Multiple sequence alignment - TraesCS6B01G225000

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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 TraesCS6B01G225000 chr6B 100.000 4369 0 0 1 4369 345627716 345623348 0.000000e+00 8069
1 TraesCS6B01G225000 chr6B 86.232 276 24 7 1 263 636972486 636972212 1.990000e-73 287
2 TraesCS6B01G225000 chr6B 84.825 257 23 7 11 260 213304500 213304747 1.210000e-60 244
3 TraesCS6B01G225000 chr6D 95.023 3657 83 26 284 3883 254136364 254139978 0.000000e+00 5653
4 TraesCS6B01G225000 chr6D 90.099 404 28 3 3885 4281 78515760 78516158 8.380000e-142 514
5 TraesCS6B01G225000 chr6D 88.599 421 33 6 3889 4302 75378877 75379289 8.440000e-137 497
6 TraesCS6B01G225000 chr6D 84.211 152 16 1 1616 1767 293805682 293805825 1.640000e-29 141
7 TraesCS6B01G225000 chr6A 94.427 3463 117 33 284 3704 340189915 340186487 0.000000e+00 5256
8 TraesCS6B01G225000 chr6A 96.377 138 4 1 3749 3885 340099399 340099262 4.400000e-55 226
9 TraesCS6B01G225000 chr6A 98.214 56 1 0 1087 1142 340189041 340188986 1.000000e-16 99
10 TraesCS6B01G225000 chr5A 89.216 510 21 6 3889 4369 53368425 53367921 1.340000e-169 606
11 TraesCS6B01G225000 chr5A 88.454 511 24 7 3889 4369 632643089 632643594 6.300000e-163 584
12 TraesCS6B01G225000 chr4D 88.155 515 26 7 3884 4369 325065289 325064781 8.140000e-162 580
13 TraesCS6B01G225000 chr4D 86.447 273 17 9 1 260 368508047 368508312 9.250000e-72 281
14 TraesCS6B01G225000 chr5D 87.759 531 15 11 3889 4369 257129604 257130134 3.790000e-160 575
15 TraesCS6B01G225000 chr5D 86.239 218 28 2 1528 1744 526035811 526036027 7.300000e-58 235
16 TraesCS6B01G225000 chr7D 91.408 419 22 6 3891 4302 562332133 562331722 2.950000e-156 562
17 TraesCS6B01G225000 chr7D 90.842 273 13 6 1 263 122524035 122523765 5.370000e-94 355
18 TraesCS6B01G225000 chr7D 89.313 262 16 8 1 260 87759363 87759614 7.050000e-83 318
19 TraesCS6B01G225000 chr7B 85.164 519 38 10 3885 4369 88311529 88311016 3.030000e-136 496
20 TraesCS6B01G225000 chr7B 88.973 263 23 5 1 258 705729487 705729226 1.960000e-83 320
21 TraesCS6B01G225000 chr7B 84.456 193 28 2 1539 1730 29232089 29231898 5.770000e-44 189
22 TraesCS6B01G225000 chr7B 83.333 192 29 3 1541 1730 603042989 603043179 1.620000e-39 174
23 TraesCS6B01G225000 chr7A 89.646 396 28 4 3910 4297 141061659 141062049 3.930000e-135 492
24 TraesCS6B01G225000 chr7A 90.076 262 21 4 1 260 704843610 704843868 7.000000e-88 335
25 TraesCS6B01G225000 chr4A 89.646 396 28 4 3910 4297 588663354 588663744 3.930000e-135 492
26 TraesCS6B01G225000 chr2D 92.395 263 18 2 1 263 37529382 37529122 1.480000e-99 374
27 TraesCS6B01G225000 chr2D 90.335 269 19 6 1 263 651638656 651638389 3.230000e-91 346
28 TraesCS6B01G225000 chr5B 89.744 273 15 6 1 263 507992855 507992586 1.950000e-88 337
29 TraesCS6B01G225000 chr5B 83.902 205 31 2 1541 1744 403648872 403648669 1.240000e-45 195
30 TraesCS6B01G225000 chr5B 83.684 190 28 3 1543 1730 95256311 95256499 4.490000e-40 176
31 TraesCS6B01G225000 chr2B 89.937 159 15 1 102 260 52601622 52601465 2.060000e-48 204
32 TraesCS6B01G225000 chr2B 90.411 146 13 1 4 149 723047887 723047743 1.600000e-44 191
33 TraesCS6B01G225000 chr3B 79.724 217 35 8 1528 1744 805419170 805419377 9.790000e-32 148
34 TraesCS6B01G225000 chr3B 79.358 218 35 9 1528 1744 805416711 805416919 1.270000e-30 145


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 TraesCS6B01G225000 chr6B 345623348 345627716 4368 True 8069.0 8069 100.0000 1 4369 1 chr6B.!!$R1 4368
1 TraesCS6B01G225000 chr6D 254136364 254139978 3614 False 5653.0 5653 95.0230 284 3883 1 chr6D.!!$F3 3599
2 TraesCS6B01G225000 chr6A 340186487 340189915 3428 True 2677.5 5256 96.3205 284 3704 2 chr6A.!!$R2 3420
3 TraesCS6B01G225000 chr5A 53367921 53368425 504 True 606.0 606 89.2160 3889 4369 1 chr5A.!!$R1 480
4 TraesCS6B01G225000 chr5A 632643089 632643594 505 False 584.0 584 88.4540 3889 4369 1 chr5A.!!$F1 480
5 TraesCS6B01G225000 chr4D 325064781 325065289 508 True 580.0 580 88.1550 3884 4369 1 chr4D.!!$R1 485
6 TraesCS6B01G225000 chr5D 257129604 257130134 530 False 575.0 575 87.7590 3889 4369 1 chr5D.!!$F1 480
7 TraesCS6B01G225000 chr7B 88311016 88311529 513 True 496.0 496 85.1640 3885 4369 1 chr7B.!!$R2 484

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
125 126 0.253894 ATGCTGGCACACATGAGCTA 59.746 50.0 0.0 0.0 31.15 3.32 F
188 189 0.319083 ACAAATCGCCAGGTCGTACA 59.681 50.0 0.0 0.0 0.00 2.90 F
193 194 0.604073 TCGCCAGGTCGTACAATCAA 59.396 50.0 0.0 0.0 0.00 2.57 F
1548 1563 0.847373 TTTGGTTCCTAGCCACACCA 59.153 50.0 0.0 0.0 37.53 4.17 F
2517 2545 0.095935 CTGCTGCTAACATGCACGAC 59.904 55.0 0.0 0.0 38.12 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1578 0.182537 CACCCACCTGACTTGACCAA 59.817 55.000 0.00 0.0 0.00 3.67 R
1567 1582 1.409521 CCAAACACCCACCTGACTTGA 60.410 52.381 0.00 0.0 0.00 3.02 R
1660 1675 2.621668 GGCTTGCCTTAGGGAATCTTGT 60.622 50.000 5.50 0.0 31.43 3.16 R
3306 3334 0.459899 TGAGGCGCGATGACTACAAT 59.540 50.000 12.10 0.0 34.35 2.71 R
