Multiple sequence alignment - TraesCS5D01G434900

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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 TraesCS5D01G434900 chr5D 100.000 2444 0 0 1 2444 490165006 490167449 0.000000e+00 4514.0
1 TraesCS5D01G434900 chr5B 91.415 1724 64 41 603 2275 604225739 604227429 0.000000e+00 2287.0
2 TraesCS5D01G434900 chr5B 89.730 185 17 2 402 584 604225498 604225682 4.060000e-58 235.0
3 TraesCS5D01G434900 chr5B 96.471 85 3 0 2357 2441 604228037 604228121 9.110000e-30 141.0
4 TraesCS5D01G434900 chr5A 92.888 1139 28 19 615 1723 611817101 611818216 0.000000e+00 1605.0
5 TraesCS5D01G434900 chr5A 89.589 365 28 5 228 584 611816672 611817034 2.860000e-124 455.0
6 TraesCS5D01G434900 chr5A 81.369 263 19 14 1870 2119 611819061 611819306 1.150000e-43 187.0
7 TraesCS5D01G434900 chr5A 82.237 152 16 6 2136 2281 611820817 611820963 1.190000e-23 121.0
8 TraesCS5D01G434900 chr7D 80.769 104 17 3 409 510 47236740 47236842 7.250000e-11 78.7


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 TraesCS5D01G434900 chr5D 490165006 490167449 2443 False 4514.000000 4514 100.000000 1 2444 1 chr5D.!!$F1 2443
1 TraesCS5D01G434900 chr5B 604225498 604228121 2623 False 887.666667 2287 92.538667 402 2441 3 chr5B.!!$F1 2039
2 TraesCS5D01G434900 chr5A 611816672 611820963 4291 False 592.000000 1605 86.520750 228 2281 4 chr5A.!!$F1 2053

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
265 267 0.038744 AGTCCCAATCCTTGTGGCTG 59.961 55.0 0.0 0.0 34.56 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1821 0.329261 TGGAAGCTCCCATGTGGAAG 59.671 55.0 0.0 0.0 44.57 3.46 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
26 27 9.170734 TGATTCAATTGACTTCTAGGATTCTTG 57.829 33.333 7.89 0.00 0.00 3.02
27 28 9.388506 GATTCAATTGACTTCTAGGATTCTTGA 57.611 33.333 7.89 0.00 0.00 3.02
28 29 9.745018 ATTCAATTGACTTCTAGGATTCTTGAA 57.255 29.630 7.89 7.73 34.54 2.69
77 78 8.667987 TTTTCTACATAACATGTTTGATTCGC 57.332 30.769 17.78 0.00 41.63 4.70
78 79 6.976636 TCTACATAACATGTTTGATTCGCA 57.023 33.333 17.78 0.00 41.63 5.10
79 80 7.003939 TCTACATAACATGTTTGATTCGCAG 57.996 36.000 17.78 4.26 41.63 5.18
80 81 4.985413 ACATAACATGTTTGATTCGCAGG 58.015 39.130 17.78 0.00 41.63 4.85
81 82 4.699735 ACATAACATGTTTGATTCGCAGGA 59.300 37.500 17.78 0.00 41.63 3.86
82 83 5.357878 ACATAACATGTTTGATTCGCAGGAT 59.642 36.000 17.78 0.00 41.63 3.24
83 84 4.789012 AACATGTTTGATTCGCAGGATT 57.211 36.364 4.92 0.00 0.00 3.01
84 85 4.100707 ACATGTTTGATTCGCAGGATTG 57.899 40.909 0.00 0.00 0.00 2.67
85 86 3.119388 ACATGTTTGATTCGCAGGATTGG 60.119 43.478 0.00 0.00 0.00 3.16
86 87 2.789213 TGTTTGATTCGCAGGATTGGA 58.211 42.857 0.00 0.00 0.00 3.53
87 88 3.153130 TGTTTGATTCGCAGGATTGGAA 58.847 40.909 0.00 0.00 0.00 3.53
88 89 3.571828 TGTTTGATTCGCAGGATTGGAAA 59.428 39.130 0.00 0.00 0.00 3.13
89 90 4.038522 TGTTTGATTCGCAGGATTGGAAAA 59.961 37.500 0.00 0.00 0.00 2.29
90 91 5.170748 GTTTGATTCGCAGGATTGGAAAAT 58.829 37.500 0.00 0.00 0.00 1.82
91 92 5.404466 TTGATTCGCAGGATTGGAAAATT 57.596 34.783 0.00 0.00 0.00 1.82
92 93 4.997565 TGATTCGCAGGATTGGAAAATTC 58.002 39.130 0.00 0.00 0.00 2.17
108 109 6.486248 GGAAAATTCCAAAAGACTGTTTTGC 58.514 36.000 7.32 0.00 46.76 3.68
109 110 6.093357 GGAAAATTCCAAAAGACTGTTTTGCA 59.907 34.615 7.32 0.00 46.76 4.08
110 111 6.421377 AAATTCCAAAAGACTGTTTTGCAC 57.579 33.333 5.97 0.00 37.89 4.57
111 112 3.518634 TCCAAAAGACTGTTTTGCACC 57.481 42.857 5.97 0.00 37.89 5.01
112 113 2.167487 TCCAAAAGACTGTTTTGCACCC 59.833 45.455 5.97 0.00 37.89 4.61
113 114 2.168313 CCAAAAGACTGTTTTGCACCCT 59.832 45.455 5.97 0.00 37.89 4.34
114 115 3.383185 CCAAAAGACTGTTTTGCACCCTA 59.617 43.478 5.97 0.00 37.89 3.53
115 116 4.039124 CCAAAAGACTGTTTTGCACCCTAT 59.961 41.667 5.97 0.00 37.89 2.57
116 117 5.453198 CCAAAAGACTGTTTTGCACCCTATT 60.453 40.000 5.97 0.00 37.89 1.73
117 118 5.869649 AAAGACTGTTTTGCACCCTATTT 57.130 34.783 0.00 0.00 0.00 1.40
118 119 5.869649 AAGACTGTTTTGCACCCTATTTT 57.130 34.783 0.00 0.00 0.00 1.82
119 120 5.200368 AGACTGTTTTGCACCCTATTTTG 57.800 39.130 0.00 0.00 0.00 2.44
