Multiple sequence alignment - TraesCS5A01G397000

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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 TraesCS5A01G397000 chr5A 100.000 4199 0 0 1 4199 591485442 591489640 0.000000e+00 7755.0
1 TraesCS5A01G397000 chr5D 94.769 3307 150 8 897 4199 472282125 472285412 0.000000e+00 5127.0
2 TraesCS5A01G397000 chr5B 92.483 2714 162 21 796 3496 578600291 578602975 0.000000e+00 3843.0
3 TraesCS5A01G397000 chr5B 84.773 683 92 9 3482 4157 578603741 578604418 0.000000e+00 675.0
4 TraesCS5A01G397000 chr7D 85.495 586 72 4 206 781 474254604 474254022 2.160000e-167 599.0
5 TraesCS5A01G397000 chr7B 85.792 549 66 3 243 781 498253754 498253208 4.710000e-159 571.0
6 TraesCS5A01G397000 chr7B 87.879 66 6 2 49 113 554757605 554757541 4.500000e-10 76.8
7 TraesCS5A01G397000 chr2B 86.173 405 48 5 194 592 150927898 150927496 8.340000e-117 431.0
8 TraesCS5A01G397000 chr2B 90.323 62 6 0 49 110 723407807 723407868 9.680000e-12 82.4
9 TraesCS5A01G397000 chr2D 81.855 496 78 7 196 687 644172463 644172950 1.410000e-109 407.0
10 TraesCS5A01G397000 chr1D 83.681 288 45 2 365 651 483851327 483851613 1.920000e-68 270.0
11 TraesCS5A01G397000 chr3D 85.088 114 6 7 1 107 426000676 426000567 5.740000e-19 106.0
12 TraesCS5A01G397000 chr3D 93.333 60 2 2 49 107 542996327 542996269 2.080000e-13 87.9
13 TraesCS5A01G397000 chr7A 96.610 59 2 0 49 107 636881836 636881894 9.610000e-17 99.0
14 TraesCS5A01G397000 chr3B 91.667 60 4 1 49 107 556366263 556366322 9.680000e-12 82.4
15 TraesCS5A01G397000 chr4D 89.062 64 7 0 49 112 469913077 469913140 3.480000e-11 80.5
16 TraesCS5A01G397000 chr2A 92.593 54 2 2 49 101 772096060 772096112 4.500000e-10 76.8
17 TraesCS5A01G397000 chr2A 92.593 54 2 2 49 101 772136461 772136513 4.500000e-10 76.8
18 TraesCS5A01G397000 chr4B 93.750 48 3 0 1 48 661196849 661196802 5.820000e-09 73.1


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 TraesCS5A01G397000 chr5A 591485442 591489640 4198 False 7755 7755 100.000 1 4199 1 chr5A.!!$F1 4198
1 TraesCS5A01G397000 chr5D 472282125 472285412 3287 False 5127 5127 94.769 897 4199 1 chr5D.!!$F1 3302
2 TraesCS5A01G397000 chr5B 578600291 578604418 4127 False 2259 3843 88.628 796 4157 2 chr5B.!!$F1 3361
3 TraesCS5A01G397000 chr7D 474254022 474254604 582 True 599 599 85.495 206 781 1 chr7D.!!$R1 575
4 TraesCS5A01G397000 chr7B 498253208 498253754 546 True 571 571 85.792 243 781 1 chr7B.!!$R1 538

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
66 67 0.460987 GGTCGCAACCTGGAGAGATG 60.461 60.0 0.0 0.0 42.8 2.90 F
67 68 0.532573 GTCGCAACCTGGAGAGATGA 59.467 55.0 0.0 0.0 0.0 2.92 F
1895 1926 0.179084 TCGGCTTAATCCTGCTTCGG 60.179 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1012 1028 0.337082 TCGGAACCCTAGGATCCACA 59.663 55.000 24.87 13.25 43.72 4.17 R
2012 2043 0.677098 AGTGCTGCCAGCTCATCAAG 60.677 55.000 18.96 0.00 42.97 3.02 R
3878 4697 2.144730 TGAAGCATGTGCCAAAAATGC 58.855 42.857 0.57 0.00 45.62 3.56 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
52 53 4.553756 AAAAGAAAAACTCTCAGGTCGC 57.446 40.909 0.00 0.00 31.02 5.19
53 54 2.910688 AGAAAAACTCTCAGGTCGCA 57.089 45.000 0.00 0.00 0.00 5.10
54 55 3.194005 AGAAAAACTCTCAGGTCGCAA 57.806 42.857 0.00 0.00 0.00 4.85
55 56 2.872858 AGAAAAACTCTCAGGTCGCAAC 59.127 45.455 0.00 0.00 0.00 4.17
56 57 1.594331 AAAACTCTCAGGTCGCAACC 58.406 50.000 0.00 0.00 46.87 3.77
57 58 7.888400 AAGAAAAACTCTCAGGTCGCAACCT 62.888 44.000 0.00 0.00 45.46 3.50
64 65 3.377656 GGTCGCAACCTGGAGAGA 58.622 61.111 0.00 0.00 42.80 3.10
65 66 1.901085 GGTCGCAACCTGGAGAGAT 59.099 57.895 0.00 0.00 42.80 2.75
66 67 0.460987 GGTCGCAACCTGGAGAGATG 60.461 60.000 0.00 0.00 42.80 2.90
67 68 0.532573 GTCGCAACCTGGAGAGATGA 59.467 55.000 0.00 0.00 0.00 2.92
68 69 0.820226 TCGCAACCTGGAGAGATGAG 59.180 55.000 0.00 0.00 0.00 2.90
69 70 0.820226 CGCAACCTGGAGAGATGAGA 59.180 55.000 0.00 0.00 0.00 3.27
70 71 1.202394 CGCAACCTGGAGAGATGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
71 72 1.830477 GCAACCTGGAGAGATGAGAGT 59.170 52.381 0.00 0.00 0.00 3.24
72 73 3.027412 GCAACCTGGAGAGATGAGAGTA 58.973 50.000 0.00 0.00 0.00 2.59
73 74 3.449018 GCAACCTGGAGAGATGAGAGTAA 59.551 47.826 0.00 0.00 0.00 2.24
74 75 4.100808 GCAACCTGGAGAGATGAGAGTAAT 59.899 45.833 0.00 0.00 0.00 1.89
75 76 5.738783 GCAACCTGGAGAGATGAGAGTAATC 60.739 48.000 0.00 0.00 0.00 1.75
76 77 5.402054 ACCTGGAGAGATGAGAGTAATCT 57.598 43.478 0.00 0.00 37.09 2.40
77 78 5.776358 ACCTGGAGAGATGAGAGTAATCTT 58.224 41.667 0.00 0.00 34.50 2.40
