Multiple sequence alignment - TraesCS1D01G376500

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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 TraesCS1D01G376500 chr1D 100.000 2816 0 0 1 2816 453133659 453136474 0.000000e+00 5201.0
1 TraesCS1D01G376500 chr1D 97.176 779 21 1 2039 2816 474814652 474813874 0.000000e+00 1315.0
2 TraesCS1D01G376500 chr1D 97.172 778 21 1 2039 2816 494311285 494312061 0.000000e+00 1314.0
3 TraesCS1D01G376500 chr1D 87.468 774 76 16 969 1728 453199585 453200351 0.000000e+00 872.0
4 TraesCS1D01G376500 chr1D 83.736 953 105 38 796 1728 453181503 453182425 0.000000e+00 856.0
5 TraesCS1D01G376500 chr1D 91.982 449 31 3 1 448 433908155 433907711 2.380000e-175 625.0
6 TraesCS1D01G376500 chr1D 91.759 449 34 3 1 448 236079950 236080396 3.080000e-174 621.0
7 TraesCS1D01G376500 chr1D 84.441 662 61 22 1001 1628 453211139 453210486 5.160000e-172 614.0
8 TraesCS1D01G376500 chr1D 91.091 449 34 4 1 448 457215689 457215246 1.120000e-168 603.0
9 TraesCS1D01G376500 chr1D 96.000 50 2 0 796 845 453199440 453199489 6.470000e-12 82.4
10 TraesCS1D01G376500 chr1A 86.960 1273 103 42 793 2031 547863708 547864951 0.000000e+00 1373.0
11 TraesCS1D01G376500 chr1A 82.235 1047 134 34 1003 2030 547886734 547887747 0.000000e+00 856.0
12 TraesCS1D01G376500 chr1A 83.129 735 56 32 1040 1716 547908414 547907690 2.400000e-170 608.0
13 TraesCS1D01G376500 chr1A 95.015 341 12 4 453 788 547863320 547863660 5.340000e-147 531.0
14 TraesCS1D01G376500 chr1A 78.780 377 46 16 796 1150 547858410 547858774 3.650000e-54 222.0
15 TraesCS1D01G376500 chr1A 90.741 54 3 1 803 854 547886575 547886628 1.400000e-08 71.3
16 TraesCS1D01G376500 chr5D 97.818 779 16 1 2039 2816 451155007 451154229 0.000000e+00 1343.0
17 TraesCS1D01G376500 chr5D 91.759 449 34 3 1 448 525594849 525595295 3.080000e-174 621.0
18 TraesCS1D01G376500 chr6D 97.558 778 16 3 2039 2816 66125149 66124375 0.000000e+00 1328.0
19 TraesCS1D01G376500 chr7D 97.301 778 21 0 2039 2816 15304472 15303695 0.000000e+00 1321.0
20 TraesCS1D01G376500 chr7D 97.301 778 20 1 2039 2816 84476820 84476044 0.000000e+00 1319.0
21 TraesCS1D01G376500 chr7D 97.301 778 17 3 2039 2816 513998881 513999654 0.000000e+00 1317.0
22 TraesCS1D01G376500 chr7D 97.301 778 18 3 2039 2816 553471773 553470999 0.000000e+00 1317.0
23 TraesCS1D01G376500 chr7D 97.176 779 20 2 2039 2816 618740550 618741327 0.000000e+00 1315.0
24 TraesCS1D01G376500 chr7D 91.314 449 36 3 1 448 397377658 397378104 6.670000e-171 610.0
25 TraesCS1D01G376500 chr1B 85.844 770 81 12 1016 1777 623672578 623673327 0.000000e+00 793.0
26 TraesCS1D01G376500 chr1B 82.732 915 99 35 1108 1975 623679684 623680586 0.000000e+00 760.0
27 TraesCS1D01G376500 chr1B 86.548 617 48 17 1035 1623 623689405 623688796 0.000000e+00 647.0
28 TraesCS1D01G376500 chr1B 84.615 247 10 19 523 754 623665905 623666138 1.310000e-53 220.0
29 TraesCS1D01G376500 chr1B 77.454 377 62 16 793 1159 623621139 623621502 1.320000e-48 204.0
30 TraesCS1D01G376500 chr1B 91.803 61 3 2 796 854 623679425 623679485 1.800000e-12 84.2
31 TraesCS1D01G376500 chr1B 94.000 50 3 0 796 845 623666217 623666266 3.010000e-10 76.8
32 TraesCS1D01G376500 chr5A 92.205 449 30 3 1 448 580928240 580927796 5.120000e-177 630.0
33 TraesCS1D01G376500 chr3D 91.295 448 37 2 1 447 402495078 402494632 6.670000e-171 610.0
34 TraesCS1D01G376500 chr3D 91.091 449 35 3 1 448 420047717 420048161 1.120000e-168 603.0
35 TraesCS1D01G376500 chr6A 91.091 449 37 3 1 448 68503909 68503463 3.100000e-169 604.0


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 TraesCS1D01G376500 chr1D 453133659 453136474 2815 False 5201.00 5201 100.0000 1 2816 1 chr1D.!!$F2 2815
1 TraesCS1D01G376500 chr1D 474813874 474814652 778 True 1315.00 1315 97.1760 2039 2816 1 chr1D.!!$R4 777
2 TraesCS1D01G376500 chr1D 494311285 494312061 776 False 1314.00 1314 97.1720 2039 2816 1 chr1D.!!$F4 777
3 TraesCS1D01G376500 chr1D 453181503 453182425 922 False 856.00 856 83.7360 796 1728 1 chr1D.!!$F3 932
4 TraesCS1D01G376500 chr1D 453210486 453211139 653 True 614.00 614 84.4410 1001 1628 1 chr1D.!!$R2 627
5 TraesCS1D01G376500 chr1D 453199440 453200351 911 False 477.20 872 91.7340 796 1728 2 chr1D.!!$F5 932
6 TraesCS1D01G376500 chr1A 547863320 547864951 1631 False 952.00 1373 90.9875 453 2031 2 chr1A.!!$F2 1578
7 TraesCS1D01G376500 chr1A 547907690 547908414 724 True 608.00 608 83.1290 1040 1716 1 chr1A.!!$R1 676
8 TraesCS1D01G376500 chr1A 547886575 547887747 1172 False 463.65 856 86.4880 803 2030 2 chr1A.!!$F3 1227
9 TraesCS1D01G376500 chr5D 451154229 451155007 778 True 1343.00 1343 97.8180 2039 2816 1 chr5D.!!$R1 777
10 TraesCS1D01G376500 chr6D 66124375 66125149 774 True 1328.00 1328 97.5580 2039 2816 1 chr6D.!!$R1 777
11 TraesCS1D01G376500 chr7D 15303695 15304472 777 True 1321.00 1321 97.3010 2039 2816 1 chr7D.!!$R1 777
12 TraesCS1D01G376500 chr7D 84476044 84476820 776 True 1319.00 1319 97.3010 2039 2816 1 chr7D.!!$R2 777
13 TraesCS1D01G376500 chr7D 513998881 513999654 773 False 1317.00 1317 97.3010 2039 2816 1 chr7D.!!$F2 777
14 TraesCS1D01G376500 chr7D 553470999 553471773 774 True 1317.00 1317 97.3010 2039 2816 1 chr7D.!!$R3 777
15 TraesCS1D01G376500 chr7D 618740550 618741327 777 False 1315.00 1315 97.1760 2039 2816 1 chr7D.!!$F3 777
16 TraesCS1D01G376500 chr1B 623672578 623673327 749 False 793.00 793 85.8440 1016 1777 1 chr1B.!!$F2 761
