Multiple sequence alignment - TraesCS7D01G175800

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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 TraesCS7D01G175800 chr7D 100.000 3422 0 0 1 3422 127701466 127698045 0.000000e+00 6320.0
1 TraesCS7D01G175800 chr7D 90.856 1203 104 6 1970 3169 127732481 127731282 0.000000e+00 1607.0
2 TraesCS7D01G175800 chr7D 90.421 1211 102 7 1970 3169 127736687 127735480 0.000000e+00 1581.0
3 TraesCS7D01G175800 chr7D 93.788 982 52 3 1970 2948 127765060 127764085 0.000000e+00 1467.0
4 TraesCS7D01G175800 chr7D 89.753 1093 94 13 1973 3054 127730216 127729131 0.000000e+00 1382.0
5 TraesCS7D01G175800 chr7D 91.967 971 75 3 1970 2940 127752557 127751590 0.000000e+00 1358.0
6 TraesCS7D01G175800 chr7D 84.196 1430 142 43 607 1972 127738131 127736722 0.000000e+00 1312.0
7 TraesCS7D01G175800 chr7D 92.720 783 42 6 681 1452 127754054 127753276 0.000000e+00 1116.0
8 TraesCS7D01G175800 chr7D 86.919 925 76 16 1058 1972 127733405 127732516 0.000000e+00 996.0
9 TraesCS7D01G175800 chr7D 93.722 446 25 2 1528 1972 127765538 127765095 0.000000e+00 665.0
10 TraesCS7D01G175800 chr7D 91.649 479 35 2 1494 1972 127753065 127752592 0.000000e+00 658.0
11 TraesCS7D01G175800 chr7D 90.289 484 32 6 2943 3422 127762686 127762214 1.350000e-173 619.0
12 TraesCS7D01G175800 chr7D 93.182 352 24 0 1101 1452 127766141 127765790 5.060000e-143 518.0
13 TraesCS7D01G175800 chr7D 86.041 394 25 10 225 594 127754608 127754221 2.470000e-106 396.0
14 TraesCS7D01G175800 chr7D 89.640 222 23 0 1751 1972 127730475 127730254 2.010000e-72 283.0
15 TraesCS7D01G175800 chr7D 83.721 215 20 1 241 440 127734364 127734150 4.510000e-44 189.0
16 TraesCS7D01G175800 chr7D 87.681 138 5 7 462 594 127277741 127277871 2.130000e-32 150.0
17 TraesCS7D01G175800 chr7D 100.000 29 0 0 565 593 127738217 127738189 2.000000e-03 54.7
18 TraesCS7D01G175800 chr7B 85.996 1421 127 35 607 1972 89561571 89560168 0.000000e+00 1456.0
19 TraesCS7D01G175800 chr7B 87.859 1219 97 27 1970 3172 89656427 89655244 0.000000e+00 1384.0
20 TraesCS7D01G175800 chr7B 88.242 944 94 10 1971 2904 89560132 89559196 0.000000e+00 1112.0
21 TraesCS7D01G175800 chr7B 81.350 874 141 19 1102 1960 89542944 89542078 0.000000e+00 691.0
22 TraesCS7D01G175800 chr7B 90.664 482 37 3 1494 1972 89656938 89656462 4.820000e-178 634.0
23 TraesCS7D01G175800 chr7B 93.466 352 23 0 1101 1452 89657521 89657170 1.090000e-144 523.0
24 TraesCS7D01G175800 chr7B 83.607 61 6 1 537 593 89561689 89561629 2.000000e-03 54.7
25 TraesCS7D01G175800 chr7A 90.132 831 72 7 2340 3169 128509519 128508698 0.000000e+00 1072.0
26 TraesCS7D01G175800 chr7A 93.114 639 41 1 1970 2605 128510369 128509731 0.000000e+00 933.0
27 TraesCS7D01G175800 chr7A 92.488 639 45 1 1970 2605 128478206 128477568 0.000000e+00 911.0
28 TraesCS7D01G175800 chr7A 92.809 445 30 2 1528 1972 128510846 128510404 0.000000e+00 643.0
29 TraesCS7D01G175800 chr7A 95.170 352 17 0 1101 1452 128511406 128511055 1.070000e-154 556.0
30 TraesCS7D01G175800 chr7A 88.068 352 41 1 1102 1452 128406114 128405763 1.900000e-112 416.0
31 TraesCS7D01G175800 chr7A 81.799 467 79 6 1974 2439 128405114 128404653 1.490000e-103 387.0
32 TraesCS7D01G175800 chr7A 89.231 260 23 2 3167 3422 6799712 6799454 1.530000e-83 320.0
33 TraesCS7D01G175800 chr7A 88.846 260 25 1 3167 3422 670686626 670686367 1.980000e-82 316.0
34 TraesCS7D01G175800 chr7A 86.897 145 7 5 455 594 127900573 127900710 5.910000e-33 152.0
35 TraesCS7D01G175800 chrUn 91.457 398 29 4 2589 2982 371050421 371050025 3.000000e-150 542.0
36 TraesCS7D01G175800 chr2D 91.457 398 29 4 2589 2982 33935784 33935388 3.000000e-150 542.0
37 TraesCS7D01G175800 chr6D 90.805 261 19 4 3166 3422 27034163 27033904 9.090000e-91 344.0
38 TraesCS7D01G175800 chr1D 90.000 260 21 4 3167 3422 375352687 375352945 7.080000e-87 331.0
39 TraesCS7D01G175800 chr1D 89.615 260 21 3 3167 3422 389330473 389330730 3.290000e-85 326.0
40 TraesCS7D01G175800 chr3D 89.313 262 24 1 3165 3422 597753247 597753508 3.290000e-85 326.0
41 TraesCS7D01G175800 chr4A 89.453 256 22 2 3172 3422 709620273 709620018 5.510000e-83 318.0
42 TraesCS7D01G175800 chr3B 89.105 257 23 2 3167 3418 372190990 372190734 7.130000e-82 315.0


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 TraesCS7D01G175800 chr7D 127698045 127701466 3421 True 6320.000000 6320 100.000000 1 3422 1 chr7D.!!$R1 3421
1 TraesCS7D01G175800 chr7D 127729131 127738217 9086 True 925.587500 1607 89.438250 241 3169 8 chr7D.!!$R2 2928
