Multiple sequence alignment - TraesCS1B01G267000

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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 TraesCS1B01G267000 chr1B 100.000 7358 0 0 1 7358 469971700 469979057 0.000000e+00 13588.0
1 TraesCS1B01G267000 chr1B 100.000 244 0 0 7623 7866 469979322 469979565 1.200000e-122 451.0
2 TraesCS1B01G267000 chr1B 82.692 104 15 2 555 658 158517655 158517555 1.090000e-13 89.8
3 TraesCS1B01G267000 chr1A 94.051 5732 214 42 518 6187 448918050 448923716 0.000000e+00 8578.0
4 TraesCS1B01G267000 chr1A 94.427 951 38 6 6225 7171 448923949 448924888 0.000000e+00 1448.0
5 TraesCS1B01G267000 chr1A 86.316 190 17 4 328 517 448916756 448916936 1.730000e-46 198.0
6 TraesCS1B01G267000 chr1A 92.241 116 9 0 7751 7866 448925244 448925359 1.760000e-36 165.0
7 TraesCS1B01G267000 chr1A 91.379 116 4 3 7644 7753 448925092 448925207 3.800000e-33 154.0
8 TraesCS1B01G267000 chr1A 87.500 104 6 1 1 97 448916643 448916746 6.450000e-21 113.0
9 TraesCS1B01G267000 chr1A 81.600 125 17 4 548 670 539977165 539977045 1.810000e-16 99.0
10 TraesCS1B01G267000 chr1A 81.416 113 17 3 547 659 155857849 155857741 1.090000e-13 89.8
11 TraesCS1B01G267000 chr1D 93.826 3110 139 23 518 3609 348055049 348058123 0.000000e+00 4630.0
12 TraesCS1B01G267000 chr1D 96.212 2508 42 16 3704 6187 348058136 348060614 0.000000e+00 4056.0
13 TraesCS1B01G267000 chr1D 95.559 1171 40 4 6200 7358 348060660 348061830 0.000000e+00 1864.0
14 TraesCS1B01G267000 chr1D 84.711 242 9 7 7653 7866 348062380 348062621 4.780000e-52 217.0
15 TraesCS1B01G267000 chr1D 86.869 198 16 4 328 523 348054834 348055023 6.180000e-51 213.0
16 TraesCS1B01G267000 chr1D 93.137 102 6 1 1 102 348054733 348054833 1.770000e-31 148.0
17 TraesCS1B01G267000 chr1D 97.368 38 0 1 7624 7661 348061908 348061944 6.590000e-06 63.9
18 TraesCS1B01G267000 chr5A 98.618 217 3 0 101 317 676174113 676173897 1.240000e-102 385.0
19 TraesCS1B01G267000 chr5A 89.100 211 14 1 106 316 605714385 605714184 3.640000e-63 254.0
20 TraesCS1B01G267000 chr7D 95.283 212 10 0 106 317 205124073 205124284 3.520000e-88 337.0
21 TraesCS1B01G267000 chr7D 87.264 212 18 1 106 317 539701120 539701322 4.750000e-57 233.0
22 TraesCS1B01G267000 chr5D 94.470 217 12 0 103 319 487171511 487171295 1.260000e-87 335.0
23 TraesCS1B01G267000 chr7B 92.593 216 16 0 102 317 443648816 443649031 2.130000e-80 311.0
24 TraesCS1B01G267000 chr7B 89.091 220 23 1 103 321 61344478 61344697 1.010000e-68 272.0
25 TraesCS1B01G267000 chr7B 82.203 118 15 4 541 658 436751649 436751760 6.500000e-16 97.1
26 TraesCS1B01G267000 chr4A 91.743 218 18 0 102 319 365446194 365445977 3.570000e-78 303.0
27 TraesCS1B01G267000 chr4A 92.473 186 2 1 107 292 684508940 684509113 1.010000e-63 255.0
28 TraesCS1B01G267000 chr4A 81.034 116 18 3 543 657 136793630 136793742 1.090000e-13 89.8
29 TraesCS1B01G267000 chr4D 89.904 208 21 0 110 317 294616013 294616220 1.300000e-67 268.0
30 TraesCS1B01G267000 chr4D 82.443 131 18 4 541 671 10977561 10977436 8.350000e-20 110.0
31 TraesCS1B01G267000 chr2A 89.286 84 5 1 5468 5547 78811451 78811534 1.400000e-17 102.0
32 TraesCS1B01G267000 chr2A 82.143 112 15 4 547 658 151267338 151267232 3.020000e-14 91.6
33 TraesCS1B01G267000 chr2D 88.095 84 6 1 5468 5547 78530005 78530088 6.500000e-16 97.1
34 TraesCS1B01G267000 chr2D 86.047 86 8 1 5466 5547 414972614 414972699 1.090000e-13 89.8
35 TraesCS1B01G267000 chr2B 88.095 84 6 1 5468 5547 121669390 121669473 6.500000e-16 97.1
36 TraesCS1B01G267000 chr6B 87.356 87 6 2 5469 5551 150637330 150637245 2.340000e-15 95.3
37 TraesCS1B01G267000 chr6A 84.158 101 8 6 5457 5551 93620940 93620842 3.020000e-14 91.6
38 TraesCS1B01G267000 chr4B 83.133 83 5 1 5469 5551 548196509 548196582 5.090000e-07 67.6
39 TraesCS1B01G267000 chr7A 96.970 33 0 1 6161 6192 561699085 561699117 4.000000e-03 54.7


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 TraesCS1B01G267000 chr1B 469971700 469979565 7865 False 7019.500000 13588 100.000000 1 7866 2 chr1B.!!$F1 7865
1 TraesCS1B01G267000 chr1A 448916643 448925359 8716 False 1776.000000 8578 90.985667 1 7866 6 chr1A.!!$F1 7865
2 TraesCS1B01G267000 chr1D 348054733 348062621 7888 False 1598.842857 4630 92.526000 1 7866 7 chr1D.!!$F1 7865

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
293 301 0.174617 GGGAGTTGAGAAGCGAGGAG 59.825 60.000 0.00 0.00 0.00 3.69 F
348 356 0.179004 ACAGTGGCGGTCCAATTCAA 60.179 50.000 0.00 0.00 45.53 2.69 F
1828 2965 0.966875 GTGCCCATCATGAACCTGCA 60.967 55.000 0.00 3.92 0.00 4.41 F
3384 4549 0.405198 ATGTGAACTCCCACCATGCA 59.595 50.000 0.00 0.00 36.26 3.96 F
4702 5893 0.110486 ATGCTGGTGAGGTTTTCGGT 59.890 50.000 0.00 0.00 0.00 4.69 F
4754 5945 1.134848 AGCTCCAATCTCGACTTCAGC 60.135 52.381 0.00 0.00 0.00 4.26 F
6734 8133 0.395586 TGAAGTTGCAAGGCCAGTGT 60.396 50.000 5.01 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 2771 0.238289 CTTCCTGTTTCACGCGCATT 59.762 50.0 5.73 0.0 0.00 3.56 R
2179 3319 0.553819 TACCACACAGCCTTTGGGTT 59.446 50.0 0.00 0.0 41.96 4.11 R
3463 4630 0.321210 TCCACATAACCACAGGCACG 60.321 55.0 0.00 0.0 0.00 5.34 R
