Multiple sequence alignment - TraesCS2D01G447100

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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 TraesCS2D01G447100 chr2D 100.000 2348 0 0 1 2348 557156563 557158910 0.000000e+00 4337
1 TraesCS2D01G447100 chr6A 89.349 2075 189 16 301 2348 586879712 586881781 0.000000e+00 2579
2 TraesCS2D01G447100 chr1B 88.905 2091 187 22 301 2348 320735228 320733140 0.000000e+00 2534
3 TraesCS2D01G447100 chr4A 89.611 1954 174 6 299 2223 541180193 541182146 0.000000e+00 2457
4 TraesCS2D01G447100 chr2A 91.294 1654 136 4 301 1946 83920351 83918698 0.000000e+00 2250
5 TraesCS2D01G447100 chr2A 83.680 337 30 13 2037 2348 83918285 83917949 6.350000e-76 294
6 TraesCS2D01G447100 chr2B 85.352 1420 181 15 679 2086 732921547 732922951 0.000000e+00 1445
7 TraesCS2D01G447100 chr2B 75.112 1784 335 72 621 2348 379299513 379301243 0.000000e+00 734
8 TraesCS2D01G447100 chr2B 74.477 717 169 11 800 1508 380252931 380253641 4.910000e-77 298
9 TraesCS2D01G447100 chr4B 84.934 1135 134 17 1251 2348 617688847 617687713 0.000000e+00 1114
10 TraesCS2D01G447100 chr4B 88.889 414 46 0 301 714 617690016 617689603 5.790000e-141 510
11 TraesCS2D01G447100 chr4B 88.764 178 20 0 2171 2348 570169828 570170005 3.930000e-53 219
12 TraesCS2D01G447100 chr6B 83.040 1138 152 22 1251 2348 255401149 255400013 0.000000e+00 994
13 TraesCS2D01G447100 chr3A 82.458 952 142 14 621 1554 469667781 469666837 0.000000e+00 809
14 TraesCS2D01G447100 chr7D 98.397 312 5 0 1 312 570791447 570791136 1.230000e-152 549
15 TraesCS2D01G447100 chr7D 96.273 322 10 2 1 322 430682081 430681762 5.750000e-146 527
16 TraesCS2D01G447100 chr6D 99.333 300 2 0 1 300 355878894 355879193 5.710000e-151 544
17 TraesCS2D01G447100 chr4D 99.333 300 2 0 1 300 378070009 378070308 5.710000e-151 544
18 TraesCS2D01G447100 chr4D 97.152 316 8 1 1 315 273562004 273562319 1.240000e-147 532
19 TraesCS2D01G447100 chr3D 99.333 300 2 0 1 300 72126286 72126585 5.710000e-151 544
20 TraesCS2D01G447100 chr1D 96.875 320 7 3 1 317 423774712 423774393 1.240000e-147 532
21 TraesCS2D01G447100 chr1D 96.865 319 7 3 1 316 226122431 226122113 4.440000e-147 531
22 TraesCS2D01G447100 chr5D 95.732 328 12 2 1 326 276445756 276446083 5.750000e-146 527
23 TraesCS2D01G447100 chr3B 74.648 710 164 12 800 1500 381026227 381026929 1.360000e-77 300


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 TraesCS2D01G447100 chr2D 557156563 557158910 2347 False 4337 4337 100.0000 1 2348 1 chr2D.!!$F1 2347
1 TraesCS2D01G447100 chr6A 586879712 586881781 2069 False 2579 2579 89.3490 301 2348 1 chr6A.!!$F1 2047
2 TraesCS2D01G447100 chr1B 320733140 320735228 2088 True 2534 2534 88.9050 301 2348 1 chr1B.!!$R1 2047
3 TraesCS2D01G447100 chr4A 541180193 541182146 1953 False 2457 2457 89.6110 299 2223 1 chr4A.!!$F1 1924
4 TraesCS2D01G447100 chr2A 83917949 83920351 2402 True 1272 2250 87.4870 301 2348 2 chr2A.!!$R1 2047
5 TraesCS2D01G447100 chr2B 732921547 732922951 1404 False 1445 1445 85.3520 679 2086 1 chr2B.!!$F3 1407
6 TraesCS2D01G447100 chr2B 379299513 379301243 1730 False 734 734 75.1120 621 2348 1 chr2B.!!$F1 1727
7 TraesCS2D01G447100 chr2B 380252931 380253641 710 False 298 298 74.4770 800 1508 1 chr2B.!!$F2 708
8 TraesCS2D01G447100 chr4B 617687713 617690016 2303 True 812 1114 86.9115 301 2348 2 chr4B.!!$R1 2047
9 TraesCS2D01G447100 chr6B 255400013 255401149 1136 True 994 994 83.0400 1251 2348 1 chr6B.!!$R1 1097
10 TraesCS2D01G447100 chr3A 469666837 469667781 944 True 809 809 82.4580 621 1554 1 chr3A.!!$R1 933
11 TraesCS2D01G447100 chr3B 381026227 381026929 702 False 300 300 74.6480 800 1500 1 chr3B.!!$F1 700

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
193 194 0.037697 TGTGATAACGCTTCCGCTGT 60.038 50.0 0.0 0.0 38.22 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2034 1.229209 GGTGGTGGAGGAGGAGTCA 60.229 63.158 0.0 0.0 0.0 3.41 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
20 21 2.905075 TGGAACATCATCATCGTCACC 58.095 47.619 0.00 0.00 0.00 4.02
21 22 2.235898 TGGAACATCATCATCGTCACCA 59.764 45.455 0.00 0.00 0.00 4.17
22 23 3.118298 TGGAACATCATCATCGTCACCAT 60.118 43.478 0.00 0.00 0.00 3.55
23 24 3.249320 GGAACATCATCATCGTCACCATG 59.751 47.826 0.00 0.00 0.00 3.66