2 TraesCS7D01G175800 chr7D 127751590 127754608 3018 True 882.000000 1358 90.594250 225 2940 4 chr7D.!!$R3 2715
3 TraesCS7D01G175800 chr7D 127762214 127766141 3927 True 817.250000 1467 92.745250 1101 3422 4 chr7D.!!$R4 2321
4 TraesCS7D01G175800 chr7B 89559196 89561689 2493 True 874.233333 1456 85.948333 537 2904 3 chr7B.!!$R2 2367
5 TraesCS7D01G175800 chr7B 89655244 89657521 2277 True 847.000000 1384 90.663000 1101 3172 3 chr7B.!!$R3 2071
6 TraesCS7D01G175800 chr7B 89542078 89542944 866 True 691.000000 691 81.350000 1102 1960 1 chr7B.!!$R1 858
7 TraesCS7D01G175800 chr7A 128477568 128478206 638 True 911.000000 911 92.488000 1970 2605 1 chr7A.!!$R2 635
8 TraesCS7D01G175800 chr7A 128508698 128511406 2708 True 801.000000 1072 92.806250 1101 3169 4 chr7A.!!$R5 2068
9 TraesCS7D01G175800 chr7A 128404653 128406114 1461 True 401.500000 416 84.933500 1102 2439 2 chr7A.!!$R4 1337

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
208 209 0.034670 GGCTGAGAGGAGTGCCAATT 60.035 55.0 0.00 0.0 44.34 2.32 F
462 471 0.040157 GCAATCGACAGTGCAAAGCA 60.040 50.0 11.56 0.0 40.58 3.91 F
1008 1175 0.250858 TCCACATGTTCAGCCACAGG 60.251 55.0 0.00 0.0 34.56 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 6898 0.387878 CGAGATCAGCATAGCCGTCC 60.388 60.0 0.00 0.0 0.00 4.79 R
2371 7156 0.253327 TACAATGCACATGCCCCGTA 59.747 50.0 0.49 0.0 41.18 4.02 R
2519 7305 1.470051 AAGGACGCACCACTGTTTTT 58.530 45.0 2.21 0.0 42.04 1.94 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
26 27 9.829507 TGACACTTTGAATTATGGTTTTCAAAT 57.170 25.926 10.26 0.00 45.60 2.32
49 50 8.546597 AATATATATTTTTCAAAATGCCGGGC 57.453 30.769 13.32 13.32 38.90 6.13
50 51 2.857186 ATTTTTCAAAATGCCGGGCT 57.143 40.000 21.46 2.61 37.24 5.19
51 52 2.629336 TTTTTCAAAATGCCGGGCTT 57.371 40.000 21.46 11.55 0.00 4.35
52 53 2.162319 TTTTCAAAATGCCGGGCTTC 57.838 45.000 21.46 0.00 0.00 3.86
53 54 1.043816 TTTCAAAATGCCGGGCTTCA 58.956 45.000 21.46 0.00 0.00 3.02
54 55 1.043816 TTCAAAATGCCGGGCTTCAA 58.956 45.000 21.46 0.00 0.00 2.69
55 56 0.602562 TCAAAATGCCGGGCTTCAAG 59.397 50.000 21.46 7.73 0.00 3.02
56 57 0.390209 CAAAATGCCGGGCTTCAAGG 60.390 55.000 21.46 1.70 0.00 3.61
57 58 0.541764 AAAATGCCGGGCTTCAAGGA 60.542 50.000 21.46 0.00 0.00 3.36
58 59 0.967380 AAATGCCGGGCTTCAAGGAG 60.967 55.000 21.46 0.00 0.00 3.69
59 60 1.852157 AATGCCGGGCTTCAAGGAGA 61.852 55.000 21.46 0.00 0.00 3.71
60 61 2.436824 GCCGGGCTTCAAGGAGAC 60.437 66.667 12.87 0.00 0.00 3.36
61 62 2.125512 CCGGGCTTCAAGGAGACG 60.126 66.667 0.00 0.00 0.00 4.18
62 63 2.125512 CGGGCTTCAAGGAGACGG 60.126 66.667 0.00 0.00 0.00 4.79
63 64 2.943978 CGGGCTTCAAGGAGACGGT 61.944 63.158 0.00 0.00 0.00 4.83
64 65 1.601419 CGGGCTTCAAGGAGACGGTA 61.601 60.000 0.00 0.00 0.00 4.02
65 66 0.175989 GGGCTTCAAGGAGACGGTAG 59.824 60.000 0.00 0.00 0.00 3.18
66 67 1.183549 GGCTTCAAGGAGACGGTAGA 58.816 55.000 0.00 0.00 0.00 2.59
67 68 1.135053 GGCTTCAAGGAGACGGTAGAC 60.135 57.143 0.00 0.00 0.00 2.59
68 69 1.544691 GCTTCAAGGAGACGGTAGACA 59.455 52.381 0.00 0.00 0.00 3.41
69 70 2.029290 GCTTCAAGGAGACGGTAGACAA 60.029 50.000 0.00 0.00 0.00 3.18
70 71 3.554337 GCTTCAAGGAGACGGTAGACAAA 60.554 47.826 0.00 0.00 0.00 2.83
71 72 4.628074 CTTCAAGGAGACGGTAGACAAAA 58.372 43.478 0.00 0.00 0.00 2.44
72 73 4.675976 TCAAGGAGACGGTAGACAAAAA 57.324 40.909 0.00 0.00 0.00 1.94
73 74 4.374399 TCAAGGAGACGGTAGACAAAAAC 58.626 43.478 0.00 0.00 0.00 2.43
74 75 4.100498 TCAAGGAGACGGTAGACAAAAACT 59.900 41.667 0.00 0.00 0.00 2.66
75 76 3.991367 AGGAGACGGTAGACAAAAACTG 58.009 45.455 0.00 0.00 0.00 3.16
76 77 3.064931 GGAGACGGTAGACAAAAACTGG 58.935 50.000 0.00 0.00 0.00 4.00
77 78 2.479275 GAGACGGTAGACAAAAACTGGC 59.521 50.000 0.00 0.00 0.00 4.85
78 79 2.158871 AGACGGTAGACAAAAACTGGCA 60.159 45.455 0.00 0.00 34.24 4.92
79 80 2.218603 ACGGTAGACAAAAACTGGCAG 58.781 47.619 14.16 14.16 34.24 4.85
80 81 2.218603 CGGTAGACAAAAACTGGCAGT 58.781 47.619 15.88 15.88 34.24 4.40
81 82 2.032030 CGGTAGACAAAAACTGGCAGTG 60.032 50.000 22.83 11.21 34.24 3.66
82 83 3.211045 GGTAGACAAAAACTGGCAGTGA 58.789 45.455 22.83 0.00 34.24 3.41
83 84 3.003378 GGTAGACAAAAACTGGCAGTGAC 59.997 47.826 22.83 8.98 34.24 3.67
84 85 1.670811 AGACAAAAACTGGCAGTGACG 59.329 47.619 22.83 12.53 34.24 4.35
85 86 1.400494 GACAAAAACTGGCAGTGACGT 59.600 47.619 22.83 15.70 30.79 4.34
86 87 2.610374 GACAAAAACTGGCAGTGACGTA 59.390 45.455 22.83 0.00 30.79 3.57
87 88 3.211045 ACAAAAACTGGCAGTGACGTAT 58.789 40.909 22.83 0.21 0.00 3.06
88 89 4.382291 ACAAAAACTGGCAGTGACGTATA 58.618 39.130 22.83 0.00 0.00 1.47
89 90 4.817464 ACAAAAACTGGCAGTGACGTATAA 59.183 37.500 22.83 0.00 0.00 0.98
