Multiple sequence alignment - TraesCS4A01G208900

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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 TraesCS4A01G208900 chr4A 100.000 3230 0 0 1 3230 501977419 501974190 0.000000e+00 5965.0
1 TraesCS4A01G208900 chr4B 91.685 2790 128 34 207 2945 126509480 126506744 0.000000e+00 3771.0
2 TraesCS4A01G208900 chr4B 83.721 129 4 6 3090 3203 126506619 126506493 4.410000e-19 106.0
3 TraesCS4A01G208900 chr4B 94.545 55 3 0 125 179 126509534 126509480 5.740000e-13 86.1
4 TraesCS4A01G208900 chr4B 100.000 30 0 0 3201 3230 126506303 126506274 4.500000e-04 56.5
5 TraesCS4A01G208900 chr4D 91.522 2760 140 31 220 2945 89436824 89434125 0.000000e+00 3714.0
6 TraesCS4A01G208900 chr4D 98.462 65 0 1 3139 3203 89433972 89433909 2.630000e-21 113.0
7 TraesCS4A01G208900 chr4D 81.818 99 11 5 3022 3119 504090710 504090802 3.460000e-10 76.8
8 TraesCS4A01G208900 chr4D 100.000 30 0 0 3201 3230 89433714 89433685 4.500000e-04 56.5
9 TraesCS4A01G208900 chr5B 82.081 1038 165 14 1192 2220 222127510 222126485 0.000000e+00 867.0
10 TraesCS4A01G208900 chr5D 81.967 1037 168 12 1192 2220 208536931 208535906 0.000000e+00 861.0
11 TraesCS4A01G208900 chr5D 94.030 134 8 0 1 134 334856210 334856343 1.520000e-48 204.0
12 TraesCS4A01G208900 chr5D 80.435 92 10 7 3023 3112 300756600 300756685 2.690000e-06 63.9
13 TraesCS4A01G208900 chr5A 81.871 1037 169 12 1192 2220 269320612 269319587 0.000000e+00 856.0
14 TraesCS4A01G208900 chr5A 95.385 130 6 0 1 130 445126825 445126954 1.170000e-49 207.0
15 TraesCS4A01G208900 chr5A 91.667 48 4 0 3072 3119 688764006 688764053 2.080000e-07 67.6
16 TraesCS4A01G208900 chr5A 92.105 38 3 0 3079 3116 689619282 689619319 2.000000e-03 54.7
17 TraesCS4A01G208900 chr3A 98.387 124 2 0 2 125 611854260 611854137 5.430000e-53 219.0
18 TraesCS4A01G208900 chr3A 96.183 131 5 0 1 131 447540996 447541126 7.020000e-52 215.0
19 TraesCS4A01G208900 chr3A 80.208 96 14 3 3023 3118 200058040 200058130 2.080000e-07 67.6
20 TraesCS4A01G208900 chr3A 78.351 97 15 4 3023 3118 200126730 200126821 1.250000e-04 58.4
21 TraesCS4A01G208900 chr1D 97.600 125 3 0 1 125 349712365 349712241 7.020000e-52 215.0
22 TraesCS4A01G208900 chr1A 96.800 125 4 0 1 125 316302625 316302749 3.270000e-50 209.0
23 TraesCS4A01G208900 chr3B 94.737 133 7 0 1 133 527883014 527882882 1.170000e-49 207.0
24 TraesCS4A01G208900 chr7B 94.697 132 6 1 1 132 129962843 129962713 1.520000e-48 204.0
25 TraesCS4A01G208900 chr2B 94.697 132 6 1 1 132 481265898 481265768 1.520000e-48 204.0
26 TraesCS4A01G208900 chr7D 94.118 51 2 1 3071 3121 514988359 514988310 3.460000e-10 76.8
27 TraesCS4A01G208900 chr7A 78.218 101 12 7 3022 3119 686783295 686783202 4.500000e-04 56.5
28 TraesCS4A01G208900 chr6B 89.130 46 2 3 3014 3059 690028490 690028448 2.000000e-03 54.7


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 TraesCS4A01G208900 chr4A 501974190 501977419 3229 True 5965.0 5965 100.000000 1 3230 1 chr4A.!!$R1 3229
1 TraesCS4A01G208900 chr4B 126506274 126509534 3260 True 1004.9 3771 92.487750 125 3230 4 chr4B.!!$R1 3105
2 TraesCS4A01G208900 chr4D 89433685 89436824 3139 True 1294.5 3714 96.661333 220 3230 3 chr4D.!!$R1 3010
3 TraesCS4A01G208900 chr5B 222126485 222127510 1025 True 867.0 867 82.081000 1192 2220 1 chr5B.!!$R1 1028
4 TraesCS4A01G208900 chr5D 208535906 208536931 1025 True 861.0 861 81.967000 1192 2220 1 chr5D.!!$R1 1028
5 TraesCS4A01G208900 chr5A 269319587 269320612 1025 True 856.0 856 81.871000 1192 2220 1 chr5A.!!$R1 1028

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
21 22 0.240145 CGTATCCGCGCTCCATCTAA 59.760 55.0 5.56 0.0 0.00 2.10 F
1515 1572 0.464735 ACCTCTCGATCCTCCTCGTG 60.465 60.0 0.00 0.0 39.62 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1689 1.215679 AGGAGGAGGAGGACGAGGAA 61.216 60.0 0.0 0.0 0.00 3.36 R
2538 2599 0.869454 GATCAGAGCAAGCGACCTCG 60.869 60.0 0.0 0.0 43.27 4.63 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.664677 GCCGTATCCGCGCTCCAT 62.665 66.667 5.56 0.00 0.00 3.41
18 19 2.430921 CCGTATCCGCGCTCCATC 60.431 66.667 5.56 0.00 0.00 3.51
19 20 2.645567 CGTATCCGCGCTCCATCT 59.354 61.111 5.56 0.00 0.00 2.90
20 21 1.583495 CCGTATCCGCGCTCCATCTA 61.583 60.000 5.56 0.00 0.00 1.98
21 22 0.240145 CGTATCCGCGCTCCATCTAA 59.760 55.000 5.56 0.00 0.00 2.10
22 23 1.699343 GTATCCGCGCTCCATCTAAC 58.301 55.000 5.56 0.00 0.00 2.34
23 24 0.601558 TATCCGCGCTCCATCTAACC 59.398 55.000 5.56 0.00 0.00 2.85
24 25 2.100879 ATCCGCGCTCCATCTAACCC 62.101 60.000 5.56 0.00 0.00 4.11
25 26 2.797278 CCGCGCTCCATCTAACCCT 61.797 63.158 5.56 0.00 0.00 4.34
26 27 1.592669 CGCGCTCCATCTAACCCTG 60.593 63.158 5.56 0.00 0.00 4.45
27 28 1.522569 GCGCTCCATCTAACCCTGT 59.477 57.895 0.00 0.00 0.00 4.00
