Multiple sequence alignment - TraesCS5A01G125000

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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 TraesCS5A01G125000 chr5A 100.000 4850 0 0 1 4850 275081583 275076734 0.000000e+00 8957.0
1 TraesCS5A01G125000 chr5A 91.429 105 6 3 146 248 392958674 392958777 1.820000e-29 141.0
2 TraesCS5A01G125000 chr5A 90.000 70 5 2 87 155 536707691 536707759 6.690000e-14 89.8
3 TraesCS5A01G125000 chr5A 86.154 65 5 3 737 799 215234440 215234502 3.130000e-07 67.6
4 TraesCS5A01G125000 chr6A 98.653 3563 47 1 867 4429 307983467 307987028 0.000000e+00 6312.0
5 TraesCS5A01G125000 chr6A 98.372 3563 57 1 867 4429 297526645 297523084 0.000000e+00 6257.0
6 TraesCS5A01G125000 chr6A 98.595 427 6 0 4424 4850 297522999 297522573 0.000000e+00 756.0
7 TraesCS5A01G125000 chr6A 98.361 427 7 0 4424 4850 307987113 307987539 0.000000e+00 750.0
8 TraesCS5A01G125000 chr6A 78.049 1025 203 18 1308 2328 447829976 447828970 1.150000e-175 627.0
9 TraesCS5A01G125000 chr6B 95.159 1198 54 2 3233 4429 304147703 304148897 0.000000e+00 1888.0
10 TraesCS5A01G125000 chr6B 93.677 427 27 0 4424 4850 304148980 304149406 1.470000e-179 640.0
11 TraesCS5A01G125000 chr6B 90.309 485 46 1 2900 3383 304146499 304146983 6.850000e-178 634.0
12 TraesCS5A01G125000 chr6B 89.803 304 27 2 3133 3435 304147554 304147854 2.120000e-103 387.0
13 TraesCS5A01G125000 chr6B 85.714 154 19 1 3281 3434 304146833 304146983 5.020000e-35 159.0
14 TraesCS5A01G125000 chr6B 89.524 105 9 2 143 246 147011498 147011601 1.100000e-26 132.0
15 TraesCS5A01G125000 chr6B 94.737 57 3 0 3232 3288 304147846 304147902 6.690000e-14 89.8
16 TraesCS5A01G125000 chr6B 88.889 72 7 1 84 155 610800706 610800636 2.400000e-13 87.9
17 TraesCS5A01G125000 chr5D 92.247 503 30 5 244 737 211978982 211978480 0.000000e+00 704.0
18 TraesCS5A01G125000 chr5D 83.871 186 28 2 252 435 312249814 312249629 4.990000e-40 176.0
19 TraesCS5A01G125000 chr5D 86.957 92 10 1 49 138 211979019 211978928 8.590000e-18 102.0
20 TraesCS5A01G125000 chr5D 97.368 38 1 0 882 919 228872178 228872215 1.130000e-06 65.8
21 TraesCS5A01G125000 chr5D 97.368 38 1 0 882 919 243575635 243575598 1.130000e-06 65.8
22 TraesCS5A01G125000 chr7D 77.799 1036 214 14 1301 2334 376085297 376084276 4.120000e-175 625.0
23 TraesCS5A01G125000 chr7D 84.409 186 27 2 252 435 588691057 588690872 1.070000e-41 182.0
24 TraesCS5A01G125000 chr7D 86.076 79 8 3 78 155 65790306 65790230 1.120000e-11 82.4
25 TraesCS5A01G125000 chr7D 89.062 64 3 3 738 799 25185358 25185419 5.210000e-10 76.8
26 TraesCS5A01G125000 chr7A 77.027 1036 206 18 1301 2334 672445994 672444989 2.530000e-157 566.0
27 TraesCS5A01G125000 chr7A 86.316 190 22 4 252 439 30660724 30660911 2.290000e-48 204.0
28 TraesCS5A01G125000 chr7A 87.850 107 11 2 143 248 452929793 452929898 1.830000e-24 124.0
29 TraesCS5A01G125000 chr7A 92.157 51 2 1 751 799 354951633 354951583 2.420000e-08 71.3
30 TraesCS5A01G125000 chr5B 86.680 503 28 7 244 737 225516676 225516204 5.560000e-144 521.0
31 TraesCS5A01G125000 chr5B 91.549 142 7 4 1 138 225516762 225516622 1.780000e-44 191.0
32 TraesCS5A01G125000 chr5B 90.909 66 6 0 90 155 30632904 30632839 6.690000e-14 89.8
33 TraesCS5A01G125000 chr5B 87.671 73 7 2 87 158 15669212 15669141 3.110000e-12 84.2
34 TraesCS5A01G125000 chr1B 75.996 1004 220 17 1321 2320 417023859 417022873 2.610000e-137 499.0
35 TraesCS5A01G125000 chr1B 97.175 177 5 0 4674 4850 332069530 332069706 2.840000e-77 300.0
36 TraesCS5A01G125000 chr1B 78.804 184 39 0 1321 1504 274864949 274865132 1.830000e-24 124.0
37 TraesCS5A01G125000 chr1B 84.536 97 9 3 883 977 274864520 274864612 1.860000e-14 91.6
38 TraesCS5A01G125000 chr3B 76.135 859 186 15 1299 2153 477621504 477620661 2.680000e-117 433.0
39 TraesCS5A01G125000 chr3B 85.027 187 26 2 250 434 764767783 764767597 6.410000e-44 189.0
40 TraesCS5A01G125000 chr3B 79.913 229 34 9 209 432 615876030 615875809 1.810000e-34 158.0
41 TraesCS5A01G125000 chr3B 100.000 28 0 0 801 828 679623527 679623554 9.000000e-03 52.8
42 TraesCS5A01G125000 chr3A 81.530 379 66 3 4430 4806 703273279 703273655 4.710000e-80 309.0
43 TraesCS5A01G125000 chr3A 100.000 28 0 0 801 828 651501585 651501612 9.000000e-03 52.8
44 TraesCS5A01G125000 chr4D 77.843 343 73 3 4495 4836 111566456 111566116 4.920000e-50 209.0
45 TraesCS5A01G125000 chr4D 88.571 70 4 3 732 799 450155645 450155712 1.120000e-11 82.4
46 TraesCS5A01G125000 chr4D 90.244 41 3 1 458 497 490257690 490257730 9.000000e-03 52.8
47 TraesCS5A01G125000 chr2A 85.641 195 21 6 252 442 249746928 249747119 1.060000e-46 198.0
48 TraesCS5A01G125000 chr2A 91.262 103 7 2 146 246 140506906 140506804 6.550000e-29 139.0
