Multiple sequence alignment - TraesCS7A01G423500

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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 TraesCS7A01G423500 chr7A 100.000 1450 0 0 830 2279 615539009 615537560 0.000000e+00 2678.0
1 TraesCS7A01G423500 chr7A 93.882 1471 68 8 830 2279 707844420 707845889 0.000000e+00 2198.0
2 TraesCS7A01G423500 chr7A 93.610 1471 72 10 830 2279 650324530 650323061 0.000000e+00 2176.0
3 TraesCS7A01G423500 chr7A 93.066 1471 78 11 830 2279 650260714 650259247 0.000000e+00 2130.0
4 TraesCS7A01G423500 chr7A 100.000 392 0 0 1 392 615539838 615539447 0.000000e+00 725.0
5 TraesCS7A01G423500 chr7A 91.495 388 19 4 1 374 107669766 107669379 2.590000e-144 521.0
6 TraesCS7A01G423500 chr2A 93.882 1471 67 14 830 2279 23796214 23797682 0.000000e+00 2196.0
7 TraesCS7A01G423500 chr2A 93.627 1475 68 16 830 2279 600113404 600111931 0.000000e+00 2180.0
8 TraesCS7A01G423500 chr2A 94.146 1435 65 11 862 2279 571019198 571020630 0.000000e+00 2167.0
9 TraesCS7A01G423500 chr2A 91.935 62 5 0 328 389 23795895 23795956 1.120000e-13 87.9
10 TraesCS7A01G423500 chr1A 93.746 1471 69 9 830 2279 531840021 531838553 0.000000e+00 2185.0
11 TraesCS7A01G423500 chr1A 93.601 1469 72 8 830 2277 380400842 380402309 0.000000e+00 2172.0
12 TraesCS7A01G423500 chr1A 95.078 1158 39 10 1139 2279 504203197 504204353 0.000000e+00 1807.0
13 TraesCS7A01G423500 chr1A 92.308 65 5 0 328 392 11026556 11026492 2.410000e-15 93.5
14 TraesCS7A01G423500 chr1A 93.333 60 4 0 333 392 380400739 380400798 3.120000e-14 89.8
15 TraesCS7A01G423500 chr1B 93.270 1471 76 9 830 2279 658504102 658502634 0.000000e+00 2146.0
16 TraesCS7A01G423500 chr1B 91.602 1155 74 9 830 1963 235897828 235898980 0.000000e+00 1574.0
17 TraesCS7A01G423500 chr4A 92.988 1469 83 11 830 2279 382145506 382146973 0.000000e+00 2124.0
18 TraesCS7A01G423500 chr4A 97.196 321 9 0 1 321 469886858 469886538 5.540000e-151 544.0
19 TraesCS7A01G423500 chr3B 94.221 1315 59 10 982 2279 59100218 59101532 0.000000e+00 1991.0
20 TraesCS7A01G423500 chr3A 95.798 1071 43 2 1211 2279 688931925 688930855 0.000000e+00 1727.0
21 TraesCS7A01G423500 chr6D 92.099 405 18 9 1 392 6098518 6098115 1.980000e-155 558.0
22 TraesCS7A01G423500 chr6D 95.639 321 14 0 1 321 294698928 294698608 1.210000e-142 516.0
23 TraesCS7A01G423500 chr6A 92.248 387 15 8 1 374 33174832 33174448 3.330000e-148 534.0
24 TraesCS7A01G423500 chr2D 93.151 365 18 5 1 358 415153888 415154252 1.550000e-146 529.0
25 TraesCS7A01G423500 chr3D 96.262 321 12 0 1 321 577325634 577325954 5.580000e-146 527.0
26 TraesCS7A01G423500 chr7D 95.652 322 13 1 1 321 567632192 567631871 1.210000e-142 516.0
27 TraesCS7A01G423500 chr7B 95.639 321 12 2 1 321 456306654 456306972 4.340000e-142 514.0
28 TraesCS7A01G423500 chr7B 92.877 351 19 5 2 348 601440862 601441210 2.610000e-139 505.0
29 TraesCS7A01G423500 chr7B 90.625 64 6 0 328 391 544972650 544972713 4.030000e-13 86.1
30 TraesCS7A01G423500 chr5B 95.364 302 13 1 1 302 61754771 61755071 1.580000e-131 479.0
31 TraesCS7A01G423500 chr5B 95.563 293 12 1 1 293 696002961 696003252 3.430000e-128 468.0
32 TraesCS7A01G423500 chr5A 92.308 65 5 0 328 392 603018962 603019026 2.410000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G423500 chr7A 615537560 615539838 2278 True 1701.50 2678 100.0000 1 2279 2 chr7A.!!$R4 2278
1 TraesCS7A01G423500 chr7A 707844420 707845889 1469 False 2198.00 2198 93.8820 830 2279 1 chr7A.!!$F1 1449
2 TraesCS7A01G423500 chr7A 650323061 650324530 1469 True 2176.00 2176 93.6100 830 2279 1 chr7A.!!$R3 1449
3 TraesCS7A01G423500 chr7A 650259247 650260714 1467 True 2130.00 2130 93.0660 830 2279 1 chr7A.!!$R2 1449
4 TraesCS7A01G423500 chr2A 600111931 600113404 1473 True 2180.00 2180 93.6270 830 2279 1 chr2A.!!$R1 1449
5 TraesCS7A01G423500 chr2A 571019198 571020630 1432 False 2167.00 2167 94.1460 862 2279 1 chr2A.!!$F1 1417
6 TraesCS7A01G423500 chr2A 23795895 23797682 1787 False 1141.95 2196 92.9085 328 2279 2 chr2A.!!$F2 1951
7 TraesCS7A01G423500 chr1A 531838553 531840021 1468 True 2185.00 2185 93.7460 830 2279 1 chr1A.!!$R2 1449
8 TraesCS7A01G423500 chr1A 504203197 504204353 1156 False 1807.00 1807 95.0780 1139 2279 1 chr1A.!!$F1 1140
9 TraesCS7A01G423500 chr1A 380400739 380402309 1570 False 1130.90 2172 93.4670 333 2277 2 chr1A.!!$F2 1944
10 TraesCS7A01G423500 chr1B 658502634 658504102 1468 True 2146.00 2146 93.2700 830 2279 1 chr1B.!!$R1 1449
11 TraesCS7A01G423500 chr1B 235897828 235898980 1152 False 1574.00 1574 91.6020 830 1963 1 chr1B.!!$F1 1133
