Multiple sequence alignment - TraesCS5D01G238800

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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 TraesCS5D01G238800 chr5D 100.000 3624 0 0 1 3624 346875401 346879024 0.000000e+00 6693.0
1 TraesCS5D01G238800 chr5A 92.633 2674 104 42 875 3528 444851541 444848941 0.000000e+00 3760.0
2 TraesCS5D01G238800 chr5A 87.179 390 39 7 462 847 444851919 444851537 2.000000e-117 433.0
3 TraesCS5D01G238800 chr5A 90.741 108 9 1 3518 3624 444848622 444848515 3.770000e-30 143.0
4 TraesCS5D01G238800 chr5A 82.432 74 7 5 2896 2965 457916153 457916082 3.910000e-05 60.2
5 TraesCS5D01G238800 chr5B 92.136 2556 122 40 524 3055 404145771 404143271 0.000000e+00 3533.0
6 TraesCS5D01G238800 chr5B 89.956 458 42 4 3062 3518 404094033 404093579 4.030000e-164 588.0
7 TraesCS5D01G238800 chr5B 91.456 316 15 7 229 539 404146386 404146078 1.200000e-114 424.0
8 TraesCS5D01G238800 chr5B 93.966 116 6 1 3510 3624 404093398 404093283 1.340000e-39 174.0
9 TraesCS5D01G238800 chr5B 97.222 36 1 0 20 55 123765173 123765208 1.090000e-05 62.1
10 TraesCS5D01G238800 chr4B 88.462 234 26 1 3344 3576 611405744 611405977 7.660000e-72 281.0
11 TraesCS5D01G238800 chr4B 77.778 162 27 8 2896 3054 134205221 134205066 1.390000e-14 91.6
12 TraesCS5D01G238800 chr3B 87.554 233 27 2 3341 3573 644018848 644018618 5.960000e-68 268.0
13 TraesCS5D01G238800 chr3B 89.011 91 8 2 1083 1172 819901652 819901563 1.060000e-20 111.0
14 TraesCS5D01G238800 chr3B 96.923 65 2 0 1108 1172 359228452 359228388 3.830000e-20 110.0
15 TraesCS5D01G238800 chr3B 100.000 28 0 0 3059 3086 46288070 46288097 7.000000e-03 52.8
16 TraesCS5D01G238800 chr3D 83.041 171 29 0 1268 1438 609215877 609215707 4.840000e-34 156.0
17 TraesCS5D01G238800 chr3D 95.385 65 3 0 1108 1172 274337213 274337277 1.780000e-18 104.0
18 TraesCS5D01G238800 chr3D 100.000 28 0 0 3059 3086 17520334 17520307 7.000000e-03 52.8
19 TraesCS5D01G238800 chr3A 83.041 171 29 0 1268 1438 742768873 742768703 4.840000e-34 156.0
20 TraesCS5D01G238800 chr3A 96.825 63 2 0 1110 1172 359082387 359082325 4.950000e-19 106.0
21 TraesCS5D01G238800 chr3A 93.548 62 4 0 1111 1172 742616982 742616921 3.850000e-15 93.5
22 TraesCS5D01G238800 chr4A 76.687 163 30 6 3342 3497 614036965 614037126 2.320000e-12 84.2
23 TraesCS5D01G238800 chr7D 86.364 66 8 1 3411 3476 244550593 244550529 1.810000e-08 71.3
24 TraesCS5D01G238800 chr7A 100.000 28 0 0 3059 3086 271642180 271642153 7.000000e-03 52.8
25 TraesCS5D01G238800 chr4D 100.000 28 0 0 3059 3086 505317417 505317444 7.000000e-03 52.8
26 TraesCS5D01G238800 chr2D 100.000 28 0 0 3059 3086 154952895 154952868 7.000000e-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 TraesCS5D01G238800 chr5D 346875401 346879024 3623 False 6693.000000 6693 100.000000 1 3624 1 chr5D.!!$F1 3623
1 TraesCS5D01G238800 chr5A 444848515 444851919 3404 True 1445.333333 3760 90.184333 462 3624 3 chr5A.!!$R2 3162
2 TraesCS5D01G238800 chr5B 404143271 404146386 3115 True 1978.500000 3533 91.796000 229 3055 2 chr5B.!!$R2 2826
3 TraesCS5D01G238800 chr5B 404093283 404094033 750 True 381.000000 588 91.961000 3062 3624 2 chr5B.!!$R1 562

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
738 1077 0.508641 CGTCCATCATTTCGCCGATC 59.491 55.000 0.00 0.00 0.00 3.69 F
740 1079 0.599991 TCCATCATTTCGCCGATCGG 60.600 55.000 30.03 30.03 39.05 4.18 F
899 1242 1.127582 AGCGAGTTACAGTCGTCGTAC 59.872 52.381 3.12 0.00 42.66 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2743 1.228245 GACCTTGGCACCTTGCTCA 60.228 57.895 0.00 0.00 44.28 4.26 R
2390 2747 1.672356 CGAGGACCTTGGCACCTTG 60.672 63.158 0.00 6.82 33.89 3.61 R
2818 3189 2.032528 ACACATGTGAGCCACCCG 59.967 61.111 31.94 2.46 32.73 5.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.796038 ATTCATTTTTCACAGGCAGGAG 57.204 40.909 0.00 0.00 0.00 3.69
23 24 1.888512 TCATTTTTCACAGGCAGGAGC 59.111 47.619 0.00 0.00 41.10 4.70
24 25 1.614903 CATTTTTCACAGGCAGGAGCA 59.385 47.619 0.00 0.00 44.61 4.26
25 26 1.032014 TTTTTCACAGGCAGGAGCAC 58.968 50.000 0.00 0.00 44.61 4.40
26 27 1.165907 TTTTCACAGGCAGGAGCACG 61.166 55.000 0.00 0.00 44.61 5.34
27 28 2.324014 TTTCACAGGCAGGAGCACGT 62.324 55.000 0.00 0.00 44.61 4.49
28 29 2.994387 TTCACAGGCAGGAGCACGTG 62.994 60.000 12.28 12.28 44.61 4.49
46 47 4.547859 CTCCCGGGAGCTGAATTG 57.452 61.111 36.90 12.91 35.31 2.32
47 48 1.821332 CTCCCGGGAGCTGAATTGC 60.821 63.158 36.90 0.00 35.31 3.56
48 49 2.045045 CCCGGGAGCTGAATTGCA 60.045 61.111 18.48 0.00 34.99 4.08
49 50 1.454479 CCCGGGAGCTGAATTGCAT 60.454 57.895 18.48 0.00 34.99 3.96
50 51 1.039233 CCCGGGAGCTGAATTGCATT 61.039 55.000 18.48 0.00 34.99 3.56
