Multiple sequence alignment - TraesCS4B01G383900

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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 TraesCS4B01G383900 chr4B 100.000 3186 0 0 1 3186 663461860 663465045 0.000000e+00 5884.0
1 TraesCS4B01G383900 chr4B 94.862 1635 79 3 706 2336 662720776 662719143 0.000000e+00 2549.0
2 TraesCS4B01G383900 chr4B 92.084 1819 107 9 706 2521 663520414 663522198 0.000000e+00 2527.0
3 TraesCS4B01G383900 chr4B 91.904 877 66 4 706 1578 663621317 663622192 0.000000e+00 1221.0
4 TraesCS4B01G383900 chr4B 92.047 679 52 2 1599 2276 663629235 663629912 0.000000e+00 953.0
5 TraesCS4B01G383900 chr4B 90.741 540 38 10 2650 3186 663522349 663522879 0.000000e+00 710.0
6 TraesCS4B01G383900 chr4B 92.013 313 22 3 2650 2962 662714683 662714374 1.360000e-118 436.0
7 TraesCS4B01G383900 chr4B 91.346 208 18 0 2961 3168 662714153 662713946 5.200000e-73 285.0
8 TraesCS4B01G383900 chr4B 90.206 194 8 5 2443 2636 662714924 662714742 3.180000e-60 243.0
9 TraesCS4B01G383900 chr4B 96.429 84 2 1 2361 2443 662718546 662718463 1.540000e-28 137.0
10 TraesCS4B01G383900 chr4B 91.781 73 6 0 2974 3046 663551608 663551680 5.620000e-18 102.0
11 TraesCS4B01G383900 chr4B 90.411 73 7 0 2974 3046 663543679 663543751 2.620000e-16 97.1
12 TraesCS4B01G383900 chr4B 93.651 63 3 1 2974 3036 662931740 662931801 3.380000e-15 93.5
13 TraesCS4B01G383900 chr5A 85.766 548 41 5 180 703 406498202 406497668 2.160000e-151 545.0
14 TraesCS4B01G383900 chr5A 85.273 550 41 10 180 703 406499449 406498914 6.050000e-147 531.0
15 TraesCS4B01G383900 chr5A 85.413 521 41 7 180 678 406496980 406496473 2.840000e-140 508.0
16 TraesCS4B01G383900 chr5B 88.136 413 47 1 270 682 120239187 120238777 1.030000e-134 490.0
17 TraesCS4B01G383900 chr5B 90.909 121 11 0 64 184 136048361 136048481 2.540000e-36 163.0
18 TraesCS4B01G383900 chr7B 74.495 1188 240 45 1038 2189 733461507 733460347 1.040000e-124 457.0
19 TraesCS4B01G383900 chr6D 85.294 442 55 7 271 707 25995078 25995514 6.270000e-122 448.0
20 TraesCS4B01G383900 chr5D 89.055 201 20 2 504 703 11015266 11015465 6.820000e-62 248.0
21 TraesCS4B01G383900 chr5D 88.000 200 22 2 504 703 11172307 11172504 5.310000e-58 235.0
22 TraesCS4B01G383900 chr3D 90.476 189 17 1 515 703 533413161 533413348 6.820000e-62 248.0
23 TraesCS4B01G383900 chr3D 94.872 39 2 0 279 317 479617758 479617796 9.540000e-06 62.1
24 TraesCS4B01G383900 chr2D 89.055 201 20 2 515 714 397963881 397964080 6.820000e-62 248.0
25 TraesCS4B01G383900 chr2D 89.947 189 18 1 515 703 6219805 6219992 3.180000e-60 243.0
26 TraesCS4B01G383900 chr2D 91.525 118 10 0 64 181 408776383 408776266 2.540000e-36 163.0
27 TraesCS4B01G383900 chr2D 90.000 120 12 0 64 183 215846387 215846506 4.260000e-34 156.0
28 TraesCS4B01G383900 chr2D 89.256 121 11 2 64 183 453759105 453758986 1.980000e-32 150.0
29 TraesCS4B01G383900 chr2D 88.983 118 13 0 64 181 443246048 443245931 2.560000e-31 147.0
30 TraesCS4B01G383900 chr3A 87.923 207 22 3 504 710 187438413 187438210 1.140000e-59 241.0
31 TraesCS4B01G383900 chr1D 89.119 193 19 2 515 707 75927625 75927435 4.110000e-59 239.0
32 TraesCS4B01G383900 chr1D 88.333 120 14 0 64 183 476229404 476229523 9.210000e-31 145.0
33 TraesCS4B01G383900 chr1A 90.678 118 11 0 64 181 65267151 65267034 1.180000e-34 158.0
34 TraesCS4B01G383900 chr6B 90.678 118 10 1 64 181 166128869 166128985 4.260000e-34 156.0
35 TraesCS4B01G383900 chr1B 89.831 118 12 0 64 181 576063422 576063305 5.500000e-33 152.0


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 TraesCS4B01G383900 chr4B 663461860 663465045 3185 False 5884.0 5884 100.0000 1 3186 1 chr4B.!!$F2 3185
1 TraesCS4B01G383900 chr4B 663520414 663522879 2465 False 1618.5 2527 91.4125 706 3186 2 chr4B.!!$F7 2480
2 TraesCS4B01G383900 chr4B 663621317 663622192 875 False 1221.0 1221 91.9040 706 1578 1 chr4B.!!$F5 872
3 TraesCS4B01G383900 chr4B 663629235 663629912 677 False 953.0 953 92.0470 1599 2276 1 chr4B.!!$F6 677
4 TraesCS4B01G383900 chr4B 662713946 662720776 6830 True 730.0 2549 92.9712 706 3168 5 chr4B.!!$R1 2462
5 TraesCS4B01G383900 chr5A 406496473 406499449 2976 True 528.0 545 85.4840 180 703 3 chr5A.!!$R1 523
6 TraesCS4B01G383900 chr7B 733460347 733461507 1160 True 457.0 457 74.4950 1038 2189 1 chr7B.!!$R1 1151

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
446 1718 0.031178 CAAAGTGAACCTGTGCTGGC 59.969 55.0 0.0 0.0 0.00 4.85 F
