Multiple sequence alignment - TraesCS5A01G088900

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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 TraesCS5A01G088900 chr5A 100.000 3858 0 0 1 3858 119219470 119215613 0.000000e+00 7125.0
1 TraesCS5A01G088900 chr5A 97.826 46 1 0 3280 3325 631328463 631328508 3.200000e-11 80.5
2 TraesCS5A01G088900 chr5A 95.833 48 0 2 3280 3325 381757741 381757694 4.130000e-10 76.8
3 TraesCS5A01G088900 chr5D 95.425 3650 90 28 156 3783 114005967 114002373 0.000000e+00 5744.0
4 TraesCS5A01G088900 chr5B 93.988 2778 86 34 217 2988 124767498 124764796 0.000000e+00 4130.0
5 TraesCS5A01G088900 chr5B 96.621 799 19 3 2986 3783 124764675 124763884 0.000000e+00 1319.0
6 TraesCS5A01G088900 chr1D 84.516 155 18 4 70 218 43282938 43282784 8.640000e-32 148.0
7 TraesCS5A01G088900 chr1D 82.468 154 18 7 69 218 107397594 107397742 4.050000e-25 126.0
8 TraesCS5A01G088900 chr3A 85.161 155 10 11 70 218 12381894 12382041 3.110000e-31 147.0
9 TraesCS5A01G088900 chr3A 83.117 154 17 7 72 220 44305519 44305370 8.700000e-27 132.0
10 TraesCS5A01G088900 chrUn 84.416 154 11 11 70 218 93062694 93062839 5.200000e-29 139.0
11 TraesCS5A01G088900 chrUn 83.226 155 13 10 70 218 129542005 129542152 3.130000e-26 130.0
12 TraesCS5A01G088900 chr6A 82.803 157 16 7 70 218 10080287 10080134 3.130000e-26 130.0
13 TraesCS5A01G088900 chr6A 91.045 67 6 0 4 70 203213298 203213232 1.480000e-14 91.6
14 TraesCS5A01G088900 chr6D 83.117 154 13 7 72 218 328823582 328823435 1.130000e-25 128.0
15 TraesCS5A01G088900 chr6D 82.895 152 14 10 70 216 444451509 444451365 4.050000e-25 126.0
16 TraesCS5A01G088900 chr3B 91.011 89 6 2 3770 3858 814892378 814892292 6.770000e-23 119.0
17 TraesCS5A01G088900 chr6B 94.737 76 2 2 3783 3858 156218432 156218505 2.440000e-22 117.0
18 TraesCS5A01G088900 chr4B 93.421 76 5 0 3783 3858 2741781 2741706 3.150000e-21 113.0
19 TraesCS5A01G088900 chr7A 93.421 76 4 1 3783 3858 225637798 225637724 1.130000e-20 111.0
20 TraesCS5A01G088900 chr3D 93.421 76 4 1 3784 3858 3102368 3102293 1.130000e-20 111.0
21 TraesCS5A01G088900 chr3D 97.917 48 1 0 3280 3327 362864577 362864624 2.470000e-12 84.2
22 TraesCS5A01G088900 chr2A 93.421 76 4 1 3783 3858 61475968 61475894 1.130000e-20 111.0
23 TraesCS5A01G088900 chr7B 93.333 75 3 1 3784 3858 640712972 640713044 4.080000e-20 110.0
24 TraesCS5A01G088900 chr4A 96.923 65 2 0 4 68 319489100 319489036 4.080000e-20 110.0
25 TraesCS5A01G088900 chr4A 92.405 79 3 3 3781 3858 606372833 606372757 4.080000e-20 110.0
26 TraesCS5A01G088900 chr4A 92.857 70 0 1 1 70 317421505 317421441 3.170000e-16 97.1
27 TraesCS5A01G088900 chr2B 93.333 75 4 1 3784 3858 82717165 82717092 4.080000e-20 110.0
28 TraesCS5A01G088900 chr7D 100.000 43 0 0 3280 3322 34070802 34070844 3.200000e-11 80.5
29 TraesCS5A01G088900 chr7D 96.000 50 0 2 3280 3329 108173793 108173840 3.200000e-11 80.5
30 TraesCS5A01G088900 chr4D 92.308 52 3 1 3267 3318 397158927 397158977 5.350000e-09 73.1
31 TraesCS5A01G088900 chr2D 88.333 60 6 1 3265 3323 196709964 196710023 1.920000e-08 71.3


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 TraesCS5A01G088900 chr5A 119215613 119219470 3857 True 7125.0 7125 100.0000 1 3858 1 chr5A.!!$R1 3857
1 TraesCS5A01G088900 chr5D 114002373 114005967 3594 True 5744.0 5744 95.4250 156 3783 1 chr5D.!!$R1 3627
2 TraesCS5A01G088900 chr5B 124763884 124767498 3614 True 2724.5 4130 95.3045 217 3783 2 chr5B.!!$R1 3566

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
813 818 0.107945 CTTCTTCGCTTCCCCTCTGG 60.108 60.0 0.0 0.0 0.00 3.86 F
1346 1353 0.100325 CTGCTGGTGTGCGTGAAAAA 59.900 50.0 0.0 0.0 35.36 1.94 F
2224 2246 0.615331 GGCTCCCAGTTCTGTCATCA 59.385 55.0 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 2474 0.392706 TTCTTCTGCTTCAGGCGACA 59.607 50.000 0.0 0.0 45.43 4.35 R
2541 2564 1.819305 GCTCCCAAACTGCCTTTGAGA 60.819 52.381 5.7 0.0 41.81 3.27 R
3790 3938 0.255890 ACAACCAGGAGCACAAGTGT 59.744 50.000 0.0 0.0 0.00 3.55 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.399046 CCGACCCATTCCAGTGGA 58.601 61.111 8.12 8.12 42.02 4.02
18 19 1.682849 CCGACCCATTCCAGTGGAA 59.317 57.895 26.54 26.54 46.39 3.53
