Multiple sequence alignment - TraesCS2A01G091800

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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 TraesCS2A01G091800 chr2A 100.000 2465 0 0 1 2465 44796893 44799357 0.000000e+00 4553
1 TraesCS2A01G091800 chr2A 80.952 336 53 9 893 1225 44719896 44720223 3.150000e-64 255
2 TraesCS2A01G091800 chr2D 93.524 1606 81 11 316 1916 43252269 43253856 0.000000e+00 2368
3 TraesCS2A01G091800 chr2D 93.950 562 29 4 1908 2465 43254424 43254984 0.000000e+00 845
4 TraesCS2A01G091800 chr2D 96.482 398 9 1 316 708 40782568 40782965 0.000000e+00 652
5 TraesCS2A01G091800 chr2D 93.557 388 17 6 697 1084 40783184 40783563 2.750000e-159 571
6 TraesCS2A01G091800 chr2D 89.487 390 38 3 1126 1514 40784174 40784561 7.920000e-135 490
7 TraesCS2A01G091800 chr2D 90.777 206 18 1 1481 1686 40784558 40784762 8.680000e-70 274
8 TraesCS2A01G091800 chr2D 94.318 88 5 0 1681 1768 40785167 40785254 4.280000e-28 135
9 TraesCS2A01G091800 chr2D 91.011 89 8 0 1024 1112 40784178 40784090 1.200000e-23 121
10 TraesCS2A01G091800 chr2B 88.306 1411 119 20 480 1869 67963613 67964998 0.000000e+00 1650
11 TraesCS2A01G091800 chr2B 79.167 408 47 21 550 934 67908624 67909016 5.260000e-62 248
12 TraesCS2A01G091800 chr6B 95.611 319 13 1 1 318 21063734 21064052 6.080000e-141 510
13 TraesCS2A01G091800 chr6B 79.554 538 91 18 1868 2391 43143342 43142810 1.390000e-97 366
14 TraesCS2A01G091800 chr6B 87.124 233 23 7 1863 2093 57421732 57421505 8.750000e-65 257
15 TraesCS2A01G091800 chr7B 95.597 318 12 2 1 316 42844030 42843713 2.190000e-140 508
16 TraesCS2A01G091800 chr1B 95.597 318 12 2 1 316 269218574 269218257 2.190000e-140 508
17 TraesCS2A01G091800 chr1B 95.570 316 14 0 1 316 25227423 25227108 7.870000e-140 507
18 TraesCS2A01G091800 chr1B 94.012 334 17 3 1 332 390272809 390273141 1.020000e-138 503
19 TraesCS2A01G091800 chr3A 95.283 318 15 0 1 318 735599218 735599535 2.830000e-139 505
20 TraesCS2A01G091800 chr4B 95.016 321 15 1 1 321 629957619 629957938 1.020000e-138 503
21 TraesCS2A01G091800 chr3D 95.298 319 12 3 1 317 533718721 533718404 1.020000e-138 503
22 TraesCS2A01G091800 chr3B 93.939 330 14 5 1 326 71213427 71213754 6.120000e-136 494
23 TraesCS2A01G091800 chr6A 86.239 218 27 3 1898 2113 32745732 32745516 1.470000e-57 233
24 TraesCS2A01G091800 chr6D 89.503 181 17 2 1872 2051 30081191 30081370 6.860000e-56 228
25 TraesCS2A01G091800 chr4D 86.294 197 23 4 1878 2072 459389133 459388939 6.910000e-51 211


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 TraesCS2A01G091800 chr2A 44796893 44799357 2464 False 4553.0 4553 100.0000 1 2465 1 chr2A.!!$F2 2464
1 TraesCS2A01G091800 chr2D 43252269 43254984 2715 False 1606.5 2368 93.7370 316 2465 2 chr2D.!!$F2 2149
2 TraesCS2A01G091800 chr2D 40782568 40785254 2686 False 424.4 652 92.9242 316 1768 5 chr2D.!!$F1 1452
3 TraesCS2A01G091800 chr2B 67963613 67964998 1385 False 1650.0 1650 88.3060 480 1869 1 chr2B.!!$F2 1389
4 TraesCS2A01G091800 chr6B 43142810 43143342 532 True 366.0 366 79.5540 1868 2391 1 chr6B.!!$R1 523

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
91 92 0.029834 GTTGCTGTTCTGTGGTGCTG 59.970 55.0 0.00 0.0 0.0 4.41 F
129 130 0.040603 ACGACGACTTTCCGACTGTC 60.041 55.0 0.00 0.0 0.0 3.51 F
130 131 0.237761 CGACGACTTTCCGACTGTCT 59.762 55.0 6.21 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1993 0.109319 GCGTTGGCATGAACCGAAAT 60.109 50.0 0.00 0.0 39.62 2.17 R
1446 2251 0.741326 GTCAGATGGCGAGCACTAGA 59.259 55.0 0.00 0.0 0.00 2.43 R
1848 3109 0.796312 CTTGTCCGCGTATTTGTGCT 59.204 50.0 4.92 0.0 0.00 4.40 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 3.596765 GTCGTTGTTCGTCTACATTCG 57.403 47.619 0.00 0.00 40.80 3.34
21 22 2.975851 GTCGTTGTTCGTCTACATTCGT 59.024 45.455 0.00 0.00 40.80 3.85
22 23 2.975193 TCGTTGTTCGTCTACATTCGTG 59.025 45.455 0.00 0.00 40.80 4.35
23 24 2.722629 CGTTGTTCGTCTACATTCGTGT 59.277 45.455 0.00 0.00 34.52 4.49
24 25 3.420035 CGTTGTTCGTCTACATTCGTGTG 60.420 47.826 0.00 0.00 34.52 3.82
25 26 3.358707 TGTTCGTCTACATTCGTGTGT 57.641 42.857 1.51 1.51 36.13 3.72
26 27 3.302555 TGTTCGTCTACATTCGTGTGTC 58.697 45.455 0.00 0.00 33.62 3.67
27 28 3.004002 TGTTCGTCTACATTCGTGTGTCT 59.996 43.478 0.00 0.00 33.62 3.41
28 29 3.909776 TCGTCTACATTCGTGTGTCTT 57.090 42.857 0.00 0.00 33.62 3.01
29 30 4.233123 TCGTCTACATTCGTGTGTCTTT 57.767 40.909 0.00 0.00 33.62 2.52
30 31 3.978855 TCGTCTACATTCGTGTGTCTTTG 59.021 43.478 0.00 0.00 33.62 2.77
31 32 3.121279 CGTCTACATTCGTGTGTCTTTGG 59.879 47.826 0.00 0.00 33.62 3.28
