Multiple sequence alignment - TraesCS5A01G481300

Loading Multiple Alignment...

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 TraesCS5A01G481300 chr5A 100.000 3968 0 0 1 3968 653847063 653851030 0.000000e+00 7328.0
1 TraesCS5A01G481300 chr5A 100.000 31 0 0 106 136 653847036 653847006 1.540000e-04 58.4
2 TraesCS5A01G481300 chr5D 91.890 3613 165 56 416 3968 526686839 526690383 0.000000e+00 4931.0
3 TraesCS5A01G481300 chr5D 84.530 181 20 5 3746 3922 526752802 526752978 5.270000e-39 172.0
4 TraesCS5A01G481300 chr5D 94.667 75 4 0 24 98 526661441 526661367 2.510000e-22 117.0
5 TraesCS5A01G481300 chr5B 89.662 2989 149 72 217 3143 662453387 662456277 0.000000e+00 3661.0
6 TraesCS5A01G481300 chr5B 93.510 832 38 10 3140 3968 662456398 662457216 0.000000e+00 1223.0


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 TraesCS5A01G481300 chr5A 653847063 653851030 3967 False 7328 7328 100.000 1 3968 1 chr5A.!!$F1 3967
1 TraesCS5A01G481300 chr5D 526686839 526690383 3544 False 4931 4931 91.890 416 3968 1 chr5D.!!$F1 3552
2 TraesCS5A01G481300 chr5B 662453387 662457216 3829 False 2442 3661 91.586 217 3968 2 chr5B.!!$F1 3751

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
22 23 0.038890 TGTGAAATGAATGGCCCCGA 59.961 50.0 0.00 0.00 0.00 5.14 F
872 913 0.039035 CCGGGAGAGCTAGCTAGGAT 59.961 60.0 19.38 3.90 0.00 3.24 F
898 939 0.041238 CCTACACAGGAGGAGGTGGA 59.959 60.0 0.00 0.00 45.91 4.02 F
1328 1385 0.110912 GACGACGACGACGAGTTCTT 60.111 55.0 25.15 2.32 42.66 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1484 0.320421 CCTGTCCTGGTACACCGTTG 60.320 60.0 0.0 0.0 39.43 4.10 R
1845 1911 0.391661 CGCAGTGTATGAGCAGGGTT 60.392 55.0 0.0 0.0 0.00 4.11 R
2379 2445 0.458669 CATCCCACTTGGCAGCAATC 59.541 55.0 0.0 0.0 0.00 2.67 R
3072 3161 1.361204 TCCATCAACTCTGCTCCCAA 58.639 50.0 0.0 0.0 0.00 4.12 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
19 20 2.896745 GGATGTGAAATGAATGGCCC 57.103 50.000 0.00 0.00 0.00 5.80
20 21 1.413812 GGATGTGAAATGAATGGCCCC 59.586 52.381 0.00 0.00 0.00 5.80
21 22 1.067516 GATGTGAAATGAATGGCCCCG 59.932 52.381 0.00 0.00 0.00 5.73
22 23 0.038890 TGTGAAATGAATGGCCCCGA 59.961 50.000 0.00 0.00 0.00 5.14
23 24 1.341877 TGTGAAATGAATGGCCCCGAT 60.342 47.619 0.00 0.00 0.00 4.18
24 25 1.338020 GTGAAATGAATGGCCCCGATC 59.662 52.381 0.00 0.00 0.00 3.69
25 26 1.215173 TGAAATGAATGGCCCCGATCT 59.785 47.619 0.00 0.00 0.00 2.75
26 27 1.610522 GAAATGAATGGCCCCGATCTG 59.389 52.381 0.00 0.00 0.00 2.90
27 28 0.825010 AATGAATGGCCCCGATCTGC 60.825 55.000 0.00 0.00 0.00 4.26
28 29 1.713005 ATGAATGGCCCCGATCTGCT 61.713 55.000 0.00 0.00 0.00 4.24
29 30 1.152881 GAATGGCCCCGATCTGCTT 60.153 57.895 0.00 0.00 0.00 3.91
30 31 1.152881 AATGGCCCCGATCTGCTTC 60.153 57.895 0.00 0.00 0.00 3.86
31 32 1.639635 AATGGCCCCGATCTGCTTCT 61.640 55.000 0.00 0.00 0.00 2.85
32 33 1.639635 ATGGCCCCGATCTGCTTCTT 61.640 55.000 0.00 0.00 0.00 2.52
33 34 1.524849 GGCCCCGATCTGCTTCTTC 60.525 63.158 0.00 0.00 0.00 2.87
34 35 1.524849 GCCCCGATCTGCTTCTTCC 60.525 63.158 0.00 0.00 0.00 3.46
35 36 1.907739 CCCCGATCTGCTTCTTCCA 59.092 57.895 0.00 0.00 0.00 3.53
36 37 0.462759 CCCCGATCTGCTTCTTCCAC 60.463 60.000 0.00 0.00 0.00 4.02
37 38 0.462759 CCCGATCTGCTTCTTCCACC 60.463 60.000 0.00 0.00 0.00 4.61
38 39 0.539051 CCGATCTGCTTCTTCCACCT 59.461 55.000 0.00 0.00 0.00 4.00
39 40 1.472376 CCGATCTGCTTCTTCCACCTC 60.472 57.143 0.00 0.00 0.00 3.85
40 41 1.472376 CGATCTGCTTCTTCCACCTCC 60.472 57.143 0.00 0.00 0.00 4.30
41 42 0.915364 ATCTGCTTCTTCCACCTCCC 59.085 55.000 0.00 0.00 0.00 4.30
42 43 1.078848 CTGCTTCTTCCACCTCCCG 60.079 63.158 0.00 0.00 0.00 5.14
43 44 1.535444 TGCTTCTTCCACCTCCCGA 60.535 57.895 0.00 0.00 0.00 5.14
44 45 1.079057 GCTTCTTCCACCTCCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
45 46 1.215647 CTTCTTCCACCTCCCGACG 59.784 63.158 0.00 0.00 0.00 5.12
46 47 2.837371 CTTCTTCCACCTCCCGACGC 62.837 65.000 0.00 0.00 0.00 5.19
47 48 3.691342 CTTCCACCTCCCGACGCA 61.691 66.667 0.00 0.00 0.00 5.24
48 49 3.234630 CTTCCACCTCCCGACGCAA 62.235 63.158 0.00 0.00 0.00 4.85
49 50 2.521958 CTTCCACCTCCCGACGCAAT 62.522 60.000 0.00 0.00 0.00 3.56
50 51 2.796483 TTCCACCTCCCGACGCAATG 62.796 60.000 0.00 0.00 0.00 2.82
51 52 3.499737 CACCTCCCGACGCAATGC 61.500 66.667 0.00 0.00 0.00 3.56
52 53 4.778143 ACCTCCCGACGCAATGCC 62.778 66.667 0.00 0.00 0.00 4.40
87 88 3.706373 GCTCCGCACTCCCTGGAA 61.706 66.667 0.00 0.00 0.00 3.53
88 89 2.266055 CTCCGCACTCCCTGGAAC 59.734 66.667 0.00 0.00 0.00 3.62
89 90 2.203788 TCCGCACTCCCTGGAACT 60.204 61.111 0.00 0.00 0.00 3.01
90 91 2.046892 CCGCACTCCCTGGAACTG 60.047 66.667 0.00 0.00 0.00 3.16
91 92 2.743718 CGCACTCCCTGGAACTGT 59.256 61.111 0.00 0.00 0.00 3.55
92 93 1.374758 CGCACTCCCTGGAACTGTC 60.375 63.158 0.00 0.00 0.00 3.51
93 94 1.003233 GCACTCCCTGGAACTGTCC 60.003 63.158 0.00 0.00 45.21 4.02
94 95 1.679898 CACTCCCTGGAACTGTCCC 59.320 63.158 0.00 0.00 44.23 4.46
95 96 1.913762 ACTCCCTGGAACTGTCCCG 60.914 63.158 0.00 0.00 44.23 5.14
96 97 3.316573 CTCCCTGGAACTGTCCCGC 62.317 68.421 0.00 0.00 44.23 6.13
97 98 3.322466 CCCTGGAACTGTCCCGCT 61.322 66.667 0.00 0.00 44.23 5.52
