Multiple sequence alignment - TraesCS4A01G435900

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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 TraesCS4A01G435900 chr4A 100.000 3454 0 0 1 3454 705707802 705711255 0.000000e+00 6379.0
1 TraesCS4A01G435900 chr4A 89.548 354 34 1 1 354 705639776 705640126 2.450000e-121 446.0
2 TraesCS4A01G435900 chr4A 81.720 372 47 10 1 354 705694849 705695217 1.210000e-74 291.0
3 TraesCS4A01G435900 chr4A 75.159 314 54 14 54 354 616896819 616896517 3.620000e-25 126.0
4 TraesCS4A01G435900 chr7B 98.580 3098 44 0 357 3454 485468510 485465413 0.000000e+00 5478.0
5 TraesCS4A01G435900 chr7B 97.754 3117 51 6 357 3454 123774253 123771137 0.000000e+00 5350.0
6 TraesCS4A01G435900 chr7B 97.466 3118 45 7 356 3454 450591816 450594918 0.000000e+00 5289.0
7 TraesCS4A01G435900 chr7B 96.296 2457 91 0 998 3454 155733209 155730753 0.000000e+00 4034.0
8 TraesCS4A01G435900 chr7B 97.059 34 1 0 923 956 348951051 348951084 1.340000e-04 58.4
9 TraesCS4A01G435900 chr2B 98.452 3101 35 2 357 3454 338741404 338744494 0.000000e+00 5448.0
10 TraesCS4A01G435900 chr2B 96.221 2461 92 1 995 3454 309476630 309479090 0.000000e+00 4028.0
11 TraesCS4A01G435900 chr2B 95.217 230 9 2 356 583 712763514 712763743 2.530000e-96 363.0
12 TraesCS4A01G435900 chr3B 98.134 3108 47 3 356 3454 141746089 141749194 0.000000e+00 5408.0
13 TraesCS4A01G435900 chr5B 97.708 3098 68 2 357 3454 560429441 560432535 0.000000e+00 5325.0
14 TraesCS4A01G435900 chr2A 97.036 2901 62 9 356 3233 448506766 448503867 0.000000e+00 4859.0
15 TraesCS4A01G435900 chr2A 92.360 445 28 4 356 797 116443085 116442644 2.260000e-176 628.0
16 TraesCS4A01G435900 chr1A 96.260 2460 92 0 995 3454 440450176 440452635 0.000000e+00 4034.0
17 TraesCS4A01G435900 chr7D 91.808 354 29 0 1 354 22655167 22655520 8.610000e-136 494.0
18 TraesCS4A01G435900 chr5D 75.069 361 62 16 11 354 551058271 551058620 3.590000e-30 143.0


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 TraesCS4A01G435900 chr4A 705707802 705711255 3453 False 6379 6379 100.000 1 3454 1 chr4A.!!$F3 3453
1 TraesCS4A01G435900 chr7B 485465413 485468510 3097 True 5478 5478 98.580 357 3454 1 chr7B.!!$R3 3097
2 TraesCS4A01G435900 chr7B 123771137 123774253 3116 True 5350 5350 97.754 357 3454 1 chr7B.!!$R1 3097
3 TraesCS4A01G435900 chr7B 450591816 450594918 3102 False 5289 5289 97.466 356 3454 1 chr7B.!!$F2 3098
4 TraesCS4A01G435900 chr7B 155730753 155733209 2456 True 4034 4034 96.296 998 3454 1 chr7B.!!$R2 2456
5 TraesCS4A01G435900 chr2B 338741404 338744494 3090 False 5448 5448 98.452 357 3454 1 chr2B.!!$F2 3097
6 TraesCS4A01G435900 chr2B 309476630 309479090 2460 False 4028 4028 96.221 995 3454 1 chr2B.!!$F1 2459
7 TraesCS4A01G435900 chr3B 141746089 141749194 3105 False 5408 5408 98.134 356 3454 1 chr3B.!!$F1 3098
8 TraesCS4A01G435900 chr5B 560429441 560432535 3094 False 5325 5325 97.708 357 3454 1 chr5B.!!$F1 3097
9 TraesCS4A01G435900 chr2A 448503867 448506766 2899 True 4859 4859 97.036 356 3233 1 chr2A.!!$R2 2877
10 TraesCS4A01G435900 chr1A 440450176 440452635 2459 False 4034 4034 96.260 995 3454 1 chr1A.!!$F1 2459

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
32 33 0.034059 CGTGCTCTGGTCTTGACCTT 59.966 55.0 19.11 0.0 0.00 3.50 F
310 311 0.037326 GGAGTTGCGTCATGGACTCA 60.037 55.0 12.58 0.0 40.13 3.41 F
1608 1682 0.178992 TGAAACTGTTGGAGGGGCTG 60.179 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2047 1.129917 CATGTGAGCCCTCTGATCCT 58.870 55.000 0.00 0.0 0.00 3.24 R
2326 2400 4.103153 ACTGAAGGAGACCAAATTGACAGA 59.897 41.667 0.00 0.0 0.00 3.41 R
2978 3053 3.249189 GAGGGGTGTCTGGGCACA 61.249 66.667 7.63 0.0 40.89 4.57 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 2.435059 GAGTGGAAGGAGCCGTGC 60.435 66.667 0.00 0.00 0.00 5.34
18 19 2.925170 AGTGGAAGGAGCCGTGCT 60.925 61.111 0.00 0.00 43.88 4.40
27 28 2.345244 AGCCGTGCTCTGGTCTTG 59.655 61.111 0.00 0.00 30.62 3.02
28 29 2.210013 AGCCGTGCTCTGGTCTTGA 61.210 57.895 0.00 0.00 30.62 3.02
29 30 2.029844 GCCGTGCTCTGGTCTTGAC 61.030 63.158 0.00 0.00 0.00 3.18
30 31 1.374758 CCGTGCTCTGGTCTTGACC 60.375 63.158 12.54 12.54 0.00 4.02
31 32 1.668294 CGTGCTCTGGTCTTGACCT 59.332 57.895 19.11 0.00 0.00 3.85
32 33 0.034059 CGTGCTCTGGTCTTGACCTT 59.966 55.000 19.11 0.00 0.00 3.50
33 34 1.517242 GTGCTCTGGTCTTGACCTTG 58.483 55.000 19.11 12.46 0.00 3.61
34 35 0.250467 TGCTCTGGTCTTGACCTTGC 60.250 55.000 19.11 18.32 0.00 4.01
35 36 0.250467 GCTCTGGTCTTGACCTTGCA 60.250 55.000 19.11 0.03 0.00 4.08
36 37 1.805869 CTCTGGTCTTGACCTTGCAG 58.194 55.000 19.11 9.36 0.00 4.41
37 38 0.250467 TCTGGTCTTGACCTTGCAGC 60.250 55.000 19.11 0.00 0.00 5.25
