Multiple sequence alignment - TraesCS1A01G045100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G045100 chr1A 100.000 3659 0 0 1 3659 25805822 25809480 0.000000e+00 6758.0
1 TraesCS1A01G045100 chr1D 90.726 2782 165 42 587 3335 25138614 25141335 0.000000e+00 3622.0
2 TraesCS1A01G045100 chr1D 91.327 392 34 0 195 586 25137808 25138199 1.500000e-148 536.0
3 TraesCS1A01G045100 chr1D 88.291 316 24 5 3349 3659 25141319 25141626 2.080000e-97 366.0
4 TraesCS1A01G045100 chr1D 100.000 37 0 0 1 37 263405280 263405244 6.560000e-08 69.4
5 TraesCS1A01G045100 chr1B 89.940 2684 173 46 587 3218 40406774 40409412 0.000000e+00 3371.0
6 TraesCS1A01G045100 chr1B 89.677 2383 139 43 658 2995 40420046 40422366 0.000000e+00 2939.0
7 TraesCS1A01G045100 chr1B 91.569 2052 141 17 1184 3218 40414092 40416128 0.000000e+00 2802.0
8 TraesCS1A01G045100 chr1B 84.629 566 30 23 658 1195 40413323 40413859 9.060000e-141 510.0
9 TraesCS1A01G045100 chr1B 88.689 389 44 0 198 586 40419234 40419622 3.310000e-130 475.0
10 TraesCS1A01G045100 chr1B 88.175 389 46 0 198 586 40412515 40412903 7.160000e-127 464.0
11 TraesCS1A01G045100 chr1B 89.101 367 38 2 220 585 40406003 40406368 4.310000e-124 455.0
12 TraesCS1A01G045100 chr1B 87.342 316 33 3 3349 3659 40409487 40409800 4.490000e-94 355.0
13 TraesCS1A01G045100 chr1B 87.342 316 33 5 3349 3659 40416203 40416516 4.490000e-94 355.0
14 TraesCS1A01G045100 chr1B 91.463 164 13 1 3494 3657 40434042 40434204 1.320000e-54 224.0
15 TraesCS1A01G045100 chr1B 87.121 132 11 2 3351 3477 40430689 40430819 1.060000e-30 145.0
16 TraesCS1A01G045100 chr1B 97.297 37 1 0 1 37 420705260 420705296 3.050000e-06 63.9
17 TraesCS1A01G045100 chr6A 82.353 119 19 2 1091 1208 61814963 61814846 6.460000e-18 102.0
18 TraesCS1A01G045100 chr5D 77.099 131 26 2 1097 1225 44488983 44489111 5.070000e-09 73.1
19 TraesCS1A01G045100 chr5B 77.099 131 26 2 1097 1225 43884307 43884435 5.070000e-09 73.1
20 TraesCS1A01G045100 chr5B 80.198 101 16 2 1130 1228 44231417 44231319 5.070000e-09 73.1
21 TraesCS1A01G045100 chr4D 97.368 38 0 1 1 38 107881773 107881737 3.050000e-06 63.9
22 TraesCS1A01G045100 chr4D 95.000 40 1 1 1 40 105050871 105050909 1.100000e-05 62.1
23 TraesCS1A01G045100 chr4A 97.368 38 0 1 1 38 522780032 522779996 3.050000e-06 63.9
24 TraesCS1A01G045100 chr3B 97.368 38 0 1 1 38 113637711 113637675 3.050000e-06 63.9
25 TraesCS1A01G045100 chr2D 97.297 37 1 0 1 37 351464588 351464552 3.050000e-06 63.9
26 TraesCS1A01G045100 chr2D 97.368 38 0 1 1 38 351477830 351477794 3.050000e-06 63.9
27 TraesCS1A01G045100 chr7A 94.872 39 2 0 1 39 474039059 474039097 1.100000e-05 62.1


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 TraesCS1A01G045100 chr1A 25805822 25809480 3658 False 6758.000000 6758 100.000000 1 3659 1 chr1A.!!$F1 3658
1 TraesCS1A01G045100 chr1D 25137808 25141626 3818 False 1508.000000 3622 90.114667 195 3659 3 chr1D.!!$F1 3464
2 TraesCS1A01G045100 chr1B 40406003 40422366 16363 False 1302.888889 3371 88.496000 198 3659 9 chr1B.!!$F2 3461

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
85 86 0.109781 ACGATGATGTTGGCAAACGC 60.110 50.0 0.00 0.0 39.30 4.84 F
341 343 0.184692 TCATGGTGTTGCCCTGTTCA 59.815 50.0 0.00 0.0 34.88 3.18 F
908 1338 0.319469 CACAAATTTGACACCCCGGC 60.319 55.0 24.64 0.0 0.00 6.13 F
1582 2036 0.106669 GAATTTTCCCCTCCTCCGGG 60.107 60.0 0.00 0.0 44.27 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1052 1506 0.586802 GATATCGCGTGCCCTTTTCC 59.413 55.000 5.77 0.0 0.0 3.13 R
1368 1822 1.066587 GAACCAGCTCTCGATCCGG 59.933 63.158 0.00 0.0 0.0 5.14 R
2635 9816 1.064357 GAAAACGAAACGCCAAGTCCA 59.936 47.619 0.00 0.0 0.0 4.02 R
3007 10197 0.602905 CTTGTTCTTCGGGCGTCCTT 60.603 55.000 3.66 0.0 0.0 3.36 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
56 57 5.898174 CCCCCATAATCGAAAAAGGTTTAC 58.102 41.667 0.00 0.00 0.00 2.01
57 58 5.655090 CCCCCATAATCGAAAAAGGTTTACT 59.345 40.000 0.00 0.00 0.00 2.24
58 59 6.829811 CCCCCATAATCGAAAAAGGTTTACTA 59.170 38.462 0.00 0.00 0.00 1.82
59 60 7.012989 CCCCCATAATCGAAAAAGGTTTACTAG 59.987 40.741 0.00 0.00 0.00 2.57
60 61 7.415229 CCCATAATCGAAAAAGGTTTACTAGC 58.585 38.462 0.00 0.00 0.00 3.42
61 62 7.066525 CCCATAATCGAAAAAGGTTTACTAGCA 59.933 37.037 0.00 0.00 0.00 3.49
62 63 8.621286 CCATAATCGAAAAAGGTTTACTAGCAT 58.379 33.333 0.00 0.00 0.00 3.79
63 64 9.438291 CATAATCGAAAAAGGTTTACTAGCATG 57.562 33.333 0.00 0.00 0.00 4.06
64 65 5.291293 TCGAAAAAGGTTTACTAGCATGC 57.709 39.130 10.51 10.51 0.00 4.06
65 66 4.155280 TCGAAAAAGGTTTACTAGCATGCC 59.845 41.667 15.66 0.00 0.00 4.40
66 67 4.083003 CGAAAAAGGTTTACTAGCATGCCA 60.083 41.667 15.66 0.00 0.00 4.92
67 68 4.783764 AAAAGGTTTACTAGCATGCCAC 57.216 40.909 15.66 1.69 0.00 5.01
68 69 2.024176 AGGTTTACTAGCATGCCACG 57.976 50.000 15.66 5.45 0.00 4.94
