Multiple sequence alignment - TraesCS3B01G459500

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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 TraesCS3B01G459500 chr3B 100.000 2213 0 0 1 2213 703008668 703006456 0.000000 4087.0
1 TraesCS3B01G459500 chr3B 94.690 1017 40 7 258 1266 201561633 201560623 0.000000 1567.0
2 TraesCS3B01G459500 chr3B 93.148 934 42 6 1285 2213 201559020 201558104 0.000000 1351.0
3 TraesCS3B01G459500 chr2D 95.553 1012 34 7 258 1265 272802513 272801509 0.000000 1609.0
4 TraesCS3B01G459500 chr2D 95.665 992 34 5 278 1265 630268391 630269377 0.000000 1585.0
5 TraesCS3B01G459500 chr1B 94.975 1015 37 7 258 1265 633729722 633728715 0.000000 1580.0
6 TraesCS3B01G459500 chr3A 95.040 1008 43 6 258 1265 672879283 672878283 0.000000 1578.0
7 TraesCS3B01G459500 chr3A 94.980 737 27 7 1285 2013 672876681 672875947 0.000000 1147.0
8 TraesCS3B01G459500 chr5D 94.523 986 50 4 280 1265 432293550 432292569 0.000000 1519.0
9 TraesCS3B01G459500 chr5B 94.428 987 49 5 279 1265 432875893 432876873 0.000000 1513.0
10 TraesCS3B01G459500 chr5B 95.508 935 35 7 1285 2213 413609191 413610124 0.000000 1487.0
11 TraesCS3B01G459500 chr5B 94.946 930 45 2 1285 2213 432878465 432879393 0.000000 1456.0
12 TraesCS3B01G459500 chr4A 94.422 986 50 4 280 1265 310761575 310762555 0.000000 1511.0
13 TraesCS3B01G459500 chr4A 93.651 1008 54 7 258 1265 219340718 219339721 0.000000 1498.0
14 TraesCS3B01G459500 chr4A 91.194 863 53 11 1353 2213 219308174 219307333 0.000000 1151.0
15 TraesCS3B01G459500 chr4D 94.307 931 49 4 1285 2213 245650435 245651363 0.000000 1423.0
16 TraesCS3B01G459500 chr1A 93.248 933 52 8 1285 2213 371922888 371923813 0.000000 1363.0
17 TraesCS3B01G459500 chr3D 90.665 932 55 17 1285 2213 182097284 182098186 0.000000 1210.0
18 TraesCS3B01G459500 chr3D 95.000 40 1 1 25 63 531430443 531430404 0.000007 62.1
19 TraesCS3B01G459500 chr7A 90.343 932 73 7 1285 2213 352675707 352674790 0.000000 1206.0
20 TraesCS3B01G459500 chr5A 96.274 671 23 2 1545 2213 482027372 482026702 0.000000 1099.0
21 TraesCS3B01G459500 chrUn 95.816 478 14 4 1300 1772 451362693 451362217 0.000000 767.0
22 TraesCS3B01G459500 chr4B 95.652 437 12 5 1285 1715 24 459 0.000000 695.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G459500 chr3B 703006456 703008668 2212 True 4087.0 4087 100.000 1 2213 1 chr3B.!!$R1 2212
1 TraesCS3B01G459500 chr3B 201558104 201561633 3529 True 1459.0 1567 93.919 258 2213 2 chr3B.!!$R2 1955
2 TraesCS3B01G459500 chr2D 272801509 272802513 1004 True 1609.0 1609 95.553 258 1265 1 chr2D.!!$R1 1007
3 TraesCS3B01G459500 chr2D 630268391 630269377 986 False 1585.0 1585 95.665 278 1265 1 chr2D.!!$F1 987
4 TraesCS3B01G459500 chr1B 633728715 633729722 1007 True 1580.0 1580 94.975 258 1265 1 chr1B.!!$R1 1007
5 TraesCS3B01G459500 chr3A 672875947 672879283 3336 True 1362.5 1578 95.010 258 2013 2 chr3A.!!$R1 1755
6 TraesCS3B01G459500 chr5D 432292569 432293550 981 True 1519.0 1519 94.523 280 1265 1 chr5D.!!$R1 985
7 TraesCS3B01G459500 chr5B 413609191 413610124 933 False 1487.0 1487 95.508 1285 2213 1 chr5B.!!$F1 928
8 TraesCS3B01G459500 chr5B 432875893 432879393 3500 False 1484.5 1513 94.687 279 2213 2 chr5B.!!$F2 1934
9 TraesCS3B01G459500 chr4A 310761575 310762555 980 False 1511.0 1511 94.422 280 1265 1 chr4A.!!$F1 985
10 TraesCS3B01G459500 chr4A 219339721 219340718 997 True 1498.0 1498 93.651 258 1265 1 chr4A.!!$R2 1007
11 TraesCS3B01G459500 chr4A 219307333 219308174 841 True 1151.0 1151 91.194 1353 2213 1 chr4A.!!$R1 860
12 TraesCS3B01G459500 chr4D 245650435 245651363 928 False 1423.0 1423 94.307 1285 2213 1 chr4D.!!$F1 928
13 TraesCS3B01G459500 chr1A 371922888 371923813 925 False 1363.0 1363 93.248 1285 2213 1 chr1A.!!$F1 928
14 TraesCS3B01G459500 chr3D 182097284 182098186 902 False 1210.0 1210 90.665 1285 2213 1 chr3D.!!$F1 928
15 TraesCS3B01G459500 chr7A 352674790 352675707 917 True 1206.0 1206 90.343 1285 2213 1 chr7A.!!$R1 928
16 TraesCS3B01G459500 chr5A 482026702 482027372 670 True 1099.0 1099 96.274 1545 2213 1 chr5A.!!$R1 668

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
222 223 0.096454 CGATCGTCTGTGCGTGTCTA 59.904 55.000 7.03 0.0 0.00 2.59 F
255 256 1.001641 GCAATCAGCCACTGGGTCT 60.002 57.895 0.00 0.0 37.23 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1168 1.133356 AGATTGCCCAGGGAAATAGGC 60.133 52.381 12.45 0.0 45.96 3.93 R
1878 3503 2.079925 GAAAGCGTGAAGAGAGCCAAT 58.920 47.619 0.00 0.0 0.00 3.16 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
26 27 3.650369 TTTTTGCGGCCGACTCTC 58.350 55.556 33.48 11.67 0.00 3.20
27 28 1.070786 TTTTTGCGGCCGACTCTCT 59.929 52.632 33.48 0.00 0.00 3.10
28 29 1.227999 TTTTTGCGGCCGACTCTCTG 61.228 55.000 33.48 0.00 0.00 3.35
29 30 2.377628 TTTTGCGGCCGACTCTCTGT 62.378 55.000 33.48 0.00 0.00 3.41
