Multiple sequence alignment - TraesCS4D01G069300

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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 TraesCS4D01G069300 chr4D 100.000 3742 0 0 1 3742 44748604 44744863 0.000000e+00 6911
1 TraesCS4D01G069300 chr4B 87.010 3472 233 87 153 3554 64699818 64696495 0.000000e+00 3712
2 TraesCS4D01G069300 chr4B 96.899 129 3 1 3615 3742 64696479 64696351 8.140000e-52 215
3 TraesCS4D01G069300 chr4A 92.284 2566 129 25 366 2906 554923532 554926053 0.000000e+00 3578
4 TraesCS4D01G069300 chr4A 89.610 462 31 6 3295 3742 554926285 554926743 4.190000e-159 571
5 TraesCS4D01G069300 chr6D 83.681 288 33 9 3464 3742 173902998 173902716 3.710000e-65 259


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 TraesCS4D01G069300 chr4D 44744863 44748604 3741 True 6911.0 6911 100.0000 1 3742 1 chr4D.!!$R1 3741
1 TraesCS4D01G069300 chr4B 64696351 64699818 3467 True 1963.5 3712 91.9545 153 3742 2 chr4B.!!$R1 3589
2 TraesCS4D01G069300 chr4A 554923532 554926743 3211 False 2074.5 3578 90.9470 366 3742 2 chr4A.!!$F1 3376

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
23 24 0.178995 TGCACACATCTCCTTTGGCA 60.179 50.0 0.0 0.0 0.00 4.92 F
30 31 0.259938 ATCTCCTTTGGCATCCCACC 59.740 55.0 0.0 0.0 41.97 4.61 F
77 78 0.396811 GCCGCCCTCCTTGTATGTAT 59.603 55.0 0.0 0.0 0.00 2.29 F
1339 1428 0.739462 TGCGTCGTATTCTTGGCTGG 60.739 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 1339 0.034476 CAGAGCTGGCTGTGAACTCA 59.966 55.0 13.41 0.00 39.36 3.41 R
1881 1970 0.394216 CCATCCGGATGCCACTGAAA 60.394 55.0 34.77 0.00 37.49 2.69 R
1890 1979 2.878406 GGATACAAACACCATCCGGATG 59.122 50.0 33.52 33.52 38.51 3.51 R
3221 3371 0.874390 AACTGCACACAATAGCACCG 59.126 50.0 0.00 0.00 36.62 4.94 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
19 20 2.936919 TCAGTGCACACATCTCCTTT 57.063 45.000 21.04 0.00 0.00 3.11
20 21 2.497138 TCAGTGCACACATCTCCTTTG 58.503 47.619 21.04 4.26 0.00 2.77
21 22 1.538512 CAGTGCACACATCTCCTTTGG 59.461 52.381 21.04 0.00 0.00 3.28
22 23 0.242017 GTGCACACATCTCCTTTGGC 59.758 55.000 13.17 0.00 0.00 4.52
23 24 0.178995 TGCACACATCTCCTTTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
24 25 1.180029 GCACACATCTCCTTTGGCAT 58.820 50.000 0.00 0.00 0.00 4.40
25 26 1.133790 GCACACATCTCCTTTGGCATC 59.866 52.381 0.00 0.00 0.00 3.91
26 27 1.747355 CACACATCTCCTTTGGCATCC 59.253 52.381 0.00 0.00 0.00 3.51
27 28 1.341383 ACACATCTCCTTTGGCATCCC 60.341 52.381 0.00 0.00 0.00 3.85
28 29 1.002069 ACATCTCCTTTGGCATCCCA 58.998 50.000 0.00 0.00 40.06 4.37
29 30 1.341383 ACATCTCCTTTGGCATCCCAC 60.341 52.381 0.00 0.00 41.97 4.61
30 31 0.259938 ATCTCCTTTGGCATCCCACC 59.740 55.000 0.00 0.00 41.97 4.61
31 32 1.750399 CTCCTTTGGCATCCCACCG 60.750 63.158 0.00 0.00 41.97 4.94
32 33 3.451894 CCTTTGGCATCCCACCGC 61.452 66.667 0.00 0.00 41.97 5.68
33 34 2.676121 CTTTGGCATCCCACCGCA 60.676 61.111 0.00 0.00 41.97 5.69
34 35 2.203552 TTTGGCATCCCACCGCAA 60.204 55.556 0.00 0.00 41.97 4.85
35 36 2.490993 CTTTGGCATCCCACCGCAAC 62.491 60.000 0.00 0.00 41.97 4.17
38 39 4.740822 GCATCCCACCGCAACCCT 62.741 66.667 0.00 0.00 0.00 4.34
39 40 2.438434 CATCCCACCGCAACCCTC 60.438 66.667 0.00 0.00 0.00 4.30
40 41 3.728373 ATCCCACCGCAACCCTCC 61.728 66.667 0.00 0.00 0.00 4.30
42 43 4.278513 CCCACCGCAACCCTCCAA 62.279 66.667 0.00 0.00 0.00 3.53
43 44 2.983592 CCACCGCAACCCTCCAAC 60.984 66.667 0.00 0.00 0.00 3.77
44 45 3.353836 CACCGCAACCCTCCAACG 61.354 66.667 0.00 0.00 0.00 4.10
48 49 3.056328 GCAACCCTCCAACGCCTC 61.056 66.667 0.00 0.00 0.00 4.70
49 50 2.359975 CAACCCTCCAACGCCTCC 60.360 66.667 0.00 0.00 0.00 4.30
50 51 2.852075 AACCCTCCAACGCCTCCA 60.852 61.111 0.00 0.00 0.00 3.86
51 52 3.192103 AACCCTCCAACGCCTCCAC 62.192 63.158 0.00 0.00 0.00 4.02
52 53 3.636231 CCCTCCAACGCCTCCACA 61.636 66.667 0.00 0.00 0.00 4.17
53 54 2.671070 CCTCCAACGCCTCCACAT 59.329 61.111 0.00 0.00 0.00 3.21
54 55 1.746615 CCTCCAACGCCTCCACATG 60.747 63.158 0.00 0.00 0.00 3.21
55 56 2.359850 TCCAACGCCTCCACATGC 60.360 61.111 0.00 0.00 0.00 4.06
56 57 2.672651 CCAACGCCTCCACATGCA 60.673 61.111 0.00 0.00 0.00 3.96
57 58 2.693762 CCAACGCCTCCACATGCAG 61.694 63.158 0.00 0.00 0.00 4.41
58 59 2.360350 AACGCCTCCACATGCAGG 60.360 61.111 0.00 0.00 0.00 4.85
72 73 3.399181 CAGGCCGCCCTCCTTGTA 61.399 66.667 5.55 0.00 40.33 2.41
73 74 2.366972 AGGCCGCCCTCCTTGTAT 60.367 61.111 5.55 0.00 36.46 2.29
74 75 2.203209 GGCCGCCCTCCTTGTATG 60.203 66.667 0.00 0.00 0.00 2.39
75 76 2.590092 GCCGCCCTCCTTGTATGT 59.410 61.111 0.00 0.00 0.00 2.29
76 77 1.692173 GGCCGCCCTCCTTGTATGTA 61.692 60.000 0.00 0.00 0.00 2.29