30 31 4.503714 TCCAGTGGAATGGAACTATTCC 57.496 45.455 10.20 18.61 46.45 3.01
45 46 7.032377 GAACTATTCCATTCCATTCCACTTC 57.968 40.000 0.00 0.00 0.00 3.01
46 47 6.078456 ACTATTCCATTCCATTCCACTTCA 57.922 37.500 0.00 0.00 0.00 3.02
47 48 6.676558 ACTATTCCATTCCATTCCACTTCAT 58.323 36.000 0.00 0.00 0.00 2.57
48 49 7.128077 ACTATTCCATTCCATTCCACTTCATT 58.872 34.615 0.00 0.00 0.00 2.57
49 50 5.920193 TTCCATTCCATTCCACTTCATTC 57.080 39.130 0.00 0.00 0.00 2.67
50 51 4.280819 TCCATTCCATTCCACTTCATTCC 58.719 43.478 0.00 0.00 0.00 3.01
51 52 3.067180 CCATTCCATTCCACTTCATTCCG 59.933 47.826 0.00 0.00 0.00 4.30
52 53 1.750193 TCCATTCCACTTCATTCCGC 58.250 50.000 0.00 0.00 0.00 5.54
53 54 1.004161 TCCATTCCACTTCATTCCGCA 59.996 47.619 0.00 0.00 0.00 5.69
54 55 1.818060 CCATTCCACTTCATTCCGCAA 59.182 47.619 0.00 0.00 0.00 4.85
55 56 2.415893 CCATTCCACTTCATTCCGCAAC 60.416 50.000 0.00 0.00 0.00 4.17
56 57 1.243902 TTCCACTTCATTCCGCAACC 58.756 50.000 0.00 0.00 0.00 3.77
57 58 0.109532 TCCACTTCATTCCGCAACCA 59.890 50.000 0.00 0.00 0.00 3.67
58 59 0.958091 CCACTTCATTCCGCAACCAA 59.042 50.000 0.00 0.00 0.00 3.67
59 60 1.339610 CCACTTCATTCCGCAACCAAA 59.660 47.619 0.00 0.00 0.00 3.28
60 61 2.393764 CACTTCATTCCGCAACCAAAC 58.606 47.619 0.00 0.00 0.00 2.93
61 62 2.028130 ACTTCATTCCGCAACCAAACA 58.972 42.857 0.00 0.00 0.00 2.83
62 63 2.223711 ACTTCATTCCGCAACCAAACAC 60.224 45.455 0.00 0.00 0.00 3.32
63 64 1.393603 TCATTCCGCAACCAAACACA 58.606 45.000 0.00 0.00 0.00 3.72
64 65 1.066303 TCATTCCGCAACCAAACACAC 59.934 47.619 0.00 0.00 0.00 3.82
65 66 0.387565 ATTCCGCAACCAAACACACC 59.612 50.000 0.00 0.00 0.00 4.16
66 67 1.668101 TTCCGCAACCAAACACACCC 61.668 55.000 0.00 0.00 0.00 4.61
67 68 2.124693 CCGCAACCAAACACACCCT 61.125 57.895 0.00 0.00 0.00 4.34
68 69 1.671901 CCGCAACCAAACACACCCTT 61.672 55.000 0.00 0.00 0.00 3.95
69 70 1.025812 CGCAACCAAACACACCCTTA 58.974 50.000 0.00 0.00 0.00 2.69
70 71 1.268845 CGCAACCAAACACACCCTTAC 60.269 52.381 0.00 0.00 0.00 2.34
71 72 1.751924 GCAACCAAACACACCCTTACA 59.248 47.619 0.00 0.00 0.00 2.41
72 73 2.364002 GCAACCAAACACACCCTTACAT 59.636 45.455 0.00 0.00 0.00 2.29
73 74 3.570550 GCAACCAAACACACCCTTACATA 59.429 43.478 0.00 0.00 0.00 2.29
74 75 4.557895 GCAACCAAACACACCCTTACATAC 60.558 45.833 0.00 0.00 0.00 2.39
75 76 3.758425 ACCAAACACACCCTTACATACC 58.242 45.455 0.00 0.00 0.00 2.73
76 77 3.138653 ACCAAACACACCCTTACATACCA 59.861 43.478 0.00 0.00 0.00 3.25
77 78 4.145807 CCAAACACACCCTTACATACCAA 58.854 43.478 0.00 0.00 0.00 3.67
78 79 4.217550 CCAAACACACCCTTACATACCAAG 59.782 45.833 0.00 0.00 0.00 3.61
79 80 4.986054 AACACACCCTTACATACCAAGA 57.014 40.909 0.00 0.00 0.00 3.02
80 81 4.281898 ACACACCCTTACATACCAAGAC 57.718 45.455 0.00 0.00 0.00 3.01
81 82 3.649023 ACACACCCTTACATACCAAGACA 59.351 43.478 0.00 0.00 0.00 3.41
82 83 4.103469 ACACACCCTTACATACCAAGACAA 59.897 41.667 0.00 0.00 0.00 3.18
83 84 4.695455 CACACCCTTACATACCAAGACAAG 59.305 45.833 0.00 0.00 0.00 3.16
84 85 4.595781 ACACCCTTACATACCAAGACAAGA 59.404 41.667 0.00 0.00 0.00 3.02
85 86 5.250774 ACACCCTTACATACCAAGACAAGAT 59.749 40.000 0.00 0.00 0.00 2.40
86 87 5.586243 CACCCTTACATACCAAGACAAGATG 59.414 44.000 0.00 0.00 0.00 2.90
87 88 5.487488 ACCCTTACATACCAAGACAAGATGA 59.513 40.000 0.00 0.00 0.00 2.92
88 89 6.051717 CCCTTACATACCAAGACAAGATGAG 58.948 44.000 0.00 0.00 0.00 2.90
89 90 6.352222 CCCTTACATACCAAGACAAGATGAGT 60.352 42.308 0.00 0.00 0.00 3.41
90 91 6.758886 CCTTACATACCAAGACAAGATGAGTC 59.241 42.308 0.00 0.00 36.26 3.36
92 93 8.589701 TTACATACCAAGACAAGATGAGTCTA 57.410 34.615 0.00 0.00 45.11 2.59
93 94 6.868622 ACATACCAAGACAAGATGAGTCTAC 58.131 40.000 0.00 0.00 45.11 2.59
94 95 6.437477 ACATACCAAGACAAGATGAGTCTACA 59.563 38.462 0.00 0.00 45.11 2.74
95 96 5.808366 ACCAAGACAAGATGAGTCTACAA 57.192 39.130 0.00 0.00 45.11 2.41
96 97 5.788450 ACCAAGACAAGATGAGTCTACAAG 58.212 41.667 0.00 0.00 45.11 3.16
97 98 4.629200 CCAAGACAAGATGAGTCTACAAGC 59.371 45.833 0.00 0.00 45.11 4.01
98 99 5.477510 CAAGACAAGATGAGTCTACAAGCT 58.522 41.667 0.00 0.00 45.11 3.74
99 100 6.350528 CCAAGACAAGATGAGTCTACAAGCTA 60.351 42.308 0.00 0.00 45.11 3.32
100 101 6.842437 AGACAAGATGAGTCTACAAGCTAA 57.158 37.500 0.00 0.00 44.10 3.09
101 102 7.416964 AGACAAGATGAGTCTACAAGCTAAT 57.583 36.000 0.00 0.00 44.10 1.73
