Multiple sequence alignment - TraesCS1B01G289500

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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 TraesCS1B01G289500 chr1B 100.000 3461 0 0 1 3461 504508117 504504657 0.000000e+00 6392
1 TraesCS1B01G289500 chr1D 91.198 2931 187 28 468 3375 377572662 377569780 0.000000e+00 3917
2 TraesCS1B01G289500 chr1D 90.323 93 2 2 216 307 377573125 377573039 7.850000e-22 115
3 TraesCS1B01G289500 chr1A 88.550 3013 175 72 511 3456 478258990 478256081 0.000000e+00 3496
4 TraesCS1B01G289500 chr1A 86.498 237 15 12 206 432 478259214 478258985 9.600000e-61 244
5 TraesCS1B01G289500 chr6B 97.183 213 6 0 1 213 695005483 695005271 9.130000e-96 361
6 TraesCS1B01G289500 chr6B 97.087 206 6 0 1 206 459059266 459059061 7.110000e-92 348
7 TraesCS1B01G289500 chr5B 98.507 201 3 0 1 201 423644804 423645004 4.250000e-94 355
8 TraesCS1B01G289500 chr5A 98.990 198 2 0 1 198 699772071 699772268 4.250000e-94 355
9 TraesCS1B01G289500 chr5A 95.755 212 8 1 1 211 662812624 662812835 1.190000e-89 340
10 TraesCS1B01G289500 chr3A 98.990 198 2 0 1 198 695744178 695743981 4.250000e-94 355
11 TraesCS1B01G289500 chr3A 97.549 204 5 0 1 204 574459957 574460160 1.980000e-92 350
12 TraesCS1B01G289500 chr7A 98.500 200 3 0 1 200 696783186 696783385 1.530000e-93 353
13 TraesCS1B01G289500 chr4A 97.115 208 4 2 1 206 685739399 685739606 1.980000e-92 350


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 TraesCS1B01G289500 chr1B 504504657 504508117 3460 True 6392 6392 100.0000 1 3461 1 chr1B.!!$R1 3460
1 TraesCS1B01G289500 chr1D 377569780 377573125 3345 True 2016 3917 90.7605 216 3375 2 chr1D.!!$R1 3159
2 TraesCS1B01G289500 chr1A 478256081 478259214 3133 True 1870 3496 87.5240 206 3456 2 chr1A.!!$R1 3250

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
200 201 0.179000 CCCACTATGACCAGCCTGAC 59.821 60.0 0.00 0.0 0.00 3.51 F
201 202 0.179000 CCACTATGACCAGCCTGACC 59.821 60.0 0.00 0.0 0.00 4.02 F
204 205 0.179062 CTATGACCAGCCTGACCAGC 60.179 60.0 0.00 0.0 0.00 4.85 F
276 281 0.440371 GCGCTCACTGCACTAGTTTC 59.560 55.0 0.00 0.0 43.06 2.78 F
1679 1914 0.521291 GTTGCATGGCGCTCTTGTTA 59.479 50.0 7.64 0.0 43.06 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 1279 0.040692 CGTCGTCCAAGAACTCGTCA 60.041 55.000 0.00 0.00 0.00 4.35 R
1280 1515 0.555769 ACCTCCTCCTGCCAAACAAA 59.444 50.000 0.00 0.00 0.00 2.83 R
2161 2397 1.081509 GCCTGCAATGACGCGAAAA 60.082 52.632 15.93 0.00 33.35 2.29 R
2308 2544 9.150348 ACTTGCCATTAATTAACACAATTAAGC 57.850 29.630 0.00 7.24 36.08 3.09 R
3069 3344 0.040781 TTGCCGCTAAAGCAACGAAC 60.041 50.000 2.44 0.00 44.95 3.95 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
22 23 5.549742 AATGAGGAGAGAGGCAAATAGAG 57.450 43.478 0.00 0.00 0.00 2.43
23 24 3.987745 TGAGGAGAGAGGCAAATAGAGT 58.012 45.455 0.00 0.00 0.00 3.24
24 25 5.130705 TGAGGAGAGAGGCAAATAGAGTA 57.869 43.478 0.00 0.00 0.00 2.59
25 26 5.519808 TGAGGAGAGAGGCAAATAGAGTAA 58.480 41.667 0.00 0.00 0.00 2.24
26 27 5.361285 TGAGGAGAGAGGCAAATAGAGTAAC 59.639 44.000 0.00 0.00 0.00 2.50
27 28 5.273208 AGGAGAGAGGCAAATAGAGTAACA 58.727 41.667 0.00 0.00 0.00 2.41
28 29 5.902431 AGGAGAGAGGCAAATAGAGTAACAT 59.098 40.000 0.00 0.00 0.00 2.71
29 30 7.069986 AGGAGAGAGGCAAATAGAGTAACATA 58.930 38.462 0.00 0.00 0.00 2.29
30 31 7.565398 AGGAGAGAGGCAAATAGAGTAACATAA 59.435 37.037 0.00 0.00 0.00 1.90
31 32 8.371699 GGAGAGAGGCAAATAGAGTAACATAAT 58.628 37.037 0.00 0.00 0.00 1.28
50 51 8.479313 ACATAATATGTTACCATCACATAGCG 57.521 34.615 0.00 0.00 41.63 4.26
51 52 7.549134 ACATAATATGTTACCATCACATAGCGG 59.451 37.037 0.00 0.00 41.63 5.52
52 53 3.838244 ATGTTACCATCACATAGCGGT 57.162 42.857 0.00 0.00 32.88 5.68
53 54 3.620427 TGTTACCATCACATAGCGGTT 57.380 42.857 0.00 0.00 32.81 4.44
54 55 3.945346 TGTTACCATCACATAGCGGTTT 58.055 40.909 0.00 0.00 32.81 3.27
55 56 3.936453 TGTTACCATCACATAGCGGTTTC 59.064 43.478 0.00 0.00 32.81 2.78
56 57 2.038387 ACCATCACATAGCGGTTTCC 57.962 50.000 0.00 0.00 0.00 3.13
57 58 1.280710 ACCATCACATAGCGGTTTCCA 59.719 47.619 0.00 0.00 0.00 3.53
58 59 2.290641 ACCATCACATAGCGGTTTCCAA 60.291 45.455 0.00 0.00 0.00 3.53
59 60 2.951642 CCATCACATAGCGGTTTCCAAT 59.048 45.455 0.00 0.00 0.00 3.16
60 61 3.243168 CCATCACATAGCGGTTTCCAATG 60.243 47.826 0.00 0.00 0.00 2.82
61 62 1.742831 TCACATAGCGGTTTCCAATGC 59.257 47.619 0.00 0.00 0.00 3.56
62 63 1.472082 CACATAGCGGTTTCCAATGCA 59.528 47.619 0.00 0.00 0.00 3.96
63 64 2.099592 CACATAGCGGTTTCCAATGCAT 59.900 45.455 0.00 0.00 0.00 3.96
