Multiple sequence alignment - TraesCS5B01G295700

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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 TraesCS5B01G295700 chr5B 100.000 5000 0 0 1 5000 479394461 479389462 0.000000e+00 9234.0
1 TraesCS5B01G295700 chr5B 86.383 3503 377 59 344 3790 479504117 479500659 0.000000e+00 3735.0
2 TraesCS5B01G295700 chr5B 74.429 1095 242 25 1553 2622 711392789 711393870 2.140000e-118 436.0
3 TraesCS5B01G295700 chr5D 90.155 3809 257 41 1237 5000 399162067 399158332 0.000000e+00 4848.0
4 TraesCS5B01G295700 chr5D 82.787 366 38 10 344 695 399210122 399209768 2.260000e-78 303.0
5 TraesCS5B01G295700 chr5D 81.410 156 14 7 853 994 399162229 399162075 4.090000e-21 113.0
6 TraesCS5B01G295700 chr5A 88.148 3375 321 43 451 3790 504855667 504852337 0.000000e+00 3943.0
7 TraesCS5B01G295700 chr5A 90.817 2853 166 34 135 2962 504784396 504781615 0.000000e+00 3729.0
8 TraesCS5B01G295700 chr5A 89.952 826 60 6 3021 3836 504781618 504780806 0.000000e+00 1044.0
9 TraesCS5B01G295700 chr5A 85.844 883 65 27 4150 5000 504780496 504779642 0.000000e+00 883.0
10 TraesCS5B01G295700 chr2A 77.473 1820 313 56 1335 3090 753694100 753695886 0.000000e+00 1000.0
11 TraesCS5B01G295700 chr7A 72.604 814 190 29 1722 2518 700085052 700085849 2.330000e-58 237.0
12 TraesCS5B01G295700 chr4A 70.049 818 203 35 1641 2434 729453824 729454623 1.140000e-21 115.0
13 TraesCS5B01G295700 chr4A 80.420 143 26 2 2292 2433 730352816 730352675 1.900000e-19 108.0
14 TraesCS5B01G295700 chr1D 96.875 32 1 0 85 116 458230966 458230935 3.000000e-03 54.7
15 TraesCS5B01G295700 chr1A 96.875 32 1 0 85 116 550794122 550794091 3.000000e-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 TraesCS5B01G295700 chr5B 479389462 479394461 4999 True 9234.000000 9234 100.0000 1 5000 1 chr5B.!!$R1 4999
1 TraesCS5B01G295700 chr5B 479500659 479504117 3458 True 3735.000000 3735 86.3830 344 3790 1 chr5B.!!$R2 3446
2 TraesCS5B01G295700 chr5B 711392789 711393870 1081 False 436.000000 436 74.4290 1553 2622 1 chr5B.!!$F1 1069
3 TraesCS5B01G295700 chr5D 399158332 399162229 3897 True 2480.500000 4848 85.7825 853 5000 2 chr5D.!!$R2 4147
4 TraesCS5B01G295700 chr5A 504852337 504855667 3330 True 3943.000000 3943 88.1480 451 3790 1 chr5A.!!$R1 3339
5 TraesCS5B01G295700 chr5A 504779642 504784396 4754 True 1885.333333 3729 88.8710 135 5000 3 chr5A.!!$R2 4865
6 TraesCS5B01G295700 chr2A 753694100 753695886 1786 False 1000.000000 1000 77.4730 1335 3090 1 chr2A.!!$F1 1755
7 TraesCS5B01G295700 chr7A 700085052 700085849 797 False 237.000000 237 72.6040 1722 2518 1 chr7A.!!$F1 796

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
61 62 0.099082 GGTGCGGTTTTTGTGTTCGA 59.901 50.0 0.0 0.0 0.00 3.71 F
74 75 0.109272 TGTTCGATCACTGACGAGGC 60.109 55.0 0.0 0.0 39.59 4.70 F
75 76 0.109272 GTTCGATCACTGACGAGGCA 60.109 55.0 0.0 0.0 39.59 4.75 F
114 115 0.179081 GGGTCCGGTTGTAGATGCTC 60.179 60.0 0.0 0.0 0.00 4.26 F
1227 1297 0.310854 CCTGGCAAAAGTGACGAACC 59.689 55.0 0.0 0.0 34.30 3.62 F
2707 2839 1.021968 AGACGCCCGCCATTTTTATC 58.978 50.0 0.0 0.0 0.00 1.75 F
3093 3244 0.166814 GCCTCATCAACTTGCGACAC 59.833 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1395 2.838386 TTCTACGGATCCGAGAAACG 57.162 50.000 39.55 19.08 42.83 3.60 R
1624 1714 2.936202 ACATTGAGCTCTGTTGGTGTT 58.064 42.857 16.19 0.00 0.00 3.32 R
1635 1725 5.907197 CGATTACGGAATAACATTGAGCT 57.093 39.130 0.00 0.00 35.72 4.09 R
2014 2125 7.441760 CAGAGCTATCAATGCATCTTTAGTTCT 59.558 37.037 16.47 16.47 30.47 3.01 R
2962 3100 0.314935 AAAACCAGCATCTTGCCGTG 59.685 50.000 0.00 0.00 46.52 4.94 R
3900 4112 0.322546 GTGTCCAGGGTGTCCATTCC 60.323 60.000 0.00 0.00 34.83 3.01 R
4786 5090 0.526954 GATGCTTTGGCCTGATTGCG 60.527 55.000 3.32 0.00 37.74 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.976356 AGTTAGTCCGGGCGTTCC 59.024 61.111 0.00 0.00 0.00 3.62
28 29 2.485122 GCGTTCCGGCCTGATTTG 59.515 61.111 0.00 0.00 0.00 2.32
29 30 3.051392 GCGTTCCGGCCTGATTTGG 62.051 63.158 0.00 0.00 0.00 3.28
30 31 2.406616 CGTTCCGGCCTGATTTGGG 61.407 63.158 0.00 0.00 0.00 4.12
31 32 2.052104 GTTCCGGCCTGATTTGGGG 61.052 63.158 0.00 0.00 0.00 4.96
32 33 3.955543 TTCCGGCCTGATTTGGGGC 62.956 63.158 0.00 0.00 46.89 5.80
37 38 3.142838 CCTGATTTGGGGCGCCTG 61.143 66.667 28.56 1.68 0.00 4.85
38 39 3.142838 CTGATTTGGGGCGCCTGG 61.143 66.667 28.56 3.87 0.00 4.45
51 52 4.974721 CCTGGCAGGGTGCGGTTT 62.975 66.667 26.34 0.00 46.21 3.27
52 53 2.912025 CTGGCAGGGTGCGGTTTT 60.912 61.111 6.61 0.00 46.21 2.43
53 54 2.443016 TGGCAGGGTGCGGTTTTT 60.443 55.556 0.00 0.00 46.21 1.94
54 55 2.028925 GGCAGGGTGCGGTTTTTG 59.971 61.111 0.00 0.00 46.21 2.44
55 56 2.791868 GGCAGGGTGCGGTTTTTGT 61.792 57.895 0.00 0.00 46.21 2.83
