Multiple sequence alignment - TraesCS6D01G223300

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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 TraesCS6D01G223300 chr6D 100.000 4462 0 0 1 4462 315365753 315361292 0.000000e+00 8240.0
1 TraesCS6D01G223300 chr6A 93.952 2348 108 16 1777 4106 452278808 452276477 0.000000e+00 3518.0
2 TraesCS6D01G223300 chr6A 91.021 1459 55 18 373 1779 452280347 452278913 0.000000e+00 1899.0
3 TraesCS6D01G223300 chr6A 88.235 323 22 7 1 309 452304198 452303878 5.450000e-99 372.0
4 TraesCS6D01G223300 chr6B 97.005 1469 38 2 2606 4074 512188662 512190124 0.000000e+00 2464.0
5 TraesCS6D01G223300 chr6B 88.775 1461 50 37 384 1776 512186110 512187524 0.000000e+00 1685.0
6 TraesCS6D01G223300 chr6B 89.483 580 44 10 1777 2352 512187645 512188211 0.000000e+00 717.0
7 TraesCS6D01G223300 chr6B 89.109 404 21 11 4080 4462 512190555 512190956 8.680000e-132 481.0
8 TraesCS6D01G223300 chr6B 87.633 283 14 10 78 341 512177700 512177980 4.330000e-80 309.0
9 TraesCS6D01G223300 chr6B 87.000 200 21 4 163 359 462130345 462130148 2.090000e-53 220.0
10 TraesCS6D01G223300 chr6B 89.189 148 15 1 2354 2500 512188249 512188396 2.740000e-42 183.0
11 TraesCS6D01G223300 chr1D 90.090 222 13 7 156 371 481454665 481454883 3.400000e-71 279.0
12 TraesCS6D01G223300 chr5D 86.047 215 20 10 157 366 500451324 500451533 5.810000e-54 222.0
13 TraesCS6D01G223300 chr5D 95.652 46 2 0 4207 4252 478164219 478164264 1.720000e-09 75.0
14 TraesCS6D01G223300 chr5D 93.333 45 3 0 4208 4252 367243808 367243852 2.880000e-07 67.6
15 TraesCS6D01G223300 chr5D 91.304 46 4 0 4207 4252 275415475 275415520 3.730000e-06 63.9
16 TraesCS6D01G223300 chr5A 85.922 206 24 5 158 359 7024076 7023872 9.720000e-52 215.0
17 TraesCS6D01G223300 chr7A 84.848 198 21 8 169 359 691612158 691612353 1.640000e-44 191.0
18 TraesCS6D01G223300 chr2B 78.889 270 53 3 1873 2140 581596947 581596680 3.550000e-41 180.0
19 TraesCS6D01G223300 chr5B 82.439 205 34 2 156 359 595286334 595286131 1.280000e-40 178.0
20 TraesCS6D01G223300 chr2A 78.545 275 55 3 1868 2140 640222242 640222514 1.280000e-40 178.0
21 TraesCS6D01G223300 chr7B 82.075 212 32 6 158 366 529826227 529826019 4.590000e-40 176.0
22 TraesCS6D01G223300 chr7B 93.478 46 3 0 4208 4253 214074912 214074957 8.010000e-08 69.4
23 TraesCS6D01G223300 chr2D 86.486 74 9 1 4184 4256 13914965 13914892 3.700000e-11 80.5
24 TraesCS6D01G223300 chr7D 93.478 46 3 0 4208 4253 237415122 237415167 8.010000e-08 69.4
25 TraesCS6D01G223300 chr3D 91.837 49 4 0 4207 4255 314619750 314619702 8.010000e-08 69.4
26 TraesCS6D01G223300 chr3A 91.837 49 4 0 4207 4255 417926939 417926891 8.010000e-08 69.4


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 TraesCS6D01G223300 chr6D 315361292 315365753 4461 True 8240.0 8240 100.0000 1 4462 1 chr6D.!!$R1 4461
1 TraesCS6D01G223300 chr6A 452276477 452280347 3870 True 2708.5 3518 92.4865 373 4106 2 chr6A.!!$R2 3733
2 TraesCS6D01G223300 chr6B 512186110 512190956 4846 False 1106.0 2464 90.7122 384 4462 5 chr6B.!!$F2 4078

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
148 149 0.028902 GTGCTTTGAACGAACCGCTT 59.971 50.000 0.00 0.00 0.0 4.68 F
600 604 0.458260 TGATACGACCACCCATCACG 59.542 55.000 0.00 0.00 0.0 4.35 F
877 891 0.466555 TTTACCAGTGGCGGCTTTGT 60.467 50.000 9.78 4.92 0.0 2.83 F
2222 2447 0.615331 GACAGGAGTGAGGCCAATGA 59.385 55.000 5.01 0.00 0.0 2.57 F
2782 3204 1.452833 GGAAGGGCCATCAGCAGAC 60.453 63.158 11.38 0.00 46.5 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 2091 1.565759 TGCTTATGGCCCTGATCAAGT 59.434 47.619 0.0 0.0 40.92 3.16 R
1945 2170 2.033194 GGGCAGCACAGTAACCGAC 61.033 63.158 0.0 0.0 0.00 4.79 R
2782 3204 2.413112 CGCTGTAGACACATGAGTTTGG 59.587 50.000 0.0 0.0 33.14 3.28 R
3316 3741 0.250727 GTCTGCTGTTGGCTTACCCA 60.251 55.000 0.0 0.0 43.51 4.51 R
4320 5199 2.289133 TGCCGTGTTACAAGATGCACTA 60.289 45.455 0.0 0.0 0.00 2.74 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
19 20 2.123726 GCAAAGGCCGGGATCCAT 60.124 61.111 15.23 0.00 0.00 3.41
20 21 2.492773 GCAAAGGCCGGGATCCATG 61.493 63.158 15.23 5.06 0.00 3.66
21 22 1.829533 CAAAGGCCGGGATCCATGG 60.830 63.158 15.23 15.75 0.00 3.66
