Multiple sequence alignment - TraesCS7A01G294500

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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 TraesCS7A01G294500 chr7A 100.000 9875 0 0 1 9875 380184413 380174539 0.000000e+00 18236.0
1 TraesCS7A01G294500 chr7A 96.134 595 8 4 9296 9875 647260120 647259526 0.000000e+00 957.0
2 TraesCS7A01G294500 chr7A 95.798 595 10 4 9296 9875 647210106 647209512 0.000000e+00 946.0
3 TraesCS7A01G294500 chr7A 89.744 117 12 0 2 118 380194928 380194812 6.180000e-32 150.0
4 TraesCS7A01G294500 chr7A 85.294 102 14 1 152 252 245048724 245048825 4.880000e-18 104.0
5 TraesCS7A01G294500 chr7A 100.000 37 0 0 1 37 217691772 217691808 1.780000e-07 69.4
6 TraesCS7A01G294500 chr7A 100.000 36 0 0 1 36 410722078 410722043 6.400000e-07 67.6
7 TraesCS7A01G294500 chr7A 97.368 38 1 0 1 38 299401689 299401726 2.300000e-06 65.8
8 TraesCS7A01G294500 chr7A 97.297 37 1 0 1 37 115740535 115740499 8.280000e-06 63.9
9 TraesCS7A01G294500 chr7B 95.660 9193 255 50 152 9288 278938327 278929223 0.000000e+00 14633.0
10 TraesCS7A01G294500 chr7B 100.000 28 0 0 3474 3501 278934911 278934884 1.800000e-02 52.8
11 TraesCS7A01G294500 chr7D 97.767 6537 99 14 1965 8492 339780273 339786771 0.000000e+00 11219.0
12 TraesCS7A01G294500 chr7D 93.301 1836 89 18 152 1972 339778381 339780197 0.000000e+00 2678.0
13 TraesCS7A01G294500 chr7D 92.849 839 27 14 8490 9298 339786929 339787764 0.000000e+00 1186.0
14 TraesCS7A01G294500 chr7D 97.727 44 1 0 8539 8582 339786929 339786972 1.060000e-09 76.8
15 TraesCS7A01G294500 chr7D 100.000 28 0 0 3474 3501 339781899 339781926 1.800000e-02 52.8
16 TraesCS7A01G294500 chr4A 95.966 595 9 1 9296 9875 12622146 12621552 0.000000e+00 952.0
17 TraesCS7A01G294500 chr4A 85.088 114 14 3 34 146 707070630 707070519 8.110000e-21 113.0
18 TraesCS7A01G294500 chr4A 83.761 117 16 3 34 148 345659141 345659026 3.770000e-19 108.0
19 TraesCS7A01G294500 chr4A 84.071 113 15 3 34 144 346534627 346534738 1.360000e-18 106.0
20 TraesCS7A01G294500 chr4A 82.075 106 17 2 34 138 548772527 548772631 1.370000e-13 89.8
21 TraesCS7A01G294500 chr4A 97.297 37 1 0 2 38 494064041 494064005 8.280000e-06 63.9
22 TraesCS7A01G294500 chr5A 95.638 596 11 7 9295 9875 15086987 15086392 0.000000e+00 942.0
23 TraesCS7A01G294500 chr5A 86.957 115 15 0 34 148 379956801 379956915 8.050000e-26 130.0
24 TraesCS7A01G294500 chr5A 84.211 114 13 4 152 261 290295117 290295229 1.360000e-18 106.0
25 TraesCS7A01G294500 chr5A 82.883 111 15 4 152 259 143122998 143123107 8.160000e-16 97.1
26 TraesCS7A01G294500 chr5A 82.301 113 18 2 152 262 290287827 290287939 8.160000e-16 97.1
27 TraesCS7A01G294500 chr3A 95.630 595 11 1 9296 9875 87787076 87786482 0.000000e+00 941.0
28 TraesCS7A01G294500 chr3A 100.000 37 0 0 2 38 737829422 737829386 1.780000e-07 69.4
29 TraesCS7A01G294500 chr3A 100.000 37 0 0 2 38 737838080 737838044 1.780000e-07 69.4
30 TraesCS7A01G294500 chr3A 100.000 37 0 0 2 38 737854918 737854882 1.780000e-07 69.4
31 TraesCS7A01G294500 chr1A 95.876 582 8 2 9310 9875 587856482 587855901 0.000000e+00 928.0
32 TraesCS7A01G294500 chr2D 95.126 595 14 1 9296 9875 645339182 645339776 0.000000e+00 924.0
33 TraesCS7A01G294500 chr2B 92.785 596 26 6 9296 9875 119512311 119512905 0.000000e+00 846.0
34 TraesCS7A01G294500 chr2B 97.500 40 0 1 9292 9330 797525947 797525986 6.400000e-07 67.6
35 TraesCS7A01G294500 chr1D 81.659 229 32 2 3899 4127 156128850 156129068 2.190000e-41 182.0
36 TraesCS7A01G294500 chr1B 81.659 229 32 4 3899 4127 250419733 250419951 2.190000e-41 182.0
37 TraesCS7A01G294500 chr6D 86.275 102 12 2 162 261 333001912 333001811 1.050000e-19 110.0
38 TraesCS7A01G294500 chr6D 85.294 102 14 1 161 261 248322901 248322800 4.880000e-18 104.0
39 TraesCS7A01G294500 chr4B 82.456 114 16 4 152 262 43069536 43069648 8.160000e-16 97.1
40 TraesCS7A01G294500 chr5B 88.525 61 6 1 9356 9415 669637043 669636983 1.380000e-08 73.1


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 TraesCS7A01G294500 chr7A 380174539 380184413 9874 True 18236.0 18236 100.000 1 9875 1 chr7A.!!$R2 9874
1 TraesCS7A01G294500 chr7A 647259526 647260120 594 True 957.0 957 96.134 9296 9875 1 chr7A.!!$R6 579
2 TraesCS7A01G294500 chr7A 647209512 647210106 594 True 946.0 946 95.798 9296 9875 1 chr7A.!!$R5 579
3 TraesCS7A01G294500 chr7B 278929223 278938327 9104 True 7342.9 14633 97.830 152 9288 2 chr7B.!!$R1 9136
4 TraesCS7A01G294500 chr7D 339778381 339786771 8390 False 6948.5 11219 95.534 152 8492 2 chr7D.!!$F2 8340
5 TraesCS7A01G294500 chr7D 339786929 339787764 835 False 631.4 1186 95.288 8490 9298 2 chr7D.!!$F3 808
6 TraesCS7A01G294500 chr4A 12621552 12622146 594 True 952.0 952 95.966 9296 9875 1 chr4A.!!$R1 579
7 TraesCS7A01G294500 chr5A 15086392 15086987 595 True 942.0 942 95.638 9295 9875 1 chr5A.!!$R1 580
8 TraesCS7A01G294500 chr3A 87786482 87787076 594 True 941.0 941 95.630 9296 9875 1 chr3A.!!$R1 579
