Multiple sequence alignment - TraesCS3A01G401200

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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 TraesCS3A01G401200 chr3A 100.000 2813 0 0 1 2813 647445026 647442214 0.000000e+00 5195.0
1 TraesCS3A01G401200 chr3A 94.203 966 49 6 1852 2813 508544489 508545451 0.000000e+00 1467.0
2 TraesCS3A01G401200 chr3A 87.488 1007 99 19 846 1841 647388765 647387775 0.000000e+00 1136.0
3 TraesCS3A01G401200 chr3A 86.891 923 111 6 917 1838 647358972 647358059 0.000000e+00 1026.0
4 TraesCS3A01G401200 chr3A 87.616 323 37 3 1496 1816 647270348 647270027 3.420000e-99 372.0
5 TraesCS3A01G401200 chr3A 76.087 552 76 27 17 550 647231852 647231339 1.300000e-58 237.0
6 TraesCS3A01G401200 chr3A 76.087 552 72 31 17 550 647374159 647373650 1.680000e-57 233.0
7 TraesCS3A01G401200 chr3A 97.619 42 1 0 1808 1849 647396009 647395968 3.890000e-09 73.1
8 TraesCS3A01G401200 chr3D 89.792 1871 159 23 1 1849 511294383 511292523 0.000000e+00 2368.0
9 TraesCS3A01G401200 chr3D 82.545 1627 209 41 198 1793 511296953 511295371 0.000000e+00 1362.0
10 TraesCS3A01G401200 chr3D 84.009 1357 170 30 511 1849 511321703 511320376 0.000000e+00 1260.0
11 TraesCS3A01G401200 chr3D 83.714 1271 169 22 598 1849 511129336 511128085 0.000000e+00 1166.0
12 TraesCS3A01G401200 chr3D 88.865 934 86 11 624 1542 511181573 511180643 0.000000e+00 1133.0
13 TraesCS3A01G401200 chr3D 87.343 877 102 7 979 1849 511266209 511265336 0.000000e+00 996.0
14 TraesCS3A01G401200 chr3D 81.134 1288 179 36 288 1537 511202890 511201629 0.000000e+00 974.0
15 TraesCS3A01G401200 chr3B 89.580 1641 123 28 244 1841 672771145 672769510 0.000000e+00 2039.0
16 TraesCS3A01G401200 chr3B 83.294 1676 204 40 207 1847 672777729 672776095 0.000000e+00 1474.0
17 TraesCS3A01G401200 chr3B 86.286 999 115 14 797 1790 672774657 672773676 0.000000e+00 1066.0
18 TraesCS3A01G401200 chr3B 86.536 973 117 11 876 1846 672517368 672516408 0.000000e+00 1059.0
19 TraesCS3A01G401200 chr3B 88.335 883 101 2 954 1835 672744788 672743907 0.000000e+00 1059.0
20 TraesCS3A01G401200 chr3B 93.925 214 13 0 3 216 672772577 672772364 9.720000e-85 324.0
21 TraesCS3A01G401200 chr3B 90.055 181 17 1 599 778 672719948 672719768 1.680000e-57 233.0
22 TraesCS3A01G401200 chr4A 94.124 953 53 3 1862 2813 288594226 288595176 0.000000e+00 1447.0
23 TraesCS3A01G401200 chr4A 93.854 960 55 4 1850 2807 288624644 288625601 0.000000e+00 1443.0
24 TraesCS3A01G401200 chr7A 93.939 957 46 12 1865 2813 426876900 426877852 0.000000e+00 1435.0
25 TraesCS3A01G401200 chr2A 93.575 965 59 3 1850 2813 481725799 481724837 0.000000e+00 1435.0
26 TraesCS3A01G401200 chr2A 100.000 28 0 0 1846 1873 448326371 448326344 5.000000e-03 52.8
27 TraesCS3A01G401200 chr6A 93.492 968 58 4 1850 2813 103920538 103919572 0.000000e+00 1434.0
28 TraesCS3A01G401200 chr6A 93.402 970 58 5 1850 2813 158127309 158126340 0.000000e+00 1432.0
29 TraesCS3A01G401200 chr6A 93.505 970 51 10 1850 2813 486993018 486993981 0.000000e+00 1432.0
30 TraesCS3A01G401200 chr6A 93.409 971 52 12 1850 2813 439708321 439709286 0.000000e+00 1428.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G401200 chr3A 647442214 647445026 2812 True 5195.00 5195 100.00000 1 2813 1 chr3A.!!$R7 2812
1 TraesCS3A01G401200 chr3A 508544489 508545451 962 False 1467.00 1467 94.20300 1852 2813 1 chr3A.!!$F1 961
2 TraesCS3A01G401200 chr3A 647387775 647388765 990 True 1136.00 1136 87.48800 846 1841 1 chr3A.!!$R5 995
3 TraesCS3A01G401200 chr3A 647358059 647358972 913 True 1026.00 1026 86.89100 917 1838 1 chr3A.!!$R3 921
4 TraesCS3A01G401200 chr3A 647231339 647231852 513 True 237.00 237 76.08700 17 550 1 chr3A.!!$R1 533
5 TraesCS3A01G401200 chr3A 647373650 647374159 509 True 233.00 233 76.08700 17 550 1 chr3A.!!$R4 533
6 TraesCS3A01G401200 chr3D 511292523 511296953 4430 True 1865.00 2368 86.16850 1 1849 2 chr3D.!!$R6 1848
7 TraesCS3A01G401200 chr3D 511320376 511321703 1327 True 1260.00 1260 84.00900 511 1849 1 chr3D.!!$R5 1338
8 TraesCS3A01G401200 chr3D 511128085 511129336 1251 True 1166.00 1166 83.71400 598 1849 1 chr3D.!!$R1 1251
9 TraesCS3A01G401200 chr3D 511180643 511181573 930 True 1133.00 1133 88.86500 624 1542 1 chr3D.!!$R2 918
10 TraesCS3A01G401200 chr3D 511265336 511266209 873 True 996.00 996 87.34300 979 1849 1 chr3D.!!$R4 870