17 TraesCS1D01G376500 chr1B 623688796 623689405 609 True 647.00 647 86.5480 1035 1623 1 chr1B.!!$R1 588
18 TraesCS1D01G376500 chr1B 623679425 623680586 1161 False 422.10 760 87.2675 796 1975 2 chr1B.!!$F4 1179

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
974 1106 0.034767 CAGCCCCTCAGCTCAATCAA 60.035 55.0 0.0 0.0 42.61 2.57 F
988 1120 0.537143 AATCAACGGCAGCAGGAACA 60.537 50.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 2080 0.035458 ACTGCCACTGGTCTAACTGC 59.965 55.0 0.00 0.0 0.0 4.40 R
2031 2318 0.163788 CGACAGCGGTGAACAACATC 59.836 55.0 23.44 5.3 0.0 3.06 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
18 19 2.388347 GTTCGAGAAGATGCAGGCC 58.612 57.895 0.00 0.00 0.00 5.19
19 20 1.153568 TTCGAGAAGATGCAGGCCG 60.154 57.895 0.00 0.00 0.00 6.13
20 21 1.604147 TTCGAGAAGATGCAGGCCGA 61.604 55.000 0.00 0.00 0.00 5.54
21 22 1.880340 CGAGAAGATGCAGGCCGAC 60.880 63.158 0.00 0.00 0.00 4.79
22 23 1.219124 GAGAAGATGCAGGCCGACA 59.781 57.895 0.00 0.00 0.00 4.35
23 24 0.179062 GAGAAGATGCAGGCCGACAT 60.179 55.000 12.73 12.73 0.00 3.06
24 25 0.463295 AGAAGATGCAGGCCGACATG 60.463 55.000 17.07 1.62 0.00 3.21
25 26 2.056481 GAAGATGCAGGCCGACATGC 62.056 60.000 17.07 12.61 42.86 4.06
26 27 2.515523 GATGCAGGCCGACATGCT 60.516 61.111 17.07 2.82 42.98 3.79
27 28 2.515523 ATGCAGGCCGACATGCTC 60.516 61.111 10.24 0.00 42.98 4.26
28 29 3.333899 ATGCAGGCCGACATGCTCA 62.334 57.895 10.24 0.00 42.98 4.26
29 30 2.747460 GCAGGCCGACATGCTCAA 60.747 61.111 0.00 0.00 39.38 3.02
30 31 2.758089 GCAGGCCGACATGCTCAAG 61.758 63.158 0.00 0.00 39.38 3.02
31 32 1.376424 CAGGCCGACATGCTCAAGT 60.376 57.895 0.00 0.00 0.00 3.16
32 33 0.957395 CAGGCCGACATGCTCAAGTT 60.957 55.000 0.00 0.00 0.00 2.66
33 34 0.674895 AGGCCGACATGCTCAAGTTC 60.675 55.000 0.00 0.00 0.00 3.01
34 35 1.421485 GCCGACATGCTCAAGTTCG 59.579 57.895 0.00 0.00 0.00 3.95
35 36 1.014044 GCCGACATGCTCAAGTTCGA 61.014 55.000 0.00 0.00 0.00 3.71
36 37 0.716108 CCGACATGCTCAAGTTCGAC 59.284 55.000 0.00 0.00 0.00 4.20
37 38 0.363512 CGACATGCTCAAGTTCGACG 59.636 55.000 0.00 0.00 0.00 5.12
38 39 1.698165 GACATGCTCAAGTTCGACGA 58.302 50.000 0.00 0.00 0.00 4.20
39 40 1.387084 GACATGCTCAAGTTCGACGAC 59.613 52.381 0.00 0.00 0.00 4.34
40 41 0.363512 CATGCTCAAGTTCGACGACG 59.636 55.000 0.00 0.00 41.26 5.12
52 53 3.537793 TCGACGACGATTGATCTATGG 57.462 47.619 5.75 0.00 43.81 2.74
53 54 1.979469 CGACGACGATTGATCTATGGC 59.021 52.381 0.00 0.00 42.66 4.40
54 55 1.979469 GACGACGATTGATCTATGGCG 59.021 52.381 0.00 11.16 0.00 5.69
55 56 1.335964 ACGACGATTGATCTATGGCGG 60.336 52.381 0.00 4.88 0.00 6.13
56 57 1.071605 GACGATTGATCTATGGCGGC 58.928 55.000 0.00 0.00 0.00 6.53
57 58 0.667487 ACGATTGATCTATGGCGGCG 60.667 55.000 0.51 0.51 0.00 6.46
58 59 0.388520 CGATTGATCTATGGCGGCGA 60.389 55.000 12.98 0.00 0.00 5.54
59 60 1.354040 GATTGATCTATGGCGGCGAG 58.646 55.000 12.98 4.23 0.00 5.03
86 87 3.043998 TTTTTGTATGCCGGCAGGT 57.956 47.368 35.36 21.86 40.50 4.00
87 88 0.600557 TTTTTGTATGCCGGCAGGTG 59.399 50.000 35.36 0.00 40.50 4.00
88 89 0.538516 TTTTGTATGCCGGCAGGTGT 60.539 50.000 35.36 20.64 40.50 4.16
89 90 1.240641 TTTGTATGCCGGCAGGTGTG 61.241 55.000 35.36 0.00 40.50 3.82
99 100 3.434319 CAGGTGTGCCGGCATGAC 61.434 66.667 35.23 29.57 40.50 3.06
100 101 4.722700 AGGTGTGCCGGCATGACC 62.723 66.667 36.43 36.43 40.50 4.02
102 103 3.737172 GTGTGCCGGCATGACCAC 61.737 66.667 35.23 29.85 39.03 4.16
107 108 4.838152 CCGGCATGACCACGGGAG 62.838 72.222 0.00 0.00 43.69 4.30
127 128 3.849953 GCGATGGCGTGGTCGAAC 61.850 66.667 0.00 0.00 40.11 3.95
128 129 2.126071 CGATGGCGTGGTCGAACT 60.126 61.111 0.33 0.00 40.11 3.01
129 130 2.158959 CGATGGCGTGGTCGAACTC 61.159 63.158 0.33 0.00 40.11 3.01
130 131 1.080093 GATGGCGTGGTCGAACTCA 60.080 57.895 0.33 0.00 39.71 3.41
131 132 0.669318 GATGGCGTGGTCGAACTCAA 60.669 55.000 0.33 0.00 39.71 3.02
132 133 0.670546 ATGGCGTGGTCGAACTCAAG 60.671 55.000 0.33 0.00 39.71 3.02
133 134 1.300697 GGCGTGGTCGAACTCAAGT 60.301 57.895 0.33 0.00 39.71 3.16
134 135 1.282930 GGCGTGGTCGAACTCAAGTC 61.283 60.000 0.33 0.00 39.71 3.01
135 136 0.596600 GCGTGGTCGAACTCAAGTCA 60.597 55.000 0.33 0.00 39.71 3.41
136 137 1.129326 CGTGGTCGAACTCAAGTCAC 58.871 55.000 0.33 0.00 39.71 3.67
137 138 1.535226 CGTGGTCGAACTCAAGTCACA 60.535 52.381 0.33 0.00 39.71 3.58
138 139 2.755650 GTGGTCGAACTCAAGTCACAT 58.244 47.619 0.33 0.00 0.00 3.21
139 140 2.731976 GTGGTCGAACTCAAGTCACATC 59.268 50.000 0.33 0.00 0.00 3.06
140 141 2.288825 TGGTCGAACTCAAGTCACATCC 60.289 50.000 0.33 0.00 0.00 3.51
141 142 2.028930 GGTCGAACTCAAGTCACATCCT 60.029 50.000 0.00 0.00 0.00 3.24
142 143 3.555168 GGTCGAACTCAAGTCACATCCTT 60.555 47.826 0.00 0.00 0.00 3.36
143 144 4.058817 GTCGAACTCAAGTCACATCCTTT 58.941 43.478 0.00 0.00 0.00 3.11
144 145 4.511826 GTCGAACTCAAGTCACATCCTTTT 59.488 41.667 0.00 0.00 0.00 2.27
145 146 5.007724 GTCGAACTCAAGTCACATCCTTTTT 59.992 40.000 0.00 0.00 0.00 1.94
161 162 1.937278 TTTTTGTGTGCTGGCATGTG 58.063 45.000 0.00 0.00 0.00 3.21
162 163 0.822811 TTTTGTGTGCTGGCATGTGT 59.177 45.000 0.00 0.00 0.00 3.72
163 164 0.102663 TTTGTGTGCTGGCATGTGTG 59.897 50.000 0.00 0.00 0.00 3.82
173 174 2.985282 CATGTGTGCCGGCCTGTT 60.985 61.111 26.77 1.45 0.00 3.16
174 175 2.985282 ATGTGTGCCGGCCTGTTG 60.985 61.111 26.77 0.00 0.00 3.33
198 199 2.253452 GCGCCAGCAAGAACTGTG 59.747 61.111 0.00 0.00 44.35 3.66