69 70 1.553248 AGGTTTACTAGCATGCCACGA 59.447 47.619 15.66 0.00 0.00 4.35
70 71 2.170607 AGGTTTACTAGCATGCCACGAT 59.829 45.455 15.66 0.00 0.00 3.73
71 72 2.287915 GGTTTACTAGCATGCCACGATG 59.712 50.000 15.66 0.89 0.00 3.84
72 73 3.194861 GTTTACTAGCATGCCACGATGA 58.805 45.455 15.66 0.00 0.00 2.92
73 74 3.751479 TTACTAGCATGCCACGATGAT 57.249 42.857 15.66 0.00 0.00 2.45
74 75 1.875009 ACTAGCATGCCACGATGATG 58.125 50.000 15.66 0.00 0.00 3.07
75 76 1.139654 ACTAGCATGCCACGATGATGT 59.860 47.619 15.66 0.00 0.00 3.06
76 77 2.216046 CTAGCATGCCACGATGATGTT 58.784 47.619 15.66 0.00 0.00 2.71
77 78 0.736636 AGCATGCCACGATGATGTTG 59.263 50.000 15.66 0.00 0.00 3.33
78 79 0.248743 GCATGCCACGATGATGTTGG 60.249 55.000 6.36 0.00 0.00 3.77
79 80 0.248743 CATGCCACGATGATGTTGGC 60.249 55.000 4.84 4.84 45.19 4.52
80 81 3.589579 GCCACGATGATGTTGGCA 58.410 55.556 6.96 0.00 44.42 4.92
81 82 1.882311 GCCACGATGATGTTGGCAA 59.118 52.632 6.96 0.00 44.42 4.52
82 83 0.243365 GCCACGATGATGTTGGCAAA 59.757 50.000 0.00 0.00 44.42 3.68
83 84 1.981254 CCACGATGATGTTGGCAAAC 58.019 50.000 0.00 0.00 36.78 2.93
84 85 1.605500 CACGATGATGTTGGCAAACG 58.394 50.000 0.00 4.27 39.30 3.60
85 86 0.109781 ACGATGATGTTGGCAAACGC 60.110 50.000 0.00 0.00 39.30 4.84
96 97 1.355210 GCAAACGCCATGATACCCG 59.645 57.895 0.00 0.00 0.00 5.28
97 98 1.373590 GCAAACGCCATGATACCCGT 61.374 55.000 0.00 0.00 35.14 5.28
98 99 1.091537 CAAACGCCATGATACCCGTT 58.908 50.000 0.00 0.00 44.66 4.44
99 100 1.091537 AAACGCCATGATACCCGTTG 58.908 50.000 0.00 0.00 42.31 4.10
100 101 1.373590 AACGCCATGATACCCGTTGC 61.374 55.000 0.00 0.00 41.67 4.17
101 102 2.881266 CGCCATGATACCCGTTGCG 61.881 63.158 0.00 0.00 39.11 4.85
102 103 1.817941 GCCATGATACCCGTTGCGT 60.818 57.895 0.00 0.00 0.00 5.24
103 104 1.373590 GCCATGATACCCGTTGCGTT 61.374 55.000 0.00 0.00 0.00 4.84
104 105 0.655733 CCATGATACCCGTTGCGTTC 59.344 55.000 0.00 0.00 0.00 3.95
105 106 0.655733 CATGATACCCGTTGCGTTCC 59.344 55.000 0.00 0.00 0.00 3.62
106 107 0.250793 ATGATACCCGTTGCGTTCCA 59.749 50.000 0.00 0.00 0.00 3.53
107 108 0.250793 TGATACCCGTTGCGTTCCAT 59.749 50.000 0.00 0.00 0.00 3.41
108 109 1.339247 TGATACCCGTTGCGTTCCATT 60.339 47.619 0.00 0.00 0.00 3.16
109 110 1.329599 GATACCCGTTGCGTTCCATTC 59.670 52.381 0.00 0.00 0.00 2.67
110 111 1.015085 TACCCGTTGCGTTCCATTCG 61.015 55.000 0.00 0.00 0.00 3.34
111 112 2.322081 CCCGTTGCGTTCCATTCGT 61.322 57.895 0.00 0.00 0.00 3.85
112 113 1.131826 CCGTTGCGTTCCATTCGTC 59.868 57.895 0.00 0.00 0.00 4.20
113 114 1.225368 CGTTGCGTTCCATTCGTCG 60.225 57.895 0.00 0.00 0.00 5.12
114 115 1.857364 GTTGCGTTCCATTCGTCGT 59.143 52.632 0.00 0.00 0.00 4.34
115 116 0.450482 GTTGCGTTCCATTCGTCGTG 60.450 55.000 0.00 0.00 0.00 4.35
116 117 1.561717 TTGCGTTCCATTCGTCGTGG 61.562 55.000 0.00 0.00 38.11 4.94
117 118 2.776072 CGTTCCATTCGTCGTGGC 59.224 61.111 0.00 0.00 36.66 5.01
118 119 2.024868 CGTTCCATTCGTCGTGGCA 61.025 57.895 0.00 0.00 36.66 4.92
119 120 1.358725 CGTTCCATTCGTCGTGGCAT 61.359 55.000 0.00 0.00 36.66 4.40
120 121 0.802494 GTTCCATTCGTCGTGGCATT 59.198 50.000 0.00 0.00 36.66 3.56
121 122 0.801872 TTCCATTCGTCGTGGCATTG 59.198 50.000 0.00 0.00 36.66 2.82
122 123 1.226379 CCATTCGTCGTGGCATTGC 60.226 57.895 0.00 0.00 0.00 3.56
133 134 3.256620 GGCATTGCCGATTACTTGC 57.743 52.632 12.82 0.00 39.62 4.01
134 135 0.740737 GGCATTGCCGATTACTTGCT 59.259 50.000 12.82 0.00 39.62 3.91
135 136 1.134946 GGCATTGCCGATTACTTGCTT 59.865 47.619 12.82 0.00 39.62 3.91
136 137 2.454055 GCATTGCCGATTACTTGCTTC 58.546 47.619 0.00 0.00 0.00 3.86
137 138 2.708514 CATTGCCGATTACTTGCTTCG 58.291 47.619 0.00 0.00 0.00 3.79
140 141 2.690326 CCGATTACTTGCTTCGGGG 58.310 57.895 2.74 0.00 46.67 5.73
141 142 0.814010 CCGATTACTTGCTTCGGGGG 60.814 60.000 2.74 0.00 46.67 5.40
155 156 3.370231 GGGGGCGCGACAAATGTT 61.370 61.111 17.00 0.00 0.00 2.71
156 157 2.648454 GGGGCGCGACAAATGTTT 59.352 55.556 17.00 0.00 0.00 2.83
157 158 1.006688 GGGGCGCGACAAATGTTTT 60.007 52.632 17.00 0.00 0.00 2.43
158 159 1.281566 GGGGCGCGACAAATGTTTTG 61.282 55.000 17.00 0.00 0.00 2.44
159 160 1.486801 GGCGCGACAAATGTTTTGC 59.513 52.632 12.10 0.00 0.00 3.68
160 161 1.486801 GCGCGACAAATGTTTTGCC 59.513 52.632 12.10 0.00 0.00 4.52
161 162 1.211818 GCGCGACAAATGTTTTGCCA 61.212 50.000 12.10 0.00 0.00 4.92
162 163 0.502275 CGCGACAAATGTTTTGCCAC 59.498 50.000 0.00 0.00 0.00 5.01
163 164 1.565305 GCGACAAATGTTTTGCCACA 58.435 45.000 0.06 0.00 0.00 4.17
164 165 2.134346 GCGACAAATGTTTTGCCACAT 58.866 42.857 0.06 0.00 39.17 3.21
165 166 2.096811 GCGACAAATGTTTTGCCACATG 60.097 45.455 0.00 0.00 37.46 3.21
166 167 2.475864 CGACAAATGTTTTGCCACATGG 59.524 45.455 0.00 0.00 37.46 3.66
178 179 1.843368 CCACATGGCATATCCCCATC 58.157 55.000 0.00 0.00 41.02 3.51
179 180 1.617804 CCACATGGCATATCCCCATCC 60.618 57.143 0.00 0.00 41.02 3.51
