Multiple sequence alignment - TraesCS4B01G056300

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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 TraesCS4B01G056300 chr4B 100.000 1584 0 0 708 2291 45771917 45773500 0.000000e+00 2926.0
1 TraesCS4B01G056300 chr4B 82.520 1476 103 66 708 2092 45515034 45516445 0.000000e+00 1153.0
2 TraesCS4B01G056300 chr4B 100.000 369 0 0 1 369 45771210 45771578 0.000000e+00 682.0
3 TraesCS4B01G056300 chr4B 97.059 34 1 0 1780 1813 45772886 45772919 8.840000e-05 58.4
4 TraesCS4B01G056300 chr4B 97.059 34 1 0 1677 1710 45772989 45773022 8.840000e-05 58.4
5 TraesCS4B01G056300 chr4D 79.787 940 66 54 712 1581 31816404 31817289 9.180000e-159 569.0
6 TraesCS4B01G056300 chr4D 90.272 257 23 2 2035 2291 31817872 31818126 3.650000e-88 335.0
7 TraesCS4B01G056300 chr4D 89.401 217 10 9 1834 2044 31817631 31817840 6.280000e-66 261.0
8 TraesCS4B01G056300 chr4D 85.393 89 9 1 1629 1717 31817290 31817374 3.130000e-14 89.8
9 TraesCS4B01G056300 chr4A 79.158 950 91 46 711 1581 570986937 570986016 1.990000e-155 558.0
10 TraesCS4B01G056300 chr4A 85.924 476 37 18 1834 2291 570985800 570985337 4.430000e-132 481.0
11 TraesCS4B01G056300 chr4A 89.333 75 7 1 1 74 154377211 154377137 2.420000e-15 93.5
12 TraesCS4B01G056300 chr4A 83.333 90 10 2 1629 1717 570986015 570985930 6.790000e-11 78.7
13 TraesCS4B01G056300 chr6A 89.333 75 8 0 1 75 398098699 398098773 6.740000e-16 95.3
14 TraesCS4B01G056300 chr2B 89.333 75 7 1 1 75 377087416 377087343 2.420000e-15 93.5
15 TraesCS4B01G056300 chr6B 91.176 68 5 1 1 68 9102938 9102872 8.720000e-15 91.6
16 TraesCS4B01G056300 chr3A 88.000 75 9 0 1 75 733185585 733185511 3.130000e-14 89.8


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 TraesCS4B01G056300 chr4B 45771210 45773500 2290 False 931.200000 2926 98.52950 1 2291 4 chr4B.!!$F2 2290
1 TraesCS4B01G056300 chr4B 45515034 45516445 1411 False 1153.000000 1153 82.52000 708 2092 1 chr4B.!!$F1 1384
2 TraesCS4B01G056300 chr4D 31816404 31818126 1722 False 313.700000 569 86.21325 712 2291 4 chr4D.!!$F1 1579
3 TraesCS4B01G056300 chr4A 570985337 570986937 1600 True 372.566667 558 82.80500 711 2291 3 chr4A.!!$R2 1580

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
274 275 0.037419 ACCACCGCAAATCATTTGGC 60.037 50.0 12.14 3.72 40.94 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1533 0.038166 GCACCCAGGATTTCACAGGA 59.962 55.0 0.0 0.0 0.0 3.86 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
41 42 8.477419 ACATTTTAGAGGAAACTTTTCATCCA 57.523 30.769 11.68 0.00 46.03 3.41
42 43 8.360390 ACATTTTAGAGGAAACTTTTCATCCAC 58.640 33.333 11.68 0.00 46.03 4.02
43 44 8.579863 CATTTTAGAGGAAACTTTTCATCCACT 58.420 33.333 11.68 0.77 46.03 4.00
44 45 7.745620 TTTAGAGGAAACTTTTCATCCACTC 57.254 36.000 11.68 5.20 46.03 3.51
45 46 5.310409 AGAGGAAACTTTTCATCCACTCA 57.690 39.130 11.68 0.00 46.03 3.41
46 47 5.694995 AGAGGAAACTTTTCATCCACTCAA 58.305 37.500 11.68 0.00 46.03 3.02
47 48 6.129179 AGAGGAAACTTTTCATCCACTCAAA 58.871 36.000 11.68 0.00 46.03 2.69
48 49 6.039829 AGAGGAAACTTTTCATCCACTCAAAC 59.960 38.462 11.68 0.00 46.03 2.93
49 50 5.893824 AGGAAACTTTTCATCCACTCAAACT 59.106 36.000 4.18 0.00 37.44 2.66
50 51 6.381133 AGGAAACTTTTCATCCACTCAAACTT 59.619 34.615 4.18 0.00 37.44 2.66
51 52 6.697455 GGAAACTTTTCATCCACTCAAACTTC 59.303 38.462 4.18 0.00 38.92 3.01
52 53 7.410120 AAACTTTTCATCCACTCAAACTTCT 57.590 32.000 0.00 0.00 0.00 2.85
53 54 7.410120 AACTTTTCATCCACTCAAACTTCTT 57.590 32.000 0.00 0.00 0.00 2.52
54 55 7.410120 ACTTTTCATCCACTCAAACTTCTTT 57.590 32.000 0.00 0.00 0.00 2.52
55 56 7.260603 ACTTTTCATCCACTCAAACTTCTTTG 58.739 34.615 0.00 0.00 38.56 2.77
56 57 6.773976 TTTCATCCACTCAAACTTCTTTGT 57.226 33.333 0.00 0.00 38.38 2.83
57 58 7.873719 TTTCATCCACTCAAACTTCTTTGTA 57.126 32.000 0.00 0.00 38.38 2.41
58 59 7.873719 TTCATCCACTCAAACTTCTTTGTAA 57.126 32.000 0.00 0.00 38.38 2.41
59 60 7.873719 TCATCCACTCAAACTTCTTTGTAAA 57.126 32.000 0.00 0.00 38.38 2.01
60 61 8.287439 TCATCCACTCAAACTTCTTTGTAAAA 57.713 30.769 0.00 0.00 38.38 1.52
61 62 8.912988 TCATCCACTCAAACTTCTTTGTAAAAT 58.087 29.630 0.00 0.00 38.38 1.82
62 63 9.533253 CATCCACTCAAACTTCTTTGTAAAATT 57.467 29.630 0.00 0.00 38.38 1.82
64 65 9.581099 TCCACTCAAACTTCTTTGTAAAATTTC 57.419 29.630 0.00 0.00 38.38 2.17
65 66 8.817100 CCACTCAAACTTCTTTGTAAAATTTCC 58.183 33.333 0.00 0.00 38.38 3.13
66 67 9.586435 CACTCAAACTTCTTTGTAAAATTTCCT 57.414 29.630 0.00 0.00 38.38 3.36
69 70 9.936759 TCAAACTTCTTTGTAAAATTTCCTTGT 57.063 25.926 0.00 0.00 38.38 3.16
79 80 9.672673 TTGTAAAATTTCCTTGTTTTTCATCCA 57.327 25.926 0.00 0.00 29.11 3.41
80 81 9.103861 TGTAAAATTTCCTTGTTTTTCATCCAC 57.896 29.630 0.00 0.00 0.00 4.02
81 82 9.325198 GTAAAATTTCCTTGTTTTTCATCCACT 57.675 29.630 0.00 0.00 0.00 4.00
82 83 8.437360 AAAATTTCCTTGTTTTTCATCCACTC 57.563 30.769 0.00 0.00 0.00 3.51
83 84 6.729690 ATTTCCTTGTTTTTCATCCACTCA 57.270 33.333 0.00 0.00 0.00 3.41
84 85 6.537453 TTTCCTTGTTTTTCATCCACTCAA 57.463 33.333 0.00 0.00 0.00 3.02
85 86 6.537453 TTCCTTGTTTTTCATCCACTCAAA 57.463 33.333 0.00 0.00 0.00 2.69
86 87 5.901552 TCCTTGTTTTTCATCCACTCAAAC 58.098 37.500 0.00 0.00 0.00 2.93
87 88 4.739716 CCTTGTTTTTCATCCACTCAAACG 59.260 41.667 0.00 0.00 31.24 3.60
88 89 4.974368 TGTTTTTCATCCACTCAAACGT 57.026 36.364 0.00 0.00 31.24 3.99