4754 5945 1.587043 TTCCTCTCGTCTGACAGCCG 61.587 60.0 8.73 0.0 0.00 5.52 R
6198 7393 0.033699 ATTCCCCTTGCCTTCTCAGC 60.034 55.0 0.00 0.0 0.00 4.26 R
6743 8142 2.092968 CCTTTCTCCCATCAACATCCGA 60.093 50.0 0.00 0.0 0.00 4.55 R
7780 9685 0.869068 TTAACACGCATGGTCGTTGG 59.131 50.0 0.00 0.0 41.21 3.77 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
54 55 1.657556 GATCTTCCTCCGAGCTCCG 59.342 63.158 8.47 1.13 38.18 4.63
102 110 6.721571 TGTTCTGAAATCGTCCTTTGATAC 57.278 37.500 0.00 0.00 0.00 2.24
103 111 6.464222 TGTTCTGAAATCGTCCTTTGATACT 58.536 36.000 0.00 0.00 0.00 2.12
106 114 8.596380 GTTCTGAAATCGTCCTTTGATACTAAG 58.404 37.037 0.00 0.00 0.00 2.18
107 115 8.063200 TCTGAAATCGTCCTTTGATACTAAGA 57.937 34.615 0.00 0.00 0.00 2.10
108 116 8.191446 TCTGAAATCGTCCTTTGATACTAAGAG 58.809 37.037 0.00 0.00 0.00 2.85
109 117 6.757010 TGAAATCGTCCTTTGATACTAAGAGC 59.243 38.462 0.00 0.00 0.00 4.09
110 118 4.650754 TCGTCCTTTGATACTAAGAGCC 57.349 45.455 0.00 0.00 0.00 4.70
111 119 4.279145 TCGTCCTTTGATACTAAGAGCCT 58.721 43.478 0.00 0.00 0.00 4.58
112 120 4.098044 TCGTCCTTTGATACTAAGAGCCTG 59.902 45.833 0.00 0.00 0.00 4.85
113 121 4.142138 CGTCCTTTGATACTAAGAGCCTGT 60.142 45.833 0.00 0.00 0.00 4.00
114 122 5.624738 CGTCCTTTGATACTAAGAGCCTGTT 60.625 44.000 0.00 0.00 0.00 3.16
115 123 5.813157 GTCCTTTGATACTAAGAGCCTGTTC 59.187 44.000 0.00 0.00 0.00 3.18
116 124 4.806247 CCTTTGATACTAAGAGCCTGTTCG 59.194 45.833 0.00 0.00 0.00 3.95
117 125 4.386867 TTGATACTAAGAGCCTGTTCGG 57.613 45.455 0.00 0.00 0.00 4.30
145 153 4.079850 CTCCGCAGCACAGCTCCT 62.080 66.667 0.00 0.00 36.40 3.69
146 154 4.383861 TCCGCAGCACAGCTCCTG 62.384 66.667 0.00 0.00 36.40 3.86
148 156 4.383861 CGCAGCACAGCTCCTGGA 62.384 66.667 0.00 0.00 36.40 3.86
149 157 2.436292 GCAGCACAGCTCCTGGAG 60.436 66.667 19.55 19.55 36.40 3.86
158 166 4.504916 CTCCTGGAGCGGCGAGTG 62.505 72.222 12.98 0.00 0.00 3.51
168 176 4.980805 GGCGAGTGTGGCACCGAA 62.981 66.667 16.26 0.00 34.49 4.30
169 177 3.712881 GCGAGTGTGGCACCGAAC 61.713 66.667 16.26 6.84 34.49 3.95
170 178 3.403057 CGAGTGTGGCACCGAACG 61.403 66.667 16.26 11.62 34.49 3.95
171 179 3.712881 GAGTGTGGCACCGAACGC 61.713 66.667 16.26 4.82 34.49 4.84
175 183 3.037249 GTGGCACCGAACGCGTTA 61.037 61.111 26.68 4.02 35.23 3.18
176 184 2.279985 TGGCACCGAACGCGTTAA 60.280 55.556 26.68 1.80 35.23 2.01
177 185 2.171701 GGCACCGAACGCGTTAAC 59.828 61.111 26.68 12.77 35.23 2.01
178 186 2.201959 GCACCGAACGCGTTAACG 60.202 61.111 26.68 23.84 43.27 3.18
189 197 3.626542 CGTTAACGTCACGCTTTCC 57.373 52.632 19.75 0.00 34.11 3.13
190 198 1.134226 CGTTAACGTCACGCTTTCCT 58.866 50.000 19.75 0.00 34.11 3.36
191 199 1.123756 CGTTAACGTCACGCTTTCCTC 59.876 52.381 19.75 0.00 34.11 3.71
192 200 1.123756 GTTAACGTCACGCTTTCCTCG 59.876 52.381 0.00 0.00 0.00 4.63
193 201 0.592637 TAACGTCACGCTTTCCTCGA 59.407 50.000 0.00 0.00 0.00 4.04
194 202 0.663568 AACGTCACGCTTTCCTCGAG 60.664 55.000 5.13 5.13 0.00 4.04
195 203 1.801913 CGTCACGCTTTCCTCGAGG 60.802 63.158 26.32 26.32 0.00 4.63
196 204 2.095252 GTCACGCTTTCCTCGAGGC 61.095 63.158 27.39 13.81 34.44 4.70
199 207 4.129737 CGCTTTCCTCGAGGCGGA 62.130 66.667 27.39 12.07 43.25 5.54
200 208 2.202810 GCTTTCCTCGAGGCGGAG 60.203 66.667 27.39 22.06 34.44 4.63
227 235 1.805254 CCAGCAGGCCATTTTCTCG 59.195 57.895 5.01 0.00 0.00 4.04
228 236 1.660560 CCAGCAGGCCATTTTCTCGG 61.661 60.000 5.01 0.00 0.00 4.63
229 237 0.677731 CAGCAGGCCATTTTCTCGGA 60.678 55.000 5.01 0.00 0.00 4.55
230 238 0.393537 AGCAGGCCATTTTCTCGGAG 60.394 55.000 5.01 0.00 0.00 4.63
231 239 1.997928 GCAGGCCATTTTCTCGGAGC 61.998 60.000 5.01 0.00 0.00 4.70
232 240 1.450312 AGGCCATTTTCTCGGAGCG 60.450 57.895 5.01 0.00 0.00 5.03
233 241 2.472909 GGCCATTTTCTCGGAGCGG 61.473 63.158 0.00 0.00 0.00 5.52
234 242 3.102097 CCATTTTCTCGGAGCGGC 58.898 61.111 0.00 0.00 0.00 6.53
235 243 2.472909 CCATTTTCTCGGAGCGGCC 61.473 63.158 0.00 0.00 0.00 6.13
236 244 2.124695 ATTTTCTCGGAGCGGCCC 60.125 61.111 0.00 0.00 0.00 5.80
237 245 2.966732 ATTTTCTCGGAGCGGCCCA 61.967 57.895 0.00 0.00 0.00 5.36
238 246 2.478335 ATTTTCTCGGAGCGGCCCAA 62.478 55.000 0.00 0.00 0.00 4.12
239 247 3.605749 TTTCTCGGAGCGGCCCAAG 62.606 63.158 0.00 0.00 0.00 3.61
269 277 3.299585 CGCTTCGCATCTACGTGG 58.700 61.111 0.00 0.00 0.00 4.94
270 278 1.226575 CGCTTCGCATCTACGTGGA 60.227 57.895 3.36 3.36 0.00 4.02
271 279 1.202973 CGCTTCGCATCTACGTGGAG 61.203 60.000 7.91 1.09 0.00 3.86
272 280 0.179134 GCTTCGCATCTACGTGGAGT 60.179 55.000 7.91 0.00 0.00 3.85
273 281 1.065102 GCTTCGCATCTACGTGGAGTA 59.935 52.381 7.91 0.00 0.00 2.59
282 290 2.719739 CTACGTGGAGTAGGGAGTTGA 58.280 52.381 0.00 0.00 46.93 3.18
283 291 1.546961 ACGTGGAGTAGGGAGTTGAG 58.453 55.000 0.00 0.00 0.00 3.02
284 292 1.075050 ACGTGGAGTAGGGAGTTGAGA 59.925 52.381 0.00 0.00 0.00 3.27
285 293 2.168496 CGTGGAGTAGGGAGTTGAGAA 58.832 52.381 0.00 0.00 0.00 2.87
286 294 2.164624 CGTGGAGTAGGGAGTTGAGAAG 59.835 54.545 0.00 0.00 0.00 2.85
287 295 2.093921 GTGGAGTAGGGAGTTGAGAAGC 60.094 54.545 0.00 0.00 0.00 3.86
288 296 1.135333 GGAGTAGGGAGTTGAGAAGCG 59.865 57.143 0.00 0.00 0.00 4.68
289 297 2.093106 GAGTAGGGAGTTGAGAAGCGA 58.907 52.381 0.00 0.00 0.00 4.93
