Multiple sequence alignment - TraesCS1B01G175800

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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 TraesCS1B01G175800 chr1B 100.000 3838 0 0 1 3838 317366123 317362286 0.000000e+00 7088.0
1 TraesCS1B01G175800 chr1D 96.047 2783 92 14 819 3597 220927637 220924869 0.000000e+00 4514.0
2 TraesCS1B01G175800 chr1D 92.734 578 23 9 247 824 220928236 220927678 0.000000e+00 817.0
3 TraesCS1B01G175800 chr1D 95.364 151 7 0 3593 3743 220924839 220924689 1.380000e-59 241.0
4 TraesCS1B01G175800 chr1D 95.238 42 1 1 51 91 24119388 24119347 8.900000e-07 65.8
5 TraesCS1B01G175800 chr1A 94.145 1298 62 7 819 2115 285355987 285354703 0.000000e+00 1964.0
6 TraesCS1B01G175800 chr1A 95.333 900 33 3 2151 3050 285354703 285353813 0.000000e+00 1421.0
7 TraesCS1B01G175800 chr1A 92.943 581 28 7 253 824 285356604 285356028 0.000000e+00 833.0
8 TraesCS1B01G175800 chr1A 93.233 399 24 3 3047 3443 285353733 285353336 5.530000e-163 584.0
9 TraesCS1B01G175800 chr1A 95.102 245 12 0 3593 3837 285340697 285340453 1.670000e-103 387.0
10 TraesCS1B01G175800 chr1A 96.667 60 1 1 3538 3597 285340785 285340727 8.770000e-17 99.0
11 TraesCS1B01G175800 chr1A 98.039 51 1 0 3440 3490 285352083 285352033 5.280000e-14 89.8
12 TraesCS1B01G175800 chr7B 95.652 46 2 0 56 101 657870405 657870360 1.480000e-09 75.0
13 TraesCS1B01G175800 chr7B 95.652 46 2 0 56 101 657870597 657870552 1.480000e-09 75.0
14 TraesCS1B01G175800 chr4B 95.349 43 2 0 57 99 376149767 376149809 6.880000e-08 69.4
15 TraesCS1B01G175800 chr5A 95.238 42 1 1 59 99 211618036 211617995 8.900000e-07 65.8
16 TraesCS1B01G175800 chr4A 88.889 54 3 3 54 107 34601648 34601698 3.200000e-06 63.9
17 TraesCS1B01G175800 chr3A 88.889 54 2 4 54 107 255509500 255509451 3.200000e-06 63.9
18 TraesCS1B01G175800 chr2A 88.889 54 2 4 54 107 732630069 732630118 3.200000e-06 63.9
19 TraesCS1B01G175800 chr5B 97.059 34 0 1 58 91 339492537 339492505 5.360000e-04 56.5


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 TraesCS1B01G175800 chr1B 317362286 317366123 3837 True 7088.000000 7088 100.0000 1 3838 1 chr1B.!!$R1 3837
1 TraesCS1B01G175800 chr1D 220924689 220928236 3547 True 1857.333333 4514 94.7150 247 3743 3 chr1D.!!$R2 3496
2 TraesCS1B01G175800 chr1A 285352033 285356604 4571 True 978.360000 1964 94.7386 253 3490 5 chr1A.!!$R2 3237

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
998 1056 0.106268 TCTGTTGGCCTGCCTTTGAA 60.106 50.0 9.97 0.0 36.94 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2893 2954 0.323302 TGCGTGGAACCAGCTAATCA 59.677 50.0 13.25 0.0 0.0 2.57 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
36 37 5.730296 TTTTTCTTTTCAACTCACCCACA 57.270 34.783 0.00 0.00 0.00 4.17
37 38 5.730296 TTTTCTTTTCAACTCACCCACAA 57.270 34.783 0.00 0.00 0.00 3.33
38 39 5.730296 TTTCTTTTCAACTCACCCACAAA 57.270 34.783 0.00 0.00 0.00 2.83
39 40 5.730296 TTCTTTTCAACTCACCCACAAAA 57.270 34.783 0.00 0.00 0.00 2.44
40 41 5.730296 TCTTTTCAACTCACCCACAAAAA 57.270 34.783 0.00 0.00 0.00 1.94
41 42 5.719173 TCTTTTCAACTCACCCACAAAAAG 58.281 37.500 0.00 0.00 34.92 2.27
42 43 5.478679 TCTTTTCAACTCACCCACAAAAAGA 59.521 36.000 0.00 0.00 38.33 2.52
43 44 5.730296 TTTCAACTCACCCACAAAAAGAA 57.270 34.783 0.00 0.00 0.00 2.52
44 45 4.981806 TCAACTCACCCACAAAAAGAAG 57.018 40.909 0.00 0.00 0.00 2.85
45 46 4.340617 TCAACTCACCCACAAAAAGAAGT 58.659 39.130 0.00 0.00 0.00 3.01
46 47 5.502079 TCAACTCACCCACAAAAAGAAGTA 58.498 37.500 0.00 0.00 0.00 2.24
47 48 5.355910 TCAACTCACCCACAAAAAGAAGTAC 59.644 40.000 0.00 0.00 0.00 2.73
48 49 5.112129 ACTCACCCACAAAAAGAAGTACT 57.888 39.130 0.00 0.00 0.00 2.73
49 50 6.243216 ACTCACCCACAAAAAGAAGTACTA 57.757 37.500 0.00 0.00 0.00 1.82
50 51 6.838382 ACTCACCCACAAAAAGAAGTACTAT 58.162 36.000 0.00 0.00 0.00 2.12
51 52 7.287810 ACTCACCCACAAAAAGAAGTACTATT 58.712 34.615 0.00 0.00 0.00 1.73
52 53 7.228706 ACTCACCCACAAAAAGAAGTACTATTG 59.771 37.037 0.00 0.12 34.14 1.90
53 54 7.284074 TCACCCACAAAAAGAAGTACTATTGA 58.716 34.615 0.00 0.00 33.04 2.57
54 55 7.776030 TCACCCACAAAAAGAAGTACTATTGAA 59.224 33.333 0.00 0.00 33.04 2.69
55 56 7.860872 CACCCACAAAAAGAAGTACTATTGAAC 59.139 37.037 0.00 0.00 33.04 3.18
56 57 7.778382 ACCCACAAAAAGAAGTACTATTGAACT 59.222 33.333 0.00 0.00 33.04 3.01
57 58 9.280174 CCCACAAAAAGAAGTACTATTGAACTA 57.720 33.333 0.00 0.00 33.04 2.24
84 85 8.848474 AAAATGTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
85 86 5.995565 TGTCTTATATTATGGGACGGAGG 57.004 43.478 0.00 0.00 0.00 4.30
86 87 5.647230 TGTCTTATATTATGGGACGGAGGA 58.353 41.667 0.00 0.00 0.00 3.71
