Multiple sequence alignment - TraesCS4B01G387700

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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 TraesCS4B01G387700 chr4B 100.000 3019 0 0 1 3019 665396693 665393675 0.000000e+00 5576.0
1 TraesCS4B01G387700 chr4B 86.957 1035 75 27 1992 3014 665353917 665352931 0.000000e+00 1109.0
2 TraesCS4B01G387700 chr3B 89.796 1225 72 23 945 2152 740107032 740108220 0.000000e+00 1520.0
3 TraesCS4B01G387700 chr3B 93.122 378 17 5 2643 3017 740134957 740135328 2.050000e-151 545.0
4 TraesCS4B01G387700 chr3B 85.783 415 25 22 2247 2635 740108608 740109014 2.800000e-110 409.0
5 TraesCS4B01G387700 chr3B 83.896 385 43 13 45 423 740103084 740103455 1.720000e-92 350.0
6 TraesCS4B01G387700 chr3B 84.946 186 15 6 429 614 740103490 740103662 3.090000e-40 176.0
7 TraesCS4B01G387700 chr3B 81.657 169 11 9 708 876 740106779 740106927 4.090000e-24 122.0
8 TraesCS4B01G387700 chr3B 95.833 72 3 0 2162 2233 740108288 740108359 1.900000e-22 117.0
9 TraesCS4B01G387700 chr3B 100.000 29 0 0 2234 2262 740108561 740108589 2.000000e-03 54.7
10 TraesCS4B01G387700 chrUn 90.407 1178 59 27 1005 2152 108546819 108547972 0.000000e+00 1500.0
11 TraesCS4B01G387700 chrUn 89.371 875 40 22 2162 3015 108548040 108548882 0.000000e+00 1051.0
12 TraesCS4B01G387700 chrUn 93.158 380 17 5 2643 3019 325517380 325517753 1.580000e-152 549.0
13 TraesCS4B01G387700 chrUn 93.158 380 17 5 2643 3019 325559123 325558750 1.580000e-152 549.0
14 TraesCS4B01G387700 chrUn 86.047 258 29 7 2573 2830 83300113 83299863 1.380000e-68 270.0
15 TraesCS4B01G387700 chr5A 89.803 1167 59 26 1008 2152 705435409 705434281 0.000000e+00 1441.0
16 TraesCS4B01G387700 chr5A 87.813 878 36 22 2162 3019 705351136 705350310 0.000000e+00 963.0
17 TraesCS4B01G387700 chr5A 91.050 581 34 8 1580 2152 705351774 705351204 0.000000e+00 769.0
18 TraesCS4B01G387700 chr7D 85.772 246 31 1 2576 2821 358677619 358677378 1.070000e-64 257.0
19 TraesCS4B01G387700 chr1D 84.064 251 35 5 2573 2822 75541976 75541730 1.400000e-58 237.0
20 TraesCS4B01G387700 chr4A 81.495 281 39 6 2573 2844 322671900 322672176 5.070000e-53 219.0
21 TraesCS4B01G387700 chr2B 90.789 76 3 1 2174 2245 671739009 671739084 6.890000e-17 99.0


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 TraesCS4B01G387700 chr4B 665393675 665396693 3018 True 5576.000000 5576 100.000000 1 3019 1 chr4B.!!$R2 3018
1 TraesCS4B01G387700 chr4B 665352931 665353917 986 True 1109.000000 1109 86.957000 1992 3014 1 chr4B.!!$R1 1022
2 TraesCS4B01G387700 chr3B 740103084 740109014 5930 False 392.671429 1520 88.844429 45 2635 7 chr3B.!!$F2 2590
3 TraesCS4B01G387700 chrUn 108546819 108548882 2063 False 1275.500000 1500 89.889000 1005 3015 2 chrUn.!!$F2 2010
4 TraesCS4B01G387700 chr5A 705434281 705435409 1128 True 1441.000000 1441 89.803000 1008 2152 1 chr5A.!!$R1 1144
5 TraesCS4B01G387700 chr5A 705350310 705351774 1464 True 866.000000 963 89.431500 1580 3019 2 chr5A.!!$R2 1439

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
319 321 0.02877 TTTTTGACGCGCAGTTCTGG 59.971 50.0 5.73 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 5354 0.105593 AGTGCCAGTGTCAGTGTCAG 59.894 55.0 6.91 0.0 0.0 3.51 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 3.720494 TATCCAGAGCGGTTGCCA 58.280 55.556 0.00 0.00 44.31 4.92
18 19 2.220953 TATCCAGAGCGGTTGCCAT 58.779 52.632 0.00 0.00 44.31 4.40
19 20 0.546122 TATCCAGAGCGGTTGCCATT 59.454 50.000 0.00 0.00 44.31 3.16
20 21 1.033746 ATCCAGAGCGGTTGCCATTG 61.034 55.000 0.00 0.00 44.31 2.82
21 22 2.180017 CAGAGCGGTTGCCATTGC 59.820 61.111 0.00 0.00 44.31 3.56
22 23 3.064324 AGAGCGGTTGCCATTGCC 61.064 61.111 0.00 0.00 44.31 4.52
23 24 3.372730 GAGCGGTTGCCATTGCCA 61.373 61.111 0.00 0.00 44.31 4.92
24 25 3.346631 GAGCGGTTGCCATTGCCAG 62.347 63.158 0.00 0.00 44.31 4.85
26 27 3.682885 CGGTTGCCATTGCCAGCA 61.683 61.111 0.00 0.00 37.18 4.41
27 28 2.047939 GGTTGCCATTGCCAGCAC 60.048 61.111 0.00 0.00 39.10 4.40
28 29 2.576832 GGTTGCCATTGCCAGCACT 61.577 57.895 0.00 0.00 39.10 4.40
29 30 1.080298 GTTGCCATTGCCAGCACTC 60.080 57.895 0.00 0.00 39.10 3.51
30 31 1.531128 TTGCCATTGCCAGCACTCA 60.531 52.632 0.00 0.00 39.10 3.41
31 32 1.808531 TTGCCATTGCCAGCACTCAC 61.809 55.000 0.00 0.00 39.10 3.51
32 33 1.975407 GCCATTGCCAGCACTCACT 60.975 57.895 0.00 0.00 0.00 3.41
33 34 0.677731 GCCATTGCCAGCACTCACTA 60.678 55.000 0.00 0.00 0.00 2.74
34 35 1.376543 CCATTGCCAGCACTCACTAG 58.623 55.000 0.00 0.00 0.00 2.57
35 36 1.065926 CCATTGCCAGCACTCACTAGA 60.066 52.381 0.00 0.00 0.00 2.43
36 37 2.421107 CCATTGCCAGCACTCACTAGAT 60.421 50.000 0.00 0.00 0.00 1.98
37 38 3.276857 CATTGCCAGCACTCACTAGATT 58.723 45.455 0.00 0.00 0.00 2.40
