Multiple sequence alignment - TraesCS1D01G414100

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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 TraesCS1D01G414100 chr1D 100.000 3647 0 0 1 3647 474265518 474269164 0.000000e+00 6735.0
1 TraesCS1D01G414100 chr1D 84.615 2639 354 29 278 2902 474307108 474309708 0.000000e+00 2577.0
2 TraesCS1D01G414100 chr1D 96.937 751 17 4 2903 3647 41910549 41909799 0.000000e+00 1254.0
3 TraesCS1D01G414100 chr1D 78.348 1949 337 55 892 2805 474289612 474291510 0.000000e+00 1182.0
4 TraesCS1D01G414100 chr1D 77.831 1042 192 24 1615 2644 474129897 474130911 3.110000e-170 608.0
5 TraesCS1D01G414100 chr1D 79.328 595 114 6 894 1485 474129170 474129758 3.390000e-110 409.0
6 TraesCS1D01G414100 chr1D 78.993 457 92 2 321 776 474289068 474289521 3.540000e-80 309.0
7 TraesCS1D01G414100 chr1D 84.298 121 16 2 1 118 132857712 132857832 8.280000e-22 115.0
8 TraesCS1D01G414100 chr1A 98.435 1278 15 2 530 1806 568686988 568688261 0.000000e+00 2244.0
9 TraesCS1D01G414100 chr1A 94.140 1058 46 4 1808 2864 568688425 568689467 0.000000e+00 1596.0
10 TraesCS1D01G414100 chr1A 78.702 1864 320 47 892 2719 568644779 568646601 0.000000e+00 1171.0
11 TraesCS1D01G414100 chr1A 77.004 1048 203 22 1616 2644 568551456 568552484 1.900000e-157 566.0
12 TraesCS1D01G414100 chr1A 95.223 314 13 1 199 512 568669093 568669404 2.530000e-136 496.0
13 TraesCS1D01G414100 chr1A 80.301 599 101 13 894 1485 568550728 568551316 1.550000e-118 436.0
14 TraesCS1D01G414100 chr1A 100.000 43 0 0 498 540 568684210 568684252 3.020000e-11 80.5
15 TraesCS1D01G414100 chrUn 80.438 2009 342 30 892 2864 8485216 8487209 0.000000e+00 1485.0
16 TraesCS1D01G414100 chrUn 79.543 1838 302 46 892 2690 8471592 8473394 0.000000e+00 1243.0
17 TraesCS1D01G414100 chr2D 97.603 751 12 4 2903 3647 116820340 116819590 0.000000e+00 1282.0
18 TraesCS1D01G414100 chr2D 97.467 750 14 3 2903 3647 5445162 5445911 0.000000e+00 1275.0
19 TraesCS1D01G414100 chr2D 97.340 752 13 4 2903 3647 594891165 594891916 0.000000e+00 1271.0
20 TraesCS1D01G414100 chr2D 96.937 751 17 4 2903 3647 66096722 66097472 0.000000e+00 1254.0
21 TraesCS1D01G414100 chr5D 97.337 751 15 3 2902 3647 311908155 311908905 0.000000e+00 1271.0
22 TraesCS1D01G414100 chr5D 86.607 112 11 3 13 121 278626879 278626769 1.780000e-23 121.0
23 TraesCS1D01G414100 chr5D 81.633 98 10 6 677 767 1882380 1882476 1.400000e-09 75.0
24 TraesCS1D01G414100 chr6D 97.333 750 15 3 2903 3647 14452849 14453598 0.000000e+00 1269.0
25 TraesCS1D01G414100 chr6D 87.963 108 10 2 13 117 93646280 93646387 1.380000e-24 124.0
26 TraesCS1D01G414100 chr6D 87.156 109 11 3 13 118 454824113 454824221 1.780000e-23 121.0
27 TraesCS1D01G414100 chr7D 97.071 751 16 4 2903 3647 23651696 23650946 0.000000e+00 1260.0
28 TraesCS1D01G414100 chr7D 96.941 752 16 5 2903 3647 631773250 631772499 0.000000e+00 1254.0
29 TraesCS1D01G414100 chr1B 77.423 1001 187 26 1615 2600 659570587 659569611 8.840000e-156 560.0
30 TraesCS1D01G414100 chr1B 78.179 582 120 4 894 1473 659571306 659570730 7.440000e-97 364.0
31 TraesCS1D01G414100 chr3B 85.950 121 14 2 1 118 8816227 8816107 3.820000e-25 126.0
32 TraesCS1D01G414100 chr3B 84.677 124 16 2 1 122 529407832 529407954 1.780000e-23 121.0
33 TraesCS1D01G414100 chr3A 86.842 114 12 2 13 123 627965029 627964916 1.380000e-24 124.0
34 TraesCS1D01G414100 chr7B 87.156 109 11 3 13 118 678722644 678722536 1.780000e-23 121.0
35 TraesCS1D01G414100 chr2B 83.333 120 17 2 1 117 797329845 797329964 1.380000e-19 108.0
36 TraesCS1D01G414100 chr5B 79.592 98 12 6 677 767 759968 760064 3.040000e-06 63.9


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 TraesCS1D01G414100 chr1D 474265518 474269164 3646 False 6735.000000 6735 100.0000 1 3647 1 chr1D.!!$F2 3646
1 TraesCS1D01G414100 chr1D 474307108 474309708 2600 False 2577.000000 2577 84.6150 278 2902 1 chr1D.!!$F3 2624
2 TraesCS1D01G414100 chr1D 41909799 41910549 750 True 1254.000000 1254 96.9370 2903 3647 1 chr1D.!!$R1 744
3 TraesCS1D01G414100 chr1D 474289068 474291510 2442 False 745.500000 1182 78.6705 321 2805 2 chr1D.!!$F5 2484
