Multiple sequence alignment - TraesCS1A01G342500

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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 TraesCS1A01G342500 chr1A 100.000 6091 0 0 1 6091 531602663 531608753 0.000000e+00 11249.0
1 TraesCS1A01G342500 chr1A 97.605 167 4 0 1 167 6645652 6645486 2.780000e-73 287.0
2 TraesCS1A01G342500 chr1A 90.769 65 6 0 2821 2885 531605396 531605460 3.020000e-13 87.9
3 TraesCS1A01G342500 chr1A 90.769 65 6 0 2734 2798 531605483 531605547 3.020000e-13 87.9
4 TraesCS1A01G342500 chr1D 93.295 3803 144 53 163 3903 433208027 433211780 0.000000e+00 5507.0
5 TraesCS1A01G342500 chr1D 95.205 1710 54 13 4389 6091 433212298 433213986 0.000000e+00 2678.0
6 TraesCS1A01G342500 chr1D 96.188 341 9 3 3900 4239 433211818 433212155 6.900000e-154 555.0
7 TraesCS1A01G342500 chr1D 92.593 135 2 2 4275 4409 433212158 433212284 2.900000e-43 187.0
8 TraesCS1A01G342500 chr1D 93.846 65 4 0 2821 2885 433210610 433210674 1.400000e-16 99.0
9 TraesCS1A01G342500 chr1D 90.769 65 6 0 2734 2798 433210697 433210761 3.020000e-13 87.9
10 TraesCS1A01G342500 chr1B 95.079 3272 100 22 2856 6091 585070783 585074029 0.000000e+00 5094.0
11 TraesCS1A01G342500 chr1B 93.219 1755 97 8 971 2719 585068990 585070728 0.000000e+00 2562.0
12 TraesCS1A01G342500 chr1B 86.435 634 47 24 271 868 585068046 585068676 0.000000e+00 658.0
13 TraesCS1A01G342500 chrUn 98.193 166 2 1 1 166 3260429 3260593 7.720000e-74 289.0
14 TraesCS1A01G342500 chr7A 98.193 166 2 1 1 166 329162788 329162624 7.720000e-74 289.0
15 TraesCS1A01G342500 chr5A 96.386 166 6 0 1 166 619412395 619412230 2.160000e-69 274.0
16 TraesCS1A01G342500 chr5A 95.783 166 5 1 1 166 431668269 431668106 3.620000e-67 267.0
17 TraesCS1A01G342500 chr3A 96.377 138 5 0 1 138 579043132 579043269 1.710000e-55 228.0
18 TraesCS1A01G342500 chr3A 80.473 169 33 0 1135 1303 505716763 505716931 4.950000e-26 130.0
19 TraesCS1A01G342500 chr3B 83.158 190 8 1 1 166 688577810 688577999 1.060000e-32 152.0
20 TraesCS1A01G342500 chr3B 91.579 95 7 1 75 168 806968653 806968747 4.950000e-26 130.0
21 TraesCS1A01G342500 chr3B 79.290 169 35 0 1135 1303 498360437 498360605 1.070000e-22 119.0
22 TraesCS1A01G342500 chr2D 82.723 191 9 1 2 168 604060456 604060266 1.370000e-31 148.0
23 TraesCS1A01G342500 chr4B 83.060 183 5 12 1 158 546124670 546124851 6.360000e-30 143.0
24 TraesCS1A01G342500 chr4B 81.053 190 11 2 2 166 636704462 636704273 1.780000e-25 128.0
25 TraesCS1A01G342500 chr7B 81.579 190 11 1 1 166 717119934 717120123 1.060000e-27 135.0
26 TraesCS1A01G342500 chr3D 79.641 167 34 0 1137 1303 382746918 382747084 2.980000e-23 121.0
27 TraesCS1A01G342500 chr3D 76.695 236 38 12 5854 6079 383110353 383110581 1.390000e-21 115.0


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 TraesCS1A01G342500 chr1A 531602663 531608753 6090 False 3808.266667 11249 93.846000 1 6091 3 chr1A.!!$F1 6090
1 TraesCS1A01G342500 chr1D 433208027 433213986 5959 False 1518.983333 5507 93.649333 163 6091 6 chr1D.!!$F1 5928
2 TraesCS1A01G342500 chr1B 585068046 585074029 5983 False 2771.333333 5094 91.577667 271 6091 3 chr1B.!!$F1 5820

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
105 106 0.033228 TTTTCGTTCGAGGCGGGTAA 59.967 50.000 10.71 2.54 0.00 2.85 F
625 675 0.035056 CGGCCTGACAGGAAAGGATT 60.035 55.000 26.25 0.00 37.67 3.01 F
703 754 0.108138 AGATCCGCTTCCGTCCAAAG 60.108 55.000 0.00 0.00 0.00 2.77 F
704 755 0.108329 GATCCGCTTCCGTCCAAAGA 60.108 55.000 0.00 0.00 0.00 2.52 F
1340 1637 0.244994 CCGATCTGATCCGATCCCAC 59.755 60.000 18.23 0.00 37.16 4.61 F
1438 1735 1.011904 CCTGTCGATGAATTGCGCG 60.012 57.895 0.00 0.00 0.00 6.86 F
1552 1859 1.098050 ATTTCTGTGCCAAGATCGCC 58.902 50.000 0.00 0.00 0.00 5.54 F
2327 2642 1.470098 CTCCCTGGAGTCGCAAATTTG 59.530 52.381 14.03 14.03 37.47 2.32 F
3936 4308 0.107263 TGCACAAGGAAGCAGTGTCA 60.107 50.000 0.00 0.00 35.51 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 2007 0.400213 ACGATCAGCAAACAGGGGAA 59.600 50.000 0.00 0.00 0.00 3.97 R
2571 2886 1.615392 AGGAACTGCTCAACAAATGCC 59.385 47.619 0.00 0.00 37.18 4.40 R
2648 2963 1.600023 TTACCACCAGAAACTTGCCG 58.400 50.000 0.00 0.00 0.00 5.69 R
2702 3017 8.009974 CGAAGAACAAAACCACTATAACTTCAG 58.990 37.037 0.00 0.00 32.98 3.02 R
3275 3606 1.066454 GCATGCTCAACATATGCTGCA 59.934 47.619 11.37 4.13 42.84 4.41 R
3710 4042 1.480789 AATGCAGCATCATGAGCCAA 58.519 45.000 8.77 0.00 0.00 4.52 R
3730 4062 1.901833 GCTGGAACAACATCCCCAAAT 59.098 47.619 0.00 0.00 38.70 2.32 R
4179 4565 2.710471 TGCACAGGCCATCCATCTTATA 59.290 45.455 5.01 0.00 40.13 0.98 R
5707 6143 0.914551 CGTCTGACGAAATGCCGTAG 59.085 55.000 24.86 0.00 46.05 3.51 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
20 21 3.418684 GGCTAGGGAGAAGTTCAACAA 57.581 47.619 5.50 0.00 0.00 2.83
21 22 3.751518 GGCTAGGGAGAAGTTCAACAAA 58.248 45.455 5.50 0.00 0.00 2.83