102 103 8.526667 AGACAAGATGAGTCTACAAGCTAATA 57.473 34.615 0.00 0.00 44.10 0.98
103 104 8.972127 AGACAAGATGAGTCTACAAGCTAATAA 58.028 33.333 0.00 0.00 44.10 1.40
104 105 9.587772 GACAAGATGAGTCTACAAGCTAATAAA 57.412 33.333 0.00 0.00 33.30 1.40
111 112 9.371136 TGAGTCTACAAGCTAATAAATGAAGTG 57.629 33.333 0.00 0.00 0.00 3.16
112 113 9.372369 GAGTCTACAAGCTAATAAATGAAGTGT 57.628 33.333 0.00 0.00 0.00 3.55
113 114 9.726438 AGTCTACAAGCTAATAAATGAAGTGTT 57.274 29.630 0.00 0.00 0.00 3.32
114 115 9.760660 GTCTACAAGCTAATAAATGAAGTGTTG 57.239 33.333 0.00 0.00 0.00 3.33
115 116 8.450964 TCTACAAGCTAATAAATGAAGTGTTGC 58.549 33.333 0.00 0.00 0.00 4.17
116 117 6.980593 ACAAGCTAATAAATGAAGTGTTGCA 58.019 32.000 0.00 0.00 0.00 4.08
117 118 7.605449 ACAAGCTAATAAATGAAGTGTTGCAT 58.395 30.769 0.00 0.00 0.00 3.96
118 119 7.543172 ACAAGCTAATAAATGAAGTGTTGCATG 59.457 33.333 0.00 0.00 0.00 4.06
119 120 7.395190 AGCTAATAAATGAAGTGTTGCATGA 57.605 32.000 0.00 0.00 0.00 3.07
120 121 7.253422 AGCTAATAAATGAAGTGTTGCATGAC 58.747 34.615 0.00 0.00 0.00 3.06
121 122 7.028962 GCTAATAAATGAAGTGTTGCATGACA 58.971 34.615 0.00 0.00 0.00 3.58
127 128 3.549997 GTGTTGCATGACACCACAC 57.450 52.632 10.05 5.22 41.13 3.82
128 129 0.737804 GTGTTGCATGACACCACACA 59.262 50.000 10.05 0.00 41.13 3.72
129 130 1.337703 GTGTTGCATGACACCACACAT 59.662 47.619 10.05 0.00 41.13 3.21
130 131 2.551887 GTGTTGCATGACACCACACATA 59.448 45.455 10.05 0.00 41.13 2.29
131 132 3.191162 GTGTTGCATGACACCACACATAT 59.809 43.478 10.05 0.00 41.13 1.78
132 133 3.190953 TGTTGCATGACACCACACATATG 59.809 43.478 0.00 0.00 0.00 1.78
133 134 3.070476 TGCATGACACCACACATATGT 57.930 42.857 1.41 1.41 40.80 2.29
134 135 3.419943 TGCATGACACCACACATATGTT 58.580 40.909 5.37 0.00 36.72 2.71
135 136 4.583871 TGCATGACACCACACATATGTTA 58.416 39.130 5.37 0.00 36.72 2.41
136 137 5.192176 TGCATGACACCACACATATGTTAT 58.808 37.500 5.37 0.00 36.72 1.89
137 138 5.651576 TGCATGACACCACACATATGTTATT 59.348 36.000 5.37 0.00 36.72 1.40
138 139 6.183360 TGCATGACACCACACATATGTTATTC 60.183 38.462 5.37 0.00 36.72 1.75
139 140 6.728200 CATGACACCACACATATGTTATTCC 58.272 40.000 5.37 0.00 36.72 3.01
140 141 5.189928 TGACACCACACATATGTTATTCCC 58.810 41.667 5.37 0.00 36.72 3.97
141 142 4.532834 ACACCACACATATGTTATTCCCC 58.467 43.478 5.37 0.00 36.72 4.81
142 143 4.017958 ACACCACACATATGTTATTCCCCA 60.018 41.667 5.37 0.00 36.72 4.96
143 144 4.338118 CACCACACATATGTTATTCCCCAC 59.662 45.833 5.37 0.00 36.72 4.61
144 145 4.229582 ACCACACATATGTTATTCCCCACT 59.770 41.667 5.37 0.00 36.72 4.00
145 146 5.430417 ACCACACATATGTTATTCCCCACTA 59.570 40.000 5.37 0.00 36.72 2.74
146 147 6.102615 ACCACACATATGTTATTCCCCACTAT 59.897 38.462 5.37 0.00 36.72 2.12
147 148 7.293771 ACCACACATATGTTATTCCCCACTATA 59.706 37.037 5.37 0.00 36.72 1.31
148 149 8.160765 CCACACATATGTTATTCCCCACTATAA 58.839 37.037 5.37 0.00 36.72 0.98
149 150 9.567776 CACACATATGTTATTCCCCACTATAAA 57.432 33.333 5.37 0.00 36.72 1.40
150 151 9.793259 ACACATATGTTATTCCCCACTATAAAG 57.207 33.333 5.37 0.00 34.46 1.85
151 152 9.231297 CACATATGTTATTCCCCACTATAAAGG 57.769 37.037 5.37 0.00 0.00 3.11
152 153 8.955794 ACATATGTTATTCCCCACTATAAAGGT 58.044 33.333 1.41 0.00 0.00 3.50
185 186 6.740110 AGTAACATAGACTAGTAGTGCATGC 58.260 40.000 11.82 11.82 0.00 4.06
186 187 5.598416 AACATAGACTAGTAGTGCATGCA 57.402 39.130 18.46 18.46 0.00 3.96
187 188 5.798125 ACATAGACTAGTAGTGCATGCAT 57.202 39.130 25.64 15.04 0.00 3.96
188 189 6.166984 ACATAGACTAGTAGTGCATGCATT 57.833 37.500 25.64 22.70 0.00 3.56
189 190 7.290110 ACATAGACTAGTAGTGCATGCATTA 57.710 36.000 25.64 21.48 0.00 1.90
204 208 5.534654 GCATGCATTACTAAGTTAATCCCCA 59.465 40.000 14.21 0.00 0.00 4.96
306 310 4.184629 ACAGCTCTTGAAATTACTAGGCG 58.815 43.478 0.00 0.00 0.00 5.52
373 378 4.738124 CGATCTGTCTAGAGCTGTTTGAA 58.262 43.478 0.00 0.00 37.20 2.69
374 379 4.797868 CGATCTGTCTAGAGCTGTTTGAAG 59.202 45.833 0.00 0.00 37.20 3.02
375 380 5.621104 CGATCTGTCTAGAGCTGTTTGAAGT 60.621 44.000 0.00 0.00 37.20 3.01
376 381 6.403746 CGATCTGTCTAGAGCTGTTTGAAGTA 60.404 42.308 0.00 0.00 37.20 2.24
377 382 6.015027 TCTGTCTAGAGCTGTTTGAAGTAC 57.985 41.667 0.00 0.00 0.00 2.73
588 593 2.745037 GACACTGGGCACGGGTAA 59.255 61.111 0.00 0.00 0.00 2.85
