Multiple sequence alignment - TraesCS3B01G492000

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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 TraesCS3B01G492000 chr3B 100.000 3167 0 0 1 3167 738127584 738124418 0.000000e+00 5849.0
1 TraesCS3B01G492000 chr3B 75.924 1217 229 44 984 2174 738110105 738108927 1.650000e-157 566.0
2 TraesCS3B01G492000 chr3B 96.875 128 4 0 1 128 55006660 55006787 6.880000e-52 215.0
3 TraesCS3B01G492000 chr3B 78.571 126 27 0 2122 2247 737335124 737334999 2.020000e-12 84.2
4 TraesCS3B01G492000 chr3B 78.788 132 21 7 2122 2247 737398461 737398331 7.280000e-12 82.4
5 TraesCS3B01G492000 chrUn 91.551 2154 150 12 127 2251 45268443 45270593 0.000000e+00 2940.0
6 TraesCS3B01G492000 chrUn 89.873 1027 72 12 127 1125 267238098 267237076 0.000000e+00 1291.0
7 TraesCS3B01G492000 chrUn 88.021 576 36 11 2599 3167 358832139 358831590 0.000000e+00 651.0
8 TraesCS3B01G492000 chrUn 87.847 576 37 11 2599 3167 45271014 45271563 0.000000e+00 645.0
9 TraesCS3B01G492000 chrUn 85.167 600 57 13 127 698 433098795 433098200 1.270000e-163 586.0
10 TraesCS3B01G492000 chrUn 88.825 349 32 5 2245 2593 45270632 45270973 3.780000e-114 422.0
11 TraesCS3B01G492000 chrUn 95.833 48 2 0 2546 2593 358832227 358832180 9.420000e-11 78.7
12 TraesCS3B01G492000 chrUn 100.000 29 0 0 1334 1362 215044890 215044862 2.000000e-03 54.7
13 TraesCS3B01G492000 chr3A 90.354 1524 118 12 740 2251 691955179 691953673 0.000000e+00 1973.0
14 TraesCS3B01G492000 chr3A 88.021 576 35 12 2599 3167 691953252 691952704 0.000000e+00 651.0
15 TraesCS3B01G492000 chr3A 89.112 349 31 5 2245 2593 691953634 691953293 8.120000e-116 427.0
16 TraesCS3B01G492000 chr3A 75.211 948 195 28 1236 2174 691837507 691836591 2.270000e-111 412.0
17 TraesCS3B01G492000 chr3A 78.967 271 47 6 972 1235 691837817 691837550 3.250000e-40 176.0
18 TraesCS3B01G492000 chr3A 82.418 91 13 2 2093 2180 691355266 691355176 3.390000e-10 76.8
19 TraesCS3B01G492000 chr3D 77.301 978 171 30 984 1942 554796600 554797545 2.160000e-146 529.0
20 TraesCS3B01G492000 chr3D 79.024 205 38 5 445 646 283385078 283385280 5.510000e-28 135.0
21 TraesCS3B01G492000 chr3D 78.986 138 23 4 2114 2247 555027113 555027248 4.350000e-14 89.8
22 TraesCS3B01G492000 chr1A 96.947 131 4 0 1 131 571781623 571781753 1.480000e-53 220.0
23 TraesCS3B01G492000 chr7D 96.923 130 4 0 1 130 422346736 422346607 5.320000e-53 219.0
24 TraesCS3B01G492000 chr7D 96.094 128 5 0 1 128 605537613 605537740 3.200000e-50 209.0
25 TraesCS3B01G492000 chr7D 100.000 30 0 0 1332 1361 581638155 581638184 4.410000e-04 56.5
26 TraesCS3B01G492000 chr7D 100.000 30 0 0 1332 1361 581665828 581665857 4.410000e-04 56.5
