Multiple sequence alignment - TraesCS7D01G502400

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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 TraesCS7D01G502400 chr7D 100.000 2615 0 0 1 2615 608105614 608103000 0.000000e+00 4830
1 TraesCS7D01G502400 chr7D 92.573 1508 108 3 1111 2615 610652121 610653627 0.000000e+00 2161
2 TraesCS7D01G502400 chr7D 88.577 534 61 0 575 1108 131618956 131619489 0.000000e+00 649
3 TraesCS7D01G502400 chr7D 80.026 756 117 23 354 1094 607933169 607933905 1.780000e-146 529
4 TraesCS7D01G502400 chrUn 91.170 2299 169 17 327 2612 77779752 77782029 0.000000e+00 3090
5 TraesCS7D01G502400 chr7B 91.219 1879 140 8 399 2273 698234655 698232798 0.000000e+00 2532
6 TraesCS7D01G502400 chr7B 92.395 1407 95 8 1216 2612 695493866 695492462 0.000000e+00 1995
7 TraesCS7D01G502400 chr7B 90.375 1465 116 10 327 1789 695285920 695287361 0.000000e+00 1901
8 TraesCS7D01G502400 chr7B 92.933 1132 74 4 1407 2537 694226933 694228059 0.000000e+00 1642
9 TraesCS7D01G502400 chr7B 93.273 773 48 4 1841 2611 697537389 697538159 0.000000e+00 1136
10 TraesCS7D01G502400 chr7B 88.511 853 74 10 327 1176 695494710 695493879 0.000000e+00 1011
11 TraesCS7D01G502400 chr7B 84.637 1048 125 21 1111 2146 697119575 697118552 0.000000e+00 1011
12 TraesCS7D01G502400 chr7B 87.848 683 77 1 432 1108 92959472 92960154 0.000000e+00 797
13 TraesCS7D01G502400 chr7B 88.095 672 71 8 437 1105 697033995 697034660 0.000000e+00 789
14 TraesCS7D01G502400 chr7B 91.721 459 31 3 2157 2609 695287433 695287890 4.750000e-177 630
15 TraesCS7D01G502400 chr7B 91.379 348 27 2 2270 2615 698231912 698231566 8.470000e-130 473
16 TraesCS7D01G502400 chr7B 89.706 272 27 1 2341 2611 694267298 694267569 1.930000e-91 346
17 TraesCS7D01G502400 chr7B 88.768 276 30 1 2341 2615 697118229 697117954 1.160000e-88 337
18 TraesCS7D01G502400 chr7B 90.741 216 18 2 2123 2337 685221738 685221524 1.180000e-73 287
19 TraesCS7D01G502400 chr7B 75.821 335 56 12 469 778 685248673 685248339 2.100000e-31 147
20 TraesCS7D01G502400 chr7A 86.743 1305 158 8 851 2146 699925152 699926450 0.000000e+00 1437
21 TraesCS7D01G502400 chr7A 85.137 1164 151 17 1111 2261 700029218 700030372 0.000000e+00 1171
22 TraesCS7D01G502400 chr7A 86.214 943 105 16 1112 2041 130384144 130385074 0.000000e+00 998
23 TraesCS7D01G502400 chr7A 86.339 915 117 5 1123 2036 700091189 700090282 0.000000e+00 990
24 TraesCS7D01G502400 chr7A 87.408 683 80 1 432 1108 130383428 130384110 0.000000e+00 780
25 TraesCS7D01G502400 chr7A 85.507 345 42 8 433 773 700045636 700045976 1.150000e-93 353


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 TraesCS7D01G502400 chr7D 608103000 608105614 2614 True 4830.0 4830 100.0000 1 2615 1 chr7D.!!$R1 2614
1 TraesCS7D01G502400 chr7D 610652121 610653627 1506 False 2161.0 2161 92.5730 1111 2615 1 chr7D.!!$F3 1504
2 TraesCS7D01G502400 chr7D 131618956 131619489 533 False 649.0 649 88.5770 575 1108 1 chr7D.!!$F1 533
3 TraesCS7D01G502400 chr7D 607933169 607933905 736 False 529.0 529 80.0260 354 1094 1 chr7D.!!$F2 740
4 TraesCS7D01G502400 chrUn 77779752 77782029 2277 False 3090.0 3090 91.1700 327 2612 1 chrUn.!!$F1 2285
5 TraesCS7D01G502400 chr7B 694226933 694228059 1126 False 1642.0 1642 92.9330 1407 2537 1 chr7B.!!$F2 1130
6 TraesCS7D01G502400 chr7B 695492462 695494710 2248 True 1503.0 1995 90.4530 327 2612 2 chr7B.!!$R3 2285
7 TraesCS7D01G502400 chr7B 698231566 698234655 3089 True 1502.5 2532 91.2990 399 2615 2 chr7B.!!$R5 2216
8 TraesCS7D01G502400 chr7B 695285920 695287890 1970 False 1265.5 1901 91.0480 327 2609 2 chr7B.!!$F6 2282
9 TraesCS7D01G502400 chr7B 697537389 697538159 770 False 1136.0 1136 93.2730 1841 2611 1 chr7B.!!$F5 770
10 TraesCS7D01G502400 chr7B 92959472 92960154 682 False 797.0 797 87.8480 432 1108 1 chr7B.!!$F1 676
11 TraesCS7D01G502400 chr7B 697033995 697034660 665 False 789.0 789 88.0950 437 1105 1 chr7B.!!$F4 668
12 TraesCS7D01G502400 chr7B 697117954 697119575 1621 True 674.0 1011 86.7025 1111 2615 2 chr7B.!!$R4 1504
13 TraesCS7D01G502400 chr7A 699925152 699926450 1298 False 1437.0 1437 86.7430 851 2146 1 chr7A.!!$F1 1295
14 TraesCS7D01G502400 chr7A 700029218 700030372 1154 False 1171.0 1171 85.1370 1111 2261 1 chr7A.!!$F2 1150
15 TraesCS7D01G502400 chr7A 700090282 700091189 907 True 990.0 990 86.3390 1123 2036 1 chr7A.!!$R1 913
16 TraesCS7D01G502400 chr7A 130383428 130385074 1646 False 889.0 998 86.8110 432 2041 2 chr7A.!!$F4 1609

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
64 65 0.032952 TTTCTCCCGTTGTCAGACCG 59.967 55.0 0.0 0.0 0.00 4.79 F
88 89 0.038251 TGCACGCAGGTGTAGAGAAG 60.038 55.0 0.0 0.0 46.13 2.85 F
201 202 0.179119 GGGGATTGTCGTCTACACCG 60.179 60.0 0.0 0.0 38.00 4.94 F
