Multiple sequence alignment - TraesCS5B01G262800

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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 TraesCS5B01G262800 chr5B 100.000 2971 0 0 1 2971 447401031 447398061 0.000000e+00 5487
1 TraesCS5B01G262800 chr5B 98.627 1020 13 1 1952 2971 680793716 680792698 0.000000e+00 1805
2 TraesCS5B01G262800 chr6A 93.357 1701 100 8 1281 2971 16623133 16621436 0.000000e+00 2503
3 TraesCS5B01G262800 chr6A 90.267 1161 101 10 135 1289 16628838 16627684 0.000000e+00 1507
4 TraesCS5B01G262800 chr1A 85.987 1206 137 18 954 2137 342597368 342596173 0.000000e+00 1262
5 TraesCS5B01G262800 chr1A 88.612 641 69 4 2333 2971 342595832 342595194 0.000000e+00 776
6 TraesCS5B01G262800 chr6B 85.230 1239 150 20 954 2170 37126610 37125383 0.000000e+00 1243
7 TraesCS5B01G262800 chr6B 87.832 641 73 5 2333 2971 37125076 37124439 0.000000e+00 747
8 TraesCS5B01G262800 chr3B 84.960 1137 141 19 950 2066 709749856 709750982 0.000000e+00 1125
9 TraesCS5B01G262800 chr2D 85.657 997 102 27 1094 2080 651035418 651036383 0.000000e+00 1011
10 TraesCS5B01G262800 chr2D 87.538 650 77 4 2324 2971 651036634 651037281 0.000000e+00 749
11 TraesCS5B01G262800 chrUn 88.144 641 72 4 2333 2971 305968019 305967381 0.000000e+00 760
12 TraesCS5B01G262800 chrUn 88.144 641 72 4 2333 2971 344608922 344609560 0.000000e+00 760
13 TraesCS5B01G262800 chr7B 76.946 989 164 43 997 1947 523629292 523630254 3.420000e-139 505
14 TraesCS5B01G262800 chr7B 86.686 338 37 8 2638 2971 66018803 66019136 4.680000e-98 368
15 TraesCS5B01G262800 chr3D 76.798 987 168 40 997 1947 41716833 41717794 5.720000e-137 497
16 TraesCS5B01G262800 chr2B 76.822 988 166 43 997 1947 776589584 776590545 5.720000e-137 497
17 TraesCS5B01G262800 chr2B 77.143 630 122 18 2359 2971 162081326 162080702 2.190000e-91 346
18 TraesCS5B01G262800 chr4D 76.417 988 167 43 997 1947 40415541 40414583 9.640000e-130 473
19 TraesCS5B01G262800 chr5A 93.902 82 4 1 56 137 476400907 476400827 4.020000e-24 122
20 TraesCS5B01G262800 chr5D 91.667 84 5 2 56 139 374660071 374659990 6.730000e-22 115


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 TraesCS5B01G262800 chr5B 447398061 447401031 2970 True 5487 5487 100.0000 1 2971 1 chr5B.!!$R1 2970
1 TraesCS5B01G262800 chr5B 680792698 680793716 1018 True 1805 1805 98.6270 1952 2971 1 chr5B.!!$R2 1019
2 TraesCS5B01G262800 chr6A 16621436 16623133 1697 True 2503 2503 93.3570 1281 2971 1 chr6A.!!$R1 1690
3 TraesCS5B01G262800 chr6A 16627684 16628838 1154 True 1507 1507 90.2670 135 1289 1 chr6A.!!$R2 1154
4 TraesCS5B01G262800 chr1A 342595194 342597368 2174 True 1019 1262 87.2995 954 2971 2 chr1A.!!$R1 2017
5 TraesCS5B01G262800 chr6B 37124439 37126610 2171 True 995 1243 86.5310 954 2971 2 chr6B.!!$R1 2017
6 TraesCS5B01G262800 chr3B 709749856 709750982 1126 False 1125 1125 84.9600 950 2066 1 chr3B.!!$F1 1116
7 TraesCS5B01G262800 chr2D 651035418 651037281 1863 False 880 1011 86.5975 1094 2971 2 chr2D.!!$F1 1877
8 TraesCS5B01G262800 chrUn 305967381 305968019 638 True 760 760 88.1440 2333 2971 1 chrUn.!!$R1 638
9 TraesCS5B01G262800 chrUn 344608922 344609560 638 False 760 760 88.1440 2333 2971 1 chrUn.!!$F1 638
10 TraesCS5B01G262800 chr7B 523629292 523630254 962 False 505 505 76.9460 997 1947 1 chr7B.!!$F2 950
11 TraesCS5B01G262800 chr3D 41716833 41717794 961 False 497 497 76.7980 997 1947 1 chr3D.!!$F1 950
12 TraesCS5B01G262800 chr2B 776589584 776590545 961 False 497 497 76.8220 997 1947 1 chr2B.!!$F1 950
13 TraesCS5B01G262800 chr2B 162080702 162081326 624 True 346 346 77.1430 2359 2971 1 chr2B.!!$R1 612
14 TraesCS5B01G262800 chr4D 40414583 40415541 958 True 473 473 76.4170 997 1947 1 chr4D.!!$R1 950

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
45 46 0.033504 TAATGCTCGCCGGGATTCTC 59.966 55.0 2.18 0.0 0.00 2.87 F
112 113 0.108424 AGCTTCGAGTGCATGAGGAC 60.108 55.0 13.56 0.0 36.16 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1166 1.486310 TCTAGGATTTCACGCCATGCT 59.514 47.619 0.0 0.0 0.0 3.79 R
