Multiple sequence alignment - TraesCS3B01G423700

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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 TraesCS3B01G423700 chr3B 100.000 5565 0 0 1 5565 661201161 661206725 0.000000e+00 10277.0
1 TraesCS3B01G423700 chr3B 100.000 161 0 0 6016 6176 661207176 661207336 1.300000e-76 298.0
2 TraesCS3B01G423700 chr3D 94.992 4812 169 28 794 5543 499989725 499994526 0.000000e+00 7485.0
3 TraesCS3B01G423700 chr3D 98.125 160 2 1 6017 6176 530153514 530153672 1.700000e-70 278.0
4 TraesCS3B01G423700 chr3D 78.981 314 42 19 385 681 499989105 499989411 6.320000e-45 193.0
5 TraesCS3B01G423700 chr3D 92.000 50 4 0 694 743 507534148 507534197 3.090000e-08 71.3
6 TraesCS3B01G423700 chr3D 100.000 31 0 0 5535 5565 455723470 455723500 2.400000e-04 58.4
7 TraesCS3B01G423700 chr3A 96.386 3403 80 11 2150 5538 639485061 639488434 0.000000e+00 5563.0
8 TraesCS3B01G423700 chr3A 90.555 1747 83 23 266 1972 639483360 639485064 0.000000e+00 2237.0
9 TraesCS3B01G423700 chr3A 96.000 200 8 0 1 200 639483156 639483355 5.970000e-85 326.0
10 TraesCS3B01G423700 chr5D 98.125 160 3 0 6017 6176 553947490 553947649 4.710000e-71 279.0
11 TraesCS3B01G423700 chr1D 98.125 160 3 0 6017 6176 457799520 457799361 4.710000e-71 279.0
12 TraesCS3B01G423700 chr2D 98.125 160 2 1 6017 6176 545763084 545763242 1.700000e-70 278.0
13 TraesCS3B01G423700 chr2D 100.000 32 0 0 175 206 320284887 320284856 6.690000e-05 60.2
14 TraesCS3B01G423700 chr2D 90.909 44 4 0 5522 5565 331604416 331604459 6.690000e-05 60.2
15 TraesCS3B01G423700 chr2D 97.059 34 1 0 5532 5565 63540731 63540764 2.400000e-04 58.4
16 TraesCS3B01G423700 chr2D 96.970 33 1 0 5533 5565 616017777 616017809 8.650000e-04 56.5
17 TraesCS3B01G423700 chr2D 92.105 38 3 0 5528 5565 2758295 2758332 3.000000e-03 54.7
18 TraesCS3B01G423700 chr2D 94.444 36 1 1 5530 5565 636790707 636790741 3.000000e-03 54.7
19 TraesCS3B01G423700 chr6D 97.531 162 2 1 6017 6176 11797428 11797589 6.100000e-70 276.0
20 TraesCS3B01G423700 chr6D 97.500 160 4 0 6017 6176 457147377 457147536 2.190000e-69 274.0
21 TraesCS3B01G423700 chr6D 96.914 162 3 1 6017 6176 11792419 11792580 2.840000e-68 270.0
22 TraesCS3B01G423700 chr6D 100.000 31 0 0 5535 5565 196359248 196359278 2.400000e-04 58.4
23 TraesCS3B01G423700 chr1B 98.101 158 2 1 6017 6174 434359571 434359727 2.190000e-69 274.0
24 TraesCS3B01G423700 chr7D 96.914 162 3 2 6017 6176 256254324 256254485 2.840000e-68 270.0
25 TraesCS3B01G423700 chr7A 95.652 46 2 0 698 743 651990042 651989997 2.390000e-09 75.0
26 TraesCS3B01G423700 chr5B 97.436 39 1 0 5527 5565 581144373 581144411 4.000000e-07 67.6
27 TraesCS3B01G423700 chr2B 93.478 46 2 1 697 742 735930848 735930804 4.000000e-07 67.6
28 TraesCS3B01G423700 chr4A 95.122 41 2 0 702 742 474726360 474726400 1.440000e-06 65.8
29 TraesCS3B01G423700 chr6A 95.000 40 0 2 175 213 455937819 455937781 1.860000e-05 62.1
30 TraesCS3B01G423700 chr6B 100.000 32 0 0 5534 5565 155175003 155174972 6.690000e-05 60.2
31 TraesCS3B01G423700 chr6B 94.444 36 2 0 179 214 149484489 149484524 8.650000e-04 56.5
32 TraesCS3B01G423700 chr2A 100.000 31 0 0 175 205 733514139 733514169 2.400000e-04 58.4


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 TraesCS3B01G423700 chr3B 661201161 661207336 6175 False 5287.500000 10277 100.000000 1 6176 2 chr3B.!!$F1 6175
1 TraesCS3B01G423700 chr3D 499989105 499994526 5421 False 3839.000000 7485 86.986500 385 5543 2 chr3D.!!$F4 5158
2 TraesCS3B01G423700 chr3A 639483156 639488434 5278 False 2708.666667 5563 94.313667 1 5538 3 chr3A.!!$F1 5537

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
975 1300 0.032813 AACGAAGGTAGGATCCGGGA 60.033 55.000 5.98 0.0 0.00 5.14 F
1357 1703 0.040204 CCTGGTTCCCCATTTGCTCT 59.960 55.000 0.00 0.0 40.90 4.09 F
1388 1735 0.321298 GCCTGGCTGAAACCGAAGTA 60.321 55.000 12.43 0.0 0.00 2.24 F
1986 2353 1.002142 GGTTCAGTTTGCCGTTGGTAC 60.002 52.381 0.00 0.0 0.00 3.34 F
2757 3124 1.165270 AGTTTATGACTGCAACCGCC 58.835 50.000 0.00 0.0 37.17 6.13 F
4098 4477 1.882623 GGTTACTCTTTTGCAGCAGCT 59.117 47.619 1.76 0.0 42.74 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2948 3315 1.238439 AGCCCTTCGTTCAATGTGTG 58.762 50.000 0.00 0.00 0.00 3.82 R
3097 3464 2.290367 TGCAACATGCTGTACAGTCAAC 59.710 45.455 23.44 7.92 45.31 3.18 R
3223 3590 4.442332 CGTGTAATATTACCAGGCTGACCA 60.442 45.833 17.94 0.00 33.59 4.02 R
3271 3638 5.355910 GTCACGGCCCTTATAATTCTTCAAA 59.644 40.000 0.00 0.00 0.00 2.69 R
4145 4524 3.011818 CCAGTTGCAGACATATGCTTGA 58.988 45.455 1.58 0.00 46.63 3.02 R
6017 6405 0.031043 TGCAGTGTACAACGTACGCT 59.969 50.000 16.72 13.20 38.66 5.07 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
65 66 5.705441 TGGAGACTGTCGAATATTTGCTTTT 59.295 36.000 1.52 0.00 0.00 2.27
66 67 6.024049 GGAGACTGTCGAATATTTGCTTTTG 58.976 40.000 1.52 0.00 0.00 2.44
91 92 2.350522 CGGCACTGCTGTAGATTTTCT 58.649 47.619 1.21 0.00 0.00 2.52
156 157 5.335583 GCACATCACAGGCAAACATAACTTA 60.336 40.000 0.00 0.00 0.00 2.24
188 189 4.684703 CCGTCCCACAAACGATCTTATATC 59.315 45.833 0.00 0.00 42.62 1.63
200 201 2.511659 TCTTATATCGTGGGACGGAGG 58.488 52.381 0.00 0.00 42.81 4.30