89 90 4.667262 TGTTTTTCATCCACTCAAACGTG 58.333 39.130 0.00 0.00 31.24 4.49
90 91 4.396478 TGTTTTTCATCCACTCAAACGTGA 59.604 37.500 0.00 0.00 37.06 4.35
102 103 4.159377 TCAAACGTGAGAAAATGCATCC 57.841 40.909 0.00 0.00 0.00 3.51
103 104 3.567585 TCAAACGTGAGAAAATGCATCCA 59.432 39.130 0.00 0.00 0.00 3.41
104 105 3.559238 AACGTGAGAAAATGCATCCAC 57.441 42.857 0.00 3.12 0.00 4.02
105 106 2.783135 ACGTGAGAAAATGCATCCACT 58.217 42.857 0.00 0.00 0.00 4.00
106 107 2.744202 ACGTGAGAAAATGCATCCACTC 59.256 45.455 0.00 9.56 0.00 3.51
107 108 2.743664 CGTGAGAAAATGCATCCACTCA 59.256 45.455 18.82 18.82 33.06 3.41
108 109 3.189080 CGTGAGAAAATGCATCCACTCAA 59.811 43.478 22.10 10.62 36.41 3.02
109 110 4.142534 CGTGAGAAAATGCATCCACTCAAT 60.143 41.667 22.10 0.00 36.41 2.57
110 111 5.620654 CGTGAGAAAATGCATCCACTCAATT 60.621 40.000 22.10 1.65 36.41 2.32
111 112 5.575606 GTGAGAAAATGCATCCACTCAATTG 59.424 40.000 22.10 0.00 36.41 2.32
112 113 4.501071 AGAAAATGCATCCACTCAATTGC 58.499 39.130 0.00 0.00 35.67 3.56
113 114 2.973694 AATGCATCCACTCAATTGCC 57.026 45.000 0.00 0.00 34.20 4.52
114 115 2.154567 ATGCATCCACTCAATTGCCT 57.845 45.000 0.00 0.00 34.20 4.75
115 116 1.927487 TGCATCCACTCAATTGCCTT 58.073 45.000 0.00 0.00 34.20 4.35
116 117 2.250031 TGCATCCACTCAATTGCCTTT 58.750 42.857 0.00 0.00 34.20 3.11
117 118 2.231964 TGCATCCACTCAATTGCCTTTC 59.768 45.455 0.00 0.00 34.20 2.62
118 119 2.733227 GCATCCACTCAATTGCCTTTCG 60.733 50.000 0.00 0.00 0.00 3.46
119 120 1.533625 TCCACTCAATTGCCTTTCGG 58.466 50.000 0.00 0.00 0.00 4.30
137 138 2.438434 CTTTCGCCCTCCGCCAAT 60.438 61.111 0.00 0.00 36.73 3.16
138 139 2.749839 TTTCGCCCTCCGCCAATG 60.750 61.111 0.00 0.00 36.73 2.82
139 140 3.261039 TTTCGCCCTCCGCCAATGA 62.261 57.895 0.00 0.00 36.73 2.57
140 141 3.969250 TTCGCCCTCCGCCAATGAC 62.969 63.158 0.00 0.00 36.73 3.06
148 149 2.279851 CGCCAATGACCGCCGATA 60.280 61.111 0.00 0.00 0.00 2.92
149 150 2.310233 CGCCAATGACCGCCGATAG 61.310 63.158 0.00 0.00 0.00 2.08
166 167 2.202703 GGTAGCGCACCTACGTGG 60.203 66.667 11.47 0.00 46.03 4.94
167 168 2.884207 GTAGCGCACCTACGTGGC 60.884 66.667 11.47 0.00 40.61 5.01
168 169 4.485834 TAGCGCACCTACGTGGCG 62.486 66.667 11.47 17.40 40.61 5.69
173 174 4.752879 CACCTACGTGGCGGGTGG 62.753 72.222 17.85 4.77 44.63 4.61
209 210 4.803426 CCTGGCGACGCTGACCTC 62.803 72.222 20.77 1.85 0.00 3.85
210 211 4.803426 CTGGCGACGCTGACCTCC 62.803 72.222 20.77 1.05 0.00 4.30
214 215 4.778415 CGACGCTGACCTCCCACG 62.778 72.222 0.00 0.00 0.00 4.94
258 259 4.659172 CGCCCAGCCCTTCAACCA 62.659 66.667 0.00 0.00 0.00 3.67
259 260 2.991540 GCCCAGCCCTTCAACCAC 60.992 66.667 0.00 0.00 0.00 4.16
260 261 2.283173 CCCAGCCCTTCAACCACC 60.283 66.667 0.00 0.00 0.00 4.61
261 262 2.672996 CCAGCCCTTCAACCACCG 60.673 66.667 0.00 0.00 0.00 4.94
262 263 3.365265 CAGCCCTTCAACCACCGC 61.365 66.667 0.00 0.00 0.00 5.68
263 264 3.884774 AGCCCTTCAACCACCGCA 61.885 61.111 0.00 0.00 0.00 5.69
264 265 2.909965 GCCCTTCAACCACCGCAA 60.910 61.111 0.00 0.00 0.00 4.85
265 266 2.494530 GCCCTTCAACCACCGCAAA 61.495 57.895 0.00 0.00 0.00 3.68
266 267 1.815817 GCCCTTCAACCACCGCAAAT 61.816 55.000 0.00 0.00 0.00 2.32
267 268 0.243636 CCCTTCAACCACCGCAAATC 59.756 55.000 0.00 0.00 0.00 2.17
268 269 0.958091 CCTTCAACCACCGCAAATCA 59.042 50.000 0.00 0.00 0.00 2.57
269 270 1.545582 CCTTCAACCACCGCAAATCAT 59.454 47.619 0.00 0.00 0.00 2.45
270 271 2.029110 CCTTCAACCACCGCAAATCATT 60.029 45.455 0.00 0.00 0.00 2.57
271 272 3.554752 CCTTCAACCACCGCAAATCATTT 60.555 43.478 0.00 0.00 0.00 2.32
272 273 3.023946 TCAACCACCGCAAATCATTTG 57.976 42.857 5.68 5.68 43.44 2.32
273 274 2.067766 CAACCACCGCAAATCATTTGG 58.932 47.619 12.14 0.00 40.94 3.28
274 275 0.037419 ACCACCGCAAATCATTTGGC 60.037 50.000 12.14 3.72 40.94 4.52
275 276 0.247185 CCACCGCAAATCATTTGGCT 59.753 50.000 12.14 0.00 40.94 4.75
276 277 1.632422 CACCGCAAATCATTTGGCTC 58.368 50.000 12.14 0.00 40.94 4.70
277 278 0.532115 ACCGCAAATCATTTGGCTCC 59.468 50.000 12.14 0.00 40.94 4.70
278 279 0.179103 CCGCAAATCATTTGGCTCCC 60.179 55.000 12.14 0.00 40.94 4.30
279 280 0.819582 CGCAAATCATTTGGCTCCCT 59.180 50.000 12.14 0.00 40.94 4.20
280 281 1.470285 CGCAAATCATTTGGCTCCCTG 60.470 52.381 12.14 0.00 40.94 4.45
281 282 1.741394 GCAAATCATTTGGCTCCCTGC 60.741 52.381 12.14 0.00 40.94 4.85
282 283 1.551430 CAAATCATTTGGCTCCCTGCA 59.449 47.619 1.73 0.00 45.15 4.41
283 284 1.941377 AATCATTTGGCTCCCTGCAA 58.059 45.000 0.00 0.00 45.15 4.08
284 285 1.188863 ATCATTTGGCTCCCTGCAAC 58.811 50.000 0.00 0.00 45.15 4.17
285 286 0.899717 TCATTTGGCTCCCTGCAACC 60.900 55.000 0.00 0.00 45.15 3.77
286 287 0.901580 CATTTGGCTCCCTGCAACCT 60.902 55.000 0.00 0.00 45.15 3.50
287 288 0.901580 ATTTGGCTCCCTGCAACCTG 60.902 55.000 0.00 0.00 45.15 4.00
288 289 4.666253 TGGCTCCCTGCAACCTGC 62.666 66.667 0.00 0.00 45.15 4.85
301 302 4.503741 GCAACCTGCATTTTCTACTTCA 57.496 40.909 0.00 0.00 44.26 3.02
302 303 5.064441 GCAACCTGCATTTTCTACTTCAT 57.936 39.130 0.00 0.00 44.26 2.57
303 304 5.098211 GCAACCTGCATTTTCTACTTCATC 58.902 41.667 0.00 0.00 44.26 2.92
304 305 5.644644 CAACCTGCATTTTCTACTTCATCC 58.355 41.667 0.00 0.00 0.00 3.51
305 306 4.922206 ACCTGCATTTTCTACTTCATCCA 58.078 39.130 0.00 0.00 0.00 3.41
306 307 4.702131 ACCTGCATTTTCTACTTCATCCAC 59.298 41.667 0.00 0.00 0.00 4.02
307 308 4.096984 CCTGCATTTTCTACTTCATCCACC 59.903 45.833 0.00 0.00 0.00 4.61
