199 TCTTCGCATCTATAACAATTACGACT 58.577 34.615 0.00 0.00 0.00 4.18
113 114 6.986424 TCGCATCTATAACAATTACGACTG 57.014 37.500 0.00 0.00 0.00 3.51
114 115 5.918576 TCGCATCTATAACAATTACGACTGG 59.081 40.000 0.00 0.00 0.00 4.00
115 116 5.690409 CGCATCTATAACAATTACGACTGGT 59.310 40.000 0.00 0.00 0.00 4.00
116 117 6.200286 CGCATCTATAACAATTACGACTGGTT 59.800 38.462 0.00 0.00 0.00 3.67
117 118 7.254319 CGCATCTATAACAATTACGACTGGTTT 60.254 37.037 0.00 0.00 0.00 3.27
118 119 8.395633 GCATCTATAACAATTACGACTGGTTTT 58.604 33.333 0.00 0.00 0.00 2.43
160 161 9.585099 TCATATTACCGTATTTTTAACGTGTCT 57.415 29.630 0.00 0.00 38.67 3.41
164 165 9.807649 ATTACCGTATTTTTAACGTGTCTAGAT 57.192 29.630 0.00 0.00 38.67 1.98
166 167 8.620533 ACCGTATTTTTAACGTGTCTAGATAC 57.379 34.615 9.46 9.46 38.67 2.24
167 168 8.243426 ACCGTATTTTTAACGTGTCTAGATACA 58.757 33.333 18.39 0.27 38.67 2.29
168 169 9.241317 CCGTATTTTTAACGTGTCTAGATACAT 57.759 33.333 18.39 9.64 38.67 2.29
172 173 9.871238 ATTTTTAACGTGTCTAGATACATCTGT 57.129 29.630 18.39 6.30 37.76 3.41
219 220 9.813826 AAGATAAATAATTCAGAACATAGGGGG 57.186 33.333 0.00 0.00 0.00 5.40
220 221 7.890655 AGATAAATAATTCAGAACATAGGGGGC 59.109 37.037 0.00 0.00 0.00 5.80
221 222 5.402054 AATAATTCAGAACATAGGGGGCA 57.598 39.130 0.00 0.00 0.00 5.36
222 223 3.979501 AATTCAGAACATAGGGGGCAT 57.020 42.857 0.00 0.00 0.00 4.40
223 224 6.718593 ATAATTCAGAACATAGGGGGCATA 57.281 37.500 0.00 0.00 0.00 3.14
224 225 5.605540 AATTCAGAACATAGGGGGCATAT 57.394 39.130 0.00 0.00 0.00 1.78
225 226 6.718593 AATTCAGAACATAGGGGGCATATA 57.281 37.500 0.00 0.00 0.00 0.86
226 227 6.718593 ATTCAGAACATAGGGGGCATATAA 57.281 37.500 0.00 0.00 0.00 0.98
227 228 6.523035 TTCAGAACATAGGGGGCATATAAA 57.477 37.500 0.00 0.00 0.00 1.40
228 229 6.523035 TCAGAACATAGGGGGCATATAAAA 57.477 37.500 0.00 0.00 0.00 1.52
229 230 6.542821 TCAGAACATAGGGGGCATATAAAAG 58.457 40.000 0.00 0.00 0.00 2.27
230 231 5.183904 CAGAACATAGGGGGCATATAAAAGC 59.816 44.000 0.00 0.00 0.00 3.51
231 232 4.740154 ACATAGGGGGCATATAAAAGCA 57.260 40.909 0.00 0.00 0.00 3.91
232 233 4.666512 ACATAGGGGGCATATAAAAGCAG 58.333 43.478 0.00 0.00 0.00 4.24
233 234 2.683211 AGGGGGCATATAAAAGCAGG 57.317 50.000 0.00 0.00 0.00 4.85
234 235 2.143602 AGGGGGCATATAAAAGCAGGA 58.856 47.619 0.00 0.00 0.00 3.86
235 236 2.108952 AGGGGGCATATAAAAGCAGGAG 59.891 50.000 0.00 0.00 0.00 3.69
236 237 1.889170 GGGGCATATAAAAGCAGGAGC 59.111 52.381 0.00 0.00 42.56 4.70
237 238 2.586425 GGGCATATAAAAGCAGGAGCA 58.414 47.619 0.00 0.00 45.49 4.26
238 239 3.160269 GGGCATATAAAAGCAGGAGCAT 58.840 45.455 0.00 0.00 45.49 3.79
239 240 3.057033 GGGCATATAAAAGCAGGAGCATG 60.057 47.826 0.00 0.00 45.49 4.06
240 241 3.057033 GGCATATAAAAGCAGGAGCATGG 60.057 47.826 0.00 0.00 45.49 3.66
241 242 3.613432 GCATATAAAAGCAGGAGCATGGC 60.613 47.826 0.00 0.00 45.49 4.40
242 243 1.027357 ATAAAAGCAGGAGCATGGCG 58.973 50.000 0.00 0.00 45.49 5.69
243 244 1.656818 TAAAAGCAGGAGCATGGCGC 61.657 55.000 0.00 0.00 45.49 6.53
244 245 4.728110 AAGCAGGAGCATGGCGCA 62.728 61.111 10.83 0.00 46.13 6.09
257 258 4.332637 GCGCACCACTGTGGCAAG 62.333 66.667 26.20 17.35 42.67 4.01
258 259 3.663176 CGCACCACTGTGGCAAGG 61.663 66.667 26.20 14.21 42.67 3.61
259 260 2.519302 GCACCACTGTGGCAAGGT 60.519 61.111 26.20 3.75 42.67 3.50
260 261 1.228124 GCACCACTGTGGCAAGGTA 60.228 57.895 26.20 0.00 42.67 3.08
261 262 1.515521 GCACCACTGTGGCAAGGTAC 61.516 60.000 26.20 4.83 42.67 3.34
262 263 1.070786 ACCACTGTGGCAAGGTACG 59.929 57.895 26.20 0.04 42.67 3.67
263 264 1.671054 CCACTGTGGCAAGGTACGG 60.671 63.158 14.87 0.00 0.00 4.02
264 265 1.671054 CACTGTGGCAAGGTACGGG 60.671 63.158 0.00 0.00 0.00 5.28
265 266 2.746277 CTGTGGCAAGGTACGGGC 60.746 66.667 0.00 0.00 0.00 6.13
266 267 4.690719 TGTGGCAAGGTACGGGCG 62.691 66.667 0.00 0.00 36.04 6.13
283 284 4.481112 GGCGGCACCGATTTGCAG 62.481 66.667 14.43 0.00 44.94 4.41
285 286 4.481112 CGGCACCGATTTGCAGCC 62.481 66.667 2.01 0.91 44.94 4.85
286 287 4.481112 GGCACCGATTTGCAGCCG 62.481 66.667 6.06 0.00 44.94 5.52
288 289 4.481112 CACCGATTTGCAGCCGCC 62.481 66.667 0.00 0.00 37.32 6.13
291 292 4.481112 CGATTTGCAGCCGCCCAC 62.481 66.667 0.00 0.00 37.32 4.61
292 293 3.372730 GATTTGCAGCCGCCCACA 61.373 61.111 0.00 0.00 37.32 4.17
