Multiple sequence alignment - TraesCS2A01G201100

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 TraesCS2A01G201100 chr2A 100.000 3571 0 0 1 3571 174243518 174247088 0.000000e+00 6595
1 TraesCS2A01G201100 chr2A 93.665 1610 92 7 734 2337 174038856 174040461 0.000000e+00 2399
2 TraesCS2A01G201100 chr2A 83.741 1144 155 20 2107 3237 174027246 174028371 0.000000e+00 1053
3 TraesCS2A01G201100 chr2A 82.538 922 135 18 2329 3237 174195615 174196523 0.000000e+00 787
4 TraesCS2A01G201100 chr2A 84.029 551 77 6 742 1289 174025654 174026196 1.470000e-143 520
5 TraesCS2A01G201100 chr2A 92.885 253 14 1 280 532 174031164 174031412 7.290000e-97 364
6 TraesCS2A01G201100 chr2A 90.071 282 23 4 1630 1910 174026488 174026765 9.420000e-96 361
7 TraesCS2A01G201100 chr2A 96.396 111 3 1 619 728 174036635 174036745 7.880000e-42 182
8 TraesCS2A01G201100 chr2A 96.703 91 3 0 531 621 174031447 174031537 6.170000e-33 152
9 TraesCS2A01G201100 chr2A 91.358 81 6 1 560 639 174024191 174024271 3.770000e-20 110
10 TraesCS2A01G201100 chr2D 94.141 1792 97 7 1120 2907 174382061 174383848 0.000000e+00 2721
11 TraesCS2A01G201100 chr2D 85.195 1101 139 15 2149 3237 174324520 174325608 0.000000e+00 1109
12 TraesCS2A01G201100 chr2D 93.971 680 27 4 2903 3571 174388348 174389024 0.000000e+00 1016
13 TraesCS2A01G201100 chr2D 84.576 791 107 10 742 1527 174321922 174322702 0.000000e+00 771
14 TraesCS2A01G201100 chr2D 86.349 630 38 15 531 1126 174330988 174331603 0.000000e+00 643
15 TraesCS2A01G201100 chr2D 95.652 253 11 0 280 532 174330704 174330956 1.190000e-109 407
16 TraesCS2A01G201100 chr2D 89.716 282 24 4 1630 1910 174322798 174323075 4.380000e-94 355
17 TraesCS2A01G201100 chr2B 84.822 1153 141 20 2107 3246 222143132 222144263 0.000000e+00 1129
18 TraesCS2A01G201100 chr2B 82.929 990 129 26 560 1527 222141528 222142499 0.000000e+00 856
19 TraesCS2A01G201100 chr2B 88.380 284 28 4 1630 1912 222142586 222142865 1.590000e-88 337
20 TraesCS2A01G201100 chr3D 83.392 849 131 8 2138 2981 307881598 307882441 0.000000e+00 778
21 TraesCS2A01G201100 chr3D 80.443 542 101 5 975 1513 307879989 307880528 3.320000e-110 409
22 TraesCS2A01G201100 chr3B 83.152 825 130 8 2160 2983 413864063 413863247 0.000000e+00 745
23 TraesCS2A01G201100 chr3B 81.400 543 96 5 974 1513 413866021 413865481 4.230000e-119 438
24 TraesCS2A01G201100 chr3B 84.848 264 40 0 1629 1892 413865390 413865127 2.110000e-67 267
25 TraesCS2A01G201100 chr3A 82.000 850 141 10 2138 2981 427193124 427193967 0.000000e+00 712
26 TraesCS2A01G201100 chr3A 80.000 545 104 5 971 1513 427191517 427192058 7.180000e-107 398
27 TraesCS2A01G201100 chr1A 76.812 828 165 20 2160 2981 534051255 534050449 1.180000e-119 440
28 TraesCS2A01G201100 chr5B 86.620 284 35 3 1 281 557519483 557519200 9.630000e-81 311


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 TraesCS2A01G201100 chr2A 174243518 174247088 3570 False 6595.000000 6595 100.000000 1 3571 1 chr2A.!!$F2 3570
1 TraesCS2A01G201100 chr2A 174036635 174040461 3826 False 1290.500000 2399 95.030500 619 2337 2 chr2A.!!$F4 1718
2 TraesCS2A01G201100 chr2A 174195615 174196523 908 False 787.000000 787 82.538000 2329 3237 1 chr2A.!!$F1 908
3 TraesCS2A01G201100 chr2A 174024191 174031537 7346 False 426.666667 1053 89.797833 280 3237 6 chr2A.!!$F3 2957
4 TraesCS2A01G201100 chr2D 174382061 174383848 1787 False 2721.000000 2721 94.141000 1120 2907 1 chr2D.!!$F1 1787
5 TraesCS2A01G201100 chr2D 174388348 174389024 676 False 1016.000000 1016 93.971000 2903 3571 1 chr2D.!!$F2 668
6 TraesCS2A01G201100 chr2D 174321922 174325608 3686 False 745.000000 1109 86.495667 742 3237 3 chr2D.!!$F3 2495
7 TraesCS2A01G201100 chr2D 174330704 174331603 899 False 525.000000 643 91.000500 280 1126 2 chr2D.!!$F4 846
8 TraesCS2A01G201100 chr2B 222141528 222144263 2735 False 774.000000 1129 85.377000 560 3246 3 chr2B.!!$F1 2686
9 TraesCS2A01G201100 chr3D 307879989 307882441 2452 False 593.500000 778 81.917500 975 2981 2 chr3D.!!$F1 2006
10 TraesCS2A01G201100 chr3B 413863247 413866021 2774 True 483.333333 745 83.133333 974 2983 3 chr3B.!!$R1 2009
11 TraesCS2A01G201100 chr3A 427191517 427193967 2450 False 555.000000 712 81.000000 971 2981 2 chr3A.!!$F1 2010
12 TraesCS2A01G201100 chr1A 534050449 534051255 806 True 440.000000 440 76.812000 2160 2981 1 chr1A.!!$R1 821

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
54 55 0.034616 CCATTCAGAGAGCGATCCCC 59.965 60.0 0.00 0.0 0.0 4.81 F
55 56 0.034616 CATTCAGAGAGCGATCCCCC 59.965 60.0 0.00 0.0 0.0 5.40 F
1464 4871 0.035439 ACGGCGAGAAATGGGTCAAT 60.035 50.0 16.62 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 4775 0.234884 CGAAGTGGCCGAACTTGTTC 59.765 55.0 12.93 3.6 40.48 3.18 R
1695 5145 0.613260 CCGTCTGAACCAAGGGATCA 59.387 55.0 0.00 0.0 33.54 2.92 R
2631 8467 0.033504 AGAATCGTGGTCACTTGCGT 59.966 50.0 0.00 0.0 0.00 5.24 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 4.383861 CTCGTGCTCTGGCCTGCA 62.384 66.667 3.32 9.55 37.74 4.41
18 19 3.677284 CTCGTGCTCTGGCCTGCAT 62.677 63.158 18.43 0.00 41.45 3.96
19 20 3.200593 CGTGCTCTGGCCTGCATC 61.201 66.667 18.43 12.38 41.45 3.91
20 21 3.200593 GTGCTCTGGCCTGCATCG 61.201 66.667 18.43 3.56 41.45 3.84