290 298 2.096248 AGTAGGGAGTTGAGAAGCGAG 58.904 52.381 0.00 0.00 0.00 5.03
291 299 1.135333 GTAGGGAGTTGAGAAGCGAGG 59.865 57.143 0.00 0.00 0.00 4.63
292 300 0.251832 AGGGAGTTGAGAAGCGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
293 301 0.174617 GGGAGTTGAGAAGCGAGGAG 59.825 60.000 0.00 0.00 0.00 3.69
321 329 4.296265 CCGAACAGGCCCTAACAC 57.704 61.111 0.00 0.00 0.00 3.32
322 330 1.373435 CCGAACAGGCCCTAACACA 59.627 57.895 0.00 0.00 0.00 3.72
323 331 0.673644 CCGAACAGGCCCTAACACAG 60.674 60.000 0.00 0.00 0.00 3.66
324 332 0.320374 CGAACAGGCCCTAACACAGA 59.680 55.000 0.00 0.00 0.00 3.41
325 333 1.809684 GAACAGGCCCTAACACAGAC 58.190 55.000 0.00 0.00 0.00 3.51
326 334 1.348036 GAACAGGCCCTAACACAGACT 59.652 52.381 0.00 0.00 0.00 3.24
332 340 2.353803 GGCCCTAACACAGACTACACAG 60.354 54.545 0.00 0.00 0.00 3.66
348 356 0.179004 ACAGTGGCGGTCCAATTCAA 60.179 50.000 0.00 0.00 45.53 2.69
358 366 4.799255 GCGGTCCAATTCAATCACCTTTTT 60.799 41.667 0.00 0.00 0.00 1.94
400 408 3.073209 TCCACCTTTACTTGCCATGTACA 59.927 43.478 0.00 0.00 0.00 2.90
401 409 3.440173 CCACCTTTACTTGCCATGTACAG 59.560 47.826 0.33 0.00 0.00 2.74
402 410 4.072131 CACCTTTACTTGCCATGTACAGT 58.928 43.478 0.33 0.00 0.00 3.55
403 411 5.242434 CACCTTTACTTGCCATGTACAGTA 58.758 41.667 0.33 0.00 0.00 2.74
404 412 5.880332 CACCTTTACTTGCCATGTACAGTAT 59.120 40.000 0.33 0.00 0.00 2.12
405 413 7.045416 CACCTTTACTTGCCATGTACAGTATA 58.955 38.462 0.33 0.00 0.00 1.47
406 414 7.011109 CACCTTTACTTGCCATGTACAGTATAC 59.989 40.741 0.33 0.00 0.00 1.47
446 454 7.277174 TCTTGAGAAAGACAATCCTTTTTCC 57.723 36.000 0.00 0.00 36.81 3.13
502 510 3.259064 GGTGATTCCAACGAAGATCGAA 58.741 45.455 6.78 0.00 38.59 3.71
503 511 3.871594 GGTGATTCCAACGAAGATCGAAT 59.128 43.478 6.78 0.00 38.59 3.34
556 1677 5.784578 ACTGTTACCTTTGTTCCCAATTC 57.215 39.130 0.00 0.00 0.00 2.17
562 1683 7.229907 TGTTACCTTTGTTCCCAATTCTAAGAC 59.770 37.037 0.00 0.00 0.00 3.01
563 1684 5.701224 ACCTTTGTTCCCAATTCTAAGACA 58.299 37.500 0.00 0.00 0.00 3.41
602 1723 7.959689 ACATGATCTATATGCAGACTGAAAC 57.040 36.000 6.65 0.00 0.00 2.78
622 1743 6.092944 TGAAACGAGTGAACAAACACACTAAT 59.907 34.615 0.00 0.00 45.54 1.73
623 1744 6.431198 AACGAGTGAACAAACACACTAATT 57.569 33.333 0.00 0.00 45.54 1.40
627 1748 8.452534 ACGAGTGAACAAACACACTAATTAAAA 58.547 29.630 0.00 0.00 45.54 1.52
628 1749 8.730427 CGAGTGAACAAACACACTAATTAAAAC 58.270 33.333 0.00 0.00 45.54 2.43
629 1750 8.609478 AGTGAACAAACACACTAATTAAAACG 57.391 30.769 0.00 0.00 44.06 3.60
630 1751 8.238631 AGTGAACAAACACACTAATTAAAACGT 58.761 29.630 0.00 0.00 44.06 3.99
687 1808 4.569162 TCATCTCACGCTATTAAAAACGGG 59.431 41.667 0.00 0.00 0.00 5.28
752 1873 3.622060 AAACCTACGCGCTGCCCAT 62.622 57.895 5.73 0.00 0.00 4.00
957 2087 4.007457 CGTGACCGGGTTCCTCTA 57.993 61.111 6.32 0.00 0.00 2.43
975 2105 4.075682 CTCTACTTCATAGCCGATCCTGA 58.924 47.826 0.00 0.00 0.00 3.86
1054 2184 1.698506 CGAGCTCTTCCCTCAGGTAT 58.301 55.000 12.85 0.00 0.00 2.73
1117 2248 2.908796 GGATGAGGAACGGGGGAC 59.091 66.667 0.00 0.00 0.00 4.46
1240 2376 1.491670 CATTCGGACGCACTAGGATG 58.508 55.000 0.00 0.00 0.00 3.51
1250 2386 2.416296 CGCACTAGGATGTTACCGTGAA 60.416 50.000 0.00 0.00 34.73 3.18
1251 2387 3.737047 CGCACTAGGATGTTACCGTGAAT 60.737 47.826 0.00 0.00 34.73 2.57
1252 2388 4.189231 GCACTAGGATGTTACCGTGAATT 58.811 43.478 0.00 0.00 34.73 2.17
1254 2390 4.570772 CACTAGGATGTTACCGTGAATTGG 59.429 45.833 0.00 0.00 34.73 3.16
1255 2391 2.999331 AGGATGTTACCGTGAATTGGG 58.001 47.619 0.00 0.00 34.73 4.12
1256 2392 2.021457 GGATGTTACCGTGAATTGGGG 58.979 52.381 0.00 0.00 0.00 4.96
1257 2393 1.404035 GATGTTACCGTGAATTGGGGC 59.596 52.381 0.00 0.00 0.00 5.80
1279 2416 1.339727 GGCCGGGTGTGATTTTAGTCT 60.340 52.381 2.18 0.00 0.00 3.24
1321 2458 8.132362 GGATTATCGCTAGATCGATTCATACTT 58.868 37.037 9.99 0.00 45.81 2.24
1365 2502 4.810345 TCCTTTTAGGGGAATTGTTGTGT 58.190 39.130 0.00 0.00 35.59 3.72
1405 2542 4.050553 CGCCATTCAGTGTTTGATTTGTT 58.949 39.130 0.00 0.00 35.27 2.83
1531 2668 2.737376 GTGGTCGCCGTCCTTGAC 60.737 66.667 1.46 0.00 0.00 3.18
1570 2707 2.486472 TAGGTTCGGTCGAAGTCTCT 57.514 50.000 6.02 5.13 34.49 3.10
1606 2743 1.066605 GCTGCGGTATCTAAGGACGAA 59.933 52.381 0.00 0.00 0.00 3.85
1618 2755 9.367444 GTATCTAAGGACGAATTTTTCAGAAGA 57.633 33.333 0.00 0.00 0.00 2.87
1634 2771 8.675705 TTTCAGAAGATTAACTGTGAATCACA 57.324 30.769 15.88 15.88 42.45 3.58
1639 2776 5.872635 AGATTAACTGTGAATCACAATGCG 58.127 37.500 17.41 8.07 44.08 4.73
1676 2813 7.603180 AGTTCATCATCTGCTGGTAAGTATA 57.397 36.000 0.00 0.00 0.00 1.47
1687 2824 8.630917 TCTGCTGGTAAGTATAAAGACTGATAC 58.369 37.037 0.00 1.19 0.00 2.24
1688 2825 7.723324 TGCTGGTAAGTATAAAGACTGATACC 58.277 38.462 4.79 0.00 35.01 2.73
1692 2829 9.263446 TGGTAAGTATAAAGACTGATACCACTT 57.737 33.333 4.84 0.00 37.66 3.16
1808 2945 2.093658 GCAGGTCCAGTCGGAATTTCTA 60.094 50.000 0.00 0.00 45.20 2.10
1828 2965 0.966875 GTGCCCATCATGAACCTGCA 60.967 55.000 0.00 3.92 0.00 4.41
1926 3063 9.077885 TGCTGGTAAGTAAAAAGATTGAGATTT 57.922 29.630 0.00 0.00 0.00 2.17
2195 3335 0.823460 AACAACCCAAAGGCTGTGTG 59.177 50.000 3.55 0.00 41.76 3.82
2196 3336 1.042559 ACAACCCAAAGGCTGTGTGG 61.043 55.000 3.55 7.25 41.04 4.17