38 39 1.572085 CTGGTCTTGACCTTGCAGCG 61.572 60.000 19.11 0.00 0.00 5.18
39 40 2.328099 GGTCTTGACCTTGCAGCGG 61.328 63.158 12.20 2.82 0.00 5.52
40 41 1.301716 GTCTTGACCTTGCAGCGGA 60.302 57.895 10.72 0.00 0.00 5.54
41 42 0.674895 GTCTTGACCTTGCAGCGGAT 60.675 55.000 10.72 0.00 0.00 4.18
42 43 0.674581 TCTTGACCTTGCAGCGGATG 60.675 55.000 10.72 0.00 0.00 3.51
57 58 2.407268 GATGCATTCATCCGGCACA 58.593 52.632 0.00 0.00 42.50 4.57
58 59 0.956633 GATGCATTCATCCGGCACAT 59.043 50.000 0.00 0.00 42.50 3.21
59 60 0.671796 ATGCATTCATCCGGCACATG 59.328 50.000 0.00 0.00 40.83 3.21
60 61 1.299620 GCATTCATCCGGCACATGC 60.300 57.895 0.00 4.16 41.14 4.06
70 71 2.673523 GCACATGCCCTCTGTCCT 59.326 61.111 0.00 0.00 34.31 3.85
71 72 1.451028 GCACATGCCCTCTGTCCTC 60.451 63.158 0.00 0.00 34.31 3.71
72 73 1.153489 CACATGCCCTCTGTCCTCG 60.153 63.158 0.00 0.00 0.00 4.63
73 74 1.610673 ACATGCCCTCTGTCCTCGT 60.611 57.895 0.00 0.00 0.00 4.18
74 75 1.142748 CATGCCCTCTGTCCTCGTC 59.857 63.158 0.00 0.00 0.00 4.20
75 76 1.305297 ATGCCCTCTGTCCTCGTCA 60.305 57.895 0.00 0.00 0.00 4.35
76 77 0.904865 ATGCCCTCTGTCCTCGTCAA 60.905 55.000 0.00 0.00 0.00 3.18
77 78 0.904865 TGCCCTCTGTCCTCGTCAAT 60.905 55.000 0.00 0.00 0.00 2.57
78 79 0.460987 GCCCTCTGTCCTCGTCAATG 60.461 60.000 0.00 0.00 0.00 2.82
79 80 1.186200 CCCTCTGTCCTCGTCAATGA 58.814 55.000 0.00 0.00 0.00 2.57
80 81 1.759445 CCCTCTGTCCTCGTCAATGAT 59.241 52.381 0.00 0.00 0.00 2.45
81 82 2.482664 CCCTCTGTCCTCGTCAATGATG 60.483 54.545 0.00 0.00 0.00 3.07
82 83 2.200067 CTCTGTCCTCGTCAATGATGC 58.800 52.381 0.00 0.00 0.00 3.91
83 84 1.550072 TCTGTCCTCGTCAATGATGCA 59.450 47.619 0.00 0.00 0.00 3.96
84 85 1.662629 CTGTCCTCGTCAATGATGCAC 59.337 52.381 0.00 0.00 0.00 4.57
85 86 1.276138 TGTCCTCGTCAATGATGCACT 59.724 47.619 0.00 0.00 0.00 4.40
86 87 1.929836 GTCCTCGTCAATGATGCACTC 59.070 52.381 0.00 0.00 0.00 3.51
87 88 1.134699 TCCTCGTCAATGATGCACTCC 60.135 52.381 0.00 0.00 0.00 3.85
88 89 1.405933 CCTCGTCAATGATGCACTCCA 60.406 52.381 0.00 0.00 0.00 3.86
89 90 1.662629 CTCGTCAATGATGCACTCCAC 59.337 52.381 0.00 0.00 0.00 4.02
90 91 1.276138 TCGTCAATGATGCACTCCACT 59.724 47.619 0.00 0.00 0.00 4.00
91 92 2.079158 CGTCAATGATGCACTCCACTT 58.921 47.619 0.00 0.00 0.00 3.16
92 93 2.094894 CGTCAATGATGCACTCCACTTC 59.905 50.000 0.00 0.00 0.00 3.01
93 94 3.076621 GTCAATGATGCACTCCACTTCA 58.923 45.455 0.00 0.00 0.00 3.02
94 95 3.503363 GTCAATGATGCACTCCACTTCAA 59.497 43.478 0.00 0.00 0.00 2.69
95 96 3.754850 TCAATGATGCACTCCACTTCAAG 59.245 43.478 0.00 0.00 0.00 3.02
96 97 1.527034 TGATGCACTCCACTTCAAGC 58.473 50.000 0.00 0.00 0.00 4.01
97 98 1.072806 TGATGCACTCCACTTCAAGCT 59.927 47.619 0.00 0.00 0.00 3.74
98 99 2.157738 GATGCACTCCACTTCAAGCTT 58.842 47.619 0.00 0.00 0.00 3.74
99 100 1.311859 TGCACTCCACTTCAAGCTTG 58.688 50.000 20.81 20.81 0.00 4.01
100 101 0.595095 GCACTCCACTTCAAGCTTGG 59.405 55.000 25.73 13.43 0.00 3.61
101 102 1.242076 CACTCCACTTCAAGCTTGGG 58.758 55.000 25.73 18.32 0.00 4.12
102 103 0.846693 ACTCCACTTCAAGCTTGGGT 59.153 50.000 25.73 20.38 0.00 4.51
103 104 2.054799 ACTCCACTTCAAGCTTGGGTA 58.945 47.619 25.73 11.01 0.00 3.69
104 105 2.224548 ACTCCACTTCAAGCTTGGGTAC 60.225 50.000 25.73 0.00 0.00 3.34
134 135 7.991084 TGATAATGATCATGTGGGAATTCTC 57.009 36.000 9.46 0.82 37.15 2.87
135 136 7.519927 TGATAATGATCATGTGGGAATTCTCA 58.480 34.615 9.46 3.16 37.15 3.27
136 137 8.000127 TGATAATGATCATGTGGGAATTCTCAA 59.000 33.333 10.26 1.02 37.15 3.02
137 138 6.710597 AATGATCATGTGGGAATTCTCAAG 57.289 37.500 10.26 3.46 0.00 3.02
138 139 5.183530 TGATCATGTGGGAATTCTCAAGT 57.816 39.130 10.26 0.00 0.00 3.16
139 140 6.312141 TGATCATGTGGGAATTCTCAAGTA 57.688 37.500 10.26 0.00 0.00 2.24
140 141 6.115446 TGATCATGTGGGAATTCTCAAGTAC 58.885 40.000 10.26 0.00 0.00 2.73
141 142 5.497464 TCATGTGGGAATTCTCAAGTACA 57.503 39.130 10.26 4.06 0.00 2.90
142 143 5.875224 TCATGTGGGAATTCTCAAGTACAA 58.125 37.500 10.26 0.00 0.00 2.41
143 144 5.705441 TCATGTGGGAATTCTCAAGTACAAC 59.295 40.000 10.26 0.00 0.00 3.32
144 145 5.304686 TGTGGGAATTCTCAAGTACAACT 57.695 39.130 10.26 0.00 0.00 3.16
145 146 5.690865 TGTGGGAATTCTCAAGTACAACTT 58.309 37.500 10.26 0.00 39.39 2.66
156 157 4.772886 AAGTACAACTTGACCTCTGGTT 57.227 40.909 0.00 0.00 37.00 3.67
157 158 4.338379 AGTACAACTTGACCTCTGGTTC 57.662 45.455 0.00 0.00 35.25 3.62
158 159 3.967987 AGTACAACTTGACCTCTGGTTCT 59.032 43.478 0.00 0.00 35.25 3.01
159 160 3.933861 ACAACTTGACCTCTGGTTCTT 57.066 42.857 0.00 0.00 35.25 2.52
160 161 4.236527 ACAACTTGACCTCTGGTTCTTT 57.763 40.909 0.00 0.00 35.25 2.52
161 162 5.367945 ACAACTTGACCTCTGGTTCTTTA 57.632 39.130 0.00 0.00 35.25 1.85
162 163 5.123936 ACAACTTGACCTCTGGTTCTTTAC 58.876 41.667 0.00 0.00 35.25 2.01
177 178 5.807011 GGTTCTTTACCATTGATTGATGTGC 59.193 40.000 0.00 0.00 46.92 4.57
