Multiple sequence alignment - TraesCS7B01G049900

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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 TraesCS7B01G049900 chr7B 100.000 2660 0 0 1 2660 51059476 51062135 0.000000e+00 4913
1 TraesCS7B01G049900 chr7B 94.845 388 11 2 1 381 372040549 372040164 4.900000e-167 597
2 TraesCS7B01G049900 chr7B 89.459 370 39 0 746 1115 638417729 638417360 4.010000e-128 468
3 TraesCS7B01G049900 chr7B 81.262 539 88 9 1142 1675 638417363 638416833 8.800000e-115 424
4 TraesCS7B01G049900 chr7A 94.417 1397 63 8 382 1766 99673012 99674405 0.000000e+00 2134
5 TraesCS7B01G049900 chr7A 89.258 391 23 11 9 382 48971281 48970893 3.100000e-129 472
6 TraesCS7B01G049900 chr6A 97.219 863 23 1 1799 2660 85581568 85580706 0.000000e+00 1459
7 TraesCS7B01G049900 chr6A 88.974 390 28 7 4 381 266761353 266760967 4.010000e-128 468
8 TraesCS7B01G049900 chr1A 96.886 867 25 2 1795 2660 23067076 23066211 0.000000e+00 1450
9 TraesCS7B01G049900 chr1A 95.921 858 29 2 1804 2660 441834752 441833900 0.000000e+00 1386
10 TraesCS7B01G049900 chr1A 95.814 860 27 3 1802 2660 586504542 586503691 0.000000e+00 1380
11 TraesCS7B01G049900 chr1A 90.026 391 23 10 4 381 486390105 486389718 2.380000e-135 492
12 TraesCS7B01G049900 chrUn 95.673 855 33 4 1808 2660 31720047 31720899 0.000000e+00 1371
13 TraesCS7B01G049900 chr3B 95.550 854 35 3 1809 2660 428201286 428200434 0.000000e+00 1363
14 TraesCS7B01G049900 chr3B 95.082 854 40 2 1809 2660 426087132 426086279 0.000000e+00 1343
15 TraesCS7B01G049900 chr1B 95.105 858 36 4 1808 2660 279905730 279906586 0.000000e+00 1347
16 TraesCS7B01G049900 chr1B 94.994 859 40 3 1805 2660 585830264 585829406 0.000000e+00 1345
17 TraesCS7B01G049900 chr7D 81.913 763 102 14 917 1675 576056693 576055963 1.750000e-171 612
18 TraesCS7B01G049900 chr7D 82.143 308 52 2 1256 1560 576089272 576089579 7.300000e-66 261
19 TraesCS7B01G049900 chr7D 78.733 442 52 21 404 827 576088301 576088718 9.450000e-65 257
20 TraesCS7B01G049900 chr4A 91.688 385 25 5 1 381 14838866 14838485 6.520000e-146 527
21 TraesCS7B01G049900 chr2A 91.349 393 22 7 1 381 604859534 604859926 6.520000e-146 527
22 TraesCS7B01G049900 chr4B 89.844 384 31 7 1 382 630534887 630535264 1.110000e-133 486
23 TraesCS7B01G049900 chr5B 89.870 385 24 7 1 381 403752549 403752176 5.150000e-132 481
24 TraesCS7B01G049900 chr3A 89.610 385 25 8 9 382 648161496 648161116 2.400000e-130 475


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 TraesCS7B01G049900 chr7B 51059476 51062135 2659 False 4913 4913 100.0000 1 2660 1 chr7B.!!$F1 2659
1 TraesCS7B01G049900 chr7B 638416833 638417729 896 True 446 468 85.3605 746 1675 2 chr7B.!!$R2 929
2 TraesCS7B01G049900 chr7A 99673012 99674405 1393 False 2134 2134 94.4170 382 1766 1 chr7A.!!$F1 1384
3 TraesCS7B01G049900 chr6A 85580706 85581568 862 True 1459 1459 97.2190 1799 2660 1 chr6A.!!$R1 861
4 TraesCS7B01G049900 chr1A 23066211 23067076 865 True 1450 1450 96.8860 1795 2660 1 chr1A.!!$R1 865
5 TraesCS7B01G049900 chr1A 441833900 441834752 852 True 1386 1386 95.9210 1804 2660 1 chr1A.!!$R2 856
6 TraesCS7B01G049900 chr1A 586503691 586504542 851 True 1380 1380 95.8140 1802 2660 1 chr1A.!!$R4 858
7 TraesCS7B01G049900 chrUn 31720047 31720899 852 False 1371 1371 95.6730 1808 2660 1 chrUn.!!$F1 852
8 TraesCS7B01G049900 chr3B 428200434 428201286 852 True 1363 1363 95.5500 1809 2660 1 chr3B.!!$R2 851
9 TraesCS7B01G049900 chr3B 426086279 426087132 853 True 1343 1343 95.0820 1809 2660 1 chr3B.!!$R1 851
10 TraesCS7B01G049900 chr1B 279905730 279906586 856 False 1347 1347 95.1050 1808 2660 1 chr1B.!!$F1 852
11 TraesCS7B01G049900 chr1B 585829406 585830264 858 True 1345 1345 94.9940 1805 2660 1 chr1B.!!$R1 855
12 TraesCS7B01G049900 chr7D 576055963 576056693 730 True 612 612 81.9130 917 1675 1 chr7D.!!$R1 758
13 TraesCS7B01G049900 chr7D 576088301 576089579 1278 False 259 261 80.4380 404 1560 2 chr7D.!!$F1 1156

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
104 105 0.033208 AGAGCAGAGAGAGTGGGGAG 60.033 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 2279 0.030908 GGACAGGATACGCGAAGGAG 59.969 60.0 15.93 0.0 46.39 3.69 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
58 59 3.494336 CGGCGAGCAAAGCAGAGG 61.494 66.667 0.00 0.00 36.08 3.69
59 60 2.046892 GGCGAGCAAAGCAGAGGA 60.047 61.111 0.00 0.00 36.08 3.71
60 61 2.105466 GGCGAGCAAAGCAGAGGAG 61.105 63.158 0.00 0.00 36.08 3.69
61 62 2.748843 GCGAGCAAAGCAGAGGAGC 61.749 63.158 0.00 0.00 34.19 4.70
62 63 1.375140 CGAGCAAAGCAGAGGAGCA 60.375 57.895 0.00 0.00 36.85 4.26
63 64 0.952497 CGAGCAAAGCAGAGGAGCAA 60.952 55.000 0.00 0.00 36.85 3.91
64 65 0.803740 GAGCAAAGCAGAGGAGCAAG 59.196 55.000 0.00 0.00 36.85 4.01
