Multiple sequence alignment - TraesCS7D01G440100

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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 TraesCS7D01G440100 chr7D 100.000 3949 0 0 1 3949 560221018 560224966 0.000000e+00 7293.0
1 TraesCS7D01G440100 chr7D 81.496 254 40 7 899 1149 5476040 5475791 6.690000e-48 202.0
2 TraesCS7D01G440100 chr7D 74.048 289 68 7 782 1067 553200010 553200294 1.160000e-20 111.0
3 TraesCS7D01G440100 chr7A 94.399 2678 107 17 428 3090 644440482 644443131 0.000000e+00 4074.0
4 TraesCS7D01G440100 chr7A 84.912 2227 221 41 1148 3321 644456175 644458339 0.000000e+00 2145.0
5 TraesCS7D01G440100 chr7A 91.369 672 32 8 3155 3817 644443185 644443839 0.000000e+00 896.0
6 TraesCS7D01G440100 chr7A 95.633 229 9 1 1 229 644424921 644425148 2.240000e-97 366.0
7 TraesCS7D01G440100 chr7A 94.737 190 9 1 227 415 644439271 644439460 1.070000e-75 294.0
8 TraesCS7D01G440100 chr7A 83.465 254 35 7 900 1149 608533560 608533310 3.070000e-56 230.0
9 TraesCS7D01G440100 chr7A 86.802 197 20 5 3696 3886 644451312 644451508 8.590000e-52 215.0
10 TraesCS7D01G440100 chr7A 91.406 128 11 0 3821 3948 644444194 644444321 4.060000e-40 176.0
11 TraesCS7D01G440100 chr7A 97.368 38 1 0 3086 3123 644443148 644443185 9.160000e-07 65.8
12 TraesCS7D01G440100 chr7B 93.798 1951 99 7 1148 3085 607909073 607911014 0.000000e+00 2913.0
13 TraesCS7D01G440100 chr7B 85.630 2199 189 49 1154 3272 608183041 608185192 0.000000e+00 2193.0
14 TraesCS7D01G440100 chr7B 82.570 2249 251 52 1148 3321 607927574 607929756 0.000000e+00 1851.0
15 TraesCS7D01G440100 chr7B 91.460 808 47 12 3155 3949 607930766 607931564 0.000000e+00 1090.0
16 TraesCS7D01G440100 chr7B 91.221 786 36 11 3155 3933 607911073 607911832 0.000000e+00 1038.0
17 TraesCS7D01G440100 chr7B 92.824 432 28 3 2655 3085 607930278 607930707 1.210000e-174 623.0
18 TraesCS7D01G440100 chr7B 83.621 232 37 1 428 658 117033222 117032991 2.390000e-52 217.0
19 TraesCS7D01G440100 chr7B 97.368 38 1 0 3086 3123 607930729 607930766 9.160000e-07 65.8
20 TraesCS7D01G440100 chrUn 76.948 1848 317 70 1289 3085 143908240 143910029 0.000000e+00 952.0
21 TraesCS7D01G440100 chrUn 75.968 1731 306 77 1203 2904 26573793 26572144 0.000000e+00 791.0
22 TraesCS7D01G440100 chrUn 73.913 2093 402 91 1348 3383 153494817 153492812 0.000000e+00 708.0
23 TraesCS7D01G440100 chrUn 75.054 1391 261 62 1722 3082 98357303 98355969 5.730000e-158 568.0
24 TraesCS7D01G440100 chrUn 73.635 1703 330 76 1349 3018 153390165 153391781 7.460000e-152 547.0
25 TraesCS7D01G440100 chrUn 75.066 1139 212 37 1289 2409 153436495 153435411 7.730000e-127 464.0
26 TraesCS7D01G440100 chrUn 75.163 1075 208 45 1852 2904 26518243 26517206 6.020000e-123 451.0
27 TraesCS7D01G440100 chr6B 75.692 1843 334 74 1289 3075 84131896 84133680 0.000000e+00 817.0
28 TraesCS7D01G440100 chr6B 73.895 1697 320 85 1349 3018 84566061 84567661 2.060000e-157 566.0
29 TraesCS7D01G440100 chr6B 74.940 1257 235 59 1855 3085 82957740 82956538 1.640000e-138 503.0
30 TraesCS7D01G440100 chr6B 85.385 390 50 7 2668 3054 171038970 171038585 7.950000e-107 398.0
31 TraesCS7D01G440100 chr6B 74.294 708 141 30 2211 2905 64008119 64007440 1.090000e-65 261.0
32 TraesCS7D01G440100 chr6B 78.341 217 37 5 3165 3380 84493188 84493395 8.900000e-27 132.0
33 TraesCS7D01G440100 chr2D 87.431 724 54 8 428 1150 617728375 617729062 0.000000e+00 798.0
34 TraesCS7D01G440100 chr2D 80.800 250 41 6 901 1147 328337010 328337255 5.210000e-44 189.0
35 TraesCS7D01G440100 chr6A 76.009 1388 247 59 1723 3085 47956538 47957864 1.200000e-179 640.0
36 TraesCS7D01G440100 chr2B 87.054 224 27 2 423 646 3643882 3643661 6.550000e-63 252.0
37 TraesCS7D01G440100 chr2B 96.364 55 1 1 253 306 693078548 693078602 5.440000e-14 89.8
38 TraesCS7D01G440100 chr5B 87.324 213 27 0 426 638 482987317 482987529 1.100000e-60 244.0
39 TraesCS7D01G440100 chr5B 78.599 257 41 11 899 1149 640539294 640539542 1.470000e-34 158.0
40 TraesCS7D01G440100 chr5B 100.000 44 0 0 263 306 446227920 446227963 9.100000e-12 82.4
41 TraesCS7D01G440100 chr6D 84.914 232 32 3 428 659 16665451 16665223 8.530000e-57 231.0
42 TraesCS7D01G440100 chr5D 84.848 231 33 2 900 1129 22426266 22426495 8.530000e-57 231.0
43 TraesCS7D01G440100 chr1D 84.549 233 29 6 900 1129 250205611 250205383 1.430000e-54 224.0
44 TraesCS7D01G440100 chr3B 85.024 207 31 0 432 638 223693430 223693224 1.110000e-50 211.0
45 TraesCS7D01G440100 chr5A 88.372 129 14 1 432 559 653884375 653884247 1.900000e-33 154.0
46 TraesCS7D01G440100 chr1B 77.985 268 39 15 901 1153 460559602 460559340 2.460000e-32 150.0
47 TraesCS7D01G440100 chr4A 87.597 129 15 1 432 559 513322613 513322741 8.840000e-32 148.0
48 TraesCS7D01G440100 chr3A 86.538 104 11 2 2 105 136002411 136002511 1.160000e-20 111.0
49 TraesCS7D01G440100 chr2A 96.364 55 1 1 253 306 714832336 714832390 5.440000e-14 89.8


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 TraesCS7D01G440100 chr7D 560221018 560224966 3948 False 7293.00 7293 100.0000 1 3949 1 chr7D.!!$F2 3948
1 TraesCS7D01G440100 chr7A 644456175 644458339 2164 False 2145.00 2145 84.9120 1148 3321 1 chr7A.!!$F3 2173