9 TraesCS7A01G294500 chr1A 587855901 587856482 581 True 928.0 928 95.876 9310 9875 1 chr1A.!!$R1 565
10 TraesCS7A01G294500 chr2D 645339182 645339776 594 False 924.0 924 95.126 9296 9875 1 chr2D.!!$F1 579
11 TraesCS7A01G294500 chr2B 119512311 119512905 594 False 846.0 846 92.785 9296 9875 1 chr2B.!!$F1 579

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
134 135 0.037303 CCATGGAGTCAACCTGTGCT 59.963 55.000 5.56 0.0 0.00 4.40 F
504 507 0.252239 GAGGGGTTGGGGCAAGATTT 60.252 55.000 0.00 0.0 0.00 2.17 F
965 1008 0.476808 TCTTCCCAAACCCTAGCCCA 60.477 55.000 0.00 0.0 0.00 5.36 F
2509 2639 0.801067 AACGACTATTCCGCGACAGC 60.801 55.000 8.23 0.0 40.74 4.40 F
3905 4036 0.820074 ATCTCTAGGAGCCGGACGTG 60.820 60.000 5.05 0.0 0.00 4.49 F
5177 5313 0.684479 AGACCACTAGAGATGCCGCA 60.684 55.000 0.00 0.0 0.00 5.69 F
6341 6484 4.996758 TCGTTTATCATCATGGGCATAGTG 59.003 41.667 0.00 0.0 0.00 2.74 F
6678 6823 1.070445 CCAGGCAATTTTGGTCTGCAA 59.930 47.619 0.00 0.0 37.83 4.08 F
7914 8059 2.143122 TGGTTAAGAGCAGCAGAAACG 58.857 47.619 0.00 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1404 2.596904 TCTACAAGTAAGCATCGGCC 57.403 50.000 0.00 0.00 42.56 6.13 R
1920 1967 6.428465 TGCAATCCTATTTTACAAGTTGACGA 59.572 34.615 10.54 0.00 0.00 4.20 R
2938 3068 1.411787 GGAAGCCAGGCTAGGAGTAGA 60.412 57.143 16.56 0.00 38.25 2.59 R
3975 4106 1.361271 CCGAAACTATAGCGGCCGA 59.639 57.895 33.48 9.86 38.46 5.54 R
5242 5378 1.702182 TCCTCAAAAGCATGTTGCCA 58.298 45.000 0.00 0.00 46.52 4.92 R
6402 6545 2.684881 CAAATGAGGTAGCCCATGACAC 59.315 50.000 0.00 0.00 0.00 3.67 R
7419 7564 1.414919 GGTAGGCCACGATGTAATGGA 59.585 52.381 5.01 0.00 38.34 3.41 R
8130 8275 2.265467 TAGGCCCCAAATGCGACCTC 62.265 60.000 0.00 0.00 0.00 3.85 R
9121 9296 0.242825 TCGGAAGTTACCAGCACTCG 59.757 55.000 0.00 0.00 0.00 4.18 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
46 47 9.765295 TTATTAGGGATAGATTAGTACCACCTC 57.235 37.037 0.00 0.00 0.00 3.85
47 48 5.681494 AGGGATAGATTAGTACCACCTCA 57.319 43.478 0.00 0.00 0.00 3.86
48 49 5.395611 AGGGATAGATTAGTACCACCTCAC 58.604 45.833 0.00 0.00 0.00 3.51
49 50 4.217983 GGGATAGATTAGTACCACCTCACG 59.782 50.000 0.00 0.00 0.00 4.35
50 51 4.826183 GGATAGATTAGTACCACCTCACGT 59.174 45.833 0.00 0.00 0.00 4.49
51 52 6.000219 GGATAGATTAGTACCACCTCACGTA 59.000 44.000 0.00 0.00 0.00 3.57
52 53 6.658391 GGATAGATTAGTACCACCTCACGTAT 59.342 42.308 0.00 0.00 0.00 3.06
53 54 7.826252 GGATAGATTAGTACCACCTCACGTATA 59.174 40.741 0.00 0.00 0.00 1.47
54 55 9.393512 GATAGATTAGTACCACCTCACGTATAT 57.606 37.037 0.00 0.00 0.00 0.86
57 58 9.750783 AGATTAGTACCACCTCACGTATATATT 57.249 33.333 0.00 0.00 0.00 1.28
81 82 9.922305 ATTTTAAATTCAAATCGAAAACGCAAA 57.078 22.222 0.00 0.00 37.12 3.68
82 83 9.922305 TTTTAAATTCAAATCGAAAACGCAAAT 57.078 22.222 0.00 0.00 37.12 2.32
83 84 9.922305 TTTAAATTCAAATCGAAAACGCAAATT 57.078 22.222 0.00 0.00 37.12 1.82
84 85 9.574401 TTAAATTCAAATCGAAAACGCAAATTC 57.426 25.926 0.00 0.00 37.12 2.17
86 87 3.118809 TCAAATCGAAAACGCAAATTCGC 59.881 39.130 9.20 0.00 45.91 4.70
87 88 2.323939 ATCGAAAACGCAAATTCGCA 57.676 40.000 9.20 1.47 45.91 5.10
88 89 1.669184 TCGAAAACGCAAATTCGCAG 58.331 45.000 9.20 0.00 45.91 5.18
89 90 1.261885 TCGAAAACGCAAATTCGCAGA 59.738 42.857 9.20 0.00 45.91 4.26
90 91 2.040524 CGAAAACGCAAATTCGCAGAA 58.959 42.857 2.44 0.00 45.90 3.02
91 92 2.465839 CGAAAACGCAAATTCGCAGAAA 59.534 40.909 2.44 0.00 45.90 2.52
92 93 3.419149 CGAAAACGCAAATTCGCAGAAAG 60.419 43.478 2.44 0.00 45.90 2.62
93 94 3.347958 AAACGCAAATTCGCAGAAAGA 57.652 38.095 0.00 0.00 45.90 2.52
94 95 3.347958 AACGCAAATTCGCAGAAAGAA 57.652 38.095 0.00 0.00 45.90 2.52
95 96 2.921126 ACGCAAATTCGCAGAAAGAAG 58.079 42.857 0.00 0.00 45.90 2.85
96 97 2.245096 CGCAAATTCGCAGAAAGAAGG 58.755 47.619 0.00 0.00 45.90 3.46
97 98 1.988467 GCAAATTCGCAGAAAGAAGGC 59.012 47.619 0.00 0.00 45.90 4.35
103 104 2.442189 CGCAGAAAGAAGGCGTATTG 57.558 50.000 0.00 0.00 45.27 1.90
104 105 1.732259 CGCAGAAAGAAGGCGTATTGT 59.268 47.619 0.00 0.00 45.27 2.71
105 106 2.474526 CGCAGAAAGAAGGCGTATTGTG 60.475 50.000 0.00 0.00 45.27 3.33
106 107 2.742053 GCAGAAAGAAGGCGTATTGTGA 59.258 45.455 1.17 0.00 0.00 3.58
107 108 3.424962 GCAGAAAGAAGGCGTATTGTGAC 60.425 47.826 1.17 0.00 0.00 3.67
108 109 3.997021 CAGAAAGAAGGCGTATTGTGACT 59.003 43.478 0.00 0.00 0.00 3.41
109 110 5.168569 CAGAAAGAAGGCGTATTGTGACTA 58.831 41.667 0.00 0.00 0.00 2.59
110 111 5.812642 CAGAAAGAAGGCGTATTGTGACTAT 59.187 40.000 0.00 0.00 0.00 2.12
111 112 5.812642 AGAAAGAAGGCGTATTGTGACTATG 59.187 40.000 0.00 0.00 0.00 2.23
112 113 5.339008 AAGAAGGCGTATTGTGACTATGA 57.661 39.130 0.00 0.00 0.00 2.15
113 114 5.339008 AGAAGGCGTATTGTGACTATGAA 57.661 39.130 0.00 0.00 0.00 2.57
114 115 5.109903 AGAAGGCGTATTGTGACTATGAAC 58.890 41.667 0.00 0.00 0.00 3.18
115 116 3.793559 AGGCGTATTGTGACTATGAACC 58.206 45.455 0.00 0.00 0.00 3.62