27 TraesCS3B01G492000 chr7D 96.875 32 1 0 1332 1363 582043318 582043349 2.000000e-03 54.7
28 TraesCS3B01G492000 chr7B 96.183 131 5 0 1 131 605109202 605109072 6.880000e-52 215.0
29 TraesCS3B01G492000 chr7B 96.154 130 5 0 1 130 147573682 147573553 2.470000e-51 213.0
30 TraesCS3B01G492000 chr7B 96.875 32 1 0 1332 1363 649322053 649322084 2.000000e-03 54.7
31 TraesCS3B01G492000 chr4A 96.154 130 5 0 1 130 631641265 631641394 2.470000e-51 213.0
32 TraesCS3B01G492000 chr4A 86.066 122 17 0 221 342 617478500 617478379 7.130000e-27 132.0
33 TraesCS3B01G492000 chr4A 82.781 151 22 2 445 595 681612088 681611942 7.130000e-27 132.0
34 TraesCS3B01G492000 chr6D 95.455 132 6 0 1 132 448352006 448351875 8.900000e-51 211.0
35 TraesCS3B01G492000 chr6D 82.927 205 32 3 444 646 412386701 412386498 6.980000e-42 182.0
36 TraesCS3B01G492000 chr6B 94.853 136 6 1 1 135 10037048 10037183 8.900000e-51 211.0
37 TraesCS3B01G492000 chr5D 71.854 906 193 40 1062 1939 497963671 497962800 1.490000e-48 204.0
38 TraesCS3B01G492000 chr4B 80.275 218 33 10 456 668 598454243 598454455 4.230000e-34 156.0
39 TraesCS3B01G492000 chr4D 80.102 196 33 6 454 647 474592478 474592669 1.180000e-29 141.0
40 TraesCS3B01G492000 chr5A 92.857 56 4 0 357 412 327906409 327906464 7.280000e-12 82.4
41 TraesCS3B01G492000 chr1D 83.951 81 13 0 1071 1151 453293151 453293071 9.420000e-11 78.7
42 TraesCS3B01G492000 chr7A 77.966 118 26 0 1066 1183 672153040 672153157 1.220000e-09 75.0
43 TraesCS3B01G492000 chr7A 100.000 32 0 0 1332 1363 648211547 648211516 3.410000e-05 60.2
44 TraesCS3B01G492000 chr7A 100.000 30 0 0 1332 1361 673310026 673310055 4.410000e-04 56.5


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 TraesCS3B01G492000 chr3B 738124418 738127584 3166 True 5849.000000 5849 100.000000 1 3167 1 chr3B.!!$R4 3166
1 TraesCS3B01G492000 chr3B 738108927 738110105 1178 True 566.000000 566 75.924000 984 2174 1 chr3B.!!$R3 1190
2 TraesCS3B01G492000 chrUn 45268443 45271563 3120 False 1335.666667 2940 89.407667 127 3167 3 chrUn.!!$F1 3040
3 TraesCS3B01G492000 chrUn 267237076 267238098 1022 True 1291.000000 1291 89.873000 127 1125 1 chrUn.!!$R2 998
4 TraesCS3B01G492000 chrUn 433098200 433098795 595 True 586.000000 586 85.167000 127 698 1 chrUn.!!$R3 571
5 TraesCS3B01G492000 chrUn 358831590 358832227 637 True 364.850000 651 91.927000 2546 3167 2 chrUn.!!$R4 621
6 TraesCS3B01G492000 chr3A 691952704 691955179 2475 True 1017.000000 1973 89.162333 740 3167 3 chr3A.!!$R3 2427
7 TraesCS3B01G492000 chr3A 691836591 691837817 1226 True 294.000000 412 77.089000 972 2174 2 chr3A.!!$R2 1202