4 TraesCS1D01G414100 chr1D 474129170 474130911 1741 False 508.500000 608 78.5795 894 2644 2 chr1D.!!$F4 1750
5 TraesCS1D01G414100 chr1A 568684210 568689467 5257 False 1306.833333 2244 97.5250 498 2864 3 chr1A.!!$F4 2366
6 TraesCS1D01G414100 chr1A 568644779 568646601 1822 False 1171.000000 1171 78.7020 892 2719 1 chr1A.!!$F1 1827
7 TraesCS1D01G414100 chr1A 568550728 568552484 1756 False 501.000000 566 78.6525 894 2644 2 chr1A.!!$F3 1750
8 TraesCS1D01G414100 chrUn 8485216 8487209 1993 False 1485.000000 1485 80.4380 892 2864 1 chrUn.!!$F2 1972
9 TraesCS1D01G414100 chrUn 8471592 8473394 1802 False 1243.000000 1243 79.5430 892 2690 1 chrUn.!!$F1 1798
10 TraesCS1D01G414100 chr2D 116819590 116820340 750 True 1282.000000 1282 97.6030 2903 3647 1 chr2D.!!$R1 744
11 TraesCS1D01G414100 chr2D 5445162 5445911 749 False 1275.000000 1275 97.4670 2903 3647 1 chr2D.!!$F1 744
12 TraesCS1D01G414100 chr2D 594891165 594891916 751 False 1271.000000 1271 97.3400 2903 3647 1 chr2D.!!$F3 744
13 TraesCS1D01G414100 chr2D 66096722 66097472 750 False 1254.000000 1254 96.9370 2903 3647 1 chr2D.!!$F2 744
14 TraesCS1D01G414100 chr5D 311908155 311908905 750 False 1271.000000 1271 97.3370 2902 3647 1 chr5D.!!$F2 745
15 TraesCS1D01G414100 chr6D 14452849 14453598 749 False 1269.000000 1269 97.3330 2903 3647 1 chr6D.!!$F1 744
16 TraesCS1D01G414100 chr7D 23650946 23651696 750 True 1260.000000 1260 97.0710 2903 3647 1 chr7D.!!$R1 744
17 TraesCS1D01G414100 chr7D 631772499 631773250 751 True 1254.000000 1254 96.9410 2903 3647 1 chr7D.!!$R2 744
18 TraesCS1D01G414100 chr1B 659569611 659571306 1695 True 462.000000 560 77.8010 894 2600 2 chr1B.!!$R1 1706

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
366 367 0.036732 TGGCGTTCTTCTCCAAGCAT 59.963 50.000 0.00 0.0 0.00 3.79 F
467 468 0.317160 CCTACCGGCATCGCTATCAA 59.683 55.000 0.00 0.0 34.56 2.57 F
2035 5020 1.723542 CTCTGCAGCTACAAGTCAACG 59.276 52.381 9.47 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 4851 1.205893 AGATGTCGAAGAAGAGCCACC 59.794 52.381 0.00 0.00 39.69 4.61 R
2120 5105 1.354337 CTTGTGGCCACGTGATCTCG 61.354 60.000 30.07 15.19 0.00 4.04 R
3107 6106 0.116940 ACCGGGACTAAAGGGTGGTA 59.883 55.000 6.32 0.00 0.00 3.25 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
20 21 2.953284 TATAGACCGCCTACAGAGCT 57.047 50.000 0.00 0.00 0.00 4.09
21 22 2.953284 ATAGACCGCCTACAGAGCTA 57.047 50.000 0.00 0.00 0.00 3.32
22 23 2.723322 TAGACCGCCTACAGAGCTAA 57.277 50.000 0.00 0.00 0.00 3.09
23 24 1.848652 AGACCGCCTACAGAGCTAAA 58.151 50.000 0.00 0.00 0.00 1.85
24 25 2.389715 AGACCGCCTACAGAGCTAAAT 58.610 47.619 0.00 0.00 0.00 1.40
25 26 2.101582 AGACCGCCTACAGAGCTAAATG 59.898 50.000 0.00 0.00 0.00 2.32
26 27 2.100916 GACCGCCTACAGAGCTAAATGA 59.899 50.000 0.00 0.00 0.00 2.57
27 28 2.101582 ACCGCCTACAGAGCTAAATGAG 59.898 50.000 0.00 0.00 0.00 2.90
28 29 2.101582 CCGCCTACAGAGCTAAATGAGT 59.898 50.000 0.00 0.00 0.00 3.41
29 30 3.119291 CGCCTACAGAGCTAAATGAGTG 58.881 50.000 0.00 0.00 0.00 3.51
30 31 3.181486 CGCCTACAGAGCTAAATGAGTGA 60.181 47.826 0.00 0.00 0.00 3.41
31 32 4.678044 CGCCTACAGAGCTAAATGAGTGAA 60.678 45.833 0.00 0.00 0.00 3.18
32 33 5.363939 GCCTACAGAGCTAAATGAGTGAAT 58.636 41.667 0.00 0.00 0.00 2.57
33 34 5.465056 GCCTACAGAGCTAAATGAGTGAATC 59.535 44.000 0.00 0.00 0.00 2.52
34 35 6.685116 GCCTACAGAGCTAAATGAGTGAATCT 60.685 42.308 0.00 0.00 0.00 2.40
35 36 7.470702 GCCTACAGAGCTAAATGAGTGAATCTA 60.471 40.741 0.00 0.00 0.00 1.98
36 37 7.865385 CCTACAGAGCTAAATGAGTGAATCTAC 59.135 40.741 0.00 0.00 0.00 2.59
37 38 7.175347 ACAGAGCTAAATGAGTGAATCTACA 57.825 36.000 0.00 0.00 0.00 2.74
38 39 7.038659 ACAGAGCTAAATGAGTGAATCTACAC 58.961 38.462 0.00 0.00 40.60 2.90
52 53 8.958506 AGTGAATCTACACTCTAAAATACGTCT 58.041 33.333 0.00 0.00 46.36 4.18
70 71 9.542462 AATACGTCTATAACATTTGTATGCAGT 57.458 29.630 0.00 0.00 35.03 4.40
71 72 7.843490 ACGTCTATAACATTTGTATGCAGTT 57.157 32.000 0.00 0.00 35.03 3.16
72 73 7.906160 ACGTCTATAACATTTGTATGCAGTTC 58.094 34.615 0.00 0.00 35.03 3.01
73 74 7.057402 CGTCTATAACATTTGTATGCAGTTCG 58.943 38.462 0.00 0.00 35.03 3.95
74 75 7.253983 CGTCTATAACATTTGTATGCAGTTCGT 60.254 37.037 0.00 0.00 35.03 3.85
