Multiple sequence alignment - TraesCS3A01G447300

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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 TraesCS3A01G447300 chr3A 100.000 3017 0 0 1 3017 687204354 687207370 0.000000e+00 5572
1 TraesCS3A01G447300 chr3A 93.833 908 49 4 2115 3017 660861855 660860950 0.000000e+00 1360
2 TraesCS3A01G447300 chr3A 85.267 862 106 14 586 1435 687130717 687131569 0.000000e+00 869
3 TraesCS3A01G447300 chr3A 81.284 919 140 18 278 1188 687224946 687224052 0.000000e+00 715
4 TraesCS3A01G447300 chr3A 90.203 296 24 5 1 295 690752750 690752459 6.100000e-102 381
5 TraesCS3A01G447300 chr3D 94.684 903 40 6 2119 3017 214958664 214959562 0.000000e+00 1395
6 TraesCS3A01G447300 chr3D 87.179 702 87 1 1372 2070 550382445 550381744 0.000000e+00 795
7 TraesCS3A01G447300 chr3D 83.279 616 73 17 588 1188 550383140 550382540 9.520000e-150 540
8 TraesCS3A01G447300 chr3D 87.857 280 32 2 2 280 239072947 239072669 8.060000e-86 327
9 TraesCS3A01G447300 chr3D 87.544 281 33 2 1 281 77066322 77066044 1.040000e-84 324
10 TraesCS3A01G447300 chr3D 80.243 329 53 6 278 602 550383500 550383180 1.400000e-58 237
11 TraesCS3A01G447300 chr7D 94.678 902 41 5 2120 3017 114467274 114468172 0.000000e+00 1393
12 TraesCS3A01G447300 chr7D 94.078 895 49 4 2125 3017 151540076 151540968 0.000000e+00 1356
13 TraesCS3A01G447300 chr7D 85.577 624 83 4 1376 1994 89831568 89832189 0.000000e+00 647
14 TraesCS3A01G447300 chr7D 83.181 547 68 11 661 1188 89830869 89831410 2.100000e-131 479
15 TraesCS3A01G447300 chr5B 94.216 899 51 1 2119 3017 669931479 669932376 0.000000e+00 1371
16 TraesCS3A01G447300 chr2D 93.716 907 48 8 2116 3017 70390877 70391779 0.000000e+00 1351
17 TraesCS3A01G447300 chr2D 93.407 910 49 11 2112 3017 623949271 623950173 0.000000e+00 1338
18 TraesCS3A01G447300 chr1D 93.882 899 45 7 2124 3017 84729901 84729008 0.000000e+00 1347
19 TraesCS3A01G447300 chr7B 93.764 898 53 2 2122 3017 154683859 154684755 0.000000e+00 1345
20 TraesCS3A01G447300 chr7B 86.334 622 82 1 1376 1994 40655438 40656059 0.000000e+00 675
21 TraesCS3A01G447300 chr7B 82.261 637 81 13 1364 1994 40887701 40888311 3.450000e-144 521
22 TraesCS3A01G447300 chr7B 82.682 537 77 8 661 1185 40654845 40655377 2.120000e-126 462
23 TraesCS3A01G447300 chr3B 90.798 815 73 2 1308 2121 729804568 729805381 0.000000e+00 1088
24 TraesCS3A01G447300 chr3B 86.484 910 103 8 278 1187 729803627 729804516 0.000000e+00 981
25 TraesCS3A01G447300 chr3B 82.974 928 121 16 278 1188 729908049 729907142 0.000000e+00 804
26 TraesCS3A01G447300 chr3B 82.131 929 129 23 278 1188 729922567 729921658 0.000000e+00 761
27 TraesCS3A01G447300 chr3B 88.189 635 73 1 1360 1994 729921564 729920932 0.000000e+00 756
28 TraesCS3A01G447300 chr3B 91.241 137 8 2 1898 2031 729912038 729912173 1.850000e-42 183
29 TraesCS3A01G447300 chr7A 85.086 637 89 3 1364 1994 91362503 91363139 0.000000e+00 645
30 TraesCS3A01G447300 chr6A 94.643 280 14 1 1 280 57750102 57750380 1.660000e-117 433
31 TraesCS3A01G447300 chr6A 89.928 278 26 2 1 278 544002653 544002928 1.030000e-94 357
32 TraesCS3A01G447300 chr6A 87.857 280 33 1 2 281 420658663 420658385 8.060000e-86 327
33 TraesCS3A01G447300 chr4A 89.643 280 27 2 1 280 429976682 429976959 3.700000e-94 355
34 TraesCS3A01G447300 chr4B 89.051 274 29 1 2 275 192994325 192994597 3.730000e-89 339
35 TraesCS3A01G447300 chr5D 87.455 279 34 1 2 280 266462407 266462130 1.350000e-83 320


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 TraesCS3A01G447300 chr3A 687204354 687207370 3016 False 5572.0 5572 100.000 1 3017 1 chr3A.!!$F2 3016
1 TraesCS3A01G447300 chr3A 660860950 660861855 905 True 1360.0 1360 93.833 2115 3017 1 chr3A.!!$R1 902
2 TraesCS3A01G447300 chr3A 687130717 687131569 852 False 869.0 869 85.267 586 1435 1 chr3A.!!$F1 849
3 TraesCS3A01G447300 chr3A 687224052 687224946 894 True 715.0 715 81.284 278 1188 1 chr3A.!!$R2 910
4 TraesCS3A01G447300 chr3D 214958664 214959562 898 False 1395.0 1395 94.684 2119 3017 1 chr3D.!!$F1 898
5 TraesCS3A01G447300 chr3D 550381744 550383500 1756 True 524.0 795 83.567 278 2070 3 chr3D.!!$R3 1792
6 TraesCS3A01G447300 chr7D 114467274 114468172 898 False 1393.0 1393 94.678 2120 3017 1 chr7D.!!$F1 897
7 TraesCS3A01G447300 chr7D 151540076 151540968 892 False 1356.0 1356 94.078 2125 3017 1 chr7D.!!$F2 892
8 TraesCS3A01G447300 chr7D 89830869 89832189 1320 False 563.0 647 84.379 661 1994 2 chr7D.!!$F3 1333
9 TraesCS3A01G447300 chr5B 669931479 669932376 897 False 1371.0 1371 94.216 2119 3017 1 chr5B.!!$F1 898
10 TraesCS3A01G447300 chr2D 70390877 70391779 902 False 1351.0 1351 93.716 2116 3017 1 chr2D.!!$F1 901
11 TraesCS3A01G447300 chr2D 623949271 623950173 902 False 1338.0 1338 93.407 2112 3017 1 chr2D.!!$F2 905
12 TraesCS3A01G447300 chr1D 84729008 84729901 893 True 1347.0 1347 93.882 2124 3017 1 chr1D.!!$R1 893
13 TraesCS3A01G447300 chr7B 154683859 154684755 896 False 1345.0 1345 93.764 2122 3017 1 chr7B.!!$F2 895
14 TraesCS3A01G447300 chr7B 40654845 40656059 1214 False 568.5 675 84.508 661 1994 2 chr7B.!!$F3 1333
15 TraesCS3A01G447300 chr7B 40887701 40888311 610 False 521.0 521 82.261 1364 1994 1 chr7B.!!$F1 630
16 TraesCS3A01G447300 chr3B 729803627 729805381 1754 False 1034.5 1088 88.641 278 2121 2 chr3B.!!$F2 1843
17 TraesCS3A01G447300 chr3B 729907142 729908049 907 True 804.0 804 82.974 278 1188 1 chr3B.!!$R1 910
