Multiple sequence alignment - TraesCS3D01G531600

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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 TraesCS3D01G531600 chr3D 100.000 3118 0 0 569 3686 607667911 607664794 0.000000e+00 5758.0
1 TraesCS3D01G531600 chr3D 89.953 1065 91 12 902 1959 610166085 610167140 0.000000e+00 1360.0
2 TraesCS3D01G531600 chr3D 100.000 163 0 0 1 163 607668479 607668317 5.980000e-78 302.0
3 TraesCS3D01G531600 chr3A 92.000 2325 135 20 784 3104 740079279 740077002 0.000000e+00 3216.0
4 TraesCS3D01G531600 chr3A 91.900 1037 75 5 998 2031 739991574 739990544 0.000000e+00 1441.0
5 TraesCS3D01G531600 chr3A 90.242 1076 91 11 902 1968 744195572 744194502 0.000000e+00 1393.0
6 TraesCS3D01G531600 chr3A 90.178 1069 93 9 902 1962 744085813 744084749 0.000000e+00 1382.0
7 TraesCS3D01G531600 chr3A 90.056 1076 94 10 902 1968 744216638 744215567 0.000000e+00 1382.0
8 TraesCS3D01G531600 chr3A 89.114 542 33 18 3159 3686 740076928 740076399 0.000000e+00 651.0
9 TraesCS3D01G531600 chr3A 89.362 188 16 3 3358 3545 649018261 649018078 2.210000e-57 233.0
10 TraesCS3D01G531600 chr3A 92.593 162 12 0 1 162 729503749 729503910 2.210000e-57 233.0
11 TraesCS3D01G531600 chr3A 90.845 142 13 0 3544 3685 649017917 649017776 1.350000e-44 191.0
12 TraesCS3D01G531600 chr3B 92.450 1457 70 23 690 2108 817353940 817352486 0.000000e+00 2045.0
13 TraesCS3D01G531600 chr3B 89.889 1078 88 16 902 1970 821978291 821979356 0.000000e+00 1367.0
14 TraesCS3D01G531600 chr3B 91.309 978 78 3 998 1968 821858263 821857286 0.000000e+00 1328.0
15 TraesCS3D01G531600 chr3B 85.683 915 69 35 2203 3105 817352298 817351434 0.000000e+00 907.0
16 TraesCS3D01G531600 chr3B 90.996 522 22 10 3176 3686 817350429 817349922 0.000000e+00 680.0
17 TraesCS3D01G531600 chr3B 82.828 297 15 13 3088 3348 817351395 817351099 2.210000e-57 233.0
18 TraesCS3D01G531600 chr3B 95.890 73 3 0 569 641 751111867 751111939 6.470000e-23 119.0
19 TraesCS3D01G531600 chr3B 91.781 73 6 0 569 641 751111367 751111439 6.510000e-18 102.0
20 TraesCS3D01G531600 chr7D 89.538 325 28 3 3361 3685 481831970 481831652 1.230000e-109 407.0
21 TraesCS3D01G531600 chr7D 92.949 156 10 1 7 162 118570000 118569846 3.700000e-55 226.0
22 TraesCS3D01G531600 chr7D 92.949 156 10 1 7 162 402684479 402684633 3.700000e-55 226.0
23 TraesCS3D01G531600 chr7D 89.103 156 17 0 2531 2686 626050738 626050583 1.040000e-45 195.0
24 TraesCS3D01G531600 chr7D 91.781 73 6 0 569 641 2857577 2857505 6.510000e-18 102.0
25 TraesCS3D01G531600 chr7B 93.210 162 11 0 1 162 711592206 711592045 4.760000e-59 239.0
26 TraesCS3D01G531600 chr7B 89.103 156 17 0 2531 2686 725854901 725855056 1.040000e-45 195.0
27 TraesCS3D01G531600 chr2D 93.590 156 9 1 7 162 571482603 571482757 7.960000e-57 231.0
28 TraesCS3D01G531600 chr2D 93.590 156 9 1 7 162 601639341 601639187 7.960000e-57 231.0
29 TraesCS3D01G531600 chr1D 92.025 163 13 0 2528 2690 452348400 452348562 2.860000e-56 230.0
30 TraesCS3D01G531600 chr7A 92.949 156 11 0 7 162 117715340 117715185 1.030000e-55 228.0
31 TraesCS3D01G531600 chr7A 92.949 156 10 1 7 162 636131913 636132067 3.700000e-55 226.0
32 TraesCS3D01G531600 chr7A 89.103 156 17 0 2531 2686 721585866 721585711 1.040000e-45 195.0
33 TraesCS3D01G531600 chr7A 89.103 156 17 0 2531 2686 721660520 721660365 1.040000e-45 195.0
34 TraesCS3D01G531600 chr7A 93.151 73 5 0 569 641 117709635 117709563 1.400000e-19 108.0
35 TraesCS3D01G531600 chr7A 88.608 79 9 0 569 647 71036889 71036811 3.030000e-16 97.1
36 TraesCS3D01G531600 chr7A 89.474 76 8 0 569 644 117704581 117704506 3.030000e-16 97.1
37 TraesCS3D01G531600 chr2B 91.925 161 13 0 2 162 781076304 781076144 3.700000e-55 226.0
38 TraesCS3D01G531600 chr1A 91.772 158 13 0 2528 2685 547277233 547277390 1.720000e-53 220.0
39 TraesCS3D01G531600 chr1A 89.474 76 8 0 569 644 22893020 22892945 3.030000e-16 97.1
40 TraesCS3D01G531600 chr5D 90.789 76 7 0 569 644 159299612 159299537 6.510000e-18 102.0
41 TraesCS3D01G531600 chr5D 90.667 75 7 0 569 643 449091320 449091394 2.340000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G531600 chr3D 607664794 607668479 3685 True 3030.00 5758 100.00000 1 3686 2 chr3D.!!$R1 3685
1 TraesCS3D01G531600 chr3D 610166085 610167140 1055 False 1360.00 1360 89.95300 902 1959 1 chr3D.!!$F1 1057
2 TraesCS3D01G531600 chr3A 740076399 740079279 2880 True 1933.50 3216 90.55700 784 3686 2 chr3A.!!$R6 2902
3 TraesCS3D01G531600 chr3A 739990544 739991574 1030 True 1441.00 1441 91.90000 998 2031 1 chr3A.!!$R1 1033
4 TraesCS3D01G531600 chr3A 744194502 744195572 1070 True 1393.00 1393 90.24200 902 1968 1 chr3A.!!$R3 1066
5 TraesCS3D01G531600 chr3A 744084749 744085813 1064 True 1382.00 1382 90.17800 902 1962 1 chr3A.!!$R2 1060
6 TraesCS3D01G531600 chr3A 744215567 744216638 1071 True 1382.00 1382 90.05600 902 1968 1 chr3A.!!$R4 1066
7 TraesCS3D01G531600 chr3B 821978291 821979356 1065 False 1367.00 1367 89.88900 902 1970 1 chr3B.!!$F1 1068
