Multiple sequence alignment - TraesCS1D01G083800

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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 TraesCS1D01G083800 chr1D 100.000 2321 0 0 501 2821 66685834 66683514 0.000000e+00 4287.0
1 TraesCS1D01G083800 chr1D 100.000 169 0 0 1 169 66686334 66686166 2.110000e-81 313.0
2 TraesCS1D01G083800 chr1A 93.419 1398 55 16 524 1909 65617102 65615730 0.000000e+00 2037.0
3 TraesCS1D01G083800 chr1A 91.429 280 21 2 2059 2338 65615625 65615349 5.700000e-102 381.0
4 TraesCS1D01G083800 chr1B 91.873 1452 67 29 501 1919 107371472 107370039 0.000000e+00 1980.0
5 TraesCS1D01G083800 chr1B 90.556 773 43 5 1916 2687 107364102 107363359 0.000000e+00 996.0
6 TraesCS1D01G083800 chr6D 88.514 148 15 2 2675 2821 455628754 455628608 8.030000e-41 178.0
7 TraesCS1D01G083800 chr6D 96.774 31 1 0 2650 2680 464820955 464820985 5.000000e-03 52.8
8 TraesCS1D01G083800 chr5D 89.630 135 10 3 2688 2821 530906855 530906986 4.830000e-38 169.0
9 TraesCS1D01G083800 chr5D 90.000 80 7 1 1 79 521151977 521152056 4.970000e-18 102.0
10 TraesCS1D01G083800 chr2D 87.681 138 13 3 2686 2821 229818941 229819076 1.050000e-34 158.0
11 TraesCS1D01G083800 chrUn 87.023 131 13 4 2693 2821 32005936 32006064 8.140000e-31 145.0
12 TraesCS1D01G083800 chrUn 87.023 131 13 4 2693 2821 333901666 333901794 8.140000e-31 145.0
13 TraesCS1D01G083800 chr3D 84.559 136 17 3 2688 2821 364957694 364957561 6.340000e-27 132.0
14 TraesCS1D01G083800 chr6A 93.827 81 3 2 2688 2768 434000737 434000815 1.370000e-23 121.0
15 TraesCS1D01G083800 chr6A 90.244 82 7 1 1 81 88127698 88127779 3.840000e-19 106.0
16 TraesCS1D01G083800 chr4A 92.045 88 4 3 2688 2774 535939576 535939661 1.370000e-23 121.0
17 TraesCS1D01G083800 chr7A 92.593 81 4 2 2688 2768 7302763 7302841 6.390000e-22 115.0
18 TraesCS1D01G083800 chr2B 92.500 80 5 1 1 79 655406192 655406271 2.300000e-21 113.0
19 TraesCS1D01G083800 chr2B 87.952 83 9 1 1 82 123152913 123152831 2.310000e-16 97.1
20 TraesCS1D01G083800 chr2B 88.750 80 8 1 1 79 606762331 606762410 2.310000e-16 97.1
21 TraesCS1D01G083800 chr4B 94.286 70 4 0 12 81 39297111 39297042 1.070000e-19 108.0
22 TraesCS1D01G083800 chr7B 94.118 68 4 0 12 79 376805401 376805334 1.380000e-18 104.0
23 TraesCS1D01G083800 chr7B 90.000 80 7 1 1 79 615386399 615386320 4.970000e-18 102.0
24 TraesCS1D01G083800 chr4D 90.000 80 7 1 1 79 384218550 384218629 4.970000e-18 102.0


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 TraesCS1D01G083800 chr1D 66683514 66686334 2820 True 2300 4287 100.000 1 2821 2 chr1D.!!$R1 2820
1 TraesCS1D01G083800 chr1A 65615349 65617102 1753 True 1209 2037 92.424 524 2338 2 chr1A.!!$R1 1814
2 TraesCS1D01G083800 chr1B 107370039 107371472 1433 True 1980 1980 91.873 501 1919 1 chr1B.!!$R2 1418
3 TraesCS1D01G083800 chr1B 107363359 107364102 743 True 996 996 90.556 1916 2687 1 chr1B.!!$R1 771

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
84 85 0.111639 GGTGGAGTTGGCCTAAACCA 59.888 55.0 3.32 6.91 38.16 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2113 0.179468 GGCGGGTATGAGTTGGCTTA 59.821 55.0 0.0 0.0 0.0 3.09 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
17 18 4.045469 ACGACCCATCACCCTACC 57.955 61.111 0.00 0.00 0.00 3.18
18 19 1.688187 ACGACCCATCACCCTACCC 60.688 63.158 0.00 0.00 0.00 3.69
19 20 1.687840 CGACCCATCACCCTACCCA 60.688 63.158 0.00 0.00 0.00 4.51
20 21 1.268992 CGACCCATCACCCTACCCAA 61.269 60.000 0.00 0.00 0.00 4.12
21 22 0.996583 GACCCATCACCCTACCCAAA 59.003 55.000 0.00 0.00 0.00 3.28
22 23 0.702316 ACCCATCACCCTACCCAAAC 59.298 55.000 0.00 0.00 0.00 2.93
23 24 0.393808 CCCATCACCCTACCCAAACG 60.394 60.000 0.00 0.00 0.00 3.60
24 25 0.616371 CCATCACCCTACCCAAACGA 59.384 55.000 0.00 0.00 0.00 3.85
25 26 1.003812 CCATCACCCTACCCAAACGAA 59.996 52.381 0.00 0.00 0.00 3.85
26 27 2.356741 CCATCACCCTACCCAAACGAAT 60.357 50.000 0.00 0.00 0.00 3.34
27 28 3.118186 CCATCACCCTACCCAAACGAATA 60.118 47.826 0.00 0.00 0.00 1.75
28 29 3.899052 TCACCCTACCCAAACGAATAG 57.101 47.619 0.00 0.00 0.00 1.73
29 30 3.443052 TCACCCTACCCAAACGAATAGA 58.557 45.455 0.00 0.00 0.00 1.98
30 31 3.839490 TCACCCTACCCAAACGAATAGAA 59.161 43.478 0.00 0.00 0.00 2.10
31 32 4.472108 TCACCCTACCCAAACGAATAGAAT 59.528 41.667 0.00 0.00 0.00 2.40
32 33 4.814771 CACCCTACCCAAACGAATAGAATC 59.185 45.833 0.00 0.00 0.00 2.52
33 34 4.141551 ACCCTACCCAAACGAATAGAATCC 60.142 45.833 0.00 0.00 0.00 3.01
34 35 4.141574 CCCTACCCAAACGAATAGAATCCA 60.142 45.833 0.00 0.00 0.00 3.41
35 36 5.057149 CCTACCCAAACGAATAGAATCCAG 58.943 45.833 0.00 0.00 0.00 3.86