78 79 6.201591 ACCTGGAGAGATGAGAGTAATCTTT 58.798 40.000 0.00 0.00 34.50 2.52
79 80 6.098124 ACCTGGAGAGATGAGAGTAATCTTTG 59.902 42.308 0.00 0.00 34.50 2.77
80 81 6.323482 CCTGGAGAGATGAGAGTAATCTTTGA 59.677 42.308 0.00 0.00 34.50 2.69
81 82 7.147759 CCTGGAGAGATGAGAGTAATCTTTGAA 60.148 40.741 0.00 0.00 34.50 2.69
82 83 8.138928 TGGAGAGATGAGAGTAATCTTTGAAA 57.861 34.615 0.00 0.00 34.50 2.69
83 84 8.256605 TGGAGAGATGAGAGTAATCTTTGAAAG 58.743 37.037 0.00 0.00 34.50 2.62
84 85 8.474025 GGAGAGATGAGAGTAATCTTTGAAAGA 58.526 37.037 10.39 10.39 42.69 2.52
85 86 9.868277 GAGAGATGAGAGTAATCTTTGAAAGAA 57.132 33.333 12.10 0.00 41.63 2.52
86 87 9.874205 AGAGATGAGAGTAATCTTTGAAAGAAG 57.126 33.333 12.10 0.00 41.63 2.85
87 88 9.651913 GAGATGAGAGTAATCTTTGAAAGAAGT 57.348 33.333 12.10 5.79 41.63 3.01
91 92 9.915629 TGAGAGTAATCTTTGAAAGAAGTACTC 57.084 33.333 30.78 30.78 46.60 2.59
92 93 9.361315 GAGAGTAATCTTTGAAAGAAGTACTCC 57.639 37.037 32.25 25.77 46.95 3.85
93 94 9.095700 AGAGTAATCTTTGAAAGAAGTACTCCT 57.904 33.333 32.25 24.40 46.95 3.69
94 95 9.713713 GAGTAATCTTTGAAAGAAGTACTCCTT 57.286 33.333 29.43 15.82 44.06 3.36
121 122 5.966636 AGTGATTTTGTTTTTCTTTCGCC 57.033 34.783 0.00 0.00 0.00 5.54
122 123 4.808895 AGTGATTTTGTTTTTCTTTCGCCC 59.191 37.500 0.00 0.00 0.00 6.13
123 124 3.799420 TGATTTTGTTTTTCTTTCGCCCG 59.201 39.130 0.00 0.00 0.00 6.13
124 125 1.562017 TTTGTTTTTCTTTCGCCCGC 58.438 45.000 0.00 0.00 0.00 6.13
125 126 0.592754 TTGTTTTTCTTTCGCCCGCG 60.593 50.000 0.00 0.00 41.35 6.46
126 127 1.009335 GTTTTTCTTTCGCCCGCGT 60.009 52.632 4.92 0.00 40.74 6.01
127 128 0.995234 GTTTTTCTTTCGCCCGCGTC 60.995 55.000 4.92 0.00 40.74 5.19
128 129 1.437772 TTTTTCTTTCGCCCGCGTCA 61.438 50.000 4.92 0.00 40.74 4.35
129 130 2.108344 TTTTCTTTCGCCCGCGTCAC 62.108 55.000 4.92 0.00 40.74 3.67
130 131 3.793775 TTCTTTCGCCCGCGTCACA 62.794 57.895 4.92 0.00 40.74 3.58
131 132 4.072088 CTTTCGCCCGCGTCACAC 62.072 66.667 4.92 0.00 40.74 3.82
141 142 2.051345 CGTCACACGCCCAAAAGC 60.051 61.111 0.00 0.00 33.65 3.51
142 143 2.542907 CGTCACACGCCCAAAAGCT 61.543 57.895 0.00 0.00 33.65 3.74
143 144 1.225376 CGTCACACGCCCAAAAGCTA 61.225 55.000 0.00 0.00 33.65 3.32
144 145 0.948678 GTCACACGCCCAAAAGCTAA 59.051 50.000 0.00 0.00 0.00 3.09
145 146 1.335496 GTCACACGCCCAAAAGCTAAA 59.665 47.619 0.00 0.00 0.00 1.85
146 147 1.335496 TCACACGCCCAAAAGCTAAAC 59.665 47.619 0.00 0.00 0.00 2.01
147 148 1.336755 CACACGCCCAAAAGCTAAACT 59.663 47.619 0.00 0.00 0.00 2.66
148 149 2.028876 ACACGCCCAAAAGCTAAACTT 58.971 42.857 0.00 0.00 41.70 2.66
149 150 2.034179 ACACGCCCAAAAGCTAAACTTC 59.966 45.455 0.00 0.00 37.75 3.01
150 151 2.293399 CACGCCCAAAAGCTAAACTTCT 59.707 45.455 0.00 0.00 37.75 2.85
151 152 2.956333 ACGCCCAAAAGCTAAACTTCTT 59.044 40.909 0.00 0.00 37.75 2.52
152 153 3.004419 ACGCCCAAAAGCTAAACTTCTTC 59.996 43.478 0.00 0.00 37.75 2.87
153 154 3.253432 CGCCCAAAAGCTAAACTTCTTCT 59.747 43.478 0.00 0.00 37.75 2.85
154 155 4.613850 CGCCCAAAAGCTAAACTTCTTCTC 60.614 45.833 0.00 0.00 37.75 2.87
155 156 4.321304 GCCCAAAAGCTAAACTTCTTCTCC 60.321 45.833 0.00 0.00 37.75 3.71
156 157 5.073428 CCCAAAAGCTAAACTTCTTCTCCT 58.927 41.667 0.00 0.00 37.75 3.69
157 158 6.238648 CCCAAAAGCTAAACTTCTTCTCCTA 58.761 40.000 0.00 0.00 37.75 2.94
158 159 6.372937 CCCAAAAGCTAAACTTCTTCTCCTAG 59.627 42.308 0.00 0.00 37.75 3.02
159 160 6.937465 CCAAAAGCTAAACTTCTTCTCCTAGT 59.063 38.462 0.00 0.00 37.75 2.57
160 161 7.095017 CCAAAAGCTAAACTTCTTCTCCTAGTG 60.095 40.741 0.00 0.00 37.75 2.74
161 162 6.919775 AAGCTAAACTTCTTCTCCTAGTGA 57.080 37.500 0.00 0.00 30.77 3.41
162 163 6.919775 AGCTAAACTTCTTCTCCTAGTGAA 57.080 37.500 0.00 0.00 0.00 3.18
163 164 7.304497 AGCTAAACTTCTTCTCCTAGTGAAA 57.696 36.000 0.00 0.00 0.00 2.69
164 165 7.736893 AGCTAAACTTCTTCTCCTAGTGAAAA 58.263 34.615 0.00 0.00 0.00 2.29
165 166 8.379331 AGCTAAACTTCTTCTCCTAGTGAAAAT 58.621 33.333 0.00 0.00 0.00 1.82
166 167 8.447053 GCTAAACTTCTTCTCCTAGTGAAAATG 58.553 37.037 0.00 0.00 0.00 2.32
167 168 9.712305 CTAAACTTCTTCTCCTAGTGAAAATGA 57.288 33.333 0.00 0.00 0.00 2.57
168 169 7.971183 AACTTCTTCTCCTAGTGAAAATGAC 57.029 36.000 0.00 0.00 0.00 3.06
169 170 7.309770 ACTTCTTCTCCTAGTGAAAATGACT 57.690 36.000 0.00 0.00 0.00 3.41
170 171 8.423906 ACTTCTTCTCCTAGTGAAAATGACTA 57.576 34.615 0.00 0.00 0.00 2.59
171 172 9.041354 ACTTCTTCTCCTAGTGAAAATGACTAT 57.959 33.333 0.00 0.00 0.00 2.12
172 173 9.311916 CTTCTTCTCCTAGTGAAAATGACTATG 57.688 37.037 0.00 0.00 0.00 2.23
173 174 8.367660 TCTTCTCCTAGTGAAAATGACTATGT 57.632 34.615 0.00 0.00 0.00 2.29