308 309 3.689161 TGCATTTTCTACTTCATCCACCG 59.311 43.478 0.00 0.00 0.00 4.94
309 310 3.689649 GCATTTTCTACTTCATCCACCGT 59.310 43.478 0.00 0.00 0.00 4.83
310 311 4.873827 GCATTTTCTACTTCATCCACCGTA 59.126 41.667 0.00 0.00 0.00 4.02
311 312 5.527582 GCATTTTCTACTTCATCCACCGTAT 59.472 40.000 0.00 0.00 0.00 3.06
312 313 6.292919 GCATTTTCTACTTCATCCACCGTATC 60.293 42.308 0.00 0.00 0.00 2.24
313 314 5.925506 TTTCTACTTCATCCACCGTATCA 57.074 39.130 0.00 0.00 0.00 2.15
314 315 5.925506 TTCTACTTCATCCACCGTATCAA 57.074 39.130 0.00 0.00 0.00 2.57
315 316 5.258456 TCTACTTCATCCACCGTATCAAC 57.742 43.478 0.00 0.00 0.00 3.18
316 317 4.954202 TCTACTTCATCCACCGTATCAACT 59.046 41.667 0.00 0.00 0.00 3.16
317 318 4.553330 ACTTCATCCACCGTATCAACTT 57.447 40.909 0.00 0.00 0.00 2.66
318 319 4.906618 ACTTCATCCACCGTATCAACTTT 58.093 39.130 0.00 0.00 0.00 2.66
319 320 4.695455 ACTTCATCCACCGTATCAACTTTG 59.305 41.667 0.00 0.00 0.00 2.77
320 321 4.280436 TCATCCACCGTATCAACTTTGT 57.720 40.909 0.00 0.00 0.00 2.83
321 322 4.647611 TCATCCACCGTATCAACTTTGTT 58.352 39.130 0.00 0.00 0.00 2.83
322 323 4.693566 TCATCCACCGTATCAACTTTGTTC 59.306 41.667 0.00 0.00 0.00 3.18
323 324 4.345859 TCCACCGTATCAACTTTGTTCT 57.654 40.909 0.00 0.00 0.00 3.01
324 325 4.312443 TCCACCGTATCAACTTTGTTCTC 58.688 43.478 0.00 0.00 0.00 2.87
325 326 4.062293 CCACCGTATCAACTTTGTTCTCA 58.938 43.478 0.00 0.00 0.00 3.27
326 327 4.084013 CCACCGTATCAACTTTGTTCTCAC 60.084 45.833 0.00 0.00 0.00 3.51
327 328 4.062991 ACCGTATCAACTTTGTTCTCACC 58.937 43.478 0.00 0.00 0.00 4.02
328 329 4.062293 CCGTATCAACTTTGTTCTCACCA 58.938 43.478 0.00 0.00 0.00 4.17
329 330 4.695455 CCGTATCAACTTTGTTCTCACCAT 59.305 41.667 0.00 0.00 0.00 3.55
330 331 5.181245 CCGTATCAACTTTGTTCTCACCATT 59.819 40.000 0.00 0.00 0.00 3.16
331 332 6.293955 CCGTATCAACTTTGTTCTCACCATTT 60.294 38.462 0.00 0.00 0.00 2.32
332 333 7.138736 CGTATCAACTTTGTTCTCACCATTTT 58.861 34.615 0.00 0.00 0.00 1.82
333 334 7.647715 CGTATCAACTTTGTTCTCACCATTTTT 59.352 33.333 0.00 0.00 0.00 1.94
364 365 5.582689 AAAAACCTTTGTTCTCTCACCAG 57.417 39.130 0.00 0.00 32.15 4.00
365 366 2.262423 ACCTTTGTTCTCTCACCAGC 57.738 50.000 0.00 0.00 0.00 4.85
366 367 1.490490 ACCTTTGTTCTCTCACCAGCA 59.510 47.619 0.00 0.00 0.00 4.41
367 368 1.876156 CCTTTGTTCTCTCACCAGCAC 59.124 52.381 0.00 0.00 0.00 4.40
368 369 1.876156 CTTTGTTCTCTCACCAGCACC 59.124 52.381 0.00 0.00 0.00 5.01
728 729 2.430367 GATCCCGCCCATACCACC 59.570 66.667 0.00 0.00 0.00 4.61
729 730 3.530910 GATCCCGCCCATACCACCG 62.531 68.421 0.00 0.00 0.00 4.94
755 756 1.019673 CAGCCGGATCTCCAAACATG 58.980 55.000 5.05 0.00 35.14 3.21
762 763 0.324645 ATCTCCAAACATGGCCCACC 60.325 55.000 0.00 0.00 0.00 4.61
767 768 1.906333 AAACATGGCCCACCGGTTC 60.906 57.895 2.97 0.00 39.70 3.62
862 863 1.000359 TCACGCCCATCCTCTCTCA 60.000 57.895 0.00 0.00 0.00 3.27
863 864 1.039785 TCACGCCCATCCTCTCTCAG 61.040 60.000 0.00 0.00 0.00 3.35
864 865 1.039785 CACGCCCATCCTCTCTCAGA 61.040 60.000 0.00 0.00 0.00 3.27
865 866 1.040339 ACGCCCATCCTCTCTCAGAC 61.040 60.000 0.00 0.00 0.00 3.51
866 867 1.739049 GCCCATCCTCTCTCAGACG 59.261 63.158 0.00 0.00 0.00 4.18
867 868 0.753479 GCCCATCCTCTCTCAGACGA 60.753 60.000 0.00 0.00 0.00 4.20
873 897 1.278337 CTCTCTCAGACGATCGCCG 59.722 63.158 16.60 3.65 45.44 6.46
885 914 1.738030 CGATCGCCGATAAATACCCCC 60.738 57.143 0.26 0.00 41.76 5.40
886 915 0.248289 ATCGCCGATAAATACCCCCG 59.752 55.000 0.00 0.00 0.00 5.73
887 916 2.030958 CGCCGATAAATACCCCCGC 61.031 63.158 0.00 0.00 0.00 6.13
888 917 1.373812 GCCGATAAATACCCCCGCT 59.626 57.895 0.00 0.00 0.00 5.52
892 923 0.953960 GATAAATACCCCCGCTGCCG 60.954 60.000 0.00 0.00 0.00 5.69
903 934 3.435186 GCTGCCGGGAAGCAAGAC 61.435 66.667 22.59 0.00 43.52 3.01
925 956 3.370527 CGAACTACATCCCAATCCAACCT 60.371 47.826 0.00 0.00 0.00 3.50
931 972 6.849697 ACTACATCCCAATCCAACCTAATCTA 59.150 38.462 0.00 0.00 0.00 1.98
949 990 7.880195 CCTAATCTAATCCAATCCAAGATCGTT 59.120 37.037 0.00 0.00 0.00 3.85
953 994 3.417069 TCCAATCCAAGATCGTTGTGT 57.583 42.857 4.81 0.00 0.00 3.72
963 1004 3.919216 AGATCGTTGTGTTCCTTCTGAG 58.081 45.455 0.00 0.00 0.00 3.35
967 1009 3.887110 TCGTTGTGTTCCTTCTGAGAGTA 59.113 43.478 0.00 0.00 0.00 2.59
973 1015 6.120220 TGTGTTCCTTCTGAGAGTATCGATA 58.880 40.000 0.00 0.00 42.67 2.92
974 1016 6.602009 TGTGTTCCTTCTGAGAGTATCGATAA 59.398 38.462 6.72 0.00 42.67 1.75
975 1017 7.136119 GTGTTCCTTCTGAGAGTATCGATAAG 58.864 42.308 6.72 0.54 42.67 1.73
979 1021 5.471797 CCTTCTGAGAGTATCGATAAGAGCA 59.528 44.000 6.72 3.26 42.67 4.26
982 1024 5.699001 TCTGAGAGTATCGATAAGAGCAGAC 59.301 44.000 17.97 4.51 42.67 3.51
984 1026 6.000840 TGAGAGTATCGATAAGAGCAGACAT 58.999 40.000 6.72 0.00 42.67 3.06
985 1027 7.162082 TGAGAGTATCGATAAGAGCAGACATA 58.838 38.462 6.72 0.00 42.67 2.29
989 1032 7.911343 AGTATCGATAAGAGCAGACATATACG 58.089 38.462 6.72 0.00 0.00 3.06
993 1036 6.313164 TCGATAAGAGCAGACATATACGTAGG 59.687 42.308 0.08 0.00 0.00 3.18
1178 1248 4.681978 GCCAGAGGCGACGGTGTT 62.682 66.667 0.00 0.00 39.62 3.32
1179 1249 2.432628 CCAGAGGCGACGGTGTTC 60.433 66.667 0.00 0.00 0.00 3.18
1180 1250 2.805353 CAGAGGCGACGGTGTTCG 60.805 66.667 0.00 0.00 45.88 3.95
1181 1251 2.981909 AGAGGCGACGGTGTTCGA 60.982 61.111 0.00 0.00 41.78 3.71
1187 1257 4.324424 GACGGTGTTCGACGGAAA 57.676 55.556 0.00 0.00 42.43 3.13