36 37 4.837093 ACCCAAACGAATAGAATCCAGA 57.163 40.909 0.00 0.00 0.00 3.86
37 38 4.514401 ACCCAAACGAATAGAATCCAGAC 58.486 43.478 0.00 0.00 0.00 3.51
38 39 4.019681 ACCCAAACGAATAGAATCCAGACA 60.020 41.667 0.00 0.00 0.00 3.41
39 40 4.941263 CCCAAACGAATAGAATCCAGACAA 59.059 41.667 0.00 0.00 0.00 3.18
40 41 5.414454 CCCAAACGAATAGAATCCAGACAAA 59.586 40.000 0.00 0.00 0.00 2.83
41 42 6.072175 CCCAAACGAATAGAATCCAGACAAAA 60.072 38.462 0.00 0.00 0.00 2.44
42 43 6.801862 CCAAACGAATAGAATCCAGACAAAAC 59.198 38.462 0.00 0.00 0.00 2.43
43 44 5.779806 ACGAATAGAATCCAGACAAAACG 57.220 39.130 0.00 0.00 0.00 3.60
44 45 4.630069 ACGAATAGAATCCAGACAAAACGG 59.370 41.667 0.00 0.00 0.00 4.44
45 46 4.868171 CGAATAGAATCCAGACAAAACGGA 59.132 41.667 0.00 0.00 0.00 4.69
46 47 5.220416 CGAATAGAATCCAGACAAAACGGAC 60.220 44.000 0.00 0.00 0.00 4.79
47 48 2.413837 AGAATCCAGACAAAACGGACG 58.586 47.619 0.00 0.00 0.00 4.79
48 49 2.140717 GAATCCAGACAAAACGGACGT 58.859 47.619 0.00 0.00 0.00 4.34
49 50 1.792006 ATCCAGACAAAACGGACGTC 58.208 50.000 7.13 7.13 0.00 4.34
50 51 0.249573 TCCAGACAAAACGGACGTCC 60.250 55.000 25.28 25.28 0.00 4.79
60 61 4.764896 GGACGTCCGTTTGAGGTT 57.235 55.556 20.85 0.00 41.94 3.50
61 62 2.231820 GGACGTCCGTTTGAGGTTG 58.768 57.895 20.85 0.00 41.94 3.77
62 63 1.568025 GACGTCCGTTTGAGGTTGC 59.432 57.895 3.51 0.00 41.94 4.17
63 64 2.154427 GACGTCCGTTTGAGGTTGCG 62.154 60.000 3.51 0.00 41.94 4.85
64 65 2.251371 GTCCGTTTGAGGTTGCGC 59.749 61.111 0.00 0.00 0.00 6.09
65 66 3.342627 TCCGTTTGAGGTTGCGCG 61.343 61.111 0.00 0.00 0.00 6.86
66 67 4.383602 CCGTTTGAGGTTGCGCGG 62.384 66.667 8.83 0.00 0.00 6.46
67 68 3.645975 CGTTTGAGGTTGCGCGGT 61.646 61.111 8.83 0.00 0.00 5.68
68 69 2.051345 GTTTGAGGTTGCGCGGTG 60.051 61.111 8.83 0.00 0.00 4.94
69 70 3.283684 TTTGAGGTTGCGCGGTGG 61.284 61.111 8.83 0.00 0.00 4.61
70 71 3.758973 TTTGAGGTTGCGCGGTGGA 62.759 57.895 8.83 0.00 0.00 4.02
71 72 4.680237 TGAGGTTGCGCGGTGGAG 62.680 66.667 8.83 0.00 0.00 3.86
72 73 4.681978 GAGGTTGCGCGGTGGAGT 62.682 66.667 8.83 0.00 0.00 3.85
73 74 4.250305 AGGTTGCGCGGTGGAGTT 62.250 61.111 8.83 0.00 0.00 3.01
74 75 4.025401 GGTTGCGCGGTGGAGTTG 62.025 66.667 8.83 0.00 0.00 3.16
75 76 4.025401 GTTGCGCGGTGGAGTTGG 62.025 66.667 8.83 0.00 0.00 3.77
79 80 4.077184 CGCGGTGGAGTTGGCCTA 62.077 66.667 3.32 0.00 0.00 3.93
80 81 2.349755 GCGGTGGAGTTGGCCTAA 59.650 61.111 3.32 0.00 0.00 2.69
81 82 1.302993 GCGGTGGAGTTGGCCTAAA 60.303 57.895 3.32 0.00 0.00 1.85
82 83 1.583495 GCGGTGGAGTTGGCCTAAAC 61.583 60.000 3.32 0.00 0.00 2.01
83 84 0.958876 CGGTGGAGTTGGCCTAAACC 60.959 60.000 3.32 4.05 0.00 3.27
84 85 0.111639 GGTGGAGTTGGCCTAAACCA 59.888 55.000 3.32 6.91 38.16 3.67
85 86 1.244816 GTGGAGTTGGCCTAAACCAC 58.755 55.000 20.97 20.97 40.19 4.16
86 87 1.145571 TGGAGTTGGCCTAAACCACT 58.854 50.000 3.32 0.00 40.19 4.00
87 88 2.039348 GTGGAGTTGGCCTAAACCACTA 59.961 50.000 25.05 8.79 41.08 2.74
88 89 2.304761 TGGAGTTGGCCTAAACCACTAG 59.695 50.000 3.32 0.00 40.19 2.57
89 90 2.305052 GGAGTTGGCCTAAACCACTAGT 59.695 50.000 3.32 0.00 40.19 2.57
90 91 3.516700 GGAGTTGGCCTAAACCACTAGTA 59.483 47.826 3.32 0.00 40.19 1.82
91 92 4.382793 GGAGTTGGCCTAAACCACTAGTAG 60.383 50.000 3.32 0.00 40.19 2.57
92 93 3.518303 AGTTGGCCTAAACCACTAGTAGG 59.482 47.826 3.32 4.50 40.19 3.18
93 94 3.478175 TGGCCTAAACCACTAGTAGGA 57.522 47.619 12.07 0.00 37.21 2.94
94 95 3.102204 TGGCCTAAACCACTAGTAGGAC 58.898 50.000 12.07 9.82 42.59 3.85
95 96 2.433604 GGCCTAAACCACTAGTAGGACC 59.566 54.545 12.07 8.88 37.09 4.46
96 97 2.100418 GCCTAAACCACTAGTAGGACCG 59.900 54.545 12.07 0.00 37.21 4.79
97 98 3.359950 CCTAAACCACTAGTAGGACCGT 58.640 50.000 15.59 3.60 37.21 4.83
98 99 3.766051 CCTAAACCACTAGTAGGACCGTT 59.234 47.826 15.59 8.13 37.21 4.44
99 100 4.949856 CCTAAACCACTAGTAGGACCGTTA 59.050 45.833 15.59 8.62 37.21 3.18
100 101 4.790765 AAACCACTAGTAGGACCGTTAC 57.209 45.455 15.59 0.00 0.00 2.50
101 102 3.439857 ACCACTAGTAGGACCGTTACA 57.560 47.619 15.59 0.00 0.00 2.41
102 103 3.973425 ACCACTAGTAGGACCGTTACAT 58.027 45.455 15.59 0.00 0.00 2.29
103 104 3.950395 ACCACTAGTAGGACCGTTACATC 59.050 47.826 15.59 0.00 0.00 3.06
104 105 4.205587 CCACTAGTAGGACCGTTACATCT 58.794 47.826 1.45 0.00 0.00 2.90
105 106 4.643784 CCACTAGTAGGACCGTTACATCTT 59.356 45.833 1.45 0.00 0.00 2.40
106 107 5.126707 CCACTAGTAGGACCGTTACATCTTT 59.873 44.000 1.45 0.00 0.00 2.52
107 108 6.034591 CACTAGTAGGACCGTTACATCTTTG 58.965 44.000 1.45 0.00 0.00 2.77
108 109 5.713861 ACTAGTAGGACCGTTACATCTTTGT 59.286 40.000 1.45 0.00 39.98 2.83