32 33 4.056050 GTCTACATTCGTGTGTCTTTGGT 58.944 43.478 0.00 0.00 33.62 3.67
33 34 4.510340 GTCTACATTCGTGTGTCTTTGGTT 59.490 41.667 0.00 0.00 33.62 3.67
34 35 5.007332 GTCTACATTCGTGTGTCTTTGGTTT 59.993 40.000 0.00 0.00 33.62 3.27
35 36 4.027572 ACATTCGTGTGTCTTTGGTTTG 57.972 40.909 0.00 0.00 0.00 2.93
36 37 3.181491 ACATTCGTGTGTCTTTGGTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
37 38 2.404923 TCGTGTGTCTTTGGTTTGGA 57.595 45.000 0.00 0.00 0.00 3.53
38 39 2.925724 TCGTGTGTCTTTGGTTTGGAT 58.074 42.857 0.00 0.00 0.00 3.41
39 40 2.875933 TCGTGTGTCTTTGGTTTGGATC 59.124 45.455 0.00 0.00 0.00 3.36
40 41 2.031157 CGTGTGTCTTTGGTTTGGATCC 60.031 50.000 4.20 4.20 0.00 3.36
41 42 3.222603 GTGTGTCTTTGGTTTGGATCCT 58.777 45.455 14.23 0.00 0.00 3.24
42 43 3.636764 GTGTGTCTTTGGTTTGGATCCTT 59.363 43.478 14.23 0.00 0.00 3.36
43 44 3.888930 TGTGTCTTTGGTTTGGATCCTTC 59.111 43.478 14.23 3.17 0.00 3.46
44 45 3.255888 GTGTCTTTGGTTTGGATCCTTCC 59.744 47.826 14.23 12.64 42.94 3.46
59 60 7.803279 GGATCCTTCCAATCTACGTTATTTT 57.197 36.000 3.84 0.00 42.12 1.82
60 61 8.221965 GGATCCTTCCAATCTACGTTATTTTT 57.778 34.615 3.84 0.00 42.12 1.94
61 62 8.343366 GGATCCTTCCAATCTACGTTATTTTTC 58.657 37.037 3.84 0.00 42.12 2.29
62 63 8.801882 ATCCTTCCAATCTACGTTATTTTTCA 57.198 30.769 0.00 0.00 0.00 2.69
63 64 8.801882 TCCTTCCAATCTACGTTATTTTTCAT 57.198 30.769 0.00 0.00 0.00 2.57
64 65 8.889717 TCCTTCCAATCTACGTTATTTTTCATC 58.110 33.333 0.00 0.00 0.00 2.92
65 66 7.850982 CCTTCCAATCTACGTTATTTTTCATCG 59.149 37.037 0.00 0.00 0.00 3.84
66 67 7.241663 TCCAATCTACGTTATTTTTCATCGG 57.758 36.000 0.00 0.00 0.00 4.18
67 68 5.907391 CCAATCTACGTTATTTTTCATCGGC 59.093 40.000 0.00 0.00 0.00 5.54
68 69 4.765281 TCTACGTTATTTTTCATCGGCG 57.235 40.909 0.00 0.00 0.00 6.46
69 70 2.817538 ACGTTATTTTTCATCGGCGG 57.182 45.000 7.21 0.00 0.00 6.13
70 71 1.202098 ACGTTATTTTTCATCGGCGGC 60.202 47.619 7.21 0.00 0.00 6.53
71 72 1.462791 GTTATTTTTCATCGGCGGCG 58.537 50.000 27.15 27.15 0.00 6.46
72 73 0.378962 TTATTTTTCATCGGCGGCGG 59.621 50.000 31.73 16.54 0.00 6.13
73 74 0.745128 TATTTTTCATCGGCGGCGGT 60.745 50.000 31.73 23.77 0.00 5.68
74 75 1.591504 ATTTTTCATCGGCGGCGGTT 61.592 50.000 31.73 16.58 0.00 4.44
75 76 2.465097 TTTTTCATCGGCGGCGGTTG 62.465 55.000 31.73 26.46 0.00 3.77
84 85 2.972505 CGGCGGTTGCTGTTCTGT 60.973 61.111 0.00 0.00 42.79 3.41
85 86 2.639286 GGCGGTTGCTGTTCTGTG 59.361 61.111 0.00 0.00 42.25 3.66
86 87 2.639286 GCGGTTGCTGTTCTGTGG 59.361 61.111 0.00 0.00 38.39 4.17
87 88 2.186826 GCGGTTGCTGTTCTGTGGT 61.187 57.895 0.00 0.00 38.39 4.16
88 89 1.648720 CGGTTGCTGTTCTGTGGTG 59.351 57.895 0.00 0.00 0.00 4.17
89 90 1.360192 GGTTGCTGTTCTGTGGTGC 59.640 57.895 0.00 0.00 0.00 5.01
90 91 1.103398 GGTTGCTGTTCTGTGGTGCT 61.103 55.000 0.00 0.00 0.00 4.40
91 92 0.029834 GTTGCTGTTCTGTGGTGCTG 59.970 55.000 0.00 0.00 0.00 4.41
92 93 1.102809 TTGCTGTTCTGTGGTGCTGG 61.103 55.000 0.00 0.00 0.00 4.85
93 94 1.526917 GCTGTTCTGTGGTGCTGGT 60.527 57.895 0.00 0.00 0.00 4.00
94 95 1.510480 GCTGTTCTGTGGTGCTGGTC 61.510 60.000 0.00 0.00 0.00 4.02
95 96 0.886490 CTGTTCTGTGGTGCTGGTCC 60.886 60.000 0.00 0.00 0.00 4.46
96 97 1.344953 TGTTCTGTGGTGCTGGTCCT 61.345 55.000 0.00 0.00 0.00 3.85
97 98 0.685097 GTTCTGTGGTGCTGGTCCTA 59.315 55.000 0.00 0.00 0.00 2.94
98 99 1.279271 GTTCTGTGGTGCTGGTCCTAT 59.721 52.381 0.00 0.00 0.00 2.57
99 100 0.904649 TCTGTGGTGCTGGTCCTATG 59.095 55.000 0.00 0.00 0.00 2.23
100 101 0.107508 CTGTGGTGCTGGTCCTATGG 60.108 60.000 0.00 0.00 0.00 2.74
101 102 1.224592 GTGGTGCTGGTCCTATGGG 59.775 63.158 0.00 0.00 0.00 4.00
102 103 2.000701 TGGTGCTGGTCCTATGGGG 61.001 63.158 0.00 0.00 0.00 4.96
103 104 2.193248 GTGCTGGTCCTATGGGGC 59.807 66.667 0.00 0.00 36.26 5.80
110 111 2.539983 GTCCTATGGGGCCTTAGCA 58.460 57.895 0.84 0.00 42.56 3.49
111 112 0.108774 GTCCTATGGGGCCTTAGCAC 59.891 60.000 0.84 0.00 43.97 4.40
112 113 1.071471 CCTATGGGGCCTTAGCACG 59.929 63.158 0.84 0.00 46.55 5.34
113 114 1.407656 CCTATGGGGCCTTAGCACGA 61.408 60.000 0.84 0.00 46.55 4.35
114 115 0.249911 CTATGGGGCCTTAGCACGAC 60.250 60.000 0.84 0.00 46.55 4.34
115 116 2.023414 TATGGGGCCTTAGCACGACG 62.023 60.000 0.84 0.00 46.55 5.12
116 117 3.766691 GGGGCCTTAGCACGACGA 61.767 66.667 0.84 0.00 46.55 4.20
117 118 2.508663 GGGCCTTAGCACGACGAC 60.509 66.667 0.84 0.00 42.56 4.34
118 119 2.572284 GGCCTTAGCACGACGACT 59.428 61.111 0.00 0.59 42.56 4.18
119 120 1.080025 GGCCTTAGCACGACGACTT 60.080 57.895 0.00 0.00 42.56 3.01
120 121 0.669625 GGCCTTAGCACGACGACTTT 60.670 55.000 0.00 0.00 42.56 2.66