75 76 9.027129 GTCTATAACATTTGTATGCAGTTCGTA 57.973 33.333 0.00 0.00 35.03 3.43
76 77 9.758651 TCTATAACATTTGTATGCAGTTCGTAT 57.241 29.630 0.00 0.00 35.03 3.06
79 80 5.879237 ACATTTGTATGCAGTTCGTATTGG 58.121 37.500 0.00 0.00 35.03 3.16
80 81 5.645929 ACATTTGTATGCAGTTCGTATTGGA 59.354 36.000 0.00 0.00 35.03 3.53
81 82 6.150307 ACATTTGTATGCAGTTCGTATTGGAA 59.850 34.615 0.00 0.00 35.03 3.53
82 83 6.751514 TTTGTATGCAGTTCGTATTGGAAT 57.248 33.333 0.00 0.00 0.00 3.01
83 84 7.851387 TTTGTATGCAGTTCGTATTGGAATA 57.149 32.000 0.00 0.00 0.00 1.75
84 85 8.445275 TTTGTATGCAGTTCGTATTGGAATAT 57.555 30.769 0.00 0.00 0.00 1.28
85 86 7.652300 TGTATGCAGTTCGTATTGGAATATC 57.348 36.000 0.00 0.00 0.00 1.63
86 87 7.441836 TGTATGCAGTTCGTATTGGAATATCT 58.558 34.615 0.00 0.00 0.00 1.98
87 88 8.581578 TGTATGCAGTTCGTATTGGAATATCTA 58.418 33.333 0.00 0.00 0.00 1.98
88 89 9.419297 GTATGCAGTTCGTATTGGAATATCTAA 57.581 33.333 0.00 0.00 0.00 2.10
89 90 8.902540 ATGCAGTTCGTATTGGAATATCTAAA 57.097 30.769 0.00 0.00 0.00 1.85
90 91 8.725405 TGCAGTTCGTATTGGAATATCTAAAA 57.275 30.769 0.00 0.00 0.00 1.52
91 92 8.609176 TGCAGTTCGTATTGGAATATCTAAAAC 58.391 33.333 0.00 0.00 0.00 2.43
92 93 7.792508 GCAGTTCGTATTGGAATATCTAAAACG 59.207 37.037 0.00 0.00 0.00 3.60
93 94 9.027129 CAGTTCGTATTGGAATATCTAAAACGA 57.973 33.333 0.00 0.00 0.00 3.85
94 95 9.028185 AGTTCGTATTGGAATATCTAAAACGAC 57.972 33.333 0.00 0.00 0.00 4.34
95 96 9.028185 GTTCGTATTGGAATATCTAAAACGACT 57.972 33.333 0.00 0.00 0.00 4.18
96 97 9.590451 TTCGTATTGGAATATCTAAAACGACTT 57.410 29.630 0.00 0.00 0.00 3.01
110 111 9.595823 TCTAAAACGACTTATTTAGGAATGGAG 57.404 33.333 0.00 0.00 38.85 3.86
111 112 9.595823 CTAAAACGACTTATTTAGGAATGGAGA 57.404 33.333 0.00 0.00 36.12 3.71
112 113 8.494016 AAAACGACTTATTTAGGAATGGAGAG 57.506 34.615 0.00 0.00 0.00 3.20
113 114 7.419711 AACGACTTATTTAGGAATGGAGAGA 57.580 36.000 0.00 0.00 0.00 3.10
114 115 7.045126 ACGACTTATTTAGGAATGGAGAGAG 57.955 40.000 0.00 0.00 0.00 3.20
115 116 6.608002 ACGACTTATTTAGGAATGGAGAGAGT 59.392 38.462 0.00 0.00 0.00 3.24
116 117 7.778853 ACGACTTATTTAGGAATGGAGAGAGTA 59.221 37.037 0.00 0.00 0.00 2.59
117 118 8.293867 CGACTTATTTAGGAATGGAGAGAGTAG 58.706 40.741 0.00 0.00 0.00 2.57
118 119 7.958088 ACTTATTTAGGAATGGAGAGAGTAGC 58.042 38.462 0.00 0.00 0.00 3.58
119 120 7.565398 ACTTATTTAGGAATGGAGAGAGTAGCA 59.435 37.037 0.00 0.00 0.00 3.49
120 121 8.497910 TTATTTAGGAATGGAGAGAGTAGCAT 57.502 34.615 0.00 0.00 0.00 3.79
121 122 9.601810 TTATTTAGGAATGGAGAGAGTAGCATA 57.398 33.333 0.00 0.00 0.00 3.14
122 123 7.531857 TTTAGGAATGGAGAGAGTAGCATAG 57.468 40.000 0.00 0.00 0.00 2.23
123 124 5.073437 AGGAATGGAGAGAGTAGCATAGT 57.927 43.478 0.00 0.00 0.00 2.12
124 125 5.076873 AGGAATGGAGAGAGTAGCATAGTC 58.923 45.833 0.00 0.00 41.38 2.59
125 126 4.830046 GGAATGGAGAGAGTAGCATAGTCA 59.170 45.833 0.00 0.00 43.52 3.41
126 127 5.480073 GGAATGGAGAGAGTAGCATAGTCAT 59.520 44.000 0.00 0.00 43.52 3.06
127 128 6.014669 GGAATGGAGAGAGTAGCATAGTCATT 60.015 42.308 0.00 0.00 43.52 2.57
128 129 6.992664 ATGGAGAGAGTAGCATAGTCATTT 57.007 37.500 0.00 0.00 43.52 2.32
129 130 6.398234 TGGAGAGAGTAGCATAGTCATTTC 57.602 41.667 0.00 0.00 43.52 2.17
130 131 5.893824 TGGAGAGAGTAGCATAGTCATTTCA 59.106 40.000 0.00 0.00 43.52 2.69
131 132 6.183360 TGGAGAGAGTAGCATAGTCATTTCAC 60.183 42.308 0.00 0.00 43.52 3.18
132 133 6.040391 GGAGAGAGTAGCATAGTCATTTCACT 59.960 42.308 0.00 0.00 43.52 3.41
133 134 7.229707 GGAGAGAGTAGCATAGTCATTTCACTA 59.770 40.741 0.00 0.00 43.52 2.74
134 135 8.704849 AGAGAGTAGCATAGTCATTTCACTAT 57.295 34.615 0.00 0.00 43.52 2.12
143 144 7.697691 CATAGTCATTTCACTATGGTCAAACC 58.302 38.462 11.31 0.00 46.95 3.27
144 145 5.010282 AGTCATTTCACTATGGTCAAACCC 58.990 41.667 0.00 0.00 37.50 4.11
145 146 4.006989 TCATTTCACTATGGTCAAACCCG 58.993 43.478 0.00 0.00 37.50 5.28
146 147 3.495434 TTTCACTATGGTCAAACCCGT 57.505 42.857 0.00 0.00 37.50 5.28
147 148 2.754946 TCACTATGGTCAAACCCGTC 57.245 50.000 0.00 0.00 37.50 4.79
148 149 1.067425 TCACTATGGTCAAACCCGTCG 60.067 52.381 0.00 0.00 37.50 5.12
149 150 1.067425 CACTATGGTCAAACCCGTCGA 60.067 52.381 0.00 0.00 37.50 4.20
150 151 1.203994 ACTATGGTCAAACCCGTCGAG 59.796 52.381 0.00 0.00 37.50 4.04