770 2050 0.321653 CGAAGGAAACCCCAGACCAG 60.322 60.0 0.0 0.0 37.41 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 2565 1.324005 TGTACCCGGCATCATCGTCA 61.324 55.0 0.00 0.0 0.0 4.35 R
2642 9060 0.457853 TGCGCAACGTCTATCCAGTC 60.458 55.0 8.16 0.0 0.0 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
21 22 4.361451 AAGCAAACTTTGTGTCTGTGAG 57.639 40.909 3.48 0.00 29.41 3.51
22 23 2.684881 AGCAAACTTTGTGTCTGTGAGG 59.315 45.455 3.48 0.00 0.00 3.86
23 24 2.682856 GCAAACTTTGTGTCTGTGAGGA 59.317 45.455 3.48 0.00 0.00 3.71
24 25 3.242870 GCAAACTTTGTGTCTGTGAGGAG 60.243 47.826 3.48 0.00 0.00 3.69
25 26 4.191544 CAAACTTTGTGTCTGTGAGGAGA 58.808 43.478 0.00 0.00 0.00 3.71
26 27 4.696479 AACTTTGTGTCTGTGAGGAGAT 57.304 40.909 0.00 0.00 0.00 2.75
27 28 4.696479 ACTTTGTGTCTGTGAGGAGATT 57.304 40.909 0.00 0.00 0.00 2.40
28 29 4.636249 ACTTTGTGTCTGTGAGGAGATTC 58.364 43.478 0.00 0.00 0.00 2.52
29 30 3.685139 TTGTGTCTGTGAGGAGATTCC 57.315 47.619 0.00 0.00 36.58 3.01
30 31 2.608623 TGTGTCTGTGAGGAGATTCCA 58.391 47.619 0.00 0.00 39.61 3.53
31 32 3.176411 TGTGTCTGTGAGGAGATTCCAT 58.824 45.455 0.00 0.00 39.61 3.41
32 33 3.055602 TGTGTCTGTGAGGAGATTCCATG 60.056 47.826 0.00 0.00 39.61 3.66
33 34 2.093288 TGTCTGTGAGGAGATTCCATGC 60.093 50.000 0.00 0.00 39.61 4.06
34 35 2.093288 GTCTGTGAGGAGATTCCATGCA 60.093 50.000 0.00 0.00 39.61 3.96
35 36 2.775960 TCTGTGAGGAGATTCCATGCAT 59.224 45.455 0.00 0.00 39.61 3.96
36 37 2.879026 CTGTGAGGAGATTCCATGCATG 59.121 50.000 20.19 20.19 39.61 4.06
37 38 2.240414 TGTGAGGAGATTCCATGCATGT 59.760 45.455 24.58 6.98 39.61 3.21
38 39 3.455543 TGTGAGGAGATTCCATGCATGTA 59.544 43.478 24.58 12.99 39.61 2.29
39 40 4.063689 GTGAGGAGATTCCATGCATGTAG 58.936 47.826 24.58 11.03 39.61 2.74
40 41 3.969312 TGAGGAGATTCCATGCATGTAGA 59.031 43.478 24.58 13.24 39.61 2.59
41 42 4.202295 TGAGGAGATTCCATGCATGTAGAC 60.202 45.833 24.58 13.16 39.61 2.59
42 43 3.072184 AGGAGATTCCATGCATGTAGACC 59.928 47.826 24.58 17.93 39.61 3.85
43 44 3.181451 GGAGATTCCATGCATGTAGACCA 60.181 47.826 24.58 3.19 36.28 4.02
44 45 4.454678 GAGATTCCATGCATGTAGACCAA 58.545 43.478 24.58 8.13 0.00 3.67
45 46 4.202441 AGATTCCATGCATGTAGACCAAC 58.798 43.478 24.58 8.06 0.00 3.77
46 47 3.431673 TTCCATGCATGTAGACCAACA 57.568 42.857 24.58 0.00 0.00 3.33
47 48 3.431673 TCCATGCATGTAGACCAACAA 57.568 42.857 24.58 0.00 32.02 2.83
48 49 3.760738 TCCATGCATGTAGACCAACAAA 58.239 40.909 24.58 0.00 32.02 2.83
49 50 4.148079 TCCATGCATGTAGACCAACAAAA 58.852 39.130 24.58 0.00 32.02 2.44
50 51 4.586421 TCCATGCATGTAGACCAACAAAAA 59.414 37.500 24.58 0.00 32.02 1.94
70 71 3.629142 AAAAATAGCGTGCTACTCCCT 57.371 42.857 3.26 0.00 0.00 4.20
71 72 2.892784 AAATAGCGTGCTACTCCCTC 57.107 50.000 3.26 0.00 0.00 4.30
72 73 1.041437 AATAGCGTGCTACTCCCTCC 58.959 55.000 3.26 0.00 0.00 4.30
73 74 1.173444 ATAGCGTGCTACTCCCTCCG 61.173 60.000 3.26 0.00 0.00 4.63
74 75 2.547640 TAGCGTGCTACTCCCTCCGT 62.548 60.000 0.00 0.00 0.00 4.69
75 76 2.799371 CGTGCTACTCCCTCCGTC 59.201 66.667 0.00 0.00 0.00 4.79
76 77 2.772691 CGTGCTACTCCCTCCGTCC 61.773 68.421 0.00 0.00 0.00 4.79
77 78 2.439701 TGCTACTCCCTCCGTCCG 60.440 66.667 0.00 0.00 0.00 4.79
78 79 3.217743 GCTACTCCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
79 80 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
80 81 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
81 82 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
82 83 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
83 84 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
84 85 1.228956 TCCCTCCGTCCGGAAAAGA 60.229 57.895 5.23 1.88 44.66 2.52
85 86 0.616679 TCCCTCCGTCCGGAAAAGAT 60.617 55.000 5.23 0.00 44.66 2.40
86 87 0.252197 CCCTCCGTCCGGAAAAGATT 59.748 55.000 5.23 0.00 44.66 2.40
87 88 1.369625 CCTCCGTCCGGAAAAGATTG 58.630 55.000 5.23 0.00 44.66 2.67
88 89 1.338769 CCTCCGTCCGGAAAAGATTGT 60.339 52.381 5.23 0.00 44.66 2.71
89 90 2.000447 CTCCGTCCGGAAAAGATTGTC 59.000 52.381 5.23 0.00 44.66 3.18
90 91 1.084289 CCGTCCGGAAAAGATTGTCC 58.916 55.000 5.23 0.00 37.50 4.02
91 92 1.084289 CGTCCGGAAAAGATTGTCCC 58.916 55.000 5.23 0.00 0.00 4.46
92 93 1.609580 CGTCCGGAAAAGATTGTCCCA 60.610 52.381 5.23 0.00 0.00 4.37
93 94 2.510613 GTCCGGAAAAGATTGTCCCAA 58.489 47.619 5.23 0.00 0.00 4.12
94 95 2.488153 GTCCGGAAAAGATTGTCCCAAG 59.512 50.000 5.23 0.00 0.00 3.61
95 96 1.202348 CCGGAAAAGATTGTCCCAAGC 59.798 52.381 0.00 0.00 0.00 4.01
96 97 2.162681 CGGAAAAGATTGTCCCAAGCT 58.837 47.619 0.00 0.00 0.00 3.74
97 98 2.558359 CGGAAAAGATTGTCCCAAGCTT 59.442 45.455 1.89 1.89 0.00 3.74
98 99 3.612479 CGGAAAAGATTGTCCCAAGCTTG 60.612 47.826 19.93 19.93 0.00 4.01
