Multiple sequence alignment - TraesCS5D01G421500

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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 TraesCS5D01G421500 chr5D 100.000 1686 0 0 489 2174 481597269 481595584 0.000000e+00 3114.0
1 TraesCS5D01G421500 chr5D 98.640 1691 15 3 489 2174 503338949 503337262 0.000000e+00 2988.0
2 TraesCS5D01G421500 chr5D 98.403 1691 21 2 489 2174 503313016 503311327 0.000000e+00 2968.0
3 TraesCS5D01G421500 chr5D 100.000 299 0 0 1 299 481597757 481597459 8.770000e-154 553.0
4 TraesCS5D01G421500 chr3A 98.584 1695 11 4 489 2174 105557449 105559139 0.000000e+00 2985.0
5 TraesCS5D01G421500 chr1A 98.463 1692 16 3 489 2174 554481766 554480079 0.000000e+00 2972.0
6 TraesCS5D01G421500 chr1B 98.167 1691 18 4 489 2174 633716480 633714798 0.000000e+00 2939.0
7 TraesCS5D01G421500 chr1D 97.930 1691 23 5 489 2174 51832450 51834133 0.000000e+00 2918.0
8 TraesCS5D01G421500 chr1D 97.395 1689 19 4 489 2174 254458924 254457258 0.000000e+00 2852.0
9 TraesCS5D01G421500 chr1D 100.000 299 0 0 1 299 3009573 3009871 8.770000e-154 553.0
10 TraesCS5D01G421500 chr1D 100.000 299 0 0 1 299 40120828 40121126 8.770000e-154 553.0
11 TraesCS5D01G421500 chr3B 98.716 1636 10 4 489 2118 101924384 101922754 0.000000e+00 2894.0
12 TraesCS5D01G421500 chr7B 97.942 1555 19 5 489 2038 662755526 662757072 0.000000e+00 2682.0
13 TraesCS5D01G421500 chr7B 99.608 255 1 0 1920 2174 137684491 137684237 1.180000e-127 466.0
14 TraesCS5D01G421500 chr7A 94.721 663 12 5 1513 2174 537849192 537848552 0.000000e+00 1009.0
15 TraesCS5D01G421500 chr6D 100.000 299 0 0 1 299 23277884 23278182 8.770000e-154 553.0
16 TraesCS5D01G421500 chr2D 100.000 299 0 0 1 299 20490503 20490801 8.770000e-154 553.0
17 TraesCS5D01G421500 chr2D 100.000 299 0 0 1 299 648434765 648434467 8.770000e-154 553.0
18 TraesCS5D01G421500 chrUn 99.666 299 1 0 1 299 20156656 20156358 4.080000e-152 547.0
19 TraesCS5D01G421500 chrUn 99.666 299 1 0 1 299 26546623 26546325 4.080000e-152 547.0
20 TraesCS5D01G421500 chrUn 99.666 299 1 0 1 299 44569917 44570215 4.080000e-152 547.0
21 TraesCS5D01G421500 chrUn 99.666 299 1 0 1 299 95842801 95843099 4.080000e-152 547.0
22 TraesCS5D01G421500 chr2B 95.549 337 13 1 1794 2130 298532914 298532580 2.460000e-149 538.0
23 TraesCS5D01G421500 chr7D 98.872 266 2 1 1792 2057 187257803 187257539 7.020000e-130 473.0
24 TraesCS5D01G421500 chr7D 99.333 150 1 0 1990 2139 17808257 17808108 2.750000e-69 272.0
25 TraesCS5D01G421500 chr4A 97.436 195 5 0 1953 2147 365760085 365759891 1.240000e-87 333.0
26 TraesCS5D01G421500 chr3D 85.606 264 14 12 1757 2020 307878302 307878063 2.770000e-64 255.0
27 TraesCS5D01G421500 chr3D 92.262 168 13 0 2007 2174 527033305 527033138 2.790000e-59 239.0
28 TraesCS5D01G421500 chr3D 98.305 59 1 0 2062 2120 310809146 310809204 1.060000e-18 104.0
29 TraesCS5D01G421500 chr6A 98.113 53 1 0 1987 2039 53804534 53804586 2.300000e-15 93.5


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 TraesCS5D01G421500 chr5D 481595584 481597757 2173 True 1833.5 3114 100.000 1 2174 2 chr5D.!!$R3 2173
1 TraesCS5D01G421500 chr5D 503337262 503338949 1687 True 2988.0 2988 98.640 489 2174 1 chr5D.!!$R2 1685
2 TraesCS5D01G421500 chr5D 503311327 503313016 1689 True 2968.0 2968 98.403 489 2174 1 chr5D.!!$R1 1685
3 TraesCS5D01G421500 chr3A 105557449 105559139 1690 False 2985.0 2985 98.584 489 2174 1 chr3A.!!$F1 1685
4 TraesCS5D01G421500 chr1A 554480079 554481766 1687 True 2972.0 2972 98.463 489 2174 1 chr1A.!!$R1 1685
5 TraesCS5D01G421500 chr1B 633714798 633716480 1682 True 2939.0 2939 98.167 489 2174 1 chr1B.!!$R1 1685
6 TraesCS5D01G421500 chr1D 51832450 51834133 1683 False 2918.0 2918 97.930 489 2174 1 chr1D.!!$F3 1685
7 TraesCS5D01G421500 chr1D 254457258 254458924 1666 True 2852.0 2852 97.395 489 2174 1 chr1D.!!$R1 1685
8 TraesCS5D01G421500 chr3B 101922754 101924384 1630 True 2894.0 2894 98.716 489 2118 1 chr3B.!!$R1 1629
9 TraesCS5D01G421500 chr7B 662755526 662757072 1546 False 2682.0 2682 97.942 489 2038 1 chr7B.!!$F1 1549
10 TraesCS5D01G421500 chr7A 537848552 537849192 640 True 1009.0 1009 94.721 1513 2174 1 chr7A.!!$R1 661

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
89 90 0.038251 TGTCGAAGCGTCTTCTGCAT 60.038 50.0 14.67 0.0 33.85 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 1480 3.123621 CAGTTGTCATAGCTGTTCGGAAC 59.876 47.826 13.86 13.86 33.41 3.62 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 2.032681 GTTTGCCGCCTCCTCAGT 59.967 61.111 0.00 0.00 0.00 3.41
18 19 2.032528 TTTGCCGCCTCCTCAGTG 59.967 61.111 0.00 0.00 0.00 3.66
19 20 2.515979 TTTGCCGCCTCCTCAGTGA 61.516 57.895 0.00 0.00 0.00 3.41
