Multiple sequence alignment - TraesCS3B01G115900

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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 TraesCS3B01G115900 chr3B 100.000 2729 0 0 1 2729 82631048 82628320 0.000000e+00 5040.0
1 TraesCS3B01G115900 chr3B 97.701 174 4 0 1 174 525834188 525834361 1.590000e-77 300.0
2 TraesCS3B01G115900 chr3B 96.610 177 6 0 1 177 822975007 822974831 7.390000e-76 294.0
3 TraesCS3B01G115900 chr3B 94.972 179 9 0 1 179 79952467 79952645 5.750000e-72 281.0
4 TraesCS3B01G115900 chr3B 84.800 125 18 1 734 857 540497588 540497464 1.030000e-24 124.0
5 TraesCS3B01G115900 chr3D 90.122 2288 124 44 464 2729 51687437 51685230 0.000000e+00 2880.0
6 TraesCS3B01G115900 chr3D 91.083 157 10 4 186 340 51688200 51688046 2.750000e-50 209.0
7 TraesCS3B01G115900 chr3A 89.541 2046 153 32 408 2420 64286114 64284097 0.000000e+00 2536.0
8 TraesCS3B01G115900 chr3A 92.896 183 8 1 2552 2729 64284066 64283884 7.500000e-66 261.0
9 TraesCS3B01G115900 chr3A 92.424 66 5 0 870 935 64285699 64285634 8.040000e-16 95.3
10 TraesCS3B01G115900 chr5A 80.102 1573 202 55 953 2462 504955196 504956720 0.000000e+00 1068.0
11 TraesCS3B01G115900 chr5A 83.175 315 42 9 532 837 119999676 119999364 7.440000e-71 278.0
12 TraesCS3B01G115900 chr5A 84.351 262 25 12 426 679 563314841 563315094 2.710000e-60 243.0
13 TraesCS3B01G115900 chr5B 80.813 1131 156 34 953 2038 479714974 479716088 0.000000e+00 830.0
14 TraesCS3B01G115900 chr5B 97.207 179 5 0 1 179 690316884 690316706 1.230000e-78 303.0
15 TraesCS3B01G115900 chr5B 83.415 205 22 7 2261 2457 479716351 479716551 2.160000e-41 180.0
16 TraesCS3B01G115900 chr5D 80.454 926 128 25 1154 2040 399327902 399328813 0.000000e+00 658.0
17 TraesCS3B01G115900 chr5D 85.259 251 31 4 953 1200 399327652 399327899 1.250000e-63 254.0
18 TraesCS3B01G115900 chr1D 83.981 412 46 9 449 857 228799265 228799659 7.130000e-101 377.0
19 TraesCS3B01G115900 chr6A 84.756 328 38 9 532 857 579956493 579956176 4.390000e-83 318.0
20 TraesCS3B01G115900 chr6A 96.045 177 7 0 1 177 602816612 602816788 3.440000e-74 289.0
21 TraesCS3B01G115900 chr6A 84.746 59 7 2 206 263 265356349 265356292 1.060000e-04 58.4
22 TraesCS3B01G115900 chr7B 85.616 292 36 5 571 857 26739080 26739370 4.420000e-78 302.0
23 TraesCS3B01G115900 chr7B 83.333 240 25 8 543 781 727001431 727001206 9.900000e-50 207.0
24 TraesCS3B01G115900 chr7A 95.977 174 7 0 1 174 135916791 135916618 1.600000e-72 283.0
25 TraesCS3B01G115900 chr4D 96.000 175 6 1 1 175 130440329 130440502 1.600000e-72 283.0
26 TraesCS3B01G115900 chrUn 95.429 175 8 0 1 175 65963186 65963012 2.070000e-71 279.0
27 TraesCS3B01G115900 chr1A 95.455 176 7 1 1 176 465399848 465399674 2.070000e-71 279.0
28 TraesCS3B01G115900 chr1B 81.982 333 51 8 532 857 551720543 551720873 9.630000e-70 274.0
29 TraesCS3B01G115900 chr6D 81.902 326 49 7 532 857 433769396 433769081 1.610000e-67 267.0
30 TraesCS3B01G115900 chr4B 86.364 66 5 3 206 269 218546526 218546589 4.880000e-08 69.4
31 TraesCS3B01G115900 chr2D 94.872 39 2 0 234 272 283899688 283899650 8.160000e-06 62.1
32 TraesCS3B01G115900 chr2B 84.211 57 7 2 206 261 672446525 672446470 1.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G115900 chr3B 82628320 82631048 2728 True 5040.0 5040 100.000000 1 2729 1 chr3B.!!$R1 2728
1 TraesCS3B01G115900 chr3D 51685230 51688200 2970 True 1544.5 2880 90.602500 186 2729 2 chr3D.!!$R1 2543
2 TraesCS3B01G115900 chr3A 64283884 64286114 2230 True 964.1 2536 91.620333 408 2729 3 chr3A.!!$R1 2321
3 TraesCS3B01G115900 chr5A 504955196 504956720 1524 False 1068.0 1068 80.102000 953 2462 1 chr5A.!!$F1 1509
4 TraesCS3B01G115900 chr5B 479714974 479716551 1577 False 505.0 830 82.114000 953 2457 2 chr5B.!!$F1 1504
5 TraesCS3B01G115900 chr5D 399327652 399328813 1161 False 456.0 658 82.856500 953 2040 2 chr5D.!!$F1 1087

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
184 185 0.036388 TCTCGTTCCCTCACAATGGC 60.036 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2701 2.068519 TGCAGAGCACAAACTGATACG 58.931 47.619 0.0 0.0 36.38 3.06 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
