Multiple sequence alignment - TraesCS3D01G288300

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 TraesCS3D01G288300 chr3D 100.000 4517 0 0 1 4517 397186339 397181823 0.000000e+00 8342
1 TraesCS3D01G288300 chr3D 99.593 246 1 0 1 246 28088950 28088705 2.480000e-122 449
2 TraesCS3D01G288300 chr3D 99.593 246 1 0 1 246 66431239 66431484 2.480000e-122 449
3 TraesCS3D01G288300 chr3D 99.593 246 1 0 1 246 291064468 291064223 2.480000e-122 449
4 TraesCS3D01G288300 chr3D 99.593 246 1 0 1 246 369775329 369775084 2.480000e-122 449
5 TraesCS3D01G288300 chr3D 99.593 246 1 0 1 246 388292266 388292511 2.480000e-122 449
6 TraesCS3D01G288300 chr3A 95.000 4280 159 17 243 4517 516785858 516781629 0.000000e+00 6667
7 TraesCS3D01G288300 chr3B 94.214 4286 219 18 243 4517 523143939 523139672 0.000000e+00 6514
8 TraesCS3D01G288300 chr3B 77.734 3310 535 111 261 3520 69640041 69636884 0.000000e+00 1844
9 TraesCS3D01G288300 chr4A 82.510 4151 532 128 243 4288 215128039 215132100 0.000000e+00 3465
10 TraesCS3D01G288300 chr4A 81.124 249 33 11 4275 4517 215132132 215132372 2.150000e-43 187
11 TraesCS3D01G288300 chr4A 88.060 134 16 0 4384 4517 694890693 694890826 4.680000e-35 159
12 TraesCS3D01G288300 chr2D 85.450 3409 383 78 243 3578 192298050 192294682 0.000000e+00 3443
13 TraesCS3D01G288300 chr2D 85.425 247 27 6 4275 4517 192293876 192293635 9.700000e-62 248
14 TraesCS3D01G288300 chr5A 82.350 4153 535 131 243 4290 604814372 604810313 0.000000e+00 3426
15 TraesCS3D01G288300 chr5A 81.929 4167 541 139 244 4290 555374716 555378790 0.000000e+00 3328
16 TraesCS3D01G288300 chr5A 90.760 671 46 14 243 904 644505382 644506045 0.000000e+00 881
17 TraesCS3D01G288300 chr5A 82.329 249 31 10 4275 4517 604810283 604810042 2.130000e-48 204
18 TraesCS3D01G288300 chr1D 85.512 2616 301 48 243 2813 2861866 2864448 0.000000e+00 2660
19 TraesCS3D01G288300 chr1D 83.515 825 104 24 2807 3606 2873205 2874022 0.000000e+00 741
20 TraesCS3D01G288300 chr1D 95.018 281 12 1 1 281 349588964 349589242 1.490000e-119 440
21 TraesCS3D01G288300 chr1D 83.871 248 29 8 4275 4517 2881472 2881713 4.550000e-55 226
22 TraesCS3D01G288300 chr6B 84.513 2770 338 60 243 2958 683641785 683639053 0.000000e+00 2654
23 TraesCS3D01G288300 chr6B 78.759 1370 188 72 2972 4290 683638773 683637456 0.000000e+00 822
24 TraesCS3D01G288300 chr6B 81.928 249 32 10 4275 4517 683637426 683637185 9.910000e-47 198
25 TraesCS3D01G288300 chr6D 84.011 2877 320 86 1633 4429 439541502 439544318 0.000000e+00 2636
26 TraesCS3D01G288300 chr6D 86.155 1394 162 26 244 1618 439521150 439522531 0.000000e+00 1476
27 TraesCS3D01G288300 chr6D 99.593 246 1 0 1 246 303558381 303558626 2.480000e-122 449
28 TraesCS3D01G288300 chr7A 86.528 2264 232 43 1438 3677 301167464 301165250 0.000000e+00 2423
29 TraesCS3D01G288300 chr7D 85.840 2267 222 51 1438 3678 271057162 271054969 0.000000e+00 2316
30 TraesCS3D01G288300 chr1A 84.109 2341 286 69 1377 3655 496060131 496062447 0.000000e+00 2183
31 TraesCS3D01G288300 chr1A 89.552 134 14 0 4384 4517 496063514 496063647 2.160000e-38 171
32 TraesCS3D01G288300 chr5D 99.593 246 1 0 1 246 26173714 26173469 2.480000e-122 449
33 TraesCS3D01G288300 chr4D 99.593 246 1 0 1 246 399334247 399334002 2.480000e-122 449


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 TraesCS3D01G288300 chr3D 397181823 397186339 4516 True 8342.000000 8342 100.000000 1 4517 1 chr3D.!!$R4 4516
1 TraesCS3D01G288300 chr3A 516781629 516785858 4229 True 6667.000000 6667 95.000000 243 4517 1 chr3A.!!$R1 4274
2 TraesCS3D01G288300 chr3B 523139672 523143939 4267 True 6514.000000 6514 94.214000 243 4517 1 chr3B.!!$R2 4274
3 TraesCS3D01G288300 chr3B 69636884 69640041 3157 True 1844.000000 1844 77.734000 261 3520 1 chr3B.!!$R1 3259
4 TraesCS3D01G288300 chr4A 215128039 215132372 4333 False 1826.000000 3465 81.817000 243 4517 2 chr4A.!!$F2 4274
