Multiple sequence alignment - TraesCS5B01G405500

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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 TraesCS5B01G405500 chr5B 100.000 2707 0 0 1 2707 580931193 580933899 0.000000e+00 5000.0
1 TraesCS5B01G405500 chr5A 86.986 2382 169 64 383 2673 593394146 593396477 0.000000e+00 2551.0
2 TraesCS5B01G405500 chr5A 94.737 57 2 1 2646 2701 593396472 593396528 1.340000e-13 87.9
3 TraesCS5B01G405500 chr5D 91.217 1651 98 22 1091 2707 474139147 474140784 0.000000e+00 2202.0
4 TraesCS5B01G405500 chr5D 89.470 1301 86 22 383 1660 473938814 473940086 0.000000e+00 1596.0
5 TraesCS5B01G405500 chr5D 94.089 626 31 6 466 1087 474138225 474138848 0.000000e+00 946.0
6 TraesCS5B01G405500 chr5D 93.103 174 12 0 1487 1660 473941113 473941286 3.460000e-64 255.0
7 TraesCS5B01G405500 chr5D 93.651 126 7 1 1350 1475 473941004 473941128 1.280000e-43 187.0
8 TraesCS5B01G405500 chr3A 87.019 208 21 6 156 357 601157874 601158081 2.100000e-56 230.0
9 TraesCS5B01G405500 chr3A 84.058 207 27 6 156 356 601134883 601135089 7.650000e-46 195.0
10 TraesCS5B01G405500 chr3A 77.872 235 44 7 151 377 271989962 271989728 3.630000e-29 139.0
11 TraesCS5B01G405500 chr1A 83.529 255 33 8 125 373 495324128 495324379 2.100000e-56 230.0
12 TraesCS5B01G405500 chr3B 86.700 203 22 5 156 353 606164564 606164766 1.260000e-53 220.0
13 TraesCS5B01G405500 chr3B 91.667 48 3 1 2521 2568 56771126 56771172 6.260000e-07 65.8
14 TraesCS5B01G405500 chr2D 82.591 247 34 6 137 378 125941627 125941385 2.730000e-50 209.0
15 TraesCS5B01G405500 chr4A 86.667 180 19 4 154 328 149658136 149657957 7.650000e-46 195.0
16 TraesCS5B01G405500 chr2A 82.000 200 25 10 130 323 572353795 572353989 2.790000e-35 159.0
17 TraesCS5B01G405500 chr6D 79.098 244 38 7 125 358 45671292 45671052 3.610000e-34 156.0


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 TraesCS5B01G405500 chr5B 580931193 580933899 2706 False 5000.000000 5000 100.000000 1 2707 1 chr5B.!!$F1 2706
1 TraesCS5B01G405500 chr5A 593394146 593396528 2382 False 1319.450000 2551 90.861500 383 2701 2 chr5A.!!$F1 2318
2 TraesCS5B01G405500 chr5D 474138225 474140784 2559 False 1574.000000 2202 92.653000 466 2707 2 chr5D.!!$F2 2241
3 TraesCS5B01G405500 chr5D 473938814 473941286 2472 False 679.333333 1596 92.074667 383 1660 3 chr5D.!!$F1 1277

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
62 63 0.029433 GCCTCCCGATCAATTTTCGC 59.971 55.0 0.0 0.0 35.31 4.70 F
545 558 0.038892 ACGAATAACCGCACACGTCT 60.039 50.0 0.0 0.0 37.70 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1515 0.176680 TGGCGAGCCAGATCTTCTTC 59.823 55.0 13.49 0.0 41.89 2.87 R
2017 3617 0.249155 TCGTCACCGTGGAGACAAAC 60.249 55.0 15.26 0.0 46.06 2.93 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
22 23 3.954258 GAGGAGGAAGAGAGAGAAAGAGG 59.046 52.174 0.00 0.00 0.00 3.69
23 24 3.596046 AGGAGGAAGAGAGAGAAAGAGGA 59.404 47.826 0.00 0.00 0.00 3.71
24 25 3.954258 GGAGGAAGAGAGAGAAAGAGGAG 59.046 52.174 0.00 0.00 0.00 3.69
25 26 4.325030 GGAGGAAGAGAGAGAAAGAGGAGA 60.325 50.000 0.00 0.00 0.00 3.71
26 27 5.261216 GAGGAAGAGAGAGAAAGAGGAGAA 58.739 45.833 0.00 0.00 0.00 2.87
27 28 5.650283 AGGAAGAGAGAGAAAGAGGAGAAA 58.350 41.667 0.00 0.00 0.00 2.52
28 29 6.081356 AGGAAGAGAGAGAAAGAGGAGAAAA 58.919 40.000 0.00 0.00 0.00 2.29
29 30 6.211384 AGGAAGAGAGAGAAAGAGGAGAAAAG 59.789 42.308 0.00 0.00 0.00 2.27
30 31 6.210584 GGAAGAGAGAGAAAGAGGAGAAAAGA 59.789 42.308 0.00 0.00 0.00 2.52
31 32 7.256154 GGAAGAGAGAGAAAGAGGAGAAAAGAA 60.256 40.741 0.00 0.00 0.00 2.52
32 33 7.610580 AGAGAGAGAAAGAGGAGAAAAGAAA 57.389 36.000 0.00 0.00 0.00 2.52
33 34 8.206126 AGAGAGAGAAAGAGGAGAAAAGAAAT 57.794 34.615 0.00 0.00 0.00 2.17
34 35 8.096414 AGAGAGAGAAAGAGGAGAAAAGAAATG 58.904 37.037 0.00 0.00 0.00 2.32
35 36 7.972301 AGAGAGAAAGAGGAGAAAAGAAATGA 58.028 34.615 0.00 0.00 0.00 2.57
36 37 8.096414 AGAGAGAAAGAGGAGAAAAGAAATGAG 58.904 37.037 0.00 0.00 0.00 2.90
37 38 6.654582 AGAGAAAGAGGAGAAAAGAAATGAGC 59.345 38.462 0.00 0.00 0.00 4.26
38 39 5.709631 AGAAAGAGGAGAAAAGAAATGAGCC 59.290 40.000 0.00 0.00 0.00 4.70
39 40 3.961849 AGAGGAGAAAAGAAATGAGCCC 58.038 45.455 0.00 0.00 0.00 5.19
40 41 3.020274 GAGGAGAAAAGAAATGAGCCCC 58.980 50.000 0.00 0.00 0.00 5.80
41 42 2.103373 GGAGAAAAGAAATGAGCCCCC 58.897 52.381 0.00 0.00 0.00 5.40
42 43 2.557452 GGAGAAAAGAAATGAGCCCCCA 60.557 50.000 0.00 0.00 0.00 4.96
43 44 2.757314 GAGAAAAGAAATGAGCCCCCAG 59.243 50.000 0.00 0.00 0.00 4.45
44 45 1.205655 GAAAAGAAATGAGCCCCCAGC 59.794 52.381 0.00 0.00 44.25 4.85
45 46 0.615827 AAAGAAATGAGCCCCCAGCC 60.616 55.000 0.00 0.00 45.47 4.85
46 47 1.513087 AAGAAATGAGCCCCCAGCCT 61.513 55.000 0.00 0.00 45.47 4.58
47 48 1.454663 GAAATGAGCCCCCAGCCTC 60.455 63.158 0.00 0.00 45.47 4.70
48 49 2.918300 GAAATGAGCCCCCAGCCTCC 62.918 65.000 0.00 0.00 45.47 4.30
55 56 3.089874 CCCCAGCCTCCCGATCAA 61.090 66.667 0.00 0.00 0.00 2.57
56 57 2.455565 CCCCAGCCTCCCGATCAAT 61.456 63.158 0.00 0.00 0.00 2.57