2262 3403 4.469657 TGAGCTCATGTGGGTTTAACTTT 58.530 39.130 13.74 0.00 0.00 2.66
2282 3423 5.063564 ACTTTAGCGCTAATCTGTACAAAGC 59.936 40.000 29.17 3.25 0.00 3.51
2333 3474 9.041354 ACATTTTCTCTGATATATACTCCCTCC 57.959 37.037 0.00 0.00 0.00 4.30
2334 3475 7.704578 TTTTCTCTGATATATACTCCCTCCG 57.295 40.000 0.00 0.00 0.00 4.63
2335 3476 6.390048 TTCTCTGATATATACTCCCTCCGT 57.610 41.667 0.00 0.00 0.00 4.69
2434 3575 6.916360 TGAAGCTAAGGGAAATGTTGATTT 57.084 33.333 0.00 0.00 34.29 2.17
2451 3592 4.289342 TGATTTTGCAATCACAACTGACG 58.711 39.130 0.00 0.00 43.32 4.35
2499 3640 8.709386 ACTAGATGTGACTTCATCATTACAAC 57.291 34.615 0.00 0.00 44.46 3.32
2557 3698 2.613595 TGCCTGCACTTAATGATAAGCG 59.386 45.455 0.00 0.00 41.92 4.68
2558 3699 2.603173 GCCTGCACTTAATGATAAGCGC 60.603 50.000 0.00 0.00 44.01 5.92
3038 4203 4.223953 AGACTTCTACTGGTGTTCCTGAA 58.776 43.478 0.00 0.00 36.65 3.02
3039 4204 4.841246 AGACTTCTACTGGTGTTCCTGAAT 59.159 41.667 0.00 0.00 36.65 2.57
3061 4226 7.606456 TGAATGTGTAGTCTCACCTAAATTTCC 59.394 37.037 0.00 0.00 37.51 3.13
3155 4320 4.282703 GGTTCTGGTGGAGTCTTAGTACAA 59.717 45.833 0.00 0.00 0.00 2.41
3243 4408 4.572389 TCTTGTCTTCTTCAAGTGAGTTGC 59.428 41.667 0.00 0.00 41.78 4.17
3245 4410 4.517285 TGTCTTCTTCAAGTGAGTTGCTT 58.483 39.130 0.00 0.00 35.94 3.91
3297 4462 2.867624 TGGCTTCAACTCATTCAAGCT 58.132 42.857 2.78 0.00 40.95 3.74
3322 4487 6.159988 ACTCTGTTAGTATTGAGTCACTTGC 58.840 40.000 0.00 0.00 36.36 4.01
3384 4549 0.405198 ATGTGAACTCCCACCATGCA 59.595 50.000 0.00 0.00 36.26 3.96
3439 4606 2.368439 TCTTGGGCACATTACTCATGC 58.632 47.619 0.00 0.00 36.14 4.06
3513 4680 3.573967 AGTTGCACACCCTTTCCTTTATG 59.426 43.478 0.00 0.00 0.00 1.90
3662 4829 2.744202 GTTAGACATGAAGGGCACTGTG 59.256 50.000 0.00 2.76 0.00 3.66
3663 4830 0.767375 AGACATGAAGGGCACTGTGT 59.233 50.000 9.86 0.00 0.00 3.72
3682 4849 6.756542 ACTGTGTTAAAAGAGAATGTTTTGCC 59.243 34.615 0.00 0.00 41.97 4.52
3774 4941 9.252962 GAAGGATCATGCTAAAAATACCATTTG 57.747 33.333 0.00 0.00 0.00 2.32
3815 4982 5.988561 AGCACTTATAGCAGAAATGAGTAGC 59.011 40.000 0.00 0.00 0.00 3.58
3941 5108 5.542635 TGTAGTAGGTTGACTGGAATCACTT 59.457 40.000 0.00 0.00 0.00 3.16
4191 5358 6.696441 CCCTTAAGGTCTGTACTAGTGTAG 57.304 45.833 20.22 3.75 0.00 2.74
4380 5570 1.789464 GATTCGCCGATAACTGCTGAG 59.211 52.381 0.00 0.00 0.00 3.35
4702 5893 0.110486 ATGCTGGTGAGGTTTTCGGT 59.890 50.000 0.00 0.00 0.00 4.69
4754 5945 1.134848 AGCTCCAATCTCGACTTCAGC 60.135 52.381 0.00 0.00 0.00 4.26
4892 6083 6.238842 GGATGGTCCATCATGTTCTATTTGTG 60.239 42.308 29.07 0.00 42.13 3.33
5399 6594 4.700213 TCTTTTATGGGTACTGCTCAAAGC 59.300 41.667 0.00 0.00 42.82 3.51
5458 6653 7.666623 TCCCTTTAAAGGTAAAAATGCTTCTG 58.333 34.615 28.41 11.19 44.98 3.02
5473 6668 8.798859 AAATGCTTCTGTATGTTTGATACTCT 57.201 30.769 0.00 0.00 0.00 3.24
5570 6765 9.864034 GGATTACGGATTATCATTATTTATGCG 57.136 33.333 0.00 0.00 36.36 4.73
5575 6770 8.255206 ACGGATTATCATTATTTATGCGGTCTA 58.745 33.333 0.00 0.00 34.90 2.59
5810 7005 1.996292 TCATGTCAGCTACTTCGTGC 58.004 50.000 0.00 0.00 0.00 5.34
5846 7041 2.906047 GCAAGACTGCCCTATAGCG 58.094 57.895 0.00 0.00 43.26 4.26
6175 7370 7.981225 ACTAATGTGAATTGAACTGCAAAAACT 59.019 29.630 0.00 0.00 40.48 2.66
6187 7382 8.682710 TGAACTGCAAAAACTTCTTACATTAGT 58.317 29.630 0.00 0.00 0.00 2.24
6189 7384 9.516314 AACTGCAAAAACTTCTTACATTAGTTC 57.484 29.630 0.00 0.00 31.26 3.01
6190 7385 8.903820 ACTGCAAAAACTTCTTACATTAGTTCT 58.096 29.630 0.00 0.00 31.26 3.01
6191 7386 9.736023 CTGCAAAAACTTCTTACATTAGTTCTT 57.264 29.630 0.00 0.00 31.26 2.52
6192 7387 9.515020 TGCAAAAACTTCTTACATTAGTTCTTG 57.485 29.630 0.00 0.00 34.53 3.02
6193 7388 9.730420 GCAAAAACTTCTTACATTAGTTCTTGA 57.270 29.630 0.00 0.00 33.70 3.02
6290 7682 9.720769 CCCCGACATATTAGTACAAAGAATAAT 57.279 33.333 0.00 0.00 0.00 1.28
6367 7759 8.570096 TCTATTTACAAATCGTGAGTATTCCG 57.430 34.615 0.00 0.00 0.00 4.30
6374 7767 6.424509 ACAAATCGTGAGTATTCCGTTTGTTA 59.575 34.615 14.97 0.00 33.85 2.41
6377 7770 7.605410 ATCGTGAGTATTCCGTTTGTTATTT 57.395 32.000 0.00 0.00 0.00 1.40
6486 7885 9.836864 TTGATAATGCTGTGTCAGTTTATAGAT 57.163 29.630 0.00 0.00 33.43 1.98
6491 7890 5.053145 GCTGTGTCAGTTTATAGATGGAGG 58.947 45.833 0.00 0.00 33.43 4.30
6688 8087 3.060866 AGGACCACTGAAGCCGTC 58.939 61.111 0.00 0.00 0.00 4.79
6734 8133 0.395586 TGAAGTTGCAAGGCCAGTGT 60.396 50.000 5.01 0.00 0.00 3.55
6743 8142 1.004044 CAAGGCCAGTGTCTGAGGATT 59.996 52.381 5.01 0.00 32.44 3.01
6751 8150 2.834549 AGTGTCTGAGGATTCGGATGTT 59.165 45.455 0.00 0.00 40.70 2.71
6754 8153 3.452264 TGTCTGAGGATTCGGATGTTGAT 59.548 43.478 0.00 0.00 40.70 2.57
6797 8196 0.546122 TGGCTGTGACAGTGAAGGTT 59.454 50.000 14.82 0.00 33.43 3.50
6877 8276 2.105477 ACTGTGCTGAACTGAAGATGGT 59.895 45.455 0.00 0.00 0.00 3.55
6885 8284 5.877012 GCTGAACTGAAGATGGTTGAAGATA 59.123 40.000 0.00 0.00 0.00 1.98
6954 8354 5.679792 GCGGTAATAATCATTTCAAACGTCC 59.320 40.000 0.00 0.00 0.00 4.79
6999 8399 4.062991 GTGAACTTACGGGACTTGTCATT 58.937 43.478 3.08 0.00 0.00 2.57
7066 8475 6.092122 TGAGATAAGTTAAAATGGTGCTGACG 59.908 38.462 0.00 0.00 0.00 4.35
7170 8579 1.923204 GTCGCTTAGTCTGAGCACATG 59.077 52.381 16.13 0.00 40.13 3.21