11 TraesCS3A01G401200 chr3D 511201629 511202890 1261 True 974.00 974 81.13400 288 1537 1 chr3D.!!$R3 1249
12 TraesCS3A01G401200 chr3B 672769510 672777729 8219 True 1225.75 2039 88.27125 3 1847 4 chr3B.!!$R4 1844
13 TraesCS3A01G401200 chr3B 672516408 672517368 960 True 1059.00 1059 86.53600 876 1846 1 chr3B.!!$R1 970
14 TraesCS3A01G401200 chr3B 672743907 672744788 881 True 1059.00 1059 88.33500 954 1835 1 chr3B.!!$R3 881
15 TraesCS3A01G401200 chr4A 288594226 288595176 950 False 1447.00 1447 94.12400 1862 2813 1 chr4A.!!$F1 951
16 TraesCS3A01G401200 chr4A 288624644 288625601 957 False 1443.00 1443 93.85400 1850 2807 1 chr4A.!!$F2 957
17 TraesCS3A01G401200 chr7A 426876900 426877852 952 False 1435.00 1435 93.93900 1865 2813 1 chr7A.!!$F1 948
18 TraesCS3A01G401200 chr2A 481724837 481725799 962 True 1435.00 1435 93.57500 1850 2813 1 chr2A.!!$R2 963
19 TraesCS3A01G401200 chr6A 103919572 103920538 966 True 1434.00 1434 93.49200 1850 2813 1 chr6A.!!$R1 963
20 TraesCS3A01G401200 chr6A 158126340 158127309 969 True 1432.00 1432 93.40200 1850 2813 1 chr6A.!!$R2 963
21 TraesCS3A01G401200 chr6A 486993018 486993981 963 False 1432.00 1432 93.50500 1850 2813 1 chr6A.!!$F2 963
22 TraesCS3A01G401200 chr6A 439708321 439709286 965 False 1428.00 1428 93.40900 1850 2813 1 chr6A.!!$F1 963

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
104 105 0.028770 GGAGAGTCTCGACGATGCTG 59.971 60.0 13.97 0.00 36.20 4.41 F
208 209 0.103208 AGAGCGGTCATGATTCGGAC 59.897 55.0 18.15 7.06 0.00 4.79 F
209 210 0.103208 GAGCGGTCATGATTCGGACT 59.897 55.0 10.30 10.67 34.49 3.85 F
634 684 0.109132 CTTGCGGCAAATCCTTCCAC 60.109 55.0 17.13 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 6507 0.027586 GCATATGAAACCGACGGTGC 59.972 55.000 22.53 16.31 35.34 5.01 R
1554 11024 0.393448 GCGAAGGAGGAATAGACCCC 59.607 60.000 0.00 0.00 0.00 4.95 R
1650 11123 1.112315 CCGGTCTCCATCTCCTCCTG 61.112 65.000 0.00 0.00 0.00 3.86 R
2187 11663 1.815408 GCAACTGAGCTCAAGTGGGAA 60.815 52.381 18.85 0.00 0.00 3.97 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
22 23 3.495331 TGCAGGCAGGTTCAAAATTCTA 58.505 40.909 0.00 0.00 0.00 2.10
32 33 5.420104 AGGTTCAAAATTCTATTCTGCCAGG 59.580 40.000 0.00 0.00 0.00 4.45
33 34 4.989279 TCAAAATTCTATTCTGCCAGGC 57.011 40.909 3.66 3.66 0.00 4.85
34 35 3.378112 TCAAAATTCTATTCTGCCAGGCG 59.622 43.478 7.03 1.56 0.00 5.52
37 38 4.623932 AATTCTATTCTGCCAGGCGATA 57.376 40.909 7.03 4.49 0.00 2.92
55 56 4.682320 GCGATAATGTAAACTCCCTCCACA 60.682 45.833 0.00 0.00 0.00 4.17
56 57 4.809426 CGATAATGTAAACTCCCTCCACAC 59.191 45.833 0.00 0.00 0.00 3.82
57 58 5.625886 CGATAATGTAAACTCCCTCCACACA 60.626 44.000 0.00 0.00 0.00 3.72
58 59 4.657814 AATGTAAACTCCCTCCACACAT 57.342 40.909 0.00 0.00 0.00 3.21
59 60 4.657814 ATGTAAACTCCCTCCACACATT 57.342 40.909 0.00 0.00 0.00 2.71
60 61 5.772393 ATGTAAACTCCCTCCACACATTA 57.228 39.130 0.00 0.00 0.00 1.90
61 62 4.901868 TGTAAACTCCCTCCACACATTAC 58.098 43.478 0.00 0.00 0.00 1.89
62 63 4.595781 TGTAAACTCCCTCCACACATTACT 59.404 41.667 0.00 0.00 0.00 2.24
63 64 3.983044 AACTCCCTCCACACATTACTC 57.017 47.619 0.00 0.00 0.00 2.59
64 65 1.825474 ACTCCCTCCACACATTACTCG 59.175 52.381 0.00 0.00 0.00 4.18
65 66 1.137086 CTCCCTCCACACATTACTCGG 59.863 57.143 0.00 0.00 0.00 4.63
66 67 0.902531 CCCTCCACACATTACTCGGT 59.097 55.000 0.00 0.00 0.00 4.69
67 68 1.405526 CCCTCCACACATTACTCGGTG 60.406 57.143 0.00 0.00 40.78 4.94
68 69 1.548719 CCTCCACACATTACTCGGTGA 59.451 52.381 0.00 0.00 38.38 4.02
69 70 2.607187 CTCCACACATTACTCGGTGAC 58.393 52.381 0.00 0.00 38.38 3.67
70 71 1.964933 TCCACACATTACTCGGTGACA 59.035 47.619 0.00 0.00 38.38 3.58
71 72 2.365941 TCCACACATTACTCGGTGACAA 59.634 45.455 0.00 0.00 38.38 3.18
72 73 3.007506 TCCACACATTACTCGGTGACAAT 59.992 43.478 0.00 0.00 38.38 2.71
73 74 3.751175 CCACACATTACTCGGTGACAATT 59.249 43.478 0.00 0.00 38.38 2.32
74 75 4.142902 CCACACATTACTCGGTGACAATTC 60.143 45.833 0.00 0.00 38.38 2.17
75 76 4.690748 CACACATTACTCGGTGACAATTCT 59.309 41.667 0.00 0.00 38.38 2.40
76 77 5.867174 CACACATTACTCGGTGACAATTCTA 59.133 40.000 0.00 0.00 38.38 2.10
77 78 5.867716 ACACATTACTCGGTGACAATTCTAC 59.132 40.000 0.00 0.00 38.38 2.59
78 79 5.291128 CACATTACTCGGTGACAATTCTACC 59.709 44.000 0.00 0.00 37.18 3.18
