Multiple sequence alignment - TraesCS3B01G367900

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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 TraesCS3B01G367900 chr3B 100.000 2993 0 0 1 2993 580061576 580064568 0.000000e+00 5528.0
1 TraesCS3B01G367900 chr3B 93.651 63 3 1 109 170 91030482 91030420 3.180000e-15 93.5
2 TraesCS3B01G367900 chr3D 90.491 2913 133 54 178 2993 442510477 442513342 0.000000e+00 3712.0
3 TraesCS3B01G367900 chr3A 88.294 1905 112 49 500 2376 583747627 583749448 0.000000e+00 2180.0
4 TraesCS3B01G367900 chr3A 88.010 1251 82 15 1047 2271 434799142 434800350 0.000000e+00 1417.0
5 TraesCS3B01G367900 chr3A 92.123 584 41 3 2411 2993 583749449 583750028 0.000000e+00 819.0
6 TraesCS3B01G367900 chr3A 87.791 172 15 4 2307 2473 434800349 434800519 2.350000e-46 196.0
7 TraesCS3B01G367900 chr3A 83.945 218 17 12 179 384 583747369 583747580 3.040000e-45 193.0
8 TraesCS3B01G367900 chr2D 89.752 1249 75 15 1047 2269 568757266 568758487 0.000000e+00 1548.0
9 TraesCS3B01G367900 chr5B 89.448 1251 73 17 1053 2271 524221799 524220576 0.000000e+00 1524.0
10 TraesCS3B01G367900 chr5B 93.548 62 2 2 114 174 392707732 392707792 1.140000e-14 91.6
11 TraesCS3B01G367900 chr5B 90.769 65 4 2 115 177 596721160 596721096 5.320000e-13 86.1
12 TraesCS3B01G367900 chr1B 89.343 1248 77 16 1053 2271 443488940 443487720 0.000000e+00 1517.0
13 TraesCS3B01G367900 chr7A 88.514 1245 75 15 1053 2271 48766857 48765655 0.000000e+00 1445.0
14 TraesCS3B01G367900 chr4D 88.169 1251 73 23 1047 2271 30394026 30395227 0.000000e+00 1421.0
15 TraesCS3B01G367900 chr7D 89.762 1094 60 17 1203 2271 207789238 207788172 0.000000e+00 1352.0
16 TraesCS3B01G367900 chr1A 90.510 706 44 15 1585 2271 512465714 512466415 0.000000e+00 911.0
17 TraesCS3B01G367900 chr6A 89.813 481 30 8 1808 2271 535421589 535421111 1.540000e-167 599.0
18 TraesCS3B01G367900 chr6A 83.554 377 22 9 1053 1414 535421938 535421587 1.730000e-82 316.0
19 TraesCS3B01G367900 chr6A 91.176 68 3 3 104 170 457399344 457399409 4.110000e-14 89.8
20 TraesCS3B01G367900 chr6B 92.424 66 3 2 114 177 52974434 52974369 3.180000e-15 93.5
21 TraesCS3B01G367900 chr2A 94.915 59 3 0 112 170 753531295 753531353 3.180000e-15 93.5
22 TraesCS3B01G367900 chr4A 94.915 59 2 1 113 170 8156307 8156365 1.140000e-14 91.6
23 TraesCS3B01G367900 chr7B 88.312 77 5 4 105 177 633011252 633011176 4.110000e-14 89.8
24 TraesCS3B01G367900 chrUn 83.158 95 12 4 85 177 88208006 88207914 1.910000e-12 84.2


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 TraesCS3B01G367900 chr3B 580061576 580064568 2992 False 5528.0 5528 100.000000 1 2993 1 chr3B.!!$F1 2992
1 TraesCS3B01G367900 chr3D 442510477 442513342 2865 False 3712.0 3712 90.491000 178 2993 1 chr3D.!!$F1 2815
2 TraesCS3B01G367900 chr3A 583747369 583750028 2659 False 1064.0 2180 88.120667 179 2993 3 chr3A.!!$F2 2814
3 TraesCS3B01G367900 chr3A 434799142 434800519 1377 False 806.5 1417 87.900500 1047 2473 2 chr3A.!!$F1 1426
4 TraesCS3B01G367900 chr2D 568757266 568758487 1221 False 1548.0 1548 89.752000 1047 2269 1 chr2D.!!$F1 1222
5 TraesCS3B01G367900 chr5B 524220576 524221799 1223 True 1524.0 1524 89.448000 1053 2271 1 chr5B.!!$R1 1218
6 TraesCS3B01G367900 chr1B 443487720 443488940 1220 True 1517.0 1517 89.343000 1053 2271 1 chr1B.!!$R1 1218
7 TraesCS3B01G367900 chr7A 48765655 48766857 1202 True 1445.0 1445 88.514000 1053 2271 1 chr7A.!!$R1 1218
8 TraesCS3B01G367900 chr4D 30394026 30395227 1201 False 1421.0 1421 88.169000 1047 2271 1 chr4D.!!$F1 1224
9 TraesCS3B01G367900 chr7D 207788172 207789238 1066 True 1352.0 1352 89.762000 1203 2271 1 chr7D.!!$R1 1068
10 TraesCS3B01G367900 chr1A 512465714 512466415 701 False 911.0 911 90.510000 1585 2271 1 chr1A.!!$F1 686
11 TraesCS3B01G367900 chr6A 535421111 535421938 827 True 457.5 599 86.683500 1053 2271 2 chr6A.!!$R1 1218

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
23 24 0.034186 TCACTTGGGCATGGACCATC 60.034 55.0 3.21 0.0 42.18 3.51 F
793 870 0.179145 CGCGCTCTATATAACCCCCG 60.179 60.0 5.56 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2097 1.053424 AGAACAGGAACGGCACCTTA 58.947 50.0 0.0 0.0 35.35 2.69 R
2052 2195 0.039326 AGCAGCCTGAATCCTTTGCT 59.961 50.0 0.0 0.0 37.09 3.91 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
17 18 2.802792 CGCATCACTTGGGCATGG 59.197 61.111 0.00 0.00 0.00 3.66
