Multiple sequence alignment - TraesCS3A01G471700

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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 TraesCS3A01G471700 chr3A 100.000 3286 0 0 1 3286 703169734 703173019 0.000000e+00 6069.0
1 TraesCS3A01G471700 chr3A 91.743 1308 79 13 1037 2320 703203807 703205109 0.000000e+00 1790.0
2 TraesCS3A01G471700 chr3A 92.009 851 51 5 2450 3286 595118045 595117198 0.000000e+00 1179.0
3 TraesCS3A01G471700 chr3A 80.033 1227 187 41 1052 2238 703304297 703303089 0.000000e+00 856.0
4 TraesCS3A01G471700 chr3A 78.536 1216 183 48 1069 2237 655637061 655635877 0.000000e+00 728.0
5 TraesCS3A01G471700 chr3D 95.758 1556 51 9 896 2443 570280876 570282424 0.000000e+00 2494.0
6 TraesCS3A01G471700 chr3D 94.922 1418 54 10 1038 2448 570328415 570329821 0.000000e+00 2204.0
7 TraesCS3A01G471700 chr3D 92.616 1246 83 7 1012 2253 570379544 570380784 0.000000e+00 1783.0
8 TraesCS3A01G471700 chr3D 90.827 1101 91 5 1142 2236 570311115 570312211 0.000000e+00 1465.0
9 TraesCS3A01G471700 chr3D 83.990 1218 147 28 1046 2225 570393676 570394883 0.000000e+00 1125.0
10 TraesCS3A01G471700 chr3D 79.542 1222 208 31 1046 2238 570496394 570495186 0.000000e+00 833.0
11 TraesCS3A01G471700 chr3D 78.485 1241 184 51 1048 2237 520191927 520190719 0.000000e+00 736.0
12 TraesCS3A01G471700 chr3D 78.739 555 93 18 1697 2238 570400497 570399955 6.750000e-92 348.0
13 TraesCS3A01G471700 chr3D 82.748 313 23 8 444 753 570280539 570280823 1.960000e-62 250.0
14 TraesCS3A01G471700 chr3D 82.584 178 8 13 856 1028 570305509 570305668 5.720000e-28 135.0
15 TraesCS3A01G471700 chr3D 100.000 42 0 0 840 881 570280837 570280878 9.780000e-11 78.7
16 TraesCS3A01G471700 chr3B 93.665 1547 76 12 910 2448 757472725 757474257 0.000000e+00 2294.0
17 TraesCS3A01G471700 chr3B 92.471 1222 84 6 1037 2253 757708069 757709287 0.000000e+00 1740.0
18 TraesCS3A01G471700 chr3B 88.490 1338 122 15 930 2253 757498177 757499496 0.000000e+00 1589.0
19 TraesCS3A01G471700 chr3B 83.990 1218 146 29 1046 2225 757734142 757735348 0.000000e+00 1123.0
20 TraesCS3A01G471700 chr3B 86.311 862 84 20 2450 3286 572803951 572803099 0.000000e+00 907.0
21 TraesCS3A01G471700 chr3B 88.780 205 18 5 512 712 757472440 757472643 2.530000e-61 246.0
22 TraesCS3A01G471700 chr3B 100.000 40 0 0 840 879 757472683 757472722 1.260000e-09 75.0
23 TraesCS3A01G471700 chr2A 92.488 852 46 5 2450 3286 678613102 678612254 0.000000e+00 1203.0
24 TraesCS3A01G471700 chr2A 86.070 804 75 21 2447 3225 485039704 485038913 0.000000e+00 830.0
25 TraesCS3A01G471700 chr5A 92.299 844 54 5 2450 3286 549582745 549583584 0.000000e+00 1188.0
26 TraesCS3A01G471700 chr5A 86.605 754 67 19 2560 3286 548773727 548772981 0.000000e+00 802.0
27 TraesCS3A01G471700 chr4D 87.791 860 77 13 2450 3286 478228505 478229359 0.000000e+00 981.0
28 TraesCS3A01G471700 chr1B 86.621 867 78 21 2447 3286 629109688 629108833 0.000000e+00 924.0
29 TraesCS3A01G471700 chr1B 84.088 861 73 29 2450 3286 401157104 401156284 0.000000e+00 773.0
30 TraesCS3A01G471700 chr1B 89.340 197 21 0 2446 2642 611129357 611129553 7.040000e-62 248.0
31 TraesCS3A01G471700 chr7A 92.369 629 44 4 2450 3075 244498326 244497699 0.000000e+00 893.0
32 TraesCS3A01G471700 chr6B 86.033 852 88 18 2461 3286 57155135 57155981 0.000000e+00 885.0
33 TraesCS3A01G471700 chr4A 85.012 854 80 22 2457 3286 102440622 102441451 0.000000e+00 824.0
34 TraesCS3A01G471700 chr7B 84.859 852 89 18 2450 3286 28934211 28933385 0.000000e+00 822.0


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 TraesCS3A01G471700 chr3A 703169734 703173019 3285 False 6069.000000 6069 100.000000 1 3286 1 chr3A.!!$F1 3285
1 TraesCS3A01G471700 chr3A 703203807 703205109 1302 False 1790.000000 1790 91.743000 1037 2320 1 chr3A.!!$F2 1283
2 TraesCS3A01G471700 chr3A 595117198 595118045 847 True 1179.000000 1179 92.009000 2450 3286 1 chr3A.!!$R1 836
3 TraesCS3A01G471700 chr3A 703303089 703304297 1208 True 856.000000 856 80.033000 1052 2238 1 chr3A.!!$R3 1186
4 TraesCS3A01G471700 chr3A 655635877 655637061 1184 True 728.000000 728 78.536000 1069 2237 1 chr3A.!!$R2 1168
5 TraesCS3A01G471700 chr3D 570328415 570329821 1406 False 2204.000000 2204 94.922000 1038 2448 1 chr3D.!!$F3 1410
6 TraesCS3A01G471700 chr3D 570379544 570380784 1240 False 1783.000000 1783 92.616000 1012 2253 1 chr3D.!!$F4 1241
7 TraesCS3A01G471700 chr3D 570311115 570312211 1096 False 1465.000000 1465 90.827000 1142 2236 1 chr3D.!!$F2 1094
8 TraesCS3A01G471700 chr3D 570393676 570394883 1207 False 1125.000000 1125 83.990000 1046 2225 1 chr3D.!!$F5 1179
9 TraesCS3A01G471700 chr3D 570280539 570282424 1885 False 940.900000 2494 92.835333 444 2443 3 chr3D.!!$F6 1999
10 TraesCS3A01G471700 chr3D 570495186 570496394 1208 True 833.000000 833 79.542000 1046 2238 1 chr3D.!!$R3 1192
11 TraesCS3A01G471700 chr3D 520190719 520191927 1208 True 736.000000 736 78.485000 1048 2237 1 chr3D.!!$R1 1189
12 TraesCS3A01G471700 chr3D 570399955 570400497 542 True 348.000000 348 78.739000 1697 2238 1 chr3D.!!$R2 541
13 TraesCS3A01G471700 chr3B 757708069 757709287 1218 False 1740.000000 1740 92.471000 1037 2253 1 chr3B.!!$F2 1216