56 57 1.591327 GCAGGGTGCGGTTTTTGTG 60.591 57.895 0.00 0.00 31.71 3.33
57 58 1.813192 CAGGGTGCGGTTTTTGTGT 59.187 52.632 0.00 0.00 0.00 3.72
58 59 0.174617 CAGGGTGCGGTTTTTGTGTT 59.825 50.000 0.00 0.00 0.00 3.32
59 60 0.458260 AGGGTGCGGTTTTTGTGTTC 59.542 50.000 0.00 0.00 0.00 3.18
60 61 0.868177 GGGTGCGGTTTTTGTGTTCG 60.868 55.000 0.00 0.00 0.00 3.95
61 62 0.099082 GGTGCGGTTTTTGTGTTCGA 59.901 50.000 0.00 0.00 0.00 3.71
62 63 1.268845 GGTGCGGTTTTTGTGTTCGAT 60.269 47.619 0.00 0.00 0.00 3.59
63 64 2.041244 GTGCGGTTTTTGTGTTCGATC 58.959 47.619 0.00 0.00 0.00 3.69
64 65 1.671328 TGCGGTTTTTGTGTTCGATCA 59.329 42.857 0.00 0.00 0.00 2.92
65 66 2.041244 GCGGTTTTTGTGTTCGATCAC 58.959 47.619 17.80 17.80 38.63 3.06
66 67 2.286772 GCGGTTTTTGTGTTCGATCACT 60.287 45.455 23.26 0.00 38.90 3.41
67 68 3.288242 CGGTTTTTGTGTTCGATCACTG 58.712 45.455 23.26 1.92 38.90 3.66
68 69 3.001838 CGGTTTTTGTGTTCGATCACTGA 59.998 43.478 23.26 12.01 38.90 3.41
69 70 4.279659 GGTTTTTGTGTTCGATCACTGAC 58.720 43.478 23.26 16.15 38.90 3.51
70 71 3.852471 TTTTGTGTTCGATCACTGACG 57.148 42.857 23.26 0.00 38.90 4.35
71 72 2.785713 TTGTGTTCGATCACTGACGA 57.214 45.000 23.26 4.22 38.90 4.20
72 73 2.331809 TGTGTTCGATCACTGACGAG 57.668 50.000 23.26 0.00 39.59 4.18
73 74 1.068541 TGTGTTCGATCACTGACGAGG 60.069 52.381 23.26 0.00 39.59 4.63
74 75 0.109272 TGTTCGATCACTGACGAGGC 60.109 55.000 0.00 0.00 39.59 4.70
75 76 0.109272 GTTCGATCACTGACGAGGCA 60.109 55.000 0.00 0.00 39.59 4.75
76 77 0.601057 TTCGATCACTGACGAGGCAA 59.399 50.000 0.00 0.00 39.59 4.52
77 78 0.817654 TCGATCACTGACGAGGCAAT 59.182 50.000 0.00 0.00 34.49 3.56
78 79 1.202302 TCGATCACTGACGAGGCAATC 60.202 52.381 0.00 0.00 34.49 2.67
79 80 1.576356 GATCACTGACGAGGCAATCC 58.424 55.000 0.00 0.00 0.00 3.01
80 81 0.179100 ATCACTGACGAGGCAATCCG 60.179 55.000 0.00 0.00 37.47 4.18
81 82 1.079819 CACTGACGAGGCAATCCGT 60.080 57.895 0.00 0.00 42.17 4.69
82 83 0.670546 CACTGACGAGGCAATCCGTT 60.671 55.000 0.00 0.00 39.30 4.44
83 84 0.389948 ACTGACGAGGCAATCCGTTC 60.390 55.000 0.00 0.00 39.30 3.95
84 85 1.413767 CTGACGAGGCAATCCGTTCG 61.414 60.000 0.00 0.00 39.30 3.95
85 86 2.125673 ACGAGGCAATCCGTTCGG 60.126 61.111 4.74 4.74 35.19 4.30
86 87 2.890474 CGAGGCAATCCGTTCGGG 60.890 66.667 11.37 0.00 37.47 5.14
87 88 3.202706 GAGGCAATCCGTTCGGGC 61.203 66.667 11.37 6.88 37.47 6.13
92 93 3.076278 AATCCGTTCGGGCGGGTA 61.076 61.111 16.17 1.55 45.77 3.69
93 94 2.437396 AATCCGTTCGGGCGGGTAT 61.437 57.895 16.17 3.59 45.77 2.73
94 95 2.653953 AATCCGTTCGGGCGGGTATG 62.654 60.000 16.17 0.00 45.77 2.39
96 97 4.903010 CGTTCGGGCGGGTATGGG 62.903 72.222 0.00 0.00 0.00 4.00
97 98 4.557385 GTTCGGGCGGGTATGGGG 62.557 72.222 0.00 0.00 0.00 4.96
104 105 3.085296 CGGGTATGGGGTCCGGTT 61.085 66.667 0.00 0.00 40.07 4.44
105 106 2.593420 GGGTATGGGGTCCGGTTG 59.407 66.667 0.00 0.00 0.00 3.77
106 107 2.303282 GGGTATGGGGTCCGGTTGT 61.303 63.158 0.00 0.00 0.00 3.32
107 108 0.982326 GGGTATGGGGTCCGGTTGTA 60.982 60.000 0.00 0.00 0.00 2.41
108 109 0.466963 GGTATGGGGTCCGGTTGTAG 59.533 60.000 0.00 0.00 0.00 2.74
109 110 1.488390 GTATGGGGTCCGGTTGTAGA 58.512 55.000 0.00 0.00 0.00 2.59
110 111 2.044758 GTATGGGGTCCGGTTGTAGAT 58.955 52.381 0.00 0.00 0.00 1.98
111 112 0.837272 ATGGGGTCCGGTTGTAGATG 59.163 55.000 0.00 0.00 0.00 2.90
112 113 1.153229 GGGGTCCGGTTGTAGATGC 60.153 63.158 0.00 0.00 0.00 3.91
113 114 1.623542 GGGGTCCGGTTGTAGATGCT 61.624 60.000 0.00 0.00 0.00 3.79
114 115 0.179081 GGGTCCGGTTGTAGATGCTC 60.179 60.000 0.00 0.00 0.00 4.26
115 116 0.824759 GGTCCGGTTGTAGATGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
116 117 1.471676 GGTCCGGTTGTAGATGCTCTG 60.472 57.143 0.00 0.00 0.00 3.35
117 118 1.476891 GTCCGGTTGTAGATGCTCTGA 59.523 52.381 0.00 0.00 0.00 3.27
118 119 1.751351 TCCGGTTGTAGATGCTCTGAG 59.249 52.381 0.00 0.00 0.00 3.35
119 120 1.202463 CCGGTTGTAGATGCTCTGAGG 60.202 57.143 6.83 0.00 0.00 3.86
120 121 1.751351 CGGTTGTAGATGCTCTGAGGA 59.249 52.381 6.83 3.64 0.00 3.71
121 122 2.363680 CGGTTGTAGATGCTCTGAGGAT 59.636 50.000 11.72 11.72 0.00 3.24
122 123 3.726607 GGTTGTAGATGCTCTGAGGATG 58.273 50.000 16.76 0.00 0.00 3.51
123 124 3.133721 GGTTGTAGATGCTCTGAGGATGT 59.866 47.826 16.76 14.78 0.00 3.06
124 125 4.367450 GTTGTAGATGCTCTGAGGATGTC 58.633 47.826 16.76 4.06 0.00 3.06
125 126 2.620585 TGTAGATGCTCTGAGGATGTCG 59.379 50.000 16.76 0.00 0.00 4.35
126 127 2.064434 AGATGCTCTGAGGATGTCGA 57.936 50.000 16.76 0.00 0.00 4.20
127 128 2.382882 AGATGCTCTGAGGATGTCGAA 58.617 47.619 16.76 0.00 0.00 3.71
128 129 2.762887 AGATGCTCTGAGGATGTCGAAA 59.237 45.455 16.76 0.00 0.00 3.46
129 130 2.370281 TGCTCTGAGGATGTCGAAAC 57.630 50.000 6.83 0.00 0.00 2.78
130 131 1.066858 TGCTCTGAGGATGTCGAAACC 60.067 52.381 6.83 0.00 0.00 3.27