98 99 1.987855 CCCTGGAACTGTCCCGCTA 60.988 63.158 0.00 0.00 44.23 4.26
99 100 1.550130 CCCTGGAACTGTCCCGCTAA 61.550 60.000 0.00 0.00 44.23 3.09
100 101 0.323629 CCTGGAACTGTCCCGCTAAA 59.676 55.000 0.00 0.00 44.23 1.85
101 102 1.676014 CCTGGAACTGTCCCGCTAAAG 60.676 57.143 0.00 0.00 44.23 1.85
102 103 0.323629 TGGAACTGTCCCGCTAAAGG 59.676 55.000 0.00 0.00 44.23 3.11
103 104 1.025113 GGAACTGTCCCGCTAAAGGC 61.025 60.000 0.00 0.00 38.08 4.35
112 113 2.203084 GCTAAAGGCGCCCTCCTC 60.203 66.667 26.15 6.30 34.82 3.71
113 114 2.506472 CTAAAGGCGCCCTCCTCC 59.494 66.667 26.15 0.00 34.82 4.30
114 115 3.087906 TAAAGGCGCCCTCCTCCC 61.088 66.667 26.15 0.00 34.82 4.30
115 116 3.935456 TAAAGGCGCCCTCCTCCCA 62.935 63.158 26.15 0.00 34.82 4.37
118 119 4.570874 GGCGCCCTCCTCCCAATC 62.571 72.222 18.11 0.00 0.00 2.67
119 120 3.483869 GCGCCCTCCTCCCAATCT 61.484 66.667 0.00 0.00 0.00 2.40
120 121 2.507944 CGCCCTCCTCCCAATCTG 59.492 66.667 0.00 0.00 0.00 2.90
121 122 2.194326 GCCCTCCTCCCAATCTGC 59.806 66.667 0.00 0.00 0.00 4.26
122 123 2.507944 CCCTCCTCCCAATCTGCG 59.492 66.667 0.00 0.00 0.00 5.18
123 124 2.507944 CCTCCTCCCAATCTGCGG 59.492 66.667 0.00 0.00 0.00 5.69
124 125 2.370445 CCTCCTCCCAATCTGCGGT 61.370 63.158 0.00 0.00 0.00 5.68
125 126 1.048724 CCTCCTCCCAATCTGCGGTA 61.049 60.000 0.00 0.00 0.00 4.02
126 127 0.830648 CTCCTCCCAATCTGCGGTAA 59.169 55.000 0.00 0.00 0.00 2.85
127 128 0.539986 TCCTCCCAATCTGCGGTAAC 59.460 55.000 0.00 0.00 0.00 2.50
128 129 0.541863 CCTCCCAATCTGCGGTAACT 59.458 55.000 0.00 0.00 0.00 2.24
129 130 1.473434 CCTCCCAATCTGCGGTAACTC 60.473 57.143 0.00 0.00 0.00 3.01
130 131 0.539986 TCCCAATCTGCGGTAACTCC 59.460 55.000 0.00 0.00 0.00 3.85
139 140 4.611961 GGTAACTCCGGTGAAGCC 57.388 61.111 11.17 5.02 0.00 4.35
140 141 1.675219 GGTAACTCCGGTGAAGCCA 59.325 57.895 11.17 0.00 36.97 4.75
141 142 0.672711 GGTAACTCCGGTGAAGCCAC 60.673 60.000 11.17 0.00 42.46 5.01
142 143 1.012486 GTAACTCCGGTGAAGCCACG 61.012 60.000 11.17 0.00 44.09 4.94
143 144 2.775032 TAACTCCGGTGAAGCCACGC 62.775 60.000 11.17 0.00 44.09 5.34
149 150 3.737172 GTGAAGCCACGCGCCATT 61.737 61.111 5.73 0.00 38.78 3.16
150 151 3.736100 TGAAGCCACGCGCCATTG 61.736 61.111 5.73 0.00 38.78 2.82
151 152 3.737172 GAAGCCACGCGCCATTGT 61.737 61.111 5.73 0.00 38.78 2.71
152 153 2.359354 AAGCCACGCGCCATTGTA 60.359 55.556 5.73 0.00 38.78 2.41
153 154 2.577763 GAAGCCACGCGCCATTGTAC 62.578 60.000 5.73 0.00 38.78 2.90
154 155 3.124921 GCCACGCGCCATTGTACT 61.125 61.111 5.73 0.00 0.00 2.73
155 156 1.812093 GCCACGCGCCATTGTACTA 60.812 57.895 5.73 0.00 0.00 1.82
156 157 1.762222 GCCACGCGCCATTGTACTAG 61.762 60.000 5.73 0.00 0.00 2.57
157 158 0.459585 CCACGCGCCATTGTACTAGT 60.460 55.000 5.73 0.00 0.00 2.57
158 159 1.202325 CCACGCGCCATTGTACTAGTA 60.202 52.381 5.73 0.00 0.00 1.82
159 160 2.117137 CACGCGCCATTGTACTAGTAG 58.883 52.381 5.73 0.00 0.00 2.57
160 161 1.747355 ACGCGCCATTGTACTAGTAGT 59.253 47.619 5.73 8.14 0.00 2.73
161 162 2.945008 ACGCGCCATTGTACTAGTAGTA 59.055 45.455 5.73 5.90 0.00 1.82
162 163 3.003068 ACGCGCCATTGTACTAGTAGTAG 59.997 47.826 10.38 2.87 30.12 2.57
163 164 3.003068 CGCGCCATTGTACTAGTAGTAGT 59.997 47.826 14.57 14.57 42.49 2.73
164 165 4.212004 CGCGCCATTGTACTAGTAGTAGTA 59.788 45.833 12.58 12.58 40.23 1.82
174 175 5.876612 ACTAGTAGTAGTACACAGTGCAC 57.123 43.478 9.40 9.40 37.76 4.57
175 176 4.699257 ACTAGTAGTAGTACACAGTGCACC 59.301 45.833 14.63 0.00 37.76 5.01
176 177 3.493334 AGTAGTAGTACACAGTGCACCA 58.507 45.455 14.63 0.00 0.00 4.17
177 178 2.814280 AGTAGTACACAGTGCACCAC 57.186 50.000 14.63 4.18 34.10 4.16
178 179 1.343465 AGTAGTACACAGTGCACCACC 59.657 52.381 14.63 0.00 34.49 4.61
179 180 0.315886 TAGTACACAGTGCACCACCG 59.684 55.000 14.63 2.17 34.49 4.94
180 181 2.280524 TACACAGTGCACCACCGC 60.281 61.111 14.63 0.00 34.49 5.68
181 182 3.095347 TACACAGTGCACCACCGCA 62.095 57.895 14.63 0.00 40.32 5.69
204 205 3.283684 CCCGTGCAAACGAGGCAA 61.284 61.111 0.00 0.00 43.91 4.52
205 206 2.718731 CCGTGCAAACGAGGCAAA 59.281 55.556 0.00 0.00 43.91 3.68
206 207 1.064946 CCGTGCAAACGAGGCAAAA 59.935 52.632 0.00 0.00 43.91 2.44
207 208 0.318614 CCGTGCAAACGAGGCAAAAT 60.319 50.000 0.00 0.00 43.91 1.82
208 209 0.777631 CGTGCAAACGAGGCAAAATG 59.222 50.000 0.00 0.00 43.91 2.32
209 210 1.139163 GTGCAAACGAGGCAAAATGG 58.861 50.000 0.00 0.00 43.91 3.16
210 211 0.599728 TGCAAACGAGGCAAAATGGC 60.600 50.000 0.00 0.00 44.10 4.40
242 243 3.436577 AATGAGCCATCCATCCATCTC 57.563 47.619 0.00 0.00 0.00 2.75
266 267 2.028733 GTTTAACCGGCGAGCGGAA 61.029 57.895 9.30 0.00 0.00 4.30
269 270 1.567746 TTAACCGGCGAGCGGAAAAC 61.568 55.000 9.30 0.00 0.00 2.43
270 271 2.438951 TAACCGGCGAGCGGAAAACT 62.439 55.000 9.30 0.00 0.00 2.66
271 272 3.488090 CCGGCGAGCGGAAAACTC 61.488 66.667 9.30 0.00 0.00 3.01
272 273 3.488090 CGGCGAGCGGAAAACTCC 61.488 66.667 0.00 0.00 0.00 3.85
273 274 2.358247 GGCGAGCGGAAAACTCCA 60.358 61.111 0.00 0.00 0.00 3.86
274 275 1.964373 GGCGAGCGGAAAACTCCAA 60.964 57.895 0.00 0.00 0.00 3.53
275 276 1.206831 GCGAGCGGAAAACTCCAAC 59.793 57.895 0.00 0.00 0.00 3.77
278 279 0.883370 GAGCGGAAAACTCCAACGGT 60.883 55.000 0.00 0.00 38.03 4.83
281 282 1.281656 GGAAAACTCCAACGGTGCG 59.718 57.895 0.00 0.00 0.00 5.34