84 85 2.889852 GGTGACAATTCTACCGAGACC 58.110 52.381 0.00 0.00 0.00 3.85
85 86 2.527100 GTGACAATTCTACCGAGACCG 58.473 52.381 0.00 0.00 0.00 4.79
97 98 4.621832 AGACCGGAGAGTCTCGAC 57.378 61.111 9.46 5.43 43.76 4.20
98 99 1.448189 AGACCGGAGAGTCTCGACG 60.448 63.158 9.46 12.19 43.76 5.12
99 100 1.447489 GACCGGAGAGTCTCGACGA 60.447 63.158 9.46 0.00 36.20 4.20
100 101 0.810823 GACCGGAGAGTCTCGACGAT 60.811 60.000 9.46 3.16 36.20 3.73
101 102 1.090625 ACCGGAGAGTCTCGACGATG 61.091 60.000 9.46 6.86 36.20 3.84
102 103 1.010574 CGGAGAGTCTCGACGATGC 60.011 63.158 13.97 0.00 36.20 3.91
103 104 1.433053 CGGAGAGTCTCGACGATGCT 61.433 60.000 13.97 0.00 36.20 3.79
104 105 0.028770 GGAGAGTCTCGACGATGCTG 59.971 60.000 13.97 0.00 36.20 4.41
105 106 0.028770 GAGAGTCTCGACGATGCTGG 59.971 60.000 3.95 0.00 36.20 4.85
106 107 1.064946 GAGTCTCGACGATGCTGGG 59.935 63.158 0.00 0.00 36.20 4.45
107 108 2.583593 GTCTCGACGATGCTGGGC 60.584 66.667 0.00 0.00 0.00 5.36
108 109 3.838271 TCTCGACGATGCTGGGCC 61.838 66.667 0.00 0.00 0.00 5.80
114 115 4.473520 CGATGCTGGGCCGGTCTT 62.474 66.667 15.16 4.61 0.00 3.01
115 116 2.044946 GATGCTGGGCCGGTCTTT 60.045 61.111 15.16 0.00 0.00 2.52
116 117 2.044946 ATGCTGGGCCGGTCTTTC 60.045 61.111 15.16 0.00 0.00 2.62
117 118 2.543067 GATGCTGGGCCGGTCTTTCT 62.543 60.000 15.16 0.00 0.00 2.52
118 119 2.747855 GCTGGGCCGGTCTTTCTG 60.748 66.667 15.16 0.00 0.00 3.02
119 120 2.747855 CTGGGCCGGTCTTTCTGC 60.748 66.667 5.77 0.00 0.00 4.26
120 121 4.344865 TGGGCCGGTCTTTCTGCC 62.345 66.667 5.77 0.00 43.26 4.85
122 123 4.699522 GGCCGGTCTTTCTGCCGT 62.700 66.667 1.90 0.00 45.91 5.68
123 124 3.423154 GCCGGTCTTTCTGCCGTG 61.423 66.667 1.90 0.00 45.91 4.94
124 125 2.030562 CCGGTCTTTCTGCCGTGT 59.969 61.111 0.00 0.00 45.91 4.49
125 126 2.317609 CCGGTCTTTCTGCCGTGTG 61.318 63.158 0.00 0.00 45.91 3.82
126 127 2.946762 GGTCTTTCTGCCGTGTGC 59.053 61.111 0.00 0.00 41.77 4.57
127 128 2.617274 GGTCTTTCTGCCGTGTGCC 61.617 63.158 0.00 0.00 40.16 5.01
128 129 1.598130 GTCTTTCTGCCGTGTGCCT 60.598 57.895 0.00 0.00 40.16 4.75
129 130 1.148273 TCTTTCTGCCGTGTGCCTT 59.852 52.632 0.00 0.00 40.16 4.35
130 131 0.884704 TCTTTCTGCCGTGTGCCTTC 60.885 55.000 0.00 0.00 40.16 3.46
131 132 0.886490 CTTTCTGCCGTGTGCCTTCT 60.886 55.000 0.00 0.00 40.16 2.85
132 133 0.465460 TTTCTGCCGTGTGCCTTCTT 60.465 50.000 0.00 0.00 40.16 2.52
133 134 1.165907 TTCTGCCGTGTGCCTTCTTG 61.166 55.000 0.00 0.00 40.16 3.02
134 135 3.259425 CTGCCGTGTGCCTTCTTGC 62.259 63.158 0.00 0.00 40.16 4.01
135 136 4.043200 GCCGTGTGCCTTCTTGCC 62.043 66.667 0.00 0.00 0.00 4.52
136 137 2.594303 CCGTGTGCCTTCTTGCCA 60.594 61.111 0.00 0.00 0.00 4.92
137 138 1.973281 CCGTGTGCCTTCTTGCCAT 60.973 57.895 0.00 0.00 0.00 4.40
138 139 0.676466 CCGTGTGCCTTCTTGCCATA 60.676 55.000 0.00 0.00 0.00 2.74
139 140 1.164411 CGTGTGCCTTCTTGCCATAA 58.836 50.000 0.00 0.00 0.00 1.90
140 141 1.745087 CGTGTGCCTTCTTGCCATAAT 59.255 47.619 0.00 0.00 0.00 1.28
141 142 2.223340 CGTGTGCCTTCTTGCCATAATC 60.223 50.000 0.00 0.00 0.00 1.75
142 143 2.016318 TGTGCCTTCTTGCCATAATCG 58.984 47.619 0.00 0.00 0.00 3.34
143 144 2.017049 GTGCCTTCTTGCCATAATCGT 58.983 47.619 0.00 0.00 0.00 3.73
144 145 2.016318 TGCCTTCTTGCCATAATCGTG 58.984 47.619 0.00 0.00 0.00 4.35
145 146 2.288666 GCCTTCTTGCCATAATCGTGA 58.711 47.619 0.00 0.00 0.00 4.35
146 147 2.032178 GCCTTCTTGCCATAATCGTGAC 59.968 50.000 0.00 0.00 0.00 3.67
147 148 3.270027 CCTTCTTGCCATAATCGTGACA 58.730 45.455 0.00 0.00 0.00 3.58
148 149 3.879295 CCTTCTTGCCATAATCGTGACAT 59.121 43.478 0.00 0.00 0.00 3.06
149 150 4.260907 CCTTCTTGCCATAATCGTGACATG 60.261 45.833 0.00 0.00 0.00 3.21
150 151 4.135747 TCTTGCCATAATCGTGACATGA 57.864 40.909 0.00 0.00 0.00 3.07
151 152 4.122046 TCTTGCCATAATCGTGACATGAG 58.878 43.478 0.00 0.00 0.00 2.90
152 153 2.837498 TGCCATAATCGTGACATGAGG 58.163 47.619 0.00 0.24 0.00 3.86
153 154 2.146342 GCCATAATCGTGACATGAGGG 58.854 52.381 0.00 3.78 0.00 4.30
154 155 2.771089 CCATAATCGTGACATGAGGGG 58.229 52.381 0.00 0.00 0.00 4.79
155 156 2.104792 CCATAATCGTGACATGAGGGGT 59.895 50.000 0.00 0.00 0.00 4.95
156 157 2.979814 TAATCGTGACATGAGGGGTG 57.020 50.000 0.00 0.00 0.00 4.61
157 158 0.392998 AATCGTGACATGAGGGGTGC 60.393 55.000 0.00 0.00 0.00 5.01
158 159 2.578163 ATCGTGACATGAGGGGTGCG 62.578 60.000 0.00 0.00 0.00 5.34
