Multiple sequence alignment - TraesCS3B01G428000

Loading Multiple Alignment...

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 TraesCS3B01G428000 chr3B 100.000 3314 0 0 1 3314 666792837 666789524 0.000000e+00 6120.0
1 TraesCS3B01G428000 chr3D 94.348 2141 86 18 419 2533 505066941 505064810 0.000000e+00 3251.0
2 TraesCS3B01G428000 chr3D 89.900 802 62 7 2528 3314 505064767 505063970 0.000000e+00 1014.0
3 TraesCS3B01G428000 chr3D 91.257 183 10 3 224 400 505067107 505066925 9.190000e-61 244.0
4 TraesCS3B01G428000 chr3A 92.316 1822 90 23 723 2533 643211000 643209218 0.000000e+00 2543.0
5 TraesCS3B01G428000 chr3A 89.077 531 29 11 213 726 643212678 643212160 1.680000e-177 632.0
6 TraesCS3B01G428000 chr3A 91.701 241 14 1 2528 2762 643209175 643208935 2.470000e-86 329.0
7 TraesCS3B01G428000 chr3A 87.448 239 29 1 3076 3314 643208936 643208699 1.170000e-69 274.0
8 TraesCS3B01G428000 chr6D 85.731 841 82 19 1081 1902 431470629 431469808 0.000000e+00 854.0
9 TraesCS3B01G428000 chr6D 100.000 28 0 0 2502 2529 263940940 263940913 6.000000e-03 52.8
10 TraesCS3B01G428000 chr6B 85.319 831 87 19 1082 1896 651423116 651423927 0.000000e+00 826.0
11 TraesCS3B01G428000 chr6B 100.000 28 0 0 2502 2529 404990437 404990410 6.000000e-03 52.8
12 TraesCS3B01G428000 chrUn 84.982 839 92 21 1081 1902 74559370 74558549 0.000000e+00 821.0
13 TraesCS3B01G428000 chr2B 81.094 841 143 15 1070 1902 485751273 485750441 0.000000e+00 658.0
14 TraesCS3B01G428000 chr2A 80.524 878 153 17 1056 1924 579583340 579584208 0.000000e+00 658.0
15 TraesCS3B01G428000 chr2D 80.090 884 158 18 1056 1930 412254627 412255501 2.790000e-180 641.0
16 TraesCS3B01G428000 chr7D 85.714 56 8 0 36 91 42928266 42928321 3.570000e-05 60.2
17 TraesCS3B01G428000 chr1B 88.000 50 4 2 3158 3206 478053232 478053184 1.280000e-04 58.4
18 TraesCS3B01G428000 chr1D 100.000 28 0 0 2502 2529 240127324 240127297 6.000000e-03 52.8


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 TraesCS3B01G428000 chr3B 666789524 666792837 3313 True 6120.0 6120 100.0000 1 3314 1 chr3B.!!$R1 3313
1 TraesCS3B01G428000 chr3D 505063970 505067107 3137 True 1503.0 3251 91.8350 224 3314 3 chr3D.!!$R1 3090
2 TraesCS3B01G428000 chr3A 643208699 643212678 3979 True 944.5 2543 90.1355 213 3314 4 chr3A.!!$R1 3101
3 TraesCS3B01G428000 chr6D 431469808 431470629 821 True 854.0 854 85.7310 1081 1902 1 chr6D.!!$R2 821
4 TraesCS3B01G428000 chr6B 651423116 651423927 811 False 826.0 826 85.3190 1082 1896 1 chr6B.!!$F1 814
5 TraesCS3B01G428000 chrUn 74558549 74559370 821 True 821.0 821 84.9820 1081 1902 1 chrUn.!!$R1 821
6 TraesCS3B01G428000 chr2B 485750441 485751273 832 True 658.0 658 81.0940 1070 1902 1 chr2B.!!$R1 832
7 TraesCS3B01G428000 chr2A 579583340 579584208 868 False 658.0 658 80.5240 1056 1924 1 chr2A.!!$F1 868
8 TraesCS3B01G428000 chr2D 412254627 412255501 874 False 641.0 641 80.0900 1056 1930 1 chr2D.!!$F1 874

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
155 156 0.109179 TGTTTCAATCATGCGGCTGC 60.109 50.0 11.65 11.65 43.20 5.25 F
156 157 0.171903 GTTTCAATCATGCGGCTGCT 59.828 50.0 20.27 0.83 43.34 4.24 F
991 2193 0.183492 TTTCTGCAGAGTTGGCCACT 59.817 50.0 17.43 6.18 39.07 4.00 F
992 2194 0.183492 TTCTGCAGAGTTGGCCACTT 59.817 50.0 17.43 0.00 35.01 3.16 F
1914 3171 0.665835 CGTTCGATCAGGAGGAGGAG 59.334 60.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 3171 0.105709 CCTCCTCCTCCTCCTCTTCC 60.106 65.0 0.00 0.0 0.00 3.46 R
1920 3177 0.336737 TCTTCACCTCCTCCTCCTCC 59.663 60.0 0.00 0.0 0.00 4.30 R
2225 3482 0.105593 CTGCGCCACCTCATCTATGT 59.894 55.0 4.18 0.0 0.00 2.29 R
2307 3564 0.807667 CTGCGTGGCTATGTCACTCC 60.808 60.0 0.89 0.0 35.84 3.85 R
3085 4407 0.031178 GATTTGACATGGCATCGGGC 59.969 55.0 0.00 0.0 43.74 6.13 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 4.917474 GCAAAATTCGGCCTGCAT 57.083 50.000 7.48 0.00 34.87 3.96
19 20 2.292103 GCAAAATTCGGCCTGCATAA 57.708 45.000 7.48 0.00 34.87 1.90
20 21 1.926510 GCAAAATTCGGCCTGCATAAC 59.073 47.619 7.48 0.00 34.87 1.89
21 22 2.539476 CAAAATTCGGCCTGCATAACC 58.461 47.619 0.00 0.00 0.00 2.85
23 24 1.724582 AATTCGGCCTGCATAACCGC 61.725 55.000 15.23 0.22 46.49 5.68
24 25 4.849310 TCGGCCTGCATAACCGCC 62.849 66.667 15.23 7.80 46.49 6.13
26 27 4.506255 GGCCTGCATAACCGCCCT 62.506 66.667 0.00 0.00 35.23 5.19
27 28 2.902343 GCCTGCATAACCGCCCTC 60.902 66.667 0.00 0.00 0.00 4.30
