Multiple sequence alignment - TraesCS7A01G532100

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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 TraesCS7A01G532100 chr7A 100.000 2690 0 0 1 2690 710959567 710956878 0.000000e+00 4968.0
1 TraesCS7A01G532100 chr7A 89.470 1472 150 5 248 1715 711172574 711171104 0.000000e+00 1855.0
2 TraesCS7A01G532100 chr7D 95.657 1819 72 6 224 2038 617197245 617199060 0.000000e+00 2915.0
3 TraesCS7A01G532100 chr7D 89.913 1497 140 9 223 1715 617378196 617376707 0.000000e+00 1917.0
4 TraesCS7A01G532100 chr7B 91.489 1504 114 11 223 1722 711489528 711488035 0.000000e+00 2056.0
5 TraesCS7A01G532100 chr7B 91.406 1408 116 5 288 1691 711475569 711476975 0.000000e+00 1925.0
6 TraesCS7A01G532100 chr4A 88.078 1275 140 6 406 1671 599612138 599613409 0.000000e+00 1502.0
7 TraesCS7A01G532100 chr4A 83.085 1277 204 10 416 1689 24557430 24556163 0.000000e+00 1151.0
8 TraesCS7A01G532100 chrUn 87.765 1275 144 6 412 1677 241849809 241848538 0.000000e+00 1480.0
9 TraesCS7A01G532100 chr4D 82.707 1278 207 12 416 1689 443206683 443207950 0.000000e+00 1123.0
10 TraesCS7A01G532100 chr4D 93.066 649 29 5 2043 2688 385487421 385486786 0.000000e+00 935.0
11 TraesCS7A01G532100 chr2A 91.020 657 53 3 2038 2690 104332188 104332842 0.000000e+00 881.0
12 TraesCS7A01G532100 chr5B 93.333 495 23 2 2196 2690 598051400 598051884 0.000000e+00 723.0
13 TraesCS7A01G532100 chr5B 89.474 114 12 0 112 225 634554196 634554083 7.760000e-31 145.0
14 TraesCS7A01G532100 chr5B 88.596 114 13 0 112 225 634458768 634458655 3.610000e-29 139.0
15 TraesCS7A01G532100 chr5B 93.590 78 4 1 2067 2144 598051329 598051405 6.090000e-22 115.0
16 TraesCS7A01G532100 chr1B 76.809 470 70 20 2047 2513 666643718 666643285 7.490000e-56 228.0
17 TraesCS7A01G532100 chr1B 90.351 114 11 0 112 225 639906418 639906531 1.670000e-32 150.0
18 TraesCS7A01G532100 chr6D 83.544 158 26 0 2174 2331 428552422 428552579 6.000000e-32 148.0
19 TraesCS7A01G532100 chr5A 89.474 114 12 0 112 225 391770363 391770250 7.760000e-31 145.0
20 TraesCS7A01G532100 chr1D 87.719 114 14 0 112 225 34663038 34663151 1.680000e-27 134.0
21 TraesCS7A01G532100 chr1D 73.711 194 41 6 2142 2328 58826026 58825836 1.730000e-07 67.6
22 TraesCS7A01G532100 chr3B 87.387 111 14 0 116 226 582462534 582462644 7.820000e-26 128.0
23 TraesCS7A01G532100 chr4B 85.965 114 16 0 112 225 499289188 499289301 3.640000e-24 122.0


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 TraesCS7A01G532100 chr7A 710956878 710959567 2689 True 4968 4968 100.0000 1 2690 1 chr7A.!!$R1 2689
1 TraesCS7A01G532100 chr7A 711171104 711172574 1470 True 1855 1855 89.4700 248 1715 1 chr7A.!!$R2 1467
2 TraesCS7A01G532100 chr7D 617197245 617199060 1815 False 2915 2915 95.6570 224 2038 1 chr7D.!!$F1 1814
3 TraesCS7A01G532100 chr7D 617376707 617378196 1489 True 1917 1917 89.9130 223 1715 1 chr7D.!!$R1 1492
4 TraesCS7A01G532100 chr7B 711488035 711489528 1493 True 2056 2056 91.4890 223 1722 1 chr7B.!!$R1 1499
5 TraesCS7A01G532100 chr7B 711475569 711476975 1406 False 1925 1925 91.4060 288 1691 1 chr7B.!!$F1 1403
6 TraesCS7A01G532100 chr4A 599612138 599613409 1271 False 1502 1502 88.0780 406 1671 1 chr4A.!!$F1 1265
7 TraesCS7A01G532100 chr4A 24556163 24557430 1267 True 1151 1151 83.0850 416 1689 1 chr4A.!!$R1 1273
8 TraesCS7A01G532100 chrUn 241848538 241849809 1271 True 1480 1480 87.7650 412 1677 1 chrUn.!!$R1 1265
9 TraesCS7A01G532100 chr4D 443206683 443207950 1267 False 1123 1123 82.7070 416 1689 1 chr4D.!!$F1 1273
10 TraesCS7A01G532100 chr4D 385486786 385487421 635 True 935 935 93.0660 2043 2688 1 chr4D.!!$R1 645
11 TraesCS7A01G532100 chr2A 104332188 104332842 654 False 881 881 91.0200 2038 2690 1 chr2A.!!$F1 652
12 TraesCS7A01G532100 chr5B 598051329 598051884 555 False 419 723 93.4615 2067 2690 2 chr5B.!!$F1 623

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
51 52 0.038159 AGTGGAAGCACTAGACGCAC 60.038 55.0 10.72 0.0 32.97 5.34 F
173 174 0.105964 CACCACCTCAACACCGAGAA 59.894 55.0 0.00 0.0 34.79 2.87 F
1416 1433 0.179045 AGCTGCAGACAAAACTCCGT 60.179 50.0 20.43 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1238 0.594028 GCGCGATCTCGGTGATGTTA 60.594 55.000 12.1 0.0 40.23 2.41 R