28 29 0.530870 GCGCTCCATCTAACCCTGTC 60.531 60.000 0.00 0.00 0.00 3.51
29 30 0.824109 CGCTCCATCTAACCCTGTCA 59.176 55.000 0.00 0.00 0.00 3.58
30 31 1.414181 CGCTCCATCTAACCCTGTCAT 59.586 52.381 0.00 0.00 0.00 3.06
31 32 2.546795 CGCTCCATCTAACCCTGTCATC 60.547 54.545 0.00 0.00 0.00 2.92
32 33 2.224402 GCTCCATCTAACCCTGTCATCC 60.224 54.545 0.00 0.00 0.00 3.51
33 34 3.041211 CTCCATCTAACCCTGTCATCCA 58.959 50.000 0.00 0.00 0.00 3.41
34 35 3.455910 CTCCATCTAACCCTGTCATCCAA 59.544 47.826 0.00 0.00 0.00 3.53
35 36 3.849574 TCCATCTAACCCTGTCATCCAAA 59.150 43.478 0.00 0.00 0.00 3.28
36 37 3.947834 CCATCTAACCCTGTCATCCAAAC 59.052 47.826 0.00 0.00 0.00 2.93
37 38 4.567537 CCATCTAACCCTGTCATCCAAACA 60.568 45.833 0.00 0.00 0.00 2.83
38 39 4.015872 TCTAACCCTGTCATCCAAACAC 57.984 45.455 0.00 0.00 0.00 3.32
39 40 1.995376 AACCCTGTCATCCAAACACC 58.005 50.000 0.00 0.00 0.00 4.16
40 41 1.149101 ACCCTGTCATCCAAACACCT 58.851 50.000 0.00 0.00 0.00 4.00
41 42 1.073923 ACCCTGTCATCCAAACACCTC 59.926 52.381 0.00 0.00 0.00 3.85
42 43 1.352352 CCCTGTCATCCAAACACCTCT 59.648 52.381 0.00 0.00 0.00 3.69
43 44 2.224867 CCCTGTCATCCAAACACCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
44 45 3.490348 CCTGTCATCCAAACACCTCTTT 58.510 45.455 0.00 0.00 0.00 2.52
45 46 3.254166 CCTGTCATCCAAACACCTCTTTG 59.746 47.826 0.00 0.00 0.00 2.77
62 63 6.166982 CCTCTTTGGTTAGAGTTAGTTCAGG 58.833 44.000 0.00 0.00 40.04 3.86
63 64 6.110411 TCTTTGGTTAGAGTTAGTTCAGGG 57.890 41.667 0.00 0.00 0.00 4.45
64 65 5.605488 TCTTTGGTTAGAGTTAGTTCAGGGT 59.395 40.000 0.00 0.00 0.00 4.34
65 66 5.899631 TTGGTTAGAGTTAGTTCAGGGTT 57.100 39.130 0.00 0.00 0.00 4.11
66 67 6.999705 TTGGTTAGAGTTAGTTCAGGGTTA 57.000 37.500 0.00 0.00 0.00 2.85
67 68 6.999705 TGGTTAGAGTTAGTTCAGGGTTAA 57.000 37.500 0.00 0.00 0.00 2.01
68 69 7.563724 TGGTTAGAGTTAGTTCAGGGTTAAT 57.436 36.000 0.00 0.00 0.00 1.40
69 70 7.981142 TGGTTAGAGTTAGTTCAGGGTTAATT 58.019 34.615 0.00 0.00 0.00 1.40
70 71 8.098912 TGGTTAGAGTTAGTTCAGGGTTAATTC 58.901 37.037 0.00 0.00 0.00 2.17
71 72 8.098912 GGTTAGAGTTAGTTCAGGGTTAATTCA 58.901 37.037 0.00 0.00 0.00 2.57
72 73 9.152595 GTTAGAGTTAGTTCAGGGTTAATTCAG 57.847 37.037 0.00 0.00 0.00 3.02
73 74 6.712276 AGAGTTAGTTCAGGGTTAATTCAGG 58.288 40.000 0.00 0.00 0.00 3.86
74 75 5.816682 AGTTAGTTCAGGGTTAATTCAGGG 58.183 41.667 0.00 0.00 0.00 4.45
75 76 5.312443 AGTTAGTTCAGGGTTAATTCAGGGT 59.688 40.000 0.00 0.00 0.00 4.34
76 77 4.741928 AGTTCAGGGTTAATTCAGGGTT 57.258 40.909 0.00 0.00 0.00 4.11
77 78 5.853572 AGTTCAGGGTTAATTCAGGGTTA 57.146 39.130 0.00 0.00 0.00 2.85
78 79 5.816682 AGTTCAGGGTTAATTCAGGGTTAG 58.183 41.667 0.00 0.00 0.00 2.34
79 80 5.550403 AGTTCAGGGTTAATTCAGGGTTAGA 59.450 40.000 0.00 0.00 0.00 2.10
80 81 6.045106 AGTTCAGGGTTAATTCAGGGTTAGAA 59.955 38.462 0.00 0.00 0.00 2.10
81 82 6.652205 TCAGGGTTAATTCAGGGTTAGAAT 57.348 37.500 0.00 0.00 37.30 2.40
82 83 6.659824 TCAGGGTTAATTCAGGGTTAGAATC 58.340 40.000 0.00 0.00 34.78 2.52
83 84 6.447084 TCAGGGTTAATTCAGGGTTAGAATCT 59.553 38.462 0.00 0.00 34.78 2.40
84 85 7.626084 TCAGGGTTAATTCAGGGTTAGAATCTA 59.374 37.037 0.00 0.00 34.78 1.98
85 86 8.272173 CAGGGTTAATTCAGGGTTAGAATCTAA 58.728 37.037 0.00 0.00 34.78 2.10
86 87 8.272889 AGGGTTAATTCAGGGTTAGAATCTAAC 58.727 37.037 21.48 21.48 34.78 2.34
87 88 8.272889 GGGTTAATTCAGGGTTAGAATCTAACT 58.727 37.037 26.42 10.32 34.78 2.24
88 89 9.327628 GGTTAATTCAGGGTTAGAATCTAACTC 57.672 37.037 26.42 24.35 34.78 3.01
101 102 7.571080 AGAATCTAACTCTAACCTCTAACCG 57.429 40.000 0.00 0.00 0.00 4.44
102 103 7.344913 AGAATCTAACTCTAACCTCTAACCGA 58.655 38.462 0.00 0.00 0.00 4.69
103 104 7.499895 AGAATCTAACTCTAACCTCTAACCGAG 59.500 40.741 0.00 0.00 39.57 4.63
104 105 6.059787 TCTAACTCTAACCTCTAACCGAGT 57.940 41.667 0.00 0.00 38.11 4.18
105 106 6.479884 TCTAACTCTAACCTCTAACCGAGTT 58.520 40.000 0.00 0.00 42.40 3.01
106 107 7.624549 TCTAACTCTAACCTCTAACCGAGTTA 58.375 38.462 0.00 0.00 40.78 2.24
107 108 6.756299 AACTCTAACCTCTAACCGAGTTAG 57.244 41.667 14.20 14.20 44.65 2.34
118 119 7.093322 TCTAACCGAGTTAGAGTATCCAAAC 57.907 40.000 17.33 0.00 46.18 2.93
119 120 5.733620 AACCGAGTTAGAGTATCCAAACA 57.266 39.130 0.00 0.00 34.84 2.83
120 121 5.326200 ACCGAGTTAGAGTATCCAAACAG 57.674 43.478 0.00 0.00 34.84 3.16
121 122 4.159879 ACCGAGTTAGAGTATCCAAACAGG 59.840 45.833 0.00 0.00 37.46 4.00
122 123 4.441634 CCGAGTTAGAGTATCCAAACAGGG 60.442 50.000 0.00 0.00 34.84 4.45
123 124 4.443621 GAGTTAGAGTATCCAAACAGGGC 58.556 47.826 0.00 0.00 34.84 5.19
127 128 1.285078 GAGTATCCAAACAGGGCCCTT 59.715 52.381 26.10 11.53 38.24 3.95
139 140 3.833304 GCCCTTGATGTGGCTAGC 58.167 61.111 6.04 6.04 44.46 3.42
146 147 2.113860 TGATGTGGCTAGCTTCCAAC 57.886 50.000 15.72 8.18 35.01 3.77
193 194 4.496670 ACGAAGTAGCCATGACGC 57.503 55.556 0.00 0.00 41.94 5.19