733 738 2.285743 GGAGGAGGAGGGGCAGTT 60.286 66.667 0.00 0.00 0.00 3.16
784 789 6.479001 CCGATTCCAATTAAAGACACGATACT 59.521 38.462 0.00 0.00 0.00 2.12
785 790 7.011109 CCGATTCCAATTAAAGACACGATACTT 59.989 37.037 0.00 0.00 0.00 2.24
786 791 8.388103 CGATTCCAATTAAAGACACGATACTTT 58.612 33.333 0.00 0.00 39.27 2.66
789 794 8.842358 TCCAATTAAAGACACGATACTTTTCT 57.158 30.769 0.00 0.00 37.49 2.52
813 818 0.107945 CTTCTTCGCTTCCCCTCTGG 60.108 60.000 0.00 0.00 0.00 3.86
814 819 2.124942 CTTCGCTTCCCCTCTGGC 60.125 66.667 0.00 0.00 0.00 4.85
815 820 3.689002 CTTCGCTTCCCCTCTGGCC 62.689 68.421 0.00 0.00 0.00 5.36
855 860 4.176752 CCCAACCCTAGCCTCCGC 62.177 72.222 0.00 0.00 0.00 5.54
856 861 4.176752 CCAACCCTAGCCTCCGCC 62.177 72.222 0.00 0.00 34.57 6.13
1197 1204 1.270518 TGACTTTGCTCTCAGTGGCTC 60.271 52.381 0.00 0.00 0.00 4.70
1199 1206 1.633852 CTTTGCTCTCAGTGGCTCGC 61.634 60.000 0.00 0.00 0.00 5.03
1236 1243 2.107726 GAGGTCCCCTGTAGTTTGGTTT 59.892 50.000 0.00 0.00 31.76 3.27
1244 1251 3.191371 CCTGTAGTTTGGTTTCTGATGGC 59.809 47.826 0.00 0.00 0.00 4.40
1249 1256 2.802247 GTTTGGTTTCTGATGGCAAAGC 59.198 45.455 0.00 0.00 0.00 3.51
1292 1299 0.464036 GAGTCGTCACCATGGCCATA 59.536 55.000 20.30 0.00 0.00 2.74
1346 1353 0.100325 CTGCTGGTGTGCGTGAAAAA 59.900 50.000 0.00 0.00 35.36 1.94
1368 1375 8.818141 AAAATAAAAGGAACAGAAGCTTTAGC 57.182 30.769 0.00 0.00 42.49 3.09
1395 1409 1.375013 CTGCATTTTGCCACTGCCC 60.375 57.895 0.00 0.00 44.23 5.36
1407 1421 2.030262 CTGCCCAGCGCCTATCTC 59.970 66.667 2.29 0.00 36.24 2.75
1594 1616 3.296322 TTCCTTGCATTGCTTTTACCG 57.704 42.857 10.49 0.00 0.00 4.02
1636 1658 4.736126 ATGGTTTAGTTGGCTTATTGGC 57.264 40.909 0.00 0.00 42.18 4.52
1954 1976 8.083828 TGGATGCTAAGTAGAAAGAAAGAGAT 57.916 34.615 0.00 0.00 0.00 2.75
2008 2030 1.737236 GCGCACACAATACTCCATGAA 59.263 47.619 0.30 0.00 0.00 2.57
2043 2065 9.120538 TCCTTATCATATTTTTGCTAACCACTC 57.879 33.333 0.00 0.00 0.00 3.51
2169 2191 3.260884 TGCCTAGTGCCTATATTGCCTAC 59.739 47.826 1.42 0.00 40.16 3.18
2171 2193 3.762288 CCTAGTGCCTATATTGCCTACGA 59.238 47.826 0.00 0.00 0.00 3.43
2192 2214 2.236395 AGTGCCGCCTACTTAATTGAGT 59.764 45.455 8.09 8.09 0.00 3.41
2224 2246 0.615331 GGCTCCCAGTTCTGTCATCA 59.385 55.000 0.00 0.00 0.00 3.07
2269 2291 3.181504 GCACACACGTGGTTTTCTTAACT 60.182 43.478 21.57 0.00 43.81 2.24
2397 2420 3.135994 CGTGCCTTTGGTACTTTACTGT 58.864 45.455 3.58 0.00 36.17 3.55
2541 2564 3.729966 GAACTCCGGTTCTTGAGAAAGT 58.270 45.455 0.00 0.00 45.90 2.66
2712 2735 2.237143 CAAACATGGCTGTAGAGGAGGA 59.763 50.000 0.00 0.00 33.36 3.71
2870 2893 4.353191 ACGGGAACTAGGAGATCTGGTATA 59.647 45.833 0.00 0.00 36.08 1.47
2879 2902 6.288096 AGGAGATCTGGTATAGTTCTTCCT 57.712 41.667 0.00 0.00 35.97 3.36
3023 3170 7.037438 CCGTGGCTTCTTTGTTTATACTACTA 58.963 38.462 0.00 0.00 0.00 1.82
3024 3171 7.009907 CCGTGGCTTCTTTGTTTATACTACTAC 59.990 40.741 0.00 0.00 0.00 2.73
3025 3172 7.758528 CGTGGCTTCTTTGTTTATACTACTACT 59.241 37.037 0.00 0.00 0.00 2.57
3139 3286 5.152623 TGGTTGACTACTTCCTGAGAATG 57.847 43.478 0.00 0.00 0.00 2.67
3690 3838 9.950680 TTATGAAGTTTCAAACAAGATTCAGTC 57.049 29.630 2.41 0.00 41.13 3.51
3692 3840 7.475015 TGAAGTTTCAAACAAGATTCAGTCAG 58.525 34.615 2.41 0.00 33.55 3.51
3693 3841 7.121168 TGAAGTTTCAAACAAGATTCAGTCAGT 59.879 33.333 2.41 0.00 33.55 3.41
3694 3842 6.789262 AGTTTCAAACAAGATTCAGTCAGTG 58.211 36.000 2.41 0.00 0.00 3.66
3696 3844 7.284034 AGTTTCAAACAAGATTCAGTCAGTGAT 59.716 33.333 2.41 0.00 34.17 3.06
3697 3845 6.791887 TCAAACAAGATTCAGTCAGTGATC 57.208 37.500 0.00 0.00 34.17 2.92
3700 3848 8.316946 TCAAACAAGATTCAGTCAGTGATCTAT 58.683 33.333 0.00 0.00 34.17 1.98
3701 3849 8.388853 CAAACAAGATTCAGTCAGTGATCTATG 58.611 37.037 0.00 0.00 34.17 2.23
3702 3850 7.180322 ACAAGATTCAGTCAGTGATCTATGT 57.820 36.000 0.00 0.39 34.17 2.29
3703 3851 7.040494 ACAAGATTCAGTCAGTGATCTATGTG 58.960 38.462 0.00 0.00 34.17 3.21
3704 3852 6.788598 AGATTCAGTCAGTGATCTATGTGT 57.211 37.500 0.00 0.00 34.17 3.72
3712 3860 4.528206 TCAGTGATCTATGTGTGGACTTGT 59.472 41.667 0.00 0.00 0.00 3.16
3792 3940 9.629878 TTAATAATAGCTTTTCCGGGAAATACA 57.370 29.630 22.08 7.55 31.34 2.29
3793 3941 5.830000 AATAGCTTTTCCGGGAAATACAC 57.170 39.130 22.08 11.99 31.34 2.90