65 66 0.399454 AGCAAAGCAGAGGAGCAAGA 59.601 50.000 0.00 0.00 36.85 3.02
66 67 0.520847 GCAAAGCAGAGGAGCAAGAC 59.479 55.000 0.00 0.00 36.85 3.01
67 68 1.888215 CAAAGCAGAGGAGCAAGACA 58.112 50.000 0.00 0.00 36.85 3.41
68 69 1.805345 CAAAGCAGAGGAGCAAGACAG 59.195 52.381 0.00 0.00 36.85 3.51
69 70 1.346062 AAGCAGAGGAGCAAGACAGA 58.654 50.000 0.00 0.00 36.85 3.41
70 71 0.896923 AGCAGAGGAGCAAGACAGAG 59.103 55.000 0.00 0.00 36.85 3.35
71 72 0.108233 GCAGAGGAGCAAGACAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
72 73 1.554836 CAGAGGAGCAAGACAGAGGA 58.445 55.000 0.00 0.00 0.00 3.71
73 74 1.477700 CAGAGGAGCAAGACAGAGGAG 59.522 57.143 0.00 0.00 0.00 3.69
74 75 0.823460 GAGGAGCAAGACAGAGGAGG 59.177 60.000 0.00 0.00 0.00 4.30
75 76 0.411452 AGGAGCAAGACAGAGGAGGA 59.589 55.000 0.00 0.00 0.00 3.71
76 77 0.823460 GGAGCAAGACAGAGGAGGAG 59.177 60.000 0.00 0.00 0.00 3.69
77 78 1.555967 GAGCAAGACAGAGGAGGAGT 58.444 55.000 0.00 0.00 0.00 3.85
78 79 1.204467 GAGCAAGACAGAGGAGGAGTG 59.796 57.143 0.00 0.00 0.00 3.51
79 80 1.203112 AGCAAGACAGAGGAGGAGTGA 60.203 52.381 0.00 0.00 0.00 3.41
80 81 1.204467 GCAAGACAGAGGAGGAGTGAG 59.796 57.143 0.00 0.00 0.00 3.51
81 82 1.204467 CAAGACAGAGGAGGAGTGAGC 59.796 57.143 0.00 0.00 0.00 4.26
82 83 0.679640 AGACAGAGGAGGAGTGAGCG 60.680 60.000 0.00 0.00 0.00 5.03
83 84 0.678366 GACAGAGGAGGAGTGAGCGA 60.678 60.000 0.00 0.00 0.00 4.93
84 85 0.251386 ACAGAGGAGGAGTGAGCGAA 60.251 55.000 0.00 0.00 0.00 4.70
85 86 0.891373 CAGAGGAGGAGTGAGCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
86 87 1.135141 CAGAGGAGGAGTGAGCGAAAG 60.135 57.143 0.00 0.00 0.00 2.62
87 88 1.178276 GAGGAGGAGTGAGCGAAAGA 58.822 55.000 0.00 0.00 0.00 2.52
88 89 1.134175 GAGGAGGAGTGAGCGAAAGAG 59.866 57.143 0.00 0.00 0.00 2.85
89 90 0.459411 GGAGGAGTGAGCGAAAGAGC 60.459 60.000 0.00 0.00 37.41 4.09
90 91 0.244994 GAGGAGTGAGCGAAAGAGCA 59.755 55.000 0.00 0.00 40.15 4.26
91 92 0.246086 AGGAGTGAGCGAAAGAGCAG 59.754 55.000 0.00 0.00 40.15 4.24
92 93 0.244994 GGAGTGAGCGAAAGAGCAGA 59.755 55.000 0.00 0.00 40.15 4.26
93 94 1.627879 GAGTGAGCGAAAGAGCAGAG 58.372 55.000 0.00 0.00 40.15 3.35
94 95 1.201181 GAGTGAGCGAAAGAGCAGAGA 59.799 52.381 0.00 0.00 40.15 3.10
95 96 1.202114 AGTGAGCGAAAGAGCAGAGAG 59.798 52.381 0.00 0.00 40.15 3.20
96 97 1.201181 GTGAGCGAAAGAGCAGAGAGA 59.799 52.381 0.00 0.00 40.15 3.10
97 98 1.472082 TGAGCGAAAGAGCAGAGAGAG 59.528 52.381 0.00 0.00 40.15 3.20
98 99 1.472480 GAGCGAAAGAGCAGAGAGAGT 59.528 52.381 0.00 0.00 40.15 3.24
99 100 1.202114 AGCGAAAGAGCAGAGAGAGTG 59.798 52.381 0.00 0.00 40.15 3.51
100 101 1.735369 GCGAAAGAGCAGAGAGAGTGG 60.735 57.143 0.00 0.00 37.05 4.00
101 102 1.135141 CGAAAGAGCAGAGAGAGTGGG 60.135 57.143 0.00 0.00 0.00 4.61
102 103 1.206849 GAAAGAGCAGAGAGAGTGGGG 59.793 57.143 0.00 0.00 0.00 4.96
103 104 0.411452 AAGAGCAGAGAGAGTGGGGA 59.589 55.000 0.00 0.00 0.00 4.81
104 105 0.033208 AGAGCAGAGAGAGTGGGGAG 60.033 60.000 0.00 0.00 0.00 4.30
105 106 0.324275 GAGCAGAGAGAGTGGGGAGT 60.324 60.000 0.00 0.00 0.00 3.85
106 107 0.614415 AGCAGAGAGAGTGGGGAGTG 60.614 60.000 0.00 0.00 0.00 3.51
107 108 1.612395 GCAGAGAGAGTGGGGAGTGG 61.612 65.000 0.00 0.00 0.00 4.00
108 109 0.975040 CAGAGAGAGTGGGGAGTGGG 60.975 65.000 0.00 0.00 0.00 4.61
109 110 1.687493 GAGAGAGTGGGGAGTGGGG 60.687 68.421 0.00 0.00 0.00 4.96
110 111 2.689034 GAGAGTGGGGAGTGGGGG 60.689 72.222 0.00 0.00 0.00 5.40
142 143 2.178912 GTCTTTTGACCGGTCCATCA 57.821 50.000 31.19 11.15 43.37 3.07
143 144 2.500229 GTCTTTTGACCGGTCCATCAA 58.500 47.619 31.19 16.87 43.37 2.57
144 145 2.882137 GTCTTTTGACCGGTCCATCAAA 59.118 45.455 31.19 21.62 43.37 2.69
145 146 2.882137 TCTTTTGACCGGTCCATCAAAC 59.118 45.455 31.19 5.34 42.87 2.93
146 147 2.350057 TTTGACCGGTCCATCAAACA 57.650 45.000 31.19 8.28 39.34 2.83
147 148 1.890876 TTGACCGGTCCATCAAACAG 58.109 50.000 31.19 0.00 31.95 3.16
148 149 1.052617 TGACCGGTCCATCAAACAGA 58.947 50.000 31.19 5.95 0.00 3.41
149 150 1.001974 TGACCGGTCCATCAAACAGAG 59.998 52.381 31.19 0.00 0.00 3.35
150 151 0.324943 ACCGGTCCATCAAACAGAGG 59.675 55.000 0.00 0.00 0.00 3.69
151 152 1.026718 CCGGTCCATCAAACAGAGGC 61.027 60.000 0.00 0.00 0.00 4.70
152 153 0.321564 CGGTCCATCAAACAGAGGCA 60.322 55.000 0.00 0.00 0.00 4.75
153 154 1.679944 CGGTCCATCAAACAGAGGCAT 60.680 52.381 0.00 0.00 0.00 4.40
154 155 2.419990 CGGTCCATCAAACAGAGGCATA 60.420 50.000 0.00 0.00 0.00 3.14
155 156 2.945668 GGTCCATCAAACAGAGGCATAC 59.054 50.000 0.00 0.00 0.00 2.39
156 157 2.609459 GTCCATCAAACAGAGGCATACG 59.391 50.000 0.00 0.00 0.00 3.06
157 158 1.942657 CCATCAAACAGAGGCATACGG 59.057 52.381 0.00 0.00 0.00 4.02
158 159 1.331756 CATCAAACAGAGGCATACGGC 59.668 52.381 0.00 0.00 43.74 5.68
159 160 0.739462 TCAAACAGAGGCATACGGCG 60.739 55.000 4.80 4.80 46.16 6.46
