Multiple sequence alignment - TraesCS3D01G173300

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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 TraesCS3D01G173300 chr3D 100.000 4495 0 0 1 4495 154183152 154178658 0.000000e+00 8301.0
1 TraesCS3D01G173300 chr3D 89.557 699 64 6 3799 4495 484630235 484630926 0.000000e+00 878.0
2 TraesCS3D01G173300 chr3A 93.616 3650 118 49 212 3798 172967018 172963421 0.000000e+00 5343.0
3 TraesCS3D01G173300 chr3A 89.828 698 59 8 3800 4495 14684820 14684133 0.000000e+00 885.0
4 TraesCS3D01G173300 chr3B 93.094 2505 87 32 201 2670 226786360 226788813 0.000000e+00 3589.0
5 TraesCS3D01G173300 chr3B 96.400 1139 33 6 2665 3798 226789090 226790225 0.000000e+00 1869.0
6 TraesCS3D01G173300 chr3B 88.000 700 74 7 3798 4495 815184899 815184208 0.000000e+00 819.0
7 TraesCS3D01G173300 chr4B 91.323 703 53 7 3795 4495 273247526 273248222 0.000000e+00 953.0
8 TraesCS3D01G173300 chr7D 90.116 688 60 8 3803 4488 215099947 215099266 0.000000e+00 887.0
9 TraesCS3D01G173300 chr7D 88.666 697 60 11 3802 4495 88077251 88076571 0.000000e+00 832.0
10 TraesCS3D01G173300 chr7D 92.093 215 13 4 1 211 7470988 7470774 2.630000e-77 300.0
11 TraesCS3D01G173300 chr2B 89.586 701 62 9 3797 4495 101158021 101157330 0.000000e+00 880.0
12 TraesCS3D01G173300 chr2B 91.981 212 13 2 1 208 435354764 435354975 1.220000e-75 294.0
13 TraesCS3D01G173300 chr2B 91.981 212 13 2 1 208 435373733 435373944 1.220000e-75 294.0
14 TraesCS3D01G173300 chr1D 89.255 698 58 13 3802 4495 489983981 489983297 0.000000e+00 857.0
15 TraesCS3D01G173300 chr1A 88.136 708 70 12 3791 4495 22647947 22647251 0.000000e+00 830.0
16 TraesCS3D01G173300 chr5D 92.891 211 11 2 1 207 19111244 19111034 2.030000e-78 303.0
17 TraesCS3D01G173300 chr5D 93.171 205 10 2 1 201 478503871 478504075 9.450000e-77 298.0
18 TraesCS3D01G173300 chr5B 93.204 206 11 3 2 204 254349320 254349115 2.630000e-77 300.0
19 TraesCS3D01G173300 chr5B 91.981 212 13 3 1 208 517190146 517190357 1.220000e-75 294.0
20 TraesCS3D01G173300 chr7B 91.981 212 13 2 1 208 23310768 23310557 1.220000e-75 294.0
21 TraesCS3D01G173300 chr7B 91.284 218 14 4 1 213 540160616 540160399 4.400000e-75 292.0
22 TraesCS3D01G173300 chr6D 91.781 73 4 2 2818 2889 415027746 415027675 2.860000e-17 100.0
23 TraesCS3D01G173300 chr6B 90.411 73 5 2 2818 2889 625779386 625779315 1.330000e-15 95.3
24 TraesCS3D01G173300 chr6A 89.041 73 6 2 2818 2889 560032829 560032758 6.190000e-14 89.8


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 TraesCS3D01G173300 chr3D 154178658 154183152 4494 True 8301 8301 100.000 1 4495 1 chr3D.!!$R1 4494
1 TraesCS3D01G173300 chr3D 484630235 484630926 691 False 878 878 89.557 3799 4495 1 chr3D.!!$F1 696
2 TraesCS3D01G173300 chr3A 172963421 172967018 3597 True 5343 5343 93.616 212 3798 1 chr3A.!!$R2 3586
3 TraesCS3D01G173300 chr3A 14684133 14684820 687 True 885 885 89.828 3800 4495 1 chr3A.!!$R1 695
4 TraesCS3D01G173300 chr3B 226786360 226790225 3865 False 2729 3589 94.747 201 3798 2 chr3B.!!$F1 3597
5 TraesCS3D01G173300 chr3B 815184208 815184899 691 True 819 819 88.000 3798 4495 1 chr3B.!!$R1 697
6 TraesCS3D01G173300 chr4B 273247526 273248222 696 False 953 953 91.323 3795 4495 1 chr4B.!!$F1 700
7 TraesCS3D01G173300 chr7D 215099266 215099947 681 True 887 887 90.116 3803 4488 1 chr7D.!!$R3 685
8 TraesCS3D01G173300 chr7D 88076571 88077251 680 True 832 832 88.666 3802 4495 1 chr7D.!!$R2 693
9 TraesCS3D01G173300 chr2B 101157330 101158021 691 True 880 880 89.586 3797 4495 1 chr2B.!!$R1 698
10 TraesCS3D01G173300 chr1D 489983297 489983981 684 True 857 857 89.255 3802 4495 1 chr1D.!!$R1 693
11 TraesCS3D01G173300 chr1A 22647251 22647947 696 True 830 830 88.136 3791 4495 1 chr1A.!!$R1 704

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
558 570 0.108662 GCCTGGTAGCAAATGTTGGC 60.109 55.0 5.04 5.04 0.0 4.52 F