51 52 0.819582 CCGGGAGCTGAATTGCATTT 59.180 50.000 0.00 0.00 34.99 2.32
52 53 1.202336 CCGGGAGCTGAATTGCATTTC 60.202 52.381 13.23 13.23 34.99 2.17
53 54 1.202336 CGGGAGCTGAATTGCATTTCC 60.202 52.381 16.52 3.79 34.99 3.13
54 55 1.202336 GGGAGCTGAATTGCATTTCCG 60.202 52.381 16.52 12.21 32.51 4.30
55 56 1.745087 GGAGCTGAATTGCATTTCCGA 59.255 47.619 16.52 1.07 34.99 4.55
56 57 2.478539 GGAGCTGAATTGCATTTCCGAC 60.479 50.000 16.52 7.71 34.99 4.79
57 58 2.161855 AGCTGAATTGCATTTCCGACA 58.838 42.857 16.52 0.71 34.99 4.35
58 59 2.557924 AGCTGAATTGCATTTCCGACAA 59.442 40.909 16.52 0.00 34.99 3.18
59 60 3.005684 AGCTGAATTGCATTTCCGACAAA 59.994 39.130 16.52 0.00 34.99 2.83
60 61 3.365820 GCTGAATTGCATTTCCGACAAAG 59.634 43.478 16.52 8.65 0.00 2.77
61 62 4.797471 CTGAATTGCATTTCCGACAAAGA 58.203 39.130 16.52 0.00 0.00 2.52
62 63 4.545610 TGAATTGCATTTCCGACAAAGAC 58.454 39.130 16.52 0.00 0.00 3.01
63 64 3.575965 ATTGCATTTCCGACAAAGACC 57.424 42.857 0.00 0.00 0.00 3.85
64 65 1.974265 TGCATTTCCGACAAAGACCA 58.026 45.000 0.00 0.00 0.00 4.02
65 66 2.513753 TGCATTTCCGACAAAGACCAT 58.486 42.857 0.00 0.00 0.00 3.55
66 67 2.487762 TGCATTTCCGACAAAGACCATC 59.512 45.455 0.00 0.00 0.00 3.51
67 68 2.749621 GCATTTCCGACAAAGACCATCT 59.250 45.455 0.00 0.00 0.00 2.90
68 69 3.938963 GCATTTCCGACAAAGACCATCTA 59.061 43.478 0.00 0.00 0.00 1.98
69 70 4.394920 GCATTTCCGACAAAGACCATCTAA 59.605 41.667 0.00 0.00 0.00 2.10
70 71 5.673818 GCATTTCCGACAAAGACCATCTAAC 60.674 44.000 0.00 0.00 0.00 2.34
71 72 4.610605 TTCCGACAAAGACCATCTAACA 57.389 40.909 0.00 0.00 0.00 2.41
72 73 4.610605 TCCGACAAAGACCATCTAACAA 57.389 40.909 0.00 0.00 0.00 2.83
73 74 4.566004 TCCGACAAAGACCATCTAACAAG 58.434 43.478 0.00 0.00 0.00 3.16
74 75 4.282449 TCCGACAAAGACCATCTAACAAGA 59.718 41.667 0.00 0.00 0.00 3.02
75 76 4.627467 CCGACAAAGACCATCTAACAAGAG 59.373 45.833 0.00 0.00 0.00 2.85
76 77 4.627467 CGACAAAGACCATCTAACAAGAGG 59.373 45.833 0.00 0.00 0.00 3.69
77 78 4.327680 ACAAAGACCATCTAACAAGAGGC 58.672 43.478 0.00 0.00 0.00 4.70
78 79 4.202461 ACAAAGACCATCTAACAAGAGGCA 60.202 41.667 0.00 0.00 0.00 4.75
79 80 4.640771 AAGACCATCTAACAAGAGGCAA 57.359 40.909 0.00 0.00 0.00 4.52
80 81 4.213564 AGACCATCTAACAAGAGGCAAG 57.786 45.455 0.00 0.00 0.00 4.01
81 82 3.054802 AGACCATCTAACAAGAGGCAAGG 60.055 47.826 0.00 0.00 0.00 3.61
82 83 2.019984 CCATCTAACAAGAGGCAAGGC 58.980 52.381 0.00 0.00 0.00 4.35
83 84 2.356535 CCATCTAACAAGAGGCAAGGCT 60.357 50.000 0.00 0.00 0.00 4.58
84 85 3.350833 CATCTAACAAGAGGCAAGGCTT 58.649 45.455 0.00 0.00 0.00 4.35
85 86 3.508845 TCTAACAAGAGGCAAGGCTTT 57.491 42.857 0.00 0.00 0.00 3.51
86 87 3.412386 TCTAACAAGAGGCAAGGCTTTC 58.588 45.455 0.00 0.00 0.00 2.62
87 88 2.371658 AACAAGAGGCAAGGCTTTCT 57.628 45.000 0.00 0.00 0.00 2.52
88 89 2.371658 ACAAGAGGCAAGGCTTTCTT 57.628 45.000 6.81 6.81 34.67 2.52
89 90 2.234143 ACAAGAGGCAAGGCTTTCTTC 58.766 47.619 9.21 5.41 33.13 2.87
90 91 2.158549 ACAAGAGGCAAGGCTTTCTTCT 60.159 45.455 5.73 5.73 33.13 2.85
91 92 3.073062 ACAAGAGGCAAGGCTTTCTTCTA 59.927 43.478 11.54 0.00 33.13 2.10
92 93 4.074970 CAAGAGGCAAGGCTTTCTTCTAA 58.925 43.478 11.54 0.00 33.13 2.10
93 94 4.582973 AGAGGCAAGGCTTTCTTCTAAT 57.417 40.909 9.63 0.00 32.41 1.73
94 95 4.522114 AGAGGCAAGGCTTTCTTCTAATC 58.478 43.478 9.63 0.00 32.41 1.75
95 96 3.274288 AGGCAAGGCTTTCTTCTAATCG 58.726 45.455 0.00 0.00 32.41 3.34
96 97 3.055094 AGGCAAGGCTTTCTTCTAATCGA 60.055 43.478 0.00 0.00 32.41 3.59
97 98 3.879892 GGCAAGGCTTTCTTCTAATCGAT 59.120 43.478 0.00 0.00 32.41 3.59
98 99 4.024472 GGCAAGGCTTTCTTCTAATCGATC 60.024 45.833 0.00 0.00 32.41 3.69
99 100 4.318404 GCAAGGCTTTCTTCTAATCGATCG 60.318 45.833 9.36 9.36 32.41 3.69
100 101 4.920640 AGGCTTTCTTCTAATCGATCGA 57.079 40.909 21.86 21.86 0.00 3.59
101 102 4.865776 AGGCTTTCTTCTAATCGATCGAG 58.134 43.478 23.84 10.20 0.00 4.04
102 103 4.580995 AGGCTTTCTTCTAATCGATCGAGA 59.419 41.667 23.84 12.51 0.00 4.04
103 104 5.067936 AGGCTTTCTTCTAATCGATCGAGAA 59.932 40.000 23.84 18.79 0.00 2.87
104 105 5.749109 GGCTTTCTTCTAATCGATCGAGAAA 59.251 40.000 23.84 21.58 0.00 2.52
105 106 6.255887 GGCTTTCTTCTAATCGATCGAGAAAA 59.744 38.462 23.84 13.12 0.00 2.29
106 107 7.334009 GCTTTCTTCTAATCGATCGAGAAAAG 58.666 38.462 23.84 20.65 0.00 2.27
107 108 7.221067 GCTTTCTTCTAATCGATCGAGAAAAGA 59.779 37.037 23.84 22.28 0.00 2.52
108 109 8.981724 TTTCTTCTAATCGATCGAGAAAAGAA 57.018 30.769 26.69 26.69 0.00 2.52
109 110 8.621921 TTCTTCTAATCGATCGAGAAAAGAAG 57.378 34.615 31.12 31.12 40.55 2.85
110 111 7.986562 TCTTCTAATCGATCGAGAAAAGAAGA 58.013 34.615 33.04 33.04 42.81 2.87
111 112 8.126074 TCTTCTAATCGATCGAGAAAAGAAGAG 58.874 37.037 33.04 22.76 41.66 2.85
112 113 7.555306 TCTAATCGATCGAGAAAAGAAGAGA 57.445 36.000 23.84 11.12 0.00 3.10
