Multiple sequence alignment - TraesCS1D01G424400

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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 TraesCS1D01G424400 chr1D 100.000 2902 0 0 1 2902 478815170 478818071 0.000000e+00 5360
1 TraesCS1D01G424400 chr1B 95.192 1248 47 8 895 2132 666823075 666824319 0.000000e+00 1960
2 TraesCS1D01G424400 chr1B 85.923 753 48 20 166 888 666822302 666823026 0.000000e+00 750
3 TraesCS1D01G424400 chr1B 89.762 420 28 6 2491 2902 666824689 666825101 9.210000e-145 523
4 TraesCS1D01G424400 chr1B 84.689 209 16 11 2195 2393 666824484 666824686 8.210000e-46 195
5 TraesCS1D01G424400 chr1A 90.306 784 45 16 2120 2885 574935887 574936657 0.000000e+00 998
6 TraesCS1D01G424400 chr1A 95.492 488 20 2 1646 2133 574935359 574935844 0.000000e+00 778
7 TraesCS1D01G424400 chr1A 84.814 619 60 12 910 1521 574934498 574935089 2.490000e-165 592
8 TraesCS1D01G424400 chr1A 83.594 128 6 4 1522 1649 574935167 574935279 3.950000e-19 106
9 TraesCS1D01G424400 chr7D 79.808 624 73 31 922 1521 63437187 63436593 3.480000e-109 405
10 TraesCS1D01G424400 chr7D 78.774 424 42 25 1683 2086 63436254 63435859 1.040000e-59 241
11 TraesCS1D01G424400 chr4A 79.866 596 80 19 934 1506 592538005 592538583 1.620000e-107 399
12 TraesCS1D01G424400 chr4A 79.698 596 81 19 934 1506 592824126 592824704 7.540000e-106 394
13 TraesCS1D01G424400 chr4A 79.500 600 79 22 934 1506 593106373 593106955 1.260000e-103 387
14 TraesCS1D01G424400 chr7B 81.010 495 58 19 1045 1521 19119424 19119900 7.640000e-96 361
15 TraesCS1D01G424400 chr7B 78.893 488 62 26 1614 2078 3795773 3795304 2.830000e-75 292
16 TraesCS1D01G424400 chr7A 78.883 573 65 33 739 1267 561607317 561607877 1.290000e-88 337
17 TraesCS1D01G424400 chr7A 78.313 498 69 24 1044 1521 34140934 34140456 4.730000e-73 285
18 TraesCS1D01G424400 chr7A 78.112 498 54 30 1614 2086 66228300 66227833 6.170000e-67 265
19 TraesCS1D01G424400 chr4B 89.773 264 21 2 2616 2879 546685106 546685363 1.670000e-87 333
20 TraesCS1D01G424400 chr6B 78.709 573 66 33 739 1267 142691591 142692151 5.990000e-87 331
21 TraesCS1D01G424400 chr6A 83.143 350 40 12 932 1267 431759915 431759571 4.700000e-78 302


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 TraesCS1D01G424400 chr1D 478815170 478818071 2901 False 5360.0 5360 100.0000 1 2902 1 chr1D.!!$F1 2901
1 TraesCS1D01G424400 chr1B 666822302 666825101 2799 False 857.0 1960 88.8915 166 2902 4 chr1B.!!$F1 2736
2 TraesCS1D01G424400 chr1A 574934498 574936657 2159 False 618.5 998 88.5515 910 2885 4 chr1A.!!$F1 1975
3 TraesCS1D01G424400 chr7D 63435859 63437187 1328 True 323.0 405 79.2910 922 2086 2 chr7D.!!$R1 1164
4 TraesCS1D01G424400 chr4A 592538005 592538583 578 False 399.0 399 79.8660 934 1506 1 chr4A.!!$F1 572
5 TraesCS1D01G424400 chr4A 592824126 592824704 578 False 394.0 394 79.6980 934 1506 1 chr4A.!!$F2 572
6 TraesCS1D01G424400 chr4A 593106373 593106955 582 False 387.0 387 79.5000 934 1506 1 chr4A.!!$F3 572
7 TraesCS1D01G424400 chr7A 561607317 561607877 560 False 337.0 337 78.8830 739 1267 1 chr7A.!!$F1 528
8 TraesCS1D01G424400 chr6B 142691591 142692151 560 False 331.0 331 78.7090 739 1267 1 chr6B.!!$F1 528

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
366 371 0.042731 TCGATTCCCCACCTTCCTCT 59.957 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2648 0.472925 TGGGACAACCACAGGCTAGA 60.473 55.0 0.0 0.0 46.8 2.43 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
20 21 3.586100 AAATGTTTGGATACCGGCAAC 57.414 42.857 0.00 0.00 0.00 4.17
21 22 2.507407 ATGTTTGGATACCGGCAACT 57.493 45.000 0.00 0.00 0.00 3.16
22 23 3.637911 ATGTTTGGATACCGGCAACTA 57.362 42.857 0.00 0.00 0.00 2.24
23 24 3.637911 TGTTTGGATACCGGCAACTAT 57.362 42.857 0.00 0.00 0.00 2.12
24 25 4.757019 TGTTTGGATACCGGCAACTATA 57.243 40.909 0.00 0.00 0.00 1.31
25 26 4.444536 TGTTTGGATACCGGCAACTATAC 58.555 43.478 0.00 0.00 0.00 1.47
26 27 4.162698 TGTTTGGATACCGGCAACTATACT 59.837 41.667 0.00 0.00 0.00 2.12
27 28 5.121105 GTTTGGATACCGGCAACTATACTT 58.879 41.667 0.00 0.00 0.00 2.24
28 29 5.362105 TTGGATACCGGCAACTATACTTT 57.638 39.130 0.00 0.00 0.00 2.66
29 30 5.362105 TGGATACCGGCAACTATACTTTT 57.638 39.130 0.00 0.00 0.00 2.27
30 31 5.120399 TGGATACCGGCAACTATACTTTTG 58.880 41.667 0.00 0.00 0.00 2.44
31 32 4.024302 GGATACCGGCAACTATACTTTTGC 60.024 45.833 0.00 0.00 46.14 3.68
41 42 8.173321 GCAACTATACTTTTGCCATGTAAAAG 57.827 34.615 21.49 21.49 45.75 2.27
42 43 8.026607 GCAACTATACTTTTGCCATGTAAAAGA 58.973 33.333 26.34 16.22 44.06 2.52
