Multiple sequence alignment - TraesCS7D01G034200

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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 TraesCS7D01G034200 chr7D 100.000 2612 0 0 1 2612 17665735 17663124 0.000000e+00 4824
1 TraesCS7D01G034200 chr7D 73.899 613 104 34 1720 2284 304147101 304146497 7.380000e-46 195
2 TraesCS7D01G034200 chr7D 75.060 417 99 4 1020 1432 12070389 12070804 3.430000e-44 189
3 TraesCS7D01G034200 chr7D 75.683 366 84 4 1071 1432 49270814 49270450 7.430000e-41 178
4 TraesCS7D01G034200 chr7D 81.560 141 23 1 1071 1208 12312488 12312348 2.120000e-21 113
5 TraesCS7D01G034200 chr7A 90.830 1952 121 12 262 2169 17162621 17160684 0.000000e+00 2560
6 TraesCS7D01G034200 chr7A 93.665 221 13 1 2383 2602 17160273 17160053 1.940000e-86 329
7 TraesCS7D01G034200 chr7A 94.737 114 6 0 2200 2313 17160687 17160574 7.430000e-41 178
8 TraesCS7D01G034200 chr7A 71.508 537 136 13 809 1332 17207986 17208518 7.590000e-26 128
9 TraesCS7D01G034200 chr7A 80.851 141 24 1 1071 1208 11761662 11761522 9.880000e-20 108
10 TraesCS7D01G034200 chr4A 76.051 1499 261 62 200 1672 716299576 716301002 0.000000e+00 689
11 TraesCS7D01G034200 chr4A 76.564 1327 247 38 365 1670 715558192 715559475 0.000000e+00 669
12 TraesCS7D01G034200 chr4A 76.471 1326 250 38 365 1670 715946141 715944858 0.000000e+00 664
13 TraesCS7D01G034200 chr4A 74.060 532 116 17 903 1424 726089452 726088933 5.700000e-47 198
14 TraesCS7D01G034200 chr4B 74.188 616 98 36 1720 2284 173614873 173615478 1.590000e-47 200
15 TraesCS7D01G034200 chr4B 87.313 134 15 1 1 134 242754925 242754794 4.500000e-33 152
16 TraesCS7D01G034200 chr4B 87.313 134 15 1 1 134 242755131 242755000 4.500000e-33 152
17 TraesCS7D01G034200 chr2D 86.131 137 15 4 1 135 286532715 286532849 7.530000e-31 145
18 TraesCS7D01G034200 chr5D 86.364 132 15 3 4 135 485609315 485609187 9.750000e-30 141
19 TraesCS7D01G034200 chr1D 85.401 137 17 3 1 135 451857205 451857340 3.510000e-29 139
20 TraesCS7D01G034200 chr1B 85.401 137 17 3 1 135 621485635 621485770 3.510000e-29 139
21 TraesCS7D01G034200 chr5A 84.286 140 19 3 1 139 567889974 567889837 1.630000e-27 134
22 TraesCS7D01G034200 chr3A 84.559 136 19 2 1 135 54356047 54356181 1.630000e-27 134
23 TraesCS7D01G034200 chr3A 84.559 136 19 2 1 135 122485086 122484952 1.630000e-27 134


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 TraesCS7D01G034200 chr7D 17663124 17665735 2611 True 4824.000000 4824 100.000000 1 2612 1 chr7D.!!$R2 2611
1 TraesCS7D01G034200 chr7A 17160053 17162621 2568 True 1022.333333 2560 93.077333 262 2602 3 chr7A.!!$R2 2340
2 TraesCS7D01G034200 chr4A 716299576 716301002 1426 False 689.000000 689 76.051000 200 1672 1 chr4A.!!$F2 1472
3 TraesCS7D01G034200 chr4A 715558192 715559475 1283 False 669.000000 669 76.564000 365 1670 1 chr4A.!!$F1 1305
4 TraesCS7D01G034200 chr4A 715944858 715946141 1283 True 664.000000 664 76.471000 365 1670 1 chr4A.!!$R1 1305

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
209 210 0.331616 GTGGGAGTTGTATGGCCCTT 59.668 55.000 0.00 0.0 41.28 3.95 F
1171 1244 1.137086 CCTACATCAAGACTGTCCCCG 59.863 57.143 3.76 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1542 0.250467 GGCAGGGTCATATGCGTCAT 60.250 55.0 0.0 0.0 43.49 3.06 R
2370 2480 0.036875 CTGGACAAGAACTCCACCCC 59.963 60.0 0.0 0.0 33.97 4.95 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
25 26 8.421249 AACACATCAAAGATAGGATTTTTGGA 57.579 30.769 3.48 0.00 33.70 3.53
26 27 8.421249 ACACATCAAAGATAGGATTTTTGGAA 57.579 30.769 3.48 0.00 33.70 3.53
27 28 9.039165 ACACATCAAAGATAGGATTTTTGGAAT 57.961 29.630 3.48 0.00 33.70 3.01
28 29 9.880157 CACATCAAAGATAGGATTTTTGGAATT 57.120 29.630 3.48 0.00 33.70 2.17
35 36 9.440773 AAGATAGGATTTTTGGAATTTCTTTGC 57.559 29.630 0.00 0.00 0.00 3.68
36 37 8.596293 AGATAGGATTTTTGGAATTTCTTTGCA 58.404 29.630 0.00 0.00 33.34 4.08
37 38 9.387257 GATAGGATTTTTGGAATTTCTTTGCAT 57.613 29.630 0.00 0.00 35.41 3.96
38 39 9.743581 ATAGGATTTTTGGAATTTCTTTGCATT 57.256 25.926 0.00 0.00 35.41 3.56
39 40 8.467963 AGGATTTTTGGAATTTCTTTGCATTT 57.532 26.923 0.00 0.00 35.41 2.32
40 41 9.571816 AGGATTTTTGGAATTTCTTTGCATTTA 57.428 25.926 0.00 0.00 35.41 1.40
68 69 8.985315 ATTCATTAGTGGAAATATCAGAGCAA 57.015 30.769 0.00 0.00 0.00 3.91
69 70 8.806429 TTCATTAGTGGAAATATCAGAGCAAA 57.194 30.769 0.00 0.00 0.00 3.68
70 71 8.985315 TCATTAGTGGAAATATCAGAGCAAAT 57.015 30.769 0.00 0.00 0.00 2.32
71 72 8.843262 TCATTAGTGGAAATATCAGAGCAAATG 58.157 33.333 0.00 0.00 0.00 2.32
72 73 8.627403 CATTAGTGGAAATATCAGAGCAAATGT 58.373 33.333 0.00 0.00 0.00 2.71
73 74 6.690194 AGTGGAAATATCAGAGCAAATGTC 57.310 37.500 0.00 0.00 0.00 3.06
74 75 6.421485 AGTGGAAATATCAGAGCAAATGTCT 58.579 36.000 0.00 0.00 0.00 3.41
75 76 6.541641 AGTGGAAATATCAGAGCAAATGTCTC 59.458 38.462 0.00 0.00 0.00 3.36
76 77 6.541641 GTGGAAATATCAGAGCAAATGTCTCT 59.458 38.462 0.00 2.77 41.28 3.10
77 78 7.066766 GTGGAAATATCAGAGCAAATGTCTCTT 59.933 37.037 5.12 0.00 38.76 2.85
78 79 7.613022 TGGAAATATCAGAGCAAATGTCTCTTT 59.387 33.333 5.12 0.00 38.76 2.52
79 80 8.465201 GGAAATATCAGAGCAAATGTCTCTTTT 58.535 33.333 5.12 4.42 38.76 2.27
80 81 9.852091 GAAATATCAGAGCAAATGTCTCTTTTT 57.148 29.630 5.12 4.44 38.76 1.94