12 TraesCS7A01G423500 chr4A 382145506 382146973 1467 False 2124.00 2124 92.9880 830 2279 1 chr4A.!!$F1 1449
13 TraesCS7A01G423500 chr3B 59100218 59101532 1314 False 1991.00 1991 94.2210 982 2279 1 chr3B.!!$F1 1297
14 TraesCS7A01G423500 chr3A 688930855 688931925 1070 True 1727.00 1727 95.7980 1211 2279 1 chr3A.!!$R1 1068

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
261 262 0.034089 CCCCGCCTCCATTCTTTCTT 60.034 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1309 0.250989 GAGACGGGATCGGAGGAGAT 60.251 60.0 0.0 0.0 41.39 2.75 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
40 41 6.462073 CTCATTTTGAGCACTGAAAAATGG 57.538 37.500 18.71 11.31 45.15 3.16
41 42 6.159299 TCATTTTGAGCACTGAAAAATGGA 57.841 33.333 18.71 8.39 45.15 3.41
42 43 6.580788 TCATTTTGAGCACTGAAAAATGGAA 58.419 32.000 18.71 6.76 45.15 3.53
43 44 7.218614 TCATTTTGAGCACTGAAAAATGGAAT 58.781 30.769 18.71 0.00 45.15 3.01
44 45 6.847956 TTTTGAGCACTGAAAAATGGAATG 57.152 33.333 0.00 0.00 0.00 2.67
45 46 5.787953 TTGAGCACTGAAAAATGGAATGA 57.212 34.783 0.00 0.00 0.00 2.57
46 47 5.787953 TGAGCACTGAAAAATGGAATGAA 57.212 34.783 0.00 0.00 0.00 2.57
47 48 6.159299 TGAGCACTGAAAAATGGAATGAAA 57.841 33.333 0.00 0.00 0.00 2.69
48 49 6.580788 TGAGCACTGAAAAATGGAATGAAAA 58.419 32.000 0.00 0.00 0.00 2.29
49 50 7.218614 TGAGCACTGAAAAATGGAATGAAAAT 58.781 30.769 0.00 0.00 0.00 1.82
50 51 7.716123 TGAGCACTGAAAAATGGAATGAAAATT 59.284 29.630 0.00 0.00 0.00 1.82
51 52 8.454570 AGCACTGAAAAATGGAATGAAAATTT 57.545 26.923 0.00 0.00 0.00 1.82
52 53 8.905850 AGCACTGAAAAATGGAATGAAAATTTT 58.094 25.926 2.28 2.28 35.55 1.82
53 54 9.518906 GCACTGAAAAATGGAATGAAAATTTTT 57.481 25.926 4.63 5.32 42.94 1.94
73 74 9.956720 AATTTTTATCTTGAATCGATCATGACC 57.043 29.630 0.00 0.00 42.87 4.02
74 75 8.504812 TTTTTATCTTGAATCGATCATGACCA 57.495 30.769 0.00 0.00 42.87 4.02
75 76 8.504812 TTTTATCTTGAATCGATCATGACCAA 57.495 30.769 0.00 2.99 42.87 3.67
76 77 8.681486 TTTATCTTGAATCGATCATGACCAAT 57.319 30.769 0.00 0.00 42.87 3.16
77 78 8.681486 TTATCTTGAATCGATCATGACCAATT 57.319 30.769 0.00 0.00 42.87 2.32
78 79 7.578310 ATCTTGAATCGATCATGACCAATTT 57.422 32.000 0.00 0.00 42.87 1.82
79 80 8.681486 ATCTTGAATCGATCATGACCAATTTA 57.319 30.769 0.00 0.00 42.87 1.40
80 81 8.681486 TCTTGAATCGATCATGACCAATTTAT 57.319 30.769 0.00 0.00 37.32 1.40
81 82 9.777297 TCTTGAATCGATCATGACCAATTTATA 57.223 29.630 0.00 0.00 37.32 0.98
84 85 8.949177 TGAATCGATCATGACCAATTTATATGG 58.051 33.333 0.00 0.00 37.25 2.74
98 99 9.519191 CCAATTTATATGGTCATAAGGTCATCA 57.481 33.333 0.00 0.00 33.08 3.07
103 104 9.519191 TTATATGGTCATAAGGTCATCAAATGG 57.481 33.333 0.00 0.00 0.00 3.16
104 105 5.191727 TGGTCATAAGGTCATCAAATGGT 57.808 39.130 0.00 0.00 0.00 3.55
105 106 5.579047 TGGTCATAAGGTCATCAAATGGTT 58.421 37.500 0.00 0.00 0.00 3.67
106 107 6.015918 TGGTCATAAGGTCATCAAATGGTTT 58.984 36.000 0.00 0.00 0.00 3.27
107 108 6.071447 TGGTCATAAGGTCATCAAATGGTTTG 60.071 38.462 0.00 0.00 41.96 2.93
108 109 5.807011 GTCATAAGGTCATCAAATGGTTTGC 59.193 40.000 0.00 0.00 40.43 3.68
109 110 5.716228 TCATAAGGTCATCAAATGGTTTGCT 59.284 36.000 0.00 0.00 40.43 3.91
110 111 3.947910 AGGTCATCAAATGGTTTGCTG 57.052 42.857 1.08 1.08 40.43 4.41
111 112 2.028748 AGGTCATCAAATGGTTTGCTGC 60.029 45.455 0.00 0.00 40.43 5.25
112 113 1.987770 GTCATCAAATGGTTTGCTGCG 59.012 47.619 0.00 0.00 40.43 5.18
113 114 1.612950 TCATCAAATGGTTTGCTGCGT 59.387 42.857 0.00 0.00 40.43 5.24
114 115 2.035704 TCATCAAATGGTTTGCTGCGTT 59.964 40.909 0.00 0.00 40.43 4.84
115 116 2.132740 TCAAATGGTTTGCTGCGTTC 57.867 45.000 0.00 0.00 40.43 3.95
116 117 1.680735 TCAAATGGTTTGCTGCGTTCT 59.319 42.857 0.00 0.00 40.43 3.01
117 118 1.788308 CAAATGGTTTGCTGCGTTCTG 59.212 47.619 0.00 0.00 33.36 3.02
118 119 1.317613 AATGGTTTGCTGCGTTCTGA 58.682 45.000 0.00 0.00 0.00 3.27
119 120 1.538047 ATGGTTTGCTGCGTTCTGAT 58.462 45.000 0.00 0.00 0.00 2.90
120 121 1.317613 TGGTTTGCTGCGTTCTGATT 58.682 45.000 0.00 0.00 0.00 2.57
121 122 1.001487 TGGTTTGCTGCGTTCTGATTG 60.001 47.619 0.00 0.00 0.00 2.67
122 123 1.666888 GGTTTGCTGCGTTCTGATTGG 60.667 52.381 0.00 0.00 0.00 3.16
123 124 1.266718 GTTTGCTGCGTTCTGATTGGA 59.733 47.619 0.00 0.00 0.00 3.53
124 125 0.874390 TTGCTGCGTTCTGATTGGAC 59.126 50.000 0.00 0.00 0.00 4.02
125 126 0.955428 TGCTGCGTTCTGATTGGACC 60.955 55.000 0.00 0.00 0.00 4.46
126 127 0.955428 GCTGCGTTCTGATTGGACCA 60.955 55.000 0.00 0.00 0.00 4.02
127 128 1.742761 CTGCGTTCTGATTGGACCAT 58.257 50.000 0.00 0.00 0.00 3.55
128 129 1.399440 CTGCGTTCTGATTGGACCATG 59.601 52.381 0.00 0.00 0.00 3.66
129 130 0.734889 GCGTTCTGATTGGACCATGG 59.265 55.000 11.19 11.19 0.00 3.66