22 23 4.142038 GGCTAGGGAGAAGTTCAACAAAA 58.858 43.478 5.50 0.00 0.00 2.44
23 24 4.583073 GGCTAGGGAGAAGTTCAACAAAAA 59.417 41.667 5.50 0.00 0.00 1.94
40 41 3.372440 AAAAACAGAGGCTAGATGGGG 57.628 47.619 0.00 0.00 0.00 4.96
41 42 1.972588 AAACAGAGGCTAGATGGGGT 58.027 50.000 0.00 0.00 0.00 4.95
42 43 1.207791 AACAGAGGCTAGATGGGGTG 58.792 55.000 0.00 0.00 0.00 4.61
43 44 1.341156 ACAGAGGCTAGATGGGGTGC 61.341 60.000 0.00 0.00 0.00 5.01
44 45 1.003442 AGAGGCTAGATGGGGTGCA 59.997 57.895 0.00 0.00 0.00 4.57
45 46 0.401105 AGAGGCTAGATGGGGTGCAT 60.401 55.000 0.00 0.00 0.00 3.96
46 47 0.250640 GAGGCTAGATGGGGTGCATG 60.251 60.000 0.00 0.00 0.00 4.06
47 48 1.228367 GGCTAGATGGGGTGCATGG 60.228 63.158 0.00 0.00 0.00 3.66
48 49 1.533711 GCTAGATGGGGTGCATGGT 59.466 57.895 0.00 0.00 0.00 3.55
49 50 0.820891 GCTAGATGGGGTGCATGGTG 60.821 60.000 0.00 0.00 0.00 4.17
50 51 0.548031 CTAGATGGGGTGCATGGTGT 59.452 55.000 0.00 0.00 0.00 4.16
51 52 0.998928 TAGATGGGGTGCATGGTGTT 59.001 50.000 0.00 0.00 0.00 3.32
52 53 0.114954 AGATGGGGTGCATGGTGTTT 59.885 50.000 0.00 0.00 0.00 2.83
53 54 0.247185 GATGGGGTGCATGGTGTTTG 59.753 55.000 0.00 0.00 0.00 2.93
54 55 0.471591 ATGGGGTGCATGGTGTTTGT 60.472 50.000 0.00 0.00 0.00 2.83
55 56 0.689080 TGGGGTGCATGGTGTTTGTT 60.689 50.000 0.00 0.00 0.00 2.83
56 57 0.249826 GGGGTGCATGGTGTTTGTTG 60.250 55.000 0.00 0.00 0.00 3.33
57 58 0.249826 GGGTGCATGGTGTTTGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
58 59 0.749649 GGTGCATGGTGTTTGTTGGA 59.250 50.000 0.00 0.00 0.00 3.53
59 60 1.137872 GGTGCATGGTGTTTGTTGGAA 59.862 47.619 0.00 0.00 0.00 3.53
60 61 2.224257 GGTGCATGGTGTTTGTTGGAAT 60.224 45.455 0.00 0.00 0.00 3.01
61 62 3.006323 GGTGCATGGTGTTTGTTGGAATA 59.994 43.478 0.00 0.00 0.00 1.75
62 63 4.236935 GTGCATGGTGTTTGTTGGAATAG 58.763 43.478 0.00 0.00 0.00 1.73
63 64 4.022416 GTGCATGGTGTTTGTTGGAATAGA 60.022 41.667 0.00 0.00 0.00 1.98
64 65 4.218200 TGCATGGTGTTTGTTGGAATAGAG 59.782 41.667 0.00 0.00 0.00 2.43
65 66 4.458989 GCATGGTGTTTGTTGGAATAGAGA 59.541 41.667 0.00 0.00 0.00 3.10
66 67 5.392380 GCATGGTGTTTGTTGGAATAGAGAG 60.392 44.000 0.00 0.00 0.00 3.20
67 68 5.560722 TGGTGTTTGTTGGAATAGAGAGA 57.439 39.130 0.00 0.00 0.00 3.10
68 69 5.935945 TGGTGTTTGTTGGAATAGAGAGAA 58.064 37.500 0.00 0.00 0.00 2.87
69 70 5.997746 TGGTGTTTGTTGGAATAGAGAGAAG 59.002 40.000 0.00 0.00 0.00 2.85
70 71 6.183361 TGGTGTTTGTTGGAATAGAGAGAAGA 60.183 38.462 0.00 0.00 0.00 2.87
71 72 6.881602 GGTGTTTGTTGGAATAGAGAGAAGAT 59.118 38.462 0.00 0.00 0.00 2.40
72 73 8.041323 GGTGTTTGTTGGAATAGAGAGAAGATA 58.959 37.037 0.00 0.00 0.00 1.98
73 74 8.874816 GTGTTTGTTGGAATAGAGAGAAGATAC 58.125 37.037 0.00 0.00 0.00 2.24
74 75 8.816894 TGTTTGTTGGAATAGAGAGAAGATACT 58.183 33.333 0.00 0.00 0.00 2.12
75 76 9.660180 GTTTGTTGGAATAGAGAGAAGATACTT 57.340 33.333 0.00 0.00 0.00 2.24
76 77 9.658799 TTTGTTGGAATAGAGAGAAGATACTTG 57.341 33.333 0.00 0.00 0.00 3.16
77 78 7.268586 TGTTGGAATAGAGAGAAGATACTTGC 58.731 38.462 0.00 0.00 0.00 4.01
78 79 6.078202 TGGAATAGAGAGAAGATACTTGCG 57.922 41.667 0.00 0.00 0.00 4.85
79 80 5.594725 TGGAATAGAGAGAAGATACTTGCGT 59.405 40.000 0.00 0.00 0.00 5.24
80 81 5.918011 GGAATAGAGAGAAGATACTTGCGTG 59.082 44.000 0.00 0.00 0.00 5.34
81 82 3.157932 AGAGAGAAGATACTTGCGTGC 57.842 47.619 0.00 0.00 0.00 5.34
82 83 2.493675 AGAGAGAAGATACTTGCGTGCA 59.506 45.455 0.00 0.00 0.00 4.57
83 84 3.056536 AGAGAGAAGATACTTGCGTGCAA 60.057 43.478 7.12 7.12 0.00 4.08
84 85 3.866651 AGAGAAGATACTTGCGTGCAAT 58.133 40.909 7.85 1.76 35.20 3.56
85 86 3.620374 AGAGAAGATACTTGCGTGCAATG 59.380 43.478 7.85 5.28 35.20 2.82
86 87 3.338249 AGAAGATACTTGCGTGCAATGT 58.662 40.909 7.85 10.51 35.20 2.71
87 88 3.753272 AGAAGATACTTGCGTGCAATGTT 59.247 39.130 7.85 0.00 35.20 2.71
88 89 4.216257 AGAAGATACTTGCGTGCAATGTTT 59.784 37.500 7.85 4.22 35.20 2.83
89 90 4.503741 AGATACTTGCGTGCAATGTTTT 57.496 36.364 7.85 1.20 35.20 2.43
90 91 4.475944 AGATACTTGCGTGCAATGTTTTC 58.524 39.130 7.85 8.82 35.20 2.29
91 92 1.476074 ACTTGCGTGCAATGTTTTCG 58.524 45.000 7.85 0.00 35.20 3.46
92 93 1.202245 ACTTGCGTGCAATGTTTTCGT 60.202 42.857 7.85 0.00 35.20 3.85
93 94 1.851666 CTTGCGTGCAATGTTTTCGTT 59.148 42.857 7.85 0.00 35.20 3.85
94 95 1.471964 TGCGTGCAATGTTTTCGTTC 58.528 45.000 0.00 0.00 0.00 3.95
95 96 0.425656 GCGTGCAATGTTTTCGTTCG 59.574 50.000 0.00 0.00 0.00 3.95
96 97 1.918112 GCGTGCAATGTTTTCGTTCGA 60.918 47.619 0.00 0.00 0.00 3.71
97 98 1.962547 CGTGCAATGTTTTCGTTCGAG 59.037 47.619 0.00 0.00 0.00 4.04
98 99 2.307049 GTGCAATGTTTTCGTTCGAGG 58.693 47.619 0.00 0.00 0.00 4.63
99 100 1.327507 GCAATGTTTTCGTTCGAGGC 58.672 50.000 0.00 0.00 0.00 4.70
100 101 1.591248 CAATGTTTTCGTTCGAGGCG 58.409 50.000 5.30 5.30 0.00 5.52
101 102 0.515564 AATGTTTTCGTTCGAGGCGG 59.484 50.000 10.71 0.00 0.00 6.13
102 103 1.296056 ATGTTTTCGTTCGAGGCGGG 61.296 55.000 10.71 0.00 0.00 6.13