174 175 8.816894 TCTTCTCCTAGTGAAAATGACTATGTT 58.183 33.333 0.00 0.00 0.00 2.71
175 176 9.442047 CTTCTCCTAGTGAAAATGACTATGTTT 57.558 33.333 0.00 0.00 0.00 2.83
176 177 9.793259 TTCTCCTAGTGAAAATGACTATGTTTT 57.207 29.630 0.00 0.00 0.00 2.43
177 178 9.793259 TCTCCTAGTGAAAATGACTATGTTTTT 57.207 29.630 0.00 0.00 0.00 1.94
178 179 9.831737 CTCCTAGTGAAAATGACTATGTTTTTG 57.168 33.333 0.00 0.00 0.00 2.44
179 180 8.792633 TCCTAGTGAAAATGACTATGTTTTTGG 58.207 33.333 0.00 0.00 0.00 3.28
180 181 8.028938 CCTAGTGAAAATGACTATGTTTTTGGG 58.971 37.037 0.00 0.00 0.00 4.12
181 182 7.360113 AGTGAAAATGACTATGTTTTTGGGT 57.640 32.000 0.00 0.00 0.00 4.51
182 183 8.472007 AGTGAAAATGACTATGTTTTTGGGTA 57.528 30.769 0.00 0.00 0.00 3.69
183 184 9.088987 AGTGAAAATGACTATGTTTTTGGGTAT 57.911 29.630 0.00 0.00 0.00 2.73
220 221 1.335496 TGTGCGGTTAAACCAAGCTTC 59.665 47.619 0.00 0.00 38.47 3.86
229 230 6.128007 CGGTTAAACCAAGCTTCATTACTCAT 60.128 38.462 0.00 0.00 38.47 2.90
231 232 8.736244 GGTTAAACCAAGCTTCATTACTCATAA 58.264 33.333 0.00 0.00 38.42 1.90
236 237 6.543831 ACCAAGCTTCATTACTCATAATCCAC 59.456 38.462 0.00 0.00 0.00 4.02
238 239 7.230108 CCAAGCTTCATTACTCATAATCCACAT 59.770 37.037 0.00 0.00 0.00 3.21
240 241 6.713903 AGCTTCATTACTCATAATCCACATGG 59.286 38.462 0.00 0.00 0.00 3.66
241 242 6.488006 GCTTCATTACTCATAATCCACATGGT 59.512 38.462 0.00 0.00 36.34 3.55
277 278 1.425448 GATTATGGGGTTGCCCTAGCT 59.575 52.381 4.02 0.00 44.66 3.32
287 288 1.414158 TGCCCTAGCTAGACATGTCC 58.586 55.000 22.70 7.34 40.80 4.02
288 289 1.062886 TGCCCTAGCTAGACATGTCCT 60.063 52.381 22.70 14.36 40.80 3.85
289 290 2.043227 GCCCTAGCTAGACATGTCCTT 58.957 52.381 22.70 7.54 35.50 3.36
294 298 3.724508 AGCTAGACATGTCCTTCATCG 57.275 47.619 22.21 0.89 34.09 3.84
313 317 3.738982 TCGAGAGAATTTGCCAACTTGA 58.261 40.909 0.00 0.00 37.03 3.02
361 365 8.627208 AGATGCTCTACATTCAAAAGAGAAAA 57.373 30.769 2.86 0.00 39.84 2.29
362 366 8.510505 AGATGCTCTACATTCAAAAGAGAAAAC 58.489 33.333 2.86 0.00 39.84 2.43
398 402 2.826128 TGTAGCTCGTTGGTTGATCTCT 59.174 45.455 0.00 0.00 0.00 3.10
399 403 4.014406 TGTAGCTCGTTGGTTGATCTCTA 58.986 43.478 0.00 0.00 0.00 2.43
401 405 4.744795 AGCTCGTTGGTTGATCTCTAAT 57.255 40.909 0.00 0.00 0.00 1.73
409 413 8.421002 TCGTTGGTTGATCTCTAATATGATTGA 58.579 33.333 0.00 0.00 0.00 2.57
424 428 2.158711 TGATTGATCCATGCTCTCCACC 60.159 50.000 0.00 0.00 0.00 4.61
431 435 1.610673 ATGCTCTCCACCGGACTGT 60.611 57.895 9.46 0.00 0.00 3.55
451 455 5.046878 ACTGTTTGGCAATGTCATTGATCAT 60.047 36.000 26.36 7.78 42.83 2.45
461 465 7.674008 GCAATGTCATTGATCATTTGCTTTGAG 60.674 37.037 26.36 0.00 42.83 3.02
468 472 4.698780 TGATCATTTGCTTTGAGTCAGAGG 59.301 41.667 12.28 0.00 0.00 3.69
475 479 3.453717 TGCTTTGAGTCAGAGGCTATGAT 59.546 43.478 15.75 4.53 0.00 2.45
476 480 3.808726 GCTTTGAGTCAGAGGCTATGATG 59.191 47.826 15.75 0.00 0.00 3.07
492 496 5.276584 GCTATGATGAAGTTGTTCAGTAGCG 60.277 44.000 11.13 0.00 45.96 4.26
499 503 2.628657 AGTTGTTCAGTAGCGAGTCCTT 59.371 45.455 0.00 0.00 0.00 3.36
501 505 2.235891 TGTTCAGTAGCGAGTCCTTGA 58.764 47.619 0.00 0.00 0.00 3.02
526 530 1.674817 CGCTAAACCTTCCCGACATGT 60.675 52.381 0.00 0.00 0.00 3.21
531 535 3.992943 AACCTTCCCGACATGTTATGA 57.007 42.857 0.00 0.00 0.00 2.15
554 558 1.374252 AAGTGTCGCGACATCCACC 60.374 57.895 40.84 28.12 43.97 4.61
555 559 3.179265 GTGTCGCGACATCCACCG 61.179 66.667 40.84 0.00 43.97 4.94
573 577 1.522668 CGTTCCTGCAATCACCAAGA 58.477 50.000 0.00 0.00 0.00 3.02
588 592 1.089920 CAAGACCGAGCTTCCAATGG 58.910 55.000 0.00 0.00 0.00 3.16
606 610 1.277273 TGGAGTTGCCAGTCTCATCAG 59.723 52.381 0.00 0.00 43.33 2.90
608 612 1.552337 GAGTTGCCAGTCTCATCAGGA 59.448 52.381 0.00 0.00 0.00 3.86
616 620 3.307269 CCAGTCTCATCAGGACACACAAT 60.307 47.826 0.00 0.00 36.29 2.71
639 643 4.864334 CTGCTCCCCGGACATGGC 62.864 72.222 0.73 0.00 0.00 4.40
652 656 3.428180 CGGACATGGCTTCTAGATATCGG 60.428 52.174 0.00 0.00 0.00 4.18
654 658 4.142271 GGACATGGCTTCTAGATATCGGAG 60.142 50.000 0.00 0.00 0.00 4.63
662 666 1.128878 CTAGATATCGGAGCGTCCACG 59.871 57.143 0.00 0.00 35.91 4.94
673 677 0.949105 GCGTCCACGTGAATCTTGGT 60.949 55.000 19.30 0.00 42.22 3.67
704 715 1.353076 GAGGCGTTTTGTAGGTACGG 58.647 55.000 0.00 0.00 35.91 4.02
708 719 1.339711 CGTTTTGTAGGTACGGTCGG 58.660 55.000 0.00 0.00 0.00 4.79
726 737 0.744874 GGTGATGTACCTCGCTGCTA 59.255 55.000 10.87 0.00 46.51 3.49
762 773 2.877168 GCAATAGTTCCAGATCAGCCAG 59.123 50.000 0.00 0.00 0.00 4.85
763 774 3.474600 CAATAGTTCCAGATCAGCCAGG 58.525 50.000 0.00 0.00 0.00 4.45
767 778 2.087646 GTTCCAGATCAGCCAGGAAAC 58.912 52.381 0.00 0.00 41.42 2.78