116 117 2.870411 GGCGTATTGTGACTATGAACCC 59.130 50.000 0.00 0.00 0.00 4.11
117 118 3.527533 GCGTATTGTGACTATGAACCCA 58.472 45.455 0.00 0.00 0.00 4.51
118 119 4.127171 GCGTATTGTGACTATGAACCCAT 58.873 43.478 0.00 0.00 36.81 4.00
119 120 4.024893 GCGTATTGTGACTATGAACCCATG 60.025 45.833 0.00 0.00 34.31 3.66
120 121 4.511454 CGTATTGTGACTATGAACCCATGG 59.489 45.833 4.14 4.14 37.30 3.66
121 122 4.860802 ATTGTGACTATGAACCCATGGA 57.139 40.909 15.22 0.00 35.51 3.41
122 123 3.912496 TGTGACTATGAACCCATGGAG 57.088 47.619 15.22 5.95 35.51 3.86
123 124 3.181329 TGTGACTATGAACCCATGGAGT 58.819 45.455 15.22 7.35 35.51 3.85
124 125 3.197766 TGTGACTATGAACCCATGGAGTC 59.802 47.826 15.22 16.92 38.20 3.36
125 126 3.197766 GTGACTATGAACCCATGGAGTCA 59.802 47.826 21.68 21.68 42.02 3.41
126 127 3.843619 TGACTATGAACCCATGGAGTCAA 59.156 43.478 22.74 11.11 41.65 3.18
127 128 4.192317 GACTATGAACCCATGGAGTCAAC 58.808 47.826 15.22 5.90 37.88 3.18
128 129 2.514458 ATGAACCCATGGAGTCAACC 57.486 50.000 15.22 1.53 0.00 3.77
129 130 1.444933 TGAACCCATGGAGTCAACCT 58.555 50.000 15.22 0.00 0.00 3.50
130 131 1.073763 TGAACCCATGGAGTCAACCTG 59.926 52.381 15.22 0.00 0.00 4.00
131 132 1.073923 GAACCCATGGAGTCAACCTGT 59.926 52.381 15.22 0.00 0.00 4.00
132 133 0.401738 ACCCATGGAGTCAACCTGTG 59.598 55.000 15.22 0.00 0.00 3.66
133 134 0.962356 CCCATGGAGTCAACCTGTGC 60.962 60.000 15.22 0.00 0.00 4.57
134 135 0.037303 CCATGGAGTCAACCTGTGCT 59.963 55.000 5.56 0.00 0.00 4.40
135 136 1.546323 CCATGGAGTCAACCTGTGCTT 60.546 52.381 5.56 0.00 0.00 3.91
136 137 2.233271 CATGGAGTCAACCTGTGCTTT 58.767 47.619 0.00 0.00 0.00 3.51
137 138 3.411446 CATGGAGTCAACCTGTGCTTTA 58.589 45.455 0.00 0.00 0.00 1.85
138 139 3.788227 TGGAGTCAACCTGTGCTTTAT 57.212 42.857 0.00 0.00 0.00 1.40
139 140 4.098914 TGGAGTCAACCTGTGCTTTATT 57.901 40.909 0.00 0.00 0.00 1.40
140 141 5.235850 TGGAGTCAACCTGTGCTTTATTA 57.764 39.130 0.00 0.00 0.00 0.98
141 142 5.815581 TGGAGTCAACCTGTGCTTTATTAT 58.184 37.500 0.00 0.00 0.00 1.28
142 143 6.245408 TGGAGTCAACCTGTGCTTTATTATT 58.755 36.000 0.00 0.00 0.00 1.40
143 144 7.398829 TGGAGTCAACCTGTGCTTTATTATTA 58.601 34.615 0.00 0.00 0.00 0.98
144 145 7.885922 TGGAGTCAACCTGTGCTTTATTATTAA 59.114 33.333 0.00 0.00 0.00 1.40
145 146 8.398665 GGAGTCAACCTGTGCTTTATTATTAAG 58.601 37.037 0.00 0.00 0.00 1.85
146 147 8.281212 AGTCAACCTGTGCTTTATTATTAAGG 57.719 34.615 0.00 0.00 0.00 2.69
147 148 8.107095 AGTCAACCTGTGCTTTATTATTAAGGA 58.893 33.333 0.00 0.00 0.00 3.36
148 149 8.398665 GTCAACCTGTGCTTTATTATTAAGGAG 58.601 37.037 0.00 0.00 0.00 3.69
149 150 7.556275 TCAACCTGTGCTTTATTATTAAGGAGG 59.444 37.037 0.00 0.00 0.00 4.30
150 151 6.365520 ACCTGTGCTTTATTATTAAGGAGGG 58.634 40.000 0.00 4.09 0.00 4.30
151 152 6.159751 ACCTGTGCTTTATTATTAAGGAGGGA 59.840 38.462 9.77 0.00 0.00 4.20
152 153 7.147123 ACCTGTGCTTTATTATTAAGGAGGGAT 60.147 37.037 9.77 0.00 0.00 3.85
153 154 7.175641 CCTGTGCTTTATTATTAAGGAGGGATG 59.824 40.741 0.00 0.00 0.00 3.51
154 155 6.490040 TGTGCTTTATTATTAAGGAGGGATGC 59.510 38.462 0.00 0.00 0.00 3.91
155 156 6.490040 GTGCTTTATTATTAAGGAGGGATGCA 59.510 38.462 0.00 0.00 0.00 3.96
156 157 7.014230 GTGCTTTATTATTAAGGAGGGATGCAA 59.986 37.037 0.00 0.00 0.00 4.08
157 158 7.563188 TGCTTTATTATTAAGGAGGGATGCAAA 59.437 33.333 0.00 0.00 0.00 3.68
158 159 8.588472 GCTTTATTATTAAGGAGGGATGCAAAT 58.412 33.333 0.00 0.00 0.00 2.32
209 210 3.980646 ACAAGCAAGCAATTAACACGA 57.019 38.095 0.00 0.00 0.00 4.35
215 216 4.083484 AGCAAGCAATTAACACGACTAACC 60.083 41.667 0.00 0.00 0.00 2.85
226 227 4.200874 ACACGACTAACCCAAAAACATGA 58.799 39.130 0.00 0.00 0.00 3.07
235 236 3.244526 ACCCAAAAACATGAAAGGCATCC 60.245 43.478 0.00 0.00 34.15 3.51
273 274 3.263489 TCGTTACAAAGGTTGTGGACA 57.737 42.857 3.90 0.00 45.03 4.02
287 289 1.633945 GTGGACAGGTTCCCCTACAAT 59.366 52.381 0.00 0.00 45.17 2.71
309 311 4.657824 CGACGACGCTGGTGGGTT 62.658 66.667 0.00 0.00 39.55 4.11
317 319 2.102588 GACGCTGGTGGGTTATGACTAT 59.897 50.000 0.00 0.00 39.55 2.12
325 327 3.808174 GTGGGTTATGACTATTTCTCCGC 59.192 47.826 0.00 0.00 0.00 5.54
329 331 0.753262 ATGACTATTTCTCCGCCGCT 59.247 50.000 0.00 0.00 0.00 5.52
358 360 4.545706 GGCCGCCATGGACGATGA 62.546 66.667 24.22 0.00 42.00 2.92
359 361 2.281070 GCCGCCATGGACGATGAT 60.281 61.111 24.22 0.00 42.00 2.45
363 365 1.338105 CCGCCATGGACGATGATGTAT 60.338 52.381 24.22 0.00 42.00 2.29
387 389 3.506096 CGCGAGTGGAGTCGGCTA 61.506 66.667 0.00 0.00 40.44 3.93
389 391 2.113433 GCGAGTGGAGTCGGCTAGA 61.113 63.158 6.04 0.00 40.44 2.43
418 420 8.924691 CACAACGACATCAATAAATTTTGGAAT 58.075 29.630 0.00 0.00 0.00 3.01
420 422 9.138062 CAACGACATCAATAAATTTTGGAATGA 57.862 29.630 0.00 0.00 0.00 2.57
421 423 9.703892 AACGACATCAATAAATTTTGGAATGAA 57.296 25.926 0.00 0.00 0.00 2.57
446 448 0.468226 GATCGGGTGGGAGCACATTA 59.532 55.000 0.00 0.00 0.00 1.90
465 468 9.450807 GCACATTAGCGACAATAAATTTTAGAT 57.549 29.630 0.00 0.00 0.00 1.98
504 507 0.252239 GAGGGGTTGGGGCAAGATTT 60.252 55.000 0.00 0.00 0.00 2.17