103 104 1.957695 GTTTTCGTTCGAGGCGGGT 60.958 57.895 10.71 0.00 0.00 5.28
104 105 0.667184 GTTTTCGTTCGAGGCGGGTA 60.667 55.000 10.71 0.00 0.00 3.69
105 106 0.033228 TTTTCGTTCGAGGCGGGTAA 59.967 50.000 10.71 2.54 0.00 2.85
106 107 0.667184 TTTCGTTCGAGGCGGGTAAC 60.667 55.000 10.71 0.00 0.00 2.50
107 108 1.526575 TTCGTTCGAGGCGGGTAACT 61.527 55.000 10.71 0.00 0.00 2.24
108 109 1.080298 CGTTCGAGGCGGGTAACTT 60.080 57.895 3.92 0.00 0.00 2.66
109 110 1.349259 CGTTCGAGGCGGGTAACTTG 61.349 60.000 3.92 0.00 0.00 3.16
110 111 0.037975 GTTCGAGGCGGGTAACTTGA 60.038 55.000 0.00 0.00 0.00 3.02
111 112 0.680618 TTCGAGGCGGGTAACTTGAA 59.319 50.000 0.00 0.00 35.34 2.69
112 113 0.037975 TCGAGGCGGGTAACTTGAAC 60.038 55.000 0.00 0.00 0.00 3.18
113 114 0.320073 CGAGGCGGGTAACTTGAACA 60.320 55.000 0.00 0.00 0.00 3.18
114 115 1.674817 CGAGGCGGGTAACTTGAACAT 60.675 52.381 0.00 0.00 0.00 2.71
115 116 2.433436 GAGGCGGGTAACTTGAACATT 58.567 47.619 0.00 0.00 0.00 2.71
116 117 2.159382 AGGCGGGTAACTTGAACATTG 58.841 47.619 0.00 0.00 0.00 2.82
117 118 1.883926 GGCGGGTAACTTGAACATTGT 59.116 47.619 0.00 0.00 0.00 2.71
118 119 2.295070 GGCGGGTAACTTGAACATTGTT 59.705 45.455 0.63 0.63 0.00 2.83
119 120 3.243602 GGCGGGTAACTTGAACATTGTTT 60.244 43.478 3.08 0.00 0.00 2.83
120 121 4.023021 GGCGGGTAACTTGAACATTGTTTA 60.023 41.667 3.08 0.00 0.00 2.01
121 122 4.913345 GCGGGTAACTTGAACATTGTTTAC 59.087 41.667 3.08 2.08 0.00 2.01
122 123 5.505985 GCGGGTAACTTGAACATTGTTTACA 60.506 40.000 3.08 0.00 0.00 2.41
123 124 6.496571 CGGGTAACTTGAACATTGTTTACAA 58.503 36.000 3.08 3.79 40.51 2.41
124 125 6.973474 CGGGTAACTTGAACATTGTTTACAAA 59.027 34.615 3.08 0.00 39.55 2.83
125 126 7.650104 CGGGTAACTTGAACATTGTTTACAAAT 59.350 33.333 3.08 0.00 39.55 2.32
126 127 9.320352 GGGTAACTTGAACATTGTTTACAAATT 57.680 29.630 3.08 3.65 39.55 1.82
135 136 9.715123 GAACATTGTTTACAAATTTTTCCTTGG 57.285 29.630 3.08 0.00 39.55 3.61
136 137 7.702386 ACATTGTTTACAAATTTTTCCTTGGC 58.298 30.769 0.00 0.00 39.55 4.52
137 138 6.685527 TTGTTTACAAATTTTTCCTTGGCC 57.314 33.333 0.00 0.00 32.11 5.36
138 139 5.126779 TGTTTACAAATTTTTCCTTGGCCC 58.873 37.500 0.00 0.00 0.00 5.80
139 140 2.542020 ACAAATTTTTCCTTGGCCCG 57.458 45.000 0.00 0.00 0.00 6.13
140 141 1.765904 ACAAATTTTTCCTTGGCCCGT 59.234 42.857 0.00 0.00 0.00 5.28
141 142 2.142319 CAAATTTTTCCTTGGCCCGTG 58.858 47.619 0.00 0.00 0.00 4.94
142 143 0.684535 AATTTTTCCTTGGCCCGTGG 59.315 50.000 0.00 0.00 0.00 4.94
160 161 2.048597 CAACGCACGGGCAGTCTA 60.049 61.111 11.77 0.00 41.24 2.59
161 162 2.048503 AACGCACGGGCAGTCTAC 60.049 61.111 11.77 0.00 41.24 2.59
162 163 2.571216 AACGCACGGGCAGTCTACT 61.571 57.895 11.77 0.00 41.24 2.57
163 164 1.246056 AACGCACGGGCAGTCTACTA 61.246 55.000 11.77 0.00 41.24 1.82
164 165 1.064296 CGCACGGGCAGTCTACTAG 59.936 63.158 11.77 0.00 41.24 2.57
165 166 1.654954 CGCACGGGCAGTCTACTAGT 61.655 60.000 11.77 0.00 41.24 2.57
166 167 1.386533 GCACGGGCAGTCTACTAGTA 58.613 55.000 3.77 1.89 40.72 1.82
167 168 1.334243 GCACGGGCAGTCTACTAGTAG 59.666 57.143 21.87 21.87 40.72 2.57
168 169 2.915349 CACGGGCAGTCTACTAGTAGA 58.085 52.381 25.58 25.58 39.67 2.59
169 170 2.873472 CACGGGCAGTCTACTAGTAGAG 59.127 54.545 29.00 20.22 42.31 2.43
170 171 2.158784 ACGGGCAGTCTACTAGTAGAGG 60.159 54.545 29.00 23.91 42.31 3.69
171 172 2.158784 CGGGCAGTCTACTAGTAGAGGT 60.159 54.545 29.00 18.19 42.31 3.85
172 173 3.070734 CGGGCAGTCTACTAGTAGAGGTA 59.929 52.174 29.00 8.72 42.31 3.08
173 174 4.644498 GGGCAGTCTACTAGTAGAGGTAG 58.356 52.174 29.00 19.71 42.31 3.18
174 175 4.347583 GGGCAGTCTACTAGTAGAGGTAGA 59.652 50.000 29.00 9.59 42.31 2.59
175 176 5.511888 GGGCAGTCTACTAGTAGAGGTAGAG 60.512 52.000 29.00 16.84 43.07 2.43
176 177 5.305128 GGCAGTCTACTAGTAGAGGTAGAGA 59.695 48.000 29.00 8.14 43.07 3.10
177 178 6.013984 GGCAGTCTACTAGTAGAGGTAGAGAT 60.014 46.154 29.00 8.40 43.07 2.75
178 179 7.447594 GCAGTCTACTAGTAGAGGTAGAGATT 58.552 42.308 29.00 5.18 43.07 2.40
179 180 7.386848 GCAGTCTACTAGTAGAGGTAGAGATTG 59.613 44.444 29.00 16.61 43.07 2.67
180 181 7.386848 CAGTCTACTAGTAGAGGTAGAGATTGC 59.613 44.444 29.00 14.60 43.07 3.56
181 182 6.366877 GTCTACTAGTAGAGGTAGAGATTGCG 59.633 46.154 29.00 1.07 43.07 4.85
182 183 5.038651 ACTAGTAGAGGTAGAGATTGCGT 57.961 43.478 3.59 0.00 0.00 5.24
183 184 4.817464 ACTAGTAGAGGTAGAGATTGCGTG 59.183 45.833 3.59 0.00 0.00 5.34
184 185 2.359531 AGTAGAGGTAGAGATTGCGTGC 59.640 50.000 0.00 0.00 0.00 5.34
185 186 0.101399 AGAGGTAGAGATTGCGTGCG 59.899 55.000 0.00 0.00 0.00 5.34
205 206 1.058695 GTGCGTGCGTTGAGTGTATAC 59.941 52.381 0.00 0.00 0.00 1.47
219 220 4.693283 AGTGTATACAATGTCCGTGGATG 58.307 43.478 7.25 0.00 0.00 3.51
241 242 4.040339 TGGCATAGGTTGATATGACACGAT 59.960 41.667 0.00 0.00 44.47 3.73
268 269 7.837898 GGTACGATATACCGTTAAACTGTAC 57.162 40.000 0.00 0.00 43.20 2.90
269 270 7.639945 GGTACGATATACCGTTAAACTGTACT 58.360 38.462 0.00 0.00 43.20 2.73