106 107 9.812347 TCATTTTAGGCTTAATCATATGGATGT 57.188 29.630 2.13 0.00 36.02 3.06
107 108 9.850628 CATTTTAGGCTTAATCATATGGATGTG 57.149 33.333 2.13 0.00 36.02 3.21
108 109 9.812347 ATTTTAGGCTTAATCATATGGATGTGA 57.188 29.630 2.13 0.00 36.02 3.58
109 110 9.639563 TTTTAGGCTTAATCATATGGATGTGAA 57.360 29.630 2.13 0.00 36.02 3.18
110 111 8.853077 TTAGGCTTAATCATATGGATGTGAAG 57.147 34.615 2.13 0.56 36.02 3.02
111 112 7.083062 AGGCTTAATCATATGGATGTGAAGA 57.917 36.000 2.13 0.00 36.02 2.87
112 113 7.520798 AGGCTTAATCATATGGATGTGAAGAA 58.479 34.615 2.13 0.00 36.02 2.52
113 114 7.664731 AGGCTTAATCATATGGATGTGAAGAAG 59.335 37.037 2.13 0.00 36.02 2.85
114 115 7.094463 GGCTTAATCATATGGATGTGAAGAAGG 60.094 40.741 2.13 0.00 36.02 3.46
115 116 7.094463 GCTTAATCATATGGATGTGAAGAAGGG 60.094 40.741 2.13 0.00 36.02 3.95
116 117 6.520021 AATCATATGGATGTGAAGAAGGGA 57.480 37.500 2.13 0.00 36.02 4.20
117 118 6.715350 ATCATATGGATGTGAAGAAGGGAT 57.285 37.500 2.13 0.00 34.06 3.85
118 119 5.872963 TCATATGGATGTGAAGAAGGGATG 58.127 41.667 2.13 0.00 34.41 3.51
119 120 5.370584 TCATATGGATGTGAAGAAGGGATGT 59.629 40.000 2.13 0.00 34.41 3.06
120 121 3.634397 TGGATGTGAAGAAGGGATGTC 57.366 47.619 0.00 0.00 0.00 3.06
121 122 2.912295 TGGATGTGAAGAAGGGATGTCA 59.088 45.455 0.00 0.00 0.00 3.58
122 123 3.054875 TGGATGTGAAGAAGGGATGTCAG 60.055 47.826 0.00 0.00 0.00 3.51
123 124 3.539604 GATGTGAAGAAGGGATGTCAGG 58.460 50.000 0.00 0.00 0.00 3.86
124 125 1.630369 TGTGAAGAAGGGATGTCAGGG 59.370 52.381 0.00 0.00 0.00 4.45
125 126 1.630878 GTGAAGAAGGGATGTCAGGGT 59.369 52.381 0.00 0.00 0.00 4.34
126 127 2.838202 GTGAAGAAGGGATGTCAGGGTA 59.162 50.000 0.00 0.00 0.00 3.69
127 128 2.838202 TGAAGAAGGGATGTCAGGGTAC 59.162 50.000 0.00 0.00 0.00 3.34
128 129 2.950990 AGAAGGGATGTCAGGGTACT 57.049 50.000 0.00 0.00 0.00 2.73
129 130 2.472029 AGAAGGGATGTCAGGGTACTG 58.528 52.381 0.00 0.00 46.30 2.74
130 131 2.188817 GAAGGGATGTCAGGGTACTGT 58.811 52.381 0.00 0.00 45.14 3.55
131 132 3.012502 AGAAGGGATGTCAGGGTACTGTA 59.987 47.826 0.00 0.00 45.14 2.74
132 133 3.033659 AGGGATGTCAGGGTACTGTAG 57.966 52.381 0.00 0.00 45.14 2.74
133 134 1.413077 GGGATGTCAGGGTACTGTAGC 59.587 57.143 8.46 8.46 45.14 3.58
134 135 2.389715 GGATGTCAGGGTACTGTAGCT 58.610 52.381 15.74 0.00 45.14 3.32
135 136 2.766828 GGATGTCAGGGTACTGTAGCTT 59.233 50.000 15.74 6.40 45.14 3.74
136 137 3.181474 GGATGTCAGGGTACTGTAGCTTC 60.181 52.174 15.74 1.62 45.14 3.86
137 138 2.176889 TGTCAGGGTACTGTAGCTTCC 58.823 52.381 15.74 0.70 45.14 3.46
138 139 1.481363 GTCAGGGTACTGTAGCTTCCC 59.519 57.143 15.74 9.60 45.14 3.97
140 141 1.867363 AGGGTACTGTAGCTTCCCTG 58.133 55.000 15.74 0.00 45.64 4.45
141 142 1.361543 AGGGTACTGTAGCTTCCCTGA 59.638 52.381 15.74 0.00 45.64 3.86
142 143 1.481363 GGGTACTGTAGCTTCCCTGAC 59.519 57.143 15.74 0.00 35.63 3.51
143 144 2.176889 GGTACTGTAGCTTCCCTGACA 58.823 52.381 9.64 0.00 0.00 3.58
144 145 2.766828 GGTACTGTAGCTTCCCTGACAT 59.233 50.000 9.64 0.00 0.00 3.06
145 146 3.181474 GGTACTGTAGCTTCCCTGACATC 60.181 52.174 9.64 0.00 0.00 3.06
146 147 1.834263 ACTGTAGCTTCCCTGACATCC 59.166 52.381 0.00 0.00 0.00 3.51
147 148 1.139853 CTGTAGCTTCCCTGACATCCC 59.860 57.143 0.00 0.00 0.00 3.85
148 149 1.273838 TGTAGCTTCCCTGACATCCCT 60.274 52.381 0.00 0.00 0.00 4.20
149 150 1.840635 GTAGCTTCCCTGACATCCCTT 59.159 52.381 0.00 0.00 0.00 3.95
150 151 0.915364 AGCTTCCCTGACATCCCTTC 59.085 55.000 0.00 0.00 0.00 3.46
151 152 0.462759 GCTTCCCTGACATCCCTTCG 60.463 60.000 0.00 0.00 0.00 3.79
152 153 0.905357 CTTCCCTGACATCCCTTCGT 59.095 55.000 0.00 0.00 0.00 3.85
153 154 0.613260 TTCCCTGACATCCCTTCGTG 59.387 55.000 0.00 0.00 0.00 4.35
154 155 0.252057 TCCCTGACATCCCTTCGTGA 60.252 55.000 0.00 0.00 0.00 4.35
155 156 0.833287 CCCTGACATCCCTTCGTGAT 59.167 55.000 0.00 0.00 0.00 3.06
156 157 1.473965 CCCTGACATCCCTTCGTGATG 60.474 57.143 0.00 0.00 44.13 3.07
163 164 3.722147 CATCCCTTCGTGATGTTAGAGG 58.278 50.000 0.00 0.00 35.86 3.69
164 165 3.095912 TCCCTTCGTGATGTTAGAGGA 57.904 47.619 0.00 0.00 0.00 3.71
165 166 3.643237 TCCCTTCGTGATGTTAGAGGAT 58.357 45.455 0.00 0.00 0.00 3.24