505 508 1.006639 GAGGGGTTGGGGCAAGATTTA 59.993 52.381 0.00 0.00 0.00 1.40
554 557 3.121019 TTTTTCCGGGTTGTGCCG 58.879 55.556 0.00 0.00 38.44 5.69
556 559 1.726533 TTTTTCCGGGTTGTGCCGTC 61.727 55.000 0.00 0.00 38.44 4.79
564 567 1.366111 GGTTGTGCCGTCGTGCATAT 61.366 55.000 10.82 0.00 44.30 1.78
569 572 1.520564 GCCGTCGTGCATATGTGGA 60.521 57.895 4.29 0.00 0.00 4.02
570 573 0.880278 GCCGTCGTGCATATGTGGAT 60.880 55.000 4.29 0.00 0.00 3.41
571 574 1.581934 CCGTCGTGCATATGTGGATT 58.418 50.000 4.29 0.00 0.00 3.01
581 584 4.274705 TGCATATGTGGATTATTTTCGCGT 59.725 37.500 5.77 0.00 0.00 6.01
588 591 1.064952 GATTATTTTCGCGTGGGGGTG 59.935 52.381 5.77 0.00 0.00 4.61
591 594 3.717695 TATTTTCGCGTGGGGGTGGAG 62.718 57.143 5.77 0.00 0.00 3.86
637 640 3.134623 TCGGTTGAGCCATCATGATAAGT 59.865 43.478 8.15 0.00 34.73 2.24
641 644 3.047857 TGAGCCATCATGATAAGTGGGA 58.952 45.455 8.15 0.00 32.35 4.37
645 648 4.166725 AGCCATCATGATAAGTGGGAAGAA 59.833 41.667 8.15 0.00 32.35 2.52
666 669 2.195727 TGGTAGGTTGAGCCATCATGA 58.804 47.619 0.00 0.00 40.61 3.07
676 679 4.512484 TGAGCCATCATGACGTTTGATTA 58.488 39.130 11.08 0.00 31.50 1.75
853 892 2.101582 AGACGATCGGGAAAAGGATCAG 59.898 50.000 20.98 0.00 39.16 2.90
889 928 6.571344 CGTGTTACAAATCCCAAATCAATCCA 60.571 38.462 0.00 0.00 0.00 3.41
891 930 7.117667 GTGTTACAAATCCCAAATCAATCCAAC 59.882 37.037 0.00 0.00 0.00 3.77
892 931 7.016072 TGTTACAAATCCCAAATCAATCCAACT 59.984 33.333 0.00 0.00 0.00 3.16
893 932 6.041423 ACAAATCCCAAATCAATCCAACTC 57.959 37.500 0.00 0.00 0.00 3.01
895 934 4.614967 ATCCCAAATCAATCCAACTCCT 57.385 40.909 0.00 0.00 0.00 3.69
897 936 4.344104 TCCCAAATCAATCCAACTCCTTC 58.656 43.478 0.00 0.00 0.00 3.46
965 1008 0.476808 TCTTCCCAAACCCTAGCCCA 60.477 55.000 0.00 0.00 0.00 5.36
1361 1404 1.792993 GCTGCTTGCTGTGCTTATTCG 60.793 52.381 0.00 0.00 38.95 3.34
1826 1873 6.437162 TGCTATTTTGGCTAGGAACTTTTGAT 59.563 34.615 0.00 0.00 41.75 2.57
1891 1938 1.703411 TGAAAGCTGGTTTTCTGGGG 58.297 50.000 6.27 0.00 37.81 4.96
1896 1943 2.627933 AGCTGGTTTTCTGGGGTACTA 58.372 47.619 0.00 0.00 0.00 1.82
1919 1966 7.984050 ACTATATTCTGTTCAGATGTCCTGTTG 59.016 37.037 3.28 0.00 43.38 3.33
1920 1967 4.422073 TTCTGTTCAGATGTCCTGTTGT 57.578 40.909 3.28 0.00 43.38 3.32
1921 1968 3.995199 TCTGTTCAGATGTCCTGTTGTC 58.005 45.455 0.00 0.00 43.38 3.18
2509 2639 0.801067 AACGACTATTCCGCGACAGC 60.801 55.000 8.23 0.00 40.74 4.40
2589 2719 1.001378 GCGCAACACCAACTCAAGAAT 60.001 47.619 0.30 0.00 0.00 2.40
2938 3068 9.533253 CTTTTGTCATATCTTTTCCTTTGTGTT 57.467 29.630 0.00 0.00 0.00 3.32
3140 3270 4.450976 ACCTTTTGCATTTTTCACCCTTC 58.549 39.130 0.00 0.00 0.00 3.46
3380 3510 7.194278 CCTTATTTGATGCTCAATCTTCACAG 58.806 38.462 0.41 0.00 36.11 3.66
3386 3516 1.471684 GCTCAATCTTCACAGCAAGGG 59.528 52.381 0.00 0.00 0.00 3.95
3396 3526 1.610522 CACAGCAAGGGGAGAAAACAG 59.389 52.381 0.00 0.00 0.00 3.16
3455 3585 6.934048 TGAACAAGTTTCATCACACATGTA 57.066 33.333 0.00 0.00 0.00 2.29
3460 3590 8.445275 ACAAGTTTCATCACACATGTACTTTA 57.555 30.769 0.00 0.00 0.00 1.85
3476 3606 7.171630 TGTACTTTACAAACACCCAAACAAT 57.828 32.000 0.00 0.00 35.38 2.71
3477 3607 7.612677 TGTACTTTACAAACACCCAAACAATT 58.387 30.769 0.00 0.00 35.38 2.32
3478 3608 6.976636 ACTTTACAAACACCCAAACAATTG 57.023 33.333 3.24 3.24 36.25 2.32
3492 3622 5.473039 CAAACAATTGGTGAATCCTTCTCC 58.527 41.667 10.83 1.89 42.28 3.71
3493 3623 3.701664 ACAATTGGTGAATCCTTCTCCC 58.298 45.455 10.83 0.00 41.48 4.30
3494 3624 3.334881 ACAATTGGTGAATCCTTCTCCCT 59.665 43.478 10.83 0.00 41.48 4.20
3495 3625 4.202716 ACAATTGGTGAATCCTTCTCCCTT 60.203 41.667 10.83 0.00 41.48 3.95
3496 3626 5.015178 ACAATTGGTGAATCCTTCTCCCTTA 59.985 40.000 10.83 0.00 41.48 2.69
3497 3627 4.844349 TTGGTGAATCCTTCTCCCTTAG 57.156 45.455 5.73 0.00 41.48 2.18
3514 3644 3.826157 CCTTAGGATCCACAAGCAACAAA 59.174 43.478 15.82 0.00 0.00 2.83
3629 3759 4.853007 CTCCAATTGGTGAATCCTTCTCT 58.147 43.478 23.76 0.00 37.07 3.10
3812 3943 4.767255 GCAGGCAGGGGTCAGACG 62.767 72.222 0.00 0.00 0.00 4.18
3869 4000 2.281070 CGTTGCTCCAGCTGGTGT 60.281 61.111 31.58 0.00 42.66 4.16
3905 4036 0.820074 ATCTCTAGGAGCCGGACGTG 60.820 60.000 5.05 0.00 0.00 4.49
3988 4119 1.358046 GACGTTCGGCCGCTATAGT 59.642 57.895 23.51 15.54 0.00 2.12
4108 4239 1.068741 CATAGAGTCCCGGTTGTAGGC 59.931 57.143 0.00 0.00 0.00 3.93
4368 4501 4.883759 TCAATCTCCCTTGGTGATCTCTA 58.116 43.478 0.00 0.00 35.24 2.43
4370 4503 2.656002 TCTCCCTTGGTGATCTCTACG 58.344 52.381 0.00 0.00 0.00 3.51
4380 4513 5.532557 TGGTGATCTCTACGCAATAATGAG 58.467 41.667 0.00 0.00 0.00 2.90
4418 4551 3.569701 CCTAACAAACATGCACCAGAACT 59.430 43.478 0.00 0.00 0.00 3.01
4532 4665 1.051556 AGGGCTAGGAGCAGGCTAAC 61.052 60.000 0.21 0.00 44.75 2.34
4638 4774 3.129813 CGTACATACTGCTTACTGACCCA 59.870 47.826 0.00 0.00 0.00 4.51
4690 4826 4.762289 AGACACAAGGAGACTGTTTCTT 57.238 40.909 0.00 0.00 42.68 2.52
4710 4846 8.630917 GTTTCTTTTATAGATTTTCCTAGGGGC 58.369 37.037 9.46 0.00 31.54 5.80
