Multiple sequence alignment - TraesCS4B01G296000

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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 TraesCS4B01G296000 chr4B 100.000 2384 0 0 1 2384 581333340 581330957 0.000000e+00 4403.0
1 TraesCS4B01G296000 chr4D 95.174 1119 42 4 745 1858 465046807 465045696 0.000000e+00 1757.0
2 TraesCS4B01G296000 chr4D 87.477 535 47 8 1857 2384 465045614 465045093 1.220000e-167 599.0
3 TraesCS4B01G296000 chr4D 85.912 433 47 8 222 651 465047645 465047224 1.300000e-122 449.0
4 TraesCS4B01G296000 chr7D 92.105 152 12 0 1 152 462301643 462301492 5.160000e-52 215.0
5 TraesCS4B01G296000 chr3B 89.583 144 13 2 11 152 738987334 738987191 5.230000e-42 182.0
6 TraesCS4B01G296000 chr1D 88.811 143 16 0 10 152 58297265 58297123 2.440000e-40 176.0
7 TraesCS4B01G296000 chr4A 82.022 89 16 0 162 250 32966772 32966860 2.540000e-10 76.8


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 TraesCS4B01G296000 chr4B 581330957 581333340 2383 True 4403 4403 100.000 1 2384 1 chr4B.!!$R1 2383
1 TraesCS4B01G296000 chr4D 465045093 465047645 2552 True 935 1757 89.521 222 2384 3 chr4D.!!$R1 2162

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
912 1238 0.105224 ACGACACCATCCAAACACGA 59.895 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2390 0.108662 TGCACTCTGATGCTACCGTG 60.109 55.0 11.45 0.0 46.28 4.94 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
17 18 3.996124 ACAGCGTGCCGAAGAGCT 61.996 61.111 0.00 0.00 41.07 4.09
18 19 3.184683 CAGCGTGCCGAAGAGCTC 61.185 66.667 5.27 5.27 37.94 4.09
19 20 3.377759 AGCGTGCCGAAGAGCTCT 61.378 61.111 11.45 11.45 34.48 4.09
20 21 2.883253 GCGTGCCGAAGAGCTCTC 60.883 66.667 18.55 9.76 0.00 3.20
21 22 2.881389 CGTGCCGAAGAGCTCTCT 59.119 61.111 18.55 7.43 42.75 3.10
32 33 3.885724 AGAGCTCTCTTTGGCTAAGAC 57.114 47.619 11.45 0.00 37.96 3.01
33 34 3.440127 AGAGCTCTCTTTGGCTAAGACT 58.560 45.455 11.45 3.90 37.96 3.24
34 35 4.605183 AGAGCTCTCTTTGGCTAAGACTA 58.395 43.478 11.45 0.00 37.96 2.59
35 36 4.644685 AGAGCTCTCTTTGGCTAAGACTAG 59.355 45.833 11.45 9.03 37.96 2.57
36 37 3.704061 AGCTCTCTTTGGCTAAGACTAGG 59.296 47.826 7.31 0.00 37.96 3.02
43 44 2.685850 GGCTAAGACTAGGCCGAAAA 57.314 50.000 0.00 0.00 43.35 2.29
44 45 2.552031 GGCTAAGACTAGGCCGAAAAG 58.448 52.381 0.00 0.00 43.35 2.27
45 46 1.934525 GCTAAGACTAGGCCGAAAAGC 59.065 52.381 0.00 0.00 0.00 3.51
54 55 1.429423 GCCGAAAAGCCCATCTTCG 59.571 57.895 0.00 0.00 41.18 3.79
62 63 3.842869 GCCCATCTTCGGCCTATAG 57.157 57.895 0.00 0.00 40.78 1.31
63 64 1.267121 GCCCATCTTCGGCCTATAGA 58.733 55.000 0.00 0.41 40.78 1.98
64 65 1.623811 GCCCATCTTCGGCCTATAGAA 59.376 52.381 0.00 0.00 40.78 2.10
65 66 2.354203 GCCCATCTTCGGCCTATAGAAG 60.354 54.545 10.87 10.87 43.70 2.85
74 75 1.965219 CCTATAGAAGGCCGACGGG 59.035 63.158 17.22 0.00 38.97 5.28
75 76 1.533469 CCTATAGAAGGCCGACGGGG 61.533 65.000 17.22 0.37 38.97 5.73
76 77 0.826672 CTATAGAAGGCCGACGGGGT 60.827 60.000 17.22 0.00 38.44 4.95
77 78 0.825010 TATAGAAGGCCGACGGGGTC 60.825 60.000 17.22 0.00 42.41 4.46
78 79 2.866523 ATAGAAGGCCGACGGGGTCA 62.867 60.000 17.22 0.00 45.54 4.02
79 80 2.866523 TAGAAGGCCGACGGGGTCAT 62.867 60.000 17.22 0.00 45.54 3.06
80 81 2.364579 AAGGCCGACGGGGTCATA 60.365 61.111 17.22 0.00 45.54 2.15
81 82 2.365095 GAAGGCCGACGGGGTCATAG 62.365 65.000 17.22 0.00 45.54 2.23
82 83 3.152400 GGCCGACGGGGTCATAGT 61.152 66.667 17.22 0.00 41.38 2.12
83 84 1.829533 GGCCGACGGGGTCATAGTA 60.830 63.158 17.22 0.00 41.38 1.82
84 85 1.183676 GGCCGACGGGGTCATAGTAT 61.184 60.000 17.22 0.00 41.38 2.12
85 86 0.677842 GCCGACGGGGTCATAGTATT 59.322 55.000 17.22 0.00 38.44 1.89
86 87 1.604693 GCCGACGGGGTCATAGTATTG 60.605 57.143 17.22 0.00 38.44 1.90
87 88 1.604693 CCGACGGGGTCATAGTATTGC 60.605 57.143 5.81 0.00 32.09 3.56
88 89 1.340248 CGACGGGGTCATAGTATTGCT 59.660 52.381 0.00 0.00 32.09 3.91
89 90 2.223971 CGACGGGGTCATAGTATTGCTT 60.224 50.000 0.00 0.00 32.09 3.91
90 91 3.740141 CGACGGGGTCATAGTATTGCTTT 60.740 47.826 0.00 0.00 32.09 3.51
91 92 4.196971 GACGGGGTCATAGTATTGCTTTT 58.803 43.478 0.00 0.00 32.09 2.27
92 93 4.595986 ACGGGGTCATAGTATTGCTTTTT 58.404 39.130 0.00 0.00 0.00 1.94
117 118 5.019785 CCCTTAGGTGCTATAGTTTTCGT 57.980 43.478 0.84 0.00 0.00 3.85
118 119 6.152932 CCCTTAGGTGCTATAGTTTTCGTA 57.847 41.667 0.84 0.00 0.00 3.43
119 120 6.756221 CCCTTAGGTGCTATAGTTTTCGTAT 58.244 40.000 0.84 0.00 0.00 3.06
120 121 7.215085 CCCTTAGGTGCTATAGTTTTCGTATT 58.785 38.462 0.84 0.00 0.00 1.89
121 122 7.713942 CCCTTAGGTGCTATAGTTTTCGTATTT 59.286 37.037 0.84 0.00 0.00 1.40
122 123 8.548721 CCTTAGGTGCTATAGTTTTCGTATTTG 58.451 37.037 0.84 0.00 0.00 2.32
123 124 6.359480 AGGTGCTATAGTTTTCGTATTTGC 57.641 37.500 0.84 0.00 0.00 3.68
124 125 6.113411 AGGTGCTATAGTTTTCGTATTTGCT 58.887 36.000 0.84 0.00 0.00 3.91