64 65 3.314913 CACATAGCGGTTTCCAATGCATA 59.685 43.478 0.00 0.00 0.00 3.14
65 66 3.951037 ACATAGCGGTTTCCAATGCATAA 59.049 39.130 0.00 0.00 0.00 1.90
66 67 4.584325 ACATAGCGGTTTCCAATGCATAAT 59.416 37.500 0.00 0.00 0.00 1.28
67 68 3.441496 AGCGGTTTCCAATGCATAATG 57.559 42.857 0.00 0.00 0.00 1.90
68 69 3.023119 AGCGGTTTCCAATGCATAATGA 58.977 40.909 0.00 0.00 0.00 2.57
69 70 3.067180 AGCGGTTTCCAATGCATAATGAG 59.933 43.478 0.00 0.00 0.00 2.90
70 71 3.181487 GCGGTTTCCAATGCATAATGAGT 60.181 43.478 0.00 0.00 0.00 3.41
71 72 4.601019 CGGTTTCCAATGCATAATGAGTC 58.399 43.478 0.00 0.00 0.00 3.36
72 73 4.336433 CGGTTTCCAATGCATAATGAGTCT 59.664 41.667 0.00 0.00 0.00 3.24
73 74 5.527214 CGGTTTCCAATGCATAATGAGTCTA 59.473 40.000 0.00 0.00 0.00 2.59
74 75 6.511767 CGGTTTCCAATGCATAATGAGTCTAC 60.512 42.308 0.00 0.00 0.00 2.59
75 76 6.318648 GGTTTCCAATGCATAATGAGTCTACA 59.681 38.462 0.00 0.00 0.00 2.74
76 77 7.148086 GGTTTCCAATGCATAATGAGTCTACAA 60.148 37.037 0.00 0.00 0.00 2.41
77 78 7.936496 TTCCAATGCATAATGAGTCTACAAA 57.064 32.000 0.00 0.00 0.00 2.83
78 79 7.558161 TCCAATGCATAATGAGTCTACAAAG 57.442 36.000 0.00 0.00 0.00 2.77
79 80 7.112122 TCCAATGCATAATGAGTCTACAAAGT 58.888 34.615 0.00 0.00 0.00 2.66
80 81 8.264347 TCCAATGCATAATGAGTCTACAAAGTA 58.736 33.333 0.00 0.00 0.00 2.24
81 82 8.892723 CCAATGCATAATGAGTCTACAAAGTAA 58.107 33.333 0.00 0.00 0.00 2.24
92 93 9.162764 TGAGTCTACAAAGTAATAAATGAAGGC 57.837 33.333 0.00 0.00 0.00 4.35
93 94 9.162764 GAGTCTACAAAGTAATAAATGAAGGCA 57.837 33.333 0.00 0.00 0.00 4.75
94 95 9.515226 AGTCTACAAAGTAATAAATGAAGGCAA 57.485 29.630 0.00 0.00 0.00 4.52
95 96 9.556030 GTCTACAAAGTAATAAATGAAGGCAAC 57.444 33.333 0.00 0.00 0.00 4.17
110 111 3.067684 GGCAACTATGTTACCACACCT 57.932 47.619 0.00 0.00 35.03 4.00
111 112 4.210724 GGCAACTATGTTACCACACCTA 57.789 45.455 0.00 0.00 35.03 3.08
112 113 4.777463 GGCAACTATGTTACCACACCTAT 58.223 43.478 0.00 0.00 35.03 2.57
113 114 4.574828 GGCAACTATGTTACCACACCTATG 59.425 45.833 0.00 0.00 35.03 2.23
114 115 5.424757 GCAACTATGTTACCACACCTATGA 58.575 41.667 0.00 0.00 35.03 2.15
115 116 5.293569 GCAACTATGTTACCACACCTATGAC 59.706 44.000 0.00 0.00 35.03 3.06
116 117 6.403049 CAACTATGTTACCACACCTATGACA 58.597 40.000 0.00 0.00 35.03 3.58
117 118 5.974108 ACTATGTTACCACACCTATGACAC 58.026 41.667 0.00 0.00 35.03 3.67
118 119 5.720041 ACTATGTTACCACACCTATGACACT 59.280 40.000 0.00 0.00 35.03 3.55
119 120 6.893554 ACTATGTTACCACACCTATGACACTA 59.106 38.462 0.00 0.00 35.03 2.74
120 121 5.395682 TGTTACCACACCTATGACACTAC 57.604 43.478 0.00 0.00 0.00 2.73
121 122 4.221262 TGTTACCACACCTATGACACTACC 59.779 45.833 0.00 0.00 0.00 3.18
122 123 2.185387 ACCACACCTATGACACTACCC 58.815 52.381 0.00 0.00 0.00 3.69
123 124 2.184533 CCACACCTATGACACTACCCA 58.815 52.381 0.00 0.00 0.00 4.51
124 125 2.093658 CCACACCTATGACACTACCCAC 60.094 54.545 0.00 0.00 0.00 4.61
125 126 2.832129 CACACCTATGACACTACCCACT 59.168 50.000 0.00 0.00 0.00 4.00
126 127 4.021229 CACACCTATGACACTACCCACTA 58.979 47.826 0.00 0.00 0.00 2.74
127 128 4.649674 CACACCTATGACACTACCCACTAT 59.350 45.833 0.00 0.00 0.00 2.12
128 129 4.649674 ACACCTATGACACTACCCACTATG 59.350 45.833 0.00 0.00 0.00 2.23
129 130 4.893524 CACCTATGACACTACCCACTATGA 59.106 45.833 0.00 0.00 0.00 2.15
130 131 5.362717 CACCTATGACACTACCCACTATGAA 59.637 44.000 0.00 0.00 0.00 2.57
131 132 5.598830 ACCTATGACACTACCCACTATGAAG 59.401 44.000 0.00 0.00 0.00 3.02
132 133 5.011125 CCTATGACACTACCCACTATGAAGG 59.989 48.000 0.00 0.00 0.00 3.46
133 134 3.786553 TGACACTACCCACTATGAAGGT 58.213 45.455 0.00 0.00 37.69 3.50
134 135 4.938028 TGACACTACCCACTATGAAGGTA 58.062 43.478 0.00 0.00 35.02 3.08
135 136 5.335261 TGACACTACCCACTATGAAGGTAA 58.665 41.667 0.00 0.00 35.76 2.85
136 137 5.962031 TGACACTACCCACTATGAAGGTAAT 59.038 40.000 0.00 0.00 35.76 1.89
137 138 7.127405 TGACACTACCCACTATGAAGGTAATA 58.873 38.462 0.00 0.00 35.76 0.98
138 139 7.620491 TGACACTACCCACTATGAAGGTAATAA 59.380 37.037 0.00 0.00 35.76 1.40
139 140 8.562949 ACACTACCCACTATGAAGGTAATAAT 57.437 34.615 0.00 0.00 35.76 1.28
140 141 9.664777 ACACTACCCACTATGAAGGTAATAATA 57.335 33.333 0.00 0.00 35.76 0.98
182 183 9.790344 TGTATGATACTAGTCTAAGTTACTCCC 57.210 37.037 0.00 0.00 0.00 4.30
183 184 9.230122 GTATGATACTAGTCTAAGTTACTCCCC 57.770 40.741 0.00 0.00 0.00 4.81
184 185 7.217028 TGATACTAGTCTAAGTTACTCCCCA 57.783 40.000 0.00 0.00 0.00 4.96
185 186 7.059156 TGATACTAGTCTAAGTTACTCCCCAC 58.941 42.308 0.00 0.00 0.00 4.61
186 187 5.533333 ACTAGTCTAAGTTACTCCCCACT 57.467 43.478 0.00 0.00 0.00 4.00