130 131 1.382522 CGTTCTGATTGGACCATGGG 58.617 55.000 18.09 0.00 0.00 4.00
131 132 1.106285 GTTCTGATTGGACCATGGGC 58.894 55.000 18.09 14.45 0.00 5.36
132 133 0.703488 TTCTGATTGGACCATGGGCA 59.297 50.000 22.13 0.00 0.00 5.36
133 134 0.928505 TCTGATTGGACCATGGGCAT 59.071 50.000 22.13 4.68 0.00 4.40
134 135 2.134354 TCTGATTGGACCATGGGCATA 58.866 47.619 22.13 6.63 0.00 3.14
135 136 2.718062 TCTGATTGGACCATGGGCATAT 59.282 45.455 22.13 11.98 0.00 1.78
136 137 3.087031 CTGATTGGACCATGGGCATATC 58.913 50.000 22.13 20.46 0.00 1.63
137 138 2.446285 TGATTGGACCATGGGCATATCA 59.554 45.455 23.17 23.17 0.00 2.15
138 139 2.363306 TTGGACCATGGGCATATCAC 57.637 50.000 22.13 0.16 0.00 3.06
139 140 0.108396 TGGACCATGGGCATATCACG 59.892 55.000 22.13 0.00 0.00 4.35
140 141 1.237285 GGACCATGGGCATATCACGC 61.237 60.000 22.13 0.00 0.00 5.34
141 142 1.568612 GACCATGGGCATATCACGCG 61.569 60.000 14.59 3.53 0.00 6.01
142 143 2.327343 CCATGGGCATATCACGCGG 61.327 63.158 12.47 0.00 0.00 6.46
143 144 1.301637 CATGGGCATATCACGCGGA 60.302 57.895 12.47 5.24 0.00 5.54
144 145 0.674581 CATGGGCATATCACGCGGAT 60.675 55.000 12.47 13.04 40.14 4.18
145 146 0.391661 ATGGGCATATCACGCGGATC 60.392 55.000 12.47 0.00 37.44 3.36
146 147 1.005037 GGGCATATCACGCGGATCA 60.005 57.895 12.47 0.00 37.44 2.92
147 148 1.291877 GGGCATATCACGCGGATCAC 61.292 60.000 12.47 3.83 37.44 3.06
157 158 4.200287 CGGATCACGCATCAACCA 57.800 55.556 0.00 0.00 34.82 3.67
158 159 1.715585 CGGATCACGCATCAACCAC 59.284 57.895 0.00 0.00 34.82 4.16
159 160 1.705337 CGGATCACGCATCAACCACC 61.705 60.000 0.00 0.00 34.82 4.61
160 161 1.705337 GGATCACGCATCAACCACCG 61.705 60.000 0.00 0.00 32.33 4.94
161 162 1.003839 ATCACGCATCAACCACCGT 60.004 52.632 0.00 0.00 0.00 4.83
162 163 1.019278 ATCACGCATCAACCACCGTC 61.019 55.000 0.00 0.00 0.00 4.79
163 164 2.736995 ACGCATCAACCACCGTCG 60.737 61.111 0.00 0.00 0.00 5.12
164 165 3.487202 CGCATCAACCACCGTCGG 61.487 66.667 10.48 10.48 0.00 4.79
165 166 2.047655 GCATCAACCACCGTCGGA 60.048 61.111 20.51 0.00 0.00 4.55
166 167 1.449601 GCATCAACCACCGTCGGAT 60.450 57.895 20.51 0.00 0.00 4.18
167 168 1.705337 GCATCAACCACCGTCGGATG 61.705 60.000 20.51 11.06 37.04 3.51
168 169 1.449601 ATCAACCACCGTCGGATGC 60.450 57.895 20.51 0.00 0.00 3.91
169 170 1.899437 ATCAACCACCGTCGGATGCT 61.899 55.000 20.51 0.13 0.00 3.79
170 171 1.671054 CAACCACCGTCGGATGCTT 60.671 57.895 20.51 3.59 0.00 3.91
171 172 1.375523 AACCACCGTCGGATGCTTC 60.376 57.895 20.51 0.00 0.00 3.86
172 173 2.511600 CCACCGTCGGATGCTTCC 60.512 66.667 20.51 8.60 38.81 3.46
182 183 2.311294 GATGCTTCCGGATCCAACG 58.689 57.895 13.41 0.00 32.39 4.10
188 189 4.418328 CCGGATCCAACGGCCCAA 62.418 66.667 13.41 0.00 45.34 4.12
189 190 2.360600 CGGATCCAACGGCCCAAA 60.361 61.111 13.41 0.00 0.00 3.28
190 191 2.696759 CGGATCCAACGGCCCAAAC 61.697 63.158 13.41 0.00 0.00 2.93
191 192 2.348104 GGATCCAACGGCCCAAACC 61.348 63.158 6.95 0.00 0.00 3.27
192 193 2.283604 ATCCAACGGCCCAAACCC 60.284 61.111 0.00 0.00 0.00 4.11
193 194 3.153629 ATCCAACGGCCCAAACCCA 62.154 57.895 0.00 0.00 0.00 4.51
194 195 3.611674 CCAACGGCCCAAACCCAC 61.612 66.667 0.00 0.00 0.00 4.61
195 196 3.611674 CAACGGCCCAAACCCACC 61.612 66.667 0.00 0.00 0.00 4.61
196 197 4.926162 AACGGCCCAAACCCACCC 62.926 66.667 0.00 0.00 0.00 4.61
200 201 3.961414 GCCCAAACCCACCCGAGA 61.961 66.667 0.00 0.00 0.00 4.04
201 202 2.033602 CCCAAACCCACCCGAGAC 59.966 66.667 0.00 0.00 0.00 3.36
202 203 2.358247 CCAAACCCACCCGAGACG 60.358 66.667 0.00 0.00 0.00 4.18
203 204 2.738480 CAAACCCACCCGAGACGA 59.262 61.111 0.00 0.00 0.00 4.20
204 205 1.070105 CAAACCCACCCGAGACGAA 59.930 57.895 0.00 0.00 0.00 3.85
205 206 0.533308 CAAACCCACCCGAGACGAAA 60.533 55.000 0.00 0.00 0.00 3.46
206 207 0.533531 AAACCCACCCGAGACGAAAC 60.534 55.000 0.00 0.00 0.00 2.78
207 208 2.047560 CCCACCCGAGACGAAACC 60.048 66.667 0.00 0.00 0.00 3.27
208 209 2.047560 CCACCCGAGACGAAACCC 60.048 66.667 0.00 0.00 0.00 4.11
209 210 2.580601 CCACCCGAGACGAAACCCT 61.581 63.158 0.00 0.00 0.00 4.34
210 211 1.252904 CCACCCGAGACGAAACCCTA 61.253 60.000 0.00 0.00 0.00 3.53
211 212 0.172803 CACCCGAGACGAAACCCTAG 59.827 60.000 0.00 0.00 0.00 3.02
212 213 0.969409 ACCCGAGACGAAACCCTAGG 60.969 60.000 0.06 0.06 0.00 3.02
213 214 0.969409 CCCGAGACGAAACCCTAGGT 60.969 60.000 8.29 0.00 37.65 3.08
214 215 0.455005 CCGAGACGAAACCCTAGGTC 59.545 60.000 8.29 0.00 33.12 3.85
215 216 1.171308 CGAGACGAAACCCTAGGTCA 58.829 55.000 8.29 0.00 33.12 4.02
216 217 1.132643 CGAGACGAAACCCTAGGTCAG 59.867 57.143 8.29 0.00 33.12 3.51
217 218 2.169330 GAGACGAAACCCTAGGTCAGT 58.831 52.381 8.29 0.09 33.12 3.41
218 219 2.164017 GAGACGAAACCCTAGGTCAGTC 59.836 54.545 8.29 9.57 33.12 3.51
