Multiple sequence alignment - TraesCS6D01G192600

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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 TraesCS6D01G192600 chr6D 100.000 4108 0 0 1 4108 266777421 266781528 0.000000e+00 7587.0
1 TraesCS6D01G192600 chr6B 90.085 1876 100 32 219 2015 414333043 414334911 0.000000e+00 2355.0
2 TraesCS6D01G192600 chr6B 94.988 1217 46 9 2034 3240 414334989 414336200 0.000000e+00 1895.0
3 TraesCS6D01G192600 chr6B 90.236 891 50 18 3237 4107 414336242 414337115 0.000000e+00 1129.0
4 TraesCS6D01G192600 chr6B 97.110 173 5 0 49 221 468734827 468734655 4.020000e-75 292.0
5 TraesCS6D01G192600 chr6B 98.160 163 3 0 59 221 229680946 229680784 6.720000e-73 285.0
6 TraesCS6D01G192600 chr6B 78.704 108 14 8 3761 3862 12986140 12986036 3.430000e-06 63.9
7 TraesCS6D01G192600 chr6A 93.149 1124 45 9 2963 4065 378170581 378171693 0.000000e+00 1620.0
8 TraesCS6D01G192600 chr6A 95.006 861 38 3 2037 2895 378167838 378168695 0.000000e+00 1347.0
9 TraesCS6D01G192600 chr6A 91.695 891 44 14 1124 2004 378166964 378167834 0.000000e+00 1208.0
10 TraesCS6D01G192600 chr6A 90.945 751 41 8 397 1123 378166149 378166896 0.000000e+00 985.0
11 TraesCS6D01G192600 chr6A 89.103 156 7 3 224 370 378161684 378161838 7.010000e-43 185.0
12 TraesCS6D01G192600 chr5D 88.679 689 42 16 1757 2436 367506088 367505427 0.000000e+00 808.0
13 TraesCS6D01G192600 chr5D 88.133 691 44 17 1757 2436 437148702 437149365 0.000000e+00 787.0
14 TraesCS6D01G192600 chr5D 94.915 177 8 1 45 221 303445427 303445252 4.040000e-70 276.0
15 TraesCS6D01G192600 chr5D 80.153 131 25 1 3974 4104 60214686 60214557 3.380000e-16 97.1
16 TraesCS6D01G192600 chr2D 88.439 692 41 18 1757 2436 181603251 181602587 0.000000e+00 798.0
17 TraesCS6D01G192600 chr7D 88.244 689 43 17 1757 2436 589200115 589199456 0.000000e+00 789.0
18 TraesCS6D01G192600 chr7D 88.244 689 43 17 1757 2436 589204371 589205030 0.000000e+00 789.0
19 TraesCS6D01G192600 chr7D 98.795 166 1 1 59 224 171308151 171307987 1.120000e-75 294.0
20 TraesCS6D01G192600 chr1D 94.363 408 21 2 2030 2436 435736414 435736820 3.490000e-175 625.0
21 TraesCS6D01G192600 chr2B 98.160 163 3 0 59 221 797534656 797534818 6.720000e-73 285.0
22 TraesCS6D01G192600 chr4B 97.041 169 4 1 56 224 618591762 618591595 2.420000e-72 283.0
23 TraesCS6D01G192600 chr3A 97.006 167 4 1 59 225 731100877 731100712 3.130000e-71 279.0
24 TraesCS6D01G192600 chr7B 95.930 172 6 1 50 221 516791755 516791925 1.120000e-70 278.0
25 TraesCS6D01G192600 chr2A 90.909 198 15 3 24 221 250729512 250729706 3.150000e-66 263.0
26 TraesCS6D01G192600 chr3D 82.031 128 20 3 3982 4107 182325831 182325705 5.620000e-19 106.0
27 TraesCS6D01G192600 chr7A 80.000 110 21 1 4000 4108 523624403 523624512 3.400000e-11 80.5


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 TraesCS6D01G192600 chr6D 266777421 266781528 4107 False 7587 7587 100.000000 1 4108 1 chr6D.!!$F1 4107
1 TraesCS6D01G192600 chr6B 414333043 414337115 4072 False 1793 2355 91.769667 219 4107 3 chr6B.!!$F1 3888
2 TraesCS6D01G192600 chr6A 378166149 378171693 5544 False 1290 1620 92.698750 397 4065 4 chr6A.!!$F2 3668
3 TraesCS6D01G192600 chr5D 367505427 367506088 661 True 808 808 88.679000 1757 2436 1 chr5D.!!$R3 679
4 TraesCS6D01G192600 chr5D 437148702 437149365 663 False 787 787 88.133000 1757 2436 1 chr5D.!!$F1 679
5 TraesCS6D01G192600 chr2D 181602587 181603251 664 True 798 798 88.439000 1757 2436 1 chr2D.!!$R1 679
6 TraesCS6D01G192600 chr7D 589199456 589200115 659 True 789 789 88.244000 1757 2436 1 chr7D.!!$R2 679
7 TraesCS6D01G192600 chr7D 589204371 589205030 659 False 789 789 88.244000 1757 2436 1 chr7D.!!$F1 679

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
367 383 0.326264 AAGGTTGAGCGAGGAAGCAT 59.674 50.000 0.0 0.0 40.15 3.79 F
1763 1885 0.407139 ACCTTGCCCAGAATCTGCTT 59.593 50.000 4.4 0.0 0.00 3.91 F
2124 2313 2.114616 CAGAGGACATGGAGCCTAAGT 58.885 52.381 0.0 0.0 33.84 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2153 0.163574 CAAATTTTGCGCGCCCTTTC 59.836 50.0 30.77 0.0 0.0 2.62 R