28 29 2.589540 CCTGCATAACCGCCCTCA 59.410 61.111 0.00 0.00 0.00 3.86
29 30 1.149174 CCTGCATAACCGCCCTCAT 59.851 57.895 0.00 0.00 0.00 2.90
30 31 1.168407 CCTGCATAACCGCCCTCATG 61.168 60.000 0.00 0.00 0.00 3.07
31 32 1.789078 CTGCATAACCGCCCTCATGC 61.789 60.000 0.00 0.00 43.22 4.06
48 49 3.568093 GCGACCTGCAAACACATTT 57.432 47.368 0.00 0.00 45.45 2.32
49 50 1.851658 GCGACCTGCAAACACATTTT 58.148 45.000 0.00 0.00 45.45 1.82
50 51 3.006659 GCGACCTGCAAACACATTTTA 57.993 42.857 0.00 0.00 45.45 1.52
51 52 2.979813 GCGACCTGCAAACACATTTTAG 59.020 45.455 0.00 0.00 45.45 1.85
52 53 3.304391 GCGACCTGCAAACACATTTTAGA 60.304 43.478 0.00 0.00 45.45 2.10
53 54 4.466828 CGACCTGCAAACACATTTTAGAG 58.533 43.478 0.00 0.00 0.00 2.43
54 55 4.613622 CGACCTGCAAACACATTTTAGAGG 60.614 45.833 0.00 0.00 0.00 3.69
55 56 4.215109 ACCTGCAAACACATTTTAGAGGT 58.785 39.130 0.00 0.00 0.00 3.85
56 57 4.278419 ACCTGCAAACACATTTTAGAGGTC 59.722 41.667 0.00 0.00 28.32 3.85
57 58 4.466828 CTGCAAACACATTTTAGAGGTCG 58.533 43.478 0.00 0.00 0.00 4.79
58 59 3.252215 TGCAAACACATTTTAGAGGTCGG 59.748 43.478 0.00 0.00 0.00 4.79
59 60 3.821841 CAAACACATTTTAGAGGTCGGC 58.178 45.455 0.00 0.00 0.00 5.54
60 61 2.851263 ACACATTTTAGAGGTCGGCA 57.149 45.000 0.00 0.00 0.00 5.69
61 62 3.134574 ACACATTTTAGAGGTCGGCAA 57.865 42.857 0.00 0.00 0.00 4.52
62 63 3.482436 ACACATTTTAGAGGTCGGCAAA 58.518 40.909 0.00 0.00 0.00 3.68
63 64 3.886505 ACACATTTTAGAGGTCGGCAAAA 59.113 39.130 0.00 0.00 0.00 2.44
64 65 4.522789 ACACATTTTAGAGGTCGGCAAAAT 59.477 37.500 0.00 0.00 32.29 1.82
65 66 4.858692 CACATTTTAGAGGTCGGCAAAATG 59.141 41.667 17.00 17.00 46.44 2.32
66 67 3.569250 TTTTAGAGGTCGGCAAAATGC 57.431 42.857 0.00 0.00 44.08 3.56
67 68 1.083489 TTAGAGGTCGGCAAAATGCG 58.917 50.000 0.00 0.00 46.21 4.73
68 69 0.742990 TAGAGGTCGGCAAAATGCGG 60.743 55.000 3.77 3.77 46.21 5.69
69 70 3.051392 GAGGTCGGCAAAATGCGGG 62.051 63.158 9.56 0.00 46.21 6.13
70 71 4.128388 GGTCGGCAAAATGCGGGG 62.128 66.667 9.56 0.00 46.21 5.73
71 72 3.370231 GTCGGCAAAATGCGGGGT 61.370 61.111 9.56 0.00 46.21 4.95
72 73 3.059386 TCGGCAAAATGCGGGGTC 61.059 61.111 9.56 0.00 46.21 4.46
73 74 3.061848 CGGCAAAATGCGGGGTCT 61.062 61.111 2.33 0.00 46.21 3.85
74 75 2.573340 GGCAAAATGCGGGGTCTG 59.427 61.111 0.00 0.00 46.21 3.51
75 76 2.125952 GCAAAATGCGGGGTCTGC 60.126 61.111 0.00 0.00 31.71 4.26
76 77 2.573340 CAAAATGCGGGGTCTGCC 59.427 61.111 0.00 0.00 0.00 4.85
77 78 2.117206 AAAATGCGGGGTCTGCCA 59.883 55.556 0.00 0.00 36.17 4.92
78 79 1.978617 AAAATGCGGGGTCTGCCAG 60.979 57.895 0.00 0.00 36.17 4.85
79 80 2.424842 AAAATGCGGGGTCTGCCAGA 62.425 55.000 0.00 0.00 36.17 3.86
80 81 2.826777 AAATGCGGGGTCTGCCAGAG 62.827 60.000 0.00 0.00 36.17 3.35
82 83 4.021925 GCGGGGTCTGCCAGAGTT 62.022 66.667 0.00 0.00 36.17 3.01
83 84 2.046892 CGGGGTCTGCCAGAGTTG 60.047 66.667 0.00 0.00 36.17 3.16
84 85 2.360475 GGGGTCTGCCAGAGTTGC 60.360 66.667 0.00 0.00 36.17 4.17
85 86 2.753029 GGGTCTGCCAGAGTTGCT 59.247 61.111 0.00 0.00 36.17 3.91
86 87 1.376553 GGGTCTGCCAGAGTTGCTC 60.377 63.158 0.00 0.00 36.17 4.26
87 88 1.676384 GGTCTGCCAGAGTTGCTCT 59.324 57.895 0.00 0.00 42.11 4.09
88 89 0.898320 GGTCTGCCAGAGTTGCTCTA 59.102 55.000 0.00 0.00 38.99 2.43
89 90 1.276421 GGTCTGCCAGAGTTGCTCTAA 59.724 52.381 0.00 0.00 38.99 2.10
90 91 2.615869 GTCTGCCAGAGTTGCTCTAAG 58.384 52.381 0.00 0.00 38.99 2.18
91 92 2.232452 GTCTGCCAGAGTTGCTCTAAGA 59.768 50.000 0.00 0.95 38.99 2.10
92 93 2.495270 TCTGCCAGAGTTGCTCTAAGAG 59.505 50.000 0.00 0.00 38.99 2.85
93 94 1.552337 TGCCAGAGTTGCTCTAAGAGG 59.448 52.381 0.00 0.00 38.99 3.69
94 95 1.827969 GCCAGAGTTGCTCTAAGAGGA 59.172 52.381 0.00 0.00 38.99 3.71
95 96 2.234908 GCCAGAGTTGCTCTAAGAGGAA 59.765 50.000 0.00 0.00 38.99 3.36
101 102 3.988976 TTGCTCTAAGAGGAACAGCAT 57.011 42.857 0.00 0.00 39.76 3.79
102 103 3.257469 TGCTCTAAGAGGAACAGCATG 57.743 47.619 0.00 0.00 46.00 4.06
103 104 2.833943 TGCTCTAAGAGGAACAGCATGA 59.166 45.455 0.00 0.00 39.69 3.07
104 105 3.453717 TGCTCTAAGAGGAACAGCATGAT 59.546 43.478 0.00 0.00 39.69 2.45
105 106 4.080695 TGCTCTAAGAGGAACAGCATGATT 60.081 41.667 0.00 0.00 39.69 2.57
106 107 4.511082 GCTCTAAGAGGAACAGCATGATTC 59.489 45.833 0.00 0.00 39.69 2.52
107 108 4.686972 TCTAAGAGGAACAGCATGATTCG 58.313 43.478 0.00 0.00 39.69 3.34
108 109 3.616956 AAGAGGAACAGCATGATTCGA 57.383 42.857 0.00 0.00 39.69 3.71
109 110 3.834489 AGAGGAACAGCATGATTCGAT 57.166 42.857 0.00 0.00 39.69 3.59
