Multiple sequence alignment - TraesCS6D01G188400

Loading Multiple Alignment...

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 TraesCS6D01G188400 chr6D 100.000 2369 0 0 1 2369 256722534 256720166 0.000000e+00 4375.0
1 TraesCS6D01G188400 chr6D 94.348 1327 49 9 219 1521 365432501 365433825 0.000000e+00 2012.0
2 TraesCS6D01G188400 chr6D 96.619 1124 20 5 414 1521 325816197 325815076 0.000000e+00 1849.0
3 TraesCS6D01G188400 chr6D 95.154 1135 26 8 414 1521 237084704 237085836 0.000000e+00 1764.0
4 TraesCS6D01G188400 chr6D 94.451 847 47 0 1523 2369 51482018 51481172 0.000000e+00 1304.0
5 TraesCS6D01G188400 chr6D 93.655 851 50 1 1523 2369 293102317 293101467 0.000000e+00 1269.0
6 TraesCS6D01G188400 chr6D 94.750 781 39 2 1590 2369 237090208 237090987 0.000000e+00 1214.0
7 TraesCS6D01G188400 chr6D 93.469 245 12 4 225 467 460227116 460227358 6.220000e-96 361.0
8 TraesCS6D01G188400 chr2D 93.997 1316 52 11 231 1521 558095501 558096814 0.000000e+00 1967.0
9 TraesCS6D01G188400 chr2D 95.385 845 39 0 1525 2369 532011556 532012400 0.000000e+00 1345.0
10 TraesCS6D01G188400 chr2D 89.902 307 30 1 1523 1829 620215722 620216027 6.140000e-106 394.0
11 TraesCS6D01G188400 chr2D 93.798 258 16 0 1521 1778 532011232 532011489 2.860000e-104 388.0
12 TraesCS6D01G188400 chr2D 87.429 350 24 4 223 552 56222810 56222461 3.690000e-103 385.0
13 TraesCS6D01G188400 chr2D 90.400 250 22 2 1546 1794 432068908 432068660 6.310000e-86 327.0
14 TraesCS6D01G188400 chr2D 98.077 52 1 0 34 85 423872499 423872448 9.020000e-15 91.6
15 TraesCS6D01G188400 chr1D 93.769 1332 47 11 225 1521 447244243 447245573 0.000000e+00 1967.0
16 TraesCS6D01G188400 chr1D 95.503 1134 21 10 414 1521 74537076 74538205 0.000000e+00 1784.0
17 TraesCS6D01G188400 chr1D 94.746 1123 40 8 413 1521 279594628 279593511 0.000000e+00 1729.0
18 TraesCS6D01G188400 chr1D 92.108 849 59 7 1521 2363 467306773 467307619 0.000000e+00 1190.0
19 TraesCS6D01G188400 chr1D 95.692 650 27 1 1555 2204 419729299 419729947 0.000000e+00 1044.0
20 TraesCS6D01G188400 chr4D 93.949 1322 44 8 224 1521 234389384 234390693 0.000000e+00 1965.0
21 TraesCS6D01G188400 chr4D 92.157 1326 53 15 222 1521 359849521 359850821 0.000000e+00 1825.0
22 TraesCS6D01G188400 chr4D 95.668 1131 24 10 414 1521 297898790 297897662 0.000000e+00 1794.0
23 TraesCS6D01G188400 chr4D 95.154 681 32 1 1684 2363 297893241 297892561 0.000000e+00 1074.0
24 TraesCS6D01G188400 chr3D 94.158 1301 44 17 227 1521 129692524 129691250 0.000000e+00 1953.0
25 TraesCS6D01G188400 chr3D 95.434 679 29 2 1692 2369 8680849 8680172 0.000000e+00 1081.0
26 TraesCS6D01G188400 chr3D 88.020 409 29 3 226 614 21809985 21809577 1.280000e-127 466.0
27 TraesCS6D01G188400 chr5D 93.593 1311 58 19 228 1521 424088619 424087318 0.000000e+00 1932.0
28 TraesCS6D01G188400 chr5D 95.230 1132 26 7 416 1521 340323899 340325028 0.000000e+00 1766.0
29 TraesCS6D01G188400 chr5D 96.195 841 32 0 1523 2363 340326919 340327759 0.000000e+00 1376.0
30 TraesCS6D01G188400 chr5D 93.443 244 14 2 225 467 394533562 394533804 6.220000e-96 361.0
31 TraesCS6D01G188400 chr7D 91.834 1347 47 30 225 1521 219905175 219906508 0.000000e+00 1820.0
32 TraesCS6D01G188400 chr7D 94.231 52 3 0 34 85 540631554 540631503 1.950000e-11 80.5
33 TraesCS6D01G188400 chr6A 99.111 225 2 0 1 225 366037134 366037358 2.840000e-109 405.0
34 TraesCS6D01G188400 chr6B 98.667 225 3 0 1 225 372571838 372571614 1.320000e-107 399.0
35 TraesCS6D01G188400 chr2A 98.077 52 1 0 34 85 564503512 564503563 9.020000e-15 91.6
36 TraesCS6D01G188400 chr2B 100.000 48 0 0 38 85 497852831 497852784 3.240000e-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 TraesCS6D01G188400 chr6D 256720166 256722534 2368 True 4375.0 4375 100.0000 1 2369 1 chr6D.!!$R2 2368
1 TraesCS6D01G188400 chr6D 365432501 365433825 1324 False 2012.0 2012 94.3480 219 1521 1 chr6D.!!$F3 1302