30 31 2.377628 TTTGCGGCCGACTCTCTGTT 62.378 55.000 33.48 0.00 0.00 3.16
31 32 2.048127 GCGGCCGACTCTCTGTTT 60.048 61.111 33.48 0.00 0.00 2.83
32 33 1.668151 GCGGCCGACTCTCTGTTTT 60.668 57.895 33.48 0.00 0.00 2.43
33 34 1.228657 GCGGCCGACTCTCTGTTTTT 61.229 55.000 33.48 0.00 0.00 1.94
52 53 5.796502 TTTTTCCTTGGAGGGTCAGATAT 57.203 39.130 0.00 0.00 35.59 1.63
53 54 5.796502 TTTTCCTTGGAGGGTCAGATATT 57.203 39.130 0.00 0.00 35.59 1.28
54 55 5.373812 TTTCCTTGGAGGGTCAGATATTC 57.626 43.478 0.00 0.00 35.59 1.75
55 56 4.286813 TCCTTGGAGGGTCAGATATTCT 57.713 45.455 0.00 0.00 35.59 2.40
56 57 4.635473 TCCTTGGAGGGTCAGATATTCTT 58.365 43.478 0.00 0.00 35.59 2.52
57 58 5.039645 TCCTTGGAGGGTCAGATATTCTTT 58.960 41.667 0.00 0.00 35.59 2.52
58 59 5.492524 TCCTTGGAGGGTCAGATATTCTTTT 59.507 40.000 0.00 0.00 35.59 2.27
59 60 6.011628 TCCTTGGAGGGTCAGATATTCTTTTT 60.012 38.462 0.00 0.00 35.59 1.94
60 61 6.319911 CCTTGGAGGGTCAGATATTCTTTTTC 59.680 42.308 0.00 0.00 0.00 2.29
61 62 5.755849 TGGAGGGTCAGATATTCTTTTTCC 58.244 41.667 0.00 0.00 0.00 3.13
62 63 5.492524 TGGAGGGTCAGATATTCTTTTTCCT 59.507 40.000 0.00 0.00 0.00 3.36
63 64 6.011628 TGGAGGGTCAGATATTCTTTTTCCTT 60.012 38.462 0.00 0.00 0.00 3.36
64 65 6.319911 GGAGGGTCAGATATTCTTTTTCCTTG 59.680 42.308 0.00 0.00 0.00 3.61
65 66 6.190587 AGGGTCAGATATTCTTTTTCCTTGG 58.809 40.000 0.00 0.00 0.00 3.61
66 67 5.360999 GGGTCAGATATTCTTTTTCCTTGGG 59.639 44.000 0.00 0.00 0.00 4.12
67 68 5.163509 GGTCAGATATTCTTTTTCCTTGGGC 60.164 44.000 0.00 0.00 0.00 5.36
68 69 4.640201 TCAGATATTCTTTTTCCTTGGGCG 59.360 41.667 0.00 0.00 0.00 6.13
69 70 4.640201 CAGATATTCTTTTTCCTTGGGCGA 59.360 41.667 0.00 0.00 0.00 5.54
70 71 5.125417 CAGATATTCTTTTTCCTTGGGCGAA 59.875 40.000 0.00 0.00 0.00 4.70
71 72 3.942130 ATTCTTTTTCCTTGGGCGAAG 57.058 42.857 1.81 1.81 0.00 3.79
78 79 3.354678 CTTGGGCGAAGGGTGTTG 58.645 61.111 0.72 0.00 0.00 3.33
79 80 2.909965 TTGGGCGAAGGGTGTTGC 60.910 61.111 0.00 0.00 0.00 4.17
80 81 3.723097 TTGGGCGAAGGGTGTTGCA 62.723 57.895 0.00 0.00 0.00 4.08
81 82 2.676471 GGGCGAAGGGTGTTGCAT 60.676 61.111 0.00 0.00 0.00 3.96
82 83 2.568090 GGCGAAGGGTGTTGCATG 59.432 61.111 0.00 0.00 0.00 4.06
83 84 2.126346 GCGAAGGGTGTTGCATGC 60.126 61.111 11.82 11.82 0.00 4.06
84 85 2.918345 GCGAAGGGTGTTGCATGCA 61.918 57.895 18.46 18.46 0.00 3.96
85 86 1.210931 CGAAGGGTGTTGCATGCAG 59.789 57.895 21.50 1.60 0.00 4.41
86 87 1.236616 CGAAGGGTGTTGCATGCAGA 61.237 55.000 21.50 9.00 0.00 4.26
87 88 0.524862 GAAGGGTGTTGCATGCAGAG 59.475 55.000 21.50 0.00 0.00 3.35
88 89 1.530013 AAGGGTGTTGCATGCAGAGC 61.530 55.000 21.50 19.43 0.00 4.09
89 90 2.177531 GGTGTTGCATGCAGAGCG 59.822 61.111 21.50 0.00 33.85 5.03
90 91 2.327343 GGTGTTGCATGCAGAGCGA 61.327 57.895 21.50 2.08 33.85 4.93
91 92 1.154338 GTGTTGCATGCAGAGCGAC 60.154 57.895 21.50 21.45 44.77 5.19
92 93 1.301953 TGTTGCATGCAGAGCGACT 60.302 52.632 25.79 0.00 44.79 4.18
93 94 1.571215 TGTTGCATGCAGAGCGACTG 61.571 55.000 25.79 6.39 44.79 3.51
94 95 2.036571 TTGCATGCAGAGCGACTGG 61.037 57.895 21.50 1.68 45.82 4.00
95 96 3.873883 GCATGCAGAGCGACTGGC 61.874 66.667 14.21 6.90 45.82 4.85
104 105 3.207354 GCGACTGGCTACTGGCTA 58.793 61.111 0.00 0.00 41.46 3.93
105 106 1.227002 GCGACTGGCTACTGGCTAC 60.227 63.158 0.00 0.00 41.46 3.58
106 107 1.668101 GCGACTGGCTACTGGCTACT 61.668 60.000 0.00 0.00 41.46 2.57
107 108 0.101399 CGACTGGCTACTGGCTACTG 59.899 60.000 0.00 0.00 41.46 2.74
108 109 0.461961 GACTGGCTACTGGCTACTGG 59.538 60.000 0.00 0.00 41.46 4.00
109 110 1.144936 CTGGCTACTGGCTACTGGC 59.855 63.158 0.00 0.00 41.46 4.85
110 111 1.306141 TGGCTACTGGCTACTGGCT 60.306 57.895 0.00 0.00 41.46 4.75
111 112 0.909610 TGGCTACTGGCTACTGGCTT 60.910 55.000 0.00 0.00 41.46 4.35
112 113 0.462759 GGCTACTGGCTACTGGCTTG 60.463 60.000 0.00 0.00 41.46 4.01
113 114 0.250513 GCTACTGGCTACTGGCTTGT 59.749 55.000 0.00 0.00 41.46 3.16
114 115 1.480954 GCTACTGGCTACTGGCTTGTA 59.519 52.381 0.00 0.00 41.46 2.41
115 116 2.738964 GCTACTGGCTACTGGCTTGTAC 60.739 54.545 0.00 0.00 41.46 2.90
116 117 1.645710 ACTGGCTACTGGCTTGTACT 58.354 50.000 0.00 0.00 41.46 2.73
117 118 1.276421 ACTGGCTACTGGCTTGTACTG 59.724 52.381 0.00 0.00 41.46 2.74
118 119 1.550524 CTGGCTACTGGCTTGTACTGA 59.449 52.381 0.00 0.00 41.46 3.41
119 120 1.974957 TGGCTACTGGCTTGTACTGAA 59.025 47.619 0.00 0.00 41.46 3.02
120 121 2.370519 TGGCTACTGGCTTGTACTGAAA 59.629 45.455 0.00 0.00 41.46 2.69
121 122 3.181449 TGGCTACTGGCTTGTACTGAAAA 60.181 43.478 0.00 0.00 41.46 2.29
122 123 3.437049 GGCTACTGGCTTGTACTGAAAAG 59.563 47.826 0.00 0.00 41.46 2.27
123 124 4.065789 GCTACTGGCTTGTACTGAAAAGT 58.934 43.478 0.00 0.00 38.06 2.66
124 125 4.515567 GCTACTGGCTTGTACTGAAAAGTT 59.484 41.667 0.00 0.00 38.06 2.66
125 126 5.008712 GCTACTGGCTTGTACTGAAAAGTTT 59.991 40.000 0.00 0.00 38.06 2.66