87 88 6.079336 TGTCTTATATTATGGGACGGAGGAA 58.921 40.000 0.00 0.00 0.00 3.36
88 89 6.210784 TGTCTTATATTATGGGACGGAGGAAG 59.789 42.308 0.00 0.00 0.00 3.46
89 90 6.210984 GTCTTATATTATGGGACGGAGGAAGT 59.789 42.308 0.00 0.00 0.00 3.01
90 91 7.395489 GTCTTATATTATGGGACGGAGGAAGTA 59.605 40.741 0.00 0.00 0.00 2.24
91 92 8.120538 TCTTATATTATGGGACGGAGGAAGTAT 58.879 37.037 0.00 0.00 0.00 2.12
92 93 9.417561 CTTATATTATGGGACGGAGGAAGTATA 57.582 37.037 0.00 0.00 0.00 1.47
93 94 9.772605 TTATATTATGGGACGGAGGAAGTATAA 57.227 33.333 0.00 0.00 0.00 0.98
94 95 8.855804 ATATTATGGGACGGAGGAAGTATAAT 57.144 34.615 0.00 0.00 0.00 1.28
95 96 4.891992 ATGGGACGGAGGAAGTATAATG 57.108 45.455 0.00 0.00 0.00 1.90
96 97 3.649843 TGGGACGGAGGAAGTATAATGT 58.350 45.455 0.00 0.00 0.00 2.71
97 98 4.806892 TGGGACGGAGGAAGTATAATGTA 58.193 43.478 0.00 0.00 0.00 2.29
98 99 5.210430 TGGGACGGAGGAAGTATAATGTAA 58.790 41.667 0.00 0.00 0.00 2.41
99 100 5.842328 TGGGACGGAGGAAGTATAATGTAAT 59.158 40.000 0.00 0.00 0.00 1.89
100 101 7.011994 TGGGACGGAGGAAGTATAATGTAATA 58.988 38.462 0.00 0.00 0.00 0.98
101 102 7.676893 TGGGACGGAGGAAGTATAATGTAATAT 59.323 37.037 0.00 0.00 0.00 1.28
102 103 9.193806 GGGACGGAGGAAGTATAATGTAATATA 57.806 37.037 0.00 0.00 0.00 0.86
127 128 6.959639 AAAAAGATACAAGCTCTGGAAACA 57.040 33.333 0.00 0.00 39.59 2.83
128 129 6.959639 AAAAGATACAAGCTCTGGAAACAA 57.040 33.333 0.00 0.00 42.06 2.83
129 130 6.959639 AAAGATACAAGCTCTGGAAACAAA 57.040 33.333 0.00 0.00 42.06 2.83
130 131 6.959639 AAGATACAAGCTCTGGAAACAAAA 57.040 33.333 0.00 0.00 42.06 2.44
131 132 6.566197 AGATACAAGCTCTGGAAACAAAAG 57.434 37.500 0.00 0.00 42.06 2.27
132 133 5.474876 AGATACAAGCTCTGGAAACAAAAGG 59.525 40.000 0.00 0.00 42.06 3.11
133 134 3.631250 ACAAGCTCTGGAAACAAAAGGA 58.369 40.909 0.00 0.00 42.06 3.36
134 135 4.023291 ACAAGCTCTGGAAACAAAAGGAA 58.977 39.130 0.00 0.00 42.06 3.36
135 136 4.651045 ACAAGCTCTGGAAACAAAAGGAAT 59.349 37.500 0.00 0.00 42.06 3.01
136 137 5.833131 ACAAGCTCTGGAAACAAAAGGAATA 59.167 36.000 0.00 0.00 42.06 1.75
137 138 6.323739 ACAAGCTCTGGAAACAAAAGGAATAA 59.676 34.615 0.00 0.00 42.06 1.40
138 139 6.976934 AGCTCTGGAAACAAAAGGAATAAA 57.023 33.333 0.00 0.00 42.06 1.40
139 140 7.360113 AGCTCTGGAAACAAAAGGAATAAAA 57.640 32.000 0.00 0.00 42.06 1.52
140 141 7.791029 AGCTCTGGAAACAAAAGGAATAAAAA 58.209 30.769 0.00 0.00 42.06 1.94
160 161 5.655893 AAAAATGGCATCGTGAAAGTTTG 57.344 34.783 0.00 0.00 0.00 2.93
161 162 4.582701 AAATGGCATCGTGAAAGTTTGA 57.417 36.364 0.00 0.00 0.00 2.69
162 163 4.789012 AATGGCATCGTGAAAGTTTGAT 57.211 36.364 0.00 0.00 0.00 2.57
163 164 4.789012 ATGGCATCGTGAAAGTTTGATT 57.211 36.364 0.00 0.00 0.00 2.57
164 165 5.895636 ATGGCATCGTGAAAGTTTGATTA 57.104 34.783 0.00 0.00 0.00 1.75
165 166 5.895636 TGGCATCGTGAAAGTTTGATTAT 57.104 34.783 0.00 0.00 0.00 1.28
166 167 6.266168 TGGCATCGTGAAAGTTTGATTATT 57.734 33.333 0.00 0.00 0.00 1.40
167 168 6.686630 TGGCATCGTGAAAGTTTGATTATTT 58.313 32.000 0.00 0.00 0.00 1.40
168 169 6.585702 TGGCATCGTGAAAGTTTGATTATTTG 59.414 34.615 0.00 0.00 0.00 2.32
169 170 6.034898 GGCATCGTGAAAGTTTGATTATTTGG 59.965 38.462 0.00 0.00 0.00 3.28
170 171 6.806249 GCATCGTGAAAGTTTGATTATTTGGA 59.194 34.615 0.00 0.00 0.00 3.53
171 172 7.489113 GCATCGTGAAAGTTTGATTATTTGGAT 59.511 33.333 0.00 0.00 0.00 3.41
172 173 9.013490 CATCGTGAAAGTTTGATTATTTGGATC 57.987 33.333 0.00 0.00 0.00 3.36
173 174 7.240674 TCGTGAAAGTTTGATTATTTGGATCG 58.759 34.615 0.00 0.00 0.00 3.69
174 175 7.021196 CGTGAAAGTTTGATTATTTGGATCGT 58.979 34.615 0.00 0.00 0.00 3.73
175 176 8.172484 CGTGAAAGTTTGATTATTTGGATCGTA 58.828 33.333 0.00 0.00 0.00 3.43
176 177 9.274065 GTGAAAGTTTGATTATTTGGATCGTAC 57.726 33.333 0.00 0.00 0.00 3.67
177 178 9.004717 TGAAAGTTTGATTATTTGGATCGTACA 57.995 29.630 0.00 0.00 0.00 2.90
178 179 9.834628 GAAAGTTTGATTATTTGGATCGTACAA 57.165 29.630 0.00 0.00 0.00 2.41
193 194 9.516546 TGGATCGTACAAATATGATACTACTCT 57.483 33.333 0.00 0.00 38.19 3.24
194 195 9.776158 GGATCGTACAAATATGATACTACTCTG 57.224 37.037 0.00 0.00 37.20 3.35
231 232 6.415573 AGGATGTTCTTGTAGTTCAATACCC 58.584 40.000 0.00 0.00 35.35 3.69
232 233 6.215636 AGGATGTTCTTGTAGTTCAATACCCT 59.784 38.462 0.00 0.00 35.35 4.34
233 234 6.884836 GGATGTTCTTGTAGTTCAATACCCTT 59.115 38.462 0.00 0.00 35.35 3.95
234 235 7.393515 GGATGTTCTTGTAGTTCAATACCCTTT 59.606 37.037 0.00 0.00 35.35 3.11
235 236 8.706322 ATGTTCTTGTAGTTCAATACCCTTTT 57.294 30.769 0.00 0.00 35.35 2.27
236 237 8.528044 TGTTCTTGTAGTTCAATACCCTTTTT 57.472 30.769 0.00 0.00 35.35 1.94
546 547 2.267351 CCAACCACTGCGGCAATCA 61.267 57.895 3.44 0.00 39.03 2.57