199 200 2.949106 CGCCAGCAAGAACTGTGG 59.051 61.111 0.00 0.00 35.83 4.17
200 201 1.893808 CGCCAGCAAGAACTGTGGT 60.894 57.895 0.00 0.00 35.83 4.16
201 202 1.656441 GCCAGCAAGAACTGTGGTG 59.344 57.895 0.00 0.00 42.73 4.17
202 203 0.819259 GCCAGCAAGAACTGTGGTGA 60.819 55.000 5.24 0.00 45.24 4.02
203 204 1.901591 CCAGCAAGAACTGTGGTGAT 58.098 50.000 5.24 0.00 45.24 3.06
204 205 2.875672 GCCAGCAAGAACTGTGGTGATA 60.876 50.000 5.24 0.00 45.24 2.15
205 206 3.614092 CCAGCAAGAACTGTGGTGATAT 58.386 45.455 5.24 0.00 45.24 1.63
206 207 4.012374 CCAGCAAGAACTGTGGTGATATT 58.988 43.478 5.24 0.00 45.24 1.28
207 208 4.460382 CCAGCAAGAACTGTGGTGATATTT 59.540 41.667 5.24 0.00 45.24 1.40
208 209 5.047802 CCAGCAAGAACTGTGGTGATATTTT 60.048 40.000 5.24 0.00 45.24 1.82
209 210 6.088824 CAGCAAGAACTGTGGTGATATTTTC 58.911 40.000 0.00 0.00 45.24 2.29
210 211 6.006449 AGCAAGAACTGTGGTGATATTTTCT 58.994 36.000 0.00 0.00 0.00 2.52
211 212 6.072286 AGCAAGAACTGTGGTGATATTTTCTG 60.072 38.462 0.00 0.00 0.00 3.02
212 213 6.072508 GCAAGAACTGTGGTGATATTTTCTGA 60.073 38.462 0.00 0.00 0.00 3.27
213 214 7.524912 CAAGAACTGTGGTGATATTTTCTGAG 58.475 38.462 0.00 0.00 0.00 3.35
214 215 6.176183 AGAACTGTGGTGATATTTTCTGAGG 58.824 40.000 0.00 0.00 0.00 3.86
215 216 5.762179 ACTGTGGTGATATTTTCTGAGGA 57.238 39.130 0.00 0.00 0.00 3.71
216 217 5.491982 ACTGTGGTGATATTTTCTGAGGAC 58.508 41.667 0.00 0.00 0.00 3.85
217 218 4.503910 TGTGGTGATATTTTCTGAGGACG 58.496 43.478 0.00 0.00 0.00 4.79
218 219 3.871594 GTGGTGATATTTTCTGAGGACGG 59.128 47.826 0.00 0.00 0.00 4.79
219 220 2.872858 GGTGATATTTTCTGAGGACGGC 59.127 50.000 0.00 0.00 0.00 5.68
220 221 3.531538 GTGATATTTTCTGAGGACGGCA 58.468 45.455 0.00 0.00 0.00 5.69
221 222 4.130118 GTGATATTTTCTGAGGACGGCAT 58.870 43.478 0.00 0.00 0.00 4.40
222 223 4.576463 GTGATATTTTCTGAGGACGGCATT 59.424 41.667 0.00 0.00 0.00 3.56
223 224 4.576053 TGATATTTTCTGAGGACGGCATTG 59.424 41.667 0.00 0.00 0.00 2.82
224 225 2.270352 TTTTCTGAGGACGGCATTGT 57.730 45.000 0.00 0.00 0.00 2.71
225 226 3.410631 TTTTCTGAGGACGGCATTGTA 57.589 42.857 0.00 0.00 0.00 2.41
226 227 3.627395 TTTCTGAGGACGGCATTGTAT 57.373 42.857 0.00 0.00 0.00 2.29
227 228 2.602257 TCTGAGGACGGCATTGTATG 57.398 50.000 0.00 0.00 0.00 2.39
236 237 4.688192 CATTGTATGCCGGCGTTG 57.312 55.556 29.18 15.46 0.00 4.10
237 238 1.063972 CATTGTATGCCGGCGTTGG 59.936 57.895 29.18 8.35 0.00 3.77
245 246 4.418401 CCGGCGTTGGCATTGGTG 62.418 66.667 6.01 0.00 42.47 4.17
254 255 3.451004 GCATTGGTGCCGGCATGA 61.451 61.111 35.23 21.56 45.76 3.07
255 256 2.802792 CATTGGTGCCGGCATGAG 59.197 61.111 35.23 17.12 0.00 2.90
256 257 1.750018 CATTGGTGCCGGCATGAGA 60.750 57.895 35.23 19.24 0.00 3.27
257 258 1.750399 ATTGGTGCCGGCATGAGAC 60.750 57.895 35.23 19.50 0.00 3.36
258 259 2.482796 ATTGGTGCCGGCATGAGACA 62.483 55.000 35.23 22.49 0.00 3.41
259 260 2.124570 GGTGCCGGCATGAGACAT 60.125 61.111 35.23 0.00 0.00 3.06
260 261 2.475466 GGTGCCGGCATGAGACATG 61.475 63.158 35.23 7.29 0.00 3.21
261 262 2.124612 TGCCGGCATGAGACATGG 60.125 61.111 29.03 0.00 0.00 3.66
262 263 3.589881 GCCGGCATGAGACATGGC 61.590 66.667 24.80 22.27 40.66 4.40
263 264 2.903855 CCGGCATGAGACATGGCC 60.904 66.667 24.71 17.98 40.95 5.36
264 265 2.124612 CGGCATGAGACATGGCCA 60.125 61.111 24.71 8.56 46.75 5.36
265 266 2.475466 CGGCATGAGACATGGCCAC 61.475 63.158 24.71 0.00 46.75 5.01
266 267 1.077212 GGCATGAGACATGGCCACT 60.077 57.895 21.83 0.00 45.70 4.00
267 268 1.381928 GGCATGAGACATGGCCACTG 61.382 60.000 21.83 10.78 45.70 3.66
268 269 1.381928 GCATGAGACATGGCCACTGG 61.382 60.000 8.16 2.83 0.00 4.00
312 313 6.576662 TTTTATTTACAGGTTGAATGCGGA 57.423 33.333 0.00 0.00 0.00 5.54
313 314 5.554822 TTATTTACAGGTTGAATGCGGAC 57.445 39.130 0.00 0.00 0.00 4.79
314 315 2.552599 TTACAGGTTGAATGCGGACA 57.447 45.000 0.00 0.00 0.00 4.02
315 316 2.779755 TACAGGTTGAATGCGGACAT 57.220 45.000 0.00 0.00 38.49 3.06
316 317 1.167851 ACAGGTTGAATGCGGACATG 58.832 50.000 0.00 0.00 36.36 3.21
317 318 1.271325 ACAGGTTGAATGCGGACATGA 60.271 47.619 0.00 0.00 36.36 3.07
318 319 1.811965 CAGGTTGAATGCGGACATGAA 59.188 47.619 0.00 0.00 36.36 2.57
319 320 2.228582 CAGGTTGAATGCGGACATGAAA 59.771 45.455 0.00 0.00 36.36 2.69
320 321 3.091545 AGGTTGAATGCGGACATGAAAT 58.908 40.909 0.00 0.00 36.36 2.17
330 331 4.929198 CATGAAATGGATCGGCGC 57.071 55.556 0.00 0.00 41.79 6.53
331 332 1.082561 CATGAAATGGATCGGCGCG 60.083 57.895 0.00 0.00 41.79 6.86
332 333 1.523711 ATGAAATGGATCGGCGCGT 60.524 52.632 8.43 0.00 0.00 6.01
333 334 1.095228 ATGAAATGGATCGGCGCGTT 61.095 50.000 8.43 0.00 0.00 4.84
334 335 1.297598 GAAATGGATCGGCGCGTTG 60.298 57.895 8.43 0.00 0.00 4.10
335 336 1.701545 GAAATGGATCGGCGCGTTGA 61.702 55.000 8.43 6.41 0.00 3.18
336 337 1.705337 AAATGGATCGGCGCGTTGAG 61.705 55.000 8.43 0.00 0.00 3.02
347 348 3.318875 CGTTGAGCGCACTGTTGA 58.681 55.556 11.47 0.00 0.00 3.18
348 349 1.862123 CGTTGAGCGCACTGTTGAT 59.138 52.632 11.47 0.00 0.00 2.57
349 350 0.179240 CGTTGAGCGCACTGTTGATC 60.179 55.000 11.47 0.00 0.00 2.92
350 351 0.166814 GTTGAGCGCACTGTTGATCC 59.833 55.000 11.47 0.00 0.00 3.36
351 352 0.250252 TTGAGCGCACTGTTGATCCA 60.250 50.000 11.47 0.00 0.00 3.41
352 353 0.250252 TGAGCGCACTGTTGATCCAA 60.250 50.000 11.47 0.00 0.00 3.53
353 354 0.874390 GAGCGCACTGTTGATCCAAA 59.126 50.000 11.47 0.00 0.00 3.28
354 355 1.470098 GAGCGCACTGTTGATCCAAAT 59.530 47.619 11.47 0.00 0.00 2.32
355 356 1.200716 AGCGCACTGTTGATCCAAATG 59.799 47.619 11.47 0.00 0.00 2.32