24 25 2.216046 ACATCATCATCGTCACCATGC 58.784 47.619 0.00 0.00 0.00 4.06
25 26 1.534163 CATCATCATCGTCACCATGCC 59.466 52.381 0.00 0.00 0.00 4.40
26 27 0.530431 TCATCATCGTCACCATGCCG 60.530 55.000 0.00 0.00 0.00 5.69
27 28 0.811219 CATCATCGTCACCATGCCGT 60.811 55.000 0.00 0.00 0.00 5.68
28 29 0.530650 ATCATCGTCACCATGCCGTC 60.531 55.000 0.00 0.00 0.00 4.79
29 30 2.202743 ATCGTCACCATGCCGTCG 60.203 61.111 0.00 0.00 0.00 5.12
30 31 3.001902 ATCGTCACCATGCCGTCGT 62.002 57.895 0.00 0.00 0.00 4.34
31 32 3.478394 CGTCACCATGCCGTCGTG 61.478 66.667 0.00 0.00 0.00 4.35
32 33 3.788766 GTCACCATGCCGTCGTGC 61.789 66.667 0.00 0.00 0.00 5.34
33 34 4.002506 TCACCATGCCGTCGTGCT 62.003 61.111 7.14 0.00 0.00 4.40
34 35 3.792047 CACCATGCCGTCGTGCTG 61.792 66.667 7.14 3.84 0.00 4.41
35 36 4.002506 ACCATGCCGTCGTGCTGA 62.003 61.111 7.14 0.00 0.00 4.26
36 37 3.490759 CCATGCCGTCGTGCTGAC 61.491 66.667 7.14 0.20 44.53 3.51
47 48 2.828933 GTGCTGACGAAACTCTCCC 58.171 57.895 0.00 0.00 0.00 4.30
48 49 0.318762 GTGCTGACGAAACTCTCCCT 59.681 55.000 0.00 0.00 0.00 4.20
49 50 0.603569 TGCTGACGAAACTCTCCCTC 59.396 55.000 0.00 0.00 0.00 4.30
50 51 0.603569 GCTGACGAAACTCTCCCTCA 59.396 55.000 0.00 0.00 0.00 3.86
51 52 1.000955 GCTGACGAAACTCTCCCTCAA 59.999 52.381 0.00 0.00 0.00 3.02
52 53 2.678324 CTGACGAAACTCTCCCTCAAC 58.322 52.381 0.00 0.00 0.00 3.18
53 54 2.035961 CTGACGAAACTCTCCCTCAACA 59.964 50.000 0.00 0.00 0.00 3.33
54 55 2.223971 TGACGAAACTCTCCCTCAACAC 60.224 50.000 0.00 0.00 0.00 3.32
55 56 2.036089 GACGAAACTCTCCCTCAACACT 59.964 50.000 0.00 0.00 0.00 3.55
56 57 2.036089 ACGAAACTCTCCCTCAACACTC 59.964 50.000 0.00 0.00 0.00 3.51
57 58 2.678324 GAAACTCTCCCTCAACACTCG 58.322 52.381 0.00 0.00 0.00 4.18
58 59 0.969894 AACTCTCCCTCAACACTCGG 59.030 55.000 0.00 0.00 0.00 4.63
59 60 1.216710 CTCTCCCTCAACACTCGGC 59.783 63.158 0.00 0.00 0.00 5.54
60 61 1.228894 TCTCCCTCAACACTCGGCT 60.229 57.895 0.00 0.00 0.00 5.52
61 62 1.079543 CTCCCTCAACACTCGGCTG 60.080 63.158 0.00 0.00 0.00 4.85
62 63 2.046892 CCCTCAACACTCGGCTGG 60.047 66.667 0.00 0.00 0.00 4.85
63 64 2.583441 CCCTCAACACTCGGCTGGA 61.583 63.158 0.00 0.00 0.00 3.86
64 65 1.599047 CCTCAACACTCGGCTGGAT 59.401 57.895 0.00 0.00 0.00 3.41
65 66 0.460987 CCTCAACACTCGGCTGGATC 60.461 60.000 0.00 0.00 0.00 3.36
66 67 0.803768 CTCAACACTCGGCTGGATCG 60.804 60.000 0.00 0.00 0.00 3.69
67 68 1.811266 CAACACTCGGCTGGATCGG 60.811 63.158 0.00 0.00 0.00 4.18
68 69 1.982395 AACACTCGGCTGGATCGGA 60.982 57.895 0.00 0.00 0.00 4.55
69 70 1.949847 AACACTCGGCTGGATCGGAG 61.950 60.000 0.00 0.00 38.77 4.63
70 71 2.043852 ACTCGGCTGGATCGGAGT 60.044 61.111 0.00 0.00 40.39 3.85
71 72 1.682684 ACTCGGCTGGATCGGAGTT 60.683 57.895 0.00 0.00 41.80 3.01
72 73 1.066587 CTCGGCTGGATCGGAGTTC 59.933 63.158 0.00 0.00 0.00 3.01
73 74 2.278857 CGGCTGGATCGGAGTTCG 60.279 66.667 0.00 0.00 40.90 3.95
81 82 2.033141 TCGGAGTTCGAGGGACGT 59.967 61.111 0.00 0.00 43.74 4.34
82 83 2.037136 TCGGAGTTCGAGGGACGTC 61.037 63.158 7.13 7.13 43.74 4.34
83 84 2.330372 CGGAGTTCGAGGGACGTCA 61.330 63.158 18.91 0.00 42.43 4.35
84 85 1.654954 CGGAGTTCGAGGGACGTCAT 61.655 60.000 18.91 4.87 42.43 3.06
85 86 0.100861 GGAGTTCGAGGGACGTCATC 59.899 60.000 18.91 13.48 43.13 2.92
86 87 0.248134 GAGTTCGAGGGACGTCATCG 60.248 60.000 27.08 27.08 43.13 3.84
87 88 0.675837 AGTTCGAGGGACGTCATCGA 60.676 55.000 29.82 29.82 43.19 3.59
88 89 0.248134 GTTCGAGGGACGTCATCGAG 60.248 60.000 30.77 16.93 45.23 4.04
89 90 1.989966 TTCGAGGGACGTCATCGAGC 61.990 60.000 30.77 10.93 45.23 5.03
90 91 2.473760 CGAGGGACGTCATCGAGCT 61.474 63.158 28.32 3.30 38.72 4.09
91 92 1.064946 GAGGGACGTCATCGAGCTG 59.935 63.158 18.91 0.00 40.62 4.24
92 93 1.377366 GAGGGACGTCATCGAGCTGA 61.377 60.000 18.91 0.00 40.62 4.26
93 94 0.965866 AGGGACGTCATCGAGCTGAA 60.966 55.000 18.91 0.00 40.62 3.02
94 95 0.802607 GGGACGTCATCGAGCTGAAC 60.803 60.000 18.91 0.00 40.62 3.18
95 96 1.134530 GGACGTCATCGAGCTGAACG 61.135 60.000 18.91 0.00 40.62 3.95
96 97 0.454620 GACGTCATCGAGCTGAACGT 60.455 55.000 11.55 12.62 40.62 3.99
97 98 0.729478 ACGTCATCGAGCTGAACGTG 60.729 55.000 12.23 3.66 40.62 4.49
98 99 0.729478 CGTCATCGAGCTGAACGTGT 60.729 55.000 0.00 0.00 39.71 4.49
99 100 0.710567 GTCATCGAGCTGAACGTGTG 59.289 55.000 0.00 0.00 0.00 3.82
100 101 0.313987 TCATCGAGCTGAACGTGTGT 59.686 50.000 0.00 0.00 0.00 3.72