2434 2498 0.108041 GTTCCGAAGCCCCGATTGTA 60.108 55.0 0.00 0.00 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2522 2589 0.037139 AGCCATGCACGTACGGTAAA 60.037 50.0 21.06 2.3 0.0 2.01 R
3840 4205 0.108186 GTGATGATGGAGGCGTGTGA 60.108 55.0 0.00 0.0 0.0 3.58 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 3.144285 CCATGCATCCATTGGCCC 58.856 61.111 0.00 0.00 0.00 5.80
18 19 2.732016 CATGCATCCATTGGCCCG 59.268 61.111 0.00 0.00 0.00 6.13
19 20 3.228759 ATGCATCCATTGGCCCGC 61.229 61.111 0.00 0.90 0.00 6.13
39 40 3.935371 ACCCCATGGTGTTGTTTGA 57.065 47.368 11.73 0.00 45.58 2.69
40 41 2.397044 ACCCCATGGTGTTGTTTGAT 57.603 45.000 11.73 0.00 45.58 2.57
41 42 2.688477 ACCCCATGGTGTTGTTTGATT 58.312 42.857 11.73 0.00 45.58 2.57
42 43 2.368221 ACCCCATGGTGTTGTTTGATTG 59.632 45.455 11.73 0.00 45.58 2.67
43 44 2.368221 CCCCATGGTGTTGTTTGATTGT 59.632 45.455 11.73 0.00 0.00 2.71
44 45 3.181456 CCCCATGGTGTTGTTTGATTGTT 60.181 43.478 11.73 0.00 0.00 2.83
45 46 4.450053 CCCATGGTGTTGTTTGATTGTTT 58.550 39.130 11.73 0.00 0.00 2.83
46 47 4.880696 CCCATGGTGTTGTTTGATTGTTTT 59.119 37.500 11.73 0.00 0.00 2.43
47 48 5.356470 CCCATGGTGTTGTTTGATTGTTTTT 59.644 36.000 11.73 0.00 0.00 1.94
70 71 7.399245 TTTTTATACTAAGGGCAACATGGTC 57.601 36.000 0.00 0.00 39.74 4.02
71 72 5.702065 TTATACTAAGGGCAACATGGTCA 57.298 39.130 0.00 0.00 39.74 4.02
72 73 4.796110 ATACTAAGGGCAACATGGTCAT 57.204 40.909 0.00 0.00 39.74 3.06
73 74 3.456380 ACTAAGGGCAACATGGTCATT 57.544 42.857 0.00 0.00 39.74 2.57
74 75 3.778265 ACTAAGGGCAACATGGTCATTT 58.222 40.909 0.00 0.00 39.74 2.32
75 76 4.929479 ACTAAGGGCAACATGGTCATTTA 58.071 39.130 0.00 0.00 39.74 1.40
76 77 5.329399 ACTAAGGGCAACATGGTCATTTAA 58.671 37.500 0.00 0.00 39.74 1.52
77 78 5.957774 ACTAAGGGCAACATGGTCATTTAAT 59.042 36.000 0.00 0.00 39.74 1.40
78 79 7.122715 ACTAAGGGCAACATGGTCATTTAATA 58.877 34.615 0.00 0.00 39.74 0.98
79 80 6.865834 AAGGGCAACATGGTCATTTAATAA 57.134 33.333 0.00 0.00 39.74 1.40
80 81 6.220726 AGGGCAACATGGTCATTTAATAAC 57.779 37.500 0.00 0.00 39.74 1.89
81 82 5.128663 AGGGCAACATGGTCATTTAATAACC 59.871 40.000 0.00 0.00 39.74 2.85
82 83 5.128663 GGGCAACATGGTCATTTAATAACCT 59.871 40.000 0.00 0.00 39.74 3.50
83 84 6.351796 GGGCAACATGGTCATTTAATAACCTT 60.352 38.462 0.00 0.00 39.74 3.50
84 85 7.102993 GGCAACATGGTCATTTAATAACCTTT 58.897 34.615 0.00 0.00 34.05 3.11
85 86 8.254508 GGCAACATGGTCATTTAATAACCTTTA 58.745 33.333 0.00 0.00 34.05 1.85
86 87 9.301153 GCAACATGGTCATTTAATAACCTTTAG 57.699 33.333 0.00 0.00 34.05 1.85
100 101 3.416414 CCTTTAGAAGGGGACTAGGGA 57.584 52.381 0.00 0.00 45.27 4.20
101 102 3.039743 CCTTTAGAAGGGGACTAGGGAC 58.960 54.545 0.00 0.00 45.27 4.46
102 103 3.310731 CCTTTAGAAGGGGACTAGGGACT 60.311 52.174 0.00 0.00 45.27 3.85
103 104 4.363573 CTTTAGAAGGGGACTAGGGACTT 58.636 47.826 0.00 0.00 42.68 3.01
104 105 4.431158 TTAGAAGGGGACTAGGGACTTT 57.569 45.455 0.00 0.00 42.68 2.66
105 106 3.293215 AGAAGGGGACTAGGGACTTTT 57.707 47.619 0.00 0.00 42.68 2.27
106 107 3.610260 AGAAGGGGACTAGGGACTTTTT 58.390 45.455 0.00 0.00 42.68 1.94
107 108 4.771338 AGAAGGGGACTAGGGACTTTTTA 58.229 43.478 0.00 0.00 42.68 1.52
108 109 4.783763 AGAAGGGGACTAGGGACTTTTTAG 59.216 45.833 0.00 0.00 42.68 1.85
109 110 4.157668 AGGGGACTAGGGACTTTTTAGT 57.842 45.455 0.00 0.00 41.75 2.24
110 111 4.102598 AGGGGACTAGGGACTTTTTAGTC 58.897 47.826 0.00 3.01 41.49 2.59
111 112 4.102598 GGGGACTAGGGACTTTTTAGTCT 58.897 47.826 9.84 0.00 41.77 3.24
112 113 4.161942 GGGGACTAGGGACTTTTTAGTCTC 59.838 50.000 9.84 6.55 41.87 3.36
120 121 6.659824 AGGGACTTTTTAGTCTCTGAAAACA 58.340 36.000 6.89 0.00 46.88 2.83
121 122 7.116736 AGGGACTTTTTAGTCTCTGAAAACAA 58.883 34.615 6.89 0.00 46.88 2.83
122 123 7.614192 AGGGACTTTTTAGTCTCTGAAAACAAA 59.386 33.333 6.89 0.00 46.88 2.83
123 124 7.915923 GGGACTTTTTAGTCTCTGAAAACAAAG 59.084 37.037 5.40 0.00 36.42 2.77
124 125 8.674607 GGACTTTTTAGTCTCTGAAAACAAAGA 58.325 33.333 5.40 0.00 38.74 2.52
