Multiple sequence alignment - TraesCS4D01G263100

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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 TraesCS4D01G263100 chr4D 100.000 5717 0 0 1 5717 434262772 434268488 0.000000e+00 10558.0
1 TraesCS4D01G263100 chr4B 94.431 3412 102 27 304 3680 533486587 533489945 0.000000e+00 5168.0
2 TraesCS4D01G263100 chr4B 92.862 1415 62 20 3682 5080 533490002 533491393 0.000000e+00 2017.0
3 TraesCS4D01G263100 chr4B 92.683 205 8 5 5517 5717 533491961 533492162 7.250000e-74 289.0
4 TraesCS4D01G263100 chr4B 86.935 199 25 1 4059 4257 18251851 18251654 7.460000e-54 222.0
5 TraesCS4D01G263100 chr4B 96.471 85 3 0 5160 5244 533491449 533491533 2.150000e-29 141.0
6 TraesCS4D01G263100 chr4A 90.412 1867 98 29 75 1904 35608137 35609959 0.000000e+00 2381.0
7 TraesCS4D01G263100 chr4A 93.805 1356 50 12 3682 5028 35616956 35618286 0.000000e+00 2008.0
8 TraesCS4D01G263100 chr4A 94.668 1069 27 7 2625 3682 35615851 35616900 0.000000e+00 1631.0
9 TraesCS4D01G263100 chr4A 93.369 754 23 2 1899 2625 35615016 35615769 0.000000e+00 1090.0
10 TraesCS4D01G263100 chr4A 86.296 467 32 17 5276 5717 35618676 35619135 4.010000e-131 479.0
11 TraesCS4D01G263100 chr5D 88.608 316 27 8 4059 4369 324753936 324753625 5.410000e-100 375.0
12 TraesCS4D01G263100 chr7B 91.457 199 16 1 4059 4257 506602711 506602908 7.300000e-69 272.0
13 TraesCS4D01G263100 chr5B 88.571 70 8 0 4160 4229 216614507 216614576 1.020000e-12 86.1


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 TraesCS4D01G263100 chr4D 434262772 434268488 5716 False 10558.00 10558 100.00000 1 5717 1 chr4D.!!$F1 5716
1 TraesCS4D01G263100 chr4B 533486587 533492162 5575 False 1903.75 5168 94.11175 304 5717 4 chr4B.!!$F1 5413
2 TraesCS4D01G263100 chr4A 35608137 35609959 1822 False 2381.00 2381 90.41200 75 1904 1 chr4A.!!$F1 1829
3 TraesCS4D01G263100 chr4A 35615016 35619135 4119 False 1302.00 2008 92.03450 1899 5717 4 chr4A.!!$F2 3818

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
182 183 0.108472 CAGCAGTTGCATCTCGGAGA 60.108 55.000 10.62 10.62 45.16 3.71 F
461 467 0.704664 GTCTCCCAATCCCACCCTTT 59.295 55.000 0.00 0.00 0.00 3.11 F
1166 1219 0.108186 CTTAGGTCGCTGGATGCACA 60.108 55.000 0.00 0.00 43.06 4.57 F
1316 1370 1.202582 ACGATGTCCTCTTCGTCCTTG 59.797 52.381 0.00 0.00 46.33 3.61 F
2950 3121 1.339631 CGGTGTTTCCATTCCCTAGCA 60.340 52.381 0.00 0.00 35.57 3.49 F
3230 3401 0.524862 CAGAAACTGACATGGCCAGC 59.475 55.000 13.05 3.55 35.14 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1093 1.336795 GGCACAGGGAAAATGGAAACG 60.337 52.381 0.00 0.0 0.0 3.60 R
1807 1863 2.254546 ATGGCAAAGACACGACTCAA 57.745 45.000 0.00 0.0 0.0 3.02 R
2836 3007 2.715749 TGAGCCATTCATACCAGGTG 57.284 50.000 0.76 0.0 0.0 4.00 R
3230 3401 2.794910 CGTACCTATGGATTTCAGTGCG 59.205 50.000 0.00 0.0 0.0 5.34 R
4632 4894 0.370273 CATCAAGACGCGTTAGTGCC 59.630 55.000 15.53 0.0 0.0 5.01 R
5100 5374 0.100503 AAAACGTGTCAGCAGCCAAC 59.899 50.000 0.00 0.0 0.0 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
19 20 1.790755 TGTTCTACGTGTGATGCACC 58.209 50.000 0.00 0.00 44.97 5.01
20 21 1.076332 GTTCTACGTGTGATGCACCC 58.924 55.000 0.00 0.00 44.97 4.61
21 22 0.973632 TTCTACGTGTGATGCACCCT 59.026 50.000 0.00 0.00 44.97 4.34
22 23 0.246360 TCTACGTGTGATGCACCCTG 59.754 55.000 0.00 0.00 44.97 4.45
23 24 0.740868 CTACGTGTGATGCACCCTGG 60.741 60.000 0.00 0.00 44.97 4.45
24 25 1.188871 TACGTGTGATGCACCCTGGA 61.189 55.000 0.00 0.00 44.97 3.86
25 26 1.078214 CGTGTGATGCACCCTGGAT 60.078 57.895 0.00 0.00 44.97 3.41
26 27 1.091771 CGTGTGATGCACCCTGGATC 61.092 60.000 0.00 0.00 44.22 3.36
27 28 0.254178 GTGTGATGCACCCTGGATCT 59.746 55.000 0.00 0.00 44.27 2.75
28 29 0.994247 TGTGATGCACCCTGGATCTT 59.006 50.000 0.00 0.00 44.27 2.40
29 30 1.065199 TGTGATGCACCCTGGATCTTC 60.065 52.381 0.00 0.77 44.27 2.87
30 31 1.065199 GTGATGCACCCTGGATCTTCA 60.065 52.381 0.00 0.00 44.27 3.02
31 32 1.848388 TGATGCACCCTGGATCTTCAT 59.152 47.619 0.00 0.00 44.27 2.57
32 33 3.047857 TGATGCACCCTGGATCTTCATA 58.952 45.455 0.00 0.00 44.27 2.15
33 34 3.654321 TGATGCACCCTGGATCTTCATAT 59.346 43.478 0.00 0.00 44.27 1.78
34 35 4.845796 TGATGCACCCTGGATCTTCATATA 59.154 41.667 0.00 0.00 44.27 0.86
35 36 5.310331 TGATGCACCCTGGATCTTCATATAA 59.690 40.000 0.00 0.00 44.27 0.98
36 37 5.645056 TGCACCCTGGATCTTCATATAAA 57.355 39.130 0.00 0.00 0.00 1.40