1188 1258 2.139210 GACGGTGTTCGACGGAAAG 58.861 57.895 0.00 0.00 42.43 2.62
1189 1259 1.883725 GACGGTGTTCGACGGAAAGC 61.884 60.000 0.00 0.00 42.43 3.51
1190 1260 1.952133 CGGTGTTCGACGGAAAGCA 60.952 57.895 0.00 0.00 42.43 3.91
1287 1369 2.505777 CTCAGCTGCTGGTCGTCG 60.506 66.667 27.79 2.06 31.51 5.12
1307 1398 2.346244 CGTGAAGCTTAATTTCCGCGTA 59.654 45.455 4.92 0.00 0.00 4.42
1308 1399 3.181528 CGTGAAGCTTAATTTCCGCGTAA 60.182 43.478 4.92 0.00 0.00 3.18
1309 1400 4.086574 GTGAAGCTTAATTTCCGCGTAAC 58.913 43.478 4.92 0.00 0.00 2.50
1320 1411 0.390735 CCGCGTAACCCTGTAGCTTT 60.391 55.000 4.92 0.00 0.00 3.51
1350 1441 2.569657 CATGCAAGCATGTGCCGT 59.430 55.556 23.25 0.00 46.20 5.68
1351 1442 1.803922 CATGCAAGCATGTGCCGTG 60.804 57.895 23.25 1.37 46.20 4.94
1352 1443 3.636313 ATGCAAGCATGTGCCGTGC 62.636 57.895 18.94 18.94 46.61 5.34
1354 1445 4.764336 CAAGCATGTGCCGTGCCG 62.764 66.667 13.65 4.56 46.38 5.69
1375 1466 2.576893 CCGATCGACGACAATGGCG 61.577 63.158 18.66 7.07 45.77 5.69
1417 1508 5.255687 TGTGACTGTGCATATGAATTTCCT 58.744 37.500 6.97 0.00 0.00 3.36
1419 1510 6.127925 TGTGACTGTGCATATGAATTTCCTTC 60.128 38.462 6.97 0.00 0.00 3.46
1434 1525 8.981659 TGAATTTCCTTCCTTTCTTTCTTTCTT 58.018 29.630 0.00 0.00 32.49 2.52
1435 1526 9.823647 GAATTTCCTTCCTTTCTTTCTTTCTTT 57.176 29.630 0.00 0.00 0.00 2.52
1436 1527 9.823647 AATTTCCTTCCTTTCTTTCTTTCTTTC 57.176 29.630 0.00 0.00 0.00 2.62
1437 1528 8.595362 TTTCCTTCCTTTCTTTCTTTCTTTCT 57.405 30.769 0.00 0.00 0.00 2.52
1438 1529 8.595362 TTCCTTCCTTTCTTTCTTTCTTTCTT 57.405 30.769 0.00 0.00 0.00 2.52
1439 1530 8.595362 TCCTTCCTTTCTTTCTTTCTTTCTTT 57.405 30.769 0.00 0.00 0.00 2.52
1440 1531 8.687242 TCCTTCCTTTCTTTCTTTCTTTCTTTC 58.313 33.333 0.00 0.00 0.00 2.62
1441 1532 8.690884 CCTTCCTTTCTTTCTTTCTTTCTTTCT 58.309 33.333 0.00 0.00 0.00 2.52
1444 1535 8.687242 TCCTTTCTTTCTTTCTTTCTTTCTTCC 58.313 33.333 0.00 0.00 0.00 3.46
1476 1570 4.321230 CCTGGGTGCTGTTTTCTGAATTAC 60.321 45.833 0.00 0.00 0.00 1.89
1503 1597 6.806739 CCGATCATAAGATTTGCTATACGTGA 59.193 38.462 0.00 0.00 33.72 4.35
1511 1605 3.710326 TTGCTATACGTGAGCTCGATT 57.290 42.857 20.74 0.00 40.76 3.34
1513 1607 3.372060 TGCTATACGTGAGCTCGATTTG 58.628 45.455 20.74 0.00 40.76 2.32
1514 1608 2.154007 GCTATACGTGAGCTCGATTTGC 59.846 50.000 9.64 3.88 36.96 3.68
1519 1628 3.372954 ACGTGAGCTCGATTTGCTATAC 58.627 45.455 9.64 0.79 41.30 1.47
1598 1707 8.417273 TCCCCTAATAAACCTCAAAAGAAAAG 57.583 34.615 0.00 0.00 0.00 2.27
1601 1710 9.914131 CCCTAATAAACCTCAAAAGAAAAGAAG 57.086 33.333 0.00 0.00 0.00 2.85
1644 1753 0.877071 CACACACCATCCTCAACTGC 59.123 55.000 0.00 0.00 0.00 4.40
1645 1754 0.767375 ACACACCATCCTCAACTGCT 59.233 50.000 0.00 0.00 0.00 4.24
1646 1755 1.977854 ACACACCATCCTCAACTGCTA 59.022 47.619 0.00 0.00 0.00 3.49
1647 1756 2.573462 ACACACCATCCTCAACTGCTAT 59.427 45.455 0.00 0.00 0.00 2.97
1670 1779 2.823829 GCGGGCCTATGAACTTGCG 61.824 63.158 0.84 0.00 0.00 4.85
1718 1828 3.419815 CGTAGTTTTCTTCACGCTCAC 57.580 47.619 0.00 0.00 0.00 3.51
1719 1829 2.792674 CGTAGTTTTCTTCACGCTCACA 59.207 45.455 0.00 0.00 0.00 3.58
1720 1830 3.428870 CGTAGTTTTCTTCACGCTCACAT 59.571 43.478 0.00 0.00 0.00 3.21
1725 1835 3.667497 TTCTTCACGCTCACATTCTCT 57.333 42.857 0.00 0.00 0.00 3.10
1726 1836 3.223423 TCTTCACGCTCACATTCTCTC 57.777 47.619 0.00 0.00 0.00 3.20
1727 1837 1.916651 CTTCACGCTCACATTCTCTCG 59.083 52.381 0.00 0.00 0.00 4.04
1728 1838 1.165270 TCACGCTCACATTCTCTCGA 58.835 50.000 0.00 0.00 0.00 4.04
1730 1840 2.030274 TCACGCTCACATTCTCTCGAAA 60.030 45.455 0.00 0.00 31.91 3.46
1732 1842 3.184379 CACGCTCACATTCTCTCGAAAAA 59.816 43.478 0.00 0.00 31.91 1.94
1776 2037 3.982576 AAAAACAAAAGAGATCGGCGT 57.017 38.095 6.85 0.00 0.00 5.68
1778 2039 4.663636 AAAACAAAAGAGATCGGCGTAG 57.336 40.909 6.85 0.00 0.00 3.51
1779 2040 3.314541 AACAAAAGAGATCGGCGTAGT 57.685 42.857 6.85 0.00 0.00 2.73
1781 2042 3.660865 ACAAAAGAGATCGGCGTAGTTT 58.339 40.909 6.85 0.00 0.00 2.66
1783 2044 2.580966 AAGAGATCGGCGTAGTTTCC 57.419 50.000 6.85 0.00 0.00 3.13
1786 2047 2.496470 AGAGATCGGCGTAGTTTCCTTT 59.504 45.455 6.85 0.00 0.00 3.11
1787 2048 2.603560 GAGATCGGCGTAGTTTCCTTTG 59.396 50.000 6.85 0.00 0.00 2.77
1788 2049 2.232941 AGATCGGCGTAGTTTCCTTTGA 59.767 45.455 6.85 0.00 0.00 2.69
1792 2053 2.159572 CGGCGTAGTTTCCTTTGAATGG 60.160 50.000 0.00 0.00 0.00 3.16
1794 2055 3.365969 GGCGTAGTTTCCTTTGAATGGTG 60.366 47.826 0.00 0.00 0.00 4.17
1795 2056 3.500680 GCGTAGTTTCCTTTGAATGGTGA 59.499 43.478 0.00 0.00 0.00 4.02
1796 2057 4.023536 GCGTAGTTTCCTTTGAATGGTGAA 60.024 41.667 0.00 0.00 0.00 3.18
1797 2058 5.335661 GCGTAGTTTCCTTTGAATGGTGAAT 60.336 40.000 0.00 0.00 0.00 2.57
1798 2059 6.677913 CGTAGTTTCCTTTGAATGGTGAATT 58.322 36.000 0.00 0.00 0.00 2.17
1799 2060 7.145323 CGTAGTTTCCTTTGAATGGTGAATTT 58.855 34.615 0.00 0.00 0.00 1.82
1800 2061 7.114811 CGTAGTTTCCTTTGAATGGTGAATTTG 59.885 37.037 0.00 0.00 0.00 2.32
1801 2062 5.759763 AGTTTCCTTTGAATGGTGAATTTGC 59.240 36.000 0.00 0.00 0.00 3.68
1802 2063 3.911868 TCCTTTGAATGGTGAATTTGCG 58.088 40.909 0.00 0.00 0.00 4.85
1803 2064 3.320541 TCCTTTGAATGGTGAATTTGCGT 59.679 39.130 0.00 0.00 0.00 5.24
1804 2065 4.520874 TCCTTTGAATGGTGAATTTGCGTA 59.479 37.500 0.00 0.00 0.00 4.42
1805 2066 4.858692 CCTTTGAATGGTGAATTTGCGTAG 59.141 41.667 0.00 0.00 0.00 3.51