126 127 5.914898 ACTGGCTTGTACTGAAAAGTTTT 57.085 34.783 0.00 0.00 0.00 2.43
127 128 7.255001 GCTACTGGCTTGTACTGAAAAGTTTTA 60.255 37.037 0.00 0.00 38.06 1.52
128 129 7.027778 ACTGGCTTGTACTGAAAAGTTTTAG 57.972 36.000 0.00 2.63 0.00 1.85
129 130 6.602009 ACTGGCTTGTACTGAAAAGTTTTAGT 59.398 34.615 0.00 7.96 39.80 2.24
130 131 7.771826 ACTGGCTTGTACTGAAAAGTTTTAGTA 59.228 33.333 0.00 7.09 37.96 1.82
131 132 8.508883 TGGCTTGTACTGAAAAGTTTTAGTAA 57.491 30.769 9.29 0.00 39.80 2.24
132 133 8.400186 TGGCTTGTACTGAAAAGTTTTAGTAAC 58.600 33.333 9.29 0.00 39.80 2.50
133 134 8.400186 GGCTTGTACTGAAAAGTTTTAGTAACA 58.600 33.333 9.29 1.94 39.80 2.41
134 135 9.218359 GCTTGTACTGAAAAGTTTTAGTAACAC 57.782 33.333 9.29 2.80 39.80 3.32
137 138 8.810427 TGTACTGAAAAGTTTTAGTAACACTCG 58.190 33.333 9.29 0.00 39.80 4.18
138 139 6.712549 ACTGAAAAGTTTTAGTAACACTCGC 58.287 36.000 0.00 0.00 35.55 5.03
139 140 5.730269 TGAAAAGTTTTAGTAACACTCGCG 58.270 37.500 0.00 0.00 0.00 5.87
140 141 5.519566 TGAAAAGTTTTAGTAACACTCGCGA 59.480 36.000 9.26 9.26 0.00 5.87
141 142 5.571778 AAAGTTTTAGTAACACTCGCGAG 57.428 39.130 33.45 33.45 0.00 5.03
142 143 4.494350 AGTTTTAGTAACACTCGCGAGA 57.506 40.909 40.58 17.41 39.12 4.04
143 144 4.863491 AGTTTTAGTAACACTCGCGAGAA 58.137 39.130 40.58 20.51 41.32 2.87
144 145 5.284079 AGTTTTAGTAACACTCGCGAGAAA 58.716 37.500 40.58 24.79 41.32 2.52
145 146 5.401674 AGTTTTAGTAACACTCGCGAGAAAG 59.598 40.000 40.58 28.98 41.32 2.62
146 147 4.754372 TTAGTAACACTCGCGAGAAAGA 57.246 40.909 40.58 20.36 41.32 2.52
147 148 3.637998 AGTAACACTCGCGAGAAAGAA 57.362 42.857 40.58 19.08 41.32 2.52
148 149 3.973657 AGTAACACTCGCGAGAAAGAAA 58.026 40.909 40.58 18.05 41.32 2.52
149 150 4.365723 AGTAACACTCGCGAGAAAGAAAA 58.634 39.130 40.58 16.52 41.32 2.29
150 151 3.861569 AACACTCGCGAGAAAGAAAAG 57.138 42.857 40.58 20.08 41.32 2.27
151 152 2.822764 ACACTCGCGAGAAAGAAAAGT 58.177 42.857 40.58 20.65 41.32 2.66
152 153 3.195661 ACACTCGCGAGAAAGAAAAGTT 58.804 40.909 40.58 13.00 41.32 2.66
153 154 3.621715 ACACTCGCGAGAAAGAAAAGTTT 59.378 39.130 40.58 12.43 41.32 2.66
154 155 4.094442 ACACTCGCGAGAAAGAAAAGTTTT 59.906 37.500 40.58 12.21 41.32 2.43
155 156 5.292589 ACACTCGCGAGAAAGAAAAGTTTTA 59.707 36.000 40.58 0.00 41.32 1.52
156 157 5.841296 CACTCGCGAGAAAGAAAAGTTTTAG 59.159 40.000 40.58 10.78 41.32 1.85
157 158 5.522824 ACTCGCGAGAAAGAAAAGTTTTAGT 59.477 36.000 40.58 11.48 41.32 2.24
158 159 6.698766 ACTCGCGAGAAAGAAAAGTTTTAGTA 59.301 34.615 40.58 0.00 41.32 1.82
159 160 7.223387 ACTCGCGAGAAAGAAAAGTTTTAGTAA 59.777 33.333 40.58 0.00 41.32 2.24
160 161 7.339953 TCGCGAGAAAGAAAAGTTTTAGTAAC 58.660 34.615 3.71 0.00 37.03 2.50
161 162 6.572621 CGCGAGAAAGAAAAGTTTTAGTAACC 59.427 38.462 0.00 0.00 0.00 2.85
162 163 7.412063 GCGAGAAAGAAAAGTTTTAGTAACCA 58.588 34.615 0.00 0.00 0.00 3.67
163 164 7.375280 GCGAGAAAGAAAAGTTTTAGTAACCAC 59.625 37.037 0.00 0.00 0.00 4.16
164 165 8.610035 CGAGAAAGAAAAGTTTTAGTAACCACT 58.390 33.333 0.00 0.00 38.91 4.00
165 166 9.717892 GAGAAAGAAAAGTTTTAGTAACCACTG 57.282 33.333 0.00 0.00 36.14 3.66
166 167 8.188799 AGAAAGAAAAGTTTTAGTAACCACTGC 58.811 33.333 0.00 0.00 36.14 4.40
167 168 7.640597 AAGAAAAGTTTTAGTAACCACTGCT 57.359 32.000 0.00 0.00 36.14 4.24
168 169 8.741603 AAGAAAAGTTTTAGTAACCACTGCTA 57.258 30.769 0.00 0.00 36.14 3.49
169 170 8.151141 AGAAAAGTTTTAGTAACCACTGCTAC 57.849 34.615 0.00 0.00 36.14 3.58
170 171 6.872628 AAAGTTTTAGTAACCACTGCTACC 57.127 37.500 0.00 0.00 36.14 3.18
171 172 5.556006 AGTTTTAGTAACCACTGCTACCA 57.444 39.130 0.00 0.00 36.14 3.25
172 173 5.932455 AGTTTTAGTAACCACTGCTACCAA 58.068 37.500 0.00 0.00 36.14 3.67
173 174 5.995897 AGTTTTAGTAACCACTGCTACCAAG 59.004 40.000 0.00 0.00 36.14 3.61
174 175 5.811796 TTTAGTAACCACTGCTACCAAGA 57.188 39.130 0.00 0.00 36.14 3.02
175 176 3.679824 AGTAACCACTGCTACCAAGAC 57.320 47.619 0.00 0.00 32.25 3.01
176 177 2.969950 AGTAACCACTGCTACCAAGACA 59.030 45.455 0.00 0.00 32.25 3.41
177 178 3.389983 AGTAACCACTGCTACCAAGACAA 59.610 43.478 0.00 0.00 32.25 3.18
178 179 3.290948 AACCACTGCTACCAAGACAAA 57.709 42.857 0.00 0.00 0.00 2.83
179 180 3.508845 ACCACTGCTACCAAGACAAAT 57.491 42.857 0.00 0.00 0.00 2.32
180 181 3.832527 ACCACTGCTACCAAGACAAATT 58.167 40.909 0.00 0.00 0.00 1.82
181 182 3.569701 ACCACTGCTACCAAGACAAATTG 59.430 43.478 0.00 0.00 0.00 2.32
182 183 3.569701 CCACTGCTACCAAGACAAATTGT 59.430 43.478 0.00 0.00 0.00 2.71
183 184 4.539870 CACTGCTACCAAGACAAATTGTG 58.460 43.478 2.20 0.00 0.00 3.33
184 185 3.569701 ACTGCTACCAAGACAAATTGTGG 59.430 43.478 2.20 1.03 37.17 4.17
185 186 3.820467 CTGCTACCAAGACAAATTGTGGA 59.180 43.478 2.20 0.00 35.04 4.02
186 187 4.406456 TGCTACCAAGACAAATTGTGGAT 58.594 39.130 2.20 0.00 35.04 3.41
187 188 5.565509 TGCTACCAAGACAAATTGTGGATA 58.434 37.500 2.20 0.00 35.04 2.59