202 203 0.179119 GGGATTGTCGTCTACACCGG 60.179 60.0 0.0 0.0 38.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1424 0.244178 GACTCGGACTCTCGCCTTTT 59.756 55.000 0.00 0.0 0.00 2.27 R
1500 1583 1.151668 GCTGCAATGTCTTGACGTCT 58.848 50.000 17.92 0.0 34.04 4.18 R
1503 1586 1.532437 TGAAGCTGCAATGTCTTGACG 59.468 47.619 1.02 0.0 34.04 4.35 R
1665 1749 4.154737 TGAAGCAATAGACAACTCATGTGC 59.845 41.667 0.00 0.0 44.12 4.57 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
29 30 2.812358 AAAAGGGTGGCATTCGAAAC 57.188 45.000 0.00 0.00 0.00 2.78
30 31 1.698506 AAAGGGTGGCATTCGAAACA 58.301 45.000 0.00 0.00 0.00 2.83
31 32 1.923356 AAGGGTGGCATTCGAAACAT 58.077 45.000 0.00 0.00 0.00 2.71
32 33 2.799126 AGGGTGGCATTCGAAACATA 57.201 45.000 0.00 0.00 0.00 2.29
33 34 2.365582 AGGGTGGCATTCGAAACATAC 58.634 47.619 0.00 0.00 0.00 2.39
34 35 2.088423 GGGTGGCATTCGAAACATACA 58.912 47.619 0.00 0.00 0.00 2.29
35 36 2.159435 GGGTGGCATTCGAAACATACAC 60.159 50.000 0.00 7.53 0.00 2.90
36 37 2.475519 GGTGGCATTCGAAACATACACG 60.476 50.000 0.00 0.00 0.00 4.49
37 38 2.158841 GTGGCATTCGAAACATACACGT 59.841 45.455 0.00 0.00 0.00 4.49
38 39 2.413796 TGGCATTCGAAACATACACGTC 59.586 45.455 0.00 0.00 0.00 4.34
39 40 2.671396 GGCATTCGAAACATACACGTCT 59.329 45.455 0.00 0.00 0.00 4.18
40 41 3.861113 GGCATTCGAAACATACACGTCTA 59.139 43.478 0.00 0.00 0.00 2.59
41 42 4.327898 GGCATTCGAAACATACACGTCTAA 59.672 41.667 0.00 0.00 0.00 2.10
42 43 5.481472 GCATTCGAAACATACACGTCTAAG 58.519 41.667 0.00 0.00 0.00 2.18
43 44 5.287752 GCATTCGAAACATACACGTCTAAGA 59.712 40.000 0.00 0.00 0.00 2.10
44 45 6.506513 GCATTCGAAACATACACGTCTAAGAG 60.507 42.308 0.00 0.00 0.00 2.85
45 46 5.618056 TCGAAACATACACGTCTAAGAGT 57.382 39.130 0.00 0.00 0.00 3.24
46 47 6.005583 TCGAAACATACACGTCTAAGAGTT 57.994 37.500 0.00 0.00 0.00 3.01
47 48 6.441274 TCGAAACATACACGTCTAAGAGTTT 58.559 36.000 0.00 0.00 0.00 2.66
48 49 6.580041 TCGAAACATACACGTCTAAGAGTTTC 59.420 38.462 13.48 13.48 39.84 2.78
49 50 6.581542 CGAAACATACACGTCTAAGAGTTTCT 59.418 38.462 17.84 0.00 40.60 2.52
50 51 7.201249 CGAAACATACACGTCTAAGAGTTTCTC 60.201 40.741 17.84 0.00 40.60 2.87
51 52 5.952033 ACATACACGTCTAAGAGTTTCTCC 58.048 41.667 0.00 0.00 0.00 3.71
52 53 3.938289 ACACGTCTAAGAGTTTCTCCC 57.062 47.619 0.00 0.00 0.00 4.30
53 54 2.228343 ACACGTCTAAGAGTTTCTCCCG 59.772 50.000 0.00 0.00 0.00 5.14
54 55 2.228343 CACGTCTAAGAGTTTCTCCCGT 59.772 50.000 0.00 0.00 0.00 5.28
55 56 2.889678 ACGTCTAAGAGTTTCTCCCGTT 59.110 45.455 0.00 0.00 0.00 4.44
56 57 3.243336 CGTCTAAGAGTTTCTCCCGTTG 58.757 50.000 0.00 0.00 0.00 4.10
57 58 3.305199 CGTCTAAGAGTTTCTCCCGTTGT 60.305 47.826 0.00 0.00 0.00 3.32
58 59 4.236147 GTCTAAGAGTTTCTCCCGTTGTC 58.764 47.826 0.00 0.00 0.00 3.18
59 60 3.893200 TCTAAGAGTTTCTCCCGTTGTCA 59.107 43.478 0.00 0.00 0.00 3.58
60 61 2.821991 AGAGTTTCTCCCGTTGTCAG 57.178 50.000 0.00 0.00 0.00 3.51
61 62 2.317040 AGAGTTTCTCCCGTTGTCAGA 58.683 47.619 0.00 0.00 0.00 3.27
62 63 2.036089 AGAGTTTCTCCCGTTGTCAGAC 59.964 50.000 0.00 0.00 0.00 3.51
63 64 1.070289 AGTTTCTCCCGTTGTCAGACC 59.930 52.381 0.00 0.00 0.00 3.85
64 65 0.032952 TTTCTCCCGTTGTCAGACCG 59.967 55.000 0.00 0.00 0.00 4.79
65 66 0.824595 TTCTCCCGTTGTCAGACCGA 60.825 55.000 0.00 0.00 0.00 4.69
66 67 0.824595 TCTCCCGTTGTCAGACCGAA 60.825 55.000 0.00 0.00 0.00 4.30
67 68 0.666577 CTCCCGTTGTCAGACCGAAC 60.667 60.000 0.00 0.00 0.00 3.95
68 69 2.019951 CCCGTTGTCAGACCGAACG 61.020 63.158 15.84 15.84 41.62 3.95
69 70 1.299620 CCGTTGTCAGACCGAACGT 60.300 57.895 19.37 0.00 40.62 3.99
70 71 1.545614 CCGTTGTCAGACCGAACGTG 61.546 60.000 19.37 10.74 40.62 4.49
71 72 1.563173 GTTGTCAGACCGAACGTGC 59.437 57.895 0.00 0.00 0.00 5.34
72 73 1.142097 TTGTCAGACCGAACGTGCA 59.858 52.632 0.00 0.00 0.00 4.57
73 74 1.149361 TTGTCAGACCGAACGTGCAC 61.149 55.000 6.82 6.82 0.00 4.57
74 75 2.354188 TCAGACCGAACGTGCACG 60.354 61.111 35.99 35.99 46.33 5.34
75 76 4.059459 CAGACCGAACGTGCACGC 62.059 66.667 37.35 21.78 44.43 5.34
76 77 4.578898 AGACCGAACGTGCACGCA 62.579 61.111 37.35 0.00 44.43 5.24
77 78 4.059459 GACCGAACGTGCACGCAG 62.059 66.667 37.35 26.73 44.43 5.18
80 81 4.354212 CGAACGTGCACGCAGGTG 62.354 66.667 37.35 19.48 43.11 4.00
81 82 3.269347 GAACGTGCACGCAGGTGT 61.269 61.111 37.35 15.76 46.13 4.16
82 83 1.952133 GAACGTGCACGCAGGTGTA 60.952 57.895 37.35 0.00 46.13 2.90
83 84 1.886861 GAACGTGCACGCAGGTGTAG 61.887 60.000 37.35 10.10 46.13 2.74
84 85 2.049526 CGTGCACGCAGGTGTAGA 60.050 61.111 28.16 0.00 46.13 2.59
85 86 2.088763 CGTGCACGCAGGTGTAGAG 61.089 63.158 28.16 0.00 46.13 2.43
86 87 1.289066 GTGCACGCAGGTGTAGAGA 59.711 57.895 0.00 0.00 46.13 3.10
87 88 0.319555 GTGCACGCAGGTGTAGAGAA 60.320 55.000 0.00 0.00 46.13 2.87
88 89 0.038251 TGCACGCAGGTGTAGAGAAG 60.038 55.000 0.00 0.00 46.13 2.85