309 324 3.702048 CGTTCCCTTCTCCCCGCA 61.702 66.667 0.00 0.00 0.00 5.69
310 325 2.998949 GTTCCCTTCTCCCCGCAT 59.001 61.111 0.00 0.00 0.00 4.73
316 331 2.040442 TTCTCCCCGCATCCTCCA 59.960 61.111 0.00 0.00 0.00 3.86
317 332 1.384502 TTCTCCCCGCATCCTCCAT 60.385 57.895 0.00 0.00 0.00 3.41
319 334 2.849162 TCCCCGCATCCTCCATCC 60.849 66.667 0.00 0.00 0.00 3.51
320 335 4.320456 CCCCGCATCCTCCATCCG 62.320 72.222 0.00 0.00 0.00 4.18
321 336 3.233980 CCCGCATCCTCCATCCGA 61.234 66.667 0.00 0.00 0.00 4.55
322 337 2.341543 CCGCATCCTCCATCCGAG 59.658 66.667 0.00 0.00 38.46 4.63
323 338 2.203082 CCGCATCCTCCATCCGAGA 61.203 63.158 0.00 0.00 41.63 4.04
324 339 1.742146 CGCATCCTCCATCCGAGAA 59.258 57.895 0.00 0.00 41.63 2.87
397 412 4.468689 CCGCCCTTCCCTCCGTTC 62.469 72.222 0.00 0.00 0.00 3.95
398 413 4.814294 CGCCCTTCCCTCCGTTCG 62.814 72.222 0.00 0.00 0.00 3.95
401 416 1.373812 CCCTTCCCTCCGTTCGTTT 59.626 57.895 0.00 0.00 0.00 3.60
402 417 0.609662 CCCTTCCCTCCGTTCGTTTA 59.390 55.000 0.00 0.00 0.00 2.01
403 418 1.002315 CCCTTCCCTCCGTTCGTTTAA 59.998 52.381 0.00 0.00 0.00 1.52
404 419 2.355412 CCCTTCCCTCCGTTCGTTTAAT 60.355 50.000 0.00 0.00 0.00 1.40
405 420 3.340928 CCTTCCCTCCGTTCGTTTAATT 58.659 45.455 0.00 0.00 0.00 1.40
406 421 3.373130 CCTTCCCTCCGTTCGTTTAATTC 59.627 47.826 0.00 0.00 0.00 2.17
407 422 3.681593 TCCCTCCGTTCGTTTAATTCA 57.318 42.857 0.00 0.00 0.00 2.57
408 423 4.210724 TCCCTCCGTTCGTTTAATTCAT 57.789 40.909 0.00 0.00 0.00 2.57
409 424 5.341872 TCCCTCCGTTCGTTTAATTCATA 57.658 39.130 0.00 0.00 0.00 2.15
410 425 5.111293 TCCCTCCGTTCGTTTAATTCATAC 58.889 41.667 0.00 0.00 0.00 2.39
411 426 4.026310 CCCTCCGTTCGTTTAATTCATACG 60.026 45.833 0.00 0.00 36.67 3.06
412 427 4.563976 CCTCCGTTCGTTTAATTCATACGT 59.436 41.667 0.00 0.00 36.70 3.57
413 428 5.743398 CCTCCGTTCGTTTAATTCATACGTA 59.257 40.000 0.00 0.00 36.70 3.57
414 429 6.418819 CCTCCGTTCGTTTAATTCATACGTAT 59.581 38.462 1.14 1.14 36.70 3.06
424 439 4.985044 ATTCATACGTATTTACTGCCGC 57.015 40.909 5.03 0.00 0.00 6.53
439 454 2.994578 CTGCCGCTAATCTGATCAGATG 59.005 50.000 33.48 23.94 46.75 2.90
443 458 4.381825 GCCGCTAATCTGATCAGATGAGAT 60.382 45.833 38.67 25.95 45.46 2.75
446 461 6.031471 CGCTAATCTGATCAGATGAGATGAG 58.969 44.000 38.67 26.05 45.46 2.90
482 508 2.477189 CGGAAAAAGACGCAACTTGTGT 60.477 45.455 7.71 7.71 44.78 3.72
483 509 3.242478 CGGAAAAAGACGCAACTTGTGTA 60.242 43.478 7.96 0.00 41.77 2.90
484 510 4.664188 GGAAAAAGACGCAACTTGTGTAA 58.336 39.130 7.96 0.00 41.77 2.41
507 533 4.543084 GGCTGCCGATCAAAGCGC 62.543 66.667 1.35 0.00 37.83 5.92
508 534 4.876081 GCTGCCGATCAAAGCGCG 62.876 66.667 0.00 0.00 0.00 6.86
509 535 3.188100 CTGCCGATCAAAGCGCGA 61.188 61.111 12.10 0.00 0.00 5.87
562 592 3.063084 GCCCGGTGACTCTCGTCT 61.063 66.667 0.00 0.00 40.86 4.18
654 695 3.735037 CTCGGGGTTTCTAGCCGCC 62.735 68.421 1.26 1.37 43.08 6.13
743 784 2.270205 GCTTGCTGCTGGCCTCTA 59.730 61.111 3.32 0.00 40.92 2.43
765 806 1.966451 GGTCCTGCAAGAACCACCG 60.966 63.158 6.88 0.00 34.07 4.94
766 807 1.966451 GTCCTGCAAGAACCACCGG 60.966 63.158 0.00 0.00 34.07 5.28
767 808 3.365265 CCTGCAAGAACCACCGGC 61.365 66.667 0.00 0.00 34.07 6.13
781 822 3.131478 CGGCACCGGGTTGGATTC 61.131 66.667 6.32 0.00 42.00 2.52
794 835 2.833943 GTTGGATTCATTTTCCCTGCCT 59.166 45.455 0.00 0.00 31.87 4.75
795 836 2.459644 TGGATTCATTTTCCCTGCCTG 58.540 47.619 0.00 0.00 31.87 4.85
798 839 0.114954 TTCATTTTCCCTGCCTGCCT 59.885 50.000 0.00 0.00 0.00 4.75
799 840 0.612732 TCATTTTCCCTGCCTGCCTG 60.613 55.000 0.00 0.00 0.00 4.85
800 841 1.986210 ATTTTCCCTGCCTGCCTGC 60.986 57.895 0.00 0.00 0.00 4.85
801 842 4.684134 TTTCCCTGCCTGCCTGCC 62.684 66.667 0.00 0.00 0.00 4.85
845 886 2.158900 GGGAGCGAGGAATCAATCTTCA 60.159 50.000 0.00 0.00 33.90 3.02
849 890 4.378774 AGCGAGGAATCAATCTTCATCTG 58.621 43.478 0.00 0.00 34.61 2.90
852 893 3.474600 AGGAATCAATCTTCATCTGCCG 58.525 45.455 0.00 0.00 0.00 5.69
854 895 1.602311 ATCAATCTTCATCTGCCGCC 58.398 50.000 0.00 0.00 0.00 6.13
856 897 1.524621 AATCTTCATCTGCCGCCGG 60.525 57.895 0.00 0.00 0.00 6.13
868 909 2.594882 CGCCGGGAGAGCTAGCTA 60.595 66.667 19.38 0.00 0.00 3.32
869 910 2.622011 CGCCGGGAGAGCTAGCTAG 61.622 68.421 19.38 16.84 0.00 3.42
870 911 2.272447 GCCGGGAGAGCTAGCTAGG 61.272 68.421 19.38 16.29 0.00 3.02
871 912 1.456726 CCGGGAGAGCTAGCTAGGA 59.543 63.158 19.38 0.00 0.00 2.94
872 913 0.039035 CCGGGAGAGCTAGCTAGGAT 59.961 60.000 19.38 3.90 0.00 3.24
873 914 1.282447 CCGGGAGAGCTAGCTAGGATA 59.718 57.143 19.38 0.00 0.00 2.59
874 915 2.291024 CCGGGAGAGCTAGCTAGGATAA 60.291 54.545 19.38 0.00 0.00 1.75
875 916 3.626222 CCGGGAGAGCTAGCTAGGATAAT 60.626 52.174 19.38 0.00 0.00 1.28
876 917 4.385421 CCGGGAGAGCTAGCTAGGATAATA 60.385 50.000 19.38 0.00 0.00 0.98
877 918 4.577283 CGGGAGAGCTAGCTAGGATAATAC 59.423 50.000 19.38 1.23 0.00 1.89
878 919 5.630539 CGGGAGAGCTAGCTAGGATAATACT 60.631 48.000 19.38 6.88 0.00 2.12
879 920 5.826208 GGGAGAGCTAGCTAGGATAATACTC 59.174 48.000 19.38 15.55 0.00 2.59
880 921 5.826208 GGAGAGCTAGCTAGGATAATACTCC 59.174 48.000 19.38 20.39 35.37 3.85
882 923 7.147444 GGAGAGCTAGCTAGGATAATACTCCTA 60.147 44.444 25.17 0.27 44.04 2.94