8 TraesCS3B01G492000 chr3D 554796600 554797545 945 False 529.000000 529 77.301000 984 1942 1 chr3D.!!$F2 958
9 TraesCS3B01G492000 chr5D 497962800 497963671 871 True 204.000000 204 71.854000 1062 1939 1 chr5D.!!$R1 877

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
448 449 0.107459 AAGAAGAATCTGGAGCCGCC 60.107 55.0 0.0 0.0 35.59 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2381 0.248498 CATGCGCTCCTTCATTGCTG 60.248 55.0 9.73 0.0 0.0 4.41 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
36 37 3.926821 GTCAAGCCGACCCATTTTAAA 57.073 42.857 0.00 0.00 38.85 1.52
37 38 4.245845 GTCAAGCCGACCCATTTTAAAA 57.754 40.909 2.51 2.51 38.85 1.52
38 39 4.816392 GTCAAGCCGACCCATTTTAAAAT 58.184 39.130 7.64 7.64 38.85 1.82
39 40 5.956642 GTCAAGCCGACCCATTTTAAAATA 58.043 37.500 12.98 0.00 38.85 1.40
40 41 5.803461 GTCAAGCCGACCCATTTTAAAATAC 59.197 40.000 12.98 5.19 38.85 1.89
41 42 4.625972 AGCCGACCCATTTTAAAATACG 57.374 40.909 12.98 14.50 0.00 3.06
42 43 3.379057 AGCCGACCCATTTTAAAATACGG 59.621 43.478 25.72 25.72 40.60 4.02
43 44 3.377798 GCCGACCCATTTTAAAATACGGA 59.622 43.478 29.73 5.26 40.16 4.69
44 45 4.731483 GCCGACCCATTTTAAAATACGGAC 60.731 45.833 29.73 22.42 40.16 4.79
45 46 4.494526 CCGACCCATTTTAAAATACGGACG 60.495 45.833 26.21 26.21 40.16 4.79
46 47 4.093261 CGACCCATTTTAAAATACGGACGT 59.907 41.667 25.55 15.06 34.14 4.34
47 48 5.299582 ACCCATTTTAAAATACGGACGTG 57.700 39.130 23.49 9.15 0.00 4.49
48 49 4.099824 CCCATTTTAAAATACGGACGTGC 58.900 43.478 12.98 0.00 0.00 5.34
49 50 4.379603 CCCATTTTAAAATACGGACGTGCA 60.380 41.667 12.98 0.00 0.00 4.57
50 51 4.555747 CCATTTTAAAATACGGACGTGCAC 59.444 41.667 12.98 6.82 0.00 4.57
51 52 3.436817 TTTAAAATACGGACGTGCACG 57.563 42.857 35.99 35.99 46.33 5.34
70 71 4.794648 CCGCCTGGCCGATCCAAA 62.795 66.667 14.12 0.00 46.01 3.28
71 72 3.508840 CGCCTGGCCGATCCAAAC 61.509 66.667 14.12 0.00 46.01 2.93
72 73 3.508840 GCCTGGCCGATCCAAACG 61.509 66.667 7.66 0.00 46.01 3.60
82 83 2.315901 CGATCCAAACGGACAAAAAGC 58.684 47.619 0.00 0.00 34.62 3.51
83 84 2.315901 GATCCAAACGGACAAAAAGCG 58.684 47.619 0.00 0.00 34.62 4.68
84 85 0.382515 TCCAAACGGACAAAAAGCGG 59.617 50.000 0.00 0.00 0.00 5.52
85 86 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
86 87 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
87 88 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
88 89 1.096416 AACGGACAAAAAGCGGACAA 58.904 45.000 0.00 0.00 0.00 3.18
89 90 1.096416 ACGGACAAAAAGCGGACAAA 58.904 45.000 0.00 0.00 0.00 2.83
90 91 1.064952 ACGGACAAAAAGCGGACAAAG 59.935 47.619 0.00 0.00 0.00 2.77
91 92 1.487482 GGACAAAAAGCGGACAAAGC 58.513 50.000 0.00 0.00 0.00 3.51