27 28 4.996434 CGGGATCCATGGCGCCTC 62.996 72.222 29.70 16.37 0.00 4.70
28 29 4.650377 GGGATCCATGGCGCCTCC 62.650 72.222 29.70 24.60 0.00 4.30
42 43 2.620234 CCTCCATGGCCCTAAGACA 58.380 57.895 6.96 0.00 0.00 3.41
43 44 0.181350 CCTCCATGGCCCTAAGACAC 59.819 60.000 6.96 0.00 0.00 3.67
44 45 0.911769 CTCCATGGCCCTAAGACACA 59.088 55.000 6.96 0.00 0.00 3.72
45 46 0.911769 TCCATGGCCCTAAGACACAG 59.088 55.000 6.96 0.00 0.00 3.66
46 47 0.911769 CCATGGCCCTAAGACACAGA 59.088 55.000 0.00 0.00 0.00 3.41
47 48 1.281867 CCATGGCCCTAAGACACAGAA 59.718 52.381 0.00 0.00 0.00 3.02
48 49 2.636830 CATGGCCCTAAGACACAGAAG 58.363 52.381 0.00 0.00 0.00 2.85
49 50 2.024176 TGGCCCTAAGACACAGAAGA 57.976 50.000 0.00 0.00 0.00 2.87
50 51 2.551270 TGGCCCTAAGACACAGAAGAT 58.449 47.619 0.00 0.00 0.00 2.40
51 52 2.237143 TGGCCCTAAGACACAGAAGATG 59.763 50.000 0.00 0.00 0.00 2.90
52 53 2.501723 GGCCCTAAGACACAGAAGATGA 59.498 50.000 0.00 0.00 0.00 2.92
53 54 3.431486 GGCCCTAAGACACAGAAGATGAG 60.431 52.174 0.00 0.00 0.00 2.90
54 55 3.431486 GCCCTAAGACACAGAAGATGAGG 60.431 52.174 0.00 0.00 0.00 3.86
55 56 3.772025 CCCTAAGACACAGAAGATGAGGT 59.228 47.826 0.00 0.00 0.00 3.85
56 57 4.956700 CCCTAAGACACAGAAGATGAGGTA 59.043 45.833 0.00 0.00 0.00 3.08
57 58 5.068460 CCCTAAGACACAGAAGATGAGGTAG 59.932 48.000 0.00 0.00 0.00 3.18
58 59 5.888724 CCTAAGACACAGAAGATGAGGTAGA 59.111 44.000 0.00 0.00 0.00 2.59
59 60 5.652994 AAGACACAGAAGATGAGGTAGAC 57.347 43.478 0.00 0.00 0.00 2.59
60 61 4.020543 AGACACAGAAGATGAGGTAGACC 58.979 47.826 0.00 0.00 0.00 3.85
61 62 2.755655 ACACAGAAGATGAGGTAGACCG 59.244 50.000 0.00 0.00 42.08 4.79
62 63 1.751924 ACAGAAGATGAGGTAGACCGC 59.248 52.381 0.00 0.00 42.08 5.68
63 64 1.067821 CAGAAGATGAGGTAGACCGCC 59.932 57.143 0.00 0.00 42.08 6.13
64 65 0.030908 GAAGATGAGGTAGACCGCCG 59.969 60.000 0.00 0.00 42.08 6.46
65 66 1.392710 AAGATGAGGTAGACCGCCGG 61.393 60.000 0.00 0.00 42.08 6.13
66 67 3.501458 GATGAGGTAGACCGCCGGC 62.501 68.421 19.07 19.07 42.08 6.13
91 92 4.944249 GCGGAAGGCACAAGAAAC 57.056 55.556 0.00 0.00 42.87 2.78
92 93 1.285950 GCGGAAGGCACAAGAAACC 59.714 57.895 0.00 0.00 42.87 3.27
93 94 1.956802 CGGAAGGCACAAGAAACCC 59.043 57.895 0.00 0.00 0.00 4.11
94 95 0.537371 CGGAAGGCACAAGAAACCCT 60.537 55.000 0.00 0.00 0.00 4.34
95 96 1.271163 CGGAAGGCACAAGAAACCCTA 60.271 52.381 0.00 0.00 0.00 3.53
96 97 2.437413 GGAAGGCACAAGAAACCCTAG 58.563 52.381 0.00 0.00 0.00 3.02
97 98 2.437413 GAAGGCACAAGAAACCCTAGG 58.563 52.381 0.06 0.06 0.00 3.02
98 99 0.698818 AGGCACAAGAAACCCTAGGG 59.301 55.000 27.36 27.36 42.03 3.53
99 100 0.965866 GGCACAAGAAACCCTAGGGC 60.966 60.000 28.88 11.96 39.32 5.19
100 101 1.305930 GCACAAGAAACCCTAGGGCG 61.306 60.000 28.88 11.62 39.32 6.13
101 102 0.676782 CACAAGAAACCCTAGGGCGG 60.677 60.000 28.88 12.92 39.32 6.13
102 103 1.131928 ACAAGAAACCCTAGGGCGGT 61.132 55.000 28.88 13.20 39.32 5.68
103 104 0.037734 CAAGAAACCCTAGGGCGGTT 59.962 55.000 28.88 18.98 45.70 4.44
104 105 0.037734 AAGAAACCCTAGGGCGGTTG 59.962 55.000 28.88 3.00 42.90 3.77
105 106 1.378119 GAAACCCTAGGGCGGTTGG 60.378 63.158 28.88 2.18 42.90 3.77
106 107 2.831894 GAAACCCTAGGGCGGTTGGG 62.832 65.000 28.88 2.29 42.90 4.12
108 109 4.109675 CCCTAGGGCGGTTGGGTG 62.110 72.222 16.90 0.00 35.13 4.61
109 110 4.796495 CCTAGGGCGGTTGGGTGC 62.796 72.222 0.00 0.00 0.00 5.01
110 111 4.028490 CTAGGGCGGTTGGGTGCA 62.028 66.667 0.00 0.00 0.00 4.57
111 112 4.338710 TAGGGCGGTTGGGTGCAC 62.339 66.667 8.80 8.80 33.73 4.57
131 132 4.362476 GCAAGCCGCCAAAGGGTG 62.362 66.667 0.00 0.00 41.82 4.61
132 133 4.362476 CAAGCCGCCAAAGGGTGC 62.362 66.667 0.00 0.00 43.62 5.01
133 134 4.603535 AAGCCGCCAAAGGGTGCT 62.604 61.111 0.00 0.00 43.62 4.40
134 135 4.603535 AGCCGCCAAAGGGTGCTT 62.604 61.111 0.00 0.00 43.62 3.91
135 136 3.615709 GCCGCCAAAGGGTGCTTT 61.616 61.111 0.00 0.00 43.62 3.51
136 137 2.339712 CCGCCAAAGGGTGCTTTG 59.660 61.111 0.00 0.00 43.62 2.77
137 138 2.199652 CCGCCAAAGGGTGCTTTGA 61.200 57.895 0.00 0.00 44.54 2.69
138 139 1.739049 CGCCAAAGGGTGCTTTGAA 59.261 52.632 0.00 0.00 44.54 2.69
139 140 0.597377 CGCCAAAGGGTGCTTTGAAC 60.597 55.000 0.00 0.00 44.54 3.18
140 141 0.597377 GCCAAAGGGTGCTTTGAACG 60.597 55.000 0.00 0.00 44.54 3.95
141 142 1.028905 CCAAAGGGTGCTTTGAACGA 58.971 50.000 0.00 0.00 44.54 3.85