356 357 1.068333 GCGCACTGTTGATCCAAATGT 60.068 47.619 0.30 0.00 0.00 2.71
357 358 2.161410 GCGCACTGTTGATCCAAATGTA 59.839 45.455 0.30 0.00 0.00 2.29
358 359 3.365868 GCGCACTGTTGATCCAAATGTAA 60.366 43.478 0.30 0.00 0.00 2.41
359 360 4.793071 CGCACTGTTGATCCAAATGTAAA 58.207 39.130 0.00 0.00 0.00 2.01
360 361 5.218885 CGCACTGTTGATCCAAATGTAAAA 58.781 37.500 0.00 0.00 0.00 1.52
361 362 5.116983 CGCACTGTTGATCCAAATGTAAAAC 59.883 40.000 0.00 0.00 0.00 2.43
362 363 6.215845 GCACTGTTGATCCAAATGTAAAACT 58.784 36.000 0.00 0.00 0.00 2.66
363 364 6.144402 GCACTGTTGATCCAAATGTAAAACTG 59.856 38.462 0.00 0.00 0.00 3.16
364 365 6.642131 CACTGTTGATCCAAATGTAAAACTGG 59.358 38.462 0.00 0.00 0.00 4.00
365 366 6.095432 TGTTGATCCAAATGTAAAACTGGG 57.905 37.500 0.00 0.00 0.00 4.45
366 367 4.799564 TGATCCAAATGTAAAACTGGGC 57.200 40.909 0.00 0.00 0.00 5.36
367 368 3.192422 TGATCCAAATGTAAAACTGGGCG 59.808 43.478 0.00 0.00 0.00 6.13
368 369 1.889829 TCCAAATGTAAAACTGGGCGG 59.110 47.619 0.00 0.00 0.00 6.13
369 370 1.889829 CCAAATGTAAAACTGGGCGGA 59.110 47.619 0.00 0.00 0.00 5.54
370 371 2.495669 CCAAATGTAAAACTGGGCGGAT 59.504 45.455 0.00 0.00 0.00 4.18
371 372 3.510719 CAAATGTAAAACTGGGCGGATG 58.489 45.455 0.00 0.00 0.00 3.51
372 373 1.102978 ATGTAAAACTGGGCGGATGC 58.897 50.000 0.00 0.00 41.71 3.91
395 396 3.192922 GGACGGCCGATCCAAACG 61.193 66.667 35.90 0.93 36.15 3.60
405 406 2.315901 CGATCCAAACGGACAAAAAGC 58.684 47.619 0.00 0.00 34.62 3.51
406 407 2.315901 GATCCAAACGGACAAAAAGCG 58.684 47.619 0.00 0.00 34.62 4.68
407 408 0.382515 TCCAAACGGACAAAAAGCGG 59.617 50.000 0.00 0.00 0.00 5.52
408 409 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
409 410 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
410 411 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
411 412 1.096416 AACGGACAAAAAGCGGACAA 58.904 45.000 0.00 0.00 0.00 3.18
412 413 1.096416 ACGGACAAAAAGCGGACAAA 58.904 45.000 0.00 0.00 0.00 2.83
413 414 1.679153 ACGGACAAAAAGCGGACAAAT 59.321 42.857 0.00 0.00 0.00 2.32
414 415 2.050691 CGGACAAAAAGCGGACAAATG 58.949 47.619 0.00 0.00 0.00 2.32
415 416 1.792367 GGACAAAAAGCGGACAAATGC 59.208 47.619 0.00 0.00 0.00 3.56
416 417 1.451651 GACAAAAAGCGGACAAATGCG 59.548 47.619 0.00 0.00 43.57 4.73
426 427 4.715892 CAAATGCGCCGCCCGTTT 62.716 61.111 6.63 2.25 39.71 3.60
427 428 4.715892 AAATGCGCCGCCCGTTTG 62.716 61.111 6.63 0.00 39.71 2.93
444 445 2.281276 GGGTCGCCCGTTGAAGTT 60.281 61.111 0.00 0.00 32.13 2.66
445 446 2.613506 GGGTCGCCCGTTGAAGTTG 61.614 63.158 0.00 0.00 32.13 3.16
446 447 2.251371 GTCGCCCGTTGAAGTTGC 59.749 61.111 0.00 0.00 0.00 4.17
447 448 2.110213 TCGCCCGTTGAAGTTGCT 59.890 55.556 0.00 0.00 0.00 3.91
448 449 0.947180 GTCGCCCGTTGAAGTTGCTA 60.947 55.000 0.00 0.00 0.00 3.49
449 450 0.249953 TCGCCCGTTGAAGTTGCTAA 60.250 50.000 0.00 0.00 0.00 3.09
450 451 0.802494 CGCCCGTTGAAGTTGCTAAT 59.198 50.000 0.00 0.00 0.00 1.73
451 452 1.465689 CGCCCGTTGAAGTTGCTAATG 60.466 52.381 0.00 0.00 0.00 1.90
497 498 5.810095 AGGAAAACCATCTAGAAGAACCAG 58.190 41.667 0.00 0.00 0.00 4.00
624 626 1.131638 GCTGTACAGATCCCATCCCA 58.868 55.000 27.08 0.00 0.00 4.37
637 639 1.708341 CATCCCATCCAAATCCCACC 58.292 55.000 0.00 0.00 0.00 4.61
721 727 1.304962 GGAGGGCAAAACCGGGATT 60.305 57.895 6.32 0.00 40.62 3.01
722 728 1.320344 GGAGGGCAAAACCGGGATTC 61.320 60.000 6.32 0.00 40.62 2.52
723 729 1.654023 GAGGGCAAAACCGGGATTCG 61.654 60.000 6.32 0.00 40.62 3.34
724 730 1.974875 GGGCAAAACCGGGATTCGT 60.975 57.895 6.32 0.00 40.62 3.85
727 733 1.131693 GGCAAAACCGGGATTCGTAAG 59.868 52.381 6.32 0.00 37.11 2.34
788 794 0.815095 CATCCCCGTTGGCCTTAAAC 59.185 55.000 3.32 0.00 0.00 2.01
789 795 0.406361 ATCCCCGTTGGCCTTAAACA 59.594 50.000 3.32 0.00 0.00 2.83
792 798 1.209127 CCGTTGGCCTTAAACAGCG 59.791 57.895 3.32 0.00 40.31 5.18
794 800 1.442017 GTTGGCCTTAAACAGCGCG 60.442 57.895 3.32 0.00 0.00 6.86
887 1004 2.035832 CCCCATCACTTCAAACAACACC 59.964 50.000 0.00 0.00 0.00 4.16
889 1006 2.692557 CCATCACTTCAAACAACACCCA 59.307 45.455 0.00 0.00 0.00 4.51
891 1008 1.740585 TCACTTCAAACAACACCCACG 59.259 47.619 0.00 0.00 0.00 4.94
900 1017 3.126703 AACACCCACGGCCATCACA 62.127 57.895 2.24 0.00 0.00 3.58
910 1027 0.607489 GGCCATCACACAGCTCAAGT 60.607 55.000 0.00 0.00 0.00 3.16
937 1054 3.038280 TCCCACTTCAGAGTTCAGACAA 58.962 45.455 0.00 0.00 32.54 3.18
974 1106 0.034767 CAGCCCCTCAGCTCAATCAA 60.035 55.000 0.00 0.00 42.61 2.57
988 1120 0.537143 AATCAACGGCAGCAGGAACA 60.537 50.000 0.00 0.00 0.00 3.18
990 1122 2.186160 CAACGGCAGCAGGAACACA 61.186 57.895 0.00 0.00 0.00 3.72
995 1127 2.633657 CAGCAGGAACACACACGC 59.366 61.111 0.00 0.00 0.00 5.34
996 1128 2.967076 AGCAGGAACACACACGCG 60.967 61.111 3.53 3.53 0.00 6.01
1009 1158 1.874019 CACGCGGAGATGACCTTCG 60.874 63.158 12.47 0.00 46.62 3.79
1012 1161 3.082579 GCGGAGATGACCTTCGGCT 62.083 63.158 0.00 0.00 44.07 5.52
1014 1163 0.744874 CGGAGATGACCTTCGGCTTA 59.255 55.000 0.00 0.00 40.21 3.09
1276 1461 4.373116 GCCTCGGGTGCGAGTTCA 62.373 66.667 0.00 0.00 34.46 3.18
1374 1586 2.303175 CGGAGGAACAAAAAGACCCAA 58.697 47.619 0.00 0.00 0.00 4.12
1545 1757 1.600636 CGCCAAGCTCAACTTCCCA 60.601 57.895 0.00 0.00 36.04 4.37
1710 1958 0.746563 AGCTAGACGAGAGCGAGCTT 60.747 55.000 0.00 0.00 44.98 3.74
1730 1978 2.038837 GCTTACTGTTCCCGGTGGC 61.039 63.158 0.00 0.00 0.00 5.01
1793 2041 2.122813 ACCAGGGGCCGATCTAGG 60.123 66.667 0.00 2.04 0.00 3.02