99 100 3.321968 GGAAAAGATTGTCCCAAGCTTGT 59.678 43.478 24.35 5.15 0.00 3.16
100 101 4.522789 GGAAAAGATTGTCCCAAGCTTGTA 59.477 41.667 24.35 10.01 0.00 2.41
101 102 5.185828 GGAAAAGATTGTCCCAAGCTTGTAT 59.814 40.000 24.35 9.75 0.00 2.29
102 103 6.295292 GGAAAAGATTGTCCCAAGCTTGTATT 60.295 38.462 24.35 6.15 0.00 1.89
103 104 6.670695 AAAGATTGTCCCAAGCTTGTATTT 57.329 33.333 24.35 11.66 0.00 1.40
104 105 5.904362 AGATTGTCCCAAGCTTGTATTTC 57.096 39.130 24.35 12.93 0.00 2.17
105 106 5.324409 AGATTGTCCCAAGCTTGTATTTCA 58.676 37.500 24.35 12.85 0.00 2.69
106 107 5.774690 AGATTGTCCCAAGCTTGTATTTCAA 59.225 36.000 24.35 19.32 34.61 2.69
107 108 5.860941 TTGTCCCAAGCTTGTATTTCAAA 57.139 34.783 24.35 7.25 35.48 2.69
108 109 6.418057 TTGTCCCAAGCTTGTATTTCAAAT 57.582 33.333 24.35 0.00 35.48 2.32
109 110 5.782047 TGTCCCAAGCTTGTATTTCAAATG 58.218 37.500 24.35 5.47 35.48 2.32
110 111 5.170748 GTCCCAAGCTTGTATTTCAAATGG 58.829 41.667 24.35 14.01 35.48 3.16
111 112 5.047377 GTCCCAAGCTTGTATTTCAAATGGA 60.047 40.000 24.35 15.96 36.92 3.41
112 113 5.721000 TCCCAAGCTTGTATTTCAAATGGAT 59.279 36.000 24.35 0.00 36.92 3.41
113 114 5.813672 CCCAAGCTTGTATTTCAAATGGATG 59.186 40.000 24.35 3.72 36.92 3.51
114 115 6.400568 CCAAGCTTGTATTTCAAATGGATGT 58.599 36.000 24.35 0.00 36.92 3.06
115 116 7.363705 CCCAAGCTTGTATTTCAAATGGATGTA 60.364 37.037 24.35 0.00 36.92 2.29
116 117 8.199449 CCAAGCTTGTATTTCAAATGGATGTAT 58.801 33.333 24.35 0.00 36.92 2.29
117 118 9.241317 CAAGCTTGTATTTCAAATGGATGTATC 57.759 33.333 18.65 0.00 35.48 2.24
118 119 8.757982 AGCTTGTATTTCAAATGGATGTATCT 57.242 30.769 0.00 0.00 35.48 1.98
119 120 9.851686 AGCTTGTATTTCAAATGGATGTATCTA 57.148 29.630 0.00 0.00 35.48 1.98
122 123 9.625747 TTGTATTTCAAATGGATGTATCTAGCA 57.374 29.630 0.00 0.00 32.64 3.49
123 124 9.056005 TGTATTTCAAATGGATGTATCTAGCAC 57.944 33.333 0.00 0.00 0.00 4.40
124 125 9.277783 GTATTTCAAATGGATGTATCTAGCACT 57.722 33.333 0.00 0.00 0.00 4.40
126 127 9.851686 ATTTCAAATGGATGTATCTAGCACTAA 57.148 29.630 0.00 0.00 0.00 2.24
127 128 9.851686 TTTCAAATGGATGTATCTAGCACTAAT 57.148 29.630 0.00 0.00 0.00 1.73
128 129 9.851686 TTCAAATGGATGTATCTAGCACTAATT 57.148 29.630 0.00 0.00 0.00 1.40
129 130 9.851686 TCAAATGGATGTATCTAGCACTAATTT 57.148 29.630 0.00 0.00 0.00 1.82
134 135 9.219603 TGGATGTATCTAGCACTAATTTTATGC 57.780 33.333 1.17 1.17 39.74 3.14
153 154 8.853077 TTTATGCTAGATACATTCATTGGAGG 57.147 34.615 0.00 0.00 0.00 4.30
154 155 5.233083 TGCTAGATACATTCATTGGAGGG 57.767 43.478 0.00 0.00 0.00 4.30
155 156 4.907269 TGCTAGATACATTCATTGGAGGGA 59.093 41.667 0.00 0.00 0.00 4.20
156 157 5.221722 TGCTAGATACATTCATTGGAGGGAC 60.222 44.000 0.00 0.00 0.00 4.46
157 158 5.221722 GCTAGATACATTCATTGGAGGGACA 60.222 44.000 0.00 0.00 0.00 4.02
158 159 5.715439 AGATACATTCATTGGAGGGACAA 57.285 39.130 0.00 0.00 34.41 3.18
159 160 5.688807 AGATACATTCATTGGAGGGACAAG 58.311 41.667 0.00 0.00 33.23 3.16
160 161 3.814504 ACATTCATTGGAGGGACAAGT 57.185 42.857 0.00 0.00 33.23 3.16
161 162 4.118168 ACATTCATTGGAGGGACAAGTT 57.882 40.909 0.00 0.00 33.23 2.66
162 163 4.482990 ACATTCATTGGAGGGACAAGTTT 58.517 39.130 0.00 0.00 33.23 2.66
163 164 4.901250 ACATTCATTGGAGGGACAAGTTTT 59.099 37.500 0.00 0.00 33.23 2.43
164 165 5.366477 ACATTCATTGGAGGGACAAGTTTTT 59.634 36.000 0.00 0.00 33.23 1.94
192 193 5.209818 TGGAGGGAGTACAAAATATAGCG 57.790 43.478 0.00 0.00 0.00 4.26
199 200 2.428544 ACAAAATATAGCGTGGCCCA 57.571 45.000 0.00 0.00 0.00 5.36
226 227 9.278978 TCTTCAAATGCTACACAAGTTATAACA 57.721 29.630 17.65 0.00 0.00 2.41
229 1477 6.417191 AATGCTACACAAGTTATAACACGG 57.583 37.500 17.65 8.65 0.00 4.94
252 1500 7.227461 CGGTAATAGCGTGCTATATTTCAAAG 58.773 38.462 14.33 0.00 38.20 2.77
274 1546 5.257864 AGTAACGTTTGCAAAACGAAGTAC 58.742 37.500 28.37 24.25 45.00 2.73
276 1548 3.931824 ACGTTTGCAAAACGAAGTACTC 58.068 40.909 28.37 9.27 45.00 2.59
304 1576 9.787435 AGTACCTTAAGACACTATCATAGAGAG 57.213 37.037 3.36 0.00 0.00 3.20
307 1579 7.722285 ACCTTAAGACACTATCATAGAGAGACC 59.278 40.741 3.36 0.00 0.00 3.85
332 1604 7.566879 CCTAATCTAGCAATAGATAGGGACCAT 59.433 40.741 0.00 0.00 35.88 3.55
396 1668 6.808008 ACATACAAACTCTGAACATTGAGG 57.192 37.500 0.00 0.00 34.84 3.86
403 1675 3.648067 ACTCTGAACATTGAGGACCAAGA 59.352 43.478 0.00 0.00 38.31 3.02
417 1689 6.027025 AGGACCAAGACTACATCTACCATA 57.973 41.667 0.00 0.00 36.27 2.74
442 1714 1.102978 ACCACAAAGTGAACCTGTGC 58.897 50.000 0.00 0.00 39.30 4.57
446 1718 0.031178 CAAAGTGAACCTGTGCTGGC 59.969 55.000 0.00 0.00 0.00 4.85
451 1723 1.377333 GAACCTGTGCTGGCCTACC 60.377 63.158 3.32 0.00 0.00 3.18