781 792 4.555262 CCAGGAAACGTGCAATAAATTGT 58.445 39.130 4.71 0.00 39.88 2.71
782 793 5.704888 CCAGGAAACGTGCAATAAATTGTA 58.295 37.500 4.71 0.00 39.88 2.41
783 794 6.329496 CCAGGAAACGTGCAATAAATTGTAT 58.671 36.000 4.71 0.00 39.88 2.29
784 795 7.476667 CCAGGAAACGTGCAATAAATTGTATA 58.523 34.615 4.71 0.00 39.88 1.47
785 796 7.431084 CCAGGAAACGTGCAATAAATTGTATAC 59.569 37.037 4.71 0.00 39.88 1.47
786 797 8.181573 CAGGAAACGTGCAATAAATTGTATACT 58.818 33.333 4.17 0.00 39.88 2.12
787 798 8.181573 AGGAAACGTGCAATAAATTGTATACTG 58.818 33.333 4.17 0.00 39.88 2.74
788 799 8.178964 GGAAACGTGCAATAAATTGTATACTGA 58.821 33.333 4.17 0.00 39.88 3.41
789 800 9.549509 GAAACGTGCAATAAATTGTATACTGAA 57.450 29.630 4.17 0.00 39.88 3.02
790 801 9.900710 AAACGTGCAATAAATTGTATACTGAAA 57.099 25.926 4.17 0.00 39.88 2.69
791 802 9.900710 AACGTGCAATAAATTGTATACTGAAAA 57.099 25.926 4.17 0.00 39.88 2.29
818 829 8.826710 TGATTATTTTTGTCCTATCGCTGTAAG 58.173 33.333 0.00 0.00 0.00 2.34
821 832 2.579207 TGTCCTATCGCTGTAAGTGC 57.421 50.000 0.00 0.00 46.11 4.40
822 833 1.822371 TGTCCTATCGCTGTAAGTGCA 59.178 47.619 0.00 0.00 46.11 4.57
825 836 1.137086 CCTATCGCTGTAAGTGCACCT 59.863 52.381 14.63 2.32 46.11 4.00
864 875 0.929244 ACTGGGCCTGCCTAATCAAT 59.071 50.000 10.71 0.00 36.10 2.57
869 880 4.555689 TGGGCCTGCCTAATCAATTTTAT 58.444 39.130 4.53 0.00 36.10 1.40
876 887 4.588528 TGCCTAATCAATTTTATCTGGGCC 59.411 41.667 0.00 0.00 35.54 5.80
879 890 6.739565 GCCTAATCAATTTTATCTGGGCCTTG 60.740 42.308 4.53 0.00 0.00 3.61
892 903 1.818642 GGCCTTGCATGCCTATAGAG 58.181 55.000 16.68 3.50 45.70 2.43
893 904 1.163554 GCCTTGCATGCCTATAGAGC 58.836 55.000 16.68 4.74 0.00 4.09
894 905 1.436600 CCTTGCATGCCTATAGAGCG 58.563 55.000 16.68 0.00 0.00 5.03
912 928 1.490693 CGATCAAGACGGCCCAATCG 61.491 60.000 0.00 2.85 0.00 3.34
922 938 2.974698 CCCAATCGGAGCCGCATC 60.975 66.667 3.59 0.00 39.59 3.91
981 997 1.819632 CTTCCCAATTCCCGCTCCG 60.820 63.158 0.00 0.00 0.00 4.63
1005 1021 2.040178 CGCCATTCCCCTTCTACTACT 58.960 52.381 0.00 0.00 0.00 2.57
1010 1026 3.463048 TTCCCCTTCTACTACTCCGTT 57.537 47.619 0.00 0.00 0.00 4.44
1012 1028 2.579860 TCCCCTTCTACTACTCCGTTCT 59.420 50.000 0.00 0.00 0.00 3.01
1020 1036 2.100989 ACTACTCCGTTCTGTGGATCC 58.899 52.381 4.20 4.20 34.32 3.36
1181 1212 0.262876 AATCCAGGCCCAAATCCTCC 59.737 55.000 0.00 0.00 0.00 4.30
1185 1216 2.042944 GGCCCAAATCCTCCCACC 60.043 66.667 0.00 0.00 0.00 4.61
1187 1218 2.978946 GCCCAAATCCTCCCACCGA 61.979 63.158 0.00 0.00 0.00 4.69
1202 1233 4.717629 CGACGCCAACTCCTCGCA 62.718 66.667 0.00 0.00 0.00 5.10
1224 1255 4.735132 CCGCCGAGCCAAACGAGA 62.735 66.667 0.00 0.00 0.00 4.04
1227 1258 2.048222 CCGAGCCAAACGAGAGCA 60.048 61.111 0.00 0.00 0.00 4.26
1230 1261 0.798776 CGAGCCAAACGAGAGCAAAT 59.201 50.000 0.00 0.00 0.00 2.32
1250 1281 3.943034 CTCGACGCGCTCCTCGAT 61.943 66.667 18.03 0.00 38.22 3.59
1259 1290 4.519437 CTCCTCGATGCGCTGCCA 62.519 66.667 9.73 0.00 0.00 4.92
1478 1509 4.742201 TCCCAGCTCAACGCGCTC 62.742 66.667 5.73 0.00 45.59 5.03
1661 1692 1.553690 TTTCCCTTCTCCTCCGCCTG 61.554 60.000 0.00 0.00 0.00 4.85
1880 1911 0.390472 CTTCCTTCCTCTGTGTCGGC 60.390 60.000 0.00 0.00 0.00 5.54
1895 1926 0.179084 TCGGCTTAATCCTGCTTCGG 60.179 55.000 0.00 0.00 0.00 4.30
1915 1946 2.948979 GGATGGATTGTGGCGTATTTCA 59.051 45.455 0.00 0.00 0.00 2.69
2012 2043 2.198304 ATTCCGGGTGACAAGGAGGC 62.198 60.000 0.00 0.00 39.37 4.70
2097 2128 2.514824 GGCGGTTCCTGATGAGGC 60.515 66.667 0.00 0.00 39.57 4.70
2335 2366 1.149101 TCTTGGCTTCAAGGAACCCT 58.851 50.000 6.32 0.00 45.84 4.34
2374 2405 1.639722 TGTTCGATTCCACTGGAGGA 58.360 50.000 0.00 0.00 35.41 3.71
2462 2493 8.793592 ACTTTGGAGACATTTTAGATGTTAACC 58.206 33.333 2.48 0.00 42.32 2.85
2497 2528 4.016790 AGGAGCTCCCAGGCCTCA 62.017 66.667 29.54 0.00 37.41 3.86
2689 2720 4.752146 TGATGTCAGATGTTCTGCTACAG 58.248 43.478 0.00 0.00 43.95 2.74
2809 2840 7.609097 AGCTCTCAAGGTGAATATCTCATAA 57.391 36.000 0.00 0.00 36.14 1.90
2810 2841 7.441017 AGCTCTCAAGGTGAATATCTCATAAC 58.559 38.462 0.00 0.00 36.14 1.89
2811 2842 7.070447 AGCTCTCAAGGTGAATATCTCATAACA 59.930 37.037 0.00 0.00 36.14 2.41
2812 2843 7.877097 GCTCTCAAGGTGAATATCTCATAACAT 59.123 37.037 0.00 0.00 36.14 2.71
2831 2862 9.650371 CATAACATTCATTTGTAACATCTACCG 57.350 33.333 0.00 0.00 0.00 4.02
2844 2875 6.630444 AACATCTACCGTATAGTACCACTG 57.370 41.667 0.00 0.00 0.00 3.66
2848 2879 4.877823 TCTACCGTATAGTACCACTGTGTG 59.122 45.833 7.08 1.06 0.00 3.82
2849 2880 3.424703 ACCGTATAGTACCACTGTGTGT 58.575 45.455 7.08 7.05 0.00 3.72
3096 3127 4.429854 TGCCCCTTGTTGCTTTAAATTT 57.570 36.364 0.00 0.00 0.00 1.82