45 46 9.461312 ACTATACTTTTGCCATGTAAAAGATGA 57.539 29.630 26.34 16.62 44.06 2.92
46 47 9.722056 CTATACTTTTGCCATGTAAAAGATGAC 57.278 33.333 26.34 0.00 44.06 3.06
47 48 5.783111 ACTTTTGCCATGTAAAAGATGACC 58.217 37.500 26.34 0.00 44.06 4.02
48 49 4.799564 TTTGCCATGTAAAAGATGACCC 57.200 40.909 0.00 0.00 0.00 4.46
49 50 3.737559 TGCCATGTAAAAGATGACCCT 57.262 42.857 0.00 0.00 0.00 4.34
50 51 4.046286 TGCCATGTAAAAGATGACCCTT 57.954 40.909 0.00 0.00 0.00 3.95
51 52 4.415596 TGCCATGTAAAAGATGACCCTTT 58.584 39.130 0.00 0.00 37.94 3.11
52 53 4.462483 TGCCATGTAAAAGATGACCCTTTC 59.538 41.667 0.00 0.00 35.50 2.62
53 54 4.706962 GCCATGTAAAAGATGACCCTTTCT 59.293 41.667 0.00 0.00 35.50 2.52
54 55 5.185828 GCCATGTAAAAGATGACCCTTTCTT 59.814 40.000 0.00 0.00 35.50 2.52
55 56 6.295292 GCCATGTAAAAGATGACCCTTTCTTT 60.295 38.462 0.00 0.00 42.46 2.52
57 58 7.599998 CCATGTAAAAGATGACCCTTTCTTTTG 59.400 37.037 16.74 4.99 46.35 2.44
58 59 6.512297 TGTAAAAGATGACCCTTTCTTTTGC 58.488 36.000 16.74 15.84 46.35 3.68
59 60 4.607293 AAAGATGACCCTTTCTTTTGCC 57.393 40.909 0.00 0.00 38.67 4.52
60 61 2.529632 AGATGACCCTTTCTTTTGCCC 58.470 47.619 0.00 0.00 0.00 5.36
61 62 2.158325 AGATGACCCTTTCTTTTGCCCA 60.158 45.455 0.00 0.00 0.00 5.36
62 63 1.703411 TGACCCTTTCTTTTGCCCAG 58.297 50.000 0.00 0.00 0.00 4.45
63 64 0.318441 GACCCTTTCTTTTGCCCAGC 59.682 55.000 0.00 0.00 0.00 4.85
64 65 0.398381 ACCCTTTCTTTTGCCCAGCA 60.398 50.000 0.00 0.00 36.47 4.41
65 66 0.978907 CCCTTTCTTTTGCCCAGCAT 59.021 50.000 0.00 0.00 38.76 3.79
66 67 1.066645 CCCTTTCTTTTGCCCAGCATC 60.067 52.381 0.00 0.00 38.76 3.91
67 68 1.619827 CCTTTCTTTTGCCCAGCATCA 59.380 47.619 0.00 0.00 38.76 3.07
68 69 2.037511 CCTTTCTTTTGCCCAGCATCAA 59.962 45.455 0.00 0.00 38.76 2.57
69 70 3.323243 CTTTCTTTTGCCCAGCATCAAG 58.677 45.455 0.00 0.00 38.76 3.02
70 71 2.291209 TCTTTTGCCCAGCATCAAGA 57.709 45.000 7.35 7.35 38.76 3.02
71 72 2.596346 TCTTTTGCCCAGCATCAAGAA 58.404 42.857 8.51 0.00 38.76 2.52
72 73 3.167485 TCTTTTGCCCAGCATCAAGAAT 58.833 40.909 8.51 0.00 38.76 2.40
73 74 3.056393 TCTTTTGCCCAGCATCAAGAATG 60.056 43.478 8.51 0.00 38.76 2.67
74 75 1.927487 TTGCCCAGCATCAAGAATGT 58.073 45.000 0.00 0.00 38.76 2.71
75 76 1.466856 TGCCCAGCATCAAGAATGTC 58.533 50.000 0.00 0.00 37.71 3.06
76 77 1.005097 TGCCCAGCATCAAGAATGTCT 59.995 47.619 0.00 0.00 37.71 3.41
77 78 2.097825 GCCCAGCATCAAGAATGTCTT 58.902 47.619 0.00 0.00 37.14 3.01
78 79 4.680434 TGCCCAGCATCAAGAATGTCTTG 61.680 47.826 11.04 11.04 43.49 3.02
92 93 8.738645 AAGAATGTCTTGATTTGGATAGTACC 57.261 34.615 0.00 0.00 34.98 3.34
93 94 8.095452 AGAATGTCTTGATTTGGATAGTACCT 57.905 34.615 0.00 0.00 0.00 3.08
94 95 8.552296 AGAATGTCTTGATTTGGATAGTACCTT 58.448 33.333 0.00 0.00 0.00 3.50
95 96 8.511604 AATGTCTTGATTTGGATAGTACCTTG 57.488 34.615 0.00 0.00 0.00 3.61
96 97 5.880332 TGTCTTGATTTGGATAGTACCTTGC 59.120 40.000 0.00 0.00 0.00 4.01
97 98 6.116126 GTCTTGATTTGGATAGTACCTTGCT 58.884 40.000 0.00 0.00 0.00 3.91
98 99 6.599638 GTCTTGATTTGGATAGTACCTTGCTT 59.400 38.462 0.00 0.00 0.00 3.91
99 100 7.121315 GTCTTGATTTGGATAGTACCTTGCTTT 59.879 37.037 0.00 0.00 0.00 3.51
100 101 7.336931 TCTTGATTTGGATAGTACCTTGCTTTC 59.663 37.037 0.00 0.00 0.00 2.62
101 102 6.480763 TGATTTGGATAGTACCTTGCTTTCA 58.519 36.000 0.00 0.00 0.00 2.69
102 103 6.945435 TGATTTGGATAGTACCTTGCTTTCAA 59.055 34.615 0.00 0.00 0.00 2.69
103 104 7.450014 TGATTTGGATAGTACCTTGCTTTCAAA 59.550 33.333 0.00 0.00 0.00 2.69
104 105 7.589958 TTTGGATAGTACCTTGCTTTCAAAA 57.410 32.000 0.00 0.00 0.00 2.44
105 106 7.589958 TTGGATAGTACCTTGCTTTCAAAAA 57.410 32.000 0.00 0.00 0.00 1.94
106 107 7.775053 TGGATAGTACCTTGCTTTCAAAAAT 57.225 32.000 0.00 0.00 0.00 1.82
107 108 7.826690 TGGATAGTACCTTGCTTTCAAAAATC 58.173 34.615 0.00 0.00 0.00 2.17
108 109 7.093945 TGGATAGTACCTTGCTTTCAAAAATCC 60.094 37.037 0.00 0.00 0.00 3.01
109 110 7.122799 GGATAGTACCTTGCTTTCAAAAATCCT 59.877 37.037 0.00 0.00 0.00 3.24
110 111 9.174166 GATAGTACCTTGCTTTCAAAAATCCTA 57.826 33.333 0.00 0.00 0.00 2.94
111 112 7.454260 AGTACCTTGCTTTCAAAAATCCTAG 57.546 36.000 0.00 0.00 0.00 3.02
112 113 5.139435 ACCTTGCTTTCAAAAATCCTAGC 57.861 39.130 0.00 0.00 0.00 3.42
113 114 4.588528 ACCTTGCTTTCAAAAATCCTAGCA 59.411 37.500 0.00 0.00 36.90 3.49
114 115 4.925646 CCTTGCTTTCAAAAATCCTAGCAC 59.074 41.667 0.00 0.00 38.25 4.40
115 116 5.509501 CCTTGCTTTCAAAAATCCTAGCACA 60.510 40.000 0.00 0.00 38.25 4.57
116 117 5.528043 TGCTTTCAAAAATCCTAGCACAA 57.472 34.783 0.00 0.00 34.05 3.33
117 118 5.911752 TGCTTTCAAAAATCCTAGCACAAA 58.088 33.333 0.00 0.00 34.05 2.83
118 119 5.984926 TGCTTTCAAAAATCCTAGCACAAAG 59.015 36.000 0.00 0.00 34.05 2.77