20 21 1.841302 TTTGCCGCCTCCTCAGTGAT 61.841 55.000 0.00 0.00 0.00 3.06
21 22 2.202987 GCCGCCTCCTCAGTGATG 60.203 66.667 0.00 0.00 0.00 3.07
22 23 2.725312 GCCGCCTCCTCAGTGATGA 61.725 63.158 0.00 0.00 0.00 2.92
23 24 1.900351 CCGCCTCCTCAGTGATGAA 59.100 57.895 0.00 0.00 0.00 2.57
24 25 0.467384 CCGCCTCCTCAGTGATGAAT 59.533 55.000 0.00 0.00 0.00 2.57
25 26 1.579698 CGCCTCCTCAGTGATGAATG 58.420 55.000 0.00 0.00 0.00 2.67
26 27 1.307097 GCCTCCTCAGTGATGAATGC 58.693 55.000 0.00 0.00 0.00 3.56
27 28 1.964552 CCTCCTCAGTGATGAATGCC 58.035 55.000 0.00 0.00 0.00 4.40
28 29 1.489649 CCTCCTCAGTGATGAATGCCT 59.510 52.381 0.00 0.00 0.00 4.75
29 30 2.485124 CCTCCTCAGTGATGAATGCCTC 60.485 54.545 0.00 0.00 0.00 4.70
30 31 2.169978 CTCCTCAGTGATGAATGCCTCA 59.830 50.000 0.00 0.00 38.81 3.86
31 32 2.169978 TCCTCAGTGATGAATGCCTCAG 59.830 50.000 0.00 0.00 37.52 3.35
32 33 1.941294 CTCAGTGATGAATGCCTCAGC 59.059 52.381 0.00 0.00 41.07 4.26
33 34 1.022735 CAGTGATGAATGCCTCAGCC 58.977 55.000 0.00 0.00 39.88 4.85
34 35 0.622136 AGTGATGAATGCCTCAGCCA 59.378 50.000 0.00 0.00 39.88 4.75
35 36 1.214673 AGTGATGAATGCCTCAGCCAT 59.785 47.619 0.00 0.00 39.88 4.40
36 37 1.607628 GTGATGAATGCCTCAGCCATC 59.392 52.381 0.00 0.00 39.88 3.51
37 38 0.873054 GATGAATGCCTCAGCCATCG 59.127 55.000 0.00 0.00 37.52 3.84
38 39 0.471191 ATGAATGCCTCAGCCATCGA 59.529 50.000 0.00 0.00 37.52 3.59
39 40 0.471191 TGAATGCCTCAGCCATCGAT 59.529 50.000 0.00 0.00 38.69 3.59
40 41 0.873054 GAATGCCTCAGCCATCGATG 59.127 55.000 18.76 18.76 38.69 3.84
41 42 1.170919 AATGCCTCAGCCATCGATGC 61.171 55.000 20.25 14.80 38.69 3.91
42 43 2.053259 ATGCCTCAGCCATCGATGCT 62.053 55.000 20.25 16.76 40.41 3.79
43 44 1.525535 GCCTCAGCCATCGATGCTT 60.526 57.895 20.25 6.96 36.81 3.91
44 45 1.505477 GCCTCAGCCATCGATGCTTC 61.505 60.000 20.25 10.66 36.81 3.86
45 46 0.179065 CCTCAGCCATCGATGCTTCA 60.179 55.000 20.25 8.49 36.81 3.02
46 47 1.660167 CTCAGCCATCGATGCTTCAA 58.340 50.000 20.25 7.70 36.81 2.69
47 48 2.219458 CTCAGCCATCGATGCTTCAAT 58.781 47.619 20.25 0.00 36.81 2.57
48 49 2.617308 CTCAGCCATCGATGCTTCAATT 59.383 45.455 20.25 0.00 36.81 2.32
49 50 2.615447 TCAGCCATCGATGCTTCAATTC 59.385 45.455 20.25 1.32 36.81 2.17
50 51 2.617308 CAGCCATCGATGCTTCAATTCT 59.383 45.455 20.25 3.44 36.81 2.40
51 52 3.811497 CAGCCATCGATGCTTCAATTCTA 59.189 43.478 20.25 0.00 36.81 2.10
52 53 3.812053 AGCCATCGATGCTTCAATTCTAC 59.188 43.478 20.25 0.00 34.87 2.59
53 54 3.363378 GCCATCGATGCTTCAATTCTACG 60.363 47.826 20.25 2.66 0.00 3.51
54 55 3.804325 CCATCGATGCTTCAATTCTACGT 59.196 43.478 20.25 0.00 0.00 3.57
55 56 4.271049 CCATCGATGCTTCAATTCTACGTT 59.729 41.667 20.25 0.00 0.00 3.99
56 57 5.220662 CCATCGATGCTTCAATTCTACGTTT 60.221 40.000 20.25 0.00 0.00 3.60
57 58 6.019075 CCATCGATGCTTCAATTCTACGTTTA 60.019 38.462 20.25 0.00 0.00 2.01
58 59 7.307396 CCATCGATGCTTCAATTCTACGTTTAT 60.307 37.037 20.25 0.00 0.00 1.40
59 60 7.534085 TCGATGCTTCAATTCTACGTTTATT 57.466 32.000 0.00 0.00 0.00 1.40
60 61 7.970384 TCGATGCTTCAATTCTACGTTTATTT 58.030 30.769 0.00 0.00 0.00 1.40
61 62 8.447833 TCGATGCTTCAATTCTACGTTTATTTT 58.552 29.630 0.00 0.00 0.00 1.82
62 63 9.061610 CGATGCTTCAATTCTACGTTTATTTTT 57.938 29.630 0.00 0.00 0.00 1.94
78 79 9.285387 CGTTTATTTTTACATTTTTGTCGAAGC 57.715 29.630 0.00 0.00 0.00 3.86
79 80 9.285387 GTTTATTTTTACATTTTTGTCGAAGCG 57.715 29.630 0.00 0.00 0.00 4.68
80 81 8.563289 TTATTTTTACATTTTTGTCGAAGCGT 57.437 26.923 0.00 0.00 0.00 5.07
81 82 6.485253 TTTTTACATTTTTGTCGAAGCGTC 57.515 33.333 0.00 0.00 0.00 5.19
82 83 5.412526 TTTACATTTTTGTCGAAGCGTCT 57.587 34.783 0.00 0.00 0.00 4.18
83 84 3.963383 ACATTTTTGTCGAAGCGTCTT 57.037 38.095 0.00 0.00 0.00 3.01
84 85 3.873529 ACATTTTTGTCGAAGCGTCTTC 58.126 40.909 8.87 8.87 0.00 2.87
85 86 3.560068 ACATTTTTGTCGAAGCGTCTTCT 59.440 39.130 14.67 0.00 0.00 2.85
86 87 3.585748 TTTTTGTCGAAGCGTCTTCTG 57.414 42.857 14.67 9.87 0.00 3.02
87 88 0.859232 TTTGTCGAAGCGTCTTCTGC 59.141 50.000 14.67 9.27 0.00 4.26
88 89 0.249280 TTGTCGAAGCGTCTTCTGCA 60.249 50.000 14.67 11.06 33.85 4.41
89 90 0.038251 TGTCGAAGCGTCTTCTGCAT 60.038 50.000 14.67 0.00 33.85 3.96
90 91 0.642800 GTCGAAGCGTCTTCTGCATC 59.357 55.000 14.67 0.00 33.85 3.91
91 92 0.458543 TCGAAGCGTCTTCTGCATCC 60.459 55.000 14.67 0.00 33.85 3.51
92 93 0.459237 CGAAGCGTCTTCTGCATCCT 60.459 55.000 14.67 0.00 33.85 3.24
93 94 1.285578 GAAGCGTCTTCTGCATCCTC 58.714 55.000 10.97 0.00 33.85 3.71
94 95 0.901124 AAGCGTCTTCTGCATCCTCT 59.099 50.000 0.00 0.00 33.85 3.69
95 96 0.459489 AGCGTCTTCTGCATCCTCTC 59.541 55.000 0.00 0.00 33.85 3.20
96 97 0.174389 GCGTCTTCTGCATCCTCTCA 59.826 55.000 0.00 0.00 0.00 3.27