120 121 4.649218 AGACTGTTTTGCACCCTATTTTGT 59.351 37.500 0.00 0.00 0.00 2.83
121 122 5.830991 AGACTGTTTTGCACCCTATTTTGTA 59.169 36.000 0.00 0.00 0.00 2.41
122 123 6.016276 AGACTGTTTTGCACCCTATTTTGTAG 60.016 38.462 0.00 0.00 0.00 2.74
123 124 5.010617 ACTGTTTTGCACCCTATTTTGTAGG 59.989 40.000 0.00 0.00 34.52 3.18
124 125 5.141182 TGTTTTGCACCCTATTTTGTAGGA 58.859 37.500 2.73 0.00 36.85 2.94
125 126 5.598830 TGTTTTGCACCCTATTTTGTAGGAA 59.401 36.000 2.73 0.00 36.85 3.36
126 127 6.098409 TGTTTTGCACCCTATTTTGTAGGAAA 59.902 34.615 2.73 0.00 36.85 3.13
127 128 6.732896 TTTGCACCCTATTTTGTAGGAAAA 57.267 33.333 2.73 0.00 36.85 2.29
128 129 6.926630 TTGCACCCTATTTTGTAGGAAAAT 57.073 33.333 2.73 0.00 36.85 1.82
129 130 6.926630 TGCACCCTATTTTGTAGGAAAATT 57.073 33.333 2.73 0.00 36.85 1.82
130 131 7.309770 TGCACCCTATTTTGTAGGAAAATTT 57.690 32.000 2.73 0.00 36.85 1.82
131 132 7.740805 TGCACCCTATTTTGTAGGAAAATTTT 58.259 30.769 2.28 2.28 36.85 1.82
132 133 7.875554 TGCACCCTATTTTGTAGGAAAATTTTC 59.124 33.333 20.51 20.51 36.85 2.29
133 134 7.875554 GCACCCTATTTTGTAGGAAAATTTTCA 59.124 33.333 27.53 9.63 38.92 2.69
134 135 9.942850 CACCCTATTTTGTAGGAAAATTTTCAT 57.057 29.630 27.53 24.16 38.92 2.57
147 148 9.702494 AGGAAAATTTTCATTCACTCAAATCTC 57.298 29.630 27.53 8.42 38.92 2.75
148 149 8.642020 GGAAAATTTTCATTCACTCAAATCTCG 58.358 33.333 27.53 0.00 38.92 4.04
149 150 9.185192 GAAAATTTTCATTCACTCAAATCTCGT 57.815 29.630 23.06 0.00 37.15 4.18
150 151 9.533253 AAAATTTTCATTCACTCAAATCTCGTT 57.467 25.926 0.00 0.00 0.00 3.85
151 152 9.533253 AAATTTTCATTCACTCAAATCTCGTTT 57.467 25.926 0.00 0.00 0.00 3.60
152 153 9.533253 AATTTTCATTCACTCAAATCTCGTTTT 57.467 25.926 0.00 0.00 0.00 2.43
154 155 9.445786 TTTTCATTCACTCAAATCTCGTTTTAC 57.554 29.630 0.00 0.00 0.00 2.01
155 156 7.722795 TCATTCACTCAAATCTCGTTTTACA 57.277 32.000 0.00 0.00 0.00 2.41
156 157 8.148807 TCATTCACTCAAATCTCGTTTTACAA 57.851 30.769 0.00 0.00 0.00 2.41
157 158 8.783093 TCATTCACTCAAATCTCGTTTTACAAT 58.217 29.630 0.00 0.00 0.00 2.71
158 159 9.398170 CATTCACTCAAATCTCGTTTTACAATT 57.602 29.630 0.00 0.00 0.00 2.32
159 160 9.612620 ATTCACTCAAATCTCGTTTTACAATTC 57.387 29.630 0.00 0.00 0.00 2.17
160 161 8.378172 TCACTCAAATCTCGTTTTACAATTCT 57.622 30.769 0.00 0.00 0.00 2.40
161 162 8.836413 TCACTCAAATCTCGTTTTACAATTCTT 58.164 29.630 0.00 0.00 0.00 2.52
162 163 9.450807 CACTCAAATCTCGTTTTACAATTCTTT 57.549 29.630 0.00 0.00 0.00 2.52
186 187 3.578286 TGGCATGTGGCACTCCCA 61.578 61.111 19.83 17.92 46.12 4.37
187 188 2.753043 GGCATGTGGCACTCCCAG 60.753 66.667 19.83 5.21 46.54 4.45
188 189 2.753043 GCATGTGGCACTCCCAGG 60.753 66.667 19.83 0.74 46.54 4.45
189 190 2.759114 CATGTGGCACTCCCAGGT 59.241 61.111 19.83 0.00 46.54 4.00
190 191 1.377725 CATGTGGCACTCCCAGGTC 60.378 63.158 19.83 0.00 46.54 3.85
191 192 2.606587 ATGTGGCACTCCCAGGTCC 61.607 63.158 19.83 0.00 46.54 4.46
192 193 4.035102 GTGGCACTCCCAGGTCCC 62.035 72.222 11.13 0.00 46.54 4.46
195 196 3.017581 GCACTCCCAGGTCCCCAT 61.018 66.667 0.00 0.00 0.00 4.00
196 197 2.616458 GCACTCCCAGGTCCCCATT 61.616 63.158 0.00 0.00 0.00 3.16
197 198 1.609783 CACTCCCAGGTCCCCATTC 59.390 63.158 0.00 0.00 0.00 2.67
198 199 1.619669 ACTCCCAGGTCCCCATTCC 60.620 63.158 0.00 0.00 0.00 3.01
199 200 1.308216 CTCCCAGGTCCCCATTCCT 60.308 63.158 0.00 0.00 33.96 3.36
201 202 1.930656 CCCAGGTCCCCATTCCTGT 60.931 63.158 9.79 0.00 46.79 4.00
202 203 1.304282 CCAGGTCCCCATTCCTGTG 59.696 63.158 9.79 0.00 46.79 3.66
203 204 1.304282 CAGGTCCCCATTCCTGTGG 59.696 63.158 3.38 0.00 44.19 4.17
204 205 2.043953 GGTCCCCATTCCTGTGGC 60.044 66.667 0.00 0.00 37.96 5.01
205 206 2.616458 GGTCCCCATTCCTGTGGCT 61.616 63.158 0.00 0.00 37.96 4.75
206 207 1.384191 GTCCCCATTCCTGTGGCTT 59.616 57.895 0.00 0.00 37.96 4.35
207 208 0.967380 GTCCCCATTCCTGTGGCTTG 60.967 60.000 0.00 0.00 37.96 4.01
208 209 1.139498 TCCCCATTCCTGTGGCTTGA 61.139 55.000 0.00 0.00 37.96 3.02
209 210 0.967380 CCCCATTCCTGTGGCTTGAC 60.967 60.000 0.00 0.00 37.96 3.18
210 211 0.251297 CCCATTCCTGTGGCTTGACA 60.251 55.000 0.00 0.00 37.96 3.58
211 212 1.619654 CCATTCCTGTGGCTTGACAA 58.380 50.000 0.00 0.00 31.43 3.18
