Multiple sequence alignment - TraesCS2B01G560100

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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 TraesCS2B01G560100 chr2B 100.000 4081 0 0 1 4081 753797969 753802049 0.000000e+00 7537.0
1 TraesCS2B01G560100 chr2B 89.916 119 7 1 83 201 104807546 104807659 9.140000e-32 148.0
2 TraesCS2B01G560100 chr2B 100.000 28 0 0 83 110 112460809 112460782 7.000000e-03 52.8
3 TraesCS2B01G560100 chr2D 94.310 2654 82 25 1462 4081 617896626 617894008 0.000000e+00 4000.0
4 TraesCS2B01G560100 chr2D 85.144 1252 63 49 208 1426 617897784 617896623 0.000000e+00 1168.0
5 TraesCS2B01G560100 chr2D 94.118 85 3 2 1 83 617897869 617897785 1.190000e-25 128.0
6 TraesCS2B01G560100 chr2A 94.282 2291 73 17 1793 4081 748446191 748443957 0.000000e+00 3452.0
7 TraesCS2B01G560100 chr2A 85.537 1535 89 60 266 1736 748447668 748446203 0.000000e+00 1482.0
8 TraesCS2B01G560100 chr2A 98.361 61 1 0 208 268 748448852 748448792 1.550000e-19 108.0
9 TraesCS2B01G560100 chr7B 89.538 1300 121 10 1795 3082 745143452 745144748 0.000000e+00 1633.0
10 TraesCS2B01G560100 chr7B 94.201 707 28 7 3140 3846 382087449 382088142 0.000000e+00 1066.0
11 TraesCS2B01G560100 chr7B 79.464 336 47 14 980 1314 745141604 745141918 6.870000e-53 219.0
12 TraesCS2B01G560100 chr7B 89.076 119 8 1 83 201 93259507 93259620 4.250000e-30 143.0
13 TraesCS2B01G560100 chr7B 87.912 91 6 1 83 173 435125516 435125431 7.220000e-18 102.0
14 TraesCS2B01G560100 chr7D 89.482 1293 123 7 1795 3082 632162713 632163997 0.000000e+00 1622.0
15 TraesCS2B01G560100 chr7D 77.962 422 53 26 998 1404 632161873 632162269 1.140000e-55 228.0
16 TraesCS2B01G560100 chr1A 89.559 1293 116 11 1795 3082 6423492 6422214 0.000000e+00 1622.0
17 TraesCS2B01G560100 chr1A 81.672 311 33 17 1005 1314 6424449 6424162 1.900000e-58 237.0
18 TraesCS2B01G560100 chr6A 94.366 710 27 7 3140 3849 477476218 477475522 0.000000e+00 1077.0
19 TraesCS2B01G560100 chr6A 93.918 707 31 6 3140 3846 239255947 239256641 0.000000e+00 1057.0
20 TraesCS2B01G560100 chr6B 93.944 710 30 7 3140 3849 714157087 714156391 0.000000e+00 1061.0
21 TraesCS2B01G560100 chr4A 93.944 710 30 7 3140 3849 29478862 29478166 0.000000e+00 1061.0
22 TraesCS2B01G560100 chr4A 93.918 707 30 7 3140 3846 51046128 51046821 0.000000e+00 1055.0
23 TraesCS2B01G560100 chr1B 93.803 710 31 7 3140 3849 82988233 82987537 0.000000e+00 1055.0
24 TraesCS2B01G560100 chr3B 77.778 324 63 9 2304 2622 779528868 779528549 1.500000e-44 191.0
25 TraesCS2B01G560100 chr3B 90.400 125 7 1 81 205 804825215 804825096 4.220000e-35 159.0
26 TraesCS2B01G560100 chrUn 90.164 122 7 1 80 201 37870593 37870477 1.960000e-33 154.0
27 TraesCS2B01G560100 chrUn 90.164 122 7 1 80 201 333563581 333563465 1.960000e-33 154.0
28 TraesCS2B01G560100 chr3D 76.856 229 47 6 2397 2622 582054310 582054535 1.540000e-24 124.0


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 TraesCS2B01G560100 chr2B 753797969 753802049 4080 False 7537.000000 7537 100.000000 1 4081 1 chr2B.!!$F2 4080
1 TraesCS2B01G560100 chr2D 617894008 617897869 3861 True 1765.333333 4000 91.190667 1 4081 3 chr2D.!!$R1 4080
2 TraesCS2B01G560100 chr2A 748443957 748448852 4895 True 1680.666667 3452 92.726667 208 4081 3 chr2A.!!$R1 3873
3 TraesCS2B01G560100 chr7B 382087449 382088142 693 False 1066.000000 1066 94.201000 3140 3846 1 chr7B.!!$F2 706
4 TraesCS2B01G560100 chr7B 745141604 745144748 3144 False 926.000000 1633 84.501000 980 3082 2 chr7B.!!$F3 2102
5 TraesCS2B01G560100 chr7D 632161873 632163997 2124 False 925.000000 1622 83.722000 998 3082 2 chr7D.!!$F1 2084
6 TraesCS2B01G560100 chr1A 6422214 6424449 2235 True 929.500000 1622 85.615500 1005 3082 2 chr1A.!!$R1 2077
7 TraesCS2B01G560100 chr6A 477475522 477476218 696 True 1077.000000 1077 94.366000 3140 3849 1 chr6A.!!$R1 709
8 TraesCS2B01G560100 chr6A 239255947 239256641 694 False 1057.000000 1057 93.918000 3140 3846 1 chr6A.!!$F1 706
9 TraesCS2B01G560100 chr6B 714156391 714157087 696 True 1061.000000 1061 93.944000 3140 3849 1 chr6B.!!$R1 709
10 TraesCS2B01G560100 chr4A 29478166 29478862 696 True 1061.000000 1061 93.944000 3140 3849 1 chr4A.!!$R1 709
11 TraesCS2B01G560100 chr4A 51046128 51046821 693 False 1055.000000 1055 93.918000 3140 3846 1 chr4A.!!$F1 706
12 TraesCS2B01G560100 chr1B 82987537 82988233 696 True 1055.000000 1055 93.803000 3140 3849 1 chr1B.!!$R1 709

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
95 98 0.108138 CCACACGGGTTGAGATCCTC 60.108 60.0 0.00 0.00 0.00 3.71 F
117 120 0.108804 CAGTACTGCACCGTACCCTG 60.109 60.0 10.54 2.88 40.42 4.45 F
145 148 0.174389 CAGATGACAGGTGAGGTCGG 59.826 60.0 0.00 0.00 38.10 4.79 F
732 1908 0.184692 TGTCACCAGGTCAATGCCAA 59.815 50.0 0.00 0.00 0.00 4.52 F