1798 2046 2.529753 GGGCCGATCTAGGGGGTA 59.470 66.667 0.00 0.00 0.00 3.69
1808 2080 3.474798 TCTAGGGGGTATCATGGCTAG 57.525 52.381 0.00 0.00 0.00 3.42
1812 2084 1.059913 GGGGTATCATGGCTAGCAGT 58.940 55.000 18.24 0.46 0.00 4.40
1818 2090 3.760580 ATCATGGCTAGCAGTTAGACC 57.239 47.619 18.24 0.00 36.48 3.85
1823 2095 1.134670 GGCTAGCAGTTAGACCAGTGG 60.135 57.143 18.24 7.91 30.47 4.00
1864 2140 2.156697 TCAATCAACACGCATGTACACG 59.843 45.455 0.00 0.07 38.45 4.49
1868 2144 1.525197 CAACACGCATGTACACGACTT 59.475 47.619 12.29 1.19 38.45 3.01
1879 2158 4.586884 TGTACACGACTTCTAGATCCTGT 58.413 43.478 0.00 0.00 0.00 4.00
1883 2162 4.523173 ACACGACTTCTAGATCCTGTTCAA 59.477 41.667 0.00 0.00 0.00 2.69
1910 2189 3.006110 TGGTTAGCACACGTACTAGCTTT 59.994 43.478 8.22 0.00 38.47 3.51
1945 2232 5.302360 TGTATAAATAGGCACCCGATCAAC 58.698 41.667 0.00 0.00 0.00 3.18
1981 2268 4.517285 TGAACCATACTCCTCTTTCATGC 58.483 43.478 0.00 0.00 0.00 4.06
2035 2322 7.886629 AGATTATTTGTTGGCACTATGATGT 57.113 32.000 0.00 0.00 0.00 3.06
2036 2323 8.297470 AGATTATTTGTTGGCACTATGATGTT 57.703 30.769 0.00 0.00 0.00 2.71
2037 2324 8.192774 AGATTATTTGTTGGCACTATGATGTTG 58.807 33.333 0.00 0.00 0.00 3.33
2363 2651 2.626266 GGTTGAACCGGAAATTCCAACT 59.374 45.455 9.46 0.00 35.91 3.16
2373 2661 5.433526 CGGAAATTCCAACTGACCCTATTA 58.566 41.667 13.04 0.00 35.91 0.98
2516 2806 1.027357 AGATGGATGCAATGCGGTTC 58.973 50.000 0.00 0.00 37.56 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.424493 CGGCCTGCATCTTCTCGAAC 61.424 60.000 0.00 0.00 0.00 3.95
2 3 2.052104 TCGGCCTGCATCTTCTCGA 61.052 57.895 0.00 0.00 0.00 4.04
4 5 0.179062 ATGTCGGCCTGCATCTTCTC 60.179 55.000 0.00 0.00 0.00 2.87
5 6 0.463295 CATGTCGGCCTGCATCTTCT 60.463 55.000 0.00 0.00 0.00 2.85
6 7 2.020131 CATGTCGGCCTGCATCTTC 58.980 57.895 0.00 0.00 0.00 2.87
7 8 2.117156 GCATGTCGGCCTGCATCTT 61.117 57.895 12.62 0.00 36.47 2.40
8 9 2.515523 GCATGTCGGCCTGCATCT 60.516 61.111 12.62 0.00 36.47 2.90
9 10 2.515523 AGCATGTCGGCCTGCATC 60.516 61.111 19.43 7.35 38.47 3.91
10 11 2.515523 GAGCATGTCGGCCTGCAT 60.516 61.111 19.43 9.89 38.47 3.96
11 12 3.549900 TTGAGCATGTCGGCCTGCA 62.550 57.895 19.43 7.94 38.47 4.41
12 13 2.747460 TTGAGCATGTCGGCCTGC 60.747 61.111 9.43 9.43 36.66 4.85
13 14 0.957395 AACTTGAGCATGTCGGCCTG 60.957 55.000 0.00 0.00 0.00 4.85
14 15 0.674895 GAACTTGAGCATGTCGGCCT 60.675 55.000 0.00 0.00 0.00 5.19
15 16 1.796796 GAACTTGAGCATGTCGGCC 59.203 57.895 0.00 0.00 0.00 6.13
16 17 1.014044 TCGAACTTGAGCATGTCGGC 61.014 55.000 0.00 0.00 0.00 5.54
17 18 0.716108 GTCGAACTTGAGCATGTCGG 59.284 55.000 0.00 0.00 0.00 4.79
18 19 0.363512 CGTCGAACTTGAGCATGTCG 59.636 55.000 0.00 0.00 0.00 4.35
19 20 1.387084 GTCGTCGAACTTGAGCATGTC 59.613 52.381 0.00 0.00 0.00 3.06
20 21 1.419374 GTCGTCGAACTTGAGCATGT 58.581 50.000 0.00 0.00 0.00 3.21
21 22 0.363512 CGTCGTCGAACTTGAGCATG 59.636 55.000 0.00 0.00 39.71 4.06
22 23 0.240145 TCGTCGTCGAACTTGAGCAT 59.760 50.000 1.37 0.00 43.34 3.79
23 24 1.650363 TCGTCGTCGAACTTGAGCA 59.350 52.632 1.37 0.00 43.34 4.26
24 25 4.528002 TCGTCGTCGAACTTGAGC 57.472 55.556 1.37 0.00 43.34 4.26
33 34 1.979469 GCCATAGATCAATCGTCGTCG 59.021 52.381 0.00 0.00 38.55 5.12
34 35 1.979469 CGCCATAGATCAATCGTCGTC 59.021 52.381 0.00 0.00 0.00 4.20
35 36 1.335964 CCGCCATAGATCAATCGTCGT 60.336 52.381 0.00 0.00 0.00 4.34
36 37 1.340658 CCGCCATAGATCAATCGTCG 58.659 55.000 0.00 0.00 0.00 5.12
37 38 1.071605 GCCGCCATAGATCAATCGTC 58.928 55.000 0.00 0.00 0.00 4.20
38 39 0.667487 CGCCGCCATAGATCAATCGT 60.667 55.000 0.00 0.00 0.00 3.73
39 40 0.388520 TCGCCGCCATAGATCAATCG 60.389 55.000 0.00 0.00 0.00 3.34
40 41 1.354040 CTCGCCGCCATAGATCAATC 58.646 55.000 0.00 0.00 0.00 2.67
41 42 0.671781 GCTCGCCGCCATAGATCAAT 60.672 55.000 0.00 0.00 0.00 2.57
42 43 1.300931 GCTCGCCGCCATAGATCAA 60.301 57.895 0.00 0.00 0.00 2.57
43 44 2.340078 GCTCGCCGCCATAGATCA 59.660 61.111 0.00 0.00 0.00 2.92
44 45 2.807045 CGCTCGCCGCCATAGATC 60.807 66.667 0.00 0.00 34.21 2.75
68 69 0.600557 CACCTGCCGGCATACAAAAA 59.399 50.000 32.87 3.62 0.00 1.94
69 70 0.538516 ACACCTGCCGGCATACAAAA 60.539 50.000 32.87 4.54 0.00 2.44
70 71 1.074072 ACACCTGCCGGCATACAAA 59.926 52.632 32.87 5.45 0.00 2.83
71 72 1.673993 CACACCTGCCGGCATACAA 60.674 57.895 32.87 6.37 0.00 2.41
72 73 2.046411 CACACCTGCCGGCATACA 60.046 61.111 32.87 6.85 0.00 2.29
73 74 3.508840 GCACACCTGCCGGCATAC 61.509 66.667 32.87 12.06 37.45 2.39
82 83 3.434319 GTCATGCCGGCACACCTG 61.434 66.667 35.50 26.35 0.00 4.00
83 84 4.722700 GGTCATGCCGGCACACCT 62.723 66.667 36.54 21.00 32.36 4.00
85 86 3.737172 GTGGTCATGCCGGCACAC 61.737 66.667 35.50 29.83 41.21 3.82
90 91 4.838152 CTCCCGTGGTCATGCCGG 62.838 72.222 0.00 0.00 41.21 6.13
110 111 3.849953 GTTCGACCACGCCATCGC 61.850 66.667 0.00 0.00 38.24 4.58
111 112 2.126071 AGTTCGACCACGCCATCG 60.126 61.111 0.00 0.00 42.43 3.84
112 113 0.669318 TTGAGTTCGACCACGCCATC 60.669 55.000 0.00 0.00 39.58 3.51
113 114 0.670546 CTTGAGTTCGACCACGCCAT 60.671 55.000 0.00 0.00 39.58 4.40
114 115 1.300620 CTTGAGTTCGACCACGCCA 60.301 57.895 0.00 0.00 39.58 5.69
115 116 1.282930 GACTTGAGTTCGACCACGCC 61.283 60.000 0.00 0.00 39.58 5.68
116 117 0.596600 TGACTTGAGTTCGACCACGC 60.597 55.000 0.00 0.00 39.58 5.34
117 118 1.129326 GTGACTTGAGTTCGACCACG 58.871 55.000 0.00 0.00 41.26 4.94
118 119 2.218953 TGTGACTTGAGTTCGACCAC 57.781 50.000 0.00 0.00 0.00 4.16