187 188 6.649041 ACTAGTCTAAGTTACTCCCCACTA 57.351 41.667 0.00 0.00 0.00 2.74
188 189 7.223472 ACTAGTCTAAGTTACTCCCCACTAT 57.777 40.000 0.00 0.00 0.00 2.12
189 190 7.061688 ACTAGTCTAAGTTACTCCCCACTATG 58.938 42.308 0.00 0.00 0.00 2.23
190 191 6.088541 AGTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
191 192 5.892686 AGTCTAAGTTACTCCCCACTATGAC 59.107 44.000 0.00 0.00 0.00 3.06
192 193 5.068855 GTCTAAGTTACTCCCCACTATGACC 59.931 48.000 0.00 0.00 0.00 4.02
193 194 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
194 195 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
195 196 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
196 197 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
197 198 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
198 199 0.982852 TCCCCACTATGACCAGCCTG 60.983 60.000 0.00 0.00 0.00 4.85
199 200 0.982852 CCCCACTATGACCAGCCTGA 60.983 60.000 0.00 0.00 0.00 3.86
200 201 0.179000 CCCACTATGACCAGCCTGAC 59.821 60.000 0.00 0.00 0.00 3.51
201 202 0.179000 CCACTATGACCAGCCTGACC 59.821 60.000 0.00 0.00 0.00 4.02
202 203 0.904649 CACTATGACCAGCCTGACCA 59.095 55.000 0.00 0.00 0.00 4.02
203 204 1.134580 CACTATGACCAGCCTGACCAG 60.135 57.143 0.00 0.00 0.00 4.00
204 205 0.179062 CTATGACCAGCCTGACCAGC 60.179 60.000 0.00 0.00 0.00 4.85
205 206 1.626356 TATGACCAGCCTGACCAGCC 61.626 60.000 0.00 0.00 0.00 4.85
206 207 3.325753 GACCAGCCTGACCAGCCT 61.326 66.667 0.00 0.00 0.00 4.58
207 208 3.618780 GACCAGCCTGACCAGCCTG 62.619 68.421 0.00 1.39 0.00 4.85
208 209 3.324930 CCAGCCTGACCAGCCTGA 61.325 66.667 9.29 0.00 0.00 3.86
209 210 2.268280 CAGCCTGACCAGCCTGAG 59.732 66.667 2.14 0.00 0.00 3.35
210 211 3.715097 AGCCTGACCAGCCTGAGC 61.715 66.667 0.00 0.00 40.32 4.26
211 212 4.792804 GCCTGACCAGCCTGAGCC 62.793 72.222 0.00 0.00 41.25 4.70
212 213 3.324930 CCTGACCAGCCTGAGCCA 61.325 66.667 0.00 0.00 41.25 4.75
213 214 2.268280 CTGACCAGCCTGAGCCAG 59.732 66.667 0.00 0.00 41.25 4.85
214 215 2.203832 TGACCAGCCTGAGCCAGA 60.204 61.111 0.00 0.00 41.25 3.86
271 276 2.262603 CAGGCGCTCACTGCACTA 59.737 61.111 7.64 0.00 43.06 2.74
276 281 0.440371 GCGCTCACTGCACTAGTTTC 59.560 55.000 0.00 0.00 43.06 2.78
300 344 3.695830 TTAGGTTTAGGTCAGTGCCTG 57.304 47.619 14.24 0.00 39.60 4.85
367 416 1.547372 GAGTGGGTTCAGCTACCGTTA 59.453 52.381 0.00 0.00 39.18 3.18
369 418 2.071540 GTGGGTTCAGCTACCGTTAAC 58.928 52.381 0.00 0.00 39.18 2.01
370 419 1.972795 TGGGTTCAGCTACCGTTAACT 59.027 47.619 3.71 0.00 39.18 2.24
419 471 4.337836 TGACATGGCGCACATAAAATGTAT 59.662 37.500 10.83 0.00 42.70 2.29
488 707 6.561737 TCTAGAACGATAGATTACAGCAGG 57.438 41.667 0.00 0.00 41.38 4.85
534 753 6.529829 GCAATTAATCGGAGCACAATTTGTAA 59.470 34.615 0.86 0.00 0.00 2.41
542 761 9.651913 ATCGGAGCACAATTTGTAAATAATTTT 57.348 25.926 0.86 0.00 0.00 1.82
623 842 9.950496 AGTCAGAATATACTTCAGAAATTGTGT 57.050 29.630 3.57 0.00 0.00 3.72
624 843 9.979270 GTCAGAATATACTTCAGAAATTGTGTG 57.021 33.333 3.57 0.00 0.00 3.82
635 854 2.831685 AATTGTGTGCAGACGAGGTA 57.168 45.000 10.08 0.00 0.00 3.08
636 855 2.080286 ATTGTGTGCAGACGAGGTAC 57.920 50.000 10.08 0.00 0.00 3.34
638 857 1.900245 TGTGTGCAGACGAGGTACTA 58.100 50.000 9.70 0.00 41.55 1.82
639 858 1.810755 TGTGTGCAGACGAGGTACTAG 59.189 52.381 9.70 0.00 41.55 2.57
648 867 1.872313 ACGAGGTACTAGTATGCGAGC 59.128 52.381 21.10 6.40 43.92 5.03
660 885 4.577246 GCGAGCTGAGCCTACCGG 62.577 72.222 0.00 0.00 0.00 5.28
678 903 1.740296 GGCTACGGTTCACACGCAT 60.740 57.895 0.00 0.00 34.00 4.73
810 1038 5.449553 CTGGCCTCTCTTTTATAAACCCAT 58.550 41.667 3.32 0.00 0.00 4.00
815 1047 5.758784 CCTCTCTTTTATAAACCCATCGGAC 59.241 44.000 0.00 0.00 0.00 4.79
824 1056 1.075970 CCCATCGGACAGAGAGGGA 60.076 63.158 9.44 0.00 45.83 4.20
848 1083 2.179018 CATTTGCACCCGCCGAAG 59.821 61.111 0.00 0.00 37.32 3.79
1089 1324 2.440430 TCCGAGGAGGAGAAGGCG 60.440 66.667 0.00 0.00 45.98 5.52
1134 1369 0.913451 ATGAGGAGGACAGCTTGGCT 60.913 55.000 0.00 0.00 40.77 4.75
1238 1473 4.111916 CAATCTTTCTGTTTGCGTGGTTT 58.888 39.130 0.00 0.00 0.00 3.27
1271 1506 4.373116 TGCGCCGGTTCCTGACTC 62.373 66.667 4.18 0.00 0.00 3.36
1274 1509 1.738099 CGCCGGTTCCTGACTCTTG 60.738 63.158 1.90 0.00 0.00 3.02
1280 1515 1.349357 GGTTCCTGACTCTTGGCTTCT 59.651 52.381 0.00 0.00 0.00 2.85
1679 1914 0.521291 GTTGCATGGCGCTCTTGTTA 59.479 50.000 7.64 0.00 43.06 2.41
1694 1929 3.380637 TCTTGTTATGCGTCTCCTACCTC 59.619 47.826 0.00 0.00 0.00 3.85
1736 1972 8.594881 AACATCTTTGTTTTGTGTTTGTGTTA 57.405 26.923 0.00 0.00 43.57 2.41