160 161 2.106683 AAACAGAGGCATACGGCGC 61.107 57.895 6.90 0.00 46.16 6.53
176 177 2.431260 GCCGTCAAACGCCGTCTA 60.431 61.111 0.00 0.00 40.91 2.59
177 178 2.023223 GCCGTCAAACGCCGTCTAA 61.023 57.895 0.00 0.00 40.91 2.10
178 179 1.777199 CCGTCAAACGCCGTCTAAC 59.223 57.895 0.00 0.00 40.91 2.34
179 180 1.409579 CGTCAAACGCCGTCTAACG 59.590 57.895 0.00 0.00 35.23 3.18
188 189 2.202570 CGTCTAACGGCTGTCGGG 60.203 66.667 6.61 0.00 44.45 5.14
189 190 2.693762 CGTCTAACGGCTGTCGGGA 61.694 63.158 6.61 0.00 44.45 5.14
190 191 1.153881 GTCTAACGGCTGTCGGGAC 60.154 63.158 6.61 7.69 44.45 4.46
237 238 2.274104 GGCCCCGCCTGTCATAAA 59.726 61.111 0.00 0.00 46.69 1.40
238 239 2.119029 GGCCCCGCCTGTCATAAAC 61.119 63.158 0.00 0.00 46.69 2.01
239 240 1.377987 GCCCCGCCTGTCATAAACA 60.378 57.895 0.00 0.00 36.18 2.83
240 241 0.963355 GCCCCGCCTGTCATAAACAA 60.963 55.000 0.00 0.00 37.45 2.83
241 242 1.094785 CCCCGCCTGTCATAAACAAG 58.905 55.000 0.00 0.00 37.45 3.16
242 243 0.451783 CCCGCCTGTCATAAACAAGC 59.548 55.000 0.00 0.00 41.16 4.01
243 244 1.453155 CCGCCTGTCATAAACAAGCT 58.547 50.000 0.00 0.00 42.19 3.74
244 245 1.812571 CCGCCTGTCATAAACAAGCTT 59.187 47.619 0.00 0.00 42.19 3.74
245 246 3.006940 CCGCCTGTCATAAACAAGCTTA 58.993 45.455 0.00 0.00 42.19 3.09
246 247 3.627577 CCGCCTGTCATAAACAAGCTTAT 59.372 43.478 0.00 0.00 42.19 1.73
247 248 4.260784 CCGCCTGTCATAAACAAGCTTATC 60.261 45.833 0.00 0.00 42.19 1.75
248 249 4.572389 CGCCTGTCATAAACAAGCTTATCT 59.428 41.667 0.00 0.00 42.19 1.98
249 250 5.503031 CGCCTGTCATAAACAAGCTTATCTG 60.503 44.000 0.00 0.00 42.19 2.90
250 251 5.586243 GCCTGTCATAAACAAGCTTATCTGA 59.414 40.000 0.00 0.00 41.33 3.27
251 252 6.238320 GCCTGTCATAAACAAGCTTATCTGAG 60.238 42.308 0.00 0.00 41.33 3.35
252 253 6.238320 CCTGTCATAAACAAGCTTATCTGAGC 60.238 42.308 0.00 0.00 37.45 4.26
253 254 5.586243 TGTCATAAACAAGCTTATCTGAGCC 59.414 40.000 0.00 0.00 36.77 4.70
254 255 5.008118 GTCATAAACAAGCTTATCTGAGCCC 59.992 44.000 0.00 0.00 43.74 5.19
255 256 2.029838 AACAAGCTTATCTGAGCCCG 57.970 50.000 0.00 0.00 43.74 6.13
256 257 1.195115 ACAAGCTTATCTGAGCCCGA 58.805 50.000 0.00 0.00 43.74 5.14
257 258 1.765314 ACAAGCTTATCTGAGCCCGAT 59.235 47.619 0.00 0.00 43.74 4.18
258 259 2.224161 ACAAGCTTATCTGAGCCCGATC 60.224 50.000 0.00 0.00 43.74 3.69
259 260 0.972883 AGCTTATCTGAGCCCGATCC 59.027 55.000 0.00 0.00 43.74 3.36
260 261 0.389166 GCTTATCTGAGCCCGATCCG 60.389 60.000 0.00 0.00 36.66 4.18
261 262 0.389166 CTTATCTGAGCCCGATCCGC 60.389 60.000 0.00 0.00 0.00 5.54
262 263 1.816863 TTATCTGAGCCCGATCCGCC 61.817 60.000 0.00 0.00 0.00 6.13
266 267 4.726351 GAGCCCGATCCGCCGATC 62.726 72.222 5.09 5.09 41.43 3.69
269 270 3.606662 CCCGATCCGCCGATCAGT 61.607 66.667 14.20 0.00 44.55 3.41
270 271 2.355126 CCGATCCGCCGATCAGTG 60.355 66.667 14.20 0.00 44.55 3.66
271 272 3.032609 CGATCCGCCGATCAGTGC 61.033 66.667 14.20 0.00 44.55 4.40
272 273 2.419198 GATCCGCCGATCAGTGCT 59.581 61.111 9.80 0.00 43.87 4.40
273 274 1.227380 GATCCGCCGATCAGTGCTT 60.227 57.895 9.80 0.00 43.87 3.91
274 275 0.811616 GATCCGCCGATCAGTGCTTT 60.812 55.000 9.80 0.00 43.87 3.51
275 276 0.811616 ATCCGCCGATCAGTGCTTTC 60.812 55.000 0.00 0.00 0.00 2.62
276 277 1.448540 CCGCCGATCAGTGCTTTCT 60.449 57.895 0.00 0.00 0.00 2.52
277 278 1.699656 CCGCCGATCAGTGCTTTCTG 61.700 60.000 0.00 0.00 36.85 3.02
278 279 1.427020 GCCGATCAGTGCTTTCTGC 59.573 57.895 0.00 0.00 43.25 4.26
292 293 4.546570 GCTTTCTGCAAAAAGATTACCGT 58.453 39.130 16.70 0.00 42.31 4.83
293 294 5.695818 GCTTTCTGCAAAAAGATTACCGTA 58.304 37.500 16.70 0.00 42.31 4.02
294 295 5.795441 GCTTTCTGCAAAAAGATTACCGTAG 59.205 40.000 16.70 0.00 42.31 3.51
295 296 6.348213 GCTTTCTGCAAAAAGATTACCGTAGA 60.348 38.462 16.70 0.00 42.31 2.59
296 297 6.476243 TTCTGCAAAAAGATTACCGTAGAC 57.524 37.500 0.00 0.00 0.00 2.59
297 298 5.543714 TCTGCAAAAAGATTACCGTAGACA 58.456 37.500 0.00 0.00 0.00 3.41
298 299 5.407387 TCTGCAAAAAGATTACCGTAGACAC 59.593 40.000 0.00 0.00 0.00 3.67
340 341 7.631915 AAAAATGTATTGTAGTGGTTTTCGC 57.368 32.000 0.00 0.00 0.00 4.70
341 342 5.950758 AATGTATTGTAGTGGTTTTCGCA 57.049 34.783 0.00 0.00 0.00 5.10
342 343 5.950758 ATGTATTGTAGTGGTTTTCGCAA 57.049 34.783 0.00 0.00 0.00 4.85
343 344 5.098218 TGTATTGTAGTGGTTTTCGCAAC 57.902 39.130 0.00 0.00 0.00 4.17
344 345 4.575236 TGTATTGTAGTGGTTTTCGCAACA 59.425 37.500 0.51 0.00 0.00 3.33
345 346 3.408288 TTGTAGTGGTTTTCGCAACAC 57.592 42.857 0.00 0.00 0.00 3.32
346 347 2.634600 TGTAGTGGTTTTCGCAACACT 58.365 42.857 5.31 5.31 45.32 3.55
347 348 3.011119 TGTAGTGGTTTTCGCAACACTT 58.989 40.909 5.28 0.00 41.03 3.16
348 349 2.559998 AGTGGTTTTCGCAACACTTG 57.440 45.000 0.00 0.00 41.03 3.16
361 362 3.795877 CAACACTTGCCTTCAAAATGGT 58.204 40.909 0.00 0.00 0.00 3.55
