Multiple sequence alignment - TraesCS4D01G280800

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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 TraesCS4D01G280800 chr4D 100.000 4010 0 0 1 4010 451687476 451683467 0.000000e+00 7406.0
1 TraesCS4D01G280800 chr4D 81.432 447 78 4 2537 2982 40568123 40567681 1.060000e-95 361.0
2 TraesCS4D01G280800 chr4D 91.209 182 15 1 98 279 154102405 154102225 3.100000e-61 246.0
3 TraesCS4D01G280800 chr4B 94.255 1932 58 17 2110 4007 565093169 565091257 0.000000e+00 2904.0
4 TraesCS4D01G280800 chr4B 91.138 1388 86 22 754 2114 565094572 565093195 0.000000e+00 1847.0
5 TraesCS4D01G280800 chr4B 80.440 455 82 6 2537 2989 59236722 59236273 1.380000e-89 340.0
6 TraesCS4D01G280800 chr4B 80.682 352 62 5 2640 2989 59227175 59226828 6.610000e-68 268.0
7 TraesCS4D01G280800 chr4B 90.805 87 8 0 1 87 565096490 565096404 2.530000e-22 117.0
8 TraesCS4D01G280800 chr4B 97.872 47 1 0 595 641 565096425 565096471 9.240000e-12 82.4
9 TraesCS4D01G280800 chr4B 100.000 28 0 0 266 293 565096389 565096362 7.000000e-03 52.8
10 TraesCS4D01G280800 chr4A 92.511 1963 73 26 2110 4007 15126723 15124770 0.000000e+00 2743.0
11 TraesCS4D01G280800 chr4A 90.989 1254 80 21 754 1987 15127995 15126755 0.000000e+00 1659.0
12 TraesCS4D01G280800 chr4A 82.781 453 75 2 2537 2989 559068210 559067761 6.240000e-108 401.0
13 TraesCS4D01G280800 chr4A 90.110 182 9 5 266 446 15129274 15129101 1.120000e-55 228.0
14 TraesCS4D01G280800 chr4A 93.617 47 2 1 595 641 15129311 15129356 7.190000e-08 69.4
15 TraesCS4D01G280800 chr3A 94.186 172 10 0 94 265 585605631 585605802 3.070000e-66 263.0
16 TraesCS4D01G280800 chr1B 94.611 167 9 0 100 266 453280603 453280769 3.980000e-65 259.0
17 TraesCS4D01G280800 chr1B 93.529 170 11 0 96 265 480970383 480970214 1.850000e-63 254.0
18 TraesCS4D01G280800 chr3B 94.578 166 9 0 100 265 326997370 326997205 1.430000e-64 257.0
19 TraesCS4D01G280800 chr6B 91.713 181 15 0 98 278 540708192 540708012 6.650000e-63 252.0
20 TraesCS4D01G280800 chr2B 90.306 196 14 4 87 277 736423736 736423931 6.650000e-63 252.0
21 TraesCS4D01G280800 chr7B 91.209 182 16 0 99 280 588861680 588861861 8.610000e-62 248.0
22 TraesCS4D01G280800 chr5D 92.045 176 12 2 100 274 181626111 181626285 3.100000e-61 246.0
23 TraesCS4D01G280800 chr1A 73.712 563 127 18 2409 2959 474427890 474428443 2.440000e-47 200.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G280800 chr4D 451683467 451687476 4009 True 7406.000000 7406 100.000000 1 4010 1 chr4D.!!$R3 4009
1 TraesCS4D01G280800 chr4B 565091257 565096490 5233 True 1230.200000 2904 94.049500 1 4007 4 chr4B.!!$R3 4006
2 TraesCS4D01G280800 chr4A 15124770 15129274 4504 True 1543.333333 2743 91.203333 266 4007 3 chr4A.!!$R2 3741

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
905 3183 0.318955 AAATCCTTGCGCACACTTGC 60.319 50.0 11.12 0.0 46.21 4.01 F
1751 4061 0.109086 CCTGAGCTGATCGTTCGTGT 60.109 55.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 4470 1.685765 TACGCCTCCTGCAGTCCAT 60.686 57.895 13.81 0.0 41.33 3.41 R
3509 5893 0.756903 AGTAAGCGTGGACACTTGGT 59.243 50.000 0.56 0.0 0.00 3.67 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
47 48 6.680810 TGCAATTCTAATTTCAGGTTCACAG 58.319 36.000 0.00 0.00 0.00 3.66
69 70 6.604795 ACAGGAACCCAATAATCAAATCTCTG 59.395 38.462 0.00 0.00 0.00 3.35
76 77 8.743714 ACCCAATAATCAAATCTCTGAAGTTTC 58.256 33.333 0.00 0.00 0.00 2.78
87 88 9.657419 AAATCTCTGAAGTTTCAAAAATGTTGT 57.343 25.926 0.00 0.00 36.64 3.32
89 90 7.825681 TCTCTGAAGTTTCAAAAATGTTGTGA 58.174 30.769 0.00 0.00 36.64 3.58
90 91 8.303156 TCTCTGAAGTTTCAAAAATGTTGTGAA 58.697 29.630 0.00 0.00 36.64 3.18
91 92 8.464770 TCTGAAGTTTCAAAAATGTTGTGAAG 57.535 30.769 0.00 0.00 36.64 3.02
118 119 8.857694 AAAAATCTACTCCATTCGTTCCTAAA 57.142 30.769 0.00 0.00 0.00 1.85
119 120 9.462606 AAAAATCTACTCCATTCGTTCCTAAAT 57.537 29.630 0.00 0.00 0.00 1.40
124 125 9.542462 TCTACTCCATTCGTTCCTAAATATTTG 57.458 33.333 11.05 1.40 0.00 2.32
125 126 9.326413 CTACTCCATTCGTTCCTAAATATTTGT 57.674 33.333 11.05 0.00 0.00 2.83
126 127 8.209917 ACTCCATTCGTTCCTAAATATTTGTC 57.790 34.615 11.05 0.00 0.00 3.18
127 128 8.047310 ACTCCATTCGTTCCTAAATATTTGTCT 58.953 33.333 11.05 0.00 0.00 3.41
128 129 8.801882 TCCATTCGTTCCTAAATATTTGTCTT 57.198 30.769 11.05 0.00 0.00 3.01