18 19 1.750018 CGCATCACTTGGGCATGGA 60.750 57.895 0.00 0.00 0.00 3.41
19 20 1.811860 GCATCACTTGGGCATGGAC 59.188 57.895 0.00 0.00 0.00 4.02
20 21 1.669999 GCATCACTTGGGCATGGACC 61.670 60.000 0.00 0.00 0.00 4.46
21 22 0.323633 CATCACTTGGGCATGGACCA 60.324 55.000 0.00 0.00 40.08 4.02
22 23 0.632835 ATCACTTGGGCATGGACCAT 59.367 50.000 0.00 0.00 42.18 3.55
23 24 0.034186 TCACTTGGGCATGGACCATC 60.034 55.000 3.21 0.00 42.18 3.51
24 25 1.039233 CACTTGGGCATGGACCATCC 61.039 60.000 3.21 9.03 42.18 3.51
32 33 4.100084 TGGACCATCCAGCTGCCG 62.100 66.667 8.66 0.00 42.67 5.69
44 45 3.865383 CTGCCGCCTGCCAGGATA 61.865 66.667 16.85 0.00 37.67 2.59
45 46 4.175337 TGCCGCCTGCCAGGATAC 62.175 66.667 16.85 2.38 37.67 2.24
66 67 9.647797 GGATACTCTATCGATCGATCTATACAT 57.352 37.037 32.50 19.11 36.03 2.29
70 71 9.203421 ACTCTATCGATCGATCTATACATCATC 57.797 37.037 32.50 0.00 36.17 2.92
71 72 8.541133 TCTATCGATCGATCTATACATCATCC 57.459 38.462 32.50 0.00 36.17 3.51
72 73 8.150945 TCTATCGATCGATCTATACATCATCCA 58.849 37.037 32.50 10.23 36.17 3.41
73 74 6.364945 TCGATCGATCTATACATCATCCAC 57.635 41.667 22.43 0.00 0.00 4.02
74 75 6.116126 TCGATCGATCTATACATCATCCACT 58.884 40.000 22.43 0.00 0.00 4.00
75 76 6.037610 TCGATCGATCTATACATCATCCACTG 59.962 42.308 22.43 1.70 0.00 3.66
76 77 5.316327 TCGATCTATACATCATCCACTGC 57.684 43.478 0.00 0.00 0.00 4.40
77 78 4.101235 CGATCTATACATCATCCACTGCG 58.899 47.826 0.00 0.00 0.00 5.18
78 79 4.379918 CGATCTATACATCATCCACTGCGT 60.380 45.833 0.00 0.00 0.00 5.24
79 80 5.163754 CGATCTATACATCATCCACTGCGTA 60.164 44.000 0.00 0.00 0.00 4.42
80 81 6.590234 ATCTATACATCATCCACTGCGTAA 57.410 37.500 0.00 0.00 0.00 3.18
81 82 6.399639 TCTATACATCATCCACTGCGTAAA 57.600 37.500 0.00 0.00 0.00 2.01
82 83 6.213677 TCTATACATCATCCACTGCGTAAAC 58.786 40.000 0.00 0.00 0.00 2.01
83 84 3.052455 ACATCATCCACTGCGTAAACA 57.948 42.857 0.00 0.00 0.00 2.83
84 85 3.609853 ACATCATCCACTGCGTAAACAT 58.390 40.909 0.00 0.00 0.00 2.71
85 86 4.009675 ACATCATCCACTGCGTAAACATT 58.990 39.130 0.00 0.00 0.00 2.71
86 87 4.142622 ACATCATCCACTGCGTAAACATTG 60.143 41.667 0.00 0.00 0.00 2.82
87 88 2.746904 TCATCCACTGCGTAAACATTGG 59.253 45.455 0.00 0.00 40.71 3.16
88 89 2.552599 TCCACTGCGTAAACATTGGA 57.447 45.000 0.00 0.00 44.46 3.53
89 90 3.066291 TCCACTGCGTAAACATTGGAT 57.934 42.857 0.00 0.00 42.54 3.41
90 91 3.417101 TCCACTGCGTAAACATTGGATT 58.583 40.909 0.00 0.00 42.54 3.01
91 92 4.580868 TCCACTGCGTAAACATTGGATTA 58.419 39.130 0.00 0.00 42.54 1.75
92 93 5.189928 TCCACTGCGTAAACATTGGATTAT 58.810 37.500 0.00 0.00 42.54 1.28
93 94 6.350103 TCCACTGCGTAAACATTGGATTATA 58.650 36.000 0.00 0.00 42.54 0.98
94 95 6.259167 TCCACTGCGTAAACATTGGATTATAC 59.741 38.462 0.00 0.00 42.54 1.47
95 96 6.037720 CCACTGCGTAAACATTGGATTATACA 59.962 38.462 0.00 0.00 41.61 2.29
96 97 7.125755 CACTGCGTAAACATTGGATTATACAG 58.874 38.462 0.00 0.00 0.00 2.74
97 98 6.821665 ACTGCGTAAACATTGGATTATACAGT 59.178 34.615 11.90 11.90 31.54 3.55
98 99 7.335924 ACTGCGTAAACATTGGATTATACAGTT 59.664 33.333 11.90 0.00 31.97 3.16
99 100 7.690228 TGCGTAAACATTGGATTATACAGTTC 58.310 34.615 0.00 0.00 0.00 3.01
100 101 6.844279 GCGTAAACATTGGATTATACAGTTCG 59.156 38.462 0.00 0.00 0.00 3.95
101 102 6.844279 CGTAAACATTGGATTATACAGTTCGC 59.156 38.462 0.00 0.00 0.00 4.70
102 103 7.254319 CGTAAACATTGGATTATACAGTTCGCT 60.254 37.037 0.00 0.00 0.00 4.93
103 104 9.037737 GTAAACATTGGATTATACAGTTCGCTA 57.962 33.333 0.00 0.00 0.00 4.26
104 105 7.715265 AACATTGGATTATACAGTTCGCTAG 57.285 36.000 0.00 0.00 0.00 3.42
105 106 6.223852 ACATTGGATTATACAGTTCGCTAGG 58.776 40.000 0.00 0.00 0.00 3.02
106 107 6.041637 ACATTGGATTATACAGTTCGCTAGGA 59.958 38.462 0.00 0.00 0.00 2.94
107 108 5.707242 TGGATTATACAGTTCGCTAGGAG 57.293 43.478 0.00 0.00 0.00 3.69
108 109 4.022242 TGGATTATACAGTTCGCTAGGAGC 60.022 45.833 0.00 0.00 38.02 4.70
109 110 4.022242 GGATTATACAGTTCGCTAGGAGCA 60.022 45.833 0.00 0.00 42.58 4.26
110 111 2.873133 ATACAGTTCGCTAGGAGCAC 57.127 50.000 0.00 0.00 42.58 4.40
111 112 1.835494 TACAGTTCGCTAGGAGCACT 58.165 50.000 0.00 0.00 42.58 4.40
112 113 1.835494 ACAGTTCGCTAGGAGCACTA 58.165 50.000 0.00 0.00 42.58 2.74
113 114 2.379972 ACAGTTCGCTAGGAGCACTAT 58.620 47.619 0.00 0.00 42.58 2.12
114 115 2.761208 ACAGTTCGCTAGGAGCACTATT 59.239 45.455 0.00 0.00 42.58 1.73
115 116 3.952323 ACAGTTCGCTAGGAGCACTATTA 59.048 43.478 0.00 0.00 42.58 0.98
116 117 4.585162 ACAGTTCGCTAGGAGCACTATTAT 59.415 41.667 0.00 0.00 42.58 1.28