3033 5067 1.103803 CTTGACCTAGTAGCCTGCGA 58.896 55.0 0.00 0.0 0.0 5.10 R
4078 6203 1.629043 ACTGCGTTGAGAGGGTCTTA 58.371 50.0 0.00 0.0 0.0 2.10 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
48 49 9.816787 TTTTATTTTACCCAGGTTCAGATTACT 57.183 29.630 0.00 0.00 0.00 2.24
49 50 8.801882 TTATTTTACCCAGGTTCAGATTACTG 57.198 34.615 0.00 0.00 44.66 2.74
50 51 5.836024 TTTACCCAGGTTCAGATTACTGT 57.164 39.130 0.00 0.00 43.81 3.55
51 52 5.836024 TTACCCAGGTTCAGATTACTGTT 57.164 39.130 0.00 0.00 43.81 3.16
52 53 4.021102 ACCCAGGTTCAGATTACTGTTG 57.979 45.455 0.00 0.00 43.81 3.33
53 54 3.394606 ACCCAGGTTCAGATTACTGTTGT 59.605 43.478 0.00 0.00 43.81 3.32
54 55 3.753272 CCCAGGTTCAGATTACTGTTGTG 59.247 47.826 0.00 0.00 43.81 3.33
55 56 4.504864 CCCAGGTTCAGATTACTGTTGTGA 60.505 45.833 0.00 0.00 43.81 3.58
56 57 5.248640 CCAGGTTCAGATTACTGTTGTGAT 58.751 41.667 0.00 0.00 43.81 3.06
57 58 5.122869 CCAGGTTCAGATTACTGTTGTGATG 59.877 44.000 0.00 0.00 43.81 3.07
58 59 5.702670 CAGGTTCAGATTACTGTTGTGATGT 59.297 40.000 0.00 0.00 43.81 3.06
59 60 6.873605 CAGGTTCAGATTACTGTTGTGATGTA 59.126 38.462 0.00 0.00 43.81 2.29
60 61 6.874134 AGGTTCAGATTACTGTTGTGATGTAC 59.126 38.462 0.00 0.00 43.81 2.90
61 62 6.874134 GGTTCAGATTACTGTTGTGATGTACT 59.126 38.462 0.00 0.00 43.81 2.73
62 63 7.063544 GGTTCAGATTACTGTTGTGATGTACTC 59.936 40.741 0.00 0.00 43.81 2.59
63 64 6.631016 TCAGATTACTGTTGTGATGTACTCC 58.369 40.000 0.00 0.00 43.81 3.85
64 65 5.812642 CAGATTACTGTTGTGATGTACTCCC 59.187 44.000 0.00 0.00 39.11 4.30
65 66 5.721960 AGATTACTGTTGTGATGTACTCCCT 59.278 40.000 0.00 0.00 0.00 4.20
66 67 3.963428 ACTGTTGTGATGTACTCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
67 68 2.567615 ACTGTTGTGATGTACTCCCTCC 59.432 50.000 0.00 0.00 0.00 4.30
68 69 1.548719 TGTTGTGATGTACTCCCTCCG 59.451 52.381 0.00 0.00 0.00 4.63
69 70 1.549170 GTTGTGATGTACTCCCTCCGT 59.451 52.381 0.00 0.00 0.00 4.69
70 71 1.933021 TGTGATGTACTCCCTCCGTT 58.067 50.000 0.00 0.00 0.00 4.44
71 72 1.822990 TGTGATGTACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
72 73 1.136500 GTGATGTACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
73 74 1.006758 TGATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
74 75 2.242965 TGATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
75 76 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
76 77 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
77 78 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
78 79 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
79 80 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
80 81 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
81 82 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
82 83 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
83 84 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
84 85 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
85 86 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
86 87 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
87 88 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
88 89 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
89 90 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
100 101 8.950208 AATATAAGTCTTTGTAGAGCTTCCAC 57.050 34.615 0.00 0.00 0.00 4.02
101 102 4.965200 AAGTCTTTGTAGAGCTTCCACT 57.035 40.909 0.00 0.00 0.00 4.00
102 103 7.719871 ATAAGTCTTTGTAGAGCTTCCACTA 57.280 36.000 0.00 0.00 0.00 2.74
103 104 6.613153 AAGTCTTTGTAGAGCTTCCACTAT 57.387 37.500 0.00 0.00 0.00 2.12
104 105 5.971763 AGTCTTTGTAGAGCTTCCACTATG 58.028 41.667 0.00 0.00 0.00 2.23
105 106 5.717178 AGTCTTTGTAGAGCTTCCACTATGA 59.283 40.000 0.00 0.00 0.00 2.15
106 107 6.211584 AGTCTTTGTAGAGCTTCCACTATGAA 59.788 38.462 0.00 0.00 0.00 2.57
107 108 6.311690 GTCTTTGTAGAGCTTCCACTATGAAC 59.688 42.308 0.00 0.00 0.00 3.18
108 109 6.211584 TCTTTGTAGAGCTTCCACTATGAACT 59.788 38.462 0.00 0.00 0.00 3.01