5042 5178 8.759481 TCATATGGACAGAGATCTATGATACC 57.241 38.462 23.69 20.41 0.00 2.73
5177 5313 0.684479 AGACCACTAGAGATGCCGCA 60.684 55.000 0.00 0.00 0.00 5.69
5242 5378 6.351286 GCCTGATAGAAATGGTTGGTTTGAAT 60.351 38.462 0.00 0.00 0.00 2.57
5510 5646 6.001460 TGTCCCGAAATAGAAACAACATTCT 58.999 36.000 0.00 0.00 42.21 2.40
5532 5668 5.602978 TCTGTCTTTACCTTCCTCTGAAACT 59.397 40.000 0.00 0.00 0.00 2.66
6047 6185 5.323382 TGATGGGCTACATATTTGTCCAT 57.677 39.130 7.45 7.45 39.45 3.41
6059 6197 7.879070 ACATATTTGTCCATATGCATCTTCAC 58.121 34.615 0.19 0.00 39.77 3.18
6172 6313 6.063404 TGGAAATGCATATATTCTGTCTGCA 58.937 36.000 0.00 0.00 45.84 4.41
6304 6447 5.744171 TGTGGCTATCTTTATTGCTTCTCA 58.256 37.500 0.00 0.00 34.69 3.27
6341 6484 4.996758 TCGTTTATCATCATGGGCATAGTG 59.003 41.667 0.00 0.00 0.00 2.74
6402 6545 7.032377 AGAGAAAGGAAACAACTTTTAGCAG 57.968 36.000 0.00 0.00 38.21 4.24
6678 6823 1.070445 CCAGGCAATTTTGGTCTGCAA 59.930 47.619 0.00 0.00 37.83 4.08
7419 7564 2.370189 AGTGTCTAGTTTTGCTCTGCCT 59.630 45.455 0.00 0.00 0.00 4.75
7914 8059 2.143122 TGGTTAAGAGCAGCAGAAACG 58.857 47.619 0.00 0.00 0.00 3.60
8130 8275 6.356556 TGATGGTAATATTGTTGGTCTCCAG 58.643 40.000 0.00 0.00 33.81 3.86
8294 8439 0.550914 ACCCTGACCTTGCAACTTGA 59.449 50.000 0.00 0.00 0.00 3.02
8300 8445 4.631813 CCTGACCTTGCAACTTGACTATAC 59.368 45.833 0.00 0.00 0.00 1.47
8449 8594 3.935203 ACGCTGAATGTGATACTCCTTTG 59.065 43.478 0.00 0.00 0.00 2.77
8795 8940 1.963515 GTTGATTGCAGGAACCCTTGT 59.036 47.619 0.00 0.00 0.00 3.16
8807 8952 3.380320 GGAACCCTTGTCCCATTATTTCG 59.620 47.826 0.00 0.00 0.00 3.46
8846 8991 7.621991 CGGCTAGACAAGACATGTAAAATTAG 58.378 38.462 0.00 0.00 44.12 1.73
9004 9150 3.716006 CGCCACAGTTGTCGCCTG 61.716 66.667 0.00 0.00 36.01 4.85
9005 9151 4.030452 GCCACAGTTGTCGCCTGC 62.030 66.667 0.00 0.00 33.09 4.85
9031 9179 9.329913 CGCTGCTTTTACATTAATATATGGAAC 57.670 33.333 0.00 0.00 28.14 3.62
9121 9296 1.589716 GCAGGACAATGTCAGCCCAC 61.590 60.000 15.86 0.00 33.68 4.61
9157 9332 1.338769 CCGAGAAAACCCAGGACGAAT 60.339 52.381 0.00 0.00 0.00 3.34
9244 9422 5.976458 TCTTTGGTTTGTCTTTCTTTGCAT 58.024 33.333 0.00 0.00 0.00 3.96
9362 9541 8.978874 ATAAATCTCCTGTTGCATGTAATACA 57.021 30.769 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.765295 GAGGTGGTACTAATCTATCCCTAATAA 57.235 37.037 0.00 0.00 0.00 1.40
21 22 8.908095 TGAGGTGGTACTAATCTATCCCTAATA 58.092 37.037 0.00 0.00 0.00 0.98
22 23 7.674772 GTGAGGTGGTACTAATCTATCCCTAAT 59.325 40.741 0.00 0.00 0.00 1.73
23 24 7.008941 GTGAGGTGGTACTAATCTATCCCTAA 58.991 42.308 0.00 0.00 0.00 2.69
24 25 6.550163 GTGAGGTGGTACTAATCTATCCCTA 58.450 44.000 0.00 0.00 0.00 3.53
25 26 5.395611 GTGAGGTGGTACTAATCTATCCCT 58.604 45.833 0.00 0.00 0.00 4.20
26 27 4.217983 CGTGAGGTGGTACTAATCTATCCC 59.782 50.000 0.00 0.00 0.00 3.85
27 28 4.826183 ACGTGAGGTGGTACTAATCTATCC 59.174 45.833 0.00 0.00 0.00 2.59
28 29 7.684937 ATACGTGAGGTGGTACTAATCTATC 57.315 40.000 0.00 0.00 0.00 2.08
31 32 9.750783 AATATATACGTGAGGTGGTACTAATCT 57.249 33.333 0.00 0.00 0.00 2.40
59 60 7.942011 CGAATTTGCGTTTTCGATTTGAATTTA 59.058 29.630 8.51 0.00 45.68 1.40
60 61 6.785164 CGAATTTGCGTTTTCGATTTGAATTT 59.215 30.769 8.51 0.00 45.68 1.82
61 62 6.288419 CGAATTTGCGTTTTCGATTTGAATT 58.712 32.000 8.51 0.00 45.68 2.17
62 63 5.665217 GCGAATTTGCGTTTTCGATTTGAAT 60.665 36.000 15.96 0.00 45.68 2.57
63 64 4.374508 GCGAATTTGCGTTTTCGATTTGAA 60.375 37.500 15.96 0.00 45.68 2.69
64 65 3.118809 GCGAATTTGCGTTTTCGATTTGA 59.881 39.130 15.96 0.00 45.68 2.69
65 66 3.121529 TGCGAATTTGCGTTTTCGATTTG 60.122 39.130 13.01 0.00 45.68 2.32
66 67 3.046390 TGCGAATTTGCGTTTTCGATTT 58.954 36.364 13.01 0.00 45.68 2.17
67 68 2.656085 TGCGAATTTGCGTTTTCGATT 58.344 38.095 13.01 0.00 45.68 3.34
68 69 2.095969 TCTGCGAATTTGCGTTTTCGAT 60.096 40.909 13.01 0.00 45.68 3.59
69 70 1.261885 TCTGCGAATTTGCGTTTTCGA 59.738 42.857 13.01 0.35 45.68 3.71
70 71 1.669184 TCTGCGAATTTGCGTTTTCG 58.331 45.000 13.01 9.53 45.61 3.46
71 72 3.728718 TCTTTCTGCGAATTTGCGTTTTC 59.271 39.130 13.01 0.00 37.81 2.29
72 73 3.701241 TCTTTCTGCGAATTTGCGTTTT 58.299 36.364 13.01 0.00 37.81 2.43
73 74 3.347958 TCTTTCTGCGAATTTGCGTTT 57.652 38.095 13.01 0.00 37.81 3.60
74 75 3.300009 CTTCTTTCTGCGAATTTGCGTT 58.700 40.909 13.01 0.00 37.81 4.84
75 76 2.350772 CCTTCTTTCTGCGAATTTGCGT 60.351 45.455 13.01 0.00 37.81 5.24
76 77 2.245096 CCTTCTTTCTGCGAATTTGCG 58.755 47.619 13.01 7.98 37.81 4.85
77 78 1.988467 GCCTTCTTTCTGCGAATTTGC 59.012 47.619 10.99 10.99 0.00 3.68
85 86 2.742053 TCACAATACGCCTTCTTTCTGC 59.258 45.455 0.00 0.00 0.00 4.26
86 87 3.997021 AGTCACAATACGCCTTCTTTCTG 59.003 43.478 0.00 0.00 0.00 3.02
87 88 4.273148 AGTCACAATACGCCTTCTTTCT 57.727 40.909 0.00 0.00 0.00 2.52
88 89 5.810587 TCATAGTCACAATACGCCTTCTTTC 59.189 40.000 0.00 0.00 0.00 2.62
89 90 5.730550 TCATAGTCACAATACGCCTTCTTT 58.269 37.500 0.00 0.00 0.00 2.52