2026 4432 0.108138 CTCAAGAAGGGGTACGCCAG 60.108 60.0 28.77 13.60 44.92 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 2580 0.879400 GCCATCAGAGAGGTCATGCG 60.879 60.000 0.00 0.0 0.00 4.73 R
1374 2589 1.817357 CAAGCAACAGCCATCAGAGA 58.183 50.000 0.00 0.0 0.00 3.10 R
1409 2629 2.009774 CAGTGCAGTATTACCAGTGGC 58.990 52.381 9.78 0.0 0.00 5.01 R
2723 5129 1.078848 GAAGACGAGCAGGTGCCAT 60.079 57.895 0.00 0.0 43.38 4.40 R
3366 5787 1.174712 TGCCTTTGCTGCCTGAGAAC 61.175 55.000 0.00 0.0 38.71 3.01 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
35 38 1.334960 GCCATGGAATTAATGGACGCG 60.335 52.381 18.40 3.53 46.44 6.01
83 86 4.128925 CATATAGATGGATCCCACACGG 57.871 50.000 9.90 0.00 35.80 4.94
93 96 4.617875 CCACACGGGTTGAGATCC 57.382 61.111 0.00 0.00 0.00 3.36
94 97 1.983224 CCACACGGGTTGAGATCCT 59.017 57.895 0.00 0.00 0.00 3.24
95 98 0.108138 CCACACGGGTTGAGATCCTC 60.108 60.000 0.00 0.00 0.00 3.71
96 99 0.898320 CACACGGGTTGAGATCCTCT 59.102 55.000 0.00 0.00 0.00 3.69
97 100 2.100197 CACACGGGTTGAGATCCTCTA 58.900 52.381 0.00 0.00 0.00 2.43
98 101 2.100989 ACACGGGTTGAGATCCTCTAC 58.899 52.381 0.00 0.00 35.97 2.59
99 102 2.100197 CACGGGTTGAGATCCTCTACA 58.900 52.381 9.86 0.00 37.82 2.74
100 103 2.099921 CACGGGTTGAGATCCTCTACAG 59.900 54.545 9.86 6.40 37.82 2.74
101 104 2.291670 ACGGGTTGAGATCCTCTACAGT 60.292 50.000 9.86 6.87 37.82 3.55
102 105 3.053842 ACGGGTTGAGATCCTCTACAGTA 60.054 47.826 9.86 0.00 37.82 2.74
103 106 3.315749 CGGGTTGAGATCCTCTACAGTAC 59.684 52.174 9.86 0.00 37.82 2.73
104 107 4.538738 GGGTTGAGATCCTCTACAGTACT 58.461 47.826 9.86 0.00 37.82 2.73
105 108 4.339814 GGGTTGAGATCCTCTACAGTACTG 59.660 50.000 21.44 21.44 37.82 2.74
106 109 4.202070 GGTTGAGATCCTCTACAGTACTGC 60.202 50.000 22.90 3.82 37.82 4.40
107 110 4.236527 TGAGATCCTCTACAGTACTGCA 57.763 45.455 22.90 9.40 0.00 4.41
108 111 3.948473 TGAGATCCTCTACAGTACTGCAC 59.052 47.826 22.90 3.38 0.00 4.57
109 112 3.292460 AGATCCTCTACAGTACTGCACC 58.708 50.000 22.90 4.01 0.00 5.01
110 113 1.460504 TCCTCTACAGTACTGCACCG 58.539 55.000 22.90 9.03 0.00 4.94
111 114 1.174783 CCTCTACAGTACTGCACCGT 58.825 55.000 22.90 5.47 0.00 4.83
112 115 2.026915 TCCTCTACAGTACTGCACCGTA 60.027 50.000 22.90 6.39 0.00 4.02
113 116 2.097142 CCTCTACAGTACTGCACCGTAC 59.903 54.545 22.90 7.92 39.97 3.67
114 117 2.086869 TCTACAGTACTGCACCGTACC 58.913 52.381 22.90 0.00 40.42 3.34
115 118 1.133790 CTACAGTACTGCACCGTACCC 59.866 57.143 22.90 0.00 40.42 3.69
116 119 0.541296 ACAGTACTGCACCGTACCCT 60.541 55.000 22.90 0.00 40.42 4.34
117 120 0.108804 CAGTACTGCACCGTACCCTG 60.109 60.000 10.54 2.88 40.42 4.45
118 121 0.541296 AGTACTGCACCGTACCCTGT 60.541 55.000 11.50 0.00 40.42 4.00
119 122 0.319405 GTACTGCACCGTACCCTGTT 59.681 55.000 5.20 0.00 34.97 3.16
120 123 0.319083 TACTGCACCGTACCCTGTTG 59.681 55.000 0.00 0.00 0.00 3.33
121 124 1.070786 CTGCACCGTACCCTGTTGT 59.929 57.895 0.00 0.00 0.00 3.32
122 125 0.319083 CTGCACCGTACCCTGTTGTA 59.681 55.000 0.00 0.00 0.00 2.41
123 126 0.319083 TGCACCGTACCCTGTTGTAG 59.681 55.000 0.00 0.00 0.00 2.74
124 127 0.319405 GCACCGTACCCTGTTGTAGT 59.681 55.000 0.00 0.00 0.00 2.73
125 128 1.938016 GCACCGTACCCTGTTGTAGTG 60.938 57.143 0.00 0.00 0.00 2.74
126 129 0.319405 ACCGTACCCTGTTGTAGTGC 59.681 55.000 0.00 0.00 0.00 4.40
127 130 0.319083 CCGTACCCTGTTGTAGTGCA 59.681 55.000 0.00 0.00 0.00 4.57
128 131 1.671850 CCGTACCCTGTTGTAGTGCAG 60.672 57.143 0.00 0.00 0.00 4.41
129 132 1.271379 CGTACCCTGTTGTAGTGCAGA 59.729 52.381 0.00 0.00 34.87 4.26
130 133 2.094182 CGTACCCTGTTGTAGTGCAGAT 60.094 50.000 0.00 0.00 34.87 2.90
131 134 2.479566 ACCCTGTTGTAGTGCAGATG 57.520 50.000 0.00 0.00 34.87 2.90
132 135 1.977854 ACCCTGTTGTAGTGCAGATGA 59.022 47.619 0.00 0.00 34.87 2.92
133 136 2.289694 ACCCTGTTGTAGTGCAGATGAC 60.290 50.000 0.00 0.00 34.87 3.06
134 137 2.289631 CCCTGTTGTAGTGCAGATGACA 60.290 50.000 0.00 0.00 34.87 3.58
135 138 2.998670 CCTGTTGTAGTGCAGATGACAG 59.001 50.000 4.35 4.35 33.97 3.51
136 139 2.998670 CTGTTGTAGTGCAGATGACAGG 59.001 50.000 3.58 0.00 34.87 4.00
137 140 2.368548 TGTTGTAGTGCAGATGACAGGT 59.631 45.455 0.00 0.00 0.00 4.00
138 141 2.738846 GTTGTAGTGCAGATGACAGGTG 59.261 50.000 0.00 0.00 0.00 4.00
139 142 2.247358 TGTAGTGCAGATGACAGGTGA 58.753 47.619 0.00 0.00 0.00 4.02
140 143 2.232208 TGTAGTGCAGATGACAGGTGAG 59.768 50.000 0.00 0.00 0.00 3.51
141 144 0.612229 AGTGCAGATGACAGGTGAGG 59.388 55.000 0.00 0.00 0.00 3.86
142 145 0.322975 GTGCAGATGACAGGTGAGGT 59.677 55.000 0.00 0.00 0.00 3.85
143 146 0.610174 TGCAGATGACAGGTGAGGTC 59.390 55.000 0.00 0.00 35.83 3.85
144 147 0.459237 GCAGATGACAGGTGAGGTCG 60.459 60.000 0.00 0.00 38.10 4.79
145 148 0.174389 CAGATGACAGGTGAGGTCGG 59.826 60.000 0.00 0.00 38.10 4.79
146 149 0.972983 AGATGACAGGTGAGGTCGGG 60.973 60.000 0.00 0.00 38.10 5.14
147 150 1.229209 ATGACAGGTGAGGTCGGGT 60.229 57.895 0.00 0.00 38.10 5.28
148 151 1.258445 ATGACAGGTGAGGTCGGGTC 61.258 60.000 0.00 0.00 38.10 4.46