159 160 2.436646 GTGACATGAGGGGTGCGG 60.437 66.667 0.00 0.00 0.00 5.69
160 161 2.606213 TGACATGAGGGGTGCGGA 60.606 61.111 0.00 0.00 0.00 5.54
161 162 2.125106 GACATGAGGGGTGCGGAC 60.125 66.667 0.00 0.00 0.00 4.79
162 163 2.927856 ACATGAGGGGTGCGGACA 60.928 61.111 9.96 0.00 0.00 4.02
163 164 2.124983 CATGAGGGGTGCGGACAG 60.125 66.667 9.96 0.00 0.00 3.51
174 175 1.300542 GCGGACAGCCTATCAGAGC 60.301 63.158 0.00 0.00 40.81 4.09
175 176 1.365633 CGGACAGCCTATCAGAGCC 59.634 63.158 0.00 0.00 0.00 4.70
176 177 1.365633 GGACAGCCTATCAGAGCCG 59.634 63.158 0.00 0.00 0.00 5.52
177 178 1.395826 GGACAGCCTATCAGAGCCGT 61.396 60.000 0.00 0.00 0.00 5.68
178 179 0.461961 GACAGCCTATCAGAGCCGTT 59.538 55.000 0.00 0.00 0.00 4.44
179 180 0.176680 ACAGCCTATCAGAGCCGTTG 59.823 55.000 0.00 0.00 0.00 4.10
180 181 0.531532 CAGCCTATCAGAGCCGTTGG 60.532 60.000 0.00 0.00 0.00 3.77
181 182 0.687757 AGCCTATCAGAGCCGTTGGA 60.688 55.000 0.00 0.00 0.00 3.53
182 183 0.394565 GCCTATCAGAGCCGTTGGAT 59.605 55.000 0.00 0.00 0.00 3.41
183 184 1.606737 GCCTATCAGAGCCGTTGGATC 60.607 57.143 0.00 0.00 38.56 3.36
184 185 1.688735 CCTATCAGAGCCGTTGGATCA 59.311 52.381 3.70 0.00 41.08 2.92
185 186 2.288702 CCTATCAGAGCCGTTGGATCAG 60.289 54.545 3.70 0.00 41.08 2.90
186 187 0.467384 ATCAGAGCCGTTGGATCAGG 59.533 55.000 3.70 0.00 41.08 3.86
190 191 4.445699 GCCGTTGGATCAGGCTAG 57.554 61.111 11.80 0.00 46.83 3.42
191 192 1.823295 GCCGTTGGATCAGGCTAGA 59.177 57.895 11.80 0.00 46.83 2.43
192 193 0.249657 GCCGTTGGATCAGGCTAGAG 60.250 60.000 11.80 0.00 46.83 2.43
193 194 0.249657 CCGTTGGATCAGGCTAGAGC 60.250 60.000 0.00 0.00 41.14 4.09
194 195 0.596083 CGTTGGATCAGGCTAGAGCG 60.596 60.000 0.00 0.00 43.26 5.03
195 196 0.249657 GTTGGATCAGGCTAGAGCGG 60.250 60.000 0.00 0.00 43.26 5.52
196 197 0.687757 TTGGATCAGGCTAGAGCGGT 60.688 55.000 0.00 0.00 43.26 5.68
197 198 1.109920 TGGATCAGGCTAGAGCGGTC 61.110 60.000 6.48 6.48 43.26 4.79
198 199 1.109920 GGATCAGGCTAGAGCGGTCA 61.110 60.000 18.15 1.99 43.26 4.02
199 200 0.965439 GATCAGGCTAGAGCGGTCAT 59.035 55.000 18.15 4.64 43.26 3.06
200 201 0.678395 ATCAGGCTAGAGCGGTCATG 59.322 55.000 18.15 9.79 43.26 3.07
201 202 0.395724 TCAGGCTAGAGCGGTCATGA 60.396 55.000 18.15 9.49 43.26 3.07
202 203 0.678395 CAGGCTAGAGCGGTCATGAT 59.322 55.000 18.15 0.00 43.26 2.45
203 204 1.069823 CAGGCTAGAGCGGTCATGATT 59.930 52.381 18.15 0.00 43.26 2.57
204 205 1.342819 AGGCTAGAGCGGTCATGATTC 59.657 52.381 18.15 1.28 43.26 2.52
205 206 1.413382 GCTAGAGCGGTCATGATTCG 58.587 55.000 18.15 14.47 0.00 3.34
206 207 1.932604 GCTAGAGCGGTCATGATTCGG 60.933 57.143 18.15 5.35 0.00 4.30
207 208 1.609072 CTAGAGCGGTCATGATTCGGA 59.391 52.381 18.15 2.22 0.00 4.55
208 209 0.103208 AGAGCGGTCATGATTCGGAC 59.897 55.000 18.15 7.06 0.00 4.79
209 210 0.103208 GAGCGGTCATGATTCGGACT 59.897 55.000 10.30 10.67 34.49 3.85
210 211 0.179100 AGCGGTCATGATTCGGACTG 60.179 55.000 18.51 10.98 42.10 3.51
211 212 0.179111 GCGGTCATGATTCGGACTGA 60.179 55.000 18.51 0.00 41.83 3.41
212 213 1.845266 CGGTCATGATTCGGACTGAG 58.155 55.000 0.00 0.00 41.83 3.35
213 214 1.405463 CGGTCATGATTCGGACTGAGA 59.595 52.381 0.00 0.00 41.83 3.27
214 215 2.796383 CGGTCATGATTCGGACTGAGAC 60.796 54.545 0.00 0.00 41.83 3.36
215 216 2.428890 GGTCATGATTCGGACTGAGACT 59.571 50.000 0.00 0.00 34.49 3.24
216 217 3.443037 GTCATGATTCGGACTGAGACTG 58.557 50.000 0.00 0.00 0.00 3.51
217 218 2.428530 TCATGATTCGGACTGAGACTGG 59.571 50.000 0.00 0.00 0.00 4.00
218 219 0.532573 TGATTCGGACTGAGACTGGC 59.467 55.000 0.00 0.00 0.00 4.85
219 220 0.179097 GATTCGGACTGAGACTGGCC 60.179 60.000 0.00 0.00 0.00 5.36
227 228 0.886490 CTGAGACTGGCCGTGCTTTT 60.886 55.000 4.94 0.00 0.00 2.27
236 237 1.858458 GGCCGTGCTTTTCAAACTTTC 59.142 47.619 0.00 0.00 0.00 2.62
238 239 2.792749 CCGTGCTTTTCAAACTTTCGT 58.207 42.857 0.00 0.00 0.00 3.85
239 240 3.789459 GCCGTGCTTTTCAAACTTTCGTA 60.789 43.478 0.00 0.00 0.00 3.43
240 241 3.722289 CCGTGCTTTTCAAACTTTCGTAC 59.278 43.478 0.00 0.00 0.00 3.67
241 242 4.336101 CGTGCTTTTCAAACTTTCGTACA 58.664 39.130 0.00 0.00 0.00 2.90
242 243 4.433304 CGTGCTTTTCAAACTTTCGTACAG 59.567 41.667 0.00 0.00 0.00 2.74
253 254 7.747799 TCAAACTTTCGTACAGTAGAAGATACG 59.252 37.037 0.00 0.00 41.31 3.06
261 262 2.031857 CAGTAGAAGATACGCTCGGGTC 60.032 54.545 0.00 0.00 0.00 4.46
274 275 2.482142 GCTCGGGTCATCTTAGAGGTTG 60.482 54.545 0.00 0.00 0.00 3.77