89 90 1.355066 GCACGCAGGTGTAGAGAAGC 61.355 60.000 0.00 0.00 46.13 3.86
90 91 0.244994 CACGCAGGTGTAGAGAAGCT 59.755 55.000 0.00 0.00 39.38 3.74
91 92 0.528470 ACGCAGGTGTAGAGAAGCTC 59.472 55.000 0.00 0.00 0.00 4.09
92 93 0.528017 CGCAGGTGTAGAGAAGCTCA 59.472 55.000 0.00 0.00 32.06 4.26
93 94 1.468908 CGCAGGTGTAGAGAAGCTCAG 60.469 57.143 0.00 0.00 32.06 3.35
94 95 1.548269 GCAGGTGTAGAGAAGCTCAGT 59.452 52.381 0.00 0.00 32.06 3.41
95 96 2.755655 GCAGGTGTAGAGAAGCTCAGTA 59.244 50.000 0.00 0.00 32.06 2.74
96 97 3.383185 GCAGGTGTAGAGAAGCTCAGTAT 59.617 47.826 0.00 0.00 32.06 2.12
97 98 4.580995 GCAGGTGTAGAGAAGCTCAGTATA 59.419 45.833 0.00 0.00 32.06 1.47
98 99 5.278266 GCAGGTGTAGAGAAGCTCAGTATAG 60.278 48.000 0.00 0.00 32.06 1.31
99 100 6.058833 CAGGTGTAGAGAAGCTCAGTATAGA 58.941 44.000 0.00 0.00 32.06 1.98
100 101 6.544197 CAGGTGTAGAGAAGCTCAGTATAGAA 59.456 42.308 0.00 0.00 32.06 2.10
101 102 7.067615 CAGGTGTAGAGAAGCTCAGTATAGAAA 59.932 40.741 0.00 0.00 32.06 2.52
102 103 7.782644 AGGTGTAGAGAAGCTCAGTATAGAAAT 59.217 37.037 0.00 0.00 32.06 2.17
103 104 8.079809 GGTGTAGAGAAGCTCAGTATAGAAATC 58.920 40.741 0.00 0.00 32.06 2.17
104 105 8.079809 GTGTAGAGAAGCTCAGTATAGAAATCC 58.920 40.741 0.00 0.00 32.06 3.01
105 106 8.001875 TGTAGAGAAGCTCAGTATAGAAATCCT 58.998 37.037 0.00 0.00 32.06 3.24
106 107 9.509956 GTAGAGAAGCTCAGTATAGAAATCCTA 57.490 37.037 0.00 0.00 32.06 2.94
108 109 9.427821 AGAGAAGCTCAGTATAGAAATCCTAAA 57.572 33.333 0.00 0.00 32.06 1.85
109 110 9.471084 GAGAAGCTCAGTATAGAAATCCTAAAC 57.529 37.037 0.00 0.00 0.00 2.01
110 111 8.425703 AGAAGCTCAGTATAGAAATCCTAAACC 58.574 37.037 0.00 0.00 0.00 3.27
111 112 7.676683 AGCTCAGTATAGAAATCCTAAACCA 57.323 36.000 0.00 0.00 0.00 3.67
112 113 8.090788 AGCTCAGTATAGAAATCCTAAACCAA 57.909 34.615 0.00 0.00 0.00 3.67
113 114 8.207545 AGCTCAGTATAGAAATCCTAAACCAAG 58.792 37.037 0.00 0.00 0.00 3.61
114 115 7.041712 GCTCAGTATAGAAATCCTAAACCAAGC 60.042 40.741 0.00 0.00 0.00 4.01
115 116 8.090788 TCAGTATAGAAATCCTAAACCAAGCT 57.909 34.615 0.00 0.00 0.00 3.74
116 117 8.204836 TCAGTATAGAAATCCTAAACCAAGCTC 58.795 37.037 0.00 0.00 0.00 4.09
117 118 7.987458 CAGTATAGAAATCCTAAACCAAGCTCA 59.013 37.037 0.00 0.00 0.00 4.26
118 119 8.548877 AGTATAGAAATCCTAAACCAAGCTCAA 58.451 33.333 0.00 0.00 0.00 3.02
119 120 9.343539 GTATAGAAATCCTAAACCAAGCTCAAT 57.656 33.333 0.00 0.00 0.00 2.57
121 122 9.920946 ATAGAAATCCTAAACCAAGCTCAATAA 57.079 29.630 0.00 0.00 0.00 1.40
122 123 8.829373 AGAAATCCTAAACCAAGCTCAATAAT 57.171 30.769 0.00 0.00 0.00 1.28
123 124 8.689972 AGAAATCCTAAACCAAGCTCAATAATG 58.310 33.333 0.00 0.00 0.00 1.90
124 125 7.961326 AATCCTAAACCAAGCTCAATAATGT 57.039 32.000 0.00 0.00 0.00 2.71
125 126 7.961326 ATCCTAAACCAAGCTCAATAATGTT 57.039 32.000 0.00 0.00 0.00 2.71
126 127 7.156876 TCCTAAACCAAGCTCAATAATGTTG 57.843 36.000 0.00 0.00 0.00 3.33
127 128 6.945435 TCCTAAACCAAGCTCAATAATGTTGA 59.055 34.615 0.00 0.00 0.00 3.18
128 129 7.615365 TCCTAAACCAAGCTCAATAATGTTGAT 59.385 33.333 0.00 0.00 0.00 2.57
129 130 8.253113 CCTAAACCAAGCTCAATAATGTTGATT 58.747 33.333 0.00 0.00 0.00 2.57
130 131 7.894376 AAACCAAGCTCAATAATGTTGATTG 57.106 32.000 0.00 0.00 35.92 2.67
131 132 6.594788 ACCAAGCTCAATAATGTTGATTGT 57.405 33.333 0.00 0.00 36.02 2.71
132 133 6.624423 ACCAAGCTCAATAATGTTGATTGTC 58.376 36.000 0.00 0.00 36.02 3.18
133 134 6.435277 ACCAAGCTCAATAATGTTGATTGTCT 59.565 34.615 0.00 0.00 36.02 3.41
134 135 7.039504 ACCAAGCTCAATAATGTTGATTGTCTT 60.040 33.333 0.00 0.00 36.02 3.01
135 136 7.816031 CCAAGCTCAATAATGTTGATTGTCTTT 59.184 33.333 0.00 0.00 36.02 2.52
136 137 9.844790 CAAGCTCAATAATGTTGATTGTCTTTA 57.155 29.630 0.00 0.00 36.02 1.85
138 139 9.453572 AGCTCAATAATGTTGATTGTCTTTAGA 57.546 29.630 0.00 0.00 36.02 2.10
173 174 8.907222 AAAAATGTTGAGCCATATTTTTGTCT 57.093 26.923 14.87 0.00 39.73 3.41
174 175 8.907222 AAAATGTTGAGCCATATTTTTGTCTT 57.093 26.923 0.00 0.00 30.86 3.01
175 176 8.907222 AAATGTTGAGCCATATTTTTGTCTTT 57.093 26.923 0.00 0.00 0.00 2.52
176 177 8.907222 AATGTTGAGCCATATTTTTGTCTTTT 57.093 26.923 0.00 0.00 0.00 2.27
177 178 8.907222 ATGTTGAGCCATATTTTTGTCTTTTT 57.093 26.923 0.00 0.00 0.00 1.94
198 199 5.486735 TTTTAAGGGGATTGTCGTCTACA 57.513 39.130 0.00 0.00 35.88 2.74
199 200 4.460948 TTAAGGGGATTGTCGTCTACAC 57.539 45.455 0.00 0.00 38.00 2.90
200 201 1.192428 AGGGGATTGTCGTCTACACC 58.808 55.000 0.00 0.00 38.00 4.16
201 202 0.179119 GGGGATTGTCGTCTACACCG 60.179 60.000 0.00 0.00 38.00 4.94
202 203 0.179119 GGGATTGTCGTCTACACCGG 60.179 60.000 0.00 0.00 38.00 5.28
203 204 0.804933 GGATTGTCGTCTACACCGGC 60.805 60.000 0.00 0.00 38.00 6.13
204 205 0.804933 GATTGTCGTCTACACCGGCC 60.805 60.000 0.00 0.00 38.00 6.13
205 206 1.537814 ATTGTCGTCTACACCGGCCA 61.538 55.000 0.00 0.00 38.00 5.36