212 213 2.173519 CCATTCCTGTGGCTTGACAAT 58.826 47.619 0.00 0.00 31.43 2.71
213 214 2.165030 CCATTCCTGTGGCTTGACAATC 59.835 50.000 0.00 0.00 31.43 2.67
214 215 1.909700 TTCCTGTGGCTTGACAATCC 58.090 50.000 0.88 0.88 0.00 3.01
215 216 1.067295 TCCTGTGGCTTGACAATCCT 58.933 50.000 9.38 0.00 0.00 3.24
216 217 2.265367 TCCTGTGGCTTGACAATCCTA 58.735 47.619 9.38 0.00 0.00 2.94
217 218 2.642311 TCCTGTGGCTTGACAATCCTAA 59.358 45.455 9.38 0.00 0.00 2.69
218 219 3.266772 TCCTGTGGCTTGACAATCCTAAT 59.733 43.478 9.38 0.00 0.00 1.73
219 220 3.379372 CCTGTGGCTTGACAATCCTAATG 59.621 47.826 9.38 0.00 0.00 1.90
220 221 4.264253 CTGTGGCTTGACAATCCTAATGA 58.736 43.478 9.38 0.00 0.00 2.57
221 222 4.661222 TGTGGCTTGACAATCCTAATGAA 58.339 39.130 9.38 0.00 0.00 2.57
222 223 5.263599 TGTGGCTTGACAATCCTAATGAAT 58.736 37.500 9.38 0.00 0.00 2.57
223 224 5.716228 TGTGGCTTGACAATCCTAATGAATT 59.284 36.000 9.38 0.00 0.00 2.17
224 225 6.127647 TGTGGCTTGACAATCCTAATGAATTC 60.128 38.462 9.38 0.00 0.00 2.17
225 226 5.951148 TGGCTTGACAATCCTAATGAATTCA 59.049 36.000 11.26 11.26 0.00 2.57
226 227 6.608405 TGGCTTGACAATCCTAATGAATTCAT 59.392 34.615 15.36 15.36 38.41 2.57
247 248 2.124151 GCATGTGGCACCCCCTAG 60.124 66.667 16.26 0.00 43.97 3.02
248 249 2.983879 GCATGTGGCACCCCCTAGT 61.984 63.158 16.26 0.00 43.97 2.57
249 250 1.224592 CATGTGGCACCCCCTAGTC 59.775 63.158 16.26 0.00 0.00 2.59
252 253 3.948360 TGGCACCCCCTAGTCCCA 61.948 66.667 0.00 0.00 0.00 4.37
254 255 2.006991 GGCACCCCCTAGTCCCAAT 61.007 63.158 0.00 0.00 0.00 3.16
255 256 1.532238 GCACCCCCTAGTCCCAATC 59.468 63.158 0.00 0.00 0.00 2.67
265 267 0.038744 AGTCCCAATCCTTGTGGCTG 59.961 55.000 0.00 0.00 34.56 4.85
267 269 2.353610 CCCAATCCTTGTGGCTGGC 61.354 63.158 0.00 0.00 35.77 4.85
269 271 2.361610 AATCCTTGTGGCTGGCCG 60.362 61.111 7.14 0.00 39.42 6.13
270 272 3.944250 AATCCTTGTGGCTGGCCGG 62.944 63.158 7.41 7.41 39.42 6.13
289 291 3.627577 CCGGTCCTATTGAATTCAAGTGG 59.372 47.826 24.17 24.54 39.47 4.00
296 298 1.927487 TGAATTCAAGTGGGCATGCT 58.073 45.000 18.92 0.00 0.00 3.79
353 356 8.610896 TGTGTTTTAAAATTCCTGCAAATCAAG 58.389 29.630 3.52 0.00 0.00 3.02
441 444 5.468072 CCAAAGGGATTGAATAGTCTCATCG 59.532 44.000 0.00 0.00 41.85 3.84
500 509 6.263168 ACTTTTCCTATGAATCAAATAGGCCG 59.737 38.462 0.00 0.00 44.37 6.13
601 636 5.467705 AGCAAAAGAACACCTAGTACGTAG 58.532 41.667 0.00 0.00 0.00 3.51
604 639 5.893897 AAAGAACACCTAGTACGTAGAGG 57.106 43.478 18.05 18.05 36.36 3.69
606 641 4.512484 AGAACACCTAGTACGTAGAGGAC 58.488 47.826 24.00 14.13 34.24 3.85
607 642 3.274095 ACACCTAGTACGTAGAGGACC 57.726 52.381 24.00 0.98 34.24 4.46
610 645 2.102252 ACCTAGTACGTAGAGGACCGAG 59.898 54.545 24.00 6.21 34.24 4.63
611 646 2.134346 CTAGTACGTAGAGGACCGAGC 58.866 57.143 0.00 0.00 0.00 5.03
612 647 0.251354 AGTACGTAGAGGACCGAGCA 59.749 55.000 0.00 0.00 0.00 4.26
613 648 1.134159 AGTACGTAGAGGACCGAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
643 689 0.170561 CCACCTCGATCGAACGAACT 59.829 55.000 19.92 3.97 41.67 3.01
715 772 7.641020 AGTCAAAACGAAAAATAAGTAACCACG 59.359 33.333 0.00 0.00 0.00 4.94
774 831 0.172578 CATCTGCCGTACTTGACCGA 59.827 55.000 0.00 0.00 0.00 4.69
944 1003 2.667318 CGCCGTACCAAGCACACAG 61.667 63.158 0.00 0.00 0.00 3.66
946 1013 1.566018 GCCGTACCAAGCACACAGAC 61.566 60.000 0.00 0.00 0.00 3.51
958 1039 2.803133 GCACACAGACAGACACAGCTAA 60.803 50.000 0.00 0.00 0.00 3.09
966 1047 3.579709 ACAGACACAGCTAACTTCATCG 58.420 45.455 0.00 0.00 0.00 3.84
983 1064 3.067601 TCATCGGCGACTAATCAAGCTAA 59.932 43.478 13.76 0.00 0.00 3.09
1271 1352 3.151710 TGGCTACGATGTCCCCGG 61.152 66.667 0.00 0.00 0.00 5.73
1284 1365 3.996124 CCCGGAGCGCCTATGGAG 61.996 72.222 0.73 0.00 0.00 3.86
1323 1404 4.711949 CCGCTGCTGCTCACCCTT 62.712 66.667 14.03 0.00 36.97 3.95
1446 1527 3.737559 ACCCCTTGTGCTAATTGATCA 57.262 42.857 0.00 0.00 0.00 2.92
1447 1528 3.624777 ACCCCTTGTGCTAATTGATCAG 58.375 45.455 0.00 0.00 0.00 2.90
1448 1529 2.360165 CCCCTTGTGCTAATTGATCAGC 59.640 50.000 0.00 0.00 38.31 4.26
1449 1530 3.018856 CCCTTGTGCTAATTGATCAGCA 58.981 45.455 3.41 3.41 45.23 4.41
1456 1537 4.325472 GTGCTAATTGATCAGCAAAGCAAC 59.675 41.667 19.35 12.84 46.31 4.17
