Multiple sequence alignment - TraesCS3D01G328900

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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 TraesCS3D01G328900 chr3D 100.000 3607 0 0 1 3607 441572378 441568772 0.000000e+00 6661
1 TraesCS3D01G328900 chr3A 89.759 3076 151 55 277 3236 582344943 582341916 0.000000e+00 3784
2 TraesCS3D01G328900 chr3A 94.722 360 17 2 3247 3606 582341480 582341123 3.150000e-155 558
3 TraesCS3D01G328900 chr3B 88.443 2639 160 52 277 2835 578986929 578989502 0.000000e+00 3049
4 TraesCS3D01G328900 chr3B 85.950 363 42 7 3228 3586 654368686 654369043 2.630000e-101 379
5 TraesCS3D01G328900 chr3B 87.619 105 9 4 156 258 578986757 578986859 6.330000e-23 119
6 TraesCS3D01G328900 chr2D 86.920 1078 102 25 1616 2678 600037927 600038980 0.000000e+00 1173
7 TraesCS3D01G328900 chr2D 80.825 412 38 15 793 1182 600036887 600037279 5.890000e-73 285
8 TraesCS3D01G328900 chr2B 86.347 1084 105 27 1616 2671 729957223 729958291 0.000000e+00 1142
9 TraesCS3D01G328900 chr2B 76.463 820 112 48 790 1553 729956282 729957076 1.580000e-98 370
10 TraesCS3D01G328900 chr2B 76.048 501 72 38 3087 3560 599202807 599203286 2.180000e-52 217
11 TraesCS3D01G328900 chr2A 85.395 1075 122 20 1616 2670 733717035 733718094 0.000000e+00 1083
12 TraesCS3D01G328900 chr2A 80.387 413 50 14 793 1182 733715959 733716363 5.890000e-73 285
13 TraesCS3D01G328900 chr4B 82.526 475 53 22 3087 3556 492226123 492225674 1.210000e-104 390
14 TraesCS3D01G328900 chr1D 82.573 482 46 32 3084 3556 17654067 17654519 1.210000e-104 390
15 TraesCS3D01G328900 chr1D 81.042 480 60 24 3087 3556 17654647 17655105 1.590000e-93 353
16 TraesCS3D01G328900 chr5B 80.753 478 60 26 3085 3551 604491162 604491618 9.590000e-91 344
17 TraesCS3D01G328900 chr4A 79.806 515 68 22 3086 3581 56512051 56511554 3.450000e-90 342
18 TraesCS3D01G328900 chr1A 80.287 487 64 22 3107 3583 348847679 348848143 4.460000e-89 339
19 TraesCS3D01G328900 chrUn 78.927 522 73 31 3087 3593 214324232 214323733 1.620000e-83 320


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 TraesCS3D01G328900 chr3D 441568772 441572378 3606 True 6661.0 6661 100.0000 1 3607 1 chr3D.!!$R1 3606
1 TraesCS3D01G328900 chr3A 582341123 582344943 3820 True 2171.0 3784 92.2405 277 3606 2 chr3A.!!$R1 3329
2 TraesCS3D01G328900 chr3B 578986757 578989502 2745 False 1584.0 3049 88.0310 156 2835 2 chr3B.!!$F2 2679
3 TraesCS3D01G328900 chr2D 600036887 600038980 2093 False 729.0 1173 83.8725 793 2678 2 chr2D.!!$F1 1885
4 TraesCS3D01G328900 chr2B 729956282 729958291 2009 False 756.0 1142 81.4050 790 2671 2 chr2B.!!$F2 1881
5 TraesCS3D01G328900 chr2A 733715959 733718094 2135 False 684.0 1083 82.8910 793 2670 2 chr2A.!!$F1 1877
6 TraesCS3D01G328900 chr1D 17654067 17655105 1038 False 371.5 390 81.8075 3084 3556 2 chr1D.!!$F1 472

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
991 1143 0.471780 TGGGTTCCTGACAGAGCTCA 60.472 55.000 17.77 0.0 0.0 4.26 F
1204 1372 0.102120 CTCTAGCTGGTTCTGCTCGG 59.898 60.000 0.00 0.0 39.3 4.63 F
1492 1828 1.003839 GACATCTGCAACCGTGGGA 60.004 57.895 0.00 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2447 0.787084 ACCTGGAGAAGTCCCTCTCA 59.213 55.000 0.00 0.0 43.19 3.27 R
2400 2901 1.067495 CAGACCTCCAACGAGAAGGAC 60.067 57.143 0.00 0.0 38.52 3.85 R
3244 3872 1.003331 GCGTTCGGACAATGTTGAACA 60.003 47.619 22.83 0.0 40.47 3.18 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
24 25 4.463050 AACCCATAGACCAAAAGTTCCA 57.537 40.909 0.00 0.00 0.00 3.53
25 26 3.763057 ACCCATAGACCAAAAGTTCCAC 58.237 45.455 0.00 0.00 0.00 4.02
27 28 4.010349 CCCATAGACCAAAAGTTCCACTC 58.990 47.826 0.00 0.00 0.00 3.51
28 29 4.010349 CCATAGACCAAAAGTTCCACTCC 58.990 47.826 0.00 0.00 0.00 3.85
29 30 2.658807 AGACCAAAAGTTCCACTCCC 57.341 50.000 0.00 0.00 0.00 4.30
30 31 1.850345 AGACCAAAAGTTCCACTCCCA 59.150 47.619 0.00 0.00 0.00 4.37
31 32 2.243736 AGACCAAAAGTTCCACTCCCAA 59.756 45.455 0.00 0.00 0.00 4.12
32 33 3.028130 GACCAAAAGTTCCACTCCCAAA 58.972 45.455 0.00 0.00 0.00 3.28
33 34 3.445987 ACCAAAAGTTCCACTCCCAAAA 58.554 40.909 0.00 0.00 0.00 2.44