201 202 1.544691 CTTATATCGTGGGACGGAGGG 59.455 57.143 0.00 0.00 42.81 4.30
202 203 0.773014 TATATCGTGGGACGGAGGGA 59.227 55.000 0.00 0.00 42.81 4.20
203 204 0.539901 ATATCGTGGGACGGAGGGAG 60.540 60.000 0.00 0.00 42.81 4.30
204 205 1.929860 TATCGTGGGACGGAGGGAGT 61.930 60.000 0.00 0.00 42.81 3.85
205 206 1.929860 ATCGTGGGACGGAGGGAGTA 61.930 60.000 0.00 0.00 42.81 2.59
206 207 1.679977 CGTGGGACGGAGGGAGTAA 60.680 63.158 0.00 0.00 38.08 2.24
207 208 1.664321 CGTGGGACGGAGGGAGTAAG 61.664 65.000 0.00 0.00 38.08 2.34
208 209 0.614134 GTGGGACGGAGGGAGTAAGT 60.614 60.000 0.00 0.00 0.00 2.24
209 210 0.115745 TGGGACGGAGGGAGTAAGTT 59.884 55.000 0.00 0.00 0.00 2.66
210 211 1.273759 GGGACGGAGGGAGTAAGTTT 58.726 55.000 0.00 0.00 0.00 2.66
211 212 1.206610 GGGACGGAGGGAGTAAGTTTC 59.793 57.143 0.00 0.00 0.00 2.78
212 213 1.897802 GGACGGAGGGAGTAAGTTTCA 59.102 52.381 0.00 0.00 0.00 2.69
213 214 2.094130 GGACGGAGGGAGTAAGTTTCAG 60.094 54.545 0.00 0.00 0.00 3.02
214 215 1.900486 ACGGAGGGAGTAAGTTTCAGG 59.100 52.381 0.00 0.00 0.00 3.86
215 216 1.900486 CGGAGGGAGTAAGTTTCAGGT 59.100 52.381 0.00 0.00 0.00 4.00
216 217 2.302157 CGGAGGGAGTAAGTTTCAGGTT 59.698 50.000 0.00 0.00 0.00 3.50
217 218 3.676093 GGAGGGAGTAAGTTTCAGGTTG 58.324 50.000 0.00 0.00 0.00 3.77
218 219 3.559384 GGAGGGAGTAAGTTTCAGGTTGG 60.559 52.174 0.00 0.00 0.00 3.77
219 220 3.053826 AGGGAGTAAGTTTCAGGTTGGT 58.946 45.455 0.00 0.00 0.00 3.67
220 221 3.072622 AGGGAGTAAGTTTCAGGTTGGTC 59.927 47.826 0.00 0.00 0.00 4.02
221 222 3.181448 GGGAGTAAGTTTCAGGTTGGTCA 60.181 47.826 0.00 0.00 0.00 4.02
222 223 4.065789 GGAGTAAGTTTCAGGTTGGTCAG 58.934 47.826 0.00 0.00 0.00 3.51
223 224 4.202326 GGAGTAAGTTTCAGGTTGGTCAGA 60.202 45.833 0.00 0.00 0.00 3.27
224 225 4.704965 AGTAAGTTTCAGGTTGGTCAGAC 58.295 43.478 0.00 0.00 0.00 3.51
225 226 3.644966 AAGTTTCAGGTTGGTCAGACA 57.355 42.857 2.17 0.00 0.00 3.41
226 227 3.199880 AGTTTCAGGTTGGTCAGACAG 57.800 47.619 2.17 0.00 0.00 3.51
227 228 2.158755 AGTTTCAGGTTGGTCAGACAGG 60.159 50.000 2.17 0.00 0.00 4.00
228 229 1.507140 TTCAGGTTGGTCAGACAGGT 58.493 50.000 2.17 0.00 0.00 4.00
229 230 1.507140 TCAGGTTGGTCAGACAGGTT 58.493 50.000 2.17 0.00 0.00 3.50
230 231 1.843851 TCAGGTTGGTCAGACAGGTTT 59.156 47.619 2.17 0.00 0.00 3.27
231 232 2.158813 TCAGGTTGGTCAGACAGGTTTC 60.159 50.000 2.17 0.00 0.00 2.78
232 233 2.127708 AGGTTGGTCAGACAGGTTTCT 58.872 47.619 2.17 0.00 0.00 2.52
233 234 2.509964 AGGTTGGTCAGACAGGTTTCTT 59.490 45.455 2.17 0.00 0.00 2.52
234 235 2.879026 GGTTGGTCAGACAGGTTTCTTC 59.121 50.000 2.17 0.00 0.00 2.87
235 236 3.433740 GGTTGGTCAGACAGGTTTCTTCT 60.434 47.826 2.17 0.00 0.00 2.85
236 237 4.200092 GTTGGTCAGACAGGTTTCTTCTT 58.800 43.478 2.17 0.00 0.00 2.52
237 238 4.073293 TGGTCAGACAGGTTTCTTCTTC 57.927 45.455 2.17 0.00 0.00 2.87
238 239 3.711704 TGGTCAGACAGGTTTCTTCTTCT 59.288 43.478 2.17 0.00 0.00 2.85
239 240 4.202264 TGGTCAGACAGGTTTCTTCTTCTC 60.202 45.833 2.17 0.00 0.00 2.87
240 241 4.311606 GTCAGACAGGTTTCTTCTTCTCC 58.688 47.826 0.00 0.00 0.00 3.71
241 242 3.325135 TCAGACAGGTTTCTTCTTCTCCC 59.675 47.826 0.00 0.00 0.00 4.30
242 243 2.640332 AGACAGGTTTCTTCTTCTCCCC 59.360 50.000 0.00 0.00 0.00 4.81
243 244 1.705745 ACAGGTTTCTTCTTCTCCCCC 59.294 52.381 0.00 0.00 0.00 5.40
261 262 4.436998 CGAGGGCGCGGAGAAAGT 62.437 66.667 8.83 0.00 0.00 2.66
262 263 2.047179 GAGGGCGCGGAGAAAGTT 60.047 61.111 8.83 0.00 0.00 2.66
263 264 1.217244 GAGGGCGCGGAGAAAGTTA 59.783 57.895 8.83 0.00 0.00 2.24
264 265 1.079336 AGGGCGCGGAGAAAGTTAC 60.079 57.895 8.83 0.00 0.00 2.50
333 334 6.983307 GTCAGTAGACTTTGATGCAGTATGAT 59.017 38.462 0.00 0.00 41.64 2.45
334 335 8.138074 GTCAGTAGACTTTGATGCAGTATGATA 58.862 37.037 0.00 0.00 41.64 2.15
335 336 8.355913 TCAGTAGACTTTGATGCAGTATGATAG 58.644 37.037 0.00 0.00 39.69 2.08
359 360 8.095937 AGTACAAACCAAAACTAATCTAGCAC 57.904 34.615 0.00 0.00 0.00 4.40
375 376 1.822990 AGCACCTGCAAAGATGAATGG 59.177 47.619 0.00 0.00 45.16 3.16
418 419 1.722464 CCAGTTTGCATCACAATTGCG 59.278 47.619 5.05 0.00 43.10 4.85
473 474 4.496336 GCCTCCGGCCAATCTGCT 62.496 66.667 2.24 0.00 44.06 4.24
482 483 1.324740 GCCAATCTGCTGGGCATCAA 61.325 55.000 0.00 0.00 46.92 2.57
512 513 3.504906 CCATTTGACTCTGTTGTGATGCT 59.495 43.478 0.00 0.00 0.00 3.79
513 514 4.022589 CCATTTGACTCTGTTGTGATGCTT 60.023 41.667 0.00 0.00 0.00 3.91
634 682 2.018542 TATGTAAGGCGTCCACAAGC 57.981 50.000 0.00 0.00 0.00 4.01
641 689 1.166531 GGCGTCCACAAGCTTCAAGT 61.167 55.000 0.00 0.00 0.00 3.16
664 712 2.157834 ACGCATTGACCGACAACTAA 57.842 45.000 0.00 0.00 41.52 2.24
665 713 2.695359 ACGCATTGACCGACAACTAAT 58.305 42.857 0.00 0.00 41.52 1.73
667 715 2.030457 CGCATTGACCGACAACTAATCC 59.970 50.000 0.00 0.00 41.52 3.01
668 716 2.030457 GCATTGACCGACAACTAATCCG 59.970 50.000 0.00 0.00 41.52 4.18
683 731 9.583765 ACAACTAATCCGAGATTTTTACTACTC 57.416 33.333 4.76 0.00 0.00 2.59
685 733 8.302515 ACTAATCCGAGATTTTTACTACTCCA 57.697 34.615 4.76 0.00 0.00 3.86
706 754 6.533730 TCCATCTGTCTCAAAATGTTAGTGT 58.466 36.000 0.00 0.00 0.00 3.55
707 755 6.650807 TCCATCTGTCTCAAAATGTTAGTGTC 59.349 38.462 0.00 0.00 0.00 3.67
708 756 6.427853 CCATCTGTCTCAAAATGTTAGTGTCA 59.572 38.462 0.00 0.00 0.00 3.58
758 813 7.505923 AGAGGGAGTAAAAACAATTTTGCTACT 59.494 33.333 12.14 9.85 46.96 2.57