121 122 0.714439 GCCTTAGCACGACGACTTTC 59.286 55.000 0.00 0.00 39.53 2.62
122 123 1.347320 CCTTAGCACGACGACTTTCC 58.653 55.000 0.00 0.00 0.00 3.13
123 124 0.982673 CTTAGCACGACGACTTTCCG 59.017 55.000 0.00 0.00 0.00 4.30
124 125 0.592637 TTAGCACGACGACTTTCCGA 59.407 50.000 0.00 0.00 0.00 4.55
125 126 0.110056 TAGCACGACGACTTTCCGAC 60.110 55.000 0.00 0.00 0.00 4.79
126 127 1.371389 GCACGACGACTTTCCGACT 60.371 57.895 0.00 0.00 0.00 4.18
127 128 1.606350 GCACGACGACTTTCCGACTG 61.606 60.000 0.00 0.00 0.00 3.51
128 129 0.317603 CACGACGACTTTCCGACTGT 60.318 55.000 0.00 0.00 0.00 3.55
129 130 0.040603 ACGACGACTTTCCGACTGTC 60.041 55.000 0.00 0.00 0.00 3.51
130 131 0.237761 CGACGACTTTCCGACTGTCT 59.762 55.000 6.21 0.00 0.00 3.41
131 132 1.462283 CGACGACTTTCCGACTGTCTA 59.538 52.381 6.21 0.00 0.00 2.59
132 133 2.724228 CGACGACTTTCCGACTGTCTAC 60.724 54.545 6.21 0.00 0.00 2.59
133 134 2.483491 GACGACTTTCCGACTGTCTACT 59.517 50.000 6.21 0.00 0.00 2.57
134 135 3.668447 ACGACTTTCCGACTGTCTACTA 58.332 45.455 6.21 0.00 0.00 1.82
135 136 3.434984 ACGACTTTCCGACTGTCTACTAC 59.565 47.826 6.21 0.00 0.00 2.73
136 137 3.434641 CGACTTTCCGACTGTCTACTACA 59.565 47.826 6.21 0.00 36.42 2.74
137 138 4.083643 CGACTTTCCGACTGTCTACTACAA 60.084 45.833 6.21 0.00 37.74 2.41
138 139 5.118642 ACTTTCCGACTGTCTACTACAAC 57.881 43.478 6.21 0.00 37.74 3.32
139 140 4.581824 ACTTTCCGACTGTCTACTACAACA 59.418 41.667 6.21 0.00 37.74 3.33
140 141 5.068198 ACTTTCCGACTGTCTACTACAACAA 59.932 40.000 6.21 0.00 37.74 2.83
141 142 4.761235 TCCGACTGTCTACTACAACAAG 57.239 45.455 6.21 0.00 37.74 3.16
142 143 4.139786 TCCGACTGTCTACTACAACAAGT 58.860 43.478 6.21 0.00 37.74 3.16
143 144 4.581824 TCCGACTGTCTACTACAACAAGTT 59.418 41.667 6.21 0.00 37.74 2.66
144 145 4.680110 CCGACTGTCTACTACAACAAGTTG 59.320 45.833 11.16 11.16 45.58 3.16
152 153 2.027460 CAACAAGTTGTGCCCGGC 59.973 61.111 9.79 1.04 35.92 6.13
153 154 2.123897 AACAAGTTGTGCCCGGCT 60.124 55.556 9.79 0.00 0.00 5.52
154 155 2.193536 AACAAGTTGTGCCCGGCTC 61.194 57.895 9.79 7.85 0.00 4.70
155 156 3.365265 CAAGTTGTGCCCGGCTCC 61.365 66.667 11.61 1.66 0.00 4.70
173 174 4.996434 GGCGATGGAGGGGCGATG 62.996 72.222 0.00 0.00 0.00 3.84
174 175 3.928779 GCGATGGAGGGGCGATGA 61.929 66.667 0.00 0.00 0.00 2.92
175 176 3.063526 CGATGGAGGGGCGATGAT 58.936 61.111 0.00 0.00 0.00 2.45
176 177 1.375140 CGATGGAGGGGCGATGATG 60.375 63.158 0.00 0.00 0.00 3.07
177 178 1.002868 GATGGAGGGGCGATGATGG 60.003 63.158 0.00 0.00 0.00 3.51
178 179 3.201707 ATGGAGGGGCGATGATGGC 62.202 63.158 0.00 0.00 0.00 4.40
179 180 4.996434 GGAGGGGCGATGATGGCG 62.996 72.222 0.00 0.00 34.76 5.69
180 181 4.996434 GAGGGGCGATGATGGCGG 62.996 72.222 0.00 0.00 34.76 6.13
202 203 4.436998 CCTTCGGCTCGCTTCGGT 62.437 66.667 0.00 0.00 0.00 4.69
203 204 3.181967 CTTCGGCTCGCTTCGGTG 61.182 66.667 0.00 0.00 0.00 4.94
207 208 3.793144 GGCTCGCTTCGGTGCTTG 61.793 66.667 0.00 0.00 0.00 4.01
208 209 3.044305 GCTCGCTTCGGTGCTTGT 61.044 61.111 0.00 0.00 0.00 3.16
209 210 1.736645 GCTCGCTTCGGTGCTTGTA 60.737 57.895 0.00 0.00 0.00 2.41
210 211 1.687494 GCTCGCTTCGGTGCTTGTAG 61.687 60.000 0.00 0.00 0.00 2.74
211 212 0.388649 CTCGCTTCGGTGCTTGTAGT 60.389 55.000 0.00 0.00 0.00 2.73
212 213 0.388134 TCGCTTCGGTGCTTGTAGTC 60.388 55.000 0.00 0.00 0.00 2.59
213 214 0.666274 CGCTTCGGTGCTTGTAGTCA 60.666 55.000 0.00 0.00 0.00 3.41
214 215 1.726853 GCTTCGGTGCTTGTAGTCAT 58.273 50.000 0.00 0.00 0.00 3.06
215 216 1.661112 GCTTCGGTGCTTGTAGTCATC 59.339 52.381 0.00 0.00 0.00 2.92
216 217 1.920574 CTTCGGTGCTTGTAGTCATCG 59.079 52.381 0.00 0.00 38.09 3.84
217 218 0.457853 TCGGTGCTTGTAGTCATCGC 60.458 55.000 0.00 0.00 36.81 4.58
218 219 0.458543 CGGTGCTTGTAGTCATCGCT 60.459 55.000 0.00 0.00 29.74 4.93
219 220 1.202256 CGGTGCTTGTAGTCATCGCTA 60.202 52.381 0.00 0.00 29.74 4.26
220 221 2.464865 GGTGCTTGTAGTCATCGCTAG 58.535 52.381 0.00 0.00 0.00 3.42
221 222 2.464865 GTGCTTGTAGTCATCGCTAGG 58.535 52.381 0.00 0.00 0.00 3.02
222 223 2.100197 TGCTTGTAGTCATCGCTAGGT 58.900 47.619 0.00 0.00 0.00 3.08
223 224 2.496070 TGCTTGTAGTCATCGCTAGGTT 59.504 45.455 0.00 0.00 0.00 3.50
224 225 2.860735 GCTTGTAGTCATCGCTAGGTTG 59.139 50.000 0.00 0.00 0.00 3.77
225 226 3.676324 GCTTGTAGTCATCGCTAGGTTGT 60.676 47.826 0.00 0.00 0.00 3.32
226 227 3.777465 TGTAGTCATCGCTAGGTTGTC 57.223 47.619 0.00 0.00 0.00 3.18
227 228 3.353557 TGTAGTCATCGCTAGGTTGTCT 58.646 45.455 0.00 0.00 0.00 3.41
228 229 4.520179 TGTAGTCATCGCTAGGTTGTCTA 58.480 43.478 0.00 0.00 0.00 2.59
229 230 4.334759 TGTAGTCATCGCTAGGTTGTCTAC 59.665 45.833 13.40 13.40 34.62 2.59
