Multiple sequence alignment - TraesCS2D01G055200

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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 TraesCS2D01G055200 chr2D 100.000 2821 0 0 1 2821 22154271 22157091 0.000000e+00 5210.0
1 TraesCS2D01G055200 chr2D 87.024 1025 110 16 1811 2821 22145273 22146288 0.000000e+00 1134.0
2 TraesCS2D01G055200 chr2D 89.189 703 73 1 1000 1702 22119376 22120075 0.000000e+00 874.0
3 TraesCS2D01G055200 chr2D 81.590 956 152 17 1865 2808 22120747 22121690 0.000000e+00 769.0
4 TraesCS2D01G055200 chr2D 87.130 676 71 10 1059 1727 22144357 22145023 0.000000e+00 752.0
5 TraesCS2D01G055200 chr2D 83.761 117 14 4 324 439 333511020 333511132 3.840000e-19 106.0
6 TraesCS2D01G055200 chr2D 100.000 31 0 0 898 928 22144224 22144254 1.090000e-04 58.4
7 TraesCS2D01G055200 chr2B 89.168 1394 103 19 1470 2821 35135149 35136536 0.000000e+00 1694.0
8 TraesCS2D01G055200 chr2B 83.201 1256 172 26 1575 2821 35283898 35285123 0.000000e+00 1114.0
9 TraesCS2D01G055200 chr2B 86.523 972 114 13 1823 2789 35276717 35277676 0.000000e+00 1053.0
10 TraesCS2D01G055200 chr2B 80.907 1257 176 34 1575 2821 35312304 35313506 0.000000e+00 933.0
11 TraesCS2D01G055200 chr2B 84.654 795 105 13 2030 2817 35309193 35309977 0.000000e+00 776.0
12 TraesCS2D01G055200 chr2B 92.213 488 22 2 889 1376 35134680 35135151 0.000000e+00 676.0
13 TraesCS2D01G055200 chr2B 91.342 462 29 8 314 774 35134173 35134624 3.090000e-174 621.0
14 TraesCS2D01G055200 chr2B 90.909 165 14 1 154 317 35133974 35134138 1.320000e-53 220.0
15 TraesCS2D01G055200 chr2A 85.700 1021 113 13 1811 2821 23971526 23972523 0.000000e+00 1046.0
16 TraesCS2D01G055200 chr2A 87.593 806 84 13 898 1700 23958705 23959497 0.000000e+00 920.0
17 TraesCS2D01G055200 chr2A 82.113 956 147 18 1865 2808 23960065 23961008 0.000000e+00 797.0
18 TraesCS2D01G055200 chr2A 87.406 667 66 11 1059 1718 23970777 23971432 0.000000e+00 750.0
19 TraesCS2D01G055200 chr2A 82.716 162 24 4 154 315 213090989 213090832 1.050000e-29 141.0
20 TraesCS2D01G055200 chr5D 86.560 811 84 20 898 1698 75913291 75912496 0.000000e+00 870.0
21 TraesCS2D01G055200 chr5D 83.611 720 103 10 1019 1730 229153992 229153280 0.000000e+00 662.0
22 TraesCS2D01G055200 chr5D 79.787 564 79 20 2048 2607 75761037 75760505 7.380000e-101 377.0
23 TraesCS2D01G055200 chr5D 84.677 124 17 1 157 280 335213993 335213872 3.820000e-24 122.0
24 TraesCS2D01G055200 chr5A 83.472 720 104 9 1019 1730 327573875 327574587 0.000000e+00 656.0
25 TraesCS2D01G055200 chr5A 82.857 140 20 4 303 438 599274609 599274470 3.820000e-24 122.0
26 TraesCS2D01G055200 chr7D 90.254 472 46 0 1104 1575 403146433 403145962 3.990000e-173 617.0
27 TraesCS2D01G055200 chr7D 77.636 313 35 17 156 438 215789381 215789688 1.050000e-34 158.0
28 TraesCS2D01G055200 chr6D 90.042 472 47 0 1104 1575 29985847 29985376 1.860000e-171 612.0
29 TraesCS2D01G055200 chr5B 83.556 450 54 11 898 1347 84623775 84623346 1.220000e-108 403.0
30 TraesCS2D01G055200 chr7A 85.470 117 15 2 324 438 514669272 514669156 1.370000e-23 121.0
31 TraesCS2D01G055200 chr3B 83.333 126 17 4 314 437 45516340 45516463 2.300000e-21 113.0
32 TraesCS2D01G055200 chr4A 86.139 101 10 4 323 421 114769084 114769182 3.840000e-19 106.0
33 TraesCS2D01G055200 chr1D 80.916 131 21 4 308 436 113922075 113922203 1.790000e-17 100.0
34 TraesCS2D01G055200 chr1B 77.778 171 26 8 300 461 24775597 24775764 8.320000e-16 95.3
35 TraesCS2D01G055200 chr4D 88.571 70 7 1 154 223 353911925 353911993 1.800000e-12 84.2
36 TraesCS2D01G055200 chr6B 81.429 70 11 2 154 223 290186654 290186587 3.930000e-04 56.5


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 TraesCS2D01G055200 chr2D 22154271 22157091 2820 False 5210.000000 5210 100.000000 1 2821 1 chr2D.!!$F1 2820
1 TraesCS2D01G055200 chr2D 22119376 22121690 2314 False 821.500000 874 85.389500 1000 2808 2 chr2D.!!$F3 1808
2 TraesCS2D01G055200 chr2D 22144224 22146288 2064 False 648.133333 1134 91.384667 898 2821 3 chr2D.!!$F4 1923