37 38 6.204852 TGCACCCTGGATCTTCATATAAAT 57.795 37.500 0.00 0.00 0.00 1.40
38 39 6.005823 TGCACCCTGGATCTTCATATAAATG 58.994 40.000 0.00 0.00 0.00 2.32
39 40 6.183361 TGCACCCTGGATCTTCATATAAATGA 60.183 38.462 0.00 0.00 40.43 2.57
40 41 6.150140 GCACCCTGGATCTTCATATAAATGAC 59.850 42.308 0.00 0.00 41.87 3.06
41 42 7.226441 CACCCTGGATCTTCATATAAATGACA 58.774 38.462 0.00 0.00 41.87 3.58
42 43 7.173907 CACCCTGGATCTTCATATAAATGACAC 59.826 40.741 0.00 0.00 41.87 3.67
43 44 6.369890 CCCTGGATCTTCATATAAATGACACG 59.630 42.308 0.00 0.00 41.87 4.49
44 45 6.931281 CCTGGATCTTCATATAAATGACACGT 59.069 38.462 0.00 0.00 41.87 4.49
45 46 7.095481 CCTGGATCTTCATATAAATGACACGTG 60.095 40.741 15.48 15.48 41.87 4.49
46 47 6.705825 TGGATCTTCATATAAATGACACGTGG 59.294 38.462 21.57 1.66 41.87 4.94
47 48 6.929049 GGATCTTCATATAAATGACACGTGGA 59.071 38.462 21.57 6.22 41.87 4.02
48 49 7.441157 GGATCTTCATATAAATGACACGTGGAA 59.559 37.037 21.57 7.77 41.87 3.53
49 50 8.908786 ATCTTCATATAAATGACACGTGGAAT 57.091 30.769 21.57 9.98 41.87 3.01
50 51 8.731275 TCTTCATATAAATGACACGTGGAATT 57.269 30.769 21.57 15.52 41.87 2.17
51 52 8.826710 TCTTCATATAAATGACACGTGGAATTC 58.173 33.333 21.57 8.76 41.87 2.17
52 53 8.731275 TTCATATAAATGACACGTGGAATTCT 57.269 30.769 21.57 11.69 41.87 2.40
53 54 9.825109 TTCATATAAATGACACGTGGAATTCTA 57.175 29.630 21.57 13.21 41.87 2.10
54 55 9.825109 TCATATAAATGACACGTGGAATTCTAA 57.175 29.630 21.57 8.57 37.20 2.10
78 79 2.818751 AAAGTGGGTTGAGTGGTTCA 57.181 45.000 0.00 0.00 0.00 3.18
79 80 3.312736 AAAGTGGGTTGAGTGGTTCAT 57.687 42.857 0.00 0.00 35.27 2.57
80 81 2.568623 AGTGGGTTGAGTGGTTCATC 57.431 50.000 0.00 0.00 35.27 2.92
86 87 2.814336 GGTTGAGTGGTTCATCTGGTTC 59.186 50.000 0.00 0.00 35.27 3.62
89 90 2.705658 TGAGTGGTTCATCTGGTTCTGT 59.294 45.455 0.00 0.00 0.00 3.41
100 101 0.402504 TGGTTCTGTATTTGGGCCGT 59.597 50.000 0.00 0.00 0.00 5.68
109 110 1.253100 ATTTGGGCCGTAAGTGGTTG 58.747 50.000 0.00 0.00 0.00 3.77
125 126 1.135333 GGTTGCAAAGTTCCAAACCGA 59.865 47.619 0.00 0.00 0.00 4.69
126 127 2.223947 GGTTGCAAAGTTCCAAACCGAT 60.224 45.455 0.00 0.00 0.00 4.18
133 134 0.322546 GTTCCAAACCGATCAGGCCT 60.323 55.000 0.00 0.00 46.52 5.19
139 140 3.016736 CAAACCGATCAGGCCTATTTGT 58.983 45.455 3.98 0.00 46.52 2.83
140 141 4.196193 CAAACCGATCAGGCCTATTTGTA 58.804 43.478 3.98 0.00 46.52 2.41
169 170 4.275508 CCCAGCACCACCAGCAGT 62.276 66.667 0.00 0.00 0.00 4.40
177 178 0.607489 ACCACCAGCAGTTGCATCTC 60.607 55.000 6.90 0.00 45.16 2.75
180 181 1.078918 CCAGCAGTTGCATCTCGGA 60.079 57.895 6.90 0.00 45.16 4.55
181 182 1.088340 CCAGCAGTTGCATCTCGGAG 61.088 60.000 6.90 0.00 45.16 4.63
182 183 0.108472 CAGCAGTTGCATCTCGGAGA 60.108 55.000 10.62 10.62 45.16 3.71
184 185 0.723981 GCAGTTGCATCTCGGAGAAC 59.276 55.000 12.40 8.04 41.59 3.01
188 189 0.976641 TTGCATCTCGGAGAACAGGT 59.023 50.000 12.40 0.00 34.09 4.00
192 193 2.416893 GCATCTCGGAGAACAGGTTTTC 59.583 50.000 12.40 0.00 34.09 2.29
194 195 3.107642 TCTCGGAGAACAGGTTTTCAC 57.892 47.619 4.96 0.00 34.09 3.18
202 203 2.203437 AGGTTTTCACGGCCCACC 60.203 61.111 0.00 0.00 0.00 4.61
266 267 2.048503 CCCTTCGAGTTTCGCCGT 60.049 61.111 0.00 0.00 40.21 5.68
335 340 4.100084 CCGCAGCCCTGTCCATCA 62.100 66.667 0.00 0.00 0.00 3.07
461 467 0.704664 GTCTCCCAATCCCACCCTTT 59.295 55.000 0.00 0.00 0.00 3.11
481 487 0.749649 CATCTCTCCTCCCCGTTGAG 59.250 60.000 0.00 0.00 0.00 3.02
514 529 2.972505 CGTGTGGGCGTGCTTCTT 60.973 61.111 0.00 0.00 0.00 2.52
748 773 1.721664 CGGCATCAATCAGTGGGCTG 61.722 60.000 0.00 0.00 43.87 4.85
897 927 7.761249 GGCAAATCTTATAGCTTTTGTGTGATT 59.239 33.333 7.84 0.00 32.88 2.57
953 983 4.400529 TCTCCAATTTGATAGCGTGCTA 57.599 40.909 3.73 3.73 0.00 3.49
1044 1091 1.605738 CCTTGCTTGCCCTCTGCTT 60.606 57.895 0.00 0.00 42.00 3.91
1046 1093 1.593296 CTTGCTTGCCCTCTGCTTCC 61.593 60.000 0.00 0.00 42.00 3.46
1057 1104 2.558359 CCTCTGCTTCCGTTTCCATTTT 59.442 45.455 0.00 0.00 0.00 1.82
1078 1125 2.170166 CCCTGTGCCATTTTAGCTTCA 58.830 47.619 0.00 0.00 0.00 3.02
1084 1131 2.295909 TGCCATTTTAGCTTCAAACGCT 59.704 40.909 0.00 0.00 41.35 5.07
1101 1152 3.305720 ACGCTTATTACCTGATCCCTCA 58.694 45.455 0.00 0.00 0.00 3.86
1159 1212 1.464997 GTTCTTTGCTTAGGTCGCTGG 59.535 52.381 0.00 0.00 0.00 4.85
1166 1219 0.108186 CTTAGGTCGCTGGATGCACA 60.108 55.000 0.00 0.00 43.06 4.57
1186 1239 4.934602 CACAATGTCCTCTTCTTCCTTCTC 59.065 45.833 0.00 0.00 0.00 2.87
1203 1256 4.262249 CCTTCTCTCGACTTCCAGAAACTT 60.262 45.833 0.00 0.00 0.00 2.66