131 132 1.914634 CTCTGAGGATGTCGAAACCG 58.085 55.000 0.00 0.00 0.00 4.44
132 133 1.472878 CTCTGAGGATGTCGAAACCGA 59.527 52.381 0.00 0.00 0.00 4.69
133 134 2.099921 CTCTGAGGATGTCGAAACCGAT 59.900 50.000 0.00 0.00 38.43 4.18
143 144 1.203052 TCGAAACCGATGTAGACCACC 59.797 52.381 0.00 0.00 0.00 4.61
174 175 2.030562 ACGCGTTTGAGGGGACAG 59.969 61.111 5.58 0.00 0.00 3.51
200 201 7.181569 TGTGAGGTTTTTCTTTCTTCCAATT 57.818 32.000 0.00 0.00 0.00 2.32
202 203 7.041721 GTGAGGTTTTTCTTTCTTCCAATTGT 58.958 34.615 4.43 0.00 0.00 2.71
211 212 3.071874 TCTTCCAATTGTGCGAGGAAT 57.928 42.857 4.43 0.00 39.26 3.01
214 215 2.513753 TCCAATTGTGCGAGGAATTGT 58.486 42.857 4.43 0.00 37.71 2.71
232 233 6.488006 GGAATTGTAGTGCACCAGATCAATAT 59.512 38.462 14.63 8.25 0.00 1.28
233 234 7.661437 GGAATTGTAGTGCACCAGATCAATATA 59.339 37.037 14.63 0.00 0.00 0.86
234 235 9.224267 GAATTGTAGTGCACCAGATCAATATAT 57.776 33.333 14.63 3.44 0.00 0.86
245 246 7.776969 CACCAGATCAATATATAATTGAGGGGG 59.223 40.741 14.82 12.66 40.80 5.40
279 280 2.140839 TAAACGAGGGAGGGAGACTC 57.859 55.000 0.00 0.00 45.84 3.36
314 315 2.282251 TCTCGCCACACCTCTCGT 60.282 61.111 0.00 0.00 0.00 4.18
325 327 2.835431 CTCTCGTCCGGCCTCCAT 60.835 66.667 0.00 0.00 0.00 3.41
452 477 3.036429 ATCAGCCGAGCACCTTCCC 62.036 63.158 0.00 0.00 0.00 3.97
453 478 4.020617 CAGCCGAGCACCTTCCCA 62.021 66.667 0.00 0.00 0.00 4.37
456 481 3.636231 CCGAGCACCTTCCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
457 482 2.671070 CGAGCACCTTCCCACCAT 59.329 61.111 0.00 0.00 0.00 3.55
492 523 1.764571 TTTGACCTGACCCTCACCGG 61.765 60.000 0.00 0.00 0.00 5.28
499 530 1.052124 TGACCCTCACCGGTTTCTGT 61.052 55.000 2.97 0.00 35.79 3.41
550 581 3.366052 AAATCAACCCCATCTACGCTT 57.634 42.857 0.00 0.00 0.00 4.68
597 634 9.950496 ATTTAATTTACTCTCATCTCGGCATAT 57.050 29.630 0.00 0.00 0.00 1.78
745 782 0.620121 AAAGCCTCCTCCCTCCTCAG 60.620 60.000 0.00 0.00 0.00 3.35
900 937 1.895798 ACGAAGCAGAGGACATCTTGA 59.104 47.619 0.00 0.00 35.47 3.02
901 938 2.266554 CGAAGCAGAGGACATCTTGAC 58.733 52.381 0.00 0.00 35.47 3.18
902 939 2.353109 CGAAGCAGAGGACATCTTGACA 60.353 50.000 0.00 0.00 35.47 3.58
904 941 2.255406 AGCAGAGGACATCTTGACAGT 58.745 47.619 0.00 0.00 35.47 3.55
972 1023 1.204312 GCCTCGACGCAACAAGAAC 59.796 57.895 1.23 0.00 0.00 3.01
1062 1116 8.438676 ACTGCCTCTATATGTGTTTGTATTTC 57.561 34.615 0.00 0.00 0.00 2.17
1078 1132 4.879545 TGTATTTCCTCTCGGGCATAAAAC 59.120 41.667 0.00 0.00 34.39 2.43
1132 1194 7.435068 TGTTAGAATTGCAAAAGGAGAGTAC 57.565 36.000 1.71 0.00 0.00 2.73
1172 1234 3.515901 TGATTTTCCGGTTTATTTGGGGG 59.484 43.478 0.00 0.00 0.00 5.40
1177 1239 1.687996 CCGGTTTATTTGGGGGCTCAT 60.688 52.381 0.00 0.00 0.00 2.90
1227 1297 0.310854 CCTGGCAAAAGTGACGAACC 59.689 55.000 0.00 0.00 34.30 3.62
1605 1695 7.948357 ACATAGTTGCAATGCTTCATGATAAT 58.052 30.769 6.82 0.00 0.00 1.28
1624 1714 6.885918 TGATAATGAAGAAGATGCTCAACCAA 59.114 34.615 0.00 0.00 0.00 3.67
1635 1725 1.748493 GCTCAACCAAACACCAACAGA 59.252 47.619 0.00 0.00 0.00 3.41
1987 2098 2.383527 CCGCTGAACGCTGGAGAAC 61.384 63.158 0.00 0.00 41.76 3.01
2014 2125 2.176889 GCAAGGTCCTGGTGACTAGTA 58.823 52.381 0.00 0.00 43.89 1.82
2267 2378 5.047377 GGCCAAACATTGATTACTGGAGAAA 60.047 40.000 0.00 0.00 0.00 2.52
2393 2504 1.131504 CCCTCGAAGACGTCTCTTGAG 59.868 57.143 20.33 22.74 36.82 3.02
2404 2515 3.178267 CGTCTCTTGAGACAAGATGAGC 58.822 50.000 24.71 1.53 38.65 4.26
2409 2520 5.125257 TCTCTTGAGACAAGATGAGCTAGTG 59.875 44.000 13.34 1.38 0.00 2.74
2436 2547 2.653115 GCTGCAGAAGGGTTTGCC 59.347 61.111 20.43 0.00 39.54 4.52
2521 2632 3.691118 GTCAGCCTCATTTCTGCAACATA 59.309 43.478 0.00 0.00 0.00 2.29
2531 2642 8.621532 TCATTTCTGCAACATAAAGTAGAGTT 57.378 30.769 0.00 0.00 0.00 3.01
2536 2647 5.616270 TGCAACATAAAGTAGAGTTCCACA 58.384 37.500 0.00 0.00 0.00 4.17
2538 2649 5.701290 GCAACATAAAGTAGAGTTCCACACT 59.299 40.000 0.00 0.00 39.07 3.55
2539 2650 6.347725 GCAACATAAAGTAGAGTTCCACACTG 60.348 42.308 0.00 0.00 35.01 3.66
2589 2700 3.552604 TTGTTGCTTGATTTAGCGGAC 57.447 42.857 0.00 0.00 44.18 4.79
2626 2737 7.026631 AGTGATTGTTTCAAAATCGAGAACA 57.973 32.000 0.00 0.00 36.93 3.18
2639 2750 2.094700 TCGAGAACAGATGGAAACGGAG 60.095 50.000 0.00 0.00 0.00 4.63
2646 2757 2.104170 AGATGGAAACGGAGAGGAGAC 58.896 52.381 0.00 0.00 0.00 3.36
2665 2797 5.033589 AGACAGCTTGATAATGGAAGGAG 57.966 43.478 0.00 0.00 0.00 3.69
2667 2799 3.782523 ACAGCTTGATAATGGAAGGAGGA 59.217 43.478 0.00 0.00 0.00 3.71
2668 2800 4.133078 CAGCTTGATAATGGAAGGAGGAC 58.867 47.826 0.00 0.00 0.00 3.85
2669 2801 3.782523 AGCTTGATAATGGAAGGAGGACA 59.217 43.478 0.00 0.00 0.00 4.02
2674 2806 6.325993 TGATAATGGAAGGAGGACATGAAA 57.674 37.500 0.00 0.00 0.00 2.69
2687 2819 4.140924 AGGACATGAAAAAGAAGTTCCCCT 60.141 41.667 0.00 0.00 0.00 4.79
