Multiple sequence alignment - TraesCS6A01G016000

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 TraesCS6A01G016000 chr6A 100.000 3173 0 0 1 3173 7985776 7988948 0.000000e+00 5860.0
1 TraesCS6A01G016000 chr6A 90.686 1836 135 13 868 2680 8202477 8200655 0.000000e+00 2410.0
2 TraesCS6A01G016000 chr6A 90.228 307 20 3 2867 3173 8200662 8200366 2.970000e-105 392.0
3 TraesCS6A01G016000 chr6B 91.257 2116 134 17 576 2681 14623157 14621083 0.000000e+00 2835.0
4 TraesCS6A01G016000 chr6B 86.325 1755 179 40 953 2658 14330391 14332133 0.000000e+00 1855.0
5 TraesCS6A01G016000 chr6B 90.944 1314 111 7 1092 2398 14550129 14548817 0.000000e+00 1760.0
6 TraesCS6A01G016000 chr6B 91.304 299 18 4 2877 3173 14548500 14548208 4.930000e-108 401.0
7 TraesCS6A01G016000 chr6B 88.599 307 25 5 2867 3173 14621091 14620795 6.470000e-97 364.0
8 TraesCS6A01G016000 chr6B 88.095 294 20 11 2397 2681 14548787 14548500 5.070000e-88 335.0
9 TraesCS6A01G016000 chr6B 88.256 281 25 4 2875 3153 14332139 14332413 2.360000e-86 329.0
10 TraesCS6A01G016000 chr6B 90.588 255 12 5 576 828 14329766 14330010 8.490000e-86 327.0
11 TraesCS6A01G016000 chr6D 89.577 2082 164 25 609 2681 7994627 7992590 0.000000e+00 2593.0
12 TraesCS6A01G016000 chr6D 91.054 1509 118 7 1185 2681 7715848 7717351 0.000000e+00 2023.0
13 TraesCS6A01G016000 chr6D 95.362 345 13 2 576 918 7715516 7715859 2.150000e-151 545.0
14 TraesCS6A01G016000 chr6D 96.078 306 9 1 2868 3173 7717344 7717646 2.200000e-136 496.0
15 TraesCS6A01G016000 chr6D 88.665 397 24 10 191 581 7713947 7714328 6.200000e-127 464.0
16 TraesCS6A01G016000 chr6D 88.274 307 26 5 2867 3173 7992598 7992302 3.010000e-95 359.0
17 TraesCS6A01G016000 chr6D 95.897 195 7 1 1 195 7698825 7699018 6.610000e-82 315.0
18 TraesCS6A01G016000 chr1B 92.523 1605 104 8 1092 2681 27752870 27751267 0.000000e+00 2285.0
19 TraesCS6A01G016000 chr1B 85.839 1829 187 40 900 2681 27678219 27676416 0.000000e+00 1877.0
20 TraesCS6A01G016000 chr1B 77.998 1159 231 20 1062 2210 630644799 630645943 0.000000e+00 706.0
21 TraesCS6A01G016000 chr1B 91.349 393 31 3 1092 1481 27364510 27364118 4.660000e-148 534.0
22 TraesCS6A01G016000 chr1B 94.313 211 7 5 2673 2881 242247014 242246807 5.110000e-83 318.0
23 TraesCS6A01G016000 chr1B 96.154 130 5 0 2868 2997 27751274 27751145 2.480000e-51 213.0
24 TraesCS6A01G016000 chr1B 92.958 142 10 0 3032 3173 27751145 27751004 1.150000e-49 207.0
25 TraesCS6A01G016000 chr5A 86.477 1649 185 21 901 2532 650824447 650826074 0.000000e+00 1775.0
26 TraesCS6A01G016000 chr5A 95.169 207 5 5 2661 2864 569174111 569174315 3.950000e-84 322.0
27 TraesCS6A01G016000 chr5D 86.328 1653 185 21 899 2532 524577419 524579049 0.000000e+00 1762.0
28 TraesCS6A01G016000 chr5D 88.971 272 25 3 2904 3173 524579050 524579318 6.560000e-87 331.0
29 TraesCS6A01G016000 chr5D 94.712 208 9 2 2680 2886 488352509 488352303 3.950000e-84 322.0
30 TraesCS6A01G016000 chr5D 90.909 77 5 2 3085 3160 42074537 42074612 5.600000e-18 102.0
31 TraesCS6A01G016000 chr5B 76.642 1096 241 13 1093 2179 556628164 556627075 2.730000e-165 592.0
32 TraesCS6A01G016000 chr4A 96.500 200 6 1 2678 2877 124610412 124610214 2.360000e-86 329.0
33 TraesCS6A01G016000 chr3A 94.860 214 6 4 2667 2878 323103759 323103969 2.360000e-86 329.0
34 TraesCS6A01G016000 chr3A 93.839 211 11 1 2670 2878 686191006 686191216 1.840000e-82 316.0
35 TraesCS6A01G016000 chr1A 96.040 202 6 2 2675 2875 290344229 290344429 8.490000e-86 327.0
36 TraesCS6A01G016000 chr2A 94.686 207 9 2 2679 2884 718110620 718110415 1.420000e-83 320.0
37 TraesCS6A01G016000 chr7A 93.458 214 10 4 2669 2879 30261654 30261866 6.610000e-82 315.0
38 TraesCS6A01G016000 chr1D 84.000 150 11 6 1 150 453543643 453543507 7.140000e-27 132.0
39 TraesCS6A01G016000 chr2B 90.698 43 2 2 225 266 647739817 647739776 4.420000e-04 56.5


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 TraesCS6A01G016000 chr6A 7985776 7988948 3172 False 5860.000000 5860 100.000000 1 3173 1 chr6A.!!$F1 3172
1 TraesCS6A01G016000 chr6A 8200366 8202477 2111 True 1401.000000 2410 90.457000 868 3173 2 chr6A.!!$R1 2305
2 TraesCS6A01G016000 chr6B 14620795 14623157 2362 True 1599.500000 2835 89.928000 576 3173 2 chr6B.!!$R2 2597
3 TraesCS6A01G016000 chr6B 14329766 14332413 2647 False 837.000000 1855 88.389667 576 3153 3 chr6B.!!$F1 2577
4 TraesCS6A01G016000 chr6B 14548208 14550129 1921 True 832.000000 1760 90.114333 1092 3173 3 chr6B.!!$R1 2081
5 TraesCS6A01G016000 chr6D 7992302 7994627 2325 True 1476.000000 2593 88.925500 609 3173 2 chr6D.!!$R1 2564
6 TraesCS6A01G016000 chr6D 7713947 7717646 3699 False 882.000000 2023 92.789750 191 3173 4 chr6D.!!$F2 2982
7 TraesCS6A01G016000 chr1B 27676416 27678219 1803 True 1877.000000 1877 85.839000 900 2681 1 chr1B.!!$R2 1781
8 TraesCS6A01G016000 chr1B 27751004 27752870 1866 True 901.666667 2285 93.878333 1092 3173 3 chr1B.!!$R4 2081