85 86 9.635520 ATCAGAGCAAATGTCTCTTTTTAAATG 57.364 29.630 5.12 0.00 38.76 2.32
86 87 8.849168 TCAGAGCAAATGTCTCTTTTTAAATGA 58.151 29.630 5.12 0.00 38.76 2.57
87 88 9.467258 CAGAGCAAATGTCTCTTTTTAAATGAA 57.533 29.630 5.12 0.00 38.76 2.57
112 113 9.816787 AAATATCTTGGTTTAAACTAAGGTGGA 57.183 29.630 31.84 18.82 44.61 4.02
113 114 9.990868 AATATCTTGGTTTAAACTAAGGTGGAT 57.009 29.630 31.84 23.56 44.61 3.41
114 115 7.703058 ATCTTGGTTTAAACTAAGGTGGATG 57.297 36.000 31.84 14.75 44.61 3.51
115 116 6.843752 TCTTGGTTTAAACTAAGGTGGATGA 58.156 36.000 31.84 16.38 44.61 2.92
116 117 6.940298 TCTTGGTTTAAACTAAGGTGGATGAG 59.060 38.462 31.84 13.70 44.61 2.90
117 118 6.195600 TGGTTTAAACTAAGGTGGATGAGT 57.804 37.500 17.50 0.00 0.00 3.41
118 119 6.001460 TGGTTTAAACTAAGGTGGATGAGTG 58.999 40.000 17.50 0.00 0.00 3.51
119 120 5.106277 GGTTTAAACTAAGGTGGATGAGTGC 60.106 44.000 17.50 0.00 0.00 4.40
120 121 3.788227 AAACTAAGGTGGATGAGTGCA 57.212 42.857 0.00 0.00 0.00 4.57
121 122 3.788227 AACTAAGGTGGATGAGTGCAA 57.212 42.857 0.00 0.00 0.00 4.08
122 123 3.788227 ACTAAGGTGGATGAGTGCAAA 57.212 42.857 0.00 0.00 0.00 3.68
123 124 4.098914 ACTAAGGTGGATGAGTGCAAAA 57.901 40.909 0.00 0.00 0.00 2.44
124 125 4.469657 ACTAAGGTGGATGAGTGCAAAAA 58.530 39.130 0.00 0.00 0.00 1.94
125 126 5.079643 ACTAAGGTGGATGAGTGCAAAAAT 58.920 37.500 0.00 0.00 0.00 1.82
126 127 6.245408 ACTAAGGTGGATGAGTGCAAAAATA 58.755 36.000 0.00 0.00 0.00 1.40
127 128 6.891908 ACTAAGGTGGATGAGTGCAAAAATAT 59.108 34.615 0.00 0.00 0.00 1.28
128 129 5.841957 AGGTGGATGAGTGCAAAAATATC 57.158 39.130 0.00 0.00 0.00 1.63
129 130 5.263599 AGGTGGATGAGTGCAAAAATATCA 58.736 37.500 0.00 0.00 0.00 2.15
130 131 5.126061 AGGTGGATGAGTGCAAAAATATCAC 59.874 40.000 0.00 0.00 0.00 3.06
131 132 5.126061 GGTGGATGAGTGCAAAAATATCACT 59.874 40.000 0.00 0.00 43.06 3.41
143 144 9.729023 TGCAAAAATATCACTCATTAATAACCG 57.271 29.630 0.00 0.00 0.00 4.44
144 145 8.690840 GCAAAAATATCACTCATTAATAACCGC 58.309 33.333 0.00 0.00 0.00 5.68
145 146 9.729023 CAAAAATATCACTCATTAATAACCGCA 57.271 29.630 0.00 0.00 0.00 5.69
147 148 9.730420 AAAATATCACTCATTAATAACCGCAAC 57.270 29.630 0.00 0.00 0.00 4.17
148 149 8.445275 AATATCACTCATTAATAACCGCAACA 57.555 30.769 0.00 0.00 0.00 3.33
149 150 6.751514 ATCACTCATTAATAACCGCAACAA 57.248 33.333 0.00 0.00 0.00 2.83
150 151 6.751514 TCACTCATTAATAACCGCAACAAT 57.248 33.333 0.00 0.00 0.00 2.71
151 152 7.851387 TCACTCATTAATAACCGCAACAATA 57.149 32.000 0.00 0.00 0.00 1.90
152 153 7.690228 TCACTCATTAATAACCGCAACAATAC 58.310 34.615 0.00 0.00 0.00 1.89
153 154 6.910433 CACTCATTAATAACCGCAACAATACC 59.090 38.462 0.00 0.00 0.00 2.73
154 155 6.038936 ACTCATTAATAACCGCAACAATACCC 59.961 38.462 0.00 0.00 0.00 3.69
155 156 6.123651 TCATTAATAACCGCAACAATACCCT 58.876 36.000 0.00 0.00 0.00 4.34
156 157 6.603997 TCATTAATAACCGCAACAATACCCTT 59.396 34.615 0.00 0.00 0.00 3.95
157 158 6.837471 TTAATAACCGCAACAATACCCTTT 57.163 33.333 0.00 0.00 0.00 3.11
158 159 4.712122 ATAACCGCAACAATACCCTTTG 57.288 40.909 0.00 0.00 0.00 2.77
159 160 1.989706 ACCGCAACAATACCCTTTGT 58.010 45.000 0.00 0.00 41.49 2.83
161 162 2.295070 ACCGCAACAATACCCTTTGTTC 59.705 45.455 0.00 0.00 45.54 3.18
162 163 2.352323 CCGCAACAATACCCTTTGTTCC 60.352 50.000 0.00 0.00 45.54 3.62
163 164 2.294791 CGCAACAATACCCTTTGTTCCA 59.705 45.455 0.00 0.00 45.54 3.53
164 165 3.056891 CGCAACAATACCCTTTGTTCCAT 60.057 43.478 0.00 0.00 45.54 3.41
165 166 4.560513 CGCAACAATACCCTTTGTTCCATT 60.561 41.667 0.00 0.00 45.54 3.16
166 167 5.304778 GCAACAATACCCTTTGTTCCATTT 58.695 37.500 0.00 0.00 45.54 2.32
167 168 5.408299 GCAACAATACCCTTTGTTCCATTTC 59.592 40.000 0.00 0.00 45.54 2.17
168 169 6.520272 CAACAATACCCTTTGTTCCATTTCA 58.480 36.000 0.00 0.00 45.54 2.69
169 170 6.933514 ACAATACCCTTTGTTCCATTTCAT 57.066 33.333 0.00 0.00 36.43 2.57
170 171 6.700352 ACAATACCCTTTGTTCCATTTCATG 58.300 36.000 0.00 0.00 36.43 3.07
171 172 6.269769 ACAATACCCTTTGTTCCATTTCATGT 59.730 34.615 0.00 0.00 36.43 3.21
172 173 4.605640 ACCCTTTGTTCCATTTCATGTG 57.394 40.909 0.00 0.00 0.00 3.21
173 174 3.324556 ACCCTTTGTTCCATTTCATGTGG 59.675 43.478 0.00 0.00 38.11 4.17
174 175 3.577848 CCCTTTGTTCCATTTCATGTGGA 59.422 43.478 0.00 0.00 43.77 4.02
175 176 4.223477 CCCTTTGTTCCATTTCATGTGGAT 59.777 41.667 4.49 0.00 44.75 3.41
176 177 5.421693 CCCTTTGTTCCATTTCATGTGGATA 59.578 40.000 4.49 0.00 44.75 2.59
177 178 6.070881 CCCTTTGTTCCATTTCATGTGGATAA 60.071 38.462 4.49 1.85 44.75 1.75
178 179 6.813152 CCTTTGTTCCATTTCATGTGGATAAC 59.187 38.462 4.49 2.39 44.75 1.89
179 180 5.913137 TGTTCCATTTCATGTGGATAACC 57.087 39.130 4.49 0.00 44.75 2.85
180 181 5.328565 TGTTCCATTTCATGTGGATAACCA 58.671 37.500 4.49 0.00 44.75 3.67
194 195 5.505780 TGGATAACCAAGACTTATTGTGGG 58.494 41.667 0.00 0.00 43.91 4.61
195 196 5.251932 TGGATAACCAAGACTTATTGTGGGA 59.748 40.000 0.00 0.00 43.91 4.37
196 197 5.823045 GGATAACCAAGACTTATTGTGGGAG 59.177 44.000 0.00 0.00 35.32 4.30
197 198 4.724279 AACCAAGACTTATTGTGGGAGT 57.276 40.909 0.00 0.00 35.32 3.85
198 199 4.724279 ACCAAGACTTATTGTGGGAGTT 57.276 40.909 0.00 0.00 35.32 3.01
204 205 5.745227 AGACTTATTGTGGGAGTTGTATGG 58.255 41.667 0.00 0.00 0.00 2.74
209 210 0.331616 GTGGGAGTTGTATGGCCCTT 59.668 55.000 0.00 0.00 41.28 3.95