4020 4105 0.104934 CTATGGGTCCTAGCAGGGGT 60.105 60.000 2.86 0.0 35.59 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
32 33 4.499037 AAAAAGATACCTCACAAACGGC 57.501 40.909 0.00 0.00 0.00 5.68
33 34 2.851263 AAGATACCTCACAAACGGCA 57.149 45.000 0.00 0.00 0.00 5.69
34 35 2.851263 AGATACCTCACAAACGGCAA 57.149 45.000 0.00 0.00 0.00 4.52
35 36 2.423577 AGATACCTCACAAACGGCAAC 58.576 47.619 0.00 0.00 0.00 4.17
36 37 2.147958 GATACCTCACAAACGGCAACA 58.852 47.619 0.00 0.00 0.00 3.33
37 38 1.588674 TACCTCACAAACGGCAACAG 58.411 50.000 0.00 0.00 0.00 3.16
38 39 1.008538 CCTCACAAACGGCAACAGC 60.009 57.895 0.00 0.00 0.00 4.40
39 40 1.447317 CCTCACAAACGGCAACAGCT 61.447 55.000 0.00 0.00 0.00 4.24
40 41 0.317269 CTCACAAACGGCAACAGCTG 60.317 55.000 13.48 13.48 40.52 4.24
51 52 1.713597 CAACAGCTGCAGTGTATCGA 58.286 50.000 15.27 0.00 0.00 3.59
52 53 1.657594 CAACAGCTGCAGTGTATCGAG 59.342 52.381 15.27 0.00 0.00 4.04
53 54 1.177401 ACAGCTGCAGTGTATCGAGA 58.823 50.000 15.27 0.00 0.00 4.04
54 55 1.135257 ACAGCTGCAGTGTATCGAGAC 60.135 52.381 15.27 2.50 0.00 3.36
55 56 1.135286 CAGCTGCAGTGTATCGAGACA 60.135 52.381 16.64 9.19 0.00 3.41
56 57 1.546029 AGCTGCAGTGTATCGAGACAA 59.454 47.619 15.52 0.00 0.00 3.18
57 58 2.167281 AGCTGCAGTGTATCGAGACAAT 59.833 45.455 15.52 11.44 0.00 2.71
58 59 3.381590 AGCTGCAGTGTATCGAGACAATA 59.618 43.478 15.52 0.00 0.00 1.90
59 60 3.487574 GCTGCAGTGTATCGAGACAATAC 59.512 47.826 15.52 9.30 0.00 1.89
60 61 4.672409 CTGCAGTGTATCGAGACAATACA 58.328 43.478 15.52 13.75 37.28 2.29
61 62 5.066968 TGCAGTGTATCGAGACAATACAA 57.933 39.130 15.52 0.00 40.33 2.41
62 63 4.862574 TGCAGTGTATCGAGACAATACAAC 59.137 41.667 15.52 4.98 40.33 3.32
63 64 4.862574 GCAGTGTATCGAGACAATACAACA 59.137 41.667 15.52 0.00 40.33 3.33
64 65 5.347635 GCAGTGTATCGAGACAATACAACAA 59.652 40.000 15.52 0.00 40.33 2.83
65 66 6.036083 GCAGTGTATCGAGACAATACAACAAT 59.964 38.462 15.52 0.00 40.33 2.71
66 67 7.222031 GCAGTGTATCGAGACAATACAACAATA 59.778 37.037 15.52 0.00 40.33 1.90
67 68 8.746751 CAGTGTATCGAGACAATACAACAATAG 58.253 37.037 15.52 0.00 40.33 1.73
68 69 8.683615 AGTGTATCGAGACAATACAACAATAGA 58.316 33.333 15.52 0.00 40.33 1.98
69 70 8.744011 GTGTATCGAGACAATACAACAATAGAC 58.256 37.037 15.52 0.00 40.33 2.59
70 71 8.463607 TGTATCGAGACAATACAACAATAGACA 58.536 33.333 11.07 0.00 36.82 3.41
71 72 9.297586 GTATCGAGACAATACAACAATAGACAA 57.702 33.333 5.07 0.00 31.30 3.18
72 73 8.771920 ATCGAGACAATACAACAATAGACAAA 57.228 30.769 0.00 0.00 0.00 2.83
73 74 8.596271 TCGAGACAATACAACAATAGACAAAA 57.404 30.769 0.00 0.00 0.00 2.44
74 75 8.708742 TCGAGACAATACAACAATAGACAAAAG 58.291 33.333 0.00 0.00 0.00 2.27
75 76 8.708742 CGAGACAATACAACAATAGACAAAAGA 58.291 33.333 0.00 0.00 0.00 2.52
78 79 9.612620 GACAATACAACAATAGACAAAAGAAGG 57.387 33.333 0.00 0.00 0.00 3.46
79 80 9.349713 ACAATACAACAATAGACAAAAGAAGGA 57.650 29.630 0.00 0.00 0.00 3.36
103 104 3.930634 AAGACAGAAAGGAAATGCAGC 57.069 42.857 0.00 0.00 0.00 5.25
104 105 2.165998 AGACAGAAAGGAAATGCAGCC 58.834 47.619 0.00 0.00 0.00 4.85
105 106 1.203287 GACAGAAAGGAAATGCAGCCC 59.797 52.381 0.00 0.00 0.00 5.19
106 107 1.259609 CAGAAAGGAAATGCAGCCCA 58.740 50.000 0.00 0.00 0.00 5.36
107 108 1.829222 CAGAAAGGAAATGCAGCCCAT 59.171 47.619 0.00 0.00 35.06 4.00
108 109 1.829222 AGAAAGGAAATGCAGCCCATG 59.171 47.619 0.00 0.00 33.49 3.66
120 121 2.889617 CCCATGCTGGCACACATG 59.110 61.111 15.56 15.56 42.82 3.21
121 122 1.679641 CCCATGCTGGCACACATGA 60.680 57.895 21.49 0.00 44.49 3.07
122 123 1.663379 CCCATGCTGGCACACATGAG 61.663 60.000 21.49 9.36 44.49 2.90
123 124 1.138883 CATGCTGGCACACATGAGC 59.861 57.895 16.95 3.10 44.49 4.26
124 125 1.001269 ATGCTGGCACACATGAGCT 60.001 52.632 0.00 0.00 31.15 4.09
125 126 0.253894 ATGCTGGCACACATGAGCTA 59.746 50.000 0.00 0.00 31.15 3.32
126 127 0.392060 TGCTGGCACACATGAGCTAG 60.392 55.000 9.72 9.72 41.58 3.42
127 128 2.391469 CTGGCACACATGAGCTAGC 58.609 57.895 6.62 6.62 34.18 3.42
128 129 1.078214 TGGCACACATGAGCTAGCC 60.078 57.895 12.13 12.69 42.32 3.93
129 130 1.821332 GGCACACATGAGCTAGCCC 60.821 63.158 12.13 0.00 36.17 5.19
130 131 1.078214 GCACACATGAGCTAGCCCA 60.078 57.895 12.13 6.15 0.00 5.36
131 132 1.372087 GCACACATGAGCTAGCCCAC 61.372 60.000 12.13 4.11 0.00 4.61
132 133 1.086067 CACACATGAGCTAGCCCACG 61.086 60.000 12.13 0.00 0.00 4.94
133 134 2.176273 CACATGAGCTAGCCCACGC 61.176 63.158 12.13 0.00 0.00 5.34
177 178 2.644707 GCGCACGCTACAAATCGC 60.645 61.111 7.96 0.00 38.26 4.58
178 179 2.021380 CGCACGCTACAAATCGCC 59.979 61.111 0.00 0.00 0.00 5.54
179 180 2.735677 CGCACGCTACAAATCGCCA 61.736 57.895 0.00 0.00 0.00 5.69
180 181 1.060937 GCACGCTACAAATCGCCAG 59.939 57.895 0.00 0.00 0.00 4.85
181 182 1.715585 CACGCTACAAATCGCCAGG 59.284 57.895 0.00 0.00 0.00 4.45
182 183 1.019278 CACGCTACAAATCGCCAGGT 61.019 55.000 0.00 0.00 0.00 4.00
183 184 0.739813 ACGCTACAAATCGCCAGGTC 60.740 55.000 0.00 0.00 0.00 3.85
184 185 1.752501 CGCTACAAATCGCCAGGTCG 61.753 60.000 0.00 0.00 0.00 4.79
185 186 0.739813 GCTACAAATCGCCAGGTCGT 60.740 55.000 3.62 0.00 0.00 4.34