178 179 5.581126 TCTTTACCATTGATTGATGTGCC 57.419 39.130 0.00 0.00 0.00 5.01
179 180 5.015515 TCTTTACCATTGATTGATGTGCCA 58.984 37.500 0.00 0.00 0.00 4.92
180 181 4.717233 TTACCATTGATTGATGTGCCAC 57.283 40.909 0.00 0.00 0.00 5.01
181 182 2.811410 ACCATTGATTGATGTGCCACT 58.189 42.857 0.00 0.00 0.00 4.00
182 183 3.167485 ACCATTGATTGATGTGCCACTT 58.833 40.909 0.00 0.00 0.00 3.16
183 184 3.056393 ACCATTGATTGATGTGCCACTTG 60.056 43.478 0.00 0.00 0.00 3.16
184 185 2.728690 TTGATTGATGTGCCACTTGC 57.271 45.000 0.00 0.00 41.77 4.01
185 186 0.889994 TGATTGATGTGCCACTTGCC 59.110 50.000 0.00 0.00 40.16 4.52
186 187 0.179156 GATTGATGTGCCACTTGCCG 60.179 55.000 0.00 0.00 40.16 5.69
187 188 2.216750 ATTGATGTGCCACTTGCCGC 62.217 55.000 0.00 0.00 40.16 6.53
188 189 3.058160 GATGTGCCACTTGCCGCT 61.058 61.111 0.00 0.00 40.16 5.52
189 190 3.044059 GATGTGCCACTTGCCGCTC 62.044 63.158 0.00 0.00 40.16 5.03
198 199 4.136511 TTGCCGCTCGTGCCGATA 62.137 61.111 3.52 0.00 34.61 2.92
199 200 3.439513 TTGCCGCTCGTGCCGATAT 62.440 57.895 3.52 0.00 34.61 1.63
200 201 3.106407 GCCGCTCGTGCCGATATC 61.106 66.667 3.52 0.00 34.61 1.63
201 202 2.645567 CCGCTCGTGCCGATATCT 59.354 61.111 3.52 0.00 34.61 1.98
202 203 1.007271 CCGCTCGTGCCGATATCTT 60.007 57.895 3.52 0.00 34.61 2.40
203 204 1.004277 CCGCTCGTGCCGATATCTTC 61.004 60.000 3.52 0.00 34.61 2.87
204 205 0.317854 CGCTCGTGCCGATATCTTCA 60.318 55.000 3.52 0.00 34.61 3.02
205 206 1.667177 CGCTCGTGCCGATATCTTCAT 60.667 52.381 3.52 0.00 34.61 2.57
206 207 1.723542 GCTCGTGCCGATATCTTCATG 59.276 52.381 0.34 4.37 34.61 3.07
207 208 1.723542 CTCGTGCCGATATCTTCATGC 59.276 52.381 0.34 0.00 34.61 4.06
208 209 0.792640 CGTGCCGATATCTTCATGCC 59.207 55.000 0.34 0.00 0.00 4.40
209 210 0.792640 GTGCCGATATCTTCATGCCG 59.207 55.000 0.34 0.00 0.00 5.69
210 211 0.678950 TGCCGATATCTTCATGCCGA 59.321 50.000 0.34 0.00 0.00 5.54
211 212 1.276138 TGCCGATATCTTCATGCCGAT 59.724 47.619 0.34 0.00 0.00 4.18
212 213 1.662629 GCCGATATCTTCATGCCGATG 59.337 52.381 0.34 0.00 0.00 3.84
213 214 2.675032 GCCGATATCTTCATGCCGATGA 60.675 50.000 0.34 0.00 36.78 2.92
214 215 3.588955 CCGATATCTTCATGCCGATGAA 58.411 45.455 0.34 0.00 44.73 2.57
220 221 1.971481 TTCATGCCGATGAAGGATGG 58.029 50.000 0.00 0.00 42.56 3.51
221 222 2.086832 TTCATGCCGATGAAGGATGGC 61.087 52.381 0.00 0.00 42.56 4.40
223 224 3.741860 GCCGATGAAGGATGGCAG 58.258 61.111 0.00 0.00 46.76 4.85
224 225 1.153086 GCCGATGAAGGATGGCAGT 60.153 57.895 0.00 0.00 46.76 4.40
225 226 1.162800 GCCGATGAAGGATGGCAGTC 61.163 60.000 0.00 0.00 46.76 3.51
226 227 0.467384 CCGATGAAGGATGGCAGTCT 59.533 55.000 0.00 0.00 0.00 3.24
227 228 1.579698 CGATGAAGGATGGCAGTCTG 58.420 55.000 0.00 0.00 0.00 3.51
228 229 1.809271 CGATGAAGGATGGCAGTCTGG 60.809 57.143 1.14 0.00 0.00 3.86
229 230 0.549950 ATGAAGGATGGCAGTCTGGG 59.450 55.000 1.14 0.00 0.00 4.45
230 231 1.225704 GAAGGATGGCAGTCTGGGG 59.774 63.158 1.14 0.00 0.00 4.96
231 232 1.229951 AAGGATGGCAGTCTGGGGA 60.230 57.895 1.14 0.00 0.00 4.81
232 233 0.625683 AAGGATGGCAGTCTGGGGAT 60.626 55.000 1.14 0.00 0.00 3.85
233 234 0.625683 AGGATGGCAGTCTGGGGATT 60.626 55.000 1.14 0.00 0.00 3.01
234 235 0.466922 GGATGGCAGTCTGGGGATTG 60.467 60.000 1.14 0.00 33.17 2.67
239 240 3.583054 CAGTCTGGGGATTGCACAT 57.417 52.632 0.00 0.00 0.00 3.21
240 241 1.100510 CAGTCTGGGGATTGCACATG 58.899 55.000 0.00 0.00 0.00 3.21
241 242 0.700564 AGTCTGGGGATTGCACATGT 59.299 50.000 0.00 0.00 0.00 3.21
242 243 1.076024 AGTCTGGGGATTGCACATGTT 59.924 47.619 0.00 0.00 0.00 2.71
243 244 1.203052 GTCTGGGGATTGCACATGTTG 59.797 52.381 0.00 0.00 0.00 3.33
244 245 1.075212 TCTGGGGATTGCACATGTTGA 59.925 47.619 0.00 0.00 0.00 3.18
245 246 1.203052 CTGGGGATTGCACATGTTGAC 59.797 52.381 0.00 0.00 0.00 3.18
246 247 1.255882 GGGGATTGCACATGTTGACA 58.744 50.000 0.00 0.00 0.00 3.58
247 248 1.203052 GGGGATTGCACATGTTGACAG 59.797 52.381 0.00 0.00 0.00 3.51
248 249 1.403249 GGGATTGCACATGTTGACAGC 60.403 52.381 0.00 0.00 0.00 4.40
249 250 1.270274 GGATTGCACATGTTGACAGCA 59.730 47.619 3.84 3.84 0.00 4.41
250 251 2.592194 GATTGCACATGTTGACAGCAG 58.408 47.619 7.72 0.00 36.47 4.24
251 252 0.669619 TTGCACATGTTGACAGCAGG 59.330 50.000 7.72 2.19 36.47 4.85
252 253 0.466007 TGCACATGTTGACAGCAGGT 60.466 50.000 3.60 3.60 0.00 4.00
253 254 0.670162 GCACATGTTGACAGCAGGTT 59.330 50.000 6.87 0.00 0.00 3.50
254 255 1.879380 GCACATGTTGACAGCAGGTTA 59.121 47.619 6.87 0.00 0.00 2.85
255 256 2.293122 GCACATGTTGACAGCAGGTTAA 59.707 45.455 6.87 0.00 0.00 2.01
256 257 3.853307 GCACATGTTGACAGCAGGTTAAC 60.853 47.826 6.87 8.60 44.02 2.01
257 258 2.884639 ACATGTTGACAGCAGGTTAACC 59.115 45.455 17.41 17.41 43.33 2.85
258 259 1.975660 TGTTGACAGCAGGTTAACCC 58.024 50.000 21.30 6.91 43.33 4.11