2083 2140 2.799978 GCAGCACCAACCAAACAAATAC 59.200 45.455 0.0 0.0 0.0 1.89 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
19 20 3.047280 GCATGGCCGACACGTCAA 61.047 61.111 0.00 0.00 0.00 3.18
20 21 3.027170 GCATGGCCGACACGTCAAG 62.027 63.158 0.00 0.00 0.00 3.02
21 22 2.047274 ATGGCCGACACGTCAAGG 60.047 61.111 0.00 0.00 0.00 3.61
22 23 2.579657 ATGGCCGACACGTCAAGGA 61.580 57.895 0.00 0.00 0.00 3.36
23 24 2.432628 GGCCGACACGTCAAGGAG 60.433 66.667 4.11 0.00 0.00 3.69
24 25 2.432628 GCCGACACGTCAAGGAGG 60.433 66.667 4.11 0.00 0.00 4.30
25 26 3.048602 CCGACACGTCAAGGAGGT 58.951 61.111 0.00 0.00 0.00 3.85
26 27 1.366366 CCGACACGTCAAGGAGGTT 59.634 57.895 0.00 0.00 0.00 3.50
27 28 0.599558 CCGACACGTCAAGGAGGTTA 59.400 55.000 0.00 0.00 0.00 2.85
28 29 1.000060 CCGACACGTCAAGGAGGTTAA 60.000 52.381 0.00 0.00 0.00 2.01
29 30 2.353406 CCGACACGTCAAGGAGGTTAAT 60.353 50.000 0.00 0.00 0.00 1.40
30 31 2.666508 CGACACGTCAAGGAGGTTAATG 59.333 50.000 0.00 0.00 0.00 1.90
31 32 2.415512 GACACGTCAAGGAGGTTAATGC 59.584 50.000 0.00 0.00 0.00 3.56
32 33 2.038557 ACACGTCAAGGAGGTTAATGCT 59.961 45.455 0.00 0.00 0.00 3.79
33 34 2.673368 CACGTCAAGGAGGTTAATGCTC 59.327 50.000 0.00 0.00 0.00 4.26
34 35 1.927174 CGTCAAGGAGGTTAATGCTCG 59.073 52.381 0.00 0.00 0.00 5.03
35 36 1.666189 GTCAAGGAGGTTAATGCTCGC 59.334 52.381 0.00 0.00 0.00 5.03
36 37 1.017387 CAAGGAGGTTAATGCTCGCC 58.983 55.000 0.00 0.00 0.00 5.54
37 38 0.462047 AAGGAGGTTAATGCTCGCCG 60.462 55.000 0.00 0.00 0.00 6.46
38 39 1.887707 GGAGGTTAATGCTCGCCGG 60.888 63.158 0.00 0.00 0.00 6.13
39 40 1.887707 GAGGTTAATGCTCGCCGGG 60.888 63.158 2.18 0.00 0.00 5.73
40 41 2.188469 GGTTAATGCTCGCCGGGA 59.812 61.111 2.18 0.00 0.00 5.14
41 42 1.227853 GGTTAATGCTCGCCGGGAT 60.228 57.895 2.18 0.00 0.00 3.85
42 43 0.818040 GGTTAATGCTCGCCGGGATT 60.818 55.000 2.18 0.00 0.00 3.01
43 44 0.586802 GTTAATGCTCGCCGGGATTC 59.413 55.000 2.18 0.00 0.00 2.52
44 45 0.468226 TTAATGCTCGCCGGGATTCT 59.532 50.000 2.18 0.00 0.00 2.40
45 46 0.033504 TAATGCTCGCCGGGATTCTC 59.966 55.000 2.18 0.00 0.00 2.87
46 47 1.690219 AATGCTCGCCGGGATTCTCT 61.690 55.000 2.18 0.00 0.00 3.10
47 48 1.690219 ATGCTCGCCGGGATTCTCTT 61.690 55.000 2.18 0.00 0.00 2.85
48 49 1.884926 GCTCGCCGGGATTCTCTTG 60.885 63.158 2.18 0.00 0.00 3.02
49 50 1.884926 CTCGCCGGGATTCTCTTGC 60.885 63.158 2.18 0.00 0.00 4.01
50 51 2.125147 CGCCGGGATTCTCTTGCA 60.125 61.111 2.18 0.00 0.00 4.08
51 52 2.176273 CGCCGGGATTCTCTTGCAG 61.176 63.158 2.18 0.00 0.00 4.41
52 53 2.476320 GCCGGGATTCTCTTGCAGC 61.476 63.158 2.18 0.00 0.00 5.25
53 54 1.222936 CCGGGATTCTCTTGCAGCT 59.777 57.895 0.00 0.00 0.00 4.24
54 55 0.393537 CCGGGATTCTCTTGCAGCTT 60.394 55.000 0.00 0.00 0.00 3.74
55 56 0.731417 CGGGATTCTCTTGCAGCTTG 59.269 55.000 0.00 0.00 0.00 4.01
56 57 0.455005 GGGATTCTCTTGCAGCTTGC 59.545 55.000 0.00 1.70 45.29 4.01
66 67 3.297620 CAGCTTGCAGGGCCGTTT 61.298 61.111 0.00 0.00 0.00 3.60
67 68 2.521708 AGCTTGCAGGGCCGTTTT 60.522 55.556 0.00 0.00 0.00 2.43
68 69 2.049156 GCTTGCAGGGCCGTTTTC 60.049 61.111 0.00 0.00 0.00 2.29
69 70 2.650778 CTTGCAGGGCCGTTTTCC 59.349 61.111 0.00 0.00 0.00 3.13
70 71 3.267597 CTTGCAGGGCCGTTTTCCG 62.268 63.158 0.00 0.00 0.00 4.30
71 72 4.572571 TGCAGGGCCGTTTTCCGT 62.573 61.111 0.00 0.00 33.66 4.69
72 73 3.733960 GCAGGGCCGTTTTCCGTC 61.734 66.667 0.00 0.00 33.66 4.79
73 74 3.419759 CAGGGCCGTTTTCCGTCG 61.420 66.667 0.00 0.00 33.66 5.12
74 75 3.618750 AGGGCCGTTTTCCGTCGA 61.619 61.111 0.00 0.00 33.66 4.20
75 76 3.417224 GGGCCGTTTTCCGTCGAC 61.417 66.667 5.18 5.18 33.66 4.20
76 77 3.770424 GGCCGTTTTCCGTCGACG 61.770 66.667 30.33 30.33 39.44 5.12
77 78 2.730604 GCCGTTTTCCGTCGACGA 60.731 61.111 37.65 21.13 43.02 4.20
78 79 2.302230 GCCGTTTTCCGTCGACGAA 61.302 57.895 37.65 25.23 43.02 3.85
79 80 1.620413 GCCGTTTTCCGTCGACGAAT 61.620 55.000 37.65 0.00 43.02 3.34
80 81 1.616620 CCGTTTTCCGTCGACGAATA 58.383 50.000 37.65 20.09 43.02 1.75
81 82 1.984990 CCGTTTTCCGTCGACGAATAA 59.015 47.619 37.65 24.29 43.02 1.40