14 TraesCS3A01G471700 chr3B 757498177 757499496 1319 False 1589.000000 1589 88.490000 930 2253 1 chr3B.!!$F1 1323
15 TraesCS3A01G471700 chr3B 757734142 757735348 1206 False 1123.000000 1123 83.990000 1046 2225 1 chr3B.!!$F3 1179
16 TraesCS3A01G471700 chr3B 572803099 572803951 852 True 907.000000 907 86.311000 2450 3286 1 chr3B.!!$R1 836
17 TraesCS3A01G471700 chr3B 757472440 757474257 1817 False 871.666667 2294 94.148333 512 2448 3 chr3B.!!$F4 1936
18 TraesCS3A01G471700 chr2A 678612254 678613102 848 True 1203.000000 1203 92.488000 2450 3286 1 chr2A.!!$R2 836
19 TraesCS3A01G471700 chr2A 485038913 485039704 791 True 830.000000 830 86.070000 2447 3225 1 chr2A.!!$R1 778
20 TraesCS3A01G471700 chr5A 549582745 549583584 839 False 1188.000000 1188 92.299000 2450 3286 1 chr5A.!!$F1 836
21 TraesCS3A01G471700 chr5A 548772981 548773727 746 True 802.000000 802 86.605000 2560 3286 1 chr5A.!!$R1 726
22 TraesCS3A01G471700 chr4D 478228505 478229359 854 False 981.000000 981 87.791000 2450 3286 1 chr4D.!!$F1 836
23 TraesCS3A01G471700 chr1B 629108833 629109688 855 True 924.000000 924 86.621000 2447 3286 1 chr1B.!!$R2 839
24 TraesCS3A01G471700 chr1B 401156284 401157104 820 True 773.000000 773 84.088000 2450 3286 1 chr1B.!!$R1 836
25 TraesCS3A01G471700 chr7A 244497699 244498326 627 True 893.000000 893 92.369000 2450 3075 1 chr7A.!!$R1 625
26 TraesCS3A01G471700 chr6B 57155135 57155981 846 False 885.000000 885 86.033000 2461 3286 1 chr6B.!!$F1 825
27 TraesCS3A01G471700 chr4A 102440622 102441451 829 False 824.000000 824 85.012000 2457 3286 1 chr4A.!!$F1 829
28 TraesCS3A01G471700 chr7B 28933385 28934211 826 True 822.000000 822 84.859000 2450 3286 1 chr7B.!!$R1 836

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
805 815 0.095245 CACGTAGAGCCATTTGTGCG 59.905 55.0 0.0 0.0 0.0 5.34 F
881 891 0.168128 GGCATGGTTTGTCTACGCAC 59.832 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2208 0.613260 CCCCTTCATCTCCACGAACA 59.387 55.000 0.0 0.0 0.00 3.18 R
2539 2664 1.065709 ACCGTATTTGAACGCCCAGAT 60.066 47.619 0.0 0.0 41.51 2.90 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
17 18 4.994744 CAGTGCACACGATCCTGA 57.005 55.556 21.04 0.00 36.20 3.86
18 19 3.215642 CAGTGCACACGATCCTGAA 57.784 52.632 21.04 0.00 36.20 3.02
19 20 0.792640 CAGTGCACACGATCCTGAAC 59.207 55.000 21.04 0.00 36.20 3.18
20 21 0.320771 AGTGCACACGATCCTGAACC 60.321 55.000 21.04 0.00 36.20 3.62
21 22 1.374125 TGCACACGATCCTGAACCG 60.374 57.895 0.00 0.00 0.00 4.44
22 23 2.100631 GCACACGATCCTGAACCGG 61.101 63.158 0.00 0.00 0.00 5.28
23 24 1.447838 CACACGATCCTGAACCGGG 60.448 63.158 6.32 0.00 0.00 5.73
24 25 2.511600 CACGATCCTGAACCGGGC 60.512 66.667 6.32 0.00 0.00 6.13
25 26 4.143333 ACGATCCTGAACCGGGCG 62.143 66.667 6.32 0.00 0.00 6.13
26 27 3.833645 CGATCCTGAACCGGGCGA 61.834 66.667 6.32 0.00 0.00 5.54
27 28 2.202892 GATCCTGAACCGGGCGAC 60.203 66.667 6.32 0.00 0.00 5.19
28 29 3.000819 ATCCTGAACCGGGCGACA 61.001 61.111 6.32 0.00 0.00 4.35
29 30 2.515996 GATCCTGAACCGGGCGACAA 62.516 60.000 6.32 0.00 0.00 3.18
30 31 1.910580 ATCCTGAACCGGGCGACAAT 61.911 55.000 6.32 0.00 0.00 2.71
31 32 2.398554 CCTGAACCGGGCGACAATG 61.399 63.158 6.32 0.00 0.00 2.82
32 33 1.375396 CTGAACCGGGCGACAATGA 60.375 57.895 6.32 0.00 0.00 2.57
33 34 1.361668 CTGAACCGGGCGACAATGAG 61.362 60.000 6.32 0.00 0.00 2.90
34 35 2.746277 AACCGGGCGACAATGAGC 60.746 61.111 6.32 0.00 0.00 4.26
41 42 4.776322 CGACAATGAGCCGGCCCA 62.776 66.667 26.15 20.75 0.00 5.36
42 43 2.361104 GACAATGAGCCGGCCCAA 60.361 61.111 26.15 9.69 0.00 4.12
43 44 1.754234 GACAATGAGCCGGCCCAAT 60.754 57.895 26.15 8.12 0.00 3.16
44 45 1.305213 ACAATGAGCCGGCCCAATT 60.305 52.632 26.15 17.65 0.00 2.32
45 46 0.904394 ACAATGAGCCGGCCCAATTT 60.904 50.000 26.15 6.95 0.00 1.82
46 47 0.249955 CAATGAGCCGGCCCAATTTT 59.750 50.000 26.15 6.06 0.00 1.82
47 48 0.536724 AATGAGCCGGCCCAATTTTC 59.463 50.000 26.15 13.16 0.00 2.29
48 49 0.614415 ATGAGCCGGCCCAATTTTCA 60.614 50.000 26.15 19.05 0.00 2.69
49 50 0.829602 TGAGCCGGCCCAATTTTCAA 60.830 50.000 26.15 0.23 0.00 2.69
50 51 0.108662 GAGCCGGCCCAATTTTCAAG 60.109 55.000 26.15 0.00 0.00 3.02
51 52 0.541764 AGCCGGCCCAATTTTCAAGA 60.542 50.000 26.15 0.00 0.00 3.02
52 53 0.108662 GCCGGCCCAATTTTCAAGAG 60.109 55.000 18.11 0.00 0.00 2.85
53 54 1.256812 CCGGCCCAATTTTCAAGAGT 58.743 50.000 0.00 0.00 0.00 3.24
54 55 1.618343 CCGGCCCAATTTTCAAGAGTT 59.382 47.619 0.00 0.00 0.00 3.01
55 56 2.352715 CCGGCCCAATTTTCAAGAGTTC 60.353 50.000 0.00 0.00 0.00 3.01
56 57 2.558359 CGGCCCAATTTTCAAGAGTTCT 59.442 45.455 0.00 0.00 0.00 3.01
57 58 3.612479 CGGCCCAATTTTCAAGAGTTCTG 60.612 47.826 0.00 0.00 0.00 3.02
58 59 3.320626 GCCCAATTTTCAAGAGTTCTGC 58.679 45.455 0.00 0.00 0.00 4.26
59 60 3.006217 GCCCAATTTTCAAGAGTTCTGCT 59.994 43.478 0.00 0.00 0.00 4.24
60 61 4.502087 GCCCAATTTTCAAGAGTTCTGCTT 60.502 41.667 0.00 0.00 0.00 3.91
61 62 4.986659 CCCAATTTTCAAGAGTTCTGCTTG 59.013 41.667 0.00 0.00 43.09 4.01
65 66 1.788258 TCAAGAGTTCTGCTTGAGCG 58.212 50.000 0.00 0.00 44.81 5.03
66 67 1.069204 TCAAGAGTTCTGCTTGAGCGT 59.931 47.619 0.00 0.00 44.81 5.07