166 167 3.637229 TCCCTTCGTGATGTTAGAGGATC 59.363 47.826 0.00 0.00 0.00 3.36
167 168 7.918888 CATCCCTTCGTGATGTTAGAGGATCT 61.919 46.154 0.00 0.00 40.97 2.75
168 169 9.601034 CATCCCTTCGTGATGTTAGAGGATCTC 62.601 48.148 0.00 0.00 39.70 2.75
179 180 1.475403 GAGGATCTCGTTCCCTCACA 58.525 55.000 0.00 0.00 44.42 3.58
180 181 1.825474 GAGGATCTCGTTCCCTCACAA 59.175 52.381 0.00 0.00 44.42 3.33
181 182 2.432510 GAGGATCTCGTTCCCTCACAAT 59.567 50.000 0.00 0.00 44.42 2.71
182 183 2.169352 AGGATCTCGTTCCCTCACAATG 59.831 50.000 0.00 0.00 36.35 2.82
183 184 2.555199 GATCTCGTTCCCTCACAATGG 58.445 52.381 0.00 0.00 0.00 3.16
184 185 0.036388 TCTCGTTCCCTCACAATGGC 60.036 55.000 0.00 0.00 0.00 4.40
207 208 4.028993 ACCTCCACGGTGATGTAAATTT 57.971 40.909 10.28 0.00 46.80 1.82
208 209 4.403734 ACCTCCACGGTGATGTAAATTTT 58.596 39.130 10.28 0.00 46.80 1.82
211 212 6.661805 ACCTCCACGGTGATGTAAATTTTAAT 59.338 34.615 10.28 0.00 46.80 1.40
213 214 7.700656 CCTCCACGGTGATGTAAATTTTAATTC 59.299 37.037 10.28 0.00 0.00 2.17
216 217 9.019764 CCACGGTGATGTAAATTTTAATTCATC 57.980 33.333 10.28 9.60 33.57 2.92
218 219 9.787532 ACGGTGATGTAAATTTTAATTCATCTG 57.212 29.630 14.41 10.89 33.85 2.90
232 233 9.567776 TTTAATTCATCTGTTGGAGTTGTAGAA 57.432 29.630 0.00 0.00 0.00 2.10
367 370 8.969260 TTTACATCATCTGTTGAATATGCTCT 57.031 30.769 0.00 0.00 39.39 4.09
368 371 8.969260 TTACATCATCTGTTGAATATGCTCTT 57.031 30.769 0.00 0.00 39.39 2.85
370 373 8.604640 ACATCATCTGTTGAATATGCTCTTAG 57.395 34.615 0.00 0.00 38.03 2.18
395 398 7.903995 CAATTTTTGCCACCAAGTACATTAT 57.096 32.000 0.00 0.00 31.52 1.28
402 405 4.442472 GCCACCAAGTACATTATAGTCCGT 60.442 45.833 0.00 0.00 0.00 4.69
415 418 2.414994 AGTCCGTCGATCCAAGAGTA 57.585 50.000 0.00 0.00 0.00 2.59
653 1186 0.421495 TCCTTCTTCCCTCATCCCCA 59.579 55.000 0.00 0.00 0.00 4.96
671 1204 4.548513 CCTCCCTCCCTCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
693 1226 3.034635 TCCTTCCTCTTGCATCCTCTAC 58.965 50.000 0.00 0.00 0.00 2.59
704 1237 5.885230 TGCATCCTCTACTTGTTCAAATG 57.115 39.130 0.00 0.00 0.00 2.32
736 1269 7.440556 CCTGATTTCTGTATTGGATGAGTACTG 59.559 40.741 0.00 0.00 0.00 2.74
740 1273 4.716784 TCTGTATTGGATGAGTACTGGCTT 59.283 41.667 0.00 0.00 0.00 4.35
810 1343 1.689984 TGCTGCATGGTTTTGACAGA 58.310 45.000 0.00 0.00 0.00 3.41
844 1377 9.965824 CAAGTTTACATGTGAAAGGATTTTAGT 57.034 29.630 9.11 0.00 39.27 2.24
846 1379 9.965824 AGTTTACATGTGAAAGGATTTTAGTTG 57.034 29.630 9.11 0.00 39.27 3.16
847 1380 9.959749 GTTTACATGTGAAAGGATTTTAGTTGA 57.040 29.630 9.11 0.00 39.27 3.18
851 1384 8.960591 ACATGTGAAAGGATTTTAGTTGATAGG 58.039 33.333 0.00 0.00 39.27 2.57
852 1385 8.960591 CATGTGAAAGGATTTTAGTTGATAGGT 58.039 33.333 0.00 0.00 39.27 3.08
853 1386 8.934023 TGTGAAAGGATTTTAGTTGATAGGTT 57.066 30.769 0.00 0.00 39.27 3.50
854 1387 9.362151 TGTGAAAGGATTTTAGTTGATAGGTTT 57.638 29.630 0.00 0.00 39.27 3.27
1103 1689 0.657840 CGCAGTTATACTTGGCTGGC 59.342 55.000 0.00 0.00 0.00 4.85
1128 1715 5.609423 AGTGCCATTAATTTTTCACTTGCA 58.391 33.333 0.00 0.00 31.51 4.08
1331 1967 5.480772 GGATGTAGTCCTAGCAGCCTAATTA 59.519 44.000 0.00 0.00 44.16 1.40
1378 2023 4.398358 CAGTCTCATTGCCATGTTGAGAAT 59.602 41.667 13.30 10.87 45.35 2.40
1437 2085 8.956533 TCAGCTTAATATACACTTGTGCATTA 57.043 30.769 0.10 0.96 0.00 1.90
1505 2158 5.767168 AGATTCAAGGTATTATGCAGAAGGC 59.233 40.000 0.00 0.00 45.13 4.35
1517 2192 3.221964 GCAGAAGGCACCATAAGTTTG 57.778 47.619 0.00 0.00 43.97 2.93
1540 2215 9.521841 TTTGTTTGTCCCTTATGTGTATGATTA 57.478 29.630 0.00 0.00 0.00 1.75
1630 2306 9.787532 TTCTGTATAATTACATCTTTGCTTTGC 57.212 29.630 0.00 0.00 37.68 3.68
1722 2398 1.678970 GGGTGTTGATGTGGGCTCC 60.679 63.158 0.00 0.00 0.00 4.70
1740 2416 1.550524 TCCGACTGAGGTCAATTCCAG 59.449 52.381 0.00 0.00 42.21 3.86
1749 2425 6.777580 ACTGAGGTCAATTCCAGTGTTTAATT 59.222 34.615 0.00 0.00 38.32 1.40
1777 2453 1.251251 CCAGTTTGAAGCTTCCTGGG 58.749 55.000 29.01 18.39 39.20 4.45
1802 2479 6.944234 ACCATAGCTAGAAAAAGGTTATGC 57.056 37.500 0.00 0.00 0.00 3.14
1819 2496 8.766994 AGGTTATGCCATTTCACTATGTTTAT 57.233 30.769 0.00 0.00 40.61 1.40