3 TraesCS2D01G055200 chr2B 35283898 35285123 1225 False 1114.000000 1114 83.201000 1575 2821 1 chr2B.!!$F2 1246
4 TraesCS2D01G055200 chr2B 35276717 35277676 959 False 1053.000000 1053 86.523000 1823 2789 1 chr2B.!!$F1 966
5 TraesCS2D01G055200 chr2B 35309193 35313506 4313 False 854.500000 933 82.780500 1575 2821 2 chr2B.!!$F4 1246
6 TraesCS2D01G055200 chr2B 35133974 35136536 2562 False 802.750000 1694 90.908000 154 2821 4 chr2B.!!$F3 2667
7 TraesCS2D01G055200 chr2A 23970777 23972523 1746 False 898.000000 1046 86.553000 1059 2821 2 chr2A.!!$F2 1762
8 TraesCS2D01G055200 chr2A 23958705 23961008 2303 False 858.500000 920 84.853000 898 2808 2 chr2A.!!$F1 1910
9 TraesCS2D01G055200 chr5D 75912496 75913291 795 True 870.000000 870 86.560000 898 1698 1 chr5D.!!$R2 800
10 TraesCS2D01G055200 chr5D 229153280 229153992 712 True 662.000000 662 83.611000 1019 1730 1 chr5D.!!$R3 711
11 TraesCS2D01G055200 chr5D 75760505 75761037 532 True 377.000000 377 79.787000 2048 2607 1 chr5D.!!$R1 559
12 TraesCS2D01G055200 chr5A 327573875 327574587 712 False 656.000000 656 83.472000 1019 1730 1 chr5A.!!$F1 711

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
870 910 0.179156 TTTGACTATCCCGACGCGAC 60.179 55.0 15.93 5.54 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 4755 0.233848 GAGGTACACCGCAAACAACG 59.766 55.0 0.0 0.0 42.08 4.1 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 2.238942 CCTGAAAAAGCAACCAACCC 57.761 50.000 0.00 0.00 0.00 4.11
20 21 1.202639 CCTGAAAAAGCAACCAACCCC 60.203 52.381 0.00 0.00 0.00 4.95
24 25 0.762842 AAAAGCAACCAACCCCTCCC 60.763 55.000 0.00 0.00 0.00 4.30
25 26 2.994643 AAAGCAACCAACCCCTCCCG 62.995 60.000 0.00 0.00 0.00 5.14
27 28 4.278513 CAACCAACCCCTCCCGCA 62.279 66.667 0.00 0.00 0.00 5.69
28 29 4.280019 AACCAACCCCTCCCGCAC 62.280 66.667 0.00 0.00 0.00 5.34
36 37 3.564027 CCTCCCGCACGCGAAATC 61.564 66.667 15.93 0.00 42.83 2.17
37 38 2.813474 CTCCCGCACGCGAAATCA 60.813 61.111 15.93 0.00 42.83 2.57
39 40 3.118454 CCCGCACGCGAAATCACT 61.118 61.111 15.93 0.00 42.83 3.41
41 42 1.151777 CCCGCACGCGAAATCACTAT 61.152 55.000 15.93 0.00 42.83 2.12
43 44 1.062002 CCGCACGCGAAATCACTATTT 59.938 47.619 15.93 0.00 42.83 1.40
51 52 2.974165 GAAATCACTATTTCGGCGCTG 58.026 47.619 10.86 10.86 41.09 5.18
52 53 2.024176 AATCACTATTTCGGCGCTGT 57.976 45.000 17.37 0.00 0.00 4.40
53 54 2.882927 ATCACTATTTCGGCGCTGTA 57.117 45.000 17.37 3.07 0.00 2.74
54 55 2.658373 TCACTATTTCGGCGCTGTAA 57.342 45.000 17.37 13.97 0.00 2.41
57 58 3.369756 TCACTATTTCGGCGCTGTAAAAG 59.630 43.478 17.37 12.25 0.00 2.27
59 60 3.749609 ACTATTTCGGCGCTGTAAAAGTT 59.250 39.130 17.37 0.18 0.00 2.66
60 61 3.636282 ATTTCGGCGCTGTAAAAGTTT 57.364 38.095 17.37 0.00 0.00 2.66
61 62 3.423996 TTTCGGCGCTGTAAAAGTTTT 57.576 38.095 17.37 6.06 0.00 2.43
62 63 3.423996 TTCGGCGCTGTAAAAGTTTTT 57.576 38.095 17.37 0.00 0.00 1.94
78 79 2.376915 TTTTTAGCGCACGTCTGTTG 57.623 45.000 11.47 0.00 0.00 3.33
79 80 0.584396 TTTTAGCGCACGTCTGTTGG 59.416 50.000 11.47 0.00 0.00 3.77
80 81 0.249531 TTTAGCGCACGTCTGTTGGA 60.250 50.000 11.47 0.00 0.00 3.53
81 82 0.666274 TTAGCGCACGTCTGTTGGAG 60.666 55.000 11.47 0.00 0.00 3.86
82 83 1.520600 TAGCGCACGTCTGTTGGAGA 61.521 55.000 11.47 0.00 0.00 3.71
84 85 1.959899 GCGCACGTCTGTTGGAGATG 61.960 60.000 0.30 0.00 42.73 2.90
85 86 1.790387 GCACGTCTGTTGGAGATGC 59.210 57.895 0.00 0.00 40.97 3.91
87 88 1.354040 CACGTCTGTTGGAGATGCTC 58.646 55.000 0.00 0.00 40.97 4.26
88 89 1.067283 CACGTCTGTTGGAGATGCTCT 60.067 52.381 0.00 0.00 40.97 4.09
89 90 1.620819 ACGTCTGTTGGAGATGCTCTT 59.379 47.619 0.00 0.00 40.97 2.85
90 91 2.826128 ACGTCTGTTGGAGATGCTCTTA 59.174 45.455 0.00 0.00 40.97 2.10
91 92 3.258372 ACGTCTGTTGGAGATGCTCTTAA 59.742 43.478 0.00 0.00 40.97 1.85
92 93 4.245660 CGTCTGTTGGAGATGCTCTTAAA 58.754 43.478 0.00 0.00 30.78 1.52
93 94 4.092091 CGTCTGTTGGAGATGCTCTTAAAC 59.908 45.833 0.00 0.00 30.78 2.01
94 95 5.241662 GTCTGTTGGAGATGCTCTTAAACT 58.758 41.667 0.00 0.00 31.63 2.66