113 114 8.160521 TCTAATCGATCGAGAAAAGAAGAGAT 57.839 34.615 23.84 0.00 0.00 2.75
114 115 9.274206 TCTAATCGATCGAGAAAAGAAGAGATA 57.726 33.333 23.84 0.00 0.00 1.98
115 116 9.325150 CTAATCGATCGAGAAAAGAAGAGATAC 57.675 37.037 23.84 0.00 0.00 2.24
116 117 6.062434 TCGATCGAGAAAAGAAGAGATACC 57.938 41.667 15.15 0.00 0.00 2.73
117 118 5.823570 TCGATCGAGAAAAGAAGAGATACCT 59.176 40.000 15.15 0.00 0.00 3.08
118 119 6.319152 TCGATCGAGAAAAGAAGAGATACCTT 59.681 38.462 15.15 0.00 0.00 3.50
119 120 6.416455 CGATCGAGAAAAGAAGAGATACCTTG 59.584 42.308 10.26 0.00 0.00 3.61
120 121 6.835819 TCGAGAAAAGAAGAGATACCTTGA 57.164 37.500 0.00 0.00 0.00 3.02
121 122 7.228314 TCGAGAAAAGAAGAGATACCTTGAA 57.772 36.000 0.00 0.00 0.00 2.69
122 123 7.841956 TCGAGAAAAGAAGAGATACCTTGAAT 58.158 34.615 0.00 0.00 0.00 2.57
123 124 8.314751 TCGAGAAAAGAAGAGATACCTTGAATT 58.685 33.333 0.00 0.00 0.00 2.17
124 125 8.940952 CGAGAAAAGAAGAGATACCTTGAATTT 58.059 33.333 0.00 0.00 0.00 1.82
139 140 8.572855 ACCTTGAATTTTGATTTTTGTTTGGA 57.427 26.923 0.00 0.00 0.00 3.53
140 141 9.018582 ACCTTGAATTTTGATTTTTGTTTGGAA 57.981 25.926 0.00 0.00 0.00 3.53
141 142 9.288124 CCTTGAATTTTGATTTTTGTTTGGAAC 57.712 29.630 0.00 0.00 0.00 3.62
143 144 9.837525 TTGAATTTTGATTTTTGTTTGGAACTG 57.162 25.926 0.00 0.00 0.00 3.16
144 145 9.007901 TGAATTTTGATTTTTGTTTGGAACTGT 57.992 25.926 0.00 0.00 0.00 3.55
147 148 8.485976 TTTTGATTTTTGTTTGGAACTGTAGG 57.514 30.769 0.00 0.00 0.00 3.18
148 149 5.596845 TGATTTTTGTTTGGAACTGTAGGC 58.403 37.500 0.00 0.00 0.00 3.93
149 150 5.127845 TGATTTTTGTTTGGAACTGTAGGCA 59.872 36.000 0.00 0.00 0.00 4.75
150 151 5.407407 TTTTTGTTTGGAACTGTAGGCAA 57.593 34.783 0.00 0.00 0.00 4.52
151 152 4.379339 TTTGTTTGGAACTGTAGGCAAC 57.621 40.909 0.00 0.00 0.00 4.17
152 153 3.006112 TGTTTGGAACTGTAGGCAACA 57.994 42.857 0.00 0.00 41.41 3.33
159 160 4.988065 TGTAGGCAACAGTCGAGC 57.012 55.556 0.00 0.00 41.41 5.03
160 161 2.351777 TGTAGGCAACAGTCGAGCT 58.648 52.632 0.00 0.00 41.41 4.09
161 162 0.679505 TGTAGGCAACAGTCGAGCTT 59.320 50.000 0.00 0.00 41.41 3.74
162 163 1.890489 TGTAGGCAACAGTCGAGCTTA 59.110 47.619 0.00 0.00 41.41 3.09
163 164 2.094700 TGTAGGCAACAGTCGAGCTTAG 60.095 50.000 0.00 0.00 41.41 2.18
164 165 0.969894 AGGCAACAGTCGAGCTTAGT 59.030 50.000 0.00 0.00 41.41 2.24
165 166 1.071605 GGCAACAGTCGAGCTTAGTG 58.928 55.000 0.00 0.00 0.00 2.74
166 167 1.605712 GGCAACAGTCGAGCTTAGTGT 60.606 52.381 5.00 5.00 31.83 3.55
167 168 2.352421 GGCAACAGTCGAGCTTAGTGTA 60.352 50.000 10.03 0.00 30.35 2.90
168 169 3.512680 GCAACAGTCGAGCTTAGTGTAT 58.487 45.455 10.03 1.03 30.35 2.29
169 170 4.439700 GGCAACAGTCGAGCTTAGTGTATA 60.440 45.833 10.03 0.00 30.35 1.47
170 171 5.282510 GCAACAGTCGAGCTTAGTGTATAT 58.717 41.667 10.03 0.00 30.35 0.86
171 172 5.399892 GCAACAGTCGAGCTTAGTGTATATC 59.600 44.000 10.03 0.00 30.35 1.63
172 173 6.495706 CAACAGTCGAGCTTAGTGTATATCA 58.504 40.000 10.03 0.00 30.35 2.15
173 174 6.694877 ACAGTCGAGCTTAGTGTATATCAA 57.305 37.500 8.33 0.00 0.00 2.57
174 175 7.096884 ACAGTCGAGCTTAGTGTATATCAAA 57.903 36.000 8.33 0.00 0.00 2.69
175 176 7.197017 ACAGTCGAGCTTAGTGTATATCAAAG 58.803 38.462 8.33 0.00 0.00 2.77
176 177 6.638873 CAGTCGAGCTTAGTGTATATCAAAGG 59.361 42.308 0.00 0.00 0.00 3.11
177 178 5.921408 GTCGAGCTTAGTGTATATCAAAGGG 59.079 44.000 0.00 0.00 0.00 3.95
178 179 5.010719 TCGAGCTTAGTGTATATCAAAGGGG 59.989 44.000 0.00 0.00 0.00 4.79
179 180 5.010719 CGAGCTTAGTGTATATCAAAGGGGA 59.989 44.000 0.00 0.00 0.00 4.81
180 181 6.462487 CGAGCTTAGTGTATATCAAAGGGGAA 60.462 42.308 0.00 0.00 0.00 3.97
181 182 6.592870 AGCTTAGTGTATATCAAAGGGGAAC 58.407 40.000 0.00 0.00 0.00 3.62
182 183 6.387220 AGCTTAGTGTATATCAAAGGGGAACT 59.613 38.462 0.00 0.00 0.00 3.01
183 184 7.054751 GCTTAGTGTATATCAAAGGGGAACTT 58.945 38.462 0.00 0.00 42.52 2.66
198 199 8.777578 AAGGGGAACTTTTTGAATTTACTACT 57.222 30.769 0.00 0.00 35.35 2.57
199 200 8.405418 AGGGGAACTTTTTGAATTTACTACTC 57.595 34.615 0.00 0.00 0.00 2.59
200 201 7.450634 AGGGGAACTTTTTGAATTTACTACTCC 59.549 37.037 0.00 0.00 0.00 3.85
201 202 7.309621 GGGGAACTTTTTGAATTTACTACTCCC 60.310 40.741 0.00 0.00 36.35 4.30
202 203 7.450634 GGGAACTTTTTGAATTTACTACTCCCT 59.549 37.037 0.00 0.00 34.61 4.20
203 204 8.512956 GGAACTTTTTGAATTTACTACTCCCTC 58.487 37.037 0.00 0.00 0.00 4.30
204 205 9.286170 GAACTTTTTGAATTTACTACTCCCTCT 57.714 33.333 0.00 0.00 0.00 3.69
209 210 9.901172 TTTTGAATTTACTACTCCCTCTATTCC 57.099 33.333 0.00 0.00 0.00 3.01
210 211 8.618240 TTGAATTTACTACTCCCTCTATTCCA 57.382 34.615 0.00 0.00 0.00 3.53
211 212 8.618240 TGAATTTACTACTCCCTCTATTCCAA 57.382 34.615 0.00 0.00 0.00 3.53
212 213 9.053472 TGAATTTACTACTCCCTCTATTCCAAA 57.947 33.333 0.00 0.00 0.00 3.28