180 181 1.075861 CACATGGCATATCCCCATCCA 59.924 52.381 0.00 0.00 41.02 3.41
181 182 2.005350 ACATGGCATATCCCCATCCAT 58.995 47.619 0.00 0.00 41.02 3.41
182 183 2.024655 ACATGGCATATCCCCATCCATC 60.025 50.000 0.00 0.00 41.02 3.51
183 184 1.757799 TGGCATATCCCCATCCATCA 58.242 50.000 0.00 0.00 0.00 3.07
184 185 2.290410 TGGCATATCCCCATCCATCAT 58.710 47.619 0.00 0.00 0.00 2.45
185 186 2.024751 TGGCATATCCCCATCCATCATG 60.025 50.000 0.00 0.00 0.00 3.07
193 194 0.748450 CCATCCATCATGGTGTTGCC 59.252 55.000 2.79 0.00 46.72 4.52
194 195 0.748450 CATCCATCATGGTGTTGCCC 59.252 55.000 2.79 0.00 39.03 5.36
195 196 0.632835 ATCCATCATGGTGTTGCCCT 59.367 50.000 2.79 0.00 39.03 5.19
196 197 0.323633 TCCATCATGGTGTTGCCCTG 60.324 55.000 2.79 0.00 39.03 4.45
197 198 0.612732 CCATCATGGTGTTGCCCTGT 60.613 55.000 5.00 0.00 34.88 4.00
198 199 1.259609 CATCATGGTGTTGCCCTGTT 58.740 50.000 0.00 0.00 34.88 3.16
199 200 1.203052 CATCATGGTGTTGCCCTGTTC 59.797 52.381 0.00 0.00 34.88 3.18
200 201 0.539438 TCATGGTGTTGCCCTGTTCC 60.539 55.000 0.00 0.00 34.88 3.62
201 202 0.827089 CATGGTGTTGCCCTGTTCCA 60.827 55.000 0.00 0.00 36.04 3.53
202 203 0.540365 ATGGTGTTGCCCTGTTCCAG 60.540 55.000 0.00 0.00 36.04 3.86
203 204 2.564721 GGTGTTGCCCTGTTCCAGC 61.565 63.158 0.00 0.00 0.00 4.85
204 205 2.594303 TGTTGCCCTGTTCCAGCG 60.594 61.111 0.00 0.00 0.00 5.18
205 206 4.043200 GTTGCCCTGTTCCAGCGC 62.043 66.667 0.00 0.00 36.02 5.92
211 212 4.069232 CTGTTCCAGCGCCGAGGA 62.069 66.667 2.29 6.78 0.00 3.71
212 213 3.589654 CTGTTCCAGCGCCGAGGAA 62.590 63.158 19.07 19.07 41.41 3.36
240 241 2.126346 GTTGATGCGCTTGCCACC 60.126 61.111 9.73 0.00 38.03 4.61
241 242 3.736100 TTGATGCGCTTGCCACCG 61.736 61.111 9.73 0.00 38.03 4.94
276 278 1.066286 TGTTTGCCAAGTGCTTGCTTT 60.066 42.857 6.42 0.00 42.00 3.51
282 284 1.321474 CAAGTGCTTGCTTTGAGGGA 58.679 50.000 0.00 0.00 33.45 4.20
287 289 3.031964 CTTGCTTTGAGGGAGCGCG 62.032 63.158 0.00 0.00 43.02 6.86
324 326 3.219281 CATGGCATGTCCTCATTCATCA 58.781 45.455 19.32 0.00 35.26 3.07
341 343 0.184692 TCATGGTGTTGCCCTGTTCA 59.815 50.000 0.00 0.00 34.88 3.18
367 369 1.802960 CGAGCAACTCAGCAGATGTTT 59.197 47.619 0.00 0.00 36.85 2.83
377 379 1.808945 AGCAGATGTTTCTTCGCTTGG 59.191 47.619 0.00 0.00 0.00 3.61
395 397 1.133869 GCACCGCCATTAACGTGTC 59.866 57.895 0.00 0.00 0.00 3.67
402 404 2.303537 GCCATTAACGTGTCGTGTTTG 58.696 47.619 0.00 0.00 39.99 2.93
436 438 1.956170 ACGGCACTCGACAAAGCTG 60.956 57.895 0.00 0.00 42.43 4.24
508 510 1.817099 GCCAGGAGACATCAAGCCG 60.817 63.158 0.00 0.00 0.00 5.52
528 530 1.729838 GTCGGTGTCTGACGAGTGC 60.730 63.158 2.98 0.00 40.09 4.40
548 550 2.726066 GCGCTTTCTCGAATGTCTTTGG 60.726 50.000 0.00 0.00 0.00 3.28
566 568 0.602372 GGCGCTTGGCAAAAATGGAA 60.602 50.000 7.64 0.00 46.16 3.53
630 1051 4.619973 ACATTGGACTTTTACGTCACGTA 58.380 39.130 5.79 5.79 41.54 3.57
664 1085 3.309296 ACCGTGAATCCATGATCCTAGT 58.691 45.455 0.00 0.00 0.00 2.57
671 1092 5.012458 TGAATCCATGATCCTAGTTAGGCTG 59.988 44.000 0.00 0.00 43.31 4.85
675 1096 4.081198 CCATGATCCTAGTTAGGCTGATCC 60.081 50.000 0.00 0.00 43.31 3.36
714 1136 5.698545 GCTTGGCTGATCTGGTACTAAATAG 59.301 44.000 1.46 0.00 0.00 1.73
715 1137 6.686632 GCTTGGCTGATCTGGTACTAAATAGT 60.687 42.308 1.46 0.00 40.24 2.12
716 1138 7.471539 GCTTGGCTGATCTGGTACTAAATAGTA 60.472 40.741 1.46 0.00 37.73 1.82
718 1140 9.596308 TTGGCTGATCTGGTACTAAATAGTATA 57.404 33.333 3.78 0.00 40.55 1.47
719 1141 9.021807 TGGCTGATCTGGTACTAAATAGTATAC 57.978 37.037 3.78 0.00 40.55 1.47
720 1142 9.245481 GGCTGATCTGGTACTAAATAGTATACT 57.755 37.037 10.87 10.87 40.55 2.12
757 1179 7.758495 ACAAAATAGTGAATCCGTAAATCCAC 58.242 34.615 0.00 0.00 0.00 4.02
790 1212 8.624776 TGACCATATGCTATGATCGAATACTAG 58.375 37.037 0.00 0.00 0.00 2.57
791 1213 8.526667 ACCATATGCTATGATCGAATACTAGT 57.473 34.615 0.00 0.00 0.00 2.57
792 1214 8.972127 ACCATATGCTATGATCGAATACTAGTT 58.028 33.333 0.00 0.00 0.00 2.24
809 1231 4.754114 ACTAGTTACTAGTAGGATTCGGCG 59.246 45.833 21.95 0.00 44.35 6.46
823 1245 0.386352 TCGGCGACAGAGTACGTTTG 60.386 55.000 4.99 0.00 0.00 2.93
906 1336 2.556189 TCATCACAAATTTGACACCCCG 59.444 45.455 24.64 6.32 0.00 5.73
907 1337 1.323412 TCACAAATTTGACACCCCGG 58.677 50.000 24.64 0.00 0.00 5.73
908 1338 0.319469 CACAAATTTGACACCCCGGC 60.319 55.000 24.64 0.00 0.00 6.13
909 1339 1.291906 CAAATTTGACACCCCGGCC 59.708 57.895 13.08 0.00 0.00 6.13
910 1340 1.911269 AAATTTGACACCCCGGCCC 60.911 57.895 0.00 0.00 0.00 5.80
924 1354 2.218066 GGCCCTCCCGTATTCTTCA 58.782 57.895 0.00 0.00 0.00 3.02
951 1381 2.125673 CCGCCGGACGTGAAGAAT 60.126 61.111 5.05 0.00 41.42 2.40
952 1382 1.740296 CCGCCGGACGTGAAGAATT 60.740 57.895 5.05 0.00 41.42 2.17
954 1384 0.921347 CGCCGGACGTGAAGAATTAG 59.079 55.000 5.05 0.00 36.87 1.73
955 1385 1.287425 GCCGGACGTGAAGAATTAGG 58.713 55.000 5.05 0.00 0.00 2.69