95 96 5.121454 GTCTGTTGGAGATGCTCTTAAACTG 59.879 44.000 0.00 0.00 31.63 3.16
96 97 4.326826 TGTTGGAGATGCTCTTAAACTGG 58.673 43.478 0.00 0.00 0.00 4.00
97 98 4.202461 TGTTGGAGATGCTCTTAAACTGGT 60.202 41.667 0.00 0.00 0.00 4.00
100 101 4.761739 TGGAGATGCTCTTAAACTGGTTTG 59.238 41.667 8.73 0.00 34.23 2.93
101 102 4.156739 GGAGATGCTCTTAAACTGGTTTGG 59.843 45.833 8.73 2.81 34.23 3.28
102 103 4.729868 AGATGCTCTTAAACTGGTTTGGT 58.270 39.130 8.73 0.00 34.23 3.67
104 105 5.598417 AGATGCTCTTAAACTGGTTTGGTTT 59.402 36.000 8.73 0.00 39.70 3.27
105 106 5.004922 TGCTCTTAAACTGGTTTGGTTTG 57.995 39.130 8.73 0.00 37.45 2.93
106 107 4.707448 TGCTCTTAAACTGGTTTGGTTTGA 59.293 37.500 8.73 0.00 37.45 2.69
107 108 5.041287 GCTCTTAAACTGGTTTGGTTTGAC 58.959 41.667 8.73 0.00 37.45 3.18
108 109 5.393678 GCTCTTAAACTGGTTTGGTTTGACA 60.394 40.000 8.73 0.00 37.45 3.58
109 110 6.202516 TCTTAAACTGGTTTGGTTTGACAG 57.797 37.500 8.73 0.00 37.45 3.51
113 114 3.958018 ACTGGTTTGGTTTGACAGTGTA 58.042 40.909 0.00 0.00 40.56 2.90
116 117 4.590918 TGGTTTGGTTTGACAGTGTAAGA 58.409 39.130 0.00 0.00 0.00 2.10
117 118 5.010933 TGGTTTGGTTTGACAGTGTAAGAA 58.989 37.500 0.00 0.00 0.00 2.52
118 119 5.477291 TGGTTTGGTTTGACAGTGTAAGAAA 59.523 36.000 0.00 0.00 0.00 2.52
119 120 6.033966 GGTTTGGTTTGACAGTGTAAGAAAG 58.966 40.000 0.00 0.00 0.00 2.62
120 121 5.828299 TTGGTTTGACAGTGTAAGAAAGG 57.172 39.130 0.00 0.00 0.00 3.11
122 123 5.690865 TGGTTTGACAGTGTAAGAAAGGAT 58.309 37.500 0.00 0.00 0.00 3.24
123 124 6.833041 TGGTTTGACAGTGTAAGAAAGGATA 58.167 36.000 0.00 0.00 0.00 2.59
124 125 6.934645 TGGTTTGACAGTGTAAGAAAGGATAG 59.065 38.462 0.00 0.00 0.00 2.08
125 126 7.159372 GGTTTGACAGTGTAAGAAAGGATAGA 58.841 38.462 0.00 0.00 0.00 1.98
127 128 7.776618 TTGACAGTGTAAGAAAGGATAGAGA 57.223 36.000 0.00 0.00 0.00 3.10
128 129 7.397892 TGACAGTGTAAGAAAGGATAGAGAG 57.602 40.000 0.00 0.00 0.00 3.20
129 130 6.378564 TGACAGTGTAAGAAAGGATAGAGAGG 59.621 42.308 0.00 0.00 0.00 3.69
130 131 5.659079 ACAGTGTAAGAAAGGATAGAGAGGG 59.341 44.000 0.00 0.00 0.00 4.30
131 132 5.894393 CAGTGTAAGAAAGGATAGAGAGGGA 59.106 44.000 0.00 0.00 0.00 4.20
132 133 6.553100 CAGTGTAAGAAAGGATAGAGAGGGAT 59.447 42.308 0.00 0.00 0.00 3.85
134 135 8.461033 AGTGTAAGAAAGGATAGAGAGGGATAT 58.539 37.037 0.00 0.00 0.00 1.63
135 136 8.527810 GTGTAAGAAAGGATAGAGAGGGATATG 58.472 40.741 0.00 0.00 0.00 1.78
136 137 8.456940 TGTAAGAAAGGATAGAGAGGGATATGA 58.543 37.037 0.00 0.00 0.00 2.15
137 138 9.487442 GTAAGAAAGGATAGAGAGGGATATGAT 57.513 37.037 0.00 0.00 0.00 2.45
138 139 7.976414 AGAAAGGATAGAGAGGGATATGATG 57.024 40.000 0.00 0.00 0.00 3.07
139 140 6.902416 AGAAAGGATAGAGAGGGATATGATGG 59.098 42.308 0.00 0.00 0.00 3.51
140 141 6.429239 AAGGATAGAGAGGGATATGATGGA 57.571 41.667 0.00 0.00 0.00 3.41
142 143 7.007580 AGGATAGAGAGGGATATGATGGAAT 57.992 40.000 0.00 0.00 0.00 3.01
143 144 7.437572 AGGATAGAGAGGGATATGATGGAATT 58.562 38.462 0.00 0.00 0.00 2.17
146 147 8.873156 ATAGAGAGGGATATGATGGAATTGAT 57.127 34.615 0.00 0.00 0.00 2.57
147 148 9.964408 ATAGAGAGGGATATGATGGAATTGATA 57.036 33.333 0.00 0.00 0.00 2.15
150 151 9.917887 GAGAGGGATATGATGGAATTGATATTT 57.082 33.333 0.00 0.00 0.00 1.40
161 162 7.156876 TGGAATTGATATTTATTGCCGATCC 57.843 36.000 0.00 0.00 0.00 3.36
162 163 6.718912 TGGAATTGATATTTATTGCCGATCCA 59.281 34.615 0.00 0.00 0.00 3.41
181 182 5.964958 TCCAGATTGAAAATGAACACCTC 57.035 39.130 0.00 0.00 0.00 3.85
183 184 5.832595 TCCAGATTGAAAATGAACACCTCAA 59.167 36.000 0.00 0.00 37.67 3.02
192 193 5.413309 AATGAACACCTCAACAAAACCAA 57.587 34.783 0.00 0.00 37.67 3.67
199 200 5.301805 ACACCTCAACAAAACCAAGATTAGG 59.698 40.000 0.00 0.00 0.00 2.69
212 213 6.246163 ACCAAGATTAGGGACGAAAGAAATT 58.754 36.000 0.00 0.00 0.00 1.82
245 246 0.525761 TATGCAAGCCTCGCCAAAAC 59.474 50.000 0.00 0.00 0.00 2.43
289 291 3.103447 TCTCATCTTATGCCAAGCGAG 57.897 47.619 0.00 7.52 0.00 5.03
291 293 3.058450 CTCATCTTATGCCAAGCGAGAG 58.942 50.000 0.00 0.00 0.00 3.20