92 93 1.120437 GACAAAAAGCGGACAAAGCG 58.880 50.000 0.00 0.00 40.04 4.68
93 94 0.869880 ACAAAAAGCGGACAAAGCGC 60.870 50.000 0.00 0.00 40.04 5.92
94 95 1.657181 AAAAAGCGGACAAAGCGCG 60.657 52.632 0.00 0.00 40.04 6.86
95 96 4.683334 AAAGCGGACAAAGCGCGC 62.683 61.111 26.66 26.66 40.04 6.86
103 104 4.659874 CAAAGCGCGCGTCCGTTT 62.660 61.111 32.35 21.22 36.67 3.60
104 105 4.659874 AAAGCGCGCGTCCGTTTG 62.660 61.111 32.35 0.04 36.67 2.93
122 123 4.324991 GGTCGCCCCGTTGGAGTT 62.325 66.667 0.00 0.00 35.07 3.01
123 124 3.047877 GTCGCCCCGTTGGAGTTG 61.048 66.667 0.00 0.00 35.07 3.16
137 138 3.774734 TGGAGTTGCTCTTAGACTACCA 58.225 45.455 0.00 0.00 0.00 3.25
143 144 5.304614 AGTTGCTCTTAGACTACCAACAAGA 59.695 40.000 12.92 1.86 36.08 3.02
155 156 4.402056 ACCAACAAGAAAGAAGACTCGA 57.598 40.909 0.00 0.00 0.00 4.04
162 163 4.402056 AGAAAGAAGACTCGACACCAAA 57.598 40.909 0.00 0.00 0.00 3.28
167 168 0.969894 AGACTCGACACCAAAGGGAG 59.030 55.000 0.00 0.00 38.05 4.30
197 198 1.891060 CTCGTTTCGCTGCTCACACC 61.891 60.000 0.00 0.00 0.00 4.16
199 200 1.862806 GTTTCGCTGCTCACACCTC 59.137 57.895 0.00 0.00 0.00 3.85
225 226 2.764547 CGGAGAGGACCCCCTTCC 60.765 72.222 0.00 0.00 44.53 3.46
226 227 2.367107 GGAGAGGACCCCCTTCCC 60.367 72.222 0.00 0.00 44.53 3.97
230 231 4.040198 AGGACCCCCTTCCCTCCC 62.040 72.222 0.00 0.00 40.78 4.30
238 239 3.532155 CTTCCCTCCCGCTCCGAG 61.532 72.222 0.00 0.00 0.00 4.63
246 247 2.721167 CCCGCTCCGAGTCATGGAA 61.721 63.158 0.00 0.00 34.44 3.53
286 287 2.026879 GAGGATCGCGTGAGGAGC 59.973 66.667 5.77 0.00 0.00 4.70
297 298 0.250513 GTGAGGAGCCAACGAGGAAT 59.749 55.000 2.86 0.00 41.22 3.01
329 330 3.437746 GGAGGCAAGTTACTCCGTC 57.562 57.895 9.34 0.00 43.37 4.79
352 353 3.473647 CAGAGCCGAGGGATGCCA 61.474 66.667 5.86 0.00 0.00 4.92
374 375 4.552365 CGCCATGACATCCCCGCT 62.552 66.667 0.00 0.00 0.00 5.52
400 401 9.832445 TTGAACATACTAGTTCCCAAATCTATC 57.168 33.333 0.00 0.00 45.62 2.08
407 408 5.614324 AGTTCCCAAATCTATCATCGACA 57.386 39.130 0.00 0.00 0.00 4.35
412 413 6.701340 TCCCAAATCTATCATCGACAATAGG 58.299 40.000 13.26 1.93 0.00 2.57
420 421 7.951591 TCTATCATCGACAATAGGAATGAACA 58.048 34.615 13.26 0.00 0.00 3.18
422 423 6.908870 TCATCGACAATAGGAATGAACAAG 57.091 37.500 0.00 0.00 0.00 3.16
428 429 5.547465 ACAATAGGAATGAACAAGTCGTCA 58.453 37.500 0.00 0.00 0.00 4.35
443 444 4.815269 AGTCGTCAAAGAAGAATCTGGAG 58.185 43.478 0.00 0.00 35.59 3.86
445 446 2.675348 CGTCAAAGAAGAATCTGGAGCC 59.325 50.000 0.00 0.00 35.59 4.70
446 447 2.675348 GTCAAAGAAGAATCTGGAGCCG 59.325 50.000 0.00 0.00 35.59 5.52
448 449 0.107459 AAGAAGAATCTGGAGCCGCC 60.107 55.000 0.00 0.00 35.59 6.13
449 450 1.884926 GAAGAATCTGGAGCCGCCG 60.885 63.158 0.00 0.00 40.66 6.46