1316 1370 1.202582 ACGATGTCCTCTTCGTCCTTG 59.797 52.381 0.00 0.00 46.33 3.61
1445 1499 6.266103 TGAATTTCATTCTTCCTCTTGCAACT 59.734 34.615 0.00 0.00 39.96 3.16
1556 1611 7.733501 AGTGGTGGGTAGCTATAATAATAGTGT 59.266 37.037 0.00 0.00 37.90 3.55
1637 1692 4.051922 AGCGAAAGGAAGATTACGCATAG 58.948 43.478 0.00 0.00 46.65 2.23
1676 1732 7.382898 TCTTTGCAGTAGTTTTCTTTGGTTTT 58.617 30.769 0.00 0.00 0.00 2.43
1992 2049 5.775195 CCCTATTTTAGATTGATCCAACCCC 59.225 44.000 0.00 0.00 0.00 4.95
2042 2099 2.954989 TCATGCTAGTGTTTGTTTGGCA 59.045 40.909 0.00 0.00 0.00 4.92
2224 2308 2.442236 TGCATTCTGGGGGAGAAATC 57.558 50.000 0.00 0.00 44.11 2.17
2225 2309 1.640149 TGCATTCTGGGGGAGAAATCA 59.360 47.619 0.00 0.00 44.11 2.57
2522 2606 6.038161 TCAAAACTCTTGGTGTGAAGTATGTG 59.962 38.462 0.00 0.00 0.00 3.21
2531 2615 5.480422 TGGTGTGAAGTATGTGTGTCTCTAT 59.520 40.000 0.00 0.00 0.00 1.98
2726 2895 6.900186 AGACTAATAGCCATACTGCCTCATAT 59.100 38.462 0.00 0.00 0.00 1.78
2836 3007 3.737774 GGAGTGCTGAAGAAATTGTTTGC 59.262 43.478 0.00 0.00 0.00 3.68
2867 3038 6.690194 ATGAATGGCTCAAGAGATAACAAC 57.310 37.500 0.32 0.00 37.67 3.32
2950 3121 1.339631 CGGTGTTTCCATTCCCTAGCA 60.340 52.381 0.00 0.00 35.57 3.49
3004 3175 3.947834 GGTTATGGCCATATGTAGGATGC 59.052 47.826 25.95 7.92 0.00 3.91
3029 3200 6.040166 CCAGTGCAAATATCAAAGCCTTAGAT 59.960 38.462 0.00 0.00 0.00 1.98
3149 3320 6.710597 AACGGTGATAGCTATACTCAAGAA 57.289 37.500 6.13 0.00 0.00 2.52
3150 3321 6.902771 ACGGTGATAGCTATACTCAAGAAT 57.097 37.500 6.13 0.00 0.00 2.40
3173 3344 9.766277 GAATATGTCAAAAGTGAAGAGAATGTC 57.234 33.333 0.00 0.00 34.87 3.06
3175 3346 7.572523 ATGTCAAAAGTGAAGAGAATGTCAA 57.427 32.000 0.00 0.00 34.87 3.18
3176 3347 7.389803 TGTCAAAAGTGAAGAGAATGTCAAA 57.610 32.000 0.00 0.00 34.87 2.69
3177 3348 7.825681 TGTCAAAAGTGAAGAGAATGTCAAAA 58.174 30.769 0.00 0.00 34.87 2.44
3178 3349 7.970061 TGTCAAAAGTGAAGAGAATGTCAAAAG 59.030 33.333 0.00 0.00 34.87 2.27
3179 3350 7.970614 GTCAAAAGTGAAGAGAATGTCAAAAGT 59.029 33.333 0.00 0.00 34.87 2.66
3180 3351 7.970061 TCAAAAGTGAAGAGAATGTCAAAAGTG 59.030 33.333 0.00 0.00 0.00 3.16
3181 3352 7.630242 AAAGTGAAGAGAATGTCAAAAGTGA 57.370 32.000 0.00 0.00 0.00 3.41
3182 3353 7.630242 AAGTGAAGAGAATGTCAAAAGTGAA 57.370 32.000 0.00 0.00 34.87 3.18
3183 3354 7.256756 AGTGAAGAGAATGTCAAAAGTGAAG 57.743 36.000 0.00 0.00 34.87 3.02
3184 3355 7.050377 AGTGAAGAGAATGTCAAAAGTGAAGA 58.950 34.615 0.00 0.00 34.87 2.87
3185 3356 7.226325 AGTGAAGAGAATGTCAAAAGTGAAGAG 59.774 37.037 0.00 0.00 34.87 2.85
3186 3357 7.225538 GTGAAGAGAATGTCAAAAGTGAAGAGA 59.774 37.037 0.00 0.00 34.87 3.10
3187 3358 7.770433 TGAAGAGAATGTCAAAAGTGAAGAGAA 59.230 33.333 0.00 0.00 34.87 2.87
3188 3359 8.688747 AAGAGAATGTCAAAAGTGAAGAGAAT 57.311 30.769 0.00 0.00 34.87 2.40
3189 3360 8.097078 AGAGAATGTCAAAAGTGAAGAGAATG 57.903 34.615 0.00 0.00 34.87 2.67
3190 3361 7.718753 AGAGAATGTCAAAAGTGAAGAGAATGT 59.281 33.333 0.00 0.00 34.87 2.71
3191 3362 7.869800 AGAATGTCAAAAGTGAAGAGAATGTC 58.130 34.615 0.00 0.00 34.87 3.06
3192 3363 5.657470 TGTCAAAAGTGAAGAGAATGTCG 57.343 39.130 0.00 0.00 34.87 4.35
3230 3401 0.524862 CAGAAACTGACATGGCCAGC 59.475 55.000 13.05 3.55 35.14 4.85
3484 3656 9.708092 GGTATACTGAGATTATGTAAGTTTCCC 57.292 37.037 2.25 0.00 0.00 3.97
3492 3664 6.389869 AGATTATGTAAGTTTCCCCATCTGGA 59.610 38.462 0.00 0.00 37.39 3.86
3523 3703 2.897969 AGTTCTAGGTGTCACGTTGGAT 59.102 45.455 3.08 0.00 0.00 3.41
3915 4151 2.040813 ACACTCCTGCATCCAAGTCATT 59.959 45.455 0.00 0.00 0.00 2.57
3920 4156 3.776969 TCCTGCATCCAAGTCATTAGTCT 59.223 43.478 0.00 0.00 0.00 3.24
3921 4157 4.225942 TCCTGCATCCAAGTCATTAGTCTT 59.774 41.667 0.00 0.00 0.00 3.01
3948 4184 4.687018 CCACGTTAGTGTTTATGTGCAGTA 59.313 41.667 0.00 0.00 46.56 2.74
3953 4189 8.347035 ACGTTAGTGTTTATGTGCAGTATTTTT 58.653 29.630 0.00 0.00 0.00 1.94
4031 4267 3.457012 GGTTGCCCCTGAAAGTATAGGTA 59.543 47.826 0.00 0.00 31.99 3.08
4158 4413 9.864034 GTGTGAGTGAATAAATTAATATCACGG 57.136 33.333 13.44 0.00 37.84 4.94
4310 4565 5.983118 ACGTTTTGATTTTGACCAGGAATTC 59.017 36.000 0.00 0.00 0.00 2.17
4343 4599 8.244113 GCAGAATATTGTTTTACCTTTAGCAGT 58.756 33.333 0.00 0.00 0.00 4.40
4352 4608 3.908643 ACCTTTAGCAGTTACCTAGGC 57.091 47.619 9.30 0.00 0.00 3.93
4370 4626 3.878778 AGGCCTTACACAGATGAACATC 58.121 45.455 0.00 6.68 38.09 3.06
4383 4639 5.064452 CAGATGAACATCTTAGCTTGTGACC 59.936 44.000 13.69 0.00 45.31 4.02
