Multiple sequence alignment - TraesCS6B01G290200

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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 TraesCS6B01G290200 chr6B 100.000 2867 0 0 1 2867 521994610 521991744 0.000000e+00 5295
1 TraesCS6B01G290200 chr6D 92.722 1951 89 24 148 2084 345791632 345789721 0.000000e+00 2767
2 TraesCS6B01G290200 chr6D 90.703 441 23 12 2440 2867 345789245 345788810 3.200000e-159 571
3 TraesCS6B01G290200 chr6D 92.038 314 8 4 2132 2442 345789725 345789426 2.640000e-115 425
4 TraesCS6B01G290200 chr6A 89.554 2020 120 31 389 2364 486280311 486278339 0.000000e+00 2477
5 TraesCS6B01G290200 chr6A 84.615 208 6 9 2417 2604 486278338 486278137 1.750000e-42 183
6 TraesCS6B01G290200 chr6A 86.458 96 11 1 2723 2816 486278065 486277970 1.410000e-18 104


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 TraesCS6B01G290200 chr6B 521991744 521994610 2866 True 5295.000000 5295 100.000000 1 2867 1 chr6B.!!$R1 2866
1 TraesCS6B01G290200 chr6D 345788810 345791632 2822 True 1254.333333 2767 91.821000 148 2867 3 chr6D.!!$R1 2719
2 TraesCS6B01G290200 chr6A 486277970 486280311 2341 True 921.333333 2477 86.875667 389 2816 3 chr6A.!!$R1 2427

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
639 654 0.099436 GTCAATTGCATCGCCCACTC 59.901 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2136 0.17576 GTAGTGATCGGGCAGCTGAA 59.824 55.0 20.43 0.0 0.0 3.02 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 2.263895 TCCCCTCCCCGAATATATGG 57.736 55.000 0.00 0.00 0.00 2.74
22 23 1.725767 TCCCCTCCCCGAATATATGGA 59.274 52.381 0.00 0.00 0.00 3.41
23 24 2.114688 TCCCCTCCCCGAATATATGGAA 59.885 50.000 0.00 0.00 0.00 3.53
24 25 2.916934 CCCCTCCCCGAATATATGGAAA 59.083 50.000 0.00 0.00 0.00 3.13
25 26 3.308188 CCCCTCCCCGAATATATGGAAAC 60.308 52.174 0.00 0.00 0.00 2.78
43 44 5.479716 GAAACAAAGTTCAGTTTCGAGGA 57.520 39.130 14.39 0.00 42.62 3.71
44 45 5.485662 AAACAAAGTTCAGTTTCGAGGAG 57.514 39.130 1.70 0.00 32.90 3.69
45 46 4.402056 ACAAAGTTCAGTTTCGAGGAGA 57.598 40.909 0.00 0.00 0.00 3.71
46 47 4.372656 ACAAAGTTCAGTTTCGAGGAGAG 58.627 43.478 0.00 0.00 0.00 3.20
47 48 4.141914 ACAAAGTTCAGTTTCGAGGAGAGT 60.142 41.667 0.00 0.00 0.00 3.24
48 49 3.926821 AGTTCAGTTTCGAGGAGAGTC 57.073 47.619 0.00 0.00 0.00 3.36
49 50 2.226912 AGTTCAGTTTCGAGGAGAGTCG 59.773 50.000 0.00 0.00 41.51 4.18
50 51 1.166129 TCAGTTTCGAGGAGAGTCGG 58.834 55.000 0.00 0.00 40.49 4.79
51 52 1.166129 CAGTTTCGAGGAGAGTCGGA 58.834 55.000 0.00 0.00 40.49 4.55
52 53 1.540267 CAGTTTCGAGGAGAGTCGGAA 59.460 52.381 0.00 0.00 40.49 4.30
53 54 2.030185 CAGTTTCGAGGAGAGTCGGAAA 60.030 50.000 0.00 0.00 39.15 3.13
54 55 2.826725 AGTTTCGAGGAGAGTCGGAAAT 59.173 45.455 0.00 0.00 39.15 2.17
55 56 4.015084 AGTTTCGAGGAGAGTCGGAAATA 58.985 43.478 0.00 0.00 39.15 1.40
56 57 4.104066 GTTTCGAGGAGAGTCGGAAATAC 58.896 47.826 0.00 0.00 39.15 1.89
57 58 3.278668 TCGAGGAGAGTCGGAAATACT 57.721 47.619 0.00 0.00 40.49 2.12
58 59 3.618351 TCGAGGAGAGTCGGAAATACTT 58.382 45.455 0.00 0.00 40.49 2.24
59 60 3.626670 TCGAGGAGAGTCGGAAATACTTC 59.373 47.826 0.00 0.00 40.49 3.01
60 61 3.243134 CGAGGAGAGTCGGAAATACTTCC 60.243 52.174 0.00 0.00 46.85 3.46
69 70 1.604278 GGAAATACTTCCGCTCATGGC 59.396 52.381 0.00 0.00 41.89 4.40
70 71 2.288666 GAAATACTTCCGCTCATGGCA 58.711 47.619 6.92 0.00 41.91 4.92
71 72 1.959042 AATACTTCCGCTCATGGCAG 58.041 50.000 0.00 0.35 41.91 4.85
72 73 0.833287 ATACTTCCGCTCATGGCAGT 59.167 50.000 0.00 5.36 41.91 4.40
73 74 0.613260 TACTTCCGCTCATGGCAGTT 59.387 50.000 0.00 0.00 41.91 3.16
74 75 0.957395 ACTTCCGCTCATGGCAGTTG 60.957 55.000 0.00 0.00 41.91 3.16
75 76 1.651240 CTTCCGCTCATGGCAGTTGG 61.651 60.000 0.00 0.00 41.91 3.77
76 77 3.818787 CCGCTCATGGCAGTTGGC 61.819 66.667 0.00 0.00 41.91 4.52
77 78 4.170062 CGCTCATGGCAGTTGGCG 62.170 66.667 11.13 11.13 46.16 5.69
78 79 3.058160 GCTCATGGCAGTTGGCGT 61.058 61.111 0.00 0.00 46.16 5.68
79 80 3.044059 GCTCATGGCAGTTGGCGTC 62.044 63.158 0.00 0.00 46.16 5.19
80 81 2.741985 TCATGGCAGTTGGCGTCG 60.742 61.111 0.00 0.00 46.16 5.12
81 82 2.741985 CATGGCAGTTGGCGTCGA 60.742 61.111 0.00 0.00 46.16 4.20
82 83 2.108514 CATGGCAGTTGGCGTCGAT 61.109 57.895 0.00 0.00 46.16 3.59
83 84 2.108514 ATGGCAGTTGGCGTCGATG 61.109 57.895 0.00 0.00 46.16 3.84
84 85 4.166011 GGCAGTTGGCGTCGATGC 62.166 66.667 21.53 21.53 46.16 3.91