142 143 1.407258 CCAAAGGGTGCTTTGAACGAA 59.593 47.619 0.00 0.00 44.54 3.85
143 144 2.459934 CAAAGGGTGCTTTGAACGAAC 58.540 47.619 0.00 0.00 44.54 3.95
144 145 1.029681 AAGGGTGCTTTGAACGAACC 58.970 50.000 0.00 0.00 0.00 3.62
145 146 1.164041 AGGGTGCTTTGAACGAACCG 61.164 55.000 0.00 0.00 0.00 4.44
146 147 1.370051 GGTGCTTTGAACGAACCGC 60.370 57.895 0.00 0.00 0.00 5.68
147 148 1.647084 GTGCTTTGAACGAACCGCT 59.353 52.632 0.00 0.00 0.00 5.52
148 149 0.028902 GTGCTTTGAACGAACCGCTT 59.971 50.000 0.00 0.00 0.00 4.68
149 150 0.736053 TGCTTTGAACGAACCGCTTT 59.264 45.000 0.00 0.00 0.00 3.51
150 151 1.133407 TGCTTTGAACGAACCGCTTTT 59.867 42.857 0.00 0.00 0.00 2.27
151 152 1.516864 GCTTTGAACGAACCGCTTTTG 59.483 47.619 0.00 0.00 0.00 2.44
152 153 2.792749 CTTTGAACGAACCGCTTTTGT 58.207 42.857 0.00 0.00 32.58 2.83
153 154 2.923605 TTGAACGAACCGCTTTTGTT 57.076 40.000 0.00 1.21 43.53 2.83
154 155 4.344448 CTTTGAACGAACCGCTTTTGTTA 58.656 39.130 0.00 0.00 41.28 2.41
155 156 4.555348 TTGAACGAACCGCTTTTGTTAT 57.445 36.364 0.00 0.00 41.28 1.89
156 157 4.136517 TGAACGAACCGCTTTTGTTATC 57.863 40.909 0.00 0.00 41.28 1.75
157 158 2.867456 ACGAACCGCTTTTGTTATCG 57.133 45.000 0.00 0.00 0.00 2.92
158 159 2.137523 ACGAACCGCTTTTGTTATCGT 58.862 42.857 0.00 0.00 0.00 3.73
159 160 2.545106 ACGAACCGCTTTTGTTATCGTT 59.455 40.909 0.00 0.00 0.00 3.85
160 161 3.002553 ACGAACCGCTTTTGTTATCGTTT 59.997 39.130 0.00 0.00 0.00 3.60
161 162 3.596562 CGAACCGCTTTTGTTATCGTTTC 59.403 43.478 0.00 0.00 0.00 2.78
162 163 4.529446 GAACCGCTTTTGTTATCGTTTCA 58.471 39.130 0.00 0.00 0.00 2.69
163 164 4.759516 ACCGCTTTTGTTATCGTTTCAT 57.240 36.364 0.00 0.00 0.00 2.57
164 165 5.866335 ACCGCTTTTGTTATCGTTTCATA 57.134 34.783 0.00 0.00 0.00 2.15
165 166 6.243811 ACCGCTTTTGTTATCGTTTCATAA 57.756 33.333 0.00 0.00 0.00 1.90
166 167 6.848451 ACCGCTTTTGTTATCGTTTCATAAT 58.152 32.000 0.00 0.00 0.00 1.28
167 168 6.745450 ACCGCTTTTGTTATCGTTTCATAATG 59.255 34.615 0.00 0.00 0.00 1.90
168 169 6.745450 CCGCTTTTGTTATCGTTTCATAATGT 59.255 34.615 0.00 0.00 0.00 2.71
169 170 7.906010 CCGCTTTTGTTATCGTTTCATAATGTA 59.094 33.333 0.00 0.00 0.00 2.29
170 171 8.933955 CGCTTTTGTTATCGTTTCATAATGTAG 58.066 33.333 0.00 0.00 0.00 2.74
171 172 9.769093 GCTTTTGTTATCGTTTCATAATGTAGT 57.231 29.630 0.00 0.00 0.00 2.73
173 174 9.549509 TTTTGTTATCGTTTCATAATGTAGTGC 57.450 29.630 0.00 0.00 0.00 4.40
174 175 7.835634 TGTTATCGTTTCATAATGTAGTGCA 57.164 32.000 0.00 0.00 0.00 4.57
175 176 8.432110 TGTTATCGTTTCATAATGTAGTGCAT 57.568 30.769 0.00 0.00 40.03 3.96
176 177 9.535878 TGTTATCGTTTCATAATGTAGTGCATA 57.464 29.630 0.00 0.00 36.67 3.14
214 215 9.868277 AAAGTCAAACATTACAAACTTTGATCA 57.132 25.926 8.55 0.00 36.06 2.92
250 251 9.988815 ACAAAAATATGCACATTTAAAGTACCA 57.011 25.926 2.84 0.00 0.00 3.25
342 343 5.099042 ACAGTTGTCTCTGTTAACTTGGT 57.901 39.130 7.22 0.00 44.92 3.67
343 344 5.497474 ACAGTTGTCTCTGTTAACTTGGTT 58.503 37.500 7.22 0.00 44.92 3.67
344 345 6.646267 ACAGTTGTCTCTGTTAACTTGGTTA 58.354 36.000 7.22 0.00 44.92 2.85
345 346 7.107542 ACAGTTGTCTCTGTTAACTTGGTTAA 58.892 34.615 7.22 0.00 44.92 2.01
346 347 7.608761 ACAGTTGTCTCTGTTAACTTGGTTAAA 59.391 33.333 7.22 0.00 44.92 1.52
347 348 8.122952 CAGTTGTCTCTGTTAACTTGGTTAAAG 58.877 37.037 7.22 5.66 39.28 1.85
362 363 8.871686 CTTGGTTAAAGTTTGCTTAGTTGAAT 57.128 30.769 0.00 0.00 33.95 2.57
363 364 9.313118 CTTGGTTAAAGTTTGCTTAGTTGAATT 57.687 29.630 0.00 0.00 33.95 2.17
364 365 9.660180 TTGGTTAAAGTTTGCTTAGTTGAATTT 57.340 25.926 0.00 0.00 33.95 1.82
365 366 9.660180 TGGTTAAAGTTTGCTTAGTTGAATTTT 57.340 25.926 0.00 0.00 33.95 1.82
475 477 2.225068 ATCCGATGACTAGTTTGGCG 57.775 50.000 0.00 0.00 0.00 5.69
515 519 1.388133 GGGGTCAAAGCCATCCCTT 59.612 57.895 0.00 0.00 37.54 3.95
563 567 3.209812 CTCTCCCGTCGCCATCGA 61.210 66.667 0.00 0.00 43.28 3.59
598 602 1.754803 GACTGATACGACCACCCATCA 59.245 52.381 0.00 0.00 0.00 3.07
599 603 1.480954 ACTGATACGACCACCCATCAC 59.519 52.381 0.00 0.00 0.00 3.06
600 604 0.458260 TGATACGACCACCCATCACG 59.542 55.000 0.00 0.00 0.00 4.35
634 638 4.961433 GTGTAACTGTAACTCCGTTCAC 57.039 45.455 0.00 0.00 0.00 3.18
641 645 4.331717 ACTGTAACTCCGTTCACAAACTTG 59.668 41.667 0.00 0.00 32.95 3.16