213 214 3.288092 GGGAGTTGTATGGCCCTTTTAG 58.712 50.000 0.00 0.00 37.59 1.85
218 219 4.044191 AGTTGTATGGCCCTTTTAGACCTT 59.956 41.667 0.00 0.00 0.00 3.50
226 227 4.401519 GGCCCTTTTAGACCTTATCCAAAC 59.598 45.833 0.00 0.00 0.00 2.93
229 231 6.194967 CCCTTTTAGACCTTATCCAAACCAT 58.805 40.000 0.00 0.00 0.00 3.55
236 238 5.014123 AGACCTTATCCAAACCATTGAGACA 59.986 40.000 0.00 0.00 38.94 3.41
240 242 7.893302 ACCTTATCCAAACCATTGAGACATAAA 59.107 33.333 0.00 0.00 38.94 1.40
244 246 4.160252 CCAAACCATTGAGACATAAAGGGG 59.840 45.833 0.00 0.00 38.94 4.79
246 248 4.946160 ACCATTGAGACATAAAGGGGAA 57.054 40.909 0.00 0.00 31.53 3.97
247 249 5.269554 ACCATTGAGACATAAAGGGGAAA 57.730 39.130 0.00 0.00 31.53 3.13
249 251 6.980577 ACCATTGAGACATAAAGGGGAAATA 58.019 36.000 0.00 0.00 31.53 1.40
250 252 7.062957 ACCATTGAGACATAAAGGGGAAATAG 58.937 38.462 0.00 0.00 31.53 1.73
252 254 8.217799 CCATTGAGACATAAAGGGGAAATAGTA 58.782 37.037 0.00 0.00 0.00 1.82
256 258 9.225682 TGAGACATAAAGGGGAAATAGTATTCT 57.774 33.333 0.00 0.00 0.00 2.40
258 260 9.453830 AGACATAAAGGGGAAATAGTATTCTCT 57.546 33.333 0.00 0.00 30.25 3.10
265 267 6.071320 GGGGAAATAGTATTCTCTGGCAAAT 58.929 40.000 0.00 0.00 30.25 2.32
300 303 3.692690 GGTCCAATACCTTGCTACCAAA 58.307 45.455 0.00 0.00 45.75 3.28
316 319 6.214819 TGCTACCAAAAATAGGAGTAGAACCT 59.785 38.462 0.00 0.00 41.05 3.50
329 332 6.841755 AGGAGTAGAACCTAGCATTACTTCAT 59.158 38.462 0.00 0.00 35.84 2.57
416 420 2.991540 GGCCCAACACCTTGCTCC 60.992 66.667 0.00 0.00 0.00 4.70
427 431 3.117512 ACACCTTGCTCCCCAATATAAGG 60.118 47.826 0.00 0.00 40.30 2.69
473 483 4.642445 TCGGCTGTCGAAATAACATAGA 57.358 40.909 0.03 0.00 45.86 1.98
502 514 4.388773 TGTTAAAAGCATGTCTAGAGTGCG 59.611 41.667 19.05 0.45 43.37 5.34
508 520 2.076100 CATGTCTAGAGTGCGCCAAAA 58.924 47.619 4.18 0.00 0.00 2.44
525 537 7.486551 TGCGCCAAAACAAATTAGACATATTAC 59.513 33.333 4.18 0.00 0.00 1.89
576 588 6.981722 TCGTATATGTGAGCATTGAGTGTAT 58.018 36.000 0.00 0.00 36.58 2.29
585 597 9.045223 TGTGAGCATTGAGTGTATAATAATCAC 57.955 33.333 0.00 0.00 34.65 3.06
679 692 4.095483 ACGAGAAGATCAAAATGATGGCAC 59.905 41.667 0.00 0.00 37.20 5.01
722 735 5.405571 AGCGTATTAATACCAAGCGATTCAG 59.594 40.000 17.91 3.02 0.00 3.02
730 743 1.629013 CAAGCGATTCAGTACGAGCA 58.371 50.000 0.00 0.00 0.00 4.26
767 780 7.717875 TGTGAATATAAAGGGCATTAGTACCAC 59.282 37.037 0.00 0.00 0.00 4.16
768 781 6.932400 TGAATATAAAGGGCATTAGTACCACG 59.068 38.462 0.00 0.00 0.00 4.94
782 795 7.818997 TTAGTACCACGATATCTGAATGAGT 57.181 36.000 0.34 0.00 0.00 3.41
968 1040 4.530946 TCTTTACCTCCCTTGGTTCTAGTG 59.469 45.833 0.00 0.00 41.22 2.74
1035 1108 3.782413 ACCTCCATCATTTTCCCCATT 57.218 42.857 0.00 0.00 0.00 3.16
1041 1114 6.463331 CCTCCATCATTTTCCCCATTATTGTG 60.463 42.308 0.00 0.00 0.00 3.33
1045 1118 5.960113 TCATTTTCCCCATTATTGTGTTCG 58.040 37.500 0.00 0.00 0.00 3.95
1061 1134 2.750166 TGTTCGTGCTTCTTTCCACAAA 59.250 40.909 0.00 0.00 32.37 2.83
1082 1155 1.957177 CATCCCTACTCAAGCTAGCGA 59.043 52.381 9.55 0.07 0.00 4.93
1111 1184 1.754226 GTGGAAACTCAAAGGCAACCA 59.246 47.619 0.00 0.00 37.17 3.67
1164 1237 7.560368 CCTCAATTAACTCCTACATCAAGACT 58.440 38.462 0.00 0.00 0.00 3.24
1171 1244 1.137086 CCTACATCAAGACTGTCCCCG 59.863 57.143 3.76 0.00 0.00 5.73
1469 1542 4.701663 GCTGGCTAGCTGTGTGAA 57.298 55.556 15.78 0.00 46.57 3.18
1473 1546 2.005451 CTGGCTAGCTGTGTGAATGAC 58.995 52.381 15.72 0.00 0.00 3.06
1479 1552 2.910199 AGCTGTGTGAATGACGCATAT 58.090 42.857 0.00 0.00 44.13 1.78
1480 1553 2.610833 AGCTGTGTGAATGACGCATATG 59.389 45.455 0.00 0.00 44.13 1.78
1554 1627 3.181501 CGCTGTTCAAGGAAAACACTGAA 60.182 43.478 0.00 0.00 33.30 3.02
1561 1634 4.402155 TCAAGGAAAACACTGAACTGCAAT 59.598 37.500 0.00 0.00 0.00 3.56
1562 1635 4.574599 AGGAAAACACTGAACTGCAATC 57.425 40.909 0.00 0.00 0.00 2.67
1570 1643 4.115516 CACTGAACTGCAATCGCTAGTAT 58.884 43.478 0.00 0.00 39.64 2.12
1579 1652 1.644509 ATCGCTAGTATGGATGGGCA 58.355 50.000 0.00 0.00 0.00 5.36
1699 1772 9.466497 AGAAATGTCTCTGGCATTAATTTTCTA 57.534 29.630 0.00 0.00 35.73 2.10
1710 1783 9.370930 TGGCATTAATTTTCTATCATTCCATCT 57.629 29.630 0.00 0.00 0.00 2.90
1767 1840 1.342819 CGGGGAAAACAAATCCTTGCA 59.657 47.619 0.00 0.00 37.14 4.08
1772 1845 3.401182 GAAAACAAATCCTTGCATGCCA 58.599 40.909 16.68 2.49 35.84 4.92
1773 1846 3.706600 AAACAAATCCTTGCATGCCAT 57.293 38.095 16.68 0.00 35.84 4.40
1795 1868 1.795768 TTGATCCTTCGCACTGTCAC 58.204 50.000 0.00 0.00 0.00 3.67
1796 1869 0.969149 TGATCCTTCGCACTGTCACT 59.031 50.000 0.00 0.00 0.00 3.41
1805 1878 1.789506 GCACTGTCACTCTCTTCACC 58.210 55.000 0.00 0.00 0.00 4.02
1810 1883 2.230025 CTGTCACTCTCTTCACCACGAT 59.770 50.000 0.00 0.00 0.00 3.73
1813 1886 2.423892 TCACTCTCTTCACCACGATAGC 59.576 50.000 0.00 0.00 42.67 2.97
1824 1897 2.156917 CCACGATAGCCGATGGTAGTA 58.843 52.381 0.00 0.00 41.76 1.82
1853 1948 6.406370 TCTCCACCTACTTAACATGAATGTG 58.594 40.000 0.00 0.00 41.61 3.21
1858 1953 7.336679 CCACCTACTTAACATGAATGTGATCAA 59.663 37.037 0.00 0.00 41.61 2.57
1861 1956 9.334947 CCTACTTAACATGAATGTGATCAATCT 57.665 33.333 0.00 0.00 41.61 2.40
1912 2007 4.715523 TTTCCCAAGCCCCTCGCG 62.716 66.667 0.00 0.00 44.76 5.87
1937 2032 6.926272 GGCACCAACTTGTAATTCAAAATACA 59.074 34.615 0.00 0.00 35.48 2.29