117 118 5.768662 ACAGTTCGCTAGGAGCACTATTATA 59.231 40.000 0.00 0.00 42.58 0.98
118 119 6.072397 ACAGTTCGCTAGGAGCACTATTATAG 60.072 42.308 0.00 0.00 42.58 1.31
119 120 6.005198 AGTTCGCTAGGAGCACTATTATAGT 58.995 40.000 0.00 0.00 42.58 2.12
120 121 6.149807 AGTTCGCTAGGAGCACTATTATAGTC 59.850 42.308 1.33 0.00 42.58 2.59
121 122 4.942483 TCGCTAGGAGCACTATTATAGTCC 59.058 45.833 1.33 1.50 42.58 3.85
122 123 4.944930 CGCTAGGAGCACTATTATAGTCCT 59.055 45.833 13.38 13.38 42.58 3.85
123 124 5.416326 CGCTAGGAGCACTATTATAGTCCTT 59.584 44.000 13.89 2.56 42.58 3.36
124 125 6.403855 CGCTAGGAGCACTATTATAGTCCTTC 60.404 46.154 13.89 5.18 42.58 3.46
125 126 6.127563 GCTAGGAGCACTATTATAGTCCTTCC 60.128 46.154 13.89 13.88 41.89 3.46
126 127 4.767928 AGGAGCACTATTATAGTCCTTCCG 59.232 45.833 1.33 0.00 36.76 4.30
127 128 4.523558 GGAGCACTATTATAGTCCTTCCGT 59.476 45.833 1.33 0.00 36.76 4.69
128 129 5.335819 GGAGCACTATTATAGTCCTTCCGTC 60.336 48.000 1.33 0.00 36.76 4.79
129 130 4.523558 AGCACTATTATAGTCCTTCCGTCC 59.476 45.833 1.33 0.00 36.76 4.79
130 131 4.615452 GCACTATTATAGTCCTTCCGTCCG 60.615 50.000 1.33 0.00 36.76 4.79
131 132 4.758674 CACTATTATAGTCCTTCCGTCCGA 59.241 45.833 1.33 0.00 36.76 4.55
132 133 5.240183 CACTATTATAGTCCTTCCGTCCGAA 59.760 44.000 1.33 0.00 36.76 4.30
133 134 5.829924 ACTATTATAGTCCTTCCGTCCGAAA 59.170 40.000 0.00 0.00 32.47 3.46
134 135 5.603170 ATTATAGTCCTTCCGTCCGAAAA 57.397 39.130 0.00 0.00 0.00 2.29
135 136 5.603170 TTATAGTCCTTCCGTCCGAAAAT 57.397 39.130 0.00 0.00 0.00 1.82
136 137 6.713762 TTATAGTCCTTCCGTCCGAAAATA 57.286 37.500 0.00 0.00 0.00 1.40
137 138 3.242549 AGTCCTTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
138 139 2.830321 AGTCCTTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
139 140 3.260128 AGTCCTTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
140 141 3.370061 GTCCTTCCGTCCGAAAATACTTG 59.630 47.826 0.00 0.00 0.00 3.16
141 142 3.007182 TCCTTCCGTCCGAAAATACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
142 143 3.370061 CCTTCCGTCCGAAAATACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
143 144 3.663995 TCCGTCCGAAAATACTTGTCA 57.336 42.857 0.00 0.00 0.00 3.58
144 145 4.196626 TCCGTCCGAAAATACTTGTCAT 57.803 40.909 0.00 0.00 0.00 3.06
145 146 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
146 147 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
147 148 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
148 149 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
149 150 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
150 151 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
151 152 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
152 153 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
153 154 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
154 155 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
155 156 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
156 157 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
157 158 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
158 159 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
159 160 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
160 161 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
161 162 7.555087 ACTTGTCATCAAAATGGACAAAAAGA 58.445 30.769 7.70 0.00 34.98 2.52
162 163 8.040132 ACTTGTCATCAAAATGGACAAAAAGAA 58.960 29.630 7.70 0.00 34.98 2.52
163 164 8.961294 TTGTCATCAAAATGGACAAAAAGAAT 57.039 26.923 4.15 0.00 33.71 2.40
164 165 8.367943 TGTCATCAAAATGGACAAAAAGAATG 57.632 30.769 0.00 0.00 33.42 2.67
165 166 7.986320 TGTCATCAAAATGGACAAAAAGAATGT 59.014 29.630 0.00 0.00 33.42 2.71
166 167 9.474920 GTCATCAAAATGGACAAAAAGAATGTA 57.525 29.630 0.00 0.00 33.42 2.29
192 193 8.650143 TCTTAATTAATTTTGGCTCCAAGAGT 57.350 30.769 5.91 0.00 37.24 3.24
262 263 4.078516 GGGTCGCGTTGCCTACCT 62.079 66.667 5.77 0.00 33.36 3.08
263 264 2.813908 GGTCGCGTTGCCTACCTG 60.814 66.667 5.77 0.00 31.11 4.00
264 265 2.048503 GTCGCGTTGCCTACCTGT 60.049 61.111 5.77 0.00 0.00 4.00
265 266 2.048597 TCGCGTTGCCTACCTGTG 60.049 61.111 5.77 0.00 0.00 3.66
266 267 2.357034 CGCGTTGCCTACCTGTGT 60.357 61.111 0.00 0.00 0.00 3.72
267 268 2.380410 CGCGTTGCCTACCTGTGTC 61.380 63.158 0.00 0.00 0.00 3.67
289 295 4.435970 TGCCCTCCCGCGTCTCTA 62.436 66.667 4.92 0.00 0.00 2.43
363 393 3.200593 CATGAGCTGGCTGCCGTC 61.201 66.667 14.98 11.08 44.23 4.79