1743 1979 6.621613 TGTTTTGTGTTTGTGTTATGCAGTA 58.378 32.000 0.00 0.00 0.00 2.74
1912 2148 2.359602 AAGACGCAGCTGCAGCAT 60.360 55.556 38.24 21.51 45.16 3.79
2151 2387 4.881850 CGTTGGTGGCTAAATATTCTTCCT 59.118 41.667 0.00 0.00 0.00 3.36
2161 2397 7.309805 GGCTAAATATTCTTCCTGTTTGGTGTT 60.310 37.037 0.00 0.00 37.07 3.32
2290 2526 4.335315 GGCATCGTTCTTGATCATGGTAAA 59.665 41.667 8.60 0.00 0.00 2.01
2301 2537 6.505048 TGATCATGGTAAACATCTCATCCT 57.495 37.500 0.00 0.00 37.84 3.24
2308 2544 6.878317 TGGTAAACATCTCATCCTGAACTAG 58.122 40.000 0.00 0.00 0.00 2.57
2309 2545 5.755861 GGTAAACATCTCATCCTGAACTAGC 59.244 44.000 0.00 0.00 0.00 3.42
2312 2548 6.798427 AACATCTCATCCTGAACTAGCTTA 57.202 37.500 0.00 0.00 0.00 3.09
2315 2551 7.800092 ACATCTCATCCTGAACTAGCTTAATT 58.200 34.615 0.00 0.00 0.00 1.40
2358 2595 0.319383 CTGACAGCGAGCTCTGTTGT 60.319 55.000 21.13 21.13 46.40 3.32
2367 2604 0.604780 AGCTCTGTTGTTGCGCAGAT 60.605 50.000 11.31 0.00 40.45 2.90
2415 2652 3.895025 GCAAGCCAGAAGATGCGA 58.105 55.556 0.00 0.00 0.00 5.10
2472 2709 0.680061 GTTCGTGAACCCAGTCTCCT 59.320 55.000 1.21 0.00 35.36 3.69
2482 2719 1.599047 CAGTCTCCTGCCGGAACAT 59.401 57.895 5.05 0.00 39.29 2.71
2500 2737 4.735132 TCCGCGTTCTTGGCTCCG 62.735 66.667 4.92 0.00 0.00 4.63
2510 2747 2.888594 TCTTGGCTCCGTTTAATCTCG 58.111 47.619 0.00 0.00 0.00 4.04
2555 2792 7.817962 AGCAGTAATTTGTAGTAGGTTGTAGTG 59.182 37.037 0.00 0.00 0.00 2.74
2557 2794 8.092687 CAGTAATTTGTAGTAGGTTGTAGTGGT 58.907 37.037 0.00 0.00 0.00 4.16
2558 2795 8.309656 AGTAATTTGTAGTAGGTTGTAGTGGTC 58.690 37.037 0.00 0.00 0.00 4.02
2559 2796 6.675413 ATTTGTAGTAGGTTGTAGTGGTCA 57.325 37.500 0.00 0.00 0.00 4.02
2560 2797 6.675413 TTTGTAGTAGGTTGTAGTGGTCAT 57.325 37.500 0.00 0.00 0.00 3.06
2561 2798 7.779754 TTTGTAGTAGGTTGTAGTGGTCATA 57.220 36.000 0.00 0.00 0.00 2.15
2562 2799 7.966339 TTGTAGTAGGTTGTAGTGGTCATAT 57.034 36.000 0.00 0.00 0.00 1.78
2563 2800 7.578310 TGTAGTAGGTTGTAGTGGTCATATC 57.422 40.000 0.00 0.00 0.00 1.63
2587 2824 8.911918 TCCTAGTAATAGAAGTAGAAGAGCAG 57.088 38.462 0.00 0.00 0.00 4.24
2588 2825 8.496088 TCCTAGTAATAGAAGTAGAAGAGCAGT 58.504 37.037 0.00 0.00 0.00 4.40
2589 2826 9.781633 CCTAGTAATAGAAGTAGAAGAGCAGTA 57.218 37.037 0.00 0.00 0.00 2.74
2679 2920 0.467384 AGCGGTGGAGATGGATGAAG 59.533 55.000 0.00 0.00 0.00 3.02
2682 2923 2.680805 GCGGTGGAGATGGATGAAGAAA 60.681 50.000 0.00 0.00 0.00 2.52
2705 2952 8.779354 AAACAAGAAATCCATGTCTAGTAGTC 57.221 34.615 0.00 0.00 0.00 2.59
2718 2965 7.275888 TGTCTAGTAGTCGGTTTGTTAGAAA 57.724 36.000 0.00 0.00 0.00 2.52
2732 2979 6.642707 TTGTTAGAAACAATAAGTGGGGTG 57.357 37.500 1.21 0.00 45.79 4.61
2736 2983 3.826729 AGAAACAATAAGTGGGGTGCTTC 59.173 43.478 0.00 0.00 0.00 3.86
2742 2989 3.319198 GTGGGGTGCTTCCGGAGA 61.319 66.667 3.34 0.00 37.00 3.71
2784 3035 4.805719 TGTTTGTAGCAAGCGAGATGATAG 59.194 41.667 0.00 0.00 0.00 2.08
2785 3036 4.918810 TTGTAGCAAGCGAGATGATAGA 57.081 40.909 0.00 0.00 0.00 1.98
2786 3037 5.459536 TTGTAGCAAGCGAGATGATAGAT 57.540 39.130 0.00 0.00 0.00 1.98
2787 3038 4.802999 TGTAGCAAGCGAGATGATAGATG 58.197 43.478 0.00 0.00 0.00 2.90
2788 3039 4.520492 TGTAGCAAGCGAGATGATAGATGA 59.480 41.667 0.00 0.00 0.00 2.92
2789 3040 4.804868 AGCAAGCGAGATGATAGATGAT 57.195 40.909 0.00 0.00 0.00 2.45
2790 3041 5.911378 AGCAAGCGAGATGATAGATGATA 57.089 39.130 0.00 0.00 0.00 2.15
2791 3042 6.278172 AGCAAGCGAGATGATAGATGATAA 57.722 37.500 0.00 0.00 0.00 1.75
2792 3043 6.876155 AGCAAGCGAGATGATAGATGATAAT 58.124 36.000 0.00 0.00 0.00 1.28
2793 3044 6.757478 AGCAAGCGAGATGATAGATGATAATG 59.243 38.462 0.00 0.00 0.00 1.90
2794 3045 6.534436 GCAAGCGAGATGATAGATGATAATGT 59.466 38.462 0.00 0.00 0.00 2.71
2795 3046 7.064371 GCAAGCGAGATGATAGATGATAATGTT 59.936 37.037 0.00 0.00 0.00 2.71
2796 3047 8.381387 CAAGCGAGATGATAGATGATAATGTTG 58.619 37.037 0.00 0.00 0.00 3.33
2797 3048 7.040494 AGCGAGATGATAGATGATAATGTTGG 58.960 38.462 0.00 0.00 0.00 3.77
2798 3049 7.038048 GCGAGATGATAGATGATAATGTTGGA 58.962 38.462 0.00 0.00 0.00 3.53
2808 3059 8.585471 AGATGATAATGTTGGAAGTGAAATGT 57.415 30.769 0.00 0.00 0.00 2.71
2890 3149 2.985847 GCCGCTTTGCCAAGGAGT 60.986 61.111 0.00 0.00 0.00 3.85
2946 3208 1.372307 CCCCCTTTTGCAGCCTTTG 59.628 57.895 0.00 0.00 0.00 2.77
3001 3263 0.800012 TGAATAAGGGCGTTCGTTGC 59.200 50.000 0.00 0.00 0.00 4.17
3025 3296 7.594758 TGCTTATGACGAAAAAGAAAGGATTTG 59.405 33.333 0.00 0.00 39.27 2.32
3036 3307 9.571810 AAAAAGAAAGGATTTGTTGATTTTTGC 57.428 25.926 0.00 0.00 41.03 3.68
