Multiple sequence alignment - TraesCS2D01G598700

Loading Multiple Alignment...

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 TraesCS2D01G598700 chr2D 100.000 3461 0 0 1 3461 650583508 650586968 0.000000e+00 6392.0
1 TraesCS2D01G598700 chr2D 79.923 782 125 17 1845 2598 650565430 650566207 2.350000e-151 545.0
2 TraesCS2D01G598700 chr2D 97.727 88 0 2 3050 3136 650586643 650586557 2.150000e-32 150.0
3 TraesCS2D01G598700 chr2A 95.292 2124 87 13 893 3011 771933045 771935160 0.000000e+00 3356.0
4 TraesCS2D01G598700 chr2A 92.881 1475 68 11 162 1626 771921627 771923074 0.000000e+00 2108.0
5 TraesCS2D01G598700 chr2A 94.741 1312 53 8 162 1463 771891728 771893033 0.000000e+00 2026.0
6 TraesCS2D01G598700 chr2A 92.908 705 41 3 162 858 771932343 771933046 0.000000e+00 1016.0
7 TraesCS2D01G598700 chr2A 96.226 371 13 1 3090 3460 771953068 771953437 1.060000e-169 606.0
8 TraesCS2D01G598700 chr2A 92.814 167 5 3 1465 1631 771906574 771906733 5.770000e-58 235.0
9 TraesCS2D01G598700 chr2A 92.357 157 9 2 1 157 771885921 771886074 1.620000e-53 220.0
10 TraesCS2D01G598700 chr2A 95.918 49 1 1 3006 3053 771953020 771953068 1.030000e-10 78.7
11 TraesCS2D01G598700 chr2B 92.945 1219 75 10 2221 3437 787050510 787049301 0.000000e+00 1764.0
12 TraesCS2D01G598700 chr2B 80.373 805 115 24 1845 2608 787098259 787099061 3.880000e-159 571.0
13 TraesCS2D01G598700 chr2B 80.795 604 93 12 1845 2431 787154314 787154911 5.270000e-123 451.0
14 TraesCS2D01G598700 chr2B 81.138 334 46 10 3109 3439 787775853 787776172 5.730000e-63 252.0


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 TraesCS2D01G598700 chr2D 650583508 650586968 3460 False 6392 6392 100.000 1 3461 1 chr2D.!!$F2 3460
1 TraesCS2D01G598700 chr2D 650565430 650566207 777 False 545 545 79.923 1845 2598 1 chr2D.!!$F1 753
2 TraesCS2D01G598700 chr2A 771932343 771935160 2817 False 2186 3356 94.100 162 3011 2 chr2A.!!$F5 2849
3 TraesCS2D01G598700 chr2A 771921627 771923074 1447 False 2108 2108 92.881 162 1626 1 chr2A.!!$F4 1464
4 TraesCS2D01G598700 chr2A 771891728 771893033 1305 False 2026 2026 94.741 162 1463 1 chr2A.!!$F2 1301
5 TraesCS2D01G598700 chr2B 787049301 787050510 1209 True 1764 1764 92.945 2221 3437 1 chr2B.!!$R1 1216
6 TraesCS2D01G598700 chr2B 787098259 787099061 802 False 571 571 80.373 1845 2608 1 chr2B.!!$F1 763
7 TraesCS2D01G598700 chr2B 787154314 787154911 597 False 451 451 80.795 1845 2431 1 chr2B.!!$F2 586

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
779 795 0.036022 GCCTTCCCAGCAGCTATAGG 59.964 60.0 0.00 0.64 0.0 2.57 F
905 921 0.249868 TAGATGATTTCGCGGGGCAG 60.250 55.0 6.13 0.00 0.0 4.85 F
2202 2238 0.250252 TCTGAAGCCGACACATGCAA 60.250 50.0 0.00 0.00 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 1991 0.460811 CGGCATGAGCAGTAGCAAGA 60.461 55.0 0.0 0.0 45.49 3.02 R
2260 2296 0.833409 CCTCCTTTTGGCAGGCCTTT 60.833 55.0 0.0 0.0 40.12 3.11 R
3053 3119 0.179004 ACACGTTCCAGCCATCCAAA 60.179 50.0 0.0 0.0 0.00 3.28 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
45 46 3.744719 CGTCGGGAGGCACGAGAA 61.745 66.667 0.00 0.00 41.50 2.87
46 47 2.654877 GTCGGGAGGCACGAGAAA 59.345 61.111 0.00 0.00 41.50 2.52
47 48 1.737008 GTCGGGAGGCACGAGAAAC 60.737 63.158 0.00 0.00 41.50 2.78
48 49 2.434359 CGGGAGGCACGAGAAACC 60.434 66.667 0.00 0.00 0.00 3.27
49 50 2.046217 GGGAGGCACGAGAAACCC 60.046 66.667 0.00 0.00 0.00 4.11
50 51 2.593956 GGGAGGCACGAGAAACCCT 61.594 63.158 0.00 0.00 35.03 4.34
51 52 1.262640 GGGAGGCACGAGAAACCCTA 61.263 60.000 0.00 0.00 35.03 3.53
52 53 0.175989 GGAGGCACGAGAAACCCTAG 59.824 60.000 0.00 0.00 0.00 3.02
53 54 0.460459 GAGGCACGAGAAACCCTAGC 60.460 60.000 0.00 0.00 0.00 3.42
54 55 1.810030 GGCACGAGAAACCCTAGCG 60.810 63.158 0.00 0.00 0.00 4.26
55 56 1.214589 GCACGAGAAACCCTAGCGA 59.785 57.895 0.00 0.00 0.00 4.93
56 57 0.389426 GCACGAGAAACCCTAGCGAA 60.389 55.000 0.00 0.00 0.00 4.70
57 58 1.938016 GCACGAGAAACCCTAGCGAAA 60.938 52.381 0.00 0.00 0.00 3.46
58 59 1.725164 CACGAGAAACCCTAGCGAAAC 59.275 52.381 0.00 0.00 0.00 2.78
59 60 0.989890 CGAGAAACCCTAGCGAAACG 59.010 55.000 0.00 0.00 0.00 3.60
60 61 1.356938 GAGAAACCCTAGCGAAACGG 58.643 55.000 0.00 0.00 0.00 4.44
61 62 0.683412 AGAAACCCTAGCGAAACGGT 59.317 50.000 0.00 0.00 41.50 4.83