1806 2067 5.446143 TTTGAATGGTGAATTTGCGTAGT 57.554 34.783 0.00 0.00 0.00 2.73
1807 2068 5.446143 TTGAATGGTGAATTTGCGTAGTT 57.554 34.783 0.00 0.00 0.00 2.24
1808 2069 5.446143 TGAATGGTGAATTTGCGTAGTTT 57.554 34.783 0.00 0.00 0.00 2.66
2011 2286 4.169696 CCAACCGCGCCATAGGGA 62.170 66.667 0.00 0.00 35.59 4.20
2128 2455 1.755179 CCATGAAGGTGGGTGATCAC 58.245 55.000 17.91 17.91 35.55 3.06
2129 2456 1.283029 CCATGAAGGTGGGTGATCACT 59.717 52.381 24.50 4.18 37.75 3.41
2141 2468 1.135333 GTGATCACTCGAACCTCTCCC 59.865 57.143 18.83 0.00 0.00 4.30
2149 2476 2.364448 AACCTCTCCCGCTCTCCC 60.364 66.667 0.00 0.00 0.00 4.30
2212 2539 1.295746 GTTCCTGGTTCGGGGAGTC 59.704 63.158 0.00 0.00 32.80 3.36
2215 2542 2.359967 CCTGGTTCGGGGAGTCTCC 61.360 68.421 10.78 10.78 35.23 3.71
2250 2577 1.076533 CGTGCTCGACGTAATGCCTT 61.077 55.000 1.00 0.00 43.50 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.581289 TGGATGAAAAGTTTCCTCTAAAATGTA 57.419 29.630 8.39 0.00 36.36 2.29
16 17 8.360390 GTGGATGAAAAGTTTCCTCTAAAATGT 58.640 33.333 8.39 0.00 36.36 2.71
17 18 8.579863 AGTGGATGAAAAGTTTCCTCTAAAATG 58.420 33.333 8.39 0.00 36.36 2.32
18 19 8.712228 AGTGGATGAAAAGTTTCCTCTAAAAT 57.288 30.769 8.39 0.00 36.36 1.82
19 20 7.777910 TGAGTGGATGAAAAGTTTCCTCTAAAA 59.222 33.333 8.39 0.00 34.43 1.52
20 21 7.287061 TGAGTGGATGAAAAGTTTCCTCTAAA 58.713 34.615 8.39 0.00 34.43 1.85
21 22 6.837312 TGAGTGGATGAAAAGTTTCCTCTAA 58.163 36.000 8.39 0.00 34.43 2.10
22 23 6.433847 TGAGTGGATGAAAAGTTTCCTCTA 57.566 37.500 8.39 1.39 34.43 2.43
23 24 5.310409 TGAGTGGATGAAAAGTTTCCTCT 57.690 39.130 8.39 0.00 36.38 3.69
24 25 6.039829 AGTTTGAGTGGATGAAAAGTTTCCTC 59.960 38.462 1.46 1.57 36.36 3.71
25 26 5.893824 AGTTTGAGTGGATGAAAAGTTTCCT 59.106 36.000 1.46 0.00 36.36 3.36
26 27 6.149129 AGTTTGAGTGGATGAAAAGTTTCC 57.851 37.500 1.46 0.00 36.36 3.13
27 28 7.484140 AGAAGTTTGAGTGGATGAAAAGTTTC 58.516 34.615 0.00 0.00 37.69 2.78
28 29 7.410120 AGAAGTTTGAGTGGATGAAAAGTTT 57.590 32.000 0.00 0.00 0.00 2.66
29 30 7.410120 AAGAAGTTTGAGTGGATGAAAAGTT 57.590 32.000 0.00 0.00 0.00 2.66
30 31 7.093771 ACAAAGAAGTTTGAGTGGATGAAAAGT 60.094 33.333 4.91 0.00 45.22 2.66
31 32 7.260603 ACAAAGAAGTTTGAGTGGATGAAAAG 58.739 34.615 4.91 0.00 45.22 2.27
32 33 7.169158 ACAAAGAAGTTTGAGTGGATGAAAA 57.831 32.000 4.91 0.00 45.22 2.29
33 34 6.773976 ACAAAGAAGTTTGAGTGGATGAAA 57.226 33.333 4.91 0.00 45.22 2.69
34 35 7.873719 TTACAAAGAAGTTTGAGTGGATGAA 57.126 32.000 4.91 0.00 45.22 2.57
35 36 7.873719 TTTACAAAGAAGTTTGAGTGGATGA 57.126 32.000 4.91 0.00 45.22 2.92
36 37 9.533253 AATTTTACAAAGAAGTTTGAGTGGATG 57.467 29.630 4.91 0.00 45.22 3.51
38 39 9.581099 GAAATTTTACAAAGAAGTTTGAGTGGA 57.419 29.630 4.91 0.00 45.22 4.02
39 40 8.817100 GGAAATTTTACAAAGAAGTTTGAGTGG 58.183 33.333 4.91 0.00 45.22 4.00
40 41 9.586435 AGGAAATTTTACAAAGAAGTTTGAGTG 57.414 29.630 4.91 0.00 45.22 3.51
43 44 9.936759 ACAAGGAAATTTTACAAAGAAGTTTGA 57.063 25.926 4.91 0.00 45.22 2.69
53 54 9.672673 TGGATGAAAAACAAGGAAATTTTACAA 57.327 25.926 0.00 0.00 0.00 2.41
54 55 9.103861 GTGGATGAAAAACAAGGAAATTTTACA 57.896 29.630 0.00 0.00 0.00 2.41
55 56 9.325198 AGTGGATGAAAAACAAGGAAATTTTAC 57.675 29.630 0.00 0.00 0.00 2.01
56 57 9.541143 GAGTGGATGAAAAACAAGGAAATTTTA 57.459 29.630 0.00 0.00 0.00 1.52
57 58 8.046107 TGAGTGGATGAAAAACAAGGAAATTTT 58.954 29.630 0.00 0.00 0.00 1.82
58 59 7.563906 TGAGTGGATGAAAAACAAGGAAATTT 58.436 30.769 0.00 0.00 0.00 1.82
59 60 7.123355 TGAGTGGATGAAAAACAAGGAAATT 57.877 32.000 0.00 0.00 0.00 1.82
60 61 6.729690 TGAGTGGATGAAAAACAAGGAAAT 57.270 33.333 0.00 0.00 0.00 2.17
61 62 6.537453 TTGAGTGGATGAAAAACAAGGAAA 57.463 33.333 0.00 0.00 0.00 3.13
62 63 6.337356 GTTTGAGTGGATGAAAAACAAGGAA 58.663 36.000 0.00 0.00 32.34 3.36
63 64 5.449862 CGTTTGAGTGGATGAAAAACAAGGA 60.450 40.000 0.00 0.00 31.69 3.36
64 65 4.739716 CGTTTGAGTGGATGAAAAACAAGG 59.260 41.667 0.00 0.00 31.69 3.61
65 66 5.229887 CACGTTTGAGTGGATGAAAAACAAG 59.770 40.000 0.00 0.00 38.40 3.16
66 67 5.098893 CACGTTTGAGTGGATGAAAAACAA 58.901 37.500 0.00 0.00 38.40 2.83
67 68 4.396478 TCACGTTTGAGTGGATGAAAAACA 59.604 37.500 0.00 0.00 42.10 2.83
68 69 4.915704 TCACGTTTGAGTGGATGAAAAAC 58.084 39.130 0.00 0.00 42.10 2.43
69 70 5.168526 CTCACGTTTGAGTGGATGAAAAA 57.831 39.130 0.00 0.00 43.95 1.94
70 71 4.811555 CTCACGTTTGAGTGGATGAAAA 57.188 40.909 0.00 0.00 43.95 2.29
81 82 3.567585 TGGATGCATTTTCTCACGTTTGA 59.432 39.130 0.00 0.00 0.00 2.69
82 83 3.670055 GTGGATGCATTTTCTCACGTTTG 59.330 43.478 0.00 0.00 0.00 2.93
83 84 3.569701 AGTGGATGCATTTTCTCACGTTT 59.430 39.130 0.00 0.00 0.00 3.60
84 85 3.149196 AGTGGATGCATTTTCTCACGTT 58.851 40.909 0.00 0.00 0.00 3.99
85 86 2.744202 GAGTGGATGCATTTTCTCACGT 59.256 45.455 0.00 0.00 0.00 4.49
86 87 2.743664 TGAGTGGATGCATTTTCTCACG 59.256 45.455 18.07 0.00 0.00 4.35
87 88 4.771590 TTGAGTGGATGCATTTTCTCAC 57.228 40.909 20.25 14.65 32.80 3.51
88 89 5.716094 CAATTGAGTGGATGCATTTTCTCA 58.284 37.500 18.07 18.07 0.00 3.27
89 90 4.565564 GCAATTGAGTGGATGCATTTTCTC 59.434 41.667 10.34 9.50 38.63 2.87
90 91 4.501071 GCAATTGAGTGGATGCATTTTCT 58.499 39.130 10.34 0.00 38.63 2.52
91 92 3.619929 GGCAATTGAGTGGATGCATTTTC 59.380 43.478 10.34 0.00 40.51 2.29
92 93 3.262405 AGGCAATTGAGTGGATGCATTTT 59.738 39.130 10.34 0.00 40.51 1.82
93 94 2.835764 AGGCAATTGAGTGGATGCATTT 59.164 40.909 10.34 0.00 40.51 2.32