883 924 7.571025 AGAGCTAGCTAGGATAATACTCCTAC 58.429 42.308 19.38 0.00 44.04 3.18
884 925 7.183112 AGAGCTAGCTAGGATAATACTCCTACA 59.817 40.741 19.38 0.00 44.04 2.74
885 926 7.114095 AGCTAGCTAGGATAATACTCCTACAC 58.886 42.308 17.69 0.00 44.04 2.90
886 927 6.885376 GCTAGCTAGGATAATACTCCTACACA 59.115 42.308 22.10 0.00 44.04 3.72
887 928 7.066525 GCTAGCTAGGATAATACTCCTACACAG 59.933 44.444 22.10 0.00 44.04 3.66
888 929 6.249951 AGCTAGGATAATACTCCTACACAGG 58.750 44.000 0.00 0.00 44.04 4.00
898 939 0.041238 CCTACACAGGAGGAGGTGGA 59.959 60.000 0.00 0.00 45.91 4.02
899 940 1.552486 CCTACACAGGAGGAGGTGGAA 60.552 57.143 0.00 0.00 45.91 3.53
905 946 0.332972 AGGAGGAGGTGGAATTTGCC 59.667 55.000 0.00 0.00 0.00 4.52
911 952 2.450476 GAGGTGGAATTTGCCTGTGAT 58.550 47.619 1.83 0.00 31.89 3.06
914 955 4.613437 AGGTGGAATTTGCCTGTGATTAT 58.387 39.130 0.00 0.00 0.00 1.28
918 959 4.222366 TGGAATTTGCCTGTGATTATTGCA 59.778 37.500 0.00 0.00 0.00 4.08
937 978 0.532573 AAGATCTCGCGCCAAGAAGA 59.467 50.000 10.80 0.00 0.00 2.87
940 981 1.323271 ATCTCGCGCCAAGAAGAGGA 61.323 55.000 10.80 0.00 0.00 3.71
941 982 1.079819 CTCGCGCCAAGAAGAGGAA 60.080 57.895 0.00 0.00 0.00 3.36
942 983 1.079819 TCGCGCCAAGAAGAGGAAG 60.080 57.895 0.00 0.00 0.00 3.46
943 984 2.744768 CGCGCCAAGAAGAGGAAGC 61.745 63.158 0.00 0.00 0.00 3.86
944 985 1.672356 GCGCCAAGAAGAGGAAGCA 60.672 57.895 0.00 0.00 33.46 3.91
945 986 1.642952 GCGCCAAGAAGAGGAAGCAG 61.643 60.000 0.00 0.00 33.46 4.24
946 987 1.642952 CGCCAAGAAGAGGAAGCAGC 61.643 60.000 0.00 0.00 0.00 5.25
947 988 0.607489 GCCAAGAAGAGGAAGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
950 991 0.399454 AAGAAGAGGAAGCAGCAGCA 59.601 50.000 3.17 0.00 45.49 4.41
953 994 2.359602 GAGGAAGCAGCAGCAGCA 60.360 61.111 12.92 0.00 45.49 4.41
965 1006 2.124653 GCAGCAGCAGGAGCAGAT 60.125 61.111 0.00 0.00 45.49 2.90
973 1014 2.419324 CAGCAGGAGCAGATTCTTCAAC 59.581 50.000 0.00 0.00 45.49 3.18
974 1015 2.039480 AGCAGGAGCAGATTCTTCAACA 59.961 45.455 0.00 0.00 45.49 3.33
980 1025 4.155644 GGAGCAGATTCTTCAACAAAGGAG 59.844 45.833 0.00 0.00 35.54 3.69
986 1031 1.073923 TCTTCAACAAAGGAGGGAGGC 59.926 52.381 0.00 0.00 35.54 4.70
1018 1063 1.303309 CATGGGTTCTTGCGAGGATC 58.697 55.000 0.00 0.00 0.00 3.36
1022 1067 0.462759 GGTTCTTGCGAGGATCTGGG 60.463 60.000 0.00 0.00 0.00 4.45
1328 1385 0.110912 GACGACGACGACGAGTTCTT 60.111 55.000 25.15 2.32 42.66 2.52
1332 1389 0.248743 ACGACGACGAGTTCTTTGCA 60.249 50.000 15.32 0.00 42.66 4.08
1337 1394 2.171489 GACGAGTTCTTTGCACCCGC 62.171 60.000 0.00 0.00 39.24 6.13
1340 1397 1.856265 GAGTTCTTTGCACCCGCCAG 61.856 60.000 0.00 0.00 37.32 4.85
1440 1503 0.320421 CAACGGTGTACCAGGACAGG 60.320 60.000 0.00 0.00 35.14 4.00
1443 1506 0.898789 CGGTGTACCAGGACAGGTCT 60.899 60.000 0.00 0.00 42.06 3.85
1461 1524 0.549950 CTTGGATGGATCCCTGCTGT 59.450 55.000 9.90 0.00 46.59 4.40
1464 1527 1.527844 GATGGATCCCTGCTGTGCC 60.528 63.158 9.90 0.00 0.00 5.01
1485 1548 2.190578 GCAACGATGGGAGGAGGG 59.809 66.667 0.00 0.00 0.00 4.30
1510 1573 1.863454 CTGATATGTTCGTCAGCAGCC 59.137 52.381 0.00 0.00 35.87 4.85
1700 1766 1.155042 GACAAAGTGCTCCTCTGCAG 58.845 55.000 7.63 7.63 44.20 4.41
1725 1791 1.002430 GTCAACTGCATCCTCCAGTCA 59.998 52.381 0.00 0.00 42.37 3.41
1728 1794 0.837691 ACTGCATCCTCCAGTCACCA 60.838 55.000 0.00 0.00 39.19 4.17
1863 1929 1.089920 CAACCCTGCTCATACACTGC 58.910 55.000 0.00 0.00 0.00 4.40
2037 2103 2.027073 CTACCGCTCGCTTGTTGCA 61.027 57.895 0.00 0.00 43.06 4.08
2079 2145 6.327154 TGACATGCTGAAAATATTCAAGCTG 58.673 36.000 14.48 12.51 44.64 4.24
2088 2154 6.321181 TGAAAATATTCAAGCTGTATGGGACC 59.679 38.462 0.00 0.00 42.47 4.46
2356 2422 2.159841 CGTGACTACGCCAAGATGTTTG 60.160 50.000 0.00 0.00 44.11 2.93
2367 2433 4.262592 GCCAAGATGTTTGATGTTCCCTTT 60.263 41.667 0.00 0.00 0.00 3.11
2373 2439 6.431234 AGATGTTTGATGTTCCCTTTGAGTAC 59.569 38.462 0.00 0.00 0.00 2.73
2376 2442 2.635915 TGATGTTCCCTTTGAGTACCGT 59.364 45.455 0.00 0.00 0.00 4.83
2379 2445 0.320073 TTCCCTTTGAGTACCGTGCG 60.320 55.000 0.00 0.00 0.00 5.34
2436 2502 2.223923 CCTCAGGATCGACAAGGATGAC 60.224 54.545 0.00 0.00 0.00 3.06
2491 2557 0.528466 CATGATGGACGAGACGGTGG 60.528 60.000 0.00 0.00 0.00 4.61
2619 2685 1.813337 GCGCTTCAAGGAGGCTCTC 60.813 63.158 15.23 4.64 32.35 3.20
2833 2899 0.322975 GGTGCCTCTGCTTCAAGAGA 59.677 55.000 2.79 0.00 45.59 3.10
3072 3161 5.799213 TGTTGTTGAATTTTGACCCTTTGT 58.201 33.333 0.00 0.00 0.00 2.83
3102 3191 6.830324 AGCAGAGTTGATGGATATTTTTGCTA 59.170 34.615 0.00 0.00 35.47 3.49
3210 3423 3.429085 GGTAGCGCTGATGTTTCATTTG 58.571 45.455 22.90 0.00 0.00 2.32
3241 3454 0.950116 GAAGGTGCATATGAGCTGCC 59.050 55.000 6.97 0.40 38.89 4.85
3332 3545 8.204160 TGAGTCAAGAGTGTGAAAAGAAGATAA 58.796 33.333 0.00 0.00 0.00 1.75
3436 3650 7.104043 CATAAATTGCTTCTCCAATCTCCAA 57.896 36.000 0.00 0.00 34.50 3.53
3527 3741 4.881273 TCATAATGCACAAGGATACACACC 59.119 41.667 0.00 0.00 41.41 4.16
3572 3788 9.921637 ATAAGCTAGAAATGTACTTATGCTCTC 57.078 33.333 0.00 0.00 33.45 3.20
3573 3789 7.353414 AGCTAGAAATGTACTTATGCTCTCA 57.647 36.000 0.00 0.00 0.00 3.27
3574 3790 7.786030 AGCTAGAAATGTACTTATGCTCTCAA 58.214 34.615 0.00 0.00 0.00 3.02