85 86 3.422303 GCAGTTGGCGTCGATGCA 61.422 61.111 29.46 13.94 36.88 3.96
86 87 2.476051 CAGTTGGCGTCGATGCAC 59.524 61.111 29.46 20.01 36.28 4.57
87 88 3.112075 AGTTGGCGTCGATGCACG 61.112 61.111 29.46 11.00 42.95 5.34
88 89 4.147322 GTTGGCGTCGATGCACGG 62.147 66.667 29.46 0.00 40.29 4.94
89 90 4.365505 TTGGCGTCGATGCACGGA 62.366 61.111 29.46 10.23 40.29 4.69
90 91 3.657448 TTGGCGTCGATGCACGGAT 62.657 57.895 29.46 0.00 40.29 4.18
91 92 3.330853 GGCGTCGATGCACGGATC 61.331 66.667 29.46 8.66 40.29 3.36
92 93 3.682315 GCGTCGATGCACGGATCG 61.682 66.667 24.45 13.95 45.43 3.69
96 97 2.355126 CGATGCACGGATCGAGGG 60.355 66.667 14.85 0.00 46.72 4.30
97 98 2.845550 CGATGCACGGATCGAGGGA 61.846 63.158 14.85 0.00 46.72 4.20
98 99 1.006805 GATGCACGGATCGAGGGAG 60.007 63.158 0.00 0.00 0.00 4.30
99 100 1.455773 ATGCACGGATCGAGGGAGA 60.456 57.895 0.00 0.00 0.00 3.71
100 101 1.043116 ATGCACGGATCGAGGGAGAA 61.043 55.000 0.00 0.00 0.00 2.87
101 102 1.254975 TGCACGGATCGAGGGAGAAA 61.255 55.000 0.00 0.00 0.00 2.52
102 103 0.105039 GCACGGATCGAGGGAGAAAT 59.895 55.000 0.00 0.00 0.00 2.17
103 104 1.870167 GCACGGATCGAGGGAGAAATC 60.870 57.143 0.00 0.00 0.00 2.17
104 105 1.409064 CACGGATCGAGGGAGAAATCA 59.591 52.381 0.00 0.00 0.00 2.57
105 106 1.683917 ACGGATCGAGGGAGAAATCAG 59.316 52.381 0.00 0.00 0.00 2.90
106 107 1.000283 CGGATCGAGGGAGAAATCAGG 60.000 57.143 0.00 0.00 0.00 3.86
107 108 2.320781 GGATCGAGGGAGAAATCAGGA 58.679 52.381 0.00 0.00 0.00 3.86
108 109 2.036604 GGATCGAGGGAGAAATCAGGAC 59.963 54.545 0.00 0.00 0.00 3.85
109 110 1.103803 TCGAGGGAGAAATCAGGACG 58.896 55.000 0.00 0.00 0.00 4.79
110 111 0.528684 CGAGGGAGAAATCAGGACGC 60.529 60.000 0.00 0.00 0.00 5.19
111 112 0.179070 GAGGGAGAAATCAGGACGCC 60.179 60.000 0.00 0.00 0.00 5.68
112 113 0.618968 AGGGAGAAATCAGGACGCCT 60.619 55.000 0.00 0.00 0.00 5.52
113 114 0.179070 GGGAGAAATCAGGACGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
114 115 0.528684 GGAGAAATCAGGACGCCTCG 60.529 60.000 0.00 0.00 0.00 4.63
115 116 1.148759 GAGAAATCAGGACGCCTCGC 61.149 60.000 0.00 0.00 0.00 5.03
116 117 1.153549 GAAATCAGGACGCCTCGCT 60.154 57.895 0.00 0.00 0.00 4.93
117 118 1.148759 GAAATCAGGACGCCTCGCTC 61.149 60.000 0.00 0.00 0.00 5.03
118 119 1.608717 AAATCAGGACGCCTCGCTCT 61.609 55.000 0.00 0.00 0.00 4.09
119 120 1.608717 AATCAGGACGCCTCGCTCTT 61.609 55.000 0.00 0.00 0.00 2.85
120 121 2.290122 ATCAGGACGCCTCGCTCTTG 62.290 60.000 0.00 0.00 0.00 3.02
121 122 2.992114 AGGACGCCTCGCTCTTGT 60.992 61.111 0.00 0.00 0.00 3.16
122 123 2.811317 GGACGCCTCGCTCTTGTG 60.811 66.667 0.00 0.00 0.00 3.33
123 124 2.811317 GACGCCTCGCTCTTGTGG 60.811 66.667 0.00 0.00 0.00 4.17
124 125 4.379243 ACGCCTCGCTCTTGTGGG 62.379 66.667 0.00 0.00 0.00 4.61
128 129 3.700109 CTCGCTCTTGTGGGGAGA 58.300 61.111 0.00 0.00 43.47 3.71
129 130 2.206635 CTCGCTCTTGTGGGGAGAT 58.793 57.895 0.00 0.00 43.47 2.75
130 131 1.403814 CTCGCTCTTGTGGGGAGATA 58.596 55.000 0.00 0.00 43.47 1.98
131 132 1.067821 CTCGCTCTTGTGGGGAGATAC 59.932 57.143 0.00 0.00 43.47 2.24
132 133 0.249073 CGCTCTTGTGGGGAGATACG 60.249 60.000 0.00 0.00 33.03 3.06
133 134 0.105039 GCTCTTGTGGGGAGATACGG 59.895 60.000 0.00 0.00 33.03 4.02
134 135 1.486211 CTCTTGTGGGGAGATACGGT 58.514 55.000 0.00 0.00 33.03 4.83
135 136 2.662866 CTCTTGTGGGGAGATACGGTA 58.337 52.381 0.00 0.00 33.03 4.02
136 137 3.028850 CTCTTGTGGGGAGATACGGTAA 58.971 50.000 0.00 0.00 33.03 2.85
137 138 3.443052 TCTTGTGGGGAGATACGGTAAA 58.557 45.455 0.00 0.00 0.00 2.01
138 139 3.839490 TCTTGTGGGGAGATACGGTAAAA 59.161 43.478 0.00 0.00 0.00 1.52
139 140 4.286549 TCTTGTGGGGAGATACGGTAAAAA 59.713 41.667 0.00 0.00 0.00 1.94
140 141 4.210724 TGTGGGGAGATACGGTAAAAAG 57.789 45.455 0.00 0.00 0.00 2.27
141 142 3.839490 TGTGGGGAGATACGGTAAAAAGA 59.161 43.478 0.00 0.00 0.00 2.52
142 143 4.081309 TGTGGGGAGATACGGTAAAAAGAG 60.081 45.833 0.00 0.00 0.00 2.85
143 144 3.118519 TGGGGAGATACGGTAAAAAGAGC 60.119 47.826 0.00 0.00 0.00 4.09
144 145 3.134262 GGGGAGATACGGTAAAAAGAGCT 59.866 47.826 0.00 0.00 0.00 4.09
145 146 4.370049 GGGAGATACGGTAAAAAGAGCTC 58.630 47.826 5.27 5.27 0.00 4.09
146 147 4.370049 GGAGATACGGTAAAAAGAGCTCC 58.630 47.826 10.93 0.00 33.45 4.70
190 191 3.322706 GAGGAAACGCGGCGCATTT 62.323 57.895 32.61 29.63 0.00 2.32
206 208 3.433598 CGCATTTCCTCCCCAAAGATAGA 60.434 47.826 0.00 0.00 0.00 1.98