125 126 9.709600 GACTTTTTAGTCTCTGAAAACAAAGAG 57.290 33.333 0.00 0.00 41.13 2.85
126 127 8.678199 ACTTTTTAGTCTCTGAAAACAAAGAGG 58.322 33.333 0.00 0.00 40.34 3.69
127 128 8.801882 TTTTTAGTCTCTGAAAACAAAGAGGA 57.198 30.769 0.00 0.00 40.34 3.71
128 129 8.801882 TTTTAGTCTCTGAAAACAAAGAGGAA 57.198 30.769 0.00 0.00 40.34 3.36
129 130 8.438676 TTTAGTCTCTGAAAACAAAGAGGAAG 57.561 34.615 0.00 0.00 40.34 3.46
130 131 5.372373 AGTCTCTGAAAACAAAGAGGAAGG 58.628 41.667 0.00 0.00 40.34 3.46
131 132 4.517075 GTCTCTGAAAACAAAGAGGAAGGG 59.483 45.833 0.00 0.00 40.34 3.95
132 133 4.412199 TCTCTGAAAACAAAGAGGAAGGGA 59.588 41.667 0.00 0.00 40.34 4.20
133 134 4.461198 TCTGAAAACAAAGAGGAAGGGAC 58.539 43.478 0.00 0.00 0.00 4.46
134 135 5.688766 CTCTGAAAACAAAGAGGAAGGGACT 60.689 44.000 0.00 0.00 37.27 3.85
135 136 7.137666 CTCTGAAAACAAAGAGGAAGGGACTT 61.138 42.308 0.00 0.00 40.71 3.01
136 137 8.553276 CTCTGAAAACAAAGAGGAAGGGACTTT 61.553 40.741 0.00 0.00 40.28 2.66
149 150 3.461824 AGGGACTTTTTAGGGACTAGGG 58.538 50.000 0.00 0.00 37.71 3.53
150 151 3.080153 AGGGACTTTTTAGGGACTAGGGA 59.920 47.826 0.00 0.00 37.71 4.20
151 152 3.199508 GGGACTTTTTAGGGACTAGGGAC 59.800 52.174 0.00 0.00 44.25 4.46
152 153 4.102598 GGACTTTTTAGGGACTAGGGACT 58.897 47.826 0.00 0.00 44.25 3.85
153 154 4.535294 GGACTTTTTAGGGACTAGGGACTT 59.465 45.833 0.00 0.00 44.25 3.01
154 155 5.013913 GGACTTTTTAGGGACTAGGGACTTT 59.986 44.000 0.00 0.00 44.25 2.66
155 156 6.466904 GGACTTTTTAGGGACTAGGGACTTTT 60.467 42.308 0.00 0.00 44.25 2.27
156 157 6.919158 ACTTTTTAGGGACTAGGGACTTTTT 58.081 36.000 0.00 0.00 44.25 1.94
157 158 8.049165 ACTTTTTAGGGACTAGGGACTTTTTA 57.951 34.615 0.00 0.00 44.25 1.52
158 159 8.162085 ACTTTTTAGGGACTAGGGACTTTTTAG 58.838 37.037 0.00 0.00 44.25 1.85
159 160 7.637548 TTTTAGGGACTAGGGACTTTTTAGT 57.362 36.000 0.00 0.00 44.25 2.24
160 161 7.637548 TTTAGGGACTAGGGACTTTTTAGTT 57.362 36.000 0.00 0.00 44.25 2.24
161 162 5.500546 AGGGACTAGGGACTTTTTAGTTG 57.499 43.478 0.00 0.00 41.75 3.16
162 163 4.288887 AGGGACTAGGGACTTTTTAGTTGG 59.711 45.833 0.00 0.00 41.75 3.77
163 164 4.567116 GGGACTAGGGACTTTTTAGTTGGG 60.567 50.000 0.00 0.00 41.75 4.12
164 165 4.287845 GGACTAGGGACTTTTTAGTTGGGA 59.712 45.833 0.00 0.00 41.75 4.37
165 166 5.045066 GGACTAGGGACTTTTTAGTTGGGAT 60.045 44.000 0.00 0.00 41.75 3.85
166 167 6.464530 ACTAGGGACTTTTTAGTTGGGATT 57.535 37.500 0.00 0.00 41.75 3.01
167 168 7.311486 GGACTAGGGACTTTTTAGTTGGGATTA 60.311 40.741 0.00 0.00 41.75 1.75
168 169 7.631007 ACTAGGGACTTTTTAGTTGGGATTAG 58.369 38.462 0.00 0.00 41.75 1.73
169 170 6.713731 AGGGACTTTTTAGTTGGGATTAGA 57.286 37.500 0.00 0.00 27.25 2.10
170 171 7.098845 AGGGACTTTTTAGTTGGGATTAGAA 57.901 36.000 0.00 0.00 27.25 2.10
171 172 7.532199 AGGGACTTTTTAGTTGGGATTAGAAA 58.468 34.615 0.00 0.00 27.25 2.52
172 173 8.008332 AGGGACTTTTTAGTTGGGATTAGAAAA 58.992 33.333 0.00 0.00 27.25 2.29
173 174 8.644216 GGGACTTTTTAGTTGGGATTAGAAAAA 58.356 33.333 0.00 0.00 0.00 1.94
174 175 9.692749 GGACTTTTTAGTTGGGATTAGAAAAAG 57.307 33.333 13.35 13.35 44.04 2.27
181 182 9.734984 TTAGTTGGGATTAGAAAAAGTCTTAGG 57.265 33.333 0.00 0.00 37.84 2.69
182 183 7.985589 AGTTGGGATTAGAAAAAGTCTTAGGA 58.014 34.615 0.00 0.00 37.84 2.94
183 184 7.883833 AGTTGGGATTAGAAAAAGTCTTAGGAC 59.116 37.037 0.00 0.00 42.41 3.85
199 200 8.705048 GTCTTAGGACTTATGAACTAAACAGG 57.295 38.462 0.00 0.00 39.24 4.00
202 203 6.051179 AGGACTTATGAACTAAACAGGGTC 57.949 41.667 0.00 0.00 0.00 4.46
208 209 8.657712 ACTTATGAACTAAACAGGGTCTTAGTT 58.342 33.333 6.87 6.87 46.18 2.24
239 240 0.603439 TGCTCCGTACCGTTTTTCCC 60.603 55.000 0.00 0.00 0.00 3.97
248 249 4.438472 CGTACCGTTTTTCCCTTTTGTTGA 60.438 41.667 0.00 0.00 0.00 3.18
279 280 2.505819 TCTAATGGGAGGAACCTTCTGC 59.494 50.000 0.00 0.00 38.98 4.26
343 344 9.118300 ACCTCAATATTCTTTCTCAATAGCAAG 57.882 33.333 0.00 0.00 0.00 4.01
363 371 4.739046 AGAGAGAATTGCTCAACAAACG 57.261 40.909 7.45 0.00 46.45 3.60