260 261 2.152016 GTTGACAGCAGGTTAACCCTC 58.848 52.381 21.30 12.80 43.86 4.30
261 262 1.729586 TGACAGCAGGTTAACCCTCT 58.270 50.000 21.30 14.86 43.86 3.69
262 263 2.897350 TGACAGCAGGTTAACCCTCTA 58.103 47.619 21.30 1.30 43.86 2.43
263 264 2.565834 TGACAGCAGGTTAACCCTCTAC 59.434 50.000 21.30 14.30 43.86 2.59
264 265 1.549170 ACAGCAGGTTAACCCTCTACG 59.451 52.381 21.30 9.62 43.86 3.51
265 266 1.549170 CAGCAGGTTAACCCTCTACGT 59.451 52.381 21.30 0.00 43.86 3.57
266 267 1.549170 AGCAGGTTAACCCTCTACGTG 59.451 52.381 21.30 11.76 43.86 4.49
267 268 1.274447 GCAGGTTAACCCTCTACGTGT 59.726 52.381 21.30 0.00 43.86 4.49
268 269 2.929592 GCAGGTTAACCCTCTACGTGTG 60.930 54.545 21.30 10.34 43.86 3.82
269 270 1.897802 AGGTTAACCCTCTACGTGTGG 59.102 52.381 21.30 0.00 40.71 4.17
270 271 1.620323 GGTTAACCCTCTACGTGTGGT 59.380 52.381 14.16 0.00 0.00 4.16
271 272 2.353109 GGTTAACCCTCTACGTGTGGTC 60.353 54.545 14.16 0.00 0.00 4.02
272 273 1.549203 TAACCCTCTACGTGTGGTCC 58.451 55.000 0.00 0.00 0.00 4.46
273 274 0.470456 AACCCTCTACGTGTGGTCCA 60.470 55.000 0.00 0.00 0.00 4.02
274 275 0.898789 ACCCTCTACGTGTGGTCCAG 60.899 60.000 0.00 0.00 0.00 3.86
275 276 0.611062 CCCTCTACGTGTGGTCCAGA 60.611 60.000 0.00 0.00 0.00 3.86
276 277 0.526662 CCTCTACGTGTGGTCCAGAC 59.473 60.000 9.15 9.15 0.00 3.51
277 278 1.244816 CTCTACGTGTGGTCCAGACA 58.755 55.000 18.58 0.00 0.00 3.41
278 279 1.611977 CTCTACGTGTGGTCCAGACAA 59.388 52.381 18.58 5.62 0.00 3.18
279 280 2.033372 TCTACGTGTGGTCCAGACAAA 58.967 47.619 18.58 5.28 0.00 2.83
280 281 2.631062 TCTACGTGTGGTCCAGACAAAT 59.369 45.455 18.58 6.41 0.00 2.32
281 282 3.827876 TCTACGTGTGGTCCAGACAAATA 59.172 43.478 18.58 7.17 0.00 1.40
282 283 3.040147 ACGTGTGGTCCAGACAAATAG 57.960 47.619 18.58 4.90 0.00 1.73
283 284 2.631062 ACGTGTGGTCCAGACAAATAGA 59.369 45.455 18.58 0.00 0.00 1.98
284 285 3.260884 ACGTGTGGTCCAGACAAATAGAT 59.739 43.478 18.58 0.00 0.00 1.98
285 286 4.253685 CGTGTGGTCCAGACAAATAGATT 58.746 43.478 18.58 0.00 0.00 2.40
286 287 4.330074 CGTGTGGTCCAGACAAATAGATTC 59.670 45.833 18.58 0.00 0.00 2.52
287 288 4.636206 GTGTGGTCCAGACAAATAGATTCC 59.364 45.833 14.17 0.00 0.00 3.01
288 289 4.288366 TGTGGTCCAGACAAATAGATTCCA 59.712 41.667 0.00 0.00 0.00 3.53
289 290 5.222027 TGTGGTCCAGACAAATAGATTCCAA 60.222 40.000 0.00 0.00 0.00 3.53
290 291 5.123979 GTGGTCCAGACAAATAGATTCCAAC 59.876 44.000 0.00 0.00 0.00 3.77
291 292 4.332819 GGTCCAGACAAATAGATTCCAACG 59.667 45.833 0.00 0.00 0.00 4.10
292 293 4.332819 GTCCAGACAAATAGATTCCAACGG 59.667 45.833 0.00 0.00 0.00 4.44
293 294 4.224147 TCCAGACAAATAGATTCCAACGGA 59.776 41.667 0.00 0.00 0.00 4.69
294 295 4.572389 CCAGACAAATAGATTCCAACGGAG 59.428 45.833 0.00 0.00 31.21 4.63
306 307 3.056458 ACGGAGTTGCGTCATGGA 58.944 55.556 0.00 0.00 37.78 3.41
307 308 1.374252 ACGGAGTTGCGTCATGGAC 60.374 57.895 0.00 0.00 37.78 4.02
308 309 1.079819 CGGAGTTGCGTCATGGACT 60.080 57.895 0.00 0.00 0.00 3.85
309 310 1.078759 CGGAGTTGCGTCATGGACTC 61.079 60.000 0.00 0.00 38.19 3.36
310 311 0.037326 GGAGTTGCGTCATGGACTCA 60.037 55.000 12.58 0.00 40.13 3.41
311 312 1.406069 GGAGTTGCGTCATGGACTCAT 60.406 52.381 12.58 0.00 40.13 2.90
325 326 2.509166 ACTCATGGTAGAGTCGTGGA 57.491 50.000 0.00 0.00 45.35 4.02
326 327 3.019799 ACTCATGGTAGAGTCGTGGAT 57.980 47.619 0.00 0.00 45.35 3.41
327 328 2.952978 ACTCATGGTAGAGTCGTGGATC 59.047 50.000 0.00 0.00 45.35 3.36
328 329 3.218453 CTCATGGTAGAGTCGTGGATCT 58.782 50.000 0.00 0.00 0.00 2.75
329 330 3.215151 TCATGGTAGAGTCGTGGATCTC 58.785 50.000 0.00 0.00 0.00 2.75
330 331 2.801077 TGGTAGAGTCGTGGATCTCA 57.199 50.000 0.00 0.00 33.63 3.27
331 332 3.081710 TGGTAGAGTCGTGGATCTCAA 57.918 47.619 0.00 0.00 33.63 3.02
332 333 3.017442 TGGTAGAGTCGTGGATCTCAAG 58.983 50.000 0.00 0.00 33.63 3.02
333 334 3.280295 GGTAGAGTCGTGGATCTCAAGA 58.720 50.000 0.00 0.00 33.63 3.02
334 335 3.695060 GGTAGAGTCGTGGATCTCAAGAA 59.305 47.826 0.00 0.00 35.75 2.52
335 336 3.859411 AGAGTCGTGGATCTCAAGAAC 57.141 47.619 0.00 0.00 35.75 3.01
336 337 2.494073 AGAGTCGTGGATCTCAAGAACC 59.506 50.000 0.00 0.00 35.75 3.62
337 338 2.494073 GAGTCGTGGATCTCAAGAACCT 59.506 50.000 7.70 0.00 37.81 3.50
338 339 2.900546 AGTCGTGGATCTCAAGAACCTT 59.099 45.455 7.70 0.00 37.81 3.50
339 340 4.087182 AGTCGTGGATCTCAAGAACCTTA 58.913 43.478 7.70 0.00 37.81 2.69
340 341 4.082136 AGTCGTGGATCTCAAGAACCTTAC 60.082 45.833 7.70 3.92 37.81 2.34
341 342 3.194968 TCGTGGATCTCAAGAACCTTACC 59.805 47.826 7.70 0.00 37.81 2.85
342 343 3.679083 CGTGGATCTCAAGAACCTTACCC 60.679 52.174 7.70 0.00 37.81 3.69
343 344 2.844348 TGGATCTCAAGAACCTTACCCC 59.156 50.000 7.70 0.00 37.81 4.95
344 345 3.116174 GGATCTCAAGAACCTTACCCCT 58.884 50.000 0.00 0.00 34.54 4.79