97 98 1.802136 GCGTCTTCTGCATCCTCTCAG 60.802 57.143 0.00 0.00 0.00 3.35
98 99 1.476085 CGTCTTCTGCATCCTCTCAGT 59.524 52.381 0.00 0.00 0.00 3.41
99 100 2.094286 CGTCTTCTGCATCCTCTCAGTT 60.094 50.000 0.00 0.00 0.00 3.16
100 101 3.260740 GTCTTCTGCATCCTCTCAGTTG 58.739 50.000 0.00 0.00 0.00 3.16
101 102 2.235650 TCTTCTGCATCCTCTCAGTTGG 59.764 50.000 0.00 0.00 0.00 3.77
102 103 0.907486 TCTGCATCCTCTCAGTTGGG 59.093 55.000 0.00 0.00 0.00 4.12
103 104 0.617413 CTGCATCCTCTCAGTTGGGT 59.383 55.000 0.00 0.00 0.00 4.51
104 105 1.833630 CTGCATCCTCTCAGTTGGGTA 59.166 52.381 0.00 0.00 0.00 3.69
105 106 1.833630 TGCATCCTCTCAGTTGGGTAG 59.166 52.381 0.00 0.00 0.00 3.18
106 107 1.474143 GCATCCTCTCAGTTGGGTAGC 60.474 57.143 0.00 0.00 0.00 3.58
107 108 1.833630 CATCCTCTCAGTTGGGTAGCA 59.166 52.381 0.00 0.00 0.00 3.49
108 109 1.267121 TCCTCTCAGTTGGGTAGCAC 58.733 55.000 0.00 0.00 0.00 4.40
109 110 0.250513 CCTCTCAGTTGGGTAGCACC 59.749 60.000 0.00 0.00 37.60 5.01
110 111 0.976641 CTCTCAGTTGGGTAGCACCA 59.023 55.000 7.49 0.00 41.02 4.17
117 118 2.279935 TTGGGTAGCACCAACGATTT 57.720 45.000 3.73 0.00 45.19 2.17
118 119 2.279935 TGGGTAGCACCAACGATTTT 57.720 45.000 7.49 0.00 41.02 1.82
119 120 1.883275 TGGGTAGCACCAACGATTTTG 59.117 47.619 7.49 0.00 41.02 2.44
120 121 1.402325 GGGTAGCACCAACGATTTTGC 60.402 52.381 7.49 0.00 41.02 3.68
121 122 1.268352 GGTAGCACCAACGATTTTGCA 59.732 47.619 0.00 0.00 38.42 4.08
122 123 2.315901 GTAGCACCAACGATTTTGCAC 58.684 47.619 0.00 0.00 37.44 4.57
123 124 0.317770 AGCACCAACGATTTTGCACG 60.318 50.000 0.00 0.00 37.44 5.34
124 125 1.274798 GCACCAACGATTTTGCACGG 61.275 55.000 0.00 0.00 34.97 4.94
125 126 0.662970 CACCAACGATTTTGCACGGG 60.663 55.000 0.00 0.00 0.00 5.28
126 127 1.732683 CCAACGATTTTGCACGGGC 60.733 57.895 0.34 0.34 41.68 6.13
127 128 1.732683 CAACGATTTTGCACGGGCC 60.733 57.895 7.46 0.00 40.13 5.80
128 129 2.926420 AACGATTTTGCACGGGCCC 61.926 57.895 13.57 13.57 40.13 5.80
129 130 4.128388 CGATTTTGCACGGGCCCC 62.128 66.667 18.66 2.06 40.13 5.80
130 131 3.770040 GATTTTGCACGGGCCCCC 61.770 66.667 18.66 5.37 40.13 5.40
145 146 2.124151 CCCCCAATCTTGCCTCGG 60.124 66.667 0.00 0.00 0.00 4.63
146 147 2.677228 CCCCAATCTTGCCTCGGT 59.323 61.111 0.00 0.00 0.00 4.69
147 148 1.452108 CCCCAATCTTGCCTCGGTC 60.452 63.158 0.00 0.00 0.00 4.79
148 149 1.815421 CCCAATCTTGCCTCGGTCG 60.815 63.158 0.00 0.00 0.00 4.79
149 150 1.815421 CCAATCTTGCCTCGGTCGG 60.815 63.158 0.00 0.00 0.00 4.79
150 151 1.815421 CAATCTTGCCTCGGTCGGG 60.815 63.158 0.00 0.00 0.00 5.14
151 152 1.987855 AATCTTGCCTCGGTCGGGA 60.988 57.895 0.00 0.00 0.00 5.14
152 153 1.961180 AATCTTGCCTCGGTCGGGAG 61.961 60.000 0.00 0.00 0.00 4.30
153 154 2.856039 ATCTTGCCTCGGTCGGGAGA 62.856 60.000 0.00 0.00 36.08 3.71
154 155 2.363795 TTGCCTCGGTCGGGAGAT 60.364 61.111 0.00 0.00 43.27 2.75
155 156 2.635229 CTTGCCTCGGTCGGGAGATG 62.635 65.000 0.00 0.00 43.27 2.90
156 157 4.593864 GCCTCGGTCGGGAGATGC 62.594 72.222 0.00 0.00 43.27 3.91
157 158 3.147595 CCTCGGTCGGGAGATGCA 61.148 66.667 0.00 0.00 43.27 3.96
158 159 2.721167 CCTCGGTCGGGAGATGCAA 61.721 63.158 0.00 0.00 43.27 4.08
159 160 1.218047 CTCGGTCGGGAGATGCAAA 59.782 57.895 0.00 0.00 43.27 3.68
160 161 0.391130 CTCGGTCGGGAGATGCAAAA 60.391 55.000 0.00 0.00 43.27 2.44
161 162 0.251916 TCGGTCGGGAGATGCAAAAT 59.748 50.000 0.00 0.00 43.27 1.82
162 163 0.657840 CGGTCGGGAGATGCAAAATC 59.342 55.000 0.00 0.00 43.27 2.17
163 164 1.750193 GGTCGGGAGATGCAAAATCA 58.250 50.000 0.00 0.00 43.27 2.57
164 165 2.091541 GGTCGGGAGATGCAAAATCAA 58.908 47.619 0.00 0.00 43.27 2.57
165 166 2.491693 GGTCGGGAGATGCAAAATCAAA 59.508 45.455 0.00 0.00 43.27 2.69
166 167 3.131046 GGTCGGGAGATGCAAAATCAAAT 59.869 43.478 0.00 0.00 43.27 2.32
167 168 4.107622 GTCGGGAGATGCAAAATCAAATG 58.892 43.478 0.00 0.00 43.27 2.32
168 169 3.763360 TCGGGAGATGCAAAATCAAATGT 59.237 39.130 0.00 0.00 0.00 2.71
169 170 4.220382 TCGGGAGATGCAAAATCAAATGTT 59.780 37.500 0.00 0.00 0.00 2.71
170 171 4.327898 CGGGAGATGCAAAATCAAATGTTG 59.672 41.667 0.00 0.00 0.00 3.33
171 172 4.093850 GGGAGATGCAAAATCAAATGTTGC 59.906 41.667 7.70 7.70 46.21 4.17
177 178 5.359716 GCAAAATCAAATGTTGCATTGGA 57.640 34.783 9.43 1.91 45.51 3.53
178 179 5.945155 GCAAAATCAAATGTTGCATTGGAT 58.055 33.333 9.43 6.04 45.51 3.41
179 180 6.383415 GCAAAATCAAATGTTGCATTGGATT 58.617 32.000 15.10 15.10 45.51 3.01
180 181 7.528307 GCAAAATCAAATGTTGCATTGGATTA 58.472 30.769 19.05 0.00 45.51 1.75
181 182 8.021973 GCAAAATCAAATGTTGCATTGGATTAA 58.978 29.630 19.05 0.00 45.51 1.40
182 183 9.894783 CAAAATCAAATGTTGCATTGGATTAAA 57.105 25.926 19.05 0.00 0.00 1.52
184 185 9.504708 AAATCAAATGTTGCATTGGATTAAAGA 57.495 25.926 19.05 1.41 0.00 2.52