411 442 2.516225 GGCGGTTGACCCTATGGC 60.516 66.667 0.00 0.00 33.59 4.40
495 539 4.444838 CCCGCCGATCCACGTTCA 62.445 66.667 0.00 0.00 40.78 3.18
496 540 3.186047 CCGCCGATCCACGTTCAC 61.186 66.667 0.00 0.00 40.78 3.18
567 617 1.793820 AAGCCTTCCCACCCTCCAAG 61.794 60.000 0.00 0.00 0.00 3.61
620 670 0.534203 GTCAACGGCCTGACAGGAAA 60.534 55.000 26.25 0.00 44.32 3.13
625 675 0.035056 CGGCCTGACAGGAAAGGATT 60.035 55.000 26.25 0.00 37.67 3.01
668 718 3.805971 CCAGGTAAATCCGTTCGGTAATC 59.194 47.826 11.04 0.70 41.99 1.75
696 747 0.676782 AAAACCCAGATCCGCTTCCG 60.677 55.000 0.00 0.00 0.00 4.30
700 751 2.721167 CCAGATCCGCTTCCGTCCA 61.721 63.158 0.00 0.00 0.00 4.02
701 752 1.218047 CAGATCCGCTTCCGTCCAA 59.782 57.895 0.00 0.00 0.00 3.53
703 754 0.108138 AGATCCGCTTCCGTCCAAAG 60.108 55.000 0.00 0.00 0.00 2.77
704 755 0.108329 GATCCGCTTCCGTCCAAAGA 60.108 55.000 0.00 0.00 0.00 2.52
714 765 1.077716 GTCCAAAGACCCCCATCCG 60.078 63.158 0.00 0.00 37.00 4.18
929 1219 4.658786 ACCGCTCCCCCTTCACCT 62.659 66.667 0.00 0.00 0.00 4.00
934 1230 4.285790 TCCCCCTTCACCTGGCCT 62.286 66.667 3.32 0.00 0.00 5.19
958 1254 1.901948 TCCAGAGCGGAGTTCGTGT 60.902 57.895 0.00 0.00 44.46 4.49
959 1255 1.444553 CCAGAGCGGAGTTCGTGTC 60.445 63.158 0.00 0.00 44.46 3.67
968 1264 4.424566 GTTCGTGTCCGGGCGCTA 62.425 66.667 18.93 3.25 33.95 4.26
978 1274 3.902086 GGGCGCTAGGGAGACGAC 61.902 72.222 11.61 0.00 31.75 4.34
979 1275 3.902086 GGCGCTAGGGAGACGACC 61.902 72.222 11.61 0.00 0.00 4.79
980 1276 4.253257 GCGCTAGGGAGACGACCG 62.253 72.222 11.61 0.00 0.00 4.79
981 1277 2.513204 CGCTAGGGAGACGACCGA 60.513 66.667 0.00 0.00 0.00 4.69
982 1278 1.892862 CGCTAGGGAGACGACCGAT 60.893 63.158 0.00 0.00 0.00 4.18
983 1279 1.843734 CGCTAGGGAGACGACCGATC 61.844 65.000 0.00 0.00 0.00 3.69
984 1280 1.517210 GCTAGGGAGACGACCGATCC 61.517 65.000 0.00 3.38 0.00 3.36
998 1294 4.148825 ATCCAGTCCAGGCGCGAC 62.149 66.667 12.10 7.34 0.00 5.19
1285 1581 0.592754 GCTCATCAGCTACGTCGACC 60.593 60.000 10.58 0.00 43.09 4.79
1287 1583 0.733150 TCATCAGCTACGTCGACCAG 59.267 55.000 10.58 8.69 0.00 4.00
1308 1604 2.676265 CCCCACCGGGTAAGGGAAG 61.676 68.421 24.03 6.54 45.80 3.46
1330 1627 1.059913 GTCCCCATTCCCGATCTGAT 58.940 55.000 0.00 0.00 0.00 2.90
1339 1636 0.900182 CCCGATCTGATCCGATCCCA 60.900 60.000 18.23 0.00 37.16 4.37
1340 1637 0.244994 CCGATCTGATCCGATCCCAC 59.755 60.000 18.23 0.00 37.16 4.61
1360 1657 2.699321 ACCCGATCCTTAGCCTTTAGTC 59.301 50.000 0.00 0.00 0.00 2.59
1372 1669 1.271656 CCTTTAGTCGTCGGGTTGACT 59.728 52.381 0.22 0.22 45.87 3.41
1438 1735 1.011904 CCTGTCGATGAATTGCGCG 60.012 57.895 0.00 0.00 0.00 6.86
1528 1825 3.270877 GGTGAAATGTGCGGATCTTAGT 58.729 45.455 0.00 0.00 0.00 2.24
1529 1826 3.063997 GGTGAAATGTGCGGATCTTAGTG 59.936 47.826 0.00 0.00 0.00 2.74
1530 1827 3.684788 GTGAAATGTGCGGATCTTAGTGT 59.315 43.478 0.00 0.00 0.00 3.55
1531 1828 3.684305 TGAAATGTGCGGATCTTAGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
1532 1829 3.610040 AATGTGCGGATCTTAGTGTGA 57.390 42.857 0.00 0.00 0.00 3.58
1533 1830 3.610040 ATGTGCGGATCTTAGTGTGAA 57.390 42.857 0.00 0.00 0.00 3.18
1534 1831 3.610040 TGTGCGGATCTTAGTGTGAAT 57.390 42.857 0.00 0.00 0.00 2.57
1535 1832 3.937814 TGTGCGGATCTTAGTGTGAATT 58.062 40.909 0.00 0.00 0.00 2.17
1536 1833 4.323417 TGTGCGGATCTTAGTGTGAATTT 58.677 39.130 0.00 0.00 0.00 1.82
1537 1834 4.391830 TGTGCGGATCTTAGTGTGAATTTC 59.608 41.667 0.00 0.00 0.00 2.17
1552 1859 1.098050 ATTTCTGTGCCAAGATCGCC 58.902 50.000 0.00 0.00 0.00 5.54
1558 1865 3.521796 GCCAAGATCGCCCCTTGC 61.522 66.667 0.00 0.00 39.60 4.01
1570 1877 2.436646 CCTTGCGGCGATTCAGGT 60.437 61.111 12.98 0.00 0.00 4.00
1609 1916 1.501582 GCCTCTTAGGTGACCTCCAT 58.498 55.000 7.77 0.00 37.80 3.41
1665 1977 8.534333 TGTGATCCTTTTATTATCTCATACGC 57.466 34.615 0.00 0.00 0.00 4.42
1923 2237 8.764524 AATCTGTACAGAAGTTCTTATGTGAC 57.235 34.615 28.43 13.87 41.36 3.67
2007 2321 9.764363 CTCCAAGTATAATCTGTTATGTGCTTA 57.236 33.333 0.00 0.00 32.84 3.09
2092 2407 9.319143 CAGGACATTTTTCCTAGACTTGTATAG 57.681 37.037 0.00 0.00 44.90 1.31
2327 2642 1.470098 CTCCCTGGAGTCGCAAATTTG 59.530 52.381 14.03 14.03 37.47 2.32
2406 2721 5.991933 TGCTTCTGTATTGGCCAAATTTA 57.008 34.783 24.71 7.84 0.00 1.40
2571 2886 5.114423 GCGGTAAAATTCAAAACACTACACG 59.886 40.000 0.00 0.00 0.00 4.49
2623 2938 6.808321 AGTTAGCATAAGTTCCACTGGATA 57.192 37.500 0.00 0.00 0.00 2.59
2702 3017 4.708726 ATGCCAATCAGAACTTAAGTGC 57.291 40.909 9.34 7.28 0.00 4.40
2728 3043 7.857569 TGAAGTTATAGTGGTTTTGTTCTTCG 58.142 34.615 0.00 0.00 32.93 3.79
2791 3106 7.224297 AGTATATGGTATCGAAGCCAATTGTT 58.776 34.615 14.04 0.00 38.38 2.83
2808 3123 6.403200 CCAATTGTTGGTCTTAAGTGGTATCG 60.403 42.308 4.43 0.00 45.93 2.92
3172 3502 5.948992 AAAACTTGTATTCTCAGGCTGAC 57.051 39.130 14.43 4.59 0.00 3.51
3275 3606 6.267471 CCATAATATTGGGCACTGGTACAAAT 59.733 38.462 0.00 0.00 32.65 2.32