125 126 7.270047 AGGTGCTATAGTTTTCGTATTTGCTA 58.730 34.615 0.84 0.00 0.00 3.49
126 127 7.224167 AGGTGCTATAGTTTTCGTATTTGCTAC 59.776 37.037 0.84 0.00 0.00 3.58
127 128 7.010738 GGTGCTATAGTTTTCGTATTTGCTACA 59.989 37.037 0.84 0.00 0.00 2.74
128 129 8.385111 GTGCTATAGTTTTCGTATTTGCTACAA 58.615 33.333 0.84 0.00 0.00 2.41
129 130 8.937884 TGCTATAGTTTTCGTATTTGCTACAAA 58.062 29.630 0.84 0.00 0.00 2.83
130 131 9.763465 GCTATAGTTTTCGTATTTGCTACAAAA 57.237 29.630 0.84 0.00 0.00 2.44
168 169 2.542020 AAATCCCGTTTTGGCTTTGG 57.458 45.000 0.00 0.00 35.87 3.28
169 170 1.710816 AATCCCGTTTTGGCTTTGGA 58.289 45.000 0.00 0.00 35.87 3.53
170 171 1.256812 ATCCCGTTTTGGCTTTGGAG 58.743 50.000 0.00 0.00 35.87 3.86
186 187 3.975168 TGGAGCTCCACCTTTACTAAC 57.025 47.619 32.00 0.74 42.01 2.34
187 188 3.517612 TGGAGCTCCACCTTTACTAACT 58.482 45.455 32.00 0.00 42.01 2.24
188 189 3.908103 TGGAGCTCCACCTTTACTAACTT 59.092 43.478 32.00 0.00 42.01 2.66
189 190 4.349930 TGGAGCTCCACCTTTACTAACTTT 59.650 41.667 32.00 0.00 42.01 2.66
190 191 4.936411 GGAGCTCCACCTTTACTAACTTTC 59.064 45.833 28.43 0.00 35.64 2.62
191 192 4.566987 AGCTCCACCTTTACTAACTTTCG 58.433 43.478 0.00 0.00 0.00 3.46
192 193 4.040095 AGCTCCACCTTTACTAACTTTCGT 59.960 41.667 0.00 0.00 0.00 3.85
193 194 4.388165 GCTCCACCTTTACTAACTTTCGTC 59.612 45.833 0.00 0.00 0.00 4.20
194 195 4.886579 TCCACCTTTACTAACTTTCGTCC 58.113 43.478 0.00 0.00 0.00 4.79
195 196 3.999001 CCACCTTTACTAACTTTCGTCCC 59.001 47.826 0.00 0.00 0.00 4.46
196 197 3.999001 CACCTTTACTAACTTTCGTCCCC 59.001 47.826 0.00 0.00 0.00 4.81
197 198 3.008375 ACCTTTACTAACTTTCGTCCCCC 59.992 47.826 0.00 0.00 0.00 5.40
198 199 3.008266 CCTTTACTAACTTTCGTCCCCCA 59.992 47.826 0.00 0.00 0.00 4.96
199 200 4.324022 CCTTTACTAACTTTCGTCCCCCAT 60.324 45.833 0.00 0.00 0.00 4.00
200 201 5.104817 CCTTTACTAACTTTCGTCCCCCATA 60.105 44.000 0.00 0.00 0.00 2.74
201 202 6.371595 TTTACTAACTTTCGTCCCCCATAA 57.628 37.500 0.00 0.00 0.00 1.90
202 203 4.914177 ACTAACTTTCGTCCCCCATAAA 57.086 40.909 0.00 0.00 0.00 1.40
203 204 5.245584 ACTAACTTTCGTCCCCCATAAAA 57.754 39.130 0.00 0.00 0.00 1.52
204 205 5.823312 ACTAACTTTCGTCCCCCATAAAAT 58.177 37.500 0.00 0.00 0.00 1.82
205 206 5.884232 ACTAACTTTCGTCCCCCATAAAATC 59.116 40.000 0.00 0.00 0.00 2.17
206 207 3.275999 ACTTTCGTCCCCCATAAAATCG 58.724 45.455 0.00 0.00 0.00 3.34
207 208 3.054948 ACTTTCGTCCCCCATAAAATCGA 60.055 43.478 0.00 0.00 0.00 3.59
208 209 2.607631 TCGTCCCCCATAAAATCGAC 57.392 50.000 0.00 0.00 0.00 4.20
209 210 2.112998 TCGTCCCCCATAAAATCGACT 58.887 47.619 0.00 0.00 0.00 4.18
210 211 2.502538 TCGTCCCCCATAAAATCGACTT 59.497 45.455 0.00 0.00 0.00 3.01
211 212 3.705579 TCGTCCCCCATAAAATCGACTTA 59.294 43.478 0.00 0.00 0.00 2.24
212 213 4.345837 TCGTCCCCCATAAAATCGACTTAT 59.654 41.667 0.00 0.00 0.00 1.73
213 214 5.061179 CGTCCCCCATAAAATCGACTTATT 58.939 41.667 0.00 0.00 0.00 1.40
214 215 5.178809 CGTCCCCCATAAAATCGACTTATTC 59.821 44.000 0.00 0.00 0.00 1.75
215 216 5.472478 GTCCCCCATAAAATCGACTTATTCC 59.528 44.000 0.00 0.00 0.00 3.01
216 217 5.132985 TCCCCCATAAAATCGACTTATTCCA 59.867 40.000 0.00 0.00 0.00 3.53
217 218 5.830991 CCCCCATAAAATCGACTTATTCCAA 59.169 40.000 0.00 0.00 0.00 3.53
218 219 6.493458 CCCCCATAAAATCGACTTATTCCAAT 59.507 38.462 0.00 0.00 0.00 3.16
219 220 7.015195 CCCCCATAAAATCGACTTATTCCAATT 59.985 37.037 0.00 0.00 0.00 2.32
220 221 8.421002 CCCCATAAAATCGACTTATTCCAATTT 58.579 33.333 0.00 0.00 0.00 1.82
259 260 9.252962 CTTATCAATAGCAAATGCCCTAAAAAG 57.747 33.333 0.94 0.00 43.38 2.27
261 262 5.719085 TCAATAGCAAATGCCCTAAAAAGGA 59.281 36.000 0.94 0.00 43.38 3.36
262 263 6.383726 TCAATAGCAAATGCCCTAAAAAGGAT 59.616 34.615 0.94 0.00 43.38 3.24
263 264 7.563188 TCAATAGCAAATGCCCTAAAAAGGATA 59.437 33.333 0.94 0.00 43.38 2.59
264 265 8.370182 CAATAGCAAATGCCCTAAAAAGGATAT 58.630 33.333 0.94 0.00 43.38 1.63
265 266 6.813293 AGCAAATGCCCTAAAAAGGATATT 57.187 33.333 0.94 0.00 43.38 1.28
266 267 6.585416 AGCAAATGCCCTAAAAAGGATATTG 58.415 36.000 0.94 0.00 43.38 1.90
267 268 6.156775 AGCAAATGCCCTAAAAAGGATATTGT 59.843 34.615 0.94 0.00 43.38 2.71
269 270 7.984617 GCAAATGCCCTAAAAAGGATATTGTTA 59.015 33.333 0.00 0.00 34.31 2.41
271 272 6.709018 TGCCCTAAAAAGGATATTGTTAGC 57.291 37.500 0.00 0.00 0.00 3.09
272 273 5.596772 TGCCCTAAAAAGGATATTGTTAGCC 59.403 40.000 0.00 0.00 33.87 3.93
273 274 5.596772 GCCCTAAAAAGGATATTGTTAGCCA 59.403 40.000 0.00 0.00 36.28 4.75
274 275 6.239036 GCCCTAAAAAGGATATTGTTAGCCAG 60.239 42.308 0.00 0.00 36.28 4.85
275 276 6.239036 CCCTAAAAAGGATATTGTTAGCCAGC 60.239 42.308 0.00 0.00 36.28 4.85
276 277 4.900635 AAAAGGATATTGTTAGCCAGCG 57.099 40.909 0.00 0.00 36.28 5.18
277 278 3.560636 AAGGATATTGTTAGCCAGCGT 57.439 42.857 0.00 0.00 36.28 5.07
279 280 3.991367 AGGATATTGTTAGCCAGCGTAC 58.009 45.455 0.00 0.00 36.28 3.67