8 TraesCS3D01G531600 chr3B 821857286 821858263 977 True 1328.00 1328 91.30900 998 1968 1 chr3B.!!$R1 970
9 TraesCS3D01G531600 chr3B 817349922 817353940 4018 True 966.25 2045 87.98925 690 3686 4 chr3B.!!$R2 2996

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
687 688 0.038166 CAGTTGCAAGAGGCCCCTAA 59.962 55.0 0.0 0.0 43.89 2.69 F
1290 1319 0.546747 AGGTGATCCCCGTCAAGGAA 60.547 55.0 0.0 0.0 45.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1568 0.806102 CGATCTTGACAACGCCGGAT 60.806 55.0 5.05 0.0 0.0 4.18 R
3124 3374 0.254178 TTCAGCTCCTCAATCTGCCC 59.746 55.0 0.00 0.0 0.0 5.36 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.889427 CGGCATGACACGAAGAGA 57.111 55.556 0.00 0.00 0.00 3.10
18 19 3.122150 CGGCATGACACGAAGAGAA 57.878 52.632 0.00 0.00 0.00 2.87
19 20 1.645034 CGGCATGACACGAAGAGAAT 58.355 50.000 0.00 0.00 0.00 2.40
20 21 1.590238 CGGCATGACACGAAGAGAATC 59.410 52.381 0.00 0.00 0.00 2.52
33 34 1.839424 GAGAATCTTGGGGTGGGTTG 58.161 55.000 0.00 0.00 0.00 3.77
34 35 0.409484 AGAATCTTGGGGTGGGTTGG 59.591 55.000 0.00 0.00 0.00 3.77
35 36 0.614697 GAATCTTGGGGTGGGTTGGG 60.615 60.000 0.00 0.00 0.00 4.12
36 37 2.746947 AATCTTGGGGTGGGTTGGGC 62.747 60.000 0.00 0.00 0.00 5.36
56 57 4.692475 GGACGGTGTTCGGGGGTG 62.692 72.222 0.00 0.00 44.45 4.61
57 58 3.932483 GACGGTGTTCGGGGGTGT 61.932 66.667 0.00 0.00 44.45 4.16
58 59 2.523902 ACGGTGTTCGGGGGTGTA 60.524 61.111 0.00 0.00 44.45 2.90
59 60 2.263540 CGGTGTTCGGGGGTGTAG 59.736 66.667 0.00 0.00 34.75 2.74
60 61 2.046604 GGTGTTCGGGGGTGTAGC 60.047 66.667 0.00 0.00 0.00 3.58
61 62 2.590114 GGTGTTCGGGGGTGTAGCT 61.590 63.158 0.00 0.00 0.00 3.32
62 63 1.259840 GGTGTTCGGGGGTGTAGCTA 61.260 60.000 0.00 0.00 0.00 3.32
63 64 0.828677 GTGTTCGGGGGTGTAGCTAT 59.171 55.000 0.00 0.00 0.00 2.97
64 65 0.828022 TGTTCGGGGGTGTAGCTATG 59.172 55.000 0.00 0.00 0.00 2.23
65 66 0.106149 GTTCGGGGGTGTAGCTATGG 59.894 60.000 0.00 0.00 0.00 2.74
66 67 1.052124 TTCGGGGGTGTAGCTATGGG 61.052 60.000 0.00 0.00 0.00 4.00
67 68 2.836888 GGGGGTGTAGCTATGGGC 59.163 66.667 0.00 0.00 42.19 5.36
78 79 2.682155 GCTATGGGCTAGGCTATGAC 57.318 55.000 23.17 12.14 38.06 3.06
79 80 1.902508 GCTATGGGCTAGGCTATGACA 59.097 52.381 23.17 9.77 38.06 3.58
80 81 2.303022 GCTATGGGCTAGGCTATGACAA 59.697 50.000 23.17 4.23 38.06 3.18
81 82 3.054802 GCTATGGGCTAGGCTATGACAAT 60.055 47.826 23.17 1.05 38.06 2.71
82 83 3.710209 ATGGGCTAGGCTATGACAATC 57.290 47.619 14.63 0.00 0.00 2.67
83 84 2.407562 TGGGCTAGGCTATGACAATCA 58.592 47.619 16.80 0.00 0.00 2.57
84 85 2.369860 TGGGCTAGGCTATGACAATCAG 59.630 50.000 16.80 0.00 0.00 2.90
85 86 2.289945 GGGCTAGGCTATGACAATCAGG 60.290 54.545 16.80 0.00 0.00 3.86
86 87 2.370189 GGCTAGGCTATGACAATCAGGT 59.630 50.000 9.46 0.00 0.00 4.00
87 88 3.397482 GCTAGGCTATGACAATCAGGTG 58.603 50.000 0.00 0.00 0.00 4.00
88 89 3.070159 GCTAGGCTATGACAATCAGGTGA 59.930 47.826 0.00 0.00 0.00 4.02
89 90 4.443457 GCTAGGCTATGACAATCAGGTGAA 60.443 45.833 0.00 0.00 0.00 3.18
90 91 4.574674 AGGCTATGACAATCAGGTGAAA 57.425 40.909 0.00 0.00 0.00 2.69
91 92 4.922206 AGGCTATGACAATCAGGTGAAAA 58.078 39.130 0.00 0.00 0.00 2.29
92 93 4.946157 AGGCTATGACAATCAGGTGAAAAG 59.054 41.667 0.00 0.00 0.00 2.27
93 94 4.096984 GGCTATGACAATCAGGTGAAAAGG 59.903 45.833 0.00 0.00 0.00 3.11
94 95 4.702131 GCTATGACAATCAGGTGAAAAGGT 59.298 41.667 0.00 0.00 0.00 3.50
95 96 5.163713 GCTATGACAATCAGGTGAAAAGGTC 60.164 44.000 0.00 0.00 0.00 3.85
96 97 3.486383 TGACAATCAGGTGAAAAGGTCC 58.514 45.455 0.00 0.00 0.00 4.46
97 98 3.117701 TGACAATCAGGTGAAAAGGTCCA 60.118 43.478 0.00 0.00 0.00 4.02
98 99 3.222603 ACAATCAGGTGAAAAGGTCCAC 58.777 45.455 0.00 0.00 0.00 4.02
101 102 4.074647 GGTGAAAAGGTCCACCGG 57.925 61.111 0.00 0.00 42.73 5.28
102 103 1.149854 GGTGAAAAGGTCCACCGGT 59.850 57.895 0.00 0.00 42.73 5.28
103 104 0.887836 GGTGAAAAGGTCCACCGGTC 60.888 60.000 2.59 0.00 42.73 4.79
104 105 0.179040 GTGAAAAGGTCCACCGGTCA 60.179 55.000 2.59 0.00 42.08 4.02
105 106 0.547075 TGAAAAGGTCCACCGGTCAA 59.453 50.000 2.59 0.00 42.08 3.18
106 107 1.064611 TGAAAAGGTCCACCGGTCAAA 60.065 47.619 2.59 0.00 42.08 2.69
107 108 1.335810 GAAAAGGTCCACCGGTCAAAC 59.664 52.381 2.59 2.57 42.08 2.93
108 109 0.466739 AAAGGTCCACCGGTCAAACC 60.467 55.000 17.91 17.91 42.08 3.27
109 110 2.281970 GGTCCACCGGTCAAACCC 60.282 66.667 2.59 0.00 33.75 4.11
110 111 2.281970 GTCCACCGGTCAAACCCC 60.282 66.667 2.59 0.00 33.75 4.95
111 112 3.943691 TCCACCGGTCAAACCCCG 61.944 66.667 2.59 0.00 45.07 5.73
112 113 4.259131 CCACCGGTCAAACCCCGT 62.259 66.667 2.59 0.00 43.98 5.28
113 114 2.667199 CACCGGTCAAACCCCGTC 60.667 66.667 2.59 0.00 43.98 4.79
114 115 2.845795 ACCGGTCAAACCCCGTCT 60.846 61.111 0.00 0.00 43.98 4.18
115 116 2.358247 CCGGTCAAACCCCGTCTG 60.358 66.667 0.00 0.00 43.98 3.51
116 117 2.358247 CGGTCAAACCCCGTCTGG 60.358 66.667 0.00 0.00 40.59 3.86
117 118 2.671963 GGTCAAACCCCGTCTGGC 60.672 66.667 0.00 0.00 30.04 4.85
118 119 3.047877 GTCAAACCCCGTCTGGCG 61.048 66.667 0.00 0.00 40.95 5.69