1539 1556 1.669760 GCCGACCATCCAAACACGA 60.670 57.895 0.0 0.0 0.00 4.35 R
2665 2693 1.688735 CTATGGACCTCCGATCAGCAA 59.311 52.381 0.0 0.0 39.43 3.91 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
43 44 8.991783 TGTACTACTATATAAGTGGAAGCACT 57.008 34.615 0.00 0.00 38.95 4.40
47 48 9.287373 ACTACTATATAAGTGGAAGCACTAGAC 57.713 37.037 0.00 0.00 38.95 2.59
48 49 7.204496 ACTATATAAGTGGAAGCACTAGACG 57.796 40.000 0.00 0.00 36.93 4.18
49 50 2.649331 TAAGTGGAAGCACTAGACGC 57.351 50.000 0.00 0.00 34.56 5.19
50 51 0.679505 AAGTGGAAGCACTAGACGCA 59.320 50.000 10.72 0.00 34.56 5.24
51 52 0.038159 AGTGGAAGCACTAGACGCAC 60.038 55.000 10.72 0.00 32.97 5.34
52 53 1.014564 GTGGAAGCACTAGACGCACC 61.015 60.000 10.72 12.33 0.00 5.01
53 54 1.292223 GGAAGCACTAGACGCACCA 59.708 57.895 10.72 0.00 0.00 4.17
54 55 0.320421 GGAAGCACTAGACGCACCAA 60.320 55.000 10.72 0.00 0.00 3.67
55 56 1.508632 GAAGCACTAGACGCACCAAA 58.491 50.000 10.72 0.00 0.00 3.28
56 57 2.076863 GAAGCACTAGACGCACCAAAT 58.923 47.619 10.72 0.00 0.00 2.32
57 58 3.259064 GAAGCACTAGACGCACCAAATA 58.741 45.455 10.72 0.00 0.00 1.40
58 59 3.328382 AGCACTAGACGCACCAAATAA 57.672 42.857 10.72 0.00 0.00 1.40
59 60 3.670625 AGCACTAGACGCACCAAATAAA 58.329 40.909 10.72 0.00 0.00 1.40
60 61 3.684788 AGCACTAGACGCACCAAATAAAG 59.315 43.478 10.72 0.00 0.00 1.85
61 62 3.682858 GCACTAGACGCACCAAATAAAGA 59.317 43.478 0.00 0.00 0.00 2.52
62 63 4.435651 GCACTAGACGCACCAAATAAAGAC 60.436 45.833 0.00 0.00 0.00 3.01
63 64 4.688879 CACTAGACGCACCAAATAAAGACA 59.311 41.667 0.00 0.00 0.00 3.41
64 65 4.689345 ACTAGACGCACCAAATAAAGACAC 59.311 41.667 0.00 0.00 0.00 3.67
65 66 3.472652 AGACGCACCAAATAAAGACACA 58.527 40.909 0.00 0.00 0.00 3.72
66 67 3.250040 AGACGCACCAAATAAAGACACAC 59.750 43.478 0.00 0.00 0.00 3.82
67 68 3.211045 ACGCACCAAATAAAGACACACT 58.789 40.909 0.00 0.00 0.00 3.55
68 69 4.382291 ACGCACCAAATAAAGACACACTA 58.618 39.130 0.00 0.00 0.00 2.74
69 70 4.817464 ACGCACCAAATAAAGACACACTAA 59.183 37.500 0.00 0.00 0.00 2.24
70 71 5.144359 CGCACCAAATAAAGACACACTAAC 58.856 41.667 0.00 0.00 0.00 2.34
71 72 5.458015 GCACCAAATAAAGACACACTAACC 58.542 41.667 0.00 0.00 0.00 2.85
72 73 5.564063 GCACCAAATAAAGACACACTAACCC 60.564 44.000 0.00 0.00 0.00 4.11
73 74 4.758165 ACCAAATAAAGACACACTAACCCG 59.242 41.667 0.00 0.00 0.00 5.28
74 75 4.998672 CCAAATAAAGACACACTAACCCGA 59.001 41.667 0.00 0.00 0.00 5.14
75 76 5.121768 CCAAATAAAGACACACTAACCCGAG 59.878 44.000 0.00 0.00 0.00 4.63
76 77 2.165319 AAAGACACACTAACCCGAGC 57.835 50.000 0.00 0.00 0.00 5.03
77 78 1.339097 AAGACACACTAACCCGAGCT 58.661 50.000 0.00 0.00 0.00 4.09
78 79 0.889306 AGACACACTAACCCGAGCTC 59.111 55.000 2.73 2.73 0.00 4.09
79 80 0.601558 GACACACTAACCCGAGCTCA 59.398 55.000 15.40 0.00 0.00 4.26
80 81 1.204941 GACACACTAACCCGAGCTCAT 59.795 52.381 15.40 0.00 0.00 2.90
81 82 2.426024 GACACACTAACCCGAGCTCATA 59.574 50.000 15.40 0.12 0.00 2.15
82 83 2.829720 ACACACTAACCCGAGCTCATAA 59.170 45.455 15.40 0.00 0.00 1.90
83 84 3.259876 ACACACTAACCCGAGCTCATAAA 59.740 43.478 15.40 0.00 0.00 1.40
84 85 3.865745 CACACTAACCCGAGCTCATAAAG 59.134 47.826 15.40 6.54 0.00 1.85
85 86 3.118738 ACACTAACCCGAGCTCATAAAGG 60.119 47.826 15.40 6.06 0.00 3.11
86 87 3.132289 CACTAACCCGAGCTCATAAAGGA 59.868 47.826 15.40 0.00 0.00 3.36
87 88 3.773119 ACTAACCCGAGCTCATAAAGGAA 59.227 43.478 15.40 0.21 0.00 3.36
88 89 3.713826 AACCCGAGCTCATAAAGGAAA 57.286 42.857 15.40 0.00 0.00 3.13
89 90 3.268023 ACCCGAGCTCATAAAGGAAAG 57.732 47.619 15.40 0.00 0.00 2.62
90 91 2.838202 ACCCGAGCTCATAAAGGAAAGA 59.162 45.455 15.40 0.00 0.00 2.52
91 92 3.118592 ACCCGAGCTCATAAAGGAAAGAG 60.119 47.826 15.40 0.00 0.00 2.85
92 93 3.118592 CCCGAGCTCATAAAGGAAAGAGT 60.119 47.826 15.40 0.00 0.00 3.24
93 94 4.099573 CCCGAGCTCATAAAGGAAAGAGTA 59.900 45.833 15.40 0.00 0.00 2.59
94 95 5.044558 CCGAGCTCATAAAGGAAAGAGTAC 58.955 45.833 15.40 0.00 0.00 2.73
95 96 5.163499 CCGAGCTCATAAAGGAAAGAGTACT 60.163 44.000 15.40 0.00 0.00 2.73
96 97 6.334202 CGAGCTCATAAAGGAAAGAGTACTT 58.666 40.000 15.40 0.00 38.05 2.24
97 98 6.474102 CGAGCTCATAAAGGAAAGAGTACTTC 59.526 42.308 15.40 0.00 35.05 3.01
98 99 6.645306 AGCTCATAAAGGAAAGAGTACTTCC 58.355 40.000 4.16 4.16 35.05 3.46
99 100 6.213600 AGCTCATAAAGGAAAGAGTACTTCCA 59.786 38.462 13.40 0.00 35.05 3.53