280 281 2.729882 GGATATTGTTAGCCAGCGTACG 59.270 50.000 11.84 11.84 33.87 3.67
287 289 0.109458 TAGCCAGCGTACGTCAACTG 60.109 55.000 17.90 14.53 0.00 3.16
289 291 1.736645 CCAGCGTACGTCAACTGGG 60.737 63.158 24.01 11.17 44.90 4.45
303 305 2.935481 TGGGAGAGGGGTGGCAAG 60.935 66.667 0.00 0.00 0.00 4.01
305 307 3.650950 GGAGAGGGGTGGCAAGCA 61.651 66.667 0.00 0.00 0.00 3.91
321 323 4.559153 GCAAGCAAACTACATTTGATGGT 58.441 39.130 3.62 0.00 46.12 3.55
324 326 5.801947 CAAGCAAACTACATTTGATGGTAGC 59.198 40.000 3.62 0.00 46.12 3.58
337 339 5.738619 TGATGGTAGCTTTAACTGTGAGA 57.261 39.130 0.00 0.00 0.00 3.27
338 340 6.109156 TGATGGTAGCTTTAACTGTGAGAA 57.891 37.500 0.00 0.00 0.00 2.87
348 350 8.131731 AGCTTTAACTGTGAGAAAAGATCAAAC 58.868 33.333 0.00 0.00 31.96 2.93
350 352 5.424121 AACTGTGAGAAAAGATCAAACGG 57.576 39.130 0.00 0.00 0.00 4.44
357 359 0.517316 AAAGATCAAACGGCGACAGC 59.483 50.000 16.62 0.00 44.18 4.40
366 368 1.301423 ACGGCGACAGCTTTAAAACA 58.699 45.000 16.62 0.00 44.37 2.83
367 369 1.671845 ACGGCGACAGCTTTAAAACAA 59.328 42.857 16.62 0.00 44.37 2.83
390 392 6.705863 AAAAACAGTCTGCTCTGAAGAAAT 57.294 33.333 0.00 0.00 38.63 2.17
392 394 5.686159 AACAGTCTGCTCTGAAGAAATTG 57.314 39.130 0.00 0.00 38.63 2.32
399 401 5.410746 TCTGCTCTGAAGAAATTGTCATGTC 59.589 40.000 0.00 0.00 0.00 3.06
400 402 4.152938 TGCTCTGAAGAAATTGTCATGTCG 59.847 41.667 0.00 0.00 0.00 4.35
401 403 4.645956 CTCTGAAGAAATTGTCATGTCGC 58.354 43.478 0.00 0.00 0.00 5.19
402 404 4.318332 TCTGAAGAAATTGTCATGTCGCT 58.682 39.130 0.00 0.00 0.00 4.93
403 405 4.389992 TCTGAAGAAATTGTCATGTCGCTC 59.610 41.667 0.00 0.00 0.00 5.03
404 406 4.318332 TGAAGAAATTGTCATGTCGCTCT 58.682 39.130 0.00 0.00 0.00 4.09
405 407 4.152938 TGAAGAAATTGTCATGTCGCTCTG 59.847 41.667 0.00 0.00 0.00 3.35
408 410 4.756642 AGAAATTGTCATGTCGCTCTGAAA 59.243 37.500 0.00 0.00 0.00 2.69
435 437 3.571590 ACCATGCCCTCACAACTAAAAA 58.428 40.909 0.00 0.00 0.00 1.94
440 442 3.572255 TGCCCTCACAACTAAAAATCCAC 59.428 43.478 0.00 0.00 0.00 4.02
448 450 8.528044 TCACAACTAAAAATCCACCTAAAACT 57.472 30.769 0.00 0.00 0.00 2.66
450 452 9.594478 CACAACTAAAAATCCACCTAAAACTTT 57.406 29.630 0.00 0.00 0.00 2.66
461 463 5.277825 CACCTAAAACTTTCGCAAATGTCA 58.722 37.500 0.00 0.00 0.00 3.58
472 475 1.442769 CAAATGTCACCTCCCTGACG 58.557 55.000 0.00 0.00 43.14 4.35
476 479 0.757561 TGTCACCTCCCTGACGAACA 60.758 55.000 0.00 0.00 43.14 3.18
479 482 1.697432 TCACCTCCCTGACGAACATTT 59.303 47.619 0.00 0.00 0.00 2.32
483 486 0.109532 TCCCTGACGAACATTTGCCA 59.890 50.000 0.00 0.00 0.00 4.92
492 495 3.880490 ACGAACATTTGCCAGTTAACAGA 59.120 39.130 8.61 0.00 0.00 3.41
495 498 5.505654 CGAACATTTGCCAGTTAACAGAGTT 60.506 40.000 8.61 1.30 0.00 3.01
498 501 6.296026 ACATTTGCCAGTTAACAGAGTTCTA 58.704 36.000 8.61 0.00 0.00 2.10
499 502 6.770785 ACATTTGCCAGTTAACAGAGTTCTAA 59.229 34.615 8.61 0.00 0.00 2.10
537 540 9.635404 TTATAACCTTACCAAAATATCCACAGG 57.365 33.333 0.00 0.00 0.00 4.00
538 541 5.789574 ACCTTACCAAAATATCCACAGGA 57.210 39.130 0.00 0.00 35.55 3.86
539 542 6.341408 ACCTTACCAAAATATCCACAGGAT 57.659 37.500 3.74 3.74 45.40 3.24
540 543 6.741724 ACCTTACCAAAATATCCACAGGATT 58.258 36.000 3.55 0.00 39.79 3.01
551 554 3.664107 TCCACAGGATTCTCGAACTTTG 58.336 45.455 0.00 0.00 0.00 2.77
619 622 1.079819 TGCCAGCTAGACGAAGCAC 60.080 57.895 10.78 2.44 45.30 4.40
651 654 2.238646 ACCCAAAGCGATACCTCAATGA 59.761 45.455 0.00 0.00 0.00 2.57
652 655 3.117888 ACCCAAAGCGATACCTCAATGAT 60.118 43.478 0.00 0.00 0.00 2.45
653 656 3.885297 CCCAAAGCGATACCTCAATGATT 59.115 43.478 0.00 0.00 0.00 2.57
654 657 4.339247 CCCAAAGCGATACCTCAATGATTT 59.661 41.667 0.00 0.00 0.00 2.17
655 658 5.506317 CCCAAAGCGATACCTCAATGATTTC 60.506 44.000 0.00 0.00 0.00 2.17
656 659 5.200454 CAAAGCGATACCTCAATGATTTCG 58.800 41.667 0.00 0.00 0.00 3.46
657 660 3.393800 AGCGATACCTCAATGATTTCGG 58.606 45.455 0.00 0.00 0.00 4.30
658 661 2.096218 GCGATACCTCAATGATTTCGGC 60.096 50.000 0.00 0.00 0.00 5.54
659 662 3.393800 CGATACCTCAATGATTTCGGCT 58.606 45.455 0.00 0.00 0.00 5.52
660 663 3.185188 CGATACCTCAATGATTTCGGCTG 59.815 47.826 0.00 0.00 0.00 4.85
661 664 1.755179 ACCTCAATGATTTCGGCTGG 58.245 50.000 0.00 0.00 0.00 4.85
662 665 1.004745 ACCTCAATGATTTCGGCTGGT 59.995 47.619 0.00 0.00 0.00 4.00
663 666 1.402968 CCTCAATGATTTCGGCTGGTG 59.597 52.381 0.00 0.00 0.00 4.17
664 667 1.402968 CTCAATGATTTCGGCTGGTGG 59.597 52.381 0.00 0.00 0.00 4.61
665 668 0.457035 CAATGATTTCGGCTGGTGGG 59.543 55.000 0.00 0.00 0.00 4.61
666 669 1.322538 AATGATTTCGGCTGGTGGGC 61.323 55.000 0.00 0.00 37.12 5.36
685 688 3.182263 CACCCCACCTCACCCCAA 61.182 66.667 0.00 0.00 0.00 4.12
686 689 3.182996 ACCCCACCTCACCCCAAC 61.183 66.667 0.00 0.00 0.00 3.77
687 690 3.979497 CCCCACCTCACCCCAACC 61.979 72.222 0.00 0.00 0.00 3.77