82 83 2.599973 CCGTTTTCCGTCGACGAATAAT 59.400 45.455 37.65 0.00 43.02 1.28
83 84 3.790820 CCGTTTTCCGTCGACGAATAATA 59.209 43.478 37.65 19.73 43.02 0.98
84 85 4.442073 CCGTTTTCCGTCGACGAATAATAT 59.558 41.667 37.65 0.00 43.02 1.28
85 86 5.386729 CCGTTTTCCGTCGACGAATAATATC 60.387 44.000 37.65 17.79 43.02 1.63
86 87 5.386729 CGTTTTCCGTCGACGAATAATATCC 60.387 44.000 37.65 14.82 43.02 2.59
87 88 5.443185 TTTCCGTCGACGAATAATATCCT 57.557 39.130 37.65 0.00 43.02 3.24
88 89 6.558771 TTTCCGTCGACGAATAATATCCTA 57.441 37.500 37.65 10.66 43.02 2.94
89 90 5.791367 TCCGTCGACGAATAATATCCTAG 57.209 43.478 37.65 16.59 43.02 3.02
90 91 4.093998 TCCGTCGACGAATAATATCCTAGC 59.906 45.833 37.65 0.00 43.02 3.42
91 92 4.094590 CCGTCGACGAATAATATCCTAGCT 59.905 45.833 37.65 0.00 43.02 3.32
92 93 5.391736 CCGTCGACGAATAATATCCTAGCTT 60.392 44.000 37.65 0.00 43.02 3.74
93 94 6.183360 CCGTCGACGAATAATATCCTAGCTTA 60.183 42.308 37.65 0.00 43.02 3.09
94 95 6.900828 CGTCGACGAATAATATCCTAGCTTAG 59.099 42.308 33.35 0.00 43.02 2.18
95 96 6.687958 GTCGACGAATAATATCCTAGCTTAGC 59.312 42.308 0.00 0.00 0.00 3.09
96 97 6.598457 TCGACGAATAATATCCTAGCTTAGCT 59.402 38.462 12.67 12.67 43.41 3.32
97 98 7.120873 TCGACGAATAATATCCTAGCTTAGCTT 59.879 37.037 13.44 0.00 40.44 3.74
98 99 7.429920 CGACGAATAATATCCTAGCTTAGCTTC 59.570 40.741 13.44 0.00 40.44 3.86
99 100 7.251994 ACGAATAATATCCTAGCTTAGCTTCG 58.748 38.462 13.44 13.55 40.44 3.79
100 101 7.120873 ACGAATAATATCCTAGCTTAGCTTCGA 59.879 37.037 13.44 8.73 40.44 3.71
101 102 7.642194 CGAATAATATCCTAGCTTAGCTTCGAG 59.358 40.741 13.44 3.52 40.44 4.04
102 103 7.948034 ATAATATCCTAGCTTAGCTTCGAGT 57.052 36.000 13.44 0.00 40.44 4.18
103 104 5.637006 ATATCCTAGCTTAGCTTCGAGTG 57.363 43.478 13.44 0.00 40.44 3.51
104 105 1.405821 TCCTAGCTTAGCTTCGAGTGC 59.594 52.381 13.44 4.59 40.44 4.40
105 106 1.135139 CCTAGCTTAGCTTCGAGTGCA 59.865 52.381 13.44 0.00 40.44 4.57
106 107 2.223923 CCTAGCTTAGCTTCGAGTGCAT 60.224 50.000 13.44 3.51 40.44 3.96
107 108 1.649664 AGCTTAGCTTCGAGTGCATG 58.350 50.000 0.00 0.00 33.89 4.06
108 109 1.205655 AGCTTAGCTTCGAGTGCATGA 59.794 47.619 0.00 0.00 33.89 3.07
109 110 1.592081 GCTTAGCTTCGAGTGCATGAG 59.408 52.381 13.56 9.21 0.00 2.90
110 111 2.200067 CTTAGCTTCGAGTGCATGAGG 58.800 52.381 13.56 0.00 0.00 3.86
111 112 1.474330 TAGCTTCGAGTGCATGAGGA 58.526 50.000 13.56 0.00 0.00 3.71
112 113 0.108424 AGCTTCGAGTGCATGAGGAC 60.108 55.000 13.56 0.00 36.16 3.85
113 114 1.086634 GCTTCGAGTGCATGAGGACC 61.087 60.000 0.00 0.00 36.65 4.46
114 115 0.803768 CTTCGAGTGCATGAGGACCG 60.804 60.000 0.00 0.00 36.65 4.79
115 116 1.248101 TTCGAGTGCATGAGGACCGA 61.248 55.000 0.00 0.00 37.15 4.69
116 117 1.215382 CGAGTGCATGAGGACCGAA 59.785 57.895 0.00 0.00 36.65 4.30
117 118 0.803768 CGAGTGCATGAGGACCGAAG 60.804 60.000 0.00 0.00 36.65 3.79
118 119 0.532573 GAGTGCATGAGGACCGAAGA 59.467 55.000 0.00 0.00 36.65 2.87
119 120 0.976641 AGTGCATGAGGACCGAAGAA 59.023 50.000 0.00 0.00 36.65 2.52
120 121 1.079503 GTGCATGAGGACCGAAGAAC 58.920 55.000 0.00 0.00 0.00 3.01
121 122 0.684535 TGCATGAGGACCGAAGAACA 59.315 50.000 0.00 0.00 0.00 3.18
122 123 1.338105 TGCATGAGGACCGAAGAACAG 60.338 52.381 0.00 0.00 0.00 3.16
123 124 1.363744 CATGAGGACCGAAGAACAGC 58.636 55.000 0.00 0.00 0.00 4.40
124 125 0.250513 ATGAGGACCGAAGAACAGCC 59.749 55.000 0.00 0.00 0.00 4.85
125 126 1.446272 GAGGACCGAAGAACAGCCG 60.446 63.158 0.00 0.00 0.00 5.52
127 128 3.119096 GACCGAAGAACAGCCGGC 61.119 66.667 21.89 21.89 46.54 6.13
128 129 4.699522 ACCGAAGAACAGCCGGCC 62.700 66.667 26.15 7.74 46.54 6.13
131 132 4.699522 GAAGAACAGCCGGCCGGT 62.700 66.667 42.53 27.53 37.65 5.28
132 133 4.699522 AAGAACAGCCGGCCGGTC 62.700 66.667 42.53 33.30 37.65 4.79
149 150 1.003928 GGTCCCCTTGTTTGGATACGT 59.996 52.381 0.00 0.00 42.51 3.57
176 177 3.202829 AGCCAAACTAGTTTTCCGTGA 57.797 42.857 18.25 0.00 0.00 4.35
177 178 3.139077 AGCCAAACTAGTTTTCCGTGAG 58.861 45.455 18.25 5.47 0.00 3.51
179 180 3.139077 CCAAACTAGTTTTCCGTGAGCT 58.861 45.455 18.25 0.00 0.00 4.09