62 63 1.073964 GAAACCCTAGCGAAACGGTC 58.926 55.000 0.00 0.00 38.83 4.79
63 64 0.321034 AAACCCTAGCGAAACGGTCC 60.321 55.000 0.00 0.00 38.83 4.46
64 65 1.190178 AACCCTAGCGAAACGGTCCT 61.190 55.000 0.00 0.00 38.83 3.85
65 66 1.141234 CCCTAGCGAAACGGTCCTC 59.859 63.158 0.00 0.00 38.83 3.71
66 67 1.321074 CCCTAGCGAAACGGTCCTCT 61.321 60.000 0.00 0.00 38.83 3.69
67 68 0.531200 CCTAGCGAAACGGTCCTCTT 59.469 55.000 0.00 0.00 38.83 2.85
68 69 1.067071 CCTAGCGAAACGGTCCTCTTT 60.067 52.381 0.00 0.00 38.83 2.52
69 70 2.260481 CTAGCGAAACGGTCCTCTTTC 58.740 52.381 0.00 0.00 38.83 2.62
70 71 0.680061 AGCGAAACGGTCCTCTTTCT 59.320 50.000 0.00 0.00 29.31 2.52
71 72 1.070289 AGCGAAACGGTCCTCTTTCTT 59.930 47.619 0.00 0.00 29.31 2.52
72 73 1.459975 GCGAAACGGTCCTCTTTCTTC 59.540 52.381 0.00 0.00 0.00 2.87
73 74 2.067013 CGAAACGGTCCTCTTTCTTCC 58.933 52.381 7.11 0.00 0.00 3.46
74 75 2.288886 CGAAACGGTCCTCTTTCTTCCT 60.289 50.000 7.11 0.00 0.00 3.36
75 76 2.841442 AACGGTCCTCTTTCTTCCTG 57.159 50.000 0.00 0.00 0.00 3.86
76 77 1.718280 ACGGTCCTCTTTCTTCCTGT 58.282 50.000 0.00 0.00 0.00 4.00
77 78 1.344763 ACGGTCCTCTTTCTTCCTGTG 59.655 52.381 0.00 0.00 0.00 3.66
78 79 1.338200 CGGTCCTCTTTCTTCCTGTGG 60.338 57.143 0.00 0.00 0.00 4.17
79 80 1.978580 GGTCCTCTTTCTTCCTGTGGA 59.021 52.381 0.00 0.00 0.00 4.02
80 81 2.372172 GGTCCTCTTTCTTCCTGTGGAA 59.628 50.000 0.00 0.00 39.66 3.53
91 92 3.386768 TCCTGTGGAAGAAAGAGAACG 57.613 47.619 0.00 0.00 0.00 3.95
92 93 1.801178 CCTGTGGAAGAAAGAGAACGC 59.199 52.381 0.00 0.00 0.00 4.84
93 94 1.457303 CTGTGGAAGAAAGAGAACGCG 59.543 52.381 3.53 3.53 0.00 6.01
94 95 1.202486 TGTGGAAGAAAGAGAACGCGT 60.202 47.619 5.58 5.58 0.00 6.01
95 96 1.865340 GTGGAAGAAAGAGAACGCGTT 59.135 47.619 26.97 26.97 0.00 4.84
96 97 2.096860 GTGGAAGAAAGAGAACGCGTTC 60.097 50.000 38.00 38.00 39.78 3.95
97 98 2.132762 GGAAGAAAGAGAACGCGTTCA 58.867 47.619 42.89 0.00 41.84 3.18
98 99 2.542595 GGAAGAAAGAGAACGCGTTCAA 59.457 45.455 42.89 0.00 41.84 2.69
99 100 3.532950 GAAGAAAGAGAACGCGTTCAAC 58.467 45.455 42.89 35.13 41.84 3.18
100 101 2.822764 AGAAAGAGAACGCGTTCAACT 58.177 42.857 42.89 36.37 41.84 3.16
101 102 3.973657 AGAAAGAGAACGCGTTCAACTA 58.026 40.909 42.89 0.00 41.84 2.24
102 103 3.982058 AGAAAGAGAACGCGTTCAACTAG 59.018 43.478 42.89 0.98 41.84 2.57
103 104 3.637998 AAGAGAACGCGTTCAACTAGA 57.362 42.857 42.89 0.00 41.84 2.43
104 105 3.851976 AGAGAACGCGTTCAACTAGAT 57.148 42.857 42.89 26.71 41.84 1.98
105 106 4.175787 AGAGAACGCGTTCAACTAGATT 57.824 40.909 42.89 26.03 41.84 2.40
106 107 4.557205 AGAGAACGCGTTCAACTAGATTT 58.443 39.130 42.89 25.36 41.84 2.17
107 108 4.989168 AGAGAACGCGTTCAACTAGATTTT 59.011 37.500 42.89 24.69 41.84 1.82
108 109 5.465724 AGAGAACGCGTTCAACTAGATTTTT 59.534 36.000 42.89 24.22 41.84 1.94
131 132 3.557577 TTGGTGACTGATTGCATTTCG 57.442 42.857 0.00 0.00 0.00 3.46
132 133 2.503331 TGGTGACTGATTGCATTTCGT 58.497 42.857 0.00 0.00 0.00 3.85
133 134 2.884012 TGGTGACTGATTGCATTTCGTT 59.116 40.909 0.00 0.00 0.00 3.85
134 135 3.317711 TGGTGACTGATTGCATTTCGTTT 59.682 39.130 0.00 0.00 0.00 3.60
135 136 4.202101 TGGTGACTGATTGCATTTCGTTTT 60.202 37.500 0.00 0.00 0.00 2.43
136 137 4.744631 GGTGACTGATTGCATTTCGTTTTT 59.255 37.500 0.00 0.00 0.00 1.94
137 138 5.332506 GGTGACTGATTGCATTTCGTTTTTG 60.333 40.000 0.00 0.00 0.00 2.44
138 139 5.458452 GTGACTGATTGCATTTCGTTTTTGA 59.542 36.000 0.00 0.00 0.00 2.69
139 140 5.458452 TGACTGATTGCATTTCGTTTTTGAC 59.542 36.000 0.00 0.00 0.00 3.18
140 141 4.744631 ACTGATTGCATTTCGTTTTTGACC 59.255 37.500 0.00 0.00 0.00 4.02
141 142 4.942852 TGATTGCATTTCGTTTTTGACCT 58.057 34.783 0.00 0.00 0.00 3.85
142 143 4.981674 TGATTGCATTTCGTTTTTGACCTC 59.018 37.500 0.00 0.00 0.00 3.85
143 144 3.363341 TGCATTTCGTTTTTGACCTCC 57.637 42.857 0.00 0.00 0.00 4.30
144 145 2.955660 TGCATTTCGTTTTTGACCTCCT 59.044 40.909 0.00 0.00 0.00 3.69
145 146 3.383185 TGCATTTCGTTTTTGACCTCCTT 59.617 39.130 0.00 0.00 0.00 3.36
146 147 4.142049 TGCATTTCGTTTTTGACCTCCTTT 60.142 37.500 0.00 0.00 0.00 3.11
147 148 4.444388 GCATTTCGTTTTTGACCTCCTTTC 59.556 41.667 0.00 0.00 0.00 2.62
148 149 5.587289 CATTTCGTTTTTGACCTCCTTTCA 58.413 37.500 0.00 0.00 0.00 2.69
149 150 5.646577 TTTCGTTTTTGACCTCCTTTCAA 57.353 34.783 0.00 0.00 0.00 2.69
150 151 4.625972 TCGTTTTTGACCTCCTTTCAAC 57.374 40.909 0.00 0.00 32.65 3.18