110 111 4.148128 AGAGGAACAGCATGATTCGATT 57.852 40.909 0.00 0.00 39.69 3.34
111 112 4.521146 AGAGGAACAGCATGATTCGATTT 58.479 39.130 0.00 0.00 39.69 2.17
112 113 4.946157 AGAGGAACAGCATGATTCGATTTT 59.054 37.500 0.00 0.00 39.69 1.82
113 114 6.115446 AGAGGAACAGCATGATTCGATTTTA 58.885 36.000 0.00 0.00 39.69 1.52
114 115 6.259608 AGAGGAACAGCATGATTCGATTTTAG 59.740 38.462 0.00 0.00 39.69 1.85
115 116 6.115446 AGGAACAGCATGATTCGATTTTAGA 58.885 36.000 0.00 0.00 39.69 2.10
116 117 6.259608 AGGAACAGCATGATTCGATTTTAGAG 59.740 38.462 0.00 0.00 39.69 2.43
117 118 5.415415 ACAGCATGATTCGATTTTAGAGC 57.585 39.130 0.00 0.00 39.69 4.09
118 119 5.121811 ACAGCATGATTCGATTTTAGAGCT 58.878 37.500 0.00 0.00 39.69 4.09
119 120 6.283694 ACAGCATGATTCGATTTTAGAGCTA 58.716 36.000 0.00 0.00 39.69 3.32
120 121 6.763135 ACAGCATGATTCGATTTTAGAGCTAA 59.237 34.615 0.00 0.00 39.69 3.09
121 122 7.443575 ACAGCATGATTCGATTTTAGAGCTAAT 59.556 33.333 0.00 0.00 39.69 1.73
122 123 7.956403 CAGCATGATTCGATTTTAGAGCTAATC 59.044 37.037 0.00 0.00 39.69 1.75
128 129 5.726489 CGATTTTAGAGCTAATCGTACGG 57.274 43.478 16.52 0.00 44.80 4.02
129 130 4.088213 CGATTTTAGAGCTAATCGTACGGC 59.912 45.833 16.52 10.81 44.80 5.68
130 131 4.374843 TTTTAGAGCTAATCGTACGGCA 57.625 40.909 16.52 0.00 0.00 5.69
131 132 3.344904 TTAGAGCTAATCGTACGGCAC 57.655 47.619 16.52 9.35 0.00 5.01
148 149 4.828291 GGCACGATTTGTTTCAATCATG 57.172 40.909 0.00 0.00 0.00 3.07
149 150 3.061161 GGCACGATTTGTTTCAATCATGC 59.939 43.478 6.03 6.03 42.01 4.06
150 151 3.241426 GCACGATTTGTTTCAATCATGCG 60.241 43.478 0.00 0.00 35.41 4.73
151 152 3.301379 CACGATTTGTTTCAATCATGCGG 59.699 43.478 0.00 0.00 0.00 5.69
152 153 2.279659 CGATTTGTTTCAATCATGCGGC 59.720 45.455 0.00 0.00 0.00 6.53
153 154 3.514645 GATTTGTTTCAATCATGCGGCT 58.485 40.909 0.00 0.00 0.00 5.52
154 155 2.350899 TTGTTTCAATCATGCGGCTG 57.649 45.000 0.00 0.00 0.00 4.85
155 156 0.109179 TGTTTCAATCATGCGGCTGC 60.109 50.000 11.65 11.65 43.20 5.25
156 157 0.171903 GTTTCAATCATGCGGCTGCT 59.828 50.000 20.27 0.83 43.34 4.24
157 158 1.401552 GTTTCAATCATGCGGCTGCTA 59.598 47.619 20.27 5.54 43.34 3.49
158 159 1.302366 TTCAATCATGCGGCTGCTAG 58.698 50.000 20.27 11.23 43.34 3.42
159 160 0.533531 TCAATCATGCGGCTGCTAGG 60.534 55.000 20.27 8.18 43.34 3.02
160 161 1.228063 AATCATGCGGCTGCTAGGG 60.228 57.895 20.27 5.54 43.34 3.53
161 162 2.687418 AATCATGCGGCTGCTAGGGG 62.687 60.000 20.27 3.68 43.34 4.79
162 163 3.865383 CATGCGGCTGCTAGGGGA 61.865 66.667 20.27 0.00 43.34 4.81
163 164 3.866582 ATGCGGCTGCTAGGGGAC 61.867 66.667 20.27 0.00 43.34 4.46
175 176 4.340246 GGGGACCGGCCGAAAGTT 62.340 66.667 30.73 4.57 40.86 2.66
176 177 2.281970 GGGACCGGCCGAAAGTTT 60.282 61.111 30.73 2.44 37.63 2.66
177 178 2.330372 GGGACCGGCCGAAAGTTTC 61.330 63.158 30.73 12.18 37.63 2.78
186 187 3.260931 GAAAGTTTCGGCCGGTCC 58.739 61.111 27.83 13.07 0.00 4.46
205 206 2.901840 CCGGCGCCTAGTACGGTA 60.902 66.667 26.68 0.00 41.34 4.02
206 207 2.635899 CGGCGCCTAGTACGGTAG 59.364 66.667 26.68 0.00 0.00 3.18
207 208 2.182842 CGGCGCCTAGTACGGTAGT 61.183 63.158 26.68 0.55 0.00 2.73
208 209 0.880278 CGGCGCCTAGTACGGTAGTA 60.880 60.000 26.68 2.90 0.00 1.82
216 217 3.281332 GTACGGTAGTACCCACCCA 57.719 57.895 13.90 0.00 45.59 4.51
270 271 1.003233 GGGTTCTTCGAAGGCAGCT 60.003 57.895 24.37 0.00 0.00 4.24
348 353 8.049117 ACAATCAGGTATCCGATAATGCAATAT 58.951 33.333 0.00 0.00 0.00 1.28
401 407 7.665559 TGTTTTGAAACATGACTAAGCTATCCT 59.334 33.333 0.00 0.00 43.45 3.24
403 409 8.635765 TTTGAAACATGACTAAGCTATCCTTT 57.364 30.769 0.00 0.00 34.95 3.11
404 410 8.635765 TTGAAACATGACTAAGCTATCCTTTT 57.364 30.769 0.00 0.00 34.95 2.27
405 411 8.635765 TGAAACATGACTAAGCTATCCTTTTT 57.364 30.769 0.00 0.00 34.95 1.94
406 412 8.730680 TGAAACATGACTAAGCTATCCTTTTTC 58.269 33.333 0.00 0.00 34.95 2.29
407 413 8.870075 AAACATGACTAAGCTATCCTTTTTCT 57.130 30.769 0.00 0.00 34.95 2.52
408 414 8.870075 AACATGACTAAGCTATCCTTTTTCTT 57.130 30.769 0.00 0.00 34.95 2.52
409 415 8.499403 ACATGACTAAGCTATCCTTTTTCTTC 57.501 34.615 0.00 0.00 34.95 2.87
450 456 4.357918 ACTATCTGTGTTTGCTGGTTCT 57.642 40.909 0.00 0.00 0.00 3.01
485 498 9.079833 GTGTATTTTTAAGAGCGAGTATGTGTA 57.920 33.333 0.00 0.00 0.00 2.90
495 508 0.611200 AGTATGTGTACCGCTTGGCA 59.389 50.000 0.00 0.00 35.53 4.92
496 509 1.006832 GTATGTGTACCGCTTGGCAG 58.993 55.000 0.00 0.00 35.53 4.85
540 554 4.450122 GCACGCATGCCTGTCACG 62.450 66.667 13.15 0.00 46.97 4.35
721 742 4.908687 ACACGAAGGCAGCACGCA 62.909 61.111 0.00 0.00 45.17 5.24