194 195 1.153628 ACGAAGTAGCCATGACGCC 60.154 57.895 0.00 0.00 41.94 5.68
195 196 1.153647 CGAAGTAGCCATGACGCCA 60.154 57.895 0.00 0.00 0.00 5.69
196 197 0.739462 CGAAGTAGCCATGACGCCAA 60.739 55.000 0.00 0.00 0.00 4.52
197 198 0.727398 GAAGTAGCCATGACGCCAAC 59.273 55.000 0.00 0.00 0.00 3.77
199 200 2.125310 TAGCCATGACGCCAACGG 60.125 61.111 0.00 0.00 46.04 4.44
200 201 2.949909 TAGCCATGACGCCAACGGT 61.950 57.895 0.00 0.00 46.04 4.83
201 202 4.101790 GCCATGACGCCAACGGTG 62.102 66.667 0.00 0.00 46.04 4.94
202 203 4.101790 CCATGACGCCAACGGTGC 62.102 66.667 0.00 0.00 46.04 5.01
203 204 3.353029 CATGACGCCAACGGTGCA 61.353 61.111 0.00 0.00 46.04 4.57
204 205 2.359850 ATGACGCCAACGGTGCAT 60.360 55.556 0.00 0.00 46.04 3.96
205 206 2.689785 ATGACGCCAACGGTGCATG 61.690 57.895 0.00 0.00 46.04 4.06
206 207 4.101790 GACGCCAACGGTGCATGG 62.102 66.667 0.00 0.00 46.04 3.66
207 208 4.947147 ACGCCAACGGTGCATGGT 62.947 61.111 5.97 0.00 46.04 3.55
208 209 2.744318 CGCCAACGGTGCATGGTA 60.744 61.111 5.97 0.00 39.00 3.25
209 210 2.112198 CGCCAACGGTGCATGGTAT 61.112 57.895 5.97 0.00 39.00 2.73
210 211 1.653094 CGCCAACGGTGCATGGTATT 61.653 55.000 5.97 0.00 39.00 1.89
211 212 1.384525 GCCAACGGTGCATGGTATTA 58.615 50.000 5.97 0.00 39.00 0.98
212 213 1.333619 GCCAACGGTGCATGGTATTAG 59.666 52.381 5.97 0.00 39.00 1.73
290 292 4.843728 AGCTCCTTTTCGACCAAATGATA 58.156 39.130 0.00 0.00 0.00 2.15
291 293 5.440610 AGCTCCTTTTCGACCAAATGATAT 58.559 37.500 0.00 0.00 0.00 1.63
298 300 9.503427 CCTTTTCGACCAAATGATATTTTCTAC 57.497 33.333 0.00 0.00 0.00 2.59
316 318 1.071605 ACTTGCGTCGATCTTCAAGC 58.928 50.000 14.51 1.74 39.45 4.01
326 328 4.441415 GTCGATCTTCAAGCCGTATAACAG 59.559 45.833 0.00 0.00 0.00 3.16
328 330 5.009710 TCGATCTTCAAGCCGTATAACAGAT 59.990 40.000 0.00 0.00 0.00 2.90
383 393 9.750125 ACTTGGATCAAATTTTGTTCTTAGTTC 57.250 29.630 16.03 3.78 31.61 3.01
400 410 6.374613 TCTTAGTTCTCTGAATGAGCTTCGTA 59.625 38.462 0.00 0.00 42.38 3.43
401 411 4.992688 AGTTCTCTGAATGAGCTTCGTAG 58.007 43.478 0.00 0.00 42.38 3.51
427 437 5.602145 TCCATCAAGGTTCCTCAAAAACATT 59.398 36.000 0.00 0.00 39.02 2.71
436 446 2.607771 CCTCAAAAACATTGCAGGTCGG 60.608 50.000 0.00 0.00 0.00 4.79
481 511 7.852945 CGATTTGAGCACTATTTCTTGAATACC 59.147 37.037 0.00 0.00 0.00 2.73
522 552 2.037901 TCAAGCACCATTTCCTTGCAA 58.962 42.857 0.00 0.00 38.81 4.08
570 600 9.528847 GCCGAATCTTTCAAATCAAAATAAAAC 57.471 29.630 0.00 0.00 0.00 2.43
654 684 5.047092 ACCATCTGCAAAAAGGGTCAAATAG 60.047 40.000 0.00 0.00 0.00 1.73
675 705 8.870075 AATAGAGCTAAACAAAAACCAGAGAT 57.130 30.769 0.00 0.00 0.00 2.75
812 851 5.758296 TCATCAATCAGTAAACTAATCGCCC 59.242 40.000 0.00 0.00 0.00 6.13
861 900 0.740868 CGCACACCTACACCCATCAG 60.741 60.000 0.00 0.00 0.00 2.90
1036 1093 3.773154 AGGGCTCCTCCTCCTCCC 61.773 72.222 0.00 0.00 37.24 4.30
1037 1094 4.095400 GGGCTCCTCCTCCTCCCA 62.095 72.222 0.00 0.00 36.96 4.37
1038 1095 2.766229 GGCTCCTCCTCCTCCCAC 60.766 72.222 0.00 0.00 0.00 4.61
1269 1326 2.125633 GAGGAGTTTCGGGCGGTC 60.126 66.667 0.00 0.00 0.00 4.79
1515 1572 0.464735 ACCTCTCGATCCTCCTCGTG 60.465 60.000 0.00 0.00 39.62 4.35
1785 1845 2.203015 CCCGTCTACGCAATGGGG 60.203 66.667 1.62 0.00 39.03 4.96
2288 2348 1.580437 GACGGCGATAGGTAGCTCC 59.420 63.158 16.62 0.00 0.00 4.70
2290 2350 0.890090 ACGGCGATAGGTAGCTCCTC 60.890 60.000 16.62 0.00 44.42 3.71
2291 2351 0.606944 CGGCGATAGGTAGCTCCTCT 60.607 60.000 0.00 0.00 44.42 3.69
2293 2353 1.170442 GCGATAGGTAGCTCCTCTCC 58.830 60.000 0.00 0.00 44.42 3.71
2294 2354 1.828979 CGATAGGTAGCTCCTCTCCC 58.171 60.000 0.00 0.00 44.42 4.30
2335 2395 1.793353 CGTGATCTGTCTCGCAGTCAG 60.793 57.143 0.00 4.79 45.23 3.51
2336 2396 0.172127 TGATCTGTCTCGCAGTCAGC 59.828 55.000 0.00 0.00 45.23 4.26
2337 2397 0.172127 GATCTGTCTCGCAGTCAGCA 59.828 55.000 5.85 0.00 46.13 4.41
2465 2526 7.037438 GCATTTGGTGTGTATCATCAGATTTT 58.963 34.615 0.00 0.00 38.49 1.82
2529 2590 0.038709 ACTTGCGTCTGTGAGCTCTC 60.039 55.000 16.19 12.36 0.00 3.20
2530 2591 0.243365 CTTGCGTCTGTGAGCTCTCT 59.757 55.000 16.19 0.00 0.00 3.10
2532 2593 1.805134 GCGTCTGTGAGCTCTCTGC 60.805 63.158 16.19 10.52 43.29 4.26
2580 2641 9.487790 GATCTTAGAATGTCATAGAAAAGAGGG 57.512 37.037 0.00 0.00 0.00 4.30
2581 2642 7.796054 TCTTAGAATGTCATAGAAAAGAGGGG 58.204 38.462 0.00 0.00 0.00 4.79
2586 2647 8.118600 AGAATGTCATAGAAAAGAGGGGAAAAT 58.881 33.333 0.00 0.00 0.00 1.82
2587 2648 7.651027 ATGTCATAGAAAAGAGGGGAAAATG 57.349 36.000 0.00 0.00 0.00 2.32
2588 2649 6.789268 TGTCATAGAAAAGAGGGGAAAATGA 58.211 36.000 0.00 0.00 0.00 2.57
2701 2762 6.567701 TTCAGTTTGAACATTAGCTTAAGGCG 60.568 38.462 4.29 0.00 37.46 5.52
2718 2780 1.154197 GCGTTGGTACTCTTTGTCCC 58.846 55.000 0.00 0.00 0.00 4.46
2723 2785 2.816411 TGGTACTCTTTGTCCCGAGAT 58.184 47.619 0.00 0.00 0.00 2.75