1974 2069 0.623324 CCACCCCTGTCTAATCCCCA 60.623 60.000 0.00 0.00 0.00 4.96
2012 2107 1.535462 CCAAGACCCATTTGTGTCGTC 59.465 52.381 0.00 0.00 36.61 4.20
2017 2112 1.019278 CCCATTTGTGTCGTCCCTCG 61.019 60.000 0.00 0.00 41.41 4.63
2032 2127 1.290955 CTCGTCCTTGGCGGTAACA 59.709 57.895 4.32 0.00 0.00 2.41
2054 2149 5.046014 ACAACCTCTCTCTTTACATGCTCAT 60.046 40.000 0.00 0.00 0.00 2.90
2104 2210 0.942252 TCATCTGATGCATGCTTCGC 59.058 50.000 23.82 10.07 0.00 4.70
2258 2368 6.827727 AGACCTGAGCTTCAAAGTAGTTTTA 58.172 36.000 0.00 0.00 0.00 1.52
2294 2404 4.767409 TCGAGTATAGCCTGCTCACATAAT 59.233 41.667 0.00 0.00 36.47 1.28
2310 2420 6.083630 TCACATAATAAAGAAAAGCGCACAC 58.916 36.000 11.47 0.00 0.00 3.82
2313 2423 0.955905 TAAAGAAAAGCGCACACCCC 59.044 50.000 11.47 0.00 0.00 4.95
2314 2424 0.755327 AAAGAAAAGCGCACACCCCT 60.755 50.000 11.47 0.00 0.00 4.79
2315 2425 1.172812 AAGAAAAGCGCACACCCCTC 61.173 55.000 11.47 0.00 0.00 4.30
2316 2426 1.600916 GAAAAGCGCACACCCCTCT 60.601 57.895 11.47 0.00 0.00 3.69
2317 2427 1.152756 AAAAGCGCACACCCCTCTT 60.153 52.632 11.47 0.00 0.00 2.85
2318 2428 0.755327 AAAAGCGCACACCCCTCTTT 60.755 50.000 11.47 0.00 0.00 2.52
2319 2429 1.172812 AAAGCGCACACCCCTCTTTC 61.173 55.000 11.47 0.00 0.00 2.62
2320 2430 3.056328 GCGCACACCCCTCTTTCC 61.056 66.667 0.30 0.00 0.00 3.13
2321 2431 2.750350 CGCACACCCCTCTTTCCT 59.250 61.111 0.00 0.00 0.00 3.36
2322 2432 1.376037 CGCACACCCCTCTTTCCTC 60.376 63.158 0.00 0.00 0.00 3.71
2323 2433 1.002011 GCACACCCCTCTTTCCTCC 60.002 63.158 0.00 0.00 0.00 4.30
2324 2434 1.685820 CACACCCCTCTTTCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
2325 2435 1.541620 ACACCCCTCTTTCCTCCCC 60.542 63.158 0.00 0.00 0.00 4.81
2326 2436 1.229984 CACCCCTCTTTCCTCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
2327 2437 1.083141 ACCCCTCTTTCCTCCCCTC 59.917 63.158 0.00 0.00 0.00 4.30
2328 2438 1.694525 CCCCTCTTTCCTCCCCTCC 60.695 68.421 0.00 0.00 0.00 4.30
2329 2439 1.694525 CCCTCTTTCCTCCCCTCCC 60.695 68.421 0.00 0.00 0.00 4.30
2330 2440 1.694525 CCTCTTTCCTCCCCTCCCC 60.695 68.421 0.00 0.00 0.00 4.81
2331 2441 1.082954 CTCTTTCCTCCCCTCCCCA 59.917 63.158 0.00 0.00 0.00 4.96
2332 2442 1.229853 TCTTTCCTCCCCTCCCCAC 60.230 63.158 0.00 0.00 0.00 4.61
2333 2443 2.204244 TTTCCTCCCCTCCCCACC 60.204 66.667 0.00 0.00 0.00 4.61
2334 2444 2.789979 CTTTCCTCCCCTCCCCACCT 62.790 65.000 0.00 0.00 0.00 4.00
2335 2445 2.782997 TTTCCTCCCCTCCCCACCTC 62.783 65.000 0.00 0.00 0.00 3.85
2337 2447 4.400251 CTCCCCTCCCCACCTCGT 62.400 72.222 0.00 0.00 0.00 4.18
2338 2448 3.925914 CTCCCCTCCCCACCTCGTT 62.926 68.421 0.00 0.00 0.00 3.85
2339 2449 3.400054 CCCCTCCCCACCTCGTTC 61.400 72.222 0.00 0.00 0.00 3.95
2340 2450 2.284699 CCCTCCCCACCTCGTTCT 60.285 66.667 0.00 0.00 0.00 3.01
2341 2451 2.359967 CCCTCCCCACCTCGTTCTC 61.360 68.421 0.00 0.00 0.00 2.87
2342 2452 2.359967 CCTCCCCACCTCGTTCTCC 61.360 68.421 0.00 0.00 0.00 3.71
2343 2453 2.284405 TCCCCACCTCGTTCTCCC 60.284 66.667 0.00 0.00 0.00 4.30
2344 2454 2.606519 CCCCACCTCGTTCTCCCA 60.607 66.667 0.00 0.00 0.00 4.37
2345 2455 2.660064 CCCCACCTCGTTCTCCCAG 61.660 68.421 0.00 0.00 0.00 4.45
2346 2456 1.609501 CCCACCTCGTTCTCCCAGA 60.610 63.158 0.00 0.00 0.00 3.86
2347 2457 0.978146 CCCACCTCGTTCTCCCAGAT 60.978 60.000 0.00 0.00 0.00 2.90
2348 2458 1.688311 CCCACCTCGTTCTCCCAGATA 60.688 57.143 0.00 0.00 0.00 1.98
2349 2459 2.320781 CCACCTCGTTCTCCCAGATAT 58.679 52.381 0.00 0.00 0.00 1.63
2350 2460 2.297597 CCACCTCGTTCTCCCAGATATC 59.702 54.545 0.00 0.00 0.00 1.63
2351 2461 2.030717 CACCTCGTTCTCCCAGATATCG 60.031 54.545 0.00 0.00 0.00 2.92
2352 2462 1.068194 CCTCGTTCTCCCAGATATCGC 60.068 57.143 0.00 0.00 0.00 4.58
2353 2463 0.959553 TCGTTCTCCCAGATATCGCC 59.040 55.000 0.00 0.00 0.00 5.54
2354 2464 0.387367 CGTTCTCCCAGATATCGCCG 60.387 60.000 0.00 0.00 0.00 6.46
2355 2465 0.667792 GTTCTCCCAGATATCGCCGC 60.668 60.000 0.00 0.00 0.00 6.53
2356 2466 1.112916 TTCTCCCAGATATCGCCGCA 61.113 55.000 0.00 0.00 0.00 5.69
2357 2467 1.373497 CTCCCAGATATCGCCGCAC 60.373 63.158 0.00 0.00 0.00 5.34
2358 2468 2.734723 CCCAGATATCGCCGCACG 60.735 66.667 0.00 0.00 45.62 5.34
2359 2469 3.406361 CCAGATATCGCCGCACGC 61.406 66.667 0.00 0.00 43.23 5.34
2360 2470 2.355126 CAGATATCGCCGCACGCT 60.355 61.111 0.00 0.00 43.23 5.07
2361 2471 1.081442 CAGATATCGCCGCACGCTA 60.081 57.895 0.00 0.00 43.23 4.26
2362 2472 0.456824 CAGATATCGCCGCACGCTAT 60.457 55.000 0.00 0.00 43.23 2.97
2363 2473 0.456824 AGATATCGCCGCACGCTATG 60.457 55.000 0.00 0.00 43.23 2.23
2364 2474 1.413767 GATATCGCCGCACGCTATGG 61.414 60.000 0.00 0.00 43.23 2.74
2365 2475 1.873270 ATATCGCCGCACGCTATGGA 61.873 55.000 0.00 0.00 43.23 3.41
2366 2476 1.873270 TATCGCCGCACGCTATGGAT 61.873 55.000 0.00 0.00 43.23 3.41
2367 2477 2.715532 ATCGCCGCACGCTATGGATT 62.716 55.000 0.00 0.00 43.23 3.01
2368 2478 1.663388 CGCCGCACGCTATGGATTA 60.663 57.895 0.00 0.00 34.21 1.75
2369 2479 1.617755 CGCCGCACGCTATGGATTAG 61.618 60.000 0.00 0.00 34.21 1.73
2370 2480 1.291877 GCCGCACGCTATGGATTAGG 61.292 60.000 0.00 0.00 0.00 2.69
2371 2481 0.670546 CCGCACGCTATGGATTAGGG 60.671 60.000 0.00 0.00 44.36 3.53
2372 2482 0.670546 CGCACGCTATGGATTAGGGG 60.671 60.000 2.40 0.00 43.39 4.79