293 294 3.346631 GATTTGCAGCCGCCCACAG 62.347 63.158 0.00 0.00 37.32 3.66
302 303 4.323477 CGCCCACAGGACCGGAAA 62.323 66.667 9.46 0.00 33.47 3.13
303 304 2.114411 GCCCACAGGACCGGAAAA 59.886 61.111 9.46 0.00 33.47 2.29
304 305 1.971695 GCCCACAGGACCGGAAAAG 60.972 63.158 9.46 0.00 33.47 2.27
305 306 1.303317 CCCACAGGACCGGAAAAGG 60.303 63.158 9.46 1.53 33.47 3.11
306 307 1.971695 CCACAGGACCGGAAAAGGC 60.972 63.158 9.46 0.00 33.69 4.35
307 308 1.228124 CACAGGACCGGAAAAGGCA 60.228 57.895 9.46 0.00 33.69 4.75
308 309 0.609131 CACAGGACCGGAAAAGGCAT 60.609 55.000 9.46 0.00 33.69 4.40
309 310 0.322546 ACAGGACCGGAAAAGGCATC 60.323 55.000 9.46 0.00 33.69 3.91
310 311 1.032114 CAGGACCGGAAAAGGCATCC 61.032 60.000 9.46 0.82 33.69 3.51
311 312 1.753078 GGACCGGAAAAGGCATCCC 60.753 63.158 9.46 0.00 33.13 3.85
312 313 1.753078 GACCGGAAAAGGCATCCCC 60.753 63.158 9.46 0.00 33.13 4.81
954 955 1.527034 CACCTCACTCACCACCATTG 58.473 55.000 0.00 0.00 0.00 2.82
955 956 1.140312 ACCTCACTCACCACCATTGT 58.860 50.000 0.00 0.00 0.00 2.71
956 957 1.494721 ACCTCACTCACCACCATTGTT 59.505 47.619 0.00 0.00 0.00 2.83
957 958 2.708861 ACCTCACTCACCACCATTGTTA 59.291 45.455 0.00 0.00 0.00 2.41
958 959 3.074412 CCTCACTCACCACCATTGTTAC 58.926 50.000 0.00 0.00 0.00 2.50
959 960 3.495983 CCTCACTCACCACCATTGTTACA 60.496 47.826 0.00 0.00 0.00 2.41
960 961 4.133820 CTCACTCACCACCATTGTTACAA 58.866 43.478 0.00 0.00 0.00 2.41
963 964 4.097135 CACTCACCACCATTGTTACAAACA 59.903 41.667 0.66 0.00 40.21 2.83
969 970 4.023622 CCACCATTGTTACAAACACATCGA 60.024 41.667 0.66 0.00 41.97 3.59
974 975 3.532542 TGTTACAAACACATCGACACCA 58.467 40.909 0.00 0.00 36.25 4.17
979 980 3.002791 CAAACACATCGACACCAGCTAT 58.997 45.455 0.00 0.00 0.00 2.97
981 982 4.672587 AACACATCGACACCAGCTATAT 57.327 40.909 0.00 0.00 0.00 0.86
996 997 3.005897 AGCTATATACCACCTCGTGCAAG 59.994 47.826 0.00 0.00 31.34 4.01
997 998 2.910688 ATATACCACCTCGTGCAAGG 57.089 50.000 2.71 2.71 42.55 3.61
1018 1019 1.139058 CCATGGACCAGTACAGCTACC 59.861 57.143 5.56 0.00 0.00 3.18
1470 1510 1.458445 CCGATGATGACGATGATGCAC 59.542 52.381 0.00 0.00 0.00 4.57
1518 1558 4.724022 CCGATGCAGTACGGGTAC 57.276 61.111 17.93 0.70 44.59 3.34
1519 1559 1.298863 CCGATGCAGTACGGGTACG 60.299 63.158 17.93 1.04 44.59 3.67
1520 1560 1.298863 CGATGCAGTACGGGTACGG 60.299 63.158 4.99 4.99 46.48 4.02
1543 1583 0.323725 CATTGGGGACTTGGACCAGG 60.324 60.000 1.23 1.23 35.37 4.45
1776 5066 7.102993 AGGATAAAGAAGAAGAAGCAGAGTTC 58.897 38.462 0.00 0.00 0.00 3.01
1777 5067 7.038373 AGGATAAAGAAGAAGAAGCAGAGTTCT 60.038 37.037 0.00 0.00 38.48 3.01
1778 5068 7.277760 GGATAAAGAAGAAGAAGCAGAGTTCTC 59.722 40.741 0.00 0.00 35.65 2.87
1779 5069 5.543507 AAGAAGAAGAAGCAGAGTTCTCA 57.456 39.130 2.64 0.00 35.65 3.27
1780 5070 5.543507 AGAAGAAGAAGCAGAGTTCTCAA 57.456 39.130 2.64 0.00 35.65 3.02
1782 5072 4.953940 AGAAGAAGCAGAGTTCTCAAGT 57.046 40.909 2.64 0.00 35.65 3.16
1785 5075 5.538433 AGAAGAAGCAGAGTTCTCAAGTAGT 59.462 40.000 2.64 0.00 35.65 2.73
1786 5076 6.717540 AGAAGAAGCAGAGTTCTCAAGTAGTA 59.282 38.462 2.64 0.00 35.65 1.82
1787 5077 6.262193 AGAAGCAGAGTTCTCAAGTAGTAC 57.738 41.667 2.64 0.00 30.55 2.73
1788 5078 6.007703 AGAAGCAGAGTTCTCAAGTAGTACT 58.992 40.000 0.00 0.00 38.44 2.73
1798 5096 9.874205 AGTTCTCAAGTAGTACTAGTAGTAGTG 57.126 37.037 22.76 18.24 39.96 2.74
1799 5097 9.651913 GTTCTCAAGTAGTACTAGTAGTAGTGT 57.348 37.037 22.76 10.67 39.96 3.55
1842 5140 1.521681 GAGAGGGAACGGGAATGCG 60.522 63.158 0.00 0.00 0.00 4.73
1857 5155 4.704007 GCGAATTGCATCAGCCTG 57.296 55.556 0.00 0.00 45.45 4.85
1858 5156 1.805254 GCGAATTGCATCAGCCTGT 59.195 52.632 0.00 0.00 45.45 4.00
1859 5157 0.171903 GCGAATTGCATCAGCCTGTT 59.828 50.000 0.00 0.00 45.45 3.16
1955 5262 7.339721 TGTTGGAGTAGAGTAATAAGAGACCAG 59.660 40.741 0.00 0.00 0.00 4.00
1973 5280 7.130681 AGACCAGCTCTGCTTTATTAGTTAT 57.869 36.000 0.00 0.00 36.40 1.89
1976 5283 8.664211 ACCAGCTCTGCTTTATTAGTTATTAC 57.336 34.615 0.00 0.00 36.40 1.89
1977 5284 7.715686 ACCAGCTCTGCTTTATTAGTTATTACC 59.284 37.037 0.00 0.00 36.40 2.85
1979 5286 9.277783 CAGCTCTGCTTTATTAGTTATTACCAT 57.722 33.333 0.00 0.00 36.40 3.55
1980 5287 9.277783 AGCTCTGCTTTATTAGTTATTACCATG 57.722 33.333 0.00 0.00 33.89 3.66
1981 5288 9.057089 GCTCTGCTTTATTAGTTATTACCATGT 57.943 33.333 0.00 0.00 0.00 3.21