418 454 1.648467 GCTCTGGTGGCCGTGAAATC 61.648 60.000 0.00 0.00 0.00 2.17
424 460 0.730265 GTGGCCGTGAAATCGCATAA 59.270 50.000 0.00 0.00 0.00 1.90
439 475 1.198867 GCATAAACCACATGACACGCA 59.801 47.619 0.00 0.00 0.00 5.24
458 494 2.605338 GCATGCAGAGTGAAGCGAAAAA 60.605 45.455 14.21 0.00 0.00 1.94
459 495 3.231965 CATGCAGAGTGAAGCGAAAAAG 58.768 45.455 0.00 0.00 0.00 2.27
460 496 2.288666 TGCAGAGTGAAGCGAAAAAGT 58.711 42.857 0.00 0.00 0.00 2.66
484 529 5.755375 TGTGTGTGTGTGACAATTTTTGTTT 59.245 32.000 0.00 0.00 45.52 2.83
488 533 5.866633 TGTGTGTGACAATTTTTGTTTCTCC 59.133 36.000 0.00 0.00 45.52 3.71
489 534 5.866633 GTGTGTGACAATTTTTGTTTCTCCA 59.133 36.000 0.00 0.00 45.52 3.86
490 535 6.534793 GTGTGTGACAATTTTTGTTTCTCCAT 59.465 34.615 0.00 0.00 45.52 3.41
492 537 5.523188 TGTGACAATTTTTGTTTCTCCATGC 59.477 36.000 0.00 0.00 45.52 4.06
494 539 4.942852 ACAATTTTTGTTTCTCCATGCGA 58.057 34.783 0.00 0.00 42.22 5.10
495 540 5.540911 ACAATTTTTGTTTCTCCATGCGAT 58.459 33.333 0.00 0.00 42.22 4.58
496 541 5.406175 ACAATTTTTGTTTCTCCATGCGATG 59.594 36.000 0.00 0.00 42.22 3.84
497 542 2.634982 TTTGTTTCTCCATGCGATGC 57.365 45.000 0.00 0.00 0.00 3.91
503 554 2.962827 CTCCATGCGATGCGATGCC 61.963 63.158 0.00 0.00 0.00 4.40
517 568 3.286694 ATGCCATGCGTGTCCCCTT 62.287 57.895 4.96 0.00 0.00 3.95
527 578 1.067071 CGTGTCCCCTTGAACTACTCC 60.067 57.143 0.00 0.00 0.00 3.85
528 579 1.975680 GTGTCCCCTTGAACTACTCCA 59.024 52.381 0.00 0.00 0.00 3.86
529 580 2.028020 GTGTCCCCTTGAACTACTCCAG 60.028 54.545 0.00 0.00 0.00 3.86
581 636 3.808466 TGCATTAACGAGCAGAGATCT 57.192 42.857 0.00 0.00 35.51 2.75
591 646 0.734253 GCAGAGATCTGTGTTCGCGT 60.734 55.000 20.02 0.00 45.45 6.01
626 681 1.813753 CTTGCCTTGCCATGCATGC 60.814 57.895 21.69 11.82 38.76 4.06
627 682 3.650907 TTGCCTTGCCATGCATGCG 62.651 57.895 21.69 15.04 38.76 4.73
628 683 4.884257 GCCTTGCCATGCATGCGG 62.884 66.667 21.69 17.34 38.76 5.69
629 684 3.142162 CCTTGCCATGCATGCGGA 61.142 61.111 21.69 12.74 38.76 5.54
630 685 2.103538 CTTGCCATGCATGCGGAC 59.896 61.111 21.69 10.31 38.76 4.79
673 728 1.107945 ACACCTTTGTTTCCCCGTTG 58.892 50.000 0.00 0.00 28.43 4.10
732 788 3.411351 CACGCGGTTTCCAGGACG 61.411 66.667 12.47 0.00 0.00 4.79
745 808 3.839432 GGACGCTCCCTCCTTCGG 61.839 72.222 0.00 0.00 0.00 4.30
749 812 3.394836 GCTCCCTCCTTCGGCAGT 61.395 66.667 0.00 0.00 0.00 4.40
793 870 0.179145 CGCGCTCTATATAACCCCCG 60.179 60.000 5.56 0.00 0.00 5.73
819 897 4.851214 GCCCTCCCCGCTCTCTCT 62.851 72.222 0.00 0.00 0.00 3.10
823 901 3.347590 TCCCCGCTCTCTCTCCCA 61.348 66.667 0.00 0.00 0.00 4.37
824 902 2.123077 CCCCGCTCTCTCTCCCAT 60.123 66.667 0.00 0.00 0.00 4.00
849 927 4.039357 ACCTCCTCGCACGTCACG 62.039 66.667 0.00 0.00 0.00 4.35
857 935 2.126424 GCACGTCACGTCCCTCTC 60.126 66.667 0.00 0.00 38.32 3.20
865 943 1.931705 ACGTCCCTCTCCTCCTCCT 60.932 63.158 0.00 0.00 0.00 3.69
866 944 1.152839 CGTCCCTCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
869 947 2.612251 CCTCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
877 955 2.444895 CCTCCTCCCCCTCCTTCG 60.445 72.222 0.00 0.00 0.00 3.79
880 958 2.764547 CCTCCCCCTCCTTCGTCC 60.765 72.222 0.00 0.00 0.00 4.79
881 959 2.038975 CTCCCCCTCCTTCGTCCA 59.961 66.667 0.00 0.00 0.00 4.02
889 967 0.320771 CTCCTTCGTCCACCACAAGG 60.321 60.000 0.00 0.00 42.21 3.61
967 1052 3.818787 GCGTCGCCGTCTTCCCTA 61.819 66.667 5.75 0.00 36.15 3.53
977 1062 1.530891 TCTTCCCTATCTCCGGCCG 60.531 63.158 21.04 21.04 0.00 6.13
995 1089 3.553922 GGCCGGATTTGTTTGTCAATTGA 60.554 43.478 5.05 3.38 35.84 2.57
1000 1094 7.312154 CCGGATTTGTTTGTCAATTGAGAATA 58.688 34.615 17.76 8.43 35.84 1.75
1001 1095 7.975616 CCGGATTTGTTTGTCAATTGAGAATAT 59.024 33.333 17.76 9.72 35.84 1.28
1008 1102 6.757897 TTGTCAATTGAGAATATGGTGACC 57.242 37.500 13.63 0.00 34.40 4.02
1009 1103 5.814481 TGTCAATTGAGAATATGGTGACCA 58.186 37.500 6.84 6.84 38.19 4.02
1010 1104 5.882000 TGTCAATTGAGAATATGGTGACCAG 59.118 40.000 11.23 0.00 36.75 4.00
1012 1106 6.375455 GTCAATTGAGAATATGGTGACCAGTT 59.625 38.462 11.23 7.64 36.75 3.16
1013 1107 6.599244 TCAATTGAGAATATGGTGACCAGTTC 59.401 38.462 19.15 19.15 36.75 3.01
1014 1108 5.762179 TTGAGAATATGGTGACCAGTTCT 57.238 39.130 25.70 25.70 41.68 3.01
1015 1109 5.089970 TGAGAATATGGTGACCAGTTCTG 57.910 43.478 28.65 0.00 40.23 3.02
1016 1110 4.080919 TGAGAATATGGTGACCAGTTCTGG 60.081 45.833 28.65 16.25 40.23 3.86