309 311 5.982516 GCGAGAGACATCTTAGAATTGACAT 59.017 40.000 0.00 0.00 35.30 3.06
310 312 6.143758 GCGAGAGACATCTTAGAATTGACATC 59.856 42.308 0.00 0.00 35.30 3.06
339 378 2.700897 CGAATGTGGGAGGAGGATAAGT 59.299 50.000 0.00 0.00 0.00 2.24
358 397 0.405198 TGGCAACACAGATGGGATGT 59.595 50.000 0.00 0.00 46.17 3.06
372 411 7.833682 ACAGATGGGATGTCATGTGTTAAATAA 59.166 33.333 2.44 0.00 45.44 1.40
377 416 7.068103 TGGGATGTCATGTGTTAAATAATGGAC 59.932 37.037 0.00 0.00 0.00 4.02
390 429 9.328845 GTTAAATAATGGACGTGGACCTATTAA 57.671 33.333 0.00 0.00 0.00 1.40
415 454 5.122396 GGTCTTGAGTCATGGTTATTGTGTC 59.878 44.000 6.21 0.00 0.00 3.67
426 465 4.142038 GGTTATTGTGTCAGGGAAGTGTT 58.858 43.478 0.00 0.00 0.00 3.32
474 513 7.648142 TCTTTTGCTAGTGACAAATAAACTGG 58.352 34.615 0.00 0.00 36.91 4.00
478 517 6.966021 TGCTAGTGACAAATAAACTGGAAAC 58.034 36.000 0.00 0.00 0.00 2.78
509 548 5.123227 TGTCTCCCTTGTGTTTGTTTAGAG 58.877 41.667 0.00 0.00 0.00 2.43
515 555 7.458397 TCCCTTGTGTTTGTTTAGAGTGATAT 58.542 34.615 0.00 0.00 0.00 1.63
599 639 4.202000 GGGGAATTGGCTTGTTTTTGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
607 647 4.376920 GGCTTGTTTTTGTTTGTGTGACAC 60.377 41.667 9.14 9.14 34.56 3.67
609 649 4.592485 TGTTTTTGTTTGTGTGACACCT 57.408 36.364 13.85 0.00 32.73 4.00
639 679 4.794648 TTGCGGGATTGGAGGGCG 62.795 66.667 0.00 0.00 0.00 6.13
655 695 2.047655 CGGGTGGCGAGCTACAAA 60.048 61.111 13.32 0.00 0.00 2.83
659 699 2.361789 GGGTGGCGAGCTACAAATTTA 58.638 47.619 13.32 0.00 0.00 1.40
660 700 2.750712 GGGTGGCGAGCTACAAATTTAA 59.249 45.455 13.32 0.00 0.00 1.52
661 701 3.427098 GGGTGGCGAGCTACAAATTTAAC 60.427 47.826 13.32 0.00 0.00 2.01
662 702 3.427098 GGTGGCGAGCTACAAATTTAACC 60.427 47.826 13.32 0.00 0.00 2.85
664 704 3.438781 TGGCGAGCTACAAATTTAACCAG 59.561 43.478 0.00 0.00 0.00 4.00
667 707 4.651994 CGAGCTACAAATTTAACCAGCAG 58.348 43.478 12.31 5.22 0.00 4.24
668 708 4.391830 CGAGCTACAAATTTAACCAGCAGA 59.608 41.667 12.31 0.00 0.00 4.26
669 709 5.446473 CGAGCTACAAATTTAACCAGCAGAG 60.446 44.000 12.31 3.29 0.00 3.35
670 710 4.702131 AGCTACAAATTTAACCAGCAGAGG 59.298 41.667 12.31 0.00 0.00 3.69
671 711 3.942130 ACAAATTTAACCAGCAGAGGC 57.058 42.857 0.00 0.00 41.61 4.70
698 738 4.172505 GAGCACTCGAGCTGATAATATGG 58.827 47.826 13.61 0.00 46.75 2.74
746 786 2.520979 GAGTGATTGTCGTCGGAAGAG 58.479 52.381 0.00 0.00 43.49 2.85
777 817 2.668212 CTTCCACTCGGCCGCAAA 60.668 61.111 23.51 1.50 0.00 3.68
778 818 2.203224 TTCCACTCGGCCGCAAAA 60.203 55.556 23.51 7.23 0.00 2.44
779 819 2.187599 CTTCCACTCGGCCGCAAAAG 62.188 60.000 23.51 15.77 0.00 2.27
780 820 2.668185 TTCCACTCGGCCGCAAAAGA 62.668 55.000 23.51 10.54 0.00 2.52
781 821 2.556287 CACTCGGCCGCAAAAGAC 59.444 61.111 23.51 0.00 0.00 3.01
783 823 2.251642 ACTCGGCCGCAAAAGACAC 61.252 57.895 23.51 0.00 0.00 3.67
784 824 2.966309 CTCGGCCGCAAAAGACACC 61.966 63.158 23.51 0.00 0.00 4.16
785 825 4.383602 CGGCCGCAAAAGACACCG 62.384 66.667 14.67 0.00 0.00 4.94
786 826 4.700365 GGCCGCAAAAGACACCGC 62.700 66.667 0.00 0.00 0.00 5.68
788 828 2.051345 CCGCAAAAGACACCGCAC 60.051 61.111 0.00 0.00 0.00 5.34
789 829 2.712539 CGCAAAAGACACCGCACA 59.287 55.556 0.00 0.00 0.00 4.57
790 830 1.369209 CGCAAAAGACACCGCACAG 60.369 57.895 0.00 0.00 0.00 3.66
791 831 1.771073 CGCAAAAGACACCGCACAGA 61.771 55.000 0.00 0.00 0.00 3.41
792 832 0.380378 GCAAAAGACACCGCACAGAA 59.620 50.000 0.00 0.00 0.00 3.02
793 833 1.202245 GCAAAAGACACCGCACAGAAA 60.202 47.619 0.00 0.00 0.00 2.52
794 834 2.543653 GCAAAAGACACCGCACAGAAAT 60.544 45.455 0.00 0.00 0.00 2.17
795 835 3.300009 CAAAAGACACCGCACAGAAATC 58.700 45.455 0.00 0.00 0.00 2.17
797 837 2.086054 AGACACCGCACAGAAATCTC 57.914 50.000 0.00 0.00 0.00 2.75
799 839 1.291877 ACACCGCACAGAAATCTCGC 61.292 55.000 0.00 0.00 0.00 5.03
800 840 2.094659 ACCGCACAGAAATCTCGCG 61.095 57.895 13.92 13.92 41.76 5.87
819 859 2.557372 TACGCAGAGCACGACACCA 61.557 57.895 0.00 0.00 0.00 4.17
854 894 4.208460 CAGTCTTCAGCAGCAACAAATTTG 59.792 41.667 16.67 16.67 0.00 2.32