119 120 2.288825 GGATGTGACTTGAGTTCGACCA 60.289 50.000 0.00 0.00 0.00 4.02
120 121 2.028930 AGGATGTGACTTGAGTTCGACC 60.029 50.000 0.00 0.00 0.00 4.79
121 122 3.305398 AGGATGTGACTTGAGTTCGAC 57.695 47.619 0.00 0.00 0.00 4.20
122 123 4.336889 AAAGGATGTGACTTGAGTTCGA 57.663 40.909 0.00 0.00 0.00 3.71
123 124 5.424121 AAAAAGGATGTGACTTGAGTTCG 57.576 39.130 0.00 0.00 0.00 3.95
142 143 1.206610 ACACATGCCAGCACACAAAAA 59.793 42.857 0.00 0.00 0.00 1.94
143 144 0.822811 ACACATGCCAGCACACAAAA 59.177 45.000 0.00 0.00 0.00 2.44
144 145 0.102663 CACACATGCCAGCACACAAA 59.897 50.000 0.00 0.00 0.00 2.83
145 146 1.734748 CACACATGCCAGCACACAA 59.265 52.632 0.00 0.00 0.00 3.33
146 147 2.847754 GCACACATGCCAGCACACA 61.848 57.895 0.00 0.00 46.97 3.72
147 148 2.049802 GCACACATGCCAGCACAC 60.050 61.111 0.00 0.00 46.97 3.82
156 157 2.985282 AACAGGCCGGCACACATG 60.985 61.111 30.85 19.55 0.00 3.21
157 158 2.985282 CAACAGGCCGGCACACAT 60.985 61.111 30.85 7.00 0.00 3.21
180 181 2.203195 ACAGTTCTTGCTGGCGCA 60.203 55.556 10.83 0.00 46.24 6.09
181 182 2.253452 CACAGTTCTTGCTGGCGC 59.747 61.111 0.00 0.00 40.59 6.53
182 183 1.893808 ACCACAGTTCTTGCTGGCG 60.894 57.895 0.00 0.00 40.59 5.69
183 184 0.819259 TCACCACAGTTCTTGCTGGC 60.819 55.000 0.00 0.00 40.59 4.85
184 185 1.901591 ATCACCACAGTTCTTGCTGG 58.098 50.000 0.00 0.00 40.59 4.85
185 186 5.633830 AAATATCACCACAGTTCTTGCTG 57.366 39.130 0.00 0.00 41.92 4.41
186 187 6.006449 AGAAAATATCACCACAGTTCTTGCT 58.994 36.000 0.00 0.00 0.00 3.91
187 188 6.072508 TCAGAAAATATCACCACAGTTCTTGC 60.073 38.462 0.00 0.00 0.00 4.01
188 189 7.361542 CCTCAGAAAATATCACCACAGTTCTTG 60.362 40.741 0.00 0.00 0.00 3.02
189 190 6.656693 CCTCAGAAAATATCACCACAGTTCTT 59.343 38.462 0.00 0.00 0.00 2.52
190 191 6.013379 TCCTCAGAAAATATCACCACAGTTCT 60.013 38.462 0.00 0.00 0.00 3.01
191 192 6.092807 GTCCTCAGAAAATATCACCACAGTTC 59.907 42.308 0.00 0.00 0.00 3.01
192 193 5.940470 GTCCTCAGAAAATATCACCACAGTT 59.060 40.000 0.00 0.00 0.00 3.16
193 194 5.491982 GTCCTCAGAAAATATCACCACAGT 58.508 41.667 0.00 0.00 0.00 3.55
194 195 4.568359 CGTCCTCAGAAAATATCACCACAG 59.432 45.833 0.00 0.00 0.00 3.66
195 196 4.503910 CGTCCTCAGAAAATATCACCACA 58.496 43.478 0.00 0.00 0.00 4.17
196 197 3.871594 CCGTCCTCAGAAAATATCACCAC 59.128 47.826 0.00 0.00 0.00 4.16
197 198 3.681594 GCCGTCCTCAGAAAATATCACCA 60.682 47.826 0.00 0.00 0.00 4.17
198 199 2.872858 GCCGTCCTCAGAAAATATCACC 59.127 50.000 0.00 0.00 0.00 4.02
199 200 3.531538 TGCCGTCCTCAGAAAATATCAC 58.468 45.455 0.00 0.00 0.00 3.06
200 201 3.904800 TGCCGTCCTCAGAAAATATCA 57.095 42.857 0.00 0.00 0.00 2.15
201 202 4.576463 ACAATGCCGTCCTCAGAAAATATC 59.424 41.667 0.00 0.00 0.00 1.63
202 203 4.526970 ACAATGCCGTCCTCAGAAAATAT 58.473 39.130 0.00 0.00 0.00 1.28
203 204 3.950397 ACAATGCCGTCCTCAGAAAATA 58.050 40.909 0.00 0.00 0.00 1.40
204 205 2.795329 ACAATGCCGTCCTCAGAAAAT 58.205 42.857 0.00 0.00 0.00 1.82
205 206 2.270352 ACAATGCCGTCCTCAGAAAA 57.730 45.000 0.00 0.00 0.00 2.29
206 207 3.270027 CATACAATGCCGTCCTCAGAAA 58.730 45.455 0.00 0.00 0.00 2.52
207 208 2.905075 CATACAATGCCGTCCTCAGAA 58.095 47.619 0.00 0.00 0.00 3.02
208 209 2.602257 CATACAATGCCGTCCTCAGA 57.398 50.000 0.00 0.00 0.00 3.27
219 220 1.063972 CCAACGCCGGCATACAATG 59.936 57.895 28.98 14.43 0.00 2.82
220 221 3.508474 CCAACGCCGGCATACAAT 58.492 55.556 28.98 1.60 0.00 2.71
228 229 4.418401 CACCAATGCCAACGCCGG 62.418 66.667 0.00 0.00 0.00 6.13
238 239 1.750018 TCTCATGCCGGCACCAATG 60.750 57.895 35.50 26.35 0.00 2.82
239 240 1.750399 GTCTCATGCCGGCACCAAT 60.750 57.895 35.50 14.18 0.00 3.16
240 241 2.359850 GTCTCATGCCGGCACCAA 60.360 61.111 35.50 19.17 0.00 3.67
241 242 2.970379 ATGTCTCATGCCGGCACCA 61.970 57.895 35.50 22.60 0.00 4.17
242 243 2.124570 ATGTCTCATGCCGGCACC 60.125 61.111 35.50 17.52 0.00 5.01
243 244 2.475466 CCATGTCTCATGCCGGCAC 61.475 63.158 35.50 19.90 0.00 5.01
244 245 2.124612 CCATGTCTCATGCCGGCA 60.125 61.111 34.80 34.80 0.00 5.69
245 246 3.589881 GCCATGTCTCATGCCGGC 61.590 66.667 22.73 22.73 0.00 6.13
246 247 2.903855 GGCCATGTCTCATGCCGG 60.904 66.667 0.00 0.00 33.59 6.13
248 249 1.077212 AGTGGCCATGTCTCATGCC 60.077 57.895 9.72 12.61 44.27 4.40
249 250 1.381928 CCAGTGGCCATGTCTCATGC 61.382 60.000 9.72 0.00 0.00 4.06
250 251 1.381928 GCCAGTGGCCATGTCTCATG 61.382 60.000 24.53 0.00 44.06 3.07
251 252 1.077212 GCCAGTGGCCATGTCTCAT 60.077 57.895 24.53 0.00 44.06 2.90
252 253 2.352422 GCCAGTGGCCATGTCTCA 59.648 61.111 24.53 0.00 44.06 3.27
288 289 6.864165 GTCCGCATTCAACCTGTAAATAAAAA 59.136 34.615 0.00 0.00 0.00 1.94
289 290 6.016192 TGTCCGCATTCAACCTGTAAATAAAA 60.016 34.615 0.00 0.00 0.00 1.52
290 291 5.473846 TGTCCGCATTCAACCTGTAAATAAA 59.526 36.000 0.00 0.00 0.00 1.40
291 292 5.004448 TGTCCGCATTCAACCTGTAAATAA 58.996 37.500 0.00 0.00 0.00 1.40
292 293 4.580868 TGTCCGCATTCAACCTGTAAATA 58.419 39.130 0.00 0.00 0.00 1.40
293 294 3.417101 TGTCCGCATTCAACCTGTAAAT 58.583 40.909 0.00 0.00 0.00 1.40
294 295 2.852449 TGTCCGCATTCAACCTGTAAA 58.148 42.857 0.00 0.00 0.00 2.01
295 296 2.552599 TGTCCGCATTCAACCTGTAA 57.447 45.000 0.00 0.00 0.00 2.41
296 297 2.027653 TCATGTCCGCATTCAACCTGTA 60.028 45.455 0.00 0.00 31.99 2.74
297 298 1.167851 CATGTCCGCATTCAACCTGT 58.832 50.000 0.00 0.00 31.99 4.00
298 299 1.452110 TCATGTCCGCATTCAACCTG 58.548 50.000 0.00 0.00 31.99 4.00
299 300 2.198827 TTCATGTCCGCATTCAACCT 57.801 45.000 0.00 0.00 31.99 3.50
300 301 3.181397 CATTTCATGTCCGCATTCAACC 58.819 45.455 0.00 0.00 31.99 3.77