5 TraesCS3D01G288300 chr2D 192293635 192298050 4415 True 1845.500000 3443 85.437500 243 4517 2 chr2D.!!$R1 4274
6 TraesCS3D01G288300 chr5A 555374716 555378790 4074 False 3328.000000 3328 81.929000 244 4290 1 chr5A.!!$F1 4046
7 TraesCS3D01G288300 chr5A 604810042 604814372 4330 True 1815.000000 3426 82.339500 243 4517 2 chr5A.!!$R1 4274
8 TraesCS3D01G288300 chr5A 644505382 644506045 663 False 881.000000 881 90.760000 243 904 1 chr5A.!!$F2 661
9 TraesCS3D01G288300 chr1D 2861866 2864448 2582 False 2660.000000 2660 85.512000 243 2813 1 chr1D.!!$F1 2570
10 TraesCS3D01G288300 chr1D 2873205 2874022 817 False 741.000000 741 83.515000 2807 3606 1 chr1D.!!$F2 799
11 TraesCS3D01G288300 chr6B 683637185 683641785 4600 True 1224.666667 2654 81.733333 243 4517 3 chr6B.!!$R1 4274
12 TraesCS3D01G288300 chr6D 439541502 439544318 2816 False 2636.000000 2636 84.011000 1633 4429 1 chr6D.!!$F3 2796
13 TraesCS3D01G288300 chr6D 439521150 439522531 1381 False 1476.000000 1476 86.155000 244 1618 1 chr6D.!!$F2 1374
14 TraesCS3D01G288300 chr7A 301165250 301167464 2214 True 2423.000000 2423 86.528000 1438 3677 1 chr7A.!!$R1 2239
15 TraesCS3D01G288300 chr7D 271054969 271057162 2193 True 2316.000000 2316 85.840000 1438 3678 1 chr7D.!!$R1 2240
16 TraesCS3D01G288300 chr1A 496060131 496063647 3516 False 1177.000000 2183 86.830500 1377 4517 2 chr1A.!!$F1 3140

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
724 741 0.396435 AACCAAGATGACGTGGCTGA 59.604 50.0 0.0 0.0 46.72 4.26 F
1364 1405 0.682209 GATGTGGTTGAGCTGGGCAT 60.682 55.0 0.0 0.0 0.00 4.40 F
1596 1638 2.285220 CCCAAATGTAGATGCGAACTCG 59.715 50.0 0.0 0.0 43.27 4.18 F
2208 2281 2.357154 GCAGGCCTCCTTTCATTAGGAA 60.357 50.0 0.0 0.0 43.57 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2008 0.539986 GCCGACATTGGACTCCCTAA 59.460 55.000 0.00 0.0 0.00 2.69 R
3047 3450 0.103208 AATCTGGCTCTTCCGTAGCG 59.897 55.000 0.00 0.0 41.03 4.26 R
3096 3499 1.133809 TAGTCAAGCAGGGGCCAGTT 61.134 55.000 4.39 0.0 42.56 3.16 R
3734 4204 2.004017 CGCACGGTTATAGCTTCCAAA 58.996 47.619 0.00 0.0 0.00 3.28 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
24 25 7.616528 TCCTAATGATGTGATCCTGTTATCA 57.383 36.000 0.00 0.00 33.48 2.15
25 26 8.033178 TCCTAATGATGTGATCCTGTTATCAA 57.967 34.615 0.00 0.00 37.61 2.57
26 27 8.663167 TCCTAATGATGTGATCCTGTTATCAAT 58.337 33.333 0.00 0.00 37.61 2.57
27 28 8.727910 CCTAATGATGTGATCCTGTTATCAATG 58.272 37.037 0.00 0.00 37.61 2.82
28 29 9.498176 CTAATGATGTGATCCTGTTATCAATGA 57.502 33.333 0.00 0.00 37.61 2.57
29 30 7.741027 ATGATGTGATCCTGTTATCAATGAC 57.259 36.000 0.00 0.00 37.61 3.06
30 31 6.652053 TGATGTGATCCTGTTATCAATGACA 58.348 36.000 0.00 0.00 37.61 3.58
31 32 7.284820 TGATGTGATCCTGTTATCAATGACAT 58.715 34.615 0.00 0.00 37.61 3.06
32 33 7.443272 TGATGTGATCCTGTTATCAATGACATC 59.557 37.037 0.00 0.00 37.61 3.06
33 34 6.057533 TGTGATCCTGTTATCAATGACATCC 58.942 40.000 0.00 0.00 37.61 3.51
34 35 6.057533 GTGATCCTGTTATCAATGACATCCA 58.942 40.000 0.00 0.00 37.61 3.41
35 36 6.543465 GTGATCCTGTTATCAATGACATCCAA 59.457 38.462 0.00 0.00 37.61 3.53
36 37 7.230108 GTGATCCTGTTATCAATGACATCCAAT 59.770 37.037 0.00 0.00 37.61 3.16
37 38 6.947644 TCCTGTTATCAATGACATCCAATG 57.052 37.500 0.00 0.00 0.00 2.82
49 50 4.428294 ACATCCAATGTCCATAGTCAGG 57.572 45.455 0.00 0.00 39.92 3.86
50 51 4.040047 ACATCCAATGTCCATAGTCAGGA 58.960 43.478 0.00 0.00 39.92 3.86
51 52 4.474651 ACATCCAATGTCCATAGTCAGGAA 59.525 41.667 0.00 0.00 39.92 3.36
52 53 5.044919 ACATCCAATGTCCATAGTCAGGAAA 60.045 40.000 0.00 0.00 39.92 3.13
53 54 4.843728 TCCAATGTCCATAGTCAGGAAAC 58.156 43.478 0.00 0.00 36.80 2.78
54 55 3.947834 CCAATGTCCATAGTCAGGAAACC 59.052 47.826 0.00 0.00 36.80 3.27
55 56 4.567537 CCAATGTCCATAGTCAGGAAACCA 60.568 45.833 0.00 0.00 36.80 3.67
56 57 5.195940 CAATGTCCATAGTCAGGAAACCAT 58.804 41.667 0.00 0.00 36.80 3.55
57 58 4.220693 TGTCCATAGTCAGGAAACCATG 57.779 45.455 0.00 0.00 36.80 3.66