188 189 5.647658 TGCTACCAAGACAAATTGTGGATAG 59.352 40.000 2.20 5.20 35.04 2.08
189 190 5.880332 GCTACCAAGACAAATTGTGGATAGA 59.120 40.000 2.20 0.00 35.04 1.98
190 191 6.037610 GCTACCAAGACAAATTGTGGATAGAG 59.962 42.308 2.20 0.00 35.04 2.43
191 192 5.256474 ACCAAGACAAATTGTGGATAGAGG 58.744 41.667 2.20 0.00 35.04 3.69
192 193 4.641989 CCAAGACAAATTGTGGATAGAGGG 59.358 45.833 2.20 0.00 32.54 4.30
193 194 4.510167 AGACAAATTGTGGATAGAGGGG 57.490 45.455 2.20 0.00 0.00 4.79
194 195 4.111577 AGACAAATTGTGGATAGAGGGGA 58.888 43.478 2.20 0.00 0.00 4.81
195 196 4.540099 AGACAAATTGTGGATAGAGGGGAA 59.460 41.667 2.20 0.00 0.00 3.97
196 197 4.600062 ACAAATTGTGGATAGAGGGGAAC 58.400 43.478 0.00 0.00 0.00 3.62
197 198 4.044065 ACAAATTGTGGATAGAGGGGAACA 59.956 41.667 0.00 0.00 0.00 3.18
198 199 4.510167 AATTGTGGATAGAGGGGAACAG 57.490 45.455 0.00 0.00 0.00 3.16
199 200 2.642171 TGTGGATAGAGGGGAACAGT 57.358 50.000 0.00 0.00 0.00 3.55
200 201 2.187958 TGTGGATAGAGGGGAACAGTG 58.812 52.381 0.00 0.00 0.00 3.66
201 202 1.486726 GTGGATAGAGGGGAACAGTGG 59.513 57.143 0.00 0.00 0.00 4.00
202 203 1.080498 TGGATAGAGGGGAACAGTGGT 59.920 52.381 0.00 0.00 0.00 4.16
203 204 1.763545 GGATAGAGGGGAACAGTGGTC 59.236 57.143 0.00 0.00 0.00 4.02
204 205 1.409427 GATAGAGGGGAACAGTGGTCG 59.591 57.143 1.17 0.00 0.00 4.79
205 206 0.406750 TAGAGGGGAACAGTGGTCGA 59.593 55.000 1.17 0.00 0.00 4.20
206 207 0.252284 AGAGGGGAACAGTGGTCGAT 60.252 55.000 1.17 0.00 0.00 3.59
207 208 0.175989 GAGGGGAACAGTGGTCGATC 59.824 60.000 1.17 0.00 0.00 3.69
208 209 1.153628 GGGGAACAGTGGTCGATCG 60.154 63.158 9.36 9.36 0.00 3.69
209 210 1.590147 GGGAACAGTGGTCGATCGT 59.410 57.895 15.94 0.00 0.00 3.73
210 211 0.458025 GGGAACAGTGGTCGATCGTC 60.458 60.000 15.94 9.66 0.00 4.20
211 212 0.526662 GGAACAGTGGTCGATCGTCT 59.473 55.000 15.94 6.99 0.00 4.18
212 213 1.618861 GAACAGTGGTCGATCGTCTG 58.381 55.000 15.94 19.05 0.00 3.51
213 214 0.959553 AACAGTGGTCGATCGTCTGT 59.040 50.000 15.94 19.61 40.40 3.41
214 215 0.241213 ACAGTGGTCGATCGTCTGTG 59.759 55.000 24.15 16.39 37.85 3.66
215 216 1.073216 CAGTGGTCGATCGTCTGTGC 61.073 60.000 15.94 2.35 0.00 4.57
216 217 2.152699 GTGGTCGATCGTCTGTGCG 61.153 63.158 15.94 0.00 0.00 5.34
217 218 2.178521 GGTCGATCGTCTGTGCGT 59.821 61.111 15.94 0.00 0.00 5.24
218 219 2.152699 GGTCGATCGTCTGTGCGTG 61.153 63.158 15.94 0.00 0.00 5.34
219 220 1.442184 GTCGATCGTCTGTGCGTGT 60.442 57.895 15.94 0.00 0.00 4.49
220 221 1.154282 TCGATCGTCTGTGCGTGTC 60.154 57.895 15.94 0.00 0.00 3.67
221 222 1.154207 CGATCGTCTGTGCGTGTCT 60.154 57.895 7.03 0.00 0.00 3.41
222 223 0.096454 CGATCGTCTGTGCGTGTCTA 59.904 55.000 7.03 0.00 0.00 2.59
223 224 1.536149 GATCGTCTGTGCGTGTCTAC 58.464 55.000 0.00 0.00 0.00 2.59
237 238 3.971150 GTGTCTACGAATCAGGATCAGG 58.029 50.000 0.00 0.00 0.00 3.86
238 239 2.362397 TGTCTACGAATCAGGATCAGGC 59.638 50.000 0.00 0.00 0.00 4.85
239 240 2.362397 GTCTACGAATCAGGATCAGGCA 59.638 50.000 0.00 0.00 0.00 4.75
240 241 3.031013 TCTACGAATCAGGATCAGGCAA 58.969 45.455 0.00 0.00 0.00 4.52
241 242 3.643320 TCTACGAATCAGGATCAGGCAAT 59.357 43.478 0.00 0.00 0.00 3.56
242 243 2.843701 ACGAATCAGGATCAGGCAATC 58.156 47.619 0.00 0.00 0.00 2.67
243 244 2.171237 ACGAATCAGGATCAGGCAATCA 59.829 45.455 0.00 0.00 0.00 2.57
244 245 2.806818 CGAATCAGGATCAGGCAATCAG 59.193 50.000 0.00 0.00 0.00 2.90
245 246 2.273538 ATCAGGATCAGGCAATCAGC 57.726 50.000 0.00 0.00 44.65 4.26
254 255 3.595819 GCAATCAGCCACTGGGTC 58.404 61.111 0.00 0.00 37.23 4.46
255 256 1.001641 GCAATCAGCCACTGGGTCT 60.002 57.895 0.00 0.00 37.23 3.85
256 257 1.310933 GCAATCAGCCACTGGGTCTG 61.311 60.000 0.00 0.00 38.73 3.51
274 275 3.935828 GTCTGGGAGTGCACTAGATTTTC 59.064 47.826 21.73 5.30 0.00 2.29
312 320 6.273026 TCCTTCCTCTATCCATATTCATGCAA 59.727 38.462 0.00 0.00 0.00 4.08
316 324 8.571461 TCCTCTATCCATATTCATGCAAAATC 57.429 34.615 0.00 0.00 0.00 2.17
339 347 5.361571 TCGCTCATGAACTAATACCCAACTA 59.638 40.000 0.00 0.00 0.00 2.24
460 469 2.672961 TGAGATCAATTCGGAAGCGT 57.327 45.000 0.00 0.00 0.00 5.07
480 489 6.398918 AGCGTCTTTTCTTATTCTAGCAGAA 58.601 36.000 1.85 1.85 38.78 3.02
553 566 1.010602 TCTATCTAGGCCCCAGGGGT 61.011 60.000 27.04 9.89 46.51 4.95
568 581 2.296190 CAGGGGTTAGGAACAAAACAGC 59.704 50.000 0.00 0.00 0.00 4.40
638 651 2.160022 TGTACGGTTTTGAAATAGCGGC 59.840 45.455 13.14 0.00 39.38 6.53
722 735 6.092259 AGTTGAAGCATAGTCAAAATACGGTC 59.908 38.462 0.00 0.00 36.77 4.79
748 761 3.625853 TGGATGGAATATTTGGCGTCAA 58.374 40.909 0.00 0.00 0.00 3.18
819 832 8.749354 GTGAAAGATTACCCTTTGATTTACCAT 58.251 33.333 0.00 0.00 36.58 3.55
862 875 7.888546 AGTAGCAGGTTACCAAACTGAATATTT 59.111 33.333 8.11 0.00 35.81 1.40
864 877 6.719370 AGCAGGTTACCAAACTGAATATTTCA 59.281 34.615 8.11 0.00 38.17 2.69
1191 1204 5.885912 GGGCAATCTCTTATTAACAACCTCA 59.114 40.000 0.00 0.00 0.00 3.86