151 152 1.203994 CTATGGTCAAACCCGTCGAGT 59.796 52.381 0.00 0.00 37.50 4.18
152 153 0.395312 ATGGTCAAACCCGTCGAGTT 59.605 50.000 0.00 0.00 37.50 3.01
153 154 0.178533 TGGTCAAACCCGTCGAGTTT 59.821 50.000 0.00 0.00 37.50 2.66
154 155 1.302366 GGTCAAACCCGTCGAGTTTT 58.698 50.000 1.71 0.00 35.28 2.43
155 156 1.003223 GGTCAAACCCGTCGAGTTTTG 60.003 52.381 1.71 4.79 35.28 2.44
156 157 1.667212 GTCAAACCCGTCGAGTTTTGT 59.333 47.619 1.71 0.00 35.28 2.83
157 158 1.935199 TCAAACCCGTCGAGTTTTGTC 59.065 47.619 1.71 0.00 35.28 3.18
158 159 1.666700 CAAACCCGTCGAGTTTTGTCA 59.333 47.619 1.71 0.00 35.28 3.58
159 160 2.249844 AACCCGTCGAGTTTTGTCAT 57.750 45.000 0.00 0.00 0.00 3.06
160 161 3.389925 AACCCGTCGAGTTTTGTCATA 57.610 42.857 0.00 0.00 0.00 2.15
161 162 3.604875 ACCCGTCGAGTTTTGTCATAT 57.395 42.857 0.00 0.00 0.00 1.78
162 163 4.724074 ACCCGTCGAGTTTTGTCATATA 57.276 40.909 0.00 0.00 0.00 0.86
163 164 5.272283 ACCCGTCGAGTTTTGTCATATAT 57.728 39.130 0.00 0.00 0.00 0.86
164 165 5.667466 ACCCGTCGAGTTTTGTCATATATT 58.333 37.500 0.00 0.00 0.00 1.28
165 166 6.808829 ACCCGTCGAGTTTTGTCATATATTA 58.191 36.000 0.00 0.00 0.00 0.98
166 167 7.439381 ACCCGTCGAGTTTTGTCATATATTAT 58.561 34.615 0.00 0.00 0.00 1.28
167 168 8.579006 ACCCGTCGAGTTTTGTCATATATTATA 58.421 33.333 0.00 0.00 0.00 0.98
168 169 9.582431 CCCGTCGAGTTTTGTCATATATTATAT 57.418 33.333 0.00 0.00 0.00 0.86
190 191 4.833478 AGTGATGAGAACACTATTGCCT 57.167 40.909 0.00 0.00 45.10 4.75
191 192 5.171339 AGTGATGAGAACACTATTGCCTT 57.829 39.130 0.00 0.00 45.10 4.35
192 193 6.299805 AGTGATGAGAACACTATTGCCTTA 57.700 37.500 0.00 0.00 45.10 2.69
193 194 6.344500 AGTGATGAGAACACTATTGCCTTAG 58.656 40.000 0.00 0.00 45.10 2.18
194 195 6.070538 AGTGATGAGAACACTATTGCCTTAGT 60.071 38.462 0.00 0.00 45.10 2.24
195 196 6.595716 GTGATGAGAACACTATTGCCTTAGTT 59.404 38.462 0.00 0.00 35.66 2.24
196 197 7.119846 GTGATGAGAACACTATTGCCTTAGTTT 59.880 37.037 0.00 0.00 35.66 2.66
197 198 7.665559 TGATGAGAACACTATTGCCTTAGTTTT 59.334 33.333 0.00 0.00 29.93 2.43
198 199 7.202016 TGAGAACACTATTGCCTTAGTTTTG 57.798 36.000 0.76 0.00 29.93 2.44
199 200 6.995686 TGAGAACACTATTGCCTTAGTTTTGA 59.004 34.615 0.76 0.00 29.93 2.69
200 201 7.665559 TGAGAACACTATTGCCTTAGTTTTGAT 59.334 33.333 0.76 0.00 29.93 2.57
201 202 8.409358 AGAACACTATTGCCTTAGTTTTGATT 57.591 30.769 0.76 0.00 29.93 2.57
202 203 8.299570 AGAACACTATTGCCTTAGTTTTGATTG 58.700 33.333 0.76 0.00 29.93 2.67
203 204 6.924111 ACACTATTGCCTTAGTTTTGATTGG 58.076 36.000 0.00 0.00 29.93 3.16
204 205 5.807011 CACTATTGCCTTAGTTTTGATTGGC 59.193 40.000 0.00 0.00 40.62 4.52
207 208 4.191033 TGCCTTAGTTTTGATTGGCATG 57.809 40.909 0.00 0.00 44.35 4.06
208 209 3.831333 TGCCTTAGTTTTGATTGGCATGA 59.169 39.130 0.00 0.00 44.35 3.07
209 210 4.467082 TGCCTTAGTTTTGATTGGCATGAT 59.533 37.500 0.00 0.00 44.35 2.45
210 211 4.807304 GCCTTAGTTTTGATTGGCATGATG 59.193 41.667 0.00 0.00 40.04 3.07
211 212 4.807304 CCTTAGTTTTGATTGGCATGATGC 59.193 41.667 9.33 9.33 44.08 3.91
233 234 7.138692 TGCATTTTGGCAATGGTATTAAAAC 57.861 32.000 0.00 0.00 41.65 2.43
234 235 6.712095 TGCATTTTGGCAATGGTATTAAAACA 59.288 30.769 0.00 0.00 41.65 2.83
235 236 7.392673 TGCATTTTGGCAATGGTATTAAAACAT 59.607 29.630 0.00 0.00 41.65 2.71
236 237 8.242739 GCATTTTGGCAATGGTATTAAAACATT 58.757 29.630 0.00 0.00 35.36 2.71
240 241 7.913674 TGGCAATGGTATTAAAACATTTTCC 57.086 32.000 0.00 0.00 32.89 3.13
241 242 6.881602 TGGCAATGGTATTAAAACATTTTCCC 59.118 34.615 0.00 0.00 32.89 3.97
242 243 6.881602 GGCAATGGTATTAAAACATTTTCCCA 59.118 34.615 0.00 0.00 32.89 4.37
243 244 7.391833 GGCAATGGTATTAAAACATTTTCCCAA 59.608 33.333 0.00 0.00 32.89 4.12
244 245 8.955388 GCAATGGTATTAAAACATTTTCCCAAT 58.045 29.630 0.00 0.00 32.89 3.16
257 258 9.454859 AACATTTTCCCAATAAAAACTTGTTCA 57.545 25.926 0.00 0.00 29.45 3.18
258 259 8.888716 ACATTTTCCCAATAAAAACTTGTTCAC 58.111 29.630 0.00 0.00 32.42 3.18
259 260 9.108284 CATTTTCCCAATAAAAACTTGTTCACT 57.892 29.630 0.00 0.00 32.42 3.41
299 300 6.490040 ACAATTAGGTCAATATACACCATGGC 59.510 38.462 13.04 0.00 34.80 4.40
301 302 2.108250 AGGTCAATATACACCATGGCCC 59.892 50.000 13.04 0.00 38.32 5.80