18 TraesCS3A01G447300 chr3B 729920932 729922567 1635 True 758.5 761 85.160 278 1994 2 chr3B.!!$R2 1716
19 TraesCS3A01G447300 chr7A 91362503 91363139 636 False 645.0 645 85.086 1364 1994 1 chr7A.!!$F1 630

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
551 563 0.321122 CTGCAGGTCAACCTCCACTC 60.321 60.0 5.57 0.0 46.65 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 2507 0.032952 TGGACGAACTGCTAAACGCT 59.967 50.0 0.0 0.0 40.11 5.07 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
25 26 4.852138 CCATGTAGGCGAAAAATCTGATG 58.148 43.478 0.00 0.00 0.00 3.07
26 27 4.336433 CCATGTAGGCGAAAAATCTGATGT 59.664 41.667 0.00 0.00 0.00 3.06
27 28 4.944962 TGTAGGCGAAAAATCTGATGTG 57.055 40.909 0.00 0.00 0.00 3.21
28 29 3.689161 TGTAGGCGAAAAATCTGATGTGG 59.311 43.478 0.00 0.00 0.00 4.17
29 30 1.474077 AGGCGAAAAATCTGATGTGGC 59.526 47.619 0.00 0.00 0.00 5.01
30 31 1.202114 GGCGAAAAATCTGATGTGGCA 59.798 47.619 0.00 0.00 0.00 4.92
31 32 2.352617 GGCGAAAAATCTGATGTGGCAA 60.353 45.455 0.00 0.00 0.00 4.52
32 33 3.316283 GCGAAAAATCTGATGTGGCAAA 58.684 40.909 0.00 0.00 0.00 3.68
33 34 3.740321 GCGAAAAATCTGATGTGGCAAAA 59.260 39.130 0.00 0.00 0.00 2.44
34 35 4.376311 GCGAAAAATCTGATGTGGCAAAAC 60.376 41.667 0.00 0.00 0.00 2.43
35 36 4.744137 CGAAAAATCTGATGTGGCAAAACA 59.256 37.500 0.00 0.00 0.00 2.83
36 37 5.233902 CGAAAAATCTGATGTGGCAAAACAA 59.766 36.000 0.00 0.00 32.81 2.83
37 38 6.073657 CGAAAAATCTGATGTGGCAAAACAAT 60.074 34.615 0.00 0.00 32.81 2.71
38 39 7.518689 CGAAAAATCTGATGTGGCAAAACAATT 60.519 33.333 0.00 0.00 32.81 2.32
39 40 8.674263 AAAAATCTGATGTGGCAAAACAATTA 57.326 26.923 0.00 0.00 32.81 1.40
40 41 8.674263 AAAATCTGATGTGGCAAAACAATTAA 57.326 26.923 0.00 0.00 32.81 1.40
41 42 8.851541 AAATCTGATGTGGCAAAACAATTAAT 57.148 26.923 0.00 0.00 32.81 1.40
42 43 9.941325 AAATCTGATGTGGCAAAACAATTAATA 57.059 25.926 0.00 0.00 32.81 0.98
44 45 8.929827 TCTGATGTGGCAAAACAATTAATATG 57.070 30.769 0.00 0.00 32.81 1.78
45 46 8.747471 TCTGATGTGGCAAAACAATTAATATGA 58.253 29.630 0.00 0.00 32.81 2.15
46 47 8.929827 TGATGTGGCAAAACAATTAATATGAG 57.070 30.769 0.00 0.00 32.81 2.90
47 48 8.747471 TGATGTGGCAAAACAATTAATATGAGA 58.253 29.630 0.00 0.00 32.81 3.27
48 49 9.241317 GATGTGGCAAAACAATTAATATGAGAG 57.759 33.333 0.00 0.00 32.81 3.20
49 50 8.347004 TGTGGCAAAACAATTAATATGAGAGA 57.653 30.769 0.00 0.00 0.00 3.10
50 51 8.801299 TGTGGCAAAACAATTAATATGAGAGAA 58.199 29.630 0.00 0.00 0.00 2.87
51 52 9.638239 GTGGCAAAACAATTAATATGAGAGAAA 57.362 29.630 0.00 0.00 0.00 2.52
68 69 9.753674 ATGAGAGAAATTAATTTGGTAACTCCA 57.246 29.630 17.98 15.14 45.60 3.86
78 79 2.696775 TGGTAACTCCAGGAAGAACCA 58.303 47.619 11.01 11.01 41.93 3.67
79 80 3.050089 TGGTAACTCCAGGAAGAACCAA 58.950 45.455 12.22 0.23 41.93 3.67
80 81 3.655777 TGGTAACTCCAGGAAGAACCAAT 59.344 43.478 12.22 0.00 41.93 3.16
81 82 4.010349 GGTAACTCCAGGAAGAACCAATG 58.990 47.826 8.35 0.00 42.04 2.82
82 83 2.206576 ACTCCAGGAAGAACCAATGC 57.793 50.000 0.00 0.00 42.04 3.56
83 84 1.272147 ACTCCAGGAAGAACCAATGCC 60.272 52.381 0.00 0.00 42.04 4.40
84 85 0.776810 TCCAGGAAGAACCAATGCCA 59.223 50.000 0.00 0.00 42.04 4.92
85 86 1.146774 TCCAGGAAGAACCAATGCCAA 59.853 47.619 0.00 0.00 42.04 4.52
86 87 1.969923 CCAGGAAGAACCAATGCCAAA 59.030 47.619 0.00 0.00 42.04 3.28
87 88 2.368221 CCAGGAAGAACCAATGCCAAAA 59.632 45.455 0.00 0.00 42.04 2.44
88 89 3.392882 CAGGAAGAACCAATGCCAAAAC 58.607 45.455 0.00 0.00 42.04 2.43
89 90 3.037549 AGGAAGAACCAATGCCAAAACA 58.962 40.909 0.00 0.00 42.04 2.83
90 91 3.130633 GGAAGAACCAATGCCAAAACAC 58.869 45.455 0.00 0.00 38.79 3.32
91 92 2.507339 AGAACCAATGCCAAAACACG 57.493 45.000 0.00 0.00 0.00 4.49
92 93 1.754226 AGAACCAATGCCAAAACACGT 59.246 42.857 0.00 0.00 0.00 4.49
93 94 1.857837 GAACCAATGCCAAAACACGTG 59.142 47.619 15.48 15.48 0.00 4.49
94 95 1.107114 ACCAATGCCAAAACACGTGA 58.893 45.000 25.01 0.00 0.00 4.35
95 96 1.478510 ACCAATGCCAAAACACGTGAA 59.521 42.857 25.01 0.00 0.00 3.18
96 97 2.102252 ACCAATGCCAAAACACGTGAAT 59.898 40.909 25.01 7.76 0.00 2.57
97 98 2.730928 CCAATGCCAAAACACGTGAATC 59.269 45.455 25.01 5.39 0.00 2.52
98 99 3.552684 CCAATGCCAAAACACGTGAATCT 60.553 43.478 25.01 0.00 0.00 2.40
99 100 4.320861 CCAATGCCAAAACACGTGAATCTA 60.321 41.667 25.01 2.36 0.00 1.98
100 101 4.685169 ATGCCAAAACACGTGAATCTAG 57.315 40.909 25.01 7.20 0.00 2.43
101 102 2.811431 TGCCAAAACACGTGAATCTAGG 59.189 45.455 25.01 16.01 0.00 3.02
102 103 2.414161 GCCAAAACACGTGAATCTAGGC 60.414 50.000 25.01 21.35 0.00 3.93
103 104 2.811431 CCAAAACACGTGAATCTAGGCA 59.189 45.455 25.01 0.00 0.00 4.75
104 105 3.252215 CCAAAACACGTGAATCTAGGCAA 59.748 43.478 25.01 0.00 0.00 4.52
105 106 4.261405 CCAAAACACGTGAATCTAGGCAAA 60.261 41.667 25.01 0.00 0.00 3.68
106 107 5.277825 CAAAACACGTGAATCTAGGCAAAA 58.722 37.500 25.01 0.00 0.00 2.44
107 108 5.705609 AAACACGTGAATCTAGGCAAAAT 57.294 34.783 25.01 0.00 0.00 1.82
108 109 6.811253 AAACACGTGAATCTAGGCAAAATA 57.189 33.333 25.01 0.00 0.00 1.40
109 110 7.391148 AAACACGTGAATCTAGGCAAAATAT 57.609 32.000 25.01 0.00 0.00 1.28
110 111 7.391148 AACACGTGAATCTAGGCAAAATATT 57.609 32.000 25.01 0.00 0.00 1.28
111 112 7.391148 ACACGTGAATCTAGGCAAAATATTT 57.609 32.000 25.01 0.00 0.00 1.40
112 113 8.500753 ACACGTGAATCTAGGCAAAATATTTA 57.499 30.769 25.01 0.00 0.00 1.40
113 114 8.952278 ACACGTGAATCTAGGCAAAATATTTAA 58.048 29.630 25.01 0.00 0.00 1.52
114 115 9.781834 CACGTGAATCTAGGCAAAATATTTAAA 57.218 29.630 10.90 0.00 0.00 1.52
124 125 7.977904 AGGCAAAATATTTAAATGAAGCAAGC 58.022 30.769 11.05 6.23 0.00 4.01