185 186 9.504708 AATCAAATGTTGCATTGGATTAAAGAA 57.495 25.926 17.90 0.00 0.00 2.52
186 187 8.537049 TCAAATGTTGCATTGGATTAAAGAAG 57.463 30.769 0.00 0.00 0.00 2.85
187 188 6.973229 AATGTTGCATTGGATTAAAGAAGC 57.027 33.333 0.00 0.00 0.00 3.86
188 189 4.819769 TGTTGCATTGGATTAAAGAAGCC 58.180 39.130 0.00 0.00 41.84 4.35
189 190 4.183865 GTTGCATTGGATTAAAGAAGCCC 58.816 43.478 0.00 0.00 40.68 5.19
190 191 2.426738 TGCATTGGATTAAAGAAGCCCG 59.573 45.455 0.00 0.00 40.68 6.13
191 192 2.223805 GCATTGGATTAAAGAAGCCCGG 60.224 50.000 0.00 0.00 40.68 5.73
192 193 2.891191 TTGGATTAAAGAAGCCCGGT 57.109 45.000 0.00 0.00 40.68 5.28
193 194 2.122783 TGGATTAAAGAAGCCCGGTG 57.877 50.000 0.00 0.00 40.68 4.94
194 195 1.340600 TGGATTAAAGAAGCCCGGTGG 60.341 52.381 0.00 0.00 40.68 4.61
195 196 1.064979 GGATTAAAGAAGCCCGGTGGA 60.065 52.381 0.00 0.00 34.86 4.02
196 197 2.619590 GGATTAAAGAAGCCCGGTGGAA 60.620 50.000 0.00 0.00 34.86 3.53
197 198 2.660670 TTAAAGAAGCCCGGTGGAAA 57.339 45.000 0.00 0.00 0.00 3.13
198 199 2.194201 TAAAGAAGCCCGGTGGAAAG 57.806 50.000 0.00 0.00 0.00 2.62
199 200 0.476771 AAAGAAGCCCGGTGGAAAGA 59.523 50.000 0.00 0.00 0.00 2.52
200 201 0.698818 AAGAAGCCCGGTGGAAAGAT 59.301 50.000 0.00 0.00 0.00 2.40
201 202 0.253327 AGAAGCCCGGTGGAAAGATC 59.747 55.000 0.00 0.00 0.00 2.75
202 203 0.253327 GAAGCCCGGTGGAAAGATCT 59.747 55.000 0.00 0.00 0.00 2.75
203 204 0.698818 AAGCCCGGTGGAAAGATCTT 59.301 50.000 0.88 0.88 0.00 2.40
204 205 0.253327 AGCCCGGTGGAAAGATCTTC 59.747 55.000 8.78 2.54 0.00 2.87
205 206 0.253327 GCCCGGTGGAAAGATCTTCT 59.747 55.000 8.78 0.00 0.00 2.85
206 207 1.744114 GCCCGGTGGAAAGATCTTCTC 60.744 57.143 8.78 8.51 0.00 2.87
207 208 1.834263 CCCGGTGGAAAGATCTTCTCT 59.166 52.381 8.78 0.00 34.96 3.10
208 209 3.031736 CCCGGTGGAAAGATCTTCTCTA 58.968 50.000 8.78 4.26 32.41 2.43
209 210 3.451178 CCCGGTGGAAAGATCTTCTCTAA 59.549 47.826 8.78 0.29 32.41 2.10
210 211 4.434520 CCGGTGGAAAGATCTTCTCTAAC 58.565 47.826 8.78 8.38 32.41 2.34
211 212 4.160626 CCGGTGGAAAGATCTTCTCTAACT 59.839 45.833 8.78 0.00 32.41 2.24
212 213 5.337652 CCGGTGGAAAGATCTTCTCTAACTT 60.338 44.000 8.78 0.00 32.41 2.66
213 214 5.578727 CGGTGGAAAGATCTTCTCTAACTTG 59.421 44.000 8.78 5.82 32.41 3.16
214 215 5.352846 GGTGGAAAGATCTTCTCTAACTTGC 59.647 44.000 8.78 0.00 32.41 4.01
215 216 5.934625 GTGGAAAGATCTTCTCTAACTTGCA 59.065 40.000 8.78 0.00 32.41 4.08
216 217 6.091986 GTGGAAAGATCTTCTCTAACTTGCAG 59.908 42.308 8.78 0.00 32.41 4.41
217 218 6.014242 TGGAAAGATCTTCTCTAACTTGCAGA 60.014 38.462 8.78 0.00 32.41 4.26
218 219 7.047271 GGAAAGATCTTCTCTAACTTGCAGAT 58.953 38.462 8.78 0.00 32.41 2.90
219 220 7.224557 GGAAAGATCTTCTCTAACTTGCAGATC 59.775 40.741 8.78 0.00 37.84 2.75
220 221 6.788598 AGATCTTCTCTAACTTGCAGATCA 57.211 37.500 9.12 0.00 39.34 2.92
221 222 7.180322 AGATCTTCTCTAACTTGCAGATCAA 57.820 36.000 9.12 0.00 39.34 2.57
222 223 7.041107 AGATCTTCTCTAACTTGCAGATCAAC 58.959 38.462 9.12 0.00 39.34 3.18
223 224 6.352016 TCTTCTCTAACTTGCAGATCAACT 57.648 37.500 0.00 0.00 0.00 3.16
224 225 6.393990 TCTTCTCTAACTTGCAGATCAACTC 58.606 40.000 0.00 0.00 0.00 3.01
225 226 5.078411 TCTCTAACTTGCAGATCAACTCC 57.922 43.478 0.00 0.00 0.00 3.85
226 227 3.849911 TCTAACTTGCAGATCAACTCCG 58.150 45.455 0.00 0.00 0.00 4.63
227 228 1.813513 AACTTGCAGATCAACTCCGG 58.186 50.000 0.00 0.00 0.00 5.14
228 229 0.687354 ACTTGCAGATCAACTCCGGT 59.313 50.000 0.00 0.00 0.00 5.28
229 230 1.081892 CTTGCAGATCAACTCCGGTG 58.918 55.000 0.00 0.00 0.00 4.94
230 231 0.955428 TTGCAGATCAACTCCGGTGC 60.955 55.000 0.00 1.15 0.00 5.01
231 232 2.109126 GCAGATCAACTCCGGTGCC 61.109 63.158 0.00 0.00 0.00 5.01
232 233 1.296392 CAGATCAACTCCGGTGCCA 59.704 57.895 0.00 0.00 0.00 4.92
233 234 0.321564 CAGATCAACTCCGGTGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
234 235 0.321653 AGATCAACTCCGGTGCCAAC 60.322 55.000 0.00 0.00 0.00 3.77
235 236 0.321653 GATCAACTCCGGTGCCAACT 60.322 55.000 0.00 0.00 0.00 3.16
236 237 0.321653 ATCAACTCCGGTGCCAACTC 60.322 55.000 0.00 0.00 0.00 3.01
237 238 1.071471 CAACTCCGGTGCCAACTCT 59.929 57.895 0.00 0.00 0.00 3.24
238 239 0.535102 CAACTCCGGTGCCAACTCTT 60.535 55.000 0.00 0.00 0.00 2.85
239 240 0.250338 AACTCCGGTGCCAACTCTTC 60.250 55.000 0.00 0.00 0.00 2.87
240 241 1.376037 CTCCGGTGCCAACTCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
241 242 2.111999 CTCCGGTGCCAACTCTTCCA 62.112 60.000 0.00 0.00 0.00 3.53
242 243 1.002134 CCGGTGCCAACTCTTCCAT 60.002 57.895 0.00 0.00 0.00 3.41
243 244 0.609131 CCGGTGCCAACTCTTCCATT 60.609 55.000 0.00 0.00 0.00 3.16
244 245 1.247567 CGGTGCCAACTCTTCCATTT 58.752 50.000 0.00 0.00 0.00 2.32
245 246 1.200020 CGGTGCCAACTCTTCCATTTC 59.800 52.381 0.00 0.00 0.00 2.17
