Multiple sequence alignment - TraesCS5D01G350500

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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 TraesCS5D01G350500 chr5D 100.000 2450 0 0 1 2450 434658147 434655698 0.000000e+00 4525.0
1 TraesCS5D01G350500 chr5D 90.373 966 37 23 1506 2450 434568164 434569094 0.000000e+00 1218.0
2 TraesCS5D01G350500 chr5D 83.197 1345 143 22 702 2012 434679572 434678277 0.000000e+00 1155.0
3 TraesCS5D01G350500 chr5D 80.080 1250 185 38 365 1569 434601575 434602805 0.000000e+00 870.0
4 TraesCS5D01G350500 chr5D 79.910 891 135 27 917 1781 434675704 434674832 4.480000e-172 614.0
5 TraesCS5D01G350500 chr5D 83.074 579 92 6 996 1569 434664543 434663966 2.790000e-144 521.0
6 TraesCS5D01G350500 chr5D 87.923 414 35 2 818 1229 434713991 434713591 7.930000e-130 473.0
7 TraesCS5D01G350500 chr5D 86.493 422 55 2 1119 1538 435345918 435345497 1.720000e-126 462.0
8 TraesCS5D01G350500 chr5D 78.940 736 89 34 263 950 434665280 434664563 8.040000e-120 440.0
9 TraesCS5D01G350500 chr5D 77.419 620 111 15 1174 1778 434551360 434551965 2.330000e-90 342.0
10 TraesCS5D01G350500 chr5D 96.571 175 6 0 1 175 217405743 217405569 8.570000e-75 291.0
11 TraesCS5D01G350500 chr5D 84.834 211 30 1 1314 1524 434713578 434713370 6.860000e-51 211.0
12 TraesCS5D01G350500 chr5D 88.312 154 12 4 2196 2348 434575531 434575679 1.940000e-41 180.0
13 TraesCS5D01G350500 chr5D 86.957 138 15 1 948 1082 435346205 435346068 4.220000e-33 152.0
14 TraesCS5D01G350500 chr5D 97.143 35 1 0 1855 1889 434663743 434663709 2.630000e-05 60.2
15 TraesCS5D01G350500 chr5B 93.921 2188 84 15 260 2423 527784350 527786512 0.000000e+00 3258.0
16 TraesCS5D01G350500 chr5B 90.179 896 45 6 1577 2450 527606769 527607643 0.000000e+00 1127.0
17 TraesCS5D01G350500 chr5B 81.134 1023 141 31 739 1733 527493729 527494727 0.000000e+00 773.0
18 TraesCS5D01G350500 chr5B 83.361 613 83 15 932 1535 527606169 527606771 1.280000e-152 549.0
19 TraesCS5D01G350500 chr5B 92.308 78 4 1 748 825 527605830 527605905 2.580000e-20 110.0
20 TraesCS5D01G350500 chr5B 88.764 89 8 1 2340 2426 527061063 527060975 9.260000e-20 108.0
21 TraesCS5D01G350500 chr4B 96.491 171 6 0 1 171 89461838 89461668 1.430000e-72 283.0
22 TraesCS5D01G350500 chr1B 96.491 171 6 0 1 171 672818961 672819131 1.430000e-72 283.0
23 TraesCS5D01G350500 chr3B 96.491 171 5 1 1 171 193571512 193571681 5.160000e-72 281.0
24 TraesCS5D01G350500 chr4D 95.322 171 8 0 1 171 67119332 67119162 3.100000e-69 272.0
25 TraesCS5D01G350500 chr1D 95.349 172 7 1 1 172 338533420 338533590 3.100000e-69 272.0
26 TraesCS5D01G350500 chr5A 94.083 169 10 0 1 169 44303678 44303846 8.690000e-65 257.0
27 TraesCS5D01G350500 chr5A 87.591 137 9 3 702 833 548665285 548665418 4.220000e-33 152.0
28 TraesCS5D01G350500 chr7A 93.023 172 12 0 1 172 164671333 164671504 4.040000e-63 252.0
29 TraesCS5D01G350500 chr6A 92.982 171 11 1 1 171 608621173 608621004 5.230000e-62 248.0


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 TraesCS5D01G350500 chr5D 434655698 434658147 2449 True 4525.000000 4525 100.000000 1 2450 1 chr5D.!!$R2 2449
1 TraesCS5D01G350500 chr5D 434568164 434569094 930 False 1218.000000 1218 90.373000 1506 2450 1 chr5D.!!$F2 944
2 TraesCS5D01G350500 chr5D 434674832 434679572 4740 True 884.500000 1155 81.553500 702 2012 2 chr5D.!!$R4 1310
3 TraesCS5D01G350500 chr5D 434601575 434602805 1230 False 870.000000 870 80.080000 365 1569 1 chr5D.!!$F4 1204
4 TraesCS5D01G350500 chr5D 434551360 434551965 605 False 342.000000 342 77.419000 1174 1778 1 chr5D.!!$F1 604
5 TraesCS5D01G350500 chr5D 434713370 434713991 621 True 342.000000 473 86.378500 818 1524 2 chr5D.!!$R5 706
6 TraesCS5D01G350500 chr5D 434663709 434665280 1571 True 340.400000 521 86.385667 263 1889 3 chr5D.!!$R3 1626
7 TraesCS5D01G350500 chr5D 435345497 435346205 708 True 307.000000 462 86.725000 948 1538 2 chr5D.!!$R6 590
8 TraesCS5D01G350500 chr5B 527784350 527786512 2162 False 3258.000000 3258 93.921000 260 2423 1 chr5B.!!$F2 2163
9 TraesCS5D01G350500 chr5B 527493729 527494727 998 False 773.000000 773 81.134000 739 1733 1 chr5B.!!$F1 994
10 TraesCS5D01G350500 chr5B 527605830 527607643 1813 False 595.333333 1127 88.616000 748 2450 3 chr5B.!!$F3 1702

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