94 95 2.463752 AGGCAATTGAGTGGATGCATT 58.536 42.857 10.34 0.00 40.51 3.56
95 96 2.154567 AGGCAATTGAGTGGATGCAT 57.845 45.000 10.34 0.00 40.51 3.96
96 97 1.927487 AAGGCAATTGAGTGGATGCA 58.073 45.000 10.34 0.00 40.51 3.96
97 98 2.733227 CGAAAGGCAATTGAGTGGATGC 60.733 50.000 10.34 0.00 38.06 3.91
98 99 3.141002 CGAAAGGCAATTGAGTGGATG 57.859 47.619 10.34 0.00 0.00 3.51
120 121 2.438434 ATTGGCGGAGGGCGAAAG 60.438 61.111 0.00 0.00 42.82 2.62
121 122 2.749839 CATTGGCGGAGGGCGAAA 60.750 61.111 0.00 0.00 42.82 3.46
122 123 3.711814 TCATTGGCGGAGGGCGAA 61.712 61.111 0.00 0.00 43.73 4.70
123 124 4.467084 GTCATTGGCGGAGGGCGA 62.467 66.667 0.00 0.00 44.92 5.54
132 133 1.961277 CCTATCGGCGGTCATTGGC 60.961 63.158 7.21 0.00 0.00 4.52
133 134 0.677288 TACCTATCGGCGGTCATTGG 59.323 55.000 7.21 6.53 35.98 3.16
134 135 1.935300 GCTACCTATCGGCGGTCATTG 60.935 57.143 7.21 0.00 35.98 2.82
135 136 0.317479 GCTACCTATCGGCGGTCATT 59.683 55.000 7.21 0.00 35.98 2.57
136 137 1.863662 CGCTACCTATCGGCGGTCAT 61.864 60.000 7.21 0.00 44.32 3.06
137 138 2.549198 CGCTACCTATCGGCGGTCA 61.549 63.158 7.21 0.00 44.32 4.02
138 139 2.254651 CGCTACCTATCGGCGGTC 59.745 66.667 7.21 0.00 44.32 4.79
142 143 2.355956 GGTGCGCTACCTATCGGC 60.356 66.667 18.16 0.00 46.51 5.54
150 151 2.884207 GCCACGTAGGTGCGCTAC 60.884 66.667 9.73 5.08 43.00 3.58
151 152 4.485834 CGCCACGTAGGTGCGCTA 62.486 66.667 9.73 0.00 43.00 4.26
192 193 4.803426 GAGGTCAGCGTCGCCAGG 62.803 72.222 14.86 4.07 0.00 4.45
193 194 4.803426 GGAGGTCAGCGTCGCCAG 62.803 72.222 14.86 7.31 0.00 4.85
197 198 4.778415 CGTGGGAGGTCAGCGTCG 62.778 72.222 0.00 0.00 0.00 5.12
241 242 4.659172 TGGTTGAAGGGCTGGGCG 62.659 66.667 0.00 0.00 0.00 6.13
242 243 2.991540 GTGGTTGAAGGGCTGGGC 60.992 66.667 0.00 0.00 0.00 5.36
243 244 2.283173 GGTGGTTGAAGGGCTGGG 60.283 66.667 0.00 0.00 0.00 4.45
244 245 2.672996 CGGTGGTTGAAGGGCTGG 60.673 66.667 0.00 0.00 0.00 4.85
245 246 3.365265 GCGGTGGTTGAAGGGCTG 61.365 66.667 0.00 0.00 0.00 4.85
246 247 2.920076 TTTGCGGTGGTTGAAGGGCT 62.920 55.000 0.00 0.00 0.00 5.19
247 248 1.815817 ATTTGCGGTGGTTGAAGGGC 61.816 55.000 0.00 0.00 0.00 5.19
248 249 0.243636 GATTTGCGGTGGTTGAAGGG 59.756 55.000 0.00 0.00 0.00 3.95
249 250 0.958091 TGATTTGCGGTGGTTGAAGG 59.042 50.000 0.00 0.00 0.00 3.46
250 251 3.302365 AATGATTTGCGGTGGTTGAAG 57.698 42.857 0.00 0.00 0.00 3.02
251 252 3.388308 CAAATGATTTGCGGTGGTTGAA 58.612 40.909 4.82 0.00 33.36 2.69
252 253 2.288702 CCAAATGATTTGCGGTGGTTGA 60.289 45.455 12.26 0.00 39.31 3.18
253 254 2.067766 CCAAATGATTTGCGGTGGTTG 58.932 47.619 12.26 0.00 39.31 3.77
254 255 1.607767 GCCAAATGATTTGCGGTGGTT 60.608 47.619 12.26 0.00 39.31 3.67
255 256 0.037419 GCCAAATGATTTGCGGTGGT 60.037 50.000 12.26 0.00 39.31 4.16
256 257 0.247185 AGCCAAATGATTTGCGGTGG 59.753 50.000 12.26 0.47 39.31 4.61
257 258 1.632422 GAGCCAAATGATTTGCGGTG 58.368 50.000 12.26 0.41 39.31 4.94
258 259 0.532115 GGAGCCAAATGATTTGCGGT 59.468 50.000 12.26 10.77 39.31 5.68
259 260 0.179103 GGGAGCCAAATGATTTGCGG 60.179 55.000 12.26 1.30 39.31 5.69
260 261 0.819582 AGGGAGCCAAATGATTTGCG 59.180 50.000 12.26 7.12 39.31 4.85
261 262 1.741394 GCAGGGAGCCAAATGATTTGC 60.741 52.381 12.26 8.06 39.31 3.68
262 263 1.551430 TGCAGGGAGCCAAATGATTTG 59.449 47.619 10.84 10.84 44.83 2.32
263 264 1.941377 TGCAGGGAGCCAAATGATTT 58.059 45.000 0.00 0.00 44.83 2.17
264 265 1.551883 GTTGCAGGGAGCCAAATGATT 59.448 47.619 0.00 0.00 44.83 2.57
265 266 1.188863 GTTGCAGGGAGCCAAATGAT 58.811 50.000 0.00 0.00 44.83 2.45
266 267 0.899717 GGTTGCAGGGAGCCAAATGA 60.900 55.000 0.00 0.00 44.83 2.57
267 268 0.901580 AGGTTGCAGGGAGCCAAATG 60.902 55.000 0.00 0.00 44.83 2.32
268 269 0.901580 CAGGTTGCAGGGAGCCAAAT 60.902 55.000 0.00 0.00 44.83 2.32
269 270 1.531365 CAGGTTGCAGGGAGCCAAA 60.531 57.895 0.00 0.00 44.83 3.28
270 271 2.115910 CAGGTTGCAGGGAGCCAA 59.884 61.111 0.00 0.00 44.83 4.52
271 272 4.666253 GCAGGTTGCAGGGAGCCA 62.666 66.667 0.00 0.00 44.26 4.75
280 281 4.503741 TGAAGTAGAAAATGCAGGTTGC 57.496 40.909 0.00 0.00 45.29 4.17
281 282 5.183713 TGGATGAAGTAGAAAATGCAGGTTG 59.816 40.000 0.00 0.00 0.00 3.77
282 283 5.183904 GTGGATGAAGTAGAAAATGCAGGTT 59.816 40.000 0.00 0.00 0.00 3.50
283 284 4.702131 GTGGATGAAGTAGAAAATGCAGGT 59.298 41.667 0.00 0.00 0.00 4.00
284 285 4.096984 GGTGGATGAAGTAGAAAATGCAGG 59.903 45.833 0.00 0.00 0.00 4.85
285 286 4.201851 CGGTGGATGAAGTAGAAAATGCAG 60.202 45.833 0.00 0.00 0.00 4.41
286 287 3.689161 CGGTGGATGAAGTAGAAAATGCA 59.311 43.478 0.00 0.00 0.00 3.96
287 288 3.689649 ACGGTGGATGAAGTAGAAAATGC 59.310 43.478 0.00 0.00 0.00 3.56
288 289 6.761242 TGATACGGTGGATGAAGTAGAAAATG 59.239 38.462 0.00 0.00 0.00 2.32
289 290 6.884832 TGATACGGTGGATGAAGTAGAAAAT 58.115 36.000 0.00 0.00 0.00 1.82
290 291 6.288941 TGATACGGTGGATGAAGTAGAAAA 57.711 37.500 0.00 0.00 0.00 2.29
291 292 5.925506 TGATACGGTGGATGAAGTAGAAA 57.074 39.130 0.00 0.00 0.00 2.52
292 293 5.421056 AGTTGATACGGTGGATGAAGTAGAA 59.579 40.000 0.00 0.00 0.00 2.10
293 294 4.954202 AGTTGATACGGTGGATGAAGTAGA 59.046 41.667 0.00 0.00 0.00 2.59
294 295 5.263968 AGTTGATACGGTGGATGAAGTAG 57.736 43.478 0.00 0.00 0.00 2.57
295 296 5.670792 AAGTTGATACGGTGGATGAAGTA 57.329 39.130 0.00 0.00 0.00 2.24
296 297 4.553330 AAGTTGATACGGTGGATGAAGT 57.447 40.909 0.00 0.00 0.00 3.01
297 298 4.695455 ACAAAGTTGATACGGTGGATGAAG 59.305 41.667 0.00 0.00 0.00 3.02