362 363 3.457610 ACACTTGCCTTCAAAATGGTG 57.542 42.857 0.00 0.00 33.48 4.17
363 364 2.102925 ACACTTGCCTTCAAAATGGTGG 59.897 45.455 0.00 0.00 32.30 4.61
364 365 2.102925 CACTTGCCTTCAAAATGGTGGT 59.897 45.455 0.00 0.00 0.00 4.16
365 366 2.771372 ACTTGCCTTCAAAATGGTGGTT 59.229 40.909 0.00 0.00 0.00 3.67
366 367 3.199727 ACTTGCCTTCAAAATGGTGGTTT 59.800 39.130 0.00 0.00 0.00 3.27
367 368 3.922171 TGCCTTCAAAATGGTGGTTTT 57.078 38.095 0.00 0.00 0.00 2.43
368 369 3.802866 TGCCTTCAAAATGGTGGTTTTC 58.197 40.909 0.00 0.00 0.00 2.29
369 370 3.454082 TGCCTTCAAAATGGTGGTTTTCT 59.546 39.130 0.00 0.00 0.00 2.52
370 371 3.809279 GCCTTCAAAATGGTGGTTTTCTG 59.191 43.478 0.00 0.00 0.00 3.02
371 372 3.809279 CCTTCAAAATGGTGGTTTTCTGC 59.191 43.478 0.00 0.00 0.00 4.26
372 373 4.440880 CTTCAAAATGGTGGTTTTCTGCA 58.559 39.130 0.00 0.00 0.00 4.41
373 374 4.478206 TCAAAATGGTGGTTTTCTGCAA 57.522 36.364 0.00 0.00 0.00 4.08
374 375 5.033589 TCAAAATGGTGGTTTTCTGCAAT 57.966 34.783 0.00 0.00 0.00 3.56
375 376 5.435291 TCAAAATGGTGGTTTTCTGCAATT 58.565 33.333 0.00 0.00 0.00 2.32
376 377 5.884792 TCAAAATGGTGGTTTTCTGCAATTT 59.115 32.000 0.00 0.00 0.00 1.82
377 378 7.050377 TCAAAATGGTGGTTTTCTGCAATTTA 58.950 30.769 0.00 0.00 0.00 1.40
378 379 6.859420 AAATGGTGGTTTTCTGCAATTTAC 57.141 33.333 0.00 0.00 0.00 2.01
379 380 5.806654 ATGGTGGTTTTCTGCAATTTACT 57.193 34.783 0.00 0.00 0.00 2.24
380 381 5.195001 TGGTGGTTTTCTGCAATTTACTC 57.805 39.130 0.00 0.00 0.00 2.59
425 426 2.444140 CCCGATCTCCCCGTCCTT 60.444 66.667 0.00 0.00 0.00 3.36
441 445 2.922503 TTCTCCTGCGTCCTGGCA 60.923 61.111 0.00 0.00 41.45 4.92
493 497 1.306482 CTCCTCCCAGCCTTCTCCA 60.306 63.158 0.00 0.00 0.00 3.86
494 498 1.613630 TCCTCCCAGCCTTCTCCAC 60.614 63.158 0.00 0.00 0.00 4.02
495 499 2.674220 CCTCCCAGCCTTCTCCACC 61.674 68.421 0.00 0.00 0.00 4.61
496 500 3.003173 TCCCAGCCTTCTCCACCG 61.003 66.667 0.00 0.00 0.00 4.94
497 501 4.785453 CCCAGCCTTCTCCACCGC 62.785 72.222 0.00 0.00 0.00 5.68
498 502 4.785453 CCAGCCTTCTCCACCGCC 62.785 72.222 0.00 0.00 0.00 6.13
499 503 4.020617 CAGCCTTCTCCACCGCCA 62.021 66.667 0.00 0.00 0.00 5.69
562 569 2.665185 GCTTTGACGTCGGCTGGT 60.665 61.111 11.62 0.00 0.00 4.00
1038 1511 3.055719 CACCCATGCGTCGGCTTT 61.056 61.111 0.00 0.00 40.82 3.51
1161 1646 2.607750 GAGGGAGGCCTGGTGACA 60.608 66.667 12.00 0.00 39.59 3.58
1233 1718 2.988839 ATTCCCAGGGCTGAGGCAC 61.989 63.158 8.68 0.00 43.32 5.01
1353 1841 1.602311 GCATGGAGGGCTACATCAAG 58.398 55.000 0.00 0.00 30.05 3.02
1408 1896 4.388499 GCCTTGACGGGAAGCCGA 62.388 66.667 0.00 0.00 36.94 5.54
1420 1908 2.172483 GAAGCCGAGAGCCCTGAACA 62.172 60.000 0.00 0.00 45.47 3.18
1432 1920 3.234630 CTGAACACCCTCCGGCGAA 62.235 63.158 9.30 0.00 0.00 4.70
1554 2042 1.507630 CGTGTCGGGGAATGTCGTA 59.492 57.895 0.00 0.00 0.00 3.43
1576 2064 1.386525 GGCATACCGTCGGTACCTCA 61.387 60.000 25.95 6.26 41.31 3.86
1642 2130 1.895798 AGCTGGAGAATCAGTTGTCGA 59.104 47.619 0.00 0.00 36.25 4.20
1660 2148 1.859383 GAAGCTGTTCGAGGGATAGC 58.141 55.000 0.00 0.00 34.65 2.97
1674 2162 3.265479 AGGGATAGCAGACTGAAAGCTTT 59.735 43.478 12.53 12.53 39.68 3.51
1693 2181 4.409570 CTTTGCACTGCATGTTGTATCTC 58.590 43.478 4.10 0.00 38.76 2.75
1739 2227 1.524621 CTGGCGCCTATCCACTTGG 60.525 63.158 29.70 0.93 0.00 3.61
1766 2254 6.036953 GCTGGATTCAGAAACTCTCAATGTAG 59.963 42.308 4.75 0.00 43.49 2.74
1767 2255 7.244886 TGGATTCAGAAACTCTCAATGTAGA 57.755 36.000 0.00 0.00 0.00 2.59
1768 2256 7.855375 TGGATTCAGAAACTCTCAATGTAGAT 58.145 34.615 0.00 0.00 0.00 1.98
1769 2257 7.767659 TGGATTCAGAAACTCTCAATGTAGATG 59.232 37.037 0.00 0.00 0.00 2.90
1770 2258 6.974932 TTCAGAAACTCTCAATGTAGATGC 57.025 37.500 0.00 0.00 0.00 3.91
1771 2259 5.423015 TCAGAAACTCTCAATGTAGATGCC 58.577 41.667 0.00 0.00 0.00 4.40
1772 2260 5.046376 TCAGAAACTCTCAATGTAGATGCCA 60.046 40.000 0.00 0.00 0.00 4.92
1773 2261 5.821470 CAGAAACTCTCAATGTAGATGCCAT 59.179 40.000 0.00 0.00 0.00 4.40
1774 2262 6.988580 CAGAAACTCTCAATGTAGATGCCATA 59.011 38.462 0.00 0.00 0.00 2.74
1775 2263 7.171167 CAGAAACTCTCAATGTAGATGCCATAG 59.829 40.741 0.00 0.00 0.00 2.23
1776 2264 5.480642 ACTCTCAATGTAGATGCCATAGG 57.519 43.478 0.00 0.00 0.00 2.57
1777 2265 5.150715 ACTCTCAATGTAGATGCCATAGGA 58.849 41.667 0.00 0.00 0.00 2.94
1778 2266 5.604231 ACTCTCAATGTAGATGCCATAGGAA 59.396 40.000 0.00 0.00 0.00 3.36
1779 2267 5.858381 TCTCAATGTAGATGCCATAGGAAC 58.142 41.667 0.00 0.00 0.00 3.62
1780 2268 5.604231 TCTCAATGTAGATGCCATAGGAACT 59.396 40.000 0.00 0.00 46.37 3.01
1781 2269 5.614308 TCAATGTAGATGCCATAGGAACTG 58.386 41.667 0.00 0.00 41.52 3.16
1782 2270 3.475566 TGTAGATGCCATAGGAACTGC 57.524 47.619 0.00 0.00 41.52 4.40
1783 2271 2.104792 TGTAGATGCCATAGGAACTGCC 59.895 50.000 0.00 0.00 41.52 4.85