759 814 8.700439 AGGGAGTAAAAACAATTTTGCTACTA 57.300 30.769 12.14 0.00 46.96 1.82
760 815 8.573885 AGGGAGTAAAAACAATTTTGCTACTAC 58.426 33.333 12.14 6.04 46.96 2.73
885 1190 4.462280 CCCGGTTGGCGTACTCCC 62.462 72.222 0.00 0.00 0.00 4.30
935 1248 0.985490 ATCCTTCAGGGTCAGAGGCC 60.985 60.000 0.00 0.00 36.25 5.19
975 1300 0.032813 AACGAAGGTAGGATCCGGGA 60.033 55.000 5.98 0.00 0.00 5.14
977 1302 0.178998 CGAAGGTAGGATCCGGGAGA 60.179 60.000 5.98 0.00 0.00 3.71
1323 1669 4.388080 GCACGCGCATTCAGCACA 62.388 61.111 5.73 0.00 46.13 4.57
1341 1687 0.464870 CACATGCTCCTCTCCTCCTG 59.535 60.000 0.00 0.00 0.00 3.86
1354 1700 0.972471 CCTCCTGGTTCCCCATTTGC 60.972 60.000 0.00 0.00 40.90 3.68
1357 1703 0.040204 CCTGGTTCCCCATTTGCTCT 59.960 55.000 0.00 0.00 40.90 4.09
1359 1705 2.648059 CTGGTTCCCCATTTGCTCTAG 58.352 52.381 0.00 0.00 40.90 2.43
1361 1708 2.290896 TGGTTCCCCATTTGCTCTAGTG 60.291 50.000 0.00 0.00 35.17 2.74
1386 1733 2.680913 CGCCTGGCTGAAACCGAAG 61.681 63.158 17.92 0.00 0.00 3.79
1387 1734 1.600916 GCCTGGCTGAAACCGAAGT 60.601 57.895 12.43 0.00 0.00 3.01
1388 1735 0.321298 GCCTGGCTGAAACCGAAGTA 60.321 55.000 12.43 0.00 0.00 2.24
1389 1736 1.726853 CCTGGCTGAAACCGAAGTAG 58.273 55.000 0.00 0.00 0.00 2.57
1390 1737 1.275291 CCTGGCTGAAACCGAAGTAGA 59.725 52.381 0.00 0.00 0.00 2.59
1391 1738 2.289444 CCTGGCTGAAACCGAAGTAGAA 60.289 50.000 0.00 0.00 0.00 2.10
1392 1739 3.600388 CTGGCTGAAACCGAAGTAGAAT 58.400 45.455 0.00 0.00 0.00 2.40
1393 1740 4.003648 CTGGCTGAAACCGAAGTAGAATT 58.996 43.478 0.00 0.00 0.00 2.17
1394 1741 4.394729 TGGCTGAAACCGAAGTAGAATTT 58.605 39.130 0.00 0.00 0.00 1.82
1396 1743 4.379499 GGCTGAAACCGAAGTAGAATTTGG 60.379 45.833 0.00 0.00 39.35 3.28
1397 1744 4.379499 GCTGAAACCGAAGTAGAATTTGGG 60.379 45.833 1.32 0.00 37.96 4.12
1398 1745 4.076394 TGAAACCGAAGTAGAATTTGGGG 58.924 43.478 1.32 0.00 37.96 4.96
1484 1844 6.061022 TGATTTAGGTGAGGTGCTTGATTA 57.939 37.500 0.00 0.00 0.00 1.75
1517 1877 3.449746 TTGGAGTGAACTAATTGGGGG 57.550 47.619 0.00 0.00 0.00 5.40
1519 1879 2.307686 TGGAGTGAACTAATTGGGGGAC 59.692 50.000 0.00 0.00 0.00 4.46
1525 1885 3.053693 TGAACTAATTGGGGGACAGATGG 60.054 47.826 0.00 0.00 0.00 3.51
1529 1895 5.173246 ACTAATTGGGGGACAGATGGATAT 58.827 41.667 0.00 0.00 0.00 1.63
1577 1943 1.142870 TGAAAGTGGCCTTAGTGTGCT 59.857 47.619 3.32 0.00 0.00 4.40
1711 2077 2.906389 TGCAGACCAGATTGTTAGAGGT 59.094 45.455 0.00 0.00 34.76 3.85
1717 2083 6.091718 GACCAGATTGTTAGAGGTCCTATC 57.908 45.833 0.00 0.00 42.21 2.08
1789 2155 2.084546 GGGTATGGTTTCAGTCAGCAC 58.915 52.381 0.00 0.00 0.00 4.40
1792 2158 3.437049 GGTATGGTTTCAGTCAGCACTTC 59.563 47.826 0.00 0.00 0.00 3.01
1814 2180 6.556974 TCAGAATTGATGATCCTTCTGTCT 57.443 37.500 23.00 4.44 43.17 3.41
1986 2353 1.002142 GGTTCAGTTTGCCGTTGGTAC 60.002 52.381 0.00 0.00 0.00 3.34
2014 2381 6.262273 GGTACCAAGTGTTTGATTCTTCTTCA 59.738 38.462 7.15 0.00 36.36 3.02
2049 2416 9.944376 TCTAAACTTGTTAGAGCAACATAGAAT 57.056 29.630 0.00 0.00 46.38 2.40
2098 2465 6.487103 GCACAAAGCAAGTCTATATAACACC 58.513 40.000 0.00 0.00 44.79 4.16
2322 2689 4.752146 TCTGATCATGCATATCGATGACC 58.248 43.478 8.54 0.00 34.73 4.02
2375 2742 3.118905 ACTGAAGAAGTGAGGCAAGAC 57.881 47.619 0.00 0.00 37.88 3.01
2475 2842 1.416813 CGCTGCAGAAGTAAGCTCGG 61.417 60.000 20.43 0.00 34.72 4.63
2734 3101 5.491070 CAAGTTAGAACACCATGAGGATGA 58.509 41.667 0.00 0.00 38.69 2.92
2757 3124 1.165270 AGTTTATGACTGCAACCGCC 58.835 50.000 0.00 0.00 37.17 6.13
2847 3214 3.422796 TGGTAGGCAGTAGCTAGCTATC 58.577 50.000 26.59 18.99 41.70 2.08
3049 3416 5.432885 TCCTTAAAAGCAAAAGGTTCTCG 57.567 39.130 1.34 0.00 42.47 4.04
3223 3590 4.503910 TCATGCACAGCTTTCGTATAAGT 58.496 39.130 0.00 0.00 0.00 2.24
3271 3638 6.525578 TTATTGAGTTGTACAGACGAGGAT 57.474 37.500 0.00 0.00 0.00 3.24
3366 3733 5.289510 AGGGGACTGGTATAAACTTCTGAT 58.710 41.667 0.00 0.00 41.13 2.90
3615 3982 5.994250 AGATTCTTATGTGGTGCTGTGTAT 58.006 37.500 0.00 0.00 0.00 2.29
4098 4477 1.882623 GGTTACTCTTTTGCAGCAGCT 59.117 47.619 1.76 0.00 42.74 4.24
4120 4499 5.523916 GCTGAGGTATGTGTAGTGGTTTATG 59.476 44.000 0.00 0.00 0.00 1.90
4145 4524 3.103742 TCCCCTTTTGTTCTTGCAACTT 58.896 40.909 0.00 0.00 0.00 2.66
4193 4572 4.093998 CACTGCATTAGAACTTACTGGCTG 59.906 45.833 0.00 0.00 0.00 4.85
4277 4656 5.013599 TGCTAGAGATAGTCTATGGAGAGCA 59.986 44.000 0.00 4.84 37.16 4.26
4280 4659 5.891198 AGAGATAGTCTATGGAGAGCATGT 58.109 41.667 0.00 0.00 31.71 3.21
4441 4820 3.997021 CGATGAACTATAAGGGCCATGAC 59.003 47.826 6.18 0.00 0.00 3.06
4467 4854 4.202141 TGTCCTTCTCTGCAAATTGGTTTG 60.202 41.667 0.00 0.00 45.92 2.93
4791 5178 4.394729 CTTTGAACAAGGCCCTGTACTTA 58.605 43.478 7.60 0.00 0.00 2.24
4854 5241 2.681848 AGGCAGCATCTCGAAGAAAATG 59.318 45.455 0.00 0.00 34.09 2.32
4905 5292 1.952296 AGAGTTACACAACGGTCGTCT 59.048 47.619 0.00 0.00 39.78 4.18
4987 5374 2.495270 AGAGCCACAGACACTGTATCAG 59.505 50.000 4.08 0.00 43.43 2.90
4996 5383 5.949952 ACAGACACTGTATCAGGTGTACATA 59.050 40.000 0.00 0.00 43.46 2.29
5097 5484 5.579511 GGTAATCTCGATGTTTTTCTCGGAA 59.420 40.000 0.00 0.00 35.64 4.30
5250 5638 5.520751 AGTCTAGAGGCTAACAACACCTAT 58.479 41.667 0.00 0.00 32.67 2.57