2701 2833 3.861797 CCCTAGACGCCCGCCATT 61.862 66.667 0.00 0.00 0.00 3.16
2705 2837 1.658994 CTAGACGCCCGCCATTTTTA 58.341 50.000 0.00 0.00 0.00 1.52
2707 2839 1.021968 AGACGCCCGCCATTTTTATC 58.978 50.000 0.00 0.00 0.00 1.75
2766 2898 1.539388 TGTAAATTGGACAAGCTGCGG 59.461 47.619 0.00 0.00 0.00 5.69
2795 2927 1.588404 CATTGACGGCGTAGATGTCAC 59.412 52.381 14.74 0.00 41.49 3.67
2811 2943 3.897239 TGTCACAAAACCAGTTGAGGAT 58.103 40.909 0.00 0.00 32.59 3.24
2817 2949 6.039270 TCACAAAACCAGTTGAGGATAAAGTG 59.961 38.462 0.00 0.00 32.59 3.16
2906 3044 5.256474 AGGTACATTTTCAGTCCCAGAATG 58.744 41.667 0.00 0.00 34.69 2.67
2951 3089 3.504906 CGGTATCTACGGCATCTTCCTTA 59.495 47.826 0.00 0.00 0.00 2.69
2962 3100 5.563867 CGGCATCTTCCTTATGAGACTAGAC 60.564 48.000 0.00 0.00 0.00 2.59
2972 3122 2.447443 TGAGACTAGACACGGCAAGAT 58.553 47.619 0.00 0.00 0.00 2.40
3019 3170 1.888512 AGCTTTACCACATGCAGGTTG 59.111 47.619 14.85 0.00 40.54 3.77
3063 3214 2.218953 TGGTGTTCAACTCTCGTGAC 57.781 50.000 0.00 0.00 0.00 3.67
3093 3244 0.166814 GCCTCATCAACTTGCGACAC 59.833 55.000 0.00 0.00 0.00 3.67
3120 3271 3.682372 GGAATGCCGTTTCTGAAGATC 57.318 47.619 0.00 0.00 0.00 2.75
3180 3331 5.237127 GCAAAAATTTGAAGTGGGAAAGGAG 59.763 40.000 9.96 0.00 40.55 3.69
3252 3403 3.256716 GAGTATCGCGGGCCTCGAG 62.257 68.421 23.95 16.17 42.43 4.04
3259 3410 3.744719 CGGGCCTCGAGAACGTCA 61.745 66.667 15.71 0.00 42.43 4.35
3309 3460 2.335712 GGGCGACAAAGAAGGGCTG 61.336 63.158 0.00 0.00 0.00 4.85
3333 3484 0.899717 CATTGGAACTGTGGTGGGGG 60.900 60.000 0.00 0.00 0.00 5.40
3360 3517 5.355630 TGATACGAGAGGAGAGTTGAAGAAG 59.644 44.000 0.00 0.00 0.00 2.85
3411 3568 2.036098 TGCCCACCCAAGCATCTG 59.964 61.111 0.00 0.00 33.08 2.90
3423 3580 3.607741 CAAGCATCTGGAATCACTGACT 58.392 45.455 0.00 0.00 0.00 3.41
3427 3584 4.040217 AGCATCTGGAATCACTGACTATCC 59.960 45.833 0.00 1.88 0.00 2.59
3499 3656 1.745653 GCTGCCCAAAGTATCTCAACC 59.254 52.381 0.00 0.00 0.00 3.77
3528 3685 1.738350 CTCTTCCATTGCAGCACAGAG 59.262 52.381 0.00 0.00 0.00 3.35
3570 3739 2.406002 TTTGGCCTCACCTCCGTTCC 62.406 60.000 3.32 0.00 40.22 3.62
3581 3750 2.233922 ACCTCCGTTCCTTCTACATGTG 59.766 50.000 9.11 0.00 0.00 3.21
3585 3754 0.727398 GTTCCTTCTACATGTGCCGC 59.273 55.000 9.11 0.00 0.00 6.53
3637 3806 1.007271 CACCTGACGTCGCTCAAGT 60.007 57.895 11.62 0.00 0.00 3.16
3644 3813 1.805945 CGTCGCTCAAGTACCTGGC 60.806 63.158 0.00 0.00 0.00 4.85
3700 3869 2.734673 CTGCCGCGTTCTCTTGAGC 61.735 63.158 4.92 0.00 0.00 4.26
3706 3875 0.436531 GCGTTCTCTTGAGCACTTCG 59.563 55.000 0.00 0.00 0.00 3.79
3795 3964 3.935203 AGATTCAGCACGTTCCTTATGTG 59.065 43.478 0.00 0.00 44.94 3.21
3804 3973 4.213270 CACGTTCCTTATGTGTGTGTCAAT 59.787 41.667 0.00 0.00 38.67 2.57
3827 3999 8.765219 CAATGACTTAGAGGTAATAAATCACCG 58.235 37.037 0.00 0.00 39.94 4.94
3840 4052 9.754382 GTAATAAATCACCGTATCTTCCTTGTA 57.246 33.333 0.00 0.00 0.00 2.41
3893 4105 4.673061 CGTTTGCTAAACTGTCAAACACCA 60.673 41.667 17.48 0.00 45.74 4.17
3900 4112 2.483876 ACTGTCAAACACCAGACGATG 58.516 47.619 0.00 0.00 37.58 3.84
3911 4123 1.656652 CAGACGATGGAATGGACACC 58.343 55.000 0.00 0.00 0.00 4.16
3912 4124 0.541863 AGACGATGGAATGGACACCC 59.458 55.000 0.00 0.00 0.00 4.61
3917 4129 0.625849 ATGGAATGGACACCCTGGAC 59.374 55.000 0.00 0.00 0.00 4.02
3921 4133 1.125093 AATGGACACCCTGGACACGA 61.125 55.000 0.00 0.00 0.00 4.35
3934 4146 1.471676 GGACACGAAGAGCCCATGTAG 60.472 57.143 0.00 0.00 0.00 2.74
3935 4147 1.476891 GACACGAAGAGCCCATGTAGA 59.523 52.381 0.00 0.00 0.00 2.59
3936 4148 2.101582 GACACGAAGAGCCCATGTAGAT 59.898 50.000 0.00 0.00 0.00 1.98
3964 4176 2.424557 GCGGCTCTTCATCATCATCAT 58.575 47.619 0.00 0.00 0.00 2.45
3981 4193 1.306141 ATCGCCCAAGACTCCCTCA 60.306 57.895 0.00 0.00 0.00 3.86
4068 4312 2.031769 TGTTGCTGATTTTGCGAGTCAG 60.032 45.455 12.00 12.00 41.69 3.51
4073 4317 1.202758 TGATTTTGCGAGTCAGGTGGT 60.203 47.619 0.00 0.00 0.00 4.16
4117 4374 7.327761 CAGAATTTGATGATCCTTGTCAACAAC 59.672 37.037 0.04 0.00 39.57 3.32
4118 4375 6.906157 ATTTGATGATCCTTGTCAACAACT 57.094 33.333 0.04 0.00 39.57 3.16
4121 4378 3.988379 TGATCCTTGTCAACAACTTGC 57.012 42.857 0.00 0.00 0.00 4.01
4122 4379 3.286353 TGATCCTTGTCAACAACTTGCA 58.714 40.909 0.00 0.00 0.00 4.08
4123 4380 3.698539 TGATCCTTGTCAACAACTTGCAA 59.301 39.130 0.00 0.00 0.00 4.08
4125 4382 3.088532 TCCTTGTCAACAACTTGCAACT 58.911 40.909 0.00 0.00 0.00 3.16
4132 4389 5.820423 TGTCAACAACTTGCAACTACTATGT 59.180 36.000 0.00 0.00 0.00 2.29
4226 4492 1.718396 TTGCACGAGAGATGCTCAAG 58.282 50.000 0.00 0.00 44.15 3.02
4238 4504 6.656902 AGAGATGCTCAAGATCCACATTTAA 58.343 36.000 0.00 0.00 32.06 1.52
4247 4513 8.187913 TCAAGATCCACATTTAATTGTTTCCA 57.812 30.769 0.25 0.00 0.00 3.53