1983 5290 9.899661 TCTGCTTTATTAGTTATTACCATGTGT 57.100 29.630 0.00 0.00 0.00 3.72
1998 5611 2.270352 TGTGTTGGAGTAGGGCTTTG 57.730 50.000 0.00 0.00 0.00 2.77
2003 5616 0.918983 TGGAGTAGGGCTTTGGATGG 59.081 55.000 0.00 0.00 0.00 3.51
2007 5620 3.217626 GAGTAGGGCTTTGGATGGAATG 58.782 50.000 0.00 0.00 0.00 2.67
2008 5621 2.852449 AGTAGGGCTTTGGATGGAATGA 59.148 45.455 0.00 0.00 0.00 2.57
2012 5625 1.269413 GGCTTTGGATGGAATGATGCG 60.269 52.381 0.00 0.00 0.00 4.73
2024 5637 7.119699 GGATGGAATGATGCGAGATTTATGTTA 59.880 37.037 0.00 0.00 0.00 2.41
2025 5638 7.189693 TGGAATGATGCGAGATTTATGTTAC 57.810 36.000 0.00 0.00 0.00 2.50
2027 5640 7.041848 TGGAATGATGCGAGATTTATGTTACAG 60.042 37.037 0.00 0.00 0.00 2.74
2029 5642 6.588348 TGATGCGAGATTTATGTTACAGTG 57.412 37.500 0.00 0.00 0.00 3.66
2030 5643 5.523552 TGATGCGAGATTTATGTTACAGTGG 59.476 40.000 0.00 0.00 0.00 4.00
2034 5659 5.462398 GCGAGATTTATGTTACAGTGGGTAG 59.538 44.000 0.00 0.00 32.49 3.18
2039 5664 3.611766 ATGTTACAGTGGGTAGTCTGC 57.388 47.619 0.00 0.00 35.37 4.26
2063 5688 1.297158 GACATCGCAAGCATGACGC 60.297 57.895 0.00 0.00 42.91 5.19
2074 5700 3.864686 ATGACGCGCCGTTGCATC 61.865 61.111 5.73 0.00 41.37 3.91
2099 5725 0.036577 CAAGCTCTGGAGTGGAGTGG 60.037 60.000 0.00 0.00 33.73 4.00
2111 5737 3.775654 GAGTGGGGAGGCGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
2123 5749 4.101448 GGAGTGCCAGCCGGTGAT 62.101 66.667 1.90 0.00 33.28 3.06
2131 5757 1.293179 CAGCCGGTGATGAGTGTCA 59.707 57.895 1.90 0.00 0.00 3.58
2136 5762 0.738762 CGGTGATGAGTGTCAGCTGG 60.739 60.000 15.13 0.00 42.78 4.85
2137 5763 0.610174 GGTGATGAGTGTCAGCTGGA 59.390 55.000 15.13 0.00 41.96 3.86
2146 5772 2.157421 GTCAGCTGGACTTGCTTCG 58.843 57.895 15.13 0.00 43.46 3.79
2191 5825 1.035932 TACTGCTACTCCACGGAGCC 61.036 60.000 13.16 2.89 45.54 4.70
2200 5834 2.168728 ACTCCACGGAGCCTAATTCTTC 59.831 50.000 13.16 0.00 45.54 2.87
2216 5850 7.878127 CCTAATTCTTCAGGCGATTAGGAATAA 59.122 37.037 13.22 0.00 41.73 1.40
2217 5851 7.497925 AATTCTTCAGGCGATTAGGAATAAC 57.502 36.000 0.00 0.00 0.00 1.89
2232 5887 1.165270 ATAACAGTTGTCGGGCAAGC 58.835 50.000 0.00 0.00 37.83 4.01
2247 5902 3.059800 GGGCAAGCGTCGATTAGTTATTC 60.060 47.826 0.00 0.00 0.00 1.75
2439 6127 0.364180 TCGCTCGCGTTGTTTATTCG 59.636 50.000 5.77 0.00 40.74 3.34
2445 6136 2.095110 TCGCGTTGTTTATTCGGAGAGA 60.095 45.455 5.77 0.00 38.43 3.10
2446 6137 2.279136 CGCGTTGTTTATTCGGAGAGAG 59.721 50.000 0.00 0.00 38.43 3.20
2448 6139 3.548268 GCGTTGTTTATTCGGAGAGAGAG 59.452 47.826 0.00 0.00 38.43 3.20
2449 6140 4.674623 GCGTTGTTTATTCGGAGAGAGAGA 60.675 45.833 0.00 0.00 38.43 3.10
2450 6141 5.399858 CGTTGTTTATTCGGAGAGAGAGAA 58.600 41.667 0.00 0.00 38.43 2.87
2451 6142 5.286558 CGTTGTTTATTCGGAGAGAGAGAAC 59.713 44.000 0.00 0.00 38.43 3.01
2452 6143 4.982999 TGTTTATTCGGAGAGAGAGAACG 58.017 43.478 0.00 0.00 38.43 3.95
2499 6223 3.898529 AGTCACAGTACAGTACGCTTTC 58.101 45.455 5.02 0.00 0.00 2.62
2515 6239 0.603172 TTTCCGGACGGCGATGAAAA 60.603 50.000 16.62 4.52 34.68 2.29
2516 6240 1.293267 TTCCGGACGGCGATGAAAAC 61.293 55.000 16.62 0.00 34.68 2.43
2518 6242 1.366111 CCGGACGGCGATGAAAACAT 61.366 55.000 16.62 0.00 0.00 2.71
2519 6243 0.247655 CGGACGGCGATGAAAACATG 60.248 55.000 16.62 0.00 0.00 3.21
2520 6244 0.802494 GGACGGCGATGAAAACATGT 59.198 50.000 16.62 0.00 0.00 3.21
2521 6245 1.202031 GGACGGCGATGAAAACATGTC 60.202 52.381 16.62 0.00 0.00 3.06
2523 6247 0.801872 CGGCGATGAAAACATGTCCA 59.198 50.000 0.00 0.00 0.00 4.02
2530 6256 1.425066 TGAAAACATGTCCAGGGAGCT 59.575 47.619 0.00 0.00 0.00 4.09
2534 6260 0.471617 ACATGTCCAGGGAGCTATGC 59.528 55.000 0.00 0.00 0.00 3.14
2540 6266 1.134401 TCCAGGGAGCTATGCTTTTCG 60.134 52.381 0.00 0.00 39.88 3.46
2545 6271 1.332065 GGAGCTATGCTTTTCGCTTCC 59.668 52.381 0.00 0.00 39.88 3.46
2578 6304 4.158025 CGTGTCCATAGTTTAGAGTGAGGT 59.842 45.833 0.00 0.00 0.00 3.85
2581 6307 5.185249 TGTCCATAGTTTAGAGTGAGGTCAC 59.815 44.000 1.60 1.60 46.77 3.67
2594 6320 4.798574 GTGAGGTCACTTGCCAAATAAAG 58.201 43.478 2.72 0.00 43.25 1.85
2603 6329 7.495135 CACTTGCCAAATAAAGTGGAAAATT 57.505 32.000 7.50 0.00 46.17 1.82
2604 6330 7.354257 CACTTGCCAAATAAAGTGGAAAATTG 58.646 34.615 7.50 0.00 46.17 2.32
2606 6332 8.207545 ACTTGCCAAATAAAGTGGAAAATTGTA 58.792 29.630 0.00 0.00 38.54 2.41