186 187 1.470285 GCTACAAATCGCCAGGTCGTA 60.470 52.381 3.62 0.00 0.00 3.43
187 188 2.190981 CTACAAATCGCCAGGTCGTAC 58.809 52.381 3.62 0.00 0.00 3.67
188 189 0.319083 ACAAATCGCCAGGTCGTACA 59.681 50.000 0.00 0.00 0.00 2.90
189 190 1.270412 ACAAATCGCCAGGTCGTACAA 60.270 47.619 0.00 0.00 0.00 2.41
190 191 2.006888 CAAATCGCCAGGTCGTACAAT 58.993 47.619 0.00 0.00 0.00 2.71
191 192 1.935933 AATCGCCAGGTCGTACAATC 58.064 50.000 0.00 0.00 0.00 2.67
192 193 0.821517 ATCGCCAGGTCGTACAATCA 59.178 50.000 0.00 0.00 0.00 2.57
193 194 0.604073 TCGCCAGGTCGTACAATCAA 59.396 50.000 0.00 0.00 0.00 2.57
194 195 1.001068 TCGCCAGGTCGTACAATCAAA 59.999 47.619 0.00 0.00 0.00 2.69
195 196 1.127951 CGCCAGGTCGTACAATCAAAC 59.872 52.381 0.00 0.00 0.00 2.93
196 197 1.127951 GCCAGGTCGTACAATCAAACG 59.872 52.381 0.00 0.00 40.40 3.60
197 198 1.127951 CCAGGTCGTACAATCAAACGC 59.872 52.381 0.00 0.00 38.94 4.84
198 199 1.065358 AGGTCGTACAATCAAACGCG 58.935 50.000 3.53 3.53 38.94 6.01
199 200 1.062258 GGTCGTACAATCAAACGCGA 58.938 50.000 15.93 0.00 38.94 5.87
200 201 1.456544 GGTCGTACAATCAAACGCGAA 59.543 47.619 15.93 0.00 38.94 4.70
201 202 2.479328 GTCGTACAATCAAACGCGAAC 58.521 47.619 15.93 0.00 38.94 3.95
202 203 2.097299 GTCGTACAATCAAACGCGAACA 60.097 45.455 15.93 0.00 38.94 3.18
203 204 2.538861 TCGTACAATCAAACGCGAACAA 59.461 40.909 15.93 0.00 38.94 2.83
204 205 3.001026 TCGTACAATCAAACGCGAACAAA 59.999 39.130 15.93 0.00 38.94 2.83
205 206 3.903644 CGTACAATCAAACGCGAACAAAT 59.096 39.130 15.93 0.00 31.66 2.32
206 207 4.027556 CGTACAATCAAACGCGAACAAATC 59.972 41.667 15.93 0.00 31.66 2.17
219 220 5.063335 CGAACAAATCGTCAGATCATCAG 57.937 43.478 0.00 0.00 46.52 2.90
220 221 4.564372 CGAACAAATCGTCAGATCATCAGT 59.436 41.667 0.00 0.00 46.52 3.41
221 222 5.276114 CGAACAAATCGTCAGATCATCAGTC 60.276 44.000 0.00 0.00 46.52 3.51
222 223 4.437239 ACAAATCGTCAGATCATCAGTCC 58.563 43.478 0.00 0.00 35.74 3.85
223 224 4.081476 ACAAATCGTCAGATCATCAGTCCA 60.081 41.667 0.00 0.00 35.74 4.02
224 225 3.724508 ATCGTCAGATCATCAGTCCAC 57.275 47.619 0.00 0.00 29.44 4.02
225 226 1.401905 TCGTCAGATCATCAGTCCACG 59.598 52.381 0.00 0.00 0.00 4.94
226 227 1.401905 CGTCAGATCATCAGTCCACGA 59.598 52.381 0.00 0.00 0.00 4.35
227 228 2.159379 CGTCAGATCATCAGTCCACGAA 60.159 50.000 0.00 0.00 0.00 3.85
228 229 3.489908 CGTCAGATCATCAGTCCACGAAT 60.490 47.826 0.00 0.00 0.00 3.34
229 230 4.437239 GTCAGATCATCAGTCCACGAATT 58.563 43.478 0.00 0.00 0.00 2.17
230 231 4.872691 GTCAGATCATCAGTCCACGAATTT 59.127 41.667 0.00 0.00 0.00 1.82
231 232 5.352569 GTCAGATCATCAGTCCACGAATTTT 59.647 40.000 0.00 0.00 0.00 1.82
232 233 6.535150 GTCAGATCATCAGTCCACGAATTTTA 59.465 38.462 0.00 0.00 0.00 1.52
233 234 7.064609 GTCAGATCATCAGTCCACGAATTTTAA 59.935 37.037 0.00 0.00 0.00 1.52
234 235 7.606073 TCAGATCATCAGTCCACGAATTTTAAA 59.394 33.333 0.00 0.00 0.00 1.52
235 236 7.907045 CAGATCATCAGTCCACGAATTTTAAAG 59.093 37.037 0.00 0.00 0.00 1.85
236 237 7.824289 AGATCATCAGTCCACGAATTTTAAAGA 59.176 33.333 0.00 0.00 0.00 2.52
237 238 7.129109 TCATCAGTCCACGAATTTTAAAGAC 57.871 36.000 0.00 0.00 0.00 3.01
238 239 5.934935 TCAGTCCACGAATTTTAAAGACC 57.065 39.130 0.00 0.00 0.00 3.85
239 240 5.369833 TCAGTCCACGAATTTTAAAGACCA 58.630 37.500 0.00 0.00 0.00 4.02
240 241 6.001460 TCAGTCCACGAATTTTAAAGACCAT 58.999 36.000 0.00 0.00 0.00 3.55
241 242 7.162761 TCAGTCCACGAATTTTAAAGACCATA 58.837 34.615 0.00 0.00 0.00 2.74
242 243 7.118680 TCAGTCCACGAATTTTAAAGACCATAC 59.881 37.037 0.00 0.00 0.00 2.39
243 244 6.938030 AGTCCACGAATTTTAAAGACCATACA 59.062 34.615 0.00 0.00 0.00 2.29
244 245 7.446013 AGTCCACGAATTTTAAAGACCATACAA 59.554 33.333 0.00 0.00 0.00 2.41
245 246 8.077386 GTCCACGAATTTTAAAGACCATACAAA 58.923 33.333 0.00 0.00 0.00 2.83
246 247 8.630917 TCCACGAATTTTAAAGACCATACAAAA 58.369 29.630 0.00 0.00 0.00 2.44
247 248 9.418045 CCACGAATTTTAAAGACCATACAAAAT 57.582 29.630 0.00 0.00 31.84 1.82
249 250 9.634163 ACGAATTTTAAAGACCATACAAAATCC 57.366 29.630 0.00 0.00 30.58 3.01
250 251 9.632807 CGAATTTTAAAGACCATACAAAATCCA 57.367 29.630 0.00 0.00 30.58 3.41
253 254 8.804688 TTTTAAAGACCATACAAAATCCAACG 57.195 30.769 0.00 0.00 0.00 4.10
254 255 7.747155 TTAAAGACCATACAAAATCCAACGA 57.253 32.000 0.00 0.00 0.00 3.85
255 256 6.834168 AAAGACCATACAAAATCCAACGAT 57.166 33.333 0.00 0.00 0.00 3.73
256 257 5.818136 AGACCATACAAAATCCAACGATG 57.182 39.130 0.00 0.00 0.00 3.84
257 258 5.496556 AGACCATACAAAATCCAACGATGA 58.503 37.500 0.00 0.00 0.00 2.92
258 259 5.586243 AGACCATACAAAATCCAACGATGAG 59.414 40.000 0.00 0.00 0.00 2.90
259 260 4.640201 ACCATACAAAATCCAACGATGAGG 59.360 41.667 0.00 0.00 0.00 3.86
260 261 4.498009 CCATACAAAATCCAACGATGAGGC 60.498 45.833 0.00 0.00 0.00 4.70
261 262 2.513753 ACAAAATCCAACGATGAGGCA 58.486 42.857 0.00 0.00 0.00 4.75
262 263 2.228822 ACAAAATCCAACGATGAGGCAC 59.771 45.455 0.00 0.00 0.00 5.01
263 264 2.198827 AAATCCAACGATGAGGCACA 57.801 45.000 0.00 0.00 0.00 4.57
264 265 2.425143 AATCCAACGATGAGGCACAT 57.575 45.000 0.00 0.00 42.47 3.21