2747 2809 1.135517 CCGCAGTTAAAAATGTCCCCG 60.136 52.381 0.00 0.00 0.00 5.73
2857 2921 7.004555 TGTCTGCTTATCAGGAGTAAAAAGA 57.995 36.000 0.00 0.00 43.06 2.52
2860 2924 6.054860 TGCTTATCAGGAGTAAAAAGAGCT 57.945 37.500 0.00 0.00 0.00 4.09
2875 2939 9.995957 GTAAAAAGAGCTTCTCAGGATAAAATC 57.004 33.333 0.00 0.00 32.06 2.17
2892 2956 7.827729 GGATAAAATCCCCACCATGTATAGTAC 59.172 40.741 0.00 0.00 43.88 2.73
2895 2959 4.274794 TCCCCACCATGTATAGTACAGT 57.725 45.455 0.00 0.00 42.77 3.55
2896 2960 5.406570 TCCCCACCATGTATAGTACAGTA 57.593 43.478 0.00 0.00 42.77 2.74
2897 2961 5.972698 TCCCCACCATGTATAGTACAGTAT 58.027 41.667 0.00 0.00 42.77 2.12
2898 2962 7.106204 TCCCCACCATGTATAGTACAGTATA 57.894 40.000 0.00 0.00 42.77 1.47
2899 2963 7.715482 TCCCCACCATGTATAGTACAGTATAT 58.285 38.462 0.00 0.00 42.77 0.86
2900 2964 8.848830 TCCCCACCATGTATAGTACAGTATATA 58.151 37.037 0.00 0.00 42.77 0.86
2901 2965 9.132923 CCCCACCATGTATAGTACAGTATATAG 57.867 40.741 0.00 0.00 42.77 1.31
2945 3009 1.728971 GTCTGCAGAGTGACAAATCGG 59.271 52.381 18.89 0.00 33.75 4.18
2946 3010 0.445436 CTGCAGAGTGACAAATCGGC 59.555 55.000 8.42 6.98 37.19 5.54
2947 3011 0.250252 TGCAGAGTGACAAATCGGCA 60.250 50.000 11.14 11.14 42.93 5.69
2949 3013 1.135859 GCAGAGTGACAAATCGGCAAG 60.136 52.381 8.53 0.00 36.74 4.01
2950 3014 2.416747 CAGAGTGACAAATCGGCAAGA 58.583 47.619 0.00 0.00 0.00 3.02
2962 3066 2.554142 TCGGCAAGAGACAATAGCATG 58.446 47.619 0.00 0.00 0.00 4.06
2963 3067 1.600957 CGGCAAGAGACAATAGCATGG 59.399 52.381 0.00 0.00 0.00 3.66
2964 3068 2.742856 CGGCAAGAGACAATAGCATGGA 60.743 50.000 0.00 0.00 0.00 3.41
2965 3069 3.282021 GGCAAGAGACAATAGCATGGAA 58.718 45.455 0.00 0.00 0.00 3.53
2966 3070 3.887716 GGCAAGAGACAATAGCATGGAAT 59.112 43.478 0.00 0.00 0.00 3.01
2968 3072 4.261489 GCAAGAGACAATAGCATGGAATGG 60.261 45.833 0.00 0.00 46.86 3.16
2969 3073 5.128205 CAAGAGACAATAGCATGGAATGGA 58.872 41.667 0.00 0.00 46.86 3.41
2970 3074 5.579753 AGAGACAATAGCATGGAATGGAT 57.420 39.130 0.00 0.00 46.86 3.41
2971 3075 5.950023 AGAGACAATAGCATGGAATGGATT 58.050 37.500 0.00 0.00 46.86 3.01
2972 3076 7.083062 AGAGACAATAGCATGGAATGGATTA 57.917 36.000 0.00 0.00 46.86 1.75
2973 3077 7.696981 AGAGACAATAGCATGGAATGGATTAT 58.303 34.615 0.00 0.00 46.86 1.28
2974 3078 7.610692 AGAGACAATAGCATGGAATGGATTATG 59.389 37.037 0.00 0.00 46.86 1.90
2975 3079 7.464273 AGACAATAGCATGGAATGGATTATGA 58.536 34.615 0.00 0.00 46.86 2.15
2976 3080 7.946219 AGACAATAGCATGGAATGGATTATGAA 59.054 33.333 0.00 0.00 46.86 2.57
2977 3081 7.889469 ACAATAGCATGGAATGGATTATGAAC 58.111 34.615 0.00 0.00 46.86 3.18
2978 3082 7.506599 ACAATAGCATGGAATGGATTATGAACA 59.493 33.333 0.00 0.00 46.86 3.18
2979 3083 8.361889 CAATAGCATGGAATGGATTATGAACAA 58.638 33.333 0.00 0.00 46.86 2.83
2980 3084 6.401047 AGCATGGAATGGATTATGAACAAG 57.599 37.500 0.00 0.00 46.86 3.16
2981 3085 6.131264 AGCATGGAATGGATTATGAACAAGA 58.869 36.000 0.00 0.00 46.86 3.02
2982 3086 6.264744 AGCATGGAATGGATTATGAACAAGAG 59.735 38.462 0.00 0.00 46.86 2.85
2983 3087 6.444633 CATGGAATGGATTATGAACAAGAGC 58.555 40.000 0.00 0.00 41.79 4.09
2984 3088 5.759059 TGGAATGGATTATGAACAAGAGCT 58.241 37.500 0.00 0.00 0.00 4.09
2985 3089 6.189859 TGGAATGGATTATGAACAAGAGCTT 58.810 36.000 0.00 0.00 0.00 3.74
2986 3090 6.664816 TGGAATGGATTATGAACAAGAGCTTT 59.335 34.615 0.00 0.00 0.00 3.51
2987 3091 7.148018 TGGAATGGATTATGAACAAGAGCTTTC 60.148 37.037 0.00 0.00 0.00 2.62
2988 3092 7.067981 GGAATGGATTATGAACAAGAGCTTTCT 59.932 37.037 0.00 0.00 0.00 2.52
2989 3093 7.951347 ATGGATTATGAACAAGAGCTTTCTT 57.049 32.000 0.00 0.00 0.00 2.52
2990 3094 7.765695 TGGATTATGAACAAGAGCTTTCTTT 57.234 32.000 0.00 0.00 0.00 2.52
2991 3095 8.181904 TGGATTATGAACAAGAGCTTTCTTTT 57.818 30.769 0.00 0.00 0.00 2.27
2992 3096 8.641541 TGGATTATGAACAAGAGCTTTCTTTTT 58.358 29.630 0.00 0.00 0.00 1.94
3012 3116 6.494893 TTTTTCGAGTTGGTATGATCAAGG 57.505 37.500 0.00 0.00 0.00 3.61
3039 3143 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3041 3145 2.023695 AGTACTCCCTCCGTCCCATAAA 60.024 50.000 0.00 0.00 0.00 1.40
3042 3146 2.191981 ACTCCCTCCGTCCCATAAAT 57.808 50.000 0.00 0.00 0.00 1.40
3043 3147 3.339713 ACTCCCTCCGTCCCATAAATA 57.660 47.619 0.00 0.00 0.00 1.40
3077 3181 8.764287 ACATTTTATCAAACTAACAAAGCTTGC 58.236 29.630 0.00 0.00 32.34 4.01
3078 3182 8.763356 CATTTTATCAAACTAACAAAGCTTGCA 58.237 29.630 0.00 0.00 32.34 4.08
3079 3183 8.709386 TTTTATCAAACTAACAAAGCTTGCAA 57.291 26.923 0.00 0.00 32.34 4.08
3080 3184 8.709386 TTTATCAAACTAACAAAGCTTGCAAA 57.291 26.923 0.00 0.00 32.34 3.68
3081 3185 8.709386 TTATCAAACTAACAAAGCTTGCAAAA 57.291 26.923 0.00 0.00 32.34 2.44
3082 3186 7.608308 ATCAAACTAACAAAGCTTGCAAAAA 57.392 28.000 0.00 0.00 32.34 1.94