67 68 1.869767 CAAGAGTTCTGCTTGAGCGTT 59.130 47.619 0.00 0.00 44.16 4.84
68 69 2.246719 AGAGTTCTGCTTGAGCGTTT 57.753 45.000 0.00 0.00 45.83 3.60
69 70 3.386768 AGAGTTCTGCTTGAGCGTTTA 57.613 42.857 0.00 0.00 45.83 2.01
70 71 3.931578 AGAGTTCTGCTTGAGCGTTTAT 58.068 40.909 0.00 0.00 45.83 1.40
71 72 4.319177 AGAGTTCTGCTTGAGCGTTTATT 58.681 39.130 0.00 0.00 45.83 1.40
72 73 4.757149 AGAGTTCTGCTTGAGCGTTTATTT 59.243 37.500 0.00 0.00 45.83 1.40
73 74 5.239525 AGAGTTCTGCTTGAGCGTTTATTTT 59.760 36.000 0.00 0.00 45.83 1.82
74 75 5.831997 AGTTCTGCTTGAGCGTTTATTTTT 58.168 33.333 0.00 0.00 45.83 1.94
102 103 7.916914 ACTAGCTATTTGATGTTTTTACCGT 57.083 32.000 0.00 0.00 0.00 4.83
103 104 9.439500 AACTAGCTATTTGATGTTTTTACCGTA 57.561 29.630 0.00 0.00 0.00 4.02
104 105 9.609346 ACTAGCTATTTGATGTTTTTACCGTAT 57.391 29.630 0.00 0.00 0.00 3.06
105 106 9.864034 CTAGCTATTTGATGTTTTTACCGTATG 57.136 33.333 0.00 0.00 0.00 2.39
106 107 8.276252 AGCTATTTGATGTTTTTACCGTATGT 57.724 30.769 0.00 0.00 0.00 2.29
107 108 8.736244 AGCTATTTGATGTTTTTACCGTATGTT 58.264 29.630 0.00 0.00 0.00 2.71
108 109 9.349145 GCTATTTGATGTTTTTACCGTATGTTT 57.651 29.630 0.00 0.00 0.00 2.83
142 143 8.907222 AAATTATTCAGAAATTTGTTGGCTGT 57.093 26.923 0.00 0.00 35.69 4.40
143 144 8.538409 AATTATTCAGAAATTTGTTGGCTGTC 57.462 30.769 0.00 0.00 0.00 3.51
144 145 5.796424 ATTCAGAAATTTGTTGGCTGTCT 57.204 34.783 0.00 0.00 0.00 3.41
145 146 4.572985 TCAGAAATTTGTTGGCTGTCTG 57.427 40.909 0.00 0.00 33.82 3.51
146 147 3.953612 TCAGAAATTTGTTGGCTGTCTGT 59.046 39.130 0.00 0.00 34.13 3.41
147 148 4.402155 TCAGAAATTTGTTGGCTGTCTGTT 59.598 37.500 0.00 0.00 34.13 3.16
148 149 5.105392 TCAGAAATTTGTTGGCTGTCTGTTT 60.105 36.000 0.00 0.00 34.13 2.83
149 150 5.581874 CAGAAATTTGTTGGCTGTCTGTTTT 59.418 36.000 0.00 0.00 0.00 2.43
150 151 6.756074 CAGAAATTTGTTGGCTGTCTGTTTTA 59.244 34.615 0.00 0.00 0.00 1.52
151 152 7.277539 CAGAAATTTGTTGGCTGTCTGTTTTAA 59.722 33.333 0.00 0.00 0.00 1.52
152 153 7.821846 AGAAATTTGTTGGCTGTCTGTTTTAAA 59.178 29.630 0.00 0.00 0.00 1.52
153 154 7.913674 AATTTGTTGGCTGTCTGTTTTAAAA 57.086 28.000 0.00 0.00 0.00 1.52
154 155 7.913674 ATTTGTTGGCTGTCTGTTTTAAAAA 57.086 28.000 1.31 0.00 0.00 1.94
212 213 9.981114 AAAAGTTCACCATACATTAAGGAAAAG 57.019 29.630 0.00 0.00 0.00 2.27
213 214 8.706322 AAGTTCACCATACATTAAGGAAAAGT 57.294 30.769 0.00 0.00 0.00 2.66
214 215 8.706322 AGTTCACCATACATTAAGGAAAAGTT 57.294 30.769 0.00 0.00 0.00 2.66
215 216 8.793592 AGTTCACCATACATTAAGGAAAAGTTC 58.206 33.333 0.00 0.00 0.00 3.01
216 217 8.573035 GTTCACCATACATTAAGGAAAAGTTCA 58.427 33.333 0.00 0.00 0.00 3.18
217 218 8.106247 TCACCATACATTAAGGAAAAGTTCAC 57.894 34.615 0.00 0.00 0.00 3.18
218 219 7.942341 TCACCATACATTAAGGAAAAGTTCACT 59.058 33.333 0.00 0.00 0.00 3.41
219 220 8.576442 CACCATACATTAAGGAAAAGTTCACTT 58.424 33.333 0.00 0.00 37.91 3.16
221 222 9.410556 CCATACATTAAGGAAAAGTTCACTTTG 57.589 33.333 5.70 0.00 44.69 2.77
222 223 9.965824 CATACATTAAGGAAAAGTTCACTTTGT 57.034 29.630 5.70 1.02 44.69 2.83
230 231 9.990360 AAGGAAAAGTTCACTTTGTAAAAGAAA 57.010 25.926 5.70 0.00 44.69 2.52
231 232 9.990360 AGGAAAAGTTCACTTTGTAAAAGAAAA 57.010 25.926 5.70 0.00 44.69 2.29
237 238 9.974980 AGTTCACTTTGTAAAAGAAAACTTTCA 57.025 25.926 6.73 0.00 39.61 2.69
239 240 9.974980 TTCACTTTGTAAAAGAAAACTTTCACT 57.025 25.926 6.73 0.00 39.61 3.41
240 241 9.405587 TCACTTTGTAAAAGAAAACTTTCACTG 57.594 29.630 6.73 0.00 39.61 3.66
241 242 9.191995 CACTTTGTAAAAGAAAACTTTCACTGT 57.808 29.630 6.73 0.00 39.61 3.55
377 378 7.809546 AAAACAAAAACAAACCCAAAAGAGA 57.190 28.000 0.00 0.00 0.00 3.10
378 379 7.809546 AAACAAAAACAAACCCAAAAGAGAA 57.190 28.000 0.00 0.00 0.00 2.87
379 380 7.809546 AACAAAAACAAACCCAAAAGAGAAA 57.190 28.000 0.00 0.00 0.00 2.52
380 381 7.809546 ACAAAAACAAACCCAAAAGAGAAAA 57.190 28.000 0.00 0.00 0.00 2.29
381 382 7.870826 ACAAAAACAAACCCAAAAGAGAAAAG 58.129 30.769 0.00 0.00 0.00 2.27
382 383 7.040755 ACAAAAACAAACCCAAAAGAGAAAAGG 60.041 33.333 0.00 0.00 0.00 3.11
383 384 6.367374 AAACAAACCCAAAAGAGAAAAGGA 57.633 33.333 0.00 0.00 0.00 3.36
384 385 6.367374 AACAAACCCAAAAGAGAAAAGGAA 57.633 33.333 0.00 0.00 0.00 3.36
385 386 6.367374 ACAAACCCAAAAGAGAAAAGGAAA 57.633 33.333 0.00 0.00 0.00 3.13
386 387 6.774673 ACAAACCCAAAAGAGAAAAGGAAAA 58.225 32.000 0.00 0.00 0.00 2.29
387 388 6.878923 ACAAACCCAAAAGAGAAAAGGAAAAG 59.121 34.615 0.00 0.00 0.00 2.27
388 389 6.867519 AACCCAAAAGAGAAAAGGAAAAGA 57.132 33.333 0.00 0.00 0.00 2.52
389 390 6.867519 ACCCAAAAGAGAAAAGGAAAAGAA 57.132 33.333 0.00 0.00 0.00 2.52
390 391 7.252612 ACCCAAAAGAGAAAAGGAAAAGAAA 57.747 32.000 0.00 0.00 0.00 2.52
391 392 7.861629 ACCCAAAAGAGAAAAGGAAAAGAAAT 58.138 30.769 0.00 0.00 0.00 2.17
392 393 8.988060 ACCCAAAAGAGAAAAGGAAAAGAAATA 58.012 29.630 0.00 0.00 0.00 1.40
393 394 9.830975 CCCAAAAGAGAAAAGGAAAAGAAATAA 57.169 29.630 0.00 0.00 0.00 1.40
456 457 2.301346 AGAGTGGCAAACAAACTGGAG 58.699 47.619 0.00 0.00 0.00 3.86
461 462 3.821033 GTGGCAAACAAACTGGAGATAGT 59.179 43.478 0.00 0.00 0.00 2.12
507 508 8.996988 TTGATATACGAACAACACAAAAGAAC 57.003 30.769 0.00 0.00 0.00 3.01
521 522 4.394920 ACAAAAGAACACGTGTGAGAATGT 59.605 37.500 24.16 20.49 0.00 2.71