58 59 3.843619 TGTCCATAGTCAGGAAACCATGA 59.156 43.478 0.00 0.00 36.80 3.07
59 60 4.192317 GTCCATAGTCAGGAAACCATGAC 58.808 47.826 0.00 2.44 44.97 3.06
66 67 5.091261 GTCAGGAAACCATGACTATCTGT 57.909 43.478 0.00 0.00 42.06 3.41
67 68 5.491982 GTCAGGAAACCATGACTATCTGTT 58.508 41.667 0.00 0.00 42.06 3.16
68 69 5.352569 GTCAGGAAACCATGACTATCTGTTG 59.647 44.000 0.00 0.00 42.06 3.33
69 70 5.248248 TCAGGAAACCATGACTATCTGTTGA 59.752 40.000 0.00 0.00 0.00 3.18
70 71 6.070021 TCAGGAAACCATGACTATCTGTTGAT 60.070 38.462 0.00 0.00 36.74 2.57
71 72 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
72 73 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
73 74 6.599244 GGAAACCATGACTATCTGTTGATCAA 59.401 38.462 3.38 3.38 34.32 2.57
74 75 6.992063 AACCATGACTATCTGTTGATCAAC 57.008 37.500 28.10 28.10 41.50 3.18
75 76 5.111989 ACCATGACTATCTGTTGATCAACG 58.888 41.667 28.55 23.04 43.94 4.10
76 77 5.105351 ACCATGACTATCTGTTGATCAACGA 60.105 40.000 28.55 26.46 43.94 3.85
77 78 5.461407 CCATGACTATCTGTTGATCAACGAG 59.539 44.000 28.55 24.84 43.94 4.18
78 79 4.424626 TGACTATCTGTTGATCAACGAGC 58.575 43.478 28.55 18.56 43.94 5.03
79 80 4.158579 TGACTATCTGTTGATCAACGAGCT 59.841 41.667 28.55 20.51 43.94 4.09
80 81 5.357032 TGACTATCTGTTGATCAACGAGCTA 59.643 40.000 28.55 20.52 43.94 3.32
81 82 5.826586 ACTATCTGTTGATCAACGAGCTAG 58.173 41.667 28.55 27.18 43.94 3.42
82 83 4.727507 ATCTGTTGATCAACGAGCTAGT 57.272 40.909 28.55 13.33 43.94 2.57
83 84 4.098055 TCTGTTGATCAACGAGCTAGTC 57.902 45.455 28.55 6.98 43.94 2.59
84 85 3.506067 TCTGTTGATCAACGAGCTAGTCA 59.494 43.478 28.55 10.88 43.94 3.41
85 86 4.022329 TCTGTTGATCAACGAGCTAGTCAA 60.022 41.667 28.55 10.18 43.94 3.18
86 87 3.987868 TGTTGATCAACGAGCTAGTCAAC 59.012 43.478 28.55 16.99 43.94 3.18
87 88 4.238514 GTTGATCAACGAGCTAGTCAACT 58.761 43.478 22.09 0.00 41.13 3.16
88 89 5.048294 TGTTGATCAACGAGCTAGTCAACTA 60.048 40.000 28.55 7.59 43.38 2.24
89 90 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
90 91 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
91 92 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
92 93 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
93 94 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
94 95 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
95 96 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
96 97 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
97 98 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
98 99 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
99 100 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
100 101 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
101 102 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
102 103 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
103 104 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
104 105 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
105 106 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
106 107 4.604784 ACTAGAGGCTTACTAGGGACAA 57.395 45.455 13.13 0.00 40.86 3.18
107 108 4.538738 ACTAGAGGCTTACTAGGGACAAG 58.461 47.826 13.13 0.00 40.86 3.16
108 109 3.476485 AGAGGCTTACTAGGGACAAGT 57.524 47.619 0.00 0.00 0.00 3.16
109 110 3.792515 AGAGGCTTACTAGGGACAAGTT 58.207 45.455 0.00 0.00 0.00 2.66
110 111 3.515901 AGAGGCTTACTAGGGACAAGTTG 59.484 47.826 0.00 0.00 0.00 3.16
111 112 3.248888 AGGCTTACTAGGGACAAGTTGT 58.751 45.455 8.61 8.61 0.00 3.32
112 113 3.008049 AGGCTTACTAGGGACAAGTTGTG 59.992 47.826 14.57 0.58 0.00 3.33
113 114 3.335579 GCTTACTAGGGACAAGTTGTGG 58.664 50.000 14.57 1.07 0.00 4.17
114 115 3.244457 GCTTACTAGGGACAAGTTGTGGT 60.244 47.826 14.57 6.79 0.00 4.16
115 116 4.566987 CTTACTAGGGACAAGTTGTGGTC 58.433 47.826 14.57 0.00 0.00 4.02
116 117 2.690840 ACTAGGGACAAGTTGTGGTCT 58.309 47.619 14.57 9.98 34.49 3.85
117 118 3.853207 ACTAGGGACAAGTTGTGGTCTA 58.147 45.455 14.57 10.56 34.49 2.59