552 553 0.378257 CACTGCGGCAATCACATACC 59.622 55.000 3.44 0.00 0.00 2.73
654 665 1.573108 CTCTCCCCTCAACCAGCTAA 58.427 55.000 0.00 0.00 0.00 3.09
668 679 1.065126 CAGCTAAGAAGAAGGTGGGGG 60.065 57.143 0.00 0.00 38.50 5.40
688 699 2.187946 GGGTCAGATGCCGGTGAG 59.812 66.667 1.90 0.00 0.00 3.51
717 728 2.890474 CGCCCCGTCGGAAAGATG 60.890 66.667 14.39 0.00 35.65 2.90
731 742 2.087461 AGATGGGATCTTGGGGCCC 61.087 63.158 18.17 18.17 42.38 5.80
733 744 2.074113 GATGGGATCTTGGGGCCCTC 62.074 65.000 25.93 12.91 42.52 4.30
751 762 0.965363 TCAGAGCGGGGAAAATTGGC 60.965 55.000 0.00 0.00 0.00 4.52
771 782 1.405661 CGCTTCTTGGGTTCTAGGGTC 60.406 57.143 0.00 0.00 0.00 4.46
800 811 1.214673 CTAGGGCCCCCTTCCTTTTAC 59.785 57.143 21.43 0.00 45.70 2.01
809 820 2.488153 CCCTTCCTTTTACTTCGCCTTG 59.512 50.000 0.00 0.00 0.00 3.61
845 902 7.675478 TCTTTACGATGAGAAAATTCGACATG 58.325 34.615 11.38 0.00 36.73 3.21
846 903 6.961359 TTACGATGAGAAAATTCGACATGT 57.039 33.333 0.00 0.00 36.73 3.21
859 916 8.786826 AAATTCGACATGTAGTTTATTCAGGA 57.213 30.769 0.00 0.00 0.00 3.86
874 931 8.897752 GTTTATTCAGGATCTAATTCTTGTGCT 58.102 33.333 0.00 0.00 0.00 4.40
901 959 4.106197 GCTATTGTTTCAGATCGTCTCGT 58.894 43.478 0.00 0.00 0.00 4.18
905 963 3.565516 TGTTTCAGATCGTCTCGTTCAG 58.434 45.455 3.70 0.00 0.00 3.02
919 977 4.450757 TCTCGTTCAGAAAATTGCGATCAA 59.549 37.500 0.00 0.00 36.51 2.57
954 1012 5.278858 CGTTTTTCTACTGAGACTGGGTAGT 60.279 44.000 9.75 0.00 40.66 2.73
978 1036 7.339466 AGTTCAAATTCAGGGGATTGTGTATAC 59.661 37.037 0.00 0.00 0.00 1.47
991 1049 2.280628 GTGTATACTCTGTTGGCCTGC 58.719 52.381 3.32 0.00 0.00 4.85
998 1056 0.106268 TCTGTTGGCCTGCCTTTGAA 60.106 50.000 9.97 0.00 36.94 2.69
1022 1080 1.683943 GCTGAAGCATGCCCTGATAA 58.316 50.000 15.66 0.00 41.59 1.75
1032 1090 0.320771 GCCCTGATAATCGGCGATGT 60.321 55.000 24.73 15.36 31.92 3.06
1053 1111 4.125703 GTCTACCTGCTTGGATGATGAAG 58.874 47.826 3.40 0.00 39.71 3.02
1056 1114 0.661552 CTGCTTGGATGATGAAGCCG 59.338 55.000 0.00 0.00 43.34 5.52
1062 1120 0.462581 GGATGATGAAGCCGTGCTCA 60.463 55.000 0.00 0.97 38.25 4.26
1071 1129 2.472695 AGCCGTGCTCAAGTAATGAA 57.527 45.000 0.00 0.00 37.67 2.57
1134 1192 1.627834 GATAAGGGATCAGGGGCTCTG 59.372 57.143 8.46 8.46 44.68 3.35
1281 1339 1.812571 GCTGTCACGGATGAATTTGGT 59.187 47.619 0.00 0.00 36.31 3.67
1323 1381 8.097662 ACTTGTAAGAATGAGAGGAAAGTTAGG 58.902 37.037 0.00 0.00 0.00 2.69
1464 1522 2.480416 GCAACGATGTCAGGGTAGAGAG 60.480 54.545 0.00 0.00 0.00 3.20
1469 1527 3.948473 CGATGTCAGGGTAGAGAGAAGAA 59.052 47.826 0.00 0.00 0.00 2.52
1501 1559 3.372206 GCGTGACAGTGCTGATTATTCTT 59.628 43.478 6.17 0.00 0.00 2.52
1706 1764 7.890655 AGCTGAAGAGGTAAACCATAATTCTTT 59.109 33.333 1.26 0.00 38.89 2.52
1779 1837 6.931840 GTGTTGTTATGCAATTCCCCTTAAAA 59.068 34.615 0.00 0.00 39.55 1.52
1854 1912 7.038659 TGCGTGCCAATTTATTAGCTTTATTT 58.961 30.769 0.00 0.00 0.00 1.40
1977 2036 4.332683 AGGAGTGACCCTAGTGAATACA 57.667 45.455 0.00 0.00 40.05 2.29
2049 2108 2.802247 CTCAAGAGACAAACATGCACGA 59.198 45.455 0.00 0.00 0.00 4.35
2117 2176 8.735692 TTGAAGACATGATTAAGCATGATGTA 57.264 30.769 33.88 16.20 46.64 2.29
2187 2246 5.016051 TCTGAGTGCTAATGACATCTTCC 57.984 43.478 0.00 0.00 0.00 3.46
2192 2251 4.660303 AGTGCTAATGACATCTTCCCCATA 59.340 41.667 0.00 0.00 0.00 2.74
2238 2297 6.451393 TGTGTGGCAGAAAATAATTTACCAC 58.549 36.000 12.47 12.47 42.16 4.16
2326 2387 7.325694 TGCTTTGAGTAACTAAGTATACCACC 58.674 38.462 0.00 0.00 34.72 4.61
2408 2469 4.303086 AGATATACGGACCACAAAGACG 57.697 45.455 0.00 0.00 0.00 4.18
2455 2516 1.341581 GCCTCCAGTCTCTACTCCTGT 60.342 57.143 0.00 0.00 31.97 4.00
2513 2574 1.902918 GGGGTTGATGCAGTGCACA 60.903 57.895 22.44 17.29 43.04 4.57
2514 2575 1.462731 GGGGTTGATGCAGTGCACAA 61.463 55.000 22.44 21.83 43.04 3.33
2577 2638 7.500992 AGTAGACAAGAACAAGAGACATGAAA 58.499 34.615 0.00 0.00 0.00 2.69
2730 2791 0.506932 CGTGAACGTGAATCTTGCGT 59.493 50.000 0.00 0.00 40.81 5.24
2869 2930 2.420642 AGTGCTGAACTGCATACACTG 58.579 47.619 9.31 0.00 45.23 3.66
2915 2976 0.036164 TTAGCTGGTTCCACGCATGT 59.964 50.000 0.00 0.35 0.00 3.21
3017 3078 7.544622 AGTAAGTCGCTTTTCTTTTCCTTTTT 58.455 30.769 0.00 0.00 0.00 1.94
3026 3087 3.035363 TCTTTTCCTTTTTGGGGGACAC 58.965 45.455 0.00 0.00 36.20 3.67
3116 3261 4.696877 TGCTGTCATTGTCATCTTACCTTG 59.303 41.667 0.00 0.00 0.00 3.61
3129 3274 7.439655 GTCATCTTACCTTGTATGATCTTGACC 59.560 40.741 0.00 0.00 31.49 4.02
3130 3275 6.867519 TCTTACCTTGTATGATCTTGACCA 57.132 37.500 0.00 0.00 0.00 4.02
3131 3276 6.878317 TCTTACCTTGTATGATCTTGACCAG 58.122 40.000 0.00 0.00 0.00 4.00
3152 3297 5.316987 CAGGTTCAGGTTCAGGTAAAGAAT 58.683 41.667 0.00 0.00 0.00 2.40