301 302 3.119531 TCCATTTCATGTCCGCATTCAAC 60.120 43.478 0.00 0.00 31.99 3.18
302 303 3.087781 TCCATTTCATGTCCGCATTCAA 58.912 40.909 0.00 0.00 31.99 2.69
303 304 2.720915 TCCATTTCATGTCCGCATTCA 58.279 42.857 0.00 0.00 31.99 2.57
304 305 3.607775 CGATCCATTTCATGTCCGCATTC 60.608 47.826 0.00 0.00 31.99 2.67
305 306 2.291465 CGATCCATTTCATGTCCGCATT 59.709 45.455 0.00 0.00 31.99 3.56
306 307 1.875514 CGATCCATTTCATGTCCGCAT 59.124 47.619 0.00 0.00 35.32 4.73
307 308 1.298602 CGATCCATTTCATGTCCGCA 58.701 50.000 0.00 0.00 0.00 5.69
308 309 0.588252 CCGATCCATTTCATGTCCGC 59.412 55.000 0.00 0.00 0.00 5.54
309 310 0.588252 GCCGATCCATTTCATGTCCG 59.412 55.000 0.00 0.00 0.00 4.79
310 311 0.588252 CGCCGATCCATTTCATGTCC 59.412 55.000 0.00 0.00 0.00 4.02
311 312 0.040958 GCGCCGATCCATTTCATGTC 60.041 55.000 0.00 0.00 0.00 3.06
312 313 1.775039 CGCGCCGATCCATTTCATGT 61.775 55.000 0.00 0.00 0.00 3.21
313 314 1.082561 CGCGCCGATCCATTTCATG 60.083 57.895 0.00 0.00 0.00 3.07
314 315 1.095228 AACGCGCCGATCCATTTCAT 61.095 50.000 5.73 0.00 0.00 2.57
315 316 1.743623 AACGCGCCGATCCATTTCA 60.744 52.632 5.73 0.00 0.00 2.69
316 317 1.297598 CAACGCGCCGATCCATTTC 60.298 57.895 5.73 0.00 0.00 2.17
317 318 1.705337 CTCAACGCGCCGATCCATTT 61.705 55.000 5.73 0.00 0.00 2.32
318 319 2.125310 TCAACGCGCCGATCCATT 60.125 55.556 5.73 0.00 0.00 3.16
319 320 2.586079 CTCAACGCGCCGATCCAT 60.586 61.111 5.73 0.00 0.00 3.41
331 332 0.166814 GGATCAACAGTGCGCTCAAC 59.833 55.000 9.73 0.00 0.00 3.18
332 333 0.250252 TGGATCAACAGTGCGCTCAA 60.250 50.000 9.73 0.00 0.00 3.02
333 334 0.250252 TTGGATCAACAGTGCGCTCA 60.250 50.000 9.73 0.00 0.00 4.26
334 335 0.874390 TTTGGATCAACAGTGCGCTC 59.126 50.000 9.73 4.74 0.00 5.03
335 336 1.200716 CATTTGGATCAACAGTGCGCT 59.799 47.619 9.73 0.00 0.00 5.92
336 337 1.068333 ACATTTGGATCAACAGTGCGC 60.068 47.619 0.00 0.00 0.00 6.09
337 338 2.995466 ACATTTGGATCAACAGTGCG 57.005 45.000 0.00 0.00 0.00 5.34
338 339 6.144402 CAGTTTTACATTTGGATCAACAGTGC 59.856 38.462 0.00 0.00 0.00 4.40
339 340 6.642131 CCAGTTTTACATTTGGATCAACAGTG 59.358 38.462 0.00 0.00 32.34 3.66
340 341 6.239289 CCCAGTTTTACATTTGGATCAACAGT 60.239 38.462 0.00 0.00 32.34 3.55
341 342 6.158598 CCCAGTTTTACATTTGGATCAACAG 58.841 40.000 0.00 0.00 32.34 3.16
342 343 5.510520 GCCCAGTTTTACATTTGGATCAACA 60.511 40.000 0.00 0.00 32.34 3.33
343 344 4.929211 GCCCAGTTTTACATTTGGATCAAC 59.071 41.667 0.00 0.00 32.34 3.18
344 345 4.321601 CGCCCAGTTTTACATTTGGATCAA 60.322 41.667 0.00 0.00 32.34 2.57
345 346 3.192422 CGCCCAGTTTTACATTTGGATCA 59.808 43.478 0.00 0.00 32.34 2.92
346 347 3.428862 CCGCCCAGTTTTACATTTGGATC 60.429 47.826 0.00 0.00 32.34 3.36
347 348 2.495669 CCGCCCAGTTTTACATTTGGAT 59.504 45.455 0.00 0.00 32.34 3.41
348 349 1.889829 CCGCCCAGTTTTACATTTGGA 59.110 47.619 0.00 0.00 32.34 3.53
349 350 1.889829 TCCGCCCAGTTTTACATTTGG 59.110 47.619 0.00 0.00 0.00 3.28
350 351 3.510719 CATCCGCCCAGTTTTACATTTG 58.489 45.455 0.00 0.00 0.00 2.32
351 352 2.094234 GCATCCGCCCAGTTTTACATTT 60.094 45.455 0.00 0.00 0.00 2.32
352 353 1.476488 GCATCCGCCCAGTTTTACATT 59.524 47.619 0.00 0.00 0.00 2.71
353 354 1.102978 GCATCCGCCCAGTTTTACAT 58.897 50.000 0.00 0.00 0.00 2.29
354 355 2.562125 GCATCCGCCCAGTTTTACA 58.438 52.632 0.00 0.00 0.00 2.41
378 379 3.192922 CGTTTGGATCGGCCGTCC 61.193 66.667 28.99 28.99 40.66 4.79
379 380 3.192922 CCGTTTGGATCGGCCGTC 61.193 66.667 27.15 20.82 41.48 4.79
380 381 3.697747 TCCGTTTGGATCGGCCGT 61.698 61.111 27.15 12.96 46.49 5.68
388 389 0.382515 CCGCTTTTTGTCCGTTTGGA 59.617 50.000 0.00 0.00 43.88 3.53
389 390 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
390 391 1.202200 TGTCCGCTTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
391 392 1.096416 TGTCCGCTTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
392 393 1.096416 TTGTCCGCTTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
393 394 1.096416 TTTGTCCGCTTTTTGTCCGT 58.904 45.000 0.00 0.00 0.00 4.69
394 395 2.050691 CATTTGTCCGCTTTTTGTCCG 58.949 47.619 0.00 0.00 0.00 4.79
395 396 1.792367 GCATTTGTCCGCTTTTTGTCC 59.208 47.619 0.00 0.00 0.00 4.02
396 397 1.451651 CGCATTTGTCCGCTTTTTGTC 59.548 47.619 0.00 0.00 0.00 3.18
397 398 1.486439 CGCATTTGTCCGCTTTTTGT 58.514 45.000 0.00 0.00 0.00 2.83
398 399 0.161446 GCGCATTTGTCCGCTTTTTG 59.839 50.000 0.30 0.00 46.14 2.44
399 400 2.516486 GCGCATTTGTCCGCTTTTT 58.484 47.368 0.30 0.00 46.14 1.94
400 401 4.243383 GCGCATTTGTCCGCTTTT 57.757 50.000 0.30 0.00 46.14 2.27
409 410 4.715892 AAACGGGCGGCGCATTTG 62.716 61.111 34.36 20.84 0.00 2.32
410 411 4.715892 CAAACGGGCGGCGCATTT 62.716 61.111 34.36 25.22 0.00 2.32
429 430 0.947180 TAGCAACTTCAACGGGCGAC 60.947 55.000 0.00 0.00 0.00 5.19
430 431 0.249953 TTAGCAACTTCAACGGGCGA 60.250 50.000 0.00 0.00 0.00 5.54
431 432 0.802494 ATTAGCAACTTCAACGGGCG 59.198 50.000 0.00 0.00 0.00 6.13
432 433 1.135402 CCATTAGCAACTTCAACGGGC 60.135 52.381 0.00 0.00 0.00 6.13
433 434 2.432444 TCCATTAGCAACTTCAACGGG 58.568 47.619 0.00 0.00 0.00 5.28
434 435 4.414852 CAATCCATTAGCAACTTCAACGG 58.585 43.478 0.00 0.00 0.00 4.44
435 436 4.082787 ACCAATCCATTAGCAACTTCAACG 60.083 41.667 0.00 0.00 0.00 4.10
436 437 5.391312 ACCAATCCATTAGCAACTTCAAC 57.609 39.130 0.00 0.00 0.00 3.18
437 438 4.155826 CGACCAATCCATTAGCAACTTCAA 59.844 41.667 0.00 0.00 0.00 2.69
438 439 3.689161 CGACCAATCCATTAGCAACTTCA 59.311 43.478 0.00 0.00 0.00 3.02