5260 5648 6.814146 GGCTAACAACACCTATATGAGCTATC 59.186 42.308 0.00 0.00 0.00 2.08
5261 5649 6.814146 GCTAACAACACCTATATGAGCTATCC 59.186 42.308 0.00 0.00 0.00 2.59
5550 5938 8.582437 TCTATACAAAATTACATACTCCCTCCG 58.418 37.037 0.00 0.00 0.00 4.63
5551 5939 5.431179 ACAAAATTACATACTCCCTCCGT 57.569 39.130 0.00 0.00 0.00 4.69
5552 5940 5.425630 ACAAAATTACATACTCCCTCCGTC 58.574 41.667 0.00 0.00 0.00 4.79
5553 5941 4.684484 AAATTACATACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
5554 5942 2.077687 TTACATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
5555 5943 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
5556 5944 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
5557 5945 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
5558 5946 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
5559 5947 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5560 5948 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
5561 5949 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
5562 5950 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
5563 5951 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
5564 5952 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
6033 6421 3.780925 GGAGCGTACGTTGTACACT 57.219 52.632 17.90 2.85 0.00 3.55
6034 6422 1.334054 GGAGCGTACGTTGTACACTG 58.666 55.000 17.90 0.00 0.00 3.66
6035 6423 0.706729 GAGCGTACGTTGTACACTGC 59.293 55.000 17.90 3.32 0.00 4.40
6036 6424 0.031043 AGCGTACGTTGTACACTGCA 59.969 50.000 17.90 0.00 0.00 4.41
6037 6425 1.065358 GCGTACGTTGTACACTGCAT 58.935 50.000 17.90 0.00 0.00 3.96
6038 6426 2.095110 AGCGTACGTTGTACACTGCATA 60.095 45.455 17.90 0.00 0.00 3.14
6039 6427 2.855963 GCGTACGTTGTACACTGCATAT 59.144 45.455 17.90 0.00 0.00 1.78
6040 6428 3.301579 GCGTACGTTGTACACTGCATATG 60.302 47.826 17.90 0.00 0.00 1.78
6041 6429 3.855379 CGTACGTTGTACACTGCATATGT 59.145 43.478 7.22 8.63 0.00 2.29
6042 6430 5.029654 CGTACGTTGTACACTGCATATGTA 58.970 41.667 7.22 6.83 0.00 2.29
6043 6431 5.684184 CGTACGTTGTACACTGCATATGTAT 59.316 40.000 7.22 1.84 35.11 2.29
6044 6432 6.852345 CGTACGTTGTACACTGCATATGTATA 59.148 38.462 7.22 8.43 35.11 1.47
6045 6433 7.059147 CGTACGTTGTACACTGCATATGTATAG 59.941 40.741 7.22 3.69 35.11 1.31
6046 6434 6.213677 ACGTTGTACACTGCATATGTATAGG 58.786 40.000 12.62 11.56 35.11 2.57
6047 6435 6.040054 ACGTTGTACACTGCATATGTATAGGA 59.960 38.462 12.62 0.00 35.11 2.94
6048 6436 6.362551 CGTTGTACACTGCATATGTATAGGAC 59.637 42.308 12.62 3.12 35.11 3.85
6049 6437 7.434492 GTTGTACACTGCATATGTATAGGACT 58.566 38.462 12.62 0.00 35.11 3.85
6050 6438 8.573885 GTTGTACACTGCATATGTATAGGACTA 58.426 37.037 12.62 0.00 35.11 2.59
6051 6439 8.336801 TGTACACTGCATATGTATAGGACTAG 57.663 38.462 12.62 0.00 35.11 2.57
6052 6440 6.842437 ACACTGCATATGTATAGGACTAGG 57.158 41.667 4.29 0.00 0.00 3.02
6053 6441 5.717178 ACACTGCATATGTATAGGACTAGGG 59.283 44.000 4.29 0.00 0.00 3.53
6054 6442 5.717178 CACTGCATATGTATAGGACTAGGGT 59.283 44.000 4.29 0.00 0.00 4.34
6055 6443 5.952947 ACTGCATATGTATAGGACTAGGGTC 59.047 44.000 4.29 0.00 41.43 4.46
6056 6444 6.153942 TGCATATGTATAGGACTAGGGTCT 57.846 41.667 4.29 0.00 41.82 3.85
6057 6445 5.952347 TGCATATGTATAGGACTAGGGTCTG 59.048 44.000 4.29 0.00 41.82 3.51
6058 6446 5.952947 GCATATGTATAGGACTAGGGTCTGT 59.047 44.000 4.29 0.00 41.82 3.41
6059 6447 7.117397 GCATATGTATAGGACTAGGGTCTGTA 58.883 42.308 4.29 0.00 41.82 2.74
6060 6448 7.780745 GCATATGTATAGGACTAGGGTCTGTAT 59.219 40.741 4.29 0.00 41.82 2.29
6061 6449 9.702253 CATATGTATAGGACTAGGGTCTGTATT 57.298 37.037 0.00 0.00 41.82 1.89
6068 6456 6.008960 AGGACTAGGGTCTGTATTTATACCG 58.991 44.000 0.00 0.00 41.82 4.02
6069 6457 5.772169 GGACTAGGGTCTGTATTTATACCGT 59.228 44.000 0.00 0.00 41.82 4.83
6070 6458 6.266330 GGACTAGGGTCTGTATTTATACCGTT 59.734 42.308 0.00 0.00 41.82 4.44
6071 6459 7.047460 ACTAGGGTCTGTATTTATACCGTTG 57.953 40.000 0.00 0.00 32.68 4.10
6072 6460 5.945144 AGGGTCTGTATTTATACCGTTGT 57.055 39.130 0.00 0.00 32.53 3.32
6073 6461 7.779798 ACTAGGGTCTGTATTTATACCGTTGTA 59.220 37.037 0.00 0.00 35.26 2.41
6074 6462 7.607615 AGGGTCTGTATTTATACCGTTGTAT 57.392 36.000 0.00 0.00 40.72 2.29
6075 6463 7.664758 AGGGTCTGTATTTATACCGTTGTATC 58.335 38.462 0.00 0.00 38.60 2.24
6076 6464 7.508296 AGGGTCTGTATTTATACCGTTGTATCT 59.492 37.037 0.00 0.00 38.60 1.98
6077 6465 7.811713 GGGTCTGTATTTATACCGTTGTATCTC 59.188 40.741 0.00 0.00 38.60 2.75
6078 6466 8.574737 GGTCTGTATTTATACCGTTGTATCTCT 58.425 37.037 0.00 0.00 38.60 3.10
6079 6467 9.609950 GTCTGTATTTATACCGTTGTATCTCTC 57.390 37.037 0.00 0.00 38.60 3.20
6080 6468 9.570468 TCTGTATTTATACCGTTGTATCTCTCT 57.430 33.333 0.00 0.00 38.60 3.10
6081 6469 9.828852 CTGTATTTATACCGTTGTATCTCTCTC 57.171 37.037 0.00 0.00 38.60 3.20
6082 6470 9.570468 TGTATTTATACCGTTGTATCTCTCTCT 57.430 33.333 0.00 0.00 38.60 3.10
6084 6472 7.507733 TTTATACCGTTGTATCTCTCTCTCC 57.492 40.000 0.00 0.00 38.60 3.71
6085 6473 2.657143 ACCGTTGTATCTCTCTCTCCC 58.343 52.381 0.00 0.00 0.00 4.30
6086 6474 1.957877 CCGTTGTATCTCTCTCTCCCC 59.042 57.143 0.00 0.00 0.00 4.81
6087 6475 1.957877 CGTTGTATCTCTCTCTCCCCC 59.042 57.143 0.00 0.00 0.00 5.40
6107 6495 5.001232 CCCCCGTATATTTGTACATCTTGG 58.999 45.833 0.00 0.00 0.00 3.61