3270 3416 0.752658 GCCTTCCCAGTTGTTTTGCT 59.247 50.000 0.00 0.00 0.00 3.91
3329 3475 6.264832 TGTGAGTGTACATTTGAGCAAAAAG 58.735 36.000 0.00 0.00 33.56 2.27
3336 3482 1.047801 TTTGAGCAAAAAGAGGGGCC 58.952 50.000 0.00 0.00 0.00 5.80
3389 3535 6.849588 AAATTTTGTGAGGCAAATGTCTTC 57.150 33.333 0.00 0.00 45.38 2.87
3447 4849 5.698741 TCCATGTCAATGTCCTTATGTCT 57.301 39.130 0.00 0.00 31.27 3.41
3521 4923 7.809331 TGTTGCATTCTTAAAATCAGTGTGATC 59.191 33.333 0.00 0.00 35.76 2.92
3527 4929 9.739276 ATTCTTAAAATCAGTGTGATCCTTGTA 57.261 29.630 0.00 0.00 35.76 2.41
3532 4934 4.128925 TCAGTGTGATCCTTGTAGATGC 57.871 45.455 0.00 0.00 0.00 3.91
3536 4938 4.159693 AGTGTGATCCTTGTAGATGCGTTA 59.840 41.667 0.00 0.00 0.00 3.18
3556 4958 7.148154 TGCGTTATCAAGGTAATATTGCAAGTT 60.148 33.333 4.94 5.19 0.00 2.66
3557 4959 8.339714 GCGTTATCAAGGTAATATTGCAAGTTA 58.660 33.333 4.94 4.16 0.00 2.24
3558 4960 9.864034 CGTTATCAAGGTAATATTGCAAGTTAG 57.136 33.333 4.94 0.00 0.00 2.34
3576 4978 8.300286 GCAAGTTAGTAGTAGATCATCATGCTA 58.700 37.037 0.00 0.00 0.00 3.49
3600 5035 3.324846 ACTCTTATCACCACAAGACAGCA 59.675 43.478 0.00 0.00 0.00 4.41
3609 5044 1.214589 CAAGACAGCATTGCAGCCC 59.785 57.895 11.91 0.00 34.23 5.19
3640 5075 6.463995 TGTTTTGTCATAGCTTTCTGGTTT 57.536 33.333 0.00 0.00 0.00 3.27
3666 5101 1.183030 TTCCTCCTCTCGCAACCGAA 61.183 55.000 0.00 0.00 43.87 4.30
3682 5117 1.795872 CCGAATGTCGTGCTGTTGTAA 59.204 47.619 0.00 0.00 38.40 2.41
3686 5121 0.528901 TGTCGTGCTGTTGTAACGCT 60.529 50.000 10.93 0.00 37.24 5.07
3689 5124 0.111266 CGTGCTGTTGTAACGCTGAC 60.111 55.000 10.93 3.99 32.44 3.51
3743 5178 2.124411 GGGCTCCCAGTTCACCTATAA 58.876 52.381 0.00 0.00 35.81 0.98
3744 5179 2.158798 GGGCTCCCAGTTCACCTATAAC 60.159 54.545 0.00 0.00 35.81 1.89
3745 5180 2.772515 GGCTCCCAGTTCACCTATAACT 59.227 50.000 0.00 0.00 37.67 2.24
3755 5190 7.907214 AGTTCACCTATAACTGATCACAAAC 57.093 36.000 0.00 0.00 35.87 2.93
3756 5191 7.680730 AGTTCACCTATAACTGATCACAAACT 58.319 34.615 0.00 0.00 35.87 2.66
3757 5192 8.812972 AGTTCACCTATAACTGATCACAAACTA 58.187 33.333 0.00 0.00 35.87 2.24
3758 5193 9.431887 GTTCACCTATAACTGATCACAAACTAA 57.568 33.333 0.00 0.00 0.00 2.24
3767 5202 8.553459 AACTGATCACAAACTAAATAGGTCAG 57.447 34.615 0.00 0.00 36.39 3.51
3768 5203 7.907389 ACTGATCACAAACTAAATAGGTCAGA 58.093 34.615 7.43 0.00 34.87 3.27
3769 5204 8.375506 ACTGATCACAAACTAAATAGGTCAGAA 58.624 33.333 7.43 0.00 34.87 3.02
3770 5205 9.219603 CTGATCACAAACTAAATAGGTCAGAAA 57.780 33.333 0.00 0.00 33.13 2.52
3771 5206 9.739276 TGATCACAAACTAAATAGGTCAGAAAT 57.261 29.630 0.00 0.00 0.00 2.17
3778 5213 8.950208 AACTAAATAGGTCAGAAATACAGAGC 57.050 34.615 0.00 0.00 33.71 4.09
3779 5214 8.312669 ACTAAATAGGTCAGAAATACAGAGCT 57.687 34.615 0.00 0.00 43.30 4.09
3780 5215 9.422681 ACTAAATAGGTCAGAAATACAGAGCTA 57.577 33.333 0.00 0.00 44.59 3.32
3781 5216 9.685828 CTAAATAGGTCAGAAATACAGAGCTAC 57.314 37.037 0.00 0.00 43.80 3.58
3782 5217 7.661536 AATAGGTCAGAAATACAGAGCTACA 57.338 36.000 0.00 0.00 43.80 2.74
3783 5218 7.847711 ATAGGTCAGAAATACAGAGCTACAT 57.152 36.000 0.00 0.00 43.80 2.29
3784 5219 8.941995 ATAGGTCAGAAATACAGAGCTACATA 57.058 34.615 0.00 0.00 43.80 2.29
3785 5220 7.847711 AGGTCAGAAATACAGAGCTACATAT 57.152 36.000 0.00 0.00 40.16 1.78
3786 5221 8.941995 AGGTCAGAAATACAGAGCTACATATA 57.058 34.615 0.00 0.00 40.16 0.86
3787 5222 9.019656 AGGTCAGAAATACAGAGCTACATATAG 57.980 37.037 0.00 0.00 40.16 1.31
3788 5223 8.247562 GGTCAGAAATACAGAGCTACATATAGG 58.752 40.741 0.00 0.00 31.46 2.57
3789 5224 9.015367 GTCAGAAATACAGAGCTACATATAGGA 57.985 37.037 0.00 0.00 0.00 2.94
3790 5225 9.588096 TCAGAAATACAGAGCTACATATAGGAA 57.412 33.333 0.00 0.00 0.00 3.36
3797 5232 7.148641 ACAGAGCTACATATAGGAAAATGTCG 58.851 38.462 0.00 0.00 37.50 4.35
3798 5233 6.090088 CAGAGCTACATATAGGAAAATGTCGC 59.910 42.308 4.37 4.37 42.17 5.19
3799 5234 5.238583 AGCTACATATAGGAAAATGTCGCC 58.761 41.667 7.95 0.00 42.58 5.54
3800 5235 4.392138 GCTACATATAGGAAAATGTCGCCC 59.608 45.833 0.00 0.00 38.29 6.13
3801 5236 3.399330 ACATATAGGAAAATGTCGCCCG 58.601 45.455 0.00 0.00 30.54 6.13
3802 5237 3.070446 ACATATAGGAAAATGTCGCCCGA 59.930 43.478 0.00 0.00 30.54 5.14
3803 5238 1.949465 ATAGGAAAATGTCGCCCGAC 58.051 50.000 13.45 13.45 44.77 4.79
3804 5239 0.899720 TAGGAAAATGTCGCCCGACT 59.100 50.000 19.88 1.50 44.80 4.18
3805 5240 0.036306 AGGAAAATGTCGCCCGACTT 59.964 50.000 19.88 12.05 44.80 3.01
3806 5241 1.276989 AGGAAAATGTCGCCCGACTTA 59.723 47.619 19.88 3.13 44.80 2.24
3807 5242 2.093128 AGGAAAATGTCGCCCGACTTAT 60.093 45.455 19.88 5.29 44.80 1.73