4558 4818 2.835764 AGCTACCCCTACGATGTTTTCA 59.164 45.455 0.00 0.00 0.00 2.69
4632 4894 9.327628 CTATATTCATCAATGATAGCCCTGAAG 57.672 37.037 0.00 0.00 36.56 3.02
4729 4994 6.577103 TCAGGTAAATGAGAGCTGATACTTG 58.423 40.000 0.00 0.00 44.33 3.16
4800 5065 3.055891 AGCTTGACAACTGTTTTGCCTTT 60.056 39.130 0.00 0.00 0.00 3.11
4843 5108 7.987649 AGTAGAGGTTAGTTAAGATCAAGTCG 58.012 38.462 0.00 0.00 0.00 4.18
4844 5109 5.652518 AGAGGTTAGTTAAGATCAAGTCGC 58.347 41.667 0.00 0.00 0.00 5.19
4845 5110 5.185249 AGAGGTTAGTTAAGATCAAGTCGCA 59.815 40.000 0.00 0.00 0.00 5.10
5032 5306 3.674753 CCGATCTTTTTGGTTGTGAATGC 59.325 43.478 0.00 0.00 0.00 3.56
5060 5334 0.931662 GCAGCTGCTGACACGTTTTG 60.932 55.000 32.30 3.79 38.21 2.44
5062 5336 1.094785 AGCTGCTGACACGTTTTGTT 58.905 45.000 0.00 0.00 39.17 2.83
5063 5337 1.472480 AGCTGCTGACACGTTTTGTTT 59.528 42.857 0.00 0.00 39.17 2.83
5088 5362 7.551035 TTTTGAATTGGAACTTTGATGTTGG 57.449 32.000 0.00 0.00 0.00 3.77
5089 5363 5.867903 TGAATTGGAACTTTGATGTTGGT 57.132 34.783 0.00 0.00 0.00 3.67
5091 5365 6.648192 TGAATTGGAACTTTGATGTTGGTTT 58.352 32.000 0.00 0.00 0.00 3.27
5092 5366 7.108847 TGAATTGGAACTTTGATGTTGGTTTT 58.891 30.769 0.00 0.00 0.00 2.43
5093 5367 7.279758 TGAATTGGAACTTTGATGTTGGTTTTC 59.720 33.333 0.00 0.00 0.00 2.29
5095 5369 5.901552 TGGAACTTTGATGTTGGTTTTCTC 58.098 37.500 0.00 0.00 0.00 2.87
5097 5371 5.163457 GGAACTTTGATGTTGGTTTTCTCCA 60.163 40.000 0.00 0.00 35.49 3.86
5098 5372 6.462909 GGAACTTTGATGTTGGTTTTCTCCAT 60.463 38.462 0.00 0.00 37.33 3.41
5099 5373 6.484364 ACTTTGATGTTGGTTTTCTCCATT 57.516 33.333 0.00 0.00 37.33 3.16
5100 5374 6.282930 ACTTTGATGTTGGTTTTCTCCATTG 58.717 36.000 0.00 0.00 37.33 2.82
5101 5375 5.867903 TTGATGTTGGTTTTCTCCATTGT 57.132 34.783 0.00 0.00 37.33 2.71
5102 5376 5.867903 TGATGTTGGTTTTCTCCATTGTT 57.132 34.783 0.00 0.00 37.33 2.83
5103 5377 5.599732 TGATGTTGGTTTTCTCCATTGTTG 58.400 37.500 0.00 0.00 37.33 3.33
5104 5378 4.399004 TGTTGGTTTTCTCCATTGTTGG 57.601 40.909 0.00 0.00 45.15 3.77
5105 5379 3.130633 GTTGGTTTTCTCCATTGTTGGC 58.869 45.455 0.00 0.00 43.29 4.52
5106 5380 2.676748 TGGTTTTCTCCATTGTTGGCT 58.323 42.857 0.00 0.00 43.29 4.75
5107 5381 2.364970 TGGTTTTCTCCATTGTTGGCTG 59.635 45.455 0.00 0.00 43.29 4.85
5108 5382 2.407090 GTTTTCTCCATTGTTGGCTGC 58.593 47.619 0.00 0.00 43.29 5.25
5109 5383 1.999648 TTTCTCCATTGTTGGCTGCT 58.000 45.000 0.00 0.00 43.29 4.24
5110 5384 1.250328 TTCTCCATTGTTGGCTGCTG 58.750 50.000 0.00 0.00 43.29 4.41
5111 5385 0.401356 TCTCCATTGTTGGCTGCTGA 59.599 50.000 0.00 0.00 43.29 4.26
5112 5386 0.524862 CTCCATTGTTGGCTGCTGAC 59.475 55.000 0.00 0.00 43.29 3.51
5113 5387 0.178995 TCCATTGTTGGCTGCTGACA 60.179 50.000 0.00 0.00 43.29 3.58
5114 5388 0.038892 CCATTGTTGGCTGCTGACAC 60.039 55.000 0.00 0.00 35.85 3.67
5115 5389 0.386352 CATTGTTGGCTGCTGACACG 60.386 55.000 0.00 0.00 0.00 4.49
5116 5390 0.819259 ATTGTTGGCTGCTGACACGT 60.819 50.000 0.00 0.00 0.00 4.49
5117 5391 1.029408 TTGTTGGCTGCTGACACGTT 61.029 50.000 0.00 0.00 0.00 3.99
5118 5392 1.029408 TGTTGGCTGCTGACACGTTT 61.029 50.000 0.00 0.00 0.00 3.60
5119 5393 0.100503 GTTGGCTGCTGACACGTTTT 59.899 50.000 0.00 0.00 0.00 2.43
5120 5394 0.814457 TTGGCTGCTGACACGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
5221 5504 6.777213 TCTGGACTCCTTTATACTCTGTTC 57.223 41.667 0.00 0.00 0.00 3.18
5244 5527 9.391006 GTTCCATATGTTCCTTTGTGTATCTAA 57.609 33.333 1.24 0.00 0.00 2.10
5275 5558 5.521906 TCAATCGATAGCTTTGCTACTCT 57.478 39.130 0.00 0.00 44.24 3.24
5349 5907 0.106918 ACCGAGCAGGGAGACTAGAG 60.107 60.000 0.00 0.00 46.96 2.43
5385 5943 6.049955 TCAGGAGTTTAGGGATGTGTTTAG 57.950 41.667 0.00 0.00 0.00 1.85
5403 5961 6.541278 GTGTTTAGAAAGGGTTGTACTGAAGT 59.459 38.462 0.00 0.00 0.00 3.01
5404 5962 7.066645 GTGTTTAGAAAGGGTTGTACTGAAGTT 59.933 37.037 0.00 0.00 0.00 2.66
5405 5963 7.612633 TGTTTAGAAAGGGTTGTACTGAAGTTT 59.387 33.333 0.00 0.00 0.00 2.66
5407 5965 9.856162 TTTAGAAAGGGTTGTACTGAAGTTTAT 57.144 29.630 0.00 0.00 0.00 1.40
5408 5966 9.856162 TTAGAAAGGGTTGTACTGAAGTTTATT 57.144 29.630 0.00 0.00 0.00 1.40
5410 5968 9.281371 AGAAAGGGTTGTACTGAAGTTTATTAC 57.719 33.333 0.00 0.00 0.00 1.89
5411 5969 9.281371 GAAAGGGTTGTACTGAAGTTTATTACT 57.719 33.333 0.00 0.00 39.32 2.24
5412 5970 8.617290 AAGGGTTGTACTGAAGTTTATTACTG 57.383 34.615 0.00 0.00 37.12 2.74
5504 6071 2.886081 GAGTAGTCGAGTGTACCGAGA 58.114 52.381 2.10 0.00 36.66 4.04