2 TraesCS7D01G440100 chr7A 644439271 644444321 5050 False 1101.16 4074 93.8558 227 3948 5 chr7A.!!$F4 3721
3 TraesCS7D01G440100 chr7B 608183041 608185192 2151 False 2193.00 2193 85.6300 1154 3272 1 chr7B.!!$F1 2118
4 TraesCS7D01G440100 chr7B 607909073 607911832 2759 False 1975.50 2913 92.5095 1148 3933 2 chr7B.!!$F2 2785
5 TraesCS7D01G440100 chr7B 607927574 607931564 3990 False 907.45 1851 91.0555 1148 3949 4 chr7B.!!$F3 2801
6 TraesCS7D01G440100 chrUn 143908240 143910029 1789 False 952.00 952 76.9480 1289 3085 1 chrUn.!!$F1 1796
7 TraesCS7D01G440100 chrUn 26572144 26573793 1649 True 791.00 791 75.9680 1203 2904 1 chrUn.!!$R2 1701
8 TraesCS7D01G440100 chrUn 153492812 153494817 2005 True 708.00 708 73.9130 1348 3383 1 chrUn.!!$R5 2035
9 TraesCS7D01G440100 chrUn 98355969 98357303 1334 True 568.00 568 75.0540 1722 3082 1 chrUn.!!$R3 1360
10 TraesCS7D01G440100 chrUn 153390165 153391781 1616 False 547.00 547 73.6350 1349 3018 1 chrUn.!!$F2 1669
11 TraesCS7D01G440100 chrUn 153435411 153436495 1084 True 464.00 464 75.0660 1289 2409 1 chrUn.!!$R4 1120
12 TraesCS7D01G440100 chrUn 26517206 26518243 1037 True 451.00 451 75.1630 1852 2904 1 chrUn.!!$R1 1052
13 TraesCS7D01G440100 chr6B 84131896 84133680 1784 False 817.00 817 75.6920 1289 3075 1 chr6B.!!$F1 1786
14 TraesCS7D01G440100 chr6B 84566061 84567661 1600 False 566.00 566 73.8950 1349 3018 1 chr6B.!!$F3 1669
15 TraesCS7D01G440100 chr6B 82956538 82957740 1202 True 503.00 503 74.9400 1855 3085 1 chr6B.!!$R2 1230
16 TraesCS7D01G440100 chr6B 64007440 64008119 679 True 261.00 261 74.2940 2211 2905 1 chr6B.!!$R1 694
17 TraesCS7D01G440100 chr2D 617728375 617729062 687 False 798.00 798 87.4310 428 1150 1 chr2D.!!$F2 722
18 TraesCS7D01G440100 chr6A 47956538 47957864 1326 False 640.00 640 76.0090 1723 3085 1 chr6A.!!$F1 1362

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
33 34 0.033601 AACTGGCCAACTCCACACAA 60.034 50.0 7.01 0.0 31.74 3.33 F
529 1540 0.035056 CCACAGGAGGCGAGGAAAAT 60.035 55.0 0.00 0.0 0.00 1.82 F
1194 2213 0.258774 CCCATTTCCCCATCCGTTCT 59.741 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 2062 0.108207 GACGGTAGGATCTCCCTCGA 59.892 60.000 9.42 0.0 43.31 4.04 R
1672 2778 1.655654 CGTAGCCGACATCGAGCTG 60.656 63.158 20.44 0.0 42.60 4.24 R
3129 5595 0.269173 AAGACCCTAGGAGGATGGGG 59.731 60.000 11.48 0.0 46.26 4.96 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.660789 ATTTGCTTCATATGAACTGGCC 57.339 40.909 19.71 0.00 0.00 5.36
22 23 2.804986 TGCTTCATATGAACTGGCCA 57.195 45.000 19.71 4.71 0.00 5.36
23 24 3.084536 TGCTTCATATGAACTGGCCAA 57.915 42.857 19.71 0.00 0.00 4.52
24 25 2.754552 TGCTTCATATGAACTGGCCAAC 59.245 45.455 19.71 1.69 0.00 3.77
25 26 3.019564 GCTTCATATGAACTGGCCAACT 58.980 45.455 14.23 0.00 0.00 3.16
26 27 3.065925 GCTTCATATGAACTGGCCAACTC 59.934 47.826 14.23 6.86 0.00 3.01
27 28 3.281727 TCATATGAACTGGCCAACTCC 57.718 47.619 7.01 0.00 0.00 3.85
28 29 2.575735 TCATATGAACTGGCCAACTCCA 59.424 45.455 7.01 2.81 34.42 3.86
29 30 2.489938 TATGAACTGGCCAACTCCAC 57.510 50.000 7.01 0.00 31.74 4.02
30 31 0.478072 ATGAACTGGCCAACTCCACA 59.522 50.000 7.01 1.95 31.74 4.17
31 32 0.465460 TGAACTGGCCAACTCCACAC 60.465 55.000 7.01 0.00 31.74 3.82
32 33 0.465460 GAACTGGCCAACTCCACACA 60.465 55.000 7.01 0.00 31.74 3.72
33 34 0.033601 AACTGGCCAACTCCACACAA 60.034 50.000 7.01 0.00 31.74 3.33
34 35 0.033601 ACTGGCCAACTCCACACAAA 60.034 50.000 7.01 0.00 31.74 2.83
35 36 1.110442 CTGGCCAACTCCACACAAAA 58.890 50.000 7.01 0.00 31.74 2.44
36 37 1.480137 CTGGCCAACTCCACACAAAAA 59.520 47.619 7.01 0.00 31.74 1.94
68 69 9.541143 AAAAACCAATACAAACATTAGACTTGG 57.459 29.630 0.00 0.00 38.26 3.61
69 70 7.833285 AACCAATACAAACATTAGACTTGGT 57.167 32.000 0.00 0.00 45.14 3.67
70 71 8.927675 AACCAATACAAACATTAGACTTGGTA 57.072 30.769 4.24 0.00 43.09 3.25
71 72 8.927675 ACCAATACAAACATTAGACTTGGTAA 57.072 30.769 1.99 0.00 42.34 2.85
72 73 9.010029 ACCAATACAAACATTAGACTTGGTAAG 57.990 33.333 1.99 0.00 42.34 2.34
73 74 7.968405 CCAATACAAACATTAGACTTGGTAAGC 59.032 37.037 0.00 0.00 0.00 3.09
74 75 5.959618 ACAAACATTAGACTTGGTAAGCC 57.040 39.130 0.00 0.00 0.00 4.35
75 76 5.381757 ACAAACATTAGACTTGGTAAGCCA 58.618 37.500 0.00 0.00 44.38 4.75
76 77 5.240844 ACAAACATTAGACTTGGTAAGCCAC 59.759 40.000 0.00 0.00 46.01 5.01
77 78 4.634012 ACATTAGACTTGGTAAGCCACA 57.366 40.909 0.00 0.00 46.01 4.17
78 79 4.980573 ACATTAGACTTGGTAAGCCACAA 58.019 39.130 0.00 0.00 46.01 3.33
79 80 4.760204 ACATTAGACTTGGTAAGCCACAAC 59.240 41.667 0.00 0.00 46.01 3.32
80 81 4.425180 TTAGACTTGGTAAGCCACAACA 57.575 40.909 0.00 0.00 46.01 3.33
81 82 2.572290 AGACTTGGTAAGCCACAACAC 58.428 47.619 0.00 0.00 46.01 3.32
82 83 2.092646 AGACTTGGTAAGCCACAACACA 60.093 45.455 0.00 0.00 46.01 3.72
83 84 2.685897 GACTTGGTAAGCCACAACACAA 59.314 45.455 0.00 0.00 46.01 3.33
84 85 2.687935 ACTTGGTAAGCCACAACACAAG 59.312 45.455 0.00 0.00 46.01 3.16
85 86 1.028905 TGGTAAGCCACAACACAAGC 58.971 50.000 0.00 0.00 40.46 4.01
86 87 0.313987 GGTAAGCCACAACACAAGCC 59.686 55.000 0.00 0.00 34.09 4.35
87 88 0.313987 GTAAGCCACAACACAAGCCC 59.686 55.000 0.00 0.00 0.00 5.19
88 89 0.106469 TAAGCCACAACACAAGCCCA 60.106 50.000 0.00 0.00 0.00 5.36