109 110 7.396339 TCTTTGTAGAGCTTCCACTATGAACTA 59.604 37.037 0.00 0.00 0.00 2.24
110 111 6.452494 TGTAGAGCTTCCACTATGAACTAC 57.548 41.667 0.00 0.00 0.00 2.73
111 112 5.949952 TGTAGAGCTTCCACTATGAACTACA 59.050 40.000 0.00 0.00 36.46 2.74
112 113 6.607600 TGTAGAGCTTCCACTATGAACTACAT 59.392 38.462 0.00 0.00 42.39 2.29
113 114 7.778382 TGTAGAGCTTCCACTATGAACTACATA 59.222 37.037 0.00 0.00 40.07 2.29
114 115 7.045126 AGAGCTTCCACTATGAACTACATAC 57.955 40.000 0.00 0.00 40.07 2.39
115 116 5.833082 AGCTTCCACTATGAACTACATACG 58.167 41.667 0.00 0.00 40.07 3.06
116 117 4.982916 GCTTCCACTATGAACTACATACGG 59.017 45.833 0.00 0.00 40.07 4.02
117 118 5.221185 GCTTCCACTATGAACTACATACGGA 60.221 44.000 0.00 0.00 40.07 4.69
118 119 6.516860 GCTTCCACTATGAACTACATACGGAT 60.517 42.308 0.00 0.00 37.58 4.18
119 120 6.327279 TCCACTATGAACTACATACGGATG 57.673 41.667 5.94 5.94 40.07 3.51
121 122 6.999871 TCCACTATGAACTACATACGGATGTA 59.000 38.462 19.32 19.32 44.77 2.29
122 123 7.668469 TCCACTATGAACTACATACGGATGTAT 59.332 37.037 20.64 7.28 45.42 2.29
123 124 8.953313 CCACTATGAACTACATACGGATGTATA 58.047 37.037 20.64 10.04 45.42 1.47
130 131 9.666626 GAACTACATACGGATGTATATAGATGC 57.333 37.037 20.64 0.00 45.42 3.91
131 132 8.747538 ACTACATACGGATGTATATAGATGCA 57.252 34.615 20.64 0.00 45.42 3.96
132 133 9.355916 ACTACATACGGATGTATATAGATGCAT 57.644 33.333 20.64 0.00 45.42 3.96
135 136 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
139 140 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
161 162 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
162 163 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
163 164 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
164 165 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
165 166 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
166 167 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
167 168 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
168 169 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
169 170 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
170 171 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
171 172 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
172 173 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
173 174 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
174 175 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
175 176 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
176 177 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
177 178 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
178 179 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
179 180 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
180 181 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
195 196 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
196 197 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
197 198 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
198 199 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
199 200 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
200 201 8.919145 CCTAGTGGAATCTCTACAAAGACTTAT 58.081 37.037 0.00 0.00 34.57 1.73
214 215 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
215 216 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
216 217 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
217 218 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
222 223 8.731591 TTATATTTAGGAACGGAGGGAGTAAT 57.268 34.615 0.00 0.00 0.00 1.89
246 247 3.007398 CCCTACTCTTGCTTGTGTTCTCT 59.993 47.826 0.00 0.00 0.00 3.10
288 296 6.141560 ACTCTTGCTTTTTCTCTTTCCTTG 57.858 37.500 0.00 0.00 0.00 3.61
292 300 4.536765 TGCTTTTTCTCTTTCCTTGTCCT 58.463 39.130 0.00 0.00 0.00 3.85
337 353 1.071385 CTATGGTCAGGTCAGGATGCC 59.929 57.143 0.00 0.00 34.76 4.40
343 359 1.202330 CAGGTCAGGATGCCTCTTCT 58.798 55.000 0.00 0.00 39.95 2.85
346 362 1.556911 GGTCAGGATGCCTCTTCTTGA 59.443 52.381 0.00 0.00 34.76 3.02