90 91 5.297278 ACAAAAACTGGCAGTGACGTATAAA 59.703 36.000 22.83 0.00 0.00 1.40
91 92 5.352643 AAAACTGGCAGTGACGTATAAAC 57.647 39.130 22.83 0.00 0.00 2.01
109 110 9.839589 CGTATAAACGTGTTTATCTTTCATACC 57.160 33.333 18.45 1.13 42.75 2.73
110 111 9.839589 GTATAAACGTGTTTATCTTTCATACCG 57.160 33.333 18.45 0.00 42.75 4.02
111 112 4.852609 ACGTGTTTATCTTTCATACCGC 57.147 40.909 0.00 0.00 0.00 5.68
112 113 4.247258 ACGTGTTTATCTTTCATACCGCA 58.753 39.130 0.00 0.00 0.00 5.69
113 114 4.691685 ACGTGTTTATCTTTCATACCGCAA 59.308 37.500 0.00 0.00 0.00 4.85
114 115 5.019498 CGTGTTTATCTTTCATACCGCAAC 58.981 41.667 0.00 0.00 0.00 4.17
115 116 5.329493 GTGTTTATCTTTCATACCGCAACC 58.671 41.667 0.00 0.00 0.00 3.77
116 117 5.004448 TGTTTATCTTTCATACCGCAACCA 58.996 37.500 0.00 0.00 0.00 3.67
117 118 5.106475 TGTTTATCTTTCATACCGCAACCAC 60.106 40.000 0.00 0.00 0.00 4.16
118 119 2.851263 TCTTTCATACCGCAACCACT 57.149 45.000 0.00 0.00 0.00 4.00
119 120 2.695359 TCTTTCATACCGCAACCACTC 58.305 47.619 0.00 0.00 0.00 3.51
120 121 2.301870 TCTTTCATACCGCAACCACTCT 59.698 45.455 0.00 0.00 0.00 3.24
121 122 2.093306 TTCATACCGCAACCACTCTG 57.907 50.000 0.00 0.00 0.00 3.35
122 123 0.391130 TCATACCGCAACCACTCTGC 60.391 55.000 0.00 0.00 36.41 4.26
123 124 0.673333 CATACCGCAACCACTCTGCA 60.673 55.000 0.00 0.00 39.91 4.41
124 125 0.253044 ATACCGCAACCACTCTGCAT 59.747 50.000 0.00 0.00 39.91 3.96
125 126 0.391130 TACCGCAACCACTCTGCATC 60.391 55.000 0.00 0.00 39.91 3.91
126 127 1.672030 CCGCAACCACTCTGCATCA 60.672 57.895 0.00 0.00 39.91 3.07
127 128 1.642037 CCGCAACCACTCTGCATCAG 61.642 60.000 0.00 0.00 39.91 2.90
128 129 0.952497 CGCAACCACTCTGCATCAGT 60.952 55.000 0.00 0.00 39.91 3.41
129 130 1.242076 GCAACCACTCTGCATCAGTT 58.758 50.000 0.00 0.00 39.69 3.16
130 131 1.610522 GCAACCACTCTGCATCAGTTT 59.389 47.619 0.00 0.00 39.69 2.66
131 132 2.351157 GCAACCACTCTGCATCAGTTTC 60.351 50.000 0.00 0.00 39.69 2.78
132 133 3.144506 CAACCACTCTGCATCAGTTTCT 58.855 45.455 0.00 0.00 32.61 2.52
133 134 3.498774 ACCACTCTGCATCAGTTTCTT 57.501 42.857 0.00 0.00 32.61 2.52
134 135 3.825328 ACCACTCTGCATCAGTTTCTTT 58.175 40.909 0.00 0.00 32.61 2.52
135 136 4.210331 ACCACTCTGCATCAGTTTCTTTT 58.790 39.130 0.00 0.00 32.61 2.27
136 137 4.646492 ACCACTCTGCATCAGTTTCTTTTT 59.354 37.500 0.00 0.00 32.61 1.94
172 173 3.810188 TGGGAACACACCGGCCAA 61.810 61.111 0.00 0.00 33.40 4.52
173 174 2.519780 GGGAACACACCGGCCAAA 60.520 61.111 0.00 0.00 0.00 3.28
174 175 2.128507 GGGAACACACCGGCCAAAA 61.129 57.895 0.00 0.00 0.00 2.44
175 176 1.066752 GGAACACACCGGCCAAAAC 59.933 57.895 0.00 0.00 0.00 2.43
176 177 1.668101 GGAACACACCGGCCAAAACA 61.668 55.000 0.00 0.00 0.00 2.83
177 178 0.173708 GAACACACCGGCCAAAACAA 59.826 50.000 0.00 0.00 0.00 2.83
178 179 0.108567 AACACACCGGCCAAAACAAC 60.109 50.000 0.00 0.00 0.00 3.32
179 180 1.251527 ACACACCGGCCAAAACAACA 61.252 50.000 0.00 0.00 0.00 3.33
180 181 0.108615 CACACCGGCCAAAACAACAA 60.109 50.000 0.00 0.00 0.00 2.83
181 182 0.174617 ACACCGGCCAAAACAACAAG 59.825 50.000 0.00 0.00 0.00 3.16
182 183 1.142965 ACCGGCCAAAACAACAAGC 59.857 52.632 0.00 0.00 0.00 4.01
183 184 1.948635 CCGGCCAAAACAACAAGCG 60.949 57.895 2.24 0.00 0.00 4.68
184 185 2.584967 CGGCCAAAACAACAAGCGC 61.585 57.895 2.24 0.00 0.00 5.92
185 186 1.227234 GGCCAAAACAACAAGCGCT 60.227 52.632 2.64 2.64 0.00 5.92
186 187 1.215014 GGCCAAAACAACAAGCGCTC 61.215 55.000 12.06 0.00 0.00 5.03
187 188 0.527385 GCCAAAACAACAAGCGCTCA 60.527 50.000 12.06 0.00 0.00 4.26
188 189 1.480205 CCAAAACAACAAGCGCTCAG 58.520 50.000 12.06 9.66 0.00 3.35
189 190 1.480205 CAAAACAACAAGCGCTCAGG 58.520 50.000 12.06 6.22 0.00 3.86
190 191 0.385390 AAAACAACAAGCGCTCAGGG 59.615 50.000 12.06 3.68 0.00 4.45
191 192 2.075426 AAACAACAAGCGCTCAGGGC 62.075 55.000 12.06 5.34 41.91 5.19
202 203 4.449638 TCAGGGCTGAGAGGAGTG 57.550 61.111 0.00 0.00 34.14 3.51
203 204 1.986757 TCAGGGCTGAGAGGAGTGC 60.987 63.158 0.00 0.00 34.14 4.40
204 205 2.686835 AGGGCTGAGAGGAGTGCC 60.687 66.667 0.00 0.00 44.22 5.01
205 206 3.005539 GGGCTGAGAGGAGTGCCA 61.006 66.667 5.21 0.00 46.53 4.92
206 207 2.596851 GGGCTGAGAGGAGTGCCAA 61.597 63.158 5.21 0.00 46.53 4.52
207 208 1.606531 GGCTGAGAGGAGTGCCAAT 59.393 57.895 0.00 0.00 44.34 3.16
208 209 0.034670 GGCTGAGAGGAGTGCCAATT 60.035 55.000 0.00 0.00 44.34 2.32
209 210 1.093159 GCTGAGAGGAGTGCCAATTG 58.907 55.000 0.00 0.00 36.29 2.32
210 211 1.612726 GCTGAGAGGAGTGCCAATTGT 60.613 52.381 4.43 0.00 36.29 2.71
211 212 2.787994 CTGAGAGGAGTGCCAATTGTT 58.212 47.619 4.43 0.00 36.29 2.83
212 213 3.869912 GCTGAGAGGAGTGCCAATTGTTA 60.870 47.826 4.43 0.00 36.29 2.41