125 126 7.825761 AGGCAAAATATTTAAATGAAGCAAGCT 59.174 29.630 11.05 0.00 0.00 3.74
126 127 8.118607 GGCAAAATATTTAAATGAAGCAAGCTC 58.881 33.333 11.05 0.00 0.00 4.09
127 128 8.658609 GCAAAATATTTAAATGAAGCAAGCTCA 58.341 29.630 11.05 0.00 0.00 4.26
128 129 9.962759 CAAAATATTTAAATGAAGCAAGCTCAC 57.037 29.630 11.05 0.00 0.00 3.51
129 130 8.707938 AAATATTTAAATGAAGCAAGCTCACC 57.292 30.769 11.05 0.00 0.00 4.02
130 131 5.726980 ATTTAAATGAAGCAAGCTCACCA 57.273 34.783 0.00 0.00 0.00 4.17
131 132 5.528043 TTTAAATGAAGCAAGCTCACCAA 57.472 34.783 0.00 0.00 0.00 3.67
132 133 5.726980 TTAAATGAAGCAAGCTCACCAAT 57.273 34.783 0.00 0.00 0.00 3.16
133 134 3.587797 AATGAAGCAAGCTCACCAATG 57.412 42.857 0.00 0.00 0.00 2.82
134 135 0.599558 TGAAGCAAGCTCACCAATGC 59.400 50.000 0.00 0.00 39.06 3.56
135 136 0.599558 GAAGCAAGCTCACCAATGCA 59.400 50.000 8.43 0.00 41.18 3.96
136 137 1.203994 GAAGCAAGCTCACCAATGCAT 59.796 47.619 8.43 0.00 41.18 3.96
137 138 0.530744 AGCAAGCTCACCAATGCATG 59.469 50.000 0.00 0.00 41.18 4.06
138 139 0.528924 GCAAGCTCACCAATGCATGA 59.471 50.000 0.00 0.00 38.63 3.07
139 140 1.067425 GCAAGCTCACCAATGCATGAA 60.067 47.619 0.00 0.00 38.63 2.57
140 141 2.610976 GCAAGCTCACCAATGCATGAAA 60.611 45.455 0.00 0.00 38.63 2.69
141 142 3.250744 CAAGCTCACCAATGCATGAAAG 58.749 45.455 0.00 0.00 30.59 2.62
142 143 2.799017 AGCTCACCAATGCATGAAAGA 58.201 42.857 0.00 0.00 0.00 2.52
143 144 2.753452 AGCTCACCAATGCATGAAAGAG 59.247 45.455 0.00 7.50 0.00 2.85
144 145 2.490903 GCTCACCAATGCATGAAAGAGT 59.509 45.455 0.00 0.00 0.00 3.24
145 146 3.057033 GCTCACCAATGCATGAAAGAGTT 60.057 43.478 0.00 0.00 0.00 3.01
146 147 4.560108 GCTCACCAATGCATGAAAGAGTTT 60.560 41.667 0.00 0.00 0.00 2.66
147 148 5.335897 GCTCACCAATGCATGAAAGAGTTTA 60.336 40.000 0.00 0.00 0.00 2.01
148 149 6.258230 TCACCAATGCATGAAAGAGTTTAG 57.742 37.500 0.00 0.00 0.00 1.85
149 150 5.769662 TCACCAATGCATGAAAGAGTTTAGT 59.230 36.000 0.00 0.00 0.00 2.24
150 151 6.939730 TCACCAATGCATGAAAGAGTTTAGTA 59.060 34.615 0.00 0.00 0.00 1.82
151 152 7.119699 TCACCAATGCATGAAAGAGTTTAGTAG 59.880 37.037 0.00 0.00 0.00 2.57
152 153 6.127897 ACCAATGCATGAAAGAGTTTAGTAGC 60.128 38.462 0.00 0.00 0.00 3.58
153 154 6.094603 CCAATGCATGAAAGAGTTTAGTAGCT 59.905 38.462 0.00 0.00 0.00 3.32
154 155 7.280876 CCAATGCATGAAAGAGTTTAGTAGCTA 59.719 37.037 0.00 0.00 0.00 3.32
155 156 8.668353 CAATGCATGAAAGAGTTTAGTAGCTAA 58.332 33.333 0.00 0.00 0.00 3.09
156 157 8.792830 ATGCATGAAAGAGTTTAGTAGCTAAA 57.207 30.769 0.00 0.00 34.12 1.85
157 158 8.792830 TGCATGAAAGAGTTTAGTAGCTAAAT 57.207 30.769 0.00 0.00 38.07 1.40
158 159 8.883731 TGCATGAAAGAGTTTAGTAGCTAAATC 58.116 33.333 0.00 0.00 38.07 2.17
159 160 8.883731 GCATGAAAGAGTTTAGTAGCTAAATCA 58.116 33.333 0.00 5.01 38.07 2.57
174 175 9.670719 GTAGCTAAATCATTAAATGAAGGAAGC 57.329 33.333 0.00 0.00 43.50 3.86
175 176 8.530804 AGCTAAATCATTAAATGAAGGAAGCT 57.469 30.769 0.00 0.00 43.50 3.74
176 177 8.975295 AGCTAAATCATTAAATGAAGGAAGCTT 58.025 29.630 0.00 0.00 43.50 3.74
180 181 7.886629 ATCATTAAATGAAGGAAGCTTAGCA 57.113 32.000 7.07 0.00 43.50 3.49
181 182 7.701539 TCATTAAATGAAGGAAGCTTAGCAA 57.298 32.000 7.07 0.00 36.11 3.91
182 183 7.538575 TCATTAAATGAAGGAAGCTTAGCAAC 58.461 34.615 7.07 0.00 36.11 4.17
183 184 6.892658 TTAAATGAAGGAAGCTTAGCAACA 57.107 33.333 7.07 0.00 0.00 3.33
184 185 5.789643 AAATGAAGGAAGCTTAGCAACAA 57.210 34.783 7.07 0.00 0.00 2.83
185 186 4.773323 ATGAAGGAAGCTTAGCAACAAC 57.227 40.909 7.07 0.00 0.00 3.32
186 187 3.550820 TGAAGGAAGCTTAGCAACAACA 58.449 40.909 7.07 0.00 0.00 3.33
187 188 3.951037 TGAAGGAAGCTTAGCAACAACAA 59.049 39.130 7.07 0.00 0.00 2.83
188 189 4.400884 TGAAGGAAGCTTAGCAACAACAAA 59.599 37.500 7.07 0.00 0.00 2.83
189 190 5.068987 TGAAGGAAGCTTAGCAACAACAAAT 59.931 36.000 7.07 0.00 0.00 2.32
190 191 5.535753 AGGAAGCTTAGCAACAACAAATT 57.464 34.783 7.07 0.00 0.00 1.82
191 192 6.648879 AGGAAGCTTAGCAACAACAAATTA 57.351 33.333 7.07 0.00 0.00 1.40
192 193 7.049799 AGGAAGCTTAGCAACAACAAATTAA 57.950 32.000 7.07 0.00 0.00 1.40
193 194 7.147976 AGGAAGCTTAGCAACAACAAATTAAG 58.852 34.615 7.07 0.00 0.00 1.85
194 195 6.128822 GGAAGCTTAGCAACAACAAATTAAGC 60.129 38.462 7.07 6.05 41.84 3.09
195 196 5.841810 AGCTTAGCAACAACAAATTAAGCA 58.158 33.333 7.07 0.00 43.18 3.91
196 197 5.691754 AGCTTAGCAACAACAAATTAAGCAC 59.308 36.000 7.07 0.00 43.18 4.40
197 198 5.107491 GCTTAGCAACAACAAATTAAGCACC 60.107 40.000 0.00 0.00 41.41 5.01
198 199 4.670896 AGCAACAACAAATTAAGCACCT 57.329 36.364 0.00 0.00 0.00 4.00
199 200 5.782893 AGCAACAACAAATTAAGCACCTA 57.217 34.783 0.00 0.00 0.00 3.08
200 201 6.345096 AGCAACAACAAATTAAGCACCTAT 57.655 33.333 0.00 0.00 0.00 2.57
201 202 6.158598 AGCAACAACAAATTAAGCACCTATG 58.841 36.000 0.00 0.00 0.00 2.23
219 220 8.484641 CACCTATGCATTATGGACTATAGTTG 57.515 38.462 3.54 1.20 0.00 3.16
220 221 7.065085 CACCTATGCATTATGGACTATAGTTGC 59.935 40.741 15.11 15.11 34.93 4.17
221 222 7.038017 ACCTATGCATTATGGACTATAGTTGCT 60.038 37.037 20.16 11.60 35.19 3.91
222 223 8.478066 CCTATGCATTATGGACTATAGTTGCTA 58.522 37.037 20.16 10.89 35.19 3.49
223 224 9.875691 CTATGCATTATGGACTATAGTTGCTAA 57.124 33.333 20.16 12.63 35.19 3.09
225 226 8.607441 TGCATTATGGACTATAGTTGCTAAAG 57.393 34.615 20.16 10.96 35.19 1.85
226 227 8.210946 TGCATTATGGACTATAGTTGCTAAAGT 58.789 33.333 20.16 0.00 35.19 2.66
227 228 9.706691 GCATTATGGACTATAGTTGCTAAAGTA 57.293 33.333 14.82 0.00 33.16 2.24
237 238 9.530129 CTATAGTTGCTAAAGTATTTAATGCGC 57.470 33.333 0.00 0.00 40.54 6.09