151 152 4.266714 TCGTTTTTGACCTCCTTTCAACT 58.733 39.130 0.00 0.00 32.65 3.16
152 153 4.334481 TCGTTTTTGACCTCCTTTCAACTC 59.666 41.667 0.00 0.00 32.65 3.01
153 154 4.095782 CGTTTTTGACCTCCTTTCAACTCA 59.904 41.667 0.00 0.00 32.65 3.41
154 155 5.582550 GTTTTTGACCTCCTTTCAACTCAG 58.417 41.667 0.00 0.00 32.65 3.35
155 156 4.503714 TTTGACCTCCTTTCAACTCAGT 57.496 40.909 0.00 0.00 32.65 3.41
156 157 3.753294 TGACCTCCTTTCAACTCAGTC 57.247 47.619 0.00 0.00 0.00 3.51
157 158 3.038280 TGACCTCCTTTCAACTCAGTCA 58.962 45.455 0.00 0.00 0.00 3.41
158 159 3.181465 TGACCTCCTTTCAACTCAGTCAC 60.181 47.826 0.00 0.00 0.00 3.67
159 160 2.104963 ACCTCCTTTCAACTCAGTCACC 59.895 50.000 0.00 0.00 0.00 4.02
160 161 2.408050 CTCCTTTCAACTCAGTCACCG 58.592 52.381 0.00 0.00 0.00 4.94
165 166 0.827925 TCAACTCAGTCACCGCTCCT 60.828 55.000 0.00 0.00 0.00 3.69
173 174 2.266055 CACCGCTCCTGGTTCCTC 59.734 66.667 0.00 0.00 41.38 3.71
195 196 1.071567 GTCGGCGTCACTTAGACTGC 61.072 60.000 6.85 0.00 45.32 4.40
213 214 3.052036 CTGCTTTTGATGTTGTTTCCCG 58.948 45.455 0.00 0.00 0.00 5.14
226 227 0.312416 TTTCCCGAACATTGGCAACG 59.688 50.000 0.00 0.00 42.51 4.10
243 244 1.360551 CGGAGAGGTGCATACGGAG 59.639 63.158 0.00 0.00 0.00 4.63
346 348 1.134431 ACGGTGGGTTTTAACGTCTGT 60.134 47.619 0.00 0.00 31.39 3.41
351 353 3.001939 GTGGGTTTTAACGTCTGTGAGTG 59.998 47.826 0.00 0.00 0.00 3.51
375 377 6.922957 TGCTTGAATTTGTTGGAATAGTGTTC 59.077 34.615 0.00 0.00 0.00 3.18
378 380 7.581213 TGAATTTGTTGGAATAGTGTTCTGT 57.419 32.000 0.00 0.00 0.00 3.41
407 409 8.743714 GGATTTTCTTGGGGAATATATGATGTC 58.256 37.037 0.00 0.00 33.53 3.06
475 477 7.896811 TGGTATATGAGTATGGTCAGTTCATC 58.103 38.462 0.00 0.00 31.49 2.92
545 561 4.209703 ACAAATTACGACCGTACACAACTG 59.790 41.667 1.35 0.00 0.00 3.16
616 632 5.941555 ACTAACATTCTCCTCTAGTTGGG 57.058 43.478 5.07 0.12 0.00 4.12
638 654 1.144691 TTCACCCCCAGAACATCACA 58.855 50.000 0.00 0.00 0.00 3.58
703 719 1.153429 CTAGTAAGCGCCCCACCAC 60.153 63.158 2.29 0.00 0.00 4.16
746 762 5.648092 ACCAAAGATTAAATCGTGGGAGAAG 59.352 40.000 0.26 0.00 41.12 2.85
779 795 0.036022 GCCTTCCCAGCAGCTATAGG 59.964 60.000 0.00 0.64 0.00 2.57
806 822 2.177394 TAGCAGGCAATCACGACAAA 57.823 45.000 0.00 0.00 0.00 2.83
807 823 1.538047 AGCAGGCAATCACGACAAAT 58.462 45.000 0.00 0.00 0.00 2.32
808 824 2.710377 AGCAGGCAATCACGACAAATA 58.290 42.857 0.00 0.00 0.00 1.40
810 826 2.792542 GCAGGCAATCACGACAAATAGC 60.793 50.000 0.00 0.00 0.00 2.97
840 856 3.555527 TCAGCTGGGAGAGATGATTTG 57.444 47.619 15.13 0.00 42.29 2.32
846 862 4.343526 GCTGGGAGAGATGATTTGTAGAGA 59.656 45.833 0.00 0.00 0.00 3.10
858 874 9.234384 GATGATTTGTAGAGATTTTTGCTCATG 57.766 33.333 0.00 0.00 34.85 3.07
880 896 6.560003 TGTTGGAGCCATTTAGAGAGATTA 57.440 37.500 0.00 0.00 0.00 1.75
881 897 6.957631 TGTTGGAGCCATTTAGAGAGATTAA 58.042 36.000 0.00 0.00 0.00 1.40
882 898 7.577303 TGTTGGAGCCATTTAGAGAGATTAAT 58.423 34.615 0.00 0.00 0.00 1.40
883 899 8.055181 TGTTGGAGCCATTTAGAGAGATTAATT 58.945 33.333 0.00 0.00 0.00 1.40
884 900 8.563732 GTTGGAGCCATTTAGAGAGATTAATTC 58.436 37.037 0.00 0.00 0.00 2.17
905 921 0.249868 TAGATGATTTCGCGGGGCAG 60.250 55.000 6.13 0.00 0.00 4.85
932 948 0.606944 ATCGTAGAGGCTCCTAGGCG 60.607 60.000 11.71 8.93 46.58 5.52
950 966 4.178545 GGCGTCTATACCGGCTATTTTA 57.821 45.455 0.00 0.00 46.12 1.52
954 970 5.622914 GCGTCTATACCGGCTATTTTATGGA 60.623 44.000 0.00 0.00 0.00 3.41
991 1007 9.625747 TCATGTGTATTGCTAGAAAATATCCAA 57.374 29.630 0.00 0.00 0.00 3.53
1059 1075 5.125578 TGCACGTAGAAGAGAGTAACATGAT 59.874 40.000 0.00 0.00 0.00 2.45
1083 1099 2.307098 ACTCTATTTGTCAAGCTGGCCT 59.693 45.455 3.32 0.00 0.00 5.19
1148 1164 7.665559 GTGGCCAATTAGAGGTCATGAATATTA 59.334 37.037 7.24 0.00 43.63 0.98
1242 1259 7.558161 TGATTGATGTTAGTAGGAATTGCTG 57.442 36.000 10.10 0.00 0.00 4.41
1290 1307 0.254747 CCGACTCCTATTTTGGGCCA 59.745 55.000 0.00 0.00 0.00 5.36
1297 1314 3.430453 TCCTATTTTGGGCCAGACTTTG 58.570 45.455 6.23 0.00 0.00 2.77
1478 1496 1.489230 AGGACCTAATAAACCTGGGCG 59.511 52.381 0.00 0.00 0.00 6.13
1525 1543 5.815233 TCCCCTTGTGCAATGAATAAAAA 57.185 34.783 0.00 0.00 0.00 1.94
1527 1545 4.694982 CCCCTTGTGCAATGAATAAAAACC 59.305 41.667 0.00 0.00 0.00 3.27
1530 1548 6.261826 CCCTTGTGCAATGAATAAAAACCAAA 59.738 34.615 0.00 0.00 0.00 3.28
1531 1549 7.040548 CCCTTGTGCAATGAATAAAAACCAAAT 60.041 33.333 0.00 0.00 0.00 2.32
