Multiple sequence alignment - TraesCS5B01G396200

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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 TraesCS5B01G396200 chr5B 100.000 6167 0 0 1 6167 573215965 573222131 0.000000e+00 11389
1 TraesCS5B01G396200 chr5D 94.408 5955 186 57 290 6167 466220500 466226384 0.000000e+00 9016
2 TraesCS5B01G396200 chr5A 93.734 6064 215 78 150 6167 586594436 586600380 0.000000e+00 8940
3 TraesCS5B01G396200 chr2D 93.023 86 6 0 1609 1694 199139691 199139776 6.490000e-25 126


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 TraesCS5B01G396200 chr5B 573215965 573222131 6166 False 11389 11389 100.000 1 6167 1 chr5B.!!$F1 6166
1 TraesCS5B01G396200 chr5D 466220500 466226384 5884 False 9016 9016 94.408 290 6167 1 chr5D.!!$F1 5877
2 TraesCS5B01G396200 chr5A 586594436 586600380 5944 False 8940 8940 93.734 150 6167 1 chr5A.!!$F1 6017

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
33 34 0.165944 CATTTTCTGACACCGACGCC 59.834 55.0 0.0 0.0 0.0 5.68 F
103 104 0.389166 CCGCCTCTGCCTAATCGATC 60.389 60.0 0.0 0.0 0.0 3.69 F
1510 1559 0.107165 AAAGCCCTTCTACGCCATCC 60.107 55.0 0.0 0.0 0.0 3.51 F
2607 2656 1.133809 AGTGGGGTGGAGCTAAGCAA 61.134 55.0 0.0 0.0 0.0 3.91 F
3333 3387 0.109532 TTTGACGGGGCACAAGATGA 59.890 50.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1540 0.107165 GGATGGCGTAGAAGGGCTTT 60.107 55.0 0.00 0.00 0.00 3.51 R
1734 1783 0.249784 CCTCACCATGCTCATCCTCG 60.250 60.0 0.00 0.00 0.00 4.63 R
2777 2826 0.888736 TGACCCTGCATTGTTGTCGG 60.889 55.0 0.00 0.00 0.00 4.79 R
4322 4392 1.243902 TCAAGGTTGAATTCCACCGC 58.756 50.0 19.93 1.22 33.55 5.68 R
5222 5302 0.176680 CCTGGTTCACATCTCGAGGG 59.823 60.0 13.56 8.03 0.00 4.30 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
23 24 6.147864 CAAAGAAGGGTCAACATTTTCTGA 57.852 37.500 0.00 0.00 0.00 3.27
24 25 5.774498 AAGAAGGGTCAACATTTTCTGAC 57.226 39.130 0.00 0.00 41.05 3.51
25 26 4.792068 AGAAGGGTCAACATTTTCTGACA 58.208 39.130 4.74 0.00 43.11 3.58
26 27 4.580580 AGAAGGGTCAACATTTTCTGACAC 59.419 41.667 4.74 0.65 44.75 3.67
27 28 3.222603 AGGGTCAACATTTTCTGACACC 58.777 45.455 0.97 2.20 45.39 4.16
28 29 2.031157 GGGTCAACATTTTCTGACACCG 60.031 50.000 4.74 0.00 43.11 4.94
29 30 2.875933 GGTCAACATTTTCTGACACCGA 59.124 45.455 4.74 0.00 43.11 4.69
30 31 3.303791 GGTCAACATTTTCTGACACCGAC 60.304 47.826 4.74 0.00 43.11 4.79
31 32 2.542178 TCAACATTTTCTGACACCGACG 59.458 45.455 0.00 0.00 0.00 5.12
32 33 0.865769 ACATTTTCTGACACCGACGC 59.134 50.000 0.00 0.00 0.00 5.19
33 34 0.165944 CATTTTCTGACACCGACGCC 59.834 55.000 0.00 0.00 0.00 5.68
34 35 0.953960 ATTTTCTGACACCGACGCCC 60.954 55.000 0.00 0.00 0.00 6.13
35 36 3.851845 TTTCTGACACCGACGCCCG 62.852 63.158 0.00 0.00 38.18 6.13
50 51 2.996734 CCGCTTGCCACCCCATTT 60.997 61.111 0.00 0.00 0.00 2.32
51 52 2.573340 CGCTTGCCACCCCATTTC 59.427 61.111 0.00 0.00 0.00 2.17
52 53 1.978617 CGCTTGCCACCCCATTTCT 60.979 57.895 0.00 0.00 0.00 2.52
53 54 1.593265 GCTTGCCACCCCATTTCTG 59.407 57.895 0.00 0.00 0.00 3.02
54 55 1.593265 CTTGCCACCCCATTTCTGC 59.407 57.895 0.00 0.00 0.00 4.26
55 56 2.216750 CTTGCCACCCCATTTCTGCG 62.217 60.000 0.00 0.00 0.00 5.18
56 57 4.133796 GCCACCCCATTTCTGCGC 62.134 66.667 0.00 0.00 0.00 6.09
57 58 3.814268 CCACCCCATTTCTGCGCG 61.814 66.667 0.00 0.00 0.00 6.86
58 59 2.745884 CACCCCATTTCTGCGCGA 60.746 61.111 12.10 0.00 0.00 5.87
59 60 2.033448 ACCCCATTTCTGCGCGAA 59.967 55.556 12.10 0.00 0.00 4.70
60 61 1.602323 ACCCCATTTCTGCGCGAAA 60.602 52.632 22.76 22.76 45.08 3.46
61 62 1.154035 CCCCATTTCTGCGCGAAAC 60.154 57.895 22.91 0.00 43.90 2.78
62 63 1.511887 CCCATTTCTGCGCGAAACG 60.512 57.895 22.91 17.38 43.90 3.60
72 73 3.126087 GCGAAACGAAAAGCACGC 58.874 55.556 0.00 0.00 39.33 5.34
73 74 1.652930 GCGAAACGAAAAGCACGCA 60.653 52.632 0.00 0.00 44.29 5.24
74 75 1.851984 GCGAAACGAAAAGCACGCAC 61.852 55.000 0.00 0.00 44.29 5.34
75 76 1.576527 CGAAACGAAAAGCACGCACG 61.577 55.000 0.00 0.00 0.00 5.34
76 77 1.851984 GAAACGAAAAGCACGCACGC 61.852 55.000 0.00 0.00 0.00 5.34
77 78 2.585170 AAACGAAAAGCACGCACGCA 62.585 50.000 0.00 0.00 0.00 5.24
78 79 3.085010 CGAAAAGCACGCACGCAC 61.085 61.111 0.00 0.00 0.00 5.34
79 80 3.085010 GAAAAGCACGCACGCACG 61.085 61.111 0.00 0.00 39.50 5.34
97 98 4.451150 CACGCCGCCTCTGCCTAA 62.451 66.667 0.00 0.00 0.00 2.69
98 99 3.470888 ACGCCGCCTCTGCCTAAT 61.471 61.111 0.00 0.00 0.00 1.73
99 100 2.663188 CGCCGCCTCTGCCTAATC 60.663 66.667 0.00 0.00 0.00 1.75
100 101 2.663188 GCCGCCTCTGCCTAATCG 60.663 66.667 0.00 0.00 0.00 3.34