452 1724 2.821679 GAACCTGTGCTGGCCTACCC 62.822 65.000 3.32 0.00 33.59 3.69
466 1738 2.772515 GCCTACCCCTACTCTGAACATT 59.227 50.000 0.00 0.00 0.00 2.71
474 1746 5.050490 CCCTACTCTGAACATTGATAACCG 58.950 45.833 0.00 0.00 0.00 4.44
492 1764 9.976511 TGATAACCGGAGTTAACATATAAAGAG 57.023 33.333 9.46 0.00 41.68 2.85
530 1802 6.126409 TGTGTTGACCCTATTTTTCTGAACT 58.874 36.000 0.00 0.00 0.00 3.01
558 1830 6.661669 TCATCATTTGAACGCTATAATGCTG 58.338 36.000 0.00 0.00 0.00 4.41
577 1849 2.532235 TGCACGCTACAACGTTATAGG 58.468 47.619 15.04 7.89 45.75 2.57
578 1850 1.856597 GCACGCTACAACGTTATAGGG 59.143 52.381 24.16 24.16 45.75 3.53
579 1851 2.466846 CACGCTACAACGTTATAGGGG 58.533 52.381 27.67 16.31 45.75 4.79
580 1852 1.202452 ACGCTACAACGTTATAGGGGC 60.202 52.381 27.67 10.20 45.75 5.80
581 1853 1.870993 CGCTACAACGTTATAGGGGCC 60.871 57.143 19.72 0.00 0.00 5.80
582 1854 1.415289 GCTACAACGTTATAGGGGCCT 59.585 52.381 15.04 0.00 0.00 5.19
583 1855 2.805657 GCTACAACGTTATAGGGGCCTG 60.806 54.545 15.04 0.00 0.00 4.85
584 1856 1.282382 ACAACGTTATAGGGGCCTGT 58.718 50.000 0.84 0.00 0.00 4.00
585 1857 2.469952 ACAACGTTATAGGGGCCTGTA 58.530 47.619 0.84 0.00 0.00 2.74
586 1858 2.433239 ACAACGTTATAGGGGCCTGTAG 59.567 50.000 0.84 0.00 0.00 2.74
587 1859 1.046204 ACGTTATAGGGGCCTGTAGC 58.954 55.000 0.84 0.00 42.60 3.58
588 1860 1.045407 CGTTATAGGGGCCTGTAGCA 58.955 55.000 0.84 0.00 46.50 3.49
589 1861 1.623811 CGTTATAGGGGCCTGTAGCAT 59.376 52.381 0.84 0.00 46.50 3.79
606 1878 7.148738 CCTGTAGCATGCTAATTACGTGAATAG 60.149 40.741 28.44 12.04 0.00 1.73
608 1880 4.150627 AGCATGCTAATTACGTGAATAGCG 59.849 41.667 21.21 9.51 31.80 4.26
657 1929 2.182014 GCGTTTCCATTCCAAATACGC 58.818 47.619 0.00 0.00 44.53 4.42
658 1930 2.792749 CGTTTCCATTCCAAATACGCC 58.207 47.619 0.00 0.00 0.00 5.68
663 1935 6.512297 GTTTCCATTCCAAATACGCCATAAT 58.488 36.000 0.00 0.00 0.00 1.28
744 2016 1.876156 GCGGAAGGAATTAGCATGGAG 59.124 52.381 0.00 0.00 0.00 3.86
745 2017 2.485479 GCGGAAGGAATTAGCATGGAGA 60.485 50.000 0.00 0.00 0.00 3.71
746 2018 3.808728 CGGAAGGAATTAGCATGGAGAA 58.191 45.455 0.00 0.00 0.00 2.87
747 2019 3.812053 CGGAAGGAATTAGCATGGAGAAG 59.188 47.826 0.00 0.00 0.00 2.85
748 2020 4.140536 GGAAGGAATTAGCATGGAGAAGG 58.859 47.826 0.00 0.00 0.00 3.46
749 2021 3.220674 AGGAATTAGCATGGAGAAGGC 57.779 47.619 0.00 0.00 0.00 4.35
750 2022 2.782341 AGGAATTAGCATGGAGAAGGCT 59.218 45.455 0.00 0.00 41.51 4.58
751 2023 3.145286 GGAATTAGCATGGAGAAGGCTC 58.855 50.000 0.00 0.00 39.01 4.70
770 2050 0.321653 CGAAGGAAACCCCAGACCAG 60.322 60.000 0.00 0.00 37.41 4.00
873 2156 9.080097 ACAGAACTTTCTAGAAGAGTTAGCTTA 57.920 33.333 22.17 1.15 35.34 3.09
889 2173 6.331837 AGTTAGCTTATTTGGCCTCCCTAATA 59.668 38.462 3.32 0.00 37.64 0.98
1191 2475 0.943673 CGTTGTCTGACATTGCCACA 59.056 50.000 11.86 0.00 0.00 4.17
1197 2481 2.880890 GTCTGACATTGCCACAGAAACT 59.119 45.455 2.24 0.00 41.31 2.66
1243 2527 3.647649 CTCCGTCGGCTGATGCACA 62.648 63.158 6.34 0.00 41.91 4.57
1281 2565 2.054232 TCTTCTCCGTCGAAGGCTAT 57.946 50.000 13.06 0.00 40.56 2.97
1321 2617 0.735632 GCTCACTCTTGTCTCCAGCG 60.736 60.000 0.00 0.00 0.00 5.18
1418 2714 4.579869 ACCATGCTCTTCGACATAAAAGT 58.420 39.130 0.00 0.00 0.00 2.66
1436 2732 2.028484 GTGGTTCACCGACGAGCA 59.972 61.111 0.00 0.00 39.43 4.26
1488 2784 2.359850 GGCTGCACACCATCGGAA 60.360 61.111 0.50 0.00 0.00 4.30
1601 2897 2.261729 GGGCATTTTTAAGGGGGTGAA 58.738 47.619 0.00 0.00 0.00 3.18
1614 2910 1.523758 GGGTGAACTCGCTTGTTGAT 58.476 50.000 0.00 0.00 0.00 2.57
1942 4226 0.179119 ATGCCGTCAAGGTACTACGC 60.179 55.000 0.00 0.00 38.89 4.42
2145 4441 6.471146 CAGGATTTGGGGACTATAAGATCAG 58.529 44.000 0.00 0.00 0.00 2.90
2230 4529 5.394883 GGGTGGTTCGTCTACTATTGAATCA 60.395 44.000 0.00 0.00 0.00 2.57
2280 4579 3.067180 CACACTTTTGAGCACTCCATTGT 59.933 43.478 0.00 0.00 0.00 2.71
2281 4580 4.275689 CACACTTTTGAGCACTCCATTGTA 59.724 41.667 0.00 0.00 0.00 2.41
2282 4581 5.048504 CACACTTTTGAGCACTCCATTGTAT 60.049 40.000 0.00 0.00 0.00 2.29
2338 4640 4.681744 TGTGACTTTCATTTTGAGCAACC 58.318 39.130 0.00 0.00 0.00 3.77
2365 4667 7.912250 CGAGATTTTCATCCTTTGTTCCATAAG 59.088 37.037 0.00 0.00 0.00 1.73
2417 5292 2.479340 TGGTCATTGGTTATACCCGGA 58.521 47.619 0.73 0.00 37.50 5.14
2528 8942 1.200948 GAAATGTCTCCACTTGCTGCC 59.799 52.381 0.00 0.00 0.00 4.85
2585 8999 5.738909 CAGTGGAGACTGGATAAGTGAAAT 58.261 41.667 0.00 0.00 45.26 2.17
2586 9000 5.814705 CAGTGGAGACTGGATAAGTGAAATC 59.185 44.000 0.00 0.00 45.26 2.17
2588 9002 6.013379 AGTGGAGACTGGATAAGTGAAATCAA 60.013 38.462 0.00 0.00 40.07 2.57