2 TraesCS6D01G188400 chr6D 325815076 325816197 1121 True 1849.0 1849 96.6190 414 1521 1 chr6D.!!$R4 1107
3 TraesCS6D01G188400 chr6D 237084704 237085836 1132 False 1764.0 1764 95.1540 414 1521 1 chr6D.!!$F1 1107
4 TraesCS6D01G188400 chr6D 51481172 51482018 846 True 1304.0 1304 94.4510 1523 2369 1 chr6D.!!$R1 846
5 TraesCS6D01G188400 chr6D 293101467 293102317 850 True 1269.0 1269 93.6550 1523 2369 1 chr6D.!!$R3 846
6 TraesCS6D01G188400 chr6D 237090208 237090987 779 False 1214.0 1214 94.7500 1590 2369 1 chr6D.!!$F2 779
7 TraesCS6D01G188400 chr2D 558095501 558096814 1313 False 1967.0 1967 93.9970 231 1521 1 chr2D.!!$F1 1290
8 TraesCS6D01G188400 chr2D 532011232 532012400 1168 False 866.5 1345 94.5915 1521 2369 2 chr2D.!!$F3 848
9 TraesCS6D01G188400 chr1D 447244243 447245573 1330 False 1967.0 1967 93.7690 225 1521 1 chr1D.!!$F3 1296
10 TraesCS6D01G188400 chr1D 74537076 74538205 1129 False 1784.0 1784 95.5030 414 1521 1 chr1D.!!$F1 1107
11 TraesCS6D01G188400 chr1D 279593511 279594628 1117 True 1729.0 1729 94.7460 413 1521 1 chr1D.!!$R1 1108
12 TraesCS6D01G188400 chr1D 467306773 467307619 846 False 1190.0 1190 92.1080 1521 2363 1 chr1D.!!$F4 842
13 TraesCS6D01G188400 chr1D 419729299 419729947 648 False 1044.0 1044 95.6920 1555 2204 1 chr1D.!!$F2 649
14 TraesCS6D01G188400 chr4D 234389384 234390693 1309 False 1965.0 1965 93.9490 224 1521 1 chr4D.!!$F1 1297
15 TraesCS6D01G188400 chr4D 359849521 359850821 1300 False 1825.0 1825 92.1570 222 1521 1 chr4D.!!$F2 1299
16 TraesCS6D01G188400 chr4D 297897662 297898790 1128 True 1794.0 1794 95.6680 414 1521 1 chr4D.!!$R2 1107
17 TraesCS6D01G188400 chr4D 297892561 297893241 680 True 1074.0 1074 95.1540 1684 2363 1 chr4D.!!$R1 679
18 TraesCS6D01G188400 chr3D 129691250 129692524 1274 True 1953.0 1953 94.1580 227 1521 1 chr3D.!!$R3 1294
19 TraesCS6D01G188400 chr3D 8680172 8680849 677 True 1081.0 1081 95.4340 1692 2369 1 chr3D.!!$R1 677
20 TraesCS6D01G188400 chr5D 424087318 424088619 1301 True 1932.0 1932 93.5930 228 1521 1 chr5D.!!$R1 1293
21 TraesCS6D01G188400 chr5D 340323899 340327759 3860 False 1571.0 1766 95.7125 416 2363 2 chr5D.!!$F2 1947
22 TraesCS6D01G188400 chr7D 219905175 219906508 1333 False 1820.0 1820 91.8340 225 1521 1 chr7D.!!$F1 1296

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
86 87 0.030369 GAGGTAGGCGTACGACATGG 59.970 60.0 25.52 0.0 0.0 3.66 F
181 182 0.178801 AAGGGAGGTGGAGGGGAATT 60.179 55.0 0.00 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1496 0.416231 TGGGGGACTACTAGCAACCT 59.584 55.000 0.0 0.0 0.0 3.50 R
1761 4100 1.203994 GGCGTACCTTCTGTTGCTCTA 59.796 52.381 0.0 0.0 0.0 2.43 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.878358 GGAGAGATTCGGGAGGGG 58.122 66.667 0.00 0.00 0.00 4.79
18 19 2.512355 GGAGAGATTCGGGAGGGGC 61.512 68.421 0.00 0.00 0.00 5.80
19 20 1.762460 GAGAGATTCGGGAGGGGCA 60.762 63.158 0.00 0.00 0.00 5.36
20 21 1.753368 GAGAGATTCGGGAGGGGCAG 61.753 65.000 0.00 0.00 0.00 4.85
21 22 2.770048 AGATTCGGGAGGGGCAGG 60.770 66.667 0.00 0.00 0.00 4.85
22 23 3.878667 GATTCGGGAGGGGCAGGG 61.879 72.222 0.00 0.00 0.00 4.45
28 29 4.095400 GGAGGGGCAGGGGAGAGA 62.095 72.222 0.00 0.00 0.00 3.10
29 30 2.288643 GAGGGGCAGGGGAGAGAT 59.711 66.667 0.00 0.00 0.00 2.75
30 31 1.385206 GAGGGGCAGGGGAGAGATT 60.385 63.158 0.00 0.00 0.00 2.40
31 32 1.695597 AGGGGCAGGGGAGAGATTG 60.696 63.158 0.00 0.00 0.00 2.67
32 33 2.003548 GGGGCAGGGGAGAGATTGT 61.004 63.158 0.00 0.00 0.00 2.71
33 34 1.225704 GGGCAGGGGAGAGATTGTG 59.774 63.158 0.00 0.00 0.00 3.33
34 35 1.452833 GGCAGGGGAGAGATTGTGC 60.453 63.158 0.00 0.00 0.00 4.57
35 36 1.817099 GCAGGGGAGAGATTGTGCG 60.817 63.158 0.00 0.00 0.00 5.34
36 37 1.900351 CAGGGGAGAGATTGTGCGA 59.100 57.895 0.00 0.00 0.00 5.10
37 38 0.250234 CAGGGGAGAGATTGTGCGAA 59.750 55.000 0.00 0.00 0.00 4.70
38 39 0.250513 AGGGGAGAGATTGTGCGAAC 59.749 55.000 0.00 0.00 0.00 3.95