1962 2659 3.021695 CAAGGCCATCAGTGTTCATGAT 58.978 45.455 5.01 0.00 37.90 2.45
1972 2670 6.426980 TCAGTGTTCATGATATGTTTGCTC 57.573 37.500 0.00 0.00 0.00 4.26
1983 2682 5.822519 TGATATGTTTGCTCTGTAACCATCC 59.177 40.000 0.00 0.00 0.00 3.51
1984 2683 3.500448 TGTTTGCTCTGTAACCATCCA 57.500 42.857 0.00 0.00 0.00 3.41
1998 2697 4.849813 ACCATCCAGATTTCATCACTGA 57.150 40.909 0.00 0.00 34.07 3.41
2002 2701 5.507482 CCATCCAGATTTCATCACTGAATGC 60.507 44.000 0.00 0.00 40.95 3.56
2079 2846 6.874134 GCTCTTTTGATGGTTCAGTTCTAGTA 59.126 38.462 0.00 0.00 32.27 1.82
2080 2847 7.550906 GCTCTTTTGATGGTTCAGTTCTAGTAT 59.449 37.037 0.00 0.00 32.27 2.12
2083 2850 8.547967 TTTTGATGGTTCAGTTCTAGTATGTC 57.452 34.615 0.00 0.00 32.27 3.06
2095 2862 9.347934 CAGTTCTAGTATGTCTAAGTTTCTGTG 57.652 37.037 0.00 0.00 0.00 3.66
2150 2929 5.689068 GGAACTTCTCAAATTCAGCAAAGTG 59.311 40.000 0.00 0.00 0.00 3.16
2151 2930 5.841957 ACTTCTCAAATTCAGCAAAGTGT 57.158 34.783 0.00 0.00 0.00 3.55
2205 2985 9.731819 CTCCTCATGATTAACAAAAGATCATTG 57.268 33.333 0.00 9.08 38.18 2.82
2206 2986 9.246670 TCCTCATGATTAACAAAAGATCATTGT 57.753 29.630 10.20 10.20 42.56 2.71
2213 2993 9.490663 GATTAACAAAAGATCATTGTACCTTCG 57.509 33.333 14.86 0.00 39.98 3.79
2215 2995 5.003804 ACAAAAGATCATTGTACCTTCGCT 58.996 37.500 13.40 0.00 39.14 4.93
2238 3018 6.569226 GCTGATACCATTATTGCTCCATGTTC 60.569 42.308 0.00 0.00 0.00 3.18
2334 3131 1.337447 ACATGCCAATTTGACAGCAGC 60.337 47.619 0.00 0.00 38.89 5.25
2351 3152 4.208686 CCGGTCGCCTGCTACCTC 62.209 72.222 10.63 0.00 33.34 3.85
2462 3266 1.967535 CTGCCTCCTCGTCTGTTGA 59.032 57.895 0.00 0.00 0.00 3.18
2480 3314 4.748798 ACCTCCCTGGAGCCCCTG 62.749 72.222 7.73 0.00 40.69 4.45
2491 3325 3.775654 GCCCCTGCTCGCAGTAGT 61.776 66.667 16.82 0.00 42.15 2.73
2492 3326 2.982130 CCCCTGCTCGCAGTAGTT 59.018 61.111 16.82 0.00 42.15 2.24
2493 3327 1.153549 CCCCTGCTCGCAGTAGTTC 60.154 63.158 16.82 0.00 42.15 3.01
2494 3328 1.608717 CCCCTGCTCGCAGTAGTTCT 61.609 60.000 16.82 0.00 42.15 3.01
2495 3329 0.179124 CCCTGCTCGCAGTAGTTCTC 60.179 60.000 16.82 0.00 42.15 2.87
2496 3330 0.528017 CCTGCTCGCAGTAGTTCTCA 59.472 55.000 16.82 0.00 42.15 3.27
2497 3331 1.468908 CCTGCTCGCAGTAGTTCTCAG 60.469 57.143 16.82 0.00 42.15 3.35
2498 3332 1.201181 CTGCTCGCAGTAGTTCTCAGT 59.799 52.381 10.65 0.00 39.10 3.41
2499 3333 1.068264 TGCTCGCAGTAGTTCTCAGTG 60.068 52.381 0.00 0.00 0.00 3.66
2500 3334 1.734047 GCTCGCAGTAGTTCTCAGTGG 60.734 57.143 0.00 0.00 0.00 4.00
2501 3335 1.542030 CTCGCAGTAGTTCTCAGTGGT 59.458 52.381 0.00 0.00 0.00 4.16
2502 3336 1.540267 TCGCAGTAGTTCTCAGTGGTC 59.460 52.381 0.00 0.00 0.00 4.02
2503 3337 1.269723 CGCAGTAGTTCTCAGTGGTCA 59.730 52.381 0.00 0.00 0.00 4.02
2504 3338 2.669670 CGCAGTAGTTCTCAGTGGTCAG 60.670 54.545 0.00 0.00 0.00 3.51
2505 3339 2.297597 GCAGTAGTTCTCAGTGGTCAGT 59.702 50.000 0.00 0.00 0.00 3.41
2506 3340 3.243907 GCAGTAGTTCTCAGTGGTCAGTT 60.244 47.826 0.00 0.00 0.00 3.16
2507 3341 4.302455 CAGTAGTTCTCAGTGGTCAGTTG 58.698 47.826 0.00 0.00 0.00 3.16
2508 3342 3.961408 AGTAGTTCTCAGTGGTCAGTTGT 59.039 43.478 0.00 0.00 0.00 3.32
2509 3343 5.009710 CAGTAGTTCTCAGTGGTCAGTTGTA 59.990 44.000 0.00 0.00 0.00 2.41
2510 3344 5.597182 AGTAGTTCTCAGTGGTCAGTTGTAA 59.403 40.000 0.00 0.00 0.00 2.41
2511 3345 5.353394 AGTTCTCAGTGGTCAGTTGTAAA 57.647 39.130 0.00 0.00 0.00 2.01
2512 3346 5.360591 AGTTCTCAGTGGTCAGTTGTAAAG 58.639 41.667 0.00 0.00 0.00 1.85
2513 3347 3.728845 TCTCAGTGGTCAGTTGTAAAGC 58.271 45.455 0.00 0.00 0.00 3.51
2514 3348 3.388024 TCTCAGTGGTCAGTTGTAAAGCT 59.612 43.478 0.00 0.00 0.00 3.74
2515 3349 4.130118 CTCAGTGGTCAGTTGTAAAGCTT 58.870 43.478 0.00 0.00 0.00 3.74
2516 3350 5.069914 TCTCAGTGGTCAGTTGTAAAGCTTA 59.930 40.000 0.00 0.00 0.00 3.09
2517 3351 5.054477 TCAGTGGTCAGTTGTAAAGCTTAC 58.946 41.667 0.00 0.00 0.00 2.34
2518 3352 4.814234 CAGTGGTCAGTTGTAAAGCTTACA 59.186 41.667 0.00 1.90 0.00 2.41
2519 3353 4.814771 AGTGGTCAGTTGTAAAGCTTACAC 59.185 41.667 0.00 1.34 0.00 2.90
2520 3354 3.805422 TGGTCAGTTGTAAAGCTTACACG 59.195 43.478 0.00 0.00 0.00 4.49