129 130 9.238368 TCCATTCGTTCCTAAATATTTGTCTTT 57.762 29.630 11.05 0.00 0.00 2.52
130 131 9.503427 CCATTCGTTCCTAAATATTTGTCTTTC 57.497 33.333 11.05 0.00 0.00 2.62
196 197 9.262358 GACATATTTTAGAGTGTAGATTCACCC 57.738 37.037 0.00 0.00 38.91 4.61
197 198 8.768397 ACATATTTTAGAGTGTAGATTCACCCA 58.232 33.333 0.00 0.00 38.91 4.51
198 199 9.784531 CATATTTTAGAGTGTAGATTCACCCAT 57.215 33.333 0.00 0.00 38.91 4.00
201 202 8.934023 TTTTAGAGTGTAGATTCACCCATTTT 57.066 30.769 0.00 0.00 38.91 1.82
202 203 7.921786 TTAGAGTGTAGATTCACCCATTTTG 57.078 36.000 0.00 0.00 38.91 2.44
203 204 4.702131 AGAGTGTAGATTCACCCATTTTGC 59.298 41.667 0.00 0.00 38.91 3.68
204 205 4.666512 AGTGTAGATTCACCCATTTTGCT 58.333 39.130 0.00 0.00 38.91 3.91
205 206 4.702131 AGTGTAGATTCACCCATTTTGCTC 59.298 41.667 0.00 0.00 38.91 4.26
206 207 4.016444 TGTAGATTCACCCATTTTGCTCC 58.984 43.478 0.00 0.00 0.00 4.70
207 208 2.094675 AGATTCACCCATTTTGCTCCG 58.905 47.619 0.00 0.00 0.00 4.63
208 209 1.818674 GATTCACCCATTTTGCTCCGT 59.181 47.619 0.00 0.00 0.00 4.69
209 210 2.570415 TTCACCCATTTTGCTCCGTA 57.430 45.000 0.00 0.00 0.00 4.02
210 211 2.799126 TCACCCATTTTGCTCCGTAT 57.201 45.000 0.00 0.00 0.00 3.06
211 212 2.364632 TCACCCATTTTGCTCCGTATG 58.635 47.619 0.00 0.00 0.00 2.39
212 213 2.091541 CACCCATTTTGCTCCGTATGT 58.908 47.619 0.00 0.00 0.00 2.29
213 214 3.055021 TCACCCATTTTGCTCCGTATGTA 60.055 43.478 0.00 0.00 0.00 2.29
214 215 3.312421 CACCCATTTTGCTCCGTATGTAG 59.688 47.826 0.00 0.00 0.00 2.74
215 216 3.054655 ACCCATTTTGCTCCGTATGTAGT 60.055 43.478 0.00 0.00 0.00 2.73
216 217 3.560068 CCCATTTTGCTCCGTATGTAGTC 59.440 47.826 0.00 0.00 0.00 2.59
217 218 4.188462 CCATTTTGCTCCGTATGTAGTCA 58.812 43.478 0.00 0.00 0.00 3.41
218 219 4.271049 CCATTTTGCTCCGTATGTAGTCAG 59.729 45.833 0.00 0.00 0.00 3.51
219 220 4.530710 TTTTGCTCCGTATGTAGTCAGT 57.469 40.909 0.00 0.00 0.00 3.41
220 221 4.530710 TTTGCTCCGTATGTAGTCAGTT 57.469 40.909 0.00 0.00 0.00 3.16
221 222 3.503827 TGCTCCGTATGTAGTCAGTTG 57.496 47.619 0.00 0.00 0.00 3.16
222 223 2.823747 TGCTCCGTATGTAGTCAGTTGT 59.176 45.455 0.00 0.00 0.00 3.32
223 224 3.257375 TGCTCCGTATGTAGTCAGTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
224 225 3.612860 GCTCCGTATGTAGTCAGTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
225 226 4.617530 GCTCCGTATGTAGTCAGTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
226 227 5.456548 TCCGTATGTAGTCAGTTGTTGAA 57.543 39.130 0.00 0.00 37.61 2.69
227 228 5.845103 TCCGTATGTAGTCAGTTGTTGAAA 58.155 37.500 0.00 0.00 37.61 2.69
228 229 6.460781 TCCGTATGTAGTCAGTTGTTGAAAT 58.539 36.000 0.00 0.00 37.61 2.17
229 230 6.588756 TCCGTATGTAGTCAGTTGTTGAAATC 59.411 38.462 0.00 0.00 37.61 2.17
230 231 6.590292 CCGTATGTAGTCAGTTGTTGAAATCT 59.410 38.462 0.00 0.00 37.61 2.40
231 232 7.201444 CCGTATGTAGTCAGTTGTTGAAATCTC 60.201 40.741 0.00 0.00 37.61 2.75
232 233 7.542477 CGTATGTAGTCAGTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 37.61 3.10
233 234 9.856488 GTATGTAGTCAGTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 37.61 2.43
234 235 8.994429 ATGTAGTCAGTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 37.61 2.43
235 236 8.178313 TGTAGTCAGTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 37.61 2.43
236 237 8.638873 TGTAGTCAGTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 37.61 2.10
237 238 9.477484 GTAGTCAGTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 37.61 2.52
238 239 8.600449 AGTCAGTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 37.61 2.62
239 240 8.424918 AGTCAGTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 37.61 2.52
240 241 8.491950 GTCAGTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 37.61 3.01
241 242 8.204160 TCAGTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 31.34 3.41
242 243 8.830580 CAGTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
243 244 9.396022 AGTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
263 264 9.981460 AGACAAATATTTAGAAATGAAGGGAGT 57.019 29.630 0.00 0.00 0.00 3.85
351 1741 6.348458 GCTCACTATCATGCACTTTTGTACAA 60.348 38.462 3.59 3.59 0.00 2.41
353 1743 6.484977 TCACTATCATGCACTTTTGTACAACA 59.515 34.615 8.07 0.13 0.00 3.33
389 1779 2.897350 CCTTTGCGATCCGGAGCC 60.897 66.667 15.35 7.71 0.00 4.70
496 1921 7.572523 AAATCATGACAGTTCAGTGAAAAGA 57.427 32.000 7.25 0.00 34.35 2.52