303 304 1.073125 TCAATATACACCATGGCCCGG 59.927 52.381 13.04 2.83 0.00 5.73
309 310 1.076777 CACCATGGCCCGGAATTCT 60.077 57.895 13.04 0.00 0.00 2.40
311 312 0.182775 ACCATGGCCCGGAATTCTAC 59.817 55.000 13.04 0.00 0.00 2.59
315 316 2.818751 TGGCCCGGAATTCTACAAAT 57.181 45.000 0.73 0.00 0.00 2.32
330 331 9.668497 AATTCTACAAATTCTACTACCCAAGAC 57.332 33.333 0.00 0.00 0.00 3.01
337 338 4.048970 TCTACTACCCAAGACTGCTCTT 57.951 45.455 0.00 0.00 37.19 2.85
345 346 2.538437 CAAGACTGCTCTTCCGATGAG 58.462 52.381 6.88 6.88 34.20 2.90
346 347 1.846007 AGACTGCTCTTCCGATGAGT 58.154 50.000 11.75 0.00 34.30 3.41
358 359 1.673033 CCGATGAGTTGGCGTTCTTCT 60.673 52.381 0.00 0.00 0.00 2.85
366 367 0.036732 TGGCGTTCTTCTCCAAGCAT 59.963 50.000 0.00 0.00 0.00 3.79
369 370 1.806542 GCGTTCTTCTCCAAGCATGAA 59.193 47.619 0.00 0.00 0.00 2.57
372 373 2.751806 GTTCTTCTCCAAGCATGAAGGG 59.248 50.000 0.00 0.00 38.10 3.95
375 376 0.549902 TCTCCAAGCATGAAGGGGGA 60.550 55.000 0.00 0.00 0.00 4.81
376 377 0.554792 CTCCAAGCATGAAGGGGGAT 59.445 55.000 0.00 0.00 0.00 3.85
377 378 1.009997 TCCAAGCATGAAGGGGGATT 58.990 50.000 0.00 0.00 0.00 3.01
379 380 1.117150 CAAGCATGAAGGGGGATTGG 58.883 55.000 0.00 0.00 0.00 3.16
466 467 1.964448 CCTACCGGCATCGCTATCA 59.036 57.895 0.00 0.00 34.56 2.15
467 468 0.317160 CCTACCGGCATCGCTATCAA 59.683 55.000 0.00 0.00 34.56 2.57
491 492 3.136443 ACCATCCTTTGATCCGCTTCATA 59.864 43.478 0.00 0.00 0.00 2.15
707 3455 4.250116 AGTTGCTGCCGATTATAGAGAG 57.750 45.455 0.00 0.00 0.00 3.20
788 3536 2.300433 GCCTACATCACCATGCAATCA 58.700 47.619 0.00 0.00 32.57 2.57
789 3537 2.889045 GCCTACATCACCATGCAATCAT 59.111 45.455 0.00 0.00 32.57 2.45
790 3538 4.074259 GCCTACATCACCATGCAATCATA 58.926 43.478 0.00 0.00 32.57 2.15
791 3539 4.703575 GCCTACATCACCATGCAATCATAT 59.296 41.667 0.00 0.00 32.57 1.78
822 3570 7.141758 ACATCCATCTGAATATACCAACTGT 57.858 36.000 0.00 0.00 0.00 3.55
1532 4322 2.689983 CCATCCCAGGTTTCAGTTATGC 59.310 50.000 0.00 0.00 0.00 3.14
1541 4331 5.008019 CAGGTTTCAGTTATGCGCAGATTAT 59.992 40.000 18.32 0.00 0.00 1.28
1559 4349 7.916977 GCAGATTATTTGTCATCAAGTGCATTA 59.083 33.333 0.00 0.00 34.88 1.90
1702 4507 3.300388 AGGGAGATCGCTTCTTACATGA 58.700 45.455 0.00 0.00 35.46 3.07
1884 4851 2.325082 CCACGCAAGGAGAAACCCG 61.325 63.158 0.00 0.00 46.39 5.28
2035 5020 1.723542 CTCTGCAGCTACAAGTCAACG 59.276 52.381 9.47 0.00 0.00 4.10
2037 5022 2.029020 TCTGCAGCTACAAGTCAACGAT 60.029 45.455 9.47 0.00 0.00 3.73
2836 5834 6.561294 TGGAATTTCCTTTGTTTCCTCCTAT 58.439 36.000 16.25 0.00 38.73 2.57
2877 5875 1.957177 TGTTGCTAATTTTGCACGGGA 59.043 42.857 4.99 0.00 40.40 5.14
3045 6044 2.034999 GGCATTGGTCCCGGTTCA 59.965 61.111 0.00 0.00 0.00 3.18
3139 6138 2.307686 AGTCCCGGTTCATACCACAAAT 59.692 45.455 0.00 0.00 45.31 2.32
3258 6257 9.295825 TCTGCCTTTTAAAGTGAAAATAGATGA 57.704 29.630 3.91 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.443145 AGCTCTGTAGGCGGTCTATAT 57.557 47.619 0.00 0.00 34.52 0.86
1 2 2.953284 AGCTCTGTAGGCGGTCTATA 57.047 50.000 0.00 0.00 34.52 1.31
2 3 2.953284 TAGCTCTGTAGGCGGTCTAT 57.047 50.000 0.00 0.00 34.52 1.98
3 4 2.723322 TTAGCTCTGTAGGCGGTCTA 57.277 50.000 0.00 0.00 34.52 2.59
4 5 1.848652 TTTAGCTCTGTAGGCGGTCT 58.151 50.000 0.00 0.00 34.52 3.85
5 6 2.100916 TCATTTAGCTCTGTAGGCGGTC 59.899 50.000 0.00 0.00 34.52 4.79
6 7 2.101582 CTCATTTAGCTCTGTAGGCGGT 59.898 50.000 0.00 0.00 34.52 5.68
7 8 2.101582 ACTCATTTAGCTCTGTAGGCGG 59.898 50.000 0.00 0.00 34.52 6.13
8 9 3.119291 CACTCATTTAGCTCTGTAGGCG 58.881 50.000 0.00 0.00 34.52 5.52
9 10 4.392921 TCACTCATTTAGCTCTGTAGGC 57.607 45.455 0.00 0.00 0.00 3.93
10 11 6.815089 AGATTCACTCATTTAGCTCTGTAGG 58.185 40.000 0.00 0.00 0.00 3.18
11 12 8.409371 TGTAGATTCACTCATTTAGCTCTGTAG 58.591 37.037 0.00 0.00 0.00 2.74
12 13 8.191446 GTGTAGATTCACTCATTTAGCTCTGTA 58.809 37.037 0.00 0.00 35.68 2.74
13 14 7.038659 GTGTAGATTCACTCATTTAGCTCTGT 58.961 38.462 0.00 0.00 35.68 3.41
14 15 7.264221 AGTGTAGATTCACTCATTTAGCTCTG 58.736 38.462 0.00 0.00 44.07 3.35
15 16 7.416964 AGTGTAGATTCACTCATTTAGCTCT 57.583 36.000 0.00 0.00 44.07 4.09
44 45 9.542462 ACTGCATACAAATGTTATAGACGTATT 57.458 29.630 0.00 0.00 35.38 1.89