21 22 3.709633 TGCTCTGGCCTGCATCGT 61.710 61.111 3.32 0.00 37.74 3.73
22 23 2.437359 GCTCTGGCCTGCATCGTT 60.437 61.111 3.32 0.00 0.00 3.85
23 24 2.467826 GCTCTGGCCTGCATCGTTC 61.468 63.158 3.32 0.00 0.00 3.95
24 25 1.078918 CTCTGGCCTGCATCGTTCA 60.079 57.895 3.32 0.00 0.00 3.18
25 26 0.463295 CTCTGGCCTGCATCGTTCAT 60.463 55.000 3.32 0.00 0.00 2.57
26 27 0.745486 TCTGGCCTGCATCGTTCATG 60.745 55.000 3.32 0.00 35.29 3.07
27 28 1.002257 TGGCCTGCATCGTTCATGT 60.002 52.632 3.32 0.00 34.56 3.21
28 29 1.026182 TGGCCTGCATCGTTCATGTC 61.026 55.000 3.32 0.00 34.56 3.06
29 30 1.026182 GGCCTGCATCGTTCATGTCA 61.026 55.000 0.00 0.00 34.56 3.58
30 31 1.019673 GCCTGCATCGTTCATGTCAT 58.980 50.000 0.00 0.00 34.56 3.06
31 32 1.268386 GCCTGCATCGTTCATGTCATG 60.268 52.381 6.47 6.47 34.56 3.07
32 33 1.332686 CCTGCATCGTTCATGTCATGG 59.667 52.381 12.90 0.00 34.56 3.66
33 34 0.734309 TGCATCGTTCATGTCATGGC 59.266 50.000 12.90 7.62 34.56 4.40
34 35 0.734309 GCATCGTTCATGTCATGGCA 59.266 50.000 12.90 0.60 34.56 4.92
35 36 1.532505 GCATCGTTCATGTCATGGCAC 60.533 52.381 12.90 9.03 34.56 5.01
36 37 1.064505 CATCGTTCATGTCATGGCACC 59.935 52.381 12.90 0.00 0.00 5.01
37 38 0.036022 TCGTTCATGTCATGGCACCA 59.964 50.000 12.90 0.00 0.00 4.17
38 39 1.097232 CGTTCATGTCATGGCACCAT 58.903 50.000 12.90 0.00 37.08 3.55
39 40 1.473677 CGTTCATGTCATGGCACCATT 59.526 47.619 12.90 0.00 33.90 3.16
40 41 2.478370 CGTTCATGTCATGGCACCATTC 60.478 50.000 12.90 0.00 33.90 2.67
41 42 2.492881 GTTCATGTCATGGCACCATTCA 59.507 45.455 12.90 3.31 33.90 2.57
42 43 2.371306 TCATGTCATGGCACCATTCAG 58.629 47.619 12.90 0.00 33.90 3.02
43 44 2.026075 TCATGTCATGGCACCATTCAGA 60.026 45.455 12.90 0.00 33.90 3.27
44 45 2.118313 TGTCATGGCACCATTCAGAG 57.882 50.000 0.00 0.00 33.90 3.35
45 46 1.629861 TGTCATGGCACCATTCAGAGA 59.370 47.619 0.00 0.00 33.90 3.10
46 47 2.286872 GTCATGGCACCATTCAGAGAG 58.713 52.381 0.00 0.00 33.90 3.20
47 48 1.022735 CATGGCACCATTCAGAGAGC 58.977 55.000 0.00 0.00 33.90 4.09
48 49 0.463295 ATGGCACCATTCAGAGAGCG 60.463 55.000 0.00 0.00 31.82 5.03
49 50 1.219124 GGCACCATTCAGAGAGCGA 59.781 57.895 0.00 0.00 0.00 4.93
50 51 0.179062 GGCACCATTCAGAGAGCGAT 60.179 55.000 0.00 0.00 0.00 4.58
51 52 1.216122 GCACCATTCAGAGAGCGATC 58.784 55.000 0.00 0.00 0.00 3.69
52 53 1.863267 CACCATTCAGAGAGCGATCC 58.137 55.000 0.00 0.00 0.00 3.36
53 54 0.755686 ACCATTCAGAGAGCGATCCC 59.244 55.000 0.00 0.00 0.00 3.85
54 55 0.034616 CCATTCAGAGAGCGATCCCC 59.965 60.000 0.00 0.00 0.00 4.81
55 56 0.034616 CATTCAGAGAGCGATCCCCC 59.965 60.000 0.00 0.00 0.00 5.40
56 57 0.105246 ATTCAGAGAGCGATCCCCCT 60.105 55.000 0.00 0.00 0.00 4.79
57 58 0.325671 TTCAGAGAGCGATCCCCCTT 60.326 55.000 0.00 0.00 0.00 3.95
58 59 1.045350 TCAGAGAGCGATCCCCCTTG 61.045 60.000 0.00 0.00 0.00 3.61
59 60 2.110006 GAGAGCGATCCCCCTTGC 59.890 66.667 0.00 0.00 0.00 4.01
60 61 2.366167 AGAGCGATCCCCCTTGCT 60.366 61.111 0.00 0.00 38.62 3.91
61 62 2.203126 GAGCGATCCCCCTTGCTG 60.203 66.667 0.00 0.00 35.97 4.41
62 63 3.764160 GAGCGATCCCCCTTGCTGG 62.764 68.421 0.00 0.00 35.97 4.85
63 64 4.115199 GCGATCCCCCTTGCTGGT 62.115 66.667 0.00 0.00 0.00 4.00
64 65 2.124570 CGATCCCCCTTGCTGGTG 60.125 66.667 0.00 0.00 0.00 4.17
65 66 2.440980 GATCCCCCTTGCTGGTGC 60.441 66.667 0.00 0.00 40.20 5.01
66 67 4.066139 ATCCCCCTTGCTGGTGCC 62.066 66.667 0.00 0.00 38.71 5.01
71 72 4.954970 CCTTGCTGGTGCCCACGT 62.955 66.667 0.00 0.00 38.71 4.49
72 73 2.906897 CTTGCTGGTGCCCACGTT 60.907 61.111 0.00 0.00 38.71 3.99
73 74 3.198236 CTTGCTGGTGCCCACGTTG 62.198 63.158 0.00 0.00 38.71 4.10
76 77 4.954970 CTGGTGCCCACGTTGCCT 62.955 66.667 4.50 0.00 0.00 4.75
83 84 3.673484 CCACGTTGCCTGCCCAAG 61.673 66.667 0.00 0.00 0.00 3.61
94 95 4.299796 GCCCAAGGCCAGGACCAA 62.300 66.667 15.35 0.00 44.06 3.67
95 96 2.283173 CCCAAGGCCAGGACCAAC 60.283 66.667 15.35 0.00 0.00 3.77
96 97 2.283173 CCAAGGCCAGGACCAACC 60.283 66.667 5.01 0.00 39.35 3.77
97 98 2.520458 CAAGGCCAGGACCAACCA 59.480 61.111 5.01 0.00 42.04 3.67
98 99 1.903404 CAAGGCCAGGACCAACCAC 60.903 63.158 5.01 0.00 42.04 4.16
99 100 3.491598 AAGGCCAGGACCAACCACG 62.492 63.158 5.01 0.00 42.04 4.94
100 101 4.265056 GGCCAGGACCAACCACGT 62.265 66.667 0.00 0.00 42.04 4.49
101 102 2.203294 GCCAGGACCAACCACGTT 60.203 61.111 0.00 0.00 42.04 3.99
102 103 2.258726 GCCAGGACCAACCACGTTC 61.259 63.158 0.00 0.00 42.04 3.95
103 104 1.599797 CCAGGACCAACCACGTTCC 60.600 63.158 0.00 0.00 42.04 3.62
104 105 1.147376 CAGGACCAACCACGTTCCA 59.853 57.895 4.61 0.00 42.04 3.53
105 106 0.250727 CAGGACCAACCACGTTCCAT 60.251 55.000 4.61 0.00 42.04 3.41
106 107 1.002659 CAGGACCAACCACGTTCCATA 59.997 52.381 4.61 0.00 42.04 2.74
107 108 1.002773 AGGACCAACCACGTTCCATAC 59.997 52.381 4.61 0.00 42.04 2.39
108 109 1.445871 GACCAACCACGTTCCATACC 58.554 55.000 0.00 0.00 0.00 2.73
109 110 1.002773 GACCAACCACGTTCCATACCT 59.997 52.381 0.00 0.00 0.00 3.08
110 111 1.271163 ACCAACCACGTTCCATACCTG 60.271 52.381 0.00 0.00 0.00 4.00
111 112 0.802494 CAACCACGTTCCATACCTGC 59.198 55.000 0.00 0.00 0.00 4.85
112 113 0.322187 AACCACGTTCCATACCTGCC 60.322 55.000 0.00 0.00 0.00 4.85
113 114 1.813753 CCACGTTCCATACCTGCCG 60.814 63.158 0.00 0.00 0.00 5.69