3808 5243 2.287103 GGAAAATGTCGCCCGACTTATC 59.713 50.000 19.88 14.63 44.80 1.75
3809 5244 1.949465 AAATGTCGCCCGACTTATCC 58.051 50.000 19.88 0.00 44.80 2.59
3810 5245 0.828022 AATGTCGCCCGACTTATCCA 59.172 50.000 19.88 1.13 44.80 3.41
3811 5246 1.048601 ATGTCGCCCGACTTATCCAT 58.951 50.000 19.88 3.36 44.80 3.41
3812 5247 1.694844 TGTCGCCCGACTTATCCATA 58.305 50.000 19.88 0.00 44.80 2.74
3813 5248 1.338973 TGTCGCCCGACTTATCCATAC 59.661 52.381 19.88 0.00 44.80 2.39
3814 5249 1.338973 GTCGCCCGACTTATCCATACA 59.661 52.381 13.10 0.00 41.57 2.29
3815 5250 2.033372 TCGCCCGACTTATCCATACAA 58.967 47.619 0.00 0.00 0.00 2.41
3816 5251 2.631062 TCGCCCGACTTATCCATACAAT 59.369 45.455 0.00 0.00 0.00 2.71
3817 5252 3.827876 TCGCCCGACTTATCCATACAATA 59.172 43.478 0.00 0.00 0.00 1.90
3818 5253 4.281435 TCGCCCGACTTATCCATACAATAA 59.719 41.667 0.00 0.00 0.00 1.40
3819 5254 4.625742 CGCCCGACTTATCCATACAATAAG 59.374 45.833 0.00 0.00 40.81 1.73
3820 5255 4.935808 GCCCGACTTATCCATACAATAAGG 59.064 45.833 7.55 0.00 39.81 2.69
3821 5256 5.512576 GCCCGACTTATCCATACAATAAGGT 60.513 44.000 7.55 0.00 39.81 3.50
3822 5257 5.932303 CCCGACTTATCCATACAATAAGGTG 59.068 44.000 7.55 0.85 39.81 4.00
3823 5258 5.932303 CCGACTTATCCATACAATAAGGTGG 59.068 44.000 7.55 5.14 39.81 4.61
3824 5259 6.239487 CCGACTTATCCATACAATAAGGTGGA 60.239 42.308 7.55 0.00 44.22 4.02
3826 5261 7.545965 CGACTTATCCATACAATAAGGTGGATC 59.454 40.741 8.86 0.00 45.81 3.36
3827 5262 8.275187 ACTTATCCATACAATAAGGTGGATCA 57.725 34.615 8.86 0.00 45.81 2.92
3828 5263 8.723365 ACTTATCCATACAATAAGGTGGATCAA 58.277 33.333 8.86 3.18 45.81 2.57
3829 5264 9.573166 CTTATCCATACAATAAGGTGGATCAAA 57.427 33.333 8.86 0.00 45.81 2.69
3830 5265 9.928618 TTATCCATACAATAAGGTGGATCAAAA 57.071 29.630 8.86 0.00 45.81 2.44
3831 5266 7.880160 TCCATACAATAAGGTGGATCAAAAG 57.120 36.000 0.00 0.00 35.91 2.27
3832 5267 7.638444 TCCATACAATAAGGTGGATCAAAAGA 58.362 34.615 0.00 0.00 35.91 2.52
3833 5268 8.112822 TCCATACAATAAGGTGGATCAAAAGAA 58.887 33.333 0.00 0.00 35.91 2.52
3834 5269 8.748412 CCATACAATAAGGTGGATCAAAAGAAA 58.252 33.333 0.00 0.00 33.53 2.52
3837 5272 7.145323 ACAATAAGGTGGATCAAAAGAAAACG 58.855 34.615 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.730296 TGTGGGTGAGTTGAAAAGAAAAA 57.270 34.783 0.00 0.00 0.00 1.94
15 16 5.730296 TTGTGGGTGAGTTGAAAAGAAAA 57.270 34.783 0.00 0.00 0.00 2.29
16 17 5.730296 TTTGTGGGTGAGTTGAAAAGAAA 57.270 34.783 0.00 0.00 0.00 2.52
17 18 5.730296 TTTTGTGGGTGAGTTGAAAAGAA 57.270 34.783 0.00 0.00 0.00 2.52
18 19 5.478679 TCTTTTTGTGGGTGAGTTGAAAAGA 59.521 36.000 0.00 0.00 38.54 2.52
19 20 5.719173 TCTTTTTGTGGGTGAGTTGAAAAG 58.281 37.500 0.00 0.00 35.22 2.27
20 21 5.730296 TCTTTTTGTGGGTGAGTTGAAAA 57.270 34.783 0.00 0.00 0.00 2.29
21 22 5.245075 ACTTCTTTTTGTGGGTGAGTTGAAA 59.755 36.000 0.00 0.00 0.00 2.69
22 23 4.770010 ACTTCTTTTTGTGGGTGAGTTGAA 59.230 37.500 0.00 0.00 0.00 2.69
23 24 4.340617 ACTTCTTTTTGTGGGTGAGTTGA 58.659 39.130 0.00 0.00 0.00 3.18
24 25 4.718940 ACTTCTTTTTGTGGGTGAGTTG 57.281 40.909 0.00 0.00 0.00 3.16
25 26 5.506708 AGTACTTCTTTTTGTGGGTGAGTT 58.493 37.500 0.00 0.00 0.00 3.01
26 27 5.112129 AGTACTTCTTTTTGTGGGTGAGT 57.888 39.130 0.00 0.00 0.00 3.41
27 28 7.444183 TCAATAGTACTTCTTTTTGTGGGTGAG 59.556 37.037 0.00 0.00 0.00 3.51
28 29 7.284074 TCAATAGTACTTCTTTTTGTGGGTGA 58.716 34.615 0.00 0.00 0.00 4.02
29 30 7.504924 TCAATAGTACTTCTTTTTGTGGGTG 57.495 36.000 0.00 0.00 0.00 4.61
30 31 7.778382 AGTTCAATAGTACTTCTTTTTGTGGGT 59.222 33.333 0.00 0.00 0.00 4.51
31 32 8.166422 AGTTCAATAGTACTTCTTTTTGTGGG 57.834 34.615 0.00 0.00 0.00 4.61
58 59 9.284968 CTCCGTCCCATAATATAAGACATTTTT 57.715 33.333 0.00 0.00 0.00 1.94
59 60 7.883311 CCTCCGTCCCATAATATAAGACATTTT 59.117 37.037 0.00 0.00 0.00 1.82
60 61 7.236847 TCCTCCGTCCCATAATATAAGACATTT 59.763 37.037 0.00 0.00 0.00 2.32
61 62 6.729100 TCCTCCGTCCCATAATATAAGACATT 59.271 38.462 0.00 0.00 0.00 2.71
62 63 6.261435 TCCTCCGTCCCATAATATAAGACAT 58.739 40.000 0.00 0.00 0.00 3.06
63 64 5.647230 TCCTCCGTCCCATAATATAAGACA 58.353 41.667 0.00 0.00 0.00 3.41
64 65 6.210984 ACTTCCTCCGTCCCATAATATAAGAC 59.789 42.308 0.00 0.00 0.00 3.01
65 66 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
66 67 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
67 68 9.772605 TTATACTTCCTCCGTCCCATAATATAA 57.227 33.333 0.00 0.00 0.00 0.98
68 69 9.947189 ATTATACTTCCTCCGTCCCATAATATA 57.053 33.333 0.00 0.00 0.00 0.86
69 70 8.705594 CATTATACTTCCTCCGTCCCATAATAT 58.294 37.037 0.00 0.00 0.00 1.28
70 71 7.676893 ACATTATACTTCCTCCGTCCCATAATA 59.323 37.037 0.00 0.00 0.00 0.98
71 72 6.500751 ACATTATACTTCCTCCGTCCCATAAT 59.499 38.462 0.00 0.00 0.00 1.28