89 90 0.975040 AAGCCACAACACAAGCCCAA 60.975 50.000 0.00 0.00 0.00 4.12
90 91 0.975040 AGCCACAACACAAGCCCAAA 60.975 50.000 0.00 0.00 0.00 3.28
91 92 0.107945 GCCACAACACAAGCCCAAAA 60.108 50.000 0.00 0.00 0.00 2.44
92 93 1.677217 GCCACAACACAAGCCCAAAAA 60.677 47.619 0.00 0.00 0.00 1.94
93 94 2.916640 CCACAACACAAGCCCAAAAAT 58.083 42.857 0.00 0.00 0.00 1.82
94 95 2.613133 CCACAACACAAGCCCAAAAATG 59.387 45.455 0.00 0.00 0.00 2.32
95 96 3.269178 CACAACACAAGCCCAAAAATGT 58.731 40.909 0.00 0.00 0.00 2.71
96 97 4.437239 CACAACACAAGCCCAAAAATGTA 58.563 39.130 0.00 0.00 0.00 2.29
97 98 4.872691 CACAACACAAGCCCAAAAATGTAA 59.127 37.500 0.00 0.00 0.00 2.41
98 99 5.352569 CACAACACAAGCCCAAAAATGTAAA 59.647 36.000 0.00 0.00 0.00 2.01
99 100 5.940470 ACAACACAAGCCCAAAAATGTAAAA 59.060 32.000 0.00 0.00 0.00 1.52
100 101 6.601217 ACAACACAAGCCCAAAAATGTAAAAT 59.399 30.769 0.00 0.00 0.00 1.82
101 102 7.770897 ACAACACAAGCCCAAAAATGTAAAATA 59.229 29.630 0.00 0.00 0.00 1.40
102 103 8.782144 CAACACAAGCCCAAAAATGTAAAATAT 58.218 29.630 0.00 0.00 0.00 1.28
103 104 8.916628 ACACAAGCCCAAAAATGTAAAATATT 57.083 26.923 0.00 0.00 0.00 1.28
119 120 9.214957 TGTAAAATATTACAGAACACACAGGAG 57.785 33.333 0.00 0.00 44.90 3.69
120 121 9.431887 GTAAAATATTACAGAACACACAGGAGA 57.568 33.333 0.00 0.00 40.93 3.71
122 123 8.498054 AAATATTACAGAACACACAGGAGATG 57.502 34.615 0.00 0.00 0.00 2.90
123 124 2.175878 ACAGAACACACAGGAGATGC 57.824 50.000 0.00 0.00 0.00 3.91
124 125 1.696336 ACAGAACACACAGGAGATGCT 59.304 47.619 0.00 0.00 0.00 3.79
125 126 2.899900 ACAGAACACACAGGAGATGCTA 59.100 45.455 0.00 0.00 0.00 3.49
126 127 3.324846 ACAGAACACACAGGAGATGCTAA 59.675 43.478 0.00 0.00 0.00 3.09
127 128 4.019860 ACAGAACACACAGGAGATGCTAAT 60.020 41.667 0.00 0.00 0.00 1.73
128 129 5.187772 ACAGAACACACAGGAGATGCTAATA 59.812 40.000 0.00 0.00 0.00 0.98
129 130 6.126940 ACAGAACACACAGGAGATGCTAATAT 60.127 38.462 0.00 0.00 0.00 1.28
130 131 7.069950 ACAGAACACACAGGAGATGCTAATATA 59.930 37.037 0.00 0.00 0.00 0.86
131 132 7.928167 CAGAACACACAGGAGATGCTAATATAA 59.072 37.037 0.00 0.00 0.00 0.98
132 133 8.654997 AGAACACACAGGAGATGCTAATATAAT 58.345 33.333 0.00 0.00 0.00 1.28
133 134 9.277783 GAACACACAGGAGATGCTAATATAATT 57.722 33.333 0.00 0.00 0.00 1.40
134 135 8.613060 ACACACAGGAGATGCTAATATAATTG 57.387 34.615 0.00 0.00 0.00 2.32
135 136 7.663081 ACACACAGGAGATGCTAATATAATTGG 59.337 37.037 0.00 0.00 0.00 3.16
136 137 7.879677 CACACAGGAGATGCTAATATAATTGGA 59.120 37.037 0.00 0.00 0.00 3.53
137 138 7.880195 ACACAGGAGATGCTAATATAATTGGAC 59.120 37.037 0.00 0.00 0.00 4.02
138 139 7.879677 CACAGGAGATGCTAATATAATTGGACA 59.120 37.037 0.00 0.00 0.00 4.02
139 140 8.099537 ACAGGAGATGCTAATATAATTGGACAG 58.900 37.037 0.00 0.00 0.00 3.51
140 141 8.316946 CAGGAGATGCTAATATAATTGGACAGA 58.683 37.037 0.00 0.00 0.00 3.41
141 142 8.884323 AGGAGATGCTAATATAATTGGACAGAA 58.116 33.333 0.00 0.00 0.00 3.02
142 143 9.507329 GGAGATGCTAATATAATTGGACAGAAA 57.493 33.333 0.00 0.00 0.00 2.52
144 145 9.007901 AGATGCTAATATAATTGGACAGAAAGC 57.992 33.333 0.00 0.00 0.00 3.51
145 146 8.930846 ATGCTAATATAATTGGACAGAAAGCT 57.069 30.769 0.00 0.00 0.00 3.74
151 152 9.512588 AATATAATTGGACAGAAAGCTATGGAG 57.487 33.333 0.00 0.00 0.00 3.86
167 168 6.872628 CTATGGAGCACACATTTGTATCAT 57.127 37.500 0.00 0.00 33.30 2.45
168 169 5.762825 ATGGAGCACACATTTGTATCATC 57.237 39.130 0.00 0.00 33.30 2.92
169 170 4.847198 TGGAGCACACATTTGTATCATCT 58.153 39.130 0.00 0.00 33.30 2.90
170 171 5.988287 TGGAGCACACATTTGTATCATCTA 58.012 37.500 0.00 0.00 33.30 1.98
171 172 6.051074 TGGAGCACACATTTGTATCATCTAG 58.949 40.000 0.00 0.00 33.30 2.43
172 173 6.051717 GGAGCACACATTTGTATCATCTAGT 58.948 40.000 0.00 0.00 33.30 2.57
173 174 7.147742 TGGAGCACACATTTGTATCATCTAGTA 60.148 37.037 0.00 0.00 33.30 1.82
174 175 7.875041 GGAGCACACATTTGTATCATCTAGTAT 59.125 37.037 0.00 0.00 33.30 2.12
175 176 9.914131 GAGCACACATTTGTATCATCTAGTATA 57.086 33.333 0.00 0.00 33.30 1.47
181 182 9.429359 ACATTTGTATCATCTAGTATAAGCTGC 57.571 33.333 0.00 0.00 0.00 5.25
182 183 9.428097 CATTTGTATCATCTAGTATAAGCTGCA 57.572 33.333 1.02 0.00 0.00 4.41
183 184 9.650539 ATTTGTATCATCTAGTATAAGCTGCAG 57.349 33.333 10.11 10.11 0.00 4.41
184 185 6.625362 TGTATCATCTAGTATAAGCTGCAGC 58.375 40.000 31.53 31.53 42.49 5.25
185 186 5.735285 ATCATCTAGTATAAGCTGCAGCA 57.265 39.130 38.24 21.24 45.16 4.41
186 187 5.131594 TCATCTAGTATAAGCTGCAGCAG 57.868 43.478 38.24 24.78 45.16 4.24
187 188 4.586421 TCATCTAGTATAAGCTGCAGCAGT 59.414 41.667 38.24 27.47 45.16 4.40
188 189 4.313277 TCTAGTATAAGCTGCAGCAGTG 57.687 45.455 38.24 18.80 45.16 3.66
200 201 1.825090 CAGCAGTGCAACCCATAAGA 58.175 50.000 19.20 0.00 37.80 2.10
201 202 1.741706 CAGCAGTGCAACCCATAAGAG 59.258 52.381 19.20 0.00 37.80 2.85
202 203 0.453390 GCAGTGCAACCCATAAGAGC 59.547 55.000 11.09 0.00 37.80 4.09
203 204 1.952367 GCAGTGCAACCCATAAGAGCT 60.952 52.381 11.09 0.00 37.80 4.09
204 205 2.440409 CAGTGCAACCCATAAGAGCTT 58.560 47.619 0.00 0.00 37.80 3.74
205 206 2.821969 CAGTGCAACCCATAAGAGCTTT 59.178 45.455 0.00 0.00 37.80 3.51
206 207 4.009675 CAGTGCAACCCATAAGAGCTTTA 58.990 43.478 0.00 0.00 37.80 1.85
207 208 4.095483 CAGTGCAACCCATAAGAGCTTTAG 59.905 45.833 0.00 0.00 37.80 1.85