219 220 1.204231 GACGAAACCCTAGGTCAGTCC 59.796 57.143 8.29 0.00 33.12 3.85
221 222 1.477295 CGAAACCCTAGGTCAGTCCTC 59.523 57.143 8.29 0.00 44.42 3.71
222 223 2.537143 GAAACCCTAGGTCAGTCCTCA 58.463 52.381 8.29 0.00 44.42 3.86
223 224 2.950990 AACCCTAGGTCAGTCCTCAT 57.049 50.000 8.29 0.00 44.42 2.90
224 225 2.166907 ACCCTAGGTCAGTCCTCATG 57.833 55.000 8.29 0.00 44.42 3.07
225 226 1.343478 ACCCTAGGTCAGTCCTCATGG 60.343 57.143 8.29 0.00 44.42 3.66
226 227 1.062886 CCCTAGGTCAGTCCTCATGGA 60.063 57.143 8.29 0.00 44.42 3.41
242 243 2.666085 GGACATTTTCCACCCACCC 58.334 57.895 0.00 0.00 45.10 4.61
243 244 0.902984 GGACATTTTCCACCCACCCC 60.903 60.000 0.00 0.00 45.10 4.95
244 245 0.902984 GACATTTTCCACCCACCCCC 60.903 60.000 0.00 0.00 0.00 5.40
258 259 2.683475 CCCCCGCCTCCATTCTTT 59.317 61.111 0.00 0.00 0.00 2.52
259 260 1.453928 CCCCCGCCTCCATTCTTTC 60.454 63.158 0.00 0.00 0.00 2.62
260 261 1.609783 CCCCGCCTCCATTCTTTCT 59.390 57.895 0.00 0.00 0.00 2.52
261 262 0.034089 CCCCGCCTCCATTCTTTCTT 60.034 55.000 0.00 0.00 0.00 2.52
262 263 1.383523 CCCGCCTCCATTCTTTCTTC 58.616 55.000 0.00 0.00 0.00 2.87
263 264 1.383523 CCGCCTCCATTCTTTCTTCC 58.616 55.000 0.00 0.00 0.00 3.46
264 265 1.340017 CCGCCTCCATTCTTTCTTCCA 60.340 52.381 0.00 0.00 0.00 3.53
265 266 2.648059 CGCCTCCATTCTTTCTTCCAT 58.352 47.619 0.00 0.00 0.00 3.41
266 267 3.019564 CGCCTCCATTCTTTCTTCCATT 58.980 45.455 0.00 0.00 0.00 3.16
267 268 3.065925 CGCCTCCATTCTTTCTTCCATTC 59.934 47.826 0.00 0.00 0.00 2.67
268 269 3.382865 GCCTCCATTCTTTCTTCCATTCC 59.617 47.826 0.00 0.00 0.00 3.01
269 270 4.864726 CCTCCATTCTTTCTTCCATTCCT 58.135 43.478 0.00 0.00 0.00 3.36
270 271 4.886489 CCTCCATTCTTTCTTCCATTCCTC 59.114 45.833 0.00 0.00 0.00 3.71
271 272 4.860022 TCCATTCTTTCTTCCATTCCTCC 58.140 43.478 0.00 0.00 0.00 4.30
272 273 3.956848 CCATTCTTTCTTCCATTCCTCCC 59.043 47.826 0.00 0.00 0.00 4.30
273 274 4.325658 CCATTCTTTCTTCCATTCCTCCCT 60.326 45.833 0.00 0.00 0.00 4.20
274 275 4.576330 TTCTTTCTTCCATTCCTCCCTC 57.424 45.455 0.00 0.00 0.00 4.30
275 276 2.846827 TCTTTCTTCCATTCCTCCCTCC 59.153 50.000 0.00 0.00 0.00 4.30
276 277 1.596496 TTCTTCCATTCCTCCCTCCC 58.404 55.000 0.00 0.00 0.00 4.30
277 278 0.327576 TCTTCCATTCCTCCCTCCCC 60.328 60.000 0.00 0.00 0.00 4.81
278 279 1.308746 TTCCATTCCTCCCTCCCCC 60.309 63.158 0.00 0.00 0.00 5.40
279 280 3.171388 CCATTCCTCCCTCCCCCG 61.171 72.222 0.00 0.00 0.00 5.73
280 281 3.878667 CATTCCTCCCTCCCCCGC 61.879 72.222 0.00 0.00 0.00 6.13
288 289 3.878667 CCTCCCCCGCCTCCATTC 61.879 72.222 0.00 0.00 0.00 2.67
289 290 2.770048 CTCCCCCGCCTCCATTCT 60.770 66.667 0.00 0.00 0.00 2.40
290 291 2.286121 TCCCCCGCCTCCATTCTT 60.286 61.111 0.00 0.00 0.00 2.52
291 292 1.926426 CTCCCCCGCCTCCATTCTTT 61.926 60.000 0.00 0.00 0.00 2.52
292 293 1.453928 CCCCCGCCTCCATTCTTTC 60.454 63.158 0.00 0.00 0.00 2.62
293 294 1.819632 CCCCGCCTCCATTCTTTCG 60.820 63.158 0.00 0.00 0.00 3.46
294 295 2.472909 CCCGCCTCCATTCTTTCGC 61.473 63.158 0.00 0.00 0.00 4.70
295 296 1.450312 CCGCCTCCATTCTTTCGCT 60.450 57.895 0.00 0.00 0.00 4.93
296 297 1.432270 CCGCCTCCATTCTTTCGCTC 61.432 60.000 0.00 0.00 0.00 5.03
297 298 1.432270 CGCCTCCATTCTTTCGCTCC 61.432 60.000 0.00 0.00 0.00 4.70
298 299 0.392998 GCCTCCATTCTTTCGCTCCA 60.393 55.000 0.00 0.00 0.00 3.86
299 300 1.661341 CCTCCATTCTTTCGCTCCAG 58.339 55.000 0.00 0.00 0.00 3.86
300 301 1.208052 CCTCCATTCTTTCGCTCCAGA 59.792 52.381 0.00 0.00 0.00 3.86
301 302 2.158842 CCTCCATTCTTTCGCTCCAGAT 60.159 50.000 0.00 0.00 0.00 2.90
302 303 3.539604 CTCCATTCTTTCGCTCCAGATT 58.460 45.455 0.00 0.00 0.00 2.40
303 304 3.535561 TCCATTCTTTCGCTCCAGATTC 58.464 45.455 0.00 0.00 0.00 2.52
304 305 2.286294 CCATTCTTTCGCTCCAGATTCG 59.714 50.000 0.00 0.00 0.00 3.34
305 306 1.359848 TTCTTTCGCTCCAGATTCGC 58.640 50.000 0.00 0.00 0.00 4.70
306 307 0.460284 TCTTTCGCTCCAGATTCGCC 60.460 55.000 0.00 0.00 0.00 5.54
307 308 0.740868 CTTTCGCTCCAGATTCGCCA 60.741 55.000 0.00 0.00 0.00 5.69
308 309 1.019278 TTTCGCTCCAGATTCGCCAC 61.019 55.000 0.00 0.00 0.00 5.01
309 310 2.852495 TTCGCTCCAGATTCGCCACC 62.852 60.000 0.00 0.00 0.00 4.61
310 311 2.514824 GCTCCAGATTCGCCACCC 60.515 66.667 0.00 0.00 0.00 4.61
311 312 2.989639 CTCCAGATTCGCCACCCA 59.010 61.111 0.00 0.00 0.00 4.51
312 313 1.450312 CTCCAGATTCGCCACCCAC 60.450 63.158 0.00 0.00 0.00 4.61
313 314 2.819595 CCAGATTCGCCACCCACG 60.820 66.667 0.00 0.00 0.00 4.94
314 315 3.499737 CAGATTCGCCACCCACGC 61.500 66.667 0.00 0.00 0.00 5.34
315 316 4.778143 AGATTCGCCACCCACGCC 62.778 66.667 0.00 0.00 0.00 5.68
317 318 4.652131 ATTCGCCACCCACGCCAA 62.652 61.111 0.00 0.00 0.00 4.52