206 207 1.746322 TTGTCGTCTACACCGGCCAA 61.746 55.000 0.00 0.00 38.00 4.52
207 208 1.445582 GTCGTCTACACCGGCCAAG 60.446 63.158 0.00 0.00 0.00 3.61
208 209 2.813908 CGTCTACACCGGCCAAGC 60.814 66.667 0.00 0.00 0.00 4.01
209 210 2.436115 GTCTACACCGGCCAAGCC 60.436 66.667 0.00 0.00 46.75 4.35
218 219 2.681421 GGCCAAGCCCAAGGAAGG 60.681 66.667 0.00 0.00 44.06 3.46
219 220 2.440599 GCCAAGCCCAAGGAAGGA 59.559 61.111 0.00 0.00 0.00 3.36
220 221 1.228862 GCCAAGCCCAAGGAAGGAA 60.229 57.895 0.00 0.00 0.00 3.36
221 222 0.831711 GCCAAGCCCAAGGAAGGAAA 60.832 55.000 0.00 0.00 0.00 3.13
222 223 1.715785 CCAAGCCCAAGGAAGGAAAA 58.284 50.000 0.00 0.00 0.00 2.29
223 224 2.259917 CCAAGCCCAAGGAAGGAAAAT 58.740 47.619 0.00 0.00 0.00 1.82
224 225 3.440127 CCAAGCCCAAGGAAGGAAAATA 58.560 45.455 0.00 0.00 0.00 1.40
225 226 3.195610 CCAAGCCCAAGGAAGGAAAATAC 59.804 47.826 0.00 0.00 0.00 1.89
226 227 4.089361 CAAGCCCAAGGAAGGAAAATACT 58.911 43.478 0.00 0.00 0.00 2.12
227 228 5.261216 CAAGCCCAAGGAAGGAAAATACTA 58.739 41.667 0.00 0.00 0.00 1.82
228 229 5.530176 AGCCCAAGGAAGGAAAATACTAA 57.470 39.130 0.00 0.00 0.00 2.24
229 230 5.510430 AGCCCAAGGAAGGAAAATACTAAG 58.490 41.667 0.00 0.00 0.00 2.18
230 231 5.015284 AGCCCAAGGAAGGAAAATACTAAGT 59.985 40.000 0.00 0.00 0.00 2.24
231 232 5.357314 GCCCAAGGAAGGAAAATACTAAGTC 59.643 44.000 0.00 0.00 0.00 3.01
232 233 5.585047 CCCAAGGAAGGAAAATACTAAGTCG 59.415 44.000 0.00 0.00 0.00 4.18
233 234 6.403878 CCAAGGAAGGAAAATACTAAGTCGA 58.596 40.000 0.00 0.00 0.00 4.20
234 235 6.313164 CCAAGGAAGGAAAATACTAAGTCGAC 59.687 42.308 7.70 7.70 0.00 4.20
235 236 6.854091 AGGAAGGAAAATACTAAGTCGACT 57.146 37.500 13.58 13.58 0.00 4.18
236 237 6.865411 AGGAAGGAAAATACTAAGTCGACTC 58.135 40.000 20.33 2.62 0.00 3.36
237 238 5.742926 GGAAGGAAAATACTAAGTCGACTCG 59.257 44.000 20.33 15.33 0.00 4.18
238 239 4.670347 AGGAAAATACTAAGTCGACTCGC 58.330 43.478 20.33 0.79 0.00 5.03
239 240 4.398673 AGGAAAATACTAAGTCGACTCGCT 59.601 41.667 20.33 5.95 0.00 4.93
240 241 4.734370 GGAAAATACTAAGTCGACTCGCTC 59.266 45.833 20.33 7.09 0.00 5.03
241 242 5.448904 GGAAAATACTAAGTCGACTCGCTCT 60.449 44.000 20.33 5.11 0.00 4.09
242 243 4.799419 AATACTAAGTCGACTCGCTCTC 57.201 45.455 20.33 0.00 0.00 3.20
243 244 1.371595 ACTAAGTCGACTCGCTCTCC 58.628 55.000 20.33 0.00 0.00 3.71
244 245 1.338864 ACTAAGTCGACTCGCTCTCCA 60.339 52.381 20.33 0.00 0.00 3.86
245 246 1.738350 CTAAGTCGACTCGCTCTCCAA 59.262 52.381 20.33 0.00 0.00 3.53
246 247 0.241481 AAGTCGACTCGCTCTCCAAC 59.759 55.000 20.33 0.00 0.00 3.77
247 248 0.889638 AGTCGACTCGCTCTCCAACA 60.890 55.000 13.58 0.00 0.00 3.33
248 249 0.455295 GTCGACTCGCTCTCCAACAG 60.455 60.000 8.70 0.00 0.00 3.16
249 250 1.153939 CGACTCGCTCTCCAACAGG 60.154 63.158 0.00 0.00 0.00 4.00
250 251 1.446966 GACTCGCTCTCCAACAGGC 60.447 63.158 0.00 0.00 0.00 4.85
251 252 2.125350 CTCGCTCTCCAACAGGCC 60.125 66.667 0.00 0.00 0.00 5.19
252 253 3.997064 CTCGCTCTCCAACAGGCCG 62.997 68.421 0.00 0.00 0.00 6.13
253 254 4.069232 CGCTCTCCAACAGGCCGA 62.069 66.667 0.00 0.00 0.00 5.54
254 255 2.435059 GCTCTCCAACAGGCCGAC 60.435 66.667 0.00 0.00 0.00 4.79
255 256 3.059982 CTCTCCAACAGGCCGACA 58.940 61.111 0.00 0.00 0.00 4.35
256 257 1.374758 CTCTCCAACAGGCCGACAC 60.375 63.158 0.00 0.00 0.00 3.67
257 258 2.358737 CTCCAACAGGCCGACACC 60.359 66.667 0.00 0.00 0.00 4.16
258 259 2.847234 TCCAACAGGCCGACACCT 60.847 61.111 0.00 0.00 42.30 4.00
269 270 2.870372 GACACCTGGCGATTGCAC 59.130 61.111 7.38 0.00 45.35 4.57
270 271 3.027170 GACACCTGGCGATTGCACG 62.027 63.158 7.38 0.00 45.35 5.34
296 297 3.058160 GCTCCTGCACACGCCATT 61.058 61.111 0.00 0.00 39.41 3.16
297 298 2.872557 CTCCTGCACACGCCATTG 59.127 61.111 0.00 0.00 37.32 2.82
298 299 3.332493 CTCCTGCACACGCCATTGC 62.332 63.158 0.00 0.00 39.33 3.56
299 300 3.672447 CCTGCACACGCCATTGCA 61.672 61.111 1.27 1.27 46.43 4.08
300 301 2.429571 CTGCACACGCCATTGCAC 60.430 61.111 0.00 0.00 43.79 4.57
301 302 4.325304 TGCACACGCCATTGCACG 62.325 61.111 0.00 0.00 43.79 5.34
303 304 4.325304 CACACGCCATTGCACGCA 62.325 61.111 0.00 0.00 37.32 5.24
304 305 4.326766 ACACGCCATTGCACGCAC 62.327 61.111 0.00 0.00 37.32 5.34
325 326 3.441290 CGGCTCTCGTCGAGGGTT 61.441 66.667 22.71 0.00 41.73 4.11
426 430 4.296690 GTTCAATACGATCCTCCTAACGG 58.703 47.826 0.00 0.00 0.00 4.44
526 536 3.612247 CTGCCCACCCCAGAAGACG 62.612 68.421 0.00 0.00 32.03 4.18
579 589 1.519455 CCGAATCTCCACCGACAGC 60.519 63.158 0.00 0.00 0.00 4.40
640 650 2.231716 TCTTGGATTCCTCGACCTCA 57.768 50.000 3.95 0.00 0.00 3.86
786 805 2.436646 CTCCTCGCCCGCAACATT 60.437 61.111 0.00 0.00 0.00 2.71
828 847 0.745486 TCTTCGGAGATCACGCGGTA 60.745 55.000 12.47 0.00 35.04 4.02
884 903 1.822613 CGCTACCTCACGGCCTAGA 60.823 63.158 0.00 0.00 0.00 2.43