72 73 5.842328 ACATTATACTTCCTCCGTCCCATAA 59.158 40.000 0.00 0.00 0.00 1.90
73 74 5.399991 ACATTATACTTCCTCCGTCCCATA 58.600 41.667 0.00 0.00 0.00 2.74
74 75 4.232091 ACATTATACTTCCTCCGTCCCAT 58.768 43.478 0.00 0.00 0.00 4.00
75 76 3.649843 ACATTATACTTCCTCCGTCCCA 58.350 45.455 0.00 0.00 0.00 4.37
76 77 5.796424 TTACATTATACTTCCTCCGTCCC 57.204 43.478 0.00 0.00 0.00 4.46
101 102 9.733556 TGTTTCCAGAGCTTGTATCTTTTTATA 57.266 29.630 0.00 0.00 0.00 0.98
102 103 8.635765 TGTTTCCAGAGCTTGTATCTTTTTAT 57.364 30.769 0.00 0.00 0.00 1.40
103 104 8.458573 TTGTTTCCAGAGCTTGTATCTTTTTA 57.541 30.769 0.00 0.00 0.00 1.52
104 105 6.959639 TGTTTCCAGAGCTTGTATCTTTTT 57.040 33.333 0.00 0.00 0.00 1.94
105 106 6.959639 TTGTTTCCAGAGCTTGTATCTTTT 57.040 33.333 0.00 0.00 0.00 2.27
106 107 6.959639 TTTGTTTCCAGAGCTTGTATCTTT 57.040 33.333 0.00 0.00 0.00 2.52
107 108 6.015940 CCTTTTGTTTCCAGAGCTTGTATCTT 60.016 38.462 0.00 0.00 0.00 2.40
108 109 5.474876 CCTTTTGTTTCCAGAGCTTGTATCT 59.525 40.000 0.00 0.00 0.00 1.98
109 110 5.473504 TCCTTTTGTTTCCAGAGCTTGTATC 59.526 40.000 0.00 0.00 0.00 2.24
110 111 5.385198 TCCTTTTGTTTCCAGAGCTTGTAT 58.615 37.500 0.00 0.00 0.00 2.29
111 112 4.787551 TCCTTTTGTTTCCAGAGCTTGTA 58.212 39.130 0.00 0.00 0.00 2.41
112 113 3.631250 TCCTTTTGTTTCCAGAGCTTGT 58.369 40.909 0.00 0.00 0.00 3.16
113 114 4.654091 TTCCTTTTGTTTCCAGAGCTTG 57.346 40.909 0.00 0.00 0.00 4.01
114 115 6.976934 TTATTCCTTTTGTTTCCAGAGCTT 57.023 33.333 0.00 0.00 0.00 3.74
115 116 6.976934 TTTATTCCTTTTGTTTCCAGAGCT 57.023 33.333 0.00 0.00 0.00 4.09
138 139 5.355596 TCAAACTTTCACGATGCCATTTTT 58.644 33.333 0.00 0.00 0.00 1.94
139 140 4.942852 TCAAACTTTCACGATGCCATTTT 58.057 34.783 0.00 0.00 0.00 1.82
140 141 4.582701 TCAAACTTTCACGATGCCATTT 57.417 36.364 0.00 0.00 0.00 2.32
141 142 4.789012 ATCAAACTTTCACGATGCCATT 57.211 36.364 0.00 0.00 0.00 3.16
142 143 4.789012 AATCAAACTTTCACGATGCCAT 57.211 36.364 0.00 0.00 0.00 4.40
143 144 5.895636 ATAATCAAACTTTCACGATGCCA 57.104 34.783 0.00 0.00 0.00 4.92
144 145 6.034898 CCAAATAATCAAACTTTCACGATGCC 59.965 38.462 0.00 0.00 0.00 4.40
145 146 6.806249 TCCAAATAATCAAACTTTCACGATGC 59.194 34.615 0.00 0.00 0.00 3.91
146 147 8.915871 ATCCAAATAATCAAACTTTCACGATG 57.084 30.769 0.00 0.00 0.00 3.84
147 148 7.910162 CGATCCAAATAATCAAACTTTCACGAT 59.090 33.333 0.00 0.00 0.00 3.73
148 149 7.094975 ACGATCCAAATAATCAAACTTTCACGA 60.095 33.333 0.00 0.00 0.00 4.35
149 150 7.021196 ACGATCCAAATAATCAAACTTTCACG 58.979 34.615 0.00 0.00 0.00 4.35
150 151 9.274065 GTACGATCCAAATAATCAAACTTTCAC 57.726 33.333 0.00 0.00 0.00 3.18
151 152 9.004717 TGTACGATCCAAATAATCAAACTTTCA 57.995 29.630 0.00 0.00 0.00 2.69
152 153 9.834628 TTGTACGATCCAAATAATCAAACTTTC 57.165 29.630 0.00 0.00 0.00 2.62
167 168 9.516546 AGAGTAGTATCATATTTGTACGATCCA 57.483 33.333 0.00 0.00 0.00 3.41
168 169 9.776158 CAGAGTAGTATCATATTTGTACGATCC 57.224 37.037 0.00 0.00 0.00 3.36
205 206 8.211629 GGGTATTGAACTACAAGAACATCCTAT 58.788 37.037 0.00 0.00 38.93 2.57
206 207 7.402071 AGGGTATTGAACTACAAGAACATCCTA 59.598 37.037 0.00 0.00 38.93 2.94
207 208 6.215636 AGGGTATTGAACTACAAGAACATCCT 59.784 38.462 0.00 0.00 38.93 3.24
208 209 6.415573 AGGGTATTGAACTACAAGAACATCC 58.584 40.000 0.00 0.00 38.93 3.51
209 210 7.923414 AAGGGTATTGAACTACAAGAACATC 57.077 36.000 0.00 0.00 38.93 3.06
210 211 8.706322 AAAAGGGTATTGAACTACAAGAACAT 57.294 30.769 0.00 0.00 38.93 2.71
211 212 8.528044 AAAAAGGGTATTGAACTACAAGAACA 57.472 30.769 0.00 0.00 38.93 3.18
273 274 7.733047 AGGGTTCAAAATTTCTAACATTACCCT 59.267 33.333 14.20 0.00 44.32 4.34
316 317 5.074791 CCGTTCGTATTGGTTAACTTTTCG 58.925 41.667 5.42 5.23 0.00 3.46
513 514 2.050350 TTGGTAGGAGCTCCGGTCG 61.050 63.158 26.95 0.00 42.08 4.79
546 547 2.744709 GCCAACGGTGCGGTATGT 60.745 61.111 0.00 0.00 0.00 2.29
654 665 3.330720 CCGCCCCCACCTTCTTCT 61.331 66.667 0.00 0.00 0.00 2.85
717 728 2.696125 TGAGGGCCCCAAGATCCC 60.696 66.667 21.43 0.00 40.36 3.85
731 742 1.098050 CCAATTTTCCCCGCTCTGAG 58.902 55.000 0.00 0.00 0.00 3.35
733 744 1.512694 GCCAATTTTCCCCGCTCTG 59.487 57.895 0.00 0.00 0.00 3.35
751 762 0.613777 ACCCTAGAACCCAAGAAGCG 59.386 55.000 0.00 0.00 0.00 4.68
800 811 5.175090 AGAAAGAAAGAAACAAGGCGAAG 57.825 39.130 0.00 0.00 0.00 3.79
809 820 9.931210 TTTCTCATCGTAAAGAAAGAAAGAAAC 57.069 29.630 5.26 0.00 38.58 2.78
859 916 3.019564 GCCACCAGCACAAGAATTAGAT 58.980 45.455 0.00 0.00 42.97 1.98
874 931 3.270027 CGATCTGAAACAATAGCCACCA 58.730 45.455 0.00 0.00 0.00 4.17
919 977 9.273016 TCTCAGTAGAAAAACGAATCAAGAAAT 57.727 29.630 0.00 0.00 0.00 2.17