7174 8583 3.539604 GCTTAGTCTGAGCACATGGAAT 58.460 45.455 11.57 0.00 39.89 3.01
7184 8593 5.255687 TGAGCACATGGAATCTTTACACAT 58.744 37.500 0.00 0.00 0.00 3.21
7192 8601 6.961359 TGGAATCTTTACACATTGTACTCG 57.039 37.500 0.00 0.00 31.69 4.18
7198 8607 0.315886 ACACATTGTACTCGGTGCGA 59.684 50.000 10.05 0.00 34.69 5.10
7250 8659 6.827727 TGAAGTTCTAGCTTTGTCCTAACTT 58.172 36.000 4.17 0.00 0.00 2.66
7350 8766 6.424207 ACCTAAGACAAAGAACTTAAAGCGAG 59.576 38.462 0.00 0.00 0.00 5.03
7758 9663 7.821595 TCTATACCTTGTAATTTGTGTGTCG 57.178 36.000 0.00 0.00 0.00 4.35
7780 9685 2.375174 TGGAGGGGTATTACATCATGGC 59.625 50.000 0.00 0.00 0.00 4.40
7797 9702 2.903547 GCCAACGACCATGCGTGTT 61.904 57.895 4.96 0.00 44.86 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.181690 TCAAAGCACCACATACTGAAAAC 57.818 39.130 0.00 0.00 0.00 2.43
141 149 4.504916 CACTCGCCGCTCCAGGAG 62.505 72.222 12.81 12.81 0.00 3.69
151 159 4.980805 TTCGGTGCCACACTCGCC 62.981 66.667 0.00 0.00 34.40 5.54
152 160 3.712881 GTTCGGTGCCACACTCGC 61.713 66.667 0.00 0.00 34.40 5.03
153 161 3.403057 CGTTCGGTGCCACACTCG 61.403 66.667 0.00 1.41 34.40 4.18
154 162 3.712881 GCGTTCGGTGCCACACTC 61.713 66.667 0.00 0.00 34.40 3.51
157 165 3.786901 TAACGCGTTCGGTGCCACA 62.787 57.895 30.28 4.17 40.69 4.17
158 166 2.596795 TTAACGCGTTCGGTGCCAC 61.597 57.895 30.28 0.00 40.69 5.01
159 167 2.279985 TTAACGCGTTCGGTGCCA 60.280 55.556 30.28 5.92 40.69 4.92
160 168 2.171701 GTTAACGCGTTCGGTGCC 59.828 61.111 30.28 7.21 40.69 5.01
161 169 2.201959 CGTTAACGCGTTCGGTGC 60.202 61.111 30.28 13.57 40.69 5.01
162 170 1.126438 GACGTTAACGCGTTCGGTG 59.874 57.895 30.28 18.53 45.79 4.94
163 171 1.299014 TGACGTTAACGCGTTCGGT 60.299 52.632 30.28 23.23 45.79 4.69
164 172 1.126438 GTGACGTTAACGCGTTCGG 59.874 57.895 30.28 20.15 45.79 4.30
165 173 1.224661 CGTGACGTTAACGCGTTCG 60.225 57.895 30.28 27.46 45.79 3.95
166 174 4.666071 CGTGACGTTAACGCGTTC 57.334 55.556 30.28 14.76 45.79 3.95
171 179 1.123756 GAGGAAAGCGTGACGTTAACG 59.876 52.381 25.68 25.68 43.81 3.18
172 180 1.123756 CGAGGAAAGCGTGACGTTAAC 59.876 52.381 6.91 0.00 0.00 2.01
173 181 1.001487 TCGAGGAAAGCGTGACGTTAA 60.001 47.619 6.91 0.00 0.00 2.01
174 182 0.592637 TCGAGGAAAGCGTGACGTTA 59.407 50.000 6.91 0.00 0.00 3.18
175 183 0.663568 CTCGAGGAAAGCGTGACGTT 60.664 55.000 6.91 0.00 0.00 3.99
176 184 1.081376 CTCGAGGAAAGCGTGACGT 60.081 57.895 6.91 0.00 0.00 4.34
177 185 1.801913 CCTCGAGGAAAGCGTGACG 60.802 63.158 28.21 0.00 37.39 4.35
178 186 2.095252 GCCTCGAGGAAAGCGTGAC 61.095 63.158 35.69 9.98 37.39 3.67
179 187 2.261671 GCCTCGAGGAAAGCGTGA 59.738 61.111 35.69 0.00 37.39 4.35
180 188 3.181967 CGCCTCGAGGAAAGCGTG 61.182 66.667 35.69 9.49 43.45 5.34
181 189 4.436998 CCGCCTCGAGGAAAGCGT 62.437 66.667 35.69 0.00 46.85 5.07
183 191 2.202810 CTCCGCCTCGAGGAAAGC 60.203 66.667 35.69 18.04 37.32 3.51
184 192 2.202810 GCTCCGCCTCGAGGAAAG 60.203 66.667 35.69 25.69 37.32 2.62
185 193 4.129737 CGCTCCGCCTCGAGGAAA 62.130 66.667 35.69 17.25 37.32 3.13
209 217 1.660560 CCGAGAAAATGGCCTGCTGG 61.661 60.000 3.32 5.03 0.00 4.85
210 218 0.677731 TCCGAGAAAATGGCCTGCTG 60.678 55.000 3.32 0.00 0.00 4.41
211 219 0.393537 CTCCGAGAAAATGGCCTGCT 60.394 55.000 3.32 0.00 0.00 4.24
212 220 1.997928 GCTCCGAGAAAATGGCCTGC 61.998 60.000 3.32 0.00 0.00 4.85
213 221 1.709147 CGCTCCGAGAAAATGGCCTG 61.709 60.000 3.32 0.00 0.00 4.85
214 222 1.450312 CGCTCCGAGAAAATGGCCT 60.450 57.895 3.32 0.00 0.00 5.19
215 223 2.472909 CCGCTCCGAGAAAATGGCC 61.473 63.158 0.00 0.00 0.00 5.36
216 224 3.102097 CCGCTCCGAGAAAATGGC 58.898 61.111 0.00 0.00 0.00 4.40
217 225 2.472909 GGCCGCTCCGAGAAAATGG 61.473 63.158 0.00 0.00 0.00 3.16
218 226 2.472909 GGGCCGCTCCGAGAAAATG 61.473 63.158 0.00 0.00 34.94 2.32
219 227 2.124695 GGGCCGCTCCGAGAAAAT 60.125 61.111 0.00 0.00 34.94 1.82
220 228 3.185299 TTGGGCCGCTCCGAGAAAA 62.185 57.895 0.00 0.00 34.94 2.29
221 229 3.605749 CTTGGGCCGCTCCGAGAAA 62.606 63.158 0.00 0.00 40.07 2.52
222 230 4.082523 CTTGGGCCGCTCCGAGAA 62.083 66.667 0.00 0.00 40.07 2.87
254 262 2.287069 CCTACTCCACGTAGATGCGAAG 60.287 54.545 0.00 0.00 46.98 3.79
255 263 1.674441 CCTACTCCACGTAGATGCGAA 59.326 52.381 0.00 0.00 46.98 4.70
256 264 1.306148 CCTACTCCACGTAGATGCGA 58.694 55.000 0.00 0.00 46.98 5.10
257 265 0.311165 CCCTACTCCACGTAGATGCG 59.689 60.000 0.00 0.00 46.98 4.73
258 266 1.609555 CTCCCTACTCCACGTAGATGC 59.390 57.143 0.00 0.00 46.98 3.91
259 267 2.933573 ACTCCCTACTCCACGTAGATG 58.066 52.381 0.00 0.00 46.98 2.90
260 268 3.053842 TCAACTCCCTACTCCACGTAGAT 60.054 47.826 0.00 0.00 46.98 1.98
261 269 2.306805 TCAACTCCCTACTCCACGTAGA 59.693 50.000 0.00 0.00 46.98 2.59
262 270 2.683867 CTCAACTCCCTACTCCACGTAG 59.316 54.545 0.00 0.00 44.26 3.51
263 271 2.306805 TCTCAACTCCCTACTCCACGTA 59.693 50.000 0.00 0.00 0.00 3.57
264 272 1.075050 TCTCAACTCCCTACTCCACGT 59.925 52.381 0.00 0.00 0.00 4.49
265 273 1.835494 TCTCAACTCCCTACTCCACG 58.165 55.000 0.00 0.00 0.00 4.94
266 274 2.093921 GCTTCTCAACTCCCTACTCCAC 60.094 54.545 0.00 0.00 0.00 4.02
267 275 2.180276 GCTTCTCAACTCCCTACTCCA 58.820 52.381 0.00 0.00 0.00 3.86