238 239 6.436843 AGTTGCTAAAGTATTTAATGCGCT 57.563 33.333 9.73 0.00 40.54 5.92
239 240 6.852664 AGTTGCTAAAGTATTTAATGCGCTT 58.147 32.000 9.73 0.00 40.54 4.68
240 241 7.981142 AGTTGCTAAAGTATTTAATGCGCTTA 58.019 30.769 9.73 1.78 40.54 3.09
241 242 8.122952 AGTTGCTAAAGTATTTAATGCGCTTAG 58.877 33.333 9.73 5.17 40.54 2.18
242 243 6.427150 TGCTAAAGTATTTAATGCGCTTAGC 58.573 36.000 22.50 22.50 40.54 3.09
259 260 7.881643 CGCTTAGCATCTTATCTAAACATCT 57.118 36.000 4.70 0.00 0.00 2.90
260 261 8.304202 CGCTTAGCATCTTATCTAAACATCTT 57.696 34.615 4.70 0.00 0.00 2.40
261 262 8.768955 CGCTTAGCATCTTATCTAAACATCTTT 58.231 33.333 4.70 0.00 0.00 2.52
266 267 9.638176 AGCATCTTATCTAAACATCTTTCCATT 57.362 29.630 0.00 0.00 0.00 3.16
267 268 9.674824 GCATCTTATCTAAACATCTTTCCATTG 57.325 33.333 0.00 0.00 0.00 2.82
270 271 9.973661 TCTTATCTAAACATCTTTCCATTGGAA 57.026 29.630 14.24 14.24 40.27 3.53
272 273 9.973661 TTATCTAAACATCTTTCCATTGGAAGA 57.026 29.630 17.29 16.20 43.06 2.87
273 274 7.928307 TCTAAACATCTTTCCATTGGAAGAG 57.072 36.000 17.29 16.36 43.06 2.85
274 275 5.990120 AAACATCTTTCCATTGGAAGAGG 57.010 39.130 17.29 18.42 43.06 3.69
275 276 4.664688 ACATCTTTCCATTGGAAGAGGT 57.335 40.909 17.29 18.94 43.06 3.85
276 277 4.593956 ACATCTTTCCATTGGAAGAGGTC 58.406 43.478 17.29 0.00 43.06 3.85
341 342 1.913419 ACCAACCGGAACCAGACATAT 59.087 47.619 9.46 0.00 35.59 1.78
394 395 2.555547 GCCTGGTGCAGTGTTCCAC 61.556 63.158 0.00 0.00 40.77 4.02
433 435 5.700832 CAGAGTGCACAACCTGTCTTAATAA 59.299 40.000 21.04 0.00 0.00 1.40
434 436 5.934625 AGAGTGCACAACCTGTCTTAATAAG 59.065 40.000 21.04 0.00 0.00 1.73
441 450 7.043325 GCACAACCTGTCTTAATAAGATCGTAG 60.043 40.741 5.96 3.50 40.18 3.51
443 452 8.407064 ACAACCTGTCTTAATAAGATCGTAGAG 58.593 37.037 5.96 0.00 43.63 2.43
453 462 1.006314 GATCGTAGAGGCGAGCATGC 61.006 60.000 10.51 10.51 45.25 4.06
470 479 1.821332 GCCTCGAAATGCCTCCCAG 60.821 63.158 0.00 0.00 0.00 4.45
522 531 1.762957 CCTACACACCCGATCCAATCT 59.237 52.381 0.00 0.00 0.00 2.40
527 536 3.199946 ACACACCCGATCCAATCTACATT 59.800 43.478 0.00 0.00 0.00 2.71
549 561 0.603975 GTCTGCAGGTCAACCTCCAC 60.604 60.000 15.13 0.00 46.65 4.02
550 562 0.764369 TCTGCAGGTCAACCTCCACT 60.764 55.000 15.13 0.00 46.65 4.00
551 563 0.321122 CTGCAGGTCAACCTCCACTC 60.321 60.000 5.57 0.00 46.65 3.51
552 564 1.003233 GCAGGTCAACCTCCACTCC 60.003 63.158 0.00 0.00 46.65 3.85
553 565 1.768684 GCAGGTCAACCTCCACTCCA 61.769 60.000 0.00 0.00 46.65 3.86
554 566 0.764890 CAGGTCAACCTCCACTCCAA 59.235 55.000 0.00 0.00 46.65 3.53
555 567 1.142870 CAGGTCAACCTCCACTCCAAA 59.857 52.381 0.00 0.00 46.65 3.28
573 585 5.683681 TCCAAATATGTGCTGCTGAATCTA 58.316 37.500 0.00 0.00 0.00 1.98
582 594 6.747125 TGTGCTGCTGAATCTAAATTTTCAA 58.253 32.000 0.00 0.00 31.85 2.69
618 684 4.670765 ACTGCTGAATCTCAATTTCCCTT 58.329 39.130 0.00 0.00 0.00 3.95
619 685 5.082425 ACTGCTGAATCTCAATTTCCCTTT 58.918 37.500 0.00 0.00 0.00 3.11
620 686 5.184671 ACTGCTGAATCTCAATTTCCCTTTC 59.815 40.000 0.00 0.00 0.00 2.62
654 729 0.540923 ATCAGGAGCTGAGTTGCCTC 59.459 55.000 0.00 0.00 44.08 4.70
655 730 1.078567 CAGGAGCTGAGTTGCCTCC 60.079 63.158 0.00 0.00 36.86 4.30
656 731 2.125350 GGAGCTGAGTTGCCTCCG 60.125 66.667 0.00 0.00 36.86 4.63
657 732 2.817396 GAGCTGAGTTGCCTCCGC 60.817 66.667 0.00 0.00 45.31 5.54
658 733 3.596066 GAGCTGAGTTGCCTCCGCA 62.596 63.158 8.60 0.00 46.80 5.69
659 734 3.602513 AGCTGAGTTGCCTCCGCAG 62.603 63.158 8.60 2.39 46.80 5.18
761 840 1.667830 CTCGGTGCGGCTCTTTTCA 60.668 57.895 0.00 0.00 0.00 2.69
788 879 3.609703 GAGAGAAGGGCTCGCTCA 58.390 61.111 11.34 0.00 46.95 4.26
819 922 1.803289 GAGGCCATGGAAAACGAGC 59.197 57.895 18.40 0.00 0.00 5.03
982 1092 2.762887 TGGCTATCAAGAGAGTGTCCAG 59.237 50.000 0.00 0.00 0.00 3.86
995 1105 1.267574 TGTCCAGGGGCTCTAAGCAG 61.268 60.000 0.86 0.00 44.75 4.24
1001 1111 1.772156 GGGCTCTAAGCAGGGGGAT 60.772 63.158 0.86 0.00 44.75 3.85
1066 1176 0.957395 CCGCAACCTTGTGCAGATCT 60.957 55.000 0.00 0.00 45.19 2.75
1137 1247 2.049063 AACAGCAGCCTCGACGTC 60.049 61.111 5.18 5.18 0.00 4.34
1181 1291 0.620556 CTATGGTGGCCAGTCAGGTT 59.379 55.000 5.11 0.00 36.75 3.50
1188 1298 0.912486 GGCCAGTCAGGTTAGGTGAT 59.088 55.000 0.00 0.00 40.61 3.06
1190 1300 1.471676 GCCAGTCAGGTTAGGTGATCG 60.472 57.143 0.00 0.00 40.61 3.69
1281 1467 8.553459 TTTGAACCAAATTTGAACTAAAGCAA 57.447 26.923 19.86 8.79 0.00 3.91
1282 1468 7.769272 TGAACCAAATTTGAACTAAAGCAAG 57.231 32.000 19.86 0.77 0.00 4.01
1283 1469 6.760770 TGAACCAAATTTGAACTAAAGCAAGG 59.239 34.615 19.86 0.39 0.00 3.61
1298 1485 8.515414 ACTAAAGCAAGGACACTATTTTTGATC 58.485 33.333 0.00 0.00 0.00 2.92
1299 1486 6.899393 AAGCAAGGACACTATTTTTGATCA 57.101 33.333 0.00 0.00 0.00 2.92
1302 1489 6.888632 AGCAAGGACACTATTTTTGATCAGAT 59.111 34.615 0.00 0.00 0.00 2.90
1356 1543 2.917971 GCGAGTTGTACAGTCTGATGAC 59.082 50.000 6.91 2.33 43.22 3.06
1414 1601 2.512515 GGATCGGCTCTGCGCTTT 60.513 61.111 9.73 0.00 39.13 3.51
1440 1627 0.332293 TGCATGAGGAATGGGAGCAA 59.668 50.000 0.00 0.00 36.71 3.91
1467 1654 2.435805 TCTGCATAGGGACATCAAGACC 59.564 50.000 0.00 0.00 0.00 3.85
1490 1677 1.133598 CAACATGATGCTGGATGCGTT 59.866 47.619 0.00 0.00 46.63 4.84
1629 1816 2.601666 AGAGCCAGCACGGAGTCA 60.602 61.111 0.00 0.00 41.61 3.41
1638 1825 2.360483 CAGCACGGAGTCAGATGTCTAT 59.640 50.000 0.00 0.00 41.61 1.98
1667 1854 2.101185 CGTGCTGCTCGAGATCGT 59.899 61.111 18.75 0.00 40.80 3.73
1674 1861 1.517257 GCTCGAGATCGTGTGTGGG 60.517 63.158 18.75 0.00 40.80 4.61