34 35 3.450817 ACCAAAAGTTCCACTCCCAAAAG 59.549 43.478 0.00 0.00 0.00 2.27
37 38 5.221244 CCAAAAGTTCCACTCCCAAAAGTAG 60.221 44.000 0.00 0.00 0.00 2.57
38 39 4.790718 AAGTTCCACTCCCAAAAGTAGT 57.209 40.909 0.00 0.00 0.00 2.73
39 40 4.353383 AGTTCCACTCCCAAAAGTAGTC 57.647 45.455 0.00 0.00 0.00 2.59
40 41 3.072622 AGTTCCACTCCCAAAAGTAGTCC 59.927 47.826 0.00 0.00 0.00 3.85
41 42 2.696775 TCCACTCCCAAAAGTAGTCCA 58.303 47.619 0.00 0.00 0.00 4.02
43 44 4.431378 TCCACTCCCAAAAGTAGTCCATA 58.569 43.478 0.00 0.00 0.00 2.74
44 45 5.036916 TCCACTCCCAAAAGTAGTCCATAT 58.963 41.667 0.00 0.00 0.00 1.78
45 46 5.104527 TCCACTCCCAAAAGTAGTCCATATG 60.105 44.000 0.00 0.00 0.00 1.78
47 48 6.126883 CCACTCCCAAAAGTAGTCCATATGTA 60.127 42.308 1.24 0.00 0.00 2.29
49 50 7.495934 CACTCCCAAAAGTAGTCCATATGTAAG 59.504 40.741 1.24 0.00 0.00 2.34
50 51 7.402071 ACTCCCAAAAGTAGTCCATATGTAAGA 59.598 37.037 1.24 0.00 0.00 2.10
51 52 7.562135 TCCCAAAAGTAGTCCATATGTAAGAC 58.438 38.462 1.24 2.39 0.00 3.01
52 53 7.181305 TCCCAAAAGTAGTCCATATGTAAGACA 59.819 37.037 11.61 0.00 32.82 3.41
53 54 7.280205 CCCAAAAGTAGTCCATATGTAAGACAC 59.720 40.741 11.61 8.31 32.82 3.67
54 55 7.822334 CCAAAAGTAGTCCATATGTAAGACACA 59.178 37.037 11.61 0.00 42.69 3.72
55 56 8.873830 CAAAAGTAGTCCATATGTAAGACACAG 58.126 37.037 11.61 0.00 41.51 3.66
56 57 7.956328 AAGTAGTCCATATGTAAGACACAGA 57.044 36.000 11.61 0.00 41.51 3.41
57 58 7.575414 AGTAGTCCATATGTAAGACACAGAG 57.425 40.000 11.61 0.00 41.51 3.35
61 62 7.324178 AGTCCATATGTAAGACACAGAGTTTC 58.676 38.462 11.61 0.00 41.51 2.78
62 63 6.535508 GTCCATATGTAAGACACAGAGTTTCC 59.464 42.308 1.24 0.00 41.51 3.13
63 64 5.817816 CCATATGTAAGACACAGAGTTTCCC 59.182 44.000 1.24 0.00 41.51 3.97
64 65 6.352222 CCATATGTAAGACACAGAGTTTCCCT 60.352 42.308 1.24 0.00 41.51 4.20
65 66 7.147724 CCATATGTAAGACACAGAGTTTCCCTA 60.148 40.741 1.24 0.00 41.51 3.53
67 68 6.282199 TGTAAGACACAGAGTTTCCCTATC 57.718 41.667 0.00 0.00 31.89 2.08
68 69 5.778241 TGTAAGACACAGAGTTTCCCTATCA 59.222 40.000 0.00 0.00 31.89 2.15
69 70 5.825593 AAGACACAGAGTTTCCCTATCAA 57.174 39.130 0.00 0.00 0.00 2.57
71 72 7.496346 AAGACACAGAGTTTCCCTATCAATA 57.504 36.000 0.00 0.00 0.00 1.90
72 73 7.118496 AGACACAGAGTTTCCCTATCAATAG 57.882 40.000 0.00 0.00 0.00 1.73
73 74 6.897966 AGACACAGAGTTTCCCTATCAATAGA 59.102 38.462 0.00 0.00 32.05 1.98
74 75 7.400339 AGACACAGAGTTTCCCTATCAATAGAA 59.600 37.037 0.00 0.00 32.05 2.10
75 76 7.918076 ACACAGAGTTTCCCTATCAATAGAAA 58.082 34.615 0.00 0.00 32.05 2.52
76 77 8.043710 ACACAGAGTTTCCCTATCAATAGAAAG 58.956 37.037 0.00 0.00 32.05 2.62
78 79 8.043710 ACAGAGTTTCCCTATCAATAGAAAGTG 58.956 37.037 0.00 0.00 32.05 3.16
79 80 8.260818 CAGAGTTTCCCTATCAATAGAAAGTGA 58.739 37.037 0.00 0.00 33.60 3.41
80 81 8.482128 AGAGTTTCCCTATCAATAGAAAGTGAG 58.518 37.037 0.00 0.00 32.39 3.51
81 82 7.569240 AGTTTCCCTATCAATAGAAAGTGAGG 58.431 38.462 0.00 0.00 32.39 3.86
85 86 7.565680 TCCCTATCAATAGAAAGTGAGGTTTC 58.434 38.462 0.00 0.00 32.39 2.78
87 88 6.768381 CCTATCAATAGAAAGTGAGGTTTCCC 59.232 42.308 0.00 0.00 37.16 3.97
88 89 5.576563 TCAATAGAAAGTGAGGTTTCCCA 57.423 39.130 0.00 0.00 37.16 4.37
89 90 5.313712 TCAATAGAAAGTGAGGTTTCCCAC 58.686 41.667 0.00 0.00 37.16 4.61
90 91 2.256117 AGAAAGTGAGGTTTCCCACG 57.744 50.000 0.00 0.00 37.16 4.94
91 92 1.202770 AGAAAGTGAGGTTTCCCACGG 60.203 52.381 0.00 0.00 37.16 4.94
92 93 0.549469 AAAGTGAGGTTTCCCACGGT 59.451 50.000 0.00 0.00 38.26 4.83
93 94 1.426751 AAGTGAGGTTTCCCACGGTA 58.573 50.000 0.00 0.00 38.26 4.02
94 95 0.683412 AGTGAGGTTTCCCACGGTAC 59.317 55.000 0.00 0.00 38.26 3.34
95 96 0.683412 GTGAGGTTTCCCACGGTACT 59.317 55.000 0.00 0.00 0.00 2.73
96 97 0.682852 TGAGGTTTCCCACGGTACTG 59.317 55.000 0.00 0.00 0.00 2.74
97 98 0.971386 GAGGTTTCCCACGGTACTGA 59.029 55.000 9.17 0.00 0.00 3.41
101 102 2.353109 GGTTTCCCACGGTACTGAGTAC 60.353 54.545 14.19 14.19 38.19 2.73
102 103 2.291209 TTCCCACGGTACTGAGTACA 57.709 50.000 22.79 0.00 40.41 2.90
103 104 1.538047 TCCCACGGTACTGAGTACAC 58.462 55.000 22.79 11.96 40.41 2.90
104 105 1.074405 TCCCACGGTACTGAGTACACT 59.926 52.381 22.79 5.45 40.41 3.55
105 106 1.471684 CCCACGGTACTGAGTACACTC 59.528 57.143 22.79 6.30 40.41 3.51