2621 6347 5.545658 AAATTGTAAGATAGCCACGTGTG 57.454 39.130 15.65 7.24 0.00 3.82
2636 6363 5.763444 CACGTGTGTTTTATAGAGTGGAG 57.237 43.478 7.58 0.00 0.00 3.86
2638 6365 5.345202 CACGTGTGTTTTATAGAGTGGAGTC 59.655 44.000 7.58 0.00 0.00 3.36
2640 6367 4.863131 GTGTGTTTTATAGAGTGGAGTCCG 59.137 45.833 4.30 0.00 0.00 4.79
2649 6376 1.164041 AGTGGAGTCCGTTTTTGCCG 61.164 55.000 4.30 0.00 0.00 5.69
2652 6379 1.082104 GAGTCCGTTTTTGCCGCTG 60.082 57.895 0.00 0.00 0.00 5.18
2658 6385 0.248866 CGTTTTTGCCGCTGGTTTCT 60.249 50.000 0.00 0.00 0.00 2.52
2659 6386 1.208259 GTTTTTGCCGCTGGTTTCTG 58.792 50.000 0.00 0.00 0.00 3.02
2660 6387 0.529555 TTTTTGCCGCTGGTTTCTGC 60.530 50.000 0.00 0.00 34.96 4.26
2666 6393 3.793144 GCTGGTTTCTGCGAGGCG 61.793 66.667 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.871238 GTCATAAAAGTTACATTGAGGTCTCTA 57.129 33.333 0.00 0.00 0.00 2.43
2 3 8.375506 TGTCATAAAAGTTACATTGAGGTCTCT 58.624 33.333 0.00 0.00 0.00 3.10
12 13 9.369904 GCATCCAAAATGTCATAAAAGTTACAT 57.630 29.630 0.00 0.00 34.11 2.29
13 14 8.584157 AGCATCCAAAATGTCATAAAAGTTACA 58.416 29.630 0.00 0.00 0.00 2.41
14 15 8.986477 AGCATCCAAAATGTCATAAAAGTTAC 57.014 30.769 0.00 0.00 0.00 2.50
15 16 9.995003 AAAGCATCCAAAATGTCATAAAAGTTA 57.005 25.926 0.00 0.00 0.00 2.24
16 17 8.907222 AAAGCATCCAAAATGTCATAAAAGTT 57.093 26.923 0.00 0.00 0.00 2.66
23 24 9.590451 CAGTAAATAAAGCATCCAAAATGTCAT 57.410 29.630 0.00 0.00 0.00 3.06
24 25 7.545265 GCAGTAAATAAAGCATCCAAAATGTCA 59.455 33.333 0.00 0.00 0.00 3.58
25 26 7.761249 AGCAGTAAATAAAGCATCCAAAATGTC 59.239 33.333 0.00 0.00 0.00 3.06
26 27 7.614494 AGCAGTAAATAAAGCATCCAAAATGT 58.386 30.769 0.00 0.00 0.00 2.71
27 28 9.754382 ATAGCAGTAAATAAAGCATCCAAAATG 57.246 29.630 0.00 0.00 0.00 2.32
28 29 9.754382 CATAGCAGTAAATAAAGCATCCAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
29 30 8.965819 TCATAGCAGTAAATAAAGCATCCAAAA 58.034 29.630 0.00 0.00 0.00 2.44
30 31 8.518430 TCATAGCAGTAAATAAAGCATCCAAA 57.482 30.769 0.00 0.00 0.00 3.28
31 32 8.570488 CATCATAGCAGTAAATAAAGCATCCAA 58.430 33.333 0.00 0.00 0.00 3.53
32 33 7.938490 TCATCATAGCAGTAAATAAAGCATCCA 59.062 33.333 0.00 0.00 0.00 3.41
33 34 8.327941 TCATCATAGCAGTAAATAAAGCATCC 57.672 34.615 0.00 0.00 0.00 3.51
36 37 9.565090 AGATTCATCATAGCAGTAAATAAAGCA 57.435 29.630 0.00 0.00 0.00 3.91
43 44 9.453572 ACAAAGAAGATTCATCATAGCAGTAAA 57.546 29.630 0.00 0.00 0.00 2.01
46 47 9.624373 AATACAAAGAAGATTCATCATAGCAGT 57.376 29.630 0.00 0.00 0.00 4.40
63 64 9.702253 AGAGACTTGGATCTACTAATACAAAGA 57.298 33.333 0.00 0.00 29.12 2.52
66 67 8.622157 CGAAGAGACTTGGATCTACTAATACAA 58.378 37.037 0.00 0.00 0.00 2.41
67 68 7.255173 GCGAAGAGACTTGGATCTACTAATACA 60.255 40.741 0.00 0.00 0.00 2.29
68 69 7.079475 GCGAAGAGACTTGGATCTACTAATAC 58.921 42.308 0.00 0.00 0.00 1.89
69 70 6.771267 TGCGAAGAGACTTGGATCTACTAATA 59.229 38.462 0.00 0.00 0.00 0.98
70 71 5.594725 TGCGAAGAGACTTGGATCTACTAAT 59.405 40.000 0.00 0.00 0.00 1.73
71 72 4.948004 TGCGAAGAGACTTGGATCTACTAA 59.052 41.667 0.00 0.00 0.00 2.24
72 73 4.524053 TGCGAAGAGACTTGGATCTACTA 58.476 43.478 0.00 0.00 0.00 1.82
73 74 3.357203 TGCGAAGAGACTTGGATCTACT 58.643 45.455 0.00 0.00 0.00 2.57
74 75 3.784701 TGCGAAGAGACTTGGATCTAC 57.215 47.619 0.00 0.00 0.00 2.59
75 76 4.211125 AGATGCGAAGAGACTTGGATCTA 58.789 43.478 12.14 0.00 37.68 1.98
76 77 3.030291 AGATGCGAAGAGACTTGGATCT 58.970 45.455 0.00 0.00 35.10 2.75
77 78 3.451141 AGATGCGAAGAGACTTGGATC 57.549 47.619 0.00 0.00 0.00 3.36
78 79 6.040955 TGTTATAGATGCGAAGAGACTTGGAT 59.959 38.462 0.00 0.00 0.00 3.41
79 80 5.359860 TGTTATAGATGCGAAGAGACTTGGA 59.640 40.000 0.00 0.00 0.00 3.53
80 81 5.592054 TGTTATAGATGCGAAGAGACTTGG 58.408 41.667 0.00 0.00 0.00 3.61
81 82 7.706281 ATTGTTATAGATGCGAAGAGACTTG 57.294 36.000 0.00 0.00 0.00 3.16
82 83 9.250624 GTAATTGTTATAGATGCGAAGAGACTT 57.749 33.333 0.00 0.00 0.00 3.01
83 84 7.591795 CGTAATTGTTATAGATGCGAAGAGACT 59.408 37.037 0.00 0.00 0.00 3.24
84 85 7.590322 TCGTAATTGTTATAGATGCGAAGAGAC 59.410 37.037 0.00 0.00 0.00 3.36
85 86 7.590322 GTCGTAATTGTTATAGATGCGAAGAGA 59.410 37.037 0.00 0.00 0.00 3.10
86 87 7.591795 AGTCGTAATTGTTATAGATGCGAAGAG 59.408 37.037 0.00 0.00 0.00 2.85
87 88 7.378728 CAGTCGTAATTGTTATAGATGCGAAGA 59.621 37.037 0.00 0.00 0.00 2.87