3397 3729 3.421919 AAAAGCCCCATGAAACATTGG 57.578 42.857 0.00 0.00 0.00 3.16
3431 3763 8.067751 TGCTGTGTTGTATTAGTCTCTCTTAT 57.932 34.615 0.00 0.00 0.00 1.73
3710 4042 6.801539 TTGTGCGAAGAATCTTACTGAAAT 57.198 33.333 0.00 0.00 0.00 2.17
3730 4062 2.351706 TGGCTCATGATGCTGCATTA 57.648 45.000 17.36 13.41 0.00 1.90
3792 4124 7.194607 TCGTACTTAGGTAATACTTGATCCG 57.805 40.000 0.00 0.00 0.00 4.18
3813 4145 3.003689 CGTTGGTCACTGAGCTTTTCATT 59.996 43.478 9.57 0.00 34.68 2.57
3936 4308 0.107263 TGCACAAGGAAGCAGTGTCA 60.107 50.000 0.00 0.00 35.51 3.58
4028 4401 3.871006 CGTGCCTTTGAAGCTATACATGA 59.129 43.478 0.00 0.00 0.00 3.07
4203 4589 0.672342 GATGGATGGCCTGTGCAATC 59.328 55.000 3.32 0.00 45.74 2.67
4321 4709 8.547967 TTGTCAAACCTATCATAAAGTCTGAC 57.452 34.615 0.00 0.00 0.00 3.51
4368 4756 8.660295 TCACCTTCTCCTTGTTAGAACTAATA 57.340 34.615 0.00 0.00 0.00 0.98
4458 4880 4.384056 CATTCTTGATACCCGATGAAGCT 58.616 43.478 0.00 0.00 29.46 3.74
4559 4988 9.120538 TCTATTTGTAGAAACTTTTCTGCTGTT 57.879 29.630 17.33 7.40 46.34 3.16
4613 5042 2.107726 AGATATGTCTGCCATGCACCAT 59.892 45.455 0.00 0.00 34.86 3.55
5324 5753 3.578688 GCATAAAAGTTTCAGTGGCAGG 58.421 45.455 0.00 0.00 0.00 4.85
5459 5889 8.556589 TGTATTTTCTCCTCCCAATAAAGATGA 58.443 33.333 0.00 0.00 0.00 2.92
5703 6139 8.078596 ACTTAGTTACTACTGAACCTTACAACG 58.921 37.037 0.00 0.00 35.78 4.10
5704 6140 6.396829 AGTTACTACTGAACCTTACAACGT 57.603 37.500 0.00 0.00 31.99 3.99
5705 6141 6.442112 AGTTACTACTGAACCTTACAACGTC 58.558 40.000 0.00 0.00 31.99 4.34
5707 6143 4.614946 ACTACTGAACCTTACAACGTCAC 58.385 43.478 0.00 0.00 0.00 3.67
5709 6145 4.924305 ACTGAACCTTACAACGTCACTA 57.076 40.909 0.00 0.00 0.00 2.74
5710 6146 4.614946 ACTGAACCTTACAACGTCACTAC 58.385 43.478 0.00 0.00 0.00 2.73
5960 6415 1.954146 GCCGAGCTTGAACACGACA 60.954 57.895 1.22 0.00 0.00 4.35
6026 6481 1.880340 GTCAGCGATGCTCTTCCCG 60.880 63.158 0.00 0.00 36.40 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.418684 TTGTTGAACTTCTCCCTAGCC 57.581 47.619 0.00 0.00 0.00 3.93
1 2 5.767816 TTTTTGTTGAACTTCTCCCTAGC 57.232 39.130 0.00 0.00 0.00 3.42
20 21 2.649816 ACCCCATCTAGCCTCTGTTTTT 59.350 45.455 0.00 0.00 0.00 1.94
21 22 2.025887 CACCCCATCTAGCCTCTGTTTT 60.026 50.000 0.00 0.00 0.00 2.43
22 23 1.561542 CACCCCATCTAGCCTCTGTTT 59.438 52.381 0.00 0.00 0.00 2.83
23 24 1.207791 CACCCCATCTAGCCTCTGTT 58.792 55.000 0.00 0.00 0.00 3.16
24 25 1.341156 GCACCCCATCTAGCCTCTGT 61.341 60.000 0.00 0.00 0.00 3.41
25 26 1.340399 TGCACCCCATCTAGCCTCTG 61.340 60.000 0.00 0.00 0.00 3.35
26 27 0.401105 ATGCACCCCATCTAGCCTCT 60.401 55.000 0.00 0.00 0.00 3.69
27 28 0.250640 CATGCACCCCATCTAGCCTC 60.251 60.000 0.00 0.00 29.71 4.70
28 29 1.713005 CCATGCACCCCATCTAGCCT 61.713 60.000 0.00 0.00 29.71 4.58
29 30 1.228367 CCATGCACCCCATCTAGCC 60.228 63.158 0.00 0.00 29.71 3.93
30 31 0.820891 CACCATGCACCCCATCTAGC 60.821 60.000 0.00 0.00 29.71 3.42
31 32 0.548031 ACACCATGCACCCCATCTAG 59.452 55.000 0.00 0.00 29.71 2.43
32 33 0.998928 AACACCATGCACCCCATCTA 59.001 50.000 0.00 0.00 29.71 1.98
33 34 0.114954 AAACACCATGCACCCCATCT 59.885 50.000 0.00 0.00 29.71 2.90
34 35 0.247185 CAAACACCATGCACCCCATC 59.753 55.000 0.00 0.00 29.71 3.51
35 36 0.471591 ACAAACACCATGCACCCCAT 60.472 50.000 0.00 0.00 33.39 4.00
36 37 0.689080 AACAAACACCATGCACCCCA 60.689 50.000 0.00 0.00 0.00 4.96
37 38 0.249826 CAACAAACACCATGCACCCC 60.250 55.000 0.00 0.00 0.00 4.95
38 39 0.249826 CCAACAAACACCATGCACCC 60.250 55.000 0.00 0.00 0.00 4.61
39 40 0.749649 TCCAACAAACACCATGCACC 59.250 50.000 0.00 0.00 0.00 5.01
40 41 2.593346 TTCCAACAAACACCATGCAC 57.407 45.000 0.00 0.00 0.00 4.57
41 42 4.148079 TCTATTCCAACAAACACCATGCA 58.852 39.130 0.00 0.00 0.00 3.96
42 43 4.458989 TCTCTATTCCAACAAACACCATGC 59.541 41.667 0.00 0.00 0.00 4.06
43 44 5.939883 TCTCTCTATTCCAACAAACACCATG 59.060 40.000 0.00 0.00 0.00 3.66
44 45 6.126863 TCTCTCTATTCCAACAAACACCAT 57.873 37.500 0.00 0.00 0.00 3.55
45 46 5.560722 TCTCTCTATTCCAACAAACACCA 57.439 39.130 0.00 0.00 0.00 4.17
46 47 6.231211 TCTTCTCTCTATTCCAACAAACACC 58.769 40.000 0.00 0.00 0.00 4.16
47 48 7.913674 ATCTTCTCTCTATTCCAACAAACAC 57.086 36.000 0.00 0.00 0.00 3.32
48 49 8.816894 AGTATCTTCTCTCTATTCCAACAAACA 58.183 33.333 0.00 0.00 0.00 2.83
49 50 9.660180 AAGTATCTTCTCTCTATTCCAACAAAC 57.340 33.333 0.00 0.00 0.00 2.93
50 51 9.658799 CAAGTATCTTCTCTCTATTCCAACAAA 57.341 33.333 0.00 0.00 0.00 2.83
51 52 7.766278 GCAAGTATCTTCTCTCTATTCCAACAA 59.234 37.037 0.00 0.00 0.00 2.83
52 53 7.268586 GCAAGTATCTTCTCTCTATTCCAACA 58.731 38.462 0.00 0.00 0.00 3.33
53 54 6.419413 CGCAAGTATCTTCTCTCTATTCCAAC 59.581 42.308 0.00 0.00 0.00 3.77
54 55 6.507900 CGCAAGTATCTTCTCTCTATTCCAA 58.492 40.000 0.00 0.00 0.00 3.53
55 56 6.078202 CGCAAGTATCTTCTCTCTATTCCA 57.922 41.667 0.00 0.00 0.00 3.53
73 74 1.476074 ACGAAAACATTGCACGCAAG 58.524 45.000 10.60 5.34 39.47 4.01