109 110 4.817517 AGTAGGACCGTTACATCTTTGTG 58.182 43.478 0.00 0.00 36.53 3.33
110 111 4.525487 AGTAGGACCGTTACATCTTTGTGA 59.475 41.667 0.00 0.00 36.53 3.58
111 112 4.345859 AGGACCGTTACATCTTTGTGAA 57.654 40.909 0.00 0.00 36.53 3.18
112 113 4.062991 AGGACCGTTACATCTTTGTGAAC 58.937 43.478 0.00 0.00 36.53 3.18
113 114 3.810941 GGACCGTTACATCTTTGTGAACA 59.189 43.478 0.00 0.00 36.53 3.18
114 115 4.084013 GGACCGTTACATCTTTGTGAACAG 60.084 45.833 0.00 0.00 36.53 3.16
115 116 4.699637 ACCGTTACATCTTTGTGAACAGA 58.300 39.130 0.00 0.00 36.53 3.41
116 117 5.120399 ACCGTTACATCTTTGTGAACAGAA 58.880 37.500 0.00 0.00 36.53 3.02
117 118 5.007332 ACCGTTACATCTTTGTGAACAGAAC 59.993 40.000 0.00 0.00 36.53 3.01
118 119 5.440685 CGTTACATCTTTGTGAACAGAACC 58.559 41.667 0.00 0.00 36.53 3.62
119 120 5.007234 CGTTACATCTTTGTGAACAGAACCA 59.993 40.000 0.00 0.00 36.53 3.67
120 121 6.293407 CGTTACATCTTTGTGAACAGAACCAT 60.293 38.462 0.00 0.00 36.53 3.55
121 122 7.425606 GTTACATCTTTGTGAACAGAACCATT 58.574 34.615 0.00 0.00 36.53 3.16
122 123 6.076981 ACATCTTTGTGAACAGAACCATTC 57.923 37.500 0.00 0.00 33.85 2.67
123 124 5.593909 ACATCTTTGTGAACAGAACCATTCA 59.406 36.000 0.00 0.00 33.85 2.57
132 133 5.412594 TGAACAGAACCATTCACTTGATAGC 59.587 40.000 0.00 0.00 29.89 2.97
133 134 4.910195 ACAGAACCATTCACTTGATAGCA 58.090 39.130 0.00 0.00 0.00 3.49
134 135 4.697352 ACAGAACCATTCACTTGATAGCAC 59.303 41.667 0.00 0.00 0.00 4.40
135 136 4.696877 CAGAACCATTCACTTGATAGCACA 59.303 41.667 0.00 0.00 0.00 4.57
136 137 4.940046 AGAACCATTCACTTGATAGCACAG 59.060 41.667 0.00 0.00 0.00 3.66
137 138 4.292186 ACCATTCACTTGATAGCACAGT 57.708 40.909 0.00 0.00 0.00 3.55
138 139 4.005650 ACCATTCACTTGATAGCACAGTG 58.994 43.478 13.64 13.64 35.92 3.66
139 140 4.256110 CCATTCACTTGATAGCACAGTGA 58.744 43.478 16.69 16.69 38.82 3.41
140 141 4.093998 CCATTCACTTGATAGCACAGTGAC 59.906 45.833 18.94 0.00 39.53 3.67
141 142 4.335400 TTCACTTGATAGCACAGTGACA 57.665 40.909 18.94 11.49 39.53 3.58
142 143 4.541973 TCACTTGATAGCACAGTGACAT 57.458 40.909 16.69 0.00 37.30 3.06
143 144 4.248058 TCACTTGATAGCACAGTGACATG 58.752 43.478 16.69 0.00 37.30 3.21
144 145 3.005554 ACTTGATAGCACAGTGACATGC 58.994 45.455 4.15 3.91 42.39 4.06
145 146 2.028420 TGATAGCACAGTGACATGCC 57.972 50.000 4.15 0.00 43.12 4.40
146 147 1.303309 GATAGCACAGTGACATGCCC 58.697 55.000 4.15 0.00 43.12 5.36
147 148 0.620030 ATAGCACAGTGACATGCCCA 59.380 50.000 4.15 0.00 43.12 5.36
148 149 0.321564 TAGCACAGTGACATGCCCAC 60.322 55.000 4.15 9.98 43.12 4.61
149 150 1.898094 GCACAGTGACATGCCCACA 60.898 57.895 17.63 0.99 37.01 4.17
150 151 1.454572 GCACAGTGACATGCCCACAA 61.455 55.000 17.63 0.00 37.01 3.33
151 152 1.250328 CACAGTGACATGCCCACAAT 58.750 50.000 17.63 5.64 37.01 2.71
152 153 1.068125 CACAGTGACATGCCCACAATG 60.068 52.381 17.63 12.70 37.01 2.82
153 154 1.202915 ACAGTGACATGCCCACAATGA 60.203 47.619 17.63 0.00 37.01 2.57
154 155 1.887854 CAGTGACATGCCCACAATGAA 59.112 47.619 17.63 0.00 37.01 2.57
155 156 2.494471 CAGTGACATGCCCACAATGAAT 59.506 45.455 17.63 0.00 37.01 2.57
156 157 2.494471 AGTGACATGCCCACAATGAATG 59.506 45.455 17.63 0.00 37.01 2.67
157 158 2.231964 GTGACATGCCCACAATGAATGT 59.768 45.455 12.37 0.00 45.34 2.71
158 159 2.492881 TGACATGCCCACAATGAATGTC 59.507 45.455 4.71 4.71 44.70 3.06
159 160 2.492881 GACATGCCCACAATGAATGTCA 59.507 45.455 6.51 0.00 44.15 3.58
160 161 2.231964 ACATGCCCACAATGAATGTCAC 59.768 45.455 0.00 0.00 41.46 3.67
161 162 0.880441 TGCCCACAATGAATGTCACG 59.120 50.000 0.00 0.00 41.46 4.35
162 163 1.164411 GCCCACAATGAATGTCACGA 58.836 50.000 0.00 0.00 41.46 4.35
163 164 1.131126 GCCCACAATGAATGTCACGAG 59.869 52.381 0.00 0.00 41.46 4.18
164 165 1.739466 CCCACAATGAATGTCACGAGG 59.261 52.381 0.00 0.00 41.46 4.63
165 166 2.426522 CCACAATGAATGTCACGAGGT 58.573 47.619 0.00 0.00 41.46 3.85
166 167 2.160219 CCACAATGAATGTCACGAGGTG 59.840 50.000 0.00 0.00 41.46 4.00
167 168 2.160219 CACAATGAATGTCACGAGGTGG 59.840 50.000 0.00 0.00 41.46 4.61
168 169 1.739466 CAATGAATGTCACGAGGTGGG 59.261 52.381 0.00 0.00 33.87 4.61
576 584 3.605749 ATGCCGCTGTACGTTGCCT 62.606 57.895 0.00 0.00 41.42 4.75
577 585 2.125832 GCCGCTGTACGTTGCCTA 60.126 61.111 0.00 0.00 41.42 3.93
578 586 2.450345 GCCGCTGTACGTTGCCTAC 61.450 63.158 0.00 0.00 41.42 3.18
580 588 1.808390 CGCTGTACGTTGCCTACCC 60.808 63.158 0.00 0.00 36.87 3.69
581 589 1.595357 GCTGTACGTTGCCTACCCT 59.405 57.895 0.00 0.00 0.00 4.34
623 631 2.670019 CATGATCCCATCCATGGTGT 57.330 50.000 12.58 0.00 46.65 4.16
624 632 3.793819 CATGATCCCATCCATGGTGTA 57.206 47.619 12.58 0.00 46.65 2.90