77 78 0.396811 GCCGCCCTCCTTGTATGTAT 59.603 55.000 0.00 0.00 0.00 2.29
78 79 1.202770 GCCGCCCTCCTTGTATGTATT 60.203 52.381 0.00 0.00 0.00 1.89
79 80 2.748465 GCCGCCCTCCTTGTATGTATTT 60.748 50.000 0.00 0.00 0.00 1.40
80 81 3.551846 CCGCCCTCCTTGTATGTATTTT 58.448 45.455 0.00 0.00 0.00 1.82
81 82 3.951680 CCGCCCTCCTTGTATGTATTTTT 59.048 43.478 0.00 0.00 0.00 1.94
82 83 4.036380 CCGCCCTCCTTGTATGTATTTTTC 59.964 45.833 0.00 0.00 0.00 2.29
83 84 4.036380 CGCCCTCCTTGTATGTATTTTTCC 59.964 45.833 0.00 0.00 0.00 3.13
84 85 4.341235 GCCCTCCTTGTATGTATTTTTCCC 59.659 45.833 0.00 0.00 0.00 3.97
85 86 4.893524 CCCTCCTTGTATGTATTTTTCCCC 59.106 45.833 0.00 0.00 0.00 4.81
86 87 4.893524 CCTCCTTGTATGTATTTTTCCCCC 59.106 45.833 0.00 0.00 0.00 5.40
87 88 5.340863 CCTCCTTGTATGTATTTTTCCCCCT 60.341 44.000 0.00 0.00 0.00 4.79
88 89 6.160483 TCCTTGTATGTATTTTTCCCCCTT 57.840 37.500 0.00 0.00 0.00 3.95
89 90 6.566914 TCCTTGTATGTATTTTTCCCCCTTT 58.433 36.000 0.00 0.00 0.00 3.11
90 91 7.020009 TCCTTGTATGTATTTTTCCCCCTTTT 58.980 34.615 0.00 0.00 0.00 2.27
91 92 7.514473 TCCTTGTATGTATTTTTCCCCCTTTTT 59.486 33.333 0.00 0.00 0.00 1.94
112 113 6.995511 TTTTTGGGGTTATAGTCGATCAAG 57.004 37.500 0.00 0.00 0.00 3.02
113 114 5.687166 TTTGGGGTTATAGTCGATCAAGT 57.313 39.130 0.00 0.00 0.00 3.16
114 115 5.687166 TTGGGGTTATAGTCGATCAAGTT 57.313 39.130 0.00 0.00 0.00 2.66
115 116 5.687166 TGGGGTTATAGTCGATCAAGTTT 57.313 39.130 0.00 0.00 0.00 2.66
116 117 6.057321 TGGGGTTATAGTCGATCAAGTTTT 57.943 37.500 0.00 0.00 0.00 2.43
117 118 7.185318 TGGGGTTATAGTCGATCAAGTTTTA 57.815 36.000 0.00 0.00 0.00 1.52
118 119 7.270047 TGGGGTTATAGTCGATCAAGTTTTAG 58.730 38.462 0.00 0.00 0.00 1.85
119 120 7.124599 TGGGGTTATAGTCGATCAAGTTTTAGA 59.875 37.037 0.00 0.00 0.00 2.10
120 121 8.148999 GGGGTTATAGTCGATCAAGTTTTAGAT 58.851 37.037 0.00 0.00 0.00 1.98
127 128 8.480643 AGTCGATCAAGTTTTAGATAAACCTG 57.519 34.615 0.00 0.00 0.00 4.00
128 129 8.311836 AGTCGATCAAGTTTTAGATAAACCTGA 58.688 33.333 4.68 4.68 35.73 3.86
129 130 8.596380 GTCGATCAAGTTTTAGATAAACCTGAG 58.404 37.037 7.49 0.00 35.03 3.35
130 131 8.528643 TCGATCAAGTTTTAGATAAACCTGAGA 58.471 33.333 7.49 0.03 35.03 3.27
131 132 9.319143 CGATCAAGTTTTAGATAAACCTGAGAT 57.681 33.333 7.49 2.27 35.03 2.75
140 141 9.436957 TTTAGATAAACCTGAGATTCTTCACAC 57.563 33.333 0.00 0.00 0.00 3.82
141 142 7.251321 AGATAAACCTGAGATTCTTCACACT 57.749 36.000 0.00 0.00 0.00 3.55
142 143 7.684529 AGATAAACCTGAGATTCTTCACACTT 58.315 34.615 0.00 0.00 0.00 3.16
143 144 8.160106 AGATAAACCTGAGATTCTTCACACTTT 58.840 33.333 0.00 0.00 0.00 2.66
144 145 9.436957 GATAAACCTGAGATTCTTCACACTTTA 57.563 33.333 0.00 0.00 0.00 1.85
145 146 7.497925 AAACCTGAGATTCTTCACACTTTAC 57.502 36.000 0.00 0.00 0.00 2.01
146 147 5.552178 ACCTGAGATTCTTCACACTTTACC 58.448 41.667 0.00 0.00 0.00 2.85
147 148 5.308237 ACCTGAGATTCTTCACACTTTACCT 59.692 40.000 0.00 0.00 0.00 3.08
148 149 6.497259 ACCTGAGATTCTTCACACTTTACCTA 59.503 38.462 0.00 0.00 0.00 3.08
149 150 7.016268 ACCTGAGATTCTTCACACTTTACCTAA 59.984 37.037 0.00 0.00 0.00 2.69
150 151 7.547370 CCTGAGATTCTTCACACTTTACCTAAG 59.453 40.741 0.00 0.00 39.87 2.18
151 152 8.190326 TGAGATTCTTCACACTTTACCTAAGA 57.810 34.615 0.00 0.00 37.30 2.10
152 153 8.647796 TGAGATTCTTCACACTTTACCTAAGAA 58.352 33.333 0.00 0.00 37.36 2.52
153 154 9.145865 GAGATTCTTCACACTTTACCTAAGAAG 57.854 37.037 0.00 0.00 36.66 2.85
154 155 8.652290 AGATTCTTCACACTTTACCTAAGAAGT 58.348 33.333 0.00 0.00 36.66 3.01
175 176 4.702131 AGTGGGTTTCATATGCTGTTTCTC 59.298 41.667 0.00 0.00 0.00 2.87
190 191 6.149197 CTGTTTCTCAGATGCACTTCCTGC 62.149 50.000 0.00 0.00 46.27 4.85
205 206 8.788409 GCACTTCCTGCAAATATAGTTATTTC 57.212 34.615 0.00 0.00 46.29 2.17
220 221 6.849085 AGTTATTTCATGGTAAATGGTGCA 57.151 33.333 3.29 0.00 31.63 4.57
223 224 8.976353 AGTTATTTCATGGTAAATGGTGCAATA 58.024 29.630 0.00 0.00 31.63 1.90
228 229 8.532186 TTCATGGTAAATGGTGCAATACTATT 57.468 30.769 0.00 0.00 41.62 1.73
231 232 7.566760 TGGTAAATGGTGCAATACTATTCAG 57.433 36.000 0.00 0.00 39.27 3.02
234 235 8.850156 GGTAAATGGTGCAATACTATTCAGAAT 58.150 33.333 0.20 0.20 39.27 2.40
256 257 9.160496 AGAATACTGAAGTTTCATGTCTTCATC 57.840 33.333 21.01 17.29 45.48 2.92
282 283 6.182627 TGCAGTCCATCTGATTTAACTTCAT 58.817 36.000 0.00 0.00 46.27 2.57
290 291 7.775093 CCATCTGATTTAACTTCATTGAGGGTA 59.225 37.037 0.55 0.00 0.00 3.69
309 310 4.774200 GGGTACTACTGACTTACTGGGAAA 59.226 45.833 0.00 0.00 0.00 3.13
335 338 2.232399 TCTGACATGCATTGCTGTTGT 58.768 42.857 10.49 10.63 0.00 3.32
344 347 4.967437 TGCATTGCTGTTGTTTTGAAAAC 58.033 34.783 13.55 13.55 0.00 2.43
346 349 5.023286 GCATTGCTGTTGTTTTGAAAACTG 58.977 37.500 20.06 9.52 0.00 3.16