212 214 3.451178 TCCTCCCCAAAGATAGAGAAACG 59.549 47.826 0.00 0.00 0.00 3.60
215 217 5.086104 TCCCCAAAGATAGAGAAACGAAG 57.914 43.478 0.00 0.00 0.00 3.79
236 238 1.540267 CTCGGTTTTGAGGAGAGTCGA 59.460 52.381 0.00 0.00 32.18 4.20
245 247 7.764901 GGTTTTGAGGAGAGTCGATAATACTTT 59.235 37.037 0.00 0.00 0.00 2.66
246 248 8.809478 GTTTTGAGGAGAGTCGATAATACTTTC 58.191 37.037 0.00 0.00 0.00 2.62
252 254 6.394025 AGAGTCGATAATACTTTCAGTCCC 57.606 41.667 0.00 0.00 0.00 4.46
254 256 4.885907 AGTCGATAATACTTTCAGTCCCGA 59.114 41.667 0.00 0.00 0.00 5.14
290 292 3.073798 TGCACAGATAAAGGGAGGAAACA 59.926 43.478 0.00 0.00 0.00 2.83
292 294 4.010349 CACAGATAAAGGGAGGAAACACC 58.990 47.826 0.00 0.00 40.88 4.16
293 295 3.655777 ACAGATAAAGGGAGGAAACACCA 59.344 43.478 0.00 0.00 43.83 4.17
309 311 1.069022 CACCACATGTTTTCCTGCTCG 60.069 52.381 0.00 0.00 0.00 5.03
318 320 5.147330 TGTTTTCCTGCTCGAAAGATAGA 57.853 39.130 0.00 0.00 40.84 1.98
321 323 6.485313 TGTTTTCCTGCTCGAAAGATAGAAAA 59.515 34.615 0.00 0.00 40.84 2.29
337 339 2.484264 AGAAAAGCGGACCTCAATTTCG 59.516 45.455 6.96 0.00 33.28 3.46
338 340 0.521735 AAAGCGGACCTCAATTTCGC 59.478 50.000 0.00 0.00 45.72 4.70
385 387 0.551396 GGGGAGTTATTGGAGGGGTG 59.449 60.000 0.00 0.00 0.00 4.61
396 398 3.039252 TGGAGGGGTGAATGTTTGTTT 57.961 42.857 0.00 0.00 0.00 2.83
447 450 7.719483 AGTATAGACATGCCAAATCCAAAATG 58.281 34.615 0.00 0.00 0.00 2.32
449 452 2.348660 ACATGCCAAATCCAAAATGCG 58.651 42.857 0.00 0.00 0.00 4.73
477 480 3.005554 CTCGGCACATTCATTGTTCTCT 58.994 45.455 0.00 0.00 36.00 3.10
479 482 3.005554 CGGCACATTCATTGTTCTCTCT 58.994 45.455 0.00 0.00 36.00 3.10
575 590 0.951558 ACGGCAAATCCACTTGTGTC 59.048 50.000 0.00 0.00 34.01 3.67
579 594 1.956477 GCAAATCCACTTGTGTCACCT 59.044 47.619 0.00 0.00 0.00 4.00
630 645 0.447801 GAAGACGCGGTCAATTGCAT 59.552 50.000 12.47 0.00 34.60 3.96
631 646 0.447801 AAGACGCGGTCAATTGCATC 59.552 50.000 12.47 0.00 34.60 3.91
633 648 2.648724 CGCGGTCAATTGCATCGC 60.649 61.111 21.30 21.30 42.51 4.58
634 649 2.278142 GCGGTCAATTGCATCGCC 60.278 61.111 20.89 9.44 40.44 5.54
635 650 2.408835 CGGTCAATTGCATCGCCC 59.591 61.111 0.00 0.00 0.00 6.13
636 651 2.405805 CGGTCAATTGCATCGCCCA 61.406 57.895 0.00 0.00 0.00 5.36
637 652 1.139520 GGTCAATTGCATCGCCCAC 59.860 57.895 0.00 0.00 0.00 4.61
638 653 1.315257 GGTCAATTGCATCGCCCACT 61.315 55.000 0.00 0.00 0.00 4.00
639 654 0.099436 GTCAATTGCATCGCCCACTC 59.901 55.000 0.00 0.00 0.00 3.51
640 655 1.031571 TCAATTGCATCGCCCACTCC 61.032 55.000 0.00 0.00 0.00 3.85
699 714 2.014857 CGTCCACGACTCCATCTTCTA 58.985 52.381 0.00 0.00 43.02 2.10
707 722 1.063567 ACTCCATCTTCTACCCGCTCT 60.064 52.381 0.00 0.00 0.00 4.09
708 723 2.035632 CTCCATCTTCTACCCGCTCTT 58.964 52.381 0.00 0.00 0.00 2.85
709 724 2.032620 TCCATCTTCTACCCGCTCTTC 58.967 52.381 0.00 0.00 0.00 2.87
710 725 2.035632 CCATCTTCTACCCGCTCTTCT 58.964 52.381 0.00 0.00 0.00 2.85
711 726 2.035321 CCATCTTCTACCCGCTCTTCTC 59.965 54.545 0.00 0.00 0.00 2.87
712 727 1.765230 TCTTCTACCCGCTCTTCTCC 58.235 55.000 0.00 0.00 0.00 3.71
716 731 1.285373 TCTACCCGCTCTTCTCCTCTT 59.715 52.381 0.00 0.00 0.00 2.85
819 839 4.704833 CCCGGACACCTGCACCAG 62.705 72.222 0.73 0.00 0.00 4.00
854 874 0.783206 TCCCATTTCCAAGAAGCCCA 59.217 50.000 0.00 0.00 0.00 5.36
858 878 0.486879 ATTTCCAAGAAGCCCACCCA 59.513 50.000 0.00 0.00 0.00 4.51
859 879 0.178964 TTTCCAAGAAGCCCACCCAG 60.179 55.000 0.00 0.00 0.00 4.45
934 954 2.171079 CGGCCGCGAGAATTTAGCA 61.171 57.895 14.67 0.00 0.00 3.49
1010 1030 2.158711 GGTGAGATGAGATGGGCATGAA 60.159 50.000 0.00 0.00 0.00 2.57
1221 1244 0.968393 GCAGGAAGTCCGACTCCTCT 60.968 60.000 13.59 5.03 42.08 3.69
1254 1277 4.335647 CACCACCCGAGCCTGCTT 62.336 66.667 0.00 0.00 0.00 3.91
1391 1414 4.885270 CAACCACCACCACCGGCA 62.885 66.667 0.00 0.00 0.00 5.69
1443 1466 2.029844 GCGCAAGAAGAGCCGTTCT 61.030 57.895 0.30 0.00 38.48 3.01
1692 1715 2.496942 CAGCATGCCTTCGGGATTT 58.503 52.632 15.66 0.00 37.25 2.17
1695 1718 1.669999 GCATGCCTTCGGGATTTGCT 61.670 55.000 6.36 0.00 37.25 3.91
1923 1948 7.010160 TCTTTAGTTTTCCTTCATCACCCAAT 58.990 34.615 0.00 0.00 0.00 3.16
1945 1973 4.702196 TCCCAATTACTACCACCCTTAGT 58.298 43.478 0.00 0.00 34.15 2.24
1983 2011 8.408043 TTTACATCTTGTCCATTTGTGAAGAT 57.592 30.769 0.00 0.00 34.42 2.40
2030 2058 5.007385 AGAACACTCCGTTGACATATACC 57.993 43.478 0.00 0.00 38.19 2.73