149 152 2.603776 ACAGGTGAGGTCGGGTCC 60.604 66.667 0.00 0.00 0.00 4.46
150 153 2.603473 CAGGTGAGGTCGGGTCCA 60.603 66.667 0.00 0.00 0.00 4.02
151 154 2.603776 AGGTGAGGTCGGGTCCAC 60.604 66.667 0.00 0.00 0.00 4.02
152 155 2.920912 GGTGAGGTCGGGTCCACA 60.921 66.667 0.00 0.00 0.00 4.17
153 156 2.291043 GGTGAGGTCGGGTCCACAT 61.291 63.158 0.00 0.00 31.51 3.21
154 157 1.079127 GTGAGGTCGGGTCCACATG 60.079 63.158 0.00 0.00 31.51 3.21
155 158 2.290287 TGAGGTCGGGTCCACATGG 61.290 63.158 0.00 0.00 0.00 3.66
156 159 3.682292 GAGGTCGGGTCCACATGGC 62.682 68.421 0.00 0.00 34.44 4.40
157 160 4.028490 GGTCGGGTCCACATGGCA 62.028 66.667 0.00 0.00 34.44 4.92
158 161 2.436646 GTCGGGTCCACATGGCAG 60.437 66.667 0.00 0.00 34.44 4.85
159 162 4.408821 TCGGGTCCACATGGCAGC 62.409 66.667 0.00 0.00 34.44 5.25
161 164 4.408821 GGGTCCACATGGCAGCGA 62.409 66.667 0.00 0.00 34.44 4.93
162 165 3.127533 GGTCCACATGGCAGCGAC 61.128 66.667 0.00 0.00 34.44 5.19
163 166 3.127533 GTCCACATGGCAGCGACC 61.128 66.667 0.00 0.00 34.44 4.79
164 167 4.758251 TCCACATGGCAGCGACCG 62.758 66.667 0.00 0.00 34.44 4.79
166 169 2.125713 CACATGGCAGCGACCGTA 60.126 61.111 0.00 0.00 0.00 4.02
167 170 2.125673 ACATGGCAGCGACCGTAC 60.126 61.111 0.00 0.00 0.00 3.67
168 171 2.890474 CATGGCAGCGACCGTACC 60.890 66.667 0.00 0.00 0.00 3.34
169 172 4.508128 ATGGCAGCGACCGTACCG 62.508 66.667 0.00 0.00 0.00 4.02
176 179 2.800053 CGACCGTACCGCACCATA 59.200 61.111 0.00 0.00 0.00 2.74
177 180 1.361271 CGACCGTACCGCACCATAT 59.639 57.895 0.00 0.00 0.00 1.78
178 181 0.937699 CGACCGTACCGCACCATATG 60.938 60.000 0.00 0.00 0.00 1.78
195 198 3.623365 TGCTACTGCAGAGGATCCT 57.377 52.632 23.35 16.13 45.31 3.24
196 199 2.755952 TGCTACTGCAGAGGATCCTA 57.244 50.000 23.35 0.00 45.31 2.94
197 200 3.032265 TGCTACTGCAGAGGATCCTAA 57.968 47.619 23.35 0.00 45.31 2.69
198 201 2.695666 TGCTACTGCAGAGGATCCTAAC 59.304 50.000 23.35 7.75 45.31 2.34
199 202 2.036604 GCTACTGCAGAGGATCCTAACC 59.963 54.545 23.35 1.92 39.41 2.85
200 203 1.501582 ACTGCAGAGGATCCTAACCC 58.498 55.000 23.35 1.49 33.66 4.11
201 204 1.273838 ACTGCAGAGGATCCTAACCCA 60.274 52.381 23.35 8.82 33.66 4.51
202 205 2.053244 CTGCAGAGGATCCTAACCCAT 58.947 52.381 16.16 0.00 33.66 4.00
203 206 2.038295 CTGCAGAGGATCCTAACCCATC 59.962 54.545 16.16 0.00 33.66 3.51
204 207 1.349357 GCAGAGGATCCTAACCCATCC 59.651 57.143 16.16 0.00 39.24 3.51
205 208 1.981495 CAGAGGATCCTAACCCATCCC 59.019 57.143 16.16 0.00 39.73 3.85
206 209 1.585592 AGAGGATCCTAACCCATCCCA 59.414 52.381 16.16 0.00 39.73 4.37
232 235 0.439214 CGCACGCACACGGTTTTATA 59.561 50.000 0.00 0.00 46.04 0.98
447 1577 9.616156 TTTCTTCTGTTTTGTGTTGGTAGTATA 57.384 29.630 0.00 0.00 0.00 1.47
468 1598 3.332761 TGAATGCGAAACACACTTGAC 57.667 42.857 0.00 0.00 0.00 3.18
469 1599 2.032799 TGAATGCGAAACACACTTGACC 59.967 45.455 0.00 0.00 0.00 4.02
470 1600 1.674359 ATGCGAAACACACTTGACCA 58.326 45.000 0.00 0.00 0.00 4.02
471 1601 1.674359 TGCGAAACACACTTGACCAT 58.326 45.000 0.00 0.00 0.00 3.55
472 1602 2.839975 TGCGAAACACACTTGACCATA 58.160 42.857 0.00 0.00 0.00 2.74
529 1693 1.805945 CAGTGGTTCGCTCGGCTAC 60.806 63.158 0.00 0.00 0.00 3.58
534 1698 0.527169 GGTTCGCTCGGCTACCTTAC 60.527 60.000 8.66 0.00 31.39 2.34
548 1712 6.371548 CGGCTACCTTACCTTGTACGTATATA 59.628 42.308 0.00 0.00 0.00 0.86
551 1715 8.186821 GCTACCTTACCTTGTACGTATATATGG 58.813 40.741 0.00 2.01 0.00 2.74
552 1716 9.236006 CTACCTTACCTTGTACGTATATATGGT 57.764 37.037 0.00 7.82 35.15 3.55
589 1765 3.528532 CTGCATGCATGTCTTCACTCTA 58.471 45.455 26.79 0.00 0.00 2.43
590 1766 3.528532 TGCATGCATGTCTTCACTCTAG 58.471 45.455 26.79 0.00 0.00 2.43
591 1767 2.287373 GCATGCATGTCTTCACTCTAGC 59.713 50.000 26.79 4.83 0.00 3.42
626 1802 3.326578 ACCGCATGCACCTACCCA 61.327 61.111 19.57 0.00 0.00 4.51
628 1804 2.824041 CGCATGCACCTACCCACC 60.824 66.667 19.57 0.00 0.00 4.61
629 1805 2.440247 GCATGCACCTACCCACCC 60.440 66.667 14.21 0.00 0.00 4.61
630 1806 2.275418 CATGCACCTACCCACCCC 59.725 66.667 0.00 0.00 0.00 4.95
631 1807 2.204228 ATGCACCTACCCACCCCA 60.204 61.111 0.00 0.00 0.00 4.96
632 1808 2.612493 ATGCACCTACCCACCCCAC 61.612 63.158 0.00 0.00 0.00 4.61
633 1809 3.253838 GCACCTACCCACCCCACA 61.254 66.667 0.00 0.00 0.00 4.17
634 1810 3.077907 CACCTACCCACCCCACAG 58.922 66.667 0.00 0.00 0.00 3.66
635 1811 1.846124 CACCTACCCACCCCACAGT 60.846 63.158 0.00 0.00 0.00 3.55
636 1812 1.846124 ACCTACCCACCCCACAGTG 60.846 63.158 0.00 0.00 37.51 3.66
637 1813 1.846124 CCTACCCACCCCACAGTGT 60.846 63.158 0.00 0.00 35.93 3.55
638 1814 0.545787 CCTACCCACCCCACAGTGTA 60.546 60.000 0.00 0.00 35.93 2.90
639 1815 1.580059 CTACCCACCCCACAGTGTAT 58.420 55.000 0.00 0.00 35.93 2.29
642 1818 1.913419 ACCCACCCCACAGTGTATTAG 59.087 52.381 0.00 0.00 35.93 1.73
694 1870 2.664402 AATCTTGCCCTCAACTGTGT 57.336 45.000 0.00 0.00 0.00 3.72