49 TraesCS5A01G125000 chr2A 90.291 103 8 2 146 246 220641148 220641046 3.050000e-27 134.0
50 TraesCS5A01G125000 chr2A 88.750 80 8 1 77 155 698075196 698075275 4.000000e-16 97.1
51 TraesCS5A01G125000 chr2A 86.842 76 10 0 80 155 193702423 193702498 8.650000e-13 86.1
52 TraesCS5A01G125000 chr2A 97.778 45 1 0 755 799 628669958 628669914 1.450000e-10 78.7
53 TraesCS5A01G125000 chr2D 87.500 168 17 4 251 415 590070505 590070671 1.780000e-44 191.0
54 TraesCS5A01G125000 chr2D 97.778 45 1 0 755 799 484372551 484372507 1.450000e-10 78.7
55 TraesCS5A01G125000 chr4A 90.566 106 8 2 146 249 210794490 210794595 6.550000e-29 139.0
56 TraesCS5A01G125000 chr4A 89.623 106 9 2 146 249 149395779 149395674 3.050000e-27 134.0
57 TraesCS5A01G125000 chr4A 87.850 107 11 2 143 248 149395770 149395875 1.830000e-24 124.0
58 TraesCS5A01G125000 chr6D 88.350 103 10 2 146 246 464990769 464990871 6.590000e-24 122.0
59 TraesCS5A01G125000 chr6D 82.955 88 11 2 883 970 396984097 396984014 5.210000e-10 76.8
60 TraesCS5A01G125000 chr1A 76.652 227 47 5 1321 1541 542180182 542179956 2.370000e-23 121.0
61 TraesCS5A01G125000 chr1A 83.505 97 10 3 883 977 542180611 542180519 8.650000e-13 86.1
62 TraesCS5A01G125000 chr7B 78.333 180 39 0 1321 1500 425166169 425165990 3.070000e-22 117.0
63 TraesCS5A01G125000 chr3D 89.011 91 9 1 883 973 475309364 475309275 1.430000e-20 111.0
64 TraesCS5A01G125000 chr3D 90.323 62 4 2 738 799 189804536 189804477 4.020000e-11 80.5
65 TraesCS5A01G125000 chr3D 93.617 47 3 0 883 929 516645968 516645922 2.420000e-08 71.3
66 TraesCS5A01G125000 chr3D 90.244 41 3 1 458 497 376824968 376825008 9.000000e-03 52.8
67 TraesCS5A01G125000 chr3D 100.000 28 0 0 801 828 516193512 516193539 9.000000e-03 52.8
68 TraesCS5A01G125000 chr1D 90.141 71 7 0 88 158 417626024 417625954 5.170000e-15 93.5
69 TraesCS5A01G125000 chr1D 91.379 58 3 2 738 795 116233160 116233215 1.450000e-10 78.7
70 TraesCS5A01G125000 chr1D 87.500 64 4 3 738 799 282466039 282466100 2.420000e-08 71.3
71 TraesCS5A01G125000 chr2B 88.889 72 8 0 87 158 373294826 373294897 6.690000e-14 89.8


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 TraesCS5A01G125000 chr5A 275076734 275081583 4849 True 8957.000000 8957 100.0000 1 4850 1 chr5A.!!$R1 4849
1 TraesCS5A01G125000 chr6A 307983467 307987539 4072 False 3531.000000 6312 98.5070 867 4850 2 chr6A.!!$F1 3983
2 TraesCS5A01G125000 chr6A 297522573 297526645 4072 True 3506.500000 6257 98.4835 867 4850 2 chr6A.!!$R2 3983
3 TraesCS5A01G125000 chr6A 447828970 447829976 1006 True 627.000000 627 78.0490 1308 2328 1 chr6A.!!$R1 1020
4 TraesCS5A01G125000 chr6B 304146499 304149406 2907 False 632.966667 1888 91.5665 2900 4850 6 chr6B.!!$F2 1950
5 TraesCS5A01G125000 chr5D 211978480 211979019 539 True 403.000000 704 89.6020 49 737 2 chr5D.!!$R3 688
6 TraesCS5A01G125000 chr7D 376084276 376085297 1021 True 625.000000 625 77.7990 1301 2334 1 chr7D.!!$R2 1033
7 TraesCS5A01G125000 chr7A 672444989 672445994 1005 True 566.000000 566 77.0270 1301 2334 1 chr7A.!!$R2 1033
8 TraesCS5A01G125000 chr5B 225516204 225516762 558 True 356.000000 521 89.1145 1 737 2 chr5B.!!$R3 736
9 TraesCS5A01G125000 chr1B 417022873 417023859 986 True 499.000000 499 75.9960 1321 2320 1 chr1B.!!$R1 999
10 TraesCS5A01G125000 chr3B 477620661 477621504 843 True 433.000000 433 76.1350 1299 2153 1 chr3B.!!$R1 854

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
104 106 0.107654 CCTAAGGCCCTGTACAGTGC 60.108 60.000 20.64 20.64 0.00 4.40 F
590 597 0.393808 GCCTTTCACTGGGCCGAATA 60.394 55.000 0.00 0.00 42.30 1.75 F
848 863 0.526524 CTCAGGAATCAGTCGACGGC 60.527 60.000 11.11 0.00 0.00 5.68 F
1075 1090 1.664306 GTCGTTTCTGGTCTCGGGT 59.336 57.895 0.00 0.00 0.00 5.28 F
3062 3089 1.968017 CGTGCACCCTGCTGATTGT 60.968 57.895 12.15 0.00 45.31 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1075 1090 4.304413 TCCCGACCCCTCCGACAA 62.304 66.667 0.00 0.0 0.00 3.18 R
1580 1597 4.451150 CCGCCTGCCGCAGAGTTA 62.451 66.667 22.35 0.0 37.30 2.24 R
2842 2869 2.047274 CGATGGGACCAACGCACT 60.047 61.111 8.06 0.0 43.86 4.40 R
3131 3158 2.046892 CTTCCTCCGGTGCAGGTG 60.047 66.667 0.00 0.0 32.20 4.00 R
4557 5546 3.090532 ACCGCCTCCAGGAATCCC 61.091 66.667 0.00 0.0 37.39 3.85 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
92 94 3.802866 CAAGGATTGTCTCTCCTAAGGC 58.197 50.000 0.00 0.00 42.42 4.35
93 95 2.403561 AGGATTGTCTCTCCTAAGGCC 58.596 52.381 0.00 0.00 41.42 5.19
94 96 1.418264 GGATTGTCTCTCCTAAGGCCC 59.582 57.143 0.00 0.00 0.00 5.80
95 97 2.403561 GATTGTCTCTCCTAAGGCCCT 58.596 52.381 0.00 0.00 0.00 5.19
96 98 1.573108 TTGTCTCTCCTAAGGCCCTG 58.427 55.000 0.00 0.00 0.00 4.45
97 99 0.413832 TGTCTCTCCTAAGGCCCTGT 59.586 55.000 0.00 0.00 0.00 4.00
98 100 1.644337 TGTCTCTCCTAAGGCCCTGTA 59.356 52.381 0.00 0.00 0.00 2.74