114 115 2.125269 ACGTTCCATACCTGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
115 116 3.261951 CGTTCCATACCTGCCGCG 61.262 66.667 0.00 0.00 0.00 6.46
116 117 3.573491 GTTCCATACCTGCCGCGC 61.573 66.667 0.00 0.00 0.00 6.86
117 118 4.089239 TTCCATACCTGCCGCGCA 62.089 61.111 8.75 1.04 36.92 6.09
118 119 3.613877 TTCCATACCTGCCGCGCAA 62.614 57.895 8.75 0.00 38.41 4.85
119 120 3.130819 CCATACCTGCCGCGCAAA 61.131 61.111 8.75 0.00 38.41 3.68
120 121 2.100216 CATACCTGCCGCGCAAAC 59.900 61.111 8.75 0.00 38.41 2.93
121 122 2.359354 ATACCTGCCGCGCAAACA 60.359 55.556 8.75 0.18 38.41 2.83
122 123 2.686816 ATACCTGCCGCGCAAACAC 61.687 57.895 8.75 0.00 38.41 3.32
124 125 4.980903 CCTGCCGCGCAAACACAC 62.981 66.667 8.75 0.00 38.41 3.82
125 126 4.249020 CTGCCGCGCAAACACACA 62.249 61.111 8.75 0.00 38.41 3.72
126 127 3.748071 CTGCCGCGCAAACACACAA 62.748 57.895 8.75 0.00 38.41 3.33
127 128 2.354539 GCCGCGCAAACACACAAT 60.355 55.556 8.75 0.00 0.00 2.71
128 129 2.364311 GCCGCGCAAACACACAATC 61.364 57.895 8.75 0.00 0.00 2.67
129 130 1.729131 CCGCGCAAACACACAATCC 60.729 57.895 8.75 0.00 0.00 3.01
130 131 1.009108 CGCGCAAACACACAATCCA 60.009 52.632 8.75 0.00 0.00 3.41
131 132 1.268113 CGCGCAAACACACAATCCAC 61.268 55.000 8.75 0.00 0.00 4.02
132 133 0.939106 GCGCAAACACACAATCCACC 60.939 55.000 0.30 0.00 0.00 4.61
133 134 0.383590 CGCAAACACACAATCCACCA 59.616 50.000 0.00 0.00 0.00 4.17
134 135 1.600164 CGCAAACACACAATCCACCAG 60.600 52.381 0.00 0.00 0.00 4.00
135 136 1.680735 GCAAACACACAATCCACCAGA 59.319 47.619 0.00 0.00 0.00 3.86
136 137 2.100584 GCAAACACACAATCCACCAGAA 59.899 45.455 0.00 0.00 0.00 3.02
137 138 3.796504 GCAAACACACAATCCACCAGAAG 60.797 47.826 0.00 0.00 0.00 2.85
138 139 2.276732 ACACACAATCCACCAGAAGG 57.723 50.000 0.00 0.00 42.21 3.46
151 152 3.721087 CCAGAAGGTACCCAATTGTCT 57.279 47.619 8.74 0.00 0.00 3.41
152 153 3.610911 CCAGAAGGTACCCAATTGTCTC 58.389 50.000 8.74 0.00 0.00 3.36
153 154 3.610911 CAGAAGGTACCCAATTGTCTCC 58.389 50.000 8.74 1.82 0.00 3.71
154 155 3.264450 CAGAAGGTACCCAATTGTCTCCT 59.736 47.826 8.74 4.07 0.00 3.69
155 156 3.519913 AGAAGGTACCCAATTGTCTCCTC 59.480 47.826 8.74 2.49 0.00 3.71
156 157 2.197465 AGGTACCCAATTGTCTCCTCC 58.803 52.381 8.74 0.00 0.00 4.30
157 158 2.197465 GGTACCCAATTGTCTCCTCCT 58.803 52.381 0.00 0.00 0.00 3.69
158 159 2.170817 GGTACCCAATTGTCTCCTCCTC 59.829 54.545 0.00 0.00 0.00 3.71
159 160 2.350863 ACCCAATTGTCTCCTCCTCT 57.649 50.000 4.43 0.00 0.00 3.69
160 161 2.637165 ACCCAATTGTCTCCTCCTCTT 58.363 47.619 4.43 0.00 0.00 2.85
161 162 2.307098 ACCCAATTGTCTCCTCCTCTTG 59.693 50.000 4.43 0.00 0.00 3.02
162 163 2.573462 CCCAATTGTCTCCTCCTCTTGA 59.427 50.000 4.43 0.00 0.00 3.02
163 164 3.201708 CCCAATTGTCTCCTCCTCTTGAT 59.798 47.826 4.43 0.00 0.00 2.57
164 165 4.450053 CCAATTGTCTCCTCCTCTTGATC 58.550 47.826 4.43 0.00 0.00 2.92
165 166 4.118410 CAATTGTCTCCTCCTCTTGATCG 58.882 47.826 0.00 0.00 0.00 3.69
166 167 1.107114 TGTCTCCTCCTCTTGATCGC 58.893 55.000 0.00 0.00 0.00 4.58
167 168 1.107114 GTCTCCTCCTCTTGATCGCA 58.893 55.000 0.00 0.00 0.00 5.10
168 169 1.686052 GTCTCCTCCTCTTGATCGCAT 59.314 52.381 0.00 0.00 0.00 4.73
169 170 2.887783 GTCTCCTCCTCTTGATCGCATA 59.112 50.000 0.00 0.00 0.00 3.14
170 171 3.319405 GTCTCCTCCTCTTGATCGCATAA 59.681 47.826 0.00 0.00 0.00 1.90
171 172 3.571828 TCTCCTCCTCTTGATCGCATAAG 59.428 47.826 0.00 0.00 0.00 1.73
172 173 2.630098 TCCTCCTCTTGATCGCATAAGG 59.370 50.000 0.00 0.00 0.00 2.69
173 174 2.289320 CCTCCTCTTGATCGCATAAGGG 60.289 54.545 0.00 0.00 30.76 3.95
174 175 1.694150 TCCTCTTGATCGCATAAGGGG 59.306 52.381 3.48 3.48 44.34 4.79
175 176 1.517242 CTCTTGATCGCATAAGGGGC 58.483 55.000 0.00 0.00 0.00 5.80
176 177 0.836606 TCTTGATCGCATAAGGGGCA 59.163 50.000 0.00 0.00 0.00 5.36
177 178 0.947244 CTTGATCGCATAAGGGGCAC 59.053 55.000 0.00 0.00 0.00 5.01
178 179 0.254462 TTGATCGCATAAGGGGCACA 59.746 50.000 0.00 0.00 0.00 4.57
179 180 0.463654 TGATCGCATAAGGGGCACAC 60.464 55.000 0.00 0.00 0.00 3.82
180 181 1.152963 ATCGCATAAGGGGCACACC 60.153 57.895 0.00 0.00 39.11 4.16
181 182 1.635817 ATCGCATAAGGGGCACACCT 61.636 55.000 0.00 0.00 44.56 4.00
182 183 1.819632 CGCATAAGGGGCACACCTC 60.820 63.158 0.00 0.00 40.87 3.85
183 184 1.453928 GCATAAGGGGCACACCTCC 60.454 63.158 0.00 0.00 40.87 4.30
184 185 1.998530 CATAAGGGGCACACCTCCA 59.001 57.895 0.00 0.00 40.87 3.86
185 186 0.552848 CATAAGGGGCACACCTCCAT 59.447 55.000 0.00 0.00 40.87 3.41
186 187 0.552848 ATAAGGGGCACACCTCCATG 59.447 55.000 0.00 0.00 40.87 3.66
187 188 0.844661 TAAGGGGCACACCTCCATGT 60.845 55.000 0.00 0.00 40.87 3.21
195 196 2.795231 ACACCTCCATGTGATCAAGG 57.205 50.000 8.57 8.57 39.57 3.61
196 197 1.340405 ACACCTCCATGTGATCAAGGC 60.340 52.381 9.84 0.00 39.57 4.35
197 198 0.994247 ACCTCCATGTGATCAAGGCA 59.006 50.000 9.84 0.00 33.05 4.75
198 199 1.567649 ACCTCCATGTGATCAAGGCAT 59.432 47.619 9.84 1.28 33.05 4.40
199 200 2.228059 CCTCCATGTGATCAAGGCATC 58.772 52.381 0.00 0.00 33.05 3.91
200 201 1.871676 CTCCATGTGATCAAGGCATCG 59.128 52.381 0.00 0.00 33.05 3.84
201 202 0.309922 CCATGTGATCAAGGCATCGC 59.690 55.000 0.00 0.00 34.39 4.58
211 212 3.567797 GGCATCGCCGAGCAAGAC 61.568 66.667 9.96 0.00 39.62 3.01
212 213 3.918220 GCATCGCCGAGCAAGACG 61.918 66.667 0.00 0.00 0.00 4.18