39 40 0.744771 GGGGAGAGATTGTGCGAACC 60.745 60.000 0.00 0.00 0.00 3.62
40 41 0.250513 GGGAGAGATTGTGCGAACCT 59.749 55.000 0.00 0.00 0.00 3.50
41 42 1.363744 GGAGAGATTGTGCGAACCTG 58.636 55.000 0.00 0.00 0.00 4.00
42 43 1.338200 GGAGAGATTGTGCGAACCTGT 60.338 52.381 0.00 0.00 0.00 4.00
43 44 1.728971 GAGAGATTGTGCGAACCTGTG 59.271 52.381 0.00 0.00 0.00 3.66
44 45 1.070758 AGAGATTGTGCGAACCTGTGT 59.929 47.619 0.00 0.00 0.00 3.72
45 46 1.461127 GAGATTGTGCGAACCTGTGTC 59.539 52.381 0.00 0.00 0.00 3.67
46 47 0.163788 GATTGTGCGAACCTGTGTCG 59.836 55.000 0.00 0.00 0.00 4.35
51 52 2.126071 CGAACCTGTGTCGCCGAT 60.126 61.111 0.00 0.00 0.00 4.18
52 53 2.444624 CGAACCTGTGTCGCCGATG 61.445 63.158 0.00 0.00 0.00 3.84
53 54 1.080093 GAACCTGTGTCGCCGATGA 60.080 57.895 0.00 0.00 0.00 2.92
54 55 0.460284 GAACCTGTGTCGCCGATGAT 60.460 55.000 0.00 0.00 0.00 2.45
55 56 0.740868 AACCTGTGTCGCCGATGATG 60.741 55.000 0.00 0.00 0.00 3.07
56 57 1.141665 CCTGTGTCGCCGATGATGA 59.858 57.895 0.00 0.00 0.00 2.92
57 58 0.249615 CCTGTGTCGCCGATGATGAT 60.250 55.000 0.00 0.00 0.00 2.45
58 59 0.857287 CTGTGTCGCCGATGATGATG 59.143 55.000 0.00 0.00 0.00 3.07
59 60 0.175531 TGTGTCGCCGATGATGATGT 59.824 50.000 0.00 0.00 0.00 3.06
60 61 1.407258 TGTGTCGCCGATGATGATGTA 59.593 47.619 0.00 0.00 0.00 2.29
61 62 1.787155 GTGTCGCCGATGATGATGTAC 59.213 52.381 0.00 0.00 0.00 2.90
62 63 1.681264 TGTCGCCGATGATGATGTACT 59.319 47.619 0.00 0.00 0.00 2.73
63 64 2.100749 TGTCGCCGATGATGATGTACTT 59.899 45.455 0.00 0.00 0.00 2.24
64 65 2.472861 GTCGCCGATGATGATGTACTTG 59.527 50.000 0.00 0.00 0.00 3.16
65 66 2.360801 TCGCCGATGATGATGTACTTGA 59.639 45.455 0.00 0.00 0.00 3.02
66 67 3.123050 CGCCGATGATGATGTACTTGAA 58.877 45.455 0.00 0.00 0.00 2.69
67 68 3.183172 CGCCGATGATGATGTACTTGAAG 59.817 47.826 0.00 0.00 0.00 3.02
68 69 4.371786 GCCGATGATGATGTACTTGAAGA 58.628 43.478 0.00 0.00 0.00 2.87
69 70 4.447054 GCCGATGATGATGTACTTGAAGAG 59.553 45.833 0.00 0.00 0.00 2.85
70 71 4.987285 CCGATGATGATGTACTTGAAGAGG 59.013 45.833 0.00 0.00 0.00 3.69
71 72 5.452496 CCGATGATGATGTACTTGAAGAGGT 60.452 44.000 0.00 0.00 0.00 3.85
72 73 6.239036 CCGATGATGATGTACTTGAAGAGGTA 60.239 42.308 0.00 0.00 0.00 3.08
73 74 6.860539 CGATGATGATGTACTTGAAGAGGTAG 59.139 42.308 0.00 0.00 0.00 3.18
74 75 6.471233 TGATGATGTACTTGAAGAGGTAGG 57.529 41.667 0.00 0.00 0.00 3.18
75 76 4.737855 TGATGTACTTGAAGAGGTAGGC 57.262 45.455 0.00 0.00 0.00 3.93
76 77 3.130516 TGATGTACTTGAAGAGGTAGGCG 59.869 47.826 0.00 0.00 0.00 5.52
77 78 2.522185 TGTACTTGAAGAGGTAGGCGT 58.478 47.619 0.00 0.00 0.00 5.68
78 79 3.689347 TGTACTTGAAGAGGTAGGCGTA 58.311 45.455 0.00 0.00 0.00 4.42
79 80 3.441572 TGTACTTGAAGAGGTAGGCGTAC 59.558 47.826 8.06 8.06 0.00 3.67
80 81 1.471684 ACTTGAAGAGGTAGGCGTACG 59.528 52.381 11.84 11.84 0.00 3.67
81 82 1.741706 CTTGAAGAGGTAGGCGTACGA 59.258 52.381 21.65 0.00 0.00 3.43
82 83 1.089920 TGAAGAGGTAGGCGTACGAC 58.910 55.000 21.65 18.43 0.00 4.34
83 84 1.089920 GAAGAGGTAGGCGTACGACA 58.910 55.000 25.52 6.51 0.00 4.35
84 85 1.674962 GAAGAGGTAGGCGTACGACAT 59.325 52.381 25.52 12.71 0.00 3.06
85 86 1.022735 AGAGGTAGGCGTACGACATG 58.977 55.000 25.52 0.00 0.00 3.21
86 87 0.030369 GAGGTAGGCGTACGACATGG 59.970 60.000 25.52 0.00 0.00 3.66
87 88 0.682209 AGGTAGGCGTACGACATGGT 60.682 55.000 25.52 4.60 0.00 3.55
88 89 0.248784 GGTAGGCGTACGACATGGTC 60.249 60.000 25.52 8.09 0.00 4.02
97 98 2.280186 GACATGGTCGATCCCGGC 60.280 66.667 0.00 0.00 40.18 6.13
98 99 4.221422 ACATGGTCGATCCCGGCG 62.221 66.667 0.00 0.00 42.18 6.46
99 100 4.969196 CATGGTCGATCCCGGCGG 62.969 72.222 21.46 21.46 42.18 6.13
121 122 2.026301 GAACGGATCGGAGGAGCG 59.974 66.667 7.35 0.00 0.00 5.03
122 123 3.486252 GAACGGATCGGAGGAGCGG 62.486 68.421 7.35 0.00 35.31 5.52
126 127 3.900892 GATCGGAGGAGCGGCGAA 61.901 66.667 12.98 0.00 0.00 4.70
127 128 3.214250 GATCGGAGGAGCGGCGAAT 62.214 63.158 12.98 0.00 0.00 3.34