1017 1111 4.104086 AGAATATGGTGACCAGTTCTGGA 58.896 43.478 25.14 3.02 39.37 3.86
1018 1112 4.536090 AGAATATGGTGACCAGTTCTGGAA 59.464 41.667 25.14 9.76 39.37 3.53
1020 1114 2.566833 TGGTGACCAGTTCTGGAATG 57.433 50.000 23.45 0.00 0.00 2.67
1029 1135 3.129287 CCAGTTCTGGAATGTACCAATGC 59.871 47.826 13.02 0.00 39.59 3.56
1040 1146 4.285807 TGTACCAATGCGCATCAATTAC 57.714 40.909 25.53 20.55 0.00 1.89
1063 1169 3.785189 GACAGTGTGGCACGGACGT 62.785 63.158 13.77 7.31 39.64 4.34
1275 1399 2.730094 CAAAACAAGCCGCAGCCT 59.270 55.556 0.00 0.00 41.25 4.58
1287 1411 2.809601 CAGCCTGGCACGTACGTC 60.810 66.667 19.94 13.15 0.00 4.34
1320 1444 0.896940 AGGACAAGGTCTTCCGCGTA 60.897 55.000 4.92 0.00 36.95 4.42
1962 2097 2.915659 TCCAGGTCCTGCGACGTT 60.916 61.111 13.99 0.00 40.17 3.99
2000 2140 1.218316 GGAGGAACTGACGCCGAAT 59.782 57.895 0.00 0.00 41.55 3.34
2065 2212 2.681848 CAGGTAGCAGCAAAGGATTCAG 59.318 50.000 0.00 0.00 0.00 3.02
2117 2265 9.566530 CGATTAATTTGTATGTTGGTTTGATCA 57.433 29.630 0.00 0.00 0.00 2.92
2399 2564 9.932207 TTCTGAATATGAAATGCATGAACTTTT 57.068 25.926 0.00 0.00 37.87 2.27
2513 2683 4.503741 AGTCCCATGACAAAATTGAACG 57.496 40.909 0.00 0.00 44.33 3.95
2524 2694 2.774439 AATTGAACGTTCAGCACCAC 57.226 45.000 28.21 1.72 38.61 4.16
2557 2727 1.950954 GCTTGTTAGTCCAGGGGAAGC 60.951 57.143 0.00 0.00 31.38 3.86
2559 2729 0.984230 TGTTAGTCCAGGGGAAGCAG 59.016 55.000 0.00 0.00 31.38 4.24
2567 2737 0.600057 CAGGGGAAGCAGCTCAAAAC 59.400 55.000 0.00 0.00 0.00 2.43
2588 2758 8.773645 CAAAACTCTGTGTAGACATGAACATAA 58.226 33.333 0.00 0.00 0.00 1.90
2598 2768 6.149129 AGACATGAACATAATCAGCTCGTA 57.851 37.500 0.00 0.00 31.76 3.43
2601 2771 6.106003 ACATGAACATAATCAGCTCGTACAA 58.894 36.000 0.00 0.00 31.76 2.41
2603 2773 5.109210 TGAACATAATCAGCTCGTACAAGG 58.891 41.667 0.00 0.00 0.00 3.61
2655 2835 7.495606 TGAACAAATCAGCTCGTACATATGATT 59.504 33.333 10.38 6.72 41.18 2.57
2670 2850 6.653020 ACATATGATTAGACTTGCAGGTCAA 58.347 36.000 28.25 19.98 38.57 3.18
2673 2853 5.885230 TGATTAGACTTGCAGGTCAAATG 57.115 39.130 28.25 0.00 38.57 2.32
2746 2927 7.011109 AGTGGTTTCGAATACATATTAGTGTGC 59.989 37.037 0.00 0.00 33.62 4.57
2753 2934 6.564709 AATACATATTAGTGTGCATGCCAG 57.435 37.500 16.68 1.99 33.62 4.85
2758 2939 6.429078 ACATATTAGTGTGCATGCCAGATTAG 59.571 38.462 16.68 0.00 0.00 1.73
2835 3016 2.484594 GGATAGAGCCTGTTCTTCTGCC 60.485 54.545 0.00 0.00 0.00 4.85
2846 3027 3.188460 TGTTCTTCTGCCGTTATCTTTGC 59.812 43.478 0.00 0.00 0.00 3.68
2867 3048 2.350772 CCGTCTGGTCAATGCTGAAAAC 60.351 50.000 0.00 0.00 31.88 2.43
2901 3082 1.544691 CCCAGCGACTAAGTGTAGTGT 59.455 52.381 0.00 0.00 40.82 3.55
2903 3084 2.415625 CCAGCGACTAAGTGTAGTGTCC 60.416 54.545 0.00 0.00 40.82 4.02
2934 3115 1.862602 GCCGGCCGAACATGAAAACT 61.863 55.000 30.73 0.00 0.00 2.66
2960 3141 6.680874 ATCAGAGAAATTGTCAGAATCTGC 57.319 37.500 5.18 1.65 34.18 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.750018 TCCATGCCCAAGTGATGCG 60.750 57.895 0.00 0.00 0.00 4.73
1 2 1.669999 GGTCCATGCCCAAGTGATGC 61.670 60.000 0.00 0.00 0.00 3.91
2 3 0.323633 TGGTCCATGCCCAAGTGATG 60.324 55.000 0.16 0.00 0.00 3.07
3 4 0.632835 ATGGTCCATGCCCAAGTGAT 59.367 50.000 2.68 0.00 35.14 3.06
6 7 1.307647 GGATGGTCCATGCCCAAGT 59.692 57.895 9.76 0.00 36.28 3.16
7 8 1.307309 TGGATGGTCCATGCCCAAG 59.693 57.895 19.72 0.00 42.67 3.61
8 9 3.518035 TGGATGGTCCATGCCCAA 58.482 55.556 19.72 0.00 42.67 4.12
15 16 4.100084 CGGCAGCTGGATGGTCCA 62.100 66.667 17.12 0.00 45.98 4.02
29 30 3.816367 GAGTATCCTGGCAGGCGGC 62.816 68.421 29.02 18.87 43.74 6.53
30 31 0.827925 TAGAGTATCCTGGCAGGCGG 60.828 60.000 29.02 6.82 34.61 6.13
31 32 1.203523 GATAGAGTATCCTGGCAGGCG 59.796 57.143 29.02 6.54 34.61 5.52
32 33 1.203523 CGATAGAGTATCCTGGCAGGC 59.796 57.143 29.02 14.98 34.10 4.85
33 34 2.796557 TCGATAGAGTATCCTGGCAGG 58.203 52.381 28.01 28.01 42.67 4.85
47 48 8.227119 GTGGATGATGTATAGATCGATCGATAG 58.773 40.741 29.45 0.00 34.60 2.08
48 49 7.934120 AGTGGATGATGTATAGATCGATCGATA 59.066 37.037 29.45 20.31 34.60 2.92
49 50 6.770303 AGTGGATGATGTATAGATCGATCGAT 59.230 38.462 29.76 29.76 37.59 3.59
50 51 6.037610 CAGTGGATGATGTATAGATCGATCGA 59.962 42.308 21.86 21.86 0.00 3.59
51 52 6.197981 CAGTGGATGATGTATAGATCGATCG 58.802 44.000 19.33 9.36 0.00 3.69
52 53 5.976534 GCAGTGGATGATGTATAGATCGATC 59.023 44.000 17.91 17.91 0.00 3.69
53 54 5.449725 CGCAGTGGATGATGTATAGATCGAT 60.450 44.000 0.00 0.00 0.00 3.59