6108 6496 5.001232 CCCCGTATATTTGTACATCTTGGG 58.999 45.833 0.00 2.38 0.00 4.12
6109 6497 5.221762 CCCCGTATATTTGTACATCTTGGGA 60.222 44.000 13.47 0.00 33.52 4.37
6110 6498 5.932303 CCCGTATATTTGTACATCTTGGGAG 59.068 44.000 0.00 0.00 33.52 4.30
6111 6499 6.239487 CCCGTATATTTGTACATCTTGGGAGA 60.239 42.308 0.00 0.00 33.52 3.71
6112 6500 6.645415 CCGTATATTTGTACATCTTGGGAGAC 59.355 42.308 0.00 0.00 33.99 3.36
6113 6501 7.207383 CGTATATTTGTACATCTTGGGAGACA 58.793 38.462 0.00 0.00 33.99 3.41
6114 6502 7.709182 CGTATATTTGTACATCTTGGGAGACAA 59.291 37.037 0.00 0.00 33.99 3.18
6123 6511 1.276622 TTGGGAGACAAGTAGAGGCC 58.723 55.000 0.00 0.00 33.18 5.19
6124 6512 0.970937 TGGGAGACAAGTAGAGGCCG 60.971 60.000 0.00 0.00 0.00 6.13
6125 6513 1.677637 GGGAGACAAGTAGAGGCCGG 61.678 65.000 0.00 0.00 0.00 6.13
6126 6514 0.971447 GGAGACAAGTAGAGGCCGGT 60.971 60.000 1.90 0.00 0.00 5.28
6127 6515 0.456628 GAGACAAGTAGAGGCCGGTC 59.543 60.000 0.00 0.00 0.00 4.79
6128 6516 0.971447 AGACAAGTAGAGGCCGGTCC 60.971 60.000 0.08 4.26 0.00 4.46
6129 6517 1.229082 ACAAGTAGAGGCCGGTCCA 60.229 57.895 15.92 0.00 37.29 4.02
6130 6518 1.218316 CAAGTAGAGGCCGGTCCAC 59.782 63.158 15.92 10.29 37.29 4.02
6131 6519 1.988406 AAGTAGAGGCCGGTCCACC 60.988 63.158 15.92 2.73 37.29 4.61
6132 6520 3.468140 GTAGAGGCCGGTCCACCC 61.468 72.222 15.92 2.35 37.29 4.61
6133 6521 3.680196 TAGAGGCCGGTCCACCCT 61.680 66.667 15.92 7.45 37.29 4.34
6134 6522 3.976490 TAGAGGCCGGTCCACCCTG 62.976 68.421 15.92 0.00 37.29 4.45
6136 6524 4.326227 AGGCCGGTCCACCCTGTA 62.326 66.667 15.92 0.00 37.29 2.74
6137 6525 4.091939 GGCCGGTCCACCCTGTAC 62.092 72.222 1.90 0.00 34.01 2.90
6138 6526 4.091939 GCCGGTCCACCCTGTACC 62.092 72.222 1.90 0.00 0.00 3.34
6139 6527 2.284405 CCGGTCCACCCTGTACCT 60.284 66.667 0.00 0.00 0.00 3.08
6140 6528 1.000739 CCGGTCCACCCTGTACCTA 59.999 63.158 0.00 0.00 0.00 3.08
6141 6529 0.398098 CCGGTCCACCCTGTACCTAT 60.398 60.000 0.00 0.00 0.00 2.57
6142 6530 1.038280 CGGTCCACCCTGTACCTATC 58.962 60.000 0.00 0.00 0.00 2.08
6143 6531 1.411216 CGGTCCACCCTGTACCTATCT 60.411 57.143 0.00 0.00 0.00 1.98
6144 6532 2.158564 CGGTCCACCCTGTACCTATCTA 60.159 54.545 0.00 0.00 0.00 1.98
6145 6533 3.499926 CGGTCCACCCTGTACCTATCTAT 60.500 52.174 0.00 0.00 0.00 1.98
6146 6534 3.833070 GGTCCACCCTGTACCTATCTATG 59.167 52.174 0.00 0.00 0.00 2.23
6147 6535 4.481072 GTCCACCCTGTACCTATCTATGT 58.519 47.826 0.00 0.00 0.00 2.29
6148 6536 4.281182 GTCCACCCTGTACCTATCTATGTG 59.719 50.000 0.00 0.00 0.00 3.21
6149 6537 3.006967 CCACCCTGTACCTATCTATGTGC 59.993 52.174 0.00 0.00 0.00 4.57
6150 6538 3.641436 CACCCTGTACCTATCTATGTGCA 59.359 47.826 0.00 0.00 0.00 4.57
6151 6539 3.641906 ACCCTGTACCTATCTATGTGCAC 59.358 47.826 10.75 10.75 0.00 4.57
6152 6540 3.006967 CCCTGTACCTATCTATGTGCACC 59.993 52.174 15.69 0.00 0.00 5.01
6153 6541 3.641436 CCTGTACCTATCTATGTGCACCA 59.359 47.826 15.69 2.61 0.00 4.17
6154 6542 4.284490 CCTGTACCTATCTATGTGCACCAT 59.716 45.833 15.69 10.45 37.58 3.55
6155 6543 5.213891 TGTACCTATCTATGTGCACCATG 57.786 43.478 15.69 4.01 34.86 3.66
6156 6544 3.131709 ACCTATCTATGTGCACCATGC 57.868 47.619 15.69 0.00 45.29 4.06
6165 6553 3.577229 GCACCATGCACACGATCA 58.423 55.556 0.00 0.00 44.26 2.92
6166 6554 1.875262 GCACCATGCACACGATCAA 59.125 52.632 0.00 0.00 44.26 2.57
6167 6555 0.452987 GCACCATGCACACGATCAAT 59.547 50.000 0.00 0.00 44.26 2.57
6168 6556 1.796253 GCACCATGCACACGATCAATG 60.796 52.381 0.00 0.00 44.26 2.82
6169 6557 1.738908 CACCATGCACACGATCAATGA 59.261 47.619 0.00 0.00 0.00 2.57
6170 6558 2.356695 CACCATGCACACGATCAATGAT 59.643 45.455 0.00 0.00 0.00 2.45
6171 6559 3.018856 ACCATGCACACGATCAATGATT 58.981 40.909 0.00 0.00 0.00 2.57
6172 6560 4.035441 CACCATGCACACGATCAATGATTA 59.965 41.667 0.00 0.00 0.00 1.75
6173 6561 4.823442 ACCATGCACACGATCAATGATTAT 59.177 37.500 0.00 0.00 0.00 1.28
6174 6562 5.049198 ACCATGCACACGATCAATGATTATC 60.049 40.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.355916 TCTCCATATATATACTTTGAGGGATCG 57.644 37.037 0.00 0.00 0.00 3.69
66 67 4.082523 TACAGCAGTGCCGGCTCC 62.083 66.667 29.70 18.26 40.23 4.70
72 73 3.604582 AGAGAAAATCTACAGCAGTGCC 58.395 45.455 12.58 0.00 36.10 5.01
156 157 0.042131 TTGTGGGACGGAGGGAGTAT 59.958 55.000 0.00 0.00 0.00 2.12
188 189 1.664321 CTTACTCCCTCCGTCCCACG 61.664 65.000 0.00 0.00 42.11 4.94
200 201 4.065789 CTGACCAACCTGAAACTTACTCC 58.934 47.826 0.00 0.00 0.00 3.85
201 202 4.750598 GTCTGACCAACCTGAAACTTACTC 59.249 45.833 0.00 0.00 0.00 2.59
202 203 4.163458 TGTCTGACCAACCTGAAACTTACT 59.837 41.667 5.17 0.00 0.00 2.24
203 204 4.448210 TGTCTGACCAACCTGAAACTTAC 58.552 43.478 5.17 0.00 0.00 2.34
204 205 4.444306 CCTGTCTGACCAACCTGAAACTTA 60.444 45.833 5.17 0.00 0.00 2.24
205 206 3.545703 CTGTCTGACCAACCTGAAACTT 58.454 45.455 5.17 0.00 0.00 2.66
206 207 2.158755 CCTGTCTGACCAACCTGAAACT 60.159 50.000 5.17 0.00 0.00 2.66
207 208 2.222027 CCTGTCTGACCAACCTGAAAC 58.778 52.381 5.17 0.00 0.00 2.78
208 209 1.843851 ACCTGTCTGACCAACCTGAAA 59.156 47.619 5.17 0.00 0.00 2.69
209 210 1.507140 ACCTGTCTGACCAACCTGAA 58.493 50.000 5.17 0.00 0.00 3.02
210 211 1.507140 AACCTGTCTGACCAACCTGA 58.493 50.000 5.17 0.00 0.00 3.86
211 212 2.158755 AGAAACCTGTCTGACCAACCTG 60.159 50.000 5.17 0.00 0.00 4.00