2038 2066 5.898174 TCCGTTGACATATACCACAACTAG 58.102 41.667 0.00 0.00 39.92 2.57
2039 2067 5.047847 CCGTTGACATATACCACAACTAGG 58.952 45.833 0.00 0.00 39.92 3.02
2040 2068 5.394883 CCGTTGACATATACCACAACTAGGT 60.395 44.000 0.00 0.00 43.14 3.08
2041 2069 6.103997 CGTTGACATATACCACAACTAGGTT 58.896 40.000 0.00 0.00 40.54 3.50
2042 2070 7.259882 CGTTGACATATACCACAACTAGGTTA 58.740 38.462 0.00 0.00 40.54 2.85
2043 2071 7.924412 CGTTGACATATACCACAACTAGGTTAT 59.076 37.037 0.00 0.00 40.54 1.89
2049 2077 9.924650 CATATACCACAACTAGGTTATTACTCC 57.075 37.037 0.00 0.00 40.54 3.85
2051 2079 6.295719 ACCACAACTAGGTTATTACTCCTG 57.704 41.667 0.00 0.00 35.33 3.86
2058 2086 2.772515 AGGTTATTACTCCTGTCCTGCC 59.227 50.000 0.00 0.00 32.29 4.85
2062 2090 1.553690 TTACTCCTGTCCTGCCTGCC 61.554 60.000 0.00 0.00 0.00 4.85
2078 2106 2.048503 CCTGCTTGCTTGCTTGCC 60.049 61.111 3.47 0.00 0.00 4.52
2079 2107 2.430244 CTGCTTGCTTGCTTGCCG 60.430 61.111 3.47 0.00 0.00 5.69
2093 2121 1.739338 TTGCCGGCCGAACAATTTGT 61.739 50.000 30.73 0.00 0.00 2.83
2100 2136 1.263217 GCCGAACAATTTGTGACGAGT 59.737 47.619 22.06 0.96 34.62 4.18
2118 2154 0.175760 GTTCAGCTGCCCGATCACTA 59.824 55.000 9.47 0.00 0.00 2.74
2120 2156 1.589993 CAGCTGCCCGATCACTACG 60.590 63.158 0.00 0.00 0.00 3.51
2124 2160 1.421410 CTGCCCGATCACTACGTTGC 61.421 60.000 0.00 0.00 0.00 4.17
2125 2161 1.447140 GCCCGATCACTACGTTGCA 60.447 57.895 0.00 0.00 0.00 4.08
2126 2162 1.693083 GCCCGATCACTACGTTGCAC 61.693 60.000 0.00 0.00 0.00 4.57
2128 2164 0.992072 CCGATCACTACGTTGCACAG 59.008 55.000 0.00 0.00 0.00 3.66
2129 2165 0.366871 CGATCACTACGTTGCACAGC 59.633 55.000 0.00 0.00 0.00 4.40
2130 2166 1.714794 GATCACTACGTTGCACAGCT 58.285 50.000 0.00 0.00 0.00 4.24
2293 2337 3.120338 CGAGTTATGAGCGAGAGAGATCC 60.120 52.174 0.00 0.00 0.00 3.36
2300 2344 2.196925 CGAGAGAGATCCGGTGGGG 61.197 68.421 0.00 0.00 37.02 4.96
2302 2346 2.041819 GAGAGATCCGGTGGGGGT 60.042 66.667 0.00 0.00 36.01 4.95
2303 2347 2.365635 AGAGATCCGGTGGGGGTG 60.366 66.667 0.00 0.00 36.01 4.61
2304 2348 2.687566 GAGATCCGGTGGGGGTGT 60.688 66.667 0.00 0.00 36.01 4.16
2305 2349 3.009115 AGATCCGGTGGGGGTGTG 61.009 66.667 0.00 0.00 36.01 3.82
2306 2350 3.327404 GATCCGGTGGGGGTGTGT 61.327 66.667 0.00 0.00 36.01 3.72
2307 2351 3.622060 GATCCGGTGGGGGTGTGTG 62.622 68.421 0.00 0.00 36.01 3.82
2308 2352 4.882396 TCCGGTGGGGGTGTGTGA 62.882 66.667 0.00 0.00 36.01 3.58
2364 2408 1.588674 TGTGCTGTCCGAACGAAATT 58.411 45.000 0.00 0.00 0.00 1.82
2366 2410 1.529438 GTGCTGTCCGAACGAAATTCA 59.471 47.619 0.00 0.00 37.12 2.57
2402 2449 6.603599 CGATGGATGGTCTATGAATACTCCTA 59.396 42.308 0.00 0.00 0.00 2.94
2403 2450 7.415765 CGATGGATGGTCTATGAATACTCCTAC 60.416 44.444 0.00 0.00 0.00 3.18
2404 2451 6.017192 TGGATGGTCTATGAATACTCCTACC 58.983 44.000 0.00 0.00 0.00 3.18
2405 2452 5.125739 GGATGGTCTATGAATACTCCTACCG 59.874 48.000 0.00 0.00 0.00 4.02
2406 2453 3.825014 TGGTCTATGAATACTCCTACCGC 59.175 47.826 0.00 0.00 0.00 5.68
2407 2454 3.193056 GGTCTATGAATACTCCTACCGCC 59.807 52.174 0.00 0.00 0.00 6.13
2408 2455 3.825014 GTCTATGAATACTCCTACCGCCA 59.175 47.826 0.00 0.00 0.00 5.69
2409 2456 4.079970 TCTATGAATACTCCTACCGCCAG 58.920 47.826 0.00 0.00 0.00 4.85
2410 2457 2.154567 TGAATACTCCTACCGCCAGT 57.845 50.000 0.00 0.00 0.00 4.00
2568 2811 3.425525 CGAACCGGACTAATCAATGATCG 59.574 47.826 9.46 0.00 0.00 3.69
2606 2849 1.899814 TGCTCTGACCCGAGTTATTGT 59.100 47.619 0.00 0.00 33.55 2.71
2611 2854 3.576982 TCTGACCCGAGTTATTGTTGAGT 59.423 43.478 0.00 0.00 0.00 3.41
2637 2880 2.354539 CCCGCCAACTTTTGCACG 60.355 61.111 0.00 0.00 0.00 5.34
2681 2936 3.011032 AGGGCCAAGAAAGAATCATCTGT 59.989 43.478 6.18 0.00 35.59 3.41
2711 2967 4.807443 ACGTCTTGTTAGAGCTTTCTACC 58.193 43.478 0.00 0.00 0.00 3.18
2725 2981 5.995897 AGCTTTCTACCGAATTAAACAGTGT 59.004 36.000 0.00 0.00 0.00 3.55
2777 3033 3.194116 GCAATTTGCAGGAGATTCTCCAA 59.806 43.478 29.87 17.81 45.54 3.53
2797 3055 1.603842 TGCTCTCGCATGATGGGTT 59.396 52.632 9.39 0.00 42.25 4.11
2799 3057 2.020131 CTCTCGCATGATGGGTTGC 58.980 57.895 9.39 0.00 35.50 4.17
2807 3065 1.887344 ATGATGGGTTGCGGTTTGCC 61.887 55.000 0.00 0.00 45.60 4.52
2817 3075 3.836151 GGTTTGCCGGTGACTTGT 58.164 55.556 1.90 0.00 0.00 3.16
2818 3076 1.358759 GGTTTGCCGGTGACTTGTG 59.641 57.895 1.90 0.00 0.00 3.33
2819 3077 1.358759 GTTTGCCGGTGACTTGTGG 59.641 57.895 1.90 0.00 0.00 4.17