927 2129 5.052304 CGTTCGTCATAGATCTTGTGCTAAC 60.052 44.000 0.00 5.43 0.00 2.34
941 2143 6.663953 TCTTGTGCTAACTATCAGTTACTCCT 59.336 38.462 0.00 0.00 39.51 3.69
984 2186 1.003003 GAGGCCTCTTTCTGCAGAGTT 59.997 52.381 26.25 0.00 39.04 3.01
985 2187 1.163554 GGCCTCTTTCTGCAGAGTTG 58.836 55.000 17.43 10.98 39.04 3.16
986 2188 1.163554 GCCTCTTTCTGCAGAGTTGG 58.836 55.000 17.43 17.36 39.04 3.77
987 2189 1.163554 CCTCTTTCTGCAGAGTTGGC 58.836 55.000 17.43 0.00 39.04 4.52
988 2190 1.163554 CTCTTTCTGCAGAGTTGGCC 58.836 55.000 17.43 0.00 36.32 5.36
989 2191 0.473755 TCTTTCTGCAGAGTTGGCCA 59.526 50.000 17.43 0.00 0.00 5.36
990 2192 0.595095 CTTTCTGCAGAGTTGGCCAC 59.405 55.000 17.43 0.00 0.00 5.01
991 2193 0.183492 TTTCTGCAGAGTTGGCCACT 59.817 50.000 17.43 6.18 39.07 4.00
992 2194 0.183492 TTCTGCAGAGTTGGCCACTT 59.817 50.000 17.43 0.00 35.01 3.16
1138 2343 2.777536 TGGAAGGACCAGATGCTGT 58.222 52.632 0.00 0.00 44.64 4.40
1140 2345 1.271543 TGGAAGGACCAGATGCTGTTG 60.272 52.381 0.00 0.00 44.64 3.33
1500 2748 0.687757 CCTCCCTCCATCGTCTCCAA 60.688 60.000 0.00 0.00 0.00 3.53
1536 2784 3.834726 CTCGGATCCGTGCTCTCT 58.165 61.111 32.15 0.00 40.74 3.10
1695 2943 4.124351 CGGAAGCCGCACGACCTA 62.124 66.667 0.00 0.00 41.17 3.08
1914 3171 0.665835 CGTTCGATCAGGAGGAGGAG 59.334 60.000 0.00 0.00 0.00 3.69
1920 3177 2.597455 GATCAGGAGGAGGAGGAAGAG 58.403 57.143 0.00 0.00 0.00 2.85
1923 3180 0.933700 AGGAGGAGGAGGAAGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
1974 3231 1.753463 GGAGAGGGACGACGATGGT 60.753 63.158 0.00 0.00 0.00 3.55
2072 3329 2.627515 TCAGAGCTGACCATAATGCC 57.372 50.000 0.00 0.00 34.14 4.40
2160 3417 4.488136 TACGGCTGCATGCAGGGG 62.488 66.667 40.59 23.00 45.15 4.79
2168 3425 2.409870 GCATGCAGGGGGTCGAAAG 61.410 63.158 14.21 0.00 0.00 2.62
2172 3429 1.449778 GCAGGGGGTCGAAAGCTAC 60.450 63.158 0.00 0.00 0.00 3.58
2199 3456 1.067142 CGGGAAAAGGACGATCTGACA 60.067 52.381 0.00 0.00 0.00 3.58
2215 3472 1.209128 GACACCGATGCATTCCGTAG 58.791 55.000 0.00 0.00 0.00 3.51
2220 3477 0.855349 CGATGCATTCCGTAGTGCTC 59.145 55.000 0.00 0.00 41.78 4.26
2287 3544 2.502295 GGAGCTGCCCTGAAATAGATG 58.498 52.381 0.00 0.00 0.00 2.90
2307 3564 3.818787 GTGCTGCGCTTGATGGGG 61.819 66.667 9.73 0.00 0.00 4.96
2338 3601 0.317160 CCACGCAGTCAGTTGTCCTA 59.683 55.000 0.00 0.00 41.61 2.94
2402 3665 9.542462 GAATACTGTTACTGCACTATTTCCATA 57.458 33.333 0.00 0.00 0.00 2.74
2521 3787 6.954944 TGTGACAACTTTGTACTAAATCAGC 58.045 36.000 0.00 0.00 42.43 4.26
2526 3792 6.426937 ACAACTTTGTACTAAATCAGCGACAT 59.573 34.615 0.00 0.00 40.16 3.06
2555 3871 1.152440 TGGCCCGGGAATTTTGTGT 60.152 52.632 29.31 0.00 0.00 3.72
2613 3935 3.869246 TCTTGTCTTTGAGTGGTTTCGAC 59.131 43.478 0.00 0.00 0.00 4.20
2619 3941 2.743636 TGAGTGGTTTCGACCAGATC 57.256 50.000 0.00 1.72 41.00 2.75
2623 3945 4.466370 TGAGTGGTTTCGACCAGATCTTAT 59.534 41.667 0.00 0.00 41.00 1.73
2640 3962 7.228108 CAGATCTTATGTATGCAAGTGGTTGAT 59.772 37.037 0.00 0.00 35.46 2.57
2671 3993 4.636435 CTTCCGGTGGGGCAACGT 62.636 66.667 0.00 0.00 43.64 3.99
2678 4000 1.964373 GTGGGGCAACGTCGATGTT 60.964 57.895 17.24 17.24 37.60 2.71
2810 4132 3.354467 CTTAGGGTCCGTACTCTGAGTT 58.646 50.000 16.53 0.37 36.93 3.01
2824 4146 4.142859 ACTCTGAGTTGTTCGTCGATAGTC 60.143 45.833 4.06 0.00 37.40 2.59
2826 4148 5.173664 TCTGAGTTGTTCGTCGATAGTCTA 58.826 41.667 0.00 0.00 37.40 2.59
2830 4152 4.940046 AGTTGTTCGTCGATAGTCTAAGGA 59.060 41.667 0.00 0.00 37.40 3.36
2837 4159 4.515944 CGTCGATAGTCTAAGGAAGGTGAT 59.484 45.833 0.00 0.00 37.40 3.06
2839 4161 6.347563 CGTCGATAGTCTAAGGAAGGTGATAC 60.348 46.154 0.00 0.00 37.40 2.24
2840 4162 6.711645 GTCGATAGTCTAAGGAAGGTGATACT 59.288 42.308 0.00 0.00 37.40 2.12
2841 4163 6.711194 TCGATAGTCTAAGGAAGGTGATACTG 59.289 42.308 0.00 0.00 37.40 2.74
2847 4169 4.985538 AAGGAAGGTGATACTGTAGTCG 57.014 45.455 0.00 0.00 0.00 4.18
2850 4172 3.242673 GGAAGGTGATACTGTAGTCGTCG 60.243 52.174 0.00 0.00 0.00 5.12
2853 4175 2.223203 GGTGATACTGTAGTCGTCGGTG 60.223 54.545 0.00 0.00 0.00 4.94
2892 4214 4.546570 TCACATATTCGCCTTGAGTATCG 58.453 43.478 0.00 0.00 38.61 2.92
2897 4219 4.859629 ATTCGCCTTGAGTATCGAAAAC 57.140 40.909 0.00 0.00 42.91 2.43
2957 4279 6.512514 AGGATAGAGCAGAAAGGAAATCAT 57.487 37.500 0.00 0.00 0.00 2.45
2999 4321 5.394993 GCTTCTACTACCCAAAACCTATCGT 60.395 44.000 0.00 0.00 0.00 3.73
3013 4335 2.609459 CCTATCGTCAACCTTGATGCAC 59.391 50.000 0.00 0.00 42.51 4.57