208 209 4.010349 GTGCAACCCATAAGAGCTTTAGT 58.990 43.478 0.00 0.00 0.00 2.24
209 210 4.459337 GTGCAACCCATAAGAGCTTTAGTT 59.541 41.667 0.00 0.00 0.00 2.24
210 211 4.458989 TGCAACCCATAAGAGCTTTAGTTG 59.541 41.667 0.00 0.00 37.12 3.16
211 212 4.459337 GCAACCCATAAGAGCTTTAGTTGT 59.541 41.667 0.00 0.00 36.58 3.32
212 213 5.619981 GCAACCCATAAGAGCTTTAGTTGTG 60.620 44.000 0.00 0.00 36.58 3.33
213 214 5.499004 ACCCATAAGAGCTTTAGTTGTGA 57.501 39.130 0.00 0.00 0.00 3.58
214 215 5.876357 ACCCATAAGAGCTTTAGTTGTGAA 58.124 37.500 0.00 0.00 0.00 3.18
215 216 5.705905 ACCCATAAGAGCTTTAGTTGTGAAC 59.294 40.000 0.00 0.00 0.00 3.18
216 217 5.705441 CCCATAAGAGCTTTAGTTGTGAACA 59.295 40.000 0.00 0.00 0.00 3.18
217 218 6.206634 CCCATAAGAGCTTTAGTTGTGAACAA 59.793 38.462 0.00 0.00 0.00 2.83
232 233 7.754069 TTGTGAACAACAAAAATTAGCTCTG 57.246 32.000 0.00 0.00 45.85 3.35
314 316 1.274167 GGTACATCCACCGAAGACACA 59.726 52.381 0.00 0.00 35.97 3.72
324 326 4.527564 CACCGAAGACACAATCAAGAAAC 58.472 43.478 0.00 0.00 0.00 2.78
326 328 4.638421 ACCGAAGACACAATCAAGAAACAA 59.362 37.500 0.00 0.00 0.00 2.83
343 345 6.400568 AGAAACAAATTGCCCACATTCATAG 58.599 36.000 0.00 0.00 0.00 2.23
370 372 6.367374 TCATCTAATCCCAAACAGTGTACA 57.633 37.500 0.00 0.00 0.00 2.90
425 427 9.847224 AGAGAAAACCATAAGTCTAAAACAGAA 57.153 29.630 0.00 0.00 34.17 3.02
529 1540 0.035056 CCACAGGAGGCGAGGAAAAT 60.035 55.000 0.00 0.00 0.00 1.82
646 1657 2.449031 AATCGAGGCGGCAACAGTGA 62.449 55.000 13.08 0.00 0.00 3.41
703 1720 1.213013 GGCGAGCGAGAGAGTTTCA 59.787 57.895 0.00 0.00 0.00 2.69
747 1766 2.438434 CTCATCCAACCACGGGCC 60.438 66.667 0.00 0.00 0.00 5.80
748 1767 3.253061 TCATCCAACCACGGGCCA 61.253 61.111 4.39 0.00 0.00 5.36
749 1768 2.282816 CATCCAACCACGGGCCAA 60.283 61.111 4.39 0.00 0.00 4.52
750 1769 2.282887 ATCCAACCACGGGCCAAC 60.283 61.111 4.39 0.00 0.00 3.77
751 1770 3.879180 ATCCAACCACGGGCCAACC 62.879 63.158 4.39 0.00 0.00 3.77
752 1771 4.904590 CCAACCACGGGCCAACCA 62.905 66.667 4.39 0.00 40.22 3.67
753 1772 3.294493 CAACCACGGGCCAACCAG 61.294 66.667 4.39 0.00 40.22 4.00
754 1773 4.596585 AACCACGGGCCAACCAGG 62.597 66.667 4.39 0.62 40.22 4.45
769 1788 4.497984 AGGCCAACCACGCACACA 62.498 61.111 5.01 0.00 39.06 3.72
796 1815 5.352643 AAAGGTGGAAAGACGAAAATACG 57.647 39.130 0.00 0.00 39.31 3.06
970 1989 5.855740 AATTCCGGAGTAAACAAAACCAA 57.144 34.783 3.34 0.00 0.00 3.67
1043 2062 1.110442 CCAACAGCCGAGATCTCTCT 58.890 55.000 20.26 13.67 40.75 3.10
1085 2104 5.931724 TCAAGAACGCATCAAGACAAAGATA 59.068 36.000 0.00 0.00 0.00 1.98
1092 2111 3.928727 TCAAGACAAAGATACGACGGT 57.071 42.857 0.00 0.00 0.00 4.83
1192 2211 1.218439 TCCCCATTTCCCCATCCGTT 61.218 55.000 0.00 0.00 0.00 4.44
1194 2213 0.258774 CCCATTTCCCCATCCGTTCT 59.741 55.000 0.00 0.00 0.00 3.01
1361 2432 1.992233 GCCGCCGATTTCATCAGCAA 61.992 55.000 0.00 0.00 32.26 3.91
1672 2778 2.747855 CCCTCGCCAACCTTCAGC 60.748 66.667 0.00 0.00 0.00 4.26
1962 3119 2.185350 CTCCATGTTCGCTCGCCT 59.815 61.111 0.00 0.00 0.00 5.52
2108 3286 1.616159 ATTTGTGCGCCTAAACTGGT 58.384 45.000 4.18 0.00 0.00 4.00
2227 3429 5.067544 AGCTAGTTTCCTACACGGAGATAAC 59.932 44.000 0.00 0.00 44.28 1.89
2266 3484 4.385358 TTGTTTGTTTTCTTCAGGGAGC 57.615 40.909 0.00 0.00 0.00 4.70
2335 3553 1.483415 TCTTAGGTGTTCCGGGTATGC 59.517 52.381 0.00 0.00 39.05 3.14
2531 3774 0.885879 AACACTACGAGACGGATGCA 59.114 50.000 0.00 0.00 0.00 3.96
2594 3840 3.554960 GCCTTCAAACCCATCTCAAAACC 60.555 47.826 0.00 0.00 0.00 3.27
2707 3953 6.655078 ATTTGAAGGAATATATGGTGCCAC 57.345 37.500 0.00 0.00 0.00 5.01
2776 4022 0.396974 AGAGCTTCTCGAGATGCCCT 60.397 55.000 36.17 31.04 43.68 5.19
2789 4035 6.064060 TCGAGATGCCCTATTTGAATTCAAT 58.936 36.000 21.10 13.38 35.55 2.57
2907 5345 2.029838 AGATTGCGCTGTTCTTAGGG 57.970 50.000 9.73 0.00 0.00 3.53
2942 5381 1.349627 GCAGGCGATGTTGATGTCG 59.650 57.895 0.00 0.00 40.62 4.35
3125 5591 2.839486 TGGAGACAGCTTGTAAGTGG 57.161 50.000 0.00 0.00 35.01 4.00
3126 5592 2.047061 TGGAGACAGCTTGTAAGTGGT 58.953 47.619 0.00 0.00 35.01 4.16
3127 5593 3.236047 TGGAGACAGCTTGTAAGTGGTA 58.764 45.455 0.00 0.00 35.01 3.25
3128 5594 3.258372 TGGAGACAGCTTGTAAGTGGTAG 59.742 47.826 0.00 0.00 35.01 3.18
3129 5595 3.254892 GAGACAGCTTGTAAGTGGTAGC 58.745 50.000 0.00 0.00 0.00 3.58
3130 5596 2.028020 AGACAGCTTGTAAGTGGTAGCC 60.028 50.000 0.00 0.00 34.19 3.93
3131 5597 1.003233 ACAGCTTGTAAGTGGTAGCCC 59.997 52.381 0.00 0.00 34.19 5.19
3132 5598 0.618981 AGCTTGTAAGTGGTAGCCCC 59.381 55.000 0.00 0.00 34.19 5.80
3133 5599 0.326927 GCTTGTAAGTGGTAGCCCCA 59.673 55.000 0.00 0.00 42.51 4.96
3140 5606 3.128991 TGGTAGCCCCATCCTCCT 58.871 61.111 0.00 0.00 38.72 3.69
3141 5607 2.349543 TGGTAGCCCCATCCTCCTA 58.650 57.895 0.00 0.00 38.72 2.94
3142 5608 0.191064 TGGTAGCCCCATCCTCCTAG 59.809 60.000 0.00 0.00 38.72 3.02
3143 5609 0.545548 GGTAGCCCCATCCTCCTAGG 60.546 65.000 0.82 0.82 36.46 3.02
3144 5610 0.545548 GTAGCCCCATCCTCCTAGGG 60.546 65.000 9.46 0.00 42.94 3.53
3145 5611 1.010602 TAGCCCCATCCTCCTAGGGT 61.011 60.000 9.46 0.00 41.99 4.34
3146 5612 1.843832 GCCCCATCCTCCTAGGGTC 60.844 68.421 9.46 0.00 41.99 4.46
3147 5613 1.950244 CCCCATCCTCCTAGGGTCT 59.050 63.158 9.46 0.00 41.16 3.85
3148 5614 0.269173 CCCCATCCTCCTAGGGTCTT 59.731 60.000 9.46 0.00 41.16 3.01