2820 3078 1.826054 TTTGCCGGTGACTTGTGGG 60.826 57.895 1.90 0.00 0.00 4.61
2821 3079 4.947147 TGCCGGTGACTTGTGGGC 62.947 66.667 1.90 0.00 44.00 5.36
2822 3080 4.643387 GCCGGTGACTTGTGGGCT 62.643 66.667 1.90 0.00 40.59 5.19
2823 3081 3.065306 CCGGTGACTTGTGGGCTA 58.935 61.111 0.00 0.00 0.00 3.93
2824 3082 1.602237 CCGGTGACTTGTGGGCTAT 59.398 57.895 0.00 0.00 0.00 2.97
2843 3106 3.555527 ATGTGAGTGTGGGATGATCAG 57.444 47.619 0.09 0.00 0.00 2.90
2851 3114 3.389329 GTGTGGGATGATCAGGATACAGT 59.611 47.826 0.09 0.00 41.41 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.123273 CCATATATTCGGGGAGGGGAAT 58.877 50.000 0.00 0.00 36.82 3.01
1 2 2.114688 TCCATATATTCGGGGAGGGGAA 59.885 50.000 0.00 0.00 0.00 3.97
3 4 2.263895 TCCATATATTCGGGGAGGGG 57.736 55.000 0.00 0.00 0.00 4.79
4 5 3.329520 TGTTTCCATATATTCGGGGAGGG 59.670 47.826 0.00 0.00 0.00 4.30
5 6 4.634012 TGTTTCCATATATTCGGGGAGG 57.366 45.455 0.00 0.00 0.00 4.30
6 7 6.062095 ACTTTGTTTCCATATATTCGGGGAG 58.938 40.000 0.00 0.00 0.00 4.30
7 8 6.008696 ACTTTGTTTCCATATATTCGGGGA 57.991 37.500 0.00 0.00 0.00 4.81
8 9 6.320164 TGAACTTTGTTTCCATATATTCGGGG 59.680 38.462 0.00 0.00 0.00 5.73
9 10 7.067008 ACTGAACTTTGTTTCCATATATTCGGG 59.933 37.037 0.00 0.00 0.00 5.14
10 11 7.985476 ACTGAACTTTGTTTCCATATATTCGG 58.015 34.615 0.00 0.00 0.00 4.30
11 12 9.840427 AAACTGAACTTTGTTTCCATATATTCG 57.160 29.630 0.00 0.00 31.65 3.34
13 14 9.840427 CGAAACTGAACTTTGTTTCCATATATT 57.160 29.630 11.39 0.00 45.22 1.28
14 15 9.226606 TCGAAACTGAACTTTGTTTCCATATAT 57.773 29.630 11.39 0.00 45.22 0.86
15 16 8.610248 TCGAAACTGAACTTTGTTTCCATATA 57.390 30.769 11.39 0.00 45.22 0.86
16 17 7.308589 CCTCGAAACTGAACTTTGTTTCCATAT 60.309 37.037 11.39 0.00 45.22 1.78
17 18 6.017440 CCTCGAAACTGAACTTTGTTTCCATA 60.017 38.462 11.39 0.35 45.22 2.74
18 19 5.221048 CCTCGAAACTGAACTTTGTTTCCAT 60.221 40.000 11.39 0.00 45.22 3.41
19 20 4.095782 CCTCGAAACTGAACTTTGTTTCCA 59.904 41.667 11.39 0.81 45.22 3.53
20 21 4.334481 TCCTCGAAACTGAACTTTGTTTCC 59.666 41.667 11.39 0.00 45.22 3.13
21 22 5.293569 TCTCCTCGAAACTGAACTTTGTTTC 59.706 40.000 8.11 8.11 44.83 2.78
22 23 5.183228 TCTCCTCGAAACTGAACTTTGTTT 58.817 37.500 0.00 0.00 38.84 2.83
23 24 4.766375 TCTCCTCGAAACTGAACTTTGTT 58.234 39.130 0.00 0.00 0.00 2.83
24 25 4.141914 ACTCTCCTCGAAACTGAACTTTGT 60.142 41.667 0.00 0.00 0.00 2.83
25 26 4.372656 ACTCTCCTCGAAACTGAACTTTG 58.627 43.478 0.00 0.00 0.00 2.77
26 27 4.623002 GACTCTCCTCGAAACTGAACTTT 58.377 43.478 0.00 0.00 0.00 2.66
27 28 3.304794 CGACTCTCCTCGAAACTGAACTT 60.305 47.826 0.00 0.00 35.58 2.66
28 29 2.226912 CGACTCTCCTCGAAACTGAACT 59.773 50.000 0.00 0.00 35.58 3.01
29 30 2.586900 CGACTCTCCTCGAAACTGAAC 58.413 52.381 0.00 0.00 35.58 3.18
30 31 1.540267 CCGACTCTCCTCGAAACTGAA 59.460 52.381 0.00 0.00 35.58 3.02
31 32 1.166129 CCGACTCTCCTCGAAACTGA 58.834 55.000 0.00 0.00 35.58 3.41
32 33 1.166129 TCCGACTCTCCTCGAAACTG 58.834 55.000 0.00 0.00 35.58 3.16
33 34 1.906990 TTCCGACTCTCCTCGAAACT 58.093 50.000 0.00 0.00 35.58 2.66
34 35 2.719426 TTTCCGACTCTCCTCGAAAC 57.281 50.000 0.00 0.00 35.58 2.78
35 36 4.015084 AGTATTTCCGACTCTCCTCGAAA 58.985 43.478 0.00 0.00 35.58 3.46
36 37 3.618351 AGTATTTCCGACTCTCCTCGAA 58.382 45.455 0.00 0.00 35.58 3.71
37 38 3.278668 AGTATTTCCGACTCTCCTCGA 57.721 47.619 0.00 0.00 35.58 4.04
38 39 3.243134 GGAAGTATTTCCGACTCTCCTCG 60.243 52.174 0.66 0.00 43.27 4.63
39 40 4.310357 GGAAGTATTTCCGACTCTCCTC 57.690 50.000 0.66 0.00 43.27 3.71
61 62 3.044059 GACGCCAACTGCCATGAGC 62.044 63.158 0.00 0.00 44.14 4.26
62 63 2.743752 CGACGCCAACTGCCATGAG 61.744 63.158 0.00 0.00 36.24 2.90
63 64 2.520465 ATCGACGCCAACTGCCATGA 62.520 55.000 0.00 0.00 36.24 3.07
64 65 2.108514 ATCGACGCCAACTGCCATG 61.109 57.895 0.00 0.00 36.24 3.66
65 66 2.108514 CATCGACGCCAACTGCCAT 61.109 57.895 0.00 0.00 36.24 4.40
66 67 2.741985 CATCGACGCCAACTGCCA 60.742 61.111 0.00 0.00 36.24 4.92
67 68 4.166011 GCATCGACGCCAACTGCC 62.166 66.667 0.00 0.00 36.24 4.85
68 69 3.422303 TGCATCGACGCCAACTGC 61.422 61.111 0.00 0.00 0.00 4.40
69 70 2.476051 GTGCATCGACGCCAACTG 59.524 61.111 0.00 0.00 0.00 3.16
70 71 3.112075 CGTGCATCGACGCCAACT 61.112 61.111 0.00 0.00 42.86 3.16
71 72 4.147322 CCGTGCATCGACGCCAAC 62.147 66.667 0.00 0.00 42.86 3.77
72 73 3.657448 ATCCGTGCATCGACGCCAA 62.657 57.895 0.00 0.00 42.86 4.52
73 74 4.141965 ATCCGTGCATCGACGCCA 62.142 61.111 0.00 0.00 42.86 5.69