369 377 5.273944 AGAATTGCTCAACAAACGAAAGAC 58.726 37.500 0.00 0.00 42.86 3.01
384 392 3.217626 GAAAGACAAGAGGCCCCATATG 58.782 50.000 0.00 0.00 0.00 1.78
407 415 4.094887 GTGTGCACAACAAAAGAGAAGAGA 59.905 41.667 23.59 0.00 41.57 3.10
408 416 4.699735 TGTGCACAACAAAAGAGAAGAGAA 59.300 37.500 19.28 0.00 35.24 2.87
415 423 5.066913 ACAAAAGAGAAGAGAACCCCATT 57.933 39.130 0.00 0.00 0.00 3.16
520 532 9.531158 GGGTTTGATAGACCATACTATACTAGT 57.469 37.037 0.00 0.00 39.58 2.57
558 570 0.108662 GCCTGGTAGCAAATGTTGGC 60.109 55.000 5.04 5.04 0.00 4.52
564 576 5.132897 TGGTAGCAAATGTTGGCTAAAAG 57.867 39.130 3.50 0.00 43.61 2.27
610 623 1.914634 TTGCGAAAATGTGCGTGTTT 58.085 40.000 0.00 0.00 0.00 2.83
710 732 1.497722 GAAAAAGGAGACGCAGCGG 59.502 57.895 21.15 0.70 0.00 5.52
711 733 0.949105 GAAAAAGGAGACGCAGCGGA 60.949 55.000 21.15 0.00 0.00 5.54
712 734 0.951040 AAAAAGGAGACGCAGCGGAG 60.951 55.000 21.15 0.00 0.00 4.63
1545 1577 7.004086 TCTTCTTCCTTCTTAAATGGCAAGAA 58.996 34.615 0.00 0.00 39.18 2.52
1734 1792 7.232737 ACGTAGTTATCCATGATCTGTCCATAA 59.767 37.037 0.00 0.00 37.78 1.90
1762 1820 1.891178 TCTCGTCGATTAGCGTTGTG 58.109 50.000 0.00 0.00 41.80 3.33
1806 1864 1.660607 CCGGTGATGTTTGACTCGATG 59.339 52.381 0.00 0.00 0.00 3.84
1807 1865 2.337583 CGGTGATGTTTGACTCGATGT 58.662 47.619 0.00 0.00 0.00 3.06
1817 1875 7.576750 TGTTTGACTCGATGTGTATTAACTC 57.423 36.000 0.00 0.00 0.00 3.01
1840 1898 4.724602 TGTCGCGTCCTGCAGCTC 62.725 66.667 8.66 2.05 46.97 4.09
1954 2012 1.370535 GATGCATCTCGTCGCGCTA 60.371 57.895 19.70 0.00 0.00 4.26
2005 2063 2.030562 CCGCAACAACCTCCGACT 59.969 61.111 0.00 0.00 0.00 4.18
2008 2066 1.284982 CGCAACAACCTCCGACTCAG 61.285 60.000 0.00 0.00 0.00 3.35
2026 2084 7.215789 CGACTCAGGAGGTACTATTCTTACTA 58.784 42.308 0.83 0.00 41.55 1.82
2031 2089 9.444668 TCAGGAGGTACTATTCTTACTACTCTA 57.555 37.037 0.00 0.00 41.55 2.43
2098 2156 6.003950 ACTGAATCAATTCCTCTTTTTCCGA 58.996 36.000 0.48 0.00 35.97 4.55
2434 2498 0.108041 GTTCCGAAGCCCCGATTGTA 60.108 55.000 0.00 0.00 0.00 2.41
2440 2504 2.100252 CGAAGCCCCGATTGTAAGACTA 59.900 50.000 0.00 0.00 0.00 2.59
2473 2540 9.688592 CTTCTTGATCATTTTCTAGTTTTTGCT 57.311 29.630 0.00 0.00 0.00 3.91
2475 2542 8.017373 TCTTGATCATTTTCTAGTTTTTGCTCG 58.983 33.333 0.00 0.00 0.00 5.03
2476 2543 7.433708 TGATCATTTTCTAGTTTTTGCTCGA 57.566 32.000 0.00 0.00 0.00 4.04
2477 2544 7.870826 TGATCATTTTCTAGTTTTTGCTCGAA 58.129 30.769 0.00 0.00 0.00 3.71
2479 2546 6.133392 TCATTTTCTAGTTTTTGCTCGAACG 58.867 36.000 0.00 0.00 0.00 3.95
2480 2547 4.461992 TTTCTAGTTTTTGCTCGAACGG 57.538 40.909 0.00 0.00 0.00 4.44
2481 2548 3.374220 TCTAGTTTTTGCTCGAACGGA 57.626 42.857 0.00 0.00 0.00 4.69
2482 2549 3.314553 TCTAGTTTTTGCTCGAACGGAG 58.685 45.455 0.00 0.00 46.06 4.63
2483 2550 2.234300 AGTTTTTGCTCGAACGGAGA 57.766 45.000 0.00 0.00 46.23 3.71
2484 2551 1.865340 AGTTTTTGCTCGAACGGAGAC 59.135 47.619 0.00 0.00 46.23 3.36
2485 2552 1.595794 GTTTTTGCTCGAACGGAGACA 59.404 47.619 0.00 0.00 46.23 3.41
2486 2553 1.214367 TTTTGCTCGAACGGAGACAC 58.786 50.000 0.00 0.00 46.23 3.67
2488 2555 2.504244 GCTCGAACGGAGACACGG 60.504 66.667 0.00 0.00 46.23 4.94
2489 2556 2.178521 CTCGAACGGAGACACGGG 59.821 66.667 0.00 0.00 46.23 5.28
2490 2557 3.966026 CTCGAACGGAGACACGGGC 62.966 68.421 0.00 0.00 46.23 6.13
2492 2559 3.692406 GAACGGAGACACGGGCCT 61.692 66.667 0.84 0.00 38.39 5.19
2493 2560 3.236003 GAACGGAGACACGGGCCTT 62.236 63.158 0.84 0.00 38.39 4.35
2494 2561 3.530910 AACGGAGACACGGGCCTTG 62.531 63.158 8.71 8.71 38.39 3.61
2495 2562 3.691342 CGGAGACACGGGCCTTGA 61.691 66.667 17.93 0.00 0.00 3.02
2496 2563 2.266055 GGAGACACGGGCCTTGAG 59.734 66.667 17.93 0.00 0.00 3.02
2497 2564 2.584391 GGAGACACGGGCCTTGAGT 61.584 63.158 17.93 2.67 0.00 3.41
2498 2565 1.079750 GAGACACGGGCCTTGAGTC 60.080 63.158 17.93 14.79 0.00 3.36
2522 2589 3.592898 TGTGTATGAATCGTGCTGACT 57.407 42.857 0.00 0.00 0.00 3.41