1784 2272 0.107456 AGATGCCATAGGAACTGCCG 59.893 55.000 0.00 0.00 41.52 5.69
1785 2273 0.106708 GATGCCATAGGAACTGCCGA 59.893 55.000 0.00 0.00 41.52 5.54
1786 2274 0.546122 ATGCCATAGGAACTGCCGAA 59.454 50.000 0.00 0.00 41.52 4.30
1787 2275 0.392461 TGCCATAGGAACTGCCGAAC 60.392 55.000 0.00 0.00 41.52 3.95
1788 2276 0.107654 GCCATAGGAACTGCCGAACT 60.108 55.000 0.00 0.00 41.52 3.01
1789 2277 1.656652 CCATAGGAACTGCCGAACTG 58.343 55.000 0.00 0.00 41.52 3.16
1790 2278 1.207089 CCATAGGAACTGCCGAACTGA 59.793 52.381 0.00 0.00 41.52 3.41
1791 2279 2.271800 CATAGGAACTGCCGAACTGAC 58.728 52.381 0.00 0.00 41.52 3.51
1792 2280 1.629043 TAGGAACTGCCGAACTGACT 58.371 50.000 0.00 0.00 41.52 3.41
1793 2281 0.318762 AGGAACTGCCGAACTGACTC 59.681 55.000 0.00 0.00 43.43 3.36
1879 2369 0.104356 TACAACCTTCCCACCTCCCA 60.104 55.000 0.00 0.00 0.00 4.37
2095 2587 3.013327 GGTAGGCCGGTTCCCCTT 61.013 66.667 1.90 0.00 32.65 3.95
2187 2679 2.764128 GGAGGCGATCCTGGTCCA 60.764 66.667 0.00 0.00 44.46 4.02
2491 2987 2.042639 GCTTGGGCATGGGGATGT 60.043 61.111 0.00 0.00 38.54 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.157958 CTCTGCTTTGCTCGCCGC 62.158 66.667 0.00 0.00 39.77 6.53
41 42 3.494336 CCTCTGCTTTGCTCGCCG 61.494 66.667 0.00 0.00 0.00 6.46
42 43 2.046892 TCCTCTGCTTTGCTCGCC 60.047 61.111 0.00 0.00 0.00 5.54
43 44 2.748843 GCTCCTCTGCTTTGCTCGC 61.749 63.158 0.00 0.00 0.00 5.03
44 45 0.952497 TTGCTCCTCTGCTTTGCTCG 60.952 55.000 0.00 0.00 0.00 5.03
45 46 0.803740 CTTGCTCCTCTGCTTTGCTC 59.196 55.000 0.00 0.00 0.00 4.26
46 47 0.399454 TCTTGCTCCTCTGCTTTGCT 59.601 50.000 0.00 0.00 0.00 3.91
47 48 0.520847 GTCTTGCTCCTCTGCTTTGC 59.479 55.000 0.00 0.00 0.00 3.68
48 49 1.805345 CTGTCTTGCTCCTCTGCTTTG 59.195 52.381 0.00 0.00 0.00 2.77
49 50 1.696336 TCTGTCTTGCTCCTCTGCTTT 59.304 47.619 0.00 0.00 0.00 3.51
50 51 1.275856 CTCTGTCTTGCTCCTCTGCTT 59.724 52.381 0.00 0.00 0.00 3.91
51 52 0.896923 CTCTGTCTTGCTCCTCTGCT 59.103 55.000 0.00 0.00 0.00 4.24
52 53 0.108233 CCTCTGTCTTGCTCCTCTGC 60.108 60.000 0.00 0.00 0.00 4.26
53 54 1.477700 CTCCTCTGTCTTGCTCCTCTG 59.522 57.143 0.00 0.00 0.00 3.35
54 55 1.619432 CCTCCTCTGTCTTGCTCCTCT 60.619 57.143 0.00 0.00 0.00 3.69
55 56 0.823460 CCTCCTCTGTCTTGCTCCTC 59.177 60.000 0.00 0.00 0.00 3.71
56 57 0.411452 TCCTCCTCTGTCTTGCTCCT 59.589 55.000 0.00 0.00 0.00 3.69
57 58 0.823460 CTCCTCCTCTGTCTTGCTCC 59.177 60.000 0.00 0.00 0.00 4.70
58 59 1.204467 CACTCCTCCTCTGTCTTGCTC 59.796 57.143 0.00 0.00 0.00 4.26
59 60 1.203112 TCACTCCTCCTCTGTCTTGCT 60.203 52.381 0.00 0.00 0.00 3.91
60 61 1.204467 CTCACTCCTCCTCTGTCTTGC 59.796 57.143 0.00 0.00 0.00 4.01
61 62 1.204467 GCTCACTCCTCCTCTGTCTTG 59.796 57.143 0.00 0.00 0.00 3.02
62 63 1.555967 GCTCACTCCTCCTCTGTCTT 58.444 55.000 0.00 0.00 0.00 3.01
63 64 0.679640 CGCTCACTCCTCCTCTGTCT 60.680 60.000 0.00 0.00 0.00 3.41
64 65 0.678366 TCGCTCACTCCTCCTCTGTC 60.678 60.000 0.00 0.00 0.00 3.51
65 66 0.251386 TTCGCTCACTCCTCCTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
66 67 0.891373 TTTCGCTCACTCCTCCTCTG 59.109 55.000 0.00 0.00 0.00 3.35
67 68 1.181786 CTTTCGCTCACTCCTCCTCT 58.818 55.000 0.00 0.00 0.00 3.69
68 69 1.134175 CTCTTTCGCTCACTCCTCCTC 59.866 57.143 0.00 0.00 0.00 3.71
69 70 1.181786 CTCTTTCGCTCACTCCTCCT 58.818 55.000 0.00 0.00 0.00 3.69
70 71 0.459411 GCTCTTTCGCTCACTCCTCC 60.459 60.000 0.00 0.00 0.00 4.30
71 72 0.244994 TGCTCTTTCGCTCACTCCTC 59.755 55.000 0.00 0.00 0.00 3.71
72 73 0.246086 CTGCTCTTTCGCTCACTCCT 59.754 55.000 0.00 0.00 0.00 3.69
73 74 0.244994 TCTGCTCTTTCGCTCACTCC 59.755 55.000 0.00 0.00 0.00 3.85
74 75 1.201181 TCTCTGCTCTTTCGCTCACTC 59.799 52.381 0.00 0.00 0.00 3.51
75 76 1.202114 CTCTCTGCTCTTTCGCTCACT 59.798 52.381 0.00 0.00 0.00 3.41
76 77 1.201181 TCTCTCTGCTCTTTCGCTCAC 59.799 52.381 0.00 0.00 0.00 3.51
77 78 1.472082 CTCTCTCTGCTCTTTCGCTCA 59.528 52.381 0.00 0.00 0.00 4.26
78 79 1.472480 ACTCTCTCTGCTCTTTCGCTC 59.528 52.381 0.00 0.00 0.00 5.03
79 80 1.202114 CACTCTCTCTGCTCTTTCGCT 59.798 52.381 0.00 0.00 0.00 4.93
80 81 1.627879 CACTCTCTCTGCTCTTTCGC 58.372 55.000 0.00 0.00 0.00 4.70
81 82 1.135141 CCCACTCTCTCTGCTCTTTCG 60.135 57.143 0.00 0.00 0.00 3.46
82 83 1.206849 CCCCACTCTCTCTGCTCTTTC 59.793 57.143 0.00 0.00 0.00 2.62
83 84 1.203237 TCCCCACTCTCTCTGCTCTTT 60.203 52.381 0.00 0.00 0.00 2.52
84 85 0.411452 TCCCCACTCTCTCTGCTCTT 59.589 55.000 0.00 0.00 0.00 2.85
85 86 0.033208 CTCCCCACTCTCTCTGCTCT 60.033 60.000 0.00 0.00 0.00 4.09
86 87 0.324275 ACTCCCCACTCTCTCTGCTC 60.324 60.000 0.00 0.00 0.00 4.26
87 88 0.614415 CACTCCCCACTCTCTCTGCT 60.614 60.000 0.00 0.00 0.00 4.24
88 89 1.612395 CCACTCCCCACTCTCTCTGC 61.612 65.000 0.00 0.00 0.00 4.26
89 90 0.975040 CCCACTCCCCACTCTCTCTG 60.975 65.000 0.00 0.00 0.00 3.35