118 119 4.426704 ACTAGGGACAAGTTGTGGTCTAT 58.573 43.478 14.57 0.00 34.49 1.98
119 120 3.703001 AGGGACAAGTTGTGGTCTATG 57.297 47.619 14.57 0.00 34.49 2.23
120 121 2.979678 AGGGACAAGTTGTGGTCTATGT 59.020 45.455 14.57 0.00 34.49 2.29
121 122 4.164981 AGGGACAAGTTGTGGTCTATGTA 58.835 43.478 14.57 0.00 34.49 2.29
122 123 4.783227 AGGGACAAGTTGTGGTCTATGTAT 59.217 41.667 14.57 0.00 34.49 2.29
123 124 5.250774 AGGGACAAGTTGTGGTCTATGTATT 59.749 40.000 14.57 0.00 34.49 1.89
124 125 5.585047 GGGACAAGTTGTGGTCTATGTATTC 59.415 44.000 14.57 0.00 34.49 1.75
125 126 6.170506 GGACAAGTTGTGGTCTATGTATTCA 58.829 40.000 14.57 0.00 34.49 2.57
126 127 6.092259 GGACAAGTTGTGGTCTATGTATTCAC 59.908 42.308 14.57 0.00 34.49 3.18
127 128 6.530120 ACAAGTTGTGGTCTATGTATTCACA 58.470 36.000 7.96 0.00 39.52 3.58
128 129 6.426937 ACAAGTTGTGGTCTATGTATTCACAC 59.573 38.462 7.96 0.00 37.96 3.82
129 130 6.109156 AGTTGTGGTCTATGTATTCACACA 57.891 37.500 0.00 0.00 37.96 3.72
130 131 6.711277 AGTTGTGGTCTATGTATTCACACAT 58.289 36.000 0.00 0.00 41.88 3.21
131 132 6.595326 AGTTGTGGTCTATGTATTCACACATG 59.405 38.462 0.00 0.00 39.46 3.21
132 133 6.048732 TGTGGTCTATGTATTCACACATGT 57.951 37.500 0.00 0.00 39.46 3.21
133 134 7.176589 TGTGGTCTATGTATTCACACATGTA 57.823 36.000 0.00 0.00 39.46 2.29
134 135 7.791029 TGTGGTCTATGTATTCACACATGTAT 58.209 34.615 0.00 0.00 39.46 2.29
135 136 8.264347 TGTGGTCTATGTATTCACACATGTATT 58.736 33.333 0.00 0.00 39.46 1.89
136 137 9.758651 GTGGTCTATGTATTCACACATGTATTA 57.241 33.333 0.00 0.00 39.46 0.98
137 138 9.758651 TGGTCTATGTATTCACACATGTATTAC 57.241 33.333 0.00 0.00 39.46 1.89
138 139 8.912658 GGTCTATGTATTCACACATGTATTACG 58.087 37.037 0.00 0.00 39.46 3.18
139 140 9.673454 GTCTATGTATTCACACATGTATTACGA 57.327 33.333 0.00 0.00 39.46 3.43
144 145 8.822855 TGTATTCACACATGTATTACGATTTCC 58.177 33.333 0.00 0.00 0.00 3.13
145 146 5.959652 TCACACATGTATTACGATTTCCG 57.040 39.130 0.00 0.00 45.44 4.30
146 147 4.806775 TCACACATGTATTACGATTTCCGG 59.193 41.667 0.00 0.00 43.93 5.14
147 148 4.806775 CACACATGTATTACGATTTCCGGA 59.193 41.667 0.00 0.00 43.93 5.14
148 149 4.807304 ACACATGTATTACGATTTCCGGAC 59.193 41.667 1.83 0.00 43.93 4.79
149 150 4.806775 CACATGTATTACGATTTCCGGACA 59.193 41.667 1.83 0.00 43.93 4.02
150 151 5.292345 CACATGTATTACGATTTCCGGACAA 59.708 40.000 1.83 2.11 43.93 3.18
151 152 6.018262 CACATGTATTACGATTTCCGGACAAT 60.018 38.462 1.83 7.66 43.93 2.71
152 153 7.170151 CACATGTATTACGATTTCCGGACAATA 59.830 37.037 1.83 0.00 43.93 1.90
153 154 7.170320 ACATGTATTACGATTTCCGGACAATAC 59.830 37.037 1.83 11.52 43.93 1.89
154 155 6.571605 TGTATTACGATTTCCGGACAATACA 58.428 36.000 1.83 13.77 42.39 2.29
155 156 7.040494 TGTATTACGATTTCCGGACAATACAA 58.960 34.615 1.83 0.00 42.09 2.41
156 157 7.711772 TGTATTACGATTTCCGGACAATACAAT 59.288 33.333 1.83 0.00 42.09 2.71
157 158 6.988622 TTACGATTTCCGGACAATACAATT 57.011 33.333 1.83 0.00 43.93 2.32
158 159 8.665643 ATTACGATTTCCGGACAATACAATTA 57.334 30.769 1.83 0.00 43.93 1.40
159 160 8.665643 TTACGATTTCCGGACAATACAATTAT 57.334 30.769 1.83 0.00 43.93 1.28
160 161 9.761504 TTACGATTTCCGGACAATACAATTATA 57.238 29.630 1.83 0.00 43.93 0.98
161 162 8.306680 ACGATTTCCGGACAATACAATTATAG 57.693 34.615 1.83 0.00 43.93 1.31
162 163 7.095355 ACGATTTCCGGACAATACAATTATAGC 60.095 37.037 1.83 0.00 43.93 2.97
163 164 7.095397 CGATTTCCGGACAATACAATTATAGCA 60.095 37.037 1.83 0.00 33.91 3.49
164 165 8.635765 ATTTCCGGACAATACAATTATAGCAT 57.364 30.769 1.83 0.00 0.00 3.79
165 166 7.433708 TTCCGGACAATACAATTATAGCATG 57.566 36.000 1.83 0.00 0.00 4.06
166 167 6.764379 TCCGGACAATACAATTATAGCATGA 58.236 36.000 0.00 0.00 0.00 3.07
167 168 7.220740 TCCGGACAATACAATTATAGCATGAA 58.779 34.615 0.00 0.00 0.00 2.57
168 169 7.882791 TCCGGACAATACAATTATAGCATGAAT 59.117 33.333 0.00 0.00 0.00 2.57
169 170 9.161629 CCGGACAATACAATTATAGCATGAATA 57.838 33.333 0.00 0.00 0.00 1.75
186 187 9.797642 AGCATGAATAATAGACAATTACCATGA 57.202 29.630 17.25 0.00 41.39 3.07