643 647 1.021968 ACTCCGTTCACAAACTTGGC 58.978 50.000 0.00 0.00 32.95 4.52
644 648 1.021202 CTCCGTTCACAAACTTGGCA 58.979 50.000 0.00 0.00 32.95 4.92
645 649 0.736053 TCCGTTCACAAACTTGGCAC 59.264 50.000 0.00 0.00 32.95 5.01
701 712 4.810191 TTCTGCTTCTTCTCTTCCTACC 57.190 45.455 0.00 0.00 0.00 3.18
703 714 3.103742 CTGCTTCTTCTCTTCCTACCCT 58.896 50.000 0.00 0.00 0.00 4.34
721 732 2.287368 CCCTTCACAGCGTAAAACCAAC 60.287 50.000 0.00 0.00 0.00 3.77
757 768 4.287238 ACAACAGCCGAAACTTAAGTTG 57.713 40.909 21.22 10.97 38.44 3.16
758 769 3.066203 ACAACAGCCGAAACTTAAGTTGG 59.934 43.478 21.22 18.67 39.18 3.77
861 875 3.123284 CCGCGTCGGTTTTATTGACTTTA 59.877 43.478 4.92 0.00 42.73 1.85
877 891 0.466555 TTTACCAGTGGCGGCTTTGT 60.467 50.000 9.78 4.92 0.00 2.83
930 970 4.803426 CTGCCGAGCGAGGTGGAC 62.803 72.222 2.58 0.00 0.00 4.02
956 1004 1.937546 GCATGGAGGAAACAAGGCCG 61.938 60.000 0.00 0.00 0.00 6.13
1038 1092 0.911045 TCAGGAGCAAGATCAGGGCA 60.911 55.000 0.00 0.00 0.00 5.36
1454 1514 2.440409 CCACCAGGTTCTCCATTTCTG 58.560 52.381 0.00 0.00 35.89 3.02
1466 1526 4.523943 TCTCCATTTCTGTTTCCATGGTTG 59.476 41.667 12.58 0.00 37.92 3.77
1494 1554 2.420722 GGAATTTCATTCGGCGGTGTTA 59.579 45.455 7.21 0.29 40.17 2.41
1519 1594 4.444388 TCTCTTGTTTCATGTTCTTCGTCG 59.556 41.667 0.00 0.00 0.00 5.12
1527 1602 2.273370 TGTTCTTCGTCGTCATAGGC 57.727 50.000 0.00 0.00 0.00 3.93
1594 1669 3.873910 AGTACTACTTGCCAATTGCGAT 58.126 40.909 0.00 0.00 45.60 4.58
1595 1670 4.261801 AGTACTACTTGCCAATTGCGATT 58.738 39.130 0.00 0.00 45.60 3.34
1615 1690 4.649088 TTTATAGTAGCAGCTCTTCGCA 57.351 40.909 0.00 0.00 42.61 5.10
1745 1847 8.613060 CAGTGTGAATTCTGCCAACTATATAT 57.387 34.615 7.05 0.00 0.00 0.86
1753 1855 6.247229 TCTGCCAACTATATATGTGGTTGT 57.753 37.500 21.51 0.00 37.80 3.32
1758 1860 6.128007 GCCAACTATATATGTGGTTGTATGCC 60.128 42.308 21.51 6.45 37.80 4.40
1833 2058 4.414846 AGGAGCCAAGGATTCATTCAGTAT 59.585 41.667 0.00 0.00 0.00 2.12
1866 2091 5.751586 ACTTCCTTTTGTCTCACTACCAAA 58.248 37.500 0.00 0.00 0.00 3.28
1878 2103 2.749621 CACTACCAAACTTGATCAGGGC 59.250 50.000 9.90 0.00 0.00 5.19
1945 2170 1.801913 CCGAACCTCGTCAAGCTCG 60.802 63.158 0.00 0.00 38.40 5.03
2074 2299 4.424711 TTCCATGGGGCGTCAGGC 62.425 66.667 13.02 0.00 42.96 4.85
2100 2325 5.125417 GGAAATAGTATTTGGTGCTGCTCAA 59.875 40.000 12.86 3.07 0.00 3.02
2143 2368 1.697982 GGTTGGAGGTTCAGGTACAGT 59.302 52.381 0.00 0.00 0.00 3.55
2160 2385 2.564947 ACAGTTTGCCAACTTTCCACAA 59.435 40.909 0.00 0.00 40.66 3.33
2168 2393 4.081198 TGCCAACTTTCCACAACATTCTTT 60.081 37.500 0.00 0.00 0.00 2.52
2169 2394 4.507756 GCCAACTTTCCACAACATTCTTTC 59.492 41.667 0.00 0.00 0.00 2.62
2207 2432 7.928167 TGAGAATACTGCATTATTGTAGGACAG 59.072 37.037 13.48 0.00 39.64 3.51
2222 2447 0.615331 GACAGGAGTGAGGCCAATGA 59.385 55.000 5.01 0.00 0.00 2.57
2433 2695 5.241728 ACTCATTCCTTTTGCTTCAACTACC 59.758 40.000 0.00 0.00 0.00 3.18
2495 2811 4.141981 TGGATTGAACAATGTTGTGCAGTT 60.142 37.500 2.20 0.00 46.79 3.16
2535 2852 6.493116 CACATAGTTGAGAGAAAATGGATGC 58.507 40.000 0.00 0.00 0.00 3.91
2554 2871 8.812513 TGGATGCCATGAATATTATTTCCTAG 57.187 34.615 0.00 0.00 0.00 3.02
2556 2873 9.905713 GGATGCCATGAATATTATTTCCTAGTA 57.094 33.333 0.00 0.00 0.00 1.82
2580 2974 9.856488 GTACTATTTTTGAAGGGAAGGATTTTC 57.144 33.333 0.00 0.00 0.00 2.29
2625 3047 7.209475 CCTTCAAGGTTTTGATTTTGCTTAGA 58.791 34.615 0.00 0.00 42.60 2.10
2782 3204 1.452833 GGAAGGGCCATCAGCAGAC 60.453 63.158 11.38 0.00 46.50 3.51
2874 3296 5.449041 GCTCCATTCACGCATTCAAGAATAA 60.449 40.000 0.00 0.00 0.00 1.40
3119 3544 6.917217 AAGCAGTTCAGCAAGATTATAGAC 57.083 37.500 0.00 0.00 36.85 2.59
3167 3592 2.685388 GCAGGGAACTAGAGAAATTGCC 59.315 50.000 0.00 0.00 40.21 4.52
3316 3741 0.977627 TCGCCACCTCATGATGTCCT 60.978 55.000 0.02 0.00 0.00 3.85
3481 3906 7.974675 ACGTGATCTTCTGTAACAATTAATGG 58.025 34.615 0.00 0.00 0.00 3.16
3557 3982 7.110155 GGTGATTTTTCCTCCTTATCAGTGTA 58.890 38.462 0.00 0.00 0.00 2.90
3558 3983 7.065923 GGTGATTTTTCCTCCTTATCAGTGTAC 59.934 40.741 0.00 0.00 0.00 2.90
3698 4133 8.830580 CAATGTAGGTATGAAATGTAAGTCTGG 58.169 37.037 0.00 0.00 0.00 3.86
3729 4164 2.389962 TACCGTGTATCCAACCTTGC 57.610 50.000 0.00 0.00 0.00 4.01
3792 4227 5.165961 TGCTAGCCATATATTTGAGGTCC 57.834 43.478 13.29 0.00 0.00 4.46