119 120 6.183360 TGCTTTCAAAAATCCTAGCACAAAGA 60.183 34.615 0.00 0.00 34.05 2.52
120 121 6.364435 GCTTTCAAAAATCCTAGCACAAAGAG 59.636 38.462 0.00 0.00 0.00 2.85
121 122 7.581213 TTTCAAAAATCCTAGCACAAAGAGA 57.419 32.000 0.00 0.00 0.00 3.10
122 123 7.581213 TTCAAAAATCCTAGCACAAAGAGAA 57.419 32.000 0.00 0.00 0.00 2.87
123 124 7.765695 TCAAAAATCCTAGCACAAAGAGAAT 57.234 32.000 0.00 0.00 0.00 2.40
124 125 7.820648 TCAAAAATCCTAGCACAAAGAGAATC 58.179 34.615 0.00 0.00 0.00 2.52
142 143 7.687005 GAGAATCTAGATTAATTATCGGCCG 57.313 40.000 22.12 22.12 38.36 6.13
143 144 6.043411 AGAATCTAGATTAATTATCGGCCGC 58.957 40.000 23.51 2.24 38.36 6.53
144 145 4.119442 TCTAGATTAATTATCGGCCGCC 57.881 45.455 23.51 0.00 38.36 6.13
145 146 3.767673 TCTAGATTAATTATCGGCCGCCT 59.232 43.478 23.51 13.16 38.36 5.52
146 147 3.418684 AGATTAATTATCGGCCGCCTT 57.581 42.857 23.51 13.04 38.36 4.35
147 148 3.751518 AGATTAATTATCGGCCGCCTTT 58.248 40.909 23.51 13.57 38.36 3.11
148 149 3.502211 AGATTAATTATCGGCCGCCTTTG 59.498 43.478 23.51 0.00 38.36 2.77
149 150 0.948678 TAATTATCGGCCGCCTTTGC 59.051 50.000 23.51 0.00 0.00 3.68
150 151 0.751643 AATTATCGGCCGCCTTTGCT 60.752 50.000 23.51 0.00 34.43 3.91
151 152 0.107831 ATTATCGGCCGCCTTTGCTA 59.892 50.000 23.51 0.00 34.43 3.49
152 153 0.107606 TTATCGGCCGCCTTTGCTAA 60.108 50.000 23.51 0.00 34.43 3.09
153 154 0.812412 TATCGGCCGCCTTTGCTAAC 60.812 55.000 23.51 0.00 34.43 2.34
154 155 2.813226 ATCGGCCGCCTTTGCTAACA 62.813 55.000 23.51 0.00 34.43 2.41
155 156 2.406616 CGGCCGCCTTTGCTAACAT 61.407 57.895 14.67 0.00 34.43 2.71
156 157 1.433471 GGCCGCCTTTGCTAACATC 59.567 57.895 0.71 0.00 34.43 3.06
157 158 1.062525 GCCGCCTTTGCTAACATCG 59.937 57.895 0.00 0.00 34.43 3.84
158 159 1.062525 CCGCCTTTGCTAACATCGC 59.937 57.895 0.00 0.00 34.43 4.58
159 160 1.062525 CGCCTTTGCTAACATCGCC 59.937 57.895 0.00 0.00 34.43 5.54
160 161 1.643868 CGCCTTTGCTAACATCGCCA 61.644 55.000 0.00 0.00 34.43 5.69
161 162 0.525761 GCCTTTGCTAACATCGCCAA 59.474 50.000 0.00 0.00 33.53 4.52
162 163 1.067915 GCCTTTGCTAACATCGCCAAA 60.068 47.619 0.00 0.00 33.53 3.28
163 164 2.417243 GCCTTTGCTAACATCGCCAAAT 60.417 45.455 0.00 0.00 33.53 2.32
164 165 3.848726 CCTTTGCTAACATCGCCAAATT 58.151 40.909 0.00 0.00 0.00 1.82
167 168 5.516339 CCTTTGCTAACATCGCCAAATTAAG 59.484 40.000 0.00 0.00 0.00 1.85
178 179 6.773976 TCGCCAAATTAAGAGAATGGAAAT 57.226 33.333 0.00 0.00 32.82 2.17
179 180 6.795399 TCGCCAAATTAAGAGAATGGAAATC 58.205 36.000 0.00 0.00 32.82 2.17
185 186 2.691409 AGAGAATGGAAATCGCGGAA 57.309 45.000 6.13 0.00 0.00 4.30
207 209 0.686789 AAGGCCCCTTGATTTTGCAC 59.313 50.000 0.00 0.00 34.60 4.57
214 216 3.554752 CCCCTTGATTTTGCACATTTCGT 60.555 43.478 0.00 0.00 0.00 3.85
215 217 3.674753 CCCTTGATTTTGCACATTTCGTC 59.325 43.478 0.00 0.00 0.00 4.20
217 219 4.618489 CCTTGATTTTGCACATTTCGTCTC 59.382 41.667 0.00 0.00 0.00 3.36
222 224 5.591643 TTTTGCACATTTCGTCTCTAGAC 57.408 39.130 0.00 0.00 41.47 2.59
245 247 5.049405 ACGCTCTAAAGTGAGTTGAAATTGG 60.049 40.000 0.00 0.00 36.80 3.16
251 253 8.567948 TCTAAAGTGAGTTGAAATTGGAACATC 58.432 33.333 3.41 0.27 39.30 3.06
263 265 1.377229 GAACATCGGTGGGTCCCAA 59.623 57.895 13.78 0.00 34.18 4.12
364 369 0.546747 TGTCGATTCCCCACCTTCCT 60.547 55.000 0.00 0.00 0.00 3.36
366 371 0.042731 TCGATTCCCCACCTTCCTCT 59.957 55.000 0.00 0.00 0.00 3.69
391 396 2.001838 GTCCCTCCCCTTTCCCCTC 61.002 68.421 0.00 0.00 0.00 4.30
406 411 2.127297 CTCCCCCTTCCCCTCCAA 59.873 66.667 0.00 0.00 0.00 3.53
445 451 4.489771 CCGCCGCCTGAATCCCTT 62.490 66.667 0.00 0.00 0.00 3.95
446 452 2.897350 CGCCGCCTGAATCCCTTC 60.897 66.667 0.00 0.00 0.00 3.46
447 453 2.517166 GCCGCCTGAATCCCTTCC 60.517 66.667 0.00 0.00 0.00 3.46
448 454 2.193248 CCGCCTGAATCCCTTCCC 59.807 66.667 0.00 0.00 0.00 3.97
449 455 2.193248 CGCCTGAATCCCTTCCCC 59.807 66.667 0.00 0.00 0.00 4.81
450 456 2.603580 GCCTGAATCCCTTCCCCC 59.396 66.667 0.00 0.00 0.00 5.40
451 457 2.009302 GCCTGAATCCCTTCCCCCT 61.009 63.158 0.00 0.00 0.00 4.79
452 458 2.000825 GCCTGAATCCCTTCCCCCTC 62.001 65.000 0.00 0.00 0.00 4.30
453 459 1.356494 CCTGAATCCCTTCCCCCTCC 61.356 65.000 0.00 0.00 0.00 4.30
454 460 0.327964 CTGAATCCCTTCCCCCTCCT 60.328 60.000 0.00 0.00 0.00 3.69
455 461 0.327576 TGAATCCCTTCCCCCTCCTC 60.328 60.000 0.00 0.00 0.00 3.71
456 462 1.006227 AATCCCTTCCCCCTCCTCC 59.994 63.158 0.00 0.00 0.00 4.30
457 463 2.585523 AATCCCTTCCCCCTCCTCCC 62.586 65.000 0.00 0.00 0.00 4.30
464 470 4.475444 CCCCTCCTCCCGCCACTA 62.475 72.222 0.00 0.00 0.00 2.74
507 513 2.227194 GTTTCCCTTCTTCCTCGCAAA 58.773 47.619 0.00 0.00 0.00 3.68