100 101 6.879458 GCTCATAAAGGAAAGAGTACTTCCAA 59.121 38.462 13.40 0.92 35.05 3.53
101 102 7.390718 GCTCATAAAGGAAAGAGTACTTCCAAA 59.609 37.037 13.40 0.61 35.05 3.28
102 103 8.848474 TCATAAAGGAAAGAGTACTTCCAAAG 57.152 34.615 13.40 1.04 35.05 2.77
103 104 8.656806 TCATAAAGGAAAGAGTACTTCCAAAGA 58.343 33.333 13.40 2.97 35.05 2.52
104 105 9.284968 CATAAAGGAAAGAGTACTTCCAAAGAA 57.715 33.333 13.40 0.00 35.05 2.52
105 106 9.862149 ATAAAGGAAAGAGTACTTCCAAAGAAA 57.138 29.630 13.40 0.00 35.05 2.52
106 107 8.589701 AAAGGAAAGAGTACTTCCAAAGAAAA 57.410 30.769 13.40 0.00 35.05 2.29
107 108 7.809546 AGGAAAGAGTACTTCCAAAGAAAAG 57.190 36.000 13.40 0.00 35.05 2.27
108 109 7.574607 AGGAAAGAGTACTTCCAAAGAAAAGA 58.425 34.615 13.40 0.00 35.05 2.52
109 110 8.053355 AGGAAAGAGTACTTCCAAAGAAAAGAA 58.947 33.333 13.40 0.00 35.05 2.52
110 111 8.683615 GGAAAGAGTACTTCCAAAGAAAAGAAA 58.316 33.333 7.14 0.00 35.05 2.52
111 112 9.723447 GAAAGAGTACTTCCAAAGAAAAGAAAG 57.277 33.333 0.00 0.00 35.05 2.62
112 113 9.462606 AAAGAGTACTTCCAAAGAAAAGAAAGA 57.537 29.630 0.00 0.00 35.05 2.52
113 114 8.669946 AGAGTACTTCCAAAGAAAAGAAAGAG 57.330 34.615 0.00 0.00 0.00 2.85
114 115 7.227711 AGAGTACTTCCAAAGAAAAGAAAGAGC 59.772 37.037 0.00 0.00 0.00 4.09
115 116 5.175090 ACTTCCAAAGAAAAGAAAGAGCG 57.825 39.130 0.00 0.00 0.00 5.03
116 117 4.640647 ACTTCCAAAGAAAAGAAAGAGCGT 59.359 37.500 0.00 0.00 0.00 5.07
117 118 5.820947 ACTTCCAAAGAAAAGAAAGAGCGTA 59.179 36.000 0.00 0.00 0.00 4.42
118 119 6.486993 ACTTCCAAAGAAAAGAAAGAGCGTAT 59.513 34.615 0.00 0.00 0.00 3.06
119 120 6.877611 TCCAAAGAAAAGAAAGAGCGTATT 57.122 33.333 0.00 0.00 0.00 1.89
120 121 7.272037 TCCAAAGAAAAGAAAGAGCGTATTT 57.728 32.000 0.00 0.00 0.00 1.40
121 122 7.360361 TCCAAAGAAAAGAAAGAGCGTATTTC 58.640 34.615 3.91 3.91 37.00 2.17
122 123 6.582672 CCAAAGAAAAGAAAGAGCGTATTTCC 59.417 38.462 7.45 0.00 37.37 3.13
123 124 5.532025 AGAAAAGAAAGAGCGTATTTCCG 57.468 39.130 7.45 0.00 37.37 4.30
135 136 4.857871 CGTATTTCCGCTGATGAAGAAA 57.142 40.909 0.00 0.00 33.13 2.52
136 137 4.826500 CGTATTTCCGCTGATGAAGAAAG 58.173 43.478 0.00 0.00 32.19 2.62
137 138 4.566759 CGTATTTCCGCTGATGAAGAAAGA 59.433 41.667 0.00 0.00 32.19 2.52
138 139 5.063438 CGTATTTCCGCTGATGAAGAAAGAA 59.937 40.000 0.00 0.00 32.19 2.52
139 140 5.557891 ATTTCCGCTGATGAAGAAAGAAG 57.442 39.130 0.00 0.00 32.19 2.85
140 141 2.350522 TCCGCTGATGAAGAAAGAAGC 58.649 47.619 0.00 0.00 0.00 3.86
141 142 1.399791 CCGCTGATGAAGAAAGAAGCC 59.600 52.381 0.00 0.00 0.00 4.35
142 143 2.079158 CGCTGATGAAGAAAGAAGCCA 58.921 47.619 0.00 0.00 0.00 4.75
143 144 2.681848 CGCTGATGAAGAAAGAAGCCAT 59.318 45.455 0.00 0.00 0.00 4.40
144 145 3.128242 CGCTGATGAAGAAAGAAGCCATT 59.872 43.478 0.00 0.00 0.00 3.16
145 146 4.670347 GCTGATGAAGAAAGAAGCCATTC 58.330 43.478 0.00 0.00 35.52 2.67
146 147 4.730035 GCTGATGAAGAAAGAAGCCATTCG 60.730 45.833 0.00 0.00 40.58 3.34
147 148 3.691118 TGATGAAGAAAGAAGCCATTCGG 59.309 43.478 0.00 0.00 40.58 4.30
148 149 3.417069 TGAAGAAAGAAGCCATTCGGA 57.583 42.857 0.00 0.00 40.58 4.55
149 150 3.074412 TGAAGAAAGAAGCCATTCGGAC 58.926 45.455 0.00 0.00 40.58 4.79
150 151 2.859165 AGAAAGAAGCCATTCGGACA 57.141 45.000 0.00 0.00 40.58 4.02
151 152 3.140325 AGAAAGAAGCCATTCGGACAA 57.860 42.857 0.00 0.00 40.58 3.18
152 153 2.814336 AGAAAGAAGCCATTCGGACAAC 59.186 45.455 0.00 0.00 40.58 3.32
153 154 1.156736 AAGAAGCCATTCGGACAACG 58.843 50.000 0.00 0.00 46.11 4.10
154 155 1.134694 GAAGCCATTCGGACAACGC 59.865 57.895 0.00 0.00 43.86 4.84
155 156 1.573829 GAAGCCATTCGGACAACGCA 61.574 55.000 0.00 0.00 43.86 5.24
156 157 1.852067 AAGCCATTCGGACAACGCAC 61.852 55.000 0.00 0.00 43.86 5.34
157 158 2.867472 CCATTCGGACAACGCACC 59.133 61.111 0.00 0.00 43.86 5.01
158 159 1.963855 CCATTCGGACAACGCACCA 60.964 57.895 0.00 0.00 43.86 4.17
159 160 1.206578 CATTCGGACAACGCACCAC 59.793 57.895 0.00 0.00 43.86 4.16
160 161 1.964373 ATTCGGACAACGCACCACC 60.964 57.895 0.00 0.00 43.86 4.61
161 162 2.391724 ATTCGGACAACGCACCACCT 62.392 55.000 0.00 0.00 43.86 4.00
162 163 2.981977 TTCGGACAACGCACCACCTC 62.982 60.000 0.00 0.00 43.86 3.85
163 164 2.110213 GGACAACGCACCACCTCA 59.890 61.111 0.00 0.00 0.00 3.86
164 165 1.525077 GGACAACGCACCACCTCAA 60.525 57.895 0.00 0.00 0.00 3.02
165 166 1.647084 GACAACGCACCACCTCAAC 59.353 57.895 0.00 0.00 0.00 3.18