106 107 2.434428 CCACGGTACTGAGTACACTCT 58.566 52.381 22.79 0.65 43.25 3.24
107 108 2.419324 CCACGGTACTGAGTACACTCTC 59.581 54.545 22.79 5.61 43.25 3.20
108 109 2.419324 CACGGTACTGAGTACACTCTCC 59.581 54.545 22.79 5.00 43.25 3.71
110 111 2.678836 CGGTACTGAGTACACTCTCCAG 59.321 54.545 22.79 3.46 43.25 3.86
111 112 3.688235 GGTACTGAGTACACTCTCCAGT 58.312 50.000 22.79 8.69 43.25 4.00
112 113 4.080687 GGTACTGAGTACACTCTCCAGTT 58.919 47.826 22.79 0.00 43.25 3.16
114 115 5.354792 GGTACTGAGTACACTCTCCAGTTAG 59.645 48.000 22.79 0.93 43.25 2.34
115 116 5.244189 ACTGAGTACACTCTCCAGTTAGA 57.756 43.478 10.55 0.00 43.25 2.10
116 117 5.632118 ACTGAGTACACTCTCCAGTTAGAA 58.368 41.667 10.55 0.00 43.25 2.10
119 120 7.094118 ACTGAGTACACTCTCCAGTTAGAATTC 60.094 40.741 10.55 0.00 43.25 2.17
120 121 6.153000 TGAGTACACTCTCCAGTTAGAATTCC 59.847 42.308 10.55 0.00 43.25 3.01
121 122 4.457834 ACACTCTCCAGTTAGAATTCCG 57.542 45.455 0.65 0.00 0.00 4.30
123 124 4.527038 ACACTCTCCAGTTAGAATTCCGAA 59.473 41.667 0.65 0.00 0.00 4.30
124 125 4.865365 CACTCTCCAGTTAGAATTCCGAAC 59.135 45.833 11.24 11.24 0.00 3.95
125 126 4.081586 ACTCTCCAGTTAGAATTCCGAACC 60.082 45.833 14.28 1.69 31.75 3.62
127 128 2.564062 TCCAGTTAGAATTCCGAACCGT 59.436 45.455 14.28 0.00 31.75 4.83
128 129 2.928116 CCAGTTAGAATTCCGAACCGTC 59.072 50.000 14.28 0.00 31.75 4.79
129 130 3.368116 CCAGTTAGAATTCCGAACCGTCT 60.368 47.826 14.28 0.00 31.75 4.18
130 131 3.612860 CAGTTAGAATTCCGAACCGTCTG 59.387 47.826 14.28 5.70 31.75 3.51
131 132 3.257624 AGTTAGAATTCCGAACCGTCTGT 59.742 43.478 14.28 0.00 31.75 3.41
132 133 2.080286 AGAATTCCGAACCGTCTGTG 57.920 50.000 0.65 0.00 0.00 3.66
134 135 1.993370 GAATTCCGAACCGTCTGTGAG 59.007 52.381 0.00 0.00 0.00 3.51
137 138 0.526211 TCCGAACCGTCTGTGAGATG 59.474 55.000 0.00 0.00 0.00 2.90
138 139 0.526211 CCGAACCGTCTGTGAGATGA 59.474 55.000 0.00 0.00 33.07 2.92
140 141 2.357952 CCGAACCGTCTGTGAGATGATA 59.642 50.000 0.00 0.00 33.07 2.15
141 142 3.181490 CCGAACCGTCTGTGAGATGATAA 60.181 47.826 0.00 0.00 33.07 1.75
142 143 4.421058 CGAACCGTCTGTGAGATGATAAA 58.579 43.478 0.00 0.00 33.07 1.40
143 144 4.862574 CGAACCGTCTGTGAGATGATAAAA 59.137 41.667 0.00 0.00 33.07 1.52
144 145 5.347635 CGAACCGTCTGTGAGATGATAAAAA 59.652 40.000 0.00 0.00 33.07 1.94
145 146 6.454318 CGAACCGTCTGTGAGATGATAAAAAG 60.454 42.308 0.00 0.00 33.07 2.27
146 147 5.794894 ACCGTCTGTGAGATGATAAAAAGT 58.205 37.500 0.00 0.00 33.07 2.66
147 148 5.639506 ACCGTCTGTGAGATGATAAAAAGTG 59.360 40.000 0.00 0.00 33.07 3.16
149 150 6.183360 CCGTCTGTGAGATGATAAAAAGTGTC 60.183 42.308 0.00 0.00 33.07 3.67
150 151 6.453003 CGTCTGTGAGATGATAAAAAGTGTCG 60.453 42.308 0.00 0.00 33.07 4.35
151 152 6.586463 GTCTGTGAGATGATAAAAAGTGTCGA 59.414 38.462 0.00 0.00 0.00 4.20
152 153 7.276658 GTCTGTGAGATGATAAAAAGTGTCGAT 59.723 37.037 0.00 0.00 0.00 3.59
153 154 7.489435 TCTGTGAGATGATAAAAAGTGTCGATC 59.511 37.037 0.00 0.00 0.00 3.69
155 156 7.276438 TGTGAGATGATAAAAAGTGTCGATCAG 59.724 37.037 0.00 0.00 30.49 2.90
156 157 7.276658 GTGAGATGATAAAAAGTGTCGATCAGT 59.723 37.037 0.00 0.00 30.49 3.41
157 158 7.276438 TGAGATGATAAAAAGTGTCGATCAGTG 59.724 37.037 0.00 0.00 30.49 3.66
158 159 7.323420 AGATGATAAAAAGTGTCGATCAGTGA 58.677 34.615 0.00 0.00 30.49 3.41
159 160 6.706055 TGATAAAAAGTGTCGATCAGTGAC 57.294 37.500 0.00 0.00 36.88 3.67
160 161 6.220201 TGATAAAAAGTGTCGATCAGTGACA 58.780 36.000 0.00 0.00 43.68 3.58
161 162 6.366061 TGATAAAAAGTGTCGATCAGTGACAG 59.634 38.462 0.00 0.00 46.25 3.51
189 190 2.935201 GCCAGTTGAGCAGAGATAGTTG 59.065 50.000 0.00 0.00 0.00 3.16
201 202 8.027524 AGCAGAGATAGTTGAGGAAATAATCA 57.972 34.615 0.00 0.00 0.00 2.57
202 203 8.658619 AGCAGAGATAGTTGAGGAAATAATCAT 58.341 33.333 0.00 0.00 0.00 2.45
203 204 8.934825 GCAGAGATAGTTGAGGAAATAATCATC 58.065 37.037 0.00 0.00 39.31 2.92
204 205 9.434420 CAGAGATAGTTGAGGAAATAATCATCC 57.566 37.037 0.00 0.00 38.07 3.51
205 206 8.601546 AGAGATAGTTGAGGAAATAATCATCCC 58.398 37.037 0.00 0.00 38.07 3.85
209 210 9.965902 ATAGTTGAGGAAATAATCATCCCATAC 57.034 33.333 0.00 0.00 38.07 2.39
210 211 6.936900 AGTTGAGGAAATAATCATCCCATACG 59.063 38.462 0.00 0.00 38.07 3.06