57 58 1.533711 CCCAGCCTCCCGATCAATT 59.466 57.895 0.00 0.00 0.00 2.32
58 59 0.106519 CCCAGCCTCCCGATCAATTT 60.107 55.000 0.00 0.00 0.00 1.82
59 60 1.686115 CCCAGCCTCCCGATCAATTTT 60.686 52.381 0.00 0.00 0.00 1.82
60 61 1.678101 CCAGCCTCCCGATCAATTTTC 59.322 52.381 0.00 0.00 0.00 2.29
61 62 1.331756 CAGCCTCCCGATCAATTTTCG 59.668 52.381 0.00 1.42 36.38 3.46
62 63 0.029433 GCCTCCCGATCAATTTTCGC 59.971 55.000 0.00 0.00 35.31 4.70
63 64 1.668419 CCTCCCGATCAATTTTCGCT 58.332 50.000 0.00 0.00 35.31 4.93
64 65 1.599542 CCTCCCGATCAATTTTCGCTC 59.400 52.381 0.00 0.00 35.31 5.03
65 66 2.555199 CTCCCGATCAATTTTCGCTCT 58.445 47.619 0.00 0.00 35.31 4.09
66 67 3.492656 CCTCCCGATCAATTTTCGCTCTA 60.493 47.826 0.00 0.00 35.31 2.43
67 68 3.717707 TCCCGATCAATTTTCGCTCTAG 58.282 45.455 0.00 0.00 35.31 2.43
68 69 2.802816 CCCGATCAATTTTCGCTCTAGG 59.197 50.000 0.00 0.00 35.31 3.02
69 70 2.221981 CCGATCAATTTTCGCTCTAGGC 59.778 50.000 0.00 0.00 35.31 3.93
70 71 2.221981 CGATCAATTTTCGCTCTAGGCC 59.778 50.000 0.00 0.00 37.74 5.19
71 72 3.471680 GATCAATTTTCGCTCTAGGCCT 58.528 45.455 11.78 11.78 37.74 5.19
72 73 2.632377 TCAATTTTCGCTCTAGGCCTG 58.368 47.619 17.99 5.60 37.74 4.85
73 74 2.027192 TCAATTTTCGCTCTAGGCCTGT 60.027 45.455 17.99 0.00 37.74 4.00
74 75 2.317530 ATTTTCGCTCTAGGCCTGTC 57.682 50.000 17.99 0.00 37.74 3.51
75 76 0.249398 TTTTCGCTCTAGGCCTGTCC 59.751 55.000 17.99 0.00 37.74 4.02
77 78 1.323271 TTCGCTCTAGGCCTGTCCTG 61.323 60.000 17.99 2.27 46.98 3.86
78 79 1.754621 CGCTCTAGGCCTGTCCTGA 60.755 63.158 17.99 4.84 46.98 3.86
79 80 1.323271 CGCTCTAGGCCTGTCCTGAA 61.323 60.000 17.99 0.00 46.98 3.02
80 81 0.176910 GCTCTAGGCCTGTCCTGAAC 59.823 60.000 17.99 0.00 46.98 3.18
81 82 1.561643 CTCTAGGCCTGTCCTGAACA 58.438 55.000 17.99 0.00 46.98 3.18
82 83 2.114616 CTCTAGGCCTGTCCTGAACAT 58.885 52.381 17.99 0.00 46.98 2.71
83 84 1.833630 TCTAGGCCTGTCCTGAACATG 59.166 52.381 17.99 0.00 46.98 3.21
84 85 0.911769 TAGGCCTGTCCTGAACATGG 59.088 55.000 17.99 0.00 46.98 3.66
85 86 0.842030 AGGCCTGTCCTGAACATGGA 60.842 55.000 3.11 0.00 45.54 3.41
91 92 1.714794 GTCCTGAACATGGACGAGTG 58.285 55.000 0.00 0.00 43.55 3.51
92 93 0.608130 TCCTGAACATGGACGAGTGG 59.392 55.000 0.00 0.00 0.00 4.00
93 94 0.608130 CCTGAACATGGACGAGTGGA 59.392 55.000 0.00 0.00 0.00 4.02
94 95 1.404717 CCTGAACATGGACGAGTGGAG 60.405 57.143 0.00 0.00 0.00 3.86
95 96 1.273606 CTGAACATGGACGAGTGGAGT 59.726 52.381 0.00 0.00 0.00 3.85
96 97 2.492088 CTGAACATGGACGAGTGGAGTA 59.508 50.000 0.00 0.00 0.00 2.59
97 98 2.894765 TGAACATGGACGAGTGGAGTAA 59.105 45.455 0.00 0.00 0.00 2.24
98 99 3.251571 GAACATGGACGAGTGGAGTAAC 58.748 50.000 0.00 0.00 0.00 2.50
99 100 2.526432 ACATGGACGAGTGGAGTAACT 58.474 47.619 0.00 0.00 0.00 2.24
100 101 2.897969 ACATGGACGAGTGGAGTAACTT 59.102 45.455 0.00 0.00 0.00 2.66
101 102 3.056749 ACATGGACGAGTGGAGTAACTTC 60.057 47.826 0.00 0.00 0.00 3.01
102 103 2.872732 TGGACGAGTGGAGTAACTTCT 58.127 47.619 0.00 0.00 0.00 2.85
103 104 2.557056 TGGACGAGTGGAGTAACTTCTG 59.443 50.000 0.00 0.00 0.00 3.02
104 105 2.818432 GGACGAGTGGAGTAACTTCTGA 59.182 50.000 0.00 0.00 0.00 3.27
105 106 3.255149 GGACGAGTGGAGTAACTTCTGAA 59.745 47.826 0.00 0.00 0.00 3.02
106 107 4.082136 GGACGAGTGGAGTAACTTCTGAAT 60.082 45.833 0.00 0.00 0.00 2.57
107 108 5.470047 ACGAGTGGAGTAACTTCTGAATT 57.530 39.130 0.00 0.00 0.00 2.17
108 109 5.855045 ACGAGTGGAGTAACTTCTGAATTT 58.145 37.500 0.00 0.00 0.00 1.82
109 110 5.927115 ACGAGTGGAGTAACTTCTGAATTTC 59.073 40.000 0.00 0.00 0.00 2.17
110 111 5.061064 CGAGTGGAGTAACTTCTGAATTTCG 59.939 44.000 0.00 0.00 0.00 3.46
111 112 6.097915 AGTGGAGTAACTTCTGAATTTCGA 57.902 37.500 0.00 0.00 0.00 3.71
112 113 6.522054 AGTGGAGTAACTTCTGAATTTCGAA 58.478 36.000 0.00 0.00 0.00 3.71
113 114 6.647067 AGTGGAGTAACTTCTGAATTTCGAAG 59.353 38.462 19.88 19.88 41.74 3.79
114 115 6.645415 GTGGAGTAACTTCTGAATTTCGAAGA 59.355 38.462 24.51 9.19 39.10 2.87
115 116 7.332182 GTGGAGTAACTTCTGAATTTCGAAGAT 59.668 37.037 24.51 19.07 39.10 2.40
116 117 7.545965 TGGAGTAACTTCTGAATTTCGAAGATC 59.454 37.037 24.51 18.25 39.10 2.75
117 118 7.545965 GGAGTAACTTCTGAATTTCGAAGATCA 59.454 37.037 24.51 12.58 39.10 2.92
118 119 8.245701 AGTAACTTCTGAATTTCGAAGATCAC 57.754 34.615 24.51 19.46 39.10 3.06
119 120 7.872993 AGTAACTTCTGAATTTCGAAGATCACA 59.127 33.333 24.51 0.00 39.10 3.58
120 121 7.496529 AACTTCTGAATTTCGAAGATCACAA 57.503 32.000 24.51 6.77 39.10 3.33
121 122 7.678947 ACTTCTGAATTTCGAAGATCACAAT 57.321 32.000 24.51 8.71 39.10 2.71
122 123 7.524912 ACTTCTGAATTTCGAAGATCACAATG 58.475 34.615 24.51 7.21 39.10 2.82
123 124 5.872635 TCTGAATTTCGAAGATCACAATGC 58.127 37.500 9.99 0.00 35.04 3.56
124 125 4.650985 TGAATTTCGAAGATCACAATGCG 58.349 39.130 9.99 0.00 35.04 4.73
125 126 4.154015 TGAATTTCGAAGATCACAATGCGT 59.846 37.500 9.99 0.00 35.04 5.24
126 127 5.350091 TGAATTTCGAAGATCACAATGCGTA 59.650 36.000 9.99 0.00 35.04 4.42
127 128 4.577687 TTTCGAAGATCACAATGCGTAC 57.422 40.909 0.00 0.00 35.04 3.67