74 75 3.330853 GATCCGTGCATCGACGCC 61.331 66.667 0.00 0.00 42.86 5.68
79 80 2.355126 CCCTCGATCCGTGCATCG 60.355 66.667 0.98 0.98 45.91 3.84
80 81 1.006805 CTCCCTCGATCCGTGCATC 60.007 63.158 0.00 0.00 0.00 3.91
81 82 1.043116 TTCTCCCTCGATCCGTGCAT 61.043 55.000 0.00 0.00 0.00 3.96
82 83 1.254975 TTTCTCCCTCGATCCGTGCA 61.255 55.000 0.00 0.00 0.00 4.57
83 84 0.105039 ATTTCTCCCTCGATCCGTGC 59.895 55.000 0.00 0.00 0.00 5.34
84 85 1.409064 TGATTTCTCCCTCGATCCGTG 59.591 52.381 0.00 0.00 0.00 4.94
85 86 1.683917 CTGATTTCTCCCTCGATCCGT 59.316 52.381 0.00 0.00 0.00 4.69
86 87 1.000283 CCTGATTTCTCCCTCGATCCG 60.000 57.143 0.00 0.00 0.00 4.18
87 88 2.036604 GTCCTGATTTCTCCCTCGATCC 59.963 54.545 0.00 0.00 0.00 3.36
88 89 2.287909 CGTCCTGATTTCTCCCTCGATC 60.288 54.545 0.00 0.00 0.00 3.69
89 90 1.683917 CGTCCTGATTTCTCCCTCGAT 59.316 52.381 0.00 0.00 0.00 3.59
90 91 1.103803 CGTCCTGATTTCTCCCTCGA 58.896 55.000 0.00 0.00 0.00 4.04
91 92 0.528684 GCGTCCTGATTTCTCCCTCG 60.529 60.000 0.00 0.00 0.00 4.63
92 93 0.179070 GGCGTCCTGATTTCTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
93 94 0.618968 AGGCGTCCTGATTTCTCCCT 60.619 55.000 0.00 0.00 29.57 4.20
94 95 0.179070 GAGGCGTCCTGATTTCTCCC 60.179 60.000 2.98 0.00 31.76 4.30
95 96 0.528684 CGAGGCGTCCTGATTTCTCC 60.529 60.000 2.98 0.00 31.76 3.71
96 97 1.148759 GCGAGGCGTCCTGATTTCTC 61.149 60.000 2.98 0.00 31.76 2.87
97 98 1.153549 GCGAGGCGTCCTGATTTCT 60.154 57.895 2.98 0.00 31.76 2.52
98 99 1.148759 GAGCGAGGCGTCCTGATTTC 61.149 60.000 2.98 0.00 31.76 2.17
99 100 1.153549 GAGCGAGGCGTCCTGATTT 60.154 57.895 2.98 0.00 31.76 2.17
100 101 1.608717 AAGAGCGAGGCGTCCTGATT 61.609 55.000 2.98 0.00 31.76 2.57
101 102 2.055042 AAGAGCGAGGCGTCCTGAT 61.055 57.895 2.98 0.00 31.76 2.90
102 103 2.676822 AAGAGCGAGGCGTCCTGA 60.677 61.111 2.98 0.00 31.76 3.86
103 104 2.507992 CAAGAGCGAGGCGTCCTG 60.508 66.667 2.98 0.00 31.76 3.86
104 105 2.992114 ACAAGAGCGAGGCGTCCT 60.992 61.111 0.00 0.00 36.03 3.85
105 106 2.811317 CACAAGAGCGAGGCGTCC 60.811 66.667 0.00 0.00 0.00 4.79
106 107 2.811317 CCACAAGAGCGAGGCGTC 60.811 66.667 0.00 0.00 0.00 5.19
107 108 4.379243 CCCACAAGAGCGAGGCGT 62.379 66.667 0.00 0.00 0.00 5.68
109 110 3.672295 CTCCCCACAAGAGCGAGGC 62.672 68.421 0.00 0.00 0.00 4.70
110 111 1.333636 ATCTCCCCACAAGAGCGAGG 61.334 60.000 0.00 0.00 0.00 4.63
111 112 1.067821 GTATCTCCCCACAAGAGCGAG 59.932 57.143 0.00 0.00 0.00 5.03
112 113 1.112113 GTATCTCCCCACAAGAGCGA 58.888 55.000 0.00 0.00 0.00 4.93
113 114 0.249073 CGTATCTCCCCACAAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
114 115 0.105039 CCGTATCTCCCCACAAGAGC 59.895 60.000 0.00 0.00 0.00 4.09
115 116 1.486211 ACCGTATCTCCCCACAAGAG 58.514 55.000 0.00 0.00 0.00 2.85
116 117 2.832643 TACCGTATCTCCCCACAAGA 57.167 50.000 0.00 0.00 0.00 3.02
117 118 3.899052 TTTACCGTATCTCCCCACAAG 57.101 47.619 0.00 0.00 0.00 3.16
118 119 4.286549 TCTTTTTACCGTATCTCCCCACAA 59.713 41.667 0.00 0.00 0.00 3.33
119 120 3.839490 TCTTTTTACCGTATCTCCCCACA 59.161 43.478 0.00 0.00 0.00 4.17
120 121 4.439968 CTCTTTTTACCGTATCTCCCCAC 58.560 47.826 0.00 0.00 0.00 4.61
121 122 3.118519 GCTCTTTTTACCGTATCTCCCCA 60.119 47.826 0.00 0.00 0.00 4.96
122 123 3.134262 AGCTCTTTTTACCGTATCTCCCC 59.866 47.826 0.00 0.00 0.00 4.81
123 124 4.370049 GAGCTCTTTTTACCGTATCTCCC 58.630 47.826 6.43 0.00 0.00 4.30
124 125 4.370049 GGAGCTCTTTTTACCGTATCTCC 58.630 47.826 14.64 0.00 0.00 3.71
125 126 4.043073 CGGAGCTCTTTTTACCGTATCTC 58.957 47.826 14.64 0.00 38.97 2.75
126 127 4.043037 CGGAGCTCTTTTTACCGTATCT 57.957 45.455 14.64 0.00 38.97 1.98
132 133 1.199327 GCCAACGGAGCTCTTTTTACC 59.801 52.381 14.64 0.00 0.00 2.85
133 134 1.136057 CGCCAACGGAGCTCTTTTTAC 60.136 52.381 14.64 0.00 34.97 2.01
134 135 1.153353 CGCCAACGGAGCTCTTTTTA 58.847 50.000 14.64 0.00 34.97 1.52
135 136 0.818040 ACGCCAACGGAGCTCTTTTT 60.818 50.000 14.64 1.36 46.04 1.94
136 137 1.227853 ACGCCAACGGAGCTCTTTT 60.228 52.632 14.64 4.05 46.04 2.27
137 138 1.668151 GACGCCAACGGAGCTCTTT 60.668 57.895 14.64 4.44 46.04 2.52
138 139 2.048127 GACGCCAACGGAGCTCTT 60.048 61.111 14.64 0.00 46.04 2.85
139 140 2.172483 ATTGACGCCAACGGAGCTCT 62.172 55.000 14.64 0.00 46.04 4.09
140 141 1.741770 ATTGACGCCAACGGAGCTC 60.742 57.895 4.71 4.71 46.04 4.09
141 142 2.034879 CATTGACGCCAACGGAGCT 61.035 57.895 0.00 0.00 46.04 4.09