246 247 2.519013 GGTGCCAACTCTTCCATTTCT 58.481 47.619 0.00 0.00 0.00 2.52
247 248 2.893489 GGTGCCAACTCTTCCATTTCTT 59.107 45.455 0.00 0.00 0.00 2.52
248 249 3.057245 GGTGCCAACTCTTCCATTTCTTC 60.057 47.826 0.00 0.00 0.00 2.87
249 250 3.823304 GTGCCAACTCTTCCATTTCTTCT 59.177 43.478 0.00 0.00 0.00 2.85
250 251 5.003804 GTGCCAACTCTTCCATTTCTTCTA 58.996 41.667 0.00 0.00 0.00 2.10
251 252 5.123027 GTGCCAACTCTTCCATTTCTTCTAG 59.877 44.000 0.00 0.00 0.00 2.43
252 253 4.095632 GCCAACTCTTCCATTTCTTCTAGC 59.904 45.833 0.00 0.00 0.00 3.42
253 254 5.248640 CCAACTCTTCCATTTCTTCTAGCA 58.751 41.667 0.00 0.00 0.00 3.49
254 255 5.123027 CCAACTCTTCCATTTCTTCTAGCAC 59.877 44.000 0.00 0.00 0.00 4.40
255 256 4.499183 ACTCTTCCATTTCTTCTAGCACG 58.501 43.478 0.00 0.00 0.00 5.34
256 257 3.262420 TCTTCCATTTCTTCTAGCACGC 58.738 45.455 0.00 0.00 0.00 5.34
257 258 2.024176 TCCATTTCTTCTAGCACGCC 57.976 50.000 0.00 0.00 0.00 5.68
258 259 1.277842 TCCATTTCTTCTAGCACGCCA 59.722 47.619 0.00 0.00 0.00 5.69
259 260 1.667724 CCATTTCTTCTAGCACGCCAG 59.332 52.381 0.00 0.00 0.00 4.85
260 261 1.667724 CATTTCTTCTAGCACGCCAGG 59.332 52.381 0.00 0.00 0.00 4.45
261 262 0.673644 TTTCTTCTAGCACGCCAGGC 60.674 55.000 0.00 0.00 0.00 4.85
274 275 0.931005 GCCAGGCGATAGTTCTTTCG 59.069 55.000 0.00 7.96 38.37 3.46
282 283 4.903638 CGATAGTTCTTTCGCACAAAGA 57.096 40.909 4.12 4.12 34.73 2.52
283 284 5.264060 CGATAGTTCTTTCGCACAAAGAA 57.736 39.130 13.94 13.94 42.15 2.52
287 288 2.730183 TCTTTCGCACAAAGAACACG 57.270 45.000 5.54 0.00 33.72 4.49
288 289 1.329292 TCTTTCGCACAAAGAACACGG 59.671 47.619 5.54 0.00 33.72 4.94
289 290 1.329292 CTTTCGCACAAAGAACACGGA 59.671 47.619 0.00 0.00 0.00 4.69
290 291 1.370609 TTCGCACAAAGAACACGGAA 58.629 45.000 0.00 0.00 0.00 4.30
291 292 0.934496 TCGCACAAAGAACACGGAAG 59.066 50.000 0.00 0.00 0.00 3.46
292 293 0.934496 CGCACAAAGAACACGGAAGA 59.066 50.000 0.00 0.00 0.00 2.87
293 294 1.329292 CGCACAAAGAACACGGAAGAA 59.671 47.619 0.00 0.00 0.00 2.52
294 295 2.223157 CGCACAAAGAACACGGAAGAAA 60.223 45.455 0.00 0.00 0.00 2.52
295 296 3.548014 CGCACAAAGAACACGGAAGAAAT 60.548 43.478 0.00 0.00 0.00 2.17
296 297 4.319190 CGCACAAAGAACACGGAAGAAATA 60.319 41.667 0.00 0.00 0.00 1.40
297 298 5.147162 GCACAAAGAACACGGAAGAAATAG 58.853 41.667 0.00 0.00 0.00 1.73
298 299 5.147162 CACAAAGAACACGGAAGAAATAGC 58.853 41.667 0.00 0.00 0.00 2.97
1135 1145 9.177608 TGAAATCTTCTAGGATGTTAATTGGTG 57.822 33.333 0.00 0.00 0.00 4.17
1470 1480 1.677633 GGTCGGGATGGTTTGTGGG 60.678 63.158 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032681 ACTGAGGAGGCGGCAAAC 59.967 61.111 13.08 0.00 0.00 2.93
1 2 1.841302 ATCACTGAGGAGGCGGCAAA 61.841 55.000 13.08 0.00 0.00 3.68
2 3 2.293318 ATCACTGAGGAGGCGGCAA 61.293 57.895 13.08 0.00 0.00 4.52
3 4 2.685017 ATCACTGAGGAGGCGGCA 60.685 61.111 13.08 0.00 0.00 5.69
4 5 2.202987 CATCACTGAGGAGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
5 6 0.467384 ATTCATCACTGAGGAGGCGG 59.533 55.000 0.00 0.00 31.68 6.13
6 7 1.579698 CATTCATCACTGAGGAGGCG 58.420 55.000 0.00 0.00 31.68 5.52
7 8 1.307097 GCATTCATCACTGAGGAGGC 58.693 55.000 4.38 4.38 31.68 4.70
8 9 1.489649 AGGCATTCATCACTGAGGAGG 59.510 52.381 0.00 0.00 31.68 4.30
9 10 2.169978 TGAGGCATTCATCACTGAGGAG 59.830 50.000 0.00 0.00 31.68 3.69
10 11 2.169978 CTGAGGCATTCATCACTGAGGA 59.830 50.000 0.00 0.00 34.68 3.71
11 12 2.562635 CTGAGGCATTCATCACTGAGG 58.437 52.381 0.00 0.00 34.68 3.86
12 13 1.941294 GCTGAGGCATTCATCACTGAG 59.059 52.381 0.00 0.00 38.54 3.35
13 14 1.407851 GGCTGAGGCATTCATCACTGA 60.408 52.381 0.00 0.00 40.87 3.41
14 15 1.022735 GGCTGAGGCATTCATCACTG 58.977 55.000 0.00 0.00 40.87 3.66
15 16 0.622136 TGGCTGAGGCATTCATCACT 59.378 50.000 3.93 0.00 40.87 3.41
16 17 1.688772 ATGGCTGAGGCATTCATCAC 58.311 50.000 16.42 0.00 46.61 3.06
24 25 2.203112 GCATCGATGGCTGAGGCA 60.203 61.111 26.00 12.23 42.34 4.75
25 26 1.505477 GAAGCATCGATGGCTGAGGC 61.505 60.000 26.00 10.36 41.66 4.70
26 27 0.179065 TGAAGCATCGATGGCTGAGG 60.179 55.000 26.00 0.00 41.66 3.86
27 28 1.660167 TTGAAGCATCGATGGCTGAG 58.340 50.000 26.00 0.38 41.66 3.35
28 29 2.336945 ATTGAAGCATCGATGGCTGA 57.663 45.000 26.00 13.11 41.66 4.26
29 30 2.617308 AGAATTGAAGCATCGATGGCTG 59.383 45.455 26.00 3.22 41.66 4.85
30 31 2.928334 AGAATTGAAGCATCGATGGCT 58.072 42.857 26.00 19.51 45.15 4.75
31 32 3.363378 CGTAGAATTGAAGCATCGATGGC 60.363 47.826 26.00 17.68 29.70 4.40
32 33 3.804325 ACGTAGAATTGAAGCATCGATGG 59.196 43.478 26.00 8.82 29.70 3.51
33 34 5.395325 AACGTAGAATTGAAGCATCGATG 57.605 39.130 21.27 21.27 29.70 3.84
34 35 7.715265 ATAAACGTAGAATTGAAGCATCGAT 57.285 32.000 0.00 0.00 0.00 3.59
35 36 7.534085 AATAAACGTAGAATTGAAGCATCGA 57.466 32.000 0.00 0.00 0.00 3.59