166 167 1.078072 ACAACGCACCACCTCAACA 60.078 52.632 0.00 0.00 0.00 3.33
167 168 1.355210 CAACGCACCACCTCAACAC 59.645 57.895 0.00 0.00 0.00 3.32
168 169 1.822186 AACGCACCACCTCAACACC 60.822 57.895 0.00 0.00 0.00 4.16
169 170 3.345808 CGCACCACCTCAACACCG 61.346 66.667 0.00 0.00 0.00 4.94
170 171 2.110213 GCACCACCTCAACACCGA 59.890 61.111 0.00 0.00 0.00 4.69
171 172 1.961277 GCACCACCTCAACACCGAG 60.961 63.158 0.00 0.00 0.00 4.63
172 173 1.745890 CACCACCTCAACACCGAGA 59.254 57.895 0.00 0.00 34.79 4.04
173 174 0.105964 CACCACCTCAACACCGAGAA 59.894 55.000 0.00 0.00 34.79 2.87
174 175 0.834612 ACCACCTCAACACCGAGAAA 59.165 50.000 0.00 0.00 34.79 2.52
175 176 1.210967 ACCACCTCAACACCGAGAAAA 59.789 47.619 0.00 0.00 34.79 2.29
176 177 2.158667 ACCACCTCAACACCGAGAAAAT 60.159 45.455 0.00 0.00 34.79 1.82
177 178 3.071892 ACCACCTCAACACCGAGAAAATA 59.928 43.478 0.00 0.00 34.79 1.40
178 179 4.069304 CCACCTCAACACCGAGAAAATAA 58.931 43.478 0.00 0.00 34.79 1.40
179 180 4.700213 CCACCTCAACACCGAGAAAATAAT 59.300 41.667 0.00 0.00 34.79 1.28
180 181 5.391950 CCACCTCAACACCGAGAAAATAATG 60.392 44.000 0.00 0.00 34.79 1.90
181 182 4.156008 ACCTCAACACCGAGAAAATAATGC 59.844 41.667 0.00 0.00 34.79 3.56
182 183 4.155826 CCTCAACACCGAGAAAATAATGCA 59.844 41.667 0.00 0.00 34.79 3.96
183 184 5.335583 CCTCAACACCGAGAAAATAATGCAA 60.336 40.000 0.00 0.00 34.79 4.08
184 185 6.078202 TCAACACCGAGAAAATAATGCAAA 57.922 33.333 0.00 0.00 0.00 3.68
185 186 6.507900 TCAACACCGAGAAAATAATGCAAAA 58.492 32.000 0.00 0.00 0.00 2.44
186 187 6.640499 TCAACACCGAGAAAATAATGCAAAAG 59.360 34.615 0.00 0.00 0.00 2.27
187 188 6.325919 ACACCGAGAAAATAATGCAAAAGA 57.674 33.333 0.00 0.00 0.00 2.52
188 189 6.149633 ACACCGAGAAAATAATGCAAAAGAC 58.850 36.000 0.00 0.00 0.00 3.01
189 190 5.572896 CACCGAGAAAATAATGCAAAAGACC 59.427 40.000 0.00 0.00 0.00 3.85
190 191 5.102313 CCGAGAAAATAATGCAAAAGACCC 58.898 41.667 0.00 0.00 0.00 4.46
191 192 5.336372 CCGAGAAAATAATGCAAAAGACCCA 60.336 40.000 0.00 0.00 0.00 4.51
192 193 6.155827 CGAGAAAATAATGCAAAAGACCCAA 58.844 36.000 0.00 0.00 0.00 4.12
193 194 6.308766 CGAGAAAATAATGCAAAAGACCCAAG 59.691 38.462 0.00 0.00 0.00 3.61
194 195 7.066307 AGAAAATAATGCAAAAGACCCAAGT 57.934 32.000 0.00 0.00 0.00 3.16
195 196 7.154656 AGAAAATAATGCAAAAGACCCAAGTC 58.845 34.615 0.00 0.00 43.89 3.01
206 207 3.040147 GACCCAAGTCTTTGATGACGA 57.960 47.619 0.00 0.00 41.47 4.20
207 208 3.399330 GACCCAAGTCTTTGATGACGAA 58.601 45.455 0.00 0.00 41.47 3.85
208 209 3.139077 ACCCAAGTCTTTGATGACGAAC 58.861 45.455 0.00 0.00 41.47 3.95
209 210 3.181454 ACCCAAGTCTTTGATGACGAACT 60.181 43.478 0.00 0.00 41.47 3.01
210 211 3.433615 CCCAAGTCTTTGATGACGAACTC 59.566 47.826 0.00 0.00 41.47 3.01
211 212 3.433615 CCAAGTCTTTGATGACGAACTCC 59.566 47.826 0.00 0.00 41.47 3.85
212 213 2.947852 AGTCTTTGATGACGAACTCCG 58.052 47.619 0.00 0.00 41.47 4.63
213 214 5.322038 CAAGTCTTTGATGACGAACTCCGT 61.322 45.833 0.00 0.00 45.01 4.69
214 215 7.290726 CAAGTCTTTGATGACGAACTCCGTG 62.291 48.000 0.00 0.00 43.50 4.94
221 222 3.449042 CGAACTCCGTGCGAAGAC 58.551 61.111 0.00 0.00 36.57 3.01
222 223 2.426183 CGAACTCCGTGCGAAGACG 61.426 63.158 0.00 0.00 36.57 4.18
223 224 1.081641 GAACTCCGTGCGAAGACGA 60.082 57.895 0.00 0.00 42.10 4.20
224 225 1.066114 GAACTCCGTGCGAAGACGAG 61.066 60.000 0.00 0.00 42.10 4.18
225 226 1.793134 AACTCCGTGCGAAGACGAGT 61.793 55.000 0.00 0.00 42.10 4.18
226 227 0.952497 ACTCCGTGCGAAGACGAGTA 60.952 55.000 0.00 0.00 42.10 2.59
227 228 0.520827 CTCCGTGCGAAGACGAGTAC 60.521 60.000 0.00 0.00 42.10 2.73
228 229 0.952497 TCCGTGCGAAGACGAGTACT 60.952 55.000 0.00 0.00 42.10 2.73
229 230 0.520827 CCGTGCGAAGACGAGTACTC 60.521 60.000 13.18 13.18 42.10 2.59
230 231 0.443088 CGTGCGAAGACGAGTACTCT 59.557 55.000 20.34 7.83 42.10 3.24
231 232 1.657594 CGTGCGAAGACGAGTACTCTA 59.342 52.381 20.34 0.00 42.10 2.43
245 247 7.369607 ACGAGTACTCTAAAGGAAGAGAAAAC 58.630 38.462 20.34 3.61 44.93 2.43
336 338 2.357034 GACAACTTCCTCGCCGCA 60.357 61.111 0.00 0.00 0.00 5.69
349 351 1.811266 GCCGCATCATGTGTCGTCT 60.811 57.895 0.00 0.00 0.00 4.18
352 354 1.349234 CGCATCATGTGTCGTCTTCA 58.651 50.000 0.00 0.00 0.00 3.02
387 389 1.744639 GGCGGAGATCATCAGCTGA 59.255 57.895 20.79 20.79 46.97 4.26
439 444 4.233635 CGGCCGTCGTCTACCTCG 62.234 72.222 19.50 0.00 0.00 4.63