54 55 4.142600 CGCAGTGGATGATGTATAGATCGA 60.143 45.833 5.48 0.00 0.00 3.59
55 56 4.101235 CGCAGTGGATGATGTATAGATCG 58.899 47.826 5.48 0.00 0.00 3.69
56 57 5.065704 ACGCAGTGGATGATGTATAGATC 57.934 43.478 2.91 2.91 42.51 2.75
57 58 6.590234 TTACGCAGTGGATGATGTATAGAT 57.410 37.500 0.00 0.00 45.73 1.98
58 59 6.183360 TGTTTACGCAGTGGATGATGTATAGA 60.183 38.462 0.00 0.00 45.73 1.98
59 60 5.983118 TGTTTACGCAGTGGATGATGTATAG 59.017 40.000 0.00 0.00 45.73 1.31
60 61 5.908341 TGTTTACGCAGTGGATGATGTATA 58.092 37.500 0.00 0.00 45.73 1.47
61 62 4.765273 TGTTTACGCAGTGGATGATGTAT 58.235 39.130 0.00 0.00 45.73 2.29
62 63 4.195225 TGTTTACGCAGTGGATGATGTA 57.805 40.909 0.00 0.00 45.73 2.29
63 64 3.052455 TGTTTACGCAGTGGATGATGT 57.948 42.857 0.00 0.00 45.73 3.06
64 65 4.345288 CAATGTTTACGCAGTGGATGATG 58.655 43.478 0.00 0.00 45.73 3.07
65 66 4.621068 CAATGTTTACGCAGTGGATGAT 57.379 40.909 0.00 0.00 45.73 2.45
71 72 7.010697 TGTATAATCCAATGTTTACGCAGTG 57.989 36.000 0.00 0.00 45.73 3.66
73 74 7.246674 ACTGTATAATCCAATGTTTACGCAG 57.753 36.000 0.00 0.00 0.00 5.18
74 75 7.464844 CGAACTGTATAATCCAATGTTTACGCA 60.465 37.037 0.00 0.00 0.00 5.24
75 76 6.844279 CGAACTGTATAATCCAATGTTTACGC 59.156 38.462 0.00 0.00 0.00 4.42
76 77 6.844279 GCGAACTGTATAATCCAATGTTTACG 59.156 38.462 0.00 0.00 0.00 3.18
77 78 7.916552 AGCGAACTGTATAATCCAATGTTTAC 58.083 34.615 0.00 0.00 0.00 2.01
78 79 9.256477 CTAGCGAACTGTATAATCCAATGTTTA 57.744 33.333 0.00 0.00 0.00 2.01
79 80 7.226720 CCTAGCGAACTGTATAATCCAATGTTT 59.773 37.037 0.00 0.00 0.00 2.83
80 81 6.706270 CCTAGCGAACTGTATAATCCAATGTT 59.294 38.462 0.00 0.00 0.00 2.71
81 82 6.041637 TCCTAGCGAACTGTATAATCCAATGT 59.958 38.462 0.00 0.00 0.00 2.71
82 83 6.455647 TCCTAGCGAACTGTATAATCCAATG 58.544 40.000 0.00 0.00 0.00 2.82
83 84 6.665992 TCCTAGCGAACTGTATAATCCAAT 57.334 37.500 0.00 0.00 0.00 3.16
84 85 5.509163 GCTCCTAGCGAACTGTATAATCCAA 60.509 44.000 0.00 0.00 0.00 3.53
85 86 4.022242 GCTCCTAGCGAACTGTATAATCCA 60.022 45.833 0.00 0.00 0.00 3.41
86 87 4.022242 TGCTCCTAGCGAACTGTATAATCC 60.022 45.833 0.00 0.00 46.26 3.01
87 88 4.918583 GTGCTCCTAGCGAACTGTATAATC 59.081 45.833 0.00 0.00 46.26 1.75
88 89 4.585162 AGTGCTCCTAGCGAACTGTATAAT 59.415 41.667 0.00 0.00 46.26 1.28
89 90 3.952323 AGTGCTCCTAGCGAACTGTATAA 59.048 43.478 0.00 0.00 46.26 0.98
90 91 3.552875 AGTGCTCCTAGCGAACTGTATA 58.447 45.455 0.00 0.00 46.26 1.47
91 92 2.379972 AGTGCTCCTAGCGAACTGTAT 58.620 47.619 0.00 0.00 46.26 2.29
92 93 1.835494 AGTGCTCCTAGCGAACTGTA 58.165 50.000 0.00 0.00 46.26 2.74
93 94 1.835494 TAGTGCTCCTAGCGAACTGT 58.165 50.000 3.01 0.00 46.26 3.55
94 95 3.444703 AATAGTGCTCCTAGCGAACTG 57.555 47.619 3.01 0.00 46.26 3.16
95 96 6.005198 ACTATAATAGTGCTCCTAGCGAACT 58.995 40.000 0.00 0.00 46.26 3.01
96 97 6.256912 ACTATAATAGTGCTCCTAGCGAAC 57.743 41.667 0.00 0.00 46.26 3.95
97 98 5.415077 GGACTATAATAGTGCTCCTAGCGAA 59.585 44.000 0.00 0.00 46.26 4.70
98 99 4.942483 GGACTATAATAGTGCTCCTAGCGA 59.058 45.833 0.00 0.00 46.26 4.93
99 100 5.238006 GGACTATAATAGTGCTCCTAGCG 57.762 47.826 0.00 0.00 46.26 4.26
107 108 4.615452 CGGACGGAAGGACTATAATAGTGC 60.615 50.000 0.00 0.00 46.12 4.40
108 109 4.758674 TCGGACGGAAGGACTATAATAGTG 59.241 45.833 0.00 0.00 39.59 2.74
109 110 4.978099 TCGGACGGAAGGACTATAATAGT 58.022 43.478 0.00 0.00 42.86 2.12
110 111 5.954296 TTCGGACGGAAGGACTATAATAG 57.046 43.478 0.00 0.00 0.00 1.73
111 112 6.713762 TTTTCGGACGGAAGGACTATAATA 57.286 37.500 0.00 0.00 35.70 0.98
112 113 5.603170 TTTTCGGACGGAAGGACTATAAT 57.397 39.130 0.00 0.00 35.70 1.28
113 114 5.603170 ATTTTCGGACGGAAGGACTATAA 57.397 39.130 0.00 0.00 35.70 0.98
114 115 5.829924 AGTATTTTCGGACGGAAGGACTATA 59.170 40.000 1.24 0.00 35.70 1.31
115 116 4.648307 AGTATTTTCGGACGGAAGGACTAT 59.352 41.667 1.24 0.00 35.70 2.12
116 117 4.019174 AGTATTTTCGGACGGAAGGACTA 58.981 43.478 1.24 0.00 35.70 2.59
117 118 2.830321 AGTATTTTCGGACGGAAGGACT 59.170 45.455 0.00 0.00 35.70 3.85
118 119 3.242549 AGTATTTTCGGACGGAAGGAC 57.757 47.619 0.00 0.00 35.70 3.85
119 120 3.007182 ACAAGTATTTTCGGACGGAAGGA 59.993 43.478 0.00 0.00 35.70 3.36
120 121 3.332034 ACAAGTATTTTCGGACGGAAGG 58.668 45.455 0.00 0.00 35.70 3.46
121 122 3.991773 TGACAAGTATTTTCGGACGGAAG 59.008 43.478 0.00 0.00 35.70 3.46
122 123 3.992643 TGACAAGTATTTTCGGACGGAA 58.007 40.909 0.00 0.00 0.00 4.30
123 124 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
124 125 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