3059 3409 4.778415 CTCGACCTCACCCACGCG 62.778 72.222 3.53 3.53 0.00 6.01
3344 3694 3.047877 CCGAACTTCACCGTGGCC 61.048 66.667 0.00 0.00 0.00 5.36
3437 3787 5.652994 ACAACAACACCAGTAACAACAAT 57.347 34.783 0.00 0.00 0.00 2.71
3442 3792 5.359576 ACAACACCAGTAACAACAATGTGAT 59.640 36.000 0.00 0.00 40.46 3.06
3496 3846 2.086869 CAACAGCGAGACCCAATGAAT 58.913 47.619 0.00 0.00 0.00 2.57
3516 3866 0.536460 GGCCTGGTCAAGTTCGGAAA 60.536 55.000 0.00 0.00 0.00 3.13
3557 3910 5.422214 AGCTAGGTTGCAAGTTATACACT 57.578 39.130 0.00 0.00 37.30 3.55
3605 3958 3.065648 AGGATTAGCTTCTCGAGACGTTC 59.934 47.826 16.36 9.22 0.00 3.95
3643 3996 4.563374 CCAAGCATGATATACGATCACCCA 60.563 45.833 0.00 0.00 0.00 4.51
3711 4068 7.448777 AGTTCATTCCTTCCCTTAGTTCTTTTC 59.551 37.037 0.00 0.00 0.00 2.29
3712 4069 7.091533 TCATTCCTTCCCTTAGTTCTTTTCT 57.908 36.000 0.00 0.00 0.00 2.52
3713 4070 7.168905 TCATTCCTTCCCTTAGTTCTTTTCTC 58.831 38.462 0.00 0.00 0.00 2.87
3814 4179 2.327568 TCTACGGAAAAACTAACGCCG 58.672 47.619 0.00 0.00 46.83 6.46
3834 4199 2.904866 ACGTGTGGGCGTTTGCAT 60.905 55.556 0.00 0.00 43.04 3.96
3879 4244 4.517075 TCACTCATTTTGCCACGTATGAAA 59.483 37.500 0.00 0.00 0.00 2.69
3999 4365 7.834068 TTCATCTGGACGAGATCTTTAAAAG 57.166 36.000 0.00 0.00 39.64 2.27
4029 4395 6.016024 CCCCATGTTGATATGTTTCGATGAAT 60.016 38.462 0.00 0.00 0.00 2.57
4064 4432 5.303971 CCCAAAAGTTGCCATGATGTTTAA 58.696 37.500 0.00 0.00 0.00 1.52
4066 4434 6.073112 CCCAAAAGTTGCCATGATGTTTAAAG 60.073 38.462 0.00 0.00 0.00 1.85
4076 4444 6.676950 CCATGATGTTTAAAGTGTAGTTGCA 58.323 36.000 0.00 0.00 0.00 4.08
4232 4601 7.821595 AAGTGCATGTATCATGTCAATTTTG 57.178 32.000 10.68 0.00 0.00 2.44
4233 4602 6.927416 AGTGCATGTATCATGTCAATTTTGT 58.073 32.000 10.68 0.00 0.00 2.83
4236 4605 9.138062 GTGCATGTATCATGTCAATTTTGTTTA 57.862 29.630 10.68 0.00 0.00 2.01
4253 4622 5.528043 TGTTTAATGGTGCATGACAAGTT 57.472 34.783 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.863346 CGGGCCAATGGATGCATGG 61.863 63.158 2.46 0.11 37.29 3.66
22 23 2.368221 ACAATCAAACAACACCATGGGG 59.632 45.455 14.08 14.08 41.29 4.96
23 24 3.749665 ACAATCAAACAACACCATGGG 57.250 42.857 18.09 7.72 0.00 4.00
24 25 6.434018 AAAAACAATCAAACAACACCATGG 57.566 33.333 11.19 11.19 0.00 3.66
46 47 6.948886 TGACCATGTTGCCCTTAGTATAAAAA 59.051 34.615 0.00 0.00 0.00 1.94
47 48 6.486056 TGACCATGTTGCCCTTAGTATAAAA 58.514 36.000 0.00 0.00 0.00 1.52
48 49 6.068461 TGACCATGTTGCCCTTAGTATAAA 57.932 37.500 0.00 0.00 0.00 1.40
49 50 5.702065 TGACCATGTTGCCCTTAGTATAA 57.298 39.130 0.00 0.00 0.00 0.98
50 51 5.904984 ATGACCATGTTGCCCTTAGTATA 57.095 39.130 0.00 0.00 0.00 1.47
51 52 4.796110 ATGACCATGTTGCCCTTAGTAT 57.204 40.909 0.00 0.00 0.00 2.12
52 53 4.584638 AATGACCATGTTGCCCTTAGTA 57.415 40.909 0.00 0.00 0.00 1.82
53 54 3.456380 AATGACCATGTTGCCCTTAGT 57.544 42.857 0.00 0.00 0.00 2.24
54 55 5.913137 TTAAATGACCATGTTGCCCTTAG 57.087 39.130 0.00 0.00 0.00 2.18
55 56 7.147811 GGTTATTAAATGACCATGTTGCCCTTA 60.148 37.037 0.00 0.00 38.68 2.69
56 57 6.351796 GGTTATTAAATGACCATGTTGCCCTT 60.352 38.462 0.00 0.00 38.68 3.95
57 58 5.128663 GGTTATTAAATGACCATGTTGCCCT 59.871 40.000 0.00 0.00 38.68 5.19
58 59 5.128663 AGGTTATTAAATGACCATGTTGCCC 59.871 40.000 6.26 0.00 41.10 5.36
59 60 6.220726 AGGTTATTAAATGACCATGTTGCC 57.779 37.500 6.26 0.00 41.10 4.52
60 61 9.301153 CTAAAGGTTATTAAATGACCATGTTGC 57.699 33.333 6.26 0.00 41.10 4.17
81 82 3.996957 AGTCCCTAGTCCCCTTCTAAAG 58.003 50.000 0.00 0.00 0.00 1.85
82 83 4.431158 AAGTCCCTAGTCCCCTTCTAAA 57.569 45.455 0.00 0.00 0.00 1.85
83 84 4.431158 AAAGTCCCTAGTCCCCTTCTAA 57.569 45.455 0.00 0.00 0.00 2.10
84 85 4.431158 AAAAGTCCCTAGTCCCCTTCTA 57.569 45.455 0.00 0.00 0.00 2.10
85 86 3.293215 AAAAGTCCCTAGTCCCCTTCT 57.707 47.619 0.00 0.00 0.00 2.85
86 87 4.535294 ACTAAAAAGTCCCTAGTCCCCTTC 59.465 45.833 0.00 0.00 0.00 3.46
87 88 4.510312 ACTAAAAAGTCCCTAGTCCCCTT 58.490 43.478 0.00 0.00 0.00 3.95