101 102 3.129300 CCGCCTCTGCCTAATCGA 58.871 61.111 0.00 0.00 0.00 3.59
102 103 1.668294 CCGCCTCTGCCTAATCGAT 59.332 57.895 0.00 0.00 0.00 3.59
103 104 0.389166 CCGCCTCTGCCTAATCGATC 60.389 60.000 0.00 0.00 0.00 3.69
104 105 0.389166 CGCCTCTGCCTAATCGATCC 60.389 60.000 0.00 0.00 0.00 3.36
105 106 0.681733 GCCTCTGCCTAATCGATCCA 59.318 55.000 0.00 0.00 0.00 3.41
106 107 1.337635 GCCTCTGCCTAATCGATCCAG 60.338 57.143 0.00 3.82 0.00 3.86
107 108 1.274728 CCTCTGCCTAATCGATCCAGG 59.725 57.143 17.71 17.71 0.00 4.45
108 109 2.242926 CTCTGCCTAATCGATCCAGGA 58.757 52.381 23.61 11.63 0.00 3.86
109 110 1.964223 TCTGCCTAATCGATCCAGGAC 59.036 52.381 23.61 16.56 0.00 3.85
110 111 0.673985 TGCCTAATCGATCCAGGACG 59.326 55.000 23.61 0.00 0.00 4.79
111 112 0.959553 GCCTAATCGATCCAGGACGA 59.040 55.000 23.61 14.15 42.49 4.20
112 113 1.336056 GCCTAATCGATCCAGGACGAC 60.336 57.143 23.61 7.56 41.17 4.34
113 114 1.069159 CCTAATCGATCCAGGACGACG 60.069 57.143 17.30 10.24 41.17 5.12
114 115 0.949397 TAATCGATCCAGGACGACGG 59.051 55.000 14.10 0.00 41.17 4.79
115 116 0.750546 AATCGATCCAGGACGACGGA 60.751 55.000 14.10 0.00 41.17 4.69
116 117 1.445716 ATCGATCCAGGACGACGGAC 61.446 60.000 14.10 0.00 41.17 4.79
129 130 3.363788 CGACGGACGGTTTCTTTATTG 57.636 47.619 0.00 0.00 38.46 1.90
130 131 2.733026 CGACGGACGGTTTCTTTATTGT 59.267 45.455 0.00 0.00 38.46 2.71
131 132 3.919804 CGACGGACGGTTTCTTTATTGTA 59.080 43.478 0.00 0.00 38.46 2.41
132 133 4.030977 CGACGGACGGTTTCTTTATTGTAG 59.969 45.833 0.00 0.00 38.46 2.74
133 134 5.138125 ACGGACGGTTTCTTTATTGTAGA 57.862 39.130 0.00 0.00 0.00 2.59
134 135 5.727434 ACGGACGGTTTCTTTATTGTAGAT 58.273 37.500 0.00 0.00 0.00 1.98
135 136 5.579511 ACGGACGGTTTCTTTATTGTAGATG 59.420 40.000 0.00 0.00 0.00 2.90
136 137 5.006358 CGGACGGTTTCTTTATTGTAGATGG 59.994 44.000 0.00 0.00 0.00 3.51
137 138 5.220796 GGACGGTTTCTTTATTGTAGATGGC 60.221 44.000 0.00 0.00 0.00 4.40
138 139 5.250200 ACGGTTTCTTTATTGTAGATGGCA 58.750 37.500 0.00 0.00 0.00 4.92
139 140 5.354234 ACGGTTTCTTTATTGTAGATGGCAG 59.646 40.000 0.00 0.00 0.00 4.85
140 141 5.354234 CGGTTTCTTTATTGTAGATGGCAGT 59.646 40.000 0.00 0.00 0.00 4.40
141 142 6.128007 CGGTTTCTTTATTGTAGATGGCAGTT 60.128 38.462 0.00 0.00 0.00 3.16
142 143 7.574967 CGGTTTCTTTATTGTAGATGGCAGTTT 60.575 37.037 0.00 0.00 0.00 2.66
143 144 8.736244 GGTTTCTTTATTGTAGATGGCAGTTTA 58.264 33.333 0.00 0.00 0.00 2.01
144 145 9.774742 GTTTCTTTATTGTAGATGGCAGTTTAG 57.225 33.333 0.00 0.00 0.00 1.85
145 146 8.506168 TTCTTTATTGTAGATGGCAGTTTAGG 57.494 34.615 0.00 0.00 0.00 2.69
146 147 7.054124 TCTTTATTGTAGATGGCAGTTTAGGG 58.946 38.462 0.00 0.00 0.00 3.53
147 148 4.862641 ATTGTAGATGGCAGTTTAGGGT 57.137 40.909 0.00 0.00 0.00 4.34
148 149 3.627395 TGTAGATGGCAGTTTAGGGTG 57.373 47.619 0.00 0.00 0.00 4.61
149 150 3.178046 TGTAGATGGCAGTTTAGGGTGA 58.822 45.455 0.00 0.00 0.00 4.02
150 151 3.780294 TGTAGATGGCAGTTTAGGGTGAT 59.220 43.478 0.00 0.00 0.00 3.06
151 152 3.567478 AGATGGCAGTTTAGGGTGATC 57.433 47.619 0.00 0.00 0.00 2.92
159 160 2.239907 AGTTTAGGGTGATCTTGGCTCC 59.760 50.000 0.00 0.00 0.00 4.70
169 170 2.951269 CTTGGCTCCAAGCATCACA 58.049 52.632 14.94 0.00 45.38 3.58
192 193 1.412343 CCACACAGTTTTGGGAAAGGG 59.588 52.381 0.00 0.00 0.00 3.95
193 194 1.412343 CACACAGTTTTGGGAAAGGGG 59.588 52.381 0.00 0.00 0.00 4.79
194 195 1.047801 CACAGTTTTGGGAAAGGGGG 58.952 55.000 0.00 0.00 0.00 5.40
195 196 0.938192 ACAGTTTTGGGAAAGGGGGA 59.062 50.000 0.00 0.00 0.00 4.81
218 219 4.201679 CACCCCGCGCACGATCTA 62.202 66.667 8.75 0.00 43.93 1.98
225 226 4.271816 CGCACGATCTAGGCCGCT 62.272 66.667 0.00 0.00 0.00 5.52
261 262 2.721167 CCGAAGATGGACGCCCTGA 61.721 63.158 0.00 0.00 0.00 3.86
262 263 1.519455 CGAAGATGGACGCCCTGAC 60.519 63.158 0.00 0.00 0.00 3.51
287 288 4.540735 GGTACGCCCCATCCACCG 62.541 72.222 0.00 0.00 0.00 4.94
288 289 4.540735 GTACGCCCCATCCACCGG 62.541 72.222 0.00 0.00 0.00 5.28
334 335 4.966787 GCCCCGACAAGCCAACCA 62.967 66.667 0.00 0.00 0.00 3.67
335 336 2.035626 CCCCGACAAGCCAACCAT 59.964 61.111 0.00 0.00 0.00 3.55
337 338 1.595093 CCCCGACAAGCCAACCATTC 61.595 60.000 0.00 0.00 0.00 2.67
338 339 0.609131 CCCGACAAGCCAACCATTCT 60.609 55.000 0.00 0.00 0.00 2.40
340 341 1.200020 CCGACAAGCCAACCATTCTTC 59.800 52.381 0.00 0.00 0.00 2.87
341 342 1.879380 CGACAAGCCAACCATTCTTCA 59.121 47.619 0.00 0.00 0.00 3.02
342 343 2.293122 CGACAAGCCAACCATTCTTCAA 59.707 45.455 0.00 0.00 0.00 2.69
396 401 2.526120 GCCGAGCTCGTGCATTACC 61.526 63.158 31.47 11.36 42.74 2.85