3069 3344 7.010552 AGCTAGTTGCAGTAGTATTTCATTTCG 59.989 37.037 0.00 0.00 45.94 3.46
3228 3507 7.993183 TCATATCTTAATCAAGGTGTTTCTCCC 59.007 37.037 0.00 0.00 32.22 4.30
3254 3533 0.325577 TGCATCTGAGGGGCACTAGA 60.326 55.000 0.00 0.00 31.58 2.43
3287 3567 1.375396 GGGTGTCATGTGTGCGCTA 60.375 57.895 9.73 0.00 0.00 4.26
3294 3574 1.012086 CATGTGTGCGCTATGCTTCT 58.988 50.000 9.73 0.00 46.63 2.85
3386 3691 3.390183 AATCTGCATCTCCGCGCCA 62.390 57.895 0.00 0.00 33.35 5.69
3399 3704 2.539338 GCGCCACCGTCTGAAAACA 61.539 57.895 0.00 0.00 36.67 2.83
3450 3756 4.052229 CTTGCTCGGACGGACGGT 62.052 66.667 0.00 0.00 0.00 4.83
3458 3764 2.408022 GACGGACGGTCGATCCAG 59.592 66.667 1.43 0.33 35.83 3.86
3459 3765 3.753070 GACGGACGGTCGATCCAGC 62.753 68.421 1.43 0.00 35.83 4.85
3460 3766 4.907034 CGGACGGTCGATCCAGCG 62.907 72.222 10.42 10.42 42.99 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.968080 ACTCTATTTGCCTCTCTCCTCATT 59.032 41.667 0.00 0.00 0.00 2.57
1 2 4.555689 ACTCTATTTGCCTCTCTCCTCAT 58.444 43.478 0.00 0.00 0.00 2.90
2 3 3.987745 ACTCTATTTGCCTCTCTCCTCA 58.012 45.455 0.00 0.00 0.00 3.86
3 4 5.361285 TGTTACTCTATTTGCCTCTCTCCTC 59.639 44.000 0.00 0.00 0.00 3.71
4 5 5.273208 TGTTACTCTATTTGCCTCTCTCCT 58.727 41.667 0.00 0.00 0.00 3.69
5 6 5.599999 TGTTACTCTATTTGCCTCTCTCC 57.400 43.478 0.00 0.00 0.00 3.71
34 35 3.311596 GGAAACCGCTATGTGATGGTAAC 59.688 47.826 0.00 0.00 33.45 2.50
35 36 3.055021 TGGAAACCGCTATGTGATGGTAA 60.055 43.478 0.00 0.00 33.45 2.85
36 37 2.502130 TGGAAACCGCTATGTGATGGTA 59.498 45.455 0.00 0.00 33.45 3.25
37 38 1.280710 TGGAAACCGCTATGTGATGGT 59.719 47.619 0.00 0.00 35.90 3.55
38 39 2.036958 TGGAAACCGCTATGTGATGG 57.963 50.000 0.00 0.00 0.00 3.51
39 40 3.793129 GCATTGGAAACCGCTATGTGATG 60.793 47.826 0.00 0.00 0.00 3.07
40 41 2.358898 GCATTGGAAACCGCTATGTGAT 59.641 45.455 0.00 0.00 0.00 3.06
41 42 1.742831 GCATTGGAAACCGCTATGTGA 59.257 47.619 0.00 0.00 0.00 3.58
42 43 1.472082 TGCATTGGAAACCGCTATGTG 59.528 47.619 0.00 0.00 0.00 3.21
43 44 1.832883 TGCATTGGAAACCGCTATGT 58.167 45.000 0.00 0.00 0.00 2.29
44 45 4.566545 TTATGCATTGGAAACCGCTATG 57.433 40.909 3.54 0.00 0.00 2.23
45 46 4.826733 TCATTATGCATTGGAAACCGCTAT 59.173 37.500 3.54 0.00 0.00 2.97
46 47 4.203226 TCATTATGCATTGGAAACCGCTA 58.797 39.130 3.54 0.00 0.00 4.26
47 48 3.023119 TCATTATGCATTGGAAACCGCT 58.977 40.909 3.54 0.00 0.00 5.52
48 49 3.181487 ACTCATTATGCATTGGAAACCGC 60.181 43.478 3.54 0.00 0.00 5.68
49 50 4.336433 AGACTCATTATGCATTGGAAACCG 59.664 41.667 3.54 0.00 0.00 4.44
50 51 5.841957 AGACTCATTATGCATTGGAAACC 57.158 39.130 3.54 0.00 0.00 3.27
51 52 7.320443 TGTAGACTCATTATGCATTGGAAAC 57.680 36.000 3.54 0.00 0.00 2.78
52 53 7.936496 TTGTAGACTCATTATGCATTGGAAA 57.064 32.000 3.54 0.00 0.00 3.13
53 54 7.611467 ACTTTGTAGACTCATTATGCATTGGAA 59.389 33.333 3.54 0.00 0.00 3.53
54 55 7.112122 ACTTTGTAGACTCATTATGCATTGGA 58.888 34.615 3.54 0.00 0.00 3.53
55 56 7.325660 ACTTTGTAGACTCATTATGCATTGG 57.674 36.000 3.54 0.00 0.00 3.16
66 67 9.162764 GCCTTCATTTATTACTTTGTAGACTCA 57.837 33.333 0.00 0.00 0.00 3.41
67 68 9.162764 TGCCTTCATTTATTACTTTGTAGACTC 57.837 33.333 0.00 0.00 0.00 3.36
68 69 9.515226 TTGCCTTCATTTATTACTTTGTAGACT 57.485 29.630 0.00 0.00 0.00 3.24
69 70 9.556030 GTTGCCTTCATTTATTACTTTGTAGAC 57.444 33.333 0.00 0.00 0.00 2.59
70 71 9.515226 AGTTGCCTTCATTTATTACTTTGTAGA 57.485 29.630 0.00 0.00 0.00 2.59
78 79 9.946165 GGTAACATAGTTGCCTTCATTTATTAC 57.054 33.333 9.36 0.00 0.00 1.89
79 80 9.688091 TGGTAACATAGTTGCCTTCATTTATTA 57.312 29.630 16.08 0.00 46.17 0.98
80 81 8.588290 TGGTAACATAGTTGCCTTCATTTATT 57.412 30.769 16.08 0.00 46.17 1.40
99 100 4.382362 GGGTAGTGTCATAGGTGTGGTAAC 60.382 50.000 0.00 0.00 0.00 2.50
100 101 3.770933 GGGTAGTGTCATAGGTGTGGTAA 59.229 47.826 0.00 0.00 0.00 2.85
101 102 3.245694 TGGGTAGTGTCATAGGTGTGGTA 60.246 47.826 0.00 0.00 0.00 3.25
102 103 2.185387 GGGTAGTGTCATAGGTGTGGT 58.815 52.381 0.00 0.00 0.00 4.16
103 104 2.093658 GTGGGTAGTGTCATAGGTGTGG 60.094 54.545 0.00 0.00 0.00 4.17
104 105 2.832129 AGTGGGTAGTGTCATAGGTGTG 59.168 50.000 0.00 0.00 0.00 3.82
105 106 3.185880 AGTGGGTAGTGTCATAGGTGT 57.814 47.619 0.00 0.00 0.00 4.16
106 107 4.893524 TCATAGTGGGTAGTGTCATAGGTG 59.106 45.833 0.00 0.00 0.00 4.00
107 108 5.138758 TCATAGTGGGTAGTGTCATAGGT 57.861 43.478 0.00 0.00 0.00 3.08
108 109 5.011125 CCTTCATAGTGGGTAGTGTCATAGG 59.989 48.000 0.00 0.00 0.00 2.57
109 110 5.598830 ACCTTCATAGTGGGTAGTGTCATAG 59.401 44.000 0.00 0.00 0.00 2.23