128 129 3.503827 TCGAAGATCACAATGCGTACT 57.496 42.857 0.00 0.00 0.00 2.73
129 130 3.435566 TCGAAGATCACAATGCGTACTC 58.564 45.455 0.00 0.00 0.00 2.59
130 131 3.128764 TCGAAGATCACAATGCGTACTCT 59.871 43.478 0.00 0.00 0.00 3.24
131 132 3.483922 CGAAGATCACAATGCGTACTCTC 59.516 47.826 0.00 0.00 0.00 3.20
132 133 4.677584 GAAGATCACAATGCGTACTCTCT 58.322 43.478 0.00 0.00 0.00 3.10
133 134 4.300189 AGATCACAATGCGTACTCTCTC 57.700 45.455 0.00 0.00 0.00 3.20
134 135 2.941453 TCACAATGCGTACTCTCTCC 57.059 50.000 0.00 0.00 0.00 3.71
135 136 1.132453 TCACAATGCGTACTCTCTCCG 59.868 52.381 0.00 0.00 0.00 4.63
136 137 1.135373 CACAATGCGTACTCTCTCCGT 60.135 52.381 0.00 0.00 0.00 4.69
137 138 1.544691 ACAATGCGTACTCTCTCCGTT 59.455 47.619 0.00 0.00 0.00 4.44
138 139 2.029290 ACAATGCGTACTCTCTCCGTTT 60.029 45.455 0.00 0.00 0.00 3.60
139 140 2.993899 CAATGCGTACTCTCTCCGTTTT 59.006 45.455 0.00 0.00 0.00 2.43
140 141 4.171005 CAATGCGTACTCTCTCCGTTTTA 58.829 43.478 0.00 0.00 0.00 1.52
141 142 4.650754 ATGCGTACTCTCTCCGTTTTAT 57.349 40.909 0.00 0.00 0.00 1.40
142 143 4.445452 TGCGTACTCTCTCCGTTTTATT 57.555 40.909 0.00 0.00 0.00 1.40
143 144 4.813027 TGCGTACTCTCTCCGTTTTATTT 58.187 39.130 0.00 0.00 0.00 1.40
144 145 5.232463 TGCGTACTCTCTCCGTTTTATTTT 58.768 37.500 0.00 0.00 0.00 1.82
145 146 6.389091 TGCGTACTCTCTCCGTTTTATTTTA 58.611 36.000 0.00 0.00 0.00 1.52
146 147 6.308766 TGCGTACTCTCTCCGTTTTATTTTAC 59.691 38.462 0.00 0.00 0.00 2.01
147 148 6.529477 GCGTACTCTCTCCGTTTTATTTTACT 59.471 38.462 0.00 0.00 0.00 2.24
148 149 7.253585 GCGTACTCTCTCCGTTTTATTTTACTC 60.254 40.741 0.00 0.00 0.00 2.59
149 150 7.219726 CGTACTCTCTCCGTTTTATTTTACTCC 59.780 40.741 0.00 0.00 0.00 3.85
150 151 7.001099 ACTCTCTCCGTTTTATTTTACTCCA 57.999 36.000 0.00 0.00 0.00 3.86
151 152 6.872547 ACTCTCTCCGTTTTATTTTACTCCAC 59.127 38.462 0.00 0.00 0.00 4.02
152 153 6.168389 TCTCTCCGTTTTATTTTACTCCACC 58.832 40.000 0.00 0.00 0.00 4.61
153 154 4.931002 TCTCCGTTTTATTTTACTCCACCG 59.069 41.667 0.00 0.00 0.00 4.94
154 155 3.436359 TCCGTTTTATTTTACTCCACCGC 59.564 43.478 0.00 0.00 0.00 5.68
155 156 3.188873 CCGTTTTATTTTACTCCACCGCA 59.811 43.478 0.00 0.00 0.00 5.69
156 157 4.142556 CCGTTTTATTTTACTCCACCGCAT 60.143 41.667 0.00 0.00 0.00 4.73
157 158 5.064962 CCGTTTTATTTTACTCCACCGCATA 59.935 40.000 0.00 0.00 0.00 3.14
158 159 6.238538 CCGTTTTATTTTACTCCACCGCATAT 60.239 38.462 0.00 0.00 0.00 1.78
159 160 7.190871 CGTTTTATTTTACTCCACCGCATATT 58.809 34.615 0.00 0.00 0.00 1.28
160 161 8.336806 CGTTTTATTTTACTCCACCGCATATTA 58.663 33.333 0.00 0.00 0.00 0.98
161 162 9.659830 GTTTTATTTTACTCCACCGCATATTAG 57.340 33.333 0.00 0.00 0.00 1.73
162 163 9.616156 TTTTATTTTACTCCACCGCATATTAGA 57.384 29.630 0.00 0.00 0.00 2.10
163 164 9.787435 TTTATTTTACTCCACCGCATATTAGAT 57.213 29.630 0.00 0.00 0.00 1.98
164 165 9.787435 TTATTTTACTCCACCGCATATTAGATT 57.213 29.630 0.00 0.00 0.00 2.40
165 166 8.691661 ATTTTACTCCACCGCATATTAGATTT 57.308 30.769 0.00 0.00 0.00 2.17
166 167 7.490962 TTTACTCCACCGCATATTAGATTTG 57.509 36.000 0.00 0.00 0.00 2.32
167 168 5.036117 ACTCCACCGCATATTAGATTTGT 57.964 39.130 0.00 0.00 0.00 2.83
168 169 5.057149 ACTCCACCGCATATTAGATTTGTC 58.943 41.667 0.00 0.00 0.00 3.18
169 170 5.163301 ACTCCACCGCATATTAGATTTGTCT 60.163 40.000 0.00 0.00 0.00 3.41
170 171 6.041637 ACTCCACCGCATATTAGATTTGTCTA 59.958 38.462 0.00 0.00 0.00 2.59
171 172 6.822442 TCCACCGCATATTAGATTTGTCTAA 58.178 36.000 0.86 0.86 36.73 2.10
172 173 7.276658 TCCACCGCATATTAGATTTGTCTAAA 58.723 34.615 2.39 0.00 36.02 1.85
173 174 7.771361 TCCACCGCATATTAGATTTGTCTAAAA 59.229 33.333 2.39 0.00 36.02 1.52
174 175 8.567948 CCACCGCATATTAGATTTGTCTAAAAT 58.432 33.333 2.39 0.00 36.02 1.82
175 176 9.599322 CACCGCATATTAGATTTGTCTAAAATC 57.401 33.333 2.39 3.18 36.02 2.17
176 177 9.337396 ACCGCATATTAGATTTGTCTAAAATCA 57.663 29.630 12.05 0.00 38.70 2.57
334 335 9.895138 ATATACTTGGTCAAACTTTATAACGGT 57.105 29.630 0.00 0.00 0.00 4.83
335 336 6.947644 ACTTGGTCAAACTTTATAACGGTT 57.052 33.333 0.00 0.00 0.00 4.44
336 337 6.731164 ACTTGGTCAAACTTTATAACGGTTG 58.269 36.000 12.34 12.34 0.00 3.77
337 338 6.543100 ACTTGGTCAAACTTTATAACGGTTGA 59.457 34.615 16.17 16.17 0.00 3.18
338 339 6.303021 TGGTCAAACTTTATAACGGTTGAC 57.697 37.500 30.58 30.58 0.00 3.18
339 340 6.056884 TGGTCAAACTTTATAACGGTTGACT 58.943 36.000 33.79 8.99 0.00 3.41
340 341 6.543100 TGGTCAAACTTTATAACGGTTGACTT 59.457 34.615 33.79 8.73 0.00 3.01
341 342 7.073883 GGTCAAACTTTATAACGGTTGACTTC 58.926 38.462 33.79 22.83 0.00 3.01
342 343 7.254863 GGTCAAACTTTATAACGGTTGACTTCA 60.255 37.037 33.79 11.51 0.00 3.02
343 344 7.797123 GTCAAACTTTATAACGGTTGACTTCAG 59.203 37.037 30.87 7.86 0.00 3.02
344 345 7.496591 TCAAACTTTATAACGGTTGACTTCAGT 59.503 33.333 16.17 0.00 0.00 3.41
345 346 7.797038 AACTTTATAACGGTTGACTTCAGTT 57.203 32.000 3.07 2.10 0.00 3.16
346 347 8.891671 AACTTTATAACGGTTGACTTCAGTTA 57.108 30.769 3.07 0.00 32.31 2.24
347 348 8.891671 ACTTTATAACGGTTGACTTCAGTTAA 57.108 30.769 3.07 0.00 31.77 2.01