218 219 2.962569 CCGAGCAAGACGGTCTGA 59.037 61.111 12.12 0.00 44.57 3.27
219 220 1.153939 CCGAGCAAGACGGTCTGAG 60.154 63.158 12.12 8.83 44.57 3.35
220 221 1.153939 CGAGCAAGACGGTCTGAGG 60.154 63.158 12.12 5.93 40.13 3.86
221 222 1.867919 CGAGCAAGACGGTCTGAGGT 61.868 60.000 12.12 12.81 40.13 3.85
222 223 0.109039 GAGCAAGACGGTCTGAGGTC 60.109 60.000 20.07 20.07 39.15 3.85
223 224 1.079750 GCAAGACGGTCTGAGGTCC 60.080 63.158 12.12 0.00 33.66 4.46
224 225 1.816863 GCAAGACGGTCTGAGGTCCA 61.817 60.000 12.12 0.00 33.66 4.02
225 226 0.244994 CAAGACGGTCTGAGGTCCAG 59.755 60.000 12.12 0.00 44.27 3.86
226 227 1.536943 AAGACGGTCTGAGGTCCAGC 61.537 60.000 12.12 0.00 42.62 4.85
227 228 2.203640 ACGGTCTGAGGTCCAGCA 60.204 61.111 0.00 0.00 42.62 4.41
228 229 2.262915 CGGTCTGAGGTCCAGCAC 59.737 66.667 0.00 0.00 42.62 4.40
242 243 4.395583 GCACCTGTTGCGCTGAGC 62.396 66.667 9.73 0.00 42.79 4.26
259 260 1.710339 GCTAGCCAAGCGAGAAACG 59.290 57.895 2.29 0.00 42.53 3.60
260 261 0.736325 GCTAGCCAAGCGAGAAACGA 60.736 55.000 2.29 0.00 42.53 3.85
261 262 0.992802 CTAGCCAAGCGAGAAACGAC 59.007 55.000 0.00 0.00 45.77 4.34
262 263 0.315886 TAGCCAAGCGAGAAACGACA 59.684 50.000 0.00 0.00 45.77 4.35
263 264 1.204312 GCCAAGCGAGAAACGACAC 59.796 57.895 0.00 0.00 45.77 3.67
264 265 1.222115 GCCAAGCGAGAAACGACACT 61.222 55.000 0.00 0.00 45.77 3.55
265 266 0.508641 CCAAGCGAGAAACGACACTG 59.491 55.000 0.00 0.00 45.77 3.66
266 267 0.508641 CAAGCGAGAAACGACACTGG 59.491 55.000 0.00 0.00 45.77 4.00
267 268 0.387929 AAGCGAGAAACGACACTGGA 59.612 50.000 0.00 0.00 45.77 3.86
268 269 0.039074 AGCGAGAAACGACACTGGAG 60.039 55.000 0.00 0.00 45.77 3.86
269 270 1.009389 GCGAGAAACGACACTGGAGG 61.009 60.000 0.00 0.00 45.77 4.30
270 271 0.388649 CGAGAAACGACACTGGAGGG 60.389 60.000 0.00 0.00 45.77 4.30
271 272 0.037232 GAGAAACGACACTGGAGGGG 60.037 60.000 0.00 0.00 0.00 4.79
272 273 1.671379 GAAACGACACTGGAGGGGC 60.671 63.158 0.00 0.00 0.00 5.80
273 274 2.113243 GAAACGACACTGGAGGGGCT 62.113 60.000 0.00 0.00 0.00 5.19
274 275 2.113243 AAACGACACTGGAGGGGCTC 62.113 60.000 0.00 0.00 0.00 4.70
275 276 2.997315 CGACACTGGAGGGGCTCA 60.997 66.667 0.00 0.00 31.08 4.26
276 277 2.665603 GACACTGGAGGGGCTCAC 59.334 66.667 0.00 0.00 31.08 3.51
277 278 3.302347 GACACTGGAGGGGCTCACG 62.302 68.421 0.00 0.00 31.08 4.35
278 279 4.087892 CACTGGAGGGGCTCACGG 62.088 72.222 0.00 0.00 31.08 4.94
279 280 4.640690 ACTGGAGGGGCTCACGGT 62.641 66.667 0.00 0.00 31.08 4.83
280 281 3.322466 CTGGAGGGGCTCACGGTT 61.322 66.667 0.00 0.00 31.08 4.44
281 282 1.987855 CTGGAGGGGCTCACGGTTA 60.988 63.158 0.00 0.00 31.08 2.85
344 345 5.359194 TGATCACCTCCTCCTTTATTCAC 57.641 43.478 0.00 0.00 0.00 3.18
363 364 2.691526 CACTCATAGCAATGGTGGCATT 59.308 45.455 0.00 0.00 33.84 3.56
413 414 1.605202 GCGCAAATTCCAGCCAAGAAA 60.605 47.619 0.30 0.00 0.00 2.52
417 418 3.367292 GCAAATTCCAGCCAAGAAATCGA 60.367 43.478 0.00 0.00 0.00 3.59
528 529 9.790344 ATCTAGAGACATAAAATAGCAGCAATT 57.210 29.630 0.00 0.00 0.00 2.32
534 568 6.934056 ACATAAAATAGCAGCAATTGAACCA 58.066 32.000 10.34 0.00 0.00 3.67
557 591 3.259876 TCAAGTAATGCTACGACCACCTT 59.740 43.478 0.00 0.00 32.87 3.50
728 2021 9.745018 ATTGTTACTAGTGGTCAGTAGTACTAA 57.255 33.333 19.55 17.30 44.84 2.24
730 2023 9.388506 TGTTACTAGTGGTCAGTAGTACTAATC 57.611 37.037 19.55 11.43 44.84 1.75
731 2024 9.388506 GTTACTAGTGGTCAGTAGTACTAATCA 57.611 37.037 19.55 0.00 44.84 2.57
732 2025 9.964354 TTACTAGTGGTCAGTAGTACTAATCAA 57.036 33.333 19.55 7.64 44.84 2.57
756 4154 7.916914 AACCGTAAATTAACTAATCAGCTGT 57.083 32.000 14.67 0.00 0.00 4.40
763 4161 8.492673 AAATTAACTAATCAGCTGTCAATCGA 57.507 30.769 14.67 0.00 0.00 3.59
770 4168 4.192429 TCAGCTGTCAATCGAATCTTCA 57.808 40.909 14.67 0.00 0.00 3.02
838 4236 2.642311 TCAGATAGGCCACAACCTTTGA 59.358 45.455 5.01 0.00 41.50 2.69
842 4240 5.471456 CAGATAGGCCACAACCTTTGATATC 59.529 44.000 5.01 0.00 41.50 1.63
848 4246 6.667414 AGGCCACAACCTTTGATATCAAATAA 59.333 34.615 26.83 9.36 43.92 1.40
849 4247 7.180051 AGGCCACAACCTTTGATATCAAATAAA 59.820 33.333 26.83 9.02 43.92 1.40
876 4278 7.771183 AGTGCAAGAACATCTCTTAAACAAAA 58.229 30.769 0.00 0.00 42.84 2.44
895 4297 7.618019 ACAAAAGGGACATCTCTATATAGCA 57.382 36.000 4.75 0.00 0.00 3.49
927 4331 6.701841 TCTCTAGCATACCGATTCAATCAAAC 59.298 38.462 0.00 0.00 0.00 2.93
985 4392 5.047448 CCTCACTTGTCAAGAGAGAGAATGA 60.047 44.000 30.44 16.09 45.48 2.57
990 4397 5.850557 TGTCAAGAGAGAGAATGATCCTC 57.149 43.478 0.00 0.00 0.00 3.71
993 4400 5.360714 GTCAAGAGAGAGAATGATCCTCAGT 59.639 44.000 0.00 0.00 33.25 3.41
995 4402 4.870636 AGAGAGAGAATGATCCTCAGTGT 58.129 43.478 0.00 0.00 33.25 3.55
1032 4439 1.003442 AGTGCCATGGAGCTCCCTA 59.997 57.895 29.95 13.16 35.38 3.53
1066 4473 0.734889 CGGCTTTGTGCTTCTATGGG 59.265 55.000 0.00 0.00 42.39 4.00
1092 4499 1.557832 AGCCGGTTGGTAGATTTGCTA 59.442 47.619 1.90 0.00 37.67 3.49
1179 4586 1.885560 TCCTCGTCGGAGATCTCATC 58.114 55.000 23.85 11.96 43.27 2.92
1248 4655 0.322456 GCTGTCACAACATAGCCCCA 60.322 55.000 0.00 0.00 34.13 4.96
1289 4696 1.899437 GACCTTGTCCGGGAGCATGA 61.899 60.000 0.00 0.00 0.00 3.07
1296 4703 0.690192 TCCGGGAGCATGAAAAGACA 59.310 50.000 0.00 0.00 0.00 3.41
1307 4714 8.502387 GGAGCATGAAAAGACATGTATATCTTC 58.498 37.037 0.00 0.73 46.25 2.87