399 404 1.519455 GAGCTCGTGCATTACCGCT 60.519 57.895 12.58 0.00 42.74 5.52
426 431 1.595993 CTCTTGCGGGGAAGACGAGA 61.596 60.000 0.00 0.00 0.00 4.04
427 432 1.446272 CTTGCGGGGAAGACGAGAC 60.446 63.158 0.00 0.00 0.00 3.36
428 433 3.277211 TTGCGGGGAAGACGAGACG 62.277 63.158 0.00 0.00 0.00 4.18
429 434 3.437795 GCGGGGAAGACGAGACGA 61.438 66.667 0.00 0.00 0.00 4.20
430 435 2.792599 CGGGGAAGACGAGACGAG 59.207 66.667 0.00 0.00 0.00 4.18
503 513 3.062500 CTCTCTTGGCTCGCTCGCT 62.063 63.158 0.00 0.00 0.00 4.93
557 568 3.487104 GAAAGCCGCCGCGTATTCG 62.487 63.158 12.58 2.69 41.18 3.34
626 654 2.568090 GAGCGGTCGGTCGGTTAA 59.432 61.111 6.81 0.00 41.12 2.01
652 680 0.801251 ATCGCTGTTGCTTGCTTCTC 59.199 50.000 0.00 0.00 36.97 2.87
675 703 2.747855 GTTTGGCGCAGGGAGGAG 60.748 66.667 10.83 0.00 0.00 3.69
676 704 4.033776 TTTGGCGCAGGGAGGAGG 62.034 66.667 10.83 0.00 0.00 4.30
749 783 1.617947 CCCCTCCTGTTCCCTTCTCG 61.618 65.000 0.00 0.00 0.00 4.04
773 807 3.925238 GCGTGTGCTTATCCGCGG 61.925 66.667 22.12 22.12 36.53 6.46
981 1024 2.764547 GAGCCTAGCTCGGGGGTT 60.765 66.667 6.39 0.00 45.85 4.11
1270 1319 4.479993 GCCTGCTCGCCATCCACT 62.480 66.667 0.00 0.00 0.00 4.00
1510 1559 0.107165 AAAGCCCTTCTACGCCATCC 60.107 55.000 0.00 0.00 0.00 3.51
1734 1783 2.423538 GGTGATGGCATACAAGTTCCAC 59.576 50.000 0.00 1.29 0.00 4.02
1824 1873 2.819595 CCGGCAACTGACATCCCG 60.820 66.667 0.00 0.00 38.71 5.14
2256 2305 2.571757 CGCACGCAGACCCTTCTA 59.428 61.111 0.00 0.00 0.00 2.10
2467 2516 2.480932 GGGCTAAGTACGGACAGCTTAC 60.481 54.545 9.73 0.00 34.41 2.34
2607 2656 1.133809 AGTGGGGTGGAGCTAAGCAA 61.134 55.000 0.00 0.00 0.00 3.91
2777 2826 2.877168 CCCTGCAAGATGAAGATGCTAC 59.123 50.000 0.00 0.00 40.66 3.58
2791 2840 1.155889 TGCTACCGACAACAATGCAG 58.844 50.000 0.00 0.00 0.00 4.41
2852 2901 3.356529 ACAGGGGCTACTTGAATTGAG 57.643 47.619 0.00 0.00 0.00 3.02
2868 2917 9.251792 CTTGAATTGAGAATTGTGACAAATGAA 57.748 29.630 0.62 0.00 0.00 2.57
2919 2968 4.800914 GCTCCTATATTGGCTGTCGACATT 60.801 45.833 20.40 4.65 0.00 2.71
3085 3134 6.294176 GCAAGGTTGTCACTATGTCTTGAATT 60.294 38.462 0.00 0.00 33.96 2.17
3091 3140 6.533730 TGTCACTATGTCTTGAATTTGGTCT 58.466 36.000 0.00 0.00 0.00 3.85
3092 3141 6.998074 TGTCACTATGTCTTGAATTTGGTCTT 59.002 34.615 0.00 0.00 0.00 3.01
3096 3145 9.219603 CACTATGTCTTGAATTTGGTCTTCTTA 57.780 33.333 0.00 0.00 0.00 2.10
3124 3173 5.297029 GCTTTCCAGCTTAGTTATAACCTGG 59.703 44.000 22.84 22.84 42.58 4.45
3125 3174 6.382919 TTTCCAGCTTAGTTATAACCTGGT 57.617 37.500 25.45 14.67 42.15 4.00
3126 3175 6.382919 TTCCAGCTTAGTTATAACCTGGTT 57.617 37.500 25.45 17.44 42.15 3.67
3163 3217 5.804979 ACGTTGTGTTTCATTTCTCCTTTTG 59.195 36.000 0.00 0.00 0.00 2.44
3185 3239 2.631160 TTTCAGGAACCGAAGAGCAA 57.369 45.000 0.00 0.00 0.00 3.91
3281 3335 4.142116 TGTTGTAGTCGTGACCTTTCAGAA 60.142 41.667 0.00 0.00 30.10 3.02
3302 3356 5.471797 AGAAAAAGTTGTTGGGGTTTGTTTG 59.528 36.000 0.00 0.00 0.00 2.93
3320 3374 4.219033 GTTTGGTAGCACAAGATTTGACG 58.781 43.478 0.00 0.00 0.00 4.35
3333 3387 0.109532 TTTGACGGGGCACAAGATGA 59.890 50.000 0.00 0.00 0.00 2.92
3335 3389 1.199615 TGACGGGGCACAAGATGATA 58.800 50.000 0.00 0.00 0.00 2.15
3359 3413 7.801893 AATGGATAAGTATACCCGGATACAA 57.198 36.000 0.73 0.00 35.16 2.41
3419 3473 8.644432 AGCTCATACCCCCTATATTTATGATT 57.356 34.615 0.00 0.00 30.68 2.57
3559 3613 3.067320 GGATGCAGGGTAAAAGATCAAGC 59.933 47.826 0.00 0.00 0.00 4.01
3713 3767 1.486211 CTGAGGGTAAGATCACCGGT 58.514 55.000 0.00 0.00 39.69 5.28
3881 3935 1.212441 ACCCGTAAGTTGTTGGAACCA 59.788 47.619 0.00 0.00 0.00 3.67
4060 4116 5.067273 TCACTAACCCCAGTAAATTGTGTG 58.933 41.667 0.00 0.00 0.00 3.82
4069 4125 4.282068 CAGTAAATTGTGTGTGTGCTGAC 58.718 43.478 0.00 0.00 0.00 3.51
4098 4154 9.757227 AGAACTGAAACTACTAATATCTCATGC 57.243 33.333 0.00 0.00 0.00 4.06
4157 4226 4.573607 AGCACACATGATATGCACTACTTG 59.426 41.667 18.20 0.00 41.97 3.16
4178 4247 3.826157 TGGACATGAAAACTTCCACCATC 59.174 43.478 0.00 0.00 33.02 3.51
4322 4392 3.170791 ACAGCTACATGGAGATGAACG 57.829 47.619 29.50 3.22 36.34 3.95
4387 4457 2.156917 CAAGGCATGTCTCTGAGCAAA 58.843 47.619 0.00 0.00 0.00 3.68
4438 4508 6.252599 TGGCCTGTAGAAGTATCATCAATT 57.747 37.500 3.32 0.00 0.00 2.32
4730 4800 7.436320 ACAGCATAAATATTTTTGGGATGGT 57.564 32.000 17.04 11.89 0.00 3.55
4745 4815 0.473755 ATGGTGACTGTGCAAGACCA 59.526 50.000 10.00 10.00 37.24 4.02
4796 4866 0.250901 AGTGGGCAGCTTGTAAGTGG 60.251 55.000 0.00 0.00 0.00 4.00
4797 4867 1.603455 TGGGCAGCTTGTAAGTGGC 60.603 57.895 0.00 10.19 34.40 5.01