1754 1941 2.436115 GCTGTACGGCCAAGGGAC 60.436 66.667 16.25 0.00 0.00 4.46
1755 1942 3.065306 CTGTACGGCCAAGGGACA 58.935 61.111 2.24 0.00 0.00 4.02
1770 1957 3.701604 GACAATCCTCGACGCGGCT 62.702 63.158 11.76 0.00 0.00 5.52
1773 1960 2.786495 AATCCTCGACGCGGCTGAT 61.786 57.895 11.76 6.53 0.00 2.90
1819 2006 3.616721 AAGAGGTGGAGCGCGTGT 61.617 61.111 8.43 0.00 0.00 4.49
1827 2014 3.335534 GAGCGCGTGTTGGTCGTT 61.336 61.111 8.43 0.00 0.00 3.85
1833 2020 2.892334 CGTGTTGGTCGTTGGCCTG 61.892 63.158 3.32 0.00 0.00 4.85
1842 2029 2.832661 GTTGGCCTGTGGTGCACA 60.833 61.111 20.43 1.62 42.45 4.57
1929 2116 3.710722 CCAGAGAGGTTGCCGCCT 61.711 66.667 0.00 0.00 42.53 5.52
2013 2203 2.749044 ACCGCTCAGCAGCCAATG 60.749 61.111 0.00 0.00 43.56 2.82
2022 2212 3.278574 TCAGCAGCCAATGTAATGGTAC 58.721 45.455 0.00 0.00 42.75 3.34
2024 2214 3.313526 CAGCAGCCAATGTAATGGTACTC 59.686 47.826 0.00 0.00 42.75 2.59
2027 2217 3.313526 CAGCCAATGTAATGGTACTCTGC 59.686 47.826 0.00 0.00 42.75 4.26
2094 2287 7.041372 GGTTAGCATCTGTCTTTTCTGTTGTAA 60.041 37.037 0.00 0.00 0.00 2.41
2101 2294 8.506168 TCTGTCTTTTCTGTTGTAAAACATCT 57.494 30.769 0.00 0.00 31.47 2.90
2108 2301 3.811083 TGTTGTAAAACATCTCCGTGGT 58.189 40.909 0.00 0.00 0.00 4.16
2117 2310 8.975439 GTAAAACATCTCCGTGGTACTATATTG 58.025 37.037 0.00 0.00 0.00 1.90
2245 2438 3.620427 TTGTATGCCACGTAGGACAAT 57.380 42.857 8.04 1.90 41.22 2.71
2249 2442 0.319083 TGCCACGTAGGACAATTCGT 59.681 50.000 8.04 0.00 41.22 3.85
2261 2454 2.867368 GACAATTCGTGTGTGTGGTGTA 59.133 45.455 0.00 0.00 41.96 2.90
2267 2460 2.362717 TCGTGTGTGTGGTGTATGAGAA 59.637 45.455 0.00 0.00 0.00 2.87
2283 2476 0.110486 AGAAAGGTCGCCCACACATT 59.890 50.000 0.00 0.00 0.00 2.71
2285 2478 0.179004 AAAGGTCGCCCACACATTCA 60.179 50.000 0.00 0.00 0.00 2.57
2291 2484 3.130340 GGTCGCCCACACATTCATTTTAT 59.870 43.478 0.00 0.00 0.00 1.40
2298 2491 5.106357 CCCACACATTCATTTTATCACACGA 60.106 40.000 0.00 0.00 0.00 4.35
2302 2495 6.429692 ACACATTCATTTTATCACACGAAGGA 59.570 34.615 0.00 0.00 0.00 3.36
2314 2507 1.658114 CGAAGGAGTCGGTGTGTGA 59.342 57.895 0.00 0.00 46.45 3.58
2339 2532 1.037493 TAGCAGTTCGTCCACACACT 58.963 50.000 0.00 0.00 0.00 3.55
2340 2533 0.249489 AGCAGTTCGTCCACACACTC 60.249 55.000 0.00 0.00 0.00 3.51
2427 2621 1.152777 CCCACACCCAAGCTGTCAA 60.153 57.895 0.00 0.00 0.00 3.18
2437 2631 0.970640 AAGCTGTCAATTGCCATGCA 59.029 45.000 11.55 0.00 36.47 3.96
2752 2956 0.391661 ATGGCAACTGCAGTAGACCG 60.392 55.000 22.01 7.73 44.36 4.79
2821 3025 3.446442 ACTTTGACCTGAGATGGCAAT 57.554 42.857 0.00 0.00 0.00 3.56
2991 3196 1.076923 ACGAGGTACGAGGCCTGAT 60.077 57.895 12.00 0.00 45.77 2.90
3007 3212 2.998480 ATGTACCGGGCGTGTGGA 60.998 61.111 6.32 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.268544 CACATCAGATTTTTCGCCTACATG 58.731 41.667 0.00 0.00 0.00 3.21
7 8 3.487544 GCCACATCAGATTTTTCGCCTAC 60.488 47.826 0.00 0.00 0.00 3.18
10 11 1.202114 TGCCACATCAGATTTTTCGCC 59.798 47.619 0.00 0.00 0.00 5.54
12 13 4.744137 TGTTTTGCCACATCAGATTTTTCG 59.256 37.500 0.00 0.00 0.00 3.46
13 14 6.601741 TTGTTTTGCCACATCAGATTTTTC 57.398 33.333 0.00 0.00 0.00 2.29
16 17 8.851541 ATTAATTGTTTTGCCACATCAGATTT 57.148 26.923 0.00 0.00 0.00 2.17
18 19 9.537192 CATATTAATTGTTTTGCCACATCAGAT 57.463 29.630 0.00 0.00 0.00 2.90
19 20 8.747471 TCATATTAATTGTTTTGCCACATCAGA 58.253 29.630 0.00 0.00 0.00 3.27
20 21 8.929827 TCATATTAATTGTTTTGCCACATCAG 57.070 30.769 0.00 0.00 0.00 2.90
21 22 8.747471 TCTCATATTAATTGTTTTGCCACATCA 58.253 29.630 0.00 0.00 0.00 3.07
22 23 9.241317 CTCTCATATTAATTGTTTTGCCACATC 57.759 33.333 0.00 0.00 0.00 3.06
23 24 8.970020 TCTCTCATATTAATTGTTTTGCCACAT 58.030 29.630 0.00 0.00 0.00 3.21
24 25 8.347004 TCTCTCATATTAATTGTTTTGCCACA 57.653 30.769 0.00 0.00 0.00 4.17
25 26 9.638239 TTTCTCTCATATTAATTGTTTTGCCAC 57.362 29.630 0.00 0.00 0.00 5.01
42 43 9.753674 TGGAGTTACCAAATTAATTTCTCTCAT 57.246 29.630 18.58 4.93 46.75 2.90
59 60 3.782656 TTGGTTCTTCCTGGAGTTACC 57.217 47.619 13.28 13.28 37.07 2.85
60 61 3.440522 GCATTGGTTCTTCCTGGAGTTAC 59.559 47.826 0.00 0.00 37.07 2.50
61 62 3.561313 GGCATTGGTTCTTCCTGGAGTTA 60.561 47.826 0.00 0.00 37.07 2.24
62 63 2.519013 GCATTGGTTCTTCCTGGAGTT 58.481 47.619 0.00 0.00 37.07 3.01
63 64 1.272147 GGCATTGGTTCTTCCTGGAGT 60.272 52.381 0.00 0.00 37.07 3.85
64 65 1.272092 TGGCATTGGTTCTTCCTGGAG 60.272 52.381 0.00 0.00 37.07 3.86
65 66 0.776810 TGGCATTGGTTCTTCCTGGA 59.223 50.000 0.00 0.00 37.07 3.86
66 67 1.631405 TTGGCATTGGTTCTTCCTGG 58.369 50.000 0.00 0.00 37.07 4.45
67 68 3.181467 TGTTTTGGCATTGGTTCTTCCTG 60.181 43.478 0.00 0.00 37.07 3.86
68 69 3.037549 TGTTTTGGCATTGGTTCTTCCT 58.962 40.909 0.00 0.00 37.07 3.36
69 70 3.130633 GTGTTTTGGCATTGGTTCTTCC 58.869 45.455 0.00 0.00 0.00 3.46
70 71 2.794350 CGTGTTTTGGCATTGGTTCTTC 59.206 45.455 0.00 0.00 0.00 2.87
71 72 2.167487 ACGTGTTTTGGCATTGGTTCTT 59.833 40.909 0.00 0.00 0.00 2.52
72 73 1.754226 ACGTGTTTTGGCATTGGTTCT 59.246 42.857 0.00 0.00 0.00 3.01
73 74 1.857837 CACGTGTTTTGGCATTGGTTC 59.142 47.619 7.58 0.00 0.00 3.62
74 75 1.478510 TCACGTGTTTTGGCATTGGTT 59.521 42.857 16.51 0.00 0.00 3.67
75 76 1.107114 TCACGTGTTTTGGCATTGGT 58.893 45.000 16.51 0.00 0.00 3.67
76 77 2.215907 TTCACGTGTTTTGGCATTGG 57.784 45.000 16.51 0.00 0.00 3.16
77 78 3.641648 AGATTCACGTGTTTTGGCATTG 58.358 40.909 16.51 0.00 0.00 2.82
78 79 4.082787 CCTAGATTCACGTGTTTTGGCATT 60.083 41.667 16.51 0.00 0.00 3.56
79 80 3.440173 CCTAGATTCACGTGTTTTGGCAT 59.560 43.478 16.51 0.00 0.00 4.40