101 102 1.538075 TCATCGAGCTGAACGTGTGTA 59.462 47.619 0.00 0.00 0.00 2.90
102 103 1.914051 CATCGAGCTGAACGTGTGTAG 59.086 52.381 0.00 0.00 0.00 2.74
103 104 1.232119 TCGAGCTGAACGTGTGTAGA 58.768 50.000 0.00 0.00 0.00 2.59
104 105 1.605232 TCGAGCTGAACGTGTGTAGAA 59.395 47.619 0.00 0.00 0.00 2.10
105 106 1.714460 CGAGCTGAACGTGTGTAGAAC 59.286 52.381 0.00 0.00 0.00 3.01
106 107 2.604855 CGAGCTGAACGTGTGTAGAACT 60.605 50.000 0.00 0.00 0.00 3.01
107 108 3.381949 GAGCTGAACGTGTGTAGAACTT 58.618 45.455 0.00 0.00 0.00 2.66
108 109 3.123804 AGCTGAACGTGTGTAGAACTTG 58.876 45.455 0.00 0.00 0.00 3.16
109 110 2.221055 GCTGAACGTGTGTAGAACTTGG 59.779 50.000 0.00 0.00 0.00 3.61
110 111 3.713288 CTGAACGTGTGTAGAACTTGGA 58.287 45.455 0.00 0.00 0.00 3.53
111 112 3.713288 TGAACGTGTGTAGAACTTGGAG 58.287 45.455 0.00 0.00 0.00 3.86
112 113 2.814280 ACGTGTGTAGAACTTGGAGG 57.186 50.000 0.00 0.00 0.00 4.30
113 114 2.037144 ACGTGTGTAGAACTTGGAGGT 58.963 47.619 0.00 0.00 0.00 3.85
114 115 2.223971 ACGTGTGTAGAACTTGGAGGTG 60.224 50.000 0.00 0.00 0.00 4.00
115 116 2.143925 GTGTGTAGAACTTGGAGGTGC 58.856 52.381 0.00 0.00 0.00 5.01
116 117 1.071699 TGTGTAGAACTTGGAGGTGCC 59.928 52.381 0.00 0.00 37.10 5.01
117 118 0.320374 TGTAGAACTTGGAGGTGCCG 59.680 55.000 0.00 0.00 40.66 5.69
118 119 0.320697 GTAGAACTTGGAGGTGCCGT 59.679 55.000 0.00 0.00 40.66 5.68
119 120 1.547372 GTAGAACTTGGAGGTGCCGTA 59.453 52.381 0.00 0.00 40.66 4.02
120 121 0.320697 AGAACTTGGAGGTGCCGTAC 59.679 55.000 0.00 0.00 40.66 3.67
121 122 1.005394 AACTTGGAGGTGCCGTACG 60.005 57.895 8.69 8.69 40.66 3.67
122 123 1.751349 AACTTGGAGGTGCCGTACGT 61.751 55.000 15.21 0.00 40.66 3.57
123 124 1.005394 CTTGGAGGTGCCGTACGTT 60.005 57.895 15.21 0.00 40.66 3.99
124 125 1.005867 TTGGAGGTGCCGTACGTTC 60.006 57.895 15.21 6.17 40.66 3.95
125 126 2.505557 GGAGGTGCCGTACGTTCG 60.506 66.667 15.21 7.68 0.00 3.95
137 138 2.444351 GTACGTTCGGTACTTGATCGG 58.556 52.381 17.26 0.00 46.50 4.18
138 139 0.883833 ACGTTCGGTACTTGATCGGT 59.116 50.000 17.26 0.00 33.92 4.69
139 140 1.135575 ACGTTCGGTACTTGATCGGTC 60.136 52.381 17.26 0.00 33.92 4.79
140 141 1.135603 CGTTCGGTACTTGATCGGTCA 60.136 52.381 0.00 0.00 30.29 4.02
141 142 2.527100 GTTCGGTACTTGATCGGTCAG 58.473 52.381 0.00 0.00 35.39 3.51
142 143 2.118313 TCGGTACTTGATCGGTCAGA 57.882 50.000 0.00 0.00 35.39 3.27
143 144 2.651455 TCGGTACTTGATCGGTCAGAT 58.349 47.619 0.00 0.00 43.51 2.90
152 153 2.722071 GATCGGTCAGATCGTGAAGAC 58.278 52.381 2.26 0.00 45.35 3.01
153 154 2.851386 GATCGGTCAGATCGTGAAGACG 60.851 54.545 2.26 0.00 45.35 4.18
154 155 0.168348 CGGTCAGATCGTGAAGACGT 59.832 55.000 0.00 0.00 46.20 4.34
155 156 1.395954 CGGTCAGATCGTGAAGACGTA 59.604 52.381 0.00 0.00 46.20 3.57
156 157 2.783333 GGTCAGATCGTGAAGACGTAC 58.217 52.381 0.00 0.00 46.20 3.67
157 158 2.429061 GTCAGATCGTGAAGACGTACG 58.571 52.381 15.01 15.01 46.20 3.67
163 164 2.403259 TCGTGAAGACGTACGACTACA 58.597 47.619 24.41 13.28 46.20 2.74
164 165 2.995939 TCGTGAAGACGTACGACTACAT 59.004 45.455 24.41 6.17 46.20 2.29
165 166 3.061295 TCGTGAAGACGTACGACTACATC 59.939 47.826 24.41 15.62 46.20 3.06
166 167 3.181527 CGTGAAGACGTACGACTACATCA 60.182 47.826 24.41 18.00 42.54 3.07
167 168 4.667415 CGTGAAGACGTACGACTACATCAA 60.667 45.833 24.41 4.49 42.54 2.57
168 169 4.552660 GTGAAGACGTACGACTACATCAAC 59.447 45.833 24.41 11.90 0.00 3.18
169 170 3.754188 AGACGTACGACTACATCAACC 57.246 47.619 24.41 0.00 0.00 3.77
170 171 2.094894 AGACGTACGACTACATCAACCG 59.905 50.000 24.41 0.00 0.00 4.44
171 172 1.186030 CGTACGACTACATCAACCGC 58.814 55.000 10.44 0.00 0.00 5.68
172 173 1.186030 GTACGACTACATCAACCGCG 58.814 55.000 0.00 0.00 0.00 6.46
173 174 0.804364 TACGACTACATCAACCGCGT 59.196 50.000 4.92 0.00 0.00 6.01
174 175 0.038892 ACGACTACATCAACCGCGTT 60.039 50.000 4.92 0.00 0.00 4.84
175 176 0.365523 CGACTACATCAACCGCGTTG 59.634 55.000 4.92 10.14 43.99 4.10
176 177 1.425412 GACTACATCAACCGCGTTGT 58.575 50.000 16.97 9.99 43.23 3.32
177 178 1.126113 GACTACATCAACCGCGTTGTG 59.874 52.381 16.97 15.92 43.23 3.33
178 179 1.269883 ACTACATCAACCGCGTTGTGA 60.270 47.619 16.97 12.14 43.23 3.58
179 180 1.999735 CTACATCAACCGCGTTGTGAT 59.000 47.619 16.97 13.59 43.23 3.06
180 181 2.087501 ACATCAACCGCGTTGTGATA 57.912 45.000 16.97 3.28 43.23 2.15
181 182 2.418692 ACATCAACCGCGTTGTGATAA 58.581 42.857 16.97 2.99 43.23 1.75