1507 1596 3.354467 ACTGCAGGTACCAGTCTAGTAC 58.646 50.000 19.93 0.33 39.19 2.73
1508 1597 2.355132 CTGCAGGTACCAGTCTAGTACG 59.645 54.545 15.94 0.00 40.84 3.67
1510 1599 3.055167 TGCAGGTACCAGTCTAGTACGTA 60.055 47.826 15.94 0.00 40.84 3.57
1511 1600 3.559242 GCAGGTACCAGTCTAGTACGTAG 59.441 52.174 15.94 0.00 40.84 3.51
1512 1601 4.681781 GCAGGTACCAGTCTAGTACGTAGA 60.682 50.000 15.94 0.00 40.84 2.59
1514 1603 5.523188 CAGGTACCAGTCTAGTACGTAGAAG 59.477 48.000 15.94 0.00 39.61 2.85
1515 1604 5.423610 AGGTACCAGTCTAGTACGTAGAAGA 59.576 44.000 15.94 0.00 39.61 2.87
1516 1605 6.099557 AGGTACCAGTCTAGTACGTAGAAGAT 59.900 42.308 15.94 0.00 39.61 2.40
1517 1606 6.765512 GGTACCAGTCTAGTACGTAGAAGATT 59.234 42.308 7.15 3.86 39.61 2.40
1518 1607 7.928706 GGTACCAGTCTAGTACGTAGAAGATTA 59.071 40.741 7.15 0.00 39.61 1.75
1628 1717 1.100510 TTCCACGAGGTCGATCGATT 58.899 50.000 22.50 12.91 45.56 3.34
1725 1814 4.829064 ACGCACAACATCTGTACATTTT 57.171 36.364 0.00 0.00 36.10 1.82
1726 1815 5.181690 ACGCACAACATCTGTACATTTTT 57.818 34.783 0.00 0.00 36.10 1.94
1755 1845 1.770658 CCACATGGGAGCTTCCAGATA 59.229 52.381 21.06 0.00 40.56 1.98
1758 1848 2.437281 ACATGGGAGCTTCCAGATACAG 59.563 50.000 21.06 7.30 40.56 2.74
1770 1860 4.229639 TCCAGATACAGAAGCATCATCCT 58.770 43.478 0.00 0.00 0.00 3.24
1773 1863 6.014755 TCCAGATACAGAAGCATCATCCTTAG 60.015 42.308 0.00 0.00 0.00 2.18
1775 1865 5.543405 AGATACAGAAGCATCATCCTTAGCT 59.457 40.000 0.00 0.00 39.37 3.32
1788 1878 6.341316 TCATCCTTAGCTTGTGTGTAAGATC 58.659 40.000 0.00 0.00 0.00 2.75
1912 2699 0.961019 ATGCATGTGCTCACGGTTTT 59.039 45.000 0.00 0.00 42.66 2.43
1923 2710 2.738846 CTCACGGTTTTGACATCAGAGG 59.261 50.000 0.00 0.00 0.00 3.69
1927 2714 1.177401 GTTTTGACATCAGAGGGGCC 58.823 55.000 0.00 0.00 0.00 5.80
1928 2715 0.322456 TTTTGACATCAGAGGGGCCG 60.322 55.000 0.00 0.00 0.00 6.13
1929 2716 2.196997 TTTGACATCAGAGGGGCCGG 62.197 60.000 0.00 0.00 0.00 6.13
1930 2717 4.554036 GACATCAGAGGGGCCGGC 62.554 72.222 21.18 21.18 0.00 6.13
1998 2787 0.315059 GACGATTTGTACGCATGCGG 60.315 55.000 39.95 23.39 44.69 5.69
2017 2806 2.872245 CGGCGATGTCAATTTGGTAGAT 59.128 45.455 0.00 0.00 0.00 1.98
2020 2809 4.516698 GGCGATGTCAATTTGGTAGATCAT 59.483 41.667 0.00 0.00 0.00 2.45
2058 2860 7.801716 TGAATGCTTGACTTTTTGTACTAGT 57.198 32.000 0.00 0.00 0.00 2.57
2130 4441 2.650608 CCGCTTTGTGCTACTTTGAAC 58.349 47.619 0.00 0.00 40.11 3.18
2133 4444 3.545633 GCTTTGTGCTACTTTGAACTCG 58.454 45.455 0.00 0.00 38.95 4.18
2134 4445 3.002348 GCTTTGTGCTACTTTGAACTCGT 59.998 43.478 0.00 0.00 38.95 4.18
2137 4448 4.841443 TGTGCTACTTTGAACTCGTCTA 57.159 40.909 0.00 0.00 0.00 2.59
2230 4547 5.625721 GCACGTACTGCTGAGTATATAACTG 59.374 44.000 9.26 0.00 43.33 3.16
2233 4550 5.625721 CGTACTGCTGAGTATATAACTGTGC 59.374 44.000 0.00 0.00 39.07 4.57
2235 4552 5.352284 ACTGCTGAGTATATAACTGTGCAC 58.648 41.667 10.75 10.75 39.07 4.57
2236 4553 5.127845 ACTGCTGAGTATATAACTGTGCACT 59.872 40.000 19.41 0.00 39.07 4.40
2237 4554 5.351458 TGCTGAGTATATAACTGTGCACTG 58.649 41.667 20.83 20.83 39.07 3.66
2239 4556 5.233050 GCTGAGTATATAACTGTGCACTGTG 59.767 44.000 27.31 15.25 39.07 3.66
2240 4557 5.109210 TGAGTATATAACTGTGCACTGTGC 58.891 41.667 27.31 25.15 40.72 4.57
2293 5103 5.684626 GTCAGAAGCAACTTGATTCAAACAG 59.315 40.000 19.30 6.30 44.52 3.16
2333 5143 2.194326 GCAATCCTCCTGGCCCTC 59.806 66.667 0.00 0.00 0.00 4.30
2348 5158 2.229792 GCCCTCGAATTATTGGATGCA 58.770 47.619 0.00 0.00 0.00 3.96
2354 5164 5.702670 CCTCGAATTATTGGATGCACATAGT 59.297 40.000 0.00 0.00 0.00 2.12
2399 5241 8.910351 AGTTAATCATCTAGGCCAAACTAATC 57.090 34.615 5.01 0.00 0.00 1.75
2425 5267 2.190578 CCTTGGGGCGATGAGGTC 59.809 66.667 0.00 0.00 0.00 3.85
2441 5283 1.206371 AGGTCCGGGTTTCTCGTTATG 59.794 52.381 0.00 0.00 0.00 1.90
2442 5284 1.066645 GGTCCGGGTTTCTCGTTATGT 60.067 52.381 0.00 0.00 0.00 2.29
2443 5285 1.997606 GTCCGGGTTTCTCGTTATGTG 59.002 52.381 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.170734 CAAGAATCCTAGAAGTCAATTGAATCA 57.829 33.333 10.35 0.00 0.00 2.57
1 2 9.388506 TCAAGAATCCTAGAAGTCAATTGAATC 57.611 33.333 10.35 11.64 0.00 2.52