36 37 8.601243 AAAATAAACGTAGAATTGAAGCATCG 57.399 30.769 0.00 0.00 0.00 3.84
52 53 9.285387 GCTTCGACAAAAATGTAAAAATAAACG 57.715 29.630 0.00 0.00 0.00 3.60
53 54 9.285387 CGCTTCGACAAAAATGTAAAAATAAAC 57.715 29.630 0.00 0.00 0.00 2.01
54 55 9.021863 ACGCTTCGACAAAAATGTAAAAATAAA 57.978 25.926 0.00 0.00 0.00 1.40
55 56 8.563289 ACGCTTCGACAAAAATGTAAAAATAA 57.437 26.923 0.00 0.00 0.00 1.40
56 57 8.071368 AGACGCTTCGACAAAAATGTAAAAATA 58.929 29.630 0.00 0.00 0.00 1.40
57 58 6.915843 AGACGCTTCGACAAAAATGTAAAAAT 59.084 30.769 0.00 0.00 0.00 1.82
58 59 6.259638 AGACGCTTCGACAAAAATGTAAAAA 58.740 32.000 0.00 0.00 0.00 1.94
59 60 5.812652 AGACGCTTCGACAAAAATGTAAAA 58.187 33.333 0.00 0.00 0.00 1.52
60 61 5.412526 AGACGCTTCGACAAAAATGTAAA 57.587 34.783 0.00 0.00 0.00 2.01
61 62 5.235616 AGAAGACGCTTCGACAAAAATGTAA 59.764 36.000 12.00 0.00 0.00 2.41
62 63 4.748102 AGAAGACGCTTCGACAAAAATGTA 59.252 37.500 12.00 0.00 0.00 2.29
63 64 3.560068 AGAAGACGCTTCGACAAAAATGT 59.440 39.130 12.00 0.00 0.00 2.71
64 65 3.902465 CAGAAGACGCTTCGACAAAAATG 59.098 43.478 12.00 2.16 0.00 2.32
65 66 3.607078 GCAGAAGACGCTTCGACAAAAAT 60.607 43.478 12.00 0.00 0.00 1.82
66 67 2.286184 GCAGAAGACGCTTCGACAAAAA 60.286 45.455 12.00 0.00 0.00 1.94
67 68 1.260561 GCAGAAGACGCTTCGACAAAA 59.739 47.619 12.00 0.00 0.00 2.44
68 69 0.859232 GCAGAAGACGCTTCGACAAA 59.141 50.000 12.00 0.00 0.00 2.83
69 70 0.249280 TGCAGAAGACGCTTCGACAA 60.249 50.000 12.00 0.90 0.00 3.18
70 71 0.038251 ATGCAGAAGACGCTTCGACA 60.038 50.000 12.00 13.43 0.00 4.35
71 72 0.642800 GATGCAGAAGACGCTTCGAC 59.357 55.000 12.00 9.54 0.00 4.20
72 73 0.458543 GGATGCAGAAGACGCTTCGA 60.459 55.000 12.00 0.00 35.10 3.71
73 74 0.459237 AGGATGCAGAAGACGCTTCG 60.459 55.000 12.00 9.20 35.10 3.79
74 75 1.134848 AGAGGATGCAGAAGACGCTTC 60.135 52.381 10.44 10.44 33.89 3.86
75 76 0.901124 AGAGGATGCAGAAGACGCTT 59.099 50.000 0.00 0.00 0.00 4.68
76 77 0.459489 GAGAGGATGCAGAAGACGCT 59.541 55.000 0.00 0.00 0.00 5.07
77 78 0.174389 TGAGAGGATGCAGAAGACGC 59.826 55.000 0.00 0.00 0.00 5.19
78 79 1.476085 ACTGAGAGGATGCAGAAGACG 59.524 52.381 0.00 0.00 36.07 4.18
79 80 3.260740 CAACTGAGAGGATGCAGAAGAC 58.739 50.000 0.00 0.00 36.07 3.01
80 81 2.235650 CCAACTGAGAGGATGCAGAAGA 59.764 50.000 0.00 0.00 36.07 2.87
81 82 2.630158 CCAACTGAGAGGATGCAGAAG 58.370 52.381 0.00 0.00 36.07 2.85
82 83 1.280133 CCCAACTGAGAGGATGCAGAA 59.720 52.381 0.00 0.00 36.07 3.02
83 84 0.907486 CCCAACTGAGAGGATGCAGA 59.093 55.000 0.00 0.00 36.07 4.26
84 85 0.617413 ACCCAACTGAGAGGATGCAG 59.383 55.000 0.00 0.00 38.10 4.41
85 86 1.833630 CTACCCAACTGAGAGGATGCA 59.166 52.381 0.00 0.00 0.00 3.96
86 87 1.474143 GCTACCCAACTGAGAGGATGC 60.474 57.143 0.00 0.00 0.00 3.91
87 88 1.833630 TGCTACCCAACTGAGAGGATG 59.166 52.381 0.00 0.00 0.00 3.51
88 89 1.834263 GTGCTACCCAACTGAGAGGAT 59.166 52.381 0.00 0.00 0.00 3.24
89 90 1.267121 GTGCTACCCAACTGAGAGGA 58.733 55.000 0.00 0.00 0.00 3.71
90 91 0.250513 GGTGCTACCCAACTGAGAGG 59.749 60.000 0.00 0.00 30.04 3.69
91 92 0.976641 TGGTGCTACCCAACTGAGAG 59.023 55.000 3.33 0.00 37.50 3.20
92 93 1.429930 TTGGTGCTACCCAACTGAGA 58.570 50.000 3.33 0.00 39.56 3.27
98 99 2.279935 AAATCGTTGGTGCTACCCAA 57.720 45.000 3.33 1.58 42.16 4.12
99 100 1.883275 CAAAATCGTTGGTGCTACCCA 59.117 47.619 3.33 0.00 37.50 4.51
100 101 1.402325 GCAAAATCGTTGGTGCTACCC 60.402 52.381 3.33 0.00 37.50 3.69
101 102 1.268352 TGCAAAATCGTTGGTGCTACC 59.732 47.619 0.00 0.00 37.87 3.18
102 103 2.315901 GTGCAAAATCGTTGGTGCTAC 58.684 47.619 0.00 0.00 37.87 3.58
103 104 1.069568 CGTGCAAAATCGTTGGTGCTA 60.070 47.619 0.00 0.00 37.87 3.49
104 105 0.317770 CGTGCAAAATCGTTGGTGCT 60.318 50.000 0.00 0.00 37.87 4.40
105 106 1.274798 CCGTGCAAAATCGTTGGTGC 61.275 55.000 0.00 0.00 37.51 5.01
106 107 0.662970 CCCGTGCAAAATCGTTGGTG 60.663 55.000 0.00 0.00 0.00 4.17
107 108 1.657556 CCCGTGCAAAATCGTTGGT 59.342 52.632 0.00 0.00 0.00 3.67
108 109 1.732683 GCCCGTGCAAAATCGTTGG 60.733 57.895 0.00 0.00 37.47 3.77
109 110 1.732683 GGCCCGTGCAAAATCGTTG 60.733 57.895 0.00 0.00 40.13 4.10
110 111 2.648454 GGCCCGTGCAAAATCGTT 59.352 55.556 0.00 0.00 40.13 3.85
111 112 3.370231 GGGCCCGTGCAAAATCGT 61.370 61.111 5.69 0.00 40.13 3.73
112 113 4.128388 GGGGCCCGTGCAAAATCG 62.128 66.667 17.79 0.00 40.13 3.34
113 114 3.770040 GGGGGCCCGTGCAAAATC 61.770 66.667 17.79 0.00 40.13 2.17
128 129 2.124151 CCGAGGCAAGATTGGGGG 60.124 66.667 0.00 0.00 0.00 5.40
129 130 1.452108 GACCGAGGCAAGATTGGGG 60.452 63.158 0.00 0.00 0.00 4.96
130 131 1.815421 CGACCGAGGCAAGATTGGG 60.815 63.158 0.00 0.00 0.00 4.12
131 132 1.815421 CCGACCGAGGCAAGATTGG 60.815 63.158 0.00 0.00 0.00 3.16