128 129 2.701163 GATCGGAGGAGCGGCGAATT 62.701 60.000 12.98 0.00 0.00 2.17
129 130 2.978452 ATCGGAGGAGCGGCGAATTG 62.978 60.000 12.98 0.00 0.00 2.32
130 131 3.577313 GGAGGAGCGGCGAATTGC 61.577 66.667 12.98 0.00 45.38 3.56
142 143 3.615849 GCGAATTGCCAAGGATTCTAG 57.384 47.619 0.00 0.00 37.76 2.43
143 144 2.287248 GCGAATTGCCAAGGATTCTAGC 60.287 50.000 0.00 0.00 37.76 3.42
144 145 2.032549 CGAATTGCCAAGGATTCTAGCG 60.033 50.000 0.00 0.00 31.63 4.26
145 146 2.717639 ATTGCCAAGGATTCTAGCGT 57.282 45.000 0.00 0.00 0.00 5.07
146 147 2.024176 TTGCCAAGGATTCTAGCGTC 57.976 50.000 0.00 0.00 0.00 5.19
147 148 1.195115 TGCCAAGGATTCTAGCGTCT 58.805 50.000 0.00 0.00 0.00 4.18
148 149 1.134699 TGCCAAGGATTCTAGCGTCTG 60.135 52.381 0.00 0.00 0.00 3.51
149 150 1.137086 GCCAAGGATTCTAGCGTCTGA 59.863 52.381 0.00 0.00 0.00 3.27
150 151 2.224161 GCCAAGGATTCTAGCGTCTGAT 60.224 50.000 0.00 0.00 0.00 2.90
151 152 3.742640 GCCAAGGATTCTAGCGTCTGATT 60.743 47.826 0.00 0.00 0.00 2.57
152 153 3.806521 CCAAGGATTCTAGCGTCTGATTG 59.193 47.826 0.00 0.00 0.00 2.67
153 154 3.742433 AGGATTCTAGCGTCTGATTGG 57.258 47.619 0.00 0.00 0.00 3.16
154 155 3.034635 AGGATTCTAGCGTCTGATTGGT 58.965 45.455 0.00 0.00 0.00 3.67
155 156 3.452627 AGGATTCTAGCGTCTGATTGGTT 59.547 43.478 0.00 0.00 0.00 3.67
156 157 4.080863 AGGATTCTAGCGTCTGATTGGTTT 60.081 41.667 0.00 0.00 0.00 3.27
157 158 5.128827 AGGATTCTAGCGTCTGATTGGTTTA 59.871 40.000 0.00 0.00 0.00 2.01
158 159 5.815740 GGATTCTAGCGTCTGATTGGTTTAA 59.184 40.000 0.00 0.00 0.00 1.52
159 160 6.018669 GGATTCTAGCGTCTGATTGGTTTAAG 60.019 42.308 0.00 0.00 0.00 1.85
160 161 5.654603 TCTAGCGTCTGATTGGTTTAAGA 57.345 39.130 0.00 0.00 0.00 2.10
161 162 5.651530 TCTAGCGTCTGATTGGTTTAAGAG 58.348 41.667 0.00 0.00 0.00 2.85
162 163 4.537135 AGCGTCTGATTGGTTTAAGAGA 57.463 40.909 0.00 0.00 0.00 3.10
163 164 4.894784 AGCGTCTGATTGGTTTAAGAGAA 58.105 39.130 0.00 0.00 0.00 2.87
164 165 4.932200 AGCGTCTGATTGGTTTAAGAGAAG 59.068 41.667 0.00 0.00 0.00 2.85
165 166 4.093556 GCGTCTGATTGGTTTAAGAGAAGG 59.906 45.833 0.00 0.00 0.00 3.46
166 167 4.631813 CGTCTGATTGGTTTAAGAGAAGGG 59.368 45.833 0.00 0.00 0.00 3.95
167 168 5.568825 CGTCTGATTGGTTTAAGAGAAGGGA 60.569 44.000 0.00 0.00 0.00 4.20
168 169 5.877564 GTCTGATTGGTTTAAGAGAAGGGAG 59.122 44.000 0.00 0.00 0.00 4.30
169 170 5.045578 TCTGATTGGTTTAAGAGAAGGGAGG 60.046 44.000 0.00 0.00 0.00 4.30
170 171 4.601857 TGATTGGTTTAAGAGAAGGGAGGT 59.398 41.667 0.00 0.00 0.00 3.85
171 172 4.367039 TTGGTTTAAGAGAAGGGAGGTG 57.633 45.455 0.00 0.00 0.00 4.00
172 173 2.642807 TGGTTTAAGAGAAGGGAGGTGG 59.357 50.000 0.00 0.00 0.00 4.61
173 174 2.910977 GGTTTAAGAGAAGGGAGGTGGA 59.089 50.000 0.00 0.00 0.00 4.02
174 175 3.055021 GGTTTAAGAGAAGGGAGGTGGAG 60.055 52.174 0.00 0.00 0.00 3.86
175 176 2.552093 TAAGAGAAGGGAGGTGGAGG 57.448 55.000 0.00 0.00 0.00 4.30
176 177 0.252927 AAGAGAAGGGAGGTGGAGGG 60.253 60.000 0.00 0.00 0.00 4.30
177 178 1.690985 GAGAAGGGAGGTGGAGGGG 60.691 68.421 0.00 0.00 0.00 4.79
178 179 2.182858 GAGAAGGGAGGTGGAGGGGA 62.183 65.000 0.00 0.00 0.00 4.81
179 180 1.229853 GAAGGGAGGTGGAGGGGAA 60.230 63.158 0.00 0.00 0.00 3.97
180 181 0.624795 GAAGGGAGGTGGAGGGGAAT 60.625 60.000 0.00 0.00 0.00 3.01
181 182 0.178801 AAGGGAGGTGGAGGGGAATT 60.179 55.000 0.00 0.00 0.00 2.17
182 183 0.921256 AGGGAGGTGGAGGGGAATTG 60.921 60.000 0.00 0.00 0.00 2.32
183 184 1.076705 GGAGGTGGAGGGGAATTGC 60.077 63.158 0.00 0.00 0.00 3.56
184 185 1.452108 GAGGTGGAGGGGAATTGCG 60.452 63.158 0.00 0.00 0.00 4.85
185 186 2.440247 GGTGGAGGGGAATTGCGG 60.440 66.667 0.00 0.00 0.00 5.69
186 187 2.440247 GTGGAGGGGAATTGCGGG 60.440 66.667 0.00 0.00 0.00 6.13
187 188 4.440829 TGGAGGGGAATTGCGGGC 62.441 66.667 0.00 0.00 0.00 6.13
192 193 4.496927 GGGAATTGCGGGCGCTTG 62.497 66.667 7.64 0.23 42.51 4.01
193 194 3.747976 GGAATTGCGGGCGCTTGT 61.748 61.111 7.64 0.00 42.51 3.16
194 195 2.504681 GAATTGCGGGCGCTTGTG 60.505 61.111 7.64 0.00 42.51 3.33