756 764 7.093771 GGAAATGATAAACAATCCTCTTGTGGT 60.094 37.037 0.00 0.00 36.37 4.16
811 829 0.600557 GCCGTCCGATCAGATGATCT 59.399 55.000 18.13 0.00 46.58 2.75
929 947 3.547737 TCTCCCCCACCTTCCCCA 61.548 66.667 0.00 0.00 0.00 4.96
945 963 0.846870 CCCACCCCTTCTTTCCCTCT 60.847 60.000 0.00 0.00 0.00 3.69
952 970 2.260822 CCTTCTTTCCCTCTCTCACCA 58.739 52.381 0.00 0.00 0.00 4.17
953 971 2.027653 CCTTCTTTCCCTCTCTCACCAC 60.028 54.545 0.00 0.00 0.00 4.16
954 972 1.645710 TCTTTCCCTCTCTCACCACC 58.354 55.000 0.00 0.00 0.00 4.61
1040 1064 3.809832 ACAGCACAGTTGAATAGACACAC 59.190 43.478 0.00 0.00 0.00 3.82
1161 1190 2.360350 AGGAAGGCGTGCACCATG 60.360 61.111 12.15 0.00 0.00 3.66
1254 1283 3.993234 CGCACGCGCCATCATCTC 61.993 66.667 5.73 0.00 33.11 2.75
1266 1295 2.650813 ATCATCTCAAGCGGTCCGGC 62.651 60.000 14.38 5.47 0.00 6.13
1415 1450 0.250338 AAAGCCAAGGTCCTCGACAC 60.250 55.000 0.00 0.00 33.68 3.67
1417 1452 2.879233 GCCAAGGTCCTCGACACCA 61.879 63.158 10.74 0.00 36.23 4.17
1442 1477 2.887568 GTGACCTCGCGCTCCATG 60.888 66.667 5.56 0.00 0.00 3.66
1444 1479 2.583593 GACCTCGCGCTCCATGAC 60.584 66.667 5.56 0.00 0.00 3.06
1448 1483 3.647649 CTCGCGCTCCATGACCACA 62.648 63.158 5.56 0.00 0.00 4.17
1449 1484 3.190849 CGCGCTCCATGACCACAG 61.191 66.667 5.56 0.00 0.00 3.66
1450 1485 2.265739 GCGCTCCATGACCACAGA 59.734 61.111 0.00 0.00 0.00 3.41
1451 1486 1.153289 GCGCTCCATGACCACAGAT 60.153 57.895 0.00 0.00 0.00 2.90
1456 1491 2.752121 CTCCATGACCACAGATCGATG 58.248 52.381 0.54 0.00 0.00 3.84
1517 1555 1.079197 TACTGCCACATCCACTGCG 60.079 57.895 0.00 0.00 0.00 5.18
1593 1631 5.050023 CCTGAAACTCTTCTCCGTTTTCTTC 60.050 44.000 0.00 0.00 33.82 2.87
1679 1719 3.871485 AGCTAGCTTGGAGTGATTTGAG 58.129 45.455 12.68 0.00 0.00 3.02
1680 1720 3.262915 AGCTAGCTTGGAGTGATTTGAGT 59.737 43.478 12.68 0.00 0.00 3.41
1685 1725 5.809001 AGCTTGGAGTGATTTGAGTGATTA 58.191 37.500 0.00 0.00 0.00 1.75
1789 1832 1.452025 GATGTATTCGGTCGTGCATCG 59.548 52.381 0.00 0.00 41.41 3.84
1910 1957 4.097286 TGTCTTACTTTGGCAAAAGGTCAC 59.903 41.667 17.89 8.90 46.01 3.67
1921 1968 3.798889 GCAAAAGGTCACCAAGCTTAACC 60.799 47.826 0.00 5.03 44.83 2.85
1922 1969 3.306472 AAAGGTCACCAAGCTTAACCA 57.694 42.857 17.02 0.00 44.83 3.67
2026 2074 3.371034 ACCCCAGGTTAATTACATTGGC 58.629 45.455 3.76 0.00 33.81 4.52
2055 2103 3.384467 AGGAGTGGTTTGTTCATGTTTGG 59.616 43.478 0.00 0.00 0.00 3.28
2076 2124 6.061022 TGGAGAACATAATAAGCCAACTCA 57.939 37.500 0.00 0.00 0.00 3.41
2081 2129 6.998673 AGAACATAATAAGCCAACTCATACCC 59.001 38.462 0.00 0.00 0.00 3.69
2170 2251 2.308570 TCTGGCAGCAGATTCCCTAAAA 59.691 45.455 10.34 0.00 0.00 1.52
2173 2254 2.625314 GGCAGCAGATTCCCTAAAATCC 59.375 50.000 0.00 0.00 36.49 3.01
2328 2409 9.076596 GCATATAAACTCAATTTCAACTCCAAC 57.923 33.333 0.00 0.00 0.00 3.77
2345 2426 2.233355 CAACATCGCATCAACGTGAAC 58.767 47.619 0.00 0.00 0.00 3.18
2346 2427 0.796312 ACATCGCATCAACGTGAACC 59.204 50.000 0.00 0.00 0.00 3.62
2388 2469 5.580297 ACACCACACAATTCAACAACATTTC 59.420 36.000 0.00 0.00 0.00 2.17
2392 2473 7.336427 ACCACACAATTCAACAACATTTCAAAT 59.664 29.630 0.00 0.00 0.00 2.32
2438 2519 2.799126 ATAGGGTCCGAATGCAACAA 57.201 45.000 0.00 0.00 0.00 2.83
2444 2525 5.197451 AGGGTCCGAATGCAACAAATAATA 58.803 37.500 0.00 0.00 0.00 0.98
2541 2622 1.400846 GTGAAGCTGCTCATGTGATGG 59.599 52.381 1.00 0.00 0.00 3.51
2545 2626 0.100682 GCTGCTCATGTGATGGCTTG 59.899 55.000 0.00 0.00 0.00 4.01
2546 2627 0.100682 CTGCTCATGTGATGGCTTGC 59.899 55.000 0.00 0.00 0.00 4.01
2571 2652 4.299155 TCAATCTTTCGATATGCCTCGAC 58.701 43.478 3.01 0.00 46.53 4.20
2584 2665 1.464997 GCCTCGACGAAAGCTTCAATT 59.535 47.619 0.00 0.00 0.00 2.32
2595 2676 4.326504 AAGCTTCAATTTGGTTCAGGTG 57.673 40.909 0.00 0.00 0.00 4.00
2596 2677 2.036346 AGCTTCAATTTGGTTCAGGTGC 59.964 45.455 0.00 0.00 0.00 5.01
2651 2732 3.382048 AGTCGTAGTTCACTTGGGAAC 57.618 47.619 7.61 7.61 45.87 3.62
2680 2761 5.173664 TCATCCTCGATGATCATGTTATGC 58.826 41.667 14.30 0.00 43.11 3.14
2690 2771 3.497103 TCATGTTATGCAGGATCCAGG 57.503 47.619 15.82 6.81 32.44 4.45
2691 2772 1.884579 CATGTTATGCAGGATCCAGGC 59.115 52.381 15.82 17.47 0.00 4.85
2692 2773 0.183492 TGTTATGCAGGATCCAGGCC 59.817 55.000 21.50 0.00 0.00 5.19
2693 2774 0.538287 GTTATGCAGGATCCAGGCCC 60.538 60.000 21.50 7.16 0.00 5.80
2694 2775 2.055689 TTATGCAGGATCCAGGCCCG 62.056 60.000 21.50 0.00 0.00 6.13
2696 2777 4.554036 GCAGGATCCAGGCCCGTC 62.554 72.222 15.82 0.00 0.00 4.79
2697 2778 4.227134 CAGGATCCAGGCCCGTCG 62.227 72.222 15.82 0.00 0.00 5.12
2698 2779 4.458829 AGGATCCAGGCCCGTCGA 62.459 66.667 15.82 0.00 0.00 4.20