535 536 7.517575 CGTGTGAGAATGTTGTGTACACATAAA 60.518 37.037 28.35 17.08 41.52 1.40
585 586 1.731098 GCCCACCAAATTTTACTCGCG 60.731 52.381 0.00 0.00 0.00 5.87
602 603 1.153667 CGGCAGGAGAGAAGTGCTC 60.154 63.158 0.00 0.00 44.29 4.26
618 619 4.425520 AGTGCTCGTAGTCAATTTCTAGC 58.574 43.478 0.00 0.00 0.00 3.42
619 620 4.082190 AGTGCTCGTAGTCAATTTCTAGCA 60.082 41.667 0.00 0.00 0.00 3.49
690 700 4.837896 AAAAAGAAGGAAGCGAGAAAGG 57.162 40.909 0.00 0.00 0.00 3.11
692 702 3.771577 AAGAAGGAAGCGAGAAAGGAA 57.228 42.857 0.00 0.00 0.00 3.36
693 703 3.771577 AGAAGGAAGCGAGAAAGGAAA 57.228 42.857 0.00 0.00 0.00 3.13
694 704 4.086706 AGAAGGAAGCGAGAAAGGAAAA 57.913 40.909 0.00 0.00 0.00 2.29
695 705 4.068599 AGAAGGAAGCGAGAAAGGAAAAG 58.931 43.478 0.00 0.00 0.00 2.27
696 706 2.784347 AGGAAGCGAGAAAGGAAAAGG 58.216 47.619 0.00 0.00 0.00 3.11
697 707 2.372172 AGGAAGCGAGAAAGGAAAAGGA 59.628 45.455 0.00 0.00 0.00 3.36
698 708 3.146847 GGAAGCGAGAAAGGAAAAGGAA 58.853 45.455 0.00 0.00 0.00 3.36
712 722 6.066032 AGGAAAAGGAAAATCTTGTCGGTAA 58.934 36.000 0.00 0.00 33.01 2.85
714 724 6.806739 GGAAAAGGAAAATCTTGTCGGTAATG 59.193 38.462 0.00 0.00 33.01 1.90
726 736 1.548719 TCGGTAATGGACTCCACACAG 59.451 52.381 0.00 2.96 35.80 3.66
753 763 0.179174 CGGGTAGTCCATTTTTGCGC 60.179 55.000 0.00 0.00 34.36 6.09
754 764 0.179174 GGGTAGTCCATTTTTGCGCG 60.179 55.000 0.00 0.00 35.00 6.86
755 765 0.796870 GGTAGTCCATTTTTGCGCGC 60.797 55.000 27.26 27.26 0.00 6.86
756 766 0.796870 GTAGTCCATTTTTGCGCGCC 60.797 55.000 30.77 11.42 0.00 6.53
757 767 1.237954 TAGTCCATTTTTGCGCGCCA 61.238 50.000 30.77 16.58 0.00 5.69
758 768 2.049618 TCCATTTTTGCGCGCCAC 60.050 55.556 30.77 0.92 0.00 5.01
759 769 2.049248 CCATTTTTGCGCGCCACT 60.049 55.556 30.77 5.72 0.00 4.00
760 770 2.374226 CCATTTTTGCGCGCCACTG 61.374 57.895 30.77 17.71 0.00 3.66
761 771 2.049248 ATTTTTGCGCGCCACTGG 60.049 55.556 30.77 0.00 0.00 4.00
762 772 2.855514 ATTTTTGCGCGCCACTGGT 61.856 52.632 30.77 7.45 0.00 4.00
763 773 3.764810 TTTTTGCGCGCCACTGGTG 62.765 57.895 30.77 4.05 36.10 4.17
773 783 1.379044 CCACTGGTGGGATCCAAGC 60.379 63.158 15.23 13.41 46.81 4.01
774 784 1.746615 CACTGGTGGGATCCAAGCG 60.747 63.158 15.23 10.97 37.01 4.68
786 796 3.188786 CAAGCGGCAGAGCGGTAC 61.189 66.667 1.45 0.00 43.00 3.34
787 797 3.691342 AAGCGGCAGAGCGGTACA 61.691 61.111 1.45 0.00 43.00 2.90
788 798 3.934391 AAGCGGCAGAGCGGTACAC 62.934 63.158 1.45 0.00 43.00 2.90
790 800 4.415332 CGGCAGAGCGGTACACGT 62.415 66.667 0.00 0.00 46.52 4.49
791 801 2.879907 GGCAGAGCGGTACACGTA 59.120 61.111 0.00 0.00 46.52 3.57
792 802 1.226603 GGCAGAGCGGTACACGTAG 60.227 63.158 0.00 0.00 46.52 3.51
793 803 1.651240 GGCAGAGCGGTACACGTAGA 61.651 60.000 0.00 0.00 46.52 2.59
794 804 0.248134 GCAGAGCGGTACACGTAGAG 60.248 60.000 0.00 0.00 46.52 2.43
795 805 0.248134 CAGAGCGGTACACGTAGAGC 60.248 60.000 0.00 0.00 46.52 4.09
796 806 1.063811 GAGCGGTACACGTAGAGCC 59.936 63.158 0.00 0.00 46.52 4.70
797 807 1.651240 GAGCGGTACACGTAGAGCCA 61.651 60.000 0.00 0.00 46.52 4.75
798 808 1.035932 AGCGGTACACGTAGAGCCAT 61.036 55.000 0.00 0.00 46.52 4.40
799 809 0.179119 GCGGTACACGTAGAGCCATT 60.179 55.000 0.00 0.00 46.52 3.16
800 810 1.738030 GCGGTACACGTAGAGCCATTT 60.738 52.381 0.00 0.00 46.52 2.32
801 811 1.924524 CGGTACACGTAGAGCCATTTG 59.075 52.381 0.00 0.00 37.93 2.32
802 812 2.673043 CGGTACACGTAGAGCCATTTGT 60.673 50.000 0.00 0.00 37.93 2.83
803 813 2.671396 GGTACACGTAGAGCCATTTGTG 59.329 50.000 0.00 0.00 0.00 3.33
804 814 1.156736 ACACGTAGAGCCATTTGTGC 58.843 50.000 0.00 0.00 0.00 4.57
805 815 0.095245 CACGTAGAGCCATTTGTGCG 59.905 55.000 0.00 0.00 0.00 5.34
806 816 1.060937 CGTAGAGCCATTTGTGCGC 59.939 57.895 0.00 0.00 0.00 6.09
807 817 1.060937 GTAGAGCCATTTGTGCGCG 59.939 57.895 0.00 0.00 33.46 6.86
808 818 2.749865 TAGAGCCATTTGTGCGCGC 61.750 57.895 27.26 27.26 33.46 6.86
812 822 4.041917 CCATTTGTGCGCGCCACT 62.042 61.111 30.77 12.61 44.92 4.00
813 823 2.685829 CCATTTGTGCGCGCCACTA 61.686 57.895 30.77 19.61 44.92 2.74
814 824 1.226101 CATTTGTGCGCGCCACTAG 60.226 57.895 30.77 10.48 44.92 2.57
815 825 1.671054 ATTTGTGCGCGCCACTAGT 60.671 52.632 30.77 16.45 44.92 2.57
816 826 1.635663 ATTTGTGCGCGCCACTAGTC 61.636 55.000 30.77 10.32 44.92 2.59
817 827 2.980213 TTTGTGCGCGCCACTAGTCA 62.980 55.000 30.77 12.79 44.92 3.41
818 828 2.736995 GTGCGCGCCACTAGTCAA 60.737 61.111 30.77 2.53 41.35 3.18
819 829 2.100631 GTGCGCGCCACTAGTCAAT 61.101 57.895 30.77 0.00 41.35 2.57
820 830 1.375396 TGCGCGCCACTAGTCAATT 60.375 52.632 30.77 0.00 0.00 2.32
821 831 0.953471 TGCGCGCCACTAGTCAATTT 60.953 50.000 30.77 0.00 0.00 1.82
822 832 0.247695 GCGCGCCACTAGTCAATTTC 60.248 55.000 23.24 0.00 0.00 2.17
823 833 1.359848 CGCGCCACTAGTCAATTTCT 58.640 50.000 0.00 0.00 0.00 2.52
824 834 1.061131 CGCGCCACTAGTCAATTTCTG 59.939 52.381 0.00 0.00 0.00 3.02
825 835 1.202076 GCGCCACTAGTCAATTTCTGC 60.202 52.381 0.00 0.00 0.00 4.26
826 836 2.076100 CGCCACTAGTCAATTTCTGCA 58.924 47.619 0.00 0.00 0.00 4.41
827 837 2.094894 CGCCACTAGTCAATTTCTGCAG 59.905 50.000 7.63 7.63 0.00 4.41
828 838 3.338249 GCCACTAGTCAATTTCTGCAGA 58.662 45.455 13.74 13.74 0.00 4.26
829 839 3.373439 GCCACTAGTCAATTTCTGCAGAG 59.627 47.826 17.43 5.37 0.00 3.35