427 438 0.108186 GTCACCATGTGAGATGCCGA 60.108 55.0 0.0 0.0 43.57 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 6452 1.839354 TGCTGGATCCAATAGCAGTGA 59.161 47.619 20.13 1.3 42.05 3.41 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 4.792068 AGTTGAACAGGGATCAAAACAGA 58.208 39.130 0.00 0.00 38.44 3.41
23 24 4.823989 AGTTGAACAGGGATCAAAACAGAG 59.176 41.667 0.00 0.00 38.44 3.35
24 25 4.437682 TGAACAGGGATCAAAACAGAGT 57.562 40.909 0.00 0.00 0.00 3.24
25 26 4.792068 TGAACAGGGATCAAAACAGAGTT 58.208 39.130 0.00 0.00 0.00 3.01
26 27 4.580167 TGAACAGGGATCAAAACAGAGTTG 59.420 41.667 0.00 0.00 0.00 3.16
27 28 2.887152 ACAGGGATCAAAACAGAGTTGC 59.113 45.455 0.00 0.00 0.00 4.17
28 29 2.229784 CAGGGATCAAAACAGAGTTGCC 59.770 50.000 0.00 0.00 0.00 4.52
29 30 1.200020 GGGATCAAAACAGAGTTGCCG 59.800 52.381 0.00 0.00 0.00 5.69
30 31 2.151202 GGATCAAAACAGAGTTGCCGA 58.849 47.619 0.00 0.00 0.00 5.54
31 32 2.749621 GGATCAAAACAGAGTTGCCGAT 59.250 45.455 0.00 0.00 0.00 4.18
32 33 3.181506 GGATCAAAACAGAGTTGCCGATC 60.182 47.826 0.00 0.00 0.00 3.69
33 34 1.798223 TCAAAACAGAGTTGCCGATCG 59.202 47.619 8.51 8.51 0.00 3.69
34 35 1.531149 CAAAACAGAGTTGCCGATCGT 59.469 47.619 15.09 0.00 0.00 3.73
35 36 1.878953 AAACAGAGTTGCCGATCGTT 58.121 45.000 15.09 0.00 0.00 3.85
36 37 1.878953 AACAGAGTTGCCGATCGTTT 58.121 45.000 15.09 0.00 0.00 3.60
37 38 1.148310 ACAGAGTTGCCGATCGTTTG 58.852 50.000 15.09 3.07 0.00 2.93
38 39 0.443869 CAGAGTTGCCGATCGTTTGG 59.556 55.000 15.09 0.00 0.00 3.28
49 50 5.418310 CCGATCGTTTGGCAAATTATAGT 57.582 39.130 16.74 0.00 0.00 2.12
50 51 5.440685 CCGATCGTTTGGCAAATTATAGTC 58.559 41.667 16.74 8.00 0.00 2.59
51 52 5.130519 CGATCGTTTGGCAAATTATAGTCG 58.869 41.667 16.74 12.65 0.00 4.18
52 53 5.276678 CGATCGTTTGGCAAATTATAGTCGT 60.277 40.000 16.74 4.24 0.00 4.34
53 54 6.074729 CGATCGTTTGGCAAATTATAGTCGTA 60.075 38.462 16.74 4.21 0.00 3.43
54 55 7.358931 CGATCGTTTGGCAAATTATAGTCGTAT 60.359 37.037 16.74 8.28 0.00 3.06
55 56 8.821147 ATCGTTTGGCAAATTATAGTCGTATA 57.179 30.769 16.74 0.00 0.00 1.47
56 57 8.289440 TCGTTTGGCAAATTATAGTCGTATAG 57.711 34.615 16.74 0.00 0.00 1.31
57 58 8.136800 TCGTTTGGCAAATTATAGTCGTATAGA 58.863 33.333 16.74 0.00 0.00 1.98
58 59 8.425491 CGTTTGGCAAATTATAGTCGTATAGAG 58.575 37.037 16.74 0.00 0.00 2.43
59 60 9.257651 GTTTGGCAAATTATAGTCGTATAGAGT 57.742 33.333 16.74 0.00 36.32 3.24
60 61 8.812147 TTGGCAAATTATAGTCGTATAGAGTG 57.188 34.615 0.00 0.00 33.80 3.51
61 62 7.948357 TGGCAAATTATAGTCGTATAGAGTGT 58.052 34.615 0.00 0.00 33.80 3.55
62 63 9.070179 TGGCAAATTATAGTCGTATAGAGTGTA 57.930 33.333 0.00 0.00 33.80 2.90
63 64 9.339492 GGCAAATTATAGTCGTATAGAGTGTAC 57.661 37.037 0.00 0.00 33.80 2.90
64 65 9.339492 GCAAATTATAGTCGTATAGAGTGTACC 57.661 37.037 0.00 0.00 33.80 3.34
67 68 7.643528 TTATAGTCGTATAGAGTGTACCACG 57.356 40.000 0.00 0.00 39.64 4.94
68 69 3.201290 AGTCGTATAGAGTGTACCACGG 58.799 50.000 0.00 0.00 39.64 4.94
69 70 1.942657 TCGTATAGAGTGTACCACGGC 59.057 52.381 0.00 0.00 39.64 5.68
70 71 1.945394 CGTATAGAGTGTACCACGGCT 59.055 52.381 0.00 0.00 39.64 5.52
71 72 2.286831 CGTATAGAGTGTACCACGGCTG 60.287 54.545 0.00 0.00 39.64 4.85
72 73 1.848652 ATAGAGTGTACCACGGCTGT 58.151 50.000 0.00 0.00 39.64 4.40
73 74 0.885879 TAGAGTGTACCACGGCTGTG 59.114 55.000 19.25 19.25 46.00 3.66
74 75 1.113517 AGAGTGTACCACGGCTGTGT 61.114 55.000 23.77 14.20 44.92 3.72
75 76 0.944311 GAGTGTACCACGGCTGTGTG 60.944 60.000 23.77 16.97 44.92 3.82
81 82 2.669229 CACGGCTGTGTGGATGCA 60.669 61.111 17.96 0.00 41.34 3.96
82 83 2.042259 CACGGCTGTGTGGATGCAT 61.042 57.895 17.96 0.00 41.34 3.96
83 84 2.042259 ACGGCTGTGTGGATGCATG 61.042 57.895 2.46 0.00 0.00 4.06
84 85 2.042259 CGGCTGTGTGGATGCATGT 61.042 57.895 2.46 0.00 0.00 3.21
85 86 0.744057 CGGCTGTGTGGATGCATGTA 60.744 55.000 2.46 0.00 0.00 2.29
86 87 1.019673 GGCTGTGTGGATGCATGTAG 58.980 55.000 2.46 0.00 0.00 2.74
87 88 1.019673 GCTGTGTGGATGCATGTAGG 58.980 55.000 2.46 0.00 0.00 3.18
88 89 1.407299 GCTGTGTGGATGCATGTAGGA 60.407 52.381 2.46 0.00 0.00 2.94
89 90 2.283298 CTGTGTGGATGCATGTAGGAC 58.717 52.381 2.46 0.00 0.00 3.85
90 91 1.065491 TGTGTGGATGCATGTAGGACC 60.065 52.381 2.46 0.00 0.00 4.46
91 92 1.065491 GTGTGGATGCATGTAGGACCA 60.065 52.381 2.46 0.09 0.00 4.02
92 93 1.065491 TGTGGATGCATGTAGGACCAC 60.065 52.381 20.61 20.61 45.16 4.16
