Multiple sequence alignment - TraesCS3D01G458000

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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 TraesCS3D01G458000 chr3D 100.000 3245 0 0 1 3245 563448290 563445046 0.000000e+00 5993.0
1 TraesCS3D01G458000 chr3D 84.167 840 107 15 1722 2554 563595543 563594723 0.000000e+00 791.0
2 TraesCS3D01G458000 chr3D 86.207 464 41 12 853 1295 563596420 563595959 6.300000e-132 481.0
3 TraesCS3D01G458000 chr3D 84.914 464 51 15 1083 1538 563435812 563435360 4.940000e-123 451.0
4 TraesCS3D01G458000 chr3D 90.878 296 27 0 1291 1586 563596011 563595716 6.520000e-107 398.0
5 TraesCS3D01G458000 chr3D 86.829 205 21 5 1087 1285 577029021 577029225 1.170000e-54 224.0
6 TraesCS3D01G458000 chr3D 82.632 190 32 1 2274 2463 563433906 563433718 2.000000e-37 167.0
7 TraesCS3D01G458000 chr3D 75.321 312 68 7 1925 2233 563834590 563834895 1.210000e-29 141.0
8 TraesCS3D01G458000 chr3D 74.453 274 63 5 1950 2221 577029800 577030068 9.520000e-21 111.0
9 TraesCS3D01G458000 chr3A 96.716 1431 46 1 833 2263 698146665 698145236 0.000000e+00 2381.0
10 TraesCS3D01G458000 chr3A 94.312 967 42 4 2280 3245 698144531 698143577 0.000000e+00 1469.0
11 TraesCS3D01G458000 chr3A 85.638 564 73 8 1722 2282 698168131 698167573 1.300000e-163 586.0
12 TraesCS3D01G458000 chr3A 82.718 596 61 23 736 1295 698169136 698168547 2.910000e-135 492.0
13 TraesCS3D01G458000 chr3A 89.717 389 19 12 275 661 698147025 698146656 8.150000e-131 477.0
14 TraesCS3D01G458000 chr3A 83.801 463 61 11 1083 1538 698032313 698031858 8.320000e-116 427.0
15 TraesCS3D01G458000 chr3A 89.189 296 32 0 1291 1586 698168599 698168304 1.420000e-98 370.0
16 TraesCS3D01G458000 chr3A 97.849 93 2 0 193 285 698147290 698147198 9.320000e-36 161.0
17 TraesCS3D01G458000 chr3A 89.231 65 7 0 2157 2221 698703510 698703446 7.460000e-12 82.4
18 TraesCS3D01G458000 chr3A 94.118 51 2 1 2925 2975 686191263 686191214 3.470000e-10 76.8
19 TraesCS3D01G458000 chr3B 81.643 1193 155 45 1722 2893 751014372 751013223 0.000000e+00 931.0
20 TraesCS3D01G458000 chr3B 87.832 452 44 10 853 1295 751015237 751014788 1.330000e-143 520.0
21 TraesCS3D01G458000 chr3B 89.865 296 30 0 1291 1586 751014840 751014545 6.570000e-102 381.0
22 TraesCS3D01G458000 chr3B 82.656 369 27 15 855 1186 751842894 751843262 3.170000e-75 292.0
23 TraesCS3D01G458000 chr3B 88.770 187 21 0 1098 1284 751511284 751511098 2.520000e-56 230.0
24 TraesCS3D01G458000 chr3B 81.356 295 32 11 2972 3245 751013221 751012929 5.450000e-53 219.0
25 TraesCS3D01G458000 chr3B 75.694 288 59 10 1950 2233 751204589 751204869 2.030000e-27 134.0
26 TraesCS3D01G458000 chr2D 83.038 395 57 7 124 514 20183302 20183690 1.850000e-92 350.0
27 TraesCS3D01G458000 chr6B 85.567 194 26 2 1092 1284 704550467 704550275 5.490000e-48 202.0
28 TraesCS3D01G458000 chr5D 92.857 56 4 0 2912 2967 526884273 526884328 7.460000e-12 82.4
29 TraesCS3D01G458000 chr4A 93.103 58 1 1 2910 2967 477033270 477033324 7.460000e-12 82.4
30 TraesCS3D01G458000 chr5B 92.982 57 1 1 2912 2968 323708818 323708765 2.680000e-11 80.5
31 TraesCS3D01G458000 chr5B 85.135 74 8 1 2894 2967 270610555 270610485 4.490000e-09 73.1
32 TraesCS3D01G458000 chr2A 92.982 57 1 1 2911 2967 28824174 28824227 2.680000e-11 80.5
33 TraesCS3D01G458000 chr2B 77.778 117 26 0 2117 2233 517436829 517436713 4.490000e-09 73.1
34 TraesCS3D01G458000 chr1B 83.784 74 12 0 2894 2967 401309868 401309795 1.620000e-08 71.3
35 TraesCS3D01G458000 chr7D 83.784 74 10 1 2894 2967 144450778 144450707 5.810000e-08 69.4


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 TraesCS3D01G458000 chr3D 563445046 563448290 3244 True 5993.000000 5993 100.000000 1 3245 1 chr3D.!!$R1 3244
1 TraesCS3D01G458000 chr3D 563594723 563596420 1697 True 556.666667 791 87.084000 853 2554 3 chr3D.!!$R3 1701
2 TraesCS3D01G458000 chr3D 563433718 563435812 2094 True 309.000000 451 83.773000 1083 2463 2 chr3D.!!$R2 1380
3 TraesCS3D01G458000 chr3A 698143577 698147290 3713 True 1122.000000 2381 94.648500 193 3245 4 chr3A.!!$R4 3052
4 TraesCS3D01G458000 chr3A 698167573 698169136 1563 True 482.666667 586 85.848333 736 2282 3 chr3A.!!$R5 1546
5 TraesCS3D01G458000 chr3B 751012929 751015237 2308 True 512.750000 931 85.174000 853 3245 4 chr3B.!!$R2 2392

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
934 1157 0.027979 CCATTACGCATTCACGCTGG 59.972 55.000 0.0 0.0 36.19 4.85 F
1035 1276 0.322906 CTGAAGCCCCTGTTCTTCCC 60.323 60.000 0.0 0.0 38.26 3.97 F
1060 1301 2.442413 CCAAAAGGAACAAGGCGGATA 58.558 47.619 0.0 0.0 0.00 2.59 F
2010 2329 1.278127 ACCCATAAGTTCCCGTCTGTG 59.722 52.381 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2188 0.036105 ATCGGTGCAGCTTGATGACA 60.036 50.000 14.92 0.0 0.00 3.58 R
2010 2329 0.543749 AGTAGATGCAGTTGGCCTCC 59.456 55.000 3.32 0.0 43.89 4.30 R