119 120 3.235481 TCAAACCCCGTCTGGCGA 61.235 61.111 1.87 0.00 44.77 5.54
120 121 2.281208 CAAACCCCGTCTGGCGAA 60.281 61.111 1.87 0.00 44.77 4.70
121 122 1.894756 CAAACCCCGTCTGGCGAAA 60.895 57.895 1.87 0.00 44.77 3.46
122 123 1.599797 AAACCCCGTCTGGCGAAAG 60.600 57.895 1.87 0.00 44.77 2.62
123 124 2.333701 AAACCCCGTCTGGCGAAAGT 62.334 55.000 1.87 0.00 44.77 2.66
124 125 2.434359 CCCCGTCTGGCGAAAGTC 60.434 66.667 1.87 0.00 44.77 3.01
131 132 3.758172 TGGCGAAAGTCAAAGGGC 58.242 55.556 0.00 0.00 46.60 5.19
132 133 1.150536 TGGCGAAAGTCAAAGGGCT 59.849 52.632 0.00 0.00 46.60 5.19
133 134 0.398696 TGGCGAAAGTCAAAGGGCTA 59.601 50.000 0.00 0.00 46.60 3.93
134 135 1.087501 GGCGAAAGTCAAAGGGCTAG 58.912 55.000 0.00 0.00 34.40 3.42
135 136 1.338769 GGCGAAAGTCAAAGGGCTAGA 60.339 52.381 0.00 0.00 34.40 2.43
136 137 2.633488 GCGAAAGTCAAAGGGCTAGAT 58.367 47.619 0.00 0.00 0.00 1.98
137 138 3.010420 GCGAAAGTCAAAGGGCTAGATT 58.990 45.455 0.00 0.00 0.00 2.40
138 139 3.064134 GCGAAAGTCAAAGGGCTAGATTC 59.936 47.826 0.00 0.00 0.00 2.52
139 140 3.307242 CGAAAGTCAAAGGGCTAGATTCG 59.693 47.826 0.00 0.00 0.00 3.34
140 141 4.504858 GAAAGTCAAAGGGCTAGATTCGA 58.495 43.478 0.00 0.00 0.00 3.71
141 142 3.528597 AGTCAAAGGGCTAGATTCGAC 57.471 47.619 0.00 0.00 0.00 4.20
142 143 2.159226 AGTCAAAGGGCTAGATTCGACG 60.159 50.000 0.00 0.00 0.00 5.12
143 144 1.136305 TCAAAGGGCTAGATTCGACGG 59.864 52.381 0.00 0.00 0.00 4.79
144 145 1.134788 CAAAGGGCTAGATTCGACGGT 60.135 52.381 0.00 0.00 0.00 4.83
145 146 0.745468 AAGGGCTAGATTCGACGGTC 59.255 55.000 0.00 0.00 0.00 4.79
146 147 1.008767 GGGCTAGATTCGACGGTCG 60.009 63.158 23.73 23.73 42.10 4.79
147 148 1.722636 GGGCTAGATTCGACGGTCGT 61.723 60.000 27.53 11.75 41.35 4.34
148 149 0.316854 GGCTAGATTCGACGGTCGTC 60.317 60.000 27.53 19.33 41.35 4.20
149 150 0.656785 GCTAGATTCGACGGTCGTCT 59.343 55.000 27.53 24.43 42.54 4.18
150 151 1.595003 GCTAGATTCGACGGTCGTCTG 60.595 57.143 27.53 18.13 42.54 3.51
151 152 1.664659 CTAGATTCGACGGTCGTCTGT 59.335 52.381 27.53 17.16 42.54 3.41
152 153 0.168348 AGATTCGACGGTCGTCTGTG 59.832 55.000 27.53 6.31 42.54 3.66
153 154 0.109873 GATTCGACGGTCGTCTGTGT 60.110 55.000 27.53 10.27 42.54 3.72
154 155 0.109873 ATTCGACGGTCGTCTGTGTC 60.110 55.000 27.53 0.00 42.54 3.67
155 156 1.438562 TTCGACGGTCGTCTGTGTCA 61.439 55.000 27.53 5.36 42.54 3.58
156 157 1.440518 CGACGGTCGTCTGTGTCAG 60.441 63.158 21.68 0.84 42.54 3.51
157 158 1.081376 GACGGTCGTCTGTGTCAGG 60.081 63.158 15.25 0.00 41.57 3.86
158 159 2.258591 CGGTCGTCTGTGTCAGGG 59.741 66.667 0.00 0.00 31.51 4.45
159 160 2.561956 CGGTCGTCTGTGTCAGGGT 61.562 63.158 0.00 0.00 31.51 4.34
160 161 1.746517 GGTCGTCTGTGTCAGGGTT 59.253 57.895 0.00 0.00 31.51 4.11
161 162 0.963962 GGTCGTCTGTGTCAGGGTTA 59.036 55.000 0.00 0.00 31.51 2.85
162 163 1.342174 GGTCGTCTGTGTCAGGGTTAA 59.658 52.381 0.00 0.00 31.51 2.01
590 591 2.654877 GCAATGCTGCCAGCTGTT 59.345 55.556 18.96 9.99 43.26 3.16
591 592 1.736645 GCAATGCTGCCAGCTGTTG 60.737 57.895 22.54 22.54 43.26 3.33
592 593 1.663739 CAATGCTGCCAGCTGTTGT 59.336 52.632 18.96 0.00 42.97 3.32
593 594 0.666274 CAATGCTGCCAGCTGTTGTG 60.666 55.000 18.96 4.90 42.97 3.33
594 595 1.812686 AATGCTGCCAGCTGTTGTGG 61.813 55.000 18.96 0.00 42.97 4.17
595 596 2.908940 GCTGCCAGCTGTTGTGGT 60.909 61.111 13.81 0.00 38.45 4.16
596 597 3.036577 CTGCCAGCTGTTGTGGTG 58.963 61.111 13.81 0.00 37.40 4.17
600 601 3.297620 CAGCTGTTGTGGTGGGCC 61.298 66.667 5.25 0.00 0.00 5.80
601 602 4.603535 AGCTGTTGTGGTGGGCCC 62.604 66.667 17.59 17.59 0.00 5.80
602 603 4.603535 GCTGTTGTGGTGGGCCCT 62.604 66.667 25.70 0.00 0.00 5.19
603 604 2.282462 CTGTTGTGGTGGGCCCTC 60.282 66.667 25.70 20.64 0.00 4.30
604 605 4.263572 TGTTGTGGTGGGCCCTCG 62.264 66.667 25.70 0.00 0.00 4.63
605 606 4.265056 GTTGTGGTGGGCCCTCGT 62.265 66.667 25.70 0.00 0.00 4.18
606 607 2.527123 TTGTGGTGGGCCCTCGTA 60.527 61.111 25.70 9.43 0.00 3.43
607 608 1.921346 TTGTGGTGGGCCCTCGTAT 60.921 57.895 25.70 0.00 0.00 3.06
608 609 2.189521 GTGGTGGGCCCTCGTATG 59.810 66.667 25.70 0.00 0.00 2.39
609 610 3.792736 TGGTGGGCCCTCGTATGC 61.793 66.667 25.70 6.72 0.00 3.14
610 611 3.480133 GGTGGGCCCTCGTATGCT 61.480 66.667 25.70 0.00 0.00 3.79
611 612 2.590092 GTGGGCCCTCGTATGCTT 59.410 61.111 25.70 0.00 0.00 3.91
612 613 1.077716 GTGGGCCCTCGTATGCTTT 60.078 57.895 25.70 0.00 0.00 3.51
613 614 0.679960 GTGGGCCCTCGTATGCTTTT 60.680 55.000 25.70 0.00 0.00 2.27
614 615 0.679640 TGGGCCCTCGTATGCTTTTG 60.680 55.000 25.70 0.00 0.00 2.44
615 616 1.384222 GGGCCCTCGTATGCTTTTGG 61.384 60.000 17.04 0.00 0.00 3.28
616 617 0.393808 GGCCCTCGTATGCTTTTGGA 60.394 55.000 0.00 0.00 0.00 3.53
617 618 1.459450 GCCCTCGTATGCTTTTGGAA 58.541 50.000 0.00 0.00 0.00 3.53
618 619 1.401905 GCCCTCGTATGCTTTTGGAAG 59.598 52.381 0.00 0.00 35.92 3.46
627 628 1.007387 CTTTTGGAAGCGTGGTGGC 60.007 57.895 0.00 0.00 0.00 5.01
628 629 1.733402 CTTTTGGAAGCGTGGTGGCA 61.733 55.000 0.00 0.00 34.64 4.92
629 630 1.733402 TTTTGGAAGCGTGGTGGCAG 61.733 55.000 0.00 0.00 34.64 4.85