1311 4718 9.642312 CATGAAAAGACATGTATATCTTCGTTG 57.358 33.333 0.00 0.00 41.59 4.10
1368 4775 2.163818 TAGCCAAGGAAGTGTTGTCG 57.836 50.000 0.00 0.00 0.00 4.35
1418 4825 0.902984 TTTCCGGCTCTGTCTAGGCA 60.903 55.000 0.00 0.00 41.95 4.75
1419 4826 0.687757 TTCCGGCTCTGTCTAGGCAT 60.688 55.000 0.00 0.00 41.95 4.40
1464 4871 0.035439 ACGGCGAGAAATGGGTCAAT 60.035 50.000 16.62 0.00 0.00 2.57
1612 5040 2.015456 AGTGTGTGACTGATCCTCCA 57.985 50.000 0.00 0.00 31.75 3.86
1695 5145 0.172803 GCTTGTCGGTAGATGGACGT 59.827 55.000 0.00 0.00 35.95 4.34
2390 8220 4.458989 GTCATGGAGGAATGCAAGTTGTTA 59.541 41.667 4.48 0.00 0.00 2.41
2636 8472 7.496263 TCTTGCAATTTATACATACCTACGCAA 59.504 33.333 0.00 0.00 33.82 4.85
2681 8517 1.883084 CCGATTGTACTCGCCTGCC 60.883 63.158 0.00 0.00 37.33 4.85
2701 8537 1.816224 CGGTGGGTTCATCCGAAAAAT 59.184 47.619 0.00 0.00 46.05 1.82
2771 8607 0.601046 TCGAGCTTCCTGTGTTGCAG 60.601 55.000 0.00 0.00 44.63 4.41
2787 8623 1.298859 GCAGATGAACCACGACCCAC 61.299 60.000 0.00 0.00 0.00 4.61
2907 8744 1.040339 GGGGCCACGGATTTGCATTA 61.040 55.000 4.39 0.00 0.00 1.90
2932 8769 1.276989 ACAATTTGCCATGCTTGAGGG 59.723 47.619 0.22 0.00 0.00 4.30
3011 8859 5.394663 GCAGTGGATAACAGTAGAGTGATGT 60.395 44.000 0.00 0.00 0.00 3.06
3266 9116 2.479837 TGCTCCTTGACACTTAACACG 58.520 47.619 0.00 0.00 0.00 4.49
3278 9128 0.466555 TTAACACGCACAAGGGCCTT 60.467 50.000 14.48 14.48 0.00 4.35
3307 9157 8.824781 CCATCAAAAATTCACACATGTGTTTTA 58.175 29.630 28.64 16.48 45.76 1.52
3396 10196 8.041323 GGGATACATATACCATGAGTACAAAGG 58.959 40.741 0.00 0.00 36.64 3.11
3403 10203 4.648651 ACCATGAGTACAAAGGTGGTTAC 58.351 43.478 0.00 0.00 37.20 2.50
3434 10455 2.957491 TTGTCAAAAGTGGCAACTGG 57.043 45.000 0.00 0.00 44.36 4.00
3444 10465 2.793946 GCAACTGGCATAGCACGG 59.206 61.111 0.00 0.00 43.97 4.94
3465 10486 7.469260 CACGGATTAACCCTTTAACTAACATG 58.531 38.462 0.00 0.00 34.64 3.21
3509 10830 8.213679 ACTCCTGCTAATCAATGCTTATCTTTA 58.786 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.677284 ATGCAGGCCAGAGCACGAG 62.677 63.158 18.05 0.00 44.49 4.18
2 3 3.200593 GATGCAGGCCAGAGCACG 61.201 66.667 18.05 0.00 44.49 5.34
3 4 3.200593 CGATGCAGGCCAGAGCAC 61.201 66.667 18.05 11.69 44.49 4.40
5 6 2.437359 AACGATGCAGGCCAGAGC 60.437 61.111 5.01 6.72 38.76 4.09
6 7 0.463295 ATGAACGATGCAGGCCAGAG 60.463 55.000 5.01 0.00 0.00 3.35
7 8 0.745486 CATGAACGATGCAGGCCAGA 60.745 55.000 5.01 0.00 0.00 3.86
8 9 1.028330 ACATGAACGATGCAGGCCAG 61.028 55.000 5.01 0.00 35.15 4.85
9 10 1.002257 ACATGAACGATGCAGGCCA 60.002 52.632 5.01 0.00 35.15 5.36
10 11 1.026182 TGACATGAACGATGCAGGCC 61.026 55.000 0.00 0.00 35.15 5.19
11 12 1.019673 ATGACATGAACGATGCAGGC 58.980 50.000 0.00 0.00 35.15 4.85
12 13 1.332686 CCATGACATGAACGATGCAGG 59.667 52.381 17.24 0.00 35.15 4.85
13 14 1.268386 GCCATGACATGAACGATGCAG 60.268 52.381 17.24 0.00 35.15 4.41
14 15 0.734309 GCCATGACATGAACGATGCA 59.266 50.000 17.24 0.00 35.15 3.96
15 16 0.734309 TGCCATGACATGAACGATGC 59.266 50.000 17.24 10.59 35.15 3.91
16 17 1.064505 GGTGCCATGACATGAACGATG 59.935 52.381 17.24 0.00 38.15 3.84
17 18 1.339920 TGGTGCCATGACATGAACGAT 60.340 47.619 17.24 0.00 0.00 3.73
18 19 0.036022 TGGTGCCATGACATGAACGA 59.964 50.000 17.24 9.03 0.00 3.85
19 20 1.097232 ATGGTGCCATGACATGAACG 58.903 50.000 17.24 1.47 35.03 3.95
20 21 2.492881 TGAATGGTGCCATGACATGAAC 59.507 45.455 17.24 13.55 36.68 3.18
21 22 2.756207 CTGAATGGTGCCATGACATGAA 59.244 45.455 17.24 1.90 36.68 2.57
22 23 2.026075 TCTGAATGGTGCCATGACATGA 60.026 45.455 17.24 0.00 36.68 3.07
23 24 2.357952 CTCTGAATGGTGCCATGACATG 59.642 50.000 8.56 8.56 36.68 3.21
24 25 2.240414 TCTCTGAATGGTGCCATGACAT 59.760 45.455 4.26 0.00 36.68 3.06
25 26 1.629861 TCTCTGAATGGTGCCATGACA 59.370 47.619 4.26 7.62 36.68 3.58
26 27 2.286872 CTCTCTGAATGGTGCCATGAC 58.713 52.381 4.26 3.53 36.68 3.06
27 28 1.407851 GCTCTCTGAATGGTGCCATGA 60.408 52.381 4.26 0.00 36.68 3.07
28 29 1.022735 GCTCTCTGAATGGTGCCATG 58.977 55.000 4.26 0.00 36.68 3.66
29 30 0.463295 CGCTCTCTGAATGGTGCCAT 60.463 55.000 0.00 0.00 38.46 4.40
30 31 1.078918 CGCTCTCTGAATGGTGCCA 60.079 57.895 0.00 0.00 0.00 4.92
31 32 0.179062 ATCGCTCTCTGAATGGTGCC 60.179 55.000 0.00 0.00 0.00 5.01
32 33 1.216122 GATCGCTCTCTGAATGGTGC 58.784 55.000 0.00 0.00 0.00 5.01
33 34 1.539929 GGGATCGCTCTCTGAATGGTG 60.540 57.143 1.84 0.00 0.00 4.17
34 35 0.755686 GGGATCGCTCTCTGAATGGT 59.244 55.000 1.84 0.00 0.00 3.55
35 36 0.034616 GGGGATCGCTCTCTGAATGG 59.965 60.000 9.90 0.00 0.00 3.16
36 37 0.034616 GGGGGATCGCTCTCTGAATG 59.965 60.000 9.90 0.00 0.00 2.67
37 38 0.105246 AGGGGGATCGCTCTCTGAAT 60.105 55.000 6.29 0.00 0.00 2.57
38 39 0.325671 AAGGGGGATCGCTCTCTGAA 60.326 55.000 13.30 0.00 34.92 3.02
39 40 1.045350 CAAGGGGGATCGCTCTCTGA 61.045 60.000 13.30 0.00 34.92 3.27
40 41 1.445095 CAAGGGGGATCGCTCTCTG 59.555 63.158 13.30 9.59 34.92 3.35
41 42 2.439104 GCAAGGGGGATCGCTCTCT 61.439 63.158 13.30 4.03 34.92 3.10
42 43 2.110006 GCAAGGGGGATCGCTCTC 59.890 66.667 13.30 0.00 34.92 3.20
43 44 2.366167 AGCAAGGGGGATCGCTCT 60.366 61.111 6.29 6.29 34.92 4.09
44 45 2.203126 CAGCAAGGGGGATCGCTC 60.203 66.667 9.90 5.49 34.92 5.03
45 46 3.801997 CCAGCAAGGGGGATCGCT 61.802 66.667 9.90 0.00 37.82 4.93