930 988 3.991367 ACCCAGTCTCAGTAGAAAAACG 58.009 45.455 0.00 0.00 32.16 3.60
936 994 4.652679 TGAACTACCCAGTCTCAGTAGA 57.347 45.455 11.23 0.00 37.50 2.59
954 1012 7.410174 AGTATACACAATCCCCTGAATTTGAA 58.590 34.615 5.50 0.00 0.00 2.69
978 1036 0.538057 TCAAAGGCAGGCCAACAGAG 60.538 55.000 13.63 0.00 38.92 3.35
991 1049 2.165167 TGCTTCAGCCATCTTCAAAGG 58.835 47.619 0.00 0.00 41.18 3.11
1022 1080 1.109920 AGCAGGTAGACATCGCCGAT 61.110 55.000 0.00 0.00 0.00 4.18
1032 1090 3.432749 GCTTCATCATCCAAGCAGGTAGA 60.433 47.826 0.00 0.00 43.87 2.59
1053 1111 2.076863 ACTTCATTACTTGAGCACGGC 58.923 47.619 0.00 0.00 35.27 5.68
1056 1114 5.673337 TTGACACTTCATTACTTGAGCAC 57.327 39.130 0.00 0.00 35.27 4.40
1062 1120 6.203723 GCTCAGTCTTTGACACTTCATTACTT 59.796 38.462 0.46 0.00 34.60 2.24
1071 1129 2.611473 CCGATGCTCAGTCTTTGACACT 60.611 50.000 0.46 0.00 34.60 3.55
1323 1381 1.153469 CTTCGGAGCAGCTCTTCCC 60.153 63.158 21.99 5.04 0.00 3.97
1438 1496 1.238439 CCCTGACATCGTTGCAAAGT 58.762 50.000 12.18 3.69 0.00 2.66
1464 1522 3.555956 TGTCACGCTTTCTTCTGTTCTTC 59.444 43.478 0.00 0.00 0.00 2.87
1469 1527 2.205074 CACTGTCACGCTTTCTTCTGT 58.795 47.619 0.00 0.00 0.00 3.41
1501 1559 8.236585 TCAATTTCTTCAAGTTCATCTTTGGA 57.763 30.769 0.00 0.00 33.63 3.53
1706 1764 8.778358 AGACAAGTAAAACAACAAAAATGCAAA 58.222 25.926 0.00 0.00 0.00 3.68
1779 1837 3.350219 AATGAACAGGAACCAGCGTAT 57.650 42.857 0.00 0.00 0.00 3.06
1854 1912 3.628008 AGATCTGCCTGCATCAATCAAA 58.372 40.909 0.00 0.00 0.00 2.69
1863 1921 3.099905 AGTTGTACTAGATCTGCCTGCA 58.900 45.455 5.18 0.00 0.00 4.41
1977 2036 1.492176 AGCCAGATCGGTCCATGAAAT 59.508 47.619 0.00 0.00 36.97 2.17
2049 2108 6.096846 ACTGAAAAACAAGAGTTTGCCTACAT 59.903 34.615 0.00 0.00 46.79 2.29
2117 2176 6.127786 GCTTTGGCAGAGAAGTTAGAAATGAT 60.128 38.462 9.54 0.00 38.54 2.45
2187 2246 7.290061 TGAAATTAGGACCTCAATTCTATGGG 58.710 38.462 0.00 0.00 0.00 4.00
2192 2251 7.671398 ACACAATGAAATTAGGACCTCAATTCT 59.329 33.333 0.00 0.00 32.46 2.40
2238 2297 1.964933 TGTAAAAAGGGGGCGAAAAGG 59.035 47.619 0.00 0.00 0.00 3.11
2326 2387 6.603237 TGTAAATGCATCAGAATACCTTCG 57.397 37.500 0.00 0.00 36.45 3.79
2455 2516 7.164122 GCTTGATATTGATCCTCCTGTATCAA 58.836 38.462 0.00 0.00 44.00 2.57
2513 2574 5.012148 AGTTTCATCTGTGGTAGTAGCTGTT 59.988 40.000 0.00 0.00 0.00 3.16
2514 2575 4.528596 AGTTTCATCTGTGGTAGTAGCTGT 59.471 41.667 0.00 0.00 0.00 4.40
2577 2638 0.535102 CTTGGTGGACGCTCTGGTTT 60.535 55.000 0.00 0.00 0.00 3.27
2730 2791 1.593209 AGTCGTTTTTCCGCTGCGA 60.593 52.632 25.45 6.86 0.00 5.10
2869 2930 3.145551 CAATGCTCCCAGGCTGCC 61.146 66.667 11.65 11.65 0.00 4.85
2893 2954 0.323302 TGCGTGGAACCAGCTAATCA 59.677 50.000 13.25 0.00 0.00 2.57
2915 2976 3.694072 GACAATAGTTACAGGCCATGCAA 59.306 43.478 5.01 0.00 0.00 4.08
2993 3054 7.253983 CCAAAAAGGAAAAGAAAAGCGACTTAC 60.254 37.037 0.00 0.00 41.22 2.34
3017 3078 1.353022 GACCAACATTAGTGTCCCCCA 59.647 52.381 0.00 0.00 37.67 4.96
3026 3087 8.547967 ACTACTGTACAAATGACCAACATTAG 57.452 34.615 0.00 0.00 46.90 1.73
3081 3226 2.340210 TGACAGCACAGGCAGTAAAA 57.660 45.000 0.00 0.00 40.14 1.52
3082 3227 2.553602 CAATGACAGCACAGGCAGTAAA 59.446 45.455 0.00 0.00 40.14 2.01
3083 3228 2.153645 CAATGACAGCACAGGCAGTAA 58.846 47.619 0.00 0.00 40.14 2.24
3116 3261 4.080863 ACCTGAACCTGGTCAAGATCATAC 60.081 45.833 0.00 0.00 29.71 2.39
3129 3274 4.351874 TCTTTACCTGAACCTGAACCTG 57.648 45.455 0.00 0.00 0.00 4.00
3130 3275 5.073144 TGATTCTTTACCTGAACCTGAACCT 59.927 40.000 0.00 0.00 0.00 3.50
3131 3276 5.181433 GTGATTCTTTACCTGAACCTGAACC 59.819 44.000 0.00 0.00 0.00 3.62
3152 3297 2.103432 TCCGTGAAAGCTAAACCTGTGA 59.897 45.455 0.00 0.00 0.00 3.58
3270 3416 3.499338 AGCTCAACAATGACCAAATCCA 58.501 40.909 0.00 0.00 0.00 3.41
3273 3419 4.401022 TCTGAGCTCAACAATGACCAAAT 58.599 39.130 18.85 0.00 0.00 2.32
3329 3475 2.294449 AGAGAAAACAAAGGCCCCTC 57.706 50.000 0.00 0.00 0.00 4.30
3336 3482 6.147000 GGAAGCTCACTCTAGAGAAAACAAAG 59.853 42.308 26.57 12.02 37.87 2.77
3447 4849 4.202010 GGAGCTAAACACTTGAAGCACAAA 60.202 41.667 0.00 0.00 38.08 2.83
3507 4909 6.094603 GCATCTACAAGGATCACACTGATTTT 59.905 38.462 0.00 0.00 37.20 1.82
3527 4929 6.710295 TGCAATATTACCTTGATAACGCATCT 59.290 34.615 0.00 0.00 34.46 2.90
3532 4934 9.864034 CTAACTTGCAATATTACCTTGATAACG 57.136 33.333 0.00 0.00 0.00 3.18
3557 4959 9.973661 AAGAGTATAGCATGATGATCTACTACT 57.026 33.333 8.44 5.85 0.00 2.57
3576 4978 5.187772 TGCTGTCTTGTGGTGATAAGAGTAT 59.812 40.000 0.00 0.00 33.90 2.12
3577 4979 4.526650 TGCTGTCTTGTGGTGATAAGAGTA 59.473 41.667 0.00 0.00 33.90 2.59
3600 5035 0.251922 ACATGACCAAGGGCTGCAAT 60.252 50.000 0.00 0.00 0.00 3.56