348 349 9.328845 ACTTTATAACGGTTGACTTCAGTTAAA 57.671 29.630 3.07 0.00 31.77 1.52
349 350 9.807386 CTTTATAACGGTTGACTTCAGTTAAAG 57.193 33.333 3.07 0.00 31.77 1.85
350 351 8.891671 TTATAACGGTTGACTTCAGTTAAAGT 57.108 30.769 3.07 0.00 42.10 2.66
351 352 9.979578 TTATAACGGTTGACTTCAGTTAAAGTA 57.020 29.630 3.07 0.00 39.55 2.24
352 353 8.891671 ATAACGGTTGACTTCAGTTAAAGTAA 57.108 30.769 3.07 0.00 39.55 2.24
353 354 7.614124 AACGGTTGACTTCAGTTAAAGTAAA 57.386 32.000 0.00 0.00 39.55 2.01
354 355 7.797038 ACGGTTGACTTCAGTTAAAGTAAAT 57.203 32.000 0.00 0.00 39.55 1.40
355 356 8.891671 ACGGTTGACTTCAGTTAAAGTAAATA 57.108 30.769 0.00 0.00 39.55 1.40
356 357 9.498176 ACGGTTGACTTCAGTTAAAGTAAATAT 57.502 29.630 0.00 0.00 39.55 1.28
357 358 9.755064 CGGTTGACTTCAGTTAAAGTAAATATG 57.245 33.333 0.00 0.00 39.55 1.78
375 376 9.498307 GTAAATATGTGGAGTAAATGAAAACGG 57.502 33.333 0.00 0.00 0.00 4.44
376 377 7.931578 AATATGTGGAGTAAATGAAAACGGA 57.068 32.000 0.00 0.00 0.00 4.69
377 378 5.880054 ATGTGGAGTAAATGAAAACGGAG 57.120 39.130 0.00 0.00 0.00 4.63
378 379 4.963373 TGTGGAGTAAATGAAAACGGAGA 58.037 39.130 0.00 0.00 0.00 3.71
379 380 5.369833 TGTGGAGTAAATGAAAACGGAGAA 58.630 37.500 0.00 0.00 0.00 2.87
380 381 5.823570 TGTGGAGTAAATGAAAACGGAGAAA 59.176 36.000 0.00 0.00 0.00 2.52
381 382 6.017440 TGTGGAGTAAATGAAAACGGAGAAAG 60.017 38.462 0.00 0.00 0.00 2.62
407 408 2.087462 ATTCATCGATCTGGCCGCGA 62.087 55.000 8.23 11.32 38.51 5.87
422 423 1.273606 CCGCGACCTAGGAATGATGAT 59.726 52.381 17.98 0.00 0.00 2.45
426 427 3.743396 GCGACCTAGGAATGATGATTGAC 59.257 47.826 17.98 0.00 0.00 3.18
431 432 2.477825 AGGAATGATGATTGACGAGCG 58.522 47.619 0.00 0.00 0.00 5.03
444 445 1.082117 ACGAGCGCCAATTACCGAAG 61.082 55.000 2.29 0.00 0.00 3.79
471 476 4.092821 TCACGACTATCTTTGGCGATTTTG 59.907 41.667 0.00 0.00 0.00 2.44
492 497 3.005554 GAGGTGGACACTTCATCATGTG 58.994 50.000 9.37 0.00 37.37 3.21
520 525 4.229096 GTGATTTCGTGCACAATGTCAAT 58.771 39.130 18.64 4.88 35.19 2.57
521 526 4.088923 GTGATTTCGTGCACAATGTCAATG 59.911 41.667 18.64 0.00 35.19 2.82
545 558 0.038892 ACGAATAACCGCACACGTCT 60.039 50.000 0.00 0.00 37.70 4.18
566 579 6.952773 TCTTCCTAGACAGCTTCTAATCTC 57.047 41.667 0.00 0.00 36.32 2.75
568 581 6.545666 TCTTCCTAGACAGCTTCTAATCTCAG 59.454 42.308 0.00 0.00 36.32 3.35
573 588 6.463995 AGACAGCTTCTAATCTCAGGTTAG 57.536 41.667 0.00 0.00 30.17 2.34
575 590 7.120051 AGACAGCTTCTAATCTCAGGTTAGTA 58.880 38.462 4.55 0.00 30.17 1.82
581 596 7.810759 GCTTCTAATCTCAGGTTAGTATACAGC 59.189 40.741 4.55 3.09 32.35 4.40
592 607 6.098409 AGGTTAGTATACAGCAGCAAGTACAT 59.902 38.462 5.50 0.00 0.00 2.29
637 658 6.073222 ACAGGTATCAGACTAAACAAAAAGCG 60.073 38.462 0.00 0.00 0.00 4.68
709 730 1.901464 GGGGACAAGCGAAAAGGCA 60.901 57.895 0.00 0.00 34.64 4.75
1089 1123 4.163427 AGATCACAGGACAAGGAGAGAAA 58.837 43.478 0.00 0.00 0.00 2.52
1304 1641 0.036483 TTCTTGCCGACAGCTGCATA 60.036 50.000 15.27 0.00 44.23 3.14
1307 1644 2.158971 TCTTGCCGACAGCTGCATATTA 60.159 45.455 15.27 0.00 44.23 0.98
1578 3135 2.261671 ACAGGACGTGACCGATGC 59.738 61.111 0.00 0.00 37.88 3.91
1600 3161 2.747686 GGAAACGGGACAGCTGGA 59.252 61.111 19.93 0.00 0.00 3.86
1655 3219 2.688446 CAGAGAGGCCGTGTGTAGATAA 59.312 50.000 0.00 0.00 0.00 1.75
1737 3305 4.801521 AATGGTCCATTGGAGATCATCA 57.198 40.909 16.63 0.00 32.39 3.07
1837 3405 7.201145 CCAAAGAAATCATATTCTCTTGCCTG 58.799 38.462 0.00 0.00 38.69 4.85
1906 3480 8.582657 AGAGAAGAGAGCTATGTTTGTAGTAA 57.417 34.615 0.00 0.00 0.00 2.24
1907 3481 9.026121 AGAGAAGAGAGCTATGTTTGTAGTAAA 57.974 33.333 0.00 0.00 0.00 2.01
1908 3482 8.989653 AGAAGAGAGCTATGTTTGTAGTAAAC 57.010 34.615 0.00 0.00 0.00 2.01
2017 3617 7.118101 CCTTTTCATTATTGTTTGTGGTGATGG 59.882 37.037 0.00 0.00 0.00 3.51
2029 3629 1.156736 GGTGATGGTTTGTCTCCACG 58.843 55.000 0.00 0.00 37.81 4.94
2060 3660 4.272991 TGCCACTTGATTTTGCATGTTTTC 59.727 37.500 0.00 0.00 0.00 2.29
2061 3661 4.272991 GCCACTTGATTTTGCATGTTTTCA 59.727 37.500 0.00 0.00 0.00 2.69
2100 3700 9.209175 TCTTTGCTTTATCTTCTCTAACTTGTC 57.791 33.333 0.00 0.00 0.00 3.18
2104 3704 6.590677 GCTTTATCTTCTCTAACTTGTCGGTT 59.409 38.462 0.00 0.00 0.00 4.44
2121 3721 5.978919 TGTCGGTTATATGGTTGAATACGTC 59.021 40.000 0.00 0.00 0.00 4.34
2128 3728 3.109044 TGGTTGAATACGTCCGAAACA 57.891 42.857 0.00 0.00 0.00 2.83
2171 3771 8.755977 AGAAAGTTCTATCAATTTGGCAATCAT 58.244 29.630 0.00 0.00 35.34 2.45
2179 3779 5.421277 TCAATTTGGCAATCATGGATGAAC 58.579 37.500 0.00 0.00 40.69 3.18
2180 3780 5.046520 TCAATTTGGCAATCATGGATGAACA 60.047 36.000 0.00 0.00 40.69 3.18
2193 3793 7.881142 TCATGGATGAACAATTTAACGTTCTT 58.119 30.769 2.82 0.00 41.67 2.52
2194 3794 8.020819 TCATGGATGAACAATTTAACGTTCTTC 58.979 33.333 2.82 13.66 41.67 2.87
2197 3797 5.098218 TGAACAATTTAACGTTCTTCGGG 57.902 39.130 2.82 0.00 41.67 5.14
2198 3798 4.575645 TGAACAATTTAACGTTCTTCGGGT 59.424 37.500 2.82 0.00 41.67 5.28
2199 3799 5.066246 TGAACAATTTAACGTTCTTCGGGTT 59.934 36.000 2.82 3.95 41.67 4.11