3175 3206 2.565841 ACCTGTTTGTCTGTGAGCTTC 58.434 47.619 0.00 0.00 0.00 3.86
3243 3277 5.189928 TCAATATGCGGTTGTAACAGGATT 58.810 37.500 7.13 0.00 36.64 3.01
3349 3383 4.154942 ACTTTGCAGATCATTCCCACTTT 58.845 39.130 0.00 0.00 0.00 2.66
3434 3468 2.593026 TCCAGTGGAACCATTTGAACC 58.407 47.619 10.20 0.00 37.80 3.62
3435 3469 2.091610 TCCAGTGGAACCATTTGAACCA 60.092 45.455 10.20 0.00 37.80 3.67
3458 3492 4.402155 ACCACTGCTTCTTTTCATGTCAAA 59.598 37.500 0.00 0.00 0.00 2.69
3502 4317 5.877012 CACATTTAGCTCTTGAGGTGTATGT 59.123 40.000 17.58 17.58 0.00 2.29
3507 4322 5.269505 AGCTCTTGAGGTGTATGTGTATC 57.730 43.478 1.23 0.00 0.00 2.24
3520 4335 2.109181 GTATCGCCCCTGTCAGCC 59.891 66.667 0.00 0.00 0.00 4.85
3532 4347 3.181497 CCCTGTCAGCCGATTAAACATTG 60.181 47.826 0.00 0.00 0.00 2.82
3578 4394 7.512746 AGGGGCTATTATGTATTTCACTCTACA 59.487 37.037 0.00 0.00 32.75 2.74
3595 4411 9.793259 TCACTCTACACCTTTATCTGAAAATTT 57.207 29.630 0.00 0.00 0.00 1.82
3596 4412 9.831737 CACTCTACACCTTTATCTGAAAATTTG 57.168 33.333 0.00 0.00 0.00 2.32
3644 4460 5.635700 GTGGACAGTTTAAAAAGTTTGTGCA 59.364 36.000 0.00 0.00 0.00 4.57
3767 4586 8.329203 ACATCTCTAACTTTGGTGATTTCTTC 57.671 34.615 0.00 0.00 0.00 2.87
3852 4671 9.634163 CAAACTACCTTTATTTTACCAACCATC 57.366 33.333 0.00 0.00 0.00 3.51
4018 4838 5.554437 TTGAGGTTTACCAGTGACACATA 57.446 39.130 8.59 0.00 38.89 2.29
4021 4841 4.312443 AGGTTTACCAGTGACACATAACG 58.688 43.478 8.59 0.00 38.89 3.18
4040 4860 1.625511 GGGGCCCTTCATGATTGATC 58.374 55.000 24.38 0.00 0.00 2.92
4068 4889 3.011818 CAGTGCTTTGATGTGATGGCTA 58.988 45.455 0.00 0.00 0.00 3.93
4125 4946 8.134202 TGATCAAGTAGACCAGTCAAGATAAA 57.866 34.615 0.00 0.00 0.00 1.40
4126 4947 8.762645 TGATCAAGTAGACCAGTCAAGATAAAT 58.237 33.333 0.00 0.00 0.00 1.40
4162 4983 3.914426 TGCCCTCCAAATACTTCTCTC 57.086 47.619 0.00 0.00 0.00 3.20
4164 4985 4.620723 TGCCCTCCAAATACTTCTCTCTA 58.379 43.478 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.398044 TGCGACCTGAGAGTTTTTCTTTTT 59.602 37.500 0.00 0.00 35.87 1.94
31 32 3.945285 TGCGACCTGAGAGTTTTTCTTTT 59.055 39.130 0.00 0.00 35.87 2.27
32 33 3.541632 TGCGACCTGAGAGTTTTTCTTT 58.458 40.909 0.00 0.00 35.87 2.52
33 34 3.194005 TGCGACCTGAGAGTTTTTCTT 57.806 42.857 0.00 0.00 35.87 2.52
34 35 2.872858 GTTGCGACCTGAGAGTTTTTCT 59.127 45.455 0.00 0.00 39.43 2.52
35 36 2.031944 GGTTGCGACCTGAGAGTTTTTC 60.032 50.000 16.57 0.00 42.99 2.29
36 37 1.947456 GGTTGCGACCTGAGAGTTTTT 59.053 47.619 16.57 0.00 42.99 1.94
37 38 1.594331 GGTTGCGACCTGAGAGTTTT 58.406 50.000 16.57 0.00 42.99 2.43
38 39 3.307379 GGTTGCGACCTGAGAGTTT 57.693 52.632 16.57 0.00 42.99 2.66
47 48 0.460987 CATCTCTCCAGGTTGCGACC 60.461 60.000 16.08 16.08 46.92 4.79
48 49 0.532573 TCATCTCTCCAGGTTGCGAC 59.467 55.000 0.00 0.00 0.00 5.19
49 50 0.820226 CTCATCTCTCCAGGTTGCGA 59.180 55.000 0.00 0.00 0.00 5.10
50 51 0.820226 TCTCATCTCTCCAGGTTGCG 59.180 55.000 0.00 0.00 0.00 4.85
51 52 1.830477 ACTCTCATCTCTCCAGGTTGC 59.170 52.381 0.00 0.00 0.00 4.17
52 53 5.598005 AGATTACTCTCATCTCTCCAGGTTG 59.402 44.000 0.00 0.00 0.00 3.77
53 54 5.776358 AGATTACTCTCATCTCTCCAGGTT 58.224 41.667 0.00 0.00 0.00 3.50
54 55 5.402054 AGATTACTCTCATCTCTCCAGGT 57.598 43.478 0.00 0.00 0.00 4.00
55 56 6.323482 TCAAAGATTACTCTCATCTCTCCAGG 59.677 42.308 0.00 0.00 30.19 4.45
56 57 7.345422 TCAAAGATTACTCTCATCTCTCCAG 57.655 40.000 0.00 0.00 30.19 3.86
57 58 7.724490 TTCAAAGATTACTCTCATCTCTCCA 57.276 36.000 0.00 0.00 30.19 3.86
58 59 8.474025 TCTTTCAAAGATTACTCTCATCTCTCC 58.526 37.037 0.00 0.00 30.19 3.71
59 60 9.868277 TTCTTTCAAAGATTACTCTCATCTCTC 57.132 33.333 0.00 0.00 37.38 3.20
60 61 9.874205 CTTCTTTCAAAGATTACTCTCATCTCT 57.126 33.333 0.00 0.00 37.38 3.10
61 62 9.651913 ACTTCTTTCAAAGATTACTCTCATCTC 57.348 33.333 0.00 0.00 37.38 2.75
65 66 9.915629 GAGTACTTCTTTCAAAGATTACTCTCA 57.084 33.333 25.71 3.92 42.81 3.27
66 67 9.361315 GGAGTACTTCTTTCAAAGATTACTCTC 57.639 37.037 28.50 21.29 43.99 3.20
67 68 9.095700 AGGAGTACTTCTTTCAAAGATTACTCT 57.904 33.333 28.50 19.80 43.99 3.24
68 69 9.713713 AAGGAGTACTTCTTTCAAAGATTACTC 57.286 33.333 25.37 25.37 43.90 2.59
95 96 8.547894 GGCGAAAGAAAAACAAAATCACTAATT 58.452 29.630 0.00 0.00 0.00 1.40
96 97 7.170828 GGGCGAAAGAAAAACAAAATCACTAAT 59.829 33.333 0.00 0.00 0.00 1.73
97 98 6.477360 GGGCGAAAGAAAAACAAAATCACTAA 59.523 34.615 0.00 0.00 0.00 2.24
98 99 5.980715 GGGCGAAAGAAAAACAAAATCACTA 59.019 36.000 0.00 0.00 0.00 2.74
99 100 4.808895 GGGCGAAAGAAAAACAAAATCACT 59.191 37.500 0.00 0.00 0.00 3.41
100 101 4.317769 CGGGCGAAAGAAAAACAAAATCAC 60.318 41.667 0.00 0.00 0.00 3.06