125 126 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
126 127 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
127 128 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
128 129 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
129 130 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
130 131 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
131 132 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
132 133 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
133 134 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
134 135 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
135 136 8.690884 TCTTTTTGTCCATTTTGATGACAAGTA 58.309 29.630 0.00 0.00 37.13 2.24
136 137 7.555087 TCTTTTTGTCCATTTTGATGACAAGT 58.445 30.769 0.00 0.00 37.13 3.16
137 138 8.422973 TTCTTTTTGTCCATTTTGATGACAAG 57.577 30.769 0.00 0.00 37.13 3.16
138 139 8.828644 CATTCTTTTTGTCCATTTTGATGACAA 58.171 29.630 0.00 0.00 34.47 3.18
139 140 7.986320 ACATTCTTTTTGTCCATTTTGATGACA 59.014 29.630 0.00 0.00 0.00 3.58
140 141 8.369218 ACATTCTTTTTGTCCATTTTGATGAC 57.631 30.769 0.00 0.00 0.00 3.06
166 167 9.259832 ACTCTTGGAGCCAAAATTAATTAAGAT 57.740 29.630 0.01 0.00 35.33 2.40
167 168 8.650143 ACTCTTGGAGCCAAAATTAATTAAGA 57.350 30.769 0.01 3.77 35.33 2.10
168 169 9.710900 AAACTCTTGGAGCCAAAATTAATTAAG 57.289 29.630 0.01 0.00 35.33 1.85
171 172 9.875691 GATAAACTCTTGGAGCCAAAATTAATT 57.124 29.630 3.24 0.00 35.33 1.40
172 173 9.259832 AGATAAACTCTTGGAGCCAAAATTAAT 57.740 29.630 3.24 0.00 35.33 1.40
173 174 8.522830 CAGATAAACTCTTGGAGCCAAAATTAA 58.477 33.333 3.24 0.00 35.33 1.40
174 175 7.888021 TCAGATAAACTCTTGGAGCCAAAATTA 59.112 33.333 3.24 1.89 35.33 1.40
175 176 6.721208 TCAGATAAACTCTTGGAGCCAAAATT 59.279 34.615 3.24 0.00 35.33 1.82
176 177 6.151817 GTCAGATAAACTCTTGGAGCCAAAAT 59.848 38.462 3.24 0.00 35.33 1.82
192 193 3.054166 CCAACACGTCACGTCAGATAAA 58.946 45.455 0.00 0.00 38.32 1.40
262 263 2.818169 GGGAGGGCACACAGACACA 61.818 63.158 0.00 0.00 0.00 3.72
263 264 2.032681 GGGAGGGCACACAGACAC 59.967 66.667 0.00 0.00 0.00 3.67
264 265 3.625897 CGGGAGGGCACACAGACA 61.626 66.667 0.00 0.00 0.00 3.41
347 377 4.827087 CGACGGCAGCCAGCTCAT 62.827 66.667 13.30 0.00 44.79 2.90
418 454 1.790123 GCGTGTCATGTGGTTTATGCG 60.790 52.381 0.00 0.00 0.00 4.73
439 475 2.880890 ACTTTTTCGCTTCACTCTGCAT 59.119 40.909 0.00 0.00 0.00 3.96
458 494 4.782019 AAAATTGTCACACACACACACT 57.218 36.364 0.00 0.00 33.41 3.55
459 495 4.683781 ACAAAAATTGTCACACACACACAC 59.316 37.500 0.00 0.00 40.56 3.82
460 496 4.876125 ACAAAAATTGTCACACACACACA 58.124 34.783 0.00 0.00 40.56 3.72
484 529 1.957695 GCATCGCATCGCATGGAGA 60.958 57.895 0.00 0.00 0.00 3.71
488 533 1.442017 CATGGCATCGCATCGCATG 60.442 57.895 0.00 0.00 0.00 4.06
489 534 2.951458 CATGGCATCGCATCGCAT 59.049 55.556 0.00 0.00 0.00 4.73
490 535 3.956317 GCATGGCATCGCATCGCA 61.956 61.111 14.33 0.00 0.00 5.10
492 537 3.642981 ACGCATGGCATCGCATCG 61.643 61.111 17.71 10.37 0.00 3.84
494 539 2.825387 ACACGCATGGCATCGCAT 60.825 55.556 17.71 4.23 0.00 4.73
495 540 3.498834 GACACGCATGGCATCGCA 61.499 61.111 17.71 0.00 32.03 5.10
496 541 4.241999 GGACACGCATGGCATCGC 62.242 66.667 15.79 13.26 34.30 4.58
497 542 3.576356 GGGACACGCATGGCATCG 61.576 66.667 14.74 14.74 34.30 3.84
503 554 0.606401 AGTTCAAGGGGACACGCATG 60.606 55.000 0.00 0.00 0.00 4.06
517 568 3.079578 CGGTGAGTACTGGAGTAGTTCA 58.920 50.000 0.00 0.00 40.89 3.18
527 578 2.181021 GGCGTCCGGTGAGTACTG 59.819 66.667 0.00 0.00 0.00 2.74
528 579 3.437795 CGGCGTCCGGTGAGTACT 61.438 66.667 0.00 0.00 44.15 2.73
581 636 1.226435 GTTGGCAAACGCGAACACA 60.226 52.632 15.93 1.62 44.68 3.72
628 683 2.579684 GATCCTGGACTGCACCGGTC 62.580 65.000 2.59 0.00 38.88 4.79
629 684 2.607750 ATCCTGGACTGCACCGGT 60.608 61.111 0.00 0.00 34.74 5.28
630 685 2.187946 GATCCTGGACTGCACCGG 59.812 66.667 0.00 0.00 36.18 5.28
673 728 5.245075 TGTGGGTTTATGGAAGGTTTTGATC 59.755 40.000 0.00 0.00 0.00 2.92
745 808 2.820037 GGTCGGGCTGCTTACTGC 60.820 66.667 0.00 0.00 43.25 4.40
749 812 3.766691 GTCGGGTCGGGCTGCTTA 61.767 66.667 0.00 0.00 0.00 3.09
769 837 1.153901 TTATATAGAGCGCGGCGGC 60.154 57.895 25.03 15.97 0.00 6.53
819 897 1.909302 GAGGAGGTGAACAAGATGGGA 59.091 52.381 0.00 0.00 0.00 4.37
823 901 0.976641 TGCGAGGAGGTGAACAAGAT 59.023 50.000 0.00 0.00 0.00 2.40
824 902 0.033504 GTGCGAGGAGGTGAACAAGA 59.966 55.000 0.00 0.00 0.00 3.02