132 133 1.815421 CCCGACCGAGGCAAGATTG 60.815 63.158 0.00 0.00 0.00 2.67
133 134 1.961180 CTCCCGACCGAGGCAAGATT 61.961 60.000 0.00 0.00 0.00 2.40
134 135 2.363795 TCCCGACCGAGGCAAGAT 60.364 61.111 0.00 0.00 0.00 2.40
135 136 2.856039 ATCTCCCGACCGAGGCAAGA 62.856 60.000 0.00 0.00 0.00 3.02
136 137 2.427245 ATCTCCCGACCGAGGCAAG 61.427 63.158 0.00 0.00 0.00 4.01
137 138 2.363795 ATCTCCCGACCGAGGCAA 60.364 61.111 0.00 0.00 0.00 4.52
138 139 3.147595 CATCTCCCGACCGAGGCA 61.148 66.667 0.00 0.00 0.00 4.75
139 140 4.593864 GCATCTCCCGACCGAGGC 62.594 72.222 0.00 0.00 0.00 4.70
140 141 2.238847 TTTGCATCTCCCGACCGAGG 62.239 60.000 0.00 0.00 0.00 4.63
141 142 0.391130 TTTTGCATCTCCCGACCGAG 60.391 55.000 0.00 0.00 0.00 4.63
142 143 0.251916 ATTTTGCATCTCCCGACCGA 59.748 50.000 0.00 0.00 0.00 4.69
143 144 0.657840 GATTTTGCATCTCCCGACCG 59.342 55.000 0.00 0.00 0.00 4.79
144 145 1.750193 TGATTTTGCATCTCCCGACC 58.250 50.000 0.00 0.00 0.00 4.79
145 146 3.848272 TTTGATTTTGCATCTCCCGAC 57.152 42.857 0.00 0.00 0.00 4.79
146 147 3.763360 ACATTTGATTTTGCATCTCCCGA 59.237 39.130 0.00 0.00 0.00 5.14
147 148 4.114058 ACATTTGATTTTGCATCTCCCG 57.886 40.909 0.00 0.00 0.00 5.14
148 149 4.093850 GCAACATTTGATTTTGCATCTCCC 59.906 41.667 6.86 0.00 44.17 4.30
149 150 5.212589 GCAACATTTGATTTTGCATCTCC 57.787 39.130 6.86 0.00 44.17 3.71
155 156 5.359716 TCCAATGCAACATTTGATTTTGC 57.640 34.783 0.00 5.16 44.84 3.68
156 157 9.894783 TTTAATCCAATGCAACATTTGATTTTG 57.105 25.926 18.85 3.47 0.00 2.44
158 159 9.504708 TCTTTAATCCAATGCAACATTTGATTT 57.495 25.926 18.85 8.49 0.00 2.17
159 160 9.504708 TTCTTTAATCCAATGCAACATTTGATT 57.495 25.926 18.12 18.12 0.00 2.57
160 161 9.158233 CTTCTTTAATCCAATGCAACATTTGAT 57.842 29.630 0.00 2.07 0.00 2.57
161 162 7.118101 GCTTCTTTAATCCAATGCAACATTTGA 59.882 33.333 0.00 0.00 0.00 2.69
162 163 7.238571 GCTTCTTTAATCCAATGCAACATTTG 58.761 34.615 0.00 0.00 0.00 2.32
163 164 6.372381 GGCTTCTTTAATCCAATGCAACATTT 59.628 34.615 0.00 0.00 0.00 2.32
164 165 5.876460 GGCTTCTTTAATCCAATGCAACATT 59.124 36.000 0.00 0.00 0.00 2.71
165 166 5.422145 GGCTTCTTTAATCCAATGCAACAT 58.578 37.500 0.00 0.00 0.00 2.71
166 167 4.322650 GGGCTTCTTTAATCCAATGCAACA 60.323 41.667 0.00 0.00 0.00 3.33
167 168 4.183865 GGGCTTCTTTAATCCAATGCAAC 58.816 43.478 0.00 0.00 0.00 4.17
168 169 3.119173 CGGGCTTCTTTAATCCAATGCAA 60.119 43.478 0.00 0.00 0.00 4.08
169 170 2.426738 CGGGCTTCTTTAATCCAATGCA 59.573 45.455 0.00 0.00 0.00 3.96
170 171 2.223805 CCGGGCTTCTTTAATCCAATGC 60.224 50.000 0.00 0.00 0.00 3.56
171 172 3.023832 ACCGGGCTTCTTTAATCCAATG 58.976 45.455 6.32 0.00 0.00 2.82
172 173 3.023832 CACCGGGCTTCTTTAATCCAAT 58.976 45.455 6.32 0.00 0.00 3.16
173 174 2.442413 CACCGGGCTTCTTTAATCCAA 58.558 47.619 6.32 0.00 0.00 3.53
174 175 1.340600 CCACCGGGCTTCTTTAATCCA 60.341 52.381 6.32 0.00 0.00 3.41
175 176 1.064979 TCCACCGGGCTTCTTTAATCC 60.065 52.381 6.32 0.00 0.00 3.01
176 177 2.413310 TCCACCGGGCTTCTTTAATC 57.587 50.000 6.32 0.00 0.00 1.75
177 178 2.891191 TTCCACCGGGCTTCTTTAAT 57.109 45.000 6.32 0.00 0.00 1.40
178 179 2.106857 TCTTTCCACCGGGCTTCTTTAA 59.893 45.455 6.32 0.00 0.00 1.52
179 180 1.700739 TCTTTCCACCGGGCTTCTTTA 59.299 47.619 6.32 0.00 0.00 1.85
180 181 0.476771 TCTTTCCACCGGGCTTCTTT 59.523 50.000 6.32 0.00 0.00 2.52
181 182 0.698818 ATCTTTCCACCGGGCTTCTT 59.301 50.000 6.32 0.00 0.00 2.52
182 183 0.253327 GATCTTTCCACCGGGCTTCT 59.747 55.000 6.32 0.00 0.00 2.85
183 184 0.253327 AGATCTTTCCACCGGGCTTC 59.747 55.000 6.32 0.00 0.00 3.86
184 185 0.698818 AAGATCTTTCCACCGGGCTT 59.301 50.000 6.32 0.00 0.00 4.35
185 186 0.253327 GAAGATCTTTCCACCGGGCT 59.747 55.000 9.87 0.00 0.00 5.19
186 187 0.253327 AGAAGATCTTTCCACCGGGC 59.747 55.000 9.87 0.00 0.00 6.13
187 188 1.834263 AGAGAAGATCTTTCCACCGGG 59.166 52.381 9.87 0.00 32.99 5.73
188 189 4.160626 AGTTAGAGAAGATCTTTCCACCGG 59.839 45.833 9.87 0.00 39.64 5.28
189 190 5.331876 AGTTAGAGAAGATCTTTCCACCG 57.668 43.478 9.87 0.00 39.64 4.94
190 191 5.352846 GCAAGTTAGAGAAGATCTTTCCACC 59.647 44.000 9.87 0.00 39.64 4.61
191 192 5.934625 TGCAAGTTAGAGAAGATCTTTCCAC 59.065 40.000 9.87 8.76 39.64 4.02
192 193 6.014242 TCTGCAAGTTAGAGAAGATCTTTCCA 60.014 38.462 9.87 0.00 35.66 3.53
193 194 6.402222 TCTGCAAGTTAGAGAAGATCTTTCC 58.598 40.000 9.87 4.75 35.66 3.13
194 195 7.763528 TGATCTGCAAGTTAGAGAAGATCTTTC 59.236 37.037 9.87 9.12 40.33 2.62
195 196 7.619050 TGATCTGCAAGTTAGAGAAGATCTTT 58.381 34.615 9.87 0.00 40.33 2.52
196 197 7.180322 TGATCTGCAAGTTAGAGAAGATCTT 57.820 36.000 7.95 7.95 40.33 2.40
197 198 6.788598 TGATCTGCAAGTTAGAGAAGATCT 57.211 37.500 10.75 0.00 40.33 2.75
198 199 7.041107 AGTTGATCTGCAAGTTAGAGAAGATC 58.959 38.462 0.00 0.00 36.79 2.75