274 275 4.722203 GATGAGGCACATCGTGAAATAG 57.278 45.455 9.14 0.00 44.46 1.73
275 276 2.279741 TGAGGCACATCGTGAAATAGC 58.720 47.619 0.00 0.00 35.23 2.97
276 277 2.279741 GAGGCACATCGTGAAATAGCA 58.720 47.619 0.00 0.00 35.23 3.49
277 278 2.677836 GAGGCACATCGTGAAATAGCAA 59.322 45.455 0.00 0.00 35.23 3.91
278 279 3.081061 AGGCACATCGTGAAATAGCAAA 58.919 40.909 0.00 0.00 35.23 3.68
279 280 3.696051 AGGCACATCGTGAAATAGCAAAT 59.304 39.130 0.00 0.00 35.23 2.32
280 281 4.037690 GGCACATCGTGAAATAGCAAATC 58.962 43.478 0.00 0.00 35.23 2.17
281 282 4.037690 GCACATCGTGAAATAGCAAATCC 58.962 43.478 0.00 0.00 35.23 3.01
282 283 4.274069 CACATCGTGAAATAGCAAATCCG 58.726 43.478 0.00 0.00 35.23 4.18
422 423 1.961277 CCATATTCGCTGGACCCGC 60.961 63.158 0.00 0.00 35.70 6.13
537 538 2.006772 GCCGAATCGCGATCTGTTT 58.993 52.632 23.92 6.87 44.57 2.83
638 639 2.886124 GCTCTCGCGGTGTTAGGC 60.886 66.667 6.13 0.00 0.00 3.93
700 701 1.909986 TGGTATCACCGGTTGGATCAA 59.090 47.619 2.97 0.00 42.58 2.57
753 754 4.392940 GAATCCACTGGCAGTAGCATTAT 58.607 43.478 21.59 0.00 44.61 1.28
797 798 2.960688 GCTGGGAGTGGGACTGGTC 61.961 68.421 0.00 0.00 0.00 4.02
965 968 3.161866 GGGTTAGAGATTTTGGTGCCAA 58.838 45.455 0.00 0.00 0.00 4.52
992 995 3.821033 GGACTCTGTAAGTGCATTTTGGT 59.179 43.478 0.00 0.00 45.15 3.67
1475 1490 5.743117 ACACTTGTACTAGACCGTATCTCT 58.257 41.667 11.43 0.00 39.04 3.10
1476 1491 5.816777 ACACTTGTACTAGACCGTATCTCTC 59.183 44.000 11.43 0.00 39.04 3.20
1521 1536 8.905702 GTTATGCTTTTTATCTCAAGTGTGTTG 58.094 33.333 0.00 0.00 0.00 3.33
1548 1563 0.847373 TTTGGTTCCTAGCCACACCA 59.153 50.000 0.00 0.00 37.53 4.17
1555 1570 4.332828 GTTCCTAGCCACACCATAAGTTT 58.667 43.478 0.00 0.00 0.00 2.66
1556 1571 3.950397 TCCTAGCCACACCATAAGTTTG 58.050 45.455 0.00 0.00 0.00 2.93
1561 1576 3.302365 CCACACCATAAGTTTGGCAAG 57.698 47.619 0.00 0.00 39.42 4.01
1562 1577 2.627699 CCACACCATAAGTTTGGCAAGT 59.372 45.455 0.00 0.00 39.42 3.16
1563 1578 3.069443 CCACACCATAAGTTTGGCAAGTT 59.931 43.478 0.00 0.99 39.42 2.66
1567 1582 3.709141 ACCATAAGTTTGGCAAGTTTGGT 59.291 39.130 13.25 13.25 40.68 3.67
1573 1588 3.119137 AGTTTGGCAAGTTTGGTCAAGTC 60.119 43.478 0.00 0.00 0.00 3.01
1641 1656 4.630923 TGTGAGCAATAAGCCCCACATATT 60.631 41.667 8.24 0.00 45.90 1.28
1779 1796 4.145052 CCCAAGAGGCACTTAGTCTTTTT 58.855 43.478 0.00 0.00 41.55 1.94
1851 1868 9.790389 GTACTGACAGTACTATCAATATATGGC 57.210 37.037 30.26 5.90 45.70 4.40
2234 2251 7.052142 AGTGGGAGTGCTACTAATATGTAAC 57.948 40.000 0.00 0.00 0.00 2.50
2235 2252 5.919141 GTGGGAGTGCTACTAATATGTAACG 59.081 44.000 0.00 0.00 0.00 3.18
2237 2254 6.772233 TGGGAGTGCTACTAATATGTAACGTA 59.228 38.462 0.00 0.00 0.00 3.57
2238 2255 7.285172 TGGGAGTGCTACTAATATGTAACGTAA 59.715 37.037 0.00 0.00 0.00 3.18
2239 2256 8.302438 GGGAGTGCTACTAATATGTAACGTAAT 58.698 37.037 0.00 0.00 0.00 1.89
2241 2258 9.339492 GAGTGCTACTAATATGTAACGTAATCC 57.661 37.037 0.00 0.00 0.00 3.01
2242 2259 8.019669 AGTGCTACTAATATGTAACGTAATCCG 58.980 37.037 0.00 0.00 44.03 4.18
2297 2325 2.161855 TCTCTACGCTTGGGAACGTAA 58.838 47.619 0.00 0.00 43.48 3.18
2362 2390 9.868277 AAGTGATGTAAAAGATTTTGTTGTTCA 57.132 25.926 0.82 0.00 0.00 3.18
2363 2391 9.868277 AGTGATGTAAAAGATTTTGTTGTTCAA 57.132 25.926 0.82 0.00 0.00 2.69
2367 2395 9.868277 ATGTAAAAGATTTTGTTGTTCAAGTGA 57.132 25.926 0.82 0.00 37.35 3.41
2368 2396 9.868277 TGTAAAAGATTTTGTTGTTCAAGTGAT 57.132 25.926 0.82 0.00 37.35 3.06
2370 2398 8.776376 AAAAGATTTTGTTGTTCAAGTGATGT 57.224 26.923 0.00 0.00 37.35 3.06
2371 2399 9.868277 AAAAGATTTTGTTGTTCAAGTGATGTA 57.132 25.926 0.00 0.00 37.35 2.29
2372 2400 9.868277 AAAGATTTTGTTGTTCAAGTGATGTAA 57.132 25.926 0.00 0.00 37.35 2.41
2373 2401 9.868277 AAGATTTTGTTGTTCAAGTGATGTAAA 57.132 25.926 0.00 0.00 37.35 2.01
2374 2402 9.868277 AGATTTTGTTGTTCAAGTGATGTAAAA 57.132 25.926 0.00 0.00 37.35 1.52
2402 2430 9.778741 ATCATTGAAGAAAAGTAGAGTTACACA 57.221 29.630 0.00 0.00 31.96 3.72
2516 2544 1.638388 GCTGCTGCTAACATGCACGA 61.638 55.000 8.53 0.00 38.12 4.35
2517 2545 0.095935 CTGCTGCTAACATGCACGAC 59.904 55.000 0.00 0.00 38.12 4.34
2626 2654 2.091222 AGTAGGAAGGCCCGACTTCTAT 60.091 50.000 10.08 2.63 46.93 1.98
2635 2663 3.002348 GGCCCGACTTCTATGAATTTTCG 59.998 47.826 0.00 0.00 0.00 3.46
2820 2848 3.740631 TGTTTGGCATGCATGTGTAAA 57.259 38.095 26.79 20.48 0.00 2.01
2863 2891 5.163152 CCAAAGTATTCTCCATCCCTAGCTT 60.163 44.000 0.00 0.00 0.00 3.74
2925 2953 2.557924 CTCCTGCTGCAATTTTACACCA 59.442 45.455 3.02 0.00 0.00 4.17
2966 2994 9.627123 TTAGCTATATTTTGCTGACCAGTAAAT 57.373 29.630 12.68 12.83 41.41 1.40
3082 3110 3.820467 TGCATTGACCACTGGTTTTCTAG 59.180 43.478 1.13 0.00 35.25 2.43
3296 3324 1.893137 TCACAGCAGACTAACGTGGAT 59.107 47.619 0.00 0.00 0.00 3.41
3306 3334 4.159693 AGACTAACGTGGATGCATCAGTTA 59.840 41.667 27.25 26.37 0.00 2.24
3457 3485 2.512885 CGCACAAAGATCTGCATCAAC 58.487 47.619 0.00 0.00 32.57 3.18
3486 3514 4.528987 ACTGACTCTAGAGGAGGGAAAAAC 59.471 45.833 23.50 3.16 45.83 2.43
3493 3521 4.968971 AGAGGAGGGAAAAACGTCTAAA 57.031 40.909 0.00 0.00 0.00 1.85