9 TraesCS6A01G016000 chr1B 630644799 630645943 1144 False 706.000000 706 77.998000 1062 2210 1 chr1B.!!$F1 1148
10 TraesCS6A01G016000 chr5A 650824447 650826074 1627 False 1775.000000 1775 86.477000 901 2532 1 chr5A.!!$F2 1631
11 TraesCS6A01G016000 chr5D 524577419 524579318 1899 False 1046.500000 1762 87.649500 899 3173 2 chr5D.!!$F2 2274
12 TraesCS6A01G016000 chr5B 556627075 556628164 1089 True 592.000000 592 76.642000 1093 2179 1 chr5B.!!$R1 1086

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
548 555 0.253044 ACATAGAGGGCAACGCACAT 59.747 50.0 0.0 0.0 32.33 3.21 F
1398 2959 0.033228 GCCTGTCAGATCCCGAGATG 59.967 60.0 0.0 0.0 30.90 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 3684 2.285977 TGCAAGCATCAGCATAGTCTG 58.714 47.619 0.00 0.00 45.49 3.51 R
2847 4497 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06 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
31 32 9.816354 AGAATTTATTGGTTATTATGTTGGCAC 57.184 29.630 0.00 0.00 0.00 5.01
32 33 9.593134 GAATTTATTGGTTATTATGTTGGCACA 57.407 29.630 0.00 0.00 37.31 4.57
55 56 9.502145 CACAAATGCACAACGAATTATACTATT 57.498 29.630 0.00 0.00 0.00 1.73
59 60 9.502145 AATGCACAACGAATTATACTATTTGTG 57.498 29.630 7.10 7.10 39.90 3.33
60 61 8.035165 TGCACAACGAATTATACTATTTGTGT 57.965 30.769 11.86 3.15 39.33 3.72
61 62 8.508062 TGCACAACGAATTATACTATTTGTGTT 58.492 29.630 11.86 0.00 39.33 3.32
62 63 8.995906 GCACAACGAATTATACTATTTGTGTTC 58.004 33.333 11.86 0.00 39.33 3.18
67 68 9.524106 ACGAATTATACTATTTGTGTTCATCGA 57.476 29.630 0.00 0.00 32.22 3.59
115 116 6.671614 AAGCATATTGTTTGAATTGCATGG 57.328 33.333 0.00 0.00 32.66 3.66
116 117 5.736813 AGCATATTGTTTGAATTGCATGGT 58.263 33.333 0.00 0.00 32.66 3.55
117 118 6.174760 AGCATATTGTTTGAATTGCATGGTT 58.825 32.000 0.00 0.00 32.66 3.67
118 119 6.314400 AGCATATTGTTTGAATTGCATGGTTC 59.686 34.615 0.00 0.00 32.66 3.62
119 120 6.457257 GCATATTGTTTGAATTGCATGGTTCC 60.457 38.462 0.00 0.00 0.00 3.62
120 121 4.412796 TTGTTTGAATTGCATGGTTCCA 57.587 36.364 0.00 0.00 0.00 3.53
121 122 4.412796 TGTTTGAATTGCATGGTTCCAA 57.587 36.364 0.00 0.00 0.00 3.53
122 123 4.774124 TGTTTGAATTGCATGGTTCCAAA 58.226 34.783 0.00 0.00 0.00 3.28
123 124 4.815308 TGTTTGAATTGCATGGTTCCAAAG 59.185 37.500 0.00 0.00 0.00 2.77
124 125 4.686191 TTGAATTGCATGGTTCCAAAGT 57.314 36.364 0.00 0.00 0.00 2.66
125 126 4.686191 TGAATTGCATGGTTCCAAAGTT 57.314 36.364 0.00 0.00 0.00 2.66
126 127 5.798125 TGAATTGCATGGTTCCAAAGTTA 57.202 34.783 0.00 0.00 0.00 2.24
127 128 6.166984 TGAATTGCATGGTTCCAAAGTTAA 57.833 33.333 0.00 0.00 0.00 2.01
128 129 6.586344 TGAATTGCATGGTTCCAAAGTTAAA 58.414 32.000 0.00 0.00 0.00 1.52
129 130 6.481644 TGAATTGCATGGTTCCAAAGTTAAAC 59.518 34.615 0.00 0.00 0.00 2.01
130 131 5.606348 TTGCATGGTTCCAAAGTTAAACT 57.394 34.783 0.00 0.00 0.00 2.66
131 132 5.606348 TGCATGGTTCCAAAGTTAAACTT 57.394 34.783 0.00 0.00 40.80 2.66
132 133 6.716934 TGCATGGTTCCAAAGTTAAACTTA 57.283 33.333 0.00 0.00 37.47 2.24
133 134 7.296628 TGCATGGTTCCAAAGTTAAACTTAT 57.703 32.000 0.00 0.00 37.47 1.73
134 135 7.731054 TGCATGGTTCCAAAGTTAAACTTATT 58.269 30.769 0.00 0.00 37.47 1.40
135 136 7.870445 TGCATGGTTCCAAAGTTAAACTTATTC 59.130 33.333 0.00 0.00 37.47 1.75
136 137 7.061789 GCATGGTTCCAAAGTTAAACTTATTCG 59.938 37.037 0.00 0.00 37.47 3.34
137 138 7.804843 TGGTTCCAAAGTTAAACTTATTCGA 57.195 32.000 0.00 0.00 37.47 3.71
138 139 7.641760 TGGTTCCAAAGTTAAACTTATTCGAC 58.358 34.615 0.00 0.00 37.47 4.20
139 140 7.282675 TGGTTCCAAAGTTAAACTTATTCGACA 59.717 33.333 0.00 0.00 37.47 4.35
140 141 8.294577 GGTTCCAAAGTTAAACTTATTCGACAT 58.705 33.333 0.00 0.00 37.47 3.06
141 142 9.673454 GTTCCAAAGTTAAACTTATTCGACATT 57.327 29.630 0.00 0.00 37.47 2.71
142 143 9.672086 TTCCAAAGTTAAACTTATTCGACATTG 57.328 29.630 0.00 0.00 37.47 2.82
143 144 8.293867 TCCAAAGTTAAACTTATTCGACATTGG 58.706 33.333 0.00 0.00 37.47 3.16
144 145 8.079809 CCAAAGTTAAACTTATTCGACATTGGT 58.920 33.333 0.00 0.00 37.47 3.67
145 146 9.458374 CAAAGTTAAACTTATTCGACATTGGTT 57.542 29.630 0.00 0.00 37.47 3.67
146 147 9.673454 AAAGTTAAACTTATTCGACATTGGTTC 57.327 29.630 0.00 0.00 37.47 3.62
147 148 8.617290 AGTTAAACTTATTCGACATTGGTTCT 57.383 30.769 0.00 0.00 0.00 3.01
148 149 9.063615 AGTTAAACTTATTCGACATTGGTTCTT 57.936 29.630 0.00 0.00 0.00 2.52
151 152 6.980051 ACTTATTCGACATTGGTTCTTACC 57.020 37.500 0.00 0.00 45.26 2.85
159 160 4.926207 GGTTCTTACCGCCATCGT 57.074 55.556 0.00 0.00 34.01 3.73
160 161 2.380081 GGTTCTTACCGCCATCGTG 58.620 57.895 0.00 0.00 34.01 4.35
161 162 1.702491 GGTTCTTACCGCCATCGTGC 61.702 60.000 0.00 0.00 34.01 5.34
170 171 3.803082 CCATCGTGCGTGGCCAAG 61.803 66.667 15.06 15.06 0.00 3.61
171 172 2.741985 CATCGTGCGTGGCCAAGA 60.742 61.111 23.82 10.47 0.00 3.02
172 173 2.031919 ATCGTGCGTGGCCAAGAA 59.968 55.556 23.82 9.61 0.00 2.52
173 174 1.599518 ATCGTGCGTGGCCAAGAAA 60.600 52.632 23.82 6.63 0.00 2.52