855 895 4.098349 AGTCTTCAGCAGCAACAAATTTGA 59.902 37.500 24.64 0.00 0.00 2.69
856 896 4.207841 GTCTTCAGCAGCAACAAATTTGAC 59.792 41.667 24.64 12.80 0.00 3.18
858 898 5.299028 TCTTCAGCAGCAACAAATTTGACTA 59.701 36.000 24.64 1.81 0.00 2.59
859 899 5.710513 TCAGCAGCAACAAATTTGACTAT 57.289 34.783 24.64 5.19 0.00 2.12
860 900 5.702865 TCAGCAGCAACAAATTTGACTATC 58.297 37.500 24.64 12.32 0.00 2.08
861 901 4.860907 CAGCAGCAACAAATTTGACTATCC 59.139 41.667 24.64 8.47 0.00 2.59
862 902 4.082026 AGCAGCAACAAATTTGACTATCCC 60.082 41.667 24.64 7.13 0.00 3.85
863 903 4.414852 CAGCAACAAATTTGACTATCCCG 58.585 43.478 24.64 4.76 0.00 5.14
864 904 4.155826 CAGCAACAAATTTGACTATCCCGA 59.844 41.667 24.64 0.00 0.00 5.14
865 905 4.156008 AGCAACAAATTTGACTATCCCGAC 59.844 41.667 24.64 2.43 0.00 4.79
866 906 4.647964 CAACAAATTTGACTATCCCGACG 58.352 43.478 24.64 0.00 0.00 5.12
868 908 1.567504 AATTTGACTATCCCGACGCG 58.432 50.000 3.53 3.53 0.00 6.01
870 910 0.179156 TTTGACTATCCCGACGCGAC 60.179 55.000 15.93 5.54 0.00 5.19
872 912 2.438975 ACTATCCCGACGCGACCA 60.439 61.111 15.93 0.00 0.00 4.02
873 913 2.025727 CTATCCCGACGCGACCAC 59.974 66.667 15.93 0.00 0.00 4.16
874 914 3.802008 CTATCCCGACGCGACCACG 62.802 68.421 15.93 12.70 42.93 4.94
994 1052 2.260869 CCAACCACCACTCCAAGCG 61.261 63.158 0.00 0.00 0.00 4.68
1052 1110 2.573869 CGTCGTCAGCCATGGAGT 59.426 61.111 18.40 0.00 0.00 3.85
1182 1240 4.082523 CTCGTCACCACCCGCCAT 62.083 66.667 0.00 0.00 0.00 4.40
1282 1340 4.293648 CGTGCCTGGACACCGACA 62.294 66.667 13.24 0.00 37.25 4.35
1755 3303 7.852971 ATGGATTTGCAAATTAACATGGAAG 57.147 32.000 24.81 0.00 0.00 3.46
1769 3348 2.340328 GGAAGTTTCCCGCCGCAAT 61.340 57.895 0.00 0.00 41.62 3.56
1771 3350 0.038618 GAAGTTTCCCGCCGCAATTT 60.039 50.000 0.00 0.00 0.00 1.82
1773 3352 0.391228 AGTTTCCCGCCGCAATTTTT 59.609 45.000 0.00 0.00 0.00 1.94
1890 4205 3.118112 AGGAGGCAGAGTACATGGAATTG 60.118 47.826 0.00 0.00 0.00 2.32
1893 4208 2.609459 GGCAGAGTACATGGAATTGACG 59.391 50.000 0.00 0.00 0.00 4.35
1986 4301 9.750125 AACAAGTCTTATGGTTTCAATCTTTTC 57.250 29.630 0.00 0.00 0.00 2.29
2017 4332 2.417243 GCACCATGTTTGGATTGGCTAC 60.417 50.000 0.00 0.00 46.92 3.58
2025 4340 4.646945 TGTTTGGATTGGCTACAAGAACAA 59.353 37.500 0.00 0.00 40.49 2.83
2214 4529 7.031975 GTGAGAAGAATGGATTGATTGTTTCC 58.968 38.462 0.00 0.00 0.00 3.13
2253 4568 3.973973 AGGTTCTAGCACATAAGGCCATA 59.026 43.478 5.01 0.00 0.00 2.74
2270 4594 5.190528 AGGCCATAGGTATGATATCACAAGG 59.809 44.000 7.78 4.89 35.75 3.61
2295 4619 5.470098 CCATATTTGTTTCCTCCTCGTATGG 59.530 44.000 0.00 0.00 32.72 2.74
2303 4627 5.429681 TTCCTCCTCGTATGGAAATGAAA 57.570 39.130 0.00 0.00 36.98 2.69
2305 4629 6.001449 TCCTCCTCGTATGGAAATGAAATT 57.999 37.500 0.00 0.00 38.98 1.82
2344 4679 8.644318 ACATATAGACTCGTAACAACATTTCC 57.356 34.615 0.00 0.00 0.00 3.13
2495 4830 3.525537 CATCGCAAAGTATGTGGAGAGT 58.474 45.455 0.00 0.00 40.07 3.24
2507 4842 2.779430 TGTGGAGAGTGCATGGGATATT 59.221 45.455 0.00 0.00 0.00 1.28
2516 4851 0.953727 CATGGGATATTGGTGTGCGG 59.046 55.000 0.00 0.00 0.00 5.69
2518 4853 2.193536 GGGATATTGGTGTGCGGGC 61.194 63.158 0.00 0.00 0.00 6.13
2540 4875 2.792542 GCGGAAGAGCGAAAATGGATTG 60.793 50.000 0.00 0.00 0.00 2.67
2551 4886 4.201950 CGAAAATGGATTGCTAAGGAGTGG 60.202 45.833 0.00 0.00 0.00 4.00
2657 4992 0.465097 CCAAGGAGGCAATGCGAGAT 60.465 55.000 0.00 0.00 0.00 2.75
2696 5031 2.304413 CATATTGCTGAATTCGCTGCG 58.696 47.619 17.25 17.25 35.75 5.18
2758 5094 8.980143 TTTATTCAAAATAAGCAAGTAGGCAC 57.020 30.769 0.00 0.00 35.83 5.01
2772 5108 0.395311 AGGCACTGATTCCAGGCATG 60.395 55.000 0.00 0.00 44.60 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202639 GGGGTTGGTTGCTTTTTCAGG 60.203 52.381 0.00 0.00 0.00 3.86
1 2 1.762370 AGGGGTTGGTTGCTTTTTCAG 59.238 47.619 0.00 0.00 0.00 3.02
2 3 1.760029 GAGGGGTTGGTTGCTTTTTCA 59.240 47.619 0.00 0.00 0.00 2.69
3 4 1.070134 GGAGGGGTTGGTTGCTTTTTC 59.930 52.381 0.00 0.00 0.00 2.29
4 5 1.128200 GGAGGGGTTGGTTGCTTTTT 58.872 50.000 0.00 0.00 0.00 1.94