2206 3806 3.121738 ACGTTCTTCGGGTTCTCAATT 57.878 42.857 0.00 0.00 44.69 2.32
2212 3812 1.803334 TCGGGTTCTCAATTTGTCCG 58.197 50.000 0.00 0.00 37.61 4.79
2232 3832 9.438228 TTGTCCGACATCAAGTTTATATTGTTA 57.562 29.630 1.09 0.00 0.00 2.41
2353 3953 8.763049 TGAGTAGTGTAACAATGATTGAAGAG 57.237 34.615 12.80 0.00 41.43 2.85
2420 4020 2.493278 ACCAATTGCAAGAAGAATCCCG 59.507 45.455 4.94 0.00 0.00 5.14
2444 4044 5.043248 AGCTTTCCAAATCGTTGTTCTTTG 58.957 37.500 0.00 0.00 32.40 2.77
2472 4072 4.351874 TCTTCATCGTTGTCTTTTCCCT 57.648 40.909 0.00 0.00 0.00 4.20
2528 4128 6.541278 CAGGAGCTCAAAGACATCATTATTCA 59.459 38.462 17.19 0.00 0.00 2.57
2534 4134 8.618677 GCTCAAAGACATCATTATTCATTCTCA 58.381 33.333 0.00 0.00 0.00 3.27
2640 4244 3.118775 ACGCATGCCAGTTCAAGTATCTA 60.119 43.478 13.15 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.954258 CCTCTTTCTCTCTCTTCCTCCTC 59.046 52.174 0.00 0.00 0.00 3.71
1 2 3.596046 TCCTCTTTCTCTCTCTTCCTCCT 59.404 47.826 0.00 0.00 0.00 3.69
2 3 3.954258 CTCCTCTTTCTCTCTCTTCCTCC 59.046 52.174 0.00 0.00 0.00 4.30
3 4 4.855340 TCTCCTCTTTCTCTCTCTTCCTC 58.145 47.826 0.00 0.00 0.00 3.71
4 5 4.946160 TCTCCTCTTTCTCTCTCTTCCT 57.054 45.455 0.00 0.00 0.00 3.36
5 6 5.993748 TTTCTCCTCTTTCTCTCTCTTCC 57.006 43.478 0.00 0.00 0.00 3.46
6 7 7.227049 TCTTTTCTCCTCTTTCTCTCTCTTC 57.773 40.000 0.00 0.00 0.00 2.87
7 8 7.610580 TTCTTTTCTCCTCTTTCTCTCTCTT 57.389 36.000 0.00 0.00 0.00 2.85
8 9 7.610580 TTTCTTTTCTCCTCTTTCTCTCTCT 57.389 36.000 0.00 0.00 0.00 3.10
9 10 8.093927 TCATTTCTTTTCTCCTCTTTCTCTCTC 58.906 37.037 0.00 0.00 0.00 3.20
10 11 7.972301 TCATTTCTTTTCTCCTCTTTCTCTCT 58.028 34.615 0.00 0.00 0.00 3.10
11 12 7.148423 GCTCATTTCTTTTCTCCTCTTTCTCTC 60.148 40.741 0.00 0.00 0.00 3.20
12 13 6.654582 GCTCATTTCTTTTCTCCTCTTTCTCT 59.345 38.462 0.00 0.00 0.00 3.10
13 14 6.128035 GGCTCATTTCTTTTCTCCTCTTTCTC 60.128 42.308 0.00 0.00 0.00 2.87
14 15 5.709631 GGCTCATTTCTTTTCTCCTCTTTCT 59.290 40.000 0.00 0.00 0.00 2.52
15 16 5.105957 GGGCTCATTTCTTTTCTCCTCTTTC 60.106 44.000 0.00 0.00 0.00 2.62
16 17 4.769488 GGGCTCATTTCTTTTCTCCTCTTT 59.231 41.667 0.00 0.00 0.00 2.52
17 18 4.339748 GGGCTCATTTCTTTTCTCCTCTT 58.660 43.478 0.00 0.00 0.00 2.85
18 19 3.308760 GGGGCTCATTTCTTTTCTCCTCT 60.309 47.826 0.00 0.00 0.00 3.69
19 20 3.020274 GGGGCTCATTTCTTTTCTCCTC 58.980 50.000 0.00 0.00 0.00 3.71
20 21 2.291865 GGGGGCTCATTTCTTTTCTCCT 60.292 50.000 0.00 0.00 0.00 3.69
21 22 2.103373 GGGGGCTCATTTCTTTTCTCC 58.897 52.381 0.00 0.00 0.00 3.71
22 23 2.757314 CTGGGGGCTCATTTCTTTTCTC 59.243 50.000 0.00 0.00 0.00 2.87
23 24 2.812658 CTGGGGGCTCATTTCTTTTCT 58.187 47.619 0.00 0.00 0.00 2.52
24 25 1.205655 GCTGGGGGCTCATTTCTTTTC 59.794 52.381 0.00 0.00 38.06 2.29
25 26 1.269958 GCTGGGGGCTCATTTCTTTT 58.730 50.000 0.00 0.00 38.06 2.27
26 27 0.615827 GGCTGGGGGCTCATTTCTTT 60.616 55.000 0.00 0.00 41.46 2.52
27 28 1.000866 GGCTGGGGGCTCATTTCTT 59.999 57.895 0.00 0.00 41.46 2.52
28 29 1.932757 AGGCTGGGGGCTCATTTCT 60.933 57.895 0.00 0.00 45.63 2.52
29 30 2.685999 AGGCTGGGGGCTCATTTC 59.314 61.111 0.00 0.00 45.63 2.17
38 39 1.999634 AATTGATCGGGAGGCTGGGG 62.000 60.000 0.00 0.00 0.00 4.96
39 40 0.106519 AAATTGATCGGGAGGCTGGG 60.107 55.000 0.00 0.00 0.00 4.45
40 41 1.678101 GAAAATTGATCGGGAGGCTGG 59.322 52.381 0.00 0.00 0.00 4.85
41 42 1.331756 CGAAAATTGATCGGGAGGCTG 59.668 52.381 0.00 0.00 36.68 4.85
42 43 1.668419 CGAAAATTGATCGGGAGGCT 58.332 50.000 6.11 0.00 36.68 4.58
43 44 0.029433 GCGAAAATTGATCGGGAGGC 59.971 55.000 13.75 0.00 40.54 4.70
44 45 1.599542 GAGCGAAAATTGATCGGGAGG 59.400 52.381 13.75 0.00 40.54 4.30
45 46 2.555199 AGAGCGAAAATTGATCGGGAG 58.445 47.619 13.75 0.00 40.54 4.30
46 47 2.691409 AGAGCGAAAATTGATCGGGA 57.309 45.000 13.75 0.00 40.54 5.14
47 48 2.802816 CCTAGAGCGAAAATTGATCGGG 59.197 50.000 13.75 4.59 40.54 5.14
48 49 2.221981 GCCTAGAGCGAAAATTGATCGG 59.778 50.000 13.75 0.58 40.54 4.18
49 50 2.221981 GGCCTAGAGCGAAAATTGATCG 59.778 50.000 0.00 9.00 45.17 3.69
50 51 3.249559 CAGGCCTAGAGCGAAAATTGATC 59.750 47.826 3.98 0.00 45.17 2.92
51 52 3.209410 CAGGCCTAGAGCGAAAATTGAT 58.791 45.455 3.98 0.00 45.17 2.57
52 53 2.027192 ACAGGCCTAGAGCGAAAATTGA 60.027 45.455 3.98 0.00 45.17 2.57
53 54 2.352960 GACAGGCCTAGAGCGAAAATTG 59.647 50.000 3.98 0.00 45.17 2.32
54 55 2.633488 GACAGGCCTAGAGCGAAAATT 58.367 47.619 3.98 0.00 45.17 1.82
55 56 1.134371 GGACAGGCCTAGAGCGAAAAT 60.134 52.381 3.98 0.00 45.17 1.82
56 57 0.249398 GGACAGGCCTAGAGCGAAAA 59.751 55.000 3.98 0.00 45.17 2.29
57 58 1.898154 GGACAGGCCTAGAGCGAAA 59.102 57.895 3.98 0.00 45.17 3.46
58 59 3.617368 GGACAGGCCTAGAGCGAA 58.383 61.111 3.98 0.00 45.17 4.70
67 68 1.685224 TCCATGTTCAGGACAGGCC 59.315 57.895 0.00 0.00 42.62 5.19
73 74 0.608130 CCACTCGTCCATGTTCAGGA 59.392 55.000 0.00 0.00 0.00 3.86
74 75 0.608130 TCCACTCGTCCATGTTCAGG 59.392 55.000 0.00 0.00 0.00 3.86
75 76 1.273606 ACTCCACTCGTCCATGTTCAG 59.726 52.381 0.00 0.00 0.00 3.02
76 77 1.338107 ACTCCACTCGTCCATGTTCA 58.662 50.000 0.00 0.00 0.00 3.18