318 319 3.936772 ATTCGCCACCCACGCCAAT 62.937 57.895 0.00 0.00 0.00 3.16
322 323 2.751436 CCACCCACGCCAATCCAG 60.751 66.667 0.00 0.00 0.00 3.86
323 324 2.350895 CACCCACGCCAATCCAGA 59.649 61.111 0.00 0.00 0.00 3.86
324 325 1.077501 CACCCACGCCAATCCAGAT 60.078 57.895 0.00 0.00 0.00 2.90
325 326 0.680921 CACCCACGCCAATCCAGATT 60.681 55.000 0.00 0.00 0.00 2.40
326 327 0.680921 ACCCACGCCAATCCAGATTG 60.681 55.000 12.51 12.51 45.77 2.67
368 369 2.378522 CCCCTCCTTCCCCATCCT 59.621 66.667 0.00 0.00 0.00 3.24
855 856 4.529219 CACCATAGCTCGCCGCCA 62.529 66.667 0.00 0.00 40.39 5.69
965 969 3.102515 CGACCTCATCGTTGTCGTT 57.897 52.632 0.00 0.00 46.25 3.85
978 983 2.808543 GTTGTCGTTGGCTTGAGATCTT 59.191 45.455 0.00 0.00 0.00 2.40
984 989 1.830279 TGGCTTGAGATCTTGCCTTG 58.170 50.000 25.29 6.04 45.11 3.61
1008 1013 3.058160 GCAGCAGCCATGGACGTT 61.058 61.111 18.40 0.00 33.58 3.99
1065 1070 1.153086 GGACAGCATCCGCCTCATT 60.153 57.895 0.00 0.00 37.88 2.57
1117 1122 2.203153 ACCAAACACTCGCGCCTT 60.203 55.556 0.00 0.00 0.00 4.35
1145 1150 1.066358 AGATCCGGTTCGTTTTCCTCC 60.066 52.381 0.00 0.00 0.00 4.30
1228 1248 1.292541 GGGTTCGTCGGCTTCTTCT 59.707 57.895 0.00 0.00 0.00 2.85
1266 1286 2.754552 CCCCATCAACAACATCATCGTT 59.245 45.455 0.00 0.00 0.00 3.85
1331 1351 3.810941 CCTCTTGTTTGCACGGTTTAGTA 59.189 43.478 0.00 0.00 0.00 1.82
1355 1375 1.691195 TTGGGTCCTGTTGTCTCGCA 61.691 55.000 0.00 0.00 0.00 5.10
1509 1533 5.163301 GGATGAGTCAAGGGTAATCAGCTAA 60.163 44.000 0.00 0.00 0.00 3.09
1540 1564 3.019564 GGGTCATGCTTAAGTCATTGCT 58.980 45.455 4.02 0.00 0.00 3.91
1549 1573 4.437930 GCTTAAGTCATTGCTGCTAGTTGG 60.438 45.833 4.02 0.00 0.00 3.77
1606 1630 4.119136 CTCACCACACAATTTGGGAAAAC 58.881 43.478 5.47 0.00 38.59 2.43
1607 1631 2.863137 CACCACACAATTTGGGAAAACG 59.137 45.455 5.47 0.00 38.59 3.60
1657 1681 1.451387 CATACCACCAGTTCGCCCC 60.451 63.158 0.00 0.00 0.00 5.80
1659 1683 1.493854 ATACCACCAGTTCGCCCCAA 61.494 55.000 0.00 0.00 0.00 4.12
1704 1728 5.700402 AAATTGGCACCTACTGAGTAGAT 57.300 39.130 20.66 0.00 38.29 1.98
1716 1740 8.721479 ACCTACTGAGTAGATAGGTTACATACA 58.279 37.037 20.66 0.00 45.22 2.29
1955 1980 1.064654 GCCAGCTTTATGTAGCAGTGC 59.935 52.381 7.13 7.13 43.68 4.40
2081 2107 4.261909 CCATTTCTTAGAATCCATGCTGGC 60.262 45.833 0.00 0.00 37.47 4.85
2102 2133 3.555956 GCGGTGTCTTCTACAATATGTGG 59.444 47.826 0.00 0.00 40.63 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.903995 TTTTCAGTGCTCAAAATGAGTTTTT 57.096 28.000 8.97 0.00 45.94 1.94
13 14 7.903995 TTTTTCAGTGCTCAAAATGAGTTTT 57.096 28.000 8.97 0.00 45.94 2.43
14 15 7.011669 CCATTTTTCAGTGCTCAAAATGAGTTT 59.988 33.333 23.24 0.00 45.94 2.66
15 16 6.480981 CCATTTTTCAGTGCTCAAAATGAGTT 59.519 34.615 23.24 0.00 45.94 3.01
16 17 5.987347 CCATTTTTCAGTGCTCAAAATGAGT 59.013 36.000 23.24 1.07 45.94 3.41
17 18 6.218019 TCCATTTTTCAGTGCTCAAAATGAG 58.782 36.000 23.24 17.16 45.03 2.90
18 19 6.159299 TCCATTTTTCAGTGCTCAAAATGA 57.841 33.333 23.24 13.73 45.03 2.57
19 20 6.847956 TTCCATTTTTCAGTGCTCAAAATG 57.152 33.333 18.72 18.72 43.21 2.32
20 21 7.218614 TCATTCCATTTTTCAGTGCTCAAAAT 58.781 30.769 0.00 0.00 31.62 1.82
21 22 6.580788 TCATTCCATTTTTCAGTGCTCAAAA 58.419 32.000 0.00 0.00 0.00 2.44
22 23 6.159299 TCATTCCATTTTTCAGTGCTCAAA 57.841 33.333 0.00 0.00 0.00 2.69
23 24 5.787953 TCATTCCATTTTTCAGTGCTCAA 57.212 34.783 0.00 0.00 0.00 3.02
24 25 5.787953 TTCATTCCATTTTTCAGTGCTCA 57.212 34.783 0.00 0.00 0.00 4.26
25 26 7.662604 ATTTTCATTCCATTTTTCAGTGCTC 57.337 32.000 0.00 0.00 0.00 4.26
26 27 8.454570 AAATTTTCATTCCATTTTTCAGTGCT 57.545 26.923 0.00 0.00 0.00 4.40
27 28 9.518906 AAAAATTTTCATTCCATTTTTCAGTGC 57.481 25.926 3.41 0.00 35.98 4.40
47 48 9.956720 GGTCATGATCGATTCAAGATAAAAATT 57.043 29.630 0.00 0.00 38.03 1.82
48 49 9.123902 TGGTCATGATCGATTCAAGATAAAAAT 57.876 29.630 0.00 0.00 38.03 1.82
49 50 8.504812 TGGTCATGATCGATTCAAGATAAAAA 57.495 30.769 0.00 0.00 38.03 1.94
50 51 8.504812 TTGGTCATGATCGATTCAAGATAAAA 57.495 30.769 0.00 0.00 38.03 1.52
51 52 8.681486 ATTGGTCATGATCGATTCAAGATAAA 57.319 30.769 2.54 2.24 38.03 1.40
52 53 8.681486 AATTGGTCATGATCGATTCAAGATAA 57.319 30.769 14.73 3.21 38.03 1.75
53 54 8.681486 AAATTGGTCATGATCGATTCAAGATA 57.319 30.769 19.69 0.00 38.03 1.98
54 55 7.578310 AAATTGGTCATGATCGATTCAAGAT 57.422 32.000 19.69 3.48 38.03 2.40
55 56 8.681486 ATAAATTGGTCATGATCGATTCAAGA 57.319 30.769 19.69 8.14 38.03 3.02
58 59 8.949177 CCATATAAATTGGTCATGATCGATTCA 58.051 33.333 19.69 8.00 39.12 2.57
59 60 8.950210 ACCATATAAATTGGTCATGATCGATTC 58.050 33.333 19.69 0.00 44.15 2.52
60 61 8.868522 ACCATATAAATTGGTCATGATCGATT 57.131 30.769 14.73 14.73 44.15 3.34