205 206 2.875087 ACCGCCCAACAAACTAAAAC 57.125 45.000 0.00 0.00 0.00 2.43
209 210 3.056304 CGCCCAACAAACTAAAACCATG 58.944 45.455 0.00 0.00 0.00 3.66
229 230 2.093235 TGTTTGGGGCCTTCAACAAAAG 60.093 45.455 0.84 0.00 34.95 2.27
238 239 4.141869 GGCCTTCAACAAAAGCATGGATAT 60.142 41.667 0.00 0.00 0.00 1.63
241 242 6.039717 GCCTTCAACAAAAGCATGGATATCTA 59.960 38.462 2.05 0.00 0.00 1.98
248 249 9.520204 AACAAAAGCATGGATATCTAAAATTCG 57.480 29.630 2.05 0.00 0.00 3.34
265 266 0.181587 TCGGTTTCCACAAAGCCAGA 59.818 50.000 0.00 0.00 38.10 3.86
271 272 3.799281 TTCCACAAAGCCAGAAAACTG 57.201 42.857 0.00 0.00 0.00 3.16
331 332 8.552034 AGAAAACAAGATTACAGAAAACTCTCG 58.448 33.333 0.00 0.00 0.00 4.04
336 337 8.095169 ACAAGATTACAGAAAACTCTCGGTAAT 58.905 33.333 8.29 8.29 44.30 1.89
341 342 9.939802 ATTACAGAAAACTCTCGGTAATAAACT 57.060 29.630 7.17 0.00 41.73 2.66
383 384 2.560542 TCAACAAACTTATTGGCGCCAT 59.439 40.909 33.25 22.08 0.00 4.40
403 404 4.785453 CTTCCCTCCCGCAGCCAC 62.785 72.222 0.00 0.00 0.00 5.01
407 408 4.785453 CCTCCCGCAGCCACTTCC 62.785 72.222 0.00 0.00 0.00 3.46
409 410 4.329545 TCCCGCAGCCACTTCCAC 62.330 66.667 0.00 0.00 0.00 4.02
418 419 2.176546 CACTTCCACGCGCCATTG 59.823 61.111 5.73 0.00 0.00 2.82
429 430 1.802636 CGCCATTGTTTCCATCGCT 59.197 52.632 0.00 0.00 0.00 4.93
445 446 6.688578 TCCATCGCTTCTATATAAACTGGAC 58.311 40.000 0.00 0.00 0.00 4.02
448 449 4.581824 TCGCTTCTATATAAACTGGACGGT 59.418 41.667 0.00 0.00 0.00 4.83
450 451 4.989168 GCTTCTATATAAACTGGACGGTGG 59.011 45.833 0.00 0.00 0.00 4.61
451 452 5.452917 GCTTCTATATAAACTGGACGGTGGT 60.453 44.000 0.00 0.00 0.00 4.16
453 454 6.889301 TCTATATAAACTGGACGGTGGTAG 57.111 41.667 0.00 0.00 0.00 3.18
461 462 1.202675 TGGACGGTGGTAGAACAAACC 60.203 52.381 0.00 0.00 37.53 3.27
464 465 1.269936 ACGGTGGTAGAACAAACCTCG 60.270 52.381 0.00 0.00 37.91 4.63
471 472 2.863401 AGAACAAACCTCGGCAAAAC 57.137 45.000 0.00 0.00 0.00 2.43
508 510 0.539518 TCAATGGCTAGCCGCTAACA 59.460 50.000 28.28 10.60 39.42 2.41
513 515 1.218316 GCTAGCCGCTAACACCTGT 59.782 57.895 2.29 0.00 35.14 4.00
559 561 2.125106 GCTAGGCTGGGAACACCG 60.125 66.667 0.00 0.00 44.64 4.94
560 562 2.656069 GCTAGGCTGGGAACACCGA 61.656 63.158 0.00 0.00 44.64 4.69
561 563 1.972660 GCTAGGCTGGGAACACCGAT 61.973 60.000 0.00 0.00 44.64 4.18
562 564 0.541863 CTAGGCTGGGAACACCGATT 59.458 55.000 0.00 0.00 44.64 3.34
571 573 1.338769 GGAACACCGATTACTGGCAGT 60.339 52.381 25.34 25.34 0.00 4.40
602 604 2.843113 CTGGGAAGACAAGGGATCTCTT 59.157 50.000 0.61 0.61 0.00 2.85
603 605 2.840651 TGGGAAGACAAGGGATCTCTTC 59.159 50.000 4.37 8.84 39.41 2.87
604 606 2.159028 GGGAAGACAAGGGATCTCTTCG 60.159 54.545 4.37 4.11 40.54 3.79
605 607 2.498078 GGAAGACAAGGGATCTCTTCGT 59.502 50.000 4.37 7.47 40.54 3.85
606 608 3.516615 GAAGACAAGGGATCTCTTCGTG 58.483 50.000 4.37 0.00 32.75 4.35
616 620 4.515567 GGGATCTCTTCGTGAACTTGTTTT 59.484 41.667 0.00 0.00 0.00 2.43
622 626 6.018751 TCTCTTCGTGAACTTGTTTTCATCAG 60.019 38.462 0.00 0.00 37.80 2.90
626 630 3.732721 GTGAACTTGTTTTCATCAGCAGC 59.267 43.478 0.00 0.00 37.80 5.25
627 631 3.380954 TGAACTTGTTTTCATCAGCAGCA 59.619 39.130 0.00 0.00 30.29 4.41
628 632 4.038282 TGAACTTGTTTTCATCAGCAGCAT 59.962 37.500 0.00 0.00 30.29 3.79
634 638 5.543714 TGTTTTCATCAGCAGCATTCAATT 58.456 33.333 0.00 0.00 0.00 2.32
660 664 5.282510 CAGATTCGTCATCCTACAGGTAAC 58.717 45.833 0.00 0.00 36.34 2.50
661 665 5.067936 CAGATTCGTCATCCTACAGGTAACT 59.932 44.000 0.00 0.00 39.62 2.24
683 687 8.812513 AACTTCCATAATCATGAACTGATCAA 57.187 30.769 0.00 0.00 44.03 2.57
695 699 9.234827 TCATGAACTGATCAACATACTGAAATT 57.765 29.630 0.00 0.00 42.54 1.82
701 705 8.454106 ACTGATCAACATACTGAAATTTGTAGC 58.546 33.333 0.00 0.00 0.00 3.58
702 706 7.463544 TGATCAACATACTGAAATTTGTAGCG 58.536 34.615 0.00 0.00 0.00 4.26
719 723 3.334583 AGCGAGAAGGTTCATGCTTTA 57.665 42.857 3.62 0.00 36.82 1.85
722 726 3.437049 GCGAGAAGGTTCATGCTTTAAGT 59.563 43.478 0.00 0.00 0.00 2.24
751 755 5.789774 GTGCAACTACGAAACTGAAATTG 57.210 39.130 0.00 0.00 0.00 2.32