212 213 2.127708 AGAAACCTGTCTGACCAACCT 58.872 47.619 5.17 0.00 0.00 3.50
213 214 2.640316 AGAAACCTGTCTGACCAACC 57.360 50.000 5.17 0.00 0.00 3.77
214 215 3.809905 AGAAGAAACCTGTCTGACCAAC 58.190 45.455 5.17 0.00 0.00 3.77
215 216 4.164221 AGAAGAAGAAACCTGTCTGACCAA 59.836 41.667 5.17 0.00 0.00 3.67
216 217 3.711704 AGAAGAAGAAACCTGTCTGACCA 59.288 43.478 5.17 0.00 0.00 4.02
217 218 4.311606 GAGAAGAAGAAACCTGTCTGACC 58.688 47.826 5.17 0.00 0.00 4.02
218 219 4.311606 GGAGAAGAAGAAACCTGTCTGAC 58.688 47.826 0.00 0.00 0.00 3.51
219 220 3.325135 GGGAGAAGAAGAAACCTGTCTGA 59.675 47.826 0.00 0.00 0.00 3.27
220 221 3.558109 GGGGAGAAGAAGAAACCTGTCTG 60.558 52.174 0.00 0.00 0.00 3.51
221 222 2.640332 GGGGAGAAGAAGAAACCTGTCT 59.360 50.000 0.00 0.00 0.00 3.41
222 223 2.290387 GGGGGAGAAGAAGAAACCTGTC 60.290 54.545 0.00 0.00 0.00 3.51
223 224 1.705745 GGGGGAGAAGAAGAAACCTGT 59.294 52.381 0.00 0.00 0.00 4.00
224 225 2.498644 GGGGGAGAAGAAGAAACCTG 57.501 55.000 0.00 0.00 0.00 4.00
244 245 2.552585 TAACTTTCTCCGCGCCCTCG 62.553 60.000 0.00 0.00 39.07 4.63
245 246 1.082679 GTAACTTTCTCCGCGCCCTC 61.083 60.000 0.00 0.00 0.00 4.30
246 247 1.079336 GTAACTTTCTCCGCGCCCT 60.079 57.895 0.00 0.00 0.00 5.19
247 248 0.174162 TAGTAACTTTCTCCGCGCCC 59.826 55.000 0.00 0.00 0.00 6.13
248 249 1.135170 AGTAGTAACTTTCTCCGCGCC 60.135 52.381 0.00 0.00 29.00 6.53
249 250 2.274920 AGTAGTAACTTTCTCCGCGC 57.725 50.000 0.00 0.00 29.00 6.86
250 251 4.093998 TCAGTAGTAGTAACTTTCTCCGCG 59.906 45.833 0.00 0.00 37.15 6.46
251 252 5.557891 TCAGTAGTAGTAACTTTCTCCGC 57.442 43.478 0.00 0.00 37.15 5.54
252 253 7.556733 AGATCAGTAGTAGTAACTTTCTCCG 57.443 40.000 0.00 0.00 37.15 4.63
281 282 2.295909 CGCCACCCAAGAAATTCTTTCA 59.704 45.455 5.36 0.00 42.10 2.69
282 283 2.296190 ACGCCACCCAAGAAATTCTTTC 59.704 45.455 5.36 0.00 33.78 2.62
301 302 2.161012 TCAAAGTCTACTGACCGCTACG 59.839 50.000 0.00 0.00 43.91 3.51
310 311 8.140628 ACTATCATACTGCATCAAAGTCTACTG 58.859 37.037 0.00 0.00 0.00 2.74
333 334 9.211485 GTGCTAGATTAGTTTTGGTTTGTACTA 57.789 33.333 0.00 0.00 0.00 1.82
334 335 7.174426 GGTGCTAGATTAGTTTTGGTTTGTACT 59.826 37.037 0.00 0.00 0.00 2.73
335 336 7.174426 AGGTGCTAGATTAGTTTTGGTTTGTAC 59.826 37.037 0.00 0.00 0.00 2.90
359 360 3.508793 ACTGTTCCATTCATCTTTGCAGG 59.491 43.478 0.00 0.00 0.00 4.85
375 376 6.371548 TGGTTATGATTGCAACTCTACTGTTC 59.628 38.462 0.00 0.00 0.00 3.18
418 419 0.888285 AGCAGCAAGTGAGTTCCAGC 60.888 55.000 0.00 0.00 0.00 4.85
476 477 3.615496 GTCAAATGGAAGCACATTGATGC 59.385 43.478 2.66 0.00 46.50 3.91
482 483 3.759581 ACAGAGTCAAATGGAAGCACAT 58.240 40.909 0.00 0.00 0.00 3.21
575 623 8.463607 ACGGGGTGTTTAACAAATAATAATCAG 58.536 33.333 0.00 0.00 0.00 2.90
634 682 3.906008 CGGTCAATGCGTAAAACTTGAAG 59.094 43.478 0.00 0.00 30.06 3.02
641 689 2.873472 AGTTGTCGGTCAATGCGTAAAA 59.127 40.909 0.00 0.00 38.38 1.52
664 712 7.070074 ACAGATGGAGTAGTAAAAATCTCGGAT 59.930 37.037 0.00 0.00 0.00 4.18
665 713 6.380274 ACAGATGGAGTAGTAAAAATCTCGGA 59.620 38.462 0.00 0.00 0.00 4.55
667 715 7.484975 AGACAGATGGAGTAGTAAAAATCTCG 58.515 38.462 0.00 0.00 0.00 4.04
668 716 8.470805 TGAGACAGATGGAGTAGTAAAAATCTC 58.529 37.037 0.00 0.00 0.00 2.75
683 731 6.427853 TGACACTAACATTTTGAGACAGATGG 59.572 38.462 0.00 0.00 0.00 3.51
685 733 8.450578 TTTGACACTAACATTTTGAGACAGAT 57.549 30.769 0.00 0.00 0.00 2.90
714 762 8.414778 ACTCCCTCTATCTTAAAATGTAAGACG 58.585 37.037 0.00 0.00 36.51 4.18
731 779 7.833285 AGCAAAATTGTTTTTACTCCCTCTA 57.167 32.000 0.00 0.00 33.29 2.43
807 1111 5.129485 TGCTGATTTTGGGTAAGGTTCAAAA 59.871 36.000 0.00 0.00 42.22 2.44
935 1248 0.601046 TCTCGCTGCTTTGTGTCTGG 60.601 55.000 0.00 0.00 0.00 3.86
937 1250 1.953559 TTTCTCGCTGCTTTGTGTCT 58.046 45.000 0.00 0.00 0.00 3.41
975 1300 2.444895 GGGGTGGCGGATCTCTCT 60.445 66.667 0.00 0.00 0.00 3.10
977 1302 3.083997 GTGGGGTGGCGGATCTCT 61.084 66.667 0.00 0.00 0.00 3.10
1323 1669 0.690411 CCAGGAGGAGAGGAGCATGT 60.690 60.000 0.00 0.00 36.89 3.21
1354 1700 2.055042 AGGCGCAGGGTCACTAGAG 61.055 63.158 10.83 0.00 0.00 2.43
1357 1703 3.390521 CCAGGCGCAGGGTCACTA 61.391 66.667 10.83 0.00 0.00 2.74
1376 1723 4.076394 CCCCAAATTCTACTTCGGTTTCA 58.924 43.478 0.00 0.00 0.00 2.69
1380 1727 1.340697 GCCCCCAAATTCTACTTCGGT 60.341 52.381 0.00 0.00 0.00 4.69
1386 1733 0.255033 AGTCCGCCCCCAAATTCTAC 59.745 55.000 0.00 0.00 0.00 2.59
1387 1734 0.254747 CAGTCCGCCCCCAAATTCTA 59.745 55.000 0.00 0.00 0.00 2.10
1388 1735 1.000896 CAGTCCGCCCCCAAATTCT 60.001 57.895 0.00 0.00 0.00 2.40
1389 1736 1.001393 TCAGTCCGCCCCCAAATTC 60.001 57.895 0.00 0.00 0.00 2.17
1390 1737 1.000896 CTCAGTCCGCCCCCAAATT 60.001 57.895 0.00 0.00 0.00 1.82
1391 1738 1.497309 TTCTCAGTCCGCCCCCAAAT 61.497 55.000 0.00 0.00 0.00 2.32
1392 1739 1.710996 TTTCTCAGTCCGCCCCCAAA 61.711 55.000 0.00 0.00 0.00 3.28
1393 1740 1.497309 ATTTCTCAGTCCGCCCCCAA 61.497 55.000 0.00 0.00 0.00 4.12
1394 1741 1.497309 AATTTCTCAGTCCGCCCCCA 61.497 55.000 0.00 0.00 0.00 4.96
1396 1743 1.209747 ACTAATTTCTCAGTCCGCCCC 59.790 52.381 0.00 0.00 0.00 5.80
1397 1744 2.678336 CAACTAATTTCTCAGTCCGCCC 59.322 50.000 0.00 0.00 0.00 6.13
1398 1745 2.096013 GCAACTAATTTCTCAGTCCGCC 59.904 50.000 0.00 0.00 0.00 6.13