45 46 9.542462 AACTGCATACAAATGTTATAGACGTAT 57.458 29.630 0.00 0.00 35.38 3.06
46 47 8.936070 AACTGCATACAAATGTTATAGACGTA 57.064 30.769 0.00 0.00 35.38 3.57
47 48 7.253983 CGAACTGCATACAAATGTTATAGACGT 60.254 37.037 0.00 0.00 35.38 4.34
48 49 7.057402 CGAACTGCATACAAATGTTATAGACG 58.943 38.462 0.00 0.00 35.38 4.18
49 50 7.906160 ACGAACTGCATACAAATGTTATAGAC 58.094 34.615 0.00 0.00 35.38 2.59
50 51 9.758651 ATACGAACTGCATACAAATGTTATAGA 57.241 29.630 0.00 0.00 35.38 1.98
53 54 8.128582 CCAATACGAACTGCATACAAATGTTAT 58.871 33.333 0.00 0.00 35.38 1.89
54 55 7.334671 TCCAATACGAACTGCATACAAATGTTA 59.665 33.333 0.00 0.00 35.38 2.41
55 56 6.150307 TCCAATACGAACTGCATACAAATGTT 59.850 34.615 0.00 0.00 35.38 2.71
56 57 5.645929 TCCAATACGAACTGCATACAAATGT 59.354 36.000 0.00 0.00 35.38 2.71
57 58 6.117911 TCCAATACGAACTGCATACAAATG 57.882 37.500 0.00 0.00 36.09 2.32
58 59 6.751514 TTCCAATACGAACTGCATACAAAT 57.248 33.333 0.00 0.00 0.00 2.32
59 60 6.751514 ATTCCAATACGAACTGCATACAAA 57.248 33.333 0.00 0.00 0.00 2.83
60 61 7.931407 AGATATTCCAATACGAACTGCATACAA 59.069 33.333 0.00 0.00 0.00 2.41
61 62 7.441836 AGATATTCCAATACGAACTGCATACA 58.558 34.615 0.00 0.00 0.00 2.29
62 63 7.891183 AGATATTCCAATACGAACTGCATAC 57.109 36.000 0.00 0.00 0.00 2.39
63 64 9.990360 TTTAGATATTCCAATACGAACTGCATA 57.010 29.630 0.00 0.00 0.00 3.14
64 65 8.902540 TTTAGATATTCCAATACGAACTGCAT 57.097 30.769 0.00 0.00 0.00 3.96
65 66 8.609176 GTTTTAGATATTCCAATACGAACTGCA 58.391 33.333 0.00 0.00 0.00 4.41
66 67 7.792508 CGTTTTAGATATTCCAATACGAACTGC 59.207 37.037 0.00 0.00 31.18 4.40
67 68 9.027129 TCGTTTTAGATATTCCAATACGAACTG 57.973 33.333 0.00 0.00 34.35 3.16
68 69 9.028185 GTCGTTTTAGATATTCCAATACGAACT 57.972 33.333 0.00 0.00 37.37 3.01
69 70 9.028185 AGTCGTTTTAGATATTCCAATACGAAC 57.972 33.333 0.00 0.00 37.37 3.95
70 71 9.590451 AAGTCGTTTTAGATATTCCAATACGAA 57.410 29.630 0.00 0.00 37.37 3.85
84 85 9.595823 CTCCATTCCTAAATAAGTCGTTTTAGA 57.404 33.333 4.45 0.00 37.53 2.10
85 86 9.595823 TCTCCATTCCTAAATAAGTCGTTTTAG 57.404 33.333 0.00 0.00 35.92 1.85
86 87 9.595823 CTCTCCATTCCTAAATAAGTCGTTTTA 57.404 33.333 0.00 0.00 0.00 1.52
87 88 8.319146 TCTCTCCATTCCTAAATAAGTCGTTTT 58.681 33.333 0.00 0.00 0.00 2.43
88 89 7.848128 TCTCTCCATTCCTAAATAAGTCGTTT 58.152 34.615 0.00 0.00 0.00 3.60
89 90 7.124448 ACTCTCTCCATTCCTAAATAAGTCGTT 59.876 37.037 0.00 0.00 0.00 3.85
90 91 6.608002 ACTCTCTCCATTCCTAAATAAGTCGT 59.392 38.462 0.00 0.00 0.00 4.34
91 92 7.045126 ACTCTCTCCATTCCTAAATAAGTCG 57.955 40.000 0.00 0.00 0.00 4.18
92 93 8.085909 GCTACTCTCTCCATTCCTAAATAAGTC 58.914 40.741 0.00 0.00 0.00 3.01
93 94 7.565398 TGCTACTCTCTCCATTCCTAAATAAGT 59.435 37.037 0.00 0.00 0.00 2.24
94 95 7.957002 TGCTACTCTCTCCATTCCTAAATAAG 58.043 38.462 0.00 0.00 0.00 1.73
95 96 7.914427 TGCTACTCTCTCCATTCCTAAATAA 57.086 36.000 0.00 0.00 0.00 1.40
96 97 9.249053 CTATGCTACTCTCTCCATTCCTAAATA 57.751 37.037 0.00 0.00 0.00 1.40
97 98 7.732593 ACTATGCTACTCTCTCCATTCCTAAAT 59.267 37.037 0.00 0.00 0.00 1.40
98 99 7.069986 ACTATGCTACTCTCTCCATTCCTAAA 58.930 38.462 0.00 0.00 0.00 1.85
99 100 6.615617 ACTATGCTACTCTCTCCATTCCTAA 58.384 40.000 0.00 0.00 0.00 2.69
100 101 6.183361 TGACTATGCTACTCTCTCCATTCCTA 60.183 42.308 0.00 0.00 0.00 2.94
101 102 5.073437 ACTATGCTACTCTCTCCATTCCT 57.927 43.478 0.00 0.00 0.00 3.36
102 103 4.830046 TGACTATGCTACTCTCTCCATTCC 59.170 45.833 0.00 0.00 0.00 3.01
103 104 6.588719 ATGACTATGCTACTCTCTCCATTC 57.411 41.667 0.00 0.00 0.00 2.67
104 105 6.992664 AATGACTATGCTACTCTCTCCATT 57.007 37.500 0.00 0.00 0.00 3.16
105 106 6.552725 TGAAATGACTATGCTACTCTCTCCAT 59.447 38.462 0.00 0.00 0.00 3.41
106 107 5.893824 TGAAATGACTATGCTACTCTCTCCA 59.106 40.000 0.00 0.00 0.00 3.86
107 108 6.040391 AGTGAAATGACTATGCTACTCTCTCC 59.960 42.308 0.00 0.00 0.00 3.71
108 109 7.038154 AGTGAAATGACTATGCTACTCTCTC 57.962 40.000 0.00 0.00 0.00 3.20
109 110 8.575589 CATAGTGAAATGACTATGCTACTCTCT 58.424 37.037 7.02 0.00 45.42 3.10
110 111 8.741101 CATAGTGAAATGACTATGCTACTCTC 57.259 38.462 7.02 0.00 45.42 3.20
119 120 6.828785 GGGTTTGACCATAGTGAAATGACTAT 59.171 38.462 0.00 0.00 41.02 2.12
120 121 6.177610 GGGTTTGACCATAGTGAAATGACTA 58.822 40.000 0.00 0.00 41.02 2.59