752 756 4.146443 GTGCAACTACGAAACTGAAATTGC 59.854 41.667 0.00 0.00 41.17 3.56
762 766 6.636850 ACGAAACTGAAATTGCAAATCTGTAC 59.363 34.615 20.63 17.22 0.00 2.90
765 769 6.594788 ACTGAAATTGCAAATCTGTACCAT 57.405 33.333 19.60 3.08 0.00 3.55
777 781 7.298122 CAAATCTGTACCATCTGTGTGTTTAC 58.702 38.462 0.00 0.00 0.00 2.01
784 788 5.437060 ACCATCTGTGTGTTTACTTGAGTT 58.563 37.500 0.00 0.00 0.00 3.01
836 841 9.860650 TTAGACACATATATAAATTGGCAGGTT 57.139 29.630 0.00 0.00 0.00 3.50
837 842 8.396272 AGACACATATATAAATTGGCAGGTTC 57.604 34.615 0.00 0.00 0.00 3.62
839 844 8.766994 ACACATATATAAATTGGCAGGTTCTT 57.233 30.769 0.00 0.00 0.00 2.52
852 857 5.298276 TGGCAGGTTCTTGTTTTTACTACAG 59.702 40.000 0.00 0.00 0.00 2.74
860 865 8.663025 GTTCTTGTTTTTACTACAGTATAGGCC 58.337 37.037 0.00 0.00 0.00 5.19
874 879 3.710209 ATAGGCCATCCTTGTAGATGC 57.290 47.619 5.01 0.00 40.66 3.91
878 883 2.295349 GGCCATCCTTGTAGATGCAATG 59.705 50.000 0.00 0.00 41.98 2.82
940 945 7.542130 CCAAAGGTAACAAAGATTGCAGTATTC 59.458 37.037 0.00 0.00 41.41 1.75
942 947 5.028375 GGTAACAAAGATTGCAGTATTCGC 58.972 41.667 0.00 0.00 0.00 4.70
948 953 2.864343 AGATTGCAGTATTCGCGTAACC 59.136 45.455 5.77 0.00 0.00 2.85
1117 1127 9.719355 TGCTGAACATACTAAAAGATCAAACTA 57.281 29.630 0.00 0.00 0.00 2.24
1407 1420 4.707105 TGCCATATCATACACTTGACCAG 58.293 43.478 0.00 0.00 0.00 4.00
1410 1423 5.696724 GCCATATCATACACTTGACCAGTAC 59.303 44.000 0.00 0.00 32.76 2.73
1529 1542 1.133761 AGCTCTACTGCATCCGGACTA 60.134 52.381 6.12 0.00 34.99 2.59
1565 1596 2.629617 CAAAGGGAAAGGTGAAGCACAT 59.370 45.455 0.00 0.00 35.86 3.21
1587 1618 9.416794 CACATATTGATCTGAATGAGGTAGTAC 57.583 37.037 8.21 0.00 0.00 2.73
1648 1688 5.950544 TGTCCTAAGAAGCCTAATAGCAA 57.049 39.130 0.00 0.00 34.23 3.91
1820 1861 6.529829 CACAACAGATAGAAGCTTACTCAGTC 59.470 42.308 0.00 0.00 0.00 3.51
1973 2020 2.147958 TGGGTTGACAATGCGTAGTTC 58.852 47.619 0.00 0.00 0.00 3.01
2074 2125 7.064371 TGTTTTCAAACAATCAATGTCAGTTGG 59.936 33.333 2.53 0.00 45.17 3.77
2083 2140 9.426837 ACAATCAATGTCAGTTGGAAATTTATG 57.573 29.630 0.00 0.00 37.96 1.90
2690 2969 7.890127 TGTTCTCCAGGATAGATTTCAACATTT 59.110 33.333 0.00 0.00 0.00 2.32
2772 3051 1.959042 CTTGCATAACTGATCCGGCT 58.041 50.000 0.00 0.00 0.00 5.52
2779 3058 4.515191 GCATAACTGATCCGGCTAATGAAA 59.485 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.027170 CTTGACGTGTCGGCCATGC 62.027 63.158 2.24 0.00 31.60 4.06
3 4 2.390599 CCTTGACGTGTCGGCCATG 61.391 63.158 2.24 0.00 31.60 3.66
4 5 2.047274 CCTTGACGTGTCGGCCAT 60.047 61.111 2.24 0.00 31.60 4.40
5 6 3.220999 CTCCTTGACGTGTCGGCCA 62.221 63.158 2.24 0.00 31.60 5.36
6 7 2.432628 CTCCTTGACGTGTCGGCC 60.433 66.667 0.00 0.00 31.60 6.13
7 8 2.432628 CCTCCTTGACGTGTCGGC 60.433 66.667 0.00 0.00 34.27 5.54
8 9 0.599558 TAACCTCCTTGACGTGTCGG 59.400 55.000 0.00 0.00 0.00 4.79
9 10 2.427232 TTAACCTCCTTGACGTGTCG 57.573 50.000 0.00 0.00 0.00 4.35
10 11 2.415512 GCATTAACCTCCTTGACGTGTC 59.584 50.000 0.00 0.00 0.00 3.67
11 12 2.038557 AGCATTAACCTCCTTGACGTGT 59.961 45.455 0.00 0.00 0.00 4.49
12 13 2.673368 GAGCATTAACCTCCTTGACGTG 59.327 50.000 0.00 0.00 0.00 4.49
13 14 2.674177 CGAGCATTAACCTCCTTGACGT 60.674 50.000 0.00 0.00 0.00 4.34
14 15 1.927174 CGAGCATTAACCTCCTTGACG 59.073 52.381 0.00 0.00 0.00 4.35
15 16 1.666189 GCGAGCATTAACCTCCTTGAC 59.334 52.381 0.00 0.00 0.00 3.18
16 17 1.406887 GGCGAGCATTAACCTCCTTGA 60.407 52.381 0.00 0.00 0.00 3.02
17 18 1.017387 GGCGAGCATTAACCTCCTTG 58.983 55.000 0.00 0.00 0.00 3.61
18 19 0.462047 CGGCGAGCATTAACCTCCTT 60.462 55.000 0.00 0.00 0.00 3.36
19 20 1.144057 CGGCGAGCATTAACCTCCT 59.856 57.895 0.00 0.00 0.00 3.69
20 21 1.887707 CCGGCGAGCATTAACCTCC 60.888 63.158 9.30 0.00 0.00 4.30
21 22 1.887707 CCCGGCGAGCATTAACCTC 60.888 63.158 9.30 0.00 0.00 3.85
22 23 1.696097 ATCCCGGCGAGCATTAACCT 61.696 55.000 9.30 0.00 0.00 3.50
23 24 0.818040 AATCCCGGCGAGCATTAACC 60.818 55.000 9.30 0.00 0.00 2.85
24 25 0.586802 GAATCCCGGCGAGCATTAAC 59.413 55.000 9.30 0.00 0.00 2.01