439 440 3.689649 ACGACCAATCCATTAGCAACTTC 59.310 43.478 0.00 0.00 0.00 3.01
440 441 3.686016 ACGACCAATCCATTAGCAACTT 58.314 40.909 0.00 0.00 0.00 2.66
441 442 3.270877 GACGACCAATCCATTAGCAACT 58.729 45.455 0.00 0.00 0.00 3.16
442 443 3.006940 TGACGACCAATCCATTAGCAAC 58.993 45.455 0.00 0.00 0.00 4.17
443 444 3.342377 TGACGACCAATCCATTAGCAA 57.658 42.857 0.00 0.00 0.00 3.91
444 445 3.342377 TTGACGACCAATCCATTAGCA 57.658 42.857 0.00 0.00 0.00 3.49
475 476 5.644206 GTCTGGTTCTTCTAGATGGTTTTCC 59.356 44.000 5.84 3.32 36.14 3.13
494 495 2.223805 GCTGGTTTTGTTGGAAGTCTGG 60.224 50.000 0.00 0.00 0.00 3.86
497 498 3.304726 GCTAGCTGGTTTTGTTGGAAGTC 60.305 47.826 7.70 0.00 0.00 3.01
624 626 3.630828 GGAAATGAGGGTGGGATTTGGAT 60.631 47.826 0.00 0.00 0.00 3.41
637 639 5.293569 GGTAATGACGTTAGTGGAAATGAGG 59.706 44.000 0.00 0.00 0.00 3.86
686 689 2.584608 CAGGGACGGGACATGACC 59.415 66.667 5.56 5.56 0.00 4.02
708 711 1.466866 GCTTACGAATCCCGGTTTTGC 60.467 52.381 0.00 0.00 43.93 3.68
711 714 2.188062 TTGCTTACGAATCCCGGTTT 57.812 45.000 0.00 0.00 43.93 3.27
721 727 1.868498 CTCGGGTTTGTTTGCTTACGA 59.132 47.619 0.00 0.00 0.00 3.43
722 728 1.069500 CCTCGGGTTTGTTTGCTTACG 60.069 52.381 0.00 0.00 0.00 3.18
723 729 1.335597 GCCTCGGGTTTGTTTGCTTAC 60.336 52.381 0.00 0.00 0.00 2.34
724 730 0.955905 GCCTCGGGTTTGTTTGCTTA 59.044 50.000 0.00 0.00 0.00 3.09
727 733 2.338620 GGCCTCGGGTTTGTTTGC 59.661 61.111 0.00 0.00 0.00 3.68
789 795 3.796443 CATGCAGAACAGCGCGCT 61.796 61.111 31.32 31.32 37.31 5.92
794 800 4.824166 CGGCGCATGCAGAACAGC 62.824 66.667 19.57 11.47 45.35 4.40
887 1004 3.434319 GCTGTGTGATGGCCGTGG 61.434 66.667 0.00 0.00 0.00 4.94
889 1006 2.046892 GAGCTGTGTGATGGCCGT 60.047 61.111 0.00 0.00 0.00 5.68
891 1008 0.607489 ACTTGAGCTGTGTGATGGCC 60.607 55.000 0.00 0.00 0.00 5.36
910 1027 0.178921 ACTCTGAAGTGGGAGCTCCA 60.179 55.000 33.29 17.15 44.79 3.86
923 1040 2.115427 TGGGTGTTGTCTGAACTCTGA 58.885 47.619 0.00 0.00 0.00 3.27
937 1054 0.760567 TGAGAGCTGACTGTGGGTGT 60.761 55.000 0.00 0.00 0.00 4.16
974 1106 2.591715 GTGTGTTCCTGCTGCCGT 60.592 61.111 0.00 0.00 0.00 5.68
988 1120 1.816863 AAGGTCATCTCCGCGTGTGT 61.817 55.000 4.92 0.00 0.00 3.72
990 1122 1.215647 GAAGGTCATCTCCGCGTGT 59.784 57.895 4.92 0.00 0.00 4.49
1012 1161 0.529773 GCATCCAGTGTCGGCGATAA 60.530 55.000 14.79 1.14 0.00 1.75
1014 1163 2.202932 GCATCCAGTGTCGGCGAT 60.203 61.111 14.79 0.00 0.00 4.58
1021 1170 2.267006 CTGGCTCGCATCCAGTGT 59.733 61.111 7.51 0.00 44.62 3.55
1134 1313 3.034923 GCGCTATGCTCCTGCTCG 61.035 66.667 0.00 0.00 41.73 5.03
1304 1489 4.465512 GTGCGTCCAATGCAGCCG 62.466 66.667 0.00 0.00 41.37 5.52
1308 1493 2.281139 TTCGGTGCGTCCAATGCA 60.281 55.556 0.00 0.00 37.87 3.96
1309 1494 2.480555 CTTCGGTGCGTCCAATGC 59.519 61.111 0.00 0.00 35.57 3.56
1310 1495 3.039202 GCCTTCGGTGCGTCCAATG 62.039 63.158 0.00 0.00 35.57 2.82
1311 1496 2.746277 GCCTTCGGTGCGTCCAAT 60.746 61.111 0.00 0.00 35.57 3.16
1374 1586 3.814615 CTGCCTGATGCCGCGGTAT 62.815 63.158 29.54 29.54 40.16 2.73
1545 1757 3.694058 CTGCTGCTGCTCGGGGAAT 62.694 63.158 17.00 0.00 40.48 3.01
1636 1857 3.310860 CTGTTTCCTCCCCGTCCGG 62.311 68.421 0.00 0.00 0.00 5.14
1710 1958 0.250553 CCACCGGGAACAGTAAGCAA 60.251 55.000 6.32 0.00 35.59 3.91
1730 1978 1.384525 TTCCAAGGTGTTGTTGACCG 58.615 50.000 0.00 0.00 38.64 4.79
1793 2041 1.059913 ACTGCTAGCCATGATACCCC 58.940 55.000 13.29 0.00 0.00 4.95
1798 2046 3.041211 TGGTCTAACTGCTAGCCATGAT 58.959 45.455 13.29 0.00 32.27 2.45
1808 2080 0.035458 ACTGCCACTGGTCTAACTGC 59.965 55.000 0.00 0.00 0.00 4.40
1812 2084 1.005037 CGCACTGCCACTGGTCTAA 60.005 57.895 0.00 0.00 0.00 2.10
1833 2105 1.125021 GTGTTGATTGAGAGACACGCG 59.875 52.381 3.53 3.53 33.88 6.01
1838 2110 2.738846 ACATGCGTGTTGATTGAGAGAC 59.261 45.455 5.51 0.00 34.01 3.36
1864 2140 6.693545 CACGTATTGAACAGGATCTAGAAGTC 59.306 42.308 0.00 0.00 0.00 3.01
1868 2144 4.954202 ACCACGTATTGAACAGGATCTAGA 59.046 41.667 0.00 0.00 0.00 2.43
1902 2181 9.953565 TTATACAGAATTACAACCAAAGCTAGT 57.046 29.630 0.00 0.00 0.00 2.57
1910 2189 9.116067 GTGCCTATTTATACAGAATTACAACCA 57.884 33.333 0.00 0.00 0.00 3.67
1945 2232 3.495670 TGGTTCAACACAACTTTTCCG 57.504 42.857 0.00 0.00 0.00 4.30
1981 2268 6.887376 AGCATTCGTGTTAAGTACATACTG 57.113 37.500 0.00 0.00 39.39 2.74
2010 2297 8.978874 ACATCATAGTGCCAACAAATAATCTA 57.021 30.769 0.00 0.00 0.00 1.98
2011 2298 7.886629 ACATCATAGTGCCAACAAATAATCT 57.113 32.000 0.00 0.00 0.00 2.40
2025 2312 3.002791 AGCGGTGAACAACATCATAGTG 58.997 45.455 0.00 0.00 0.00 2.74
2031 2318 0.163788 CGACAGCGGTGAACAACATC 59.836 55.000 23.44 5.30 0.00 3.06
2032 2319 0.249699 TCGACAGCGGTGAACAACAT 60.250 50.000 23.44 0.00 38.28 2.71
2033 2320 0.249699 ATCGACAGCGGTGAACAACA 60.250 50.000 23.44 0.00 38.28 3.33
2034 2321 0.438830 GATCGACAGCGGTGAACAAC 59.561 55.000 23.44 5.91 38.28 3.32
2035 2322 1.006825 CGATCGACAGCGGTGAACAA 61.007 55.000 23.44 3.91 38.28 2.83
2036 2323 1.443702 CGATCGACAGCGGTGAACA 60.444 57.895 23.44 4.03 38.28 3.18
2037 2324 2.789203 GCGATCGACAGCGGTGAAC 61.789 63.158 23.44 13.41 38.28 3.18
2176 2464 9.944376 AGAACCATCGCACTATATAATAACAAT 57.056 29.630 0.00 0.00 0.00 2.71
2363 2651 7.850935 ATTTAACCTCTCGATAATAGGGTCA 57.149 36.000 7.81 0.00 34.52 4.02
2373 2661 9.720769 TTCTTCAACTAAATTTAACCTCTCGAT 57.279 29.630 0.00 0.00 0.00 3.59
2619 2909 8.816640 AACTATGTAAAACCTTTCAATGCAAG 57.183 30.769 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.