Multiple sequence alignment - TraesCS5D01G195400

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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 TraesCS5D01G195400 chr5D 100.000 4111 0 0 948 5058 298939600 298943710 0.000000e+00 7592.0
1 TraesCS5D01G195400 chr5D 100.000 643 0 0 1 643 298938653 298939295 0.000000e+00 1188.0
2 TraesCS5D01G195400 chr5A 93.012 4164 174 57 948 5058 398887550 398883451 0.000000e+00 5969.0
3 TraesCS5D01G195400 chr5A 92.291 454 19 8 202 643 398888053 398887604 9.240000e-177 630.0
4 TraesCS5D01G195400 chr5B 93.080 2312 100 24 2794 5058 339905691 339907989 0.000000e+00 3328.0
5 TraesCS5D01G195400 chr5B 89.363 1335 97 22 948 2255 339903782 339905098 0.000000e+00 1637.0
6 TraesCS5D01G195400 chr5B 92.500 520 30 4 2254 2764 339905179 339905698 0.000000e+00 736.0
7 TraesCS5D01G195400 chr5B 93.154 409 20 4 229 636 339903308 339903709 1.210000e-165 593.0
8 TraesCS5D01G195400 chr4D 74.754 610 87 43 4442 5004 220344370 220343781 1.430000e-50 211.0
9 TraesCS5D01G195400 chr3B 79.649 285 35 18 4551 4820 479293763 479293487 3.110000e-42 183.0
10 TraesCS5D01G195400 chr4B 81.159 207 27 6 4546 4745 20229052 20229253 6.780000e-34 156.0
11 TraesCS5D01G195400 chr1D 91.111 45 3 1 4696 4740 484320128 484320171 5.470000e-05 60.2


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 TraesCS5D01G195400 chr5D 298938653 298943710 5057 False 4390.0 7592 100.00000 1 5058 2 chr5D.!!$F1 5057
1 TraesCS5D01G195400 chr5A 398883451 398888053 4602 True 3299.5 5969 92.65150 202 5058 2 chr5A.!!$R1 4856
2 TraesCS5D01G195400 chr5B 339903308 339907989 4681 False 1573.5 3328 92.02425 229 5058 4 chr5B.!!$F1 4829
3 TraesCS5D01G195400 chr4D 220343781 220344370 589 True 211.0 211 74.75400 4442 5004 1 chr4D.!!$R1 562


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
297 298 0.173708 ACGAAAGCTCCGAGCCTTAG 59.826 55.0 16.99 12.82 43.77 2.18 F
628 650 0.983378 CCCTCCCGACCTTCATCCTT 60.983 60.0 0.00 0.00 0.00 3.36 F
2041 2091 0.035317 AATGGCACGCAGAGAAGTCA 59.965 50.0 0.00 0.00 0.00 3.41 F
2163 2216 0.188342 AAGCCTGGATGTGGTTTGGT 59.812 50.0 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1317 0.036306 AAATCCGGTCTCCCACACAC 59.964 55.0 0.00 0.0 0.00 3.82 R
2147 2200 0.318120 GCAACCAAACCACATCCAGG 59.682 55.0 0.00 0.0 0.00 4.45 R
3134 3318 1.114119 TTGCTGGCAGGTGCAATTCA 61.114 50.0 17.64 0.0 43.17 2.57 R
4157 4362 0.036952 CGGTGACAACAGGCATCTCT 60.037 55.0 0.00 0.0 0.00 3.10 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
20 21 3.034721 ACAACTAAAGTCGCCATTCGA 57.965 42.857 0.00 0.00 46.29 3.71
58 59 6.908870 AAGAAAAACTGAAACTTGCAATCC 57.091 33.333 0.00 0.00 0.00 3.01
59 60 5.043248 AGAAAAACTGAAACTTGCAATCCG 58.957 37.500 0.00 0.00 0.00 4.18
60 61 4.647424 AAAACTGAAACTTGCAATCCGA 57.353 36.364 0.00 0.00 0.00 4.55
61 62 4.647424 AAACTGAAACTTGCAATCCGAA 57.353 36.364 0.00 0.00 0.00 4.30
62 63 4.647424 AACTGAAACTTGCAATCCGAAA 57.353 36.364 0.00 0.00 0.00 3.46
63 64 4.647424 ACTGAAACTTGCAATCCGAAAA 57.353 36.364 0.00 0.00 0.00 2.29
64 65 4.610945 ACTGAAACTTGCAATCCGAAAAG 58.389 39.130 0.00 0.00 0.00 2.27
65 66 4.338118 ACTGAAACTTGCAATCCGAAAAGA 59.662 37.500 0.00 0.00 0.00 2.52
66 67 5.163561 ACTGAAACTTGCAATCCGAAAAGAA 60.164 36.000 0.00 0.00 0.00 2.52
67 68 5.280945 TGAAACTTGCAATCCGAAAAGAAG 58.719 37.500 0.00 0.00 0.00 2.85
68 69 4.918810 AACTTGCAATCCGAAAAGAAGT 57.081 36.364 0.00 0.00 0.00 3.01
69 70 4.918810 ACTTGCAATCCGAAAAGAAGTT 57.081 36.364 0.00 0.00 0.00 2.66
70 71 4.610945 ACTTGCAATCCGAAAAGAAGTTG 58.389 39.130 0.00 0.00 0.00 3.16
71 72 4.097892 ACTTGCAATCCGAAAAGAAGTTGT 59.902 37.500 0.00 0.00 0.00 3.32
72 73 4.223320 TGCAATCCGAAAAGAAGTTGTC 57.777 40.909 0.00 0.00 0.00 3.18
73 74 3.226347 GCAATCCGAAAAGAAGTTGTCG 58.774 45.455 0.00 0.00 0.00 4.35
74 75 3.303791 GCAATCCGAAAAGAAGTTGTCGT 60.304 43.478 0.00 0.00 0.00 4.34