80 81 2.811431 CCTAGATTCACGTGTTTTGGCA 59.189 45.455 16.51 0.00 0.00 4.92
81 82 2.414161 GCCTAGATTCACGTGTTTTGGC 60.414 50.000 16.51 17.45 0.00 4.52
82 83 2.811431 TGCCTAGATTCACGTGTTTTGG 59.189 45.455 16.51 12.11 0.00 3.28
83 84 4.481930 TTGCCTAGATTCACGTGTTTTG 57.518 40.909 16.51 2.58 0.00 2.44
84 85 5.508200 TTTTGCCTAGATTCACGTGTTTT 57.492 34.783 16.51 1.11 0.00 2.43
85 86 5.705609 ATTTTGCCTAGATTCACGTGTTT 57.294 34.783 16.51 3.90 0.00 2.83
86 87 7.391148 AATATTTTGCCTAGATTCACGTGTT 57.609 32.000 16.51 4.31 0.00 3.32
87 88 7.391148 AAATATTTTGCCTAGATTCACGTGT 57.609 32.000 16.51 0.00 0.00 4.49
88 89 9.781834 TTTAAATATTTTGCCTAGATTCACGTG 57.218 29.630 9.94 9.94 0.00 4.49
98 99 9.097257 GCTTGCTTCATTTAAATATTTTGCCTA 57.903 29.630 5.91 0.00 0.00 3.93
99 100 7.825761 AGCTTGCTTCATTTAAATATTTTGCCT 59.174 29.630 5.91 0.00 0.00 4.75
100 101 7.977904 AGCTTGCTTCATTTAAATATTTTGCC 58.022 30.769 5.91 0.00 0.00 4.52
101 102 8.658609 TGAGCTTGCTTCATTTAAATATTTTGC 58.341 29.630 5.91 2.78 0.00 3.68
102 103 9.962759 GTGAGCTTGCTTCATTTAAATATTTTG 57.037 29.630 5.91 0.00 0.00 2.44
103 104 9.154847 GGTGAGCTTGCTTCATTTAAATATTTT 57.845 29.630 5.91 0.00 0.00 1.82
104 105 8.313292 TGGTGAGCTTGCTTCATTTAAATATTT 58.687 29.630 5.89 5.89 0.00 1.40
105 106 7.839907 TGGTGAGCTTGCTTCATTTAAATATT 58.160 30.769 0.00 0.00 0.00 1.28
106 107 7.408756 TGGTGAGCTTGCTTCATTTAAATAT 57.591 32.000 0.00 0.00 0.00 1.28
107 108 6.832520 TGGTGAGCTTGCTTCATTTAAATA 57.167 33.333 0.00 0.00 0.00 1.40
108 109 5.726980 TGGTGAGCTTGCTTCATTTAAAT 57.273 34.783 0.00 0.00 0.00 1.40
109 110 5.528043 TTGGTGAGCTTGCTTCATTTAAA 57.472 34.783 0.00 0.00 0.00 1.52
110 111 5.472148 CATTGGTGAGCTTGCTTCATTTAA 58.528 37.500 0.00 0.00 0.00 1.52
111 112 4.618927 GCATTGGTGAGCTTGCTTCATTTA 60.619 41.667 0.00 0.00 32.41 1.40
112 113 3.863400 GCATTGGTGAGCTTGCTTCATTT 60.863 43.478 0.00 0.00 32.41 2.32
113 114 2.353406 GCATTGGTGAGCTTGCTTCATT 60.353 45.455 0.00 0.00 32.41 2.57
114 115 1.203994 GCATTGGTGAGCTTGCTTCAT 59.796 47.619 0.00 0.00 32.41 2.57
115 116 0.599558 GCATTGGTGAGCTTGCTTCA 59.400 50.000 0.00 0.00 32.41 3.02
116 117 0.599558 TGCATTGGTGAGCTTGCTTC 59.400 50.000 7.30 0.00 36.10 3.86
117 118 1.067142 CATGCATTGGTGAGCTTGCTT 60.067 47.619 0.00 0.00 36.10 3.91
118 119 0.530744 CATGCATTGGTGAGCTTGCT 59.469 50.000 0.00 0.00 36.10 3.91
119 120 0.528924 TCATGCATTGGTGAGCTTGC 59.471 50.000 0.00 0.00 36.28 4.01
120 121 3.057104 TCTTTCATGCATTGGTGAGCTTG 60.057 43.478 0.00 0.00 37.28 4.01
121 122 3.159472 TCTTTCATGCATTGGTGAGCTT 58.841 40.909 0.00 0.00 0.00 3.74
122 123 2.753452 CTCTTTCATGCATTGGTGAGCT 59.247 45.455 0.00 0.00 0.00 4.09
123 124 2.490903 ACTCTTTCATGCATTGGTGAGC 59.509 45.455 0.00 0.00 0.00 4.26
124 125 4.778534 AACTCTTTCATGCATTGGTGAG 57.221 40.909 0.00 5.76 0.00 3.51
125 126 5.769662 ACTAAACTCTTTCATGCATTGGTGA 59.230 36.000 0.00 0.00 0.00 4.02
126 127 6.017400 ACTAAACTCTTTCATGCATTGGTG 57.983 37.500 0.00 0.00 0.00 4.17
127 128 6.127897 GCTACTAAACTCTTTCATGCATTGGT 60.128 38.462 0.00 0.00 0.00 3.67
128 129 6.094603 AGCTACTAAACTCTTTCATGCATTGG 59.905 38.462 0.00 0.00 0.00 3.16
129 130 7.081526 AGCTACTAAACTCTTTCATGCATTG 57.918 36.000 0.00 0.00 0.00 2.82
130 131 8.792830 TTAGCTACTAAACTCTTTCATGCATT 57.207 30.769 0.00 0.00 0.00 3.56
131 132 8.792830 TTTAGCTACTAAACTCTTTCATGCAT 57.207 30.769 0.00 0.00 31.94 3.96
132 133 8.792830 ATTTAGCTACTAAACTCTTTCATGCA 57.207 30.769 0.00 0.00 38.51 3.96
133 134 8.883731 TGATTTAGCTACTAAACTCTTTCATGC 58.116 33.333 0.00 0.00 38.51 4.06
148 149 9.670719 GCTTCCTTCATTTAATGATTTAGCTAC 57.329 33.333 8.56 0.00 39.39 3.58
149 150 9.632638 AGCTTCCTTCATTTAATGATTTAGCTA 57.367 29.630 21.41 0.00 37.85 3.32
150 151 8.530804 AGCTTCCTTCATTTAATGATTTAGCT 57.469 30.769 19.16 19.16 39.39 3.32
154 155 8.752187 TGCTAAGCTTCCTTCATTTAATGATTT 58.248 29.630 8.56 0.00 39.39 2.17
155 156 8.297470 TGCTAAGCTTCCTTCATTTAATGATT 57.703 30.769 8.56 1.25 39.39 2.57
156 157 7.886629 TGCTAAGCTTCCTTCATTTAATGAT 57.113 32.000 8.56 0.00 39.39 2.45
157 158 7.176515 TGTTGCTAAGCTTCCTTCATTTAATGA 59.823 33.333 0.00 3.20 37.55 2.57
158 159 7.315142 TGTTGCTAAGCTTCCTTCATTTAATG 58.685 34.615 0.00 0.00 32.47 1.90
159 160 7.466746 TGTTGCTAAGCTTCCTTCATTTAAT 57.533 32.000 0.00 0.00 32.47 1.40
160 161 6.892658 TGTTGCTAAGCTTCCTTCATTTAA 57.107 33.333 0.00 0.00 32.47 1.52
161 162 6.264292 TGTTGTTGCTAAGCTTCCTTCATTTA 59.736 34.615 0.00 0.00 32.47 1.40
162 163 5.068987 TGTTGTTGCTAAGCTTCCTTCATTT 59.931 36.000 0.00 0.00 32.47 2.32
163 164 4.584325 TGTTGTTGCTAAGCTTCCTTCATT 59.416 37.500 0.00 0.00 32.47 2.57
164 165 4.144297 TGTTGTTGCTAAGCTTCCTTCAT 58.856 39.130 0.00 0.00 32.47 2.57
165 166 3.550820 TGTTGTTGCTAAGCTTCCTTCA 58.449 40.909 0.00 0.00 32.47 3.02
166 167 4.568152 TTGTTGTTGCTAAGCTTCCTTC 57.432 40.909 0.00 0.00 32.47 3.46
167 168 5.535753 ATTTGTTGTTGCTAAGCTTCCTT 57.464 34.783 0.00 0.00 35.05 3.36
168 169 5.535753 AATTTGTTGTTGCTAAGCTTCCT 57.464 34.783 0.00 0.00 0.00 3.36
169 170 6.128822 GCTTAATTTGTTGTTGCTAAGCTTCC 60.129 38.462 0.00 0.00 38.65 3.46
170 171 6.420604 TGCTTAATTTGTTGTTGCTAAGCTTC 59.579 34.615 0.00 0.00 41.04 3.86
171 172 6.200854 GTGCTTAATTTGTTGTTGCTAAGCTT 59.799 34.615 3.48 3.48 41.04 3.74
172 173 5.691754 GTGCTTAATTTGTTGTTGCTAAGCT 59.308 36.000 11.60 0.00 41.04 3.74
173 174 5.107491 GGTGCTTAATTTGTTGTTGCTAAGC 60.107 40.000 4.99 4.99 40.91 3.09
174 175 6.215845 AGGTGCTTAATTTGTTGTTGCTAAG 58.784 36.000 0.00 0.00 0.00 2.18