195 196 4.722855 AATTGCGGGCGCTTGTGC 62.723 61.111 7.64 7.07 42.51 4.57
202 203 4.683334 GGCGCTTGTGCAACCGAC 62.683 66.667 7.64 0.00 39.64 4.79
205 206 3.947841 GCTTGTGCAACCGACGCA 61.948 61.111 0.00 0.00 39.41 5.24
217 218 2.579787 GACGCACGCGACAGCTAT 60.580 61.111 19.66 4.71 42.83 2.97
218 219 2.126071 ACGCACGCGACAGCTATT 60.126 55.556 19.66 0.00 42.83 1.73
219 220 1.683790 GACGCACGCGACAGCTATTT 61.684 55.000 19.66 0.00 42.83 1.40
220 221 1.289109 ACGCACGCGACAGCTATTTT 61.289 50.000 19.66 0.00 42.83 1.82
296 297 3.482436 TGGGTGCGAAACTATTTCACTT 58.518 40.909 2.50 0.00 39.63 3.16
322 323 1.512156 CCTTTTTGTGTAGCGCCCGT 61.512 55.000 2.29 0.00 0.00 5.28
358 359 0.527600 CGTATTGTGCAGCGCCTAGA 60.528 55.000 2.29 0.00 0.00 2.43
515 542 4.659172 CCCCGCCACACCACACAT 62.659 66.667 0.00 0.00 0.00 3.21
546 603 4.293671 CCCCGAGTTTTGGCCCCA 62.294 66.667 0.00 0.00 0.00 4.96
548 605 2.203422 CCGAGTTTTGGCCCCACA 60.203 61.111 0.00 0.00 0.00 4.17
598 656 6.590068 TCTCCCAAATCTTGCAAATTTGAAA 58.410 32.000 28.95 16.63 43.60 2.69
626 684 3.435671 GTCCGTGGATTTCGAAGTCAAAT 59.564 43.478 20.53 0.91 0.00 2.32
634 692 4.367039 TTTCGAAGTCAAATCCTCCCTT 57.633 40.909 0.00 0.00 0.00 3.95
709 767 3.255642 GCTCATTTGTTGCTAGTTTGGGA 59.744 43.478 0.00 0.00 0.00 4.37
710 768 4.261994 GCTCATTTGTTGCTAGTTTGGGAA 60.262 41.667 0.00 0.00 0.00 3.97
885 1009 5.429435 TGGTTATGGTTAGGGTTAGGGTTAG 59.571 44.000 0.00 0.00 0.00 2.34
965 1094 5.032846 TCCTTGGATTAGTCTCATGGAAGT 58.967 41.667 0.00 0.00 33.60 3.01
1170 1299 6.332635 TGAATTGGATGGACCCTAGTGATATT 59.667 38.462 0.00 0.00 38.00 1.28
1367 1496 2.041596 CCGGAACCCCTCCCCTTA 59.958 66.667 0.00 0.00 41.87 2.69
1380 1509 3.630311 CCTCCCCTTAGGTTGCTAGTAGT 60.630 52.174 0.00 0.00 36.75 2.73
1518 1647 1.575244 ATGCGGACGATGACAATGAG 58.425 50.000 0.00 0.00 0.00 2.90
1519 1648 0.246360 TGCGGACGATGACAATGAGT 59.754 50.000 0.00 0.00 0.00 3.41
1761 4100 3.452264 TGCACAAGTCTGTAGCTATCCAT 59.548 43.478 0.00 0.00 33.22 3.41
1793 4132 2.038837 GTACGCCTCCAGTTTGGGC 61.039 63.158 0.00 0.00 38.32 5.36
1895 4234 2.125512 CTGTAGAGTGTGGCGCCC 60.126 66.667 26.77 16.24 0.00 6.13
2119 4459 9.899661 ACAAATTCCACATTACTAATAGCTACA 57.100 29.630 0.00 0.00 0.00 2.74
2197 4537 5.236478 ACTCCAAGTTCAACGACATAACAAG 59.764 40.000 0.00 0.00 0.00 3.16
2319 4663 2.283676 AAGAGGAACCCGCTCCGA 60.284 61.111 0.00 0.00 40.75 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.512355 GCCCCTCCCGAATCTCTCC 61.512 68.421 0.00 0.00 0.00 3.71
1 2 1.753368 CTGCCCCTCCCGAATCTCTC 61.753 65.000 0.00 0.00 0.00 3.20
2 3 1.764054 CTGCCCCTCCCGAATCTCT 60.764 63.158 0.00 0.00 0.00 3.10
5 6 3.878667 CCCTGCCCCTCCCGAATC 61.879 72.222 0.00 0.00 0.00 2.52
11 12 2.923852 AATCTCTCCCCTGCCCCTCC 62.924 65.000 0.00 0.00 0.00 4.30
12 13 1.385206 AATCTCTCCCCTGCCCCTC 60.385 63.158 0.00 0.00 0.00 4.30
13 14 1.695597 CAATCTCTCCCCTGCCCCT 60.696 63.158 0.00 0.00 0.00 4.79
14 15 2.003548 ACAATCTCTCCCCTGCCCC 61.004 63.158 0.00 0.00 0.00 5.80
15 16 1.225704 CACAATCTCTCCCCTGCCC 59.774 63.158 0.00 0.00 0.00 5.36
16 17 1.452833 GCACAATCTCTCCCCTGCC 60.453 63.158 0.00 0.00 0.00 4.85
17 18 1.817099 CGCACAATCTCTCCCCTGC 60.817 63.158 0.00 0.00 0.00 4.85
18 19 0.250234 TTCGCACAATCTCTCCCCTG 59.750 55.000 0.00 0.00 0.00 4.45
19 20 0.250513 GTTCGCACAATCTCTCCCCT 59.749 55.000 0.00 0.00 0.00 4.79
20 21 0.744771 GGTTCGCACAATCTCTCCCC 60.745 60.000 0.00 0.00 0.00 4.81
21 22 0.250513 AGGTTCGCACAATCTCTCCC 59.749 55.000 0.00 0.00 0.00 4.30
22 23 1.338200 ACAGGTTCGCACAATCTCTCC 60.338 52.381 0.00 0.00 0.00 3.71
23 24 1.728971 CACAGGTTCGCACAATCTCTC 59.271 52.381 0.00 0.00 0.00 3.20
24 25 1.070758 ACACAGGTTCGCACAATCTCT 59.929 47.619 0.00 0.00 0.00 3.10
25 26 1.461127 GACACAGGTTCGCACAATCTC 59.539 52.381 0.00 0.00 0.00 2.75
26 27 1.512926 GACACAGGTTCGCACAATCT 58.487 50.000 0.00 0.00 0.00 2.40
27 28 0.163788 CGACACAGGTTCGCACAATC 59.836 55.000 0.00 0.00 0.00 2.67