830 840 3.373439 CCACTAGTCAATTTCTGCAGAGC 59.627 47.826 17.43 4.68 0.00 4.09
831 841 3.373439 CACTAGTCAATTTCTGCAGAGCC 59.627 47.826 17.43 0.00 0.00 4.70
832 842 2.574006 AGTCAATTTCTGCAGAGCCA 57.426 45.000 17.43 5.65 0.00 4.75
833 843 3.083122 AGTCAATTTCTGCAGAGCCAT 57.917 42.857 17.43 7.85 0.00 4.40
834 844 3.428532 AGTCAATTTCTGCAGAGCCATT 58.571 40.909 17.43 13.30 0.00 3.16
835 845 3.830755 AGTCAATTTCTGCAGAGCCATTT 59.169 39.130 17.43 2.50 0.00 2.32
836 846 3.924686 GTCAATTTCTGCAGAGCCATTTG 59.075 43.478 17.43 14.24 0.00 2.32
837 847 3.575256 TCAATTTCTGCAGAGCCATTTGT 59.425 39.130 17.43 0.00 0.00 2.83
838 848 3.587797 ATTTCTGCAGAGCCATTTGTG 57.412 42.857 17.43 0.00 0.00 3.33
879 889 1.017177 TCGGCATGGTTTGTCTACGC 61.017 55.000 0.00 0.00 0.00 4.42
880 890 1.295357 CGGCATGGTTTGTCTACGCA 61.295 55.000 0.00 0.00 0.00 5.24
881 891 0.168128 GGCATGGTTTGTCTACGCAC 59.832 55.000 0.00 0.00 0.00 5.34
882 892 0.871722 GCATGGTTTGTCTACGCACA 59.128 50.000 0.00 0.00 0.00 4.57
883 893 1.468520 GCATGGTTTGTCTACGCACAT 59.531 47.619 0.00 0.00 0.00 3.21
884 894 2.095263 GCATGGTTTGTCTACGCACATT 60.095 45.455 0.00 0.00 0.00 2.71
885 895 3.491356 CATGGTTTGTCTACGCACATTG 58.509 45.455 0.00 0.00 0.00 2.82
886 896 1.265635 TGGTTTGTCTACGCACATTGC 59.734 47.619 0.00 0.00 40.69 3.56
887 897 1.265635 GGTTTGTCTACGCACATTGCA 59.734 47.619 0.00 0.00 45.36 4.08
888 898 2.095263 GGTTTGTCTACGCACATTGCAT 60.095 45.455 0.00 0.00 45.36 3.96
889 899 2.898181 TTGTCTACGCACATTGCATG 57.102 45.000 0.00 0.00 45.36 4.06
890 900 1.807139 TGTCTACGCACATTGCATGT 58.193 45.000 0.00 0.00 45.36 3.21
928 938 0.824759 GTAGGGTCGCCAGTGAATCT 59.175 55.000 0.00 0.00 0.00 2.40
1030 1054 4.334203 ACTTCACACACTCGCAAACAATTA 59.666 37.500 0.00 0.00 0.00 1.40
1383 1429 2.753701 CCATCCAACCCGGTCACA 59.246 61.111 0.00 0.00 35.57 3.58
1614 1664 1.073199 CGCCAACAGGTTCCTCCTT 59.927 57.895 0.00 0.00 45.67 3.36
2196 2300 1.579932 GAGGACTTCGTGCTCGACA 59.420 57.895 10.88 1.99 46.03 4.35
2240 2344 2.045045 TTTAGCAGGCTGCCGCAT 60.045 55.556 34.33 19.34 46.52 4.73
2304 2428 5.709011 GACAGTGTATTCGTCGACTACTA 57.291 43.478 19.59 0.00 0.00 1.82
2329 2453 7.170277 ACGTGTAATAAATAAGGGAAACACCT 58.830 34.615 0.00 0.00 44.56 4.00
2351 2475 3.812156 CCACCAGTGGTATGAATCGTA 57.188 47.619 16.22 0.00 45.53 3.43
2771 2944 2.689983 GCAGGGAATTCGAACATGGAAT 59.310 45.455 0.00 0.00 35.71 3.01
2831 3004 3.502211 ACGGTCTGGTTTGCTCTTAATTG 59.498 43.478 0.00 0.00 0.00 2.32
2882 3059 1.260033 GTATCGCTCTGCACATGCTTC 59.740 52.381 5.31 0.00 42.66 3.86
3155 3339 9.748708 CAGTGGAGAATTTTTCTGAAATAAACA 57.251 29.630 3.31 0.00 40.87 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.792640 GTTCAGGATCGTGTGCACTG 59.207 55.000 19.41 10.84 0.00 3.66
1 2 0.320771 GGTTCAGGATCGTGTGCACT 60.321 55.000 19.41 0.00 0.00 4.40
2 3 1.626654 CGGTTCAGGATCGTGTGCAC 61.627 60.000 10.75 10.75 0.00 4.57
3 4 1.374125 CGGTTCAGGATCGTGTGCA 60.374 57.895 14.67 0.00 0.00 4.57
4 5 2.100631 CCGGTTCAGGATCGTGTGC 61.101 63.158 14.67 8.84 0.00 4.57
5 6 1.447838 CCCGGTTCAGGATCGTGTG 60.448 63.158 14.67 4.49 0.00 3.82
6 7 2.978824 CCCGGTTCAGGATCGTGT 59.021 61.111 14.67 0.00 0.00 4.49
7 8 2.511600 GCCCGGTTCAGGATCGTG 60.512 66.667 9.16 9.16 0.00 4.35
8 9 4.143333 CGCCCGGTTCAGGATCGT 62.143 66.667 0.00 0.00 0.00 3.73
9 10 3.833645 TCGCCCGGTTCAGGATCG 61.834 66.667 0.00 0.00 0.00 3.69
10 11 2.202892 GTCGCCCGGTTCAGGATC 60.203 66.667 0.00 0.00 0.00 3.36
11 12 1.910580 ATTGTCGCCCGGTTCAGGAT 61.911 55.000 0.00 0.00 0.00 3.24
12 13 2.589157 ATTGTCGCCCGGTTCAGGA 61.589 57.895 0.00 0.00 0.00 3.86
13 14 2.046314 ATTGTCGCCCGGTTCAGG 60.046 61.111 0.00 0.00 0.00 3.86
14 15 1.361668 CTCATTGTCGCCCGGTTCAG 61.362 60.000 0.00 0.00 0.00 3.02
15 16 1.375396 CTCATTGTCGCCCGGTTCA 60.375 57.895 0.00 0.00 0.00 3.18
16 17 2.750888 GCTCATTGTCGCCCGGTTC 61.751 63.158 0.00 0.00 0.00 3.62
17 18 2.746277 GCTCATTGTCGCCCGGTT 60.746 61.111 0.00 0.00 0.00 4.44
18 19 4.778143 GGCTCATTGTCGCCCGGT 62.778 66.667 0.00 0.00 40.43 5.28
24 25 4.776322 TGGGCCGGCTCATTGTCG 62.776 66.667 29.29 0.00 44.42 4.35
25 26 1.322538 AATTGGGCCGGCTCATTGTC 61.323 55.000 33.55 9.29 0.00 3.18
26 27 0.904394 AAATTGGGCCGGCTCATTGT 60.904 50.000 33.55 20.17 0.00 2.71
27 28 0.249955 AAAATTGGGCCGGCTCATTG 59.750 50.000 33.55 0.00 0.00 2.82
28 29 0.536724 GAAAATTGGGCCGGCTCATT 59.463 50.000 33.55 25.18 0.00 2.57
29 30 0.614415 TGAAAATTGGGCCGGCTCAT 60.614 50.000 33.55 16.54 0.00 2.90
30 31 0.829602 TTGAAAATTGGGCCGGCTCA 60.830 50.000 29.29 29.29 0.00 4.26
31 32 0.108662 CTTGAAAATTGGGCCGGCTC 60.109 55.000 28.56 25.91 0.00 4.70
32 33 0.541764 TCTTGAAAATTGGGCCGGCT 60.542 50.000 28.56 3.45 0.00 5.52
33 34 0.108662 CTCTTGAAAATTGGGCCGGC 60.109 55.000 21.18 21.18 0.00 6.13
34 35 1.256812 ACTCTTGAAAATTGGGCCGG 58.743 50.000 0.00 0.00 0.00 6.13
35 36 2.558359 AGAACTCTTGAAAATTGGGCCG 59.442 45.455 0.00 0.00 0.00 6.13
36 37 3.862264 GCAGAACTCTTGAAAATTGGGCC 60.862 47.826 0.00 0.00 0.00 5.80
37 38 3.006217 AGCAGAACTCTTGAAAATTGGGC 59.994 43.478 0.00 0.00 0.00 5.36
38 39 4.861102 AGCAGAACTCTTGAAAATTGGG 57.139 40.909 0.00 0.00 0.00 4.12
39 40 5.835257 TCAAGCAGAACTCTTGAAAATTGG 58.165 37.500 3.26 0.00 44.70 3.16