367 383 0.326264 AAGGTTGAGCGAGGAAGCAT 59.674 50.000 0.00 0.00 40.15 3.79
370 386 1.869767 GGTTGAGCGAGGAAGCATATG 59.130 52.381 0.00 0.00 40.15 1.78
381 397 4.899502 AGGAAGCATATGGAAATCCGTAG 58.100 43.478 4.56 1.99 40.55 3.51
413 429 6.331369 TGCCTAAAGGAAACTCAGAAAATG 57.669 37.500 0.00 0.00 42.68 2.32
418 434 6.469782 AAAGGAAACTCAGAAAATGCTGAA 57.530 33.333 0.00 0.00 43.75 3.02
470 486 3.855689 AGCCTGTATGTGATTTGTTGC 57.144 42.857 0.00 0.00 0.00 4.17
474 490 5.418524 AGCCTGTATGTGATTTGTTGCAATA 59.581 36.000 0.59 0.00 0.00 1.90
577 593 4.039852 GGTGTGTTCATTGGGGTTTACAAT 59.960 41.667 0.00 0.00 39.00 2.71
581 597 6.951198 TGTGTTCATTGGGGTTTACAATCTAT 59.049 34.615 0.00 0.00 36.47 1.98
646 662 1.802960 ACTGCATTTCTCTTGAGTGCG 59.197 47.619 0.00 5.32 38.00 5.34
660 676 1.061711 GAGTGCGCAATACAAGCAGAG 59.938 52.381 14.00 0.00 41.93 3.35
661 677 1.078709 GTGCGCAATACAAGCAGAGA 58.921 50.000 14.00 0.00 41.93 3.10
728 767 4.957684 AAGCAACCTAGTACAAGACACT 57.042 40.909 0.00 0.00 0.00 3.55
769 818 3.106242 CCCAAACAAAGGGTAAACAGC 57.894 47.619 0.00 0.00 41.61 4.40
772 821 3.181485 CCAAACAAAGGGTAAACAGCGAA 60.181 43.478 0.00 0.00 0.00 4.70
786 835 1.225637 GCGAACAACGGTGCATACG 60.226 57.895 0.00 11.53 42.83 3.06
953 1002 2.296920 TGGGGCTCCATGTGAGTAC 58.703 57.895 0.00 6.38 43.48 2.73
1024 1073 1.362406 GAAAGCGGTGCTCTGCCTAC 61.362 60.000 15.72 4.19 46.23 3.18
1038 1087 3.196469 TCTGCCTACTCTTGATCTTGGTG 59.804 47.826 0.00 0.00 0.00 4.17
1086 1135 6.115446 TCCAGATATTGTCACAGGTTTGATC 58.885 40.000 0.00 0.00 0.00 2.92
1090 1139 7.224362 CAGATATTGTCACAGGTTTGATCTCTC 59.776 40.741 0.00 0.00 0.00 3.20
1130 1179 5.722021 GAGGTTTTCTCTCTCTCTCAAGT 57.278 43.478 0.00 0.00 39.38 3.16
1131 1180 6.827586 GAGGTTTTCTCTCTCTCTCAAGTA 57.172 41.667 0.00 0.00 39.38 2.24
1134 1183 7.463431 AGGTTTTCTCTCTCTCTCAAGTACTA 58.537 38.462 0.00 0.00 0.00 1.82
1136 1185 8.745590 GGTTTTCTCTCTCTCTCAAGTACTAAT 58.254 37.037 0.00 0.00 0.00 1.73
1171 1286 6.484308 CCTTCATTTTTGAAATTGCAGAAGGT 59.516 34.615 17.67 0.00 0.00 3.50
1238 1359 5.047021 TGCATATATACTTGGACAGAGCTCC 60.047 44.000 10.93 0.00 0.00 4.70
1763 1885 0.407139 ACCTTGCCCAGAATCTGCTT 59.593 50.000 4.40 0.00 0.00 3.91
1788 1914 9.832445 TTAGTAAGAAGGATCCATCATGTTTAC 57.168 33.333 18.78 16.22 0.00 2.01
1790 1916 8.552296 AGTAAGAAGGATCCATCATGTTTACTT 58.448 33.333 18.78 4.70 32.03 2.24
1798 1924 7.041508 GGATCCATCATGTTTACTTAAGCTCTG 60.042 40.741 6.95 0.00 0.00 3.35
1799 1925 6.711277 TCCATCATGTTTACTTAAGCTCTGT 58.289 36.000 1.29 0.00 0.00 3.41
1822 1948 8.239038 TGTAGCTAGCTAGAGTGTTGAATTAT 57.761 34.615 24.78 0.00 0.00 1.28
1933 2063 2.285220 CAGGTTTCTTCACACACACTCG 59.715 50.000 0.00 0.00 0.00 4.18
1979 2109 4.823989 ACATTAAGGTGAGCATATCCTTGC 59.176 41.667 11.04 0.00 41.04 4.01
2005 2135 3.667497 TGATCCCTCGACATAAGCATC 57.333 47.619 0.00 0.00 0.00 3.91
2018 2148 2.897350 GCATCCGCTCCTTTCCGG 60.897 66.667 0.00 0.00 45.64 5.14
2124 2313 2.114616 CAGAGGACATGGAGCCTAAGT 58.885 52.381 0.00 0.00 33.84 2.24
2174 2363 2.819348 GCAAATGGAGGAGACCAAGGTT 60.819 50.000 0.00 0.00 43.47 3.50
2333 2525 2.276617 ATTGTTGCGCGCGATTCG 60.277 55.556 37.18 4.97 42.12 3.34
2370 2563 5.573337 AAGTTCAGGCATATCTTTTCAGC 57.427 39.130 0.00 0.00 0.00 4.26
2447 2641 7.781324 ATTCTCACCATTGGTTGTTCTTATT 57.219 32.000 5.34 0.00 31.02 1.40
2448 2642 8.877864 ATTCTCACCATTGGTTGTTCTTATTA 57.122 30.769 5.34 0.00 31.02 0.98
2449 2643 8.877864 TTCTCACCATTGGTTGTTCTTATTAT 57.122 30.769 5.34 0.00 31.02 1.28
2731 2925 5.463061 CACAAAGGTTTGAATCATTGACACC 59.537 40.000 9.42 0.00 40.55 4.16
2735 2929 6.029346 AGGTTTGAATCATTGACACCATTC 57.971 37.500 0.00 0.00 0.00 2.67
2942 4976 4.378874 GCTCAAAGTTGCATACTGAAGGTC 60.379 45.833 0.00 0.00 37.12 3.85
2943 4977 4.713553 TCAAAGTTGCATACTGAAGGTCA 58.286 39.130 0.00 0.00 37.12 4.02
2954 4988 8.046708 TGCATACTGAAGGTCATGTAAAGTAAT 58.953 33.333 0.00 0.00 0.00 1.89
3018 5052 9.349713 ACTCACTGTCCATTGTTTCTAAAAATA 57.650 29.630 0.00 0.00 0.00 1.40
3080 5114 8.425577 AGGAGATAAATTCGTCAAATACAGTG 57.574 34.615 0.00 0.00 0.00 3.66