5 6 0.762842 GGGAGGGGTTGGTTGCTTTT 60.763 55.000 0.00 0.00 0.00 2.27
6 7 1.152333 GGGAGGGGTTGGTTGCTTT 60.152 57.895 0.00 0.00 0.00 3.51
7 8 2.526110 GGGAGGGGTTGGTTGCTT 59.474 61.111 0.00 0.00 0.00 3.91
8 9 3.966543 CGGGAGGGGTTGGTTGCT 61.967 66.667 0.00 0.00 0.00 3.91
10 11 4.278513 TGCGGGAGGGGTTGGTTG 62.279 66.667 0.00 0.00 0.00 3.77
11 12 4.280019 GTGCGGGAGGGGTTGGTT 62.280 66.667 0.00 0.00 0.00 3.67
19 20 3.564027 GATTTCGCGTGCGGGAGG 61.564 66.667 14.89 0.00 38.30 4.30
20 21 2.813474 TGATTTCGCGTGCGGGAG 60.813 61.111 14.89 0.00 38.30 4.30
24 25 2.354196 GAAATAGTGATTTCGCGTGCG 58.646 47.619 5.77 8.14 41.12 5.34
31 32 2.351726 ACAGCGCCGAAATAGTGATTTC 59.648 45.455 2.29 1.13 45.13 2.17
32 33 2.356135 ACAGCGCCGAAATAGTGATTT 58.644 42.857 2.29 0.00 38.00 2.17
33 34 2.024176 ACAGCGCCGAAATAGTGATT 57.976 45.000 2.29 0.00 0.00 2.57
34 35 2.882927 TACAGCGCCGAAATAGTGAT 57.117 45.000 2.29 0.00 0.00 3.06
35 36 2.658373 TTACAGCGCCGAAATAGTGA 57.342 45.000 2.29 0.00 0.00 3.41
36 37 3.124636 ACTTTTACAGCGCCGAAATAGTG 59.875 43.478 2.29 0.00 0.00 2.74
37 38 3.332034 ACTTTTACAGCGCCGAAATAGT 58.668 40.909 2.29 3.66 0.00 2.12
39 40 4.752661 AAACTTTTACAGCGCCGAAATA 57.247 36.364 2.29 0.00 0.00 1.40
41 42 3.423996 AAAACTTTTACAGCGCCGAAA 57.576 38.095 2.29 0.00 0.00 3.46
59 60 1.003331 CCAACAGACGTGCGCTAAAAA 60.003 47.619 9.73 0.00 0.00 1.94
60 61 0.584396 CCAACAGACGTGCGCTAAAA 59.416 50.000 9.73 0.00 0.00 1.52
61 62 0.249531 TCCAACAGACGTGCGCTAAA 60.250 50.000 9.73 0.00 0.00 1.85
62 63 0.666274 CTCCAACAGACGTGCGCTAA 60.666 55.000 9.73 0.00 0.00 3.09
63 64 1.080772 CTCCAACAGACGTGCGCTA 60.081 57.895 9.73 0.00 0.00 4.26
67 68 0.671781 AGCATCTCCAACAGACGTGC 60.672 55.000 0.00 0.00 32.26 5.34
68 69 1.354040 GAGCATCTCCAACAGACGTG 58.646 55.000 0.00 0.00 32.26 4.49
69 70 3.822607 GAGCATCTCCAACAGACGT 57.177 52.632 0.00 0.00 32.26 4.34
78 79 9.085797 AAACCAAACCAGTTTAAGAGCATCTCC 62.086 40.741 0.00 0.00 36.81 3.71
79 80 6.239036 AAACCAAACCAGTTTAAGAGCATCTC 60.239 38.462 0.00 0.00 36.81 2.75
80 81 5.598417 AAACCAAACCAGTTTAAGAGCATCT 59.402 36.000 0.00 0.00 37.21 2.90
81 82 5.453567 AACCAAACCAGTTTAAGAGCATC 57.546 39.130 0.00 0.00 0.00 3.91
82 83 5.362430 TCAAACCAAACCAGTTTAAGAGCAT 59.638 36.000 0.00 0.00 35.71 3.79
84 85 5.041287 GTCAAACCAAACCAGTTTAAGAGC 58.959 41.667 0.00 0.00 35.71 4.09
85 86 6.127730 ACTGTCAAACCAAACCAGTTTAAGAG 60.128 38.462 0.00 0.00 35.71 2.85
87 88 5.804979 CACTGTCAAACCAAACCAGTTTAAG 59.195 40.000 0.00 0.00 35.71 1.85
88 89 5.244178 ACACTGTCAAACCAAACCAGTTTAA 59.756 36.000 0.00 0.00 35.71 1.52
89 90 4.767928 ACACTGTCAAACCAAACCAGTTTA 59.232 37.500 0.00 0.00 35.71 2.01
90 91 3.576550 ACACTGTCAAACCAAACCAGTTT 59.423 39.130 0.00 0.00 37.93 2.66
91 92 3.161866 ACACTGTCAAACCAAACCAGTT 58.838 40.909 0.00 0.00 34.31 3.16
92 93 2.802719 ACACTGTCAAACCAAACCAGT 58.197 42.857 0.00 0.00 36.85 4.00
93 94 4.638421 TCTTACACTGTCAAACCAAACCAG 59.362 41.667 0.00 0.00 0.00 4.00
94 95 4.590918 TCTTACACTGTCAAACCAAACCA 58.409 39.130 0.00 0.00 0.00 3.67
95 96 5.570234 TTCTTACACTGTCAAACCAAACC 57.430 39.130 0.00 0.00 0.00 3.27
96 97 6.033966 CCTTTCTTACACTGTCAAACCAAAC 58.966 40.000 0.00 0.00 0.00 2.93
97 98 5.946972 TCCTTTCTTACACTGTCAAACCAAA 59.053 36.000 0.00 0.00 0.00 3.28
100 101 7.159372 TCTATCCTTTCTTACACTGTCAAACC 58.841 38.462 0.00 0.00 0.00 3.27
101 102 8.088981 TCTCTATCCTTTCTTACACTGTCAAAC 58.911 37.037 0.00 0.00 0.00 2.93
102 103 8.190326 TCTCTATCCTTTCTTACACTGTCAAA 57.810 34.615 0.00 0.00 0.00 2.69
104 105 6.378564 CCTCTCTATCCTTTCTTACACTGTCA 59.621 42.308 0.00 0.00 0.00 3.58
105 106 6.183360 CCCTCTCTATCCTTTCTTACACTGTC 60.183 46.154 0.00 0.00 0.00 3.51
106 107 5.659079 CCCTCTCTATCCTTTCTTACACTGT 59.341 44.000 0.00 0.00 0.00 3.55
107 108 5.894393 TCCCTCTCTATCCTTTCTTACACTG 59.106 44.000 0.00 0.00 0.00 3.66
108 109 6.093617 TCCCTCTCTATCCTTTCTTACACT 57.906 41.667 0.00 0.00 0.00 3.55
109 110 6.987403 ATCCCTCTCTATCCTTTCTTACAC 57.013 41.667 0.00 0.00 0.00 2.90