93 94 0.546122 TGGATGCATGTAGGACCACC 59.454 55.000 2.46 0.00 0.00 4.61
94 95 0.546122 GGATGCATGTAGGACCACCA 59.454 55.000 2.46 0.00 38.94 4.17
95 96 1.143684 GGATGCATGTAGGACCACCAT 59.856 52.381 2.46 0.00 38.94 3.55
96 97 2.224606 GATGCATGTAGGACCACCATG 58.775 52.381 2.46 15.54 39.13 3.66
97 98 0.991146 TGCATGTAGGACCACCATGT 59.009 50.000 19.02 0.00 38.53 3.21
98 99 2.192263 TGCATGTAGGACCACCATGTA 58.808 47.619 19.02 14.40 38.53 2.29
99 100 2.777114 TGCATGTAGGACCACCATGTAT 59.223 45.455 19.02 0.00 38.53 2.29
100 101 3.201930 TGCATGTAGGACCACCATGTATT 59.798 43.478 19.02 0.00 38.53 1.89
101 102 3.565482 GCATGTAGGACCACCATGTATTG 59.435 47.826 19.02 2.39 38.53 1.90
102 103 4.685848 GCATGTAGGACCACCATGTATTGA 60.686 45.833 19.02 0.00 38.53 2.57
103 104 4.753516 TGTAGGACCACCATGTATTGAG 57.246 45.455 0.00 0.00 38.94 3.02
104 105 3.454447 TGTAGGACCACCATGTATTGAGG 59.546 47.826 0.00 0.00 38.94 3.86
105 106 2.845659 AGGACCACCATGTATTGAGGA 58.154 47.619 0.00 0.00 38.94 3.71
106 107 3.397527 AGGACCACCATGTATTGAGGAT 58.602 45.455 0.00 0.00 38.94 3.24
107 108 3.392616 AGGACCACCATGTATTGAGGATC 59.607 47.826 0.00 0.00 38.94 3.36
108 109 3.392616 GGACCACCATGTATTGAGGATCT 59.607 47.826 0.00 0.00 33.79 2.75
109 110 4.141390 GGACCACCATGTATTGAGGATCTT 60.141 45.833 0.00 0.00 33.79 2.40
110 111 5.440610 GACCACCATGTATTGAGGATCTTT 58.559 41.667 0.00 0.00 34.92 2.52
111 112 5.831103 ACCACCATGTATTGAGGATCTTTT 58.169 37.500 0.00 0.00 34.92 2.27
112 113 6.969043 ACCACCATGTATTGAGGATCTTTTA 58.031 36.000 0.00 0.00 34.92 1.52
113 114 6.828785 ACCACCATGTATTGAGGATCTTTTAC 59.171 38.462 0.00 0.00 34.92 2.01
114 115 6.263168 CCACCATGTATTGAGGATCTTTTACC 59.737 42.308 0.00 0.00 34.92 2.85
115 116 7.056635 CACCATGTATTGAGGATCTTTTACCT 58.943 38.462 0.00 0.00 39.41 3.08
123 124 4.927422 GAGGATCTTTTACCTCTCGACTG 58.073 47.826 0.00 0.00 46.28 3.51
124 125 4.345854 AGGATCTTTTACCTCTCGACTGT 58.654 43.478 0.00 0.00 0.00 3.55
125 126 5.507637 AGGATCTTTTACCTCTCGACTGTA 58.492 41.667 0.00 0.00 0.00 2.74
126 127 5.950549 AGGATCTTTTACCTCTCGACTGTAA 59.049 40.000 0.00 0.00 0.00 2.41
127 128 6.035217 GGATCTTTTACCTCTCGACTGTAAC 58.965 44.000 0.00 0.00 0.00 2.50
128 129 6.127675 GGATCTTTTACCTCTCGACTGTAACT 60.128 42.308 0.00 0.00 0.00 2.24
129 130 6.251655 TCTTTTACCTCTCGACTGTAACTC 57.748 41.667 0.00 0.00 0.00 3.01
130 131 6.002704 TCTTTTACCTCTCGACTGTAACTCT 58.997 40.000 0.00 0.00 0.00 3.24
131 132 5.876612 TTTACCTCTCGACTGTAACTCTC 57.123 43.478 0.00 0.00 0.00 3.20
132 133 3.706600 ACCTCTCGACTGTAACTCTCT 57.293 47.619 0.00 0.00 0.00 3.10
133 134 3.602483 ACCTCTCGACTGTAACTCTCTC 58.398 50.000 0.00 0.00 0.00 3.20
134 135 3.008157 ACCTCTCGACTGTAACTCTCTCA 59.992 47.826 0.00 0.00 0.00 3.27
135 136 4.004314 CCTCTCGACTGTAACTCTCTCAA 58.996 47.826 0.00 0.00 0.00 3.02
136 137 4.638421 CCTCTCGACTGTAACTCTCTCAAT 59.362 45.833 0.00 0.00 0.00 2.57
137 138 5.818336 CCTCTCGACTGTAACTCTCTCAATA 59.182 44.000 0.00 0.00 0.00 1.90
138 139 6.485313 CCTCTCGACTGTAACTCTCTCAATAT 59.515 42.308 0.00 0.00 0.00 1.28
139 140 7.252965 TCTCGACTGTAACTCTCTCAATATG 57.747 40.000 0.00 0.00 0.00 1.78
140 141 6.261158 TCTCGACTGTAACTCTCTCAATATGG 59.739 42.308 0.00 0.00 0.00 2.74
141 142 6.120220 TCGACTGTAACTCTCTCAATATGGA 58.880 40.000 0.00 0.00 0.00 3.41
142 143 6.602009 TCGACTGTAACTCTCTCAATATGGAA 59.398 38.462 0.00 0.00 0.00 3.53
143 144 7.285629 TCGACTGTAACTCTCTCAATATGGAAT 59.714 37.037 0.00 0.00 0.00 3.01
144 145 8.568794 CGACTGTAACTCTCTCAATATGGAATA 58.431 37.037 0.00 0.00 0.00 1.75
151 152 9.620259 AACTCTCTCAATATGGAATAAAACTCC 57.380 33.333 0.00 0.00 29.06 3.85
152 153 8.997734 ACTCTCTCAATATGGAATAAAACTCCT 58.002 33.333 0.00 0.00 33.77 3.69
153 154 9.844257 CTCTCTCAATATGGAATAAAACTCCTT 57.156 33.333 0.00 0.00 33.77 3.36
158 159 8.977412 TCAATATGGAATAAAACTCCTTTTCCC 58.023 33.333 0.00 0.00 33.77 3.97
159 160 8.981659 CAATATGGAATAAAACTCCTTTTCCCT 58.018 33.333 0.00 0.00 33.77 4.20
160 161 9.560860 AATATGGAATAAAACTCCTTTTCCCTT 57.439 29.630 0.00 0.00 33.77 3.95
161 162 6.664428 TGGAATAAAACTCCTTTTCCCTTG 57.336 37.500 0.00 0.00 33.77 3.61
162 163 5.011635 TGGAATAAAACTCCTTTTCCCTTGC 59.988 40.000 0.00 0.00 33.77 4.01
163 164 5.011635 GGAATAAAACTCCTTTTCCCTTGCA 59.988 40.000 0.00 0.00 31.74 4.08
164 165 6.463755 GGAATAAAACTCCTTTTCCCTTGCAA 60.464 38.462 0.00 0.00 31.74 4.08