350 353 6.221858 TGCTGTTGTTTTGAAAACTGAAAC 57.778 33.333 20.06 15.97 34.67 2.78
351 354 5.755375 TGCTGTTGTTTTGAAAACTGAAACA 59.245 32.000 20.06 18.95 40.39 2.83
371 390 5.835113 ACAATAATACAATGTCAGGGCAC 57.165 39.130 0.00 0.00 0.00 5.01
728 779 4.153986 CGATCTTGTTGTCACATCAAAGC 58.846 43.478 2.95 0.00 31.06 3.51
740 791 4.130118 CACATCAAAGCTATCCAGTACCC 58.870 47.826 0.00 0.00 0.00 3.69
759 810 3.791545 ACCCAACTACCCAATCCATACAT 59.208 43.478 0.00 0.00 0.00 2.29
802 853 4.320788 GCATTCCACTTGTCCTTTTCTCTG 60.321 45.833 0.00 0.00 0.00 3.35
873 924 4.654915 TGACCAGAAGCATCTCAAAATCA 58.345 39.130 0.00 0.00 32.03 2.57
874 925 5.072055 TGACCAGAAGCATCTCAAAATCAA 58.928 37.500 0.00 0.00 32.03 2.57
875 926 5.535783 TGACCAGAAGCATCTCAAAATCAAA 59.464 36.000 0.00 0.00 32.03 2.69
876 927 6.040729 TGACCAGAAGCATCTCAAAATCAAAA 59.959 34.615 0.00 0.00 32.03 2.44
877 928 7.001099 ACCAGAAGCATCTCAAAATCAAAAT 57.999 32.000 0.00 0.00 32.03 1.82
878 929 7.095270 ACCAGAAGCATCTCAAAATCAAAATC 58.905 34.615 0.00 0.00 32.03 2.17
905 956 5.841810 TCAATTTGGTTTCTGCGAAGAAAT 58.158 33.333 21.37 2.41 39.58 2.17
959 1012 3.523972 GTCCCCTTTTGTAATCTCCTCCT 59.476 47.826 0.00 0.00 0.00 3.69
987 1040 0.991920 AATCGGAAAGGAAGGGCTCA 59.008 50.000 0.00 0.00 0.00 4.26
1182 1263 2.289320 GCAGGATATTCGGTGATCTGCT 60.289 50.000 0.00 0.00 33.18 4.24
1258 1339 0.984230 TCCGGATTCAGAAAGCCTGT 59.016 50.000 0.00 0.00 43.38 4.00
1326 1415 4.072088 GAACGGCAAGGTGCGTCG 62.072 66.667 0.00 0.00 46.21 5.12
1339 1428 0.739462 TGCGTCGTATTCTTGGCTGG 60.739 55.000 0.00 0.00 0.00 4.85
1358 1447 2.224769 TGGGTTCTTCTTGATGGTGGTC 60.225 50.000 0.00 0.00 0.00 4.02
1359 1448 2.040412 GGGTTCTTCTTGATGGTGGTCT 59.960 50.000 0.00 0.00 0.00 3.85
1382 1471 6.498651 TCTGGCCATTTCCTTTGGTTTAATAA 59.501 34.615 5.51 0.00 36.57 1.40
1383 1472 7.181845 TCTGGCCATTTCCTTTGGTTTAATAAT 59.818 33.333 5.51 0.00 36.57 1.28
1384 1473 8.380742 TGGCCATTTCCTTTGGTTTAATAATA 57.619 30.769 0.00 0.00 36.57 0.98
1609 1698 6.545666 TCACCATATTCTGAAATACGGCAATT 59.454 34.615 0.00 0.00 34.68 2.32
1615 1704 5.446143 TCTGAAATACGGCAATTGTTGTT 57.554 34.783 7.40 0.00 0.00 2.83
1616 1705 5.218885 TCTGAAATACGGCAATTGTTGTTG 58.781 37.500 7.40 0.00 0.00 3.33
1709 1798 3.895232 AGCGTACATCAAAGGTGATCT 57.105 42.857 0.00 0.00 42.88 2.75
1717 1806 7.904977 CGTACATCAAAGGTGATCTTGTTATTG 59.095 37.037 0.00 0.00 42.88 1.90
1727 1816 8.147058 AGGTGATCTTGTTATTGTATAGCTGAG 58.853 37.037 0.00 0.00 0.00 3.35
1750 1839 7.609146 TGAGTATTCTTGATGTTGAAAGAGCAT 59.391 33.333 0.00 0.00 34.09 3.79
1763 1852 9.017509 TGTTGAAAGAGCATTTCTAATCTGATT 57.982 29.630 8.14 8.14 34.14 2.57
1764 1853 9.286946 GTTGAAAGAGCATTTCTAATCTGATTG 57.713 33.333 13.01 3.75 34.14 2.67
1818 1907 6.378280 GGACAGAAATGAAGGTGGATAAACAT 59.622 38.462 0.00 0.00 0.00 2.71
1821 1910 4.637483 AATGAAGGTGGATAAACATGCG 57.363 40.909 0.00 0.00 0.00 4.73
1824 1913 2.507407 AGGTGGATAAACATGCGGTT 57.493 45.000 0.00 0.00 42.98 4.44
1876 1965 1.200760 AGGAGCTGTGGCCATGTACA 61.201 55.000 9.72 0.00 39.73 2.90
1881 1970 3.885297 GAGCTGTGGCCATGTACATAAAT 59.115 43.478 9.72 0.00 39.73 1.40
1890 1979 5.043248 GCCATGTACATAAATTTCAGTGGC 58.957 41.667 8.32 10.85 41.16 5.01
1908 1997 1.680555 GGCATCCGGATGGTGTTTGTA 60.681 52.381 38.49 0.00 39.16 2.41
1931 2020 1.466856 TGCCATCTTGCAGGTTGATC 58.533 50.000 8.37 1.40 36.04 2.92
1960 2050 6.835488 AGCTTCTGGCAATCCATTTCTTATTA 59.165 34.615 0.00 0.00 42.51 0.98
1961 2051 7.014038 AGCTTCTGGCAATCCATTTCTTATTAG 59.986 37.037 0.00 0.00 42.51 1.73
1962 2052 7.201857 GCTTCTGGCAATCCATTTCTTATTAGT 60.202 37.037 0.00 0.00 42.51 2.24
1963 2053 9.342308 CTTCTGGCAATCCATTTCTTATTAGTA 57.658 33.333 0.00 0.00 42.51 1.82
1964 2054 9.866655 TTCTGGCAATCCATTTCTTATTAGTAT 57.133 29.630 0.00 0.00 42.51 2.12
1965 2055 9.507329 TCTGGCAATCCATTTCTTATTAGTATC 57.493 33.333 0.00 0.00 42.51 2.24
1966 2056 9.288576 CTGGCAATCCATTTCTTATTAGTATCA 57.711 33.333 0.00 0.00 42.51 2.15
1967 2057 9.066892 TGGCAATCCATTTCTTATTAGTATCAC 57.933 33.333 0.00 0.00 37.47 3.06
1968 2058 8.515414 GGCAATCCATTTCTTATTAGTATCACC 58.485 37.037 0.00 0.00 0.00 4.02
1969 2059 9.066892 GCAATCCATTTCTTATTAGTATCACCA 57.933 33.333 0.00 0.00 0.00 4.17
2001 2091 5.105064 TGGGTCTTATTACCTCAGTGCTAAC 60.105 44.000 0.00 0.00 39.65 2.34
2015 2105 3.363178 GTGCTAACACTGAAAGCAACAC 58.637 45.455 10.38 0.00 47.00 3.32
2020 2110 6.708502 TGCTAACACTGAAAGCAACACTAATA 59.291 34.615 7.37 0.00 42.96 0.98
2282 2383 3.181520 CGCCAAAGTGTAAGTGTATGCTC 60.182 47.826 0.00 0.00 0.00 4.26
2285 2386 4.688879 CCAAAGTGTAAGTGTATGCTCGAA 59.311 41.667 0.00 0.00 0.00 3.71