38 39 3.423539 TTGCCAGCACTCACTAGATTT 57.576 42.857 0.00 0.00 0.00 2.17
39 40 4.551702 TTGCCAGCACTCACTAGATTTA 57.448 40.909 0.00 0.00 0.00 1.40
40 41 4.760530 TGCCAGCACTCACTAGATTTAT 57.239 40.909 0.00 0.00 0.00 1.40
41 42 5.102953 TGCCAGCACTCACTAGATTTATT 57.897 39.130 0.00 0.00 0.00 1.40
42 43 5.118990 TGCCAGCACTCACTAGATTTATTC 58.881 41.667 0.00 0.00 0.00 1.75
43 44 5.118990 GCCAGCACTCACTAGATTTATTCA 58.881 41.667 0.00 0.00 0.00 2.57
52 53 9.965902 ACTCACTAGATTTATTCAGGAAACATT 57.034 29.630 0.00 0.00 0.00 2.71
58 59 7.978982 AGATTTATTCAGGAAACATTCTCACG 58.021 34.615 0.00 0.00 0.00 4.35
66 67 1.238439 AACATTCTCACGCCCAGTTG 58.762 50.000 0.00 0.00 0.00 3.16
93 94 0.535797 GAACCCGGTTCGAATCCTCT 59.464 55.000 14.56 0.00 32.81 3.69
94 95 0.249398 AACCCGGTTCGAATCCTCTG 59.751 55.000 0.00 0.00 0.00 3.35
96 97 1.218047 CCGGTTCGAATCCTCTGCA 59.782 57.895 0.00 0.00 0.00 4.41
108 109 1.677576 TCCTCTGCAGCAACAAAGTTG 59.322 47.619 9.47 5.56 0.00 3.16
130 132 3.393426 AATCCAGCCCTGTTTGATGAT 57.607 42.857 0.00 0.00 0.00 2.45
136 138 2.025037 AGCCCTGTTTGATGATAAGCCA 60.025 45.455 0.00 0.00 0.00 4.75
137 139 2.360165 GCCCTGTTTGATGATAAGCCAG 59.640 50.000 0.00 0.00 0.00 4.85
138 140 2.360165 CCCTGTTTGATGATAAGCCAGC 59.640 50.000 0.00 0.00 0.00 4.85
140 142 2.360165 CTGTTTGATGATAAGCCAGCCC 59.640 50.000 0.00 0.00 0.00 5.19
142 144 0.546122 TTGATGATAAGCCAGCCCGT 59.454 50.000 0.00 0.00 0.00 5.28
143 145 0.546122 TGATGATAAGCCAGCCCGTT 59.454 50.000 0.00 0.00 0.00 4.44
144 146 1.064758 TGATGATAAGCCAGCCCGTTT 60.065 47.619 0.00 0.00 0.00 3.60
146 148 0.326595 TGATAAGCCAGCCCGTTTGA 59.673 50.000 0.00 0.00 0.00 2.69
147 149 0.733150 GATAAGCCAGCCCGTTTGAC 59.267 55.000 0.00 0.00 0.00 3.18
148 150 0.037590 ATAAGCCAGCCCGTTTGACA 59.962 50.000 0.00 0.00 0.00 3.58
149 151 0.179015 TAAGCCAGCCCGTTTGACAA 60.179 50.000 0.00 0.00 0.00 3.18
150 152 1.455383 AAGCCAGCCCGTTTGACAAG 61.455 55.000 0.00 0.00 0.00 3.16
151 153 2.193536 GCCAGCCCGTTTGACAAGT 61.194 57.895 0.00 0.00 0.00 3.16
152 154 1.654220 CCAGCCCGTTTGACAAGTG 59.346 57.895 0.00 0.00 0.00 3.16
153 155 1.101049 CCAGCCCGTTTGACAAGTGT 61.101 55.000 0.00 0.00 0.00 3.55
154 156 0.738389 CAGCCCGTTTGACAAGTGTT 59.262 50.000 0.00 0.00 0.00 3.32
155 157 1.134175 CAGCCCGTTTGACAAGTGTTT 59.866 47.619 0.00 0.00 0.00 2.83
156 158 1.822371 AGCCCGTTTGACAAGTGTTTT 59.178 42.857 0.00 0.00 0.00 2.43
191 193 2.906691 TTGTGTTGGGAGGCATTTTG 57.093 45.000 0.00 0.00 0.00 2.44
194 196 2.890311 TGTGTTGGGAGGCATTTTGTAG 59.110 45.455 0.00 0.00 0.00 2.74
210 212 2.917933 TGTAGGGCCATTGAAATCTCG 58.082 47.619 6.18 0.00 0.00 4.04
216 218 1.597663 GCCATTGAAATCTCGTACCCG 59.402 52.381 0.00 0.00 0.00 5.28
230 232 4.278513 CCCGGGAGTGGTTGCCAA 62.279 66.667 18.48 0.00 37.05 4.52
235 237 1.907807 GGAGTGGTTGCCAATGCCA 60.908 57.895 0.00 0.00 34.00 4.92
238 240 3.682885 TGGTTGCCAATGCCAGCG 61.683 61.111 0.00 0.00 33.62 5.18
247 249 1.135024 CCAATGCCAGCGCTACATTTT 60.135 47.619 26.61 12.13 31.82 1.82
248 250 2.098934 CCAATGCCAGCGCTACATTTTA 59.901 45.455 26.61 5.79 31.82 1.52
249 251 3.243501 CCAATGCCAGCGCTACATTTTAT 60.244 43.478 26.61 10.64 31.82 1.40
250 252 4.023279 CCAATGCCAGCGCTACATTTTATA 60.023 41.667 26.61 1.53 31.82 0.98
252 254 5.964958 ATGCCAGCGCTACATTTTATATT 57.035 34.783 10.99 0.00 35.36 1.28
253 255 5.356882 TGCCAGCGCTACATTTTATATTC 57.643 39.130 10.99 0.00 35.36 1.75
254 256 4.215399 TGCCAGCGCTACATTTTATATTCC 59.785 41.667 10.99 0.00 35.36 3.01
256 258 4.394795 CAGCGCTACATTTTATATTCCGC 58.605 43.478 10.99 0.00 39.23 5.54
257 259 3.122948 AGCGCTACATTTTATATTCCGCG 59.877 43.478 8.99 0.00 43.13 6.46
260 262 4.384846 CGCTACATTTTATATTCCGCGAGT 59.615 41.667 8.23 0.00 40.38 4.18
275 277 0.249073 CGAGTTTGGCGAGATCCGAT 60.249 55.000 7.64 0.00 41.76 4.18
277 279 2.543031 CGAGTTTGGCGAGATCCGATTA 60.543 50.000 7.64 0.00 41.76 1.75
291 293 5.634020 AGATCCGATTACGAAATTCGAATCC 59.366 40.000 22.92 12.18 43.74 3.01
293 295 4.743151 TCCGATTACGAAATTCGAATCCTG 59.257 41.667 22.92 16.02 43.74 3.86
294 296 4.084537 CCGATTACGAAATTCGAATCCTGG 60.085 45.833 22.92 16.76 43.74 4.45
295 297 4.743151 CGATTACGAAATTCGAATCCTGGA 59.257 41.667 22.92 0.00 43.74 3.86
297 299 6.562270 CGATTACGAAATTCGAATCCTGGAAG 60.562 42.308 22.92 8.68 43.74 3.46
298 300 3.939066 ACGAAATTCGAATCCTGGAAGT 58.061 40.909 22.92 2.75 43.74 3.01
299 301 3.684788 ACGAAATTCGAATCCTGGAAGTG 59.315 43.478 22.92 0.00 43.74 3.16
300 302 3.684788 CGAAATTCGAATCCTGGAAGTGT 59.315 43.478 11.83 0.00 43.74 3.55
305 307 4.829064 TCGAATCCTGGAAGTGTTTTTG 57.171 40.909 0.00 0.00 0.00 2.44
312 314 0.248296 GGAAGTGTTTTTGACGCGCA 60.248 50.000 5.73 1.71 43.57 6.09
313 315 1.112459 GAAGTGTTTTTGACGCGCAG 58.888 50.000 5.73 2.42 43.57 5.18