345 346 4.265124 TGGATCTCAAGAACCTTACCCCTA 60.265 45.833 7.70 0.00 37.81 3.53
346 347 4.908481 GGATCTCAAGAACCTTACCCCTAT 59.092 45.833 0.00 0.00 34.54 2.57
347 348 5.369993 GGATCTCAAGAACCTTACCCCTATT 59.630 44.000 0.00 0.00 34.54 1.73
348 349 6.557633 GGATCTCAAGAACCTTACCCCTATTA 59.442 42.308 0.00 0.00 34.54 0.98
349 350 7.072076 GGATCTCAAGAACCTTACCCCTATTAA 59.928 40.741 0.00 0.00 34.54 1.40
350 351 7.817910 TCTCAAGAACCTTACCCCTATTAAA 57.182 36.000 0.00 0.00 0.00 1.52
351 352 8.222138 TCTCAAGAACCTTACCCCTATTAAAA 57.778 34.615 0.00 0.00 0.00 1.52
352 353 8.671409 TCTCAAGAACCTTACCCCTATTAAAAA 58.329 33.333 0.00 0.00 0.00 1.94
353 354 9.475620 CTCAAGAACCTTACCCCTATTAAAAAT 57.524 33.333 0.00 0.00 0.00 1.82
354 355 9.831682 TCAAGAACCTTACCCCTATTAAAAATT 57.168 29.630 0.00 0.00 0.00 1.82
366 367 7.094118 CCCCTATTAAAAATTCTGTTGAACCGA 60.094 37.037 0.00 0.00 34.71 4.69
441 442 1.500474 CTGACCTAGAAGGGGCATCA 58.500 55.000 0.00 0.00 44.35 3.07
755 814 1.004560 CGAAGGAGGAGTGCTTGCA 60.005 57.895 0.00 0.00 33.83 4.08
1122 1196 0.537188 AGATCGAACTGCCGTCCATT 59.463 50.000 0.00 0.00 0.00 3.16
1573 1647 1.377202 TCAGGGCGCAAGTGGATTC 60.377 57.895 10.83 0.00 41.68 2.52
1608 1682 0.178992 TGAAACTGTTGGAGGGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
1782 1856 2.236223 CTGAGCGCATGGAGTGGAGT 62.236 60.000 11.47 0.00 0.00 3.85
1973 2047 1.075536 TGGCTACTCAGGACACTCAGA 59.924 52.381 0.00 0.00 0.00 3.27
2326 2400 4.126437 GGTTTTACATGTGCCAGCTTTTT 58.874 39.130 9.11 0.00 0.00 1.94
2758 2833 5.981315 CCAGTTGTATCAATGAATGGAATGC 59.019 40.000 0.00 0.00 0.00 3.56
2792 2867 5.698089 TGACATTCATCGATTGCTATTCTCC 59.302 40.000 0.00 0.00 0.00 3.71
2978 3053 9.300681 TGATCAAGGTATTCTTCATCAAACTTT 57.699 29.630 0.00 0.00 39.49 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.435059 GCACGGCTCCTTCCACTC 60.435 66.667 0.00 0.00 0.00 3.51
1 2 2.925170 AGCACGGCTCCTTCCACT 60.925 61.111 0.00 0.00 30.62 4.00
10 11 2.210013 TCAAGACCAGAGCACGGCT 61.210 57.895 0.00 0.00 43.88 5.52
11 12 2.029844 GTCAAGACCAGAGCACGGC 61.030 63.158 0.00 0.00 0.00 5.68
12 13 4.268687 GTCAAGACCAGAGCACGG 57.731 61.111 0.00 0.00 0.00 4.94
22 23 0.674895 ATCCGCTGCAAGGTCAAGAC 60.675 55.000 0.00 0.00 0.00 3.01
23 24 0.674581 CATCCGCTGCAAGGTCAAGA 60.675 55.000 0.00 0.00 0.00 3.02
24 25 1.798735 CATCCGCTGCAAGGTCAAG 59.201 57.895 0.00 0.00 0.00 3.02
25 26 3.985877 CATCCGCTGCAAGGTCAA 58.014 55.556 0.00 0.00 0.00 3.18
40 41 0.671796 CATGTGCCGGATGAATGCAT 59.328 50.000 5.05 0.00 37.34 3.96
41 42 2.007113 GCATGTGCCGGATGAATGCA 62.007 55.000 20.35 0.00 42.48 3.96
42 43 1.299620 GCATGTGCCGGATGAATGC 60.300 57.895 5.05 10.94 37.12 3.56
53 54 1.451028 GAGGACAGAGGGCATGTGC 60.451 63.158 0.00 0.00 39.10 4.57
54 55 1.153489 CGAGGACAGAGGGCATGTG 60.153 63.158 0.00 0.00 0.00 3.21
55 56 1.608717 GACGAGGACAGAGGGCATGT 61.609 60.000 0.00 0.00 0.00 3.21
56 57 1.142748 GACGAGGACAGAGGGCATG 59.857 63.158 0.00 0.00 0.00 4.06
57 58 0.904865 TTGACGAGGACAGAGGGCAT 60.905 55.000 0.00 0.00 0.00 4.40
58 59 0.904865 ATTGACGAGGACAGAGGGCA 60.905 55.000 0.00 0.00 0.00 5.36
59 60 0.460987 CATTGACGAGGACAGAGGGC 60.461 60.000 0.00 0.00 0.00 5.19
60 61 1.186200 TCATTGACGAGGACAGAGGG 58.814 55.000 0.00 0.00 0.00 4.30
61 62 2.819115 CATCATTGACGAGGACAGAGG 58.181 52.381 0.00 0.00 0.00 3.69
62 63 2.200067 GCATCATTGACGAGGACAGAG 58.800 52.381 0.00 0.00 0.00 3.35
63 64 1.550072 TGCATCATTGACGAGGACAGA 59.450 47.619 0.00 0.00 0.00 3.41
64 65 1.662629 GTGCATCATTGACGAGGACAG 59.337 52.381 0.00 0.00 0.00 3.51
65 66 1.276138 AGTGCATCATTGACGAGGACA 59.724 47.619 0.00 0.00 0.00 4.02
66 67 1.929836 GAGTGCATCATTGACGAGGAC 59.070 52.381 0.00 0.00 0.00 3.85
67 68 1.134699 GGAGTGCATCATTGACGAGGA 60.135 52.381 0.00 0.00 0.00 3.71
68 69 1.293924 GGAGTGCATCATTGACGAGG 58.706 55.000 0.00 0.00 0.00 4.63
69 70 1.662629 GTGGAGTGCATCATTGACGAG 59.337 52.381 0.00 0.00 0.00 4.18
70 71 1.276138 AGTGGAGTGCATCATTGACGA 59.724 47.619 0.00 0.00 0.00 4.20
71 72 1.730501 AGTGGAGTGCATCATTGACG 58.269 50.000 0.00 0.00 0.00 4.35
72 73 3.076621 TGAAGTGGAGTGCATCATTGAC 58.923 45.455 0.00 0.00 0.00 3.18
73 74 3.421919 TGAAGTGGAGTGCATCATTGA 57.578 42.857 0.00 0.00 0.00 2.57
74 75 3.672511 GCTTGAAGTGGAGTGCATCATTG 60.673 47.826 0.00 0.00 0.00 2.82
75 76 2.490903 GCTTGAAGTGGAGTGCATCATT 59.509 45.455 0.00 0.00 0.00 2.57
76 77 2.089980 GCTTGAAGTGGAGTGCATCAT 58.910 47.619 0.00 0.00 0.00 2.45
77 78 1.072806 AGCTTGAAGTGGAGTGCATCA 59.927 47.619 0.00 0.00 0.00 3.07
78 79 1.818642 AGCTTGAAGTGGAGTGCATC 58.181 50.000 0.00 0.00 0.00 3.91
79 80 1.884579 CAAGCTTGAAGTGGAGTGCAT 59.115 47.619 22.31 0.00 0.00 3.96
80 81 1.311859 CAAGCTTGAAGTGGAGTGCA 58.688 50.000 22.31 0.00 0.00 4.57