1532 1550 7.804129 CCTTGTGCAATGAATAAAAACCAAATG 59.196 33.333 0.00 0.00 0.00 2.32
1533 1551 7.199541 TGTGCAATGAATAAAAACCAAATGG 57.800 32.000 0.00 0.00 42.17 3.16
1534 1552 6.994496 TGTGCAATGAATAAAAACCAAATGGA 59.006 30.769 6.42 0.00 38.94 3.41
1535 1553 7.664731 TGTGCAATGAATAAAAACCAAATGGAT 59.335 29.630 6.42 0.00 38.94 3.41
1536 1554 7.964011 GTGCAATGAATAAAAACCAAATGGATG 59.036 33.333 6.42 0.00 38.94 3.51
1537 1555 7.120873 TGCAATGAATAAAAACCAAATGGATGG 59.879 33.333 6.42 0.00 46.38 3.51
1571 1589 7.664552 AAATCATGCATCTTAGGAAATCCAA 57.335 32.000 0.00 0.00 38.89 3.53
1795 1813 6.781014 AGATGGGATCATGCAAACATATCTTT 59.219 34.615 0.00 0.00 33.67 2.52
1796 1814 6.151663 TGGGATCATGCAAACATATCTTTG 57.848 37.500 0.00 0.00 33.67 2.77
1847 1867 4.835056 AGTGCCTCCTTTTCTAAAAGCATT 59.165 37.500 9.26 0.86 43.07 3.56
1851 1871 6.183360 TGCCTCCTTTTCTAAAAGCATTATCG 60.183 38.462 9.26 0.00 43.07 2.92
1915 1935 2.390696 TCTATACCCGCTTACTTGGCA 58.609 47.619 0.00 0.00 0.00 4.92
1925 1945 4.486090 CGCTTACTTGGCATCGATACTAT 58.514 43.478 0.00 0.00 0.00 2.12
1971 1991 2.576191 TCAAGGTGCCAAGCCTACTATT 59.424 45.455 0.00 0.00 34.81 1.73
1997 2020 1.744368 CTGCTCATGCCGCTCTTGT 60.744 57.895 8.05 0.00 38.71 3.16
2010 2033 2.504367 GCTCTTGTTTCCTGGTAAGCA 58.496 47.619 0.00 0.00 0.00 3.91
2067 2100 4.635223 TCCTCAATGCATGATGTAGCTAC 58.365 43.478 17.30 17.30 37.44 3.58
2101 2135 2.025155 TCGTACTCCTTGCCTCATCTC 58.975 52.381 0.00 0.00 0.00 2.75
2110 2144 3.688673 CCTTGCCTCATCTCTTTGTCTTC 59.311 47.826 0.00 0.00 0.00 2.87
2202 2238 0.250252 TCTGAAGCCGACACATGCAA 60.250 50.000 0.00 0.00 0.00 4.08
2260 2296 3.002038 TGCAAGCATGATCCATGTGTA 57.998 42.857 0.00 0.00 43.10 2.90
2461 2516 6.070309 AGCAATGGAAGAAGTTGAGACTCTAT 60.070 38.462 3.68 0.00 34.21 1.98
2462 2517 6.597280 GCAATGGAAGAAGTTGAGACTCTATT 59.403 38.462 3.68 0.00 34.21 1.73
2706 2771 0.039618 GTTTGATTGGAGGGCTGGGA 59.960 55.000 0.00 0.00 0.00 4.37
2725 2790 7.014615 GGCTGGGAAATTAATCAATAGTGTCAT 59.985 37.037 0.00 0.00 0.00 3.06
2741 2806 9.905713 AATAGTGTCATGGTAGATTAACACAAT 57.094 29.630 11.27 0.00 39.48 2.71
2767 2832 7.100458 ACCATTAGAGATGGCATGTAAAAAC 57.900 36.000 3.81 0.00 42.82 2.43
2768 2833 6.663093 ACCATTAGAGATGGCATGTAAAAACA 59.337 34.615 3.81 0.00 42.82 2.83
2769 2834 7.148018 ACCATTAGAGATGGCATGTAAAAACAG 60.148 37.037 3.81 0.00 42.82 3.16
2772 2837 6.506500 AGAGATGGCATGTAAAAACAGAAG 57.493 37.500 3.81 0.00 0.00 2.85
2774 2839 5.324409 AGATGGCATGTAAAAACAGAAGGA 58.676 37.500 3.81 0.00 0.00 3.36
2859 2925 2.349886 CAGGAACACATAAAGAGCGCTC 59.650 50.000 30.01 30.01 0.00 5.03
3022 3088 4.729881 TGAGGGCTAAGTAATTAACCCCAT 59.270 41.667 16.01 0.94 34.13 4.00
3046 3112 3.523564 AGCACCTAAGAATTCCAGCCTTA 59.476 43.478 0.65 0.00 0.00 2.69
3049 3115 5.501156 CACCTAAGAATTCCAGCCTTAAGT 58.499 41.667 0.65 0.00 0.00 2.24
3050 3116 6.650120 CACCTAAGAATTCCAGCCTTAAGTA 58.350 40.000 0.65 0.00 0.00 2.24
3052 3118 7.775561 CACCTAAGAATTCCAGCCTTAAGTAAT 59.224 37.037 0.65 0.00 0.00 1.89
3053 3119 8.336987 ACCTAAGAATTCCAGCCTTAAGTAATT 58.663 33.333 0.65 0.21 0.00 1.40
3054 3120 9.190317 CCTAAGAATTCCAGCCTTAAGTAATTT 57.810 33.333 0.65 0.00 0.00 1.82
3057 3123 7.840931 AGAATTCCAGCCTTAAGTAATTTTGG 58.159 34.615 0.65 0.63 0.00 3.28
3058 3124 7.673926 AGAATTCCAGCCTTAAGTAATTTTGGA 59.326 33.333 0.65 2.86 0.00 3.53
3059 3125 7.978099 ATTCCAGCCTTAAGTAATTTTGGAT 57.022 32.000 0.97 0.00 33.83 3.41
3060 3126 6.773976 TCCAGCCTTAAGTAATTTTGGATG 57.226 37.500 0.97 5.52 31.61 3.51
3061 3127 5.656416 TCCAGCCTTAAGTAATTTTGGATGG 59.344 40.000 18.72 18.72 43.28 3.51
3062 3128 5.351458 CAGCCTTAAGTAATTTTGGATGGC 58.649 41.667 0.97 0.00 37.15 4.40
3063 3129 5.127682 CAGCCTTAAGTAATTTTGGATGGCT 59.872 40.000 0.97 0.00 46.50 4.75
3064 3130 5.127682 AGCCTTAAGTAATTTTGGATGGCTG 59.872 40.000 0.00 0.00 44.27 4.85
3065 3131 5.682212 GCCTTAAGTAATTTTGGATGGCTGG 60.682 44.000 0.97 0.00 34.42 4.85
3066 3132 5.656416 CCTTAAGTAATTTTGGATGGCTGGA 59.344 40.000 0.97 0.00 0.00 3.86
3067 3133 6.154363 CCTTAAGTAATTTTGGATGGCTGGAA 59.846 38.462 0.97 0.00 0.00 3.53
3068 3134 5.405935 AAGTAATTTTGGATGGCTGGAAC 57.594 39.130 0.00 0.00 0.00 3.62
3069 3135 3.443681 AGTAATTTTGGATGGCTGGAACG 59.556 43.478 0.00 0.00 0.00 3.95
3070 3136 1.923356 ATTTTGGATGGCTGGAACGT 58.077 45.000 0.00 0.00 0.00 3.99