3838 4273 6.069905 TGCAGATGGTACCTTAGGTATGAAAA 60.070 38.462 14.78 0.00 40.54 2.29
3884 4319 4.990426 ACTGCTTATTTTCAACATGCCAAC 59.010 37.500 0.00 0.00 0.00 3.77
4090 4950 5.880054 TGAACTCTTATGCCAAAGTAAGC 57.120 39.130 0.00 0.00 0.00 3.09
4101 4961 2.424956 CCAAAGTAAGCATGCCCTCTTC 59.575 50.000 15.66 0.00 0.00 2.87
4181 5041 6.474102 GCTAGAAGAAGAAAGGAACAGATACG 59.526 42.308 0.00 0.00 0.00 3.06
4202 5062 5.770417 ACGAAGTACTTCCTCTGTAACTTG 58.230 41.667 26.12 12.19 41.94 3.16
4204 5064 6.208994 ACGAAGTACTTCCTCTGTAACTTGAT 59.791 38.462 26.12 0.00 41.94 2.57
4205 5065 6.528423 CGAAGTACTTCCTCTGTAACTTGATG 59.472 42.308 26.12 5.95 36.27 3.07
4209 5069 9.036980 AGTACTTCCTCTGTAACTTGATGTAAT 57.963 33.333 0.00 0.00 0.00 1.89
4268 5146 6.990341 GGTAGTATTACCCAACGACAAAAT 57.010 37.500 3.01 0.00 43.06 1.82
4320 5199 9.274206 CATGTCTTGATCAGAGAAACATCATAT 57.726 33.333 8.55 0.00 29.34 1.78
4337 5216 8.370493 ACATCATATAGTGCATCTTGTAACAC 57.630 34.615 0.00 0.00 0.00 3.32
4357 5236 5.719173 ACACGGCAGCAAATTATTAAACAT 58.281 33.333 0.00 0.00 0.00 2.71
4409 5289 9.967346 GAGTTGAATATGTACATCAGTAGCTTA 57.033 33.333 12.68 0.00 0.00 3.09
4428 5308 5.244626 AGCTTAACAAAATGACCAGCAATCT 59.755 36.000 0.00 0.00 0.00 2.40
4440 5321 4.826556 ACCAGCAATCTAGAAACAGAGAC 58.173 43.478 0.00 0.00 0.00 3.36
4446 5327 4.734398 ATCTAGAAACAGAGACTGCTGG 57.266 45.455 0.00 0.00 40.20 4.85
4447 5328 3.501349 TCTAGAAACAGAGACTGCTGGT 58.499 45.455 0.00 0.00 40.20 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.123726 ATGGATCCCGGCCTTTGC 60.124 61.111 9.90 0.00 0.00 3.68
3 4 1.829533 CCATGGATCCCGGCCTTTG 60.830 63.158 5.56 0.00 0.00 2.77
4 5 2.603008 CCATGGATCCCGGCCTTT 59.397 61.111 5.56 0.00 0.00 3.11
5 6 4.209866 GCCATGGATCCCGGCCTT 62.210 66.667 25.35 0.00 40.07 4.35
10 11 4.996434 GAGGCGCCATGGATCCCG 62.996 72.222 31.54 10.78 0.00 5.14
11 12 4.650377 GGAGGCGCCATGGATCCC 62.650 72.222 31.54 11.80 36.34 3.85
12 13 3.877450 TGGAGGCGCCATGGATCC 61.877 66.667 31.54 25.89 43.33 3.36
24 25 0.181350 GTGTCTTAGGGCCATGGAGG 59.819 60.000 18.40 0.00 41.84 4.30
25 26 0.911769 TGTGTCTTAGGGCCATGGAG 59.088 55.000 18.40 3.03 0.00 3.86
26 27 0.911769 CTGTGTCTTAGGGCCATGGA 59.088 55.000 18.40 0.00 0.00 3.41
27 28 0.911769 TCTGTGTCTTAGGGCCATGG 59.088 55.000 7.63 7.63 0.00 3.66
28 29 2.237143 TCTTCTGTGTCTTAGGGCCATG 59.763 50.000 6.18 0.00 0.00 3.66
29 30 2.551270 TCTTCTGTGTCTTAGGGCCAT 58.449 47.619 6.18 0.00 0.00 4.40
30 31 2.024176 TCTTCTGTGTCTTAGGGCCA 57.976 50.000 6.18 0.00 0.00 5.36
31 32 2.501723 TCATCTTCTGTGTCTTAGGGCC 59.498 50.000 0.00 0.00 0.00 5.80
32 33 3.431486 CCTCATCTTCTGTGTCTTAGGGC 60.431 52.174 0.00 0.00 0.00 5.19
33 34 3.772025 ACCTCATCTTCTGTGTCTTAGGG 59.228 47.826 0.00 0.00 0.00 3.53
34 35 5.888724 TCTACCTCATCTTCTGTGTCTTAGG 59.111 44.000 0.00 0.00 0.00 2.69
35 36 6.183360 GGTCTACCTCATCTTCTGTGTCTTAG 60.183 46.154 0.00 0.00 0.00 2.18
36 37 5.652891 GGTCTACCTCATCTTCTGTGTCTTA 59.347 44.000 0.00 0.00 0.00 2.10
37 38 4.464597 GGTCTACCTCATCTTCTGTGTCTT 59.535 45.833 0.00 0.00 0.00 3.01
38 39 4.020543 GGTCTACCTCATCTTCTGTGTCT 58.979 47.826 0.00 0.00 0.00 3.41
39 40 3.181495 CGGTCTACCTCATCTTCTGTGTC 60.181 52.174 0.00 0.00 0.00 3.67
40 41 2.755655 CGGTCTACCTCATCTTCTGTGT 59.244 50.000 0.00 0.00 0.00 3.72
41 42 2.480416 GCGGTCTACCTCATCTTCTGTG 60.480 54.545 0.00 0.00 0.00 3.66
42 43 1.751924 GCGGTCTACCTCATCTTCTGT 59.248 52.381 0.00 0.00 0.00 3.41
43 44 1.067821 GGCGGTCTACCTCATCTTCTG 59.932 57.143 0.00 0.00 0.00 3.02
44 45 1.404843 GGCGGTCTACCTCATCTTCT 58.595 55.000 0.00 0.00 0.00 2.85
45 46 0.030908 CGGCGGTCTACCTCATCTTC 59.969 60.000 0.00 0.00 0.00 2.87
46 47 1.392710 CCGGCGGTCTACCTCATCTT 61.393 60.000 19.97 0.00 0.00 2.40
47 48 1.828660 CCGGCGGTCTACCTCATCT 60.829 63.158 19.97 0.00 0.00 2.90
48 49 2.728817 CCGGCGGTCTACCTCATC 59.271 66.667 19.97 0.00 0.00 2.92
49 50 3.537874 GCCGGCGGTCTACCTCAT 61.538 66.667 28.82 0.00 0.00 2.90
71 72 4.697756 TCTTGTGCCTTCCGCCGG 62.698 66.667 0.00 0.00 36.24 6.13
72 73 2.258013 TTTCTTGTGCCTTCCGCCG 61.258 57.895 0.00 0.00 36.24 6.46
73 74 1.285950 GTTTCTTGTGCCTTCCGCC 59.714 57.895 0.00 0.00 36.24 6.13
74 75 1.285950 GGTTTCTTGTGCCTTCCGC 59.714 57.895 0.00 0.00 38.31 5.54