182 183 2.158841 ACATCAACCGCGTTGTGATAAC 59.841 45.455 16.97 0.00 43.23 1.89
183 184 0.785378 TCAACCGCGTTGTGATAACG 59.215 50.000 10.16 10.16 43.23 3.18
189 190 3.850207 CGTTGTGATAACGCTTCCG 57.150 52.632 0.75 0.00 36.82 4.30
190 191 0.247145 CGTTGTGATAACGCTTCCGC 60.247 55.000 0.75 0.00 36.82 5.54
191 192 1.076332 GTTGTGATAACGCTTCCGCT 58.924 50.000 0.00 0.00 38.22 5.52
192 193 1.075542 TTGTGATAACGCTTCCGCTG 58.924 50.000 0.00 0.00 38.22 5.18
193 194 0.037697 TGTGATAACGCTTCCGCTGT 60.038 50.000 0.00 0.00 38.22 4.40
194 195 0.645868 GTGATAACGCTTCCGCTGTC 59.354 55.000 0.00 0.00 38.22 3.51
195 196 0.800683 TGATAACGCTTCCGCTGTCG 60.801 55.000 0.00 0.00 38.22 4.35
213 214 2.101700 GGTCTACGAGGGTACGTGG 58.898 63.158 0.00 0.00 46.02 4.94
214 215 1.379642 GGTCTACGAGGGTACGTGGG 61.380 65.000 0.00 0.00 46.02 4.61
215 216 1.750399 TCTACGAGGGTACGTGGGC 60.750 63.158 0.00 0.00 46.02 5.36
216 217 2.035469 TACGAGGGTACGTGGGCA 59.965 61.111 0.00 0.00 46.02 5.36
217 218 1.597797 CTACGAGGGTACGTGGGCAA 61.598 60.000 0.00 0.00 46.02 4.52
218 219 1.876497 TACGAGGGTACGTGGGCAAC 61.876 60.000 0.00 0.00 46.02 4.17
219 220 2.745037 GAGGGTACGTGGGCAACA 59.255 61.111 0.00 0.00 39.74 3.33
220 221 1.670083 GAGGGTACGTGGGCAACAC 60.670 63.158 0.00 1.02 46.78 3.32
227 228 2.034221 GTGGGCAACACTCTCCCC 59.966 66.667 3.76 0.00 46.72 4.81
228 229 2.121963 TGGGCAACACTCTCCCCT 60.122 61.111 0.00 0.00 39.30 4.79
229 230 2.224159 TGGGCAACACTCTCCCCTC 61.224 63.158 0.00 0.00 39.30 4.30
230 231 1.920835 GGGCAACACTCTCCCCTCT 60.921 63.158 0.00 0.00 39.74 3.69
231 232 1.599576 GGCAACACTCTCCCCTCTC 59.400 63.158 0.00 0.00 0.00 3.20
232 233 1.216710 GCAACACTCTCCCCTCTCG 59.783 63.158 0.00 0.00 0.00 4.04
233 234 1.536943 GCAACACTCTCCCCTCTCGT 61.537 60.000 0.00 0.00 0.00 4.18
234 235 0.969894 CAACACTCTCCCCTCTCGTT 59.030 55.000 0.00 0.00 0.00 3.85
235 236 0.969894 AACACTCTCCCCTCTCGTTG 59.030 55.000 0.00 0.00 0.00 4.10
236 237 1.216710 CACTCTCCCCTCTCGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
237 238 1.077625 ACTCTCCCCTCTCGTTGCT 59.922 57.895 0.00 0.00 0.00 3.91
238 239 0.331954 ACTCTCCCCTCTCGTTGCTA 59.668 55.000 0.00 0.00 0.00 3.49
239 240 1.063567 ACTCTCCCCTCTCGTTGCTAT 60.064 52.381 0.00 0.00 0.00 2.97
240 241 1.339610 CTCTCCCCTCTCGTTGCTATG 59.660 57.143 0.00 0.00 0.00 2.23
241 242 0.249657 CTCCCCTCTCGTTGCTATGC 60.250 60.000 0.00 0.00 0.00 3.14
242 243 0.975556 TCCCCTCTCGTTGCTATGCA 60.976 55.000 0.00 0.00 36.47 3.96
243 244 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
244 245 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
245 246 1.202568 CCCTCTCGTTGCTATGCATCA 60.203 52.381 0.19 0.00 38.76 3.07
246 247 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
247 248 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
248 249 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
249 250 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
250 251 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
251 252 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
252 253 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
253 254 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
254 255 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
255 256 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
256 257 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
257 258 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
258 259 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
259 260 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
260 261 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
261 262 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
262 263 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
263 264 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
275 276 2.325509 GCGTGTGCGTAGGAATTTTT 57.674 45.000 0.00 0.00 40.81 1.94
296 297 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
297 298 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
392 393 1.183030 TTCGACGGCCTCTTCTTCCA 61.183 55.000 0.00 0.00 0.00 3.53
436 437 3.173965 CGGGTAGATTGTAGGGATCCAT 58.826 50.000 15.23 9.63 0.00 3.41
521 522 0.976073 CAAGGTAGGAAGGGAGGCGA 60.976 60.000 0.00 0.00 0.00 5.54
553 554 3.948719 GGTCACCACGGGGCAGAA 61.949 66.667 1.73 0.00 37.90 3.02