2045 2364 1.415289 TGCAGATGTAGGCAGATGAGG 59.585 52.381 0.00 0.0 34.58 3.86 R
3147 4406 2.524306 TGATTGAAGTCGGCCCAATTT 58.476 42.857 0.00 0.0 31.40 1.82 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 4.675404 AGGCAGCACGAACAGTAC 57.325 55.556 0.00 0.00 0.00 2.73
18 19 1.745890 AGGCAGCACGAACAGTACA 59.254 52.632 0.00 0.00 0.00 2.90
19 20 0.321671 AGGCAGCACGAACAGTACAT 59.678 50.000 0.00 0.00 0.00 2.29
20 21 0.443869 GGCAGCACGAACAGTACATG 59.556 55.000 0.00 0.00 0.00 3.21
21 22 1.148310 GCAGCACGAACAGTACATGT 58.852 50.000 2.69 2.69 46.97 3.21
29 30 2.999356 ACAGTACATGTTGCGCACA 58.001 47.368 11.12 12.74 39.96 4.57
35 36 4.402851 ATGTTGCGCACATGGACT 57.597 50.000 11.12 0.00 45.12 3.85
36 37 1.878070 ATGTTGCGCACATGGACTG 59.122 52.632 11.12 0.00 45.12 3.51
37 38 0.606130 ATGTTGCGCACATGGACTGA 60.606 50.000 11.12 0.00 45.12 3.41
38 39 1.207593 GTTGCGCACATGGACTGAC 59.792 57.895 11.12 0.00 0.00 3.51
39 40 1.227793 TTGCGCACATGGACTGACA 60.228 52.632 11.12 0.00 0.00 3.58
40 41 0.606130 TTGCGCACATGGACTGACAT 60.606 50.000 11.12 0.00 0.00 3.06
41 42 0.248843 TGCGCACATGGACTGACATA 59.751 50.000 5.66 0.00 0.00 2.29
42 43 1.134431 TGCGCACATGGACTGACATAT 60.134 47.619 5.66 0.00 0.00 1.78
43 44 2.102252 TGCGCACATGGACTGACATATA 59.898 45.455 5.66 0.00 0.00 0.86
44 45 3.244181 TGCGCACATGGACTGACATATAT 60.244 43.478 5.66 0.00 0.00 0.86
45 46 3.369147 GCGCACATGGACTGACATATATC 59.631 47.826 0.30 0.00 0.00 1.63
46 47 3.928992 CGCACATGGACTGACATATATCC 59.071 47.826 0.00 0.00 0.00 2.59
47 48 4.322273 CGCACATGGACTGACATATATCCT 60.322 45.833 0.00 0.00 32.06 3.24
48 49 5.555017 GCACATGGACTGACATATATCCTT 58.445 41.667 0.00 0.00 32.06 3.36
49 50 5.410746 GCACATGGACTGACATATATCCTTG 59.589 44.000 0.00 0.00 40.49 3.61
50 51 5.936372 CACATGGACTGACATATATCCTTGG 59.064 44.000 0.00 0.00 39.52 3.61
51 52 5.846164 ACATGGACTGACATATATCCTTGGA 59.154 40.000 0.00 0.00 39.52 3.53
52 53 6.503217 ACATGGACTGACATATATCCTTGGAT 59.497 38.462 7.37 7.37 39.52 3.41
53 54 6.611613 TGGACTGACATATATCCTTGGATC 57.388 41.667 5.30 0.00 32.06 3.36
54 55 6.326161 TGGACTGACATATATCCTTGGATCT 58.674 40.000 5.30 0.00 32.06 2.75
55 56 6.789457 TGGACTGACATATATCCTTGGATCTT 59.211 38.462 5.30 0.00 32.06 2.40
56 57 7.293299 TGGACTGACATATATCCTTGGATCTTT 59.707 37.037 5.30 0.00 32.06 2.52
57 58 8.160106 GGACTGACATATATCCTTGGATCTTTT 58.840 37.037 5.30 0.00 0.00 2.27
58 59 9.566432 GACTGACATATATCCTTGGATCTTTTT 57.434 33.333 5.30 0.00 0.00 1.94
59 60 9.347240 ACTGACATATATCCTTGGATCTTTTTG 57.653 33.333 5.30 1.93 0.00 2.44
60 61 8.696043 TGACATATATCCTTGGATCTTTTTGG 57.304 34.615 5.30 0.00 0.00 3.28
61 62 7.725397 TGACATATATCCTTGGATCTTTTTGGG 59.275 37.037 5.30 0.00 0.00 4.12
62 63 7.825709 ACATATATCCTTGGATCTTTTTGGGA 58.174 34.615 5.30 0.00 0.00 4.37
63 64 7.725844 ACATATATCCTTGGATCTTTTTGGGAC 59.274 37.037 5.30 0.00 0.00 4.46
64 65 3.893753 TCCTTGGATCTTTTTGGGACA 57.106 42.857 0.00 0.00 0.00 4.02
80 81 3.596310 GGACAAACTCCCACTCTAGAC 57.404 52.381 0.00 0.00 31.83 2.59
81 82 2.094649 GGACAAACTCCCACTCTAGACG 60.095 54.545 0.00 0.00 31.83 4.18
82 83 1.893801 ACAAACTCCCACTCTAGACGG 59.106 52.381 0.00 0.00 0.00 4.79
83 84 2.168496 CAAACTCCCACTCTAGACGGA 58.832 52.381 5.19 2.40 0.00 4.69
84 85 2.561419 CAAACTCCCACTCTAGACGGAA 59.439 50.000 5.19 0.00 0.00 4.30
85 86 2.830651 ACTCCCACTCTAGACGGAAT 57.169 50.000 5.19 0.00 0.00 3.01
86 87 2.379972 ACTCCCACTCTAGACGGAATG 58.620 52.381 5.19 0.00 0.00 2.67
87 88 1.683917 CTCCCACTCTAGACGGAATGG 59.316 57.143 5.19 1.30 32.99 3.16
88 89 0.105039 CCCACTCTAGACGGAATGGC 59.895 60.000 5.19 0.00 31.98 4.40
89 90 0.249073 CCACTCTAGACGGAATGGCG 60.249 60.000 0.00 0.00 0.00 5.69
90 91 0.738975 CACTCTAGACGGAATGGCGA 59.261 55.000 0.00 0.00 0.00 5.54
91 92 1.338337 CACTCTAGACGGAATGGCGAT 59.662 52.381 0.00 0.00 0.00 4.58
92 93 2.032620 ACTCTAGACGGAATGGCGATT 58.967 47.619 0.00 0.00 0.00 3.34
93 94 2.034812 ACTCTAGACGGAATGGCGATTC 59.965 50.000 12.62 12.62 37.80 2.52
94 95 2.294791 CTCTAGACGGAATGGCGATTCT 59.705 50.000 19.21 3.91 38.48 2.40
95 96 2.693591 TCTAGACGGAATGGCGATTCTT 59.306 45.455 19.21 8.31 38.48 2.52
96 97 1.656652 AGACGGAATGGCGATTCTTG 58.343 50.000 19.21 14.61 38.48 3.02
97 98 1.207089 AGACGGAATGGCGATTCTTGA 59.793 47.619 19.21 0.00 38.48 3.02
98 99 2.006888 GACGGAATGGCGATTCTTGAA 58.993 47.619 19.21 0.00 38.48 2.69
99 100 2.009774 ACGGAATGGCGATTCTTGAAG 58.990 47.619 19.21 9.57 38.48 3.02
100 101 1.331756 CGGAATGGCGATTCTTGAAGG 59.668 52.381 19.21 1.47 38.48 3.46
101 102 2.643551 GGAATGGCGATTCTTGAAGGA 58.356 47.619 19.21 0.00 38.48 3.36
102 103 2.615912 GGAATGGCGATTCTTGAAGGAG 59.384 50.000 19.21 0.00 38.48 3.69
103 104 1.673168 ATGGCGATTCTTGAAGGAGC 58.327 50.000 0.00 0.00 0.00 4.70
104 105 0.740868 TGGCGATTCTTGAAGGAGCG 60.741 55.000 6.79 6.79 0.00 5.03
105 106 1.432270 GGCGATTCTTGAAGGAGCGG 61.432 60.000 13.45 0.00 0.00 5.52