4798 4868 1.603455 GGGCAGCTTGTAAGTGGCA 60.603 57.895 16.28 0.00 35.72 4.92
4799 4869 1.589716 GGGCAGCTTGTAAGTGGCAG 61.590 60.000 16.28 0.00 35.72 4.85
4800 4870 0.890996 GGCAGCTTGTAAGTGGCAGT 60.891 55.000 12.37 0.00 34.88 4.40
4801 4871 1.610624 GGCAGCTTGTAAGTGGCAGTA 60.611 52.381 0.00 0.00 34.88 2.74
4802 4872 1.734465 GCAGCTTGTAAGTGGCAGTAG 59.266 52.381 0.00 0.00 0.00 2.57
4803 4873 2.872038 GCAGCTTGTAAGTGGCAGTAGT 60.872 50.000 0.00 0.00 0.00 2.73
4804 4874 2.738846 CAGCTTGTAAGTGGCAGTAGTG 59.261 50.000 0.00 0.00 0.00 2.74
4822 4901 1.352622 TGACAGGAGGTTGCCCTTGT 61.353 55.000 0.00 0.00 42.86 3.16
4872 4951 4.773674 TGATGAGTTTTCTGGGATGCAATT 59.226 37.500 0.00 0.00 0.00 2.32
4920 4999 1.459450 GTTTGCTGGATAGGCCGAAA 58.541 50.000 0.00 0.00 40.66 3.46
4981 5060 2.669569 CTTGTCCACCCAGCACCG 60.670 66.667 0.00 0.00 0.00 4.94
5213 5292 4.184629 CAAGAGTAACTTCTGAATCCCGG 58.815 47.826 0.00 0.00 36.61 5.73
5259 5339 1.266867 GGGCCATTGATTGGGTTGCT 61.267 55.000 4.39 0.00 46.55 3.91
5260 5340 0.108041 GGCCATTGATTGGGTTGCTG 60.108 55.000 0.00 0.00 46.55 4.41
5261 5341 0.108041 GCCATTGATTGGGTTGCTGG 60.108 55.000 0.00 0.00 46.55 4.85
5321 5401 1.357137 TGTGTAGCTGGGAACATGGA 58.643 50.000 0.00 0.00 41.51 3.41
5414 5497 1.135373 CACGGCAACTCTACGAGTGAT 60.135 52.381 0.00 0.00 42.59 3.06
5472 5556 0.109532 TCAATTCTCGGGTGGTTGCA 59.890 50.000 0.00 0.00 0.00 4.08
5476 5560 1.243902 TTCTCGGGTGGTTGCAAATC 58.756 50.000 0.00 0.00 0.00 2.17
5506 5590 6.367149 CGTTCAGTCTGATTTGAGATTCTTGA 59.633 38.462 2.68 0.00 0.00 3.02
5546 5646 2.724977 TGCAGTGCAGAGTACACTAC 57.275 50.000 15.37 0.00 46.44 2.73
5547 5647 2.239400 TGCAGTGCAGAGTACACTACT 58.761 47.619 15.37 0.00 46.44 2.57
5548 5648 3.418047 TGCAGTGCAGAGTACACTACTA 58.582 45.455 15.37 0.00 46.44 1.82
5549 5649 4.017126 TGCAGTGCAGAGTACACTACTAT 58.983 43.478 15.37 0.00 46.44 2.12
5550 5650 4.462834 TGCAGTGCAGAGTACACTACTATT 59.537 41.667 15.37 0.00 46.44 1.73
5551 5651 5.047306 TGCAGTGCAGAGTACACTACTATTT 60.047 40.000 15.37 0.00 46.44 1.40
5552 5652 5.869888 GCAGTGCAGAGTACACTACTATTTT 59.130 40.000 11.09 0.00 46.44 1.82
5553 5653 7.033791 GCAGTGCAGAGTACACTACTATTTTA 58.966 38.462 11.09 0.00 46.44 1.52
5554 5654 7.707035 GCAGTGCAGAGTACACTACTATTTTAT 59.293 37.037 11.09 0.00 46.44 1.40
5555 5655 9.587772 CAGTGCAGAGTACACTACTATTTTATT 57.412 33.333 0.00 0.00 46.44 1.40
5571 5671 9.110502 ACTATTTTATTTAGGCTTGCAGAGTAC 57.889 33.333 0.00 0.00 0.00 2.73
5580 5680 3.192844 GGCTTGCAGAGTACACTACACTA 59.807 47.826 0.00 0.00 0.00 2.74
5581 5681 4.167268 GCTTGCAGAGTACACTACACTAC 58.833 47.826 0.00 0.00 0.00 2.73
5582 5682 4.321008 GCTTGCAGAGTACACTACACTACA 60.321 45.833 0.00 0.00 0.00 2.74
5583 5683 5.769367 CTTGCAGAGTACACTACACTACAA 58.231 41.667 0.00 0.00 33.57 2.41
5593 5693 8.082852 AGTACACTACACTACAATTGTGAAGAG 58.917 37.037 21.42 12.49 38.65 2.85
5594 5694 6.223852 ACACTACACTACAATTGTGAAGAGG 58.776 40.000 21.42 11.13 38.65 3.69
5599 5699 7.639113 ACACTACAATTGTGAAGAGGAAAAA 57.361 32.000 21.42 0.00 38.65 1.94
5622 5760 1.165270 CCGTTCTAAACAGGCCTTGG 58.835 55.000 0.00 0.00 0.00 3.61
5632 5770 1.539869 AGGCCTTGGAGCAGAGGAA 60.540 57.895 0.00 0.00 34.91 3.36
5829 5967 2.507484 CTCCACAAGATCAAAGGTGCA 58.493 47.619 0.00 0.00 0.00 4.57
5830 5968 2.486982 CTCCACAAGATCAAAGGTGCAG 59.513 50.000 0.00 0.00 0.00 4.41
5833 5971 3.128242 CCACAAGATCAAAGGTGCAGATC 59.872 47.826 5.05 5.05 38.70 2.75
5871 6009 3.689346 GATCGACTGTAAACCCTCGTAC 58.311 50.000 0.00 0.00 0.00 3.67
5913 6051 0.459063 ATCGGAGTTAACGCGGGTTC 60.459 55.000 22.08 8.53 37.58 3.62
6076 6217 1.076549 TCCACATGGTTTGGCTCCC 59.923 57.895 0.00 0.00 33.71 4.30
6077 6218 1.077265 CCACATGGTTTGGCTCCCT 59.923 57.895 0.00 0.00 0.00 4.20
6080 6221 0.779997 ACATGGTTTGGCTCCCTCTT 59.220 50.000 0.00 0.00 0.00 2.85
6083 6224 1.000771 GGTTTGGCTCCCTCTTCCC 60.001 63.158 0.00 0.00 0.00 3.97
6085 6226 1.465188 TTTGGCTCCCTCTTCCCCA 60.465 57.895 0.00 0.00 0.00 4.96
6099 6240 1.984570 CCCCACTCTCTCGCCTTCA 60.985 63.158 0.00 0.00 0.00 3.02
6137 6278 1.142748 CTGTCAGATCCTCACCGGC 59.857 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.656416 TGTCAGAAAATGTTGACCCTTCTTT 59.344 36.000 2.56 0.00 42.30 2.52
2 3 5.067805 GTGTCAGAAAATGTTGACCCTTCTT 59.932 40.000 2.56 0.00 42.30 2.52
3 4 4.580580 GTGTCAGAAAATGTTGACCCTTCT 59.419 41.667 2.56 0.00 42.30 2.85
4 5 4.261614 GGTGTCAGAAAATGTTGACCCTTC 60.262 45.833 2.56 0.00 42.30 3.46
5 6 3.636764 GGTGTCAGAAAATGTTGACCCTT 59.363 43.478 2.56 0.00 42.30 3.95