77 78 3.056749 AGTTACTCCACTCGTCCATGTTC 60.057 47.826 0.00 0.00 0.00 3.18
78 79 2.897969 AGTTACTCCACTCGTCCATGTT 59.102 45.455 0.00 0.00 0.00 2.71
79 80 2.526432 AGTTACTCCACTCGTCCATGT 58.474 47.619 0.00 0.00 0.00 3.21
80 81 3.193691 AGAAGTTACTCCACTCGTCCATG 59.806 47.826 0.00 0.00 0.00 3.66
81 82 3.193691 CAGAAGTTACTCCACTCGTCCAT 59.806 47.826 0.00 0.00 0.00 3.41
82 83 2.557056 CAGAAGTTACTCCACTCGTCCA 59.443 50.000 0.00 0.00 0.00 4.02
83 84 2.818432 TCAGAAGTTACTCCACTCGTCC 59.182 50.000 0.00 0.00 0.00 4.79
84 85 4.500603 TTCAGAAGTTACTCCACTCGTC 57.499 45.455 0.00 0.00 0.00 4.20
85 86 5.470047 AATTCAGAAGTTACTCCACTCGT 57.530 39.130 0.00 0.00 0.00 4.18
86 87 5.061064 CGAAATTCAGAAGTTACTCCACTCG 59.939 44.000 0.00 0.00 0.00 4.18
87 88 6.157211 TCGAAATTCAGAAGTTACTCCACTC 58.843 40.000 0.00 0.00 0.00 3.51
88 89 6.097915 TCGAAATTCAGAAGTTACTCCACT 57.902 37.500 0.00 0.00 0.00 4.00
89 90 6.645415 TCTTCGAAATTCAGAAGTTACTCCAC 59.355 38.462 19.08 0.00 43.07 4.02
90 91 6.755206 TCTTCGAAATTCAGAAGTTACTCCA 58.245 36.000 19.08 4.39 43.07 3.86
91 92 7.545965 TGATCTTCGAAATTCAGAAGTTACTCC 59.454 37.037 19.08 7.29 43.07 3.85
92 93 8.376942 GTGATCTTCGAAATTCAGAAGTTACTC 58.623 37.037 19.08 14.32 43.07 2.59
93 94 7.872993 TGTGATCTTCGAAATTCAGAAGTTACT 59.127 33.333 19.08 9.11 43.07 2.24
94 95 8.018677 TGTGATCTTCGAAATTCAGAAGTTAC 57.981 34.615 19.08 16.73 43.07 2.50
95 96 8.601845 TTGTGATCTTCGAAATTCAGAAGTTA 57.398 30.769 19.08 8.40 43.07 2.24
96 97 7.496529 TTGTGATCTTCGAAATTCAGAAGTT 57.503 32.000 19.08 14.30 43.07 2.66
97 98 7.524912 CATTGTGATCTTCGAAATTCAGAAGT 58.475 34.615 18.31 11.50 43.07 3.01
98 99 6.468319 GCATTGTGATCTTCGAAATTCAGAAG 59.532 38.462 18.31 15.98 43.70 2.85
99 100 6.317088 GCATTGTGATCTTCGAAATTCAGAA 58.683 36.000 16.74 16.74 0.00 3.02
100 101 5.446340 CGCATTGTGATCTTCGAAATTCAGA 60.446 40.000 9.32 6.39 0.00 3.27
101 102 4.727179 CGCATTGTGATCTTCGAAATTCAG 59.273 41.667 9.32 0.00 0.00 3.02
102 103 4.154015 ACGCATTGTGATCTTCGAAATTCA 59.846 37.500 3.82 2.35 0.00 2.57
103 104 4.651994 ACGCATTGTGATCTTCGAAATTC 58.348 39.130 3.82 0.00 0.00 2.17
104 105 4.685169 ACGCATTGTGATCTTCGAAATT 57.315 36.364 3.82 0.00 0.00 1.82
105 106 4.870426 AGTACGCATTGTGATCTTCGAAAT 59.130 37.500 3.82 0.00 0.00 2.17
106 107 4.242475 AGTACGCATTGTGATCTTCGAAA 58.758 39.130 3.82 0.00 0.00 3.46
107 108 3.845178 AGTACGCATTGTGATCTTCGAA 58.155 40.909 3.82 0.00 0.00 3.71
108 109 3.128764 AGAGTACGCATTGTGATCTTCGA 59.871 43.478 3.82 0.00 0.00 3.71
109 110 3.439293 AGAGTACGCATTGTGATCTTCG 58.561 45.455 3.82 0.00 0.00 3.79
110 111 4.677584 AGAGAGTACGCATTGTGATCTTC 58.322 43.478 3.82 0.00 29.74 2.87
111 112 4.440802 GGAGAGAGTACGCATTGTGATCTT 60.441 45.833 3.82 0.00 29.74 2.40
112 113 3.067461 GGAGAGAGTACGCATTGTGATCT 59.933 47.826 3.82 4.39 31.57 2.75
113 114 3.376540 GGAGAGAGTACGCATTGTGATC 58.623 50.000 3.82 0.00 0.00 2.92
114 115 2.223595 CGGAGAGAGTACGCATTGTGAT 60.224 50.000 3.82 0.00 0.00 3.06
115 116 1.132453 CGGAGAGAGTACGCATTGTGA 59.868 52.381 3.82 0.00 0.00 3.58
116 117 1.135373 ACGGAGAGAGTACGCATTGTG 60.135 52.381 0.00 0.00 0.00 3.33
117 118 1.174783 ACGGAGAGAGTACGCATTGT 58.825 50.000 0.00 0.00 0.00 2.71
118 119 2.279582 AACGGAGAGAGTACGCATTG 57.720 50.000 0.00 0.00 0.00 2.82
119 120 3.314541 AAAACGGAGAGAGTACGCATT 57.685 42.857 0.00 0.00 0.00 3.56
120 121 4.650754 ATAAAACGGAGAGAGTACGCAT 57.349 40.909 0.00 0.00 0.00 4.73
121 122 4.445452 AATAAAACGGAGAGAGTACGCA 57.555 40.909 0.00 0.00 0.00 5.24
122 123 5.774878 AAAATAAAACGGAGAGAGTACGC 57.225 39.130 0.00 0.00 0.00 4.42
123 124 7.219726 GGAGTAAAATAAAACGGAGAGAGTACG 59.780 40.741 0.00 0.00 0.00 3.67
124 125 8.031277 TGGAGTAAAATAAAACGGAGAGAGTAC 58.969 37.037 0.00 0.00 0.00 2.73
125 126 8.031277 GTGGAGTAAAATAAAACGGAGAGAGTA 58.969 37.037 0.00 0.00 0.00 2.59
126 127 6.872547 GTGGAGTAAAATAAAACGGAGAGAGT 59.127 38.462 0.00 0.00 0.00 3.24
127 128 6.313164 GGTGGAGTAAAATAAAACGGAGAGAG 59.687 42.308 0.00 0.00 0.00 3.20
128 129 6.168389 GGTGGAGTAAAATAAAACGGAGAGA 58.832 40.000 0.00 0.00 0.00 3.10
129 130 5.063060 CGGTGGAGTAAAATAAAACGGAGAG 59.937 44.000 0.00 0.00 0.00 3.20
130 131 4.931002 CGGTGGAGTAAAATAAAACGGAGA 59.069 41.667 0.00 0.00 0.00 3.71
131 132 4.436451 GCGGTGGAGTAAAATAAAACGGAG 60.436 45.833 0.00 0.00 0.00 4.63
132 133 3.436359 GCGGTGGAGTAAAATAAAACGGA 59.564 43.478 0.00 0.00 0.00 4.69
133 134 3.188873 TGCGGTGGAGTAAAATAAAACGG 59.811 43.478 0.00 0.00 0.00 4.44
134 135 4.407496 TGCGGTGGAGTAAAATAAAACG 57.593 40.909 0.00 0.00 0.00 3.60
135 136 9.659830 CTAATATGCGGTGGAGTAAAATAAAAC 57.340 33.333 0.00 0.00 0.00 2.43
136 137 9.616156 TCTAATATGCGGTGGAGTAAAATAAAA 57.384 29.630 0.00 0.00 0.00 1.52
137 138 9.787435 ATCTAATATGCGGTGGAGTAAAATAAA 57.213 29.630 0.00 0.00 0.00 1.40
138 139 9.787435 AATCTAATATGCGGTGGAGTAAAATAA 57.213 29.630 0.00 0.00 0.00 1.40
139 140 9.787435 AAATCTAATATGCGGTGGAGTAAAATA 57.213 29.630 0.00 0.00 0.00 1.40
140 141 8.567948 CAAATCTAATATGCGGTGGAGTAAAAT 58.432 33.333 0.00 0.00 0.00 1.82