230 231 2.355132 AGTCATCGCTAGGTTGTCTACG 59.645 50.000 0.00 0.00 0.00 3.51
231 232 2.353889 GTCATCGCTAGGTTGTCTACGA 59.646 50.000 0.00 0.00 36.62 3.43
232 233 3.011818 TCATCGCTAGGTTGTCTACGAA 58.988 45.455 0.00 0.00 36.18 3.85
233 234 3.441222 TCATCGCTAGGTTGTCTACGAAA 59.559 43.478 0.00 0.00 36.18 3.46
234 235 3.207474 TCGCTAGGTTGTCTACGAAAC 57.793 47.619 0.00 0.00 32.69 2.78
235 236 2.816087 TCGCTAGGTTGTCTACGAAACT 59.184 45.455 0.00 0.00 32.69 2.66
236 237 2.915463 CGCTAGGTTGTCTACGAAACTG 59.085 50.000 0.00 0.00 0.00 3.16
237 238 3.251571 GCTAGGTTGTCTACGAAACTGG 58.748 50.000 0.00 0.00 0.00 4.00
238 239 3.057033 GCTAGGTTGTCTACGAAACTGGA 60.057 47.826 0.00 0.00 0.00 3.86
239 240 4.381718 GCTAGGTTGTCTACGAAACTGGAT 60.382 45.833 0.00 0.00 0.00 3.41
240 241 3.926616 AGGTTGTCTACGAAACTGGATG 58.073 45.455 0.00 0.00 0.00 3.51
241 242 3.323979 AGGTTGTCTACGAAACTGGATGT 59.676 43.478 0.00 0.00 0.00 3.06
242 243 4.525487 AGGTTGTCTACGAAACTGGATGTA 59.475 41.667 0.00 0.00 0.00 2.29
243 244 5.011329 AGGTTGTCTACGAAACTGGATGTAA 59.989 40.000 0.00 0.00 0.00 2.41
244 245 5.873164 GGTTGTCTACGAAACTGGATGTAAT 59.127 40.000 0.00 0.00 0.00 1.89
245 246 6.370718 GGTTGTCTACGAAACTGGATGTAATT 59.629 38.462 0.00 0.00 0.00 1.40
246 247 7.094933 GGTTGTCTACGAAACTGGATGTAATTT 60.095 37.037 0.00 0.00 0.00 1.82
247 248 7.972832 TGTCTACGAAACTGGATGTAATTTT 57.027 32.000 0.00 0.00 0.00 1.82
248 249 8.385898 TGTCTACGAAACTGGATGTAATTTTT 57.614 30.769 0.00 0.00 0.00 1.94
249 250 9.491675 TGTCTACGAAACTGGATGTAATTTTTA 57.508 29.630 0.00 0.00 0.00 1.52
271 272 5.796350 ATTTCTGGTATTCGTTGTACTGC 57.204 39.130 0.00 0.00 0.00 4.40
272 273 3.241067 TCTGGTATTCGTTGTACTGCC 57.759 47.619 0.00 0.00 0.00 4.85
273 274 2.563620 TCTGGTATTCGTTGTACTGCCA 59.436 45.455 0.00 0.00 0.00 4.92
274 275 3.196901 TCTGGTATTCGTTGTACTGCCAT 59.803 43.478 0.00 0.00 0.00 4.40
275 276 3.266636 TGGTATTCGTTGTACTGCCATG 58.733 45.455 0.00 0.00 0.00 3.66
276 277 3.055747 TGGTATTCGTTGTACTGCCATGA 60.056 43.478 0.00 0.00 0.00 3.07
277 278 4.127171 GGTATTCGTTGTACTGCCATGAT 58.873 43.478 0.00 0.00 0.00 2.45
278 279 4.574828 GGTATTCGTTGTACTGCCATGATT 59.425 41.667 0.00 0.00 0.00 2.57
279 280 4.621068 ATTCGTTGTACTGCCATGATTG 57.379 40.909 0.00 0.00 0.00 2.67
280 281 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
281 282 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
282 283 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
283 284 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
284 285 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
285 286 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
286 287 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
287 288 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
288 289 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
289 290 7.281841 TGTACTGCCATGATTGAAGATGAATA 58.718 34.615 0.00 0.00 0.00 1.75
290 291 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
291 292 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
292 293 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
293 294 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
294 295 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
295 296 7.039993 TGCCATGATTGAAGATGAATAGATTGG 60.040 37.037 0.00 0.00 0.00 3.16
296 297 7.176165 GCCATGATTGAAGATGAATAGATTGGA 59.824 37.037 0.00 0.00 0.00 3.53
297 298 9.074576 CCATGATTGAAGATGAATAGATTGGAA 57.925 33.333 0.00 0.00 0.00 3.53
299 300 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
300 301 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
738 974 8.469125 CGACTTACAGTTCAGCAAATTAAAAAC 58.531 33.333 0.00 0.00 0.00 2.43
889 1125 5.399858 CACACACCAGCCTATATATACGTC 58.600 45.833 0.00 0.00 0.00 4.34
941 1177 4.400251 AGCTCTCTCAAGTTCTCATCTCAG 59.600 45.833 0.00 0.00 0.00 3.35
957 1193 2.648304 TCTCAGGTACAGGACACTAGGT 59.352 50.000 0.00 0.00 0.00 3.08
965 1201 5.067544 GGTACAGGACACTAGGTTACTCATC 59.932 48.000 0.00 0.00 0.00 2.92
966 1202 4.673968 ACAGGACACTAGGTTACTCATCA 58.326 43.478 0.00 0.00 0.00 3.07
967 1203 5.273208 ACAGGACACTAGGTTACTCATCAT 58.727 41.667 0.00 0.00 0.00 2.45
973 1209 7.606456 GGACACTAGGTTACTCATCATTTTTCA 59.394 37.037 0.00 0.00 0.00 2.69
1199 2004 0.527565 GCTGTGGCATTTCGGTTCAT 59.472 50.000 0.00 0.00 38.54 2.57
1322 2127 1.018752 CACGACGGCATCATCACCAA 61.019 55.000 0.00 0.00 0.00 3.67
1443 2248 4.845580 AAGAGCCGCTCCATGCCG 62.846 66.667 16.99 0.00 38.78 5.69
1615 2451 7.096884 ACTTTTGAGAGTTGGTCTTTTTACC 57.903 36.000 0.00 0.00 40.19 2.85