213 214 4.326826 CTGAGAGGAGTGCCAATTGTTAA 58.673 43.478 4.43 0.00 36.29 2.01
214 215 4.326826 TGAGAGGAGTGCCAATTGTTAAG 58.673 43.478 4.43 0.00 36.29 1.85
215 216 4.041567 TGAGAGGAGTGCCAATTGTTAAGA 59.958 41.667 4.43 0.00 36.29 2.10
216 217 4.583871 AGAGGAGTGCCAATTGTTAAGAG 58.416 43.478 4.43 0.00 36.29 2.85
217 218 3.084786 AGGAGTGCCAATTGTTAAGAGC 58.915 45.455 4.43 0.00 36.29 4.09
218 219 2.819608 GGAGTGCCAATTGTTAAGAGCA 59.180 45.455 4.43 2.68 0.00 4.26
219 220 3.255642 GGAGTGCCAATTGTTAAGAGCAA 59.744 43.478 4.43 0.00 31.03 3.91
220 221 4.261994 GGAGTGCCAATTGTTAAGAGCAAA 60.262 41.667 4.43 0.00 31.03 3.68
221 222 4.620982 AGTGCCAATTGTTAAGAGCAAAC 58.379 39.130 4.43 0.00 31.03 2.93
222 223 3.425193 GTGCCAATTGTTAAGAGCAAACG 59.575 43.478 4.43 0.00 31.03 3.60
223 224 2.986479 GCCAATTGTTAAGAGCAAACGG 59.014 45.455 4.43 0.00 0.00 4.44
251 252 2.532193 CGCAGTCAACTATACGTTTGCG 60.532 50.000 0.00 13.23 46.92 4.85
261 262 2.928361 CGTTTGCGCTGACGTTCT 59.072 55.556 22.08 0.00 42.83 3.01
262 263 1.154836 CGTTTGCGCTGACGTTCTC 60.155 57.895 22.08 0.00 42.83 2.87
303 304 6.916387 GCAATCACTATCAAACTGATGGAATG 59.084 38.462 6.97 3.78 37.52 2.67
311 312 6.519679 TCAAACTGATGGAATGATGGAAAG 57.480 37.500 0.00 0.00 0.00 2.62
314 315 5.715439 ACTGATGGAATGATGGAAAGGTA 57.285 39.130 0.00 0.00 0.00 3.08
320 321 5.261216 TGGAATGATGGAAAGGTAAGGAAC 58.739 41.667 0.00 0.00 0.00 3.62
376 377 3.602205 AGCCTTCCAGGAAAGAAGTTT 57.398 42.857 2.72 0.00 37.67 2.66
408 409 1.560505 ATGCTAAGCCACAAAAGGGG 58.439 50.000 0.00 0.00 0.00 4.79
409 410 0.187361 TGCTAAGCCACAAAAGGGGT 59.813 50.000 0.00 0.00 37.86 4.95
410 411 1.338107 GCTAAGCCACAAAAGGGGTT 58.662 50.000 0.00 0.00 46.94 4.11
411 412 1.000843 GCTAAGCCACAAAAGGGGTTG 59.999 52.381 6.16 0.00 45.15 3.77
455 464 2.401766 GCTGGGGCAATCGACAGTG 61.402 63.158 0.00 0.00 38.54 3.66
457 466 2.359850 GGGGCAATCGACAGTGCA 60.360 61.111 16.67 0.00 42.74 4.57
458 467 1.971167 GGGGCAATCGACAGTGCAA 60.971 57.895 16.67 0.00 42.74 4.08
459 468 1.523154 GGGGCAATCGACAGTGCAAA 61.523 55.000 16.67 0.00 42.74 3.68
460 469 0.109597 GGGCAATCGACAGTGCAAAG 60.110 55.000 16.67 0.00 42.74 2.77
462 471 0.040157 GCAATCGACAGTGCAAAGCA 60.040 50.000 11.56 0.00 40.58 3.91
463 472 1.600164 GCAATCGACAGTGCAAAGCAA 60.600 47.619 11.56 0.00 41.47 3.91
464 473 2.730069 CAATCGACAGTGCAAAGCAAA 58.270 42.857 0.00 0.00 41.47 3.68
465 474 3.311106 CAATCGACAGTGCAAAGCAAAT 58.689 40.909 0.00 0.00 41.47 2.32
466 475 4.475028 CAATCGACAGTGCAAAGCAAATA 58.525 39.130 0.00 0.00 41.47 1.40
467 476 3.536158 TCGACAGTGCAAAGCAAATAC 57.464 42.857 0.00 0.00 41.47 1.89
491 516 7.857456 ACCATTCCATAAAAGGGGTTAAATTC 58.143 34.615 0.00 0.00 34.40 2.17
515 540 6.540189 TCTTTTTCCATAAGCTACAGAGATGC 59.460 38.462 0.00 0.00 0.00 3.91
531 556 6.862209 CAGAGATGCTGTAAGAACTAGAACT 58.138 40.000 0.00 0.00 39.85 3.01
554 579 5.312120 ACTACTACTGAACTTGATGACCG 57.688 43.478 0.00 0.00 0.00 4.79
658 754 6.644248 ATGATCAACAGATCTCTCTCTGAG 57.356 41.667 0.00 0.00 44.48 3.35
669 765 5.317733 TCTCTCTCTGAGATTCCGTTTTC 57.682 43.478 8.00 0.00 46.03 2.29
680 776 5.805728 AGATTCCGTTTTCCTGAAGTACAT 58.194 37.500 0.00 0.00 0.00 2.29
704 826 4.320275 GCTGTACAAACCAGAAAAGGCTAC 60.320 45.833 0.00 0.00 31.38 3.58
719 841 2.067013 GGCTACGACACCAGAAGTTTC 58.933 52.381 0.00 0.00 0.00 2.78
737 859 2.537560 CCGTCATCGCTTCCATGCC 61.538 63.158 0.00 0.00 35.54 4.40
760 915 1.469703 TGAATCGCAATCAGCACCAAG 59.530 47.619 0.00 0.00 46.13 3.61
896 1051 2.162809 GAGAGAGTGACGAGAGGAAACC 59.837 54.545 0.00 0.00 0.00 3.27
1008 1175 0.250858 TCCACATGTTCAGCCACAGG 60.251 55.000 0.00 0.00 34.56 4.00
1034 1208 3.136763 CAGAGCAGAGTTCAGAAGCAAA 58.863 45.455 0.00 0.00 0.00 3.68
1038 1212 6.093771 CAGAGCAGAGTTCAGAAGCAAATAAT 59.906 38.462 0.00 0.00 0.00 1.28
1087 1290 2.872370 GCACAATCTGCATCCAGTTTC 58.128 47.619 0.00 0.00 46.29 2.78
1646 6351 1.043816 CCGAGTCTGGCATGGTCTAT 58.956 55.000 0.00 0.00 0.00 1.98
1944 6649 4.901250 TCATGGACTATATGGACTGCTTCA 59.099 41.667 0.00 0.00 0.00 3.02
1977 6756 2.890808 TGCACTCGGGATGTCTATTC 57.109 50.000 0.00 0.00 0.00 1.75
2216 6995 4.055360 CGACTCACCATTGAACAAGTACA 58.945 43.478 0.00 0.00 0.00 2.90
2219 6998 5.189928 ACTCACCATTGAACAAGTACAACA 58.810 37.500 0.00 0.00 0.00 3.33
2229 7008 8.774890 TTGAACAAGTACAACAGTAACACTTA 57.225 30.769 0.00 0.00 0.00 2.24
2261 7040 3.264193 AGATCCTGTCATTGGCTACACAA 59.736 43.478 0.00 0.00 34.41 3.33
2307 7092 0.320697 GCCGAGTAGTTCACCCACTT 59.679 55.000 0.00 0.00 0.00 3.16
2440 7226 4.081406 TCTCCCATGTAATGCCAATATGC 58.919 43.478 0.00 0.00 44.97 3.14