72 73 9.519191 TGATGACCTTATGACCATATAAATTGG 57.481 33.333 0.00 0.00 40.26 3.16
77 78 9.519191 CCATTTGATGACCTTATGACCATATAA 57.481 33.333 0.00 0.00 0.00 0.98
78 79 8.668653 ACCATTTGATGACCTTATGACCATATA 58.331 33.333 0.00 0.00 0.00 0.86
79 80 7.529555 ACCATTTGATGACCTTATGACCATAT 58.470 34.615 0.00 0.00 0.00 1.78
80 81 6.910191 ACCATTTGATGACCTTATGACCATA 58.090 36.000 0.00 0.00 0.00 2.74
81 82 5.769835 ACCATTTGATGACCTTATGACCAT 58.230 37.500 0.00 0.00 0.00 3.55
82 83 5.191727 ACCATTTGATGACCTTATGACCA 57.808 39.130 0.00 0.00 0.00 4.02
83 84 6.332630 CAAACCATTTGATGACCTTATGACC 58.667 40.000 0.00 0.00 43.26 4.02
84 85 5.807011 GCAAACCATTTGATGACCTTATGAC 59.193 40.000 5.49 0.00 43.26 3.06
85 86 5.716228 AGCAAACCATTTGATGACCTTATGA 59.284 36.000 5.49 0.00 43.26 2.15
86 87 5.969423 AGCAAACCATTTGATGACCTTATG 58.031 37.500 5.49 0.00 43.26 1.90
95 96 2.297033 AGAACGCAGCAAACCATTTGAT 59.703 40.909 5.49 0.00 43.26 2.57
96 97 1.680735 AGAACGCAGCAAACCATTTGA 59.319 42.857 5.49 0.00 43.26 2.69
97 98 1.788308 CAGAACGCAGCAAACCATTTG 59.212 47.619 0.00 0.00 43.44 2.32
98 99 1.680735 TCAGAACGCAGCAAACCATTT 59.319 42.857 0.00 0.00 0.00 2.32
99 100 1.317613 TCAGAACGCAGCAAACCATT 58.682 45.000 0.00 0.00 0.00 3.16
100 101 1.538047 ATCAGAACGCAGCAAACCAT 58.462 45.000 0.00 0.00 0.00 3.55
101 102 1.001487 CAATCAGAACGCAGCAAACCA 60.001 47.619 0.00 0.00 0.00 3.67
102 103 1.666888 CCAATCAGAACGCAGCAAACC 60.667 52.381 0.00 0.00 0.00 3.27
103 104 1.266718 TCCAATCAGAACGCAGCAAAC 59.733 47.619 0.00 0.00 0.00 2.93
104 105 1.266718 GTCCAATCAGAACGCAGCAAA 59.733 47.619 0.00 0.00 0.00 3.68
105 106 0.874390 GTCCAATCAGAACGCAGCAA 59.126 50.000 0.00 0.00 0.00 3.91
106 107 0.955428 GGTCCAATCAGAACGCAGCA 60.955 55.000 0.00 0.00 0.00 4.41
107 108 0.955428 TGGTCCAATCAGAACGCAGC 60.955 55.000 0.00 0.00 0.00 5.25
108 109 1.399440 CATGGTCCAATCAGAACGCAG 59.601 52.381 0.00 0.00 0.00 5.18
109 110 1.452110 CATGGTCCAATCAGAACGCA 58.548 50.000 0.00 0.00 0.00 5.24
110 111 0.734889 CCATGGTCCAATCAGAACGC 59.265 55.000 2.57 0.00 0.00 4.84
111 112 1.382522 CCCATGGTCCAATCAGAACG 58.617 55.000 11.73 0.00 0.00 3.95
112 113 1.106285 GCCCATGGTCCAATCAGAAC 58.894 55.000 11.73 0.00 0.00 3.01
113 114 0.703488 TGCCCATGGTCCAATCAGAA 59.297 50.000 11.73 0.00 0.00 3.02
114 115 0.928505 ATGCCCATGGTCCAATCAGA 59.071 50.000 11.73 0.00 0.00 3.27
115 116 2.662535 TATGCCCATGGTCCAATCAG 57.337 50.000 11.73 0.00 0.00 2.90
116 117 2.446285 TGATATGCCCATGGTCCAATCA 59.554 45.455 11.73 11.36 0.00 2.57
117 118 2.821969 GTGATATGCCCATGGTCCAATC 59.178 50.000 11.73 8.94 0.00 2.67
118 119 2.815215 CGTGATATGCCCATGGTCCAAT 60.815 50.000 11.73 0.00 0.00 3.16
119 120 1.476652 CGTGATATGCCCATGGTCCAA 60.477 52.381 11.73 0.00 0.00 3.53
120 121 0.108396 CGTGATATGCCCATGGTCCA 59.892 55.000 11.73 7.93 0.00 4.02
121 122 1.237285 GCGTGATATGCCCATGGTCC 61.237 60.000 11.73 1.51 0.00 4.46
122 123 1.568612 CGCGTGATATGCCCATGGTC 61.569 60.000 11.73 0.00 0.00 4.02
123 124 1.597854 CGCGTGATATGCCCATGGT 60.598 57.895 11.73 0.00 0.00 3.55
124 125 2.327343 CCGCGTGATATGCCCATGG 61.327 63.158 4.14 4.14 0.00 3.66
125 126 0.674581 ATCCGCGTGATATGCCCATG 60.675 55.000 4.92 0.00 0.00 3.66
126 127 0.391661 GATCCGCGTGATATGCCCAT 60.392 55.000 4.92 0.00 32.41 4.00
127 128 1.005037 GATCCGCGTGATATGCCCA 60.005 57.895 4.92 0.00 32.41 5.36
128 129 1.005037 TGATCCGCGTGATATGCCC 60.005 57.895 4.92 0.00 32.41 5.36
129 130 1.617755 CGTGATCCGCGTGATATGCC 61.618 60.000 4.92 0.00 32.41 4.40
130 131 1.775344 CGTGATCCGCGTGATATGC 59.225 57.895 4.92 0.00 32.41 3.14
140 141 1.705337 GGTGGTTGATGCGTGATCCG 61.705 60.000 0.00 0.00 40.40 4.18
141 142 1.705337 CGGTGGTTGATGCGTGATCC 61.705 60.000 0.00 0.00 0.00 3.36
142 143 1.019278 ACGGTGGTTGATGCGTGATC 61.019 55.000 0.00 0.00 0.00 2.92
143 144 1.003839 ACGGTGGTTGATGCGTGAT 60.004 52.632 0.00 0.00 0.00 3.06
144 145 1.666553 GACGGTGGTTGATGCGTGA 60.667 57.895 0.00 0.00 0.00 4.35
145 146 2.860293 GACGGTGGTTGATGCGTG 59.140 61.111 0.00 0.00 0.00 5.34
146 147 2.736995 CGACGGTGGTTGATGCGT 60.737 61.111 0.00 0.00 0.00 5.24
147 148 3.487202 CCGACGGTGGTTGATGCG 61.487 66.667 5.48 0.00 0.00 4.73
148 149 1.449601 ATCCGACGGTGGTTGATGC 60.450 57.895 14.79 0.00 0.00 3.91
149 150 1.705337 GCATCCGACGGTGGTTGATG 61.705 60.000 14.79 10.05 38.09 3.07
150 151 1.449601 GCATCCGACGGTGGTTGAT 60.450 57.895 14.79 0.00 31.58 2.57
151 152 2.047655 GCATCCGACGGTGGTTGA 60.048 61.111 14.79 0.00 31.58 3.18
152 153 1.635663 GAAGCATCCGACGGTGGTTG 61.636 60.000 26.93 16.79 36.31 3.77
153 154 1.375523 GAAGCATCCGACGGTGGTT 60.376 57.895 24.08 24.08 38.61 3.67