688 691 3.979497 CCCACCTCACCCCAACCC 61.979 72.222 0.00 0.00 0.00 4.11
689 692 3.979497 CCACCTCACCCCAACCCC 61.979 72.222 0.00 0.00 0.00 4.95
690 693 4.344865 CACCTCACCCCAACCCCG 62.345 72.222 0.00 0.00 0.00 5.73
711 714 4.128388 CCGGCCCGCCATTTGAAC 62.128 66.667 6.52 0.00 35.37 3.18
712 715 4.128388 CGGCCCGCCATTTGAACC 62.128 66.667 6.52 0.00 35.37 3.62
713 716 3.770040 GGCCCGCCATTTGAACCC 61.770 66.667 0.00 0.00 35.81 4.11
714 717 3.770040 GCCCGCCATTTGAACCCC 61.770 66.667 0.00 0.00 0.00 4.95
715 718 3.074369 CCCGCCATTTGAACCCCC 61.074 66.667 0.00 0.00 0.00 5.40
716 719 2.283532 CCGCCATTTGAACCCCCA 60.284 61.111 0.00 0.00 0.00 4.96
717 720 2.645192 CCGCCATTTGAACCCCCAC 61.645 63.158 0.00 0.00 0.00 4.61
718 721 1.606313 CGCCATTTGAACCCCCACT 60.606 57.895 0.00 0.00 0.00 4.00
719 722 0.322997 CGCCATTTGAACCCCCACTA 60.323 55.000 0.00 0.00 0.00 2.74
720 723 1.182667 GCCATTTGAACCCCCACTAC 58.817 55.000 0.00 0.00 0.00 2.73
721 724 1.549037 GCCATTTGAACCCCCACTACA 60.549 52.381 0.00 0.00 0.00 2.74
722 725 2.167662 CCATTTGAACCCCCACTACAC 58.832 52.381 0.00 0.00 0.00 2.90
723 726 2.225017 CCATTTGAACCCCCACTACACT 60.225 50.000 0.00 0.00 0.00 3.55
724 727 3.496331 CATTTGAACCCCCACTACACTT 58.504 45.455 0.00 0.00 0.00 3.16
725 728 2.943036 TTGAACCCCCACTACACTTC 57.057 50.000 0.00 0.00 0.00 3.01
726 729 1.809133 TGAACCCCCACTACACTTCA 58.191 50.000 0.00 0.00 0.00 3.02
727 730 1.418637 TGAACCCCCACTACACTTCAC 59.581 52.381 0.00 0.00 0.00 3.18
728 731 1.418637 GAACCCCCACTACACTTCACA 59.581 52.381 0.00 0.00 0.00 3.58
729 732 0.763035 ACCCCCACTACACTTCACAC 59.237 55.000 0.00 0.00 0.00 3.82
730 733 1.056660 CCCCCACTACACTTCACACT 58.943 55.000 0.00 0.00 0.00 3.55
731 734 1.002087 CCCCCACTACACTTCACACTC 59.998 57.143 0.00 0.00 0.00 3.51
732 735 1.002087 CCCCACTACACTTCACACTCC 59.998 57.143 0.00 0.00 0.00 3.85
733 736 1.002087 CCCACTACACTTCACACTCCC 59.998 57.143 0.00 0.00 0.00 4.30
734 737 1.002087 CCACTACACTTCACACTCCCC 59.998 57.143 0.00 0.00 0.00 4.81
735 738 1.002087 CACTACACTTCACACTCCCCC 59.998 57.143 0.00 0.00 0.00 5.40
902 1228 2.163815 CGTCTTCCTCTAACGACACCAT 59.836 50.000 0.00 0.00 38.65 3.55
907 1233 2.901192 TCCTCTAACGACACCATCCAAA 59.099 45.455 0.00 0.00 0.00 3.28
912 1238 0.105224 ACGACACCATCCAAACACGA 59.895 50.000 0.00 0.00 0.00 4.35
920 1246 0.389948 ATCCAAACACGAGAGGCGAC 60.390 55.000 0.00 0.00 44.57 5.19
934 1260 1.065926 AGGCGACAAGAATCAGCATCA 60.066 47.619 0.00 0.00 0.00 3.07
964 1295 1.001764 TAGAGCCGTCCTCGACCAA 60.002 57.895 0.00 0.00 45.54 3.67
986 1317 3.919554 AGATCCAAGAAGAGGGAGGTTTT 59.080 43.478 0.00 0.00 36.45 2.43
987 1318 4.355287 AGATCCAAGAAGAGGGAGGTTTTT 59.645 41.667 0.00 0.00 36.45 1.94
1016 1347 2.668212 CATGTCGGCGGTGGTTGT 60.668 61.111 7.21 0.00 0.00 3.32
1026 1357 2.251642 GGTGGTTGTGCAGGACGTC 61.252 63.158 7.13 7.13 0.00 4.34
1028 1359 2.279918 GGTTGTGCAGGACGTCGT 60.280 61.111 9.92 7.31 0.00 4.34
1248 1579 2.499827 GGAGGTAGAGGCGGCGATT 61.500 63.158 12.98 0.00 0.00 3.34
1345 1676 4.168291 GCCAGAGCGGGAGGAAGG 62.168 72.222 0.00 0.00 34.06 3.46
1531 1862 4.003648 AGACGCTTAATTTGGAGACCAAG 58.996 43.478 3.49 0.00 44.84 3.61
1618 1949 9.516314 TGTAGATGACACGAGAAAAATGTATAG 57.484 33.333 0.00 0.00 31.20 1.31
1630 1961 7.222872 AGAAAAATGTATAGATGGAGCTGAGG 58.777 38.462 0.00 0.00 0.00 3.86
1644 1975 4.054671 GAGCTGAGGTCGAATAATTCCAG 58.945 47.826 0.00 0.00 0.00 3.86
1653 1984 8.857694 AGGTCGAATAATTCCAGTTTAAGAAA 57.142 30.769 0.00 0.00 0.00 2.52
1654 1985 9.462606 AGGTCGAATAATTCCAGTTTAAGAAAT 57.537 29.630 0.00 0.00 0.00 2.17
1692 2023 5.347342 TCAAATAATGGCAAAGGTATTGCG 58.653 37.500 7.04 0.00 45.78 4.85
1696 2027 0.519519 TGGCAAAGGTATTGCGTTCG 59.480 50.000 7.04 0.00 45.78 3.95
1703 2034 0.448990 GGTATTGCGTTCGGGGTTTC 59.551 55.000 0.00 0.00 0.00 2.78
1725 2056 2.031120 CTTTTGACCTGGCACTTTGGA 58.969 47.619 0.00 0.00 0.00 3.53
1733 2064 2.575532 CTGGCACTTTGGAACTTCAGA 58.424 47.619 0.00 0.00 0.00 3.27
1750 2081 1.000385 CAGACTTTGCGGAATTTGGCA 60.000 47.619 0.00 0.73 37.39 4.92
1751 2082 1.895131 AGACTTTGCGGAATTTGGCAT 59.105 42.857 5.36 0.00 39.21 4.40
1785 2116 2.275134 TTCAGACAAGCATGCCAGAA 57.725 45.000 15.66 4.74 0.00 3.02
1816 2147 1.268079 GCAGCTGTCTTTTTCTCACCC 59.732 52.381 16.64 0.00 0.00 4.61
1818 2149 1.141053 AGCTGTCTTTTTCTCACCCGT 59.859 47.619 0.00 0.00 0.00 5.28
1902 2316 4.621460 AGTATCATTCACGACAAACGAGTG 59.379 41.667 0.00 0.00 45.77 3.51
1941 2355 1.270826 CGGACAGGTCGATGCATCTAT 59.729 52.381 23.73 4.71 0.00 1.98
2038 2452 5.560724 AGCCACTTCAAGTAGAAAGCAATA 58.439 37.500 0.00 0.00 35.40 1.90
2039 2453 5.412904 AGCCACTTCAAGTAGAAAGCAATAC 59.587 40.000 0.00 0.00 35.40 1.89
2054 2468 8.774586 AGAAAGCAATACTAGTAACAAGTTGTG 58.225 33.333 9.79 0.00 0.00 3.33
2063 2477 2.965572 AACAAGTTGTGCATTGCAGT 57.034 40.000 12.53 2.13 40.08 4.40