90 91 1.390125 CCCACTCCCCACTCTCTCT 59.610 63.158 0.00 0.00 0.00 3.10
91 92 1.687493 CCCCACTCCCCACTCTCTC 60.687 68.421 0.00 0.00 0.00 3.20
92 93 2.452114 CCCCACTCCCCACTCTCT 59.548 66.667 0.00 0.00 0.00 3.10
93 94 2.689034 CCCCCACTCCCCACTCTC 60.689 72.222 0.00 0.00 0.00 3.20
109 110 3.537206 AAGACCTGTCGGTGCTGCC 62.537 63.158 0.00 0.00 45.73 4.85
110 111 1.166531 AAAAGACCTGTCGGTGCTGC 61.167 55.000 0.00 0.00 45.73 5.25
111 112 0.588252 CAAAAGACCTGTCGGTGCTG 59.412 55.000 0.00 0.00 45.73 4.41
112 113 0.468226 TCAAAAGACCTGTCGGTGCT 59.532 50.000 0.00 0.00 45.73 4.40
113 114 0.586802 GTCAAAAGACCTGTCGGTGC 59.413 55.000 0.00 0.00 45.73 5.01
114 115 1.226746 GGTCAAAAGACCTGTCGGTG 58.773 55.000 7.39 0.00 45.73 4.94
116 117 0.949105 CCGGTCAAAAGACCTGTCGG 60.949 60.000 12.36 5.13 42.87 4.79
117 118 0.249741 ACCGGTCAAAAGACCTGTCG 60.250 55.000 0.00 0.01 38.06 4.35
118 119 1.509703 GACCGGTCAAAAGACCTGTC 58.490 55.000 29.75 18.78 46.63 3.51
119 120 0.108019 GGACCGGTCAAAAGACCTGT 59.892 55.000 34.40 10.82 43.72 4.00
120 121 0.107831 TGGACCGGTCAAAAGACCTG 59.892 55.000 34.40 8.55 42.87 4.00
121 122 1.003233 GATGGACCGGTCAAAAGACCT 59.997 52.381 34.40 8.73 42.87 3.85
122 123 1.271163 TGATGGACCGGTCAAAAGACC 60.271 52.381 34.40 17.58 41.68 3.85
123 124 2.178912 TGATGGACCGGTCAAAAGAC 57.821 50.000 34.40 17.23 0.00 3.01
124 125 2.882137 GTTTGATGGACCGGTCAAAAGA 59.118 45.455 34.40 15.18 43.56 2.52
125 126 2.621055 TGTTTGATGGACCGGTCAAAAG 59.379 45.455 34.40 0.00 43.56 2.27
126 127 2.621055 CTGTTTGATGGACCGGTCAAAA 59.379 45.455 34.40 23.71 43.56 2.44
127 128 2.158740 TCTGTTTGATGGACCGGTCAAA 60.159 45.455 34.40 23.35 40.81 2.69
128 129 1.418264 TCTGTTTGATGGACCGGTCAA 59.582 47.619 34.40 26.34 32.86 3.18
129 130 1.001974 CTCTGTTTGATGGACCGGTCA 59.998 52.381 34.40 21.15 0.00 4.02
130 131 1.676014 CCTCTGTTTGATGGACCGGTC 60.676 57.143 27.04 27.04 0.00 4.79
131 132 0.324943 CCTCTGTTTGATGGACCGGT 59.675 55.000 6.92 6.92 0.00 5.28
132 133 1.026718 GCCTCTGTTTGATGGACCGG 61.027 60.000 0.00 0.00 0.00 5.28
133 134 0.321564 TGCCTCTGTTTGATGGACCG 60.322 55.000 0.00 0.00 0.00 4.79
134 135 2.134789 ATGCCTCTGTTTGATGGACC 57.865 50.000 0.00 0.00 0.00 4.46
135 136 2.609459 CGTATGCCTCTGTTTGATGGAC 59.391 50.000 0.00 0.00 0.00 4.02
136 137 2.419990 CCGTATGCCTCTGTTTGATGGA 60.420 50.000 0.00 0.00 0.00 3.41
137 138 1.942657 CCGTATGCCTCTGTTTGATGG 59.057 52.381 0.00 0.00 0.00 3.51
138 139 1.331756 GCCGTATGCCTCTGTTTGATG 59.668 52.381 0.00 0.00 0.00 3.07
139 140 1.668419 GCCGTATGCCTCTGTTTGAT 58.332 50.000 0.00 0.00 0.00 2.57
140 141 0.739462 CGCCGTATGCCTCTGTTTGA 60.739 55.000 0.00 0.00 36.24 2.69
141 142 1.715585 CGCCGTATGCCTCTGTTTG 59.284 57.895 0.00 0.00 36.24 2.93
142 143 2.106683 GCGCCGTATGCCTCTGTTT 61.107 57.895 0.00 0.00 36.24 2.83
143 144 2.511600 GCGCCGTATGCCTCTGTT 60.512 61.111 0.00 0.00 36.24 3.16
171 172 2.202570 CCCGACAGCCGTTAGACG 60.203 66.667 0.00 0.00 42.11 4.18
172 173 1.153881 GTCCCGACAGCCGTTAGAC 60.154 63.158 0.00 0.00 36.31 2.59
173 174 2.693762 CGTCCCGACAGCCGTTAGA 61.694 63.158 0.00 0.00 36.31 2.10
174 175 2.202570 CGTCCCGACAGCCGTTAG 60.203 66.667 0.00 0.00 36.31 2.34
175 176 3.751246 CCGTCCCGACAGCCGTTA 61.751 66.667 0.00 0.00 36.31 3.18
198 199 4.560856 TTTTGCGCACGTGGCACC 62.561 61.111 24.98 6.08 45.17 5.01
199 200 2.580867 TTTTTGCGCACGTGGCAC 60.581 55.556 24.98 7.79 45.17 5.01
221 222 0.963355 TTGTTTATGACAGGCGGGGC 60.963 55.000 0.00 0.00 39.94 5.80
222 223 1.094785 CTTGTTTATGACAGGCGGGG 58.905 55.000 0.00 0.00 39.94 5.73
227 228 6.238320 GCTCAGATAAGCTTGTTTATGACAGG 60.238 42.308 9.86 0.00 39.27 4.00
228 229 6.238320 GGCTCAGATAAGCTTGTTTATGACAG 60.238 42.308 9.86 0.17 42.13 3.51
229 230 5.586243 GGCTCAGATAAGCTTGTTTATGACA 59.414 40.000 9.86 0.00 42.13 3.58
230 231 5.008118 GGGCTCAGATAAGCTTGTTTATGAC 59.992 44.000 9.86 0.00 42.13 3.06
231 232 5.126067 GGGCTCAGATAAGCTTGTTTATGA 58.874 41.667 9.86 7.74 42.13 2.15
232 233 4.024556 CGGGCTCAGATAAGCTTGTTTATG 60.025 45.833 9.86 3.59 42.13 1.90
233 234 4.130118 CGGGCTCAGATAAGCTTGTTTAT 58.870 43.478 9.86 0.00 42.13 1.40
234 235 3.196901 TCGGGCTCAGATAAGCTTGTTTA 59.803 43.478 9.86 0.00 42.13 2.01
235 236 2.027192 TCGGGCTCAGATAAGCTTGTTT 60.027 45.455 9.86 0.00 42.13 2.83
236 237 1.555075 TCGGGCTCAGATAAGCTTGTT 59.445 47.619 9.86 0.00 42.13 2.83
237 238 1.195115 TCGGGCTCAGATAAGCTTGT 58.805 50.000 9.86 0.92 42.13 3.16
238 239 2.411904 GATCGGGCTCAGATAAGCTTG 58.588 52.381 9.86 0.00 42.13 4.01
239 240 1.346068 GGATCGGGCTCAGATAAGCTT 59.654 52.381 3.48 3.48 42.13 3.74
240 241 0.972883 GGATCGGGCTCAGATAAGCT 59.027 55.000 0.00 0.00 42.13 3.74
241 242 0.389166 CGGATCGGGCTCAGATAAGC 60.389 60.000 0.00 0.00 41.73 3.09
242 243 0.389166 GCGGATCGGGCTCAGATAAG 60.389 60.000 2.13 0.00 0.00 1.73