2487 7273 2.816087 GTGACATCACTGCCTTCAACAT 59.184 45.455 4.72 0.00 43.25 2.71
2519 7305 4.019141 ACAAATTCTATTCCCACGGTACCA 60.019 41.667 13.54 0.00 0.00 3.25
2634 7894 5.278758 GCAAGGGCTATAACAAAGTTTGTGA 60.279 40.000 21.53 15.06 39.63 3.58
2646 7908 8.887036 AACAAAGTTTGTGAAAAATATCTCCC 57.113 30.769 21.53 0.00 44.59 4.30
3075 9758 3.922171 TCCCTTTTTGTTGTGCCATTT 57.078 38.095 0.00 0.00 0.00 2.32
3084 9767 2.158534 TGTTGTGCCATTTCAGGTAGGT 60.159 45.455 0.00 0.00 0.00 3.08
3096 9779 1.482182 CAGGTAGGTGCTGTGCTGATA 59.518 52.381 0.00 0.00 0.00 2.15
3132 9815 1.960689 AGGTAAACCTTGCACGCATTT 59.039 42.857 0.00 0.00 46.09 2.32
3145 9829 7.063308 CCTTGCACGCATTTCTAATGTAAAAAT 59.937 33.333 0.00 0.00 0.00 1.82
3175 9859 9.148104 AGCTTTCTATTGATTCATTTTCTTTGC 57.852 29.630 0.00 0.00 0.00 3.68
3178 9862 6.563422 TCTATTGATTCATTTTCTTTGCGGG 58.437 36.000 0.00 0.00 0.00 6.13
3180 9864 4.862902 TGATTCATTTTCTTTGCGGGAA 57.137 36.364 0.00 0.00 0.00 3.97
3181 9865 5.207110 TGATTCATTTTCTTTGCGGGAAA 57.793 34.783 0.00 0.00 0.00 3.13
3182 9866 5.792741 TGATTCATTTTCTTTGCGGGAAAT 58.207 33.333 0.00 0.00 33.51 2.17
3284 9972 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
3349 10037 2.687935 CCAGGCACAACTTGTTGTAGTT 59.312 45.455 17.26 4.89 38.87 2.24
3365 10053 3.635373 TGTAGTTGACAGTCGGAAAGTCT 59.365 43.478 11.01 0.00 32.86 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.998377 GCCCGGCATTTTGAAAAATATATATTT 58.002 29.630 13.85 13.85 36.52 1.40
24 25 8.374743 AGCCCGGCATTTTGAAAAATATATATT 58.625 29.630 13.15 1.91 36.52 1.28
25 26 7.906327 AGCCCGGCATTTTGAAAAATATATAT 58.094 30.769 13.15 0.00 36.52 0.86
26 27 7.296628 AGCCCGGCATTTTGAAAAATATATA 57.703 32.000 13.15 0.00 36.52 0.86
27 28 6.173427 AGCCCGGCATTTTGAAAAATATAT 57.827 33.333 13.15 0.00 36.52 0.86
28 29 5.606348 AGCCCGGCATTTTGAAAAATATA 57.394 34.783 13.15 0.00 36.52 0.86
29 30 4.486125 AGCCCGGCATTTTGAAAAATAT 57.514 36.364 13.15 0.00 36.52 1.28
30 31 3.971245 AGCCCGGCATTTTGAAAAATA 57.029 38.095 13.15 0.00 36.52 1.40
31 32 2.857186 AGCCCGGCATTTTGAAAAAT 57.143 40.000 13.15 0.00 39.07 1.82
32 33 2.158900 TGAAGCCCGGCATTTTGAAAAA 60.159 40.909 13.15 0.00 0.00 1.94
33 34 1.414181 TGAAGCCCGGCATTTTGAAAA 59.586 42.857 13.15 0.00 0.00 2.29
34 35 1.043816 TGAAGCCCGGCATTTTGAAA 58.956 45.000 13.15 0.00 0.00 2.69
35 36 1.000731 CTTGAAGCCCGGCATTTTGAA 59.999 47.619 13.15 0.00 0.00 2.69
36 37 0.602562 CTTGAAGCCCGGCATTTTGA 59.397 50.000 13.15 0.00 0.00 2.69
37 38 0.390209 CCTTGAAGCCCGGCATTTTG 60.390 55.000 13.15 0.00 0.00 2.44
38 39 0.541764 TCCTTGAAGCCCGGCATTTT 60.542 50.000 13.15 0.00 0.00 1.82
39 40 0.967380 CTCCTTGAAGCCCGGCATTT 60.967 55.000 13.15 0.00 0.00 2.32
40 41 1.379044 CTCCTTGAAGCCCGGCATT 60.379 57.895 13.15 2.85 0.00 3.56
41 42 2.273449 CTCCTTGAAGCCCGGCAT 59.727 61.111 13.15 0.00 0.00 4.40
42 43 2.927856 TCTCCTTGAAGCCCGGCA 60.928 61.111 13.15 0.00 0.00 5.69
43 44 2.436824 GTCTCCTTGAAGCCCGGC 60.437 66.667 0.00 0.00 0.00 6.13
44 45 2.125512 CGTCTCCTTGAAGCCCGG 60.126 66.667 0.00 0.00 0.00 5.73
45 46 1.601419 TACCGTCTCCTTGAAGCCCG 61.601 60.000 0.00 0.00 0.00 6.13
46 47 0.175989 CTACCGTCTCCTTGAAGCCC 59.824 60.000 0.00 0.00 0.00 5.19
47 48 1.135053 GTCTACCGTCTCCTTGAAGCC 60.135 57.143 0.00 0.00 0.00 4.35
48 49 1.544691 TGTCTACCGTCTCCTTGAAGC 59.455 52.381 0.00 0.00 0.00 3.86
49 50 3.936372 TTGTCTACCGTCTCCTTGAAG 57.064 47.619 0.00 0.00 0.00 3.02
50 51 4.675976 TTTTGTCTACCGTCTCCTTGAA 57.324 40.909 0.00 0.00 0.00 2.69
51 52 4.100498 AGTTTTTGTCTACCGTCTCCTTGA 59.900 41.667 0.00 0.00 0.00 3.02
52 53 4.211374 CAGTTTTTGTCTACCGTCTCCTTG 59.789 45.833 0.00 0.00 0.00 3.61
53 54 4.377897 CAGTTTTTGTCTACCGTCTCCTT 58.622 43.478 0.00 0.00 0.00 3.36
54 55 3.244112 CCAGTTTTTGTCTACCGTCTCCT 60.244 47.826 0.00 0.00 0.00 3.69
55 56 3.064931 CCAGTTTTTGTCTACCGTCTCC 58.935 50.000 0.00 0.00 0.00 3.71
56 57 2.479275 GCCAGTTTTTGTCTACCGTCTC 59.521 50.000 0.00 0.00 0.00 3.36
57 58 2.158871 TGCCAGTTTTTGTCTACCGTCT 60.159 45.455 0.00 0.00 0.00 4.18
58 59 2.215196 TGCCAGTTTTTGTCTACCGTC 58.785 47.619 0.00 0.00 0.00 4.79
59 60 2.218603 CTGCCAGTTTTTGTCTACCGT 58.781 47.619 0.00 0.00 0.00 4.83
60 61 2.032030 CACTGCCAGTTTTTGTCTACCG 60.032 50.000 0.00 0.00 0.00 4.02
61 62 3.003378 GTCACTGCCAGTTTTTGTCTACC 59.997 47.826 0.00 0.00 0.00 3.18
62 63 3.303132 CGTCACTGCCAGTTTTTGTCTAC 60.303 47.826 0.00 0.00 0.00 2.59
63 64 2.869801 CGTCACTGCCAGTTTTTGTCTA 59.130 45.455 0.00 0.00 0.00 2.59
64 65 1.670811 CGTCACTGCCAGTTTTTGTCT 59.329 47.619 0.00 0.00 0.00 3.41
65 66 1.400494 ACGTCACTGCCAGTTTTTGTC 59.600 47.619 0.00 0.00 0.00 3.18