142 143 2.480555 CATTGACGCCAACGGAGC 59.519 61.111 0.00 0.00 46.04 4.70
143 144 2.480555 GCATTGACGCCAACGGAG 59.519 61.111 0.00 0.00 46.04 4.63
144 145 3.418913 CGCATTGACGCCAACGGA 61.419 61.111 0.00 0.00 46.04 4.69
163 164 1.153147 GCGTTTCCTCCCTCCATCC 60.153 63.158 0.00 0.00 0.00 3.51
190 191 3.451178 CGTTTCTCTATCTTTGGGGAGGA 59.549 47.826 0.00 0.00 0.00 3.71
196 198 4.266502 CGAGCTTCGTTTCTCTATCTTTGG 59.733 45.833 0.00 0.00 34.72 3.28
206 208 2.544267 CTCAAAACCGAGCTTCGTTTCT 59.456 45.455 11.26 2.26 38.40 2.52
212 214 2.289133 ACTCTCCTCAAAACCGAGCTTC 60.289 50.000 0.00 0.00 0.00 3.86
215 217 1.715993 GACTCTCCTCAAAACCGAGC 58.284 55.000 0.00 0.00 0.00 5.03
224 226 7.265647 CTGAAAGTATTATCGACTCTCCTCA 57.734 40.000 0.00 0.00 0.00 3.86
236 238 5.450137 CGACTGTCGGGACTGAAAGTATTAT 60.450 44.000 21.78 0.00 41.87 1.28
252 254 3.853330 CAATGGCGCCGACTGTCG 61.853 66.667 23.90 22.49 40.07 4.35
264 266 2.954318 CCTCCCTTTATCTGTGCAATGG 59.046 50.000 0.00 0.00 0.00 3.16
267 269 4.079253 GTTTCCTCCCTTTATCTGTGCAA 58.921 43.478 0.00 0.00 0.00 4.08
273 275 3.655777 TGTGGTGTTTCCTCCCTTTATCT 59.344 43.478 0.00 0.00 37.07 1.98
290 292 1.202758 TCGAGCAGGAAAACATGTGGT 60.203 47.619 0.00 0.00 0.00 4.16
292 294 3.250762 TCTTTCGAGCAGGAAAACATGTG 59.749 43.478 0.00 0.00 35.64 3.21
293 295 3.476552 TCTTTCGAGCAGGAAAACATGT 58.523 40.909 0.00 0.00 35.64 3.21
305 307 3.000423 GTCCGCTTTTCTATCTTTCGAGC 60.000 47.826 0.00 0.00 0.00 5.03
309 311 4.504858 TGAGGTCCGCTTTTCTATCTTTC 58.495 43.478 0.00 0.00 0.00 2.62
318 320 1.068541 GCGAAATTGAGGTCCGCTTTT 60.069 47.619 0.00 0.00 42.24 2.27
321 323 2.100631 CGCGAAATTGAGGTCCGCT 61.101 57.895 0.00 0.00 43.19 5.52
337 339 4.806342 TTCCTTATTATCCGCTTTTCGC 57.194 40.909 0.00 0.00 36.73 4.70
338 340 6.954944 TCAATTCCTTATTATCCGCTTTTCG 58.045 36.000 0.00 0.00 38.08 3.46
352 354 4.855298 AACTCCCCGAATCAATTCCTTA 57.145 40.909 0.00 0.00 33.28 2.69
447 450 1.060698 GAATGTGCCGAGTAAAGTCGC 59.939 52.381 1.62 0.00 38.69 5.19
449 452 4.154195 ACAATGAATGTGCCGAGTAAAGTC 59.846 41.667 0.00 0.00 41.93 3.01
549 564 1.969064 TGGATTTGCCGTTGGACCG 60.969 57.895 0.00 0.00 40.66 4.79
575 590 5.151389 GGTTTGCGTTTCAGTTATAAGGTG 58.849 41.667 0.00 0.00 0.00 4.00
579 594 6.073167 TCGATTGGTTTGCGTTTCAGTTATAA 60.073 34.615 0.00 0.00 0.00 0.98
611 626 0.447801 ATGCAATTGACCGCGTCTTC 59.552 50.000 10.34 0.00 33.15 2.87
630 645 4.332543 AAGAGGGGGAGTGGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
631 646 3.787001 GAAGAGGGGGAGTGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
633 648 1.997874 CAGGAAGAGGGGGAGTGGG 60.998 68.421 0.00 0.00 0.00 4.61
634 649 2.674220 GCAGGAAGAGGGGGAGTGG 61.674 68.421 0.00 0.00 0.00 4.00
635 650 1.908340 CTGCAGGAAGAGGGGGAGTG 61.908 65.000 5.57 0.00 0.00 3.51
636 651 1.614824 CTGCAGGAAGAGGGGGAGT 60.615 63.158 5.57 0.00 0.00 3.85
637 652 2.373707 CCTGCAGGAAGAGGGGGAG 61.374 68.421 29.88 0.00 37.39 4.30
638 653 1.821966 TACCTGCAGGAAGAGGGGGA 61.822 60.000 39.19 1.56 38.94 4.81
639 654 0.695803 ATACCTGCAGGAAGAGGGGG 60.696 60.000 39.19 10.78 38.94 5.40
640 655 0.761802 GATACCTGCAGGAAGAGGGG 59.238 60.000 39.19 11.60 38.94 4.79
644 659 3.430790 CGACAATGATACCTGCAGGAAGA 60.431 47.826 39.19 22.77 38.94 2.87
699 714 0.040499 AGAAGAGGAGAAGAGCGGGT 59.960 55.000 0.00 0.00 0.00 5.28
707 722 4.658063 ACGAAGAGAAGAGAAGAGGAGAA 58.342 43.478 0.00 0.00 0.00 2.87
708 723 4.019681 AGACGAAGAGAAGAGAAGAGGAGA 60.020 45.833 0.00 0.00 0.00 3.71
709 724 4.261801 AGACGAAGAGAAGAGAAGAGGAG 58.738 47.826 0.00 0.00 0.00 3.69
710 725 4.258543 GAGACGAAGAGAAGAGAAGAGGA 58.741 47.826 0.00 0.00 0.00 3.71
711 726 3.377172 GGAGACGAAGAGAAGAGAAGAGG 59.623 52.174 0.00 0.00 0.00 3.69
712 727 4.616181 GGAGACGAAGAGAAGAGAAGAG 57.384 50.000 0.00 0.00 0.00 2.85
877 897 0.036875 CCGTCCTCCTTTGCTTTCCT 59.963 55.000 0.00 0.00 0.00 3.36
990 1010 2.924757 TCATGCCCATCTCATCTCAC 57.075 50.000 0.00 0.00 0.00 3.51
1254 1277 4.302509 TGCGGCGTCCGGAAGAAA 62.303 61.111 22.33 0.00 45.82 2.52
1389 1412 3.311110 TCCTCCGGTCTGTGGTGC 61.311 66.667 0.00 0.00 0.00 5.01
1391 1414 1.458777 TTGTCCTCCGGTCTGTGGT 60.459 57.895 0.00 0.00 0.00 4.16
1413 1436 1.398692 TCTTGCGCTCCTTGGTTTTT 58.601 45.000 9.73 0.00 0.00 1.94
1417 1440 0.321122 CTCTTCTTGCGCTCCTTGGT 60.321 55.000 9.73 0.00 0.00 3.67
1443 1466 3.419580 ATGATCCCGGCCAGCCAA 61.420 61.111 9.78 0.00 35.37 4.52