211 212 6.680148 TGAGGAAATAATCATCCCATACGA 57.320 37.500 0.00 0.00 38.07 3.43
213 214 7.513856 TGAGGAAATAATCATCCCATACGAAA 58.486 34.615 0.00 0.00 38.07 3.46
220 221 3.869065 TCATCCCATACGAAACTGTTCC 58.131 45.455 0.00 0.00 0.00 3.62
251 252 2.885676 GCTGCGTCACCACACTGTG 61.886 63.158 6.19 6.19 37.59 3.66
271 278 5.508567 TGTGCAATGAAATTATCTCCCTCA 58.491 37.500 0.00 0.00 32.46 3.86
274 281 5.591472 TGCAATGAAATTATCTCCCTCACTG 59.409 40.000 0.00 0.00 32.46 3.66
349 409 0.525668 CCACGTATCAGTCGACAGGC 60.526 60.000 19.50 3.43 0.00 4.85
461 521 0.746204 GGCTTAGCTCAAGACCCAGC 60.746 60.000 3.59 0.00 36.10 4.85
464 525 0.615331 TTAGCTCAAGACCCAGCCAG 59.385 55.000 0.00 0.00 36.17 4.85
466 527 1.376553 GCTCAAGACCCAGCCAGAC 60.377 63.158 0.00 0.00 0.00 3.51
480 541 3.107601 AGCCAGACCTCATTAGCAAGTA 58.892 45.455 0.00 0.00 0.00 2.24
481 542 3.713764 AGCCAGACCTCATTAGCAAGTAT 59.286 43.478 0.00 0.00 0.00 2.12
482 543 4.901849 AGCCAGACCTCATTAGCAAGTATA 59.098 41.667 0.00 0.00 0.00 1.47
483 544 4.991687 GCCAGACCTCATTAGCAAGTATAC 59.008 45.833 0.00 0.00 0.00 1.47
484 545 5.223382 CCAGACCTCATTAGCAAGTATACG 58.777 45.833 0.00 0.00 0.00 3.06
485 546 5.221263 CCAGACCTCATTAGCAAGTATACGT 60.221 44.000 0.00 0.00 0.00 3.57
490 551 8.632906 ACCTCATTAGCAAGTATACGTACTAT 57.367 34.615 0.00 0.00 40.24 2.12
508 569 7.492669 ACGTACTATTAGTACTTAACAGCTCGA 59.507 37.037 24.46 0.00 46.68 4.04
522 583 1.550524 AGCTCGAACTAATCAGGCACA 59.449 47.619 0.00 0.00 0.00 4.57
523 584 1.929836 GCTCGAACTAATCAGGCACAG 59.070 52.381 0.00 0.00 0.00 3.66
524 585 1.929836 CTCGAACTAATCAGGCACAGC 59.070 52.381 0.00 0.00 0.00 4.40
525 586 1.275010 TCGAACTAATCAGGCACAGCA 59.725 47.619 0.00 0.00 0.00 4.41
526 587 1.662629 CGAACTAATCAGGCACAGCAG 59.337 52.381 0.00 0.00 0.00 4.24
600 667 1.197721 CGGTCCAATTCACACTTGAGC 59.802 52.381 0.00 0.00 31.71 4.26
736 833 2.042464 TGACACAGGAGCACTCTTTCT 58.958 47.619 0.00 0.00 0.00 2.52
785 890 3.748568 ACTCGAGAAATGCAGGTCTTTTC 59.251 43.478 21.68 2.88 38.44 2.29
901 1029 1.153208 CTGAGCTTAGCTGCAGGGG 60.153 63.158 13.01 0.00 39.88 4.79
933 1061 1.446966 GCAGAACAGAGAGGCGACC 60.447 63.158 0.00 0.00 0.00 4.79
938 1066 1.251527 AACAGAGAGGCGACCATCGT 61.252 55.000 0.00 0.00 42.81 3.73
944 1072 1.964223 AGAGGCGACCATCGTATTCAT 59.036 47.619 0.00 0.00 42.81 2.57
961 1089 5.590530 ATTCATACTCTCTGACCACACTC 57.409 43.478 0.00 0.00 0.00 3.51
962 1090 3.357203 TCATACTCTCTGACCACACTCC 58.643 50.000 0.00 0.00 0.00 3.85
991 1143 0.471780 TGGGTTCCTGACAGAGCTCA 60.472 55.000 17.77 0.00 0.00 4.26
1155 1307 1.377366 CCGCGTCTCTCCTCTTGCTA 61.377 60.000 4.92 0.00 0.00 3.49
1158 1310 1.464734 CGTCTCTCCTCTTGCTACCA 58.535 55.000 0.00 0.00 0.00 3.25
1202 1370 2.099405 ACTCTCTAGCTGGTTCTGCTC 58.901 52.381 0.00 0.00 39.30 4.26
1204 1372 0.102120 CTCTAGCTGGTTCTGCTCGG 59.898 60.000 0.00 0.00 39.30 4.63
1209 1377 1.153549 CTGGTTCTGCTCGGGCTAC 60.154 63.158 9.62 3.82 39.59 3.58
1230 1404 2.030363 CCTAGCACTAGCAAGAGGATCG 60.030 54.545 0.00 0.00 45.49 3.69
1232 1406 2.656002 AGCACTAGCAAGAGGATCGTA 58.344 47.619 0.00 0.00 45.49 3.43
1268 1459 2.124122 GATTTTGCAGGAAAAACGCGT 58.876 42.857 5.58 5.58 37.10 6.01
1271 1462 2.050442 GCAGGAAAAACGCGTGGG 60.050 61.111 14.98 0.00 0.00 4.61
1359 1675 2.475864 GCATGCTTCTCGATCTCATCAC 59.524 50.000 11.37 0.00 0.00 3.06
1390 1726 2.712057 GTGCAACAAAGTGGAGATGG 57.288 50.000 0.00 0.00 36.32 3.51
1391 1727 2.229792 GTGCAACAAAGTGGAGATGGA 58.770 47.619 0.00 0.00 36.32 3.41
1392 1728 2.227388 GTGCAACAAAGTGGAGATGGAG 59.773 50.000 0.00 0.00 36.32 3.86
1393 1729 2.106338 TGCAACAAAGTGGAGATGGAGA 59.894 45.455 0.00 0.00 0.00 3.71
1394 1730 3.245016 TGCAACAAAGTGGAGATGGAGAT 60.245 43.478 0.00 0.00 0.00 2.75
1395 1731 3.128242 GCAACAAAGTGGAGATGGAGATG 59.872 47.826 0.00 0.00 0.00 2.90
1396 1732 3.641434 ACAAAGTGGAGATGGAGATGG 57.359 47.619 0.00 0.00 0.00 3.51
1399 1735 4.229123 ACAAAGTGGAGATGGAGATGGATT 59.771 41.667 0.00 0.00 0.00 3.01
1420 1756 7.549134 TGGATTACTGATCGATGTTAATATGGC 59.451 37.037 0.54 0.00 35.49 4.40
1428 1764 8.128582 TGATCGATGTTAATATGGCTTTGTTTC 58.871 33.333 0.54 0.00 0.00 2.78
1492 1828 1.003839 GACATCTGCAACCGTGGGA 60.004 57.895 0.00 0.00 0.00 4.37