40 41 5.401674 GCTCAAGCAGAACTCTTGAAAATTG 59.598 40.000 6.84 0.00 46.25 2.32
41 42 5.527033 GCTCAAGCAGAACTCTTGAAAATT 58.473 37.500 6.84 0.00 46.25 1.82
42 43 4.320057 CGCTCAAGCAGAACTCTTGAAAAT 60.320 41.667 2.50 0.00 46.25 1.82
43 44 3.002656 CGCTCAAGCAGAACTCTTGAAAA 59.997 43.478 2.50 0.00 46.25 2.29
44 45 2.545526 CGCTCAAGCAGAACTCTTGAAA 59.454 45.455 2.50 0.00 46.25 2.69
45 46 2.138320 CGCTCAAGCAGAACTCTTGAA 58.862 47.619 2.50 0.00 46.25 2.69
46 47 1.069204 ACGCTCAAGCAGAACTCTTGA 59.931 47.619 2.50 5.48 45.25 3.02
47 48 1.506493 ACGCTCAAGCAGAACTCTTG 58.494 50.000 2.50 0.00 42.21 3.02
48 49 2.246719 AACGCTCAAGCAGAACTCTT 57.753 45.000 2.50 0.00 42.21 2.85
49 50 2.246719 AAACGCTCAAGCAGAACTCT 57.753 45.000 2.50 0.00 42.21 3.24
50 51 4.670227 AATAAACGCTCAAGCAGAACTC 57.330 40.909 2.50 0.00 42.21 3.01
51 52 5.438761 AAAATAAACGCTCAAGCAGAACT 57.561 34.783 2.50 0.00 42.21 3.01
76 77 8.789762 ACGGTAAAAACATCAAATAGCTAGTTT 58.210 29.630 3.16 2.34 0.00 2.66
77 78 8.331730 ACGGTAAAAACATCAAATAGCTAGTT 57.668 30.769 0.00 0.00 0.00 2.24
78 79 7.916914 ACGGTAAAAACATCAAATAGCTAGT 57.083 32.000 0.00 0.00 0.00 2.57
79 80 9.864034 CATACGGTAAAAACATCAAATAGCTAG 57.136 33.333 0.00 0.00 0.00 3.42
80 81 9.386010 ACATACGGTAAAAACATCAAATAGCTA 57.614 29.630 0.00 0.00 0.00 3.32
81 82 8.276252 ACATACGGTAAAAACATCAAATAGCT 57.724 30.769 0.00 0.00 0.00 3.32
82 83 8.905103 AACATACGGTAAAAACATCAAATAGC 57.095 30.769 0.00 0.00 0.00 2.97
116 117 9.341078 ACAGCCAACAAATTTCTGAATAATTTT 57.659 25.926 9.99 0.00 34.01 1.82
117 118 8.907222 ACAGCCAACAAATTTCTGAATAATTT 57.093 26.923 9.99 0.00 36.03 1.82
118 119 8.370182 AGACAGCCAACAAATTTCTGAATAATT 58.630 29.630 9.99 0.00 0.00 1.40
119 120 7.816031 CAGACAGCCAACAAATTTCTGAATAAT 59.184 33.333 9.99 0.00 32.42 1.28
120 121 7.147312 CAGACAGCCAACAAATTTCTGAATAA 58.853 34.615 9.99 0.00 32.42 1.40
121 122 6.265196 ACAGACAGCCAACAAATTTCTGAATA 59.735 34.615 9.99 0.00 34.41 1.75
122 123 5.069516 ACAGACAGCCAACAAATTTCTGAAT 59.930 36.000 9.99 0.00 34.41 2.57
123 124 4.402155 ACAGACAGCCAACAAATTTCTGAA 59.598 37.500 9.99 0.00 34.41 3.02
124 125 3.953612 ACAGACAGCCAACAAATTTCTGA 59.046 39.130 9.99 0.00 34.41 3.27
125 126 4.311816 ACAGACAGCCAACAAATTTCTG 57.688 40.909 3.06 3.06 36.02 3.02
126 127 5.343307 AAACAGACAGCCAACAAATTTCT 57.657 34.783 0.00 0.00 0.00 2.52
127 128 7.532682 TTAAAACAGACAGCCAACAAATTTC 57.467 32.000 0.00 0.00 0.00 2.17
128 129 7.913674 TTTAAAACAGACAGCCAACAAATTT 57.086 28.000 0.00 0.00 0.00 1.82
129 130 7.913674 TTTTAAAACAGACAGCCAACAAATT 57.086 28.000 0.00 0.00 0.00 1.82
130 131 7.913674 TTTTTAAAACAGACAGCCAACAAAT 57.086 28.000 0.00 0.00 0.00 2.32
186 187 9.981114 CTTTTCCTTAATGTATGGTGAACTTTT 57.019 29.630 0.00 0.00 0.00 2.27
187 188 9.143155 ACTTTTCCTTAATGTATGGTGAACTTT 57.857 29.630 0.00 0.00 0.00 2.66
188 189 8.706322 ACTTTTCCTTAATGTATGGTGAACTT 57.294 30.769 0.00 0.00 0.00 2.66
189 190 8.706322 AACTTTTCCTTAATGTATGGTGAACT 57.294 30.769 0.00 0.00 0.00 3.01
190 191 8.573035 TGAACTTTTCCTTAATGTATGGTGAAC 58.427 33.333 0.00 0.00 0.00 3.18
191 192 8.573035 GTGAACTTTTCCTTAATGTATGGTGAA 58.427 33.333 0.00 0.00 0.00 3.18
192 193 7.942341 AGTGAACTTTTCCTTAATGTATGGTGA 59.058 33.333 0.00 0.00 0.00 4.02
193 194 8.110860 AGTGAACTTTTCCTTAATGTATGGTG 57.889 34.615 0.00 0.00 0.00 4.17
194 195 8.706322 AAGTGAACTTTTCCTTAATGTATGGT 57.294 30.769 0.00 0.00 30.82 3.55
195 196 9.410556 CAAAGTGAACTTTTCCTTAATGTATGG 57.589 33.333 5.70 0.00 43.07 2.74
196 197 9.965824 ACAAAGTGAACTTTTCCTTAATGTATG 57.034 29.630 5.70 0.00 43.07 2.39
204 205 9.990360 TTTCTTTTACAAAGTGAACTTTTCCTT 57.010 25.926 5.70 0.00 43.07 3.36
205 206 9.990360 TTTTCTTTTACAAAGTGAACTTTTCCT 57.010 25.926 5.70 0.00 43.07 3.36
352 353 8.226819 TCTCTTTTGGGTTTGTTTTTGTTTTT 57.773 26.923 0.00 0.00 0.00 1.94
353 354 7.809546 TCTCTTTTGGGTTTGTTTTTGTTTT 57.190 28.000 0.00 0.00 0.00 2.43
354 355 7.809546 TTCTCTTTTGGGTTTGTTTTTGTTT 57.190 28.000 0.00 0.00 0.00 2.83
355 356 7.809546 TTTCTCTTTTGGGTTTGTTTTTGTT 57.190 28.000 0.00 0.00 0.00 2.83
356 357 7.040755 CCTTTTCTCTTTTGGGTTTGTTTTTGT 60.041 33.333 0.00 0.00 0.00 2.83
357 358 7.174080 TCCTTTTCTCTTTTGGGTTTGTTTTTG 59.826 33.333 0.00 0.00 0.00 2.44
358 359 7.227873 TCCTTTTCTCTTTTGGGTTTGTTTTT 58.772 30.769 0.00 0.00 0.00 1.94
359 360 6.774673 TCCTTTTCTCTTTTGGGTTTGTTTT 58.225 32.000 0.00 0.00 0.00 2.43
360 361 6.367374 TCCTTTTCTCTTTTGGGTTTGTTT 57.633 33.333 0.00 0.00 0.00 2.83
361 362 6.367374 TTCCTTTTCTCTTTTGGGTTTGTT 57.633 33.333 0.00 0.00 0.00 2.83
362 363 6.367374 TTTCCTTTTCTCTTTTGGGTTTGT 57.633 33.333 0.00 0.00 0.00 2.83
363 364 7.102993 TCTTTTCCTTTTCTCTTTTGGGTTTG 58.897 34.615 0.00 0.00 0.00 2.93
364 365 7.252612 TCTTTTCCTTTTCTCTTTTGGGTTT 57.747 32.000 0.00 0.00 0.00 3.27
365 366 6.867519 TCTTTTCCTTTTCTCTTTTGGGTT 57.132 33.333 0.00 0.00 0.00 4.11
366 367 6.867519 TTCTTTTCCTTTTCTCTTTTGGGT 57.132 33.333 0.00 0.00 0.00 4.51
367 368 9.830975 TTATTTCTTTTCCTTTTCTCTTTTGGG 57.169 29.630 0.00 0.00 0.00 4.12
432 433 4.020662 TCCAGTTTGTTTGCCACTCTTTTT 60.021 37.500 0.00 0.00 0.00 1.94
433 434 3.513515 TCCAGTTTGTTTGCCACTCTTTT 59.486 39.130 0.00 0.00 0.00 2.27
434 435 3.096092 TCCAGTTTGTTTGCCACTCTTT 58.904 40.909 0.00 0.00 0.00 2.52