3071 3137 0.958091 TTTTGGATGGCTGGAACGTG 59.042 50.000 0.00 0.00 0.00 4.49
3072 3138 0.179004 TTTGGATGGCTGGAACGTGT 60.179 50.000 0.00 0.00 0.00 4.49
3073 3139 0.888736 TTGGATGGCTGGAACGTGTG 60.889 55.000 0.00 0.00 0.00 3.82
3074 3140 1.302511 GGATGGCTGGAACGTGTGT 60.303 57.895 0.00 0.00 0.00 3.72
3075 3141 0.889186 GGATGGCTGGAACGTGTGTT 60.889 55.000 0.00 0.00 42.23 3.32
3076 3142 1.609580 GGATGGCTGGAACGTGTGTTA 60.610 52.381 0.00 0.00 38.78 2.41
3077 3143 1.732259 GATGGCTGGAACGTGTGTTAG 59.268 52.381 0.00 0.00 38.78 2.34
3078 3144 0.753867 TGGCTGGAACGTGTGTTAGA 59.246 50.000 0.00 0.00 38.78 2.10
3079 3145 1.346395 TGGCTGGAACGTGTGTTAGAT 59.654 47.619 0.00 0.00 38.78 1.98
3080 3146 1.732259 GGCTGGAACGTGTGTTAGATG 59.268 52.381 0.00 0.00 38.78 2.90
3081 3147 2.611971 GGCTGGAACGTGTGTTAGATGA 60.612 50.000 0.00 0.00 38.78 2.92
3082 3148 3.262420 GCTGGAACGTGTGTTAGATGAT 58.738 45.455 0.00 0.00 38.78 2.45
3083 3149 3.307242 GCTGGAACGTGTGTTAGATGATC 59.693 47.826 0.00 0.00 38.78 2.92
3084 3150 3.507786 TGGAACGTGTGTTAGATGATCG 58.492 45.455 0.00 0.00 38.78 3.69
3085 3151 3.057104 TGGAACGTGTGTTAGATGATCGT 60.057 43.478 0.00 0.00 38.78 3.73
3086 3152 3.303495 GGAACGTGTGTTAGATGATCGTG 59.697 47.826 0.00 0.00 38.78 4.35
3087 3153 3.570926 ACGTGTGTTAGATGATCGTGT 57.429 42.857 0.00 0.00 0.00 4.49
3088 3154 3.909430 ACGTGTGTTAGATGATCGTGTT 58.091 40.909 0.00 0.00 0.00 3.32
3112 3208 6.699895 TGTACAAACACGATCATCTAACAC 57.300 37.500 0.00 0.00 0.00 3.32
3113 3209 6.217294 TGTACAAACACGATCATCTAACACA 58.783 36.000 0.00 0.00 0.00 3.72
3164 3260 1.089920 GGACAGGCAGTGCAATACAG 58.910 55.000 18.61 0.00 38.62 2.74
3216 3312 4.410228 ACAGTAGATACACCATCCAATGCT 59.590 41.667 0.00 0.00 33.75 3.79
3219 3315 6.425114 CAGTAGATACACCATCCAATGCTAAC 59.575 42.308 0.00 0.00 33.75 2.34
3220 3316 4.718961 AGATACACCATCCAATGCTAACC 58.281 43.478 0.00 0.00 33.75 2.85
3229 3325 5.508489 CCATCCAATGCTAACCATTCATCAC 60.508 44.000 0.00 0.00 42.15 3.06
3350 3446 4.725790 ATAAATGCAAAGGGTTCTCAGC 57.274 40.909 0.00 0.00 0.00 4.26
3412 3508 5.880901 ACTTCTCAAGGGTTGTGATAATGT 58.119 37.500 0.00 0.00 33.69 2.71
3421 3517 5.714333 AGGGTTGTGATAATGTGCATTACAA 59.286 36.000 6.76 7.08 43.77 2.41
3437 3533 9.931210 GTGCATTACAATTAAGTTAGTCATACC 57.069 33.333 0.00 0.00 0.00 2.73
3438 3534 9.899661 TGCATTACAATTAAGTTAGTCATACCT 57.100 29.630 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.277211 TTTCTCGTGCCTCCCGACG 62.277 63.158 0.00 0.00 36.91 5.12
29 30 1.737008 GTTTCTCGTGCCTCCCGAC 60.737 63.158 0.00 0.00 0.00 4.79
30 31 2.654877 GTTTCTCGTGCCTCCCGA 59.345 61.111 0.00 0.00 0.00 5.14
31 32 2.434359 GGTTTCTCGTGCCTCCCG 60.434 66.667 0.00 0.00 0.00 5.14
32 33 1.262640 TAGGGTTTCTCGTGCCTCCC 61.263 60.000 0.00 0.00 35.56 4.30
33 34 0.175989 CTAGGGTTTCTCGTGCCTCC 59.824 60.000 0.00 0.00 0.00 4.30
34 35 0.460459 GCTAGGGTTTCTCGTGCCTC 60.460 60.000 0.00 0.00 0.00 4.70
35 36 1.597461 GCTAGGGTTTCTCGTGCCT 59.403 57.895 0.00 0.00 0.00 4.75
36 37 1.810030 CGCTAGGGTTTCTCGTGCC 60.810 63.158 0.00 0.00 0.00 5.01
37 38 0.389426 TTCGCTAGGGTTTCTCGTGC 60.389 55.000 6.70 0.00 0.00 5.34
38 39 1.725164 GTTTCGCTAGGGTTTCTCGTG 59.275 52.381 6.70 0.00 0.00 4.35
39 40 1.668047 CGTTTCGCTAGGGTTTCTCGT 60.668 52.381 6.70 0.00 0.00 4.18
40 41 0.989890 CGTTTCGCTAGGGTTTCTCG 59.010 55.000 6.70 3.15 0.00 4.04
41 42 1.337541 ACCGTTTCGCTAGGGTTTCTC 60.338 52.381 6.70 0.00 32.61 2.87
42 43 0.683412 ACCGTTTCGCTAGGGTTTCT 59.317 50.000 6.70 0.00 32.61 2.52
43 44 1.073964 GACCGTTTCGCTAGGGTTTC 58.926 55.000 6.70 0.00 36.48 2.78
44 45 0.321034 GGACCGTTTCGCTAGGGTTT 60.321 55.000 6.70 0.00 36.48 3.27
45 46 1.190178 AGGACCGTTTCGCTAGGGTT 61.190 55.000 6.70 0.00 36.48 4.11
46 47 1.602327 GAGGACCGTTTCGCTAGGGT 61.602 60.000 6.70 0.00 38.90 4.34
47 48 1.141234 GAGGACCGTTTCGCTAGGG 59.859 63.158 0.00 0.00 0.00 3.53
48 49 0.531200 AAGAGGACCGTTTCGCTAGG 59.469 55.000 0.00 0.00 0.00 3.02
49 50 2.094649 AGAAAGAGGACCGTTTCGCTAG 60.095 50.000 13.62 0.00 37.67 3.42
50 51 1.891150 AGAAAGAGGACCGTTTCGCTA 59.109 47.619 13.62 0.00 37.67 4.26
51 52 0.680061 AGAAAGAGGACCGTTTCGCT 59.320 50.000 13.62 0.00 37.67 4.93
52 53 1.459975 GAAGAAAGAGGACCGTTTCGC 59.540 52.381 13.62 8.59 37.67 4.70
53 54 2.067013 GGAAGAAAGAGGACCGTTTCG 58.933 52.381 13.62 0.00 37.67 3.46