2293 2394 7.435488 GTGTAAGTGTATGCTCGAACTATTCAT 59.565 37.037 0.00 0.00 0.00 2.57
2294 2395 8.626526 TGTAAGTGTATGCTCGAACTATTCATA 58.373 33.333 0.00 0.00 0.00 2.15
2402 2503 3.058224 GTCAAGTGTTCAATGGGTACTGC 60.058 47.826 0.00 0.00 0.00 4.40
2426 2527 1.810755 GGGACCTTGTCTTTTAAGCCG 59.189 52.381 0.00 0.00 32.47 5.52
2462 2563 2.907910 TCGGAAGTAGCAACTACGAC 57.092 50.000 0.00 0.00 41.37 4.34
2538 2639 9.958180 TCTGAAAGAAATTGTACATATTCTGGA 57.042 29.630 18.89 13.54 42.31 3.86
2645 2764 1.372087 CTTCTGGCTTGGATGCGGTC 61.372 60.000 0.00 0.00 0.00 4.79
2711 2830 2.399916 AGCCTGTGAAAGCTCATCTC 57.600 50.000 0.00 0.00 32.71 2.75
2732 2851 1.145803 GTCTGAAAGTACGTGGTGGC 58.854 55.000 0.00 0.00 33.76 5.01
2733 2852 0.753867 TCTGAAAGTACGTGGTGGCA 59.246 50.000 0.00 0.00 33.76 4.92
2736 2855 3.007074 TCTGAAAGTACGTGGTGGCAATA 59.993 43.478 0.00 0.00 33.76 1.90
2910 3029 5.379003 CGTGTATTCATGTTGTTGTGTACC 58.621 41.667 0.00 0.00 0.00 3.34
2937 3085 2.101750 TGATGTTATATGGTGACGCGGT 59.898 45.455 12.47 0.00 0.00 5.68
2959 3107 1.474332 TTTCGAACCGGTAGGCAGGT 61.474 55.000 8.00 0.00 45.04 4.00
3024 3173 9.646522 AAAAAGAAATACCCAGCATATACAGAT 57.353 29.630 0.00 0.00 0.00 2.90
3080 3230 4.763279 TCAATATGGCATTGACATAGCAGG 59.237 41.667 16.95 7.13 36.93 4.85
3098 3248 5.509498 AGCAGGGCAGATTCTTTATTACAA 58.491 37.500 0.00 0.00 0.00 2.41
3104 3254 6.322491 GGCAGATTCTTTATTACAACACACC 58.678 40.000 0.00 0.00 0.00 4.16
3107 3257 8.726988 GCAGATTCTTTATTACAACACACCTTA 58.273 33.333 0.00 0.00 0.00 2.69
3126 3276 1.995376 ATTTCCCATTGATACCCGGC 58.005 50.000 0.00 0.00 0.00 6.13
3127 3277 0.106419 TTTCCCATTGATACCCGGCC 60.106 55.000 0.00 0.00 0.00 6.13
3128 3278 0.991355 TTCCCATTGATACCCGGCCT 60.991 55.000 0.00 0.00 0.00 5.19
3129 3279 1.228245 CCCATTGATACCCGGCCTG 60.228 63.158 0.00 0.00 0.00 4.85
3130 3280 1.705002 CCCATTGATACCCGGCCTGA 61.705 60.000 0.00 0.00 0.00 3.86
3133 3283 2.586425 CATTGATACCCGGCCTGAAAT 58.414 47.619 0.00 0.00 0.00 2.17
3135 3285 2.818751 TGATACCCGGCCTGAAATTT 57.181 45.000 0.00 0.00 0.00 1.82
3139 3289 2.296073 ACCCGGCCTGAAATTTGTTA 57.704 45.000 0.00 0.00 0.00 2.41
3145 3295 3.243569 CGGCCTGAAATTTGTTACACCAA 60.244 43.478 0.00 0.00 0.00 3.67
3155 3305 6.892658 ATTTGTTACACCAACTAGCAATCA 57.107 33.333 0.00 0.00 38.05 2.57
3165 3315 7.093640 ACACCAACTAGCAATCATTTGATCAAT 60.094 33.333 9.40 0.00 34.60 2.57
3169 3319 8.592155 CAACTAGCAATCATTTGATCAATTGTG 58.408 33.333 22.99 17.72 34.60 3.33
3176 3326 9.797556 CAATCATTTGATCAATTGTGATAGTGT 57.202 29.630 22.99 10.59 44.83 3.55
3177 3327 9.797556 AATCATTTGATCAATTGTGATAGTGTG 57.202 29.630 22.99 0.82 44.83 3.82
3178 3328 7.252708 TCATTTGATCAATTGTGATAGTGTGC 58.747 34.615 22.99 0.00 44.83 4.57
3179 3329 6.822667 TTTGATCAATTGTGATAGTGTGCT 57.177 33.333 9.40 0.00 44.83 4.40
3180 3330 7.920160 TTTGATCAATTGTGATAGTGTGCTA 57.080 32.000 9.40 0.00 44.83 3.49
3181 3331 6.908870 TGATCAATTGTGATAGTGTGCTAC 57.091 37.500 5.13 0.00 44.83 3.58
3182 3332 6.643388 TGATCAATTGTGATAGTGTGCTACT 58.357 36.000 5.13 0.12 44.83 2.57
3183 3333 7.105588 TGATCAATTGTGATAGTGTGCTACTT 58.894 34.615 5.13 0.00 44.83 2.24
3184 3334 6.726258 TCAATTGTGATAGTGTGCTACTTG 57.274 37.500 5.13 0.00 40.89 3.16
3185 3335 6.230472 TCAATTGTGATAGTGTGCTACTTGT 58.770 36.000 5.13 0.00 40.89 3.16
3186 3336 6.147656 TCAATTGTGATAGTGTGCTACTTGTG 59.852 38.462 5.13 0.00 40.89 3.33
3189 3339 3.123621 GTGATAGTGTGCTACTTGTGTGC 59.876 47.826 0.00 0.00 40.89 4.57
3209 3359 7.012138 TGTGTGCAAAATTTGTAAATCAGCAAT 59.988 29.630 7.60 0.00 33.93 3.56
3318 3470 6.916360 TGGAGTTTAAGGCTCAAATTGAAT 57.084 33.333 0.00 0.00 34.83 2.57
3343 3495 5.705905 GGGACCTCCATATTAGGAATTTTCG 59.294 44.000 7.71 0.00 37.20 3.46
3344 3496 5.181433 GGACCTCCATATTAGGAATTTTCGC 59.819 44.000 7.71 0.00 37.20 4.70
3358 3510 5.748630 GGAATTTTCGCTTTCAAGAACAGTT 59.251 36.000 0.00 0.00 0.00 3.16
3359 3511 6.915843 GGAATTTTCGCTTTCAAGAACAGTTA 59.084 34.615 0.00 0.00 0.00 2.24
3360 3512 7.595130 GGAATTTTCGCTTTCAAGAACAGTTAT 59.405 33.333 0.00 0.00 0.00 1.89
3361 3513 8.871686 AATTTTCGCTTTCAAGAACAGTTATT 57.128 26.923 0.00 0.00 0.00 1.40
3362 3514 7.678194 TTTTCGCTTTCAAGAACAGTTATTG 57.322 32.000 13.56 13.56 33.35 1.90
3363 3515 6.371809 TTCGCTTTCAAGAACAGTTATTGT 57.628 33.333 18.04 0.00 43.45 2.71
3387 3539 8.474025 TGTGTTTGGATTTCACAATTTCTAACT 58.526 29.630 0.00 0.00 38.80 2.24
3515 3683 9.748708 CAAAAGAATTTCACCTATCTCACAAAA 57.251 29.630 0.00 0.00 37.28 2.44
3576 3746 4.117685 ACGGTTTGAGTACAGAAACAGAC 58.882 43.478 19.44 7.55 0.00 3.51
3588 3758 3.489785 CAGAAACAGACGGTACACACTTC 59.510 47.826 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.497138 CAAAGGAGATGTGTGCACTGA 58.503 47.619 19.41 4.48 0.00 3.41