99 101 2.033372 GTCTCTCCTAAGGCCCTGTAC 58.967 57.143 0.00 0.00 0.00 2.90
100 102 1.644337 TCTCTCCTAAGGCCCTGTACA 59.356 52.381 0.00 0.00 0.00 2.90
101 103 2.035632 CTCTCCTAAGGCCCTGTACAG 58.964 57.143 16.34 16.34 0.00 2.74
102 104 1.361543 TCTCCTAAGGCCCTGTACAGT 59.638 52.381 21.18 5.19 0.00 3.55
103 105 1.482593 CTCCTAAGGCCCTGTACAGTG 59.517 57.143 21.18 11.65 0.00 3.66
104 106 0.107654 CCTAAGGCCCTGTACAGTGC 60.108 60.000 20.64 20.64 0.00 4.40
105 107 0.613260 CTAAGGCCCTGTACAGTGCA 59.387 55.000 27.94 10.15 33.31 4.57
106 108 0.613260 TAAGGCCCTGTACAGTGCAG 59.387 55.000 27.94 11.56 33.31 4.41
123 125 2.338577 CAGGATGCTTAGGGAAGGTG 57.661 55.000 0.00 0.00 32.84 4.00
124 126 0.548510 AGGATGCTTAGGGAAGGTGC 59.451 55.000 0.00 0.00 32.84 5.01
125 127 0.548510 GGATGCTTAGGGAAGGTGCT 59.451 55.000 0.00 0.00 32.84 4.40
126 128 1.064389 GGATGCTTAGGGAAGGTGCTT 60.064 52.381 0.00 0.00 32.84 3.91
127 129 2.172717 GGATGCTTAGGGAAGGTGCTTA 59.827 50.000 0.00 0.00 32.84 3.09
128 130 3.471680 GATGCTTAGGGAAGGTGCTTAG 58.528 50.000 0.00 0.00 32.84 2.18
129 131 2.546899 TGCTTAGGGAAGGTGCTTAGA 58.453 47.619 0.00 0.00 32.84 2.10
130 132 2.501723 TGCTTAGGGAAGGTGCTTAGAG 59.498 50.000 0.00 0.00 32.84 2.43
131 133 2.766828 GCTTAGGGAAGGTGCTTAGAGA 59.233 50.000 0.00 0.00 32.84 3.10
132 134 3.197983 GCTTAGGGAAGGTGCTTAGAGAA 59.802 47.826 0.00 0.00 32.84 2.87
133 135 4.323562 GCTTAGGGAAGGTGCTTAGAGAAA 60.324 45.833 0.00 0.00 32.84 2.52
134 136 5.630304 GCTTAGGGAAGGTGCTTAGAGAAAT 60.630 44.000 0.00 0.00 32.84 2.17
135 137 6.408206 GCTTAGGGAAGGTGCTTAGAGAAATA 60.408 42.308 0.00 0.00 32.84 1.40
136 138 7.504926 TTAGGGAAGGTGCTTAGAGAAATAA 57.495 36.000 0.00 0.00 0.00 1.40
137 139 6.388619 AGGGAAGGTGCTTAGAGAAATAAA 57.611 37.500 0.00 0.00 0.00 1.40
138 140 6.974795 AGGGAAGGTGCTTAGAGAAATAAAT 58.025 36.000 0.00 0.00 0.00 1.40
139 141 7.057264 AGGGAAGGTGCTTAGAGAAATAAATC 58.943 38.462 0.00 0.00 0.00 2.17
140 142 6.828785 GGGAAGGTGCTTAGAGAAATAAATCA 59.171 38.462 0.00 0.00 0.00 2.57
141 143 7.012799 GGGAAGGTGCTTAGAGAAATAAATCAG 59.987 40.741 0.00 0.00 0.00 2.90
142 144 7.012799 GGAAGGTGCTTAGAGAAATAAATCAGG 59.987 40.741 0.00 0.00 0.00 3.86
143 145 5.825151 AGGTGCTTAGAGAAATAAATCAGGC 59.175 40.000 0.00 0.00 0.00 4.85
144 146 5.825151 GGTGCTTAGAGAAATAAATCAGGCT 59.175 40.000 0.00 0.00 0.00 4.58
145 147 6.319911 GGTGCTTAGAGAAATAAATCAGGCTT 59.680 38.462 0.00 0.00 0.00 4.35
146 148 7.148000 GGTGCTTAGAGAAATAAATCAGGCTTT 60.148 37.037 0.00 0.00 0.00 3.51
147 149 8.893727 GTGCTTAGAGAAATAAATCAGGCTTTA 58.106 33.333 0.00 0.00 0.00 1.85
148 150 8.893727 TGCTTAGAGAAATAAATCAGGCTTTAC 58.106 33.333 0.00 0.00 0.00 2.01
149 151 9.114952 GCTTAGAGAAATAAATCAGGCTTTACT 57.885 33.333 0.00 0.00 0.00 2.24
165 167 5.069501 CTTTACTTAAGCGTCTACCCTGT 57.930 43.478 1.29 0.00 0.00 4.00
166 168 6.199937 CTTTACTTAAGCGTCTACCCTGTA 57.800 41.667 1.29 0.00 0.00 2.74
167 169 5.567138 TTACTTAAGCGTCTACCCTGTAC 57.433 43.478 1.29 0.00 0.00 2.90
168 170 3.424703 ACTTAAGCGTCTACCCTGTACA 58.575 45.455 1.29 0.00 0.00 2.90
169 171 3.828451 ACTTAAGCGTCTACCCTGTACAA 59.172 43.478 1.29 0.00 0.00 2.41
170 172 4.281688 ACTTAAGCGTCTACCCTGTACAAA 59.718 41.667 1.29 0.00 0.00 2.83
171 173 3.975168 AAGCGTCTACCCTGTACAAAT 57.025 42.857 0.00 0.00 0.00 2.32
172 174 6.153340 ACTTAAGCGTCTACCCTGTACAAATA 59.847 38.462 1.29 0.00 0.00 1.40
173 175 4.650754 AGCGTCTACCCTGTACAAATAG 57.349 45.455 0.00 0.00 0.00 1.73
174 176 3.383825 AGCGTCTACCCTGTACAAATAGG 59.616 47.826 0.00 0.00 33.85 2.57
175 177 3.714391 CGTCTACCCTGTACAAATAGGC 58.286 50.000 0.00 0.00 32.73 3.93
176 178 3.131577 CGTCTACCCTGTACAAATAGGCA 59.868 47.826 0.00 0.00 32.73 4.75
177 179 4.439968 GTCTACCCTGTACAAATAGGCAC 58.560 47.826 0.00 0.00 32.73 5.01
178 180 4.161754 GTCTACCCTGTACAAATAGGCACT 59.838 45.833 0.00 0.00 46.37 4.40
179 181 3.350219 ACCCTGTACAAATAGGCACTG 57.650 47.619 0.00 0.00 41.52 3.66
180 182 2.026262 ACCCTGTACAAATAGGCACTGG 60.026 50.000 0.00 0.00 41.52 4.00
181 183 2.026262 CCCTGTACAAATAGGCACTGGT 60.026 50.000 0.00 0.00 41.52 4.00
182 184 3.009723 CCTGTACAAATAGGCACTGGTG 58.990 50.000 0.00 0.00 41.52 4.17
212 214 5.562506 AAAGCCGGTTTATTCTTCTAAGC 57.437 39.130 3.14 0.00 0.00 3.09
213 215 4.216411 AGCCGGTTTATTCTTCTAAGCA 57.784 40.909 1.90 0.00 0.00 3.91
214 216 3.939592 AGCCGGTTTATTCTTCTAAGCAC 59.060 43.478 1.90 0.00 0.00 4.40
215 217 3.064958 GCCGGTTTATTCTTCTAAGCACC 59.935 47.826 1.90 0.00 0.00 5.01
216 218 4.514401 CCGGTTTATTCTTCTAAGCACCT 58.486 43.478 0.00 0.00 0.00 4.00
217 219 4.571176 CCGGTTTATTCTTCTAAGCACCTC 59.429 45.833 0.00 0.00 0.00 3.85
218 220 4.571176 CGGTTTATTCTTCTAAGCACCTCC 59.429 45.833 0.00 0.00 0.00 4.30
219 221 5.627040 CGGTTTATTCTTCTAAGCACCTCCT 60.627 44.000 0.00 0.00 0.00 3.69