280 281 3.471680 GTCATCTTAGAGGTTGCCATCC 58.528 50.000 0.00 0.00 0.00 3.51
290 291 0.539438 GTTGCCATCCTTGGTCCACA 60.539 55.000 0.00 0.00 45.57 4.17
342 349 8.998377 GTATTTTTGCCCAATGTGAAAAAGTAT 58.002 29.630 0.00 0.00 32.43 2.12
346 353 8.545229 TTTGCCCAATGTGAAAAAGTATATTG 57.455 30.769 0.00 0.00 0.00 1.90
418 442 4.536489 AGTTAGGACTGGGAAAAGCACTAT 59.464 41.667 0.00 0.00 33.99 2.12
457 481 4.041691 AGTTTTACCTGCCTGTCACATACT 59.958 41.667 0.00 0.00 0.00 2.12
458 482 3.887621 TTACCTGCCTGTCACATACTC 57.112 47.619 0.00 0.00 0.00 2.59
472 505 6.262496 TGTCACATACTCCCTCGTAAATAGAG 59.738 42.308 0.00 0.00 35.60 2.43
522 555 3.695830 ACACCTATTTTTCTCTCGGCA 57.304 42.857 0.00 0.00 0.00 5.69
552 588 5.304357 TGACTGGTTACTGATGAAGTCTTCA 59.696 40.000 17.46 17.46 45.01 3.02
553 589 5.542779 ACTGGTTACTGATGAAGTCTTCAC 58.457 41.667 17.49 11.71 43.48 3.18
619 669 5.488341 TGTCTTTCTTCCCTGTATACTTGC 58.512 41.667 4.17 0.00 0.00 4.01
634 684 0.109132 CTTGCGGCAAATCCTTCCAC 60.109 55.000 17.13 0.00 0.00 4.02
648 698 4.566004 TCCTTCCACGTCAATAAGACTTG 58.434 43.478 0.00 0.00 45.32 3.16
677 727 2.617532 GGCAGAAGAGAAGTCCATGCTT 60.618 50.000 0.00 0.00 32.89 3.91
778 832 2.945008 CTGGTGAGTTTTCTGAAGCACA 59.055 45.455 13.03 4.54 0.00 4.57
788 852 3.510388 TCTGAAGCACATCGGAAGTAG 57.490 47.619 0.00 0.00 31.84 2.57
831 900 8.840833 ACAAGTGTTTTCCAACTTTGTTATTT 57.159 26.923 0.00 0.00 37.76 1.40
874 943 7.041721 GTCTACTTTGTGGTGTCATCATATCA 58.958 38.462 0.00 0.00 0.00 2.15
939 3475 3.753272 TCTTACACAAGCTTTGATCAGGC 59.247 43.478 12.84 12.84 0.00 4.85
1030 6371 3.998913 TGGCTGATGATACCAAGTTCA 57.001 42.857 0.00 0.00 0.00 3.18
1162 6503 6.264067 ACTCAAATCCTCTTGGAACTTTGAAG 59.736 38.462 12.16 9.79 44.27 3.02
1166 6507 4.655963 TCCTCTTGGAACTTTGAAGATGG 58.344 43.478 0.00 0.00 39.87 3.51
1219 10689 1.303561 GAATGCTGGCACCCTGACA 60.304 57.895 0.00 0.00 32.24 3.58
1233 10703 3.117512 ACCCTGACAAGAACATGGTTCTT 60.118 43.478 16.36 16.36 39.16 2.52
1311 10781 2.124736 GCAAGCATGACCGGCCTA 60.125 61.111 0.00 0.00 0.00 3.93
1329 10799 5.007682 GGCCTAGACCTGTCAAATAACAAA 58.992 41.667 0.00 0.00 0.00 2.83
1542 11012 2.761559 TCGACGTTCAATGTTGTGGAT 58.238 42.857 0.00 0.00 0.00 3.41
1554 11024 7.747888 TCAATGTTGTGGATAACTTGTTATCG 58.252 34.615 20.48 8.96 35.34 2.92
1592 11065 2.673368 CGCTACTAAGGTTTCCAGCTTG 59.327 50.000 0.00 0.00 41.02 4.01
1650 11123 1.227973 GGATGATTGTCCCCGCTCC 60.228 63.158 0.00 0.00 31.82 4.70
1699 11172 2.661537 TGCACAGGCTCAACGACG 60.662 61.111 0.00 0.00 41.91 5.12
1767 11240 0.608640 CCTTCTACTTCCCGCACTGT 59.391 55.000 0.00 0.00 0.00 3.55
1846 11319 6.039616 TGTTCTGAAACTTTGTTTGGCATAC 58.960 36.000 0.75 0.75 36.30 2.39
2187 11663 2.695666 ACGATCAAGATCTTCATCGGGT 59.304 45.455 34.96 19.33 41.97 5.28
2228 11704 3.251729 GCGTCATCTGCATGGTTATCATT 59.748 43.478 0.00 0.00 32.92 2.57
2236 11712 3.221771 GCATGGTTATCATTGGCACCTA 58.778 45.455 0.00 0.00 32.92 3.08
2339 11822 3.323775 AGGAAAAGGTAGTGAGGTGGAA 58.676 45.455 0.00 0.00 0.00 3.53
2340 11823 3.720002 AGGAAAAGGTAGTGAGGTGGAAA 59.280 43.478 0.00 0.00 0.00 3.13
2408 11891 2.874701 GTGAGAAGAGAAGCAAAGCACA 59.125 45.455 0.00 0.00 0.00 4.57
2417 11900 1.953559 AGCAAAGCACAGTCGAGAAA 58.046 45.000 0.00 0.00 0.00 2.52
2525 12010 0.037697 GACCATCACGGCTACACACA 60.038 55.000 0.00 0.00 39.03 3.72
2592 12077 7.255660 GCAACCGGATATTAACAAATTCCCATA 60.256 37.037 9.46 0.00 0.00 2.74
2777 12263 3.168528 ACCAGCAAGACCACCCGT 61.169 61.111 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.699846 AGAATTTTGAACCTGCCTGCAA 59.300 40.909 0.00 0.00 0.00 4.08
1 2 2.318908 AGAATTTTGAACCTGCCTGCA 58.681 42.857 0.00 0.00 0.00 4.41
2 3 4.725790 ATAGAATTTTGAACCTGCCTGC 57.274 40.909 0.00 0.00 0.00 4.85
3 4 6.327934 CAGAATAGAATTTTGAACCTGCCTG 58.672 40.000 0.00 0.00 0.00 4.85
5 6 5.105063 GCAGAATAGAATTTTGAACCTGCC 58.895 41.667 0.00 0.00 38.69 4.85
8 9 5.420104 CCTGGCAGAATAGAATTTTGAACCT 59.580 40.000 17.94 0.00 0.00 3.50
10 11 5.105063 GCCTGGCAGAATAGAATTTTGAAC 58.895 41.667 17.94 0.00 0.00 3.18
13 14 3.378112 TCGCCTGGCAGAATAGAATTTTG 59.622 43.478 20.29 0.00 0.00 2.44
15 16 3.281727 TCGCCTGGCAGAATAGAATTT 57.718 42.857 20.29 0.00 0.00 1.82
22 23 2.645838 ACATTATCGCCTGGCAGAAT 57.354 45.000 20.29 11.29 0.00 2.40