213 214 9.901172 GAATTTACTACTCCCTCTATTCCAAAA 57.099 33.333 0.00 0.00 0.00 2.44
260 261 5.520376 AATCACCTTTTGTCCTTCTGTTG 57.480 39.130 0.00 0.00 0.00 3.33
274 275 6.094186 GTCCTTCTGTTGAGTGTTTTTCTTCT 59.906 38.462 0.00 0.00 0.00 2.85
280 281 5.525745 TGTTGAGTGTTTTTCTTCTATGCGA 59.474 36.000 0.00 0.00 0.00 5.10
343 344 7.012894 GTGTGAGTGAGATGCTAGTATTCTACT 59.987 40.741 0.00 0.18 42.68 2.57
361 362 8.856490 ATTCTACTGTTTGTTTTTGATGTGTC 57.144 30.769 0.00 0.00 0.00 3.67
394 395 9.372541 CAATTAATCTTCAATGTTGTTGTTTGC 57.627 29.630 0.00 0.00 0.00 3.68
418 419 5.834169 TGTTTGAACGATGAGTACTACACA 58.166 37.500 0.00 0.00 0.00 3.72
419 420 5.688621 TGTTTGAACGATGAGTACTACACAC 59.311 40.000 0.00 0.00 0.00 3.82
420 421 5.441709 TTGAACGATGAGTACTACACACA 57.558 39.130 0.00 0.00 31.98 3.72
421 422 4.790878 TGAACGATGAGTACTACACACAC 58.209 43.478 0.00 0.00 30.06 3.82
422 423 4.276431 TGAACGATGAGTACTACACACACA 59.724 41.667 0.00 0.00 30.06 3.72
423 424 4.156664 ACGATGAGTACTACACACACAC 57.843 45.455 0.00 0.00 30.06 3.82
424 425 3.566742 ACGATGAGTACTACACACACACA 59.433 43.478 0.00 0.00 30.06 3.72
425 426 3.912563 CGATGAGTACTACACACACACAC 59.087 47.826 0.00 0.00 30.06 3.82
433 434 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
441 442 4.094294 ACACACACACACACACAAATCTAC 59.906 41.667 0.00 0.00 0.00 2.59
454 455 5.086058 CACAAATCTACGTGCAAACCATAC 58.914 41.667 0.00 0.00 0.00 2.39
532 538 8.129496 TGTAGTAGTTACCATCAATCAAGTGA 57.871 34.615 0.00 0.00 0.00 3.41
585 923 2.033065 GCATGCGCAAATGTTGTTTTCA 60.033 40.909 17.11 0.00 38.36 2.69
590 928 3.661419 GCGCAAATGTTGTTTTCATTCGG 60.661 43.478 0.30 0.00 34.92 4.30
665 1003 7.198390 ACAATAATAATGTCTGTACGTACGCT 58.802 34.615 20.18 5.36 0.00 5.07
706 1045 4.838665 AAACAAACAAAACGATGCACAG 57.161 36.364 0.00 0.00 0.00 3.66
707 1046 3.502191 ACAAACAAAACGATGCACAGT 57.498 38.095 0.00 0.00 0.00 3.55
708 1047 4.624336 ACAAACAAAACGATGCACAGTA 57.376 36.364 0.00 0.00 0.00 2.74
711 1050 4.893424 AACAAAACGATGCACAGTAGTT 57.107 36.364 0.00 0.00 0.00 2.24
713 1052 3.874543 ACAAAACGATGCACAGTAGTTGA 59.125 39.130 18.40 0.00 0.00 3.18
717 1056 2.028112 ACGATGCACAGTAGTTGATGGT 60.028 45.455 0.00 0.00 0.00 3.55
738 1077 0.508641 CGTCCATCATTTCGCCGATC 59.491 55.000 0.00 0.00 0.00 3.69
740 1079 0.599991 TCCATCATTTCGCCGATCGG 60.600 55.000 30.03 30.03 39.05 4.18
784 1123 1.933181 TGTGCATCCAATCGAATCGAC 59.067 47.619 7.77 0.00 39.18 4.20
823 1163 2.806745 CGGCCGGAACATCAGTGATATT 60.807 50.000 20.10 0.00 0.00 1.28
899 1242 1.127582 AGCGAGTTACAGTCGTCGTAC 59.872 52.381 3.12 0.00 42.66 3.67
1184 1531 2.203538 CCAGGCAGGCACCAAGTT 60.204 61.111 0.00 0.00 0.00 2.66
1229 1576 9.829507 CTTAATTACTCTCATGGAGAATGTTCT 57.170 33.333 15.51 0.00 44.45 3.01
1231 1578 6.857437 TTACTCTCATGGAGAATGTTCTGA 57.143 37.500 15.51 0.00 44.45 3.27
1244 1591 8.719648 GGAGAATGTTCTGATCATATTGCTTAG 58.280 37.037 0.00 0.00 37.73 2.18
1609 1956 6.109359 CAGGGATCCTCGGTAAAATATCATC 58.891 44.000 12.58 0.00 0.00 2.92
1630 1983 6.331042 TCATCCCATCTCCATCAATCTTTACT 59.669 38.462 0.00 0.00 0.00 2.24
1661 2014 1.533625 TCTTTTCTTGCATCGTGGGG 58.466 50.000 0.00 0.00 0.00 4.96
1762 2119 2.734673 GCTGGAGAAGAAGCACGCG 61.735 63.158 3.53 3.53 39.31 6.01
1850 2207 3.740128 CTCCTCCCGGGCAACATCG 62.740 68.421 18.49 0.00 39.74 3.84
2109 2466 3.755628 GCAGTACGGCGACCTGGA 61.756 66.667 23.94 0.00 0.00 3.86
2386 2743 2.762043 GGCCTCCTCTTCGGCTCT 60.762 66.667 0.00 0.00 45.57 4.09
2390 2747 1.437160 CTCCTCTTCGGCTCTGAGC 59.563 63.158 21.17 21.17 41.46 4.26
2527 2884 2.827051 CGGGATGAAGCACATGCGG 61.827 63.158 0.00 8.32 46.05 5.69
2617 2974 2.365617 CGCTGCTAATCCTTCCTCCTTA 59.634 50.000 0.00 0.00 0.00 2.69
2833 3204 3.952508 TGCGGGTGGCTCACATGT 61.953 61.111 0.00 0.00 44.05 3.21
2854 3225 2.222931 TGTCTTCTTGTGTTTTCGCACG 60.223 45.455 0.00 0.00 41.94 5.34
2877 3248 3.651803 CTCTATCGTGAGGGTTGGATC 57.348 52.381 0.00 0.00 0.00 3.36
2878 3249 2.959030 CTCTATCGTGAGGGTTGGATCA 59.041 50.000 0.00 0.00 0.00 2.92
2886 3257 2.562298 TGAGGGTTGGATCAATGTTTGC 59.438 45.455 0.00 0.00 0.00 3.68
2890 3261 3.244526 GGGTTGGATCAATGTTTGCCTTT 60.245 43.478 0.00 0.00 0.00 3.11
2945 3316 1.402896 GGATGATGACGCCTCCAGGA 61.403 60.000 0.00 0.00 37.39 3.86
2967 3338 3.624861 AGAGAAATGGTTGACGATGATGC 59.375 43.478 0.00 0.00 0.00 3.91
3026 3398 3.934579 TGTGTCAGATATCATGTGTGTGC 59.065 43.478 5.32 0.00 0.00 4.57
3080 3452 3.869272 GCGCTCGTCCATGGCAAG 61.869 66.667 6.96 5.17 0.00 4.01
3104 3476 5.065988 GGCGATTTAGAGTTTCAGGCAAATA 59.934 40.000 0.00 0.00 0.00 1.40
3124 3496 9.328721 GCAAATATTTAGCAAAACCAATGTTTC 57.671 29.630 14.05 0.00 43.80 2.78
3139 3511 9.859427 AACCAATGTTTCATTATACAACTCATG 57.141 29.630 0.00 0.00 0.00 3.07