88 89 7.358435 CCAGTCGTAATTGTTATAGATGCGAAG 60.358 40.741 0.00 0.00 0.00 3.79
89 90 6.419710 CCAGTCGTAATTGTTATAGATGCGAA 59.580 38.462 0.00 0.00 0.00 4.70
90 91 5.918576 CCAGTCGTAATTGTTATAGATGCGA 59.081 40.000 0.00 0.00 0.00 5.10
91 92 5.690409 ACCAGTCGTAATTGTTATAGATGCG 59.310 40.000 0.00 0.00 0.00 4.73
92 93 7.478520 AACCAGTCGTAATTGTTATAGATGC 57.521 36.000 0.00 0.00 0.00 3.91
134 135 9.585099 AGACACGTTAAAAATACGGTAATATGA 57.415 29.630 0.00 0.00 42.99 2.15
138 139 9.807649 ATCTAGACACGTTAAAAATACGGTAAT 57.192 29.630 0.00 0.00 42.99 1.89
140 141 9.716507 GTATCTAGACACGTTAAAAATACGGTA 57.283 33.333 0.00 0.00 42.99 4.02
141 142 8.243426 TGTATCTAGACACGTTAAAAATACGGT 58.757 33.333 0.00 0.00 42.99 4.83
142 143 8.619146 TGTATCTAGACACGTTAAAAATACGG 57.381 34.615 0.00 0.00 42.99 4.02
146 147 9.871238 ACAGATGTATCTAGACACGTTAAAAAT 57.129 29.630 0.00 0.00 34.85 1.82
193 194 9.813826 CCCCCTATGTTCTGAATTATTTATCTT 57.186 33.333 0.00 0.00 0.00 2.40
194 195 7.890655 GCCCCCTATGTTCTGAATTATTTATCT 59.109 37.037 0.00 0.00 0.00 1.98
195 196 7.669722 TGCCCCCTATGTTCTGAATTATTTATC 59.330 37.037 0.00 0.00 0.00 1.75
196 197 7.534852 TGCCCCCTATGTTCTGAATTATTTAT 58.465 34.615 0.00 0.00 0.00 1.40
197 198 6.916909 TGCCCCCTATGTTCTGAATTATTTA 58.083 36.000 0.00 0.00 0.00 1.40
198 199 5.776358 TGCCCCCTATGTTCTGAATTATTT 58.224 37.500 0.00 0.00 0.00 1.40
199 200 5.402054 TGCCCCCTATGTTCTGAATTATT 57.598 39.130 0.00 0.00 0.00 1.40
200 201 5.605540 ATGCCCCCTATGTTCTGAATTAT 57.394 39.130 0.00 0.00 0.00 1.28
201 202 6.718593 ATATGCCCCCTATGTTCTGAATTA 57.281 37.500 0.00 0.00 0.00 1.40
202 203 3.979501 ATGCCCCCTATGTTCTGAATT 57.020 42.857 0.00 0.00 0.00 2.17
203 204 6.718593 TTATATGCCCCCTATGTTCTGAAT 57.281 37.500 0.00 0.00 0.00 2.57
204 205 6.523035 TTTATATGCCCCCTATGTTCTGAA 57.477 37.500 0.00 0.00 0.00 3.02
205 206 6.523035 TTTTATATGCCCCCTATGTTCTGA 57.477 37.500 0.00 0.00 0.00 3.27
206 207 5.183904 GCTTTTATATGCCCCCTATGTTCTG 59.816 44.000 0.00 0.00 0.00 3.02
207 208 5.162991 TGCTTTTATATGCCCCCTATGTTCT 60.163 40.000 0.00 0.00 0.00 3.01
208 209 5.076873 TGCTTTTATATGCCCCCTATGTTC 58.923 41.667 0.00 0.00 0.00 3.18
209 210 5.073437 TGCTTTTATATGCCCCCTATGTT 57.927 39.130 0.00 0.00 0.00 2.71
210 211 4.509122 CCTGCTTTTATATGCCCCCTATGT 60.509 45.833 0.00 0.00 0.00 2.29
211 212 4.019174 CCTGCTTTTATATGCCCCCTATG 58.981 47.826 0.00 0.00 0.00 2.23
212 213 3.922778 TCCTGCTTTTATATGCCCCCTAT 59.077 43.478 0.00 0.00 0.00 2.57
213 214 3.330701 CTCCTGCTTTTATATGCCCCCTA 59.669 47.826 0.00 0.00 0.00 3.53
214 215 2.108952 CTCCTGCTTTTATATGCCCCCT 59.891 50.000 0.00 0.00 0.00 4.79
215 216 2.519013 CTCCTGCTTTTATATGCCCCC 58.481 52.381 0.00 0.00 0.00 5.40
216 217 1.889170 GCTCCTGCTTTTATATGCCCC 59.111 52.381 0.00 0.00 36.03 5.80
217 218 2.586425 TGCTCCTGCTTTTATATGCCC 58.414 47.619 0.00 0.00 40.48 5.36
218 219 3.057033 CCATGCTCCTGCTTTTATATGCC 60.057 47.826 0.00 0.00 40.48 4.40
219 220 3.613432 GCCATGCTCCTGCTTTTATATGC 60.613 47.826 0.00 0.00 40.48 3.14
220 221 3.365666 CGCCATGCTCCTGCTTTTATATG 60.366 47.826 0.00 0.00 40.48 1.78
221 222 2.816087 CGCCATGCTCCTGCTTTTATAT 59.184 45.455 0.00 0.00 40.48 0.86
222 223 2.221169 CGCCATGCTCCTGCTTTTATA 58.779 47.619 0.00 0.00 40.48 0.98
223 224 1.027357 CGCCATGCTCCTGCTTTTAT 58.973 50.000 0.00 0.00 40.48 1.40
224 225 1.656818 GCGCCATGCTCCTGCTTTTA 61.657 55.000 0.00 0.00 41.73 1.52
225 226 2.998279 GCGCCATGCTCCTGCTTTT 61.998 57.895 0.00 0.00 41.73 2.27
226 227 3.446570 GCGCCATGCTCCTGCTTT 61.447 61.111 0.00 0.00 41.73 3.51
227 228 4.728110 TGCGCCATGCTCCTGCTT 62.728 61.111 4.18 0.00 46.63 3.91
240 241 4.332637 CTTGCCACAGTGGTGCGC 62.333 66.667 21.26 0.00 43.88 6.09
241 242 3.663176 CCTTGCCACAGTGGTGCG 61.663 66.667 21.26 9.00 43.88 5.34
242 243 1.228124 TACCTTGCCACAGTGGTGC 60.228 57.895 21.26 8.12 43.88 5.01
243 244 1.227999 CGTACCTTGCCACAGTGGTG 61.228 60.000 21.26 11.23 44.85 4.17
244 245 1.070786 CGTACCTTGCCACAGTGGT 59.929 57.895 21.26 3.07 40.46 4.16
245 246 1.671054 CCGTACCTTGCCACAGTGG 60.671 63.158 16.16 16.16 41.55 4.00
246 247 1.671054 CCCGTACCTTGCCACAGTG 60.671 63.158 0.00 0.00 0.00 3.66
247 248 2.747686 CCCGTACCTTGCCACAGT 59.252 61.111 0.00 0.00 0.00 3.55
248 249 2.746277 GCCCGTACCTTGCCACAG 60.746 66.667 0.00 0.00 0.00 3.66