154 155 2.264794 GAAGCATCCGACGGTGGT 59.735 61.111 14.79 13.79 0.00 4.16
155 156 2.511600 GGAAGCATCCGACGGTGG 60.512 66.667 14.79 8.45 35.59 4.61
163 164 1.160329 CGTTGGATCCGGAAGCATCC 61.160 60.000 9.01 12.10 42.80 3.51
164 165 2.311294 CGTTGGATCCGGAAGCATC 58.689 57.895 9.01 0.00 0.00 3.91
165 166 4.540153 CGTTGGATCCGGAAGCAT 57.460 55.556 9.01 0.00 0.00 3.79
172 173 2.360600 TTTGGGCCGTTGGATCCG 60.361 61.111 7.39 0.00 0.00 4.18
173 174 2.348104 GGTTTGGGCCGTTGGATCC 61.348 63.158 4.20 4.20 0.00 3.36
174 175 2.348104 GGGTTTGGGCCGTTGGATC 61.348 63.158 0.00 0.00 0.00 3.36
175 176 2.283604 GGGTTTGGGCCGTTGGAT 60.284 61.111 0.00 0.00 0.00 3.41
176 177 3.822035 TGGGTTTGGGCCGTTGGA 61.822 61.111 0.00 0.00 0.00 3.53
177 178 3.611674 GTGGGTTTGGGCCGTTGG 61.612 66.667 0.00 0.00 0.00 3.77
178 179 3.611674 GGTGGGTTTGGGCCGTTG 61.612 66.667 0.00 0.00 0.00 4.10
179 180 4.926162 GGGTGGGTTTGGGCCGTT 62.926 66.667 0.00 0.00 0.00 4.44
183 184 3.961414 TCTCGGGTGGGTTTGGGC 61.961 66.667 0.00 0.00 0.00 5.36
184 185 2.033602 GTCTCGGGTGGGTTTGGG 59.966 66.667 0.00 0.00 0.00 4.12
185 186 2.358247 CGTCTCGGGTGGGTTTGG 60.358 66.667 0.00 0.00 0.00 3.28
186 187 0.533308 TTTCGTCTCGGGTGGGTTTG 60.533 55.000 0.00 0.00 0.00 2.93
187 188 0.533531 GTTTCGTCTCGGGTGGGTTT 60.534 55.000 0.00 0.00 0.00 3.27
188 189 1.070275 GTTTCGTCTCGGGTGGGTT 59.930 57.895 0.00 0.00 0.00 4.11
189 190 2.739132 GTTTCGTCTCGGGTGGGT 59.261 61.111 0.00 0.00 0.00 4.51
190 191 2.047560 GGTTTCGTCTCGGGTGGG 60.048 66.667 0.00 0.00 0.00 4.61
191 192 1.252904 TAGGGTTTCGTCTCGGGTGG 61.253 60.000 0.00 0.00 0.00 4.61
192 193 0.172803 CTAGGGTTTCGTCTCGGGTG 59.827 60.000 0.00 0.00 0.00 4.61
193 194 0.969409 CCTAGGGTTTCGTCTCGGGT 60.969 60.000 0.00 0.00 0.00 5.28
194 195 0.969409 ACCTAGGGTTTCGTCTCGGG 60.969 60.000 14.81 0.00 27.29 5.14
195 196 0.455005 GACCTAGGGTTTCGTCTCGG 59.545 60.000 14.81 0.00 35.25 4.63
196 197 1.132643 CTGACCTAGGGTTTCGTCTCG 59.867 57.143 14.81 0.00 35.25 4.04
197 198 2.164017 GACTGACCTAGGGTTTCGTCTC 59.836 54.545 14.81 0.00 35.25 3.36
198 199 2.169330 GACTGACCTAGGGTTTCGTCT 58.831 52.381 14.81 0.00 35.25 4.18
199 200 1.204231 GGACTGACCTAGGGTTTCGTC 59.796 57.143 14.81 12.42 35.25 4.20
200 201 1.264295 GGACTGACCTAGGGTTTCGT 58.736 55.000 14.81 4.61 35.25 3.85
225 226 0.902984 GGGGGTGGGTGGAAAATGTC 60.903 60.000 0.00 0.00 0.00 3.06
226 227 1.157513 GGGGGTGGGTGGAAAATGT 59.842 57.895 0.00 0.00 0.00 2.71
227 228 4.128580 GGGGGTGGGTGGAAAATG 57.871 61.111 0.00 0.00 0.00 2.32
241 242 1.453928 GAAAGAATGGAGGCGGGGG 60.454 63.158 0.00 0.00 0.00 5.40
242 243 0.034089 AAGAAAGAATGGAGGCGGGG 60.034 55.000 0.00 0.00 0.00 5.73
243 244 1.383523 GAAGAAAGAATGGAGGCGGG 58.616 55.000 0.00 0.00 0.00 6.13
244 245 1.340017 TGGAAGAAAGAATGGAGGCGG 60.340 52.381 0.00 0.00 0.00 6.13
245 246 2.113860 TGGAAGAAAGAATGGAGGCG 57.886 50.000 0.00 0.00 0.00 5.52
246 247 3.382865 GGAATGGAAGAAAGAATGGAGGC 59.617 47.826 0.00 0.00 0.00 4.70
247 248 4.864726 AGGAATGGAAGAAAGAATGGAGG 58.135 43.478 0.00 0.00 0.00 4.30
248 249 4.886489 GGAGGAATGGAAGAAAGAATGGAG 59.114 45.833 0.00 0.00 0.00 3.86
249 250 4.325344 GGGAGGAATGGAAGAAAGAATGGA 60.325 45.833 0.00 0.00 0.00 3.41
250 251 3.956848 GGGAGGAATGGAAGAAAGAATGG 59.043 47.826 0.00 0.00 0.00 3.16
251 252 4.864726 AGGGAGGAATGGAAGAAAGAATG 58.135 43.478 0.00 0.00 0.00 2.67
252 253 4.079500 GGAGGGAGGAATGGAAGAAAGAAT 60.080 45.833 0.00 0.00 0.00 2.40
253 254 3.267031 GGAGGGAGGAATGGAAGAAAGAA 59.733 47.826 0.00 0.00 0.00 2.52
254 255 2.846827 GGAGGGAGGAATGGAAGAAAGA 59.153 50.000 0.00 0.00 0.00 2.52
255 256 2.092158 GGGAGGGAGGAATGGAAGAAAG 60.092 54.545 0.00 0.00 0.00 2.62
256 257 1.923148 GGGAGGGAGGAATGGAAGAAA 59.077 52.381 0.00 0.00 0.00 2.52
257 258 1.596496 GGGAGGGAGGAATGGAAGAA 58.404 55.000 0.00 0.00 0.00 2.52
258 259 0.327576 GGGGAGGGAGGAATGGAAGA 60.328 60.000 0.00 0.00 0.00 2.87
259 260 1.356494 GGGGGAGGGAGGAATGGAAG 61.356 65.000 0.00 0.00 0.00 3.46
260 261 1.308746 GGGGGAGGGAGGAATGGAA 60.309 63.158 0.00 0.00 0.00 3.53
261 262 2.376842 GGGGGAGGGAGGAATGGA 59.623 66.667 0.00 0.00 0.00 3.41
262 263 3.171388 CGGGGGAGGGAGGAATGG 61.171 72.222 0.00 0.00 0.00 3.16
263 264 3.878667 GCGGGGGAGGGAGGAATG 61.879 72.222 0.00 0.00 0.00 2.67
271 272 3.878667 GAATGGAGGCGGGGGAGG 61.879 72.222 0.00 0.00 0.00 4.30
272 273 1.926426 AAAGAATGGAGGCGGGGGAG 61.926 60.000 0.00 0.00 0.00 4.30
273 274 1.921869 GAAAGAATGGAGGCGGGGGA 61.922 60.000 0.00 0.00 0.00 4.81
274 275 1.453928 GAAAGAATGGAGGCGGGGG 60.454 63.158 0.00 0.00 0.00 5.40
275 276 1.819632 CGAAAGAATGGAGGCGGGG 60.820 63.158 0.00 0.00 0.00 5.73
276 277 2.472909 GCGAAAGAATGGAGGCGGG 61.473 63.158 0.00 0.00 0.00 6.13
