Multiple sequence alignment - TraesCS4D01G221400

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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 TraesCS4D01G221400 chr4D 100.000 2872 0 0 1 2872 378498815 378501686 0.000000e+00 5304.0
1 TraesCS4D01G221400 chr4B 93.650 1937 87 18 201 2113 465021563 465023487 0.000000e+00 2863.0
2 TraesCS4D01G221400 chr4A 97.461 1024 20 3 650 1668 86869576 86868554 0.000000e+00 1742.0
3 TraesCS4D01G221400 chr4A 87.581 620 53 11 1700 2301 86868555 86867942 0.000000e+00 697.0
4 TraesCS4D01G221400 chr4A 92.174 460 23 6 201 658 86875120 86874672 3.120000e-179 638.0
5 TraesCS4D01G221400 chr4A 85.953 598 47 18 2297 2870 86855490 86854906 3.170000e-169 604.0
6 TraesCS4D01G221400 chr4A 93.434 198 13 0 2 199 86930130 86929933 7.780000e-76 294.0
7 TraesCS4D01G221400 chr4A 94.340 53 3 0 2791 2843 310771653 310771705 6.600000e-12 82.4
8 TraesCS4D01G221400 chr2A 79.959 489 57 20 253 714 31960198 31960672 3.570000e-84 322.0
9 TraesCS4D01G221400 chr2B 85.522 297 39 3 1417 1710 47834179 47834474 1.000000e-79 307.0
10 TraesCS4D01G221400 chr2B 90.683 161 15 0 30 190 424494558 424494398 6.230000e-52 215.0
11 TraesCS4D01G221400 chr3D 87.562 201 20 3 3 199 387151404 387151603 8.010000e-56 228.0
12 TraesCS4D01G221400 chr3D 84.496 129 19 1 61 189 308970759 308970886 3.000000e-25 126.0
13 TraesCS4D01G221400 chr3D 94.340 53 3 0 2791 2843 158940967 158941019 6.600000e-12 82.4
14 TraesCS4D01G221400 chr3D 94.340 53 3 0 2791 2843 589251912 589251964 6.600000e-12 82.4
15 TraesCS4D01G221400 chr7A 87.368 190 21 3 12 199 692943567 692943379 6.230000e-52 215.0
16 TraesCS4D01G221400 chr7A 94.340 53 3 0 2791 2843 381056937 381056989 6.600000e-12 82.4
17 TraesCS4D01G221400 chr7D 88.028 142 17 0 58 199 599881942 599881801 4.920000e-38 169.0
18 TraesCS4D01G221400 chr6D 84.091 176 27 1 24 199 308908842 308909016 4.920000e-38 169.0
19 TraesCS4D01G221400 chr6D 97.436 39 1 0 2717 2755 447855306 447855268 1.850000e-07 67.6
20 TraesCS4D01G221400 chr3B 89.916 119 12 0 81 199 363321620 363321738 1.380000e-33 154.0
21 TraesCS4D01G221400 chr2D 85.816 141 20 0 58 198 646273749 646273889 1.780000e-32 150.0
22 TraesCS4D01G221400 chr7B 94.444 54 3 0 2790 2843 71816844 71816791 1.830000e-12 84.2
23 TraesCS4D01G221400 chrUn 94.340 53 3 0 2791 2843 331841693 331841745 6.600000e-12 82.4
24 TraesCS4D01G221400 chrUn 94.340 53 3 0 2791 2843 354742570 354742622 6.600000e-12 82.4
25 TraesCS4D01G221400 chrUn 93.023 43 3 0 2717 2759 452435257 452435299 2.390000e-06 63.9
26 TraesCS4D01G221400 chr6B 94.340 53 3 0 2791 2843 515378307 515378359 6.600000e-12 82.4
27 TraesCS4D01G221400 chr5D 94.340 53 3 0 2791 2843 503256508 503256560 6.600000e-12 82.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G221400 chr4D 378498815 378501686 2871 False 5304.0 5304 100.000 1 2872 1 chr4D.!!$F1 2871
1 TraesCS4D01G221400 chr4B 465021563 465023487 1924 False 2863.0 2863 93.650 201 2113 1 chr4B.!!$F1 1912
2 TraesCS4D01G221400 chr4A 86867942 86869576 1634 True 1219.5 1742 92.521 650 2301 2 chr4A.!!$R4 1651
3 TraesCS4D01G221400 chr4A 86854906 86855490 584 True 604.0 604 85.953 2297 2870 1 chr4A.!!$R1 573

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
175 176 0.027194 CGCATCACGGCAAAGATCTG 59.973 55.0 0.00 0.00 38.44 2.90 F
192 193 0.033228 CTGCATGATCGGTCCTCCTC 59.967 60.0 0.00 0.00 0.00 3.71 F
207 208 0.105593 TCCTCGATCTGCATGCTTCC 59.894 55.0 20.33 4.66 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1409 0.108615 ATCTCGCACTCTTCAACCCG 60.109 55.0 0.00 0.00 0.00 5.28 R
1843 1868 0.238289 CAGCCGACGATGCTTTGTTT 59.762 50.0 0.00 0.00 36.81 2.83 R
2014 2040 0.734889 AATAGAGCATGGCACGTTGC 59.265 50.0 3.39 3.39 44.08 4.17 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
37 38 4.309950 GGCTGGTGTCGGTTCCGT 62.310 66.667 11.04 0.00 0.00 4.69
38 39 2.737376 GCTGGTGTCGGTTCCGTC 60.737 66.667 11.04 6.35 0.00 4.79
39 40 2.732016 CTGGTGTCGGTTCCGTCA 59.268 61.111 11.04 8.96 0.00 4.35
40 41 1.372997 CTGGTGTCGGTTCCGTCAG 60.373 63.158 10.89 10.38 0.00 3.51
41 42 1.802337 CTGGTGTCGGTTCCGTCAGA 61.802 60.000 10.89 1.85 0.00 3.27
42 43 1.183030 TGGTGTCGGTTCCGTCAGAT 61.183 55.000 10.89 0.00 0.00 2.90