5505 6072 2.602660 GAGTAGTCGAGTGTACCGAGAC 59.397 54.545 2.10 0.00 36.66 3.36
5506 6073 1.663135 GTAGTCGAGTGTACCGAGACC 59.337 57.143 2.10 0.00 36.66 3.85
5507 6074 1.018226 AGTCGAGTGTACCGAGACCG 61.018 60.000 0.00 0.00 36.66 4.79
5508 6075 1.016130 GTCGAGTGTACCGAGACCGA 61.016 60.000 0.00 0.00 36.66 4.69
5509 6076 0.738762 TCGAGTGTACCGAGACCGAG 60.739 60.000 0.00 0.00 38.22 4.63
5510 6077 0.738762 CGAGTGTACCGAGACCGAGA 60.739 60.000 0.00 0.00 38.22 4.04
5511 6078 1.008329 GAGTGTACCGAGACCGAGAG 58.992 60.000 0.00 0.00 38.22 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.994247 AAGATCCAGGGTGCATCACA 59.006 50.000 0.00 0.00 35.86 3.58
10 11 1.065199 TGAAGATCCAGGGTGCATCAC 60.065 52.381 0.00 0.00 0.00 3.06
11 12 1.288188 TGAAGATCCAGGGTGCATCA 58.712 50.000 0.00 0.00 0.00 3.07
12 13 2.653234 ATGAAGATCCAGGGTGCATC 57.347 50.000 0.00 0.00 0.00 3.91
13 14 5.848286 TTATATGAAGATCCAGGGTGCAT 57.152 39.130 0.00 0.00 0.00 3.96
14 15 5.645056 TTTATATGAAGATCCAGGGTGCA 57.355 39.130 0.00 0.00 0.00 4.57
15 16 6.150140 GTCATTTATATGAAGATCCAGGGTGC 59.850 42.308 0.00 0.00 42.23 5.01
16 17 7.173907 GTGTCATTTATATGAAGATCCAGGGTG 59.826 40.741 0.00 0.00 42.23 4.61
17 18 7.227156 GTGTCATTTATATGAAGATCCAGGGT 58.773 38.462 0.00 0.00 42.23 4.34
18 19 6.369890 CGTGTCATTTATATGAAGATCCAGGG 59.630 42.308 0.00 0.00 42.23 4.45
19 20 6.931281 ACGTGTCATTTATATGAAGATCCAGG 59.069 38.462 0.00 0.99 42.23 4.45
20 21 7.095481 CCACGTGTCATTTATATGAAGATCCAG 60.095 40.741 15.65 0.00 42.23 3.86
21 22 6.705825 CCACGTGTCATTTATATGAAGATCCA 59.294 38.462 15.65 0.00 42.23 3.41
22 23 6.929049 TCCACGTGTCATTTATATGAAGATCC 59.071 38.462 15.65 0.00 42.23 3.36
23 24 7.946655 TCCACGTGTCATTTATATGAAGATC 57.053 36.000 15.65 0.00 42.23 2.75
24 25 8.908786 ATTCCACGTGTCATTTATATGAAGAT 57.091 30.769 15.65 0.00 42.23 2.40
25 26 8.731275 AATTCCACGTGTCATTTATATGAAGA 57.269 30.769 15.65 0.00 42.23 2.87
26 27 8.830580 AGAATTCCACGTGTCATTTATATGAAG 58.169 33.333 15.65 0.00 42.23 3.02
27 28 8.731275 AGAATTCCACGTGTCATTTATATGAA 57.269 30.769 15.65 6.89 42.23 2.57
28 29 9.825109 TTAGAATTCCACGTGTCATTTATATGA 57.175 29.630 15.65 0.00 38.45 2.15
57 58 3.436243 TGAACCACTCAACCCACTTTTT 58.564 40.909 0.00 0.00 0.00 1.94
58 59 3.094484 TGAACCACTCAACCCACTTTT 57.906 42.857 0.00 0.00 0.00 2.27
59 60 2.818751 TGAACCACTCAACCCACTTT 57.181 45.000 0.00 0.00 0.00 2.66
60 61 2.443255 AGATGAACCACTCAACCCACTT 59.557 45.455 0.00 0.00 37.67 3.16
61 62 2.057922 AGATGAACCACTCAACCCACT 58.942 47.619 0.00 0.00 37.67 4.00
62 63 2.154462 CAGATGAACCACTCAACCCAC 58.846 52.381 0.00 0.00 37.67 4.61
63 64 1.073763 CCAGATGAACCACTCAACCCA 59.926 52.381 0.00 0.00 37.67 4.51
64 65 1.073923 ACCAGATGAACCACTCAACCC 59.926 52.381 0.00 0.00 37.67 4.11
65 66 2.568623 ACCAGATGAACCACTCAACC 57.431 50.000 0.00 0.00 37.67 3.77
66 67 3.499918 CAGAACCAGATGAACCACTCAAC 59.500 47.826 0.00 0.00 37.67 3.18
67 68 3.136443 ACAGAACCAGATGAACCACTCAA 59.864 43.478 0.00 0.00 37.67 3.02
68 69 2.705658 ACAGAACCAGATGAACCACTCA 59.294 45.455 0.00 0.00 38.81 3.41
69 70 3.409026 ACAGAACCAGATGAACCACTC 57.591 47.619 0.00 0.00 0.00 3.51
70 71 5.505181 AATACAGAACCAGATGAACCACT 57.495 39.130 0.00 0.00 0.00 4.00
71 72 5.106157 CCAAATACAGAACCAGATGAACCAC 60.106 44.000 0.00 0.00 0.00 4.16
72 73 5.009631 CCAAATACAGAACCAGATGAACCA 58.990 41.667 0.00 0.00 0.00 3.67
73 74 4.399303 CCCAAATACAGAACCAGATGAACC 59.601 45.833 0.00 0.00 0.00 3.62
74 75 4.142381 GCCCAAATACAGAACCAGATGAAC 60.142 45.833 0.00 0.00 0.00 3.18
75 76 4.016444 GCCCAAATACAGAACCAGATGAA 58.984 43.478 0.00 0.00 0.00 2.57
76 77 3.620488 GCCCAAATACAGAACCAGATGA 58.380 45.455 0.00 0.00 0.00 2.92
77 78 2.689983 GGCCCAAATACAGAACCAGATG 59.310 50.000 0.00 0.00 0.00 2.90
78 79 2.683742 CGGCCCAAATACAGAACCAGAT 60.684 50.000 0.00 0.00 0.00 2.90
79 80 1.339631 CGGCCCAAATACAGAACCAGA 60.340 52.381 0.00 0.00 0.00 3.86
80 81 1.094785 CGGCCCAAATACAGAACCAG 58.905 55.000 0.00 0.00 0.00 4.00
86 87 2.014128 CCACTTACGGCCCAAATACAG 58.986 52.381 0.00 0.00 0.00 2.74
89 90 2.438411 CAACCACTTACGGCCCAAATA 58.562 47.619 0.00 0.00 0.00 1.40
100 101 4.382147 GGTTTGGAACTTTGCAACCACTTA 60.382 41.667 6.03 0.00 38.25 2.24
109 110 2.351738 CCTGATCGGTTTGGAACTTTGC 60.352 50.000 0.00 0.00 0.00 3.68
125 126 4.747931 GCCTGACATACAAATAGGCCTGAT 60.748 45.833 17.99 0.00 46.29 2.90
126 127 3.433598 GCCTGACATACAAATAGGCCTGA 60.434 47.826 17.99 0.00 46.29 3.86
133 134 2.422803 GGGCTGGCCTGACATACAAATA 60.423 50.000 18.40 0.00 36.10 1.40