1265 1278 4.882671 TCAACACAAAAGCTCTCTCAAC 57.117 40.909 0.00 0.00 0.00 3.18
1266 1279 4.517285 TCAACACAAAAGCTCTCTCAACT 58.483 39.130 0.00 0.00 0.00 3.16
1267 1280 4.943705 TCAACACAAAAGCTCTCTCAACTT 59.056 37.500 0.00 0.00 0.00 2.66
1268 1281 4.889832 ACACAAAAGCTCTCTCAACTTG 57.110 40.909 0.00 0.00 0.00 3.16
1269 1282 4.517285 ACACAAAAGCTCTCTCAACTTGA 58.483 39.130 0.00 0.00 0.00 3.02
1270 1283 4.333926 ACACAAAAGCTCTCTCAACTTGAC 59.666 41.667 0.00 0.00 0.00 3.18
1271 1284 3.879892 ACAAAAGCTCTCTCAACTTGACC 59.120 43.478 0.00 0.00 0.00 4.02
1272 1285 4.133078 CAAAAGCTCTCTCAACTTGACCT 58.867 43.478 0.00 0.00 0.00 3.85
1274 1287 5.753721 AAAGCTCTCTCAACTTGACCTAT 57.246 39.130 0.00 0.00 0.00 2.57
1276 1289 4.093011 AGCTCTCTCAACTTGACCTATGT 58.907 43.478 0.00 0.00 0.00 2.29
1278 1291 5.126384 AGCTCTCTCAACTTGACCTATGTAC 59.874 44.000 0.00 0.00 0.00 2.90
1280 1293 5.580998 TCTCTCAACTTGACCTATGTACCT 58.419 41.667 0.00 0.00 0.00 3.08
1357 2957 1.336440 TCACAAGCCGAAACATGGTTG 59.664 47.619 0.00 0.00 43.62 3.77
1363 2963 1.948611 GCCGAAACATGGTTGGAGCTA 60.949 52.381 7.12 0.00 0.00 3.32
1369 2969 6.147821 CCGAAACATGGTTGGAGCTATAATAG 59.852 42.308 7.12 0.00 0.00 1.73
1458 3058 8.749354 AGTCGCCAATTAAAAGGAGATATTTTT 58.251 29.630 6.33 0.00 36.14 1.94
1527 3127 6.360618 ACTATCCATTCTTTCTTCCATCCAC 58.639 40.000 0.00 0.00 0.00 4.02
1819 3440 9.904647 CAATTTATTGGCTAATTCAAATTCGTG 57.095 29.630 11.31 2.04 34.22 4.35
1912 3537 3.970610 CACGCTTTCTCACAAACAGATTG 59.029 43.478 0.00 0.00 44.95 2.67
1977 3602 4.993905 TCGTCTGGTGTCTACAATACATG 58.006 43.478 0.00 0.00 0.00 3.21
2135 3766 9.109393 GCTTGTCCAACAGATGTATTAGAAATA 57.891 33.333 0.00 0.00 0.00 1.40
2170 3801 4.040217 TGGATGTAAAGCCAAGCAAATTGT 59.960 37.500 0.00 0.00 37.17 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.070786 AGAGAGTCGGCCGCAAAAA 59.929 52.632 23.51 0.00 0.00 1.94
10 11 1.667830 CAGAGAGTCGGCCGCAAAA 60.668 57.895 23.51 0.00 0.00 2.44
11 12 2.048222 CAGAGAGTCGGCCGCAAA 60.048 61.111 23.51 0.00 0.00 3.68
12 13 2.377628 AAACAGAGAGTCGGCCGCAA 62.378 55.000 23.51 0.00 0.00 4.85
13 14 2.377628 AAAACAGAGAGTCGGCCGCA 62.378 55.000 23.51 6.75 0.00 5.69
14 15 1.228657 AAAAACAGAGAGTCGGCCGC 61.229 55.000 23.51 16.31 0.00 6.53
15 16 2.914379 AAAAACAGAGAGTCGGCCG 58.086 52.632 22.12 22.12 0.00 6.13
30 31 5.796502 ATATCTGACCCTCCAAGGAAAAA 57.203 39.130 0.00 0.00 37.67 1.94
31 32 5.492524 AGAATATCTGACCCTCCAAGGAAAA 59.507 40.000 0.00 0.00 37.67 2.29
32 33 5.039645 AGAATATCTGACCCTCCAAGGAAA 58.960 41.667 0.00 0.00 37.67 3.13
33 34 4.635473 AGAATATCTGACCCTCCAAGGAA 58.365 43.478 0.00 0.00 37.67 3.36
34 35 4.286813 AGAATATCTGACCCTCCAAGGA 57.713 45.455 0.00 0.00 37.67 3.36
35 36 5.379706 AAAGAATATCTGACCCTCCAAGG 57.620 43.478 0.00 0.00 34.30 3.61
36 37 6.319911 GGAAAAAGAATATCTGACCCTCCAAG 59.680 42.308 0.00 0.00 0.00 3.61
37 38 6.011628 AGGAAAAAGAATATCTGACCCTCCAA 60.012 38.462 0.00 0.00 0.00 3.53
38 39 5.492524 AGGAAAAAGAATATCTGACCCTCCA 59.507 40.000 0.00 0.00 0.00 3.86
39 40 6.007485 AGGAAAAAGAATATCTGACCCTCC 57.993 41.667 0.00 0.00 0.00 4.30
40 41 6.319911 CCAAGGAAAAAGAATATCTGACCCTC 59.680 42.308 0.00 0.00 0.00 4.30
41 42 6.190587 CCAAGGAAAAAGAATATCTGACCCT 58.809 40.000 0.00 0.00 0.00 4.34
42 43 5.360999 CCCAAGGAAAAAGAATATCTGACCC 59.639 44.000 0.00 0.00 0.00 4.46
43 44 5.163509 GCCCAAGGAAAAAGAATATCTGACC 60.164 44.000 0.00 0.00 0.00 4.02
44 45 5.449177 CGCCCAAGGAAAAAGAATATCTGAC 60.449 44.000 0.00 0.00 0.00 3.51
45 46 4.640201 CGCCCAAGGAAAAAGAATATCTGA 59.360 41.667 0.00 0.00 0.00 3.27
46 47 4.640201 TCGCCCAAGGAAAAAGAATATCTG 59.360 41.667 0.00 0.00 0.00 2.90
47 48 4.855340 TCGCCCAAGGAAAAAGAATATCT 58.145 39.130 0.00 0.00 0.00 1.98
48 49 5.576447 TTCGCCCAAGGAAAAAGAATATC 57.424 39.130 0.00 0.00 0.00 1.63
49 50 5.582689 CTTCGCCCAAGGAAAAAGAATAT 57.417 39.130 0.00 0.00 0.00 1.28
51 52 3.942130 CTTCGCCCAAGGAAAAAGAAT 57.058 42.857 0.00 0.00 0.00 2.40
61 62 2.919494 GCAACACCCTTCGCCCAAG 61.919 63.158 0.00 0.00 0.00 3.61
62 63 2.909965 GCAACACCCTTCGCCCAA 60.910 61.111 0.00 0.00 0.00 4.12
63 64 3.505790 ATGCAACACCCTTCGCCCA 62.506 57.895 0.00 0.00 0.00 5.36
64 65 2.676471 ATGCAACACCCTTCGCCC 60.676 61.111 0.00 0.00 0.00 6.13
65 66 2.568090 CATGCAACACCCTTCGCC 59.432 61.111 0.00 0.00 0.00 5.54
66 67 2.126346 GCATGCAACACCCTTCGC 60.126 61.111 14.21 0.00 0.00 4.70
67 68 1.210931 CTGCATGCAACACCCTTCG 59.789 57.895 22.88 2.34 0.00 3.79
68 69 0.524862 CTCTGCATGCAACACCCTTC 59.475 55.000 22.88 0.00 0.00 3.46
69 70 1.530013 GCTCTGCATGCAACACCCTT 61.530 55.000 22.88 0.00 0.00 3.95
70 71 1.975407 GCTCTGCATGCAACACCCT 60.975 57.895 22.88 0.00 0.00 4.34
71 72 2.570181 GCTCTGCATGCAACACCC 59.430 61.111 22.88 4.86 0.00 4.61
72 73 2.177531 CGCTCTGCATGCAACACC 59.822 61.111 22.88 9.30 0.00 4.16
73 74 1.154338 GTCGCTCTGCATGCAACAC 60.154 57.895 22.88 12.26 0.00 3.32