3141 5175 7.639113 TGTCCAAACAAAGAAGAACAATAGT 57.361 32.000 0.00 0.00 30.70 2.12
3178 5212 3.696051 AGCACACTTTTCACATGAACTGT 59.304 39.130 0.00 0.00 39.20 3.55
3191 5225 7.386059 TCACATGAACTGTAGAAGATGCTTAA 58.614 34.615 0.00 0.00 35.91 1.85
3192 5226 8.043113 TCACATGAACTGTAGAAGATGCTTAAT 58.957 33.333 0.00 0.00 35.91 1.40
3205 5241 6.566197 AGATGCTTAATATGCCAAAGCTAC 57.434 37.500 7.68 2.64 44.66 3.58
3233 5270 2.094417 GGAGTATTGCACTTCGAACTGC 59.906 50.000 19.18 19.18 37.72 4.40
3333 5415 9.654663 AGTAGAAGTTCAGTTATGTAATTCACC 57.345 33.333 5.50 0.00 34.45 4.02
3467 5549 4.023792 CAGAATGCTACTCTGCAAACACAA 60.024 41.667 0.00 0.00 46.61 3.33
3473 5555 4.261572 GCTACTCTGCAAACACAATGGAAA 60.262 41.667 0.00 0.00 0.00 3.13
3618 5723 6.175712 TGTTTTCAATGTTTGCCAAGTTTC 57.824 33.333 0.00 0.00 0.00 2.78
3639 5744 7.987458 AGTTTCGTCATAGAATACATTCATGGT 59.013 33.333 4.85 0.00 39.23 3.55
3930 6053 9.179909 TGAATTTGTTATACGGGAATGTACAAT 57.820 29.630 0.00 0.00 0.00 2.71
4015 6140 6.151817 GCTCACCTTTCTTCATTAGTTTGGAT 59.848 38.462 0.00 0.00 0.00 3.41
4035 6160 7.510549 TGGATATTTAGAGTAATTGGCTTGC 57.489 36.000 0.00 0.00 0.00 4.01
4041 6166 3.347216 AGAGTAATTGGCTTGCGAATGT 58.653 40.909 3.76 0.00 0.00 2.71
4093 6218 5.932303 TCTTGAATTTAAGACCCTCTCAACG 59.068 40.000 8.50 0.00 32.02 4.10
4101 6226 3.362706 AGACCCTCTCAACGCAGTATTA 58.637 45.455 0.00 0.00 45.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.816787 AGTAATCTGAACCTGGGTAAAATAAAA 57.183 29.630 0.00 0.00 0.00 1.52
23 24 9.238368 CAGTAATCTGAACCTGGGTAAAATAAA 57.762 33.333 0.00 0.00 43.76 1.40
24 25 8.387813 ACAGTAATCTGAACCTGGGTAAAATAA 58.612 33.333 0.00 0.00 43.76 1.40
25 26 7.924541 ACAGTAATCTGAACCTGGGTAAAATA 58.075 34.615 0.00 0.00 43.76 1.40
26 27 6.790319 ACAGTAATCTGAACCTGGGTAAAAT 58.210 36.000 0.00 0.00 43.76 1.82
27 28 6.195600 ACAGTAATCTGAACCTGGGTAAAA 57.804 37.500 0.00 0.00 43.76 1.52
28 29 5.836024 ACAGTAATCTGAACCTGGGTAAA 57.164 39.130 0.00 0.00 43.76 2.01
29 30 5.072600 ACAACAGTAATCTGAACCTGGGTAA 59.927 40.000 0.00 0.00 43.76 2.85
30 31 4.595781 ACAACAGTAATCTGAACCTGGGTA 59.404 41.667 0.00 0.00 43.76 3.69
31 32 3.394606 ACAACAGTAATCTGAACCTGGGT 59.605 43.478 0.00 0.00 43.76 4.51
32 33 3.753272 CACAACAGTAATCTGAACCTGGG 59.247 47.826 0.00 0.00 43.76 4.45
33 34 4.641396 TCACAACAGTAATCTGAACCTGG 58.359 43.478 2.17 0.00 43.76 4.45
34 35 5.702670 ACATCACAACAGTAATCTGAACCTG 59.297 40.000 2.17 0.00 43.76 4.00
35 36 5.869579 ACATCACAACAGTAATCTGAACCT 58.130 37.500 2.17 0.00 43.76 3.50
36 37 6.874134 AGTACATCACAACAGTAATCTGAACC 59.126 38.462 0.00 0.00 43.76 3.62
37 38 7.063544 GGAGTACATCACAACAGTAATCTGAAC 59.936 40.741 0.00 0.00 43.76 3.18
38 39 7.097192 GGAGTACATCACAACAGTAATCTGAA 58.903 38.462 0.00 0.00 43.76 3.02
39 40 6.351033 GGGAGTACATCACAACAGTAATCTGA 60.351 42.308 0.00 0.00 43.76 3.27
40 41 5.812642 GGGAGTACATCACAACAGTAATCTG 59.187 44.000 0.00 0.00 46.18 2.90
41 42 5.721960 AGGGAGTACATCACAACAGTAATCT 59.278 40.000 0.00 0.00 34.38 2.40
42 43 5.978814 AGGGAGTACATCACAACAGTAATC 58.021 41.667 0.00 0.00 31.63 1.75
43 44 5.104900 GGAGGGAGTACATCACAACAGTAAT 60.105 44.000 0.00 0.00 31.63 1.89
44 45 4.222145 GGAGGGAGTACATCACAACAGTAA 59.778 45.833 0.00 0.00 31.63 2.24
45 46 3.767673 GGAGGGAGTACATCACAACAGTA 59.232 47.826 0.00 0.00 31.63 2.74
46 47 2.567615 GGAGGGAGTACATCACAACAGT 59.432 50.000 0.00 0.00 31.63 3.55
47 48 2.417379 CGGAGGGAGTACATCACAACAG 60.417 54.545 0.00 0.00 31.63 3.16
48 49 1.548719 CGGAGGGAGTACATCACAACA 59.451 52.381 0.00 0.00 31.63 3.33
49 50 1.549170 ACGGAGGGAGTACATCACAAC 59.451 52.381 0.00 0.00 31.63 3.32
50 51 1.933021 ACGGAGGGAGTACATCACAA 58.067 50.000 0.00 0.00 31.63 3.33
51 52 1.822990 GAACGGAGGGAGTACATCACA 59.177 52.381 0.00 0.00 31.63 3.58
52 53 1.136500 GGAACGGAGGGAGTACATCAC 59.864 57.143 0.00 0.00 0.00 3.06
53 54 1.006758 AGGAACGGAGGGAGTACATCA 59.993 52.381 0.00 0.00 0.00 3.07
54 55 1.777941 AGGAACGGAGGGAGTACATC 58.222 55.000 0.00 0.00 0.00 3.06