43 44 0.458025 GGTGTCGGTTCCGTCAGATC 60.458 60.000 10.89 1.32 0.00 2.75
44 45 0.526662 GTGTCGGTTCCGTCAGATCT 59.473 55.000 10.89 0.00 0.00 2.75
45 46 0.526211 TGTCGGTTCCGTCAGATCTG 59.474 55.000 17.07 17.07 0.00 2.90
46 47 0.179134 GTCGGTTCCGTCAGATCTGG 60.179 60.000 22.42 7.07 0.00 3.86
47 48 1.519455 CGGTTCCGTCAGATCTGGC 60.519 63.158 22.42 20.11 0.00 4.85
53 54 3.805267 GTCAGATCTGGCGCTTGG 58.195 61.111 22.42 0.00 0.00 3.61
54 55 1.219124 GTCAGATCTGGCGCTTGGA 59.781 57.895 22.42 3.46 0.00 3.53
55 56 0.809241 GTCAGATCTGGCGCTTGGAG 60.809 60.000 22.42 0.00 0.00 3.86
56 57 1.220206 CAGATCTGGCGCTTGGAGT 59.780 57.895 15.38 0.00 0.00 3.85
57 58 0.809241 CAGATCTGGCGCTTGGAGTC 60.809 60.000 15.38 0.00 0.00 3.36
58 59 1.880340 GATCTGGCGCTTGGAGTCG 60.880 63.158 7.64 0.00 0.00 4.18
66 67 4.379243 CTTGGAGTCGCGGGCTGT 62.379 66.667 6.13 0.00 0.00 4.40
67 68 4.680237 TTGGAGTCGCGGGCTGTG 62.680 66.667 6.13 0.00 0.00 3.66
69 70 4.803426 GGAGTCGCGGGCTGTGAG 62.803 72.222 10.39 0.00 37.89 3.51
80 81 2.125753 CTGTGAGCAGCGAGGACC 60.126 66.667 0.00 0.00 35.77 4.46
81 82 3.978723 CTGTGAGCAGCGAGGACCG 62.979 68.421 0.00 0.00 42.21 4.79
82 83 4.803426 GTGAGCAGCGAGGACCGG 62.803 72.222 0.00 0.00 39.04 5.28
97 98 4.415332 CGGTGTCCTCCGTCGTGG 62.415 72.222 0.00 0.00 44.77 4.94
98 99 4.736896 GGTGTCCTCCGTCGTGGC 62.737 72.222 0.00 0.00 37.80 5.01
119 120 2.890474 GATGGCGTCGGCGTGATT 60.890 61.111 19.23 0.00 41.24 2.57
120 121 3.155470 GATGGCGTCGGCGTGATTG 62.155 63.158 19.23 0.00 41.24 2.67
121 122 3.657448 ATGGCGTCGGCGTGATTGA 62.657 57.895 12.58 0.00 41.24 2.57
122 123 3.554692 GGCGTCGGCGTGATTGAG 61.555 66.667 12.58 0.00 41.24 3.02
123 124 3.554692 GCGTCGGCGTGATTGAGG 61.555 66.667 12.58 0.00 40.81 3.86
124 125 3.554692 CGTCGGCGTGATTGAGGC 61.555 66.667 6.85 0.00 34.52 4.70
125 126 2.434185 GTCGGCGTGATTGAGGCA 60.434 61.111 6.85 0.00 37.18 4.75
126 127 2.125552 TCGGCGTGATTGAGGCAG 60.126 61.111 6.85 0.00 37.18 4.85
127 128 3.869272 CGGCGTGATTGAGGCAGC 61.869 66.667 0.00 0.00 37.18 5.25
128 129 3.869272 GGCGTGATTGAGGCAGCG 61.869 66.667 0.00 0.00 37.18 5.18
129 130 3.869272 GCGTGATTGAGGCAGCGG 61.869 66.667 0.00 0.00 35.42 5.52
130 131 2.434884 CGTGATTGAGGCAGCGGT 60.435 61.111 0.00 0.00 0.00 5.68
131 132 2.743752 CGTGATTGAGGCAGCGGTG 61.744 63.158 10.98 10.98 0.00 4.94
132 133 1.672356 GTGATTGAGGCAGCGGTGT 60.672 57.895 17.07 0.00 0.00 4.16
133 134 1.672030 TGATTGAGGCAGCGGTGTG 60.672 57.895 17.07 0.00 0.00 3.82
134 135 2.360350 ATTGAGGCAGCGGTGTGG 60.360 61.111 17.07 0.00 0.00 4.17
147 148 4.572571 TGTGGCGGCGGTCCTTTT 62.573 61.111 9.78 0.00 0.00 2.27
148 149 3.292159 GTGGCGGCGGTCCTTTTT 61.292 61.111 9.78 0.00 0.00 1.94
149 150 2.981350 TGGCGGCGGTCCTTTTTC 60.981 61.111 9.78 0.00 0.00 2.29
150 151 2.671963 GGCGGCGGTCCTTTTTCT 60.672 61.111 9.78 0.00 0.00 2.52
151 152 2.687805 GGCGGCGGTCCTTTTTCTC 61.688 63.158 9.78 0.00 0.00 2.87
152 153 1.671379 GCGGCGGTCCTTTTTCTCT 60.671 57.895 9.78 0.00 0.00 3.10
153 154 1.235281 GCGGCGGTCCTTTTTCTCTT 61.235 55.000 9.78 0.00 0.00 2.85
154 155 0.517316 CGGCGGTCCTTTTTCTCTTG 59.483 55.000 0.00 0.00 0.00 3.02
155 156 1.605753 GGCGGTCCTTTTTCTCTTGT 58.394 50.000 0.00 0.00 0.00 3.16
156 157 1.535896 GGCGGTCCTTTTTCTCTTGTC 59.464 52.381 0.00 0.00 0.00 3.18
157 158 1.194772 GCGGTCCTTTTTCTCTTGTCG 59.805 52.381 0.00 0.00 0.00 4.35
158 159 1.194772 CGGTCCTTTTTCTCTTGTCGC 59.805 52.381 0.00 0.00 0.00 5.19
159 160 2.218603 GGTCCTTTTTCTCTTGTCGCA 58.781 47.619 0.00 0.00 0.00 5.10
160 161 2.814336 GGTCCTTTTTCTCTTGTCGCAT 59.186 45.455 0.00 0.00 0.00 4.73
161 162 3.120165 GGTCCTTTTTCTCTTGTCGCATC 60.120 47.826 0.00 0.00 0.00 3.91
162 163 3.498397 GTCCTTTTTCTCTTGTCGCATCA 59.502 43.478 0.00 0.00 0.00 3.07
163 164 3.498397 TCCTTTTTCTCTTGTCGCATCAC 59.502 43.478 0.00 0.00 0.00 3.06
164 165 3.473367 CTTTTTCTCTTGTCGCATCACG 58.527 45.455 0.00 0.00 45.62 4.35
165 166 1.428448 TTTCTCTTGTCGCATCACGG 58.572 50.000 0.00 0.00 43.89 4.94
172 173 4.615901 TCGCATCACGGCAAAGAT 57.384 50.000 0.00 0.00 43.89 2.40
173 174 2.383170 TCGCATCACGGCAAAGATC 58.617 52.632 0.00 0.00 43.89 2.75
174 175 0.108186 TCGCATCACGGCAAAGATCT 60.108 50.000 0.00 0.00 43.89 2.75
175 176 0.027194 CGCATCACGGCAAAGATCTG 59.973 55.000 0.00 0.00 38.44 2.90
176 177 0.248377 GCATCACGGCAAAGATCTGC 60.248 55.000 0.00 0.00 41.85 4.26