499 1924 7.572523 TCATGACAGTTCAGTGAAAAGATTT 57.427 32.000 7.25 0.00 34.35 2.17
547 1972 4.497473 TTTCGTGGTCAAATGACATTCC 57.503 40.909 14.93 0.00 46.47 3.01
616 2042 7.116075 AGGATTTGATTATTGGGTTCATGTG 57.884 36.000 0.00 0.00 0.00 3.21
617 2043 6.896860 AGGATTTGATTATTGGGTTCATGTGA 59.103 34.615 0.00 0.00 0.00 3.58
618 2044 7.399765 AGGATTTGATTATTGGGTTCATGTGAA 59.600 33.333 0.00 0.00 0.00 3.18
630 2056 5.356882 GTTCATGTGAACCTGAAATTCGA 57.643 39.130 13.56 0.00 46.42 3.71
631 2057 5.757886 GTTCATGTGAACCTGAAATTCGAA 58.242 37.500 13.56 0.00 46.42 3.71
632 2058 6.381801 GTTCATGTGAACCTGAAATTCGAAT 58.618 36.000 13.56 4.39 46.42 3.34
633 2059 6.573664 TCATGTGAACCTGAAATTCGAATT 57.426 33.333 17.60 17.60 0.00 2.17
634 2060 6.380995 TCATGTGAACCTGAAATTCGAATTG 58.619 36.000 23.38 13.33 0.00 2.32
635 2061 4.545610 TGTGAACCTGAAATTCGAATTGC 58.454 39.130 23.38 21.75 0.00 3.56
636 2062 4.037327 TGTGAACCTGAAATTCGAATTGCA 59.963 37.500 26.33 26.33 33.03 4.08
637 2063 5.163513 GTGAACCTGAAATTCGAATTGCAT 58.836 37.500 27.79 16.02 33.58 3.96
638 2064 5.634859 GTGAACCTGAAATTCGAATTGCATT 59.365 36.000 27.79 20.97 33.58 3.56
639 2065 6.146021 GTGAACCTGAAATTCGAATTGCATTT 59.854 34.615 27.79 22.90 33.58 2.32
640 2066 6.365789 TGAACCTGAAATTCGAATTGCATTTC 59.634 34.615 27.79 27.79 33.58 2.17
641 2067 5.782047 ACCTGAAATTCGAATTGCATTTCA 58.218 33.333 27.79 22.39 42.13 2.69
645 2071 7.107834 TGAAATTCGAATTGCATTTCAGTTG 57.892 32.000 24.80 5.25 40.41 3.16
646 2072 6.700960 TGAAATTCGAATTGCATTTCAGTTGT 59.299 30.769 24.80 5.14 40.41 3.32
647 2073 6.695292 AATTCGAATTGCATTTCAGTTGTC 57.305 33.333 22.16 0.00 0.00 3.18
648 2074 4.827304 TCGAATTGCATTTCAGTTGTCA 57.173 36.364 18.57 0.00 0.00 3.58
649 2075 5.180367 TCGAATTGCATTTCAGTTGTCAA 57.820 34.783 18.57 0.00 0.00 3.18
650 2076 5.771469 TCGAATTGCATTTCAGTTGTCAAT 58.229 33.333 18.57 0.00 0.00 2.57
651 2077 5.630264 TCGAATTGCATTTCAGTTGTCAATG 59.370 36.000 18.57 1.99 0.00 2.82
652 2078 5.630264 CGAATTGCATTTCAGTTGTCAATGA 59.370 36.000 18.57 0.00 30.66 2.57
653 2079 6.144241 CGAATTGCATTTCAGTTGTCAATGAA 59.856 34.615 18.57 6.42 33.73 2.57
654 2080 7.306690 CGAATTGCATTTCAGTTGTCAATGAAA 60.307 33.333 18.57 17.69 46.29 2.69
655 2081 6.586868 TTGCATTTCAGTTGTCAATGAAAC 57.413 33.333 17.72 11.20 45.38 2.78
656 2082 5.904941 TGCATTTCAGTTGTCAATGAAACT 58.095 33.333 17.72 5.44 45.38 2.66
657 2083 5.978919 TGCATTTCAGTTGTCAATGAAACTC 59.021 36.000 17.72 14.31 45.38 3.01
658 2084 6.183360 TGCATTTCAGTTGTCAATGAAACTCT 60.183 34.615 17.72 7.02 45.38 3.24
659 2085 6.698766 GCATTTCAGTTGTCAATGAAACTCTT 59.301 34.615 17.72 6.79 45.38 2.85
660 2086 7.306399 GCATTTCAGTTGTCAATGAAACTCTTG 60.306 37.037 17.72 14.62 45.38 3.02
661 2087 7.389803 TTTCAGTTGTCAATGAAACTCTTGA 57.610 32.000 14.16 3.03 39.76 3.02
662 2088 7.389803 TTCAGTTGTCAATGAAACTCTTGAA 57.610 32.000 7.50 7.23 34.41 2.69
663 2089 7.389803 TCAGTTGTCAATGAAACTCTTGAAA 57.610 32.000 7.50 0.00 34.41 2.69
664 2090 7.825681 TCAGTTGTCAATGAAACTCTTGAAAA 58.174 30.769 7.50 0.00 34.41 2.29
665 2091 8.303156 TCAGTTGTCAATGAAACTCTTGAAAAA 58.697 29.630 7.50 0.00 34.41 1.94
695 2121 6.979817 TCAATTGTTCAGACCTGATTTTTGTG 59.020 34.615 5.13 0.00 39.64 3.33
706 2132 4.484236 CTGATTTTTGTGTGTGTGTGTGT 58.516 39.130 0.00 0.00 0.00 3.72
707 2133 4.233005 TGATTTTTGTGTGTGTGTGTGTG 58.767 39.130 0.00 0.00 0.00 3.82
708 2134 3.717400 TTTTTGTGTGTGTGTGTGTGT 57.283 38.095 0.00 0.00 0.00 3.72
709 2135 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
710 2136 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
711 2137 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
712 2138 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
713 2139 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
714 2140 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
725 2151 2.163211 TGTGTGTGTGTGTGTTGAATGG 59.837 45.455 0.00 0.00 0.00 3.16
742 2168 5.791666 TGAATGGCATTTTCTTAACATGCA 58.208 33.333 14.93 0.00 44.37 3.96
743 2169 6.228995 TGAATGGCATTTTCTTAACATGCAA 58.771 32.000 14.93 2.43 44.37 4.08
745 2171 8.039538 TGAATGGCATTTTCTTAACATGCAATA 58.960 29.630 14.93 0.61 44.37 1.90
746 2172 8.428186 AATGGCATTTTCTTAACATGCAATAG 57.572 30.769 6.96 0.00 44.37 1.73
747 2173 7.167924 TGGCATTTTCTTAACATGCAATAGA 57.832 32.000 11.58 0.00 44.37 1.98