110 111 5.525484 ACCTTCATAGTGGGTAGTGTCATA 58.475 41.667 0.00 0.00 0.00 2.15
111 112 4.362677 ACCTTCATAGTGGGTAGTGTCAT 58.637 43.478 0.00 0.00 0.00 3.06
112 113 3.786553 ACCTTCATAGTGGGTAGTGTCA 58.213 45.455 0.00 0.00 0.00 3.58
113 114 5.927281 TTACCTTCATAGTGGGTAGTGTC 57.073 43.478 0.00 0.00 37.00 3.67
114 115 7.983166 TTATTACCTTCATAGTGGGTAGTGT 57.017 36.000 0.00 0.00 37.00 3.55
156 157 9.790344 GGGAGTAACTTAGACTAGTATCATACA 57.210 37.037 0.00 0.00 0.00 2.29
157 158 9.230122 GGGGAGTAACTTAGACTAGTATCATAC 57.770 40.741 0.00 0.00 0.00 2.39
158 159 8.952602 TGGGGAGTAACTTAGACTAGTATCATA 58.047 37.037 0.00 0.00 0.00 2.15
159 160 7.724951 GTGGGGAGTAACTTAGACTAGTATCAT 59.275 40.741 0.00 0.00 0.00 2.45
160 161 7.059156 GTGGGGAGTAACTTAGACTAGTATCA 58.941 42.308 0.00 0.00 0.00 2.15
161 162 7.289310 AGTGGGGAGTAACTTAGACTAGTATC 58.711 42.308 0.00 0.00 0.00 2.24
162 163 7.223472 AGTGGGGAGTAACTTAGACTAGTAT 57.777 40.000 0.00 0.00 0.00 2.12
163 164 6.649041 AGTGGGGAGTAACTTAGACTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
164 165 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
165 166 7.229106 GTCATAGTGGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 31.58 2.57
166 167 7.059156 GTCATAGTGGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 31.58 2.59
167 168 5.892686 GTCATAGTGGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 31.58 3.24
168 169 5.068855 GGTCATAGTGGGGAGTAACTTAGAC 59.931 48.000 0.00 0.00 32.58 2.59
169 170 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
170 171 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
171 172 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
172 173 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
173 174 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
174 175 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
175 176 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
176 177 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
177 178 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
178 179 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
179 180 0.982852 CAGGCTGGTCATAGTGGGGA 60.983 60.000 6.61 0.00 0.00 4.81
180 181 0.982852 TCAGGCTGGTCATAGTGGGG 60.983 60.000 15.73 0.00 0.00 4.96
181 182 0.179000 GTCAGGCTGGTCATAGTGGG 59.821 60.000 15.73 0.00 0.00 4.61
182 183 0.179000 GGTCAGGCTGGTCATAGTGG 59.821 60.000 15.73 0.00 0.00 4.00
183 184 0.904649 TGGTCAGGCTGGTCATAGTG 59.095 55.000 15.73 0.00 0.00 2.74
184 185 1.198713 CTGGTCAGGCTGGTCATAGT 58.801 55.000 15.73 0.00 0.00 2.12
185 186 0.179062 GCTGGTCAGGCTGGTCATAG 60.179 60.000 15.73 10.97 0.00 2.23
186 187 1.907739 GCTGGTCAGGCTGGTCATA 59.092 57.895 15.73 0.00 0.00 2.15
187 188 2.673523 GCTGGTCAGGCTGGTCAT 59.326 61.111 15.73 0.00 0.00 3.06
195 196 3.324930 TGGCTCAGGCTGGTCAGG 61.325 66.667 15.73 1.69 38.73 3.86
196 197 2.241479 CTCTGGCTCAGGCTGGTCAG 62.241 65.000 23.32 23.32 38.73 3.51
197 198 2.203832 TCTGGCTCAGGCTGGTCA 60.204 61.111 15.73 12.02 38.73 4.02
198 199 2.583520 CTCTGGCTCAGGCTGGTC 59.416 66.667 15.73 7.65 38.73 4.02
199 200 3.715097 GCTCTGGCTCAGGCTGGT 61.715 66.667 15.73 0.00 38.73 4.00
200 201 3.683966 CTGCTCTGGCTCAGGCTGG 62.684 68.421 15.73 6.64 39.59 4.85
201 202 2.125065 CTGCTCTGGCTCAGGCTG 60.125 66.667 8.58 8.58 39.59 4.85
202 203 2.284478 TCTGCTCTGGCTCAGGCT 60.284 61.111 0.00 0.00 39.59 4.58
203 204 2.187424 CTCTGCTCTGGCTCAGGC 59.813 66.667 0.00 0.00 39.59 4.85
204 205 2.187424 GCTCTGCTCTGGCTCAGG 59.813 66.667 2.86 0.00 39.59 3.86
205 206 1.153529 CTGCTCTGCTCTGGCTCAG 60.154 63.158 0.00 0.00 39.59 3.35
206 207 1.478526 AACTGCTCTGCTCTGGCTCA 61.479 55.000 0.00 0.00 39.59 4.26
207 208 1.020333 CAACTGCTCTGCTCTGGCTC 61.020 60.000 0.00 0.00 39.59 4.70
208 209 1.003597 CAACTGCTCTGCTCTGGCT 60.004 57.895 0.00 0.00 39.59 4.75
209 210 2.688794 GCAACTGCTCTGCTCTGGC 61.689 63.158 0.00 0.00 36.84 4.85
210 211 1.302271 TGCAACTGCTCTGCTCTGG 60.302 57.895 2.95 0.00 42.66 3.86
211 212 1.867615 GTGCAACTGCTCTGCTCTG 59.132 57.895 2.95 0.00 42.66 3.35
212 213 4.375569 GTGCAACTGCTCTGCTCT 57.624 55.556 2.95 0.00 42.66 4.09
271 276 5.163269 ACTGACCTAAACCTAAACCGAAACT 60.163 40.000 0.00 0.00 0.00 2.66
276 281 2.740447 GCACTGACCTAAACCTAAACCG 59.260 50.000 0.00 0.00 0.00 4.44
300 344 4.505313 AGGCAAATTTTCTTCCTTCGTC 57.495 40.909 0.00 0.00 0.00 4.20
307 351 2.736721 GCGGGAAAGGCAAATTTTCTTC 59.263 45.455 4.57 0.00 35.42 2.87
367 416 1.909302 CCACCCACTCACCAGATAGTT 59.091 52.381 0.00 0.00 0.00 2.24