2615 9033 9.691362 TTATTATTTCAGTTGTTCTGCCTTTTC 57.309 29.630 0.00 0.00 43.32 2.29
2633 9051 2.038387 TCTTTGCGATAAAGGCCTCC 57.962 50.000 5.23 0.00 0.00 4.30
2636 9054 0.326595 TTGCGATAAAGGCCTCCACA 59.673 50.000 5.23 0.00 0.00 4.17
2637 9055 0.107703 TGCGATAAAGGCCTCCACAG 60.108 55.000 5.23 0.00 0.00 3.66
2638 9056 0.107654 GCGATAAAGGCCTCCACAGT 60.108 55.000 5.23 0.00 0.00 3.55
2639 9057 1.656652 CGATAAAGGCCTCCACAGTG 58.343 55.000 5.23 0.00 0.00 3.66
2699 9162 3.963374 TCTCTAGTGATTGGTGAGGATGG 59.037 47.826 0.00 0.00 0.00 3.51
2715 9178 2.203153 GGGCCGTGAACACACACT 60.203 61.111 0.00 0.00 38.47 3.55
2716 9179 2.542907 GGGCCGTGAACACACACTG 61.543 63.158 0.00 0.00 38.47 3.66
2753 9216 1.896660 AACACTGGAAACGGCGCAT 60.897 52.632 10.83 0.00 41.93 4.73
2763 9226 4.012895 CGGCGCATACGATTGGCC 62.013 66.667 10.83 0.00 43.93 5.36
2767 9230 0.165944 GCGCATACGATTGGCCATAC 59.834 55.000 6.09 2.44 43.93 2.39
2810 9276 7.905126 TGATGTTGTCACATACGATTTATGTC 58.095 34.615 0.00 0.00 44.22 3.06
2860 9326 7.614494 AGCTTGCAAACCATTTCATATTTAGT 58.386 30.769 0.00 0.00 0.00 2.24
2891 9357 4.049546 TGTGCTACTTTACTGTTGTCGT 57.950 40.909 0.00 0.00 0.00 4.34
2898 9364 3.732721 ACTTTACTGTTGTCGTACGCTTC 59.267 43.478 11.24 4.25 0.00 3.86
2901 9367 2.391879 ACTGTTGTCGTACGCTTCTTC 58.608 47.619 11.24 0.00 0.00 2.87
2904 9370 3.047796 TGTTGTCGTACGCTTCTTCTTC 58.952 45.455 11.24 0.00 0.00 2.87
2907 9373 3.562505 TGTCGTACGCTTCTTCTTCTTC 58.437 45.455 11.24 0.00 0.00 2.87
2908 9374 3.252701 TGTCGTACGCTTCTTCTTCTTCT 59.747 43.478 11.24 0.00 0.00 2.85
2909 9375 4.228317 GTCGTACGCTTCTTCTTCTTCTT 58.772 43.478 11.24 0.00 0.00 2.52
2910 9376 4.321480 GTCGTACGCTTCTTCTTCTTCTTC 59.679 45.833 11.24 0.00 0.00 2.87
2911 9377 3.298499 CGTACGCTTCTTCTTCTTCTTCG 59.702 47.826 0.52 0.00 0.00 3.79
2912 9378 3.372660 ACGCTTCTTCTTCTTCTTCGT 57.627 42.857 0.00 0.00 0.00 3.85
2913 9379 3.310246 ACGCTTCTTCTTCTTCTTCGTC 58.690 45.455 0.00 0.00 0.00 4.20
2943 9413 1.354040 TTTGTGTTTGCTTGTTGCCG 58.646 45.000 0.00 0.00 42.00 5.69
3012 9705 3.365265 CACAGGTTTCCGCAGCCC 61.365 66.667 0.00 0.00 0.00 5.19
3024 9717 1.300963 GCAGCCCCTGATTCACTCA 59.699 57.895 0.00 0.00 32.44 3.41
3028 9721 2.229784 CAGCCCCTGATTCACTCAAAAC 59.770 50.000 0.00 0.00 32.44 2.43
3072 9765 0.251877 CCACCGGTAACCCCCAAAAT 60.252 55.000 6.87 0.00 0.00 1.82
3088 9781 0.749649 AAATTTGACTGGCAACCGCA 59.250 45.000 0.00 0.00 41.24 5.69
3168 9861 1.977854 CACCGGAGATCCCCAATGATA 59.022 52.381 9.46 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.129287 CCTCACAGACACAAAGTTTGCTT 59.871 43.478 15.59 2.33 35.84 3.91
5 6 4.696479 ATCTCCTCACAGACACAAAGTT 57.304 40.909 0.00 0.00 0.00 2.66
6 7 4.503991 GGAATCTCCTCACAGACACAAAGT 60.504 45.833 0.00 0.00 32.53 2.66
7 8 3.999663 GGAATCTCCTCACAGACACAAAG 59.000 47.826 0.00 0.00 32.53 2.77
8 9 3.390967 TGGAATCTCCTCACAGACACAAA 59.609 43.478 0.00 0.00 37.46 2.83
9 10 2.972021 TGGAATCTCCTCACAGACACAA 59.028 45.455 0.00 0.00 37.46 3.33
10 11 2.608623 TGGAATCTCCTCACAGACACA 58.391 47.619 0.00 0.00 37.46 3.72
11 12 3.529533 CATGGAATCTCCTCACAGACAC 58.470 50.000 0.00 0.00 37.46 3.67
12 13 2.093288 GCATGGAATCTCCTCACAGACA 60.093 50.000 0.00 0.00 37.46 3.41
13 14 2.093288 TGCATGGAATCTCCTCACAGAC 60.093 50.000 0.00 0.00 37.46 3.51
14 15 2.190538 TGCATGGAATCTCCTCACAGA 58.809 47.619 0.00 0.00 37.46 3.41
15 16 2.704464 TGCATGGAATCTCCTCACAG 57.296 50.000 0.00 0.00 37.46 3.66
16 17 2.240414 ACATGCATGGAATCTCCTCACA 59.760 45.455 29.41 0.00 37.46 3.58
17 18 2.928334 ACATGCATGGAATCTCCTCAC 58.072 47.619 29.41 0.00 37.46 3.51
18 19 3.969312 TCTACATGCATGGAATCTCCTCA 59.031 43.478 29.41 0.00 37.46 3.86
19 20 4.314121 GTCTACATGCATGGAATCTCCTC 58.686 47.826 29.41 7.20 37.46 3.71
20 21 3.072184 GGTCTACATGCATGGAATCTCCT 59.928 47.826 29.41 9.36 37.46 3.69
21 22 3.181451 TGGTCTACATGCATGGAATCTCC 60.181 47.826 29.41 21.30 36.96 3.71
22 23 4.077300 TGGTCTACATGCATGGAATCTC 57.923 45.455 29.41 14.62 0.00 2.75
23 24 4.202441 GTTGGTCTACATGCATGGAATCT 58.798 43.478 29.41 11.55 0.00 2.40
24 25 3.947196 TGTTGGTCTACATGCATGGAATC 59.053 43.478 29.41 16.39 0.00 2.52
25 26 3.966979 TGTTGGTCTACATGCATGGAAT 58.033 40.909 29.41 12.30 0.00 3.01
26 27 3.431673 TGTTGGTCTACATGCATGGAA 57.568 42.857 29.41 16.46 0.00 3.53
27 28 3.431673 TTGTTGGTCTACATGCATGGA 57.568 42.857 29.41 21.69 0.00 3.41
28 29 4.517952 TTTTGTTGGTCTACATGCATGG 57.482 40.909 29.41 13.66 0.00 3.66
50 51 3.532542 GAGGGAGTAGCACGCTATTTTT 58.467 45.455 1.43 0.00 0.00 1.94