630 631 4.641645 TGGAAGCGTGGTGGCAGG 62.642 66.667 0.00 0.00 34.64 4.85
647 648 4.082523 GCGCAGGCACCTGGTAGA 62.083 66.667 18.14 0.00 43.77 2.59
648 649 2.662596 CGCAGGCACCTGGTAGAA 59.337 61.111 18.14 0.00 43.77 2.10
649 650 1.448540 CGCAGGCACCTGGTAGAAG 60.449 63.158 18.14 0.00 43.77 2.85
650 651 1.679898 GCAGGCACCTGGTAGAAGT 59.320 57.895 18.14 0.00 43.77 3.01
651 652 0.391793 GCAGGCACCTGGTAGAAGTC 60.392 60.000 18.14 0.00 43.77 3.01
652 653 0.976641 CAGGCACCTGGTAGAAGTCA 59.023 55.000 8.93 0.00 40.17 3.41
653 654 1.556911 CAGGCACCTGGTAGAAGTCAT 59.443 52.381 8.93 0.00 40.17 3.06
654 655 2.766263 CAGGCACCTGGTAGAAGTCATA 59.234 50.000 8.93 0.00 40.17 2.15
655 656 3.197766 CAGGCACCTGGTAGAAGTCATAA 59.802 47.826 8.93 0.00 40.17 1.90
656 657 3.844211 AGGCACCTGGTAGAAGTCATAAA 59.156 43.478 0.00 0.00 0.00 1.40
657 658 4.475016 AGGCACCTGGTAGAAGTCATAAAT 59.525 41.667 0.00 0.00 0.00 1.40
658 659 4.816925 GGCACCTGGTAGAAGTCATAAATC 59.183 45.833 0.00 0.00 0.00 2.17
659 660 5.396884 GGCACCTGGTAGAAGTCATAAATCT 60.397 44.000 0.00 0.00 0.00 2.40
660 661 6.116126 GCACCTGGTAGAAGTCATAAATCTT 58.884 40.000 0.00 0.00 0.00 2.40
661 662 6.258947 GCACCTGGTAGAAGTCATAAATCTTC 59.741 42.308 0.00 0.00 39.93 2.87
663 664 8.043710 CACCTGGTAGAAGTCATAAATCTTCTT 58.956 37.037 11.66 0.00 45.13 2.52
664 665 9.268282 ACCTGGTAGAAGTCATAAATCTTCTTA 57.732 33.333 11.66 1.34 45.13 2.10
680 681 6.808008 TCTTCTTATTTCAGTTGCAAGAGG 57.192 37.500 0.00 0.00 0.00 3.69
681 682 5.182001 TCTTCTTATTTCAGTTGCAAGAGGC 59.818 40.000 0.00 0.00 45.13 4.70
682 683 3.758554 TCTTATTTCAGTTGCAAGAGGCC 59.241 43.478 0.00 0.00 43.89 5.19
683 684 1.260544 ATTTCAGTTGCAAGAGGCCC 58.739 50.000 0.00 0.00 43.89 5.80
684 685 0.827507 TTTCAGTTGCAAGAGGCCCC 60.828 55.000 0.00 0.00 43.89 5.80
685 686 1.719063 TTCAGTTGCAAGAGGCCCCT 61.719 55.000 0.00 0.00 43.89 4.79
686 687 0.840288 TCAGTTGCAAGAGGCCCCTA 60.840 55.000 0.00 0.00 43.89 3.53
687 688 0.038166 CAGTTGCAAGAGGCCCCTAA 59.962 55.000 0.00 0.00 43.89 2.69
688 689 0.777446 AGTTGCAAGAGGCCCCTAAA 59.223 50.000 0.00 0.00 43.89 1.85
703 704 4.388689 GCCCCTAAAAATCCTAAATCCCCT 60.389 45.833 0.00 0.00 0.00 4.79
733 739 5.230942 AGATAATCTAAATCCGTTCCTGCG 58.769 41.667 0.00 0.00 0.00 5.18
762 772 1.799181 CGATCATGGCGAAGTCGTTCT 60.799 52.381 2.25 0.00 42.22 3.01
919 936 3.428870 GTGACGCAGCTATAAATACGCAT 59.571 43.478 0.00 0.00 0.00 4.73
925 942 4.932200 GCAGCTATAAATACGCATCCTTCT 59.068 41.667 0.00 0.00 0.00 2.85
933 950 1.867363 ACGCATCCTTCTACCTCCTT 58.133 50.000 0.00 0.00 0.00 3.36
1029 1058 4.379243 AGCTCCAACGCCGAGGTG 62.379 66.667 0.46 0.46 36.74 4.00
1194 1223 2.041405 GCCCTCCCCAGCTACTCT 60.041 66.667 0.00 0.00 0.00 3.24
1290 1319 0.546747 AGGTGATCCCCGTCAAGGAA 60.547 55.000 0.00 0.00 45.00 3.36
1533 1568 2.607750 GTCTCCACCCAGCCTGGA 60.608 66.667 13.74 0.00 40.96 3.86
1579 1614 3.390521 ACAAGATGCCCGAGCCGA 61.391 61.111 0.00 0.00 38.69 5.54
1836 1871 4.760047 GTGGGCATCGACGGCACT 62.760 66.667 7.52 0.00 35.15 4.40
2043 2108 2.082231 ACTCTTGAGCATGCATGTGTC 58.918 47.619 26.79 22.37 0.00 3.67
2044 2109 2.081462 CTCTTGAGCATGCATGTGTCA 58.919 47.619 26.79 24.41 0.00 3.58
2045 2110 2.683362 CTCTTGAGCATGCATGTGTCAT 59.317 45.455 26.79 9.08 0.00 3.06
2046 2111 2.422127 TCTTGAGCATGCATGTGTCATG 59.578 45.455 26.79 25.84 43.02 3.07
2047 2112 1.828979 TGAGCATGCATGTGTCATGT 58.171 45.000 26.79 4.40 42.34 3.21
2048 2113 1.470890 TGAGCATGCATGTGTCATGTG 59.529 47.619 26.79 0.85 42.34 3.21
2049 2114 1.471287 GAGCATGCATGTGTCATGTGT 59.529 47.619 26.79 0.00 42.34 3.72
2050 2115 1.201414 AGCATGCATGTGTCATGTGTG 59.799 47.619 26.79 0.00 42.34 3.82
2068 2133 5.114081 TGTGTGTCTGATCTGATGCATTAG 58.886 41.667 12.14 12.14 0.00 1.73
2076 2141 6.760298 TCTGATCTGATGCATTAGTTCTGTTC 59.240 38.462 22.78 11.11 0.00 3.18
2092 2157 8.029642 AGTTCTGTTCTGTATATTTTGGTTCG 57.970 34.615 0.00 0.00 0.00 3.95
2113 2178 5.285651 TCGGTTTTGCAAAATTCAACTAGG 58.714 37.500 26.24 8.75 0.00 3.02
2163 2228 2.097825 GCTCCAGAATTCTGTGGCATT 58.902 47.619 29.03 0.00 42.27 3.56
2255 2428 6.461927 CCATATATGCTCAACATTGCAAGGTT 60.462 38.462 22.84 22.84 42.74 3.50
2294 2467 6.681729 AGTAAATACTCCACAAGGAACAGA 57.318 37.500 0.00 0.00 45.19 3.41
2299 2481 7.973048 AATACTCCACAAGGAACAGATACTA 57.027 36.000 0.00 0.00 45.19 1.82
2300 2482 7.973048 ATACTCCACAAGGAACAGATACTAA 57.027 36.000 0.00 0.00 45.19 2.24
2301 2483 6.681729 ACTCCACAAGGAACAGATACTAAA 57.318 37.500 0.00 0.00 45.19 1.85
2302 2484 7.074653 ACTCCACAAGGAACAGATACTAAAA 57.925 36.000 0.00 0.00 45.19 1.52
2303 2485 7.514721 ACTCCACAAGGAACAGATACTAAAAA 58.485 34.615 0.00 0.00 45.19 1.94
2354 2536 9.562408 TCTCCTACTGTCATATACTTTCTGTAG 57.438 37.037 0.00 0.00 34.24 2.74
2355 2537 9.344772 CTCCTACTGTCATATACTTTCTGTAGT 57.655 37.037 0.00 0.00 34.24 2.73
2398 2583 9.892130 TCTTGAAGGGAGTTATAGAAAAAGATC 57.108 33.333 0.00 0.00 0.00 2.75
2403 2588 7.001073 AGGGAGTTATAGAAAAAGATCATGCC 58.999 38.462 0.00 0.00 0.00 4.40
2409 2594 9.468532 GTTATAGAAAAAGATCATGCCAATTCC 57.531 33.333 0.00 0.00 0.00 3.01