174 175 0.960364 ATCGTGCGTGGCCAAGAAAT 60.960 50.000 23.82 0.00 0.00 2.17
175 176 0.320858 TCGTGCGTGGCCAAGAAATA 60.321 50.000 23.82 0.00 0.00 1.40
176 177 0.519519 CGTGCGTGGCCAAGAAATAA 59.480 50.000 23.82 0.00 0.00 1.40
177 178 1.132262 CGTGCGTGGCCAAGAAATAAT 59.868 47.619 23.82 0.00 0.00 1.28
178 179 2.791158 CGTGCGTGGCCAAGAAATAATC 60.791 50.000 23.82 2.99 0.00 1.75
179 180 1.748493 TGCGTGGCCAAGAAATAATCC 59.252 47.619 23.82 2.21 0.00 3.01
180 181 1.748493 GCGTGGCCAAGAAATAATCCA 59.252 47.619 23.82 0.00 0.00 3.41
181 182 2.165437 GCGTGGCCAAGAAATAATCCAA 59.835 45.455 23.82 0.00 0.00 3.53
182 183 3.769536 CGTGGCCAAGAAATAATCCAAC 58.230 45.455 14.14 0.00 0.00 3.77
183 184 3.443681 CGTGGCCAAGAAATAATCCAACT 59.556 43.478 14.14 0.00 0.00 3.16
184 185 4.638421 CGTGGCCAAGAAATAATCCAACTA 59.362 41.667 14.14 0.00 0.00 2.24
185 186 5.220854 CGTGGCCAAGAAATAATCCAACTAG 60.221 44.000 14.14 0.00 0.00 2.57
186 187 5.885912 GTGGCCAAGAAATAATCCAACTAGA 59.114 40.000 7.24 0.00 0.00 2.43
187 188 6.547510 GTGGCCAAGAAATAATCCAACTAGAT 59.452 38.462 7.24 0.00 0.00 1.98
188 189 7.719633 GTGGCCAAGAAATAATCCAACTAGATA 59.280 37.037 7.24 0.00 0.00 1.98
189 190 8.448008 TGGCCAAGAAATAATCCAACTAGATAT 58.552 33.333 0.61 0.00 0.00 1.63
302 305 8.006564 ACAATCATAATACCCTCAAATGTGGAT 58.993 33.333 3.15 0.00 0.00 3.41
313 316 4.331968 TCAAATGTGGATCCTGGTTGTAC 58.668 43.478 14.23 0.88 0.00 2.90
367 370 8.948401 AGATACATACATGACCTAACTCAGAT 57.052 34.615 0.00 0.00 0.00 2.90
371 374 8.484214 ACATACATGACCTAACTCAGATACAT 57.516 34.615 0.00 0.00 0.00 2.29
372 375 9.588096 ACATACATGACCTAACTCAGATACATA 57.412 33.333 0.00 0.00 0.00 2.29
374 377 7.898014 ACATGACCTAACTCAGATACATACA 57.102 36.000 0.00 0.00 0.00 2.29
375 378 8.484214 ACATGACCTAACTCAGATACATACAT 57.516 34.615 0.00 0.00 0.00 2.29
376 379 9.588096 ACATGACCTAACTCAGATACATACATA 57.412 33.333 0.00 0.00 0.00 2.29
377 380 9.847706 CATGACCTAACTCAGATACATACATAC 57.152 37.037 0.00 0.00 0.00 2.39
378 381 8.990163 TGACCTAACTCAGATACATACATACA 57.010 34.615 0.00 0.00 0.00 2.29
379 382 9.588096 TGACCTAACTCAGATACATACATACAT 57.412 33.333 0.00 0.00 0.00 2.29
418 421 4.871933 ACATACATACATCGATCTGCCA 57.128 40.909 0.00 0.00 0.00 4.92
460 467 4.681978 GACGGGCGCTTGGTGTCT 62.682 66.667 7.64 0.00 0.00 3.41
540 547 3.008835 ACACGTACTACATAGAGGGCA 57.991 47.619 0.00 0.00 0.00 5.36
546 553 1.134788 ACTACATAGAGGGCAACGCAC 60.135 52.381 0.00 0.00 37.60 5.34
548 555 0.253044 ACATAGAGGGCAACGCACAT 59.747 50.000 0.00 0.00 32.33 3.21
551 558 0.323302 TAGAGGGCAACGCACATGAA 59.677 50.000 0.00 0.00 32.33 2.57
594 1794 3.959535 AGCAGACAGAAGAGAAGGAAG 57.040 47.619 0.00 0.00 0.00 3.46
601 1801 1.349357 AGAAGAGAAGGAAGCCCACAC 59.651 52.381 0.00 0.00 33.88 3.82
828 2033 5.743026 TGCACAAACATAACGAGAGAAAA 57.257 34.783 0.00 0.00 0.00 2.29
1176 2737 4.767255 GTCTCCACCTGCGGCCTG 62.767 72.222 0.00 0.00 0.00 4.85
1398 2959 0.033228 GCCTGTCAGATCCCGAGATG 59.967 60.000 0.00 0.00 30.90 2.90
1399 2960 0.678395 CCTGTCAGATCCCGAGATGG 59.322 60.000 0.00 0.00 30.90 3.51
1571 3138 4.481112 CAAGCCCAATGTCGCGGC 62.481 66.667 2.29 2.29 43.35 6.53
1654 3221 0.038159 GCTCACCTGCAACGTAGAGT 60.038 55.000 0.00 0.00 0.00 3.24
1954 3521 1.065701 CCGTAATGCTCTCGTACAGCT 59.934 52.381 5.40 0.00 37.79 4.24
2117 3684 4.783621 TGCACCATGCCTCGCTCC 62.784 66.667 0.00 0.00 44.23 4.70
2197 3766 4.610945 CAAGGATTGGTTATGGAAATCGC 58.389 43.478 0.00 0.00 43.94 4.58
2334 3921 1.026182 TTGGTCGCTGCTAATGCCTG 61.026 55.000 0.00 0.00 38.71 4.85
2429 4066 3.461061 CATCGCCTGCAATCTCTAGAAA 58.539 45.455 0.00 0.00 0.00 2.52
2430 4067 3.827008 TCGCCTGCAATCTCTAGAAAT 57.173 42.857 0.00 0.00 0.00 2.17
2440 4077 6.099413 TGCAATCTCTAGAAATGAGAGTCCAT 59.901 38.462 0.00 0.00 42.85 3.41
2686 4336 8.934023 TCCAGGTTATGTTTAGAAAAATCAGT 57.066 30.769 0.00 0.00 0.00 3.41
2687 4337 9.362151 TCCAGGTTATGTTTAGAAAAATCAGTT 57.638 29.630 0.00 0.00 0.00 3.16
2688 4338 9.981114 CCAGGTTATGTTTAGAAAAATCAGTTT 57.019 29.630 0.00 0.00 0.00 2.66
2724 4374 8.992835 CATCTAGATGTGCTATAAGTATTGCA 57.007 34.615 22.42 3.73 40.96 4.08
2734 4384 8.818141 TGCTATAAGTATTGCACATCTAAGTC 57.182 34.615 3.73 0.00 38.99 3.01
2735 4385 7.872993 TGCTATAAGTATTGCACATCTAAGTCC 59.127 37.037 3.73 0.00 38.99 3.85
2736 4386 8.091449 GCTATAAGTATTGCACATCTAAGTCCT 58.909 37.037 0.00 0.00 35.12 3.85
2739 4389 9.935241 ATAAGTATTGCACATCTAAGTCCTATG 57.065 33.333 0.00 0.00 0.00 2.23
2740 4390 7.366847 AGTATTGCACATCTAAGTCCTATGT 57.633 36.000 0.00 0.00 34.22 2.29
2741 4391 7.437748 AGTATTGCACATCTAAGTCCTATGTC 58.562 38.462 0.00 0.00 31.60 3.06
2742 4392 5.675684 TTGCACATCTAAGTCCTATGTCA 57.324 39.130 0.00 0.00 31.60 3.58
2743 4393 5.876651 TGCACATCTAAGTCCTATGTCAT 57.123 39.130 0.00 0.00 31.60 3.06
2744 4394 6.239217 TGCACATCTAAGTCCTATGTCATT 57.761 37.500 0.00 0.00 31.60 2.57