315 317 0.450184 AGTGTTTTTGACGCGCAGTT 59.550 45.000 5.73 0.00 43.57 3.16
319 321 0.028770 TTTTTGACGCGCAGTTCTGG 59.971 50.000 5.73 0.00 0.00 3.86
320 322 2.387125 TTTTGACGCGCAGTTCTGGC 62.387 55.000 5.73 0.00 0.00 4.85
322 324 3.782244 GACGCGCAGTTCTGGCTG 61.782 66.667 5.73 0.00 39.37 4.85
423 429 2.569853 TCCTGTAACGGATCATGGTTGT 59.430 45.455 0.00 0.00 0.00 3.32
425 431 3.126858 CCTGTAACGGATCATGGTTGTTG 59.873 47.826 7.56 0.00 0.00 3.33
426 432 3.078097 TGTAACGGATCATGGTTGTTGG 58.922 45.455 7.56 0.00 0.00 3.77
437 472 5.441500 TCATGGTTGTTGGTTTTCTACTCA 58.558 37.500 0.00 0.00 0.00 3.41
439 474 5.766150 TGGTTGTTGGTTTTCTACTCATG 57.234 39.130 0.00 0.00 0.00 3.07
459 494 2.933769 GCGAAGTGCTTTGCAAGTAAT 58.066 42.857 16.79 0.00 46.55 1.89
460 495 3.308530 GCGAAGTGCTTTGCAAGTAATT 58.691 40.909 16.79 0.00 46.55 1.40
461 496 4.472286 GCGAAGTGCTTTGCAAGTAATTA 58.528 39.130 16.79 0.00 46.55 1.40
462 497 4.554973 GCGAAGTGCTTTGCAAGTAATTAG 59.445 41.667 16.79 1.79 46.55 1.73
468 503 7.360361 AGTGCTTTGCAAGTAATTAGTTACAC 58.640 34.615 10.38 7.47 41.47 2.90
487 522 3.953775 CACTGCCCCCGGTCAACT 61.954 66.667 0.00 0.00 0.00 3.16
488 523 2.203877 ACTGCCCCCGGTCAACTA 60.204 61.111 0.00 0.00 0.00 2.24
492 527 2.608368 CCCCCGGTCAACTACCCA 60.608 66.667 0.00 0.00 46.62 4.51
523 558 4.899239 CTCATCTGGACCGCCCGC 62.899 72.222 0.00 0.00 37.93 6.13
533 568 4.776322 CCGCCCGCTGGATGACAA 62.776 66.667 0.00 0.00 0.00 3.18
614 649 1.597937 GCTTTGCTTGGACGACACAAG 60.598 52.381 11.99 11.99 46.15 3.16
615 650 1.670811 CTTTGCTTGGACGACACAAGT 59.329 47.619 15.72 0.00 45.38 3.16
616 651 1.013596 TTGCTTGGACGACACAAGTG 58.986 50.000 15.72 0.00 45.38 3.16
628 676 5.289595 ACGACACAAGTGTATATATGCAGG 58.710 41.667 5.74 0.35 45.05 4.85
629 677 5.068591 ACGACACAAGTGTATATATGCAGGA 59.931 40.000 5.74 0.00 45.05 3.86
630 678 5.631096 CGACACAAGTGTATATATGCAGGAG 59.369 44.000 5.74 0.06 45.05 3.69
631 679 6.515035 CGACACAAGTGTATATATGCAGGAGA 60.515 42.308 5.74 0.00 45.05 3.71
632 680 6.753180 ACACAAGTGTATATATGCAGGAGAG 58.247 40.000 3.64 0.00 42.90 3.20
641 689 2.018727 ATGCAGGAGAGAGCTCAGCG 62.019 60.000 17.77 0.00 42.87 5.18
642 690 2.413963 GCAGGAGAGAGCTCAGCGA 61.414 63.158 17.77 0.00 43.14 4.93
643 691 1.729276 CAGGAGAGAGCTCAGCGAG 59.271 63.158 17.77 0.00 43.14 5.03
647 3301 1.032014 GAGAGAGCTCAGCGAGGATT 58.968 55.000 17.77 0.00 40.96 3.01
667 3321 1.971505 AATGCCGCCGAGGATTCTCA 61.972 55.000 0.96 0.00 45.00 3.27
678 3332 2.393646 AGGATTCTCACCTCACCTAGC 58.606 52.381 0.00 0.00 31.43 3.42
679 3333 2.023501 AGGATTCTCACCTCACCTAGCT 60.024 50.000 0.00 0.00 31.43 3.32
681 3335 0.898320 TTCTCACCTCACCTAGCTGC 59.102 55.000 0.00 0.00 0.00 5.25
682 3336 0.040351 TCTCACCTCACCTAGCTGCT 59.960 55.000 7.57 7.57 0.00 4.24
683 3337 1.285078 TCTCACCTCACCTAGCTGCTA 59.715 52.381 9.34 9.34 0.00 3.49
684 3338 1.680735 CTCACCTCACCTAGCTGCTAG 59.319 57.143 26.08 26.08 34.16 3.42
692 3349 4.452825 TCACCTAGCTGCTAGTAGTACAG 58.547 47.826 29.21 17.27 32.62 2.74
708 3365 2.772739 CAGTATCACTGTGGCAGGC 58.227 57.895 8.11 0.00 41.19 4.85
739 3796 1.901650 GCCACACTGCTAGCAACGTC 61.902 60.000 19.86 4.23 0.00 4.34
783 3840 4.695928 GGTGAATTACCCAACTCTCAAGTC 59.304 45.833 0.00 0.00 44.15 3.01
785 3842 5.639931 GTGAATTACCCAACTCTCAAGTCTC 59.360 44.000 0.00 0.00 33.48 3.36
786 3843 5.306937 TGAATTACCCAACTCTCAAGTCTCA 59.693 40.000 0.00 0.00 33.48 3.27
787 3844 5.825593 ATTACCCAACTCTCAAGTCTCAA 57.174 39.130 0.00 0.00 33.48 3.02
788 3845 3.760580 ACCCAACTCTCAAGTCTCAAG 57.239 47.619 0.00 0.00 33.48 3.02
789 3846 3.041946 ACCCAACTCTCAAGTCTCAAGT 58.958 45.455 0.00 0.00 33.48 3.16
790 3847 4.223953 ACCCAACTCTCAAGTCTCAAGTA 58.776 43.478 0.00 0.00 33.48 2.24
791 3848 4.039366 ACCCAACTCTCAAGTCTCAAGTAC 59.961 45.833 0.00 0.00 33.48 2.73
792 3849 4.282195 CCCAACTCTCAAGTCTCAAGTACT 59.718 45.833 0.00 0.00 33.48 2.73
793 3850 5.477291 CCCAACTCTCAAGTCTCAAGTACTA 59.523 44.000 0.00 0.00 33.48 1.82
794 3851 6.383415 CCAACTCTCAAGTCTCAAGTACTAC 58.617 44.000 0.00 0.00 33.48 2.73
795 3852 5.866335 ACTCTCAAGTCTCAAGTACTACG 57.134 43.478 0.00 0.00 0.00 3.51
796 3853 5.307204 ACTCTCAAGTCTCAAGTACTACGT 58.693 41.667 0.00 0.00 0.00 3.57
797 3854 6.462500 ACTCTCAAGTCTCAAGTACTACGTA 58.538 40.000 0.00 0.00 0.00 3.57
798 3855 7.104939 ACTCTCAAGTCTCAAGTACTACGTAT 58.895 38.462 0.00 0.00 0.00 3.06
799 3856 8.256605 ACTCTCAAGTCTCAAGTACTACGTATA 58.743 37.037 0.00 0.00 0.00 1.47
800 3857 9.263538 CTCTCAAGTCTCAAGTACTACGTATAT 57.736 37.037 0.00 0.00 0.00 0.86
801 3858 9.043079 TCTCAAGTCTCAAGTACTACGTATATG 57.957 37.037 0.00 0.00 0.00 1.78
802 3859 8.151141 TCAAGTCTCAAGTACTACGTATATGG 57.849 38.462 0.00 0.00 0.00 2.74
803 3860 7.772292 TCAAGTCTCAAGTACTACGTATATGGT 59.228 37.037 0.00 0.00 0.00 3.55