268 276 1.135333 CGCTTCTCAACTCCCTACTCC 59.865 57.143 0.00 0.00 0.00 3.85
269 277 2.093106 TCGCTTCTCAACTCCCTACTC 58.907 52.381 0.00 0.00 0.00 2.59
270 278 2.096248 CTCGCTTCTCAACTCCCTACT 58.904 52.381 0.00 0.00 0.00 2.57
271 279 1.135333 CCTCGCTTCTCAACTCCCTAC 59.865 57.143 0.00 0.00 0.00 3.18
272 280 1.005569 TCCTCGCTTCTCAACTCCCTA 59.994 52.381 0.00 0.00 0.00 3.53
273 281 0.251832 TCCTCGCTTCTCAACTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
274 282 0.174617 CTCCTCGCTTCTCAACTCCC 59.825 60.000 0.00 0.00 0.00 4.30
275 283 0.459411 GCTCCTCGCTTCTCAACTCC 60.459 60.000 0.00 0.00 35.14 3.85
276 284 0.244994 TGCTCCTCGCTTCTCAACTC 59.755 55.000 0.00 0.00 40.11 3.01
277 285 0.246086 CTGCTCCTCGCTTCTCAACT 59.754 55.000 0.00 0.00 40.11 3.16
278 286 0.244994 TCTGCTCCTCGCTTCTCAAC 59.755 55.000 0.00 0.00 40.11 3.18
279 287 0.529833 CTCTGCTCCTCGCTTCTCAA 59.470 55.000 0.00 0.00 40.11 3.02
280 288 1.318886 CCTCTGCTCCTCGCTTCTCA 61.319 60.000 0.00 0.00 40.11 3.27
281 289 1.437160 CCTCTGCTCCTCGCTTCTC 59.563 63.158 0.00 0.00 40.11 2.87
282 290 2.057408 CCCTCTGCTCCTCGCTTCT 61.057 63.158 0.00 0.00 40.11 2.85
283 291 2.498726 CCCTCTGCTCCTCGCTTC 59.501 66.667 0.00 0.00 40.11 3.86
284 292 3.780173 GCCCTCTGCTCCTCGCTT 61.780 66.667 0.00 0.00 40.11 4.68
294 302 2.435586 CTGTTCGGCAGCCCTCTG 60.436 66.667 5.63 0.00 43.16 3.35
295 303 3.710722 CCTGTTCGGCAGCCCTCT 61.711 66.667 5.63 0.00 43.71 3.69
304 312 0.673644 CTGTGTTAGGGCCTGTTCGG 60.674 60.000 18.53 5.34 0.00 4.30
305 313 0.320374 TCTGTGTTAGGGCCTGTTCG 59.680 55.000 18.53 0.00 0.00 3.95
306 314 1.348036 AGTCTGTGTTAGGGCCTGTTC 59.652 52.381 18.53 6.90 0.00 3.18
307 315 1.435256 AGTCTGTGTTAGGGCCTGTT 58.565 50.000 18.53 0.00 0.00 3.16
308 316 1.900486 GTAGTCTGTGTTAGGGCCTGT 59.100 52.381 18.53 0.00 0.00 4.00
309 317 1.899814 TGTAGTCTGTGTTAGGGCCTG 59.100 52.381 18.53 0.00 0.00 4.85
310 318 1.900486 GTGTAGTCTGTGTTAGGGCCT 59.100 52.381 12.58 12.58 0.00 5.19
311 319 1.621814 TGTGTAGTCTGTGTTAGGGCC 59.378 52.381 0.00 0.00 0.00 5.80
312 320 2.299297 ACTGTGTAGTCTGTGTTAGGGC 59.701 50.000 0.00 0.00 28.79 5.19
313 321 3.306088 CCACTGTGTAGTCTGTGTTAGGG 60.306 52.174 7.08 0.00 34.07 3.53
314 322 3.861131 GCCACTGTGTAGTCTGTGTTAGG 60.861 52.174 7.08 0.00 34.07 2.69
315 323 3.318017 GCCACTGTGTAGTCTGTGTTAG 58.682 50.000 7.08 0.00 34.07 2.34
316 324 2.287970 CGCCACTGTGTAGTCTGTGTTA 60.288 50.000 7.08 0.00 34.07 2.41
317 325 1.538204 CGCCACTGTGTAGTCTGTGTT 60.538 52.381 7.08 0.00 34.07 3.32
318 326 0.032130 CGCCACTGTGTAGTCTGTGT 59.968 55.000 7.08 0.00 34.07 3.72
319 327 0.667487 CCGCCACTGTGTAGTCTGTG 60.667 60.000 7.08 0.00 34.07 3.66
320 328 1.113517 ACCGCCACTGTGTAGTCTGT 61.114 55.000 7.08 0.00 34.07 3.41
321 329 0.388649 GACCGCCACTGTGTAGTCTG 60.389 60.000 7.08 0.00 34.07 3.51
322 330 1.533469 GGACCGCCACTGTGTAGTCT 61.533 60.000 16.53 0.00 34.07 3.24
323 331 1.080025 GGACCGCCACTGTGTAGTC 60.080 63.158 7.08 9.74 34.07 2.59
324 332 1.404479 TTGGACCGCCACTGTGTAGT 61.404 55.000 7.08 0.74 45.94 2.73
325 333 0.036388 ATTGGACCGCCACTGTGTAG 60.036 55.000 7.08 0.04 45.94 2.74
326 334 0.398696 AATTGGACCGCCACTGTGTA 59.601 50.000 7.08 0.00 45.94 2.90
332 340 1.135402 GTGATTGAATTGGACCGCCAC 60.135 52.381 0.00 0.00 45.94 5.01
358 366 5.238650 GTGGAGGATGTTCTCGAAAAAGAAA 59.761 40.000 0.00 0.00 37.04 2.52
400 408 8.709646 CAAGAAGAAAACTGCGTAAAGTATACT 58.290 33.333 0.00 0.00 0.00 2.12
401 409 8.706035 TCAAGAAGAAAACTGCGTAAAGTATAC 58.294 33.333 0.00 0.00 0.00 1.47
402 410 8.821147 TCAAGAAGAAAACTGCGTAAAGTATA 57.179 30.769 0.00 0.00 0.00 1.47
403 411 7.656137 TCTCAAGAAGAAAACTGCGTAAAGTAT 59.344 33.333 0.00 0.00 0.00 2.12
404 412 6.982141 TCTCAAGAAGAAAACTGCGTAAAGTA 59.018 34.615 0.00 0.00 0.00 2.24
405 413 5.815740 TCTCAAGAAGAAAACTGCGTAAAGT 59.184 36.000 0.00 0.00 0.00 2.66
406 414 6.287107 TCTCAAGAAGAAAACTGCGTAAAG 57.713 37.500 0.00 0.00 0.00 1.85
480 488 1.933853 CGATCTTCGTTGGAATCACCC 59.066 52.381 0.00 0.00 34.70 4.61
481 489 2.888594 TCGATCTTCGTTGGAATCACC 58.111 47.619 0.00 0.00 41.35 4.02
482 490 5.749109 ACTATTCGATCTTCGTTGGAATCAC 59.251 40.000 0.00 0.00 41.35 3.06
530 1651 5.113446 TGGGAACAAAGGTAACAGTAACA 57.887 39.130 0.00 0.00 37.44 2.41
576 1697 7.958053 TTCAGTCTGCATATAGATCATGTTG 57.042 36.000 0.00 0.00 0.00 3.33
579 1700 6.865205 TCGTTTCAGTCTGCATATAGATCATG 59.135 38.462 0.00 0.00 0.00 3.07
584 1705 5.357032 TCACTCGTTTCAGTCTGCATATAGA 59.643 40.000 0.00 0.00 0.00 1.98
602 1723 8.730427 GTTTTAATTAGTGTGTTTGTTCACTCG 58.270 33.333 1.08 0.00 42.77 4.18
627 1748 8.095937 TCGTGAATCAGATGTATATAGAACGT 57.904 34.615 0.00 0.00 0.00 3.99
628 1749 8.950403 TTCGTGAATCAGATGTATATAGAACG 57.050 34.615 0.00 0.00 0.00 3.95
658 1779 9.774742 GTTTTTAATAGCGTGAGATGATCTTTT 57.225 29.630 0.00 0.00 0.00 2.27
659 1780 8.116753 CGTTTTTAATAGCGTGAGATGATCTTT 58.883 33.333 0.00 0.00 0.00 2.52
660 1781 7.254455 CCGTTTTTAATAGCGTGAGATGATCTT 60.254 37.037 0.00 0.00 0.00 2.40
664 1785 4.569162 CCCGTTTTTAATAGCGTGAGATGA 59.431 41.667 2.01 0.00 0.00 2.92
687 1808 8.358582 TCCTCTTTTCGTAATATATACTCCCC 57.641 38.462 0.00 0.00 0.00 4.81
696 1817 8.368668 CCTCCTTGTATCCTCTTTTCGTAATAT 58.631 37.037 0.00 0.00 0.00 1.28