1832 3089 0.538287 AGAAGGAAGGGCAAGCACAC 60.538 55.000 0.00 0.00 0.00 3.82
1962 3800 1.840635 AGGAGTACCCAGCCAAAGATC 59.159 52.381 3.60 0.00 37.41 2.75
1974 3812 1.032114 CAAAGATCCCTCCCAACCGC 61.032 60.000 0.00 0.00 0.00 5.68
2104 3945 1.371558 GATGATGCCGTAGTCCCCC 59.628 63.158 0.00 0.00 0.00 5.40
2132 3973 9.623350 CAACTCTCTGATGTATATGATGTACTG 57.377 37.037 1.14 0.00 0.00 2.74
2158 3999 1.089112 TGCAATCTGAAGCGACATGG 58.911 50.000 0.00 0.00 0.00 3.66
2186 4030 0.109132 CCCAAGATCTTGCGCCAAAC 60.109 55.000 27.01 0.00 39.16 2.93
2203 4047 1.115326 AACAAAGGCCTTCCCTGCAC 61.115 55.000 20.79 0.00 45.62 4.57
2239 4083 0.250989 TCGGTGGATCCAACAAACCC 60.251 55.000 29.00 17.47 32.16 4.11
2240 4084 1.582610 CGGTGGATCCAACAAACCCG 61.583 60.000 29.00 24.52 32.16 5.28
2278 4122 0.746659 GAGCCCAAATAAGCGCCATT 59.253 50.000 2.29 0.40 0.00 3.16
2333 4178 1.786937 ATGGTTGGTGGAAACTGCAA 58.213 45.000 0.00 0.00 0.00 4.08
2365 4211 8.116026 ACATTAATCTTTATGGAACCCTGAACT 58.884 33.333 0.00 0.00 0.00 3.01
2431 4277 2.656069 TAGTGGAGGTTCTGGCCGC 61.656 63.158 0.00 0.00 0.00 6.53
2446 4292 2.456119 CCGCGCACTCAACTGATCC 61.456 63.158 8.75 0.00 0.00 3.36
2449 4295 1.089920 GCGCACTCAACTGATCCAAT 58.910 50.000 0.30 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.722629 ACACGAATGTAGACGAACAACG 59.277 45.455 0.00 4.37 42.17 4.10
3 4 3.488310 ACACACGAATGTAGACGAACAAC 59.512 43.478 0.00 0.00 36.72 3.32
5 6 3.004002 AGACACACGAATGTAGACGAACA 59.996 43.478 0.00 0.00 36.72 3.18
6 7 3.562505 AGACACACGAATGTAGACGAAC 58.437 45.455 0.00 0.00 36.72 3.95
7 8 3.909776 AGACACACGAATGTAGACGAA 57.090 42.857 0.00 0.00 36.72 3.85
8 9 3.909776 AAGACACACGAATGTAGACGA 57.090 42.857 0.00 0.00 36.72 4.20
9 10 3.121279 CCAAAGACACACGAATGTAGACG 59.879 47.826 0.00 0.00 36.72 4.18
10 11 4.056050 ACCAAAGACACACGAATGTAGAC 58.944 43.478 0.00 0.00 36.72 2.59
11 12 4.330944 ACCAAAGACACACGAATGTAGA 57.669 40.909 0.00 0.00 36.72 2.59
12 13 5.204833 CAAACCAAAGACACACGAATGTAG 58.795 41.667 0.00 0.00 36.72 2.74
13 14 4.035792 CCAAACCAAAGACACACGAATGTA 59.964 41.667 0.00 0.00 36.72 2.29
14 15 3.181491 CCAAACCAAAGACACACGAATGT 60.181 43.478 0.00 0.00 40.80 2.71
15 16 3.066064 TCCAAACCAAAGACACACGAATG 59.934 43.478 0.00 0.00 0.00 2.67
16 17 3.283751 TCCAAACCAAAGACACACGAAT 58.716 40.909 0.00 0.00 0.00 3.34
17 18 2.712709 TCCAAACCAAAGACACACGAA 58.287 42.857 0.00 0.00 0.00 3.85
18 19 2.404923 TCCAAACCAAAGACACACGA 57.595 45.000 0.00 0.00 0.00 4.35
19 20 2.031157 GGATCCAAACCAAAGACACACG 60.031 50.000 6.95 0.00 0.00 4.49
20 21 3.222603 AGGATCCAAACCAAAGACACAC 58.777 45.455 15.82 0.00 0.00 3.82
21 22 3.593442 AGGATCCAAACCAAAGACACA 57.407 42.857 15.82 0.00 0.00 3.72
22 23 3.255888 GGAAGGATCCAAACCAAAGACAC 59.744 47.826 15.82 0.00 45.79 3.67
23 24 3.496331 GGAAGGATCCAAACCAAAGACA 58.504 45.455 15.82 0.00 45.79 3.41
35 36 7.803279 AAAATAACGTAGATTGGAAGGATCC 57.197 36.000 2.48 2.48 46.76 3.36
36 37 8.889717 TGAAAAATAACGTAGATTGGAAGGATC 58.110 33.333 0.00 0.00 0.00 3.36
37 38 8.801882 TGAAAAATAACGTAGATTGGAAGGAT 57.198 30.769 0.00 0.00 0.00 3.24
38 39 8.801882 ATGAAAAATAACGTAGATTGGAAGGA 57.198 30.769 0.00 0.00 0.00 3.36
39 40 7.850982 CGATGAAAAATAACGTAGATTGGAAGG 59.149 37.037 0.00 0.00 0.00 3.46
40 41 7.850982 CCGATGAAAAATAACGTAGATTGGAAG 59.149 37.037 0.00 0.00 0.00 3.46
41 42 7.677747 GCCGATGAAAAATAACGTAGATTGGAA 60.678 37.037 0.00 0.00 0.00 3.53
42 43 6.238266 GCCGATGAAAAATAACGTAGATTGGA 60.238 38.462 0.00 0.00 0.00 3.53
43 44 5.907391 GCCGATGAAAAATAACGTAGATTGG 59.093 40.000 0.00 0.00 0.00 3.16
44 45 5.615581 CGCCGATGAAAAATAACGTAGATTG 59.384 40.000 0.00 0.00 0.00 2.67
45 46 5.277154 CCGCCGATGAAAAATAACGTAGATT 60.277 40.000 0.00 0.00 0.00 2.40
46 47 4.210537 CCGCCGATGAAAAATAACGTAGAT 59.789 41.667 0.00 0.00 0.00 1.98
47 48 3.552699 CCGCCGATGAAAAATAACGTAGA 59.447 43.478 0.00 0.00 0.00 2.59
48 49 3.843510 GCCGCCGATGAAAAATAACGTAG 60.844 47.826 0.00 0.00 0.00 3.51
49 50 2.030701 GCCGCCGATGAAAAATAACGTA 59.969 45.455 0.00 0.00 0.00 3.57
50 51 1.202098 GCCGCCGATGAAAAATAACGT 60.202 47.619 0.00 0.00 0.00 3.99
51 52 1.462791 GCCGCCGATGAAAAATAACG 58.537 50.000 0.00 0.00 0.00 3.18
52 53 1.462791 CGCCGCCGATGAAAAATAAC 58.537 50.000 0.00 0.00 36.29 1.89
53 54 0.378962 CCGCCGCCGATGAAAAATAA 59.621 50.000 0.00 0.00 36.29 1.40
54 55 0.745128 ACCGCCGCCGATGAAAAATA 60.745 50.000 0.00 0.00 36.29 1.40
55 56 1.591504 AACCGCCGCCGATGAAAAAT 61.592 50.000 0.00 0.00 36.29 1.82
56 57 2.262303 AACCGCCGCCGATGAAAAA 61.262 52.632 0.00 0.00 36.29 1.94
57 58 2.670251 AACCGCCGCCGATGAAAA 60.670 55.556 0.00 0.00 36.29 2.29