804 3861 9.049523 CAAGTCTCAAGTACTACGTATATGGTA 57.950 37.037 0.00 0.00 0.00 3.25
808 3865 7.875041 TCTCAAGTACTACGTATATGGTAGTCC 59.125 40.741 18.95 11.70 45.52 3.85
817 3874 9.474920 CTACGTATATGGTAGTCCTACTATAGC 57.525 40.741 13.65 9.35 40.93 2.97
823 3880 7.999450 ATGGTAGTCCTACTATAGCTGTTAC 57.001 40.000 0.00 0.00 35.82 2.50
837 3894 2.735134 GCTGTTACGATCAACGAAACCT 59.265 45.455 0.00 0.00 45.77 3.50
876 3933 5.757850 AGAAGTTTTAGTCCAAACTGCTG 57.242 39.130 6.08 0.00 46.86 4.41
877 3934 5.193679 AGAAGTTTTAGTCCAAACTGCTGT 58.806 37.500 6.08 0.00 46.86 4.40
878 3935 6.354130 AGAAGTTTTAGTCCAAACTGCTGTA 58.646 36.000 6.08 0.00 46.86 2.74
879 3936 6.260271 AGAAGTTTTAGTCCAAACTGCTGTAC 59.740 38.462 6.08 0.00 46.86 2.90
880 3937 5.433526 AGTTTTAGTCCAAACTGCTGTACA 58.566 37.500 0.00 0.00 43.88 2.90
881 3938 6.062095 AGTTTTAGTCCAAACTGCTGTACAT 58.938 36.000 0.00 0.00 43.88 2.29
883 3940 7.172703 AGTTTTAGTCCAAACTGCTGTACATAC 59.827 37.037 0.00 0.00 43.88 2.39
884 3941 4.617253 AGTCCAAACTGCTGTACATACA 57.383 40.909 0.00 0.00 33.32 2.29
886 3943 5.560724 AGTCCAAACTGCTGTACATACAAT 58.439 37.500 0.00 0.00 32.91 2.71
887 3944 5.412594 AGTCCAAACTGCTGTACATACAATG 59.587 40.000 0.00 0.00 32.91 2.82
889 3946 4.156556 CCAAACTGCTGTACATACAATGCT 59.843 41.667 0.00 0.00 35.50 3.79
890 3947 5.335897 CCAAACTGCTGTACATACAATGCTT 60.336 40.000 0.00 0.00 35.50 3.91
891 3948 4.952262 ACTGCTGTACATACAATGCTTG 57.048 40.909 0.00 0.00 35.50 4.01
892 3949 3.691118 ACTGCTGTACATACAATGCTTGG 59.309 43.478 0.00 0.00 35.50 3.61
893 3950 3.684908 TGCTGTACATACAATGCTTGGT 58.315 40.909 0.00 0.00 35.50 3.67
894 3951 4.078537 TGCTGTACATACAATGCTTGGTT 58.921 39.130 0.00 0.00 35.50 3.67
895 3952 5.249420 TGCTGTACATACAATGCTTGGTTA 58.751 37.500 0.00 0.00 35.50 2.85
896 3953 5.885352 TGCTGTACATACAATGCTTGGTTAT 59.115 36.000 0.00 0.00 35.50 1.89
897 3954 7.051000 TGCTGTACATACAATGCTTGGTTATA 58.949 34.615 0.00 0.00 35.50 0.98
898 3955 7.011950 TGCTGTACATACAATGCTTGGTTATAC 59.988 37.037 0.00 0.00 35.50 1.47
899 3956 7.226720 GCTGTACATACAATGCTTGGTTATACT 59.773 37.037 0.00 0.00 35.50 2.12
900 3957 9.758651 CTGTACATACAATGCTTGGTTATACTA 57.241 33.333 0.00 0.00 35.50 1.82
901 3958 9.537192 TGTACATACAATGCTTGGTTATACTAC 57.463 33.333 0.00 0.00 32.40 2.73
902 3959 7.709269 ACATACAATGCTTGGTTATACTACG 57.291 36.000 1.84 0.00 34.12 3.51
903 3960 7.494211 ACATACAATGCTTGGTTATACTACGA 58.506 34.615 0.00 0.00 34.12 3.43
904 3961 8.148351 ACATACAATGCTTGGTTATACTACGAT 58.852 33.333 0.00 0.00 34.12 3.73
905 3962 8.988934 CATACAATGCTTGGTTATACTACGATT 58.011 33.333 0.00 0.00 34.12 3.34
906 3963 7.859325 ACAATGCTTGGTTATACTACGATTT 57.141 32.000 0.00 0.00 34.12 2.17
907 3964 7.693952 ACAATGCTTGGTTATACTACGATTTG 58.306 34.615 0.00 0.00 34.12 2.32
908 3965 7.335924 ACAATGCTTGGTTATACTACGATTTGT 59.664 33.333 0.00 0.00 34.12 2.83
909 3966 6.656314 TGCTTGGTTATACTACGATTTGTG 57.344 37.500 0.00 0.00 0.00 3.33
910 3967 6.167685 TGCTTGGTTATACTACGATTTGTGT 58.832 36.000 0.00 0.00 0.00 3.72
911 3968 7.321908 TGCTTGGTTATACTACGATTTGTGTA 58.678 34.615 0.00 0.00 0.00 2.90
912 3969 7.818446 TGCTTGGTTATACTACGATTTGTGTAA 59.182 33.333 0.00 0.00 0.00 2.41
923 3980 8.692710 ACTACGATTTGTGTAAGATTCCTGATA 58.307 33.333 0.00 0.00 0.00 2.15
925 3982 7.556844 ACGATTTGTGTAAGATTCCTGATAGT 58.443 34.615 0.00 0.00 0.00 2.12
926 3983 7.707035 ACGATTTGTGTAAGATTCCTGATAGTC 59.293 37.037 0.00 0.00 0.00 2.59
932 4053 5.819379 TGTAAGATTCCTGATAGTCGTACGT 59.181 40.000 16.05 0.00 31.22 3.57
933 4054 6.986231 TGTAAGATTCCTGATAGTCGTACGTA 59.014 38.462 16.05 1.13 31.22 3.57
943 4064 0.041488 GTCGTACGTATAGCGCTGCT 60.041 55.000 22.90 10.07 46.11 4.24
944 4065 0.659427 TCGTACGTATAGCGCTGCTT 59.341 50.000 22.90 7.41 46.11 3.91
945 4066 0.770590 CGTACGTATAGCGCTGCTTG 59.229 55.000 22.90 10.14 46.11 4.01
946 4067 0.503117 GTACGTATAGCGCTGCTTGC 59.497 55.000 22.90 7.51 46.11 4.01
975 4096 7.756722 GCATGCATTTACTCTAATGAAAACTGT 59.243 33.333 14.21 0.00 37.65 3.55
1208 4351 2.357517 CTCGCCAACGCCAAGTCT 60.358 61.111 0.00 0.00 39.84 3.24
1225 4368 1.229336 CTCACTCCCACTCCCACCT 60.229 63.158 0.00 0.00 0.00 4.00
1226 4369 1.229209 TCACTCCCACTCCCACCTC 60.229 63.158 0.00 0.00 0.00 3.85
1227 4370 1.536418 CACTCCCACTCCCACCTCA 60.536 63.158 0.00 0.00 0.00 3.86
1253 4411 2.346541 CCTCAGCTCCGACTGCTCA 61.347 63.158 0.00 0.00 38.92 4.26
1280 4438 3.210528 GACGACCGCTCCTCCGAT 61.211 66.667 0.00 0.00 0.00 4.18
1304 4462 1.557269 GCAGCTCCCTCTCCTTCCAA 61.557 60.000 0.00 0.00 0.00 3.53
1336 4494 1.198094 ATCACCGATGACCACCACCA 61.198 55.000 0.00 0.00 37.79 4.17
1338 4496 2.046314 CCGATGACCACCACCACC 60.046 66.667 0.00 0.00 0.00 4.61
1339 4497 2.747022 CGATGACCACCACCACCA 59.253 61.111 0.00 0.00 0.00 4.17