165 166 4.835284 AAAACTCCTTTTCCCTTGCAAA 57.165 36.364 0.00 0.00 0.00 3.68
166 167 4.835284 AAACTCCTTTTCCCTTGCAAAA 57.165 36.364 0.00 0.00 0.00 2.44
167 168 4.835284 AACTCCTTTTCCCTTGCAAAAA 57.165 36.364 0.00 0.00 0.00 1.94
197 198 9.481340 GGAATTAATCATTCTTATTTTCTGGGC 57.519 33.333 0.00 0.00 41.22 5.36
198 199 9.481340 GAATTAATCATTCTTATTTTCTGGGCC 57.519 33.333 0.00 0.00 38.69 5.80
199 200 7.969690 TTAATCATTCTTATTTTCTGGGCCA 57.030 32.000 5.85 5.85 0.00 5.36
200 201 8.551682 TTAATCATTCTTATTTTCTGGGCCAT 57.448 30.769 6.72 0.00 0.00 4.40
201 202 9.653516 TTAATCATTCTTATTTTCTGGGCCATA 57.346 29.630 6.72 0.00 0.00 2.74
202 203 8.731591 AATCATTCTTATTTTCTGGGCCATAT 57.268 30.769 6.72 1.04 0.00 1.78
203 204 7.528996 TCATTCTTATTTTCTGGGCCATATG 57.471 36.000 6.72 0.00 0.00 1.78
204 205 6.494491 TCATTCTTATTTTCTGGGCCATATGG 59.506 38.462 18.07 18.07 38.53 2.74
205 206 5.402054 TCTTATTTTCTGGGCCATATGGT 57.598 39.130 22.79 2.37 37.57 3.55
206 207 5.385198 TCTTATTTTCTGGGCCATATGGTC 58.615 41.667 22.79 20.81 39.63 4.02
207 208 3.686227 ATTTTCTGGGCCATATGGTCA 57.314 42.857 27.14 20.60 42.93 4.02
208 209 3.686227 TTTTCTGGGCCATATGGTCAT 57.314 42.857 27.14 0.00 42.93 3.06
209 210 2.662535 TTCTGGGCCATATGGTCATG 57.337 50.000 27.14 18.13 42.93 3.07
210 211 1.521764 TCTGGGCCATATGGTCATGT 58.478 50.000 27.14 0.00 42.93 3.21
211 212 1.421268 TCTGGGCCATATGGTCATGTC 59.579 52.381 27.14 10.77 42.93 3.06
212 213 0.478072 TGGGCCATATGGTCATGTCC 59.522 55.000 27.14 15.77 42.93 4.02
213 214 0.478072 GGGCCATATGGTCATGTCCA 59.522 55.000 27.14 14.21 42.93 4.02
214 215 1.133513 GGGCCATATGGTCATGTCCAA 60.134 52.381 27.14 6.12 42.93 3.53
215 216 2.233271 GGCCATATGGTCATGTCCAAG 58.767 52.381 21.74 8.73 40.23 3.61
216 217 2.158623 GGCCATATGGTCATGTCCAAGA 60.159 50.000 21.74 7.50 40.23 3.02
217 218 3.554934 GCCATATGGTCATGTCCAAGAA 58.445 45.455 22.79 5.29 41.09 2.52
218 219 3.953612 GCCATATGGTCATGTCCAAGAAA 59.046 43.478 22.79 2.92 41.09 2.52
219 220 4.402155 GCCATATGGTCATGTCCAAGAAAA 59.598 41.667 22.79 0.59 41.09 2.29
220 221 5.069516 GCCATATGGTCATGTCCAAGAAAAT 59.930 40.000 22.79 0.99 41.09 1.82
221 222 6.407299 GCCATATGGTCATGTCCAAGAAAATT 60.407 38.462 22.79 0.27 41.09 1.82
222 223 7.201902 GCCATATGGTCATGTCCAAGAAAATTA 60.202 37.037 22.79 2.56 41.09 1.40
223 224 8.694540 CCATATGGTCATGTCCAAGAAAATTAA 58.305 33.333 15.77 0.00 41.09 1.40
249 250 8.893219 ATATTAACTGAGAAGATCGCATTTCA 57.107 30.769 0.00 0.00 0.00 2.69
250 251 7.615582 ATTAACTGAGAAGATCGCATTTCAA 57.384 32.000 0.00 0.00 0.00 2.69
251 252 5.947228 AACTGAGAAGATCGCATTTCAAA 57.053 34.783 0.00 0.00 0.00 2.69
252 253 6.506500 AACTGAGAAGATCGCATTTCAAAT 57.493 33.333 0.00 0.00 0.00 2.32
253 254 7.615582 AACTGAGAAGATCGCATTTCAAATA 57.384 32.000 0.00 0.00 0.00 1.40
254 255 7.009568 ACTGAGAAGATCGCATTTCAAATAC 57.990 36.000 0.00 0.00 0.00 1.89
255 256 6.820656 ACTGAGAAGATCGCATTTCAAATACT 59.179 34.615 0.00 0.00 0.00 2.12
256 257 7.981789 ACTGAGAAGATCGCATTTCAAATACTA 59.018 33.333 0.00 0.00 0.00 1.82
257 258 8.131455 TGAGAAGATCGCATTTCAAATACTAC 57.869 34.615 0.00 0.00 0.00 2.73
258 259 7.763985 TGAGAAGATCGCATTTCAAATACTACA 59.236 33.333 0.00 0.00 0.00 2.74
290 291 1.925185 CACACATCAGAGACATCAGCG 59.075 52.381 0.00 0.00 0.00 5.18
327 331 1.069049 ACATGCCACTTTTTCACAGGC 59.931 47.619 0.00 0.00 45.41 4.85
355 359 3.508762 CAAGAAGCAGAAATCACCATGC 58.491 45.455 0.00 0.00 38.97 4.06
363 367 4.122046 CAGAAATCACCATGCGAGATGTA 58.878 43.478 0.00 0.00 0.00 2.29
427 438 0.108186 GTCACCATGTGAGATGCCGA 60.108 55.000 0.00 0.00 43.57 5.54
428 439 0.612744 TCACCATGTGAGATGCCGAA 59.387 50.000 0.00 0.00 37.67 4.30
429 440 1.012086 CACCATGTGAGATGCCGAAG 58.988 55.000 0.00 0.00 35.23 3.79
430 441 0.745845 ACCATGTGAGATGCCGAAGC 60.746 55.000 0.00 0.00 40.48 3.86
431 442 1.442526 CCATGTGAGATGCCGAAGCC 61.443 60.000 0.00 0.00 38.69 4.35
445 456 3.308530 CCGAAGCCAAAATCAAACAGAC 58.691 45.455 0.00 0.00 0.00 3.51
501 512 7.010830 TCGATGTTCAGAAAGAATAGATTGCTG 59.989 37.037 0.00 0.00 38.76 4.41
503 514 6.475504 TGTTCAGAAAGAATAGATTGCTGGA 58.524 36.000 0.00 0.00 38.76 3.86
533 544 4.338012 ACAATTGCATGTCTCCATCTCAA 58.662 39.130 5.05 0.00 0.00 3.02
560 571 7.558807 GGGCCGCCCTATATACTTAAAATTATT 59.441 37.037 22.31 0.00 41.34 1.40
561 572 9.617523 GGCCGCCCTATATACTTAAAATTATTA 57.382 33.333 0.00 0.00 0.00 0.98