25 26 0.468226 AGAATCCCGGCGAGCATTAA 59.532 50.000 9.30 0.00 0.00 1.40
26 27 0.033504 GAGAATCCCGGCGAGCATTA 59.966 55.000 9.30 0.00 0.00 1.90
27 28 1.227674 GAGAATCCCGGCGAGCATT 60.228 57.895 9.30 2.69 0.00 3.56
28 29 1.690219 AAGAGAATCCCGGCGAGCAT 61.690 55.000 9.30 0.00 33.66 3.79
29 30 2.359169 AAGAGAATCCCGGCGAGCA 61.359 57.895 9.30 0.00 33.66 4.26
30 31 1.884926 CAAGAGAATCCCGGCGAGC 60.885 63.158 9.30 0.00 33.66 5.03
31 32 1.884926 GCAAGAGAATCCCGGCGAG 60.885 63.158 9.30 0.00 33.66 5.03
32 33 2.186903 GCAAGAGAATCCCGGCGA 59.813 61.111 9.30 0.00 33.66 5.54
33 34 2.125147 TGCAAGAGAATCCCGGCG 60.125 61.111 0.00 0.00 33.66 6.46
34 35 2.476320 GCTGCAAGAGAATCCCGGC 61.476 63.158 0.00 0.00 34.07 6.13
35 36 0.393537 AAGCTGCAAGAGAATCCCGG 60.394 55.000 1.02 0.00 34.07 5.73
36 37 0.731417 CAAGCTGCAAGAGAATCCCG 59.269 55.000 1.02 0.00 34.07 5.14
37 38 0.455005 GCAAGCTGCAAGAGAATCCC 59.545 55.000 1.02 0.00 44.26 3.85
49 50 2.753931 GAAAACGGCCCTGCAAGCTG 62.754 60.000 14.17 14.17 42.55 4.24
50 51 2.521708 AAAACGGCCCTGCAAGCT 60.522 55.556 8.19 0.00 0.00 3.74
51 52 2.049156 GAAAACGGCCCTGCAAGC 60.049 61.111 0.00 0.00 0.00 4.01
52 53 2.650778 GGAAAACGGCCCTGCAAG 59.349 61.111 0.00 0.00 0.00 4.01
53 54 3.291383 CGGAAAACGGCCCTGCAA 61.291 61.111 0.00 0.00 39.42 4.08
63 64 5.689068 AGGATATTATTCGTCGACGGAAAAC 59.311 40.000 35.05 18.67 40.29 2.43
64 65 5.835257 AGGATATTATTCGTCGACGGAAAA 58.165 37.500 35.05 25.15 40.29 2.29
65 66 5.443185 AGGATATTATTCGTCGACGGAAA 57.557 39.130 35.05 24.10 40.29 3.13
66 67 5.391310 GCTAGGATATTATTCGTCGACGGAA 60.391 44.000 35.05 26.44 40.29 4.30
67 68 4.093998 GCTAGGATATTATTCGTCGACGGA 59.906 45.833 35.05 29.79 40.29 4.69
68 69 4.094590 AGCTAGGATATTATTCGTCGACGG 59.905 45.833 35.05 18.25 40.29 4.79
69 70 5.219226 AGCTAGGATATTATTCGTCGACG 57.781 43.478 31.30 31.30 41.45 5.12
70 71 6.687958 GCTAAGCTAGGATATTATTCGTCGAC 59.312 42.308 5.18 5.18 0.00 4.20
71 72 6.598457 AGCTAAGCTAGGATATTATTCGTCGA 59.402 38.462 0.00 0.00 36.99 4.20
72 73 6.787225 AGCTAAGCTAGGATATTATTCGTCG 58.213 40.000 0.00 0.00 36.99 5.12
73 74 7.429920 CGAAGCTAAGCTAGGATATTATTCGTC 59.570 40.741 0.00 0.00 38.25 4.20
74 75 7.120873 TCGAAGCTAAGCTAGGATATTATTCGT 59.879 37.037 0.00 0.00 38.25 3.85
75 76 7.473366 TCGAAGCTAAGCTAGGATATTATTCG 58.527 38.462 0.00 0.00 38.25 3.34
76 77 8.463607 ACTCGAAGCTAAGCTAGGATATTATTC 58.536 37.037 0.00 0.00 38.25 1.75
77 78 8.247562 CACTCGAAGCTAAGCTAGGATATTATT 58.752 37.037 0.00 0.00 38.25 1.40
78 79 7.629652 GCACTCGAAGCTAAGCTAGGATATTAT 60.630 40.741 2.49 0.00 38.25 1.28
79 80 6.349445 GCACTCGAAGCTAAGCTAGGATATTA 60.349 42.308 2.49 0.00 38.25 0.98
80 81 5.565834 GCACTCGAAGCTAAGCTAGGATATT 60.566 44.000 2.49 0.00 38.25 1.28
81 82 4.082463 GCACTCGAAGCTAAGCTAGGATAT 60.082 45.833 2.49 0.00 38.25 1.63
82 83 3.253677 GCACTCGAAGCTAAGCTAGGATA 59.746 47.826 2.49 0.00 38.25 2.59
83 84 2.035321 GCACTCGAAGCTAAGCTAGGAT 59.965 50.000 2.49 0.00 38.25 3.24
84 85 1.405821 GCACTCGAAGCTAAGCTAGGA 59.594 52.381 2.49 0.00 38.25 2.94
85 86 1.135139 TGCACTCGAAGCTAAGCTAGG 59.865 52.381 10.42 0.00 38.25 3.02
86 87 2.568696 TGCACTCGAAGCTAAGCTAG 57.431 50.000 10.42 0.00 38.25 3.42
87 88 2.427095 TCATGCACTCGAAGCTAAGCTA 59.573 45.455 10.42 0.00 38.25 3.32
88 89 1.205655 TCATGCACTCGAAGCTAAGCT 59.794 47.619 10.42 0.00 42.56 3.74
89 90 1.592081 CTCATGCACTCGAAGCTAAGC 59.408 52.381 10.42 0.00 0.00 3.09
90 91 2.159184 TCCTCATGCACTCGAAGCTAAG 60.159 50.000 10.42 5.59 0.00 2.18
91 92 1.824852 TCCTCATGCACTCGAAGCTAA 59.175 47.619 10.42 0.00 0.00 3.09
92 93 1.135139 GTCCTCATGCACTCGAAGCTA 59.865 52.381 10.42 0.00 0.00 3.32
93 94 0.108424 GTCCTCATGCACTCGAAGCT 60.108 55.000 10.42 0.00 0.00 3.74
94 95 1.086634 GGTCCTCATGCACTCGAAGC 61.087 60.000 0.00 2.74 0.00 3.86
95 96 0.803768 CGGTCCTCATGCACTCGAAG 60.804 60.000 0.00 0.00 0.00 3.79
96 97 1.215382 CGGTCCTCATGCACTCGAA 59.785 57.895 0.00 0.00 0.00 3.71
97 98 1.248101 TTCGGTCCTCATGCACTCGA 61.248 55.000 0.00 0.00 0.00 4.04
98 99 0.803768 CTTCGGTCCTCATGCACTCG 60.804 60.000 0.00 0.00 0.00 4.18