2511 2696 6.370442 TGATCAATCTGGTTAACTAACGTTGG 59.630 38.462 11.99 11.17 37.07 3.77
2518 2703 7.675062 TCTGGTTAACTAACGTTGGGTTATTA 58.325 34.615 20.88 8.31 40.22 0.98
2813 3001 8.607441 TGAATTCGCAGATGTAATAATAAGCT 57.393 30.769 0.04 0.00 35.04 3.74
2971 3164 1.003118 TCTCAAATGGTTGGAGTCGGG 59.997 52.381 0.00 0.00 35.29 5.14
3017 3210 4.277921 TTTTCATTGAAAATTGGCCAAGCC 59.722 37.500 24.94 12.56 41.46 4.35
3124 3374 2.040544 GGTGACGGGGAGTTGCATG 61.041 63.158 0.00 0.00 0.00 4.06
3150 3400 4.752604 CAGATTGAGGAGCTGAAGATCATG 59.247 45.833 0.00 0.00 44.56 3.07
3177 3427 8.715191 AAGTGATATGCTCTTCAAACTTCTAG 57.285 34.615 0.00 0.00 0.00 2.43
3178 3428 8.072321 AGTGATATGCTCTTCAAACTTCTAGA 57.928 34.615 0.00 0.00 0.00 2.43
3180 3430 9.973450 GTGATATGCTCTTCAAACTTCTAGATA 57.027 33.333 0.00 0.00 0.00 1.98
3207 3484 9.584839 GTTAGTTACGTTTATGGTTTTACACTG 57.415 33.333 0.00 0.00 0.00 3.66
3208 3485 9.539825 TTAGTTACGTTTATGGTTTTACACTGA 57.460 29.630 0.00 0.00 0.00 3.41
3209 3486 8.611654 AGTTACGTTTATGGTTTTACACTGAT 57.388 30.769 0.00 0.00 0.00 2.90
3210 3487 8.500773 AGTTACGTTTATGGTTTTACACTGATG 58.499 33.333 0.00 0.00 0.00 3.07
3242 4375 2.791383 ATAGTCGATCTGCAGACAGC 57.209 50.000 20.97 10.70 44.10 4.40
3293 4428 2.190325 GTACCTGCAGTACGTAGCTG 57.810 55.000 13.81 16.19 41.94 4.24
3432 4572 0.465460 GCAATATCCGGCAGAACCCA 60.465 55.000 0.00 0.00 33.26 4.51
3457 4598 2.039624 AGATGGCGACCCACCTCT 59.960 61.111 0.00 0.00 45.77 3.69
3496 4637 2.371841 TGCTAGAGAGTGGGCTTCAAAA 59.628 45.455 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.590238 GATTCTCTTCGTGTCATGCCG 59.410 52.381 0.00 0.00 0.00 5.69
1 2 2.898705 AGATTCTCTTCGTGTCATGCC 58.101 47.619 0.00 0.00 0.00 4.40
2 3 3.063180 CCAAGATTCTCTTCGTGTCATGC 59.937 47.826 0.00 0.00 33.78 4.06
3 4 3.620374 CCCAAGATTCTCTTCGTGTCATG 59.380 47.826 0.00 0.00 33.78 3.07
4 5 3.369892 CCCCAAGATTCTCTTCGTGTCAT 60.370 47.826 0.00 0.00 33.78 3.06
5 6 2.028112 CCCCAAGATTCTCTTCGTGTCA 60.028 50.000 0.00 0.00 33.78 3.58
6 7 2.028020 ACCCCAAGATTCTCTTCGTGTC 60.028 50.000 0.00 0.00 33.78 3.67
7 8 1.978580 ACCCCAAGATTCTCTTCGTGT 59.021 47.619 0.00 0.00 33.78 4.49
8 9 2.350522 CACCCCAAGATTCTCTTCGTG 58.649 52.381 0.00 0.00 33.78 4.35
9 10 1.279271 CCACCCCAAGATTCTCTTCGT 59.721 52.381 0.00 0.00 33.78 3.85
10 11 1.407437 CCCACCCCAAGATTCTCTTCG 60.407 57.143 0.00 0.00 33.78 3.79
11 12 1.636003 ACCCACCCCAAGATTCTCTTC 59.364 52.381 0.00 0.00 33.78 2.87
12 13 1.760405 ACCCACCCCAAGATTCTCTT 58.240 50.000 0.00 0.00 37.14 2.85
13 14 1.355720 CAACCCACCCCAAGATTCTCT 59.644 52.381 0.00 0.00 0.00 3.10
14 15 1.616994 CCAACCCACCCCAAGATTCTC 60.617 57.143 0.00 0.00 0.00 2.87
15 16 0.409484 CCAACCCACCCCAAGATTCT 59.591 55.000 0.00 0.00 0.00 2.40
16 17 0.614697 CCCAACCCACCCCAAGATTC 60.615 60.000 0.00 0.00 0.00 2.52
17 18 1.469251 CCCAACCCACCCCAAGATT 59.531 57.895 0.00 0.00 0.00 2.40
18 19 3.190349 CCCAACCCACCCCAAGAT 58.810 61.111 0.00 0.00 0.00 2.40
19 20 3.909651 GCCCAACCCACCCCAAGA 61.910 66.667 0.00 0.00 0.00 3.02
39 40 4.692475 CACCCCCGAACACCGTCC 62.692 72.222 0.00 0.00 36.31 4.79
40 41 2.496828 CTACACCCCCGAACACCGTC 62.497 65.000 0.00 0.00 36.31 4.79
41 42 2.523902 TACACCCCCGAACACCGT 60.524 61.111 0.00 0.00 36.31 4.83
42 43 2.263540 CTACACCCCCGAACACCG 59.736 66.667 0.00 0.00 38.18 4.94
43 44 1.259840 TAGCTACACCCCCGAACACC 61.260 60.000 0.00 0.00 0.00 4.16
44 45 0.828677 ATAGCTACACCCCCGAACAC 59.171 55.000 0.00 0.00 0.00 3.32
45 46 0.828022 CATAGCTACACCCCCGAACA 59.172 55.000 0.00 0.00 0.00 3.18
46 47 0.106149 CCATAGCTACACCCCCGAAC 59.894 60.000 0.00 0.00 0.00 3.95
47 48 1.052124 CCCATAGCTACACCCCCGAA 61.052 60.000 0.00 0.00 0.00 4.30
48 49 1.458777 CCCATAGCTACACCCCCGA 60.459 63.158 0.00 0.00 0.00 5.14
49 50 3.148084 CCCATAGCTACACCCCCG 58.852 66.667 0.00 0.00 0.00 5.73
50 51 2.836888 GCCCATAGCTACACCCCC 59.163 66.667 0.00 0.00 38.99 5.40
59 60 1.902508 TGTCATAGCCTAGCCCATAGC 59.097 52.381 0.00 0.00 44.25 2.97
60 61 4.223700 TGATTGTCATAGCCTAGCCCATAG 59.776 45.833 0.00 0.00 0.00 2.23
61 62 4.167319 TGATTGTCATAGCCTAGCCCATA 58.833 43.478 0.00 0.00 0.00 2.74
62 63 2.981784 TGATTGTCATAGCCTAGCCCAT 59.018 45.455 0.00 0.00 0.00 4.00
63 64 2.369860 CTGATTGTCATAGCCTAGCCCA 59.630 50.000 0.00 0.00 0.00 5.36
64 65 2.289945 CCTGATTGTCATAGCCTAGCCC 60.290 54.545 0.00 0.00 0.00 5.19
65 66 2.370189 ACCTGATTGTCATAGCCTAGCC 59.630 50.000 0.00 0.00 0.00 3.93
66 67 3.070159 TCACCTGATTGTCATAGCCTAGC 59.930 47.826 0.00 0.00 0.00 3.42
67 68 4.944619 TCACCTGATTGTCATAGCCTAG 57.055 45.455 0.00 0.00 0.00 3.02
68 69 5.692115 TTTCACCTGATTGTCATAGCCTA 57.308 39.130 0.00 0.00 0.00 3.93
69 70 4.574674 TTTCACCTGATTGTCATAGCCT 57.425 40.909 0.00 0.00 0.00 4.58
70 71 4.096984 CCTTTTCACCTGATTGTCATAGCC 59.903 45.833 0.00 0.00 0.00 3.93
71 72 4.702131 ACCTTTTCACCTGATTGTCATAGC 59.298 41.667 0.00 0.00 0.00 2.97
72 73 5.355350 GGACCTTTTCACCTGATTGTCATAG 59.645 44.000 0.00 0.00 0.00 2.23
73 74 5.222027 TGGACCTTTTCACCTGATTGTCATA 60.222 40.000 0.00 0.00 0.00 2.15