4300 4569 0.263172 TTCTTCCTTGCCCCAAACCA 59.737 50.000 0.00 0.00 0.00 3.67
4318 4587 2.821969 ACCACAAGACATTGCTCAATCC 59.178 45.455 0.00 0.00 40.27 3.01
4322 4591 4.885907 CACAAGACATTGCTCAATCCCTAT 59.114 41.667 0.00 0.00 40.27 2.57
4324 4593 5.104193 ACAAGACATTGCTCAATCCCTATCT 60.104 40.000 0.00 0.00 40.27 1.98
4331 4600 7.071698 ACATTGCTCAATCCCTATCTTTCTCTA 59.928 37.037 0.00 0.00 0.00 2.43
4338 4607 8.010697 TCAATCCCTATCTTTCTCTATGGTGTA 58.989 37.037 0.00 0.00 0.00 2.90
4348 4617 8.437575 TCTTTCTCTATGGTGTATTTATTCCCC 58.562 37.037 0.00 0.00 0.00 4.81
4349 4618 6.354794 TCTCTATGGTGTATTTATTCCCCG 57.645 41.667 0.00 0.00 0.00 5.73
4350 4619 5.842328 TCTCTATGGTGTATTTATTCCCCGT 59.158 40.000 0.00 0.00 0.00 5.28
4351 4620 5.860611 TCTATGGTGTATTTATTCCCCGTG 58.139 41.667 0.00 0.00 0.00 4.94
4354 4630 3.009253 TGGTGTATTTATTCCCCGTGTGT 59.991 43.478 0.00 0.00 0.00 3.72
4417 4694 1.897560 AGCCAAGCAGACCACTTTAC 58.102 50.000 0.00 0.00 0.00 2.01
4425 4702 2.293122 GCAGACCACTTTACATGCACAA 59.707 45.455 0.00 0.00 33.92 3.33
4438 4715 3.875727 ACATGCACAATATGACTGAGAGC 59.124 43.478 0.00 0.00 0.00 4.09
4500 4786 0.620556 TCAAGAGGCTGAATGGACCC 59.379 55.000 0.00 0.00 0.00 4.46
4504 4790 0.038166 GAGGCTGAATGGACCCAACA 59.962 55.000 0.00 0.00 0.00 3.33
4555 4841 6.265196 ACAAATTTACTCAGCATTCAGACCAA 59.735 34.615 0.00 0.00 0.00 3.67
4558 4844 6.500684 TTTACTCAGCATTCAGACCAATTC 57.499 37.500 0.00 0.00 0.00 2.17
4589 4887 2.798680 ACGACGAGATCAGCAACATAC 58.201 47.619 0.00 0.00 0.00 2.39
4681 4979 6.128090 ACACAATTGTCTGACATCATCATCAC 60.128 38.462 11.86 0.00 36.48 3.06
4715 5015 3.840078 TCCATCACATCCTTCAGTGAGAA 59.160 43.478 0.00 0.00 46.70 2.87
4786 5090 4.145876 TCATCGAAAACACATGCACTTC 57.854 40.909 0.00 0.00 0.00 3.01
4819 5123 0.736325 AGCATCAGTACGCGTTGTCC 60.736 55.000 20.78 3.12 0.00 4.02
4860 5164 2.037620 CTCCTCAGCTGGGATTCCGG 62.038 65.000 17.43 0.00 42.40 5.14
4914 5218 2.959507 TGTGGATCGACATACCTGTG 57.040 50.000 6.44 0.00 35.14 3.66
4972 5279 2.343625 GGGAATAGCTGGAAGGAGGAT 58.656 52.381 0.00 0.00 0.00 3.24
4974 5281 3.262151 GGGAATAGCTGGAAGGAGGATAC 59.738 52.174 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.052104 CCCCAAATCAGGCCGGAAC 61.052 63.158 10.42 0.00 0.00 3.62
14 15 2.358619 CCCCAAATCAGGCCGGAA 59.641 61.111 10.42 0.00 0.00 4.30
15 16 4.440829 GCCCCAAATCAGGCCGGA 62.441 66.667 8.42 8.42 43.76 5.14
20 21 3.142838 CAGGCGCCCCAAATCAGG 61.143 66.667 26.15 0.00 0.00 3.86
21 22 3.142838 CCAGGCGCCCCAAATCAG 61.143 66.667 26.15 2.71 0.00 2.90
34 35 4.974721 AAACCGCACCCTGCCAGG 62.975 66.667 2.91 2.91 41.12 4.45
35 36 2.498056 AAAAACCGCACCCTGCCAG 61.498 57.895 0.00 0.00 41.12 4.85
36 37 2.443016 AAAAACCGCACCCTGCCA 60.443 55.556 0.00 0.00 41.12 4.92
37 38 2.028925 CAAAAACCGCACCCTGCC 59.971 61.111 0.00 0.00 41.12 4.85
38 39 1.591327 CACAAAAACCGCACCCTGC 60.591 57.895 0.00 0.00 40.69 4.85
39 40 0.174617 AACACAAAAACCGCACCCTG 59.825 50.000 0.00 0.00 0.00 4.45
40 41 0.458260 GAACACAAAAACCGCACCCT 59.542 50.000 0.00 0.00 0.00 4.34
41 42 0.868177 CGAACACAAAAACCGCACCC 60.868 55.000 0.00 0.00 0.00 4.61
42 43 0.099082 TCGAACACAAAAACCGCACC 59.901 50.000 0.00 0.00 0.00 5.01
43 44 2.041244 GATCGAACACAAAAACCGCAC 58.959 47.619 0.00 0.00 0.00 5.34
44 45 1.671328 TGATCGAACACAAAAACCGCA 59.329 42.857 0.00 0.00 0.00 5.69
45 46 2.041244 GTGATCGAACACAAAAACCGC 58.959 47.619 19.68 0.00 40.11 5.68
46 47 3.001838 TCAGTGATCGAACACAAAAACCG 59.998 43.478 25.22 6.84 42.45 4.44
47 48 4.279659 GTCAGTGATCGAACACAAAAACC 58.720 43.478 25.22 5.61 42.45 3.27
48 49 3.960002 CGTCAGTGATCGAACACAAAAAC 59.040 43.478 25.22 15.85 42.45 2.43
49 50 3.866327 TCGTCAGTGATCGAACACAAAAA 59.134 39.130 25.22 6.92 42.45 1.94
50 51 3.449632 TCGTCAGTGATCGAACACAAAA 58.550 40.909 25.22 9.19 42.45 2.44
51 52 3.049912 CTCGTCAGTGATCGAACACAAA 58.950 45.455 25.22 11.51 42.45 2.83
52 53 2.607038 CCTCGTCAGTGATCGAACACAA 60.607 50.000 25.22 11.84 42.45 3.33
53 54 1.068541 CCTCGTCAGTGATCGAACACA 60.069 52.381 25.22 5.24 42.45 3.72
54 55 1.618861 CCTCGTCAGTGATCGAACAC 58.381 55.000 17.27 17.27 40.60 3.32
55 56 0.109272 GCCTCGTCAGTGATCGAACA 60.109 55.000 15.35 0.00 35.69 3.18
56 57 0.109272 TGCCTCGTCAGTGATCGAAC 60.109 55.000 15.35 11.98 35.69 3.95
57 58 0.601057 TTGCCTCGTCAGTGATCGAA 59.399 50.000 15.35 2.95 35.69 3.71
58 59 0.817654 ATTGCCTCGTCAGTGATCGA 59.182 50.000 14.28 14.28 34.88 3.59
59 60 1.203928 GATTGCCTCGTCAGTGATCG 58.796 55.000 0.00 2.36 0.00 3.69
60 61 1.576356 GGATTGCCTCGTCAGTGATC 58.424 55.000 0.00 0.00 0.00 2.92
61 62 0.179100 CGGATTGCCTCGTCAGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
62 63 1.215382 CGGATTGCCTCGTCAGTGA 59.785 57.895 0.00 0.00 0.00 3.41
63 64 0.670546 AACGGATTGCCTCGTCAGTG 60.671 55.000 0.00 0.00 38.78 3.66