3371 3744 4.270084 TGAAATAGAGGCGTAAGATTTGCG 59.730 41.667 0.00 0.00 41.83 4.85
3377 3750 1.332028 GGCGTAAGATTTGCGTGATCG 60.332 52.381 1.65 0.00 40.97 3.69
3411 3784 9.520515 AAGAGGAGAATAGAATTTTACAAAGCA 57.479 29.630 0.00 0.00 0.00 3.91
3421 3794 4.810191 TTTTACAAAGCACCCACAAAGT 57.190 36.364 0.00 0.00 0.00 2.66
3460 3833 6.646267 ACTCGCACAAAATAATAGACCCTAA 58.354 36.000 0.00 0.00 0.00 2.69
3465 3838 9.019764 CGCACAAAATAATAGACCCTAATTTTG 57.980 33.333 14.13 14.13 45.94 2.44
3476 3849 1.933115 CTAATTTTGTGGCGCCCGCT 61.933 55.000 26.77 3.63 41.60 5.52
3481 3854 0.677098 TTTGTGGCGCCCGCTATAAA 60.677 50.000 26.77 13.15 39.45 1.40
3529 3902 5.368523 TGACATTAAGGAGTATAGTTGGGGG 59.631 44.000 0.00 0.00 0.00 5.40
3530 3903 5.544682 ACATTAAGGAGTATAGTTGGGGGA 58.455 41.667 0.00 0.00 0.00 4.81
3531 3904 5.607171 ACATTAAGGAGTATAGTTGGGGGAG 59.393 44.000 0.00 0.00 0.00 4.30
3542 4244 2.067932 TTGGGGGAGCACTCTTGTGG 62.068 60.000 0.00 0.00 43.97 4.17
3589 4292 5.488341 GTTCTATTTGGTGGAGCACTCTTA 58.512 41.667 0.00 0.00 34.40 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.056322 GCTCCTGCCTGTGAAAAATGAAT 60.056 43.478 0.00 0.00 0.00 2.57
4 5 1.614903 TGCTCCTGCCTGTGAAAAATG 59.385 47.619 0.00 0.00 38.71 2.32
5 6 1.615392 GTGCTCCTGCCTGTGAAAAAT 59.385 47.619 0.00 0.00 38.71 1.82
6 7 1.032014 GTGCTCCTGCCTGTGAAAAA 58.968 50.000 0.00 0.00 38.71 1.94
7 8 1.165907 CGTGCTCCTGCCTGTGAAAA 61.166 55.000 0.00 0.00 38.71 2.29
8 9 1.597854 CGTGCTCCTGCCTGTGAAA 60.598 57.895 0.00 0.00 38.71 2.69
9 10 2.031012 CGTGCTCCTGCCTGTGAA 59.969 61.111 0.00 0.00 38.71 3.18
10 11 3.233980 ACGTGCTCCTGCCTGTGA 61.234 61.111 0.00 0.00 38.71 3.58
11 12 3.046087 CACGTGCTCCTGCCTGTG 61.046 66.667 0.82 0.00 38.71 3.66
12 13 4.996434 GCACGTGCTCCTGCCTGT 62.996 66.667 32.55 0.00 38.71 4.00
29 30 1.821332 GCAATTCAGCTCCCGGGAG 60.821 63.158 41.29 41.29 44.56 4.30
30 31 1.925285 ATGCAATTCAGCTCCCGGGA 61.925 55.000 25.06 25.06 34.99 5.14
31 32 1.039233 AATGCAATTCAGCTCCCGGG 61.039 55.000 16.85 16.85 34.99 5.73
32 33 0.819582 AAATGCAATTCAGCTCCCGG 59.180 50.000 0.00 0.00 33.67 5.73
33 34 1.202336 GGAAATGCAATTCAGCTCCCG 60.202 52.381 16.10 0.00 33.67 5.14
34 35 1.202336 CGGAAATGCAATTCAGCTCCC 60.202 52.381 16.10 0.00 33.67 4.30
35 36 1.745087 TCGGAAATGCAATTCAGCTCC 59.255 47.619 16.10 0.00 33.67 4.70
36 37 2.162208 TGTCGGAAATGCAATTCAGCTC 59.838 45.455 16.10 9.07 33.67 4.09
37 38 2.161855 TGTCGGAAATGCAATTCAGCT 58.838 42.857 16.10 0.00 33.67 4.24
38 39 2.634982 TGTCGGAAATGCAATTCAGC 57.365 45.000 16.10 8.91 33.67 4.26
39 40 4.618489 GTCTTTGTCGGAAATGCAATTCAG 59.382 41.667 16.10 12.15 33.67 3.02
40 41 4.545610 GTCTTTGTCGGAAATGCAATTCA 58.454 39.130 16.10 0.00 33.67 2.57
41 42 3.920412 GGTCTTTGTCGGAAATGCAATTC 59.080 43.478 5.92 5.92 33.67 2.17
42 43 3.320541 TGGTCTTTGTCGGAAATGCAATT 59.679 39.130 0.00 0.00 38.98 2.32
43 44 2.890311 TGGTCTTTGTCGGAAATGCAAT 59.110 40.909 0.00 0.00 0.00 3.56
44 45 2.302260 TGGTCTTTGTCGGAAATGCAA 58.698 42.857 0.00 0.00 0.00 4.08
45 46 1.974265 TGGTCTTTGTCGGAAATGCA 58.026 45.000 0.00 0.00 0.00 3.96
46 47 2.749621 AGATGGTCTTTGTCGGAAATGC 59.250 45.455 0.00 0.00 0.00 3.56
47 48 5.411361 TGTTAGATGGTCTTTGTCGGAAATG 59.589 40.000 0.00 0.00 0.00 2.32
48 49 5.556915 TGTTAGATGGTCTTTGTCGGAAAT 58.443 37.500 0.00 0.00 0.00 2.17
49 50 4.963373 TGTTAGATGGTCTTTGTCGGAAA 58.037 39.130 0.00 0.00 0.00 3.13
50 51 4.610605 TGTTAGATGGTCTTTGTCGGAA 57.389 40.909 0.00 0.00 0.00 4.30
51 52 4.282449 TCTTGTTAGATGGTCTTTGTCGGA 59.718 41.667 0.00 0.00 0.00 4.55
52 53 4.566004 TCTTGTTAGATGGTCTTTGTCGG 58.434 43.478 0.00 0.00 0.00 4.79
53 54 4.627467 CCTCTTGTTAGATGGTCTTTGTCG 59.373 45.833 0.00 0.00 0.00 4.35
54 55 4.393371 GCCTCTTGTTAGATGGTCTTTGTC 59.607 45.833 0.00 0.00 0.00 3.18
55 56 4.202461 TGCCTCTTGTTAGATGGTCTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
56 57 4.326826 TGCCTCTTGTTAGATGGTCTTTG 58.673 43.478 0.00 0.00 0.00 2.77
57 58 4.640771 TGCCTCTTGTTAGATGGTCTTT 57.359 40.909 0.00 0.00 0.00 2.52
58 59 4.566488 CCTTGCCTCTTGTTAGATGGTCTT 60.566 45.833 0.00 0.00 0.00 3.01
59 60 3.054802 CCTTGCCTCTTGTTAGATGGTCT 60.055 47.826 0.00 0.00 0.00 3.85
60 61 3.274288 CCTTGCCTCTTGTTAGATGGTC 58.726 50.000 0.00 0.00 0.00 4.02
61 62 2.619074 GCCTTGCCTCTTGTTAGATGGT 60.619 50.000 0.00 0.00 0.00 3.55
62 63 2.019984 GCCTTGCCTCTTGTTAGATGG 58.980 52.381 0.00 0.00 0.00 3.51
63 64 2.996631 AGCCTTGCCTCTTGTTAGATG 58.003 47.619 0.00 0.00 0.00 2.90
64 65 3.728385 AAGCCTTGCCTCTTGTTAGAT 57.272 42.857 0.00 0.00 0.00 1.98
65 66 3.073062 AGAAAGCCTTGCCTCTTGTTAGA 59.927 43.478 0.00 0.00 0.00 2.10
66 67 3.416156 AGAAAGCCTTGCCTCTTGTTAG 58.584 45.455 0.00 0.00 0.00 2.34
67 68 3.508845 AGAAAGCCTTGCCTCTTGTTA 57.491 42.857 0.00 0.00 0.00 2.41