74 75 4.082125 GGACCTTTTCACCTGATTGTCAT 58.918 43.478 0.00 0.00 0.00 3.06
75 76 3.117701 TGGACCTTTTCACCTGATTGTCA 60.118 43.478 0.00 0.00 0.00 3.58
76 77 3.253432 GTGGACCTTTTCACCTGATTGTC 59.747 47.826 0.00 0.00 0.00 3.18
77 78 3.222603 GTGGACCTTTTCACCTGATTGT 58.777 45.455 0.00 0.00 0.00 2.71
78 79 3.923017 GTGGACCTTTTCACCTGATTG 57.077 47.619 0.00 0.00 0.00 2.67
85 86 0.179040 TGACCGGTGGACCTTTTCAC 60.179 55.000 14.63 0.00 0.00 3.18
86 87 0.547075 TTGACCGGTGGACCTTTTCA 59.453 50.000 14.63 0.00 0.00 2.69
87 88 1.335810 GTTTGACCGGTGGACCTTTTC 59.664 52.381 14.63 0.00 0.00 2.29
88 89 1.395635 GTTTGACCGGTGGACCTTTT 58.604 50.000 14.63 0.00 0.00 2.27
89 90 0.466739 GGTTTGACCGGTGGACCTTT 60.467 55.000 14.63 0.00 0.00 3.11
90 91 1.149854 GGTTTGACCGGTGGACCTT 59.850 57.895 14.63 0.00 0.00 3.50
91 92 2.826003 GGGTTTGACCGGTGGACCT 61.826 63.158 14.63 0.00 39.83 3.85
92 93 2.281970 GGGTTTGACCGGTGGACC 60.282 66.667 14.63 16.91 39.83 4.46
93 94 2.281970 GGGGTTTGACCGGTGGAC 60.282 66.667 14.63 7.51 39.83 4.02
100 101 2.671963 GCCAGACGGGGTTTGACC 60.672 66.667 0.00 0.00 37.60 4.02
101 102 2.999739 TTCGCCAGACGGGGTTTGAC 63.000 60.000 0.00 0.00 45.44 3.18
102 103 2.326773 TTTCGCCAGACGGGGTTTGA 62.327 55.000 0.00 0.00 45.44 2.69
103 104 1.852067 CTTTCGCCAGACGGGGTTTG 61.852 60.000 0.00 0.00 45.44 2.93
104 105 1.599797 CTTTCGCCAGACGGGGTTT 60.600 57.895 0.00 0.00 45.44 3.27
105 106 2.032071 CTTTCGCCAGACGGGGTT 59.968 61.111 0.00 0.00 45.44 4.11
106 107 3.236003 GACTTTCGCCAGACGGGGT 62.236 63.158 0.00 0.00 45.44 4.95
107 108 2.434359 GACTTTCGCCAGACGGGG 60.434 66.667 0.00 0.00 46.62 5.73
108 109 0.882927 TTTGACTTTCGCCAGACGGG 60.883 55.000 0.00 0.00 43.89 5.28
109 110 0.512952 CTTTGACTTTCGCCAGACGG 59.487 55.000 0.00 0.00 43.89 4.79
110 111 0.512952 CCTTTGACTTTCGCCAGACG 59.487 55.000 0.00 0.00 45.62 4.18
111 112 0.875059 CCCTTTGACTTTCGCCAGAC 59.125 55.000 0.00 0.00 0.00 3.51
112 113 0.889186 GCCCTTTGACTTTCGCCAGA 60.889 55.000 0.00 0.00 0.00 3.86
113 114 0.890996 AGCCCTTTGACTTTCGCCAG 60.891 55.000 0.00 0.00 0.00 4.85
114 115 0.398696 TAGCCCTTTGACTTTCGCCA 59.601 50.000 0.00 0.00 0.00 5.69
115 116 1.087501 CTAGCCCTTTGACTTTCGCC 58.912 55.000 0.00 0.00 0.00 5.54
116 117 2.094762 TCTAGCCCTTTGACTTTCGC 57.905 50.000 0.00 0.00 0.00 4.70
117 118 3.307242 CGAATCTAGCCCTTTGACTTTCG 59.693 47.826 0.00 0.00 0.00 3.46
118 119 4.330347 GTCGAATCTAGCCCTTTGACTTTC 59.670 45.833 10.38 0.00 34.36 2.62
119 120 4.254492 GTCGAATCTAGCCCTTTGACTTT 58.746 43.478 10.38 0.00 34.36 2.66
120 121 3.676324 CGTCGAATCTAGCCCTTTGACTT 60.676 47.826 13.50 0.00 34.81 3.01
121 122 2.159226 CGTCGAATCTAGCCCTTTGACT 60.159 50.000 13.50 0.00 34.81 3.41
122 123 2.194271 CGTCGAATCTAGCCCTTTGAC 58.806 52.381 0.00 8.66 34.00 3.18
123 124 1.136305 CCGTCGAATCTAGCCCTTTGA 59.864 52.381 0.00 0.00 0.00 2.69
124 125 1.134788 ACCGTCGAATCTAGCCCTTTG 60.135 52.381 0.00 0.00 0.00 2.77
125 126 1.136500 GACCGTCGAATCTAGCCCTTT 59.864 52.381 0.00 0.00 0.00 3.11
126 127 0.745468 GACCGTCGAATCTAGCCCTT 59.255 55.000 0.00 0.00 0.00 3.95
127 128 1.445716 CGACCGTCGAATCTAGCCCT 61.446 60.000 16.03 0.00 43.74 5.19
128 129 1.008767 CGACCGTCGAATCTAGCCC 60.009 63.158 16.03 0.00 43.74 5.19
129 130 0.316854 GACGACCGTCGAATCTAGCC 60.317 60.000 27.03 2.59 43.74 3.93
130 131 3.145806 GACGACCGTCGAATCTAGC 57.854 57.895 27.03 4.01 43.74 3.42
139 140 1.081376 CCTGACACAGACGACCGTC 60.081 63.158 14.03 14.03 44.86 4.79
140 141 2.561956 CCCTGACACAGACGACCGT 61.562 63.158 0.00 0.00 32.44 4.83
141 142 2.083835 AACCCTGACACAGACGACCG 62.084 60.000 0.00 0.00 32.44 4.79
142 143 0.963962 TAACCCTGACACAGACGACC 59.036 55.000 0.00 0.00 32.44 4.79
143 144 2.806608 TTAACCCTGACACAGACGAC 57.193 50.000 0.00 0.00 32.44 4.34
573 574 1.736645 CAACAGCTGGCAGCATTGC 60.737 57.895 38.09 15.00 45.56 3.56
574 575 0.666274 CACAACAGCTGGCAGCATTG 60.666 55.000 35.58 35.58 45.56 2.82
575 576 1.663739 CACAACAGCTGGCAGCATT 59.336 52.632 38.09 28.37 45.56 3.56
576 577 2.273179 CCACAACAGCTGGCAGCAT 61.273 57.895 38.09 24.51 45.56 3.79
577 578 2.908428 CCACAACAGCTGGCAGCA 60.908 61.111 38.09 0.00 45.56 4.41
578 579 2.908940 ACCACAACAGCTGGCAGC 60.909 61.111 31.56 31.56 42.84 5.25
579 580 2.558286 CCACCACAACAGCTGGCAG 61.558 63.158 19.93 10.94 31.13 4.85
580 581 2.519063 CCACCACAACAGCTGGCA 60.519 61.111 19.93 0.00 31.13 4.92
581 582 3.297620 CCCACCACAACAGCTGGC 61.298 66.667 19.93 0.00 31.13 4.85
582 583 3.297620 GCCCACCACAACAGCTGG 61.298 66.667 19.93 2.50 34.62 4.85
583 584 3.297620 GGCCCACCACAACAGCTG 61.298 66.667 13.48 13.48 35.26 4.24
584 585 4.603535 GGGCCCACCACAACAGCT 62.604 66.667 19.95 0.00 39.85 4.24
585 586 4.603535 AGGGCCCACCACAACAGC 62.604 66.667 27.56 0.00 43.89 4.40
586 587 2.282462 GAGGGCCCACCACAACAG 60.282 66.667 27.56 0.00 43.89 3.16
587 588 4.263572 CGAGGGCCCACCACAACA 62.264 66.667 27.56 0.00 43.89 3.33
588 589 2.193087 ATACGAGGGCCCACCACAAC 62.193 60.000 27.56 4.94 43.89 3.32
589 590 1.921346 ATACGAGGGCCCACCACAA 60.921 57.895 27.56 4.02 43.89 3.33