141 142 7.554835 ACAAATCTAATATGCGGTGGAGTAAAA 59.445 33.333 0.00 0.00 0.00 1.52
142 143 7.051623 ACAAATCTAATATGCGGTGGAGTAAA 58.948 34.615 0.00 0.00 0.00 2.01
143 144 6.588204 ACAAATCTAATATGCGGTGGAGTAA 58.412 36.000 0.00 0.00 0.00 2.24
144 145 6.041637 AGACAAATCTAATATGCGGTGGAGTA 59.958 38.462 0.00 0.00 31.46 2.59
145 146 5.036117 ACAAATCTAATATGCGGTGGAGT 57.964 39.130 0.00 0.00 0.00 3.85
146 147 5.300752 AGACAAATCTAATATGCGGTGGAG 58.699 41.667 0.00 0.00 31.46 3.86
147 148 5.290493 AGACAAATCTAATATGCGGTGGA 57.710 39.130 0.00 0.00 31.46 4.02
148 149 7.490962 TTTAGACAAATCTAATATGCGGTGG 57.509 36.000 0.00 0.00 44.99 4.61
149 150 9.599322 GATTTTAGACAAATCTAATATGCGGTG 57.401 33.333 5.18 0.00 44.99 4.94
150 151 9.337396 TGATTTTAGACAAATCTAATATGCGGT 57.663 29.630 8.40 0.00 44.99 5.68
222 223 9.077885 GTGAATCCAATATATATTTGGTGGTGT 57.922 33.333 18.32 0.00 0.00 4.16
223 224 9.300681 AGTGAATCCAATATATATTTGGTGGTG 57.699 33.333 18.32 0.00 0.00 4.17
308 309 9.895138 ACCGTTATAAAGTTTGACCAAGTATAT 57.105 29.630 0.00 0.00 0.00 0.86
309 310 9.723601 AACCGTTATAAAGTTTGACCAAGTATA 57.276 29.630 0.00 0.00 0.00 1.47
310 311 8.508875 CAACCGTTATAAAGTTTGACCAAGTAT 58.491 33.333 3.17 0.00 0.00 2.12
311 312 7.714377 TCAACCGTTATAAAGTTTGACCAAGTA 59.286 33.333 7.17 0.00 0.00 2.24
312 313 6.543100 TCAACCGTTATAAAGTTTGACCAAGT 59.457 34.615 7.17 0.00 0.00 3.16
313 314 6.854381 GTCAACCGTTATAAAGTTTGACCAAG 59.146 38.462 22.40 3.79 0.00 3.61
314 315 6.543100 AGTCAACCGTTATAAAGTTTGACCAA 59.457 34.615 26.34 2.33 0.00 3.67
315 316 6.056884 AGTCAACCGTTATAAAGTTTGACCA 58.943 36.000 26.34 2.61 0.00 4.02
316 317 6.549912 AGTCAACCGTTATAAAGTTTGACC 57.450 37.500 26.34 15.27 0.00 4.02
317 318 7.632721 TGAAGTCAACCGTTATAAAGTTTGAC 58.367 34.615 24.22 24.22 0.00 3.18
318 319 7.496591 ACTGAAGTCAACCGTTATAAAGTTTGA 59.503 33.333 7.17 7.17 0.00 2.69
319 320 7.636326 ACTGAAGTCAACCGTTATAAAGTTTG 58.364 34.615 0.00 2.92 0.00 2.93
320 321 7.797038 ACTGAAGTCAACCGTTATAAAGTTT 57.203 32.000 0.00 0.00 0.00 2.66
321 322 7.797038 AACTGAAGTCAACCGTTATAAAGTT 57.203 32.000 0.00 0.00 0.00 2.66
322 323 8.891671 TTAACTGAAGTCAACCGTTATAAAGT 57.108 30.769 0.00 0.00 0.00 2.66
323 324 9.807386 CTTTAACTGAAGTCAACCGTTATAAAG 57.193 33.333 0.00 0.00 0.00 1.85
324 325 9.328845 ACTTTAACTGAAGTCAACCGTTATAAA 57.671 29.630 0.00 0.00 34.94 1.40
325 326 8.891671 ACTTTAACTGAAGTCAACCGTTATAA 57.108 30.769 0.00 0.00 34.94 0.98
326 327 9.979578 TTACTTTAACTGAAGTCAACCGTTATA 57.020 29.630 0.00 0.00 40.24 0.98
327 328 8.891671 TTACTTTAACTGAAGTCAACCGTTAT 57.108 30.769 0.00 0.00 40.24 1.89
328 329 8.715191 TTTACTTTAACTGAAGTCAACCGTTA 57.285 30.769 0.00 0.00 40.24 3.18
329 330 7.614124 TTTACTTTAACTGAAGTCAACCGTT 57.386 32.000 0.00 0.00 40.24 4.44
330 331 7.797038 ATTTACTTTAACTGAAGTCAACCGT 57.203 32.000 0.00 0.00 40.24 4.83
331 332 9.755064 CATATTTACTTTAACTGAAGTCAACCG 57.245 33.333 0.00 0.00 40.24 4.44
349 350 9.498307 CCGTTTTCATTTACTCCACATATTTAC 57.502 33.333 0.00 0.00 0.00 2.01
350 351 9.451002 TCCGTTTTCATTTACTCCACATATTTA 57.549 29.630 0.00 0.00 0.00 1.40
351 352 8.343168 TCCGTTTTCATTTACTCCACATATTT 57.657 30.769 0.00 0.00 0.00 1.40
352 353 7.827236 TCTCCGTTTTCATTTACTCCACATATT 59.173 33.333 0.00 0.00 0.00 1.28
353 354 7.335627 TCTCCGTTTTCATTTACTCCACATAT 58.664 34.615 0.00 0.00 0.00 1.78
354 355 6.703319 TCTCCGTTTTCATTTACTCCACATA 58.297 36.000 0.00 0.00 0.00 2.29
355 356 5.556915 TCTCCGTTTTCATTTACTCCACAT 58.443 37.500 0.00 0.00 0.00 3.21
356 357 4.963373 TCTCCGTTTTCATTTACTCCACA 58.037 39.130 0.00 0.00 0.00 4.17
357 358 5.934935 TTCTCCGTTTTCATTTACTCCAC 57.065 39.130 0.00 0.00 0.00 4.02
358 359 6.059484 ACTTTCTCCGTTTTCATTTACTCCA 58.941 36.000 0.00 0.00 0.00 3.86
359 360 6.555812 ACTTTCTCCGTTTTCATTTACTCC 57.444 37.500 0.00 0.00 0.00 3.85
360 361 9.152595 AGATACTTTCTCCGTTTTCATTTACTC 57.847 33.333 0.00 0.00 0.00 2.59
366 367 9.667107 TGAATTAGATACTTTCTCCGTTTTCAT 57.333 29.630 0.00 0.00 35.79 2.57
367 368 9.667107 ATGAATTAGATACTTTCTCCGTTTTCA 57.333 29.630 0.00 0.00 35.79 2.69
369 370 8.818057 CGATGAATTAGATACTTTCTCCGTTTT 58.182 33.333 0.00 0.00 35.79 2.43
370 371 8.195436 TCGATGAATTAGATACTTTCTCCGTTT 58.805 33.333 0.00 0.00 35.79 3.60
371 372 7.713750 TCGATGAATTAGATACTTTCTCCGTT 58.286 34.615 0.00 0.00 35.79 4.44
372 373 7.273320 TCGATGAATTAGATACTTTCTCCGT 57.727 36.000 0.00 0.00 35.79 4.69
373 374 8.240682 AGATCGATGAATTAGATACTTTCTCCG 58.759 37.037 0.54 0.00 35.79 4.63
374 375 9.352784 CAGATCGATGAATTAGATACTTTCTCC 57.647 37.037 0.54 0.00 35.79 3.71
375 376 9.352784 CCAGATCGATGAATTAGATACTTTCTC 57.647 37.037 0.54 0.00 35.79 2.87
376 377 7.816995 GCCAGATCGATGAATTAGATACTTTCT 59.183 37.037 0.54 0.00 38.57 2.52
377 378 7.064016 GGCCAGATCGATGAATTAGATACTTTC 59.936 40.741 0.54 0.00 0.00 2.62
378 379 6.876257 GGCCAGATCGATGAATTAGATACTTT 59.124 38.462 0.54 0.00 0.00 2.66
379 380 6.402222 GGCCAGATCGATGAATTAGATACTT 58.598 40.000 0.54 0.00 0.00 2.24