74 75 1.849219 GAACGAAAACATTGCACGCAA 59.151 42.857 6.95 6.95 40.47 4.85
75 76 1.471964 GAACGAAAACATTGCACGCA 58.528 45.000 0.00 0.00 0.00 5.24
76 77 0.425656 CGAACGAAAACATTGCACGC 59.574 50.000 0.00 0.00 0.00 5.34
77 78 1.962547 CTCGAACGAAAACATTGCACG 59.037 47.619 0.00 0.00 0.00 5.34
78 79 2.307049 CCTCGAACGAAAACATTGCAC 58.693 47.619 0.00 0.00 0.00 4.57
79 80 1.334599 GCCTCGAACGAAAACATTGCA 60.335 47.619 0.00 0.00 0.00 4.08
80 81 1.327507 GCCTCGAACGAAAACATTGC 58.672 50.000 0.00 0.00 0.00 3.56
81 82 1.591248 CGCCTCGAACGAAAACATTG 58.409 50.000 1.42 0.00 0.00 2.82
82 83 0.515564 CCGCCTCGAACGAAAACATT 59.484 50.000 8.94 0.00 0.00 2.71
83 84 1.296056 CCCGCCTCGAACGAAAACAT 61.296 55.000 8.94 0.00 0.00 2.71
84 85 1.957186 CCCGCCTCGAACGAAAACA 60.957 57.895 8.94 0.00 0.00 2.83
85 86 0.667184 TACCCGCCTCGAACGAAAAC 60.667 55.000 8.94 0.00 0.00 2.43
86 87 0.033228 TTACCCGCCTCGAACGAAAA 59.967 50.000 8.94 0.00 0.00 2.29
87 88 0.667184 GTTACCCGCCTCGAACGAAA 60.667 55.000 8.94 0.00 0.00 3.46
88 89 1.080569 GTTACCCGCCTCGAACGAA 60.081 57.895 8.94 0.00 0.00 3.85
89 90 1.526575 AAGTTACCCGCCTCGAACGA 61.527 55.000 8.94 0.00 0.00 3.85
90 91 1.080298 AAGTTACCCGCCTCGAACG 60.080 57.895 0.69 0.69 0.00 3.95
91 92 0.037975 TCAAGTTACCCGCCTCGAAC 60.038 55.000 0.00 0.00 0.00 3.95
92 93 0.680618 TTCAAGTTACCCGCCTCGAA 59.319 50.000 0.00 0.00 0.00 3.71
93 94 0.037975 GTTCAAGTTACCCGCCTCGA 60.038 55.000 0.00 0.00 0.00 4.04
94 95 0.320073 TGTTCAAGTTACCCGCCTCG 60.320 55.000 0.00 0.00 0.00 4.63
95 96 2.109425 ATGTTCAAGTTACCCGCCTC 57.891 50.000 0.00 0.00 0.00 4.70
96 97 2.159382 CAATGTTCAAGTTACCCGCCT 58.841 47.619 0.00 0.00 0.00 5.52
97 98 1.883926 ACAATGTTCAAGTTACCCGCC 59.116 47.619 0.00 0.00 0.00 6.13
98 99 3.636282 AACAATGTTCAAGTTACCCGC 57.364 42.857 0.00 0.00 0.00 6.13
99 100 6.062434 TGTAAACAATGTTCAAGTTACCCG 57.938 37.500 0.00 0.00 0.00 5.28
100 101 8.880878 ATTTGTAAACAATGTTCAAGTTACCC 57.119 30.769 0.00 0.00 35.55 3.69
109 110 9.715123 CCAAGGAAAAATTTGTAAACAATGTTC 57.285 29.630 0.00 0.00 35.55 3.18
110 111 8.187480 GCCAAGGAAAAATTTGTAAACAATGTT 58.813 29.630 0.00 0.00 35.55 2.71
111 112 7.201776 GGCCAAGGAAAAATTTGTAAACAATGT 60.202 33.333 0.00 0.00 35.55 2.71
112 113 7.138081 GGCCAAGGAAAAATTTGTAAACAATG 58.862 34.615 0.00 0.00 35.55 2.82
113 114 6.264292 GGGCCAAGGAAAAATTTGTAAACAAT 59.736 34.615 4.39 0.00 35.55 2.71
114 115 5.590663 GGGCCAAGGAAAAATTTGTAAACAA 59.409 36.000 4.39 0.00 0.00 2.83
115 116 5.126779 GGGCCAAGGAAAAATTTGTAAACA 58.873 37.500 4.39 0.00 0.00 2.83
116 117 4.212425 CGGGCCAAGGAAAAATTTGTAAAC 59.788 41.667 4.39 0.00 0.00 2.01
117 118 4.141688 ACGGGCCAAGGAAAAATTTGTAAA 60.142 37.500 4.39 0.00 0.00 2.01
118 119 3.388350 ACGGGCCAAGGAAAAATTTGTAA 59.612 39.130 4.39 0.00 0.00 2.41
119 120 2.966516 ACGGGCCAAGGAAAAATTTGTA 59.033 40.909 4.39 0.00 0.00 2.41
120 121 1.765904 ACGGGCCAAGGAAAAATTTGT 59.234 42.857 4.39 0.00 0.00 2.83
121 122 2.142319 CACGGGCCAAGGAAAAATTTG 58.858 47.619 4.39 0.00 0.00 2.32
122 123 1.071542 CCACGGGCCAAGGAAAAATTT 59.928 47.619 4.39 0.00 0.00 1.82
123 124 0.684535 CCACGGGCCAAGGAAAAATT 59.315 50.000 4.39 0.00 0.00 1.82
124 125 1.826340 GCCACGGGCCAAGGAAAAAT 61.826 55.000 14.94 0.00 44.06 1.82
125 126 2.503382 GCCACGGGCCAAGGAAAAA 61.503 57.895 14.94 0.00 44.06 1.94
126 127 2.915137 GCCACGGGCCAAGGAAAA 60.915 61.111 14.94 0.00 44.06 2.29
143 144 2.048597 TAGACTGCCCGTGCGTTG 60.049 61.111 0.00 0.00 41.78 4.10
144 145 1.246056 TAGTAGACTGCCCGTGCGTT 61.246 55.000 0.00 0.00 41.78 4.84
145 146 1.654954 CTAGTAGACTGCCCGTGCGT 61.655 60.000 0.00 0.00 41.78 5.24
146 147 1.064296 CTAGTAGACTGCCCGTGCG 59.936 63.158 0.00 0.00 41.78 5.34
147 148 1.334243 CTACTAGTAGACTGCCCGTGC 59.666 57.143 23.20 0.00 35.21 5.34
148 149 2.873472 CTCTACTAGTAGACTGCCCGTG 59.127 54.545 25.58 11.74 37.28 4.94
149 150 2.158784 CCTCTACTAGTAGACTGCCCGT 60.159 54.545 25.58 0.00 37.28 5.28
150 151 2.158784 ACCTCTACTAGTAGACTGCCCG 60.159 54.545 25.58 15.71 37.28 6.13
151 152 3.581265 ACCTCTACTAGTAGACTGCCC 57.419 52.381 25.58 0.00 37.28 5.36
152 153 5.305128 TCTCTACCTCTACTAGTAGACTGCC 59.695 48.000 25.58 0.00 39.95 4.85
153 154 6.409524 TCTCTACCTCTACTAGTAGACTGC 57.590 45.833 25.58 0.00 39.95 4.40
154 155 7.386848 GCAATCTCTACCTCTACTAGTAGACTG 59.613 44.444 25.58 20.92 39.95 3.51
155 156 7.447594 GCAATCTCTACCTCTACTAGTAGACT 58.552 42.308 25.58 16.61 39.95 3.24
156 157 6.366877 CGCAATCTCTACCTCTACTAGTAGAC 59.633 46.154 25.58 12.12 39.95 2.59
157 158 6.041865 ACGCAATCTCTACCTCTACTAGTAGA 59.958 42.308 27.03 27.03 42.00 2.59
158 159 6.146510 CACGCAATCTCTACCTCTACTAGTAG 59.853 46.154 21.87 21.87 37.83 2.57
159 160 5.990386 CACGCAATCTCTACCTCTACTAGTA 59.010 44.000 1.89 1.89 0.00 1.82
160 161 4.817464 CACGCAATCTCTACCTCTACTAGT 59.183 45.833 0.00 0.00 0.00 2.57
161 162 4.319911 GCACGCAATCTCTACCTCTACTAG 60.320 50.000 0.00 0.00 0.00 2.57