2373 2483 0.321653 GCACGCTATGGATTAGGGGG 60.322 60.000 2.40 0.00 44.92 5.40
2374 2484 1.056660 CACGCTATGGATTAGGGGGT 58.943 55.000 2.40 0.00 43.39 4.95
2375 2485 1.056660 ACGCTATGGATTAGGGGGTG 58.943 55.000 2.40 0.00 43.39 4.61
2376 2486 0.324943 CGCTATGGATTAGGGGGTGG 59.675 60.000 0.00 0.00 37.25 4.61
2377 2487 1.742308 GCTATGGATTAGGGGGTGGA 58.258 55.000 0.00 0.00 0.00 4.02
2378 2488 1.630878 GCTATGGATTAGGGGGTGGAG 59.369 57.143 0.00 0.00 0.00 3.86
2379 2489 2.991580 CTATGGATTAGGGGGTGGAGT 58.008 52.381 0.00 0.00 0.00 3.85
2380 2490 2.303660 ATGGATTAGGGGGTGGAGTT 57.696 50.000 0.00 0.00 0.00 3.01
2381 2491 1.591768 TGGATTAGGGGGTGGAGTTC 58.408 55.000 0.00 0.00 0.00 3.01
2406 2747 3.499918 GTCCAGGAAGAACACAACTCATG 59.500 47.826 0.00 0.00 0.00 3.07
2407 2748 2.227388 CCAGGAAGAACACAACTCATGC 59.773 50.000 0.00 0.00 0.00 4.06
2412 2753 4.033358 GGAAGAACACAACTCATGCGATAG 59.967 45.833 0.00 0.00 0.00 2.08
2426 2768 9.039870 ACTCATGCGATAGAAAAGAAAATCTAG 57.960 33.333 0.00 0.00 39.76 2.43
2438 2780 4.013050 AGAAAATCTAGCCAGCAAGGTTC 58.987 43.478 0.00 0.00 40.61 3.62
2508 2850 2.610859 GGGGCCCAAGACTCTGGA 60.611 66.667 26.86 0.00 38.96 3.86
2565 2907 8.052748 AGTTGCAAAAATCTCCCTATACACATA 58.947 33.333 0.00 0.00 0.00 2.29
2603 2945 3.741029 CACTCTCCGTGTACCCATG 57.259 57.895 0.00 0.00 38.84 3.66
2604 2946 0.895530 CACTCTCCGTGTACCCATGT 59.104 55.000 0.00 0.00 38.84 3.21
2605 2947 0.895530 ACTCTCCGTGTACCCATGTG 59.104 55.000 0.00 0.00 0.00 3.21
2606 2948 0.895530 CTCTCCGTGTACCCATGTGT 59.104 55.000 0.00 0.00 0.00 3.72
2607 2949 2.097036 CTCTCCGTGTACCCATGTGTA 58.903 52.381 0.00 0.00 0.00 2.90
2608 2950 2.693591 CTCTCCGTGTACCCATGTGTAT 59.306 50.000 0.00 0.00 0.00 2.29
2609 2951 2.429250 TCTCCGTGTACCCATGTGTATG 59.571 50.000 0.00 0.00 0.00 2.39
2610 2952 1.134640 TCCGTGTACCCATGTGTATGC 60.135 52.381 0.00 0.00 32.79 3.14
2611 2953 1.406205 CCGTGTACCCATGTGTATGCA 60.406 52.381 0.00 0.00 32.79 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.421249 TCCAAAAATCCTATCTTTGATGTGTT 57.579 30.769 0.00 0.00 32.87 3.32
1 2 8.421249 TTCCAAAAATCCTATCTTTGATGTGT 57.579 30.769 0.00 0.00 32.87 3.72
2 3 9.880157 AATTCCAAAAATCCTATCTTTGATGTG 57.120 29.630 0.00 0.00 32.87 3.21
9 10 9.440773 GCAAAGAAATTCCAAAAATCCTATCTT 57.559 29.630 0.00 0.00 0.00 2.40
10 11 8.596293 TGCAAAGAAATTCCAAAAATCCTATCT 58.404 29.630 0.00 0.00 0.00 1.98
11 12 8.776376 TGCAAAGAAATTCCAAAAATCCTATC 57.224 30.769 0.00 0.00 0.00 2.08
12 13 9.743581 AATGCAAAGAAATTCCAAAAATCCTAT 57.256 25.926 0.00 0.00 0.00 2.57
13 14 9.571816 AAATGCAAAGAAATTCCAAAAATCCTA 57.428 25.926 0.00 0.00 0.00 2.94
14 15 8.467963 AAATGCAAAGAAATTCCAAAAATCCT 57.532 26.923 0.00 0.00 0.00 3.24
43 44 8.985315 TTGCTCTGATATTTCCACTAATGAAT 57.015 30.769 0.00 0.00 0.00 2.57
44 45 8.806429 TTTGCTCTGATATTTCCACTAATGAA 57.194 30.769 0.00 0.00 0.00 2.57
45 46 8.843262 CATTTGCTCTGATATTTCCACTAATGA 58.157 33.333 0.00 0.00 0.00 2.57
46 47 8.627403 ACATTTGCTCTGATATTTCCACTAATG 58.373 33.333 0.00 0.00 0.00 1.90
47 48 8.757982 ACATTTGCTCTGATATTTCCACTAAT 57.242 30.769 0.00 0.00 0.00 1.73
48 49 8.049117 AGACATTTGCTCTGATATTTCCACTAA 58.951 33.333 0.00 0.00 0.00 2.24
49 50 7.568349 AGACATTTGCTCTGATATTTCCACTA 58.432 34.615 0.00 0.00 0.00 2.74
50 51 6.421485 AGACATTTGCTCTGATATTTCCACT 58.579 36.000 0.00 0.00 0.00 4.00
51 52 6.541641 AGAGACATTTGCTCTGATATTTCCAC 59.458 38.462 0.00 0.00 41.00 4.02
52 53 6.656902 AGAGACATTTGCTCTGATATTTCCA 58.343 36.000 0.00 0.00 41.00 3.53
53 54 7.565323 AAGAGACATTTGCTCTGATATTTCC 57.435 36.000 0.00 0.00 41.66 3.13
54 55 9.852091 AAAAAGAGACATTTGCTCTGATATTTC 57.148 29.630 0.00 0.00 41.66 2.17
59 60 9.635520 CATTTAAAAAGAGACATTTGCTCTGAT 57.364 29.630 0.00 0.00 41.66 2.90
60 61 8.849168 TCATTTAAAAAGAGACATTTGCTCTGA 58.151 29.630 0.00 0.00 41.66 3.27
61 62 9.467258 TTCATTTAAAAAGAGACATTTGCTCTG 57.533 29.630 0.00 0.00 41.66 3.35
86 87 9.816787 TCCACCTTAGTTTAAACCAAGATATTT 57.183 29.630 22.96 2.78 30.62 1.40
87 88 9.990868 ATCCACCTTAGTTTAAACCAAGATATT 57.009 29.630 22.96 6.22 30.62 1.28
88 89 9.408648 CATCCACCTTAGTTTAAACCAAGATAT 57.591 33.333 22.96 9.19 30.62 1.63
89 90 8.607713 TCATCCACCTTAGTTTAAACCAAGATA 58.392 33.333 22.96 9.25 30.62 1.98
90 91 7.466804 TCATCCACCTTAGTTTAAACCAAGAT 58.533 34.615 22.96 7.72 30.62 2.40
91 92 6.843752 TCATCCACCTTAGTTTAAACCAAGA 58.156 36.000 22.96 7.99 30.62 3.02
92 93 6.715264 ACTCATCCACCTTAGTTTAAACCAAG 59.285 38.462 16.71 16.71 0.00 3.61
93 94 6.488683 CACTCATCCACCTTAGTTTAAACCAA 59.511 38.462 14.72 6.87 0.00 3.67
94 95 6.001460 CACTCATCCACCTTAGTTTAAACCA 58.999 40.000 14.72 0.00 0.00 3.67
95 96 5.106277 GCACTCATCCACCTTAGTTTAAACC 60.106 44.000 14.72 0.00 0.00 3.27
96 97 5.472137 TGCACTCATCCACCTTAGTTTAAAC 59.528 40.000 10.47 10.47 0.00 2.01
97 98 5.626142 TGCACTCATCCACCTTAGTTTAAA 58.374 37.500 0.00 0.00 0.00 1.52
98 99 5.235850 TGCACTCATCCACCTTAGTTTAA 57.764 39.130 0.00 0.00 0.00 1.52
99 100 4.901197 TGCACTCATCCACCTTAGTTTA 57.099 40.909 0.00 0.00 0.00 2.01
100 101 3.788227 TGCACTCATCCACCTTAGTTT 57.212 42.857 0.00 0.00 0.00 2.66
101 102 3.788227 TTGCACTCATCCACCTTAGTT 57.212 42.857 0.00 0.00 0.00 2.24
102 103 3.788227 TTTGCACTCATCCACCTTAGT 57.212 42.857 0.00 0.00 0.00 2.24
103 104 5.649782 ATTTTTGCACTCATCCACCTTAG 57.350 39.130 0.00 0.00 0.00 2.18