2 3 9.745018 TTCAAGAATCCTAGAAGTCAATTGAAT 57.255 29.630 10.35 6.06 30.43 2.57
3 4 9.224267 CTTCAAGAATCCTAGAAGTCAATTGAA 57.776 33.333 10.35 0.00 34.32 2.69
4 5 7.826252 CCTTCAAGAATCCTAGAAGTCAATTGA 59.174 37.037 3.38 3.38 36.60 2.57
5 6 7.826252 TCCTTCAAGAATCCTAGAAGTCAATTG 59.174 37.037 0.00 0.00 36.60 2.32
6 7 7.922382 TCCTTCAAGAATCCTAGAAGTCAATT 58.078 34.615 0.00 0.00 36.60 2.32
7 8 7.502060 TCCTTCAAGAATCCTAGAAGTCAAT 57.498 36.000 0.00 0.00 36.60 2.57
8 9 6.935240 TCCTTCAAGAATCCTAGAAGTCAA 57.065 37.500 0.00 0.00 36.60 3.18
9 10 7.502060 AATCCTTCAAGAATCCTAGAAGTCA 57.498 36.000 0.00 0.00 36.60 3.41
10 11 6.699642 CGAATCCTTCAAGAATCCTAGAAGTC 59.300 42.308 0.00 0.00 36.60 3.01
11 12 6.407525 CCGAATCCTTCAAGAATCCTAGAAGT 60.408 42.308 0.00 0.00 36.60 3.01
12 13 5.988561 CCGAATCCTTCAAGAATCCTAGAAG 59.011 44.000 0.00 0.00 37.74 2.85
13 14 5.661312 TCCGAATCCTTCAAGAATCCTAGAA 59.339 40.000 0.00 0.00 0.00 2.10
14 15 5.208890 TCCGAATCCTTCAAGAATCCTAGA 58.791 41.667 0.00 0.00 0.00 2.43
15 16 5.537300 TCCGAATCCTTCAAGAATCCTAG 57.463 43.478 0.00 0.00 0.00 3.02
16 17 5.012148 GGATCCGAATCCTTCAAGAATCCTA 59.988 44.000 0.00 0.00 46.97 2.94
17 18 4.202409 GGATCCGAATCCTTCAAGAATCCT 60.202 45.833 0.00 0.00 46.97 3.24
18 19 4.068599 GGATCCGAATCCTTCAAGAATCC 58.931 47.826 0.00 0.00 46.97 3.01
51 52 9.123709 GCGAATCAAACATGTTATGTAGAAAAA 57.876 29.630 12.39 0.00 44.07 1.94
52 53 8.293157 TGCGAATCAAACATGTTATGTAGAAAA 58.707 29.630 12.39 0.00 44.07 2.29
53 54 7.811653 TGCGAATCAAACATGTTATGTAGAAA 58.188 30.769 12.39 0.00 44.07 2.52
54 55 7.371126 TGCGAATCAAACATGTTATGTAGAA 57.629 32.000 12.39 0.00 44.07 2.10
55 56 6.037062 CCTGCGAATCAAACATGTTATGTAGA 59.963 38.462 12.39 5.86 44.07 2.59
56 57 6.037062 TCCTGCGAATCAAACATGTTATGTAG 59.963 38.462 12.39 7.05 44.07 2.74
57 58 5.877564 TCCTGCGAATCAAACATGTTATGTA 59.122 36.000 12.39 0.00 44.07 2.29
59 60 5.233957 TCCTGCGAATCAAACATGTTATG 57.766 39.130 12.39 12.15 0.00 1.90
60 61 6.267817 CAATCCTGCGAATCAAACATGTTAT 58.732 36.000 12.39 0.00 0.00 1.89
61 62 5.392919 CCAATCCTGCGAATCAAACATGTTA 60.393 40.000 12.39 0.00 0.00 2.41
62 63 4.487948 CAATCCTGCGAATCAAACATGTT 58.512 39.130 4.92 4.92 0.00 2.71
63 64 3.119388 CCAATCCTGCGAATCAAACATGT 60.119 43.478 0.00 0.00 0.00 3.21
64 65 3.129113 TCCAATCCTGCGAATCAAACATG 59.871 43.478 0.00 0.00 0.00 3.21
65 66 3.355378 TCCAATCCTGCGAATCAAACAT 58.645 40.909 0.00 0.00 0.00 2.71
66 67 2.789213 TCCAATCCTGCGAATCAAACA 58.211 42.857 0.00 0.00 0.00 2.83
67 68 3.848272 TTCCAATCCTGCGAATCAAAC 57.152 42.857 0.00 0.00 0.00 2.93
68 69 4.862902 TTTTCCAATCCTGCGAATCAAA 57.137 36.364 0.00 0.00 0.00 2.69
69 70 5.404466 AATTTTCCAATCCTGCGAATCAA 57.596 34.783 0.00 0.00 0.00 2.57
70 71 4.142182 GGAATTTTCCAATCCTGCGAATCA 60.142 41.667 4.43 0.00 46.76 2.57
71 72 4.363138 GGAATTTTCCAATCCTGCGAATC 58.637 43.478 4.43 0.00 46.76 2.52
72 73 4.391405 GGAATTTTCCAATCCTGCGAAT 57.609 40.909 4.43 0.00 46.76 3.34
73 74 3.866883 GGAATTTTCCAATCCTGCGAA 57.133 42.857 4.43 0.00 46.76 4.70
85 86 6.960992 GTGCAAAACAGTCTTTTGGAATTTTC 59.039 34.615 5.86 0.00 40.46 2.29
86 87 6.128035 GGTGCAAAACAGTCTTTTGGAATTTT 60.128 34.615 5.86 0.00 40.46 1.82
87 88 5.353956 GGTGCAAAACAGTCTTTTGGAATTT 59.646 36.000 5.86 0.00 40.46 1.82
88 89 4.875536 GGTGCAAAACAGTCTTTTGGAATT 59.124 37.500 5.86 0.00 40.46 2.17
89 90 4.441792 GGTGCAAAACAGTCTTTTGGAAT 58.558 39.130 5.86 0.00 40.46 3.01
90 91 3.368948 GGGTGCAAAACAGTCTTTTGGAA 60.369 43.478 5.86 0.00 40.46 3.53
91 92 2.167487 GGGTGCAAAACAGTCTTTTGGA 59.833 45.455 5.86 0.21 39.19 3.53
92 93 2.168313 AGGGTGCAAAACAGTCTTTTGG 59.832 45.455 5.86 0.00 39.19 3.28
93 94 3.525268 AGGGTGCAAAACAGTCTTTTG 57.475 42.857 0.00 0.00 41.09 2.44
94 95 5.869649 AATAGGGTGCAAAACAGTCTTTT 57.130 34.783 0.00 0.00 0.00 2.27
95 96 5.869649 AAATAGGGTGCAAAACAGTCTTT 57.130 34.783 0.00 0.00 0.00 2.52
96 97 5.128663 ACAAAATAGGGTGCAAAACAGTCTT 59.871 36.000 0.00 0.00 0.00 3.01
97 98 4.649218 ACAAAATAGGGTGCAAAACAGTCT 59.351 37.500 0.00 0.00 0.00 3.24
98 99 4.944048 ACAAAATAGGGTGCAAAACAGTC 58.056 39.130 0.00 0.00 0.00 3.51