58 59 3.427425 CAACCGCCGCCGATGAAA 61.427 61.111 0.00 0.00 36.29 2.69
66 67 4.389576 CAGAACAGCAACCGCCGC 62.390 66.667 0.00 0.00 39.83 6.53
67 68 2.972505 ACAGAACAGCAACCGCCG 60.973 61.111 0.00 0.00 39.83 6.46
68 69 2.639286 CACAGAACAGCAACCGCC 59.361 61.111 0.00 0.00 39.83 6.13
69 70 2.186826 ACCACAGAACAGCAACCGC 61.187 57.895 0.00 0.00 38.99 5.68
70 71 1.648720 CACCACAGAACAGCAACCG 59.351 57.895 0.00 0.00 0.00 4.44
71 72 1.103398 AGCACCACAGAACAGCAACC 61.103 55.000 0.00 0.00 0.00 3.77
72 73 0.029834 CAGCACCACAGAACAGCAAC 59.970 55.000 0.00 0.00 0.00 4.17
73 74 1.102809 CCAGCACCACAGAACAGCAA 61.103 55.000 0.00 0.00 0.00 3.91
74 75 1.526686 CCAGCACCACAGAACAGCA 60.527 57.895 0.00 0.00 0.00 4.41
75 76 1.510480 GACCAGCACCACAGAACAGC 61.510 60.000 0.00 0.00 0.00 4.40
76 77 0.886490 GGACCAGCACCACAGAACAG 60.886 60.000 0.00 0.00 0.00 3.16
77 78 1.148273 GGACCAGCACCACAGAACA 59.852 57.895 0.00 0.00 0.00 3.18
78 79 0.685097 TAGGACCAGCACCACAGAAC 59.315 55.000 0.00 0.00 0.00 3.01
79 80 1.278985 CATAGGACCAGCACCACAGAA 59.721 52.381 0.00 0.00 0.00 3.02
80 81 0.904649 CATAGGACCAGCACCACAGA 59.095 55.000 0.00 0.00 0.00 3.41
81 82 0.107508 CCATAGGACCAGCACCACAG 60.108 60.000 0.00 0.00 0.00 3.66
82 83 1.561769 CCCATAGGACCAGCACCACA 61.562 60.000 0.00 0.00 33.47 4.17
83 84 1.224592 CCCATAGGACCAGCACCAC 59.775 63.158 0.00 0.00 33.47 4.16
84 85 2.000701 CCCCATAGGACCAGCACCA 61.001 63.158 0.00 0.00 38.24 4.17
85 86 2.919043 CCCCATAGGACCAGCACC 59.081 66.667 0.00 0.00 38.24 5.01
86 87 2.193248 GCCCCATAGGACCAGCAC 59.807 66.667 0.00 0.00 38.24 4.40
87 88 3.096495 GGCCCCATAGGACCAGCA 61.096 66.667 0.00 0.00 37.96 4.41
93 94 1.407656 CGTGCTAAGGCCCCATAGGA 61.408 60.000 0.00 0.00 38.24 2.94
94 95 1.071471 CGTGCTAAGGCCCCATAGG 59.929 63.158 0.00 0.00 37.74 2.57
95 96 0.249911 GTCGTGCTAAGGCCCCATAG 60.250 60.000 0.00 0.67 37.74 2.23
96 97 1.827394 GTCGTGCTAAGGCCCCATA 59.173 57.895 0.00 0.00 37.74 2.74
97 98 2.590092 GTCGTGCTAAGGCCCCAT 59.410 61.111 0.00 0.00 37.74 4.00
98 99 4.077184 CGTCGTGCTAAGGCCCCA 62.077 66.667 0.00 0.00 37.74 4.96
99 100 3.766691 TCGTCGTGCTAAGGCCCC 61.767 66.667 0.00 0.00 37.74 5.80
100 101 2.502692 AAGTCGTCGTGCTAAGGCCC 62.503 60.000 0.00 0.00 37.74 5.80
101 102 0.669625 AAAGTCGTCGTGCTAAGGCC 60.670 55.000 0.00 0.00 37.74 5.19
102 103 0.714439 GAAAGTCGTCGTGCTAAGGC 59.286 55.000 0.00 0.00 39.26 4.35
103 104 1.347320 GGAAAGTCGTCGTGCTAAGG 58.653 55.000 0.00 0.00 0.00 2.69
104 105 0.982673 CGGAAAGTCGTCGTGCTAAG 59.017 55.000 0.00 0.00 0.00 2.18
105 106 0.592637 TCGGAAAGTCGTCGTGCTAA 59.407 50.000 0.00 0.00 0.00 3.09
106 107 0.110056 GTCGGAAAGTCGTCGTGCTA 60.110 55.000 0.00 0.00 0.00 3.49
107 108 1.371389 GTCGGAAAGTCGTCGTGCT 60.371 57.895 0.00 0.00 0.00 4.40
108 109 1.371389 AGTCGGAAAGTCGTCGTGC 60.371 57.895 0.00 0.00 0.00 5.34
109 110 0.317603 ACAGTCGGAAAGTCGTCGTG 60.318 55.000 0.00 0.00 0.00 4.35
110 111 0.040603 GACAGTCGGAAAGTCGTCGT 60.041 55.000 0.00 0.00 0.00 4.34
111 112 0.237761 AGACAGTCGGAAAGTCGTCG 59.762 55.000 0.00 0.00 37.36 5.12
112 113 2.483491 AGTAGACAGTCGGAAAGTCGTC 59.517 50.000 0.00 0.00 37.36 4.20
113 114 2.502295 AGTAGACAGTCGGAAAGTCGT 58.498 47.619 0.00 0.00 37.36 4.34
114 115 3.434641 TGTAGTAGACAGTCGGAAAGTCG 59.565 47.826 0.00 0.00 37.36 4.18
115 116 5.152804 GTTGTAGTAGACAGTCGGAAAGTC 58.847 45.833 0.00 3.60 39.88 3.01
116 117 4.581824 TGTTGTAGTAGACAGTCGGAAAGT 59.418 41.667 0.00 0.00 39.88 2.66
117 118 5.117355 TGTTGTAGTAGACAGTCGGAAAG 57.883 43.478 0.00 0.00 39.88 2.62
118 119 5.068198 ACTTGTTGTAGTAGACAGTCGGAAA 59.932 40.000 0.00 0.00 39.88 3.13
119 120 4.581824 ACTTGTTGTAGTAGACAGTCGGAA 59.418 41.667 0.00 0.00 39.88 4.30
120 121 4.139786 ACTTGTTGTAGTAGACAGTCGGA 58.860 43.478 0.00 0.00 39.88 4.55
121 122 4.500603 ACTTGTTGTAGTAGACAGTCGG 57.499 45.455 0.00 0.00 39.88 4.79
122 123 5.173312 CACAACTTGTTGTAGTAGACAGTCG 59.827 44.000 17.26 0.00 39.88 4.18
123 124 5.050972 GCACAACTTGTTGTAGTAGACAGTC 60.051 44.000 17.26 0.00 39.88 3.51
124 125 4.809426 GCACAACTTGTTGTAGTAGACAGT 59.191 41.667 17.26 0.00 39.88 3.55
125 126 4.211374 GGCACAACTTGTTGTAGTAGACAG 59.789 45.833 17.26 5.63 39.88 3.51
126 127 4.124238 GGCACAACTTGTTGTAGTAGACA 58.876 43.478 17.26 0.00 35.78 3.41
127 128 3.497262 GGGCACAACTTGTTGTAGTAGAC 59.503 47.826 17.26 8.51 33.17 2.59
128 129 3.735591 GGGCACAACTTGTTGTAGTAGA 58.264 45.455 17.26 0.00 33.17 2.59
129 130 2.478894 CGGGCACAACTTGTTGTAGTAG 59.521 50.000 17.26 7.80 33.17 2.57
130 131 2.485903 CGGGCACAACTTGTTGTAGTA 58.514 47.619 17.26 0.00 33.17 1.82