106 107 0.741221 GCGATTCTTGAAGGAGCGGT 60.741 55.000 13.45 0.00 0.00 5.68
107 108 1.002366 CGATTCTTGAAGGAGCGGTG 58.998 55.000 2.67 0.00 0.00 4.94
108 109 1.373570 GATTCTTGAAGGAGCGGTGG 58.626 55.000 0.00 0.00 0.00 4.61
109 110 0.693049 ATTCTTGAAGGAGCGGTGGT 59.307 50.000 0.00 0.00 0.00 4.16
110 111 0.472471 TTCTTGAAGGAGCGGTGGTT 59.528 50.000 0.00 0.00 0.00 3.67
111 112 0.250295 TCTTGAAGGAGCGGTGGTTG 60.250 55.000 0.00 0.00 0.00 3.77
112 113 0.535102 CTTGAAGGAGCGGTGGTTGT 60.535 55.000 0.00 0.00 0.00 3.32
113 114 0.817634 TTGAAGGAGCGGTGGTTGTG 60.818 55.000 0.00 0.00 0.00 3.33
114 115 1.966451 GAAGGAGCGGTGGTTGTGG 60.966 63.158 0.00 0.00 0.00 4.17
115 116 4.643387 AGGAGCGGTGGTTGTGGC 62.643 66.667 0.00 0.00 0.00 5.01
120 121 4.326766 CGGTGGTTGTGGCGCTTG 62.327 66.667 7.64 0.00 0.00 4.01
121 122 4.645921 GGTGGTTGTGGCGCTTGC 62.646 66.667 7.64 0.00 38.11 4.01
122 123 4.980903 GTGGTTGTGGCGCTTGCG 62.981 66.667 7.64 10.90 40.46 4.85
125 126 4.389576 GTTGTGGCGCTTGCGGAG 62.390 66.667 16.79 0.00 40.46 4.63
129 130 4.838152 TGGCGCTTGCGGAGGATC 62.838 66.667 16.79 0.00 40.46 3.36
130 131 4.537433 GGCGCTTGCGGAGGATCT 62.537 66.667 16.79 0.00 40.46 2.75
131 132 2.512515 GCGCTTGCGGAGGATCTT 60.513 61.111 16.79 0.00 33.73 2.40
132 133 2.109126 GCGCTTGCGGAGGATCTTT 61.109 57.895 16.79 0.00 33.73 2.52
133 134 1.648467 GCGCTTGCGGAGGATCTTTT 61.648 55.000 16.79 0.00 33.73 2.27
134 135 0.375106 CGCTTGCGGAGGATCTTTTC 59.625 55.000 7.16 0.00 33.73 2.29
135 136 1.743996 GCTTGCGGAGGATCTTTTCT 58.256 50.000 0.00 0.00 33.73 2.52
136 137 2.087646 GCTTGCGGAGGATCTTTTCTT 58.912 47.619 0.00 0.00 33.73 2.52
137 138 2.159462 GCTTGCGGAGGATCTTTTCTTG 60.159 50.000 0.00 0.00 33.73 3.02
138 139 2.859165 TGCGGAGGATCTTTTCTTGT 57.141 45.000 0.00 0.00 33.73 3.16
139 140 3.140325 TGCGGAGGATCTTTTCTTGTT 57.860 42.857 0.00 0.00 33.73 2.83
140 141 4.280436 TGCGGAGGATCTTTTCTTGTTA 57.720 40.909 0.00 0.00 33.73 2.41
141 142 4.647611 TGCGGAGGATCTTTTCTTGTTAA 58.352 39.130 0.00 0.00 33.73 2.01
142 143 5.253330 TGCGGAGGATCTTTTCTTGTTAAT 58.747 37.500 0.00 0.00 33.73 1.40
143 144 6.411376 TGCGGAGGATCTTTTCTTGTTAATA 58.589 36.000 0.00 0.00 33.73 0.98
144 145 6.882140 TGCGGAGGATCTTTTCTTGTTAATAA 59.118 34.615 0.00 0.00 33.73 1.40
145 146 7.148306 TGCGGAGGATCTTTTCTTGTTAATAAC 60.148 37.037 0.00 0.00 33.73 1.89
146 147 7.399523 CGGAGGATCTTTTCTTGTTAATAACG 58.600 38.462 0.00 0.00 33.73 3.18
147 148 7.064253 CGGAGGATCTTTTCTTGTTAATAACGT 59.936 37.037 0.00 0.00 33.73 3.99
148 149 8.175716 GGAGGATCTTTTCTTGTTAATAACGTG 58.824 37.037 0.00 0.00 33.73 4.49
149 150 8.842358 AGGATCTTTTCTTGTTAATAACGTGA 57.158 30.769 0.00 0.00 0.00 4.35
150 151 9.449719 AGGATCTTTTCTTGTTAATAACGTGAT 57.550 29.630 0.00 0.00 0.00 3.06
154 155 9.872757 TCTTTTCTTGTTAATAACGTGATTGAC 57.127 29.630 12.55 12.55 0.00 3.18
155 156 9.878599 CTTTTCTTGTTAATAACGTGATTGACT 57.121 29.630 18.49 0.00 0.00 3.41
168 169 7.568267 ACGTGATTGACTATAATTATGAGCG 57.432 36.000 8.28 3.12 0.00 5.03
169 170 6.089551 ACGTGATTGACTATAATTATGAGCGC 59.910 38.462 8.28 0.00 0.00 5.92
170 171 6.461816 GTGATTGACTATAATTATGAGCGCG 58.538 40.000 8.28 0.00 0.00 6.86
171 172 6.089551 GTGATTGACTATAATTATGAGCGCGT 59.910 38.462 8.43 0.00 0.00 6.01
172 173 5.822584 TTGACTATAATTATGAGCGCGTG 57.177 39.130 8.43 0.00 0.00 5.34
173 174 5.116069 TGACTATAATTATGAGCGCGTGA 57.884 39.130 8.43 0.00 0.00 4.35
174 175 5.154222 TGACTATAATTATGAGCGCGTGAG 58.846 41.667 8.43 0.00 0.00 3.51
175 176 5.048991 TGACTATAATTATGAGCGCGTGAGA 60.049 40.000 8.43 0.00 0.00 3.27
176 177 5.154932 ACTATAATTATGAGCGCGTGAGAC 58.845 41.667 8.43 0.00 0.00 3.36
177 178 2.293677 AATTATGAGCGCGTGAGACA 57.706 45.000 8.43 1.52 0.00 3.41
178 179 2.293677 ATTATGAGCGCGTGAGACAA 57.706 45.000 8.43 0.00 0.00 3.18
179 180 2.293677 TTATGAGCGCGTGAGACAAT 57.706 45.000 8.43 0.00 0.00 2.71
180 181 2.293677 TATGAGCGCGTGAGACAATT 57.706 45.000 8.43 0.00 0.00 2.32
181 182 1.442769 ATGAGCGCGTGAGACAATTT 58.557 45.000 8.43 0.00 0.00 1.82
182 183 1.225855 TGAGCGCGTGAGACAATTTT 58.774 45.000 8.43 0.00 0.00 1.82
183 184 1.069973 TGAGCGCGTGAGACAATTTTG 60.070 47.619 8.43 0.00 0.00 2.44
184 185 0.944386 AGCGCGTGAGACAATTTTGT 59.056 45.000 8.43 0.00 45.65 2.83
185 186 1.044725 GCGCGTGAGACAATTTTGTG 58.955 50.000 8.43 0.00 42.43 3.33
186 187 1.596954 GCGCGTGAGACAATTTTGTGT 60.597 47.619 8.43 0.00 42.43 3.72
187 188 2.715268 CGCGTGAGACAATTTTGTGTT 58.285 42.857 0.00 0.00 42.43 3.32
188 189 2.463653 CGCGTGAGACAATTTTGTGTTG 59.536 45.455 0.00 0.00 42.43 3.33
189 190 2.788786 GCGTGAGACAATTTTGTGTTGG 59.211 45.455 0.00 0.00 42.43 3.77
190 191 3.488384 GCGTGAGACAATTTTGTGTTGGA 60.488 43.478 0.00 0.00 42.43 3.53
191 192 4.667262 CGTGAGACAATTTTGTGTTGGAA 58.333 39.130 0.00 0.00 42.43 3.53
238 239 9.817365 GATCATATCTTTTAATGACGTGATTGG 57.183 33.333 10.71 0.00 35.06 3.16