298 299 4.647611 ACAAAGTTGATACGGTGGATGAA 58.352 39.130 0.00 0.00 0.00 2.57
299 300 4.280436 ACAAAGTTGATACGGTGGATGA 57.720 40.909 0.00 0.00 0.00 2.92
300 301 4.695455 AGAACAAAGTTGATACGGTGGATG 59.305 41.667 0.00 0.00 0.00 3.51
301 302 4.906618 AGAACAAAGTTGATACGGTGGAT 58.093 39.130 0.00 0.00 0.00 3.41
302 303 4.202274 TGAGAACAAAGTTGATACGGTGGA 60.202 41.667 0.00 0.00 0.00 4.02
303 304 4.062293 TGAGAACAAAGTTGATACGGTGG 58.938 43.478 0.00 0.00 0.00 4.61
304 305 4.084013 GGTGAGAACAAAGTTGATACGGTG 60.084 45.833 0.00 0.00 0.00 4.94
305 306 4.062991 GGTGAGAACAAAGTTGATACGGT 58.937 43.478 0.00 0.00 0.00 4.83
306 307 4.062293 TGGTGAGAACAAAGTTGATACGG 58.938 43.478 0.00 0.00 0.00 4.02
307 308 5.862924 ATGGTGAGAACAAAGTTGATACG 57.137 39.130 0.00 0.00 0.00 3.06
308 309 8.871686 AAAAATGGTGAGAACAAAGTTGATAC 57.128 30.769 0.00 0.00 0.00 2.24
342 343 4.142160 GCTGGTGAGAGAACAAAGGTTTTT 60.142 41.667 0.00 0.00 37.36 1.94
343 344 3.381590 GCTGGTGAGAGAACAAAGGTTTT 59.618 43.478 0.00 0.00 37.36 2.43
344 345 2.952310 GCTGGTGAGAGAACAAAGGTTT 59.048 45.455 0.00 0.00 37.36 3.27
345 346 2.092429 TGCTGGTGAGAGAACAAAGGTT 60.092 45.455 0.00 0.00 40.76 3.50
346 347 1.490490 TGCTGGTGAGAGAACAAAGGT 59.510 47.619 0.00 0.00 0.00 3.50
347 348 1.876156 GTGCTGGTGAGAGAACAAAGG 59.124 52.381 0.00 0.00 0.00 3.11
348 349 1.876156 GGTGCTGGTGAGAGAACAAAG 59.124 52.381 0.00 0.00 0.00 2.77
349 350 1.967319 GGTGCTGGTGAGAGAACAAA 58.033 50.000 0.00 0.00 0.00 2.83
350 351 3.706055 GGTGCTGGTGAGAGAACAA 57.294 52.632 0.00 0.00 0.00 2.83
709 710 2.852075 TGGTATGGGCGGGATCCC 60.852 66.667 22.12 22.12 46.73 3.85
744 745 1.076549 GGTGGGCCATGTTTGGAGA 59.923 57.895 10.70 0.00 46.92 3.71
767 768 3.782443 CCGGGGTTTCTCGAGGGG 61.782 72.222 13.56 0.00 0.00 4.79
828 829 1.999735 CGTGACGTGGCTGTTGAATAT 59.000 47.619 0.00 0.00 0.00 1.28
862 863 2.094854 GGGTATTTATCGGCGATCGTCT 60.095 50.000 27.61 12.03 40.32 4.18
863 864 2.257034 GGGTATTTATCGGCGATCGTC 58.743 52.381 27.61 14.29 40.32 4.20
864 865 1.067354 GGGGTATTTATCGGCGATCGT 60.067 52.381 27.61 15.38 40.32 3.73
865 866 1.636988 GGGGTATTTATCGGCGATCG 58.363 55.000 27.61 11.69 40.90 3.69
866 867 1.738030 CGGGGGTATTTATCGGCGATC 60.738 57.143 27.61 11.42 0.00 3.69
867 868 0.248289 CGGGGGTATTTATCGGCGAT 59.752 55.000 26.95 26.95 0.00 4.58
873 897 0.953960 CGGCAGCGGGGGTATTTATC 60.954 60.000 0.00 0.00 0.00 1.75
886 915 3.435186 GTCTTGCTTCCCGGCAGC 61.435 66.667 15.32 15.32 43.39 5.25
887 916 3.121030 CGTCTTGCTTCCCGGCAG 61.121 66.667 0.00 0.00 43.39 4.85
888 917 3.171828 TTCGTCTTGCTTCCCGGCA 62.172 57.895 0.00 0.00 40.74 5.69
892 923 2.450609 TGTAGTTCGTCTTGCTTCCC 57.549 50.000 0.00 0.00 0.00 3.97
893 924 2.930682 GGATGTAGTTCGTCTTGCTTCC 59.069 50.000 0.00 0.00 33.00 3.46
902 933 3.606687 GTTGGATTGGGATGTAGTTCGT 58.393 45.455 0.00 0.00 0.00 3.85
903 934 2.943033 GGTTGGATTGGGATGTAGTTCG 59.057 50.000 0.00 0.00 0.00 3.95
925 956 8.210946 ACAACGATCTTGGATTGGATTAGATTA 58.789 33.333 0.00 0.00 0.00 1.75
931 972 4.335416 ACACAACGATCTTGGATTGGATT 58.665 39.130 0.00 0.00 0.00 3.01
949 990 4.332828 TCGATACTCTCAGAAGGAACACA 58.667 43.478 0.00 0.00 0.00 3.72
953 994 6.205853 GCTCTTATCGATACTCTCAGAAGGAA 59.794 42.308 4.16 0.00 0.00 3.36
963 1004 8.059502 CGTATATGTCTGCTCTTATCGATACTC 58.940 40.741 4.16 0.00 0.00 2.59
967 1009 6.745159 ACGTATATGTCTGCTCTTATCGAT 57.255 37.500 2.16 2.16 0.00 3.59
973 1015 5.706369 CCTACCTACGTATATGTCTGCTCTT 59.294 44.000 0.00 0.00 0.00 2.85
974 1016 5.247084 CCTACCTACGTATATGTCTGCTCT 58.753 45.833 0.00 0.00 0.00 4.09
975 1017 4.142643 GCCTACCTACGTATATGTCTGCTC 60.143 50.000 0.00 0.00 0.00 4.26
979 1021 4.277515 TCGCCTACCTACGTATATGTCT 57.722 45.455 0.00 0.00 0.00 3.41
982 1024 3.488721 GCCATCGCCTACCTACGTATATG 60.489 52.174 0.00 0.00 0.00 1.78
984 1026 2.086869 GCCATCGCCTACCTACGTATA 58.913 52.381 0.00 0.00 0.00 1.47
985 1027 0.886563 GCCATCGCCTACCTACGTAT 59.113 55.000 0.00 0.00 0.00 3.06
1162 1232 2.432628 GAACACCGTCGCCTCTGG 60.433 66.667 0.00 0.00 0.00 3.86
1163 1233 2.805353 CGAACACCGTCGCCTCTG 60.805 66.667 0.00 0.00 33.66 3.35
1164 1234 2.981909 TCGAACACCGTCGCCTCT 60.982 61.111 0.00 0.00 40.88 3.69
1165 1235 2.804090 GTCGAACACCGTCGCCTC 60.804 66.667 0.00 0.00 40.88 4.70
1169 1239 1.602877 CTTTCCGTCGAACACCGTCG 61.603 60.000 0.00 0.00 46.28 5.12
1170 1240 1.883725 GCTTTCCGTCGAACACCGTC 61.884 60.000 0.00 0.00 39.75 4.79
1171 1241 1.952635 GCTTTCCGTCGAACACCGT 60.953 57.895 0.00 0.00 39.75 4.83
1172 1242 1.886861 CTGCTTTCCGTCGAACACCG 61.887 60.000 0.00 0.00 40.25 4.94
1173 1243 0.599204 TCTGCTTTCCGTCGAACACC 60.599 55.000 0.00 0.00 0.00 4.16
1174 1244 1.192534 CTTCTGCTTTCCGTCGAACAC 59.807 52.381 0.00 0.00 0.00 3.32
1175 1245 1.497991 CTTCTGCTTTCCGTCGAACA 58.502 50.000 0.00 0.00 0.00 3.18
1176 1246 0.164002 GCTTCTGCTTTCCGTCGAAC 59.836 55.000 0.00 0.00 36.03 3.95
1177 1247 0.249699 TGCTTCTGCTTTCCGTCGAA 60.250 50.000 0.00 0.00 40.48 3.71
1178 1248 0.667487 CTGCTTCTGCTTTCCGTCGA 60.667 55.000 0.00 0.00 40.48 4.20
1179 1249 0.667487 TCTGCTTCTGCTTTCCGTCG 60.667 55.000 0.00 0.00 40.48 5.12
1180 1250 1.074752 CTCTGCTTCTGCTTTCCGTC 58.925 55.000 0.00 0.00 40.48 4.79
1181 1251 0.321122 CCTCTGCTTCTGCTTTCCGT 60.321 55.000 0.00 0.00 40.48 4.69
1182 1252 1.023513 CCCTCTGCTTCTGCTTTCCG 61.024 60.000 0.00 0.00 40.48 4.30