3508 3536 7.417496 AACGTCTAAATCTTGTACTGGAAAC 57.583 36.000 0.00 0.00 0.00 2.78
3526 3554 6.942976 TGGAAACAGAGGAATAGTCGTATTT 58.057 36.000 0.00 0.00 35.01 1.40
3575 3619 4.202090 ACGTTCTTTTCGTGTTACTCCTCT 60.202 41.667 0.00 0.00 40.07 3.69
3576 3620 4.148348 CGTTCTTTTCGTGTTACTCCTCTG 59.852 45.833 0.00 0.00 0.00 3.35
3588 3657 7.595502 CGTGTTACTCCTCTGATCCATATTAAC 59.404 40.741 0.00 0.00 0.00 2.01
3675 3748 5.050644 TGTAGTGGTACATACACTTGTCG 57.949 43.478 8.31 0.00 46.38 4.35
3676 3749 4.520111 TGTAGTGGTACATACACTTGTCGT 59.480 41.667 8.31 0.00 46.38 4.34
3677 3750 4.170292 AGTGGTACATACACTTGTCGTC 57.830 45.455 0.00 0.00 46.38 4.20
3706 3779 3.199727 TCGACCTTGAATTGGATCATGGA 59.800 43.478 14.05 0.00 43.74 3.41
3735 3808 6.627243 AGCACAAATATAGTGACACGTCTTA 58.373 36.000 11.29 0.00 39.30 2.10
3741 3814 9.741168 CAAATATAGTGACACGTCTTAAACAAG 57.259 33.333 0.00 0.00 0.00 3.16
3883 3956 3.998913 TGATTAGAGTGGGCAACATCA 57.001 42.857 0.00 0.00 39.74 3.07
3884 3957 4.508551 TGATTAGAGTGGGCAACATCAT 57.491 40.909 0.00 0.00 39.74 2.45
3885 3958 4.858850 TGATTAGAGTGGGCAACATCATT 58.141 39.130 0.00 0.00 39.74 2.57
3886 3959 5.263599 TGATTAGAGTGGGCAACATCATTT 58.736 37.500 0.00 0.00 39.74 2.32
3887 3960 5.125900 TGATTAGAGTGGGCAACATCATTTG 59.874 40.000 0.00 0.00 39.74 2.32
4020 4105 4.462483 GCATTAGAGGACCCAAATGTTTCA 59.538 41.667 10.91 0.00 32.99 2.69
4040 4125 0.104934 CCCCTGCTAGGACCCATAGT 60.105 60.000 4.00 0.00 37.67 2.12
4076 4161 5.957771 TGATAGCTTGGAGAGTGGTAAAT 57.042 39.130 0.00 0.00 0.00 1.40
4126 4211 2.231235 GTGCGTTCCTTTCATCCCAAAT 59.769 45.455 0.00 0.00 0.00 2.32
4127 4212 2.491693 TGCGTTCCTTTCATCCCAAATC 59.508 45.455 0.00 0.00 0.00 2.17
4254 4369 3.131046 GCCCAACCTGAAGTATCCAAATG 59.869 47.826 0.00 0.00 0.00 2.32
4297 4412 3.244561 TGACCATCTCCCAAACTCTCAAC 60.245 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.886505 TGCCGTTTGTGAGGTATCTTTTT 59.113 39.130 0.00 0.00 0.00 1.94
12 13 3.482436 TGCCGTTTGTGAGGTATCTTTT 58.518 40.909 0.00 0.00 0.00 2.27
13 14 3.134574 TGCCGTTTGTGAGGTATCTTT 57.865 42.857 0.00 0.00 0.00 2.52
14 15 2.812011 GTTGCCGTTTGTGAGGTATCTT 59.188 45.455 0.00 0.00 0.00 2.40
15 16 2.224426 TGTTGCCGTTTGTGAGGTATCT 60.224 45.455 0.00 0.00 0.00 1.98
16 17 2.147958 TGTTGCCGTTTGTGAGGTATC 58.852 47.619 0.00 0.00 0.00 2.24
17 18 2.151202 CTGTTGCCGTTTGTGAGGTAT 58.849 47.619 0.00 0.00 0.00 2.73
18 19 1.588674 CTGTTGCCGTTTGTGAGGTA 58.411 50.000 0.00 0.00 0.00 3.08
19 20 1.724582 GCTGTTGCCGTTTGTGAGGT 61.725 55.000 0.00 0.00 0.00 3.85
20 21 1.008538 GCTGTTGCCGTTTGTGAGG 60.009 57.895 0.00 0.00 0.00 3.86
21 22 0.317269 CAGCTGTTGCCGTTTGTGAG 60.317 55.000 5.25 0.00 40.80 3.51
22 23 1.726865 CAGCTGTTGCCGTTTGTGA 59.273 52.632 5.25 0.00 40.80 3.58
23 24 4.307258 CAGCTGTTGCCGTTTGTG 57.693 55.556 5.25 0.00 40.80 3.33
32 33 1.657594 CTCGATACACTGCAGCTGTTG 59.342 52.381 21.50 12.56 0.00 3.33
33 34 1.546029 TCTCGATACACTGCAGCTGTT 59.454 47.619 21.50 12.55 0.00 3.16
34 35 1.135257 GTCTCGATACACTGCAGCTGT 60.135 52.381 15.27 18.68 0.00 4.40
35 36 1.135286 TGTCTCGATACACTGCAGCTG 60.135 52.381 15.27 10.11 0.00 4.24
36 37 1.177401 TGTCTCGATACACTGCAGCT 58.823 50.000 15.27 0.98 0.00 4.24
37 38 1.996292 TTGTCTCGATACACTGCAGC 58.004 50.000 15.27 0.00 0.00 5.25
38 39 4.672409 TGTATTGTCTCGATACACTGCAG 58.328 43.478 13.48 13.48 36.24 4.41
39 40 4.712122 TGTATTGTCTCGATACACTGCA 57.288 40.909 2.71 5.63 36.24 4.41
40 41 4.862574 TGTTGTATTGTCTCGATACACTGC 59.137 41.667 2.71 3.00 39.55 4.40
41 42 6.944557 TTGTTGTATTGTCTCGATACACTG 57.055 37.500 2.71 0.00 39.55 3.66
42 43 8.683615 TCTATTGTTGTATTGTCTCGATACACT 58.316 33.333 2.71 1.06 39.55 3.55
43 44 8.744011 GTCTATTGTTGTATTGTCTCGATACAC 58.256 37.037 2.71 0.00 39.55 2.90
44 45 8.463607 TGTCTATTGTTGTATTGTCTCGATACA 58.536 33.333 0.00 0.00 38.50 2.29
45 46 8.851960 TGTCTATTGTTGTATTGTCTCGATAC 57.148 34.615 0.00 0.00 32.83 2.24
46 47 9.863845 TTTGTCTATTGTTGTATTGTCTCGATA 57.136 29.630 0.00 0.00 0.00 2.92
47 48 8.771920 TTTGTCTATTGTTGTATTGTCTCGAT 57.228 30.769 0.00 0.00 0.00 3.59
48 49 8.596271 TTTTGTCTATTGTTGTATTGTCTCGA 57.404 30.769 0.00 0.00 0.00 4.04
49 50 8.708742 TCTTTTGTCTATTGTTGTATTGTCTCG 58.291 33.333 0.00 0.00 0.00 4.04
52 53 9.612620 CCTTCTTTTGTCTATTGTTGTATTGTC 57.387 33.333 0.00 0.00 0.00 3.18
53 54 9.349713 TCCTTCTTTTGTCTATTGTTGTATTGT 57.650 29.630 0.00 0.00 0.00 2.71
80 81 5.052481 GCTGCATTTCCTTTCTGTCTTTTT 58.948 37.500 0.00 0.00 0.00 1.94
81 82 4.502087 GGCTGCATTTCCTTTCTGTCTTTT 60.502 41.667 0.50 0.00 0.00 2.27
82 83 3.006217 GGCTGCATTTCCTTTCTGTCTTT 59.994 43.478 0.50 0.00 0.00 2.52
83 84 2.560105 GGCTGCATTTCCTTTCTGTCTT 59.440 45.455 0.50 0.00 0.00 3.01
84 85 2.165998 GGCTGCATTTCCTTTCTGTCT 58.834 47.619 0.50 0.00 0.00 3.41
85 86 1.203287 GGGCTGCATTTCCTTTCTGTC 59.797 52.381 0.50 0.00 0.00 3.51
86 87 1.260544 GGGCTGCATTTCCTTTCTGT 58.739 50.000 0.50 0.00 0.00 3.41
87 88 1.259609 TGGGCTGCATTTCCTTTCTG 58.740 50.000 0.50 0.00 0.00 3.02
88 89 1.829222 CATGGGCTGCATTTCCTTTCT 59.171 47.619 0.50 0.00 0.00 2.52