1343 4501 1.863155 ATGACCACCACCACCATCCC 61.863 60.000 0.00 0.00 0.00 3.85
1363 4542 2.740714 CTGCTCCGGCTGTTTACGC 61.741 63.158 0.00 0.00 39.59 4.42
1505 4684 4.244802 CTCGAGTCGGAGCGCCTC 62.245 72.222 13.54 1.49 0.00 4.70
2022 5207 3.164026 TGCTTCTGCATGTAGGCTG 57.836 52.632 11.15 3.05 45.31 4.85
2023 5208 1.028330 TGCTTCTGCATGTAGGCTGC 61.028 55.000 11.15 12.46 45.31 5.25
2115 5310 5.046159 CCCTTGGATTATGGCGGTATTACTA 60.046 44.000 0.00 0.00 0.00 1.82
2152 5349 0.466372 GAGATGGTTTAGGCTGGGGC 60.466 60.000 0.00 0.00 37.82 5.80
2153 5350 1.214305 AGATGGTTTAGGCTGGGGCA 61.214 55.000 0.00 0.00 40.87 5.36
2154 5351 1.000359 ATGGTTTAGGCTGGGGCAC 60.000 57.895 0.00 0.00 40.87 5.01
2225 5484 3.495806 GGAGATGGAGATGGGCAAAGTAG 60.496 52.174 0.00 0.00 0.00 2.57
2279 5771 8.943909 AGTAGTATTAAGCAGTAATGTCCAAC 57.056 34.615 3.57 0.00 34.18 3.77
2358 5851 6.831353 TCTGTTTACCTCCAACTTTTCAATCA 59.169 34.615 0.00 0.00 0.00 2.57
2390 5908 3.632145 ACAAACTGTTCGAATTCCTGCTT 59.368 39.130 0.00 0.00 0.00 3.91
2391 5909 3.904136 AACTGTTCGAATTCCTGCTTG 57.096 42.857 0.00 0.00 0.00 4.01
2392 5910 1.537202 ACTGTTCGAATTCCTGCTTGC 59.463 47.619 0.00 0.00 0.00 4.01
2393 5911 1.808945 CTGTTCGAATTCCTGCTTGCT 59.191 47.619 0.00 0.00 0.00 3.91
2536 6064 6.127925 TGCATAAAAGCAGGTTAACATCTCTG 60.128 38.462 8.10 6.58 40.11 3.35
2548 6076 0.798776 CATCTCTGGGCGTCACAAAC 59.201 55.000 0.00 0.00 0.00 2.93
2565 6093 2.458892 ACCCATTGGTCTCAACGGA 58.541 52.632 1.20 0.00 43.06 4.69
2568 6096 2.093128 ACCCATTGGTCTCAACGGATAC 60.093 50.000 1.20 0.00 43.06 2.24
2569 6097 2.170607 CCCATTGGTCTCAACGGATACT 59.829 50.000 1.20 0.00 38.41 2.12
2570 6098 3.458189 CCATTGGTCTCAACGGATACTC 58.542 50.000 0.00 0.00 38.41 2.59
2571 6099 3.133003 CCATTGGTCTCAACGGATACTCT 59.867 47.826 0.00 0.00 38.41 3.24
2586 6130 4.426313 TCTCTCCCTCCGCTCGCA 62.426 66.667 0.00 0.00 0.00 5.10
2622 6166 9.507329 ACATCTAGCTCTTGTCTTAAATCAAAA 57.493 29.630 0.00 0.00 0.00 2.44
2623 6167 9.766277 CATCTAGCTCTTGTCTTAAATCAAAAC 57.234 33.333 0.00 0.00 0.00 2.43
2698 6243 5.801947 GCACAAAATTCGCATCACTAGATTT 59.198 36.000 0.00 0.00 30.20 2.17
2825 6370 7.956328 AGGTAGATGTACACTTATTCACAGA 57.044 36.000 0.00 0.00 0.00 3.41
2946 6494 2.954318 GACCGTCTATAACAGGTGCCTA 59.046 50.000 0.00 0.00 35.72 3.93
3016 6564 2.016318 CCAACGGCTTCAATCATGCTA 58.984 47.619 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.546122 AATGGCAACCGCTCTGGATA 59.454 50.000 0.00 0.00 42.00 2.59
1 2 1.033746 CAATGGCAACCGCTCTGGAT 61.034 55.000 0.00 0.00 42.00 3.41
3 4 2.879907 CAATGGCAACCGCTCTGG 59.120 61.111 0.00 0.00 46.41 3.86
4 5 2.180017 GCAATGGCAACCGCTCTG 59.820 61.111 0.00 0.00 40.72 3.35
5 6 3.064324 GGCAATGGCAACCGCTCT 61.064 61.111 0.58 0.00 43.71 4.09
6 7 3.346631 CTGGCAATGGCAACCGCTC 62.347 63.158 11.45 0.00 43.71 5.03
7 8 3.376078 CTGGCAATGGCAACCGCT 61.376 61.111 11.45 0.00 43.71 5.52
9 10 3.682885 TGCTGGCAATGGCAACCG 61.683 61.111 11.45 0.18 43.71 4.44
10 11 2.047939 GTGCTGGCAATGGCAACC 60.048 61.111 11.45 5.60 43.71 3.77
11 12 1.080298 GAGTGCTGGCAATGGCAAC 60.080 57.895 11.45 7.14 43.71 4.17
12 13 1.531128 TGAGTGCTGGCAATGGCAA 60.531 52.632 11.45 0.00 43.71 4.52
13 14 2.115695 TGAGTGCTGGCAATGGCA 59.884 55.556 9.67 9.67 43.71 4.92
14 15 0.677731 TAGTGAGTGCTGGCAATGGC 60.678 55.000 0.00 0.00 40.13 4.40
15 16 1.065926 TCTAGTGAGTGCTGGCAATGG 60.066 52.381 0.00 0.00 0.00 3.16
16 17 2.391616 TCTAGTGAGTGCTGGCAATG 57.608 50.000 0.00 0.00 0.00 2.82
17 18 3.641434 AATCTAGTGAGTGCTGGCAAT 57.359 42.857 0.00 0.00 0.00 3.56
18 19 3.423539 AAATCTAGTGAGTGCTGGCAA 57.576 42.857 0.00 0.00 0.00 4.52
19 20 4.760530 ATAAATCTAGTGAGTGCTGGCA 57.239 40.909 0.00 0.00 0.00 4.92
20 21 5.118990 TGAATAAATCTAGTGAGTGCTGGC 58.881 41.667 0.00 0.00 0.00 4.85
21 22 5.757320 CCTGAATAAATCTAGTGAGTGCTGG 59.243 44.000 0.00 0.00 0.00 4.85
22 23 6.577103 TCCTGAATAAATCTAGTGAGTGCTG 58.423 40.000 0.00 0.00 0.00 4.41
23 24 6.798427 TCCTGAATAAATCTAGTGAGTGCT 57.202 37.500 0.00 0.00 0.00 4.40
24 25 7.334421 TGTTTCCTGAATAAATCTAGTGAGTGC 59.666 37.037 0.00 0.00 0.00 4.40
25 26 8.777865 TGTTTCCTGAATAAATCTAGTGAGTG 57.222 34.615 0.00 0.00 0.00 3.51
26 27 9.965902 AATGTTTCCTGAATAAATCTAGTGAGT 57.034 29.630 0.00 0.00 0.00 3.41
32 33 9.098355 CGTGAGAATGTTTCCTGAATAAATCTA 57.902 33.333 0.00 0.00 0.00 1.98
33 34 7.414540 GCGTGAGAATGTTTCCTGAATAAATCT 60.415 37.037 0.00 0.00 0.00 2.40
34 35 6.688813 GCGTGAGAATGTTTCCTGAATAAATC 59.311 38.462 0.00 0.00 0.00 2.17
35 36 6.404734 GGCGTGAGAATGTTTCCTGAATAAAT 60.405 38.462 0.00 0.00 0.00 1.40
36 37 5.106317 GGCGTGAGAATGTTTCCTGAATAAA 60.106 40.000 0.00 0.00 0.00 1.40
37 38 4.394920 GGCGTGAGAATGTTTCCTGAATAA 59.605 41.667 0.00 0.00 0.00 1.40