249 250 4.690719 CGCCCGTACCTTGCCACA 62.691 66.667 0.00 0.00 0.00 4.17
266 267 4.481112 CTGCAAATCGGTGCCGCC 62.481 66.667 5.64 0.00 44.26 6.13
268 269 4.481112 GGCTGCAAATCGGTGCCG 62.481 66.667 3.94 3.94 44.26 5.69
269 270 4.481112 CGGCTGCAAATCGGTGCC 62.481 66.667 0.50 0.91 44.26 5.01
271 272 4.481112 GGCGGCTGCAAATCGGTG 62.481 66.667 21.31 0.00 45.35 4.94
274 275 4.481112 GTGGGCGGCTGCAAATCG 62.481 66.667 21.31 0.00 45.35 3.34
275 276 3.346631 CTGTGGGCGGCTGCAAATC 62.347 63.158 21.31 7.05 45.35 2.17
276 277 3.376078 CTGTGGGCGGCTGCAAAT 61.376 61.111 21.31 0.00 45.35 2.32
285 286 3.835790 TTTTCCGGTCCTGTGGGCG 62.836 63.158 0.00 0.00 0.00 6.13
286 287 1.971695 CTTTTCCGGTCCTGTGGGC 60.972 63.158 0.00 0.00 0.00 5.36
287 288 1.303317 CCTTTTCCGGTCCTGTGGG 60.303 63.158 0.00 0.00 0.00 4.61
288 289 1.971695 GCCTTTTCCGGTCCTGTGG 60.972 63.158 0.00 0.00 0.00 4.17
289 290 0.609131 ATGCCTTTTCCGGTCCTGTG 60.609 55.000 0.00 0.00 0.00 3.66
290 291 0.322546 GATGCCTTTTCCGGTCCTGT 60.323 55.000 0.00 0.00 0.00 4.00
291 292 1.032114 GGATGCCTTTTCCGGTCCTG 61.032 60.000 0.00 0.00 0.00 3.86
292 293 1.303282 GGATGCCTTTTCCGGTCCT 59.697 57.895 0.00 0.00 0.00 3.85
293 294 1.753078 GGGATGCCTTTTCCGGTCC 60.753 63.158 0.00 0.00 33.82 4.46
294 295 1.753078 GGGGATGCCTTTTCCGGTC 60.753 63.158 2.19 0.00 33.82 4.79
295 296 2.359011 GGGGATGCCTTTTCCGGT 59.641 61.111 2.19 0.00 33.82 5.28
935 936 1.202806 ACAATGGTGGTGAGTGAGGTG 60.203 52.381 0.00 0.00 0.00 4.00
936 937 1.140312 ACAATGGTGGTGAGTGAGGT 58.860 50.000 0.00 0.00 0.00 3.85
937 938 2.276732 AACAATGGTGGTGAGTGAGG 57.723 50.000 0.00 0.00 0.00 3.86
938 939 3.738982 TGTAACAATGGTGGTGAGTGAG 58.261 45.455 0.00 0.00 0.00 3.51
939 940 3.847671 TGTAACAATGGTGGTGAGTGA 57.152 42.857 0.00 0.00 0.00 3.41
940 941 4.097135 TGTTTGTAACAATGGTGGTGAGTG 59.903 41.667 0.00 0.00 38.72 3.51
941 942 4.097286 GTGTTTGTAACAATGGTGGTGAGT 59.903 41.667 0.00 0.00 44.16 3.41
942 943 4.097135 TGTGTTTGTAACAATGGTGGTGAG 59.903 41.667 0.00 0.00 44.16 3.51
943 944 4.017126 TGTGTTTGTAACAATGGTGGTGA 58.983 39.130 0.00 0.00 44.16 4.02
944 945 4.377839 TGTGTTTGTAACAATGGTGGTG 57.622 40.909 0.00 0.00 44.16 4.17
945 946 4.261405 CGATGTGTTTGTAACAATGGTGGT 60.261 41.667 0.00 0.00 44.16 4.16
946 947 4.023622 TCGATGTGTTTGTAACAATGGTGG 60.024 41.667 0.00 0.00 44.16 4.61
947 948 4.909305 GTCGATGTGTTTGTAACAATGGTG 59.091 41.667 0.00 0.00 44.16 4.17
948 949 4.576873 TGTCGATGTGTTTGTAACAATGGT 59.423 37.500 0.00 0.00 44.16 3.55
949 950 4.909305 GTGTCGATGTGTTTGTAACAATGG 59.091 41.667 0.00 0.00 44.16 3.16
950 951 4.909305 GGTGTCGATGTGTTTGTAACAATG 59.091 41.667 0.00 0.00 44.16 2.82
951 952 4.576873 TGGTGTCGATGTGTTTGTAACAAT 59.423 37.500 0.00 0.00 44.16 2.71
952 953 3.939592 TGGTGTCGATGTGTTTGTAACAA 59.060 39.130 0.00 0.00 44.16 2.83
953 954 3.532542 TGGTGTCGATGTGTTTGTAACA 58.467 40.909 0.00 0.00 39.52 2.41
954 955 3.606153 GCTGGTGTCGATGTGTTTGTAAC 60.606 47.826 0.00 0.00 0.00 2.50
955 956 2.546368 GCTGGTGTCGATGTGTTTGTAA 59.454 45.455 0.00 0.00 0.00 2.41
956 957 2.139917 GCTGGTGTCGATGTGTTTGTA 58.860 47.619 0.00 0.00 0.00 2.41
957 958 0.944386 GCTGGTGTCGATGTGTTTGT 59.056 50.000 0.00 0.00 0.00 2.83
958 959 1.229428 AGCTGGTGTCGATGTGTTTG 58.771 50.000 0.00 0.00 0.00 2.93
959 960 2.831685 TAGCTGGTGTCGATGTGTTT 57.168 45.000 0.00 0.00 0.00 2.83
960 961 4.672587 ATATAGCTGGTGTCGATGTGTT 57.327 40.909 0.00 0.00 0.00 3.32
963 964 4.022242 GTGGTATATAGCTGGTGTCGATGT 60.022 45.833 12.87 0.00 0.00 3.06
969 970 2.891580 CGAGGTGGTATATAGCTGGTGT 59.108 50.000 12.87 0.00 0.00 4.16
974 975 2.594131 TGCACGAGGTGGTATATAGCT 58.406 47.619 12.87 0.00 33.64 3.32
979 980 0.177141 GCCTTGCACGAGGTGGTATA 59.823 55.000 6.32 0.00 39.11 1.47
981 982 2.345991 GCCTTGCACGAGGTGGTA 59.654 61.111 6.32 0.00 39.11 3.25
996 997 1.452108 GCTGTACTGGTCCATGGCC 60.452 63.158 6.96 12.55 0.00 5.36
997 998 0.830648 TAGCTGTACTGGTCCATGGC 59.169 55.000 6.96 1.78 0.00 4.40
1028 1029 2.438434 CCTGGCCATTGTCGTCCC 60.438 66.667 5.51 0.00 0.00 4.46
1029 1030 2.438434 CCCTGGCCATTGTCGTCC 60.438 66.667 5.51 0.00 0.00 4.79
1095 1102 1.374252 CGTCTCCCGGAACTTGGTG 60.374 63.158 0.73 0.00 0.00 4.17
1488 1528 0.041488 GCATCGGGTAGTCGTCGTAG 60.041 60.000 0.00 0.00 0.00 3.51