252 253 6.540551 TGACGTGATTGGCTATATTTTTAGCA 59.459 34.615 0.00 0.00 45.21 3.49
324 509 5.305585 TCTATTTCTGGCGTGGGAATAATC 58.694 41.667 0.00 0.00 0.00 1.75
472 657 4.530553 TCTGAGCCATTATAATTCGGCCTA 59.469 41.667 18.58 10.17 46.08 3.93
473 658 4.575885 TGAGCCATTATAATTCGGCCTAC 58.424 43.478 18.58 12.83 46.08 3.18
483 669 4.497291 AATTCGGCCTACCAGATTAACA 57.503 40.909 0.00 0.00 34.57 2.41
507 693 8.246180 ACAGCTCACAATTTCTAATTAACATGG 58.754 33.333 0.00 0.00 0.00 3.66
510 696 8.416329 GCTCACAATTTCTAATTAACATGGGAT 58.584 33.333 0.00 0.00 0.00 3.85
619 815 2.080654 TGTTTCTTTTGTGGGGGAGG 57.919 50.000 0.00 0.00 0.00 4.30
653 849 7.801716 ATGTTAATGGTCGTATAGCAATGTT 57.198 32.000 0.00 0.00 39.48 2.71
660 856 6.993079 TGGTCGTATAGCAATGTTATCATCT 58.007 36.000 0.00 0.00 32.56 2.90
661 857 6.868339 TGGTCGTATAGCAATGTTATCATCTG 59.132 38.462 0.00 0.00 32.56 2.90
662 858 6.183360 GGTCGTATAGCAATGTTATCATCTGC 60.183 42.308 0.00 10.47 37.82 4.26
663 859 5.572896 TCGTATAGCAATGTTATCATCTGCG 59.427 40.000 0.00 0.00 39.99 5.18
664 860 5.346011 CGTATAGCAATGTTATCATCTGCGT 59.654 40.000 0.00 9.13 39.99 5.24
665 861 6.128822 CGTATAGCAATGTTATCATCTGCGTT 60.129 38.462 0.00 8.26 39.99 4.84
666 862 4.970662 AGCAATGTTATCATCTGCGTTT 57.029 36.364 11.71 0.00 39.99 3.60
667 863 5.314923 AGCAATGTTATCATCTGCGTTTT 57.685 34.783 11.71 0.00 39.99 2.43
668 864 5.097529 AGCAATGTTATCATCTGCGTTTTG 58.902 37.500 11.71 0.00 39.99 2.44
669 865 4.858692 GCAATGTTATCATCTGCGTTTTGT 59.141 37.500 5.68 0.00 32.87 2.83
670 866 6.027131 GCAATGTTATCATCTGCGTTTTGTA 58.973 36.000 5.68 0.00 32.87 2.41
671 867 6.021468 GCAATGTTATCATCTGCGTTTTGTAC 60.021 38.462 0.00 0.00 32.87 2.90
672 868 6.985188 ATGTTATCATCTGCGTTTTGTACT 57.015 33.333 0.00 0.00 0.00 2.73
673 869 6.164408 TGTTATCATCTGCGTTTTGTACTG 57.836 37.500 0.00 0.00 0.00 2.74
674 870 5.699001 TGTTATCATCTGCGTTTTGTACTGT 59.301 36.000 0.00 0.00 0.00 3.55
675 871 4.668576 ATCATCTGCGTTTTGTACTGTG 57.331 40.909 0.00 0.00 0.00 3.66
676 872 3.462982 TCATCTGCGTTTTGTACTGTGT 58.537 40.909 0.00 0.00 0.00 3.72
677 873 3.874543 TCATCTGCGTTTTGTACTGTGTT 59.125 39.130 0.00 0.00 0.00 3.32
678 874 4.334203 TCATCTGCGTTTTGTACTGTGTTT 59.666 37.500 0.00 0.00 0.00 2.83
679 875 5.524281 TCATCTGCGTTTTGTACTGTGTTTA 59.476 36.000 0.00 0.00 0.00 2.01
680 876 5.798015 TCTGCGTTTTGTACTGTGTTTAA 57.202 34.783 0.00 0.00 0.00 1.52
681 877 6.179504 TCTGCGTTTTGTACTGTGTTTAAA 57.820 33.333 0.00 0.00 0.00 1.52
682 878 6.609533 TCTGCGTTTTGTACTGTGTTTAAAA 58.390 32.000 0.00 0.00 0.00 1.52
683 879 7.251994 TCTGCGTTTTGTACTGTGTTTAAAAT 58.748 30.769 0.00 0.00 0.00 1.82
684 880 8.396390 TCTGCGTTTTGTACTGTGTTTAAAATA 58.604 29.630 0.00 0.00 0.00 1.40
685 881 8.906636 TGCGTTTTGTACTGTGTTTAAAATAA 57.093 26.923 0.00 0.00 0.00 1.40
686 882 9.517609 TGCGTTTTGTACTGTGTTTAAAATAAT 57.482 25.926 0.00 0.00 0.00 1.28
764 962 6.494893 TTTAAGAAGATTGGTCATGGTTCG 57.505 37.500 0.00 0.00 0.00 3.95
765 963 2.991250 AGAAGATTGGTCATGGTTCGG 58.009 47.619 0.00 0.00 0.00 4.30
787 985 2.648304 AGTCCAGTCCACTACTCTACCA 59.352 50.000 0.00 0.00 35.76 3.25
788 986 2.754002 GTCCAGTCCACTACTCTACCAC 59.246 54.545 0.00 0.00 35.76 4.16
789 987 2.100989 CCAGTCCACTACTCTACCACC 58.899 57.143 0.00 0.00 35.76 4.61
790 988 2.100989 CAGTCCACTACTCTACCACCC 58.899 57.143 0.00 0.00 35.76 4.61
793 991 1.192428 CCACTACTCTACCACCCACC 58.808 60.000 0.00 0.00 0.00 4.61
794 992 0.815734 CACTACTCTACCACCCACCG 59.184 60.000 0.00 0.00 0.00 4.94
811 1009 2.044946 GGGCACTGGCGATCCTTT 60.045 61.111 0.00 0.00 42.47 3.11
812 1010 2.409870 GGGCACTGGCGATCCTTTG 61.410 63.158 0.00 0.00 42.47 2.77
814 1012 1.244019 GGCACTGGCGATCCTTTGTT 61.244 55.000 0.00 0.00 42.47 2.83
818 1016 1.001393 TGGCGATCCTTTGTTCCCC 60.001 57.895 0.00 0.00 0.00 4.81
823 1021 2.092323 CGATCCTTTGTTCCCCTTTCC 58.908 52.381 0.00 0.00 0.00 3.13
824 1022 2.457598 GATCCTTTGTTCCCCTTTCCC 58.542 52.381 0.00 0.00 0.00 3.97
825 1023 1.541275 TCCTTTGTTCCCCTTTCCCT 58.459 50.000 0.00 0.00 0.00 4.20
826 1024 1.427753 TCCTTTGTTCCCCTTTCCCTC 59.572 52.381 0.00 0.00 0.00 4.30
827 1025 1.429299 CCTTTGTTCCCCTTTCCCTCT 59.571 52.381 0.00 0.00 0.00 3.69
828 1026 2.519013 CTTTGTTCCCCTTTCCCTCTG 58.481 52.381 0.00 0.00 0.00 3.35
829 1027 0.777446 TTGTTCCCCTTTCCCTCTGG 59.223 55.000 0.00 0.00 0.00 3.86
830 1028 1.000771 GTTCCCCTTTCCCTCTGGC 60.001 63.158 0.00 0.00 0.00 4.85
831 1029 2.602676 TTCCCCTTTCCCTCTGGCG 61.603 63.158 0.00 0.00 0.00 5.69
832 1030 4.115199 CCCCTTTCCCTCTGGCGG 62.115 72.222 0.00 0.00 0.00 6.13
833 1031 3.330720 CCCTTTCCCTCTGGCGGT 61.331 66.667 0.00 0.00 0.00 5.68
834 1032 2.045926 CCTTTCCCTCTGGCGGTG 60.046 66.667 0.00 0.00 0.00 4.94
835 1033 2.747855 CTTTCCCTCTGGCGGTGC 60.748 66.667 0.00 0.00 0.00 5.01
888 1111 0.107214 TGATCCGGTGAGCAAATCCC 60.107 55.000 0.00 0.00 33.08 3.85