101 102 3.799420 CGGGCGAAAGAAAAACAAAATCA 59.201 39.130 0.00 0.00 0.00 2.57
102 103 3.362596 GCGGGCGAAAGAAAAACAAAATC 60.363 43.478 0.00 0.00 0.00 2.17
103 104 2.542178 GCGGGCGAAAGAAAAACAAAAT 59.458 40.909 0.00 0.00 0.00 1.82
104 105 1.927838 GCGGGCGAAAGAAAAACAAAA 59.072 42.857 0.00 0.00 0.00 2.44
105 106 1.562017 GCGGGCGAAAGAAAAACAAA 58.438 45.000 0.00 0.00 0.00 2.83
106 107 0.592754 CGCGGGCGAAAGAAAAACAA 60.593 50.000 7.38 0.00 42.83 2.83
107 108 1.009449 CGCGGGCGAAAGAAAAACA 60.009 52.632 7.38 0.00 42.83 2.83
108 109 0.995234 GACGCGGGCGAAAGAAAAAC 60.995 55.000 20.98 0.00 42.83 2.43
109 110 1.280444 GACGCGGGCGAAAGAAAAA 59.720 52.632 20.98 0.00 42.83 1.94
110 111 1.888172 TGACGCGGGCGAAAGAAAA 60.888 52.632 20.98 0.00 42.83 2.29
111 112 2.280254 TGACGCGGGCGAAAGAAA 60.280 55.556 20.98 0.00 42.83 2.52
112 113 3.039588 GTGACGCGGGCGAAAGAA 61.040 61.111 20.98 0.00 42.83 2.52
113 114 4.287781 TGTGACGCGGGCGAAAGA 62.288 61.111 20.98 2.84 42.83 2.52
114 115 4.072088 GTGTGACGCGGGCGAAAG 62.072 66.667 20.98 0.00 42.83 2.62
124 125 1.225376 TAGCTTTTGGGCGTGTGACG 61.225 55.000 0.00 0.00 45.88 4.35
125 126 0.948678 TTAGCTTTTGGGCGTGTGAC 59.051 50.000 0.00 0.00 37.29 3.67
126 127 1.335496 GTTTAGCTTTTGGGCGTGTGA 59.665 47.619 0.00 0.00 37.29 3.58
127 128 1.336755 AGTTTAGCTTTTGGGCGTGTG 59.663 47.619 0.00 0.00 37.29 3.82
128 129 1.687563 AGTTTAGCTTTTGGGCGTGT 58.312 45.000 0.00 0.00 37.29 4.49
129 130 2.293399 AGAAGTTTAGCTTTTGGGCGTG 59.707 45.455 0.00 0.00 37.59 5.34
130 131 2.583143 AGAAGTTTAGCTTTTGGGCGT 58.417 42.857 0.00 0.00 37.59 5.68
131 132 3.253432 AGAAGAAGTTTAGCTTTTGGGCG 59.747 43.478 0.00 0.00 37.59 6.13
132 133 4.321304 GGAGAAGAAGTTTAGCTTTTGGGC 60.321 45.833 0.00 0.00 37.59 5.36
133 134 5.073428 AGGAGAAGAAGTTTAGCTTTTGGG 58.927 41.667 0.00 0.00 37.59 4.12
134 135 6.937465 ACTAGGAGAAGAAGTTTAGCTTTTGG 59.063 38.462 0.00 0.00 37.59 3.28
135 136 7.657761 TCACTAGGAGAAGAAGTTTAGCTTTTG 59.342 37.037 0.00 0.00 37.59 2.44
136 137 7.736893 TCACTAGGAGAAGAAGTTTAGCTTTT 58.263 34.615 0.00 0.00 37.59 2.27
137 138 7.304497 TCACTAGGAGAAGAAGTTTAGCTTT 57.696 36.000 0.00 0.00 37.59 3.51
138 139 6.919775 TCACTAGGAGAAGAAGTTTAGCTT 57.080 37.500 0.00 0.00 40.76 3.74
139 140 6.919775 TTCACTAGGAGAAGAAGTTTAGCT 57.080 37.500 0.00 0.00 0.00 3.32
140 141 7.964604 TTTTCACTAGGAGAAGAAGTTTAGC 57.035 36.000 0.00 0.00 0.00 3.09
141 142 9.712305 TCATTTTCACTAGGAGAAGAAGTTTAG 57.288 33.333 0.00 0.00 0.00 1.85
142 143 9.490379 GTCATTTTCACTAGGAGAAGAAGTTTA 57.510 33.333 0.00 0.00 0.00 2.01
143 144 8.214364 AGTCATTTTCACTAGGAGAAGAAGTTT 58.786 33.333 0.00 0.00 0.00 2.66
144 145 7.740805 AGTCATTTTCACTAGGAGAAGAAGTT 58.259 34.615 0.00 0.00 0.00 2.66
145 146 7.309770 AGTCATTTTCACTAGGAGAAGAAGT 57.690 36.000 0.00 0.00 0.00 3.01
146 147 9.311916 CATAGTCATTTTCACTAGGAGAAGAAG 57.688 37.037 0.00 0.00 31.14 2.85
147 148 8.816894 ACATAGTCATTTTCACTAGGAGAAGAA 58.183 33.333 0.00 0.00 33.34 2.52
148 149 8.367660 ACATAGTCATTTTCACTAGGAGAAGA 57.632 34.615 0.00 0.00 33.34 2.87
149 150 9.442047 AAACATAGTCATTTTCACTAGGAGAAG 57.558 33.333 0.00 0.00 33.34 2.85
150 151 9.793259 AAAACATAGTCATTTTCACTAGGAGAA 57.207 29.630 0.00 0.00 33.34 2.87
151 152 9.793259 AAAAACATAGTCATTTTCACTAGGAGA 57.207 29.630 0.00 0.00 33.34 3.71
152 153 9.831737 CAAAAACATAGTCATTTTCACTAGGAG 57.168 33.333 0.00 0.00 33.34 3.69
153 154 8.792633 CCAAAAACATAGTCATTTTCACTAGGA 58.207 33.333 0.00 0.00 33.34 2.94
154 155 8.028938 CCCAAAAACATAGTCATTTTCACTAGG 58.971 37.037 0.00 0.00 34.88 3.02
155 156 8.576442 ACCCAAAAACATAGTCATTTTCACTAG 58.424 33.333 0.00 0.00 29.82 2.57
156 157 8.472007 ACCCAAAAACATAGTCATTTTCACTA 57.528 30.769 0.00 0.00 0.00 2.74
157 158 7.360113 ACCCAAAAACATAGTCATTTTCACT 57.640 32.000 0.00 0.00 0.00 3.41
196 197 2.930682 GCTTGGTTTAACCGCACAAAAA 59.069 40.909 9.77 0.00 42.58 1.94
197 198 2.166664 AGCTTGGTTTAACCGCACAAAA 59.833 40.909 14.57 0.46 42.58 2.44
198 199 1.751924 AGCTTGGTTTAACCGCACAAA 59.248 42.857 14.57 1.10 42.58 2.83
199 200 1.394618 AGCTTGGTTTAACCGCACAA 58.605 45.000 14.57 1.43 42.58 3.33
200 201 1.335496 GAAGCTTGGTTTAACCGCACA 59.665 47.619 2.10 0.00 42.58 4.57
201 202 1.335496 TGAAGCTTGGTTTAACCGCAC 59.665 47.619 2.10 9.38 42.58 5.34
202 203 1.681538 TGAAGCTTGGTTTAACCGCA 58.318 45.000 2.10 1.87 42.58 5.69
203 204 3.297830 AATGAAGCTTGGTTTAACCGC 57.702 42.857 2.10 7.72 42.58 5.68
204 205 5.180492 TGAGTAATGAAGCTTGGTTTAACCG 59.820 40.000 2.10 0.00 42.58 4.44
220 221 6.962686 CACACCATGTGGATTATGAGTAATG 58.037 40.000 5.96 0.00 44.27 1.90