32 33 3.808174 GTGGAGGGAGTTTACATTATCGC 59.192 47.826 0.00 0.00 0.00 4.58
33 34 4.809426 GTGTGGAGGGAGTTTACATTATCG 59.191 45.833 0.00 0.00 0.00 2.92
34 35 5.741011 TGTGTGGAGGGAGTTTACATTATC 58.259 41.667 0.00 0.00 0.00 1.75
37 38 4.657814 ATGTGTGGAGGGAGTTTACATT 57.342 40.909 0.00 0.00 0.00 2.71
55 56 5.416947 GGTAGAATTGTCACCGAGTAATGT 58.583 41.667 0.00 0.00 0.00 2.71
56 57 5.968387 GGTAGAATTGTCACCGAGTAATG 57.032 43.478 0.00 0.00 0.00 1.90
64 65 2.734492 CGGTCTCGGTAGAATTGTCACC 60.734 54.545 0.00 0.00 32.16 4.02
65 66 2.527100 CGGTCTCGGTAGAATTGTCAC 58.473 52.381 0.00 0.00 32.16 3.67
66 67 2.933495 CGGTCTCGGTAGAATTGTCA 57.067 50.000 0.00 0.00 32.16 3.58
81 82 0.810823 ATCGTCGAGACTCTCCGGTC 60.811 60.000 0.00 0.00 36.56 4.79
82 83 1.090625 CATCGTCGAGACTCTCCGGT 61.091 60.000 0.00 0.00 0.00 5.28
83 84 1.644372 CATCGTCGAGACTCTCCGG 59.356 63.158 0.00 0.00 0.00 5.14
84 85 1.010574 GCATCGTCGAGACTCTCCG 60.011 63.158 0.00 2.79 0.00 4.63
85 86 0.028770 CAGCATCGTCGAGACTCTCC 59.971 60.000 0.00 0.00 0.00 3.71
86 87 0.028770 CCAGCATCGTCGAGACTCTC 59.971 60.000 0.00 0.00 0.00 3.20
87 88 1.380403 CCCAGCATCGTCGAGACTCT 61.380 60.000 0.00 0.00 0.00 3.24
88 89 1.064946 CCCAGCATCGTCGAGACTC 59.935 63.158 0.00 0.00 0.00 3.36
89 90 3.069980 GCCCAGCATCGTCGAGACT 62.070 63.158 0.00 0.00 0.00 3.24
90 91 2.583593 GCCCAGCATCGTCGAGAC 60.584 66.667 0.00 0.00 0.00 3.36
91 92 3.838271 GGCCCAGCATCGTCGAGA 61.838 66.667 0.00 0.00 0.00 4.04
97 98 3.976701 AAAGACCGGCCCAGCATCG 62.977 63.158 0.00 0.00 0.00 3.84
98 99 2.044946 AAAGACCGGCCCAGCATC 60.045 61.111 0.00 0.00 0.00 3.91
99 100 2.044946 GAAAGACCGGCCCAGCAT 60.045 61.111 0.00 0.00 0.00 3.79
100 101 3.249189 AGAAAGACCGGCCCAGCA 61.249 61.111 0.00 0.00 0.00 4.41
101 102 2.747855 CAGAAAGACCGGCCCAGC 60.748 66.667 0.00 0.00 0.00 4.85
102 103 2.747855 GCAGAAAGACCGGCCCAG 60.748 66.667 0.00 0.00 0.00 4.45
103 104 4.344865 GGCAGAAAGACCGGCCCA 62.345 66.667 0.00 0.00 40.55 5.36
109 110 2.946762 GCACACGGCAGAAAGACC 59.053 61.111 0.00 0.00 43.97 3.85
118 119 4.043200 GGCAAGAAGGCACACGGC 62.043 66.667 0.00 0.00 43.51 5.68
125 126 2.032178 GTCACGATTATGGCAAGAAGGC 59.968 50.000 0.00 0.00 44.50 4.35
126 127 3.270027 TGTCACGATTATGGCAAGAAGG 58.730 45.455 0.00 0.00 29.24 3.46
127 128 4.571984 TCATGTCACGATTATGGCAAGAAG 59.428 41.667 0.00 0.00 37.82 2.85
128 129 4.512484 TCATGTCACGATTATGGCAAGAA 58.488 39.130 0.00 0.00 37.82 2.52
129 130 4.122046 CTCATGTCACGATTATGGCAAGA 58.878 43.478 0.00 0.00 37.82 3.02
130 131 3.249320 CCTCATGTCACGATTATGGCAAG 59.751 47.826 0.00 0.00 37.82 4.01
131 132 3.205338 CCTCATGTCACGATTATGGCAA 58.795 45.455 0.00 0.00 37.82 4.52
132 133 2.485302 CCCTCATGTCACGATTATGGCA 60.485 50.000 0.00 0.00 38.87 4.92
133 134 2.146342 CCCTCATGTCACGATTATGGC 58.854 52.381 0.00 0.00 0.00 4.40
134 135 2.104792 ACCCCTCATGTCACGATTATGG 59.895 50.000 0.00 0.00 0.00 2.74
135 136 3.133691 CACCCCTCATGTCACGATTATG 58.866 50.000 0.00 0.00 0.00 1.90
136 137 2.485479 GCACCCCTCATGTCACGATTAT 60.485 50.000 0.00 0.00 0.00 1.28
137 138 1.134521 GCACCCCTCATGTCACGATTA 60.135 52.381 0.00 0.00 0.00 1.75
138 139 0.392998 GCACCCCTCATGTCACGATT 60.393 55.000 0.00 0.00 0.00 3.34
139 140 1.221840 GCACCCCTCATGTCACGAT 59.778 57.895 0.00 0.00 0.00 3.73
140 141 2.662596 GCACCCCTCATGTCACGA 59.337 61.111 0.00 0.00 0.00 4.35
141 142 2.815211 CGCACCCCTCATGTCACG 60.815 66.667 0.00 0.00 0.00 4.35
142 143 2.436646 CCGCACCCCTCATGTCAC 60.437 66.667 0.00 0.00 0.00 3.67
143 144 2.606213 TCCGCACCCCTCATGTCA 60.606 61.111 0.00 0.00 0.00 3.58
144 145 2.125106 GTCCGCACCCCTCATGTC 60.125 66.667 0.00 0.00 0.00 3.06
145 146 2.927856 TGTCCGCACCCCTCATGT 60.928 61.111 0.00 0.00 0.00 3.21
146 147 2.124983 CTGTCCGCACCCCTCATG 60.125 66.667 0.00 0.00 0.00 3.07
147 148 4.101448 GCTGTCCGCACCCCTCAT 62.101 66.667 0.00 0.00 38.92 2.90
150 151 4.715130 TAGGCTGTCCGCACCCCT 62.715 66.667 0.00 0.00 41.67 4.79
151 152 3.462199 GATAGGCTGTCCGCACCCC 62.462 68.421 0.00 0.00 41.67 4.95
152 153 2.109181 GATAGGCTGTCCGCACCC 59.891 66.667 0.00 0.00 41.67 4.61
153 154 1.227380 CTGATAGGCTGTCCGCACC 60.227 63.158 8.89 0.00 41.67 5.01
154 155 0.249238 CTCTGATAGGCTGTCCGCAC 60.249 60.000 8.89 0.00 41.67 5.34
155 156 2.021068 GCTCTGATAGGCTGTCCGCA 62.021 60.000 8.89 0.00 41.67 5.69
156 157 1.300542 GCTCTGATAGGCTGTCCGC 60.301 63.158 8.89 5.32 37.47 5.54