934 1157 0.027979 CCATTACGCATTCACGCTGG 59.972 55.000 0.00 0.00 36.19 4.85
1035 1276 0.322906 CTGAAGCCCCTGTTCTTCCC 60.323 60.000 0.00 0.00 38.26 3.97
1060 1301 2.442413 CCAAAAGGAACAAGGCGGATA 58.558 47.619 0.00 0.00 0.00 2.59
1131 1372 3.518998 CTGCCCGATCTCGTCCGT 61.519 66.667 0.00 0.00 37.74 4.69
1428 1702 3.681835 GTCGTCGCCACCACTCCT 61.682 66.667 0.00 0.00 0.00 3.69
1612 1895 2.509569 TCTGCGACTCTTCTCTGAACT 58.490 47.619 0.00 0.00 0.00 3.01
1656 1939 9.301153 GTCAGTGAAAGTTTCAACAAACATAAT 57.699 29.630 19.63 0.00 43.98 1.28
1828 2147 3.645975 GGCACACCAACGACCACG 61.646 66.667 0.00 0.00 39.84 4.94
1911 2230 4.952957 TGTGTCAAGGTTTTCAAGATGGAA 59.047 37.500 0.00 0.00 0.00 3.53
2010 2329 1.278127 ACCCATAAGTTCCCGTCTGTG 59.722 52.381 0.00 0.00 0.00 3.66
2086 2405 3.868757 TGTACAATCTCAAGGACGAGG 57.131 47.619 0.00 0.00 33.59 4.63
2152 2471 0.109597 CAAGCTGTTCGTCATTGCCC 60.110 55.000 0.00 0.00 0.00 5.36
2308 3316 6.993079 TGCTATGAAACAGACTTGACTCTAA 58.007 36.000 0.00 0.00 0.00 2.10
2358 3428 1.005450 TGTGGCCCAAATTAGGACCTC 59.995 52.381 0.00 1.98 0.00 3.85
2486 3557 8.738645 ATATCTGGTTCAGTTTATTCCACTTC 57.261 34.615 0.00 0.00 32.61 3.01
2600 3680 4.370364 TTTCCGCCTTTCTGAATATTGC 57.630 40.909 0.00 0.00 0.00 3.56
2667 3758 7.494298 GGCTTTGTTCCTTGTTTCTTTTTCATA 59.506 33.333 0.00 0.00 0.00 2.15
2743 3834 6.128007 CCGTTAAGATTTGCTGTTTATGTCCT 60.128 38.462 0.00 0.00 0.00 3.85
2888 3979 8.902540 ATAAAGGCGTACAGATTGAATCATAA 57.097 30.769 8.03 0.00 0.00 1.90
2928 4019 2.333389 CGTGTCTAGATACGGCATCC 57.667 55.000 28.37 0.00 41.29 3.51
2947 4038 6.809196 GGCATCCGTATCTAGACAAATCTAAG 59.191 42.308 0.00 0.00 36.98 2.18
2952 4043 8.963725 TCCGTATCTAGACAAATCTAAGACAAA 58.036 33.333 0.00 0.00 36.98 2.83
2999 4090 8.924511 AATGTTGGTTCAGTATAGGGATATTG 57.075 34.615 0.00 0.00 0.00 1.90
3000 4091 6.296026 TGTTGGTTCAGTATAGGGATATTGC 58.704 40.000 0.00 0.00 0.00 3.56
3005 4096 2.838202 CAGTATAGGGATATTGCCGGGT 59.162 50.000 2.18 0.00 30.73 5.28
3006 4097 3.263425 CAGTATAGGGATATTGCCGGGTT 59.737 47.826 2.18 0.00 30.73 4.11
3007 4098 4.468510 CAGTATAGGGATATTGCCGGGTTA 59.531 45.833 2.18 0.00 30.73 2.85
3076 4311 4.083271 GCGTAGATTCTGTTTTTCCTGCTT 60.083 41.667 0.00 0.00 0.00 3.91
3087 4342 3.883830 TTTCCTGCTTGCTGTTTTTCA 57.116 38.095 0.00 0.00 0.00 2.69
3147 4406 6.661777 TCAGCTTATATATATGCATTGGCCA 58.338 36.000 24.64 0.00 40.13 5.36
3215 4474 2.330440 TGCAACTTCACTCTTGCTCA 57.670 45.000 4.19 0.00 42.77 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321671 ATGTACTGTTCGTGCTGCCT 59.678 50.000 0.00 0.00 0.00 4.75
1 2 0.443869 CATGTACTGTTCGTGCTGCC 59.556 55.000 0.00 0.00 0.00 4.85
2 3 1.148310 ACATGTACTGTTCGTGCTGC 58.852 50.000 0.00 0.00 32.90 5.25
3 4 2.662791 GCAACATGTACTGTTCGTGCTG 60.663 50.000 0.00 6.19 44.99 4.41
4 5 1.531149 GCAACATGTACTGTTCGTGCT 59.469 47.619 0.00 0.00 44.99 4.40
5 6 1.721489 CGCAACATGTACTGTTCGTGC 60.721 52.381 0.00 1.32 44.99 5.34
6 7 1.721489 GCGCAACATGTACTGTTCGTG 60.721 52.381 0.30 5.25 44.99 4.35
7 8 0.511221 GCGCAACATGTACTGTTCGT 59.489 50.000 0.30 0.00 44.99 3.85
8 9 0.510790 TGCGCAACATGTACTGTTCG 59.489 50.000 8.16 16.12 44.99 3.95
9 10 1.262950 TGTGCGCAACATGTACTGTTC 59.737 47.619 14.00 0.00 44.99 3.18
11 12 2.999356 TGTGCGCAACATGTACTGT 58.001 47.368 14.00 0.00 40.84 3.55
19 20 1.227793 TCAGTCCATGTGCGCAACA 60.228 52.632 14.00 13.76 44.79 3.33
20 21 1.207593 GTCAGTCCATGTGCGCAAC 59.792 57.895 14.00 6.31 0.00 4.17
21 22 0.606130 ATGTCAGTCCATGTGCGCAA 60.606 50.000 14.00 2.60 0.00 4.85
22 23 0.248843 TATGTCAGTCCATGTGCGCA 59.751 50.000 5.66 5.66 0.00 6.09
23 24 1.586422 ATATGTCAGTCCATGTGCGC 58.414 50.000 0.00 0.00 0.00 6.09
24 25 3.928992 GGATATATGTCAGTCCATGTGCG 59.071 47.826 1.63 0.00 0.00 5.34
25 26 5.157940 AGGATATATGTCAGTCCATGTGC 57.842 43.478 1.63 0.00 33.12 4.57
26 27 5.936372 CCAAGGATATATGTCAGTCCATGTG 59.064 44.000 1.63 0.00 33.12 3.21
27 28 5.846164 TCCAAGGATATATGTCAGTCCATGT 59.154 40.000 1.63 0.00 33.12 3.21
28 29 6.364568 TCCAAGGATATATGTCAGTCCATG 57.635 41.667 1.63 0.00 33.12 3.66
29 30 6.964679 AGATCCAAGGATATATGTCAGTCCAT 59.035 38.462 0.68 0.00 34.60 3.41
30 31 6.326161 AGATCCAAGGATATATGTCAGTCCA 58.674 40.000 0.68 0.00 34.60 4.02
31 32 6.865834 AGATCCAAGGATATATGTCAGTCC 57.134 41.667 0.68 0.00 34.60 3.85
32 33 9.566432 AAAAAGATCCAAGGATATATGTCAGTC 57.434 33.333 0.68 0.00 34.60 3.51
33 34 9.347240 CAAAAAGATCCAAGGATATATGTCAGT 57.653 33.333 0.68 0.00 34.60 3.41
34 35 8.790718 CCAAAAAGATCCAAGGATATATGTCAG 58.209 37.037 0.68 0.00 34.60 3.51
35 36 7.725397 CCCAAAAAGATCCAAGGATATATGTCA 59.275 37.037 0.68 0.00 34.60 3.58
36 37 7.944554 TCCCAAAAAGATCCAAGGATATATGTC 59.055 37.037 0.68 0.00 34.60 3.06
37 38 7.725844 GTCCCAAAAAGATCCAAGGATATATGT 59.274 37.037 0.68 0.00 34.60 2.29
38 39 7.725397 TGTCCCAAAAAGATCCAAGGATATATG 59.275 37.037 0.68 0.23 34.60 1.78