99 100 5.010617 CCTACAAAATAGGGTGCAAAACAGT 59.989 40.000 0.00 0.00 0.00 3.55
100 101 5.242838 TCCTACAAAATAGGGTGCAAAACAG 59.757 40.000 0.00 0.00 35.45 3.16
101 102 5.141182 TCCTACAAAATAGGGTGCAAAACA 58.859 37.500 0.00 0.00 35.45 2.83
102 103 5.715434 TCCTACAAAATAGGGTGCAAAAC 57.285 39.130 0.00 0.00 35.45 2.43
103 104 6.732896 TTTCCTACAAAATAGGGTGCAAAA 57.267 33.333 0.00 0.00 35.45 2.44
104 105 6.732896 TTTTCCTACAAAATAGGGTGCAAA 57.267 33.333 0.00 0.00 35.45 3.68
105 106 6.926630 ATTTTCCTACAAAATAGGGTGCAA 57.073 33.333 0.00 0.00 35.45 4.08
106 107 6.926630 AATTTTCCTACAAAATAGGGTGCA 57.073 33.333 0.21 0.00 35.45 4.57
107 108 7.875554 TGAAAATTTTCCTACAAAATAGGGTGC 59.124 33.333 24.51 0.00 36.36 5.01
108 109 9.942850 ATGAAAATTTTCCTACAAAATAGGGTG 57.057 29.630 24.51 0.00 36.36 4.61
121 122 9.702494 GAGATTTGAGTGAATGAAAATTTTCCT 57.298 29.630 24.51 14.49 36.36 3.36
122 123 8.642020 CGAGATTTGAGTGAATGAAAATTTTCC 58.358 33.333 24.51 12.26 36.36 3.13
123 124 9.185192 ACGAGATTTGAGTGAATGAAAATTTTC 57.815 29.630 21.60 21.60 37.69 2.29
124 125 9.533253 AACGAGATTTGAGTGAATGAAAATTTT 57.467 25.926 2.28 2.28 0.00 1.82
125 126 9.533253 AAACGAGATTTGAGTGAATGAAAATTT 57.467 25.926 0.00 0.00 0.00 1.82
126 127 9.533253 AAAACGAGATTTGAGTGAATGAAAATT 57.467 25.926 0.00 0.00 0.00 1.82
128 129 9.445786 GTAAAACGAGATTTGAGTGAATGAAAA 57.554 29.630 0.00 0.00 0.00 2.29
129 130 8.616942 TGTAAAACGAGATTTGAGTGAATGAAA 58.383 29.630 0.00 0.00 0.00 2.69
130 131 8.148807 TGTAAAACGAGATTTGAGTGAATGAA 57.851 30.769 0.00 0.00 0.00 2.57
131 132 7.722795 TGTAAAACGAGATTTGAGTGAATGA 57.277 32.000 0.00 0.00 0.00 2.57
132 133 8.955061 ATTGTAAAACGAGATTTGAGTGAATG 57.045 30.769 0.00 0.00 0.00 2.67
133 134 9.612620 GAATTGTAAAACGAGATTTGAGTGAAT 57.387 29.630 0.00 0.00 0.00 2.57
134 135 8.836413 AGAATTGTAAAACGAGATTTGAGTGAA 58.164 29.630 0.00 0.00 0.00 3.18
135 136 8.378172 AGAATTGTAAAACGAGATTTGAGTGA 57.622 30.769 0.00 0.00 0.00 3.41
136 137 9.450807 AAAGAATTGTAAAACGAGATTTGAGTG 57.549 29.630 0.00 0.00 0.00 3.51
162 163 0.249238 GTGCCACATGCCACGAAAAA 60.249 50.000 0.00 0.00 40.16 1.94
163 164 1.106351 AGTGCCACATGCCACGAAAA 61.106 50.000 0.00 0.00 40.16 2.29
164 165 1.514678 GAGTGCCACATGCCACGAAA 61.515 55.000 0.00 0.00 40.16 3.46
165 166 1.965930 GAGTGCCACATGCCACGAA 60.966 57.895 0.00 0.00 40.16 3.85
166 167 2.358615 GAGTGCCACATGCCACGA 60.359 61.111 0.00 0.00 40.16 4.35
167 168 3.434319 GGAGTGCCACATGCCACG 61.434 66.667 0.00 0.00 40.16 4.94
168 169 3.064324 GGGAGTGCCACATGCCAC 61.064 66.667 0.00 0.00 40.16 5.01
169 170 3.572447 CTGGGAGTGCCACATGCCA 62.572 63.158 0.00 2.58 40.16 4.92
170 171 2.753043 CTGGGAGTGCCACATGCC 60.753 66.667 0.00 0.00 40.16 4.40
171 172 2.753043 CCTGGGAGTGCCACATGC 60.753 66.667 0.00 0.00 41.77 4.06
172 173 1.377725 GACCTGGGAGTGCCACATG 60.378 63.158 0.00 0.00 35.15 3.21
173 174 2.606587 GGACCTGGGAGTGCCACAT 61.607 63.158 0.00 0.00 35.15 3.21
174 175 3.249189 GGACCTGGGAGTGCCACA 61.249 66.667 0.00 0.00 35.15 4.17
175 176 4.035102 GGGACCTGGGAGTGCCAC 62.035 72.222 0.00 0.00 46.81 5.01
188 189 0.967380 CAAGCCACAGGAATGGGGAC 60.967 60.000 0.00 0.00 40.43 4.46
189 190 1.139498 TCAAGCCACAGGAATGGGGA 61.139 55.000 0.00 0.00 40.43 4.81
190 191 0.967380 GTCAAGCCACAGGAATGGGG 60.967 60.000 0.00 0.00 40.43 4.96
191 192 0.251297 TGTCAAGCCACAGGAATGGG 60.251 55.000 0.00 0.00 40.43 4.00
192 193 1.619654 TTGTCAAGCCACAGGAATGG 58.380 50.000 0.00 0.00 43.26 3.16
193 194 2.165030 GGATTGTCAAGCCACAGGAATG 59.835 50.000 15.07 0.00 36.80 2.67
194 195 2.042162 AGGATTGTCAAGCCACAGGAAT 59.958 45.455 21.51 0.00 40.13 3.01
195 196 1.425066 AGGATTGTCAAGCCACAGGAA 59.575 47.619 21.51 0.00 40.13 3.36
196 197 1.067295 AGGATTGTCAAGCCACAGGA 58.933 50.000 21.51 0.00 40.13 3.86
197 198 2.787473 TAGGATTGTCAAGCCACAGG 57.213 50.000 21.51 0.00 40.13 4.00
198 199 4.264253 TCATTAGGATTGTCAAGCCACAG 58.736 43.478 21.51 8.62 40.13 3.66
199 200 4.299586 TCATTAGGATTGTCAAGCCACA 57.700 40.909 21.51 7.96 40.13 4.17
200 201 5.841957 ATTCATTAGGATTGTCAAGCCAC 57.158 39.130 21.51 0.00 40.13 5.01
201 202 5.951148 TGAATTCATTAGGATTGTCAAGCCA 59.049 36.000 21.51 2.41 40.13 4.75