1515 1555 4.476752 TCCCCAATGCCGCCGTAC 62.477 66.667 0.00 0.00 0.00 3.67
1516 1556 4.476752 GTCCCCAATGCCGCCGTA 62.477 66.667 0.00 0.00 0.00 4.02
1519 1559 3.451894 CAAGTCCCCAATGCCGCC 61.452 66.667 0.00 0.00 0.00 6.13
1520 1560 3.451894 CCAAGTCCCCAATGCCGC 61.452 66.667 0.00 0.00 0.00 6.53
1543 1583 3.733337 TCCCGTCGTAGTAGTAGGAATC 58.267 50.000 1.61 0.00 0.00 2.52
1798 5096 7.419204 TGCTTTACGGCCACATAAATAATAAC 58.581 34.615 2.24 0.00 0.00 1.89
1799 5097 7.499563 TCTGCTTTACGGCCACATAAATAATAA 59.500 33.333 2.24 0.00 0.00 1.40
1802 5100 5.186942 TCTGCTTTACGGCCACATAAATAA 58.813 37.500 2.24 0.00 0.00 1.40
1813 5111 0.249398 TTCCCTCTCTGCTTTACGGC 59.751 55.000 0.00 0.00 0.00 5.68
1814 5112 1.736032 CGTTCCCTCTCTGCTTTACGG 60.736 57.143 0.00 0.00 0.00 4.02
1842 5140 3.308438 ACAAACAGGCTGATGCAATTC 57.692 42.857 23.66 0.00 41.91 2.17
1910 5212 6.051717 CCAACACATGTTACAAAATTCCCAA 58.948 36.000 0.00 0.00 36.32 4.12
1914 5216 8.564574 TCTACTCCAACACATGTTACAAAATTC 58.435 33.333 0.00 0.00 36.32 2.17
1955 5262 9.057089 ACATGGTAATAACTAATAAAGCAGAGC 57.943 33.333 0.00 0.00 0.00 4.09
1977 5284 2.489329 CAAAGCCCTACTCCAACACATG 59.511 50.000 0.00 0.00 0.00 3.21
1979 5286 1.202879 CCAAAGCCCTACTCCAACACA 60.203 52.381 0.00 0.00 0.00 3.72
1980 5287 1.073284 TCCAAAGCCCTACTCCAACAC 59.927 52.381 0.00 0.00 0.00 3.32
1981 5288 1.440618 TCCAAAGCCCTACTCCAACA 58.559 50.000 0.00 0.00 0.00 3.33
1982 5289 2.369394 CATCCAAAGCCCTACTCCAAC 58.631 52.381 0.00 0.00 0.00 3.77
1983 5290 1.284785 CCATCCAAAGCCCTACTCCAA 59.715 52.381 0.00 0.00 0.00 3.53
1985 5292 1.213296 TCCATCCAAAGCCCTACTCC 58.787 55.000 0.00 0.00 0.00 3.85
1986 5293 3.117888 TCATTCCATCCAAAGCCCTACTC 60.118 47.826 0.00 0.00 0.00 2.59
1987 5294 2.852449 TCATTCCATCCAAAGCCCTACT 59.148 45.455 0.00 0.00 0.00 2.57
1988 5295 3.297134 TCATTCCATCCAAAGCCCTAC 57.703 47.619 0.00 0.00 0.00 3.18
1989 5296 3.836146 CATCATTCCATCCAAAGCCCTA 58.164 45.455 0.00 0.00 0.00 3.53
1991 5298 1.069668 GCATCATTCCATCCAAAGCCC 59.930 52.381 0.00 0.00 0.00 5.19
1993 5300 1.677576 TCGCATCATTCCATCCAAAGC 59.322 47.619 0.00 0.00 0.00 3.51
1998 5611 5.413833 ACATAAATCTCGCATCATTCCATCC 59.586 40.000 0.00 0.00 0.00 3.51
2003 5616 7.795734 CACTGTAACATAAATCTCGCATCATTC 59.204 37.037 0.00 0.00 0.00 2.67
2007 5620 5.050091 CCCACTGTAACATAAATCTCGCATC 60.050 44.000 0.00 0.00 0.00 3.91
2008 5621 4.816385 CCCACTGTAACATAAATCTCGCAT 59.184 41.667 0.00 0.00 0.00 4.73
2012 5625 7.707035 CAGACTACCCACTGTAACATAAATCTC 59.293 40.741 0.00 0.00 0.00 2.75
2024 5637 0.969894 GAGTGCAGACTACCCACTGT 59.030 55.000 7.17 0.00 39.72 3.55
2025 5638 0.109086 CGAGTGCAGACTACCCACTG 60.109 60.000 7.17 0.00 39.72 3.66
2027 5640 1.215647 CCGAGTGCAGACTACCCAC 59.784 63.158 0.00 0.00 30.16 4.61
2029 5642 1.248785 TGTCCGAGTGCAGACTACCC 61.249 60.000 5.54 0.00 34.02 3.69
2030 5643 0.818296 ATGTCCGAGTGCAGACTACC 59.182 55.000 5.54 0.00 34.02 3.18
2034 5659 2.161486 GCGATGTCCGAGTGCAGAC 61.161 63.158 0.00 0.00 41.76 3.51
2039 5664 1.086067 ATGCTTGCGATGTCCGAGTG 61.086 55.000 0.00 0.00 41.76 3.51
2063 5688 4.596180 GGATGCGATGCAACGGCG 62.596 66.667 18.44 4.80 43.62 6.46
2064 5689 2.924922 CTTGGATGCGATGCAACGGC 62.925 60.000 18.44 10.69 43.62 5.68
2065 5690 1.063006 CTTGGATGCGATGCAACGG 59.937 57.895 18.44 0.06 43.62 4.44
2107 5733 2.821366 CATCACCGGCTGGCACTC 60.821 66.667 12.89 0.00 39.70 3.51
2108 5734 3.320879 CTCATCACCGGCTGGCACT 62.321 63.158 12.89 0.00 39.70 4.40
2109 5735 2.821366 CTCATCACCGGCTGGCAC 60.821 66.667 12.89 0.00 39.70 5.01
2110 5736 3.321648 ACTCATCACCGGCTGGCA 61.322 61.111 12.89 0.00 39.70 4.92
2111 5737 2.821366 CACTCATCACCGGCTGGC 60.821 66.667 12.89 0.00 39.70 4.85
2112 5738 1.448540 GACACTCATCACCGGCTGG 60.449 63.158 11.02 11.02 42.84 4.85
2113 5739 0.738762 CTGACACTCATCACCGGCTG 60.739 60.000 0.00 0.00 0.00 4.85
2114 5740 1.593787 CTGACACTCATCACCGGCT 59.406 57.895 0.00 0.00 0.00 5.52
2115 5741 2.103042 GCTGACACTCATCACCGGC 61.103 63.158 0.00 0.00 0.00 6.13
2116 5742 0.738762 CAGCTGACACTCATCACCGG 60.739 60.000 8.42 0.00 0.00 5.28
2117 5743 0.738762 CCAGCTGACACTCATCACCG 60.739 60.000 17.39 0.00 0.00 4.94
2118 5744 0.610174 TCCAGCTGACACTCATCACC 59.390 55.000 17.39 0.00 0.00 4.02
2119 5745 1.719600 GTCCAGCTGACACTCATCAC 58.280 55.000 17.39 0.00 43.85 3.06