28 29 2.234613 CGACACAGGTTCGCACAAT 58.765 52.632 0.00 0.00 0.00 2.71
29 30 3.712655 CGACACAGGTTCGCACAA 58.287 55.556 0.00 0.00 0.00 3.33
34 35 2.126071 ATCGGCGACACAGGTTCG 60.126 61.111 13.76 0.00 0.00 3.95
35 36 0.460284 ATCATCGGCGACACAGGTTC 60.460 55.000 13.76 0.00 0.00 3.62
36 37 0.740868 CATCATCGGCGACACAGGTT 60.741 55.000 13.76 0.00 0.00 3.50
37 38 1.153568 CATCATCGGCGACACAGGT 60.154 57.895 13.76 0.00 0.00 4.00
38 39 0.249615 ATCATCATCGGCGACACAGG 60.250 55.000 13.76 0.04 0.00 4.00
39 40 0.857287 CATCATCATCGGCGACACAG 59.143 55.000 13.76 2.98 0.00 3.66
40 41 0.175531 ACATCATCATCGGCGACACA 59.824 50.000 13.76 0.00 0.00 3.72
41 42 1.787155 GTACATCATCATCGGCGACAC 59.213 52.381 13.76 0.00 0.00 3.67
42 43 1.681264 AGTACATCATCATCGGCGACA 59.319 47.619 13.76 1.25 0.00 4.35
43 44 2.423926 AGTACATCATCATCGGCGAC 57.576 50.000 13.76 0.00 0.00 5.19
44 45 2.360801 TCAAGTACATCATCATCGGCGA 59.639 45.455 13.87 13.87 0.00 5.54
45 46 2.742774 TCAAGTACATCATCATCGGCG 58.257 47.619 0.00 0.00 0.00 6.46
46 47 4.371786 TCTTCAAGTACATCATCATCGGC 58.628 43.478 0.00 0.00 0.00 5.54
47 48 4.987285 CCTCTTCAAGTACATCATCATCGG 59.013 45.833 0.00 0.00 0.00 4.18
48 49 5.595885 ACCTCTTCAAGTACATCATCATCG 58.404 41.667 0.00 0.00 0.00 3.84
49 50 7.151308 CCTACCTCTTCAAGTACATCATCATC 58.849 42.308 0.00 0.00 0.00 2.92
50 51 6.463614 GCCTACCTCTTCAAGTACATCATCAT 60.464 42.308 0.00 0.00 0.00 2.45
51 52 5.163405 GCCTACCTCTTCAAGTACATCATCA 60.163 44.000 0.00 0.00 0.00 3.07
52 53 5.293560 GCCTACCTCTTCAAGTACATCATC 58.706 45.833 0.00 0.00 0.00 2.92
53 54 4.202161 CGCCTACCTCTTCAAGTACATCAT 60.202 45.833 0.00 0.00 0.00 2.45
54 55 3.130516 CGCCTACCTCTTCAAGTACATCA 59.869 47.826 0.00 0.00 0.00 3.07
55 56 3.130693 ACGCCTACCTCTTCAAGTACATC 59.869 47.826 0.00 0.00 0.00 3.06
56 57 3.097614 ACGCCTACCTCTTCAAGTACAT 58.902 45.455 0.00 0.00 0.00 2.29
57 58 2.522185 ACGCCTACCTCTTCAAGTACA 58.478 47.619 0.00 0.00 0.00 2.90
58 59 3.486542 CGTACGCCTACCTCTTCAAGTAC 60.487 52.174 0.52 0.00 0.00 2.73
59 60 2.679837 CGTACGCCTACCTCTTCAAGTA 59.320 50.000 0.52 0.00 0.00 2.24
60 61 1.471684 CGTACGCCTACCTCTTCAAGT 59.528 52.381 0.52 0.00 0.00 3.16
61 62 1.741706 TCGTACGCCTACCTCTTCAAG 59.258 52.381 11.24 0.00 0.00 3.02
62 63 1.470098 GTCGTACGCCTACCTCTTCAA 59.530 52.381 11.24 0.00 0.00 2.69
63 64 1.089920 GTCGTACGCCTACCTCTTCA 58.910 55.000 11.24 0.00 0.00 3.02
64 65 1.089920 TGTCGTACGCCTACCTCTTC 58.910 55.000 11.24 0.00 0.00 2.87
65 66 1.404391 CATGTCGTACGCCTACCTCTT 59.596 52.381 11.24 0.00 0.00 2.85
66 67 1.022735 CATGTCGTACGCCTACCTCT 58.977 55.000 11.24 0.00 0.00 3.69
67 68 0.030369 CCATGTCGTACGCCTACCTC 59.970 60.000 11.24 0.00 0.00 3.85
68 69 0.682209 ACCATGTCGTACGCCTACCT 60.682 55.000 11.24 0.00 0.00 3.08
69 70 0.248784 GACCATGTCGTACGCCTACC 60.249 60.000 11.24 0.00 0.00 3.18
70 71 3.247033 GACCATGTCGTACGCCTAC 57.753 57.895 11.24 4.36 0.00 3.18
80 81 2.280186 GCCGGGATCGACCATGTC 60.280 66.667 2.18 0.00 41.20 3.06
81 82 4.221422 CGCCGGGATCGACCATGT 62.221 66.667 2.18 0.00 41.20 3.21
82 83 4.969196 CCGCCGGGATCGACCATG 62.969 72.222 2.18 0.00 41.20 3.66
100 101 4.925576 CCTCCGATCCGTTCGCCG 62.926 72.222 0.00 0.00 46.71 6.46
101 102 3.486252 CTCCTCCGATCCGTTCGCC 62.486 68.421 0.00 0.00 46.71 5.54
102 103 2.026301 CTCCTCCGATCCGTTCGC 59.974 66.667 0.00 0.00 46.71 4.70
104 105 2.026301 CGCTCCTCCGATCCGTTC 59.974 66.667 0.00 0.00 0.00 3.95
105 106 3.528370 CCGCTCCTCCGATCCGTT 61.528 66.667 0.00 0.00 0.00 4.44
109 110 2.701163 AATTCGCCGCTCCTCCGATC 62.701 60.000 0.00 0.00 0.00 3.69
110 111 2.797278 AATTCGCCGCTCCTCCGAT 61.797 57.895 0.00 0.00 0.00 4.18
111 112 3.458163 AATTCGCCGCTCCTCCGA 61.458 61.111 0.00 0.00 0.00 4.55
112 113 3.264897 CAATTCGCCGCTCCTCCG 61.265 66.667 0.00 0.00 0.00 4.63
113 114 3.577313 GCAATTCGCCGCTCCTCC 61.577 66.667 0.00 0.00 32.94 4.30
122 123 2.287248 GCTAGAATCCTTGGCAATTCGC 60.287 50.000 0.00 0.00 37.06 4.70