202 203 6.455360 TGAATTCATTAGGATTGTCAAGCC 57.545 37.500 12.11 12.11 37.16 4.35
203 204 7.434307 CACATGAATTCATTAGGATTGTCAAGC 59.566 37.037 18.41 0.00 33.61 4.01
204 205 7.919091 CCACATGAATTCATTAGGATTGTCAAG 59.081 37.037 22.87 9.91 33.61 3.02
205 206 7.631161 GCCACATGAATTCATTAGGATTGTCAA 60.631 37.037 28.06 0.00 33.61 3.18
206 207 6.183360 GCCACATGAATTCATTAGGATTGTCA 60.183 38.462 28.06 0.00 33.61 3.58
207 208 6.183360 TGCCACATGAATTCATTAGGATTGTC 60.183 38.462 28.06 16.16 33.61 3.18
208 209 5.657745 TGCCACATGAATTCATTAGGATTGT 59.342 36.000 28.06 17.44 33.61 2.71
209 210 6.151663 TGCCACATGAATTCATTAGGATTG 57.848 37.500 28.06 16.91 33.61 2.67
210 211 6.325545 ACATGCCACATGAATTCATTAGGATT 59.674 34.615 28.06 16.75 33.61 3.01
211 212 5.836898 ACATGCCACATGAATTCATTAGGAT 59.163 36.000 28.06 18.98 33.61 3.24
212 213 5.068067 CACATGCCACATGAATTCATTAGGA 59.932 40.000 28.06 17.90 33.61 2.94
213 214 5.286438 CACATGCCACATGAATTCATTAGG 58.714 41.667 22.93 22.93 33.61 2.69
214 215 5.286438 CCACATGCCACATGAATTCATTAG 58.714 41.667 18.41 13.01 33.61 1.73
215 216 4.441773 GCCACATGCCACATGAATTCATTA 60.442 41.667 18.41 3.77 33.61 1.90
216 217 3.680475 GCCACATGCCACATGAATTCATT 60.680 43.478 18.41 7.62 33.61 2.57
217 218 2.159014 GCCACATGCCACATGAATTCAT 60.159 45.455 15.36 15.36 36.96 2.57
218 219 1.205179 GCCACATGCCACATGAATTCA 59.795 47.619 11.26 11.26 0.00 2.57
219 220 1.205179 TGCCACATGCCACATGAATTC 59.795 47.619 14.17 0.00 40.16 2.17
220 221 1.066716 GTGCCACATGCCACATGAATT 60.067 47.619 14.17 0.00 40.16 2.17
221 222 0.533491 GTGCCACATGCCACATGAAT 59.467 50.000 14.17 0.00 40.16 2.57
222 223 1.534336 GGTGCCACATGCCACATGAA 61.534 55.000 14.17 0.00 40.16 2.57
223 224 1.978080 GGTGCCACATGCCACATGA 60.978 57.895 14.17 0.00 40.16 3.07
224 225 2.574929 GGTGCCACATGCCACATG 59.425 61.111 6.03 6.03 40.16 3.21
225 226 2.681064 GGGTGCCACATGCCACAT 60.681 61.111 12.10 0.00 40.16 3.21
226 227 4.992740 GGGGTGCCACATGCCACA 62.993 66.667 12.10 0.00 40.16 4.17
252 253 2.361610 CGGCCAGCCACAAGGATT 60.362 61.111 9.78 0.00 36.89 3.01
265 267 2.341846 TGAATTCAATAGGACCGGCC 57.658 50.000 5.45 3.58 0.00 6.13
267 269 3.627577 CCACTTGAATTCAATAGGACCGG 59.372 47.826 24.32 13.25 35.02 5.28
269 271 3.381590 GCCCACTTGAATTCAATAGGACC 59.618 47.826 27.76 18.82 35.02 4.46
270 272 4.016444 TGCCCACTTGAATTCAATAGGAC 58.984 43.478 27.76 21.34 35.02 3.85
289 291 5.002464 ACACAGAAATGAAATAGCATGCC 57.998 39.130 15.66 0.00 0.00 4.40
318 321 9.474920 CAGGAATTTTAAAACACAGCAATAGAA 57.525 29.630 1.97 0.00 0.00 2.10
319 322 7.598493 GCAGGAATTTTAAAACACAGCAATAGA 59.402 33.333 1.97 0.00 0.00 1.98
327 330 8.498054 TTGATTTGCAGGAATTTTAAAACACA 57.502 26.923 1.97 0.00 0.00 3.72
328 331 8.069574 CCTTGATTTGCAGGAATTTTAAAACAC 58.930 33.333 1.97 0.51 0.00 3.32
335 338 4.285260 AGCTCCTTGATTTGCAGGAATTTT 59.715 37.500 0.00 0.00 0.00 1.82
415 418 5.745227 TGAGACTATTCAATCCCTTTGGTC 58.255 41.667 0.00 0.00 35.92 4.02
417 420 5.468072 CGATGAGACTATTCAATCCCTTTGG 59.532 44.000 0.00 0.00 35.92 3.28
452 458 7.848128 AGTAGAGAAAAATCGTAGGAATGGAA 58.152 34.615 0.00 0.00 0.00 3.53
494 503 3.262405 AGTGTTCCAAGATTTACGGCCTA 59.738 43.478 0.00 0.00 0.00 3.93
500 509 6.142320 CGCTTTCAAAGTGTTCCAAGATTTAC 59.858 38.462 2.24 0.00 34.37 2.01
601 636 0.745845 AACATGCATGCTCGGTCCTC 60.746 55.000 26.53 0.00 0.00 3.71
604 639 0.179156 CCAAACATGCATGCTCGGTC 60.179 55.000 26.53 0.00 0.00 4.79
606 641 1.517694 GCCAAACATGCATGCTCGG 60.518 57.895 26.53 22.46 0.00 4.63
607 642 1.517694 GGCCAAACATGCATGCTCG 60.518 57.895 26.53 13.97 0.00 5.03
610 645 1.742510 GGTGGCCAAACATGCATGC 60.743 57.895 26.53 11.82 0.00 4.06
611 646 0.108520 GAGGTGGCCAAACATGCATG 60.109 55.000 25.09 25.09 0.00 4.06
612 647 1.597797 CGAGGTGGCCAAACATGCAT 61.598 55.000 7.24 0.00 0.00 3.96
613 648 2.267351 CGAGGTGGCCAAACATGCA 61.267 57.895 7.24 0.00 0.00 3.96
643 689 4.390603 GTGTATAATCAACGTGCCTTCACA 59.609 41.667 0.00 0.00 43.28 3.58
715 772 0.323957 AAAGCGAGGGTAGGTTGGAC 59.676 55.000 0.00 0.00 0.00 4.02
944 1003 3.610242 CGATGAAGTTAGCTGTGTCTGTC 59.390 47.826 0.00 0.00 0.00 3.51
946 1013 2.926200 CCGATGAAGTTAGCTGTGTCTG 59.074 50.000 0.00 0.00 0.00 3.51