139 140 3.047807 GCTGGGCTGGCCTGACATA 62.048 63.158 27.43 4.65 36.10 2.29
140 141 4.437587 GCTGGGCTGGCCTGACAT 62.438 66.667 27.43 0.00 36.10 3.06
158 159 0.607489 GAGATGCAACTGCTGGTGGT 60.607 55.000 10.91 0.00 42.66 4.16
159 160 1.642037 CGAGATGCAACTGCTGGTGG 61.642 60.000 10.91 0.00 42.66 4.61
160 161 1.642037 CCGAGATGCAACTGCTGGTG 61.642 60.000 0.00 3.92 42.66 4.17
161 162 1.376424 CCGAGATGCAACTGCTGGT 60.376 57.895 0.00 0.00 42.66 4.00
163 164 0.108472 TCTCCGAGATGCAACTGCTG 60.108 55.000 0.00 0.00 42.66 4.41
164 165 0.610174 TTCTCCGAGATGCAACTGCT 59.390 50.000 0.00 0.00 42.66 4.24
165 166 0.723981 GTTCTCCGAGATGCAACTGC 59.276 55.000 0.00 0.00 42.50 4.40
166 167 1.998315 CTGTTCTCCGAGATGCAACTG 59.002 52.381 0.00 0.00 0.00 3.16
167 168 1.066573 CCTGTTCTCCGAGATGCAACT 60.067 52.381 0.00 0.00 0.00 3.16
168 169 1.338200 ACCTGTTCTCCGAGATGCAAC 60.338 52.381 0.00 0.00 0.00 4.17
169 170 0.976641 ACCTGTTCTCCGAGATGCAA 59.023 50.000 0.00 0.00 0.00 4.08
177 178 0.865769 CCGTGAAAACCTGTTCTCCG 59.134 55.000 0.00 0.00 0.00 4.63
180 181 0.822121 GGGCCGTGAAAACCTGTTCT 60.822 55.000 0.00 0.00 0.00 3.01
181 182 1.104577 TGGGCCGTGAAAACCTGTTC 61.105 55.000 0.00 0.00 0.00 3.18
182 183 1.076632 TGGGCCGTGAAAACCTGTT 60.077 52.632 0.00 0.00 0.00 3.16
184 185 2.561037 GGTGGGCCGTGAAAACCTG 61.561 63.158 0.00 0.00 0.00 4.00
202 203 0.784778 GACCAGAAAAGACTGACGCG 59.215 55.000 3.53 3.53 39.94 6.01
205 206 3.206150 TGCTTGACCAGAAAAGACTGAC 58.794 45.455 0.00 0.00 39.94 3.51
266 267 2.093500 CCCTGAATTCACGATCTGGACA 60.093 50.000 3.38 0.00 36.95 4.02
327 332 1.302752 GGTGCTGTGCTGATGGACA 60.303 57.895 0.00 0.00 42.20 4.02
332 337 3.052082 GTGCGGTGCTGTGCTGAT 61.052 61.111 0.00 0.00 0.00 2.90
461 467 0.335019 TCAACGGGGAGGAGAGATGA 59.665 55.000 0.00 0.00 0.00 2.92
481 487 1.979693 ACGAGCAGGTCTCCCAGTC 60.980 63.158 0.00 0.00 38.62 3.51
498 504 2.186826 ACAAGAAGCACGCCCACAC 61.187 57.895 0.00 0.00 0.00 3.82
499 505 2.186160 CACAAGAAGCACGCCCACA 61.186 57.895 0.00 0.00 0.00 4.17
500 506 2.639286 CACAAGAAGCACGCCCAC 59.361 61.111 0.00 0.00 0.00 4.61
501 507 2.594303 CCACAAGAAGCACGCCCA 60.594 61.111 0.00 0.00 0.00 5.36
502 508 2.281484 TCCACAAGAAGCACGCCC 60.281 61.111 0.00 0.00 0.00 6.13
514 529 4.063967 CTACCGTGCGGCTCCACA 62.064 66.667 10.87 0.00 39.32 4.17
748 773 7.586664 ACGAAAAGAAAGTTTATTCGAAGCTTC 59.413 33.333 25.14 16.84 43.99 3.86
897 927 0.895530 CGGGCTGAGGAAGAACTACA 59.104 55.000 0.00 0.00 0.00 2.74
1044 1091 2.235016 CACAGGGAAAATGGAAACGGA 58.765 47.619 0.00 0.00 0.00 4.69
1046 1093 1.336795 GGCACAGGGAAAATGGAAACG 60.337 52.381 0.00 0.00 0.00 3.60
1078 1125 4.163458 TGAGGGATCAGGTAATAAGCGTTT 59.837 41.667 0.00 0.00 0.00 3.60
1084 1131 5.726560 TCTGGATGAGGGATCAGGTAATAA 58.273 41.667 0.00 0.00 31.91 1.40
1124 1175 7.307493 AGCAAAGAACAAATTTTGGAAGTTC 57.693 32.000 13.42 9.27 38.99 3.01
1159 1212 3.376546 GGAAGAAGAGGACATTGTGCATC 59.623 47.826 11.08 5.97 0.00 3.91
1166 1219 4.159506 CGAGAGAAGGAAGAAGAGGACATT 59.840 45.833 0.00 0.00 0.00 2.71
1186 1239 5.993106 AAGAAAAGTTTCTGGAAGTCGAG 57.007 39.130 7.05 0.00 46.22 4.04
1203 1256 9.772973 ACATATATAACGACCTATGCAAAGAAA 57.227 29.630 0.00 0.00 0.00 2.52
1316 1370 8.911247 AACCACGAGATTAATATTTTTCAAGC 57.089 30.769 0.00 0.00 0.00 4.01
1445 1499 5.385198 AGAGGGAAATGAAGCTAACAACAA 58.615 37.500 0.00 0.00 0.00 2.83
1556 1611 2.557056 ACTACTCACTGCTGCGTTTCTA 59.443 45.455 0.00 0.00 0.00 2.10
1637 1692 3.074412 TGCAAAGAAGCTAAGGTACTGC 58.926 45.455 0.00 0.00 34.80 4.40
1676 1732 8.925700 CAAGCGATTCAGTTGCACTATATATAA 58.074 33.333 0.00 0.00 39.90 0.98
1802 1858 2.607635 GCAAAGACACGACTCAAGTCAA 59.392 45.455 10.56 0.00 44.99 3.18
1807 1863 2.254546 ATGGCAAAGACACGACTCAA 57.745 45.000 0.00 0.00 0.00 3.02
2198 2282 5.865977 TCTCCCCCAGAATGCATTAATAT 57.134 39.130 12.97 0.00 31.97 1.28
2224 2308 8.694394 GCACAGAGAAATAAAACTTTTTAGCTG 58.306 33.333 0.00 0.00 36.22 4.24
2225 2309 8.413229 TGCACAGAGAAATAAAACTTTTTAGCT 58.587 29.630 0.00 0.00 36.22 3.32
2531 2615 3.319689 TCAGTGTCTTACCGTCAATGTCA 59.680 43.478 0.00 0.00 30.69 3.58
2763 2932 5.696724 ACAGATCTTGTACACTGTTAAGTGC 59.303 40.000 10.24 0.00 44.34 4.40
2836 3007 2.715749 TGAGCCATTCATACCAGGTG 57.284 50.000 0.76 0.00 0.00 4.00
2867 3038 4.432980 ACTTACCAAATAATCTCCGGGG 57.567 45.455 0.00 0.00 0.00 5.73
2903 3074 6.581712 AGGCTTTTGATAGAAAACAAAGCAA 58.418 32.000 14.88 0.00 37.32 3.91