1467 1827 1.065126 GCCTAATCAAGCACCTCACCT 60.065 52.381 0.00 0.00 0.00 4.00
1484 1844 1.228988 CTCCAAAAAGGGCCTGCCT 60.229 57.895 6.92 0.00 38.24 4.75
1517 1877 4.511617 TCGAAGCTCATATCCATCTGTC 57.488 45.455 0.00 0.00 0.00 3.51
1519 1879 5.131594 TCTTCGAAGCTCATATCCATCTG 57.868 43.478 20.56 0.00 0.00 2.90
1525 1885 6.219473 TGAGGAAATCTTCGAAGCTCATATC 58.781 40.000 20.56 13.63 0.00 1.63
1529 1895 3.961480 TGAGGAAATCTTCGAAGCTCA 57.039 42.857 20.56 21.00 0.00 4.26
1577 1943 3.917988 TGCACACACAAAATGACACAAA 58.082 36.364 0.00 0.00 0.00 2.83
1711 2077 3.388024 CGAGTTCCCAAGGAATGATAGGA 59.612 47.826 0.00 0.00 44.04 2.94
1714 2080 3.380393 TCCGAGTTCCCAAGGAATGATA 58.620 45.455 0.00 0.00 44.04 2.15
1717 2083 2.014068 GCTCCGAGTTCCCAAGGAATG 61.014 57.143 0.00 0.00 44.04 2.67
1986 2353 4.398319 AGAATCAAACACTTGGTACCAGG 58.602 43.478 21.74 21.74 33.01 4.45
2014 2381 8.157476 TGCTCTAACAAGTTTAGAAAGAAGGAT 58.843 33.333 0.00 0.00 31.36 3.24
2375 2742 3.485463 TTAGTTGACCAGTGGGACTTG 57.515 47.619 15.21 0.00 38.05 3.16
2475 2842 8.744008 TGCATAATATAGCGAAGAAGAGTAAC 57.256 34.615 0.00 0.00 0.00 2.50
2734 3101 4.755123 GGCGGTTGCAGTCATAAACTATAT 59.245 41.667 0.00 0.00 45.35 0.86
2757 3124 3.181439 GGGAATGGAGGTGGAGGAAATAG 60.181 52.174 0.00 0.00 0.00 1.73
2847 3214 8.589335 AGTAACATTAAATAGTCGCATACAGG 57.411 34.615 0.00 0.00 0.00 4.00
2948 3315 1.238439 AGCCCTTCGTTCAATGTGTG 58.762 50.000 0.00 0.00 0.00 3.82
3049 3416 4.151867 CAGTACTTTGGTTTCGTAAGCTCC 59.848 45.833 5.57 0.00 32.98 4.70
3097 3464 2.290367 TGCAACATGCTGTACAGTCAAC 59.710 45.455 23.44 7.92 45.31 3.18
3223 3590 4.442332 CGTGTAATATTACCAGGCTGACCA 60.442 45.833 17.94 0.00 33.59 4.02
3271 3638 5.355910 GTCACGGCCCTTATAATTCTTCAAA 59.644 40.000 0.00 0.00 0.00 2.69
3366 3733 7.170658 AGCAAAAGTTTTGAGCGCATTATTAAA 59.829 29.630 28.36 0.00 0.00 1.52
4098 4477 6.614694 ACATAAACCACTACACATACCTCA 57.385 37.500 0.00 0.00 0.00 3.86
4120 4499 3.867857 TGCAAGAACAAAAGGGGAAAAC 58.132 40.909 0.00 0.00 0.00 2.43
4145 4524 3.011818 CCAGTTGCAGACATATGCTTGA 58.988 45.455 1.58 0.00 46.63 3.02
4173 4552 4.286297 ACAGCCAGTAAGTTCTAATGCA 57.714 40.909 0.00 0.00 0.00 3.96
4277 4656 9.757227 CTAGCTTTCTAGAACTTATTAGCACAT 57.243 33.333 20.95 8.10 43.95 3.21
4280 4659 7.782049 TGCTAGCTTTCTAGAACTTATTAGCA 58.218 34.615 20.95 20.88 43.95 3.49
4441 4820 3.057033 CCAATTTGCAGAGAAGGACAAGG 60.057 47.826 0.00 0.00 0.00 3.61
4574 4961 7.065683 GCCCATAATGGAAAACCTTGTAATTTG 59.934 37.037 0.00 0.00 40.96 2.32
4785 5172 1.192980 CGGCGTTTGTGGTGTAAGTAC 59.807 52.381 0.00 0.00 0.00 2.73
4791 5178 0.741915 AATTTCGGCGTTTGTGGTGT 59.258 45.000 6.85 0.00 0.00 4.16
4905 5292 5.346551 CACATTTCGTCCAATTGTAGTCGTA 59.653 40.000 4.43 0.00 29.28 3.43
4987 5374 7.142680 GCTAGTCTCTTTGATCTATGTACACC 58.857 42.308 0.00 0.00 0.00 4.16
4996 5383 5.207354 TGATCTGGCTAGTCTCTTTGATCT 58.793 41.667 0.00 0.00 32.74 2.75
5097 5484 7.176589 AGATCTTGAAATACTTCTCCTTCGT 57.823 36.000 0.00 0.00 32.33 3.85
5110 5497 4.723789 TCTGGAAGCCCTAGATCTTGAAAT 59.276 41.667 0.00 0.00 0.00 2.17
5250 5638 2.229062 CGGCTTCTTCGGATAGCTCATA 59.771 50.000 0.00 0.00 35.30 2.15
5524 5912 8.582437 CGGAGGGAGTATGTAATTTTGTATAGA 58.418 37.037 0.00 0.00 0.00 1.98
5543 5931 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
5544 5932 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
6015 6403 1.334054 CAGTGTACAACGTACGCTCC 58.666 55.000 16.72 0.00 36.27 4.70
6016 6404 0.706729 GCAGTGTACAACGTACGCTC 59.293 55.000 16.72 8.66 36.27 5.03
6017 6405 0.031043 TGCAGTGTACAACGTACGCT 59.969 50.000 16.72 13.20 38.66 5.07
6018 6406 1.065358 ATGCAGTGTACAACGTACGC 58.935 50.000 16.72 9.30 0.00 4.42
6019 6407 3.855379 ACATATGCAGTGTACAACGTACG 59.145 43.478 15.01 15.01 0.00 3.67
6020 6408 7.325338 CCTATACATATGCAGTGTACAACGTAC 59.675 40.741 14.73 0.00 35.11 3.67
6021 6409 7.229106 TCCTATACATATGCAGTGTACAACGTA 59.771 37.037 14.73 0.00 35.11 3.57
6022 6410 6.040054 TCCTATACATATGCAGTGTACAACGT 59.960 38.462 14.73 4.34 35.11 3.99
6023 6411 6.362551 GTCCTATACATATGCAGTGTACAACG 59.637 42.308 14.73 0.00 35.11 4.10
6024 6412 7.434492 AGTCCTATACATATGCAGTGTACAAC 58.566 38.462 14.73 11.00 35.11 3.32
6025 6413 7.597288 AGTCCTATACATATGCAGTGTACAA 57.403 36.000 14.73 7.47 35.11 2.41
6026 6414 7.393515 CCTAGTCCTATACATATGCAGTGTACA 59.606 40.741 14.73 5.17 35.11 2.90
6027 6415 7.148052 CCCTAGTCCTATACATATGCAGTGTAC 60.148 44.444 14.73 6.77 35.11 2.90
6028 6416 6.890268 CCCTAGTCCTATACATATGCAGTGTA 59.110 42.308 14.77 14.77 36.58 2.90
6029 6417 5.717178 CCCTAGTCCTATACATATGCAGTGT 59.283 44.000 11.66 11.66 0.00 3.55
6030 6418 5.717178 ACCCTAGTCCTATACATATGCAGTG 59.283 44.000 1.58 0.00 0.00 3.66
6031 6419 5.905088 ACCCTAGTCCTATACATATGCAGT 58.095 41.667 1.58 0.00 0.00 4.40
6032 6420 6.096141 CAGACCCTAGTCCTATACATATGCAG 59.904 46.154 1.58 0.00 44.72 4.41
6033 6421 5.952347 CAGACCCTAGTCCTATACATATGCA 59.048 44.000 1.58 0.00 44.72 3.96
6034 6422 5.952947 ACAGACCCTAGTCCTATACATATGC 59.047 44.000 1.58 0.00 44.72 3.14
6035 6423 9.702253 AATACAGACCCTAGTCCTATACATATG 57.298 37.037 0.00 0.00 44.72 1.78
6042 6430 7.833183 CGGTATAAATACAGACCCTAGTCCTAT 59.167 40.741 2.74 0.00 44.72 2.57
6043 6431 7.170965 CGGTATAAATACAGACCCTAGTCCTA 58.829 42.308 2.74 0.00 44.72 2.94