175 176 6.155475 AGGTGCTTAATTTGTTGTTGCTAA 57.845 33.333 0.00 0.00 0.00 3.09
176 177 5.782893 AGGTGCTTAATTTGTTGTTGCTA 57.217 34.783 0.00 0.00 0.00 3.49
177 178 4.670896 AGGTGCTTAATTTGTTGTTGCT 57.329 36.364 0.00 0.00 0.00 3.91
178 179 6.393720 CATAGGTGCTTAATTTGTTGTTGC 57.606 37.500 0.00 0.00 0.00 4.17
194 195 7.065085 GCAACTATAGTCCATAATGCATAGGTG 59.935 40.741 16.48 0.00 36.96 4.00
195 196 7.038017 AGCAACTATAGTCCATAATGCATAGGT 60.038 37.037 21.18 3.74 35.74 3.08
196 197 7.334090 AGCAACTATAGTCCATAATGCATAGG 58.666 38.462 21.18 2.72 35.74 2.57
197 198 9.875691 TTAGCAACTATAGTCCATAATGCATAG 57.124 33.333 21.18 0.00 35.74 2.23
199 200 9.224267 CTTTAGCAACTATAGTCCATAATGCAT 57.776 33.333 21.18 12.03 35.74 3.96
200 201 8.210946 ACTTTAGCAACTATAGTCCATAATGCA 58.789 33.333 21.18 9.19 35.74 3.96
201 202 8.608844 ACTTTAGCAACTATAGTCCATAATGC 57.391 34.615 14.43 14.43 34.48 3.56
211 212 9.530129 GCGCATTAAATACTTTAGCAACTATAG 57.470 33.333 0.30 0.00 0.00 1.31
212 213 9.268268 AGCGCATTAAATACTTTAGCAACTATA 57.732 29.630 11.47 0.00 0.00 1.31
213 214 8.154649 AGCGCATTAAATACTTTAGCAACTAT 57.845 30.769 11.47 0.00 0.00 2.12
214 215 7.548196 AGCGCATTAAATACTTTAGCAACTA 57.452 32.000 11.47 0.00 0.00 2.24
215 216 6.436843 AGCGCATTAAATACTTTAGCAACT 57.563 33.333 11.47 0.00 0.00 3.16
216 217 7.097006 GCTAAGCGCATTAAATACTTTAGCAAC 60.097 37.037 19.53 0.00 38.92 4.17
217 218 6.910433 GCTAAGCGCATTAAATACTTTAGCAA 59.090 34.615 19.53 0.00 38.92 3.91
218 219 6.037720 TGCTAAGCGCATTAAATACTTTAGCA 59.962 34.615 21.87 21.87 45.47 3.49
219 220 6.427150 TGCTAAGCGCATTAAATACTTTAGC 58.573 36.000 18.32 18.32 45.47 3.09
234 235 5.907197 TGTTTAGATAAGATGCTAAGCGC 57.093 39.130 0.00 0.00 32.57 5.92
235 236 7.881643 AGATGTTTAGATAAGATGCTAAGCG 57.118 36.000 0.00 0.00 32.57 4.68
240 241 9.638176 AATGGAAAGATGTTTAGATAAGATGCT 57.362 29.630 0.00 0.00 0.00 3.79
241 242 9.674824 CAATGGAAAGATGTTTAGATAAGATGC 57.325 33.333 0.00 0.00 0.00 3.91
244 245 9.973661 TTCCAATGGAAAGATGTTTAGATAAGA 57.026 29.630 13.04 0.00 38.93 2.10
246 247 9.973661 TCTTCCAATGGAAAGATGTTTAGATAA 57.026 29.630 16.30 0.00 41.54 1.75
247 248 9.618890 CTCTTCCAATGGAAAGATGTTTAGATA 57.381 33.333 16.30 0.00 41.54 1.98
248 249 7.559170 CCTCTTCCAATGGAAAGATGTTTAGAT 59.441 37.037 16.30 0.00 41.54 1.98
249 250 6.886459 CCTCTTCCAATGGAAAGATGTTTAGA 59.114 38.462 16.30 5.36 41.54 2.10
250 251 6.660949 ACCTCTTCCAATGGAAAGATGTTTAG 59.339 38.462 16.30 0.82 41.54 1.85
251 252 6.552008 ACCTCTTCCAATGGAAAGATGTTTA 58.448 36.000 16.30 0.00 41.54 2.01
252 253 5.397360 ACCTCTTCCAATGGAAAGATGTTT 58.603 37.500 16.30 0.00 41.54 2.83
253 254 5.003096 ACCTCTTCCAATGGAAAGATGTT 57.997 39.130 16.30 0.00 41.54 2.71
254 255 4.290722 AGACCTCTTCCAATGGAAAGATGT 59.709 41.667 16.30 16.08 41.54 3.06
255 256 4.853007 AGACCTCTTCCAATGGAAAGATG 58.147 43.478 16.30 13.49 41.54 2.90
256 257 6.418946 GTTAGACCTCTTCCAATGGAAAGAT 58.581 40.000 16.30 3.65 41.54 2.40
257 258 5.280521 GGTTAGACCTCTTCCAATGGAAAGA 60.281 44.000 16.30 13.53 36.92 2.52
258 259 4.944317 GGTTAGACCTCTTCCAATGGAAAG 59.056 45.833 16.30 14.67 36.92 2.62
259 260 4.263771 GGGTTAGACCTCTTCCAATGGAAA 60.264 45.833 16.30 6.47 38.70 3.13
260 261 3.265995 GGGTTAGACCTCTTCCAATGGAA 59.734 47.826 14.73 14.73 37.65 3.53
261 262 2.844348 GGGTTAGACCTCTTCCAATGGA 59.156 50.000 0.00 0.00 38.64 3.41
262 263 2.576191 TGGGTTAGACCTCTTCCAATGG 59.424 50.000 0.00 0.00 38.64 3.16
263 264 3.878778 CTGGGTTAGACCTCTTCCAATG 58.121 50.000 0.00 0.00 38.64 2.82
264 265 2.239907 GCTGGGTTAGACCTCTTCCAAT 59.760 50.000 0.00 0.00 38.64 3.16
265 266 1.628846 GCTGGGTTAGACCTCTTCCAA 59.371 52.381 0.00 0.00 38.64 3.53
266 267 1.203313 AGCTGGGTTAGACCTCTTCCA 60.203 52.381 0.00 0.00 38.64 3.53
267 268 1.483004 GAGCTGGGTTAGACCTCTTCC 59.517 57.143 0.00 0.00 38.64 3.46
268 269 2.180276 TGAGCTGGGTTAGACCTCTTC 58.820 52.381 0.00 0.00 38.64 2.87
269 270 2.327325 TGAGCTGGGTTAGACCTCTT 57.673 50.000 0.00 0.00 38.64 2.85
270 271 2.114616 CATGAGCTGGGTTAGACCTCT 58.885 52.381 0.00 0.00 38.64 3.69
271 272 1.139853 CCATGAGCTGGGTTAGACCTC 59.860 57.143 0.00 0.00 41.82 3.85
272 273 1.207791 CCATGAGCTGGGTTAGACCT 58.792 55.000 0.00 0.00 41.82 3.85
273 274 3.788672 CCATGAGCTGGGTTAGACC 57.211 57.895 0.00 0.00 41.82 3.85
321 322 1.354101 TATGTCTGGTTCCGGTTGGT 58.646 50.000 0.00 0.00 36.30 3.67
331 332 1.137086 GCGAGTCCACATATGTCTGGT 59.863 52.381 5.07 0.00 0.00 4.00
363 364 1.072505 CCAGGCCGTACAACACCTT 59.927 57.895 0.00 0.00 0.00 3.50
389 390 1.070786 GGGCGACAAGTCTGTGGAA 59.929 57.895 0.00 0.00 35.30 3.53
394 395 0.668706 CTCTGTGGGCGACAAGTCTG 60.669 60.000 3.39 0.00 32.80 3.51
433 435 0.595588 CATGCTCGCCTCTACGATCT 59.404 55.000 0.00 0.00 42.02 2.75
434 436 1.006314 GCATGCTCGCCTCTACGATC 61.006 60.000 11.37 0.00 42.02 3.69
453 462 1.153086 CCTGGGAGGCATTTCGAGG 60.153 63.158 0.00 0.00 0.00 4.63
454 463 4.547859 CCTGGGAGGCATTTCGAG 57.452 61.111 0.00 0.00 0.00 4.04
478 487 0.249489 GTAGCAGCCGTACCTCATGG 60.249 60.000 0.00 0.00 39.83 3.66
522 531 1.262417 TGACCTGCAGACCGAATGTA 58.738 50.000 17.39 0.00 0.00 2.29
527 536 1.837051 AGGTTGACCTGCAGACCGA 60.837 57.895 17.39 3.04 46.55 4.69
549 561 4.579340 AGATTCAGCAGCACATATTTGGAG 59.421 41.667 0.00 0.00 0.00 3.86
550 562 4.529897 AGATTCAGCAGCACATATTTGGA 58.470 39.130 0.00 0.00 0.00 3.53
551 563 4.913335 AGATTCAGCAGCACATATTTGG 57.087 40.909 0.00 0.00 0.00 3.28
552 564 8.867112 AATTTAGATTCAGCAGCACATATTTG 57.133 30.769 0.00 0.00 0.00 2.32
553 565 9.880157 AAAATTTAGATTCAGCAGCACATATTT 57.120 25.926 0.00 0.00 0.00 1.40