220 222 6.181190 GGTTTATTCTTCTAAGCACCTCCTT 58.819 40.000 0.00 0.00 0.00 3.36
221 223 7.336396 GGTTTATTCTTCTAAGCACCTCCTTA 58.664 38.462 0.00 0.00 0.00 2.69
222 224 7.827729 GGTTTATTCTTCTAAGCACCTCCTTAA 59.172 37.037 0.00 0.00 0.00 1.85
223 225 8.884726 GTTTATTCTTCTAAGCACCTCCTTAAG 58.115 37.037 0.00 0.00 0.00 1.85
224 226 4.473477 TCTTCTAAGCACCTCCTTAAGC 57.527 45.455 0.00 0.00 0.00 3.09
225 227 3.838317 TCTTCTAAGCACCTCCTTAAGCA 59.162 43.478 0.00 0.00 0.00 3.91
226 228 3.611766 TCTAAGCACCTCCTTAAGCAC 57.388 47.619 0.00 0.00 0.00 4.40
227 229 2.236395 TCTAAGCACCTCCTTAAGCACC 59.764 50.000 0.00 0.00 0.00 5.01
228 230 1.068121 AAGCACCTCCTTAAGCACCT 58.932 50.000 0.00 0.00 0.00 4.00
229 231 1.952621 AGCACCTCCTTAAGCACCTA 58.047 50.000 0.00 0.00 0.00 3.08
230 232 1.555533 AGCACCTCCTTAAGCACCTAC 59.444 52.381 0.00 0.00 0.00 3.18
231 233 1.407025 GCACCTCCTTAAGCACCTACC 60.407 57.143 0.00 0.00 0.00 3.18
232 234 1.906574 CACCTCCTTAAGCACCTACCA 59.093 52.381 0.00 0.00 0.00 3.25
233 235 2.505819 CACCTCCTTAAGCACCTACCAT 59.494 50.000 0.00 0.00 0.00 3.55
234 236 3.054361 CACCTCCTTAAGCACCTACCATT 60.054 47.826 0.00 0.00 0.00 3.16
235 237 3.054361 ACCTCCTTAAGCACCTACCATTG 60.054 47.826 0.00 0.00 0.00 2.82
236 238 3.054361 CCTCCTTAAGCACCTACCATTGT 60.054 47.826 0.00 0.00 0.00 2.71
237 239 4.163458 CCTCCTTAAGCACCTACCATTGTA 59.837 45.833 0.00 0.00 0.00 2.41
238 240 5.093849 TCCTTAAGCACCTACCATTGTAC 57.906 43.478 0.00 0.00 0.00 2.90
239 241 4.532916 TCCTTAAGCACCTACCATTGTACA 59.467 41.667 0.00 0.00 0.00 2.90
240 242 5.013287 TCCTTAAGCACCTACCATTGTACAA 59.987 40.000 11.41 11.41 0.00 2.41
241 243 5.354234 CCTTAAGCACCTACCATTGTACAAG 59.646 44.000 14.65 3.88 0.00 3.16
242 244 3.350219 AGCACCTACCATTGTACAAGG 57.650 47.619 14.65 13.92 0.00 3.61
360 362 6.243811 AGACGCTTAATTAGGTATCTCTCG 57.756 41.667 0.00 0.00 0.00 4.04
373 375 6.603224 AGGTATCTCTCGTGTAGAAATAGGT 58.397 40.000 0.00 0.00 32.46 3.08
381 383 3.129287 CGTGTAGAAATAGGTACCGGTGT 59.871 47.826 19.93 4.02 0.00 4.16
393 395 3.748048 GGTACCGGTGTTTAAGAGAAACC 59.252 47.826 19.93 8.30 0.00 3.27
497 503 6.170506 CCTAAACACCTAGCATTGTACAAGA 58.829 40.000 14.65 0.00 0.00 3.02
502 508 5.178061 CACCTAGCATTGTACAAGACATCA 58.822 41.667 14.65 0.00 38.07 3.07
552 559 6.827762 AGTTTTCAATTTCCTGCAATCCAAAA 59.172 30.769 0.00 0.00 0.00 2.44
590 597 0.393808 GCCTTTCACTGGGCCGAATA 60.394 55.000 0.00 0.00 42.30 1.75
595 602 1.507140 TCACTGGGCCGAATAGGATT 58.493 50.000 0.00 0.00 45.00 3.01
614 621 1.968704 TTGCGTCCACCACAACAATA 58.031 45.000 0.00 0.00 0.00 1.90
636 643 2.161609 CCCAAGTCGACAATAAGCCAAC 59.838 50.000 19.50 0.00 0.00 3.77
644 651 5.986135 GTCGACAATAAGCCAACATCTCTAT 59.014 40.000 11.55 0.00 0.00 1.98
655 662 4.753610 CCAACATCTCTATGCACAATCGAT 59.246 41.667 0.00 0.00 36.50 3.59
658 666 5.228665 ACATCTCTATGCACAATCGATCAG 58.771 41.667 0.00 0.00 36.50 2.90
708 717 1.965754 GAATCGGCTCTGGCTCTGGT 61.966 60.000 0.00 0.00 38.73 4.00
709 718 2.249413 AATCGGCTCTGGCTCTGGTG 62.249 60.000 0.00 0.00 38.73 4.17
710 719 3.699894 CGGCTCTGGCTCTGGTGT 61.700 66.667 0.00 0.00 38.73 4.16
754 769 9.636789 AAAAACTACTACTCCCTACACATTTTT 57.363 29.630 0.00 0.00 0.00 1.94
785 800 9.956720 ATTTGTCTTTCTAGATTTCAACAAGTG 57.043 29.630 0.00 0.00 31.86 3.16
786 801 8.731275 TTGTCTTTCTAGATTTCAACAAGTGA 57.269 30.769 0.00 0.00 31.86 3.41
787 802 8.142994 TGTCTTTCTAGATTTCAACAAGTGAC 57.857 34.615 0.00 0.00 31.82 3.67
788 803 7.987458 TGTCTTTCTAGATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 31.82 3.41
789 804 9.477484 GTCTTTCTAGATTTCAACAAGTGACTA 57.523 33.333 0.00 0.00 31.82 2.59
790 805 9.477484 TCTTTCTAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
791 806 9.261180 CTTTCTAGATTTCAACAAGTGACTACA 57.739 33.333 0.00 0.00 35.39 2.74
792 807 9.778741 TTTCTAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
794 809 9.856488 TCTAGATTTCAACAAGTGACTACATAC 57.144 33.333 0.00 0.00 35.39 2.39
795 810 9.862371 CTAGATTTCAACAAGTGACTACATACT 57.138 33.333 0.00 0.00 35.39 2.12
796 811 8.539770 AGATTTCAACAAGTGACTACATACTG 57.460 34.615 0.00 0.00 35.39 2.74
797 812 8.367911 AGATTTCAACAAGTGACTACATACTGA 58.632 33.333 0.00 0.00 35.39 3.41
798 813 7.946655 TTTCAACAAGTGACTACATACTGAG 57.053 36.000 0.00 0.00 35.39 3.35
799 814 6.025749 TCAACAAGTGACTACATACTGAGG 57.974 41.667 0.00 0.00 0.00 3.86
800 815 5.047306 TCAACAAGTGACTACATACTGAGGG 60.047 44.000 0.00 0.00 0.00 4.30
801 816 3.195825 ACAAGTGACTACATACTGAGGGC 59.804 47.826 0.00 0.00 0.00 5.19
802 817 3.390175 AGTGACTACATACTGAGGGCT 57.610 47.619 0.00 0.00 0.00 5.19
803 818 3.027412 AGTGACTACATACTGAGGGCTG 58.973 50.000 0.00 0.00 0.00 4.85
804 819 1.757118 TGACTACATACTGAGGGCTGC 59.243 52.381 0.00 0.00 0.00 5.25