38 39 3.938963 GGCGTGAGAATGTTTCCTGAATA 59.061 43.478 0.00 0.00 0.00 1.75
39 40 2.749621 GGCGTGAGAATGTTTCCTGAAT 59.250 45.455 0.00 0.00 0.00 2.57
40 41 2.151202 GGCGTGAGAATGTTTCCTGAA 58.849 47.619 0.00 0.00 0.00 3.02
41 42 1.610624 GGGCGTGAGAATGTTTCCTGA 60.611 52.381 0.00 0.00 0.00 3.86
42 43 0.804989 GGGCGTGAGAATGTTTCCTG 59.195 55.000 0.00 0.00 0.00 3.86
43 44 0.400213 TGGGCGTGAGAATGTTTCCT 59.600 50.000 0.00 0.00 0.00 3.36
52 53 2.425592 CCACAACTGGGCGTGAGA 59.574 61.111 0.00 0.00 35.02 3.27
88 89 1.677576 CAACTTTGTTGCTGCAGAGGA 59.322 47.619 20.43 0.00 0.00 3.71
93 94 3.118847 TGGATTTCAACTTTGTTGCTGCA 60.119 39.130 0.00 0.00 0.00 4.41
94 95 3.456280 TGGATTTCAACTTTGTTGCTGC 58.544 40.909 5.65 0.00 0.00 5.25
96 97 3.493176 GGCTGGATTTCAACTTTGTTGCT 60.493 43.478 5.65 0.00 0.00 3.91
108 109 3.091545 TCATCAAACAGGGCTGGATTTC 58.908 45.455 0.00 0.00 34.19 2.17
130 132 0.179015 TTGTCAAACGGGCTGGCTTA 60.179 50.000 0.00 0.00 0.00 3.09
136 138 1.470051 AAACACTTGTCAAACGGGCT 58.530 45.000 0.00 0.00 0.00 5.19
137 139 2.287393 AAAACACTTGTCAAACGGGC 57.713 45.000 0.00 0.00 0.00 6.13
162 164 3.828451 CCTCCCAACACAATGATTTCTGT 59.172 43.478 0.00 0.00 0.00 3.41
170 172 3.068560 CAAAATGCCTCCCAACACAATG 58.931 45.455 0.00 0.00 0.00 2.82
174 176 2.231235 CCTACAAAATGCCTCCCAACAC 59.769 50.000 0.00 0.00 0.00 3.32
176 178 1.824852 CCCTACAAAATGCCTCCCAAC 59.175 52.381 0.00 0.00 0.00 3.77
181 183 1.780503 ATGGCCCTACAAAATGCCTC 58.219 50.000 0.00 0.00 44.32 4.70
191 193 2.919228 ACGAGATTTCAATGGCCCTAC 58.081 47.619 0.00 0.00 0.00 3.18
194 196 1.947456 GGTACGAGATTTCAATGGCCC 59.053 52.381 0.00 0.00 0.00 5.80
210 212 2.046604 GCAACCACTCCCGGGTAC 60.047 66.667 22.86 0.00 37.77 3.34
216 218 2.649129 GGCATTGGCAACCACTCCC 61.649 63.158 0.00 0.00 43.71 4.30
230 232 5.106157 GGAATATAAAATGTAGCGCTGGCAT 60.106 40.000 22.90 20.64 43.41 4.40
235 237 3.122948 CGCGGAATATAAAATGTAGCGCT 59.877 43.478 17.26 17.26 38.69 5.92
238 240 5.840940 ACTCGCGGAATATAAAATGTAGC 57.159 39.130 6.13 0.00 0.00 3.58
247 249 1.493772 CGCCAAACTCGCGGAATATA 58.506 50.000 6.13 0.00 45.80 0.86
248 250 2.307363 CGCCAAACTCGCGGAATAT 58.693 52.632 6.13 0.00 45.80 1.28
249 251 3.788817 CGCCAAACTCGCGGAATA 58.211 55.556 6.13 0.00 45.80 1.75
256 258 0.249073 ATCGGATCTCGCCAAACTCG 60.249 55.000 0.00 0.00 39.05 4.18
257 259 1.941325 AATCGGATCTCGCCAAACTC 58.059 50.000 0.00 0.00 39.05 3.01
260 262 1.406180 TCGTAATCGGATCTCGCCAAA 59.594 47.619 9.00 0.00 39.05 3.28
275 277 5.350365 CACTTCCAGGATTCGAATTTCGTAA 59.650 40.000 17.61 11.26 41.35 3.18
277 279 3.684788 CACTTCCAGGATTCGAATTTCGT 59.315 43.478 17.61 0.00 41.35 3.85
291 293 1.741993 CGCGTCAAAAACACTTCCAG 58.258 50.000 0.00 0.00 0.00 3.86
293 295 0.248296 TGCGCGTCAAAAACACTTCC 60.248 50.000 8.43 0.00 0.00 3.46
294 296 1.112459 CTGCGCGTCAAAAACACTTC 58.888 50.000 8.43 0.00 0.00 3.01
295 297 0.450184 ACTGCGCGTCAAAAACACTT 59.550 45.000 8.43 0.00 0.00 3.16
297 299 0.837605 GAACTGCGCGTCAAAAACAC 59.162 50.000 8.43 0.00 0.00 3.32
298 300 0.730265 AGAACTGCGCGTCAAAAACA 59.270 45.000 8.43 0.00 0.00 2.83
299 301 1.112459 CAGAACTGCGCGTCAAAAAC 58.888 50.000 8.43 0.00 0.00 2.43
300 302 0.028770 CCAGAACTGCGCGTCAAAAA 59.971 50.000 8.43 0.00 0.00 1.94
305 307 3.782244 CAGCCAGAACTGCGCGTC 61.782 66.667 8.43 0.00 33.82 5.19
330 332 2.265904 GCCTTCCAACGGAACACCC 61.266 63.158 0.00 0.00 36.71 4.61
331 333 1.228154 AGCCTTCCAACGGAACACC 60.228 57.895 0.00 0.00 36.71 4.16
332 334 1.566018 CGAGCCTTCCAACGGAACAC 61.566 60.000 0.00 0.00 36.71 3.32
342 348 3.119096 GTTGCGGACGAGCCTTCC 61.119 66.667 0.00 0.00 36.02 3.46
343 349 3.119096 GGTTGCGGACGAGCCTTC 61.119 66.667 0.00 0.00 36.02 3.46
367 373 2.353208 GGCGCCATTCATTTTACACCAA 60.353 45.455 24.80 0.00 0.00 3.67
374 380 5.606348 TTATTAAGGGCGCCATTCATTTT 57.394 34.783 32.02 13.66 0.00 1.82
379 385 2.288213 GGCTTTATTAAGGGCGCCATTC 60.288 50.000 32.02 13.87 37.48 2.67
415 421 5.766150 TGAGTAGAAAACCAACAACCATG 57.234 39.130 0.00 0.00 0.00 3.66
423 429 4.213270 CACTTCGCATGAGTAGAAAACCAA 59.787 41.667 9.95 0.00 0.00 3.67
425 431 3.424962 GCACTTCGCATGAGTAGAAAACC 60.425 47.826 9.95 0.00 41.79 3.27
426 432 3.433615 AGCACTTCGCATGAGTAGAAAAC 59.566 43.478 9.95 0.00 46.13 2.43
437 472 3.484524 CTTGCAAAGCACTTCGCAT 57.515 47.368 0.00 0.00 46.13 4.73
462 497 1.375523 CGGGGGCAGTGAGTGTAAC 60.376 63.158 0.00 0.00 0.00 2.50
468 503 3.636231 TTGACCGGGGGCAGTGAG 61.636 66.667 6.32 0.00 0.00 3.51
505 540 4.899239 CGGGCGGTCCAGATGAGC 62.899 72.222 0.00 0.00 38.14 4.26
523 558 1.021390 GCCGTCCACTTGTCATCCAG 61.021 60.000 0.00 0.00 0.00 3.86
526 561 1.021390 CCAGCCGTCCACTTGTCATC 61.021 60.000 0.00 0.00 0.00 2.92
528 563 2.425592 CCAGCCGTCCACTTGTCA 59.574 61.111 0.00 0.00 0.00 3.58