131 132 1.305201 CGGGCACAACTTGTTGTAGT 58.695 50.000 17.26 0.00 33.17 2.73
132 133 0.591170 CCGGGCACAACTTGTTGTAG 59.409 55.000 17.26 12.96 33.17 2.74
133 134 1.448922 GCCGGGCACAACTTGTTGTA 61.449 55.000 15.62 0.00 33.17 2.41
134 135 2.781158 GCCGGGCACAACTTGTTGT 61.781 57.895 15.62 12.73 35.14 3.32
135 136 2.027460 GCCGGGCACAACTTGTTG 59.973 61.111 15.62 11.44 0.00 3.33
136 137 2.123897 AGCCGGGCACAACTTGTT 60.124 55.556 23.09 0.00 0.00 2.83
137 138 2.594592 GAGCCGGGCACAACTTGT 60.595 61.111 23.09 0.00 0.00 3.16
138 139 3.365265 GGAGCCGGGCACAACTTG 61.365 66.667 23.09 0.00 0.00 3.16
156 157 4.996434 CATCGCCCCTCCATCGCC 62.996 72.222 0.00 0.00 0.00 5.54
157 158 3.245668 ATCATCGCCCCTCCATCGC 62.246 63.158 0.00 0.00 0.00 4.58
158 159 1.375140 CATCATCGCCCCTCCATCG 60.375 63.158 0.00 0.00 0.00 3.84
159 160 1.002868 CCATCATCGCCCCTCCATC 60.003 63.158 0.00 0.00 0.00 3.51
160 161 3.164479 CCATCATCGCCCCTCCAT 58.836 61.111 0.00 0.00 0.00 3.41
161 162 3.877450 GCCATCATCGCCCCTCCA 61.877 66.667 0.00 0.00 0.00 3.86
162 163 4.996434 CGCCATCATCGCCCCTCC 62.996 72.222 0.00 0.00 0.00 4.30
163 164 4.996434 CCGCCATCATCGCCCCTC 62.996 72.222 0.00 0.00 0.00 4.30
186 187 3.181967 CACCGAAGCGAGCCGAAG 61.182 66.667 0.00 0.00 0.00 3.79
190 191 3.793144 CAAGCACCGAAGCGAGCC 61.793 66.667 0.00 0.00 40.15 4.70
191 192 1.687494 CTACAAGCACCGAAGCGAGC 61.687 60.000 0.00 0.00 40.15 5.03
192 193 0.388649 ACTACAAGCACCGAAGCGAG 60.389 55.000 0.00 0.00 40.15 5.03
193 194 0.388134 GACTACAAGCACCGAAGCGA 60.388 55.000 0.00 0.00 40.15 4.93
194 195 0.666274 TGACTACAAGCACCGAAGCG 60.666 55.000 0.00 0.00 40.15 4.68
195 196 1.661112 GATGACTACAAGCACCGAAGC 59.339 52.381 0.00 0.00 0.00 3.86
196 197 1.920574 CGATGACTACAAGCACCGAAG 59.079 52.381 0.00 0.00 0.00 3.79
197 198 1.990799 CGATGACTACAAGCACCGAA 58.009 50.000 0.00 0.00 0.00 4.30
198 199 0.457853 GCGATGACTACAAGCACCGA 60.458 55.000 0.00 0.00 35.16 4.69
199 200 0.458543 AGCGATGACTACAAGCACCG 60.459 55.000 0.00 0.00 36.63 4.94
200 201 2.464865 CTAGCGATGACTACAAGCACC 58.535 52.381 0.00 0.00 36.63 5.01
201 202 2.159226 ACCTAGCGATGACTACAAGCAC 60.159 50.000 0.00 0.00 36.63 4.40
202 203 2.100197 ACCTAGCGATGACTACAAGCA 58.900 47.619 0.00 0.00 36.63 3.91
203 204 2.860735 CAACCTAGCGATGACTACAAGC 59.139 50.000 0.00 0.00 35.24 4.01
204 205 4.106197 GACAACCTAGCGATGACTACAAG 58.894 47.826 0.00 0.00 0.00 3.16
205 206 3.762288 AGACAACCTAGCGATGACTACAA 59.238 43.478 0.00 0.00 0.00 2.41
206 207 3.353557 AGACAACCTAGCGATGACTACA 58.646 45.455 0.00 0.00 0.00 2.74
207 208 4.552378 CGTAGACAACCTAGCGATGACTAC 60.552 50.000 14.43 14.43 38.26 2.73
208 209 3.558829 CGTAGACAACCTAGCGATGACTA 59.441 47.826 0.00 0.00 0.00 2.59
209 210 2.355132 CGTAGACAACCTAGCGATGACT 59.645 50.000 0.00 0.00 0.00 3.41
210 211 2.353889 TCGTAGACAACCTAGCGATGAC 59.646 50.000 0.00 0.00 31.20 3.06
211 212 2.635714 TCGTAGACAACCTAGCGATGA 58.364 47.619 0.00 0.00 31.20 2.92
212 213 3.416119 TTCGTAGACAACCTAGCGATG 57.584 47.619 0.00 0.00 34.32 3.84
213 214 3.442977 AGTTTCGTAGACAACCTAGCGAT 59.557 43.478 0.00 0.00 34.32 4.58
214 215 2.816087 AGTTTCGTAGACAACCTAGCGA 59.184 45.455 0.00 0.00 34.32 4.93
215 216 2.915463 CAGTTTCGTAGACAACCTAGCG 59.085 50.000 0.00 0.00 34.32 4.26
216 217 3.057033 TCCAGTTTCGTAGACAACCTAGC 60.057 47.826 0.00 0.00 34.32 3.42
217 218 4.778534 TCCAGTTTCGTAGACAACCTAG 57.221 45.455 0.00 0.00 34.32 3.02
218 219 4.525487 ACATCCAGTTTCGTAGACAACCTA 59.475 41.667 0.00 0.00 34.32 3.08
219 220 3.323979 ACATCCAGTTTCGTAGACAACCT 59.676 43.478 0.00 0.00 34.32 3.50
220 221 3.660865 ACATCCAGTTTCGTAGACAACC 58.339 45.455 0.00 0.00 34.32 3.77
221 222 6.963049 ATTACATCCAGTTTCGTAGACAAC 57.037 37.500 0.00 0.00 34.32 3.32
222 223 7.972832 AAATTACATCCAGTTTCGTAGACAA 57.027 32.000 0.00 0.00 34.32 3.18
223 224 7.972832 AAAATTACATCCAGTTTCGTAGACA 57.027 32.000 0.00 0.00 34.32 3.41
245 246 8.231837 GCAGTACAACGAATACCAGAAATAAAA 58.768 33.333 0.00 0.00 0.00 1.52
246 247 7.148373 GGCAGTACAACGAATACCAGAAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
247 248 6.314400 GGCAGTACAACGAATACCAGAAATAA 59.686 38.462 0.00 0.00 0.00 1.40
248 249 5.813672 GGCAGTACAACGAATACCAGAAATA 59.186 40.000 0.00 0.00 0.00 1.40
249 250 4.634443 GGCAGTACAACGAATACCAGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
250 251 3.998341 GGCAGTACAACGAATACCAGAAA 59.002 43.478 0.00 0.00 0.00 2.52
251 252 3.007074 TGGCAGTACAACGAATACCAGAA 59.993 43.478 0.00 0.00 0.00 3.02
252 253 2.563620 TGGCAGTACAACGAATACCAGA 59.436 45.455 0.00 0.00 0.00 3.86
253 254 2.967362 TGGCAGTACAACGAATACCAG 58.033 47.619 0.00 0.00 0.00 4.00