46 47 4.115199 ACCAGCAAGGGGGATCGC 62.115 66.667 0.06 0.06 43.89 4.58
47 48 2.124570 CACCAGCAAGGGGGATCG 60.125 66.667 0.04 0.00 43.89 3.69
48 49 2.440980 GCACCAGCAAGGGGGATC 60.441 66.667 0.00 0.00 42.99 3.36
49 50 4.066139 GGCACCAGCAAGGGGGAT 62.066 66.667 0.00 0.00 42.99 3.85
66 67 3.673484 CTTGGGCAGGCAACGTGG 61.673 66.667 0.00 0.00 46.39 4.94
67 68 3.673484 CCTTGGGCAGGCAACGTG 61.673 66.667 0.00 0.00 46.39 4.49
78 79 2.283173 GTTGGTCCTGGCCTTGGG 60.283 66.667 3.32 3.76 0.00 4.12
79 80 2.283173 GGTTGGTCCTGGCCTTGG 60.283 66.667 3.32 6.67 0.00 3.61
80 81 1.903404 GTGGTTGGTCCTGGCCTTG 60.903 63.158 3.32 0.00 37.07 3.61
81 82 2.520968 GTGGTTGGTCCTGGCCTT 59.479 61.111 3.32 0.00 37.07 4.35
82 83 3.953775 CGTGGTTGGTCCTGGCCT 61.954 66.667 3.32 0.00 37.07 5.19
83 84 3.785122 AACGTGGTTGGTCCTGGCC 62.785 63.158 0.00 0.00 37.07 5.36
84 85 2.203294 AACGTGGTTGGTCCTGGC 60.203 61.111 0.00 0.00 37.07 4.85
85 86 1.599797 GGAACGTGGTTGGTCCTGG 60.600 63.158 0.00 0.00 37.07 4.45
86 87 0.250727 ATGGAACGTGGTTGGTCCTG 60.251 55.000 3.53 0.00 37.07 3.86
87 88 1.002773 GTATGGAACGTGGTTGGTCCT 59.997 52.381 3.53 0.00 37.07 3.85
88 89 1.445871 GTATGGAACGTGGTTGGTCC 58.554 55.000 0.00 0.00 0.00 4.46
89 90 1.002773 AGGTATGGAACGTGGTTGGTC 59.997 52.381 0.00 0.00 0.00 4.02
90 91 1.061546 AGGTATGGAACGTGGTTGGT 58.938 50.000 0.00 0.00 0.00 3.67
91 92 1.448985 CAGGTATGGAACGTGGTTGG 58.551 55.000 0.00 0.00 39.73 3.77
92 93 0.802494 GCAGGTATGGAACGTGGTTG 59.198 55.000 0.00 0.00 42.88 3.77
93 94 0.322187 GGCAGGTATGGAACGTGGTT 60.322 55.000 0.00 0.00 42.88 3.67
94 95 1.298667 GGCAGGTATGGAACGTGGT 59.701 57.895 0.00 0.00 42.88 4.16
95 96 1.813753 CGGCAGGTATGGAACGTGG 60.814 63.158 0.00 0.00 42.88 4.94
96 97 2.461110 GCGGCAGGTATGGAACGTG 61.461 63.158 0.00 0.00 44.94 4.49
97 98 2.125269 GCGGCAGGTATGGAACGT 60.125 61.111 0.00 0.00 0.00 3.99
98 99 3.261951 CGCGGCAGGTATGGAACG 61.262 66.667 0.00 0.00 0.00 3.95
99 100 3.573491 GCGCGGCAGGTATGGAAC 61.573 66.667 8.83 0.00 0.00 3.62
100 101 3.613877 TTGCGCGGCAGGTATGGAA 62.614 57.895 8.83 0.00 40.61 3.53
101 102 3.613877 TTTGCGCGGCAGGTATGGA 62.614 57.895 8.83 0.00 40.61 3.41
102 103 3.130819 TTTGCGCGGCAGGTATGG 61.131 61.111 8.83 0.00 40.61 2.74
103 104 2.100216 GTTTGCGCGGCAGGTATG 59.900 61.111 8.83 0.00 40.61 2.39
104 105 2.359354 TGTTTGCGCGGCAGGTAT 60.359 55.556 8.83 0.00 40.61 2.73
105 106 3.350612 GTGTTTGCGCGGCAGGTA 61.351 61.111 8.83 0.00 40.61 3.08
107 108 4.980903 GTGTGTTTGCGCGGCAGG 62.981 66.667 8.83 0.00 40.61 4.85
108 109 3.748071 TTGTGTGTTTGCGCGGCAG 62.748 57.895 8.83 0.00 40.61 4.85
109 110 2.997621 GATTGTGTGTTTGCGCGGCA 62.998 55.000 8.83 3.20 36.47 5.69
110 111 2.354539 ATTGTGTGTTTGCGCGGC 60.355 55.556 8.83 0.00 0.00 6.53
111 112 1.729131 GGATTGTGTGTTTGCGCGG 60.729 57.895 8.83 0.00 0.00 6.46
112 113 1.009108 TGGATTGTGTGTTTGCGCG 60.009 52.632 0.00 0.00 0.00 6.86
113 114 0.939106 GGTGGATTGTGTGTTTGCGC 60.939 55.000 0.00 0.00 0.00 6.09
114 115 0.383590 TGGTGGATTGTGTGTTTGCG 59.616 50.000 0.00 0.00 0.00 4.85
115 116 1.680735 TCTGGTGGATTGTGTGTTTGC 59.319 47.619 0.00 0.00 0.00 3.68
116 117 3.243501 CCTTCTGGTGGATTGTGTGTTTG 60.244 47.826 0.00 0.00 0.00 2.93
117 118 2.958355 CCTTCTGGTGGATTGTGTGTTT 59.042 45.455 0.00 0.00 0.00 2.83
118 119 2.091885 ACCTTCTGGTGGATTGTGTGTT 60.092 45.455 0.00 0.00 46.51 3.32
119 120 1.494721 ACCTTCTGGTGGATTGTGTGT 59.505 47.619 0.00 0.00 46.51 3.72
120 121 2.276732 ACCTTCTGGTGGATTGTGTG 57.723 50.000 0.00 0.00 46.51 3.82
138 139 3.108376 AGAGGAGGAGACAATTGGGTAC 58.892 50.000 10.83 0.00 0.00 3.34
139 140 3.491766 AGAGGAGGAGACAATTGGGTA 57.508 47.619 10.83 0.00 0.00 3.69
140 141 2.307098 CAAGAGGAGGAGACAATTGGGT 59.693 50.000 10.83 0.00 0.00 4.51
141 142 2.573462 TCAAGAGGAGGAGACAATTGGG 59.427 50.000 10.83 0.00 0.00 4.12
142 143 3.988976 TCAAGAGGAGGAGACAATTGG 57.011 47.619 10.83 0.00 0.00 3.16
143 144 4.118410 CGATCAAGAGGAGGAGACAATTG 58.882 47.826 3.24 3.24 0.00 2.32
144 145 3.431486 GCGATCAAGAGGAGGAGACAATT 60.431 47.826 0.00 0.00 0.00 2.32
145 146 2.102252 GCGATCAAGAGGAGGAGACAAT 59.898 50.000 0.00 0.00 0.00 2.71
146 147 1.478510 GCGATCAAGAGGAGGAGACAA 59.521 52.381 0.00 0.00 0.00 3.18
147 148 1.107114 GCGATCAAGAGGAGGAGACA 58.893 55.000 0.00 0.00 0.00 3.41
148 149 1.107114 TGCGATCAAGAGGAGGAGAC 58.893 55.000 0.00 0.00 0.00 3.36
149 150 2.079170 ATGCGATCAAGAGGAGGAGA 57.921 50.000 0.00 0.00 0.00 3.71
150 151 3.305950 CCTTATGCGATCAAGAGGAGGAG 60.306 52.174 0.00 0.00 32.95 3.69
151 152 2.630098 CCTTATGCGATCAAGAGGAGGA 59.370 50.000 0.00 0.00 32.95 3.71
152 153 2.289320 CCCTTATGCGATCAAGAGGAGG 60.289 54.545 0.00 0.00 32.95 4.30
153 154 2.289320 CCCCTTATGCGATCAAGAGGAG 60.289 54.545 0.00 0.00 32.95 3.69
154 155 1.694150 CCCCTTATGCGATCAAGAGGA 59.306 52.381 0.00 0.00 32.95 3.71
155 156 1.879796 GCCCCTTATGCGATCAAGAGG 60.880 57.143 0.00 0.00 0.00 3.69
156 157 1.202687 TGCCCCTTATGCGATCAAGAG 60.203 52.381 0.00 0.00 0.00 2.85
157 158 0.836606 TGCCCCTTATGCGATCAAGA 59.163 50.000 0.00 0.00 0.00 3.02
158 159 0.947244 GTGCCCCTTATGCGATCAAG 59.053 55.000 0.00 0.00 0.00 3.02
159 160 0.254462 TGTGCCCCTTATGCGATCAA 59.746 50.000 0.00 0.00 0.00 2.57
160 161 0.463654 GTGTGCCCCTTATGCGATCA 60.464 55.000 0.00 0.00 0.00 2.92