89 90 2.304751 CATGGGCTGCATTTCCTTTC 57.695 50.000 0.50 0.00 0.00 2.62
105 106 1.138883 GCTCATGTGTGCCAGCATG 59.861 57.895 0.00 3.53 42.62 4.06
106 107 0.253894 TAGCTCATGTGTGCCAGCAT 59.746 50.000 0.00 0.00 35.33 3.79
107 108 0.392060 CTAGCTCATGTGTGCCAGCA 60.392 55.000 0.00 0.00 35.33 4.41
108 109 1.712977 GCTAGCTCATGTGTGCCAGC 61.713 60.000 7.70 10.64 40.63 4.85
109 110 1.094073 GGCTAGCTCATGTGTGCCAG 61.094 60.000 15.72 9.87 40.04 4.85
110 111 1.078214 GGCTAGCTCATGTGTGCCA 60.078 57.895 15.72 1.66 40.04 4.92
111 112 1.821332 GGGCTAGCTCATGTGTGCC 60.821 63.158 15.72 15.25 39.61 5.01
112 113 1.078214 TGGGCTAGCTCATGTGTGC 60.078 57.895 14.93 0.00 35.00 4.57
113 114 1.086067 CGTGGGCTAGCTCATGTGTG 61.086 60.000 26.01 8.69 0.00 3.82
114 115 1.219124 CGTGGGCTAGCTCATGTGT 59.781 57.895 26.01 0.00 0.00 3.72
115 116 2.176273 GCGTGGGCTAGCTCATGTG 61.176 63.158 32.17 20.83 35.92 3.21
116 117 2.187946 GCGTGGGCTAGCTCATGT 59.812 61.111 32.17 0.00 35.92 3.21
160 161 2.644707 GCGATTTGTAGCGTGCGC 60.645 61.111 8.67 8.67 42.33 6.09
161 162 2.021380 GGCGATTTGTAGCGTGCG 59.979 61.111 0.00 0.00 35.17 5.34
162 163 1.060937 CTGGCGATTTGTAGCGTGC 59.939 57.895 0.00 0.00 35.17 5.34
163 164 1.019278 ACCTGGCGATTTGTAGCGTG 61.019 55.000 0.00 0.00 35.17 5.34
164 165 0.739813 GACCTGGCGATTTGTAGCGT 60.740 55.000 0.00 0.00 35.17 5.07
165 166 1.752501 CGACCTGGCGATTTGTAGCG 61.753 60.000 4.82 0.00 35.98 4.26
166 167 0.739813 ACGACCTGGCGATTTGTAGC 60.740 55.000 15.53 0.00 34.83 3.58
167 168 2.190981 GTACGACCTGGCGATTTGTAG 58.809 52.381 15.53 0.00 34.83 2.74
168 169 1.545136 TGTACGACCTGGCGATTTGTA 59.455 47.619 15.53 0.00 34.83 2.41
169 170 0.319083 TGTACGACCTGGCGATTTGT 59.681 50.000 15.53 0.00 34.83 2.83
170 171 1.434555 TTGTACGACCTGGCGATTTG 58.565 50.000 15.53 0.00 34.83 2.32
171 172 2.277084 GATTGTACGACCTGGCGATTT 58.723 47.619 15.53 0.00 34.83 2.17
172 173 1.206132 TGATTGTACGACCTGGCGATT 59.794 47.619 15.53 0.00 34.83 3.34
173 174 0.821517 TGATTGTACGACCTGGCGAT 59.178 50.000 15.53 1.05 34.83 4.58
174 175 0.604073 TTGATTGTACGACCTGGCGA 59.396 50.000 15.53 0.00 34.83 5.54
175 176 1.127951 GTTTGATTGTACGACCTGGCG 59.872 52.381 8.60 8.60 37.29 5.69
176 177 1.127951 CGTTTGATTGTACGACCTGGC 59.872 52.381 0.00 0.00 40.03 4.85
177 178 1.127951 GCGTTTGATTGTACGACCTGG 59.872 52.381 0.00 0.00 40.03 4.45
178 179 1.201769 CGCGTTTGATTGTACGACCTG 60.202 52.381 0.00 0.00 40.03 4.00
179 180 1.065358 CGCGTTTGATTGTACGACCT 58.935 50.000 0.00 0.00 40.03 3.85
180 181 1.062258 TCGCGTTTGATTGTACGACC 58.938 50.000 5.77 0.00 40.03 4.79
181 182 2.097299 TGTTCGCGTTTGATTGTACGAC 60.097 45.455 5.77 0.00 40.03 4.34
182 183 2.125685 TGTTCGCGTTTGATTGTACGA 58.874 42.857 5.77 0.00 40.03 3.43
183 184 2.563670 TGTTCGCGTTTGATTGTACG 57.436 45.000 5.77 0.00 40.55 3.67
184 185 4.027556 CGATTTGTTCGCGTTTGATTGTAC 59.972 41.667 5.77 0.00 41.69 2.90
185 186 4.145276 CGATTTGTTCGCGTTTGATTGTA 58.855 39.130 5.77 0.00 41.69 2.41
186 187 2.970609 CGATTTGTTCGCGTTTGATTGT 59.029 40.909 5.77 0.00 41.69 2.71
187 188 3.583798 CGATTTGTTCGCGTTTGATTG 57.416 42.857 5.77 0.00 41.69 2.67
198 199 5.006165 GGACTGATGATCTGACGATTTGTTC 59.994 44.000 6.32 0.00 0.00 3.18
199 200 4.872691 GGACTGATGATCTGACGATTTGTT 59.127 41.667 6.32 0.00 0.00 2.83
200 201 4.081476 TGGACTGATGATCTGACGATTTGT 60.081 41.667 6.32 0.00 0.00 2.83
201 202 4.269603 GTGGACTGATGATCTGACGATTTG 59.730 45.833 6.32 0.00 0.00 2.32
202 203 4.437239 GTGGACTGATGATCTGACGATTT 58.563 43.478 6.32 0.00 0.00 2.17
203 204 3.489908 CGTGGACTGATGATCTGACGATT 60.490 47.826 6.32 0.00 0.00 3.34
204 205 2.033927 CGTGGACTGATGATCTGACGAT 59.966 50.000 6.32 0.00 0.00 3.73
205 206 1.401905 CGTGGACTGATGATCTGACGA 59.598 52.381 6.32 0.00 0.00 4.20
206 207 1.401905 TCGTGGACTGATGATCTGACG 59.598 52.381 6.32 6.10 0.00 4.35
207 208 3.510388 TTCGTGGACTGATGATCTGAC 57.490 47.619 6.32 0.00 0.00 3.51
208 209 4.743057 AATTCGTGGACTGATGATCTGA 57.257 40.909 6.32 0.00 0.00 3.27
209 210 5.808042 AAAATTCGTGGACTGATGATCTG 57.192 39.130 0.00 0.00 0.00 2.90
210 211 7.824289 TCTTTAAAATTCGTGGACTGATGATCT 59.176 33.333 0.00 0.00 0.00 2.75
211 212 7.905493 GTCTTTAAAATTCGTGGACTGATGATC 59.095 37.037 0.00 0.00 0.00 2.92
212 213 7.148239 GGTCTTTAAAATTCGTGGACTGATGAT 60.148 37.037 0.00 0.00 0.00 2.45
213 214 6.148811 GGTCTTTAAAATTCGTGGACTGATGA 59.851 38.462 0.00 0.00 0.00 2.92
214 215 6.072728 TGGTCTTTAAAATTCGTGGACTGATG 60.073 38.462 0.00 0.00 0.00 3.07
215 216 6.001460 TGGTCTTTAAAATTCGTGGACTGAT 58.999 36.000 0.00 0.00 0.00 2.90
216 217 5.369833 TGGTCTTTAAAATTCGTGGACTGA 58.630 37.500 0.00 0.00 0.00 3.41
217 218 5.682943 TGGTCTTTAAAATTCGTGGACTG 57.317 39.130 0.00 0.00 0.00 3.51
218 219 6.938030 TGTATGGTCTTTAAAATTCGTGGACT 59.062 34.615 0.00 0.00 0.00 3.85
219 220 7.136289 TGTATGGTCTTTAAAATTCGTGGAC 57.864 36.000 0.00 0.00 0.00 4.02
220 221 7.747155 TTGTATGGTCTTTAAAATTCGTGGA 57.253 32.000 0.00 0.00 0.00 4.02
221 222 8.804688 TTTTGTATGGTCTTTAAAATTCGTGG 57.195 30.769 0.00 0.00 0.00 4.94
223 224 9.634163 GGATTTTGTATGGTCTTTAAAATTCGT 57.366 29.630 0.00 0.00 32.79 3.85