177 178 1.089112 CATCACGGCAAAGATCTGCA 58.911 50.000 8.97 0.00 44.52 4.41
178 179 1.674441 CATCACGGCAAAGATCTGCAT 59.326 47.619 8.97 0.00 44.52 3.96
179 180 1.089112 TCACGGCAAAGATCTGCATG 58.911 50.000 8.97 6.67 44.52 4.06
180 181 1.089112 CACGGCAAAGATCTGCATGA 58.911 50.000 8.97 0.00 44.52 3.07
181 182 1.674441 CACGGCAAAGATCTGCATGAT 59.326 47.619 8.97 0.00 44.52 2.45
189 190 2.077413 GATCTGCATGATCGGTCCTC 57.923 55.000 0.00 0.00 41.68 3.71
190 191 0.683973 ATCTGCATGATCGGTCCTCC 59.316 55.000 0.00 0.00 0.00 4.30
191 192 0.397675 TCTGCATGATCGGTCCTCCT 60.398 55.000 0.00 0.00 0.00 3.69
192 193 0.033228 CTGCATGATCGGTCCTCCTC 59.967 60.000 0.00 0.00 0.00 3.71
193 194 1.006805 GCATGATCGGTCCTCCTCG 60.007 63.158 0.00 0.00 0.00 4.63
194 195 1.456196 GCATGATCGGTCCTCCTCGA 61.456 60.000 0.00 0.00 39.79 4.04
195 196 1.252175 CATGATCGGTCCTCCTCGAT 58.748 55.000 0.00 0.00 46.96 3.59
198 199 3.028916 ATCGGTCCTCCTCGATCTG 57.971 57.895 0.00 0.00 41.56 2.90
199 200 1.175983 ATCGGTCCTCCTCGATCTGC 61.176 60.000 0.00 0.00 41.56 4.26
200 201 2.121538 CGGTCCTCCTCGATCTGCA 61.122 63.158 0.00 0.00 0.00 4.41
201 202 1.459455 CGGTCCTCCTCGATCTGCAT 61.459 60.000 0.00 0.00 0.00 3.96
202 203 0.033228 GGTCCTCCTCGATCTGCATG 59.967 60.000 0.00 0.00 0.00 4.06
203 204 0.599728 GTCCTCCTCGATCTGCATGC 60.600 60.000 11.82 11.82 0.00 4.06
204 205 0.758310 TCCTCCTCGATCTGCATGCT 60.758 55.000 20.33 0.00 0.00 3.79
205 206 0.106335 CCTCCTCGATCTGCATGCTT 59.894 55.000 20.33 3.46 0.00 3.91
206 207 1.500108 CTCCTCGATCTGCATGCTTC 58.500 55.000 20.33 11.96 0.00 3.86
207 208 0.105593 TCCTCGATCTGCATGCTTCC 59.894 55.000 20.33 4.66 0.00 3.46
208 209 0.106335 CCTCGATCTGCATGCTTCCT 59.894 55.000 20.33 0.45 0.00 3.36
213 214 0.395311 ATCTGCATGCTTCCTGTGGG 60.395 55.000 20.33 0.00 0.00 4.61
263 264 7.643764 CCCAAATGTGCATTTTCGTACTTATAG 59.356 37.037 7.36 0.00 38.84 1.31
297 298 8.918202 TGACACACTTCAAATACTTTTAGGAT 57.082 30.769 0.00 0.00 0.00 3.24
312 313 5.756195 TTTAGGATCTCCGATGCATTTTG 57.244 39.130 0.00 0.00 42.08 2.44
331 332 8.268738 GCATTTTGCGCTTTTTATTAGATAAGG 58.731 33.333 9.73 0.00 31.71 2.69
332 333 7.749539 TTTTGCGCTTTTTATTAGATAAGGC 57.250 32.000 9.73 0.00 0.00 4.35
377 380 3.469008 TCTCAAAGGTTCGCTTTCTCA 57.531 42.857 0.00 0.00 0.00 3.27
382 385 4.024048 TCAAAGGTTCGCTTTCTCAATGTC 60.024 41.667 0.00 0.00 0.00 3.06
388 391 1.470098 CGCTTTCTCAATGTCCCAAGG 59.530 52.381 0.00 0.00 0.00 3.61
500 503 4.058817 ACTGCTCTAACTTTGTTCTTCCG 58.941 43.478 0.00 0.00 0.00 4.30
529 532 5.708948 TGTATTACAGCAAAATGAGCCAAC 58.291 37.500 0.00 0.00 0.00 3.77
541 544 3.306917 TGAGCCAACGTTATTTCTCGA 57.693 42.857 0.00 0.00 0.00 4.04
569 572 6.595326 GTCTTGTGTATGGAGAAACATCATCA 59.405 38.462 0.00 0.00 32.39 3.07
575 578 2.019984 GGAGAAACATCATCACTGGGC 58.980 52.381 0.00 0.00 0.00 5.36
578 581 2.040813 AGAAACATCATCACTGGGCACT 59.959 45.455 0.00 0.00 0.00 4.40
582 585 2.773661 ACATCATCACTGGGCACTGATA 59.226 45.455 0.00 0.00 0.00 2.15
742 745 2.619147 TCGTGACGGTGTGAAAAAGAA 58.381 42.857 4.70 0.00 0.00 2.52
748 751 2.108700 CGGTGTGAAAAAGAAGTTGCG 58.891 47.619 0.00 0.00 0.00 4.85
807 810 7.205992 TCTGATGCAGACTATTGTTGATACTC 58.794 38.462 0.00 0.00 35.39 2.59
1359 1369 1.734465 GGTATCAAGTCACAGCAGTGC 59.266 52.381 7.13 7.13 45.49 4.40
1397 1407 0.547471 TGGAGTTGGAGAGATGGGCA 60.547 55.000 0.00 0.00 0.00 5.36
1399 1409 0.463474 GAGTTGGAGAGATGGGCAGC 60.463 60.000 0.00 0.00 0.00 5.25
1663 1673 7.970614 GCCTAGAAATATTTGAGTTTTCAGGTG 59.029 37.037 5.17 0.00 34.15 4.00
1673 1683 4.709397 TGAGTTTTCAGGTGTTTGGAATGT 59.291 37.500 0.00 0.00 0.00 2.71
1676 1686 5.654650 AGTTTTCAGGTGTTTGGAATGTGTA 59.345 36.000 0.00 0.00 0.00 2.90
1682 1692 5.241506 CAGGTGTTTGGAATGTGTATGAACT 59.758 40.000 0.00 0.00 0.00 3.01
1740 1750 6.338146 CCATGATGCACTTTTGATCTCAAAT 58.662 36.000 6.21 0.00 44.30 2.32
1840 1865 2.829120 GGAGAGGTAAAGAGACTGCACT 59.171 50.000 0.00 0.00 0.00 4.40
1841 1866 3.367910 GGAGAGGTAAAGAGACTGCACTG 60.368 52.174 0.00 0.00 0.00 3.66
1843 1868 3.898123 AGAGGTAAAGAGACTGCACTGAA 59.102 43.478 0.00 0.00 0.00 3.02
1950 1975 5.048434 GCTAGGCCCATTGAATAATGTCTTC 60.048 44.000 0.00 0.00 41.68 2.87
1952 1977 6.266131 AGGCCCATTGAATAATGTCTTCTA 57.734 37.500 0.00 0.00 41.68 2.10