75 76 0.537371 AGGGTTTCTTGTGCCTTCCG 60.537 55.000 0.00 0.00 0.00 4.30
76 77 2.437413 CTAGGGTTTCTTGTGCCTTCC 58.563 52.381 0.00 0.00 0.00 3.46
77 78 2.437413 CCTAGGGTTTCTTGTGCCTTC 58.563 52.381 0.00 0.00 0.00 3.46
78 79 1.075536 CCCTAGGGTTTCTTGTGCCTT 59.924 52.381 20.88 0.00 0.00 4.35
79 80 0.698818 CCCTAGGGTTTCTTGTGCCT 59.301 55.000 20.88 0.00 0.00 4.75
80 81 0.965866 GCCCTAGGGTTTCTTGTGCC 60.966 60.000 28.96 4.28 37.65 5.01
81 82 1.305930 CGCCCTAGGGTTTCTTGTGC 61.306 60.000 28.96 10.08 37.65 4.57
82 83 0.676782 CCGCCCTAGGGTTTCTTGTG 60.677 60.000 28.96 7.56 37.65 3.33
83 84 1.131928 ACCGCCCTAGGGTTTCTTGT 61.132 55.000 28.96 13.71 32.70 3.16
84 85 0.037734 AACCGCCCTAGGGTTTCTTG 59.962 55.000 28.96 13.10 45.25 3.02
85 86 0.037734 CAACCGCCCTAGGGTTTCTT 59.962 55.000 28.96 12.29 45.25 2.52
86 87 1.683441 CAACCGCCCTAGGGTTTCT 59.317 57.895 28.96 9.13 45.25 2.52
87 88 1.378119 CCAACCGCCCTAGGGTTTC 60.378 63.158 28.96 11.69 45.25 2.78
88 89 2.761160 CCAACCGCCCTAGGGTTT 59.239 61.111 28.96 16.47 45.25 3.27
91 92 4.109675 CACCCAACCGCCCTAGGG 62.110 72.222 24.89 24.89 46.96 3.53
92 93 4.796495 GCACCCAACCGCCCTAGG 62.796 72.222 0.06 0.06 37.30 3.02
93 94 4.028490 TGCACCCAACCGCCCTAG 62.028 66.667 0.00 0.00 0.00 3.02
94 95 4.338710 GTGCACCCAACCGCCCTA 62.339 66.667 5.22 0.00 0.00 3.53
114 115 4.362476 CACCCTTTGGCGGCTTGC 62.362 66.667 11.43 0.00 45.38 4.01
115 116 4.362476 GCACCCTTTGGCGGCTTG 62.362 66.667 11.43 0.00 33.61 4.01
116 117 4.603535 AGCACCCTTTGGCGGCTT 62.604 61.111 11.43 0.00 41.39 4.35
117 118 4.603535 AAGCACCCTTTGGCGGCT 62.604 61.111 11.43 0.00 44.82 5.52
118 119 3.615709 AAAGCACCCTTTGGCGGC 61.616 61.111 0.00 0.00 39.72 6.53
124 125 1.407618 GGTTCGTTCAAAGCACCCTTT 59.592 47.619 0.00 0.00 41.86 3.11
125 126 1.029681 GGTTCGTTCAAAGCACCCTT 58.970 50.000 0.00 0.00 0.00 3.95
126 127 1.164041 CGGTTCGTTCAAAGCACCCT 61.164 55.000 0.00 0.00 0.00 4.34
127 128 1.281656 CGGTTCGTTCAAAGCACCC 59.718 57.895 0.00 0.00 0.00 4.61
128 129 1.370051 GCGGTTCGTTCAAAGCACC 60.370 57.895 0.00 0.00 0.00 5.01
129 130 0.028902 AAGCGGTTCGTTCAAAGCAC 59.971 50.000 0.00 0.00 0.00 4.40
130 131 0.736053 AAAGCGGTTCGTTCAAAGCA 59.264 45.000 0.00 0.00 0.00 3.91
131 132 1.516864 CAAAAGCGGTTCGTTCAAAGC 59.483 47.619 0.00 0.00 0.00 3.51
132 133 2.792749 ACAAAAGCGGTTCGTTCAAAG 58.207 42.857 0.00 0.00 0.00 2.77
133 134 2.923605 ACAAAAGCGGTTCGTTCAAA 57.076 40.000 0.00 0.00 0.00 2.69
134 135 2.923605 AACAAAAGCGGTTCGTTCAA 57.076 40.000 0.00 0.00 0.00 2.69
135 136 3.363182 CGATAACAAAAGCGGTTCGTTCA 60.363 43.478 15.71 6.40 0.00 3.18
136 137 3.150731 CGATAACAAAAGCGGTTCGTTC 58.849 45.455 15.71 5.36 0.00 3.95
137 138 2.545106 ACGATAACAAAAGCGGTTCGTT 59.455 40.909 16.28 16.28 28.31 3.85
138 139 2.137523 ACGATAACAAAAGCGGTTCGT 58.862 42.857 0.00 0.73 0.00 3.85
139 140 2.867456 ACGATAACAAAAGCGGTTCG 57.133 45.000 0.00 0.00 0.00 3.95
141 142 4.555348 TGAAACGATAACAAAAGCGGTT 57.445 36.364 0.00 0.00 36.24 4.44
142 143 4.759516 ATGAAACGATAACAAAAGCGGT 57.240 36.364 0.00 0.00 0.00 5.68
143 144 6.745450 ACATTATGAAACGATAACAAAAGCGG 59.255 34.615 0.00 0.00 0.00 5.52
144 145 7.719689 ACATTATGAAACGATAACAAAAGCG 57.280 32.000 0.00 0.00 0.00 4.68
145 146 9.769093 ACTACATTATGAAACGATAACAAAAGC 57.231 29.630 0.00 0.00 0.00 3.51
147 148 9.549509 GCACTACATTATGAAACGATAACAAAA 57.450 29.630 0.00 0.00 0.00 2.44
148 149 8.722394 TGCACTACATTATGAAACGATAACAAA 58.278 29.630 0.00 0.00 0.00 2.83
149 150 8.257830 TGCACTACATTATGAAACGATAACAA 57.742 30.769 0.00 0.00 0.00 2.83
150 151 7.835634 TGCACTACATTATGAAACGATAACA 57.164 32.000 0.00 0.00 0.00 2.41
188 189 9.868277 TGATCAAAGTTTGTAATGTTTGACTTT 57.132 25.926 15.08 0.00 40.67 2.66
224 225 9.988815 TGGTACTTTAAATGTGCATATTTTTGT 57.011 25.926 23.95 20.14 32.79 2.83
321 322 7.548196 TTAACCAAGTTAACAGAGACAACTG 57.452 36.000 8.61 0.00 42.78 3.16
322 323 7.827729 ACTTTAACCAAGTTAACAGAGACAACT 59.172 33.333 8.61 0.00 43.89 3.16
323 324 7.982224 ACTTTAACCAAGTTAACAGAGACAAC 58.018 34.615 8.61 0.00 43.89 3.32
337 338 8.871686 ATTCAACTAAGCAAACTTTAACCAAG 57.128 30.769 0.00 0.00 37.33 3.61
338 339 9.660180 AAATTCAACTAAGCAAACTTTAACCAA 57.340 25.926 0.00 0.00 37.33 3.67
339 340 9.660180 AAAATTCAACTAAGCAAACTTTAACCA 57.340 25.926 0.00 0.00 37.33 3.67