55 56 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
56 57 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
57 58 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
58 59 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
59 60 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
60 61 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
61 62 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
62 63 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
63 64 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
64 65 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
74 75 9.384764 GTGGAAGCTCTACAAAGACTTATATTT 57.615 33.333 0.00 0.00 0.00 1.40
75 76 8.763601 AGTGGAAGCTCTACAAAGACTTATATT 58.236 33.333 0.00 0.00 29.47 1.28
76 77 8.312669 AGTGGAAGCTCTACAAAGACTTATAT 57.687 34.615 0.00 0.00 29.47 0.86
77 78 7.719871 AGTGGAAGCTCTACAAAGACTTATA 57.280 36.000 0.00 0.00 29.47 0.98
78 79 6.613153 AGTGGAAGCTCTACAAAGACTTAT 57.387 37.500 0.00 0.00 29.47 1.73
79 80 7.396339 TCATAGTGGAAGCTCTACAAAGACTTA 59.604 37.037 0.00 0.00 29.47 2.24
80 81 4.965200 AGTGGAAGCTCTACAAAGACTT 57.035 40.909 0.00 0.00 29.47 3.01
81 82 5.717178 TCATAGTGGAAGCTCTACAAAGACT 59.283 40.000 0.00 0.00 29.47 3.24
82 83 5.967088 TCATAGTGGAAGCTCTACAAAGAC 58.033 41.667 0.00 0.00 29.47 3.01
83 84 6.211584 AGTTCATAGTGGAAGCTCTACAAAGA 59.788 38.462 0.00 0.00 29.47 2.52
84 85 6.402222 AGTTCATAGTGGAAGCTCTACAAAG 58.598 40.000 0.00 0.00 29.47 2.77
85 86 6.360370 AGTTCATAGTGGAAGCTCTACAAA 57.640 37.500 0.00 0.00 29.47 2.83
86 87 6.436218 TGTAGTTCATAGTGGAAGCTCTACAA 59.564 38.462 0.00 0.00 34.07 2.41
87 88 5.949952 TGTAGTTCATAGTGGAAGCTCTACA 59.050 40.000 0.00 0.00 34.35 2.74
88 89 6.452494 TGTAGTTCATAGTGGAAGCTCTAC 57.548 41.667 0.00 0.00 30.52 2.59
89 90 7.041303 CGTATGTAGTTCATAGTGGAAGCTCTA 60.041 40.741 0.00 0.00 39.36 2.43
90 91 6.238786 CGTATGTAGTTCATAGTGGAAGCTCT 60.239 42.308 0.00 0.00 39.36 4.09
91 92 5.915758 CGTATGTAGTTCATAGTGGAAGCTC 59.084 44.000 0.00 0.00 39.36 4.09
92 93 5.221263 CCGTATGTAGTTCATAGTGGAAGCT 60.221 44.000 3.20 0.00 39.36 3.74
93 94 4.982916 CCGTATGTAGTTCATAGTGGAAGC 59.017 45.833 3.20 0.00 39.36 3.86
94 95 6.387041 TCCGTATGTAGTTCATAGTGGAAG 57.613 41.667 7.73 0.00 39.60 3.46
95 96 6.322969 ACATCCGTATGTAGTTCATAGTGGAA 59.677 38.462 12.08 0.00 44.66 3.53
96 97 5.831525 ACATCCGTATGTAGTTCATAGTGGA 59.168 40.000 11.01 11.01 44.66 4.02
97 98 6.085555 ACATCCGTATGTAGTTCATAGTGG 57.914 41.667 0.00 2.99 44.66 4.00
113 114 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
135 136 8.677300 GGAGCAAAATGAATGAATCTACACTTA 58.323 33.333 0.00 0.00 0.00 2.24
136 137 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
137 138 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
138 139 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
139 140 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
140 141 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
141 142 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
142 143 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
143 144 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
144 145 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
145 146 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
146 147 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
147 148 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
148 149 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
149 150 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
150 151 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
151 152 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
152 153 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
153 154 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
154 155 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
155 156 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
156 157 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
157 158 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