957 1387 1.404986 CCGGACGTGAAGAATTAGGCA 60.405 52.381 0.00 0.00 0.00 4.75
983 1437 2.811542 AAGAAGGAAGCCGAGGCAGC 62.812 60.000 17.18 7.25 44.88 5.25
1018 1472 1.919600 GATGAGGGCAGCCAAGAGGT 61.920 60.000 15.19 0.00 37.19 3.85
1069 1523 1.812093 CGGAAAAGGGCACGCGATA 60.812 57.895 15.93 0.00 0.00 2.92
1226 1680 3.878519 GCCTCTCGACCTCGACGG 61.879 72.222 0.00 0.00 44.22 4.79
1334 1788 1.128692 GTTCGAAAACATCTGCCTCCG 59.871 52.381 0.00 0.00 35.36 4.63
1343 1797 1.065102 CATCTGCCTCCGCAAATCAAG 59.935 52.381 0.00 0.00 46.66 3.02
1351 1805 1.272212 TCCGCAAATCAAGAAAAGGGC 59.728 47.619 0.00 0.00 0.00 5.19
1353 1807 2.061028 CGCAAATCAAGAAAAGGGCAC 58.939 47.619 0.00 0.00 0.00 5.01
1408 1862 4.308458 CCCGGTGCCTCGACAACA 62.308 66.667 0.00 0.00 0.00 3.33
1452 1906 1.839424 GGCTGTTGGGTAAAGCAGAT 58.161 50.000 0.00 0.00 38.73 2.90
1485 1939 4.201679 TACCCGCTGCCATCGTCG 62.202 66.667 0.00 0.00 0.00 5.12
1582 2036 0.106669 GAATTTTCCCCTCCTCCGGG 60.107 60.000 0.00 0.00 44.27 5.73
1707 2161 0.969894 ACTGCCTTCGTGTTAGCTCT 59.030 50.000 0.00 0.00 0.00 4.09
1743 2197 4.560739 TCATCTGGTTCATCCCTACTCAT 58.439 43.478 0.00 0.00 34.77 2.90
1757 2211 2.887151 ACTCATTTGGGGAGACAAGG 57.113 50.000 0.00 0.00 36.26 3.61
1946 2404 5.183713 CACCCTTATTGTCTCTTGCATTGAA 59.816 40.000 0.00 0.00 0.00 2.69
1995 2453 7.384660 TGTTTCTAATGTCCATGCATTGTTTTC 59.615 33.333 0.00 0.00 39.20 2.29
1997 2455 6.623486 TCTAATGTCCATGCATTGTTTTCTG 58.377 36.000 0.00 0.00 39.20 3.02
2078 2539 0.971386 AGTTTGCTGGCCCAGATTTG 59.029 50.000 16.85 0.00 32.44 2.32
2101 2562 2.115427 TGCGGTTCTCAATATCCTCCA 58.885 47.619 0.00 0.00 0.00 3.86
2127 2588 1.253593 CCCCTGCTTGGAAAAGCTCC 61.254 60.000 11.39 0.00 45.66 4.70
2168 2629 9.301153 GACCATTTTGTTCGCTTTAAATGATAT 57.699 29.630 0.00 0.00 39.26 1.63
2259 2721 2.027625 CCTTTCGCAGTGGGACGAC 61.028 63.158 9.78 0.00 38.17 4.34
2331 2793 1.538047 TCAAATGCCTTGAGAGCCAC 58.462 50.000 0.00 0.00 39.20 5.01
2403 2866 3.932089 GCTTTGCCAAGTTCTTTGTTTCA 59.068 39.130 0.00 0.00 34.87 2.69
2605 9786 0.400213 AATTGCTGACCCCTTCGACA 59.600 50.000 0.00 0.00 0.00 4.35
2635 9816 3.473113 ACTTTGCCAATGGGGTAGATT 57.527 42.857 0.00 0.00 39.65 2.40
2636 9817 3.099141 ACTTTGCCAATGGGGTAGATTG 58.901 45.455 0.00 0.00 39.65 2.67
2666 9847 4.638963 CGTTTCGTTTTCTAGATCCTTGC 58.361 43.478 0.00 0.00 0.00 4.01
2681 9862 5.705441 AGATCCTTGCGAACAGTAAAATTGA 59.295 36.000 0.00 0.00 0.00 2.57
2818 10008 6.092944 TCAACGTGTCATACTTTTGTTGAAGT 59.907 34.615 2.71 0.00 40.63 3.01
2970 10160 0.966920 TCCCTCGTCTTCAACTCCAC 59.033 55.000 0.00 0.00 0.00 4.02
2974 10164 2.352814 CCTCGTCTTCAACTCCACGAAT 60.353 50.000 0.00 0.00 40.55 3.34
3007 10197 1.100463 TTGTTCTCAAAGCTGCGCCA 61.100 50.000 4.18 0.00 0.00 5.69
3025 10216 0.882927 CAAGGACGCCCGAAGAACAA 60.883 55.000 0.00 0.00 37.58 2.83
3066 10258 3.678056 TCTCAAACGACTAATGGTGCT 57.322 42.857 0.00 0.00 0.00 4.40
3117 10309 2.034066 TTGGTAGCAGCCTGGTGC 59.966 61.111 13.14 13.14 44.35 5.01
3244 10438 4.087892 CTGGTCTCAGGCCCACCG 62.088 72.222 0.00 0.00 42.76 4.94
3318 10512 9.853177 AATTCTATATTTCTCTTACACCCTTGG 57.147 33.333 0.00 0.00 0.00 3.61
3319 10513 7.989947 TCTATATTTCTCTTACACCCTTGGT 57.010 36.000 0.00 0.00 35.62 3.67
3320 10514 8.019656 TCTATATTTCTCTTACACCCTTGGTC 57.980 38.462 0.00 0.00 31.02 4.02
3321 10515 3.782656 TTTCTCTTACACCCTTGGTCC 57.217 47.619 0.00 0.00 31.02 4.46
3322 10516 1.652947 TCTCTTACACCCTTGGTCCC 58.347 55.000 0.00 0.00 31.02 4.46
3323 10517 1.151413 TCTCTTACACCCTTGGTCCCT 59.849 52.381 0.00 0.00 31.02 4.20
3324 10518 2.384375 TCTCTTACACCCTTGGTCCCTA 59.616 50.000 0.00 0.00 31.02 3.53
3325 10519 3.013648 TCTCTTACACCCTTGGTCCCTAT 59.986 47.826 0.00 0.00 31.02 2.57
3326 10520 3.780850 CTCTTACACCCTTGGTCCCTATT 59.219 47.826 0.00 0.00 31.02 1.73
3327 10521 3.521937 TCTTACACCCTTGGTCCCTATTG 59.478 47.826 0.00 0.00 31.02 1.90
3328 10522 2.053747 ACACCCTTGGTCCCTATTGA 57.946 50.000 0.00 0.00 31.02 2.57
3329 10523 2.354328 ACACCCTTGGTCCCTATTGAA 58.646 47.619 0.00 0.00 31.02 2.69
3330 10524 2.041216 ACACCCTTGGTCCCTATTGAAC 59.959 50.000 0.00 0.00 31.02 3.18
3331 10525 2.041081 CACCCTTGGTCCCTATTGAACA 59.959 50.000 0.00 0.00 31.02 3.18
3332 10526 2.719705 ACCCTTGGTCCCTATTGAACAA 59.280 45.455 0.00 0.00 39.55 2.83
3333 10527 3.336694 ACCCTTGGTCCCTATTGAACAAT 59.663 43.478 5.40 5.40 40.92 2.71
3334 10528 4.202781 ACCCTTGGTCCCTATTGAACAATT 60.203 41.667 5.37 0.00 40.92 2.32
3335 10529 4.777366 CCCTTGGTCCCTATTGAACAATTT 59.223 41.667 5.37 0.00 40.92 1.82
3336 10530 5.248248 CCCTTGGTCCCTATTGAACAATTTT 59.752 40.000 5.37 0.00 40.92 1.82
3337 10531 6.239858 CCCTTGGTCCCTATTGAACAATTTTT 60.240 38.462 5.37 0.00 40.92 1.94
3387 10581 5.706916 TGATCGAGTTGTTCTAGTGGTTAC 58.293 41.667 0.00 0.00 0.00 2.50
3398 10592 7.262772 TGTTCTAGTGGTTACAGTATATGTGC 58.737 38.462 0.00 0.00 43.80 4.57