1562 1898 2.141535 GCTGAGGTACTAATCCAGCG 57.858 55.000 0.00 0.00 41.55 5.18
1564 1900 2.287909 GCTGAGGTACTAATCCAGCGAG 60.288 54.545 0.00 0.00 41.55 5.03
1565 1901 2.952978 CTGAGGTACTAATCCAGCGAGT 59.047 50.000 0.00 0.00 41.55 4.18
1566 1902 4.135306 CTGAGGTACTAATCCAGCGAGTA 58.865 47.826 0.00 0.00 41.55 2.59
1570 1906 6.086785 AGGTACTAATCCAGCGAGTAAATC 57.913 41.667 0.00 0.00 36.02 2.17
1926 2390 2.620112 CCCCAACAAGCTGCTCGTG 61.620 63.158 1.00 0.37 0.00 4.35
2088 2576 4.264253 TGTCTTGTCAATGGTGATGGATC 58.736 43.478 0.00 0.00 35.80 3.36
2376 2877 8.361592 AGTTCATTTGCTCTTCTTTTTCATTG 57.638 30.769 0.00 0.00 0.00 2.82
2400 2901 2.787473 TTGCAGTATCTTGGGTGGAG 57.213 50.000 0.00 0.00 0.00 3.86
2578 3085 1.757699 GAGGGAGCACGATAAGGAAGT 59.242 52.381 0.00 0.00 0.00 3.01
2585 3092 4.360563 AGCACGATAAGGAAGTAACGATG 58.639 43.478 0.00 0.00 0.00 3.84
2639 3146 3.116977 TGAAGGAGGCTCCATCTATCTCA 60.117 47.826 31.96 19.88 39.61 3.27
2640 3147 3.850917 AGGAGGCTCCATCTATCTCAT 57.149 47.619 33.86 7.57 39.61 2.90
2641 3148 4.144825 AGGAGGCTCCATCTATCTCATT 57.855 45.455 33.86 7.01 39.61 2.57
2642 3149 4.095946 AGGAGGCTCCATCTATCTCATTC 58.904 47.826 33.86 2.92 39.61 2.67
2705 3212 8.908786 ATTCAACTCAATACACAAAGAAGAGA 57.091 30.769 0.00 0.00 0.00 3.10
2864 3375 9.771534 TGCAACTTGTAGCATGTATGTTATATA 57.228 29.630 0.00 0.00 35.51 0.86
2945 3456 5.666969 TGCGATTTATAAAAGTCCGATGG 57.333 39.130 1.21 0.00 0.00 3.51
2967 3478 6.280643 TGGAAATCAATAGACCGTGATACAG 58.719 40.000 0.00 0.00 33.31 2.74
2976 3487 2.354821 GACCGTGATACAGGATTTTGCC 59.645 50.000 0.00 0.00 0.00 4.52
2998 3509 4.576463 CCTGTTCTTATGTATTGCAGGGTC 59.424 45.833 0.00 0.00 38.56 4.46
3004 3515 1.220749 GTATTGCAGGGTCGCCTCA 59.779 57.895 0.00 0.00 0.00 3.86
3152 3758 7.481275 TGTTTGCTTTTCATTTTTCATCTCC 57.519 32.000 0.00 0.00 0.00 3.71
3422 4515 8.555166 TGTTCAACATTTTTCAAATACTCGTC 57.445 30.769 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.436218 GTGGAACTTTTGGTCTATGGGTTTAT 59.564 38.462 0.00 0.00 36.15 1.40
2 3 4.587262 GTGGAACTTTTGGTCTATGGGTTT 59.413 41.667 0.00 0.00 36.15 3.27
4 5 3.763057 GTGGAACTTTTGGTCTATGGGT 58.237 45.455 0.00 0.00 36.15 4.51
22 23 3.721087 ATGGACTACTTTTGGGAGTGG 57.279 47.619 0.00 0.00 34.64 4.00
23 24 5.745227 ACATATGGACTACTTTTGGGAGTG 58.255 41.667 7.80 0.00 0.00 3.51
24 25 7.402071 TCTTACATATGGACTACTTTTGGGAGT 59.598 37.037 7.80 0.00 0.00 3.85
25 26 7.711339 GTCTTACATATGGACTACTTTTGGGAG 59.289 40.741 7.80 0.00 0.00 4.30
27 28 7.280205 GTGTCTTACATATGGACTACTTTTGGG 59.720 40.741 7.80 0.00 0.00 4.12
28 29 7.822334 TGTGTCTTACATATGGACTACTTTTGG 59.178 37.037 7.80 0.00 33.42 3.28
29 30 8.771920 TGTGTCTTACATATGGACTACTTTTG 57.228 34.615 7.80 0.00 33.42 2.44
30 31 8.812972 TCTGTGTCTTACATATGGACTACTTTT 58.187 33.333 7.80 0.00 38.92 2.27
31 32 8.362464 TCTGTGTCTTACATATGGACTACTTT 57.638 34.615 7.80 0.00 38.92 2.66
32 33 7.616150 ACTCTGTGTCTTACATATGGACTACTT 59.384 37.037 7.80 0.00 38.92 2.24
33 34 7.120051 ACTCTGTGTCTTACATATGGACTACT 58.880 38.462 7.80 0.00 38.92 2.57
34 35 7.336161 ACTCTGTGTCTTACATATGGACTAC 57.664 40.000 7.80 0.00 38.92 2.73
37 38 6.535508 GGAAACTCTGTGTCTTACATATGGAC 59.464 42.308 7.80 5.71 38.92 4.02
38 39 6.351881 GGGAAACTCTGTGTCTTACATATGGA 60.352 42.308 7.80 0.00 38.92 3.41
39 40 5.817816 GGGAAACTCTGTGTCTTACATATGG 59.182 44.000 7.80 0.00 38.92 2.74
40 41 6.644347 AGGGAAACTCTGTGTCTTACATATG 58.356 40.000 0.00 0.00 38.92 1.78
41 42 6.875972 AGGGAAACTCTGTGTCTTACATAT 57.124 37.500 0.00 0.00 38.92 1.78
43 44 6.440647 TGATAGGGAAACTCTGTGTCTTACAT 59.559 38.462 0.00 0.00 38.92 2.29
44 45 5.778241 TGATAGGGAAACTCTGTGTCTTACA 59.222 40.000 0.00 0.00 37.78 2.41
45 46 6.282199 TGATAGGGAAACTCTGTGTCTTAC 57.718 41.667 0.00 0.00 0.00 2.34
47 48 5.825593 TTGATAGGGAAACTCTGTGTCTT 57.174 39.130 0.00 0.00 0.00 3.01
49 50 7.113658 TCTATTGATAGGGAAACTCTGTGTC 57.886 40.000 0.00 0.00 0.00 3.67
50 51 7.496346 TTCTATTGATAGGGAAACTCTGTGT 57.504 36.000 0.00 0.00 0.00 3.72
51 52 8.043710 ACTTTCTATTGATAGGGAAACTCTGTG 58.956 37.037 0.46 0.00 0.00 3.66
52 53 8.043710 CACTTTCTATTGATAGGGAAACTCTGT 58.956 37.037 0.46 0.00 27.94 3.41