3083 3187 6.826612 TCAAACTAACAAAGCTTGCAAAAAC 58.173 32.000 0.00 0.00 32.34 2.43
3084 3188 6.425114 TCAAACTAACAAAGCTTGCAAAAACA 59.575 30.769 0.00 0.00 32.34 2.83
3085 3189 6.983474 AACTAACAAAGCTTGCAAAAACAT 57.017 29.167 0.00 0.00 0.00 2.71
3086 3190 6.588348 ACTAACAAAGCTTGCAAAAACATC 57.412 33.333 0.00 0.00 0.00 3.06
3087 3191 4.519191 AACAAAGCTTGCAAAAACATCG 57.481 36.364 0.00 0.00 0.00 3.84
3088 3192 3.520569 ACAAAGCTTGCAAAAACATCGT 58.479 36.364 0.00 0.00 0.00 3.73
3089 3193 4.677584 ACAAAGCTTGCAAAAACATCGTA 58.322 34.783 0.00 0.00 0.00 3.43
3090 3194 4.502645 ACAAAGCTTGCAAAAACATCGTAC 59.497 37.500 0.00 0.00 0.00 3.67
3091 3195 3.980646 AGCTTGCAAAAACATCGTACA 57.019 38.095 0.00 0.00 0.00 2.90
3092 3196 4.503741 AGCTTGCAAAAACATCGTACAT 57.496 36.364 0.00 0.00 0.00 2.29
3093 3197 4.870363 AGCTTGCAAAAACATCGTACATT 58.130 34.783 0.00 0.00 0.00 2.71
3094 3198 6.007936 AGCTTGCAAAAACATCGTACATTA 57.992 33.333 0.00 0.00 0.00 1.90
3095 3199 6.620678 AGCTTGCAAAAACATCGTACATTAT 58.379 32.000 0.00 0.00 0.00 1.28
3096 3200 6.527722 AGCTTGCAAAAACATCGTACATTATG 59.472 34.615 0.00 0.00 0.00 1.90
3129 3233 4.810790 AGTATATAGCAACAGATCACGGC 58.189 43.478 0.00 0.00 0.00 5.68
3131 3235 2.698855 ATAGCAACAGATCACGGCTT 57.301 45.000 6.52 0.00 36.10 4.35
3134 3238 2.283298 AGCAACAGATCACGGCTTATG 58.717 47.619 0.00 0.00 0.00 1.90
3137 3241 3.485877 GCAACAGATCACGGCTTATGAAC 60.486 47.826 0.00 0.00 0.00 3.18
3157 3276 6.629128 TGAACAAGAAATTGCAGAACAGAAA 58.371 32.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.669211 GGTTAGATGGAGCGCGGATAC 60.669 57.143 8.83 0.00 0.00 2.24
4 5 0.601558 GGTTAGATGGAGCGCGGATA 59.398 55.000 8.83 0.00 0.00 2.59
5 6 1.367840 GGTTAGATGGAGCGCGGAT 59.632 57.895 8.83 0.00 0.00 4.18
6 7 2.792947 GGGTTAGATGGAGCGCGGA 61.793 63.158 8.83 0.00 0.00 5.54
7 8 2.280186 GGGTTAGATGGAGCGCGG 60.280 66.667 8.83 0.00 0.00 6.46
8 9 1.592669 CAGGGTTAGATGGAGCGCG 60.593 63.158 0.00 0.00 0.00 6.86
9 10 0.530870 GACAGGGTTAGATGGAGCGC 60.531 60.000 0.00 0.00 0.00 5.92
10 11 0.824109 TGACAGGGTTAGATGGAGCG 59.176 55.000 0.00 0.00 0.00 5.03
11 12 2.224402 GGATGACAGGGTTAGATGGAGC 60.224 54.545 0.00 0.00 0.00 4.70
12 13 3.041211 TGGATGACAGGGTTAGATGGAG 58.959 50.000 0.00 0.00 0.00 3.86
13 14 3.129262 TGGATGACAGGGTTAGATGGA 57.871 47.619 0.00 0.00 0.00 3.41
14 15 3.931907 TTGGATGACAGGGTTAGATGG 57.068 47.619 0.00 0.00 0.00 3.51
15 16 4.396166 GTGTTTGGATGACAGGGTTAGATG 59.604 45.833 0.00 0.00 0.00 2.90
16 17 4.567747 GGTGTTTGGATGACAGGGTTAGAT 60.568 45.833 0.00 0.00 0.00 1.98
17 18 3.244770 GGTGTTTGGATGACAGGGTTAGA 60.245 47.826 0.00 0.00 0.00 2.10
18 19 3.081804 GGTGTTTGGATGACAGGGTTAG 58.918 50.000 0.00 0.00 0.00 2.34
19 20 2.714250 AGGTGTTTGGATGACAGGGTTA 59.286 45.455 0.00 0.00 0.00 2.85
20 21 1.499007 AGGTGTTTGGATGACAGGGTT 59.501 47.619 0.00 0.00 0.00 4.11
21 22 1.073923 GAGGTGTTTGGATGACAGGGT 59.926 52.381 0.00 0.00 0.00 4.34
22 23 1.352352 AGAGGTGTTTGGATGACAGGG 59.648 52.381 0.00 0.00 0.00 4.45
23 24 2.867109 AGAGGTGTTTGGATGACAGG 57.133 50.000 0.00 0.00 0.00 4.00
24 25 4.494350 CAAAGAGGTGTTTGGATGACAG 57.506 45.455 0.00 0.00 34.34 3.51
38 39 6.166982 CCTGAACTAACTCTAACCAAAGAGG 58.833 44.000 5.90 0.00 46.11 3.69
40 41 5.605488 ACCCTGAACTAACTCTAACCAAAGA 59.395 40.000 0.00 0.00 0.00 2.52
41 42 5.866207 ACCCTGAACTAACTCTAACCAAAG 58.134 41.667 0.00 0.00 0.00 2.77
42 43 5.899631 ACCCTGAACTAACTCTAACCAAA 57.100 39.130 0.00 0.00 0.00 3.28
43 44 5.899631 AACCCTGAACTAACTCTAACCAA 57.100 39.130 0.00 0.00 0.00 3.67
44 45 6.999705 TTAACCCTGAACTAACTCTAACCA 57.000 37.500 0.00 0.00 0.00 3.67
45 46 8.098912 TGAATTAACCCTGAACTAACTCTAACC 58.901 37.037 0.00 0.00 0.00 2.85
46 47 9.152595 CTGAATTAACCCTGAACTAACTCTAAC 57.847 37.037 0.00 0.00 0.00 2.34
47 48 8.319146 CCTGAATTAACCCTGAACTAACTCTAA 58.681 37.037 0.00 0.00 0.00 2.10
48 49 7.093024 CCCTGAATTAACCCTGAACTAACTCTA 60.093 40.741 0.00 0.00 0.00 2.43
49 50 6.296489 CCCTGAATTAACCCTGAACTAACTCT 60.296 42.308 0.00 0.00 0.00 3.24
50 51 5.880887 CCCTGAATTAACCCTGAACTAACTC 59.119 44.000 0.00 0.00 0.00 3.01
51 52 5.312443 ACCCTGAATTAACCCTGAACTAACT 59.688 40.000 0.00 0.00 0.00 2.24
52 53 5.567430 ACCCTGAATTAACCCTGAACTAAC 58.433 41.667 0.00 0.00 0.00 2.34
53 54 5.853572 ACCCTGAATTAACCCTGAACTAA 57.146 39.130 0.00 0.00 0.00 2.24
54 55 5.853572 AACCCTGAATTAACCCTGAACTA 57.146 39.130 0.00 0.00 0.00 2.24
55 56 4.741928 AACCCTGAATTAACCCTGAACT 57.258 40.909 0.00 0.00 0.00 3.01
56 57 5.812286 TCTAACCCTGAATTAACCCTGAAC 58.188 41.667 0.00 0.00 0.00 3.18
57 58 6.457159 TTCTAACCCTGAATTAACCCTGAA 57.543 37.500 0.00 0.00 0.00 3.02
58 59 6.447084 AGATTCTAACCCTGAATTAACCCTGA 59.553 38.462 0.00 0.00 34.67 3.86
59 60 6.663734 AGATTCTAACCCTGAATTAACCCTG 58.336 40.000 0.00 0.00 34.67 4.45
60 61 6.910259 AGATTCTAACCCTGAATTAACCCT 57.090 37.500 0.00 0.00 34.67 4.34