3794 3942 3.434940 AGCTTTTCCGGGAAATACACT 57.565 42.857 22.08 13.82 31.34 3.55
3795 3943 3.763057 AGCTTTTCCGGGAAATACACTT 58.237 40.909 22.08 3.84 31.34 3.16
3796 3944 3.506067 AGCTTTTCCGGGAAATACACTTG 59.494 43.478 22.08 8.43 31.34 3.16
3797 3945 3.254903 GCTTTTCCGGGAAATACACTTGT 59.745 43.478 22.08 0.00 31.34 3.16
3798 3946 4.794169 CTTTTCCGGGAAATACACTTGTG 58.206 43.478 22.08 0.00 31.34 3.33
3799 3947 1.816074 TCCGGGAAATACACTTGTGC 58.184 50.000 0.00 0.00 0.00 4.57
3800 3948 1.349688 TCCGGGAAATACACTTGTGCT 59.650 47.619 0.00 0.00 0.00 4.40
3801 3949 1.737793 CCGGGAAATACACTTGTGCTC 59.262 52.381 0.00 0.00 0.00 4.26
3802 3950 1.737793 CGGGAAATACACTTGTGCTCC 59.262 52.381 0.10 2.68 0.00 4.70
3803 3951 2.615493 CGGGAAATACACTTGTGCTCCT 60.615 50.000 0.10 0.00 0.00 3.69
3804 3952 2.749621 GGGAAATACACTTGTGCTCCTG 59.250 50.000 0.10 0.00 0.00 3.86
3805 3953 2.749621 GGAAATACACTTGTGCTCCTGG 59.250 50.000 0.10 0.00 0.00 4.45
3806 3954 3.412386 GAAATACACTTGTGCTCCTGGT 58.588 45.455 0.10 0.00 0.00 4.00
3807 3955 3.508845 AATACACTTGTGCTCCTGGTT 57.491 42.857 0.10 0.00 0.00 3.67
3808 3956 2.254546 TACACTTGTGCTCCTGGTTG 57.745 50.000 0.10 0.00 0.00 3.77
3809 3957 0.255890 ACACTTGTGCTCCTGGTTGT 59.744 50.000 0.10 0.00 0.00 3.32
3810 3958 1.488812 ACACTTGTGCTCCTGGTTGTA 59.511 47.619 0.10 0.00 0.00 2.41
3811 3959 2.106511 ACACTTGTGCTCCTGGTTGTAT 59.893 45.455 0.10 0.00 0.00 2.29
3812 3960 3.326588 ACACTTGTGCTCCTGGTTGTATA 59.673 43.478 0.10 0.00 0.00 1.47
3813 3961 4.019321 ACACTTGTGCTCCTGGTTGTATAT 60.019 41.667 0.10 0.00 0.00 0.86
3814 3962 4.333649 CACTTGTGCTCCTGGTTGTATATG 59.666 45.833 0.00 0.00 0.00 1.78
3815 3963 2.917933 TGTGCTCCTGGTTGTATATGC 58.082 47.619 0.00 0.00 0.00 3.14
3816 3964 2.238395 TGTGCTCCTGGTTGTATATGCA 59.762 45.455 0.00 0.00 0.00 3.96
3817 3965 2.614057 GTGCTCCTGGTTGTATATGCAC 59.386 50.000 0.00 0.00 41.72 4.57
3818 3966 2.222027 GCTCCTGGTTGTATATGCACC 58.778 52.381 0.00 0.00 0.00 5.01
3819 3967 2.851195 CTCCTGGTTGTATATGCACCC 58.149 52.381 0.12 0.12 0.00 4.61
3820 3968 2.439507 CTCCTGGTTGTATATGCACCCT 59.560 50.000 8.77 0.00 0.00 4.34
3821 3969 3.646162 CTCCTGGTTGTATATGCACCCTA 59.354 47.826 8.77 0.00 0.00 3.53
3822 3970 4.239495 TCCTGGTTGTATATGCACCCTAT 58.761 43.478 8.77 0.00 0.00 2.57
3823 3971 5.407936 TCCTGGTTGTATATGCACCCTATA 58.592 41.667 8.77 0.00 0.00 1.31
3824 3972 6.029431 TCCTGGTTGTATATGCACCCTATAT 58.971 40.000 8.77 0.00 0.00 0.86
3825 3973 6.070251 TCCTGGTTGTATATGCACCCTATATG 60.070 42.308 8.77 0.00 0.00 1.78
3826 3974 6.061022 TGGTTGTATATGCACCCTATATGG 57.939 41.667 8.77 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.682849 TTCCACTGGAATGGGTCGG 59.317 57.895 6.39 0.00 40.49 4.79
21 22 6.603201 TGAAGTGGAATGGAATGGAATAGTTC 59.397 38.462 0.00 0.00 0.00 3.01
22 23 6.493166 TGAAGTGGAATGGAATGGAATAGTT 58.507 36.000 0.00 0.00 0.00 2.24
23 24 6.078456 TGAAGTGGAATGGAATGGAATAGT 57.922 37.500 0.00 0.00 0.00 2.12
24 25 7.255730 GGAATGAAGTGGAATGGAATGGAATAG 60.256 40.741 0.00 0.00 0.00 1.73
25 26 6.550854 GGAATGAAGTGGAATGGAATGGAATA 59.449 38.462 0.00 0.00 0.00 1.75
26 27 5.364735 GGAATGAAGTGGAATGGAATGGAAT 59.635 40.000 0.00 0.00 0.00 3.01
27 28 4.711355 GGAATGAAGTGGAATGGAATGGAA 59.289 41.667 0.00 0.00 0.00 3.53
28 29 4.280819 GGAATGAAGTGGAATGGAATGGA 58.719 43.478 0.00 0.00 0.00 3.41
29 30 3.067180 CGGAATGAAGTGGAATGGAATGG 59.933 47.826 0.00 0.00 0.00 3.16
30 31 3.489738 GCGGAATGAAGTGGAATGGAATG 60.490 47.826 0.00 0.00 0.00 2.67
31 32 2.689983 GCGGAATGAAGTGGAATGGAAT 59.310 45.455 0.00 0.00 0.00 3.01
32 33 2.091541 GCGGAATGAAGTGGAATGGAA 58.908 47.619 0.00 0.00 0.00 3.53
33 34 1.004161 TGCGGAATGAAGTGGAATGGA 59.996 47.619 0.00 0.00 0.00 3.41
34 35 1.462616 TGCGGAATGAAGTGGAATGG 58.537 50.000 0.00 0.00 0.00 3.16
35 36 2.415893 GGTTGCGGAATGAAGTGGAATG 60.416 50.000 0.00 0.00 0.00 2.67
36 37 1.818674 GGTTGCGGAATGAAGTGGAAT 59.181 47.619 0.00 0.00 0.00 3.01
37 38 1.243902 GGTTGCGGAATGAAGTGGAA 58.756 50.000 0.00 0.00 0.00 3.53
38 39 0.109532 TGGTTGCGGAATGAAGTGGA 59.890 50.000 0.00 0.00 0.00 4.02
39 40 0.958091 TTGGTTGCGGAATGAAGTGG 59.042 50.000 0.00 0.00 0.00 4.00
40 41 2.223688 TGTTTGGTTGCGGAATGAAGTG 60.224 45.455 0.00 0.00 0.00 3.16