6 7 3.222603 GGTGTCAGAAAATGTTGACCCT 58.777 45.455 2.56 0.00 42.30 4.34
7 8 2.031157 CGGTGTCAGAAAATGTTGACCC 60.031 50.000 2.56 3.12 42.30 4.46
8 9 2.875933 TCGGTGTCAGAAAATGTTGACC 59.124 45.455 2.56 0.00 42.30 4.02
9 10 3.603857 CGTCGGTGTCAGAAAATGTTGAC 60.604 47.826 0.00 0.00 43.07 3.18
10 11 2.542178 CGTCGGTGTCAGAAAATGTTGA 59.458 45.455 0.00 0.00 0.00 3.18
11 12 2.903678 CGTCGGTGTCAGAAAATGTTG 58.096 47.619 0.00 0.00 0.00 3.33
12 13 1.263217 GCGTCGGTGTCAGAAAATGTT 59.737 47.619 0.00 0.00 0.00 2.71
13 14 0.865769 GCGTCGGTGTCAGAAAATGT 59.134 50.000 0.00 0.00 0.00 2.71
14 15 0.165944 GGCGTCGGTGTCAGAAAATG 59.834 55.000 0.00 0.00 0.00 2.32
15 16 0.953960 GGGCGTCGGTGTCAGAAAAT 60.954 55.000 0.00 0.00 0.00 1.82
16 17 1.595929 GGGCGTCGGTGTCAGAAAA 60.596 57.895 0.00 0.00 0.00 2.29
17 18 2.029964 GGGCGTCGGTGTCAGAAA 59.970 61.111 0.00 0.00 0.00 2.52
18 19 4.351938 CGGGCGTCGGTGTCAGAA 62.352 66.667 0.00 0.00 34.75 3.02
33 34 2.996734 AAATGGGGTGGCAAGCGG 60.997 61.111 0.00 0.00 0.00 5.52
34 35 1.978617 AGAAATGGGGTGGCAAGCG 60.979 57.895 0.00 0.00 0.00 4.68
35 36 1.593265 CAGAAATGGGGTGGCAAGC 59.407 57.895 0.00 0.00 0.00 4.01
36 37 1.593265 GCAGAAATGGGGTGGCAAG 59.407 57.895 0.00 0.00 0.00 4.01
37 38 2.274645 CGCAGAAATGGGGTGGCAA 61.275 57.895 0.00 0.00 0.00 4.52
38 39 2.676121 CGCAGAAATGGGGTGGCA 60.676 61.111 0.00 0.00 0.00 4.92
39 40 4.133796 GCGCAGAAATGGGGTGGC 62.134 66.667 0.30 0.00 0.00 5.01
40 41 3.814268 CGCGCAGAAATGGGGTGG 61.814 66.667 8.75 0.00 0.00 4.61
41 42 1.861542 TTTCGCGCAGAAATGGGGTG 61.862 55.000 18.75 0.00 43.35 4.61
42 43 1.602323 TTTCGCGCAGAAATGGGGT 60.602 52.632 18.75 0.00 43.35 4.95
43 44 3.273048 TTTCGCGCAGAAATGGGG 58.727 55.556 18.75 0.00 43.35 4.96
48 49 1.737249 CTTTTCGTTTCGCGCAGAAA 58.263 45.000 18.75 18.75 45.76 2.52
49 50 0.656205 GCTTTTCGTTTCGCGCAGAA 60.656 50.000 8.75 9.50 41.07 3.02
50 51 1.083015 GCTTTTCGTTTCGCGCAGA 60.083 52.632 8.75 2.49 41.07 4.26
51 52 1.368731 TGCTTTTCGTTTCGCGCAG 60.369 52.632 8.75 0.00 41.07 5.18
52 53 1.652930 GTGCTTTTCGTTTCGCGCA 60.653 52.632 8.75 0.00 41.07 6.09
53 54 2.684217 CGTGCTTTTCGTTTCGCGC 61.684 57.895 0.00 0.00 41.07 6.86
54 55 2.684217 GCGTGCTTTTCGTTTCGCG 61.684 57.895 0.00 0.00 43.01 5.87
55 56 1.652930 TGCGTGCTTTTCGTTTCGC 60.653 52.632 0.00 0.00 43.14 4.70
56 57 1.576527 CGTGCGTGCTTTTCGTTTCG 61.577 55.000 0.00 0.00 0.00 3.46
57 58 1.851984 GCGTGCGTGCTTTTCGTTTC 61.852 55.000 0.00 0.00 0.00 2.78
58 59 1.937362 GCGTGCGTGCTTTTCGTTT 60.937 52.632 0.00 0.00 0.00 3.60
59 60 2.351888 GCGTGCGTGCTTTTCGTT 60.352 55.556 0.00 0.00 0.00 3.85
60 61 3.568743 TGCGTGCGTGCTTTTCGT 61.569 55.556 1.52 0.00 35.36 3.85
61 62 3.085010 GTGCGTGCGTGCTTTTCG 61.085 61.111 1.52 0.00 35.36 3.46
62 63 3.085010 CGTGCGTGCGTGCTTTTC 61.085 61.111 1.52 0.00 35.36 2.29
80 81 3.740128 ATTAGGCAGAGGCGGCGTG 62.740 63.158 9.37 6.67 42.47 5.34
81 82 3.447025 GATTAGGCAGAGGCGGCGT 62.447 63.158 9.37 0.00 42.47 5.68
82 83 2.663188 GATTAGGCAGAGGCGGCG 60.663 66.667 0.51 0.51 42.47 6.46
83 84 2.441822 ATCGATTAGGCAGAGGCGGC 62.442 60.000 0.00 0.00 42.47 6.53
84 85 0.389166 GATCGATTAGGCAGAGGCGG 60.389 60.000 0.00 0.00 42.47 6.13
85 86 0.389166 GGATCGATTAGGCAGAGGCG 60.389 60.000 0.00 0.00 42.47 5.52
86 87 0.681733 TGGATCGATTAGGCAGAGGC 59.318 55.000 0.00 0.00 40.13 4.70
87 88 1.274728 CCTGGATCGATTAGGCAGAGG 59.725 57.143 14.39 2.03 0.00 3.69
88 89 2.029470 GTCCTGGATCGATTAGGCAGAG 60.029 54.545 19.47 2.59 0.00 3.35
89 90 1.964223 GTCCTGGATCGATTAGGCAGA 59.036 52.381 19.47 5.49 0.00 4.26
90 91 1.336332 CGTCCTGGATCGATTAGGCAG 60.336 57.143 19.47 13.59 0.00 4.85
91 92 0.673985 CGTCCTGGATCGATTAGGCA 59.326 55.000 19.47 9.74 0.00 4.75
92 93 0.959553 TCGTCCTGGATCGATTAGGC 59.040 55.000 19.47 14.77 0.00 3.93
93 94 1.069159 CGTCGTCCTGGATCGATTAGG 60.069 57.143 18.62 18.62 38.32 2.69
94 95 1.069159 CCGTCGTCCTGGATCGATTAG 60.069 57.143 19.16 14.58 38.32 1.73
95 96 0.949397 CCGTCGTCCTGGATCGATTA 59.051 55.000 19.16 0.00 38.32 1.75
96 97 0.750546 TCCGTCGTCCTGGATCGATT 60.751 55.000 19.16 0.00 38.32 3.34
97 98 1.153025 TCCGTCGTCCTGGATCGAT 60.153 57.895 19.16 0.00 38.32 3.59
98 99 2.110967 GTCCGTCGTCCTGGATCGA 61.111 63.158 14.47 14.47 36.48 3.59
99 100 2.408022 GTCCGTCGTCCTGGATCG 59.592 66.667 0.00 6.01 36.48 3.69
100 101 2.408022 CGTCCGTCGTCCTGGATC 59.592 66.667 0.00 0.00 36.48 3.36
101 102 3.138798 CCGTCCGTCGTCCTGGAT 61.139 66.667 0.00 0.00 36.48 3.41
102 103 4.648626 ACCGTCCGTCGTCCTGGA 62.649 66.667 0.00 0.00 37.94 3.86