748 2174 7.259882 TGGCATTTTCTTAACATGCAATAGAG 58.740 34.615 11.58 0.00 44.37 2.43
749 2175 7.122501 TGGCATTTTCTTAACATGCAATAGAGA 59.877 33.333 11.58 0.00 44.37 3.10
752 3026 9.512435 CATTTTCTTAACATGCAATAGAGAAGG 57.488 33.333 0.00 0.00 0.00 3.46
756 3030 7.044181 TCTTAACATGCAATAGAGAAGGACAG 58.956 38.462 0.00 0.00 0.00 3.51
783 3057 1.091537 AACGCGGATTACAATGTGGG 58.908 50.000 12.47 0.00 0.00 4.61
905 3183 0.318955 AAATCCTTGCGCACACTTGC 60.319 50.000 11.12 0.00 46.21 4.01
989 3269 0.320421 TTAGCCTTCGCGTTCAAGCT 60.320 50.000 5.77 11.25 41.18 3.74
990 3270 0.528924 TAGCCTTCGCGTTCAAGCTA 59.471 50.000 5.77 10.23 41.18 3.32
991 3271 0.737715 AGCCTTCGCGTTCAAGCTAG 60.738 55.000 5.77 0.00 41.18 3.42
992 3272 1.710339 CCTTCGCGTTCAAGCTAGC 59.290 57.895 6.62 6.62 34.40 3.42
993 3273 0.737715 CCTTCGCGTTCAAGCTAGCT 60.738 55.000 12.68 12.68 34.40 3.32
1008 3288 2.283298 CTAGCTAGTGCAATGGTGGTG 58.717 52.381 12.92 0.00 42.74 4.17
1655 3935 6.431234 ACTTACTTGATTCTTTAAGCACTGGG 59.569 38.462 0.00 0.00 28.88 4.45
1660 3940 7.451566 ACTTGATTCTTTAAGCACTGGGTAAAT 59.548 33.333 0.00 0.00 28.88 1.40
1751 4061 0.109086 CCTGAGCTGATCGTTCGTGT 60.109 55.000 0.00 0.00 0.00 4.49
1756 4066 2.784380 GAGCTGATCGTTCGTGTCATAC 59.216 50.000 0.00 0.00 0.00 2.39
1764 4074 2.473868 CGTTCGTGTCATACCATGTTGC 60.474 50.000 0.00 0.00 0.00 4.17
1765 4075 2.742053 GTTCGTGTCATACCATGTTGCT 59.258 45.455 0.00 0.00 0.00 3.91
1837 4150 9.776158 CAGCTTATAGGAGTACTAAACATATCG 57.224 37.037 0.00 0.00 34.79 2.92
1843 4156 6.817184 AGGAGTACTAAACATATCGTGCATT 58.183 36.000 0.00 0.00 0.00 3.56
1853 4166 1.495878 ATCGTGCATTCATCTCTCGC 58.504 50.000 0.00 0.00 0.00 5.03
2017 4331 5.241064 TGCCATTTTTGCATGCTTTTATTGT 59.759 32.000 20.33 0.00 32.85 2.71
2020 4334 7.361116 GCCATTTTTGCATGCTTTTATTGTAGT 60.361 33.333 20.33 0.00 0.00 2.73
2021 4335 9.149225 CCATTTTTGCATGCTTTTATTGTAGTA 57.851 29.630 20.33 0.00 0.00 1.82
2053 4367 6.321181 TCTTCTTGTGCAAACTAACCATTTCT 59.679 34.615 0.00 0.00 0.00 2.52
2054 4368 6.463995 TCTTGTGCAAACTAACCATTTCTT 57.536 33.333 0.00 0.00 0.00 2.52
2058 4372 6.039616 TGTGCAAACTAACCATTTCTTGTTC 58.960 36.000 0.00 0.00 0.00 3.18
2063 4377 7.115378 GCAAACTAACCATTTCTTGTTCATCTG 59.885 37.037 0.00 0.00 0.00 2.90
2070 4384 7.433680 ACCATTTCTTGTTCATCTGGTTAAAC 58.566 34.615 0.00 0.00 31.69 2.01
2075 4389 5.827797 TCTTGTTCATCTGGTTAAACTGCTT 59.172 36.000 0.00 0.00 0.00 3.91
2076 4390 6.995686 TCTTGTTCATCTGGTTAAACTGCTTA 59.004 34.615 0.00 0.00 0.00 3.09
2078 4392 5.472137 TGTTCATCTGGTTAAACTGCTTACC 59.528 40.000 0.00 0.00 0.00 2.85
2079 4393 5.235850 TCATCTGGTTAAACTGCTTACCA 57.764 39.130 0.00 0.00 0.00 3.25
2091 4405 3.751518 CTGCTTACCAGTAACCAAAGGT 58.248 45.455 0.00 0.00 35.45 3.50
2092 4406 3.746940 TGCTTACCAGTAACCAAAGGTC 58.253 45.455 0.00 0.00 33.12 3.85
2093 4407 3.393278 TGCTTACCAGTAACCAAAGGTCT 59.607 43.478 0.00 0.00 33.12 3.85
2096 4413 5.803470 GCTTACCAGTAACCAAAGGTCTGAT 60.803 44.000 6.49 0.00 33.12 2.90
2103 4420 3.814504 ACCAAAGGTCTGATCATGGTT 57.185 42.857 10.07 0.00 37.92 3.67
3025 5372 3.740044 CGTGAACGTGATTGCCTATTT 57.260 42.857 0.00 0.00 34.11 1.40
3026 5373 3.416277 CGTGAACGTGATTGCCTATTTG 58.584 45.455 0.00 0.00 34.11 2.32
3027 5374 3.171277 GTGAACGTGATTGCCTATTTGC 58.829 45.455 0.00 0.00 0.00 3.68
3028 5375 2.163412 TGAACGTGATTGCCTATTTGCC 59.837 45.455 0.00 0.00 0.00 4.52
3029 5376 2.128771 ACGTGATTGCCTATTTGCCT 57.871 45.000 0.00 0.00 0.00 4.75
3032 5379 2.164219 CGTGATTGCCTATTTGCCTTGT 59.836 45.455 0.00 0.00 0.00 3.16
3110 5473 9.394477 GATATTTTATTTCGATTAACCACCTGC 57.606 33.333 0.00 0.00 0.00 4.85
3111 5474 4.868450 TTATTTCGATTAACCACCTGCG 57.132 40.909 0.00 0.00 0.00 5.18
3112 5475 2.459060 TTTCGATTAACCACCTGCGA 57.541 45.000 0.00 0.00 0.00 5.10
3119 5497 4.493545 CGATTAACCACCTGCGATTACAAC 60.494 45.833 0.00 0.00 0.00 3.32
3129 5507 5.109210 CCTGCGATTACAACTCTACAATGA 58.891 41.667 0.00 0.00 0.00 2.57
3203 5581 0.179081 GACCATGTAGCGAGGGTTCC 60.179 60.000 0.00 0.00 32.77 3.62
3331 5712 2.126031 GTCGCCGACCACTTCTCC 60.126 66.667 5.81 0.00 0.00 3.71
3334 5715 4.097361 GCCGACCACTTCTCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
3385 5766 3.994853 GGGTCCGTCGTCCCGTTT 61.995 66.667 6.93 0.00 33.97 3.60
3465 5846 5.948992 AAGAAATCAGTACTCCAAAGTGC 57.051 39.130 0.00 0.00 38.30 4.40
3486 5867 2.799978 CAGTGTAGTGCGTCACATCAAA 59.200 45.455 11.58 0.00 36.74 2.69