3575 3791 7.925483 AGCTAGAAATGTACTTATGCTCTCAAG 59.075 37.037 0.00 0.00 0.00 3.02
3576 3792 7.708752 GCTAGAAATGTACTTATGCTCTCAAGT 59.291 37.037 0.00 0.00 38.50 3.16
3650 3866 3.835790 TTTCGTTGGGGTGCCCTCG 62.836 63.158 7.26 9.77 45.70 4.63
3704 3920 5.152623 TGAACTTCACCTCTTCATACTGG 57.847 43.478 0.00 0.00 0.00 4.00
3759 3976 1.073923 GGTTGTCCTCAAGTGGTCCAT 59.926 52.381 0.00 0.00 33.97 3.41
3766 3986 5.724370 TGTCCTCAAGTGGTCCATAGAATAA 59.276 40.000 0.00 0.00 0.00 1.40
3832 4052 2.074948 AGCCACATCAGCCCTAGGG 61.075 63.158 24.89 24.89 38.57 3.53
3874 4094 2.437281 GAGAAGCTCATCATCCTTCCCA 59.563 50.000 0.00 0.00 36.50 4.37
3897 4117 3.465403 CAGCTCCCTCACTCCCCG 61.465 72.222 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.413812 GGGGCCATTCATTTCACATCC 59.586 52.381 4.39 0.00 0.00 3.51
1 2 1.067516 CGGGGCCATTCATTTCACATC 59.932 52.381 4.39 0.00 0.00 3.06
2 3 1.113788 CGGGGCCATTCATTTCACAT 58.886 50.000 4.39 0.00 0.00 3.21
3 4 0.038890 TCGGGGCCATTCATTTCACA 59.961 50.000 4.39 0.00 0.00 3.58
4 5 1.338020 GATCGGGGCCATTCATTTCAC 59.662 52.381 4.39 0.00 0.00 3.18
5 6 1.215173 AGATCGGGGCCATTCATTTCA 59.785 47.619 4.39 0.00 0.00 2.69
6 7 1.610522 CAGATCGGGGCCATTCATTTC 59.389 52.381 4.39 0.00 0.00 2.17
7 8 1.696063 CAGATCGGGGCCATTCATTT 58.304 50.000 4.39 0.00 0.00 2.32
8 9 0.825010 GCAGATCGGGGCCATTCATT 60.825 55.000 4.39 0.00 0.00 2.57
9 10 1.228367 GCAGATCGGGGCCATTCAT 60.228 57.895 4.39 0.00 0.00 2.57
10 11 1.925285 AAGCAGATCGGGGCCATTCA 61.925 55.000 4.39 0.00 0.00 2.57
11 12 1.152881 AAGCAGATCGGGGCCATTC 60.153 57.895 4.39 0.00 0.00 2.67
12 13 1.152881 GAAGCAGATCGGGGCCATT 60.153 57.895 4.39 0.00 0.00 3.16
13 14 1.639635 AAGAAGCAGATCGGGGCCAT 61.640 55.000 4.39 0.00 0.00 4.40
14 15 2.257409 GAAGAAGCAGATCGGGGCCA 62.257 60.000 4.39 0.00 0.00 5.36
15 16 1.524849 GAAGAAGCAGATCGGGGCC 60.525 63.158 0.00 0.00 0.00 5.80
16 17 1.524849 GGAAGAAGCAGATCGGGGC 60.525 63.158 0.00 0.00 0.00 5.80
17 18 0.462759 GTGGAAGAAGCAGATCGGGG 60.463 60.000 0.00 0.00 0.00 5.73
18 19 0.462759 GGTGGAAGAAGCAGATCGGG 60.463 60.000 0.00 0.00 0.00 5.14
19 20 0.539051 AGGTGGAAGAAGCAGATCGG 59.461 55.000 0.00 0.00 0.00 4.18
20 21 1.472376 GGAGGTGGAAGAAGCAGATCG 60.472 57.143 0.00 0.00 0.00 3.69
21 22 1.134250 GGGAGGTGGAAGAAGCAGATC 60.134 57.143 0.00 0.00 0.00 2.75
22 23 0.915364 GGGAGGTGGAAGAAGCAGAT 59.085 55.000 0.00 0.00 0.00 2.90
23 24 1.544825 CGGGAGGTGGAAGAAGCAGA 61.545 60.000 0.00 0.00 0.00 4.26
24 25 1.078848 CGGGAGGTGGAAGAAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
25 26 1.535444 TCGGGAGGTGGAAGAAGCA 60.535 57.895 0.00 0.00 0.00 3.91
26 27 1.079057 GTCGGGAGGTGGAAGAAGC 60.079 63.158 0.00 0.00 0.00 3.86
27 28 1.215647 CGTCGGGAGGTGGAAGAAG 59.784 63.158 0.00 0.00 0.00 2.85
28 29 2.939261 GCGTCGGGAGGTGGAAGAA 61.939 63.158 0.00 0.00 0.00 2.52
29 30 3.379445 GCGTCGGGAGGTGGAAGA 61.379 66.667 0.00 0.00 0.00 2.87
30 31 2.521958 ATTGCGTCGGGAGGTGGAAG 62.522 60.000 0.00 0.00 0.00 3.46
31 32 2.589157 ATTGCGTCGGGAGGTGGAA 61.589 57.895 0.00 0.00 0.00 3.53
32 33 3.000819 ATTGCGTCGGGAGGTGGA 61.001 61.111 0.00 0.00 0.00 4.02
33 34 2.819595 CATTGCGTCGGGAGGTGG 60.820 66.667 0.00 0.00 0.00 4.61
34 35 3.499737 GCATTGCGTCGGGAGGTG 61.500 66.667 0.00 0.00 0.00 4.00
35 36 4.778143 GGCATTGCGTCGGGAGGT 62.778 66.667 1.91 0.00 0.00 3.85
71 72 2.266055 GTTCCAGGGAGTGCGGAG 59.734 66.667 0.00 0.00 0.00 4.63
72 73 2.203788 AGTTCCAGGGAGTGCGGA 60.204 61.111 0.00 0.00 0.00 5.54
73 74 2.046892 CAGTTCCAGGGAGTGCGG 60.047 66.667 0.00 0.00 0.00 5.69
74 75 1.374758 GACAGTTCCAGGGAGTGCG 60.375 63.158 1.83 0.00 0.00 5.34
75 76 1.003233 GGACAGTTCCAGGGAGTGC 60.003 63.158 1.83 0.00 42.30 4.40
76 77 1.679898 GGGACAGTTCCAGGGAGTG 59.320 63.158 0.13 0.13 44.98 3.51
77 78 1.913762 CGGGACAGTTCCAGGGAGT 60.914 63.158 0.00 0.00 44.98 3.85
78 79 2.982130 CGGGACAGTTCCAGGGAG 59.018 66.667 0.00 0.00 44.98 4.30
79 80 2.449967 TAGCGGGACAGTTCCAGGGA 62.450 60.000 0.00 0.00 44.98 4.20
80 81 1.550130 TTAGCGGGACAGTTCCAGGG 61.550 60.000 0.00 0.00 44.98 4.45
81 82 0.323629 TTTAGCGGGACAGTTCCAGG 59.676 55.000 0.00 0.00 44.98 4.45
82 83 1.676014 CCTTTAGCGGGACAGTTCCAG 60.676 57.143 0.00 0.00 44.98 3.86
83 84 0.323629 CCTTTAGCGGGACAGTTCCA 59.676 55.000 0.00 0.00 44.98 3.53
84 85 1.025113 GCCTTTAGCGGGACAGTTCC 61.025 60.000 0.00 0.00 41.95 3.62
85 86 2.467962 GCCTTTAGCGGGACAGTTC 58.532 57.895 0.00 0.00 0.00 3.01
86 87 4.716003 GCCTTTAGCGGGACAGTT 57.284 55.556 0.00 0.00 0.00 3.16
95 96 2.203084 GAGGAGGGCGCCTTTAGC 60.203 66.667 28.56 9.28 38.73 3.09
96 97 2.506472 GGAGGAGGGCGCCTTTAG 59.494 66.667 28.56 0.00 38.73 1.85
97 98 3.087906 GGGAGGAGGGCGCCTTTA 61.088 66.667 28.56 0.00 38.73 1.85
101 102 4.570874 GATTGGGAGGAGGGCGCC 62.571 72.222 21.18 21.18 0.00 6.53
102 103 3.483869 AGATTGGGAGGAGGGCGC 61.484 66.667 0.00 0.00 0.00 6.53
103 104 2.507944 CAGATTGGGAGGAGGGCG 59.492 66.667 0.00 0.00 0.00 6.13
104 105 2.194326 GCAGATTGGGAGGAGGGC 59.806 66.667 0.00 0.00 0.00 5.19
105 106 2.507944 CGCAGATTGGGAGGAGGG 59.492 66.667 0.00 0.00 31.21 4.30
106 107 1.048724 TACCGCAGATTGGGAGGAGG 61.049 60.000 0.00 0.00 31.21 4.30
107 108 0.830648 TTACCGCAGATTGGGAGGAG 59.169 55.000 0.00 0.00 31.21 3.69