103 104 3.216944 AAACCGTCCGTCGTCCTGG 62.217 63.158 0.00 0.00 37.94 4.45
104 105 1.731969 GAAACCGTCCGTCGTCCTG 60.732 63.158 0.00 0.00 37.94 3.86
105 106 1.458639 AAGAAACCGTCCGTCGTCCT 61.459 55.000 0.00 0.00 37.94 3.85
106 107 0.598419 AAAGAAACCGTCCGTCGTCC 60.598 55.000 0.00 0.00 37.94 4.79
107 108 2.050477 TAAAGAAACCGTCCGTCGTC 57.950 50.000 0.00 0.00 37.94 4.20
108 109 2.730550 ATAAAGAAACCGTCCGTCGT 57.269 45.000 0.00 0.00 37.94 4.34
109 110 2.733026 ACAATAAAGAAACCGTCCGTCG 59.267 45.455 0.00 0.00 39.52 5.12
110 111 5.163513 TCTACAATAAAGAAACCGTCCGTC 58.836 41.667 0.00 0.00 0.00 4.79
111 112 5.138125 TCTACAATAAAGAAACCGTCCGT 57.862 39.130 0.00 0.00 0.00 4.69
112 113 5.006358 CCATCTACAATAAAGAAACCGTCCG 59.994 44.000 0.00 0.00 0.00 4.79
113 114 5.220796 GCCATCTACAATAAAGAAACCGTCC 60.221 44.000 0.00 0.00 0.00 4.79
114 115 5.353123 TGCCATCTACAATAAAGAAACCGTC 59.647 40.000 0.00 0.00 0.00 4.79
115 116 5.250200 TGCCATCTACAATAAAGAAACCGT 58.750 37.500 0.00 0.00 0.00 4.83
116 117 5.354234 ACTGCCATCTACAATAAAGAAACCG 59.646 40.000 0.00 0.00 0.00 4.44
117 118 6.759497 ACTGCCATCTACAATAAAGAAACC 57.241 37.500 0.00 0.00 0.00 3.27
118 119 9.774742 CTAAACTGCCATCTACAATAAAGAAAC 57.225 33.333 0.00 0.00 0.00 2.78
119 120 8.956426 CCTAAACTGCCATCTACAATAAAGAAA 58.044 33.333 0.00 0.00 0.00 2.52
120 121 7.556275 CCCTAAACTGCCATCTACAATAAAGAA 59.444 37.037 0.00 0.00 0.00 2.52
121 122 7.054124 CCCTAAACTGCCATCTACAATAAAGA 58.946 38.462 0.00 0.00 0.00 2.52
122 123 6.828785 ACCCTAAACTGCCATCTACAATAAAG 59.171 38.462 0.00 0.00 0.00 1.85
123 124 6.601613 CACCCTAAACTGCCATCTACAATAAA 59.398 38.462 0.00 0.00 0.00 1.40
124 125 6.069905 TCACCCTAAACTGCCATCTACAATAA 60.070 38.462 0.00 0.00 0.00 1.40
125 126 5.427157 TCACCCTAAACTGCCATCTACAATA 59.573 40.000 0.00 0.00 0.00 1.90
126 127 4.227300 TCACCCTAAACTGCCATCTACAAT 59.773 41.667 0.00 0.00 0.00 2.71
127 128 3.585289 TCACCCTAAACTGCCATCTACAA 59.415 43.478 0.00 0.00 0.00 2.41
128 129 3.178046 TCACCCTAAACTGCCATCTACA 58.822 45.455 0.00 0.00 0.00 2.74
129 130 3.906720 TCACCCTAAACTGCCATCTAC 57.093 47.619 0.00 0.00 0.00 2.59
130 131 4.298626 AGATCACCCTAAACTGCCATCTA 58.701 43.478 0.00 0.00 0.00 1.98
131 132 3.118531 AGATCACCCTAAACTGCCATCT 58.881 45.455 0.00 0.00 0.00 2.90
132 133 3.567478 AGATCACCCTAAACTGCCATC 57.433 47.619 0.00 0.00 0.00 3.51
133 134 3.624777 CAAGATCACCCTAAACTGCCAT 58.375 45.455 0.00 0.00 0.00 4.40
134 135 2.290896 CCAAGATCACCCTAAACTGCCA 60.291 50.000 0.00 0.00 0.00 4.92
135 136 2.369394 CCAAGATCACCCTAAACTGCC 58.631 52.381 0.00 0.00 0.00 4.85
136 137 1.745653 GCCAAGATCACCCTAAACTGC 59.254 52.381 0.00 0.00 0.00 4.40
137 138 3.274288 GAGCCAAGATCACCCTAAACTG 58.726 50.000 0.00 0.00 0.00 3.16
138 139 2.239907 GGAGCCAAGATCACCCTAAACT 59.760 50.000 0.00 0.00 0.00 2.66
139 140 2.026262 TGGAGCCAAGATCACCCTAAAC 60.026 50.000 0.00 0.00 0.00 2.01
140 141 2.274542 TGGAGCCAAGATCACCCTAAA 58.725 47.619 0.00 0.00 0.00 1.85
141 142 1.965414 TGGAGCCAAGATCACCCTAA 58.035 50.000 0.00 0.00 0.00 2.69
142 143 1.965414 TTGGAGCCAAGATCACCCTA 58.035 50.000 0.00 0.00 0.00 3.53
143 144 2.791253 TTGGAGCCAAGATCACCCT 58.209 52.632 0.00 0.00 0.00 4.34
159 160 1.002142 CTGTGTGGTGTGTGATGCTTG 60.002 52.381 0.00 0.00 0.00 4.01
169 170 2.223803 TTCCCAAAACTGTGTGGTGT 57.776 45.000 9.27 0.00 32.60 4.16
201 202 4.201679 TAGATCGTGCGCGGGGTG 62.202 66.667 21.04 0.00 38.89 4.61
202 203 3.900892 CTAGATCGTGCGCGGGGT 61.901 66.667 21.04 6.32 38.89 4.95
210 211 2.050895 CGAGCGGCCTAGATCGTG 60.051 66.667 9.76 0.00 43.94 4.35
233 234 1.889105 CATCTTCGGCCGGTGGATG 60.889 63.158 27.83 27.53 0.00 3.51
245 246 1.519455 CGTCAGGGCGTCCATCTTC 60.519 63.158 9.71 0.00 34.83 2.87
269 270 4.540735 GGTGGATGGGGCGTACCG 62.541 72.222 0.00 0.00 41.60 4.02
279 280 1.595382 GATCTTCGGCCGGTGGATG 60.595 63.158 27.83 8.27 0.00 3.51
280 281 2.822399 GATCTTCGGCCGGTGGAT 59.178 61.111 27.83 23.95 0.00 3.41
283 284 4.812476 TGCGATCTTCGGCCGGTG 62.812 66.667 27.83 18.35 40.84 4.94
284 285 4.514577 CTGCGATCTTCGGCCGGT 62.515 66.667 27.83 9.29 40.84 5.28
286 287 4.880537 AGCTGCGATCTTCGGCCG 62.881 66.667 22.12 22.12 40.84 6.13
287 288 3.267860 CAGCTGCGATCTTCGGCC 61.268 66.667 0.00 0.00 40.84 6.13
288 289 3.267860 CCAGCTGCGATCTTCGGC 61.268 66.667 8.66 7.36 40.84 5.54
289 290 3.267860 GCCAGCTGCGATCTTCGG 61.268 66.667 8.66 0.00 40.84 4.30
292 293 4.845580 CCGGCCAGCTGCGATCTT 62.846 66.667 8.66 0.00 42.61 2.40
335 336 9.177608 ACTTGATCGGAATAATTGATTGAAGAA 57.822 29.630 0.00 0.00 0.00 2.52