123 124 2.032549 CGCTAGAATCCTTGGCAATTCG 60.033 50.000 0.00 0.00 37.06 3.34
124 125 2.945668 ACGCTAGAATCCTTGGCAATTC 59.054 45.455 0.00 1.81 33.06 2.17
125 126 2.945668 GACGCTAGAATCCTTGGCAATT 59.054 45.455 0.00 0.00 0.00 2.32
126 127 2.171448 AGACGCTAGAATCCTTGGCAAT 59.829 45.455 0.00 0.00 0.00 3.56
127 128 1.555075 AGACGCTAGAATCCTTGGCAA 59.445 47.619 0.00 0.00 0.00 4.52
128 129 1.134699 CAGACGCTAGAATCCTTGGCA 60.135 52.381 0.00 0.00 0.00 4.92
129 130 1.137086 TCAGACGCTAGAATCCTTGGC 59.863 52.381 0.00 0.00 0.00 4.52
130 131 3.742433 ATCAGACGCTAGAATCCTTGG 57.258 47.619 0.00 0.00 0.00 3.61
131 132 3.806521 CCAATCAGACGCTAGAATCCTTG 59.193 47.826 0.00 0.00 0.00 3.61
132 133 3.452627 ACCAATCAGACGCTAGAATCCTT 59.547 43.478 0.00 0.00 0.00 3.36
133 134 3.034635 ACCAATCAGACGCTAGAATCCT 58.965 45.455 0.00 0.00 0.00 3.24
134 135 3.460857 ACCAATCAGACGCTAGAATCC 57.539 47.619 0.00 0.00 0.00 3.01
135 136 6.757010 TCTTAAACCAATCAGACGCTAGAATC 59.243 38.462 0.00 0.00 0.00 2.52
136 137 6.640518 TCTTAAACCAATCAGACGCTAGAAT 58.359 36.000 0.00 0.00 0.00 2.40
137 138 6.032956 TCTTAAACCAATCAGACGCTAGAA 57.967 37.500 0.00 0.00 0.00 2.10
138 139 5.417894 TCTCTTAAACCAATCAGACGCTAGA 59.582 40.000 0.00 0.00 0.00 2.43
139 140 5.651530 TCTCTTAAACCAATCAGACGCTAG 58.348 41.667 0.00 0.00 0.00 3.42
140 141 5.654603 TCTCTTAAACCAATCAGACGCTA 57.345 39.130 0.00 0.00 0.00 4.26
141 142 4.537135 TCTCTTAAACCAATCAGACGCT 57.463 40.909 0.00 0.00 0.00 5.07
142 143 4.093556 CCTTCTCTTAAACCAATCAGACGC 59.906 45.833 0.00 0.00 0.00 5.19
143 144 4.631813 CCCTTCTCTTAAACCAATCAGACG 59.368 45.833 0.00 0.00 0.00 4.18
144 145 5.805728 TCCCTTCTCTTAAACCAATCAGAC 58.194 41.667 0.00 0.00 0.00 3.51
145 146 5.045578 CCTCCCTTCTCTTAAACCAATCAGA 60.046 44.000 0.00 0.00 0.00 3.27
146 147 5.189180 CCTCCCTTCTCTTAAACCAATCAG 58.811 45.833 0.00 0.00 0.00 2.90
147 148 4.601857 ACCTCCCTTCTCTTAAACCAATCA 59.398 41.667 0.00 0.00 0.00 2.57
148 149 4.944317 CACCTCCCTTCTCTTAAACCAATC 59.056 45.833 0.00 0.00 0.00 2.67
149 150 4.263949 CCACCTCCCTTCTCTTAAACCAAT 60.264 45.833 0.00 0.00 0.00 3.16
150 151 3.073946 CCACCTCCCTTCTCTTAAACCAA 59.926 47.826 0.00 0.00 0.00 3.67
151 152 2.642807 CCACCTCCCTTCTCTTAAACCA 59.357 50.000 0.00 0.00 0.00 3.67
152 153 2.910977 TCCACCTCCCTTCTCTTAAACC 59.089 50.000 0.00 0.00 0.00 3.27
153 154 3.055021 CCTCCACCTCCCTTCTCTTAAAC 60.055 52.174 0.00 0.00 0.00 2.01
154 155 3.182152 CCTCCACCTCCCTTCTCTTAAA 58.818 50.000 0.00 0.00 0.00 1.52
155 156 2.562214 CCCTCCACCTCCCTTCTCTTAA 60.562 54.545 0.00 0.00 0.00 1.85
156 157 1.008449 CCCTCCACCTCCCTTCTCTTA 59.992 57.143 0.00 0.00 0.00 2.10
157 158 0.252927 CCCTCCACCTCCCTTCTCTT 60.253 60.000 0.00 0.00 0.00 2.85
158 159 1.394151 CCCTCCACCTCCCTTCTCT 59.606 63.158 0.00 0.00 0.00 3.10
159 160 1.690985 CCCCTCCACCTCCCTTCTC 60.691 68.421 0.00 0.00 0.00 2.87
160 161 1.761780 TTCCCCTCCACCTCCCTTCT 61.762 60.000 0.00 0.00 0.00 2.85
161 162 0.624795 ATTCCCCTCCACCTCCCTTC 60.625 60.000 0.00 0.00 0.00 3.46
162 163 0.178801 AATTCCCCTCCACCTCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
163 164 0.921256 CAATTCCCCTCCACCTCCCT 60.921 60.000 0.00 0.00 0.00 4.20
164 165 1.615262 CAATTCCCCTCCACCTCCC 59.385 63.158 0.00 0.00 0.00 4.30
165 166 1.076705 GCAATTCCCCTCCACCTCC 60.077 63.158 0.00 0.00 0.00 4.30
166 167 1.452108 CGCAATTCCCCTCCACCTC 60.452 63.158 0.00 0.00 0.00 3.85
167 168 2.677228 CGCAATTCCCCTCCACCT 59.323 61.111 0.00 0.00 0.00 4.00
168 169 2.440247 CCGCAATTCCCCTCCACC 60.440 66.667 0.00 0.00 0.00 4.61
169 170 2.440247 CCCGCAATTCCCCTCCAC 60.440 66.667 0.00 0.00 0.00 4.02
170 171 4.440829 GCCCGCAATTCCCCTCCA 62.441 66.667 0.00 0.00 0.00 3.86
175 176 4.496927 CAAGCGCCCGCAATTCCC 62.497 66.667 15.50 0.00 44.88 3.97
176 177 3.747976 ACAAGCGCCCGCAATTCC 61.748 61.111 15.50 0.00 44.88 3.01
177 178 2.504681 CACAAGCGCCCGCAATTC 60.505 61.111 15.50 0.00 44.88 2.17