3149 5615 1.508185 CCCCATCCTCCTAGGGTCTTA 59.492 57.143 9.46 0.00 41.16 2.10
3150 5616 2.114506 CCCCATCCTCCTAGGGTCTTAT 59.885 54.545 9.46 0.00 41.16 1.73
3151 5617 3.445987 CCCATCCTCCTAGGGTCTTATC 58.554 54.545 9.46 0.00 37.81 1.75
3152 5618 3.445987 CCATCCTCCTAGGGTCTTATCC 58.554 54.545 9.46 0.00 35.59 2.59
3153 5619 3.078305 CCATCCTCCTAGGGTCTTATCCT 59.922 52.174 9.46 0.00 35.59 3.24
3230 5743 6.255215 TGTGTCGAAAACTTCATTGTCTTTC 58.745 36.000 0.00 0.00 0.00 2.62
3380 5897 5.810095 AGGAAGGAGAGGTTTCTGTTATTG 58.190 41.667 0.00 0.00 32.53 1.90
3515 6041 2.789409 AGGACCTGCATCTTGGTAAC 57.211 50.000 0.00 0.00 36.59 2.50
3526 6052 4.345257 GCATCTTGGTAACTGATCCTCCTA 59.655 45.833 0.00 0.00 37.61 2.94
3538 6064 2.198980 CTCCTACCTCCCCTCCCG 59.801 72.222 0.00 0.00 0.00 5.14
3571 6097 4.458295 GCATCTTGGTATAGTCGCCTACTA 59.542 45.833 0.00 0.00 44.76 1.82
3637 6164 3.489416 TGATTCGATCGCCATCTTTTACG 59.511 43.478 20.95 0.00 0.00 3.18
3681 6208 2.163818 TCCTGTACCAAGAAACAGCG 57.836 50.000 0.00 0.00 41.45 5.18
3684 6211 3.069872 TCCTGTACCAAGAAACAGCGTTA 59.930 43.478 0.00 0.00 41.45 3.18
3687 6214 4.890088 TGTACCAAGAAACAGCGTTAGAT 58.110 39.130 0.00 0.00 0.00 1.98
3688 6215 5.302360 TGTACCAAGAAACAGCGTTAGATT 58.698 37.500 0.00 0.00 0.00 2.40
3689 6216 4.749245 ACCAAGAAACAGCGTTAGATTG 57.251 40.909 0.00 2.02 0.00 2.67
3690 6217 3.502211 ACCAAGAAACAGCGTTAGATTGG 59.498 43.478 18.91 18.91 41.33 3.16
3691 6218 3.119849 CCAAGAAACAGCGTTAGATTGGG 60.120 47.826 15.90 0.00 33.82 4.12
3692 6219 2.084546 AGAAACAGCGTTAGATTGGGC 58.915 47.619 0.00 0.00 0.00 5.36
3693 6220 1.810151 GAAACAGCGTTAGATTGGGCA 59.190 47.619 0.00 0.00 0.00 5.36
3694 6221 2.128771 AACAGCGTTAGATTGGGCAT 57.871 45.000 0.00 0.00 0.00 4.40
3732 6259 1.463674 AGATGATGTTGGTTTCGGCC 58.536 50.000 0.00 0.00 0.00 6.13
3756 6294 1.068055 GGTTATCCTCGTGTCGTGTGT 60.068 52.381 0.00 0.00 0.00 3.72
3757 6295 1.983605 GTTATCCTCGTGTCGTGTGTG 59.016 52.381 0.00 0.00 0.00 3.82
3758 6296 0.109458 TATCCTCGTGTCGTGTGTGC 60.109 55.000 0.00 0.00 0.00 4.57
3759 6297 2.765250 ATCCTCGTGTCGTGTGTGCC 62.765 60.000 0.00 0.00 0.00 5.01
3760 6298 3.394874 CTCGTGTCGTGTGTGCCG 61.395 66.667 0.00 0.00 0.00 5.69
3763 6301 3.269347 GTGTCGTGTGTGCCGCTT 61.269 61.111 0.00 0.00 0.00 4.68
3764 6302 3.268603 TGTCGTGTGTGCCGCTTG 61.269 61.111 0.00 0.00 0.00 4.01
3793 6332 3.870419 TCAACTTGTTTTTCTGCATTGCC 59.130 39.130 6.12 0.00 0.00 4.52
3806 6345 0.867086 CATTGCCGTTTGCCAAAAGG 59.133 50.000 16.58 16.58 42.08 3.11
3817 6356 3.733443 TGCCAAAAGGAAAGAGAAAGC 57.267 42.857 0.00 0.00 0.00 3.51
3820 6359 3.068732 GCCAAAAGGAAAGAGAAAGCTGT 59.931 43.478 0.00 0.00 0.00 4.40
3839 6730 3.446799 TGTTTTTCTGCATTGCTGACAC 58.553 40.909 16.67 13.71 36.32 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.025360 TGGCCAGTTCATATGAAGCAAAT 58.975 39.130 18.47 0.00 34.27 2.32
2 3 3.084536 TGGCCAGTTCATATGAAGCAA 57.915 42.857 18.47 9.52 34.27 3.91
3 4 2.754552 GTTGGCCAGTTCATATGAAGCA 59.245 45.455 18.47 7.16 34.27 3.91
5 6 3.629398 GGAGTTGGCCAGTTCATATGAAG 59.371 47.826 18.47 8.44 34.27 3.02
6 7 3.010027 TGGAGTTGGCCAGTTCATATGAA 59.990 43.478 14.23 14.23 33.10 2.57
7 8 2.575735 TGGAGTTGGCCAGTTCATATGA 59.424 45.455 17.33 0.00 33.10 2.15
8 9 2.684881 GTGGAGTTGGCCAGTTCATATG 59.315 50.000 17.33 0.00 38.95 1.78
10 11 1.702401 TGTGGAGTTGGCCAGTTCATA 59.298 47.619 17.33 5.97 38.95 2.15
11 12 0.478072 TGTGGAGTTGGCCAGTTCAT 59.522 50.000 17.33 0.00 38.95 2.57
12 13 0.465460 GTGTGGAGTTGGCCAGTTCA 60.465 55.000 17.33 7.37 38.95 3.18
13 14 0.465460 TGTGTGGAGTTGGCCAGTTC 60.465 55.000 5.11 7.84 38.95 3.01
14 15 0.033601 TTGTGTGGAGTTGGCCAGTT 60.034 50.000 5.11 0.00 38.95 3.16
15 16 0.033601 TTTGTGTGGAGTTGGCCAGT 60.034 50.000 5.11 0.00 38.95 4.00
16 17 1.110442 TTTTGTGTGGAGTTGGCCAG 58.890 50.000 5.11 0.00 38.95 4.85
17 18 1.561643 TTTTTGTGTGGAGTTGGCCA 58.438 45.000 0.00 0.00 35.02 5.36
42 43 9.541143 CCAAGTCTAATGTTTGTATTGGTTTTT 57.459 29.630 0.00 0.00 33.00 1.94
43 44 8.700973 ACCAAGTCTAATGTTTGTATTGGTTTT 58.299 29.630 0.58 0.00 45.07 2.43
44 45 8.245195 ACCAAGTCTAATGTTTGTATTGGTTT 57.755 30.769 0.58 0.00 45.07 3.27
45 46 7.833285 ACCAAGTCTAATGTTTGTATTGGTT 57.167 32.000 0.58 0.00 45.07 3.67
47 48 7.968405 GCTTACCAAGTCTAATGTTTGTATTGG 59.032 37.037 0.00 0.00 41.33 3.16
48 49 7.968405 GGCTTACCAAGTCTAATGTTTGTATTG 59.032 37.037 0.00 0.00 35.26 1.90
49 50 7.668052 TGGCTTACCAAGTCTAATGTTTGTATT 59.332 33.333 0.00 0.00 45.37 1.89
50 51 7.172342 TGGCTTACCAAGTCTAATGTTTGTAT 58.828 34.615 0.00 0.00 45.37 2.29
51 52 6.535540 TGGCTTACCAAGTCTAATGTTTGTA 58.464 36.000 0.00 0.00 45.37 2.41
52 53 5.381757 TGGCTTACCAAGTCTAATGTTTGT 58.618 37.500 0.00 0.00 45.37 2.83
53 54 5.957842 TGGCTTACCAAGTCTAATGTTTG 57.042 39.130 0.00 0.00 45.37 2.93
66 67 1.028905 GCTTGTGTTGTGGCTTACCA 58.971 50.000 0.00 0.00 46.51 3.25
67 68 0.313987 GGCTTGTGTTGTGGCTTACC 59.686 55.000 0.00 0.00 0.00 2.85
68 69 0.313987 GGGCTTGTGTTGTGGCTTAC 59.686 55.000 0.00 0.00 0.00 2.34
69 70 0.106469 TGGGCTTGTGTTGTGGCTTA 60.106 50.000 0.00 0.00 0.00 3.09
70 71 0.975040 TTGGGCTTGTGTTGTGGCTT 60.975 50.000 0.00 0.00 0.00 4.35
71 72 0.975040 TTTGGGCTTGTGTTGTGGCT 60.975 50.000 0.00 0.00 0.00 4.75