277 278 1.432270 GAGCGAAAGAATGGAGGCGG 61.432 60.000 0.00 0.00 0.00 6.13
278 279 1.432270 GGAGCGAAAGAATGGAGGCG 61.432 60.000 0.00 0.00 0.00 5.52
279 280 0.392998 TGGAGCGAAAGAATGGAGGC 60.393 55.000 0.00 0.00 0.00 4.70
280 281 1.208052 TCTGGAGCGAAAGAATGGAGG 59.792 52.381 0.00 0.00 0.00 4.30
281 282 2.680312 TCTGGAGCGAAAGAATGGAG 57.320 50.000 0.00 0.00 0.00 3.86
282 283 3.535561 GAATCTGGAGCGAAAGAATGGA 58.464 45.455 0.00 0.00 0.00 3.41
283 284 2.286294 CGAATCTGGAGCGAAAGAATGG 59.714 50.000 0.00 0.00 0.00 3.16
284 285 2.286067 GCGAATCTGGAGCGAAAGAATG 60.286 50.000 0.00 0.00 0.00 2.67
285 286 1.936547 GCGAATCTGGAGCGAAAGAAT 59.063 47.619 0.00 0.00 0.00 2.40
286 287 1.359848 GCGAATCTGGAGCGAAAGAA 58.640 50.000 0.00 0.00 0.00 2.52
287 288 0.460284 GGCGAATCTGGAGCGAAAGA 60.460 55.000 0.00 0.00 0.00 2.52
288 289 0.740868 TGGCGAATCTGGAGCGAAAG 60.741 55.000 0.00 0.00 0.00 2.62
289 290 1.019278 GTGGCGAATCTGGAGCGAAA 61.019 55.000 0.00 0.00 0.00 3.46
290 291 1.447838 GTGGCGAATCTGGAGCGAA 60.448 57.895 0.00 0.00 0.00 4.70
291 292 2.184322 GTGGCGAATCTGGAGCGA 59.816 61.111 0.00 0.00 0.00 4.93
292 293 2.892425 GGTGGCGAATCTGGAGCG 60.892 66.667 0.00 0.00 0.00 5.03
293 294 2.514824 GGGTGGCGAATCTGGAGC 60.515 66.667 0.00 0.00 0.00 4.70
294 295 1.450312 GTGGGTGGCGAATCTGGAG 60.450 63.158 0.00 0.00 0.00 3.86
295 296 2.668632 GTGGGTGGCGAATCTGGA 59.331 61.111 0.00 0.00 0.00 3.86
296 297 2.819595 CGTGGGTGGCGAATCTGG 60.820 66.667 0.00 0.00 0.00 3.86
297 298 3.499737 GCGTGGGTGGCGAATCTG 61.500 66.667 0.00 0.00 0.00 2.90
298 299 4.778143 GGCGTGGGTGGCGAATCT 62.778 66.667 0.00 0.00 0.00 2.40
300 301 3.936772 ATTGGCGTGGGTGGCGAAT 62.937 57.895 0.00 0.00 34.58 3.34
301 302 4.652131 ATTGGCGTGGGTGGCGAA 62.652 61.111 0.00 0.00 37.19 4.70
305 306 2.556840 ATCTGGATTGGCGTGGGTGG 62.557 60.000 0.00 0.00 0.00 4.61
306 307 0.680921 AATCTGGATTGGCGTGGGTG 60.681 55.000 0.00 0.00 0.00 4.61
307 308 0.680921 CAATCTGGATTGGCGTGGGT 60.681 55.000 13.68 0.00 43.25 4.51
308 309 0.394216 TCAATCTGGATTGGCGTGGG 60.394 55.000 19.21 0.00 46.08 4.61
309 310 0.734889 GTCAATCTGGATTGGCGTGG 59.265 55.000 19.21 0.00 46.08 4.94
313 314 2.564771 TCATCGTCAATCTGGATTGGC 58.435 47.619 19.21 17.36 46.73 4.52
314 315 3.562973 CCTTCATCGTCAATCTGGATTGG 59.437 47.826 19.21 7.92 46.08 3.16
316 317 3.209410 GCCTTCATCGTCAATCTGGATT 58.791 45.455 0.00 0.00 0.00 3.01
317 318 2.486191 GGCCTTCATCGTCAATCTGGAT 60.486 50.000 0.00 0.00 0.00 3.41
318 319 1.134401 GGCCTTCATCGTCAATCTGGA 60.134 52.381 0.00 0.00 0.00 3.86
319 320 1.303309 GGCCTTCATCGTCAATCTGG 58.697 55.000 0.00 0.00 0.00 3.86
320 321 1.303309 GGGCCTTCATCGTCAATCTG 58.697 55.000 0.84 0.00 0.00 2.90
321 322 0.181350 GGGGCCTTCATCGTCAATCT 59.819 55.000 0.84 0.00 0.00 2.40
322 323 0.819666 GGGGGCCTTCATCGTCAATC 60.820 60.000 0.84 0.00 0.00 2.67
323 324 1.227383 GGGGGCCTTCATCGTCAAT 59.773 57.895 0.84 0.00 0.00 2.57
324 325 2.674754 GGGGGCCTTCATCGTCAA 59.325 61.111 0.84 0.00 0.00 3.18
855 856 3.773154 GAGGAGGGGAGGAGGCCT 61.773 72.222 3.86 3.86 36.03 5.19
924 928 2.454941 GTGAGGGGAAGGGAGGGA 59.545 66.667 0.00 0.00 0.00 4.20
1007 1012 1.829096 TCCACCACGGAGTCGACAA 60.829 57.895 19.50 0.00 41.61 3.18
1008 1013 2.203379 TCCACCACGGAGTCGACA 60.203 61.111 19.50 0.00 41.61 4.35
1063 1068 3.051392 GCTTGTGGCGGCGCTTAAT 62.051 57.895 32.30 0.00 0.00 1.40
1084 1089 1.377612 GGTCCTTACCCTTGCGGTT 59.622 57.895 0.00 0.00 45.36 4.44
1117 1122 1.032794 CGAACCGGATCTGGATGAGA 58.967 55.000 27.90 0.00 34.25 3.27
1228 1248 2.577563 TGGGGATGAAGATGAGCTTGAA 59.422 45.455 0.00 0.00 36.83 2.69
1289 1309 0.250989 GAGACGGGATCGGAGGAGAT 60.251 60.000 0.00 0.00 41.39 2.75
1331 1351 2.104963 GAGACAACAGGACCCAAGTCTT 59.895 50.000 7.62 0.00 43.05 3.01
1509 1533 2.616458 GCATGACCCCAGTTCCCCT 61.616 63.158 0.00 0.00 0.00 4.79
1606 1630 2.061028 GAAACATTGCAAAAGCTCCCG 58.939 47.619 1.71 0.00 0.00 5.14
1607 1631 2.061028 CGAAACATTGCAAAAGCTCCC 58.939 47.619 1.71 0.00 0.00 4.30
1657 1681 2.226200 TGCACTGAATCGACACCAATTG 59.774 45.455 0.00 0.00 0.00 2.32
1659 1683 2.183478 TGCACTGAATCGACACCAAT 57.817 45.000 0.00 0.00 0.00 3.16
1716 1740 2.018515 ACGAACCATGGACAAACGTTT 58.981 42.857 21.47 7.96 0.00 3.60
1828 1853 7.441017 TCTTATTTTACAAAAGCTTGCCATGT 58.559 30.769 0.00 6.22 35.84 3.21
1955 1980 2.018544 TTTTTGAGGTCACACGCGG 58.981 52.632 12.47 1.27 0.00 6.46
2081 2107 5.006153 TCCACATATTGTAGAAGACACCG 57.994 43.478 0.00 0.00 37.96 4.94
2123 2154 1.685765 AGACTGGTCGGCCATAGCA 60.686 57.895 10.40 5.05 45.05 3.49


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

AutoCloner maintained by Alex Coulton.