3609 5044 5.633830 AGCTATGACAAAACATGACCAAG 57.366 39.130 0.00 0.00 0.00 3.61
3640 5075 1.063942 TGCGAGAGGAGGAAGATGGTA 60.064 52.381 0.00 0.00 0.00 3.25
3666 5101 0.511221 GCGTTACAACAGCACGACAT 59.489 50.000 0.00 0.00 35.93 3.06
3682 5117 1.885850 GTGGTGGTTTCGTCAGCGT 60.886 57.895 0.00 0.00 39.49 5.07
3686 5121 0.462937 CAGGTGTGGTGGTTTCGTCA 60.463 55.000 0.00 0.00 0.00 4.35
3689 5124 0.179056 ACTCAGGTGTGGTGGTTTCG 60.179 55.000 0.00 0.00 0.00 3.46
3743 5178 7.907389 TCTGACCTATTTAGTTTGTGATCAGT 58.093 34.615 0.00 0.00 33.28 3.41
3744 5179 8.777865 TTCTGACCTATTTAGTTTGTGATCAG 57.222 34.615 0.00 0.00 32.88 2.90
3745 5180 9.739276 ATTTCTGACCTATTTAGTTTGTGATCA 57.261 29.630 0.00 0.00 0.00 2.92
3752 5187 9.384764 GCTCTGTATTTCTGACCTATTTAGTTT 57.615 33.333 0.00 0.00 0.00 2.66
3753 5188 8.763601 AGCTCTGTATTTCTGACCTATTTAGTT 58.236 33.333 0.00 0.00 0.00 2.24
3754 5189 8.312669 AGCTCTGTATTTCTGACCTATTTAGT 57.687 34.615 0.00 0.00 0.00 2.24
3755 5190 9.685828 GTAGCTCTGTATTTCTGACCTATTTAG 57.314 37.037 0.00 0.00 0.00 1.85
3756 5191 9.197306 TGTAGCTCTGTATTTCTGACCTATTTA 57.803 33.333 0.00 0.00 0.00 1.40
3757 5192 8.079211 TGTAGCTCTGTATTTCTGACCTATTT 57.921 34.615 0.00 0.00 0.00 1.40
3758 5193 7.661536 TGTAGCTCTGTATTTCTGACCTATT 57.338 36.000 0.00 0.00 0.00 1.73
3759 5194 7.847711 ATGTAGCTCTGTATTTCTGACCTAT 57.152 36.000 0.00 0.00 0.00 2.57
3760 5195 8.941995 ATATGTAGCTCTGTATTTCTGACCTA 57.058 34.615 0.00 0.00 0.00 3.08
3761 5196 7.847711 ATATGTAGCTCTGTATTTCTGACCT 57.152 36.000 0.00 0.00 0.00 3.85
3762 5197 8.247562 CCTATATGTAGCTCTGTATTTCTGACC 58.752 40.741 0.00 0.00 0.00 4.02
3763 5198 9.015367 TCCTATATGTAGCTCTGTATTTCTGAC 57.985 37.037 0.00 0.00 0.00 3.51
3764 5199 9.588096 TTCCTATATGTAGCTCTGTATTTCTGA 57.412 33.333 0.00 0.00 0.00 3.27
3771 5206 8.297426 CGACATTTTCCTATATGTAGCTCTGTA 58.703 37.037 0.00 0.00 35.24 2.74
3772 5207 7.148641 CGACATTTTCCTATATGTAGCTCTGT 58.851 38.462 0.00 0.00 35.24 3.41
3773 5208 6.090088 GCGACATTTTCCTATATGTAGCTCTG 59.910 42.308 11.37 0.00 44.65 3.35
3774 5209 6.159988 GCGACATTTTCCTATATGTAGCTCT 58.840 40.000 11.37 0.00 44.65 4.09
3775 5210 5.348997 GGCGACATTTTCCTATATGTAGCTC 59.651 44.000 16.05 6.64 46.17 4.09
3776 5211 5.238583 GGCGACATTTTCCTATATGTAGCT 58.761 41.667 16.05 0.00 46.17 3.32
3777 5212 4.392138 GGGCGACATTTTCCTATATGTAGC 59.608 45.833 10.52 10.52 46.19 3.58
3778 5213 4.625742 CGGGCGACATTTTCCTATATGTAG 59.374 45.833 0.00 0.00 35.24 2.74
3779 5214 4.281435 TCGGGCGACATTTTCCTATATGTA 59.719 41.667 0.00 0.00 35.24 2.29
3780 5215 3.070446 TCGGGCGACATTTTCCTATATGT 59.930 43.478 0.00 0.00 37.68 2.29
3781 5216 3.432252 GTCGGGCGACATTTTCCTATATG 59.568 47.826 0.00 0.00 44.02 1.78
3782 5217 3.323979 AGTCGGGCGACATTTTCCTATAT 59.676 43.478 0.00 0.00 46.76 0.86
3783 5218 2.696707 AGTCGGGCGACATTTTCCTATA 59.303 45.455 0.00 0.00 46.76 1.31
3784 5219 1.485066 AGTCGGGCGACATTTTCCTAT 59.515 47.619 0.00 0.00 46.76 2.57
3785 5220 0.899720 AGTCGGGCGACATTTTCCTA 59.100 50.000 0.00 0.00 46.76 2.94
3786 5221 0.036306 AAGTCGGGCGACATTTTCCT 59.964 50.000 0.00 0.00 46.76 3.36
3787 5222 1.729284 TAAGTCGGGCGACATTTTCC 58.271 50.000 0.00 0.00 46.76 3.13
3788 5223 2.287103 GGATAAGTCGGGCGACATTTTC 59.713 50.000 0.00 0.00 46.76 2.29
3789 5224 2.285977 GGATAAGTCGGGCGACATTTT 58.714 47.619 0.00 0.00 46.76 1.82
3790 5225 1.208535 TGGATAAGTCGGGCGACATTT 59.791 47.619 0.00 0.00 46.76 2.32
3791 5226 0.828022 TGGATAAGTCGGGCGACATT 59.172 50.000 0.00 0.00 46.76 2.71
3792 5227 1.048601 ATGGATAAGTCGGGCGACAT 58.951 50.000 0.00 0.00 46.76 3.06
3793 5228 1.338973 GTATGGATAAGTCGGGCGACA 59.661 52.381 0.00 0.00 46.76 4.35
3794 5229 1.338973 TGTATGGATAAGTCGGGCGAC 59.661 52.381 0.00 0.00 44.86 5.19
3795 5230 1.694844 TGTATGGATAAGTCGGGCGA 58.305 50.000 0.00 0.00 0.00 5.54
3796 5231 2.519377 TTGTATGGATAAGTCGGGCG 57.481 50.000 0.00 0.00 0.00 6.13
3797 5232 4.935808 CCTTATTGTATGGATAAGTCGGGC 59.064 45.833 0.00 0.00 36.03 6.13
3798 5233 5.932303 CACCTTATTGTATGGATAAGTCGGG 59.068 44.000 0.00 0.00 36.03 5.14
3799 5234 5.932303 CCACCTTATTGTATGGATAAGTCGG 59.068 44.000 0.00 0.00 36.03 4.79
3800 5235 6.755206 TCCACCTTATTGTATGGATAAGTCG 58.245 40.000 0.00 0.00 36.30 4.18
3807 5242 7.638444 TCTTTTGATCCACCTTATTGTATGGA 58.362 34.615 0.00 0.00 45.12 3.41
3808 5243 7.880160 TCTTTTGATCCACCTTATTGTATGG 57.120 36.000 0.00 0.00 0.00 2.74
3811 5246 8.293867 CGTTTTCTTTTGATCCACCTTATTGTA 58.706 33.333 0.00 0.00 0.00 2.41
3812 5247 7.145323 CGTTTTCTTTTGATCCACCTTATTGT 58.855 34.615 0.00 0.00 0.00 2.71
3813 5248 7.566858 CGTTTTCTTTTGATCCACCTTATTG 57.433 36.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.