825 839 4.745170 CGACATCATCGTGAACAAGTAG 57.255 45.455 0.00 0.00 46.25 2.57
1223 1237 1.991230 CCGGGAATTCACTCCAGGT 59.009 57.895 6.07 0.00 43.68 4.00
1224 1238 0.328258 CCGGGAATTCACTCCAGGTT 59.672 55.000 6.07 0.00 43.68 3.50
1335 1352 1.492176 CATGTCAAGCCCTACATCCCT 59.508 52.381 0.00 0.00 34.12 4.20
1360 1377 1.228094 TCCATGGCGTTCAAGCACA 60.228 52.632 6.96 0.00 39.27 4.57
1410 1427 0.249280 TCGACGAGCTGCAGACAAAA 60.249 50.000 20.43 0.00 0.00 2.44
1416 1433 0.179045 AGCTGCAGACAAAACTCCGT 60.179 50.000 20.43 0.00 0.00 4.69
1452 1469 4.492160 GAGGCGTCGCGGATGACA 62.492 66.667 11.75 0.00 38.84 3.58
1715 1736 9.833917 GCTTACTATCTTTACAGAATAAACCCT 57.166 33.333 0.00 0.00 30.76 4.34
1722 1743 5.703730 TTACAGAATAAACCCTACCCAGG 57.296 43.478 0.00 0.00 42.22 4.45
1724 1745 4.380791 ACAGAATAAACCCTACCCAGGAT 58.619 43.478 0.00 0.00 45.91 3.24
1803 1824 1.669115 TCGCTGCTGCTTTGAGACC 60.669 57.895 14.03 0.00 36.97 3.85
1826 1847 6.070481 ACCCTTACCACATTTTCTGTTTTGTT 60.070 34.615 0.00 0.00 35.29 2.83
1953 1975 6.183360 TGCTAAACCACTAGCTTACTATCCTG 60.183 42.308 0.00 0.00 43.96 3.86
1954 1976 6.183360 GCTAAACCACTAGCTTACTATCCTGT 60.183 42.308 0.00 0.00 41.01 4.00
1955 1977 7.014038 GCTAAACCACTAGCTTACTATCCTGTA 59.986 40.741 0.00 0.00 41.01 2.74
1956 1978 6.963083 AACCACTAGCTTACTATCCTGTAG 57.037 41.667 0.00 0.00 0.00 2.74
2015 2037 0.396435 AGAATGAACACAGCCGGTCA 59.604 50.000 1.90 0.00 0.00 4.02
2038 2060 9.477484 GTCATGTAGTCCTAACAAATATACCAG 57.523 37.037 0.00 0.00 0.00 4.00
2039 2061 8.647796 TCATGTAGTCCTAACAAATATACCAGG 58.352 37.037 0.00 0.00 0.00 4.45
2040 2062 7.369551 TGTAGTCCTAACAAATATACCAGGG 57.630 40.000 0.00 0.00 0.00 4.45
2041 2063 7.134162 TGTAGTCCTAACAAATATACCAGGGA 58.866 38.462 0.00 0.00 0.00 4.20
2127 2152 2.283676 TCGCCGTCTTCCCTCCTT 60.284 61.111 0.00 0.00 0.00 3.36
2129 2154 2.943978 CGCCGTCTTCCCTCCTTGT 61.944 63.158 0.00 0.00 0.00 3.16
2215 2243 3.374402 CGCAGTCCTCCTCGTGGT 61.374 66.667 2.99 0.00 34.23 4.16
2243 2271 4.025401 GAGTGCCGTTGCGTTGGG 62.025 66.667 0.00 0.00 41.78 4.12
2244 2272 4.868116 AGTGCCGTTGCGTTGGGT 62.868 61.111 0.00 0.00 41.78 4.51
2682 2710 1.596934 GTTGCTGATCGGAGGTCCA 59.403 57.895 5.48 0.00 35.14 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.014564 GGTGCGTCTAGTGCTTCCAC 61.015 60.000 10.29 1.80 42.39 4.02
34 35 1.292223 GGTGCGTCTAGTGCTTCCA 59.708 57.895 10.29 0.00 0.00 3.53
35 36 0.320421 TTGGTGCGTCTAGTGCTTCC 60.320 55.000 10.29 11.81 0.00 3.46
36 37 1.508632 TTTGGTGCGTCTAGTGCTTC 58.491 50.000 10.29 4.83 0.00 3.86
37 38 2.185004 ATTTGGTGCGTCTAGTGCTT 57.815 45.000 10.29 0.00 0.00 3.91
38 39 3.328382 TTATTTGGTGCGTCTAGTGCT 57.672 42.857 10.29 0.00 0.00 4.40
39 40 3.682858 TCTTTATTTGGTGCGTCTAGTGC 59.317 43.478 3.25 3.25 0.00 4.40
40 41 4.688879 TGTCTTTATTTGGTGCGTCTAGTG 59.311 41.667 0.00 0.00 0.00 2.74
41 42 4.689345 GTGTCTTTATTTGGTGCGTCTAGT 59.311 41.667 0.00 0.00 0.00 2.57
42 43 4.688879 TGTGTCTTTATTTGGTGCGTCTAG 59.311 41.667 0.00 0.00 0.00 2.43
43 44 4.449743 GTGTGTCTTTATTTGGTGCGTCTA 59.550 41.667 0.00 0.00 0.00 2.59
44 45 3.250040 GTGTGTCTTTATTTGGTGCGTCT 59.750 43.478 0.00 0.00 0.00 4.18
45 46 3.250040 AGTGTGTCTTTATTTGGTGCGTC 59.750 43.478 0.00 0.00 0.00 5.19
46 47 3.211045 AGTGTGTCTTTATTTGGTGCGT 58.789 40.909 0.00 0.00 0.00 5.24
47 48 3.896648 AGTGTGTCTTTATTTGGTGCG 57.103 42.857 0.00 0.00 0.00 5.34
48 49 5.458015 GGTTAGTGTGTCTTTATTTGGTGC 58.542 41.667 0.00 0.00 0.00 5.01
49 50 5.334569 CGGGTTAGTGTGTCTTTATTTGGTG 60.335 44.000 0.00 0.00 0.00 4.17
50 51 4.758165 CGGGTTAGTGTGTCTTTATTTGGT 59.242 41.667 0.00 0.00 0.00 3.67
51 52 4.998672 TCGGGTTAGTGTGTCTTTATTTGG 59.001 41.667 0.00 0.00 0.00 3.28
52 53 5.390567 GCTCGGGTTAGTGTGTCTTTATTTG 60.391 44.000 0.00 0.00 0.00 2.32
53 54 4.694037 GCTCGGGTTAGTGTGTCTTTATTT 59.306 41.667 0.00 0.00 0.00 1.40
54 55 4.020485 AGCTCGGGTTAGTGTGTCTTTATT 60.020 41.667 0.00 0.00 0.00 1.40
55 56 3.514309 AGCTCGGGTTAGTGTGTCTTTAT 59.486 43.478 0.00 0.00 0.00 1.40
56 57 2.895404 AGCTCGGGTTAGTGTGTCTTTA 59.105 45.455 0.00 0.00 0.00 1.85
57 58 1.692519 AGCTCGGGTTAGTGTGTCTTT 59.307 47.619 0.00 0.00 0.00 2.52
58 59 1.272769 GAGCTCGGGTTAGTGTGTCTT 59.727 52.381 0.00 0.00 0.00 3.01
59 60 0.889306 GAGCTCGGGTTAGTGTGTCT 59.111 55.000 0.00 0.00 0.00 3.41