61 62 8.272889 AGTTAGATTCTAACCCTGAATTAACCC 58.727 37.037 25.81 3.69 34.67 4.11
62 63 9.327628 GAGTTAGATTCTAACCCTGAATTAACC 57.672 37.037 25.81 4.05 34.67 2.85
75 76 9.118300 CGGTTAGAGGTTAGAGTTAGATTCTAA 57.882 37.037 1.90 1.90 35.39 2.10
76 77 8.489489 TCGGTTAGAGGTTAGAGTTAGATTCTA 58.511 37.037 0.00 0.00 0.00 2.10
77 78 7.344913 TCGGTTAGAGGTTAGAGTTAGATTCT 58.655 38.462 0.00 0.00 0.00 2.40
78 79 7.565323 TCGGTTAGAGGTTAGAGTTAGATTC 57.435 40.000 0.00 0.00 0.00 2.52
79 80 7.571080 CTCGGTTAGAGGTTAGAGTTAGATT 57.429 40.000 0.00 0.00 43.20 2.40
80 81 7.118060 AACTCGGTTAGAGGTTAGAGTTAGAT 58.882 38.462 6.84 0.00 46.78 1.98
81 82 6.479884 AACTCGGTTAGAGGTTAGAGTTAGA 58.520 40.000 6.84 0.00 46.78 2.10
82 83 6.756299 AACTCGGTTAGAGGTTAGAGTTAG 57.244 41.667 6.84 0.00 46.78 2.34
83 84 7.624549 TCTAACTCGGTTAGAGGTTAGAGTTA 58.375 38.462 17.33 13.10 46.78 2.24
84 85 6.479884 TCTAACTCGGTTAGAGGTTAGAGTT 58.520 40.000 17.33 12.32 46.78 3.01
85 86 6.059787 TCTAACTCGGTTAGAGGTTAGAGT 57.940 41.667 17.33 0.00 46.78 3.24
95 96 6.860080 TGTTTGGATACTCTAACTCGGTTAG 58.140 40.000 14.20 14.20 44.65 2.34
96 97 6.127535 CCTGTTTGGATACTCTAACTCGGTTA 60.128 42.308 0.00 0.00 38.35 2.85
97 98 5.337330 CCTGTTTGGATACTCTAACTCGGTT 60.337 44.000 0.00 0.00 38.35 4.44
98 99 4.159879 CCTGTTTGGATACTCTAACTCGGT 59.840 45.833 0.00 0.00 38.35 4.69
99 100 4.441634 CCCTGTTTGGATACTCTAACTCGG 60.442 50.000 0.00 0.00 38.35 4.63
100 101 4.683832 CCCTGTTTGGATACTCTAACTCG 58.316 47.826 0.00 0.00 38.35 4.18
101 102 4.443621 GCCCTGTTTGGATACTCTAACTC 58.556 47.826 0.00 0.00 38.35 3.01
102 103 3.200165 GGCCCTGTTTGGATACTCTAACT 59.800 47.826 0.00 0.00 38.35 2.24
103 104 3.542648 GGCCCTGTTTGGATACTCTAAC 58.457 50.000 0.00 0.00 38.35 2.34
104 105 2.508300 GGGCCCTGTTTGGATACTCTAA 59.492 50.000 17.04 0.00 38.35 2.10
105 106 2.124411 GGGCCCTGTTTGGATACTCTA 58.876 52.381 17.04 0.00 38.35 2.43
106 107 0.919710 GGGCCCTGTTTGGATACTCT 59.080 55.000 17.04 0.00 38.35 3.24
107 108 0.919710 AGGGCCCTGTTTGGATACTC 59.080 55.000 28.05 0.00 38.35 2.59
108 109 1.005924 CAAGGGCCCTGTTTGGATACT 59.994 52.381 29.50 1.08 38.35 2.12
109 110 1.005450 TCAAGGGCCCTGTTTGGATAC 59.995 52.381 29.50 0.00 38.35 2.24
110 111 1.377690 TCAAGGGCCCTGTTTGGATA 58.622 50.000 29.50 0.71 38.35 2.59
111 112 0.712380 ATCAAGGGCCCTGTTTGGAT 59.288 50.000 29.50 19.73 38.35 3.41
112 113 0.251742 CATCAAGGGCCCTGTTTGGA 60.252 55.000 29.50 18.30 38.35 3.53
113 114 0.542702 ACATCAAGGGCCCTGTTTGG 60.543 55.000 29.50 16.89 0.00 3.28
114 115 0.604578 CACATCAAGGGCCCTGTTTG 59.395 55.000 29.50 24.11 0.00 2.93
115 116 0.542702 CCACATCAAGGGCCCTGTTT 60.543 55.000 29.50 6.93 0.00 2.83
116 117 1.077265 CCACATCAAGGGCCCTGTT 59.923 57.895 29.50 7.92 0.00 3.16
117 118 2.765969 CCACATCAAGGGCCCTGT 59.234 61.111 29.50 17.90 0.00 4.00
118 119 2.757099 GCCACATCAAGGGCCCTG 60.757 66.667 29.50 19.84 44.53 4.45
123 124 1.673168 GAAGCTAGCCACATCAAGGG 58.327 55.000 12.13 0.00 0.00 3.95
127 128 1.630369 AGTTGGAAGCTAGCCACATCA 59.370 47.619 12.13 0.29 34.56 3.07
146 147 1.937278 CACTCTAGCAGCACCATCAG 58.063 55.000 0.00 0.00 0.00 2.90
179 180 1.019278 CGTTGGCGTCATGGCTACTT 61.019 55.000 0.00 0.00 44.61 2.24
181 182 2.461110 CCGTTGGCGTCATGGCTAC 61.461 63.158 0.00 0.00 45.14 3.58
182 183 2.125310 CCGTTGGCGTCATGGCTA 60.125 61.111 0.00 0.00 45.14 3.93
184 185 4.101790 CACCGTTGGCGTCATGGC 62.102 66.667 8.59 0.00 45.12 4.40
185 186 4.101790 GCACCGTTGGCGTCATGG 62.102 66.667 7.22 7.22 36.15 3.66
186 187 2.689785 ATGCACCGTTGGCGTCATG 61.690 57.895 0.00 0.00 36.15 3.07
187 188 2.359850 ATGCACCGTTGGCGTCAT 60.360 55.556 0.00 0.00 36.15 3.06
188 189 3.353029 CATGCACCGTTGGCGTCA 61.353 61.111 0.00 0.00 36.15 4.35
189 190 4.101790 CCATGCACCGTTGGCGTC 62.102 66.667 0.00 0.00 36.15 5.19
190 191 2.813226 ATACCATGCACCGTTGGCGT 62.813 55.000 3.91 0.00 36.41 5.68
191 192 1.653094 AATACCATGCACCGTTGGCG 61.653 55.000 3.91 0.00 36.41 5.69
192 193 1.333619 CTAATACCATGCACCGTTGGC 59.666 52.381 3.91 0.00 36.41 4.52
193 194 2.639065 ACTAATACCATGCACCGTTGG 58.361 47.619 2.41 2.41 39.02 3.77
194 195 5.295787 ACATAACTAATACCATGCACCGTTG 59.704 40.000 0.00 0.00 0.00 4.10
195 196 5.295787 CACATAACTAATACCATGCACCGTT 59.704 40.000 0.00 0.00 0.00 4.44
196 197 4.814234 CACATAACTAATACCATGCACCGT 59.186 41.667 0.00 0.00 0.00 4.83
197 198 4.814234 ACACATAACTAATACCATGCACCG 59.186 41.667 0.00 0.00 0.00 4.94
198 199 6.094881 ACAACACATAACTAATACCATGCACC 59.905 38.462 0.00 0.00 0.00 5.01
199 200 7.083875 ACAACACATAACTAATACCATGCAC 57.916 36.000 0.00 0.00 0.00 4.57
200 201 7.413548 CGAACAACACATAACTAATACCATGCA 60.414 37.037 0.00 0.00 0.00 3.96
201 202 6.905076 CGAACAACACATAACTAATACCATGC 59.095 38.462 0.00 0.00 0.00 4.06
202 203 7.065324 ACCGAACAACACATAACTAATACCATG 59.935 37.037 0.00 0.00 0.00 3.66