75 76 4.455124 CAATCCGAAAAGAAGTTGTCGTC 58.545 43.478 0.00 0.00 0.00 4.20
76 77 3.447918 TCCGAAAAGAAGTTGTCGTCT 57.552 42.857 0.00 0.00 34.13 4.18
77 78 3.788937 TCCGAAAAGAAGTTGTCGTCTT 58.211 40.909 0.00 0.00 42.36 3.01
79 80 4.269363 TCCGAAAAGAAGTTGTCGTCTTTC 59.731 41.667 8.87 0.00 46.03 2.62
80 81 4.033587 CCGAAAAGAAGTTGTCGTCTTTCA 59.966 41.667 8.87 0.00 46.03 2.69
81 82 5.446741 CCGAAAAGAAGTTGTCGTCTTTCAA 60.447 40.000 8.87 0.00 46.03 2.69
82 83 5.448162 CGAAAAGAAGTTGTCGTCTTTCAAC 59.552 40.000 8.87 0.00 46.03 3.18
103 104 5.786401 ACTAAAGTTGTCATCATCGCTTC 57.214 39.130 0.00 0.00 0.00 3.86
104 105 5.237815 ACTAAAGTTGTCATCATCGCTTCA 58.762 37.500 0.00 0.00 0.00 3.02
105 106 4.410492 AAAGTTGTCATCATCGCTTCAC 57.590 40.909 0.00 0.00 0.00 3.18
106 107 3.325293 AGTTGTCATCATCGCTTCACT 57.675 42.857 0.00 0.00 0.00 3.41
107 108 4.456280 AGTTGTCATCATCGCTTCACTA 57.544 40.909 0.00 0.00 0.00 2.74
108 109 4.820897 AGTTGTCATCATCGCTTCACTAA 58.179 39.130 0.00 0.00 0.00 2.24
109 110 5.237815 AGTTGTCATCATCGCTTCACTAAA 58.762 37.500 0.00 0.00 0.00 1.85
110 111 5.877012 AGTTGTCATCATCGCTTCACTAAAT 59.123 36.000 0.00 0.00 0.00 1.40
111 112 5.973651 TGTCATCATCGCTTCACTAAATC 57.026 39.130 0.00 0.00 0.00 2.17
112 113 5.664457 TGTCATCATCGCTTCACTAAATCT 58.336 37.500 0.00 0.00 0.00 2.40
113 114 5.521372 TGTCATCATCGCTTCACTAAATCTG 59.479 40.000 0.00 0.00 0.00 2.90
114 115 4.509230 TCATCATCGCTTCACTAAATCTGC 59.491 41.667 0.00 0.00 0.00 4.26
115 116 3.198068 TCATCGCTTCACTAAATCTGCC 58.802 45.455 0.00 0.00 0.00 4.85
116 117 2.760634 TCGCTTCACTAAATCTGCCA 57.239 45.000 0.00 0.00 0.00 4.92
117 118 3.266510 TCGCTTCACTAAATCTGCCAT 57.733 42.857 0.00 0.00 0.00 4.40
118 119 4.400529 TCGCTTCACTAAATCTGCCATA 57.599 40.909 0.00 0.00 0.00 2.74
119 120 4.765273 TCGCTTCACTAAATCTGCCATAA 58.235 39.130 0.00 0.00 0.00 1.90
120 121 5.182487 TCGCTTCACTAAATCTGCCATAAA 58.818 37.500 0.00 0.00 0.00 1.40
121 122 5.645929 TCGCTTCACTAAATCTGCCATAAAA 59.354 36.000 0.00 0.00 0.00 1.52
122 123 6.150307 TCGCTTCACTAAATCTGCCATAAAAA 59.850 34.615 0.00 0.00 0.00 1.94
123 124 6.974622 CGCTTCACTAAATCTGCCATAAAAAT 59.025 34.615 0.00 0.00 0.00 1.82
124 125 7.043854 CGCTTCACTAAATCTGCCATAAAAATG 60.044 37.037 0.00 0.00 0.00 2.32
125 126 7.761249 GCTTCACTAAATCTGCCATAAAAATGT 59.239 33.333 0.00 0.00 0.00 2.71
126 127 9.643693 CTTCACTAAATCTGCCATAAAAATGTT 57.356 29.630 0.00 0.00 0.00 2.71
127 128 9.995003 TTCACTAAATCTGCCATAAAAATGTTT 57.005 25.926 0.00 0.00 0.00 2.83
128 129 9.995003 TCACTAAATCTGCCATAAAAATGTTTT 57.005 25.926 0.00 0.00 0.00 2.43
130 131 9.995003 ACTAAATCTGCCATAAAAATGTTTTGA 57.005 25.926 0.00 0.00 0.00 2.69
135 136 7.583230 TCTGCCATAAAAATGTTTTGAATTGC 58.417 30.769 0.00 0.00 0.00 3.56
136 137 6.675987 TGCCATAAAAATGTTTTGAATTGCC 58.324 32.000 0.00 0.00 0.00 4.52
137 138 6.263842 TGCCATAAAAATGTTTTGAATTGCCA 59.736 30.769 0.00 0.00 0.00 4.92
138 139 7.039923 TGCCATAAAAATGTTTTGAATTGCCAT 60.040 29.630 0.00 0.00 0.00 4.40
139 140 7.273815 GCCATAAAAATGTTTTGAATTGCCATG 59.726 33.333 0.00 0.00 0.00 3.66
140 141 8.298140 CCATAAAAATGTTTTGAATTGCCATGT 58.702 29.630 0.00 0.00 0.00 3.21
141 142 9.119329 CATAAAAATGTTTTGAATTGCCATGTG 57.881 29.630 0.00 0.00 0.00 3.21
142 143 6.696441 AAAATGTTTTGAATTGCCATGTGT 57.304 29.167 0.00 0.00 0.00 3.72
143 144 6.696441 AAATGTTTTGAATTGCCATGTGTT 57.304 29.167 0.00 0.00 0.00 3.32
144 145 6.696441 AATGTTTTGAATTGCCATGTGTTT 57.304 29.167 0.00 0.00 0.00 2.83
145 146 7.798596 AATGTTTTGAATTGCCATGTGTTTA 57.201 28.000 0.00 0.00 0.00 2.01
146 147 7.982761 ATGTTTTGAATTGCCATGTGTTTAT 57.017 28.000 0.00 0.00 0.00 1.40
147 148 7.187244 TGTTTTGAATTGCCATGTGTTTATG 57.813 32.000 0.00 0.00 0.00 1.90
148 149 5.859521 TTTGAATTGCCATGTGTTTATGC 57.140 34.783 0.00 0.00 0.00 3.14
149 150 3.859443 TGAATTGCCATGTGTTTATGCC 58.141 40.909 0.00 0.00 0.00 4.40