72 73 0.107945 TTTTGGGCTTGTGTTGTGGC 60.108 50.000 0.00 0.00 0.00 5.01
73 74 2.393271 TTTTTGGGCTTGTGTTGTGG 57.607 45.000 0.00 0.00 0.00 4.17
74 75 3.269178 ACATTTTTGGGCTTGTGTTGTG 58.731 40.909 0.00 0.00 0.00 3.33
75 76 3.625649 ACATTTTTGGGCTTGTGTTGT 57.374 38.095 0.00 0.00 0.00 3.32
76 77 6.428385 TTTTACATTTTTGGGCTTGTGTTG 57.572 33.333 0.00 0.00 0.00 3.33
77 78 8.916628 ATATTTTACATTTTTGGGCTTGTGTT 57.083 26.923 0.00 0.00 0.00 3.32
78 79 8.916628 AATATTTTACATTTTTGGGCTTGTGT 57.083 26.923 0.00 0.00 0.00 3.72
92 93 9.733556 TCCTGTGTGTTCTGTAATATTTTACAT 57.266 29.630 8.88 0.00 44.99 2.29
93 94 9.214957 CTCCTGTGTGTTCTGTAATATTTTACA 57.785 33.333 8.25 8.25 44.16 2.41
94 95 9.431887 TCTCCTGTGTGTTCTGTAATATTTTAC 57.568 33.333 0.00 0.00 38.56 2.01
96 97 8.950210 CATCTCCTGTGTGTTCTGTAATATTTT 58.050 33.333 0.00 0.00 0.00 1.82
97 98 7.066284 GCATCTCCTGTGTGTTCTGTAATATTT 59.934 37.037 0.00 0.00 0.00 1.40
98 99 6.540189 GCATCTCCTGTGTGTTCTGTAATATT 59.460 38.462 0.00 0.00 0.00 1.28
99 100 6.051717 GCATCTCCTGTGTGTTCTGTAATAT 58.948 40.000 0.00 0.00 0.00 1.28
100 101 5.187772 AGCATCTCCTGTGTGTTCTGTAATA 59.812 40.000 0.00 0.00 0.00 0.98
101 102 4.019860 AGCATCTCCTGTGTGTTCTGTAAT 60.020 41.667 0.00 0.00 0.00 1.89
102 103 3.324846 AGCATCTCCTGTGTGTTCTGTAA 59.675 43.478 0.00 0.00 0.00 2.41
103 104 2.899900 AGCATCTCCTGTGTGTTCTGTA 59.100 45.455 0.00 0.00 0.00 2.74
104 105 1.696336 AGCATCTCCTGTGTGTTCTGT 59.304 47.619 0.00 0.00 0.00 3.41
105 106 2.469274 AGCATCTCCTGTGTGTTCTG 57.531 50.000 0.00 0.00 0.00 3.02
106 107 4.833478 ATTAGCATCTCCTGTGTGTTCT 57.167 40.909 0.00 0.00 0.00 3.01
107 108 8.839310 ATTATATTAGCATCTCCTGTGTGTTC 57.161 34.615 0.00 0.00 0.00 3.18
108 109 9.060347 CAATTATATTAGCATCTCCTGTGTGTT 57.940 33.333 0.00 0.00 0.00 3.32
109 110 7.663081 CCAATTATATTAGCATCTCCTGTGTGT 59.337 37.037 0.00 0.00 0.00 3.72
110 111 7.879677 TCCAATTATATTAGCATCTCCTGTGTG 59.120 37.037 0.00 0.00 0.00 3.82
111 112 7.880195 GTCCAATTATATTAGCATCTCCTGTGT 59.120 37.037 0.00 0.00 0.00 3.72
112 113 7.879677 TGTCCAATTATATTAGCATCTCCTGTG 59.120 37.037 0.00 0.00 0.00 3.66
113 114 7.977818 TGTCCAATTATATTAGCATCTCCTGT 58.022 34.615 0.00 0.00 0.00 4.00
114 115 8.316946 TCTGTCCAATTATATTAGCATCTCCTG 58.683 37.037 0.00 0.00 0.00 3.86
115 116 8.441311 TCTGTCCAATTATATTAGCATCTCCT 57.559 34.615 0.00 0.00 0.00 3.69
116 117 9.507329 TTTCTGTCCAATTATATTAGCATCTCC 57.493 33.333 0.00 0.00 0.00 3.71
118 119 9.007901 GCTTTCTGTCCAATTATATTAGCATCT 57.992 33.333 0.00 0.00 0.00 2.90
119 120 9.007901 AGCTTTCTGTCCAATTATATTAGCATC 57.992 33.333 0.00 0.00 0.00 3.91
120 121 8.930846 AGCTTTCTGTCCAATTATATTAGCAT 57.069 30.769 0.00 0.00 0.00 3.79
125 126 9.512588 CTCCATAGCTTTCTGTCCAATTATATT 57.487 33.333 0.00 0.00 0.00 1.28
126 127 7.609532 GCTCCATAGCTTTCTGTCCAATTATAT 59.390 37.037 0.00 0.00 45.85 0.86
127 128 6.936900 GCTCCATAGCTTTCTGTCCAATTATA 59.063 38.462 0.00 0.00 45.85 0.98
128 129 5.767168 GCTCCATAGCTTTCTGTCCAATTAT 59.233 40.000 0.00 0.00 45.85 1.28
129 130 5.126067 GCTCCATAGCTTTCTGTCCAATTA 58.874 41.667 0.00 0.00 45.85 1.40
130 131 3.950395 GCTCCATAGCTTTCTGTCCAATT 59.050 43.478 0.00 0.00 45.85 2.32
131 132 3.549794 GCTCCATAGCTTTCTGTCCAAT 58.450 45.455 0.00 0.00 45.85 3.16
132 133 2.991250 GCTCCATAGCTTTCTGTCCAA 58.009 47.619 0.00 0.00 45.85 3.53
133 134 2.698855 GCTCCATAGCTTTCTGTCCA 57.301 50.000 0.00 0.00 45.85 4.02
144 145 6.709397 AGATGATACAAATGTGTGCTCCATAG 59.291 38.462 0.00 0.00 38.82 2.23
145 146 6.594744 AGATGATACAAATGTGTGCTCCATA 58.405 36.000 0.00 0.00 38.82 2.74
146 147 5.443283 AGATGATACAAATGTGTGCTCCAT 58.557 37.500 0.00 0.00 38.82 3.41
147 148 4.847198 AGATGATACAAATGTGTGCTCCA 58.153 39.130 0.00 0.00 38.82 3.86
148 149 6.051717 ACTAGATGATACAAATGTGTGCTCC 58.948 40.000 0.00 0.00 38.82 4.70
149 150 8.824159 ATACTAGATGATACAAATGTGTGCTC 57.176 34.615 0.00 0.00 38.82 4.26
155 156 9.429359 GCAGCTTATACTAGATGATACAAATGT 57.571 33.333 0.00 0.00 33.46 2.71
156 157 9.428097 TGCAGCTTATACTAGATGATACAAATG 57.572 33.333 0.00 0.00 33.46 2.32
157 158 9.650539 CTGCAGCTTATACTAGATGATACAAAT 57.349 33.333 0.00 0.00 33.46 2.32
158 159 7.600375 GCTGCAGCTTATACTAGATGATACAAA 59.400 37.037 31.33 0.00 33.46 2.83
159 160 7.093354 GCTGCAGCTTATACTAGATGATACAA 58.907 38.462 31.33 0.00 33.46 2.41
160 161 6.209391 TGCTGCAGCTTATACTAGATGATACA 59.791 38.462 36.61 9.39 42.66 2.29
161 162 6.625362 TGCTGCAGCTTATACTAGATGATAC 58.375 40.000 36.61 4.35 42.66 2.24
162 163 6.435591 ACTGCTGCAGCTTATACTAGATGATA 59.564 38.462 36.61 11.82 42.66 2.15
163 164 5.245751 ACTGCTGCAGCTTATACTAGATGAT 59.754 40.000 36.61 7.52 42.66 2.45
164 165 4.586421 ACTGCTGCAGCTTATACTAGATGA 59.414 41.667 36.61 12.92 42.66 2.92
165 166 4.685165 CACTGCTGCAGCTTATACTAGATG 59.315 45.833 36.61 19.48 42.66 2.90
166 167 4.798924 GCACTGCTGCAGCTTATACTAGAT 60.799 45.833 36.61 13.17 43.62 1.98
167 168 3.491619 GCACTGCTGCAGCTTATACTAGA 60.492 47.826 36.61 14.40 43.62 2.43
168 169 2.799412 GCACTGCTGCAGCTTATACTAG 59.201 50.000 36.61 25.74 43.62 2.57
169 170 2.826428 GCACTGCTGCAGCTTATACTA 58.174 47.619 36.61 15.90 43.62 1.82
170 171 1.661341 GCACTGCTGCAGCTTATACT 58.339 50.000 36.61 11.73 43.62 2.12
180 181 0.171903 CTTATGGGTTGCACTGCTGC 59.828 55.000 1.98 0.00 44.52 5.25