164 165 1.688735 TGATCCAACGGCTCTGATAGG 59.311 52.381 0.00 0.00 0.00 2.57
165 166 2.288702 CCTGATCCAACGGCTCTGATAG 60.289 54.545 0.00 0.00 0.00 2.08
166 167 1.688735 CCTGATCCAACGGCTCTGATA 59.311 52.381 0.00 0.00 0.00 2.15
167 168 0.467384 CCTGATCCAACGGCTCTGAT 59.533 55.000 0.00 0.00 0.00 2.90
168 169 1.900351 CCTGATCCAACGGCTCTGA 59.100 57.895 0.00 0.00 0.00 3.27
169 170 1.817099 GCCTGATCCAACGGCTCTG 60.817 63.158 5.48 0.00 40.62 3.35
170 171 2.586792 GCCTGATCCAACGGCTCT 59.413 61.111 5.48 0.00 40.62 4.09
173 174 0.249657 CTCTAGCCTGATCCAACGGC 60.250 60.000 4.75 4.75 44.09 5.68
174 175 0.249657 GCTCTAGCCTGATCCAACGG 60.250 60.000 0.00 0.00 34.31 4.44
175 176 0.596083 CGCTCTAGCCTGATCCAACG 60.596 60.000 0.00 0.00 37.91 4.10
176 177 0.249657 CCGCTCTAGCCTGATCCAAC 60.250 60.000 0.00 0.00 37.91 3.77
177 178 0.687757 ACCGCTCTAGCCTGATCCAA 60.688 55.000 0.00 0.00 37.91 3.53
178 179 1.075970 ACCGCTCTAGCCTGATCCA 60.076 57.895 0.00 0.00 37.91 3.41
179 180 1.109920 TGACCGCTCTAGCCTGATCC 61.110 60.000 0.00 0.00 37.91 3.36
180 181 0.965439 ATGACCGCTCTAGCCTGATC 59.035 55.000 0.00 0.00 37.91 2.92
181 182 0.678395 CATGACCGCTCTAGCCTGAT 59.322 55.000 0.00 0.00 37.91 2.90
182 183 0.395724 TCATGACCGCTCTAGCCTGA 60.396 55.000 0.00 0.00 37.91 3.86
183 184 0.678395 ATCATGACCGCTCTAGCCTG 59.322 55.000 0.00 0.00 37.91 4.85
184 185 1.342819 GAATCATGACCGCTCTAGCCT 59.657 52.381 0.00 0.00 37.91 4.58
185 186 1.789506 GAATCATGACCGCTCTAGCC 58.210 55.000 0.00 0.00 37.91 3.93
186 187 1.413382 CGAATCATGACCGCTCTAGC 58.587 55.000 0.00 0.00 37.78 3.42
187 188 1.609072 TCCGAATCATGACCGCTCTAG 59.391 52.381 12.36 1.50 0.00 2.43
188 189 1.337071 GTCCGAATCATGACCGCTCTA 59.663 52.381 12.36 0.00 0.00 2.43
189 190 0.103208 GTCCGAATCATGACCGCTCT 59.897 55.000 12.36 0.00 0.00 4.09
190 191 0.103208 AGTCCGAATCATGACCGCTC 59.897 55.000 12.36 8.18 31.76 5.03
191 192 0.179100 CAGTCCGAATCATGACCGCT 60.179 55.000 12.36 4.40 31.76 5.52
192 193 0.179111 TCAGTCCGAATCATGACCGC 60.179 55.000 12.36 2.50 31.76 5.68
193 194 1.405463 TCTCAGTCCGAATCATGACCG 59.595 52.381 0.00 4.85 31.76 4.79
194 195 2.428890 AGTCTCAGTCCGAATCATGACC 59.571 50.000 0.00 0.00 31.76 4.02
195 196 3.443037 CAGTCTCAGTCCGAATCATGAC 58.557 50.000 0.00 0.00 0.00 3.06
196 197 2.428530 CCAGTCTCAGTCCGAATCATGA 59.571 50.000 0.00 0.00 0.00 3.07
197 198 2.819115 CCAGTCTCAGTCCGAATCATG 58.181 52.381 0.00 0.00 0.00 3.07
198 199 1.137872 GCCAGTCTCAGTCCGAATCAT 59.862 52.381 0.00 0.00 0.00 2.45
199 200 0.532573 GCCAGTCTCAGTCCGAATCA 59.467 55.000 0.00 0.00 0.00 2.57
200 201 0.179097 GGCCAGTCTCAGTCCGAATC 60.179 60.000 0.00 0.00 0.00 2.52
201 202 1.901085 GGCCAGTCTCAGTCCGAAT 59.099 57.895 0.00 0.00 0.00 3.34
202 203 2.636412 CGGCCAGTCTCAGTCCGAA 61.636 63.158 2.24 0.00 42.43 4.30
203 204 3.062466 CGGCCAGTCTCAGTCCGA 61.062 66.667 2.24 0.00 42.43 4.55
204 205 3.374402 ACGGCCAGTCTCAGTCCG 61.374 66.667 2.24 0.00 45.04 4.79
205 206 2.262915 CACGGCCAGTCTCAGTCC 59.737 66.667 2.24 0.00 0.00 3.85
206 207 2.433318 GCACGGCCAGTCTCAGTC 60.433 66.667 2.24 0.00 0.00 3.51
207 208 2.044806 AAAGCACGGCCAGTCTCAGT 62.045 55.000 2.24 0.00 0.00 3.41
208 209 0.886490 AAAAGCACGGCCAGTCTCAG 60.886 55.000 2.24 0.00 0.00 3.35
209 210 0.884704 GAAAAGCACGGCCAGTCTCA 60.885 55.000 2.24 0.00 0.00 3.27
210 211 0.884704 TGAAAAGCACGGCCAGTCTC 60.885 55.000 2.24 0.00 0.00 3.36
211 212 0.465460 TTGAAAAGCACGGCCAGTCT 60.465 50.000 2.24 0.00 0.00 3.24
212 213 0.383949 TTTGAAAAGCACGGCCAGTC 59.616 50.000 2.24 0.00 0.00 3.51
213 214 0.102300 GTTTGAAAAGCACGGCCAGT 59.898 50.000 2.24 0.00 0.00 4.00
214 215 0.385390 AGTTTGAAAAGCACGGCCAG 59.615 50.000 2.24 0.00 0.00 4.85
215 216 0.820871 AAGTTTGAAAAGCACGGCCA 59.179 45.000 2.24 0.00 0.00 5.36
216 217 1.858458 GAAAGTTTGAAAAGCACGGCC 59.142 47.619 0.00 0.00 0.00 6.13
217 218 1.516864 CGAAAGTTTGAAAAGCACGGC 59.483 47.619 0.00 0.00 0.00 5.68
218 219 2.792749 ACGAAAGTTTGAAAAGCACGG 58.207 42.857 0.00 0.00 46.40 4.94
219 220 4.336101 TGTACGAAAGTTTGAAAAGCACG 58.664 39.130 0.00 0.00 46.40 5.34
227 228 7.747799 CGTATCTTCTACTGTACGAAAGTTTGA 59.252 37.037 0.00 0.00 46.40 2.69
236 237 3.362791 CCGAGCGTATCTTCTACTGTACG 60.363 52.174 0.00 0.00 41.89 3.67
238 239 3.136763 CCCGAGCGTATCTTCTACTGTA 58.863 50.000 0.00 0.00 0.00 2.74
239 240 1.948145 CCCGAGCGTATCTTCTACTGT 59.052 52.381 0.00 0.00 0.00 3.55