41 42 2.028130 TGTTTGGTTGCGGAATGAAGT 58.972 42.857 0.00 0.00 0.00 3.01
42 43 2.223688 TGTGTTTGGTTGCGGAATGAAG 60.224 45.455 0.00 0.00 0.00 3.02
43 44 1.751351 TGTGTTTGGTTGCGGAATGAA 59.249 42.857 0.00 0.00 0.00 2.57
44 45 1.066303 GTGTGTTTGGTTGCGGAATGA 59.934 47.619 0.00 0.00 0.00 2.57
45 46 1.486439 GTGTGTTTGGTTGCGGAATG 58.514 50.000 0.00 0.00 0.00 2.67
46 47 0.387565 GGTGTGTTTGGTTGCGGAAT 59.612 50.000 0.00 0.00 0.00 3.01
47 48 1.668101 GGGTGTGTTTGGTTGCGGAA 61.668 55.000 0.00 0.00 0.00 4.30
48 49 2.122167 GGGTGTGTTTGGTTGCGGA 61.122 57.895 0.00 0.00 0.00 5.54
49 50 1.671901 AAGGGTGTGTTTGGTTGCGG 61.672 55.000 0.00 0.00 0.00 5.69
50 51 1.025812 TAAGGGTGTGTTTGGTTGCG 58.974 50.000 0.00 0.00 0.00 4.85
51 52 1.751924 TGTAAGGGTGTGTTTGGTTGC 59.248 47.619 0.00 0.00 0.00 4.17
52 53 4.022676 GGTATGTAAGGGTGTGTTTGGTTG 60.023 45.833 0.00 0.00 0.00 3.77
53 54 4.146564 GGTATGTAAGGGTGTGTTTGGTT 58.853 43.478 0.00 0.00 0.00 3.67
54 55 3.138653 TGGTATGTAAGGGTGTGTTTGGT 59.861 43.478 0.00 0.00 0.00 3.67
55 56 3.757270 TGGTATGTAAGGGTGTGTTTGG 58.243 45.455 0.00 0.00 0.00 3.28
56 57 5.048991 GTCTTGGTATGTAAGGGTGTGTTTG 60.049 44.000 0.00 0.00 0.00 2.93
57 58 5.067954 GTCTTGGTATGTAAGGGTGTGTTT 58.932 41.667 0.00 0.00 0.00 2.83
58 59 4.103469 TGTCTTGGTATGTAAGGGTGTGTT 59.897 41.667 0.00 0.00 0.00 3.32
59 60 3.649023 TGTCTTGGTATGTAAGGGTGTGT 59.351 43.478 0.00 0.00 0.00 3.72
60 61 4.280436 TGTCTTGGTATGTAAGGGTGTG 57.720 45.455 0.00 0.00 0.00 3.82
61 62 4.595781 TCTTGTCTTGGTATGTAAGGGTGT 59.404 41.667 0.00 0.00 0.00 4.16
62 63 5.160607 TCTTGTCTTGGTATGTAAGGGTG 57.839 43.478 0.00 0.00 0.00 4.61
63 64 5.487488 TCATCTTGTCTTGGTATGTAAGGGT 59.513 40.000 0.00 0.00 0.00 4.34
64 65 5.989477 TCATCTTGTCTTGGTATGTAAGGG 58.011 41.667 0.00 0.00 0.00 3.95
65 66 6.644347 ACTCATCTTGTCTTGGTATGTAAGG 58.356 40.000 0.00 0.00 0.00 2.69
66 67 7.551585 AGACTCATCTTGTCTTGGTATGTAAG 58.448 38.462 0.00 0.00 41.45 2.34
67 68 7.482169 AGACTCATCTTGTCTTGGTATGTAA 57.518 36.000 0.00 0.00 41.45 2.41
68 69 7.614192 TGTAGACTCATCTTGTCTTGGTATGTA 59.386 37.037 1.67 0.00 41.45 2.29
69 70 6.437477 TGTAGACTCATCTTGTCTTGGTATGT 59.563 38.462 1.67 0.00 41.45 2.29
70 71 6.867550 TGTAGACTCATCTTGTCTTGGTATG 58.132 40.000 1.67 0.00 41.45 2.39
71 72 7.482169 TTGTAGACTCATCTTGTCTTGGTAT 57.518 36.000 1.67 0.00 41.45 2.73
72 73 6.572509 GCTTGTAGACTCATCTTGTCTTGGTA 60.573 42.308 1.67 0.00 41.45 3.25
73 74 5.788450 CTTGTAGACTCATCTTGTCTTGGT 58.212 41.667 1.67 0.00 41.45 3.67
74 75 4.629200 GCTTGTAGACTCATCTTGTCTTGG 59.371 45.833 1.67 0.00 41.45 3.61
75 76 5.477510 AGCTTGTAGACTCATCTTGTCTTG 58.522 41.667 1.67 0.00 41.45 3.02
76 77 5.736951 AGCTTGTAGACTCATCTTGTCTT 57.263 39.130 1.67 0.00 41.45 3.01
77 78 6.842437 TTAGCTTGTAGACTCATCTTGTCT 57.158 37.500 0.00 0.00 45.48 3.41
78 79 9.587772 TTTATTAGCTTGTAGACTCATCTTGTC 57.412 33.333 0.00 0.00 36.29 3.18
85 86 9.371136 CACTTCATTTATTAGCTTGTAGACTCA 57.629 33.333 0.00 0.00 0.00 3.41
86 87 9.372369 ACACTTCATTTATTAGCTTGTAGACTC 57.628 33.333 0.00 0.00 0.00 3.36
87 88 9.726438 AACACTTCATTTATTAGCTTGTAGACT 57.274 29.630 0.00 0.00 0.00 3.24
88 89 9.760660 CAACACTTCATTTATTAGCTTGTAGAC 57.239 33.333 0.00 0.00 0.00 2.59
89 90 8.450964 GCAACACTTCATTTATTAGCTTGTAGA 58.549 33.333 0.00 0.00 0.00 2.59
90 91 8.236586 TGCAACACTTCATTTATTAGCTTGTAG 58.763 33.333 0.00 0.00 0.00 2.74
91 92 8.105097 TGCAACACTTCATTTATTAGCTTGTA 57.895 30.769 0.00 0.00 0.00 2.41
92 93 6.980593 TGCAACACTTCATTTATTAGCTTGT 58.019 32.000 0.00 0.00 0.00 3.16
93 94 7.756272 TCATGCAACACTTCATTTATTAGCTTG 59.244 33.333 0.00 0.00 0.00 4.01
94 95 7.756722 GTCATGCAACACTTCATTTATTAGCTT 59.243 33.333 0.00 0.00 0.00 3.74
95 96 7.094248 TGTCATGCAACACTTCATTTATTAGCT 60.094 33.333 0.00 0.00 0.00 3.32
96 97 7.008628 GTGTCATGCAACACTTCATTTATTAGC 59.991 37.037 13.31 0.00 44.90 3.09
97 98 7.485913 GGTGTCATGCAACACTTCATTTATTAG 59.514 37.037 18.55 0.00 46.96 1.73
98 99 7.040132 TGGTGTCATGCAACACTTCATTTATTA 60.040 33.333 18.55 0.00 46.96 0.98
99 100 6.158598 GGTGTCATGCAACACTTCATTTATT 58.841 36.000 18.55 0.00 46.96 1.40
100 101 5.243507 TGGTGTCATGCAACACTTCATTTAT 59.756 36.000 18.55 0.00 46.96 1.40
101 102 4.582240 TGGTGTCATGCAACACTTCATTTA 59.418 37.500 18.55 0.00 46.96 1.40