53 54 8.260818 TCACTTTCTATTGATAGGGAAACTCTG 58.739 37.037 0.00 0.00 32.19 3.35
54 55 8.380742 TCACTTTCTATTGATAGGGAAACTCT 57.619 34.615 0.00 0.00 32.19 3.24
55 56 7.713073 CCTCACTTTCTATTGATAGGGAAACTC 59.287 40.741 1.79 0.00 34.23 3.01
56 57 7.182930 ACCTCACTTTCTATTGATAGGGAAACT 59.817 37.037 1.79 0.00 34.23 2.66
57 58 7.339482 ACCTCACTTTCTATTGATAGGGAAAC 58.661 38.462 1.79 0.00 34.23 2.78
61 62 6.768381 GGAAACCTCACTTTCTATTGATAGGG 59.232 42.308 0.00 0.00 31.76 3.53
62 63 7.793927 GGAAACCTCACTTTCTATTGATAGG 57.206 40.000 0.46 0.00 31.76 2.57
78 79 6.403318 GTACTCAGTACCGTGGGAAACCTC 62.403 54.167 3.25 0.00 41.24 3.85
79 80 4.626631 GTACTCAGTACCGTGGGAAACCT 61.627 52.174 3.25 0.00 41.24 3.50
80 81 2.353109 GTACTCAGTACCGTGGGAAACC 60.353 54.545 3.25 0.00 41.13 3.27
81 82 2.297033 TGTACTCAGTACCGTGGGAAAC 59.703 50.000 12.62 0.00 38.14 2.78
85 86 1.471684 GAGTGTACTCAGTACCGTGGG 59.528 57.143 12.62 0.00 42.42 4.61
87 88 2.419324 GGAGAGTGTACTCAGTACCGTG 59.581 54.545 12.62 0.00 45.21 4.94
88 89 2.039480 TGGAGAGTGTACTCAGTACCGT 59.961 50.000 12.62 0.00 45.21 4.83
89 90 2.678836 CTGGAGAGTGTACTCAGTACCG 59.321 54.545 12.62 5.46 45.21 4.02
90 91 3.688235 ACTGGAGAGTGTACTCAGTACC 58.312 50.000 12.62 4.11 45.21 3.34
91 92 6.171921 TCTAACTGGAGAGTGTACTCAGTAC 58.828 44.000 8.15 8.15 45.21 2.73
92 93 6.370186 TCTAACTGGAGAGTGTACTCAGTA 57.630 41.667 13.95 0.00 45.21 2.74
93 94 5.244189 TCTAACTGGAGAGTGTACTCAGT 57.756 43.478 13.95 6.87 45.21 3.41
94 95 6.767524 ATTCTAACTGGAGAGTGTACTCAG 57.232 41.667 13.95 6.29 45.21 3.35
95 96 6.153000 GGAATTCTAACTGGAGAGTGTACTCA 59.847 42.308 13.95 0.00 45.21 3.41
96 97 6.566141 GGAATTCTAACTGGAGAGTGTACTC 58.434 44.000 5.23 3.85 43.17 2.59
97 98 5.125739 CGGAATTCTAACTGGAGAGTGTACT 59.874 44.000 5.23 0.00 30.61 2.73
101 102 4.720649 TCGGAATTCTAACTGGAGAGTG 57.279 45.455 5.23 0.00 30.61 3.51
102 103 4.081586 GGTTCGGAATTCTAACTGGAGAGT 60.082 45.833 17.76 0.00 0.00 3.24
103 104 4.434520 GGTTCGGAATTCTAACTGGAGAG 58.565 47.826 17.76 0.00 0.00 3.20
104 105 3.119245 CGGTTCGGAATTCTAACTGGAGA 60.119 47.826 18.03 1.53 0.00 3.71
105 106 3.187700 CGGTTCGGAATTCTAACTGGAG 58.812 50.000 18.03 8.69 0.00 3.86
106 107 2.564062 ACGGTTCGGAATTCTAACTGGA 59.436 45.455 24.36 6.79 34.47 3.86
107 108 2.928116 GACGGTTCGGAATTCTAACTGG 59.072 50.000 24.36 17.43 34.47 4.00
108 109 3.612860 CAGACGGTTCGGAATTCTAACTG 59.387 47.826 21.48 21.48 35.94 3.16
110 111 3.367025 CACAGACGGTTCGGAATTCTAAC 59.633 47.826 5.23 9.99 0.00 2.34
111 112 3.256383 TCACAGACGGTTCGGAATTCTAA 59.744 43.478 5.23 0.00 0.00 2.10
112 113 2.821378 TCACAGACGGTTCGGAATTCTA 59.179 45.455 5.23 0.00 0.00 2.10
114 115 1.993370 CTCACAGACGGTTCGGAATTC 59.007 52.381 0.00 0.00 0.00 2.17
115 116 1.616865 TCTCACAGACGGTTCGGAATT 59.383 47.619 0.00 0.00 0.00 2.17
116 117 1.254026 TCTCACAGACGGTTCGGAAT 58.746 50.000 0.00 0.00 0.00 3.01
119 120 0.526211 TCATCTCACAGACGGTTCGG 59.474 55.000 0.00 0.00 0.00 4.30
120 121 2.568696 ATCATCTCACAGACGGTTCG 57.431 50.000 0.00 0.00 0.00 3.95
121 122 6.369065 ACTTTTTATCATCTCACAGACGGTTC 59.631 38.462 0.00 0.00 0.00 3.62
123 124 5.639506 CACTTTTTATCATCTCACAGACGGT 59.360 40.000 0.00 0.00 0.00 4.83
124 125 5.639506 ACACTTTTTATCATCTCACAGACGG 59.360 40.000 0.00 0.00 0.00 4.79
125 126 6.453003 CGACACTTTTTATCATCTCACAGACG 60.453 42.308 0.00 0.00 0.00 4.18
127 128 6.687604 TCGACACTTTTTATCATCTCACAGA 58.312 36.000 0.00 0.00 0.00 3.41
128 129 6.951256 TCGACACTTTTTATCATCTCACAG 57.049 37.500 0.00 0.00 0.00 3.66
129 130 7.096551 TGATCGACACTTTTTATCATCTCACA 58.903 34.615 0.00 0.00 0.00 3.58
130 131 7.276658 ACTGATCGACACTTTTTATCATCTCAC 59.723 37.037 0.00 0.00 0.00 3.51
131 132 7.276438 CACTGATCGACACTTTTTATCATCTCA 59.724 37.037 0.00 0.00 0.00 3.27
132 133 7.489435 TCACTGATCGACACTTTTTATCATCTC 59.511 37.037 0.00 0.00 0.00 2.75
134 135 7.063426 TGTCACTGATCGACACTTTTTATCATC 59.937 37.037 0.00 0.00 38.45 2.92
137 138 6.586463 TCTGTCACTGATCGACACTTTTTATC 59.414 38.462 0.00 0.00 38.45 1.75
138 139 6.455647 TCTGTCACTGATCGACACTTTTTAT 58.544 36.000 0.00 0.00 38.45 1.40
140 141 4.693283 TCTGTCACTGATCGACACTTTTT 58.307 39.130 0.00 0.00 38.45 1.94