161 162 1.166531 GGTGTGCCCCTTATGCGATC 61.167 60.000 0.00 0.00 0.00 3.69
162 163 1.152963 GGTGTGCCCCTTATGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
163 164 2.252072 GAGGTGTGCCCCTTATGCGA 62.252 60.000 0.00 0.00 34.03 5.10
164 165 1.819632 GAGGTGTGCCCCTTATGCG 60.820 63.158 0.00 0.00 34.03 4.73
165 166 1.453928 GGAGGTGTGCCCCTTATGC 60.454 63.158 0.00 0.00 34.03 3.14
166 167 0.552848 ATGGAGGTGTGCCCCTTATG 59.447 55.000 0.00 0.00 34.03 1.90
167 168 0.552848 CATGGAGGTGTGCCCCTTAT 59.447 55.000 0.00 0.00 34.03 1.73
168 169 0.844661 ACATGGAGGTGTGCCCCTTA 60.845 55.000 0.00 0.00 34.03 2.69
169 170 2.162906 ACATGGAGGTGTGCCCCTT 61.163 57.895 0.00 0.00 34.03 3.95
170 171 2.532715 ACATGGAGGTGTGCCCCT 60.533 61.111 0.00 0.00 37.62 4.79
171 172 2.215451 ATCACATGGAGGTGTGCCCC 62.215 60.000 0.00 0.00 46.97 5.80
172 173 0.749454 GATCACATGGAGGTGTGCCC 60.749 60.000 0.00 0.00 46.97 5.36
173 174 0.035152 TGATCACATGGAGGTGTGCC 60.035 55.000 0.00 0.00 46.97 5.01
174 175 1.741706 CTTGATCACATGGAGGTGTGC 59.258 52.381 0.00 0.00 46.97 4.57
176 177 1.340405 GCCTTGATCACATGGAGGTGT 60.340 52.381 11.22 0.00 41.88 4.16
177 178 1.340308 TGCCTTGATCACATGGAGGTG 60.340 52.381 11.22 0.00 41.88 4.00
178 179 0.994247 TGCCTTGATCACATGGAGGT 59.006 50.000 11.22 0.00 41.88 3.85
179 180 2.228059 GATGCCTTGATCACATGGAGG 58.772 52.381 11.49 8.95 41.88 4.30
180 181 1.871676 CGATGCCTTGATCACATGGAG 59.128 52.381 11.49 0.00 41.88 3.86
181 182 1.957668 CGATGCCTTGATCACATGGA 58.042 50.000 11.49 0.00 41.88 3.41
182 183 0.309922 GCGATGCCTTGATCACATGG 59.690 55.000 0.00 0.00 42.12 3.66
183 184 0.309922 GGCGATGCCTTGATCACATG 59.690 55.000 0.00 0.00 46.69 3.21
184 185 2.711711 GGCGATGCCTTGATCACAT 58.288 52.632 0.00 0.00 46.69 3.21
185 186 4.223800 GGCGATGCCTTGATCACA 57.776 55.556 0.00 0.00 46.69 3.58
194 195 3.567797 GTCTTGCTCGGCGATGCC 61.568 66.667 22.19 10.94 46.75 4.40
195 196 3.918220 CGTCTTGCTCGGCGATGC 61.918 66.667 11.27 16.69 0.00 3.91
196 197 3.257561 CCGTCTTGCTCGGCGATG 61.258 66.667 11.27 5.99 41.48 3.84
202 203 1.153939 CCTCAGACCGTCTTGCTCG 60.154 63.158 0.00 0.00 0.00 5.03
203 204 0.109039 GACCTCAGACCGTCTTGCTC 60.109 60.000 0.00 0.00 0.00 4.26
204 205 1.536943 GGACCTCAGACCGTCTTGCT 61.537 60.000 0.00 0.00 0.00 3.91
205 206 1.079750 GGACCTCAGACCGTCTTGC 60.080 63.158 0.00 0.00 0.00 4.01
206 207 0.244994 CTGGACCTCAGACCGTCTTG 59.755 60.000 0.00 0.00 46.18 3.02
207 208 1.536943 GCTGGACCTCAGACCGTCTT 61.537 60.000 0.00 0.00 46.18 3.01
208 209 1.979693 GCTGGACCTCAGACCGTCT 60.980 63.158 0.00 0.00 46.18 4.18
209 210 2.276116 TGCTGGACCTCAGACCGTC 61.276 63.158 0.00 0.00 46.18 4.79
210 211 2.203640 TGCTGGACCTCAGACCGT 60.204 61.111 0.00 0.00 46.18 4.83
211 212 2.262915 GTGCTGGACCTCAGACCG 59.737 66.667 0.00 0.00 46.18 4.79
212 213 2.665603 GGTGCTGGACCTCAGACC 59.334 66.667 11.48 0.00 46.18 3.85
226 227 1.357258 CTAGCTCAGCGCAACAGGTG 61.357 60.000 11.47 0.00 42.61 4.00
227 228 1.079543 CTAGCTCAGCGCAACAGGT 60.080 57.895 11.47 10.22 42.61 4.00
228 229 2.459442 GCTAGCTCAGCGCAACAGG 61.459 63.158 11.47 0.00 41.37 4.00
229 230 3.088044 GCTAGCTCAGCGCAACAG 58.912 61.111 11.47 2.57 41.37 3.16
241 242 0.736325 TCGTTTCTCGCTTGGCTAGC 60.736 55.000 11.03 11.03 46.83 3.42
242 243 0.992802 GTCGTTTCTCGCTTGGCTAG 59.007 55.000 0.00 0.00 39.67 3.42
243 244 0.315886 TGTCGTTTCTCGCTTGGCTA 59.684 50.000 0.00 0.00 39.67 3.93
244 245 1.069090 TGTCGTTTCTCGCTTGGCT 59.931 52.632 0.00 0.00 39.67 4.75
245 246 1.204312 GTGTCGTTTCTCGCTTGGC 59.796 57.895 0.00 0.00 39.67 4.52
246 247 0.508641 CAGTGTCGTTTCTCGCTTGG 59.491 55.000 0.00 0.00 39.67 3.61
247 248 0.508641 CCAGTGTCGTTTCTCGCTTG 59.491 55.000 0.00 0.00 39.67 4.01
248 249 0.387929 TCCAGTGTCGTTTCTCGCTT 59.612 50.000 0.00 0.00 39.67 4.68
249 250 0.039074 CTCCAGTGTCGTTTCTCGCT 60.039 55.000 0.00 0.00 39.67 4.93
250 251 1.009389 CCTCCAGTGTCGTTTCTCGC 61.009 60.000 0.00 0.00 39.67 5.03
251 252 0.388649 CCCTCCAGTGTCGTTTCTCG 60.389 60.000 0.00 0.00 41.41 4.04
252 253 0.037232 CCCCTCCAGTGTCGTTTCTC 60.037 60.000 0.00 0.00 0.00 2.87
253 254 2.058675 CCCCTCCAGTGTCGTTTCT 58.941 57.895 0.00 0.00 0.00 2.52
254 255 1.671379 GCCCCTCCAGTGTCGTTTC 60.671 63.158 0.00 0.00 0.00 2.78
255 256 2.113243 GAGCCCCTCCAGTGTCGTTT 62.113 60.000 0.00 0.00 0.00 3.60
256 257 2.526873 AGCCCCTCCAGTGTCGTT 60.527 61.111 0.00 0.00 0.00 3.85
257 258 2.997897 GAGCCCCTCCAGTGTCGT 60.998 66.667 0.00 0.00 0.00 4.34
258 259 2.997315 TGAGCCCCTCCAGTGTCG 60.997 66.667 0.00 0.00 0.00 4.35
259 260 2.665603 GTGAGCCCCTCCAGTGTC 59.334 66.667 0.00 0.00 0.00 3.67
260 261 3.314331 CGTGAGCCCCTCCAGTGT 61.314 66.667 0.00 0.00 0.00 3.55
261 262 4.087892 CCGTGAGCCCCTCCAGTG 62.088 72.222 0.00 0.00 0.00 3.66
262 263 2.741878 TAACCGTGAGCCCCTCCAGT 62.742 60.000 0.00 0.00 0.00 4.00
263 264 1.338136 ATAACCGTGAGCCCCTCCAG 61.338 60.000 0.00 0.00 0.00 3.86
264 265 0.031917 TATAACCGTGAGCCCCTCCA 60.032 55.000 0.00 0.00 0.00 3.86
265 266 1.275573 GATATAACCGTGAGCCCCTCC 59.724 57.143 0.00 0.00 0.00 4.30
266 267 1.968493 TGATATAACCGTGAGCCCCTC 59.032 52.381 0.00 0.00 0.00 4.30
267 268 2.097110 TGATATAACCGTGAGCCCCT 57.903 50.000 0.00 0.00 0.00 4.79
268 269 3.418684 AATGATATAACCGTGAGCCCC 57.581 47.619 0.00 0.00 0.00 5.80