102 103 3.384146 TGGTGTCATGCAACACTTCATTT 59.616 39.130 18.55 0.00 46.96 2.32
103 104 2.957680 TGGTGTCATGCAACACTTCATT 59.042 40.909 18.55 0.00 46.96 2.57
104 105 2.585330 TGGTGTCATGCAACACTTCAT 58.415 42.857 18.55 0.00 46.96 2.57
105 106 2.049888 TGGTGTCATGCAACACTTCA 57.950 45.000 18.55 8.56 46.96 3.02
110 111 1.689984 ATGTGTGGTGTCATGCAACA 58.310 45.000 4.08 4.08 43.58 3.33
111 112 3.191162 ACATATGTGTGGTGTCATGCAAC 59.809 43.478 7.78 0.00 37.14 4.17
112 113 3.419943 ACATATGTGTGGTGTCATGCAA 58.580 40.909 7.78 0.00 37.14 4.08
113 114 3.070476 ACATATGTGTGGTGTCATGCA 57.930 42.857 7.78 0.00 37.14 3.96
114 115 5.756195 ATAACATATGTGTGGTGTCATGC 57.244 39.130 9.63 0.00 38.92 4.06
115 116 6.238731 GGGAATAACATATGTGTGGTGTCATG 60.239 42.308 9.63 0.00 38.92 3.07
116 117 5.827797 GGGAATAACATATGTGTGGTGTCAT 59.172 40.000 9.63 0.00 38.92 3.06
117 118 5.189928 GGGAATAACATATGTGTGGTGTCA 58.810 41.667 9.63 0.00 38.92 3.58
118 119 4.578928 GGGGAATAACATATGTGTGGTGTC 59.421 45.833 9.63 1.90 38.92 3.67
119 120 4.017958 TGGGGAATAACATATGTGTGGTGT 60.018 41.667 9.63 0.00 38.92 4.16
120 121 4.338118 GTGGGGAATAACATATGTGTGGTG 59.662 45.833 9.63 0.00 38.92 4.17
121 122 4.229582 AGTGGGGAATAACATATGTGTGGT 59.770 41.667 9.63 0.00 38.92 4.16
122 123 4.792068 AGTGGGGAATAACATATGTGTGG 58.208 43.478 9.63 0.00 38.92 4.17
123 124 9.567776 TTTATAGTGGGGAATAACATATGTGTG 57.432 33.333 9.63 0.00 38.92 3.82
124 125 9.793259 CTTTATAGTGGGGAATAACATATGTGT 57.207 33.333 9.63 2.63 41.28 3.72
125 126 9.231297 CCTTTATAGTGGGGAATAACATATGTG 57.769 37.037 9.63 0.00 0.00 3.21
126 127 8.955794 ACCTTTATAGTGGGGAATAACATATGT 58.044 33.333 1.41 1.41 0.00 2.29
129 130 9.449896 TGTACCTTTATAGTGGGGAATAACATA 57.550 33.333 0.00 0.00 0.00 2.29
130 131 8.339720 TGTACCTTTATAGTGGGGAATAACAT 57.660 34.615 0.00 0.00 0.00 2.71
131 132 7.403813 ACTGTACCTTTATAGTGGGGAATAACA 59.596 37.037 0.00 0.00 29.00 2.41
132 133 7.799081 ACTGTACCTTTATAGTGGGGAATAAC 58.201 38.462 0.00 0.00 29.00 1.89
133 134 8.927411 GTACTGTACCTTTATAGTGGGGAATAA 58.073 37.037 6.70 0.00 32.33 1.40
134 135 8.291745 AGTACTGTACCTTTATAGTGGGGAATA 58.708 37.037 14.05 0.00 32.33 1.75
135 136 7.137567 AGTACTGTACCTTTATAGTGGGGAAT 58.862 38.462 14.05 0.00 32.33 3.01
136 137 6.505754 AGTACTGTACCTTTATAGTGGGGAA 58.494 40.000 14.05 0.00 32.33 3.97
137 138 6.096164 AGTACTGTACCTTTATAGTGGGGA 57.904 41.667 14.05 0.00 32.33 4.81
138 139 7.065504 ACTAGTACTGTACCTTTATAGTGGGG 58.934 42.308 14.05 0.00 32.33 4.96
139 140 9.632638 TTACTAGTACTGTACCTTTATAGTGGG 57.367 37.037 19.13 0.00 32.33 4.61
147 148 9.972106 AGTCTATGTTACTAGTACTGTACCTTT 57.028 33.333 14.05 0.00 0.00 3.11
178 179 6.438763 GGGATTAACTTAGTAATGCATGCAC 58.561 40.000 25.37 10.95 34.46 4.57
179 180 5.534654 GGGGATTAACTTAGTAATGCATGCA 59.465 40.000 25.04 25.04 34.46 3.96
180 181 5.534654 TGGGGATTAACTTAGTAATGCATGC 59.465 40.000 11.82 11.82 34.46 4.06
181 182 7.765695 ATGGGGATTAACTTAGTAATGCATG 57.234 36.000 0.00 0.00 34.46 4.06
183 184 9.295825 CATAATGGGGATTAACTTAGTAATGCA 57.704 33.333 0.00 0.00 34.46 3.96
184 185 8.739972 CCATAATGGGGATTAACTTAGTAATGC 58.260 37.037 0.00 0.00 32.67 3.56
204 208 5.473273 TGTACCCATGAGACTACCCATAAT 58.527 41.667 0.00 0.00 0.00 1.28
306 310 2.939103 ACAAAATACTCAGATGCTCGCC 59.061 45.455 0.00 0.00 0.00 5.54
733 738 0.953471 CTGCGGACCCAAATGACGAA 60.953 55.000 0.00 0.00 0.00 3.85
784 789 4.037565 GGGAAGCGAAGAAGGAAAAGAAAA 59.962 41.667 0.00 0.00 0.00 2.29
785 790 3.568430 GGGAAGCGAAGAAGGAAAAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
786 791 3.146847 GGGAAGCGAAGAAGGAAAAGAA 58.853 45.455 0.00 0.00 0.00 2.52
787 792 2.552373 GGGGAAGCGAAGAAGGAAAAGA 60.552 50.000 0.00 0.00 0.00 2.52
788 793 1.813178 GGGGAAGCGAAGAAGGAAAAG 59.187 52.381 0.00 0.00 0.00 2.27
789 794 1.423921 AGGGGAAGCGAAGAAGGAAAA 59.576 47.619 0.00 0.00 0.00 2.29
792 797 0.252284 AGAGGGGAAGCGAAGAAGGA 60.252 55.000 0.00 0.00 0.00 3.36
1236 1243 3.126879 CGCCGCTTTGCCATCAGA 61.127 61.111 0.00 0.00 0.00 3.27
1244 1251 3.567797 GCTCTAGCCGCCGCTTTG 61.568 66.667 4.51 0.00 45.55 2.77
1249 1256 2.775856 TTCTCTGCTCTAGCCGCCG 61.776 63.158 0.00 0.00 41.18 6.46
1257 1264 4.013728 ACGACTCTATTGTTCTCTGCTCT 58.986 43.478 0.00 0.00 0.00 4.09
1407 1421 0.447801 AAAGAAAGCGTGCTATGGCG 59.552 50.000 0.00 0.00 42.25 5.69