590 591 2.285069 ATACGAGGGCCCACCACA 60.285 61.111 27.56 4.87 43.89 4.17
591 592 2.189521 CATACGAGGGCCCACCAC 59.810 66.667 27.56 11.36 43.89 4.16
592 593 3.792736 GCATACGAGGGCCCACCA 61.793 66.667 27.56 7.69 43.89 4.17
593 594 2.552231 AAAGCATACGAGGGCCCACC 62.552 60.000 27.56 14.75 40.67 4.61
594 595 0.679960 AAAAGCATACGAGGGCCCAC 60.680 55.000 27.56 18.56 0.00 4.61
595 596 0.679640 CAAAAGCATACGAGGGCCCA 60.680 55.000 27.56 2.25 0.00 5.36
596 597 1.384222 CCAAAAGCATACGAGGGCCC 61.384 60.000 16.46 16.46 0.00 5.80
597 598 0.393808 TCCAAAAGCATACGAGGGCC 60.394 55.000 0.00 0.00 0.00 5.80
598 599 1.401905 CTTCCAAAAGCATACGAGGGC 59.598 52.381 0.00 0.00 0.00 5.19
609 610 1.007387 GCCACCACGCTTCCAAAAG 60.007 57.895 0.00 0.00 35.47 2.27
610 611 1.733402 CTGCCACCACGCTTCCAAAA 61.733 55.000 0.00 0.00 0.00 2.44
611 612 2.124109 TGCCACCACGCTTCCAAA 60.124 55.556 0.00 0.00 0.00 3.28
612 613 2.594303 CTGCCACCACGCTTCCAA 60.594 61.111 0.00 0.00 0.00 3.53
613 614 4.641645 CCTGCCACCACGCTTCCA 62.642 66.667 0.00 0.00 0.00 3.53
630 631 3.605749 TTCTACCAGGTGCCTGCGC 62.606 63.158 12.54 0.00 42.35 6.09
631 632 1.448540 CTTCTACCAGGTGCCTGCG 60.449 63.158 12.54 8.57 42.35 5.18
632 633 0.391793 GACTTCTACCAGGTGCCTGC 60.392 60.000 12.54 0.00 42.35 4.85
633 634 0.976641 TGACTTCTACCAGGTGCCTG 59.023 55.000 11.13 11.13 43.26 4.85
634 635 1.958288 ATGACTTCTACCAGGTGCCT 58.042 50.000 0.76 0.00 0.00 4.75
635 636 3.906720 TTATGACTTCTACCAGGTGCC 57.093 47.619 0.76 0.00 0.00 5.01
636 637 5.675538 AGATTTATGACTTCTACCAGGTGC 58.324 41.667 0.76 0.00 0.00 5.01
637 638 7.560368 AGAAGATTTATGACTTCTACCAGGTG 58.440 38.462 0.76 0.00 46.99 4.00
638 639 7.741554 AGAAGATTTATGACTTCTACCAGGT 57.258 36.000 0.00 0.00 46.99 4.00
654 655 8.302438 CCTCTTGCAACTGAAATAAGAAGATTT 58.698 33.333 0.00 0.00 0.00 2.17
655 656 7.576477 GCCTCTTGCAACTGAAATAAGAAGATT 60.576 37.037 0.00 0.00 40.77 2.40
656 657 6.127786 GCCTCTTGCAACTGAAATAAGAAGAT 60.128 38.462 0.00 0.00 40.77 2.40
657 658 5.182001 GCCTCTTGCAACTGAAATAAGAAGA 59.818 40.000 0.00 0.00 40.77 2.87
658 659 5.397326 GCCTCTTGCAACTGAAATAAGAAG 58.603 41.667 0.00 0.00 40.77 2.85
659 660 4.218417 GGCCTCTTGCAACTGAAATAAGAA 59.782 41.667 0.00 0.00 43.89 2.52
660 661 3.758554 GGCCTCTTGCAACTGAAATAAGA 59.241 43.478 0.00 0.00 43.89 2.10
661 662 3.119352 GGGCCTCTTGCAACTGAAATAAG 60.119 47.826 0.84 0.00 43.89 1.73
662 663 2.825532 GGGCCTCTTGCAACTGAAATAA 59.174 45.455 0.84 0.00 43.89 1.40
663 664 2.446435 GGGCCTCTTGCAACTGAAATA 58.554 47.619 0.84 0.00 43.89 1.40
664 665 1.260544 GGGCCTCTTGCAACTGAAAT 58.739 50.000 0.84 0.00 43.89 2.17
665 666 0.827507 GGGGCCTCTTGCAACTGAAA 60.828 55.000 0.84 0.00 43.89 2.69
666 667 1.228552 GGGGCCTCTTGCAACTGAA 60.229 57.895 0.84 0.00 43.89 3.02
667 668 0.840288 TAGGGGCCTCTTGCAACTGA 60.840 55.000 12.52 0.00 43.89 3.41
668 669 0.038166 TTAGGGGCCTCTTGCAACTG 59.962 55.000 12.52 0.00 43.89 3.16
669 670 0.777446 TTTAGGGGCCTCTTGCAACT 59.223 50.000 12.52 0.00 43.89 3.16
670 671 1.627864 TTTTAGGGGCCTCTTGCAAC 58.372 50.000 12.52 0.00 43.89 4.17
671 672 2.390225 TTTTTAGGGGCCTCTTGCAA 57.610 45.000 12.52 0.00 43.89 4.08
672 673 2.456577 GATTTTTAGGGGCCTCTTGCA 58.543 47.619 12.52 0.00 43.89 4.08
673 674 1.757118 GGATTTTTAGGGGCCTCTTGC 59.243 52.381 12.52 0.00 40.16 4.01
674 675 3.388552 AGGATTTTTAGGGGCCTCTTG 57.611 47.619 12.52 0.00 0.00 3.02
675 676 5.546035 TTTAGGATTTTTAGGGGCCTCTT 57.454 39.130 12.52 0.00 0.00 2.85
676 677 5.400305 GGATTTAGGATTTTTAGGGGCCTCT 60.400 44.000 11.71 11.71 0.00 3.69
677 678 4.833380 GGATTTAGGATTTTTAGGGGCCTC 59.167 45.833 0.84 0.00 0.00 4.70
678 679 4.388689 GGGATTTAGGATTTTTAGGGGCCT 60.389 45.833 0.84 0.00 0.00 5.19
679 680 3.901844 GGGATTTAGGATTTTTAGGGGCC 59.098 47.826 0.00 0.00 0.00 5.80
680 681 3.901844 GGGGATTTAGGATTTTTAGGGGC 59.098 47.826 0.00 0.00 0.00 5.80
681 682 5.418692 AGGGGATTTAGGATTTTTAGGGG 57.581 43.478 0.00 0.00 0.00 4.79
682 683 8.847982 TTTTAGGGGATTTAGGATTTTTAGGG 57.152 34.615 0.00 0.00 0.00 3.53
713 714 4.116961 CACGCAGGAACGGATTTAGATTA 58.883 43.478 0.00 0.00 37.37 1.75
715 716 2.550978 CACGCAGGAACGGATTTAGAT 58.449 47.619 0.00 0.00 37.37 1.98
716 717 2.004583 CACGCAGGAACGGATTTAGA 57.995 50.000 0.00 0.00 37.37 2.10
717 718 0.373716 GCACGCAGGAACGGATTTAG 59.626 55.000 0.00 0.00 37.37 1.85
718 719 0.320858 TGCACGCAGGAACGGATTTA 60.321 50.000 0.00 0.00 37.37 1.40
722 728 0.529773 GATATGCACGCAGGAACGGA 60.530 55.000 0.00 0.00 37.37 4.69
733 739 0.723414 CGCCATGATCGGATATGCAC 59.277 55.000 0.00 0.00 0.00 4.57
762 772 4.771114 ATCATCCCGTTGAATAGGAACA 57.229 40.909 0.00 0.00 32.26 3.18
919 936 2.032620 GCGATGAAGGAGGTAGAAGGA 58.967 52.381 0.00 0.00 0.00 3.36
925 942 2.666317 TGAGATGCGATGAAGGAGGTA 58.334 47.619 0.00 0.00 0.00 3.08
933 950 3.070590 AGGATGTGAATGAGATGCGATGA 59.929 43.478 0.00 0.00 0.00 2.92
1029 1058 1.709147 GCGACAGGTCCATGCACATC 61.709 60.000 0.00 0.00 0.00 3.06
1194 1223 4.373116 GCGACCTTGGCGGAGTCA 62.373 66.667 0.00 0.00 45.30 3.41