588 589 4.033776 CTGCGCTTTCCCTCCCCA 62.034 66.667 9.73 0.00 0.00 4.96
591 592 4.426313 CGCTTTCCCTCCCCACCC 62.426 72.222 0.00 0.00 0.00 4.61
837 876 0.322546 GCCATGACCCCGAAGACTTT 60.323 55.000 0.00 0.00 0.00 2.66
982 1021 4.794439 CGCTCCATGTCCGCGTCA 62.794 66.667 4.92 4.31 41.78 4.35
1013 1052 2.233566 TCCCCATGCAGCTCTGGTT 61.234 57.895 12.10 0.00 0.00 3.67
1025 1064 3.260100 CTGGTTGCTGGAGGGGGT 61.260 66.667 0.00 0.00 0.00 4.95
1145 1184 1.614711 ATGTCGCCAACATCCCCAT 59.385 52.632 0.00 0.00 45.78 4.00
1468 1779 4.666253 GGCTGCCAGGGTCTGCAA 62.666 66.667 15.17 0.00 0.00 4.08
1533 1844 4.569023 CGGCAGCCGTCGCTCATA 62.569 66.667 26.69 0.00 43.95 2.15
1599 1910 1.958205 CATCGAAGGATCAGGCGCC 60.958 63.158 21.89 21.89 0.00 6.53
1706 2024 4.124351 CTCTCCCGTTACGCCGCA 62.124 66.667 0.00 0.00 0.00 5.69
1726 2044 2.360980 CCGTCCCTGACTCCTCCT 59.639 66.667 0.00 0.00 0.00 3.69
1863 2187 4.749310 CCGCTGCGAGCTGGAAGT 62.749 66.667 25.45 0.00 39.60 3.01
1924 2248 2.048127 GAGCCCGTCAACGCTCTT 60.048 61.111 1.88 0.00 46.48 2.85
1991 2315 3.491208 GACTCCATCCAAGCATGCT 57.509 52.632 16.30 16.30 0.00 3.79
2140 2825 3.330720 CTCCGCCCCTCCCAAGTT 61.331 66.667 0.00 0.00 0.00 2.66
2223 2908 3.952508 TCGCACAGTGGGCCACAT 61.953 61.111 36.28 22.33 36.74 3.21
2225 2910 1.673993 CGCACAGTGGGCCACATTA 60.674 57.895 36.28 0.00 36.74 1.90
2235 2920 1.153628 GCCACATTACGCCTCGTCT 60.154 57.895 0.00 0.00 41.54 4.18
2264 2949 3.327404 GTCCTCGGCCCAAGGGAA 61.327 66.667 16.87 0.00 37.50 3.97
2273 2958 1.303236 CCCAAGGGAACGCATGACA 60.303 57.895 0.00 0.00 37.50 3.58
2320 3005 2.024319 GCTTCGACGAGCAGCTGTT 61.024 57.895 16.64 9.79 42.25 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.235898 TGGTGACGATGATGATGTTCCA 59.764 45.455 0.00 0.00 0.00 3.53
2 3 3.303593 GCATGGTGACGATGATGATGTTC 60.304 47.826 11.88 0.00 0.00 3.18
3 4 2.615447 GCATGGTGACGATGATGATGTT 59.385 45.455 11.88 0.00 0.00 2.71
4 5 2.216046 GCATGGTGACGATGATGATGT 58.784 47.619 11.88 0.00 0.00 3.06
5 6 1.534163 GGCATGGTGACGATGATGATG 59.466 52.381 11.88 0.00 0.00 3.07
6 7 1.888215 GGCATGGTGACGATGATGAT 58.112 50.000 11.88 0.00 0.00 2.45
7 8 3.384816 GGCATGGTGACGATGATGA 57.615 52.632 11.88 0.00 0.00 2.92
15 16 3.788766 GCACGACGGCATGGTGAC 61.789 66.667 0.00 0.00 39.28 3.67
16 17 4.002506 AGCACGACGGCATGGTGA 62.003 61.111 0.00 0.00 39.28 4.02
17 18 3.792047 CAGCACGACGGCATGGTG 61.792 66.667 0.63 0.63 39.89 4.17
18 19 4.002506 TCAGCACGACGGCATGGT 62.003 61.111 10.28 0.00 35.83 3.55
19 20 3.490759 GTCAGCACGACGGCATGG 61.491 66.667 10.28 1.29 34.19 3.66
29 30 0.318762 AGGGAGAGTTTCGTCAGCAC 59.681 55.000 0.00 0.00 0.00 4.40
30 31 0.603569 GAGGGAGAGTTTCGTCAGCA 59.396 55.000 0.00 0.00 0.00 4.41
31 32 0.603569 TGAGGGAGAGTTTCGTCAGC 59.396 55.000 0.00 0.00 0.00 4.26
32 33 2.035961 TGTTGAGGGAGAGTTTCGTCAG 59.964 50.000 0.00 0.00 0.00 3.51
33 34 2.036387 TGTTGAGGGAGAGTTTCGTCA 58.964 47.619 0.00 0.00 0.00 4.35
34 35 2.036089 AGTGTTGAGGGAGAGTTTCGTC 59.964 50.000 0.00 0.00 0.00 4.20
35 36 2.036089 GAGTGTTGAGGGAGAGTTTCGT 59.964 50.000 0.00 0.00 0.00 3.85
36 37 2.678324 GAGTGTTGAGGGAGAGTTTCG 58.322 52.381 0.00 0.00 0.00 3.46
37 38 2.610727 CCGAGTGTTGAGGGAGAGTTTC 60.611 54.545 0.00 0.00 0.00 2.78
38 39 1.344763 CCGAGTGTTGAGGGAGAGTTT 59.655 52.381 0.00 0.00 0.00 2.66
39 40 0.969894 CCGAGTGTTGAGGGAGAGTT 59.030 55.000 0.00 0.00 0.00 3.01
40 41 1.536943 GCCGAGTGTTGAGGGAGAGT 61.537 60.000 0.00 0.00 0.00 3.24
41 42 1.216710 GCCGAGTGTTGAGGGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
42 43 1.228894 AGCCGAGTGTTGAGGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
43 44 1.079543 CAGCCGAGTGTTGAGGGAG 60.080 63.158 0.00 0.00 0.00 4.30
44 45 2.583441 CCAGCCGAGTGTTGAGGGA 61.583 63.158 0.00 0.00 0.00 4.20
45 46 1.903877 ATCCAGCCGAGTGTTGAGGG 61.904 60.000 0.00 0.00 0.00 4.30
46 47 0.460987 GATCCAGCCGAGTGTTGAGG 60.461 60.000 0.00 0.00 0.00 3.86
47 48 0.803768 CGATCCAGCCGAGTGTTGAG 60.804 60.000 0.00 0.00 0.00 3.02
48 49 1.215382 CGATCCAGCCGAGTGTTGA 59.785 57.895 0.00 0.00 0.00 3.18
49 50 1.811266 CCGATCCAGCCGAGTGTTG 60.811 63.158 0.00 0.00 0.00 3.33
50 51 1.949847 CTCCGATCCAGCCGAGTGTT 61.950 60.000 0.00 0.00 0.00 3.32
51 52 2.362503 TCCGATCCAGCCGAGTGT 60.363 61.111 0.00 0.00 0.00 3.55
52 53 1.949847 AACTCCGATCCAGCCGAGTG 61.950 60.000 0.00 0.00 0.00 3.51