108 109 0.539986 GTTACCGCAGATTGGGAGGA 59.460 55.000 0.00 0.00 31.21 3.71
109 110 0.541863 AGTTACCGCAGATTGGGAGG 59.458 55.000 0.00 0.00 31.21 4.30
110 111 1.473434 GGAGTTACCGCAGATTGGGAG 60.473 57.143 0.00 0.00 31.21 4.30
111 112 0.539986 GGAGTTACCGCAGATTGGGA 59.460 55.000 0.00 0.00 31.21 4.37
112 113 3.080647 GGAGTTACCGCAGATTGGG 57.919 57.895 0.00 0.00 0.00 4.12
122 123 0.672711 GTGGCTTCACCGGAGTTACC 60.673 60.000 9.46 4.31 43.94 2.85
123 124 1.012486 CGTGGCTTCACCGGAGTTAC 61.012 60.000 9.46 0.00 43.94 2.50
124 125 1.290955 CGTGGCTTCACCGGAGTTA 59.709 57.895 9.46 0.00 43.94 2.24
125 126 2.030562 CGTGGCTTCACCGGAGTT 59.969 61.111 9.46 0.00 43.94 3.01
126 127 4.681978 GCGTGGCTTCACCGGAGT 62.682 66.667 9.46 0.00 43.94 3.85
132 133 3.737172 AATGGCGCGTGGCTTCAC 61.737 61.111 23.71 0.00 42.94 3.18
133 134 3.736100 CAATGGCGCGTGGCTTCA 61.736 61.111 23.71 3.54 42.94 3.02
134 135 2.395360 TACAATGGCGCGTGGCTTC 61.395 57.895 23.71 0.00 42.94 3.86
135 136 2.359354 TACAATGGCGCGTGGCTT 60.359 55.556 23.71 14.70 42.94 4.35
136 137 2.233605 TAGTACAATGGCGCGTGGCT 62.234 55.000 23.71 5.64 42.94 4.75
137 138 1.762222 CTAGTACAATGGCGCGTGGC 61.762 60.000 16.64 16.64 42.51 5.01
138 139 0.459585 ACTAGTACAATGGCGCGTGG 60.460 55.000 8.43 0.00 0.00 4.94
139 140 2.117137 CTACTAGTACAATGGCGCGTG 58.883 52.381 8.43 0.00 0.00 5.34
140 141 1.747355 ACTACTAGTACAATGGCGCGT 59.253 47.619 8.43 0.00 0.00 6.01
141 142 2.486951 ACTACTAGTACAATGGCGCG 57.513 50.000 0.00 0.00 0.00 6.86
142 143 4.564940 ACTACTACTAGTACAATGGCGC 57.435 45.455 0.00 0.00 30.81 6.53
151 152 5.877012 GGTGCACTGTGTACTACTACTAGTA 59.123 44.000 24.55 1.89 34.79 1.82
152 153 4.699257 GGTGCACTGTGTACTACTACTAGT 59.301 45.833 24.55 0.00 37.04 2.57
153 154 4.698780 TGGTGCACTGTGTACTACTACTAG 59.301 45.833 24.55 0.00 33.35 2.57
154 155 4.456911 GTGGTGCACTGTGTACTACTACTA 59.543 45.833 28.63 1.88 40.26 1.82
155 156 3.255149 GTGGTGCACTGTGTACTACTACT 59.745 47.826 28.63 0.00 40.26 2.57
156 157 3.572584 GTGGTGCACTGTGTACTACTAC 58.427 50.000 28.63 18.28 40.26 2.73
157 158 2.559668 GGTGGTGCACTGTGTACTACTA 59.440 50.000 32.02 14.92 42.30 1.82
158 159 1.343465 GGTGGTGCACTGTGTACTACT 59.657 52.381 32.02 0.00 42.30 2.57
159 160 1.792006 GGTGGTGCACTGTGTACTAC 58.208 55.000 28.26 28.26 42.03 2.73
160 161 0.315886 CGGTGGTGCACTGTGTACTA 59.684 55.000 24.55 18.22 36.14 1.82
161 162 1.069090 CGGTGGTGCACTGTGTACT 59.931 57.895 24.55 0.00 36.14 2.73
162 163 2.604174 GCGGTGGTGCACTGTGTAC 61.604 63.158 18.99 18.99 42.21 2.90
163 164 2.280524 GCGGTGGTGCACTGTGTA 60.281 61.111 17.98 1.30 42.21 2.90
164 165 4.481617 TGCGGTGGTGCACTGTGT 62.482 61.111 17.98 0.00 42.21 3.72
190 191 1.139163 CCATTTTGCCTCGTTTGCAC 58.861 50.000 0.00 0.00 38.72 4.57
191 192 0.599728 GCCATTTTGCCTCGTTTGCA 60.600 50.000 0.00 0.00 36.84 4.08
192 193 0.319813 AGCCATTTTGCCTCGTTTGC 60.320 50.000 0.00 0.00 0.00 3.68
193 194 1.000385 TCAGCCATTTTGCCTCGTTTG 60.000 47.619 0.00 0.00 0.00 2.93
194 195 1.327303 TCAGCCATTTTGCCTCGTTT 58.673 45.000 0.00 0.00 0.00 3.60
195 196 1.000274 GTTCAGCCATTTTGCCTCGTT 60.000 47.619 0.00 0.00 0.00 3.85
196 197 0.598065 GTTCAGCCATTTTGCCTCGT 59.402 50.000 0.00 0.00 0.00 4.18
197 198 0.597568 TGTTCAGCCATTTTGCCTCG 59.402 50.000 0.00 0.00 0.00 4.63
198 199 1.337167 GGTGTTCAGCCATTTTGCCTC 60.337 52.381 0.00 0.00 0.00 4.70
199 200 0.681175 GGTGTTCAGCCATTTTGCCT 59.319 50.000 0.00 0.00 0.00 4.75
200 201 0.392336 TGGTGTTCAGCCATTTTGCC 59.608 50.000 0.00 0.00 0.00 4.52
201 202 2.237393 TTGGTGTTCAGCCATTTTGC 57.763 45.000 0.00 0.00 35.71 3.68
202 203 5.296283 TCATTTTTGGTGTTCAGCCATTTTG 59.704 36.000 0.00 0.00 35.71 2.44
203 204 5.435291 TCATTTTTGGTGTTCAGCCATTTT 58.565 33.333 0.00 0.00 35.71 1.82
204 205 5.033589 TCATTTTTGGTGTTCAGCCATTT 57.966 34.783 0.00 0.00 35.71 2.32
205 206 4.634199 CTCATTTTTGGTGTTCAGCCATT 58.366 39.130 0.00 0.00 35.71 3.16
206 207 3.555586 GCTCATTTTTGGTGTTCAGCCAT 60.556 43.478 0.00 0.00 35.71 4.40
207 208 2.224018 GCTCATTTTTGGTGTTCAGCCA 60.224 45.455 0.00 0.00 0.00 4.75
208 209 2.407090 GCTCATTTTTGGTGTTCAGCC 58.593 47.619 0.00 0.00 0.00 4.85
209 210 2.224018 TGGCTCATTTTTGGTGTTCAGC 60.224 45.455 0.00 0.00 0.00 4.26
210 211 3.731652 TGGCTCATTTTTGGTGTTCAG 57.268 42.857 0.00 0.00 0.00 3.02
211 212 3.006752 GGATGGCTCATTTTTGGTGTTCA 59.993 43.478 0.00 0.00 0.00 3.18
212 213 3.006752 TGGATGGCTCATTTTTGGTGTTC 59.993 43.478 0.00 0.00 0.00 3.18
213 214 2.971330 TGGATGGCTCATTTTTGGTGTT 59.029 40.909 0.00 0.00 0.00 3.32
214 215 2.607499 TGGATGGCTCATTTTTGGTGT 58.393 42.857 0.00 0.00 0.00 4.16
215 216 3.431207 GGATGGATGGCTCATTTTTGGTG 60.431 47.826 0.00 0.00 0.00 4.17
266 267 3.284449 GGCGCACCGTTGGAGTTT 61.284 61.111 10.83 0.00 0.00 2.66
293 308 1.153147 GATGCGGGGAGAAGGGAAC 60.153 63.158 0.00 0.00 0.00 3.62
309 324 2.593026 GTCTCTTCTCGGATGGAGGAT 58.407 52.381 0.00 0.00 43.34 3.24
310 325 1.747552 CGTCTCTTCTCGGATGGAGGA 60.748 57.143 0.00 0.00 43.34 3.71
316 331 1.384525 CTGGTCGTCTCTTCTCGGAT 58.615 55.000 0.00 0.00 0.00 4.18
317 332 0.677098 CCTGGTCGTCTCTTCTCGGA 60.677 60.000 0.00 0.00 0.00 4.55
319 334 0.448593 GACCTGGTCGTCTCTTCTCG 59.551 60.000 11.71 0.00 0.00 4.04