51 52 2.158943 GGAGGGAGTAGCACGCTATTTT 60.159 50.000 1.43 0.00 0.00 1.82
52 53 1.413077 GGAGGGAGTAGCACGCTATTT 59.587 52.381 1.43 0.00 0.00 1.40
53 54 1.041437 GGAGGGAGTAGCACGCTATT 58.959 55.000 1.43 0.00 0.00 1.73
54 55 1.173444 CGGAGGGAGTAGCACGCTAT 61.173 60.000 1.43 0.00 0.00 2.97
55 56 1.822613 CGGAGGGAGTAGCACGCTA 60.823 63.158 0.00 0.00 0.00 4.26
56 57 3.141488 CGGAGGGAGTAGCACGCT 61.141 66.667 0.00 0.00 0.00 5.07
57 58 3.412879 GACGGAGGGAGTAGCACGC 62.413 68.421 0.00 0.00 0.00 5.34
58 59 2.772691 GGACGGAGGGAGTAGCACG 61.773 68.421 0.00 0.00 0.00 5.34
59 60 2.772691 CGGACGGAGGGAGTAGCAC 61.773 68.421 0.00 0.00 0.00 4.40
60 61 2.439701 CGGACGGAGGGAGTAGCA 60.440 66.667 0.00 0.00 0.00 3.49
61 62 3.217743 CCGGACGGAGGGAGTAGC 61.218 72.222 4.40 0.00 37.50 3.58
62 63 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
63 64 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
64 65 1.534717 TTTTCCGGACGGAGGGAGT 60.535 57.895 13.64 0.00 46.06 3.85
65 66 1.218316 CTTTTCCGGACGGAGGGAG 59.782 63.158 13.64 9.15 46.06 4.30
66 67 0.616679 ATCTTTTCCGGACGGAGGGA 60.617 55.000 13.64 12.75 46.06 4.20
67 68 0.252197 AATCTTTTCCGGACGGAGGG 59.748 55.000 13.64 8.17 46.06 4.30
68 69 1.338769 ACAATCTTTTCCGGACGGAGG 60.339 52.381 13.64 8.49 46.06 4.30
69 70 2.000447 GACAATCTTTTCCGGACGGAG 59.000 52.381 13.64 2.12 46.06 4.63
70 71 1.338389 GGACAATCTTTTCCGGACGGA 60.338 52.381 1.83 9.76 43.52 4.69
71 72 1.084289 GGACAATCTTTTCCGGACGG 58.916 55.000 1.83 3.96 0.00 4.79
72 73 1.084289 GGGACAATCTTTTCCGGACG 58.916 55.000 1.83 0.00 32.00 4.79
73 74 2.194201 TGGGACAATCTTTTCCGGAC 57.806 50.000 1.83 0.00 31.92 4.79
80 81 7.201992 TTGAAATACAAGCTTGGGACAATCTTT 60.202 33.333 29.18 12.35 37.48 2.52
81 82 6.267471 TTGAAATACAAGCTTGGGACAATCTT 59.733 34.615 29.18 8.41 37.48 2.40
82 83 5.774690 TTGAAATACAAGCTTGGGACAATCT 59.225 36.000 29.18 9.13 37.48 2.40
83 84 6.024552 TTGAAATACAAGCTTGGGACAATC 57.975 37.500 29.18 18.39 37.48 2.67
84 85 6.418057 TTTGAAATACAAGCTTGGGACAAT 57.582 33.333 29.18 10.59 41.27 2.71
85 86 5.860941 TTTGAAATACAAGCTTGGGACAA 57.139 34.783 29.18 21.59 41.27 3.18
86 87 5.279406 CCATTTGAAATACAAGCTTGGGACA 60.279 40.000 29.18 17.71 39.77 4.02
87 88 5.047377 TCCATTTGAAATACAAGCTTGGGAC 60.047 40.000 29.18 15.60 39.77 4.46
88 89 5.083122 TCCATTTGAAATACAAGCTTGGGA 58.917 37.500 29.18 18.26 39.77 4.37
89 90 5.404466 TCCATTTGAAATACAAGCTTGGG 57.596 39.130 29.18 16.37 39.77 4.12
90 91 6.400568 ACATCCATTTGAAATACAAGCTTGG 58.599 36.000 29.18 12.28 39.77 3.61
91 92 9.241317 GATACATCCATTTGAAATACAAGCTTG 57.759 33.333 24.84 24.84 39.77 4.01
92 93 9.193806 AGATACATCCATTTGAAATACAAGCTT 57.806 29.630 0.00 0.00 39.77 3.74
93 94 8.757982 AGATACATCCATTTGAAATACAAGCT 57.242 30.769 0.00 0.00 39.77 3.74
96 97 9.625747 TGCTAGATACATCCATTTGAAATACAA 57.374 29.630 0.00 0.00 36.65 2.41
97 98 9.056005 GTGCTAGATACATCCATTTGAAATACA 57.944 33.333 0.00 0.00 0.00 2.29
98 99 9.277783 AGTGCTAGATACATCCATTTGAAATAC 57.722 33.333 0.00 0.00 0.00 1.89
100 101 9.851686 TTAGTGCTAGATACATCCATTTGAAAT 57.148 29.630 0.00 0.00 0.00 2.17
101 102 9.851686 ATTAGTGCTAGATACATCCATTTGAAA 57.148 29.630 0.00 0.00 0.00 2.69
102 103 9.851686 AATTAGTGCTAGATACATCCATTTGAA 57.148 29.630 0.00 0.00 0.00 2.69
103 104 9.851686 AAATTAGTGCTAGATACATCCATTTGA 57.148 29.630 0.00 0.00 0.00 2.69
108 109 9.219603 GCATAAAATTAGTGCTAGATACATCCA 57.780 33.333 0.00 0.00 36.02 3.41
109 110 9.442047 AGCATAAAATTAGTGCTAGATACATCC 57.558 33.333 9.58 0.00 46.54 3.51
127 128 9.288576 CCTCCAATGAATGTATCTAGCATAAAA 57.711 33.333 0.00 0.00 0.00 1.52
128 129 7.884877 CCCTCCAATGAATGTATCTAGCATAAA 59.115 37.037 0.00 0.00 0.00 1.40
129 130 7.237471 TCCCTCCAATGAATGTATCTAGCATAA 59.763 37.037 0.00 0.00 0.00 1.90
130 131 6.730507 TCCCTCCAATGAATGTATCTAGCATA 59.269 38.462 0.00 0.00 0.00 3.14
131 132 5.549228 TCCCTCCAATGAATGTATCTAGCAT 59.451 40.000 0.00 0.00 0.00 3.79
132 133 4.907269 TCCCTCCAATGAATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
133 134 5.221722 TGTCCCTCCAATGAATGTATCTAGC 60.222 44.000 0.00 0.00 0.00 3.42
134 135 6.425210 TGTCCCTCCAATGAATGTATCTAG 57.575 41.667 0.00 0.00 0.00 2.43
135 136 6.386927 ACTTGTCCCTCCAATGAATGTATCTA 59.613 38.462 0.00 0.00 0.00 1.98
136 137 5.192522 ACTTGTCCCTCCAATGAATGTATCT 59.807 40.000 0.00 0.00 0.00 1.98
137 138 5.440610 ACTTGTCCCTCCAATGAATGTATC 58.559 41.667 0.00 0.00 0.00 2.24
138 139 5.456921 ACTTGTCCCTCCAATGAATGTAT 57.543 39.130 0.00 0.00 0.00 2.29
139 140 4.927267 ACTTGTCCCTCCAATGAATGTA 57.073 40.909 0.00 0.00 0.00 2.29