3411 10605 8.560355 ACAGTATATGTGCATTCACTAACAAA 57.440 30.769 0.00 0.00 41.91 2.83
3457 10656 6.530120 TGCGTGATTATTATGGGAAGTACAT 58.470 36.000 0.00 0.00 0.00 2.29
3459 10658 6.620733 GCGTGATTATTATGGGAAGTACATGC 60.621 42.308 0.00 0.00 0.00 4.06
3460 10659 6.426633 CGTGATTATTATGGGAAGTACATGCA 59.573 38.462 0.00 0.00 0.00 3.96
3466 10665 2.256306 TGGGAAGTACATGCAGAGACA 58.744 47.619 0.00 0.00 0.00 3.41
3481 10680 6.283694 TGCAGAGACAATATTTCTTAGCGAT 58.716 36.000 0.00 0.00 0.00 4.58
3485 10684 8.272176 CAGAGACAATATTTCTTAGCGATGTTC 58.728 37.037 0.00 0.00 0.00 3.18
3486 10685 7.981789 AGAGACAATATTTCTTAGCGATGTTCA 59.018 33.333 0.00 0.00 0.00 3.18
3487 10686 8.136057 AGACAATATTTCTTAGCGATGTTCAG 57.864 34.615 0.00 0.00 0.00 3.02
3488 10687 7.766278 AGACAATATTTCTTAGCGATGTTCAGT 59.234 33.333 0.00 0.00 0.00 3.41
3489 10688 7.688372 ACAATATTTCTTAGCGATGTTCAGTG 58.312 34.615 0.00 0.00 0.00 3.66
3490 10689 7.549134 ACAATATTTCTTAGCGATGTTCAGTGA 59.451 33.333 0.00 0.00 0.00 3.41
3491 10690 5.786401 ATTTCTTAGCGATGTTCAGTGAC 57.214 39.130 0.00 0.00 0.00 3.67
3497 10696 0.792640 CGATGTTCAGTGACCAGTGC 59.207 55.000 0.00 0.00 0.00 4.40
3561 10767 7.577979 TGTGTACTTAAATCGACAAATCAACC 58.422 34.615 0.00 0.00 0.00 3.77
3592 10798 3.984633 GTCAAGGCTATTAGACGCATCTC 59.015 47.826 0.00 0.00 36.29 2.75
3601 10807 1.681538 AGACGCATCTCGACCACTAT 58.318 50.000 0.00 0.00 41.67 2.12
3613 10819 0.833287 ACCACTATGCCAGCCTACAG 59.167 55.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.655090 AGTAAACCTTTTTCGATTATGGGGG 59.345 40.000 0.00 0.00 0.00 5.40
34 35 6.769134 AGTAAACCTTTTTCGATTATGGGG 57.231 37.500 0.00 0.00 0.00 4.96
35 36 7.066525 TGCTAGTAAACCTTTTTCGATTATGGG 59.933 37.037 0.00 0.00 0.00 4.00
36 37 7.981142 TGCTAGTAAACCTTTTTCGATTATGG 58.019 34.615 0.00 0.00 0.00 2.74
37 38 9.438291 CATGCTAGTAAACCTTTTTCGATTATG 57.562 33.333 0.00 0.00 0.00 1.90
38 39 8.129211 GCATGCTAGTAAACCTTTTTCGATTAT 58.871 33.333 11.37 0.00 0.00 1.28
39 40 7.414762 GGCATGCTAGTAAACCTTTTTCGATTA 60.415 37.037 18.92 0.00 0.00 1.75
40 41 6.322491 GCATGCTAGTAAACCTTTTTCGATT 58.678 36.000 11.37 0.00 0.00 3.34
41 42 5.163652 GGCATGCTAGTAAACCTTTTTCGAT 60.164 40.000 18.92 0.00 0.00 3.59
42 43 4.155280 GGCATGCTAGTAAACCTTTTTCGA 59.845 41.667 18.92 0.00 0.00 3.71
43 44 4.083003 TGGCATGCTAGTAAACCTTTTTCG 60.083 41.667 18.92 0.00 0.00 3.46
44 45 5.161358 GTGGCATGCTAGTAAACCTTTTTC 58.839 41.667 18.92 0.00 0.00 2.29
45 46 4.320935 CGTGGCATGCTAGTAAACCTTTTT 60.321 41.667 18.92 0.00 0.00 1.94
46 47 3.190535 CGTGGCATGCTAGTAAACCTTTT 59.809 43.478 18.92 0.00 0.00 2.27
47 48 2.747446 CGTGGCATGCTAGTAAACCTTT 59.253 45.455 18.92 0.00 0.00 3.11
48 49 2.027561 TCGTGGCATGCTAGTAAACCTT 60.028 45.455 18.92 0.00 0.00 3.50
49 50 1.553248 TCGTGGCATGCTAGTAAACCT 59.447 47.619 18.92 0.00 0.00 3.50
50 51 2.018542 TCGTGGCATGCTAGTAAACC 57.981 50.000 18.92 0.00 0.00 3.27
51 52 3.194861 TCATCGTGGCATGCTAGTAAAC 58.805 45.455 18.92 5.96 0.00 2.01
52 53 3.535280 TCATCGTGGCATGCTAGTAAA 57.465 42.857 18.92 0.00 0.00 2.01
53 54 3.181466 ACATCATCGTGGCATGCTAGTAA 60.181 43.478 18.92 0.00 0.00 2.24
54 55 2.365293 ACATCATCGTGGCATGCTAGTA 59.635 45.455 18.92 2.35 0.00 1.82
55 56 1.139654 ACATCATCGTGGCATGCTAGT 59.860 47.619 18.92 0.36 0.00 2.57
56 57 1.875009 ACATCATCGTGGCATGCTAG 58.125 50.000 18.92 9.35 0.00 3.42
57 58 1.941975 CAACATCATCGTGGCATGCTA 59.058 47.619 18.92 9.16 0.00 3.49
58 59 0.736636 CAACATCATCGTGGCATGCT 59.263 50.000 18.92 0.00 0.00 3.79
59 60 0.248743 CCAACATCATCGTGGCATGC 60.249 55.000 9.90 9.90 0.00 4.06
60 61 0.248743 GCCAACATCATCGTGGCATG 60.249 55.000 8.98 0.00 44.42 4.06
61 62 2.109431 GCCAACATCATCGTGGCAT 58.891 52.632 8.98 0.00 44.42 4.40
62 63 3.589579 GCCAACATCATCGTGGCA 58.410 55.556 8.98 0.00 44.42 4.92
63 64 0.243365 TTTGCCAACATCATCGTGGC 59.757 50.000 6.96 6.96 45.19 5.01
64 65 1.728825 CGTTTGCCAACATCATCGTGG 60.729 52.381 1.21 0.00 32.54 4.94
65 66 1.605500 CGTTTGCCAACATCATCGTG 58.394 50.000 1.21 0.00 32.54 4.35
66 67 0.109781 GCGTTTGCCAACATCATCGT 60.110 50.000 1.21 0.00 32.54 3.73
67 68 2.640684 GCGTTTGCCAACATCATCG 58.359 52.632 1.21 0.00 32.54 3.84
78 79 1.355210 CGGGTATCATGGCGTTTGC 59.645 57.895 0.00 0.00 41.71 3.68
79 80 1.091537 AACGGGTATCATGGCGTTTG 58.908 50.000 0.00 0.00 0.00 2.93
80 81 1.091537 CAACGGGTATCATGGCGTTT 58.908 50.000 0.00 0.00 0.00 3.60
81 82 1.373590 GCAACGGGTATCATGGCGTT 61.374 55.000 0.00 0.00 0.00 4.84
82 83 1.817941 GCAACGGGTATCATGGCGT 60.818 57.895 0.00 0.00 0.00 5.68
83 84 2.881266 CGCAACGGGTATCATGGCG 61.881 63.158 0.00 0.00 36.93 5.69
84 85 1.373590 AACGCAACGGGTATCATGGC 61.374 55.000 0.00 0.00 0.00 4.40
85 86 0.655733 GAACGCAACGGGTATCATGG 59.344 55.000 0.00 0.00 0.00 3.66
86 87 0.655733 GGAACGCAACGGGTATCATG 59.344 55.000 0.00 0.00 0.00 3.07