141 142 4.322080 TCTGTCACTGATCGACACTTTT 57.678 40.909 0.00 0.00 38.45 2.27
142 143 4.038042 TCTTCTGTCACTGATCGACACTTT 59.962 41.667 0.00 0.00 38.45 2.66
143 144 3.570125 TCTTCTGTCACTGATCGACACTT 59.430 43.478 0.00 0.00 38.45 3.16
144 145 3.149981 TCTTCTGTCACTGATCGACACT 58.850 45.455 0.00 0.00 38.45 3.55
145 146 3.189495 TCTCTTCTGTCACTGATCGACAC 59.811 47.826 0.00 0.00 38.45 3.67
146 147 3.412386 TCTCTTCTGTCACTGATCGACA 58.588 45.455 0.00 2.53 41.00 4.35
147 148 3.730662 GCTCTCTTCTGTCACTGATCGAC 60.731 52.174 0.00 0.00 0.00 4.20
149 150 2.479389 GGCTCTCTTCTGTCACTGATCG 60.479 54.545 0.00 0.00 0.00 3.69
150 151 2.495270 TGGCTCTCTTCTGTCACTGATC 59.505 50.000 0.00 0.00 0.00 2.92
151 152 2.496871 CTGGCTCTCTTCTGTCACTGAT 59.503 50.000 0.00 0.00 0.00 2.90
152 153 1.891811 CTGGCTCTCTTCTGTCACTGA 59.108 52.381 0.00 0.00 0.00 3.41
153 154 1.617850 ACTGGCTCTCTTCTGTCACTG 59.382 52.381 0.00 0.00 0.00 3.66
155 156 2.036475 TCAACTGGCTCTCTTCTGTCAC 59.964 50.000 0.00 0.00 0.00 3.67
156 157 2.298446 CTCAACTGGCTCTCTTCTGTCA 59.702 50.000 0.00 0.00 0.00 3.58
157 158 2.930455 GCTCAACTGGCTCTCTTCTGTC 60.930 54.545 0.00 0.00 0.00 3.51
158 159 1.001860 GCTCAACTGGCTCTCTTCTGT 59.998 52.381 0.00 0.00 0.00 3.41
159 160 1.001746 TGCTCAACTGGCTCTCTTCTG 59.998 52.381 0.00 0.00 0.00 3.02
160 161 1.275856 CTGCTCAACTGGCTCTCTTCT 59.724 52.381 0.00 0.00 0.00 2.85
161 162 1.274728 TCTGCTCAACTGGCTCTCTTC 59.725 52.381 0.00 0.00 0.00 2.87
189 190 7.661847 AGTTTCGTATGGGATGATTATTTCCTC 59.338 37.037 0.00 0.00 32.34 3.71
201 202 2.235402 ACGGAACAGTTTCGTATGGGAT 59.765 45.455 18.46 0.00 31.78 3.85
202 203 1.619827 ACGGAACAGTTTCGTATGGGA 59.380 47.619 18.46 0.00 31.78 4.37
203 204 1.730064 CACGGAACAGTTTCGTATGGG 59.270 52.381 19.43 3.58 31.78 4.00
204 205 2.679450 TCACGGAACAGTTTCGTATGG 58.321 47.619 19.43 7.88 31.78 2.74
205 206 5.004440 CACTATCACGGAACAGTTTCGTATG 59.996 44.000 19.43 8.66 31.78 2.39
208 209 3.314553 CACTATCACGGAACAGTTTCGT 58.685 45.455 14.26 14.26 31.78 3.85
209 210 2.092211 GCACTATCACGGAACAGTTTCG 59.908 50.000 12.75 12.75 31.78 3.46
210 211 3.064207 TGCACTATCACGGAACAGTTTC 58.936 45.455 0.00 0.00 0.00 2.78
211 212 3.120321 TGCACTATCACGGAACAGTTT 57.880 42.857 0.00 0.00 0.00 2.66
213 214 2.621338 CATGCACTATCACGGAACAGT 58.379 47.619 0.00 0.00 0.00 3.55
251 252 5.506982 GCAGTGAGGGAGATAATTTCATTGC 60.507 44.000 5.98 5.98 41.80 3.56
349 409 2.993471 GCCACATGTTTGCTCCCGG 61.993 63.158 9.37 0.00 0.00 5.73
446 506 0.252239 TCTGGCTGGGTCTTGAGCTA 60.252 55.000 0.00 0.00 35.42 3.32
451 511 1.298014 GAGGTCTGGCTGGGTCTTG 59.702 63.158 0.00 0.00 0.00 3.02
461 521 5.221263 ACGTATACTTGCTAATGAGGTCTGG 60.221 44.000 0.56 0.00 0.00 3.86
464 525 6.968250 AGTACGTATACTTGCTAATGAGGTC 58.032 40.000 0.00 0.00 38.59 3.85
485 546 9.388506 AGTTCGAGCTGTTAAGTACTAATAGTA 57.611 33.333 0.00 0.00 32.68 1.82
490 551 8.733458 TGATTAGTTCGAGCTGTTAAGTACTAA 58.267 33.333 12.54 6.75 33.10 2.24
492 553 7.154435 TGATTAGTTCGAGCTGTTAAGTACT 57.846 36.000 12.54 0.00 0.00 2.73
493 554 6.472808 CCTGATTAGTTCGAGCTGTTAAGTAC 59.527 42.308 12.54 0.00 0.00 2.73
496 557 4.268884 GCCTGATTAGTTCGAGCTGTTAAG 59.731 45.833 12.54 4.71 0.00 1.85
505 566 1.275010 TGCTGTGCCTGATTAGTTCGA 59.725 47.619 0.00 0.00 0.00 3.71
506 567 1.662629 CTGCTGTGCCTGATTAGTTCG 59.337 52.381 0.00 0.00 0.00 3.95
508 569 2.938756 GCTCTGCTGTGCCTGATTAGTT 60.939 50.000 6.39 0.00 0.00 2.24
522 583 0.399454 ATTGGTCACACTGCTCTGCT 59.601 50.000 0.00 0.00 0.00 4.24
523 584 0.520404 CATTGGTCACACTGCTCTGC 59.480 55.000 0.00 0.00 0.00 4.26
524 585 0.520404 GCATTGGTCACACTGCTCTG 59.480 55.000 3.26 0.00 46.28 3.35
525 586 2.938354 GCATTGGTCACACTGCTCT 58.062 52.632 3.26 0.00 46.28 4.09
736 833 6.195700 ACAGGAGTACCTCTCAGCTAATTTA 58.804 40.000 0.00 0.00 45.94 1.40
901 1029 0.880278 TTCTGCGCTGGTGTCTGAAC 60.880 55.000 14.70 0.00 0.00 3.18
933 1061 6.146216 GTGGTCAGAGAGTATGAATACGATG 58.854 44.000 0.00 0.00 38.28 3.84
938 1066 5.594725 GGAGTGTGGTCAGAGAGTATGAATA 59.405 44.000 0.00 0.00 0.00 1.75
944 1072 1.350019 TCGGAGTGTGGTCAGAGAGTA 59.650 52.381 0.00 0.00 0.00 2.59
961 1089 0.905357 AGGAACCCAACAGAGATCGG 59.095 55.000 0.00 0.00 0.00 4.18