624 635 2.838386 ATCTCATTGCGCAATCACAC 57.162 45.000 31.88 0.00 0.00 3.82
662 683 6.323996 CCACTTCCAGGTCATGTAAGTCTATA 59.676 42.308 0.00 0.00 0.00 1.31
705 758 4.848357 AGTCAGTATGCCAGCAATTAGTT 58.152 39.130 0.00 0.00 34.76 2.24
728 786 2.101249 CCAACAAGTGGCAAACTCATGT 59.899 45.455 0.00 0.00 41.72 3.21
732 790 0.773644 AGTGGCAAACTCATGTCCCT 59.226 50.000 0.00 0.00 31.64 4.20
761 821 6.696148 GGAATCAAATCAAGATCACATTGCTC 59.304 38.462 0.00 0.00 0.00 4.26
849 921 7.873739 TGTCATGATATTGATAGCTACAACG 57.126 36.000 0.00 0.00 0.00 4.10
914 995 2.578021 AGCTTACCACCACCATCTCATT 59.422 45.455 0.00 0.00 0.00 2.57
931 1188 7.283807 CCATCTCATTATCACTTCATCCACAAA 59.716 37.037 0.00 0.00 0.00 2.83
1082 1365 2.472029 GAGGAAGAGGATCACCCAGAA 58.528 52.381 0.00 0.00 37.82 3.02
1207 1613 1.078918 CTGGCATTCCTCAGCACGA 60.079 57.895 0.00 0.00 0.00 4.35
1697 5806 7.210718 AGGCATACACTTTAAAACTACAACC 57.789 36.000 0.00 0.00 0.00 3.77
1708 5817 4.616181 AAACTACAACCAATATGCGCTC 57.384 40.909 9.73 0.00 0.00 5.03
1792 5901 4.439289 GGAGCTTTGCCTATCATTGAACAC 60.439 45.833 0.00 0.00 0.00 3.32
1793 5902 3.127548 AGCTTTGCCTATCATTGAACACG 59.872 43.478 0.00 0.00 0.00 4.49
1931 6041 4.248859 GCAGATTGAGCAACTGAGAACTA 58.751 43.478 13.29 0.00 34.07 2.24
1932 6042 4.329528 GCAGATTGAGCAACTGAGAACTAG 59.670 45.833 13.29 0.00 34.07 2.57
1933 6043 5.477510 CAGATTGAGCAACTGAGAACTAGT 58.522 41.667 0.00 0.00 34.07 2.57
1934 6044 5.931146 CAGATTGAGCAACTGAGAACTAGTT 59.069 40.000 8.13 8.13 38.84 2.24
1935 6045 7.093354 CAGATTGAGCAACTGAGAACTAGTTA 58.907 38.462 8.42 0.00 36.29 2.24
1936 6046 7.275341 CAGATTGAGCAACTGAGAACTAGTTAG 59.725 40.741 8.42 5.20 36.29 2.34
1937 6047 6.406692 TTGAGCAACTGAGAACTAGTTAGT 57.593 37.500 8.42 5.89 36.29 2.24
2206 6337 0.179100 AGGCGACCGATCATTGACAG 60.179 55.000 0.00 0.00 0.00 3.51
2211 6342 3.795488 GCGACCGATCATTGACAGTGATA 60.795 47.826 12.92 0.00 36.49 2.15
2216 6347 7.008719 CGACCGATCATTGACAGTGATAATATC 59.991 40.741 12.92 8.14 36.49 1.63
2371 6502 4.051661 ACATTTGACCCCATCACAATCT 57.948 40.909 0.00 0.00 36.92 2.40
2423 6554 1.152138 GCTGATCCCATGGCCATGA 59.848 57.895 41.32 26.13 41.20 3.07
2424 6555 1.177256 GCTGATCCCATGGCCATGAC 61.177 60.000 41.32 28.03 41.20 3.06
2425 6556 0.538977 CTGATCCCATGGCCATGACC 60.539 60.000 41.32 26.54 41.20 4.02
2426 6557 1.287773 TGATCCCATGGCCATGACCA 61.288 55.000 41.32 28.41 45.82 4.02
2435 6566 2.195727 TGGCCATGACCATGTCTCTTA 58.804 47.619 0.00 0.00 37.11 2.10
2436 6567 2.779430 TGGCCATGACCATGTCTCTTAT 59.221 45.455 0.00 0.00 37.11 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.580580 ACTCTGTTTTGATCCCTGTTCAAC 59.419 41.667 0.00 0.00 33.03 3.18
3 4 4.437682 ACTCTGTTTTGATCCCTGTTCA 57.562 40.909 0.00 0.00 0.00 3.18
4 5 4.557496 GCAACTCTGTTTTGATCCCTGTTC 60.557 45.833 0.00 0.00 0.00 3.18
6 7 2.887152 GCAACTCTGTTTTGATCCCTGT 59.113 45.455 0.00 0.00 0.00 4.00
7 8 2.229784 GGCAACTCTGTTTTGATCCCTG 59.770 50.000 0.00 0.00 0.00 4.45
8 9 2.519013 GGCAACTCTGTTTTGATCCCT 58.481 47.619 0.00 0.00 0.00 4.20
9 10 1.200020 CGGCAACTCTGTTTTGATCCC 59.800 52.381 0.00 0.00 0.00 3.85
10 11 2.151202 TCGGCAACTCTGTTTTGATCC 58.849 47.619 0.00 0.00 0.00 3.36
11 12 3.484229 CGATCGGCAACTCTGTTTTGATC 60.484 47.826 7.38 0.00 0.00 2.92
13 14 1.798223 CGATCGGCAACTCTGTTTTGA 59.202 47.619 7.38 0.00 0.00 2.69
14 15 1.531149 ACGATCGGCAACTCTGTTTTG 59.469 47.619 20.98 0.00 0.00 2.44
15 16 1.878953 ACGATCGGCAACTCTGTTTT 58.121 45.000 20.98 0.00 0.00 2.43
17 18 1.531149 CAAACGATCGGCAACTCTGTT 59.469 47.619 20.98 0.00 0.00 3.16
18 19 1.148310 CAAACGATCGGCAACTCTGT 58.852 50.000 20.98 0.00 0.00 3.41
19 20 0.443869 CCAAACGATCGGCAACTCTG 59.556 55.000 20.98 5.35 0.00 3.35
20 21 2.840974 CCAAACGATCGGCAACTCT 58.159 52.632 20.98 0.00 0.00 3.24
27 28 5.418310 ACTATAATTTGCCAAACGATCGG 57.582 39.130 20.98 2.04 0.00 4.18
28 29 5.130519 CGACTATAATTTGCCAAACGATCG 58.869 41.667 14.88 14.88 0.00 3.69
29 30 6.044512 ACGACTATAATTTGCCAAACGATC 57.955 37.500 0.00 0.00 0.00 3.69
30 31 7.724305 ATACGACTATAATTTGCCAAACGAT 57.276 32.000 0.00 0.00 0.00 3.73
31 32 8.136800 TCTATACGACTATAATTTGCCAAACGA 58.863 33.333 0.00 0.00 0.00 3.85
32 33 8.289440 TCTATACGACTATAATTTGCCAAACG 57.711 34.615 0.00 0.00 0.00 3.60
33 34 9.257651 ACTCTATACGACTATAATTTGCCAAAC 57.742 33.333 0.00 0.00 0.00 2.93