805 820 1.069358 GACTACATACTGAGGGCTGCC 59.931 57.143 11.05 11.05 0.00 4.85
806 821 1.123077 CTACATACTGAGGGCTGCCA 58.877 55.000 22.05 0.00 0.00 4.92
807 822 0.830648 TACATACTGAGGGCTGCCAC 59.169 55.000 22.05 14.12 0.00 5.01
808 823 1.153086 CATACTGAGGGCTGCCACC 60.153 63.158 22.05 11.67 0.00 4.61
809 824 1.616327 ATACTGAGGGCTGCCACCA 60.616 57.895 22.05 15.70 0.00 4.17
810 825 1.630126 ATACTGAGGGCTGCCACCAG 61.630 60.000 27.14 27.14 42.13 4.00
821 836 1.153706 GCCACCAGCAACATGATGC 60.154 57.895 19.41 19.41 46.78 3.91
829 844 2.556534 GCAACATGATGCTTGAGGAC 57.443 50.000 19.70 0.00 43.06 3.85
830 845 2.089980 GCAACATGATGCTTGAGGACT 58.910 47.619 19.70 0.00 43.06 3.85
831 846 2.097142 GCAACATGATGCTTGAGGACTC 59.903 50.000 19.70 0.00 43.06 3.36
832 847 3.340928 CAACATGATGCTTGAGGACTCA 58.659 45.455 0.00 0.00 37.91 3.41
833 848 3.263489 ACATGATGCTTGAGGACTCAG 57.737 47.619 0.00 0.00 41.13 3.35
834 849 2.093075 ACATGATGCTTGAGGACTCAGG 60.093 50.000 0.00 7.04 41.13 3.86
835 850 1.942776 TGATGCTTGAGGACTCAGGA 58.057 50.000 14.67 5.72 41.13 3.86
836 851 2.259917 TGATGCTTGAGGACTCAGGAA 58.740 47.619 14.67 5.14 41.13 3.36
837 852 2.842496 TGATGCTTGAGGACTCAGGAAT 59.158 45.455 14.67 9.85 37.62 3.01
838 853 3.118482 TGATGCTTGAGGACTCAGGAATC 60.118 47.826 20.01 20.01 46.35 2.52
839 854 2.259917 TGCTTGAGGACTCAGGAATCA 58.740 47.619 14.67 1.67 41.13 2.57
840 855 2.235650 TGCTTGAGGACTCAGGAATCAG 59.764 50.000 14.67 4.22 41.13 2.90
841 856 2.235898 GCTTGAGGACTCAGGAATCAGT 59.764 50.000 14.67 0.00 41.13 3.41
842 857 3.678529 GCTTGAGGACTCAGGAATCAGTC 60.679 52.174 14.67 0.00 41.13 3.51
843 858 2.095461 TGAGGACTCAGGAATCAGTCG 58.905 52.381 0.00 0.00 40.11 4.18
844 859 2.290960 TGAGGACTCAGGAATCAGTCGA 60.291 50.000 0.00 0.00 40.11 4.20
845 860 2.096248 AGGACTCAGGAATCAGTCGAC 58.904 52.381 7.70 7.70 40.11 4.20
846 861 1.202200 GGACTCAGGAATCAGTCGACG 60.202 57.143 10.46 5.48 40.11 5.12
847 862 0.811915 ACTCAGGAATCAGTCGACGG 59.188 55.000 10.46 10.03 0.00 4.79
848 863 0.526524 CTCAGGAATCAGTCGACGGC 60.527 60.000 11.11 0.00 0.00 5.68
849 864 1.874019 CAGGAATCAGTCGACGGCG 60.874 63.158 2.87 2.87 39.35 6.46
850 865 2.582498 GGAATCAGTCGACGGCGG 60.582 66.667 12.58 0.00 38.28 6.13
851 866 2.181021 GAATCAGTCGACGGCGGT 59.819 61.111 12.58 0.00 38.28 5.68
852 867 2.126071 AATCAGTCGACGGCGGTG 60.126 61.111 12.58 9.55 38.28 4.94
853 868 2.537792 GAATCAGTCGACGGCGGTGA 62.538 60.000 12.58 15.51 38.28 4.02
854 869 2.149803 AATCAGTCGACGGCGGTGAA 62.150 55.000 18.58 0.07 35.52 3.18
855 870 2.149803 ATCAGTCGACGGCGGTGAAA 62.150 55.000 18.58 0.00 35.52 2.69
856 871 2.355481 AGTCGACGGCGGTGAAAC 60.355 61.111 12.58 0.00 38.28 2.78
1075 1090 1.664306 GTCGTTTCTGGTCTCGGGT 59.336 57.895 0.00 0.00 0.00 5.28
2397 2424 2.931649 ACGTTTGGGGTCCGGGAT 60.932 61.111 0.00 0.00 0.00 3.85
2716 2743 3.112075 CGATCGTGGCAAGTGCGT 61.112 61.111 7.03 0.00 43.26 5.24
2721 2748 4.374702 GTGGCAAGTGCGTCGCAG 62.375 66.667 22.42 10.56 40.08 5.18
3062 3089 1.968017 CGTGCACCCTGCTGATTGT 60.968 57.895 12.15 0.00 45.31 2.71
3131 3158 0.659957 GCTGAGATTTCGATGGTGGC 59.340 55.000 0.00 0.00 0.00 5.01
3135 3162 0.620556 AGATTTCGATGGTGGCACCT 59.379 50.000 34.69 21.39 39.58 4.00
3347 4245 0.688749 ATGCAAGGATCTTTGGGGGC 60.689 55.000 18.18 5.32 0.00 5.80
3483 4381 2.223805 GGAGGTGGTTGCTTTTGACAAG 60.224 50.000 0.00 0.00 0.00 3.16
3534 4432 0.610687 AGCTAGCACCACCACTTCTC 59.389 55.000 18.83 0.00 0.00 2.87
3656 4554 3.337398 CTACTCCAGCTGAGAACGC 57.663 57.895 17.39 0.00 44.42 4.84
4128 5027 0.674269 TGGCGTGGGATAAAACGGTC 60.674 55.000 0.00 0.00 40.12 4.79
4602 5591 1.473257 GCTTGGGTATGCGATGACTCA 60.473 52.381 0.00 0.00 0.00 3.41
4731 5720 3.196901 TGGCCAACTATGTGATACTTCGT 59.803 43.478 0.61 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 0.548510 ACCTTCCCTAAGCATCCTGC 59.451 55.000 0.00 0.00 45.46 4.85
104 106 1.748591 GCACCTTCCCTAAGCATCCTG 60.749 57.143 0.00 0.00 0.00 3.86
105 107 0.548510 GCACCTTCCCTAAGCATCCT 59.451 55.000 0.00 0.00 0.00 3.24
106 108 0.548510 AGCACCTTCCCTAAGCATCC 59.451 55.000 0.00 0.00 0.00 3.51
107 109 2.426842 AAGCACCTTCCCTAAGCATC 57.573 50.000 0.00 0.00 0.00 3.91
108 110 3.115390 TCTAAGCACCTTCCCTAAGCAT 58.885 45.455 0.00 0.00 0.00 3.79
109 111 2.501723 CTCTAAGCACCTTCCCTAAGCA 59.498 50.000 0.00 0.00 0.00 3.91
110 112 2.766828 TCTCTAAGCACCTTCCCTAAGC 59.233 50.000 0.00 0.00 0.00 3.09
111 113 5.422214 TTTCTCTAAGCACCTTCCCTAAG 57.578 43.478 0.00 0.00 0.00 2.18
112 114 7.504926 TTATTTCTCTAAGCACCTTCCCTAA 57.495 36.000 0.00 0.00 0.00 2.69
113 115 7.504926 TTTATTTCTCTAAGCACCTTCCCTA 57.495 36.000 0.00 0.00 0.00 3.53
114 116 6.388619 TTTATTTCTCTAAGCACCTTCCCT 57.611 37.500 0.00 0.00 0.00 4.20
115 117 6.828785 TGATTTATTTCTCTAAGCACCTTCCC 59.171 38.462 0.00 0.00 0.00 3.97