1 2 1.538512 CCAAAGGAGATGTGTGCACTG 59.461 52.381 19.41 3.36 0.00 3.66
2 3 1.901591 CCAAAGGAGATGTGTGCACT 58.098 50.000 19.41 0.00 0.00 4.40
4 5 0.178995 TGCCAAAGGAGATGTGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
5 6 1.133790 GATGCCAAAGGAGATGTGTGC 59.866 52.381 0.00 0.00 0.00 4.57
6 7 1.747355 GGATGCCAAAGGAGATGTGTG 59.253 52.381 0.00 0.00 0.00 3.82
7 8 1.341383 GGGATGCCAAAGGAGATGTGT 60.341 52.381 0.00 0.00 0.00 3.72
8 9 1.341285 TGGGATGCCAAAGGAGATGTG 60.341 52.381 2.13 0.00 0.00 3.21
9 10 1.002069 TGGGATGCCAAAGGAGATGT 58.998 50.000 2.13 0.00 0.00 3.06
10 11 1.396653 GTGGGATGCCAAAGGAGATG 58.603 55.000 7.86 0.00 0.00 2.90
11 12 0.259938 GGTGGGATGCCAAAGGAGAT 59.740 55.000 7.86 0.00 0.00 2.75
12 13 1.691219 GGTGGGATGCCAAAGGAGA 59.309 57.895 7.86 0.00 0.00 3.71
13 14 1.750399 CGGTGGGATGCCAAAGGAG 60.750 63.158 7.86 0.00 0.00 3.69
14 15 2.354729 CGGTGGGATGCCAAAGGA 59.645 61.111 7.86 0.00 0.00 3.36
15 16 3.451894 GCGGTGGGATGCCAAAGG 61.452 66.667 7.86 0.82 0.00 3.11
16 17 2.274645 TTGCGGTGGGATGCCAAAG 61.275 57.895 7.86 6.16 0.00 2.77
17 18 2.203552 TTGCGGTGGGATGCCAAA 60.204 55.556 7.86 0.00 0.00 3.28
18 19 2.988684 GTTGCGGTGGGATGCCAA 60.989 61.111 7.86 0.00 0.00 4.52
21 22 4.740822 AGGGTTGCGGTGGGATGC 62.741 66.667 0.00 0.00 0.00 3.91
22 23 2.438434 GAGGGTTGCGGTGGGATG 60.438 66.667 0.00 0.00 0.00 3.51
23 24 3.728373 GGAGGGTTGCGGTGGGAT 61.728 66.667 0.00 0.00 0.00 3.85
25 26 4.278513 TTGGAGGGTTGCGGTGGG 62.279 66.667 0.00 0.00 0.00 4.61
26 27 2.983592 GTTGGAGGGTTGCGGTGG 60.984 66.667 0.00 0.00 0.00 4.61
27 28 3.353836 CGTTGGAGGGTTGCGGTG 61.354 66.667 0.00 0.00 0.00 4.94
31 32 3.056328 GAGGCGTTGGAGGGTTGC 61.056 66.667 0.00 0.00 0.00 4.17
32 33 2.359975 GGAGGCGTTGGAGGGTTG 60.360 66.667 0.00 0.00 0.00 3.77
33 34 2.852075 TGGAGGCGTTGGAGGGTT 60.852 61.111 0.00 0.00 0.00 4.11
34 35 3.637273 GTGGAGGCGTTGGAGGGT 61.637 66.667 0.00 0.00 0.00 4.34
35 36 2.971598 ATGTGGAGGCGTTGGAGGG 61.972 63.158 0.00 0.00 0.00 4.30
36 37 1.746615 CATGTGGAGGCGTTGGAGG 60.747 63.158 0.00 0.00 0.00 4.30
37 38 2.401766 GCATGTGGAGGCGTTGGAG 61.402 63.158 0.00 0.00 0.00 3.86
38 39 2.359850 GCATGTGGAGGCGTTGGA 60.360 61.111 0.00 0.00 0.00 3.53
39 40 2.672651 TGCATGTGGAGGCGTTGG 60.673 61.111 0.00 0.00 0.00 3.77
40 41 2.693762 CCTGCATGTGGAGGCGTTG 61.694 63.158 7.65 0.00 46.55 4.10
41 42 2.360350 CCTGCATGTGGAGGCGTT 60.360 61.111 7.65 0.00 46.55 4.84
55 56 2.746375 ATACAAGGAGGGCGGCCTG 61.746 63.158 38.01 24.06 35.50 4.85
56 57 2.366972 ATACAAGGAGGGCGGCCT 60.367 61.111 33.40 33.40 37.35 5.19
57 58 1.692173 TACATACAAGGAGGGCGGCC 61.692 60.000 22.67 22.67 0.00 6.13
58 59 0.396811 ATACATACAAGGAGGGCGGC 59.603 55.000 0.00 0.00 0.00 6.53
59 60 2.930826 AATACATACAAGGAGGGCGG 57.069 50.000 0.00 0.00 0.00 6.13
60 61 4.036380 GGAAAAATACATACAAGGAGGGCG 59.964 45.833 0.00 0.00 0.00 6.13
61 62 4.341235 GGGAAAAATACATACAAGGAGGGC 59.659 45.833 0.00 0.00 0.00 5.19
62 63 4.893524 GGGGAAAAATACATACAAGGAGGG 59.106 45.833 0.00 0.00 0.00 4.30
63 64 4.893524 GGGGGAAAAATACATACAAGGAGG 59.106 45.833 0.00 0.00 0.00 4.30
64 65 5.766590 AGGGGGAAAAATACATACAAGGAG 58.233 41.667 0.00 0.00 0.00 3.69
65 66 5.806955 AGGGGGAAAAATACATACAAGGA 57.193 39.130 0.00 0.00 0.00 3.36
66 67 6.867519 AAAGGGGGAAAAATACATACAAGG 57.132 37.500 0.00 0.00 0.00 3.61
89 90 6.478129 ACTTGATCGACTATAACCCCAAAAA 58.522 36.000 0.00 0.00 0.00 1.94
90 91 6.057321 ACTTGATCGACTATAACCCCAAAA 57.943 37.500 0.00 0.00 0.00 2.44
91 92 5.687166 ACTTGATCGACTATAACCCCAAA 57.313 39.130 0.00 0.00 0.00 3.28
92 93 5.687166 AACTTGATCGACTATAACCCCAA 57.313 39.130 0.00 0.00 0.00 4.12
93 94 5.687166 AAACTTGATCGACTATAACCCCA 57.313 39.130 0.00 0.00 0.00 4.96
94 95 7.495055 TCTAAAACTTGATCGACTATAACCCC 58.505 38.462 0.00 0.00 0.00 4.95
101 102 9.582431 CAGGTTTATCTAAAACTTGATCGACTA 57.418 33.333 6.85 0.00 40.09 2.59
102 103 8.311836 TCAGGTTTATCTAAAACTTGATCGACT 58.688 33.333 10.29 0.00 40.09 4.18
103 104 8.475331 TCAGGTTTATCTAAAACTTGATCGAC 57.525 34.615 10.29 0.00 40.09 4.20
104 105 8.528643 TCTCAGGTTTATCTAAAACTTGATCGA 58.471 33.333 13.56 7.76 40.09 3.59
105 106 8.703604 TCTCAGGTTTATCTAAAACTTGATCG 57.296 34.615 13.56 6.01 40.09 3.69
114 115 9.436957 GTGTGAAGAATCTCAGGTTTATCTAAA 57.563 33.333 0.00 0.00 30.21 1.85
115 116 8.816894 AGTGTGAAGAATCTCAGGTTTATCTAA 58.183 33.333 0.00 0.00 30.21 2.10
116 117 8.367660 AGTGTGAAGAATCTCAGGTTTATCTA 57.632 34.615 0.00 0.00 30.21 1.98
117 118 7.251321 AGTGTGAAGAATCTCAGGTTTATCT 57.749 36.000 0.00 0.00 30.21 1.98