74 75 1.301953 AGTCGCTCTGCATGCAACA 60.302 52.632 22.88 10.32 0.00 3.33
75 76 1.134075 CAGTCGCTCTGCATGCAAC 59.866 57.895 22.88 16.26 37.36 4.17
76 77 2.036571 CCAGTCGCTCTGCATGCAA 61.037 57.895 22.88 11.70 42.38 4.08
77 78 2.435410 CCAGTCGCTCTGCATGCA 60.435 61.111 21.29 21.29 42.38 3.96
78 79 3.873883 GCCAGTCGCTCTGCATGC 61.874 66.667 11.82 11.82 42.38 4.06
87 88 1.227002 GTAGCCAGTAGCCAGTCGC 60.227 63.158 0.00 0.00 45.47 5.19
88 89 0.101399 CAGTAGCCAGTAGCCAGTCG 59.899 60.000 0.00 0.00 45.47 4.18
89 90 0.461961 CCAGTAGCCAGTAGCCAGTC 59.538 60.000 0.00 0.00 45.47 3.51
90 91 1.617947 GCCAGTAGCCAGTAGCCAGT 61.618 60.000 0.00 0.00 45.47 4.00
91 92 1.144936 GCCAGTAGCCAGTAGCCAG 59.855 63.158 0.00 0.00 45.47 4.85
92 93 0.909610 AAGCCAGTAGCCAGTAGCCA 60.910 55.000 0.00 0.00 45.47 4.75
93 94 0.462759 CAAGCCAGTAGCCAGTAGCC 60.463 60.000 0.00 0.00 45.47 3.93
94 95 0.250513 ACAAGCCAGTAGCCAGTAGC 59.749 55.000 0.00 0.00 45.47 3.58
95 96 2.761208 AGTACAAGCCAGTAGCCAGTAG 59.239 50.000 0.00 0.00 45.47 2.57
96 97 2.496070 CAGTACAAGCCAGTAGCCAGTA 59.504 50.000 0.00 0.00 45.47 2.74
97 98 1.276421 CAGTACAAGCCAGTAGCCAGT 59.724 52.381 0.00 0.00 45.47 4.00
98 99 1.550524 TCAGTACAAGCCAGTAGCCAG 59.449 52.381 0.00 0.00 45.47 4.85
99 100 1.639722 TCAGTACAAGCCAGTAGCCA 58.360 50.000 0.00 0.00 45.47 4.75
100 101 2.762535 TTCAGTACAAGCCAGTAGCC 57.237 50.000 0.00 0.00 45.47 3.93
101 102 4.065789 ACTTTTCAGTACAAGCCAGTAGC 58.934 43.478 0.00 0.00 44.25 3.58
102 103 6.619801 AAACTTTTCAGTACAAGCCAGTAG 57.380 37.500 0.00 0.00 30.68 2.57
103 104 7.771826 ACTAAAACTTTTCAGTACAAGCCAGTA 59.228 33.333 0.00 0.00 30.68 2.74
104 105 5.914898 AAAACTTTTCAGTACAAGCCAGT 57.085 34.783 0.00 0.00 30.68 4.00
105 106 7.027778 ACTAAAACTTTTCAGTACAAGCCAG 57.972 36.000 0.00 0.00 30.68 4.85
106 107 8.400186 GTTACTAAAACTTTTCAGTACAAGCCA 58.600 33.333 0.00 0.00 30.68 4.75
107 108 8.400186 TGTTACTAAAACTTTTCAGTACAAGCC 58.600 33.333 0.00 0.00 30.68 4.35
108 109 9.218359 GTGTTACTAAAACTTTTCAGTACAAGC 57.782 33.333 0.00 0.00 30.68 4.01
111 112 8.810427 CGAGTGTTACTAAAACTTTTCAGTACA 58.190 33.333 0.00 0.00 30.68 2.90
112 113 7.791131 GCGAGTGTTACTAAAACTTTTCAGTAC 59.209 37.037 0.00 0.00 30.68 2.73
113 114 7.306167 CGCGAGTGTTACTAAAACTTTTCAGTA 60.306 37.037 0.00 0.00 30.68 2.74
114 115 6.509039 CGCGAGTGTTACTAAAACTTTTCAGT 60.509 38.462 0.00 0.00 33.11 3.41
115 116 5.839239 CGCGAGTGTTACTAAAACTTTTCAG 59.161 40.000 0.00 0.00 0.00 3.02
116 117 5.519566 TCGCGAGTGTTACTAAAACTTTTCA 59.480 36.000 3.71 0.00 0.00 2.69
117 118 5.966335 TCGCGAGTGTTACTAAAACTTTTC 58.034 37.500 3.71 0.00 0.00 2.29
118 119 5.750067 TCTCGCGAGTGTTACTAAAACTTTT 59.250 36.000 33.33 0.00 0.00 2.27
119 120 5.284079 TCTCGCGAGTGTTACTAAAACTTT 58.716 37.500 33.33 0.00 0.00 2.66
120 121 4.863491 TCTCGCGAGTGTTACTAAAACTT 58.137 39.130 33.33 0.00 0.00 2.66
121 122 4.494350 TCTCGCGAGTGTTACTAAAACT 57.506 40.909 33.33 0.00 0.00 2.66
122 123 5.400485 TCTTTCTCGCGAGTGTTACTAAAAC 59.600 40.000 33.33 0.00 0.00 2.43
123 124 5.522456 TCTTTCTCGCGAGTGTTACTAAAA 58.478 37.500 33.33 21.86 0.00 1.52
124 125 5.112220 TCTTTCTCGCGAGTGTTACTAAA 57.888 39.130 33.33 22.51 0.00 1.85
125 126 4.754372 TCTTTCTCGCGAGTGTTACTAA 57.246 40.909 33.33 17.09 0.00 2.24
126 127 4.754372 TTCTTTCTCGCGAGTGTTACTA 57.246 40.909 33.33 11.70 0.00 1.82
127 128 3.637998 TTCTTTCTCGCGAGTGTTACT 57.362 42.857 33.33 0.00 0.00 2.24
128 129 4.208666 ACTTTTCTTTCTCGCGAGTGTTAC 59.791 41.667 33.33 0.00 0.00 2.50
129 130 4.365723 ACTTTTCTTTCTCGCGAGTGTTA 58.634 39.130 33.33 13.67 0.00 2.41
130 131 3.195661 ACTTTTCTTTCTCGCGAGTGTT 58.804 40.909 33.33 7.99 0.00 3.32
131 132 2.822764 ACTTTTCTTTCTCGCGAGTGT 58.177 42.857 33.33 17.07 0.00 3.55
132 133 3.861569 AACTTTTCTTTCTCGCGAGTG 57.138 42.857 33.33 23.58 0.00 3.51
133 134 4.877323 AAAACTTTTCTTTCTCGCGAGT 57.123 36.364 33.33 11.00 0.00 4.18
134 135 5.975442 ACTAAAACTTTTCTTTCTCGCGAG 58.025 37.500 30.03 30.03 0.00 5.03
135 136 5.978934 ACTAAAACTTTTCTTTCTCGCGA 57.021 34.783 9.26 9.26 0.00 5.87
136 137 6.572621 GGTTACTAAAACTTTTCTTTCTCGCG 59.427 38.462 0.00 0.00 0.00 5.87
137 138 7.375280 GTGGTTACTAAAACTTTTCTTTCTCGC 59.625 37.037 0.00 0.00 0.00 5.03
138 139 8.610035 AGTGGTTACTAAAACTTTTCTTTCTCG 58.390 33.333 0.00 0.00 34.74 4.04
139 140 9.717892 CAGTGGTTACTAAAACTTTTCTTTCTC 57.282 33.333 0.00 0.00 34.74 2.87
140 141 8.188799 GCAGTGGTTACTAAAACTTTTCTTTCT 58.811 33.333 0.00 0.00 34.74 2.52
141 142 8.188799 AGCAGTGGTTACTAAAACTTTTCTTTC 58.811 33.333 0.00 0.00 34.74 2.62
142 143 8.063200 AGCAGTGGTTACTAAAACTTTTCTTT 57.937 30.769 0.00 0.00 34.74 2.52
143 144 7.640597 AGCAGTGGTTACTAAAACTTTTCTT 57.359 32.000 0.00 0.00 34.74 2.52
144 145 7.228108 GGTAGCAGTGGTTACTAAAACTTTTCT 59.772 37.037 0.00 0.00 34.74 2.52
145 146 7.012610 TGGTAGCAGTGGTTACTAAAACTTTTC 59.987 37.037 0.00 0.00 34.74 2.29