962 1090 1.550524 TCAGGAACCCAACAGAGATCG 59.449 52.381 0.00 0.00 0.00 3.69
1014 1166 1.189403 CGATCACGTACGGCTTCTTC 58.811 55.000 21.06 6.53 34.56 2.87
1155 1307 3.628646 GAGGGCAATGGCGAGTGGT 62.629 63.158 0.00 0.00 42.47 4.16
1158 1310 3.376935 CTCGAGGGCAATGGCGAGT 62.377 63.158 3.91 0.00 43.65 4.18
1185 1351 0.102120 CCGAGCAGAACCAGCTAGAG 59.898 60.000 0.00 0.00 43.58 2.43
1190 1356 3.019003 TAGCCCGAGCAGAACCAGC 62.019 63.158 0.00 0.00 43.56 4.85
1209 1377 2.030363 CGATCCTCTTGCTAGTGCTAGG 60.030 54.545 8.16 0.00 41.25 3.02
1215 1389 7.448777 TGATTCTTATACGATCCTCTTGCTAGT 59.551 37.037 0.00 0.00 0.00 2.57
1226 1400 3.610242 CAGCGCCTGATTCTTATACGATC 59.390 47.826 2.29 0.00 32.44 3.69
1359 1675 4.805192 ACTTTGTTGCACATAAACAGCTTG 59.195 37.500 0.00 0.00 38.67 4.01
1381 1717 4.590647 TCAGTAATCCATCTCCATCTCCAC 59.409 45.833 0.00 0.00 0.00 4.02
1390 1726 8.994429 ATTAACATCGATCAGTAATCCATCTC 57.006 34.615 0.00 0.00 0.00 2.75
1393 1729 9.605275 CCATATTAACATCGATCAGTAATCCAT 57.395 33.333 0.00 0.00 0.00 3.41
1394 1730 7.549134 GCCATATTAACATCGATCAGTAATCCA 59.451 37.037 0.00 0.00 0.00 3.41
1395 1731 7.766278 AGCCATATTAACATCGATCAGTAATCC 59.234 37.037 0.00 0.00 0.00 3.01
1396 1732 8.709386 AGCCATATTAACATCGATCAGTAATC 57.291 34.615 0.00 0.00 0.00 1.75
1399 1735 7.931407 ACAAAGCCATATTAACATCGATCAGTA 59.069 33.333 0.00 0.00 0.00 2.74
1420 1756 6.431234 AGCTAAATGTAGTCCTGGAAACAAAG 59.569 38.462 14.89 13.23 42.06 2.77
1428 1764 6.259608 CAGATTCAAGCTAAATGTAGTCCTGG 59.740 42.308 0.00 0.00 0.00 4.45
1562 1898 1.202545 GGGAGCTGGGTCGATTTACTC 60.203 57.143 0.00 0.00 0.00 2.59
1564 1900 0.831307 AGGGAGCTGGGTCGATTTAC 59.169 55.000 0.00 0.00 0.00 2.01
1565 1901 2.037144 GTAGGGAGCTGGGTCGATTTA 58.963 52.381 0.00 0.00 0.00 1.40
1566 1902 0.831307 GTAGGGAGCTGGGTCGATTT 59.169 55.000 0.00 0.00 0.00 2.17
1570 1906 2.363795 TGGTAGGGAGCTGGGTCG 60.364 66.667 0.00 0.00 0.00 4.79
1573 1909 0.325296 TACAGTGGTAGGGAGCTGGG 60.325 60.000 0.00 0.00 33.62 4.45
1579 1915 2.812836 TGATCGTACAGTGGTAGGGA 57.187 50.000 0.00 0.00 36.33 4.20
1983 2447 0.787084 ACCTGGAGAAGTCCCTCTCA 59.213 55.000 0.00 0.00 43.19 3.27
2088 2576 1.742880 CAGTCCACTCCATGCACCG 60.743 63.158 0.00 0.00 0.00 4.94
2315 2813 2.416747 GTGTGTAGATCAGCAGTGCAA 58.583 47.619 19.20 5.15 0.00 4.08
2360 2861 7.632721 TGCAAAAATCAATGAAAAAGAAGAGC 58.367 30.769 0.00 0.00 0.00 4.09
2376 2877 4.462483 TCCACCCAAGATACTGCAAAAATC 59.538 41.667 0.00 0.00 0.00 2.17
2400 2901 1.067495 CAGACCTCCAACGAGAAGGAC 60.067 57.143 0.00 0.00 38.52 3.85
2578 3085 2.202690 CAGCCGGCGACATCGTTA 60.203 61.111 23.20 0.00 42.22 3.18
2585 3092 2.665185 ACTTGTTCAGCCGGCGAC 60.665 61.111 23.20 20.93 0.00 5.19
2691 3198 2.798283 CGCCGTTTCTCTTCTTTGTGTA 59.202 45.455 0.00 0.00 0.00 2.90
2692 3199 1.597663 CGCCGTTTCTCTTCTTTGTGT 59.402 47.619 0.00 0.00 0.00 3.72
2705 3212 2.444700 ATCAGGTCCGTTCGCCGTTT 62.445 55.000 0.00 0.00 33.66 3.60
2718 3225 5.456921 ACTGATCATAAACCCAATCAGGT 57.543 39.130 13.88 0.00 46.02 4.00
2864 3375 2.094675 GCCATGTCCAAGTTACTGCAT 58.905 47.619 0.00 0.00 0.00 3.96
2867 3378 3.119388 CCATTGCCATGTCCAAGTTACTG 60.119 47.826 0.00 0.00 0.00 2.74
2934 3445 5.823045 GGTCTATTGATTTCCATCGGACTTT 59.177 40.000 0.00 0.00 31.08 2.66
2945 3456 6.513180 TCCTGTATCACGGTCTATTGATTTC 58.487 40.000 0.00 0.00 34.28 2.17
2967 3478 6.476706 GCAATACATAAGAACAGGCAAAATCC 59.523 38.462 0.00 0.00 0.00 3.01
2976 3487 4.271049 CGACCCTGCAATACATAAGAACAG 59.729 45.833 0.00 0.00 0.00 3.16
2982 3493 1.488812 AGGCGACCCTGCAATACATAA 59.511 47.619 0.00 0.00 40.94 1.90
3027 3539 6.803154 AAAACGTGAAAACCAATGGAAAAA 57.197 29.167 6.16 0.00 0.00 1.94
3237 3865 7.465379 CGTTCGGACAATGTTGAACATGTATAT 60.465 37.037 22.83 0.00 37.97 0.86
3239 3867 5.390461 CGTTCGGACAATGTTGAACATGTAT 60.390 40.000 22.83 0.19 37.97 2.29
3244 3872 1.003331 GCGTTCGGACAATGTTGAACA 60.003 47.619 22.83 0.00 40.47 3.18
3245 3873 1.263217 AGCGTTCGGACAATGTTGAAC 59.737 47.619 17.10 17.10 37.84 3.18
3481 4574 9.134734 TGAACAAGTATTTGAAAACTGTTGAAC 57.865 29.630 4.81 0.00 37.73 3.18


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

AutoCloner maintained by Alex Coulton.