140 141 3.814504 ACTTGTCCCTCCAATGAATGT 57.185 42.857 0.00 0.00 0.00 2.71
141 142 5.473066 AAAACTTGTCCCTCCAATGAATG 57.527 39.130 0.00 0.00 0.00 2.67
161 162 2.907696 TGTACTCCCTCCATCCGAAAAA 59.092 45.455 0.00 0.00 0.00 1.94
162 163 2.542550 TGTACTCCCTCCATCCGAAAA 58.457 47.619 0.00 0.00 0.00 2.29
163 164 2.241281 TGTACTCCCTCCATCCGAAA 57.759 50.000 0.00 0.00 0.00 3.46
164 165 2.241281 TTGTACTCCCTCCATCCGAA 57.759 50.000 0.00 0.00 0.00 4.30
165 166 2.241281 TTTGTACTCCCTCCATCCGA 57.759 50.000 0.00 0.00 0.00 4.55
166 167 3.560636 ATTTTGTACTCCCTCCATCCG 57.439 47.619 0.00 0.00 0.00 4.18
167 168 6.174049 GCTATATTTTGTACTCCCTCCATCC 58.826 44.000 0.00 0.00 0.00 3.51
168 169 5.869888 CGCTATATTTTGTACTCCCTCCATC 59.130 44.000 0.00 0.00 0.00 3.51
169 170 5.307196 ACGCTATATTTTGTACTCCCTCCAT 59.693 40.000 0.00 0.00 0.00 3.41
170 171 4.652421 ACGCTATATTTTGTACTCCCTCCA 59.348 41.667 0.00 0.00 0.00 3.86
171 172 4.989168 CACGCTATATTTTGTACTCCCTCC 59.011 45.833 0.00 0.00 0.00 4.30
172 173 4.989168 CCACGCTATATTTTGTACTCCCTC 59.011 45.833 0.00 0.00 0.00 4.30
173 174 4.742743 GCCACGCTATATTTTGTACTCCCT 60.743 45.833 0.00 0.00 0.00 4.20
174 175 3.497262 GCCACGCTATATTTTGTACTCCC 59.503 47.826 0.00 0.00 0.00 4.30
175 176 3.497262 GGCCACGCTATATTTTGTACTCC 59.503 47.826 0.00 0.00 0.00 3.85
176 177 3.497262 GGGCCACGCTATATTTTGTACTC 59.503 47.826 4.39 0.00 0.00 2.59
177 178 3.118186 TGGGCCACGCTATATTTTGTACT 60.118 43.478 0.00 0.00 0.00 2.73
178 179 3.207778 TGGGCCACGCTATATTTTGTAC 58.792 45.455 0.00 0.00 0.00 2.90
192 193 1.188863 AGCATTTGAAGATGGGCCAC 58.811 50.000 9.28 2.67 0.00 5.01
226 227 5.775686 TGAAATATAGCACGCTATTACCGT 58.224 37.500 16.26 0.00 39.65 4.83
252 1500 5.257864 AGTACTTCGTTTTGCAAACGTTAC 58.742 37.500 23.62 21.35 43.47 2.50
255 1503 3.242511 GGAGTACTTCGTTTTGCAAACGT 60.243 43.478 23.62 14.25 43.47 3.99
274 1546 7.589958 ATGATAGTGTCTTAAGGTACTGGAG 57.410 40.000 17.43 0.00 40.86 3.86
276 1548 8.693120 TCTATGATAGTGTCTTAAGGTACTGG 57.307 38.462 17.43 6.07 40.86 4.00
304 1576 7.068962 GGTCCCTATCTATTGCTAGATTAGGTC 59.931 44.444 0.00 2.01 41.05 3.85
307 1579 7.962995 TGGTCCCTATCTATTGCTAGATTAG 57.037 40.000 0.00 0.00 41.05 1.73
378 1650 4.136796 TGGTCCTCAATGTTCAGAGTTTG 58.863 43.478 0.00 0.00 0.00 2.93
386 1658 4.894784 TGTAGTCTTGGTCCTCAATGTTC 58.105 43.478 0.00 0.00 34.45 3.18
396 1668 8.405418 TGTATATGGTAGATGTAGTCTTGGTC 57.595 38.462 0.00 0.00 38.42 4.02
403 1675 8.313944 TGTGGTTTGTATATGGTAGATGTAGT 57.686 34.615 0.00 0.00 0.00 2.73
417 1689 4.953579 ACAGGTTCACTTTGTGGTTTGTAT 59.046 37.500 0.00 0.00 33.87 2.29
442 1714 0.261991 TCAGAGTAGGGGTAGGCCAG 59.738 60.000 5.01 0.00 36.17 4.85
446 1718 4.030913 TCAATGTTCAGAGTAGGGGTAGG 58.969 47.826 0.00 0.00 0.00 3.18
451 1723 5.050490 CGGTTATCAATGTTCAGAGTAGGG 58.950 45.833 0.00 0.00 0.00 3.53
452 1724 5.050490 CCGGTTATCAATGTTCAGAGTAGG 58.950 45.833 0.00 0.00 0.00 3.18
466 1738 9.976511 CTCTTTATATGTTAACTCCGGTTATCA 57.023 33.333 7.22 0.00 40.01 2.15
474 1746 6.278363 TCGGTGCTCTTTATATGTTAACTCC 58.722 40.000 7.22 0.00 0.00 3.85
492 1764 2.125512 CACAGGTAGGCTCGGTGC 60.126 66.667 0.00 0.00 41.94 5.01
558 1830 1.856597 CCCTATAACGTTGTAGCGTGC 59.143 52.381 22.54 0.00 45.00 5.34
577 1849 1.986882 AATTAGCATGCTACAGGCCC 58.013 50.000 26.87 0.00 42.45 5.80
578 1850 2.480419 CGTAATTAGCATGCTACAGGCC 59.520 50.000 26.87 12.59 42.45 5.19
579 1851 3.059597 CACGTAATTAGCATGCTACAGGC 60.060 47.826 26.87 15.70 41.74 4.85
580 1852 4.368315 TCACGTAATTAGCATGCTACAGG 58.632 43.478 26.87 20.10 0.00 4.00
581 1853 5.966636 TTCACGTAATTAGCATGCTACAG 57.033 39.130 26.87 17.12 0.00 2.74
582 1854 6.145534 GCTATTCACGTAATTAGCATGCTACA 59.854 38.462 26.87 17.53 30.70 2.74
583 1855 6.526222 GCTATTCACGTAATTAGCATGCTAC 58.474 40.000 26.87 16.90 30.70 3.58
584 1856 5.344933 CGCTATTCACGTAATTAGCATGCTA 59.655 40.000 23.52 23.52 30.70 3.49
585 1857 4.150627 CGCTATTCACGTAATTAGCATGCT 59.849 41.667 25.99 25.99 30.70 3.79
586 1858 4.386230 CGCTATTCACGTAATTAGCATGC 58.614 43.478 10.51 10.51 30.70 4.06
587 1859 4.386230 GCGCTATTCACGTAATTAGCATG 58.614 43.478 17.62 0.00 30.70 4.06
588 1860 3.432252 GGCGCTATTCACGTAATTAGCAT 59.568 43.478 7.64 0.00 30.70 3.79
589 1861 2.798283 GGCGCTATTCACGTAATTAGCA 59.202 45.455 7.64 0.00 30.70 3.49
608 1880 6.515035 ATTTTAGTAAATTCAGCCGCTATGGC 60.515 38.462 0.00 0.00 46.96 4.40
626 1898 8.514330 TTGGAATGGAAACGCTATATTTTAGT 57.486 30.769 0.00 0.00 0.00 2.24
667 1939 2.539346 CGCTATAACCGCGCTATAGT 57.461 50.000 23.43 7.12 44.33 2.12
676 1948 3.515071 AAAAATAGCGCGCTATAACCG 57.485 42.857 43.81 0.00 38.20 4.44