958 1039 3.448686 CTTGATTAGTCGCCGATGAAGT 58.551 45.455 0.00 0.00 0.00 3.01
966 1047 4.209495 GCTTACTTAGCTTGATTAGTCGCC 59.791 45.833 0.00 0.00 46.77 5.54
983 1064 3.376935 ATGGCTGCTCGCGCTTACT 62.377 57.895 5.56 0.00 40.44 2.24
1007 1088 2.357517 CGCCGGCCATAGTCATCC 60.358 66.667 23.46 0.00 0.00 3.51
1271 1352 2.578714 CCCTCCTCCATAGGCGCTC 61.579 68.421 7.64 0.00 43.31 5.03
1284 1365 0.469144 CTCCTACTCCAGCTCCCTCC 60.469 65.000 0.00 0.00 0.00 4.30
1446 1527 2.173519 ACTGCATATGGTTGCTTTGCT 58.826 42.857 4.56 0.00 43.18 3.91
1447 1528 2.660189 ACTGCATATGGTTGCTTTGC 57.340 45.000 4.56 0.00 43.18 3.68
1448 1529 4.177165 TCAACTGCATATGGTTGCTTTG 57.823 40.909 15.93 7.09 43.18 2.77
1449 1530 4.708421 AGATCAACTGCATATGGTTGCTTT 59.292 37.500 15.93 3.94 43.18 3.51
1450 1531 4.097437 CAGATCAACTGCATATGGTTGCTT 59.903 41.667 15.93 8.82 43.18 3.91
1456 1537 3.812262 TGTCCAGATCAACTGCATATGG 58.188 45.455 4.56 0.00 44.52 2.74
1559 1648 3.375299 CCTGGCTAACTGATTTGTACTGC 59.625 47.826 0.00 0.00 0.00 4.40
1625 1714 5.277058 CGAAATTTCAGTCCCTCGATCAATC 60.277 44.000 17.99 0.00 0.00 2.67
1628 1717 3.521560 CGAAATTTCAGTCCCTCGATCA 58.478 45.455 17.99 0.00 0.00 2.92
1725 1814 2.627699 GCTCCCATGTGGAAGAACAAAA 59.372 45.455 0.00 0.00 44.57 2.44
1726 1815 2.158475 AGCTCCCATGTGGAAGAACAAA 60.158 45.455 0.00 0.00 44.57 2.83
1732 1821 0.329261 TGGAAGCTCCCATGTGGAAG 59.671 55.000 0.00 0.00 44.57 3.46
1738 1827 2.702478 TCTGTATCTGGAAGCTCCCATG 59.298 50.000 0.00 0.00 35.03 3.66
1755 1845 4.197750 CAAGCTAAGGATGATGCTTCTGT 58.802 43.478 1.43 0.00 42.89 3.41
1758 1848 3.944015 ACACAAGCTAAGGATGATGCTTC 59.056 43.478 1.43 0.00 42.89 3.86
1766 1856 5.189736 TGGATCTTACACACAAGCTAAGGAT 59.810 40.000 0.00 0.00 0.00 3.24
1770 1860 4.575885 GGTGGATCTTACACACAAGCTAA 58.424 43.478 0.00 0.00 40.54 3.09
1773 1863 1.732259 CGGTGGATCTTACACACAAGC 59.268 52.381 3.47 0.00 40.54 4.01
1775 1865 3.395639 GAACGGTGGATCTTACACACAA 58.604 45.455 3.47 0.00 40.54 3.33
1776 1866 2.608506 CGAACGGTGGATCTTACACACA 60.609 50.000 3.47 0.00 40.54 3.72
1788 1878 0.515564 AAGCGAAAATCGAACGGTGG 59.484 50.000 3.61 0.00 43.74 4.61
1912 2699 3.083349 CCGGCCCCTCTGATGTCA 61.083 66.667 0.00 0.00 0.00 3.58
1927 2714 0.521867 CAGTTCATGCATTGTCGCCG 60.522 55.000 0.00 0.00 0.00 6.46
1928 2715 3.317608 CAGTTCATGCATTGTCGCC 57.682 52.632 0.00 0.00 0.00 5.54
1998 2787 5.446709 CATGATCTACCAAATTGACATCGC 58.553 41.667 0.00 0.00 0.00 4.58
2000 2789 5.278660 GGGCATGATCTACCAAATTGACATC 60.279 44.000 0.00 0.00 0.00 3.06
2017 2806 4.023279 GCATTCATAAATGTACGGGCATGA 60.023 41.667 0.00 0.00 43.54 3.07
2020 2809 3.550820 AGCATTCATAAATGTACGGGCA 58.449 40.909 0.00 0.00 43.54 5.36
2056 2858 7.121315 GCACCCTACAATTTGAAATCTTCTACT 59.879 37.037 2.79 0.00 0.00 2.57
2058 2860 6.093495 CGCACCCTACAATTTGAAATCTTCTA 59.907 38.462 2.79 0.00 0.00 2.10
2070 2883 1.248101 GGCAACCGCACCCTACAATT 61.248 55.000 0.00 0.00 41.24 2.32
2074 2887 2.436115 GAGGCAACCGCACCCTAC 60.436 66.667 0.00 0.00 41.24 3.18
2130 4441 1.081892 TCCCGTTCGAACTAGACGAG 58.918 55.000 24.80 8.26 40.72 4.18
2133 4444 1.475682 ACCATCCCGTTCGAACTAGAC 59.524 52.381 24.80 0.00 0.00 2.59
2134 4445 1.475280 CACCATCCCGTTCGAACTAGA 59.525 52.381 24.80 20.24 0.00 2.43
2137 4448 1.189524 TCCACCATCCCGTTCGAACT 61.190 55.000 24.80 4.29 0.00 3.01
2233 4550 1.064505 CTCAGGTTTGTGTGCACAGTG 59.935 52.381 22.40 10.90 42.94 3.66
2235 4552 0.664761 CCTCAGGTTTGTGTGCACAG 59.335 55.000 22.40 6.73 42.94 3.66
2236 4553 0.751277 CCCTCAGGTTTGTGTGCACA 60.751 55.000 17.42 17.42 39.98 4.57
2237 4554 2.032981 CCCTCAGGTTTGTGTGCAC 58.967 57.895 10.75 10.75 0.00 4.57
2239 4556 1.181098 ATGCCCTCAGGTTTGTGTGC 61.181 55.000 0.00 0.00 34.57 4.57
2240 4557 0.599558 CATGCCCTCAGGTTTGTGTG 59.400 55.000 0.00 0.00 34.57 3.82
2248 4565 1.107538 CCTGAATGCATGCCCTCAGG 61.108 60.000 33.67 33.67 46.66 3.86
2333 5143 6.544038 TGACTATGTGCATCCAATAATTCG 57.456 37.500 0.00 0.00 0.00 3.34
2399 5241 4.785453 GCCCCAAGGAGACGGCAG 62.785 72.222 0.00 0.00 41.25 4.85


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

AutoCloner maintained by Alex Coulton.