363 364 3.007614 CCCTCCCTCTGTTCGTCTAAAAA 59.992 47.826 0.00 0.00 0.00 1.94
364 365 2.565834 CCCTCCCTCTGTTCGTCTAAAA 59.434 50.000 0.00 0.00 0.00 1.52
365 366 2.176889 CCCTCCCTCTGTTCGTCTAAA 58.823 52.381 0.00 0.00 0.00 1.85
366 367 1.356738 TCCCTCCCTCTGTTCGTCTAA 59.643 52.381 0.00 0.00 0.00 2.10
367 368 0.997363 TCCCTCCCTCTGTTCGTCTA 59.003 55.000 0.00 0.00 0.00 2.59
368 369 0.323908 CTCCCTCCCTCTGTTCGTCT 60.324 60.000 0.00 0.00 0.00 4.18
369 370 0.612453 ACTCCCTCCCTCTGTTCGTC 60.612 60.000 0.00 0.00 0.00 4.20
370 371 0.702902 TACTCCCTCCCTCTGTTCGT 59.297 55.000 0.00 0.00 0.00 3.85
371 372 1.104630 GTACTCCCTCCCTCTGTTCG 58.895 60.000 0.00 0.00 0.00 3.95
441 442 6.326583 AGTCATCGGATATCTTCCCTAAAACA 59.673 38.462 2.05 0.00 42.06 2.83
442 443 6.760291 AGTCATCGGATATCTTCCCTAAAAC 58.240 40.000 2.05 0.00 42.06 2.43
458 460 0.739462 TGCGCCAAACTAGTCATCGG 60.739 55.000 4.18 0.00 0.00 4.18
563 567 5.120208 CGTATCAGTCAAACGAAATGGTCTT 59.880 40.000 0.00 0.00 38.89 3.01
598 602 3.194968 AGTTACACTAACTAGGCATGCGT 59.805 43.478 18.09 18.09 46.53 5.24
599 603 3.551890 CAGTTACACTAACTAGGCATGCG 59.448 47.826 12.44 0.00 46.66 4.73
600 604 4.504858 ACAGTTACACTAACTAGGCATGC 58.495 43.478 9.90 9.90 46.66 4.06
625 629 1.021202 TGCCAAGTTTGTGAACGGAG 58.979 50.000 0.00 0.00 40.75 4.63
626 630 0.736053 GTGCCAAGTTTGTGAACGGA 59.264 50.000 0.00 0.00 40.75 4.69
634 638 5.063060 GGATTACTACTACGTGCCAAGTTTG 59.937 44.000 0.00 0.00 0.00 2.93
641 645 3.561725 ACTACGGATTACTACTACGTGCC 59.438 47.826 0.00 0.00 38.34 5.01
643 647 6.256539 TGAAGACTACGGATTACTACTACGTG 59.743 42.308 0.00 0.00 38.34 4.49
644 648 6.256757 GTGAAGACTACGGATTACTACTACGT 59.743 42.308 0.00 0.00 41.10 3.57
645 649 6.256539 TGTGAAGACTACGGATTACTACTACG 59.743 42.308 0.00 0.00 0.00 3.51
701 712 2.356382 TGTTGGTTTTACGCTGTGAAGG 59.644 45.455 0.00 0.00 0.00 3.46
703 714 4.640789 AATGTTGGTTTTACGCTGTGAA 57.359 36.364 0.00 0.00 0.00 3.18
721 732 5.399301 CGGCTGTTGTTTCTGAACTTAAATG 59.601 40.000 0.00 0.00 36.70 2.32
757 768 3.496331 TGAATTTCACCAACCTTCCTCC 58.504 45.455 0.00 0.00 0.00 4.30
758 769 4.142600 CGATGAATTTCACCAACCTTCCTC 60.143 45.833 0.15 0.00 0.00 3.71
861 875 2.906897 CACAAAGCCGCCACTGGT 60.907 61.111 0.00 0.00 0.00 4.00
1038 1092 2.759795 GGTCTCTTGCCCTTGCCT 59.240 61.111 0.00 0.00 36.33 4.75
1141 1195 4.767255 CTGGGACTGGCTCGTGGC 62.767 72.222 3.80 3.80 40.90 5.01
1142 1196 3.302347 GACTGGGACTGGCTCGTGG 62.302 68.421 0.00 0.00 30.30 4.94
1143 1197 2.262915 GACTGGGACTGGCTCGTG 59.737 66.667 0.00 0.00 30.30 4.35
1144 1198 2.997897 GGACTGGGACTGGCTCGT 60.998 66.667 0.00 0.00 34.87 4.18
1145 1199 3.775654 GGGACTGGGACTGGCTCG 61.776 72.222 0.00 0.00 34.87 5.03
1146 1200 2.607750 TGGGACTGGGACTGGCTC 60.608 66.667 0.00 0.00 35.77 4.70
1147 1201 2.608988 CTGGGACTGGGACTGGCT 60.609 66.667 0.00 0.00 34.87 4.75
1148 1202 3.721706 CCTGGGACTGGGACTGGC 61.722 72.222 0.00 0.00 44.20 4.85
1302 1362 2.571757 CGGCTGAAGTCGCTGGTA 59.428 61.111 0.00 0.00 35.94 3.25
1454 1514 8.846943 AAATTCCTAATTTCAACCATGGAAAC 57.153 30.769 21.47 0.00 36.38 2.78
1494 1554 6.346919 CGACGAAGAACATGAAACAAGAGAAT 60.347 38.462 0.00 0.00 0.00 2.40
1519 1594 5.907207 TCTTACACTGAATCAGCCTATGAC 58.093 41.667 10.62 0.00 41.91 3.06
1527 1602 5.537188 GGGCTAGATCTTACACTGAATCAG 58.463 45.833 8.98 8.98 37.52 2.90
1615 1690 1.636148 ACAATTGTGGAAGCCAGCAT 58.364 45.000 11.07 0.00 32.34 3.79
1704 1806 5.062528 TCACACTGCACAGATGTTTCATTA 58.937 37.500 4.31 0.00 0.00 1.90
1708 1810 3.969117 TTCACACTGCACAGATGTTTC 57.031 42.857 4.31 0.00 0.00 2.78
1744 1846 3.439857 ACTGAAGGCATACAACCACAT 57.560 42.857 0.00 0.00 0.00 3.21
1745 1847 2.949177 ACTGAAGGCATACAACCACA 57.051 45.000 0.00 0.00 0.00 4.17
1753 1855 7.822161 ACAATGCAATAATACTGAAGGCATA 57.178 32.000 0.00 0.00 39.36 3.14
1792 2014 7.031270 GGCTCCTAGTAGCAAATAGCCAGAT 62.031 48.000 9.75 0.00 45.81 2.90
1795 2017 2.368875 GGCTCCTAGTAGCAAATAGCCA 59.631 50.000 9.75 0.00 45.81 4.75
1797 2019 3.753294 TGGCTCCTAGTAGCAAATAGC 57.247 47.619 9.75 0.00 44.64 2.97
1833 2058 8.188139 GTGAGACAAAAGGAAGTCAAATACAAA 58.812 33.333 0.00 0.00 37.23 2.83
1866 2091 1.565759 TGCTTATGGCCCTGATCAAGT 59.434 47.619 0.00 0.00 40.92 3.16