88 89 4.102598 GACTAAAAAGTCCCTAGTCCCCT 58.897 47.826 0.00 0.00 36.91 4.79
89 90 4.102598 AGACTAAAAAGTCCCTAGTCCCC 58.897 47.826 2.00 0.00 41.59 4.81
90 91 5.024785 AGAGACTAAAAAGTCCCTAGTCCC 58.975 45.833 2.00 0.00 41.59 4.46
91 92 5.715753 TCAGAGACTAAAAAGTCCCTAGTCC 59.284 44.000 2.00 0.00 41.59 3.85
92 93 6.837471 TCAGAGACTAAAAAGTCCCTAGTC 57.163 41.667 2.00 0.00 41.17 2.59
93 94 7.613551 TTTCAGAGACTAAAAAGTCCCTAGT 57.386 36.000 2.00 0.00 39.50 2.57
94 95 7.931948 TGTTTTCAGAGACTAAAAAGTCCCTAG 59.068 37.037 2.00 0.00 39.50 3.02
95 96 7.798071 TGTTTTCAGAGACTAAAAAGTCCCTA 58.202 34.615 2.00 0.00 39.50 3.53
96 97 6.659824 TGTTTTCAGAGACTAAAAAGTCCCT 58.340 36.000 2.00 0.00 39.50 4.20
97 98 6.937436 TGTTTTCAGAGACTAAAAAGTCCC 57.063 37.500 2.00 0.00 39.50 4.46
98 99 8.674607 TCTTTGTTTTCAGAGACTAAAAAGTCC 58.325 33.333 2.00 0.00 36.36 3.85
99 100 9.709600 CTCTTTGTTTTCAGAGACTAAAAAGTC 57.290 33.333 0.00 0.00 36.36 3.01
100 101 8.678199 CCTCTTTGTTTTCAGAGACTAAAAAGT 58.322 33.333 0.00 0.00 36.36 2.66
101 102 8.893727 TCCTCTTTGTTTTCAGAGACTAAAAAG 58.106 33.333 0.00 0.00 36.36 2.27
102 103 8.801882 TCCTCTTTGTTTTCAGAGACTAAAAA 57.198 30.769 0.00 0.00 36.36 1.94
103 104 8.801882 TTCCTCTTTGTTTTCAGAGACTAAAA 57.198 30.769 0.00 0.00 36.36 1.52
104 105 7.499232 CCTTCCTCTTTGTTTTCAGAGACTAAA 59.501 37.037 0.00 0.00 36.36 1.85
105 106 6.992715 CCTTCCTCTTTGTTTTCAGAGACTAA 59.007 38.462 0.00 0.00 36.36 2.24
106 107 6.464465 CCCTTCCTCTTTGTTTTCAGAGACTA 60.464 42.308 0.00 0.00 36.36 2.59
107 108 5.372373 CCTTCCTCTTTGTTTTCAGAGACT 58.628 41.667 0.00 0.00 36.36 3.24
108 109 4.517075 CCCTTCCTCTTTGTTTTCAGAGAC 59.483 45.833 0.00 0.00 36.36 3.36
109 110 4.412199 TCCCTTCCTCTTTGTTTTCAGAGA 59.588 41.667 0.00 0.00 38.47 3.10
110 111 4.517075 GTCCCTTCCTCTTTGTTTTCAGAG 59.483 45.833 0.00 0.00 33.92 3.35
111 112 4.166144 AGTCCCTTCCTCTTTGTTTTCAGA 59.834 41.667 0.00 0.00 0.00 3.27
112 113 4.464947 AGTCCCTTCCTCTTTGTTTTCAG 58.535 43.478 0.00 0.00 0.00 3.02
113 114 4.519906 AGTCCCTTCCTCTTTGTTTTCA 57.480 40.909 0.00 0.00 0.00 2.69
114 115 5.854010 AAAGTCCCTTCCTCTTTGTTTTC 57.146 39.130 0.00 0.00 31.47 2.29
115 116 6.620877 AAAAAGTCCCTTCCTCTTTGTTTT 57.379 33.333 0.00 0.00 32.74 2.43
116 117 6.323996 CCTAAAAAGTCCCTTCCTCTTTGTTT 59.676 38.462 0.00 0.00 32.74 2.83
117 118 5.833667 CCTAAAAAGTCCCTTCCTCTTTGTT 59.166 40.000 0.00 0.00 32.74 2.83
118 119 5.386060 CCTAAAAAGTCCCTTCCTCTTTGT 58.614 41.667 0.00 0.00 32.74 2.83
119 120 4.767409 CCCTAAAAAGTCCCTTCCTCTTTG 59.233 45.833 0.00 0.00 32.74 2.77
120 121 4.668335 TCCCTAAAAAGTCCCTTCCTCTTT 59.332 41.667 0.00 0.00 33.61 2.52
121 122 4.043059 GTCCCTAAAAAGTCCCTTCCTCTT 59.957 45.833 0.00 0.00 0.00 2.85
122 123 3.587951 GTCCCTAAAAAGTCCCTTCCTCT 59.412 47.826 0.00 0.00 0.00 3.69
123 124 3.587951 AGTCCCTAAAAAGTCCCTTCCTC 59.412 47.826 0.00 0.00 0.00 3.71
124 125 3.610260 AGTCCCTAAAAAGTCCCTTCCT 58.390 45.455 0.00 0.00 0.00 3.36
125 126 4.080469 CCTAGTCCCTAAAAAGTCCCTTCC 60.080 50.000 0.00 0.00 0.00 3.46
126 127 4.080469 CCCTAGTCCCTAAAAAGTCCCTTC 60.080 50.000 0.00 0.00 0.00 3.46
127 128 3.850774 CCCTAGTCCCTAAAAAGTCCCTT 59.149 47.826 0.00 0.00 0.00 3.95
128 129 3.080153 TCCCTAGTCCCTAAAAAGTCCCT 59.920 47.826 0.00 0.00 0.00 4.20
129 130 3.199508 GTCCCTAGTCCCTAAAAAGTCCC 59.800 52.174 0.00 0.00 0.00 4.46
130 131 4.102598 AGTCCCTAGTCCCTAAAAAGTCC 58.897 47.826 0.00 0.00 0.00 3.85
131 132 5.758790 AAGTCCCTAGTCCCTAAAAAGTC 57.241 43.478 0.00 0.00 0.00 3.01
132 133 6.526056 AAAAGTCCCTAGTCCCTAAAAAGT 57.474 37.500 0.00 0.00 0.00 2.66
133 134 8.162085 ACTAAAAAGTCCCTAGTCCCTAAAAAG 58.838 37.037 0.00 0.00 0.00 2.27
134 135 8.049165 ACTAAAAAGTCCCTAGTCCCTAAAAA 57.951 34.615 0.00 0.00 0.00 1.94
135 136 7.637548 ACTAAAAAGTCCCTAGTCCCTAAAA 57.362 36.000 0.00 0.00 0.00 1.52
136 137 7.455891 CAACTAAAAAGTCCCTAGTCCCTAAA 58.544 38.462 0.00 0.00 0.00 1.85