533 539 2.641746 CCAGGTCTCCTCCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
534 540 1.075600 CAGGTCTCCTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
535 541 2.284151 GGTCTCCTCCCTCCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
536 542 2.284151 GTCTCCTCCCTCCCTCCC 59.716 72.222 0.00 0.00 0.00 4.30
541 547 1.082954 CCTCCCTCCCTCCCTTTGA 59.917 63.158 0.00 0.00 0.00 2.69
561 567 5.728637 TGAGGTATGTATGTATGAGCAGG 57.271 43.478 0.00 0.00 0.00 4.85
582 588 2.543777 AGCTAGGTTGTTTCTTCGCA 57.456 45.000 0.00 0.00 0.00 5.10
614 620 2.565391 TCTCTGTCAAACCAATCGGCTA 59.435 45.455 0.00 0.00 34.57 3.93
615 621 2.932614 CTCTGTCAAACCAATCGGCTAG 59.067 50.000 0.00 0.00 34.57 3.42
616 622 1.398390 CTGTCAAACCAATCGGCTAGC 59.602 52.381 6.04 6.04 34.57 3.42
653 662 0.684479 GGGACCTTCCAATTCTGGGC 60.684 60.000 0.00 0.00 43.71 5.36
693 714 2.264480 CGCGTGTTCCTGGATCCA 59.736 61.111 15.27 15.27 0.00 3.41
702 723 2.558359 GTTCCTGGATCCAAGTTTGTGG 59.442 50.000 17.00 11.65 40.33 4.17
715 736 5.520288 CCAAGTTTGTGGATGATACGAGTAG 59.480 44.000 0.00 0.00 41.65 2.57
735 756 2.909006 AGGATTGGTCTGCGGATGATAT 59.091 45.455 0.00 0.00 0.00 1.63
754 775 6.202226 TGATATGATCTATATCTTGCGTCGC 58.798 40.000 11.10 11.10 45.24 5.19
788 819 6.320164 TCGGTTGATTTTATTACAAGGGATGG 59.680 38.462 0.00 0.00 0.00 3.51
797 828 0.677731 ACAAGGGATGGTGCGTGATG 60.678 55.000 0.00 0.00 0.00 3.07
801 832 2.182842 GGATGGTGCGTGATGGCTC 61.183 63.158 0.00 0.00 0.00 4.70
813 844 3.181511 CGTGATGGCTCGATGCTTTTTAA 60.182 43.478 6.78 0.00 42.39 1.52
1042 1126 2.467880 CTAAGCCACCACCTAGGAAGA 58.532 52.381 17.98 0.00 41.22 2.87
1104 1188 2.110967 CCATGGGAGCAGCGTTGAG 61.111 63.158 2.85 0.00 0.00 3.02
1129 1213 5.361571 TGCCGGATGTTAGTACTATCTTCAA 59.638 40.000 20.21 0.59 0.00 2.69
1147 1231 7.496529 TCTTCAACTGTTCTCCTGTTAATTG 57.503 36.000 0.00 0.00 33.91 2.32
1154 1247 4.462483 TGTTCTCCTGTTAATTGGGAATGC 59.538 41.667 0.00 0.00 0.00 3.56
1335 1456 3.028130 TGGACGTAGATGCCATACTGAA 58.972 45.455 0.00 0.00 0.00 3.02
1402 1524 5.046304 TGGTTTTGTTCCATCTCAACCAAAA 60.046 36.000 0.00 0.00 40.51 2.44
1563 1771 6.471233 TTATCATGTCCCTAGTCTGAGTTG 57.529 41.667 0.00 0.00 0.00 3.16
1923 2255 8.854312 CATGAGCATGTGTAACTATAATACTCG 58.146 37.037 2.34 0.00 38.04 4.18
1928 2260 9.073368 GCATGTGTAACTATAATACTCGTATGG 57.927 37.037 0.00 0.00 38.04 2.74
2136 2607 9.665264 GTACCTGCAAAGAATTTATACTTATGC 57.335 33.333 0.00 0.00 35.03 3.14
2152 2623 4.462483 ACTTATGCTATGGTGGTTGTTTGG 59.538 41.667 0.00 0.00 0.00 3.28
2177 2648 3.319122 GGCCTTTCATGTGAGTTGTTTCT 59.681 43.478 0.00 0.00 0.00 2.52
2251 2722 2.368439 GGATGTGCAAGCCAGTATGAA 58.632 47.619 0.00 0.00 39.69 2.57
2252 2723 2.754552 GGATGTGCAAGCCAGTATGAAA 59.245 45.455 0.00 0.00 39.69 2.69
2282 2754 2.615986 TACCAGCTCAGGGACAGTAA 57.384 50.000 0.00 0.00 0.00 2.24
2283 2755 1.958288 ACCAGCTCAGGGACAGTAAT 58.042 50.000 0.00 0.00 0.00 1.89
2306 2778 5.605564 TTTCGAAGTATGTCATGTGGTTG 57.394 39.130 0.00 0.00 0.00 3.77
2318 2790 2.079170 TGTGGTTGAAAGGATTGCCA 57.921 45.000 0.00 0.00 36.29 4.92
2319 2791 2.607499 TGTGGTTGAAAGGATTGCCAT 58.393 42.857 0.00 0.00 36.29 4.40
2321 2793 3.509575 TGTGGTTGAAAGGATTGCCATAC 59.490 43.478 0.00 0.00 36.29 2.39
2323 2795 4.160252 GTGGTTGAAAGGATTGCCATACAT 59.840 41.667 0.00 0.00 36.29 2.29
2326 2798 5.581874 GGTTGAAAGGATTGCCATACATTTG 59.418 40.000 0.00 0.00 36.29 2.32
2327 2799 5.999205 TGAAAGGATTGCCATACATTTGT 57.001 34.783 0.00 0.00 36.29 2.83
2331 2803 8.538701 TGAAAGGATTGCCATACATTTGTTAAT 58.461 29.630 0.00 0.00 36.29 1.40
2334 2806 7.719483 AGGATTGCCATACATTTGTTAATCAG 58.281 34.615 0.00 0.00 36.29 2.90
2335 2807 7.342799 AGGATTGCCATACATTTGTTAATCAGT 59.657 33.333 0.00 0.00 36.29 3.41
2336 2808 7.649306 GGATTGCCATACATTTGTTAATCAGTC 59.351 37.037 0.00 0.00 0.00 3.51
2338 2810 7.459795 TGCCATACATTTGTTAATCAGTCAA 57.540 32.000 0.00 0.00 0.00 3.18
2340 2812 7.812191 TGCCATACATTTGTTAATCAGTCAAAC 59.188 33.333 0.00 0.00 34.63 2.93
2341 2813 8.028938 GCCATACATTTGTTAATCAGTCAAACT 58.971 33.333 0.00 0.00 34.63 2.66
2346 2818 6.569179 TTTGTTAATCAGTCAAACTAGCCC 57.431 37.500 0.00 0.00 0.00 5.19
2381 2861 7.390918 CTGTTCTCAGCAATTTTTCAAAGAG 57.609 36.000 0.00 0.00 34.79 2.85
2383 2863 7.546358 TGTTCTCAGCAATTTTTCAAAGAGAA 58.454 30.769 0.00 0.00 38.22 2.87
2384 2864 8.199449 TGTTCTCAGCAATTTTTCAAAGAGAAT 58.801 29.630 0.00 0.00 41.27 2.40
2525 3005 5.221224 TGCCTGATAGAAACAGTTTGGTTTG 60.221 40.000 2.34 0.00 40.85 2.93
2541 3021 2.290367 GGTTTGATTTGTTTGCAAGGCC 59.710 45.455 0.00 0.00 35.82 5.19
2591 3071 9.970395 TTGCAGCCAAGATTATTAATCAATTAG 57.030 29.630 16.68 5.28 40.42 1.73