81 82 0.595095 CCAAGCTTGAAGTGGAGTGC 59.405 55.000 28.05 0.00 34.05 4.40
82 83 1.242076 CCCAAGCTTGAAGTGGAGTG 58.758 55.000 28.05 7.28 34.05 3.51
83 84 0.846693 ACCCAAGCTTGAAGTGGAGT 59.153 50.000 28.05 8.62 34.05 3.85
84 85 2.427506 GTACCCAAGCTTGAAGTGGAG 58.572 52.381 28.05 8.76 34.05 3.86
85 86 1.073284 GGTACCCAAGCTTGAAGTGGA 59.927 52.381 28.05 7.03 34.05 4.02
86 87 1.202879 TGGTACCCAAGCTTGAAGTGG 60.203 52.381 28.05 21.03 0.00 4.00
87 88 2.270352 TGGTACCCAAGCTTGAAGTG 57.730 50.000 28.05 14.56 0.00 3.16
94 95 7.961457 GATCATTATCATCTTGGTACCCAAGCT 60.961 40.741 16.46 5.90 44.17 3.74
95 96 6.150140 GATCATTATCATCTTGGTACCCAAGC 59.850 42.308 16.46 0.00 44.17 4.01
96 97 7.678947 GATCATTATCATCTTGGTACCCAAG 57.321 40.000 15.38 15.38 44.89 3.61
97 98 7.147958 TGATCATTATCATCTTGGTACCCAA 57.852 36.000 10.07 3.05 37.94 4.12
98 99 6.762077 TGATCATTATCATCTTGGTACCCA 57.238 37.500 10.07 0.00 37.20 4.51
110 111 7.519927 TGAGAATTCCCACATGATCATTATCA 58.480 34.615 5.16 0.02 46.01 2.15
111 112 7.991084 TGAGAATTCCCACATGATCATTATC 57.009 36.000 5.16 0.00 0.00 1.75
112 113 8.003044 ACTTGAGAATTCCCACATGATCATTAT 58.997 33.333 5.16 0.00 0.00 1.28
113 114 7.348815 ACTTGAGAATTCCCACATGATCATTA 58.651 34.615 5.16 0.00 0.00 1.90
114 115 6.192773 ACTTGAGAATTCCCACATGATCATT 58.807 36.000 5.16 0.00 0.00 2.57
115 116 5.763355 ACTTGAGAATTCCCACATGATCAT 58.237 37.500 1.18 1.18 0.00 2.45
116 117 5.183530 ACTTGAGAATTCCCACATGATCA 57.816 39.130 0.00 0.00 0.00 2.92
117 118 6.115446 TGTACTTGAGAATTCCCACATGATC 58.885 40.000 0.00 0.00 0.00 2.92
118 119 6.065976 TGTACTTGAGAATTCCCACATGAT 57.934 37.500 0.00 0.00 0.00 2.45
119 120 5.497464 TGTACTTGAGAATTCCCACATGA 57.503 39.130 0.00 0.00 0.00 3.07
120 121 5.707298 AGTTGTACTTGAGAATTCCCACATG 59.293 40.000 0.65 5.71 0.00 3.21
121 122 5.880901 AGTTGTACTTGAGAATTCCCACAT 58.119 37.500 0.65 0.00 0.00 3.21
122 123 5.304686 AGTTGTACTTGAGAATTCCCACA 57.695 39.130 0.65 0.00 0.00 4.17
135 136 4.409247 AGAACCAGAGGTCAAGTTGTACTT 59.591 41.667 2.11 0.00 34.79 2.24
136 137 3.967987 AGAACCAGAGGTCAAGTTGTACT 59.032 43.478 2.11 2.33 33.12 2.73
137 138 4.338379 AGAACCAGAGGTCAAGTTGTAC 57.662 45.455 2.11 0.15 33.12 2.90
138 139 5.367945 AAAGAACCAGAGGTCAAGTTGTA 57.632 39.130 2.11 0.00 33.12 2.41
139 140 3.933861 AAGAACCAGAGGTCAAGTTGT 57.066 42.857 2.11 0.00 33.12 3.32
140 141 5.674933 GTAAAGAACCAGAGGTCAAGTTG 57.325 43.478 0.00 0.00 33.12 3.16
154 155 5.807011 GGCACATCAATCAATGGTAAAGAAC 59.193 40.000 0.00 0.00 0.00 3.01
155 156 5.479724 TGGCACATCAATCAATGGTAAAGAA 59.520 36.000 0.00 0.00 0.00 2.52
156 157 5.015515 TGGCACATCAATCAATGGTAAAGA 58.984 37.500 0.00 0.00 0.00 2.52
157 158 5.104374 GTGGCACATCAATCAATGGTAAAG 58.896 41.667 13.86 0.00 44.52 1.85
158 159 4.771577 AGTGGCACATCAATCAATGGTAAA 59.228 37.500 21.41 0.00 44.52 2.01
159 160 4.343231 AGTGGCACATCAATCAATGGTAA 58.657 39.130 21.41 0.00 44.52 2.85
160 161 3.966979 AGTGGCACATCAATCAATGGTA 58.033 40.909 21.41 0.00 44.52 3.25
161 162 2.811410 AGTGGCACATCAATCAATGGT 58.189 42.857 21.41 0.00 44.52 3.55
162 163 3.517602 CAAGTGGCACATCAATCAATGG 58.482 45.455 21.41 0.00 44.52 3.16
163 164 2.927477 GCAAGTGGCACATCAATCAATG 59.073 45.455 21.41 5.41 44.52 2.82
164 165 3.241067 GCAAGTGGCACATCAATCAAT 57.759 42.857 21.41 0.00 44.52 2.57
165 166 2.728690 GCAAGTGGCACATCAATCAA 57.271 45.000 21.41 0.00 44.52 2.57
190 191 0.792640 CGGCATGAAGATATCGGCAC 59.207 55.000 0.00 0.00 33.85 5.01
191 192 0.678950 TCGGCATGAAGATATCGGCA 59.321 50.000 0.00 0.02 33.85 5.69
192 193 1.662629 CATCGGCATGAAGATATCGGC 59.337 52.381 0.00 0.00 30.57 5.54
193 194 3.236632 TCATCGGCATGAAGATATCGG 57.763 47.619 0.00 0.00 35.99 4.18
201 202 1.971481 CCATCCTTCATCGGCATGAA 58.029 50.000 0.00 10.49 45.20 2.57
202 203 0.535780 GCCATCCTTCATCGGCATGA 60.536 55.000 0.00 0.00 44.25 3.07
203 204 1.954528 GCCATCCTTCATCGGCATG 59.045 57.895 0.00 0.00 44.25 4.06
204 205 4.488790 GCCATCCTTCATCGGCAT 57.511 55.556 0.00 0.00 44.25 4.40
206 207 1.153086 ACTGCCATCCTTCATCGGC 60.153 57.895 0.00 0.00 45.11 5.54
207 208 0.467384 AGACTGCCATCCTTCATCGG 59.533 55.000 0.00 0.00 0.00 4.18
208 209 1.579698 CAGACTGCCATCCTTCATCG 58.420 55.000 0.00 0.00 0.00 3.84
209 210 1.476471 CCCAGACTGCCATCCTTCATC 60.476 57.143 0.00 0.00 0.00 2.92
210 211 0.549950 CCCAGACTGCCATCCTTCAT 59.450 55.000 0.00 0.00 0.00 2.57
211 212 1.565390 CCCCAGACTGCCATCCTTCA 61.565 60.000 0.00 0.00 0.00 3.02
212 213 1.225704 CCCCAGACTGCCATCCTTC 59.774 63.158 0.00 0.00 0.00 3.46
213 214 0.625683 ATCCCCAGACTGCCATCCTT 60.626 55.000 0.00 0.00 0.00 3.36
214 215 0.625683 AATCCCCAGACTGCCATCCT 60.626 55.000 0.00 0.00 0.00 3.24
215 216 0.466922 CAATCCCCAGACTGCCATCC 60.467 60.000 0.00 0.00 0.00 3.51
216 217 1.105759 GCAATCCCCAGACTGCCATC 61.106 60.000 0.00 0.00 39.34 3.51