2019 2045 4.094146 ACAGGGAAACAAAAATTTGCAACG 59.906 37.500 0.00 0.00 41.79 4.10
2024 2050 2.350522 ACAAAAATTTGCAACGTGCCA 58.649 38.095 0.00 0.00 44.23 4.92
2032 2058 0.392863 TGCAACGTGCCATGCTCTAT 60.393 50.000 10.97 0.00 44.23 1.98
2042 2068 8.256611 ACGTGCCATGCTCTATTATATAAAAG 57.743 34.615 0.00 0.00 0.00 2.27
2118 2146 2.090349 CACGCGGCAAAATTTACACATG 59.910 45.455 12.47 0.00 0.00 3.21
2122 2150 4.318404 CGCGGCAAAATTTACACATGTTTT 60.318 37.500 0.00 0.00 0.00 2.43
2123 2151 4.903016 GCGGCAAAATTTACACATGTTTTG 59.097 37.500 12.14 12.14 41.84 2.44
2126 2154 7.621991 CGGCAAAATTTACACATGTTTTGTAA 58.378 30.769 15.99 10.49 41.30 2.41
2127 2155 8.279103 CGGCAAAATTTACACATGTTTTGTAAT 58.721 29.630 15.99 2.75 41.30 1.89
2128 2156 9.379811 GGCAAAATTTACACATGTTTTGTAATG 57.620 29.630 15.99 9.50 41.30 1.90
2129 2157 9.928236 GCAAAATTTACACATGTTTTGTAATGT 57.072 25.926 15.99 4.05 41.30 2.71
2137 2165 8.312896 ACACATGTTTTGTAATGTACATACGA 57.687 30.769 9.21 5.22 38.68 3.43
2138 2166 8.225107 ACACATGTTTTGTAATGTACATACGAC 58.775 33.333 9.21 8.46 38.68 4.34
2175 2203 8.954950 TGTTTTAAGATGGAAAATTTCTTGCA 57.045 26.923 5.65 0.00 32.28 4.08
2184 2212 5.884792 TGGAAAATTTCTTGCATTTTGGTGT 59.115 32.000 5.65 0.00 34.61 4.16
2193 2221 7.459795 TCTTGCATTTTGGTGTATATGACAA 57.540 32.000 0.00 0.00 40.66 3.18
2203 2231 6.862209 TGGTGTATATGACAAGGCAATTTTC 58.138 36.000 0.00 0.00 40.66 2.29
2208 2236 4.806640 ATGACAAGGCAATTTTCGGAAT 57.193 36.364 0.00 0.00 0.00 3.01
2210 2238 4.954875 TGACAAGGCAATTTTCGGAATTT 58.045 34.783 0.00 0.00 0.00 1.82
2291 2319 8.992073 ACACATGGCAAATTTAGAATTTTTCTC 58.008 29.630 0.00 0.00 41.14 2.87
2292 2320 8.445493 CACATGGCAAATTTAGAATTTTTCTCC 58.555 33.333 0.00 0.00 41.14 3.71
2307 2335 4.453480 TTTCTCCTGGTCACAAGGAAAT 57.547 40.909 1.40 0.00 0.00 2.17
2363 2391 1.522676 GCAAGCTTGCGTTCTTTTTCC 59.477 47.619 33.75 6.12 45.11 3.13
2365 2393 0.673985 AGCTTGCGTTCTTTTTCCCC 59.326 50.000 0.00 0.00 0.00 4.81
2366 2394 0.319555 GCTTGCGTTCTTTTTCCCCC 60.320 55.000 0.00 0.00 0.00 5.40
2367 2395 1.036707 CTTGCGTTCTTTTTCCCCCA 58.963 50.000 0.00 0.00 0.00 4.96
2375 2403 2.888212 TCTTTTTCCCCCAGAACCATG 58.112 47.619 0.00 0.00 32.95 3.66
2376 2404 2.448961 TCTTTTTCCCCCAGAACCATGA 59.551 45.455 0.00 0.00 32.95 3.07
2377 2405 2.302587 TTTTCCCCCAGAACCATGAC 57.697 50.000 0.00 0.00 32.95 3.06
2379 2407 1.153539 TTCCCCCAGAACCATGACAA 58.846 50.000 0.00 0.00 0.00 3.18
2380 2408 1.381867 TCCCCCAGAACCATGACAAT 58.618 50.000 0.00 0.00 0.00 2.71
2381 2409 1.715931 TCCCCCAGAACCATGACAATT 59.284 47.619 0.00 0.00 0.00 2.32
2382 2410 2.111613 TCCCCCAGAACCATGACAATTT 59.888 45.455 0.00 0.00 0.00 1.82
2383 2411 2.905736 CCCCCAGAACCATGACAATTTT 59.094 45.455 0.00 0.00 0.00 1.82
2384 2412 3.306919 CCCCCAGAACCATGACAATTTTG 60.307 47.826 0.00 0.00 0.00 2.44
2385 2413 3.306919 CCCCAGAACCATGACAATTTTGG 60.307 47.826 0.00 0.00 36.56 3.28
2421 2449 6.523840 ACTTTGTCACATGGCAATTTTACAT 58.476 32.000 0.00 0.00 39.61 2.29
2422 2450 6.991531 ACTTTGTCACATGGCAATTTTACATT 59.008 30.769 0.00 0.00 39.61 2.71
2423 2451 7.171337 ACTTTGTCACATGGCAATTTTACATTC 59.829 33.333 0.00 0.00 39.61 2.67
2471 2499 6.894339 AATGAAGTTAACACGAGGGAATTT 57.106 33.333 8.61 0.00 0.00 1.82
2517 2545 0.975887 ATTTGCCAAGGCGGTGAAAT 59.024 45.000 6.60 4.15 45.51 2.17
2525 2553 4.142924 GCCAAGGCGGTGAAATTAAATTTG 60.143 41.667 0.00 0.00 36.97 2.32
2536 2564 6.092533 GTGAAATTAAATTTGCCATGGTCCAG 59.907 38.462 14.67 0.00 31.47 3.86
2537 2565 6.013898 TGAAATTAAATTTGCCATGGTCCAGA 60.014 34.615 14.67 0.00 31.47 3.86
2552 2580 6.084326 TGGTCCAGAGAAAAACTAAATTGC 57.916 37.500 0.00 0.00 0.00 3.56
2556 2584 7.116805 GGTCCAGAGAAAAACTAAATTGCAATG 59.883 37.037 13.82 2.97 0.00 2.82
2557 2585 7.116805 GTCCAGAGAAAAACTAAATTGCAATGG 59.883 37.037 13.82 6.15 0.00 3.16
2558 2586 6.128472 CCAGAGAAAAACTAAATTGCAATGGC 60.128 38.462 13.82 0.00 41.68 4.40
2560 2588 6.870439 AGAGAAAAACTAAATTGCAATGGCTC 59.130 34.615 13.82 9.04 41.91 4.70
2562 2590 7.219322 AGAAAAACTAAATTGCAATGGCTCTT 58.781 30.769 13.82 5.61 41.91 2.85
2563 2591 6.790285 AAAACTAAATTGCAATGGCTCTTG 57.210 33.333 13.82 2.42 41.91 3.02
2595 2635 2.093869 GCCATGGTCTGTCAATGCAAAT 60.094 45.455 14.67 0.00 0.00 2.32
2622 2662 6.277605 CCATGATCTAGCAATGCAATTTTCA 58.722 36.000 8.35 4.26 31.22 2.69