64 65 0.389948 GAACGGATTGCCTCGTCAGT 60.390 55.000 0.00 0.00 38.78 3.41
65 66 1.413767 CGAACGGATTGCCTCGTCAG 61.414 60.000 0.00 0.00 38.78 3.51
66 67 1.445410 CGAACGGATTGCCTCGTCA 60.445 57.895 0.00 0.00 38.78 4.35
67 68 2.165301 CCGAACGGATTGCCTCGTC 61.165 63.158 7.53 0.00 38.78 4.20
68 69 2.125673 CCGAACGGATTGCCTCGT 60.126 61.111 7.53 0.00 41.71 4.18
69 70 2.890474 CCCGAACGGATTGCCTCG 60.890 66.667 15.07 0.00 37.50 4.63
70 71 3.202706 GCCCGAACGGATTGCCTC 61.203 66.667 15.07 0.00 37.50 4.70
79 80 4.903010 CCCATACCCGCCCGAACG 62.903 72.222 0.00 0.00 0.00 3.95
80 81 4.557385 CCCCATACCCGCCCGAAC 62.557 72.222 0.00 0.00 0.00 3.95
87 88 3.085296 AACCGGACCCCATACCCG 61.085 66.667 9.46 0.00 42.64 5.28
88 89 0.982326 TACAACCGGACCCCATACCC 60.982 60.000 9.46 0.00 0.00 3.69
89 90 0.466963 CTACAACCGGACCCCATACC 59.533 60.000 9.46 0.00 0.00 2.73
90 91 1.488390 TCTACAACCGGACCCCATAC 58.512 55.000 9.46 0.00 0.00 2.39
91 92 2.043992 CATCTACAACCGGACCCCATA 58.956 52.381 9.46 0.00 0.00 2.74
92 93 0.837272 CATCTACAACCGGACCCCAT 59.163 55.000 9.46 0.00 0.00 4.00
93 94 1.906105 GCATCTACAACCGGACCCCA 61.906 60.000 9.46 0.00 0.00 4.96
94 95 1.153229 GCATCTACAACCGGACCCC 60.153 63.158 9.46 0.00 0.00 4.95
95 96 0.179081 GAGCATCTACAACCGGACCC 60.179 60.000 9.46 0.00 0.00 4.46
96 97 3.364277 GAGCATCTACAACCGGACC 57.636 57.895 9.46 0.00 0.00 4.46
108 109 2.863137 GTTTCGACATCCTCAGAGCATC 59.137 50.000 0.00 0.00 0.00 3.91
109 110 2.419297 GGTTTCGACATCCTCAGAGCAT 60.419 50.000 0.00 0.00 0.00 3.79
110 111 1.066858 GGTTTCGACATCCTCAGAGCA 60.067 52.381 0.00 0.00 0.00 4.26
111 112 1.646189 GGTTTCGACATCCTCAGAGC 58.354 55.000 0.00 0.00 0.00 4.09
112 113 1.472878 TCGGTTTCGACATCCTCAGAG 59.527 52.381 0.00 0.00 40.88 3.35
113 114 1.541379 TCGGTTTCGACATCCTCAGA 58.459 50.000 0.00 0.00 40.88 3.27
124 125 1.203994 AGGTGGTCTACATCGGTTTCG 59.796 52.381 0.00 0.00 34.56 3.46
125 126 3.329929 AAGGTGGTCTACATCGGTTTC 57.670 47.619 0.00 0.00 34.56 2.78
126 127 3.071892 TCAAAGGTGGTCTACATCGGTTT 59.928 43.478 0.00 0.00 34.56 3.27
127 128 2.635915 TCAAAGGTGGTCTACATCGGTT 59.364 45.455 0.00 0.00 34.56 4.44
128 129 2.028385 GTCAAAGGTGGTCTACATCGGT 60.028 50.000 0.00 0.00 34.56 4.69
129 130 2.233922 AGTCAAAGGTGGTCTACATCGG 59.766 50.000 0.00 0.00 34.56 4.18
130 131 3.254060 CAGTCAAAGGTGGTCTACATCG 58.746 50.000 0.00 0.00 34.56 3.84
131 132 4.273148 ACAGTCAAAGGTGGTCTACATC 57.727 45.455 0.00 0.00 0.00 3.06
132 133 4.141482 ACAACAGTCAAAGGTGGTCTACAT 60.141 41.667 0.00 0.00 0.00 2.29
133 134 3.199071 ACAACAGTCAAAGGTGGTCTACA 59.801 43.478 0.00 0.00 0.00 2.74
143 144 0.650512 ACGCGTGACAACAGTCAAAG 59.349 50.000 12.93 0.00 43.37 2.77
174 175 4.097892 TGGAAGAAAGAAAAACCTCACAGC 59.902 41.667 0.00 0.00 0.00 4.40
200 201 1.270571 TGCACTACAATTCCTCGCACA 60.271 47.619 0.00 0.00 0.00 4.57
202 203 1.438651 GTGCACTACAATTCCTCGCA 58.561 50.000 10.32 0.00 0.00 5.10
245 246 4.738252 CCTCGTTTAACTTTTCAAACTGCC 59.262 41.667 0.00 0.00 33.43 4.85
259 260 2.454538 GAGTCTCCCTCCCTCGTTTAA 58.545 52.381 0.00 0.00 33.79 1.52
279 280 2.343101 AGAGTGAAGTCTCGACTCTCG 58.657 52.381 7.59 0.00 42.22 4.04
294 295 1.214062 GAGAGGTGTGGCGAGAGTG 59.786 63.158 0.00 0.00 0.00 3.51
331 333 3.273048 CGGAGCCGGAAATGCAAA 58.727 55.556 5.05 0.00 35.56 3.68
452 477 2.825836 GGCGGCTGAAGGATGGTG 60.826 66.667 0.00 0.00 0.00 4.17
453 478 4.473520 CGGCGGCTGAAGGATGGT 62.474 66.667 7.61 0.00 0.00 3.55
455 480 2.947938 AATCCGGCGGCTGAAGGATG 62.948 60.000 23.83 0.00 42.17 3.51
456 481 2.270874 AAATCCGGCGGCTGAAGGAT 62.271 55.000 23.83 14.29 44.64 3.24
457 482 2.966732 AAATCCGGCGGCTGAAGGA 61.967 57.895 23.83 11.15 37.17 3.36
517 548 0.258774 TTGATTTAGAGGCTGGGGGC 59.741 55.000 0.00 0.00 40.90 5.80
531 562 2.238646 TCAAGCGTAGATGGGGTTGATT 59.761 45.455 1.95 0.00 43.38 2.57
567 604 7.095439 GCCGAGATGAGAGTAAATTAAATCCAG 60.095 40.741 0.00 0.00 0.00 3.86
575 612 7.675062 AGAATATGCCGAGATGAGAGTAAATT 58.325 34.615 0.00 0.00 0.00 1.82
597 634 3.889227 CGGCGATTTGCTGGAGAA 58.111 55.556 0.00 0.00 46.76 2.87
745 782 1.823828 CTTCTGCGATGCATCAAAGC 58.176 50.000 25.70 20.29 38.13 3.51
900 937 7.451877 TCTTGTATCTGTTTCTCTAGGAACTGT 59.548 37.037 2.93 0.00 41.52 3.55
901 938 7.831753 TCTTGTATCTGTTTCTCTAGGAACTG 58.168 38.462 2.93 2.68 41.52 3.16
902 939 8.474025 CATCTTGTATCTGTTTCTCTAGGAACT 58.526 37.037 2.93 0.00 46.37 3.01
904 941 8.470805 GTCATCTTGTATCTGTTTCTCTAGGAA 58.529 37.037 0.00 0.00 0.00 3.36
972 1023 2.414481 CGTCAAGAGCTTCTTCACATGG 59.586 50.000 0.00 0.00 33.78 3.66
1062 1116 6.108247 AAAAACCGTTTTATGCCCGAGAGG 62.108 45.833 9.63 0.00 42.51 3.69
1172 1234 4.082787 TGCTAAGTTGTAAAGCCAATGAGC 60.083 41.667 0.00 0.00 35.33 4.26
1177 1239 3.954904 TGGTTGCTAAGTTGTAAAGCCAA 59.045 39.130 0.00 0.00 35.33 4.52