181 182 1.741706 CTCTTATGGGTTGCACTGCTG 59.258 52.381 1.98 0.00 0.00 4.41
182 183 1.952367 GCTCTTATGGGTTGCACTGCT 60.952 52.381 1.98 0.00 0.00 4.24
183 184 0.453390 GCTCTTATGGGTTGCACTGC 59.547 55.000 0.00 0.00 0.00 4.40
184 185 2.119801 AGCTCTTATGGGTTGCACTG 57.880 50.000 0.00 0.00 0.00 3.66
185 186 2.887151 AAGCTCTTATGGGTTGCACT 57.113 45.000 0.00 0.00 0.00 4.40
186 187 4.010349 ACTAAAGCTCTTATGGGTTGCAC 58.990 43.478 0.00 0.00 0.00 4.57
187 188 4.301072 ACTAAAGCTCTTATGGGTTGCA 57.699 40.909 0.00 0.00 0.00 4.08
188 189 4.459337 ACAACTAAAGCTCTTATGGGTTGC 59.541 41.667 0.00 0.00 37.06 4.17
189 190 5.705441 TCACAACTAAAGCTCTTATGGGTTG 59.295 40.000 0.00 0.00 38.75 3.77
190 191 5.876357 TCACAACTAAAGCTCTTATGGGTT 58.124 37.500 0.00 0.00 0.00 4.11
191 192 5.499004 TCACAACTAAAGCTCTTATGGGT 57.501 39.130 0.00 0.00 0.00 4.51
192 193 5.705441 TGTTCACAACTAAAGCTCTTATGGG 59.295 40.000 0.00 0.00 0.00 4.00
193 194 6.801539 TGTTCACAACTAAAGCTCTTATGG 57.198 37.500 0.00 0.00 0.00 2.74
208 209 7.275341 CACAGAGCTAATTTTTGTTGTTCACAA 59.725 33.333 0.00 0.00 44.11 3.33
209 210 6.751425 CACAGAGCTAATTTTTGTTGTTCACA 59.249 34.615 0.00 0.00 0.00 3.58
210 211 6.291796 GCACAGAGCTAATTTTTGTTGTTCAC 60.292 38.462 0.00 0.00 41.15 3.18
211 212 5.748152 GCACAGAGCTAATTTTTGTTGTTCA 59.252 36.000 0.00 0.00 41.15 3.18
212 213 5.748152 TGCACAGAGCTAATTTTTGTTGTTC 59.252 36.000 0.00 0.00 45.94 3.18
213 214 5.659463 TGCACAGAGCTAATTTTTGTTGTT 58.341 33.333 0.00 0.00 45.94 2.83
214 215 5.163519 ACTGCACAGAGCTAATTTTTGTTGT 60.164 36.000 4.31 0.00 45.94 3.32
215 216 5.174398 CACTGCACAGAGCTAATTTTTGTTG 59.826 40.000 4.31 0.00 45.94 3.33
216 217 5.067674 TCACTGCACAGAGCTAATTTTTGTT 59.932 36.000 4.31 0.00 45.94 2.83
217 218 4.580167 TCACTGCACAGAGCTAATTTTTGT 59.420 37.500 4.31 0.00 45.94 2.83
218 219 5.112220 TCACTGCACAGAGCTAATTTTTG 57.888 39.130 4.31 0.00 45.94 2.44
219 220 5.067674 TGTTCACTGCACAGAGCTAATTTTT 59.932 36.000 4.31 0.00 45.94 1.94
220 221 4.580167 TGTTCACTGCACAGAGCTAATTTT 59.420 37.500 4.31 0.00 45.94 1.82
221 222 4.136796 TGTTCACTGCACAGAGCTAATTT 58.863 39.130 4.31 0.00 45.94 1.82
222 223 3.743521 TGTTCACTGCACAGAGCTAATT 58.256 40.909 4.31 0.00 45.94 1.40
223 224 3.407424 TGTTCACTGCACAGAGCTAAT 57.593 42.857 4.31 0.00 45.94 1.73
224 225 2.908688 TGTTCACTGCACAGAGCTAA 57.091 45.000 4.31 0.00 45.94 3.09
225 226 2.908688 TTGTTCACTGCACAGAGCTA 57.091 45.000 4.31 0.00 45.94 3.32
232 233 4.488126 TTAGATGCTTTGTTCACTGCAC 57.512 40.909 0.00 0.00 38.29 4.57
301 303 2.766313 TCTTGATTGTGTCTTCGGTGG 58.234 47.619 0.00 0.00 0.00 4.61
306 308 7.339953 GCAATTTGTTTCTTGATTGTGTCTTC 58.660 34.615 0.00 0.00 33.25 2.87
314 316 5.033589 TGTGGGCAATTTGTTTCTTGATT 57.966 34.783 0.00 0.00 0.00 2.57
324 326 5.327616 TGACTATGAATGTGGGCAATTTG 57.672 39.130 0.00 0.00 0.00 2.32
326 328 5.202765 TGATGACTATGAATGTGGGCAATT 58.797 37.500 0.00 0.00 0.00 2.32
343 345 5.882557 ACACTGTTTGGGATTAGATGATGAC 59.117 40.000 0.00 0.00 0.00 3.06
415 417 1.957877 TGCCCCGGTTTTCTGTTTTAG 59.042 47.619 0.00 0.00 0.00 1.85
417 419 1.134640 GTTGCCCCGGTTTTCTGTTTT 60.135 47.619 0.00 0.00 0.00 2.43
418 420 0.462375 GTTGCCCCGGTTTTCTGTTT 59.538 50.000 0.00 0.00 0.00 2.83
419 421 1.730451 CGTTGCCCCGGTTTTCTGTT 61.730 55.000 0.00 0.00 0.00 3.16
420 422 2.190841 CGTTGCCCCGGTTTTCTGT 61.191 57.895 0.00 0.00 0.00 3.41
421 423 1.852067 CTCGTTGCCCCGGTTTTCTG 61.852 60.000 0.00 0.00 0.00 3.02
423 425 2.951458 CTCGTTGCCCCGGTTTTC 59.049 61.111 0.00 0.00 0.00 2.29
425 427 4.572571 TGCTCGTTGCCCCGGTTT 62.573 61.111 0.00 0.00 42.00 3.27
529 1540 2.366533 AGCTTCACCTCGTCGATCTAA 58.633 47.619 0.00 0.00 0.00 2.10
627 1638 2.034879 CACTGTTGCCGCCTCGATT 61.035 57.895 0.00 0.00 0.00 3.34
646 1657 2.215196 GTACTTCTCTCGCTCGATCCT 58.785 52.381 0.00 0.00 0.00 3.24
680 1697 2.124109 TCTCTCGCTCGCCCAGAT 60.124 61.111 0.00 0.00 0.00 2.90
681 1698 2.826287 CTCTCTCGCTCGCCCAGA 60.826 66.667 0.00 0.00 0.00 3.86
747 1766 3.977244 GCGTGGTTGGCCTGGTTG 61.977 66.667 3.32 0.00 35.27 3.77
748 1767 4.514585 TGCGTGGTTGGCCTGGTT 62.515 61.111 3.32 0.00 35.27 3.67
751 1770 3.964875 GTGTGCGTGGTTGGCCTG 61.965 66.667 3.32 0.00 35.27 4.85
752 1771 4.497984 TGTGTGCGTGGTTGGCCT 62.498 61.111 3.32 0.00 35.27 5.19
753 1772 3.964875 CTGTGTGCGTGGTTGGCC 61.965 66.667 0.00 0.00 0.00 5.36
754 1773 3.964875 CCTGTGTGCGTGGTTGGC 61.965 66.667 0.00 0.00 0.00 4.52
755 1774 3.964875 GCCTGTGTGCGTGGTTGG 61.965 66.667 0.00 0.00 0.00 3.77
769 1788 1.133915 TCGTCTTTCCACCTTTTGCCT 60.134 47.619 0.00 0.00 0.00 4.75
905 1924 2.298661 GGGTCGATTCCTGGTGGGT 61.299 63.158 0.00 0.00 36.25 4.51
970 1989 4.600062 AGCTTCCATCCGGTTTTTCTTAT 58.400 39.130 0.00 0.00 0.00 1.73
980 1999 4.543590 ATGAATAGTAGCTTCCATCCGG 57.456 45.455 0.00 0.00 0.00 5.14
1043 2062 0.108207 GACGGTAGGATCTCCCTCGA 59.892 60.000 9.42 0.00 43.31 4.04
1048 2067 3.439895 GTTCTTGACGGTAGGATCTCC 57.560 52.381 0.00 0.00 0.00 3.71
1085 2104 2.707849 CCGGATTCCTGACCGTCGT 61.708 63.158 0.00 0.00 46.53 4.34
1672 2778 1.655654 CGTAGCCGACATCGAGCTG 60.656 63.158 20.44 0.00 42.60 4.24
2108 3286 3.270960 AGGTAACAAAGGGCCCAATATCA 59.729 43.478 27.56 0.99 41.41 2.15
2266 3484 3.862124 CCAAGTCGGCTGAACTCG 58.138 61.111 0.00 0.00 0.00 4.18