118 119 7.913674 AAGTGTGAAGAATCTCAGGTTTATC 57.086 36.000 0.00 0.00 30.21 1.75
119 120 9.220767 GTAAAGTGTGAAGAATCTCAGGTTTAT 57.779 33.333 0.00 0.00 29.94 1.40
120 121 7.660208 GGTAAAGTGTGAAGAATCTCAGGTTTA 59.340 37.037 0.00 0.00 30.21 2.01
121 122 6.486993 GGTAAAGTGTGAAGAATCTCAGGTTT 59.513 38.462 0.00 0.00 30.21 3.27
122 123 5.998363 GGTAAAGTGTGAAGAATCTCAGGTT 59.002 40.000 0.00 0.00 30.21 3.50
123 124 5.308237 AGGTAAAGTGTGAAGAATCTCAGGT 59.692 40.000 0.00 0.00 30.21 4.00
124 125 5.799213 AGGTAAAGTGTGAAGAATCTCAGG 58.201 41.667 0.00 0.00 30.21 3.86
125 126 8.307483 TCTTAGGTAAAGTGTGAAGAATCTCAG 58.693 37.037 0.00 0.00 36.51 3.35
126 127 8.190326 TCTTAGGTAAAGTGTGAAGAATCTCA 57.810 34.615 0.00 0.00 36.51 3.27
127 128 9.145865 CTTCTTAGGTAAAGTGTGAAGAATCTC 57.854 37.037 0.00 0.00 36.51 2.75
128 129 8.652290 ACTTCTTAGGTAAAGTGTGAAGAATCT 58.348 33.333 0.00 0.00 34.52 2.40
129 130 8.713271 CACTTCTTAGGTAAAGTGTGAAGAATC 58.287 37.037 0.00 0.00 44.65 2.52
130 131 8.608844 CACTTCTTAGGTAAAGTGTGAAGAAT 57.391 34.615 0.00 0.00 44.65 2.40
139 140 6.256643 TGAAACCCACTTCTTAGGTAAAGT 57.743 37.500 0.00 0.00 36.51 2.66
140 141 8.893727 CATATGAAACCCACTTCTTAGGTAAAG 58.106 37.037 0.00 0.00 36.45 1.85
141 142 7.338449 GCATATGAAACCCACTTCTTAGGTAAA 59.662 37.037 6.97 0.00 32.21 2.01
142 143 6.826741 GCATATGAAACCCACTTCTTAGGTAA 59.173 38.462 6.97 0.00 32.21 2.85
143 144 6.157994 AGCATATGAAACCCACTTCTTAGGTA 59.842 38.462 6.97 0.00 32.21 3.08
144 145 5.044846 AGCATATGAAACCCACTTCTTAGGT 60.045 40.000 6.97 0.00 34.60 3.08
145 146 5.297776 CAGCATATGAAACCCACTTCTTAGG 59.702 44.000 6.97 0.00 0.00 2.69
146 147 5.882557 ACAGCATATGAAACCCACTTCTTAG 59.117 40.000 6.97 0.00 0.00 2.18
147 148 5.815581 ACAGCATATGAAACCCACTTCTTA 58.184 37.500 6.97 0.00 0.00 2.10
148 149 4.666512 ACAGCATATGAAACCCACTTCTT 58.333 39.130 6.97 0.00 0.00 2.52
149 150 4.307032 ACAGCATATGAAACCCACTTCT 57.693 40.909 6.97 0.00 0.00 2.85
150 151 5.183904 AGAAACAGCATATGAAACCCACTTC 59.816 40.000 6.97 0.00 0.00 3.01
151 152 5.079643 AGAAACAGCATATGAAACCCACTT 58.920 37.500 6.97 0.00 0.00 3.16
152 153 4.666512 AGAAACAGCATATGAAACCCACT 58.333 39.130 6.97 0.00 0.00 4.00
153 154 4.458989 TGAGAAACAGCATATGAAACCCAC 59.541 41.667 6.97 0.00 0.00 4.61
154 155 4.661222 TGAGAAACAGCATATGAAACCCA 58.339 39.130 6.97 0.00 0.00 4.51
155 156 4.943705 TCTGAGAAACAGCATATGAAACCC 59.056 41.667 6.97 0.00 45.38 4.11
156 157 6.493116 CATCTGAGAAACAGCATATGAAACC 58.507 40.000 6.97 0.00 45.38 3.27
157 158 5.970023 GCATCTGAGAAACAGCATATGAAAC 59.030 40.000 6.97 0.00 45.38 2.78
158 159 5.648960 TGCATCTGAGAAACAGCATATGAAA 59.351 36.000 6.97 0.00 45.38 2.69
199 200 8.976353 AGTATTGCACCATTTACCATGAAATAA 58.024 29.630 0.00 0.00 0.00 1.40
205 206 7.939782 TGAATAGTATTGCACCATTTACCATG 58.060 34.615 0.00 0.00 0.00 3.66
244 245 3.008266 TGGACTGCAAGATGAAGACATGA 59.992 43.478 0.00 0.00 36.82 3.07
256 257 6.149973 TGAAGTTAAATCAGATGGACTGCAAG 59.850 38.462 0.00 0.00 45.38 4.01
282 283 5.014858 CCAGTAAGTCAGTAGTACCCTCAA 58.985 45.833 0.00 0.00 0.00 3.02
290 291 4.283722 CAGGTTTCCCAGTAAGTCAGTAGT 59.716 45.833 0.00 0.00 0.00 2.73
309 310 1.542915 GCAATGCATGTCAGAACAGGT 59.457 47.619 0.00 0.00 39.36 4.00
313 314 2.984471 CAACAGCAATGCATGTCAGAAC 59.016 45.455 8.35 0.00 0.00 3.01
319 320 3.794717 TCAAAACAACAGCAATGCATGT 58.205 36.364 8.35 6.76 0.00 3.21
320 321 4.797693 TTCAAAACAACAGCAATGCATG 57.202 36.364 8.35 6.07 0.00 4.06
344 347 6.974622 GCCCTGACATTGTATTATTGTTTCAG 59.025 38.462 0.00 0.00 0.00 3.02
346 349 6.751888 GTGCCCTGACATTGTATTATTGTTTC 59.248 38.462 0.00 0.00 0.00 2.78
350 353 5.734220 GCAGTGCCCTGACATTGTATTATTG 60.734 44.000 2.85 0.00 41.50 1.90
351 354 4.339247 GCAGTGCCCTGACATTGTATTATT 59.661 41.667 2.85 0.00 41.50 1.40
353 356 3.278574 GCAGTGCCCTGACATTGTATTA 58.721 45.455 2.85 0.00 41.50 0.98
358 377 0.892755 AATGCAGTGCCCTGACATTG 59.107 50.000 13.72 0.00 40.58 2.82
371 390 7.514125 GCGTATTTTTAATGAGCAGAAATGCAG 60.514 37.037 2.73 0.00 37.25 4.41
728 779 3.649843 TGGGTAGTTGGGTACTGGATAG 58.350 50.000 0.00 0.00 37.73 2.08
740 791 5.445069 TGGAATGTATGGATTGGGTAGTTG 58.555 41.667 0.00 0.00 0.00 3.16
802 853 3.426525 GTGCAAAGTTTCAACATAGCAGC 59.573 43.478 0.00 0.00 33.77 5.25
840 891 7.844100 GATGCTTCTGGTCATCACGTTTTCG 62.844 48.000 0.00 0.00 39.02 3.46
873 924 6.366877 CGCAGAAACCAAATTGATCAGATTTT 59.633 34.615 11.01 4.56 0.00 1.82
874 925 5.865552 CGCAGAAACCAAATTGATCAGATTT 59.134 36.000 0.00 3.09 0.00 2.17
875 926 5.183713 TCGCAGAAACCAAATTGATCAGATT 59.816 36.000 0.00 0.00 0.00 2.40
876 927 4.701651 TCGCAGAAACCAAATTGATCAGAT 59.298 37.500 0.00 0.00 0.00 2.90
877 928 4.071423 TCGCAGAAACCAAATTGATCAGA 58.929 39.130 0.00 0.00 0.00 3.27