697 1818 7.201974 CCCTCCTTGTATCCTCTTTTCGTAATA 60.202 40.741 0.00 0.00 0.00 0.98
940 2070 0.964358 AGTAGAGGAACCCGGTCACG 60.964 60.000 0.00 0.00 40.55 4.35
944 2074 2.249309 ATGAAGTAGAGGAACCCGGT 57.751 50.000 0.00 0.00 0.00 5.28
957 2087 3.007398 GGAATCAGGATCGGCTATGAAGT 59.993 47.826 0.00 0.00 0.00 3.01
975 2105 2.092914 CGAACCCTAGAAGCCAAGGAAT 60.093 50.000 0.00 0.00 34.58 3.01
1054 2184 4.483243 GGAAAGGCGGATCGGGCA 62.483 66.667 25.41 0.00 34.40 5.36
1128 2259 2.634777 CTCGCCGCCGAACAAAAA 59.365 55.556 0.00 0.00 43.87 1.94
1194 2328 5.018539 TCCACTATTCCCAATCTGTAACG 57.981 43.478 0.00 0.00 0.00 3.18
1240 2376 1.650314 CCGCCCCAATTCACGGTAAC 61.650 60.000 0.00 0.00 40.77 2.50
1257 2393 1.373590 CTAAAATCACACCCGGCCCG 61.374 60.000 0.00 0.00 0.00 6.13
1262 2398 3.262420 CAGGAGACTAAAATCACACCCG 58.738 50.000 0.00 0.00 40.21 5.28
1288 2425 5.754406 TCGATCTAGCGATAATCCTAGTAGC 59.246 44.000 0.00 0.00 35.01 3.58
1302 2439 6.958752 CAGAGTAAGTATGAATCGATCTAGCG 59.041 42.308 0.00 0.00 0.00 4.26
1303 2440 8.035165 TCAGAGTAAGTATGAATCGATCTAGC 57.965 38.462 0.00 0.00 0.00 3.42
1345 2482 6.265422 AGAAGACACAACAATTCCCCTAAAAG 59.735 38.462 0.00 0.00 0.00 2.27
1347 2484 5.534654 CAGAAGACACAACAATTCCCCTAAA 59.465 40.000 0.00 0.00 0.00 1.85
1365 2502 1.475034 GCGGATTACCCATGCAGAAGA 60.475 52.381 0.00 0.00 34.14 2.87
1405 2542 2.125552 CTTCGACCGCAGCCATGA 60.126 61.111 0.00 0.00 0.00 3.07
1531 2668 5.107824 CCTATCATAGATGGCATGACTTCG 58.892 45.833 3.81 0.00 35.33 3.79
1570 2707 3.538614 GCCTCCTGATGGACGCTA 58.461 61.111 0.00 0.00 39.98 4.26
1618 2755 4.414852 GCGCATTGTGATTCACAGTTAAT 58.585 39.130 18.27 7.60 45.39 1.40
1634 2771 0.238289 CTTCCTGTTTCACGCGCATT 59.762 50.000 5.73 0.00 0.00 3.56
1639 2776 2.548057 TGATGAACTTCCTGTTTCACGC 59.452 45.455 0.00 0.00 39.30 5.34
1676 2813 6.212388 ACAGAGATCAAGTGGTATCAGTCTTT 59.788 38.462 0.00 0.00 0.00 2.52
1687 2824 4.397481 TCAGCATACAGAGATCAAGTGG 57.603 45.455 0.00 0.00 0.00 4.00
1688 2825 4.809958 CCTTCAGCATACAGAGATCAAGTG 59.190 45.833 0.00 0.00 0.00 3.16
1692 2829 3.465742 GCCTTCAGCATACAGAGATCA 57.534 47.619 0.00 0.00 42.97 2.92
1808 2945 0.682209 GCAGGTTCATGATGGGCACT 60.682 55.000 0.00 0.00 0.00 4.40
1926 3063 4.350816 ACACTAAGCATAGATTGGCCCATA 59.649 41.667 0.00 0.00 33.15 2.74
2158 3298 9.054922 TGGGTTGTTACTTAACACTTGTATAAC 57.945 33.333 1.18 0.00 45.01 1.89
2179 3319 0.553819 TACCACACAGCCTTTGGGTT 59.446 50.000 0.00 0.00 41.96 4.11
2195 3335 6.122964 AGTCAAGAATAAGAAAGCCCATACC 58.877 40.000 0.00 0.00 0.00 2.73
2196 3336 7.631717 AAGTCAAGAATAAGAAAGCCCATAC 57.368 36.000 0.00 0.00 0.00 2.39
2262 3403 3.454375 GGCTTTGTACAGATTAGCGCTA 58.546 45.455 14.45 14.45 32.74 4.26
2282 3423 9.305925 GTTCTTGCAATTTATTGAAGATAAGGG 57.694 33.333 0.00 0.00 40.14 3.95
2326 3467 2.362717 GGTTCTAATGAGACGGAGGGAG 59.637 54.545 0.00 0.00 0.00 4.30
2328 3469 2.389715 AGGTTCTAATGAGACGGAGGG 58.610 52.381 0.00 0.00 0.00 4.30
2329 3470 4.434520 GAAAGGTTCTAATGAGACGGAGG 58.565 47.826 0.00 0.00 0.00 4.30
2330 3471 4.434520 GGAAAGGTTCTAATGAGACGGAG 58.565 47.826 0.00 0.00 0.00 4.63
2331 3472 3.197116 GGGAAAGGTTCTAATGAGACGGA 59.803 47.826 0.00 0.00 0.00 4.69
2332 3473 3.532542 GGGAAAGGTTCTAATGAGACGG 58.467 50.000 0.00 0.00 0.00 4.79
2333 3474 3.187700 CGGGAAAGGTTCTAATGAGACG 58.812 50.000 0.00 0.00 0.00 4.18
2334 3475 4.203654 ACGGGAAAGGTTCTAATGAGAC 57.796 45.455 0.00 0.00 0.00 3.36
2335 3476 4.903045 AACGGGAAAGGTTCTAATGAGA 57.097 40.909 0.00 0.00 0.00 3.27
2420 3561 5.469421 TGTGATTGCAAAATCAACATTTCCC 59.531 36.000 1.71 0.00 40.49 3.97
2434 3575 1.268488 GCACGTCAGTTGTGATTGCAA 60.268 47.619 0.00 0.00 41.24 4.08
2451 3592 2.865551 CACCCACAACATTTTCTTGCAC 59.134 45.455 0.00 0.00 0.00 4.57
2499 3640 6.261826 GGGAAATCTAGTTGTCCATTCATCAG 59.738 42.308 11.46 0.00 31.30 2.90
2557 3698 0.313672 TTGAACGGCCAAATCACAGC 59.686 50.000 2.24 0.00 0.00 4.40
2558 3699 1.879380 TCTTGAACGGCCAAATCACAG 59.121 47.619 2.24 4.75 0.00 3.66
2789 3954 7.066645 CCAACTTGATTAGCTGAATGATCTGAA 59.933 37.037 0.00 0.00 0.00 3.02
2863 4028 0.968405 GCTGTTGCTCCCATTTTCCA 59.032 50.000 0.00 0.00 36.03 3.53
2865 4030 4.454728 TTATGCTGTTGCTCCCATTTTC 57.545 40.909 0.00 0.00 40.48 2.29
3038 4203 6.012858 TGGGAAATTTAGGTGAGACTACACAT 60.013 38.462 0.00 0.00 41.88 3.21
3039 4204 5.308497 TGGGAAATTTAGGTGAGACTACACA 59.692 40.000 0.00 0.00 41.88 3.72
3061 4226 4.086706 AGGGTGTCTTTTTCAGTACTGG 57.913 45.455 22.48 6.39 0.00 4.00
3155 4320 6.534475 ACATCAGCACAATTGTTATCCATT 57.466 33.333 8.77 0.00 0.00 3.16
3191 4356 3.133542 CACCATGCTCAACTCTATCCTCA 59.866 47.826 0.00 0.00 0.00 3.86
3243 4408 7.081526 AGTGATTCGAATTCAAATCAGGAAG 57.918 36.000 19.69 0.00 41.28 3.46
3245 4410 7.307694 CAAAGTGATTCGAATTCAAATCAGGA 58.692 34.615 19.69 0.00 41.28 3.86
3297 4462 7.313646 GCAAGTGACTCAATACTAACAGAGTA 58.686 38.462 0.00 0.00 44.87 2.59
3322 4487 3.859650 GCATCAGCAATGGAATCCG 57.140 52.632 0.00 0.00 41.58 4.18
3439 4606 1.062365 CCATACACGCATGCAACCG 59.938 57.895 19.57 3.36 0.00 4.44
3463 4630 0.321210 TCCACATAACCACAGGCACG 60.321 55.000 0.00 0.00 0.00 5.34
3682 4849 6.861065 TTGAGGTTAGCTTGTGAGTTTAAG 57.139 37.500 0.00 0.00 0.00 1.85