60 61 0.601558 TGAGCTCGGGTTAGTGTGTC 59.398 55.000 9.64 0.00 0.00 3.67
61 62 1.267121 ATGAGCTCGGGTTAGTGTGT 58.733 50.000 9.64 0.00 0.00 3.72
62 63 3.520290 TTATGAGCTCGGGTTAGTGTG 57.480 47.619 9.64 0.00 0.00 3.82
63 64 3.118738 CCTTTATGAGCTCGGGTTAGTGT 60.119 47.826 9.64 0.00 0.00 3.55
64 65 3.132289 TCCTTTATGAGCTCGGGTTAGTG 59.868 47.826 9.64 0.00 0.00 2.74
65 66 3.371965 TCCTTTATGAGCTCGGGTTAGT 58.628 45.455 9.64 0.00 0.00 2.24
66 67 4.402056 TTCCTTTATGAGCTCGGGTTAG 57.598 45.455 9.64 2.69 0.00 2.34
67 68 4.468510 TCTTTCCTTTATGAGCTCGGGTTA 59.531 41.667 9.64 0.00 0.00 2.85
68 69 3.263425 TCTTTCCTTTATGAGCTCGGGTT 59.737 43.478 9.64 0.00 0.00 4.11
69 70 2.838202 TCTTTCCTTTATGAGCTCGGGT 59.162 45.455 9.64 0.00 0.00 5.28
70 71 3.118592 ACTCTTTCCTTTATGAGCTCGGG 60.119 47.826 9.64 6.23 0.00 5.14
71 72 4.130286 ACTCTTTCCTTTATGAGCTCGG 57.870 45.455 9.64 3.58 0.00 4.63
72 73 5.897050 AGTACTCTTTCCTTTATGAGCTCG 58.103 41.667 9.64 0.00 0.00 5.03
73 74 6.759356 GGAAGTACTCTTTCCTTTATGAGCTC 59.241 42.308 6.82 6.82 33.64 4.09
74 75 6.213600 TGGAAGTACTCTTTCCTTTATGAGCT 59.786 38.462 12.31 0.00 33.64 4.09
75 76 6.407202 TGGAAGTACTCTTTCCTTTATGAGC 58.593 40.000 12.31 0.00 33.64 4.26
76 77 8.848474 TTTGGAAGTACTCTTTCCTTTATGAG 57.152 34.615 12.31 0.00 33.64 2.90
77 78 8.656806 TCTTTGGAAGTACTCTTTCCTTTATGA 58.343 33.333 12.31 4.68 33.64 2.15
78 79 8.848474 TCTTTGGAAGTACTCTTTCCTTTATG 57.152 34.615 12.31 2.94 33.64 1.90
79 80 9.862149 TTTCTTTGGAAGTACTCTTTCCTTTAT 57.138 29.630 12.31 0.00 33.64 1.40
80 81 9.689501 TTTTCTTTGGAAGTACTCTTTCCTTTA 57.310 29.630 12.31 0.00 33.64 1.85
81 82 8.589701 TTTTCTTTGGAAGTACTCTTTCCTTT 57.410 30.769 12.31 0.00 33.64 3.11
82 83 8.053355 TCTTTTCTTTGGAAGTACTCTTTCCTT 58.947 33.333 12.31 0.00 33.64 3.36
83 84 7.574607 TCTTTTCTTTGGAAGTACTCTTTCCT 58.425 34.615 12.31 0.00 33.64 3.36
84 85 7.803279 TCTTTTCTTTGGAAGTACTCTTTCC 57.197 36.000 5.28 5.28 33.64 3.13
85 86 9.723447 CTTTCTTTTCTTTGGAAGTACTCTTTC 57.277 33.333 0.00 0.00 33.64 2.62
86 87 9.462606 TCTTTCTTTTCTTTGGAAGTACTCTTT 57.537 29.630 0.00 0.00 33.64 2.52
87 88 9.114952 CTCTTTCTTTTCTTTGGAAGTACTCTT 57.885 33.333 0.00 0.00 36.51 2.85
88 89 7.227711 GCTCTTTCTTTTCTTTGGAAGTACTCT 59.772 37.037 0.00 0.00 32.61 3.24
89 90 7.356540 GCTCTTTCTTTTCTTTGGAAGTACTC 58.643 38.462 0.00 0.00 32.61 2.59
90 91 6.017852 CGCTCTTTCTTTTCTTTGGAAGTACT 60.018 38.462 0.00 0.00 32.61 2.73
91 92 6.136743 CGCTCTTTCTTTTCTTTGGAAGTAC 58.863 40.000 0.00 0.00 32.61 2.73
92 93 5.820947 ACGCTCTTTCTTTTCTTTGGAAGTA 59.179 36.000 0.00 0.00 32.61 2.24
93 94 4.640647 ACGCTCTTTCTTTTCTTTGGAAGT 59.359 37.500 0.00 0.00 32.61 3.01
94 95 5.175090 ACGCTCTTTCTTTTCTTTGGAAG 57.825 39.130 0.00 0.00 32.61 3.46
95 96 6.877611 ATACGCTCTTTCTTTTCTTTGGAA 57.122 33.333 0.00 0.00 0.00 3.53
96 97 6.877611 AATACGCTCTTTCTTTTCTTTGGA 57.122 33.333 0.00 0.00 0.00 3.53
97 98 6.582672 GGAAATACGCTCTTTCTTTTCTTTGG 59.417 38.462 5.33 0.00 33.93 3.28
98 99 6.303259 CGGAAATACGCTCTTTCTTTTCTTTG 59.697 38.462 5.33 0.00 33.93 2.77
99 100 6.371389 CGGAAATACGCTCTTTCTTTTCTTT 58.629 36.000 5.33 0.00 33.93 2.52
100 101 5.928153 CGGAAATACGCTCTTTCTTTTCTT 58.072 37.500 5.33 0.00 33.93 2.52
101 102 5.532025 CGGAAATACGCTCTTTCTTTTCT 57.468 39.130 5.33 0.00 33.93 2.52
114 115 4.566759 TCTTTCTTCATCAGCGGAAATACG 59.433 41.667 0.00 0.00 0.00 3.06
115 116 6.422776 TTCTTTCTTCATCAGCGGAAATAC 57.577 37.500 0.00 0.00 0.00 1.89
116 117 5.065218 GCTTCTTTCTTCATCAGCGGAAATA 59.935 40.000 0.00 0.00 0.00 1.40
117 118 4.142513 GCTTCTTTCTTCATCAGCGGAAAT 60.143 41.667 0.00 0.00 0.00 2.17
118 119 3.189287 GCTTCTTTCTTCATCAGCGGAAA 59.811 43.478 0.00 0.00 0.00 3.13
119 120 2.744202 GCTTCTTTCTTCATCAGCGGAA 59.256 45.455 0.00 0.00 0.00 4.30
120 121 2.350522 GCTTCTTTCTTCATCAGCGGA 58.649 47.619 0.00 0.00 0.00 5.54
121 122 1.399791 GGCTTCTTTCTTCATCAGCGG 59.600 52.381 0.00 0.00 0.00 5.52
122 123 2.079158 TGGCTTCTTTCTTCATCAGCG 58.921 47.619 0.00 0.00 0.00 5.18
123 124 4.670347 GAATGGCTTCTTTCTTCATCAGC 58.330 43.478 0.00 0.00 0.00 4.26
124 125 4.201891 CCGAATGGCTTCTTTCTTCATCAG 60.202 45.833 0.00 0.00 0.00 2.90
125 126 3.691118 CCGAATGGCTTCTTTCTTCATCA 59.309 43.478 0.00 0.00 0.00 3.07
126 127 3.941483 TCCGAATGGCTTCTTTCTTCATC 59.059 43.478 0.00 0.00 34.14 2.92