150 151 3.260128 TGAATTGCCATGTGTTTATGCCA 59.740 39.130 0.00 0.00 0.00 4.92
151 152 4.081031 TGAATTGCCATGTGTTTATGCCAT 60.081 37.500 0.00 0.00 0.00 4.40
152 153 3.523606 TTGCCATGTGTTTATGCCATC 57.476 42.857 0.00 0.00 0.00 3.51
153 154 1.755959 TGCCATGTGTTTATGCCATCC 59.244 47.619 0.00 0.00 0.00 3.51
154 155 1.755959 GCCATGTGTTTATGCCATCCA 59.244 47.619 0.00 0.00 0.00 3.41
155 156 2.366266 GCCATGTGTTTATGCCATCCAT 59.634 45.455 0.00 0.00 37.97 3.41
156 157 3.800949 GCCATGTGTTTATGCCATCCATG 60.801 47.826 0.00 0.00 35.34 3.66
157 158 3.385433 CCATGTGTTTATGCCATCCATGT 59.615 43.478 0.00 0.00 35.34 3.21
158 159 4.364860 CATGTGTTTATGCCATCCATGTG 58.635 43.478 0.00 0.00 35.34 3.21
159 160 3.694926 TGTGTTTATGCCATCCATGTGA 58.305 40.909 0.00 0.00 35.34 3.58
160 161 4.279982 TGTGTTTATGCCATCCATGTGAT 58.720 39.130 0.00 0.00 35.34 3.06
161 162 5.444176 TGTGTTTATGCCATCCATGTGATA 58.556 37.500 0.00 0.00 35.34 2.15
162 163 6.069994 TGTGTTTATGCCATCCATGTGATAT 58.930 36.000 0.00 0.00 35.34 1.63
163 164 6.550481 TGTGTTTATGCCATCCATGTGATATT 59.450 34.615 0.00 0.00 35.34 1.28
164 165 7.069702 TGTGTTTATGCCATCCATGTGATATTT 59.930 33.333 0.00 0.00 35.34 1.40
165 166 8.575589 GTGTTTATGCCATCCATGTGATATTTA 58.424 33.333 0.00 0.00 35.34 1.40
166 167 9.311676 TGTTTATGCCATCCATGTGATATTTAT 57.688 29.630 0.00 0.00 35.34 1.40
167 168 9.793252 GTTTATGCCATCCATGTGATATTTATC 57.207 33.333 0.00 0.00 35.34 1.75
168 169 9.531158 TTTATGCCATCCATGTGATATTTATCA 57.469 29.630 0.00 0.00 36.60 2.15
169 170 7.640597 ATGCCATCCATGTGATATTTATCAG 57.359 36.000 0.52 0.00 42.84 2.90
170 171 5.947566 TGCCATCCATGTGATATTTATCAGG 59.052 40.000 0.52 0.33 42.84 3.86
171 172 5.359009 GCCATCCATGTGATATTTATCAGGG 59.641 44.000 0.52 4.16 42.84 4.45
172 173 6.487828 CCATCCATGTGATATTTATCAGGGT 58.512 40.000 0.52 0.00 42.84 4.34
173 174 6.600822 CCATCCATGTGATATTTATCAGGGTC 59.399 42.308 0.52 0.00 42.84 4.46
174 175 7.400439 CATCCATGTGATATTTATCAGGGTCT 58.600 38.462 0.52 0.00 42.84 3.85
175 176 8.542926 CATCCATGTGATATTTATCAGGGTCTA 58.457 37.037 0.52 0.00 42.84 2.59
176 177 8.504811 TCCATGTGATATTTATCAGGGTCTAA 57.495 34.615 0.52 0.00 42.84 2.10
177 178 8.944138 TCCATGTGATATTTATCAGGGTCTAAA 58.056 33.333 0.52 0.00 42.84 1.85
178 179 9.573166 CCATGTGATATTTATCAGGGTCTAAAA 57.427 33.333 0.52 0.00 42.84 1.52
246 247 6.409704 ACCAATCCAATGGATATCGATGTAG 58.590 40.000 16.10 1.03 42.27 2.74
247 248 6.013379 ACCAATCCAATGGATATCGATGTAGT 60.013 38.462 16.10 1.62 42.27 2.73
248 249 7.180229 ACCAATCCAATGGATATCGATGTAGTA 59.820 37.037 16.10 0.00 42.27 1.82
262 263 8.858003 ATCGATGTAGTATAAACAACTGACAG 57.142 34.615 0.00 0.00 0.00 3.51
297 298 0.173708 ACGAAAGCTCCGAGCCTTAG 59.826 55.000 16.99 12.82 43.77 2.18
375 377 1.051556 GTCAGTCCCCTCTCCCATCC 61.052 65.000 0.00 0.00 0.00 3.51
378 381 2.964039 TCCCCTCTCCCATCCCCA 60.964 66.667 0.00 0.00 0.00 4.96
628 650 0.983378 CCCTCCCGACCTTCATCCTT 60.983 60.000 0.00 0.00 0.00 3.36
631 653 1.834263 CTCCCGACCTTCATCCTTCTT 59.166 52.381 0.00 0.00 0.00 2.52
636 658 2.545731 GACCTTCATCCTTCTTCTCGC 58.454 52.381 0.00 0.00 0.00 5.03
638 660 1.474143 CCTTCATCCTTCTTCTCGCCC 60.474 57.143 0.00 0.00 0.00 6.13
1193 1226 1.431036 GCTCCTTCTTTCATGGCGC 59.569 57.895 0.00 0.00 0.00 6.53
1209 1242 1.333115 GCGCGGTTGTTGATTAAACC 58.667 50.000 8.83 0.00 42.07 3.27
1277 1317 2.355197 TGACTTGTGTTGTGTCAGTGG 58.645 47.619 0.00 0.00 36.03 4.00
1278 1318 2.290008 TGACTTGTGTTGTGTCAGTGGT 60.290 45.455 0.00 0.00 36.03 4.16
1393 1433 4.837972 AGGAATTTGAGTGCTAGAACCTC 58.162 43.478 0.00 0.00 0.00 3.85
1394 1434 4.534103 AGGAATTTGAGTGCTAGAACCTCT 59.466 41.667 0.00 0.00 0.00 3.69
1396 1436 5.123027 GGAATTTGAGTGCTAGAACCTCTTG 59.877 44.000 0.00 0.00 0.00 3.02
1397 1437 4.689612 TTTGAGTGCTAGAACCTCTTGT 57.310 40.909 0.00 0.00 0.00 3.16
1398 1438 3.667497 TGAGTGCTAGAACCTCTTGTG 57.333 47.619 0.00 0.00 0.00 3.33