240 241 1.948145 ACCCGAGCGTATCTTCTACTG 59.052 52.381 0.00 0.00 0.00 2.74
241 242 2.220313 GACCCGAGCGTATCTTCTACT 58.780 52.381 0.00 0.00 0.00 2.57
242 243 1.945394 TGACCCGAGCGTATCTTCTAC 59.055 52.381 0.00 0.00 0.00 2.59
253 254 1.404843 ACCTCTAAGATGACCCGAGC 58.595 55.000 0.00 0.00 0.00 5.03
261 262 3.853355 AGGATGGCAACCTCTAAGATG 57.147 47.619 10.99 0.00 31.43 2.90
290 291 3.044156 ACTGATATGATGCCACTCTGGT 58.956 45.455 0.00 0.00 40.46 4.00
298 299 4.833478 ATACTGGGACTGATATGATGCC 57.167 45.455 0.00 0.00 0.00 4.40
392 407 5.014228 AGTGCTTTTCCCAGTCCTAACTATT 59.986 40.000 0.00 0.00 33.25 1.73
393 408 4.536489 AGTGCTTTTCCCAGTCCTAACTAT 59.464 41.667 0.00 0.00 33.25 2.12
409 430 8.677148 TTTGTCAAGAGTAAAGATAGTGCTTT 57.323 30.769 0.00 0.00 40.85 3.51
418 442 8.889717 CAGGTAAAACTTTGTCAAGAGTAAAGA 58.110 33.333 11.46 0.00 35.82 2.52
457 481 6.239600 CCATGAAATCCTCTATTTACGAGGGA 60.240 42.308 6.27 0.00 46.43 4.20
458 482 5.934625 CCATGAAATCCTCTATTTACGAGGG 59.065 44.000 6.27 0.00 46.43 4.30
483 516 6.779860 AGGTGTATAACTTGTGGAACTGATT 58.220 36.000 0.00 0.00 38.04 2.57
522 555 4.152647 TCATCAGTAACCAGTCACTCACT 58.847 43.478 0.00 0.00 34.67 3.41
552 588 1.079490 TCCCCATCCTGAGAAGTCTGT 59.921 52.381 0.00 0.00 0.00 3.41
553 589 1.484240 GTCCCCATCCTGAGAAGTCTG 59.516 57.143 0.00 0.00 0.00 3.51
559 595 1.062886 CCAGTAGTCCCCATCCTGAGA 60.063 57.143 0.00 0.00 0.00 3.27
619 669 0.953471 TGACGTGGAAGGATTTGCCG 60.953 55.000 0.00 0.00 43.43 5.69
648 698 2.224646 ACTTCTCTTCTGCCAAACCCTC 60.225 50.000 0.00 0.00 0.00 4.30
677 727 1.078918 CAGAGAATGCCTCCACGCA 60.079 57.895 0.00 0.00 42.97 5.24
735 789 3.726557 TGATCCAGGCAAATCAGAAGT 57.273 42.857 0.00 0.00 0.00 3.01
778 832 6.597672 TGTTAATTTCATGTGCTACTTCCGAT 59.402 34.615 0.00 0.00 0.00 4.18
788 852 7.683746 ACACTTGTTTTGTTAATTTCATGTGC 58.316 30.769 0.00 0.00 35.72 4.57
818 886 4.148696 CCAAGAGCGCAAATAACAAAGTTG 59.851 41.667 11.47 0.00 36.25 3.16
819 887 4.202111 ACCAAGAGCGCAAATAACAAAGTT 60.202 37.500 11.47 0.00 0.00 2.66
825 894 3.492313 CAAGACCAAGAGCGCAAATAAC 58.508 45.455 11.47 0.00 0.00 1.89
831 900 1.004560 CTCCAAGACCAAGAGCGCA 60.005 57.895 11.47 0.00 0.00 6.09
888 957 8.995220 ACTTGAACGCACTACTTGAAAAATATA 58.005 29.630 0.00 0.00 0.00 0.86
889 958 7.803189 CACTTGAACGCACTACTTGAAAAATAT 59.197 33.333 0.00 0.00 0.00 1.28
939 3475 1.990563 AGCTTGTAAATTCCGACGTCG 59.009 47.619 30.33 30.33 39.44 5.12
1030 6371 6.306987 TGCTTAAGAGGAGAAACAAAAGGAT 58.693 36.000 6.67 0.00 0.00 3.24
1162 6503 1.024579 ATGAAACCGACGGTGCCATC 61.025 55.000 22.53 16.42 35.34 3.51
1166 6507 0.027586 GCATATGAAACCGACGGTGC 59.972 55.000 22.53 16.31 35.34 5.01
1219 10689 3.499918 CGCAGAGAAAGAACCATGTTCTT 59.500 43.478 14.70 14.70 40.20 2.52
1233 10703 1.372997 GTTGCCGAGACGCAGAGAA 60.373 57.895 0.00 0.00 40.53 2.87
1311 10781 8.143835 CCTGAAAATTTGTTATTTGACAGGTCT 58.856 33.333 18.19 0.00 39.14 3.85
1329 10799 3.309410 CCTGAGGGATTGGTCCTGAAAAT 60.309 47.826 0.00 0.00 44.44 1.82
1542 11012 5.901276 AGGAATAGACCCCGATAACAAGTTA 59.099 40.000 0.00 0.00 0.00 2.24
1554 11024 0.393448 GCGAAGGAGGAATAGACCCC 59.607 60.000 0.00 0.00 0.00 4.95
1592 11065 3.509967 CCCTTGGTTACCATCAAAGTTCC 59.490 47.826 4.38 0.00 31.53 3.62
1650 11123 1.112315 CCGGTCTCCATCTCCTCCTG 61.112 65.000 0.00 0.00 0.00 3.86
1699 11172 2.352915 CGCTCCGATGCTCGACTC 60.353 66.667 7.07 0.00 43.74 3.36
1767 11240 1.883732 CCTCTCGGAGCAGACGAAA 59.116 57.895 0.00 0.00 40.16 3.46
1846 11319 2.026822 ACAAGTTGGTATCAGAGCCAGG 60.027 50.000 7.96 0.00 36.00 4.45
2041 11514 6.903516 ACCTTGATTGTATTCTGGATGATGA 58.096 36.000 0.00 0.00 0.00 2.92
2187 11663 1.815408 GCAACTGAGCTCAAGTGGGAA 60.815 52.381 18.85 0.00 0.00 3.97
2228 11704 2.719531 TCAAACAGTTGTAGGTGCCA 57.280 45.000 0.00 0.00 36.07 4.92
2236 11712 6.823689 ACTCACAGATTACTTCAAACAGTTGT 59.176 34.615 0.00 0.00 36.07 3.32
2339 11822 6.596888 CCATATATGCTAGTGCTTGCTACATT 59.403 38.462 7.24 0.00 40.48 2.71
2340 11823 6.111382 CCATATATGCTAGTGCTTGCTACAT 58.889 40.000 7.24 0.00 40.48 2.29
2408 11891 9.743057 CTTCTTGATCATTATAGTTTCTCGACT 57.257 33.333 0.00 0.00 0.00 4.18
2525 12010 9.915629 TTAACTTAATTAAAATGCATCAACCGT 57.084 25.926 0.00 0.00 29.46 4.83
2777 12263 2.631160 ATCGGGATTTGTCGGCATAA 57.369 45.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.