529 564 2.185310 ATCCCAGCCGTCCACTTGTC 62.185 60.000 0.00 0.00 0.00 3.18
530 565 2.224159 ATCCCAGCCGTCCACTTGT 61.224 57.895 0.00 0.00 0.00 3.16
531 566 1.746615 CATCCCAGCCGTCCACTTG 60.747 63.158 0.00 0.00 0.00 3.16
532 567 1.488705 TTCATCCCAGCCGTCCACTT 61.489 55.000 0.00 0.00 0.00 3.16
533 568 1.903877 CTTCATCCCAGCCGTCCACT 61.904 60.000 0.00 0.00 0.00 4.00
576 611 1.675641 CTTCCTTCGGCCACAAGGG 60.676 63.158 24.29 10.40 40.93 3.95
577 612 2.335712 GCTTCCTTCGGCCACAAGG 61.336 63.158 20.48 20.48 41.81 3.61
578 613 0.890996 AAGCTTCCTTCGGCCACAAG 60.891 55.000 2.24 3.72 0.00 3.16
582 617 2.268076 GCAAAGCTTCCTTCGGCCA 61.268 57.895 2.24 0.00 0.00 5.36
598 633 0.107897 ACACTTGTGTCGTCCAAGCA 60.108 50.000 0.00 0.00 42.41 3.91
614 649 5.417266 TGAGCTCTCTCCTGCATATATACAC 59.583 44.000 16.19 0.00 38.58 2.90
615 650 5.574188 TGAGCTCTCTCCTGCATATATACA 58.426 41.667 16.19 0.00 38.58 2.29
616 651 5.450412 GCTGAGCTCTCTCCTGCATATATAC 60.450 48.000 16.19 0.00 38.58 1.47
628 676 1.032014 AATCCTCGCTGAGCTCTCTC 58.968 55.000 16.19 2.91 39.78 3.20
629 677 2.356665 TAATCCTCGCTGAGCTCTCT 57.643 50.000 16.19 0.00 0.00 3.10
630 678 3.316283 CATTAATCCTCGCTGAGCTCTC 58.684 50.000 16.19 5.89 0.00 3.20
631 679 2.547642 GCATTAATCCTCGCTGAGCTCT 60.548 50.000 16.19 0.00 0.00 4.09
632 680 1.797635 GCATTAATCCTCGCTGAGCTC 59.202 52.381 6.82 6.82 0.00 4.09
641 689 0.951040 CCTCGGCGGCATTAATCCTC 60.951 60.000 10.53 0.00 0.00 3.71
642 690 1.071471 CCTCGGCGGCATTAATCCT 59.929 57.895 10.53 0.00 0.00 3.24
643 691 0.321653 ATCCTCGGCGGCATTAATCC 60.322 55.000 10.53 0.00 0.00 3.01
647 3301 0.033504 GAGAATCCTCGGCGGCATTA 59.966 55.000 10.53 0.00 0.00 1.90
667 3321 2.242708 ACTACTAGCAGCTAGGTGAGGT 59.757 50.000 29.36 19.41 38.30 3.85
692 3349 1.372087 GCTGCCTGCCACAGTGATAC 61.372 60.000 0.62 0.00 37.47 2.24
708 3365 2.281276 TGTGGCACTGCAGAGCTG 60.281 61.111 30.75 16.15 0.00 4.24
724 3781 1.260206 CTACGACGTTGCTAGCAGTG 58.740 55.000 18.45 16.24 0.00 3.66
730 3787 2.158559 TGTTACCCTACGACGTTGCTA 58.841 47.619 5.50 0.00 0.00 3.49
739 3796 3.057033 CCGGGATAGATTGTTACCCTACG 60.057 52.174 0.00 0.00 38.51 3.51
773 3830 5.307204 ACGTAGTACTTGAGACTTGAGAGT 58.693 41.667 0.00 0.00 41.94 3.24
783 3840 8.027440 GGACTACCATATACGTAGTACTTGAG 57.973 42.308 13.54 0.00 44.98 3.02
791 3848 9.474920 GCTATAGTAGGACTACCATATACGTAG 57.525 40.741 0.08 7.11 39.32 3.51
792 3849 9.206690 AGCTATAGTAGGACTACCATATACGTA 57.793 37.037 0.00 0.00 38.94 3.57
793 3850 7.986320 CAGCTATAGTAGGACTACCATATACGT 59.014 40.741 5.90 0.00 38.94 3.57
794 3851 7.986320 ACAGCTATAGTAGGACTACCATATACG 59.014 40.741 5.90 0.00 38.94 3.06
795 3852 9.683870 AACAGCTATAGTAGGACTACCATATAC 57.316 37.037 5.90 0.00 38.94 1.47
797 3854 9.683870 GTAACAGCTATAGTAGGACTACCATAT 57.316 37.037 5.90 2.14 38.94 1.78
798 3855 7.821359 CGTAACAGCTATAGTAGGACTACCATA 59.179 40.741 5.90 2.28 38.94 2.74
799 3856 6.654161 CGTAACAGCTATAGTAGGACTACCAT 59.346 42.308 5.90 1.20 38.94 3.55
800 3857 5.994054 CGTAACAGCTATAGTAGGACTACCA 59.006 44.000 5.90 0.00 38.94 3.25
801 3858 6.226787 TCGTAACAGCTATAGTAGGACTACC 58.773 44.000 5.90 0.00 36.75 3.18
802 3859 7.601886 TGATCGTAACAGCTATAGTAGGACTAC 59.398 40.741 0.84 1.25 32.84 2.73
803 3860 7.674120 TGATCGTAACAGCTATAGTAGGACTA 58.326 38.462 0.84 0.00 34.82 2.59
804 3861 6.531923 TGATCGTAACAGCTATAGTAGGACT 58.468 40.000 0.84 0.00 0.00 3.85
808 3865 6.885247 TCGTTGATCGTAACAGCTATAGTAG 58.115 40.000 0.84 0.00 40.80 2.57
817 3874 3.985279 TCAGGTTTCGTTGATCGTAACAG 59.015 43.478 7.51 1.09 46.40 3.16
823 3880 9.370126 GATTAATTAATCAGGTTTCGTTGATCG 57.630 33.333 26.36 0.00 41.25 3.69
855 3912 5.500645 ACAGCAGTTTGGACTAAAACTTC 57.499 39.130 0.00 0.00 45.84 3.01
858 3915 5.744666 TGTACAGCAGTTTGGACTAAAAC 57.255 39.130 0.00 0.00 39.80 2.43
867 3924 5.300969 AGCATTGTATGTACAGCAGTTTG 57.699 39.130 0.33 4.21 37.52 2.93
871 3928 3.691118 ACCAAGCATTGTATGTACAGCAG 59.309 43.478 0.33 0.00 46.99 4.24
876 3933 8.697067 CGTAGTATAACCAAGCATTGTATGTAC 58.303 37.037 0.00 0.00 46.99 2.90
877 3934 8.631797 TCGTAGTATAACCAAGCATTGTATGTA 58.368 33.333 0.00 0.00 46.99 2.29
878 3935 7.494211 TCGTAGTATAACCAAGCATTGTATGT 58.506 34.615 0.00 0.00 46.99 2.29
879 3936 7.940178 TCGTAGTATAACCAAGCATTGTATG 57.060 36.000 0.00 0.00 46.99 2.39
880 3937 9.555727 AAATCGTAGTATAACCAAGCATTGTAT 57.444 29.630 0.00 0.00 46.99 2.29
881 3938 8.822855 CAAATCGTAGTATAACCAAGCATTGTA 58.177 33.333 0.00 0.00 46.99 2.41
884 3941 7.335924 ACACAAATCGTAGTATAACCAAGCATT 59.664 33.333 0.00 0.00 0.00 3.56
886 3943 6.167685 ACACAAATCGTAGTATAACCAAGCA 58.832 36.000 0.00 0.00 0.00 3.91
887 3944 6.657836 ACACAAATCGTAGTATAACCAAGC 57.342 37.500 0.00 0.00 0.00 4.01
894 3951 9.961265 CAGGAATCTTACACAAATCGTAGTATA 57.039 33.333 0.00 0.00 0.00 1.47