39 40 7.825709 TGTCCCAAAAAGATCCAAGGATATAT 58.174 34.615 0.68 0.00 34.60 0.86
40 41 7.219601 TGTCCCAAAAAGATCCAAGGATATA 57.780 36.000 0.68 0.00 34.60 0.86
41 42 6.091076 TGTCCCAAAAAGATCCAAGGATAT 57.909 37.500 0.68 0.00 34.60 1.63
42 43 5.528600 TGTCCCAAAAAGATCCAAGGATA 57.471 39.130 0.68 0.00 34.60 2.59
43 44 4.402616 TGTCCCAAAAAGATCCAAGGAT 57.597 40.909 0.16 0.16 37.59 3.24
44 45 3.893753 TGTCCCAAAAAGATCCAAGGA 57.106 42.857 0.00 0.00 0.00 3.36
45 46 4.344968 AGTTTGTCCCAAAAAGATCCAAGG 59.655 41.667 0.00 0.00 0.00 3.61
46 47 5.509670 GGAGTTTGTCCCAAAAAGATCCAAG 60.510 44.000 0.00 0.00 39.88 3.61
47 48 4.343814 GGAGTTTGTCCCAAAAAGATCCAA 59.656 41.667 0.00 0.00 39.88 3.53
48 49 3.895041 GGAGTTTGTCCCAAAAAGATCCA 59.105 43.478 0.00 0.00 39.88 3.41
49 50 4.521130 GGAGTTTGTCCCAAAAAGATCC 57.479 45.455 0.00 0.00 39.88 3.36
60 61 2.094649 CGTCTAGAGTGGGAGTTTGTCC 60.095 54.545 0.00 0.00 46.10 4.02
61 62 2.094649 CCGTCTAGAGTGGGAGTTTGTC 60.095 54.545 0.00 0.00 0.00 3.18
62 63 1.893801 CCGTCTAGAGTGGGAGTTTGT 59.106 52.381 0.00 0.00 0.00 2.83
63 64 2.168496 TCCGTCTAGAGTGGGAGTTTG 58.832 52.381 10.35 0.00 0.00 2.93
64 65 2.599408 TCCGTCTAGAGTGGGAGTTT 57.401 50.000 10.35 0.00 0.00 2.66
65 66 2.599408 TTCCGTCTAGAGTGGGAGTT 57.401 50.000 10.35 0.00 0.00 3.01
66 67 2.379972 CATTCCGTCTAGAGTGGGAGT 58.620 52.381 10.35 4.36 0.00 3.85
67 68 1.683917 CCATTCCGTCTAGAGTGGGAG 59.316 57.143 10.35 0.61 39.37 4.30
68 69 1.776662 CCATTCCGTCTAGAGTGGGA 58.223 55.000 10.35 6.99 39.37 4.37
69 70 0.105039 GCCATTCCGTCTAGAGTGGG 59.895 60.000 10.35 4.88 42.39 4.61
70 71 0.249073 CGCCATTCCGTCTAGAGTGG 60.249 60.000 4.81 4.81 44.35 4.00
71 72 0.738975 TCGCCATTCCGTCTAGAGTG 59.261 55.000 0.00 0.00 0.00 3.51
72 73 1.693627 ATCGCCATTCCGTCTAGAGT 58.306 50.000 0.00 0.00 0.00 3.24
73 74 2.294791 AGAATCGCCATTCCGTCTAGAG 59.705 50.000 0.00 0.00 39.58 2.43
74 75 2.307768 AGAATCGCCATTCCGTCTAGA 58.692 47.619 0.00 0.00 39.58 2.43
75 76 2.797156 CAAGAATCGCCATTCCGTCTAG 59.203 50.000 0.00 0.00 39.58 2.43
76 77 2.429250 TCAAGAATCGCCATTCCGTCTA 59.571 45.455 0.00 0.00 39.58 2.59
77 78 1.207089 TCAAGAATCGCCATTCCGTCT 59.793 47.619 0.00 0.00 39.58 4.18
78 79 1.651987 TCAAGAATCGCCATTCCGTC 58.348 50.000 0.00 0.00 39.58 4.79
79 80 2.009774 CTTCAAGAATCGCCATTCCGT 58.990 47.619 0.00 0.00 39.58 4.69
80 81 1.331756 CCTTCAAGAATCGCCATTCCG 59.668 52.381 0.00 0.00 39.58 4.30
81 82 2.615912 CTCCTTCAAGAATCGCCATTCC 59.384 50.000 0.00 0.00 39.58 3.01
82 83 2.032675 GCTCCTTCAAGAATCGCCATTC 59.967 50.000 0.00 0.00 39.10 2.67
83 84 2.019984 GCTCCTTCAAGAATCGCCATT 58.980 47.619 0.00 0.00 0.00 3.16
84 85 1.673168 GCTCCTTCAAGAATCGCCAT 58.327 50.000 0.00 0.00 0.00 4.40
85 86 0.740868 CGCTCCTTCAAGAATCGCCA 60.741 55.000 0.00 0.00 0.00 5.69
86 87 1.432270 CCGCTCCTTCAAGAATCGCC 61.432 60.000 0.00 0.00 0.00 5.54
87 88 0.741221 ACCGCTCCTTCAAGAATCGC 60.741 55.000 0.00 0.00 0.00 4.58
88 89 1.002366 CACCGCTCCTTCAAGAATCG 58.998 55.000 0.00 0.00 0.00 3.34
89 90 1.339151 ACCACCGCTCCTTCAAGAATC 60.339 52.381 0.00 0.00 0.00 2.52
90 91 0.693049 ACCACCGCTCCTTCAAGAAT 59.307 50.000 0.00 0.00 0.00 2.40
91 92 0.472471 AACCACCGCTCCTTCAAGAA 59.528 50.000 0.00 0.00 0.00 2.52
92 93 0.250295 CAACCACCGCTCCTTCAAGA 60.250 55.000 0.00 0.00 0.00 3.02
93 94 0.535102 ACAACCACCGCTCCTTCAAG 60.535 55.000 0.00 0.00 0.00 3.02
94 95 0.817634 CACAACCACCGCTCCTTCAA 60.818 55.000 0.00 0.00 0.00 2.69
95 96 1.227823 CACAACCACCGCTCCTTCA 60.228 57.895 0.00 0.00 0.00 3.02
96 97 1.966451 CCACAACCACCGCTCCTTC 60.966 63.158 0.00 0.00 0.00 3.46
97 98 2.113139 CCACAACCACCGCTCCTT 59.887 61.111 0.00 0.00 0.00 3.36
98 99 4.643387 GCCACAACCACCGCTCCT 62.643 66.667 0.00 0.00 0.00 3.69
103 104 4.326766 CAAGCGCCACAACCACCG 62.327 66.667 2.29 0.00 0.00 4.94
104 105 4.645921 GCAAGCGCCACAACCACC 62.646 66.667 2.29 0.00 0.00 4.61
105 106 4.980903 CGCAAGCGCCACAACCAC 62.981 66.667 2.29 0.00 33.11 4.16
108 109 4.389576 CTCCGCAAGCGCCACAAC 62.390 66.667 9.26 0.00 38.24 3.32
112 113 4.838152 GATCCTCCGCAAGCGCCA 62.838 66.667 9.26 0.00 38.24 5.69
113 114 4.537433 AGATCCTCCGCAAGCGCC 62.537 66.667 9.26 0.00 38.24 6.53
114 115 1.648467 AAAAGATCCTCCGCAAGCGC 61.648 55.000 9.26 0.00 38.24 5.92
115 116 0.375106 GAAAAGATCCTCCGCAAGCG 59.625 55.000 7.60 7.60 39.44 4.68
116 117 1.743996 AGAAAAGATCCTCCGCAAGC 58.256 50.000 0.00 0.00 0.00 4.01
117 118 3.077359 ACAAGAAAAGATCCTCCGCAAG 58.923 45.455 0.00 0.00 0.00 4.01
118 119 3.140325 ACAAGAAAAGATCCTCCGCAA 57.860 42.857 0.00 0.00 0.00 4.85
119 120 2.859165 ACAAGAAAAGATCCTCCGCA 57.141 45.000 0.00 0.00 0.00 5.69
120 121 5.819825 ATTAACAAGAAAAGATCCTCCGC 57.180 39.130 0.00 0.00 0.00 5.54
121 122 7.064253 ACGTTATTAACAAGAAAAGATCCTCCG 59.936 37.037 7.31 0.00 0.00 4.63
122 123 8.175716 CACGTTATTAACAAGAAAAGATCCTCC 58.824 37.037 7.31 0.00 0.00 4.30
123 124 8.932791 TCACGTTATTAACAAGAAAAGATCCTC 58.067 33.333 7.31 0.00 0.00 3.71