1399 1439 2.289072 TGAGTGCTAGAACCTCTTGTGC 60.289 50.000 0.00 0.00 0.00 4.57
1405 1449 4.202315 TGCTAGAACCTCTTGTGCTTTGTA 60.202 41.667 0.00 0.00 33.62 2.41
1412 1456 3.743396 CCTCTTGTGCTTTGTAGTGAGTC 59.257 47.826 0.00 0.00 0.00 3.36
1471 1515 1.152881 ATGGCCCTTTCGCTGGATC 60.153 57.895 0.00 0.00 0.00 3.36
1472 1516 1.925285 ATGGCCCTTTCGCTGGATCA 61.925 55.000 0.00 0.00 0.00 2.92
1473 1517 1.152881 GGCCCTTTCGCTGGATCAT 60.153 57.895 0.00 0.00 0.00 2.45
1507 1551 5.324409 TGTTTCAGTTCTGGGCATATTTCT 58.676 37.500 0.00 0.00 0.00 2.52
1510 1554 5.441718 TCAGTTCTGGGCATATTTCTTCT 57.558 39.130 0.00 0.00 0.00 2.85
1515 1559 5.902613 TCTGGGCATATTTCTTCTGTTTG 57.097 39.130 0.00 0.00 0.00 2.93
1554 1599 1.503818 CTTTGCGGTTACGTGTGGCT 61.504 55.000 0.00 0.00 43.45 4.75
1555 1600 1.500512 TTTGCGGTTACGTGTGGCTC 61.501 55.000 0.00 0.00 43.45 4.70
1556 1601 2.356553 GCGGTTACGTGTGGCTCA 60.357 61.111 0.00 0.00 43.45 4.26
1557 1602 2.664436 GCGGTTACGTGTGGCTCAC 61.664 63.158 9.57 9.57 43.45 3.51
1568 1613 2.880890 GTGTGGCTCACAATTCTGAGTT 59.119 45.455 14.37 0.00 46.28 3.01
1570 1615 3.565482 TGTGGCTCACAATTCTGAGTTTC 59.435 43.478 11.72 4.04 41.69 2.78
1574 1619 5.360714 TGGCTCACAATTCTGAGTTTCTTTT 59.639 36.000 11.72 0.00 40.03 2.27
1581 1626 3.963476 TCTGAGTTTCTTTTTGGGGGA 57.037 42.857 0.00 0.00 0.00 4.81
1587 1637 4.411013 AGTTTCTTTTTGGGGGAGATGAG 58.589 43.478 0.00 0.00 0.00 2.90
1595 1645 2.358258 TGGGGGAGATGAGGACTTTTT 58.642 47.619 0.00 0.00 0.00 1.94
1628 1678 2.609825 CACACTGTGTGCTCTGACC 58.390 57.895 26.02 0.00 41.89 4.02
1639 1689 3.771479 TGTGCTCTGACCTCACTGAATAT 59.229 43.478 0.00 0.00 0.00 1.28
1642 1692 6.070824 TGTGCTCTGACCTCACTGAATATTAA 60.071 38.462 0.00 0.00 0.00 1.40
1644 1694 7.497249 GTGCTCTGACCTCACTGAATATTAAAT 59.503 37.037 0.00 0.00 0.00 1.40
1666 1716 7.775397 AATTTGATGTGCAATAGCCAATAAC 57.225 32.000 0.00 0.00 41.13 1.89
1691 1741 1.274728 AGAGCACTCTTGTACTGCTGG 59.725 52.381 10.93 0.00 36.31 4.85
1731 1781 4.613437 AGAATTGGCCATCTTTGTATGGT 58.387 39.130 6.09 0.00 46.93 3.55
1739 1789 5.376625 GCCATCTTTGTATGGTTATGGAGA 58.623 41.667 0.00 0.00 46.93 3.71
1752 1802 2.988010 ATGGAGAGTATGCAAAGCGA 57.012 45.000 0.00 0.00 30.55 4.93
1798 1848 0.326264 AGGTTGCTTCTGGGCTAGTG 59.674 55.000 0.00 0.00 0.00 2.74
1806 1856 1.486211 TCTGGGCTAGTGCTAAGGAC 58.514 55.000 0.00 0.00 39.59 3.85
1925 1975 6.942532 TGGCATTGGAATTCAGTATCTTAC 57.057 37.500 7.93 0.00 0.00 2.34
1926 1976 6.422333 TGGCATTGGAATTCAGTATCTTACA 58.578 36.000 7.93 0.00 0.00 2.41
1928 1978 7.013559 TGGCATTGGAATTCAGTATCTTACATG 59.986 37.037 7.93 0.00 0.00 3.21
1929 1979 7.013655 GGCATTGGAATTCAGTATCTTACATGT 59.986 37.037 7.93 2.69 0.00 3.21
2012 2062 4.942483 GCCTCTTCCTAGTTTTAGTTTCCC 59.058 45.833 0.00 0.00 0.00 3.97
2034 2084 1.548719 AGTACTACAATGGCACGCAGA 59.451 47.619 0.00 0.00 0.00 4.26
2036 2086 0.608130 ACTACAATGGCACGCAGAGA 59.392 50.000 0.00 0.00 0.00 3.10
2038 2088 1.662629 CTACAATGGCACGCAGAGAAG 59.337 52.381 0.00 0.00 0.00 2.85
2040 2090 0.445436 CAATGGCACGCAGAGAAGTC 59.555 55.000 0.00 0.00 0.00 3.01
2041 2091 0.035317 AATGGCACGCAGAGAAGTCA 59.965 50.000 0.00 0.00 0.00 3.41
2042 2092 0.390866 ATGGCACGCAGAGAAGTCAG 60.391 55.000 0.00 0.00 0.00 3.51
2062 2113 9.435688 AAGTCAGTTGCATTAAAATATTTTCCC 57.564 29.630 16.56 5.21 0.00 3.97
2113 2164 5.106555 CGAAACACTAGAAGATGCACCAATT 60.107 40.000 0.00 0.00 0.00 2.32
2147 2200 3.436700 ACAAACTGGCAAGTGTAAAGC 57.563 42.857 0.00 0.00 36.51 3.51
2163 2216 0.188342 AAGCCTGGATGTGGTTTGGT 59.812 50.000 0.00 0.00 0.00 3.67
2165 2218 0.318120 GCCTGGATGTGGTTTGGTTG 59.682 55.000 0.00 0.00 0.00 3.77
2166 2219 0.318120 CCTGGATGTGGTTTGGTTGC 59.682 55.000 0.00 0.00 0.00 4.17
2167 2220 1.331214 CTGGATGTGGTTTGGTTGCT 58.669 50.000 0.00 0.00 0.00 3.91
2212 2270 6.619446 GCACTCACTTGTGTTCATATGACTTC 60.619 42.308 4.48 0.07 39.89 3.01