203 204 7.065324 CACCGAACAACACATAACTAATACCAT 59.935 37.037 0.00 0.00 0.00 3.55
204 205 6.369340 CACCGAACAACACATAACTAATACCA 59.631 38.462 0.00 0.00 0.00 3.25
205 206 6.673796 GCACCGAACAACACATAACTAATACC 60.674 42.308 0.00 0.00 0.00 2.73
206 207 6.245724 GCACCGAACAACACATAACTAATAC 58.754 40.000 0.00 0.00 0.00 1.89
207 208 5.352016 GGCACCGAACAACACATAACTAATA 59.648 40.000 0.00 0.00 0.00 0.98
208 209 4.155280 GGCACCGAACAACACATAACTAAT 59.845 41.667 0.00 0.00 0.00 1.73
209 210 3.499157 GGCACCGAACAACACATAACTAA 59.501 43.478 0.00 0.00 0.00 2.24
210 211 3.068560 GGCACCGAACAACACATAACTA 58.931 45.455 0.00 0.00 0.00 2.24
211 212 1.877443 GGCACCGAACAACACATAACT 59.123 47.619 0.00 0.00 0.00 2.24
212 213 1.399215 CGGCACCGAACAACACATAAC 60.399 52.381 2.01 0.00 42.83 1.89
316 318 7.747888 TCAAACATGAAACATCTGTTATACGG 58.252 34.615 0.00 0.00 37.25 4.02
326 328 7.064966 GGGAAATTGGATCAAACATGAAACATC 59.935 37.037 0.00 0.00 0.00 3.06
328 330 6.229733 GGGAAATTGGATCAAACATGAAACA 58.770 36.000 0.00 0.00 0.00 2.83
400 410 1.661463 TGAGGAACCTTGATGGAGCT 58.339 50.000 0.00 0.00 39.71 4.09
401 411 2.496899 TTGAGGAACCTTGATGGAGC 57.503 50.000 0.00 0.00 39.71 4.70
403 413 4.541705 TGTTTTTGAGGAACCTTGATGGA 58.458 39.130 0.00 0.00 39.71 3.41
427 437 0.104855 GATGCTCATACCGACCTGCA 59.895 55.000 0.00 0.00 34.88 4.41
436 446 3.588955 TCGCCACATATGATGCTCATAC 58.411 45.455 10.38 0.00 41.62 2.39
447 457 2.923121 AGTGCTCAAATCGCCACATAT 58.077 42.857 0.00 0.00 0.00 1.78
456 466 8.897752 AGGTATTCAAGAAATAGTGCTCAAATC 58.102 33.333 0.00 0.00 30.39 2.17
481 511 6.317789 TGACTTTAGGCAGAAATTTGTCAG 57.682 37.500 0.00 0.00 0.00 3.51
522 552 6.460123 CGGCCAATACTAGCTTCAATGATTTT 60.460 38.462 2.24 0.00 0.00 1.82
570 600 3.837213 AGTGGACGATGCTTGATTTTG 57.163 42.857 0.00 0.00 0.00 2.44
593 623 8.907222 TTAGTAATTACGGACAAGTTCCTTTT 57.093 30.769 9.91 0.00 43.25 2.27
624 654 3.160269 CCTTTTTGCAGATGGTCCTTCT 58.840 45.455 1.33 1.33 0.00 2.85
637 667 4.790765 AGCTCTATTTGACCCTTTTTGC 57.209 40.909 0.00 0.00 0.00 3.68
654 684 8.184848 GGAATATCTCTGGTTTTTGTTTAGCTC 58.815 37.037 0.00 0.00 0.00 4.09
675 705 9.486123 TGGTGATATTCTTTTGGAATTGGAATA 57.514 29.630 0.00 0.00 41.42 1.75
715 747 4.919774 TTAGTTTAATGGTGGCCTCTGA 57.080 40.909 3.32 0.00 0.00 3.27
718 750 6.071616 TGTTGAATTAGTTTAATGGTGGCCTC 60.072 38.462 3.32 0.00 0.00 4.70
724 756 6.266558 TGCACCTGTTGAATTAGTTTAATGGT 59.733 34.615 0.00 0.00 0.00 3.55
812 851 0.923358 TATGGGGTTGTGCTTAGGGG 59.077 55.000 0.00 0.00 0.00 4.79
861 900 4.264638 GGTGCGGTGTGGTGTTGC 62.265 66.667 0.00 0.00 0.00 4.17
1036 1093 2.663196 GAACGGGGAGTGGGAGTG 59.337 66.667 0.00 0.00 0.00 3.51
1037 1094 2.995574 CGAACGGGGAGTGGGAGT 60.996 66.667 0.00 0.00 0.00 3.85
1038 1095 4.452733 GCGAACGGGGAGTGGGAG 62.453 72.222 0.00 0.00 0.00 4.30
1177 1234 3.465403 CTCCCCGTCCCTCAGCTG 61.465 72.222 7.63 7.63 0.00 4.24
1449 1506 3.144120 CTGGCCCTCGTGGATCTCG 62.144 68.421 4.76 0.00 35.39 4.04
1632 1689 1.215679 AGGAGGAGGAGGACGAGGAA 61.216 60.000 0.00 0.00 0.00 3.36
2116 2176 2.671070 CAGGCCGTCCTTCATGGT 59.329 61.111 0.00 0.00 41.93 3.55
2271 2331 3.760917 GGAGCTACCTATCGCCGT 58.239 61.111 0.00 0.00 35.41 5.68
2288 2348 0.250166 AAAAACCACGGACGGGAGAG 60.250 55.000 0.00 0.00 0.00 3.20
2289 2349 0.533308 CAAAAACCACGGACGGGAGA 60.533 55.000 0.00 0.00 0.00 3.71
2290 2350 0.533308 TCAAAAACCACGGACGGGAG 60.533 55.000 0.00 0.00 0.00 4.30
2291 2351 0.108963 ATCAAAAACCACGGACGGGA 59.891 50.000 0.00 0.00 0.00 5.14
2293 2353 1.069500 GTGATCAAAAACCACGGACGG 60.069 52.381 0.00 0.00 0.00 4.79
2294 2354 1.069500 GGTGATCAAAAACCACGGACG 60.069 52.381 0.00 0.00 36.41 4.79
2487 2548 3.925238 AAGAATTAGCCGCGCGCG 61.925 61.111 43.73 43.73 44.76 6.86
2538 2599 0.869454 GATCAGAGCAAGCGACCTCG 60.869 60.000 0.00 0.00 43.27 4.63
2705 2766 4.299978 GCATATCTCGGGACAAAGAGTAC 58.700 47.826 0.00 0.00 0.00 2.73
2718 2780 4.530094 TTTTTAACTGCGGCATATCTCG 57.470 40.909 1.75 0.00 0.00 4.04
2723 2785 3.129638 GGGACATTTTTAACTGCGGCATA 59.870 43.478 1.75 0.00 0.00 3.14
2807 2871 4.899352 ATCCACATATAGAGAACTGGGC 57.101 45.455 0.00 0.00 0.00 5.36
2875 2939 7.973048 ATATACTGTACTATACATGGTGGGG 57.027 40.000 0.00 0.00 38.15 4.96
2910 2974 7.493971 CACTCTGCAGACTGCTTTATTAGTAAT 59.506 37.037 26.94 0.17 45.31 1.89
2914 2978 5.290643 GTCACTCTGCAGACTGCTTTATTAG 59.709 44.000 26.94 15.24 45.31 1.73
2923 2987 2.411069 CGATTTGTCACTCTGCAGACTG 59.589 50.000 13.74 14.55 35.81 3.51
2945 3009 4.261489 CCATTCCATGCTATTGTCTCTTGC 60.261 45.833 0.00 0.00 0.00 4.01
2946 3010 5.128205 TCCATTCCATGCTATTGTCTCTTG 58.872 41.667 0.00 0.00 0.00 3.02
2947 3011 5.378230 TCCATTCCATGCTATTGTCTCTT 57.622 39.130 0.00 0.00 0.00 2.85
2949 3013 7.609146 TCATAATCCATTCCATGCTATTGTCTC 59.391 37.037 0.00 0.00 0.00 3.36