68 69 2.371658 AGAAAGCCTTGCCTCTTGTT 57.628 45.000 0.00 0.00 0.00 2.83
69 70 2.158549 AGAAGAAAGCCTTGCCTCTTGT 60.159 45.455 5.93 0.65 33.37 3.16
70 71 2.512705 AGAAGAAAGCCTTGCCTCTTG 58.487 47.619 5.93 0.00 33.37 3.02
71 72 2.967745 AGAAGAAAGCCTTGCCTCTT 57.032 45.000 1.84 1.84 35.07 2.85
72 73 4.522114 GATTAGAAGAAAGCCTTGCCTCT 58.478 43.478 0.00 0.00 34.68 3.69
73 74 3.311048 CGATTAGAAGAAAGCCTTGCCTC 59.689 47.826 0.00 0.00 34.68 4.70
74 75 3.055094 TCGATTAGAAGAAAGCCTTGCCT 60.055 43.478 0.00 0.00 34.68 4.75
75 76 3.270877 TCGATTAGAAGAAAGCCTTGCC 58.729 45.455 0.00 0.00 34.68 4.52
76 77 4.318404 CGATCGATTAGAAGAAAGCCTTGC 60.318 45.833 10.26 0.00 34.68 4.01
77 78 5.043903 TCGATCGATTAGAAGAAAGCCTTG 58.956 41.667 15.15 0.00 34.68 3.61
78 79 5.067936 TCTCGATCGATTAGAAGAAAGCCTT 59.932 40.000 19.78 0.00 37.93 4.35
79 80 4.580995 TCTCGATCGATTAGAAGAAAGCCT 59.419 41.667 19.78 0.00 0.00 4.58
80 81 4.861210 TCTCGATCGATTAGAAGAAAGCC 58.139 43.478 19.78 0.00 0.00 4.35
81 82 6.814076 TTTCTCGATCGATTAGAAGAAAGC 57.186 37.500 19.78 0.00 31.75 3.51
82 83 8.621921 TCTTTTCTCGATCGATTAGAAGAAAG 57.378 34.615 19.78 17.53 35.72 2.62
83 84 8.981724 TTCTTTTCTCGATCGATTAGAAGAAA 57.018 30.769 26.67 23.06 33.69 2.52
84 85 8.459635 TCTTCTTTTCTCGATCGATTAGAAGAA 58.540 33.333 31.99 29.46 41.75 2.52
85 86 7.986562 TCTTCTTTTCTCGATCGATTAGAAGA 58.013 34.615 31.31 31.31 42.19 2.87
86 87 8.126074 TCTCTTCTTTTCTCGATCGATTAGAAG 58.874 37.037 29.38 29.38 38.96 2.85
87 88 7.986562 TCTCTTCTTTTCTCGATCGATTAGAA 58.013 34.615 19.78 20.18 0.00 2.10
88 89 7.555306 TCTCTTCTTTTCTCGATCGATTAGA 57.445 36.000 19.78 14.88 0.00 2.10
89 90 9.325150 GTATCTCTTCTTTTCTCGATCGATTAG 57.675 37.037 19.78 12.91 0.00 1.73
90 91 8.291032 GGTATCTCTTCTTTTCTCGATCGATTA 58.709 37.037 19.78 7.26 0.00 1.75
91 92 7.013846 AGGTATCTCTTCTTTTCTCGATCGATT 59.986 37.037 19.78 0.00 0.00 3.34
92 93 6.488683 AGGTATCTCTTCTTTTCTCGATCGAT 59.511 38.462 19.78 0.00 0.00 3.59
93 94 5.823570 AGGTATCTCTTCTTTTCTCGATCGA 59.176 40.000 18.32 18.32 0.00 3.59
94 95 6.067263 AGGTATCTCTTCTTTTCTCGATCG 57.933 41.667 9.36 9.36 0.00 3.69
95 96 7.484975 TCAAGGTATCTCTTCTTTTCTCGATC 58.515 38.462 0.00 0.00 0.00 3.69
96 97 7.411486 TCAAGGTATCTCTTCTTTTCTCGAT 57.589 36.000 0.00 0.00 0.00 3.59
97 98 6.835819 TCAAGGTATCTCTTCTTTTCTCGA 57.164 37.500 0.00 0.00 0.00 4.04
98 99 8.485976 AATTCAAGGTATCTCTTCTTTTCTCG 57.514 34.615 0.00 0.00 0.00 4.04
113 114 9.672673 TCCAAACAAAAATCAAAATTCAAGGTA 57.327 25.926 0.00 0.00 0.00 3.08
114 115 8.572855 TCCAAACAAAAATCAAAATTCAAGGT 57.427 26.923 0.00 0.00 0.00 3.50
115 116 9.288124 GTTCCAAACAAAAATCAAAATTCAAGG 57.712 29.630 0.00 0.00 0.00 3.61
117 118 9.837525 CAGTTCCAAACAAAAATCAAAATTCAA 57.162 25.926 0.00 0.00 0.00 2.69
118 119 9.007901 ACAGTTCCAAACAAAAATCAAAATTCA 57.992 25.926 0.00 0.00 0.00 2.57
121 122 9.108284 CCTACAGTTCCAAACAAAAATCAAAAT 57.892 29.630 0.00 0.00 0.00 1.82
122 123 7.065204 GCCTACAGTTCCAAACAAAAATCAAAA 59.935 33.333 0.00 0.00 0.00 2.44
123 124 6.536941 GCCTACAGTTCCAAACAAAAATCAAA 59.463 34.615 0.00 0.00 0.00 2.69
124 125 6.045955 GCCTACAGTTCCAAACAAAAATCAA 58.954 36.000 0.00 0.00 0.00 2.57
125 126 5.127845 TGCCTACAGTTCCAAACAAAAATCA 59.872 36.000 0.00 0.00 0.00 2.57
126 127 5.596845 TGCCTACAGTTCCAAACAAAAATC 58.403 37.500 0.00 0.00 0.00 2.17
127 128 5.606348 TGCCTACAGTTCCAAACAAAAAT 57.394 34.783 0.00 0.00 0.00 1.82
128 129 5.172205 GTTGCCTACAGTTCCAAACAAAAA 58.828 37.500 0.00 0.00 0.00 1.94
129 130 4.220821 TGTTGCCTACAGTTCCAAACAAAA 59.779 37.500 0.00 0.00 31.68 2.44
130 131 3.764434 TGTTGCCTACAGTTCCAAACAAA 59.236 39.130 0.00 0.00 31.68 2.83
131 132 3.357203 TGTTGCCTACAGTTCCAAACAA 58.643 40.909 0.00 0.00 31.68 2.83
132 133 3.006112 TGTTGCCTACAGTTCCAAACA 57.994 42.857 0.00 0.00 31.68 2.83
142 143 0.679505 AAGCTCGACTGTTGCCTACA 59.320 50.000 0.00 0.00 34.95 2.74
143 144 2.094649 ACTAAGCTCGACTGTTGCCTAC 60.095 50.000 0.00 0.00 0.00 3.18
144 145 2.094700 CACTAAGCTCGACTGTTGCCTA 60.095 50.000 0.00 0.00 0.00 3.93
145 146 0.969894 ACTAAGCTCGACTGTTGCCT 59.030 50.000 0.00 0.00 0.00 4.75
146 147 1.071605 CACTAAGCTCGACTGTTGCC 58.928 55.000 0.00 0.00 0.00 4.52
147 148 1.784525 ACACTAAGCTCGACTGTTGC 58.215 50.000 0.00 0.00 0.00 4.17
148 149 6.495706 TGATATACACTAAGCTCGACTGTTG 58.504 40.000 0.00 0.00 0.00 3.33
149 150 6.694877 TGATATACACTAAGCTCGACTGTT 57.305 37.500 0.00 0.00 0.00 3.16
150 151 6.694877 TTGATATACACTAAGCTCGACTGT 57.305 37.500 0.00 0.00 0.00 3.55
151 152 6.638873 CCTTTGATATACACTAAGCTCGACTG 59.361 42.308 0.00 0.00 0.00 3.51
152 153 6.239064 CCCTTTGATATACACTAAGCTCGACT 60.239 42.308 0.00 0.00 0.00 4.18
153 154 5.921408 CCCTTTGATATACACTAAGCTCGAC 59.079 44.000 0.00 0.00 0.00 4.20