380 381 5.393569 CGGCCAGATCGATGAATTAGATACT 60.394 44.000 0.54 0.00 0.00 2.12
381 382 4.800993 CGGCCAGATCGATGAATTAGATAC 59.199 45.833 0.54 0.00 0.00 2.24
407 408 4.502259 GCTCGTCAATCATCATTCCTAGGT 60.502 45.833 9.08 0.00 0.00 3.08
422 423 1.355796 CGGTAATTGGCGCTCGTCAA 61.356 55.000 11.77 11.77 44.19 3.18
426 427 1.636340 CTTCGGTAATTGGCGCTCG 59.364 57.895 7.64 0.64 0.00 5.03
431 432 2.007608 GTGAGTCCTTCGGTAATTGGC 58.992 52.381 0.00 0.00 0.00 4.52
444 445 2.541556 GCCAAAGATAGTCGTGAGTCC 58.458 52.381 0.00 0.00 0.00 3.85
452 453 4.636206 ACCTCAAAATCGCCAAAGATAGTC 59.364 41.667 0.00 0.00 0.00 2.59
455 456 3.694072 CCACCTCAAAATCGCCAAAGATA 59.306 43.478 0.00 0.00 0.00 1.98
471 476 3.005554 CACATGATGAAGTGTCCACCTC 58.994 50.000 0.00 0.00 0.00 3.85
520 525 1.374378 TGCGGTTATTCGTTCGCCA 60.374 52.632 0.00 0.00 46.51 5.69
521 526 1.059838 GTGCGGTTATTCGTTCGCC 59.940 57.895 0.00 0.00 46.51 5.54
545 558 5.596361 CCTGAGATTAGAAGCTGTCTAGGAA 59.404 44.000 0.00 0.00 40.04 3.36
557 570 8.762481 TGCTGTATACTAACCTGAGATTAGAA 57.238 34.615 0.00 0.00 34.36 2.10
565 578 4.466370 ACTTGCTGCTGTATACTAACCTGA 59.534 41.667 4.17 0.00 0.00 3.86
566 579 4.759782 ACTTGCTGCTGTATACTAACCTG 58.240 43.478 4.17 0.00 0.00 4.00
568 581 5.657474 TGTACTTGCTGCTGTATACTAACC 58.343 41.667 4.17 0.00 0.00 2.85
573 588 5.117745 CGATCATGTACTTGCTGCTGTATAC 59.882 44.000 0.00 0.00 0.00 1.47
575 590 4.053983 CGATCATGTACTTGCTGCTGTAT 58.946 43.478 0.00 0.00 0.00 2.29
581 596 0.940126 GCCCGATCATGTACTTGCTG 59.060 55.000 3.90 0.00 0.00 4.41
637 658 0.924090 GATCCGTCACATGTTCGCTC 59.076 55.000 12.84 8.90 0.00 5.03
698 719 0.827368 TTGGGTTTTGCCTTTTCGCT 59.173 45.000 0.00 0.00 37.43 4.93
709 730 3.636764 AGTCAAAGCTCGATTTGGGTTTT 59.363 39.130 10.71 0.00 39.99 2.43
964 998 0.250166 CGGAGGCGGGGTTTTATAGG 60.250 60.000 0.00 0.00 0.00 2.57
1089 1123 7.777440 GGAAATCTCTGAAAATATCACTCCCTT 59.223 37.037 0.00 0.00 33.47 3.95
1184 1515 0.176680 TGGCGAGCCAGATCTTCTTC 59.823 55.000 13.49 0.00 41.89 2.87
1304 1641 9.981114 AAACAAATCCAAACGAAGAGAAATAAT 57.019 25.926 0.00 0.00 0.00 1.28
1307 1644 7.649306 CAGAAACAAATCCAAACGAAGAGAAAT 59.351 33.333 0.00 0.00 0.00 2.17
1451 1812 4.168291 GGCGGCCTCCTTCTCCTG 62.168 72.222 12.87 0.00 0.00 3.86
1501 1862 2.551071 CCACGCCTTCTTCTTCTTCCTT 60.551 50.000 0.00 0.00 0.00 3.36
1578 3135 3.411351 CTGTCCCGTTTCCGCGTG 61.411 66.667 4.92 0.00 0.00 5.34
1655 3219 1.260544 GAGAGGGCCAATGCTGTTTT 58.739 50.000 6.18 0.00 37.74 2.43
1737 3305 2.818130 ATCCTGTTTTTGCGCACAAT 57.182 40.000 11.12 0.00 35.21 2.71
1823 3391 5.189180 GTGGTTCTTCAGGCAAGAGAATAT 58.811 41.667 0.00 0.00 42.37 1.28
1837 3405 3.311596 GTGCCGGTAATATGTGGTTCTTC 59.688 47.826 1.90 0.00 0.00 2.87
1941 3515 7.092891 TGGGCAAGATCCGATGTTATAGATTAT 60.093 37.037 0.00 0.00 0.00 1.28
1942 3516 6.212589 TGGGCAAGATCCGATGTTATAGATTA 59.787 38.462 0.00 0.00 0.00 1.75
2017 3617 0.249155 TCGTCACCGTGGAGACAAAC 60.249 55.000 15.26 0.00 46.06 2.93
2029 3629 1.453155 AATCAAGTGGCATCGTCACC 58.547 50.000 0.00 0.00 39.18 4.02
2039 3639 5.987777 TGAAAACATGCAAAATCAAGTGG 57.012 34.783 0.00 0.00 0.00 4.00
2097 3697 5.904941 ACGTATTCAACCATATAACCGACA 58.095 37.500 0.00 0.00 0.00 4.35
2100 3700 4.383649 CGGACGTATTCAACCATATAACCG 59.616 45.833 0.00 0.00 0.00 4.44
2104 3704 6.571605 TGTTTCGGACGTATTCAACCATATA 58.428 36.000 0.00 0.00 0.00 0.86
2121 3721 5.878116 TGGTATGTTCTATTTCCTGTTTCGG 59.122 40.000 0.00 0.00 0.00 4.30
2128 3728 8.606830 AGAACTTTCTGGTATGTTCTATTTCCT 58.393 33.333 5.56 0.00 44.70 3.36
2171 3771 6.367421 CGAAGAACGTTAAATTGTTCATCCA 58.633 36.000 0.00 0.00 45.34 3.41
2179 3779 5.049954 TGAGAACCCGAAGAACGTTAAATTG 60.050 40.000 0.00 0.00 40.78 2.32
2180 3780 5.058490 TGAGAACCCGAAGAACGTTAAATT 58.942 37.500 0.00 0.00 40.78 1.82
2193 3793 1.345089 TCGGACAAATTGAGAACCCGA 59.655 47.619 0.00 6.99 41.64 5.14
2194 3794 1.463444 GTCGGACAAATTGAGAACCCG 59.537 52.381 2.62 4.82 37.08 5.28
2197 3797 5.049405 ACTTGATGTCGGACAAATTGAGAAC 60.049 40.000 15.72 0.08 0.00 3.01
2198 3798 5.063204 ACTTGATGTCGGACAAATTGAGAA 58.937 37.500 15.72 0.29 0.00 2.87
2199 3799 4.641396 ACTTGATGTCGGACAAATTGAGA 58.359 39.130 15.72 0.00 0.00 3.27
2206 3806 7.915293 ACAATATAAACTTGATGTCGGACAA 57.085 32.000 15.72 0.00 0.00 3.18
2343 3943 8.884124 AAAGGATTACAATTCCTCTTCAATCA 57.116 30.769 0.00 0.00 32.62 2.57
2349 3949 8.884124 TGATCAAAAGGATTACAATTCCTCTT 57.116 30.769 0.00 0.00 36.00 2.85
2353 3953 9.657419 ACAATTGATCAAAAGGATTACAATTCC 57.343 29.630 13.09 0.00 37.89 3.01
2420 4020 4.489679 AGAACAACGATTTGGAAAGCTC 57.510 40.909 0.00 0.00 37.00 4.09
2444 4044 3.201290 AGACAACGATGAAGATGGATGC 58.799 45.455 0.00 0.00 0.00 3.91
2472 4072 3.829311 AAAGAGGGGTGGGAGGGCA 62.829 63.158 0.00 0.00 0.00 5.36
2528 4128 8.115490 AGTTCATCGGAAAAGAAAATGAGAAT 57.885 30.769 0.00 0.00 34.13 2.40
2534 4134 8.359642 TGAATTGAGTTCATCGGAAAAGAAAAT 58.640 29.630 0.00 0.00 41.79 1.82


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

AutoCloner maintained by Alex Coulton.