113 114 7.402650 CCATCATATCCCTCTCTATCCTTTCTT 59.597 40.741 0.00 0.00 0.00 2.52
116 117 6.820205 TCCATCATATCCCTCTCTATCCTTT 58.180 40.000 0.00 0.00 0.00 3.11
117 118 6.429239 TCCATCATATCCCTCTCTATCCTT 57.571 41.667 0.00 0.00 0.00 3.36
118 119 6.429239 TTCCATCATATCCCTCTCTATCCT 57.571 41.667 0.00 0.00 0.00 3.24
119 120 7.346698 TCAATTCCATCATATCCCTCTCTATCC 59.653 40.741 0.00 0.00 0.00 2.59
120 121 8.316497 TCAATTCCATCATATCCCTCTCTATC 57.684 38.462 0.00 0.00 0.00 2.08
122 123 9.964408 ATATCAATTCCATCATATCCCTCTCTA 57.036 33.333 0.00 0.00 0.00 2.43
123 124 8.873156 ATATCAATTCCATCATATCCCTCTCT 57.127 34.615 0.00 0.00 0.00 3.10
124 125 9.917887 AAATATCAATTCCATCATATCCCTCTC 57.082 33.333 0.00 0.00 0.00 3.20
132 133 9.460019 TCGGCAATAAATATCAATTCCATCATA 57.540 29.630 0.00 0.00 0.00 2.15
134 135 7.757941 TCGGCAATAAATATCAATTCCATCA 57.242 32.000 0.00 0.00 0.00 3.07
135 136 7.917505 GGATCGGCAATAAATATCAATTCCATC 59.082 37.037 0.00 0.00 0.00 3.51
136 137 7.396907 TGGATCGGCAATAAATATCAATTCCAT 59.603 33.333 0.00 0.00 0.00 3.41
137 138 6.718912 TGGATCGGCAATAAATATCAATTCCA 59.281 34.615 0.00 0.00 0.00 3.53
138 139 7.121168 TCTGGATCGGCAATAAATATCAATTCC 59.879 37.037 0.00 0.00 0.00 3.01
139 140 8.044060 TCTGGATCGGCAATAAATATCAATTC 57.956 34.615 0.00 0.00 0.00 2.17
140 141 8.585471 ATCTGGATCGGCAATAAATATCAATT 57.415 30.769 0.00 0.00 0.00 2.32
142 143 7.665145 TCAATCTGGATCGGCAATAAATATCAA 59.335 33.333 0.00 0.00 0.00 2.57
143 144 7.167535 TCAATCTGGATCGGCAATAAATATCA 58.832 34.615 0.00 0.00 0.00 2.15
146 147 7.815840 TTTCAATCTGGATCGGCAATAAATA 57.184 32.000 0.00 0.00 0.00 1.40
147 148 6.713762 TTTCAATCTGGATCGGCAATAAAT 57.286 33.333 0.00 0.00 0.00 1.40
150 151 5.827267 TCATTTTCAATCTGGATCGGCAATA 59.173 36.000 0.00 0.00 0.00 1.90
151 152 4.646040 TCATTTTCAATCTGGATCGGCAAT 59.354 37.500 0.00 0.00 0.00 3.56
152 153 4.015764 TCATTTTCAATCTGGATCGGCAA 58.984 39.130 0.00 0.00 0.00 4.52
161 162 6.506147 TGTTGAGGTGTTCATTTTCAATCTG 58.494 36.000 0.00 0.00 35.27 2.90
162 163 6.713762 TGTTGAGGTGTTCATTTTCAATCT 57.286 33.333 0.00 0.00 35.27 2.40
181 182 4.517453 TCGTCCCTAATCTTGGTTTTGTTG 59.483 41.667 0.00 0.00 0.00 3.33
183 184 4.360951 TCGTCCCTAATCTTGGTTTTGT 57.639 40.909 0.00 0.00 0.00 2.83
192 193 8.487028 ACAGATAATTTCTTTCGTCCCTAATCT 58.513 33.333 0.00 0.00 29.93 2.40
199 200 6.702897 CGGTTACAGATAATTTCTTTCGTCC 58.297 40.000 0.00 0.00 29.93 4.79
212 213 3.745975 GCTTGCATATGCGGTTACAGATA 59.254 43.478 22.21 0.00 45.83 1.98
262 263 5.506982 GCTTGGCATAAGATGAGAAATCACC 60.507 44.000 4.33 0.00 0.00 4.02
273 275 2.432146 TGTCTCTCGCTTGGCATAAGAT 59.568 45.455 4.33 0.00 0.00 2.40
289 291 8.486383 CGAATGATGTCAATTCTAAGATGTCTC 58.514 37.037 0.00 0.00 0.00 3.36
291 293 8.357796 TCGAATGATGTCAATTCTAAGATGTC 57.642 34.615 0.00 0.00 0.00 3.06
339 378 0.405198 ACATCCCATCTGTGTTGCCA 59.595 50.000 0.00 0.00 0.00 4.92
358 397 6.092944 GTCCACGTCCATTATTTAACACATGA 59.907 38.462 0.00 0.00 0.00 3.07
390 429 5.221925 ACACAATAACCATGACTCAAGACCT 60.222 40.000 0.00 0.00 0.00 3.85
474 513 2.767505 AGGGAGACATTGACACGTTTC 58.232 47.619 0.00 0.00 0.00 2.78
528 568 6.325993 TCCAATCTTCCCATGACAGAAATA 57.674 37.500 0.00 0.00 0.00 1.40
575 615 2.142319 CAAAAACAAGCCAATTCCCCG 58.858 47.619 0.00 0.00 0.00 5.73
607 647 3.673484 CAACAACAGCGGCCCAGG 61.673 66.667 0.00 0.00 0.00 4.45
639 679 1.173913 AAATTTGTAGCTCGCCACCC 58.826 50.000 0.00 0.00 0.00 4.61
671 711 1.090728 TCAGCTCGAGTGCTCACTAG 58.909 55.000 15.13 3.20 42.66 2.57
674 714 2.568696 TTATCAGCTCGAGTGCTCAC 57.431 50.000 15.13 0.00 41.98 3.51
675 715 4.321527 CCATATTATCAGCTCGAGTGCTCA 60.322 45.833 15.13 0.00 41.98 4.26
698 738 2.111932 TTGCGCGTGATGTGGACAAC 62.112 55.000 8.43 0.00 0.00 3.32
746 786 1.002792 GTGGAAGCAACGAGGAAACAC 60.003 52.381 0.00 0.00 0.00 3.32
774 814 2.842208 TTTCTGTGCGGTGTCTTTTG 57.158 45.000 0.00 0.00 0.00 2.44
775 815 3.214328 AGATTTCTGTGCGGTGTCTTTT 58.786 40.909 0.00 0.00 0.00 2.27
776 816 2.808543 GAGATTTCTGTGCGGTGTCTTT 59.191 45.455 0.00 0.00 0.00 2.52