224 225 9.632807 TGGATTTTGTATGGTCTTTAAAATTCG 57.367 29.630 0.00 0.00 31.80 3.34
227 228 9.418045 CGTTGGATTTTGTATGGTCTTTAAAAT 57.582 29.630 0.00 0.00 34.65 1.82
228 229 8.630917 TCGTTGGATTTTGTATGGTCTTTAAAA 58.369 29.630 0.00 0.00 0.00 1.52
229 230 8.167605 TCGTTGGATTTTGTATGGTCTTTAAA 57.832 30.769 0.00 0.00 0.00 1.52
230 231 7.747155 TCGTTGGATTTTGTATGGTCTTTAA 57.253 32.000 0.00 0.00 0.00 1.52
231 232 7.608376 TCATCGTTGGATTTTGTATGGTCTTTA 59.392 33.333 0.00 0.00 0.00 1.85
232 233 6.432783 TCATCGTTGGATTTTGTATGGTCTTT 59.567 34.615 0.00 0.00 0.00 2.52
233 234 5.943416 TCATCGTTGGATTTTGTATGGTCTT 59.057 36.000 0.00 0.00 0.00 3.01
234 235 5.496556 TCATCGTTGGATTTTGTATGGTCT 58.503 37.500 0.00 0.00 0.00 3.85
235 236 5.220854 CCTCATCGTTGGATTTTGTATGGTC 60.221 44.000 0.00 0.00 0.00 4.02
236 237 4.640201 CCTCATCGTTGGATTTTGTATGGT 59.360 41.667 0.00 0.00 0.00 3.55
237 238 4.498009 GCCTCATCGTTGGATTTTGTATGG 60.498 45.833 0.00 0.00 0.00 2.74
238 239 4.096231 TGCCTCATCGTTGGATTTTGTATG 59.904 41.667 0.00 0.00 0.00 2.39
239 240 4.096382 GTGCCTCATCGTTGGATTTTGTAT 59.904 41.667 0.00 0.00 0.00 2.29
240 241 3.438781 GTGCCTCATCGTTGGATTTTGTA 59.561 43.478 0.00 0.00 0.00 2.41
241 242 2.228822 GTGCCTCATCGTTGGATTTTGT 59.771 45.455 0.00 0.00 0.00 2.83
242 243 2.228582 TGTGCCTCATCGTTGGATTTTG 59.771 45.455 0.00 0.00 0.00 2.44
243 244 2.513753 TGTGCCTCATCGTTGGATTTT 58.486 42.857 0.00 0.00 0.00 1.82
244 245 2.198827 TGTGCCTCATCGTTGGATTT 57.801 45.000 0.00 0.00 0.00 2.17
245 246 2.292267 GATGTGCCTCATCGTTGGATT 58.708 47.619 3.80 0.00 42.57 3.01
246 247 1.959042 GATGTGCCTCATCGTTGGAT 58.041 50.000 3.80 0.00 42.57 3.41
247 248 3.458872 GATGTGCCTCATCGTTGGA 57.541 52.632 3.80 0.00 42.57 3.53
253 254 3.059325 GCTATTTCACGATGTGCCTCATC 60.059 47.826 8.38 8.38 46.68 2.92
254 255 2.874701 GCTATTTCACGATGTGCCTCAT 59.125 45.455 0.00 0.00 39.77 2.90
255 256 2.279741 GCTATTTCACGATGTGCCTCA 58.720 47.619 0.00 0.00 32.98 3.86
256 257 2.279741 TGCTATTTCACGATGTGCCTC 58.720 47.619 0.00 0.00 32.98 4.70
257 258 2.401583 TGCTATTTCACGATGTGCCT 57.598 45.000 0.00 0.00 32.98 4.75
258 259 3.485947 TTTGCTATTTCACGATGTGCC 57.514 42.857 0.00 0.00 32.98 5.01
259 260 4.037690 GGATTTGCTATTTCACGATGTGC 58.962 43.478 0.00 0.00 32.98 4.57
260 261 4.033932 TCGGATTTGCTATTTCACGATGTG 59.966 41.667 0.00 0.00 34.45 3.21
261 262 4.188462 TCGGATTTGCTATTTCACGATGT 58.812 39.130 0.00 0.00 0.00 3.06
262 263 4.794248 TCGGATTTGCTATTTCACGATG 57.206 40.909 0.00 0.00 0.00 3.84
263 264 5.584649 TCTTTCGGATTTGCTATTTCACGAT 59.415 36.000 0.00 0.00 0.00 3.73
264 265 4.932799 TCTTTCGGATTTGCTATTTCACGA 59.067 37.500 0.00 0.00 0.00 4.35
265 266 5.216566 TCTTTCGGATTTGCTATTTCACG 57.783 39.130 0.00 0.00 0.00 4.35
266 267 7.867445 TTTTCTTTCGGATTTGCTATTTCAC 57.133 32.000 0.00 0.00 0.00 3.18
269 270 9.586435 CCTATTTTTCTTTCGGATTTGCTATTT 57.414 29.630 0.00 0.00 0.00 1.40
270 271 7.706607 GCCTATTTTTCTTTCGGATTTGCTATT 59.293 33.333 0.00 0.00 0.00 1.73
271 272 7.068716 AGCCTATTTTTCTTTCGGATTTGCTAT 59.931 33.333 0.00 0.00 0.00 2.97
272 273 6.377146 AGCCTATTTTTCTTTCGGATTTGCTA 59.623 34.615 0.00 0.00 0.00 3.49
273 274 5.185828 AGCCTATTTTTCTTTCGGATTTGCT 59.814 36.000 0.00 0.00 0.00 3.91
274 275 5.289434 CAGCCTATTTTTCTTTCGGATTTGC 59.711 40.000 0.00 0.00 0.00 3.68
275 276 5.807011 CCAGCCTATTTTTCTTTCGGATTTG 59.193 40.000 0.00 0.00 0.00 2.32
276 277 5.624509 GCCAGCCTATTTTTCTTTCGGATTT 60.625 40.000 0.00 0.00 0.00 2.17
277 278 4.142160 GCCAGCCTATTTTTCTTTCGGATT 60.142 41.667 0.00 0.00 0.00 3.01
278 279 3.381590 GCCAGCCTATTTTTCTTTCGGAT 59.618 43.478 0.00 0.00 0.00 4.18
279 280 2.752903 GCCAGCCTATTTTTCTTTCGGA 59.247 45.455 0.00 0.00 0.00 4.55
280 281 2.159240 GGCCAGCCTATTTTTCTTTCGG 60.159 50.000 0.00 0.00 0.00 4.30
281 282 2.477863 CGGCCAGCCTATTTTTCTTTCG 60.478 50.000 2.24 0.00 0.00 3.46
282 283 2.159240 CCGGCCAGCCTATTTTTCTTTC 60.159 50.000 2.24 0.00 0.00 2.62
422 423 2.202892 GAGGAGTTTAGGGCGCCG 60.203 66.667 22.54 0.00 0.00 6.46
423 424 1.144276 GAGAGGAGTTTAGGGCGCC 59.856 63.158 21.18 21.18 0.00 6.53
424 425 0.103390 GAGAGAGGAGTTTAGGGCGC 59.897 60.000 0.00 0.00 0.00 6.53
425 426 0.382515 CGAGAGAGGAGTTTAGGGCG 59.617 60.000 0.00 0.00 0.00 6.13
426 427 1.476477 ACGAGAGAGGAGTTTAGGGC 58.524 55.000 0.00 0.00 0.00 5.19
427 428 3.358118 AGAACGAGAGAGGAGTTTAGGG 58.642 50.000 0.00 0.00 0.00 3.53
431 432 2.630580 AGCAAGAACGAGAGAGGAGTTT 59.369 45.455 0.00 0.00 0.00 2.66
537 538 1.199615 TTGGCACGAGATGGGTATGA 58.800 50.000 0.00 0.00 0.00 2.15
638 639 1.458588 GAGGACCTCCCCAGCCTAG 60.459 68.421 10.74 0.00 36.42 3.02
700 701 2.088674 AAACACGCGCTCCTCTCTGT 62.089 55.000 5.73 0.00 0.00 3.41
753 754 5.221925 ACCTAGCAACCTGATCAAAGAGAAA 60.222 40.000 0.00 0.00 0.00 2.52
797 798 2.863740 GGAAAGCCAACGAAAAACAAGG 59.136 45.455 0.00 0.00 0.00 3.61
965 968 5.700402 AATGCACTTACAGAGTCCCTAAT 57.300 39.130 0.00 0.00 36.10 1.73
992 995 4.469657 AGTACAAGAAGACATGGCCAAAA 58.530 39.130 10.96 0.00 0.00 2.44