2745 4395 6.051074 TGCACATCTAAGTCCTATGTCATTG 58.949 40.000 0.00 0.00 31.60 2.82
2746 4396 6.127083 TGCACATCTAAGTCCTATGTCATTGA 60.127 38.462 0.00 0.00 31.60 2.57
2747 4397 6.933521 GCACATCTAAGTCCTATGTCATTGAT 59.066 38.462 0.00 0.00 31.60 2.57
2748 4398 7.117523 GCACATCTAAGTCCTATGTCATTGATC 59.882 40.741 0.00 0.00 31.60 2.92
2749 4399 8.366401 CACATCTAAGTCCTATGTCATTGATCT 58.634 37.037 0.00 0.00 31.60 2.75
2750 4400 8.932610 ACATCTAAGTCCTATGTCATTGATCTT 58.067 33.333 0.00 0.82 0.00 2.40
2753 4403 8.568794 TCTAAGTCCTATGTCATTGATCTTACG 58.431 37.037 0.00 0.00 0.00 3.18
2754 4404 6.716934 AGTCCTATGTCATTGATCTTACGT 57.283 37.500 0.00 0.00 0.00 3.57
2755 4405 7.113658 AGTCCTATGTCATTGATCTTACGTT 57.886 36.000 0.00 0.00 0.00 3.99
2756 4406 6.980978 AGTCCTATGTCATTGATCTTACGTTG 59.019 38.462 0.00 0.00 0.00 4.10
2757 4407 6.978659 GTCCTATGTCATTGATCTTACGTTGA 59.021 38.462 0.00 0.00 0.00 3.18
2758 4408 7.168302 GTCCTATGTCATTGATCTTACGTTGAG 59.832 40.741 0.00 0.00 0.00 3.02
2759 4409 7.068226 TCCTATGTCATTGATCTTACGTTGAGA 59.932 37.037 0.00 0.00 0.00 3.27
2760 4410 7.869937 CCTATGTCATTGATCTTACGTTGAGAT 59.130 37.037 12.34 12.34 36.60 2.75
2761 4411 9.254133 CTATGTCATTGATCTTACGTTGAGATT 57.746 33.333 13.35 0.00 34.13 2.40
2762 4412 7.525688 TGTCATTGATCTTACGTTGAGATTC 57.474 36.000 13.35 8.73 34.13 2.52
2763 4413 6.253512 TGTCATTGATCTTACGTTGAGATTCG 59.746 38.462 13.35 5.46 34.13 3.34
2764 4414 6.253727 GTCATTGATCTTACGTTGAGATTCGT 59.746 38.462 13.35 0.00 42.82 3.85
2765 4415 6.253512 TCATTGATCTTACGTTGAGATTCGTG 59.746 38.462 13.35 11.92 40.50 4.35
2766 4416 5.055642 TGATCTTACGTTGAGATTCGTGT 57.944 39.130 13.35 0.00 40.50 4.49
2767 4417 4.857037 TGATCTTACGTTGAGATTCGTGTG 59.143 41.667 13.35 0.00 40.50 3.82
2768 4418 3.571571 TCTTACGTTGAGATTCGTGTGG 58.428 45.455 0.00 0.00 40.50 4.17
2769 4419 3.253921 TCTTACGTTGAGATTCGTGTGGA 59.746 43.478 0.00 0.00 40.50 4.02
2770 4420 2.743636 ACGTTGAGATTCGTGTGGAT 57.256 45.000 0.00 0.00 38.85 3.41
2771 4421 3.861276 ACGTTGAGATTCGTGTGGATA 57.139 42.857 0.00 0.00 38.85 2.59
2772 4422 4.386867 ACGTTGAGATTCGTGTGGATAT 57.613 40.909 0.00 0.00 38.85 1.63
2773 4423 4.755411 ACGTTGAGATTCGTGTGGATATT 58.245 39.130 0.00 0.00 38.85 1.28
2774 4424 5.175859 ACGTTGAGATTCGTGTGGATATTT 58.824 37.500 0.00 0.00 38.85 1.40
2775 4425 5.642063 ACGTTGAGATTCGTGTGGATATTTT 59.358 36.000 0.00 0.00 38.85 1.82
2776 4426 6.183360 ACGTTGAGATTCGTGTGGATATTTTC 60.183 38.462 0.00 0.00 38.85 2.29
2777 4427 6.036083 CGTTGAGATTCGTGTGGATATTTTCT 59.964 38.462 0.00 0.00 0.00 2.52
2778 4428 7.413000 CGTTGAGATTCGTGTGGATATTTTCTT 60.413 37.037 0.00 0.00 0.00 2.52
2779 4429 7.921786 TGAGATTCGTGTGGATATTTTCTTT 57.078 32.000 0.00 0.00 0.00 2.52
2780 4430 8.335532 TGAGATTCGTGTGGATATTTTCTTTT 57.664 30.769 0.00 0.00 0.00 2.27
2781 4431 8.792633 TGAGATTCGTGTGGATATTTTCTTTTT 58.207 29.630 0.00 0.00 0.00 1.94
2782 4432 9.278734 GAGATTCGTGTGGATATTTTCTTTTTC 57.721 33.333 0.00 0.00 0.00 2.29
2783 4433 9.014297 AGATTCGTGTGGATATTTTCTTTTTCT 57.986 29.630 0.00 0.00 0.00 2.52
2784 4434 9.626045 GATTCGTGTGGATATTTTCTTTTTCTT 57.374 29.630 0.00 0.00 0.00 2.52
2785 4435 9.981114 ATTCGTGTGGATATTTTCTTTTTCTTT 57.019 25.926 0.00 0.00 0.00 2.52
2786 4436 9.810545 TTCGTGTGGATATTTTCTTTTTCTTTT 57.189 25.926 0.00 0.00 0.00 2.27
2787 4437 9.810545 TCGTGTGGATATTTTCTTTTTCTTTTT 57.189 25.926 0.00 0.00 0.00 1.94
2811 4461 9.696917 TTTTCTTTTCCTCTTTATGCTTGATTC 57.303 29.630 0.00 0.00 0.00 2.52
2812 4462 8.408043 TTCTTTTCCTCTTTATGCTTGATTCA 57.592 30.769 0.00 0.00 0.00 2.57
2813 4463 7.820648 TCTTTTCCTCTTTATGCTTGATTCAC 58.179 34.615 0.00 0.00 0.00 3.18
2814 4464 7.667219 TCTTTTCCTCTTTATGCTTGATTCACT 59.333 33.333 0.00 0.00 0.00 3.41
2815 4465 6.992063 TTCCTCTTTATGCTTGATTCACTC 57.008 37.500 0.00 0.00 0.00 3.51
2816 4466 6.053632 TCCTCTTTATGCTTGATTCACTCA 57.946 37.500 0.00 0.00 0.00 3.41
2817 4467 5.877012 TCCTCTTTATGCTTGATTCACTCAC 59.123 40.000 0.00 0.00 32.17 3.51
2818 4468 5.879223 CCTCTTTATGCTTGATTCACTCACT 59.121 40.000 0.00 0.00 32.17 3.41
2819 4469 6.373774 CCTCTTTATGCTTGATTCACTCACTT 59.626 38.462 0.00 0.00 32.17 3.16
2820 4470 7.550551 CCTCTTTATGCTTGATTCACTCACTTA 59.449 37.037 0.00 0.00 32.17 2.24
2821 4471 8.484641 TCTTTATGCTTGATTCACTCACTTAG 57.515 34.615 0.00 0.00 32.17 2.18
2822 4472 8.314021 TCTTTATGCTTGATTCACTCACTTAGA 58.686 33.333 0.00 0.00 32.17 2.10
2823 4473 9.107177 CTTTATGCTTGATTCACTCACTTAGAT 57.893 33.333 0.00 0.00 32.17 1.98
2824 4474 6.922247 ATGCTTGATTCACTCACTTAGATG 57.078 37.500 0.00 0.00 32.17 2.90
2825 4475 5.798132 TGCTTGATTCACTCACTTAGATGT 58.202 37.500 0.00 0.00 32.17 3.06
2826 4476 5.640783 TGCTTGATTCACTCACTTAGATGTG 59.359 40.000 0.00 0.00 39.15 3.21
2827 4477 5.447010 GCTTGATTCACTCACTTAGATGTGC 60.447 44.000 0.00 0.00 37.81 4.57
2828 4478 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
2829 4479 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