228 229 9.533831 AATAACCATTTATTATTGCCTCTAGGG 57.466 33.333 0.00 0.00 36.34 3.53
241 242 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
404 405 2.916702 AAGCTTTCTTTGGGCAAAGG 57.083 45.000 0.00 0.00 45.80 3.11
491 506 7.669089 TGTTTCTTCCCAATTTTTACCTTCT 57.331 32.000 0.00 0.00 0.00 2.85
571 588 2.039084 AGTTTCGCCCTCTGTCAAAGAT 59.961 45.455 0.00 0.00 33.29 2.40
692 709 6.899089 TCAAGATTGTGGAGCTGGAAATATA 58.101 36.000 0.00 0.00 0.00 0.86
724 741 0.396435 AACCAAGATGACGTGGCTGA 59.604 50.000 0.00 0.00 46.72 4.26
1069 1104 1.742308 AGGGGCTCCAAGTTCTTACA 58.258 50.000 4.79 0.00 34.83 2.41
1157 1192 3.126831 CGTCAAGTTCTCAAGAAGCAGT 58.873 45.455 0.00 0.00 34.27 4.40
1176 1211 4.941263 GCAGTGGATGTTACCTTTGATGTA 59.059 41.667 0.00 0.00 0.00 2.29
1181 1216 5.057149 GGATGTTACCTTTGATGTATCGCT 58.943 41.667 0.00 0.00 0.00 4.93
1364 1405 0.682209 GATGTGGTTGAGCTGGGCAT 60.682 55.000 0.00 0.00 0.00 4.40
1445 1487 3.963428 AGTGTCCAGTGGTGAAGATAC 57.037 47.619 9.54 0.00 0.00 2.24
1518 1560 2.440409 GCTGGACATTGGAGTGATGTT 58.560 47.619 0.00 0.00 37.83 2.71
1596 1638 2.285220 CCCAAATGTAGATGCGAACTCG 59.715 50.000 0.00 0.00 43.27 4.18
2208 2281 2.357154 GCAGGCCTCCTTTCATTAGGAA 60.357 50.000 0.00 0.00 43.57 3.36
2610 2698 5.010282 CCTAGTAAGTTTGCTCCCAACAAT 58.990 41.667 0.00 0.00 0.00 2.71
2687 2784 9.620259 ATTCCATTTAACCTCTATCTTGTCTTC 57.380 33.333 0.00 0.00 0.00 2.87
2766 2864 2.875933 CGTTAACCTCTTGCACAAGGAA 59.124 45.455 18.28 5.25 38.88 3.36
2955 3086 5.758784 GTCTGAAGTTTTAGTGGTTGTAGCT 59.241 40.000 0.00 0.00 0.00 3.32
3047 3450 7.174946 TGTCAGTTTACCAATTTCAAGAGGATC 59.825 37.037 0.00 0.00 0.00 3.36
3053 3456 3.246226 CCAATTTCAAGAGGATCGCTACG 59.754 47.826 0.00 0.00 42.67 3.51
3096 3499 8.477419 AGTGGATTTATCTTCTTTCAAACCAA 57.523 30.769 0.00 0.00 0.00 3.67
3155 3559 3.653344 GTGAGCTCTAATCACACACACA 58.347 45.455 16.19 0.00 45.18 3.72
3363 3803 3.068873 TGGGTACTTTTTCATGTGTTGCC 59.931 43.478 0.00 0.00 0.00 4.52
3368 3808 4.932146 ACTTTTTCATGTGTTGCCTGTAC 58.068 39.130 0.00 0.00 0.00 2.90
3577 4037 4.111916 CGGTTTTGAAGATGCAACTTTGT 58.888 39.130 10.85 0.00 0.00 2.83
3579 4039 5.399301 CGGTTTTGAAGATGCAACTTTGTAG 59.601 40.000 10.85 0.00 0.00 2.74
3662 4127 7.611467 ACTCCATGTAAAGCAAATCAGTTATGA 59.389 33.333 0.00 0.00 40.50 2.15
3773 4245 1.134965 CGGTGGTTTGTTGGAAGCAAA 60.135 47.619 0.00 0.00 38.58 3.68
3875 4350 9.554395 TTTCATGTCTGTTTTTCTAGTATGTGA 57.446 29.630 0.00 0.00 0.00 3.58
4030 4518 4.081198 TGTTGTTGGAAGAAGCATTTTGGT 60.081 37.500 0.00 0.00 0.00 3.67
4055 4702 9.482627 GTAGCTTTGACATAATACTAGAAGCAT 57.517 33.333 0.00 0.00 40.36 3.79
4295 5452 5.376854 AATGAGCAGTAACATGAACCAAC 57.623 39.130 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.727910 CATTGATAACAGGATCACATCATTAGG 58.272 37.037 0.00 0.00 35.56 2.69
5 6 7.284820 TGTCATTGATAACAGGATCACATCAT 58.715 34.615 0.00 0.00 35.56 2.45
7 8 7.094890 GGATGTCATTGATAACAGGATCACATC 60.095 40.741 0.00 0.48 36.17 3.06
8 9 6.713903 GGATGTCATTGATAACAGGATCACAT 59.286 38.462 0.00 0.00 35.56 3.21
9 10 6.057533 GGATGTCATTGATAACAGGATCACA 58.942 40.000 0.00 0.00 35.56 3.58
10 11 6.057533 TGGATGTCATTGATAACAGGATCAC 58.942 40.000 0.00 0.00 35.56 3.06
11 12 6.251255 TGGATGTCATTGATAACAGGATCA 57.749 37.500 0.00 0.00 33.96 2.92
12 13 7.230108 ACATTGGATGTCATTGATAACAGGATC 59.770 37.037 0.00 0.00 39.92 3.36
13 14 7.064866 ACATTGGATGTCATTGATAACAGGAT 58.935 34.615 0.00 0.00 39.92 3.24
14 15 6.425735 ACATTGGATGTCATTGATAACAGGA 58.574 36.000 0.00 0.00 39.92 3.86
15 16 6.704289 ACATTGGATGTCATTGATAACAGG 57.296 37.500 0.00 0.00 39.92 4.00
29 30 4.694760 TCCTGACTATGGACATTGGATG 57.305 45.455 0.00 0.00 0.00 3.51
30 31 5.440610 GTTTCCTGACTATGGACATTGGAT 58.559 41.667 0.00 0.00 32.65 3.41
31 32 4.324254 GGTTTCCTGACTATGGACATTGGA 60.324 45.833 0.00 0.00 32.65 3.53
32 33 3.947834 GGTTTCCTGACTATGGACATTGG 59.052 47.826 0.00 0.00 32.65 3.16