3774 4941 2.413453 GTGCTTCTGAATCCGTTGACTC 59.587 50.000 0.00 0.00 0.00 3.36
3815 4982 8.470002 TCCATACGATCATATCAGTAATTCCTG 58.530 37.037 0.00 0.00 0.00 3.86
3941 5108 4.326826 GAGAATCACTGACAATGACCCAA 58.673 43.478 0.00 0.00 33.17 4.12
4191 5358 4.256920 TCTCTATGGCAACTTCAGAAAGC 58.743 43.478 0.00 0.00 35.81 3.51
4380 5570 4.762251 ACAGCAGAAGAATAAGTTCCAACC 59.238 41.667 0.00 0.00 34.81 3.77
4702 5893 4.709886 TCCGTGGTCAAAATAGATCTCTCA 59.290 41.667 0.00 0.00 0.00 3.27
4754 5945 1.587043 TTCCTCTCGTCTGACAGCCG 61.587 60.000 8.73 0.00 0.00 5.52
4884 6075 6.795399 AGGACAAACAACTGAACACAAATAG 58.205 36.000 0.00 0.00 0.00 1.73
4892 6083 7.920682 ACATCATTAAAGGACAAACAACTGAAC 59.079 33.333 0.00 0.00 0.00 3.18
5399 6594 8.858003 TGCTCTGTAGATTTAATTAAGAGACG 57.142 34.615 10.81 0.00 33.14 4.18
5458 6653 5.978322 GGAACGGAGAGAGTATCAAACATAC 59.022 44.000 0.00 0.00 37.82 2.39
5473 6668 3.549423 CGACGCTTAATATGGAACGGAGA 60.549 47.826 0.00 0.00 0.00 3.71
5570 6765 7.886970 ACTACCCATAAAACCTTTTCTTAGACC 59.113 37.037 0.00 0.00 0.00 3.85
5575 6770 7.343574 ACAACACTACCCATAAAACCTTTTCTT 59.656 33.333 0.00 0.00 0.00 2.52
5810 7005 4.394920 TCTTGCTATGGAAAACTTTAGCGG 59.605 41.667 0.00 0.00 33.64 5.52
5868 7063 9.098355 CCAGAGTCATCGAAATTCAGTTTAATA 57.902 33.333 0.00 0.00 0.00 0.98
5883 7078 3.857549 TCTGAAGTTCCAGAGTCATCG 57.142 47.619 0.00 0.00 38.18 3.84
6155 7350 6.892310 AGAAGTTTTTGCAGTTCAATTCAC 57.108 33.333 0.00 0.00 34.12 3.18
6187 7382 4.847198 TGCCTTCTCAGCATTATCAAGAA 58.153 39.130 0.00 0.00 34.69 2.52
6189 7384 4.036498 CCTTGCCTTCTCAGCATTATCAAG 59.964 45.833 0.00 0.00 40.59 3.02
6190 7385 3.949754 CCTTGCCTTCTCAGCATTATCAA 59.050 43.478 0.00 0.00 40.59 2.57
6191 7386 3.548770 CCTTGCCTTCTCAGCATTATCA 58.451 45.455 0.00 0.00 40.59 2.15
6192 7387 2.883386 CCCTTGCCTTCTCAGCATTATC 59.117 50.000 0.00 0.00 40.59 1.75
6193 7388 2.423947 CCCCTTGCCTTCTCAGCATTAT 60.424 50.000 0.00 0.00 40.59 1.28
6194 7389 1.064463 CCCCTTGCCTTCTCAGCATTA 60.064 52.381 0.00 0.00 40.59 1.90
6195 7390 0.324091 CCCCTTGCCTTCTCAGCATT 60.324 55.000 0.00 0.00 40.59 3.56
6197 7392 1.426251 TTCCCCTTGCCTTCTCAGCA 61.426 55.000 0.00 0.00 38.81 4.41
6198 7393 0.033699 ATTCCCCTTGCCTTCTCAGC 60.034 55.000 0.00 0.00 0.00 4.26
6260 7652 4.757019 TGTACTAATATGTCGGGGCAAA 57.243 40.909 0.00 0.00 0.00 3.68
6262 7654 4.406326 TCTTTGTACTAATATGTCGGGGCA 59.594 41.667 0.00 0.00 0.00 5.36
6290 7682 6.488683 CCACTTCCCAATGTCTAACTTTAACA 59.511 38.462 0.00 0.00 0.00 2.41
6451 7846 8.969260 TGACACAGCATTATCAAGAATCTAAT 57.031 30.769 0.00 0.00 0.00 1.73
6486 7885 4.536090 ACAAGGATATGTTTCAGTCCTCCA 59.464 41.667 6.85 0.00 40.10 3.86
6491 7890 7.254932 GCATAAGGACAAGGATATGTTTCAGTC 60.255 40.741 0.00 0.00 32.57 3.51
6604 8003 4.892433 AGGAGAGACTTGACATTGTTGAG 58.108 43.478 0.00 0.00 0.00 3.02
6688 8087 7.096966 GCGACTGTATGTTTATCTTTAGACTCG 60.097 40.741 0.00 0.00 0.00 4.18
6734 8133 3.181462 CCATCAACATCCGAATCCTCAGA 60.181 47.826 0.00 0.00 0.00 3.27
6743 8142 2.092968 CCTTTCTCCCATCAACATCCGA 60.093 50.000 0.00 0.00 0.00 4.55
6751 8150 4.739793 ACATTTCAACCTTTCTCCCATCA 58.260 39.130 0.00 0.00 0.00 3.07
6754 8153 5.947663 TCTAACATTTCAACCTTTCTCCCA 58.052 37.500 0.00 0.00 0.00 4.37
6797 8196 1.070758 GTCTTCACCCACTGAGCTTGA 59.929 52.381 0.00 0.00 0.00 3.02
6877 8276 3.330701 AGGCAAACCCTGACTATCTTCAA 59.669 43.478 0.00 0.00 43.93 2.69
6946 8345 2.224549 TCGCACAAAATAGGGACGTTTG 59.775 45.455 0.00 0.00 38.06 2.93
6947 8346 2.482721 CTCGCACAAAATAGGGACGTTT 59.517 45.455 0.00 0.00 0.00 3.60
6999 8399 2.437281 TCCCAAAAGGCAAAGCAATTCA 59.563 40.909 0.00 0.00 34.51 2.57
7039 8448 8.296713 GTCAGCACCATTTTAACTTATCTCAAA 58.703 33.333 0.00 0.00 0.00 2.69
7040 8449 7.360861 CGTCAGCACCATTTTAACTTATCTCAA 60.361 37.037 0.00 0.00 0.00 3.02
7041 8450 6.092122 CGTCAGCACCATTTTAACTTATCTCA 59.908 38.462 0.00 0.00 0.00 3.27
7042 8451 6.092259 ACGTCAGCACCATTTTAACTTATCTC 59.908 38.462 0.00 0.00 0.00 2.75
7043 8452 5.938125 ACGTCAGCACCATTTTAACTTATCT 59.062 36.000 0.00 0.00 0.00 1.98
7044 8453 6.021596 CACGTCAGCACCATTTTAACTTATC 58.978 40.000 0.00 0.00 0.00 1.75
7045 8454 5.703592 TCACGTCAGCACCATTTTAACTTAT 59.296 36.000 0.00 0.00 0.00 1.73
7046 8455 5.057819 TCACGTCAGCACCATTTTAACTTA 58.942 37.500 0.00 0.00 0.00 2.24
7047 8456 3.880490 TCACGTCAGCACCATTTTAACTT 59.120 39.130 0.00 0.00 0.00 2.66
7122 8531 5.481105 CAGTAAAATTGGCATTGACATGGT 58.519 37.500 0.00 0.00 0.00 3.55
7170 8579 5.873164 ACCGAGTACAATGTGTAAAGATTCC 59.127 40.000 0.00 0.00 34.21 3.01
7174 8583 3.991773 GCACCGAGTACAATGTGTAAAGA 59.008 43.478 0.00 0.00 34.21 2.52
7184 8593 0.599060 TGTGATCGCACCGAGTACAA 59.401 50.000 4.45 0.00 44.51 2.41
7192 8601 7.985634 ACAATAAATAAAATGTGATCGCACC 57.014 32.000 11.96 0.00 44.51 5.01
7629 9045 9.696917 AAGCCTTTACAATTTGTAATCTGAAAG 57.303 29.630 19.73 14.90 41.83 2.62
7733 9599 7.874016 ACGACACACAAATTACAAGGTATAGAA 59.126 33.333 0.00 0.00 0.00 2.10
7758 9663 3.810743 GCCATGATGTAATACCCCTCCAC 60.811 52.174 0.00 0.00 0.00 4.02
7780 9685 0.869068 TTAACACGCATGGTCGTTGG 59.131 50.000 0.00 0.00 41.21 3.77
7797 9702 9.150348 CACGTCATGCCTATATTCACATATTTA 57.850 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.