154 155 5.010719 CCCCTTTGATATACACTAAGCTCGA 59.989 44.000 0.00 0.00 0.00 4.04
155 156 5.010719 TCCCCTTTGATATACACTAAGCTCG 59.989 44.000 0.00 0.00 0.00 5.03
156 157 6.420913 TCCCCTTTGATATACACTAAGCTC 57.579 41.667 0.00 0.00 0.00 4.09
157 158 6.387220 AGTTCCCCTTTGATATACACTAAGCT 59.613 38.462 0.00 0.00 0.00 3.74
158 159 6.592870 AGTTCCCCTTTGATATACACTAAGC 58.407 40.000 0.00 0.00 0.00 3.09
159 160 9.462606 AAAAGTTCCCCTTTGATATACACTAAG 57.537 33.333 0.00 0.00 42.62 2.18
160 161 9.816787 AAAAAGTTCCCCTTTGATATACACTAA 57.183 29.630 0.00 0.00 42.62 2.24
161 162 9.238368 CAAAAAGTTCCCCTTTGATATACACTA 57.762 33.333 0.00 0.00 42.62 2.74
162 163 7.947890 TCAAAAAGTTCCCCTTTGATATACACT 59.052 33.333 0.00 0.00 42.62 3.55
163 164 8.117813 TCAAAAAGTTCCCCTTTGATATACAC 57.882 34.615 0.00 0.00 42.62 2.90
164 165 8.713708 TTCAAAAAGTTCCCCTTTGATATACA 57.286 30.769 2.19 0.00 42.62 2.29
168 169 9.990360 GTAAATTCAAAAAGTTCCCCTTTGATA 57.010 29.630 2.19 0.00 42.62 2.15
169 170 8.713971 AGTAAATTCAAAAAGTTCCCCTTTGAT 58.286 29.630 2.19 0.00 42.62 2.57
170 171 8.084985 AGTAAATTCAAAAAGTTCCCCTTTGA 57.915 30.769 0.00 0.00 42.62 2.69
171 172 9.256477 GTAGTAAATTCAAAAAGTTCCCCTTTG 57.744 33.333 0.00 0.00 42.62 2.77
172 173 9.209048 AGTAGTAAATTCAAAAAGTTCCCCTTT 57.791 29.630 0.00 0.00 45.39 3.11
173 174 8.777578 AGTAGTAAATTCAAAAAGTTCCCCTT 57.222 30.769 0.00 0.00 33.79 3.95
174 175 7.450634 GGAGTAGTAAATTCAAAAAGTTCCCCT 59.549 37.037 0.00 0.00 0.00 4.79
175 176 7.309621 GGGAGTAGTAAATTCAAAAAGTTCCCC 60.310 40.741 0.00 0.00 0.00 4.81
176 177 7.450634 AGGGAGTAGTAAATTCAAAAAGTTCCC 59.549 37.037 0.00 0.00 0.00 3.97
177 178 8.405418 AGGGAGTAGTAAATTCAAAAAGTTCC 57.595 34.615 0.00 0.00 0.00 3.62
178 179 9.286170 AGAGGGAGTAGTAAATTCAAAAAGTTC 57.714 33.333 0.00 0.00 0.00 3.01
183 184 9.901172 GGAATAGAGGGAGTAGTAAATTCAAAA 57.099 33.333 0.00 0.00 0.00 2.44
184 185 9.053472 TGGAATAGAGGGAGTAGTAAATTCAAA 57.947 33.333 0.00 0.00 0.00 2.69
185 186 8.618240 TGGAATAGAGGGAGTAGTAAATTCAA 57.382 34.615 0.00 0.00 0.00 2.69
186 187 8.618240 TTGGAATAGAGGGAGTAGTAAATTCA 57.382 34.615 0.00 0.00 0.00 2.57
187 188 9.901172 TTTTGGAATAGAGGGAGTAGTAAATTC 57.099 33.333 0.00 0.00 0.00 2.17
232 233 8.536175 ACAGAAGGACAAAAGGTGATTTAAAAA 58.464 29.630 0.00 0.00 0.00 1.94
236 237 6.831353 TCAACAGAAGGACAAAAGGTGATTTA 59.169 34.615 0.00 0.00 0.00 1.40
260 261 4.434330 CCGTCGCATAGAAGAAAAACACTC 60.434 45.833 0.00 0.00 0.00 3.51
274 275 2.664568 CGAAGAGAAAAACCGTCGCATA 59.335 45.455 0.00 0.00 0.00 3.14
280 281 2.350498 CACACACGAAGAGAAAAACCGT 59.650 45.455 0.00 0.00 0.00 4.83
343 344 5.352846 TCTCTCGACACATCAAAAACAAACA 59.647 36.000 0.00 0.00 0.00 2.83
361 362 8.446273 ACAACATTGAAGATTAATTGTCTCTCG 58.554 33.333 0.00 0.00 0.00 4.04
369 370 9.328845 AGCAAACAACAACATTGAAGATTAATT 57.671 25.926 0.00 0.00 0.00 1.40
374 375 5.663456 ACAGCAAACAACAACATTGAAGAT 58.337 33.333 0.00 0.00 0.00 2.40
375 376 5.070770 ACAGCAAACAACAACATTGAAGA 57.929 34.783 0.00 0.00 0.00 2.87
376 377 5.783100 AACAGCAAACAACAACATTGAAG 57.217 34.783 0.00 0.00 0.00 3.02
383 384 3.670991 TCGTTCAAACAGCAAACAACAAC 59.329 39.130 0.00 0.00 0.00 3.32
394 395 5.918576 TGTGTAGTACTCATCGTTCAAACAG 59.081 40.000 0.00 0.00 0.00 3.16
418 419 3.081061 AGATTTGTGTGTGTGTGTGTGT 58.919 40.909 0.00 0.00 0.00 3.72
419 420 3.763097 AGATTTGTGTGTGTGTGTGTG 57.237 42.857 0.00 0.00 0.00 3.82
420 421 3.308595 CGTAGATTTGTGTGTGTGTGTGT 59.691 43.478 0.00 0.00 0.00 3.72
421 422 3.308595 ACGTAGATTTGTGTGTGTGTGTG 59.691 43.478 0.00 0.00 0.00 3.82
422 423 3.308595 CACGTAGATTTGTGTGTGTGTGT 59.691 43.478 0.00 0.00 0.00 3.72
423 424 3.844585 GCACGTAGATTTGTGTGTGTGTG 60.845 47.826 0.00 0.00 38.36 3.82
424 425 2.286833 GCACGTAGATTTGTGTGTGTGT 59.713 45.455 0.00 0.00 38.36 3.72
425 426 2.286563 TGCACGTAGATTTGTGTGTGTG 59.713 45.455 0.00 0.00 38.36 3.82
433 434 4.092237 TCGTATGGTTTGCACGTAGATTTG 59.908 41.667 0.00 0.00 37.02 2.32
441 442 1.602191 GCTTTCGTATGGTTTGCACG 58.398 50.000 0.00 0.00 37.03 5.34
454 455 2.705826 GCTCATCGCAGGCTTTCG 59.294 61.111 0.00 0.00 38.92 3.46
532 538 3.704061 ACAAACAGCCACACTTAATTGGT 59.296 39.130 0.00 0.00 35.09 3.67
570 908 3.186205 CCCCGAATGAAAACAACATTTGC 59.814 43.478 0.00 0.00 37.96 3.68
585 923 4.165486 CCGTAACCGCCCCCGAAT 62.165 66.667 0.00 0.00 36.29 3.34
665 1003 1.945387 TTGTTTTACGTGGCGTACCA 58.055 45.000 0.00 0.00 46.51 3.25
717 1056 0.456628 TCGGCGAAATGATGGACGTA 59.543 50.000 7.35 0.00 39.60 3.57
738 1077 0.462759 GTGGAAGAGGAATCTGCCCG 60.463 60.000 0.00 0.00 34.39 6.13
740 1079 2.016096 GCAGTGGAAGAGGAATCTGCC 61.016 57.143 0.00 0.00 41.26 4.85
784 1123 2.282462 GCCTGTGTTGGGTGGAGG 60.282 66.667 0.00 0.00 0.00 4.30
860 1203 6.642131 ACTCGCTTACATACGTTGAGTAAAAA 59.358 34.615 0.00 0.00 39.04 1.94