254 255 3.055747 TCATGGCAGTACAACGAATACCA 60.056 43.478 0.00 0.00 0.00 3.25
255 256 3.527533 TCATGGCAGTACAACGAATACC 58.472 45.455 0.00 0.00 0.00 2.73
256 257 5.293324 TCAATCATGGCAGTACAACGAATAC 59.707 40.000 0.00 0.00 0.00 1.89
257 258 5.423886 TCAATCATGGCAGTACAACGAATA 58.576 37.500 0.00 0.00 0.00 1.75
258 259 4.260985 TCAATCATGGCAGTACAACGAAT 58.739 39.130 0.00 0.00 0.00 3.34
259 260 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
260 261 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
261 262 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
262 263 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
263 264 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
264 265 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
265 266 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
266 267 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
267 268 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
268 269 7.689446 ATCTATTCATCTTCAATCATGGCAG 57.311 36.000 0.00 0.00 0.00 4.85
269 270 7.039993 CCAATCTATTCATCTTCAATCATGGCA 60.040 37.037 0.00 0.00 0.00 4.92
270 271 7.176165 TCCAATCTATTCATCTTCAATCATGGC 59.824 37.037 0.00 0.00 0.00 4.40
271 272 8.631480 TCCAATCTATTCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
273 274 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
274 275 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
310 311 8.624776 CCTTTGTCACTTTCACTAATCTTCTTT 58.375 33.333 0.00 0.00 0.00 2.52
311 312 7.229506 CCCTTTGTCACTTTCACTAATCTTCTT 59.770 37.037 0.00 0.00 0.00 2.52
312 313 6.712547 CCCTTTGTCACTTTCACTAATCTTCT 59.287 38.462 0.00 0.00 0.00 2.85
313 314 6.568653 GCCCTTTGTCACTTTCACTAATCTTC 60.569 42.308 0.00 0.00 0.00 2.87
314 315 5.241728 GCCCTTTGTCACTTTCACTAATCTT 59.758 40.000 0.00 0.00 0.00 2.40
738 974 7.063898 CGGTGATATCTATGAGTTGCTATTTGG 59.936 40.741 3.98 0.00 0.00 3.28
889 1125 3.748568 GTGTTGAAGAAGAAGGTAGGCAG 59.251 47.826 0.00 0.00 0.00 4.85
941 1177 4.338879 TGAGTAACCTAGTGTCCTGTACC 58.661 47.826 0.00 0.00 0.00 3.34
957 1193 8.143193 AGTGCAAACATGAAAAATGATGAGTAA 58.857 29.630 0.00 0.00 0.00 2.24
965 1201 4.043761 GCGAGTGCAAACATGAAAAATG 57.956 40.909 0.00 0.00 42.15 2.32
1146 1951 1.447140 GGTCAACAGGCGTCGCATA 60.447 57.895 20.50 0.00 0.00 3.14
1188 1993 0.109319 GCGTTGGCATGAACCGAAAT 60.109 50.000 0.00 0.00 39.62 2.17
1312 2117 2.303022 ACTCACGGAAGTTGGTGATGAT 59.697 45.455 6.77 0.00 46.40 2.45
1383 2188 1.271840 ATATGGCCCACACCACGTCT 61.272 55.000 0.00 0.00 44.17 4.18
1443 2248 1.068250 GATGGCGAGCACTAGACCC 59.932 63.158 0.00 0.00 0.00 4.46
1446 2251 0.741326 GTCAGATGGCGAGCACTAGA 59.259 55.000 0.00 0.00 0.00 2.43
1509 2345 5.701855 CGTTGTCCGGGTAAAAACAATATT 58.298 37.500 0.00 0.00 34.45 1.28
1512 2348 3.629438 CGTTGTCCGGGTAAAAACAAT 57.371 42.857 0.00 0.00 34.45 2.71
1615 2451 4.754372 TTCACAAAGAACATGCTAGCAG 57.246 40.909 23.89 16.67 0.00 4.24
1795 3044 1.075536 TCTTTTCTCTTCCCCAAGCCC 59.924 52.381 0.00 0.00 0.00 5.19
1796 3045 2.586648 TCTTTTCTCTTCCCCAAGCC 57.413 50.000 0.00 0.00 0.00 4.35
1797 3046 2.822561 CCTTCTTTTCTCTTCCCCAAGC 59.177 50.000 0.00 0.00 0.00 4.01
1798 3047 4.373156 TCCTTCTTTTCTCTTCCCCAAG 57.627 45.455 0.00 0.00 0.00 3.61
1848 3109 0.796312 CTTGTCCGCGTATTTGTGCT 59.204 50.000 4.92 0.00 0.00 4.40
1922 3760 4.288366 TCCTCATGACCCAGTTGTAATTCA 59.712 41.667 0.00 0.00 0.00 2.57
1974 3812 2.737252 GCTAGGTTTGGTGTTTCTCTCG 59.263 50.000 0.00 0.00 0.00 4.04
2104 3945 9.838975 GTACATCATATACATCAGAGAGTTGAG 57.161 37.037 0.00 0.00 0.00 3.02
2132 3973 1.706443 GCTTCAGATTGCAAACAGGC 58.294 50.000 1.71 0.00 0.00 4.85
2158 3999 2.424956 GCAAGATCTTGGGATGGTTCAC 59.575 50.000 31.41 11.18 40.74 3.18
2186 4030 2.629656 CGTGCAGGGAAGGCCTTTG 61.630 63.158 21.54 15.44 0.00 2.77
2203 4047 1.723542 CCGATGCTAGAAGCTATTGCG 59.276 52.381 0.00 0.00 42.97 4.85
2239 4083 1.399440 CTTCCATGCTGGTCATTCACG 59.601 52.381 2.68 0.00 39.03 4.35
2240 4084 2.681848 CTCTTCCATGCTGGTCATTCAC 59.318 50.000 2.68 0.00 39.03 3.18
2295 4140 0.460635 TAATGTTGGTACGGCCGCTC 60.461 55.000 28.58 18.52 41.21 5.03
2328 4173 7.218773 CCATAAAGATTAATGTTGACGTTGCAG 59.781 37.037 0.00 0.00 0.00 4.41
2333 4178 7.148137 GGGTTCCATAAAGATTAATGTTGACGT 60.148 37.037 0.00 0.00 0.00 4.34
2365 4211 0.331278 ATTTCAAGTGGATCCCGCCA 59.669 50.000 9.90 0.00 33.99 5.69
2405 4251 1.203025 AGAACCTCCACTACAGACGGT 60.203 52.381 0.00 0.00 0.00 4.83
2431 4277 2.743664 TGAATTGGATCAGTTGAGTGCG 59.256 45.455 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.