2066 2480 2.363038 ACAAGTTGTGCATTGCAGTGAT 59.637 40.909 12.53 0.00 40.08 3.06
2073 2487 3.189080 TGTGCATTGCAGTGATGTTACTC 59.811 43.478 12.53 0.00 40.08 2.59
2079 2493 6.348458 GCATTGCAGTGATGTTACTCAAAGTA 60.348 38.462 14.15 0.00 0.00 2.24
2097 2511 6.884295 TCAAAGTAGAAAATGTATCCACCTGG 59.116 38.462 0.00 0.00 0.00 4.45
2098 2512 5.373812 AGTAGAAAATGTATCCACCTGGG 57.626 43.478 0.00 0.00 35.41 4.45
2110 2524 1.463674 CACCTGGGATTGTGGTAAGC 58.536 55.000 0.00 0.00 32.13 3.09
2111 2525 1.004745 CACCTGGGATTGTGGTAAGCT 59.995 52.381 0.00 0.00 32.13 3.74
2115 2529 1.207089 TGGGATTGTGGTAAGCTCTCG 59.793 52.381 0.00 0.00 0.00 4.04
2117 2531 2.093658 GGGATTGTGGTAAGCTCTCGAA 60.094 50.000 0.00 0.00 0.00 3.71
2120 2534 2.672961 TGTGGTAAGCTCTCGAATGG 57.327 50.000 0.00 0.00 0.00 3.16
2125 2539 2.166664 GGTAAGCTCTCGAATGGAGTGT 59.833 50.000 2.55 0.00 43.60 3.55
2129 2543 4.537135 AGCTCTCGAATGGAGTGTAAAA 57.463 40.909 2.55 0.00 43.60 1.52
2133 2547 5.122396 GCTCTCGAATGGAGTGTAAAATGTT 59.878 40.000 2.55 0.00 43.60 2.71
2138 2552 6.263392 TCGAATGGAGTGTAAAATGTTTCCAA 59.737 34.615 0.00 0.00 38.14 3.53
2160 2574 7.281549 TCCAACTAAGTTACTTGAAGTGGAAAC 59.718 37.037 8.33 4.76 0.00 2.78
2161 2575 7.066525 CCAACTAAGTTACTTGAAGTGGAAACA 59.933 37.037 8.33 0.00 38.70 2.83
2163 2577 8.209917 ACTAAGTTACTTGAAGTGGAAACAAG 57.790 34.615 8.33 8.66 46.06 3.16
2184 2603 4.016444 AGAACTTGCACACAGAAAAGGAA 58.984 39.130 0.00 0.00 0.00 3.36
2215 2634 6.551385 AGAAGTGTAAAGCAAGAACAGATG 57.449 37.500 0.00 0.00 0.00 2.90
2221 2640 4.595762 AAAGCAAGAACAGATGTGCAAT 57.404 36.364 0.00 0.00 39.50 3.56
2222 2641 4.595762 AAGCAAGAACAGATGTGCAATT 57.404 36.364 0.00 0.00 39.50 2.32
2223 2642 4.595762 AGCAAGAACAGATGTGCAATTT 57.404 36.364 0.00 0.00 39.50 1.82
2252 2671 2.750948 CAGCAAGCAAGCAAGATTTGT 58.249 42.857 3.19 0.00 36.85 2.83
2275 2694 1.762522 TATCTGCTAGCTGGCCTGCC 61.763 60.000 28.96 15.61 0.00 4.85
2306 2725 3.491208 GCATGTTCTGATGCTCCCT 57.509 52.632 0.00 0.00 44.57 4.20
2310 2729 1.942776 TGTTCTGATGCTCCCTCTCA 58.057 50.000 0.00 0.00 0.00 3.27
2311 2730 2.259917 TGTTCTGATGCTCCCTCTCAA 58.740 47.619 0.00 0.00 0.00 3.02
2318 2737 3.760151 TGATGCTCCCTCTCAATTGTTTG 59.240 43.478 5.13 0.00 0.00 2.93
2320 2739 4.038271 TGCTCCCTCTCAATTGTTTGAT 57.962 40.909 5.13 0.00 40.95 2.57
2327 2746 8.284945 TCCCTCTCAATTGTTTGATTAATCAG 57.715 34.615 17.28 5.42 40.95 2.90
2339 2758 9.973661 TGTTTGATTAATCAGGAAATAGAAGGA 57.026 29.630 17.28 0.00 38.19 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.827383 AAGAGAGCTCTTCGGCACGC 62.827 60.000 19.36 1.83 46.13 5.34
4 5 1.214062 AAGAGAGCTCTTCGGCACG 59.786 57.895 19.36 0.00 46.13 5.34
12 13 3.440127 AGTCTTAGCCAAAGAGAGCTCT 58.560 45.455 18.28 18.28 44.94 4.09
13 14 3.885724 AGTCTTAGCCAAAGAGAGCTC 57.114 47.619 5.27 5.27 44.94 4.09
14 15 3.704061 CCTAGTCTTAGCCAAAGAGAGCT 59.296 47.826 0.00 0.00 44.94 4.09
15 16 3.739830 GCCTAGTCTTAGCCAAAGAGAGC 60.740 52.174 0.00 0.00 44.94 4.09
16 17 3.181470 GGCCTAGTCTTAGCCAAAGAGAG 60.181 52.174 0.00 1.63 44.94 3.20
17 18 2.766828 GGCCTAGTCTTAGCCAAAGAGA 59.233 50.000 0.00 0.00 44.94 3.10
18 19 2.482142 CGGCCTAGTCTTAGCCAAAGAG 60.482 54.545 0.00 0.00 44.94 2.85
19 20 1.480954 CGGCCTAGTCTTAGCCAAAGA 59.519 52.381 0.00 0.00 42.07 2.52
20 21 1.480954 TCGGCCTAGTCTTAGCCAAAG 59.519 52.381 0.00 0.00 36.45 2.77
21 22 1.563924 TCGGCCTAGTCTTAGCCAAA 58.436 50.000 0.00 0.00 0.00 3.28
22 23 1.563924 TTCGGCCTAGTCTTAGCCAA 58.436 50.000 0.00 4.46 0.00 4.52
23 24 1.563924 TTTCGGCCTAGTCTTAGCCA 58.436 50.000 0.00 0.00 0.00 4.75
24 25 2.552031 CTTTTCGGCCTAGTCTTAGCC 58.448 52.381 0.00 3.27 0.00 3.93
25 26 1.934525 GCTTTTCGGCCTAGTCTTAGC 59.065 52.381 0.00 0.00 0.00 3.09
36 37 1.429423 CGAAGATGGGCTTTTCGGC 59.571 57.895 0.00 0.00 39.82 5.54
45 46 2.234908 CCTTCTATAGGCCGAAGATGGG 59.765 54.545 16.97 12.36 39.10 4.00
46 47 3.601443 CCTTCTATAGGCCGAAGATGG 57.399 52.381 16.97 16.94 39.10 3.51
57 58 0.826672 ACCCCGTCGGCCTTCTATAG 60.827 60.000 5.50 0.00 33.26 1.31
58 59 0.825010 GACCCCGTCGGCCTTCTATA 60.825 60.000 5.50 0.00 33.26 1.31
59 60 2.042230 ACCCCGTCGGCCTTCTAT 60.042 61.111 5.50 0.00 33.26 1.98
60 61 2.757099 GACCCCGTCGGCCTTCTA 60.757 66.667 5.50 0.00 33.26 2.10
61 62 2.866523 TATGACCCCGTCGGCCTTCT 62.867 60.000 5.50 0.00 34.95 2.85
62 63 2.365095 CTATGACCCCGTCGGCCTTC 62.365 65.000 5.50 1.83 34.95 3.46
63 64 2.364579 TATGACCCCGTCGGCCTT 60.365 61.111 5.50 0.00 34.95 4.35
64 65 2.288642 TACTATGACCCCGTCGGCCT 62.289 60.000 5.50 0.00 34.95 5.19
65 66 1.183676 ATACTATGACCCCGTCGGCC 61.184 60.000 5.50 0.00 34.95 6.13
66 67 0.677842 AATACTATGACCCCGTCGGC 59.322 55.000 5.50 0.00 34.95 5.54
67 68 1.604693 GCAATACTATGACCCCGTCGG 60.605 57.143 3.60 3.60 34.95 4.79
68 69 1.340248 AGCAATACTATGACCCCGTCG 59.660 52.381 0.00 0.00 34.95 5.12