217 218 1.076485 GCAATCCCCAGACTGCCAT 60.076 57.895 0.00 0.00 39.34 4.40
218 219 2.356278 GCAATCCCCAGACTGCCA 59.644 61.111 0.00 0.00 39.34 4.92
219 220 2.048603 GTGCAATCCCCAGACTGCC 61.049 63.158 0.00 0.00 44.63 4.85
220 221 0.682209 ATGTGCAATCCCCAGACTGC 60.682 55.000 0.00 0.00 45.45 4.40
221 222 1.100510 CATGTGCAATCCCCAGACTG 58.899 55.000 0.00 0.00 0.00 3.51
222 223 0.700564 ACATGTGCAATCCCCAGACT 59.299 50.000 0.00 0.00 0.00 3.24
223 224 1.203052 CAACATGTGCAATCCCCAGAC 59.797 52.381 0.00 0.00 0.00 3.51
224 225 1.075212 TCAACATGTGCAATCCCCAGA 59.925 47.619 0.00 0.00 0.00 3.86
225 226 1.203052 GTCAACATGTGCAATCCCCAG 59.797 52.381 0.00 0.00 0.00 4.45
226 227 1.255882 GTCAACATGTGCAATCCCCA 58.744 50.000 0.00 0.00 0.00 4.96
227 228 1.203052 CTGTCAACATGTGCAATCCCC 59.797 52.381 0.00 0.00 0.00 4.81
228 229 1.403249 GCTGTCAACATGTGCAATCCC 60.403 52.381 0.00 0.00 0.00 3.85
229 230 1.270274 TGCTGTCAACATGTGCAATCC 59.730 47.619 0.00 0.00 0.00 3.01
230 231 2.592194 CTGCTGTCAACATGTGCAATC 58.408 47.619 0.00 0.00 33.07 2.67
231 232 1.271379 CCTGCTGTCAACATGTGCAAT 59.729 47.619 0.00 0.00 33.07 3.56
232 233 0.669619 CCTGCTGTCAACATGTGCAA 59.330 50.000 0.00 0.00 33.07 4.08
233 234 0.466007 ACCTGCTGTCAACATGTGCA 60.466 50.000 0.00 3.03 0.00 4.57
234 235 0.670162 AACCTGCTGTCAACATGTGC 59.330 50.000 0.00 0.00 0.00 4.57
235 236 3.304659 GGTTAACCTGCTGTCAACATGTG 60.305 47.826 17.83 0.00 0.00 3.21
236 237 2.884639 GGTTAACCTGCTGTCAACATGT 59.115 45.455 17.83 0.00 0.00 3.21
237 238 2.228822 GGGTTAACCTGCTGTCAACATG 59.771 50.000 23.69 0.00 35.85 3.21
238 239 2.514803 GGGTTAACCTGCTGTCAACAT 58.485 47.619 23.69 0.00 35.85 2.71
239 240 1.975660 GGGTTAACCTGCTGTCAACA 58.024 50.000 23.69 0.00 35.85 3.33
250 251 1.620323 ACCACACGTAGAGGGTTAACC 59.380 52.381 16.85 16.85 31.20 2.85
251 252 2.353109 GGACCACACGTAGAGGGTTAAC 60.353 54.545 0.00 0.00 31.20 2.01
252 253 1.895131 GGACCACACGTAGAGGGTTAA 59.105 52.381 0.00 0.00 31.20 2.01
253 254 1.203038 TGGACCACACGTAGAGGGTTA 60.203 52.381 0.00 0.00 31.20 2.85
254 255 0.470456 TGGACCACACGTAGAGGGTT 60.470 55.000 0.00 0.00 31.20 4.11
255 256 0.898789 CTGGACCACACGTAGAGGGT 60.899 60.000 0.00 0.00 36.52 4.34
256 257 0.611062 TCTGGACCACACGTAGAGGG 60.611 60.000 0.00 0.00 0.00 4.30
257 258 0.526662 GTCTGGACCACACGTAGAGG 59.473 60.000 0.00 0.00 0.00 3.69
258 259 1.244816 TGTCTGGACCACACGTAGAG 58.755 55.000 0.00 0.00 0.00 2.43
259 260 1.694844 TTGTCTGGACCACACGTAGA 58.305 50.000 0.00 0.00 0.00 2.59
260 261 2.519377 TTTGTCTGGACCACACGTAG 57.481 50.000 0.00 0.00 0.00 3.51
261 262 3.827876 TCTATTTGTCTGGACCACACGTA 59.172 43.478 0.00 0.00 0.00 3.57
262 263 2.631062 TCTATTTGTCTGGACCACACGT 59.369 45.455 0.00 0.00 0.00 4.49
263 264 3.313012 TCTATTTGTCTGGACCACACG 57.687 47.619 0.00 0.00 0.00 4.49
264 265 4.636206 GGAATCTATTTGTCTGGACCACAC 59.364 45.833 0.00 0.00 0.00 3.82
265 266 4.288366 TGGAATCTATTTGTCTGGACCACA 59.712 41.667 0.00 0.00 0.00 4.17
266 267 4.843728 TGGAATCTATTTGTCTGGACCAC 58.156 43.478 0.00 0.00 0.00 4.16
267 268 5.253330 GTTGGAATCTATTTGTCTGGACCA 58.747 41.667 0.00 0.00 0.00 4.02
268 269 4.332819 CGTTGGAATCTATTTGTCTGGACC 59.667 45.833 0.00 0.00 0.00 4.46
269 270 4.332819 CCGTTGGAATCTATTTGTCTGGAC 59.667 45.833 0.00 0.00 0.00 4.02
270 271 4.224147 TCCGTTGGAATCTATTTGTCTGGA 59.776 41.667 0.00 0.00 0.00 3.86
271 272 4.513442 TCCGTTGGAATCTATTTGTCTGG 58.487 43.478 0.00 0.00 0.00 3.86
272 273 5.178797 ACTCCGTTGGAATCTATTTGTCTG 58.821 41.667 0.00 0.00 0.00 3.51
273 274 5.422214 ACTCCGTTGGAATCTATTTGTCT 57.578 39.130 0.00 0.00 0.00 3.41
274 275 5.673818 GCAACTCCGTTGGAATCTATTTGTC 60.674 44.000 8.60 0.00 42.99 3.18
275 276 4.156008 GCAACTCCGTTGGAATCTATTTGT 59.844 41.667 8.60 0.00 42.99 2.83
276 277 4.662145 GCAACTCCGTTGGAATCTATTTG 58.338 43.478 8.60 0.00 42.99 2.32
277 278 3.374058 CGCAACTCCGTTGGAATCTATTT 59.626 43.478 8.60 0.00 42.99 1.40
278 279 2.936498 CGCAACTCCGTTGGAATCTATT 59.064 45.455 8.60 0.00 42.99 1.73
279 280 2.093658 ACGCAACTCCGTTGGAATCTAT 60.094 45.455 8.60 0.00 42.99 1.98
280 281 1.274167 ACGCAACTCCGTTGGAATCTA 59.726 47.619 8.60 0.00 42.99 1.98
281 282 0.034896 ACGCAACTCCGTTGGAATCT 59.965 50.000 8.60 0.00 42.99 2.40
282 283 0.442699 GACGCAACTCCGTTGGAATC 59.557 55.000 8.60 0.00 42.99 2.52
283 284 0.250124 TGACGCAACTCCGTTGGAAT 60.250 50.000 8.60 0.00 42.99 3.01
284 285 0.250124 ATGACGCAACTCCGTTGGAA 60.250 50.000 8.60 0.00 42.99 3.53
285 286 0.948623 CATGACGCAACTCCGTTGGA 60.949 55.000 8.60 0.00 42.99 3.53
286 287 1.497278 CATGACGCAACTCCGTTGG 59.503 57.895 8.60 2.29 42.99 3.77
287 288 0.948623 TCCATGACGCAACTCCGTTG 60.949 55.000 0.00 2.51 45.24 4.10
288 289 0.949105 GTCCATGACGCAACTCCGTT 60.949 55.000 0.00 0.00 42.24 4.44