2699 2780 3.234730 GGATCCAGGCCCGTCGAT 61.235 66.667 6.95 0.00 0.00 3.59
2700 2781 2.029666 GATCCAGGCCCGTCGATG 59.970 66.667 0.00 0.00 0.00 3.84
2701 2782 2.443952 ATCCAGGCCCGTCGATGA 60.444 61.111 6.11 0.00 0.00 2.92
2702 2783 2.427540 GATCCAGGCCCGTCGATGAG 62.428 65.000 6.11 0.00 0.00 2.90
2703 2784 4.227134 CCAGGCCCGTCGATGAGG 62.227 72.222 6.11 6.99 0.00 3.86
2745 2826 3.726004 GGGGCCCCCAAAATCTTG 58.274 61.111 33.01 0.00 44.65 3.02
2753 2834 3.726004 CAAAATCTTGGGGCCCCC 58.274 61.111 38.81 20.71 45.71 5.40
2763 2844 3.878667 GGGCCCCCGATTGGAGAG 61.879 72.222 12.23 0.00 37.49 3.20
2764 2845 2.768344 GGCCCCCGATTGGAGAGA 60.768 66.667 0.00 0.00 37.49 3.10
2765 2846 2.375345 GGCCCCCGATTGGAGAGAA 61.375 63.158 0.00 0.00 37.49 2.87
2766 2847 1.607612 GCCCCCGATTGGAGAGAAA 59.392 57.895 0.00 0.00 37.49 2.52
2767 2848 0.034477 GCCCCCGATTGGAGAGAAAA 60.034 55.000 0.00 0.00 37.49 2.29
2768 2849 1.751437 CCCCCGATTGGAGAGAAAAC 58.249 55.000 0.00 0.00 37.49 2.43
2769 2850 1.369625 CCCCGATTGGAGAGAAAACG 58.630 55.000 0.00 0.00 37.49 3.60
2770 2851 0.727398 CCCGATTGGAGAGAAAACGC 59.273 55.000 0.00 0.00 37.49 4.84
2771 2852 1.438651 CCGATTGGAGAGAAAACGCA 58.561 50.000 0.00 0.00 37.49 5.24
2772 2853 1.804151 CCGATTGGAGAGAAAACGCAA 59.196 47.619 0.00 0.00 37.49 4.85
2773 2854 2.159653 CCGATTGGAGAGAAAACGCAAG 60.160 50.000 0.00 0.00 40.53 4.01
2774 2855 2.159653 CGATTGGAGAGAAAACGCAAGG 60.160 50.000 0.00 0.00 46.39 3.61
2775 2856 2.341846 TTGGAGAGAAAACGCAAGGT 57.658 45.000 0.00 0.00 46.39 3.50
2817 2898 5.549742 AAAGAGAGATAATCTGCCTCTGG 57.450 43.478 0.00 0.00 38.84 3.86
2818 2899 3.509442 AGAGAGATAATCTGCCTCTGGG 58.491 50.000 0.00 0.00 38.84 4.45
2819 2900 2.566724 GAGAGATAATCTGCCTCTGGGG 59.433 54.545 0.00 0.00 38.84 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.688187 GGGTAGGGTGATGGGTCGT 60.688 63.158 0.00 0.00 0.00 4.34
1 2 1.268992 TTGGGTAGGGTGATGGGTCG 61.269 60.000 0.00 0.00 0.00 4.79
2 3 0.996583 TTTGGGTAGGGTGATGGGTC 59.003 55.000 0.00 0.00 0.00 4.46
3 4 0.702316 GTTTGGGTAGGGTGATGGGT 59.298 55.000 0.00 0.00 0.00 4.51
4 5 0.393808 CGTTTGGGTAGGGTGATGGG 60.394 60.000 0.00 0.00 0.00 4.00
5 6 0.616371 TCGTTTGGGTAGGGTGATGG 59.384 55.000 0.00 0.00 0.00 3.51
6 7 2.483014 TTCGTTTGGGTAGGGTGATG 57.517 50.000 0.00 0.00 0.00 3.07
7 8 4.035112 TCTATTCGTTTGGGTAGGGTGAT 58.965 43.478 0.00 0.00 0.00 3.06
8 9 3.443052 TCTATTCGTTTGGGTAGGGTGA 58.557 45.455 0.00 0.00 0.00 4.02
9 10 3.899052 TCTATTCGTTTGGGTAGGGTG 57.101 47.619 0.00 0.00 0.00 4.61
10 11 4.141551 GGATTCTATTCGTTTGGGTAGGGT 60.142 45.833 0.00 0.00 0.00 4.34
11 12 4.141574 TGGATTCTATTCGTTTGGGTAGGG 60.142 45.833 0.00 0.00 0.00 3.53
12 13 5.031066 TGGATTCTATTCGTTTGGGTAGG 57.969 43.478 0.00 0.00 0.00 3.18
13 14 5.753921 GTCTGGATTCTATTCGTTTGGGTAG 59.246 44.000 0.00 0.00 0.00 3.18
14 15 5.188163 TGTCTGGATTCTATTCGTTTGGGTA 59.812 40.000 0.00 0.00 0.00 3.69
15 16 4.019681 TGTCTGGATTCTATTCGTTTGGGT 60.020 41.667 0.00 0.00 0.00 4.51
16 17 4.513442 TGTCTGGATTCTATTCGTTTGGG 58.487 43.478 0.00 0.00 0.00 4.12
17 18 6.494893 TTTGTCTGGATTCTATTCGTTTGG 57.505 37.500 0.00 0.00 0.00 3.28
18 19 6.519761 CGTTTTGTCTGGATTCTATTCGTTTG 59.480 38.462 0.00 0.00 0.00 2.93
19 20 6.348213 CCGTTTTGTCTGGATTCTATTCGTTT 60.348 38.462 0.00 0.00 0.00 3.60
20 21 5.121768 CCGTTTTGTCTGGATTCTATTCGTT 59.878 40.000 0.00 0.00 0.00 3.85
21 22 4.630069 CCGTTTTGTCTGGATTCTATTCGT 59.370 41.667 0.00 0.00 0.00 3.85
22 23 4.868171 TCCGTTTTGTCTGGATTCTATTCG 59.132 41.667 0.00 0.00 0.00 3.34
23 24 5.220416 CGTCCGTTTTGTCTGGATTCTATTC 60.220 44.000 0.00 0.00 33.63 1.75
24 25 4.630069 CGTCCGTTTTGTCTGGATTCTATT 59.370 41.667 0.00 0.00 33.63 1.73
25 26 4.181578 CGTCCGTTTTGTCTGGATTCTAT 58.818 43.478 0.00 0.00 33.63 1.98
26 27 3.006110 ACGTCCGTTTTGTCTGGATTCTA 59.994 43.478 0.00 0.00 33.63 2.10
27 28 2.224209 ACGTCCGTTTTGTCTGGATTCT 60.224 45.455 0.00 0.00 33.63 2.40
28 29 2.140717 ACGTCCGTTTTGTCTGGATTC 58.859 47.619 0.00 0.00 33.63 2.52
29 30 2.140717 GACGTCCGTTTTGTCTGGATT 58.859 47.619 3.51 0.00 33.63 3.01
30 31 1.607251 GGACGTCCGTTTTGTCTGGAT 60.607 52.381 20.85 0.00 33.63 3.41
31 32 0.249573 GGACGTCCGTTTTGTCTGGA 60.250 55.000 20.85 0.00 33.21 3.86
32 33 2.231820 GGACGTCCGTTTTGTCTGG 58.768 57.895 20.85 0.00 33.21 3.86
43 44 1.838568 GCAACCTCAAACGGACGTCC 61.839 60.000 25.28 25.28 0.00 4.79
44 45 1.568025 GCAACCTCAAACGGACGTC 59.432 57.895 7.13 7.13 0.00 4.34
45 46 2.241880 CGCAACCTCAAACGGACGT 61.242 57.895 0.00 0.00 0.00 4.34
46 47 2.549282 CGCAACCTCAAACGGACG 59.451 61.111 0.00 0.00 0.00 4.79