3004 3175 4.460948 AAGGCTTTGATATTTGCACTGG 57.539 40.909 0.00 0.00 0.00 4.00
3029 3200 4.438148 TCGTCATCTGTTTCTGACAACAA 58.562 39.130 3.87 1.46 41.46 2.83
3149 3320 8.853077 TGACATTCTCTTCACTTTTGACATAT 57.147 30.769 0.00 0.00 0.00 1.78
3150 3321 8.675705 TTGACATTCTCTTCACTTTTGACATA 57.324 30.769 0.00 0.00 0.00 2.29
3173 3344 7.857389 TCATTTTCGACATTCTCTTCACTTTTG 59.143 33.333 0.00 0.00 0.00 2.44
3175 3346 7.496529 TCATTTTCGACATTCTCTTCACTTT 57.503 32.000 0.00 0.00 0.00 2.66
3176 3347 6.348050 GCTCATTTTCGACATTCTCTTCACTT 60.348 38.462 0.00 0.00 0.00 3.16
3177 3348 5.121454 GCTCATTTTCGACATTCTCTTCACT 59.879 40.000 0.00 0.00 0.00 3.41
3178 3349 5.319931 GCTCATTTTCGACATTCTCTTCAC 58.680 41.667 0.00 0.00 0.00 3.18
3179 3350 4.393062 GGCTCATTTTCGACATTCTCTTCA 59.607 41.667 0.00 0.00 0.00 3.02
3180 3351 4.393062 TGGCTCATTTTCGACATTCTCTTC 59.607 41.667 0.00 0.00 0.00 2.87
3181 3352 4.326826 TGGCTCATTTTCGACATTCTCTT 58.673 39.130 0.00 0.00 0.00 2.85
3182 3353 3.937706 CTGGCTCATTTTCGACATTCTCT 59.062 43.478 0.00 0.00 0.00 3.10
3183 3354 3.686726 ACTGGCTCATTTTCGACATTCTC 59.313 43.478 0.00 0.00 0.00 2.87
3184 3355 3.679389 ACTGGCTCATTTTCGACATTCT 58.321 40.909 0.00 0.00 0.00 2.40
3185 3356 5.741388 ATACTGGCTCATTTTCGACATTC 57.259 39.130 0.00 0.00 0.00 2.67
3186 3357 6.515272 AAATACTGGCTCATTTTCGACATT 57.485 33.333 0.00 0.00 0.00 2.71
3187 3358 6.597672 TGTAAATACTGGCTCATTTTCGACAT 59.402 34.615 0.00 0.00 0.00 3.06
3188 3359 5.935206 TGTAAATACTGGCTCATTTTCGACA 59.065 36.000 0.00 0.00 0.00 4.35
3189 3360 6.312918 TCTGTAAATACTGGCTCATTTTCGAC 59.687 38.462 0.00 0.00 0.00 4.20
3190 3361 6.403049 TCTGTAAATACTGGCTCATTTTCGA 58.597 36.000 0.00 0.00 0.00 3.71
3191 3362 6.662414 TCTGTAAATACTGGCTCATTTTCG 57.338 37.500 0.00 0.00 0.00 3.46
3192 3363 8.515414 AGTTTCTGTAAATACTGGCTCATTTTC 58.485 33.333 0.00 0.00 0.00 2.29
3230 3401 2.794910 CGTACCTATGGATTTCAGTGCG 59.205 50.000 0.00 0.00 0.00 5.34
3649 3829 3.683365 AATTTTCTTCCAAAGCGGCAT 57.317 38.095 1.45 0.00 33.14 4.40
3799 4035 7.880160 ATTAGCCAGCAAGAACATGTATAAA 57.120 32.000 0.00 0.00 0.00 1.40
3896 4132 3.521126 ACTAATGACTTGGATGCAGGAGT 59.479 43.478 2.61 0.00 0.00 3.85
3915 4151 3.759581 ACACTAACGTGGGAGAAGACTA 58.240 45.455 0.00 0.00 45.50 2.59
3920 4156 4.992319 CACATAAACACTAACGTGGGAGAA 59.008 41.667 0.00 0.00 45.50 2.87
3921 4157 4.562082 CACATAAACACTAACGTGGGAGA 58.438 43.478 0.00 0.00 45.50 3.71
3948 4184 2.029828 TGCGTTGCCACGGAATAAAAAT 60.030 40.909 12.66 0.00 44.68 1.82
3971 4207 8.386264 ACCATTATATCAACTAGCTAAATGCCT 58.614 33.333 0.00 0.00 44.23 4.75
4011 4247 5.987019 ATTACCTATACTTTCAGGGGCAA 57.013 39.130 0.00 0.00 36.15 4.52
4042 4297 9.829507 CAGAATCTAAAGTGGTATTCAGAATCT 57.170 33.333 0.00 0.00 32.04 2.40
4043 4298 9.823647 TCAGAATCTAAAGTGGTATTCAGAATC 57.176 33.333 0.00 0.00 32.04 2.52
4046 4301 9.605275 CATTCAGAATCTAAAGTGGTATTCAGA 57.395 33.333 0.00 0.00 32.04 3.27
4047 4302 9.388506 ACATTCAGAATCTAAAGTGGTATTCAG 57.611 33.333 0.00 0.00 32.04 3.02
4048 4303 9.739276 AACATTCAGAATCTAAAGTGGTATTCA 57.261 29.630 0.00 0.00 32.04 2.57
4053 4308 8.918202 TTGTAACATTCAGAATCTAAAGTGGT 57.082 30.769 0.00 0.00 0.00 4.16
4054 4309 9.003658 ACTTGTAACATTCAGAATCTAAAGTGG 57.996 33.333 0.00 0.00 0.00 4.00
4157 4412 6.434340 AGAGTTTTCAATGGTGGAAATAGACC 59.566 38.462 0.00 0.00 34.66 3.85
4158 4413 7.362142 GGAGAGTTTTCAATGGTGGAAATAGAC 60.362 40.741 0.00 0.00 34.66 2.59
4343 4599 4.616553 TCATCTGTGTAAGGCCTAGGTAA 58.383 43.478 5.16 0.00 0.00 2.85
4352 4608 6.344500 AGCTAAGATGTTCATCTGTGTAAGG 58.656 40.000 14.82 3.91 0.00 2.69
4370 4626 1.549170 AGGGTACGGTCACAAGCTAAG 59.451 52.381 0.00 0.00 0.00 2.18
4383 4639 2.304221 TCCCATAGGATCAGGGTACG 57.696 55.000 10.43 0.00 43.31 3.67
4444 4700 5.047731 TCCTATAGCGATGAAACAGAGGATG 60.048 44.000 0.00 0.00 0.00 3.51
4445 4701 5.080337 TCCTATAGCGATGAAACAGAGGAT 58.920 41.667 0.00 0.00 0.00 3.24
4532 4792 6.736110 AAACATCGTAGGGGTAGCTTATTA 57.264 37.500 0.00 0.00 0.00 0.98
4558 4818 6.992715 AGCAAAGTATCAGTACTGTTGAAAGT 59.007 34.615 21.99 5.25 40.24 2.66
4632 4894 0.370273 CATCAAGACGCGTTAGTGCC 59.630 55.000 15.53 0.00 0.00 5.01
4729 4994 4.184629 CAACAGCCTGGTCTTCAGTATAC 58.815 47.826 0.00 0.00 41.83 1.47
4745 5010 3.304057 GGAGTGCTTTTCTACACAACAGC 60.304 47.826 0.00 0.00 39.30 4.40
4800 5065 8.209584 ACCTCTACTAGTATAATCACGAACAGA 58.790 37.037 2.33 0.00 0.00 3.41
4843 5108 7.986085 AAGATATTACAACATGGGTATCTGC 57.014 36.000 0.00 0.00 31.36 4.26