146 147 6.829811 TGGTAGCAGTGGTTACTAAAACTTTT 59.170 34.615 0.00 0.00 34.74 2.27
147 148 6.358991 TGGTAGCAGTGGTTACTAAAACTTT 58.641 36.000 0.00 0.00 34.74 2.66
148 149 5.932455 TGGTAGCAGTGGTTACTAAAACTT 58.068 37.500 0.00 0.00 34.74 2.66
149 150 5.556006 TGGTAGCAGTGGTTACTAAAACT 57.444 39.130 0.00 0.00 34.74 2.66
150 151 5.993441 TCTTGGTAGCAGTGGTTACTAAAAC 59.007 40.000 0.00 0.00 32.46 2.43
151 152 5.993441 GTCTTGGTAGCAGTGGTTACTAAAA 59.007 40.000 0.00 0.00 32.46 1.52
152 153 5.070714 TGTCTTGGTAGCAGTGGTTACTAAA 59.929 40.000 0.00 0.00 32.46 1.85
153 154 4.589798 TGTCTTGGTAGCAGTGGTTACTAA 59.410 41.667 0.00 0.93 34.74 2.24
154 155 4.154176 TGTCTTGGTAGCAGTGGTTACTA 58.846 43.478 0.00 0.00 34.74 1.82
155 156 2.969950 TGTCTTGGTAGCAGTGGTTACT 59.030 45.455 0.00 0.00 37.75 2.24
156 157 3.396260 TGTCTTGGTAGCAGTGGTTAC 57.604 47.619 0.00 0.00 0.00 2.50
157 158 4.425180 TTTGTCTTGGTAGCAGTGGTTA 57.575 40.909 0.00 0.00 0.00 2.85
158 159 3.290948 TTTGTCTTGGTAGCAGTGGTT 57.709 42.857 0.00 0.00 0.00 3.67
159 160 3.508845 ATTTGTCTTGGTAGCAGTGGT 57.491 42.857 0.00 0.00 0.00 4.16
160 161 3.569701 ACAATTTGTCTTGGTAGCAGTGG 59.430 43.478 0.00 0.00 0.00 4.00
161 162 4.539870 CACAATTTGTCTTGGTAGCAGTG 58.460 43.478 0.00 0.00 0.00 3.66
162 163 3.569701 CCACAATTTGTCTTGGTAGCAGT 59.430 43.478 0.00 0.00 0.00 4.40
163 164 3.820467 TCCACAATTTGTCTTGGTAGCAG 59.180 43.478 0.00 0.00 0.00 4.24
164 165 3.826524 TCCACAATTTGTCTTGGTAGCA 58.173 40.909 0.00 0.00 0.00 3.49
165 166 5.880332 TCTATCCACAATTTGTCTTGGTAGC 59.120 40.000 0.00 0.00 0.00 3.58
166 167 6.540189 CCTCTATCCACAATTTGTCTTGGTAG 59.460 42.308 0.00 2.32 0.00 3.18
167 168 6.414732 CCTCTATCCACAATTTGTCTTGGTA 58.585 40.000 0.00 0.00 0.00 3.25
168 169 5.256474 CCTCTATCCACAATTTGTCTTGGT 58.744 41.667 0.00 0.00 0.00 3.67
169 170 4.641989 CCCTCTATCCACAATTTGTCTTGG 59.358 45.833 0.00 0.00 0.00 3.61
170 171 4.641989 CCCCTCTATCCACAATTTGTCTTG 59.358 45.833 0.00 0.00 0.00 3.02
171 172 4.540099 TCCCCTCTATCCACAATTTGTCTT 59.460 41.667 0.00 0.00 0.00 3.01
172 173 4.111577 TCCCCTCTATCCACAATTTGTCT 58.888 43.478 0.00 0.00 0.00 3.41
173 174 4.503714 TCCCCTCTATCCACAATTTGTC 57.496 45.455 0.00 0.00 0.00 3.18
174 175 4.044065 TGTTCCCCTCTATCCACAATTTGT 59.956 41.667 0.00 0.00 0.00 2.83
175 176 4.599041 TGTTCCCCTCTATCCACAATTTG 58.401 43.478 0.00 0.00 0.00 2.32
176 177 4.292306 ACTGTTCCCCTCTATCCACAATTT 59.708 41.667 0.00 0.00 0.00 1.82
177 178 3.852578 ACTGTTCCCCTCTATCCACAATT 59.147 43.478 0.00 0.00 0.00 2.32
178 179 3.200825 CACTGTTCCCCTCTATCCACAAT 59.799 47.826 0.00 0.00 0.00 2.71
179 180 2.571653 CACTGTTCCCCTCTATCCACAA 59.428 50.000 0.00 0.00 0.00 3.33
180 181 2.187958 CACTGTTCCCCTCTATCCACA 58.812 52.381 0.00 0.00 0.00 4.17
181 182 1.486726 CCACTGTTCCCCTCTATCCAC 59.513 57.143 0.00 0.00 0.00 4.02
182 183 1.080498 ACCACTGTTCCCCTCTATCCA 59.920 52.381 0.00 0.00 0.00 3.41
183 184 1.763545 GACCACTGTTCCCCTCTATCC 59.236 57.143 0.00 0.00 0.00 2.59
184 185 1.409427 CGACCACTGTTCCCCTCTATC 59.591 57.143 0.00 0.00 0.00 2.08
185 186 1.006758 TCGACCACTGTTCCCCTCTAT 59.993 52.381 0.00 0.00 0.00 1.98
186 187 0.406750 TCGACCACTGTTCCCCTCTA 59.593 55.000 0.00 0.00 0.00 2.43
187 188 0.252284 ATCGACCACTGTTCCCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
188 189 0.175989 GATCGACCACTGTTCCCCTC 59.824 60.000 0.00 0.00 0.00 4.30
189 190 1.605058 CGATCGACCACTGTTCCCCT 61.605 60.000 10.26 0.00 0.00 4.79
190 191 1.153628 CGATCGACCACTGTTCCCC 60.154 63.158 10.26 0.00 0.00 4.81
191 192 0.458025 GACGATCGACCACTGTTCCC 60.458 60.000 24.34 0.00 0.00 3.97
192 193 0.526662 AGACGATCGACCACTGTTCC 59.473 55.000 24.34 0.00 0.00 3.62
193 194 1.068472 ACAGACGATCGACCACTGTTC 60.068 52.381 24.34 6.02 38.41 3.18
194 195 0.959553 ACAGACGATCGACCACTGTT 59.040 50.000 24.34 11.95 38.41 3.16
195 196 0.241213 CACAGACGATCGACCACTGT 59.759 55.000 24.34 23.88 41.52 3.55
196 197 1.073216 GCACAGACGATCGACCACTG 61.073 60.000 24.34 23.31 35.14 3.66
197 198 1.213013 GCACAGACGATCGACCACT 59.787 57.895 24.34 12.00 0.00 4.00
198 199 2.152699 CGCACAGACGATCGACCAC 61.153 63.158 24.34 9.90 34.06 4.16
199 200 2.178273 CGCACAGACGATCGACCA 59.822 61.111 24.34 0.00 34.06 4.02
200 201 2.152699 CACGCACAGACGATCGACC 61.153 63.158 24.34 12.94 36.70 4.79
201 202 1.396543 GACACGCACAGACGATCGAC 61.397 60.000 24.34 16.66 36.70 4.20
202 203 1.154282 GACACGCACAGACGATCGA 60.154 57.895 24.34 0.00 36.70 3.59
203 204 0.096454 TAGACACGCACAGACGATCG 59.904 55.000 14.88 14.88 36.70 3.69
204 205 1.536149 GTAGACACGCACAGACGATC 58.464 55.000 0.00 0.00 36.70 3.69
205 206 0.179197 CGTAGACACGCACAGACGAT 60.179 55.000 0.00 0.00 42.05 3.73
206 207 1.205820 CGTAGACACGCACAGACGA 59.794 57.895 0.00 0.00 42.05 4.20
207 208 3.737182 CGTAGACACGCACAGACG 58.263 61.111 0.00 0.00 42.05 4.18
216 217 3.797184 GCCTGATCCTGATTCGTAGACAC 60.797 52.174 0.00 0.00 34.32 3.67