116 118 7.012799 CCTGATTTATTTCTCTAAGCACCTTCC 59.987 40.741 0.00 0.00 0.00 3.46
117 119 7.467947 GCCTGATTTATTTCTCTAAGCACCTTC 60.468 40.741 0.00 0.00 0.00 3.46
118 120 6.319911 GCCTGATTTATTTCTCTAAGCACCTT 59.680 38.462 0.00 0.00 0.00 3.50
119 121 5.825151 GCCTGATTTATTTCTCTAAGCACCT 59.175 40.000 0.00 0.00 0.00 4.00
120 122 5.825151 AGCCTGATTTATTTCTCTAAGCACC 59.175 40.000 0.00 0.00 0.00 5.01
121 123 6.934048 AGCCTGATTTATTTCTCTAAGCAC 57.066 37.500 0.00 0.00 0.00 4.40
122 124 7.944729 AAAGCCTGATTTATTTCTCTAAGCA 57.055 32.000 0.00 0.00 0.00 3.91
123 125 9.114952 AGTAAAGCCTGATTTATTTCTCTAAGC 57.885 33.333 0.00 0.00 0.00 3.09
143 145 5.069501 ACAGGGTAGACGCTTAAGTAAAG 57.930 43.478 4.02 0.00 37.00 1.85
144 146 5.476599 TGTACAGGGTAGACGCTTAAGTAAA 59.523 40.000 4.02 0.00 37.00 2.01
145 147 5.009631 TGTACAGGGTAGACGCTTAAGTAA 58.990 41.667 4.02 0.00 37.00 2.24
146 148 4.588899 TGTACAGGGTAGACGCTTAAGTA 58.411 43.478 4.02 0.00 37.00 2.24
147 149 3.424703 TGTACAGGGTAGACGCTTAAGT 58.575 45.455 4.02 0.00 37.00 2.24
148 150 4.445452 TTGTACAGGGTAGACGCTTAAG 57.555 45.455 0.00 0.00 37.00 1.85
149 151 4.870123 TTTGTACAGGGTAGACGCTTAA 57.130 40.909 0.00 0.00 37.00 1.85
150 152 5.068198 CCTATTTGTACAGGGTAGACGCTTA 59.932 44.000 10.90 0.00 37.00 3.09
151 153 3.975168 ATTTGTACAGGGTAGACGCTT 57.025 42.857 0.00 0.00 37.00 4.68
152 154 3.383825 CCTATTTGTACAGGGTAGACGCT 59.616 47.826 10.90 0.00 39.95 5.07
153 155 3.714391 CCTATTTGTACAGGGTAGACGC 58.286 50.000 10.90 0.00 0.00 5.19
154 156 3.131577 TGCCTATTTGTACAGGGTAGACG 59.868 47.826 10.90 0.00 32.15 4.18
155 157 4.161754 AGTGCCTATTTGTACAGGGTAGAC 59.838 45.833 10.90 3.11 32.15 2.59
156 158 4.161565 CAGTGCCTATTTGTACAGGGTAGA 59.838 45.833 10.90 0.00 32.15 2.59
157 159 4.442706 CAGTGCCTATTTGTACAGGGTAG 58.557 47.826 0.00 0.39 32.15 3.18
158 160 3.199071 CCAGTGCCTATTTGTACAGGGTA 59.801 47.826 0.00 0.00 32.15 3.69
159 161 2.026262 CCAGTGCCTATTTGTACAGGGT 60.026 50.000 0.00 0.00 32.15 4.34
160 162 2.026262 ACCAGTGCCTATTTGTACAGGG 60.026 50.000 0.00 0.00 32.15 4.45
161 163 3.009723 CACCAGTGCCTATTTGTACAGG 58.990 50.000 0.00 0.00 34.85 4.00
188 190 6.015772 TGCTTAGAAGAATAAACCGGCTTTTT 60.016 34.615 0.00 0.00 0.00 1.94
189 191 5.475564 TGCTTAGAAGAATAAACCGGCTTTT 59.524 36.000 0.00 0.00 0.00 2.27
190 192 5.007682 TGCTTAGAAGAATAAACCGGCTTT 58.992 37.500 0.00 4.17 0.00 3.51
191 193 4.395231 GTGCTTAGAAGAATAAACCGGCTT 59.605 41.667 0.00 0.00 0.00 4.35
192 194 3.939592 GTGCTTAGAAGAATAAACCGGCT 59.060 43.478 0.00 0.00 0.00 5.52
193 195 3.064958 GGTGCTTAGAAGAATAAACCGGC 59.935 47.826 0.00 0.00 0.00 6.13
194 196 4.514401 AGGTGCTTAGAAGAATAAACCGG 58.486 43.478 0.00 0.00 0.00 5.28
195 197 4.571176 GGAGGTGCTTAGAAGAATAAACCG 59.429 45.833 0.00 0.00 0.00 4.44
196 198 5.746284 AGGAGGTGCTTAGAAGAATAAACC 58.254 41.667 0.00 0.00 0.00 3.27
197 199 8.788325 TTAAGGAGGTGCTTAGAAGAATAAAC 57.212 34.615 0.00 0.00 0.00 2.01
198 200 7.553044 GCTTAAGGAGGTGCTTAGAAGAATAAA 59.447 37.037 4.29 0.00 0.00 1.40
199 201 7.048512 GCTTAAGGAGGTGCTTAGAAGAATAA 58.951 38.462 4.29 0.00 0.00 1.40
200 202 6.156256 TGCTTAAGGAGGTGCTTAGAAGAATA 59.844 38.462 4.29 0.00 0.00 1.75
201 203 5.045578 TGCTTAAGGAGGTGCTTAGAAGAAT 60.046 40.000 4.29 0.00 0.00 2.40
202 204 4.286032 TGCTTAAGGAGGTGCTTAGAAGAA 59.714 41.667 4.29 0.00 0.00 2.52
203 205 3.838317 TGCTTAAGGAGGTGCTTAGAAGA 59.162 43.478 4.29 0.00 0.00 2.87
204 206 3.935828 GTGCTTAAGGAGGTGCTTAGAAG 59.064 47.826 4.29 0.00 0.00 2.85
205 207 3.307480 GGTGCTTAAGGAGGTGCTTAGAA 60.307 47.826 4.29 0.00 0.00 2.10
206 208 2.236395 GGTGCTTAAGGAGGTGCTTAGA 59.764 50.000 4.29 0.00 0.00 2.10
207 209 2.237392 AGGTGCTTAAGGAGGTGCTTAG 59.763 50.000 4.29 0.00 0.00 2.18
208 210 2.266279 AGGTGCTTAAGGAGGTGCTTA 58.734 47.619 4.29 0.00 0.00 3.09
209 211 1.068121 AGGTGCTTAAGGAGGTGCTT 58.932 50.000 4.29 0.00 0.00 3.91
210 212 1.555533 GTAGGTGCTTAAGGAGGTGCT 59.444 52.381 4.29 0.00 0.00 4.40
211 213 1.407025 GGTAGGTGCTTAAGGAGGTGC 60.407 57.143 4.29 0.00 0.00 5.01
212 214 1.906574 TGGTAGGTGCTTAAGGAGGTG 59.093 52.381 4.29 0.00 0.00 4.00
213 215 2.337359 TGGTAGGTGCTTAAGGAGGT 57.663 50.000 4.29 0.00 0.00 3.85
214 216 3.054361 ACAATGGTAGGTGCTTAAGGAGG 60.054 47.826 4.29 0.00 0.00 4.30
215 217 4.222124 ACAATGGTAGGTGCTTAAGGAG 57.778 45.455 4.29 0.00 0.00 3.69
216 218 4.532916 TGTACAATGGTAGGTGCTTAAGGA 59.467 41.667 4.29 0.00 0.00 3.36
217 219 4.839121 TGTACAATGGTAGGTGCTTAAGG 58.161 43.478 4.29 0.00 0.00 2.69
218 220 5.354234 CCTTGTACAATGGTAGGTGCTTAAG 59.646 44.000 9.13 0.00 0.00 1.85
219 221 5.250200 CCTTGTACAATGGTAGGTGCTTAA 58.750 41.667 9.13 0.00 0.00 1.85
220 222 4.839121 CCTTGTACAATGGTAGGTGCTTA 58.161 43.478 9.13 0.00 0.00 3.09
221 223 3.686016 CCTTGTACAATGGTAGGTGCTT 58.314 45.455 9.13 0.00 0.00 3.91