732 1908 0.184692 TGTCACCAGGTCAATGCCAA 59.815 50.000 0.00 0.00 0.00 4.52
733 1909 1.327303 GTCACCAGGTCAATGCCAAA 58.673 50.000 0.00 0.00 0.00 3.28
734 1910 1.895131 GTCACCAGGTCAATGCCAAAT 59.105 47.619 0.00 0.00 0.00 2.32
735 1911 1.894466 TCACCAGGTCAATGCCAAATG 59.106 47.619 0.00 0.00 0.00 2.32
743 1919 1.275856 TCAATGCCAAATGCCCAAGTC 59.724 47.619 0.00 0.00 40.16 3.01
797 1973 3.085296 GGCCCCCAATTGCATGCT 61.085 61.111 20.33 0.00 0.00 3.79
798 1974 2.672181 GGCCCCCAATTGCATGCTT 61.672 57.895 20.33 2.28 0.00 3.91
801 1977 1.455248 CCCCCAATTGCATGCTTTTG 58.545 50.000 20.33 20.05 0.00 2.44
808 1984 6.095720 CCCCAATTGCATGCTTTTGAAATAAT 59.904 34.615 25.24 10.44 0.00 1.28
811 1987 9.710979 CCAATTGCATGCTTTTGAAATAATTAG 57.289 29.630 25.24 9.12 0.00 1.73
812 1988 9.710979 CAATTGCATGCTTTTGAAATAATTAGG 57.289 29.630 20.33 0.00 0.00 2.69
813 1989 9.669887 AATTGCATGCTTTTGAAATAATTAGGA 57.330 25.926 20.33 0.00 0.00 2.94
814 1990 8.706492 TTGCATGCTTTTGAAATAATTAGGAG 57.294 30.769 20.33 0.00 0.00 3.69
815 1991 6.757947 TGCATGCTTTTGAAATAATTAGGAGC 59.242 34.615 20.33 0.00 0.00 4.70
816 1992 6.757947 GCATGCTTTTGAAATAATTAGGAGCA 59.242 34.615 11.37 0.00 41.22 4.26
817 1993 7.042925 GCATGCTTTTGAAATAATTAGGAGCAG 60.043 37.037 11.37 0.00 40.44 4.24
818 1994 7.701539 TGCTTTTGAAATAATTAGGAGCAGA 57.298 32.000 0.00 0.00 33.20 4.26
819 1995 8.121305 TGCTTTTGAAATAATTAGGAGCAGAA 57.879 30.769 0.00 0.00 33.20 3.02
820 1996 8.246180 TGCTTTTGAAATAATTAGGAGCAGAAG 58.754 33.333 0.00 0.00 33.20 2.85
824 2000 9.739276 TTTGAAATAATTAGGAGCAGAAGAAGA 57.261 29.630 0.00 0.00 0.00 2.87
825 2001 9.739276 TTGAAATAATTAGGAGCAGAAGAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
826 2002 9.388506 TGAAATAATTAGGAGCAGAAGAAGAAG 57.611 33.333 0.00 0.00 0.00 2.85
827 2003 9.606631 GAAATAATTAGGAGCAGAAGAAGAAGA 57.393 33.333 0.00 0.00 0.00 2.87
828 2004 9.965902 AAATAATTAGGAGCAGAAGAAGAAGAA 57.034 29.630 0.00 0.00 0.00 2.52
829 2005 9.612066 AATAATTAGGAGCAGAAGAAGAAGAAG 57.388 33.333 0.00 0.00 0.00 2.85
830 2006 6.865834 ATTAGGAGCAGAAGAAGAAGAAGA 57.134 37.500 0.00 0.00 0.00 2.87
831 2007 4.806640 AGGAGCAGAAGAAGAAGAAGAG 57.193 45.455 0.00 0.00 0.00 2.85
832 2008 4.415596 AGGAGCAGAAGAAGAAGAAGAGA 58.584 43.478 0.00 0.00 0.00 3.10
833 2009 4.837860 AGGAGCAGAAGAAGAAGAAGAGAA 59.162 41.667 0.00 0.00 0.00 2.87
834 2010 5.047092 AGGAGCAGAAGAAGAAGAAGAGAAG 60.047 44.000 0.00 0.00 0.00 2.85
835 2011 5.047377 GGAGCAGAAGAAGAAGAAGAGAAGA 60.047 44.000 0.00 0.00 0.00 2.87
836 2012 6.418057 AGCAGAAGAAGAAGAAGAGAAGAA 57.582 37.500 0.00 0.00 0.00 2.52
837 2013 6.458210 AGCAGAAGAAGAAGAAGAGAAGAAG 58.542 40.000 0.00 0.00 0.00 2.85
838 2014 6.041979 AGCAGAAGAAGAAGAAGAGAAGAAGT 59.958 38.462 0.00 0.00 0.00 3.01
839 2015 6.705825 GCAGAAGAAGAAGAAGAGAAGAAGTT 59.294 38.462 0.00 0.00 0.00 2.66
846 2022 8.831715 AAGAAGAAGAGAAGAAGTTCAATCTC 57.168 34.615 21.96 21.96 38.84 2.75
850 2026 7.830739 AGAAGAGAAGAAGTTCAATCTCTCTC 58.169 38.462 27.72 24.86 45.90 3.20
883 2059 4.192317 GCACCTACCAAGATCAGTTTAGG 58.808 47.826 0.00 2.37 33.60 2.69
888 2064 7.611855 CACCTACCAAGATCAGTTTAGGAAAAT 59.388 37.037 14.24 0.00 32.06 1.82
893 2069 9.981460 ACCAAGATCAGTTTAGGAAAATTCTAT 57.019 29.630 0.00 0.00 0.00 1.98
925 2101 7.547227 TCCAAGCTTTTGAAATAATTAGGAGC 58.453 34.615 0.00 0.00 0.00 4.70
934 2110 9.739276 TTTGAAATAATTAGGAGCAGAAGAAGA 57.261 29.630 0.00 0.00 0.00 2.87
935 2111 9.739276 TTGAAATAATTAGGAGCAGAAGAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
936 2112 9.388506 TGAAATAATTAGGAGCAGAAGAAGAAG 57.611 33.333 0.00 0.00 0.00 2.85
937 2113 9.606631 GAAATAATTAGGAGCAGAAGAAGAAGA 57.393 33.333 0.00 0.00 0.00 2.87
938 2114 9.965902 AAATAATTAGGAGCAGAAGAAGAAGAA 57.034 29.630 0.00 0.00 0.00 2.52
939 2115 9.612066 AATAATTAGGAGCAGAAGAAGAAGAAG 57.388 33.333 0.00 0.00 0.00 2.85
940 2116 6.865834 ATTAGGAGCAGAAGAAGAAGAAGA 57.134 37.500 0.00 0.00 0.00 2.87
941 2117 6.672266 TTAGGAGCAGAAGAAGAAGAAGAA 57.328 37.500 0.00 0.00 0.00 2.52
942 2118 5.151297 AGGAGCAGAAGAAGAAGAAGAAG 57.849 43.478 0.00 0.00 0.00 2.85
943 2119 4.837860 AGGAGCAGAAGAAGAAGAAGAAGA 59.162 41.667 0.00 0.00 0.00 2.87
944 2120 5.047092 AGGAGCAGAAGAAGAAGAAGAAGAG 60.047 44.000 0.00 0.00 0.00 2.85
945 2121 5.151297 AGCAGAAGAAGAAGAAGAAGAGG 57.849 43.478 0.00 0.00 0.00 3.69
977 2162 5.327616 TCAATCTCTCTCTTGCTCTCTTG 57.672 43.478 0.00 0.00 0.00 3.02
988 2182 1.270907 GCTCTCTTGTGGAGGAGGAA 58.729 55.000 0.00 0.00 42.10 3.36
989 2183 1.836802 GCTCTCTTGTGGAGGAGGAAT 59.163 52.381 0.00 0.00 42.10 3.01
990 2184 2.238395 GCTCTCTTGTGGAGGAGGAATT 59.762 50.000 0.00 0.00 42.10 2.17
1008 2206 4.660771 GGAATTAGAAGAAGGATGAGGGGA 59.339 45.833 0.00 0.00 0.00 4.81
1223 2421 4.430765 CAAGGGGGACGACGACGG 62.431 72.222 12.58 0.00 44.46 4.79
1365 2580 7.807433 GCTCGTCTATGATGGATGATATGATAC 59.193 40.741 1.02 0.00 0.00 2.24