3492 5873 5.576774 TGTAGTGCGTCACATCAAAAGATAG 59.423 40.000 11.58 0.00 36.74 2.08
3527 5911 1.145803 GACCAAGTGTCCACGCTTAC 58.854 55.000 5.22 0.00 44.06 2.34
3674 6059 5.050490 GCTAGGAAACAGATCTGCGATTAA 58.950 41.667 22.83 4.09 0.00 1.40
3985 6399 1.091537 GGCGATCCTCTCCTCTATCG 58.908 60.000 0.00 0.00 43.05 2.92
3997 6411 1.534175 CCTCTATCGTCGCCACAACTC 60.534 57.143 0.00 0.00 0.00 3.01
4004 6418 2.738521 CGCCACAACTCGGTCCTG 60.739 66.667 0.00 0.00 0.00 3.86
4007 6421 1.293498 CCACAACTCGGTCCTGGAG 59.707 63.158 0.00 0.00 37.54 3.86
4008 6422 1.472662 CCACAACTCGGTCCTGGAGT 61.473 60.000 0.00 0.00 46.27 3.85
4009 6423 1.254026 CACAACTCGGTCCTGGAGTA 58.746 55.000 0.00 0.00 43.66 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.585416 AGAATTGCATTTCTCAACCTTGTTT 58.415 32.000 16.26 0.00 29.99 2.83
13 14 8.761575 TGAAATTAGAATTGCATTTCTCAACC 57.238 30.769 23.34 12.68 37.66 3.77
15 16 8.587608 ACCTGAAATTAGAATTGCATTTCTCAA 58.412 29.630 23.34 16.61 37.66 3.02
47 48 7.340487 ACTTCAGAGATTTGATTATTGGGTTCC 59.660 37.037 0.00 0.00 0.00 3.62
98 99 9.542462 CAAATATTTAGGAACGAATGGAGTAGA 57.458 33.333 0.00 0.00 0.00 2.59
99 100 9.326413 ACAAATATTTAGGAACGAATGGAGTAG 57.674 33.333 0.00 0.00 0.00 2.57
100 101 9.321562 GACAAATATTTAGGAACGAATGGAGTA 57.678 33.333 0.00 0.00 0.00 2.59
101 102 8.047310 AGACAAATATTTAGGAACGAATGGAGT 58.953 33.333 0.00 0.00 0.00 3.85
102 103 8.438676 AGACAAATATTTAGGAACGAATGGAG 57.561 34.615 0.00 0.00 0.00 3.86
103 104 8.801882 AAGACAAATATTTAGGAACGAATGGA 57.198 30.769 0.00 0.00 0.00 3.41
104 105 9.503427 GAAAGACAAATATTTAGGAACGAATGG 57.497 33.333 0.00 0.00 0.00 3.16
170 171 9.262358 GGGTGAATCTACACTCTAAAATATGTC 57.738 37.037 0.00 0.00 38.14 3.06
171 172 8.768397 TGGGTGAATCTACACTCTAAAATATGT 58.232 33.333 0.00 0.00 41.33 2.29
172 173 9.784531 ATGGGTGAATCTACACTCTAAAATATG 57.215 33.333 0.00 0.00 41.33 1.78
175 176 9.533831 AAAATGGGTGAATCTACACTCTAAAAT 57.466 29.630 0.00 0.00 41.33 1.82
176 177 8.792633 CAAAATGGGTGAATCTACACTCTAAAA 58.207 33.333 0.00 0.00 41.33 1.52
177 178 7.094377 GCAAAATGGGTGAATCTACACTCTAAA 60.094 37.037 0.00 0.00 41.33 1.85
178 179 6.374333 GCAAAATGGGTGAATCTACACTCTAA 59.626 38.462 0.00 0.00 41.33 2.10
179 180 5.880332 GCAAAATGGGTGAATCTACACTCTA 59.120 40.000 0.00 0.00 41.33 2.43
180 181 4.702131 GCAAAATGGGTGAATCTACACTCT 59.298 41.667 0.00 0.00 41.33 3.24
181 182 4.702131 AGCAAAATGGGTGAATCTACACTC 59.298 41.667 0.00 0.00 41.16 3.51
182 183 4.666512 AGCAAAATGGGTGAATCTACACT 58.333 39.130 0.00 0.00 40.22 3.55
183 184 4.142381 GGAGCAAAATGGGTGAATCTACAC 60.142 45.833 0.00 0.00 39.70 2.90
184 185 4.016444 GGAGCAAAATGGGTGAATCTACA 58.984 43.478 0.00 0.00 0.00 2.74
185 186 3.065371 CGGAGCAAAATGGGTGAATCTAC 59.935 47.826 0.00 0.00 0.00 2.59
186 187 3.278574 CGGAGCAAAATGGGTGAATCTA 58.721 45.455 0.00 0.00 0.00 1.98
187 188 2.094675 CGGAGCAAAATGGGTGAATCT 58.905 47.619 0.00 0.00 0.00 2.40
188 189 1.818674 ACGGAGCAAAATGGGTGAATC 59.181 47.619 0.00 0.00 0.00 2.52
189 190 1.923356 ACGGAGCAAAATGGGTGAAT 58.077 45.000 0.00 0.00 0.00 2.57
190 191 2.570415 TACGGAGCAAAATGGGTGAA 57.430 45.000 0.00 0.00 0.00 3.18
191 192 2.290641 ACATACGGAGCAAAATGGGTGA 60.291 45.455 0.00 0.00 0.00 4.02
192 193 2.091541 ACATACGGAGCAAAATGGGTG 58.908 47.619 0.00 0.00 0.00 4.61
193 194 2.507407 ACATACGGAGCAAAATGGGT 57.493 45.000 0.00 0.00 0.00 4.51
194 195 3.541632 ACTACATACGGAGCAAAATGGG 58.458 45.455 0.00 0.00 0.00 4.00
195 196 4.188462 TGACTACATACGGAGCAAAATGG 58.812 43.478 0.00 0.00 0.00 3.16
196 197 4.870426 ACTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
197 198 5.086104 ACTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
198 199 4.530710 ACTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
199 200 4.242475 CAACTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
200 201 3.257375 ACAACTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
201 202 2.823747 ACAACTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
202 203 3.505464 ACAACTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
203 204 5.055642 TCAACAACTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
204 205 5.456548 TTCAACAACTGACTACATACGGA 57.543 39.130 0.00 0.00 32.21 4.69
205 206 6.590292 AGATTTCAACAACTGACTACATACGG 59.410 38.462 0.00 0.00 32.21 4.02