2693 2733 2.992164 GCAATTTGCCATGGCCCT 59.008 55.556 33.44 15.32 37.42 5.19
2694 2734 1.450669 GCAATTTGCCATGGCCCTG 60.451 57.895 33.44 23.45 37.42 4.45
2707 2747 3.749665 TGGCCCTGAAAAGTTTGAATG 57.250 42.857 0.00 0.00 0.00 2.67
2709 2749 4.219115 TGGCCCTGAAAAGTTTGAATGTA 58.781 39.130 0.00 0.00 0.00 2.29
2711 2751 5.129485 TGGCCCTGAAAAGTTTGAATGTAAA 59.871 36.000 0.00 0.00 0.00 2.01
2713 2753 6.710295 GGCCCTGAAAAGTTTGAATGTAAAAT 59.290 34.615 0.00 0.00 0.00 1.82
2714 2754 7.228507 GGCCCTGAAAAGTTTGAATGTAAAATT 59.771 33.333 0.00 0.00 30.10 1.82
2715 2755 8.620416 GCCCTGAAAAGTTTGAATGTAAAATTT 58.380 29.630 0.00 0.00 38.86 1.82
2716 2756 9.934190 CCCTGAAAAGTTTGAATGTAAAATTTG 57.066 29.630 0.00 0.00 37.73 2.32
2822 2873 9.606631 CCTCTTCTTATATTACTGCTTTTCACT 57.393 33.333 0.00 0.00 0.00 3.41
2845 2896 3.213506 TGTTCATTGGATTCATAGGCCG 58.786 45.455 0.00 0.00 0.00 6.13
2853 2904 2.213499 GATTCATAGGCCGTGGTGAAG 58.787 52.381 16.31 0.00 34.45 3.02
2870 2921 5.010922 TGGTGAAGGAAAAAGTCAATCATGG 59.989 40.000 0.00 0.00 0.00 3.66
2871 2922 4.925646 GTGAAGGAAAAAGTCAATCATGGC 59.074 41.667 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.309950 ACGGAACCGACACCAGCC 62.310 66.667 20.14 0.00 42.83 4.85
21 22 2.737376 GACGGAACCGACACCAGC 60.737 66.667 20.14 0.00 42.83 4.85
22 23 1.372997 CTGACGGAACCGACACCAG 60.373 63.158 20.14 14.99 42.83 4.00
23 24 1.183030 ATCTGACGGAACCGACACCA 61.183 55.000 20.14 7.51 42.83 4.17
24 25 0.458025 GATCTGACGGAACCGACACC 60.458 60.000 20.14 6.32 42.83 4.16
25 26 0.526662 AGATCTGACGGAACCGACAC 59.473 55.000 20.14 8.21 42.83 3.67
26 27 0.526211 CAGATCTGACGGAACCGACA 59.474 55.000 18.34 17.79 42.83 4.35
27 28 0.179134 CCAGATCTGACGGAACCGAC 60.179 60.000 24.62 14.04 42.83 4.79
28 29 1.945354 GCCAGATCTGACGGAACCGA 61.945 60.000 24.62 0.00 42.83 4.69
29 30 1.519455 GCCAGATCTGACGGAACCG 60.519 63.158 24.62 11.83 46.03 4.44
30 31 1.519455 CGCCAGATCTGACGGAACC 60.519 63.158 24.62 2.57 32.81 3.62
31 32 2.167861 GCGCCAGATCTGACGGAAC 61.168 63.158 28.90 11.89 36.95 3.62
32 33 1.888436 AAGCGCCAGATCTGACGGAA 61.888 55.000 28.90 0.00 36.95 4.30
33 34 2.351244 AAGCGCCAGATCTGACGGA 61.351 57.895 28.90 0.00 36.95 4.69
34 35 2.169789 CAAGCGCCAGATCTGACGG 61.170 63.158 28.90 16.09 36.95 4.79
35 36 2.169789 CCAAGCGCCAGATCTGACG 61.170 63.158 24.97 24.97 39.46 4.35
36 37 0.809241 CTCCAAGCGCCAGATCTGAC 60.809 60.000 24.62 12.06 0.00 3.51
37 38 1.260538 ACTCCAAGCGCCAGATCTGA 61.261 55.000 24.62 0.07 0.00 3.27
38 39 0.809241 GACTCCAAGCGCCAGATCTG 60.809 60.000 16.24 16.24 0.00 2.90
39 40 1.519719 GACTCCAAGCGCCAGATCT 59.480 57.895 2.29 0.00 0.00 2.75
40 41 1.880340 CGACTCCAAGCGCCAGATC 60.880 63.158 2.29 0.00 0.00 2.75
41 42 2.185350 CGACTCCAAGCGCCAGAT 59.815 61.111 2.29 0.00 0.00 2.90
42 43 4.742201 GCGACTCCAAGCGCCAGA 62.742 66.667 2.29 0.00 46.93 3.86
49 50 4.379243 ACAGCCCGCGACTCCAAG 62.379 66.667 8.23 0.00 0.00 3.61
50 51 4.680237 CACAGCCCGCGACTCCAA 62.680 66.667 8.23 0.00 0.00 3.53
52 53 4.803426 CTCACAGCCCGCGACTCC 62.803 72.222 8.23 0.00 0.00 3.85
64 65 4.056125 CGGTCCTCGCTGCTCACA 62.056 66.667 0.00 0.00 0.00 3.58
65 66 4.803426 CCGGTCCTCGCTGCTCAC 62.803 72.222 0.00 0.00 37.59 3.51
67 68 4.803426 CACCGGTCCTCGCTGCTC 62.803 72.222 2.59 0.00 37.59 4.26
81 82 4.736896 GCCACGACGGAGGACACC 62.737 72.222 12.16 0.00 36.56 4.16
102 103 2.890474 AATCACGCCGACGCCATC 60.890 61.111 0.00 0.00 45.53 3.51
103 104 3.195002 CAATCACGCCGACGCCAT 61.195 61.111 0.00 0.00 45.53 4.40
104 105 4.365505 TCAATCACGCCGACGCCA 62.366 61.111 0.00 0.00 45.53 5.69
105 106 3.554692 CTCAATCACGCCGACGCC 61.555 66.667 0.00 0.00 45.53 5.68
106 107 3.554692 CCTCAATCACGCCGACGC 61.555 66.667 0.00 0.00 45.53 5.19
108 109 2.434185 TGCCTCAATCACGCCGAC 60.434 61.111 0.00 0.00 0.00 4.79
109 110 2.125552 CTGCCTCAATCACGCCGA 60.126 61.111 0.00 0.00 0.00 5.54
110 111 3.869272 GCTGCCTCAATCACGCCG 61.869 66.667 0.00 0.00 0.00 6.46
111 112 3.869272 CGCTGCCTCAATCACGCC 61.869 66.667 0.00 0.00 0.00 5.68
112 113 3.869272 CCGCTGCCTCAATCACGC 61.869 66.667 0.00 0.00 0.00 5.34
113 114 2.434884 ACCGCTGCCTCAATCACG 60.435 61.111 0.00 0.00 0.00 4.35
114 115 1.672356 ACACCGCTGCCTCAATCAC 60.672 57.895 0.00 0.00 0.00 3.06
115 116 1.672030 CACACCGCTGCCTCAATCA 60.672 57.895 0.00 0.00 0.00 2.57