1374 2589 4.467438 TGGATGATATGATACGCATGACCT 59.533 41.667 0.00 0.00 37.87 3.85
1409 2629 3.197092 TGCTGCACGCATGATCCG 61.197 61.111 0.00 0.00 45.47 4.18
1410 2630 4.602696 GCTGCACGCATGATCCGC 62.603 66.667 0.00 0.00 38.92 5.54
1415 2635 2.512286 ACGCATGATCCGCCACTG 60.512 61.111 0.00 0.00 0.00 3.66
1418 2638 1.146041 GCATGATCCGCCACTGGTA 59.854 57.895 0.00 0.00 0.00 3.25
1457 2677 4.498520 CCTGCGATCGAGCGGTGT 62.499 66.667 25.73 0.00 41.72 4.16
1458 2678 3.250323 CTGCGATCGAGCGGTGTG 61.250 66.667 25.73 0.00 40.67 3.82
1512 2774 4.358851 TGATTTTGTTGCCTTCTTCAACG 58.641 39.130 0.00 0.00 44.88 4.10
1517 2779 2.807967 TGTTGCCTTCTTCAACGATCAG 59.192 45.455 0.00 0.00 44.88 2.90
1746 3241 9.567848 AACATACTTACAAAAGTTTTGTCTGTG 57.432 29.630 31.73 23.88 43.60 3.66
1747 3242 8.952278 ACATACTTACAAAAGTTTTGTCTGTGA 58.048 29.630 31.73 15.38 43.60 3.58
1750 3245 7.305474 ACTTACAAAAGTTTTGTCTGTGAGTG 58.695 34.615 31.73 17.48 43.60 3.51
1752 3247 6.325919 ACAAAAGTTTTGTCTGTGAGTGAA 57.674 33.333 24.92 0.00 0.00 3.18
1753 3248 6.381801 ACAAAAGTTTTGTCTGTGAGTGAAG 58.618 36.000 24.92 0.33 0.00 3.02
1754 3249 4.622701 AAGTTTTGTCTGTGAGTGAAGC 57.377 40.909 0.00 0.00 0.00 3.86
1755 3250 3.609853 AGTTTTGTCTGTGAGTGAAGCA 58.390 40.909 0.00 0.00 0.00 3.91
1756 3251 4.202441 AGTTTTGTCTGTGAGTGAAGCAT 58.798 39.130 0.00 0.00 0.00 3.79
1757 3252 4.036027 AGTTTTGTCTGTGAGTGAAGCATG 59.964 41.667 0.00 0.00 0.00 4.06
1759 3254 1.202675 TGTCTGTGAGTGAAGCATGCA 60.203 47.619 21.98 0.00 0.00 3.96
1760 3255 1.875514 GTCTGTGAGTGAAGCATGCAA 59.124 47.619 21.98 1.49 0.00 4.08
1761 3256 1.875514 TCTGTGAGTGAAGCATGCAAC 59.124 47.619 21.98 14.79 0.00 4.17
1762 3257 1.878088 CTGTGAGTGAAGCATGCAACT 59.122 47.619 21.98 19.34 0.00 3.16
1763 3258 2.292569 CTGTGAGTGAAGCATGCAACTT 59.707 45.455 21.98 5.25 0.00 2.66
2026 4432 0.108138 CTCAAGAAGGGGTACGCCAG 60.108 60.000 28.77 13.60 44.92 4.85
2348 4754 2.187946 GAGGACATGGACCTGGCG 59.812 66.667 16.50 0.00 37.93 5.69
2612 5018 0.888619 TCCTCTTCTACTGCGTGGTG 59.111 55.000 0.00 0.00 0.00 4.17
2723 5129 3.311110 GTCTGCACCCCGAGGTCA 61.311 66.667 0.00 0.00 46.45 4.02
2870 5282 2.930562 GTGACCTCCACCCCTGCT 60.931 66.667 0.00 0.00 39.86 4.24
2936 5351 1.224039 GAGCCAGAGCAGCATCCTT 59.776 57.895 0.00 0.00 43.56 3.36
3100 5515 2.559998 AGTGACGCCAACAAAACAAG 57.440 45.000 0.00 0.00 0.00 3.16
3102 5517 2.490115 AGTGACGCCAACAAAACAAGAA 59.510 40.909 0.00 0.00 0.00 2.52
3103 5518 2.596862 GTGACGCCAACAAAACAAGAAC 59.403 45.455 0.00 0.00 0.00 3.01
3200 5619 5.712152 AGATAGCTTGTTGTTTTTCAGGG 57.288 39.130 0.00 0.00 0.00 4.45
3267 5688 2.507407 TCCAAGGCAGGACAATTACC 57.493 50.000 0.00 0.00 31.23 2.85
3366 5787 2.547826 TCGAAGCAGATGAGCATTCTG 58.452 47.619 6.28 6.28 36.85 3.02
3441 5862 6.180771 ACAATTTCTTTGTTTGTTGCAAGG 57.819 33.333 0.00 0.00 46.51 3.61
3462 5883 5.121811 AGGTGAATGATCCGAAAGAAGATG 58.878 41.667 0.00 0.00 0.00 2.90
3471 5892 2.945008 CCGAAAGAAGATGGCAATAGCA 59.055 45.455 0.00 0.00 44.61 3.49
3501 5922 5.353123 AGCCACCTAATTGTTTGTATACACG 59.647 40.000 4.68 0.00 0.00 4.49
3548 5970 7.935755 AGTGTTGAAGATGATCAGAAAGAAGAA 59.064 33.333 0.09 0.00 0.00 2.52
3549 5971 8.562892 GTGTTGAAGATGATCAGAAAGAAGAAA 58.437 33.333 0.09 0.00 0.00 2.52
3550 5972 8.781196 TGTTGAAGATGATCAGAAAGAAGAAAG 58.219 33.333 0.09 0.00 0.00 2.62
3576 5998 5.169836 ACAAGTCAAACCTTCAAATCGAC 57.830 39.130 0.00 0.00 0.00 4.20
3652 6074 5.006153 TGGTTGATAGTATCTTCACACGG 57.994 43.478 11.40 0.00 0.00 4.94
3878 6300 2.347490 TGCCCTTCTTCCGCAGAC 59.653 61.111 0.00 0.00 0.00 3.51
4007 6429 6.308766 CAGCTGCCAGAAAATGTGTAAATTAC 59.691 38.462 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 2.507547 GTCGTGCCGCGTCCATTA 60.508 61.111 4.92 0.00 42.13 1.90
88 91 6.690068 ACGGTGCAGTACTGTAGAGGATCT 62.690 50.000 23.44 0.00 46.95 2.75
89 92 2.033550 CGGTGCAGTACTGTAGAGGATC 59.966 54.545 23.44 6.60 0.00 3.36
90 93 2.025155 CGGTGCAGTACTGTAGAGGAT 58.975 52.381 23.44 0.00 0.00 3.24
91 94 1.271762 ACGGTGCAGTACTGTAGAGGA 60.272 52.381 23.44 0.00 46.95 3.71
92 95 1.174783 ACGGTGCAGTACTGTAGAGG 58.825 55.000 23.44 13.16 46.95 3.69
96 99 1.176527 GGGTACGGTGCAGTACTGTA 58.823 55.000 23.44 17.20 46.95 2.74
98 101 0.108804 CAGGGTACGGTGCAGTACTG 60.109 60.000 18.93 18.93 44.59 2.74
99 102 0.541296 ACAGGGTACGGTGCAGTACT 60.541 55.000 13.97 0.00 44.59 2.73
100 103 0.319405 AACAGGGTACGGTGCAGTAC 59.681 55.000 7.54 7.54 44.50 2.73
101 104 0.319083 CAACAGGGTACGGTGCAGTA 59.681 55.000 0.00 0.00 0.00 2.74
102 105 1.070786 CAACAGGGTACGGTGCAGT 59.929 57.895 0.00 0.00 0.00 4.40
103 106 0.319083 TACAACAGGGTACGGTGCAG 59.681 55.000 0.00 0.00 0.00 4.41
104 107 0.319083 CTACAACAGGGTACGGTGCA 59.681 55.000 0.00 0.00 0.00 4.57
105 108 0.319405 ACTACAACAGGGTACGGTGC 59.681 55.000 0.00 0.00 0.00 5.01
106 109 1.938016 GCACTACAACAGGGTACGGTG 60.938 57.143 0.00 0.00 0.00 4.94