66 67 1.459450 ACGTCACTGCCAGTTTTTGT 58.541 45.000 0.00 0.00 0.00 2.83
67 68 3.896648 ATACGTCACTGCCAGTTTTTG 57.103 42.857 0.00 0.00 0.00 2.44
68 69 5.559417 CGTTTATACGTCACTGCCAGTTTTT 60.559 40.000 0.00 0.00 42.72 1.94
69 70 4.084223 CGTTTATACGTCACTGCCAGTTTT 60.084 41.667 0.00 0.00 42.72 2.43
70 71 3.430895 CGTTTATACGTCACTGCCAGTTT 59.569 43.478 0.00 0.00 42.72 2.66
71 72 2.991190 CGTTTATACGTCACTGCCAGTT 59.009 45.455 0.00 0.00 42.72 3.16
72 73 2.602878 CGTTTATACGTCACTGCCAGT 58.397 47.619 0.00 0.00 42.72 4.00
84 85 9.839589 CGGTATGAAAGATAAACACGTTTATAC 57.160 33.333 13.68 7.67 43.52 1.47
85 86 8.542132 GCGGTATGAAAGATAAACACGTTTATA 58.458 33.333 13.68 1.02 43.52 0.98
86 87 7.064847 TGCGGTATGAAAGATAAACACGTTTAT 59.935 33.333 13.60 13.60 45.43 1.40
87 88 6.368243 TGCGGTATGAAAGATAAACACGTTTA 59.632 34.615 4.93 4.93 39.12 2.01
88 89 5.179742 TGCGGTATGAAAGATAAACACGTTT 59.820 36.000 0.22 0.22 36.63 3.60
89 90 4.691685 TGCGGTATGAAAGATAAACACGTT 59.308 37.500 0.00 0.00 0.00 3.99
90 91 4.247258 TGCGGTATGAAAGATAAACACGT 58.753 39.130 0.00 0.00 0.00 4.49
91 92 4.850859 TGCGGTATGAAAGATAAACACG 57.149 40.909 0.00 0.00 0.00 4.49
92 93 5.106475 TGGTTGCGGTATGAAAGATAAACAC 60.106 40.000 0.00 0.00 0.00 3.32
93 94 5.004448 TGGTTGCGGTATGAAAGATAAACA 58.996 37.500 0.00 0.00 0.00 2.83
94 95 5.123344 AGTGGTTGCGGTATGAAAGATAAAC 59.877 40.000 0.00 0.00 0.00 2.01
95 96 5.250200 AGTGGTTGCGGTATGAAAGATAAA 58.750 37.500 0.00 0.00 0.00 1.40
96 97 4.839121 AGTGGTTGCGGTATGAAAGATAA 58.161 39.130 0.00 0.00 0.00 1.75
97 98 4.161565 AGAGTGGTTGCGGTATGAAAGATA 59.838 41.667 0.00 0.00 0.00 1.98
98 99 3.055094 AGAGTGGTTGCGGTATGAAAGAT 60.055 43.478 0.00 0.00 0.00 2.40
99 100 2.301870 AGAGTGGTTGCGGTATGAAAGA 59.698 45.455 0.00 0.00 0.00 2.52
100 101 2.416547 CAGAGTGGTTGCGGTATGAAAG 59.583 50.000 0.00 0.00 0.00 2.62
101 102 2.422597 CAGAGTGGTTGCGGTATGAAA 58.577 47.619 0.00 0.00 0.00 2.69
102 103 1.943968 GCAGAGTGGTTGCGGTATGAA 60.944 52.381 0.00 0.00 0.00 2.57
103 104 0.391130 GCAGAGTGGTTGCGGTATGA 60.391 55.000 0.00 0.00 0.00 2.15
104 105 0.673333 TGCAGAGTGGTTGCGGTATG 60.673 55.000 0.00 0.00 44.40 2.39
105 106 0.253044 ATGCAGAGTGGTTGCGGTAT 59.747 50.000 0.00 0.00 44.40 2.73
106 107 0.391130 GATGCAGAGTGGTTGCGGTA 60.391 55.000 0.00 0.00 44.40 4.02
107 108 1.672356 GATGCAGAGTGGTTGCGGT 60.672 57.895 0.00 0.00 44.40 5.68
108 109 1.642037 CTGATGCAGAGTGGTTGCGG 61.642 60.000 0.00 0.00 44.40 5.69
109 110 0.952497 ACTGATGCAGAGTGGTTGCG 60.952 55.000 0.82 0.00 44.40 4.85
110 111 1.242076 AACTGATGCAGAGTGGTTGC 58.758 50.000 0.82 0.00 41.86 4.17
111 112 3.144506 AGAAACTGATGCAGAGTGGTTG 58.855 45.455 0.82 0.00 35.18 3.77
112 113 3.498774 AGAAACTGATGCAGAGTGGTT 57.501 42.857 0.82 0.00 35.18 3.67
113 114 3.498774 AAGAAACTGATGCAGAGTGGT 57.501 42.857 0.82 0.00 35.18 4.16
114 115 4.843220 AAAAGAAACTGATGCAGAGTGG 57.157 40.909 0.82 0.00 35.18 4.00
141 142 9.810545 CGGTGTGTTCCCATAAATAAAATAAAT 57.189 29.630 0.00 0.00 0.00 1.40
142 143 8.251721 CCGGTGTGTTCCCATAAATAAAATAAA 58.748 33.333 0.00 0.00 0.00 1.40
143 144 7.630944 GCCGGTGTGTTCCCATAAATAAAATAA 60.631 37.037 1.90 0.00 0.00 1.40
144 145 6.183360 GCCGGTGTGTTCCCATAAATAAAATA 60.183 38.462 1.90 0.00 0.00 1.40
145 146 5.394773 GCCGGTGTGTTCCCATAAATAAAAT 60.395 40.000 1.90 0.00 0.00 1.82
146 147 4.082136 GCCGGTGTGTTCCCATAAATAAAA 60.082 41.667 1.90 0.00 0.00 1.52
147 148 3.444388 GCCGGTGTGTTCCCATAAATAAA 59.556 43.478 1.90 0.00 0.00 1.40
148 149 3.018149 GCCGGTGTGTTCCCATAAATAA 58.982 45.455 1.90 0.00 0.00 1.40
149 150 2.645802 GCCGGTGTGTTCCCATAAATA 58.354 47.619 1.90 0.00 0.00 1.40
150 151 1.470051 GCCGGTGTGTTCCCATAAAT 58.530 50.000 1.90 0.00 0.00 1.40
151 152 0.609681 GGCCGGTGTGTTCCCATAAA 60.610 55.000 1.90 0.00 0.00 1.40
152 153 1.001887 GGCCGGTGTGTTCCCATAA 60.002 57.895 1.90 0.00 0.00 1.90
153 154 1.780107 TTGGCCGGTGTGTTCCCATA 61.780 55.000 1.90 0.00 0.00 2.74
154 155 2.648613 TTTGGCCGGTGTGTTCCCAT 62.649 55.000 1.90 0.00 0.00 4.00
155 156 2.856039 TTTTGGCCGGTGTGTTCCCA 62.856 55.000 1.90 0.00 0.00 4.37
156 157 2.128507 TTTTGGCCGGTGTGTTCCC 61.129 57.895 1.90 0.00 0.00 3.97
157 158 1.066752 GTTTTGGCCGGTGTGTTCC 59.933 57.895 1.90 0.00 0.00 3.62
158 159 0.173708 TTGTTTTGGCCGGTGTGTTC 59.826 50.000 1.90 0.00 0.00 3.18
159 160 0.108567 GTTGTTTTGGCCGGTGTGTT 60.109 50.000 1.90 0.00 0.00 3.32
160 161 1.251527 TGTTGTTTTGGCCGGTGTGT 61.252 50.000 1.90 0.00 0.00 3.72
161 162 0.108615 TTGTTGTTTTGGCCGGTGTG 60.109 50.000 1.90 0.00 0.00 3.82
162 163 0.174617 CTTGTTGTTTTGGCCGGTGT 59.825 50.000 1.90 0.00 0.00 4.16
163 164 1.151172 GCTTGTTGTTTTGGCCGGTG 61.151 55.000 1.90 0.00 0.00 4.94