1154 1157 0.250684 TTGCGAGGACTGCCAATTCA 60.251 50.000 0.00 0.00 36.29 2.57
1475 1490 9.571810 GCATAACAAGTGATTGTTAATTGATGA 57.428 29.630 15.26 0.00 46.54 2.92
1476 1491 9.577110 AGCATAACAAGTGATTGTTAATTGATG 57.423 29.630 15.26 11.43 46.54 3.07
1499 1514 5.592282 TCCAACACACTTGAGATAAAAAGCA 59.408 36.000 0.00 0.00 0.00 3.91
1507 1522 3.389329 ACAGTCTCCAACACACTTGAGAT 59.611 43.478 0.00 0.00 0.00 2.75
1514 1529 2.365582 ACCAAACAGTCTCCAACACAC 58.634 47.619 0.00 0.00 0.00 3.82
1521 1536 2.615747 GGCTAGGAACCAAACAGTCTCC 60.616 54.545 0.00 0.00 0.00 3.71
1548 1563 5.128663 ACTTGACCAAACTTGCCAAACTTAT 59.871 36.000 0.00 0.00 0.00 1.73
1555 1570 2.023673 CTGACTTGACCAAACTTGCCA 58.976 47.619 0.00 0.00 0.00 4.92
1556 1571 1.338020 CCTGACTTGACCAAACTTGCC 59.662 52.381 0.00 0.00 0.00 4.52
1557 1572 2.024414 ACCTGACTTGACCAAACTTGC 58.976 47.619 0.00 0.00 0.00 4.01
1558 1573 2.358898 CCACCTGACTTGACCAAACTTG 59.641 50.000 0.00 0.00 0.00 3.16
1559 1574 2.654863 CCACCTGACTTGACCAAACTT 58.345 47.619 0.00 0.00 0.00 2.66
1560 1575 1.133792 CCCACCTGACTTGACCAAACT 60.134 52.381 0.00 0.00 0.00 2.66
1561 1576 1.318576 CCCACCTGACTTGACCAAAC 58.681 55.000 0.00 0.00 0.00 2.93
1562 1577 0.923358 ACCCACCTGACTTGACCAAA 59.077 50.000 0.00 0.00 0.00 3.28
1563 1578 0.182537 CACCCACCTGACTTGACCAA 59.817 55.000 0.00 0.00 0.00 3.67
1567 1582 1.409521 CCAAACACCCACCTGACTTGA 60.410 52.381 0.00 0.00 0.00 3.02
1573 1588 2.752903 GCTATAACCAAACACCCACCTG 59.247 50.000 0.00 0.00 0.00 4.00
1641 1656 7.793927 TCTTGTGACATTTTGTGTGTGTATA 57.206 32.000 0.00 0.00 42.36 1.47
1660 1675 2.621668 GGCTTGCCTTAGGGAATCTTGT 60.622 50.000 5.50 0.00 31.43 3.16
1716 1731 5.984926 CCACATTATTTTTGTCACACTTGCT 59.015 36.000 0.00 0.00 0.00 3.91
1851 1868 8.955061 AAGTTCAACTTCAAATCATCATTACG 57.045 30.769 0.00 0.00 31.77 3.18
2092 2109 6.258947 GTGCCAACTGAAGGATCTCTATTTAC 59.741 42.308 0.00 0.00 0.00 2.01
2235 2252 4.388378 AAGAAGCTAGTCCACGGATTAC 57.612 45.455 0.00 0.00 0.00 1.89
2237 2254 3.983044 AAAGAAGCTAGTCCACGGATT 57.017 42.857 0.00 0.00 0.00 3.01
2238 2255 4.279145 TCTAAAGAAGCTAGTCCACGGAT 58.721 43.478 0.00 0.00 0.00 4.18
2239 2256 3.693807 TCTAAAGAAGCTAGTCCACGGA 58.306 45.455 0.00 0.00 0.00 4.69
2241 2258 5.227908 TGTTTCTAAAGAAGCTAGTCCACG 58.772 41.667 7.87 0.00 36.42 4.94
2242 2259 7.492352 TTTGTTTCTAAAGAAGCTAGTCCAC 57.508 36.000 7.87 0.00 36.42 4.02
2297 2325 9.585099 AAATGACATCATGCATTTTTATTACGT 57.415 25.926 11.87 0.00 40.68 3.57
2402 2430 4.402056 AGTACACTATTTATGCACGCCT 57.598 40.909 0.00 0.00 0.00 5.52
2516 2544 5.217978 TGTTGGTTAGAAATAGACCGTGT 57.782 39.130 0.00 0.00 36.22 4.49
2517 2545 7.548075 ACTTATGTTGGTTAGAAATAGACCGTG 59.452 37.037 0.00 0.00 36.22 4.94
2635 2663 5.163663 TCCAAGCGGAAATGACATATTTGTC 60.164 40.000 9.14 9.14 44.79 3.18
2820 2848 4.574674 TGGCAGAAGTAGTGATGGAAAT 57.425 40.909 0.00 0.00 0.00 2.17
2863 2891 8.195436 GGCTAACACATATAGTTGTAGTGAGAA 58.805 37.037 0.00 0.00 34.47 2.87
2958 2986 4.202050 GCACCTGGCAAGAATATTTACTGG 60.202 45.833 0.00 0.00 43.97 4.00
3082 3110 2.814336 CAAAGAGGGCAAGTAGTGTTCC 59.186 50.000 0.00 0.00 0.00 3.62
3149 3177 1.464997 GCTTGTGTTTCCAGATCGGTC 59.535 52.381 0.00 0.00 35.57 4.79
3193 3221 2.101575 CCACATGATGCTGCGCAC 59.898 61.111 5.66 4.25 43.04 5.34
3296 3324 4.507756 GCGATGACTACAATAACTGATGCA 59.492 41.667 0.00 0.00 0.00 3.96
3306 3334 0.459899 TGAGGCGCGATGACTACAAT 59.540 50.000 12.10 0.00 34.35 2.71
3457 3485 3.628487 CCTCCTCTAGAGTCAGTTTACCG 59.372 52.174 18.42 0.00 41.47 4.02
3486 3514 6.866770 TCTGTTTCCAGTACAAGATTTAGACG 59.133 38.462 0.00 0.00 39.82 4.18
3493 3521 5.825593 TTCCTCTGTTTCCAGTACAAGAT 57.174 39.130 0.00 0.00 39.82 2.40
3540 3584 4.438145 CGAAAAGAACGTCTCCGATATCAG 59.562 45.833 3.12 0.00 37.88 2.90
3575 3619 8.255111 AGATCAGTGACAGTTAATATGGATCA 57.745 34.615 0.00 0.00 32.10 2.92
3614 3683 5.900437 AGTTTACTCCCTCCGATCCATATA 58.100 41.667 0.00 0.00 0.00 0.86
3675 3748 4.142816 CCAATTCAAGGTCGAGATTGTGAC 60.143 45.833 8.85 0.00 0.00 3.67
3676 3749 4.002982 CCAATTCAAGGTCGAGATTGTGA 58.997 43.478 8.85 1.77 0.00 3.58
3677 3750 4.002982 TCCAATTCAAGGTCGAGATTGTG 58.997 43.478 8.85 2.02 0.00 3.33
3706 3779 6.816640 ACGTGTCACTATATTTGTGCTTATGT 59.183 34.615 0.65 3.04 35.58 2.29
3735 3808 8.519526 TCCATATATTTTTCGCACTTCTTGTTT 58.480 29.630 0.00 0.00 0.00 2.83
3741 3814 5.050363 TCGCTCCATATATTTTTCGCACTTC 60.050 40.000 0.00 0.00 0.00 3.01
3799 3872 0.329261 TCACAAATGAGAGGCCAGGG 59.671 55.000 5.01 0.00 0.00 4.45
3807 3880 7.549134 GGTCAGTACATGTAATCACAAATGAGA 59.451 37.037 9.54 0.00 38.57 3.27
3968 4044 3.566742 ACGGCTTGTATTTTCTTTTCGGT 59.433 39.130 0.00 0.00 0.00 4.69
4020 4105 0.104934 CTATGGGTCCTAGCAGGGGT 60.105 60.000 2.86 0.00 35.59 4.95
4126 4211 3.242903 TGCTCGTTTCGAAAGCAATTTGA 60.243 39.130 18.21 5.16 34.95 2.69
4127 4212 3.042189 TGCTCGTTTCGAAAGCAATTTG 58.958 40.909 18.21 4.21 34.95 2.32
4254 4369 3.080319 AGAGCTTGGCTTCAACTCATTC 58.920 45.455 0.00 0.00 39.88 2.67
4297 4412 1.006102 AAGAGACCGTTGAGCACCG 60.006 57.895 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.