346 361 4.487412 GATTGCGCCACCTGCTGC 62.487 66.667 4.18 0.00 39.09 5.25
347 362 3.818787 GGATTGCGCCACCTGCTG 61.819 66.667 4.18 0.00 38.05 4.41
380 395 4.468689 GAACGGAGGGAAGGGCGG 62.469 72.222 0.00 0.00 0.00 6.13
381 396 4.814294 CGAACGGAGGGAAGGGCG 62.814 72.222 0.00 0.00 0.00 6.13
382 397 2.743126 AAACGAACGGAGGGAAGGGC 62.743 60.000 0.00 0.00 0.00 5.19
396 411 8.542132 GGCAGTAAATACGTATGAATTAAACGA 58.458 33.333 9.24 0.00 39.80 3.85
397 412 7.524861 CGGCAGTAAATACGTATGAATTAAACG 59.475 37.037 9.24 5.07 42.17 3.60
398 413 7.319615 GCGGCAGTAAATACGTATGAATTAAAC 59.680 37.037 9.24 0.00 0.00 2.01
401 416 6.218019 AGCGGCAGTAAATACGTATGAATTA 58.782 36.000 9.24 1.46 0.00 1.40
402 417 5.054477 AGCGGCAGTAAATACGTATGAATT 58.946 37.500 9.24 2.48 0.00 2.17
403 418 4.628074 AGCGGCAGTAAATACGTATGAAT 58.372 39.130 9.24 1.55 0.00 2.57
404 419 4.049546 AGCGGCAGTAAATACGTATGAA 57.950 40.909 9.24 0.00 0.00 2.57
405 420 3.720949 AGCGGCAGTAAATACGTATGA 57.279 42.857 9.24 0.00 0.00 2.15
406 421 5.862323 AGATTAGCGGCAGTAAATACGTATG 59.138 40.000 9.24 0.00 0.00 2.39
407 422 5.862323 CAGATTAGCGGCAGTAAATACGTAT 59.138 40.000 1.14 1.14 0.00 3.06
408 423 5.008911 TCAGATTAGCGGCAGTAAATACGTA 59.991 40.000 1.45 0.00 0.00 3.57
409 424 4.049186 CAGATTAGCGGCAGTAAATACGT 58.951 43.478 1.45 0.00 0.00 3.57
410 425 4.295870 TCAGATTAGCGGCAGTAAATACG 58.704 43.478 1.45 0.00 0.00 3.06
411 426 5.926542 TGATCAGATTAGCGGCAGTAAATAC 59.073 40.000 1.45 0.00 0.00 1.89
412 427 6.015434 TCTGATCAGATTAGCGGCAGTAAATA 60.015 38.462 21.67 0.00 31.41 1.40
413 428 4.960938 TGATCAGATTAGCGGCAGTAAAT 58.039 39.130 1.45 0.00 0.00 1.40
414 429 4.099419 TCTGATCAGATTAGCGGCAGTAAA 59.901 41.667 21.67 0.00 31.41 2.01
424 439 8.962679 TGATCTCATCTCATCTGATCAGATTAG 58.037 37.037 31.37 30.32 45.31 1.73
439 454 5.006165 CCGCTTTGTTTAGTGATCTCATCTC 59.994 44.000 0.00 0.00 0.00 2.75
443 458 4.265904 TCCGCTTTGTTTAGTGATCTCA 57.734 40.909 0.00 0.00 0.00 3.27
446 461 6.359883 GTCTTTTTCCGCTTTGTTTAGTGATC 59.640 38.462 0.00 0.00 0.00 2.92
479 505 1.641677 CGGCAGCCGCTTATTACAC 59.358 57.895 23.64 0.00 41.17 2.90
508 534 4.451150 TGGGATGGCGACGTGCTC 62.451 66.667 0.67 0.00 45.43 4.26
509 535 4.760047 GTGGGATGGCGACGTGCT 62.760 66.667 0.67 0.00 45.43 4.40
527 553 4.394712 GTGCTGGTCTCGGTGGGG 62.395 72.222 0.00 0.00 0.00 4.96
578 609 1.609783 GGTGATTGGTGGGGAGGAG 59.390 63.158 0.00 0.00 0.00 3.69
579 610 1.928567 GGGTGATTGGTGGGGAGGA 60.929 63.158 0.00 0.00 0.00 3.71
580 611 2.683475 GGGTGATTGGTGGGGAGG 59.317 66.667 0.00 0.00 0.00 4.30
733 774 2.787567 GGACCGAGTAGAGGCCAGC 61.788 68.421 5.01 0.00 0.00 4.85
743 784 1.371558 GGTTCTTGCAGGACCGAGT 59.628 57.895 0.00 0.00 0.00 4.18
765 806 0.970427 AATGAATCCAACCCGGTGCC 60.970 55.000 0.00 0.00 35.57 5.01
766 807 0.894835 AAATGAATCCAACCCGGTGC 59.105 50.000 0.00 0.00 35.57 5.01
767 808 2.094234 GGAAAATGAATCCAACCCGGTG 60.094 50.000 0.00 0.00 36.92 4.94
778 819 1.197812 GGCAGGCAGGGAAAATGAAT 58.802 50.000 0.00 0.00 0.00 2.57
781 822 1.895238 CAGGCAGGCAGGGAAAATG 59.105 57.895 0.00 0.00 0.00 2.32
795 836 1.871126 GACAAGAAAGGCAGGCAGGC 61.871 60.000 0.00 0.00 44.61 4.85
798 839 0.538057 CTGGACAAGAAAGGCAGGCA 60.538 55.000 0.00 0.00 0.00 4.75
799 840 0.538287 ACTGGACAAGAAAGGCAGGC 60.538 55.000 0.00 0.00 0.00 4.85
800 841 1.882623 GAACTGGACAAGAAAGGCAGG 59.117 52.381 0.00 0.00 0.00 4.85
801 842 1.532868 CGAACTGGACAAGAAAGGCAG 59.467 52.381 0.00 0.00 0.00 4.85
802 843 1.593196 CGAACTGGACAAGAAAGGCA 58.407 50.000 0.00 0.00 0.00 4.75
803 844 0.238553 GCGAACTGGACAAGAAAGGC 59.761 55.000 0.00 0.00 0.00 4.35
852 893 2.272447 CCTAGCTAGCTCTCCCGGC 61.272 68.421 23.26 0.00 0.00 6.13
854 895 2.791347 TATCCTAGCTAGCTCTCCCG 57.209 55.000 23.26 5.32 0.00 5.14
856 897 5.826208 GGAGTATTATCCTAGCTAGCTCTCC 59.174 48.000 23.26 21.80 36.35 3.71
879 920 0.041238 TCCACCTCCTCCTGTGTAGG 59.959 60.000 0.00 0.00 46.06 3.18
880 921 1.938585 TTCCACCTCCTCCTGTGTAG 58.061 55.000 0.00 0.00 0.00 2.74
881 922 2.642171 ATTCCACCTCCTCCTGTGTA 57.358 50.000 0.00 0.00 0.00 2.90
882 923 1.747444 AATTCCACCTCCTCCTGTGT 58.253 50.000 0.00 0.00 0.00 3.72
883 924 2.440409 CAAATTCCACCTCCTCCTGTG 58.560 52.381 0.00 0.00 0.00 3.66
884 925 1.272147 GCAAATTCCACCTCCTCCTGT 60.272 52.381 0.00 0.00 0.00 4.00
885 926 1.467920 GCAAATTCCACCTCCTCCTG 58.532 55.000 0.00 0.00 0.00 3.86
886 927 0.332972 GGCAAATTCCACCTCCTCCT 59.667 55.000 0.00 0.00 0.00 3.69
887 928 0.332972 AGGCAAATTCCACCTCCTCC 59.667 55.000 0.00 0.00 0.00 4.30
888 929 1.272147 ACAGGCAAATTCCACCTCCTC 60.272 52.381 0.00 0.00 0.00 3.71
889 930 0.779997 ACAGGCAAATTCCACCTCCT 59.220 50.000 0.00 0.00 0.00 3.69
898 939 6.040209 TCTTGCAATAATCACAGGCAAATT 57.960 33.333 0.00 0.00 43.08 1.82
899 940 5.664294 TCTTGCAATAATCACAGGCAAAT 57.336 34.783 0.00 0.00 43.08 2.32
905 946 4.607778 CGCGAGATCTTGCAATAATCACAG 60.608 45.833 29.99 9.68 39.96 3.66
911 952 0.937304 GGCGCGAGATCTTGCAATAA 59.063 50.000 29.99 0.00 39.96 1.40
914 955 1.638388 CTTGGCGCGAGATCTTGCAA 61.638 55.000 29.99 17.90 39.96 4.08
918 959 0.532573 TCTTCTTGGCGCGAGATCTT 59.467 50.000 12.10 0.00 0.00 2.40
937 978 2.360100 CTGCTGCTGCTGCTTCCT 60.360 61.111 27.67 0.00 40.48 3.36