289 290 1.374252 GTCCATGACGCAACTCCGT 60.374 57.895 0.00 0.00 45.30 4.69
290 291 1.078759 GAGTCCATGACGCAACTCCG 61.079 60.000 0.00 0.00 37.67 4.63
291 292 0.037326 TGAGTCCATGACGCAACTCC 60.037 55.000 0.00 0.00 39.20 3.85
292 293 2.015736 ATGAGTCCATGACGCAACTC 57.984 50.000 4.82 0.05 44.47 3.01
307 308 3.218453 AGATCCACGACTCTACCATGAG 58.782 50.000 0.00 0.00 39.78 2.90
308 309 3.215151 GAGATCCACGACTCTACCATGA 58.785 50.000 0.00 0.00 0.00 3.07
309 310 2.952310 TGAGATCCACGACTCTACCATG 59.048 50.000 0.00 0.00 34.65 3.66
310 311 3.298686 TGAGATCCACGACTCTACCAT 57.701 47.619 0.00 0.00 34.65 3.55
311 312 2.801077 TGAGATCCACGACTCTACCA 57.199 50.000 0.00 0.00 34.65 3.25
312 313 3.280295 TCTTGAGATCCACGACTCTACC 58.720 50.000 0.00 0.00 34.65 3.18
313 314 4.439016 GGTTCTTGAGATCCACGACTCTAC 60.439 50.000 0.00 0.00 34.75 2.59
314 315 3.695060 GGTTCTTGAGATCCACGACTCTA 59.305 47.826 0.00 0.00 34.75 2.43
315 316 2.494073 GGTTCTTGAGATCCACGACTCT 59.506 50.000 0.00 0.00 34.75 3.24
316 317 2.494073 AGGTTCTTGAGATCCACGACTC 59.506 50.000 10.01 0.00 36.59 3.36
317 318 2.530701 AGGTTCTTGAGATCCACGACT 58.469 47.619 10.01 0.00 36.59 4.18
318 319 3.320673 AAGGTTCTTGAGATCCACGAC 57.679 47.619 10.01 0.00 36.59 4.34
319 320 3.194968 GGTAAGGTTCTTGAGATCCACGA 59.805 47.826 10.01 0.00 36.59 4.35
320 321 3.522553 GGTAAGGTTCTTGAGATCCACG 58.477 50.000 10.01 0.00 36.59 4.94
321 322 3.370633 GGGGTAAGGTTCTTGAGATCCAC 60.371 52.174 10.01 1.88 36.59 4.02
322 323 2.844348 GGGGTAAGGTTCTTGAGATCCA 59.156 50.000 10.01 0.00 36.59 3.41
323 324 3.116174 AGGGGTAAGGTTCTTGAGATCC 58.884 50.000 0.69 0.69 34.82 3.36
324 325 6.502074 AATAGGGGTAAGGTTCTTGAGATC 57.498 41.667 0.00 0.00 0.00 2.75
325 326 8.401955 TTTAATAGGGGTAAGGTTCTTGAGAT 57.598 34.615 0.00 0.00 0.00 2.75
326 327 7.817910 TTTAATAGGGGTAAGGTTCTTGAGA 57.182 36.000 0.00 0.00 0.00 3.27
327 328 8.873186 TTTTTAATAGGGGTAAGGTTCTTGAG 57.127 34.615 0.00 0.00 0.00 3.02
328 329 9.831682 AATTTTTAATAGGGGTAAGGTTCTTGA 57.168 29.630 0.00 0.00 0.00 3.02
331 332 9.475620 CAGAATTTTTAATAGGGGTAAGGTTCT 57.524 33.333 0.00 0.00 0.00 3.01
332 333 9.251440 ACAGAATTTTTAATAGGGGTAAGGTTC 57.749 33.333 0.00 0.00 0.00 3.62
333 334 9.610104 AACAGAATTTTTAATAGGGGTAAGGTT 57.390 29.630 0.00 0.00 0.00 3.50
334 335 9.031537 CAACAGAATTTTTAATAGGGGTAAGGT 57.968 33.333 0.00 0.00 0.00 3.50
335 336 9.250246 TCAACAGAATTTTTAATAGGGGTAAGG 57.750 33.333 0.00 0.00 0.00 2.69
338 339 9.027202 GGTTCAACAGAATTTTTAATAGGGGTA 57.973 33.333 0.00 0.00 0.00 3.69
339 340 7.309560 CGGTTCAACAGAATTTTTAATAGGGGT 60.310 37.037 0.00 0.00 0.00 4.95
340 341 7.033185 CGGTTCAACAGAATTTTTAATAGGGG 58.967 38.462 0.00 0.00 0.00 4.79
341 342 7.822658 TCGGTTCAACAGAATTTTTAATAGGG 58.177 34.615 0.00 0.00 0.00 3.53
345 346 9.801873 CCATATCGGTTCAACAGAATTTTTAAT 57.198 29.630 0.00 0.00 0.00 1.40
346 347 8.247562 CCCATATCGGTTCAACAGAATTTTTAA 58.752 33.333 0.00 0.00 0.00 1.52
347 348 7.629652 GCCCATATCGGTTCAACAGAATTTTTA 60.630 37.037 0.00 0.00 0.00 1.52
348 349 6.630071 CCCATATCGGTTCAACAGAATTTTT 58.370 36.000 0.00 0.00 0.00 1.94
349 350 5.394115 GCCCATATCGGTTCAACAGAATTTT 60.394 40.000 0.00 0.00 0.00 1.82
350 351 4.097892 GCCCATATCGGTTCAACAGAATTT 59.902 41.667 0.00 0.00 0.00 1.82
351 352 3.632145 GCCCATATCGGTTCAACAGAATT 59.368 43.478 0.00 0.00 0.00 2.17
352 353 3.214328 GCCCATATCGGTTCAACAGAAT 58.786 45.455 0.00 0.00 0.00 2.40
353 354 2.639065 GCCCATATCGGTTCAACAGAA 58.361 47.619 0.00 0.00 0.00 3.02
354 355 1.134220 GGCCCATATCGGTTCAACAGA 60.134 52.381 0.00 0.00 0.00 3.41
441 442 1.152096 ACTGGGAACGGGAGGACTT 60.152 57.895 0.00 0.00 42.76 3.01
1122 1196 1.559682 GCCCCCTCTAACTTCATGTCA 59.440 52.381 0.00 0.00 0.00 3.58
1488 1562 1.458639 GCTCTGCCCACAAAGCTTGT 61.459 55.000 0.00 0.00 46.75 3.16
1491 1565 1.602888 CTGCTCTGCCCACAAAGCT 60.603 57.895 0.00 0.00 35.76 3.74
1521 1595 2.025155 GCATCGTAGAGTTCCAGAGGA 58.975 52.381 0.00 0.00 43.63 3.71
1608 1682 2.229784 CCTGCCATGAAAACAACCTCTC 59.770 50.000 0.00 0.00 0.00 3.20
1743 1817 3.062763 AGTGACTGCAAATGTCGAAGAG 58.937 45.455 0.00 0.00 36.95 2.85
1782 1856 6.319405 CACAGATATGACATTTGTTGGGATCA 59.681 38.462 0.00 0.00 0.00 2.92
1973 2047 1.129917 CATGTGAGCCCTCTGATCCT 58.870 55.000 0.00 0.00 0.00 3.24
2326 2400 4.103153 ACTGAAGGAGACCAAATTGACAGA 59.897 41.667 0.00 0.00 0.00 3.41
2758 2833 7.044510 GCAATCGATGAATGTCACAAAGTATTG 60.045 37.037 0.00 0.00 42.46 1.90
2792 2867 6.205464 ACGCATCAAATAAATCCAGGTCATAG 59.795 38.462 0.00 0.00 0.00 2.23
2978 3053 3.249189 GAGGGGTGTCTGGGCACA 61.249 66.667 7.63 0.00 40.89 4.57
3213 3298 5.693104 GTGATCACGAACAAAACAGGTACTA 59.307 40.000 10.69 0.00 36.02 1.82


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

AutoCloner maintained by Alex Coulton.