127 128 3.691609 GTCCGAATGGCTTCTTTCTTCAT 59.308 43.478 0.00 0.00 34.14 2.57
128 129 3.074412 GTCCGAATGGCTTCTTTCTTCA 58.926 45.455 0.00 0.00 34.14 3.02
129 130 3.074412 TGTCCGAATGGCTTCTTTCTTC 58.926 45.455 0.00 0.00 34.14 2.87
130 131 3.140325 TGTCCGAATGGCTTCTTTCTT 57.860 42.857 0.00 0.00 34.14 2.52
131 132 2.814336 GTTGTCCGAATGGCTTCTTTCT 59.186 45.455 0.00 0.00 34.14 2.52
132 133 2.412847 CGTTGTCCGAATGGCTTCTTTC 60.413 50.000 0.00 0.00 39.56 2.62
133 134 1.535462 CGTTGTCCGAATGGCTTCTTT 59.465 47.619 0.00 0.00 39.56 2.52
134 135 1.156736 CGTTGTCCGAATGGCTTCTT 58.843 50.000 0.00 0.00 39.56 2.52
135 136 1.298859 GCGTTGTCCGAATGGCTTCT 61.299 55.000 0.00 0.00 39.56 2.85
136 137 1.134694 GCGTTGTCCGAATGGCTTC 59.865 57.895 0.00 0.00 39.56 3.86
137 138 1.599518 TGCGTTGTCCGAATGGCTT 60.600 52.632 0.00 0.00 39.56 4.35
138 139 2.031919 TGCGTTGTCCGAATGGCT 59.968 55.556 0.00 0.00 39.56 4.75
139 140 2.175811 GTGCGTTGTCCGAATGGC 59.824 61.111 0.00 0.00 39.56 4.40
140 141 1.963855 TGGTGCGTTGTCCGAATGG 60.964 57.895 0.00 0.00 39.56 3.16
141 142 1.206578 GTGGTGCGTTGTCCGAATG 59.793 57.895 0.00 0.00 39.56 2.67
142 143 1.964373 GGTGGTGCGTTGTCCGAAT 60.964 57.895 0.00 0.00 39.56 3.34
143 144 2.589442 GGTGGTGCGTTGTCCGAA 60.589 61.111 0.00 0.00 39.56 4.30
144 145 3.509137 GAGGTGGTGCGTTGTCCGA 62.509 63.158 0.00 0.00 39.56 4.55
145 146 3.041940 GAGGTGGTGCGTTGTCCG 61.042 66.667 0.00 0.00 40.40 4.79
146 147 1.525077 TTGAGGTGGTGCGTTGTCC 60.525 57.895 0.00 0.00 0.00 4.02
147 148 1.092921 TGTTGAGGTGGTGCGTTGTC 61.093 55.000 0.00 0.00 0.00 3.18
148 149 1.078072 TGTTGAGGTGGTGCGTTGT 60.078 52.632 0.00 0.00 0.00 3.32
149 150 1.355210 GTGTTGAGGTGGTGCGTTG 59.645 57.895 0.00 0.00 0.00 4.10
150 151 1.822186 GGTGTTGAGGTGGTGCGTT 60.822 57.895 0.00 0.00 0.00 4.84
151 152 2.203153 GGTGTTGAGGTGGTGCGT 60.203 61.111 0.00 0.00 0.00 5.24
152 153 3.345808 CGGTGTTGAGGTGGTGCG 61.346 66.667 0.00 0.00 0.00 5.34
153 154 1.961277 CTCGGTGTTGAGGTGGTGC 60.961 63.158 0.00 0.00 32.18 5.01
154 155 0.105964 TTCTCGGTGTTGAGGTGGTG 59.894 55.000 0.00 0.00 36.61 4.17
155 156 0.834612 TTTCTCGGTGTTGAGGTGGT 59.165 50.000 0.00 0.00 36.61 4.16
156 157 1.961793 TTTTCTCGGTGTTGAGGTGG 58.038 50.000 0.00 0.00 36.61 4.61
157 158 5.631026 CATTATTTTCTCGGTGTTGAGGTG 58.369 41.667 0.00 0.00 36.61 4.00
158 159 4.156008 GCATTATTTTCTCGGTGTTGAGGT 59.844 41.667 0.00 0.00 36.61 3.85
159 160 4.155826 TGCATTATTTTCTCGGTGTTGAGG 59.844 41.667 0.00 0.00 36.61 3.86
160 161 5.295431 TGCATTATTTTCTCGGTGTTGAG 57.705 39.130 0.00 0.00 37.33 3.02
161 162 5.697473 TTGCATTATTTTCTCGGTGTTGA 57.303 34.783 0.00 0.00 0.00 3.18
162 163 6.640499 TCTTTTGCATTATTTTCTCGGTGTTG 59.360 34.615 0.00 0.00 0.00 3.33
163 164 6.640907 GTCTTTTGCATTATTTTCTCGGTGTT 59.359 34.615 0.00 0.00 0.00 3.32
164 165 6.149633 GTCTTTTGCATTATTTTCTCGGTGT 58.850 36.000 0.00 0.00 0.00 4.16
165 166 5.572896 GGTCTTTTGCATTATTTTCTCGGTG 59.427 40.000 0.00 0.00 0.00 4.94
166 167 5.336451 GGGTCTTTTGCATTATTTTCTCGGT 60.336 40.000 0.00 0.00 0.00 4.69
167 168 5.102313 GGGTCTTTTGCATTATTTTCTCGG 58.898 41.667 0.00 0.00 0.00 4.63
168 169 5.708948 TGGGTCTTTTGCATTATTTTCTCG 58.291 37.500 0.00 0.00 0.00 4.04
169 170 7.154656 ACTTGGGTCTTTTGCATTATTTTCTC 58.845 34.615 0.00 0.00 0.00 2.87
170 171 7.066307 ACTTGGGTCTTTTGCATTATTTTCT 57.934 32.000 0.00 0.00 0.00 2.52
171 172 7.351414 GACTTGGGTCTTTTGCATTATTTTC 57.649 36.000 0.00 0.00 39.24 2.29
186 187 3.040147 TCGTCATCAAAGACTTGGGTC 57.960 47.619 0.00 0.00 42.41 4.46
187 188 3.139077 GTTCGTCATCAAAGACTTGGGT 58.861 45.455 0.00 0.00 36.38 4.51
188 189 3.403038 AGTTCGTCATCAAAGACTTGGG 58.597 45.455 0.00 0.00 36.38 4.12
189 190 3.433615 GGAGTTCGTCATCAAAGACTTGG 59.566 47.826 0.00 0.00 36.38 3.61
190 191 3.121944 CGGAGTTCGTCATCAAAGACTTG 59.878 47.826 0.00 0.00 36.38 3.16
191 192 3.318017 CGGAGTTCGTCATCAAAGACTT 58.682 45.455 0.00 0.00 36.38 3.01
192 193 2.947852 CGGAGTTCGTCATCAAAGACT 58.052 47.619 0.00 0.00 36.38 3.24
205 206 1.066114 CTCGTCTTCGCACGGAGTTC 61.066 60.000 0.00 0.00 40.35 3.01
206 207 1.081376 CTCGTCTTCGCACGGAGTT 60.081 57.895 0.00 0.00 40.35 3.01
207 208 0.952497 TACTCGTCTTCGCACGGAGT 60.952 55.000 0.00 1.63 40.35 3.85
208 209 0.520827 GTACTCGTCTTCGCACGGAG 60.521 60.000 0.00 0.00 40.35 4.63
209 210 0.952497 AGTACTCGTCTTCGCACGGA 60.952 55.000 0.00 0.00 40.35 4.69