2521 3355 3.363673 GGTCAGTTGTAAAGCTTACACGC 60.364 47.826 0.00 0.00 0.00 5.34
2522 3356 2.473609 TCAGTTGTAAAGCTTACACGCG 59.526 45.455 3.53 3.53 34.40 6.01
2523 3357 1.193874 AGTTGTAAAGCTTACACGCGC 59.806 47.619 5.73 0.00 34.40 6.86
2524 3358 0.513820 TTGTAAAGCTTACACGCGCC 59.486 50.000 5.73 0.00 34.40 6.53
2525 3359 0.320073 TGTAAAGCTTACACGCGCCT 60.320 50.000 5.73 0.00 34.40 5.52
2611 3447 3.577667 TGTTGCTTAAACATGCATGCTC 58.422 40.909 26.53 9.57 43.96 4.26
2612 3448 2.925563 GTTGCTTAAACATGCATGCTCC 59.074 45.455 26.53 9.58 39.07 4.70
2613 3449 2.449464 TGCTTAAACATGCATGCTCCT 58.551 42.857 26.53 10.70 33.94 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 9.812347 ACATCCATATGATTAAGCCTAAAATGA 57.188 29.630 3.65 0.00 36.54 2.57
81 82 9.850628 CACATCCATATGATTAAGCCTAAAATG 57.149 33.333 3.65 0.00 36.54 2.32
82 83 9.812347 TCACATCCATATGATTAAGCCTAAAAT 57.188 29.630 3.65 0.00 36.54 1.82
83 84 9.639563 TTCACATCCATATGATTAAGCCTAAAA 57.360 29.630 3.65 0.00 36.54 1.52
84 85 9.288576 CTTCACATCCATATGATTAAGCCTAAA 57.711 33.333 3.65 0.00 36.54 1.85
85 86 8.659527 TCTTCACATCCATATGATTAAGCCTAA 58.340 33.333 3.65 0.00 36.54 2.69
86 87 8.206126 TCTTCACATCCATATGATTAAGCCTA 57.794 34.615 3.65 0.00 36.54 3.93
87 88 7.083062 TCTTCACATCCATATGATTAAGCCT 57.917 36.000 3.65 0.00 36.54 4.58
88 89 7.094463 CCTTCTTCACATCCATATGATTAAGCC 60.094 40.741 3.65 0.00 36.54 4.35
89 90 7.094463 CCCTTCTTCACATCCATATGATTAAGC 60.094 40.741 3.65 0.00 36.54 3.09
90 91 8.159447 TCCCTTCTTCACATCCATATGATTAAG 58.841 37.037 3.65 0.00 36.54 1.85
91 92 8.044574 TCCCTTCTTCACATCCATATGATTAA 57.955 34.615 3.65 0.00 36.54 1.40
92 93 7.631510 TCCCTTCTTCACATCCATATGATTA 57.368 36.000 3.65 0.00 36.54 1.75
93 94 6.520021 TCCCTTCTTCACATCCATATGATT 57.480 37.500 3.65 0.00 36.54 2.57
94 95 6.045224 ACATCCCTTCTTCACATCCATATGAT 59.955 38.462 3.65 0.00 36.54 2.45
95 96 5.370584 ACATCCCTTCTTCACATCCATATGA 59.629 40.000 3.65 0.00 36.54 2.15
96 97 5.628130 ACATCCCTTCTTCACATCCATATG 58.372 41.667 0.00 0.00 39.17 1.78
97 98 5.370584 TGACATCCCTTCTTCACATCCATAT 59.629 40.000 0.00 0.00 0.00 1.78
98 99 4.721274 TGACATCCCTTCTTCACATCCATA 59.279 41.667 0.00 0.00 0.00 2.74
99 100 3.524789 TGACATCCCTTCTTCACATCCAT 59.475 43.478 0.00 0.00 0.00 3.41
100 101 2.912295 TGACATCCCTTCTTCACATCCA 59.088 45.455 0.00 0.00 0.00 3.41
101 102 3.539604 CTGACATCCCTTCTTCACATCC 58.460 50.000 0.00 0.00 0.00 3.51
102 103 3.539604 CCTGACATCCCTTCTTCACATC 58.460 50.000 0.00 0.00 0.00 3.06
103 104 2.240667 CCCTGACATCCCTTCTTCACAT 59.759 50.000 0.00 0.00 0.00 3.21
104 105 1.630369 CCCTGACATCCCTTCTTCACA 59.370 52.381 0.00 0.00 0.00 3.58
105 106 1.630878 ACCCTGACATCCCTTCTTCAC 59.369 52.381 0.00 0.00 0.00 3.18
106 107 2.044793 ACCCTGACATCCCTTCTTCA 57.955 50.000 0.00 0.00 0.00 3.02
107 108 3.108376 AGTACCCTGACATCCCTTCTTC 58.892 50.000 0.00 0.00 0.00 2.87
108 109 2.840651 CAGTACCCTGACATCCCTTCTT 59.159 50.000 0.00 0.00 41.50 2.52
109 110 2.225650 ACAGTACCCTGACATCCCTTCT 60.226 50.000 0.00 0.00 41.50 2.85
110 111 2.188817 ACAGTACCCTGACATCCCTTC 58.811 52.381 0.00 0.00 41.50 3.46
111 112 2.344093 ACAGTACCCTGACATCCCTT 57.656 50.000 0.00 0.00 41.50 3.95
112 113 2.955461 GCTACAGTACCCTGACATCCCT 60.955 54.545 0.00 0.00 41.50 4.20
113 114 1.413077 GCTACAGTACCCTGACATCCC 59.587 57.143 0.00 0.00 41.50 3.85
114 115 2.389715 AGCTACAGTACCCTGACATCC 58.610 52.381 0.00 0.00 41.50 3.51
115 116 3.181474 GGAAGCTACAGTACCCTGACATC 60.181 52.174 0.00 0.00 41.50 3.06
116 117 2.766828 GGAAGCTACAGTACCCTGACAT 59.233 50.000 0.00 0.00 41.50 3.06
117 118 2.176889 GGAAGCTACAGTACCCTGACA 58.823 52.381 0.00 0.00 41.50 3.58
118 119 1.481363 GGGAAGCTACAGTACCCTGAC 59.519 57.143 0.00 0.00 41.50 3.51
119 120 1.861982 GGGAAGCTACAGTACCCTGA 58.138 55.000 0.00 0.00 41.50 3.86
122 123 1.481363 GTCAGGGAAGCTACAGTACCC 59.519 57.143 0.00 0.00 40.71 3.69
123 124 2.176889 TGTCAGGGAAGCTACAGTACC 58.823 52.381 0.00 0.00 0.00 3.34
124 125 3.181474 GGATGTCAGGGAAGCTACAGTAC 60.181 52.174 0.00 0.00 0.00 2.73
125 126 3.031736 GGATGTCAGGGAAGCTACAGTA 58.968 50.000 0.00 0.00 0.00 2.74
126 127 1.834263 GGATGTCAGGGAAGCTACAGT 59.166 52.381 0.00 0.00 0.00 3.55