158 159 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
159 160 3.548770 CACTAGGTGGACTACATACGGA 58.451 50.000 0.00 0.00 0.00 4.69
160 161 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
172 173 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
173 174 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
174 175 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
189 190 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
190 191 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
191 192 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
192 193 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
193 194 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
194 195 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
195 196 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
196 197 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
197 198 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
198 199 9.247861 GTATTACTCCCTCCGTTCCTAAATATA 57.752 37.037 0.00 0.00 0.00 0.86
199 200 7.179872 GGTATTACTCCCTCCGTTCCTAAATAT 59.820 40.741 0.00 0.00 0.00 1.28
200 201 6.494835 GGTATTACTCCCTCCGTTCCTAAATA 59.505 42.308 0.00 0.00 0.00 1.40
201 202 5.306419 GGTATTACTCCCTCCGTTCCTAAAT 59.694 44.000 0.00 0.00 0.00 1.40
202 203 4.651045 GGTATTACTCCCTCCGTTCCTAAA 59.349 45.833 0.00 0.00 0.00 1.85
203 204 4.218312 GGTATTACTCCCTCCGTTCCTAA 58.782 47.826 0.00 0.00 0.00 2.69
204 205 3.437052 GGGTATTACTCCCTCCGTTCCTA 60.437 52.174 0.00 0.00 41.58 2.94
205 206 2.675583 GGTATTACTCCCTCCGTTCCT 58.324 52.381 0.00 0.00 0.00 3.36
206 207 1.690893 GGGTATTACTCCCTCCGTTCC 59.309 57.143 0.00 0.00 41.58 3.62
214 215 4.224762 AGCAAGAGTAGGGTATTACTCCC 58.775 47.826 9.01 0.00 46.95 4.30
215 216 5.128991 ACAAGCAAGAGTAGGGTATTACTCC 59.871 44.000 9.01 0.00 46.95 3.85
216 217 6.043411 CACAAGCAAGAGTAGGGTATTACTC 58.957 44.000 5.30 5.30 46.39 2.59
217 218 5.484290 ACACAAGCAAGAGTAGGGTATTACT 59.516 40.000 0.00 0.00 36.61 2.24
222 223 3.901844 AGAACACAAGCAAGAGTAGGGTA 59.098 43.478 0.00 0.00 0.00 3.69
226 227 6.393990 ACATAGAGAACACAAGCAAGAGTAG 58.606 40.000 0.00 0.00 0.00 2.57
232 233 9.371136 CTATTAGAACATAGAGAACACAAGCAA 57.629 33.333 0.00 0.00 0.00 3.91
234 235 9.757227 ATCTATTAGAACATAGAGAACACAAGC 57.243 33.333 0.00 0.00 38.81 4.01
266 274 6.141560 ACAAGGAAAGAGAAAAAGCAAGAG 57.858 37.500 0.00 0.00 0.00 2.85
288 296 1.277557 AGCACTCATCACTTGGAGGAC 59.722 52.381 0.00 0.00 35.45 3.85
292 300 4.623932 AAACTAGCACTCATCACTTGGA 57.376 40.909 0.00 0.00 0.00 3.53
337 353 3.809832 TCGCTCAACCTTTTCAAGAAGAG 59.190 43.478 0.00 0.00 0.00 2.85
343 359 2.631160 TCCTCGCTCAACCTTTTCAA 57.369 45.000 0.00 0.00 0.00 2.69
346 362 1.239347 GCTTCCTCGCTCAACCTTTT 58.761 50.000 0.00 0.00 0.00 2.27
367 383 6.464222 CAGGATTAAGCTACGGATTTCCATA 58.536 40.000 0.00 0.00 35.14 2.74
370 386 3.498777 GCAGGATTAAGCTACGGATTTCC 59.501 47.826 0.00 0.00 0.00 3.13
381 397 4.950475 AGTTTCCTTTAGGCAGGATTAAGC 59.050 41.667 0.00 0.00 42.89 3.09
413 429 6.867550 AGGAAAATTAGCCAACTTATTCAGC 58.132 36.000 0.01 0.00 0.00 4.26
418 434 6.857437 AGCAAGGAAAATTAGCCAACTTAT 57.143 33.333 0.00 0.00 0.00 1.73
470 486 7.097834 TGCATCAAGAGAGATATGAGCTATTG 58.902 38.462 0.00 0.00 33.46 1.90
474 490 5.748670 ATGCATCAAGAGAGATATGAGCT 57.251 39.130 0.00 0.00 0.00 4.09
532 548 5.774690 ACCAATAACAACACTGTTCATCCAT 59.225 36.000 0.00 0.00 42.25 3.41
533 549 5.009510 CACCAATAACAACACTGTTCATCCA 59.990 40.000 0.00 0.00 42.25 3.41
534 550 5.009610 ACACCAATAACAACACTGTTCATCC 59.990 40.000 0.00 0.00 42.25 3.51
535 551 5.914635 CACACCAATAACAACACTGTTCATC 59.085 40.000 0.00 0.00 42.25 2.92
577 593 5.023452 TCTTGGCTGAGTTGGACTTATAGA 58.977 41.667 0.00 0.00 0.00 1.98
581 597 2.972713 AGTCTTGGCTGAGTTGGACTTA 59.027 45.455 0.00 0.00 31.14 2.24
628 644 0.518636 GCGCACTCAAGAGAAATGCA 59.481 50.000 0.30 0.00 36.30 3.96
629 645 0.518636 TGCGCACTCAAGAGAAATGC 59.481 50.000 5.66 2.81 34.28 3.56
646 662 1.740025 GTGGGTCTCTGCTTGTATTGC 59.260 52.381 0.00 0.00 0.00 3.56