1683 1706 2.555123 GCAGACAGCAAATCCCGAA 58.445 52.632 0.00 0.00 44.79 4.30
1923 1948 4.702196 ACTAAGGGTGGTAGTAATTGGGA 58.298 43.478 0.00 0.00 29.89 4.37
1983 2011 4.201920 CGAGTATGAAATCTCACGGACTCA 60.202 45.833 7.82 0.00 38.18 3.41
2030 2058 6.154706 AGGACAGGAGTAATAACCTAGTTGTG 59.845 42.308 0.00 0.00 34.87 3.33
2038 2066 2.772515 AGGCAGGACAGGAGTAATAACC 59.227 50.000 0.00 0.00 0.00 2.85
2039 2067 3.798202 CAGGCAGGACAGGAGTAATAAC 58.202 50.000 0.00 0.00 0.00 1.89
2040 2068 2.170607 GCAGGCAGGACAGGAGTAATAA 59.829 50.000 0.00 0.00 0.00 1.40
2041 2069 1.762957 GCAGGCAGGACAGGAGTAATA 59.237 52.381 0.00 0.00 0.00 0.98
2042 2070 0.543749 GCAGGCAGGACAGGAGTAAT 59.456 55.000 0.00 0.00 0.00 1.89
2043 2071 1.553690 GGCAGGCAGGACAGGAGTAA 61.554 60.000 0.00 0.00 0.00 2.24
2046 2074 3.007920 AGGCAGGCAGGACAGGAG 61.008 66.667 0.00 0.00 0.00 3.69
2049 2077 3.564345 AAGCAGGCAGGCAGGACAG 62.564 63.158 0.00 0.00 35.83 3.51
2051 2079 3.060615 CAAGCAGGCAGGCAGGAC 61.061 66.667 0.00 0.00 35.83 3.85
2058 2086 1.372997 CAAGCAAGCAAGCAGGCAG 60.373 57.895 9.92 0.00 36.85 4.85
2062 2090 2.430244 CGGCAAGCAAGCAAGCAG 60.430 61.111 10.15 3.46 36.85 4.24
2069 2097 4.404654 GTTCGGCCGGCAAGCAAG 62.405 66.667 30.85 11.66 0.00 4.01
2078 2106 0.724453 CGTCACAAATTGTTCGGCCG 60.724 55.000 22.12 22.12 0.00 6.13
2079 2107 0.589223 TCGTCACAAATTGTTCGGCC 59.411 50.000 16.16 0.00 0.00 6.13
2093 2121 2.343758 GGGCAGCTGAACTCGTCA 59.656 61.111 20.43 0.00 34.17 4.35
2100 2136 0.175760 GTAGTGATCGGGCAGCTGAA 59.824 55.000 20.43 0.00 0.00 3.02
2118 2154 2.738521 CGGCTAGCTGTGCAACGT 60.739 61.111 15.85 0.00 42.39 3.99
2120 2156 1.374758 AGACGGCTAGCTGTGCAAC 60.375 57.895 33.39 18.44 35.39 4.17
2124 2160 1.153745 GACCAGACGGCTAGCTGTG 60.154 63.158 33.39 20.80 35.39 3.66
2125 2161 2.352032 GGACCAGACGGCTAGCTGT 61.352 63.158 29.14 29.14 38.41 4.40
2126 2162 2.055042 AGGACCAGACGGCTAGCTG 61.055 63.158 22.26 22.26 34.57 4.24
2128 2164 1.395826 ATCAGGACCAGACGGCTAGC 61.396 60.000 6.04 6.04 34.57 3.42
2129 2165 0.671251 GATCAGGACCAGACGGCTAG 59.329 60.000 0.00 0.00 34.57 3.42
2130 2166 0.755698 GGATCAGGACCAGACGGCTA 60.756 60.000 0.00 0.00 34.57 3.93
2257 2301 2.214376 AACTCGGGCATTCAATTCCA 57.786 45.000 0.00 0.00 0.00 3.53
2293 2337 3.556306 ACTCACACACCCCCACCG 61.556 66.667 0.00 0.00 0.00 4.94
2300 2344 2.534019 CGGCACACACTCACACACC 61.534 63.158 0.00 0.00 0.00 4.16
2302 2346 0.179059 AATCGGCACACACTCACACA 60.179 50.000 0.00 0.00 0.00 3.72
2303 2347 1.790755 TAATCGGCACACACTCACAC 58.209 50.000 0.00 0.00 0.00 3.82
2304 2348 2.535012 TTAATCGGCACACACTCACA 57.465 45.000 0.00 0.00 0.00 3.58
2305 2349 3.889196 TTTTAATCGGCACACACTCAC 57.111 42.857 0.00 0.00 0.00 3.51
2306 2350 4.130857 TCTTTTTAATCGGCACACACTCA 58.869 39.130 0.00 0.00 0.00 3.41
2307 2351 4.742438 TCTTTTTAATCGGCACACACTC 57.258 40.909 0.00 0.00 0.00 3.51
2308 2352 4.023193 CCTTCTTTTTAATCGGCACACACT 60.023 41.667 0.00 0.00 0.00 3.55
2364 2408 1.780503 TCCATCGGCTCAGATTCTGA 58.219 50.000 15.39 15.39 38.25 3.27
2366 2410 1.347050 CCATCCATCGGCTCAGATTCT 59.653 52.381 0.00 0.00 0.00 2.40
2423 2470 3.317603 TCAATTGATGCGTCTCTCACA 57.682 42.857 3.38 0.00 0.00 3.58
2556 2799 3.136443 AGAGGTTGGGCGATCATTGATTA 59.864 43.478 0.00 0.00 0.00 1.75
2568 2811 0.600057 CAAGCAGAAAGAGGTTGGGC 59.400 55.000 0.00 0.00 39.94 5.36
2711 2967 8.500837 TCAAGCAAAATACACTGTTTAATTCG 57.499 30.769 0.00 0.00 0.00 3.34
2725 2981 7.254227 ACTTTCGTGTAACTCAAGCAAAATA 57.746 32.000 0.00 0.00 29.34 1.40
2788 3046 1.591183 GCAAACCGCAACCCATCAT 59.409 52.632 0.00 0.00 41.79 2.45
2807 3065 0.036388 ACATAGCCCACAAGTCACCG 60.036 55.000 0.00 0.00 0.00 4.94
2817 3075 0.546507 TCCCACACTCACATAGCCCA 60.547 55.000 0.00 0.00 0.00 5.36
2818 3076 0.839946 ATCCCACACTCACATAGCCC 59.160 55.000 0.00 0.00 0.00 5.19
2819 3077 1.486310 TCATCCCACACTCACATAGCC 59.514 52.381 0.00 0.00 0.00 3.93
2820 3078 2.988010 TCATCCCACACTCACATAGC 57.012 50.000 0.00 0.00 0.00 2.97
2821 3079 4.502777 CCTGATCATCCCACACTCACATAG 60.503 50.000 0.00 0.00 0.00 2.23
2822 3080 3.389002 CCTGATCATCCCACACTCACATA 59.611 47.826 0.00 0.00 0.00 2.29
2823 3081 2.172082 CCTGATCATCCCACACTCACAT 59.828 50.000 0.00 0.00 0.00 3.21
2824 3082 1.556451 CCTGATCATCCCACACTCACA 59.444 52.381 0.00 0.00 0.00 3.58
2843 3106 5.920312 CACATCGAATGCAATACTGTATCC 58.080 41.667 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.