127 128 1.139853 GGGATGTCAGGGAAGCTACAG 59.860 57.143 0.00 0.00 0.00 2.74
128 129 1.204146 GGGATGTCAGGGAAGCTACA 58.796 55.000 0.00 0.00 0.00 2.74
129 130 1.501582 AGGGATGTCAGGGAAGCTAC 58.498 55.000 0.00 0.00 0.00 3.58
130 131 2.119495 GAAGGGATGTCAGGGAAGCTA 58.881 52.381 0.00 0.00 0.00 3.32
131 132 0.915364 GAAGGGATGTCAGGGAAGCT 59.085 55.000 0.00 0.00 0.00 3.74
132 133 0.462759 CGAAGGGATGTCAGGGAAGC 60.463 60.000 0.00 0.00 0.00 3.86
133 134 0.905357 ACGAAGGGATGTCAGGGAAG 59.095 55.000 0.00 0.00 0.00 3.46
134 135 0.613260 CACGAAGGGATGTCAGGGAA 59.387 55.000 0.00 0.00 0.00 3.97
135 136 0.252057 TCACGAAGGGATGTCAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
136 137 0.833287 ATCACGAAGGGATGTCAGGG 59.167 55.000 0.00 0.00 0.00 4.45
137 138 1.945387 CATCACGAAGGGATGTCAGG 58.055 55.000 4.23 0.00 37.85 3.86
142 143 3.384789 TCCTCTAACATCACGAAGGGATG 59.615 47.826 10.41 10.41 45.93 3.51
143 144 3.643237 TCCTCTAACATCACGAAGGGAT 58.357 45.455 0.00 0.00 0.00 3.85
144 145 3.095912 TCCTCTAACATCACGAAGGGA 57.904 47.619 0.00 0.00 0.00 4.20
145 146 3.639094 AGATCCTCTAACATCACGAAGGG 59.361 47.826 0.00 0.00 0.00 3.95
146 147 4.555708 CGAGATCCTCTAACATCACGAAGG 60.556 50.000 0.00 0.00 35.79 3.46
147 148 4.035792 ACGAGATCCTCTAACATCACGAAG 59.964 45.833 5.88 0.00 36.82 3.79
148 149 3.945921 ACGAGATCCTCTAACATCACGAA 59.054 43.478 5.88 0.00 36.82 3.85
149 150 3.542648 ACGAGATCCTCTAACATCACGA 58.457 45.455 5.88 0.00 36.82 4.35
150 151 3.972950 ACGAGATCCTCTAACATCACG 57.027 47.619 0.00 0.00 38.56 4.35
151 152 4.500035 GGGAACGAGATCCTCTAACATCAC 60.500 50.000 0.00 0.00 39.57 3.06
152 153 3.637229 GGGAACGAGATCCTCTAACATCA 59.363 47.826 0.00 0.00 39.57 3.07
153 154 3.892588 AGGGAACGAGATCCTCTAACATC 59.107 47.826 0.00 0.00 39.57 3.06
154 155 3.892588 GAGGGAACGAGATCCTCTAACAT 59.107 47.826 0.00 0.00 42.70 2.71
155 156 3.288964 GAGGGAACGAGATCCTCTAACA 58.711 50.000 0.00 0.00 42.70 2.41
156 157 3.067040 GTGAGGGAACGAGATCCTCTAAC 59.933 52.174 15.48 7.89 45.36 2.34
157 158 3.288964 GTGAGGGAACGAGATCCTCTAA 58.711 50.000 15.48 1.61 45.36 2.10
158 159 2.241430 TGTGAGGGAACGAGATCCTCTA 59.759 50.000 15.48 6.45 45.36 2.43
159 160 1.006043 TGTGAGGGAACGAGATCCTCT 59.994 52.381 15.48 8.12 45.36 3.69
160 161 1.475403 TGTGAGGGAACGAGATCCTC 58.525 55.000 0.00 0.00 45.36 3.71
161 162 1.938585 TTGTGAGGGAACGAGATCCT 58.061 50.000 0.00 0.00 39.57 3.24
162 163 2.555199 CATTGTGAGGGAACGAGATCC 58.445 52.381 0.00 0.00 38.86 3.36
163 164 2.555199 CCATTGTGAGGGAACGAGATC 58.445 52.381 0.00 0.00 0.00 2.75
164 165 1.407437 GCCATTGTGAGGGAACGAGAT 60.407 52.381 0.00 0.00 0.00 2.75
165 166 0.036388 GCCATTGTGAGGGAACGAGA 60.036 55.000 0.00 0.00 0.00 4.04
166 167 1.026718 GGCCATTGTGAGGGAACGAG 61.027 60.000 0.00 0.00 0.00 4.18
167 168 1.002624 GGCCATTGTGAGGGAACGA 60.003 57.895 0.00 0.00 0.00 3.85
168 169 1.303236 TGGCCATTGTGAGGGAACG 60.303 57.895 0.00 0.00 0.00 3.95
169 170 1.250840 GGTGGCCATTGTGAGGGAAC 61.251 60.000 9.72 0.00 0.00 3.62
170 171 1.076549 GGTGGCCATTGTGAGGGAA 59.923 57.895 9.72 0.00 0.00 3.97
171 172 1.852157 AGGTGGCCATTGTGAGGGA 60.852 57.895 9.72 0.00 0.00 4.20
172 173 1.379044 GAGGTGGCCATTGTGAGGG 60.379 63.158 9.72 0.00 0.00 4.30
173 174 1.379044 GGAGGTGGCCATTGTGAGG 60.379 63.158 9.72 0.00 0.00 3.86
174 175 0.962356 GTGGAGGTGGCCATTGTGAG 60.962 60.000 9.72 0.00 40.68 3.51
175 176 1.074775 GTGGAGGTGGCCATTGTGA 59.925 57.895 9.72 0.00 40.68 3.58
176 177 2.334946 CGTGGAGGTGGCCATTGTG 61.335 63.158 9.72 0.00 40.68 3.33
177 178 2.034066 CGTGGAGGTGGCCATTGT 59.966 61.111 9.72 0.00 40.68 2.71
178 179 2.751436 CCGTGGAGGTGGCCATTG 60.751 66.667 9.72 0.00 40.68 2.82
207 208 9.739276 ATTCTACAACTCCAACAGATGAATTAA 57.261 29.630 0.00 0.00 0.00 1.40
208 209 9.739276 AATTCTACAACTCCAACAGATGAATTA 57.261 29.630 0.00 0.00 31.42 1.40
211 212 8.463930 AAAATTCTACAACTCCAACAGATGAA 57.536 30.769 0.00 0.00 0.00 2.57
213 214 7.596248 CCAAAAATTCTACAACTCCAACAGATG 59.404 37.037 0.00 0.00 0.00 2.90
216 217 6.697019 CACCAAAAATTCTACAACTCCAACAG 59.303 38.462 0.00 0.00 0.00 3.16
218 219 6.801575 TCACCAAAAATTCTACAACTCCAAC 58.198 36.000 0.00 0.00 0.00 3.77