217 218 2.362397 GCCTGATCCTGATTCGTAGACA 59.638 50.000 0.00 0.00 34.32 3.41
218 219 2.362397 TGCCTGATCCTGATTCGTAGAC 59.638 50.000 0.00 0.00 34.32 2.59
219 220 2.666317 TGCCTGATCCTGATTCGTAGA 58.334 47.619 0.00 0.00 0.00 2.59
220 221 3.459232 TTGCCTGATCCTGATTCGTAG 57.541 47.619 0.00 0.00 0.00 3.51
221 222 3.387699 TGATTGCCTGATCCTGATTCGTA 59.612 43.478 0.00 0.00 0.00 3.43
222 223 2.171237 TGATTGCCTGATCCTGATTCGT 59.829 45.455 0.00 0.00 0.00 3.85
223 224 2.806818 CTGATTGCCTGATCCTGATTCG 59.193 50.000 0.00 0.00 0.00 3.34
224 225 2.553172 GCTGATTGCCTGATCCTGATTC 59.447 50.000 0.00 0.00 35.15 2.52
225 226 2.584236 GCTGATTGCCTGATCCTGATT 58.416 47.619 0.00 0.00 35.15 2.57
226 227 2.273538 GCTGATTGCCTGATCCTGAT 57.726 50.000 0.00 0.00 35.15 2.90
227 228 3.794737 GCTGATTGCCTGATCCTGA 57.205 52.632 0.00 0.00 35.15 3.86
237 238 1.001641 AGACCCAGTGGCTGATTGC 60.002 57.895 2.61 0.00 41.94 3.56
238 239 0.679002 CCAGACCCAGTGGCTGATTG 60.679 60.000 16.10 4.82 37.74 2.67
239 240 1.687612 CCAGACCCAGTGGCTGATT 59.312 57.895 16.10 0.00 37.74 2.57
240 241 2.304056 CCCAGACCCAGTGGCTGAT 61.304 63.158 16.10 0.00 37.74 2.90
241 242 2.930019 CCCAGACCCAGTGGCTGA 60.930 66.667 16.10 0.00 37.74 4.26
242 243 2.930019 TCCCAGACCCAGTGGCTG 60.930 66.667 2.61 6.73 36.27 4.85
243 244 2.608988 CTCCCAGACCCAGTGGCT 60.609 66.667 2.61 0.00 33.24 4.75
244 245 2.930562 ACTCCCAGACCCAGTGGC 60.931 66.667 2.61 0.00 33.24 5.01
245 246 3.072476 CACTCCCAGACCCAGTGG 58.928 66.667 0.63 0.63 34.96 4.00
246 247 2.348998 GCACTCCCAGACCCAGTG 59.651 66.667 0.00 0.00 40.53 3.66
247 248 2.122413 TGCACTCCCAGACCCAGT 60.122 61.111 0.00 0.00 0.00 4.00
248 249 0.904865 TAGTGCACTCCCAGACCCAG 60.905 60.000 25.56 0.00 0.00 4.45
249 250 0.904865 CTAGTGCACTCCCAGACCCA 60.905 60.000 25.56 0.59 0.00 4.51
250 251 0.614979 TCTAGTGCACTCCCAGACCC 60.615 60.000 25.56 0.00 0.00 4.46
251 252 1.490574 ATCTAGTGCACTCCCAGACC 58.509 55.000 25.56 0.00 0.00 3.85
252 253 3.618690 AAATCTAGTGCACTCCCAGAC 57.381 47.619 25.56 0.00 0.00 3.51
253 254 3.840666 AGAAAATCTAGTGCACTCCCAGA 59.159 43.478 25.56 21.01 0.00 3.86
254 255 4.213564 AGAAAATCTAGTGCACTCCCAG 57.786 45.455 25.56 15.92 0.00 4.45
255 256 4.640771 AAGAAAATCTAGTGCACTCCCA 57.359 40.909 25.56 8.81 0.00 4.37
256 257 5.966742 AAAAGAAAATCTAGTGCACTCCC 57.033 39.130 25.56 5.82 0.00 4.30
312 320 5.680619 TGGGTATTAGTTCATGAGCGATTT 58.319 37.500 3.72 0.00 0.00 2.17
316 324 4.442706 AGTTGGGTATTAGTTCATGAGCG 58.557 43.478 3.72 0.00 0.00 5.03
460 469 9.965902 AATTCCTTCTGCTAGAATAAGAAAAGA 57.034 29.630 0.00 0.00 33.13 2.52
553 566 3.639561 GGAAAGGGCTGTTTTGTTCCTAA 59.360 43.478 0.00 0.00 33.28 2.69
568 581 7.341805 TCTCTATGATCAGAAAAAGGAAAGGG 58.658 38.462 0.09 0.00 0.00 3.95
707 720 7.094549 CCATCCAAAAAGACCGTATTTTGACTA 60.095 37.037 17.47 7.98 45.09 2.59
722 735 5.418676 ACGCCAAATATTCCATCCAAAAAG 58.581 37.500 0.00 0.00 0.00 2.27
819 832 4.647853 TGCTACTAATTCTTCCTCCGCTTA 59.352 41.667 0.00 0.00 0.00 3.09
939 952 0.898326 AAATTCCACCCGCCCAAGTC 60.898 55.000 0.00 0.00 0.00 3.01
996 1009 9.558396 AAAATTCCAACTGCTTTATTCATTTGA 57.442 25.926 0.00 0.00 0.00 2.69
1155 1168 1.133356 AGATTGCCCAGGGAAATAGGC 60.133 52.381 12.45 0.00 45.96 3.93
1265 1278 7.671302 ACATGCTATAAGGTACATAGGTCAAG 58.329 38.462 0.00 0.00 0.00 3.02
1266 1279 7.612065 ACATGCTATAAGGTACATAGGTCAA 57.388 36.000 0.00 0.00 0.00 3.18
1267 1280 7.948447 AGTACATGCTATAAGGTACATAGGTCA 59.052 37.037 0.00 0.00 38.78 4.02
1268 1281 8.350852 AGTACATGCTATAAGGTACATAGGTC 57.649 38.462 0.00 0.00 38.78 3.85
1269 1282 8.722622 AAGTACATGCTATAAGGTACATAGGT 57.277 34.615 0.00 0.00 38.78 3.08
1270 1283 9.998106 AAAAGTACATGCTATAAGGTACATAGG 57.002 33.333 0.00 0.00 38.78 2.57
1317 2917 9.293404 CTTGTGATCAATCCATAGATACCAATT 57.707 33.333 0.00 0.00 32.82 2.32
1418 3018 9.554395 TTAATTGGCGACTATCAAATAGATCAA 57.446 29.630 0.00 0.00 38.19 2.57
1458 3058 5.406780 CGCAAGGGTTATAACAAAAATTGCA 59.593 36.000 25.19 0.00 40.27 4.08
1527 3127 4.317671 ACGAGTGGATTTCCTATTACGG 57.682 45.455 0.00 0.00 36.82 4.02
1592 3209 8.204836 GCCTTTGTTTAGAGGATTCTATGTCTA 58.795 37.037 0.00 0.00 35.88 2.59
1593 3210 7.051000 GCCTTTGTTTAGAGGATTCTATGTCT 58.949 38.462 0.00 0.00 35.88 3.41
1594 3211 6.823689 TGCCTTTGTTTAGAGGATTCTATGTC 59.176 38.462 0.00 0.00 35.88 3.06
1811 3432 9.453325 AATTTTACGAATTGTACACACGAATTT 57.547 25.926 17.93 6.79 31.20 1.82
1878 3503 2.079925 GAAAGCGTGAAGAGAGCCAAT 58.920 47.619 0.00 0.00 0.00 3.16
2106 3737 2.936919 ACATCTGTTGGACAAGCTCA 57.063 45.000 0.00 0.00 0.00 4.26
2135 3766 4.447762 GCTTTACATCCATCCCAGGGTATT 60.448 45.833 5.01 0.00 0.00 1.89
2170 3801 2.702751 TTCGGTTCTCAGCGCGGAAA 62.703 55.000 12.27 6.40 43.85 3.13


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

AutoCloner maintained by Alex Coulton.