2830 4480 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
2831 4481 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
2832 4482 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
2833 4483 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
2834 4484 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
2835 4485 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
2836 4486 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
2837 4487 7.976175 CACTCACTTAGATGTGCAATAACTAGA 59.024 37.037 0.00 0.00 37.81 2.43
2838 4488 8.194104 ACTCACTTAGATGTGCAATAACTAGAG 58.806 37.037 0.00 0.00 37.81 2.43
2839 4489 6.980978 TCACTTAGATGTGCAATAACTAGAGC 59.019 38.462 0.00 0.00 37.81 4.09
2840 4490 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
2862 4512 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
2866 4516 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
2867 4517 1.152118 TGTGCCCTAGACACACCCT 60.152 57.895 12.81 0.00 42.88 4.34
2868 4518 0.766674 TGTGCCCTAGACACACCCTT 60.767 55.000 12.81 0.00 42.88 3.95
2869 4519 1.272807 GTGCCCTAGACACACCCTTA 58.727 55.000 10.07 0.00 37.96 2.69
2870 4520 1.207329 GTGCCCTAGACACACCCTTAG 59.793 57.143 10.07 0.00 37.96 2.18
2925 4575 4.065088 GCCTTTTGGTTTCTTTCCCATTC 58.935 43.478 0.00 0.00 42.99 2.67
2927 4577 5.687441 GCCTTTTGGTTTCTTTCCCATTCTT 60.687 40.000 0.00 0.00 42.99 2.52
2980 4630 6.636454 ATCCTGTACCTGATTTTACTTCCA 57.364 37.500 0.00 0.00 0.00 3.53
3045 4697 6.404734 GGGACTAAACCATGATCAACAATGAC 60.405 42.308 0.00 0.00 38.69 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.816354 GTGCCAACATAATAACCAATAAATTCT 57.184 29.630 0.00 0.00 0.00 2.40
6 7 9.593134 TGTGCCAACATAATAACCAATAAATTC 57.407 29.630 0.00 0.00 0.00 2.17
7 8 9.950496 TTGTGCCAACATAATAACCAATAAATT 57.050 25.926 0.00 0.00 35.83 1.82
8 9 9.950496 TTTGTGCCAACATAATAACCAATAAAT 57.050 25.926 0.00 0.00 35.83 1.40
9 10 9.950496 ATTTGTGCCAACATAATAACCAATAAA 57.050 25.926 0.00 0.00 35.83 1.40
10 11 9.376075 CATTTGTGCCAACATAATAACCAATAA 57.624 29.630 0.00 0.00 35.83 1.40
11 12 7.493971 GCATTTGTGCCAACATAATAACCAATA 59.506 33.333 0.00 0.00 35.83 1.90
12 13 6.315891 GCATTTGTGCCAACATAATAACCAAT 59.684 34.615 0.00 0.00 35.83 3.16
13 14 5.641209 GCATTTGTGCCAACATAATAACCAA 59.359 36.000 0.00 0.00 35.83 3.67
14 15 5.174395 GCATTTGTGCCAACATAATAACCA 58.826 37.500 0.00 0.00 35.83 3.67
15 16 5.063312 GTGCATTTGTGCCAACATAATAACC 59.937 40.000 0.00 0.00 35.83 2.85
16 17 5.636965 TGTGCATTTGTGCCAACATAATAAC 59.363 36.000 0.00 0.00 35.83 1.89
17 18 5.787380 TGTGCATTTGTGCCAACATAATAA 58.213 33.333 0.00 0.00 35.83 1.40
18 19 5.397142 TGTGCATTTGTGCCAACATAATA 57.603 34.783 0.00 0.00 35.83 0.98
19 20 4.268797 TGTGCATTTGTGCCAACATAAT 57.731 36.364 0.00 0.00 35.83 1.28
20 21 3.740631 TGTGCATTTGTGCCAACATAA 57.259 38.095 0.00 0.00 35.83 1.90
21 22 3.388308 GTTGTGCATTTGTGCCAACATA 58.612 40.909 19.94 2.90 41.32 2.29
22 23 2.211806 GTTGTGCATTTGTGCCAACAT 58.788 42.857 19.94 0.00 41.32 2.71
23 24 1.649664 GTTGTGCATTTGTGCCAACA 58.350 45.000 19.94 8.77 41.32 3.33
24 25 0.576328 CGTTGTGCATTTGTGCCAAC 59.424 50.000 17.20 17.20 39.87 3.77
25 26 0.457443 TCGTTGTGCATTTGTGCCAA 59.543 45.000 0.00 0.00 0.00 4.52
26 27 0.457443 TTCGTTGTGCATTTGTGCCA 59.543 45.000 0.00 0.00 0.00 4.92
27 28 1.782044 ATTCGTTGTGCATTTGTGCC 58.218 45.000 0.00 0.00 0.00 5.01
28 29 5.799936 AGTATAATTCGTTGTGCATTTGTGC 59.200 36.000 0.00 0.00 0.00 4.57
29 30 9.502145 AATAGTATAATTCGTTGTGCATTTGTG 57.498 29.630 0.00 0.00 0.00 3.33
33 34 9.502145 CACAAATAGTATAATTCGTTGTGCATT 57.498 29.630 9.18 0.00 32.34 3.56
34 35 8.673711 ACACAAATAGTATAATTCGTTGTGCAT 58.326 29.630 17.27 3.25 40.38 3.96
35 36 8.035165 ACACAAATAGTATAATTCGTTGTGCA 57.965 30.769 17.27 0.00 40.38 4.57
36 37 8.889849 AACACAAATAGTATAATTCGTTGTGC 57.110 30.769 17.27 0.00 40.38 4.57
41 42 9.524106 TCGATGAACACAAATAGTATAATTCGT 57.476 29.630 0.00 0.00 0.00 3.85
89 90 8.832521 CCATGCAATTCAAACAATATGCTTTAT 58.167 29.630 0.00 0.00 34.97 1.40
90 91 7.823310 ACCATGCAATTCAAACAATATGCTTTA 59.177 29.630 0.00 0.00 34.97 1.85
91 92 6.655848 ACCATGCAATTCAAACAATATGCTTT 59.344 30.769 0.00 0.00 34.97 3.51
92 93 6.174760 ACCATGCAATTCAAACAATATGCTT 58.825 32.000 0.00 0.00 34.97 3.91
93 94 5.736813 ACCATGCAATTCAAACAATATGCT 58.263 33.333 0.00 0.00 34.97 3.79
94 95 6.425577 AACCATGCAATTCAAACAATATGC 57.574 33.333 0.00 0.00 0.00 3.14
95 96 6.594547 TGGAACCATGCAATTCAAACAATATG 59.405 34.615 9.98 0.00 0.00 1.78
96 97 6.709281 TGGAACCATGCAATTCAAACAATAT 58.291 32.000 9.98 0.00 0.00 1.28
97 98 6.106648 TGGAACCATGCAATTCAAACAATA 57.893 33.333 9.98 0.00 0.00 1.90
98 99 4.970711 TGGAACCATGCAATTCAAACAAT 58.029 34.783 9.98 0.00 0.00 2.71
99 100 4.412796 TGGAACCATGCAATTCAAACAA 57.587 36.364 9.98 0.00 0.00 2.83
100 101 4.412796 TTGGAACCATGCAATTCAAACA 57.587 36.364 9.98 0.00 31.30 2.83