210 211 0.520827 GAGTACTCGTCTTCGCACGG 60.521 60.000 7.22 0.00 40.35 4.94
211 212 0.443088 AGAGTACTCGTCTTCGCACG 59.557 55.000 17.07 0.00 41.36 5.34
212 213 3.736530 TTAGAGTACTCGTCTTCGCAC 57.263 47.619 17.07 0.00 36.96 5.34
213 214 3.126514 CCTTTAGAGTACTCGTCTTCGCA 59.873 47.826 17.07 0.00 36.96 5.10
214 215 3.373439 TCCTTTAGAGTACTCGTCTTCGC 59.627 47.826 17.07 0.00 36.96 4.70
215 216 5.350914 TCTTCCTTTAGAGTACTCGTCTTCG 59.649 44.000 17.07 5.11 38.55 3.79
216 217 6.594937 TCTCTTCCTTTAGAGTACTCGTCTTC 59.405 42.308 17.07 0.00 41.91 2.87
217 218 6.474630 TCTCTTCCTTTAGAGTACTCGTCTT 58.525 40.000 17.07 2.42 41.91 3.01
218 219 6.052405 TCTCTTCCTTTAGAGTACTCGTCT 57.948 41.667 17.07 2.80 41.91 4.18
219 220 6.740411 TTCTCTTCCTTTAGAGTACTCGTC 57.260 41.667 17.07 0.00 41.91 4.20
220 221 7.014038 TGTTTTCTCTTCCTTTAGAGTACTCGT 59.986 37.037 17.07 8.42 41.91 4.18
221 222 7.368833 TGTTTTCTCTTCCTTTAGAGTACTCG 58.631 38.462 17.07 2.89 41.91 4.18
222 223 9.198837 CTTGTTTTCTCTTCCTTTAGAGTACTC 57.801 37.037 15.41 15.41 41.91 2.59
223 224 7.658167 GCTTGTTTTCTCTTCCTTTAGAGTACT 59.342 37.037 0.00 0.00 41.91 2.73
224 225 7.441458 TGCTTGTTTTCTCTTCCTTTAGAGTAC 59.559 37.037 0.00 0.00 41.91 2.73
225 226 7.506114 TGCTTGTTTTCTCTTCCTTTAGAGTA 58.494 34.615 0.00 0.00 41.91 2.59
226 227 6.357367 TGCTTGTTTTCTCTTCCTTTAGAGT 58.643 36.000 0.00 0.00 41.91 3.24
227 228 6.567511 GCTGCTTGTTTTCTCTTCCTTTAGAG 60.568 42.308 0.00 0.00 42.46 2.43
228 229 5.239525 GCTGCTTGTTTTCTCTTCCTTTAGA 59.760 40.000 0.00 0.00 0.00 2.10
229 230 5.009010 TGCTGCTTGTTTTCTCTTCCTTTAG 59.991 40.000 0.00 0.00 0.00 1.85
230 231 4.887071 TGCTGCTTGTTTTCTCTTCCTTTA 59.113 37.500 0.00 0.00 0.00 1.85
231 232 3.701040 TGCTGCTTGTTTTCTCTTCCTTT 59.299 39.130 0.00 0.00 0.00 3.11
245 247 3.372676 GACGACCGCATGCTGCTTG 62.373 63.158 17.13 10.85 42.25 4.01
336 338 3.264947 CACCATGAAGACGACACATGAT 58.735 45.455 19.42 6.44 42.41 2.45
825 839 3.088500 GATGTCGCAGCGCAGGTTC 62.089 63.158 10.87 2.98 33.74 3.62
996 1010 2.042831 GTTTGGCAGGAGCATCGCT 61.043 57.895 0.00 0.00 44.61 4.93
1223 1237 1.835121 CGCGATCTCGGTGATGTTAA 58.165 50.000 0.00 0.00 40.23 2.01
1224 1238 0.594028 GCGCGATCTCGGTGATGTTA 60.594 55.000 12.10 0.00 40.23 2.41
1316 1330 1.898863 AGGGATGTAGGGCTTGACAT 58.101 50.000 0.21 0.21 38.99 3.06
1335 1352 3.334691 CTTGAACGCCATGGAGAAGTTA 58.665 45.455 23.45 0.90 0.00 2.24
1360 1377 3.814268 GCCCGCGTGAATGCACAT 61.814 61.111 4.92 0.00 45.41 3.21
1416 1433 2.041115 CACCTGCTCGTCCGAGAGA 61.041 63.158 20.07 4.98 44.53 3.10
1539 1556 1.669760 GCCGACCATCCAAACACGA 60.670 57.895 0.00 0.00 0.00 4.35
1552 1569 4.821589 CCCTGAGCCGAAGCCGAC 62.822 72.222 0.00 0.00 41.25 4.79
1715 1736 3.009695 ACGAAAACCATTCATCCTGGGTA 59.990 43.478 0.00 0.00 38.14 3.69
1722 1743 5.006358 ACGCATAGTACGAAAACCATTCATC 59.994 40.000 0.00 0.00 0.00 2.92
1724 1745 4.092237 CACGCATAGTACGAAAACCATTCA 59.908 41.667 0.00 0.00 0.00 2.57
1803 1824 9.191995 GATAACAAAACAGAAAATGTGGTAAGG 57.808 33.333 0.00 0.00 43.00 2.69
1953 1975 8.876790 GTCTGGGTTGTGTTTATTATGTACTAC 58.123 37.037 0.00 0.00 0.00 2.73
1954 1976 7.760794 CGTCTGGGTTGTGTTTATTATGTACTA 59.239 37.037 0.00 0.00 0.00 1.82
1955 1977 6.592607 CGTCTGGGTTGTGTTTATTATGTACT 59.407 38.462 0.00 0.00 0.00 2.73
1956 1978 6.183360 CCGTCTGGGTTGTGTTTATTATGTAC 60.183 42.308 0.00 0.00 0.00 2.90
2015 2037 7.792736 TCCCTGGTATATTTGTTAGGACTACAT 59.207 37.037 0.00 0.00 0.00 2.29
2193 2221 4.459089 GAGGAGGACTGCGCCCAC 62.459 72.222 4.18 0.00 0.00 4.61
2227 2255 4.868116 ACCCAACGCAACGGCACT 62.868 61.111 0.00 0.00 41.24 4.40
2234 2262 3.578272 GCACGACACCCAACGCAA 61.578 61.111 0.00 0.00 0.00 4.85
2243 2271 3.712881 GCTCAACCCGCACGACAC 61.713 66.667 0.00 0.00 0.00 3.67
2244 2272 4.980805 GGCTCAACCCGCACGACA 62.981 66.667 0.00 0.00 0.00 4.35
2424 2452 3.518998 AGATCCGCGTGTCCCGAG 61.519 66.667 4.92 0.00 39.56 4.63
2514 2542 2.126812 CGCCTAGTAGATCCGCGC 60.127 66.667 0.00 0.00 36.02 6.86
2569 2597 2.058001 AGATCCACGGCGTCCATGA 61.058 57.895 10.85 4.94 0.00 3.07
2610 2638 1.757118 CAGATCGGGGCAAAGAGACTA 59.243 52.381 0.00 0.00 0.00 2.59
2665 2693 1.688735 CTATGGACCTCCGATCAGCAA 59.311 52.381 0.00 0.00 39.43 3.91


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

AutoCloner maintained by Alex Coulton.