99 100 0.532573 TCTTCGGTCCTCATGCACTC 59.467 55.000 0.00 0.00 0.00 3.51
100 101 0.976641 TTCTTCGGTCCTCATGCACT 59.023 50.000 0.00 0.00 0.00 4.40
101 102 1.079503 GTTCTTCGGTCCTCATGCAC 58.920 55.000 0.00 0.00 0.00 4.57
102 103 0.684535 TGTTCTTCGGTCCTCATGCA 59.315 50.000 0.00 0.00 0.00 3.96
103 104 1.363744 CTGTTCTTCGGTCCTCATGC 58.636 55.000 0.00 0.00 0.00 4.06
104 105 1.363744 GCTGTTCTTCGGTCCTCATG 58.636 55.000 0.00 0.00 0.00 3.07
105 106 0.250513 GGCTGTTCTTCGGTCCTCAT 59.749 55.000 0.00 0.00 0.00 2.90
106 107 1.671742 GGCTGTTCTTCGGTCCTCA 59.328 57.895 0.00 0.00 0.00 3.86
107 108 1.446272 CGGCTGTTCTTCGGTCCTC 60.446 63.158 0.00 0.00 0.00 3.71
108 109 2.657237 CGGCTGTTCTTCGGTCCT 59.343 61.111 0.00 0.00 0.00 3.85
109 110 2.434359 CCGGCTGTTCTTCGGTCC 60.434 66.667 0.00 0.00 39.04 4.46
110 111 3.119096 GCCGGCTGTTCTTCGGTC 61.119 66.667 22.15 0.00 44.97 4.79
111 112 4.699522 GGCCGGCTGTTCTTCGGT 62.700 66.667 28.56 0.00 44.97 4.69
114 115 4.699522 ACCGGCCGGCTGTTCTTC 62.700 66.667 43.58 10.60 39.32 2.87
115 116 4.699522 GACCGGCCGGCTGTTCTT 62.700 66.667 43.58 23.47 39.32 2.52
130 131 2.484742 ACGTATCCAAACAAGGGGAC 57.515 50.000 0.00 0.00 35.67 4.46
131 132 2.553466 CCAACGTATCCAAACAAGGGGA 60.553 50.000 0.00 0.00 37.64 4.81
132 133 1.816224 CCAACGTATCCAAACAAGGGG 59.184 52.381 0.00 0.00 0.00 4.79
133 134 2.785562 TCCAACGTATCCAAACAAGGG 58.214 47.619 0.00 0.00 0.00 3.95
172 173 1.419374 GGCGGTTATATGAGCTCACG 58.581 55.000 20.97 17.68 0.00 4.35
176 177 1.488812 TGTTGGGCGGTTATATGAGCT 59.511 47.619 0.00 0.00 0.00 4.09
177 178 1.961793 TGTTGGGCGGTTATATGAGC 58.038 50.000 0.00 0.00 0.00 4.26
179 180 3.958018 AGTTTGTTGGGCGGTTATATGA 58.042 40.909 0.00 0.00 0.00 2.15
205 206 0.321346 GTTGAAGGCCCCAAACATGG 59.679 55.000 9.47 0.00 0.00 3.66
209 210 2.560504 CTTTTGTTGAAGGCCCCAAAC 58.439 47.619 9.47 7.31 0.00 2.93
216 217 2.818130 TCCATGCTTTTGTTGAAGGC 57.182 45.000 0.00 0.00 40.50 4.35
229 230 7.084486 GGAAACCGAATTTTAGATATCCATGC 58.916 38.462 0.00 0.00 0.00 4.06
238 239 5.508320 GGCTTTGTGGAAACCGAATTTTAGA 60.508 40.000 0.00 0.00 0.00 2.10
241 242 3.118592 TGGCTTTGTGGAAACCGAATTTT 60.119 39.130 0.00 0.00 0.00 1.82
247 248 1.028905 TTCTGGCTTTGTGGAAACCG 58.971 50.000 0.00 0.00 0.00 4.44
248 249 3.118775 AGTTTTCTGGCTTTGTGGAAACC 60.119 43.478 0.00 0.00 0.00 3.27
319 320 9.946165 AAAAAGTTTATTACCGAGAGTTTTCTG 57.054 29.630 0.00 0.00 32.53 3.02
346 347 1.864263 TTGAGGGAGGAGCGGAGAGA 61.864 60.000 0.00 0.00 0.00 3.10
359 360 2.671070 GCGCCAATAAGTTTGTTGAGGG 60.671 50.000 0.00 3.80 31.84 4.30
383 384 2.351276 GCTGCGGGAGGGAAGAAA 59.649 61.111 0.00 0.00 0.00 2.52
403 404 0.729140 GAAACAATGGCGCGTGGAAG 60.729 55.000 8.43 0.00 0.00 3.46
407 408 2.642129 TGGAAACAATGGCGCGTG 59.358 55.556 8.43 0.00 37.44 5.34
418 419 7.656137 TCCAGTTTATATAGAAGCGATGGAAAC 59.344 37.037 3.44 0.00 30.50 2.78
429 430 7.062322 TCTACCACCGTCCAGTTTATATAGAA 58.938 38.462 0.00 0.00 0.00 2.10
445 446 1.425412 CGAGGTTTGTTCTACCACCG 58.575 55.000 0.00 0.00 38.16 4.94
448 449 0.759959 TGCCGAGGTTTGTTCTACCA 59.240 50.000 0.00 0.00 38.16 3.25
450 451 3.065648 TGTTTTGCCGAGGTTTGTTCTAC 59.934 43.478 0.00 0.00 0.00 2.59
451 452 3.280295 TGTTTTGCCGAGGTTTGTTCTA 58.720 40.909 0.00 0.00 0.00 2.10
453 454 2.098443 TCTGTTTTGCCGAGGTTTGTTC 59.902 45.455 0.00 0.00 0.00 3.18
461 462 2.099141 TCCAGATCTGTTTTGCCGAG 57.901 50.000 21.11 2.94 0.00 4.63
464 465 2.893489 AGGTTTCCAGATCTGTTTTGCC 59.107 45.455 21.11 15.06 0.00 4.52
471 472 5.587844 CCATTGAACTAGGTTTCCAGATCTG 59.412 44.000 16.24 16.24 0.00 2.90
508 510 3.535561 GGAATCGATGATCACAACAGGT 58.464 45.455 0.00 0.00 0.00 4.00
513 515 2.746142 GCCAGGGAATCGATGATCACAA 60.746 50.000 0.00 0.00 0.00 3.33
521 523 4.256180 GGCGGCCAGGGAATCGAT 62.256 66.667 15.62 0.00 0.00 3.59
541 543 2.125106 GGTGTTCCCAGCCTAGCG 60.125 66.667 0.00 0.00 32.87 4.26
543 545 0.541863 AATCGGTGTTCCCAGCCTAG 59.458 55.000 0.00 0.00 35.65 3.02
554 556 1.610624 CCAACTGCCAGTAATCGGTGT 60.611 52.381 0.00 0.00 0.00 4.16