33 34 4.588899 TGGTTTCCTGACTATGGACATTG 58.411 43.478 0.00 0.00 32.65 2.82
34 35 4.927267 TGGTTTCCTGACTATGGACATT 57.073 40.909 0.00 0.00 32.65 2.71
35 36 4.474651 TCATGGTTTCCTGACTATGGACAT 59.525 41.667 0.00 0.00 38.56 3.06
36 37 3.843619 TCATGGTTTCCTGACTATGGACA 59.156 43.478 0.00 0.00 38.56 4.02
37 38 4.192317 GTCATGGTTTCCTGACTATGGAC 58.808 47.826 0.00 0.00 38.56 4.02
38 39 4.487714 GTCATGGTTTCCTGACTATGGA 57.512 45.455 0.00 0.00 38.56 3.41
44 45 5.091261 ACAGATAGTCATGGTTTCCTGAC 57.909 43.478 10.65 8.96 41.65 3.51
45 46 5.248248 TCAACAGATAGTCATGGTTTCCTGA 59.752 40.000 10.65 0.00 0.00 3.86
46 47 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
47 48 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
48 49 6.115446 TGATCAACAGATAGTCATGGTTTCC 58.885 40.000 0.00 0.00 0.00 3.13
49 50 7.467623 GTTGATCAACAGATAGTCATGGTTTC 58.532 38.462 29.43 0.00 40.84 2.78
50 51 6.092670 CGTTGATCAACAGATAGTCATGGTTT 59.907 38.462 32.06 0.00 41.20 3.27
51 52 5.582269 CGTTGATCAACAGATAGTCATGGTT 59.418 40.000 32.06 0.00 41.20 3.67
52 53 5.105351 TCGTTGATCAACAGATAGTCATGGT 60.105 40.000 32.06 0.00 41.20 3.55
53 54 5.351458 TCGTTGATCAACAGATAGTCATGG 58.649 41.667 32.06 15.04 41.20 3.66
54 55 5.051173 GCTCGTTGATCAACAGATAGTCATG 60.051 44.000 32.06 18.25 41.20 3.07
55 56 5.046529 GCTCGTTGATCAACAGATAGTCAT 58.953 41.667 32.06 0.00 41.20 3.06
56 57 4.158579 AGCTCGTTGATCAACAGATAGTCA 59.841 41.667 32.06 11.38 41.20 3.41
57 58 4.677584 AGCTCGTTGATCAACAGATAGTC 58.322 43.478 32.06 19.15 41.20 2.59
58 59 4.727507 AGCTCGTTGATCAACAGATAGT 57.272 40.909 32.06 16.47 41.20 2.12
59 60 5.826586 ACTAGCTCGTTGATCAACAGATAG 58.173 41.667 33.05 33.05 40.27 2.08
60 61 5.357032 TGACTAGCTCGTTGATCAACAGATA 59.643 40.000 32.06 26.63 41.20 1.98
61 62 4.158579 TGACTAGCTCGTTGATCAACAGAT 59.841 41.667 32.06 26.87 41.20 2.90
62 63 3.506067 TGACTAGCTCGTTGATCAACAGA 59.494 43.478 32.06 26.81 41.20 3.41
63 64 3.838120 TGACTAGCTCGTTGATCAACAG 58.162 45.455 32.06 26.93 41.20 3.16
64 65 3.934457 TGACTAGCTCGTTGATCAACA 57.066 42.857 32.06 20.24 41.20 3.33
65 66 4.238514 AGTTGACTAGCTCGTTGATCAAC 58.761 43.478 25.68 25.68 43.94 3.18
66 67 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
67 68 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
68 69 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
69 70 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
70 71 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
71 72 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
72 73 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
73 74 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
74 75 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
75 76 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
76 77 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
77 78 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
78 79 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
79 80 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
80 81 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
81 82 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
82 83 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
83 84 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
84 85 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
85 86 4.017314 ACTTGTCCCTAGTAAGCCTCTAGT 60.017 45.833 0.00 0.00 34.72 2.57
86 87 4.538738 ACTTGTCCCTAGTAAGCCTCTAG 58.461 47.826 0.00 0.00 35.86 2.43
87 88 4.604784 ACTTGTCCCTAGTAAGCCTCTA 57.395 45.455 0.00 0.00 0.00 2.43
88 89 3.476485 ACTTGTCCCTAGTAAGCCTCT 57.524 47.619 0.00 0.00 0.00 3.69
89 90 3.261137 ACAACTTGTCCCTAGTAAGCCTC 59.739 47.826 0.00 0.00 0.00 4.70
90 91 3.008049 CACAACTTGTCCCTAGTAAGCCT 59.992 47.826 0.00 0.00 0.00 4.58
91 92 3.335579 CACAACTTGTCCCTAGTAAGCC 58.664 50.000 0.00 0.00 0.00 4.35
92 93 3.244457 ACCACAACTTGTCCCTAGTAAGC 60.244 47.826 0.00 0.00 0.00 3.09