369 418 1.866015 TCCACCCACTCACCAGATAG 58.134 55.000 0.00 0.00 0.00 2.08
370 419 2.335681 TTCCACCCACTCACCAGATA 57.664 50.000 0.00 0.00 0.00 1.98
459 511 8.673711 GCTGTAATCTATCGTTCTAGATCTGAT 58.326 37.037 5.18 1.48 37.45 2.90
460 512 7.661847 TGCTGTAATCTATCGTTCTAGATCTGA 59.338 37.037 5.18 0.00 37.45 3.27
461 513 7.811653 TGCTGTAATCTATCGTTCTAGATCTG 58.188 38.462 5.18 0.00 37.45 2.90
463 515 7.247728 CCTGCTGTAATCTATCGTTCTAGATC 58.752 42.308 0.00 0.00 37.45 2.75
464 516 6.349777 GCCTGCTGTAATCTATCGTTCTAGAT 60.350 42.308 0.00 0.00 39.59 1.98
466 518 5.157781 GCCTGCTGTAATCTATCGTTCTAG 58.842 45.833 0.00 0.00 0.00 2.43
547 766 6.814644 CCGAACTTTTTCTTTTACCCACTTTT 59.185 34.615 0.00 0.00 0.00 2.27
550 769 5.195185 TCCGAACTTTTTCTTTTACCCACT 58.805 37.500 0.00 0.00 0.00 4.00
551 770 5.503662 TCCGAACTTTTTCTTTTACCCAC 57.496 39.130 0.00 0.00 0.00 4.61
552 771 4.037089 GCTCCGAACTTTTTCTTTTACCCA 59.963 41.667 0.00 0.00 0.00 4.51
553 772 4.037089 TGCTCCGAACTTTTTCTTTTACCC 59.963 41.667 0.00 0.00 0.00 3.69
554 773 4.974275 GTGCTCCGAACTTTTTCTTTTACC 59.026 41.667 0.00 0.00 0.00 2.85
601 820 8.565896 TGCACACAATTTCTGAAGTATATTCT 57.434 30.769 0.00 0.00 0.00 2.40
623 842 2.617308 GCATACTAGTACCTCGTCTGCA 59.383 50.000 14.54 0.00 32.47 4.41
624 843 2.349627 CGCATACTAGTACCTCGTCTGC 60.350 54.545 4.31 8.40 30.19 4.26
635 854 0.671251 GGCTCAGCTCGCATACTAGT 59.329 55.000 0.00 0.00 0.00 2.57
636 855 0.958091 AGGCTCAGCTCGCATACTAG 59.042 55.000 0.00 0.00 0.00 2.57
637 856 1.880675 GTAGGCTCAGCTCGCATACTA 59.119 52.381 17.40 4.32 40.38 1.82
638 857 0.671251 GTAGGCTCAGCTCGCATACT 59.329 55.000 17.40 5.09 40.38 2.12
639 858 0.319125 GGTAGGCTCAGCTCGCATAC 60.319 60.000 16.74 16.74 42.15 2.39
640 859 1.796190 CGGTAGGCTCAGCTCGCATA 61.796 60.000 0.00 1.27 0.00 3.14
660 885 1.693083 GATGCGTGTGAACCGTAGCC 61.693 60.000 0.00 0.00 0.00 3.93
678 903 2.340078 GAGCTGTGCCTGTGACGA 59.660 61.111 0.00 0.00 0.00 4.20
810 1038 1.077357 GCTCTCCCTCTCTGTCCGA 60.077 63.158 0.00 0.00 0.00 4.55
815 1047 0.831966 AATGCTGCTCTCCCTCTCTG 59.168 55.000 0.00 0.00 0.00 3.35
842 1074 1.776034 GAATGTCGATGGGCTTCGGC 61.776 60.000 7.80 7.80 43.79 5.54
844 1076 1.160329 GGGAATGTCGATGGGCTTCG 61.160 60.000 0.00 4.39 40.46 3.79
848 1083 1.227973 GAGGGGAATGTCGATGGGC 60.228 63.158 0.00 0.00 0.00 5.36
964 1199 0.765510 AATCCTAGTCCGGGCAATCC 59.234 55.000 9.71 0.00 0.00 3.01
977 1212 3.181329 TGCTCCACCTTGAAGAATCCTA 58.819 45.455 0.00 0.00 0.00 2.94
979 1214 2.496899 TGCTCCACCTTGAAGAATCC 57.503 50.000 0.00 0.00 0.00 3.01
1038 1273 2.296471 GTCCAAGAACTCGTCAGGAAGA 59.704 50.000 0.00 0.00 35.28 2.87
1044 1279 0.040692 CGTCGTCCAAGAACTCGTCA 60.041 55.000 0.00 0.00 0.00 4.35
1170 1405 1.947146 CGTGACGGCGAGTTTGTCA 60.947 57.895 16.62 1.90 40.12 3.58
1238 1473 2.197792 CGCAGGTACTACGCATAACA 57.802 50.000 0.00 0.00 38.82 2.41
1269 1504 2.101249 TGCCAAACAAAGAAGCCAAGAG 59.899 45.455 0.00 0.00 0.00 2.85
1271 1506 2.476821 CTGCCAAACAAAGAAGCCAAG 58.523 47.619 0.00 0.00 0.00 3.61
1274 1509 1.000171 CTCCTGCCAAACAAAGAAGCC 60.000 52.381 0.00 0.00 0.00 4.35
1280 1515 0.555769 ACCTCCTCCTGCCAAACAAA 59.444 50.000 0.00 0.00 0.00 2.83
1447 1682 4.335647 CTGTTGACCAGCCCGGCT 62.336 66.667 5.94 5.94 40.77 5.52
1455 1690 2.350895 CCGGGATGCTGTTGACCA 59.649 61.111 0.00 0.00 0.00 4.02
1679 1914 2.145397 TCTTGAGGTAGGAGACGCAT 57.855 50.000 0.00 0.00 0.00 4.73
1718 1954 5.928839 ACTGCATAACACAAACACAAAACAA 59.071 32.000 0.00 0.00 0.00 2.83
1721 1957 7.484140 TGATACTGCATAACACAAACACAAAA 58.516 30.769 0.00 0.00 0.00 2.44
1736 1972 5.363562 TGTTTGAGGAGATGATACTGCAT 57.636 39.130 0.00 0.00 0.00 3.96
1743 1979 2.026542 TGCTGCTGTTTGAGGAGATGAT 60.027 45.455 0.00 0.00 42.77 2.45
1846 2082 4.235762 TCAATAGGAGCGGCGCCC 62.236 66.667 30.40 27.53 0.00 6.13
1892 2128 2.610694 GCTGCAGCTGCGTCTTCAA 61.611 57.895 32.11 13.14 45.83 2.69
2151 2387 1.199327 TGACGCGAAAAACACCAAACA 59.801 42.857 15.93 0.00 0.00 2.83
2161 2397 1.081509 GCCTGCAATGACGCGAAAA 60.082 52.632 15.93 0.00 33.35 2.29
2308 2544 9.150348 ACTTGCCATTAATTAACACAATTAAGC 57.850 29.630 0.00 7.24 36.08 3.09
2315 2551 9.853555 CAGATTAACTTGCCATTAATTAACACA 57.146 29.630 0.00 0.00 33.39 3.72
2358 2595 0.677414 TGATCAAGGCATCTGCGCAA 60.677 50.000 13.05 2.72 43.26 4.85
2367 2604 1.219124 GCTCCGACTGATCAAGGCA 59.781 57.895 0.00 0.00 30.58 4.75
2482 2719 2.358247 GGAGCCAAGAACGCGGAA 60.358 61.111 12.47 0.00 0.00 4.30
2487 2724 3.000727 AGATTAAACGGAGCCAAGAACG 58.999 45.455 0.00 0.00 0.00 3.95
2527 2764 6.765403 ACAACCTACTACAAATTACTGCTGA 58.235 36.000 0.00 0.00 0.00 4.26