2131 5757 0.106708 TGAACGAAGCAAGTCCAGCT 59.893 50.000 0.00 0.00 45.97 4.24
2136 5762 0.234884 CCCGTTGAACGAAGCAAGTC 59.765 55.000 20.47 0.00 46.05 3.01
2137 5763 1.782028 GCCCGTTGAACGAAGCAAGT 61.782 55.000 20.47 0.00 46.05 3.16
2138 5764 1.082104 GCCCGTTGAACGAAGCAAG 60.082 57.895 20.47 0.55 46.05 4.01
2139 5765 2.887889 CGCCCGTTGAACGAAGCAA 61.888 57.895 24.58 0.00 46.05 3.91
2146 5772 4.322385 GTGCACCGCCCGTTGAAC 62.322 66.667 5.22 0.00 0.00 3.18
2168 5794 0.098376 CCGTGGAGTAGCAGTACGTC 59.902 60.000 0.00 0.00 33.97 4.34
2169 5795 0.321919 TCCGTGGAGTAGCAGTACGT 60.322 55.000 0.00 0.00 33.97 3.57
2170 5796 0.377554 CTCCGTGGAGTAGCAGTACG 59.622 60.000 7.79 0.00 37.47 3.67
2171 5797 0.100861 GCTCCGTGGAGTAGCAGTAC 59.899 60.000 16.88 0.00 43.70 2.73
2172 5798 1.035932 GGCTCCGTGGAGTAGCAGTA 61.036 60.000 16.88 0.00 43.70 2.74
2173 5799 2.352032 GGCTCCGTGGAGTAGCAGT 61.352 63.158 16.88 0.00 43.70 4.40
2174 5800 0.752009 TAGGCTCCGTGGAGTAGCAG 60.752 60.000 16.88 0.00 43.70 4.24
2175 5801 0.323999 TTAGGCTCCGTGGAGTAGCA 60.324 55.000 16.88 0.00 43.70 3.49
2176 5802 1.041437 ATTAGGCTCCGTGGAGTAGC 58.959 55.000 16.88 4.05 43.70 3.58
2177 5803 2.959707 AGAATTAGGCTCCGTGGAGTAG 59.040 50.000 16.88 0.00 43.70 2.57
2191 5825 8.713271 GTTATTCCTAATCGCCTGAAGAATTAG 58.287 37.037 0.00 0.00 0.00 1.73
2200 5834 4.876107 ACAACTGTTATTCCTAATCGCCTG 59.124 41.667 0.00 0.00 0.00 4.85
2210 5844 1.816074 TGCCCGACAACTGTTATTCC 58.184 50.000 0.00 0.00 0.00 3.01
2216 5850 2.972505 CGCTTGCCCGACAACTGT 60.973 61.111 0.00 0.00 33.68 3.55
2217 5851 2.954753 GACGCTTGCCCGACAACTG 61.955 63.158 0.00 0.00 33.68 3.16
2232 5887 2.150611 CGGTGCGAATAACTAATCGACG 59.849 50.000 0.00 0.00 41.43 5.12
2354 6029 3.431922 TCATTCACCGACCGAATCTAC 57.568 47.619 0.00 0.00 30.65 2.59
2439 6127 0.452585 CCGTTCCGTTCTCTCTCTCC 59.547 60.000 0.00 0.00 0.00 3.71
2445 6136 1.174712 TCCGTTCCGTTCCGTTCTCT 61.175 55.000 0.00 0.00 0.00 3.10
2446 6137 0.318955 TTCCGTTCCGTTCCGTTCTC 60.319 55.000 0.00 0.00 0.00 2.87
2448 6139 0.509929 CTTTCCGTTCCGTTCCGTTC 59.490 55.000 0.00 0.00 0.00 3.95
2449 6140 0.104671 TCTTTCCGTTCCGTTCCGTT 59.895 50.000 0.00 0.00 0.00 4.44
2450 6141 0.319297 CTCTTTCCGTTCCGTTCCGT 60.319 55.000 0.00 0.00 0.00 4.69
2451 6142 0.038892 TCTCTTTCCGTTCCGTTCCG 60.039 55.000 0.00 0.00 0.00 4.30
2452 6143 1.269936 TGTCTCTTTCCGTTCCGTTCC 60.270 52.381 0.00 0.00 0.00 3.62
2476 6195 3.284323 AGCGTACTGTACTGTGACTTG 57.716 47.619 15.01 0.00 0.00 3.16
2499 6223 1.366111 ATGTTTTCATCGCCGTCCGG 61.366 55.000 0.24 0.24 35.32 5.14
2505 6229 1.133025 CCTGGACATGTTTTCATCGCC 59.867 52.381 0.00 0.00 38.64 5.54
2515 6239 0.471617 GCATAGCTCCCTGGACATGT 59.528 55.000 0.00 0.00 0.00 3.21
2516 6240 0.763652 AGCATAGCTCCCTGGACATG 59.236 55.000 0.00 0.00 30.62 3.21
2518 6242 1.289160 AAAGCATAGCTCCCTGGACA 58.711 50.000 0.00 0.00 38.25 4.02
2519 6243 2.293170 GAAAAGCATAGCTCCCTGGAC 58.707 52.381 0.00 0.00 38.25 4.02
2520 6244 1.134401 CGAAAAGCATAGCTCCCTGGA 60.134 52.381 0.00 0.00 38.25 3.86
2521 6245 1.303309 CGAAAAGCATAGCTCCCTGG 58.697 55.000 0.00 0.00 38.25 4.45
2530 6256 4.916702 CCCCTGGGAAGCGAAAAGCATA 62.917 54.545 16.20 0.00 43.13 3.14
2534 6260 1.378762 TCCCCTGGGAAGCGAAAAG 59.621 57.895 16.20 0.00 42.05 2.27
2581 6307 7.495135 ACAATTTTCCACTTTATTTGGCAAG 57.505 32.000 0.00 0.00 33.71 4.01
2584 6310 8.825667 TCTTACAATTTTCCACTTTATTTGGC 57.174 30.769 0.00 0.00 33.71 4.52
2594 6320 5.123344 ACGTGGCTATCTTACAATTTTCCAC 59.877 40.000 0.00 0.00 38.37 4.02
2603 6329 3.671008 AACACACGTGGCTATCTTACA 57.329 42.857 21.57 0.00 34.19 2.41
2604 6330 6.657836 ATAAAACACACGTGGCTATCTTAC 57.342 37.500 21.57 0.00 34.19 2.34
2606 6332 6.636705 TCTATAAAACACACGTGGCTATCTT 58.363 36.000 21.57 7.69 34.19 2.40
2621 6347 7.295930 CAAAAACGGACTCCACTCTATAAAAC 58.704 38.462 0.00 0.00 0.00 2.43
2636 6363 2.050442 CCAGCGGCAAAAACGGAC 60.050 61.111 1.45 0.00 0.00 4.79
2638 6365 1.212455 GAAACCAGCGGCAAAAACGG 61.212 55.000 1.45 0.00 0.00 4.44
2640 6367 1.208259 CAGAAACCAGCGGCAAAAAC 58.792 50.000 1.45 0.00 0.00 2.43
2649 6376 3.793144 CGCCTCGCAGAAACCAGC 61.793 66.667 0.00 0.00 34.09 4.85


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

AutoCloner maintained by Alex Coulton.