164 165 1.142965 GCTTGTTGTTTTGGCCGGT 59.857 52.632 1.90 0.00 0.00 5.28
165 166 1.948635 CGCTTGTTGTTTTGGCCGG 60.949 57.895 0.00 0.00 0.00 6.13
166 167 2.584967 GCGCTTGTTGTTTTGGCCG 61.585 57.895 0.00 0.00 0.00 6.13
167 168 1.215014 GAGCGCTTGTTGTTTTGGCC 61.215 55.000 13.26 0.00 0.00 5.36
168 169 0.527385 TGAGCGCTTGTTGTTTTGGC 60.527 50.000 13.26 0.00 0.00 4.52
169 170 1.480205 CTGAGCGCTTGTTGTTTTGG 58.520 50.000 13.26 0.00 0.00 3.28
170 171 1.480205 CCTGAGCGCTTGTTGTTTTG 58.520 50.000 13.26 0.00 0.00 2.44
171 172 0.385390 CCCTGAGCGCTTGTTGTTTT 59.615 50.000 13.26 0.00 0.00 2.43
172 173 2.032981 CCCTGAGCGCTTGTTGTTT 58.967 52.632 13.26 0.00 0.00 2.83
173 174 2.555547 GCCCTGAGCGCTTGTTGTT 61.556 57.895 13.26 0.00 0.00 2.83
174 175 2.980233 GCCCTGAGCGCTTGTTGT 60.980 61.111 13.26 0.00 0.00 3.32
185 186 1.986757 GCACTCCTCTCAGCCCTGA 60.987 63.158 0.00 0.00 38.06 3.86
186 187 2.583520 GCACTCCTCTCAGCCCTG 59.416 66.667 0.00 0.00 0.00 4.45
187 188 2.686835 GGCACTCCTCTCAGCCCT 60.687 66.667 0.00 0.00 41.25 5.19
188 189 1.919600 ATTGGCACTCCTCTCAGCCC 61.920 60.000 0.00 0.00 46.45 5.19
190 191 1.093159 CAATTGGCACTCCTCTCAGC 58.907 55.000 0.00 0.00 0.00 4.26
191 192 2.486472 ACAATTGGCACTCCTCTCAG 57.514 50.000 10.83 0.00 0.00 3.35
192 193 2.957402 AACAATTGGCACTCCTCTCA 57.043 45.000 10.83 0.00 0.00 3.27
193 194 4.579869 TCTTAACAATTGGCACTCCTCTC 58.420 43.478 10.83 0.00 0.00 3.20
194 195 4.583871 CTCTTAACAATTGGCACTCCTCT 58.416 43.478 10.83 0.00 0.00 3.69
195 196 3.127721 GCTCTTAACAATTGGCACTCCTC 59.872 47.826 10.83 0.00 0.00 3.71
196 197 3.084786 GCTCTTAACAATTGGCACTCCT 58.915 45.455 10.83 0.00 0.00 3.69
197 198 2.819608 TGCTCTTAACAATTGGCACTCC 59.180 45.455 10.83 0.00 0.00 3.85
198 199 4.503741 TTGCTCTTAACAATTGGCACTC 57.496 40.909 10.83 0.00 0.00 3.51
199 200 4.620982 GTTTGCTCTTAACAATTGGCACT 58.379 39.130 10.83 0.00 0.00 4.40
200 201 3.425193 CGTTTGCTCTTAACAATTGGCAC 59.575 43.478 10.83 0.00 0.00 5.01
201 202 3.551863 CCGTTTGCTCTTAACAATTGGCA 60.552 43.478 10.83 5.56 0.00 4.92
202 203 2.986479 CCGTTTGCTCTTAACAATTGGC 59.014 45.455 10.83 2.75 0.00 4.52
203 204 2.986479 GCCGTTTGCTCTTAACAATTGG 59.014 45.455 10.83 0.00 36.87 3.16
204 205 3.637432 TGCCGTTTGCTCTTAACAATTG 58.363 40.909 3.24 3.24 42.00 2.32
205 206 3.857010 GCTGCCGTTTGCTCTTAACAATT 60.857 43.478 0.00 0.00 42.00 2.32
206 207 2.351738 GCTGCCGTTTGCTCTTAACAAT 60.352 45.455 0.00 0.00 42.00 2.71
207 208 1.001815 GCTGCCGTTTGCTCTTAACAA 60.002 47.619 0.00 0.00 42.00 2.83
208 209 0.591170 GCTGCCGTTTGCTCTTAACA 59.409 50.000 0.00 0.00 42.00 2.41
209 210 0.591170 TGCTGCCGTTTGCTCTTAAC 59.409 50.000 0.00 0.00 42.00 2.01
210 211 0.874390 CTGCTGCCGTTTGCTCTTAA 59.126 50.000 0.00 0.00 42.00 1.85
211 212 1.577328 GCTGCTGCCGTTTGCTCTTA 61.577 55.000 3.85 0.00 42.00 2.10
212 213 2.912624 GCTGCTGCCGTTTGCTCTT 61.913 57.895 3.85 0.00 42.00 2.85
213 214 3.360340 GCTGCTGCCGTTTGCTCT 61.360 61.111 3.85 0.00 42.00 4.09
214 215 4.748679 CGCTGCTGCCGTTTGCTC 62.749 66.667 10.24 0.00 42.00 4.26
222 223 4.395583 GTTGACTGCGCTGCTGCC 62.396 66.667 14.80 3.70 35.36 4.85
223 224 1.364626 ATAGTTGACTGCGCTGCTGC 61.365 55.000 14.80 5.34 0.00 5.25
233 234 2.666508 CAGCGCAAACGTATAGTTGACT 59.333 45.455 11.47 0.00 43.37 3.41
261 262 1.218047 GCACCTGCCTACATCGTGA 59.782 57.895 0.00 0.00 30.96 4.35
262 263 0.673333 TTGCACCTGCCTACATCGTG 60.673 55.000 0.00 0.00 41.18 4.35
265 266 1.672881 GTGATTGCACCTGCCTACATC 59.327 52.381 0.00 0.00 39.14 3.06
267 268 0.692476 AGTGATTGCACCTGCCTACA 59.308 50.000 0.00 0.00 46.32 2.74
275 276 5.449588 CCATCAGTTTGATAGTGATTGCACC 60.450 44.000 0.00 0.00 42.98 5.01
314 315 0.765510 AAGCCACGAGAAGGTTCCTT 59.234 50.000 3.55 3.55 0.00 3.36
320 321 0.391793 GGGAAGAAGCCACGAGAAGG 60.392 60.000 0.00 0.00 0.00 3.46
370 371 9.182933 CTTAGCATAGATAACGACCTAAACTTC 57.817 37.037 0.00 0.00 0.00 3.01
373 374 6.365518 GGCTTAGCATAGATAACGACCTAAAC 59.634 42.308 6.53 0.00 0.00 2.01
376 377 5.048224 GTGGCTTAGCATAGATAACGACCTA 60.048 44.000 6.53 0.00 0.00 3.08
408 409 9.764363 ACCTCTTTTATGGAAAAAGAAATCAAC 57.236 29.630 12.50 0.00 43.28 3.18
409 410 9.762933 CACCTCTTTTATGGAAAAAGAAATCAA 57.237 29.630 12.50 0.00 43.28 2.57
410 411 9.142014 TCACCTCTTTTATGGAAAAAGAAATCA 57.858 29.630 12.50 0.00 43.28 2.57
411 412 9.631452 CTCACCTCTTTTATGGAAAAAGAAATC 57.369 33.333 12.50 0.00 43.28 2.17
455 464 7.201635 CCTTTTATGGAATGGTATTTGCTTTGC 60.202 37.037 0.00 0.00 0.00 3.68
457 466 7.337938 CCCTTTTATGGAATGGTATTTGCTTT 58.662 34.615 0.00 0.00 32.09 3.51
458 467 6.126796 CCCCTTTTATGGAATGGTATTTGCTT 60.127 38.462 0.00 0.00 32.09 3.91