2578 2725 4.576879 ACTCTATGACTATGCATGCCATG 58.423 43.478 16.68 0.00 35.34 3.66
2582 2729 7.124750 ACTCTATGACTATGCATGCCATGTATA 59.875 37.037 16.68 13.74 36.90 1.47
2787 2938 8.927411 AGTACTAAAGTTTGTAGGAGTTGGTAA 58.073 33.333 0.00 0.00 0.00 2.85
3049 3200 1.274167 CGGGTGCCGGCTATATTAAGA 59.726 52.381 29.70 0.00 44.15 2.10
3076 3260 5.917447 CCACATGACATAGTGATTCTAGACG 59.083 44.000 15.37 0.00 37.97 4.18
3098 3282 3.781079 CGGTATACGTCCCAAGTGTTA 57.219 47.619 0.00 0.00 37.93 2.41
3119 3303 6.042093 TGTTAAACCATTTAATCCTGCCAACA 59.958 34.615 0.00 0.00 37.44 3.33
3141 3325 3.067180 ACGTGGAATCCATCATGAATTGC 59.933 43.478 4.81 1.06 35.28 3.56
3148 3332 1.202486 CCATCATGAATTGCACCTGCC 60.202 52.381 0.00 0.00 41.18 4.85
3518 3715 5.947228 TGCCATCTTGTTTCTTAGTGAAG 57.053 39.130 0.00 0.00 35.89 3.02
3544 3741 8.459911 AATGATGCATAATGAACAAGATGAGA 57.540 30.769 0.00 0.00 0.00 3.27
3558 3755 6.516718 ACAAGATGAGATTACCATCCTTACG 58.483 40.000 0.00 0.00 40.85 3.18
3563 3760 4.051922 GAGATTACCATCCTTACGCACAG 58.948 47.826 0.00 0.00 0.00 3.66
3786 3983 0.389426 GCAAGCCAAAGCACTCATGG 60.389 55.000 0.00 0.00 43.56 3.66
3790 3987 0.811281 GCCAAAGCACTCATGGTACC 59.189 55.000 4.43 4.43 39.53 3.34
3979 4176 0.602905 ACTTTGCGAACGGCTTAGCT 60.603 50.000 3.59 0.00 44.05 3.32
4157 4362 0.951558 GAAAGAAGAAACCGGCTGCA 59.048 50.000 0.00 0.00 0.00 4.41
4178 4383 1.965930 GATGCCTGTTGTCACCGCA 60.966 57.895 0.00 0.00 0.00 5.69
4211 4416 1.473550 TCAATTTAACCCCCACCCCT 58.526 50.000 0.00 0.00 0.00 4.79
4390 4596 2.752354 CTGTTGTCAAGTGTTTGGTGGA 59.248 45.455 0.00 0.00 34.97 4.02
4468 4674 1.614996 TACAGTGCACCAACCCAATG 58.385 50.000 14.63 4.99 33.66 2.82
4661 4887 7.125507 ACAAAGATGGCCATATATTTTGAACCA 59.874 33.333 30.86 2.01 0.00 3.67
4830 5068 1.541672 GGAGAGGGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.045223 GGATTGCAAGTTTCAGTTTTTCTTATT 57.955 29.630 4.94 0.00 0.00 1.40
33 34 7.382218 CGGATTGCAAGTTTCAGTTTTTCTTAT 59.618 33.333 4.94 0.00 0.00 1.73
34 35 6.695278 CGGATTGCAAGTTTCAGTTTTTCTTA 59.305 34.615 4.94 0.00 0.00 2.10
35 36 5.519927 CGGATTGCAAGTTTCAGTTTTTCTT 59.480 36.000 4.94 0.00 0.00 2.52
36 37 5.043248 CGGATTGCAAGTTTCAGTTTTTCT 58.957 37.500 4.94 0.00 0.00 2.52
37 38 5.040635 TCGGATTGCAAGTTTCAGTTTTTC 58.959 37.500 4.94 0.00 0.00 2.29
38 39 5.004922 TCGGATTGCAAGTTTCAGTTTTT 57.995 34.783 4.94 0.00 0.00 1.94
39 40 4.647424 TCGGATTGCAAGTTTCAGTTTT 57.353 36.364 4.94 0.00 0.00 2.43
40 41 4.647424 TTCGGATTGCAAGTTTCAGTTT 57.353 36.364 4.94 0.00 0.00 2.66
41 42 4.647424 TTTCGGATTGCAAGTTTCAGTT 57.353 36.364 4.94 0.00 0.00 3.16
42 43 4.338118 TCTTTTCGGATTGCAAGTTTCAGT 59.662 37.500 4.94 0.00 0.00 3.41
43 44 4.858935 TCTTTTCGGATTGCAAGTTTCAG 58.141 39.130 4.94 0.00 0.00 3.02
44 45 4.909696 TCTTTTCGGATTGCAAGTTTCA 57.090 36.364 4.94 0.00 0.00 2.69
45 46 5.281727 ACTTCTTTTCGGATTGCAAGTTTC 58.718 37.500 4.94 0.00 0.00 2.78
46 47 5.262588 ACTTCTTTTCGGATTGCAAGTTT 57.737 34.783 4.94 0.00 0.00 2.66
47 48 4.918810 ACTTCTTTTCGGATTGCAAGTT 57.081 36.364 4.94 0.00 0.00 2.66
48 49 4.097892 ACAACTTCTTTTCGGATTGCAAGT 59.902 37.500 4.94 0.00 0.00 3.16
49 50 4.610945 ACAACTTCTTTTCGGATTGCAAG 58.389 39.130 4.94 0.00 0.00 4.01
50 51 4.606961 GACAACTTCTTTTCGGATTGCAA 58.393 39.130 0.00 0.00 0.00 4.08
51 52 3.303725 CGACAACTTCTTTTCGGATTGCA 60.304 43.478 0.00 0.00 0.00 4.08
52 53 3.226347 CGACAACTTCTTTTCGGATTGC 58.774 45.455 0.00 0.00 0.00 3.56
53 54 4.211374 AGACGACAACTTCTTTTCGGATTG 59.789 41.667 0.00 0.00 35.77 2.67
54 55 4.377897 AGACGACAACTTCTTTTCGGATT 58.622 39.130 0.00 0.00 35.77 3.01
55 56 3.991367 AGACGACAACTTCTTTTCGGAT 58.009 40.909 0.00 0.00 35.77 4.18
56 57 3.447918 AGACGACAACTTCTTTTCGGA 57.552 42.857 0.00 0.00 35.77 4.55
57 58 4.033587 TGAAAGACGACAACTTCTTTTCGG 59.966 41.667 0.00 0.00 42.07 4.30
58 59 5.138800 TGAAAGACGACAACTTCTTTTCG 57.861 39.130 0.00 0.00 42.07 3.46