124 125 8.842358 TCACGTTATTAACAAGAAAAGATCCT 57.158 30.769 7.31 0.00 0.00 3.24
128 129 9.872757 GTCAATCACGTTATTAACAAGAAAAGA 57.127 29.630 7.31 2.20 0.00 2.52
129 130 9.878599 AGTCAATCACGTTATTAACAAGAAAAG 57.121 29.630 7.31 0.33 0.00 2.27
142 143 9.124807 CGCTCATAATTATAGTCAATCACGTTA 57.875 33.333 0.00 0.00 0.00 3.18
143 144 7.359264 GCGCTCATAATTATAGTCAATCACGTT 60.359 37.037 0.00 0.00 0.00 3.99
144 145 6.089551 GCGCTCATAATTATAGTCAATCACGT 59.910 38.462 0.00 0.00 0.00 4.49
145 146 6.461816 GCGCTCATAATTATAGTCAATCACG 58.538 40.000 0.00 0.00 0.00 4.35
146 147 6.089551 ACGCGCTCATAATTATAGTCAATCAC 59.910 38.462 5.73 0.00 0.00 3.06
147 148 6.089417 CACGCGCTCATAATTATAGTCAATCA 59.911 38.462 5.73 0.00 0.00 2.57
148 149 6.308041 TCACGCGCTCATAATTATAGTCAATC 59.692 38.462 5.73 0.00 0.00 2.67
149 150 6.156519 TCACGCGCTCATAATTATAGTCAAT 58.843 36.000 5.73 0.00 0.00 2.57
150 151 5.525199 TCACGCGCTCATAATTATAGTCAA 58.475 37.500 5.73 0.00 0.00 3.18
151 152 5.048991 TCTCACGCGCTCATAATTATAGTCA 60.049 40.000 5.73 0.00 0.00 3.41
152 153 5.284188 GTCTCACGCGCTCATAATTATAGTC 59.716 44.000 5.73 0.00 0.00 2.59
153 154 5.154932 GTCTCACGCGCTCATAATTATAGT 58.845 41.667 5.73 0.00 0.00 2.12
154 155 5.154222 TGTCTCACGCGCTCATAATTATAG 58.846 41.667 5.73 0.00 0.00 1.31
155 156 5.116069 TGTCTCACGCGCTCATAATTATA 57.884 39.130 5.73 0.00 0.00 0.98
156 157 3.977427 TGTCTCACGCGCTCATAATTAT 58.023 40.909 5.73 0.00 0.00 1.28
157 158 3.430333 TGTCTCACGCGCTCATAATTA 57.570 42.857 5.73 0.00 0.00 1.40
158 159 2.293677 TGTCTCACGCGCTCATAATT 57.706 45.000 5.73 0.00 0.00 1.40
159 160 2.293677 TTGTCTCACGCGCTCATAAT 57.706 45.000 5.73 0.00 0.00 1.28
160 161 2.293677 ATTGTCTCACGCGCTCATAA 57.706 45.000 5.73 0.00 0.00 1.90
161 162 2.293677 AATTGTCTCACGCGCTCATA 57.706 45.000 5.73 0.00 0.00 2.15
162 163 1.442769 AAATTGTCTCACGCGCTCAT 58.557 45.000 5.73 0.00 0.00 2.90
163 164 1.069973 CAAAATTGTCTCACGCGCTCA 60.070 47.619 5.73 0.00 0.00 4.26
164 165 1.069906 ACAAAATTGTCTCACGCGCTC 60.070 47.619 5.73 0.00 36.50 5.03
165 166 0.944386 ACAAAATTGTCTCACGCGCT 59.056 45.000 5.73 0.00 36.50 5.92
166 167 1.044725 CACAAAATTGTCTCACGCGC 58.955 50.000 5.73 0.00 39.91 6.86
167 168 2.383298 ACACAAAATTGTCTCACGCG 57.617 45.000 3.53 3.53 39.91 6.01
168 169 2.788786 CCAACACAAAATTGTCTCACGC 59.211 45.455 0.00 0.00 39.91 5.34
169 170 4.285807 TCCAACACAAAATTGTCTCACG 57.714 40.909 0.00 0.00 39.91 4.35
170 171 5.650543 AGTTCCAACACAAAATTGTCTCAC 58.349 37.500 0.00 0.00 39.91 3.51
171 172 5.913137 AGTTCCAACACAAAATTGTCTCA 57.087 34.783 0.00 0.00 39.91 3.27
172 173 7.595311 AAAAGTTCCAACACAAAATTGTCTC 57.405 32.000 0.00 0.00 39.91 3.36
173 174 7.977789 AAAAAGTTCCAACACAAAATTGTCT 57.022 28.000 0.00 0.00 39.91 3.41
238 239 9.971922 AATGTCTTTCCATGCTAAAAATATAGC 57.028 29.630 0.00 0.00 46.78 2.97
252 253 7.729116 AGTTCATCACAAAAATGTCTTTCCAT 58.271 30.769 0.00 0.00 0.00 3.41
285 286 6.417930 CAGAAATAGAGCGAATCACGTCATTA 59.582 38.462 0.00 0.00 44.60 1.90
286 287 5.233050 CAGAAATAGAGCGAATCACGTCATT 59.767 40.000 0.00 0.00 44.60 2.57
287 288 4.742167 CAGAAATAGAGCGAATCACGTCAT 59.258 41.667 0.00 0.00 44.60 3.06
472 657 6.006449 AGAAATTGTGAGCTGTTAATCTGGT 58.994 36.000 0.00 0.00 0.00 4.00
473 658 6.506500 AGAAATTGTGAGCTGTTAATCTGG 57.493 37.500 0.00 0.00 0.00 3.86
483 669 7.615365 TCCCATGTTAATTAGAAATTGTGAGCT 59.385 33.333 0.00 0.00 0.00 4.09
573 769 9.967451 TTGTTTGTTCCCAATAACATCTATCTA 57.033 29.630 0.00 0.00 39.04 1.98
574 770 8.877864 TTGTTTGTTCCCAATAACATCTATCT 57.122 30.769 0.00 0.00 39.04 1.98
575 771 9.520204 CATTGTTTGTTCCCAATAACATCTATC 57.480 33.333 0.00 0.00 39.04 2.08
576 772 9.034800 ACATTGTTTGTTCCCAATAACATCTAT 57.965 29.630 0.00 0.00 39.04 1.98
577 773 8.415950 ACATTGTTTGTTCCCAATAACATCTA 57.584 30.769 0.00 0.00 39.04 1.98
578 774 7.301868 ACATTGTTTGTTCCCAATAACATCT 57.698 32.000 0.00 0.00 39.04 2.90
579 775 7.961325 AACATTGTTTGTTCCCAATAACATC 57.039 32.000 0.00 0.00 45.55 3.06
611 807 0.863956 ATTGTTTGTTCCCTCCCCCA 59.136 50.000 0.00 0.00 0.00 4.96
619 815 5.525199 ACGACCATTAACATTGTTTGTTCC 58.475 37.500 7.45 0.00 45.55 3.62
653 849 5.234752 ACACAGTACAAAACGCAGATGATA 58.765 37.500 0.00 0.00 0.00 2.15
660 856 8.906636 TTATTTTAAACACAGTACAAAACGCA 57.093 26.923 0.00 0.00 0.00 5.24
731 927 9.184523 TGACCAATCTTCTTAAAAAGAAAGACA 57.815 29.630 0.00 0.00 46.13 3.41
734 930 9.415544 CCATGACCAATCTTCTTAAAAAGAAAG 57.584 33.333 0.00 0.00 46.13 2.62
744 940 3.009033 TCCGAACCATGACCAATCTTCTT 59.991 43.478 0.00 0.00 0.00 2.52
745 941 2.571653 TCCGAACCATGACCAATCTTCT 59.428 45.455 0.00 0.00 0.00 2.85
746 942 2.939103 CTCCGAACCATGACCAATCTTC 59.061 50.000 0.00 0.00 0.00 2.87
748 944 1.909302 ACTCCGAACCATGACCAATCT 59.091 47.619 0.00 0.00 0.00 2.40
755 953 0.895530 GACTGGACTCCGAACCATGA 59.104 55.000 0.00 0.00 35.54 3.07