459 468 5.366477 CCCCTTTTATGGAATGGTATTTGCT 59.634 40.000 0.00 0.00 32.09 3.91
460 469 5.130311 ACCCCTTTTATGGAATGGTATTTGC 59.870 40.000 0.00 0.00 32.09 3.68
462 471 8.919018 TTAACCCCTTTTATGGAATGGTATTT 57.081 30.769 0.00 0.00 32.09 1.40
463 472 8.919018 TTTAACCCCTTTTATGGAATGGTATT 57.081 30.769 0.00 0.00 32.09 1.89
464 473 9.514093 AATTTAACCCCTTTTATGGAATGGTAT 57.486 29.630 0.00 0.00 32.09 2.73
465 474 8.919018 AATTTAACCCCTTTTATGGAATGGTA 57.081 30.769 0.00 0.00 32.09 3.25
466 475 7.682459 AGAATTTAACCCCTTTTATGGAATGGT 59.318 33.333 0.00 0.00 32.09 3.55
467 476 8.089625 AGAATTTAACCCCTTTTATGGAATGG 57.910 34.615 0.00 0.00 33.43 3.16
491 516 6.541641 AGCATCTCTGTAGCTTATGGAAAAAG 59.458 38.462 0.00 0.00 34.37 2.27
522 547 9.790344 TCAAGTTCAGTAGTAGTAGTTCTAGTT 57.210 33.333 0.00 0.00 34.51 2.24
523 548 9.962809 ATCAAGTTCAGTAGTAGTAGTTCTAGT 57.037 33.333 0.00 0.00 36.41 2.57
525 550 9.955102 TCATCAAGTTCAGTAGTAGTAGTTCTA 57.045 33.333 0.00 0.00 0.00 2.10
531 556 5.942236 ACGGTCATCAAGTTCAGTAGTAGTA 59.058 40.000 0.00 0.00 0.00 1.82
658 754 5.673818 GCATGTACTTCAGGAAAACGGAATC 60.674 44.000 0.00 0.00 32.84 2.52
680 776 2.360801 GCCTTTTCTGGTTTGTACAGCA 59.639 45.455 0.00 0.00 35.94 4.41
693 815 1.968493 TCTGGTGTCGTAGCCTTTTCT 59.032 47.619 0.00 0.00 0.00 2.52
694 816 2.450609 TCTGGTGTCGTAGCCTTTTC 57.549 50.000 0.00 0.00 0.00 2.29
695 817 2.104281 ACTTCTGGTGTCGTAGCCTTTT 59.896 45.455 0.00 0.00 0.00 2.27
704 826 1.137513 GACGGAAACTTCTGGTGTCG 58.862 55.000 3.43 0.00 37.89 4.35
719 841 2.537560 GGCATGGAAGCGATGACGG 61.538 63.158 0.00 0.00 40.15 4.79
760 915 2.707849 CCATCAGGGCAACAGCAGC 61.708 63.158 0.00 0.00 39.74 5.25
791 946 1.433053 TTCCGTTTGCACACCAGTCG 61.433 55.000 0.00 0.00 0.00 4.18
880 1035 0.538977 TCCGGTTTCCTCTCGTCACT 60.539 55.000 0.00 0.00 0.00 3.41
896 1051 0.388649 CAGACTCTGTTCCCGTTCCG 60.389 60.000 0.00 0.00 0.00 4.30
1008 1175 3.516981 TCTGAACTCTGCTCTGTATGC 57.483 47.619 0.00 0.00 0.00 3.14
1034 1208 6.754702 ACGTACGATGGTATGCTCTATTAT 57.245 37.500 24.41 0.00 38.89 1.28
1038 1212 6.376177 CAAATACGTACGATGGTATGCTCTA 58.624 40.000 24.41 0.00 38.89 2.43
1553 2045 4.037923 GGCTGGAAATCTGTTTTGTTCAGA 59.962 41.667 0.00 0.00 44.37 3.27
1646 6351 2.829384 AAGCTGTCGGGGCTTGGAA 61.829 57.895 8.98 0.00 46.53 3.53
1892 6597 1.485124 ACCTGATGCCTACACGATCA 58.515 50.000 0.00 0.00 0.00 2.92
1944 6649 1.302511 GTGCATGTGGGTCGGAGTT 60.303 57.895 0.00 0.00 0.00 3.01
1977 6756 1.079819 CGCGGCTCTACCATATGGG 60.080 63.158 25.55 9.11 44.81 4.00
2015 6794 1.330655 CCGTGGGGTATCTGTCTGCT 61.331 60.000 0.00 0.00 0.00 4.24
2119 6898 0.387878 CGAGATCAGCATAGCCGTCC 60.388 60.000 0.00 0.00 0.00 4.79
2216 6995 4.935702 TGCGTGTAGTAAGTGTTACTGTT 58.064 39.130 9.19 0.00 45.58 3.16
2229 7008 1.893137 TGACAGGATCTTGCGTGTAGT 59.107 47.619 4.46 0.00 37.05 2.73
2261 7040 4.884164 CGAGCCTTCAAGGAAAGGATAATT 59.116 41.667 7.98 0.00 44.83 1.40
2307 7092 8.969260 ATCAAGCATATCACTAATTCAAGTCA 57.031 30.769 0.00 0.00 0.00 3.41
2371 7156 0.253327 TACAATGCACATGCCCCGTA 59.747 50.000 0.49 0.00 41.18 4.02
2487 7273 7.110155 GTGGGAATAGAATTTGTCTTACAGGA 58.890 38.462 0.00 0.00 37.84 3.86
2519 7305 1.470051 AAGGACGCACCACTGTTTTT 58.530 45.000 2.21 0.00 42.04 1.94
2634 7894 8.825774 AGTTGCCAATTAAAGGGAGATATTTTT 58.174 29.630 0.22 0.00 0.00 1.94
2970 9644 2.227865 GGGCAGACGCAAATAACTGAAA 59.772 45.455 0.00 0.00 41.24 2.69
3020 9702 2.417933 AGATCTAACAACGCGTACGAGT 59.582 45.455 21.65 20.39 43.93 4.18
3075 9758 0.831711 TCAGCACAGCACCTACCTGA 60.832 55.000 0.00 0.00 34.47 3.86
3084 9767 0.732538 CGTCGTGTATCAGCACAGCA 60.733 55.000 0.00 0.00 39.19 4.41
3096 9779 1.248785 ACCTACCTGCATCGTCGTGT 61.249 55.000 0.00 0.00 0.00 4.49
3152 9836 7.545265 CCCGCAAAGAAAATGAATCAATAGAAA 59.455 33.333 0.00 0.00 0.00 2.52
3174 9858 4.391140 GAATAGATCGACAATTTCCCGC 57.609 45.455 0.00 0.00 0.00 6.13
3196 9880 6.097356 TCGTTGTACTACCATGATTGAAGAC 58.903 40.000 0.00 0.00 0.00 3.01
3249 9937 4.268797 AGTCGTCGCTAGGTGATCTATA 57.731 45.455 0.00 0.00 0.00 1.31
3255 9943 1.736126 CTTGTAGTCGTCGCTAGGTGA 59.264 52.381 0.00 0.00 0.00 4.02
3303 9991 2.764128 GAGGGAGGGGCGATGACA 60.764 66.667 0.00 0.00 0.00 3.58
3349 10037 1.679680 ACGAAGACTTTCCGACTGTCA 59.320 47.619 8.73 0.00 33.56 3.58
3350 10038 2.052157 CACGAAGACTTTCCGACTGTC 58.948 52.381 3.55 0.00 0.00 3.51
3365 10053 1.760613 CCTATGGGACCTTAGCACGAA 59.239 52.381 5.90 0.00 33.58 3.85
3393 10081 1.748879 GGCGCTTGCTGTTATGGGA 60.749 57.895 7.64 0.00 39.13 4.37


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

AutoCloner maintained by Alex Coulton.