262 263 7.734942 ACATTACCAAAACATTCAACTCCAAT 58.265 30.769 0.00 0.00 0.00 3.16
341 344 9.399797 AGAGCATATTCAACAGATGATGTAAAA 57.600 29.630 0.00 0.00 43.00 1.52
343 346 8.969260 AAGAGCATATTCAACAGATGATGTAA 57.031 30.769 0.00 0.00 43.00 2.41
345 348 7.172875 GCTAAGAGCATATTCAACAGATGATGT 59.827 37.037 0.00 0.00 42.38 3.06
346 349 7.519843 GCTAAGAGCATATTCAACAGATGATG 58.480 38.462 0.00 0.00 41.89 3.07
347 350 7.670009 GCTAAGAGCATATTCAACAGATGAT 57.330 36.000 0.00 0.00 41.89 2.45
379 382 4.056050 CGGACTATAATGTACTTGGTGGC 58.944 47.826 0.00 0.00 0.00 5.01
384 387 6.084925 GGATCGACGGACTATAATGTACTTG 58.915 44.000 0.00 0.00 0.00 3.16
395 398 2.414994 ACTCTTGGATCGACGGACTA 57.585 50.000 0.00 0.00 0.00 2.59
402 405 2.681848 GACGTCCTTACTCTTGGATCGA 59.318 50.000 3.51 0.00 34.58 3.59
415 418 0.616964 GGAACCCTAGGGACGTCCTT 60.617 60.000 35.38 28.27 45.47 3.36
653 1186 3.369388 GGAGGGAGGGAGGGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
671 1204 1.836802 AGAGGATGCAAGAGGAAGGAC 59.163 52.381 0.00 0.00 0.00 3.85
693 1226 5.972107 ATCAGGGAGAACATTTGAACAAG 57.028 39.130 0.00 0.00 0.00 3.16
704 1237 5.745227 TCCAATACAGAAATCAGGGAGAAC 58.255 41.667 0.00 0.00 0.00 3.01
736 1269 6.624352 TCTCACAATATGCAATCTAAAGCC 57.376 37.500 0.00 0.00 0.00 4.35
781 1314 2.362736 ACCATGCAGCAAGTACTCATG 58.637 47.619 12.39 12.39 35.55 3.07
853 1386 8.973182 ACCTATCAACTTTACCTCAAACAAAAA 58.027 29.630 0.00 0.00 0.00 1.94
854 1387 8.410141 CACCTATCAACTTTACCTCAAACAAAA 58.590 33.333 0.00 0.00 0.00 2.44
855 1388 7.558444 ACACCTATCAACTTTACCTCAAACAAA 59.442 33.333 0.00 0.00 0.00 2.83
856 1389 7.057894 ACACCTATCAACTTTACCTCAAACAA 58.942 34.615 0.00 0.00 0.00 2.83
857 1390 6.597562 ACACCTATCAACTTTACCTCAAACA 58.402 36.000 0.00 0.00 0.00 2.83
858 1391 7.506328 AACACCTATCAACTTTACCTCAAAC 57.494 36.000 0.00 0.00 0.00 2.93
859 1392 8.528044 AAAACACCTATCAACTTTACCTCAAA 57.472 30.769 0.00 0.00 0.00 2.69
860 1393 8.410141 CAAAAACACCTATCAACTTTACCTCAA 58.590 33.333 0.00 0.00 0.00 3.02
861 1394 7.776030 TCAAAAACACCTATCAACTTTACCTCA 59.224 33.333 0.00 0.00 0.00 3.86
862 1395 8.161699 TCAAAAACACCTATCAACTTTACCTC 57.838 34.615 0.00 0.00 0.00 3.85
863 1396 8.706322 ATCAAAAACACCTATCAACTTTACCT 57.294 30.769 0.00 0.00 0.00 3.08
867 1400 9.423061 GCATTATCAAAAACACCTATCAACTTT 57.577 29.630 0.00 0.00 0.00 2.66
868 1401 8.806146 AGCATTATCAAAAACACCTATCAACTT 58.194 29.630 0.00 0.00 0.00 2.66
935 1468 6.073873 CGAATTAGAGCCTAAAATGCAGAGAG 60.074 42.308 0.00 0.00 0.00 3.20
1103 1689 5.164061 GCAAGTGAAAAATTAATGGCACTCG 60.164 40.000 11.00 4.51 35.73 4.18
1505 2158 5.529581 AAGGGACAAACAAACTTATGGTG 57.470 39.130 0.00 0.00 0.00 4.17
1630 2306 7.012327 TCGAGCACAAATAATTAGAAATGGGAG 59.988 37.037 0.00 0.00 0.00 4.30
1722 2398 2.289072 ACACTGGAATTGACCTCAGTCG 60.289 50.000 0.00 0.00 46.74 4.18
1749 2425 6.323739 AGGAAGCTTCAAACTGGTCATAAAAA 59.676 34.615 27.02 0.00 0.00 1.94
1777 2453 7.041303 GGCATAACCTTTTTCTAGCTATGGTAC 60.041 40.741 0.00 0.00 34.51 3.34
1945 2642 5.762825 AACATATCATGAACACTGATGGC 57.237 39.130 0.00 0.00 35.12 4.40
1962 2659 5.045942 TCTGGATGGTTACAGAGCAAACATA 60.046 40.000 0.00 0.00 38.71 2.29
1972 2670 6.037940 CAGTGATGAAATCTGGATGGTTACAG 59.962 42.308 0.00 0.00 45.81 2.74
1983 2682 4.611310 ACGCATTCAGTGATGAAATCTG 57.389 40.909 0.00 0.00 45.81 2.90
1984 2683 6.051074 TGATACGCATTCAGTGATGAAATCT 58.949 36.000 0.00 0.00 45.81 2.40
1998 2697 3.125829 CAGAGCACAAACTGATACGCATT 59.874 43.478 0.00 0.00 36.38 3.56
2002 2701 2.068519 TGCAGAGCACAAACTGATACG 58.931 47.619 0.00 0.00 36.38 3.06
2079 2846 3.499918 GCACTGCACAGAAACTTAGACAT 59.500 43.478 4.31 0.00 0.00 3.06
2080 2847 2.872245 GCACTGCACAGAAACTTAGACA 59.128 45.455 4.31 0.00 0.00 3.41
2083 2850 3.133691 TCTGCACTGCACAGAAACTTAG 58.866 45.455 4.31 0.00 41.10 2.18
2095 2862 4.387862 CCAAATGAAAGAAATCTGCACTGC 59.612 41.667 0.00 0.00 0.00 4.40
2150 2929 3.988379 TCAAAGTGCCAATGAGACAAC 57.012 42.857 0.00 0.00 0.00 3.32
2151 2930 3.953612 ACTTCAAAGTGCCAATGAGACAA 59.046 39.130 0.00 0.00 37.98 3.18
2205 2985 5.107065 GCAATAATGGTATCAGCGAAGGTAC 60.107 44.000 0.00 0.00 35.08 3.34