107 110 0.319405 GCACTACAACAGGGTACGGT 59.681 55.000 0.00 0.00 0.00 4.83
108 111 0.319083 TGCACTACAACAGGGTACGG 59.681 55.000 0.00 0.00 0.00 4.02
109 112 1.271379 TCTGCACTACAACAGGGTACG 59.729 52.381 0.00 0.00 34.57 3.67
110 113 3.056107 TCATCTGCACTACAACAGGGTAC 60.056 47.826 0.00 0.00 34.57 3.34
111 114 3.056107 GTCATCTGCACTACAACAGGGTA 60.056 47.826 0.00 0.00 34.57 3.69
112 115 1.977854 TCATCTGCACTACAACAGGGT 59.022 47.619 0.00 0.00 34.57 4.34
113 116 2.289631 TGTCATCTGCACTACAACAGGG 60.290 50.000 0.00 0.00 34.57 4.45
114 117 2.998670 CTGTCATCTGCACTACAACAGG 59.001 50.000 0.00 0.00 32.18 4.00
115 118 2.998670 CCTGTCATCTGCACTACAACAG 59.001 50.000 0.00 0.00 34.51 3.16
116 119 2.368548 ACCTGTCATCTGCACTACAACA 59.631 45.455 0.00 0.00 0.00 3.33
117 120 2.738846 CACCTGTCATCTGCACTACAAC 59.261 50.000 0.00 0.00 0.00 3.32
118 121 2.632512 TCACCTGTCATCTGCACTACAA 59.367 45.455 0.00 0.00 0.00 2.41
119 122 2.232208 CTCACCTGTCATCTGCACTACA 59.768 50.000 0.00 0.00 0.00 2.74
120 123 2.417924 CCTCACCTGTCATCTGCACTAC 60.418 54.545 0.00 0.00 0.00 2.73
121 124 1.827344 CCTCACCTGTCATCTGCACTA 59.173 52.381 0.00 0.00 0.00 2.74
122 125 0.612229 CCTCACCTGTCATCTGCACT 59.388 55.000 0.00 0.00 0.00 4.40
123 126 0.322975 ACCTCACCTGTCATCTGCAC 59.677 55.000 0.00 0.00 0.00 4.57
124 127 0.610174 GACCTCACCTGTCATCTGCA 59.390 55.000 0.00 0.00 32.91 4.41
125 128 0.459237 CGACCTCACCTGTCATCTGC 60.459 60.000 0.00 0.00 32.91 4.26
126 129 0.174389 CCGACCTCACCTGTCATCTG 59.826 60.000 0.00 0.00 32.91 2.90
127 130 0.972983 CCCGACCTCACCTGTCATCT 60.973 60.000 0.00 0.00 32.91 2.90
128 131 1.258445 ACCCGACCTCACCTGTCATC 61.258 60.000 0.00 0.00 32.91 2.92
129 132 1.229209 ACCCGACCTCACCTGTCAT 60.229 57.895 0.00 0.00 32.91 3.06
130 133 1.906824 GACCCGACCTCACCTGTCA 60.907 63.158 0.00 0.00 32.91 3.58
131 134 2.647158 GGACCCGACCTCACCTGTC 61.647 68.421 0.00 0.00 0.00 3.51
132 135 2.603776 GGACCCGACCTCACCTGT 60.604 66.667 0.00 0.00 0.00 4.00
133 136 2.603473 TGGACCCGACCTCACCTG 60.603 66.667 0.00 0.00 0.00 4.00
134 137 2.603776 GTGGACCCGACCTCACCT 60.604 66.667 0.00 0.00 0.00 4.00
135 138 2.291043 ATGTGGACCCGACCTCACC 61.291 63.158 0.00 0.00 36.48 4.02
136 139 1.079127 CATGTGGACCCGACCTCAC 60.079 63.158 0.00 0.00 36.48 3.51
137 140 2.290287 CCATGTGGACCCGACCTCA 61.290 63.158 0.00 0.00 37.73 3.86
138 141 2.584608 CCATGTGGACCCGACCTC 59.415 66.667 0.00 0.00 37.39 3.85
139 142 3.717294 GCCATGTGGACCCGACCT 61.717 66.667 2.55 0.00 37.39 3.85
140 143 3.976701 CTGCCATGTGGACCCGACC 62.977 68.421 2.55 0.00 37.39 4.79
141 144 2.436646 CTGCCATGTGGACCCGAC 60.437 66.667 2.55 0.00 37.39 4.79
142 145 4.408821 GCTGCCATGTGGACCCGA 62.409 66.667 2.55 0.00 37.39 5.14
144 147 4.408821 TCGCTGCCATGTGGACCC 62.409 66.667 2.55 0.00 37.39 4.46
145 148 3.127533 GTCGCTGCCATGTGGACC 61.128 66.667 2.55 0.00 37.39 4.46
146 149 3.127533 GGTCGCTGCCATGTGGAC 61.128 66.667 2.55 0.00 37.39 4.02
147 150 4.758251 CGGTCGCTGCCATGTGGA 62.758 66.667 2.55 0.00 37.39 4.02
148 151 3.657448 TACGGTCGCTGCCATGTGG 62.657 63.158 0.00 0.00 38.53 4.17
149 152 2.125713 TACGGTCGCTGCCATGTG 60.126 61.111 0.00 0.00 0.00 3.21
150 153 2.125673 GTACGGTCGCTGCCATGT 60.126 61.111 0.00 0.00 0.00 3.21
151 154 2.890474 GGTACGGTCGCTGCCATG 60.890 66.667 0.00 0.00 0.00 3.66
178 181 2.036604 GGTTAGGATCCTCTGCAGTAGC 59.963 54.545 20.22 0.00 42.57 3.58
179 182 2.630580 GGGTTAGGATCCTCTGCAGTAG 59.369 54.545 20.22 9.71 0.00 2.57
180 183 2.023404 TGGGTTAGGATCCTCTGCAGTA 60.023 50.000 20.22 0.00 0.00 2.74
181 184 1.273838 TGGGTTAGGATCCTCTGCAGT 60.274 52.381 20.22 0.00 0.00 4.40
182 185 1.500474 TGGGTTAGGATCCTCTGCAG 58.500 55.000 20.22 7.63 0.00 4.41
183 186 2.050144 GATGGGTTAGGATCCTCTGCA 58.950 52.381 20.22 0.00 0.00 4.41
184 187 1.349357 GGATGGGTTAGGATCCTCTGC 59.651 57.143 20.22 9.52 36.04 4.26
185 188 1.981495 GGGATGGGTTAGGATCCTCTG 59.019 57.143 20.22 0.00 38.61 3.35
186 189 1.585592 TGGGATGGGTTAGGATCCTCT 59.414 52.381 20.22 0.00 38.61 3.69
187 190 1.700186 GTGGGATGGGTTAGGATCCTC 59.300 57.143 20.22 4.44 38.61 3.71
188 191 1.010793 TGTGGGATGGGTTAGGATCCT 59.989 52.381 20.48 20.48 38.61 3.24
189 192 1.143073 GTGTGGGATGGGTTAGGATCC 59.857 57.143 2.48 2.48 37.94 3.36
190 193 1.202651 CGTGTGGGATGGGTTAGGATC 60.203 57.143 0.00 0.00 0.00 3.36
191 194 0.837272 CGTGTGGGATGGGTTAGGAT 59.163 55.000 0.00 0.00 0.00 3.24
192 195 1.906105 GCGTGTGGGATGGGTTAGGA 61.906 60.000 0.00 0.00 0.00 2.94
193 196 1.451387 GCGTGTGGGATGGGTTAGG 60.451 63.158 0.00 0.00 0.00 2.69
194 197 1.024579 GTGCGTGTGGGATGGGTTAG 61.025 60.000 0.00 0.00 0.00 2.34
195 198 1.003112 GTGCGTGTGGGATGGGTTA 60.003 57.895 0.00 0.00 0.00 2.85
196 199 2.282180 GTGCGTGTGGGATGGGTT 60.282 61.111 0.00 0.00 0.00 4.11
197 200 4.697756 CGTGCGTGTGGGATGGGT 62.698 66.667 0.00 0.00 0.00 4.51
200 203 4.088762 GTGCGTGCGTGTGGGATG 62.089 66.667 0.00 0.00 0.00 3.51