34 35 9.256477 CACTCTATACGACTATAATTTGCCAAA 57.744 33.333 0.00 0.00 0.00 3.28
35 36 8.418662 ACACTCTATACGACTATAATTTGCCAA 58.581 33.333 0.00 0.00 0.00 4.52
36 37 7.948357 ACACTCTATACGACTATAATTTGCCA 58.052 34.615 0.00 0.00 0.00 4.92
37 38 9.339492 GTACACTCTATACGACTATAATTTGCC 57.661 37.037 0.00 0.00 0.00 4.52
38 39 9.339492 GGTACACTCTATACGACTATAATTTGC 57.661 37.037 0.00 0.00 0.00 3.68
65 66 2.042259 CATGCATCCACACAGCCGT 61.042 57.895 0.00 0.00 0.00 5.68
66 67 0.744057 TACATGCATCCACACAGCCG 60.744 55.000 0.00 0.00 0.00 5.52
67 68 1.019673 CTACATGCATCCACACAGCC 58.980 55.000 0.00 0.00 0.00 4.85
68 69 1.019673 CCTACATGCATCCACACAGC 58.980 55.000 0.00 0.00 0.00 4.40
69 70 2.283298 GTCCTACATGCATCCACACAG 58.717 52.381 0.00 0.00 0.00 3.66
70 71 1.065491 GGTCCTACATGCATCCACACA 60.065 52.381 0.00 0.00 0.00 3.72
71 72 1.065491 TGGTCCTACATGCATCCACAC 60.065 52.381 0.00 0.00 0.00 3.82
72 73 1.065491 GTGGTCCTACATGCATCCACA 60.065 52.381 21.86 3.21 43.03 4.17
73 74 1.668419 GTGGTCCTACATGCATCCAC 58.332 55.000 14.97 14.97 38.47 4.02
74 75 0.546122 GGTGGTCCTACATGCATCCA 59.454 55.000 0.00 0.00 0.00 3.41
75 76 0.546122 TGGTGGTCCTACATGCATCC 59.454 55.000 0.00 0.00 34.23 3.51
76 77 2.224606 CATGGTGGTCCTACATGCATC 58.775 52.381 11.68 0.00 36.03 3.91
77 78 1.565759 ACATGGTGGTCCTACATGCAT 59.434 47.619 19.81 0.00 44.32 3.96
78 79 0.991146 ACATGGTGGTCCTACATGCA 59.009 50.000 19.81 0.00 44.32 3.96
79 80 3.492102 ATACATGGTGGTCCTACATGC 57.508 47.619 19.81 0.00 44.32 4.06
80 81 5.034852 TCAATACATGGTGGTCCTACATG 57.965 43.478 18.84 18.84 45.56 3.21
81 82 4.103153 CCTCAATACATGGTGGTCCTACAT 59.897 45.833 0.00 0.00 34.23 2.29
82 83 3.454447 CCTCAATACATGGTGGTCCTACA 59.546 47.826 0.00 0.00 34.23 2.74
83 84 3.709653 TCCTCAATACATGGTGGTCCTAC 59.290 47.826 0.00 0.00 34.23 3.18
84 85 4.002256 TCCTCAATACATGGTGGTCCTA 57.998 45.455 0.00 0.00 34.23 2.94
85 86 2.845659 TCCTCAATACATGGTGGTCCT 58.154 47.619 0.00 0.00 34.23 3.85
86 87 3.392616 AGATCCTCAATACATGGTGGTCC 59.607 47.826 0.00 0.00 0.00 4.46
87 88 4.696479 AGATCCTCAATACATGGTGGTC 57.304 45.455 0.00 0.00 0.00 4.02
88 89 5.456921 AAAGATCCTCAATACATGGTGGT 57.543 39.130 0.00 0.00 0.00 4.16
89 90 6.263168 GGTAAAAGATCCTCAATACATGGTGG 59.737 42.308 0.00 0.00 0.00 4.61
90 91 7.056635 AGGTAAAAGATCCTCAATACATGGTG 58.943 38.462 0.00 0.00 0.00 4.17
91 92 7.213178 AGGTAAAAGATCCTCAATACATGGT 57.787 36.000 0.00 0.00 0.00 3.55
92 93 7.736447 GAGGTAAAAGATCCTCAATACATGG 57.264 40.000 0.00 0.00 46.59 3.66
102 103 4.345854 ACAGTCGAGAGGTAAAAGATCCT 58.654 43.478 0.00 0.00 36.70 3.24
103 104 4.722361 ACAGTCGAGAGGTAAAAGATCC 57.278 45.455 0.00 0.00 0.00 3.36
104 105 6.854778 AGTTACAGTCGAGAGGTAAAAGATC 58.145 40.000 5.39 0.00 0.00 2.75
105 106 6.660094 AGAGTTACAGTCGAGAGGTAAAAGAT 59.340 38.462 5.39 0.00 0.00 2.40
106 107 6.002704 AGAGTTACAGTCGAGAGGTAAAAGA 58.997 40.000 5.39 0.00 0.00 2.52
107 108 6.149807 AGAGAGTTACAGTCGAGAGGTAAAAG 59.850 42.308 5.39 0.00 0.00 2.27
108 109 6.002704 AGAGAGTTACAGTCGAGAGGTAAAA 58.997 40.000 5.39 0.00 0.00 1.52
109 110 5.558818 AGAGAGTTACAGTCGAGAGGTAAA 58.441 41.667 5.39 0.00 0.00 2.01
110 111 5.163281 AGAGAGTTACAGTCGAGAGGTAA 57.837 43.478 0.00 0.00 0.00 2.85
111 112 4.222366 TGAGAGAGTTACAGTCGAGAGGTA 59.778 45.833 0.00 0.00 0.00 3.08
112 113 3.008157 TGAGAGAGTTACAGTCGAGAGGT 59.992 47.826 0.00 0.00 0.00 3.85
113 114 3.601435 TGAGAGAGTTACAGTCGAGAGG 58.399 50.000 0.00 0.00 0.00 3.69
114 115 5.811399 ATTGAGAGAGTTACAGTCGAGAG 57.189 43.478 0.00 0.00 0.00 3.20
115 116 6.261158 CCATATTGAGAGAGTTACAGTCGAGA 59.739 42.308 0.00 0.00 0.00 4.04
116 117 6.261158 TCCATATTGAGAGAGTTACAGTCGAG 59.739 42.308 0.00 0.00 0.00 4.04
117 118 6.120220 TCCATATTGAGAGAGTTACAGTCGA 58.880 40.000 0.00 0.00 0.00 4.20
118 119 6.378710 TCCATATTGAGAGAGTTACAGTCG 57.621 41.667 0.00 0.00 0.00 4.18
125 126 9.620259 GGAGTTTTATTCCATATTGAGAGAGTT 57.380 33.333 0.00 0.00 34.74 3.01
126 127 8.997734 AGGAGTTTTATTCCATATTGAGAGAGT 58.002 33.333 0.00 0.00 37.18 3.24
127 128 9.844257 AAGGAGTTTTATTCCATATTGAGAGAG 57.156 33.333 0.00 0.00 37.18 3.20
132 133 8.977412 GGGAAAAGGAGTTTTATTCCATATTGA 58.023 33.333 5.34 0.00 35.94 2.57
133 134 8.981659 AGGGAAAAGGAGTTTTATTCCATATTG 58.018 33.333 5.34 0.00 35.94 1.90
134 135 9.560860 AAGGGAAAAGGAGTTTTATTCCATATT 57.439 29.630 5.34 0.00 35.94 1.28