69 70 3.470645 AAGCAATACTATGACCCCGTC 57.529 47.619 0.00 0.00 0.00 4.79
70 71 3.926058 AAAGCAATACTATGACCCCGT 57.074 42.857 0.00 0.00 0.00 5.28
89 90 9.234827 GAAAACTATAGCACCTAAGGGTAAAAA 57.765 33.333 0.00 0.00 45.41 1.94
90 91 7.550196 CGAAAACTATAGCACCTAAGGGTAAAA 59.450 37.037 0.00 0.00 45.41 1.52
91 92 7.043565 CGAAAACTATAGCACCTAAGGGTAAA 58.956 38.462 0.00 0.00 45.41 2.01
92 93 6.155049 ACGAAAACTATAGCACCTAAGGGTAA 59.845 38.462 0.00 0.00 45.41 2.85
93 94 5.658190 ACGAAAACTATAGCACCTAAGGGTA 59.342 40.000 0.00 0.00 45.41 3.69
95 96 5.019785 ACGAAAACTATAGCACCTAAGGG 57.980 43.478 0.00 0.00 38.88 3.95
96 97 8.548721 CAAATACGAAAACTATAGCACCTAAGG 58.451 37.037 0.00 0.00 0.00 2.69
97 98 8.062448 GCAAATACGAAAACTATAGCACCTAAG 58.938 37.037 0.00 0.00 0.00 2.18
98 99 7.767198 AGCAAATACGAAAACTATAGCACCTAA 59.233 33.333 0.00 0.00 0.00 2.69
99 100 7.270047 AGCAAATACGAAAACTATAGCACCTA 58.730 34.615 0.00 0.00 0.00 3.08
100 101 6.113411 AGCAAATACGAAAACTATAGCACCT 58.887 36.000 0.00 0.00 0.00 4.00
101 102 6.359480 AGCAAATACGAAAACTATAGCACC 57.641 37.500 0.00 0.00 0.00 5.01
102 103 7.902032 TGTAGCAAATACGAAAACTATAGCAC 58.098 34.615 0.00 0.00 37.17 4.40
103 104 8.481974 TTGTAGCAAATACGAAAACTATAGCA 57.518 30.769 0.00 0.00 37.17 3.49
104 105 9.763465 TTTTGTAGCAAATACGAAAACTATAGC 57.237 29.630 0.00 0.00 42.37 2.97
147 148 3.118223 TCCAAAGCCAAAACGGGATTTTT 60.118 39.130 0.00 0.00 43.61 1.94
148 149 2.436173 TCCAAAGCCAAAACGGGATTTT 59.564 40.909 0.00 0.00 43.61 1.82
149 150 2.037121 CTCCAAAGCCAAAACGGGATTT 59.963 45.455 0.00 0.00 46.80 2.17
150 151 1.618343 CTCCAAAGCCAAAACGGGATT 59.382 47.619 0.00 0.00 38.41 3.01
151 152 1.256812 CTCCAAAGCCAAAACGGGAT 58.743 50.000 0.00 0.00 34.06 3.85
152 153 1.460273 GCTCCAAAGCCAAAACGGGA 61.460 55.000 0.00 0.00 43.10 5.14
153 154 1.006220 GCTCCAAAGCCAAAACGGG 60.006 57.895 0.00 0.00 43.10 5.28
154 155 4.653555 GCTCCAAAGCCAAAACGG 57.346 55.556 0.00 0.00 43.10 4.44
166 167 3.517612 AGTTAGTAAAGGTGGAGCTCCA 58.482 45.455 32.00 32.00 45.30 3.86
167 168 4.554960 AAGTTAGTAAAGGTGGAGCTCC 57.445 45.455 26.78 26.78 0.00 4.70
168 169 4.626172 CGAAAGTTAGTAAAGGTGGAGCTC 59.374 45.833 4.71 4.71 0.00 4.09
169 170 4.040095 ACGAAAGTTAGTAAAGGTGGAGCT 59.960 41.667 0.00 0.00 46.40 4.09
170 171 4.313282 ACGAAAGTTAGTAAAGGTGGAGC 58.687 43.478 0.00 0.00 46.40 4.70
186 187 3.311596 GTCGATTTTATGGGGGACGAAAG 59.688 47.826 0.00 0.00 0.00 2.62
187 188 3.054948 AGTCGATTTTATGGGGGACGAAA 60.055 43.478 0.00 0.00 0.00 3.46
188 189 2.502538 AGTCGATTTTATGGGGGACGAA 59.497 45.455 0.00 0.00 0.00 3.85
189 190 2.112998 AGTCGATTTTATGGGGGACGA 58.887 47.619 0.00 0.00 0.00 4.20
190 191 2.614829 AGTCGATTTTATGGGGGACG 57.385 50.000 0.00 0.00 0.00 4.79
191 192 5.472478 GGAATAAGTCGATTTTATGGGGGAC 59.528 44.000 0.00 0.00 0.00 4.46
192 193 5.132985 TGGAATAAGTCGATTTTATGGGGGA 59.867 40.000 0.00 0.00 0.00 4.81
193 194 5.381757 TGGAATAAGTCGATTTTATGGGGG 58.618 41.667 0.00 0.00 0.00 5.40
194 195 6.952773 TTGGAATAAGTCGATTTTATGGGG 57.047 37.500 0.00 0.00 0.00 4.96
205 206 9.796120 TGCCTAAAAATAAATTGGAATAAGTCG 57.204 29.630 0.00 0.00 0.00 4.18
259 260 2.729882 CGTACGCTGGCTAACAATATCC 59.270 50.000 0.52 0.00 0.00 2.59
261 262 3.181484 TGACGTACGCTGGCTAACAATAT 60.181 43.478 16.72 0.00 0.00 1.28
262 263 2.164017 TGACGTACGCTGGCTAACAATA 59.836 45.455 16.72 0.00 0.00 1.90
263 264 1.067425 TGACGTACGCTGGCTAACAAT 60.067 47.619 16.72 0.00 0.00 2.71
264 265 0.314618 TGACGTACGCTGGCTAACAA 59.685 50.000 16.72 0.00 0.00 2.83
265 266 0.314618 TTGACGTACGCTGGCTAACA 59.685 50.000 16.72 0.46 0.00 2.41
266 267 0.712222 GTTGACGTACGCTGGCTAAC 59.288 55.000 16.72 7.98 0.00 2.34
267 268 0.599558 AGTTGACGTACGCTGGCTAA 59.400 50.000 16.72 0.00 0.00 3.09
269 270 1.372997 CAGTTGACGTACGCTGGCT 60.373 57.895 16.72 6.18 0.00 4.75
271 272 1.736645 CCCAGTTGACGTACGCTGG 60.737 63.158 24.49 24.49 45.86 4.85
272 273 0.732880 CTCCCAGTTGACGTACGCTG 60.733 60.000 16.72 13.93 0.00 5.18
273 274 0.892358 TCTCCCAGTTGACGTACGCT 60.892 55.000 16.72 0.54 0.00 5.07
274 275 0.456312 CTCTCCCAGTTGACGTACGC 60.456 60.000 16.72 8.98 0.00 4.42
275 276 0.170561 CCTCTCCCAGTTGACGTACG 59.829 60.000 15.01 15.01 0.00 3.67
276 277 0.531200 CCCTCTCCCAGTTGACGTAC 59.469 60.000 0.00 0.00 0.00 3.67
277 278 0.613853 CCCCTCTCCCAGTTGACGTA 60.614 60.000 0.00 0.00 0.00 3.57
279 280 1.913762 ACCCCTCTCCCAGTTGACG 60.914 63.158 0.00 0.00 0.00 4.35
280 281 1.679898 CACCCCTCTCCCAGTTGAC 59.320 63.158 0.00 0.00 0.00 3.18
287 289 4.432741 GCTTGCCACCCCTCTCCC 62.433 72.222 0.00 0.00 0.00 4.30
289 291 1.228552 TTTGCTTGCCACCCCTCTC 60.229 57.895 0.00 0.00 0.00 3.20
303 305 5.567138 AGCTACCATCAAATGTAGTTTGC 57.433 39.130 0.00 0.00 45.45 3.68
305 307 9.297037 AGTTAAAGCTACCATCAAATGTAGTTT 57.703 29.630 0.00 0.00 0.00 2.66
321 323 8.902540 TTGATCTTTTCTCACAGTTAAAGCTA 57.097 30.769 0.00 0.00 0.00 3.32