104 105 6.889177 TGATATTTTTGCACTCATCCACCTTA 59.111 34.615 0.00 0.00 0.00 2.69
105 106 5.716228 TGATATTTTTGCACTCATCCACCTT 59.284 36.000 0.00 0.00 0.00 3.50
106 107 5.126061 GTGATATTTTTGCACTCATCCACCT 59.874 40.000 0.00 0.00 0.00 4.00
107 108 5.126061 AGTGATATTTTTGCACTCATCCACC 59.874 40.000 0.00 0.00 38.41 4.61
108 109 6.199937 AGTGATATTTTTGCACTCATCCAC 57.800 37.500 0.00 0.00 38.41 4.02
117 118 9.729023 CGGTTATTAATGAGTGATATTTTTGCA 57.271 29.630 0.00 0.00 0.00 4.08
118 119 8.690840 GCGGTTATTAATGAGTGATATTTTTGC 58.309 33.333 0.00 0.00 0.00 3.68
119 120 9.729023 TGCGGTTATTAATGAGTGATATTTTTG 57.271 29.630 0.00 0.00 0.00 2.44
121 122 9.730420 GTTGCGGTTATTAATGAGTGATATTTT 57.270 29.630 0.00 0.00 0.00 1.82
122 123 8.898761 TGTTGCGGTTATTAATGAGTGATATTT 58.101 29.630 0.00 0.00 0.00 1.40
123 124 8.445275 TGTTGCGGTTATTAATGAGTGATATT 57.555 30.769 0.00 0.00 0.00 1.28
124 125 8.445275 TTGTTGCGGTTATTAATGAGTGATAT 57.555 30.769 0.00 0.00 0.00 1.63
125 126 7.851387 TTGTTGCGGTTATTAATGAGTGATA 57.149 32.000 0.00 0.00 0.00 2.15
126 127 6.751514 TTGTTGCGGTTATTAATGAGTGAT 57.248 33.333 0.00 0.00 0.00 3.06
127 128 6.751514 ATTGTTGCGGTTATTAATGAGTGA 57.248 33.333 0.00 0.00 0.00 3.41
128 129 6.910433 GGTATTGTTGCGGTTATTAATGAGTG 59.090 38.462 0.00 0.00 0.00 3.51
129 130 6.038936 GGGTATTGTTGCGGTTATTAATGAGT 59.961 38.462 0.00 0.00 0.00 3.41
130 131 6.262273 AGGGTATTGTTGCGGTTATTAATGAG 59.738 38.462 0.00 0.00 0.00 2.90
131 132 6.123651 AGGGTATTGTTGCGGTTATTAATGA 58.876 36.000 0.00 0.00 0.00 2.57
132 133 6.385649 AGGGTATTGTTGCGGTTATTAATG 57.614 37.500 0.00 0.00 0.00 1.90
133 134 7.093684 ACAAAGGGTATTGTTGCGGTTATTAAT 60.094 33.333 0.00 0.00 40.52 1.40
134 135 6.208994 ACAAAGGGTATTGTTGCGGTTATTAA 59.791 34.615 0.00 0.00 40.52 1.40
135 136 5.711036 ACAAAGGGTATTGTTGCGGTTATTA 59.289 36.000 0.00 0.00 40.52 0.98
136 137 4.525100 ACAAAGGGTATTGTTGCGGTTATT 59.475 37.500 0.00 0.00 40.52 1.40
137 138 4.083565 ACAAAGGGTATTGTTGCGGTTAT 58.916 39.130 0.00 0.00 40.52 1.89
138 139 3.488363 ACAAAGGGTATTGTTGCGGTTA 58.512 40.909 0.00 0.00 40.52 2.85
139 140 2.312390 ACAAAGGGTATTGTTGCGGTT 58.688 42.857 0.00 0.00 40.52 4.44
140 141 1.989706 ACAAAGGGTATTGTTGCGGT 58.010 45.000 0.00 0.00 40.52 5.68
163 164 9.479549 AATAAGTCTTGGTTATCCACATGAAAT 57.520 29.630 0.00 0.00 44.22 2.17
164 165 8.739039 CAATAAGTCTTGGTTATCCACATGAAA 58.261 33.333 0.00 0.00 44.22 2.69
165 166 7.888021 ACAATAAGTCTTGGTTATCCACATGAA 59.112 33.333 0.00 0.00 44.22 2.57
166 167 7.336679 CACAATAAGTCTTGGTTATCCACATGA 59.663 37.037 0.00 0.00 44.22 3.07
167 168 7.415541 CCACAATAAGTCTTGGTTATCCACATG 60.416 40.741 0.00 0.00 44.22 3.21
168 169 6.603201 CCACAATAAGTCTTGGTTATCCACAT 59.397 38.462 0.00 0.00 44.22 3.21
169 170 5.943416 CCACAATAAGTCTTGGTTATCCACA 59.057 40.000 0.00 0.00 44.22 4.17
170 171 5.357032 CCCACAATAAGTCTTGGTTATCCAC 59.643 44.000 0.00 0.00 44.22 4.02
171 172 5.251932 TCCCACAATAAGTCTTGGTTATCCA 59.748 40.000 0.00 0.00 42.66 3.41
172 173 5.751586 TCCCACAATAAGTCTTGGTTATCC 58.248 41.667 0.00 0.00 0.00 2.59
173 174 6.415573 ACTCCCACAATAAGTCTTGGTTATC 58.584 40.000 0.00 0.00 0.00 1.75
174 175 6.388619 ACTCCCACAATAAGTCTTGGTTAT 57.611 37.500 0.00 0.00 0.00 1.89
175 176 5.836024 ACTCCCACAATAAGTCTTGGTTA 57.164 39.130 0.00 0.00 0.00 2.85
176 177 4.724279 ACTCCCACAATAAGTCTTGGTT 57.276 40.909 0.00 0.00 0.00 3.67
177 178 4.141251 ACAACTCCCACAATAAGTCTTGGT 60.141 41.667 0.00 0.00 0.00 3.67
178 179 4.398319 ACAACTCCCACAATAAGTCTTGG 58.602 43.478 0.00 0.00 0.00 3.61
179 180 6.094048 CCATACAACTCCCACAATAAGTCTTG 59.906 42.308 0.00 0.00 0.00 3.02
180 181 6.180472 CCATACAACTCCCACAATAAGTCTT 58.820 40.000 0.00 0.00 0.00 3.01
181 182 5.745227 CCATACAACTCCCACAATAAGTCT 58.255 41.667 0.00 0.00 0.00 3.24
182 183 4.335594 GCCATACAACTCCCACAATAAGTC 59.664 45.833 0.00 0.00 0.00 3.01
183 184 4.270008 GCCATACAACTCCCACAATAAGT 58.730 43.478 0.00 0.00 0.00 2.24
184 185 3.632145 GGCCATACAACTCCCACAATAAG 59.368 47.826 0.00 0.00 0.00 1.73
185 186 3.626222 GGGCCATACAACTCCCACAATAA 60.626 47.826 4.39 0.00 38.62 1.40
186 187 2.092103 GGGCCATACAACTCCCACAATA 60.092 50.000 4.39 0.00 38.62 1.90
187 188 1.341976 GGGCCATACAACTCCCACAAT 60.342 52.381 4.39 0.00 38.62 2.71
188 189 0.039035 GGGCCATACAACTCCCACAA 59.961 55.000 4.39 0.00 38.62 3.33
189 190 0.844661 AGGGCCATACAACTCCCACA 60.845 55.000 6.18 0.00 41.22 4.17
190 191 0.331616 AAGGGCCATACAACTCCCAC 59.668 55.000 6.18 0.00 41.22 4.61
191 192 1.080638 AAAGGGCCATACAACTCCCA 58.919 50.000 6.18 0.00 41.22 4.37
192 193 2.231716 AAAAGGGCCATACAACTCCC 57.768 50.000 6.18 0.00 39.05 4.30
193 194 3.945921 GTCTAAAAGGGCCATACAACTCC 59.054 47.826 6.18 0.00 0.00 3.85
194 195 3.945921 GGTCTAAAAGGGCCATACAACTC 59.054 47.826 6.18 0.00 0.00 3.01
195 196 3.591977 AGGTCTAAAAGGGCCATACAACT 59.408 43.478 6.18 0.00 0.00 3.16
196 197 3.964411 AGGTCTAAAAGGGCCATACAAC 58.036 45.455 6.18 0.00 0.00 3.32
197 198 4.668138 AAGGTCTAAAAGGGCCATACAA 57.332 40.909 6.18 0.00 0.00 2.41
198 199 5.163131 GGATAAGGTCTAAAAGGGCCATACA 60.163 44.000 6.18 0.00 0.00 2.29
204 205 4.401519 GGTTTGGATAAGGTCTAAAAGGGC 59.598 45.833 0.00 0.00 38.76 5.19
209 210 7.610305 GTCTCAATGGTTTGGATAAGGTCTAAA 59.390 37.037 0.00 0.00 35.26 1.85