3033 4355 4.907010 GCACAATACGAAATTCGAACACAA 59.093 37.500 22.92 0.62 43.74 3.33
3035 4357 5.056330 CACAATACGAAATTCGAACACAACG 59.944 40.000 22.92 5.32 43.74 4.10
3037 4359 3.228878 ACGAAATTCGAACACAACGTC 57.771 42.857 22.92 0.00 43.74 4.34
3085 4407 1.843753 GTTTCAAAGACAACAACCGCG 59.156 47.619 0.00 0.00 0.00 6.46
3087 4409 1.657181 CAAAGACAACAACCGCGCC 60.657 57.895 0.00 0.00 0.00 6.53
3092 4414 4.459331 CAACAACCGCGCCCGATG 62.459 66.667 0.00 0.00 36.29 3.84
3112 4434 4.906065 TGCCATGTCAAATCTTGCTATC 57.094 40.909 0.00 0.00 0.00 2.08
3142 4464 5.063564 GTGTTGGGACGATTAGAACTTGATC 59.936 44.000 0.00 0.00 0.00 2.92
3153 4475 1.057847 GAACTTGATCGCGAGACAACG 59.942 52.381 21.60 19.11 46.97 4.10
3190 4512 2.413310 ACACGGACCTTCAAAACAGT 57.587 45.000 0.00 0.00 0.00 3.55
3193 4515 1.137479 ACGGACCTTCAAAACAGTCGA 59.863 47.619 0.00 0.00 0.00 4.20
3197 4519 4.348656 GGACCTTCAAAACAGTCGAAAAC 58.651 43.478 0.00 0.00 0.00 2.43
3200 4522 4.026407 CCTTCAAAACAGTCGAAAACGTC 58.974 43.478 0.00 0.00 0.00 4.34
3217 4539 0.319641 GTCCGGACTGAGGTGTTCAC 60.320 60.000 27.64 0.00 0.00 3.18
3227 4557 4.595629 GTGTTCACACGCTGCAAG 57.404 55.556 0.00 0.00 37.10 4.01
3249 4579 0.323725 ATCCAAGGCGGCACTTCATT 60.324 50.000 13.08 0.00 33.14 2.57
3263 4593 2.514592 CATTGGTCCGCGGATGCT 60.515 61.111 33.58 13.85 39.65 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.926510 GTTATGCAGGCCGAATTTTGC 59.073 47.619 5.48 5.48 37.09 3.68
2 3 2.959507 GGTTATGCAGGCCGAATTTT 57.040 45.000 0.00 0.00 0.00 1.82
10 11 2.902343 GAGGGCGGTTATGCAGGC 60.902 66.667 0.00 0.00 36.28 4.85
11 12 1.149174 ATGAGGGCGGTTATGCAGG 59.851 57.895 0.00 0.00 36.28 4.85
12 13 1.789078 GCATGAGGGCGGTTATGCAG 61.789 60.000 0.00 0.00 43.93 4.41
13 14 1.823470 GCATGAGGGCGGTTATGCA 60.823 57.895 0.00 0.00 43.93 3.96
14 15 3.034030 GCATGAGGGCGGTTATGC 58.966 61.111 0.00 0.00 39.08 3.14
30 31 1.851658 AAAATGTGTTTGCAGGTCGC 58.148 45.000 0.00 0.00 42.89 5.19
31 32 4.466828 CTCTAAAATGTGTTTGCAGGTCG 58.533 43.478 0.00 0.00 0.00 4.79
32 33 4.278419 ACCTCTAAAATGTGTTTGCAGGTC 59.722 41.667 0.00 0.00 30.96 3.85
33 34 4.215109 ACCTCTAAAATGTGTTTGCAGGT 58.785 39.130 0.00 0.00 31.45 4.00
34 35 4.613622 CGACCTCTAAAATGTGTTTGCAGG 60.614 45.833 0.00 0.00 0.00 4.85
35 36 4.466828 CGACCTCTAAAATGTGTTTGCAG 58.533 43.478 0.00 0.00 0.00 4.41
36 37 3.252215 CCGACCTCTAAAATGTGTTTGCA 59.748 43.478 0.00 0.00 0.00 4.08
37 38 3.821841 CCGACCTCTAAAATGTGTTTGC 58.178 45.455 0.00 0.00 0.00 3.68
38 39 3.252215 TGCCGACCTCTAAAATGTGTTTG 59.748 43.478 0.00 0.00 0.00 2.93
39 40 3.482436 TGCCGACCTCTAAAATGTGTTT 58.518 40.909 0.00 0.00 0.00 2.83
40 41 3.134574 TGCCGACCTCTAAAATGTGTT 57.865 42.857 0.00 0.00 0.00 3.32
41 42 2.851263 TGCCGACCTCTAAAATGTGT 57.149 45.000 0.00 0.00 0.00 3.72
42 43 4.497473 TTTTGCCGACCTCTAAAATGTG 57.503 40.909 0.00 0.00 0.00 3.21
43 44 4.618227 GCATTTTGCCGACCTCTAAAATGT 60.618 41.667 17.36 0.00 45.38 2.71
44 45 3.859386 GCATTTTGCCGACCTCTAAAATG 59.141 43.478 13.83 13.83 45.92 2.32
45 46 3.427503 CGCATTTTGCCGACCTCTAAAAT 60.428 43.478 0.00 0.00 41.12 1.82
46 47 2.095466 CGCATTTTGCCGACCTCTAAAA 60.095 45.455 0.00 0.00 41.12 1.52
47 48 1.466950 CGCATTTTGCCGACCTCTAAA 59.533 47.619 0.00 0.00 41.12 1.85
48 49 1.083489 CGCATTTTGCCGACCTCTAA 58.917 50.000 0.00 0.00 41.12 2.10
49 50 0.742990 CCGCATTTTGCCGACCTCTA 60.743 55.000 0.00 0.00 41.12 2.43
50 51 2.040544 CCGCATTTTGCCGACCTCT 61.041 57.895 0.00 0.00 41.12 3.69
51 52 2.485122 CCGCATTTTGCCGACCTC 59.515 61.111 0.00 0.00 41.12 3.85
52 53 3.061848 CCCGCATTTTGCCGACCT 61.062 61.111 0.00 0.00 41.12 3.85
53 54 4.128388 CCCCGCATTTTGCCGACC 62.128 66.667 0.00 0.00 41.12 4.79
54 55 3.336715 GACCCCGCATTTTGCCGAC 62.337 63.158 0.00 0.00 41.12 4.79
55 56 3.059386 GACCCCGCATTTTGCCGA 61.059 61.111 0.00 0.00 41.12 5.54
56 57 3.061848 AGACCCCGCATTTTGCCG 61.062 61.111 0.00 0.00 41.12 5.69
57 58 2.573340 CAGACCCCGCATTTTGCC 59.427 61.111 0.00 0.00 41.12 4.52
58 59 2.125952 GCAGACCCCGCATTTTGC 60.126 61.111 0.00 0.00 40.69 3.68
59 60 2.216750 CTGGCAGACCCCGCATTTTG 62.217 60.000 9.42 0.00 33.59 2.44
60 61 1.978617 CTGGCAGACCCCGCATTTT 60.979 57.895 9.42 0.00 33.59 1.82
61 62 2.361610 CTGGCAGACCCCGCATTT 60.362 61.111 9.42 0.00 33.59 2.32
62 63 3.329889 TCTGGCAGACCCCGCATT 61.330 61.111 14.43 0.00 33.59 3.56
63 64 3.790437 CTCTGGCAGACCCCGCAT 61.790 66.667 14.43 0.00 33.59 4.73
65 66 4.021925 AACTCTGGCAGACCCCGC 62.022 66.667 14.43 0.00 33.59 6.13