135 136 8.981659 CAAGGGAAAAGGAGTTTTATTCCATAT 58.018 33.333 5.34 0.00 35.94 1.78
136 137 7.093509 GCAAGGGAAAAGGAGTTTTATTCCATA 60.094 37.037 5.34 0.00 35.94 2.74
137 138 6.295859 GCAAGGGAAAAGGAGTTTTATTCCAT 60.296 38.462 5.34 0.00 35.94 3.41
138 139 5.011635 GCAAGGGAAAAGGAGTTTTATTCCA 59.988 40.000 5.34 0.00 35.94 3.53
139 140 5.011635 TGCAAGGGAAAAGGAGTTTTATTCC 59.988 40.000 0.00 0.00 35.94 3.01
140 141 6.096673 TGCAAGGGAAAAGGAGTTTTATTC 57.903 37.500 0.00 0.00 35.94 1.75
141 142 6.493189 TTGCAAGGGAAAAGGAGTTTTATT 57.507 33.333 0.00 0.00 35.94 1.40
142 143 6.493189 TTTGCAAGGGAAAAGGAGTTTTAT 57.507 33.333 0.00 0.00 35.94 1.40
143 144 5.941555 TTTGCAAGGGAAAAGGAGTTTTA 57.058 34.783 0.00 0.00 35.94 1.52
144 145 4.835284 TTTGCAAGGGAAAAGGAGTTTT 57.165 36.364 0.00 0.00 38.65 2.43
145 146 4.835284 TTTTGCAAGGGAAAAGGAGTTT 57.165 36.364 0.00 0.00 0.00 2.66
146 147 4.835284 TTTTTGCAAGGGAAAAGGAGTT 57.165 36.364 0.00 0.00 0.00 3.01
171 172 9.481340 GCCCAGAAAATAAGAATGATTAATTCC 57.519 33.333 0.00 0.00 45.10 3.01
172 173 9.481340 GGCCCAGAAAATAAGAATGATTAATTC 57.519 33.333 0.00 0.00 44.44 2.17
173 174 8.991275 TGGCCCAGAAAATAAGAATGATTAATT 58.009 29.630 0.00 0.00 0.00 1.40
174 175 8.551682 TGGCCCAGAAAATAAGAATGATTAAT 57.448 30.769 0.00 0.00 0.00 1.40
175 176 7.969690 TGGCCCAGAAAATAAGAATGATTAA 57.030 32.000 0.00 0.00 0.00 1.40
176 177 9.827198 ATATGGCCCAGAAAATAAGAATGATTA 57.173 29.630 0.00 0.00 0.00 1.75
177 178 8.591072 CATATGGCCCAGAAAATAAGAATGATT 58.409 33.333 0.00 0.00 0.00 2.57
178 179 7.179694 CCATATGGCCCAGAAAATAAGAATGAT 59.820 37.037 9.29 0.00 0.00 2.45
179 180 6.494491 CCATATGGCCCAGAAAATAAGAATGA 59.506 38.462 9.29 0.00 0.00 2.57
180 181 6.268387 ACCATATGGCCCAGAAAATAAGAATG 59.732 38.462 22.18 0.00 39.32 2.67
181 182 6.384603 ACCATATGGCCCAGAAAATAAGAAT 58.615 36.000 22.18 0.00 39.32 2.40
182 183 5.776358 ACCATATGGCCCAGAAAATAAGAA 58.224 37.500 22.18 0.00 39.32 2.52
183 184 5.103728 TGACCATATGGCCCAGAAAATAAGA 60.104 40.000 22.18 0.00 39.32 2.10
184 185 5.139727 TGACCATATGGCCCAGAAAATAAG 58.860 41.667 22.18 0.00 39.32 1.73
185 186 5.136068 TGACCATATGGCCCAGAAAATAA 57.864 39.130 22.18 0.00 39.32 1.40
186 187 4.805140 TGACCATATGGCCCAGAAAATA 57.195 40.909 22.18 0.00 39.32 1.40
187 188 3.686227 TGACCATATGGCCCAGAAAAT 57.314 42.857 22.18 0.00 39.32 1.82
188 189 3.298619 CATGACCATATGGCCCAGAAAA 58.701 45.455 22.18 0.00 39.32 2.29
189 190 2.244510 ACATGACCATATGGCCCAGAAA 59.755 45.455 22.18 0.00 39.32 2.52
190 191 1.852309 ACATGACCATATGGCCCAGAA 59.148 47.619 22.18 1.55 39.32 3.02
191 192 1.421268 GACATGACCATATGGCCCAGA 59.579 52.381 22.18 1.53 39.32 3.86
192 193 1.901591 GACATGACCATATGGCCCAG 58.098 55.000 22.18 11.90 39.32 4.45
196 197 3.213206 TCTTGGACATGACCATATGGC 57.787 47.619 22.18 14.55 39.82 4.40
197 198 6.720112 ATTTTCTTGGACATGACCATATGG 57.280 37.500 20.68 20.68 39.82 2.74
223 224 9.330063 TGAAATGCGATCTTCTCAGTTAATATT 57.670 29.630 0.00 0.00 0.00 1.28
224 225 8.893219 TGAAATGCGATCTTCTCAGTTAATAT 57.107 30.769 0.00 0.00 0.00 1.28
225 226 8.716646 TTGAAATGCGATCTTCTCAGTTAATA 57.283 30.769 0.00 0.00 0.00 0.98
226 227 7.615582 TTGAAATGCGATCTTCTCAGTTAAT 57.384 32.000 0.00 0.00 0.00 1.40
227 228 7.433708 TTTGAAATGCGATCTTCTCAGTTAA 57.566 32.000 0.00 0.00 0.00 2.01
228 229 7.615582 ATTTGAAATGCGATCTTCTCAGTTA 57.384 32.000 0.00 0.00 0.00 2.24
229 230 5.947228 TTTGAAATGCGATCTTCTCAGTT 57.053 34.783 0.00 0.00 0.00 3.16
230 231 6.820656 AGTATTTGAAATGCGATCTTCTCAGT 59.179 34.615 0.00 0.00 0.00 3.41
231 232 7.244166 AGTATTTGAAATGCGATCTTCTCAG 57.756 36.000 0.00 0.00 0.00 3.35
232 233 7.763985 TGTAGTATTTGAAATGCGATCTTCTCA 59.236 33.333 0.00 0.00 0.00 3.27
233 234 8.131455 TGTAGTATTTGAAATGCGATCTTCTC 57.869 34.615 0.00 0.00 0.00 2.87
234 235 8.492673 TTGTAGTATTTGAAATGCGATCTTCT 57.507 30.769 0.00 0.00 0.00 2.85
235 236 8.391106 ACTTGTAGTATTTGAAATGCGATCTTC 58.609 33.333 0.00 0.00 0.00 2.87
236 237 8.268850 ACTTGTAGTATTTGAAATGCGATCTT 57.731 30.769 0.00 0.00 0.00 2.40
237 238 7.549134 TGACTTGTAGTATTTGAAATGCGATCT 59.451 33.333 0.00 0.00 0.00 2.75
238 239 7.684670 TGACTTGTAGTATTTGAAATGCGATC 58.315 34.615 0.00 0.00 0.00 3.69
239 240 7.609760 TGACTTGTAGTATTTGAAATGCGAT 57.390 32.000 0.00 0.00 0.00 4.58
240 241 7.041712 TGTTGACTTGTAGTATTTGAAATGCGA 60.042 33.333 0.00 0.00 0.00 5.10
241 242 7.059488 GTGTTGACTTGTAGTATTTGAAATGCG 59.941 37.037 0.00 0.00 0.00 4.73