1303 1385 3.973135 CGGATCCGAGAAACGTACATAAG 59.027 47.826 30.62 0.00 42.83 1.73
1305 1389 2.945008 ACGGATCCGAGAAACGTACATA 59.055 45.455 39.55 0.00 42.83 2.29
1311 1395 2.838386 TTCTACGGATCCGAGAAACG 57.162 50.000 39.55 19.08 42.83 3.60
1548 1638 4.277672 TCTTTATCTCGTCCGATTACCAGG 59.722 45.833 0.00 0.00 0.00 4.45
1605 1695 4.036734 GTGTTTGGTTGAGCATCTTCTTCA 59.963 41.667 0.00 0.00 34.92 3.02
1624 1714 2.936202 ACATTGAGCTCTGTTGGTGTT 58.064 42.857 16.19 0.00 0.00 3.32
1635 1725 5.907197 CGATTACGGAATAACATTGAGCT 57.093 39.130 0.00 0.00 35.72 4.09
2014 2125 7.441760 CAGAGCTATCAATGCATCTTTAGTTCT 59.558 37.037 16.47 16.47 30.47 3.01
2436 2547 2.743636 TCCCTTCGTTGCTACTTCTG 57.256 50.000 0.00 0.00 0.00 3.02
2448 2559 3.895232 TCTTCTGAATCCTTCCCTTCG 57.105 47.619 0.00 0.00 0.00 3.79
2521 2632 5.145564 TCTACCAGTGTGGAACTCTACTTT 58.854 41.667 0.00 0.00 40.96 2.66
2531 2642 2.367567 GTGTCCTTTCTACCAGTGTGGA 59.632 50.000 0.00 0.00 40.96 4.02
2536 2647 9.490083 AACTATATAAGTGTCCTTTCTACCAGT 57.510 33.333 0.00 0.00 38.88 4.00
2538 2649 9.483489 TGAACTATATAAGTGTCCTTTCTACCA 57.517 33.333 0.00 0.00 38.88 3.25
2569 2680 2.881513 TGTCCGCTAAATCAAGCAACAA 59.118 40.909 0.00 0.00 42.91 2.83
2589 2700 1.466167 CAATCACTTCCAGCGACCTTG 59.534 52.381 0.00 0.00 0.00 3.61
2615 2726 3.684788 CCGTTTCCATCTGTTCTCGATTT 59.315 43.478 0.00 0.00 0.00 2.17
2626 2737 2.104170 GTCTCCTCTCCGTTTCCATCT 58.896 52.381 0.00 0.00 0.00 2.90
2639 2750 4.679373 TCCATTATCAAGCTGTCTCCTC 57.321 45.455 0.00 0.00 0.00 3.71
2646 2757 4.133078 GTCCTCCTTCCATTATCAAGCTG 58.867 47.826 0.00 0.00 0.00 4.24
2665 2797 4.152647 AGGGGAACTTCTTTTTCATGTCC 58.847 43.478 0.00 0.00 0.00 4.02
2667 2799 6.004574 GTCTAGGGGAACTTCTTTTTCATGT 58.995 40.000 0.00 0.00 0.00 3.21
2668 2800 5.122396 CGTCTAGGGGAACTTCTTTTTCATG 59.878 44.000 0.00 0.00 0.00 3.07
2669 2801 5.246307 CGTCTAGGGGAACTTCTTTTTCAT 58.754 41.667 0.00 0.00 0.00 2.57
2674 2806 1.278413 GGCGTCTAGGGGAACTTCTTT 59.722 52.381 0.00 0.00 0.00 2.52
2687 2819 2.158871 AGATAAAAATGGCGGGCGTCTA 60.159 45.455 0.00 0.00 0.00 2.59
2705 2837 8.712103 TCAATTCTGAATCATAGGTCTGAAGAT 58.288 33.333 2.92 0.00 35.85 2.40
2707 2839 8.905660 ATCAATTCTGAATCATAGGTCTGAAG 57.094 34.615 2.92 0.00 35.85 3.02
2766 2898 1.203928 CGCCGTCAATGATGAGAGTC 58.796 55.000 3.65 0.00 35.88 3.36
2795 2927 5.301805 ACCACTTTATCCTCAACTGGTTTTG 59.698 40.000 0.00 0.00 0.00 2.44
2811 2943 5.584649 CACAAACAGACTCTTGACCACTTTA 59.415 40.000 1.62 0.00 0.00 1.85
2817 2949 3.134458 CCTCACAAACAGACTCTTGACC 58.866 50.000 1.62 0.00 0.00 4.02
2906 3044 4.078639 AGATGCCTTAGCTGACCAATAC 57.921 45.455 0.00 0.00 40.80 1.89
2951 3089 2.447443 TCTTGCCGTGTCTAGTCTCAT 58.553 47.619 0.00 0.00 0.00 2.90
2962 3100 0.314935 AAAACCAGCATCTTGCCGTG 59.685 50.000 0.00 0.00 46.52 4.94
3042 3193 3.131396 GTCACGAGAGTTGAACACCAAT 58.869 45.455 0.00 0.00 46.40 3.16
3063 3214 1.452110 TGATGAGGCCAAACATGTCG 58.548 50.000 5.01 0.00 0.00 4.35
3180 3331 1.576421 CTTCAACTCGCACCCTTGC 59.424 57.895 0.00 0.00 46.21 4.01
3252 3403 0.951040 CCTGCTGGGTCTTGACGTTC 60.951 60.000 0.71 0.00 0.00 3.95
3259 3410 2.759795 GGCTTCCTGCTGGGTCTT 59.240 61.111 10.07 0.00 42.39 3.01
3309 3460 2.034558 CCACCACAGTTCCAATGTTGTC 59.965 50.000 0.00 0.00 0.00 3.18
3333 3484 1.301423 ACTCTCCTCTCGTATCACGC 58.699 55.000 0.00 0.00 42.21 5.34
3335 3486 4.636648 TCTTCAACTCTCCTCTCGTATCAC 59.363 45.833 0.00 0.00 0.00 3.06
3360 3517 3.071206 TCCGTCTGAGCCTCCTGC 61.071 66.667 0.00 0.00 41.71 4.85
3375 3532 2.284995 AGACCCTCCAGCACCTCC 60.285 66.667 0.00 0.00 0.00 4.30
3411 3568 5.606348 AAGAGTGGATAGTCAGTGATTCC 57.394 43.478 11.04 11.04 0.00 3.01
3423 3580 4.037222 TCAAGCCATGGTAAGAGTGGATA 58.963 43.478 14.67 0.00 34.94 2.59
3427 3584 3.616956 TCTCAAGCCATGGTAAGAGTG 57.383 47.619 14.67 3.11 0.00 3.51
3481 3638 3.153919 GTTGGTTGAGATACTTTGGGCA 58.846 45.455 0.00 0.00 0.00 5.36
3499 3656 1.471684 GCAATGGAAGAGGCTGAGTTG 59.528 52.381 0.00 0.00 0.00 3.16
3536 3693 1.413118 CCAAAACCCACCAAGCTCTT 58.587 50.000 0.00 0.00 0.00 2.85
3570 3739 1.717937 GCAGCGGCACATGTAGAAG 59.282 57.895 3.18 0.00 40.72 2.85
3585 3754 2.104859 CATGGTGGACGAGCTGCAG 61.105 63.158 10.11 10.11 0.00 4.41
3637 3806 2.363795 CCAGTCGAGGGCCAGGTA 60.364 66.667 6.18 0.00 0.00 3.08
3690 3859 3.507622 TGAGATCGAAGTGCTCAAGAGAA 59.492 43.478 0.32 0.00 36.32 2.87
3700 3869 1.925847 GCAGAAGCTGAGATCGAAGTG 59.074 52.381 0.00 0.00 37.91 3.16
3706 3875 3.794717 TCTCATTGCAGAAGCTGAGATC 58.205 45.455 5.61 0.00 43.21 2.75
3795 3964 8.997621 TTATTACCTCTAAGTCATTGACACAC 57.002 34.615 18.57 0.00 34.60 3.82
3804 3973 7.414222 ACGGTGATTTATTACCTCTAAGTCA 57.586 36.000 2.68 0.00 34.54 3.41
3827 3999 8.660373 CATGACAACTCTTTACAAGGAAGATAC 58.340 37.037 0.00 0.00 33.05 2.24