199 200 6.945218 AGTTGATCTGCAAGTTAGAGAAGAT 58.055 36.000 0.00 0.00 36.79 2.40
200 201 6.352016 AGTTGATCTGCAAGTTAGAGAAGA 57.648 37.500 0.00 0.00 36.79 2.87
201 202 5.580297 GGAGTTGATCTGCAAGTTAGAGAAG 59.420 44.000 0.00 0.00 40.20 2.85
202 203 5.482908 GGAGTTGATCTGCAAGTTAGAGAA 58.517 41.667 0.00 0.00 40.20 2.87
203 204 4.380973 CGGAGTTGATCTGCAAGTTAGAGA 60.381 45.833 0.00 0.00 40.20 3.10
204 205 3.862267 CGGAGTTGATCTGCAAGTTAGAG 59.138 47.826 0.00 0.00 40.20 2.43
205 206 3.368427 CCGGAGTTGATCTGCAAGTTAGA 60.368 47.826 0.00 0.00 40.20 2.10
206 207 2.932614 CCGGAGTTGATCTGCAAGTTAG 59.067 50.000 0.00 0.00 40.20 2.34
207 208 2.301870 ACCGGAGTTGATCTGCAAGTTA 59.698 45.455 9.46 0.00 40.20 2.24
208 209 1.072331 ACCGGAGTTGATCTGCAAGTT 59.928 47.619 9.46 0.00 40.20 2.66
209 210 0.687354 ACCGGAGTTGATCTGCAAGT 59.313 50.000 9.46 0.00 42.75 3.16
210 211 1.081892 CACCGGAGTTGATCTGCAAG 58.918 55.000 9.46 0.00 37.12 4.01
211 212 0.955428 GCACCGGAGTTGATCTGCAA 60.955 55.000 9.46 0.00 34.03 4.08
212 213 1.375908 GCACCGGAGTTGATCTGCA 60.376 57.895 9.46 0.00 34.03 4.41
213 214 2.109126 GGCACCGGAGTTGATCTGC 61.109 63.158 9.46 4.28 32.37 4.26
214 215 0.321564 TTGGCACCGGAGTTGATCTG 60.322 55.000 9.46 0.00 0.00 2.90
215 216 0.321653 GTTGGCACCGGAGTTGATCT 60.322 55.000 9.46 0.00 0.00 2.75
216 217 0.321653 AGTTGGCACCGGAGTTGATC 60.322 55.000 9.46 0.00 0.00 2.92
217 218 0.321653 GAGTTGGCACCGGAGTTGAT 60.322 55.000 9.46 0.00 0.00 2.57
218 219 1.070786 GAGTTGGCACCGGAGTTGA 59.929 57.895 9.46 0.00 0.00 3.18
219 220 0.535102 AAGAGTTGGCACCGGAGTTG 60.535 55.000 9.46 0.00 0.00 3.16
220 221 0.250338 GAAGAGTTGGCACCGGAGTT 60.250 55.000 9.46 0.00 0.00 3.01
221 222 1.371558 GAAGAGTTGGCACCGGAGT 59.628 57.895 9.46 0.00 0.00 3.85
222 223 1.376037 GGAAGAGTTGGCACCGGAG 60.376 63.158 9.46 0.00 0.00 4.63
223 224 1.488705 ATGGAAGAGTTGGCACCGGA 61.489 55.000 9.46 0.00 0.00 5.14
224 225 0.609131 AATGGAAGAGTTGGCACCGG 60.609 55.000 0.00 0.00 0.00 5.28
225 226 1.200020 GAAATGGAAGAGTTGGCACCG 59.800 52.381 0.00 0.00 0.00 4.94
226 227 2.519013 AGAAATGGAAGAGTTGGCACC 58.481 47.619 0.00 0.00 0.00 5.01
227 228 3.823304 AGAAGAAATGGAAGAGTTGGCAC 59.177 43.478 0.00 0.00 0.00 5.01
228 229 4.104383 AGAAGAAATGGAAGAGTTGGCA 57.896 40.909 0.00 0.00 0.00 4.92
229 230 4.095632 GCTAGAAGAAATGGAAGAGTTGGC 59.904 45.833 0.00 0.00 0.00 4.52
230 231 5.123027 GTGCTAGAAGAAATGGAAGAGTTGG 59.877 44.000 0.00 0.00 0.00 3.77
231 232 5.163913 CGTGCTAGAAGAAATGGAAGAGTTG 60.164 44.000 0.00 0.00 0.00 3.16
232 233 4.932200 CGTGCTAGAAGAAATGGAAGAGTT 59.068 41.667 0.00 0.00 0.00 3.01
233 234 4.499183 CGTGCTAGAAGAAATGGAAGAGT 58.501 43.478 0.00 0.00 0.00 3.24
234 235 3.308323 GCGTGCTAGAAGAAATGGAAGAG 59.692 47.826 0.00 0.00 0.00 2.85
235 236 3.262420 GCGTGCTAGAAGAAATGGAAGA 58.738 45.455 0.00 0.00 0.00 2.87
236 237 2.352960 GGCGTGCTAGAAGAAATGGAAG 59.647 50.000 0.00 0.00 0.00 3.46
237 238 2.290008 TGGCGTGCTAGAAGAAATGGAA 60.290 45.455 0.00 0.00 0.00 3.53
238 239 1.277842 TGGCGTGCTAGAAGAAATGGA 59.722 47.619 0.00 0.00 0.00 3.41
239 240 1.667724 CTGGCGTGCTAGAAGAAATGG 59.332 52.381 0.00 0.00 0.00 3.16
240 241 1.667724 CCTGGCGTGCTAGAAGAAATG 59.332 52.381 6.80 0.00 0.00 2.32
241 242 2.014068 GCCTGGCGTGCTAGAAGAAAT 61.014 52.381 1.35 0.00 0.00 2.17
242 243 0.673644 GCCTGGCGTGCTAGAAGAAA 60.674 55.000 1.35 0.00 0.00 2.52
243 244 1.079127 GCCTGGCGTGCTAGAAGAA 60.079 57.895 1.35 0.00 0.00 2.52
244 245 2.579201 GCCTGGCGTGCTAGAAGA 59.421 61.111 1.35 0.00 0.00 2.87
255 256 0.931005 CGAAAGAACTATCGCCTGGC 59.069 55.000 9.11 9.11 31.71 4.85
261 262 4.903638 TCTTTGTGCGAAAGAACTATCG 57.096 40.909 7.98 0.00 41.55 2.92
267 268 2.223157 CCGTGTTCTTTGTGCGAAAGAA 60.223 45.455 15.83 15.83 42.15 2.52
268 269 1.329292 CCGTGTTCTTTGTGCGAAAGA 59.671 47.619 6.63 6.63 34.73 2.52
269 270 1.329292 TCCGTGTTCTTTGTGCGAAAG 59.671 47.619 2.32 2.32 0.00 2.62
270 271 1.370609 TCCGTGTTCTTTGTGCGAAA 58.629 45.000 0.00 0.00 0.00 3.46
271 272 1.329292 CTTCCGTGTTCTTTGTGCGAA 59.671 47.619 0.00 0.00 0.00 4.70
272 273 0.934496 CTTCCGTGTTCTTTGTGCGA 59.066 50.000 0.00 0.00 0.00 5.10
273 274 0.934496 TCTTCCGTGTTCTTTGTGCG 59.066 50.000 0.00 0.00 0.00 5.34
274 275 3.414549 TTTCTTCCGTGTTCTTTGTGC 57.585 42.857 0.00 0.00 0.00 4.57
275 276 5.147162 GCTATTTCTTCCGTGTTCTTTGTG 58.853 41.667 0.00 0.00 0.00 3.33
276 277 5.358298 GCTATTTCTTCCGTGTTCTTTGT 57.642 39.130 0.00 0.00 0.00 2.83
1238 1248 8.186163 CGCCCACGAATGATATAAATACTACTA 58.814 37.037 0.00 0.00 43.93 1.82
1470 1480 3.123621 CAGTTGTCATAGCTGTTCGGAAC 59.876 47.826 13.86 13.86 33.41 3.62
1865 1877 8.609176 TGCGTAAATTTATGGAATCACTTACTC 58.391 33.333 17.14 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.