703 1975 2.614134 AGCTTGGAGTCTGTCTACCT 57.386 50.000 0.00 0.00 0.00 3.08
704 1976 2.100087 GCTAGCTTGGAGTCTGTCTACC 59.900 54.545 7.70 0.00 0.00 3.18
744 2016 0.677098 GGGGTTTCCTTCGAGCCTTC 60.677 60.000 0.00 0.00 33.97 3.46
745 2017 1.379146 GGGGTTTCCTTCGAGCCTT 59.621 57.895 0.00 0.00 33.97 4.35
746 2018 1.842381 CTGGGGTTTCCTTCGAGCCT 61.842 60.000 0.00 0.00 36.20 4.58
747 2019 1.377333 CTGGGGTTTCCTTCGAGCC 60.377 63.158 0.00 0.00 36.20 4.70
748 2020 0.673956 GTCTGGGGTTTCCTTCGAGC 60.674 60.000 0.00 0.00 36.20 5.03
749 2021 0.036294 GGTCTGGGGTTTCCTTCGAG 60.036 60.000 0.00 0.00 36.20 4.04
750 2022 0.765135 TGGTCTGGGGTTTCCTTCGA 60.765 55.000 0.00 0.00 36.20 3.71
751 2023 0.321653 CTGGTCTGGGGTTTCCTTCG 60.322 60.000 0.00 0.00 36.20 3.79
795 2075 5.955959 GGTTTACAATTTCATAGGAGGGGTT 59.044 40.000 0.00 0.00 0.00 4.11
796 2076 5.255443 AGGTTTACAATTTCATAGGAGGGGT 59.745 40.000 0.00 0.00 0.00 4.95
857 2140 6.587273 AGGCCAAATAAGCTAACTCTTCTAG 58.413 40.000 5.01 0.00 0.00 2.43
873 2156 6.536684 AGATTTCTATTAGGGAGGCCAAAT 57.463 37.500 5.01 0.00 0.00 2.32
874 2157 5.994416 AGATTTCTATTAGGGAGGCCAAA 57.006 39.130 5.01 0.00 0.00 3.28
889 2173 3.560105 GGGCCAAAGCTGATAGATTTCT 58.440 45.455 4.39 0.00 30.47 2.52
1209 2493 0.984995 GGAGGTGGGAGTACTTGCTT 59.015 55.000 0.00 0.00 0.00 3.91
1236 2520 2.730672 GACGGTGAGCGTGTGCATC 61.731 63.158 16.53 0.00 46.23 3.91
1257 2541 1.515954 TTCGACGGAGAAGATGCCC 59.484 57.895 0.00 0.00 0.00 5.36
1281 2565 1.324005 TGTACCCGGCATCATCGTCA 61.324 55.000 0.00 0.00 0.00 4.35
1335 2631 2.037136 GTTGCACATGCTCTCGCCT 61.037 57.895 5.31 0.00 42.66 5.52
1418 2714 2.028484 GCTCGTCGGTGAACCACA 59.972 61.111 0.00 0.00 35.86 4.17
1651 2947 3.256960 GTGTGGGAGGGCCTTGGA 61.257 66.667 7.89 0.00 0.00 3.53
1857 4141 8.586744 TGAACAACAACACATATAGTAGGTACA 58.413 33.333 0.00 0.00 0.00 2.90
1942 4226 1.583054 GTATAGCTTCCTTGCACCGG 58.417 55.000 0.00 0.00 34.99 5.28
2248 4547 5.748152 GTGCTCAAAAGTGTGCTTATTTTGA 59.252 36.000 10.76 10.76 45.66 2.69
2281 4580 8.311109 GGTGTGTGAAAGAACCCAAATAATAAT 58.689 33.333 0.00 0.00 0.00 1.28
2282 4581 7.662897 GGTGTGTGAAAGAACCCAAATAATAA 58.337 34.615 0.00 0.00 0.00 1.40
2338 4640 4.458989 TGGAACAAAGGATGAAAATCTCGG 59.541 41.667 0.00 0.00 31.92 4.63
2417 5292 2.807837 GCGTATAGCCACGGGGTAATTT 60.808 50.000 5.12 0.00 42.18 1.82
2605 9020 4.082787 CCTTTATCGCAAAGAAAAGGCAGA 60.083 41.667 9.99 0.00 38.73 4.26
2615 9033 1.401905 GTGGAGGCCTTTATCGCAAAG 59.598 52.381 6.77 3.18 0.00 2.77
2636 9054 2.755655 CAACGTCTATCCAGTCTCCACT 59.244 50.000 0.00 0.00 0.00 4.00
2637 9055 2.735762 GCAACGTCTATCCAGTCTCCAC 60.736 54.545 0.00 0.00 0.00 4.02
2638 9056 1.476891 GCAACGTCTATCCAGTCTCCA 59.523 52.381 0.00 0.00 0.00 3.86
2639 9057 1.534175 CGCAACGTCTATCCAGTCTCC 60.534 57.143 0.00 0.00 0.00 3.71
2642 9060 0.457853 TGCGCAACGTCTATCCAGTC 60.458 55.000 8.16 0.00 0.00 3.51
2643 9061 0.736325 GTGCGCAACGTCTATCCAGT 60.736 55.000 14.00 0.00 0.00 4.00
2644 9062 1.999051 GTGCGCAACGTCTATCCAG 59.001 57.895 14.00 0.00 0.00 3.86
2645 9063 4.178861 GTGCGCAACGTCTATCCA 57.821 55.556 14.00 0.00 0.00 3.41
2699 9162 2.542907 CCAGTGTGTGTTCACGGCC 61.543 63.158 0.00 0.00 46.49 6.13
2735 9198 0.604243 TATGCGCCGTTTCCAGTGTT 60.604 50.000 4.18 0.00 0.00 3.32
2753 9216 4.994217 CACACATATGTATGGCCAATCGTA 59.006 41.667 10.96 12.11 36.72 3.43
2763 9226 9.389570 CATCAATTTAGCACACACATATGTATG 57.610 33.333 12.58 12.58 36.72 2.39
2767 9230 7.756272 ACAACATCAATTTAGCACACACATATG 59.244 33.333 0.00 0.00 0.00 1.78
2810 9276 1.728426 GAAGCAAACGCAGCAGCAG 60.728 57.895 0.82 0.00 42.27 4.24
2891 9357 4.215827 AGACGAAGAAGAAGAAGAAGCGTA 59.784 41.667 0.00 0.00 0.00 4.42
2957 9427 4.157656 TGCAAGCCGAGTTTAAATGCTAAT 59.842 37.500 8.64 0.00 33.66 1.73
2971 9663 0.874390 CAGCTAACTTTGCAAGCCGA 59.126 50.000 0.00 0.00 36.92 5.54
3012 9705 6.320171 CAGCAATAGTTTTGAGTGAATCAGG 58.680 40.000 0.00 0.00 39.68 3.86
3024 9717 2.744202 CCAGACGAGCAGCAATAGTTTT 59.256 45.455 0.00 0.00 0.00 2.43
3028 9721 1.850377 CTCCAGACGAGCAGCAATAG 58.150 55.000 0.00 0.00 0.00 1.73
3072 9765 2.485795 GGTGCGGTTGCCAGTCAAA 61.486 57.895 0.00 0.00 41.78 2.69
3088 9781 3.213402 CCCAACAACGTTGCCGGT 61.213 61.111 27.61 5.70 38.78 5.28
3107 9800 3.370231 GCGGATTTGGGCGTTGGT 61.370 61.111 0.00 0.00 0.00 3.67
3154 9847 5.668135 TGGATTGTTATCATTGGGGATCT 57.332 39.130 0.00 0.00 32.09 2.75
3155 9848 6.729690 TTTGGATTGTTATCATTGGGGATC 57.270 37.500 0.00 0.00 32.09 3.36


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

AutoCloner maintained by Alex Coulton.