3840 4052 5.829924 AGAAACACCATCATGACAACTCTTT 59.170 36.000 0.00 0.00 0.00 2.52
3845 4057 7.029563 GGATTAAGAAACACCATCATGACAAC 58.970 38.462 0.00 0.00 0.00 3.32
3856 4068 4.499037 AGCAAACGGATTAAGAAACACC 57.501 40.909 0.00 0.00 0.00 4.16
3857 4069 7.112984 CAGTTTAGCAAACGGATTAAGAAACAC 59.887 37.037 6.20 0.00 45.88 3.32
3858 4070 7.136119 CAGTTTAGCAAACGGATTAAGAAACA 58.864 34.615 6.20 0.00 45.88 2.83
3893 4105 0.541863 GGGTGTCCATTCCATCGTCT 59.458 55.000 0.00 0.00 0.00 4.18
3900 4112 0.322546 GTGTCCAGGGTGTCCATTCC 60.323 60.000 0.00 0.00 34.83 3.01
3901 4113 0.673644 CGTGTCCAGGGTGTCCATTC 60.674 60.000 0.00 0.00 34.83 2.67
3903 4115 1.125093 TTCGTGTCCAGGGTGTCCAT 61.125 55.000 0.00 0.00 34.83 3.41
3911 4123 1.903877 ATGGGCTCTTCGTGTCCAGG 61.904 60.000 0.00 0.00 0.00 4.45
3912 4124 0.742281 CATGGGCTCTTCGTGTCCAG 60.742 60.000 0.00 0.00 0.00 3.86
3917 4129 2.101415 TCATCTACATGGGCTCTTCGTG 59.899 50.000 0.00 0.00 0.00 4.35
3921 4133 2.224719 GCCATCATCTACATGGGCTCTT 60.225 50.000 0.00 0.00 41.23 2.85
3934 4146 4.615815 AGAGCCGCCGCCATCATC 62.616 66.667 0.00 0.00 34.57 2.92
3935 4147 4.181010 AAGAGCCGCCGCCATCAT 62.181 61.111 0.00 0.00 34.57 2.45
3936 4148 4.838152 GAAGAGCCGCCGCCATCA 62.838 66.667 0.00 0.00 34.57 3.07
3964 4176 1.535444 TTGAGGGAGTCTTGGGCGA 60.535 57.895 0.00 0.00 0.00 5.54
3981 4193 4.988598 CACACGGCCTCCACGCTT 62.989 66.667 0.00 0.00 34.00 4.68
4045 4259 2.912967 GACTCGCAAAATCAGCAACATG 59.087 45.455 0.00 0.00 0.00 3.21
4056 4300 1.444119 GCACCACCTGACTCGCAAAA 61.444 55.000 0.00 0.00 0.00 2.44
4068 4312 2.032528 TGTAGCAGCAGCACCACC 59.967 61.111 3.17 0.00 45.49 4.61
4073 4317 2.357396 CACCGTGTAGCAGCAGCA 60.357 61.111 3.17 0.00 45.49 4.41
4142 4399 5.804639 TGGTTTCACAGCATTATACTCACT 58.195 37.500 0.00 0.00 0.00 3.41
4143 4400 6.683974 ATGGTTTCACAGCATTATACTCAC 57.316 37.500 0.00 0.00 41.00 3.51
4144 4401 8.673711 GTTTATGGTTTCACAGCATTATACTCA 58.326 33.333 0.00 0.00 41.00 3.41
4145 4402 8.673711 TGTTTATGGTTTCACAGCATTATACTC 58.326 33.333 0.00 0.00 41.00 2.59
4146 4403 8.458843 GTGTTTATGGTTTCACAGCATTATACT 58.541 33.333 0.00 0.00 41.00 2.12
4147 4404 8.458843 AGTGTTTATGGTTTCACAGCATTATAC 58.541 33.333 0.00 0.00 41.00 1.47
4148 4405 8.458052 CAGTGTTTATGGTTTCACAGCATTATA 58.542 33.333 0.00 0.00 41.00 0.98
4300 4569 3.446442 AGGGATTGAGCAATGTCTTGT 57.554 42.857 0.00 0.00 34.69 3.16
4322 4591 8.437575 GGGGAATAAATACACCATAGAGAAAGA 58.562 37.037 0.00 0.00 0.00 2.52
4324 4593 7.147444 ACGGGGAATAAATACACCATAGAGAAA 60.147 37.037 0.00 0.00 0.00 2.52
4331 4600 4.204012 CACACGGGGAATAAATACACCAT 58.796 43.478 0.00 0.00 0.00 3.55
4338 4607 5.946972 TGTAATCAACACACGGGGAATAAAT 59.053 36.000 0.00 0.00 31.43 1.40
4348 4617 3.059188 GTGTCCCTTGTAATCAACACACG 60.059 47.826 0.00 0.00 38.00 4.49
4349 4618 4.134563 AGTGTCCCTTGTAATCAACACAC 58.865 43.478 6.26 0.00 38.00 3.82
4350 4619 4.431416 AGTGTCCCTTGTAATCAACACA 57.569 40.909 6.26 0.00 38.00 3.72
4351 4620 5.408604 CACTAGTGTCCCTTGTAATCAACAC 59.591 44.000 15.06 0.00 38.00 3.32
4354 4630 4.286032 AGCACTAGTGTCCCTTGTAATCAA 59.714 41.667 23.44 0.00 0.00 2.57
4417 4694 4.127907 AGCTCTCAGTCATATTGTGCATG 58.872 43.478 0.00 0.00 0.00 4.06
4425 4702 3.244491 GGATGGCAAGCTCTCAGTCATAT 60.244 47.826 0.00 0.00 0.00 1.78
4438 4715 2.514458 ACCAAACCTAGGATGGCAAG 57.486 50.000 27.66 12.36 37.77 4.01
4500 4786 2.753989 TGAGATGTGTGCGTTTGTTG 57.246 45.000 0.00 0.00 0.00 3.33
4504 4790 2.618241 ACATGTTGAGATGTGTGCGTTT 59.382 40.909 0.00 0.00 35.17 3.60
4555 4841 8.604640 TGATCTCGTCGTATAGAGTTAAGAAT 57.395 34.615 0.00 0.00 36.03 2.40
4558 4844 6.073711 TGCTGATCTCGTCGTATAGAGTTAAG 60.074 42.308 0.00 0.00 36.03 1.85
4589 4887 2.719739 ACAAGGTGATCTGCTGGATTG 58.280 47.619 0.00 0.00 34.33 2.67
4652 4950 3.884693 TGATGTCAGACAATTGTGTGCTT 59.115 39.130 26.45 19.26 38.41 3.91
4654 4952 3.902261 TGATGTCAGACAATTGTGTGC 57.098 42.857 26.45 21.36 38.41 4.57
4668 4966 9.619316 GAAGTATAGTAGTGTGATGATGATGTC 57.381 37.037 0.00 0.00 0.00 3.06
4681 4979 7.531857 AGGATGTGATGGAAGTATAGTAGTG 57.468 40.000 0.00 0.00 0.00 2.74
4715 5015 3.822735 CTGTTTGGTGTCATTCTGGTGAT 59.177 43.478 0.00 0.00 0.00 3.06
4720 5020 7.859377 GCAATATATCTGTTTGGTGTCATTCTG 59.141 37.037 0.00 0.00 0.00 3.02
4721 5021 7.776969 AGCAATATATCTGTTTGGTGTCATTCT 59.223 33.333 0.00 0.00 30.53 2.40
4786 5090 0.526954 GATGCTTTGGCCTGATTGCG 60.527 55.000 3.32 0.00 37.74 4.85
4906 5210 3.055094 GGTGGTCTGATGTTCACAGGTAT 60.055 47.826 0.00 0.00 36.22 2.73
4914 5218 2.037772 ACTCACTGGTGGTCTGATGTTC 59.962 50.000 0.70 0.00 0.00 3.18
4972 5279 4.588899 CACCAATCTGACATTTCCCAGTA 58.411 43.478 0.00 0.00 0.00 2.74
4974 5281 2.165030 GCACCAATCTGACATTTCCCAG 59.835 50.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.