764 962 2.517998 AGAGTAGTGGACTGGACTCC 57.482 55.000 6.22 0.00 39.06 3.85
765 963 3.281158 GGTAGAGTAGTGGACTGGACTC 58.719 54.545 2.63 2.63 39.06 3.36
793 991 3.976701 AAAGGATCGCCAGTGCCCG 62.977 63.158 0.00 0.00 36.29 6.13
794 992 2.044946 AAAGGATCGCCAGTGCCC 60.045 61.111 0.00 0.00 36.29 5.36
798 996 0.322546 GGGAACAAAGGATCGCCAGT 60.323 55.000 0.00 0.00 36.29 4.00
801 999 0.323451 AAGGGGAACAAAGGATCGCC 60.323 55.000 1.01 1.01 45.65 5.54
803 1001 2.092323 GGAAAGGGGAACAAAGGATCG 58.908 52.381 0.00 0.00 0.00 3.69
811 1009 1.789576 GCCAGAGGGAAAGGGGAACA 61.790 60.000 0.00 0.00 35.59 3.18
812 1010 1.000771 GCCAGAGGGAAAGGGGAAC 60.001 63.158 0.00 0.00 35.59 3.62
814 1012 3.009115 CGCCAGAGGGAAAGGGGA 61.009 66.667 0.00 0.00 37.54 4.81
818 1016 2.747855 GCACCGCCAGAGGGAAAG 60.748 66.667 0.00 0.00 35.59 2.62
823 1021 4.154347 GAGGAGCACCGCCAGAGG 62.154 72.222 0.00 0.00 41.83 3.69
824 1022 2.570582 GAAGAGGAGCACCGCCAGAG 62.571 65.000 0.00 0.00 41.83 3.35
825 1023 2.604686 AAGAGGAGCACCGCCAGA 60.605 61.111 0.00 0.00 41.83 3.86
826 1024 2.125350 GAAGAGGAGCACCGCCAG 60.125 66.667 0.00 0.00 41.83 4.85
827 1025 2.217038 AAGAAGAGGAGCACCGCCA 61.217 57.895 0.00 0.00 41.83 5.69
828 1026 1.743252 CAAGAAGAGGAGCACCGCC 60.743 63.158 0.00 0.00 41.83 6.13
829 1027 1.743252 CCAAGAAGAGGAGCACCGC 60.743 63.158 0.00 0.00 41.83 5.68
830 1028 1.078848 CCCAAGAAGAGGAGCACCG 60.079 63.158 0.00 0.00 41.83 4.94
831 1029 1.377856 GCCCAAGAAGAGGAGCACC 60.378 63.158 0.00 0.00 0.00 5.01
832 1030 0.392327 GAGCCCAAGAAGAGGAGCAC 60.392 60.000 0.00 0.00 0.00 4.40
833 1031 1.557269 GGAGCCCAAGAAGAGGAGCA 61.557 60.000 0.00 0.00 0.00 4.26
834 1032 1.223211 GGAGCCCAAGAAGAGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
835 1033 0.540923 CAGGAGCCCAAGAAGAGGAG 59.459 60.000 0.00 0.00 0.00 3.69
839 1037 1.130054 ACAGCAGGAGCCCAAGAAGA 61.130 55.000 0.00 0.00 43.56 2.87
891 1114 0.102481 AACGGAATCGATCGAGTGGG 59.898 55.000 24.20 15.89 40.11 4.61
934 1157 5.640357 TCGATAGTACAAATTTGTGGGTGAC 59.360 40.000 29.72 20.20 42.31 3.67
1015 1238 0.402121 GGAAGAACAGGGGCTTCAGT 59.598 55.000 0.00 0.00 41.69 3.41
1035 1276 1.665442 CTTGTTCCTTTTGGCGGGG 59.335 57.895 0.00 0.00 40.12 5.73
1060 1301 2.425312 CTGAGGTATGCAGAAGACTCGT 59.575 50.000 0.00 0.00 35.39 4.18
1064 1305 1.565305 CGCTGAGGTATGCAGAAGAC 58.435 55.000 0.00 0.00 35.39 3.01
1320 1591 3.479269 GCGCCGTCGTTCAGGAAG 61.479 66.667 0.00 0.00 38.14 3.46
1612 1895 0.107831 ACAGGAGCAGCCACGTAAAA 59.892 50.000 0.00 0.00 40.02 1.52
1656 1939 9.504708 TTCCGTAAGAAATAATAAGTGGAAACA 57.495 29.630 0.00 0.00 43.02 2.83
1828 2147 0.534203 TCGACAAGGAAACACCAGCC 60.534 55.000 0.00 0.00 42.04 4.85
1869 2188 0.036105 ATCGGTGCAGCTTGATGACA 60.036 50.000 14.92 0.00 0.00 3.58
2010 2329 0.543749 AGTAGATGCAGTTGGCCTCC 59.456 55.000 3.32 0.00 43.89 4.30
2045 2364 1.415289 TGCAGATGTAGGCAGATGAGG 59.585 52.381 0.00 0.00 34.58 3.86
2046 2365 2.904697 TGCAGATGTAGGCAGATGAG 57.095 50.000 0.00 0.00 34.58 2.90
2086 2405 3.550639 CCAGCTGAGATCATCTCGTCTTC 60.551 52.174 17.39 0.00 46.25 2.87
2152 2471 2.983592 GGTGAAAGGGCGGTGTGG 60.984 66.667 0.00 0.00 0.00 4.17
2278 2597 6.868864 GTCAAGTCTGTTTCATAGCAAGACTA 59.131 38.462 4.21 0.00 34.55 2.59
2308 3316 8.215736 AGTAGTTCCACCACAGTTAAAATAACT 58.784 33.333 0.00 0.00 0.00 2.24
2358 3428 5.221601 ACAGATAGAGCACTGGGTTCATATG 60.222 44.000 0.00 0.00 38.30 1.78
2486 3557 3.350833 AGTTGCAGGGCTAAATTCAGAG 58.649 45.455 0.00 0.00 0.00 3.35
2600 3680 5.824429 TGTTCAAAGATTCAGTTGCAGAAG 58.176 37.500 0.00 0.00 0.00 2.85
2667 3758 2.037772 CAGTAGCGCCTGGAATTAGGAT 59.962 50.000 2.29 0.00 40.42 3.24
2719 3810 6.842163 AGGACATAAACAGCAAATCTTAACG 58.158 36.000 0.00 0.00 0.00 3.18
2743 3834 7.013178 TCAGCAATCACAAACTGTCAGAAATTA 59.987 33.333 6.91 0.00 0.00 1.40
2888 3979 7.341805 ACACGGACGGAGGTAATACTATATAT 58.658 38.462 0.00 0.00 0.00 0.86
2923 4014 7.539366 GTCTTAGATTTGTCTAGATACGGATGC 59.461 40.741 0.00 0.00 0.00 3.91
2927 4018 9.751542 ATTTGTCTTAGATTTGTCTAGATACGG 57.248 33.333 0.00 0.00 0.00 4.02
2938 4029 9.289303 CGTCCCAAATTATTTGTCTTAGATTTG 57.711 33.333 15.40 0.00 38.98 2.32
2947 4038 8.989653 TTAAATTCCGTCCCAAATTATTTGTC 57.010 30.769 15.40 5.99 38.98 3.18
3005 4096 4.348461 TGATATTACTCCAACCCGGCATAA 59.652 41.667 0.00 0.00 33.14 1.90
3006 4097 3.904965 TGATATTACTCCAACCCGGCATA 59.095 43.478 0.00 0.00 33.14 3.14
3007 4098 2.708861 TGATATTACTCCAACCCGGCAT 59.291 45.455 0.00 0.00 33.14 4.40
3046 4147 5.551760 AAAACAGAATCTACGCCAATCTG 57.448 39.130 0.00 0.00 42.43 2.90
3087 4342 9.649167 CCCGGTTCGAATCTAAATATAATAAGT 57.351 33.333 6.88 0.00 0.00 2.24
3147 4406 2.524306 TGATTGAAGTCGGCCCAATTT 58.476 42.857 0.00 0.00 31.40 1.82
3162 4421 5.106515 TGCCAATGTTCAAATTGCATGATTG 60.107 36.000 0.00 0.00 36.42 2.67


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

AutoCloner maintained by Alex Coulton.