878 929 4.424061 TCGCAGAAACCAAATTGATCAG 57.576 40.909 0.00 0.00 0.00 2.90
954 1007 5.992217 CCTTTCCGATTATCTTACAAGGAGG 59.008 44.000 0.00 0.00 32.72 4.30
959 1012 6.354130 CCCTTCCTTTCCGATTATCTTACAA 58.646 40.000 0.00 0.00 0.00 2.41
969 1022 0.543749 CTGAGCCCTTCCTTTCCGAT 59.456 55.000 0.00 0.00 0.00 4.18
987 1040 0.625316 TGCCCATGTCTATGTTGGCT 59.375 50.000 6.86 0.00 40.34 4.75
1182 1263 0.896923 GGAAACCATGCCATTGCTGA 59.103 50.000 0.00 0.00 38.71 4.26
1258 1339 0.034476 CAGAGCTGGCTGTGAACTCA 59.966 55.000 13.41 0.00 39.36 3.41
1282 1363 4.193865 TCCATGTGATAATGCAGACACAG 58.806 43.478 17.79 12.09 44.39 3.66
1326 1415 3.956744 AGAAGAACCCAGCCAAGAATAC 58.043 45.455 0.00 0.00 0.00 1.89
1339 1428 3.077359 CAGACCACCATCAAGAAGAACC 58.923 50.000 0.00 0.00 0.00 3.62
1358 1447 4.615588 TTAAACCAAAGGAAATGGCCAG 57.384 40.909 13.05 0.00 41.89 4.85
1359 1448 6.688073 TTATTAAACCAAAGGAAATGGCCA 57.312 33.333 8.56 8.56 41.89 5.36
1382 1471 5.352284 ACATCTTCGCGAAAGAACAGATAT 58.648 37.500 23.54 7.10 46.85 1.63
1383 1472 4.744570 ACATCTTCGCGAAAGAACAGATA 58.255 39.130 23.54 0.00 46.85 1.98
1384 1473 3.589988 ACATCTTCGCGAAAGAACAGAT 58.410 40.909 23.54 17.10 46.85 2.90
1566 1655 6.293004 TGGTGAAAACCTTCAGAATGTTTT 57.707 33.333 22.25 22.25 42.27 2.43
1567 1656 5.930837 TGGTGAAAACCTTCAGAATGTTT 57.069 34.783 9.98 9.98 42.27 2.83
1572 1661 7.230747 TCAGAATATGGTGAAAACCTTCAGAA 58.769 34.615 0.00 0.00 42.27 3.02
1574 1663 7.452880 TTCAGAATATGGTGAAAACCTTCAG 57.547 36.000 0.00 0.00 42.27 3.02
1609 1698 7.254387 GCATAACAAGCTGAAATTTCAACAACA 60.254 33.333 20.82 5.01 36.64 3.33
1615 1704 5.243507 TCTGGCATAACAAGCTGAAATTTCA 59.756 36.000 19.45 19.45 35.57 2.69
1616 1705 5.713025 TCTGGCATAACAAGCTGAAATTTC 58.287 37.500 11.41 11.41 0.00 2.17
1717 1806 9.534565 TTCAACATCAAGAATACTCAGCTATAC 57.465 33.333 0.00 0.00 0.00 1.47
1727 1816 8.976986 AAATGCTCTTTCAACATCAAGAATAC 57.023 30.769 0.00 0.00 0.00 1.89
1736 1825 8.571461 TCAGATTAGAAATGCTCTTTCAACAT 57.429 30.769 12.73 4.03 35.41 2.71
1783 1872 7.010160 ACCTTCATTTCTGTCCAAATTTAGGA 58.990 34.615 5.55 5.55 32.65 2.94
1787 1876 5.602145 TCCACCTTCATTTCTGTCCAAATTT 59.398 36.000 0.00 0.00 0.00 1.82
1876 1965 3.897239 TCCGGATGCCACTGAAATTTAT 58.103 40.909 0.00 0.00 0.00 1.40
1881 1970 0.394216 CCATCCGGATGCCACTGAAA 60.394 55.000 34.77 0.00 37.49 2.69
1890 1979 2.878406 GGATACAAACACCATCCGGATG 59.122 50.000 33.52 33.52 38.51 3.51
1965 2055 7.559897 AGGTAATAAGACCCAACAATATTGGTG 59.440 37.037 24.01 24.01 45.32 4.17
1966 2056 7.648770 AGGTAATAAGACCCAACAATATTGGT 58.351 34.615 19.37 10.56 40.74 3.67
1967 2057 7.777910 TGAGGTAATAAGACCCAACAATATTGG 59.222 37.037 19.37 3.50 40.74 3.16
1968 2058 8.746052 TGAGGTAATAAGACCCAACAATATTG 57.254 34.615 14.01 14.01 40.74 1.90
1969 2059 8.557450 ACTGAGGTAATAAGACCCAACAATATT 58.443 33.333 0.00 0.00 40.74 1.28
1970 2060 7.993183 CACTGAGGTAATAAGACCCAACAATAT 59.007 37.037 0.00 0.00 40.74 1.28
1971 2061 7.335627 CACTGAGGTAATAAGACCCAACAATA 58.664 38.462 0.00 0.00 40.74 1.90
1972 2062 6.180472 CACTGAGGTAATAAGACCCAACAAT 58.820 40.000 0.00 0.00 40.74 2.71
1973 2063 5.556915 CACTGAGGTAATAAGACCCAACAA 58.443 41.667 0.00 0.00 40.74 2.83
1974 2064 4.564821 GCACTGAGGTAATAAGACCCAACA 60.565 45.833 0.00 0.00 40.74 3.33
2001 2091 8.721478 ACAGTTATATTAGTGTTGCTTTCAGTG 58.279 33.333 0.00 0.00 0.00 3.66
2293 2394 9.183368 TGTCAGGCATTTATGTCATGTAAAATA 57.817 29.630 0.00 0.00 34.11 1.40
2294 2395 8.065473 TGTCAGGCATTTATGTCATGTAAAAT 57.935 30.769 0.00 0.00 34.11 1.82
2402 2503 3.188667 GCTTAAAAGACAAGGTCCCTTCG 59.811 47.826 0.00 0.00 33.42 3.79
2462 2563 5.855045 ACTGAAGGTACCTTGTAACTTGAG 58.145 41.667 31.81 11.92 36.26 3.02
2527 2628 9.965902 AGAAGACATTAAGTTTCCAGAATATGT 57.034 29.630 0.00 0.00 0.00 2.29
2529 2630 8.897752 GCAGAAGACATTAAGTTTCCAGAATAT 58.102 33.333 0.00 0.00 0.00 1.28
2530 2631 7.882791 TGCAGAAGACATTAAGTTTCCAGAATA 59.117 33.333 0.00 0.00 0.00 1.75
2531 2632 6.716628 TGCAGAAGACATTAAGTTTCCAGAAT 59.283 34.615 0.00 0.00 0.00 2.40
2532 2633 6.061441 TGCAGAAGACATTAAGTTTCCAGAA 58.939 36.000 0.00 0.00 0.00 3.02
2533 2634 5.620206 TGCAGAAGACATTAAGTTTCCAGA 58.380 37.500 0.00 0.00 0.00 3.86
2534 2635 5.947228 TGCAGAAGACATTAAGTTTCCAG 57.053 39.130 0.00 0.00 0.00 3.86
2535 2636 7.415541 GCATATGCAGAAGACATTAAGTTTCCA 60.416 37.037 22.84 0.00 41.59 3.53
2536 2637 6.914757 GCATATGCAGAAGACATTAAGTTTCC 59.085 38.462 22.84 0.00 41.59 3.13
2537 2638 7.701445 AGCATATGCAGAAGACATTAAGTTTC 58.299 34.615 28.62 0.00 45.16 2.78
2538 2639 7.555554 AGAGCATATGCAGAAGACATTAAGTTT 59.444 33.333 28.62 2.11 45.16 2.66