222 224 2.618045 GCCTTGTACAATGGTAGGTGCT 60.618 50.000 9.13 0.00 0.00 4.40
223 225 1.743394 GCCTTGTACAATGGTAGGTGC 59.257 52.381 9.13 0.00 0.00 5.01
224 226 2.026262 AGGCCTTGTACAATGGTAGGTG 60.026 50.000 9.13 0.00 0.00 4.00
225 227 2.275466 AGGCCTTGTACAATGGTAGGT 58.725 47.619 9.13 0.00 0.00 3.08
226 228 4.497291 TTAGGCCTTGTACAATGGTAGG 57.503 45.455 12.58 7.48 0.00 3.18
227 229 6.204882 GCTTATTAGGCCTTGTACAATGGTAG 59.795 42.308 12.58 5.18 0.00 3.18
228 230 6.059484 GCTTATTAGGCCTTGTACAATGGTA 58.941 40.000 12.58 0.54 0.00 3.25
229 231 4.887655 GCTTATTAGGCCTTGTACAATGGT 59.112 41.667 12.58 1.42 0.00 3.55
230 232 4.278419 GGCTTATTAGGCCTTGTACAATGG 59.722 45.833 12.58 13.26 45.57 3.16
231 233 5.438761 GGCTTATTAGGCCTTGTACAATG 57.561 43.478 12.58 7.68 45.57 2.82
241 243 6.668544 TGCATTGTACAAGGCTTATTAGGCC 61.669 44.000 36.19 8.73 46.93 5.19
242 244 4.338118 TGCATTGTACAAGGCTTATTAGGC 59.662 41.667 36.19 15.65 46.93 3.93
317 319 6.084925 CGTCTACCCTCTATAAATAAGCACG 58.915 44.000 0.00 0.00 0.00 5.34
328 330 6.313324 ACCTAATTAAGCGTCTACCCTCTAT 58.687 40.000 0.00 0.00 0.00 1.98
360 362 4.725790 ACACCGGTACCTATTTCTACAC 57.274 45.455 6.87 0.00 0.00 2.90
373 375 3.647590 AGGGTTTCTCTTAAACACCGGTA 59.352 43.478 6.87 0.00 34.20 4.02
381 383 8.129496 AGAAAACAAACAGGGTTTCTCTTAAA 57.871 30.769 0.61 0.00 37.47 1.52
393 395 4.918810 AGGTGCTTAGAAAACAAACAGG 57.081 40.909 0.00 0.00 0.00 4.00
425 431 5.627040 GCTTATGCACCAGTACTTAGGACTT 60.627 44.000 6.26 0.27 39.41 3.01
426 432 4.141914 GCTTATGCACCAGTACTTAGGACT 60.142 45.833 6.26 0.00 39.41 3.85
427 433 4.120589 GCTTATGCACCAGTACTTAGGAC 58.879 47.826 6.26 0.00 39.41 3.85
428 434 3.772572 TGCTTATGCACCAGTACTTAGGA 59.227 43.478 6.26 0.00 45.31 2.94
478 484 4.617253 TGTCTTGTACAATGCTAGGTGT 57.383 40.909 9.13 0.00 34.29 4.16
497 503 8.441312 AATGAGAAAAGCACAAAATTTGATGT 57.559 26.923 13.19 0.00 0.00 3.06
552 559 2.179427 GCCAATCTGTTTAAGGGCCTT 58.821 47.619 24.44 24.44 35.42 4.35
590 597 0.179004 TTGTGGTGGACGCAAATCCT 60.179 50.000 0.78 0.00 45.89 3.24
595 602 1.604755 GTATTGTTGTGGTGGACGCAA 59.395 47.619 0.00 0.00 46.63 4.85
614 621 1.349688 TGGCTTATTGTCGACTTGGGT 59.650 47.619 17.92 0.84 0.00 4.51
636 643 5.467705 TCTGATCGATTGTGCATAGAGATG 58.532 41.667 0.00 0.00 36.02 2.90
664 672 7.876068 TCGTTGGTAATCTAAAACAGAGATGTT 59.124 33.333 0.00 0.00 36.48 2.71
666 674 7.827819 TCGTTGGTAATCTAAAACAGAGATG 57.172 36.000 0.00 0.00 36.48 2.90
759 774 9.956720 CACTTGTTGAAATCTAGAAAGACAAAT 57.043 29.630 0.00 0.00 33.57 2.32
760 775 9.173021 TCACTTGTTGAAATCTAGAAAGACAAA 57.827 29.630 0.00 0.00 33.57 2.83
761 776 8.612619 GTCACTTGTTGAAATCTAGAAAGACAA 58.387 33.333 0.00 3.79 35.39 3.18
762 777 7.987458 AGTCACTTGTTGAAATCTAGAAAGACA 59.013 33.333 0.00 0.00 35.39 3.41
763 778 8.371770 AGTCACTTGTTGAAATCTAGAAAGAC 57.628 34.615 0.00 0.00 35.39 3.01
764 779 9.477484 GTAGTCACTTGTTGAAATCTAGAAAGA 57.523 33.333 0.00 0.00 35.39 2.52
765 780 9.261180 TGTAGTCACTTGTTGAAATCTAGAAAG 57.739 33.333 0.00 0.00 35.39 2.62
766 781 9.778741 ATGTAGTCACTTGTTGAAATCTAGAAA 57.221 29.630 0.00 0.00 35.39 2.52
768 783 9.856488 GTATGTAGTCACTTGTTGAAATCTAGA 57.144 33.333 0.00 0.00 35.39 2.43
769 784 9.862371 AGTATGTAGTCACTTGTTGAAATCTAG 57.138 33.333 0.00 0.00 35.39 2.43
770 785 9.639601 CAGTATGTAGTCACTTGTTGAAATCTA 57.360 33.333 0.00 0.00 35.39 1.98
771 786 8.367911 TCAGTATGTAGTCACTTGTTGAAATCT 58.632 33.333 0.00 0.00 34.37 2.40
772 787 8.534333 TCAGTATGTAGTCACTTGTTGAAATC 57.466 34.615 0.00 0.00 34.37 2.17
773 788 7.604164 CCTCAGTATGTAGTCACTTGTTGAAAT 59.396 37.037 0.00 0.00 34.37 2.17
774 789 6.929049 CCTCAGTATGTAGTCACTTGTTGAAA 59.071 38.462 0.00 0.00 34.37 2.69
775 790 6.455647 CCTCAGTATGTAGTCACTTGTTGAA 58.544 40.000 0.00 0.00 34.37 2.69
776 791 5.047306 CCCTCAGTATGTAGTCACTTGTTGA 60.047 44.000 0.00 0.00 37.40 3.18
777 792 5.171476 CCCTCAGTATGTAGTCACTTGTTG 58.829 45.833 0.00 0.00 37.40 3.33
778 793 4.322801 GCCCTCAGTATGTAGTCACTTGTT 60.323 45.833 0.00 0.00 37.40 2.83
779 794 3.195825 GCCCTCAGTATGTAGTCACTTGT 59.804 47.826 0.00 0.00 37.40 3.16
780 795 3.449018 AGCCCTCAGTATGTAGTCACTTG 59.551 47.826 0.00 0.00 37.40 3.16
781 796 3.449018 CAGCCCTCAGTATGTAGTCACTT 59.551 47.826 0.00 0.00 37.40 3.16
782 797 3.027412 CAGCCCTCAGTATGTAGTCACT 58.973 50.000 0.00 0.00 37.40 3.41
783 798 2.482142 GCAGCCCTCAGTATGTAGTCAC 60.482 54.545 0.00 0.00 37.40 3.67
784 799 1.757118 GCAGCCCTCAGTATGTAGTCA 59.243 52.381 0.00 0.00 37.40 3.41
785 800 1.069358 GGCAGCCCTCAGTATGTAGTC 59.931 57.143 0.00 0.00 37.40 2.59
786 801 1.123928 GGCAGCCCTCAGTATGTAGT 58.876 55.000 0.00 0.00 37.40 2.73
787 802 1.123077 TGGCAGCCCTCAGTATGTAG 58.877 55.000 9.64 0.00 37.40 2.74
788 803 0.830648 GTGGCAGCCCTCAGTATGTA 59.169 55.000 9.64 0.00 37.40 2.29