206 207 7.542477 AGAGATTTCAACAACTGACTACATACG 59.458 37.037 0.00 0.00 32.21 3.06
207 208 8.764524 AGAGATTTCAACAACTGACTACATAC 57.235 34.615 0.00 0.00 32.21 2.39
209 210 8.807118 TCTAGAGATTTCAACAACTGACTACAT 58.193 33.333 0.00 0.00 32.21 2.29
210 211 8.178313 TCTAGAGATTTCAACAACTGACTACA 57.822 34.615 0.00 0.00 32.21 2.74
211 212 9.477484 TTTCTAGAGATTTCAACAACTGACTAC 57.523 33.333 0.00 0.00 32.21 2.73
212 213 9.698309 CTTTCTAGAGATTTCAACAACTGACTA 57.302 33.333 0.00 0.00 32.21 2.59
213 214 8.424918 TCTTTCTAGAGATTTCAACAACTGACT 58.575 33.333 0.00 0.00 32.21 3.41
214 215 8.491950 GTCTTTCTAGAGATTTCAACAACTGAC 58.508 37.037 0.00 0.00 32.21 3.51
215 216 8.204160 TGTCTTTCTAGAGATTTCAACAACTGA 58.796 33.333 0.00 0.00 0.00 3.41
216 217 8.370493 TGTCTTTCTAGAGATTTCAACAACTG 57.630 34.615 0.00 0.00 0.00 3.16
217 218 8.964476 TTGTCTTTCTAGAGATTTCAACAACT 57.036 30.769 0.00 0.00 0.00 3.16
237 238 9.981460 ACTCCCTTCATTTCTAAATATTTGTCT 57.019 29.630 11.05 0.00 0.00 3.41
241 242 9.920946 TGCTACTCCCTTCATTTCTAAATATTT 57.079 29.630 5.89 5.89 0.00 1.40
244 245 9.998106 GTATGCTACTCCCTTCATTTCTAAATA 57.002 33.333 0.00 0.00 0.00 1.40
245 246 8.494433 TGTATGCTACTCCCTTCATTTCTAAAT 58.506 33.333 0.00 0.00 0.00 1.40
246 247 7.857456 TGTATGCTACTCCCTTCATTTCTAAA 58.143 34.615 0.00 0.00 0.00 1.85
247 248 7.432148 TGTATGCTACTCCCTTCATTTCTAA 57.568 36.000 0.00 0.00 0.00 2.10
248 249 7.432148 TTGTATGCTACTCCCTTCATTTCTA 57.568 36.000 0.00 0.00 0.00 2.10
249 250 5.957771 TGTATGCTACTCCCTTCATTTCT 57.042 39.130 0.00 0.00 0.00 2.52
250 251 6.599638 ACTTTGTATGCTACTCCCTTCATTTC 59.400 38.462 0.00 0.00 0.00 2.17
251 252 6.485171 ACTTTGTATGCTACTCCCTTCATTT 58.515 36.000 0.00 0.00 0.00 2.32
252 253 6.067217 ACTTTGTATGCTACTCCCTTCATT 57.933 37.500 0.00 0.00 0.00 2.57
253 254 5.700402 ACTTTGTATGCTACTCCCTTCAT 57.300 39.130 0.00 0.00 0.00 2.57
254 255 6.382859 TCATACTTTGTATGCTACTCCCTTCA 59.617 38.462 11.57 0.00 0.00 3.02
255 256 6.817184 TCATACTTTGTATGCTACTCCCTTC 58.183 40.000 11.57 0.00 0.00 3.46
256 257 6.384305 ACTCATACTTTGTATGCTACTCCCTT 59.616 38.462 11.57 0.00 0.00 3.95
257 258 5.900123 ACTCATACTTTGTATGCTACTCCCT 59.100 40.000 11.57 0.00 0.00 4.20
258 259 6.163135 ACTCATACTTTGTATGCTACTCCC 57.837 41.667 11.57 0.00 0.00 4.30
259 260 8.167605 TCTACTCATACTTTGTATGCTACTCC 57.832 38.462 11.57 0.00 0.00 3.85
260 261 9.058174 TCTCTACTCATACTTTGTATGCTACTC 57.942 37.037 11.57 0.00 0.00 2.59
261 262 8.842280 GTCTCTACTCATACTTTGTATGCTACT 58.158 37.037 11.57 0.00 0.00 2.57
262 263 8.622157 TGTCTCTACTCATACTTTGTATGCTAC 58.378 37.037 11.57 4.50 0.00 3.58
263 264 8.622157 GTGTCTCTACTCATACTTTGTATGCTA 58.378 37.037 11.57 4.64 0.00 3.49
264 265 7.122799 TGTGTCTCTACTCATACTTTGTATGCT 59.877 37.037 11.57 3.89 0.00 3.79
316 1706 9.293404 AGTGCATGATAGTGAGCATAAATAAAT 57.707 29.630 0.00 0.00 39.43 1.40
317 1707 8.681486 AGTGCATGATAGTGAGCATAAATAAA 57.319 30.769 0.00 0.00 39.43 1.40
353 1743 8.234546 CGCAAAGGAGTACAATACAATTTACTT 58.765 33.333 0.00 0.00 0.00 2.24
374 1764 3.680620 CTGGGCTCCGGATCGCAAA 62.681 63.158 23.14 7.72 29.82 3.68
389 1779 4.486503 GGGAGCAGCTGAGCCTGG 62.487 72.222 20.43 0.00 33.44 4.45
482 1907 6.208204 CCATCTCCAAATCTTTTCACTGAACT 59.792 38.462 0.00 0.00 0.00 3.01
488 1913 5.316327 GGACCATCTCCAAATCTTTTCAC 57.684 43.478 0.00 0.00 39.21 3.18
517 1942 5.757320 TCATTTGACCACGAAATTTTGCATT 59.243 32.000 5.27 0.00 0.00 3.56
518 1943 5.177327 GTCATTTGACCACGAAATTTTGCAT 59.823 36.000 5.27 0.00 39.07 3.96
526 1951 3.885901 TGGAATGTCATTTGACCACGAAA 59.114 39.130 8.16 0.00 44.15 3.46
530 1955 3.420893 TCCTGGAATGTCATTTGACCAC 58.579 45.455 8.16 0.50 44.15 4.16
592 2018 6.896860 TCACATGAACCCAATAATCAAATCCT 59.103 34.615 0.00 0.00 0.00 3.24
609 2035 6.573664 ATTCGAATTTCAGGTTCACATGAA 57.426 33.333 4.39 2.96 43.72 2.57
610 2036 6.380995 CAATTCGAATTTCAGGTTCACATGA 58.619 36.000 20.56 0.00 34.60 3.07
611 2037 5.061311 GCAATTCGAATTTCAGGTTCACATG 59.939 40.000 20.56 6.92 0.00 3.21
612 2038 5.163513 GCAATTCGAATTTCAGGTTCACAT 58.836 37.500 20.56 0.00 0.00 3.21
614 2040 4.545610 TGCAATTCGAATTTCAGGTTCAC 58.454 39.130 20.56 3.39 0.00 3.18
616 2042 6.365789 TGAAATGCAATTCGAATTTCAGGTTC 59.634 34.615 25.65 25.65 42.44 3.62
617 2043 6.222389 TGAAATGCAATTCGAATTTCAGGTT 58.778 32.000 23.80 19.89 42.44 3.50
618 2044 5.782047 TGAAATGCAATTCGAATTTCAGGT 58.218 33.333 23.80 15.79 42.44 4.00