90 91 5.339008 TCATAGTCACAATACGCCTTCTT 57.661 39.130 0.00 0.00 0.00 2.52
91 92 5.109903 GTTCATAGTCACAATACGCCTTCT 58.890 41.667 0.00 0.00 0.00 2.85
92 93 4.270325 GGTTCATAGTCACAATACGCCTTC 59.730 45.833 0.00 0.00 0.00 3.46
93 94 4.189231 GGTTCATAGTCACAATACGCCTT 58.811 43.478 0.00 0.00 0.00 4.35
94 95 3.431766 GGGTTCATAGTCACAATACGCCT 60.432 47.826 0.00 0.00 0.00 5.52
95 96 2.870411 GGGTTCATAGTCACAATACGCC 59.130 50.000 0.00 0.00 0.00 5.68
96 97 3.527533 TGGGTTCATAGTCACAATACGC 58.472 45.455 0.00 0.00 0.00 4.42
97 98 4.511454 CCATGGGTTCATAGTCACAATACG 59.489 45.833 2.85 0.00 31.33 3.06
98 99 5.680619 TCCATGGGTTCATAGTCACAATAC 58.319 41.667 13.02 0.00 31.33 1.89
99 100 5.428457 ACTCCATGGGTTCATAGTCACAATA 59.572 40.000 13.02 0.00 31.33 1.90
100 101 4.228210 ACTCCATGGGTTCATAGTCACAAT 59.772 41.667 13.02 0.00 31.33 2.71
101 102 3.587061 ACTCCATGGGTTCATAGTCACAA 59.413 43.478 13.02 0.00 31.33 3.33
102 103 3.181329 ACTCCATGGGTTCATAGTCACA 58.819 45.455 13.02 0.00 31.33 3.58
103 104 3.197766 TGACTCCATGGGTTCATAGTCAC 59.802 47.826 21.68 4.74 40.89 3.67
104 105 3.449918 TGACTCCATGGGTTCATAGTCA 58.550 45.455 21.68 21.68 42.28 3.41
105 106 4.192317 GTTGACTCCATGGGTTCATAGTC 58.808 47.826 17.88 17.88 38.51 2.59
106 107 3.054361 GGTTGACTCCATGGGTTCATAGT 60.054 47.826 13.02 6.56 31.33 2.12
107 108 3.200825 AGGTTGACTCCATGGGTTCATAG 59.799 47.826 13.02 2.81 31.33 2.23
108 109 3.054434 CAGGTTGACTCCATGGGTTCATA 60.054 47.826 13.02 3.62 31.33 2.15
109 110 1.995542 AGGTTGACTCCATGGGTTCAT 59.004 47.619 13.02 0.00 0.00 2.57
110 111 1.073763 CAGGTTGACTCCATGGGTTCA 59.926 52.381 13.02 11.87 0.00 3.18
111 112 1.073923 ACAGGTTGACTCCATGGGTTC 59.926 52.381 13.02 9.20 0.00 3.62
112 113 1.149101 ACAGGTTGACTCCATGGGTT 58.851 50.000 13.02 0.00 0.00 4.11
113 114 0.401738 CACAGGTTGACTCCATGGGT 59.598 55.000 13.02 8.85 0.00 4.51
114 115 0.962356 GCACAGGTTGACTCCATGGG 60.962 60.000 13.02 5.22 0.00 4.00
115 116 0.037303 AGCACAGGTTGACTCCATGG 59.963 55.000 4.97 4.97 0.00 3.66
116 117 1.901591 AAGCACAGGTTGACTCCATG 58.098 50.000 0.00 0.00 0.00 3.66
117 118 2.664402 AAAGCACAGGTTGACTCCAT 57.336 45.000 0.00 0.00 0.00 3.41
118 119 3.788227 ATAAAGCACAGGTTGACTCCA 57.212 42.857 0.00 0.00 0.00 3.86
119 120 6.759497 AATAATAAAGCACAGGTTGACTCC 57.241 37.500 0.00 0.00 0.00 3.85
120 121 8.398665 CCTTAATAATAAAGCACAGGTTGACTC 58.601 37.037 0.00 0.00 0.00 3.36
121 122 8.107095 TCCTTAATAATAAAGCACAGGTTGACT 58.893 33.333 0.00 0.00 0.00 3.41
122 123 8.276252 TCCTTAATAATAAAGCACAGGTTGAC 57.724 34.615 0.00 0.00 0.00 3.18
123 124 7.556275 CCTCCTTAATAATAAAGCACAGGTTGA 59.444 37.037 0.00 0.00 0.00 3.18
124 125 7.201821 CCCTCCTTAATAATAAAGCACAGGTTG 60.202 40.741 0.00 0.00 0.00 3.77
125 126 6.833933 CCCTCCTTAATAATAAAGCACAGGTT 59.166 38.462 0.00 0.00 0.00 3.50
126 127 6.159751 TCCCTCCTTAATAATAAAGCACAGGT 59.840 38.462 0.00 0.00 0.00 4.00
127 128 6.601332 TCCCTCCTTAATAATAAAGCACAGG 58.399 40.000 0.00 0.00 0.00 4.00
128 129 7.308830 GCATCCCTCCTTAATAATAAAGCACAG 60.309 40.741 0.00 0.00 0.00 3.66
129 130 6.490040 GCATCCCTCCTTAATAATAAAGCACA 59.510 38.462 0.00 0.00 0.00 4.57
130 131 6.490040 TGCATCCCTCCTTAATAATAAAGCAC 59.510 38.462 0.00 0.00 0.00 4.40
131 132 6.609876 TGCATCCCTCCTTAATAATAAAGCA 58.390 36.000 0.00 0.00 0.00 3.91
132 133 7.524717 TTGCATCCCTCCTTAATAATAAAGC 57.475 36.000 0.00 0.00 0.00 3.51
137 138 9.605951 ATTGTATTTGCATCCCTCCTTAATAAT 57.394 29.630 0.00 0.00 0.00 1.28
138 139 8.859090 CATTGTATTTGCATCCCTCCTTAATAA 58.141 33.333 0.00 0.00 0.00 1.40
139 140 7.039784 GCATTGTATTTGCATCCCTCCTTAATA 60.040 37.037 0.00 0.00 39.90 0.98
140 141 6.239402 GCATTGTATTTGCATCCCTCCTTAAT 60.239 38.462 0.00 0.00 39.90 1.40
141 142 5.068987 GCATTGTATTTGCATCCCTCCTTAA 59.931 40.000 0.00 0.00 39.90 1.85
142 143 4.584325 GCATTGTATTTGCATCCCTCCTTA 59.416 41.667 0.00 0.00 39.90 2.69
143 144 3.385755 GCATTGTATTTGCATCCCTCCTT 59.614 43.478 0.00 0.00 39.90 3.36
144 145 2.961062 GCATTGTATTTGCATCCCTCCT 59.039 45.455 0.00 0.00 39.90 3.69
145 146 2.287788 CGCATTGTATTTGCATCCCTCC 60.288 50.000 0.00 0.00 40.14 4.30
146 147 2.859806 GCGCATTGTATTTGCATCCCTC 60.860 50.000 0.30 0.00 40.14 4.30
147 148 1.067516 GCGCATTGTATTTGCATCCCT 59.932 47.619 0.30 0.00 40.14 4.20
148 149 1.202394 TGCGCATTGTATTTGCATCCC 60.202 47.619 5.66 0.00 40.14 3.85
149 150 2.206815 TGCGCATTGTATTTGCATCC 57.793 45.000 5.66 0.00 40.14 3.51
150 151 3.373849 TCATGCGCATTGTATTTGCATC 58.626 40.909 22.81 0.00 43.89 3.91
151 152 3.439895 TCATGCGCATTGTATTTGCAT 57.560 38.095 22.81 0.00 46.43 3.96
152 153 2.935481 TCATGCGCATTGTATTTGCA 57.065 40.000 22.81 0.00 40.14 4.08
153 154 2.097104 GCATCATGCGCATTGTATTTGC 60.097 45.455 22.81 18.08 31.71 3.68
154 155 2.473609 GGCATCATGCGCATTGTATTTG 59.526 45.455 22.81 9.63 46.21 2.32
155 156 2.101082 TGGCATCATGCGCATTGTATTT 59.899 40.909 22.81 0.00 46.21 1.40
156 157 1.682323 TGGCATCATGCGCATTGTATT 59.318 42.857 22.81 0.00 46.21 1.89