59 60 6.776271 GTTGAAAGACGACAACTTCTTTTC 57.224 37.500 0.00 0.00 42.07 2.29
80 81 5.700832 TGAAGCGATGATGACAACTTTAGTT 59.299 36.000 0.00 0.00 39.12 2.24
81 82 5.120830 GTGAAGCGATGATGACAACTTTAGT 59.879 40.000 0.00 0.00 0.00 2.24
82 83 5.349817 AGTGAAGCGATGATGACAACTTTAG 59.650 40.000 0.00 0.00 0.00 1.85
83 84 5.237815 AGTGAAGCGATGATGACAACTTTA 58.762 37.500 0.00 0.00 0.00 1.85
84 85 4.067896 AGTGAAGCGATGATGACAACTTT 58.932 39.130 0.00 0.00 0.00 2.66
85 86 3.668447 AGTGAAGCGATGATGACAACTT 58.332 40.909 0.00 0.00 0.00 2.66
86 87 3.325293 AGTGAAGCGATGATGACAACT 57.675 42.857 0.00 0.00 0.00 3.16
87 88 5.530519 TTTAGTGAAGCGATGATGACAAC 57.469 39.130 0.00 0.00 0.00 3.32
88 89 6.036408 CAGATTTAGTGAAGCGATGATGACAA 59.964 38.462 0.00 0.00 0.00 3.18
89 90 5.521372 CAGATTTAGTGAAGCGATGATGACA 59.479 40.000 0.00 0.00 0.00 3.58
90 91 5.557893 GCAGATTTAGTGAAGCGATGATGAC 60.558 44.000 0.00 0.00 0.00 3.06
91 92 4.509230 GCAGATTTAGTGAAGCGATGATGA 59.491 41.667 0.00 0.00 0.00 2.92
92 93 4.319333 GGCAGATTTAGTGAAGCGATGATG 60.319 45.833 0.00 0.00 0.00 3.07
93 94 3.812053 GGCAGATTTAGTGAAGCGATGAT 59.188 43.478 0.00 0.00 0.00 2.45
94 95 3.198068 GGCAGATTTAGTGAAGCGATGA 58.802 45.455 0.00 0.00 0.00 2.92
95 96 2.938451 TGGCAGATTTAGTGAAGCGATG 59.062 45.455 0.00 0.00 0.00 3.84
96 97 3.266510 TGGCAGATTTAGTGAAGCGAT 57.733 42.857 0.00 0.00 0.00 4.58
97 98 2.760634 TGGCAGATTTAGTGAAGCGA 57.239 45.000 0.00 0.00 0.00 4.93
98 99 5.484173 TTTATGGCAGATTTAGTGAAGCG 57.516 39.130 0.00 0.00 0.00 4.68
99 100 7.761249 ACATTTTTATGGCAGATTTAGTGAAGC 59.239 33.333 0.00 0.00 0.00 3.86
100 101 9.643693 AACATTTTTATGGCAGATTTAGTGAAG 57.356 29.630 0.00 0.00 0.00 3.02
101 102 9.995003 AAACATTTTTATGGCAGATTTAGTGAA 57.005 25.926 0.00 0.00 0.00 3.18
102 103 9.995003 AAAACATTTTTATGGCAGATTTAGTGA 57.005 25.926 0.00 0.00 0.00 3.41
104 105 9.995003 TCAAAACATTTTTATGGCAGATTTAGT 57.005 25.926 0.00 0.00 0.00 2.24
109 110 8.238631 GCAATTCAAAACATTTTTATGGCAGAT 58.761 29.630 0.00 0.00 0.00 2.90
110 111 7.308469 GGCAATTCAAAACATTTTTATGGCAGA 60.308 33.333 0.00 0.00 0.00 4.26
111 112 6.802834 GGCAATTCAAAACATTTTTATGGCAG 59.197 34.615 0.00 0.00 0.00 4.85
112 113 6.263842 TGGCAATTCAAAACATTTTTATGGCA 59.736 30.769 0.00 0.00 0.00 4.92
113 114 6.675987 TGGCAATTCAAAACATTTTTATGGC 58.324 32.000 0.00 0.00 0.00 4.40
114 115 8.298140 ACATGGCAATTCAAAACATTTTTATGG 58.702 29.630 0.00 0.00 0.00 2.74
115 116 9.119329 CACATGGCAATTCAAAACATTTTTATG 57.881 29.630 0.00 0.00 0.00 1.90
116 117 8.848182 ACACATGGCAATTCAAAACATTTTTAT 58.152 25.926 0.00 0.00 0.00 1.40
117 118 8.218338 ACACATGGCAATTCAAAACATTTTTA 57.782 26.923 0.00 0.00 0.00 1.52
118 119 7.098074 ACACATGGCAATTCAAAACATTTTT 57.902 28.000 0.00 0.00 0.00 1.94
119 120 6.696441 ACACATGGCAATTCAAAACATTTT 57.304 29.167 0.00 0.00 0.00 1.82
120 121 6.696441 AACACATGGCAATTCAAAACATTT 57.304 29.167 0.00 0.00 0.00 2.32
121 122 6.696441 AAACACATGGCAATTCAAAACATT 57.304 29.167 0.00 0.00 0.00 2.71
122 123 7.573469 GCATAAACACATGGCAATTCAAAACAT 60.573 33.333 0.00 0.00 0.00 2.71
123 124 6.293298 GCATAAACACATGGCAATTCAAAACA 60.293 34.615 0.00 0.00 0.00 2.83
124 125 6.079120 GCATAAACACATGGCAATTCAAAAC 58.921 36.000 0.00 0.00 0.00 2.43
125 126 6.238610 GCATAAACACATGGCAATTCAAAA 57.761 33.333 0.00 0.00 0.00 2.44
126 127 5.859521 GCATAAACACATGGCAATTCAAA 57.140 34.783 0.00 0.00 0.00 2.69
135 136 3.385433 ACATGGATGGCATAAACACATGG 59.615 43.478 21.57 11.26 38.72 3.66
136 137 4.098196 TCACATGGATGGCATAAACACATG 59.902 41.667 18.59 18.59 39.88 3.21
137 138 4.279982 TCACATGGATGGCATAAACACAT 58.720 39.130 0.00 0.00 0.00 3.21
138 139 3.694926 TCACATGGATGGCATAAACACA 58.305 40.909 0.00 0.00 0.00 3.72
139 140 4.924305 ATCACATGGATGGCATAAACAC 57.076 40.909 0.00 0.00 34.06 3.32
140 141 7.600231 AAATATCACATGGATGGCATAAACA 57.400 32.000 0.00 0.14 36.72 2.83
141 142 9.793252 GATAAATATCACATGGATGGCATAAAC 57.207 33.333 0.00 0.00 36.72 2.01