1945 2170 2.033194 GGGCAGCACAGTAACCGAC 61.033 63.158 0.00 0.00 0.00 4.79
2074 2299 4.641989 AGCAGCACCAAATACTATTTCCAG 59.358 41.667 0.00 0.00 0.00 3.86
2100 2325 5.398353 CCCTTCATGGAGATACATCAAACCT 60.398 44.000 1.24 0.00 38.35 3.50
2143 2368 3.902881 ATGTTGTGGAAAGTTGGCAAA 57.097 38.095 0.00 0.00 0.00 3.68
2168 2393 5.871524 GCAGTATTCTCATTTCTCACACAGA 59.128 40.000 0.00 0.00 0.00 3.41
2169 2394 5.640783 TGCAGTATTCTCATTTCTCACACAG 59.359 40.000 0.00 0.00 0.00 3.66
2207 2432 3.144506 CATACATCATTGGCCTCACTCC 58.855 50.000 3.32 0.00 0.00 3.85
2310 2535 5.931724 CAGCATTTACCGATATGATGTGGTA 59.068 40.000 0.00 0.00 35.93 3.25
2418 2679 4.727507 TGCAAAGGTAGTTGAAGCAAAA 57.272 36.364 0.00 0.00 0.00 2.44
2477 2793 5.764487 TGATAACTGCACAACATTGTTCA 57.236 34.783 0.00 0.00 39.91 3.18
2495 2811 9.665719 TCAACTATGTGCTTCAATTAGTTGATA 57.334 29.630 20.84 10.50 44.63 2.15
2510 2827 6.493116 CATCCATTTTCTCTCAACTATGTGC 58.507 40.000 0.00 0.00 0.00 4.57
2554 2871 9.856488 GAAAATCCTTCCCTTCAAAAATAGTAC 57.144 33.333 0.00 0.00 0.00 2.73
2556 2873 8.491045 TGAAAATCCTTCCCTTCAAAAATAGT 57.509 30.769 0.00 0.00 0.00 2.12
2558 2875 9.554395 GTTTGAAAATCCTTCCCTTCAAAAATA 57.446 29.630 9.65 0.00 44.79 1.40
2559 2876 8.052141 TGTTTGAAAATCCTTCCCTTCAAAAAT 58.948 29.630 9.65 0.00 44.79 1.82
2560 2877 7.398024 TGTTTGAAAATCCTTCCCTTCAAAAA 58.602 30.769 9.65 3.33 44.79 1.94
2562 2879 6.552445 TGTTTGAAAATCCTTCCCTTCAAA 57.448 33.333 5.05 5.05 42.49 2.69
2564 2881 5.660864 ACTTGTTTGAAAATCCTTCCCTTCA 59.339 36.000 0.00 0.00 0.00 3.02
2565 2882 5.985530 CACTTGTTTGAAAATCCTTCCCTTC 59.014 40.000 0.00 0.00 0.00 3.46
2580 2974 6.039270 TGAAGGTTGGAGATAACACTTGTTTG 59.961 38.462 0.00 0.00 39.31 2.93
2782 3204 2.413112 CGCTGTAGACACATGAGTTTGG 59.587 50.000 0.00 0.00 33.14 3.28
2820 3242 6.091986 GGAAACTCTGTTATCTTGCTCTGAAG 59.908 42.308 0.00 0.00 0.00 3.02
2874 3296 7.121463 ACGATAGAGCGAGTTATCATAAGGAAT 59.879 37.037 0.00 0.00 41.38 3.01
3119 3544 0.600255 AACGGCCTTCGAGTCTTGTG 60.600 55.000 0.00 0.00 42.43 3.33
3167 3592 1.067916 GCAGGTGTTGGCCAACTTG 59.932 57.895 40.40 33.70 38.15 3.16
3316 3741 0.250727 GTCTGCTGTTGGCTTACCCA 60.251 55.000 0.00 0.00 43.51 4.51
3481 3906 2.165845 ACAATGTACACGGAGTCTAGGC 59.834 50.000 0.00 0.00 41.61 3.93
3557 3982 9.574516 AAACATTAGATCTTCTAAAGGTTGTGT 57.425 29.630 0.00 6.07 41.72 3.72
3698 4133 7.599630 TGGATACACGGTAAAACATAGAAAC 57.400 36.000 0.00 0.00 46.17 2.78
3729 4164 5.713025 CCACCATTTTCAATGTCTACCTTG 58.287 41.667 0.00 0.00 0.00 3.61
3792 4227 4.772434 CAAAGTGCCATTTACCGATATCG 58.228 43.478 18.31 18.31 39.44 2.92
4074 4509 3.491447 GGGCATGCTTACTTTGGCATAAG 60.491 47.826 18.92 2.65 45.82 1.73
4090 4950 2.602257 TACATGTCGAAGAGGGCATG 57.398 50.000 0.00 9.23 42.93 4.06
4146 5006 8.375506 TCCTTTCTTCTTCTAGCAGACAAAATA 58.624 33.333 0.00 0.00 0.00 1.40
4147 5007 7.227156 TCCTTTCTTCTTCTAGCAGACAAAAT 58.773 34.615 0.00 0.00 0.00 1.82
4149 5009 6.174720 TCCTTTCTTCTTCTAGCAGACAAA 57.825 37.500 0.00 0.00 0.00 2.83
4150 5010 5.808366 TCCTTTCTTCTTCTAGCAGACAA 57.192 39.130 0.00 0.00 0.00 3.18
4181 5041 7.379750 ACATCAAGTTACAGAGGAAGTACTTC 58.620 38.462 24.73 24.73 38.80 3.01
4194 5054 7.935520 TGCAGTTCAAATTACATCAAGTTACA 58.064 30.769 0.00 0.00 0.00 2.41
4202 5062 8.981647 AGACATTTTTGCAGTTCAAATTACATC 58.018 29.630 0.00 0.00 43.53 3.06
4204 5064 8.715191 AAGACATTTTTGCAGTTCAAATTACA 57.285 26.923 0.00 0.00 43.53 2.41
4209 5069 8.715191 AATGTAAGACATTTTTGCAGTTCAAA 57.285 26.923 0.00 0.00 45.80 2.69
4237 5115 7.489435 GTCGTTGGGTAATACTACCTCTTTAAC 59.511 40.741 0.00 0.00 46.20 2.01
4241 5119 5.018809 TGTCGTTGGGTAATACTACCTCTT 58.981 41.667 0.00 0.00 46.20 2.85
4294 5173 6.980051 TGATGTTTCTCTGATCAAGACATG 57.020 37.500 6.74 0.00 0.00 3.21
4320 5199 2.289133 TGCCGTGTTACAAGATGCACTA 60.289 45.455 0.00 0.00 0.00 2.74
4337 5216 5.804473 TGTGATGTTTAATAATTTGCTGCCG 59.196 36.000 0.00 0.00 0.00 5.69
4373 5253 8.196802 TGTACATATTCAACTCATTTTCCTCG 57.803 34.615 0.00 0.00 0.00 4.63
4409 5289 6.899393 TTCTAGATTGCTGGTCATTTTGTT 57.101 33.333 0.00 0.00 0.00 2.83
4428 5308 3.944055 GACCAGCAGTCTCTGTTTCTA 57.056 47.619 0.00 0.00 42.69 2.10


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

AutoCloner maintained by Alex Coulton.