121 122 5.010282 GGGTTTGACCATAGTGAAATGACT 58.990 41.667 0.00 0.00 41.02 3.41
122 123 4.142687 CGGGTTTGACCATAGTGAAATGAC 60.143 45.833 0.00 0.00 41.02 3.06
123 124 4.006989 CGGGTTTGACCATAGTGAAATGA 58.993 43.478 0.00 0.00 41.02 2.57
124 125 3.756434 ACGGGTTTGACCATAGTGAAATG 59.244 43.478 0.00 0.00 41.02 2.32
125 126 4.007659 GACGGGTTTGACCATAGTGAAAT 58.992 43.478 0.00 0.00 41.02 2.17
126 127 3.404899 GACGGGTTTGACCATAGTGAAA 58.595 45.455 0.00 0.00 41.02 2.69
127 128 2.610976 CGACGGGTTTGACCATAGTGAA 60.611 50.000 0.00 0.00 41.02 3.18
128 129 1.067425 CGACGGGTTTGACCATAGTGA 60.067 52.381 0.00 0.00 41.02 3.41
129 130 1.067425 TCGACGGGTTTGACCATAGTG 60.067 52.381 0.00 0.00 41.02 2.74
130 131 1.203994 CTCGACGGGTTTGACCATAGT 59.796 52.381 0.00 0.00 41.02 2.12
131 132 1.203994 ACTCGACGGGTTTGACCATAG 59.796 52.381 0.00 0.00 41.02 2.23
132 133 1.259609 ACTCGACGGGTTTGACCATA 58.740 50.000 0.00 0.00 41.02 2.74
133 134 0.395312 AACTCGACGGGTTTGACCAT 59.605 50.000 7.44 0.00 41.02 3.55
134 135 0.178533 AAACTCGACGGGTTTGACCA 59.821 50.000 24.34 0.00 41.02 4.02
135 136 1.003223 CAAAACTCGACGGGTTTGACC 60.003 52.381 25.51 0.00 37.05 4.02
136 137 1.667212 ACAAAACTCGACGGGTTTGAC 59.333 47.619 25.51 0.00 37.05 3.18
137 138 1.935199 GACAAAACTCGACGGGTTTGA 59.065 47.619 25.51 0.00 37.05 2.69
138 139 1.666700 TGACAAAACTCGACGGGTTTG 59.333 47.619 25.51 21.67 37.05 2.93
139 140 2.027003 TGACAAAACTCGACGGGTTT 57.973 45.000 19.90 19.90 38.35 3.27
140 141 2.249844 ATGACAAAACTCGACGGGTT 57.750 45.000 7.44 7.44 0.00 4.11
141 142 3.604875 ATATGACAAAACTCGACGGGT 57.395 42.857 0.00 0.00 0.00 5.28
142 143 7.884816 ATAATATATGACAAAACTCGACGGG 57.115 36.000 0.00 0.00 0.00 5.28
169 170 4.833478 AGGCAATAGTGTTCTCATCACT 57.167 40.909 4.11 4.11 46.10 3.41
170 171 6.109359 ACTAAGGCAATAGTGTTCTCATCAC 58.891 40.000 2.63 0.00 34.86 3.06
171 172 6.299805 ACTAAGGCAATAGTGTTCTCATCA 57.700 37.500 2.63 0.00 34.86 3.07
172 173 7.617041 AAACTAAGGCAATAGTGTTCTCATC 57.383 36.000 4.08 0.00 36.28 2.92
173 174 7.665559 TCAAAACTAAGGCAATAGTGTTCTCAT 59.334 33.333 4.08 0.00 36.28 2.90
174 175 6.995686 TCAAAACTAAGGCAATAGTGTTCTCA 59.004 34.615 4.08 0.00 36.28 3.27
175 176 7.435068 TCAAAACTAAGGCAATAGTGTTCTC 57.565 36.000 4.08 0.00 36.28 2.87
176 177 8.299570 CAATCAAAACTAAGGCAATAGTGTTCT 58.700 33.333 4.08 0.00 36.28 3.01
177 178 7.542130 CCAATCAAAACTAAGGCAATAGTGTTC 59.458 37.037 4.08 0.00 36.28 3.18
178 179 7.378181 CCAATCAAAACTAAGGCAATAGTGTT 58.622 34.615 4.08 2.64 36.28 3.32
179 180 6.572314 GCCAATCAAAACTAAGGCAATAGTGT 60.572 38.462 4.08 0.00 41.63 3.55
180 181 5.807011 GCCAATCAAAACTAAGGCAATAGTG 59.193 40.000 4.08 0.00 41.63 2.74
181 182 5.965922 GCCAATCAAAACTAAGGCAATAGT 58.034 37.500 0.00 0.00 41.63 2.12
187 188 4.454728 TCATGCCAATCAAAACTAAGGC 57.545 40.909 0.00 0.00 42.32 4.35
188 189 4.807304 GCATCATGCCAATCAAAACTAAGG 59.193 41.667 0.00 0.00 37.42 2.69
189 190 5.412640 TGCATCATGCCAATCAAAACTAAG 58.587 37.500 7.30 0.00 44.23 2.18
190 191 5.402997 TGCATCATGCCAATCAAAACTAA 57.597 34.783 7.30 0.00 44.23 2.24
191 192 5.601583 ATGCATCATGCCAATCAAAACTA 57.398 34.783 7.30 0.00 44.23 2.24
192 193 3.965379 TGCATCATGCCAATCAAAACT 57.035 38.095 7.30 0.00 44.23 2.66
193 194 5.554822 AAATGCATCATGCCAATCAAAAC 57.445 34.783 7.30 0.00 44.23 2.43
194 195 5.106118 CCAAAATGCATCATGCCAATCAAAA 60.106 36.000 7.30 0.00 44.23 2.44
195 196 4.396478 CCAAAATGCATCATGCCAATCAAA 59.604 37.500 7.30 0.00 44.23 2.69
196 197 3.942115 CCAAAATGCATCATGCCAATCAA 59.058 39.130 7.30 0.00 44.23 2.57
197 198 3.536570 CCAAAATGCATCATGCCAATCA 58.463 40.909 7.30 0.00 44.23 2.57
198 199 2.289547 GCCAAAATGCATCATGCCAATC 59.710 45.455 7.30 0.00 44.23 2.67
199 200 2.294074 GCCAAAATGCATCATGCCAAT 58.706 42.857 7.30 0.00 44.23 3.16
200 201 1.003233 TGCCAAAATGCATCATGCCAA 59.997 42.857 7.30 0.00 44.23 4.52
201 202 0.613777 TGCCAAAATGCATCATGCCA 59.386 45.000 7.30 0.00 44.23 4.92
202 203 1.740297 TTGCCAAAATGCATCATGCC 58.260 45.000 7.30 0.00 44.23 4.40
203 204 2.032799 CCATTGCCAAAATGCATCATGC 59.967 45.455 1.35 1.35 45.29 4.06
204 205 3.275143 ACCATTGCCAAAATGCATCATG 58.725 40.909 0.00 1.83 41.70 3.07