1543 1565 9.671279 TGATGAGAAACACATGTCTATAACATT 57.329 29.630 0.00 0.00 46.73 2.71
1594 1616 5.509163 CCATTCCATTGATCAAGCCAATCTC 60.509 44.000 14.54 0.00 32.40 2.75
1636 1658 9.703892 AGAAATCCGATATGAGAAGATTTAGTG 57.296 33.333 0.00 0.00 37.30 2.74
1643 1665 9.402320 CTCCTATAGAAATCCGATATGAGAAGA 57.598 37.037 0.00 0.00 31.62 2.87
2008 2030 9.807649 GCAAAAATATGATAAGGAAATGTGTCT 57.192 29.630 0.00 0.00 0.00 3.41
2043 2065 3.560068 ACCGCAGTACTTTCAGAACAAAG 59.440 43.478 0.00 0.00 39.03 2.77
2169 2191 1.593006 CAATTAAGTAGGCGGCACTCG 59.407 52.381 13.08 0.00 42.76 4.18
2171 2193 2.236395 ACTCAATTAAGTAGGCGGCACT 59.764 45.455 13.08 10.01 0.00 4.40
2192 2214 1.635817 GGGAGCCTTGACCCTATGCA 61.636 60.000 0.00 0.00 42.56 3.96
2224 2246 3.066190 TGTGCCTACGCGCTAGGT 61.066 61.111 25.39 11.95 46.08 3.08
2269 2291 9.643735 ACCAAATATTAACCCGTATATTCCAAA 57.356 29.630 0.00 0.00 0.00 3.28
2397 2420 6.439675 AAAACTCAAAACGCTGGTAAAGTA 57.560 33.333 0.00 0.00 0.00 2.24
2451 2474 0.392706 TTCTTCTGCTTCAGGCGACA 59.607 50.000 0.00 0.00 45.43 4.35
2541 2564 1.819305 GCTCCCAAACTGCCTTTGAGA 60.819 52.381 5.70 0.00 41.81 3.27
2712 2735 5.950549 GCATCCATTTCCATATCCTTCTGAT 59.049 40.000 0.00 0.00 37.49 2.90
2870 2893 7.213678 TGAAAAACACAACAAAAGGAAGAACT 58.786 30.769 0.00 0.00 0.00 3.01
2879 2902 8.087982 TGCAATAACTGAAAAACACAACAAAA 57.912 26.923 0.00 0.00 0.00 2.44
2961 2985 8.102484 ACAACCCTAGATTGTGGAACTATATT 57.898 34.615 10.52 0.00 38.84 1.28
3023 3170 7.387948 CAGCCACTTACATAACTTTTCACTAGT 59.612 37.037 0.00 0.00 0.00 2.57
3024 3171 7.624344 GCAGCCACTTACATAACTTTTCACTAG 60.624 40.741 0.00 0.00 0.00 2.57
3025 3172 6.148811 GCAGCCACTTACATAACTTTTCACTA 59.851 38.462 0.00 0.00 0.00 2.74
3139 3286 5.695363 GTGTCAAGTACCCAAGAGTAAGTTC 59.305 44.000 0.00 0.00 0.00 3.01
3246 3393 9.941664 CTTACTAAATAGCAATTCAATGGTCTG 57.058 33.333 0.00 0.00 32.43 3.51
3368 3515 4.998051 ACTATTTTCTGAGGAAAGGCCAA 58.002 39.130 5.01 0.00 41.66 4.52
3690 3838 4.825422 ACAAGTCCACACATAGATCACTG 58.175 43.478 0.00 0.00 0.00 3.66
3692 3840 6.208988 TCTACAAGTCCACACATAGATCAC 57.791 41.667 0.00 0.00 0.00 3.06
3693 3841 7.343057 AGAATCTACAAGTCCACACATAGATCA 59.657 37.037 0.00 0.00 30.12 2.92
3694 3842 7.721402 AGAATCTACAAGTCCACACATAGATC 58.279 38.462 0.00 0.00 30.12 2.75
3696 3844 7.482169 AAGAATCTACAAGTCCACACATAGA 57.518 36.000 0.00 0.00 0.00 1.98
3697 3845 7.604164 ACAAAGAATCTACAAGTCCACACATAG 59.396 37.037 0.00 0.00 0.00 2.23
3700 3848 5.527214 CACAAAGAATCTACAAGTCCACACA 59.473 40.000 0.00 0.00 0.00 3.72
3701 3849 5.527582 ACACAAAGAATCTACAAGTCCACAC 59.472 40.000 0.00 0.00 0.00 3.82
3702 3850 5.680619 ACACAAAGAATCTACAAGTCCACA 58.319 37.500 0.00 0.00 0.00 4.17
3703 3851 6.430451 CAACACAAAGAATCTACAAGTCCAC 58.570 40.000 0.00 0.00 0.00 4.02
3704 3852 5.008613 GCAACACAAAGAATCTACAAGTCCA 59.991 40.000 0.00 0.00 0.00 4.02
3712 3860 9.409312 CAAACATATTGCAACACAAAGAATCTA 57.591 29.630 0.00 0.00 42.86 1.98
3783 3931 2.749621 CAGGAGCACAAGTGTATTTCCC 59.250 50.000 1.79 0.00 0.00 3.97
3784 3932 2.749621 CCAGGAGCACAAGTGTATTTCC 59.250 50.000 1.79 4.95 0.00 3.13
3785 3933 3.412386 ACCAGGAGCACAAGTGTATTTC 58.588 45.455 0.00 0.00 0.00 2.17
3786 3934 3.508845 ACCAGGAGCACAAGTGTATTT 57.491 42.857 0.00 0.00 0.00 1.40
3787 3935 3.149196 CAACCAGGAGCACAAGTGTATT 58.851 45.455 0.00 0.00 0.00 1.89
3788 3936 2.106511 ACAACCAGGAGCACAAGTGTAT 59.893 45.455 0.00 0.00 0.00 2.29
3789 3937 1.488812 ACAACCAGGAGCACAAGTGTA 59.511 47.619 0.00 0.00 0.00 2.90
3790 3938 0.255890 ACAACCAGGAGCACAAGTGT 59.744 50.000 0.00 0.00 0.00 3.55
3791 3939 2.254546 TACAACCAGGAGCACAAGTG 57.745 50.000 0.00 0.00 0.00 3.16
3792 3940 4.517285 CATATACAACCAGGAGCACAAGT 58.483 43.478 0.00 0.00 0.00 3.16
3793 3941 3.313526 GCATATACAACCAGGAGCACAAG 59.686 47.826 0.00 0.00 0.00 3.16
3794 3942 3.278574 GCATATACAACCAGGAGCACAA 58.721 45.455 0.00 0.00 0.00 3.33
3795 3943 2.238395 TGCATATACAACCAGGAGCACA 59.762 45.455 0.00 0.00 0.00 4.57
3796 3944 2.614057 GTGCATATACAACCAGGAGCAC 59.386 50.000 0.00 0.00 43.27 4.40
3797 3945 2.421388 GGTGCATATACAACCAGGAGCA 60.421 50.000 0.00 0.00 0.00 4.26
3798 3946 2.222027 GGTGCATATACAACCAGGAGC 58.778 52.381 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.