101 102 4.815846 ACTTTGGAACCATGCAATTCAAAC 59.184 37.500 9.98 0.00 36.71 2.93
102 103 5.033589 ACTTTGGAACCATGCAATTCAAA 57.966 34.783 9.98 3.53 36.71 2.69
103 104 4.686191 ACTTTGGAACCATGCAATTCAA 57.314 36.364 9.98 0.00 36.71 2.69
104 105 4.686191 AACTTTGGAACCATGCAATTCA 57.314 36.364 9.98 0.00 36.71 2.57
105 106 6.705825 AGTTTAACTTTGGAACCATGCAATTC 59.294 34.615 0.00 0.00 36.71 2.17
106 107 6.591001 AGTTTAACTTTGGAACCATGCAATT 58.409 32.000 0.00 0.00 36.71 2.32
107 108 6.173427 AGTTTAACTTTGGAACCATGCAAT 57.827 33.333 0.00 0.00 36.71 3.56
108 109 5.606348 AGTTTAACTTTGGAACCATGCAA 57.394 34.783 0.00 0.00 34.82 4.08
109 110 5.606348 AAGTTTAACTTTGGAACCATGCA 57.394 34.783 4.30 0.00 34.11 3.96
110 111 7.061789 CGAATAAGTTTAACTTTGGAACCATGC 59.938 37.037 15.83 0.00 39.51 4.06
111 112 8.293867 TCGAATAAGTTTAACTTTGGAACCATG 58.706 33.333 15.83 0.00 39.51 3.66
112 113 8.294577 GTCGAATAAGTTTAACTTTGGAACCAT 58.705 33.333 15.83 0.00 39.51 3.55
113 114 7.282675 TGTCGAATAAGTTTAACTTTGGAACCA 59.717 33.333 15.83 4.60 39.51 3.67
114 115 7.641760 TGTCGAATAAGTTTAACTTTGGAACC 58.358 34.615 15.83 2.22 39.51 3.62
115 116 9.673454 AATGTCGAATAAGTTTAACTTTGGAAC 57.327 29.630 15.83 8.80 39.51 3.62
116 117 9.672086 CAATGTCGAATAAGTTTAACTTTGGAA 57.328 29.630 15.83 0.00 39.51 3.53
117 118 8.293867 CCAATGTCGAATAAGTTTAACTTTGGA 58.706 33.333 15.83 3.16 39.51 3.53
118 119 8.079809 ACCAATGTCGAATAAGTTTAACTTTGG 58.920 33.333 15.83 14.87 39.51 3.28
119 120 9.458374 AACCAATGTCGAATAAGTTTAACTTTG 57.542 29.630 15.83 4.76 39.51 2.77
120 121 9.673454 GAACCAATGTCGAATAAGTTTAACTTT 57.327 29.630 15.83 0.00 39.51 2.66
121 122 9.063615 AGAACCAATGTCGAATAAGTTTAACTT 57.936 29.630 14.99 14.99 41.97 2.66
122 123 8.617290 AGAACCAATGTCGAATAAGTTTAACT 57.383 30.769 0.00 0.00 0.00 2.24
125 126 8.938906 GGTAAGAACCAATGTCGAATAAGTTTA 58.061 33.333 0.00 0.00 45.98 2.01
126 127 7.813645 GGTAAGAACCAATGTCGAATAAGTTT 58.186 34.615 0.00 0.00 45.98 2.66
127 128 7.373778 GGTAAGAACCAATGTCGAATAAGTT 57.626 36.000 0.00 0.00 45.98 2.66
128 129 6.980051 GGTAAGAACCAATGTCGAATAAGT 57.020 37.500 0.00 0.00 45.98 2.24
142 143 1.702491 GCACGATGGCGGTAAGAACC 61.702 60.000 0.00 0.00 43.17 3.62
143 144 1.713830 GCACGATGGCGGTAAGAAC 59.286 57.895 0.00 0.00 43.17 3.01
144 145 4.195308 GCACGATGGCGGTAAGAA 57.805 55.556 0.00 0.00 43.17 2.52
153 154 3.803082 CTTGGCCACGCACGATGG 61.803 66.667 3.88 2.23 40.50 3.51
154 155 1.851021 TTTCTTGGCCACGCACGATG 61.851 55.000 3.88 0.00 0.00 3.84
155 156 0.960364 ATTTCTTGGCCACGCACGAT 60.960 50.000 3.88 0.00 0.00 3.73
156 157 0.320858 TATTTCTTGGCCACGCACGA 60.321 50.000 3.88 0.00 0.00 4.35
157 158 0.519519 TTATTTCTTGGCCACGCACG 59.480 50.000 3.88 0.00 0.00 5.34
158 159 2.479560 GGATTATTTCTTGGCCACGCAC 60.480 50.000 3.88 0.00 0.00 5.34
159 160 1.748493 GGATTATTTCTTGGCCACGCA 59.252 47.619 3.88 0.00 0.00 5.24
160 161 1.748493 TGGATTATTTCTTGGCCACGC 59.252 47.619 3.88 0.00 0.00 5.34
161 162 3.443681 AGTTGGATTATTTCTTGGCCACG 59.556 43.478 3.88 2.81 0.00 4.94
162 163 5.885912 TCTAGTTGGATTATTTCTTGGCCAC 59.114 40.000 3.88 0.00 0.00 5.01
163 164 6.073447 TCTAGTTGGATTATTTCTTGGCCA 57.927 37.500 0.00 0.00 0.00 5.36
164 165 8.734386 CATATCTAGTTGGATTATTTCTTGGCC 58.266 37.037 0.00 0.00 0.00 5.36
165 166 9.507329 TCATATCTAGTTGGATTATTTCTTGGC 57.493 33.333 0.00 0.00 0.00 4.52
203 204 1.928503 CATGGCCGCAATTTGTCAATC 59.071 47.619 0.00 0.00 0.00 2.67
205 206 0.964700 TCATGGCCGCAATTTGTCAA 59.035 45.000 0.00 0.00 0.00 3.18
206 207 0.964700 TTCATGGCCGCAATTTGTCA 59.035 45.000 0.00 0.00 0.00 3.58
281 284 6.432162 CAGGATCCACATTTGAGGGTATTATG 59.568 42.308 15.82 0.00 0.00 1.90
290 293 3.424703 ACAACCAGGATCCACATTTGAG 58.575 45.455 15.82 0.20 0.00 3.02
292 295 4.078537 TGTACAACCAGGATCCACATTTG 58.921 43.478 15.82 13.27 0.00 2.32
302 305 5.508489 CGTTCTCTAAACTGTACAACCAGGA 60.508 44.000 0.00 0.00 36.75 3.86
313 316 7.869016 TGTGTAATTCTCGTTCTCTAAACTG 57.131 36.000 0.00 0.00 0.00 3.16
388 391 9.764363 AGATCGATGTATGTATGTTAATTGTGT 57.236 29.630 0.54 0.00 0.00 3.72
390 393 8.712363 GCAGATCGATGTATGTATGTTAATTGT 58.288 33.333 0.54 0.00 0.00 2.71
391 394 8.171196 GGCAGATCGATGTATGTATGTTAATTG 58.829 37.037 0.54 0.00 0.00 2.32
392 395 7.877612 TGGCAGATCGATGTATGTATGTTAATT 59.122 33.333 0.54 0.00 0.00 1.40
393 396 7.386059 TGGCAGATCGATGTATGTATGTTAAT 58.614 34.615 0.54 0.00 0.00 1.40
394 397 6.754193 TGGCAGATCGATGTATGTATGTTAA 58.246 36.000 0.54 0.00 0.00 2.01
395 398 6.339587 TGGCAGATCGATGTATGTATGTTA 57.660 37.500 0.54 0.00 0.00 2.41
396 399 5.213891 TGGCAGATCGATGTATGTATGTT 57.786 39.130 0.54 0.00 0.00 2.71
397 400 4.871933 TGGCAGATCGATGTATGTATGT 57.128 40.909 0.54 0.00 0.00 2.29
398 401 5.233225 AGTTGGCAGATCGATGTATGTATG 58.767 41.667 0.54 0.00 0.00 2.39
399 402 5.473931 GAGTTGGCAGATCGATGTATGTAT 58.526 41.667 0.54 0.00 0.00 2.29
400 403 4.262036 GGAGTTGGCAGATCGATGTATGTA 60.262 45.833 0.54 0.00 0.00 2.29