93 94 4.283722 AGACCACAACTTGTCCCTAGTAAG 59.716 45.833 0.00 0.00 31.76 2.34
94 95 4.228824 AGACCACAACTTGTCCCTAGTAA 58.771 43.478 0.00 0.00 31.76 2.24
95 96 3.853207 AGACCACAACTTGTCCCTAGTA 58.147 45.455 0.00 0.00 31.76 1.82
96 97 2.690840 AGACCACAACTTGTCCCTAGT 58.309 47.619 0.00 0.00 31.76 2.57
97 98 4.223032 ACATAGACCACAACTTGTCCCTAG 59.777 45.833 0.00 0.00 31.76 3.02
98 99 4.164981 ACATAGACCACAACTTGTCCCTA 58.835 43.478 0.00 0.00 31.76 3.53
99 100 2.979678 ACATAGACCACAACTTGTCCCT 59.020 45.455 0.00 0.00 31.76 4.20
100 101 3.418684 ACATAGACCACAACTTGTCCC 57.581 47.619 0.00 0.00 31.76 4.46
101 102 6.092259 GTGAATACATAGACCACAACTTGTCC 59.908 42.308 0.00 0.00 31.76 4.02
102 103 6.649141 TGTGAATACATAGACCACAACTTGTC 59.351 38.462 0.00 0.00 35.16 3.18
103 104 6.426937 GTGTGAATACATAGACCACAACTTGT 59.573 38.462 0.00 0.00 39.13 3.16
104 105 6.426633 TGTGTGAATACATAGACCACAACTTG 59.573 38.462 0.00 0.00 39.13 3.16
105 106 6.530120 TGTGTGAATACATAGACCACAACTT 58.470 36.000 0.00 0.00 39.13 2.66
106 107 6.109156 TGTGTGAATACATAGACCACAACT 57.891 37.500 0.00 0.00 39.13 3.16
107 108 6.371548 ACATGTGTGAATACATAGACCACAAC 59.628 38.462 0.00 0.00 39.17 3.32
108 109 6.472016 ACATGTGTGAATACATAGACCACAA 58.528 36.000 0.00 0.00 39.17 3.33
109 110 6.048732 ACATGTGTGAATACATAGACCACA 57.951 37.500 0.00 0.00 39.17 4.17
110 111 8.662781 AATACATGTGTGAATACATAGACCAC 57.337 34.615 9.11 0.00 39.17 4.16
111 112 9.758651 GTAATACATGTGTGAATACATAGACCA 57.241 33.333 9.11 0.00 39.17 4.02
112 113 8.912658 CGTAATACATGTGTGAATACATAGACC 58.087 37.037 9.11 0.00 39.17 3.85
113 114 9.673454 TCGTAATACATGTGTGAATACATAGAC 57.327 33.333 9.11 0.00 39.17 2.59
118 119 8.822855 GGAAATCGTAATACATGTGTGAATACA 58.177 33.333 9.11 0.00 34.63 2.29
119 120 8.002107 CGGAAATCGTAATACATGTGTGAATAC 58.998 37.037 9.11 0.76 0.00 1.89
120 121 7.170151 CCGGAAATCGTAATACATGTGTGAATA 59.830 37.037 9.11 0.00 37.11 1.75
121 122 6.018262 CCGGAAATCGTAATACATGTGTGAAT 60.018 38.462 9.11 0.00 37.11 2.57
122 123 5.292345 CCGGAAATCGTAATACATGTGTGAA 59.708 40.000 9.11 0.00 37.11 3.18
123 124 4.806775 CCGGAAATCGTAATACATGTGTGA 59.193 41.667 9.11 0.00 37.11 3.58
124 125 4.806775 TCCGGAAATCGTAATACATGTGTG 59.193 41.667 9.11 0.00 37.11 3.82
125 126 4.807304 GTCCGGAAATCGTAATACATGTGT 59.193 41.667 5.23 0.00 37.11 3.72
126 127 4.806775 TGTCCGGAAATCGTAATACATGTG 59.193 41.667 5.23 0.00 37.11 3.21
127 128 5.013568 TGTCCGGAAATCGTAATACATGT 57.986 39.130 5.23 2.69 37.11 3.21
128 129 5.977171 TTGTCCGGAAATCGTAATACATG 57.023 39.130 5.23 0.00 37.11 3.21
129 130 7.211573 TGTATTGTCCGGAAATCGTAATACAT 58.788 34.615 5.23 0.00 39.85 2.29
130 131 6.571605 TGTATTGTCCGGAAATCGTAATACA 58.428 36.000 5.23 16.25 40.93 2.29
131 132 7.467557 TTGTATTGTCCGGAAATCGTAATAC 57.532 36.000 5.23 14.10 37.96 1.89
132 133 8.665643 AATTGTATTGTCCGGAAATCGTAATA 57.334 30.769 5.23 2.30 37.11 0.98
133 134 7.562454 AATTGTATTGTCCGGAAATCGTAAT 57.438 32.000 5.23 0.74 37.11 1.89
134 135 6.988622 AATTGTATTGTCCGGAAATCGTAA 57.011 33.333 5.23 0.00 37.11 3.18
135 136 9.414295 CTATAATTGTATTGTCCGGAAATCGTA 57.586 33.333 5.23 0.00 37.11 3.43
136 137 7.095355 GCTATAATTGTATTGTCCGGAAATCGT 60.095 37.037 5.23 0.00 37.11 3.73
137 138 7.095397 TGCTATAATTGTATTGTCCGGAAATCG 60.095 37.037 5.23 0.00 38.88 3.34
138 139 8.094798 TGCTATAATTGTATTGTCCGGAAATC 57.905 34.615 5.23 0.00 0.00 2.17
139 140 8.514594 CATGCTATAATTGTATTGTCCGGAAAT 58.485 33.333 5.23 11.20 0.00 2.17
140 141 7.717436 TCATGCTATAATTGTATTGTCCGGAAA 59.283 33.333 5.23 0.00 0.00 3.13
141 142 7.220740 TCATGCTATAATTGTATTGTCCGGAA 58.779 34.615 5.23 0.00 0.00 4.30
142 143 6.764379 TCATGCTATAATTGTATTGTCCGGA 58.236 36.000 0.00 0.00 0.00 5.14
143 144 7.433708 TTCATGCTATAATTGTATTGTCCGG 57.566 36.000 0.00 0.00 0.00 5.14
160 161 9.797642 TCATGGTAATTGTCTATTATTCATGCT 57.202 29.630 17.71 0.00 39.63 3.79
202 203 9.533831 CCCTAGAGGCAATAATAAATGGTTATT 57.466 33.333 0.00 0.00 41.71 1.40