414 1544 6.466308 ACACAAAACAGAAGAAAAGCAAAC 57.534 33.333 0.00 0.00 0.00 2.93
447 1577 3.304659 GGTCAAGTGTGTTTCGCATTCAT 60.305 43.478 0.00 0.00 0.00 2.57
468 1598 6.142818 TGGTGAAGAAACAAACAAGTATGG 57.857 37.500 0.00 0.00 0.00 2.74
469 1599 7.920151 TGATTGGTGAAGAAACAAACAAGTATG 59.080 33.333 0.00 0.00 0.00 2.39
470 1600 8.006298 TGATTGGTGAAGAAACAAACAAGTAT 57.994 30.769 0.00 0.00 0.00 2.12
471 1601 7.397892 TGATTGGTGAAGAAACAAACAAGTA 57.602 32.000 0.00 0.00 0.00 2.24
472 1602 6.279513 TGATTGGTGAAGAAACAAACAAGT 57.720 33.333 0.00 0.00 0.00 3.16
529 1693 7.889469 ACACCATATATACGTACAAGGTAAGG 58.111 38.462 0.00 0.00 0.00 2.69
548 1712 4.016444 CAGGCCAGTACAAATTACACCAT 58.984 43.478 5.01 0.00 0.00 3.55
551 1715 2.817258 TGCAGGCCAGTACAAATTACAC 59.183 45.455 5.01 0.00 0.00 2.90
552 1716 3.147553 TGCAGGCCAGTACAAATTACA 57.852 42.857 5.01 0.00 0.00 2.41
590 1766 4.353437 GTGCAGCCAGCCACAAGC 62.353 66.667 0.00 0.00 44.83 4.01
591 1767 3.677648 GGTGCAGCCAGCCACAAG 61.678 66.667 4.03 0.00 44.83 3.16
609 1785 3.326578 TGGGTAGGTGCATGCGGT 61.327 61.111 14.09 2.09 0.00 5.68
615 1791 3.253838 GTGGGGTGGGTAGGTGCA 61.254 66.667 0.00 0.00 0.00 4.57
616 1792 3.253838 TGTGGGGTGGGTAGGTGC 61.254 66.667 0.00 0.00 0.00 5.01
621 1797 2.047769 AATACACTGTGGGGTGGGTA 57.952 50.000 13.09 0.00 41.09 3.69
626 1802 5.582953 TGTACTACTAATACACTGTGGGGT 58.417 41.667 13.09 5.82 0.00 4.95
628 1804 7.584122 ATCTGTACTACTAATACACTGTGGG 57.416 40.000 13.09 0.00 0.00 4.61
629 1805 8.291032 GCTATCTGTACTACTAATACACTGTGG 58.709 40.741 13.09 0.00 0.00 4.17
630 1806 8.837389 TGCTATCTGTACTACTAATACACTGTG 58.163 37.037 6.19 6.19 0.00 3.66
631 1807 8.975663 TGCTATCTGTACTACTAATACACTGT 57.024 34.615 0.00 0.00 0.00 3.55
632 1808 9.885934 CTTGCTATCTGTACTACTAATACACTG 57.114 37.037 0.00 0.00 0.00 3.66
633 1809 8.569641 GCTTGCTATCTGTACTACTAATACACT 58.430 37.037 0.00 0.00 0.00 3.55
634 1810 8.350722 TGCTTGCTATCTGTACTACTAATACAC 58.649 37.037 0.00 0.00 0.00 2.90
635 1811 8.350722 GTGCTTGCTATCTGTACTACTAATACA 58.649 37.037 0.00 0.00 0.00 2.29
636 1812 8.569641 AGTGCTTGCTATCTGTACTACTAATAC 58.430 37.037 0.00 0.00 0.00 1.89
637 1813 8.693120 AGTGCTTGCTATCTGTACTACTAATA 57.307 34.615 0.00 0.00 0.00 0.98
638 1814 7.589958 AGTGCTTGCTATCTGTACTACTAAT 57.410 36.000 0.00 0.00 0.00 1.73
639 1815 8.515695 TTAGTGCTTGCTATCTGTACTACTAA 57.484 34.615 0.00 0.00 30.86 2.24
642 1818 7.630470 CATTAGTGCTTGCTATCTGTACTAC 57.370 40.000 0.00 0.00 30.86 2.73
694 1870 2.568956 ACAGCCAGAAAGCACTATCTGA 59.431 45.455 4.43 0.00 44.64 3.27
732 1908 4.386424 GGGAAGGTTATAGACTTGGGCATT 60.386 45.833 0.00 0.00 0.00 3.56
733 1909 3.138468 GGGAAGGTTATAGACTTGGGCAT 59.862 47.826 0.00 0.00 0.00 4.40
734 1910 2.508300 GGGAAGGTTATAGACTTGGGCA 59.492 50.000 0.00 0.00 0.00 5.36
735 1911 2.158652 GGGGAAGGTTATAGACTTGGGC 60.159 54.545 0.00 0.00 0.00 5.36
762 1938 2.546162 GGCCAGGCTAGATTAGAACGAC 60.546 54.545 12.43 0.00 0.00 4.34
763 1939 1.687123 GGCCAGGCTAGATTAGAACGA 59.313 52.381 12.43 0.00 0.00 3.85
764 1940 1.270358 GGGCCAGGCTAGATTAGAACG 60.270 57.143 12.43 0.00 0.00 3.95
798 1974 9.739276 TCTTCTTCTGCTCCTAATTATTTCAAA 57.261 29.630 0.00 0.00 0.00 2.69
801 1977 9.606631 TCTTCTTCTTCTGCTCCTAATTATTTC 57.393 33.333 0.00 0.00 0.00 2.17
808 1984 6.013379 TCTCTTCTTCTTCTTCTGCTCCTAA 58.987 40.000 0.00 0.00 0.00 2.69
811 1987 4.799564 TCTCTTCTTCTTCTTCTGCTCC 57.200 45.455 0.00 0.00 0.00 4.70
812 1988 6.024552 TCTTCTCTTCTTCTTCTTCTGCTC 57.975 41.667 0.00 0.00 0.00 4.26
813 1989 6.041979 ACTTCTTCTCTTCTTCTTCTTCTGCT 59.958 38.462 0.00 0.00 0.00 4.24
814 1990 6.223120 ACTTCTTCTCTTCTTCTTCTTCTGC 58.777 40.000 0.00 0.00 0.00 4.26
815 1991 7.925483 TGAACTTCTTCTCTTCTTCTTCTTCTG 59.075 37.037 0.00 0.00 0.00 3.02
816 1992 8.017418 TGAACTTCTTCTCTTCTTCTTCTTCT 57.983 34.615 0.00 0.00 0.00 2.85
817 1993 8.655651 TTGAACTTCTTCTCTTCTTCTTCTTC 57.344 34.615 0.00 0.00 0.00 2.87
818 1994 9.271828 GATTGAACTTCTTCTCTTCTTCTTCTT 57.728 33.333 0.00 0.00 0.00 2.52
819 1995 8.650490 AGATTGAACTTCTTCTCTTCTTCTTCT 58.350 33.333 0.00 0.00 0.00 2.85
820 1996 8.831715 AGATTGAACTTCTTCTCTTCTTCTTC 57.168 34.615 0.00 0.00 0.00 2.87
822 1998 8.193953 AGAGATTGAACTTCTTCTCTTCTTCT 57.806 34.615 14.36 0.00 41.59 2.85
823 1999 8.306761 AGAGAGATTGAACTTCTTCTCTTCTTC 58.693 37.037 18.29 10.71 43.71 2.87
824 2000 8.193953 AGAGAGATTGAACTTCTTCTCTTCTT 57.806 34.615 18.29 10.03 43.71 2.52
825 2001 7.671398 AGAGAGAGATTGAACTTCTTCTCTTCT 59.329 37.037 18.29 17.77 43.71 2.85
826 2002 7.830739 AGAGAGAGATTGAACTTCTTCTCTTC 58.169 38.462 18.29 16.67 43.71 2.87
827 2003 7.781324 AGAGAGAGATTGAACTTCTTCTCTT 57.219 36.000 18.29 12.10 43.71 2.85
839 2015 8.911965 GGTGCATCATATATAGAGAGAGATTGA 58.088 37.037 0.00 0.00 0.00 2.57
846 2022 7.888250 TGGTAGGTGCATCATATATAGAGAG 57.112 40.000 0.00 0.00 0.00 3.20
850 2026 8.699130 TGATCTTGGTAGGTGCATCATATATAG 58.301 37.037 0.00 0.00 0.00 1.31