943 984 3.128188 CTCCTGCTGCTGCTGCTG 61.128 66.667 27.67 25.97 40.48 4.41
946 987 2.878089 ATCTGCTCCTGCTGCTGCTG 62.878 60.000 17.00 15.58 40.48 4.41
947 988 2.199613 AATCTGCTCCTGCTGCTGCT 62.200 55.000 17.00 0.00 40.48 4.24
950 991 0.619505 AAGAATCTGCTCCTGCTGCT 59.380 50.000 0.00 0.00 40.48 4.24
953 994 2.039480 TGTTGAAGAATCTGCTCCTGCT 59.961 45.455 0.00 0.00 40.48 4.24
956 997 4.077822 CCTTTGTTGAAGAATCTGCTCCT 58.922 43.478 0.00 0.00 37.57 3.69
958 999 4.155644 CCTCCTTTGTTGAAGAATCTGCTC 59.844 45.833 0.00 0.00 37.57 4.26
965 1006 2.489073 GCCTCCCTCCTTTGTTGAAGAA 60.489 50.000 0.00 0.00 37.57 2.52
973 1014 1.147153 GATCCGCCTCCCTCCTTTG 59.853 63.158 0.00 0.00 0.00 2.77
974 1015 2.435693 CGATCCGCCTCCCTCCTTT 61.436 63.158 0.00 0.00 0.00 3.11
1157 1214 0.600255 CTGGTAATAGGCGGCGGAAG 60.600 60.000 9.78 0.00 0.00 3.46
1159 1216 3.134879 CTGGTAATAGGCGGCGGA 58.865 61.111 9.78 0.00 0.00 5.54
1377 1440 1.179152 TGATGTCGACGAAGGGCTTA 58.821 50.000 11.62 0.00 0.00 3.09
1417 1480 3.419759 CTGGTACACCGTTGCCGC 61.420 66.667 0.00 0.00 39.43 6.53
1418 1481 2.740826 CCTGGTACACCGTTGCCG 60.741 66.667 0.00 0.00 39.43 5.69
1419 1482 1.670083 GTCCTGGTACACCGTTGCC 60.670 63.158 0.00 0.00 39.43 4.52
1420 1483 0.949105 CTGTCCTGGTACACCGTTGC 60.949 60.000 0.00 0.00 39.43 4.17
1421 1484 0.320421 CCTGTCCTGGTACACCGTTG 60.320 60.000 0.00 0.00 39.43 4.10
1422 1485 0.761702 ACCTGTCCTGGTACACCGTT 60.762 55.000 0.00 0.00 38.79 4.44
1423 1486 1.152398 ACCTGTCCTGGTACACCGT 60.152 57.895 0.00 0.00 38.79 4.83
1424 1487 0.898789 AGACCTGTCCTGGTACACCG 60.899 60.000 0.00 0.00 41.00 4.94
1425 1488 1.002087 CAAGACCTGTCCTGGTACACC 59.998 57.143 0.00 0.00 41.00 4.16
1426 1489 1.002087 CCAAGACCTGTCCTGGTACAC 59.998 57.143 6.75 0.00 41.00 2.90
1427 1490 1.132977 TCCAAGACCTGTCCTGGTACA 60.133 52.381 13.27 0.00 41.02 2.90
1435 1498 2.629336 GGATCCATCCAAGACCTGTC 57.371 55.000 6.95 0.00 46.38 3.51
1464 1527 0.807667 CTCCTCCCATCGTTGCGAAG 60.808 60.000 0.00 0.00 39.99 3.79
1470 1533 1.689582 GGACCCTCCTCCCATCGTT 60.690 63.158 0.00 0.00 32.53 3.85
1471 1534 2.041819 GGACCCTCCTCCCATCGT 60.042 66.667 0.00 0.00 32.53 3.73
1485 1548 2.803492 GCTGACGAACATATCAGGGGAC 60.803 54.545 3.61 0.00 42.25 4.46
1700 1766 1.639298 GAGGATGCAGTTGACACCGC 61.639 60.000 0.00 0.00 0.00 5.68
1734 1800 1.143620 GCTGATCTCTGCTTCGGCT 59.856 57.895 0.00 0.00 40.38 5.52
1845 1911 0.391661 CGCAGTGTATGAGCAGGGTT 60.392 55.000 0.00 0.00 0.00 4.11
2037 2103 2.737376 GCGGAAGAAGTTCGCCGT 60.737 61.111 28.58 6.60 39.93 5.68
2079 2145 2.594592 GGGCATGCGGTCCCATAC 60.595 66.667 12.44 0.00 42.18 2.39
2088 2154 2.711311 CTGATGAACGGGCATGCG 59.289 61.111 12.44 0.62 0.00 4.73
2262 2328 1.488527 GTAAGTCGATGGCGGTGATC 58.511 55.000 0.00 0.00 38.28 2.92
2337 2403 3.394674 TCAAACATCTTGGCGTAGTCA 57.605 42.857 0.00 0.00 45.30 3.41
2340 2406 4.437390 GGAACATCAAACATCTTGGCGTAG 60.437 45.833 0.00 0.00 0.00 3.51
2356 2422 3.000727 CACGGTACTCAAAGGGAACATC 58.999 50.000 0.00 0.00 0.00 3.06
2367 2433 0.735978 CAGCAATCGCACGGTACTCA 60.736 55.000 0.00 0.00 42.27 3.41
2373 2439 3.672255 CTTGGCAGCAATCGCACGG 62.672 63.158 0.00 0.00 42.27 4.94
2376 2442 2.628696 CCACTTGGCAGCAATCGCA 61.629 57.895 0.00 0.00 42.27 5.10
2379 2445 0.458669 CATCCCACTTGGCAGCAATC 59.541 55.000 0.00 0.00 0.00 2.67
2436 2502 5.695851 ACAAGCAGTTGACAATAAGAAGG 57.304 39.130 0.00 0.00 37.10 3.46
2491 2557 4.292178 CCTCGGGCTCTCATCGGC 62.292 72.222 0.00 0.00 0.00 5.54
2619 2685 4.512198 TCGTAGAGCGAGGAGAAATAGAAG 59.488 45.833 0.00 0.00 45.68 2.85
3072 3161 1.361204 TCCATCAACTCTGCTCCCAA 58.639 50.000 0.00 0.00 0.00 4.12
3102 3191 6.587273 AGAAGCTTCTGTTCTAGTCAAGTTT 58.413 36.000 27.96 0.00 35.89 2.66
3210 3423 2.229792 TGCACCTTCCATTGAACTGAC 58.770 47.619 0.00 0.00 0.00 3.51
3241 3454 4.917998 ACGCAACAGCTAATATATCACTCG 59.082 41.667 0.00 0.00 0.00 4.18
3332 3545 9.261180 CATTGATACAGTTTAACGGATATGACT 57.739 33.333 1.74 0.00 0.00 3.41
3370 3583 2.289072 CGAGGAGGAGAAGTCAGCAAAA 60.289 50.000 0.00 0.00 0.00 2.44
3384 3597 1.067821 CCGAGATTTTCTCCGAGGAGG 59.932 57.143 18.16 1.34 40.34 4.30
3436 3650 5.858381 TGAAAATAGCCTTCTATCGATGCT 58.142 37.500 8.54 10.26 34.53 3.79
3571 3787 7.226720 GGTTTTGAGTCATCAGTTAAGACTTGA 59.773 37.037 0.00 0.00 42.29 3.02
3572 3788 7.355778 GGTTTTGAGTCATCAGTTAAGACTTG 58.644 38.462 0.00 0.00 42.29 3.16
3573 3789 6.202954 CGGTTTTGAGTCATCAGTTAAGACTT 59.797 38.462 0.00 0.00 42.29 3.01
3574 3790 5.696724 CGGTTTTGAGTCATCAGTTAAGACT 59.303 40.000 0.00 0.00 44.71 3.24
3575 3791 5.107065 CCGGTTTTGAGTCATCAGTTAAGAC 60.107 44.000 0.00 0.00 36.61 3.01
3576 3792 4.994852 CCGGTTTTGAGTCATCAGTTAAGA 59.005 41.667 0.00 0.00 36.61 2.10
3704 3920 2.224646 ACTTCTCTTGAAACAGGCCCTC 60.225 50.000 0.00 0.00 0.00 4.30
3736 3952 2.427506 GACCACTTGAGGACAACCATC 58.572 52.381 0.00 0.00 38.94 3.51
3766 3986 9.224267 CCTACTATATGATAATTGCTGCAACTT 57.776 33.333 18.51 14.64 0.00 2.66
3791 4011 6.870971 TGAAGTTTGTGTTCAGGTATAACC 57.129 37.500 0.00 0.00 38.99 2.85
3832 4052 3.055819 TCCAGACTGACACTAAGGCAATC 60.056 47.826 3.32 0.00 32.28 2.67
3874 4094 1.280421 GGAGTGAGGGAGCTGATTGTT 59.720 52.381 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.