2206 2986 4.994852 GCAATAATGGTATCAGCGAAGGTA 59.005 41.667 0.00 0.00 35.08 3.08
2212 2992 3.402110 TGGAGCAATAATGGTATCAGCG 58.598 45.455 0.00 0.00 37.41 5.18
2213 2993 4.763793 ACATGGAGCAATAATGGTATCAGC 59.236 41.667 0.00 0.00 37.41 4.26
2215 2995 6.262944 GTGAACATGGAGCAATAATGGTATCA 59.737 38.462 0.00 0.00 37.41 2.15
2238 3018 7.167968 CACAGTCCATTCTACAATTGTTTTGTG 59.832 37.037 17.78 10.88 34.11 3.33
2334 3131 4.208686 GAGGTAGCAGGCGACCGG 62.209 72.222 16.21 0.00 44.71 5.28
2371 3172 1.228675 CAGCCTCAAACAAGCCCCT 60.229 57.895 0.00 0.00 0.00 4.79
2375 3176 0.823356 TGGACCAGCCTCAAACAAGC 60.823 55.000 0.00 0.00 37.63 4.01
2462 3266 3.960313 AGGGGCTCCAGGGAGGTT 61.960 66.667 16.70 0.00 42.19 3.50
2480 3314 1.623359 CACTGAGAACTACTGCGAGC 58.377 55.000 0.00 0.00 0.00 5.03
2481 3315 1.542030 ACCACTGAGAACTACTGCGAG 59.458 52.381 0.00 0.00 0.00 5.03
2482 3316 1.540267 GACCACTGAGAACTACTGCGA 59.460 52.381 0.00 0.00 0.00 5.10
2483 3317 1.269723 TGACCACTGAGAACTACTGCG 59.730 52.381 0.00 0.00 0.00 5.18
2484 3318 2.297597 ACTGACCACTGAGAACTACTGC 59.702 50.000 0.00 0.00 0.00 4.40
2485 3319 4.202161 ACAACTGACCACTGAGAACTACTG 60.202 45.833 0.00 0.00 0.00 2.74
2486 3320 3.961408 ACAACTGACCACTGAGAACTACT 59.039 43.478 0.00 0.00 0.00 2.57
2487 3321 4.323553 ACAACTGACCACTGAGAACTAC 57.676 45.455 0.00 0.00 0.00 2.73
2488 3322 6.474140 TTTACAACTGACCACTGAGAACTA 57.526 37.500 0.00 0.00 0.00 2.24
2489 3323 5.353394 TTTACAACTGACCACTGAGAACT 57.647 39.130 0.00 0.00 0.00 3.01
2490 3324 4.024809 GCTTTACAACTGACCACTGAGAAC 60.025 45.833 0.00 0.00 0.00 3.01
2491 3325 4.127171 GCTTTACAACTGACCACTGAGAA 58.873 43.478 0.00 0.00 0.00 2.87
2492 3326 3.388024 AGCTTTACAACTGACCACTGAGA 59.612 43.478 0.00 0.00 0.00 3.27
2493 3327 3.733337 AGCTTTACAACTGACCACTGAG 58.267 45.455 0.00 0.00 0.00 3.35
2494 3328 3.838244 AGCTTTACAACTGACCACTGA 57.162 42.857 0.00 0.00 0.00 3.41
2495 3329 4.814234 TGTAAGCTTTACAACTGACCACTG 59.186 41.667 3.20 0.00 0.00 3.66
2496 3330 4.814771 GTGTAAGCTTTACAACTGACCACT 59.185 41.667 3.20 0.00 0.00 4.00
2497 3331 4.318546 CGTGTAAGCTTTACAACTGACCAC 60.319 45.833 3.20 0.00 0.00 4.16
2498 3332 3.805422 CGTGTAAGCTTTACAACTGACCA 59.195 43.478 3.20 0.00 0.00 4.02
2499 3333 3.363673 GCGTGTAAGCTTTACAACTGACC 60.364 47.826 3.20 0.00 0.00 4.02
2500 3334 3.660904 CGCGTGTAAGCTTTACAACTGAC 60.661 47.826 3.20 0.00 34.40 3.51
2501 3335 2.473609 CGCGTGTAAGCTTTACAACTGA 59.526 45.455 3.20 0.00 34.40 3.41
2502 3336 2.822827 CGCGTGTAAGCTTTACAACTG 58.177 47.619 3.20 2.80 34.40 3.16
2503 3337 1.193874 GCGCGTGTAAGCTTTACAACT 59.806 47.619 3.20 0.00 34.40 3.16
2504 3338 1.587991 GCGCGTGTAAGCTTTACAAC 58.412 50.000 3.20 0.00 34.40 3.32
2505 3339 0.513820 GGCGCGTGTAAGCTTTACAA 59.486 50.000 3.20 0.00 34.40 2.41
2506 3340 0.320073 AGGCGCGTGTAAGCTTTACA 60.320 50.000 3.20 4.44 34.40 2.41
2507 3341 0.794473 AAGGCGCGTGTAAGCTTTAC 59.206 50.000 3.20 3.74 30.81 2.01
2508 3342 0.793861 CAAGGCGCGTGTAAGCTTTA 59.206 50.000 3.20 0.00 31.41 1.85
2509 3343 1.574428 CAAGGCGCGTGTAAGCTTT 59.426 52.632 3.20 0.00 32.82 3.51
2510 3344 2.325082 CCAAGGCGCGTGTAAGCTT 61.325 57.895 8.43 3.48 34.40 3.74
2511 3345 2.742372 CCAAGGCGCGTGTAAGCT 60.742 61.111 8.43 0.00 34.40 3.74
2512 3346 3.799755 CCCAAGGCGCGTGTAAGC 61.800 66.667 8.43 0.00 0.00 3.09
2513 3347 3.799755 GCCCAAGGCGCGTGTAAG 61.800 66.667 8.43 0.00 39.62 2.34
2523 3357 2.990967 ACATGCAACGGCCCAAGG 60.991 61.111 0.00 0.00 40.13 3.61
2524 3358 2.259204 CACATGCAACGGCCCAAG 59.741 61.111 0.00 0.00 40.13 3.61
2525 3359 3.988525 GCACATGCAACGGCCCAA 61.989 61.111 0.00 0.00 41.59 4.12
2549 3385 9.858247 GGTATACGAAACACACAACATATATTG 57.142 33.333 0.00 0.00 35.59 1.90
2550 3386 9.826574 AGGTATACGAAACACACAACATATATT 57.173 29.630 0.00 0.00 0.00 1.28
2605 3441 2.027377 AGGAACAGAACAGAGGAGCATG 60.027 50.000 0.00 0.00 0.00 4.06
2611 3447 2.880890 CAAACCAGGAACAGAACAGAGG 59.119 50.000 0.00 0.00 0.00 3.69
2612 3448 2.880890 CCAAACCAGGAACAGAACAGAG 59.119 50.000 0.00 0.00 0.00 3.35
2613 3449 2.930950 CCAAACCAGGAACAGAACAGA 58.069 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.