241 242 4.397730 CCATAATCCGATTTGTGTTCCACA 59.602 41.667 0.00 0.00 43.02 4.17
248 249 3.490761 GCAACCCCATAATCCGATTTGTG 60.491 47.826 0.00 0.00 0.00 3.33
277 278 4.781934 TCTCTCGATGAAGGACATGTCTA 58.218 43.478 24.50 9.92 39.56 2.59
287 288 4.394300 AGTTGGCAAATTCTCTCGATGAAG 59.606 41.667 0.00 0.00 0.00 3.02
288 289 4.326826 AGTTGGCAAATTCTCTCGATGAA 58.673 39.130 0.00 3.94 0.00 2.57
289 290 3.942829 AGTTGGCAAATTCTCTCGATGA 58.057 40.909 0.00 0.00 0.00 2.92
294 298 6.374578 GTTAGTCAAGTTGGCAAATTCTCTC 58.625 40.000 10.33 1.86 0.00 3.20
302 306 4.585879 GGATAGGTTAGTCAAGTTGGCAA 58.414 43.478 10.65 0.00 0.00 4.52
306 310 3.857052 TGCGGATAGGTTAGTCAAGTTG 58.143 45.455 0.00 0.00 0.00 3.16
313 317 6.895756 TCTAATATGGATGCGGATAGGTTAGT 59.104 38.462 0.00 0.00 0.00 2.24
380 384 4.744795 ATTAGAGATCAACCAACGAGCT 57.255 40.909 0.00 0.00 0.00 4.09
398 402 7.108194 GTGGAGAGCATGGATCAATCATATTA 58.892 38.462 0.00 0.00 0.00 0.98
399 403 5.944599 GTGGAGAGCATGGATCAATCATATT 59.055 40.000 0.00 0.00 0.00 1.28
401 405 4.263199 GGTGGAGAGCATGGATCAATCATA 60.263 45.833 0.00 0.00 0.00 2.15
409 413 1.383109 TCCGGTGGAGAGCATGGAT 60.383 57.895 0.00 0.00 0.00 3.41
415 419 0.951040 CAAACAGTCCGGTGGAGAGC 60.951 60.000 0.00 0.00 29.39 4.09
424 428 0.950836 TGACATTGCCAAACAGTCCG 59.049 50.000 5.84 0.00 0.00 4.79
431 435 5.122554 GCAAATGATCAATGACATTGCCAAA 59.877 36.000 21.17 6.53 40.05 3.28
451 455 2.645838 AGCCTCTGACTCAAAGCAAA 57.354 45.000 0.00 0.00 0.00 3.68
461 465 4.764172 ACAACTTCATCATAGCCTCTGAC 58.236 43.478 0.00 0.00 0.00 3.51
468 472 5.276584 CGCTACTGAACAACTTCATCATAGC 60.277 44.000 9.41 9.41 38.02 2.97
475 479 3.552273 GGACTCGCTACTGAACAACTTCA 60.552 47.826 0.00 0.00 35.04 3.02
476 480 2.987821 GGACTCGCTACTGAACAACTTC 59.012 50.000 0.00 0.00 0.00 3.01
492 496 0.170561 TTAGCGCTCGTCAAGGACTC 59.829 55.000 16.34 0.00 0.00 3.36
499 503 0.389426 GGAAGGTTTAGCGCTCGTCA 60.389 55.000 16.34 0.00 0.00 4.35
501 505 1.079336 GGGAAGGTTTAGCGCTCGT 60.079 57.895 16.34 0.00 0.00 4.18
526 530 1.542472 TCGCGACACTTGAGGTCATAA 59.458 47.619 3.71 0.00 34.97 1.90
531 535 0.388649 GATGTCGCGACACTTGAGGT 60.389 55.000 41.29 25.29 45.05 3.85
554 558 1.197721 GTCTTGGTGATTGCAGGAACG 59.802 52.381 0.00 0.00 0.00 3.95
555 559 1.541588 GGTCTTGGTGATTGCAGGAAC 59.458 52.381 0.00 0.00 0.00 3.62
573 577 0.693049 AACTCCATTGGAAGCTCGGT 59.307 50.000 6.88 0.00 0.00 4.69
588 592 1.552337 TCCTGATGAGACTGGCAACTC 59.448 52.381 12.47 12.47 37.61 3.01
606 610 1.982073 GCAGCGGCTATTGTGTGTCC 61.982 60.000 0.26 0.00 36.96 4.02
608 612 3.578456 GCAGCGGCTATTGTGTGT 58.422 55.556 0.26 0.00 36.96 3.72
639 643 3.075148 TGGACGCTCCGATATCTAGAAG 58.925 50.000 0.00 0.00 40.17 2.85
652 656 0.716108 CAAGATTCACGTGGACGCTC 59.284 55.000 17.00 1.17 44.43 5.03
662 666 1.815003 CAGGGCTTCACCAAGATTCAC 59.185 52.381 0.00 0.00 42.05 3.18
673 677 4.020617 CGCCTCCACAGGGCTTCA 62.021 66.667 3.25 0.00 46.73 3.02
708 719 2.802787 ATAGCAGCGAGGTACATCAC 57.197 50.000 8.44 0.00 32.12 3.06
726 737 7.615365 TGGAACTATTGCCAAAGAAGAATGTAT 59.385 33.333 0.00 0.00 0.00 2.29
762 773 8.178964 TCAGTATACAATTTATTGCACGTTTCC 58.821 33.333 5.50 0.00 41.38 3.13
763 774 9.549509 TTCAGTATACAATTTATTGCACGTTTC 57.450 29.630 5.50 0.00 41.38 2.78
786 797 9.515020 GCGATAGGACAAAAATAATCATTTTCA 57.485 29.630 0.00 0.00 42.29 2.69
787 798 9.736023 AGCGATAGGACAAAAATAATCATTTTC 57.264 29.630 0.00 0.00 42.29 2.29
788 799 9.520204 CAGCGATAGGACAAAAATAATCATTTT 57.480 29.630 0.00 0.00 44.45 1.82
789 800 8.686334 ACAGCGATAGGACAAAAATAATCATTT 58.314 29.630 0.00 0.00 35.84 2.32
790 801 8.225603 ACAGCGATAGGACAAAAATAATCATT 57.774 30.769 0.00 0.00 0.00 2.57
791 802 7.807977 ACAGCGATAGGACAAAAATAATCAT 57.192 32.000 0.00 0.00 0.00 2.45
792 803 8.725405 TTACAGCGATAGGACAAAAATAATCA 57.275 30.769 0.00 0.00 0.00 2.57
793 804 8.827677 ACTTACAGCGATAGGACAAAAATAATC 58.172 33.333 0.00 0.00 0.00 1.75
794 805 8.612619 CACTTACAGCGATAGGACAAAAATAAT 58.387 33.333 0.00 0.00 0.00 1.28
795 806 7.413657 GCACTTACAGCGATAGGACAAAAATAA 60.414 37.037 0.00 0.00 0.00 1.40
796 807 6.036735 GCACTTACAGCGATAGGACAAAAATA 59.963 38.462 0.00 0.00 0.00 1.40
797 808 5.163754 GCACTTACAGCGATAGGACAAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
798 809 4.153475 GCACTTACAGCGATAGGACAAAAA 59.847 41.667 0.00 0.00 0.00 1.94
799 810 3.682858 GCACTTACAGCGATAGGACAAAA 59.317 43.478 0.00 0.00 0.00 2.44
800 811 3.259064 GCACTTACAGCGATAGGACAAA 58.741 45.455 0.00 0.00 0.00 2.83
801 812 2.232696 TGCACTTACAGCGATAGGACAA 59.767 45.455 0.00 0.00 33.85 3.18
804 815 1.136305 GGTGCACTTACAGCGATAGGA 59.864 52.381 17.98 0.00 33.85 2.94