54 55 3.067833 CAGGAAGAAAGAGGACCGTTTC 58.932 50.000 12.26 12.26 33.59 2.78
55 56 2.438392 ACAGGAAGAAAGAGGACCGTTT 59.562 45.455 0.00 0.00 0.00 3.60
56 57 2.047830 ACAGGAAGAAAGAGGACCGTT 58.952 47.619 0.00 0.00 0.00 4.44
57 58 1.344763 CACAGGAAGAAAGAGGACCGT 59.655 52.381 0.00 0.00 0.00 4.83
58 59 1.338200 CCACAGGAAGAAAGAGGACCG 60.338 57.143 0.00 0.00 0.00 4.79
59 60 1.978580 TCCACAGGAAGAAAGAGGACC 59.021 52.381 0.00 0.00 0.00 4.46
60 61 3.771577 TTCCACAGGAAGAAAGAGGAC 57.228 47.619 0.00 0.00 36.71 3.85
70 71 3.728845 CGTTCTCTTTCTTCCACAGGAA 58.271 45.455 0.00 0.00 39.66 3.36
71 72 2.548067 GCGTTCTCTTTCTTCCACAGGA 60.548 50.000 0.00 0.00 0.00 3.86
72 73 1.801178 GCGTTCTCTTTCTTCCACAGG 59.199 52.381 0.00 0.00 0.00 4.00
73 74 1.457303 CGCGTTCTCTTTCTTCCACAG 59.543 52.381 0.00 0.00 0.00 3.66
74 75 1.202486 ACGCGTTCTCTTTCTTCCACA 60.202 47.619 5.58 0.00 0.00 4.17
75 76 1.499049 ACGCGTTCTCTTTCTTCCAC 58.501 50.000 5.58 0.00 0.00 4.02
76 77 2.132762 GAACGCGTTCTCTTTCTTCCA 58.867 47.619 37.61 0.00 36.69 3.53
77 78 2.132762 TGAACGCGTTCTCTTTCTTCC 58.867 47.619 41.46 20.30 40.14 3.46
78 79 3.245519 AGTTGAACGCGTTCTCTTTCTTC 59.754 43.478 41.46 24.84 40.14 2.87
79 80 3.195661 AGTTGAACGCGTTCTCTTTCTT 58.804 40.909 41.46 22.51 40.14 2.52
80 81 2.822764 AGTTGAACGCGTTCTCTTTCT 58.177 42.857 41.46 29.36 40.14 2.52
81 82 3.979495 TCTAGTTGAACGCGTTCTCTTTC 59.021 43.478 41.46 28.07 40.14 2.62
82 83 3.973657 TCTAGTTGAACGCGTTCTCTTT 58.026 40.909 41.46 28.70 40.14 2.52
83 84 3.637998 TCTAGTTGAACGCGTTCTCTT 57.362 42.857 41.46 30.12 40.14 2.85
84 85 3.851976 ATCTAGTTGAACGCGTTCTCT 57.148 42.857 41.46 36.86 40.14 3.10
85 86 4.905412 AAATCTAGTTGAACGCGTTCTC 57.095 40.909 41.46 33.64 40.14 2.87
86 87 5.668558 AAAAATCTAGTTGAACGCGTTCT 57.331 34.783 41.46 28.90 40.14 3.01
108 109 4.744137 CGAAATGCAATCAGTCACCAAAAA 59.256 37.500 0.00 0.00 0.00 1.94
109 110 4.202101 ACGAAATGCAATCAGTCACCAAAA 60.202 37.500 0.00 0.00 0.00 2.44
110 111 3.317711 ACGAAATGCAATCAGTCACCAAA 59.682 39.130 0.00 0.00 0.00 3.28
111 112 2.884012 ACGAAATGCAATCAGTCACCAA 59.116 40.909 0.00 0.00 0.00 3.67
112 113 2.503331 ACGAAATGCAATCAGTCACCA 58.497 42.857 0.00 0.00 0.00 4.17
113 114 3.559238 AACGAAATGCAATCAGTCACC 57.441 42.857 0.00 0.00 0.00 4.02
114 115 5.458452 TCAAAAACGAAATGCAATCAGTCAC 59.542 36.000 0.00 0.00 0.00 3.67
115 116 5.458452 GTCAAAAACGAAATGCAATCAGTCA 59.542 36.000 0.00 0.00 0.00 3.41
116 117 5.107875 GGTCAAAAACGAAATGCAATCAGTC 60.108 40.000 0.00 0.00 0.00 3.51
117 118 4.744631 GGTCAAAAACGAAATGCAATCAGT 59.255 37.500 0.00 0.00 0.00 3.41
118 119 4.984161 AGGTCAAAAACGAAATGCAATCAG 59.016 37.500 0.00 0.00 0.00 2.90
119 120 4.942852 AGGTCAAAAACGAAATGCAATCA 58.057 34.783 0.00 0.00 0.00 2.57
120 121 4.385748 GGAGGTCAAAAACGAAATGCAATC 59.614 41.667 0.00 0.00 0.00 2.67
121 122 4.039124 AGGAGGTCAAAAACGAAATGCAAT 59.961 37.500 0.00 0.00 0.00 3.56
122 123 3.383185 AGGAGGTCAAAAACGAAATGCAA 59.617 39.130 0.00 0.00 0.00 4.08
123 124 2.955660 AGGAGGTCAAAAACGAAATGCA 59.044 40.909 0.00 0.00 0.00 3.96
124 125 3.643159 AGGAGGTCAAAAACGAAATGC 57.357 42.857 0.00 0.00 0.00 3.56
125 126 5.587289 TGAAAGGAGGTCAAAAACGAAATG 58.413 37.500 0.00 0.00 0.00 2.32
126 127 5.845391 TGAAAGGAGGTCAAAAACGAAAT 57.155 34.783 0.00 0.00 0.00 2.17
127 128 5.184287 AGTTGAAAGGAGGTCAAAAACGAAA 59.816 36.000 0.00 0.00 36.77 3.46
128 129 4.703093 AGTTGAAAGGAGGTCAAAAACGAA 59.297 37.500 0.00 0.00 36.77 3.85
129 130 4.266714 AGTTGAAAGGAGGTCAAAAACGA 58.733 39.130 0.00 0.00 36.77 3.85
130 131 4.095782 TGAGTTGAAAGGAGGTCAAAAACG 59.904 41.667 0.00 0.00 36.77 3.60
131 132 5.125578 ACTGAGTTGAAAGGAGGTCAAAAAC 59.874 40.000 0.00 0.00 36.77 2.43
132 133 5.261216 ACTGAGTTGAAAGGAGGTCAAAAA 58.739 37.500 0.00 0.00 36.77 1.94
133 134 4.855340 ACTGAGTTGAAAGGAGGTCAAAA 58.145 39.130 0.00 0.00 36.77 2.44
134 135 4.080582 TGACTGAGTTGAAAGGAGGTCAAA 60.081 41.667 0.00 0.00 36.77 2.69
135 136 3.454447 TGACTGAGTTGAAAGGAGGTCAA 59.546 43.478 0.00 0.00 32.62 3.18
136 137 3.038280 TGACTGAGTTGAAAGGAGGTCA 58.962 45.455 0.00 0.00 0.00 4.02
137 138 3.394719 GTGACTGAGTTGAAAGGAGGTC 58.605 50.000 0.00 0.00 0.00 3.85
138 139 2.104963 GGTGACTGAGTTGAAAGGAGGT 59.895 50.000 0.00 0.00 0.00 3.85
139 140 2.772287 GGTGACTGAGTTGAAAGGAGG 58.228 52.381 0.00 0.00 0.00 4.30