1183 1253 1.311651 GCCCTCTGCTTCTGCTTTCC 61.312 60.000 0.00 0.00 40.48 3.13
1184 1254 1.642952 CGCCCTCTGCTTCTGCTTTC 61.643 60.000 0.00 0.00 40.48 2.62
1185 1255 1.673665 CGCCCTCTGCTTCTGCTTT 60.674 57.895 0.00 0.00 40.48 3.51
1186 1256 2.046507 CGCCCTCTGCTTCTGCTT 60.047 61.111 0.00 0.00 40.48 3.91
1187 1257 4.774503 GCGCCCTCTGCTTCTGCT 62.775 66.667 0.00 0.00 40.48 4.24
1189 1259 4.749310 ACGCGCCCTCTGCTTCTG 62.749 66.667 5.73 0.00 38.05 3.02
1190 1260 4.443266 GACGCGCCCTCTGCTTCT 62.443 66.667 5.73 0.00 38.05 2.85
1287 1369 2.894307 ACGCGGAAATTAAGCTTCAC 57.106 45.000 12.47 0.00 0.00 3.18
1307 1398 1.425448 AGAGGCAAAAGCTACAGGGTT 59.575 47.619 0.00 0.00 37.22 4.11
1308 1399 1.068121 AGAGGCAAAAGCTACAGGGT 58.932 50.000 0.00 0.00 0.00 4.34
1309 1400 2.206576 AAGAGGCAAAAGCTACAGGG 57.793 50.000 0.00 0.00 0.00 4.45
1334 1425 2.569657 CACGGCACATGCTTGCAT 59.430 55.556 10.16 1.81 44.94 3.96
1364 1455 0.463654 ACATATGCCGCCATTGTCGT 60.464 50.000 1.58 0.00 32.85 4.34
1365 1456 0.041047 CACATATGCCGCCATTGTCG 60.041 55.000 1.58 0.00 32.85 4.35
1375 1466 8.285394 CAGTCACATTTTATCTACACATATGCC 58.715 37.037 1.58 0.00 0.00 4.40
1419 1510 8.690884 AGGAAGAAAGAAAGAAAGAAAGAAAGG 58.309 33.333 0.00 0.00 0.00 3.11
1434 1525 5.072741 CCAGGATTTCACAGGAAGAAAGAA 58.927 41.667 0.00 0.00 38.27 2.52
1435 1526 4.507335 CCCAGGATTTCACAGGAAGAAAGA 60.507 45.833 0.00 0.00 38.27 2.52
1436 1527 3.760684 CCCAGGATTTCACAGGAAGAAAG 59.239 47.826 0.00 0.00 38.27 2.62
1437 1528 3.140144 ACCCAGGATTTCACAGGAAGAAA 59.860 43.478 0.00 0.00 39.11 2.52
1438 1529 2.716424 ACCCAGGATTTCACAGGAAGAA 59.284 45.455 0.00 0.00 33.82 2.52
1439 1530 2.040278 CACCCAGGATTTCACAGGAAGA 59.960 50.000 0.00 0.00 33.82 2.87
1440 1531 2.440409 CACCCAGGATTTCACAGGAAG 58.560 52.381 0.00 0.00 33.82 3.46
1441 1532 1.547675 GCACCCAGGATTTCACAGGAA 60.548 52.381 0.00 0.00 0.00 3.36
1442 1533 0.038166 GCACCCAGGATTTCACAGGA 59.962 55.000 0.00 0.00 0.00 3.86
1443 1534 0.038744 AGCACCCAGGATTTCACAGG 59.961 55.000 0.00 0.00 0.00 4.00
1444 1535 1.171308 CAGCACCCAGGATTTCACAG 58.829 55.000 0.00 0.00 0.00 3.66
1476 1570 5.520288 CGTATAGCAAATCTTATGATCGGGG 59.480 44.000 0.00 0.00 31.51 5.73
1503 1597 4.342378 TCAGAAGGTATAGCAAATCGAGCT 59.658 41.667 4.48 2.99 45.77 4.09
1511 1605 5.643777 GCTTCAAGTTCAGAAGGTATAGCAA 59.356 40.000 4.48 0.00 42.08 3.91
1513 1607 4.268884 CGCTTCAAGTTCAGAAGGTATAGC 59.731 45.833 0.00 0.00 42.08 2.97
1514 1608 4.268884 GCGCTTCAAGTTCAGAAGGTATAG 59.731 45.833 0.00 0.00 42.08 1.31
1519 1628 0.519077 GGCGCTTCAAGTTCAGAAGG 59.481 55.000 7.64 0.00 42.08 3.46
1582 1691 6.183360 CCGTCTCTTCTTTTCTTTTGAGGTTT 60.183 38.462 0.00 0.00 0.00 3.27
1598 1707 2.552031 GGGTAATTCAGCCGTCTCTTC 58.448 52.381 0.00 0.00 34.44 2.87
1644 1753 3.511934 AGTTCATAGGCCCGCTTAGATAG 59.488 47.826 0.00 0.00 0.00 2.08
1645 1754 3.507411 AGTTCATAGGCCCGCTTAGATA 58.493 45.455 0.00 0.00 0.00 1.98
1646 1755 2.330216 AGTTCATAGGCCCGCTTAGAT 58.670 47.619 0.00 0.00 0.00 1.98
1647 1756 1.789523 AGTTCATAGGCCCGCTTAGA 58.210 50.000 0.00 0.00 0.00 2.10
1653 1762 0.742990 TTCGCAAGTTCATAGGCCCG 60.743 55.000 0.00 0.00 39.48 6.13
1670 1779 8.437360 AATTCACCATTCAAAGGAAAAACTTC 57.563 30.769 0.00 0.00 36.43 3.01
1677 1786 4.202202 ACGCAAATTCACCATTCAAAGGAA 60.202 37.500 0.00 0.00 37.45 3.36
1772 2033 2.817844 ACCATTCAAAGGAAACTACGCC 59.182 45.455 0.00 0.00 42.68 5.68
1774 2035 5.682943 TTCACCATTCAAAGGAAACTACG 57.317 39.130 0.00 0.00 42.68 3.51
1775 2036 7.095649 GCAAATTCACCATTCAAAGGAAACTAC 60.096 37.037 0.00 0.00 42.68 2.73
1776 2037 6.928492 GCAAATTCACCATTCAAAGGAAACTA 59.072 34.615 0.00 0.00 42.68 2.24
1778 2039 5.333263 CGCAAATTCACCATTCAAAGGAAAC 60.333 40.000 0.00 0.00 36.43 2.78
1779 2040 4.749099 CGCAAATTCACCATTCAAAGGAAA 59.251 37.500 0.00 0.00 36.43 3.13
1781 2042 3.320541 ACGCAAATTCACCATTCAAAGGA 59.679 39.130 0.00 0.00 0.00 3.36
1783 2044 5.460646 ACTACGCAAATTCACCATTCAAAG 58.539 37.500 0.00 0.00 0.00 2.77
1786 2047 5.446143 AAACTACGCAAATTCACCATTCA 57.554 34.783 0.00 0.00 0.00 2.57
1787 2048 4.857037 GGAAACTACGCAAATTCACCATTC 59.143 41.667 0.00 0.00 0.00 2.67
1788 2049 4.522789 AGGAAACTACGCAAATTCACCATT 59.477 37.500 0.00 0.00 40.61 3.16
1792 2053 4.909880 GTCAAGGAAACTACGCAAATTCAC 59.090 41.667 0.00 0.00 42.68 3.18
1794 2055 5.103290 TGTCAAGGAAACTACGCAAATTC 57.897 39.130 0.00 0.00 42.68 2.17
1795 2056 5.705609 ATGTCAAGGAAACTACGCAAATT 57.294 34.783 0.00 0.00 42.68 1.82
1796 2057 5.705609 AATGTCAAGGAAACTACGCAAAT 57.294 34.783 0.00 0.00 42.68 2.32
1797 2058 5.508200 AAATGTCAAGGAAACTACGCAAA 57.492 34.783 0.00 0.00 42.68 3.68
1798 2059 5.508200 AAAATGTCAAGGAAACTACGCAA 57.492 34.783 0.00 0.00 42.68 4.85
1799 2060 5.508200 AAAAATGTCAAGGAAACTACGCA 57.492 34.783 0.00 0.00 42.68 5.24
1831 2092 8.877864 AAACTGTAAATCATGTCAAGGGATAA 57.122 30.769 0.00 0.00 0.00 1.75
2120 2447 1.135333 GGAGAGGTTCGAGTGATCACC 59.865 57.143 22.21 12.53 0.00 4.02
2128 2455 1.720694 GAGAGCGGGAGAGGTTCGAG 61.721 65.000 0.00 0.00 0.00 4.04
2129 2456 1.749638 GAGAGCGGGAGAGGTTCGA 60.750 63.158 0.00 0.00 0.00 3.71
2141 2468 1.118838 ATCCAGAGAAAGGGAGAGCG 58.881 55.000 0.00 0.00 36.45 5.03
2149 2476 0.392193 ACGGCTGCATCCAGAGAAAG 60.392 55.000 7.47 0.00 41.77 2.62
2250 2577 4.196778 TGCACAGGAAACCCGGCA 62.197 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.