337 338 7.859377 CCACTTGATCGGAATAATTGATTGAAG 59.141 37.037 0.00 0.00 0.00 3.02
338 339 7.681782 GCCACTTGATCGGAATAATTGATTGAA 60.682 37.037 0.00 0.00 0.00 2.69
340 341 5.916883 GCCACTTGATCGGAATAATTGATTG 59.083 40.000 0.00 0.00 0.00 2.67
341 342 5.277974 CGCCACTTGATCGGAATAATTGATT 60.278 40.000 0.00 0.00 0.00 2.57
342 343 4.214119 CGCCACTTGATCGGAATAATTGAT 59.786 41.667 0.00 0.00 0.00 2.57
515 525 2.683933 GGAGGAAGTGGCGGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
610 638 0.738412 CAATTAACCGACCGACCGCT 60.738 55.000 0.00 0.00 0.00 5.52
615 643 0.741574 ATGCGCAATTAACCGACCGA 60.742 50.000 17.11 0.00 0.00 4.69
652 680 3.124921 CCTGCGCCAAACGGTAGG 61.125 66.667 4.18 0.00 43.93 3.18
675 703 2.658321 TATCCCCACGCTCCTCCTCC 62.658 65.000 0.00 0.00 0.00 4.30
676 704 0.759436 TTATCCCCACGCTCCTCCTC 60.759 60.000 0.00 0.00 0.00 3.71
677 705 1.049289 GTTATCCCCACGCTCCTCCT 61.049 60.000 0.00 0.00 0.00 3.69
678 706 1.335132 TGTTATCCCCACGCTCCTCC 61.335 60.000 0.00 0.00 0.00 4.30
679 707 0.759346 ATGTTATCCCCACGCTCCTC 59.241 55.000 0.00 0.00 0.00 3.71
680 708 0.759346 GATGTTATCCCCACGCTCCT 59.241 55.000 0.00 0.00 0.00 3.69
773 807 3.287520 GGGATTGGATTCGCCCGC 61.288 66.667 0.00 0.00 34.97 6.13
954 997 1.228306 GCTAGGCTCCTCGCTCCTA 60.228 63.158 5.30 0.00 39.13 2.94
1056 1105 3.782244 CGCTCGCTGTGCTTGGAC 61.782 66.667 0.00 0.00 0.00 4.02
1270 1319 4.116328 CAGCGCGAAGGACTCCGA 62.116 66.667 12.10 0.00 0.00 4.55
1491 1540 0.107165 GGATGGCGTAGAAGGGCTTT 60.107 55.000 0.00 0.00 0.00 3.51
1510 1559 3.545481 GACGTCGATGCGGTGCAG 61.545 66.667 4.06 0.00 43.65 4.41
1734 1783 0.249784 CCTCACCATGCTCATCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
1824 1873 1.251251 ACAGAAACCTGGATGCTTGC 58.749 50.000 0.00 0.00 36.01 4.01
2061 2110 1.572085 CTTTCGGCTGCTGGTCACTG 61.572 60.000 8.89 0.00 0.00 3.66
2118 2167 3.703127 GGGACGAACCTCGGGCTT 61.703 66.667 0.67 0.00 45.59 4.35
2304 2353 3.117550 TCACCAGATCCATTACATTGGGG 60.118 47.826 0.00 0.00 37.37 4.96
2478 2527 1.589993 CGCAGACGCACCAGGATAG 60.590 63.158 0.00 0.00 38.40 2.08
2607 2656 1.911357 TCATCTGCATCACCTGGTTCT 59.089 47.619 0.00 0.00 0.00 3.01
2652 2701 1.280457 AGAAGGCCCTGAACGAAGAT 58.720 50.000 0.00 0.00 0.00 2.40
2777 2826 0.888736 TGACCCTGCATTGTTGTCGG 60.889 55.000 0.00 0.00 0.00 4.79
2791 2840 2.238521 TGGAGCTTCAACAATTGACCC 58.761 47.619 13.59 1.99 39.87 4.46
2852 2901 5.388682 CGCACCATTTCATTTGTCACAATTC 60.389 40.000 0.00 0.00 0.00 2.17
2868 2917 2.017049 GTCTCAATTAGGCGCACCATT 58.983 47.619 10.83 0.00 39.06 3.16
2919 2968 4.907809 TCCATCCGTTTATGTTACCAACA 58.092 39.130 0.00 0.00 46.94 3.33
2967 3016 1.673337 GGCTTCCGTGGTGGGTAAC 60.673 63.158 0.00 0.00 38.76 2.50
3085 3134 5.590259 GCTGGAAAGCATATAAGAAGACCAA 59.410 40.000 0.00 0.00 34.41 3.67
3096 3145 8.440771 AGGTTATAACTAAGCTGGAAAGCATAT 58.559 33.333 15.05 0.00 42.56 1.78
3133 3186 4.155099 AGAAATGAAACACAACGTGTCACA 59.845 37.500 3.42 4.80 44.85 3.58
3141 3194 8.871686 ATACAAAAGGAGAAATGAAACACAAC 57.128 30.769 0.00 0.00 0.00 3.32
3163 3217 3.596214 TGCTCTTCGGTTCCTGAAATAC 58.404 45.455 0.00 0.00 0.00 1.89
3281 3335 4.075682 CCAAACAAACCCCAACAACTTTT 58.924 39.130 0.00 0.00 0.00 2.27
3302 3356 1.737793 CCCGTCAAATCTTGTGCTACC 59.262 52.381 0.00 0.00 0.00 3.18
3320 3374 3.228188 TCCATTATCATCTTGTGCCCC 57.772 47.619 0.00 0.00 0.00 5.80
3333 3387 9.496710 TTGTATCCGGGTATACTTATCCATTAT 57.503 33.333 12.95 0.00 34.13 1.28
3335 3389 7.093024 CCTTGTATCCGGGTATACTTATCCATT 60.093 40.741 12.95 0.00 34.13 3.16
3359 3413 3.543680 ACTATTGCAACATAGTCGCCT 57.456 42.857 0.00 0.00 0.00 5.52
3419 3473 8.896744 CATTCTAAGCAAGAACCAAGATCATTA 58.103 33.333 3.87 0.00 46.90 1.90
3559 3613 8.467598 TCAGTATGCTAAGTTTGGTTAGAGTAG 58.532 37.037 0.00 0.00 34.76 2.57
3881 3935 2.496871 CTGCTCCTCTGTCAAGTCAGAT 59.503 50.000 0.00 0.00 42.47 2.90
4069 4125 7.915923 TGAGATATTAGTAGTTTCAGTTCTGCG 59.084 37.037 0.00 0.00 0.00 5.18
4136 4192 5.007039 GTCCAAGTAGTGCATATCATGTGTG 59.993 44.000 0.00 0.00 0.00 3.82
4157 4226 3.826157 TGATGGTGGAAGTTTTCATGTCC 59.174 43.478 0.00 0.00 0.00 4.02
4178 4247 9.624697 TTTTCTAGCACTATAAGCATTTTGTTG 57.375 29.630 0.00 0.00 0.00 3.33
4211 4280 5.941948 AAGGTATGCTAAACTGTTGTGTC 57.058 39.130 0.00 0.00 0.00 3.67
4296 4366 6.985188 TCATCTCCATGTAGCTGTAAAAAC 57.015 37.500 0.00 0.00 0.00 2.43
4322 4392 1.243902 TCAAGGTTGAATTCCACCGC 58.756 50.000 19.93 1.22 33.55 5.68
4387 4457 8.405531 TCACGATCAAGAGAAATTTGTTTTTCT 58.594 29.630 0.00 0.00 46.08 2.52
4438 4508 9.401496 AGCCTTAAGTTATCCCCATATAAGTAA 57.599 33.333 0.97 0.00 0.00 2.24