242 243 7.860373 TGTGTTGACTTGTAGTATTTGAAATGC 59.140 33.333 0.00 0.00 0.00 3.56
243 244 9.729023 TTGTGTTGACTTGTAGTATTTGAAATG 57.271 29.630 0.00 0.00 0.00 2.32
244 245 9.730420 GTTGTGTTGACTTGTAGTATTTGAAAT 57.270 29.630 0.00 0.00 0.00 2.17
245 246 8.731605 TGTTGTGTTGACTTGTAGTATTTGAAA 58.268 29.630 0.00 0.00 0.00 2.69
246 247 8.178964 GTGTTGTGTTGACTTGTAGTATTTGAA 58.821 33.333 0.00 0.00 0.00 2.69
247 248 7.334671 TGTGTTGTGTTGACTTGTAGTATTTGA 59.665 33.333 0.00 0.00 0.00 2.69
248 249 7.428183 GTGTGTTGTGTTGACTTGTAGTATTTG 59.572 37.037 0.00 0.00 0.00 2.32
249 250 7.119992 TGTGTGTTGTGTTGACTTGTAGTATTT 59.880 33.333 0.00 0.00 0.00 1.40
250 251 6.596106 TGTGTGTTGTGTTGACTTGTAGTATT 59.404 34.615 0.00 0.00 0.00 1.89
251 252 6.110033 TGTGTGTTGTGTTGACTTGTAGTAT 58.890 36.000 0.00 0.00 0.00 2.12
252 253 5.480205 TGTGTGTTGTGTTGACTTGTAGTA 58.520 37.500 0.00 0.00 0.00 1.82
253 254 4.320023 TGTGTGTTGTGTTGACTTGTAGT 58.680 39.130 0.00 0.00 0.00 2.73
254 255 4.937696 TGTGTGTTGTGTTGACTTGTAG 57.062 40.909 0.00 0.00 0.00 2.74
255 256 4.938226 TGATGTGTGTTGTGTTGACTTGTA 59.062 37.500 0.00 0.00 0.00 2.41
256 257 3.755905 TGATGTGTGTTGTGTTGACTTGT 59.244 39.130 0.00 0.00 0.00 3.16
257 258 4.094739 TCTGATGTGTGTTGTGTTGACTTG 59.905 41.667 0.00 0.00 0.00 3.16
258 259 4.260985 TCTGATGTGTGTTGTGTTGACTT 58.739 39.130 0.00 0.00 0.00 3.01
290 291 2.798976 TGTCACATTTTCAAGCTGGC 57.201 45.000 0.00 0.00 0.00 4.85
375 384 2.413453 GCATTTCTCGTCTCTTGGACAC 59.587 50.000 0.00 0.00 44.70 3.67
380 389 4.668686 GCTTCTTGCATTTCTCGTCTCTTG 60.669 45.833 0.00 0.00 42.31 3.02
406 417 1.661341 GGCATCTCACATGGTGACTC 58.339 55.000 0.00 0.00 37.67 3.36
427 438 4.101430 ACATGGTCTGTTTGATTTTGGCTT 59.899 37.500 0.00 0.00 32.90 4.35
428 439 3.642848 ACATGGTCTGTTTGATTTTGGCT 59.357 39.130 0.00 0.00 32.90 4.75
429 440 3.742369 CACATGGTCTGTTTGATTTTGGC 59.258 43.478 0.00 0.00 35.29 4.52
430 441 3.742369 GCACATGGTCTGTTTGATTTTGG 59.258 43.478 0.00 0.00 35.29 3.28
431 442 4.624015 AGCACATGGTCTGTTTGATTTTG 58.376 39.130 0.00 0.00 35.29 2.44
472 483 8.538856 CAATCTATTCTTTCTGAACATCGAGTC 58.461 37.037 0.00 0.00 37.52 3.36
477 488 7.281774 TCCAGCAATCTATTCTTTCTGAACATC 59.718 37.037 0.00 0.00 37.52 3.06
501 512 3.592059 ACATGCAATTGTTGATGCTTCC 58.408 40.909 14.84 0.00 42.97 3.46
503 514 4.491676 GAGACATGCAATTGTTGATGCTT 58.508 39.130 14.84 4.88 42.97 3.91
624 635 1.595093 GAAGTGGGCCCATTTCCGTG 61.595 60.000 37.86 0.00 36.90 4.94
662 683 3.290948 TGTTTCAAGTAGTGGCCAAGT 57.709 42.857 7.24 0.00 0.00 3.16
728 786 6.616959 TGATCTTGATTTGATTCCTCTAGGGA 59.383 38.462 0.00 0.00 43.41 4.20
732 790 9.117183 CAATGTGATCTTGATTTGATTCCTCTA 57.883 33.333 0.00 0.00 0.00 2.43
793 863 3.443037 GGACAGAGACATGATGAACTCG 58.557 50.000 0.00 6.96 32.96 4.18
849 921 2.548904 GAGAGAAGCATCATGATGTGCC 59.451 50.000 31.09 20.93 42.20 5.01
914 995 4.764823 GGTTGGTTTGTGGATGAAGTGATA 59.235 41.667 0.00 0.00 0.00 2.15
931 1188 0.108585 CAGGTGCTGTAGTGGTTGGT 59.891 55.000 0.00 0.00 0.00 3.67
1116 1518 2.109181 GCTACTGGGGTCATCGGC 59.891 66.667 0.00 0.00 0.00 5.54
1117 1519 1.330655 ACTGCTACTGGGGTCATCGG 61.331 60.000 0.00 0.00 0.00 4.18
1194 1600 1.261480 AGACTGTCGTGCTGAGGAAT 58.739 50.000 1.52 0.00 0.00 3.01
1207 1613 0.897863 AGGAGCTCGCTGAAGACTGT 60.898 55.000 7.83 0.00 0.00 3.55
1555 5650 6.367695 TGATCAGAAAGCTTGCAAATTTCATG 59.632 34.615 26.39 21.85 35.79 3.07
1666 5763 5.856126 TTTAAAGTGTATGCCTTGACTCG 57.144 39.130 0.00 0.00 0.00 4.18
1722 5831 6.741992 TGTGCAGGACTCATTAGTTTTATG 57.258 37.500 0.00 0.00 35.56 1.90
1792 5901 7.042335 ACTTGAATCTATACCCTCTGTTTTCG 58.958 38.462 0.00 0.00 0.00 3.46
1935 6045 9.227777 GGATTATTCAAGTGTTTGGTAACTACT 57.772 33.333 0.00 0.00 35.24 2.57
1936 6046 9.227777 AGGATTATTCAAGTGTTTGGTAACTAC 57.772 33.333 0.00 0.00 35.24 2.73
2206 6337 6.037786 TGGATCGGGTTGAGATATTATCAC 57.962 41.667 6.46 0.68 0.00 3.06
2211 6342 3.909995 TGGATGGATCGGGTTGAGATATT 59.090 43.478 0.00 0.00 0.00 1.28
2216 6347 3.369892 GGATATGGATGGATCGGGTTGAG 60.370 52.174 0.00 0.00 0.00 3.02
2321 6452 1.839354 TGCTGGATCCAATAGCAGTGA 59.161 47.619 20.13 1.30 42.05 3.41
2357 6488 4.879295 TTGGATTAGATTGTGATGGGGT 57.121 40.909 0.00 0.00 0.00 4.95
2423 6554 9.911788 ATTACAAAAGATGATAAGAGACATGGT 57.088 29.630 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.