435 436 2.689983 CTCCAGTTTGTTTGCCACTCTT 59.310 45.455 0.00 0.00 0.00 2.85
436 437 2.092429 TCTCCAGTTTGTTTGCCACTCT 60.092 45.455 0.00 0.00 0.00 3.24
437 438 2.297701 TCTCCAGTTTGTTTGCCACTC 58.702 47.619 0.00 0.00 0.00 3.51
438 439 2.435372 TCTCCAGTTTGTTTGCCACT 57.565 45.000 0.00 0.00 0.00 4.00
439 440 3.821033 ACTATCTCCAGTTTGTTTGCCAC 59.179 43.478 0.00 0.00 0.00 5.01
440 441 4.098914 ACTATCTCCAGTTTGTTTGCCA 57.901 40.909 0.00 0.00 0.00 4.92
441 442 4.798574 CAACTATCTCCAGTTTGTTTGCC 58.201 43.478 0.00 0.00 36.61 4.52
442 443 4.229876 GCAACTATCTCCAGTTTGTTTGC 58.770 43.478 0.00 0.00 36.61 3.68
474 475 4.652421 TGTTCGTATATCAAAGGCGGTA 57.348 40.909 0.00 0.00 0.00 4.02
475 476 3.530265 TGTTCGTATATCAAAGGCGGT 57.470 42.857 0.00 0.00 0.00 5.68
476 477 3.619483 TGTTGTTCGTATATCAAAGGCGG 59.381 43.478 0.00 0.00 0.00 6.13
477 478 4.092237 TGTGTTGTTCGTATATCAAAGGCG 59.908 41.667 0.00 0.00 0.00 5.52
485 486 7.067116 CGTGTTCTTTTGTGTTGTTCGTATAT 58.933 34.615 0.00 0.00 0.00 0.86
507 508 3.553917 TGTACACAACATTCTCACACGTG 59.446 43.478 15.48 15.48 31.43 4.49
535 536 8.943002 CGACTAGGGAAACTTTACAACATTATT 58.057 33.333 0.00 0.00 0.00 1.40
585 586 1.153667 CGAGCACTTCTCTCCTGCC 60.154 63.158 0.00 0.00 39.70 4.85
602 603 2.866762 GGGCTGCTAGAAATTGACTACG 59.133 50.000 0.00 0.00 0.00 3.51
618 619 2.564975 CGAGCAAAAGCAGGGCTG 59.435 61.111 0.00 0.00 39.62 4.85
619 620 2.674380 CCGAGCAAAAGCAGGGCT 60.674 61.111 0.00 0.00 42.56 5.19
674 684 3.189495 CCTTTTCCTTTCTCGCTTCCTTC 59.811 47.826 0.00 0.00 0.00 3.46
690 700 6.806739 CCATTACCGACAAGATTTTCCTTTTC 59.193 38.462 0.00 0.00 0.00 2.29
692 702 6.007703 TCCATTACCGACAAGATTTTCCTTT 58.992 36.000 0.00 0.00 0.00 3.11
693 703 5.414765 GTCCATTACCGACAAGATTTTCCTT 59.585 40.000 0.00 0.00 0.00 3.36
694 704 4.941873 GTCCATTACCGACAAGATTTTCCT 59.058 41.667 0.00 0.00 0.00 3.36
695 705 4.941873 AGTCCATTACCGACAAGATTTTCC 59.058 41.667 0.00 0.00 32.41 3.13
696 706 5.064834 GGAGTCCATTACCGACAAGATTTTC 59.935 44.000 3.60 0.00 32.41 2.29
697 707 4.941873 GGAGTCCATTACCGACAAGATTTT 59.058 41.667 3.60 0.00 32.41 1.82
698 708 4.019681 TGGAGTCCATTACCGACAAGATTT 60.020 41.667 8.12 0.00 32.41 2.17
731 741 1.161843 CAAAAATGGACTACCCGCGT 58.838 50.000 4.92 0.00 37.93 6.01
736 746 0.796870 GCGCGCAAAAATGGACTACC 60.797 55.000 29.10 0.00 0.00 3.18
756 766 1.746615 CGCTTGGATCCCACCAGTG 60.747 63.158 9.90 3.01 41.19 3.66
757 767 2.671070 CGCTTGGATCCCACCAGT 59.329 61.111 9.90 0.00 41.19 4.00
758 768 2.124570 CCGCTTGGATCCCACCAG 60.125 66.667 9.90 1.05 41.19 4.00
759 769 4.424711 GCCGCTTGGATCCCACCA 62.425 66.667 9.90 0.00 38.24 4.17
760 770 4.424711 TGCCGCTTGGATCCCACC 62.425 66.667 9.90 0.00 30.78 4.61
761 771 2.825836 CTGCCGCTTGGATCCCAC 60.826 66.667 9.90 0.00 30.78 4.61
762 772 3.008517 TCTGCCGCTTGGATCCCA 61.009 61.111 9.90 0.00 33.02 4.37
763 773 2.203126 CTCTGCCGCTTGGATCCC 60.203 66.667 9.90 0.00 33.02 3.85
764 774 2.899339 GCTCTGCCGCTTGGATCC 60.899 66.667 4.20 4.20 33.02 3.36
765 775 3.267860 CGCTCTGCCGCTTGGATC 61.268 66.667 0.00 0.00 33.02 3.36
766 776 4.845580 CCGCTCTGCCGCTTGGAT 62.846 66.667 0.00 0.00 33.02 3.41
768 778 4.451150 TACCGCTCTGCCGCTTGG 62.451 66.667 0.00 0.00 0.00 3.61
769 779 3.188786 GTACCGCTCTGCCGCTTG 61.189 66.667 0.00 0.00 0.00 4.01
770 780 3.691342 TGTACCGCTCTGCCGCTT 61.691 61.111 0.00 0.00 0.00 4.68
771 781 4.436998 GTGTACCGCTCTGCCGCT 62.437 66.667 0.00 0.00 0.00 5.52
773 783 2.914797 CTACGTGTACCGCTCTGCCG 62.915 65.000 0.00 0.00 41.42 5.69
774 784 1.226603 CTACGTGTACCGCTCTGCC 60.227 63.158 0.00 0.00 41.42 4.85
786 796 0.095245 CGCACAAATGGCTCTACGTG 59.905 55.000 0.00 0.00 0.00 4.49
787 797 1.635663 GCGCACAAATGGCTCTACGT 61.636 55.000 0.30 0.00 0.00 3.57
788 798 1.060937 GCGCACAAATGGCTCTACG 59.939 57.895 0.30 0.00 0.00 3.51
789 799 1.060937 CGCGCACAAATGGCTCTAC 59.939 57.895 8.75 0.00 0.00 2.59
790 800 2.749865 GCGCGCACAAATGGCTCTA 61.750 57.895 29.10 0.00 0.00 2.43
791 801 4.107051 GCGCGCACAAATGGCTCT 62.107 61.111 29.10 0.00 0.00 4.09
795 805 2.582202 CTAGTGGCGCGCACAAATGG 62.582 60.000 34.42 14.93 0.00 3.16
796 806 1.226101 CTAGTGGCGCGCACAAATG 60.226 57.895 34.42 13.87 0.00 2.32
797 807 1.635663 GACTAGTGGCGCGCACAAAT 61.636 55.000 34.42 19.00 0.00 2.32
798 808 2.280524 ACTAGTGGCGCGCACAAA 60.281 55.556 34.42 18.14 0.00 2.83
799 809 2.736995 GACTAGTGGCGCGCACAA 60.737 61.111 34.42 15.33 0.00 3.33
800 810 2.779951 ATTGACTAGTGGCGCGCACA 62.780 55.000 34.42 24.72 0.00 4.57
801 811 1.635663 AATTGACTAGTGGCGCGCAC 61.636 55.000 34.42 26.65 0.00 5.34
802 812 0.953471 AAATTGACTAGTGGCGCGCA 60.953 50.000 34.42 16.55 0.00 6.09
803 813 0.247695 GAAATTGACTAGTGGCGCGC 60.248 55.000 25.94 25.94 0.00 6.86
804 814 1.061131 CAGAAATTGACTAGTGGCGCG 59.939 52.381 0.00 0.00 0.00 6.86
805 815 1.202076 GCAGAAATTGACTAGTGGCGC 60.202 52.381 0.00 0.00 0.00 6.53
806 816 2.076100 TGCAGAAATTGACTAGTGGCG 58.924 47.619 0.00 0.00 0.00 5.69
807 817 3.338249 TCTGCAGAAATTGACTAGTGGC 58.662 45.455 15.67 0.00 0.00 5.01
808 818 3.373439 GCTCTGCAGAAATTGACTAGTGG 59.627 47.826 18.85 2.06 0.00 4.00
809 819 3.373439 GGCTCTGCAGAAATTGACTAGTG 59.627 47.826 18.85 2.27 0.00 2.74