825 836 2.282446 TTTTTCGGGGGTGGGCAA 59.718 55.556 0.00 0.00 0.00 4.52
843 854 0.704076 TGATTAGGCAGGCCCAGTTT 59.296 50.000 6.70 0.00 36.58 2.66
857 868 5.660417 TGCAAGGCCCAGATAAAATTGATTA 59.340 36.000 0.00 0.00 0.00 1.75
864 875 1.481772 GCATGCAAGGCCCAGATAAAA 59.518 47.619 14.21 0.00 37.93 1.52
876 887 2.445565 TCGCTCTATAGGCATGCAAG 57.554 50.000 21.36 10.85 0.00 4.01
879 890 2.662006 TGATCGCTCTATAGGCATGC 57.338 50.000 9.90 9.90 0.00 4.06
886 897 1.540267 GGCCGTCTTGATCGCTCTATA 59.460 52.381 0.00 0.00 0.00 1.31
888 899 1.734137 GGCCGTCTTGATCGCTCTA 59.266 57.895 0.00 0.00 0.00 2.43
889 900 2.496817 GGCCGTCTTGATCGCTCT 59.503 61.111 0.00 0.00 0.00 4.09
890 901 2.586357 GGGCCGTCTTGATCGCTC 60.586 66.667 0.00 0.00 0.00 5.03
891 902 2.257409 ATTGGGCCGTCTTGATCGCT 62.257 55.000 0.00 0.00 0.00 4.93
892 903 1.776034 GATTGGGCCGTCTTGATCGC 61.776 60.000 0.00 0.00 0.00 4.58
893 904 1.490693 CGATTGGGCCGTCTTGATCG 61.491 60.000 0.00 3.62 0.00 3.69
894 905 1.160329 CCGATTGGGCCGTCTTGATC 61.160 60.000 0.00 0.00 0.00 2.92
922 938 2.751837 GGAGAAAAGGCCTGCGGG 60.752 66.667 5.69 7.41 0.00 6.13
981 997 2.306255 TAGAAGGGGAATGGCGACGC 62.306 60.000 12.43 12.43 0.00 5.19
1005 1021 1.688311 CCCTAGGATCCACAGAACGGA 60.688 57.143 15.82 0.00 36.84 4.69
1010 1026 1.688311 CGGAACCCTAGGATCCACAGA 60.688 57.143 24.87 0.00 43.72 3.41
1012 1028 0.337082 TCGGAACCCTAGGATCCACA 59.663 55.000 24.87 13.25 43.72 4.17
1020 1036 1.382692 GGAGGTCGTCGGAACCCTAG 61.383 65.000 0.00 0.00 0.00 3.02
1081 1112 4.738998 TTGGCTGGGACATGGCGG 62.739 66.667 0.00 0.00 38.20 6.13
1181 1212 3.934391 GAGGAGTTGGCGTCGGTGG 62.934 68.421 0.00 0.00 0.00 4.61
1185 1216 4.717629 TGCGAGGAGTTGGCGTCG 62.718 66.667 0.00 0.00 45.73 5.12
1213 1244 1.168714 GGATTTGCTCTCGTTTGGCT 58.831 50.000 0.00 0.00 0.00 4.75
1224 1255 2.509336 CGCGTCGAGGGATTTGCT 60.509 61.111 7.31 0.00 34.27 3.91
1227 1258 2.202756 GAGCGCGTCGAGGGATTT 60.203 61.111 8.43 0.00 34.27 2.17
1640 1671 1.222113 GCGGAGGAGAAGGGAAAGG 59.778 63.158 0.00 0.00 0.00 3.11
1880 1911 3.475566 TCCATCCGAAGCAGGATTAAG 57.524 47.619 5.76 0.16 45.23 1.85
1895 1926 3.376859 TGTGAAATACGCCACAATCCATC 59.623 43.478 0.00 0.00 39.97 3.51
1915 1946 6.293698 TCATTAAGTATGCTGCTCATGATGT 58.706 36.000 0.00 0.00 36.63 3.06
2012 2043 0.677098 AGTGCTGCCAGCTCATCAAG 60.677 55.000 18.96 0.00 42.97 3.02
2097 2128 3.797039 TCAAACAATCGCCTCCTCATAG 58.203 45.455 0.00 0.00 0.00 2.23
2335 2366 1.403814 AAGCCGCATCTAGAGTAGCA 58.596 50.000 13.08 0.00 0.00 3.49
2374 2405 1.108727 TGCGGTTACGGGTATCGGAT 61.109 55.000 0.00 0.00 44.45 4.18
2447 2478 9.830975 AAAAACAGCAAGGTTAACATCTAAAAT 57.169 25.926 8.10 0.00 0.00 1.82
2497 2528 5.370880 AGCCATGGTATCCTTTCTGTCTATT 59.629 40.000 14.67 0.00 0.00 1.73
2689 2720 1.780860 GAATTGCACAGCGTTGACAAC 59.219 47.619 6.16 8.34 30.71 3.32
2809 2840 8.958119 ATACGGTAGATGTTACAAATGAATGT 57.042 30.769 0.00 0.00 37.32 2.71
2864 2895 5.526115 CATTCACAAAACTGAGAGCACAAT 58.474 37.500 0.00 0.00 0.00 2.71
3111 3142 5.779241 ACCATACTCAATCTTTCAAGGGA 57.221 39.130 0.00 0.00 0.00 4.20
3140 3171 9.020731 AGACAAACAGGTACATAAAATTTAGGG 57.979 33.333 2.45 0.00 0.00 3.53
3319 3353 6.034591 GGAATGATCTGCAAAGTCAGAATTG 58.965 40.000 0.00 0.00 45.17 2.32
3356 3390 9.784680 GAACGAGATACAGATAAAAGTAACTCA 57.215 33.333 0.00 0.00 38.99 3.41
3364 3398 9.878667 TTGGTAATGAACGAGATACAGATAAAA 57.121 29.630 0.00 0.00 0.00 1.52
3434 3468 3.316029 TGACATGAAAAGAAGCAGTGGTG 59.684 43.478 0.00 0.00 0.00 4.17
3435 3469 3.554934 TGACATGAAAAGAAGCAGTGGT 58.445 40.909 0.00 0.00 0.00 4.16
3502 4317 2.731571 GGCTGACAGGGGCGATACA 61.732 63.158 4.26 0.00 0.00 2.29
3520 4335 9.941991 CTAAAAAGAATGTGCAATGTTTAATCG 57.058 29.630 0.00 0.00 0.00 3.34
3532 4347 5.696270 CCCCTTGAAACTAAAAAGAATGTGC 59.304 40.000 0.00 0.00 0.00 4.57
3548 4363 7.582719 AGTGAAATACATAATAGCCCCTTGAA 58.417 34.615 0.00 0.00 0.00 2.69
3801 4620 8.570488 TGGCTTCATCATTGTATACATGAAATC 58.430 33.333 16.47 12.76 0.00 2.17
3852 4671 5.674068 GACCATCAGTCTGTACAGAAGTACG 60.674 48.000 26.74 14.88 43.52 3.67
3878 4697 2.144730 TGAAGCATGTGCCAAAAATGC 58.855 42.857 0.57 0.00 45.62 3.56
4018 4838 0.684153 CAATCATGAAGGGCCCCGTT 60.684 55.000 21.43 7.19 0.00 4.44
4021 4841 1.625511 GATCAATCATGAAGGGCCCC 58.374 55.000 21.43 4.15 39.49 5.80
4040 4860 3.187022 TCACATCAAAGCACTGTCAATCG 59.813 43.478 0.00 0.00 0.00 3.34
4125 4946 5.456763 GGAGGGCAAAGATCATACCTTGTAT 60.457 44.000 0.00 0.00 0.00 2.29
4126 4947 4.141482 GGAGGGCAAAGATCATACCTTGTA 60.141 45.833 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.