2602 3082 9.933723 ATTATTAATCAATTAGCAATTGCCTCC 57.066 29.630 26.45 0.00 46.09 4.30
2608 3088 4.526438 ATTAGCAATTGCCTCCTAAGGT 57.474 40.909 26.45 7.51 45.34 3.50
2689 3169 0.603707 TGCAGCCACTCTAACAGCAC 60.604 55.000 0.00 0.00 0.00 4.40
2758 3245 2.675056 CGGTGTGCAGCAGAGCTTC 61.675 63.158 18.61 0.00 36.40 3.86
2777 3264 2.937591 TCGCGAAGGTAGTGTACTTTG 58.062 47.619 6.20 0.00 0.00 2.77
2786 3273 9.415544 CGAAGGTAGTGTACTTTGTTTACTTAT 57.584 33.333 0.00 0.00 0.00 1.73
2871 3366 7.413446 ACAGTGTAGTAGTAGTATTTGGGGTA 58.587 38.462 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.161866 AGTTGCCGGTATCCAAACATTT 58.838 40.909 1.90 0.00 0.00 2.32
1 2 2.802719 AGTTGCCGGTATCCAAACATT 58.197 42.857 1.90 0.00 0.00 2.71
2 3 2.507407 AGTTGCCGGTATCCAAACAT 57.493 45.000 1.90 0.00 0.00 2.71
4 5 4.700700 AGTATAGTTGCCGGTATCCAAAC 58.299 43.478 1.90 0.00 0.00 2.93
5 6 5.362105 AAGTATAGTTGCCGGTATCCAAA 57.638 39.130 1.90 0.00 0.00 3.28
6 7 5.362105 AAAGTATAGTTGCCGGTATCCAA 57.638 39.130 1.90 0.00 0.00 3.53
7 8 5.120399 CAAAAGTATAGTTGCCGGTATCCA 58.880 41.667 1.90 0.00 0.00 3.41
8 9 4.024302 GCAAAAGTATAGTTGCCGGTATCC 60.024 45.833 1.90 0.00 43.49 2.59
9 10 5.091910 GCAAAAGTATAGTTGCCGGTATC 57.908 43.478 1.90 0.00 43.49 2.24
19 20 9.461312 TCATCTTTTACATGGCAAAAGTATAGT 57.539 29.630 23.32 10.89 41.59 2.12
20 21 9.722056 GTCATCTTTTACATGGCAAAAGTATAG 57.278 33.333 23.32 15.80 41.59 1.31
21 22 8.682710 GGTCATCTTTTACATGGCAAAAGTATA 58.317 33.333 23.32 12.43 41.59 1.47
22 23 7.363793 GGGTCATCTTTTACATGGCAAAAGTAT 60.364 37.037 23.32 16.49 41.59 2.12
23 24 6.071616 GGGTCATCTTTTACATGGCAAAAGTA 60.072 38.462 23.32 15.51 41.59 2.24
24 25 5.279456 GGGTCATCTTTTACATGGCAAAAGT 60.279 40.000 23.32 14.11 41.59 2.66
25 26 5.047092 AGGGTCATCTTTTACATGGCAAAAG 60.047 40.000 20.53 20.53 42.02 2.27
26 27 4.837860 AGGGTCATCTTTTACATGGCAAAA 59.162 37.500 0.00 2.58 0.00 2.44
27 28 4.415596 AGGGTCATCTTTTACATGGCAAA 58.584 39.130 0.00 0.00 0.00 3.68
28 29 4.046286 AGGGTCATCTTTTACATGGCAA 57.954 40.909 0.00 0.00 0.00 4.52
29 30 3.737559 AGGGTCATCTTTTACATGGCA 57.262 42.857 0.00 0.00 0.00 4.92
30 31 4.706962 AGAAAGGGTCATCTTTTACATGGC 59.293 41.667 0.00 0.00 37.13 4.40
31 32 6.840780 AAGAAAGGGTCATCTTTTACATGG 57.159 37.500 0.00 0.00 37.13 3.66
38 39 3.324846 GGGCAAAAGAAAGGGTCATCTTT 59.675 43.478 0.00 0.00 45.30 2.52
39 40 2.899900 GGGCAAAAGAAAGGGTCATCTT 59.100 45.455 0.00 0.00 37.49 2.40
40 41 2.158325 TGGGCAAAAGAAAGGGTCATCT 60.158 45.455 0.00 0.00 0.00 2.90
41 42 2.232208 CTGGGCAAAAGAAAGGGTCATC 59.768 50.000 0.00 0.00 0.00 2.92
42 43 2.250924 CTGGGCAAAAGAAAGGGTCAT 58.749 47.619 0.00 0.00 0.00 3.06
43 44 1.703411 CTGGGCAAAAGAAAGGGTCA 58.297 50.000 0.00 0.00 0.00 4.02
44 45 0.318441 GCTGGGCAAAAGAAAGGGTC 59.682 55.000 0.00 0.00 0.00 4.46
45 46 0.398381 TGCTGGGCAAAAGAAAGGGT 60.398 50.000 0.00 0.00 34.76 4.34
46 47 0.978907 ATGCTGGGCAAAAGAAAGGG 59.021 50.000 0.00 0.00 43.62 3.95
47 48 1.619827 TGATGCTGGGCAAAAGAAAGG 59.380 47.619 0.00 0.00 43.62 3.11
48 49 3.006110 TCTTGATGCTGGGCAAAAGAAAG 59.994 43.478 14.32 7.26 43.62 2.62
49 50 2.964464 TCTTGATGCTGGGCAAAAGAAA 59.036 40.909 14.32 0.08 43.62 2.52
50 51 2.596346 TCTTGATGCTGGGCAAAAGAA 58.404 42.857 14.32 4.01 43.62 2.52
51 52 2.291209 TCTTGATGCTGGGCAAAAGA 57.709 45.000 13.31 13.31 43.62 2.52
52 53 3.259064 CATTCTTGATGCTGGGCAAAAG 58.741 45.455 10.20 10.20 43.62 2.27
53 54 2.633967 ACATTCTTGATGCTGGGCAAAA 59.366 40.909 0.00 0.00 43.62 2.44
54 55 2.231964 GACATTCTTGATGCTGGGCAAA 59.768 45.455 0.00 0.00 43.62 3.68
55 56 1.820519 GACATTCTTGATGCTGGGCAA 59.179 47.619 0.00 0.00 43.62 4.52
56 57 1.005097 AGACATTCTTGATGCTGGGCA 59.995 47.619 0.00 0.00 44.86 5.36
57 58 1.760192 AGACATTCTTGATGCTGGGC 58.240 50.000 0.00 0.00 39.47 5.36
67 68 8.552296 AGGTACTATCCAAATCAAGACATTCTT 58.448 33.333 0.00 0.00 34.46 2.52
68 69 8.095452 AGGTACTATCCAAATCAAGACATTCT 57.905 34.615 0.00 0.00 36.02 2.40
69 70 8.616076 CAAGGTACTATCCAAATCAAGACATTC 58.384 37.037 0.00 0.00 38.49 2.67
70 71 7.067494 GCAAGGTACTATCCAAATCAAGACATT 59.933 37.037 0.00 0.00 38.49 2.71
71 72 6.543831 GCAAGGTACTATCCAAATCAAGACAT 59.456 38.462 0.00 0.00 38.49 3.06
72 73 5.880332 GCAAGGTACTATCCAAATCAAGACA 59.120 40.000 0.00 0.00 38.49 3.41
73 74 6.116126 AGCAAGGTACTATCCAAATCAAGAC 58.884 40.000 0.00 0.00 38.49 3.01
74 75 6.313519 AGCAAGGTACTATCCAAATCAAGA 57.686 37.500 0.00 0.00 38.49 3.02
75 76 7.121168 TGAAAGCAAGGTACTATCCAAATCAAG 59.879 37.037 0.00 0.00 38.49 3.02
76 77 6.945435 TGAAAGCAAGGTACTATCCAAATCAA 59.055 34.615 0.00 0.00 38.49 2.57