178 179 4.722855 GCACAAGCGCCCGCAATT 62.723 61.111 15.50 0.00 44.88 2.32
188 189 3.947841 TGCGTCGGTTGCACAAGC 61.948 61.111 2.51 2.51 37.44 4.01
200 201 1.683790 AAATAGCTGTCGCGTGCGTC 61.684 55.000 14.47 9.37 42.32 5.19
201 202 1.289109 AAAATAGCTGTCGCGTGCGT 61.289 50.000 14.47 1.69 42.32 5.24
202 203 0.853224 CAAAATAGCTGTCGCGTGCG 60.853 55.000 5.77 8.14 42.32 5.34
203 204 0.442310 TCAAAATAGCTGTCGCGTGC 59.558 50.000 5.77 9.73 42.32 5.34
204 205 2.537529 CCATCAAAATAGCTGTCGCGTG 60.538 50.000 5.77 0.00 42.32 5.34
205 206 1.665679 CCATCAAAATAGCTGTCGCGT 59.334 47.619 5.77 0.00 42.32 6.01
206 207 1.595489 GCCATCAAAATAGCTGTCGCG 60.595 52.381 0.00 0.00 42.32 5.87
207 208 1.401552 TGCCATCAAAATAGCTGTCGC 59.598 47.619 0.00 0.00 0.00 5.19
208 209 3.763097 TTGCCATCAAAATAGCTGTCG 57.237 42.857 0.00 0.00 0.00 4.35
209 210 6.591062 TCAAATTTGCCATCAAAATAGCTGTC 59.409 34.615 13.54 0.00 44.44 3.51
210 211 6.369615 GTCAAATTTGCCATCAAAATAGCTGT 59.630 34.615 13.54 0.00 44.44 4.40
211 212 6.369340 TGTCAAATTTGCCATCAAAATAGCTG 59.631 34.615 13.54 0.00 44.44 4.24
212 213 6.465948 TGTCAAATTTGCCATCAAAATAGCT 58.534 32.000 13.54 0.00 44.44 3.32
213 214 6.724694 TGTCAAATTTGCCATCAAAATAGC 57.275 33.333 13.54 0.00 44.44 2.97
216 217 9.250624 CAAAATTGTCAAATTTGCCATCAAAAT 57.749 25.926 13.54 0.27 43.63 1.82
217 218 7.705325 CCAAAATTGTCAAATTTGCCATCAAAA 59.295 29.630 17.25 0.00 43.63 2.44
218 219 7.201145 CCAAAATTGTCAAATTTGCCATCAAA 58.799 30.769 17.25 0.00 43.63 2.69
219 220 6.735145 GCCAAAATTGTCAAATTTGCCATCAA 60.735 34.615 17.25 14.34 43.63 2.57
220 221 5.278364 GCCAAAATTGTCAAATTTGCCATCA 60.278 36.000 17.25 7.10 43.63 3.07
243 244 1.330829 GAAATGATTTCGTCCCGAGGC 59.669 52.381 1.71 0.00 37.14 4.70
269 270 2.623878 TAGTTTCGCACCCAGTTCAA 57.376 45.000 0.00 0.00 0.00 2.69
296 297 3.390135 CGCTACACAAAAAGGTCAGAGA 58.610 45.455 0.00 0.00 0.00 3.10
343 344 2.434884 GCTCTAGGCGCTGCACAA 60.435 61.111 7.64 0.00 0.00 3.33
407 408 3.654173 CTAGGCGCTGCACTGCTGA 62.654 63.158 7.64 0.00 0.00 4.26
502 518 1.244019 GGGAGAATGTGTGGTGTGGC 61.244 60.000 0.00 0.00 0.00 5.01
515 542 1.000486 CGGGGAGAGAGTGGGAGAA 60.000 63.158 0.00 0.00 0.00 2.87
546 603 2.122954 GGGGGAGAGAGTGGGTGT 59.877 66.667 0.00 0.00 0.00 4.16
548 605 1.864559 AGAGGGGGAGAGAGTGGGT 60.865 63.158 0.00 0.00 0.00 4.51
598 656 4.277423 ACTTCGAAATCCACGGACAAATTT 59.723 37.500 0.00 0.00 0.00 1.82
626 684 5.778750 CGGAGAATATTACCTTAAGGGAGGA 59.221 44.000 25.31 9.19 39.25 3.71
634 692 5.912103 AGGGGATCGGAGAATATTACCTTA 58.088 41.667 8.78 0.09 43.58 2.69
885 1009 2.108776 ACAACAACCCTAACCCTAACCC 59.891 50.000 0.00 0.00 0.00 4.11
965 1094 7.865385 GCATTCAAAGAACACAAGGTAACATTA 59.135 33.333 0.00 0.00 41.41 1.90
1045 1174 6.605594 TCCGGTTCTATATTGCCTTTCAAAAT 59.394 34.615 0.00 0.00 38.34 1.82
1170 1299 2.274542 TGCCTTCCCTCCAACTCAATA 58.725 47.619 0.00 0.00 0.00 1.90
1367 1496 0.416231 TGGGGGACTACTAGCAACCT 59.584 55.000 0.00 0.00 0.00 3.50
1380 1509 3.646715 CGCTTCAAGGGTGGGGGA 61.647 66.667 0.00 0.00 0.00 4.81
1518 1647 2.175811 CAACGCCTAGCCGCAAAC 59.824 61.111 0.00 0.00 0.00 2.93
1519 1648 3.732892 GCAACGCCTAGCCGCAAA 61.733 61.111 0.00 0.00 0.00 3.68
1563 3412 2.376228 TACAGACTTGTGCAGCGCCA 62.376 55.000 2.29 0.00 38.23 5.69
1710 4049 2.786495 CGGAGGCGCCACACTCTAT 61.786 63.158 31.54 4.27 35.94 1.98
1761 4100 1.203994 GGCGTACCTTCTGTTGCTCTA 59.796 52.381 0.00 0.00 0.00 2.43
1800 4139 3.308530 GCTGCACAAAAACTTAGCGAAT 58.691 40.909 0.00 0.00 0.00 3.34
1991 4331 7.434492 TGTCTTTGGTGAACACTTTTTAAACA 58.566 30.769 4.96 0.25 0.00 2.83
1995 4335 7.397892 TGATGTCTTTGGTGAACACTTTTTA 57.602 32.000 4.96 0.00 0.00 1.52
2119 4459 2.285977 GTCGTTGAACTTGGAGTGGTT 58.714 47.619 0.00 0.00 0.00 3.67
2272 4616 4.246458 AGGTGAAGAAGATAAGCGTCAAC 58.754 43.478 0.00 0.00 31.65 3.18


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

AutoCloner maintained by Alex Coulton.