137 138 6.013119 CCAACTAAAAAGTCCCTAGTCCCTAA 60.013 42.308 0.00 0.00 0.00 2.69
138 139 5.486419 CCAACTAAAAAGTCCCTAGTCCCTA 59.514 44.000 0.00 0.00 0.00 3.53
139 140 4.288887 CCAACTAAAAAGTCCCTAGTCCCT 59.711 45.833 0.00 0.00 0.00 4.20
140 141 4.567116 CCCAACTAAAAAGTCCCTAGTCCC 60.567 50.000 0.00 0.00 0.00 4.46
141 142 4.287845 TCCCAACTAAAAAGTCCCTAGTCC 59.712 45.833 0.00 0.00 0.00 3.85
142 143 5.494390 TCCCAACTAAAAAGTCCCTAGTC 57.506 43.478 0.00 0.00 0.00 2.59
143 144 6.464530 AATCCCAACTAAAAAGTCCCTAGT 57.535 37.500 0.00 0.00 0.00 2.57
144 145 7.858498 TCTAATCCCAACTAAAAAGTCCCTAG 58.142 38.462 0.00 0.00 0.00 3.02
145 146 7.817910 TCTAATCCCAACTAAAAAGTCCCTA 57.182 36.000 0.00 0.00 0.00 3.53
146 147 6.713731 TCTAATCCCAACTAAAAAGTCCCT 57.286 37.500 0.00 0.00 0.00 4.20
147 148 7.770366 TTTCTAATCCCAACTAAAAAGTCCC 57.230 36.000 0.00 0.00 0.00 4.46
148 149 9.692749 CTTTTTCTAATCCCAACTAAAAAGTCC 57.307 33.333 0.00 0.00 38.32 3.85
155 156 9.734984 CCTAAGACTTTTTCTAATCCCAACTAA 57.265 33.333 0.00 0.00 32.51 2.24
156 157 9.108111 TCCTAAGACTTTTTCTAATCCCAACTA 57.892 33.333 0.00 0.00 32.51 2.24
157 158 7.883833 GTCCTAAGACTTTTTCTAATCCCAACT 59.116 37.037 0.00 0.00 40.10 3.16
158 159 8.041829 GTCCTAAGACTTTTTCTAATCCCAAC 57.958 38.462 0.00 0.00 40.10 3.77
174 175 7.764901 CCCTGTTTAGTTCATAAGTCCTAAGAC 59.235 40.741 0.00 0.00 43.89 3.01
175 176 7.456902 ACCCTGTTTAGTTCATAAGTCCTAAGA 59.543 37.037 0.00 0.00 0.00 2.10
176 177 7.621796 ACCCTGTTTAGTTCATAAGTCCTAAG 58.378 38.462 0.00 0.00 0.00 2.18
177 178 7.456902 AGACCCTGTTTAGTTCATAAGTCCTAA 59.543 37.037 0.00 0.00 0.00 2.69
178 179 6.958192 AGACCCTGTTTAGTTCATAAGTCCTA 59.042 38.462 0.00 0.00 0.00 2.94
179 180 5.785940 AGACCCTGTTTAGTTCATAAGTCCT 59.214 40.000 0.00 0.00 0.00 3.85
180 181 6.051179 AGACCCTGTTTAGTTCATAAGTCC 57.949 41.667 0.00 0.00 0.00 3.85
181 182 8.312564 ACTAAGACCCTGTTTAGTTCATAAGTC 58.687 37.037 0.00 0.00 36.90 3.01
182 183 8.203681 ACTAAGACCCTGTTTAGTTCATAAGT 57.796 34.615 0.00 0.00 36.90 2.24
183 184 9.503399 AAACTAAGACCCTGTTTAGTTCATAAG 57.497 33.333 9.33 0.00 44.84 1.73
186 187 8.877195 TCTAAACTAAGACCCTGTTTAGTTCAT 58.123 33.333 18.25 0.35 44.84 2.57
187 188 8.146412 GTCTAAACTAAGACCCTGTTTAGTTCA 58.854 37.037 18.25 3.89 44.84 3.18
188 189 8.531622 GTCTAAACTAAGACCCTGTTTAGTTC 57.468 38.462 18.25 12.11 44.84 3.01
202 203 4.382147 GGAGCAGGTCAGGTCTAAACTAAG 60.382 50.000 1.20 0.00 36.33 2.18
208 209 0.251653 ACGGAGCAGGTCAGGTCTAA 60.252 55.000 4.72 0.00 36.33 2.10
239 240 6.721571 TTAGATTACTCGCCTCAACAAAAG 57.278 37.500 0.00 0.00 0.00 2.27
248 249 2.900546 CCTCCCATTAGATTACTCGCCT 59.099 50.000 0.00 0.00 0.00 5.52
343 344 4.732285 TCGTTTGTTGAGCAATTCTCTC 57.268 40.909 6.50 2.92 42.38 3.20
363 371 3.217626 CATATGGGGCCTCTTGTCTTTC 58.782 50.000 3.07 0.00 0.00 2.62
369 377 1.683943 CACACATATGGGGCCTCTTG 58.316 55.000 10.35 1.14 0.00 3.02
384 392 4.094887 TCTCTTCTCTTTTGTTGTGCACAC 59.905 41.667 21.56 15.21 33.98 3.82
443 455 2.536365 TCGATGACTCGCCATTTGTAC 58.464 47.619 0.00 0.00 44.65 2.90
530 542 2.673523 CTACCAGGCCAGCTGCTT 59.326 61.111 8.66 0.00 40.92 3.91
558 570 6.303903 TGTTTACTAGGGGTAGCCTTTTAG 57.696 41.667 11.48 12.34 0.00 1.85
564 576 4.458397 GGAAATGTTTACTAGGGGTAGCC 58.542 47.826 1.07 1.07 0.00 3.93
657 678 2.436087 CTTCGCCTGTCGGTCCAACT 62.436 60.000 0.00 0.00 39.05 3.16
719 741 2.082366 GTGCAATGCAAAGCGACGG 61.082 57.895 10.44 0.00 41.47 4.79
1428 1460 1.450312 GGCCTGATCCTTGTGGTCG 60.450 63.158 0.00 0.00 34.23 4.79
1545 1577 9.057089 GTATATATAGAAAAACAAGCAGTGCCT 57.943 33.333 12.58 0.00 0.00 4.75
1546 1578 8.009974 CGTATATATAGAAAAACAAGCAGTGCC 58.990 37.037 12.58 0.00 0.00 5.01
1547 1579 8.009974 CCGTATATATAGAAAAACAAGCAGTGC 58.990 37.037 7.13 7.13 0.00 4.40
1548 1580 8.009974 GCCGTATATATAGAAAAACAAGCAGTG 58.990 37.037 0.00 0.00 0.00 3.66
1552 1596 7.342318 TCGCCGTATATATAGAAAAACAAGC 57.658 36.000 0.00 0.00 0.00 4.01
1762 1820 2.869503 ATCCACCATGTTCGCCGTCC 62.870 60.000 0.00 0.00 0.00 4.79