140 141 2.408050 CGGTGACTGAGTTGAAAGGAG 58.592 52.381 0.00 0.00 0.00 3.69
141 142 1.540363 GCGGTGACTGAGTTGAAAGGA 60.540 52.381 0.00 0.00 0.00 3.36
142 143 0.868406 GCGGTGACTGAGTTGAAAGG 59.132 55.000 0.00 0.00 0.00 3.11
143 144 1.795286 GAGCGGTGACTGAGTTGAAAG 59.205 52.381 0.00 0.00 0.00 2.62
144 145 1.540363 GGAGCGGTGACTGAGTTGAAA 60.540 52.381 0.00 0.00 0.00 2.69
145 146 0.033504 GGAGCGGTGACTGAGTTGAA 59.966 55.000 0.00 0.00 0.00 2.69
146 147 0.827925 AGGAGCGGTGACTGAGTTGA 60.828 55.000 0.00 0.00 0.00 3.18
147 148 0.668706 CAGGAGCGGTGACTGAGTTG 60.669 60.000 9.61 0.00 34.21 3.16
148 149 1.668294 CAGGAGCGGTGACTGAGTT 59.332 57.895 9.61 0.00 34.21 3.01
149 150 2.279069 CCAGGAGCGGTGACTGAGT 61.279 63.158 15.25 0.00 34.21 3.41
150 151 1.821061 AACCAGGAGCGGTGACTGAG 61.821 60.000 15.25 9.14 39.95 3.35
151 152 1.816863 GAACCAGGAGCGGTGACTGA 61.817 60.000 15.25 0.00 39.95 3.41
152 153 1.374758 GAACCAGGAGCGGTGACTG 60.375 63.158 8.50 8.50 39.95 3.51
153 154 2.584391 GGAACCAGGAGCGGTGACT 61.584 63.158 0.00 0.00 39.95 3.41
154 155 2.047179 GGAACCAGGAGCGGTGAC 60.047 66.667 0.00 0.00 39.95 3.67
155 156 2.203788 AGGAACCAGGAGCGGTGA 60.204 61.111 0.00 0.00 39.95 4.02
156 157 2.266055 GAGGAACCAGGAGCGGTG 59.734 66.667 0.00 0.00 39.95 4.94
157 158 3.382832 CGAGGAACCAGGAGCGGT 61.383 66.667 0.00 0.00 42.71 5.68
158 159 4.148825 CCGAGGAACCAGGAGCGG 62.149 72.222 0.00 0.00 0.00 5.52
159 160 4.148825 CCCGAGGAACCAGGAGCG 62.149 72.222 0.00 0.00 0.00 5.03
160 161 3.003763 ACCCGAGGAACCAGGAGC 61.004 66.667 0.00 0.00 0.00 4.70
173 174 2.202570 CTAAGTGACGCCGACCCG 60.203 66.667 0.00 0.00 0.00 5.28
195 196 4.677584 TGTTCGGGAAACAACATCAAAAG 58.322 39.130 0.00 0.00 44.83 2.27
213 214 0.804989 CCTCTCCGTTGCCAATGTTC 59.195 55.000 0.00 0.00 0.00 3.18
226 227 0.824759 AACTCCGTATGCACCTCTCC 59.175 55.000 0.00 0.00 0.00 3.71
243 244 0.666577 ACTCGCGCACAGACCTAAAC 60.667 55.000 8.75 0.00 0.00 2.01
346 348 4.998671 TTCCAACAAATTCAAGCACTCA 57.001 36.364 0.00 0.00 0.00 3.41
351 353 7.115378 CAGAACACTATTCCAACAAATTCAAGC 59.885 37.037 0.00 0.00 0.00 4.01
375 377 4.316025 TTCCCCAAGAAAATCCCTACAG 57.684 45.455 0.00 0.00 0.00 2.74
378 380 8.532774 TCATATATTCCCCAAGAAAATCCCTA 57.467 34.615 0.00 0.00 38.21 3.53
475 477 8.012957 ACTATCACTCCTCAAATACCACTTAG 57.987 38.462 0.00 0.00 0.00 2.18
545 561 6.092807 CCCTAGAAAAACACTTGTAGATGCTC 59.907 42.308 0.00 0.00 0.00 4.26
616 632 2.296190 GTGATGTTCTGGGGGTGAAAAC 59.704 50.000 0.00 0.00 0.00 2.43
638 654 4.899502 ACATCGAGAATTTCTTCCACACT 58.100 39.130 0.00 0.00 31.27 3.55
703 719 7.819415 TCTTTGGTAATACACTGAGAGATTGTG 59.181 37.037 0.00 0.00 37.67 3.33
746 762 2.668261 GAAGGCCGGCATGAAATCGC 62.668 60.000 30.85 7.16 0.00 4.58
806 822 2.159198 CCAGCTGAAAAATTGCCGCTAT 60.159 45.455 17.39 0.00 0.00 2.97
807 823 1.202114 CCAGCTGAAAAATTGCCGCTA 59.798 47.619 17.39 0.00 0.00 4.26
808 824 0.037975 CCAGCTGAAAAATTGCCGCT 60.038 50.000 17.39 0.00 0.00 5.52
810 826 0.602562 TCCCAGCTGAAAAATTGCCG 59.397 50.000 17.39 0.00 0.00 5.69
840 856 6.500684 TCCAACATGAGCAAAAATCTCTAC 57.499 37.500 0.00 0.00 0.00 2.59
858 874 8.457238 AATTAATCTCTCTAAATGGCTCCAAC 57.543 34.615 0.00 0.00 0.00 3.77
880 896 2.800544 CCCGCGAAATCATCTACGAATT 59.199 45.455 8.23 0.00 0.00 2.17
881 897 2.404215 CCCGCGAAATCATCTACGAAT 58.596 47.619 8.23 0.00 0.00 3.34
882 898 1.537348 CCCCGCGAAATCATCTACGAA 60.537 52.381 8.23 0.00 0.00 3.85
883 899 0.031585 CCCCGCGAAATCATCTACGA 59.968 55.000 8.23 0.00 0.00 3.43
884 900 1.557443 GCCCCGCGAAATCATCTACG 61.557 60.000 8.23 0.00 0.00 3.51
905 921 0.605589 AGCCTCTACGATGCTATGGC 59.394 55.000 0.00 0.00 32.16 4.40
932 948 8.611654 TTTTCCATAAAATAGCCGGTATAGAC 57.388 34.615 1.90 0.00 29.59 2.59
1059 1075 3.849911 CCAGCTTGACAAATAGAGTCGA 58.150 45.455 0.00 0.00 38.83 4.20
1066 1082 2.877097 TCAGGCCAGCTTGACAAATA 57.123 45.000 5.01 0.00 0.00 1.40
1083 1099 8.865090 TCCAAGTTAATTCAATTTTAGCCTTCA 58.135 29.630 0.00 0.00 0.00 3.02
1148 1164 6.690530 CAACATCAACCAAATACATGTTCCT 58.309 36.000 2.30 0.00 35.89 3.36
1571 1589 2.095567 GCTGCTTCATCACATGTTCGTT 60.096 45.455 0.00 0.00 0.00 3.85
1676 1694 5.992729 TCTTTGCTCCACGTTTTTGTATAC 58.007 37.500 0.00 0.00 0.00 1.47
1681 1699 5.069485 CAATTCTTTGCTCCACGTTTTTG 57.931 39.130 0.00 0.00 0.00 2.44
1769 1787 6.312529 AGATATGTTTGCATGATCCCATCTT 58.687 36.000 0.00 0.00 36.58 2.40