66 67 2.046892 CAACTCTGGCAGACCCCG 60.047 66.667 14.43 6.51 33.59 5.73
67 68 2.360475 GCAACTCTGGCAGACCCC 60.360 66.667 14.43 0.00 33.59 4.95
68 69 1.376553 GAGCAACTCTGGCAGACCC 60.377 63.158 14.43 2.07 33.59 4.46
69 70 0.898320 TAGAGCAACTCTGGCAGACC 59.102 55.000 14.43 2.43 41.37 3.85
70 71 2.232452 TCTTAGAGCAACTCTGGCAGAC 59.768 50.000 14.43 3.68 41.37 3.51
71 72 2.495270 CTCTTAGAGCAACTCTGGCAGA 59.505 50.000 17.68 17.68 41.37 4.26
72 73 2.418471 CCTCTTAGAGCAACTCTGGCAG 60.418 54.545 8.58 8.58 41.37 4.85
73 74 1.552337 CCTCTTAGAGCAACTCTGGCA 59.448 52.381 3.26 0.00 41.37 4.92
74 75 1.827969 TCCTCTTAGAGCAACTCTGGC 59.172 52.381 3.26 0.00 41.37 4.85
75 76 3.259374 TGTTCCTCTTAGAGCAACTCTGG 59.741 47.826 15.94 0.39 41.37 3.86
76 77 4.493547 CTGTTCCTCTTAGAGCAACTCTG 58.506 47.826 15.94 4.33 41.37 3.35
77 78 3.056179 GCTGTTCCTCTTAGAGCAACTCT 60.056 47.826 15.94 2.23 43.83 3.24
78 79 3.258228 GCTGTTCCTCTTAGAGCAACTC 58.742 50.000 15.94 5.60 32.14 3.01
79 80 2.634940 TGCTGTTCCTCTTAGAGCAACT 59.365 45.455 15.94 0.00 38.74 3.16
80 81 3.045601 TGCTGTTCCTCTTAGAGCAAC 57.954 47.619 8.98 8.98 38.74 4.17
81 82 3.261643 TCATGCTGTTCCTCTTAGAGCAA 59.738 43.478 3.26 0.00 43.84 3.91
82 83 2.833943 TCATGCTGTTCCTCTTAGAGCA 59.166 45.455 3.26 0.00 44.59 4.26
83 84 3.533606 TCATGCTGTTCCTCTTAGAGC 57.466 47.619 3.26 0.00 32.91 4.09
84 85 4.744137 CGAATCATGCTGTTCCTCTTAGAG 59.256 45.833 1.56 1.56 0.00 2.43
85 86 4.402474 TCGAATCATGCTGTTCCTCTTAGA 59.598 41.667 0.00 0.00 0.00 2.10
86 87 4.686972 TCGAATCATGCTGTTCCTCTTAG 58.313 43.478 0.00 0.00 0.00 2.18
87 88 4.736126 TCGAATCATGCTGTTCCTCTTA 57.264 40.909 0.00 0.00 0.00 2.10
88 89 3.616956 TCGAATCATGCTGTTCCTCTT 57.383 42.857 0.00 0.00 0.00 2.85
89 90 3.834489 ATCGAATCATGCTGTTCCTCT 57.166 42.857 0.00 0.00 0.00 3.69
90 91 4.889832 AAATCGAATCATGCTGTTCCTC 57.110 40.909 0.00 0.00 0.00 3.71
91 92 6.115446 TCTAAAATCGAATCATGCTGTTCCT 58.885 36.000 0.00 0.00 0.00 3.36
92 93 6.363577 TCTAAAATCGAATCATGCTGTTCC 57.636 37.500 0.00 0.00 0.00 3.62
93 94 5.906285 GCTCTAAAATCGAATCATGCTGTTC 59.094 40.000 0.00 0.00 0.00 3.18
94 95 5.587844 AGCTCTAAAATCGAATCATGCTGTT 59.412 36.000 0.00 0.00 0.00 3.16
95 96 5.121811 AGCTCTAAAATCGAATCATGCTGT 58.878 37.500 0.00 0.00 0.00 4.40
96 97 5.670149 AGCTCTAAAATCGAATCATGCTG 57.330 39.130 0.00 0.00 0.00 4.41
97 98 7.976135 ATTAGCTCTAAAATCGAATCATGCT 57.024 32.000 0.00 0.00 0.00 3.79
107 108 4.980434 TGCCGTACGATTAGCTCTAAAATC 59.020 41.667 18.76 0.00 0.00 2.17
108 109 4.743644 GTGCCGTACGATTAGCTCTAAAAT 59.256 41.667 18.76 0.00 0.00 1.82
109 110 4.107622 GTGCCGTACGATTAGCTCTAAAA 58.892 43.478 18.76 0.00 0.00 1.52
110 111 3.699067 GTGCCGTACGATTAGCTCTAAA 58.301 45.455 18.76 0.00 0.00 1.85
111 112 3.344904 GTGCCGTACGATTAGCTCTAA 57.655 47.619 18.76 0.00 0.00 2.10
113 114 3.940723 GTGCCGTACGATTAGCTCT 57.059 52.632 18.76 0.00 0.00 4.09
123 124 2.953640 TGAAACAAATCGTGCCGTAC 57.046 45.000 0.00 0.00 0.00 3.67
124 125 3.498777 TGATTGAAACAAATCGTGCCGTA 59.501 39.130 0.00 0.00 39.06 4.02
125 126 2.292016 TGATTGAAACAAATCGTGCCGT 59.708 40.909 0.00 0.00 39.06 5.68
126 127 2.927429 TGATTGAAACAAATCGTGCCG 58.073 42.857 0.00 0.00 39.06 5.69
127 128 4.828291 CATGATTGAAACAAATCGTGCC 57.172 40.909 6.27 0.00 43.16 5.01
130 131 3.500982 CCGCATGATTGAAACAAATCGT 58.499 40.909 0.00 0.00 39.06 3.73
131 132 2.279659 GCCGCATGATTGAAACAAATCG 59.720 45.455 0.00 0.00 39.06 3.34
132 133 3.305094 CAGCCGCATGATTGAAACAAATC 59.695 43.478 0.00 0.00 37.13 2.17
133 134 3.255725 CAGCCGCATGATTGAAACAAAT 58.744 40.909 0.00 0.00 0.00 2.32
134 135 2.674954 CAGCCGCATGATTGAAACAAA 58.325 42.857 0.00 0.00 0.00 2.83
135 136 1.669502 GCAGCCGCATGATTGAAACAA 60.670 47.619 0.00 0.00 38.36 2.83
136 137 0.109179 GCAGCCGCATGATTGAAACA 60.109 50.000 0.00 0.00 38.36 2.83
137 138 0.171903 AGCAGCCGCATGATTGAAAC 59.828 50.000 0.00 0.00 42.27 2.78
138 139 1.672363 CTAGCAGCCGCATGATTGAAA 59.328 47.619 0.00 0.00 42.27 2.69
139 140 1.302366 CTAGCAGCCGCATGATTGAA 58.698 50.000 0.00 0.00 42.27 2.69
140 141 0.533531 CCTAGCAGCCGCATGATTGA 60.534 55.000 0.00 0.00 42.27 2.57
141 142 1.512996 CCCTAGCAGCCGCATGATTG 61.513 60.000 0.00 0.00 42.27 2.67
142 143 1.228063 CCCTAGCAGCCGCATGATT 60.228 57.895 0.00 0.00 42.27 2.57
143 144 2.429058 CCCTAGCAGCCGCATGAT 59.571 61.111 0.00 0.00 42.27 2.45
144 145 3.865383 CCCCTAGCAGCCGCATGA 61.865 66.667 0.00 0.00 42.27 3.07
145 146 3.865383 TCCCCTAGCAGCCGCATG 61.865 66.667 0.00 0.00 42.27 4.06