621 2047 6.700960 ACAACTGAAATGCAATTCGAATTTCA 59.299 30.769 22.33 22.33 44.11 2.69
622 2048 7.096106 TGACAACTGAAATGCAATTCGAATTTC 60.096 33.333 20.56 16.46 39.61 2.17
623 2049 6.700960 TGACAACTGAAATGCAATTCGAATTT 59.299 30.769 20.56 7.02 33.67 1.82
624 2050 6.215121 TGACAACTGAAATGCAATTCGAATT 58.785 32.000 17.60 17.60 33.67 2.17
625 2051 5.771469 TGACAACTGAAATGCAATTCGAAT 58.229 33.333 4.39 4.39 33.67 3.34
626 2052 5.180367 TGACAACTGAAATGCAATTCGAA 57.820 34.783 9.85 0.00 33.67 3.71
627 2053 4.827304 TGACAACTGAAATGCAATTCGA 57.173 36.364 9.85 0.00 33.67 3.71
628 2054 5.630264 TCATTGACAACTGAAATGCAATTCG 59.370 36.000 9.85 7.28 33.67 3.34
629 2055 7.410800 TTCATTGACAACTGAAATGCAATTC 57.589 32.000 7.59 7.59 33.67 2.17
630 2056 7.496591 AGTTTCATTGACAACTGAAATGCAATT 59.503 29.630 19.49 0.00 41.80 2.32
631 2057 6.987992 AGTTTCATTGACAACTGAAATGCAAT 59.012 30.769 19.49 0.00 41.80 3.56
632 2058 6.339730 AGTTTCATTGACAACTGAAATGCAA 58.660 32.000 19.49 0.00 41.80 4.08
633 2059 5.904941 AGTTTCATTGACAACTGAAATGCA 58.095 33.333 19.49 0.00 41.80 3.96
634 2060 6.211515 AGAGTTTCATTGACAACTGAAATGC 58.788 36.000 19.49 15.98 41.80 3.56
635 2061 7.916977 TCAAGAGTTTCATTGACAACTGAAATG 59.083 33.333 19.49 15.70 41.80 2.32
636 2062 7.999679 TCAAGAGTTTCATTGACAACTGAAAT 58.000 30.769 19.49 12.97 41.80 2.17
637 2063 7.389803 TCAAGAGTTTCATTGACAACTGAAA 57.610 32.000 15.67 15.67 38.64 2.69
638 2064 7.389803 TTCAAGAGTTTCATTGACAACTGAA 57.610 32.000 14.71 11.41 35.25 3.02
639 2065 7.389803 TTTCAAGAGTTTCATTGACAACTGA 57.610 32.000 14.71 7.78 35.25 3.41
640 2066 8.464770 TTTTTCAAGAGTTTCATTGACAACTG 57.535 30.769 14.71 6.25 35.25 3.16
665 2091 9.617523 AAAATCAGGTCTGAACAATTGATTTTT 57.382 25.926 19.92 10.42 42.27 1.94
666 2092 9.617523 AAAAATCAGGTCTGAACAATTGATTTT 57.382 25.926 19.92 19.92 44.05 1.82
667 2093 9.048446 CAAAAATCAGGTCTGAACAATTGATTT 57.952 29.630 13.59 12.85 43.58 2.17
668 2094 8.206189 ACAAAAATCAGGTCTGAACAATTGATT 58.794 29.630 13.59 2.61 43.58 2.57
669 2095 7.654520 CACAAAAATCAGGTCTGAACAATTGAT 59.345 33.333 13.59 0.00 43.58 2.57
670 2096 6.979817 CACAAAAATCAGGTCTGAACAATTGA 59.020 34.615 13.59 0.00 43.58 2.57
679 2105 4.142403 ACACACACACAAAAATCAGGTCTG 60.142 41.667 0.00 0.00 0.00 3.51
684 2110 4.324135 CACACACACACACACAAAAATCAG 59.676 41.667 0.00 0.00 0.00 2.90
695 2121 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
706 2132 1.133982 GCCATTCAACACACACACACA 59.866 47.619 0.00 0.00 0.00 3.72
707 2133 1.133982 TGCCATTCAACACACACACAC 59.866 47.619 0.00 0.00 0.00 3.82
708 2134 1.467920 TGCCATTCAACACACACACA 58.532 45.000 0.00 0.00 0.00 3.72
709 2135 2.798976 ATGCCATTCAACACACACAC 57.201 45.000 0.00 0.00 0.00 3.82
710 2136 3.815856 AAATGCCATTCAACACACACA 57.184 38.095 0.00 0.00 0.00 3.72
711 2137 4.370917 AGAAAATGCCATTCAACACACAC 58.629 39.130 0.00 0.00 0.00 3.82
712 2138 4.669206 AGAAAATGCCATTCAACACACA 57.331 36.364 0.00 0.00 0.00 3.72
713 2139 6.478344 TGTTAAGAAAATGCCATTCAACACAC 59.522 34.615 0.00 0.00 0.00 3.82
714 2140 6.577103 TGTTAAGAAAATGCCATTCAACACA 58.423 32.000 0.00 0.00 0.00 3.72
725 2151 8.915871 TTCTCTATTGCATGTTAAGAAAATGC 57.084 30.769 7.30 7.30 45.51 3.56
742 2168 6.391537 GTTTCTTCGTCTGTCCTTCTCTATT 58.608 40.000 0.00 0.00 0.00 1.73
743 2169 5.392165 CGTTTCTTCGTCTGTCCTTCTCTAT 60.392 44.000 0.00 0.00 0.00 1.98
745 2171 3.304794 CGTTTCTTCGTCTGTCCTTCTCT 60.305 47.826 0.00 0.00 0.00 3.10
746 2172 2.981140 CGTTTCTTCGTCTGTCCTTCTC 59.019 50.000 0.00 0.00 0.00 2.87
747 2173 2.862921 GCGTTTCTTCGTCTGTCCTTCT 60.863 50.000 0.00 0.00 0.00 2.85
748 2174 1.456165 GCGTTTCTTCGTCTGTCCTTC 59.544 52.381 0.00 0.00 0.00 3.46
749 2175 1.499049 GCGTTTCTTCGTCTGTCCTT 58.501 50.000 0.00 0.00 0.00 3.36
752 3026 0.662374 TCCGCGTTTCTTCGTCTGTC 60.662 55.000 4.92 0.00 0.00 3.51
756 3030 1.987770 TGTAATCCGCGTTTCTTCGTC 59.012 47.619 4.92 0.00 0.00 4.20
783 3057 2.577450 GCGGTAAAATTGTGGACGAAC 58.423 47.619 0.00 0.00 0.00 3.95
905 3183 0.453793 TCTGTGGTTTGGTTTGTGCG 59.546 50.000 0.00 0.00 0.00 5.34
908 3186 1.111277 GCCTCTGTGGTTTGGTTTGT 58.889 50.000 0.00 0.00 38.35 2.83
954 3232 1.334689 GCTAACCCGTTTGTGTTGAGC 60.335 52.381 0.00 0.00 0.00 4.26
960 3240 0.515564 CGAAGGCTAACCCGTTTGTG 59.484 55.000 0.00 0.00 39.21 3.33
989 3269 1.065491 CCACCACCATTGCACTAGCTA 60.065 52.381 0.00 0.00 42.74 3.32