777 817 2.417719 GAGATTTCTGTGCGGTGTCTT 58.582 47.619 0.00 0.00 0.00 3.01
778 818 1.670087 CGAGATTTCTGTGCGGTGTCT 60.670 52.381 0.00 0.00 0.00 3.41
779 819 0.716108 CGAGATTTCTGTGCGGTGTC 59.284 55.000 0.00 0.00 0.00 3.67
780 820 1.291877 GCGAGATTTCTGTGCGGTGT 61.292 55.000 0.00 0.00 0.00 4.16
781 821 1.421485 GCGAGATTTCTGTGCGGTG 59.579 57.895 0.00 0.00 0.00 4.94
783 823 0.800683 TACGCGAGATTTCTGTGCGG 60.801 55.000 15.93 8.93 45.78 5.69
784 824 0.294887 GTACGCGAGATTTCTGTGCG 59.705 55.000 15.93 17.36 46.45 5.34
785 825 0.294887 CGTACGCGAGATTTCTGTGC 59.705 55.000 15.93 0.00 41.33 4.57
786 826 0.294887 GCGTACGCGAGATTTCTGTG 59.705 55.000 26.17 0.00 41.33 3.66
788 828 0.567968 CTGCGTACGCGAGATTTCTG 59.432 55.000 32.65 11.56 45.51 3.02
789 829 0.450583 TCTGCGTACGCGAGATTTCT 59.549 50.000 32.65 0.00 45.51 2.52
790 830 0.840729 CTCTGCGTACGCGAGATTTC 59.159 55.000 36.34 14.82 45.51 2.17
791 831 1.140407 GCTCTGCGTACGCGAGATTT 61.140 55.000 39.97 0.00 45.51 2.17
792 832 1.586564 GCTCTGCGTACGCGAGATT 60.587 57.895 39.97 0.00 45.51 2.40
793 833 2.024871 GCTCTGCGTACGCGAGAT 59.975 61.111 39.97 0.00 45.51 2.75
794 834 3.428282 TGCTCTGCGTACGCGAGA 61.428 61.111 39.97 34.32 45.51 4.04
795 835 3.241059 GTGCTCTGCGTACGCGAG 61.241 66.667 35.73 35.73 45.51 5.03
800 840 2.087009 GGTGTCGTGCTCTGCGTAC 61.087 63.158 0.00 0.00 0.00 3.67
819 859 1.639298 GAAGACTGGCGCGCAAGATT 61.639 55.000 40.59 31.22 43.02 2.40
854 894 2.330745 GGTCGCGTCGGGATAGTC 59.669 66.667 15.53 2.29 0.00 2.59
855 895 2.438975 TGGTCGCGTCGGGATAGT 60.439 61.111 15.53 0.00 0.00 2.12
856 896 2.025727 GTGGTCGCGTCGGGATAG 59.974 66.667 15.53 0.00 0.00 2.08
880 920 8.570488 GGTTTCTCTTCGGGATAGTTTTAAAAA 58.430 33.333 1.31 0.00 0.00 1.94
882 922 7.455891 AGGTTTCTCTTCGGGATAGTTTTAAA 58.544 34.615 0.00 0.00 0.00 1.52
884 924 6.616237 AGGTTTCTCTTCGGGATAGTTTTA 57.384 37.500 0.00 0.00 0.00 1.52
885 925 5.500546 AGGTTTCTCTTCGGGATAGTTTT 57.499 39.130 0.00 0.00 0.00 2.43
887 927 4.833390 CAAGGTTTCTCTTCGGGATAGTT 58.167 43.478 0.00 0.00 0.00 2.24
994 1052 1.520342 GCGTGCTCTCCATGTCTCC 60.520 63.158 0.00 0.00 32.85 3.71
997 1055 2.887568 CGGCGTGCTCTCCATGTC 60.888 66.667 0.00 0.00 32.85 3.06
1182 1240 3.311110 GGGGTGACGGAGAGCACA 61.311 66.667 0.00 0.00 37.87 4.57
1282 1340 0.252103 TCCAGCCGGGAGAAGTACTT 60.252 55.000 8.13 8.13 42.15 2.24
1338 1396 2.183555 GCGGTCGTTTCCTCCGAT 59.816 61.111 7.01 0.00 46.05 4.18
1590 3128 3.240134 GAACCCTGGCTGCGACTCA 62.240 63.158 0.00 0.00 0.00 3.41
1755 3303 2.907431 AAAAATTGCGGCGGGAAAC 58.093 47.368 9.78 0.00 0.00 2.78
1773 3352 9.965824 GATCAAGAAAGAAGTTCCATGTTAAAA 57.034 29.630 0.00 0.00 36.86 1.52
1890 4205 2.126031 GTCTTCGCTCCCCACGTC 60.126 66.667 0.00 0.00 0.00 4.34
1893 4208 2.280823 CTACGGTCTTCGCTCCCCAC 62.281 65.000 0.00 0.00 43.89 4.61
1986 4301 3.928769 CATGGTGCATCGTCGCCG 61.929 66.667 0.00 0.00 39.42 6.46
2017 4332 4.070716 ACAGAGGAGATGCTTTGTTCTTG 58.929 43.478 0.00 0.00 0.00 3.02
2025 4340 1.350351 AGCACAACAGAGGAGATGCTT 59.650 47.619 0.00 0.00 40.39 3.91
2253 4568 6.898171 ATATGGCCTTGTGATATCATACCT 57.102 37.500 9.02 0.00 0.00 3.08
2270 4594 3.279434 ACGAGGAGGAAACAAATATGGC 58.721 45.455 0.00 0.00 0.00 4.40
2326 4655 9.673454 AATAAAAAGGAAATGTTGTTACGAGTC 57.327 29.630 0.00 0.00 0.00 3.36
2420 4755 0.233848 GAGGTACACCGCAAACAACG 59.766 55.000 0.00 0.00 42.08 4.10
2470 4805 2.083774 CCACATACTTTGCGATGGTGT 58.916 47.619 0.00 0.00 0.00 4.16
2495 4830 1.401761 GCACACCAATATCCCATGCA 58.598 50.000 0.00 0.00 0.00 3.96
2540 4875 1.677637 CGACCTCCCCACTCCTTAGC 61.678 65.000 0.00 0.00 0.00 3.09
2551 4886 0.690077 AATACACCTCCCGACCTCCC 60.690 60.000 0.00 0.00 0.00 4.30
2657 4992 1.371183 CTTGTCCGAGCTTCCACCA 59.629 57.895 0.00 0.00 0.00 4.17
2732 5067 9.586435 GTGCCTACTTGCTTATTTTGAATAAAT 57.414 29.630 0.00 0.00 0.00 1.40
2758 5094 6.057533 TCTAAACATACATGCCTGGAATCAG 58.942 40.000 0.00 0.00 40.59 2.90
2772 5108 9.010029 TGGAAAAATTGTCTCCTCTAAACATAC 57.990 33.333 3.22 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.