47 48 2.251371 GCGCAACCTCAAACGGAC 59.749 61.111 0.30 0.00 0.00 4.79
48 49 3.342627 CGCGCAACCTCAAACGGA 61.343 61.111 8.75 0.00 0.00 4.69
49 50 4.383602 CCGCGCAACCTCAAACGG 62.384 66.667 8.75 0.00 0.00 4.44
50 51 3.645975 ACCGCGCAACCTCAAACG 61.646 61.111 8.75 0.00 0.00 3.60
51 52 2.051345 CACCGCGCAACCTCAAAC 60.051 61.111 8.75 0.00 0.00 2.93
52 53 3.283684 CCACCGCGCAACCTCAAA 61.284 61.111 8.75 0.00 0.00 2.69
53 54 4.243008 TCCACCGCGCAACCTCAA 62.243 61.111 8.75 0.00 0.00 3.02
54 55 4.680237 CTCCACCGCGCAACCTCA 62.680 66.667 8.75 0.00 0.00 3.86
55 56 4.681978 ACTCCACCGCGCAACCTC 62.682 66.667 8.75 0.00 0.00 3.85
56 57 4.250305 AACTCCACCGCGCAACCT 62.250 61.111 8.75 0.00 0.00 3.50
57 58 4.025401 CAACTCCACCGCGCAACC 62.025 66.667 8.75 0.00 0.00 3.77
58 59 4.025401 CCAACTCCACCGCGCAAC 62.025 66.667 8.75 0.00 0.00 4.17
62 63 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
63 64 1.302993 TTTAGGCCAACTCCACCGC 60.303 57.895 5.01 0.00 0.00 5.68
64 65 0.958876 GGTTTAGGCCAACTCCACCG 60.959 60.000 5.01 0.00 0.00 4.94
65 66 0.111639 TGGTTTAGGCCAACTCCACC 59.888 55.000 5.01 2.33 35.25 4.61
66 67 1.202891 AGTGGTTTAGGCCAACTCCAC 60.203 52.381 23.40 23.40 40.68 4.02
67 68 1.145571 AGTGGTTTAGGCCAACTCCA 58.854 50.000 5.01 5.51 40.68 3.86
68 69 2.305052 ACTAGTGGTTTAGGCCAACTCC 59.695 50.000 5.01 2.48 40.68 3.85
69 70 3.697619 ACTAGTGGTTTAGGCCAACTC 57.302 47.619 5.01 0.00 40.68 3.01
70 71 3.518303 CCTACTAGTGGTTTAGGCCAACT 59.482 47.826 5.01 0.82 40.68 3.16
71 72 3.516700 TCCTACTAGTGGTTTAGGCCAAC 59.483 47.826 5.01 0.36 40.68 3.77
72 73 3.516700 GTCCTACTAGTGGTTTAGGCCAA 59.483 47.826 5.01 0.00 40.68 4.52
73 74 3.102204 GTCCTACTAGTGGTTTAGGCCA 58.898 50.000 5.01 0.00 35.93 5.36
74 75 2.433604 GGTCCTACTAGTGGTTTAGGCC 59.566 54.545 5.39 0.00 0.00 5.19
75 76 2.100418 CGGTCCTACTAGTGGTTTAGGC 59.900 54.545 5.39 0.65 0.00 3.93
76 77 3.359950 ACGGTCCTACTAGTGGTTTAGG 58.640 50.000 5.39 3.79 0.00 2.69
77 78 5.415701 TGTAACGGTCCTACTAGTGGTTTAG 59.584 44.000 5.39 0.00 0.00 1.85
78 79 5.321102 TGTAACGGTCCTACTAGTGGTTTA 58.679 41.667 5.39 1.10 0.00 2.01
79 80 4.151883 TGTAACGGTCCTACTAGTGGTTT 58.848 43.478 5.39 1.89 0.00 3.27
80 81 3.766545 TGTAACGGTCCTACTAGTGGTT 58.233 45.455 5.39 3.07 0.00 3.67
81 82 3.439857 TGTAACGGTCCTACTAGTGGT 57.560 47.619 5.39 0.00 0.00 4.16
82 83 4.205587 AGATGTAACGGTCCTACTAGTGG 58.794 47.826 5.39 1.52 0.00 4.00
83 84 5.831702 AAGATGTAACGGTCCTACTAGTG 57.168 43.478 5.39 0.00 0.00 2.74
84 85 5.713861 ACAAAGATGTAACGGTCCTACTAGT 59.286 40.000 0.00 0.00 38.24 2.57
85 86 6.034591 CACAAAGATGTAACGGTCCTACTAG 58.965 44.000 0.00 0.00 37.82 2.57
86 87 5.711506 TCACAAAGATGTAACGGTCCTACTA 59.288 40.000 0.00 0.00 37.82 1.82
87 88 4.525487 TCACAAAGATGTAACGGTCCTACT 59.475 41.667 0.00 0.00 37.82 2.57
88 89 4.813027 TCACAAAGATGTAACGGTCCTAC 58.187 43.478 0.00 0.00 37.82 3.18
89 90 5.221481 TGTTCACAAAGATGTAACGGTCCTA 60.221 40.000 0.00 0.00 37.82 2.94
90 91 4.062991 GTTCACAAAGATGTAACGGTCCT 58.937 43.478 0.00 0.00 37.82 3.85
91 92 3.810941 TGTTCACAAAGATGTAACGGTCC 59.189 43.478 0.00 0.00 37.82 4.46
92 93 4.748102 TCTGTTCACAAAGATGTAACGGTC 59.252 41.667 0.00 0.00 37.82 4.79
93 94 4.699637 TCTGTTCACAAAGATGTAACGGT 58.300 39.130 0.00 0.00 37.82 4.83
94 95 5.440685 GTTCTGTTCACAAAGATGTAACGG 58.559 41.667 0.00 0.00 37.82 4.44
95 96 5.007234 TGGTTCTGTTCACAAAGATGTAACG 59.993 40.000 0.00 0.00 37.82 3.18
96 97 6.371809 TGGTTCTGTTCACAAAGATGTAAC 57.628 37.500 0.00 0.00 37.82 2.50
97 98 7.284261 TGAATGGTTCTGTTCACAAAGATGTAA 59.716 33.333 0.00 0.00 37.82 2.41
98 99 6.770303 TGAATGGTTCTGTTCACAAAGATGTA 59.230 34.615 0.00 0.00 37.82 2.29
99 100 5.593909 TGAATGGTTCTGTTCACAAAGATGT 59.406 36.000 0.00 0.00 41.61 3.06
100 101 6.075762 TGAATGGTTCTGTTCACAAAGATG 57.924 37.500 0.00 0.00 29.93 2.90
108 109 5.412594 GCTATCAAGTGAATGGTTCTGTTCA 59.587 40.000 0.00 0.00 32.31 3.18
109 110 5.412594 TGCTATCAAGTGAATGGTTCTGTTC 59.587 40.000 0.00 0.00 0.00 3.18
110 111 5.182001 GTGCTATCAAGTGAATGGTTCTGTT 59.818 40.000 0.00 0.00 0.00 3.16
111 112 4.697352 GTGCTATCAAGTGAATGGTTCTGT 59.303 41.667 0.00 0.00 0.00 3.41
112 113 4.696877 TGTGCTATCAAGTGAATGGTTCTG 59.303 41.667 0.00 0.00 0.00 3.02
113 114 4.910195 TGTGCTATCAAGTGAATGGTTCT 58.090 39.130 0.00 0.00 0.00 3.01
114 115 4.697352 ACTGTGCTATCAAGTGAATGGTTC 59.303 41.667 0.00 0.00 0.00 3.62
115 116 4.456911 CACTGTGCTATCAAGTGAATGGTT 59.543 41.667 0.00 0.00 32.77 3.67
116 117 4.005650 CACTGTGCTATCAAGTGAATGGT 58.994 43.478 0.00 0.00 32.77 3.55
117 118 4.093998 GTCACTGTGCTATCAAGTGAATGG 59.906 45.833 2.12 0.00 40.54 3.16