900 919 0.732880 TAGACGCTTCGCTTGAGCAC 60.733 55.000 3.65 0.00 42.21 4.40
901 920 3.016474 GACGCTTCGCTTGAGCACC 62.016 63.158 3.65 0.00 42.21 5.01
902 921 3.793144 CGCTTCGCTTGAGCACCC 61.793 66.667 3.65 0.00 42.21 4.61
903 922 3.793144 GCTTCGCTTGAGCACCCG 61.793 66.667 3.65 0.00 42.21 5.28
904 923 2.357517 CTTCGCTTGAGCACCCGT 60.358 61.111 3.65 0.00 42.21 5.28
905 924 1.961277 CTTCGCTTGAGCACCCGTT 60.961 57.895 3.65 0.00 42.21 4.44
906 925 1.901650 CTTCGCTTGAGCACCCGTTC 61.902 60.000 3.65 0.00 42.21 3.95
907 926 3.423154 CGCTTGAGCACCCGTTCC 61.423 66.667 3.65 0.00 42.21 3.62
908 927 3.056328 GCTTGAGCACCCGTTCCC 61.056 66.667 0.00 0.00 41.59 3.97
948 985 1.079750 GAAGCGCTTCCTCGTTCCT 60.080 57.895 34.88 4.54 33.64 3.36
1027 1064 2.281484 GCGAAACCAGTCTGGCCA 60.281 61.111 19.40 4.71 42.67 5.36
1050 1087 2.791347 TCTACTTCTCCTCGAGCACT 57.209 50.000 6.99 0.00 0.00 4.40
1097 1134 2.773661 AGGATTTGAATGATTTGGCCCC 59.226 45.455 0.00 0.00 0.00 5.80
1120 1187 2.106511 GGCAAGGGCTATATTCACAGGA 59.893 50.000 0.00 0.00 40.87 3.86
1146 1213 7.458409 CCATTATGCTTATGGCTGTTTCTAT 57.542 36.000 0.00 0.00 42.39 1.98
1167 1234 1.501170 TGGGACTGGGTGAATTTTGGA 59.499 47.619 0.00 0.00 0.00 3.53
1197 1270 2.928801 TGCTCTTGCTTAACACCAGA 57.071 45.000 0.00 0.00 40.48 3.86
1315 1395 5.415221 TTGGTTTCCACTGTGAAATTTCAC 58.585 37.500 34.41 34.41 44.80 3.18
1673 1757 8.659925 ACTTCTCTTCATAATTAGCACATGAG 57.340 34.615 0.00 0.00 30.77 2.90
1710 1794 5.776208 TCATGCTCATTATGGCAATTGGTAT 59.224 36.000 7.72 0.00 41.90 2.73
1713 1797 6.887013 TGCTCATTATGGCAATTGGTATTTT 58.113 32.000 7.72 0.00 35.40 1.82
2041 2143 8.412456 TCAAGTCAAAGATTGCTCATTTTGTAA 58.588 29.630 0.00 0.00 33.46 2.41
2220 2447 2.359531 CCGATCTCTCCACCACTCTTAC 59.640 54.545 0.00 0.00 0.00 2.34
2316 3432 5.673514 AGAAGTTTTCATGTGGTTGCATTT 58.326 33.333 0.00 0.00 0.00 2.32
2317 3433 6.114767 AGAAGTTTTCATGTGGTTGCATTTT 58.885 32.000 0.00 0.00 0.00 1.82
2387 3542 3.316308 ACTTCTGCACAACCAATTCTGTC 59.684 43.478 0.00 0.00 0.00 3.51
2435 3590 1.375908 TTCATGTGCCTCTGTCCGC 60.376 57.895 0.00 0.00 0.00 5.54
2478 3639 3.054875 TGATGCTAAGCTCACTGAACCAT 60.055 43.478 0.00 0.00 0.00 3.55
2479 3640 3.423539 TGCTAAGCTCACTGAACCATT 57.576 42.857 0.00 0.00 0.00 3.16
2544 3705 0.541863 CTATTCTGCCCCGTCCTGTT 59.458 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.432510 TGTTTCGAATGCCACCCTTTTT 59.567 40.909 0.00 0.00 0.00 1.94
10 11 2.035632 TGTTTCGAATGCCACCCTTTT 58.964 42.857 0.00 0.00 0.00 2.27
11 12 1.698506 TGTTTCGAATGCCACCCTTT 58.301 45.000 0.00 0.00 0.00 3.11
12 13 1.923356 ATGTTTCGAATGCCACCCTT 58.077 45.000 0.00 0.00 0.00 3.95
13 14 2.290641 TGTATGTTTCGAATGCCACCCT 60.291 45.455 0.00 0.00 0.00 4.34
14 15 2.088423 TGTATGTTTCGAATGCCACCC 58.912 47.619 0.00 0.00 0.00 4.61
15 16 2.475519 CGTGTATGTTTCGAATGCCACC 60.476 50.000 0.00 0.00 0.00 4.61
16 17 2.158841 ACGTGTATGTTTCGAATGCCAC 59.841 45.455 0.00 1.61 0.00 5.01
17 18 2.413796 GACGTGTATGTTTCGAATGCCA 59.586 45.455 0.00 0.00 0.00 4.92
18 19 2.671396 AGACGTGTATGTTTCGAATGCC 59.329 45.455 0.00 0.00 0.00 4.40
19 20 3.991605 AGACGTGTATGTTTCGAATGC 57.008 42.857 0.00 0.00 0.00 3.56
20 21 6.527023 ACTCTTAGACGTGTATGTTTCGAATG 59.473 38.462 0.00 0.00 0.00 2.67
21 22 6.618811 ACTCTTAGACGTGTATGTTTCGAAT 58.381 36.000 0.00 0.00 0.00 3.34
22 23 6.005583 ACTCTTAGACGTGTATGTTTCGAA 57.994 37.500 0.00 0.00 0.00 3.71
23 24 5.618056 ACTCTTAGACGTGTATGTTTCGA 57.382 39.130 0.00 0.00 0.00 3.71
24 25 6.581542 AGAAACTCTTAGACGTGTATGTTTCG 59.418 38.462 23.73 10.32 43.57 3.46
25 26 7.062022 GGAGAAACTCTTAGACGTGTATGTTTC 59.938 40.741 23.23 23.23 40.99 2.78
26 27 6.867293 GGAGAAACTCTTAGACGTGTATGTTT 59.133 38.462 14.23 14.23 0.00 2.83
27 28 6.388278 GGAGAAACTCTTAGACGTGTATGTT 58.612 40.000 0.00 0.00 0.00 2.71
28 29 5.105837 GGGAGAAACTCTTAGACGTGTATGT 60.106 44.000 0.00 0.00 0.00 2.29
29 30 5.341617 GGGAGAAACTCTTAGACGTGTATG 58.658 45.833 0.00 0.00 0.00 2.39
30 31 4.096081 CGGGAGAAACTCTTAGACGTGTAT 59.904 45.833 0.00 0.00 0.00 2.29
31 32 3.438087 CGGGAGAAACTCTTAGACGTGTA 59.562 47.826 0.00 0.00 0.00 2.90
32 33 2.228343 CGGGAGAAACTCTTAGACGTGT 59.772 50.000 0.00 0.00 0.00 4.49
33 34 2.228343 ACGGGAGAAACTCTTAGACGTG 59.772 50.000 0.00 0.00 0.00 4.49
34 35 2.512705 ACGGGAGAAACTCTTAGACGT 58.487 47.619 0.00 0.00 0.00 4.34
35 36 3.243336 CAACGGGAGAAACTCTTAGACG 58.757 50.000 0.00 0.00 0.00 4.18
36 37 4.236147 GACAACGGGAGAAACTCTTAGAC 58.764 47.826 0.00 0.00 0.00 2.59
37 38 3.893200 TGACAACGGGAGAAACTCTTAGA 59.107 43.478 0.00 0.00 0.00 2.10
38 39 4.022242 TCTGACAACGGGAGAAACTCTTAG 60.022 45.833 0.00 0.00 0.00 2.18
39 40 3.893200 TCTGACAACGGGAGAAACTCTTA 59.107 43.478 0.00 0.00 0.00 2.10
40 41 2.698797 TCTGACAACGGGAGAAACTCTT 59.301 45.455 0.00 0.00 0.00 2.85