243 244 1.666011 GCGGATCGGGCTCAGATAA 59.334 57.895 2.13 0.00 0.00 1.75
244 245 2.276116 GGCGGATCGGGCTCAGATA 61.276 63.158 18.13 0.00 0.00 1.98
245 246 3.620785 GGCGGATCGGGCTCAGAT 61.621 66.667 18.13 0.00 0.00 2.90
249 250 4.726351 GATCGGCGGATCGGGCTC 62.726 72.222 21.82 11.67 39.72 4.70
256 257 0.811616 GAAAGCACTGATCGGCGGAT 60.812 55.000 7.21 6.45 34.96 4.18
257 258 1.447838 GAAAGCACTGATCGGCGGA 60.448 57.895 7.21 0.00 34.54 5.54
258 259 1.448540 AGAAAGCACTGATCGGCGG 60.449 57.895 7.21 0.00 34.54 6.13
259 260 1.712081 CAGAAAGCACTGATCGGCG 59.288 57.895 0.00 0.00 39.94 6.46
260 261 1.427020 GCAGAAAGCACTGATCGGC 59.573 57.895 0.00 0.00 44.79 5.54
270 271 4.546570 ACGGTAATCTTTTTGCAGAAAGC 58.453 39.130 21.68 9.88 45.96 3.51
271 272 7.015877 GTCTACGGTAATCTTTTTGCAGAAAG 58.984 38.462 20.73 20.73 37.85 2.62
272 273 6.483974 TGTCTACGGTAATCTTTTTGCAGAAA 59.516 34.615 2.07 2.07 0.00 2.52
273 274 5.992829 TGTCTACGGTAATCTTTTTGCAGAA 59.007 36.000 0.00 0.00 0.00 3.02
274 275 5.407387 GTGTCTACGGTAATCTTTTTGCAGA 59.593 40.000 0.00 0.00 0.00 4.26
275 276 5.618561 GTGTCTACGGTAATCTTTTTGCAG 58.381 41.667 0.00 0.00 0.00 4.41
276 277 4.150980 CGTGTCTACGGTAATCTTTTTGCA 59.849 41.667 0.00 0.00 46.23 4.08
277 278 4.634991 CGTGTCTACGGTAATCTTTTTGC 58.365 43.478 0.00 0.00 46.23 3.68
316 317 7.203910 TGCGAAAACCACTACAATACATTTTT 58.796 30.769 0.00 0.00 0.00 1.94
317 318 6.740110 TGCGAAAACCACTACAATACATTTT 58.260 32.000 0.00 0.00 0.00 1.82
318 319 6.320494 TGCGAAAACCACTACAATACATTT 57.680 33.333 0.00 0.00 0.00 2.32
319 320 5.950758 TGCGAAAACCACTACAATACATT 57.049 34.783 0.00 0.00 0.00 2.71
320 321 5.239744 TGTTGCGAAAACCACTACAATACAT 59.760 36.000 0.00 0.00 0.00 2.29
321 322 4.575236 TGTTGCGAAAACCACTACAATACA 59.425 37.500 0.00 0.00 0.00 2.29
322 323 4.907582 GTGTTGCGAAAACCACTACAATAC 59.092 41.667 0.00 0.00 0.00 1.89
323 324 4.817464 AGTGTTGCGAAAACCACTACAATA 59.183 37.500 0.00 0.00 0.00 1.90
324 325 3.630312 AGTGTTGCGAAAACCACTACAAT 59.370 39.130 0.00 0.00 0.00 2.71
325 326 3.011119 AGTGTTGCGAAAACCACTACAA 58.989 40.909 0.00 0.00 0.00 2.41
326 327 2.634600 AGTGTTGCGAAAACCACTACA 58.365 42.857 0.00 0.00 0.00 2.74
327 328 3.359654 CAAGTGTTGCGAAAACCACTAC 58.640 45.455 0.08 0.00 0.00 2.73
328 329 3.684103 CAAGTGTTGCGAAAACCACTA 57.316 42.857 0.08 0.00 0.00 2.74
329 330 2.559998 CAAGTGTTGCGAAAACCACT 57.440 45.000 0.00 0.00 0.00 4.00
340 341 3.556775 CACCATTTTGAAGGCAAGTGTTG 59.443 43.478 0.00 0.00 35.04 3.33
341 342 3.432046 CCACCATTTTGAAGGCAAGTGTT 60.432 43.478 0.00 0.00 35.04 3.32
342 343 2.102925 CCACCATTTTGAAGGCAAGTGT 59.897 45.455 0.00 0.00 35.04 3.55
343 344 2.102925 ACCACCATTTTGAAGGCAAGTG 59.897 45.455 0.00 0.00 35.04 3.16
344 345 2.397597 ACCACCATTTTGAAGGCAAGT 58.602 42.857 0.00 0.00 35.04 3.16
345 346 3.473923 AACCACCATTTTGAAGGCAAG 57.526 42.857 0.00 0.00 35.04 4.01
346 347 3.922171 AAACCACCATTTTGAAGGCAA 57.078 38.095 0.00 0.00 0.00 4.52
347 348 3.454082 AGAAAACCACCATTTTGAAGGCA 59.546 39.130 0.00 0.00 31.90 4.75
348 349 3.809279 CAGAAAACCACCATTTTGAAGGC 59.191 43.478 0.00 0.00 31.90 4.35
349 350 3.809279 GCAGAAAACCACCATTTTGAAGG 59.191 43.478 0.00 0.00 31.90 3.46
350 351 4.440880 TGCAGAAAACCACCATTTTGAAG 58.559 39.130 0.00 0.00 31.90 3.02
351 352 4.478206 TGCAGAAAACCACCATTTTGAA 57.522 36.364 0.00 0.00 31.90 2.69
352 353 4.478206 TTGCAGAAAACCACCATTTTGA 57.522 36.364 0.00 0.00 31.90 2.69
353 354 5.754543 AATTGCAGAAAACCACCATTTTG 57.245 34.783 0.00 0.00 31.90 2.44
354 355 7.053498 AGTAAATTGCAGAAAACCACCATTTT 58.947 30.769 0.00 0.00 34.46 1.82
355 356 6.591001 AGTAAATTGCAGAAAACCACCATTT 58.409 32.000 0.00 0.00 0.00 2.32
356 357 6.173427 AGTAAATTGCAGAAAACCACCATT 57.827 33.333 0.00 0.00 0.00 3.16
357 358 5.279456 GGAGTAAATTGCAGAAAACCACCAT 60.279 40.000 0.00 0.00 0.00 3.55
358 359 4.038642 GGAGTAAATTGCAGAAAACCACCA 59.961 41.667 0.00 0.00 0.00 4.17
359 360 4.556233 GGAGTAAATTGCAGAAAACCACC 58.444 43.478 0.00 0.00 0.00 4.61
360 361 4.226761 CGGAGTAAATTGCAGAAAACCAC 58.773 43.478 0.00 0.00 0.00 4.16
361 362 3.305064 GCGGAGTAAATTGCAGAAAACCA 60.305 43.478 0.00 0.00 0.00 3.67
362 363 3.242518 GCGGAGTAAATTGCAGAAAACC 58.757 45.455 0.00 0.00 0.00 3.27
363 364 3.242518 GGCGGAGTAAATTGCAGAAAAC 58.757 45.455 0.00 0.00 0.00 2.43
364 365 2.095466 CGGCGGAGTAAATTGCAGAAAA 60.095 45.455 0.00 0.00 0.00 2.29
365 366 1.466950 CGGCGGAGTAAATTGCAGAAA 59.533 47.619 0.00 0.00 0.00 2.52
366 367 1.083489 CGGCGGAGTAAATTGCAGAA 58.917 50.000 0.00 0.00 0.00 3.02
367 368 0.248012 TCGGCGGAGTAAATTGCAGA 59.752 50.000 7.21 0.00 0.00 4.26
368 369 0.652592 CTCGGCGGAGTAAATTGCAG 59.347 55.000 12.89 0.00 35.48 4.41
369 370 0.742990 CCTCGGCGGAGTAAATTGCA 60.743 55.000 18.79 0.00 38.70 4.08