895 3952 8.692710 TCAGGAATCTTACACAAATCGTAGTAT 58.307 33.333 0.00 0.00 0.00 2.12
896 3953 8.058667 TCAGGAATCTTACACAAATCGTAGTA 57.941 34.615 0.00 0.00 0.00 1.82
897 3954 6.931838 TCAGGAATCTTACACAAATCGTAGT 58.068 36.000 0.00 0.00 0.00 2.73
898 3955 9.186323 CTATCAGGAATCTTACACAAATCGTAG 57.814 37.037 0.00 0.00 0.00 3.51
899 3956 8.692710 ACTATCAGGAATCTTACACAAATCGTA 58.307 33.333 0.00 0.00 0.00 3.43
900 3957 7.556844 ACTATCAGGAATCTTACACAAATCGT 58.443 34.615 0.00 0.00 0.00 3.73
901 3958 7.096436 CGACTATCAGGAATCTTACACAAATCG 60.096 40.741 0.00 0.00 0.00 3.34
902 3959 7.707035 ACGACTATCAGGAATCTTACACAAATC 59.293 37.037 0.00 0.00 0.00 2.17
903 3960 7.556844 ACGACTATCAGGAATCTTACACAAAT 58.443 34.615 0.00 0.00 0.00 2.32
904 3961 6.931838 ACGACTATCAGGAATCTTACACAAA 58.068 36.000 0.00 0.00 0.00 2.83
905 3962 6.525578 ACGACTATCAGGAATCTTACACAA 57.474 37.500 0.00 0.00 0.00 3.33
906 3963 6.238293 CGTACGACTATCAGGAATCTTACACA 60.238 42.308 10.44 0.00 0.00 3.72
907 3964 6.134730 CGTACGACTATCAGGAATCTTACAC 58.865 44.000 10.44 0.00 0.00 2.90
908 3965 5.819379 ACGTACGACTATCAGGAATCTTACA 59.181 40.000 24.41 0.00 0.00 2.41
909 3966 6.297694 ACGTACGACTATCAGGAATCTTAC 57.702 41.667 24.41 0.00 0.00 2.34
910 3967 9.363763 CTATACGTACGACTATCAGGAATCTTA 57.636 37.037 24.41 0.00 0.00 2.10
911 3968 7.148440 GCTATACGTACGACTATCAGGAATCTT 60.148 40.741 24.41 0.00 0.00 2.40
912 3969 6.313411 GCTATACGTACGACTATCAGGAATCT 59.687 42.308 24.41 0.00 0.00 2.40
923 3980 0.041488 GCAGCGCTATACGTACGACT 60.041 55.000 24.41 10.84 46.11 4.18
925 3982 0.659427 AAGCAGCGCTATACGTACGA 59.341 50.000 24.41 6.04 46.11 3.43
926 3983 0.770590 CAAGCAGCGCTATACGTACG 59.229 55.000 10.99 15.01 46.11 3.67
946 4067 8.537223 GTTTTCATTAGAGTAAATGCATGCATG 58.463 33.333 32.79 22.70 36.89 4.06
975 4096 3.327626 ACACTTGTCACACACAAACGTA 58.672 40.909 0.00 0.00 44.71 3.57
1181 4312 2.203788 TTGGCGAGGAGGGACTGT 60.204 61.111 0.00 0.00 41.55 3.55
1208 4351 1.229209 GAGGTGGGAGTGGGAGTGA 60.229 63.158 0.00 0.00 0.00 3.41
1225 4368 1.194781 GGAGCTGAGGTGGAGGTTGA 61.195 60.000 0.00 0.00 0.00 3.18
1226 4369 1.298014 GGAGCTGAGGTGGAGGTTG 59.702 63.158 0.00 0.00 0.00 3.77
1227 4370 2.286523 CGGAGCTGAGGTGGAGGTT 61.287 63.158 0.00 0.00 0.00 3.50
1253 4411 3.857854 CGGTCGTCGACGTCGGAT 61.858 66.667 35.05 0.00 42.43 4.18
1304 4462 2.298661 GGTGATTCCGGAGTGGGGT 61.299 63.158 3.25 0.00 38.76 4.95
1343 4501 2.434185 TAAACAGCCGGAGCAGCG 60.434 61.111 5.05 0.00 43.56 5.18
1355 4516 1.666553 CACCAGCTCGGCGTAAACA 60.667 57.895 6.85 0.00 39.03 2.83
1359 4538 4.063967 CACCACCAGCTCGGCGTA 62.064 66.667 6.85 0.00 39.03 4.42
1505 4684 4.069232 TTCTCGCCCAGCAGGACG 62.069 66.667 0.00 0.00 38.24 4.79
2013 5198 4.864334 GCCGCCTGCAGCCTACAT 62.864 66.667 8.66 0.00 40.77 2.29
2053 5240 2.930950 CACCAAAAACAGAGACCCTCA 58.069 47.619 0.00 0.00 32.06 3.86
2115 5310 1.683917 CTCTTCGTCGATCATCCCCTT 59.316 52.381 0.00 0.00 0.00 3.95
2152 5349 1.575244 CAGTGTCAGTGTCAGTGGTG 58.425 55.000 15.07 0.00 33.96 4.17
2153 5350 0.465705 CCAGTGTCAGTGTCAGTGGT 59.534 55.000 26.87 0.00 45.83 4.16
2154 5351 3.295734 CCAGTGTCAGTGTCAGTGG 57.704 57.895 23.90 23.90 45.76 4.00
2155 5352 0.179076 TGCCAGTGTCAGTGTCAGTG 60.179 55.000 15.71 15.71 36.39 3.66
2156 5353 0.179073 GTGCCAGTGTCAGTGTCAGT 60.179 55.000 6.91 0.00 0.00 3.41
2157 5354 0.105593 AGTGCCAGTGTCAGTGTCAG 59.894 55.000 6.91 0.00 0.00 3.51
2166 5421 0.987294 AGCTCCATTAGTGCCAGTGT 59.013 50.000 0.00 0.00 35.51 3.55
2279 5771 3.854286 AAGTAACAACTTTGCGTCTCG 57.146 42.857 0.00 0.00 0.00 4.04
2305 5797 4.914540 ACTCATGTGCGAGATATATAGCG 58.085 43.478 0.00 3.12 36.47 4.26
2309 5801 5.221521 ACACCAACTCATGTGCGAGATATAT 60.222 40.000 0.00 0.00 36.47 0.86
2358 5851 6.730960 TTCGAACAGTTTGTACTCAAAACT 57.269 33.333 0.00 4.44 43.78 2.66
2391 5909 3.957468 GCAATTTAGTGCTGTGGATAGC 58.043 45.455 0.00 0.00 41.51 2.97
2536 6064 1.288752 CAATGGGTTTGTGACGCCC 59.711 57.895 3.23 3.23 40.28 6.13
2563 6091 0.111639 AGCGGAGGGAGAGAGTATCC 59.888 60.000 0.00 0.00 33.66 2.59
2565 6093 0.250553 CGAGCGGAGGGAGAGAGTAT 60.251 60.000 0.00 0.00 0.00 2.12
2568 6096 3.591835 GCGAGCGGAGGGAGAGAG 61.592 72.222 0.00 0.00 0.00 3.20
2569 6097 4.426313 TGCGAGCGGAGGGAGAGA 62.426 66.667 0.00 0.00 0.00 3.10
2570 6098 3.898509 CTGCGAGCGGAGGGAGAG 61.899 72.222 3.33 0.00 0.00 3.20
2571 6099 2.339275 TATCTGCGAGCGGAGGGAGA 62.339 60.000 12.42 0.00 34.49 3.71
2586 6130 9.142014 AGACAAGAGCTAGATGTACATTTATCT 57.858 33.333 10.30 9.51 37.42 1.98
2678 6223 8.702438 CAAAACAAATCTAGTGATGCGAATTTT 58.298 29.630 0.00 0.00 32.44 1.82
2721 6266 7.654568 AGCATACATGACATCAAATTGGTATG 58.345 34.615 0.00 12.26 0.00 2.39


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

AutoCloner maintained by Alex Coulton.