41 42 2.036089 GTCTGACAACGGGAGAAACTCT 59.964 50.000 2.24 0.00 0.00 3.24
42 43 2.405172 GTCTGACAACGGGAGAAACTC 58.595 52.381 2.24 0.00 0.00 3.01
43 44 1.070289 GGTCTGACAACGGGAGAAACT 59.930 52.381 10.38 0.00 0.00 2.66
44 45 1.509703 GGTCTGACAACGGGAGAAAC 58.490 55.000 10.38 0.00 0.00 2.78
45 46 0.032952 CGGTCTGACAACGGGAGAAA 59.967 55.000 10.38 0.00 0.00 2.52
46 47 0.824595 TCGGTCTGACAACGGGAGAA 60.825 55.000 10.38 0.00 0.00 2.87
47 48 0.824595 TTCGGTCTGACAACGGGAGA 60.825 55.000 10.38 0.00 0.00 3.71
48 49 0.666577 GTTCGGTCTGACAACGGGAG 60.667 60.000 10.38 0.00 0.00 4.30
49 50 1.364901 GTTCGGTCTGACAACGGGA 59.635 57.895 10.38 0.00 0.00 5.14
50 51 2.019951 CGTTCGGTCTGACAACGGG 61.020 63.158 19.65 0.62 39.36 5.28
51 52 1.299620 ACGTTCGGTCTGACAACGG 60.300 57.895 26.52 14.86 45.67 4.44
52 53 1.844003 CACGTTCGGTCTGACAACG 59.156 57.895 23.45 23.45 46.57 4.10
53 54 1.149361 TGCACGTTCGGTCTGACAAC 61.149 55.000 10.38 5.61 0.00 3.32
54 55 1.142097 TGCACGTTCGGTCTGACAA 59.858 52.632 10.38 0.00 0.00 3.18
55 56 1.590525 GTGCACGTTCGGTCTGACA 60.591 57.895 10.38 0.00 0.00 3.58
56 57 2.645510 CGTGCACGTTCGGTCTGAC 61.646 63.158 30.50 0.00 34.11 3.51
57 58 2.354188 CGTGCACGTTCGGTCTGA 60.354 61.111 30.50 0.00 34.11 3.27
58 59 4.059459 GCGTGCACGTTCGGTCTG 62.059 66.667 36.80 9.58 42.22 3.51
59 60 4.578898 TGCGTGCACGTTCGGTCT 62.579 61.111 36.80 0.00 42.22 3.85
60 61 4.059459 CTGCGTGCACGTTCGGTC 62.059 66.667 36.80 21.22 42.22 4.79
63 64 4.354212 CACCTGCGTGCACGTTCG 62.354 66.667 36.80 25.73 42.22 3.95
64 65 1.886861 CTACACCTGCGTGCACGTTC 61.887 60.000 36.80 23.35 44.40 3.95
65 66 1.954146 CTACACCTGCGTGCACGTT 60.954 57.895 36.80 18.35 44.40 3.99
66 67 2.355837 CTACACCTGCGTGCACGT 60.356 61.111 36.80 20.60 44.40 4.49
67 68 2.049526 TCTACACCTGCGTGCACG 60.050 61.111 34.01 34.01 44.40 5.34
68 69 0.319555 TTCTCTACACCTGCGTGCAC 60.320 55.000 6.82 6.82 44.40 4.57
69 70 0.038251 CTTCTCTACACCTGCGTGCA 60.038 55.000 0.00 0.00 44.40 4.57
70 71 1.355066 GCTTCTCTACACCTGCGTGC 61.355 60.000 0.00 0.00 44.40 5.34
71 72 0.244994 AGCTTCTCTACACCTGCGTG 59.755 55.000 0.00 0.00 46.11 5.34
72 73 0.528470 GAGCTTCTCTACACCTGCGT 59.472 55.000 0.00 0.00 0.00 5.24
73 74 0.528017 TGAGCTTCTCTACACCTGCG 59.472 55.000 0.00 0.00 0.00 5.18
74 75 1.548269 ACTGAGCTTCTCTACACCTGC 59.452 52.381 0.00 0.00 0.00 4.85
75 76 6.058833 TCTATACTGAGCTTCTCTACACCTG 58.941 44.000 0.00 0.00 0.00 4.00
76 77 6.255294 TCTATACTGAGCTTCTCTACACCT 57.745 41.667 0.00 0.00 0.00 4.00
77 78 6.945938 TTCTATACTGAGCTTCTCTACACC 57.054 41.667 0.00 0.00 0.00 4.16
78 79 8.079809 GGATTTCTATACTGAGCTTCTCTACAC 58.920 40.741 0.00 0.00 0.00 2.90
79 80 8.001875 AGGATTTCTATACTGAGCTTCTCTACA 58.998 37.037 0.00 0.00 0.00 2.74
80 81 8.404107 AGGATTTCTATACTGAGCTTCTCTAC 57.596 38.462 0.00 0.00 0.00 2.59
82 83 9.427821 TTTAGGATTTCTATACTGAGCTTCTCT 57.572 33.333 0.00 0.00 0.00 3.10
83 84 9.471084 GTTTAGGATTTCTATACTGAGCTTCTC 57.529 37.037 0.00 0.00 30.47 2.87
84 85 8.425703 GGTTTAGGATTTCTATACTGAGCTTCT 58.574 37.037 0.00 0.00 32.69 2.85
85 86 8.204836 TGGTTTAGGATTTCTATACTGAGCTTC 58.795 37.037 0.00 0.00 32.69 3.86
86 87 8.090788 TGGTTTAGGATTTCTATACTGAGCTT 57.909 34.615 0.00 0.00 32.69 3.74
87 88 7.676683 TGGTTTAGGATTTCTATACTGAGCT 57.323 36.000 0.00 0.00 32.69 4.09
88 89 7.041712 GCTTGGTTTAGGATTTCTATACTGAGC 60.042 40.741 5.61 5.61 34.57 4.26
89 90 8.207545 AGCTTGGTTTAGGATTTCTATACTGAG 58.792 37.037 0.00 0.00 32.69 3.35
90 91 8.090788 AGCTTGGTTTAGGATTTCTATACTGA 57.909 34.615 0.00 0.00 32.69 3.41
91 92 7.987458 TGAGCTTGGTTTAGGATTTCTATACTG 59.013 37.037 0.00 0.00 32.69 2.74
92 93 8.090788 TGAGCTTGGTTTAGGATTTCTATACT 57.909 34.615 0.00 0.00 32.69 2.12
93 94 8.732746 TTGAGCTTGGTTTAGGATTTCTATAC 57.267 34.615 0.00 0.00 31.74 1.47
95 96 9.920946 TTATTGAGCTTGGTTTAGGATTTCTAT 57.079 29.630 0.00 0.00 0.00 1.98
96 97 9.920946 ATTATTGAGCTTGGTTTAGGATTTCTA 57.079 29.630 0.00 0.00 0.00 2.10
97 98 8.689972 CATTATTGAGCTTGGTTTAGGATTTCT 58.310 33.333 0.00 0.00 0.00 2.52
98 99 8.470002 ACATTATTGAGCTTGGTTTAGGATTTC 58.530 33.333 0.00 0.00 0.00 2.17
99 100 8.366359 ACATTATTGAGCTTGGTTTAGGATTT 57.634 30.769 0.00 0.00 0.00 2.17
100 101 7.961326 ACATTATTGAGCTTGGTTTAGGATT 57.039 32.000 0.00 0.00 0.00 3.01
101 102 7.615365 TCAACATTATTGAGCTTGGTTTAGGAT 59.385 33.333 0.00 0.00 0.00 3.24
102 103 6.945435 TCAACATTATTGAGCTTGGTTTAGGA 59.055 34.615 0.00 0.00 0.00 2.94
103 104 7.156876 TCAACATTATTGAGCTTGGTTTAGG 57.843 36.000 0.00 0.00 0.00 2.69
104 105 9.079833 CAATCAACATTATTGAGCTTGGTTTAG 57.920 33.333 0.00 0.00 36.61 1.85
105 106 8.584157 ACAATCAACATTATTGAGCTTGGTTTA 58.416 29.630 3.01 0.00 37.68 2.01
106 107 7.444299 ACAATCAACATTATTGAGCTTGGTTT 58.556 30.769 3.01 0.00 37.68 3.27
107 108 6.996509 ACAATCAACATTATTGAGCTTGGTT 58.003 32.000 3.01 0.00 37.68 3.67