118 119 4.692155 TGTCACTGTGCTATCAAGTGAATG 59.308 41.667 2.12 0.00 40.54 2.67
119 120 4.898320 TGTCACTGTGCTATCAAGTGAAT 58.102 39.130 2.12 0.00 40.54 2.57
120 121 4.335400 TGTCACTGTGCTATCAAGTGAA 57.665 40.909 2.12 0.00 40.54 3.18
121 122 4.248058 CATGTCACTGTGCTATCAAGTGA 58.752 43.478 2.12 0.76 37.20 3.41
122 123 3.181513 GCATGTCACTGTGCTATCAAGTG 60.182 47.826 2.12 0.00 38.30 3.16
123 124 3.005554 GCATGTCACTGTGCTATCAAGT 58.994 45.455 2.12 0.00 38.30 3.16
124 125 2.353889 GGCATGTCACTGTGCTATCAAG 59.646 50.000 2.12 0.00 41.04 3.02
125 126 2.358957 GGCATGTCACTGTGCTATCAA 58.641 47.619 2.12 0.00 41.04 2.57
126 127 1.407299 GGGCATGTCACTGTGCTATCA 60.407 52.381 2.12 0.59 41.04 2.15
127 128 1.303309 GGGCATGTCACTGTGCTATC 58.697 55.000 2.12 0.00 41.04 2.08
128 129 0.620030 TGGGCATGTCACTGTGCTAT 59.380 50.000 2.12 0.00 41.04 2.97
129 130 0.321564 GTGGGCATGTCACTGTGCTA 60.322 55.000 2.12 0.00 41.04 3.49
130 131 1.601759 GTGGGCATGTCACTGTGCT 60.602 57.895 2.12 0.00 41.04 4.40
131 132 1.454572 TTGTGGGCATGTCACTGTGC 61.455 55.000 17.65 0.00 40.55 4.57
132 133 1.068125 CATTGTGGGCATGTCACTGTG 60.068 52.381 17.65 0.17 36.21 3.66
133 134 1.202915 TCATTGTGGGCATGTCACTGT 60.203 47.619 17.65 7.58 36.21 3.55
134 135 1.536940 TCATTGTGGGCATGTCACTG 58.463 50.000 17.65 11.21 36.21 3.66
135 136 2.291209 TTCATTGTGGGCATGTCACT 57.709 45.000 17.65 1.72 36.21 3.41
136 137 2.231964 ACATTCATTGTGGGCATGTCAC 59.768 45.455 0.00 7.00 37.11 3.67
137 138 2.492881 GACATTCATTGTGGGCATGTCA 59.507 45.455 0.00 0.00 42.21 3.58
138 139 2.492881 TGACATTCATTGTGGGCATGTC 59.507 45.455 4.04 4.04 42.72 3.06
139 140 2.231964 GTGACATTCATTGTGGGCATGT 59.768 45.455 0.00 0.00 39.18 3.21
140 141 2.732912 CGTGACATTCATTGTGGGCATG 60.733 50.000 0.00 0.00 39.18 4.06
141 142 1.473677 CGTGACATTCATTGTGGGCAT 59.526 47.619 0.00 0.00 39.18 4.40
142 143 0.880441 CGTGACATTCATTGTGGGCA 59.120 50.000 0.00 0.00 39.18 5.36
143 144 1.131126 CTCGTGACATTCATTGTGGGC 59.869 52.381 0.00 0.00 39.18 5.36
144 145 1.739466 CCTCGTGACATTCATTGTGGG 59.261 52.381 0.00 0.00 39.18 4.61
145 146 2.160219 CACCTCGTGACATTCATTGTGG 59.840 50.000 0.00 0.00 39.18 4.17
146 147 2.160219 CCACCTCGTGACATTCATTGTG 59.840 50.000 0.00 0.00 39.18 3.33
147 148 2.426522 CCACCTCGTGACATTCATTGT 58.573 47.619 0.00 0.00 42.79 2.71
148 149 1.739466 CCCACCTCGTGACATTCATTG 59.261 52.381 0.00 0.00 35.23 2.82
149 150 2.113860 CCCACCTCGTGACATTCATT 57.886 50.000 0.00 0.00 35.23 2.57
150 151 3.861341 CCCACCTCGTGACATTCAT 57.139 52.632 0.00 0.00 35.23 2.57
571 579 0.834687 AGTGGACGAAGGGTAGGCAA 60.835 55.000 0.00 0.00 0.00 4.52
576 584 1.100510 CGATGAGTGGACGAAGGGTA 58.899 55.000 0.00 0.00 0.00 3.69
577 585 1.605058 CCGATGAGTGGACGAAGGGT 61.605 60.000 0.00 0.00 0.00 4.34
578 586 1.141881 CCGATGAGTGGACGAAGGG 59.858 63.158 0.00 0.00 0.00 3.95
580 588 0.803768 CTGCCGATGAGTGGACGAAG 60.804 60.000 0.00 0.00 0.00 3.79
581 589 1.215382 CTGCCGATGAGTGGACGAA 59.785 57.895 0.00 0.00 0.00 3.85
623 631 0.815213 GGAGCAAGCGCACATGGATA 60.815 55.000 11.47 0.00 42.27 2.59
624 632 2.117156 GGAGCAAGCGCACATGGAT 61.117 57.895 11.47 0.00 42.27 3.41
687 695 6.350528 GGTGAGTGAGTGAGAACAGAATCATA 60.351 42.308 0.00 0.00 0.00 2.15
811 829 2.667199 TCTCGTCGACAGCCGTCA 60.667 61.111 17.16 0.00 42.74 4.35
929 947 1.152271 TGAGAGAGGGAAAGAAGGGGT 59.848 52.381 0.00 0.00 0.00 4.95
1030 1048 6.042093 TGGAAGTTTCTCTCTGTGTGTCTATT 59.958 38.462 0.00 0.00 0.00 1.73
1034 1058 4.060038 TGGAAGTTTCTCTCTGTGTGTC 57.940 45.455 0.00 0.00 0.00 3.67
1040 1064 5.240183 TCAAAGCAATGGAAGTTTCTCTCTG 59.760 40.000 0.00 0.00 0.00 3.35
1082 1109 5.882040 TCTATGTGGTATGTCTAGCTAGCT 58.118 41.667 23.12 23.12 0.00 3.32
1083 1110 6.576662 TTCTATGTGGTATGTCTAGCTAGC 57.423 41.667 16.35 6.62 0.00 3.42
1218 1247 2.357034 GGCGTCTTCTTGCCGTCA 60.357 61.111 0.00 0.00 42.22 4.35
1248 1277 2.892640 CCGGACCGCTTGAGATGA 59.107 61.111 8.86 0.00 0.00 2.92
1415 1450 4.436998 GAGGTCACGAGGCGGTGG 62.437 72.222 10.98 0.00 38.46 4.61
1517 1555 2.094854 CCAAAGGCTCTGAAATCTGCAC 60.095 50.000 0.00 0.00 0.00 4.57
1593 1631 5.166398 GGATTCATTTCAGGCTCAACAAAG 58.834 41.667 0.00 0.00 0.00 2.77
1789 1832 1.939934 TCATTGATTGGCGAATCGGAC 59.060 47.619 15.54 0.00 40.96 4.79
1910 1957 8.695456 AGGAATTAACAATATGGTTAAGCTTGG 58.305 33.333 18.15 0.00 43.99 3.61
2055 2103 7.173390 GGGTATGAGTTGGCTTATTATGTTCTC 59.827 40.741 0.00 0.00 0.00 2.87
2065 2113 0.179468 GGCGGGTATGAGTTGGCTTA 59.821 55.000 0.00 0.00 0.00 3.09
2066 2114 1.077716 GGCGGGTATGAGTTGGCTT 60.078 57.895 0.00 0.00 0.00 4.35
2067 2115 2.590092 GGCGGGTATGAGTTGGCT 59.410 61.111 0.00 0.00 0.00 4.75