590 592 3.601443 AGTTCACGAAGAGATCCCTTG 57.399 47.619 0.00 0.00 0.00 3.61
602 604 3.625313 TGCTGATGAAAACAAGTTCACGA 59.375 39.130 0.00 0.00 40.22 4.35
603 605 3.951306 TGCTGATGAAAACAAGTTCACG 58.049 40.909 0.00 0.00 40.22 4.35
604 606 3.732721 GCTGCTGATGAAAACAAGTTCAC 59.267 43.478 0.00 0.00 40.22 3.18
605 607 3.380954 TGCTGCTGATGAAAACAAGTTCA 59.619 39.130 0.00 0.00 41.59 3.18
606 608 3.968649 TGCTGCTGATGAAAACAAGTTC 58.031 40.909 0.00 0.00 0.00 3.01
616 620 3.056465 TGCAAATTGAATGCTGCTGATGA 60.056 39.130 12.08 0.00 44.14 2.92
622 626 3.000078 CGAATCTGCAAATTGAATGCTGC 60.000 43.478 0.00 5.75 44.14 5.25
626 630 5.457799 GGATGACGAATCTGCAAATTGAATG 59.542 40.000 0.00 0.00 35.43 2.67
627 631 5.359009 AGGATGACGAATCTGCAAATTGAAT 59.641 36.000 0.00 0.00 35.43 2.57
628 632 4.701651 AGGATGACGAATCTGCAAATTGAA 59.298 37.500 0.00 0.00 35.43 2.69
634 638 3.430790 CCTGTAGGATGACGAATCTGCAA 60.431 47.826 0.00 0.00 37.39 4.08
672 676 8.849168 ACAAATTTCAGTATGTTGATCAGTTCA 58.151 29.630 0.00 0.00 37.40 3.18
683 687 6.313905 CCTTCTCGCTACAAATTTCAGTATGT 59.686 38.462 0.00 0.00 37.40 2.29
690 694 5.607119 TGAACCTTCTCGCTACAAATTTC 57.393 39.130 0.00 0.00 0.00 2.17
695 699 2.028112 AGCATGAACCTTCTCGCTACAA 60.028 45.455 0.00 0.00 34.93 2.41
701 705 5.637810 TGTACTTAAAGCATGAACCTTCTCG 59.362 40.000 0.00 0.00 0.00 4.04
702 706 7.334421 TCATGTACTTAAAGCATGAACCTTCTC 59.666 37.037 0.00 0.00 43.84 2.87
719 723 4.514781 TCGTAGTTGCACTCATGTACTT 57.485 40.909 0.00 0.00 0.00 2.24
722 726 4.684242 CAGTTTCGTAGTTGCACTCATGTA 59.316 41.667 0.00 0.00 0.00 2.29
729 733 4.146443 GCAATTTCAGTTTCGTAGTTGCAC 59.854 41.667 0.00 0.00 40.13 4.57
762 766 7.387673 TCATAACTCAAGTAAACACACAGATGG 59.612 37.037 0.00 0.00 0.00 3.51
765 769 8.902540 ATTCATAACTCAAGTAAACACACAGA 57.097 30.769 0.00 0.00 0.00 3.41
814 819 8.632679 CAAGAACCTGCCAATTTATATATGTGT 58.367 33.333 0.00 0.00 0.00 3.72
822 827 8.428852 AGTAAAAACAAGAACCTGCCAATTTAT 58.571 29.630 0.00 0.00 0.00 1.40
830 835 6.373186 ACTGTAGTAAAAACAAGAACCTGC 57.627 37.500 0.00 0.00 0.00 4.85
833 838 8.663025 GCCTATACTGTAGTAAAAACAAGAACC 58.337 37.037 0.00 0.00 33.76 3.62
836 841 7.909518 TGGCCTATACTGTAGTAAAAACAAGA 58.090 34.615 3.32 0.00 33.76 3.02
837 842 8.732746 ATGGCCTATACTGTAGTAAAAACAAG 57.267 34.615 3.32 0.00 33.76 3.16
839 844 7.126726 AGGATGGCCTATACTGTAGTAAAAACA 59.873 37.037 3.32 0.00 44.74 2.83
852 857 4.020218 TGCATCTACAAGGATGGCCTATAC 60.020 45.833 3.32 0.00 46.28 1.47
860 865 2.295349 GGGCATTGCATCTACAAGGATG 59.705 50.000 11.39 0.00 44.08 3.51
874 879 6.415206 AGGAAATTATCATGAAGGGCATTG 57.585 37.500 0.00 0.00 34.15 2.82
878 883 7.667219 TGATCTAAGGAAATTATCATGAAGGGC 59.333 37.037 0.00 0.00 0.00 5.19
910 915 4.501400 GCAATCTTTGTTACCTTTGGCACT 60.501 41.667 0.00 0.00 0.00 4.40
940 945 5.961395 AGTTAAATCATGTAGGTTACGCG 57.039 39.130 3.53 3.53 0.00 6.01
1117 1127 4.544152 TGTTCCTTCCTTCCCTCCATTTAT 59.456 41.667 0.00 0.00 0.00 1.40
1155 1166 1.486310 TCTAGGATTTCACGCCATGCT 59.514 47.619 0.00 0.00 0.00 3.79
1380 1393 7.228507 TGGTCAAGTGTATGATATGGCAATTAC 59.771 37.037 0.00 0.00 0.00 1.89
1407 1420 9.646336 CAGTTTGTAAGTTCATTGTTAGTGTAC 57.354 33.333 0.00 0.00 0.00 2.90
1410 1423 7.192913 TGCAGTTTGTAAGTTCATTGTTAGTG 58.807 34.615 0.00 0.00 0.00 2.74
1463 1476 3.585289 TCCAACTAGGCCACACTTTATCA 59.415 43.478 5.01 0.00 37.29 2.15
1565 1596 9.201989 ACTTGTACTACCTCATTCAGATCAATA 57.798 33.333 0.00 0.00 0.00 1.90
1624 1664 6.500589 TGCTATTAGGCTTCTTAGGACAAT 57.499 37.500 0.00 0.00 0.00 2.71
1648 1688 6.072230 GCACTTCTTCTTTTTCTCTGCCTTAT 60.072 38.462 0.00 0.00 0.00 1.73
1973 2020 6.018180 ACTCAAAGGTACGCTACAAGAAAAAG 60.018 38.462 0.00 0.00 0.00 2.27
2083 2140 2.799978 GCAGCACCAACCAAACAAATAC 59.200 45.455 0.00 0.00 0.00 1.89
2690 2969 4.529377 AGTGTCGACTAATTGTTTCCCCTA 59.471 41.667 17.92 0.00 0.00 3.53
2779 3058 4.282195 TCGCCCAATATTTTTGTTGGAACT 59.718 37.500 5.74 0.00 46.15 3.01


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

AutoCloner maintained by Alex Coulton.