6044 6432 6.008960 CGGTATAAATACAGACCCTAGTCCT 58.991 44.000 2.74 0.00 44.72 3.85
6045 6433 5.772169 ACGGTATAAATACAGACCCTAGTCC 59.228 44.000 7.18 0.00 44.72 3.85
6046 6434 6.890979 ACGGTATAAATACAGACCCTAGTC 57.109 41.667 7.18 0.00 43.89 2.59
6047 6435 6.608808 ACAACGGTATAAATACAGACCCTAGT 59.391 38.462 7.18 0.00 34.98 2.57
6048 6436 7.047460 ACAACGGTATAAATACAGACCCTAG 57.953 40.000 7.18 0.00 34.98 3.02
6049 6437 8.710749 ATACAACGGTATAAATACAGACCCTA 57.289 34.615 7.18 0.00 38.43 3.53
6050 6438 5.945144 ACAACGGTATAAATACAGACCCT 57.055 39.130 7.18 0.00 34.98 4.34
6051 6439 7.664758 AGATACAACGGTATAAATACAGACCC 58.335 38.462 7.18 0.00 40.28 4.46
6052 6440 8.574737 AGAGATACAACGGTATAAATACAGACC 58.425 37.037 7.18 0.00 40.28 3.85
6053 6441 9.609950 GAGAGATACAACGGTATAAATACAGAC 57.390 37.037 7.18 0.00 40.28 3.51
6054 6442 9.570468 AGAGAGATACAACGGTATAAATACAGA 57.430 33.333 7.18 0.00 40.28 3.41
6055 6443 9.828852 GAGAGAGATACAACGGTATAAATACAG 57.171 37.037 2.74 1.13 40.28 2.74
6056 6444 9.570468 AGAGAGAGATACAACGGTATAAATACA 57.430 33.333 2.74 0.00 40.28 2.29
6058 6446 9.228949 GGAGAGAGAGATACAACGGTATAAATA 57.771 37.037 0.00 0.00 40.28 1.40
6059 6447 7.177041 GGGAGAGAGAGATACAACGGTATAAAT 59.823 40.741 0.00 0.00 40.28 1.40
6060 6448 6.489361 GGGAGAGAGAGATACAACGGTATAAA 59.511 42.308 0.00 0.00 40.28 1.40
6061 6449 6.002704 GGGAGAGAGAGATACAACGGTATAA 58.997 44.000 0.00 0.00 40.28 0.98
6062 6450 5.514484 GGGGAGAGAGAGATACAACGGTATA 60.514 48.000 0.00 0.00 40.28 1.47
6063 6451 4.400120 GGGAGAGAGAGATACAACGGTAT 58.600 47.826 0.00 0.00 42.86 2.73
6064 6452 3.434739 GGGGAGAGAGAGATACAACGGTA 60.435 52.174 0.00 0.00 0.00 4.02
6065 6453 2.657143 GGGAGAGAGAGATACAACGGT 58.343 52.381 0.00 0.00 0.00 4.83
6066 6454 1.957877 GGGGAGAGAGAGATACAACGG 59.042 57.143 0.00 0.00 0.00 4.44
6067 6455 1.957877 GGGGGAGAGAGAGATACAACG 59.042 57.143 0.00 0.00 0.00 4.10
6084 6472 5.001232 CCAAGATGTACAAATATACGGGGG 58.999 45.833 0.00 0.00 0.00 5.40
6085 6473 5.001232 CCCAAGATGTACAAATATACGGGG 58.999 45.833 0.00 0.00 0.00 5.73
6086 6474 5.860611 TCCCAAGATGTACAAATATACGGG 58.139 41.667 0.00 4.25 0.00 5.28
6087 6475 6.645415 GTCTCCCAAGATGTACAAATATACGG 59.355 42.308 0.00 0.00 33.08 4.02
6088 6476 7.207383 TGTCTCCCAAGATGTACAAATATACG 58.793 38.462 0.00 0.00 33.08 3.06
6089 6477 8.958119 TTGTCTCCCAAGATGTACAAATATAC 57.042 34.615 0.00 0.00 33.08 1.47
6104 6492 1.276622 GGCCTCTACTTGTCTCCCAA 58.723 55.000 0.00 0.00 0.00 4.12
6105 6493 0.970937 CGGCCTCTACTTGTCTCCCA 60.971 60.000 0.00 0.00 0.00 4.37
6106 6494 1.677637 CCGGCCTCTACTTGTCTCCC 61.678 65.000 0.00 0.00 0.00 4.30
6107 6495 0.971447 ACCGGCCTCTACTTGTCTCC 60.971 60.000 0.00 0.00 0.00 3.71
6108 6496 0.456628 GACCGGCCTCTACTTGTCTC 59.543 60.000 0.00 0.00 0.00 3.36
6109 6497 0.971447 GGACCGGCCTCTACTTGTCT 60.971 60.000 0.00 0.00 0.00 3.41
6110 6498 1.255667 TGGACCGGCCTCTACTTGTC 61.256 60.000 14.76 0.00 37.63 3.18
6111 6499 1.229082 TGGACCGGCCTCTACTTGT 60.229 57.895 14.76 0.00 37.63 3.16
6112 6500 1.218316 GTGGACCGGCCTCTACTTG 59.782 63.158 14.76 0.00 37.63 3.16
6113 6501 1.988406 GGTGGACCGGCCTCTACTT 60.988 63.158 14.76 0.00 37.63 2.24
6114 6502 2.363925 GGTGGACCGGCCTCTACT 60.364 66.667 14.76 0.00 37.63 2.57
6115 6503 3.468140 GGGTGGACCGGCCTCTAC 61.468 72.222 14.76 8.05 37.63 2.59
6116 6504 3.680196 AGGGTGGACCGGCCTCTA 61.680 66.667 14.76 0.00 46.96 2.43
6119 6507 4.326227 TACAGGGTGGACCGGCCT 62.326 66.667 14.76 4.20 46.96 5.19
6120 6508 4.091939 GTACAGGGTGGACCGGCC 62.092 72.222 0.00 4.32 46.96 6.13
6121 6509 4.091939 GGTACAGGGTGGACCGGC 62.092 72.222 0.00 0.00 42.36 6.13
6125 6513 4.281182 CACATAGATAGGTACAGGGTGGAC 59.719 50.000 0.00 0.00 0.00 4.02
6126 6514 4.480115 CACATAGATAGGTACAGGGTGGA 58.520 47.826 0.00 0.00 0.00 4.02
6127 6515 3.006967 GCACATAGATAGGTACAGGGTGG 59.993 52.174 0.00 0.00 0.00 4.61
6128 6516 3.641436 TGCACATAGATAGGTACAGGGTG 59.359 47.826 0.00 0.00 0.00 4.61
6129 6517 3.641906 GTGCACATAGATAGGTACAGGGT 59.358 47.826 13.17 0.00 0.00 4.34
6130 6518 3.006967 GGTGCACATAGATAGGTACAGGG 59.993 52.174 20.43 0.00 0.00 4.45
6131 6519 3.641436 TGGTGCACATAGATAGGTACAGG 59.359 47.826 20.43 0.00 0.00 4.00
6132 6520 4.937201 TGGTGCACATAGATAGGTACAG 57.063 45.455 20.43 0.00 0.00 2.74
6133 6521 4.503123 GCATGGTGCACATAGATAGGTACA 60.503 45.833 20.43 2.66 44.26 2.90
6134 6522 3.997021 GCATGGTGCACATAGATAGGTAC 59.003 47.826 20.43 0.00 44.26 3.34
6135 6523 4.271696 GCATGGTGCACATAGATAGGTA 57.728 45.455 20.43 0.00 44.26 3.08
6136 6524 3.131709 GCATGGTGCACATAGATAGGT 57.868 47.619 20.43 0.00 44.26 3.08
6148 6536 0.452987 ATTGATCGTGTGCATGGTGC 59.547 50.000 0.00 0.00 45.29 5.01
6149 6537 1.738908 TCATTGATCGTGTGCATGGTG 59.261 47.619 0.00 0.00 0.00 4.17
6150 6538 2.112380 TCATTGATCGTGTGCATGGT 57.888 45.000 0.00 0.00 0.00 3.55
6151 6539 3.703286 AATCATTGATCGTGTGCATGG 57.297 42.857 0.00 0.00 0.00 3.66
6152 6540 5.077424 CGATAATCATTGATCGTGTGCATG 58.923 41.667 0.00 0.00 40.02 4.06
6153 6541 5.273523 CGATAATCATTGATCGTGTGCAT 57.726 39.130 0.00 0.00 40.02 3.96
6154 6542 4.713854 CGATAATCATTGATCGTGTGCA 57.286 40.909 0.00 0.00 40.02 4.57


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

AutoCloner maintained by Alex Coulton.