554 566 9.525409 GAAAATTTAGATTCAGCAGCACATATT 57.475 29.630 0.00 0.00 0.00 1.28
555 567 8.689061 TGAAAATTTAGATTCAGCAGCACATAT 58.311 29.630 0.00 0.00 32.14 1.78
618 684 4.588106 TCCTGATCAATGCACAAAAAGGAA 59.412 37.500 0.00 0.00 0.00 3.36
619 685 4.151121 TCCTGATCAATGCACAAAAAGGA 58.849 39.130 0.00 0.00 0.00 3.36
620 686 4.491676 CTCCTGATCAATGCACAAAAAGG 58.508 43.478 0.00 0.00 0.00 3.11
717 796 6.301486 TGCTAATGCAGATCAACAATAGGAT 58.699 36.000 10.41 0.00 45.31 3.24
761 840 1.118356 CCCTTCTCTCTAGGCGGCAT 61.118 60.000 13.08 0.00 0.00 4.40
784 863 1.192534 CCTCGTCGTCTTGTTTTGAGC 59.807 52.381 0.00 0.00 0.00 4.26
788 879 0.179067 TGGCCTCGTCGTCTTGTTTT 60.179 50.000 3.32 0.00 0.00 2.43
819 922 1.597461 GTCCGGTCCCTTTCCTGAG 59.403 63.158 0.00 0.00 0.00 3.35
876 986 5.379732 TTTTTGTTGTCGGAGAAGTTGTT 57.620 34.783 0.00 0.00 39.69 2.83
926 1036 6.996282 TCAAGTCTTTAAGGAACCCTTTGTAG 59.004 38.462 3.34 0.52 41.69 2.74
941 1051 5.003804 GCCACCTCAATTCTCAAGTCTTTA 58.996 41.667 0.00 0.00 0.00 1.85
982 1092 3.493303 CCCCCTGCTTAGAGCCCC 61.493 72.222 0.00 0.00 41.51 5.80
995 1105 1.446366 GCGTACTCCTTCATCCCCC 59.554 63.158 0.00 0.00 0.00 5.40
1026 1136 0.179108 GCCGAAGCCGACTTATGACT 60.179 55.000 0.00 0.00 35.82 3.41
1137 1247 0.871722 TTTTCGTGCCGTGAAGATGG 59.128 50.000 0.00 0.00 0.00 3.51
1153 1263 4.672899 ACTGGCCACCATAGTACATTTTT 58.327 39.130 0.00 0.00 30.82 1.94
1155 1265 3.265737 TGACTGGCCACCATAGTACATTT 59.734 43.478 0.00 0.00 30.82 2.32
1181 1291 6.778834 TTACATTAAGGTCACGATCACCTA 57.221 37.500 3.76 0.00 44.03 3.08
1234 1420 0.040781 TGAACTAAAGCCGCAAACGC 60.041 50.000 0.00 0.00 38.22 4.84
1235 1421 2.392933 TTGAACTAAAGCCGCAAACG 57.607 45.000 0.00 0.00 39.67 3.60
1236 1422 5.233263 TCAAATTTGAACTAAAGCCGCAAAC 59.767 36.000 18.45 0.00 33.55 2.93
1237 1423 5.352284 TCAAATTTGAACTAAAGCCGCAAA 58.648 33.333 18.45 0.00 33.55 3.68
1238 1424 4.938080 TCAAATTTGAACTAAAGCCGCAA 58.062 34.783 18.45 0.00 33.55 4.85
1239 1425 4.576216 TCAAATTTGAACTAAAGCCGCA 57.424 36.364 18.45 0.00 33.55 5.69
1277 1463 6.240894 TCTGATCAAAAATAGTGTCCTTGCT 58.759 36.000 0.00 0.00 0.00 3.91
1278 1464 6.500684 TCTGATCAAAAATAGTGTCCTTGC 57.499 37.500 0.00 0.00 0.00 4.01
1279 1465 7.337689 TCCATCTGATCAAAAATAGTGTCCTTG 59.662 37.037 0.00 0.00 0.00 3.61
1281 1467 6.962182 TCCATCTGATCAAAAATAGTGTCCT 58.038 36.000 0.00 0.00 0.00 3.85
1282 1468 6.825721 ACTCCATCTGATCAAAAATAGTGTCC 59.174 38.462 0.00 0.00 0.00 4.02
1283 1469 7.856145 ACTCCATCTGATCAAAAATAGTGTC 57.144 36.000 0.00 0.00 0.00 3.67
1302 1489 9.094578 TCCAAATCCAAACAAATTATTACTCCA 57.905 29.630 0.00 0.00 0.00 3.86
1319 1506 2.766263 ACTCGCTAGTGATCCAAATCCA 59.234 45.455 6.42 0.00 33.57 3.41
1356 1543 6.018180 GCCTGAAGTAAAACCATTAGATACGG 60.018 42.308 0.00 0.00 0.00 4.02
1414 1601 2.173356 CCCATTCCTCATGCAGGTAGAA 59.827 50.000 0.00 3.24 43.95 2.10
1452 1639 1.951209 TGCTGGTCTTGATGTCCCTA 58.049 50.000 0.00 0.00 0.00 3.53
1503 1690 3.591254 GAGCCCGAAGTCGCCAAGT 62.591 63.158 0.00 0.00 38.18 3.16
1560 1747 2.036571 CAATGTGCCAGCGAGCTCA 61.037 57.895 15.40 7.96 40.23 4.26
1629 1816 2.226912 GACGCCGAAGCTATAGACATCT 59.773 50.000 3.21 0.00 36.60 2.90
1638 1825 3.744719 AGCACGACGCCGAAGCTA 61.745 61.111 12.94 0.00 44.04 3.32
1754 1941 2.960957 ATCAGCCGCGTCGAGGATTG 62.961 60.000 20.01 15.18 0.00 2.67
1755 1942 2.786495 ATCAGCCGCGTCGAGGATT 61.786 57.895 20.01 2.80 0.00 3.01
1785 1972 2.764637 CTTGGGGGTGGAAGTTCCCG 62.765 65.000 19.42 0.00 44.27 5.14
1819 2006 2.203280 CCACAGGCCAACGACCAA 60.203 61.111 5.01 0.00 0.00 3.67
1833 2020 1.213537 GTCATGGCATGTGCACCAC 59.786 57.895 25.62 12.53 44.36 4.16
1842 2029 0.180406 GTAGGTTCCGGTCATGGCAT 59.820 55.000 0.00 0.00 0.00 4.40
2013 2203 1.935933 CCCACGCAGAGTACCATTAC 58.064 55.000 0.00 0.00 0.00 1.89
2022 2212 1.798735 CAATCAAGCCCACGCAGAG 59.201 57.895 0.00 0.00 37.52 3.35
2024 2214 2.144833 TTGCAATCAAGCCCACGCAG 62.145 55.000 0.00 0.00 37.52 5.18
2027 2217 1.442520 CGTTGCAATCAAGCCCACG 60.443 57.895 0.59 0.00 35.02 4.94
2094 2287 7.120923 ACAATATAGTACCACGGAGATGTTT 57.879 36.000 0.00 0.00 0.00 2.83
2117 2310 5.793457 GTGTGAGCATTAACATTTCCGTAAC 59.207 40.000 0.00 0.00 0.00 2.50
2163 2356 3.127533 GTGATGGAGGCGTGTGGC 61.128 66.667 0.00 0.00 42.51 5.01
2245 2438 2.362717 TCTCATACACCACACACACGAA 59.637 45.455 0.00 0.00 0.00 3.85
2249 2442 3.135712 ACCTTTCTCATACACCACACACA 59.864 43.478 0.00 0.00 0.00 3.72
2283 2476 4.862574 CGACTCCTTCGTGTGATAAAATGA 59.137 41.667 0.00 0.00 43.24 2.57
2298 2491 1.367840 GCTCACACACCGACTCCTT 59.632 57.895 0.00 0.00 0.00 3.36
2302 2495 0.386476 TAAACGCTCACACACCGACT 59.614 50.000 0.00 0.00 0.00 4.18
2314 2507 0.032952 TGGACGAACTGCTAAACGCT 59.967 50.000 0.00 0.00 40.11 5.07
2330 2523 2.093921 TGACTGAAAACGAGTGTGTGGA 60.094 45.455 0.00 0.00 0.00 4.02
2339 2532 1.326245 CTTGTGCGTGACTGAAAACGA 59.674 47.619 0.00 0.00 42.32 3.85
2340 2533 1.594518 CCTTGTGCGTGACTGAAAACG 60.595 52.381 0.00 0.00 42.61 3.60
2407 2601 1.150536 GACAGCTTGGGTGTGGGAA 59.849 57.895 7.10 0.00 44.55 3.97
2437 2631 3.321682 AGTTGCCATGTACACTGCAAAAT 59.678 39.130 26.49 18.58 44.44 1.82
2469 2663 0.527113 TTGCCATCTGGTTGCAATCG 59.473 50.000 0.59 0.00 39.86 3.34
2502 2703 4.639755 ACATATGGCAAATGACATGTTCGA 59.360 37.500 12.01 0.00 44.95 3.71
2939 3144 1.066257 ACGTGACACTTTACCGCGT 59.934 52.632 4.92 0.00 41.39 6.01
2991 3196 3.993584 GTCCACACGCCCGGTACA 61.994 66.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.