142 143 9.531158 TGATAAATATCACATGGATGGCATAAA 57.469 29.630 0.00 0.00 37.76 1.40
143 144 9.181061 CTGATAAATATCACATGGATGGCATAA 57.819 33.333 0.00 0.00 37.76 1.90
144 145 7.776500 CCTGATAAATATCACATGGATGGCATA 59.224 37.037 0.00 0.00 37.76 3.14
145 146 6.605995 CCTGATAAATATCACATGGATGGCAT 59.394 38.462 0.00 0.00 37.76 4.40
146 147 5.947566 CCTGATAAATATCACATGGATGGCA 59.052 40.000 0.00 0.00 37.76 4.92
147 148 5.359009 CCCTGATAAATATCACATGGATGGC 59.641 44.000 0.00 0.00 37.76 4.40
148 149 6.487828 ACCCTGATAAATATCACATGGATGG 58.512 40.000 0.00 6.04 37.76 3.51
149 150 7.400439 AGACCCTGATAAATATCACATGGATG 58.600 38.462 0.00 0.00 37.76 3.51
150 151 7.579940 AGACCCTGATAAATATCACATGGAT 57.420 36.000 0.00 0.00 37.76 3.41
151 152 8.504811 TTAGACCCTGATAAATATCACATGGA 57.495 34.615 0.00 0.00 37.76 3.41
152 153 9.573166 TTTTAGACCCTGATAAATATCACATGG 57.427 33.333 0.00 3.93 37.76 3.66
208 209 8.859090 CCATTGGATTGGTAAGCTAATCAATAA 58.141 33.333 8.76 2.61 42.24 1.40
209 210 8.224025 TCCATTGGATTGGTAAGCTAATCAATA 58.776 33.333 0.00 0.00 42.24 1.90
219 220 6.881065 ACATCGATATCCATTGGATTGGTAAG 59.119 38.462 22.87 12.01 39.79 2.34
220 221 6.778821 ACATCGATATCCATTGGATTGGTAA 58.221 36.000 22.87 5.55 39.79 2.85
246 247 8.161699 TCCTTTTTCCTGTCAGTTGTTTATAC 57.838 34.615 0.00 0.00 0.00 1.47
247 248 7.996644 ACTCCTTTTTCCTGTCAGTTGTTTATA 59.003 33.333 0.00 0.00 0.00 0.98
248 249 6.833933 ACTCCTTTTTCCTGTCAGTTGTTTAT 59.166 34.615 0.00 0.00 0.00 1.40
262 263 0.601841 TCGTGCCGACTCCTTTTTCC 60.602 55.000 0.00 0.00 0.00 3.13
297 298 1.193874 CTACTCGGCGGTGTGTTTTTC 59.806 52.381 7.21 0.00 0.00 2.29
375 377 0.325933 TGAGGCTGATGTGACTTGGG 59.674 55.000 0.00 0.00 0.00 4.12
378 381 0.681733 ACGTGAGGCTGATGTGACTT 59.318 50.000 0.00 0.00 0.00 3.01
621 630 1.338136 GGGGGCGAGAAGAAGGATGA 61.338 60.000 0.00 0.00 0.00 2.92
985 1007 2.123077 CATCTCTCCCCCGCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
988 1010 2.835431 CGTCATCTCTCCCCCGCT 60.835 66.667 0.00 0.00 0.00 5.52
1176 1207 1.709147 CCGCGCCATGAAAGAAGGAG 61.709 60.000 0.00 0.00 0.00 3.69
1179 1212 0.454957 CAACCGCGCCATGAAAGAAG 60.455 55.000 0.00 0.00 0.00 2.85
1209 1242 2.568696 ATCAGTCCGTCAGTCAATCG 57.431 50.000 0.00 0.00 0.00 3.34
1224 1260 2.031314 AGCGCACGAATCAATCAATCAG 59.969 45.455 11.47 0.00 0.00 2.90
1277 1317 0.036306 AAATCCGGTCTCCCACACAC 59.964 55.000 0.00 0.00 0.00 3.82
1278 1318 0.768622 AAAATCCGGTCTCCCACACA 59.231 50.000 0.00 0.00 0.00 3.72
1393 1433 5.773575 TCTAGACTCACTACAAAGCACAAG 58.226 41.667 0.00 0.00 0.00 3.16
1394 1434 5.784578 TCTAGACTCACTACAAAGCACAA 57.215 39.130 0.00 0.00 0.00 3.33
1396 1436 6.159988 ACAATCTAGACTCACTACAAAGCAC 58.840 40.000 0.00 0.00 0.00 4.40
1397 1437 6.346477 ACAATCTAGACTCACTACAAAGCA 57.654 37.500 0.00 0.00 0.00 3.91
1398 1438 7.093992 AGAACAATCTAGACTCACTACAAAGC 58.906 38.462 0.00 0.00 32.88 3.51
1399 1439 8.920665 CAAGAACAATCTAGACTCACTACAAAG 58.079 37.037 0.00 0.00 33.77 2.77
1435 1479 1.841302 ATCTCGCTTGCCCCTGAACA 61.841 55.000 0.00 0.00 0.00 3.18
1494 1538 4.427312 GCAAACAGAAGAAATATGCCCAG 58.573 43.478 0.00 0.00 0.00 4.45
1507 1551 3.719924 CAGAATTTGCAGGCAAACAGAA 58.280 40.909 20.45 0.00 46.80 3.02
1532 1576 1.064357 CCACACGTAACCGCAAAGTTT 59.936 47.619 0.00 0.00 37.70 2.66
1554 1599 6.406849 CCCCAAAAAGAAACTCAGAATTGTGA 60.407 38.462 5.05 5.05 0.00 3.58
1555 1600 5.754890 CCCCAAAAAGAAACTCAGAATTGTG 59.245 40.000 0.00 0.00 0.00 3.33
1556 1601 5.163311 CCCCCAAAAAGAAACTCAGAATTGT 60.163 40.000 0.00 0.00 0.00 2.71
1557 1602 5.070313 TCCCCCAAAAAGAAACTCAGAATTG 59.930 40.000 0.00 0.00 0.00 2.32
1568 1613 2.993146 TCCTCATCTCCCCCAAAAAGAA 59.007 45.455 0.00 0.00 0.00 2.52
1570 1615 2.310052 AGTCCTCATCTCCCCCAAAAAG 59.690 50.000 0.00 0.00 0.00 2.27
1574 1619 2.059756 AAAGTCCTCATCTCCCCCAA 57.940 50.000 0.00 0.00 0.00 4.12