1455 1490 0.170561 CGACGAACTCGGTGGAGAAT 59.829 55.000 3.88 0.00 43.27 2.40
1482 1517 2.283676 TCCTGGTCGAGGTCCCAC 60.284 66.667 0.26 0.00 43.37 4.61
1533 1568 0.806102 CGATCTTGACAACGCCGGAT 60.806 55.000 5.05 0.00 0.00 4.18
1542 1577 4.812476 CCCGCGGCGATCTTGACA 62.812 66.667 25.92 0.00 0.00 3.58
2043 2108 3.267483 TGCATCAGATCAGACACACATG 58.733 45.455 0.00 0.00 0.00 3.21
2044 2109 3.622166 TGCATCAGATCAGACACACAT 57.378 42.857 0.00 0.00 0.00 3.21
2045 2110 3.622166 ATGCATCAGATCAGACACACA 57.378 42.857 0.00 0.00 0.00 3.72
2046 2111 5.114780 ACTAATGCATCAGATCAGACACAC 58.885 41.667 3.12 0.00 0.00 3.82
2047 2112 5.349061 ACTAATGCATCAGATCAGACACA 57.651 39.130 3.12 0.00 0.00 3.72
2048 2113 6.018913 CAGAACTAATGCATCAGATCAGACAC 60.019 42.308 3.12 0.00 0.00 3.67
2049 2114 6.047231 CAGAACTAATGCATCAGATCAGACA 58.953 40.000 3.12 0.00 0.00 3.41
2050 2115 6.047870 ACAGAACTAATGCATCAGATCAGAC 58.952 40.000 3.12 0.00 0.00 3.51
2068 2133 7.094933 ACCGAACCAAAATATACAGAACAGAAC 60.095 37.037 0.00 0.00 0.00 3.01
2076 2141 6.153067 TGCAAAACCGAACCAAAATATACAG 58.847 36.000 0.00 0.00 0.00 2.74
2092 2157 6.761242 AGTTCCTAGTTGAATTTTGCAAAACC 59.239 34.615 26.05 19.88 0.00 3.27
2128 2193 9.174166 GAATTCTGGAGCTAATTAAAGTGGTAA 57.826 33.333 0.00 0.00 0.00 2.85
2131 2196 7.701445 CAGAATTCTGGAGCTAATTAAAGTGG 58.299 38.462 25.14 0.00 40.20 4.00
2279 2452 7.979444 TTTTTAGTATCTGTTCCTTGTGGAG 57.021 36.000 0.00 0.00 44.24 3.86
2304 2486 9.588096 AGATTAGTTTTCAGTTTTCCCATTAGT 57.412 29.630 0.00 0.00 0.00 2.24
2306 2488 9.020731 GGAGATTAGTTTTCAGTTTTCCCATTA 57.979 33.333 0.00 0.00 0.00 1.90
2307 2489 7.730332 AGGAGATTAGTTTTCAGTTTTCCCATT 59.270 33.333 0.00 0.00 0.00 3.16
2308 2490 7.241628 AGGAGATTAGTTTTCAGTTTTCCCAT 58.758 34.615 0.00 0.00 0.00 4.00
2309 2491 6.610830 AGGAGATTAGTTTTCAGTTTTCCCA 58.389 36.000 0.00 0.00 0.00 4.37
2310 2492 7.883833 AGTAGGAGATTAGTTTTCAGTTTTCCC 59.116 37.037 0.00 0.00 0.00 3.97
2311 2493 8.722394 CAGTAGGAGATTAGTTTTCAGTTTTCC 58.278 37.037 0.00 0.00 0.00 3.13
2312 2494 9.274206 ACAGTAGGAGATTAGTTTTCAGTTTTC 57.726 33.333 0.00 0.00 0.00 2.29
2313 2495 9.274206 GACAGTAGGAGATTAGTTTTCAGTTTT 57.726 33.333 0.00 0.00 0.00 2.43
2314 2496 8.429641 TGACAGTAGGAGATTAGTTTTCAGTTT 58.570 33.333 0.00 0.00 0.00 2.66
2315 2497 7.963532 TGACAGTAGGAGATTAGTTTTCAGTT 58.036 34.615 0.00 0.00 0.00 3.16
2316 2498 7.540474 TGACAGTAGGAGATTAGTTTTCAGT 57.460 36.000 0.00 0.00 0.00 3.41
2373 2558 9.672673 TGATCTTTTTCTATAACTCCCTTCAAG 57.327 33.333 0.00 0.00 0.00 3.02
2389 2574 6.091713 CACAAGGAATTGGCATGATCTTTTTC 59.908 38.462 0.00 0.00 0.00 2.29
2423 2608 9.177304 CATGCAGCAAGATTACAATAATTGTAG 57.823 33.333 0.00 0.00 45.92 2.74
2511 2696 6.035975 GGCTGCATTTGTTTGACATAATAACC 59.964 38.462 0.50 0.00 0.00 2.85
2518 2703 1.693062 TGGGCTGCATTTGTTTGACAT 59.307 42.857 0.50 0.00 0.00 3.06
2556 2741 2.048503 CACACCGACGTCTTCCCC 60.049 66.667 14.70 0.00 0.00 4.81
2809 2997 3.951775 GATCATACCGATCTCCAGCTT 57.048 47.619 0.00 0.00 46.16 3.74
2951 3139 1.003118 CCCGACTCCAACCATTTGAGA 59.997 52.381 0.00 0.00 34.24 3.27
2971 3164 2.501610 GCGAGAGGATCACACCCC 59.498 66.667 0.00 0.00 37.82 4.95
2977 3170 3.055167 TGAAAATTCAGGCGAGAGGATCA 60.055 43.478 0.00 0.00 32.49 2.92
2982 3175 4.952262 TCAATGAAAATTCAGGCGAGAG 57.048 40.909 1.98 0.00 41.08 3.20
2983 3176 5.703978 TTTCAATGAAAATTCAGGCGAGA 57.296 34.783 5.87 0.00 41.08 4.04
3014 3207 8.951614 TGTTGTAATCTACCTACTATATGGCT 57.048 34.615 0.00 0.00 0.00 4.75
3017 3210 9.529823 TCCCTGTTGTAATCTACCTACTATATG 57.470 37.037 0.00 0.00 0.00 1.78
3028 3221 6.214278 TCCCCTTTATCCCTGTTGTAATCTA 58.786 40.000 0.00 0.00 0.00 1.98
3108 3358 2.350895 CCATGCAACTCCCCGTCA 59.649 61.111 0.00 0.00 0.00 4.35
3124 3374 0.254178 TTCAGCTCCTCAATCTGCCC 59.746 55.000 0.00 0.00 0.00 5.36
3130 3380 5.369409 TTCATGATCTTCAGCTCCTCAAT 57.631 39.130 0.00 0.00 0.00 2.57
3150 3400 8.038492 AGAAGTTTGAAGAGCATATCACTTTC 57.962 34.615 0.00 0.00 0.00 2.62
3180 3430 9.546428 AGTGTAAAACCATAAACGTAACTAACT 57.454 29.630 0.00 0.00 0.00 2.24
3181 3431 9.584839 CAGTGTAAAACCATAAACGTAACTAAC 57.415 33.333 0.00 0.00 0.00 2.34
3182 3432 9.539825 TCAGTGTAAAACCATAAACGTAACTAA 57.460 29.630 0.00 0.00 0.00 2.24
3183 3433 9.709495 ATCAGTGTAAAACCATAAACGTAACTA 57.291 29.630 0.00 0.00 0.00 2.24
3184 3434 8.500773 CATCAGTGTAAAACCATAAACGTAACT 58.499 33.333 0.00 0.00 0.00 2.24
3222 4355 2.224314 CGCTGTCTGCAGATCGACTATA 59.776 50.000 21.47 0.00 45.28 1.31
3244 4377 3.682377 CAGAAATGTACGGTGTGCATACA 59.318 43.478 15.93 7.72 37.86 2.29
3245 4378 3.063452 CCAGAAATGTACGGTGTGCATAC 59.937 47.826 4.79 4.79 37.86 2.39
3368 4508 9.682465 GATTTCTGAATAAACCCTAGTTACCTT 57.318 33.333 0.00 0.00 34.19 3.50
3369 4509 8.832735 TGATTTCTGAATAAACCCTAGTTACCT 58.167 33.333 0.00 0.00 34.19 3.08
3457 4598 4.689612 AGCAAAAGGAGTTGTGTCTCTA 57.310 40.909 0.00 0.00 35.11 2.43
3518 4659 8.635765 AGTAACTTTGCTTTCATAGATTTCCA 57.364 30.769 0.00 0.00 0.00 3.53
3595 4736 4.062991 AGGTCGTCACAAACATAAGGAAC 58.937 43.478 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.