87 88 0.250793 TGGAACGCAACGGGTATCAT 59.749 50.000 0.00 0.00 0.00 2.45
88 89 0.250793 ATGGAACGCAACGGGTATCA 59.749 50.000 0.00 0.00 0.00 2.15
89 90 1.329599 GAATGGAACGCAACGGGTATC 59.670 52.381 0.00 0.00 0.00 2.24
90 91 1.375551 GAATGGAACGCAACGGGTAT 58.624 50.000 0.00 0.00 0.00 2.73
91 92 1.015085 CGAATGGAACGCAACGGGTA 61.015 55.000 0.00 0.00 0.00 3.69
92 93 2.322081 CGAATGGAACGCAACGGGT 61.322 57.895 0.00 0.00 0.00 5.28
93 94 2.235536 GACGAATGGAACGCAACGGG 62.236 60.000 0.00 0.00 0.00 5.28
94 95 1.131826 GACGAATGGAACGCAACGG 59.868 57.895 0.00 0.00 0.00 4.44
95 96 1.225368 CGACGAATGGAACGCAACG 60.225 57.895 0.00 0.00 0.00 4.10
96 97 0.450482 CACGACGAATGGAACGCAAC 60.450 55.000 0.00 0.00 0.00 4.17
97 98 1.561717 CCACGACGAATGGAACGCAA 61.562 55.000 0.00 0.00 39.87 4.85
98 99 2.024868 CCACGACGAATGGAACGCA 61.025 57.895 0.00 0.00 39.87 5.24
99 100 2.776072 CCACGACGAATGGAACGC 59.224 61.111 0.00 0.00 39.87 4.84
100 101 1.358725 ATGCCACGACGAATGGAACG 61.359 55.000 8.58 0.00 39.87 3.95
101 102 0.802494 AATGCCACGACGAATGGAAC 59.198 50.000 8.58 0.00 39.87 3.62
102 103 0.801872 CAATGCCACGACGAATGGAA 59.198 50.000 8.58 0.00 39.87 3.53
103 104 1.643868 GCAATGCCACGACGAATGGA 61.644 55.000 8.58 0.00 39.87 3.41
104 105 1.226379 GCAATGCCACGACGAATGG 60.226 57.895 0.00 0.00 40.50 3.16
105 106 4.365287 GCAATGCCACGACGAATG 57.635 55.556 0.00 0.00 0.00 2.67
115 116 0.740737 AGCAAGTAATCGGCAATGCC 59.259 50.000 15.52 15.52 46.75 4.40
116 117 2.454055 GAAGCAAGTAATCGGCAATGC 58.546 47.619 0.00 0.00 0.00 3.56
117 118 2.708514 CGAAGCAAGTAATCGGCAATG 58.291 47.619 0.00 0.00 33.15 2.82
123 124 2.690326 CCCCCGAAGCAAGTAATCG 58.310 57.895 0.00 0.00 36.39 3.34
138 139 2.428960 AAAACATTTGTCGCGCCCCC 62.429 55.000 0.00 0.00 0.00 5.40
139 140 1.006688 AAAACATTTGTCGCGCCCC 60.007 52.632 0.00 0.00 0.00 5.80
140 141 1.885814 GCAAAACATTTGTCGCGCCC 61.886 55.000 0.00 0.00 0.00 6.13
141 142 1.486801 GCAAAACATTTGTCGCGCC 59.513 52.632 0.00 0.00 0.00 6.53
142 143 1.211818 TGGCAAAACATTTGTCGCGC 61.212 50.000 0.00 0.00 0.00 6.86
143 144 0.502275 GTGGCAAAACATTTGTCGCG 59.498 50.000 0.00 0.00 0.00 5.87
144 145 1.565305 TGTGGCAAAACATTTGTCGC 58.435 45.000 12.60 12.60 35.32 5.19
145 146 2.475864 CCATGTGGCAAAACATTTGTCG 59.524 45.455 3.33 0.00 38.75 4.35
159 160 1.617804 GGATGGGGATATGCCATGTGG 60.618 57.143 15.93 0.00 38.95 4.17
160 161 1.075861 TGGATGGGGATATGCCATGTG 59.924 52.381 15.93 0.00 38.95 3.21
161 162 1.459117 TGGATGGGGATATGCCATGT 58.541 50.000 15.93 0.00 38.95 3.21
162 163 2.024751 TGATGGATGGGGATATGCCATG 60.025 50.000 15.93 0.00 39.32 3.66
163 164 2.290410 TGATGGATGGGGATATGCCAT 58.710 47.619 15.93 6.74 41.76 4.40
164 165 1.757799 TGATGGATGGGGATATGCCA 58.242 50.000 15.93 1.75 38.95 4.92
165 166 2.662866 CATGATGGATGGGGATATGCC 58.337 52.381 4.31 4.31 0.00 4.40
175 176 0.748450 GGGCAACACCATGATGGATG 59.252 55.000 20.11 14.58 41.78 3.51
176 177 0.632835 AGGGCAACACCATGATGGAT 59.367 50.000 20.11 2.50 41.78 3.41
177 178 2.086363 AGGGCAACACCATGATGGA 58.914 52.632 20.11 0.00 41.78 3.41
178 179 4.770540 AGGGCAACACCATGATGG 57.229 55.556 10.53 10.53 45.02 3.51
183 184 1.541169 TGGAACAGGGCAACACCAT 59.459 52.632 0.00 0.00 42.05 3.55
184 185 3.011014 TGGAACAGGGCAACACCA 58.989 55.556 0.00 0.00 42.05 4.17
195 196 3.621805 TTCCTCGGCGCTGGAACA 61.622 61.111 23.25 8.89 37.42 3.18
197 198 3.296709 GAGTTCCTCGGCGCTGGAA 62.297 63.158 23.25 23.25 39.73 3.53
198 199 3.760035 GAGTTCCTCGGCGCTGGA 61.760 66.667 17.88 14.40 0.00 3.86
199 200 3.589654 TTGAGTTCCTCGGCGCTGG 62.590 63.158 17.88 12.16 32.35 4.85
200 201 2.048222 TTGAGTTCCTCGGCGCTG 60.048 61.111 10.86 10.86 32.35 5.18
201 202 2.048127 GTTGAGTTCCTCGGCGCT 60.048 61.111 7.64 0.00 32.35 5.92
202 203 1.503818 TTTGTTGAGTTCCTCGGCGC 61.504 55.000 0.00 0.00 32.35 6.53
203 204 1.135972 CATTTGTTGAGTTCCTCGGCG 60.136 52.381 0.00 0.00 32.35 6.46
204 205 1.880027 ACATTTGTTGAGTTCCTCGGC 59.120 47.619 0.00 0.00 32.35 5.54
215 216 2.410517 GCAAGCGCATCAACATTTGTTG 60.411 45.455 11.47 15.63 46.11 3.33
216 217 1.794116 GCAAGCGCATCAACATTTGTT 59.206 42.857 11.47 0.00 37.05 2.83
217 218 1.421382 GCAAGCGCATCAACATTTGT 58.579 45.000 11.47 0.00 38.36 2.83
218 219 0.717224 GGCAAGCGCATCAACATTTG 59.283 50.000 11.47 3.47 41.24 2.32
219 220 0.317799 TGGCAAGCGCATCAACATTT 59.682 45.000 11.47 0.00 41.24 2.32
220 221 0.388907 GTGGCAAGCGCATCAACATT 60.389 50.000 11.47 0.00 41.24 2.71
221 222 1.213537 GTGGCAAGCGCATCAACAT 59.786 52.632 11.47 0.00 41.24 2.71
222 223 2.644418 GTGGCAAGCGCATCAACA 59.356 55.556 11.47 0.00 41.24 3.33
223 224 2.126346 GGTGGCAAGCGCATCAAC 60.126 61.111 11.47 0.83 41.24 3.18
276 278 1.741401 CATTTGTCGCGCTCCCTCA 60.741 57.895 5.56 0.00 0.00 3.86
282 284 1.066303 TGGAAAAACATTTGTCGCGCT 59.934 42.857 5.56 0.00 0.00 5.92
287 289 4.125703 TGCCATGTGGAAAAACATTTGTC 58.874 39.130 2.55 0.00 37.39 3.18