53 54 1.668101 GAACTCCGATCCAGCCGAGT 61.668 60.000 0.00 0.00 0.00 4.18
54 55 1.066587 GAACTCCGATCCAGCCGAG 59.933 63.158 0.00 0.00 0.00 4.63
55 56 2.771639 CGAACTCCGATCCAGCCGA 61.772 63.158 0.00 0.00 41.76 5.54
56 57 2.278857 CGAACTCCGATCCAGCCG 60.279 66.667 0.00 0.00 41.76 5.52
57 58 3.207354 TCGAACTCCGATCCAGCC 58.793 61.111 0.00 0.00 43.23 4.85
64 65 2.033141 ACGTCCCTCGAACTCCGA 59.967 61.111 1.88 0.00 46.35 4.55
65 66 1.654954 ATGACGTCCCTCGAACTCCG 61.655 60.000 14.12 0.00 42.86 4.63
66 67 0.100861 GATGACGTCCCTCGAACTCC 59.899 60.000 14.12 0.00 42.86 3.85
67 68 0.248134 CGATGACGTCCCTCGAACTC 60.248 60.000 24.99 5.48 42.86 3.01
68 69 0.675837 TCGATGACGTCCCTCGAACT 60.676 55.000 27.70 0.60 42.86 3.01
69 70 0.248134 CTCGATGACGTCCCTCGAAC 60.248 60.000 28.71 6.04 40.52 3.95
70 71 1.989966 GCTCGATGACGTCCCTCGAA 61.990 60.000 28.71 18.23 40.52 3.71
71 72 2.470362 GCTCGATGACGTCCCTCGA 61.470 63.158 27.81 27.81 42.86 4.04
72 73 2.024871 GCTCGATGACGTCCCTCG 59.975 66.667 23.88 23.88 46.00 4.63
73 74 1.064946 CAGCTCGATGACGTCCCTC 59.935 63.158 14.12 9.05 40.69 4.30
74 75 0.965866 TTCAGCTCGATGACGTCCCT 60.966 55.000 14.12 0.00 40.69 4.20
75 76 0.802607 GTTCAGCTCGATGACGTCCC 60.803 60.000 14.12 3.95 40.69 4.46
76 77 1.134530 CGTTCAGCTCGATGACGTCC 61.135 60.000 14.12 0.00 40.69 4.79
77 78 0.454620 ACGTTCAGCTCGATGACGTC 60.455 55.000 9.11 9.11 40.69 4.34
78 79 0.729478 CACGTTCAGCTCGATGACGT 60.729 55.000 0.00 5.49 37.39 4.34
79 80 0.729478 ACACGTTCAGCTCGATGACG 60.729 55.000 0.00 4.93 41.26 4.35
80 81 0.710567 CACACGTTCAGCTCGATGAC 59.289 55.000 0.00 0.00 0.00 3.06
81 82 0.313987 ACACACGTTCAGCTCGATGA 59.686 50.000 0.00 0.00 0.00 2.92
82 83 1.914051 CTACACACGTTCAGCTCGATG 59.086 52.381 0.00 1.36 0.00 3.84
83 84 1.810755 TCTACACACGTTCAGCTCGAT 59.189 47.619 0.00 0.00 0.00 3.59
84 85 1.232119 TCTACACACGTTCAGCTCGA 58.768 50.000 0.00 0.00 0.00 4.04
85 86 1.714460 GTTCTACACACGTTCAGCTCG 59.286 52.381 0.00 0.00 0.00 5.03
86 87 3.014604 AGTTCTACACACGTTCAGCTC 57.985 47.619 0.00 0.00 0.00 4.09
87 88 3.123804 CAAGTTCTACACACGTTCAGCT 58.876 45.455 0.00 0.00 0.00 4.24
88 89 2.221055 CCAAGTTCTACACACGTTCAGC 59.779 50.000 0.00 0.00 0.00 4.26
89 90 3.713288 TCCAAGTTCTACACACGTTCAG 58.287 45.455 0.00 0.00 0.00 3.02
90 91 3.491964 CCTCCAAGTTCTACACACGTTCA 60.492 47.826 0.00 0.00 0.00 3.18
91 92 3.057734 CCTCCAAGTTCTACACACGTTC 58.942 50.000 0.00 0.00 0.00 3.95
92 93 2.433239 ACCTCCAAGTTCTACACACGTT 59.567 45.455 0.00 0.00 0.00 3.99
93 94 2.037144 ACCTCCAAGTTCTACACACGT 58.963 47.619 0.00 0.00 0.00 4.49
94 95 2.404215 CACCTCCAAGTTCTACACACG 58.596 52.381 0.00 0.00 0.00 4.49
95 96 2.143925 GCACCTCCAAGTTCTACACAC 58.856 52.381 0.00 0.00 0.00 3.82
96 97 1.071699 GGCACCTCCAAGTTCTACACA 59.928 52.381 0.00 0.00 34.01 3.72
97 98 1.809684 GGCACCTCCAAGTTCTACAC 58.190 55.000 0.00 0.00 34.01 2.90
98 99 0.320374 CGGCACCTCCAAGTTCTACA 59.680 55.000 0.00 0.00 34.01 2.74
99 100 0.320697 ACGGCACCTCCAAGTTCTAC 59.679 55.000 0.00 0.00 34.01 2.59
100 101 1.547372 GTACGGCACCTCCAAGTTCTA 59.453 52.381 0.00 0.00 34.01 2.10
101 102 0.320697 GTACGGCACCTCCAAGTTCT 59.679 55.000 0.00 0.00 34.01 3.01
102 103 1.012486 CGTACGGCACCTCCAAGTTC 61.012 60.000 7.57 0.00 34.01 3.01
103 104 1.005394 CGTACGGCACCTCCAAGTT 60.005 57.895 7.57 0.00 34.01 2.66
104 105 1.751349 AACGTACGGCACCTCCAAGT 61.751 55.000 21.06 0.00 34.01 3.16
105 106 1.005394 AACGTACGGCACCTCCAAG 60.005 57.895 21.06 0.00 34.01 3.61
106 107 1.005867 GAACGTACGGCACCTCCAA 60.006 57.895 21.06 0.00 34.01 3.53
107 108 2.652530 GAACGTACGGCACCTCCA 59.347 61.111 21.06 0.00 34.01 3.86
108 109 2.505557 CGAACGTACGGCACCTCC 60.506 66.667 21.06 0.00 0.00 4.30
109 110 2.505557 CCGAACGTACGGCACCTC 60.506 66.667 21.06 6.84 46.20 3.85
117 118 2.159517 ACCGATCAAGTACCGAACGTAC 60.160 50.000 10.35 0.00 46.69 3.67
118 119 2.083774 ACCGATCAAGTACCGAACGTA 58.916 47.619 10.35 0.00 0.00 3.57
119 120 0.883833 ACCGATCAAGTACCGAACGT 59.116 50.000 10.35 0.00 0.00 3.99
120 121 1.135603 TGACCGATCAAGTACCGAACG 60.136 52.381 5.81 5.81 0.00 3.95
121 122 2.163010 TCTGACCGATCAAGTACCGAAC 59.837 50.000 0.00 0.00 33.30 3.95
122 123 2.439409 TCTGACCGATCAAGTACCGAA 58.561 47.619 0.00 0.00 33.30 4.30
123 124 2.118313 TCTGACCGATCAAGTACCGA 57.882 50.000 0.00 0.00 33.30 4.69
124 125 3.001395 GATCTGACCGATCAAGTACCG 57.999 52.381 2.27 0.00 46.35 4.02