2538 2775 7.069085 GGATATGACCACTACAACCTACTACAA 59.931 40.741 0.00 0.00 0.00 2.41
2543 2780 6.776603 ACTAGGATATGACCACTACAACCTAC 59.223 42.308 0.00 0.00 0.00 3.18
2561 2798 9.515226 CTGCTCTTCTACTTCTATTACTAGGAT 57.485 37.037 0.00 0.00 0.00 3.24
2562 2799 8.496088 ACTGCTCTTCTACTTCTATTACTAGGA 58.504 37.037 0.00 0.00 0.00 2.94
2563 2800 8.685838 ACTGCTCTTCTACTTCTATTACTAGG 57.314 38.462 0.00 0.00 0.00 3.02
2580 2817 2.166459 TGACGCTGCTAATACTGCTCTT 59.834 45.455 0.00 0.00 32.81 2.85
2583 2820 1.478510 ACTGACGCTGCTAATACTGCT 59.521 47.619 0.00 0.00 32.81 4.24
2584 2821 1.927895 ACTGACGCTGCTAATACTGC 58.072 50.000 0.00 0.00 0.00 4.40
2585 2822 4.928661 AAAACTGACGCTGCTAATACTG 57.071 40.909 0.00 0.00 0.00 2.74
2586 2823 4.567159 GCTAAAACTGACGCTGCTAATACT 59.433 41.667 0.00 0.00 0.00 2.12
2587 2824 4.328983 TGCTAAAACTGACGCTGCTAATAC 59.671 41.667 0.00 0.00 0.00 1.89
2588 2825 4.500127 TGCTAAAACTGACGCTGCTAATA 58.500 39.130 0.00 0.00 0.00 0.98
2589 2826 3.334691 TGCTAAAACTGACGCTGCTAAT 58.665 40.909 0.00 0.00 0.00 1.73
2590 2827 2.736721 CTGCTAAAACTGACGCTGCTAA 59.263 45.455 0.00 0.00 0.00 3.09
2594 2831 1.195448 CACCTGCTAAAACTGACGCTG 59.805 52.381 0.00 0.00 0.00 5.18
2679 2920 8.779354 ACTACTAGACATGGATTTCTTGTTTC 57.221 34.615 0.00 0.00 34.42 2.78
2682 2923 6.405953 CCGACTACTAGACATGGATTTCTTGT 60.406 42.308 0.00 0.64 36.59 3.16
2718 2965 1.613255 CGGAAGCACCCCACTTATTGT 60.613 52.381 0.00 0.00 34.64 2.71
2731 2978 1.002502 TCTCTCGTCTCCGGAAGCA 60.003 57.895 5.23 0.00 33.95 3.91
2732 2979 0.745128 TCTCTCTCGTCTCCGGAAGC 60.745 60.000 5.23 0.00 33.95 3.86
2736 2983 0.660488 CACATCTCTCTCGTCTCCGG 59.340 60.000 0.00 0.00 33.95 5.14
2742 2989 3.085533 ACAGCTAACACATCTCTCTCGT 58.914 45.455 0.00 0.00 0.00 4.18
2784 3035 7.703621 CCACATTTCACTTCCAACATTATCATC 59.296 37.037 0.00 0.00 0.00 2.92
2785 3036 7.549839 CCACATTTCACTTCCAACATTATCAT 58.450 34.615 0.00 0.00 0.00 2.45
2786 3037 6.572119 GCCACATTTCACTTCCAACATTATCA 60.572 38.462 0.00 0.00 0.00 2.15
2787 3038 5.807011 GCCACATTTCACTTCCAACATTATC 59.193 40.000 0.00 0.00 0.00 1.75
2788 3039 5.481473 AGCCACATTTCACTTCCAACATTAT 59.519 36.000 0.00 0.00 0.00 1.28
2789 3040 4.832266 AGCCACATTTCACTTCCAACATTA 59.168 37.500 0.00 0.00 0.00 1.90
2790 3041 3.642848 AGCCACATTTCACTTCCAACATT 59.357 39.130 0.00 0.00 0.00 2.71
2791 3042 3.233507 AGCCACATTTCACTTCCAACAT 58.766 40.909 0.00 0.00 0.00 2.71
2792 3043 2.665165 AGCCACATTTCACTTCCAACA 58.335 42.857 0.00 0.00 0.00 3.33
2793 3044 4.846779 TTAGCCACATTTCACTTCCAAC 57.153 40.909 0.00 0.00 0.00 3.77
2794 3045 5.324409 AGATTAGCCACATTTCACTTCCAA 58.676 37.500 0.00 0.00 0.00 3.53
2795 3046 4.922206 AGATTAGCCACATTTCACTTCCA 58.078 39.130 0.00 0.00 0.00 3.53
2796 3047 5.415701 TCAAGATTAGCCACATTTCACTTCC 59.584 40.000 0.00 0.00 0.00 3.46
2797 3048 6.500684 TCAAGATTAGCCACATTTCACTTC 57.499 37.500 0.00 0.00 0.00 3.01
2798 3049 6.071728 CCTTCAAGATTAGCCACATTTCACTT 60.072 38.462 0.00 0.00 0.00 3.16
2808 3059 2.840038 TCTGCTCCTTCAAGATTAGCCA 59.160 45.455 4.51 0.00 32.14 4.75
2890 3149 4.783621 GCTGGATGTGCGCTGGGA 62.784 66.667 9.73 0.00 0.00 4.37
2955 3217 3.442441 CCCACGGCAAAGCTTCAA 58.558 55.556 0.00 0.00 0.00 2.69
2977 3239 3.541632 ACGAACGCCCTTATTCATTCAT 58.458 40.909 0.00 0.00 0.00 2.57
2978 3240 2.980568 ACGAACGCCCTTATTCATTCA 58.019 42.857 0.00 0.00 0.00 2.57
2979 3241 3.680789 CAACGAACGCCCTTATTCATTC 58.319 45.455 0.00 0.00 0.00 2.67
2980 3242 2.159435 GCAACGAACGCCCTTATTCATT 60.159 45.455 0.00 0.00 0.00 2.57
3001 3263 9.463443 AACAAATCCTTTCTTTTTCGTCATAAG 57.537 29.630 0.00 0.00 0.00 1.73
3011 3277 8.959548 AGCAAAAATCAACAAATCCTTTCTTTT 58.040 25.926 0.00 0.00 0.00 2.27
3015 3281 7.250445 ACAGCAAAAATCAACAAATCCTTTC 57.750 32.000 0.00 0.00 0.00 2.62
3036 3307 9.751542 AAATACTACTGCAACTAGCTATTACAG 57.248 33.333 10.67 10.67 45.94 2.74
3052 3323 6.461698 GCAACGAACGAAATGAAATACTACTG 59.538 38.462 0.14 0.00 0.00 2.74
3069 3344 0.040781 TTGCCGCTAAAGCAACGAAC 60.041 50.000 2.44 0.00 44.95 3.95
3131 3409 7.649533 TTCCGAGGACAAGTACAATTCTATA 57.350 36.000 0.00 0.00 0.00 1.31
3228 3507 0.679002 CCCCTCAGATGCACACAAGG 60.679 60.000 0.00 0.00 0.00 3.61
3254 3533 5.687166 TGACACCCCGATTAAGATAAACT 57.313 39.130 0.00 0.00 0.00 2.66
3287 3567 2.749044 CCACAGCCGCAGAAGCAT 60.749 61.111 0.00 0.00 42.27 3.79
3386 3691 0.463116 AGGCGTTGTTTTCAGACGGT 60.463 50.000 0.00 0.00 36.05 4.83


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

AutoCloner maintained by Alex Coulton.