146 147 3.866582 GTCCCCTAGCAGCCGCAT 61.867 66.667 0.00 0.00 42.27 4.73
155 156 3.078836 TTTCGGCCGGTCCCCTAG 61.079 66.667 27.83 0.00 0.00 3.02
156 157 3.078836 CTTTCGGCCGGTCCCCTA 61.079 66.667 27.83 0.00 0.00 3.53
158 159 3.855503 AAACTTTCGGCCGGTCCCC 62.856 63.158 27.83 0.00 0.00 4.81
159 160 2.281970 AAACTTTCGGCCGGTCCC 60.282 61.111 27.83 0.00 0.00 4.46
160 161 3.260931 GAAACTTTCGGCCGGTCC 58.739 61.111 27.83 7.41 0.00 4.46
169 170 3.260931 GGACCGGCCGAAACTTTC 58.739 61.111 30.73 12.18 0.00 2.62
188 189 2.901292 CTACCGTACTAGGCGCCGG 61.901 68.421 23.20 19.76 45.72 6.13
189 190 0.880278 TACTACCGTACTAGGCGCCG 60.880 60.000 23.20 10.77 33.69 6.46
190 191 0.588737 GTACTACCGTACTAGGCGCC 59.411 60.000 21.89 21.89 42.16 6.53
191 192 0.588737 GGTACTACCGTACTAGGCGC 59.411 60.000 0.00 0.00 44.30 6.53
192 193 1.230324 GGGTACTACCGTACTAGGCG 58.770 60.000 0.00 0.00 44.30 5.52
193 194 1.950216 GTGGGTACTACCGTACTAGGC 59.050 57.143 0.00 0.00 44.30 3.93
203 204 0.688487 TTGCTGTGGGTGGGTACTAC 59.312 55.000 0.00 0.00 39.89 2.73
204 205 1.349688 CTTTGCTGTGGGTGGGTACTA 59.650 52.381 0.00 0.00 0.00 1.82
205 206 0.110486 CTTTGCTGTGGGTGGGTACT 59.890 55.000 0.00 0.00 0.00 2.73
206 207 1.524008 GCTTTGCTGTGGGTGGGTAC 61.524 60.000 0.00 0.00 0.00 3.34
207 208 1.228429 GCTTTGCTGTGGGTGGGTA 60.228 57.895 0.00 0.00 0.00 3.69
208 209 2.521708 GCTTTGCTGTGGGTGGGT 60.522 61.111 0.00 0.00 0.00 4.51
209 210 3.305516 GGCTTTGCTGTGGGTGGG 61.306 66.667 0.00 0.00 0.00 4.61
210 211 2.132996 TTGGCTTTGCTGTGGGTGG 61.133 57.895 0.00 0.00 0.00 4.61
211 212 1.067916 GTTGGCTTTGCTGTGGGTG 59.932 57.895 0.00 0.00 0.00 4.61
212 213 0.184933 TAGTTGGCTTTGCTGTGGGT 59.815 50.000 0.00 0.00 0.00 4.51
213 214 1.203052 CATAGTTGGCTTTGCTGTGGG 59.797 52.381 0.00 0.00 0.00 4.61
214 215 1.203052 CCATAGTTGGCTTTGCTGTGG 59.797 52.381 0.00 0.00 35.85 4.17
215 216 2.642139 CCATAGTTGGCTTTGCTGTG 57.358 50.000 0.00 0.00 35.85 3.66
242 243 4.928020 CCTTCGAAGAACCCTAACTGTTAC 59.072 45.833 26.61 0.00 45.90 2.50
348 353 2.839486 AAGATCACTTTGCTGGACGA 57.161 45.000 0.00 0.00 31.71 4.20
416 422 7.566760 AACACAGATAGTTTTGTCATGTTCA 57.433 32.000 0.00 0.00 27.36 3.18
426 432 5.594317 AGAACCAGCAAACACAGATAGTTTT 59.406 36.000 0.00 0.00 37.10 2.43
429 435 4.357918 AGAACCAGCAAACACAGATAGT 57.642 40.909 0.00 0.00 0.00 2.12
450 456 6.237996 CGCTCTTAAAAATACACGCTATGGAA 60.238 38.462 0.00 0.00 0.00 3.53
496 509 1.655597 GCAAATTTTCTAAGCAGCGGC 59.344 47.619 0.00 0.00 41.61 6.53
555 569 1.175654 ATGCGTTCATGTGGATGCAA 58.824 45.000 11.90 0.00 39.66 4.08
721 742 6.346477 TGAGCTCTATGTTTCTGTGTAAGT 57.654 37.500 16.19 0.00 0.00 2.24
821 2016 3.508840 GAATTCAGTGGCCGCCCG 61.509 66.667 14.07 4.61 0.00 6.13
822 2017 2.044946 AGAATTCAGTGGCCGCCC 60.045 61.111 14.07 0.00 0.00 6.13
823 2018 2.115291 GGAGAATTCAGTGGCCGCC 61.115 63.158 14.07 1.04 0.00 6.13
824 2019 1.078143 AGGAGAATTCAGTGGCCGC 60.078 57.895 8.71 8.71 0.00 6.53
825 2020 0.807667 CGAGGAGAATTCAGTGGCCG 60.808 60.000 8.44 0.00 0.00 6.13
826 2021 0.537188 TCGAGGAGAATTCAGTGGCC 59.463 55.000 8.44 0.00 0.00 5.36
827 2022 1.205893 AGTCGAGGAGAATTCAGTGGC 59.794 52.381 8.44 0.00 0.00 5.01
868 2070 1.005975 CGAGCTATTTATATGCGCGCC 60.006 52.381 30.77 11.42 42.07 6.53
869 2071 2.337728 CGAGCTATTTATATGCGCGC 57.662 50.000 27.26 27.26 42.07 6.86
871 2073 1.005975 CGGCGAGCTATTTATATGCGC 60.006 52.381 0.00 0.00 41.95 6.09
941 2143 1.748493 GCCGTGAATGCCTTTATCCAA 59.252 47.619 0.00 0.00 0.00 3.53
987 2189 4.738998 TCCATGCCGGCCAAGTGG 62.739 66.667 26.77 24.77 38.53 4.00
988 2190 3.136123 CTCCATGCCGGCCAAGTG 61.136 66.667 26.77 16.91 33.14 3.16
1138 2343 3.760035 GCCCTCGAGCCTCGTCAA 61.760 66.667 14.64 0.00 41.35 3.18
1195 2419 2.956964 CGACGAGGAAGATGCGCC 60.957 66.667 4.18 0.00 0.00 6.53
1203 2427 3.425713 CCCGACGACGACGAGGAA 61.426 66.667 20.63 0.00 42.66 3.36
1224 2448 4.049817 ACGTCGGGAGGCTCCTCT 62.050 66.667 31.39 8.16 42.38 3.69
1500 2748 0.671781 GCGTGCTGTCTTGGATGTCT 60.672 55.000 0.00 0.00 0.00 3.41
1695 2943 2.355209 GGAGATCTTCCACGCCTTCTTT 60.355 50.000 0.00 0.00 46.01 2.52
1914 3171 0.105709 CCTCCTCCTCCTCCTCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
1920 3177 0.336737 TCTTCACCTCCTCCTCCTCC 59.663 60.000 0.00 0.00 0.00 4.30
1923 3180 2.239681 TCTTCTTCACCTCCTCCTCC 57.760 55.000 0.00 0.00 0.00 4.30
1974 3231 2.049156 CGCACAACGCTCTCCAGA 60.049 61.111 0.00 0.00 39.08 3.86