132 133 2.722071 GTCTTCACGATCTGACCGATC 58.278 52.381 0.00 0.00 44.16 3.69
133 134 2.853731 GTCTTCACGATCTGACCGAT 57.146 50.000 0.00 0.00 34.25 4.18
145 146 4.332186 TGATGTAGTCGTACGTCTTCAC 57.668 45.455 19.61 13.19 43.23 3.18
146 147 4.378770 GGTTGATGTAGTCGTACGTCTTCA 60.379 45.833 19.61 19.79 43.23 3.02
147 148 4.094212 GGTTGATGTAGTCGTACGTCTTC 58.906 47.826 19.61 15.02 43.23 2.87
148 149 3.425359 CGGTTGATGTAGTCGTACGTCTT 60.425 47.826 19.61 2.66 43.23 3.01
149 150 2.094894 CGGTTGATGTAGTCGTACGTCT 59.905 50.000 18.54 18.54 43.23 4.18
150 151 2.434761 CGGTTGATGTAGTCGTACGTC 58.565 52.381 16.05 10.06 43.16 4.34
151 152 1.466360 GCGGTTGATGTAGTCGTACGT 60.466 52.381 16.05 0.00 30.95 3.57
152 153 1.186030 GCGGTTGATGTAGTCGTACG 58.814 55.000 9.53 9.53 30.95 3.67
153 154 1.186030 CGCGGTTGATGTAGTCGTAC 58.814 55.000 0.00 0.00 0.00 3.67
154 155 0.804364 ACGCGGTTGATGTAGTCGTA 59.196 50.000 12.47 0.00 0.00 3.43
155 156 0.038892 AACGCGGTTGATGTAGTCGT 60.039 50.000 12.47 0.00 0.00 4.34
156 157 0.365523 CAACGCGGTTGATGTAGTCG 59.634 55.000 12.47 0.00 45.28 4.18
157 158 1.126113 CACAACGCGGTTGATGTAGTC 59.874 52.381 22.26 0.00 45.28 2.59
158 159 1.144969 CACAACGCGGTTGATGTAGT 58.855 50.000 22.26 2.04 45.28 2.73
159 160 1.424403 TCACAACGCGGTTGATGTAG 58.576 50.000 22.26 1.41 45.28 2.74
160 161 2.087501 ATCACAACGCGGTTGATGTA 57.912 45.000 22.26 9.09 45.28 2.29
161 162 2.087501 TATCACAACGCGGTTGATGT 57.912 45.000 23.23 12.81 45.28 3.06
162 163 2.769376 GTTATCACAACGCGGTTGATG 58.231 47.619 23.23 17.53 45.28 3.07
163 164 1.392168 CGTTATCACAACGCGGTTGAT 59.608 47.619 22.26 21.20 45.28 2.57
164 165 0.785378 CGTTATCACAACGCGGTTGA 59.215 50.000 22.26 16.83 45.28 3.18
171 172 3.850207 CGGAAGCGTTATCACAACG 57.150 52.632 5.22 5.22 45.56 4.10
188 189 2.403987 CCTCGTAGACCGACAGCG 59.596 66.667 0.00 0.00 41.60 5.18
189 190 0.745845 TACCCTCGTAGACCGACAGC 60.746 60.000 0.00 0.00 41.60 4.40
190 191 1.012841 GTACCCTCGTAGACCGACAG 58.987 60.000 0.00 0.00 41.60 3.51
191 192 0.740868 CGTACCCTCGTAGACCGACA 60.741 60.000 0.00 0.00 41.60 4.35
192 193 0.741221 ACGTACCCTCGTAGACCGAC 60.741 60.000 0.00 0.00 41.60 4.79
193 194 0.740868 CACGTACCCTCGTAGACCGA 60.741 60.000 0.00 0.00 45.00 4.69
194 195 1.709147 CCACGTACCCTCGTAGACCG 61.709 65.000 0.00 0.00 42.27 4.79
195 196 1.379642 CCCACGTACCCTCGTAGACC 61.380 65.000 0.00 0.00 42.27 3.85
196 197 1.997928 GCCCACGTACCCTCGTAGAC 61.998 65.000 0.00 0.00 42.27 2.59
197 198 1.750399 GCCCACGTACCCTCGTAGA 60.750 63.158 0.00 0.00 42.27 2.59
198 199 1.597797 TTGCCCACGTACCCTCGTAG 61.598 60.000 0.00 0.00 42.27 3.51
199 200 1.606025 TTGCCCACGTACCCTCGTA 60.606 57.895 0.00 0.00 42.27 3.43
200 201 2.918802 TTGCCCACGTACCCTCGT 60.919 61.111 0.00 0.00 45.10 4.18
201 202 2.433664 GTTGCCCACGTACCCTCG 60.434 66.667 0.00 0.00 0.00 4.63
202 203 1.670083 GTGTTGCCCACGTACCCTC 60.670 63.158 0.00 0.00 33.61 4.30
203 204 2.428622 GTGTTGCCCACGTACCCT 59.571 61.111 0.00 0.00 33.61 4.34
213 214 1.599576 GAGAGGGGAGAGTGTTGCC 59.400 63.158 0.00 0.00 0.00 4.52
214 215 1.216710 CGAGAGGGGAGAGTGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
215 216 0.969894 AACGAGAGGGGAGAGTGTTG 59.030 55.000 0.00 0.00 0.00 3.33
216 217 0.969894 CAACGAGAGGGGAGAGTGTT 59.030 55.000 0.00 0.00 0.00 3.32
217 218 1.536943 GCAACGAGAGGGGAGAGTGT 61.537 60.000 0.00 0.00 0.00 3.55
218 219 1.216710 GCAACGAGAGGGGAGAGTG 59.783 63.158 0.00 0.00 0.00 3.51
219 220 0.331954 TAGCAACGAGAGGGGAGAGT 59.668 55.000 0.00 0.00 0.00 3.24
220 221 1.339610 CATAGCAACGAGAGGGGAGAG 59.660 57.143 0.00 0.00 0.00 3.20
221 222 1.403814 CATAGCAACGAGAGGGGAGA 58.596 55.000 0.00 0.00 0.00 3.71
222 223 0.249657 GCATAGCAACGAGAGGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
223 224 0.975556 TGCATAGCAACGAGAGGGGA 60.976 55.000 0.00 0.00 34.76 4.81
224 225 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
225 226 1.202568 TGATGCATAGCAACGAGAGGG 60.203 52.381 0.00 0.00 43.62 4.30
226 227 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
227 228 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
228 229 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
229 230 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
230 231 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
231 232 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