108 109 6.435277 AGACAATCAACATTATTGAGCTTGGT 59.565 34.615 3.01 0.00 37.68 3.67
109 110 6.860080 AGACAATCAACATTATTGAGCTTGG 58.140 36.000 3.01 0.00 37.68 3.61
110 111 8.752766 AAAGACAATCAACATTATTGAGCTTG 57.247 30.769 3.01 0.00 37.68 4.01
112 113 9.453572 TCTAAAGACAATCAACATTATTGAGCT 57.546 29.630 3.01 0.00 37.68 4.09
148 149 8.907222 AGACAAAAATATGGCTCAACATTTTT 57.093 26.923 12.56 12.56 39.78 1.94
149 150 8.907222 AAGACAAAAATATGGCTCAACATTTT 57.093 26.923 0.00 0.00 37.83 1.82
150 151 8.907222 AAAGACAAAAATATGGCTCAACATTT 57.093 26.923 0.00 0.00 37.83 2.32
151 152 8.907222 AAAAGACAAAAATATGGCTCAACATT 57.093 26.923 0.00 0.00 37.83 2.71
152 153 8.907222 AAAAAGACAAAAATATGGCTCAACAT 57.093 26.923 0.00 0.00 37.83 2.71
175 176 5.702209 GTGTAGACGACAATCCCCTTAAAAA 59.298 40.000 0.00 0.00 40.66 1.94
176 177 5.240121 GTGTAGACGACAATCCCCTTAAAA 58.760 41.667 0.00 0.00 40.66 1.52
177 178 4.322953 GGTGTAGACGACAATCCCCTTAAA 60.323 45.833 0.00 0.00 40.66 1.52
178 179 3.196254 GGTGTAGACGACAATCCCCTTAA 59.804 47.826 0.00 0.00 40.66 1.85
179 180 2.762327 GGTGTAGACGACAATCCCCTTA 59.238 50.000 0.00 0.00 40.66 2.69
180 181 1.553704 GGTGTAGACGACAATCCCCTT 59.446 52.381 0.00 0.00 40.66 3.95
181 182 1.192428 GGTGTAGACGACAATCCCCT 58.808 55.000 0.00 0.00 40.66 4.79
182 183 0.179119 CGGTGTAGACGACAATCCCC 60.179 60.000 0.00 0.00 40.66 4.81
183 184 0.179119 CCGGTGTAGACGACAATCCC 60.179 60.000 0.00 0.00 40.66 3.85
184 185 0.804933 GCCGGTGTAGACGACAATCC 60.805 60.000 1.90 0.00 40.66 3.01
185 186 0.804933 GGCCGGTGTAGACGACAATC 60.805 60.000 1.90 0.00 40.66 2.67
186 187 1.217244 GGCCGGTGTAGACGACAAT 59.783 57.895 1.90 0.00 40.66 2.71
187 188 1.746322 TTGGCCGGTGTAGACGACAA 61.746 55.000 1.90 0.00 40.66 3.18
188 189 2.149803 CTTGGCCGGTGTAGACGACA 62.150 60.000 1.90 0.00 34.94 4.35
189 190 1.445582 CTTGGCCGGTGTAGACGAC 60.446 63.158 1.90 0.00 0.00 4.34
190 191 2.967397 CTTGGCCGGTGTAGACGA 59.033 61.111 1.90 0.00 0.00 4.20
191 192 2.813908 GCTTGGCCGGTGTAGACG 60.814 66.667 1.90 0.00 0.00 4.18
192 193 2.436115 GGCTTGGCCGGTGTAGAC 60.436 66.667 1.90 0.00 39.62 2.59
202 203 0.831711 TTTCCTTCCTTGGGCTTGGC 60.832 55.000 0.00 0.00 0.00 4.52
203 204 1.715785 TTTTCCTTCCTTGGGCTTGG 58.284 50.000 0.00 0.00 0.00 3.61
204 205 4.089361 AGTATTTTCCTTCCTTGGGCTTG 58.911 43.478 0.00 0.00 0.00 4.01
205 206 4.404185 AGTATTTTCCTTCCTTGGGCTT 57.596 40.909 0.00 0.00 0.00 4.35
206 207 5.015284 ACTTAGTATTTTCCTTCCTTGGGCT 59.985 40.000 0.00 0.00 0.00 5.19
207 208 5.262009 ACTTAGTATTTTCCTTCCTTGGGC 58.738 41.667 0.00 0.00 0.00 5.36
208 209 5.585047 CGACTTAGTATTTTCCTTCCTTGGG 59.415 44.000 0.00 0.00 0.00 4.12
209 210 6.313164 GTCGACTTAGTATTTTCCTTCCTTGG 59.687 42.308 8.70 0.00 0.00 3.61
210 211 7.097834 AGTCGACTTAGTATTTTCCTTCCTTG 58.902 38.462 13.58 0.00 0.00 3.61
211 212 7.242322 AGTCGACTTAGTATTTTCCTTCCTT 57.758 36.000 13.58 0.00 0.00 3.36
212 213 6.404513 CGAGTCGACTTAGTATTTTCCTTCCT 60.405 42.308 21.08 0.00 0.00 3.36
213 214 5.742926 CGAGTCGACTTAGTATTTTCCTTCC 59.257 44.000 21.08 0.00 0.00 3.46
214 215 5.229678 GCGAGTCGACTTAGTATTTTCCTTC 59.770 44.000 21.08 0.40 0.00 3.46
215 216 5.100943 GCGAGTCGACTTAGTATTTTCCTT 58.899 41.667 21.08 0.00 0.00 3.36
216 217 4.398673 AGCGAGTCGACTTAGTATTTTCCT 59.601 41.667 21.08 5.10 0.00 3.36
217 218 4.670347 AGCGAGTCGACTTAGTATTTTCC 58.330 43.478 21.08 1.32 0.00 3.13
218 219 5.571277 AGAGCGAGTCGACTTAGTATTTTC 58.429 41.667 21.08 9.11 0.00 2.29
219 220 5.448904 GGAGAGCGAGTCGACTTAGTATTTT 60.449 44.000 21.08 1.11 0.00 1.82
220 221 4.035441 GGAGAGCGAGTCGACTTAGTATTT 59.965 45.833 21.08 5.93 0.00 1.40
221 222 3.560896 GGAGAGCGAGTCGACTTAGTATT 59.439 47.826 21.08 4.35 0.00 1.89
222 223 3.132925 GGAGAGCGAGTCGACTTAGTAT 58.867 50.000 21.08 10.00 0.00 2.12
223 224 2.093816 TGGAGAGCGAGTCGACTTAGTA 60.094 50.000 21.08 0.00 0.00 1.82
224 225 1.338864 TGGAGAGCGAGTCGACTTAGT 60.339 52.381 21.08 6.87 0.00 2.24
225 226 1.370609 TGGAGAGCGAGTCGACTTAG 58.629 55.000 21.08 17.51 0.00 2.18
226 227 1.467734 GTTGGAGAGCGAGTCGACTTA 59.532 52.381 21.08 5.52 0.00 2.24
227 228 0.241481 GTTGGAGAGCGAGTCGACTT 59.759 55.000 21.08 3.21 0.00 3.01
228 229 0.889638 TGTTGGAGAGCGAGTCGACT 60.890 55.000 20.18 20.18 0.00 4.18
229 230 0.455295 CTGTTGGAGAGCGAGTCGAC 60.455 60.000 18.61 7.70 0.00 4.20
230 231 1.587043 CCTGTTGGAGAGCGAGTCGA 61.587 60.000 18.61 0.00 34.57 4.20
231 232 1.153939 CCTGTTGGAGAGCGAGTCG 60.154 63.158 8.54 8.54 34.57 4.18
232 233 1.446966 GCCTGTTGGAGAGCGAGTC 60.447 63.158 0.00 0.00 34.57 3.36
233 234 2.659610 GCCTGTTGGAGAGCGAGT 59.340 61.111 0.00 0.00 34.57 4.18
234 235 2.125350 GGCCTGTTGGAGAGCGAG 60.125 66.667 0.00 0.00 34.57 5.03
235 236 4.069232 CGGCCTGTTGGAGAGCGA 62.069 66.667 0.00 0.00 34.57 4.93