2076 2124 1.818555 GACCTACAACGGCGGGTAT 59.181 57.895 13.24 0.00 31.60 2.73
2081 2129 0.797249 CTTCTCGACCTACAACGGCG 60.797 60.000 4.80 4.80 0.00 6.46
2129 2210 8.870116 TGCCAGAGTTGCTCTTATAATAGATAA 58.130 33.333 2.20 0.00 38.99 1.75
2137 2218 2.501316 TGCTGCCAGAGTTGCTCTTATA 59.499 45.455 0.00 0.00 38.99 0.98
2138 2219 1.280133 TGCTGCCAGAGTTGCTCTTAT 59.720 47.619 0.00 0.00 38.99 1.73
2170 2251 7.067737 TCGAAAACAAGTTTTAAAGTCAGGGAT 59.932 33.333 10.60 0.00 42.26 3.85
2173 2254 6.471198 GGTCGAAAACAAGTTTTAAAGTCAGG 59.529 38.462 10.60 0.00 42.26 3.86
2216 2297 4.286707 TGCCCACTTGCTCTATAGACTTA 58.713 43.478 0.00 0.00 0.00 2.24
2224 2305 3.559171 CCTTAGTTTGCCCACTTGCTCTA 60.559 47.826 0.00 0.00 0.00 2.43
2302 2383 9.076596 GTTGGAGTTGAAATTGAGTTTATATGC 57.923 33.333 0.00 0.00 0.00 3.14
2314 2395 4.218200 TGATGCGATGTTGGAGTTGAAATT 59.782 37.500 0.00 0.00 0.00 1.82
2328 2409 0.247262 CGGTTCACGTTGATGCGATG 60.247 55.000 0.00 0.00 37.93 3.84
2345 2426 3.179599 GTGTCGCAAAATGAAAACTTCGG 59.820 43.478 0.00 0.00 0.00 4.30
2346 2427 3.179599 GGTGTCGCAAAATGAAAACTTCG 59.820 43.478 0.00 0.00 0.00 3.79
2412 2493 5.766150 TGCATTCGGACCCTATTTATTTG 57.234 39.130 0.00 0.00 0.00 2.32
2485 2566 2.871022 GCATCAGTGGAAGCTACATGAG 59.129 50.000 0.00 0.00 34.98 2.90
2499 2580 0.665835 GGATCTCGTCGAGCATCAGT 59.334 55.000 23.77 7.83 33.17 3.41
2571 2652 3.983344 CCTGAACCAAATTGAAGCTTTCG 59.017 43.478 0.00 0.00 0.00 3.46
2584 2665 1.373435 CCGTAGGCACCTGAACCAA 59.627 57.895 0.00 0.00 46.14 3.67
2651 2732 3.446658 TCATCGAGGATGAGAGGGG 57.553 57.895 0.00 0.00 43.11 4.79
2680 2761 4.227134 CGACGGGCCTGGATCCTG 62.227 72.222 18.00 12.81 36.07 3.86
2687 2768 4.227134 CCCTCATCGACGGGCCTG 62.227 72.222 11.02 11.02 32.83 4.85
2709 2790 4.025401 GTGCGGTCGGCCACTTTG 62.025 66.667 6.96 0.00 42.61 2.77
2710 2791 4.555709 TGTGCGGTCGGCCACTTT 62.556 61.111 6.96 0.00 42.61 2.66
2711 2792 4.988598 CTGTGCGGTCGGCCACTT 62.989 66.667 6.96 0.00 42.61 3.16
2723 2804 4.952102 TTTTGGGGGCCCCTGTGC 62.952 66.667 40.43 23.95 45.70 4.57
2724 2805 1.989508 GATTTTGGGGGCCCCTGTG 60.990 63.158 40.43 0.00 45.70 3.66
2725 2806 1.750087 AAGATTTTGGGGGCCCCTGT 61.750 55.000 40.43 23.71 45.70 4.00
2726 2807 1.080907 AAGATTTTGGGGGCCCCTG 59.919 57.895 40.43 0.00 45.70 4.45
2727 2808 1.080907 CAAGATTTTGGGGGCCCCT 59.919 57.895 40.43 22.72 45.70 4.79
2728 2809 3.726004 CAAGATTTTGGGGGCCCC 58.274 61.111 36.02 36.02 45.71 5.80
2736 2817 2.358372 CGGGGGCCCCAAGATTTTG 61.358 63.158 41.80 18.29 45.83 2.44
2737 2818 1.885593 ATCGGGGGCCCCAAGATTTT 61.886 55.000 41.80 21.71 45.83 1.82
2738 2819 1.885593 AATCGGGGGCCCCAAGATTT 61.886 55.000 38.14 28.04 45.83 2.17
2739 2820 2.324560 AATCGGGGGCCCCAAGATT 61.325 57.895 38.14 38.14 45.83 2.40
2740 2821 2.699938 AATCGGGGGCCCCAAGAT 60.700 61.111 41.80 37.00 45.83 2.40
2741 2822 3.738481 CAATCGGGGGCCCCAAGA 61.738 66.667 41.80 36.55 45.83 3.02
2742 2823 4.839706 CCAATCGGGGGCCCCAAG 62.840 72.222 41.80 32.87 45.83 3.61
2746 2827 3.878667 CTCTCCAATCGGGGGCCC 61.879 72.222 15.76 15.76 36.91 5.80
2747 2828 1.921869 TTTCTCTCCAATCGGGGGCC 61.922 60.000 0.00 0.00 36.91 5.80
2748 2829 0.034477 TTTTCTCTCCAATCGGGGGC 60.034 55.000 0.00 0.00 36.91 5.80
2749 2830 1.751437 GTTTTCTCTCCAATCGGGGG 58.249 55.000 0.00 0.00 39.19 5.40
2750 2831 1.369625 CGTTTTCTCTCCAATCGGGG 58.630 55.000 0.00 0.00 37.22 5.73
2751 2832 0.727398 GCGTTTTCTCTCCAATCGGG 59.273 55.000 0.00 0.00 38.37 5.14
2752 2833 1.438651 TGCGTTTTCTCTCCAATCGG 58.561 50.000 0.00 0.00 0.00 4.18
2753 2834 2.159653 CCTTGCGTTTTCTCTCCAATCG 60.160 50.000 0.00 0.00 0.00 3.34
2754 2835 2.814336 ACCTTGCGTTTTCTCTCCAATC 59.186 45.455 0.00 0.00 0.00 2.67
2755 2836 2.863809 ACCTTGCGTTTTCTCTCCAAT 58.136 42.857 0.00 0.00 0.00 3.16
2756 2837 2.341846 ACCTTGCGTTTTCTCTCCAA 57.658 45.000 0.00 0.00 0.00 3.53
2757 2838 2.341846 AACCTTGCGTTTTCTCTCCA 57.658 45.000 0.00 0.00 0.00 3.86
2793 2874 6.355747 CCAGAGGCAGATTATCTCTCTTTTT 58.644 40.000 9.79 0.00 35.89 1.94
2794 2875 5.163216 CCCAGAGGCAGATTATCTCTCTTTT 60.163 44.000 9.79 0.00 35.89 2.27
2795 2876 4.347583 CCCAGAGGCAGATTATCTCTCTTT 59.652 45.833 9.79 0.00 35.89 2.52
2796 2877 3.903090 CCCAGAGGCAGATTATCTCTCTT 59.097 47.826 9.79 0.00 35.89 2.85
2797 2878 3.509442 CCCAGAGGCAGATTATCTCTCT 58.491 50.000 7.40 7.40 35.89 3.10
2798 2879 2.566724 CCCCAGAGGCAGATTATCTCTC 59.433 54.545 3.55 3.55 35.89 3.20
2799 2880 2.618794 CCCCAGAGGCAGATTATCTCT 58.381 52.381 0.00 0.00 38.29 3.10


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

AutoCloner maintained by Alex Coulton.