232 233 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
233 234 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
234 235 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
235 236 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
236 237 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
237 238 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
238 239 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
239 240 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
240 241 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
241 242 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
242 243 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
243 244 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
244 245 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
245 246 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
246 247 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
247 248 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
248 249 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
249 250 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
250 251 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
251 252 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
252 253 0.037697 ATTCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
253 254 0.796312 AATTCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
254 255 1.231221 AAATTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
255 256 1.231221 AAAATTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
256 257 2.325509 AAAAATTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
273 274 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
274 275 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
275 276 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
276 277 5.239087 GTGTTGGGGAACGTAGTAATTTCAA 59.761 40.000 0.00 0.00 45.00 2.69
277 278 4.756135 GTGTTGGGGAACGTAGTAATTTCA 59.244 41.667 0.00 0.00 45.00 2.69
278 279 4.154737 GGTGTTGGGGAACGTAGTAATTTC 59.845 45.833 0.00 0.00 45.00 2.17
279 280 4.074259 GGTGTTGGGGAACGTAGTAATTT 58.926 43.478 0.00 0.00 45.00 1.82
280 281 3.072768 TGGTGTTGGGGAACGTAGTAATT 59.927 43.478 0.00 0.00 45.00 1.40
281 282 2.638855 TGGTGTTGGGGAACGTAGTAAT 59.361 45.455 0.00 0.00 45.00 1.89
282 283 2.045524 TGGTGTTGGGGAACGTAGTAA 58.954 47.619 0.00 0.00 45.00 2.24
283 284 1.344114 GTGGTGTTGGGGAACGTAGTA 59.656 52.381 0.00 0.00 45.00 1.82
285 286 0.604511 GGTGGTGTTGGGGAACGTAG 60.605 60.000 0.00 0.00 0.00 3.51
286 287 1.451072 GGTGGTGTTGGGGAACGTA 59.549 57.895 0.00 0.00 0.00 3.57
287 288 2.193786 GGTGGTGTTGGGGAACGT 59.806 61.111 0.00 0.00 0.00 3.99
288 289 2.975799 CGGTGGTGTTGGGGAACG 60.976 66.667 0.00 0.00 0.00 3.95
289 290 2.596338 CCGGTGGTGTTGGGGAAC 60.596 66.667 0.00 0.00 0.00 3.62
290 291 4.589675 GCCGGTGGTGTTGGGGAA 62.590 66.667 1.90 0.00 0.00 3.97
386 387 3.890313 TGCTGAGGCAGTGGAAGA 58.110 55.556 0.00 0.00 44.28 2.87
745 783 3.017581 GATGGACAGGGGGCTGGT 61.018 66.667 0.00 0.00 0.00 4.00
769 807 1.446099 GCAACTGCTCGTCGATGGA 60.446 57.895 4.48 0.00 38.21 3.41
1025 1064 1.822186 TCGCCGATGATCTCCGTCA 60.822 57.895 0.00 0.00 0.00 4.35
1145 1184 2.089017 CGCCAAATGATGCGTCTGA 58.911 52.632 7.58 0.00 45.43 3.27
1533 1844 2.345244 CCAGCAGCGTGTCCTTCT 59.655 61.111 0.00 0.00 0.00 2.85
1608 1921 1.452108 GGGGTTCTGCTGCGCTTAT 60.452 57.895 9.73 0.00 0.00 1.73
1706 2024 4.680537 AGGAGTCAGGGACGGCGT 62.681 66.667 14.65 14.65 37.67 5.68
1716 2034 1.229209 GGTGGTGGAGGAGGAGTCA 60.229 63.158 0.00 0.00 0.00 3.41
1908 2232 2.048127 GAAGAGCGTTGACGGGCT 60.048 61.111 5.62 0.00 43.42 5.19
1924 2248 3.557903 GACCTTGCTGCCAGCCTGA 62.558 63.158 15.29 0.00 41.51 3.86
2210 2895 1.674322 GCGTAATGTGGCCCACTGT 60.674 57.895 16.23 5.26 35.11 3.55
2223 2908 0.107312 AGCTCCTAGACGAGGCGTAA 60.107 55.000 0.00 0.00 46.25 3.18
2225 2910 1.820481 GAGCTCCTAGACGAGGCGT 60.820 63.158 0.87 0.00 46.25 5.68
2235 2920 1.146485 CGAGGACTCCGAGCTCCTA 59.854 63.158 8.47 0.00 37.00 2.94
2264 2949 2.029288 CGCCTTGACTGTCATGCGT 61.029 57.895 30.62 0.00 40.65 5.24
2320 3005 0.659417 GCAGTTGACGTCGTCTTCGA 60.659 55.000 24.75 2.94 44.12 3.71


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

AutoCloner maintained by Alex Coulton.