213 214 5.253330 TGTCTCAATGGTTTGGATAAGGTC 58.747 41.667 0.00 0.00 33.44 3.85
218 219 6.833416 CCCTTTATGTCTCAATGGTTTGGATA 59.167 38.462 0.00 0.00 33.44 2.59
226 227 7.062957 ACTATTTCCCCTTTATGTCTCAATGG 58.937 38.462 0.00 0.00 0.00 3.16
229 231 9.847224 GAATACTATTTCCCCTTTATGTCTCAA 57.153 33.333 0.00 0.00 0.00 3.02
236 238 7.073725 TGCCAGAGAATACTATTTCCCCTTTAT 59.926 37.037 0.00 0.00 0.00 1.40
240 242 4.307259 TGCCAGAGAATACTATTTCCCCT 58.693 43.478 0.00 0.00 0.00 4.79
244 246 9.727627 CAAAGATTTGCCAGAGAATACTATTTC 57.272 33.333 0.00 0.00 0.00 2.17
265 267 0.836606 TGGACCACAGAGTGCAAAGA 59.163 50.000 0.00 0.00 34.92 2.52
300 303 8.785184 AGTAATGCTAGGTTCTACTCCTATTT 57.215 34.615 0.00 0.00 37.01 1.40
337 340 6.773200 TCTCGAGTAGGTGATCTAATGTCATT 59.227 38.462 13.13 3.06 0.00 2.57
340 343 5.992829 TCTCTCGAGTAGGTGATCTAATGTC 59.007 44.000 13.13 0.00 0.00 3.06
358 361 7.421530 TGAAGTAGGAAACAATTTTCTCTCG 57.578 36.000 0.00 0.00 40.98 4.04
416 420 6.207417 CCATGTTTGCTACTCCTTATATTGGG 59.793 42.308 0.00 0.00 0.00 4.12
427 431 5.412594 TCAAGTTGATCCATGTTTGCTACTC 59.587 40.000 0.08 0.00 0.00 2.59
455 459 8.391106 ACAGATTTTCTATGTTATTTCGACAGC 58.609 33.333 0.00 0.00 0.00 4.40
473 483 9.289782 ACTCTAGACATGCTTTTAACAGATTTT 57.710 29.630 0.00 0.00 0.00 1.82
545 557 4.255833 TGCTCACATATACGATGATGCA 57.744 40.909 0.00 0.00 0.00 3.96
585 597 7.434492 ACACACCTTGATTACGGATATCTAAG 58.566 38.462 2.05 0.00 0.00 2.18
674 686 8.352201 GCTTTATATTCTCAAATACATGTGCCA 58.648 33.333 9.11 0.00 30.27 4.92
676 688 8.070171 ACGCTTTATATTCTCAAATACATGTGC 58.930 33.333 9.11 0.00 30.27 4.57
722 735 4.862574 TCACAAGTACATTCATGCTCGTAC 59.137 41.667 0.00 9.19 35.53 3.67
730 743 8.850156 GCCCTTTATATTCACAAGTACATTCAT 58.150 33.333 0.00 0.00 0.00 2.57
893 965 5.704515 CAGAGTTGGATGGATGATTGGATAC 59.295 44.000 0.00 0.00 0.00 2.24
968 1040 3.866327 GCTAGCTACAAGCCTTGAACTAC 59.134 47.826 12.25 0.00 43.77 2.73
995 1068 6.016276 GGAGGTATTCGATATTGCCATTTTGT 60.016 38.462 0.00 0.00 0.00 2.83
996 1069 6.016360 TGGAGGTATTCGATATTGCCATTTTG 60.016 38.462 0.00 0.00 0.00 2.44
1035 1108 4.024387 GTGGAAAGAAGCACGAACACAATA 60.024 41.667 0.00 0.00 0.00 1.90
1041 1114 3.105937 GTTTGTGGAAAGAAGCACGAAC 58.894 45.455 0.00 0.00 35.59 3.95
1045 1118 3.552890 GGGATGTTTGTGGAAAGAAGCAC 60.553 47.826 0.00 0.00 0.00 4.40
1061 1134 1.683917 CGCTAGCTTGAGTAGGGATGT 59.316 52.381 13.93 0.00 33.37 3.06
1082 1155 4.202367 CCTTTGAGTTTCCACTACCAGAGT 60.202 45.833 0.00 0.00 39.82 3.24
1164 1237 3.702045 ACAAACAAAATTCTTCGGGGACA 59.298 39.130 0.00 0.00 0.00 4.02
1171 1244 5.183014 AGGGTCGACAAACAAAATTCTTC 57.817 39.130 18.91 0.00 0.00 2.87
1468 1541 1.597742 GCAGGGTCATATGCGTCATT 58.402 50.000 0.00 0.00 31.87 2.57
1469 1542 0.250467 GGCAGGGTCATATGCGTCAT 60.250 55.000 0.00 0.00 43.49 3.06
1473 1546 2.666190 CCGGCAGGGTCATATGCG 60.666 66.667 0.00 0.00 43.49 4.73
1503 1576 3.071312 CCTCTGGCATATCTTGAAGCTCT 59.929 47.826 0.00 0.00 0.00 4.09
1554 1627 3.555795 CCATCCATACTAGCGATTGCAGT 60.556 47.826 7.90 10.89 46.23 4.40
1561 1634 0.679505 GTGCCCATCCATACTAGCGA 59.320 55.000 0.00 0.00 0.00 4.93
1562 1635 0.681733 AGTGCCCATCCATACTAGCG 59.318 55.000 0.00 0.00 0.00 4.26
1570 1643 1.668826 AGGAAGTTAGTGCCCATCCA 58.331 50.000 0.00 0.00 0.00 3.41
1579 1652 4.436079 ACCATTGGGACTAGGAAGTTAGT 58.564 43.478 7.78 0.00 35.56 2.24
1672 1745 9.466497 AGAAAATTAATGCCAGAGACATTTCTA 57.534 29.630 0.00 0.00 38.62 2.10
1673 1746 8.358582 AGAAAATTAATGCCAGAGACATTTCT 57.641 30.769 0.00 0.00 38.62 2.52
1732 1805 2.507547 CCGTTGCCATGCACATGC 60.508 61.111 5.06 0.00 38.71 4.06
1767 1840 3.254166 GTGCGAAGGATCAATTATGGCAT 59.746 43.478 4.88 4.88 0.00 4.40
1772 1845 4.572389 GTGACAGTGCGAAGGATCAATTAT 59.428 41.667 0.00 0.00 0.00 1.28
1773 1846 3.932710 GTGACAGTGCGAAGGATCAATTA 59.067 43.478 0.00 0.00 0.00 1.40
1795 1868 1.268794 CGGCTATCGTGGTGAAGAGAG 60.269 57.143 0.00 0.00 0.00 3.20
1796 1869 0.738975 CGGCTATCGTGGTGAAGAGA 59.261 55.000 0.00 0.00 0.00 3.10
1805 1878 3.909776 TTACTACCATCGGCTATCGTG 57.090 47.619 0.00 0.00 40.32 4.35
1810 1883 4.340381 GGAGAACTTTACTACCATCGGCTA 59.660 45.833 0.00 0.00 0.00 3.93
1813 1886 4.430908 GTGGAGAACTTTACTACCATCGG 58.569 47.826 0.00 0.00 0.00 4.18
1824 1897 7.074653 TCATGTTAAGTAGGTGGAGAACTTT 57.925 36.000 0.00 0.00 35.23 2.66
1858 1953 7.615039 AAGTATGATGACCAAGATCAGAGAT 57.385 36.000 0.00 0.00 33.38 2.75
1861 1956 9.383519 GTTAAAAGTATGATGACCAAGATCAGA 57.616 33.333 0.00 0.00 33.38 3.27
1912 2007 6.926272 TGTATTTTGAATTACAAGTTGGTGCC 59.074 34.615 7.96 0.00 39.77 5.01
1937 2032 5.112129 GGTGGTTCCCTACTTCATTACAT 57.888 43.478 0.00 0.00 0.00 2.29
1974 2069 0.398318 GGACTTGGAGGCAAGAGTGT 59.602 55.000 0.00 0.00 36.16 3.55
2012 2107 2.652095 TTACCGCCAAGGACGAGGG 61.652 63.158 0.00 0.00 45.00 4.30
2017 2112 2.250646 GGTTGTTACCGCCAAGGAC 58.749 57.895 0.00 0.00 45.00 3.85
2032 2127 5.690464 ATGAGCATGTAAAGAGAGAGGTT 57.310 39.130 0.00 0.00 0.00 3.50
2054 2149 8.896320 ATGTACGCCATCATTACAAGTAATTA 57.104 30.769 2.82 0.00 33.79 1.40
2219 2329 1.149288 AGGTCTTGGTAGTGGTCCTGA 59.851 52.381 0.00 0.00 0.00 3.86
2224 2334 0.977395 GCTCAGGTCTTGGTAGTGGT 59.023 55.000 0.00 0.00 0.00 4.16
2272 2382 4.505313 TTATGTGAGCAGGCTATACTCG 57.495 45.455 0.00 0.00 32.98 4.18