324 326 7.587757 CCGTTTGATCTTTTCTCACAGTTAAAG 59.412 37.037 0.00 0.00 0.00 1.85
330 332 3.665323 CGCCGTTTGATCTTTTCTCACAG 60.665 47.826 0.00 0.00 0.00 3.66
337 339 1.069227 GCTGTCGCCGTTTGATCTTTT 60.069 47.619 0.00 0.00 0.00 2.27
338 340 0.517316 GCTGTCGCCGTTTGATCTTT 59.483 50.000 0.00 0.00 0.00 2.52
348 350 2.392933 TTGTTTTAAAGCTGTCGCCG 57.607 45.000 3.62 0.00 36.60 6.46
367 369 6.705863 ATTTCTTCAGAGCAGACTGTTTTT 57.294 33.333 3.99 0.00 38.79 1.94
372 374 4.753610 TGACAATTTCTTCAGAGCAGACTG 59.246 41.667 0.00 0.00 39.02 3.51
373 375 4.965814 TGACAATTTCTTCAGAGCAGACT 58.034 39.130 0.00 0.00 0.00 3.24
378 380 4.645956 CGACATGACAATTTCTTCAGAGC 58.354 43.478 0.00 0.00 0.00 4.09
380 382 4.318332 AGCGACATGACAATTTCTTCAGA 58.682 39.130 0.00 0.00 0.00 3.27
408 410 2.890945 GTTGTGAGGGCATGGTAGTTTT 59.109 45.455 0.00 0.00 0.00 2.43
417 419 4.220602 GTGGATTTTTAGTTGTGAGGGCAT 59.779 41.667 0.00 0.00 0.00 4.40
419 421 3.056821 GGTGGATTTTTAGTTGTGAGGGC 60.057 47.826 0.00 0.00 0.00 5.19
435 437 5.010617 ACATTTGCGAAAGTTTTAGGTGGAT 59.989 36.000 0.00 0.00 0.00 3.41
440 442 4.679654 GGTGACATTTGCGAAAGTTTTAGG 59.320 41.667 0.00 0.00 0.00 2.69
448 450 1.202879 AGGGAGGTGACATTTGCGAAA 60.203 47.619 0.00 0.00 0.00 3.46
450 452 0.321564 CAGGGAGGTGACATTTGCGA 60.322 55.000 0.00 0.00 0.00 5.10
461 463 1.882352 GCAAATGTTCGTCAGGGAGGT 60.882 52.381 0.00 0.00 0.00 3.85
472 475 5.438761 ACTCTGTTAACTGGCAAATGTTC 57.561 39.130 12.00 0.00 0.00 3.18
476 479 7.817418 TTTAGAACTCTGTTAACTGGCAAAT 57.183 32.000 12.00 0.62 0.00 2.32
514 517 7.273457 TCCTGTGGATATTTTGGTAAGGTTA 57.727 36.000 0.00 0.00 0.00 2.85
534 537 5.004821 CACGATACAAAGTTCGAGAATCCTG 59.995 44.000 0.00 0.00 38.67 3.86
535 538 5.103000 CACGATACAAAGTTCGAGAATCCT 58.897 41.667 0.00 0.00 38.67 3.24
537 540 4.267928 CCCACGATACAAAGTTCGAGAATC 59.732 45.833 0.00 0.00 38.67 2.52
538 541 4.181578 CCCACGATACAAAGTTCGAGAAT 58.818 43.478 0.00 0.00 38.67 2.40
539 542 3.581755 CCCACGATACAAAGTTCGAGAA 58.418 45.455 0.00 0.00 38.67 2.87
540 543 2.673043 GCCCACGATACAAAGTTCGAGA 60.673 50.000 0.00 0.00 38.67 4.04
619 622 1.501741 CTTTGGGTGTTCGATGCGG 59.498 57.895 0.00 0.00 0.00 5.69
668 671 3.182263 TTGGGGTGAGGTGGGGTG 61.182 66.667 0.00 0.00 0.00 4.61
669 672 3.182996 GTTGGGGTGAGGTGGGGT 61.183 66.667 0.00 0.00 0.00 4.95
670 673 3.979497 GGTTGGGGTGAGGTGGGG 61.979 72.222 0.00 0.00 0.00 4.96
671 674 3.979497 GGGTTGGGGTGAGGTGGG 61.979 72.222 0.00 0.00 0.00 4.61
672 675 3.979497 GGGGTTGGGGTGAGGTGG 61.979 72.222 0.00 0.00 0.00 4.61
673 676 4.344865 CGGGGTTGGGGTGAGGTG 62.345 72.222 0.00 0.00 0.00 4.00
694 697 4.128388 GTTCAAATGGCGGGCCGG 62.128 66.667 29.48 9.91 39.42 6.13
695 698 4.128388 GGTTCAAATGGCGGGCCG 62.128 66.667 24.35 24.35 39.42 6.13
696 699 3.770040 GGGTTCAAATGGCGGGCC 61.770 66.667 1.86 1.86 0.00 5.80
697 700 3.770040 GGGGTTCAAATGGCGGGC 61.770 66.667 0.00 0.00 0.00 6.13
698 701 3.074369 GGGGGTTCAAATGGCGGG 61.074 66.667 0.00 0.00 0.00 6.13
699 702 2.283532 TGGGGGTTCAAATGGCGG 60.284 61.111 0.00 0.00 0.00 6.13
700 703 0.322997 TAGTGGGGGTTCAAATGGCG 60.323 55.000 0.00 0.00 0.00 5.69
701 704 1.182667 GTAGTGGGGGTTCAAATGGC 58.817 55.000 0.00 0.00 0.00 4.40
702 705 2.167662 GTGTAGTGGGGGTTCAAATGG 58.832 52.381 0.00 0.00 0.00 3.16
703 706 3.154827 AGTGTAGTGGGGGTTCAAATG 57.845 47.619 0.00 0.00 0.00 2.32
704 707 3.139397 TGAAGTGTAGTGGGGGTTCAAAT 59.861 43.478 0.00 0.00 0.00 2.32
705 708 2.510382 TGAAGTGTAGTGGGGGTTCAAA 59.490 45.455 0.00 0.00 0.00 2.69
706 709 2.128535 TGAAGTGTAGTGGGGGTTCAA 58.871 47.619 0.00 0.00 0.00 2.69
707 710 1.418637 GTGAAGTGTAGTGGGGGTTCA 59.581 52.381 0.00 0.00 0.00 3.18
708 711 1.418637 TGTGAAGTGTAGTGGGGGTTC 59.581 52.381 0.00 0.00 0.00 3.62
709 712 1.142262 GTGTGAAGTGTAGTGGGGGTT 59.858 52.381 0.00 0.00 0.00 4.11
710 713 0.763035 GTGTGAAGTGTAGTGGGGGT 59.237 55.000 0.00 0.00 0.00 4.95
711 714 1.002087 GAGTGTGAAGTGTAGTGGGGG 59.998 57.143 0.00 0.00 0.00 5.40
712 715 1.002087 GGAGTGTGAAGTGTAGTGGGG 59.998 57.143 0.00 0.00 0.00 4.96
713 716 1.002087 GGGAGTGTGAAGTGTAGTGGG 59.998 57.143 0.00 0.00 0.00 4.61
714 717 1.002087 GGGGAGTGTGAAGTGTAGTGG 59.998 57.143 0.00 0.00 0.00 4.00
715 718 1.002087 GGGGGAGTGTGAAGTGTAGTG 59.998 57.143 0.00 0.00 0.00 2.74
716 719 1.349067 GGGGGAGTGTGAAGTGTAGT 58.651 55.000 0.00 0.00 0.00 2.73
902 1228 1.006571 GTCGCCTCTCGTGTTTGGA 60.007 57.895 0.00 0.00 39.67 3.53
907 1233 0.603569 ATTCTTGTCGCCTCTCGTGT 59.396 50.000 0.00 0.00 39.67 4.49
912 1238 0.610174 TGCTGATTCTTGTCGCCTCT 59.390 50.000 0.00 0.00 0.00 3.69
920 1246 1.030457 GGCCCTGATGCTGATTCTTG 58.970 55.000 0.00 0.00 0.00 3.02
934 1260 1.118356 CGGCTCTAGATCAAGGCCCT 61.118 60.000 12.89 0.00 39.64 5.19
964 1295 2.959421 ACCTCCCTCTTCTTGGATCT 57.041 50.000 0.00 0.00 0.00 2.75