401 404 3.493350 GGAGTTGGCAGATCGATGTATGT 60.493 47.826 0.54 0.00 0.00 2.29
402 405 3.062763 GGAGTTGGCAGATCGATGTATG 58.937 50.000 0.54 0.00 0.00 2.39
418 421 1.313812 CCTCGGTCGCTACTGGAGTT 61.314 60.000 0.00 0.00 32.40 3.01
510 517 1.981533 GTAGTACGTGTTCTGTTCGGC 59.018 52.381 0.00 0.00 0.00 5.54
516 523 4.497674 GCCCTCTATGTAGTACGTGTTCTG 60.498 50.000 5.21 0.00 0.00 3.02
540 547 0.537143 TCAAGCCCTTCATGTGCGTT 60.537 50.000 0.00 0.00 0.00 4.84
546 553 3.702548 TCAATTGGATCAAGCCCTTCATG 59.297 43.478 5.42 0.00 0.00 3.07
548 555 3.091545 GTCAATTGGATCAAGCCCTTCA 58.908 45.455 5.42 0.00 0.00 3.02
551 558 1.342374 GGGTCAATTGGATCAAGCCCT 60.342 52.381 5.42 0.00 32.47 5.19
557 564 2.827322 CTGCTTTGGGTCAATTGGATCA 59.173 45.455 5.42 0.00 0.00 2.92
594 1794 3.480133 ATCTAGGGGCGTGTGGGC 61.480 66.667 0.00 0.00 41.35 5.36
828 2033 0.824595 GTGGGCCCGTTTACAAGGTT 60.825 55.000 19.37 0.00 0.00 3.50
1481 3045 3.456644 AGAGAGGAGATTCTCGTAGGACA 59.543 47.826 8.78 0.00 46.51 4.02
1571 3138 2.747855 GCCCAAACTCTCGCAGGG 60.748 66.667 0.00 0.00 42.55 4.45
1954 3521 3.407967 CCTTAGCCGGCCCTCCAA 61.408 66.667 26.15 8.82 0.00 3.53
2117 3684 2.285977 TGCAAGCATCAGCATAGTCTG 58.714 47.619 0.00 0.00 45.49 3.51
2197 3766 4.507710 ACTGTCATGCCATACACAGTTAG 58.492 43.478 13.37 0.00 45.77 2.34
2429 4066 9.857656 AACACAAATATATTCATGGACTCTCAT 57.142 29.630 0.00 0.00 0.00 2.90
2430 4067 9.685276 AAACACAAATATATTCATGGACTCTCA 57.315 29.630 0.00 0.00 0.00 3.27
2440 4077 9.513906 TGGAAGTCAGAAACACAAATATATTCA 57.486 29.630 0.00 0.00 0.00 2.57
2699 4349 8.992835 TGCAATACTTATAGCACATCTAGATG 57.007 34.615 27.63 27.63 44.15 2.90
2709 4359 7.872993 GGACTTAGATGTGCAATACTTATAGCA 59.127 37.037 0.00 0.00 34.10 3.49
2710 4360 8.091449 AGGACTTAGATGTGCAATACTTATAGC 58.909 37.037 0.00 0.00 0.00 2.97
2713 4363 9.935241 CATAGGACTTAGATGTGCAATACTTAT 57.065 33.333 0.00 0.00 0.00 1.73
2714 4364 8.924303 ACATAGGACTTAGATGTGCAATACTTA 58.076 33.333 0.00 0.00 32.62 2.24
2715 4365 7.796054 ACATAGGACTTAGATGTGCAATACTT 58.204 34.615 0.00 0.00 32.62 2.24
2716 4366 7.069950 TGACATAGGACTTAGATGTGCAATACT 59.930 37.037 0.00 0.00 33.99 2.12
2717 4367 7.210174 TGACATAGGACTTAGATGTGCAATAC 58.790 38.462 0.00 0.00 33.99 1.89
2718 4368 7.360113 TGACATAGGACTTAGATGTGCAATA 57.640 36.000 0.00 0.00 33.99 1.90
2719 4369 6.239217 TGACATAGGACTTAGATGTGCAAT 57.761 37.500 0.00 0.00 33.99 3.56
2720 4370 5.675684 TGACATAGGACTTAGATGTGCAA 57.324 39.130 0.00 0.00 33.99 4.08
2721 4371 5.876651 ATGACATAGGACTTAGATGTGCA 57.123 39.130 0.00 0.00 33.99 4.57
2722 4372 6.283694 TCAATGACATAGGACTTAGATGTGC 58.716 40.000 0.00 0.00 33.99 4.57
2723 4373 8.366401 AGATCAATGACATAGGACTTAGATGTG 58.634 37.037 0.00 0.00 33.99 3.21
2724 4374 8.489676 AGATCAATGACATAGGACTTAGATGT 57.510 34.615 0.00 0.00 36.52 3.06
2727 4377 8.568794 CGTAAGATCAATGACATAGGACTTAGA 58.431 37.037 0.00 0.00 43.02 2.10
2728 4378 8.353684 ACGTAAGATCAATGACATAGGACTTAG 58.646 37.037 0.00 0.00 43.62 2.18
2729 4379 8.234136 ACGTAAGATCAATGACATAGGACTTA 57.766 34.615 0.00 0.00 43.62 2.24
2730 4380 7.113658 ACGTAAGATCAATGACATAGGACTT 57.886 36.000 0.00 0.00 43.62 3.01
2731 4381 6.716934 ACGTAAGATCAATGACATAGGACT 57.283 37.500 0.00 0.00 43.62 3.85
2732 4382 6.978659 TCAACGTAAGATCAATGACATAGGAC 59.021 38.462 0.00 0.00 43.62 3.85
2733 4383 7.068226 TCTCAACGTAAGATCAATGACATAGGA 59.932 37.037 0.00 0.00 43.62 2.94
2734 4384 7.203218 TCTCAACGTAAGATCAATGACATAGG 58.797 38.462 0.00 0.00 43.62 2.57
2735 4385 8.809159 ATCTCAACGTAAGATCAATGACATAG 57.191 34.615 7.39 0.00 43.62 2.23
2736 4386 9.249457 GAATCTCAACGTAAGATCAATGACATA 57.751 33.333 12.34 0.00 43.62 2.29
2737 4387 7.043125 CGAATCTCAACGTAAGATCAATGACAT 60.043 37.037 12.34 0.00 43.62 3.06
2738 4388 6.253512 CGAATCTCAACGTAAGATCAATGACA 59.746 38.462 12.34 0.00 43.62 3.58
2739 4389 6.253727 ACGAATCTCAACGTAAGATCAATGAC 59.746 38.462 12.34 2.89 40.92 3.06
2740 4390 6.253512 CACGAATCTCAACGTAAGATCAATGA 59.746 38.462 12.34 0.00 40.76 2.57
2741 4391 6.035005 ACACGAATCTCAACGTAAGATCAATG 59.965 38.462 12.34 12.21 40.76 2.82
2742 4392 6.035005 CACACGAATCTCAACGTAAGATCAAT 59.965 38.462 12.34 0.02 40.76 2.57
2743 4393 5.344933 CACACGAATCTCAACGTAAGATCAA 59.655 40.000 12.34 0.00 40.76 2.57
2744 4394 4.857037 CACACGAATCTCAACGTAAGATCA 59.143 41.667 12.34 0.00 40.76 2.92
2745 4395 4.265556 CCACACGAATCTCAACGTAAGATC 59.734 45.833 12.34 6.90 40.76 2.75
2746 4396 4.082408 TCCACACGAATCTCAACGTAAGAT 60.082 41.667 7.39 7.39 40.76 2.40
2747 4397 3.253921 TCCACACGAATCTCAACGTAAGA 59.746 43.478 3.32 3.32 40.76 2.10
2748 4398 3.571571 TCCACACGAATCTCAACGTAAG 58.428 45.455 0.00 0.00 40.76 2.34
2749 4399 3.646611 TCCACACGAATCTCAACGTAA 57.353 42.857 0.00 0.00 40.76 3.18
2750 4400 3.861276 ATCCACACGAATCTCAACGTA 57.139 42.857 0.00 0.00 40.76 3.57
2751 4401 2.743636 ATCCACACGAATCTCAACGT 57.256 45.000 0.00 0.00 43.50 3.99
2752 4402 5.718649 AAATATCCACACGAATCTCAACG 57.281 39.130 0.00 0.00 0.00 4.10