789 804 1.604378 GTGGCAGCCCTCAGTATGT 59.396 57.895 9.64 0.00 37.40 2.29
790 805 1.153086 GGTGGCAGCCCTCAGTATG 60.153 63.158 9.64 0.00 37.54 2.39
791 806 1.616327 TGGTGGCAGCCCTCAGTAT 60.616 57.895 14.97 0.00 0.00 2.12
792 807 2.203922 TGGTGGCAGCCCTCAGTA 60.204 61.111 14.97 0.00 0.00 2.74
793 808 3.644606 CTGGTGGCAGCCCTCAGT 61.645 66.667 14.97 0.00 32.38 3.41
803 818 1.153706 GCATCATGTTGCTGGTGGC 60.154 57.895 19.34 0.00 39.57 5.01
810 825 2.089980 AGTCCTCAAGCATCATGTTGC 58.910 47.619 19.05 19.05 43.09 4.17
811 826 3.340928 TGAGTCCTCAAGCATCATGTTG 58.659 45.455 0.00 0.00 36.53 3.33
812 827 3.607741 CTGAGTCCTCAAGCATCATGTT 58.392 45.455 0.00 0.00 39.39 2.71
813 828 2.093075 CCTGAGTCCTCAAGCATCATGT 60.093 50.000 0.00 0.00 39.39 3.21
814 829 2.169978 TCCTGAGTCCTCAAGCATCATG 59.830 50.000 0.00 0.00 39.39 3.07
815 830 2.475155 TCCTGAGTCCTCAAGCATCAT 58.525 47.619 0.00 0.00 39.39 2.45
816 831 1.942776 TCCTGAGTCCTCAAGCATCA 58.057 50.000 0.00 0.00 39.39 3.07
817 832 3.118482 TGATTCCTGAGTCCTCAAGCATC 60.118 47.826 0.00 0.00 39.39 3.91
818 833 2.842496 TGATTCCTGAGTCCTCAAGCAT 59.158 45.455 0.00 0.00 39.39 3.79
819 834 2.235650 CTGATTCCTGAGTCCTCAAGCA 59.764 50.000 0.00 0.00 39.39 3.91
820 835 2.235898 ACTGATTCCTGAGTCCTCAAGC 59.764 50.000 0.00 0.00 39.39 4.01
821 836 3.428725 CGACTGATTCCTGAGTCCTCAAG 60.429 52.174 0.00 0.00 39.39 3.02
822 837 2.493675 CGACTGATTCCTGAGTCCTCAA 59.506 50.000 0.00 0.00 39.39 3.02
823 838 2.095461 CGACTGATTCCTGAGTCCTCA 58.905 52.381 0.00 0.00 36.07 3.86
824 839 2.098443 GTCGACTGATTCCTGAGTCCTC 59.902 54.545 8.70 0.00 36.07 3.71
825 840 2.096248 GTCGACTGATTCCTGAGTCCT 58.904 52.381 8.70 0.00 36.07 3.85
826 841 1.202200 CGTCGACTGATTCCTGAGTCC 60.202 57.143 14.70 0.00 36.07 3.85
827 842 1.202200 CCGTCGACTGATTCCTGAGTC 60.202 57.143 14.70 0.00 36.10 3.36
828 843 0.811915 CCGTCGACTGATTCCTGAGT 59.188 55.000 14.70 0.00 0.00 3.41
829 844 0.526524 GCCGTCGACTGATTCCTGAG 60.527 60.000 14.70 0.00 0.00 3.35
830 845 1.511305 GCCGTCGACTGATTCCTGA 59.489 57.895 14.70 0.00 0.00 3.86
831 846 1.874019 CGCCGTCGACTGATTCCTG 60.874 63.158 14.70 0.00 38.10 3.86
832 847 2.490217 CGCCGTCGACTGATTCCT 59.510 61.111 14.70 0.00 38.10 3.36
833 848 2.582498 CCGCCGTCGACTGATTCC 60.582 66.667 14.70 0.00 38.10 3.01
834 849 2.158959 CACCGCCGTCGACTGATTC 61.159 63.158 14.70 0.00 38.10 2.52
835 850 2.126071 CACCGCCGTCGACTGATT 60.126 61.111 14.70 0.00 38.10 2.57
836 851 2.149803 TTTCACCGCCGTCGACTGAT 62.150 55.000 14.70 0.00 38.10 2.90
837 852 2.847754 TTTCACCGCCGTCGACTGA 61.848 57.895 14.70 7.18 38.10 3.41
838 853 2.355363 TTTCACCGCCGTCGACTG 60.355 61.111 14.70 8.48 38.10 3.51
839 854 2.355481 GTTTCACCGCCGTCGACT 60.355 61.111 14.70 0.00 38.10 4.18
840 855 3.408851 GGTTTCACCGCCGTCGAC 61.409 66.667 5.18 5.18 38.10 4.20
849 864 1.503818 TTCAAGCGAGCGGTTTCACC 61.504 55.000 4.42 0.00 33.16 4.02
850 865 0.110644 CTTCAAGCGAGCGGTTTCAC 60.111 55.000 4.42 0.00 33.16 3.18
851 866 1.841663 GCTTCAAGCGAGCGGTTTCA 61.842 55.000 4.42 0.00 33.16 2.69
852 867 1.154395 GCTTCAAGCGAGCGGTTTC 60.154 57.895 4.42 0.00 33.16 2.78
853 868 2.946762 GCTTCAAGCGAGCGGTTT 59.053 55.556 4.42 0.00 33.16 3.27
862 877 3.843240 CGACGGAGCGCTTCAAGC 61.843 66.667 17.68 0.00 38.02 4.01
863 878 2.126463 TCGACGGAGCGCTTCAAG 60.126 61.111 17.68 6.10 0.00 3.02
864 879 2.430244 GTCGACGGAGCGCTTCAA 60.430 61.111 17.68 0.00 0.00 2.69
865 880 4.415332 GGTCGACGGAGCGCTTCA 62.415 66.667 17.68 0.00 0.00 3.02
993 1008 0.912486 GACTAGAACCCATGGCCACT 59.088 55.000 8.16 1.00 0.00 4.00
1075 1090 4.304413 TCCCGACCCCTCCGACAA 62.304 66.667 0.00 0.00 0.00 3.18
1580 1597 4.451150 CCGCCTGCCGCAGAGTTA 62.451 66.667 22.35 0.00 37.30 2.24
2221 2248 5.235850 TGGATTAGAACCTTGTACTGCAA 57.764 39.130 0.00 0.00 35.50 4.08
2842 2869 2.047274 CGATGGGACCAACGCACT 60.047 61.111 8.06 0.00 43.86 4.40
3131 3158 2.046892 CTTCCTCCGGTGCAGGTG 60.047 66.667 0.00 0.00 32.20 4.00
3135 3162 1.533033 TGTCTCTTCCTCCGGTGCA 60.533 57.895 0.00 0.00 0.00 4.57
3187 3215 2.270923 GTTCATCTGCATGCACGAGTA 58.729 47.619 18.46 7.98 0.00 2.59
3483 4381 4.158579 AGGCTAGAGCAAAACCATTTTAGC 59.841 41.667 3.54 0.00 44.36 3.09
3534 4432 1.205064 CGACGCTTGCACTTCCTTG 59.795 57.895 0.00 0.00 0.00 3.61
3656 4554 2.610694 CCGAGCGCATGCATAAGGG 61.611 63.158 19.57 7.92 46.23 3.95
4034 4933 3.498397 GGACGGTCCAATACATTGCATAG 59.502 47.826 22.10 0.00 36.28 2.23
4128 5027 6.662414 AGTGTTATGTTATCAACGTCCATG 57.338 37.500 0.00 0.00 0.00 3.66
4557 5546 3.090532 ACCGCCTCCAGGAATCCC 61.091 66.667 0.00 0.00 37.39 3.85
4602 5591 3.435671 GTCGTTTGAAAGGATCCGTGATT 59.564 43.478 5.98 0.24 0.00 2.57
4731 5720 4.986783 TGAACTCTTGGACTCTGTCTAGA 58.013 43.478 0.00 0.00 32.47 2.43


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

AutoCloner maintained by Alex Coulton.