1806 1864 2.026038 CGACACGCGTGAGTTAATACAC 59.974 50.000 42.94 18.34 34.64 2.90
1807 1865 2.244251 CGACACGCGTGAGTTAATACA 58.756 47.619 42.94 0.00 34.64 2.29
1954 2012 0.112995 TCTGGGTCCTTTGCTGCATT 59.887 50.000 1.84 0.00 0.00 3.56
2005 2063 8.334522 AGAGTAGTAAGAATAGTACCTCCTGA 57.665 38.462 0.00 0.00 38.28 3.86
2026 2084 5.103430 AGTGATCCCTAGCTAGGTTTAGAGT 60.103 44.000 33.00 15.66 42.03 3.24
2031 2089 5.145513 ACTAGTGATCCCTAGCTAGGTTT 57.854 43.478 33.00 22.00 42.03 3.27
2098 2156 7.054124 TCTCGTTCTTGCCATCCTAATAAAAT 58.946 34.615 0.00 0.00 0.00 1.82
2350 2414 3.429372 TTGCTGGTCGTGGCCCTTT 62.429 57.895 0.00 0.00 0.00 3.11
2416 2480 0.614294 TTACAATCGGGGCTTCGGAA 59.386 50.000 0.00 0.00 0.00 4.30
2473 2540 4.047059 GCCCGTGTCTCCGTTCGA 62.047 66.667 0.00 0.00 0.00 3.71
2475 2542 3.236003 AAGGCCCGTGTCTCCGTTC 62.236 63.158 0.00 0.00 0.00 3.95
2476 2543 3.239253 AAGGCCCGTGTCTCCGTT 61.239 61.111 0.00 0.00 0.00 4.44
2477 2544 4.003788 CAAGGCCCGTGTCTCCGT 62.004 66.667 0.00 0.00 0.00 4.69
2479 2546 2.266055 CTCAAGGCCCGTGTCTCC 59.734 66.667 0.00 0.00 0.00 3.71
2480 2547 1.079750 GACTCAAGGCCCGTGTCTC 60.080 63.158 14.63 3.83 0.00 3.36
2481 2548 2.584391 GGACTCAAGGCCCGTGTCT 61.584 63.158 19.00 1.79 0.00 3.41
2482 2549 2.047179 GGACTCAAGGCCCGTGTC 60.047 66.667 13.87 13.87 0.00 3.67
2483 2550 3.637273 GGGACTCAAGGCCCGTGT 61.637 66.667 4.84 0.00 34.00 4.49
2488 2555 0.690762 TACACAAGGGACTCAAGGCC 59.309 55.000 0.00 0.00 38.49 5.19
2489 2556 2.027192 TCATACACAAGGGACTCAAGGC 60.027 50.000 0.00 0.00 38.49 4.35
2490 2557 3.981071 TCATACACAAGGGACTCAAGG 57.019 47.619 0.00 0.00 38.49 3.61
2491 2558 4.568359 CGATTCATACACAAGGGACTCAAG 59.432 45.833 0.00 0.00 38.49 3.02
2492 2559 4.020573 ACGATTCATACACAAGGGACTCAA 60.021 41.667 0.00 0.00 38.49 3.02
2493 2560 3.513912 ACGATTCATACACAAGGGACTCA 59.486 43.478 0.00 0.00 38.49 3.41
2494 2561 3.865745 CACGATTCATACACAAGGGACTC 59.134 47.826 0.00 0.00 38.49 3.36
2496 2563 2.351726 GCACGATTCATACACAAGGGAC 59.648 50.000 0.00 0.00 0.00 4.46
2497 2564 2.236146 AGCACGATTCATACACAAGGGA 59.764 45.455 0.00 0.00 0.00 4.20
2498 2565 2.352651 CAGCACGATTCATACACAAGGG 59.647 50.000 0.00 0.00 0.00 3.95
2522 2589 0.037139 AGCCATGCACGTACGGTAAA 60.037 50.000 21.06 2.30 0.00 2.01
2614 2681 0.106708 CCATGGTGCAGCGGTAGTAT 59.893 55.000 11.91 0.00 0.00 2.12
2666 3015 2.289195 CCAGTCGTGGCCAGTTAGTTAA 60.289 50.000 5.11 0.00 36.89 2.01
3113 3463 1.002134 CGGAACATGGAACTGCCCT 60.002 57.895 0.00 0.00 34.97 5.19
3329 3679 1.671379 GAGGGCCACGGTGAAGTTC 60.671 63.158 10.28 0.00 0.00 3.01
3437 3787 3.181474 TGTTGTTACTGGTCGTCATCACA 60.181 43.478 0.00 0.00 0.00 3.58
3442 3792 1.404748 TCGTGTTGTTACTGGTCGTCA 59.595 47.619 0.00 0.00 0.00 4.35
3496 3846 1.701031 TTCCGAACTTGACCAGGCCA 61.701 55.000 5.01 0.00 0.00 5.36
3516 3866 5.753721 AGCTATCTGGTTTCTCAACTCTT 57.246 39.130 0.00 0.00 32.90 2.85
3643 3996 3.428534 GCCGCAAAATCACGAAAGAAAAT 59.571 39.130 0.00 0.00 0.00 1.82
3834 4199 1.391933 ATGGAGGCGTGTGAGCGATA 61.392 55.000 0.00 0.00 38.18 2.92
3840 4205 0.108186 GTGATGATGGAGGCGTGTGA 60.108 55.000 0.00 0.00 0.00 3.58
3879 4244 7.463961 AAAAGATTTCTGCTGATGTCATCTT 57.536 32.000 13.90 3.65 0.00 2.40
3959 4325 8.306761 GTCCAGATGAATTTAATGGTGAAAACT 58.693 33.333 5.18 0.00 32.68 2.66
3978 4344 8.192110 GTCTACTTTTAAAGATCTCGTCCAGAT 58.808 37.037 12.02 0.00 45.41 2.90
3999 4365 5.236478 CGAAACATATCAACATGGGGTCTAC 59.764 44.000 0.00 0.00 0.00 2.59
4076 4444 7.519032 TGGCAACTTTAGTTTAAGCACTATT 57.481 32.000 5.98 0.00 35.83 1.73
4224 4593 6.988580 TGTCATGCACCATTAAACAAAATTGA 59.011 30.769 0.00 0.00 0.00 2.57
4232 4601 7.145323 ACTAAACTTGTCATGCACCATTAAAC 58.855 34.615 0.00 0.00 0.00 2.01
4233 4602 7.283625 ACTAAACTTGTCATGCACCATTAAA 57.716 32.000 0.00 0.00 0.00 1.52
4236 4605 5.789643 AACTAAACTTGTCATGCACCATT 57.210 34.783 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.