2040 3297 3.144120 CTCTGATCCGCTCCCACCG 62.144 68.421 0.00 0.00 0.00 4.94
2139 3396 0.461870 CCTGCATGCAGCCGTAGTAA 60.462 55.000 37.11 4.47 44.83 2.24
2160 3417 0.735287 GGTCACCGTAGCTTTCGACC 60.735 60.000 11.58 8.24 36.46 4.79
2168 3425 1.004679 TTTTCCCGGTCACCGTAGC 60.005 57.895 16.87 0.00 46.80 3.58
2199 3456 0.810031 GCACTACGGAATGCATCGGT 60.810 55.000 11.88 11.84 43.31 4.69
2215 3472 3.126831 CCTCATCTATGTTTCCGAGCAC 58.873 50.000 0.00 0.00 0.00 4.40
2220 3477 2.213499 GCCACCTCATCTATGTTTCCG 58.787 52.381 0.00 0.00 0.00 4.30
2223 3480 1.065491 TGCGCCACCTCATCTATGTTT 60.065 47.619 4.18 0.00 0.00 2.83
2224 3481 0.541392 TGCGCCACCTCATCTATGTT 59.459 50.000 4.18 0.00 0.00 2.71
2225 3482 0.105593 CTGCGCCACCTCATCTATGT 59.894 55.000 4.18 0.00 0.00 2.29
2307 3564 0.807667 CTGCGTGGCTATGTCACTCC 60.808 60.000 0.89 0.00 35.84 3.85
2338 3601 3.806625 ATAACCGTGCGTAACATAGGT 57.193 42.857 0.00 0.00 41.94 3.08
2383 3646 6.016276 CCCCAATATGGAAATAGTGCAGTAAC 60.016 42.308 5.12 0.73 40.96 2.50
2402 3665 3.552132 AAACGAAAAAGCAACCCCAAT 57.448 38.095 0.00 0.00 0.00 3.16
2475 3738 6.144563 CACATAAGAGAAATGATCATACGCGT 59.855 38.462 19.17 19.17 0.00 6.01
2476 3739 6.363357 TCACATAAGAGAAATGATCATACGCG 59.637 38.462 9.04 3.53 0.00 6.01
2521 3787 1.135689 GGCCACTAGCACAAAATGTCG 60.136 52.381 0.00 0.00 46.50 4.35
2574 3890 6.624423 AGACAAGATTGTTTGGATTGCATAC 58.376 36.000 0.00 0.00 42.43 2.39
2613 3935 5.371526 ACCACTTGCATACATAAGATCTGG 58.628 41.667 0.00 0.00 0.00 3.86
2619 3941 6.682423 TCATCAACCACTTGCATACATAAG 57.318 37.500 0.00 0.00 0.00 1.73
2623 3945 4.587891 TGATCATCAACCACTTGCATACA 58.412 39.130 0.00 0.00 0.00 2.29
2640 3962 2.567169 ACCGGAAGACAACATCTGATCA 59.433 45.455 9.46 0.00 37.88 2.92
2726 4048 1.361993 GGCAACCGCAACATTGTGA 59.638 52.632 6.74 0.00 41.01 3.58
2776 4098 4.530857 CTAAGGGTGCCCGGCTCG 62.531 72.222 11.61 0.00 41.95 5.03
2789 4111 3.002038 ACTCAGAGTACGGACCCTAAG 57.998 52.381 0.00 0.00 0.00 2.18
2790 4112 3.087031 CAACTCAGAGTACGGACCCTAA 58.913 50.000 2.64 0.00 0.00 2.69
2810 4132 4.334759 CCTTCCTTAGACTATCGACGAACA 59.665 45.833 0.00 0.00 0.00 3.18
2824 4146 5.589452 ACGACTACAGTATCACCTTCCTTAG 59.411 44.000 0.00 0.00 0.00 2.18
2826 4148 4.342359 ACGACTACAGTATCACCTTCCTT 58.658 43.478 0.00 0.00 0.00 3.36
2830 4152 2.681848 CCGACGACTACAGTATCACCTT 59.318 50.000 0.00 0.00 0.00 3.50
2837 4159 1.159285 CACCACCGACGACTACAGTA 58.841 55.000 0.00 0.00 0.00 2.74
2839 4161 1.443872 GCACCACCGACGACTACAG 60.444 63.158 0.00 0.00 0.00 2.74
2840 4162 2.646719 GCACCACCGACGACTACA 59.353 61.111 0.00 0.00 0.00 2.74
2841 4163 2.503375 CGCACCACCGACGACTAC 60.503 66.667 0.00 0.00 0.00 2.73
2847 4169 4.760047 ATCAGCCGCACCACCGAC 62.760 66.667 0.00 0.00 0.00 4.79
2850 4172 3.434319 CACATCAGCCGCACCACC 61.434 66.667 0.00 0.00 0.00 4.61
2853 4175 2.672996 AACCACATCAGCCGCACC 60.673 61.111 0.00 0.00 0.00 5.01
2892 4214 3.884169 TCTTGTATTGCGTGCAGTTTTC 58.116 40.909 0.00 0.00 0.00 2.29
2957 4279 3.806949 AGCCATTGTTCCTTACCTTCA 57.193 42.857 0.00 0.00 0.00 3.02
2999 4321 3.669536 TCGTATTGTGCATCAAGGTTGA 58.330 40.909 0.00 0.00 42.14 3.18
3013 4335 5.134640 ACGTTGTGTTCGAATTTCGTATTG 58.865 37.500 17.61 4.89 41.35 1.90
3035 4357 4.097361 GGCAAGGGAGGACGGGAC 62.097 72.222 0.00 0.00 0.00 4.46
3037 4359 3.330720 AAGGCAAGGGAGGACGGG 61.331 66.667 0.00 0.00 0.00 5.28
3085 4407 0.031178 GATTTGACATGGCATCGGGC 59.969 55.000 0.00 0.00 43.74 6.13
3087 4409 2.797087 GCAAGATTTGACATGGCATCGG 60.797 50.000 0.00 0.00 0.00 4.18
3092 4414 4.577693 TCAGATAGCAAGATTTGACATGGC 59.422 41.667 0.00 0.00 0.00 4.40
3112 4434 4.566004 TCTAATCGTCCCAACACTTTCAG 58.434 43.478 0.00 0.00 0.00 3.02
3142 4464 1.683790 CCTTAAGCCGTTGTCTCGCG 61.684 60.000 0.00 0.00 0.00 5.87
3153 4475 3.181500 CGTGTTAAAGATGCCCTTAAGCC 60.181 47.826 0.00 0.00 34.00 4.35
3193 4515 0.249741 CACCTCAGTCCGGACGTTTT 60.250 55.000 28.26 8.74 36.20 2.43
3197 4519 1.080705 GAACACCTCAGTCCGGACG 60.081 63.158 28.26 22.00 36.20 4.79
3200 4522 0.600255 GTGTGAACACCTCAGTCCGG 60.600 60.000 0.00 0.00 40.85 5.14
3217 4539 2.537792 CTTGGATGGCTTGCAGCGTG 62.538 60.000 0.00 0.00 43.62 5.34
3236 4566 2.700773 GGACCAATGAAGTGCCGCC 61.701 63.158 0.00 0.00 0.00 6.13
3244 4574 2.112198 GCATCCGCGGACCAATGAA 61.112 57.895 33.75 5.46 0.00 2.57
3267 4597 3.149196 ACGGTGAGCATTTCAGACAAAT 58.851 40.909 0.00 0.00 36.21 2.32


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

AutoCloner maintained by Alex Coulton.