1092 1423 2.267324 GCAGTGCACTCCTCCCTC 59.733 66.667 18.64 0.00 0.00 4.30
1205 1536 4.220163 CCGATCCTCCTCCCCCGA 62.220 72.222 0.00 0.00 0.00 5.14
1209 1540 3.551407 GTGGCCGATCCTCCTCCC 61.551 72.222 0.00 0.00 35.26 4.30
1531 1862 7.642978 CACAAATAAGCTGAAGATATTGCAGAC 59.357 37.037 0.00 0.00 0.00 3.51
1618 1949 3.735237 TTATTCGACCTCAGCTCCATC 57.265 47.619 0.00 0.00 0.00 3.51
1620 1951 3.181465 GGAATTATTCGACCTCAGCTCCA 60.181 47.826 0.00 0.00 0.00 3.86
1654 1985 9.585099 GCCATTATTTGATTCAATAGTTTGACA 57.415 29.630 0.00 0.00 41.50 3.58
1703 2034 1.069049 CAAAGTGCCAGGTCAAAAGGG 59.931 52.381 0.00 0.00 0.00 3.95
1705 2036 2.031120 TCCAAAGTGCCAGGTCAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
1706 2037 2.151502 TCCAAAGTGCCAGGTCAAAA 57.848 45.000 0.00 0.00 0.00 2.44
1725 2056 4.499696 CCAAATTCCGCAAAGTCTGAAGTT 60.500 41.667 0.00 0.00 0.00 2.66
1733 2064 5.531634 CATATATGCCAAATTCCGCAAAGT 58.468 37.500 0.00 0.00 38.75 2.66
1760 2091 2.019249 GCATGCTTGTCTGAATGCCTA 58.981 47.619 11.37 0.00 41.85 3.93
1785 2116 8.579863 AGAAAAAGACAGCTGCTATTAAAATGT 58.420 29.630 15.27 0.00 0.00 2.71
1816 2147 8.996988 TGTTGCTTGTAAATTTTAGAACTACG 57.003 30.769 0.00 0.00 0.00 3.51
1866 2280 7.226918 TCGTGAATGATACTCTTCGAGTCTATT 59.773 37.037 0.00 0.98 42.40 1.73
1871 2285 4.395231 TGTCGTGAATGATACTCTTCGAGT 59.605 41.667 1.82 1.82 45.54 4.18
1874 2288 5.497126 CGTTTGTCGTGAATGATACTCTTCG 60.497 44.000 0.00 0.00 34.52 3.79
1916 2330 4.796231 ATCGACCTGTCCGCGTGC 62.796 66.667 4.92 0.00 0.00 5.34
1941 2355 2.101415 CAGTGTCAGTGACTCTGTTGGA 59.899 50.000 32.76 8.92 44.23 3.53
1957 2371 2.943033 GTGTAAGGAAGCACAACAGTGT 59.057 45.455 0.00 0.00 39.07 3.55
1958 2372 2.032894 CGTGTAAGGAAGCACAACAGTG 60.033 50.000 0.00 0.00 35.51 3.66
1959 2373 2.210116 CGTGTAAGGAAGCACAACAGT 58.790 47.619 0.00 0.00 35.51 3.55
1960 2374 1.531149 CCGTGTAAGGAAGCACAACAG 59.469 52.381 0.00 0.00 35.51 3.16
1961 2375 1.134340 ACCGTGTAAGGAAGCACAACA 60.134 47.619 0.00 0.00 35.51 3.33
1962 2376 1.589803 ACCGTGTAAGGAAGCACAAC 58.410 50.000 0.00 0.00 35.51 3.32
1976 2390 0.108662 TGCACTCTGATGCTACCGTG 60.109 55.000 11.45 0.00 46.28 4.94
1996 2410 0.250252 TCGCACATCTGCAAGTGGAA 60.250 50.000 13.45 0.00 44.50 3.53
1997 2411 0.671472 CTCGCACATCTGCAAGTGGA 60.671 55.000 13.45 9.00 44.50 4.02
1998 2412 1.792301 CTCGCACATCTGCAAGTGG 59.208 57.895 13.45 5.99 44.50 4.00
1999 2413 1.134075 GCTCGCACATCTGCAAGTG 59.866 57.895 8.73 8.73 44.50 3.16
2008 2422 0.250467 ACTTGAAGTGGCTCGCACAT 60.250 50.000 0.00 0.00 0.00 3.21
2038 2452 4.578516 TGCAATGCACAACTTGTTACTAGT 59.421 37.500 2.72 0.00 31.71 2.57
2039 2453 5.107109 TGCAATGCACAACTTGTTACTAG 57.893 39.130 2.72 0.00 31.71 2.57
2054 2468 4.424061 TTGAGTAACATCACTGCAATGC 57.576 40.909 0.00 0.00 0.00 3.56
2097 2511 2.961526 TCGAGAGCTTACCACAATCC 57.038 50.000 0.00 0.00 0.00 3.01
2098 2512 3.557595 CCATTCGAGAGCTTACCACAATC 59.442 47.826 0.00 0.00 0.00 2.67
2099 2513 3.197766 TCCATTCGAGAGCTTACCACAAT 59.802 43.478 0.00 0.00 0.00 2.71
2110 2524 6.727824 AACATTTTACACTCCATTCGAGAG 57.272 37.500 0.00 0.00 41.63 3.20
2111 2525 6.148811 GGAAACATTTTACACTCCATTCGAGA 59.851 38.462 0.00 0.00 41.63 4.04
2133 2547 6.891388 TCCACTTCAAGTAACTTAGTTGGAA 58.109 36.000 8.00 5.71 39.12 3.53
2138 2552 8.044908 TCTTGTTTCCACTTCAAGTAACTTAGT 58.955 33.333 3.84 0.00 39.36 2.24
2160 2574 4.107622 CCTTTTCTGTGTGCAAGTTCTTG 58.892 43.478 8.04 8.04 0.00 3.02
2161 2575 4.016444 TCCTTTTCTGTGTGCAAGTTCTT 58.984 39.130 0.00 0.00 0.00 2.52
2163 2577 4.096382 TCTTCCTTTTCTGTGTGCAAGTTC 59.904 41.667 0.00 0.00 0.00 3.01
2184 2603 7.291411 TCTTGCTTTACACTTCTAGTCTTCT 57.709 36.000 0.00 0.00 0.00 2.85
2246 2665 5.277731 GCCAGCTAGCAGATAAGAACAAATC 60.278 44.000 18.83 0.00 0.00 2.17
2252 2671 2.103771 CAGGCCAGCTAGCAGATAAGAA 59.896 50.000 18.83 0.00 0.00 2.52
2275 2694 2.498481 AGAACATGCATGGTTCCCATTG 59.502 45.455 29.41 3.23 42.23 2.82
2327 2746 8.478066 ACTTGGCAATTTTATCCTTCTATTTCC 58.522 33.333 0.00 0.00 0.00 3.13
2332 2751 7.669722 AGTTGACTTGGCAATTTTATCCTTCTA 59.330 33.333 0.00 0.00 0.00 2.10
2335 2754 6.670695 AGTTGACTTGGCAATTTTATCCTT 57.329 33.333 0.00 0.00 0.00 3.36
2338 2757 7.041848 AGCAAAAGTTGACTTGGCAATTTTATC 60.042 33.333 17.52 5.66 36.91 1.75
2339 2758 6.767423 AGCAAAAGTTGACTTGGCAATTTTAT 59.233 30.769 17.52 0.00 36.91 1.40
2340 2759 6.112058 AGCAAAAGTTGACTTGGCAATTTTA 58.888 32.000 17.52 0.00 36.91 1.52
2341 2760 4.943093 AGCAAAAGTTGACTTGGCAATTTT 59.057 33.333 17.52 4.22 38.71 1.82
2344 2763 3.132646 TGAGCAAAAGTTGACTTGGCAAT 59.867 39.130 17.52 0.00 38.66 3.56
2347 2766 2.159254 TGTGAGCAAAAGTTGACTTGGC 60.159 45.455 10.90 10.90 37.35 4.52
2348 2767 3.781079 TGTGAGCAAAAGTTGACTTGG 57.219 42.857 0.00 0.00 36.12 3.61


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

AutoCloner maintained by Alex Coulton.