4845 5110 9.354673 CCAAAAGATATTACAACATGGGTATCT 57.645 33.333 0.00 0.00 32.03 1.98
4971 5245 8.680001 GCATAACATTGCTGATATCAATCCATA 58.320 33.333 6.90 0.00 39.57 2.74
5063 5337 7.609532 ACCAACATCAAAGTTCCAATTCAAAAA 59.390 29.630 0.00 0.00 0.00 1.94
5073 5347 5.163457 TGGAGAAAACCAACATCAAAGTTCC 60.163 40.000 0.00 0.00 36.96 3.62
5074 5348 5.901552 TGGAGAAAACCAACATCAAAGTTC 58.098 37.500 0.00 0.00 36.96 3.01
5080 5354 5.599732 CAACAATGGAGAAAACCAACATCA 58.400 37.500 0.00 0.00 43.47 3.07
5097 5371 0.819259 ACGTGTCAGCAGCCAACAAT 60.819 50.000 0.00 0.00 0.00 2.71
5098 5372 1.029408 AACGTGTCAGCAGCCAACAA 61.029 50.000 0.00 0.00 0.00 2.83
5099 5373 1.029408 AAACGTGTCAGCAGCCAACA 61.029 50.000 0.00 0.00 0.00 3.33
5100 5374 0.100503 AAAACGTGTCAGCAGCCAAC 59.899 50.000 0.00 0.00 0.00 3.77
5101 5375 0.814457 AAAAACGTGTCAGCAGCCAA 59.186 45.000 0.00 0.00 0.00 4.52
5102 5376 2.487918 AAAAACGTGTCAGCAGCCA 58.512 47.368 0.00 0.00 0.00 4.75
5117 5391 8.760569 GCTAAAATCGAAGTTCCAATTCAAAAA 58.239 29.630 0.00 0.00 0.00 1.94
5118 5392 8.141268 AGCTAAAATCGAAGTTCCAATTCAAAA 58.859 29.630 0.00 0.00 0.00 2.44
5119 5393 7.657336 AGCTAAAATCGAAGTTCCAATTCAAA 58.343 30.769 0.00 0.00 0.00 2.69
5120 5394 7.214467 AGCTAAAATCGAAGTTCCAATTCAA 57.786 32.000 0.00 0.00 0.00 2.69
5121 5395 6.817765 AGCTAAAATCGAAGTTCCAATTCA 57.182 33.333 0.00 0.00 0.00 2.57
5122 5396 8.023706 AGAAAGCTAAAATCGAAGTTCCAATTC 58.976 33.333 0.00 0.00 0.00 2.17
5123 5397 7.886338 AGAAAGCTAAAATCGAAGTTCCAATT 58.114 30.769 0.00 0.00 0.00 2.32
5124 5398 7.362142 GGAGAAAGCTAAAATCGAAGTTCCAAT 60.362 37.037 0.00 0.00 0.00 3.16
5125 5399 6.072673 GGAGAAAGCTAAAATCGAAGTTCCAA 60.073 38.462 0.00 0.00 0.00 3.53
5126 5400 5.411669 GGAGAAAGCTAAAATCGAAGTTCCA 59.588 40.000 0.00 0.00 0.00 3.53
5127 5401 5.411669 TGGAGAAAGCTAAAATCGAAGTTCC 59.588 40.000 0.00 0.00 0.00 3.62
5128 5402 6.481954 TGGAGAAAGCTAAAATCGAAGTTC 57.518 37.500 0.00 0.00 0.00 3.01
5129 5403 7.040409 ACAATGGAGAAAGCTAAAATCGAAGTT 60.040 33.333 0.00 0.00 0.00 2.66
5134 5408 5.287035 GCAACAATGGAGAAAGCTAAAATCG 59.713 40.000 0.00 0.00 0.00 3.34
5141 5415 1.891150 CCAGCAACAATGGAGAAAGCT 59.109 47.619 0.00 0.00 40.51 3.74
5244 5527 7.012704 AGCAAAGCTATCGATTGAACATGTTAT 59.987 33.333 11.95 1.81 36.99 1.89
5257 5540 7.444487 TCTGTTATAGAGTAGCAAAGCTATCGA 59.556 37.037 1.68 0.00 43.30 3.59
5295 5850 6.075918 CGAAGACAAACATGACTCAGATTTG 58.924 40.000 0.00 12.92 36.54 2.32
5349 5907 9.121658 CCCTAAACTCCTGATTTATTTAGAACC 57.878 37.037 0.00 0.00 35.70 3.62
5385 5943 9.281371 AGTAATAAACTTCAGTACAACCCTTTC 57.719 33.333 0.00 0.00 33.35 2.62
5416 5974 8.506437 TGTTTGTTCATGTCTTTCATCATAGAC 58.494 33.333 0.00 0.00 40.89 2.59
5417 5975 8.620116 TGTTTGTTCATGTCTTTCATCATAGA 57.380 30.769 0.00 0.00 34.09 1.98
5418 5976 9.681692 TTTGTTTGTTCATGTCTTTCATCATAG 57.318 29.630 0.00 0.00 34.09 2.23
5454 6021 0.037447 GGCTGGGATCAGGATTAGGC 59.963 60.000 0.00 0.00 41.19 3.93
5500 6067 2.438614 TCCAGCCTCTCGGTCTCG 60.439 66.667 0.00 0.00 37.82 4.04
5501 6068 2.781158 GCTCCAGCCTCTCGGTCTC 61.781 68.421 0.00 0.00 34.31 3.36
5502 6069 2.757917 GCTCCAGCCTCTCGGTCT 60.758 66.667 0.00 0.00 34.31 3.85
5503 6070 2.757917 AGCTCCAGCCTCTCGGTC 60.758 66.667 0.00 0.00 43.38 4.79
5504 6071 2.757917 GAGCTCCAGCCTCTCGGT 60.758 66.667 0.87 0.00 43.38 4.69
5505 6072 2.441901 AGAGCTCCAGCCTCTCGG 60.442 66.667 10.93 0.00 43.38 4.63
5506 6073 1.727511 CTGAGAGCTCCAGCCTCTCG 61.728 65.000 10.93 11.06 42.64 4.04
5507 6074 0.684153 ACTGAGAGCTCCAGCCTCTC 60.684 60.000 23.94 15.56 43.38 3.20
5508 6075 0.628522 TACTGAGAGCTCCAGCCTCT 59.371 55.000 23.94 12.45 43.38 3.69
5509 6076 1.032014 CTACTGAGAGCTCCAGCCTC 58.968 60.000 23.94 11.39 43.38 4.70
5510 6077 0.396974 CCTACTGAGAGCTCCAGCCT 60.397 60.000 23.94 13.24 43.38 4.58
5511 6078 0.686112 ACCTACTGAGAGCTCCAGCC 60.686 60.000 23.94 8.55 43.38 4.85
5512 6079 0.744281 GACCTACTGAGAGCTCCAGC 59.256 60.000 23.94 10.90 42.49 4.85
5513 6080 1.021202 CGACCTACTGAGAGCTCCAG 58.979 60.000 22.96 22.96 37.64 3.86
5514 6081 0.394488 CCGACCTACTGAGAGCTCCA 60.394 60.000 10.93 7.41 0.00 3.86
5515 6082 1.104577 CCCGACCTACTGAGAGCTCC 61.105 65.000 10.93 2.40 0.00 4.70
5553 6120 3.685214 CTCTCACGCGAAGACCCCG 62.685 68.421 15.93 0.00 0.00 5.73
5555 6122 2.507324 GCTCTCACGCGAAGACCC 60.507 66.667 15.93 3.49 0.00 4.46


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

AutoCloner maintained by Alex Coulton.