660 676 1.017701 GGACCAATCGTTCGTGGGTC 61.018 60.000 17.02 17.02 45.68 4.46
661 677 1.004200 GGACCAATCGTTCGTGGGT 60.004 57.895 6.76 6.04 39.39 4.51
728 767 0.106719 GGGGAATCTTGGGCGAATCA 60.107 55.000 0.00 0.00 0.00 2.57
769 818 1.319374 CTACGTATGCACCGTTGTTCG 59.681 52.381 17.14 0.00 39.60 3.95
772 821 0.245539 AGCTACGTATGCACCGTTGT 59.754 50.000 17.14 1.80 39.60 3.32
786 835 0.806492 GTCTTGGCGCACCTAGCTAC 60.806 60.000 10.83 0.00 42.61 3.58
947 996 2.606308 GGACGAACTTTGCGAGTACTCA 60.606 50.000 22.37 1.68 37.72 3.41
953 1002 3.562635 GGGGACGAACTTTGCGAG 58.437 61.111 0.00 0.00 0.00 5.03
1024 1073 1.280133 TGAGGCCACCAAGATCAAGAG 59.720 52.381 5.01 0.00 0.00 2.85
1086 1135 1.916651 CGTGATTGACGCTTCTGAGAG 59.083 52.381 0.00 0.00 42.21 3.20
1151 1266 6.585416 AGTCACCTTCTGCAATTTCAAAAAT 58.415 32.000 0.00 0.00 0.00 1.82
1156 1271 3.745975 CGTAGTCACCTTCTGCAATTTCA 59.254 43.478 0.00 0.00 0.00 2.69
1260 1381 9.289782 GTTAGGCTGGATTAATTCATTGACTAT 57.710 33.333 0.00 0.00 0.00 2.12
1264 1385 6.889177 TGTGTTAGGCTGGATTAATTCATTGA 59.111 34.615 0.00 0.00 0.00 2.57
1500 1622 1.741770 GGCTGTTGGCGTAGTCCAG 60.742 63.158 0.00 0.00 42.94 3.86
1760 1882 6.529220 ACATGATGGATCCTTCTTACTAAGC 58.471 40.000 23.94 0.66 0.00 3.09
1763 1885 9.213777 AGTAAACATGATGGATCCTTCTTACTA 57.786 33.333 24.17 10.77 0.00 1.82
1822 1948 9.342308 CCTACCAATCAAGAGCAAATCTTATAA 57.658 33.333 0.00 0.00 46.91 0.98
1829 1955 5.416952 CACTTCCTACCAATCAAGAGCAAAT 59.583 40.000 0.00 0.00 0.00 2.32
1845 1975 3.085533 GAGAGCACAGAGTCACTTCCTA 58.914 50.000 0.00 0.00 0.00 2.94
1912 2042 2.285220 CGAGTGTGTGTGAAGAAACCTG 59.715 50.000 0.00 0.00 0.00 4.00
1933 2063 5.641209 GTCTCTATGTACAATGCATCCATCC 59.359 44.000 0.00 0.00 0.00 3.51
1979 2109 5.066375 TGCTTATGTCGAGGGATCAAAAATG 59.934 40.000 0.00 0.00 0.00 2.32
2021 2151 2.779951 AATTTTGCGCGCCCTTTCCC 62.780 55.000 30.77 0.00 0.00 3.97
2022 2152 0.948623 AAATTTTGCGCGCCCTTTCC 60.949 50.000 30.77 0.00 0.00 3.13
2023 2153 0.163574 CAAATTTTGCGCGCCCTTTC 59.836 50.000 30.77 0.00 0.00 2.62
2031 2161 7.310006 TAAGATGGCTTTGCAAATTTTGCGC 62.310 40.000 24.67 21.34 46.11 6.09
2124 2313 0.968405 GCCAGCCCAAAATCAGACAA 59.032 50.000 0.00 0.00 0.00 3.18
2174 2363 3.396276 TGGTTCCCCTCACATCTGTAAAA 59.604 43.478 0.00 0.00 0.00 1.52
2370 2563 6.410942 TCTCAGTGTAACAGGGATATGATG 57.589 41.667 0.00 0.00 41.43 3.07
2472 2666 7.945033 TCAAATTAGGTGCATCAAAAACTTC 57.055 32.000 0.00 0.00 0.00 3.01
2551 2745 0.427504 CGCGCGAGTCTATGAATTCG 59.572 55.000 28.94 0.00 36.23 3.34
2731 2925 3.909776 AGTGTGTGTGATGCAAGAATG 57.090 42.857 0.00 0.00 0.00 2.67
2735 2929 4.754372 AATGTAGTGTGTGTGATGCAAG 57.246 40.909 0.00 0.00 0.00 4.01
2914 4941 4.036262 TCAGTATGCAACTTTGAGCGTTTT 59.964 37.500 0.00 0.00 35.76 2.43
2954 4988 6.710295 CCCTCGGATCAAAATACATGACATTA 59.290 38.462 0.00 0.00 0.00 1.90
3018 5052 4.159879 AGCCTGCGAAAGTATAACAGTAGT 59.840 41.667 0.00 0.00 0.00 2.73
3033 5067 1.103803 CTTGACCTAGTAGCCTGCGA 58.896 55.000 0.00 0.00 0.00 5.10
3080 5114 6.183360 ACACATCTATCACTTTTGCATACTGC 60.183 38.462 0.00 0.00 45.29 4.40
3178 5212 7.000472 AGCTTTGGCATATTAAGCATCTTCTA 59.000 34.615 20.27 0.00 45.08 2.10
3226 5262 2.802787 AGAGGGAATATCGCAGTTCG 57.197 50.000 0.00 0.00 40.15 3.95
3233 5270 5.106237 CGTAGGAAACCTAGAGGGAATATCG 60.106 48.000 0.00 0.00 36.71 2.92
3333 5415 1.944024 TGTGTTAGGTTTCGCCAAGTG 59.056 47.619 0.00 0.00 40.61 3.16
3473 5555 3.827008 ATGTGCTTCTGTCGATGGTAT 57.173 42.857 0.00 0.00 0.00 2.73
3520 5624 6.671614 ATCGTTTCAGTTTTACTGTTCACA 57.328 33.333 6.71 0.00 46.03 3.58
3618 5723 8.703336 CAACTACCATGAATGTATTCTATGACG 58.297 37.037 0.00 0.00 37.67 4.35
4015 6140 7.282224 ACATTCGCAAGCCAATTACTCTAAATA 59.718 33.333 0.00 0.00 37.18 1.40
4069 6194 5.932303 CGTTGAGAGGGTCTTAAATTCAAGA 59.068 40.000 0.00 0.00 32.11 3.02
4075 6200 3.008049 ACTGCGTTGAGAGGGTCTTAAAT 59.992 43.478 0.00 0.00 0.00 1.40
4078 6203 1.629043 ACTGCGTTGAGAGGGTCTTA 58.371 50.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.