116 117 2.401766 CCACACCGCTGCCTCAATC 61.402 63.158 0.00 0.00 0.00 2.67
117 118 2.360350 CCACACCGCTGCCTCAAT 60.360 61.111 0.00 0.00 0.00 2.57
130 131 4.572571 AAAAGGACCGCCGCCACA 62.573 61.111 0.00 0.00 39.96 4.17
131 132 3.263503 GAAAAAGGACCGCCGCCAC 62.264 63.158 0.00 0.00 39.96 5.01
132 133 2.981350 GAAAAAGGACCGCCGCCA 60.981 61.111 0.00 0.00 39.96 5.69
133 134 2.671963 AGAAAAAGGACCGCCGCC 60.672 61.111 0.00 0.00 39.96 6.13
134 135 1.235281 AAGAGAAAAAGGACCGCCGC 61.235 55.000 0.00 0.00 39.96 6.53
135 136 0.517316 CAAGAGAAAAAGGACCGCCG 59.483 55.000 0.00 0.00 39.96 6.46
136 137 1.535896 GACAAGAGAAAAAGGACCGCC 59.464 52.381 0.00 0.00 0.00 6.13
137 138 1.194772 CGACAAGAGAAAAAGGACCGC 59.805 52.381 0.00 0.00 0.00 5.68
138 139 1.194772 GCGACAAGAGAAAAAGGACCG 59.805 52.381 0.00 0.00 0.00 4.79
139 140 2.218603 TGCGACAAGAGAAAAAGGACC 58.781 47.619 0.00 0.00 0.00 4.46
140 141 3.498397 TGATGCGACAAGAGAAAAAGGAC 59.502 43.478 0.00 0.00 0.00 3.85
141 142 3.498397 GTGATGCGACAAGAGAAAAAGGA 59.502 43.478 0.00 0.00 0.00 3.36
142 143 3.665323 CGTGATGCGACAAGAGAAAAAGG 60.665 47.826 0.00 0.00 44.77 3.11
143 144 3.473367 CGTGATGCGACAAGAGAAAAAG 58.527 45.455 0.00 0.00 44.77 2.27
144 145 2.223144 CCGTGATGCGACAAGAGAAAAA 59.777 45.455 0.00 0.00 44.77 1.94
145 146 1.798223 CCGTGATGCGACAAGAGAAAA 59.202 47.619 0.00 0.00 44.77 2.29
146 147 1.428448 CCGTGATGCGACAAGAGAAA 58.572 50.000 0.00 0.00 44.77 2.52
147 148 1.014044 GCCGTGATGCGACAAGAGAA 61.014 55.000 0.00 0.00 44.77 2.87
148 149 1.446099 GCCGTGATGCGACAAGAGA 60.446 57.895 0.00 0.00 44.77 3.10
149 150 1.291184 TTGCCGTGATGCGACAAGAG 61.291 55.000 0.00 0.00 44.77 2.85
150 151 0.882484 TTTGCCGTGATGCGACAAGA 60.882 50.000 0.00 0.00 43.31 3.02
151 152 0.453282 CTTTGCCGTGATGCGACAAG 60.453 55.000 0.00 0.00 43.31 3.16
152 153 0.882484 TCTTTGCCGTGATGCGACAA 60.882 50.000 0.00 0.00 41.00 3.18
153 154 0.673333 ATCTTTGCCGTGATGCGACA 60.673 50.000 0.00 0.00 44.77 4.35
154 155 0.026803 GATCTTTGCCGTGATGCGAC 59.973 55.000 0.00 0.00 44.77 5.19
155 156 0.108186 AGATCTTTGCCGTGATGCGA 60.108 50.000 0.00 0.00 44.77 5.10
156 157 0.027194 CAGATCTTTGCCGTGATGCG 59.973 55.000 0.00 0.00 40.95 4.73
157 158 0.248377 GCAGATCTTTGCCGTGATGC 60.248 55.000 0.00 0.00 38.13 3.91
158 159 1.089112 TGCAGATCTTTGCCGTGATG 58.911 50.000 4.64 0.00 43.43 3.07
159 160 1.674441 CATGCAGATCTTTGCCGTGAT 59.326 47.619 4.64 0.00 43.43 3.06
160 161 1.089112 CATGCAGATCTTTGCCGTGA 58.911 50.000 4.64 0.00 43.43 4.35
161 162 1.089112 TCATGCAGATCTTTGCCGTG 58.911 50.000 4.64 4.36 43.43 4.94
162 163 2.048444 ATCATGCAGATCTTTGCCGT 57.952 45.000 4.64 0.00 43.43 5.68
171 172 0.683973 GGAGGACCGATCATGCAGAT 59.316 55.000 0.00 0.00 40.48 2.90
172 173 0.397675 AGGAGGACCGATCATGCAGA 60.398 55.000 0.00 0.00 41.83 4.26
173 174 0.033228 GAGGAGGACCGATCATGCAG 59.967 60.000 0.00 0.00 41.83 4.41
174 175 1.738346 CGAGGAGGACCGATCATGCA 61.738 60.000 0.00 0.00 41.83 3.96
175 176 1.006805 CGAGGAGGACCGATCATGC 60.007 63.158 0.00 0.00 41.83 4.06
176 177 1.252175 ATCGAGGAGGACCGATCATG 58.748 55.000 0.00 0.00 41.05 3.07
177 178 3.755810 ATCGAGGAGGACCGATCAT 57.244 52.632 0.00 0.00 41.05 2.45
180 181 1.175983 GCAGATCGAGGAGGACCGAT 61.176 60.000 0.00 0.00 46.67 4.18
181 182 1.824329 GCAGATCGAGGAGGACCGA 60.824 63.158 0.00 0.00 41.83 4.69
182 183 1.459455 ATGCAGATCGAGGAGGACCG 61.459 60.000 0.00 0.00 41.83 4.79
183 184 0.033228 CATGCAGATCGAGGAGGACC 59.967 60.000 0.00 0.00 0.00 4.46
184 185 0.599728 GCATGCAGATCGAGGAGGAC 60.600 60.000 14.21 0.00 0.00 3.85
185 186 0.758310 AGCATGCAGATCGAGGAGGA 60.758 55.000 21.98 0.00 0.00 3.71
186 187 0.106335 AAGCATGCAGATCGAGGAGG 59.894 55.000 21.98 0.00 0.00 4.30
187 188 1.500108 GAAGCATGCAGATCGAGGAG 58.500 55.000 21.98 0.00 0.00 3.69
188 189 0.105593 GGAAGCATGCAGATCGAGGA 59.894 55.000 21.98 0.00 0.00 3.71
189 190 0.106335 AGGAAGCATGCAGATCGAGG 59.894 55.000 21.98 0.00 0.00 4.63
190 191 1.218763 CAGGAAGCATGCAGATCGAG 58.781 55.000 21.98 7.18 0.00 4.04
191 192 0.538584 ACAGGAAGCATGCAGATCGA 59.461 50.000 21.98 0.00 0.00 3.59
192 193 0.656259 CACAGGAAGCATGCAGATCG 59.344 55.000 21.98 7.68 0.00 3.69
193 194 1.022735 CCACAGGAAGCATGCAGATC 58.977 55.000 21.98 14.48 0.00 2.75
194 195 0.395311 CCCACAGGAAGCATGCAGAT 60.395 55.000 21.98 5.29 33.47 2.90