220 221 4.141390 ACTGTTGGAAATATGCCCTAGAGG 60.141 45.833 0.00 0.00 39.47 3.69
221 222 5.041191 ACTGTTGGAAATATGCCCTAGAG 57.959 43.478 0.00 0.00 0.00 2.43
222 223 4.721776 AGACTGTTGGAAATATGCCCTAGA 59.278 41.667 0.00 0.00 0.00 2.43
223 224 5.041191 AGACTGTTGGAAATATGCCCTAG 57.959 43.478 0.00 0.00 0.00 3.02
224 225 5.191722 AGAAGACTGTTGGAAATATGCCCTA 59.808 40.000 0.00 0.00 0.00 3.53
225 226 4.018050 AGAAGACTGTTGGAAATATGCCCT 60.018 41.667 0.00 0.00 0.00 5.19
226 227 4.273318 AGAAGACTGTTGGAAATATGCCC 58.727 43.478 0.00 0.00 0.00 5.36
227 228 5.904362 AAGAAGACTGTTGGAAATATGCC 57.096 39.130 0.00 0.00 0.00 4.40
228 229 8.677300 TGAATAAGAAGACTGTTGGAAATATGC 58.323 33.333 0.00 0.00 0.00 3.14
229 230 9.994432 GTGAATAAGAAGACTGTTGGAAATATG 57.006 33.333 0.00 0.00 0.00 1.78
230 231 8.883731 CGTGAATAAGAAGACTGTTGGAAATAT 58.116 33.333 0.00 0.00 0.00 1.28
231 232 7.876068 ACGTGAATAAGAAGACTGTTGGAAATA 59.124 33.333 0.00 0.00 0.00 1.40
232 233 6.710744 ACGTGAATAAGAAGACTGTTGGAAAT 59.289 34.615 0.00 0.00 0.00 2.17
233 234 6.053005 ACGTGAATAAGAAGACTGTTGGAAA 58.947 36.000 0.00 0.00 0.00 3.13
234 235 5.607477 ACGTGAATAAGAAGACTGTTGGAA 58.393 37.500 0.00 0.00 0.00 3.53
235 236 5.209818 ACGTGAATAAGAAGACTGTTGGA 57.790 39.130 0.00 0.00 0.00 3.53
236 237 5.924475 AACGTGAATAAGAAGACTGTTGG 57.076 39.130 0.00 0.00 0.00 3.77
239 240 9.701098 TGTAAATAACGTGAATAAGAAGACTGT 57.299 29.630 0.00 0.00 0.00 3.55
284 285 1.159285 CTCGTTGATGGCAGCTTGAA 58.841 50.000 3.69 0.00 0.00 2.69
404 405 0.389948 ACGACACTTCCCGAATGAGC 60.390 55.000 0.00 0.00 0.00 4.26
491 506 7.721402 ACCATGAGTACACAAGCAAAAATAAA 58.279 30.769 0.00 0.00 0.00 1.40
692 709 8.956426 ACGTCATCTTGGTTATCATTAATGTTT 58.044 29.630 14.97 7.05 0.00 2.83
872 901 9.877178 AAGGTATGTGACAAAATTAAACAACAA 57.123 25.926 0.00 0.00 0.00 2.83
1157 1192 4.814234 GCGATACATCAAAGGTAACATCCA 59.186 41.667 0.00 0.00 41.41 3.41
1176 1211 1.339438 ACATTGCTGTGAGGAAGCGAT 60.339 47.619 0.00 0.00 44.08 4.58
1181 1216 4.065088 GTCTACAACATTGCTGTGAGGAA 58.935 43.478 2.97 0.00 35.22 3.36
1364 1405 3.895656 ACTGACAACAGCACTAGTTCCTA 59.104 43.478 0.00 0.00 46.95 2.94
1445 1487 1.271001 TGAGTTGGTGACCATGCTCAG 60.271 52.381 25.41 0.00 39.29 3.35
1518 1560 3.786368 TGGAACACACTCATTGATGGA 57.214 42.857 0.00 0.00 0.00 3.41
1949 2008 0.539986 GCCGACATTGGACTCCCTAA 59.460 55.000 0.00 0.00 0.00 2.69
2208 2281 5.885912 GTGTAGGTAATGTGGAAATCACCAT 59.114 40.000 0.00 0.00 45.48 3.55
2367 2440 5.049680 GGAGCAACAAAAGATGAACTAACGA 60.050 40.000 0.00 0.00 0.00 3.85
2687 2784 7.135467 GGTGAAGAAAAGCTAGAAAAAGAGTG 58.865 38.462 0.00 0.00 0.00 3.51
2766 2864 6.653526 TCCAATGAGTCAAACATGTTGAAT 57.346 33.333 12.82 10.85 0.00 2.57
2916 3030 4.520492 ACTTCAGACACATTTGGATTCACC 59.480 41.667 0.00 0.00 39.54 4.02
2962 3096 7.581213 TTGTCAAACATAAAAGAGTGATGGT 57.419 32.000 0.00 0.00 0.00 3.55
3047 3450 0.103208 AATCTGGCTCTTCCGTAGCG 59.897 55.000 0.00 0.00 41.03 4.26
3053 3456 3.192212 CCACTTTGAAATCTGGCTCTTCC 59.808 47.826 0.00 0.00 0.00 3.46
3096 3499 1.133809 TAGTCAAGCAGGGGCCAGTT 61.134 55.000 4.39 0.00 42.56 3.16
3155 3559 8.989131 ACATGTAAACACTACTATTATGGAGGT 58.011 33.333 0.00 0.00 0.00 3.85
3227 3640 2.058829 AAAGCTGTTTCGTGGTGCCG 62.059 55.000 0.00 0.00 0.00 5.69
3368 3808 7.148705 TGGTGAAAAGAGAACAAACGTATATCG 60.149 37.037 0.00 0.00 46.00 2.92
3577 4037 7.954788 GGCAACAATGTATTTCCAAAAACTA 57.045 32.000 0.00 0.00 0.00 2.24
3734 4204 2.004017 CGCACGGTTATAGCTTCCAAA 58.996 47.619 0.00 0.00 0.00 3.28
3857 4331 6.992063 AGGCATCACATACTAGAAAAACAG 57.008 37.500 0.00 0.00 0.00 3.16
3875 4350 6.350445 GGACAATTTGTGACAAGATAAGGCAT 60.350 38.462 6.80 0.00 0.00 4.40
4012 4500 4.151883 AGCTACCAAAATGCTTCTTCCAA 58.848 39.130 0.00 0.00 32.61 3.53
4335 5550 8.842280 ACTTTCGAAAAAGACATATTTGTACCA 58.158 29.630 12.41 0.00 43.90 3.25


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

AutoCloner maintained by Alex Coulton.