324 326 0.540365 CCTGAACAGGGCAACACCAT 60.540 55.000 12.54 0.00 44.87 3.55
341 343 4.749310 CTGAGTTGCTCGGCGCCT 62.749 66.667 26.68 2.51 38.05 5.52
348 350 3.072944 AGAAACATCTGCTGAGTTGCTC 58.927 45.455 9.25 5.63 0.00 4.26
351 353 3.666374 GCGAAGAAACATCTGCTGAGTTG 60.666 47.826 0.00 0.00 0.00 3.16
377 379 1.133869 GACACGTTAATGGCGGTGC 59.866 57.895 0.00 0.00 0.00 5.01
395 397 0.232303 GAGTGAACTCGGCAAACACG 59.768 55.000 0.00 0.00 36.71 4.49
508 510 0.110147 CACTCGTCAGACACCGACTC 60.110 60.000 0.41 0.00 0.00 3.36
528 530 2.726066 GCCAAAGACATTCGAGAAAGCG 60.726 50.000 0.00 0.00 0.00 4.68
548 550 1.224965 TTTCCATTTTTGCCAAGCGC 58.775 45.000 0.00 0.00 38.31 5.92
561 563 7.400339 TCTCCTACTCACTACTGAAATTTCCAT 59.600 37.037 15.48 6.17 0.00 3.41
566 568 8.282982 TCCTATCTCCTACTCACTACTGAAATT 58.717 37.037 0.00 0.00 0.00 1.82
612 1031 4.082841 TGCTATACGTGACGTAAAAGTCCA 60.083 41.667 22.28 12.76 45.39 4.02
630 1051 3.603158 TTCACGGTACACATGTGCTAT 57.397 42.857 25.68 9.21 33.69 2.97
757 1179 3.119495 TCATAGCATATGGTCACGGATCG 60.119 47.826 11.40 0.00 0.00 3.69
765 1187 8.625651 ACTAGTATTCGATCATAGCATATGGTC 58.374 37.037 11.40 0.77 0.00 4.02
766 1188 8.526667 ACTAGTATTCGATCATAGCATATGGT 57.473 34.615 12.78 12.78 0.00 3.55
772 1194 9.722184 ACTAGTAACTAGTATTCGATCATAGCA 57.278 33.333 0.00 0.00 44.35 3.49
790 1212 3.313526 TGTCGCCGAATCCTACTAGTAAC 59.686 47.826 3.76 0.00 0.00 2.50
791 1213 3.544684 TGTCGCCGAATCCTACTAGTAA 58.455 45.455 3.76 0.00 0.00 2.24
792 1214 3.136763 CTGTCGCCGAATCCTACTAGTA 58.863 50.000 1.89 1.89 0.00 1.82
793 1215 1.948145 CTGTCGCCGAATCCTACTAGT 59.052 52.381 0.00 0.00 0.00 2.57
794 1216 2.219458 TCTGTCGCCGAATCCTACTAG 58.781 52.381 0.00 0.00 0.00 2.57
795 1217 2.219458 CTCTGTCGCCGAATCCTACTA 58.781 52.381 0.00 0.00 0.00 1.82
796 1218 1.025812 CTCTGTCGCCGAATCCTACT 58.974 55.000 0.00 0.00 0.00 2.57
797 1219 0.739561 ACTCTGTCGCCGAATCCTAC 59.260 55.000 0.00 0.00 0.00 3.18
809 1231 1.672145 GCCTCCCAAACGTACTCTGTC 60.672 57.143 0.00 0.00 0.00 3.51
823 1245 2.181021 CGTGAGTGTACGCCTCCC 59.819 66.667 1.98 0.00 37.24 4.30
884 1314 3.193267 CGGGGTGTCAAATTTGTGATGAT 59.807 43.478 17.47 0.00 0.00 2.45
885 1315 2.556189 CGGGGTGTCAAATTTGTGATGA 59.444 45.455 17.47 0.00 0.00 2.92
886 1316 2.352617 CCGGGGTGTCAAATTTGTGATG 60.353 50.000 17.47 3.48 0.00 3.07
906 1336 0.765510 ATGAAGAATACGGGAGGGCC 59.234 55.000 0.00 0.00 0.00 5.80
907 1337 1.694696 AGATGAAGAATACGGGAGGGC 59.305 52.381 0.00 0.00 0.00 5.19
908 1338 2.700897 ACAGATGAAGAATACGGGAGGG 59.299 50.000 0.00 0.00 0.00 4.30
909 1339 3.243907 GGACAGATGAAGAATACGGGAGG 60.244 52.174 0.00 0.00 0.00 4.30
910 1340 3.384789 TGGACAGATGAAGAATACGGGAG 59.615 47.826 0.00 0.00 0.00 4.30
922 1352 4.147449 CGGCGGCTGGACAGATGA 62.147 66.667 7.61 0.00 0.00 2.92
943 1373 7.391148 TCTTATTGGTTGCCTAATTCTTCAC 57.609 36.000 0.00 0.00 0.00 3.18
951 1381 4.705023 GCTTCCTTCTTATTGGTTGCCTAA 59.295 41.667 0.00 0.00 0.00 2.69
952 1382 4.270008 GCTTCCTTCTTATTGGTTGCCTA 58.730 43.478 0.00 0.00 0.00 3.93
954 1384 2.166459 GGCTTCCTTCTTATTGGTTGCC 59.834 50.000 0.00 0.00 36.42 4.52
955 1385 2.159379 CGGCTTCCTTCTTATTGGTTGC 60.159 50.000 0.00 0.00 0.00 4.17
957 1387 3.610911 CTCGGCTTCCTTCTTATTGGTT 58.389 45.455 0.00 0.00 0.00 3.67
983 1437 0.745845 CATCTTCTTGGCCGTGGGAG 60.746 60.000 0.00 0.00 0.00 4.30
1052 1506 0.586802 GATATCGCGTGCCCTTTTCC 59.413 55.000 5.77 0.00 0.00 3.13
1069 1523 3.411517 CTGGGTGGGCTTCGGGAT 61.412 66.667 0.00 0.00 0.00 3.85
1226 1680 1.375908 TTGGAGCAGATGTCGGTGC 60.376 57.895 0.00 0.00 40.17 5.01
1308 1762 3.364964 GGCAGATGTTTTCGAACGTGAAT 60.365 43.478 0.00 0.00 0.00 2.57
1334 1788 2.061028 CGTGCCCTTTTCTTGATTTGC 58.939 47.619 0.00 0.00 0.00 3.68
1343 1797 1.901464 TCCTTGGCGTGCCCTTTTC 60.901 57.895 8.69 0.00 34.56 2.29
1365 1819 4.637489 CAGCTCTCGATCCGGGCG 62.637 72.222 0.00 6.44 0.00 6.13
1368 1822 1.066587 GAACCAGCTCTCGATCCGG 59.933 63.158 0.00 0.00 0.00 5.14
1369 1823 1.066587 GGAACCAGCTCTCGATCCG 59.933 63.158 0.00 0.00 0.00 4.18
1378 1832 3.322466 CCGGGAGTGGAACCAGCT 61.322 66.667 0.00 0.00 37.80 4.24
1408 1862 3.164268 AGCTGATATCAAGCTCCTCGAT 58.836 45.455 18.33 0.00 32.98 3.59
1452 1906 1.474332 GGTACCGGTTCCTGGACACA 61.474 60.000 22.13 0.00 0.00 3.72
1528 1982 2.306805 TCTCACTTGGGAATCTGCACAT 59.693 45.455 0.00 0.00 0.00 3.21
1536 1990 2.042162 AGGTGCAATCTCACTTGGGAAT 59.958 45.455 0.00 0.00 37.16 3.01
1600 2054 1.576356 GCTTCCTCCGACATGCTAAG 58.424 55.000 0.00 0.00 0.00 2.18
1608 2062 1.078143 ATGCAAGGCTTCCTCCGAC 60.078 57.895 0.00 0.00 30.89 4.79
1707 2161 3.036819 CCAGATGATCCTCAGAGTTGGA 58.963 50.000 0.62 0.00 36.72 3.53
1735 2189 3.370953 CCTTGTCTCCCCAAATGAGTAGG 60.371 52.174 0.00 0.00 0.00 3.18
1743 2197 1.786441 ACCAATCCTTGTCTCCCCAAA 59.214 47.619 0.00 0.00 0.00 3.28