990 3270 0.322816 CCACCACCATTGCACTAGCT 60.323 55.000 0.00 0.00 42.74 3.32
991 3271 1.937546 GCCACCACCATTGCACTAGC 61.938 60.000 0.00 0.00 42.57 3.42
992 3272 1.315257 GGCCACCACCATTGCACTAG 61.315 60.000 0.00 0.00 0.00 2.57
993 3273 1.304052 GGCCACCACCATTGCACTA 60.304 57.895 0.00 0.00 0.00 2.74
1008 3288 2.044946 AACGGCTCCTCAATGGCC 60.045 61.111 0.00 0.00 42.18 5.36
1655 3935 5.104485 ACTCTGGGTAACATCAGGGATTTAC 60.104 44.000 0.00 0.00 35.20 2.01
1660 3940 2.642171 ACTCTGGGTAACATCAGGGA 57.358 50.000 0.00 0.00 35.20 4.20
1821 4134 7.694388 TGAATGCACGATATGTTTAGTACTC 57.306 36.000 0.00 0.00 0.00 2.59
1823 4136 8.299262 AGATGAATGCACGATATGTTTAGTAC 57.701 34.615 0.00 0.00 0.00 2.73
1837 4150 1.931906 TGAGCGAGAGATGAATGCAC 58.068 50.000 0.00 0.00 0.00 4.57
1843 4156 2.030096 GCTGATGATGAGCGAGAGATGA 60.030 50.000 0.00 0.00 0.00 2.92
1853 4166 3.439129 TGCACAAAAGAGCTGATGATGAG 59.561 43.478 0.00 0.00 0.00 2.90
2017 4331 8.148351 AGTTTGCACAAGAAGAACAGTATACTA 58.852 33.333 4.74 0.00 0.00 1.82
2020 4334 8.770828 GTTAGTTTGCACAAGAAGAACAGTATA 58.229 33.333 0.00 0.00 0.00 1.47
2021 4335 7.255139 GGTTAGTTTGCACAAGAAGAACAGTAT 60.255 37.037 0.00 0.00 0.00 2.12
2033 4347 5.971763 ACAAGAAATGGTTAGTTTGCACAA 58.028 33.333 0.00 0.00 0.00 3.33
2053 4367 6.016610 GGTAAGCAGTTTAACCAGATGAACAA 60.017 38.462 0.00 0.00 0.00 2.83
2054 4368 5.472137 GGTAAGCAGTTTAACCAGATGAACA 59.528 40.000 0.00 0.00 0.00 3.18
2058 4372 5.003804 ACTGGTAAGCAGTTTAACCAGATG 58.996 41.667 23.30 2.56 39.90 2.90
2063 4377 5.065235 TGGTTACTGGTAAGCAGTTTAACC 58.935 41.667 17.70 11.93 45.23 2.85
2075 4389 4.841813 TGATCAGACCTTTGGTTACTGGTA 59.158 41.667 0.00 0.00 35.25 3.25
2076 4390 3.650942 TGATCAGACCTTTGGTTACTGGT 59.349 43.478 0.00 0.00 35.25 4.00
2078 4392 4.637534 CCATGATCAGACCTTTGGTTACTG 59.362 45.833 0.09 0.00 35.25 2.74
2079 4393 4.289672 ACCATGATCAGACCTTTGGTTACT 59.710 41.667 10.07 0.00 35.25 2.24
2080 4394 4.589908 ACCATGATCAGACCTTTGGTTAC 58.410 43.478 10.07 0.00 35.25 2.50
2081 4395 4.927267 ACCATGATCAGACCTTTGGTTA 57.073 40.909 10.07 0.00 35.25 2.85
2082 4396 3.814504 ACCATGATCAGACCTTTGGTT 57.185 42.857 10.07 0.00 35.25 3.67
2083 4397 3.814504 AACCATGATCAGACCTTTGGT 57.185 42.857 10.07 10.07 39.07 3.67
2084 4398 4.848357 AGTAACCATGATCAGACCTTTGG 58.152 43.478 8.86 8.86 0.00 3.28
2085 4399 6.644347 AGTAGTAACCATGATCAGACCTTTG 58.356 40.000 0.09 0.00 0.00 2.77
2103 4420 8.873144 AGTCCATAACCAAAGTTACAAGTAGTA 58.127 33.333 0.00 0.00 41.19 1.82
2123 4470 1.685765 TACGCCTCCTGCAGTCCAT 60.686 57.895 13.81 0.00 41.33 3.41
2487 4834 3.663176 GTGACGACGGACACGGGA 61.663 66.667 10.57 0.00 46.48 5.14
3022 5369 3.430473 TTGTCCGGACAAGGCAAAT 57.570 47.368 39.59 0.00 45.42 2.32
3023 5370 4.988744 TTGTCCGGACAAGGCAAA 57.011 50.000 39.59 21.79 45.42 3.68
3032 5379 9.519191 AAATATATCATCAAATCATTGTCCGGA 57.481 29.630 0.00 0.00 37.79 5.14
3102 5465 1.623811 AGAGTTGTAATCGCAGGTGGT 59.376 47.619 0.00 0.00 0.00 4.16
3106 5469 5.109210 TCATTGTAGAGTTGTAATCGCAGG 58.891 41.667 0.00 0.00 0.00 4.85
3107 5470 6.311445 AGTTCATTGTAGAGTTGTAATCGCAG 59.689 38.462 0.00 0.00 0.00 5.18
3108 5471 6.090763 CAGTTCATTGTAGAGTTGTAATCGCA 59.909 38.462 0.00 0.00 0.00 5.10
3109 5472 6.455646 CCAGTTCATTGTAGAGTTGTAATCGC 60.456 42.308 0.00 0.00 0.00 4.58
3110 5473 6.590292 ACCAGTTCATTGTAGAGTTGTAATCG 59.410 38.462 0.00 0.00 0.00 3.34
3111 5474 7.624344 GCACCAGTTCATTGTAGAGTTGTAATC 60.624 40.741 0.00 0.00 0.00 1.75
3112 5475 6.149474 GCACCAGTTCATTGTAGAGTTGTAAT 59.851 38.462 0.00 0.00 0.00 1.89
3119 5497 2.413112 CGTGCACCAGTTCATTGTAGAG 59.587 50.000 12.15 0.00 0.00 2.43
3334 5715 3.781770 GAGCTGCCCCGTGATCGAG 62.782 68.421 0.00 0.00 39.71 4.04
3385 5766 1.228245 GTTCTTCAGCCTGCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
3465 5846 2.064573 TGATGTGACGCACTACACTG 57.935 50.000 10.54 0.00 37.81 3.66
3492 5873 5.521735 CACTTGGTCATGCAGATAGTCTTAC 59.478 44.000 0.00 0.00 0.00 2.34
3509 5893 0.756903 AGTAAGCGTGGACACTTGGT 59.243 50.000 0.56 0.00 0.00 3.67
3599 5983 7.480542 CCTACGACCTCGAAATTAATTTGTTTG 59.519 37.037 17.98 8.74 43.02 2.93
3674 6059 0.822164 CTTCCCCAACTCCGACGTAT 59.178 55.000 0.00 0.00 0.00 3.06
3906 6318 2.738521 CCCGGTGCACTGAACTCG 60.739 66.667 27.46 15.13 0.00 4.18
3985 6399 2.737376 GGACCGAGTTGTGGCGAC 60.737 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.