1595 1645 5.116180 CACAGTGTGACAAGGAACTTAGAA 58.884 41.667 18.83 0.00 41.06 2.10
1596 1646 4.161565 ACACAGTGTGACAAGGAACTTAGA 59.838 41.667 29.58 0.00 41.50 2.10
1598 1648 4.481368 ACACAGTGTGACAAGGAACTTA 57.519 40.909 29.58 0.00 41.50 2.24
1614 1664 0.678395 AGTGAGGTCAGAGCACACAG 59.322 55.000 25.81 0.00 35.08 3.66
1628 1678 9.791820 TGCACATCAAATTTAATATTCAGTGAG 57.208 29.630 0.00 0.00 0.00 3.51
1639 1689 9.881649 TTATTGGCTATTGCACATCAAATTTAA 57.118 25.926 0.66 0.00 41.91 1.52
1642 1692 7.558604 AGTTATTGGCTATTGCACATCAAATT 58.441 30.769 0.66 0.00 41.91 1.82
1644 1694 6.152492 TGAGTTATTGGCTATTGCACATCAAA 59.848 34.615 0.66 0.00 41.91 2.69
1691 1741 7.626452 GCCAATTCTAATCAGAGTTGTTGTACC 60.626 40.741 0.87 0.00 43.47 3.34
1731 1781 4.400529 TCGCTTTGCATACTCTCCATAA 57.599 40.909 0.00 0.00 0.00 1.90
1739 1789 2.359900 CCCTCTTTCGCTTTGCATACT 58.640 47.619 0.00 0.00 0.00 2.12
1752 1802 1.353091 AAGCGAAGTCTCCCCTCTTT 58.647 50.000 0.00 0.00 0.00 2.52
1806 1856 6.808008 TGAAGTAAAGCTGAAAAGGATGAG 57.192 37.500 0.00 0.00 0.00 2.90
1925 1975 6.739112 TCTGACCAGAACGATAGATAACATG 58.261 40.000 0.00 0.00 33.91 3.21
1926 1976 6.961360 TCTGACCAGAACGATAGATAACAT 57.039 37.500 0.00 0.00 33.91 2.71
2012 2062 3.116300 CTGCGTGCCATTGTAGTACTAG 58.884 50.000 1.87 0.00 0.00 2.57
2036 2086 9.435688 GGGAAAATATTTTAATGCAACTGACTT 57.564 29.630 13.34 0.00 0.00 3.01
2038 2088 7.757624 TCGGGAAAATATTTTAATGCAACTGAC 59.242 33.333 13.34 0.00 0.00 3.51
2040 2090 7.973388 TCTCGGGAAAATATTTTAATGCAACTG 59.027 33.333 13.34 4.36 0.00 3.16
2041 2091 8.062065 TCTCGGGAAAATATTTTAATGCAACT 57.938 30.769 13.34 0.00 0.00 3.16
2042 2092 8.696410 TTCTCGGGAAAATATTTTAATGCAAC 57.304 30.769 13.34 0.00 0.00 4.17
2062 2113 3.778618 TGAGTTGAGCAGATGATTCTCG 58.221 45.455 0.00 0.00 0.00 4.04
2113 2164 8.948631 TTGCCAGTTTGTAAATAAATGTTTGA 57.051 26.923 0.00 0.00 0.00 2.69
2147 2200 0.318120 GCAACCAAACCACATCCAGG 59.682 55.000 0.00 0.00 0.00 4.45
2149 2202 1.786937 AAGCAACCAAACCACATCCA 58.213 45.000 0.00 0.00 0.00 3.41
2176 2234 3.062763 CAAGTGAGTGCTTCTACACCAG 58.937 50.000 0.00 0.00 41.67 4.00
2212 2270 9.950680 CTGCAATGTAAACCCACTATAAAATAG 57.049 33.333 0.00 0.00 0.00 1.73
2553 2700 4.101430 TGGCATGCATAGTCATAGAGTTGA 59.899 41.667 21.36 0.00 0.00 3.18
2578 2725 8.375465 GTGAAGTACCGTGTGTGTAAAATATAC 58.625 37.037 0.00 0.00 0.00 1.47
2582 2729 5.117584 TGTGAAGTACCGTGTGTGTAAAAT 58.882 37.500 0.00 0.00 0.00 1.82
2666 2816 7.822658 ACACGGCTGTTAATTACATACAAAAT 58.177 30.769 0.00 0.00 35.85 1.82
2680 2830 0.398696 ATGACCCAACACGGCTGTTA 59.601 50.000 0.00 0.00 38.66 2.41
2812 2963 6.434302 TCATGTGATGAATTAATCCCCTGTT 58.566 36.000 0.00 0.00 36.11 3.16
2864 3015 9.147364 CGTATCAGATTCGTATTTTGATTGTTG 57.853 33.333 1.40 0.00 31.49 3.33
2967 3118 3.681594 CGCCCAAGCAGTTAGGATAAGAA 60.682 47.826 0.00 0.00 39.83 2.52
3049 3200 5.901413 AGAATCACTATGTCATGTGGGAT 57.099 39.130 12.51 7.30 35.15 3.85
3098 3282 4.560513 CGTGTTGGCAGGATTAAATGGTTT 60.561 41.667 0.00 0.00 32.67 3.27
3119 3303 3.067180 GCAATTCATGATGGATTCCACGT 59.933 43.478 7.76 1.05 35.80 4.49
3134 3318 1.114119 TTGCTGGCAGGTGCAATTCA 61.114 50.000 17.64 0.00 43.17 2.57
3518 3715 8.565416 TCTCATCTTGTTCATTATGCATCATTC 58.435 33.333 0.19 0.00 0.00 2.67
3544 3741 2.093181 TGCTGTGCGTAAGGATGGTAAT 60.093 45.455 0.00 0.00 42.42 1.89
3979 4176 4.508128 GTGGGATTCGGCTCGCGA 62.508 66.667 9.26 9.26 0.00 5.87
4157 4362 0.036952 CGGTGACAACAGGCATCTCT 60.037 55.000 0.00 0.00 0.00 3.10
4178 4383 7.832685 GGGGTTAAATTGAATACTCCTACTTGT 59.167 37.037 0.00 0.00 0.00 3.16
4359 4565 1.860950 CTTGACAACAGACCGACAGTG 59.139 52.381 0.00 0.00 0.00 3.66
4830 5068 6.403878 TGTCTTATAAGTTCTGTAACCCTGC 58.596 40.000 12.19 0.00 36.15 4.85
4913 5169 3.567585 TGTTCGAAACAAGATCAATGCCA 59.432 39.130 0.00 0.00 38.72 4.92



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

AutoCloner maintained by Alex Coulton.