269 270 5.063880 AGAAAATGATATAACCGTGAGCCC 58.936 41.667 0.00 0.00 0.00 5.19
270 271 6.619801 AAGAAAATGATATAACCGTGAGCC 57.380 37.500 0.00 0.00 0.00 4.70
271 272 8.589335 TCTAAGAAAATGATATAACCGTGAGC 57.411 34.615 0.00 0.00 0.00 4.26
275 276 9.209175 GCTCATCTAAGAAAATGATATAACCGT 57.791 33.333 0.00 0.00 31.79 4.83
276 277 9.429359 AGCTCATCTAAGAAAATGATATAACCG 57.571 33.333 0.00 0.00 31.79 4.44
322 323 5.032846 AGTGAATAAAGGAGGAGGTGATCA 58.967 41.667 0.00 0.00 0.00 2.92
328 329 5.070981 TGCTATGAGTGAATAAAGGAGGAGG 59.929 44.000 0.00 0.00 0.00 4.30
363 364 4.998672 CGGTTACTCCCTTGATTGTAAACA 59.001 41.667 0.00 0.00 33.61 2.83
413 414 5.279256 GGCTAGCTAGATTTTCTCCTTCGAT 60.279 44.000 25.15 0.00 0.00 3.59
417 418 6.664428 CTAGGCTAGCTAGATTTTCTCCTT 57.336 41.667 25.15 2.98 0.00 3.36
528 529 4.868171 GTCGTAGCATTACTTGATGGTTCA 59.132 41.667 0.00 0.00 38.56 3.18
534 568 3.451178 AGGTGGTCGTAGCATTACTTGAT 59.549 43.478 0.00 0.00 0.00 2.57
547 581 0.106149 AAAAGAGCGAAGGTGGTCGT 59.894 50.000 0.00 0.00 43.06 4.34
557 591 4.385825 ACAACCAACTGATAAAAGAGCGA 58.614 39.130 0.00 0.00 0.00 4.93
681 1973 9.773328 AACAATATGTGATCAAAGTTTACATCG 57.227 29.630 0.00 0.59 34.22 3.84
728 2021 9.174166 AGCTGATTAGTTAATTTACGGTTTGAT 57.826 29.630 0.00 0.00 0.00 2.57
730 2023 8.234546 ACAGCTGATTAGTTAATTTACGGTTTG 58.765 33.333 23.35 0.00 0.00 2.93
731 2024 8.331730 ACAGCTGATTAGTTAATTTACGGTTT 57.668 30.769 23.35 0.00 0.00 3.27
732 2025 7.604927 TGACAGCTGATTAGTTAATTTACGGTT 59.395 33.333 23.35 0.00 0.00 4.44
752 4150 3.484229 CGGTTGAAGATTCGATTGACAGC 60.484 47.826 0.00 0.00 0.00 4.40
756 4154 2.672874 CTGCGGTTGAAGATTCGATTGA 59.327 45.455 0.00 0.00 0.00 2.57
763 4161 2.568623 AGGAACTGCGGTTGAAGATT 57.431 45.000 17.49 0.00 37.18 2.40
770 4168 2.835764 TGGTAGATAAGGAACTGCGGTT 59.164 45.455 11.62 11.62 40.86 4.44
848 4246 8.621532 TGTTTAAGAGATGTTCTTGCACTATT 57.378 30.769 0.00 0.00 45.66 1.73
849 4247 8.621532 TTGTTTAAGAGATGTTCTTGCACTAT 57.378 30.769 0.00 0.00 45.66 2.12
876 4278 5.896678 GGTCATGCTATATAGAGATGTCCCT 59.103 44.000 14.16 0.00 0.00 4.20
895 4297 3.767711 TCGGTATGCTAGAGATGGTCAT 58.232 45.455 0.00 0.00 0.00 3.06
944 4349 0.540597 AGGGAAGAAAGGCCAGTTGC 60.541 55.000 5.01 0.00 40.16 4.17
990 4397 1.723220 CTGGACTCATCAGCACACTG 58.277 55.000 0.00 0.00 45.95 3.66
1066 4473 1.041447 TCTACCAACCGGCTAGCCTC 61.041 60.000 30.55 6.55 34.57 4.70
1195 4602 0.526524 CTCGATCGTGCCTCCTTGTC 60.527 60.000 15.94 0.00 0.00 3.18
1248 4655 2.603776 AGGAACGGCGGGAAGAGT 60.604 61.111 13.24 0.00 0.00 3.24
1289 4696 8.873830 CACTCAACGAAGATATACATGTCTTTT 58.126 33.333 0.00 0.00 38.19 2.27
1296 4703 6.757010 GGAACACACTCAACGAAGATATACAT 59.243 38.462 0.00 0.00 0.00 2.29
1307 4714 0.944386 CTTGGGGAACACACTCAACG 59.056 55.000 0.00 0.00 0.00 4.10
1311 4718 0.472471 TGACCTTGGGGAACACACTC 59.528 55.000 0.00 0.00 36.25 3.51
1368 4775 0.234884 CGAAGTGGCCGAACTTGTTC 59.765 55.000 12.93 3.60 40.48 3.18
1418 4825 1.739338 CGCTAGTCCTCGGGCAAGAT 61.739 60.000 0.00 0.00 0.00 2.40
1419 4826 2.415608 CGCTAGTCCTCGGGCAAGA 61.416 63.158 0.00 0.00 0.00 3.02
1426 4833 1.009900 CGTAAGCCGCTAGTCCTCG 60.010 63.158 0.00 0.00 0.00 4.63
1464 4871 3.901844 CGGGGTTAAGGATCCTTCTATGA 59.098 47.826 30.35 10.17 37.47 2.15
1612 5040 3.853831 TCAATTTGATGATGTGCGCTT 57.146 38.095 9.73 0.00 0.00 4.68
1695 5145 0.613260 CCGTCTGAACCAAGGGATCA 59.387 55.000 0.00 0.00 33.54 2.92
2080 7877 9.872721 AATCATATTGCACATTTACAAATCACA 57.127 25.926 0.00 0.00 0.00 3.58
2390 8220 6.711277 TGTTGTTTCTGTCCTAGCAAGATAT 58.289 36.000 0.00 0.00 0.00 1.63
2399 8229 6.371548 GCAGTATTGATGTTGTTTCTGTCCTA 59.628 38.462 0.00 0.00 0.00 2.94
2400 8230 5.182001 GCAGTATTGATGTTGTTTCTGTCCT 59.818 40.000 0.00 0.00 0.00 3.85
2631 8467 0.033504 AGAATCGTGGTCACTTGCGT 59.966 50.000 0.00 0.00 0.00 5.24
2636 8472 3.367087 CCTCGTAAAGAATCGTGGTCACT 60.367 47.826 0.00 0.00 36.42 3.41
2681 8517 1.240256 TTTTTCGGATGAACCCACCG 58.760 50.000 0.00 0.00 46.71 4.94
2701 8537 5.248248 TCACCAATCTTCATCTCCTTGTACA 59.752 40.000 0.00 0.00 0.00 2.90
2740 8576 0.976641 AAGCTCGATGAGGACACCAA 59.023 50.000 0.00 0.00 0.00 3.67
2771 8607 0.250124 TGTGTGGGTCGTGGTTCATC 60.250 55.000 0.00 0.00 0.00 2.92
2787 8623 2.260844 ACATCGCTTCCCCATATGTG 57.739 50.000 1.24 0.00 29.93 3.21
2932 8769 1.134936 TCATGCACAATGCCATCTTGC 60.135 47.619 0.00 4.01 44.23 4.01
3011 8859 4.306967 TGCGCCATGTGTCGGACA 62.307 61.111 6.76 6.76 39.53 4.02
3096 8944 9.640952 AATTATATGTTTAGGTACATGGCAACT 57.359 29.630 0.00 0.00 39.06 3.16
3142 8990 6.097554 TGGTTGGTTCACATGAAATACAAACT 59.902 34.615 16.95 0.00 35.27 2.66
3278 9128 4.202336 ACATGTGTGAATTTTTGATGGGCA 60.202 37.500 0.00 0.00 0.00 5.36
3396 10196 3.320826 ACAATTGCCTCCTTTGTAACCAC 59.679 43.478 5.05 0.00 32.09 4.16
3403 10203 4.508861 CACTTTTGACAATTGCCTCCTTTG 59.491 41.667 5.05 0.00 0.00 2.77
3434 10455 2.256117 AGGGTTAATCCGTGCTATGC 57.744 50.000 0.00 0.00 37.00 3.14
3465 10486 9.343539 AGCAGGAGTGTTAGGAATTAATTAATC 57.656 33.333 11.08 5.39 0.00 1.75
3478 10499 5.121811 AGCATTGATTAGCAGGAGTGTTAG 58.878 41.667 0.00 0.00 0.00 2.34
3482 10503 5.996513 AGATAAGCATTGATTAGCAGGAGTG 59.003 40.000 11.94 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.