855 2031 4.655649 ACTGATCTTGGTAGGTGCATCATA 59.344 41.667 0.00 0.00 0.00 2.15
856 2032 3.457380 ACTGATCTTGGTAGGTGCATCAT 59.543 43.478 0.00 0.00 0.00 2.45
857 2033 2.840038 ACTGATCTTGGTAGGTGCATCA 59.160 45.455 0.00 0.00 0.00 3.07
858 2034 3.550437 ACTGATCTTGGTAGGTGCATC 57.450 47.619 0.00 0.00 0.00 3.91
859 2035 4.307032 AAACTGATCTTGGTAGGTGCAT 57.693 40.909 0.00 0.00 0.00 3.96
860 2036 3.788227 AAACTGATCTTGGTAGGTGCA 57.212 42.857 0.00 0.00 0.00 4.57
925 2101 6.588719 TCTCCTCTTCTTCTTCTTCTTCTG 57.411 41.667 0.00 0.00 0.00 3.02
934 2110 6.739331 TGAACTTCTTCTCCTCTTCTTCTT 57.261 37.500 0.00 0.00 0.00 2.52
935 2111 6.739331 TTGAACTTCTTCTCCTCTTCTTCT 57.261 37.500 0.00 0.00 0.00 2.85
936 2112 7.386059 AGATTGAACTTCTTCTCCTCTTCTTC 58.614 38.462 0.00 0.00 0.00 2.87
937 2113 7.235399 AGAGATTGAACTTCTTCTCCTCTTCTT 59.765 37.037 14.06 0.00 36.16 2.52
938 2114 6.725834 AGAGATTGAACTTCTTCTCCTCTTCT 59.274 38.462 14.06 0.00 36.16 2.85
939 2115 6.935167 AGAGATTGAACTTCTTCTCCTCTTC 58.065 40.000 14.06 0.00 36.16 2.87
940 2116 6.725834 AGAGAGATTGAACTTCTTCTCCTCTT 59.274 38.462 14.06 2.39 36.16 2.85
941 2117 6.256053 AGAGAGATTGAACTTCTTCTCCTCT 58.744 40.000 14.06 13.06 36.16 3.69
942 2118 6.378280 AGAGAGAGATTGAACTTCTTCTCCTC 59.622 42.308 18.36 18.36 36.16 3.71
943 2119 6.256053 AGAGAGAGATTGAACTTCTTCTCCT 58.744 40.000 14.06 11.86 36.16 3.69
944 2120 6.530019 AGAGAGAGATTGAACTTCTTCTCC 57.470 41.667 14.06 8.96 36.16 3.71
945 2121 6.311200 GCAAGAGAGAGATTGAACTTCTTCTC 59.689 42.308 11.48 11.48 35.84 2.87
977 2162 4.717280 TCCTTCTTCTAATTCCTCCTCCAC 59.283 45.833 0.00 0.00 0.00 4.02
988 2182 4.657969 CACTCCCCTCATCCTTCTTCTAAT 59.342 45.833 0.00 0.00 0.00 1.73
989 2183 4.033709 CACTCCCCTCATCCTTCTTCTAA 58.966 47.826 0.00 0.00 0.00 2.10
990 2184 3.272285 TCACTCCCCTCATCCTTCTTCTA 59.728 47.826 0.00 0.00 0.00 2.10
1008 2206 1.730501 CCATCGTCAACATGCTCACT 58.269 50.000 0.00 0.00 0.00 3.41
1253 2451 1.997874 ACCATGGGCAGGTCCTCTC 60.998 63.158 18.09 0.00 32.90 3.20
1365 2580 0.879400 GCCATCAGAGAGGTCATGCG 60.879 60.000 0.00 0.00 0.00 4.73
1374 2589 1.817357 CAAGCAACAGCCATCAGAGA 58.183 50.000 0.00 0.00 0.00 3.10
1409 2629 2.009774 CAGTGCAGTATTACCAGTGGC 58.990 52.381 9.78 0.00 0.00 5.01
1410 2630 2.009774 GCAGTGCAGTATTACCAGTGG 58.990 52.381 11.09 7.91 32.07 4.00
1453 2673 2.668212 TTACCAGCAGCGCACACC 60.668 61.111 11.47 0.00 0.00 4.16
1458 2678 2.508439 TAGCGTTACCAGCAGCGC 60.508 61.111 0.00 0.00 46.86 5.92
1579 2847 2.287308 TGGACGTAGCAATGCAACAAAC 60.287 45.455 8.35 0.00 0.00 2.93
1746 3241 3.004106 ACTCAAAGTTGCATGCTTCACTC 59.996 43.478 20.33 3.05 0.00 3.51
1747 3242 2.954318 ACTCAAAGTTGCATGCTTCACT 59.046 40.909 20.33 14.80 0.00 3.41
1750 3245 3.631145 TCACTCAAAGTTGCATGCTTC 57.369 42.857 20.33 11.64 0.00 3.86
1752 3247 3.130869 TGTTTCACTCAAAGTTGCATGCT 59.869 39.130 20.33 0.00 0.00 3.79
1753 3248 3.446799 TGTTTCACTCAAAGTTGCATGC 58.553 40.909 11.82 11.82 0.00 4.06
1754 3249 5.104374 ACTTGTTTCACTCAAAGTTGCATG 58.896 37.500 0.00 0.00 0.00 4.06
1755 3250 5.329035 ACTTGTTTCACTCAAAGTTGCAT 57.671 34.783 0.00 0.00 0.00 3.96
1756 3251 4.782019 ACTTGTTTCACTCAAAGTTGCA 57.218 36.364 0.00 0.00 0.00 4.08
1757 3252 6.119144 TCTACTTGTTTCACTCAAAGTTGC 57.881 37.500 0.00 0.00 0.00 4.17
2026 4432 4.767255 CCACCAGCTCGCAGTCCC 62.767 72.222 0.00 0.00 0.00 4.46
2303 4709 3.861797 CGGTCCTTCCATCCCCCG 61.862 72.222 0.00 0.00 35.57 5.73
2309 4715 2.351276 GTGGTGCGGTCCTTCCAT 59.649 61.111 0.00 0.00 35.57 3.41
2483 4889 3.452474 CACGATCTCCCAGAACATCTTC 58.548 50.000 0.00 0.00 0.00 2.87
2612 5018 3.537874 AGCACGTAGGCCGGGATC 61.538 66.667 2.18 0.00 45.03 3.36
2723 5129 1.078848 GAAGACGAGCAGGTGCCAT 60.079 57.895 0.00 0.00 43.38 4.40
3200 5619 4.893424 ATGTATGTATTGTTCGGTTGGC 57.107 40.909 0.00 0.00 0.00 4.52
3293 5714 5.243507 TGGTTCTGTACATGATGCAAAATGT 59.756 36.000 18.35 18.35 40.13 2.71
3366 5787 1.174712 TGCCTTTGCTGCCTGAGAAC 61.175 55.000 0.00 0.00 38.71 3.01
3441 5862 4.260948 GCCATCTTCTTTCGGATCATTCAC 60.261 45.833 0.00 0.00 0.00 3.18
3462 5883 2.543641 GTGGCTTTGAATGCTATTGCC 58.456 47.619 3.04 0.00 38.71 4.52
3471 5892 6.173427 ACAAACAATTAGGTGGCTTTGAAT 57.827 33.333 0.00 0.00 0.00 2.57
3501 5922 5.789774 CTGTAAGTTTTGCAATTCACGTC 57.210 39.130 0.00 0.00 0.00 4.34
3548 5970 2.243736 TGAAGGTTTGACTTGTCCCCTT 59.756 45.455 12.89 12.89 35.09 3.95
3549 5971 1.850345 TGAAGGTTTGACTTGTCCCCT 59.150 47.619 0.00 0.00 0.00 4.79
3550 5972 2.358322 TGAAGGTTTGACTTGTCCCC 57.642 50.000 0.00 0.00 0.00 4.81
3652 6074 3.785859 TGGGAGCGAGGCATGGTC 61.786 66.667 0.00 0.22 0.00 4.02
3878 6300 2.612672 CAGCATCTAGTGTTGCATCCTG 59.387 50.000 14.39 3.94 40.35 3.86
4007 6429 4.184629 GAGTGGCAGTAATACCAACTCTG 58.815 47.826 0.00 0.00 37.79 3.35


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

AutoCloner maintained by Alex Coulton.