4655 4725 9.822727 TCCCTATGTGTTCTTCTGATATACATA 57.177 33.333 0.00 0.00 0.00 2.29
4656 4726 8.727100 TCCCTATGTGTTCTTCTGATATACAT 57.273 34.615 0.00 0.00 0.00 2.29
4657 4727 8.421784 GTTCCCTATGTGTTCTTCTGATATACA 58.578 37.037 0.00 0.00 0.00 2.29
4658 4728 8.421784 TGTTCCCTATGTGTTCTTCTGATATAC 58.578 37.037 0.00 0.00 0.00 1.47
4730 4800 0.250038 GCTCTGGTCTTGCACAGTCA 60.250 55.000 2.37 0.48 36.17 3.41
4782 4852 1.734465 CTACTGCCACTTACAAGCTGC 59.266 52.381 0.00 0.00 0.00 5.25
4796 4866 1.941668 GCAACCTCCTGTCACTACTGC 60.942 57.143 0.00 0.00 0.00 4.40
4797 4867 1.338200 GGCAACCTCCTGTCACTACTG 60.338 57.143 0.00 0.00 0.00 2.74
4798 4868 0.977395 GGCAACCTCCTGTCACTACT 59.023 55.000 0.00 0.00 0.00 2.57
4799 4869 3.534721 GGCAACCTCCTGTCACTAC 57.465 57.895 0.00 0.00 0.00 2.73
4822 4901 8.730680 GGCAATCTAAACACTATCAAAGAAGAA 58.269 33.333 0.00 0.00 0.00 2.52
4872 4951 7.566760 TTCAGATTGCTTTCAGTTAAGTGAA 57.433 32.000 19.59 19.59 34.56 3.18
4920 4999 6.715347 AAACAGCTGTTATTTTCAAGGAGT 57.285 33.333 31.31 9.07 37.25 3.85
4990 5069 2.836636 TCTCCTGTATCAGTGCCTCT 57.163 50.000 0.00 0.00 0.00 3.69
5222 5302 0.176680 CCTGGTTCACATCTCGAGGG 59.823 60.000 13.56 8.03 0.00 4.30
5259 5339 0.540365 CCAAAGGGCTTGCTCTTCCA 60.540 55.000 8.28 0.00 33.27 3.53
5260 5340 1.253593 CCCAAAGGGCTTGCTCTTCC 61.254 60.000 8.28 0.00 35.35 3.46
5261 5341 0.251341 TCCCAAAGGGCTTGCTCTTC 60.251 55.000 8.28 0.00 43.94 2.87
5332 5412 1.280421 AGCTCCTCCTCAACCATCAAC 59.720 52.381 0.00 0.00 0.00 3.18
5450 5534 2.710377 CAACCACCCGAGAATTGATCA 58.290 47.619 0.00 0.00 0.00 2.92
5462 5546 0.603065 GTCTGGATTTGCAACCACCC 59.397 55.000 0.00 0.00 32.44 4.61
5539 5639 9.893634 TGCAAGCCTAAATAAAATAGTAGTGTA 57.106 29.630 0.00 0.00 0.00 2.90
5540 5640 8.801882 TGCAAGCCTAAATAAAATAGTAGTGT 57.198 30.769 0.00 0.00 0.00 3.55
5541 5641 9.109393 TCTGCAAGCCTAAATAAAATAGTAGTG 57.891 33.333 0.00 0.00 0.00 2.74
5542 5642 9.331282 CTCTGCAAGCCTAAATAAAATAGTAGT 57.669 33.333 0.00 0.00 0.00 2.73
5543 5643 9.331282 ACTCTGCAAGCCTAAATAAAATAGTAG 57.669 33.333 0.00 0.00 0.00 2.57
5545 5645 9.110502 GTACTCTGCAAGCCTAAATAAAATAGT 57.889 33.333 0.00 0.00 0.00 2.12
5546 5646 9.109393 TGTACTCTGCAAGCCTAAATAAAATAG 57.891 33.333 0.00 0.00 0.00 1.73
5547 5647 8.889717 GTGTACTCTGCAAGCCTAAATAAAATA 58.110 33.333 0.00 0.00 0.00 1.40
5548 5648 7.611855 AGTGTACTCTGCAAGCCTAAATAAAAT 59.388 33.333 0.00 0.00 0.00 1.82
5549 5649 6.940298 AGTGTACTCTGCAAGCCTAAATAAAA 59.060 34.615 0.00 0.00 0.00 1.52
5550 5650 6.472887 AGTGTACTCTGCAAGCCTAAATAAA 58.527 36.000 0.00 0.00 0.00 1.40
5551 5651 6.049955 AGTGTACTCTGCAAGCCTAAATAA 57.950 37.500 0.00 0.00 0.00 1.40
5552 5652 5.677319 AGTGTACTCTGCAAGCCTAAATA 57.323 39.130 0.00 0.00 0.00 1.40
5553 5653 4.559862 AGTGTACTCTGCAAGCCTAAAT 57.440 40.909 0.00 0.00 0.00 1.40
5554 5654 4.282449 TGTAGTGTACTCTGCAAGCCTAAA 59.718 41.667 12.47 0.00 0.00 1.85
5555 5655 3.830178 TGTAGTGTACTCTGCAAGCCTAA 59.170 43.478 12.47 0.00 0.00 2.69
5556 5656 3.192844 GTGTAGTGTACTCTGCAAGCCTA 59.807 47.826 15.81 0.00 32.48 3.93
5557 5657 2.028930 GTGTAGTGTACTCTGCAAGCCT 60.029 50.000 15.81 0.00 32.48 4.58
5558 5658 2.028930 AGTGTAGTGTACTCTGCAAGCC 60.029 50.000 15.81 5.83 32.48 4.35
5559 5659 3.305398 AGTGTAGTGTACTCTGCAAGC 57.695 47.619 15.81 6.45 32.48 4.01
5560 5660 5.372547 TGTAGTGTAGTGTACTCTGCAAG 57.627 43.478 15.81 0.00 40.27 4.01
5571 5671 6.455647 TCCTCTTCACAATTGTAGTGTAGTG 58.544 40.000 11.53 3.94 36.27 2.74
5599 5699 2.940158 AGGCCTGTTTAGAACGGTTTT 58.060 42.857 3.11 0.00 35.99 2.43
5603 5733 1.165270 CCAAGGCCTGTTTAGAACGG 58.835 55.000 5.69 0.00 37.52 4.44
5608 5746 1.003580 TCTGCTCCAAGGCCTGTTTAG 59.996 52.381 5.69 2.82 0.00 1.85
5622 5760 2.175878 TGTGAAAGCTTCCTCTGCTC 57.824 50.000 0.00 0.00 40.22 4.26
5829 5967 0.938926 AGGAGAGGGAAGGGGGATCT 60.939 60.000 0.00 0.00 0.00 2.75
5830 5968 0.472925 GAGGAGAGGGAAGGGGGATC 60.473 65.000 0.00 0.00 0.00 3.36
5833 5971 2.319410 ATCGAGGAGAGGGAAGGGGG 62.319 65.000 0.00 0.00 0.00 5.40
6076 6217 1.671901 GGCGAGAGAGTGGGGAAGAG 61.672 65.000 0.00 0.00 0.00 2.85
6077 6218 1.682684 GGCGAGAGAGTGGGGAAGA 60.683 63.158 0.00 0.00 0.00 2.87
6080 6221 1.682684 GAAGGCGAGAGAGTGGGGA 60.683 63.158 0.00 0.00 0.00 4.81
6083 6224 2.169832 TTTTGAAGGCGAGAGAGTGG 57.830 50.000 0.00 0.00 0.00 4.00
6085 6226 3.513515 AGAGATTTTGAAGGCGAGAGAGT 59.486 43.478 0.00 0.00 0.00 3.24
6099 6240 1.168714 GCTTGGTCGGCAGAGATTTT 58.831 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.