2753 4403 7.308782 AGAAAATATCCACACGAATCTCAAC 57.691 36.000 0.00 0.00 0.00 3.18
2754 4404 7.921786 AAGAAAATATCCACACGAATCTCAA 57.078 32.000 0.00 0.00 0.00 3.02
2755 4405 7.921786 AAAGAAAATATCCACACGAATCTCA 57.078 32.000 0.00 0.00 0.00 3.27
2756 4406 9.278734 GAAAAAGAAAATATCCACACGAATCTC 57.721 33.333 0.00 0.00 0.00 2.75
2757 4407 9.014297 AGAAAAAGAAAATATCCACACGAATCT 57.986 29.630 0.00 0.00 0.00 2.40
2758 4408 9.626045 AAGAAAAAGAAAATATCCACACGAATC 57.374 29.630 0.00 0.00 0.00 2.52
2759 4409 9.981114 AAAGAAAAAGAAAATATCCACACGAAT 57.019 25.926 0.00 0.00 0.00 3.34
2760 4410 9.810545 AAAAGAAAAAGAAAATATCCACACGAA 57.189 25.926 0.00 0.00 0.00 3.85
2761 4411 9.810545 AAAAAGAAAAAGAAAATATCCACACGA 57.189 25.926 0.00 0.00 0.00 4.35
2785 4435 9.696917 GAATCAAGCATAAAGAGGAAAAGAAAA 57.303 29.630 0.00 0.00 0.00 2.29
2786 4436 8.859090 TGAATCAAGCATAAAGAGGAAAAGAAA 58.141 29.630 0.00 0.00 0.00 2.52
2787 4437 8.299570 GTGAATCAAGCATAAAGAGGAAAAGAA 58.700 33.333 0.00 0.00 0.00 2.52
2788 4438 7.667219 AGTGAATCAAGCATAAAGAGGAAAAGA 59.333 33.333 0.00 0.00 0.00 2.52
2789 4439 7.824672 AGTGAATCAAGCATAAAGAGGAAAAG 58.175 34.615 0.00 0.00 0.00 2.27
2790 4440 7.448161 TGAGTGAATCAAGCATAAAGAGGAAAA 59.552 33.333 0.00 0.00 34.02 2.29
2791 4441 6.942005 TGAGTGAATCAAGCATAAAGAGGAAA 59.058 34.615 0.00 0.00 34.02 3.13
2792 4442 6.372659 GTGAGTGAATCAAGCATAAAGAGGAA 59.627 38.462 0.00 0.00 40.43 3.36
2793 4443 5.877012 GTGAGTGAATCAAGCATAAAGAGGA 59.123 40.000 0.00 0.00 40.43 3.71
2794 4444 5.879223 AGTGAGTGAATCAAGCATAAAGAGG 59.121 40.000 0.00 0.00 40.43 3.69
2795 4445 6.981762 AGTGAGTGAATCAAGCATAAAGAG 57.018 37.500 0.00 0.00 40.43 2.85
2796 4446 8.314021 TCTAAGTGAGTGAATCAAGCATAAAGA 58.686 33.333 0.00 0.00 40.43 2.52
2797 4447 8.484641 TCTAAGTGAGTGAATCAAGCATAAAG 57.515 34.615 0.00 0.00 40.43 1.85
2798 4448 8.886719 CATCTAAGTGAGTGAATCAAGCATAAA 58.113 33.333 0.00 0.00 40.43 1.40
2799 4449 8.043113 ACATCTAAGTGAGTGAATCAAGCATAA 58.957 33.333 0.00 0.00 40.43 1.90
2800 4450 7.493645 CACATCTAAGTGAGTGAATCAAGCATA 59.506 37.037 0.00 0.00 42.05 3.14
2801 4451 6.315642 CACATCTAAGTGAGTGAATCAAGCAT 59.684 38.462 0.00 0.00 42.05 3.79
2802 4452 5.640783 CACATCTAAGTGAGTGAATCAAGCA 59.359 40.000 0.00 0.00 42.05 3.91
2803 4453 5.447010 GCACATCTAAGTGAGTGAATCAAGC 60.447 44.000 0.00 0.00 42.05 4.01
2804 4454 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
2805 4455 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
2806 4456 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
2807 4457 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
2808 4458 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
2809 4459 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
2810 4460 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
2811 4461 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
2812 4462 8.067751 TCTAGTTATTGCACATCTAAGTGAGT 57.932 34.615 0.00 0.00 42.05 3.41
2813 4463 7.168972 GCTCTAGTTATTGCACATCTAAGTGAG 59.831 40.741 0.00 0.00 42.05 3.51
2814 4464 6.980978 GCTCTAGTTATTGCACATCTAAGTGA 59.019 38.462 0.00 0.00 42.05 3.41
2815 4465 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
2816 4466 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
2841 4491 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
2842 4492 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
2843 4493 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
2844 4494 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
2845 4495 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
2846 4496 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
2847 4497 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
2848 4498 0.547712 AGGGTGTGTCTAGGGCACAT 60.548 55.000 18.92 5.97 46.66 3.21
2849 4499 0.766674 AAGGGTGTGTCTAGGGCACA 60.767 55.000 14.22 14.22 43.60 4.57
2850 4500 1.207329 CTAAGGGTGTGTCTAGGGCAC 59.793 57.143 10.20 10.20 37.37 5.01
2851 4501 1.078159 TCTAAGGGTGTGTCTAGGGCA 59.922 52.381 0.00 0.00 0.00 5.36
2852 4502 1.861982 TCTAAGGGTGTGTCTAGGGC 58.138 55.000 0.00 0.00 0.00 5.19
2853 4503 4.903045 TTTTCTAAGGGTGTGTCTAGGG 57.097 45.455 0.00 0.00 0.00 3.53
2854 4504 9.712305 CATATATTTTCTAAGGGTGTGTCTAGG 57.288 37.037 0.00 0.00 0.00 3.02
2857 4507 9.975218 AAACATATATTTTCTAAGGGTGTGTCT 57.025 29.630 0.00 0.00 0.00 3.41
2859 4509 9.975218 AGAAACATATATTTTCTAAGGGTGTGT 57.025 29.630 15.41 0.00 40.72 3.72
2942 4592 7.066284 CAGGTACAGGATTTAGGAACAAAGATG 59.934 40.741 0.00 0.00 0.00 2.90
3011 4663 8.281531 TGATCATGGTTTAGTCCCAAATAGATT 58.718 33.333 0.00 0.00 35.14 2.40
3012 4664 7.815383 TGATCATGGTTTAGTCCCAAATAGAT 58.185 34.615 0.00 0.00 35.14 1.98
3013 4665 7.206789 TGATCATGGTTTAGTCCCAAATAGA 57.793 36.000 0.00 0.00 35.14 1.98


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

AutoCloner maintained by Alex Coulton.