861 1204 6.151691 ACTCGCTTACATACGTTGAGTAAAA 58.848 36.000 0.00 0.00 39.04 1.52
862 1205 5.702865 ACTCGCTTACATACGTTGAGTAAA 58.297 37.500 0.00 0.00 39.04 2.01
863 1206 5.300969 ACTCGCTTACATACGTTGAGTAA 57.699 39.130 0.00 0.00 39.04 2.24
864 1207 4.952262 ACTCGCTTACATACGTTGAGTA 57.048 40.909 0.00 0.00 40.03 2.59
865 1208 3.844577 ACTCGCTTACATACGTTGAGT 57.155 42.857 0.00 0.00 0.00 3.41
866 1209 5.090757 TGTAACTCGCTTACATACGTTGAG 58.909 41.667 0.00 0.00 39.93 3.02
867 1210 5.045668 TGTAACTCGCTTACATACGTTGA 57.954 39.130 0.00 0.00 39.93 3.18
868 1211 4.855388 ACTGTAACTCGCTTACATACGTTG 59.145 41.667 0.00 0.00 43.15 4.10
869 1212 5.051891 ACTGTAACTCGCTTACATACGTT 57.948 39.130 0.00 0.00 43.15 3.99
870 1213 4.656041 GACTGTAACTCGCTTACATACGT 58.344 43.478 0.00 0.00 43.15 3.57
871 1214 3.717890 CGACTGTAACTCGCTTACATACG 59.282 47.826 6.11 9.83 43.15 3.06
872 1215 4.656041 ACGACTGTAACTCGCTTACATAC 58.344 43.478 6.11 3.99 43.15 2.39
873 1216 4.493057 CGACGACTGTAACTCGCTTACATA 60.493 45.833 6.11 0.00 43.15 2.29
889 1232 5.469421 CCCTCTTTATATGAGTACGACGACT 59.531 44.000 0.00 0.16 0.00 4.18
890 1233 5.468072 TCCCTCTTTATATGAGTACGACGAC 59.532 44.000 0.00 0.00 0.00 4.34
899 1242 5.841237 TCCTTCCTGTCCCTCTTTATATGAG 59.159 44.000 0.00 0.00 0.00 2.90
968 1312 1.999048 CTCTCTGCTTCAGTCAGCTG 58.001 55.000 7.63 7.63 43.87 4.24
975 1319 0.037139 ACTGCTGCTCTCTGCTTCAG 60.037 55.000 0.00 0.00 42.67 3.02
994 1338 0.960364 GAAAGGCGAGCCATGGTGAA 60.960 55.000 17.18 0.00 38.92 3.18
1178 1525 7.072581 AGGAGGAGTATTTAATAGGGAACTTGG 59.927 40.741 0.00 0.00 43.67 3.61
1211 1558 5.915175 TGATCAGAACATTCTCCATGAGAG 58.085 41.667 0.00 0.00 39.98 3.20
1244 1591 5.901884 CACTTACGCGGATTCATTGATTAAC 59.098 40.000 12.47 0.00 0.00 2.01
1253 1600 0.739462 CCTGCACTTACGCGGATTCA 60.739 55.000 12.47 0.00 41.00 2.57
1609 1956 4.993584 CGAGTAAAGATTGATGGAGATGGG 59.006 45.833 0.00 0.00 0.00 4.00
1630 1983 5.053811 TGCAAGAAAAGAATACACACTCGA 58.946 37.500 0.00 0.00 0.00 4.04
1661 2014 4.134187 CGTCACGCCATGTCACGC 62.134 66.667 0.00 0.00 0.00 5.34
2109 2466 1.534235 AGGCTCTGGTCGTTGAGGT 60.534 57.895 0.00 0.00 0.00 3.85
2216 2573 2.432628 GTCCCGCTGGTTCACTCG 60.433 66.667 0.00 0.00 0.00 4.18
2386 2743 1.228245 GACCTTGGCACCTTGCTCA 60.228 57.895 0.00 0.00 44.28 4.26
2390 2747 1.672356 CGAGGACCTTGGCACCTTG 60.672 63.158 0.00 6.82 33.89 3.61
2464 2821 4.308458 TGGAACCTCCGCACCACG 62.308 66.667 0.00 0.00 40.17 4.94
2527 2884 2.811317 CAGAGGTTGGCGAGCGAC 60.811 66.667 0.00 0.00 0.00 5.19
2617 2974 5.482006 TCGATCACACAGTTTGATCAGAAT 58.518 37.500 23.51 0.00 46.70 2.40
2818 3189 2.032528 ACACATGTGAGCCACCCG 59.967 61.111 31.94 2.46 32.73 5.28
2833 3204 2.222931 CGTGCGAAAACACAAGAAGACA 60.223 45.455 0.00 0.00 40.73 3.41
2875 3246 6.105397 ACTTCATCAAAGGCAAACATTGAT 57.895 33.333 0.00 0.00 42.80 2.57
2877 3248 4.383649 CGACTTCATCAAAGGCAAACATTG 59.616 41.667 0.00 0.00 43.97 2.82
2878 3249 4.549458 CGACTTCATCAAAGGCAAACATT 58.451 39.130 0.00 0.00 43.97 2.71
2886 3257 2.263077 CGACTCCGACTTCATCAAAGG 58.737 52.381 0.00 0.00 39.47 3.11
2890 3261 2.672714 CAAACGACTCCGACTTCATCA 58.327 47.619 0.00 0.00 39.50 3.07
2945 3316 3.624861 GCATCATCGTCAACCATTTCTCT 59.375 43.478 0.00 0.00 0.00 3.10
3034 3406 0.458260 AAAACCGTCACAAACTGCCC 59.542 50.000 0.00 0.00 0.00 5.36
3080 3452 2.356135 TGCCTGAAACTCTAAATCGCC 58.644 47.619 0.00 0.00 0.00 5.54
3292 3665 4.285020 TCCTCTGCTAGTGTGATCAATCT 58.715 43.478 0.00 1.32 0.00 2.40
3353 3726 2.164827 TCACGCAAATCTTACGCCTCTA 59.835 45.455 0.00 0.00 0.00 2.43
3354 3727 1.067142 TCACGCAAATCTTACGCCTCT 60.067 47.619 0.00 0.00 0.00 3.69
3360 3733 9.858247 TTATTTAATCGATCACGCAAATCTTAC 57.142 29.630 0.00 0.00 39.58 2.34
3367 3740 6.277605 TCCTCTTATTTAATCGATCACGCAA 58.722 36.000 0.00 0.00 39.58 4.85
3399 3772 5.351948 ACTTTGTGGGTGCTTTGTAAAAT 57.648 34.783 0.00 0.00 0.00 1.82
3411 3784 0.398696 TCATGCCGTACTTTGTGGGT 59.601 50.000 0.00 0.00 0.00 4.51
3421 3794 2.198406 GCGAGTAATTGTCATGCCGTA 58.802 47.619 0.00 0.00 0.00 4.02
3460 3833 0.464735 TATAGCGGGCGCCACAAAAT 60.465 50.000 30.85 16.44 43.17 1.82
3465 3838 2.540228 GGTTTATAGCGGGCGCCAC 61.540 63.158 30.85 20.20 43.17 5.01
3508 3881 5.513267 GCTCCCCCAACTATACTCCTTAATG 60.513 48.000 0.00 0.00 0.00 1.90
3529 3902 1.301716 TTCCGCCACAAGAGTGCTC 60.302 57.895 0.00 0.00 44.53 4.26
3530 3903 1.598130 GTTCCGCCACAAGAGTGCT 60.598 57.895 0.00 0.00 44.53 4.40
3531 3904 1.891919 TGTTCCGCCACAAGAGTGC 60.892 57.895 0.00 0.00 44.53 4.40
3542 4244 0.452784 GAAATGCTCGTGTGTTCCGC 60.453 55.000 0.00 0.00 0.00 5.54
3589 4292 8.975663 TCTCCTCGGTCATAATAATCGTATAT 57.024 34.615 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.