77 78 6.480763 TGAAAGCAAGGTACTATCCAAATCA 58.519 36.000 0.00 0.00 38.49 2.57
78 79 7.391148 TTGAAAGCAAGGTACTATCCAAATC 57.609 36.000 0.00 0.00 38.49 2.17
79 80 7.775053 TTTGAAAGCAAGGTACTATCCAAAT 57.225 32.000 0.00 0.00 38.49 2.32
80 81 7.589958 TTTTGAAAGCAAGGTACTATCCAAA 57.410 32.000 0.00 0.00 38.49 3.28
81 82 7.589958 TTTTTGAAAGCAAGGTACTATCCAA 57.410 32.000 0.00 0.00 38.49 3.53
82 83 7.093945 GGATTTTTGAAAGCAAGGTACTATCCA 60.094 37.037 0.00 0.00 38.49 3.41
83 84 7.122799 AGGATTTTTGAAAGCAAGGTACTATCC 59.877 37.037 0.00 0.00 38.49 2.59
84 85 8.056407 AGGATTTTTGAAAGCAAGGTACTATC 57.944 34.615 0.00 0.00 38.49 2.08
85 86 9.178758 CTAGGATTTTTGAAAGCAAGGTACTAT 57.821 33.333 0.00 0.00 38.49 2.12
86 87 7.120726 GCTAGGATTTTTGAAAGCAAGGTACTA 59.879 37.037 0.00 0.00 38.49 1.82
88 89 6.093404 GCTAGGATTTTTGAAAGCAAGGTAC 58.907 40.000 0.00 0.00 35.04 3.34
89 90 5.772672 TGCTAGGATTTTTGAAAGCAAGGTA 59.227 36.000 0.00 0.00 37.05 3.08
90 91 4.588528 TGCTAGGATTTTTGAAAGCAAGGT 59.411 37.500 0.00 0.00 37.05 3.50
91 92 4.925646 GTGCTAGGATTTTTGAAAGCAAGG 59.074 41.667 0.00 0.00 41.24 3.61
92 93 5.531634 TGTGCTAGGATTTTTGAAAGCAAG 58.468 37.500 0.00 0.00 41.24 4.01
93 94 5.528043 TGTGCTAGGATTTTTGAAAGCAA 57.472 34.783 0.00 0.00 41.24 3.91
94 95 5.528043 TTGTGCTAGGATTTTTGAAAGCA 57.472 34.783 0.00 0.00 37.62 3.91
95 96 6.215845 TCTTTGTGCTAGGATTTTTGAAAGC 58.784 36.000 0.00 0.00 0.00 3.51
96 97 7.651808 TCTCTTTGTGCTAGGATTTTTGAAAG 58.348 34.615 0.00 0.00 0.00 2.62
97 98 7.581213 TCTCTTTGTGCTAGGATTTTTGAAA 57.419 32.000 0.00 0.00 0.00 2.69
98 99 7.581213 TTCTCTTTGTGCTAGGATTTTTGAA 57.419 32.000 0.00 0.00 0.00 2.69
99 100 7.667219 AGATTCTCTTTGTGCTAGGATTTTTGA 59.333 33.333 0.00 0.00 0.00 2.69
100 101 7.824672 AGATTCTCTTTGTGCTAGGATTTTTG 58.175 34.615 0.00 0.00 0.00 2.44
101 102 9.171877 CTAGATTCTCTTTGTGCTAGGATTTTT 57.828 33.333 0.00 0.00 0.00 1.94
102 103 8.543774 TCTAGATTCTCTTTGTGCTAGGATTTT 58.456 33.333 0.00 0.00 0.00 1.82
103 104 8.083828 TCTAGATTCTCTTTGTGCTAGGATTT 57.916 34.615 0.00 0.00 0.00 2.17
104 105 7.667575 TCTAGATTCTCTTTGTGCTAGGATT 57.332 36.000 0.00 0.00 0.00 3.01
105 106 7.854166 ATCTAGATTCTCTTTGTGCTAGGAT 57.146 36.000 0.00 0.00 0.00 3.24
106 107 7.667575 AATCTAGATTCTCTTTGTGCTAGGA 57.332 36.000 12.37 0.00 0.00 2.94
107 108 9.995003 ATTAATCTAGATTCTCTTTGTGCTAGG 57.005 33.333 21.17 0.00 32.50 3.02
115 116 9.660180 GGCCGATAATTAATCTAGATTCTCTTT 57.340 33.333 21.17 12.57 31.87 2.52
116 117 7.976734 CGGCCGATAATTAATCTAGATTCTCTT 59.023 37.037 24.07 14.56 31.87 2.85
117 118 7.484975 CGGCCGATAATTAATCTAGATTCTCT 58.515 38.462 24.07 9.32 31.87 3.10
118 119 6.199342 GCGGCCGATAATTAATCTAGATTCTC 59.801 42.308 33.48 10.43 31.87 2.87
119 120 6.043411 GCGGCCGATAATTAATCTAGATTCT 58.957 40.000 33.48 9.98 31.87 2.40
120 121 5.234543 GGCGGCCGATAATTAATCTAGATTC 59.765 44.000 33.48 5.57 31.87 2.52
121 122 5.104900 AGGCGGCCGATAATTAATCTAGATT 60.105 40.000 33.48 21.28 31.87 2.40
122 123 4.406003 AGGCGGCCGATAATTAATCTAGAT 59.594 41.667 33.48 0.00 31.87 1.98
123 124 3.767673 AGGCGGCCGATAATTAATCTAGA 59.232 43.478 33.48 0.00 31.87 2.43
124 125 4.124851 AGGCGGCCGATAATTAATCTAG 57.875 45.455 33.48 0.00 31.87 2.43
125 126 4.546829 AAGGCGGCCGATAATTAATCTA 57.453 40.909 33.48 0.00 31.87 1.98
126 127 3.418684 AAGGCGGCCGATAATTAATCT 57.581 42.857 33.48 7.89 31.87 2.40
127 128 3.821841 CAAAGGCGGCCGATAATTAATC 58.178 45.455 33.48 7.28 0.00 1.75
128 129 2.030274 GCAAAGGCGGCCGATAATTAAT 60.030 45.455 33.48 2.22 0.00 1.40
129 130 1.335496 GCAAAGGCGGCCGATAATTAA 59.665 47.619 33.48 0.00 0.00 1.40
130 131 0.948678 GCAAAGGCGGCCGATAATTA 59.051 50.000 33.48 0.00 0.00 1.40
131 132 1.733526 GCAAAGGCGGCCGATAATT 59.266 52.632 33.48 14.81 0.00 1.40
132 133 3.432186 GCAAAGGCGGCCGATAAT 58.568 55.556 33.48 8.99 0.00 1.28
142 143 0.525761 TTGGCGATGTTAGCAAAGGC 59.474 50.000 0.00 4.75 41.61 4.35
143 144 3.508744 ATTTGGCGATGTTAGCAAAGG 57.491 42.857 0.00 0.00 36.08 3.11
144 145 6.321717 TCTTAATTTGGCGATGTTAGCAAAG 58.678 36.000 0.00 0.00 36.08 2.77
145 146 6.150307 TCTCTTAATTTGGCGATGTTAGCAAA 59.850 34.615 0.00 0.00 36.08 3.68
146 147 5.645929 TCTCTTAATTTGGCGATGTTAGCAA 59.354 36.000 0.00 0.00 36.08 3.91
147 148 5.182487 TCTCTTAATTTGGCGATGTTAGCA 58.818 37.500 0.00 0.00 36.08 3.49
148 149 5.734855 TCTCTTAATTTGGCGATGTTAGC 57.265 39.130 0.00 0.00 0.00 3.09
149 150 7.012327 TCCATTCTCTTAATTTGGCGATGTTAG 59.988 37.037 0.00 0.00 0.00 2.34
150 151 6.826231 TCCATTCTCTTAATTTGGCGATGTTA 59.174 34.615 0.00 0.00 0.00 2.41
151 152 5.652014 TCCATTCTCTTAATTTGGCGATGTT 59.348 36.000 0.00 0.00 0.00 2.71