195 196 1.001764 CCCACAGGAAGCATGCAGA 60.002 57.895 21.98 0.00 33.47 4.26
196 197 2.707849 GCCCACAGGAAGCATGCAG 61.708 63.158 21.98 6.52 33.47 4.41
197 198 2.677524 GCCCACAGGAAGCATGCA 60.678 61.111 21.98 0.00 33.47 3.96
198 199 3.818787 CGCCCACAGGAAGCATGC 61.819 66.667 10.51 10.51 33.47 4.06
199 200 1.078497 TACGCCCACAGGAAGCATG 60.078 57.895 0.00 0.00 33.47 4.06
200 201 1.221840 CTACGCCCACAGGAAGCAT 59.778 57.895 0.00 0.00 33.47 3.79
201 202 1.911269 TCTACGCCCACAGGAAGCA 60.911 57.895 0.00 0.00 33.47 3.91
202 203 1.448013 GTCTACGCCCACAGGAAGC 60.448 63.158 0.00 0.00 33.47 3.86
203 204 0.608640 AAGTCTACGCCCACAGGAAG 59.391 55.000 0.00 0.00 33.47 3.46
204 205 1.927487 TAAGTCTACGCCCACAGGAA 58.073 50.000 0.00 0.00 33.47 3.36
205 206 2.029623 GATAAGTCTACGCCCACAGGA 58.970 52.381 0.00 0.00 33.47 3.86
206 207 2.032620 AGATAAGTCTACGCCCACAGG 58.967 52.381 0.00 0.00 31.36 4.00
207 208 4.913335 TTAGATAAGTCTACGCCCACAG 57.087 45.455 0.00 0.00 36.69 3.66
208 209 5.864418 ATTTAGATAAGTCTACGCCCACA 57.136 39.130 0.00 0.00 36.69 4.17
213 214 7.598118 GGGTCCTAAATTTAGATAAGTCTACGC 59.402 40.741 23.95 12.84 36.69 4.42
263 264 0.603975 GAAGTGTGTCAGCTGGGTCC 60.604 60.000 15.13 0.18 0.00 4.46
297 298 1.026182 AGCGCAAAATGCATCGGAGA 61.026 50.000 11.47 0.00 45.36 3.71
312 313 5.470437 AGAGGCCTTATCTAATAAAAAGCGC 59.530 40.000 6.77 0.00 0.00 5.92
323 324 5.884322 TCGGTGTATTAGAGGCCTTATCTA 58.116 41.667 6.77 0.35 0.00 1.98
324 325 4.737578 TCGGTGTATTAGAGGCCTTATCT 58.262 43.478 6.77 1.58 0.00 1.98
325 326 5.464030 TTCGGTGTATTAGAGGCCTTATC 57.536 43.478 6.77 0.00 0.00 1.75
327 328 7.549147 AATATTCGGTGTATTAGAGGCCTTA 57.451 36.000 6.77 0.00 0.00 2.69
329 330 6.042781 TCAAATATTCGGTGTATTAGAGGCCT 59.957 38.462 3.86 3.86 0.00 5.19
330 331 6.228258 TCAAATATTCGGTGTATTAGAGGCC 58.772 40.000 0.00 0.00 0.00 5.19
331 332 6.929606 ACTCAAATATTCGGTGTATTAGAGGC 59.070 38.462 0.00 0.00 0.00 4.70
332 333 8.888579 AACTCAAATATTCGGTGTATTAGAGG 57.111 34.615 0.00 0.00 0.00 3.69
377 380 2.557452 CCACTTAAGCCCTTGGGACATT 60.557 50.000 10.36 3.43 39.30 2.71
382 385 0.623723 TAGCCACTTAAGCCCTTGGG 59.376 55.000 10.84 0.32 0.00 4.12
388 391 4.033990 GCAAGATTTAGCCACTTAAGCC 57.966 45.455 1.29 0.00 0.00 4.35
413 416 6.830912 AGTATGCTATTATCTCCAACTGCAA 58.169 36.000 0.00 0.00 32.88 4.08
414 417 6.425210 AGTATGCTATTATCTCCAACTGCA 57.575 37.500 0.00 0.00 0.00 4.41
415 418 7.329717 GTGTAGTATGCTATTATCTCCAACTGC 59.670 40.741 0.00 0.00 0.00 4.40
416 419 8.580720 AGTGTAGTATGCTATTATCTCCAACTG 58.419 37.037 0.00 0.00 0.00 3.16
417 420 8.580720 CAGTGTAGTATGCTATTATCTCCAACT 58.419 37.037 0.00 0.00 0.00 3.16
420 423 8.706322 TTCAGTGTAGTATGCTATTATCTCCA 57.294 34.615 0.00 0.00 0.00 3.86
421 424 9.982651 TTTTCAGTGTAGTATGCTATTATCTCC 57.017 33.333 0.00 0.00 0.00 3.71
491 494 5.845103 TGTAATACAGTCAACGGAAGAACA 58.155 37.500 0.00 0.00 0.00 3.18
529 532 4.680110 ACACAAGACAGTCGAGAAATAACG 59.320 41.667 0.00 0.00 0.00 3.18
541 544 5.290493 TGTTTCTCCATACACAAGACAGT 57.710 39.130 0.00 0.00 0.00 3.55
569 572 5.360714 CCATATTTTGTTATCAGTGCCCAGT 59.639 40.000 0.00 0.00 0.00 4.00
575 578 8.292448 GCACCTATCCATATTTTGTTATCAGTG 58.708 37.037 0.00 0.00 0.00 3.66
578 581 8.217111 TCTGCACCTATCCATATTTTGTTATCA 58.783 33.333 0.00 0.00 0.00 2.15
582 585 6.543831 GTCTCTGCACCTATCCATATTTTGTT 59.456 38.462 0.00 0.00 0.00 2.83
642 645 3.560251 ACCAGGCGGTGCTTCAGT 61.560 61.111 0.23 0.00 46.79 3.41
742 745 2.980233 GGGCTTCAGCACGCAACT 60.980 61.111 0.30 0.00 44.36 3.16
748 751 2.362120 ATGCCAGGGCTTCAGCAC 60.362 61.111 12.19 0.00 46.94 4.40
807 810 8.112016 TCGTGATAGAAATAAGGATAGGTCTG 57.888 38.462 0.00 0.00 0.00 3.51
1095 1100 4.890988 TGTCCCATCCAGGAAGTAAGATA 58.109 43.478 0.00 0.00 41.22 1.98
1359 1369 6.102663 ACTCCAAGTCTTGACATAATCTTCG 58.897 40.000 14.42 0.00 0.00 3.79
1397 1407 2.357517 CGCACTCTTCAACCCGCT 60.358 61.111 0.00 0.00 0.00 5.52
1399 1409 0.108615 ATCTCGCACTCTTCAACCCG 60.109 55.000 0.00 0.00 0.00 5.28
1691 1701 3.091545 AGGCAAGTAAATCATGTGGGTG 58.908 45.455 0.00 0.00 0.00 4.61
1692 1702 3.456380 AGGCAAGTAAATCATGTGGGT 57.544 42.857 0.00 0.00 0.00 4.51
1740 1750 6.853872 CAGCAGCGTTATACAACTTACAAAAA 59.146 34.615 0.00 0.00 32.09 1.94
1782 1796 1.064832 GCTGATCCTCCTTTGCTCCTT 60.065 52.381 0.00 0.00 0.00 3.36