2950 3014 7.464273 TCATAATCCATTCCATGCTATTGTCT 58.536 34.615 0.00 0.00 0.00 3.41
2962 3066 6.705863 AAGCTCTTGTTCATAATCCATTCC 57.294 37.500 0.00 0.00 0.00 3.01
2963 3067 7.994194 AGAAAGCTCTTGTTCATAATCCATTC 58.006 34.615 0.00 0.00 0.00 2.67
2964 3068 7.951347 AGAAAGCTCTTGTTCATAATCCATT 57.049 32.000 0.00 0.00 0.00 3.16
2965 3069 7.951347 AAGAAAGCTCTTGTTCATAATCCAT 57.049 32.000 0.00 0.00 40.54 3.41
2966 3070 7.765695 AAAGAAAGCTCTTGTTCATAATCCA 57.234 32.000 0.00 0.00 41.23 3.41
2989 3093 5.414454 CCCTTGATCATACCAACTCGAAAAA 59.586 40.000 0.00 0.00 0.00 1.94
2990 3094 4.941263 CCCTTGATCATACCAACTCGAAAA 59.059 41.667 0.00 0.00 0.00 2.29
2991 3095 4.513442 CCCTTGATCATACCAACTCGAAA 58.487 43.478 0.00 0.00 0.00 3.46
2992 3096 3.681594 GCCCTTGATCATACCAACTCGAA 60.682 47.826 0.00 0.00 0.00 3.71
2993 3097 2.158957 GCCCTTGATCATACCAACTCGA 60.159 50.000 0.00 0.00 0.00 4.04
2994 3098 2.158900 AGCCCTTGATCATACCAACTCG 60.159 50.000 0.00 0.00 0.00 4.18
2995 3099 3.567478 AGCCCTTGATCATACCAACTC 57.433 47.619 0.00 0.00 0.00 3.01
2996 3100 3.780294 TGTAGCCCTTGATCATACCAACT 59.220 43.478 0.00 0.00 0.00 3.16
2997 3101 4.150897 TGTAGCCCTTGATCATACCAAC 57.849 45.455 0.00 0.00 0.00 3.77
2998 3102 4.853468 TTGTAGCCCTTGATCATACCAA 57.147 40.909 0.00 0.00 0.00 3.67
2999 3103 4.227300 ACTTTGTAGCCCTTGATCATACCA 59.773 41.667 0.00 0.00 0.00 3.25
3000 3104 4.781934 ACTTTGTAGCCCTTGATCATACC 58.218 43.478 0.00 0.00 0.00 2.73
3001 3105 6.583562 AGTACTTTGTAGCCCTTGATCATAC 58.416 40.000 0.00 0.00 0.00 2.39
3012 3116 1.136500 CGGAGGGAGTACTTTGTAGCC 59.864 57.143 0.00 0.00 0.00 3.93
3058 3162 7.118971 TGTTTTTGCAAGCTTTGTTAGTTTGAT 59.881 29.630 0.00 0.00 45.02 2.57
3059 3163 6.425114 TGTTTTTGCAAGCTTTGTTAGTTTGA 59.575 30.769 0.00 0.00 45.02 2.69
3065 3169 5.105752 ACGATGTTTTTGCAAGCTTTGTTA 58.894 33.333 0.00 0.00 0.00 2.41
3066 3170 3.932089 ACGATGTTTTTGCAAGCTTTGTT 59.068 34.783 0.00 0.00 0.00 2.83
3067 3171 3.520569 ACGATGTTTTTGCAAGCTTTGT 58.479 36.364 0.00 0.72 0.00 2.83
3068 3172 4.502282 TGTACGATGTTTTTGCAAGCTTTG 59.498 37.500 0.00 0.00 0.00 2.77
3069 3173 4.677584 TGTACGATGTTTTTGCAAGCTTT 58.322 34.783 0.00 0.00 0.00 3.51
3070 3174 4.300189 TGTACGATGTTTTTGCAAGCTT 57.700 36.364 0.00 0.00 0.00 3.74
3071 3175 3.980646 TGTACGATGTTTTTGCAAGCT 57.019 38.095 0.00 0.00 0.00 3.74
3072 3176 6.237542 CCATAATGTACGATGTTTTTGCAAGC 60.238 38.462 0.00 0.00 0.00 4.01
3073 3177 6.253298 CCCATAATGTACGATGTTTTTGCAAG 59.747 38.462 0.00 0.00 0.00 4.01
3074 3178 6.071896 TCCCATAATGTACGATGTTTTTGCAA 60.072 34.615 0.00 0.00 0.00 4.08
3075 3179 5.416013 TCCCATAATGTACGATGTTTTTGCA 59.584 36.000 0.00 0.00 0.00 4.08
3076 3180 5.741982 GTCCCATAATGTACGATGTTTTTGC 59.258 40.000 0.00 0.00 0.00 3.68
3077 3181 5.963004 CGTCCCATAATGTACGATGTTTTTG 59.037 40.000 0.00 0.00 37.53 2.44
3078 3182 5.065474 CCGTCCCATAATGTACGATGTTTTT 59.935 40.000 0.00 0.00 37.53 1.94
3079 3183 4.573201 CCGTCCCATAATGTACGATGTTTT 59.427 41.667 0.00 0.00 37.53 2.43
3080 3184 4.124238 CCGTCCCATAATGTACGATGTTT 58.876 43.478 0.00 0.00 37.53 2.83
3081 3185 3.385433 TCCGTCCCATAATGTACGATGTT 59.615 43.478 0.00 0.00 37.53 2.71
3082 3186 2.960384 TCCGTCCCATAATGTACGATGT 59.040 45.455 0.00 0.00 37.53 3.06
3083 3187 3.575630 CTCCGTCCCATAATGTACGATG 58.424 50.000 0.00 0.00 37.53 3.84
3084 3188 2.561419 CCTCCGTCCCATAATGTACGAT 59.439 50.000 0.00 0.00 37.53 3.73
3085 3189 1.958579 CCTCCGTCCCATAATGTACGA 59.041 52.381 0.00 0.00 37.53 3.43
3086 3190 1.000506 CCCTCCGTCCCATAATGTACG 59.999 57.143 0.00 0.00 35.20 3.67
3087 3191 2.299297 CTCCCTCCGTCCCATAATGTAC 59.701 54.545 0.00 0.00 0.00 2.90
3088 3192 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3089 3193 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3090 3194 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3091 3195 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3092 3196 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
3093 3197 4.386088 GCTATATACTCCCTCCGTCCCATA 60.386 50.000 0.00 0.00 0.00 2.74
3094 3198 3.627747 GCTATATACTCCCTCCGTCCCAT 60.628 52.174 0.00 0.00 0.00 4.00
3095 3199 2.291411 GCTATATACTCCCTCCGTCCCA 60.291 54.545 0.00 0.00 0.00 4.37
3096 3200 2.291411 TGCTATATACTCCCTCCGTCCC 60.291 54.545 0.00 0.00 0.00 4.46
3129 3233 8.077991 TCTGTTCTGCAATTTCTTGTTCATAAG 58.922 33.333 0.00 0.00 34.69 1.73
3131 3235 7.509141 TCTGTTCTGCAATTTCTTGTTCATA 57.491 32.000 0.00 0.00 34.69 2.15
3134 3238 6.292008 GCTTTCTGTTCTGCAATTTCTTGTTC 60.292 38.462 0.00 0.00 34.69 3.18
3137 3241 5.045215 TGCTTTCTGTTCTGCAATTTCTTG 58.955 37.500 0.00 0.00 35.36 3.02
3157 3276 5.066505 GGTATTTGGATTCAGTCGAATTGCT 59.933 40.000 0.00 0.00 42.06 3.91


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

AutoCloner maintained by Alex Coulton.