370 371 0.743345 ACCTCGGCGGAGTAAATTGC 60.743 55.000 18.79 0.00 38.70 3.56
371 372 1.287425 GACCTCGGCGGAGTAAATTG 58.713 55.000 18.79 6.06 38.70 2.32
372 373 0.179119 CGACCTCGGCGGAGTAAATT 60.179 55.000 18.79 0.00 38.70 1.82
373 374 1.033746 TCGACCTCGGCGGAGTAAAT 61.034 55.000 18.79 2.90 38.70 1.40
374 375 1.675310 TCGACCTCGGCGGAGTAAA 60.675 57.895 18.79 0.51 38.70 2.01
375 376 2.046023 TCGACCTCGGCGGAGTAA 60.046 61.111 18.79 0.18 38.70 2.24
376 377 2.821366 GTCGACCTCGGCGGAGTA 60.821 66.667 18.79 0.48 38.70 2.59
441 445 1.007271 CAGGTGCTTGTCGACGTCT 60.007 57.895 14.70 0.00 0.00 4.18
562 569 1.003839 GGTCGTCCATGTCCAGCAA 60.004 57.895 0.00 0.00 0.00 3.91
634 653 4.015406 TTCCATGGTGCCGAGCGT 62.015 61.111 12.58 0.00 0.00 5.07
676 695 2.741211 GACCGGGTTGCGGACTTC 60.741 66.667 6.32 0.00 0.00 3.01
677 696 3.109592 TTGACCGGGTTGCGGACTT 62.110 57.895 6.32 0.00 0.00 3.01
678 697 3.552384 TTGACCGGGTTGCGGACT 61.552 61.111 6.32 0.00 0.00 3.85
862 884 1.296715 GCCACGAGAACATCCTGGT 59.703 57.895 0.00 0.00 36.69 4.00
1026 1499 1.656818 CCATCCAAAAGCCGACGCAT 61.657 55.000 0.00 0.00 37.52 4.73
1038 1511 2.742116 GCGGAGGTAGCCCATCCAA 61.742 63.158 5.64 0.00 31.77 3.53
1103 1576 4.986587 CGTTGCCGTCGTGGTCGA 62.987 66.667 0.00 0.00 44.12 4.20
1149 1634 2.203907 AGCTCTGTCACCAGGCCT 60.204 61.111 0.00 0.00 39.31 5.19
1161 1646 1.674764 CCAGGCACGAGATCAGCTCT 61.675 60.000 0.00 0.00 41.66 4.09
1215 1700 2.614969 TGCCTCAGCCCTGGGAAT 60.615 61.111 19.27 0.00 38.69 3.01
1233 1718 3.187022 TCGTGTTGTTGAGCATGAAGATG 59.813 43.478 0.00 0.00 0.00 2.90
1407 1895 1.599576 GAGGGTGTTCAGGGCTCTC 59.400 63.158 0.00 0.00 0.00 3.20
1408 1896 1.920835 GGAGGGTGTTCAGGGCTCT 60.921 63.158 0.00 0.00 0.00 4.09
1576 2064 2.845795 AACCTCCGGGTGGTCGTT 60.846 61.111 20.34 3.26 46.67 3.85
1642 2130 1.137872 CTGCTATCCCTCGAACAGCTT 59.862 52.381 0.00 0.00 33.38 3.74
1653 2141 2.998316 AGCTTTCAGTCTGCTATCCC 57.002 50.000 0.00 0.00 35.05 3.85
1660 2148 2.857489 GCAGTGCAAAGCTTTCAGTCTG 60.857 50.000 9.23 15.17 0.00 3.51
1674 2162 3.056588 TGAGATACAACATGCAGTGCA 57.943 42.857 22.22 22.22 44.86 4.57
1693 2181 3.008330 CTGGTCTCTGGCTCAGAATTTG 58.992 50.000 6.39 0.00 40.18 2.32
1739 2227 4.199432 TGAGAGTTTCTGAATCCAGCTC 57.801 45.455 0.00 0.00 40.20 4.09
1741 2229 4.699257 ACATTGAGAGTTTCTGAATCCAGC 59.301 41.667 0.00 0.00 40.20 4.85
1766 2254 0.106708 TCGGCAGTTCCTATGGCATC 59.893 55.000 1.65 0.00 43.01 3.91
1767 2255 0.546122 TTCGGCAGTTCCTATGGCAT 59.454 50.000 4.88 4.88 43.01 4.40
1768 2256 0.392461 GTTCGGCAGTTCCTATGGCA 60.392 55.000 0.00 0.00 43.01 4.92
1769 2257 0.107654 AGTTCGGCAGTTCCTATGGC 60.108 55.000 0.00 0.00 39.69 4.40
1770 2258 1.207089 TCAGTTCGGCAGTTCCTATGG 59.793 52.381 0.00 0.00 0.00 2.74
1771 2259 2.093973 AGTCAGTTCGGCAGTTCCTATG 60.094 50.000 0.00 0.00 0.00 2.23
1772 2260 2.166664 GAGTCAGTTCGGCAGTTCCTAT 59.833 50.000 0.00 0.00 0.00 2.57
1773 2261 1.544691 GAGTCAGTTCGGCAGTTCCTA 59.455 52.381 0.00 0.00 0.00 2.94
1774 2262 0.318762 GAGTCAGTTCGGCAGTTCCT 59.681 55.000 0.00 0.00 0.00 3.36
1775 2263 0.670854 GGAGTCAGTTCGGCAGTTCC 60.671 60.000 0.00 0.00 0.00 3.62
1776 2264 0.318762 AGGAGTCAGTTCGGCAGTTC 59.681 55.000 0.00 0.00 0.00 3.01
1777 2265 0.759346 AAGGAGTCAGTTCGGCAGTT 59.241 50.000 0.00 0.00 0.00 3.16
1778 2266 0.318762 GAAGGAGTCAGTTCGGCAGT 59.681 55.000 0.00 0.00 0.00 4.40
1779 2267 0.734253 CGAAGGAGTCAGTTCGGCAG 60.734 60.000 15.62 0.00 41.47 4.85
1780 2268 1.289066 CGAAGGAGTCAGTTCGGCA 59.711 57.895 15.62 0.00 41.47 5.69
1781 2269 2.095252 GCGAAGGAGTCAGTTCGGC 61.095 63.158 21.62 13.51 44.55 5.54
1782 2270 1.801913 CGCGAAGGAGTCAGTTCGG 60.802 63.158 21.62 12.09 44.55 4.30
1783 2271 0.167470 TACGCGAAGGAGTCAGTTCG 59.833 55.000 15.93 17.99 46.60 3.95
1784 2272 2.452105 GATACGCGAAGGAGTCAGTTC 58.548 52.381 15.93 0.00 0.00 3.01
1785 2273 1.134560 GGATACGCGAAGGAGTCAGTT 59.865 52.381 15.93 0.00 0.00 3.16
1786 2274 0.739561 GGATACGCGAAGGAGTCAGT 59.260 55.000 15.93 0.00 0.00 3.41
1787 2275 1.025812 AGGATACGCGAAGGAGTCAG 58.974 55.000 15.93 0.00 46.39 3.51
1788 2276 0.738975 CAGGATACGCGAAGGAGTCA 59.261 55.000 15.93 0.00 46.39 3.41
1789 2277 0.739561 ACAGGATACGCGAAGGAGTC 59.260 55.000 15.93 0.69 46.39 3.36
1790 2278 0.739561 GACAGGATACGCGAAGGAGT 59.260 55.000 15.93 3.53 46.39 3.85
1791 2279 0.030908 GGACAGGATACGCGAAGGAG 59.969 60.000 15.93 0.00 46.39 3.69
1792 2280 1.389609 GGGACAGGATACGCGAAGGA 61.390 60.000 15.93 0.00 46.39 3.36
1793 2281 1.067582 GGGACAGGATACGCGAAGG 59.932 63.158 15.93 0.00 46.39 3.46
2187 2679 1.737029 CGAAGGTCATGCATCACGAGT 60.737 52.381 0.00 0.00 0.00 4.18
2458 2954 3.361977 GCCGGCGCCTTCAAGAAA 61.362 61.111 26.68 0.00 0.00 2.52
2491 2987 3.293714 CACGCCATGCACACCCAA 61.294 61.111 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.