2335 3553 8.930846 AAGGATATTAAGAACTCCATCCAATG 57.069 34.615 0.00 0.00 35.44 2.82
2531 3774 4.273480 CGGTCATATTGAGGCTCGATTTTT 59.727 41.667 21.91 5.74 0.00 1.94
2594 3840 2.781101 CACGAATGTTTCAAACACCACG 59.219 45.455 4.73 13.40 45.50 4.94
2776 4022 9.218440 TGCGATATCTGCTATTGAATTCAAATA 57.782 29.630 23.91 15.63 39.55 1.40
2907 5345 2.195922 CTGCAAAACAAGCACAAGACC 58.804 47.619 0.00 0.00 37.02 3.85
2942 5381 3.126858 TGCGGAAGACAGTGCAATTATTC 59.873 43.478 0.00 0.00 33.80 1.75
3022 5464 4.139038 TCTTGCAGTTTTAACAGGGGTAC 58.861 43.478 0.00 0.00 0.00 3.34
3124 5590 0.545548 CCTAGGAGGATGGGGCTACC 60.546 65.000 1.05 0.00 37.67 3.18
3125 5591 0.545548 CCCTAGGAGGATGGGGCTAC 60.546 65.000 11.48 0.00 37.67 3.58
3126 5592 1.010602 ACCCTAGGAGGATGGGGCTA 61.011 60.000 11.48 0.00 44.73 3.93
3127 5593 2.333695 GACCCTAGGAGGATGGGGCT 62.334 65.000 11.48 0.00 44.73 5.19
3128 5594 1.843832 GACCCTAGGAGGATGGGGC 60.844 68.421 11.48 0.00 44.73 5.80
3129 5595 0.269173 AAGACCCTAGGAGGATGGGG 59.731 60.000 11.48 0.00 46.26 4.96
3130 5596 3.445987 GATAAGACCCTAGGAGGATGGG 58.554 54.545 11.48 0.00 46.07 4.00
3131 5597 3.078305 AGGATAAGACCCTAGGAGGATGG 59.922 52.174 11.48 0.00 37.67 3.51
3132 5598 4.093011 CAGGATAAGACCCTAGGAGGATG 58.907 52.174 11.48 0.00 37.67 3.51
3133 5599 3.503227 GCAGGATAAGACCCTAGGAGGAT 60.503 52.174 11.48 0.00 37.67 3.24
3134 5600 2.158295 GCAGGATAAGACCCTAGGAGGA 60.158 54.545 11.48 0.00 37.67 3.71
3135 5601 2.252714 GCAGGATAAGACCCTAGGAGG 58.747 57.143 11.48 0.00 34.30 4.30
3136 5602 2.630580 GTGCAGGATAAGACCCTAGGAG 59.369 54.545 11.48 2.69 31.64 3.69
3137 5603 2.023404 TGTGCAGGATAAGACCCTAGGA 60.023 50.000 11.48 0.00 31.64 2.94
3138 5604 2.398588 TGTGCAGGATAAGACCCTAGG 58.601 52.381 0.06 0.06 31.64 3.02
3139 5605 4.696479 ATTGTGCAGGATAAGACCCTAG 57.304 45.455 0.00 0.00 31.64 3.02
3140 5606 4.227300 ACAATTGTGCAGGATAAGACCCTA 59.773 41.667 11.07 0.00 31.64 3.53
3141 5607 3.010584 ACAATTGTGCAGGATAAGACCCT 59.989 43.478 11.07 0.00 0.00 4.34
3142 5608 3.356290 ACAATTGTGCAGGATAAGACCC 58.644 45.455 11.07 0.00 0.00 4.46
3143 5609 5.391312 AAACAATTGTGCAGGATAAGACC 57.609 39.130 12.82 0.00 0.00 3.85
3144 5610 6.974622 CCATAAACAATTGTGCAGGATAAGAC 59.025 38.462 12.82 0.00 0.00 3.01
3145 5611 6.405731 GCCATAAACAATTGTGCAGGATAAGA 60.406 38.462 12.82 0.00 0.00 2.10
3146 5612 5.750067 GCCATAAACAATTGTGCAGGATAAG 59.250 40.000 12.82 0.00 0.00 1.73
3147 5613 5.421693 AGCCATAAACAATTGTGCAGGATAA 59.578 36.000 12.82 0.00 0.00 1.75
3148 5614 4.955450 AGCCATAAACAATTGTGCAGGATA 59.045 37.500 12.82 0.00 0.00 2.59
3149 5615 3.770933 AGCCATAAACAATTGTGCAGGAT 59.229 39.130 12.82 8.11 0.00 3.24
3150 5616 3.164268 AGCCATAAACAATTGTGCAGGA 58.836 40.909 12.82 0.00 0.00 3.86
3151 5617 3.598019 AGCCATAAACAATTGTGCAGG 57.402 42.857 12.82 12.72 0.00 4.85
3152 5618 4.377635 GCAAAGCCATAAACAATTGTGCAG 60.378 41.667 12.82 6.28 0.00 4.41
3153 5619 3.497640 GCAAAGCCATAAACAATTGTGCA 59.502 39.130 12.82 3.19 0.00 4.57
3230 5743 4.550831 CGCGCTTTTCTATGTGATAACTGG 60.551 45.833 5.56 0.00 0.00 4.00
3276 5790 7.543868 AGATTCTGTATGAACACTCGAAGAAAG 59.456 37.037 0.00 0.00 37.52 2.62
3380 5897 4.006319 AGCAAAACTTGAGCCTGATAGAC 58.994 43.478 0.00 0.00 0.00 2.59
3494 6020 3.010420 GTTACCAAGATGCAGGTCCTTC 58.990 50.000 0.00 0.00 39.31 3.46
3515 6041 0.863956 AGGGGAGGTAGGAGGATCAG 59.136 60.000 0.00 0.00 36.25 2.90
3538 6064 3.207669 CAAGATGCTGAGCGGGGC 61.208 66.667 0.00 0.00 0.00 5.80
3542 6068 3.312828 GACTATACCAAGATGCTGAGCG 58.687 50.000 0.00 0.00 0.00 5.03
3571 6097 4.384647 GGATGAAAGATCAACTACCAGGCT 60.385 45.833 0.00 0.00 39.49 4.58
3681 6208 2.110578 AGCCCAAATGCCCAATCTAAC 58.889 47.619 0.00 0.00 0.00 2.34
3684 6211 2.548464 TAAGCCCAAATGCCCAATCT 57.452 45.000 0.00 0.00 0.00 2.40
3687 6214 1.203237 TCCTTAAGCCCAAATGCCCAA 60.203 47.619 0.00 0.00 0.00 4.12
3688 6215 0.411452 TCCTTAAGCCCAAATGCCCA 59.589 50.000 0.00 0.00 0.00 5.36
3689 6216 0.824109 GTCCTTAAGCCCAAATGCCC 59.176 55.000 0.00 0.00 0.00 5.36
3690 6217 0.824109 GGTCCTTAAGCCCAAATGCC 59.176 55.000 0.00 0.00 0.00 4.40
3691 6218 1.478105 CAGGTCCTTAAGCCCAAATGC 59.522 52.381 10.89 0.00 0.00 3.56
3692 6219 3.085952 TCAGGTCCTTAAGCCCAAATG 57.914 47.619 10.89 2.83 0.00 2.32
3693 6220 3.333680 TCTTCAGGTCCTTAAGCCCAAAT 59.666 43.478 7.83 0.00 0.00 2.32
3694 6221 2.714250 TCTTCAGGTCCTTAAGCCCAAA 59.286 45.455 7.83 5.24 0.00 3.28
3732 6259 1.065102 ACGACACGAGGATAACCATCG 59.935 52.381 8.58 8.58 40.18 3.84
3761 6299 0.661187 AACAAGTTGATGCGCGCAAG 60.661 50.000 39.68 21.98 43.44 4.01
3762 6300 0.248825 AAACAAGTTGATGCGCGCAA 60.249 45.000 39.68 21.19 0.00 4.85
3763 6301 0.248825 AAAACAAGTTGATGCGCGCA 60.249 45.000 38.27 38.27 0.00 6.09
3764 6302 0.852136 AAAAACAAGTTGATGCGCGC 59.148 45.000 27.26 27.26 0.00 6.86
3793 6332 3.708563 TCTCTTTCCTTTTGGCAAACG 57.291 42.857 13.10 11.00 40.12 3.60
3806 6345 5.343249 TGCAGAAAAACAGCTTTCTCTTTC 58.657 37.500 0.00 0.00 42.47 2.62
3817 6356 3.488310 GTGTCAGCAATGCAGAAAAACAG 59.512 43.478 8.35 0.00 0.00 3.16
3820 6359 3.380954 TCTGTGTCAGCAATGCAGAAAAA 59.619 39.130 8.35 0.00 33.84 1.94


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

AutoCloner maintained by Alex Coulton.