810 820 3.008375 TGGCTCTGCAGAAATTGACTAGT 59.992 43.478 18.85 0.00 0.00 2.57
811 821 3.603532 TGGCTCTGCAGAAATTGACTAG 58.396 45.455 18.85 3.60 0.00 2.57
812 822 3.701205 TGGCTCTGCAGAAATTGACTA 57.299 42.857 18.85 0.00 0.00 2.59
813 823 2.574006 TGGCTCTGCAGAAATTGACT 57.426 45.000 18.85 0.00 0.00 3.41
814 824 3.863142 AATGGCTCTGCAGAAATTGAC 57.137 42.857 18.85 8.82 0.00 3.18
815 825 3.575256 ACAAATGGCTCTGCAGAAATTGA 59.425 39.130 18.85 0.44 0.00 2.57
816 826 3.678072 CACAAATGGCTCTGCAGAAATTG 59.322 43.478 18.85 18.17 0.00 2.32
817 827 3.575256 TCACAAATGGCTCTGCAGAAATT 59.425 39.130 18.85 14.35 0.00 1.82
818 828 3.159472 TCACAAATGGCTCTGCAGAAAT 58.841 40.909 18.85 9.01 0.00 2.17
819 829 2.555325 CTCACAAATGGCTCTGCAGAAA 59.445 45.455 18.85 6.87 0.00 2.52
820 830 2.156917 CTCACAAATGGCTCTGCAGAA 58.843 47.619 18.85 3.02 0.00 3.02
821 831 1.072806 ACTCACAAATGGCTCTGCAGA 59.927 47.619 17.19 17.19 0.00 4.26
822 832 1.531423 ACTCACAAATGGCTCTGCAG 58.469 50.000 7.63 7.63 0.00 4.41
823 833 2.426522 GTACTCACAAATGGCTCTGCA 58.573 47.619 0.00 0.00 0.00 4.41
824 834 1.740025 GGTACTCACAAATGGCTCTGC 59.260 52.381 0.00 0.00 0.00 4.26
825 835 3.057969 TGGTACTCACAAATGGCTCTG 57.942 47.619 0.00 0.00 0.00 3.35
826 836 3.370953 GGATGGTACTCACAAATGGCTCT 60.371 47.826 0.00 0.00 0.00 4.09
827 837 2.945668 GGATGGTACTCACAAATGGCTC 59.054 50.000 0.00 0.00 0.00 4.70
828 838 2.308570 TGGATGGTACTCACAAATGGCT 59.691 45.455 0.00 0.00 0.00 4.75
829 839 2.722094 TGGATGGTACTCACAAATGGC 58.278 47.619 0.00 0.00 0.00 4.40
830 840 3.129287 GCTTGGATGGTACTCACAAATGG 59.871 47.826 0.00 0.00 0.00 3.16
831 841 4.012374 AGCTTGGATGGTACTCACAAATG 58.988 43.478 0.00 0.00 0.00 2.32
832 842 4.012374 CAGCTTGGATGGTACTCACAAAT 58.988 43.478 0.00 0.00 0.00 2.32
833 843 3.181445 ACAGCTTGGATGGTACTCACAAA 60.181 43.478 0.00 0.00 0.00 2.83
834 844 2.371841 ACAGCTTGGATGGTACTCACAA 59.628 45.455 0.00 0.00 0.00 3.33
835 845 1.977854 ACAGCTTGGATGGTACTCACA 59.022 47.619 0.00 0.00 0.00 3.58
836 846 2.770164 ACAGCTTGGATGGTACTCAC 57.230 50.000 0.00 0.00 0.00 3.51
837 847 2.766263 CCTACAGCTTGGATGGTACTCA 59.234 50.000 0.00 0.00 0.00 3.41
838 848 2.103263 CCCTACAGCTTGGATGGTACTC 59.897 54.545 0.00 0.00 0.00 2.59
886 896 2.095415 CGGGAAGATATGCATGCACATG 60.095 50.000 25.37 6.25 41.60 3.21
887 897 2.156917 CGGGAAGATATGCATGCACAT 58.843 47.619 25.37 18.86 0.00 3.21
888 898 1.596603 CGGGAAGATATGCATGCACA 58.403 50.000 25.37 13.37 0.00 4.57
889 899 0.239347 GCGGGAAGATATGCATGCAC 59.761 55.000 25.37 10.95 0.00 4.57
890 900 1.229975 CGCGGGAAGATATGCATGCA 61.230 55.000 25.04 25.04 0.00 3.96
891 901 1.230635 ACGCGGGAAGATATGCATGC 61.231 55.000 11.82 11.82 0.00 4.06
892 902 1.995484 CTACGCGGGAAGATATGCATG 59.005 52.381 12.47 0.00 0.00 4.06
893 903 1.066858 CCTACGCGGGAAGATATGCAT 60.067 52.381 12.47 3.79 0.00 3.96
894 904 0.317160 CCTACGCGGGAAGATATGCA 59.683 55.000 12.47 0.00 0.00 3.96
895 905 3.123674 CCTACGCGGGAAGATATGC 57.876 57.895 12.47 0.00 0.00 3.14
928 938 3.059099 TGCGATCTCTGCACACCA 58.941 55.556 0.00 0.00 37.44 4.17
1030 1054 0.952497 CTTGCACAGATGGAGCGTGT 60.952 55.000 0.00 0.00 33.13 4.49
1830 1933 3.458163 CGGAGCAAGGCGTAGGGA 61.458 66.667 0.00 0.00 0.00 4.20
1876 1979 2.113139 CCAGGCCTTGGTGAACGT 59.887 61.111 0.00 0.00 42.41 3.99
2045 2149 1.153628 CTTCCCGGTCATCGTCCAC 60.154 63.158 0.00 0.00 37.11 4.02
2104 2208 0.613260 CCCCTTCATCTCCACGAACA 59.387 55.000 0.00 0.00 0.00 3.18
2196 2300 1.202463 CCGCTTCTTCTCCATGTCGAT 60.202 52.381 0.00 0.00 0.00 3.59
2240 2344 3.355455 CCGCCGCAACCCGTAAAA 61.355 61.111 0.00 0.00 34.38 1.52
2304 2428 7.170277 AGGTGTTTCCCTTATTTATTACACGT 58.830 34.615 0.00 0.00 36.42 4.49
2332 2456 4.944048 TCATACGATTCATACCACTGGTG 58.056 43.478 11.32 0.00 36.19 4.17
2333 2457 5.808366 ATCATACGATTCATACCACTGGT 57.192 39.130 5.88 5.88 40.16 4.00
2336 2460 7.815068 GCTTCTTATCATACGATTCATACCACT 59.185 37.037 0.00 0.00 32.73 4.00
2337 2461 7.598869 TGCTTCTTATCATACGATTCATACCAC 59.401 37.037 0.00 0.00 32.73 4.16
2338 2462 7.666623 TGCTTCTTATCATACGATTCATACCA 58.333 34.615 0.00 0.00 32.73 3.25
2339 2463 7.815068 ACTGCTTCTTATCATACGATTCATACC 59.185 37.037 0.00 0.00 32.73 2.73
2340 2464 8.749841 ACTGCTTCTTATCATACGATTCATAC 57.250 34.615 0.00 0.00 32.73 2.39
2341 2465 8.576442 TGACTGCTTCTTATCATACGATTCATA 58.424 33.333 0.00 0.00 32.73 2.15
2344 2468 7.596621 TGATGACTGCTTCTTATCATACGATTC 59.403 37.037 0.00 0.00 31.96 2.52
2348 2472 6.362016 GTCTGATGACTGCTTCTTATCATACG 59.638 42.308 0.00 0.00 39.94 3.06
2351 2475 5.366186 AGGTCTGATGACTGCTTCTTATCAT 59.634 40.000 0.00 0.00 42.54 2.45
2470 2594 4.853507 CGCGTCGGACAAGTTAGA 57.146 55.556 9.10 0.00 0.00 2.10
2539 2664 1.065709 ACCGTATTTGAACGCCCAGAT 60.066 47.619 0.00 0.00 41.51 2.90
2669 2839 9.635404 TCGTGAGAATTAATTAAAATATGGGGT 57.365 29.630 1.21 0.00 37.03 4.95
2771 2944 3.055458 TCGATTGTCAGGCAACAAGGATA 60.055 43.478 10.55 0.00 42.09 2.59
2938 3117 8.188139 TCATGAAAACTAAACAGAAACTTCACC 58.812 33.333 0.00 0.00 0.00 4.02
3139 3323 9.574458 TGAACGTGAATGTTTATTTCAGAAAAA 57.426 25.926 0.00 0.00 30.75 1.94
3155 3339 9.859427 AATATGAAAATGAATGTGAACGTGAAT 57.141 25.926 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.