162 163 3.564644 GCACGCAATCTCTACCTCTACTA 59.435 47.826 0.00 0.00 0.00 1.82
163 164 2.359531 GCACGCAATCTCTACCTCTACT 59.640 50.000 0.00 0.00 0.00 2.57
164 165 2.733517 GCACGCAATCTCTACCTCTAC 58.266 52.381 0.00 0.00 0.00 2.59
165 166 1.333931 CGCACGCAATCTCTACCTCTA 59.666 52.381 0.00 0.00 0.00 2.43
166 167 0.101399 CGCACGCAATCTCTACCTCT 59.899 55.000 0.00 0.00 0.00 3.69
167 168 0.179134 ACGCACGCAATCTCTACCTC 60.179 55.000 0.00 0.00 0.00 3.85
168 169 0.458543 CACGCACGCAATCTCTACCT 60.459 55.000 0.00 0.00 0.00 3.08
169 170 1.999051 CACGCACGCAATCTCTACC 59.001 57.895 0.00 0.00 0.00 3.18
170 171 1.345176 GCACGCACGCAATCTCTAC 59.655 57.895 0.00 0.00 0.00 2.59
171 172 2.158330 CGCACGCACGCAATCTCTA 61.158 57.895 0.00 0.00 0.00 2.43
172 173 3.481903 CGCACGCACGCAATCTCT 61.482 61.111 0.00 0.00 0.00 3.10
173 174 3.777925 ACGCACGCACGCAATCTC 61.778 61.111 0.00 0.00 36.19 2.75
174 175 4.075910 CACGCACGCACGCAATCT 62.076 61.111 0.00 0.00 36.19 2.40
181 182 4.993945 CTCAACGCACGCACGCAC 62.994 66.667 0.00 0.00 36.19 5.34
183 184 4.993945 CACTCAACGCACGCACGC 62.994 66.667 0.00 0.00 36.19 5.34
184 185 1.614227 ATACACTCAACGCACGCACG 61.614 55.000 0.00 0.00 39.50 5.34
185 186 1.058695 GTATACACTCAACGCACGCAC 59.941 52.381 0.00 0.00 0.00 5.34
205 206 1.875514 CTATGCCATCCACGGACATTG 59.124 52.381 0.00 0.00 0.00 2.82
219 220 3.990092 TCGTGTCATATCAACCTATGCC 58.010 45.455 0.00 0.00 0.00 4.40
252 253 8.071177 AGGATTACAGTACAGTTTAACGGTAT 57.929 34.615 10.85 0.00 31.87 2.73
254 255 6.350629 AGGATTACAGTACAGTTTAACGGT 57.649 37.500 6.13 6.13 0.00 4.83
260 261 3.057033 ACGCGAGGATTACAGTACAGTTT 60.057 43.478 15.93 0.00 0.00 2.66
263 264 2.717530 GACGCGAGGATTACAGTACAG 58.282 52.381 15.93 0.00 0.00 2.74
264 265 1.063027 CGACGCGAGGATTACAGTACA 59.937 52.381 15.93 0.00 0.00 2.90
265 266 1.739618 CGACGCGAGGATTACAGTAC 58.260 55.000 15.93 0.00 0.00 2.73
266 267 0.028505 GCGACGCGAGGATTACAGTA 59.971 55.000 15.93 0.00 0.00 2.74
267 268 1.226603 GCGACGCGAGGATTACAGT 60.227 57.895 15.93 0.00 0.00 3.55
268 269 3.601981 GCGACGCGAGGATTACAG 58.398 61.111 15.93 0.00 0.00 2.74
411 442 3.728373 GGGGTGGTGCCAGTAGGG 61.728 72.222 0.00 0.00 39.65 3.53
493 537 1.364269 AGGTTGGGAAATACGGGTGA 58.636 50.000 0.00 0.00 0.00 4.02
494 538 2.209690 AAGGTTGGGAAATACGGGTG 57.790 50.000 0.00 0.00 0.00 4.61
495 539 2.984435 AAAGGTTGGGAAATACGGGT 57.016 45.000 0.00 0.00 0.00 5.28
496 540 4.082081 GGTAAAAAGGTTGGGAAATACGGG 60.082 45.833 0.00 0.00 0.00 5.28
594 644 1.525995 CAGGCCGTTGACTTGTGGT 60.526 57.895 0.00 0.00 0.00 4.16
620 670 2.009774 CATCGCGGTGAAAAGAATCCT 58.990 47.619 15.97 0.00 0.00 3.24
625 675 4.202172 TGGATATACATCGCGGTGAAAAGA 60.202 41.667 28.98 8.66 31.33 2.52
668 718 3.306019 CGGATCTGGGTTTTCCTTTTTGG 60.306 47.826 0.00 0.00 40.46 3.28
679 730 2.240162 GACGGAAGCGGATCTGGGTT 62.240 60.000 3.14 2.60 0.00 4.11
696 747 1.077716 CGGATGGGGGTCTTTGGAC 60.078 63.158 0.00 0.00 41.43 4.02
913 1203 4.101448 CAGGTGAAGGGGGAGCGG 62.101 72.222 0.00 0.00 0.00 5.52
915 1205 4.432741 GCCAGGTGAAGGGGGAGC 62.433 72.222 0.00 0.00 0.00 4.70
920 1210 4.101448 CGGAGGCCAGGTGAAGGG 62.101 72.222 5.01 0.00 0.00 3.95
961 1257 3.902086 GTCGTCTCCCTAGCGCCC 61.902 72.222 2.29 0.00 0.00 6.13
963 1259 4.253257 CGGTCGTCTCCCTAGCGC 62.253 72.222 0.00 0.00 0.00 5.92
968 1264 1.454111 CTGGATCGGTCGTCTCCCT 60.454 63.158 10.43 0.00 0.00 4.20
972 1268 1.001269 TGGACTGGATCGGTCGTCT 60.001 57.895 4.10 0.00 40.37 4.18
973 1269 1.433879 CTGGACTGGATCGGTCGTC 59.566 63.158 10.08 0.00 40.37 4.20
974 1270 2.052690 CCTGGACTGGATCGGTCGT 61.053 63.158 10.08 0.00 40.37 4.34
975 1271 2.808315 CCTGGACTGGATCGGTCG 59.192 66.667 10.08 0.00 40.37 4.79
976 1272 2.501610 GCCTGGACTGGATCGGTC 59.498 66.667 0.00 8.40 38.88 4.79
977 1273 3.461773 CGCCTGGACTGGATCGGT 61.462 66.667 0.00 0.00 0.00 4.69
978 1274 4.899239 GCGCCTGGACTGGATCGG 62.899 72.222 0.00 0.00 0.00 4.18
980 1276 3.838271 TCGCGCCTGGACTGGATC 61.838 66.667 0.00 0.00 0.00 3.36
981 1277 4.148825 GTCGCGCCTGGACTGGAT 62.149 66.667 0.00 0.00 0.00 3.41
984 1280 4.498520 ATCGTCGCGCCTGGACTG 62.499 66.667 0.00 0.90 32.24 3.51
1308 1604 3.826926 GATCGGGAATGGGGACGGC 62.827 68.421 0.00 0.00 0.00 5.68
1312 1609 1.352083 GATCAGATCGGGAATGGGGA 58.648 55.000 0.00 0.00 0.00 4.81
1330 1627 2.523412 GGATCGGGTGGGATCGGA 60.523 66.667 0.00 0.00 43.00 4.55
1339 1636 2.699321 GACTAAAGGCTAAGGATCGGGT 59.301 50.000 0.00 0.00 0.00 5.28
1340 1637 2.288273 CGACTAAAGGCTAAGGATCGGG 60.288 54.545 0.00 0.00 0.00 5.14
1372 1669 2.668632 GGATCACGAGGCCCACAA 59.331 61.111 0.00 0.00 0.00 3.33
1438 1735 3.484547 CGTACGCGGCCAAGGAAC 61.485 66.667 12.47 0.00 0.00 3.62
1471 1768 1.487976 TGCCTAATCAAGAGCAGGAGG 59.512 52.381 4.42 0.00 30.74 4.30
1528 1825 3.189080 CGATCTTGGCACAGAAATTCACA 59.811 43.478 0.00 0.00 42.39 3.58
1529 1826 3.751621 CGATCTTGGCACAGAAATTCAC 58.248 45.455 0.00 0.00 42.39 3.18