157 158 1.320507 TGGCATCATGCGCATTGTAT 58.679 45.000 22.81 11.92 46.21 2.29
158 159 1.001158 CATGGCATCATGCGCATTGTA 60.001 47.619 22.81 9.87 46.21 2.41
159 160 0.249280 CATGGCATCATGCGCATTGT 60.249 50.000 22.81 9.51 46.21 2.71
209 210 4.407296 TGCCTTTCATGTTTTTGGGTTAGT 59.593 37.500 0.00 0.00 0.00 2.24
215 216 2.995258 CGGATGCCTTTCATGTTTTTGG 59.005 45.455 0.00 0.00 35.05 3.28
226 227 2.125106 GACGCTCCGGATGCCTTT 60.125 61.111 3.57 0.00 0.00 3.11
300 302 5.368989 GGAGAAATAGTCATAACCCACCAG 58.631 45.833 0.00 0.00 0.00 4.00
307 309 2.475487 GCGGCGGAGAAATAGTCATAAC 59.525 50.000 9.78 0.00 0.00 1.89
309 311 1.961394 AGCGGCGGAGAAATAGTCATA 59.039 47.619 9.78 0.00 0.00 2.15
317 319 1.143183 GACCATAGCGGCGGAGAAA 59.857 57.895 9.78 0.00 39.03 2.52
325 327 1.302033 GCCATGGAGACCATAGCGG 60.302 63.158 18.40 3.94 43.15 5.52
329 331 2.818169 GGCGGCCATGGAGACCATA 61.818 63.158 18.40 0.00 43.15 2.74
358 360 1.337071 CCACTCGCGTCCTACATACAT 59.663 52.381 5.77 0.00 0.00 2.29
359 361 0.736636 CCACTCGCGTCCTACATACA 59.263 55.000 5.77 0.00 0.00 2.29
363 365 1.303074 ACTCCACTCGCGTCCTACA 60.303 57.895 5.77 0.00 0.00 2.74
387 389 5.940192 TTTATTGATGTCGTTGTGCTTCT 57.060 34.783 0.00 0.00 0.00 2.85
389 391 7.095691 CCAAAATTTATTGATGTCGTTGTGCTT 60.096 33.333 0.00 0.00 31.84 3.91
418 420 1.344953 CCCACCCGATCCCATCTTCA 61.345 60.000 0.00 0.00 0.00 3.02
420 422 1.004230 TCCCACCCGATCCCATCTT 59.996 57.895 0.00 0.00 0.00 2.40
421 423 1.460305 CTCCCACCCGATCCCATCT 60.460 63.158 0.00 0.00 0.00 2.90
446 448 8.948631 TCTCTCATCTAAAATTTATTGTCGCT 57.051 30.769 0.00 0.00 0.00 4.93
465 468 0.829602 GGCCTCGATCCCATCTCTCA 60.830 60.000 0.00 0.00 0.00 3.27
504 507 2.503331 CAACCCATGCACACACTTCTA 58.497 47.619 0.00 0.00 0.00 2.10
505 508 1.321474 CAACCCATGCACACACTTCT 58.679 50.000 0.00 0.00 0.00 2.85
554 557 5.845953 CGAAAATAATCCACATATGCACGAC 59.154 40.000 1.58 0.00 0.00 4.34
556 559 4.612614 GCGAAAATAATCCACATATGCACG 59.387 41.667 1.58 0.00 0.00 5.34
561 564 4.215399 CCCACGCGAAAATAATCCACATAT 59.785 41.667 15.93 0.00 0.00 1.78
564 567 1.740585 CCCACGCGAAAATAATCCACA 59.259 47.619 15.93 0.00 0.00 4.17
569 572 1.099689 CACCCCCACGCGAAAATAAT 58.900 50.000 15.93 0.00 0.00 1.28
570 573 0.961358 CCACCCCCACGCGAAAATAA 60.961 55.000 15.93 0.00 0.00 1.40
571 574 1.377463 CCACCCCCACGCGAAAATA 60.377 57.895 15.93 0.00 0.00 1.40
588 591 4.825679 CTCCCTCCCCACCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
591 594 4.825679 CTCCTCCCTCCCCACCCC 62.826 77.778 0.00 0.00 0.00 4.95
592 595 4.825679 CCTCCTCCCTCCCCACCC 62.826 77.778 0.00 0.00 0.00 4.61
593 596 2.974435 GATCCTCCTCCCTCCCCACC 62.974 70.000 0.00 0.00 0.00 4.61
594 597 1.460497 GATCCTCCTCCCTCCCCAC 60.460 68.421 0.00 0.00 0.00 4.61
595 598 2.727071 GGATCCTCCTCCCTCCCCA 61.727 68.421 3.84 0.00 32.53 4.96
596 599 2.054834 ATGGATCCTCCTCCCTCCCC 62.055 65.000 14.23 0.00 37.46 4.81
597 600 0.546507 GATGGATCCTCCTCCCTCCC 60.547 65.000 14.23 0.00 37.46 4.30
598 601 0.902516 CGATGGATCCTCCTCCCTCC 60.903 65.000 14.23 0.00 37.46 4.30
599 602 0.902516 CCGATGGATCCTCCTCCCTC 60.903 65.000 14.23 0.00 37.46 4.30
600 603 1.157276 CCGATGGATCCTCCTCCCT 59.843 63.158 14.23 0.00 37.46 4.20
604 607 1.418334 CTCAACCGATGGATCCTCCT 58.582 55.000 14.23 0.00 37.46 3.69
613 616 1.957668 TCATGATGGCTCAACCGATG 58.042 50.000 0.00 0.00 43.94 3.84
637 640 2.026262 GCTCAACCTACCATTCTTCCCA 60.026 50.000 0.00 0.00 0.00 4.37
641 644 3.266772 TGATGGCTCAACCTACCATTCTT 59.733 43.478 0.00 0.00 44.20 2.52
645 648 2.779430 TCATGATGGCTCAACCTACCAT 59.221 45.455 0.00 0.00 46.82 3.55
705 708 9.869757 TTGACGATCTCTATTTTCATTTCAGTA 57.130 29.630 0.00 0.00 0.00 2.74
706 709 8.777865 TTGACGATCTCTATTTTCATTTCAGT 57.222 30.769 0.00 0.00 0.00 3.41
709 712 9.362911 CGAATTGACGATCTCTATTTTCATTTC 57.637 33.333 0.00 0.00 35.09 2.17
710 713 7.852945 GCGAATTGACGATCTCTATTTTCATTT 59.147 33.333 0.00 0.00 35.09 2.32
711 714 7.348201 GCGAATTGACGATCTCTATTTTCATT 58.652 34.615 0.00 0.00 35.09 2.57
712 715 6.073548 GGCGAATTGACGATCTCTATTTTCAT 60.074 38.462 0.00 0.00 35.09 2.57
889 928 2.757077 CCAAGCCGGGAAGGAGTT 59.243 61.111 2.18 0.00 45.00 3.01
891 930 3.273788 AAGCCAAGCCGGGAAGGAG 62.274 63.158 2.18 0.00 45.00 3.69
892 931 3.256960 AAGCCAAGCCGGGAAGGA 61.257 61.111 2.18 0.00 45.00 3.36
893 932 3.064324 CAAGCCAAGCCGGGAAGG 61.064 66.667 2.18 0.00 44.97 3.46
1361 1404 2.596904 TCTACAAGTAAGCATCGGCC 57.403 50.000 0.00 0.00 42.56 6.13
1826 1873 8.871629 TGCTAATTTTATTCAGTTTCACCCTA 57.128 30.769 0.00 0.00 0.00 3.53
1891 1938 8.634444 ACAGGACATCTGAACAGAATATAGTAC 58.366 37.037 8.59 4.36 46.18 2.73
1896 1943 6.715280 ACAACAGGACATCTGAACAGAATAT 58.285 36.000 8.59 0.00 46.18 1.28
1919 1966 6.741358 GCAATCCTATTTTACAAGTTGACGAC 59.259 38.462 10.54 0.00 0.00 4.34
1920 1967 6.428465 TGCAATCCTATTTTACAAGTTGACGA 59.572 34.615 10.54 0.00 0.00 4.20
1921 1968 6.607689 TGCAATCCTATTTTACAAGTTGACG 58.392 36.000 10.54 0.00 0.00 4.35