152 153 5.192927 TCCATTCTCTTAATTTGGCGATGT 58.807 37.500 0.00 0.00 0.00 3.06
153 154 5.756195 TCCATTCTCTTAATTTGGCGATG 57.244 39.130 0.00 0.00 0.00 3.84
154 155 6.773976 TTTCCATTCTCTTAATTTGGCGAT 57.226 33.333 0.00 0.00 0.00 4.58
155 156 6.458206 CGATTTCCATTCTCTTAATTTGGCGA 60.458 38.462 0.00 0.00 0.00 5.54
156 157 5.682862 CGATTTCCATTCTCTTAATTTGGCG 59.317 40.000 0.00 0.00 0.00 5.69
157 158 5.460091 GCGATTTCCATTCTCTTAATTTGGC 59.540 40.000 0.00 0.00 0.00 4.52
158 159 5.682862 CGCGATTTCCATTCTCTTAATTTGG 59.317 40.000 0.00 0.00 0.00 3.28
159 160 5.682862 CCGCGATTTCCATTCTCTTAATTTG 59.317 40.000 8.23 0.00 0.00 2.32
160 161 5.588648 TCCGCGATTTCCATTCTCTTAATTT 59.411 36.000 8.23 0.00 0.00 1.82
161 162 5.123227 TCCGCGATTTCCATTCTCTTAATT 58.877 37.500 8.23 0.00 0.00 1.40
162 163 4.703897 TCCGCGATTTCCATTCTCTTAAT 58.296 39.130 8.23 0.00 0.00 1.40
163 164 4.131649 TCCGCGATTTCCATTCTCTTAA 57.868 40.909 8.23 0.00 0.00 1.85
164 165 3.812156 TCCGCGATTTCCATTCTCTTA 57.188 42.857 8.23 0.00 0.00 2.10
167 168 1.330829 GGTTCCGCGATTTCCATTCTC 59.669 52.381 8.23 0.00 0.00 2.87
214 216 4.834534 ACTCACTTTAGAGCGTCTAGAGA 58.165 43.478 14.88 3.71 39.26 3.10
215 217 5.122554 TCAACTCACTTTAGAGCGTCTAGAG 59.877 44.000 0.00 9.49 39.26 2.43
217 219 5.298197 TCAACTCACTTTAGAGCGTCTAG 57.702 43.478 0.00 0.00 39.26 2.43
222 224 5.179368 TCCAATTTCAACTCACTTTAGAGCG 59.821 40.000 0.00 0.00 39.26 5.03
227 229 7.359595 CGATGTTCCAATTTCAACTCACTTTA 58.640 34.615 0.00 0.00 0.00 1.85
245 247 0.034477 ATTGGGACCCACCGATGTTC 60.034 55.000 14.59 0.00 40.11 3.18
251 253 2.428544 TATCAAATTGGGACCCACCG 57.571 50.000 14.59 1.71 40.11 4.94
263 265 4.786068 CGCAATCGTCGTTGTTTATCAAAT 59.214 37.500 8.60 0.00 37.81 2.32
342 346 1.810755 GAAGGTGGGGAATCGACAAAC 59.189 52.381 0.00 0.00 0.00 2.93
345 350 0.546747 AGGAAGGTGGGGAATCGACA 60.547 55.000 0.00 0.00 0.00 4.35
364 369 3.752167 GGGAGGGACGAGGGGAGA 61.752 72.222 0.00 0.00 0.00 3.71
391 396 3.728373 CGTTGGAGGGGAAGGGGG 61.728 72.222 0.00 0.00 0.00 5.40
447 453 4.475444 TAGTGGCGGGAGGAGGGG 62.475 72.222 0.00 0.00 0.00 4.79
448 454 2.840102 CTAGTGGCGGGAGGAGGG 60.840 72.222 0.00 0.00 0.00 4.30
449 455 2.840102 CCTAGTGGCGGGAGGAGG 60.840 72.222 0.00 0.00 31.45 4.30
450 456 2.840102 CCCTAGTGGCGGGAGGAG 60.840 72.222 0.29 0.00 44.90 3.69
451 457 4.475444 CCCCTAGTGGCGGGAGGA 62.475 72.222 0.00 0.00 44.90 3.71
452 458 4.475444 TCCCCTAGTGGCGGGAGG 62.475 72.222 0.58 0.00 43.72 4.30
454 460 4.791069 GGTCCCCTAGTGGCGGGA 62.791 72.222 0.58 0.58 46.52 5.14
455 461 4.798682 AGGTCCCCTAGTGGCGGG 62.799 72.222 0.00 0.00 41.59 6.13
456 462 3.470888 CAGGTCCCCTAGTGGCGG 61.471 72.222 0.00 0.00 29.64 6.13
457 463 4.162690 GCAGGTCCCCTAGTGGCG 62.163 72.222 0.00 0.00 29.64 5.69
458 464 4.162690 CGCAGGTCCCCTAGTGGC 62.163 72.222 0.00 0.00 29.64 5.01
459 465 4.162690 GCGCAGGTCCCCTAGTGG 62.163 72.222 0.30 0.00 29.64 4.00
460 466 4.162690 GGCGCAGGTCCCCTAGTG 62.163 72.222 10.83 0.00 29.64 2.74
479 485 0.036671 AAGAAGGGAAACGGCTACGG 60.037 55.000 0.00 0.00 46.48 4.02
483 489 0.325272 GAGGAAGAAGGGAAACGGCT 59.675 55.000 0.00 0.00 0.00 5.52
492 498 1.160137 CCTGTTTGCGAGGAAGAAGG 58.840 55.000 0.00 0.00 31.48 3.46
507 513 0.543174 GAGGAGACCTGGTGACCTGT 60.543 60.000 21.13 0.00 31.76 4.00
533 539 6.239600 GCTCATACATACATACCTCAAAGGGA 60.240 42.308 0.00 0.00 40.58 4.20
534 540 5.934625 GCTCATACATACATACCTCAAAGGG 59.065 44.000 0.00 0.00 40.58 3.95
535 541 6.524734 TGCTCATACATACATACCTCAAAGG 58.475 40.000 0.00 0.00 42.49 3.11
536 542 6.648310 CCTGCTCATACATACATACCTCAAAG 59.352 42.308 0.00 0.00 0.00 2.77
541 547 5.186021 GCTACCTGCTCATACATACATACCT 59.814 44.000 0.00 0.00 38.95 3.08
561 567 3.323243 TGCGAAGAAACAACCTAGCTAC 58.677 45.455 0.00 0.00 0.00 3.58
575 581 1.406898 AGAGAATCGATGCTGCGAAGA 59.593 47.619 11.71 0.00 44.22 2.87
582 588 4.180057 GTTTGACAGAGAGAATCGATGCT 58.820 43.478 5.29 5.29 42.67 3.79
616 622 1.897615 CGTCCCTACCCTAGCGGAG 60.898 68.421 4.45 0.00 34.64 4.63
670 679 2.279851 CAGGAACACGCGACACCA 60.280 61.111 15.93 0.00 0.00 4.17
671 680 2.781595 ATCCAGGAACACGCGACACC 62.782 60.000 15.93 10.70 0.00 4.16
693 714 5.421056 TCCTACTCGTATCATCCACAAACTT 59.579 40.000 0.00 0.00 0.00 2.66
702 723 5.704888 CAGACCAATCCTACTCGTATCATC 58.295 45.833 0.00 0.00 0.00 2.92
703 724 4.021894 GCAGACCAATCCTACTCGTATCAT 60.022 45.833 0.00 0.00 0.00 2.45
704 725 3.318275 GCAGACCAATCCTACTCGTATCA 59.682 47.826 0.00 0.00 0.00 2.15
715 736 2.839486 TATCATCCGCAGACCAATCC 57.161 50.000 0.00 0.00 0.00 3.01
735 756 4.454504 TGTAGCGACGCAAGATATAGATCA 59.545 41.667 23.70 0.00 43.62 2.92