205 206 3.637911 ACCATTGCCAAAATGCATCAT 57.362 38.095 0.00 0.00 41.70 2.45
206 207 4.757019 ATACCATTGCCAAAATGCATCA 57.243 36.364 0.00 0.00 41.70 3.07
207 208 7.551035 TTTAATACCATTGCCAAAATGCATC 57.449 32.000 0.00 0.00 41.70 3.91
208 209 7.392673 TGTTTTAATACCATTGCCAAAATGCAT 59.607 29.630 0.00 0.00 41.70 3.96
209 210 6.712095 TGTTTTAATACCATTGCCAAAATGCA 59.288 30.769 0.00 0.00 40.07 3.96
210 211 7.138692 TGTTTTAATACCATTGCCAAAATGC 57.861 32.000 0.00 0.00 0.00 3.56
214 215 8.787852 GGAAAATGTTTTAATACCATTGCCAAA 58.212 29.630 4.19 0.00 30.38 3.28
215 216 7.391833 GGGAAAATGTTTTAATACCATTGCCAA 59.608 33.333 8.96 0.00 31.01 4.52
216 217 6.881602 GGGAAAATGTTTTAATACCATTGCCA 59.118 34.615 8.96 0.00 31.01 4.92
217 218 6.881602 TGGGAAAATGTTTTAATACCATTGCC 59.118 34.615 8.19 8.19 0.00 4.52
218 219 7.913674 TGGGAAAATGTTTTAATACCATTGC 57.086 32.000 0.00 0.00 0.00 3.56
231 232 9.454859 TGAACAAGTTTTTATTGGGAAAATGTT 57.545 25.926 0.00 0.00 34.47 2.71
232 233 8.888716 GTGAACAAGTTTTTATTGGGAAAATGT 58.111 29.630 0.00 0.00 31.76 2.71
233 234 9.108284 AGTGAACAAGTTTTTATTGGGAAAATG 57.892 29.630 0.00 0.00 31.76 2.32
272 273 7.719193 CCATGGTGTATATTGACCTAATTGTCA 59.281 37.037 2.57 0.00 43.26 3.58
273 274 7.308589 GCCATGGTGTATATTGACCTAATTGTC 60.309 40.741 14.67 0.00 35.77 3.18
274 275 6.490040 GCCATGGTGTATATTGACCTAATTGT 59.510 38.462 14.67 0.00 32.98 2.71
275 276 6.071952 GGCCATGGTGTATATTGACCTAATTG 60.072 42.308 14.67 0.00 32.98 2.32
276 277 6.010219 GGCCATGGTGTATATTGACCTAATT 58.990 40.000 14.67 0.00 32.98 1.40
287 288 1.440618 ATTCCGGGCCATGGTGTATA 58.559 50.000 14.67 0.00 0.00 1.47
289 290 0.106918 GAATTCCGGGCCATGGTGTA 60.107 55.000 14.67 0.00 0.00 2.90
294 295 2.051334 TTGTAGAATTCCGGGCCATG 57.949 50.000 4.39 0.00 0.00 3.66
299 300 6.704937 GGTAGTAGAATTTGTAGAATTCCGGG 59.295 42.308 0.00 0.00 37.36 5.73
301 302 7.270047 TGGGTAGTAGAATTTGTAGAATTCCG 58.730 38.462 0.65 0.00 37.36 4.30
303 304 9.886132 TCTTGGGTAGTAGAATTTGTAGAATTC 57.114 33.333 0.00 0.00 37.01 2.17
309 310 6.212791 AGCAGTCTTGGGTAGTAGAATTTGTA 59.787 38.462 0.00 0.00 0.00 2.41
311 312 5.491982 AGCAGTCTTGGGTAGTAGAATTTG 58.508 41.667 0.00 0.00 0.00 2.32
315 316 4.048970 AGAGCAGTCTTGGGTAGTAGAA 57.951 45.455 0.00 0.00 0.00 2.10
337 338 0.320374 AAGAACGCCAACTCATCGGA 59.680 50.000 0.00 0.00 0.00 4.55
358 359 1.009997 AATCCCCCTTCATGCTTGGA 58.990 50.000 0.00 0.00 0.00 3.53
366 367 1.529744 GATACCCCAATCCCCCTTCA 58.470 55.000 0.00 0.00 0.00 3.02
369 370 4.794274 GGATACCCCAATCCCCCT 57.206 61.111 0.00 0.00 39.74 4.79
390 391 0.796927 GCCACAAGGAGAGCGTTAAC 59.203 55.000 0.00 0.00 36.89 2.01
392 393 0.394938 TTGCCACAAGGAGAGCGTTA 59.605 50.000 0.00 0.00 36.89 3.18
466 467 1.004745 AGCGGATCAAAGGATGGTGTT 59.995 47.619 0.00 0.00 32.67 3.32
467 468 0.620556 AGCGGATCAAAGGATGGTGT 59.379 50.000 0.00 0.00 32.67 4.16
491 492 0.642710 AGGTGGTGGCTCCTAGGTAT 59.357 55.000 9.08 0.00 37.07 2.73
707 3455 2.700773 GGGTGCAATGCTTCGACCC 61.701 63.158 14.52 14.52 39.65 4.46
822 3570 5.596845 GGAGCAACCACAAAAGTTTGATAA 58.403 37.500 10.66 0.00 41.23 1.75
1313 4079 1.959899 CTCGAGCAACACATGGCGTC 61.960 60.000 0.00 0.00 34.54 5.19
1532 4322 4.731961 GCACTTGATGACAAATAATCTGCG 59.268 41.667 0.00 0.00 35.49 5.18
1541 4331 5.476254 TGATGGTAATGCACTTGATGACAAA 59.524 36.000 0.00 0.00 35.49 2.83
1559 4349 5.842874 TGTAGAGGATCAGATTCATGATGGT 59.157 40.000 0.00 0.00 40.02 3.55
1884 4851 1.205893 AGATGTCGAAGAAGAGCCACC 59.794 52.381 0.00 0.00 39.69 4.61
2120 5105 1.354337 CTTGTGGCCACGTGATCTCG 61.354 60.000 30.07 15.19 0.00 4.04
2265 5250 1.741770 ACGCGTGGCATCCTTCTTC 60.742 57.895 12.93 0.00 0.00 2.87
2836 5834 6.533819 ACAACAAATAAGTCATCGACGAAA 57.466 33.333 0.00 0.00 37.67 3.46
2877 5875 8.959548 TGACAGCACATACTTTATCATTTCATT 58.040 29.630 0.00 0.00 0.00 2.57
3107 6106 0.116940 ACCGGGACTAAAGGGTGGTA 59.883 55.000 6.32 0.00 0.00 3.25
3139 6138 1.229400 ACCAGCCCTTTAGTCCCGA 60.229 57.895 0.00 0.00 0.00 5.14
3258 6257 7.519347 TTAGGTCAAATTCCCTGTATAAGGT 57.481 36.000 2.40 0.00 45.78 3.50
3549 6556 3.818210 TGGATGCACTTCGTGTACAAAAT 59.182 39.130 0.00 0.00 35.75 1.82


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

AutoCloner maintained by Alex Coulton.