1840 1865 1.334599 GCCGACGATGCTTTGTTTTCA 60.335 47.619 0.00 0.00 0.00 2.69
1841 1866 1.069227 AGCCGACGATGCTTTGTTTTC 60.069 47.619 0.00 0.00 34.87 2.29
1843 1868 0.238289 CAGCCGACGATGCTTTGTTT 59.762 50.000 0.00 0.00 36.81 2.83
1868 1893 6.302269 AGCAGGATAAGAATGGTCCAATTAG 58.698 40.000 0.00 0.00 34.42 1.73
1876 1901 5.184892 ACTCAAAGCAGGATAAGAATGGT 57.815 39.130 0.00 0.00 0.00 3.55
2014 2040 0.734889 AATAGAGCATGGCACGTTGC 59.265 50.000 3.39 3.39 44.08 4.17
2056 2082 9.323985 TCATAACTTTTTCCCAGTTTCAAATTG 57.676 29.630 0.00 0.00 35.95 2.32
2057 2083 9.898152 TTCATAACTTTTTCCCAGTTTCAAATT 57.102 25.926 0.00 0.00 35.95 1.82
2074 2100 8.707839 CGTGGCATGTTTAAAAATTCATAACTT 58.292 29.630 0.00 0.00 0.00 2.66
2076 2102 6.953189 GCGTGGCATGTTTAAAAATTCATAAC 59.047 34.615 8.75 0.00 0.00 1.89
2169 2197 7.362834 CCTTGTCATATACACCAAAATGCAAGA 60.363 37.037 14.31 0.00 38.00 3.02
2175 2203 6.849085 TTGCCTTGTCATATACACCAAAAT 57.151 33.333 0.00 0.00 38.00 1.82
2184 2212 7.581213 ATTCCGAAAATTGCCTTGTCATATA 57.419 32.000 0.00 0.00 0.00 0.86
2291 2319 5.723295 CCATTAAATTTCCTTGTGACCAGG 58.277 41.667 0.00 0.00 0.00 4.45
2292 2320 5.170748 GCCATTAAATTTCCTTGTGACCAG 58.829 41.667 0.00 0.00 0.00 4.00
2352 2380 1.611977 GGTTCTGGGGGAAAAAGAACG 59.388 52.381 8.27 0.00 46.98 3.95
2363 2391 3.306919 CCAAAATTGTCATGGTTCTGGGG 60.307 47.826 0.00 0.00 0.00 4.96
2365 2393 4.870123 TCCAAAATTGTCATGGTTCTGG 57.130 40.909 0.00 0.00 35.66 3.86
2366 2394 7.227116 ACATTTTCCAAAATTGTCATGGTTCTG 59.773 33.333 0.00 0.00 36.52 3.02
2367 2395 7.281841 ACATTTTCCAAAATTGTCATGGTTCT 58.718 30.769 0.00 0.00 36.52 3.01
2379 2407 9.883142 TGACAAAGTAGAAACATTTTCCAAAAT 57.117 25.926 0.00 0.00 39.07 1.82
2380 2408 9.145865 GTGACAAAGTAGAAACATTTTCCAAAA 57.854 29.630 0.00 0.00 0.00 2.44
2381 2409 8.307483 TGTGACAAAGTAGAAACATTTTCCAAA 58.693 29.630 0.00 0.00 0.00 3.28
2382 2410 7.831753 TGTGACAAAGTAGAAACATTTTCCAA 58.168 30.769 0.00 0.00 0.00 3.53
2383 2411 7.397892 TGTGACAAAGTAGAAACATTTTCCA 57.602 32.000 0.00 0.00 0.00 3.53
2384 2412 7.382218 CCATGTGACAAAGTAGAAACATTTTCC 59.618 37.037 0.00 0.00 0.00 3.13
2385 2413 7.096065 GCCATGTGACAAAGTAGAAACATTTTC 60.096 37.037 0.00 0.00 0.00 2.29
2445 2473 5.471556 TCCCTCGTGTTAACTTCATTACA 57.528 39.130 7.22 0.00 0.00 2.41
2454 2482 8.347771 ACTTAAAAGAAATTCCCTCGTGTTAAC 58.652 33.333 0.00 0.00 0.00 2.01
2457 2485 6.954487 ACTTAAAAGAAATTCCCTCGTGTT 57.046 33.333 0.00 0.00 0.00 3.32
2487 2515 3.003585 GCCTTGGCAAATTCAGTTTTTGG 59.996 43.478 6.79 0.00 35.18 3.28
2496 2524 0.316841 TTCACCGCCTTGGCAAATTC 59.683 50.000 12.45 0.00 43.94 2.17
2517 2545 4.671831 TCTCTGGACCATGGCAAATTTAA 58.328 39.130 13.04 0.00 0.00 1.52
2525 2553 2.519013 AGTTTTTCTCTGGACCATGGC 58.481 47.619 13.04 4.47 0.00 4.40
2536 2564 6.870439 AGAGCCATTGCAATTTAGTTTTTCTC 59.130 34.615 9.83 5.98 41.13 2.87
2537 2565 6.762333 AGAGCCATTGCAATTTAGTTTTTCT 58.238 32.000 9.83 2.20 41.13 2.52
2552 2580 6.372103 TGGCAAATTTATTTCAAGAGCCATTG 59.628 34.615 8.53 0.00 38.27 2.82
2556 2584 5.295045 CCATGGCAAATTTATTTCAAGAGCC 59.705 40.000 0.00 0.00 35.56 4.70
2557 2585 5.876460 ACCATGGCAAATTTATTTCAAGAGC 59.124 36.000 13.04 0.00 0.00 4.09
2558 2586 7.277098 CAGACCATGGCAAATTTATTTCAAGAG 59.723 37.037 13.04 0.00 0.00 2.85
2560 2588 6.875195 ACAGACCATGGCAAATTTATTTCAAG 59.125 34.615 13.04 0.00 0.00 3.02
2562 2590 6.014755 TGACAGACCATGGCAAATTTATTTCA 60.015 34.615 13.04 0.00 46.85 2.69
2563 2591 6.397272 TGACAGACCATGGCAAATTTATTTC 58.603 36.000 13.04 0.00 46.85 2.17
2777 2828 5.903923 AGAGGGGATAATTCCTTGTTTGTT 58.096 37.500 0.00 0.00 42.20 2.83
2779 2830 6.190587 AGAAGAGGGGATAATTCCTTGTTTG 58.809 40.000 0.00 0.00 42.20 2.93
2794 2845 7.993183 TGAAAAGCAGTAATATAAGAAGAGGGG 59.007 37.037 0.00 0.00 0.00 4.79
2795 2846 8.831550 GTGAAAAGCAGTAATATAAGAAGAGGG 58.168 37.037 0.00 0.00 0.00 4.30
2813 2864 6.479660 TGAATCCAATGAACAAAGTGAAAAGC 59.520 34.615 0.00 0.00 0.00 3.51
2822 2873 4.097741 CGGCCTATGAATCCAATGAACAAA 59.902 41.667 0.00 0.00 0.00 2.83
2828 2879 1.881973 CCACGGCCTATGAATCCAATG 59.118 52.381 0.00 0.00 0.00 2.82
2829 2880 1.494721 ACCACGGCCTATGAATCCAAT 59.505 47.619 0.00 0.00 0.00 3.16
2845 2896 5.514274 TGATTGACTTTTTCCTTCACCAC 57.486 39.130 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.