1530 1827 2.162208 GCGATCTTGGCACAGAAATTCA 59.838 45.455 0.00 0.00 42.39 2.57
1531 1828 2.478539 GGCGATCTTGGCACAGAAATTC 60.479 50.000 0.00 0.00 42.39 2.17
1532 1829 1.474077 GGCGATCTTGGCACAGAAATT 59.526 47.619 0.00 0.00 42.39 1.82
1533 1830 1.098050 GGCGATCTTGGCACAGAAAT 58.902 50.000 0.00 0.00 42.39 2.17
1534 1831 0.960364 GGGCGATCTTGGCACAGAAA 60.960 55.000 0.00 0.00 42.39 2.52
1535 1832 1.377202 GGGCGATCTTGGCACAGAA 60.377 57.895 0.00 0.00 42.39 3.02
1536 1833 2.268920 GGGCGATCTTGGCACAGA 59.731 61.111 0.00 0.00 42.39 3.41
1537 1834 2.825836 GGGGCGATCTTGGCACAG 60.826 66.667 0.00 0.00 42.39 3.66
1558 1865 0.577269 GAATTCGACCTGAATCGCCG 59.423 55.000 0.00 0.00 46.65 6.46
1570 1877 1.667756 CGACGGTGTTCCTGAATTCGA 60.668 52.381 0.04 0.00 0.00 3.71
1575 1882 2.029964 GGCGACGGTGTTCCTGAA 59.970 61.111 0.00 0.00 0.00 3.02
1609 1916 3.694043 TGATGATTCACCGAGAACCAA 57.306 42.857 0.00 0.00 39.49 3.67
1663 1975 2.983136 GAGATCGGTCAGTTCATATGCG 59.017 50.000 0.00 0.00 0.00 4.73
1664 1976 2.983136 CGAGATCGGTCAGTTCATATGC 59.017 50.000 0.00 0.00 35.37 3.14
1665 1977 2.983136 GCGAGATCGGTCAGTTCATATG 59.017 50.000 0.00 0.00 40.23 1.78
1695 2007 0.400213 ACGATCAGCAAACAGGGGAA 59.600 50.000 0.00 0.00 0.00 3.97
1838 2152 2.922740 TCCCTGCCATAATCGGTTAC 57.077 50.000 0.00 0.00 0.00 2.50
1959 2273 3.964031 GAGGATGAGTTCTACTGGTGGAT 59.036 47.826 0.00 0.00 0.00 3.41
1960 2274 3.011821 AGAGGATGAGTTCTACTGGTGGA 59.988 47.826 0.00 0.00 0.00 4.02
2007 2321 7.339466 ACAGGTTACAATTTGTCTTGAGAAACT 59.661 33.333 5.07 0.00 0.00 2.66
2092 2407 7.334171 AGCACCCAAATGATTAAACAATAAAGC 59.666 33.333 0.00 0.00 0.00 3.51
2327 2642 6.651755 AGTTAAATTAGCAAACATGCATGC 57.348 33.333 26.53 14.42 42.87 4.06
2406 2721 4.073293 ACTCGTCACCTTCAGTTTCAAT 57.927 40.909 0.00 0.00 0.00 2.57
2571 2886 1.615392 AGGAACTGCTCAACAAATGCC 59.385 47.619 0.00 0.00 37.18 4.40
2623 2938 9.236006 CGAGGGAATCAATGGATTTATAAGAAT 57.764 33.333 0.00 0.00 43.69 2.40
2648 2963 1.600023 TTACCACCAGAAACTTGCCG 58.400 50.000 0.00 0.00 0.00 5.69
2702 3017 8.009974 CGAAGAACAAAACCACTATAACTTCAG 58.990 37.037 0.00 0.00 32.98 3.02
2728 3043 8.911247 ACACTTAAGTTCTGATTGACAAAAAC 57.089 30.769 5.07 0.00 0.00 2.43
2791 3106 6.594788 AACTTACGATACCACTTAAGACCA 57.405 37.500 10.09 0.00 0.00 4.02
2793 3108 8.699283 ATGAAACTTACGATACCACTTAAGAC 57.301 34.615 10.09 0.00 0.00 3.01
2808 3123 9.807649 AAATTCTGATTGGCATATGAAACTTAC 57.192 29.630 6.97 0.00 0.00 2.34
3172 3502 8.349245 TGTCATTAACCTACAAAACATCAACAG 58.651 33.333 0.00 0.00 0.00 3.16
3275 3606 1.066454 GCATGCTCAACATATGCTGCA 59.934 47.619 11.37 4.13 42.84 4.41
3710 4042 1.480789 AATGCAGCATCATGAGCCAA 58.519 45.000 8.77 0.00 0.00 4.52
3730 4062 1.901833 GCTGGAACAACATCCCCAAAT 59.098 47.619 0.00 0.00 38.70 2.32
3792 4124 4.276926 AGAATGAAAAGCTCAGTGACCAAC 59.723 41.667 0.00 0.00 37.52 3.77
3813 4145 5.850557 TTTTTCCATGTCAAGAAGCAAGA 57.149 34.783 0.00 0.00 0.00 3.02
3894 4226 6.967199 GCAGTTTGACTATTATTGGCACTTAC 59.033 38.462 0.00 0.00 0.00 2.34
4028 4401 6.406370 TCACATGGATTACTCGAATGAAGTT 58.594 36.000 0.00 0.00 0.00 2.66
4178 4564 3.138098 TGCACAGGCCATCCATCTTATAA 59.862 43.478 5.01 0.00 40.13 0.98
4179 4565 2.710471 TGCACAGGCCATCCATCTTATA 59.290 45.455 5.01 0.00 40.13 0.98
4203 4589 7.961827 ACGAAACAAACTCTATCTAACTAGACG 59.038 37.037 0.00 0.00 34.72 4.18
4250 4638 4.119136 AGTTTGGCTTTGGTTTCGAATTG 58.881 39.130 0.00 0.00 0.00 2.32
4288 4676 9.453325 TTTATGATAGGTTTGACAAAAACGAAC 57.547 29.630 1.27 0.00 38.08 3.95
4321 4709 7.012421 GGTGAAAATTACTCATTAGGCCACTAG 59.988 40.741 5.01 0.00 0.00 2.57
4458 4880 3.900601 AGTGGTGTTAATGGCAATGGAAA 59.099 39.130 0.00 0.00 0.00 3.13
4613 5042 6.778834 ATTTTAAGGTCATGTGATGCATCA 57.221 33.333 25.42 25.42 35.19 3.07
5162 5591 4.788679 AGGTTCGAAGGGAAAAGAAAAGA 58.211 39.130 0.00 0.00 36.14 2.52
5163 5592 5.507482 GGAAGGTTCGAAGGGAAAAGAAAAG 60.507 44.000 0.00 0.00 36.14 2.27
5324 5753 4.823989 CCAAACCTCCATCTCCATATGTTC 59.176 45.833 1.24 0.00 0.00 3.18
5459 5889 5.765182 GGTTAAATTGGATGATGTCGATCCT 59.235 40.000 3.79 0.00 40.26 3.24
5602 6032 1.072159 AGTGTGCCAGCCTTGAGAC 59.928 57.895 0.00 0.00 0.00 3.36
5703 6139 1.654105 CTGACGAAATGCCGTAGTGAC 59.346 52.381 0.00 0.00 43.49 3.67
5704 6140 1.542472 TCTGACGAAATGCCGTAGTGA 59.458 47.619 0.00 0.00 43.49 3.41
5705 6141 1.654105 GTCTGACGAAATGCCGTAGTG 59.346 52.381 0.00 0.00 43.49 2.74
5707 6143 0.914551 CGTCTGACGAAATGCCGTAG 59.085 55.000 24.86 0.00 46.05 3.51
5709 6145 3.856508 CGTCTGACGAAATGCCGT 58.143 55.556 24.86 0.00 46.05 5.68
5924 6379 4.166888 ATCATCTGCACCGGCGCT 62.167 61.111 16.69 0.00 45.35 5.92
5960 6415 1.000955 AGGCAAAGTGACGACTTCGAT 59.999 47.619 5.47 0.00 41.87 3.59
6011 6466 2.759973 TCCGGGAAGAGCATCGCT 60.760 61.111 0.00 0.00 43.88 4.93


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

AutoCloner maintained by Alex Coulton.