782 803 3.211963 GCCATCACGCACCATCCC 61.212 66.667 0.00 0.00 0.00 3.85
788 819 3.009140 CATCGAGCCATCACGCAC 58.991 61.111 0.00 0.00 0.00 5.34
1032 1116 3.379452 CTTGTCCATCCTCTTCCTAGGT 58.621 50.000 9.08 0.00 37.91 3.08
1042 1126 1.689273 GGTATCGAGCTTGTCCATCCT 59.311 52.381 0.00 0.00 0.00 3.24
1104 1188 4.850347 AGATAGTACTAACATCCGGCAC 57.150 45.455 6.70 0.00 0.00 5.01
1129 1213 4.993705 TCCCAATTAACAGGAGAACAGT 57.006 40.909 0.00 0.00 0.00 3.55
1147 1231 3.565307 TGTTGAATGGATAGGCATTCCC 58.435 45.455 0.00 0.00 37.09 3.97
1154 1247 6.127810 CAGTCACAATGTTGAATGGATAGG 57.872 41.667 0.00 0.00 37.82 2.57
1202 1312 4.012374 GCCTCACCAATCAGATTCTTCAA 58.988 43.478 0.00 0.00 0.00 2.69
1357 1478 4.267536 CAATGAGATGTCTGGTGTGGAAT 58.732 43.478 0.00 0.00 0.00 3.01
1402 1524 7.058525 TCCTAGAGTTGCAATCAATCAATCAT 58.941 34.615 0.59 0.00 34.29 2.45
1563 1771 6.363473 CAGGTTTGTTTCGAGTAATTCAGTC 58.637 40.000 0.00 0.00 0.00 3.51
1923 2255 7.852531 ATGACATCAACACATTGAGGCCATAC 61.853 42.308 5.01 0.00 44.54 2.39
2136 2607 2.752903 GCCTACCAAACAACCACCATAG 59.247 50.000 0.00 0.00 0.00 2.23
2152 2623 3.412386 ACAACTCACATGAAAGGCCTAC 58.588 45.455 5.16 3.96 0.00 3.18
2177 2648 0.472925 TGGGACAACCACAGGCTAGA 60.473 55.000 0.00 0.00 46.80 2.43
2252 2723 4.505742 CCCTGAGCTGGTAAGAGAGTTTTT 60.506 45.833 0.00 0.00 0.00 1.94
2257 2728 1.754226 GTCCCTGAGCTGGTAAGAGAG 59.246 57.143 0.00 0.00 0.00 3.20
2270 2742 5.223449 ACTTCGAAAATTACTGTCCCTGA 57.777 39.130 0.00 0.00 0.00 3.86
2282 2754 6.429692 TCAACCACATGACATACTTCGAAAAT 59.570 34.615 0.00 0.00 0.00 1.82
2283 2755 5.760743 TCAACCACATGACATACTTCGAAAA 59.239 36.000 0.00 0.00 0.00 2.29
2306 2778 8.947055 ATTAACAAATGTATGGCAATCCTTTC 57.053 30.769 0.00 0.00 0.00 2.62
2319 2791 8.726988 GGCTAGTTTGACTGATTAACAAATGTA 58.273 33.333 0.00 0.00 36.25 2.29
2321 2793 7.029563 GGGCTAGTTTGACTGATTAACAAATG 58.970 38.462 0.00 0.00 36.25 2.32
2323 2795 6.065374 TGGGCTAGTTTGACTGATTAACAAA 58.935 36.000 0.00 0.00 0.00 2.83
2326 2798 5.705905 AGTTGGGCTAGTTTGACTGATTAAC 59.294 40.000 0.00 0.00 0.00 2.01
2327 2799 5.876357 AGTTGGGCTAGTTTGACTGATTAA 58.124 37.500 0.00 0.00 0.00 1.40
2331 2803 3.118038 ACAAGTTGGGCTAGTTTGACTGA 60.118 43.478 7.96 0.00 0.00 3.41
2334 2806 4.320275 GCTAACAAGTTGGGCTAGTTTGAC 60.320 45.833 7.96 0.00 0.00 3.18
2335 2807 3.818773 GCTAACAAGTTGGGCTAGTTTGA 59.181 43.478 7.96 0.00 0.00 2.69
2336 2808 3.821033 AGCTAACAAGTTGGGCTAGTTTG 59.179 43.478 15.25 0.28 33.62 2.93
2338 2810 3.181443 ACAGCTAACAAGTTGGGCTAGTT 60.181 43.478 16.03 6.30 33.88 2.24
2340 2812 3.059352 ACAGCTAACAAGTTGGGCTAG 57.941 47.619 16.03 10.62 33.88 3.42
2341 2813 3.072476 AGAACAGCTAACAAGTTGGGCTA 59.928 43.478 16.03 1.97 33.88 3.93
2342 2814 2.158608 AGAACAGCTAACAAGTTGGGCT 60.159 45.455 7.96 10.61 34.89 5.19
2343 2815 2.226674 GAGAACAGCTAACAAGTTGGGC 59.773 50.000 7.96 8.52 0.00 5.36
2344 2816 3.476552 TGAGAACAGCTAACAAGTTGGG 58.523 45.455 7.96 0.00 0.00 4.12
2381 2861 7.648510 CCAACCGATAGAGTAGTCTTGTTATTC 59.351 40.741 5.16 0.00 39.76 1.75
2383 2863 6.040616 CCCAACCGATAGAGTAGTCTTGTTAT 59.959 42.308 5.16 0.00 39.76 1.89
2384 2864 5.359009 CCCAACCGATAGAGTAGTCTTGTTA 59.641 44.000 5.16 0.00 39.76 2.41
2525 3005 1.000274 AGTCGGCCTTGCAAACAAATC 60.000 47.619 0.00 0.00 34.74 2.17
2541 3021 6.291067 TCAGCATAGCATAAAATCAAGTCG 57.709 37.500 0.00 0.00 0.00 4.18
2602 3082 7.883311 TCTCTGAAATTAAACCAGGAACCTTAG 59.117 37.037 0.00 0.00 0.00 2.18
2642 3122 8.632906 TTGGAATAAACCGTTTCAATTACCTA 57.367 30.769 0.00 0.00 0.00 3.08
2643 3123 7.527568 TTGGAATAAACCGTTTCAATTACCT 57.472 32.000 0.00 0.00 0.00 3.08
2644 3124 7.868922 AGTTTGGAATAAACCGTTTCAATTACC 59.131 33.333 0.00 1.78 0.00 2.85
2652 3132 4.616953 CTGCAGTTTGGAATAAACCGTTT 58.383 39.130 5.25 1.40 0.00 3.60
2655 3135 2.595386 GCTGCAGTTTGGAATAAACCG 58.405 47.619 16.64 0.00 0.00 4.44
2689 3169 0.798776 CCTGGAAAACTAGTGCAGCG 59.201 55.000 0.00 0.00 33.43 5.18
2723 3210 3.504520 ACACCGCGATAAATTCCTTTTGT 59.495 39.130 8.23 0.00 0.00 2.83
2758 3245 2.669364 ACAAAGTACACTACCTTCGCG 58.331 47.619 0.00 0.00 0.00 5.87
2786 3273 8.856103 TGCATATACTGTGTTAGTGAGCTATAA 58.144 33.333 0.00 0.00 40.65 0.98
2787 3274 8.404107 TGCATATACTGTGTTAGTGAGCTATA 57.596 34.615 0.00 0.00 40.65 1.31
2788 3275 7.290110 TGCATATACTGTGTTAGTGAGCTAT 57.710 36.000 0.00 0.00 40.65 2.97
2789 3276 6.709018 TGCATATACTGTGTTAGTGAGCTA 57.291 37.500 0.00 0.00 40.65 3.32
2790 3277 5.598416 TGCATATACTGTGTTAGTGAGCT 57.402 39.130 0.00 0.00 40.65 4.09
2871 3366 3.196685 GCAGTCACTCCCTTACTTCTGAT 59.803 47.826 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.