236 237 4.069232 TCGGCCTGTTGGAGAGCG 62.069 66.667 0.00 0.00 34.57 5.03
237 238 2.435059 GTCGGCCTGTTGGAGAGC 60.435 66.667 0.00 0.00 34.57 4.09
238 239 1.374758 GTGTCGGCCTGTTGGAGAG 60.375 63.158 0.00 0.00 34.57 3.20
239 240 2.741092 GTGTCGGCCTGTTGGAGA 59.259 61.111 0.00 0.00 34.57 3.71
240 241 2.358737 GGTGTCGGCCTGTTGGAG 60.359 66.667 0.00 0.00 34.57 3.86
241 242 2.847234 AGGTGTCGGCCTGTTGGA 60.847 61.111 0.00 0.00 37.50 3.53
249 250 3.499737 CAATCGCCAGGTGTCGGC 61.500 66.667 0.00 0.00 46.62 5.54
250 251 3.499737 GCAATCGCCAGGTGTCGG 61.500 66.667 0.00 0.00 0.00 4.79
251 252 2.741985 TGCAATCGCCAGGTGTCG 60.742 61.111 0.00 0.00 37.32 4.35
252 253 2.870372 GTGCAATCGCCAGGTGTC 59.130 61.111 0.00 0.00 37.32 3.67
253 254 3.049674 CGTGCAATCGCCAGGTGT 61.050 61.111 0.00 0.00 37.32 4.16
279 280 3.058160 AATGGCGTGTGCAGGAGC 61.058 61.111 0.00 0.00 45.35 4.70
280 281 2.872557 CAATGGCGTGTGCAGGAG 59.127 61.111 0.00 0.00 45.35 3.69
281 282 3.364441 GCAATGGCGTGTGCAGGA 61.364 61.111 8.39 0.00 45.35 3.86
282 283 3.672447 TGCAATGGCGTGTGCAGG 61.672 61.111 10.97 0.00 45.52 4.85
286 287 4.325304 TGCGTGCAATGGCGTGTG 62.325 61.111 0.00 0.00 45.35 3.82
287 288 4.326766 GTGCGTGCAATGGCGTGT 62.327 61.111 0.00 0.00 45.35 4.49
308 309 2.868999 GAAACCCTCGACGAGAGCCG 62.869 65.000 26.11 12.12 45.54 5.52
309 310 1.153804 GAAACCCTCGACGAGAGCC 60.154 63.158 26.11 6.68 45.54 4.70
310 311 1.153804 GGAAACCCTCGACGAGAGC 60.154 63.158 26.11 9.61 45.54 4.09
311 312 1.401199 GTAGGAAACCCTCGACGAGAG 59.599 57.143 26.11 15.97 46.44 3.20
312 313 1.457346 GTAGGAAACCCTCGACGAGA 58.543 55.000 26.11 0.12 35.26 4.04
313 314 0.098376 CGTAGGAAACCCTCGACGAG 59.902 60.000 18.08 18.08 37.77 4.18
314 315 1.926511 GCGTAGGAAACCCTCGACGA 61.927 60.000 10.04 0.00 37.77 4.20
315 316 1.515736 GCGTAGGAAACCCTCGACG 60.516 63.158 0.00 0.00 38.29 5.12
316 317 0.179142 GAGCGTAGGAAACCCTCGAC 60.179 60.000 0.00 0.00 35.26 4.20
317 318 0.609957 TGAGCGTAGGAAACCCTCGA 60.610 55.000 0.00 0.00 36.03 4.04
318 319 0.245539 TTGAGCGTAGGAAACCCTCG 59.754 55.000 0.00 0.00 36.03 4.63
319 320 2.467566 TTTGAGCGTAGGAAACCCTC 57.532 50.000 0.00 0.00 34.19 4.30
320 321 2.943036 TTTTGAGCGTAGGAAACCCT 57.057 45.000 0.00 0.00 37.84 4.34
483 493 0.820074 GGAAGATCTCGGCGAGGAGA 60.820 60.000 33.93 17.92 46.37 3.71
579 589 1.153469 GAAGCAGCGGAGGAAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
696 715 3.560025 GGAAGGAGAAGGTGAAATCTGCA 60.560 47.826 0.00 0.00 36.58 4.41
699 718 3.521531 GGAGGAAGGAGAAGGTGAAATCT 59.478 47.826 0.00 0.00 0.00 2.40
786 805 2.742403 GGCTGCCCATGTTTTGCA 59.258 55.556 7.66 0.00 0.00 4.08
814 833 3.938112 GCATACCGCGTGATCTCC 58.062 61.111 4.92 0.00 0.00 3.71
848 867 2.363925 GGGGGAGCAGGACGTACT 60.364 66.667 0.00 0.00 0.00 2.73
907 926 3.793888 GGGCTCACTTACCGGGGG 61.794 72.222 6.32 0.00 0.00 5.40
908 927 2.687566 AGGGCTCACTTACCGGGG 60.688 66.667 6.32 0.00 0.00 5.73
922 959 3.130160 GAAGCGCTTCCAGCAGGG 61.130 66.667 34.88 0.00 42.58 4.45
948 985 2.326773 CTACCTCCTCCTCGCCGAGA 62.327 65.000 17.19 0.68 30.97 4.04
1027 1064 2.291024 TGCTCGAGGAGAAGTAGAAGGT 60.291 50.000 15.58 0.00 0.00 3.50
1050 1087 3.199551 GCGGCTTGCCATTGATCA 58.800 55.556 12.45 0.00 37.76 2.92
1097 1134 3.144506 CTGTGAATATAGCCCTTGCCAG 58.855 50.000 0.00 0.00 38.69 4.85
1146 1213 2.091055 TCCAAAATTCACCCAGTCCCAA 60.091 45.455 0.00 0.00 0.00 4.12
1315 1395 1.535833 ACGGTATAGCTGAGATCGGG 58.464 55.000 0.00 0.00 0.00 5.14
1344 1424 0.244178 GACTCGGACTCTCGCCTTTT 59.756 55.000 0.00 0.00 0.00 2.27
1359 1439 1.189752 TCTCCATCTGCCACTGACTC 58.810 55.000 0.00 0.00 0.00 3.36
1500 1583 1.151668 GCTGCAATGTCTTGACGTCT 58.848 50.000 17.92 0.00 34.04 4.18
1503 1586 1.532437 TGAAGCTGCAATGTCTTGACG 59.468 47.619 1.02 0.00 34.04 4.35
1665 1749 4.154737 TGAAGCAATAGACAACTCATGTGC 59.845 41.667 0.00 0.00 44.12 4.57
1741 1825 4.518970 TCTTAGTTTTCCCAATGAGCACAC 59.481 41.667 0.00 0.00 0.00 3.82
2117 2230 5.819901 GCAGGTTTATCTCTAGACAGCAATT 59.180 40.000 0.00 0.00 0.00 2.32
2118 2231 5.104776 TGCAGGTTTATCTCTAGACAGCAAT 60.105 40.000 0.00 0.00 28.50 3.56
2128 2241 6.656632 TCGATCTTATGCAGGTTTATCTCT 57.343 37.500 0.00 0.00 0.00 3.10
2220 2447 3.273434 CACAACCATGGTACTGAGGATG 58.727 50.000 20.12 12.60 0.00 3.51
2316 3432 4.097286 GGTGTGTTGGTAGAGCAAGAAAAA 59.903 41.667 0.00 0.00 0.00 1.94
2317 3433 3.630312 GGTGTGTTGGTAGAGCAAGAAAA 59.370 43.478 0.00 0.00 0.00 2.29
2368 3522 2.880268 CAGACAGAATTGGTTGTGCAGA 59.120 45.455 0.00 0.00 32.15 4.26
2435 3590 5.496556 TCAATACAAGTTGGGATACACTGG 58.503 41.667 7.96 0.00 39.74 4.00
2478 3639 4.814147 TGAAACATGTGACTGCAAACAAA 58.186 34.783 0.00 0.00 0.00 2.83
2479 3640 4.157472 TCTGAAACATGTGACTGCAAACAA 59.843 37.500 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.