2294 2404 0.955905 GGGGTGTGCGCTTTTCTTTA 59.044 50.000 9.73 0.00 0.00 1.85
2310 2420 1.694525 GGAGGGGAGGAAAGAGGGG 60.695 68.421 0.00 0.00 0.00 4.79
2313 2423 1.082954 TGGGGAGGGGAGGAAAGAG 59.917 63.158 0.00 0.00 0.00 2.85
2314 2424 1.229853 GTGGGGAGGGGAGGAAAGA 60.230 63.158 0.00 0.00 0.00 2.52
2315 2425 2.309504 GGTGGGGAGGGGAGGAAAG 61.310 68.421 0.00 0.00 0.00 2.62
2316 2426 2.204244 GGTGGGGAGGGGAGGAAA 60.204 66.667 0.00 0.00 0.00 3.13
2317 2427 3.216371 AGGTGGGGAGGGGAGGAA 61.216 66.667 0.00 0.00 0.00 3.36
2318 2428 3.695825 GAGGTGGGGAGGGGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
2320 2430 3.925914 AACGAGGTGGGGAGGGGAG 62.926 68.421 0.00 0.00 0.00 4.30
2321 2431 3.918328 GAACGAGGTGGGGAGGGGA 62.918 68.421 0.00 0.00 0.00 4.81
2322 2432 3.400054 GAACGAGGTGGGGAGGGG 61.400 72.222 0.00 0.00 0.00 4.79
2323 2433 2.284699 AGAACGAGGTGGGGAGGG 60.285 66.667 0.00 0.00 0.00 4.30
2324 2434 2.359967 GGAGAACGAGGTGGGGAGG 61.360 68.421 0.00 0.00 0.00 4.30
2325 2435 2.359967 GGGAGAACGAGGTGGGGAG 61.360 68.421 0.00 0.00 0.00 4.30
2326 2436 2.284405 GGGAGAACGAGGTGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
2327 2437 2.606519 TGGGAGAACGAGGTGGGG 60.607 66.667 0.00 0.00 0.00 4.96
2328 2438 0.978146 ATCTGGGAGAACGAGGTGGG 60.978 60.000 0.00 0.00 0.00 4.61
2329 2439 1.776662 TATCTGGGAGAACGAGGTGG 58.223 55.000 0.00 0.00 0.00 4.61
2330 2440 2.030717 CGATATCTGGGAGAACGAGGTG 60.031 54.545 0.34 0.00 0.00 4.00
2331 2441 2.231529 CGATATCTGGGAGAACGAGGT 58.768 52.381 0.34 0.00 0.00 3.85
2332 2442 1.068194 GCGATATCTGGGAGAACGAGG 60.068 57.143 0.34 0.00 0.00 4.63
2333 2443 1.068194 GGCGATATCTGGGAGAACGAG 60.068 57.143 0.34 0.00 0.00 4.18
2334 2444 0.959553 GGCGATATCTGGGAGAACGA 59.040 55.000 0.34 0.00 0.00 3.85
2335 2445 0.387367 CGGCGATATCTGGGAGAACG 60.387 60.000 0.00 0.00 0.00 3.95
2336 2446 0.667792 GCGGCGATATCTGGGAGAAC 60.668 60.000 12.98 0.00 0.00 3.01
2337 2447 1.112916 TGCGGCGATATCTGGGAGAA 61.113 55.000 12.98 0.00 0.00 2.87
2338 2448 1.530655 TGCGGCGATATCTGGGAGA 60.531 57.895 12.98 0.00 0.00 3.71
2339 2449 1.373497 GTGCGGCGATATCTGGGAG 60.373 63.158 12.98 0.00 0.00 4.30
2340 2450 2.734591 GTGCGGCGATATCTGGGA 59.265 61.111 12.98 0.00 0.00 4.37
2341 2451 2.734723 CGTGCGGCGATATCTGGG 60.735 66.667 12.98 0.00 44.77 4.45
2342 2452 3.406361 GCGTGCGGCGATATCTGG 61.406 66.667 12.98 0.00 44.77 3.86
2351 2461 1.291877 CCTAATCCATAGCGTGCGGC 61.292 60.000 0.00 0.00 44.05 6.53
2352 2462 0.670546 CCCTAATCCATAGCGTGCGG 60.671 60.000 0.00 0.00 0.00 5.69
2353 2463 0.670546 CCCCTAATCCATAGCGTGCG 60.671 60.000 0.00 0.00 0.00 5.34
2354 2464 0.321653 CCCCCTAATCCATAGCGTGC 60.322 60.000 0.00 0.00 0.00 5.34
2355 2465 1.056660 ACCCCCTAATCCATAGCGTG 58.943 55.000 0.00 0.00 0.00 5.34
2356 2466 1.056660 CACCCCCTAATCCATAGCGT 58.943 55.000 0.00 0.00 0.00 5.07
2357 2467 0.324943 CCACCCCCTAATCCATAGCG 59.675 60.000 0.00 0.00 0.00 4.26
2358 2468 1.630878 CTCCACCCCCTAATCCATAGC 59.369 57.143 0.00 0.00 0.00 2.97
2359 2469 2.991580 ACTCCACCCCCTAATCCATAG 58.008 52.381 0.00 0.00 0.00 2.23
2360 2470 3.050564 AGAACTCCACCCCCTAATCCATA 60.051 47.826 0.00 0.00 0.00 2.74
2361 2471 2.136026 GAACTCCACCCCCTAATCCAT 58.864 52.381 0.00 0.00 0.00 3.41
2362 2472 1.082194 AGAACTCCACCCCCTAATCCA 59.918 52.381 0.00 0.00 0.00 3.41
2363 2473 1.894699 AGAACTCCACCCCCTAATCC 58.105 55.000 0.00 0.00 0.00 3.01
2364 2474 2.576648 ACAAGAACTCCACCCCCTAATC 59.423 50.000 0.00 0.00 0.00 1.75
2365 2475 2.576648 GACAAGAACTCCACCCCCTAAT 59.423 50.000 0.00 0.00 0.00 1.73
2366 2476 1.982958 GACAAGAACTCCACCCCCTAA 59.017 52.381 0.00 0.00 0.00 2.69
2367 2477 1.652947 GACAAGAACTCCACCCCCTA 58.347 55.000 0.00 0.00 0.00 3.53
2368 2478 1.134438 GGACAAGAACTCCACCCCCT 61.134 60.000 0.00 0.00 0.00 4.79
2369 2479 1.379146 GGACAAGAACTCCACCCCC 59.621 63.158 0.00 0.00 0.00 5.40
2370 2480 0.036875 CTGGACAAGAACTCCACCCC 59.963 60.000 0.00 0.00 33.97 4.95
2371 2481 0.036875 CCTGGACAAGAACTCCACCC 59.963 60.000 0.00 0.00 33.97 4.61
2372 2482 1.056660 TCCTGGACAAGAACTCCACC 58.943 55.000 0.00 0.00 33.97 4.61
2373 2483 2.368875 TCTTCCTGGACAAGAACTCCAC 59.631 50.000 0.00 0.00 33.97 4.02
2374 2484 2.689658 TCTTCCTGGACAAGAACTCCA 58.310 47.619 0.00 0.00 36.34 3.86
2375 2485 3.771577 TTCTTCCTGGACAAGAACTCC 57.228 47.619 6.72 0.00 35.40 3.85
2379 2489 3.924114 TGTGTTCTTCCTGGACAAGAA 57.076 42.857 6.72 6.72 37.50 2.52
2380 2490 3.199946 AGTTGTGTTCTTCCTGGACAAGA 59.800 43.478 0.00 0.00 0.00 3.02
2381 2491 3.545703 AGTTGTGTTCTTCCTGGACAAG 58.454 45.455 0.00 0.00 0.00 3.16
2406 2747 6.604735 TGGCTAGATTTTCTTTTCTATCGC 57.395 37.500 0.00 0.00 0.00 4.58
2407 2748 6.258727 TGCTGGCTAGATTTTCTTTTCTATCG 59.741 38.462 0.00 0.00 0.00 2.92
2412 2753 5.047731 ACCTTGCTGGCTAGATTTTCTTTTC 60.048 40.000 0.00 0.00 40.22 2.29
2426 2768 1.006922 GTTGCAGAACCTTGCTGGC 60.007 57.895 0.00 0.00 44.38 4.85
2438 2780 2.223377 GGTCGGTAACAAAGAGTTGCAG 59.777 50.000 0.00 0.00 43.66 4.41
2541 2883 8.849168 CATATGTGTATAGGGAGATTTTTGCAA 58.151 33.333 0.00 0.00 0.00 4.08
2572 2914 6.446781 CACGGAGAGTGTATAAGGAAGTTA 57.553 41.667 0.00 0.00 45.51 2.24
2589 2931 2.821546 CATACACATGGGTACACGGAG 58.178 52.381 10.71 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.