2539 2640 7.052873 AGAGCATATGCAGAAGACATTAAGTT 58.947 34.615 28.62 2.51 45.16 2.66
2540 2641 6.590068 AGAGCATATGCAGAAGACATTAAGT 58.410 36.000 28.62 3.20 45.16 2.24
2541 2642 7.226128 TGAAGAGCATATGCAGAAGACATTAAG 59.774 37.037 28.62 0.00 45.16 1.85
2552 2671 3.806380 AGGAAGTGAAGAGCATATGCAG 58.194 45.455 28.62 0.00 45.16 4.41
2645 2764 9.499585 CAATCAAGTGCTTCATATGAACTTAAG 57.500 33.333 14.23 5.57 0.00 1.85
2711 2830 2.404215 CCACCACGTACTTTCAGACAG 58.596 52.381 0.00 0.00 0.00 3.51
2834 2953 7.772332 TCTAGCGAAATCATTTTAAGAGGAC 57.228 36.000 0.00 0.00 0.00 3.85
2910 3029 5.347093 GCGTCACCATATAACATCATGAGAG 59.653 44.000 0.09 0.00 0.00 3.20
2952 3100 2.949644 GTTGTTTGTAGAACACCTGCCT 59.050 45.455 0.00 0.00 0.00 4.75
2959 3107 6.597672 ACACATCAGAAGTTGTTTGTAGAACA 59.402 34.615 0.00 0.00 30.29 3.18
3001 3150 8.322091 GGTATCTGTATATGCTGGGTATTTCTT 58.678 37.037 0.00 0.00 0.00 2.52
3041 3190 6.403964 GCCATATTGACATGGTACTATGCATG 60.404 42.308 18.24 12.64 46.21 4.06
3043 3192 5.003160 GCCATATTGACATGGTACTATGCA 58.997 41.667 18.24 13.96 46.21 3.96
3044 3193 5.003160 TGCCATATTGACATGGTACTATGC 58.997 41.667 18.24 11.76 46.21 3.14
3080 3230 6.151144 AGGTGTGTTGTAATAAAGAATCTGCC 59.849 38.462 0.00 0.00 0.00 4.85
3098 3248 5.891551 GGTATCAATGGGAAATAAGGTGTGT 59.108 40.000 0.00 0.00 0.00 3.72
3104 3254 3.506067 GCCGGGTATCAATGGGAAATAAG 59.494 47.826 2.18 0.00 0.00 1.73
3107 3257 1.480498 GGCCGGGTATCAATGGGAAAT 60.480 52.381 2.18 0.00 0.00 2.17
3126 3276 6.149633 GCTAGTTGGTGTAACAAATTTCAGG 58.850 40.000 0.00 0.00 41.88 3.86
3127 3277 6.734137 TGCTAGTTGGTGTAACAAATTTCAG 58.266 36.000 0.00 0.00 41.88 3.02
3128 3278 6.701145 TGCTAGTTGGTGTAACAAATTTCA 57.299 33.333 0.00 0.00 41.88 2.69
3129 3279 7.865385 TGATTGCTAGTTGGTGTAACAAATTTC 59.135 33.333 0.00 0.00 41.88 2.17
3130 3280 7.721402 TGATTGCTAGTTGGTGTAACAAATTT 58.279 30.769 0.00 0.00 41.88 1.82
3133 3283 6.892658 ATGATTGCTAGTTGGTGTAACAAA 57.107 33.333 0.00 0.00 41.88 2.83
3135 3285 6.488344 TCAAATGATTGCTAGTTGGTGTAACA 59.512 34.615 0.00 0.00 37.82 2.41
3139 3289 5.711506 TGATCAAATGATTGCTAGTTGGTGT 59.288 36.000 0.00 0.00 36.45 4.16
3145 3295 8.058667 TCACAATTGATCAAATGATTGCTAGT 57.941 30.769 26.44 2.32 36.45 2.57
3155 3305 7.400599 AGCACACTATCACAATTGATCAAAT 57.599 32.000 13.09 0.02 41.87 2.32
3165 3315 4.749598 CACACAAGTAGCACACTATCACAA 59.250 41.667 0.00 0.00 36.04 3.33
3169 3319 3.325870 TGCACACAAGTAGCACACTATC 58.674 45.455 0.00 0.00 36.04 2.08
3172 3322 2.036958 TTGCACACAAGTAGCACACT 57.963 45.000 0.00 0.00 38.11 3.55
3176 3326 4.753233 ACAAATTTTGCACACAAGTAGCA 58.247 34.783 9.04 0.00 37.04 3.49
3177 3327 6.820470 TTACAAATTTTGCACACAAGTAGC 57.180 33.333 9.04 0.00 37.04 3.58
3178 3328 9.029243 TGATTTACAAATTTTGCACACAAGTAG 57.971 29.630 9.04 0.00 37.04 2.57
3179 3329 8.932945 TGATTTACAAATTTTGCACACAAGTA 57.067 26.923 9.04 0.00 37.04 2.24
3180 3330 7.465781 GCTGATTTACAAATTTTGCACACAAGT 60.466 33.333 9.04 0.00 37.04 3.16
3181 3331 6.847289 GCTGATTTACAAATTTTGCACACAAG 59.153 34.615 9.04 2.84 37.04 3.16
3182 3332 6.314648 TGCTGATTTACAAATTTTGCACACAA 59.685 30.769 9.04 0.00 0.00 3.33
3183 3333 5.814188 TGCTGATTTACAAATTTTGCACACA 59.186 32.000 9.04 3.53 0.00 3.72
3184 3334 6.284475 TGCTGATTTACAAATTTTGCACAC 57.716 33.333 9.04 0.00 0.00 3.82
3185 3335 6.915544 TTGCTGATTTACAAATTTTGCACA 57.084 29.167 9.04 2.62 32.40 4.57
3209 3359 6.989759 ACACAATAGCACCGATATGAACAATA 59.010 34.615 0.00 0.00 0.00 1.90
3221 3371 0.874390 AACTGCACACAATAGCACCG 59.126 50.000 0.00 0.00 36.62 4.94
3266 3418 9.618890 CCTGGATATAAACATGGATATCGATTT 57.381 33.333 1.71 0.00 36.35 2.17
3267 3419 8.772250 ACCTGGATATAAACATGGATATCGATT 58.228 33.333 1.71 0.00 36.35 3.34
3288 3440 3.199946 TGAGCCTTAAACTCCATACCTGG 59.800 47.826 0.00 0.00 44.64 4.45
3298 3450 5.779771 TCCCATTCAATTTGAGCCTTAAACT 59.220 36.000 0.00 0.00 0.00 2.66
3307 3459 3.700538 TGGAGGTCCCATTCAATTTGAG 58.299 45.455 0.00 0.00 40.82 3.02
3343 3495 7.254084 CCAAACACAATAACTGTTCTTGAAAGC 60.254 37.037 20.98 0.00 35.47 3.51
3344 3496 7.973388 TCCAAACACAATAACTGTTCTTGAAAG 59.027 33.333 20.98 13.70 35.47 2.62
3361 3513 8.474025 AGTTAGAAATTGTGAAATCCAAACACA 58.526 29.630 0.00 0.00 41.70 3.72
3362 3514 8.871686 AGTTAGAAATTGTGAAATCCAAACAC 57.128 30.769 0.00 0.00 35.45 3.32
3387 3539 8.846211 CAAGGAAGTTAAGAATTGTGTTCCTTA 58.154 33.333 15.45 1.33 43.62 2.69
3409 3565 7.065324 TCTGTAGTGAAACACAAAAGTACAAGG 59.935 37.037 0.00 0.00 41.43 3.61
3515 3683 6.777580 AGTTTCCTTGTTTCTGTACCATGAAT 59.222 34.615 0.00 0.00 0.00 2.57
3588 3758 6.626302 TGGTTTTCTGAGTTTTGTTAACTGG 58.374 36.000 7.22 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.