1815 1833 4.225942 AGAAAAGGAGGCACTGATGATGTA 59.774 41.667 0.00 0.00 41.55 2.29
1847 1867 3.131577 ACGATCTTTTGTAGGCACCGATA 59.868 43.478 0.00 0.00 0.00 2.92
1851 1871 1.130561 GCACGATCTTTTGTAGGCACC 59.869 52.381 0.00 0.00 0.00 5.01
1887 1907 7.309867 CCAAGTAAGCGGGTATAGAATAGATGT 60.310 40.741 0.00 0.00 0.00 3.06
1925 1945 5.163195 GGCCCCTCATCTCTTTAGTCATAAA 60.163 44.000 0.00 0.00 0.00 1.40
1971 1991 0.460811 CGGCATGAGCAGTAGCAAGA 60.461 55.000 0.00 0.00 45.49 3.02
1997 2020 5.186256 TCCATACAATGCTTACCAGGAAA 57.814 39.130 0.00 0.00 0.00 3.13
2010 2033 8.814931 TCTTTGTGGATGAAATTTCCATACAAT 58.185 29.630 15.48 1.08 44.75 2.71
2067 2100 7.517417 GCAAGGAGTACGAATTTCACATATGAG 60.517 40.741 10.38 0.87 35.83 2.90
2101 2135 9.145865 GGTGTTCTATAGAGAAAGAAGACAAAG 57.854 37.037 0.38 0.00 43.91 2.77
2110 2144 7.296628 AGGCTATGGTGTTCTATAGAGAAAG 57.703 40.000 0.38 0.00 43.38 2.62
2202 2238 1.794714 ATAGGTCCTGCTGAACCGAT 58.205 50.000 0.00 0.00 0.00 4.18
2260 2296 0.833409 CCTCCTTTTGGCAGGCCTTT 60.833 55.000 0.00 0.00 40.12 3.11
2725 2790 8.544622 TCTAATGGTCATTGTGTTAATCTACCA 58.455 33.333 6.46 0.00 39.87 3.25
2741 2806 5.628797 TTACATGCCATCTCTAATGGTCA 57.371 39.130 5.98 5.13 41.17 4.02
3022 3088 2.356125 GGCTGGAATTCTTAGGTGCTCA 60.356 50.000 5.23 0.00 0.00 4.26
3046 3112 4.082245 CGTTCCAGCCATCCAAAATTACTT 60.082 41.667 0.00 0.00 0.00 2.24
3049 3115 3.192422 CACGTTCCAGCCATCCAAAATTA 59.808 43.478 0.00 0.00 0.00 1.40
3050 3116 2.029110 CACGTTCCAGCCATCCAAAATT 60.029 45.455 0.00 0.00 0.00 1.82
3052 3118 0.958091 CACGTTCCAGCCATCCAAAA 59.042 50.000 0.00 0.00 0.00 2.44
3053 3119 0.179004 ACACGTTCCAGCCATCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
3054 3120 0.888736 CACACGTTCCAGCCATCCAA 60.889 55.000 0.00 0.00 0.00 3.53
3055 3121 1.302431 CACACGTTCCAGCCATCCA 60.302 57.895 0.00 0.00 0.00 3.41
3056 3122 0.889186 AACACACGTTCCAGCCATCC 60.889 55.000 0.00 0.00 0.00 3.51
3057 3123 1.732259 CTAACACACGTTCCAGCCATC 59.268 52.381 0.00 0.00 36.52 3.51
3058 3124 1.346395 TCTAACACACGTTCCAGCCAT 59.654 47.619 0.00 0.00 36.52 4.40
3059 3125 0.753867 TCTAACACACGTTCCAGCCA 59.246 50.000 0.00 0.00 36.52 4.75
3060 3126 1.732259 CATCTAACACACGTTCCAGCC 59.268 52.381 0.00 0.00 36.52 4.85
3061 3127 2.683968 TCATCTAACACACGTTCCAGC 58.316 47.619 0.00 0.00 36.52 4.85
3062 3128 3.547868 CGATCATCTAACACACGTTCCAG 59.452 47.826 0.00 0.00 36.52 3.86
3063 3129 3.057104 ACGATCATCTAACACACGTTCCA 60.057 43.478 0.00 0.00 36.52 3.53
3064 3130 3.303495 CACGATCATCTAACACACGTTCC 59.697 47.826 0.00 0.00 36.52 3.62
3065 3131 3.918591 ACACGATCATCTAACACACGTTC 59.081 43.478 0.00 0.00 36.52 3.95
3066 3132 3.909430 ACACGATCATCTAACACACGTT 58.091 40.909 0.00 0.00 39.24 3.99
3067 3133 3.570926 ACACGATCATCTAACACACGT 57.429 42.857 0.00 0.00 0.00 4.49
3068 3134 4.149922 ACAAACACGATCATCTAACACACG 59.850 41.667 0.00 0.00 0.00 4.49
3069 3135 5.591643 ACAAACACGATCATCTAACACAC 57.408 39.130 0.00 0.00 0.00 3.82
3070 3136 6.217294 TGTACAAACACGATCATCTAACACA 58.783 36.000 0.00 0.00 0.00 3.72
3071 3137 6.699895 TGTACAAACACGATCATCTAACAC 57.300 37.500 0.00 0.00 0.00 3.32
3072 3138 7.716768 TTTGTACAAACACGATCATCTAACA 57.283 32.000 17.01 0.00 34.61 2.41
3087 3153 7.224949 TGTGTTAGATGATCGTGTTTGTACAAA 59.775 33.333 17.01 17.01 35.69 2.83
3088 3154 6.702282 TGTGTTAGATGATCGTGTTTGTACAA 59.298 34.615 3.59 3.59 35.69 2.41
3106 3202 1.732259 GATGGCTGGAACGTGTGTTAG 59.268 52.381 0.00 0.00 38.78 2.34
3112 3208 0.888736 TGTTGGATGGCTGGAACGTG 60.889 55.000 0.00 0.00 0.00 4.49
3113 3209 0.179004 TTGTTGGATGGCTGGAACGT 60.179 50.000 0.00 0.00 0.00 3.99
3196 3292 5.701290 GGTTAGCATTGGATGGTGTATCTAC 59.299 44.000 3.10 0.00 41.73 2.59
3201 3297 4.518278 ATGGTTAGCATTGGATGGTGTA 57.482 40.909 3.10 0.00 41.73 2.90
3216 3312 4.195225 TGTGTAGCGTGATGAATGGTTA 57.805 40.909 0.00 0.00 0.00 2.85
3219 3315 3.302675 CGATTGTGTAGCGTGATGAATGG 60.303 47.826 0.00 0.00 0.00 3.16
3220 3316 3.551485 TCGATTGTGTAGCGTGATGAATG 59.449 43.478 0.00 0.00 0.00 2.67
3229 3325 4.675565 ACGAATATTCTCGATTGTGTAGCG 59.324 41.667 13.45 0.00 41.44 4.26
3375 3471 6.436532 CCCTTGAGAAGTACAAGACCTAACTA 59.563 42.308 0.00 0.00 44.92 2.24
3412 3508 9.899661 AGGTATGACTAACTTAATTGTAATGCA 57.100 29.630 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.