2154 2284 7.872881 AGATAATTGATAGAAGCAAGCATGTG 58.127 34.615 0.00 0.00 0.00 3.21
2509 2639 2.554893 GCCTAGGAGATAACGACTCTGG 59.445 54.545 14.75 0.00 35.10 3.86
2938 3068 1.411787 GGAAGCCAGGCTAGGAGTAGA 60.412 57.143 16.56 0.00 38.25 2.59
3074 3204 3.243336 CAAGTACTCCGCTACTGACAAC 58.757 50.000 0.00 0.00 0.00 3.32
3140 3270 5.180117 GCAGGTGATATGTTGCATACCTAAG 59.820 44.000 0.00 0.00 36.46 2.18
3380 3510 4.380973 GCTATTTCTGTTTTCTCCCCTTGC 60.381 45.833 0.00 0.00 0.00 4.01
3386 3516 7.440523 TTCTTGAGCTATTTCTGTTTTCTCC 57.559 36.000 0.00 0.00 0.00 3.71
3396 3526 6.428159 TCCTCTTGTGTTTCTTGAGCTATTTC 59.572 38.462 0.00 0.00 0.00 2.17
3455 3585 6.976636 CAATTGTTTGGGTGTTTGTAAAGT 57.023 33.333 0.00 0.00 0.00 2.66
3479 3609 6.404126 TGGATCCTAAGGGAGAAGGATTCAC 61.404 48.000 14.23 2.66 46.57 3.18
3484 3614 2.317900 TGTGGATCCTAAGGGAGAAGGA 59.682 50.000 14.23 0.00 45.86 3.36
3485 3615 2.764269 TGTGGATCCTAAGGGAGAAGG 58.236 52.381 14.23 0.00 45.86 3.46
3486 3616 3.432890 GCTTGTGGATCCTAAGGGAGAAG 60.433 52.174 22.55 13.17 45.86 2.85
3487 3617 2.505819 GCTTGTGGATCCTAAGGGAGAA 59.494 50.000 22.55 4.70 45.86 2.87
3488 3618 2.119495 GCTTGTGGATCCTAAGGGAGA 58.881 52.381 22.55 0.00 45.86 3.71
3489 3619 1.839994 TGCTTGTGGATCCTAAGGGAG 59.160 52.381 22.55 10.77 45.86 4.30
3490 3620 1.965414 TGCTTGTGGATCCTAAGGGA 58.035 50.000 22.55 8.42 46.81 4.20
3491 3621 2.290896 TGTTGCTTGTGGATCCTAAGGG 60.291 50.000 22.55 8.85 0.00 3.95
3492 3622 3.071874 TGTTGCTTGTGGATCCTAAGG 57.928 47.619 22.55 10.44 0.00 2.69
3493 3623 5.649782 ATTTGTTGCTTGTGGATCCTAAG 57.350 39.130 14.23 17.30 0.00 2.18
3494 3624 5.652014 CCTATTTGTTGCTTGTGGATCCTAA 59.348 40.000 14.23 7.53 0.00 2.69
3495 3625 5.045213 TCCTATTTGTTGCTTGTGGATCCTA 60.045 40.000 14.23 0.00 0.00 2.94
3496 3626 4.019174 CCTATTTGTTGCTTGTGGATCCT 58.981 43.478 14.23 0.00 0.00 3.24
3497 3627 4.016444 TCCTATTTGTTGCTTGTGGATCC 58.984 43.478 4.20 4.20 0.00 3.36
3629 3759 2.250273 AGCCTCCCAAGGTATCCTAAGA 59.750 50.000 0.00 0.00 45.34 2.10
3808 3939 1.983224 CCATCCAACCCAGACGTCT 59.017 57.895 13.58 13.58 0.00 4.18
3812 3943 2.270874 ATCCGCCATCCAACCCAGAC 62.271 60.000 0.00 0.00 0.00 3.51
3905 4036 4.496336 ATCCAGCTTCCAGCCCGC 62.496 66.667 0.00 0.00 43.77 6.13
3975 4106 1.361271 CCGAAACTATAGCGGCCGA 59.639 57.895 33.48 9.86 38.46 5.54
3988 4119 1.909700 AGGAAGAAATGCAGCCGAAA 58.090 45.000 0.00 0.00 0.00 3.46
4108 4239 1.764723 TCCCATGAGACATGGCTACTG 59.235 52.381 21.09 1.31 37.85 2.74
4194 4325 2.406596 AATGCCAATTGGACCAATGC 57.593 45.000 29.02 19.24 34.04 3.56
4638 4774 2.093764 GGAGCACAATCAGACTACTGCT 60.094 50.000 0.00 0.00 43.17 4.24
5042 5178 7.770801 TGTTGATCAGGATTTTCAGTATACG 57.229 36.000 0.00 0.00 0.00 3.06
5177 5313 3.118112 CCCCAATACAGAATGAGACAGCT 60.118 47.826 0.00 0.00 39.69 4.24
5242 5378 1.702182 TCCTCAAAAGCATGTTGCCA 58.298 45.000 0.00 0.00 46.52 4.92
5249 5385 3.689347 TGTGCACTATCCTCAAAAGCAT 58.311 40.909 19.41 0.00 32.75 3.79
5510 5646 5.888982 AGTTTCAGAGGAAGGTAAAGACA 57.111 39.130 0.00 0.00 33.82 3.41
5532 5668 2.291153 CCCAGGAAATCCAGCTCTCAAA 60.291 50.000 1.67 0.00 38.89 2.69
5677 5813 7.602644 AGTGTTGTGTCGATGTTACTATTCATT 59.397 33.333 0.00 0.00 0.00 2.57
5692 5828 3.914312 AGGTATGAGAAGTGTTGTGTCG 58.086 45.455 0.00 0.00 0.00 4.35
5955 6093 8.383175 AGACAGATACCCTTTTCAGTCATAAAA 58.617 33.333 0.00 0.00 32.57 1.52
6059 6197 5.290493 TCCCTAACATTGTATGCAGGTAG 57.710 43.478 0.00 0.00 35.22 3.18
6304 6447 9.173021 TGATGATAAACGACATAACTCCATTTT 57.827 29.630 0.00 0.00 0.00 1.82
6402 6545 2.684881 CAAATGAGGTAGCCCATGACAC 59.315 50.000 0.00 0.00 0.00 3.67
6678 6823 6.313519 TGGTACTCTGAAATAGCTCCATTT 57.686 37.500 0.00 0.00 0.00 2.32
7419 7564 1.414919 GGTAGGCCACGATGTAATGGA 59.585 52.381 5.01 0.00 38.34 3.41
7914 8059 4.236527 AGGAACACCATCATTTCCTACC 57.763 45.455 0.11 0.00 46.03 3.18
8130 8275 2.265467 TAGGCCCCAAATGCGACCTC 62.265 60.000 0.00 0.00 0.00 3.85
8514 8659 4.952262 TGCACAGAAGCAGTATTTGATC 57.048 40.909 0.00 0.00 40.11 2.92
8795 8940 5.081032 ACCAAAGAAACCGAAATAATGGGA 58.919 37.500 0.00 0.00 0.00 4.37
8807 8952 0.955905 TAGCCGCAACCAAAGAAACC 59.044 50.000 0.00 0.00 0.00 3.27
8846 8991 6.096001 AGCATACCAAAATCTGATTTCTCCAC 59.904 38.462 15.43 3.94 0.00 4.02
9004 9150 7.526608 TCCATATATTAATGTAAAAGCAGCGC 58.473 34.615 0.00 0.00 0.00 5.92
9005 9151 9.329913 GTTCCATATATTAATGTAAAAGCAGCG 57.670 33.333 0.00 0.00 0.00 5.18
9031 9179 4.402056 TGTTTCGCCTAGATTAAGAGGG 57.598 45.455 0.00 0.00 33.04 4.30
9121 9296 0.242825 TCGGAAGTTACCAGCACTCG 59.757 55.000 0.00 0.00 0.00 4.18
9157 9332 2.083774 GTTGACGGATGCCTTGATTCA 58.916 47.619 0.00 0.00 0.00 2.57
9217 9395 7.015289 GCAAAGAAAGACAAACCAAAGAAAAC 58.985 34.615 0.00 0.00 0.00 2.43
9244 9422 3.809279 CACACTGTTACAATGCAGAGACA 59.191 43.478 0.00 0.00 36.62 3.41
9362 9541 5.067413 CCTCTTTGCAGAATTGACATGCTAT 59.933 40.000 0.00 0.00 40.62 2.97


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

AutoCloner maintained by Alex Coulton.