849 927 1.231928 GGAGGAGGAGGAGAGGGAC 59.768 68.421 0.00 0.00 0.00 4.46
853 931 2.018086 AGGGGGAGGAGGAGGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
857 935 2.613576 GAAGGAGGGGGAGGAGGAGG 62.614 70.000 0.00 0.00 0.00 4.30
865 943 2.284405 GTGGACGAAGGAGGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
866 944 3.400054 GGTGGACGAAGGAGGGGG 61.400 72.222 0.00 0.00 0.00 5.40
869 947 0.320771 CTTGTGGTGGACGAAGGAGG 60.321 60.000 0.00 0.00 0.00 4.30
877 955 1.605753 GTTTCTCCCTTGTGGTGGAC 58.394 55.000 0.00 0.00 34.77 4.02
889 967 0.112412 TTCTGGCTTGGGGTTTCTCC 59.888 55.000 0.00 0.00 0.00 3.71
977 1062 9.090692 CCATATTCTCAATTGACAAACAAATCC 57.909 33.333 3.38 0.00 42.03 3.01
995 1089 4.494091 CCAGAACTGGTCACCATATTCT 57.506 45.455 15.06 15.06 45.53 2.40
1008 1102 3.181507 CGCATTGGTACATTCCAGAACTG 60.182 47.826 0.00 0.00 39.30 3.16
1009 1103 3.009723 CGCATTGGTACATTCCAGAACT 58.990 45.455 0.00 0.00 39.30 3.01
1010 1104 2.477863 GCGCATTGGTACATTCCAGAAC 60.478 50.000 0.30 0.00 39.30 3.01
1012 1106 1.339535 TGCGCATTGGTACATTCCAGA 60.340 47.619 5.66 0.00 39.30 3.86
1013 1107 1.093972 TGCGCATTGGTACATTCCAG 58.906 50.000 5.66 0.00 39.30 3.86
1014 1108 1.675483 GATGCGCATTGGTACATTCCA 59.325 47.619 26.12 0.00 39.30 3.53
1015 1109 1.675483 TGATGCGCATTGGTACATTCC 59.325 47.619 26.12 7.91 39.30 3.01
1016 1110 3.419264 TTGATGCGCATTGGTACATTC 57.581 42.857 26.12 9.74 39.30 2.67
1017 1111 4.389890 AATTGATGCGCATTGGTACATT 57.610 36.364 26.12 10.65 39.30 2.71
1018 1112 4.337836 TGTAATTGATGCGCATTGGTACAT 59.662 37.500 26.12 9.89 39.30 2.29
1020 1114 4.285807 TGTAATTGATGCGCATTGGTAC 57.714 40.909 26.12 21.75 0.00 3.34
1029 1135 4.083855 ACACTGTCAGTTGTAATTGATGCG 60.084 41.667 1.67 0.00 0.00 4.73
1040 1146 1.643292 CGTGCCACACTGTCAGTTG 59.357 57.895 1.67 5.58 31.34 3.16
1063 1169 4.033243 CGAATCAATCTGCGACATCAGAAA 59.967 41.667 0.00 0.00 45.17 2.52
1260 1375 3.297620 CCAGGCTGCGGCTTGTTT 61.298 61.111 25.98 1.44 42.88 2.83
1423 1558 3.213402 GACGGCGAGGGAGAGGAG 61.213 72.222 16.62 0.00 0.00 3.69
1467 1602 2.098831 GGGCTTGAACGCGAGGTAC 61.099 63.158 15.93 0.00 0.00 3.34
1939 2074 2.959484 CGCAGGACCTGGACACCAT 61.959 63.158 23.09 0.00 30.82 3.55
1962 2097 1.053424 AGAACAGGAACGGCACCTTA 58.947 50.000 0.00 0.00 35.35 2.69
2000 2140 4.038642 GGCCAGTAACCATTTTTGTCTTGA 59.961 41.667 0.00 0.00 0.00 3.02
2052 2195 0.039326 AGCAGCCTGAATCCTTTGCT 59.961 50.000 0.00 0.00 37.09 3.91
2065 2212 0.598065 AAAACATCACGGAAGCAGCC 59.402 50.000 0.00 0.00 0.00 4.85
2117 2265 6.512297 ACGGACAAAAGAATTAACATTGCTT 58.488 32.000 0.00 0.00 0.00 3.91
2296 2461 8.964476 ACCATATGACAAAACTTATACTCCTG 57.036 34.615 3.65 0.00 0.00 3.86
2425 2595 6.777213 ATGACCTAGTGTAAACTGGAGTAG 57.223 41.667 0.00 0.00 0.00 2.57
2513 2683 2.331451 GTTGCCGTGGTGCTGAAC 59.669 61.111 0.00 0.00 0.00 3.18
2524 2694 2.126228 CAAGCATGCCTGTTGCCG 60.126 61.111 15.66 0.00 41.06 5.69
2541 2711 0.393132 GCTGCTTCCCCTGGACTAAC 60.393 60.000 0.00 0.00 0.00 2.34
2557 2727 4.371786 TGTCTACACAGAGTTTTGAGCTG 58.628 43.478 0.00 0.00 35.81 4.24
2559 2729 4.991056 TCATGTCTACACAGAGTTTTGAGC 59.009 41.667 0.00 0.00 35.41 4.26
2567 2737 7.042858 GCTGATTATGTTCATGTCTACACAGAG 60.043 40.741 0.00 0.00 35.41 3.35
2588 2758 2.447443 TCAGTCCTTGTACGAGCTGAT 58.553 47.619 13.56 0.00 0.00 2.90
2655 2835 4.318332 CAGACATTTGACCTGCAAGTCTA 58.682 43.478 16.18 6.26 38.95 2.59
2670 2850 2.579873 AGTGCTTGAACTGCAGACATT 58.420 42.857 23.35 3.80 41.41 2.71
2673 2853 2.032204 CAGAAGTGCTTGAACTGCAGAC 60.032 50.000 23.35 14.31 41.41 3.51
2736 2917 6.173427 TCTAATCTGGCATGCACACTAATA 57.827 37.500 21.36 2.63 0.00 0.98
2746 2927 3.741249 AGTGCTGATCTAATCTGGCATG 58.259 45.455 0.00 0.00 39.39 4.06
2753 2934 4.186926 TGTGCTGAAGTGCTGATCTAATC 58.813 43.478 0.00 0.00 0.00 1.75
2758 2939 1.875514 TGTTGTGCTGAAGTGCTGATC 59.124 47.619 0.00 0.00 0.00 2.92
2835 3016 1.659098 GACCAGACGGCAAAGATAACG 59.341 52.381 0.00 0.00 34.57 3.18
2846 3027 1.522668 TTTCAGCATTGACCAGACGG 58.477 50.000 0.00 0.00 38.77 4.79
2867 3048 0.524862 GCTGGGAGCTCACAACATTG 59.475 55.000 21.33 9.04 38.45 2.82
2901 3082 2.342279 CGGCCAAGACGTGAAGGA 59.658 61.111 2.24 0.00 0.00 3.36
2903 3084 3.423154 GCCGGCCAAGACGTGAAG 61.423 66.667 18.11 0.00 28.54 3.02
2934 3115 9.486497 GCAGATTCTGACAATTTCTCTGATATA 57.514 33.333 17.87 0.00 32.44 0.86
2960 3141 2.376808 ATCCGAACAGAAGTGCAGAG 57.623 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.