1757 2211 2.545322 GGGACGTCCTCGATAACCAATC 60.545 54.545 32.52 8.65 40.62 2.67
1917 2371 1.282157 AGAGACAATAAGGGTGGTGCC 59.718 52.381 0.00 0.00 0.00 5.01
1946 2404 4.471904 TTCTGCATCGTCTAGGATTTGT 57.528 40.909 0.00 0.00 0.00 2.83
2078 2539 3.748568 GGAGGATATTGAGAACCGCATTC 59.251 47.826 0.00 0.00 37.62 2.67
2101 2562 1.719063 TTCCAAGCAGGGGAAGCACT 61.719 55.000 0.18 0.00 39.44 4.40
2127 2588 7.147312 ACAAAATGGTCACTTACAATGACATG 58.853 34.615 7.38 0.00 46.89 3.21
2190 2651 9.635520 GTTGCTAACTAGTTGACTTAGAATACA 57.364 33.333 18.56 0.00 0.00 2.29
2191 2652 9.857957 AGTTGCTAACTAGTTGACTTAGAATAC 57.142 33.333 18.56 6.21 40.69 1.89
2193 2654 9.857957 GTAGTTGCTAACTAGTTGACTTAGAAT 57.142 33.333 18.56 0.36 44.16 2.40
2195 2656 8.632906 AGTAGTTGCTAACTAGTTGACTTAGA 57.367 34.615 18.56 0.00 43.36 2.10
2239 2701 2.430367 GTCCCACTGCGAAAGGGT 59.570 61.111 0.62 0.00 43.31 4.34
2259 2721 7.470702 ATGTCGATCATCTCTACCTTTAAGGTG 60.471 40.741 25.38 15.26 39.90 4.00
2331 2793 7.687941 ATTATTCAACACCAGTACTTTGAGG 57.312 36.000 8.03 2.18 29.96 3.86
2403 2866 7.136119 TGATTTCTTTTACGACTTTCGCATTT 58.864 30.769 0.00 0.00 45.12 2.32
2565 9746 4.182693 TGGTAAGTCACTTGTATCCACG 57.817 45.455 0.00 0.00 0.00 4.94
2605 9786 4.500716 CCCATTGGCAAAGTTAAAACGACT 60.501 41.667 3.01 0.00 0.00 4.18
2635 9816 1.064357 GAAAACGAAACGCCAAGTCCA 59.936 47.619 0.00 0.00 0.00 4.02
2636 9817 1.332686 AGAAAACGAAACGCCAAGTCC 59.667 47.619 0.00 0.00 0.00 3.85
2640 9821 3.434299 GGATCTAGAAAACGAAACGCCAA 59.566 43.478 0.00 0.00 0.00 4.52
2698 9879 5.710099 ACTCTTCTTTTGAGAACACAAACCA 59.290 36.000 0.00 0.00 39.08 3.67
2699 9880 6.196079 ACTCTTCTTTTGAGAACACAAACC 57.804 37.500 0.00 0.00 39.08 3.27
2700 9881 7.857885 CCATACTCTTCTTTTGAGAACACAAAC 59.142 37.037 0.00 0.00 39.08 2.93
2701 9882 7.773224 TCCATACTCTTCTTTTGAGAACACAAA 59.227 33.333 0.00 0.00 37.87 2.83
2702 9883 7.279615 TCCATACTCTTCTTTTGAGAACACAA 58.720 34.615 0.00 0.00 35.66 3.33
2703 9884 6.826668 TCCATACTCTTCTTTTGAGAACACA 58.173 36.000 0.00 0.00 35.66 3.72
2704 9885 7.625185 GCATCCATACTCTTCTTTTGAGAACAC 60.625 40.741 0.00 0.00 35.66 3.32
2779 9969 2.673368 CACGTTGATTGGAACTAGCCTC 59.327 50.000 0.00 0.00 0.00 4.70
2818 10008 4.816385 GCGAACAAGGATGGATAATTCAGA 59.184 41.667 0.00 0.00 0.00 3.27
2938 10128 6.544564 TGAAGACGAGGGAGTTTATTGTTTTT 59.455 34.615 0.00 0.00 0.00 1.94
2947 10137 2.037381 GGAGTTGAAGACGAGGGAGTTT 59.963 50.000 0.00 0.00 0.00 2.66
2970 10160 4.910746 ACAACATCGAGTTTCTCATTCG 57.089 40.909 0.00 0.00 38.74 3.34
2974 10164 4.944048 TGAGAACAACATCGAGTTTCTCA 58.056 39.130 18.20 18.20 45.22 3.27
3007 10197 0.602905 CTTGTTCTTCGGGCGTCCTT 60.603 55.000 3.66 0.00 0.00 3.36
3066 10258 6.925610 ATTATAGCAGATGAGCAACGAAAA 57.074 33.333 0.00 0.00 36.85 2.29
3117 10309 8.936864 AGAGTTCAAGTTTAATCAAAGGTATCG 58.063 33.333 0.00 0.00 0.00 2.92
3305 10499 3.502051 ATAGGGACCAAGGGTGTAAGA 57.498 47.619 0.00 0.00 35.25 2.10
3347 10541 5.989477 TCGATCAATTGTTCAATAGGGACT 58.011 37.500 15.11 0.00 46.37 3.85
3430 10624 6.959639 ACTTCCCATAATAATCACGCAATT 57.040 33.333 0.00 0.00 0.00 2.32
3436 10630 7.661437 TCTGCATGTACTTCCCATAATAATCAC 59.339 37.037 0.00 0.00 0.00 3.06
3449 10648 8.430801 AGAAATATTGTCTCTGCATGTACTTC 57.569 34.615 0.00 0.00 0.00 3.01
3457 10656 5.660460 TCGCTAAGAAATATTGTCTCTGCA 58.340 37.500 15.75 0.00 0.00 4.41
3459 10658 7.706281 ACATCGCTAAGAAATATTGTCTCTG 57.294 36.000 0.00 0.00 0.00 3.35
3460 10659 7.981789 TGAACATCGCTAAGAAATATTGTCTCT 59.018 33.333 0.00 0.00 0.00 3.10
3466 10665 7.011482 GGTCACTGAACATCGCTAAGAAATATT 59.989 37.037 0.00 0.00 0.00 1.28
3481 10680 1.070134 GTAGGCACTGGTCACTGAACA 59.930 52.381 0.00 0.00 41.52 3.18
3485 10684 2.289631 TGAATGTAGGCACTGGTCACTG 60.290 50.000 0.00 0.00 41.52 3.66
3486 10685 1.977854 TGAATGTAGGCACTGGTCACT 59.022 47.619 0.00 0.00 41.52 3.41
3487 10686 2.076863 GTGAATGTAGGCACTGGTCAC 58.923 52.381 0.00 0.00 41.52 3.67
3488 10687 1.696884 TGTGAATGTAGGCACTGGTCA 59.303 47.619 0.00 0.00 41.52 4.02
3489 10688 2.472695 TGTGAATGTAGGCACTGGTC 57.527 50.000 0.00 0.00 41.52 4.02
3490 10689 2.618816 CCATGTGAATGTAGGCACTGGT 60.619 50.000 0.00 0.00 41.52 4.00
3491 10690 2.019249 CCATGTGAATGTAGGCACTGG 58.981 52.381 0.00 0.00 41.52 4.00
3497 10696 3.812262 TCTCATGCCATGTGAATGTAGG 58.188 45.455 6.97 0.00 30.64 3.18
3561 10767 4.937620 TCTAATAGCCTTGACAAGCTTGTG 59.062 41.667 35.67 21.69 42.43 3.33
3592 10798 0.249489 GTAGGCTGGCATAGTGGTCG 60.249 60.000 3.38 0.00 0.00 4.79
3601 10807 0.179084 GTAATCGCTGTAGGCTGGCA 60.179 55.000 3.38 0.00 39.13 4.92
3631 10837 9.553064 CTTGTGTAGGCTAAATAGAAGATCAAT 57.447 33.333 0.00 0.00 0.00 2.57
3632 10838 7.495934 GCTTGTGTAGGCTAAATAGAAGATCAA 59.504 37.037 12.66 0.02 0.00 2.57


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

AutoCloner maintained by Alex Coulton.