450 451 4.537433 AGAATCTGGAGCCGCCGC 62.537 66.667 0.00 0.00 40.66 6.53
464 483 4.404654 CCGCCAAAGCCAAGACGC 62.405 66.667 0.00 0.00 34.57 5.19
469 488 1.082104 CAAAGCCAAGACGCCGAAC 60.082 57.895 0.00 0.00 0.00 3.95
490 509 3.834231 ACGACCCAAAACCTAAGCTACTA 59.166 43.478 0.00 0.00 0.00 1.82
515 534 4.882427 GGCCCTAGAACCTAAAGCTAAAAG 59.118 45.833 0.00 0.00 0.00 2.27
524 543 6.002653 ACCTAAAGCTAAAAGGATCCGAAT 57.997 37.500 14.17 0.00 34.34 3.34
525 544 5.823045 ACCTAAAGCTAAAAGGATCCGAATG 59.177 40.000 14.17 0.00 34.34 2.67
526 545 4.639135 AAAGCTAAAAGGATCCGAATGC 57.361 40.909 5.98 8.72 0.00 3.56
527 546 2.213499 AGCTAAAAGGATCCGAATGCG 58.787 47.619 5.98 0.00 37.24 4.73
532 551 2.591715 GGATCCGAATGCGTGGGG 60.592 66.667 0.00 0.00 35.23 4.96
593 612 2.444140 GGAGGGGAGCCGCTAGAA 60.444 66.667 6.04 0.00 39.38 2.10
613 632 1.476085 AGACAGCGACAGAAGGATCAG 59.524 52.381 0.00 0.00 0.00 2.90
649 677 1.041447 TAGGGTTCCTAGCCGCTCAC 61.041 60.000 0.00 0.00 46.76 3.51
653 681 0.822164 GTTCCTAGCCGCTCACCTAA 59.178 55.000 0.00 0.00 0.00 2.69
663 691 2.412089 CCGCTCACCTAAGAGAAAAACG 59.588 50.000 0.00 0.00 37.87 3.60
692 720 5.163457 CCAAGCTTCAAAGGGACTGTTTTTA 60.163 40.000 0.00 0.00 40.86 1.52
723 752 2.307098 ACTTTCAAGGGACTGCTATGCT 59.693 45.455 0.00 0.00 40.86 3.79
928 957 0.890090 GTAGATCCTCCCGTCCCTCG 60.890 65.000 0.00 0.00 39.52 4.63
1130 1178 2.672996 GTCCACCCGCTGTTGCAT 60.673 61.111 0.00 0.00 39.64 3.96
1302 1399 1.198713 GCATCAACTCCTCCCTCTCA 58.801 55.000 0.00 0.00 0.00 3.27
1312 1409 2.037620 CTCCCTCTCATTCCTGCCCG 62.038 65.000 0.00 0.00 0.00 6.13
1317 1414 0.982852 TCTCATTCCTGCCCGGATGT 60.983 55.000 0.73 0.00 42.70 3.06
1371 1480 2.503356 CCTCCTCCTCTGTAAATGCTGT 59.497 50.000 0.00 0.00 0.00 4.40
1416 1525 2.080693 GATTACGTGGTGTGCAATCCA 58.919 47.619 0.00 6.98 0.00 3.41
1466 1575 0.249911 ACAAACTGGTCCAGCGAGTC 60.250 55.000 19.40 0.00 35.01 3.36
1538 1647 5.051816 TGTTTTTGAGTTCGTACCTACCTG 58.948 41.667 0.00 0.00 0.00 4.00
1709 1818 4.777463 ACCGGGATCCTGTATTTAACTTG 58.223 43.478 19.51 2.42 0.00 3.16
1784 1893 4.281435 TCGTGTTCCTAAACCACACTATCA 59.719 41.667 0.00 0.00 38.97 2.15
1785 1894 4.992319 CGTGTTCCTAAACCACACTATCAA 59.008 41.667 0.00 0.00 38.97 2.57
1809 1918 6.193514 TGTGGTGCTTATGATGTTTATGTG 57.806 37.500 0.00 0.00 0.00 3.21
1835 1944 2.539476 GGGCCATTTGTATTTCGCAAG 58.461 47.619 4.39 0.00 0.00 4.01
1860 1969 8.746530 AGTTGTGATGCTTCTGAAATATCAATT 58.253 29.630 14.19 2.03 34.49 2.32
2057 2198 3.602483 TGGTGGAACTATTTTCCTACGC 58.398 45.455 4.73 0.00 39.31 4.42
2061 2202 5.818857 GGTGGAACTATTTTCCTACGCAATA 59.181 40.000 4.73 0.00 39.31 1.90
2064 2205 6.759827 TGGAACTATTTTCCTACGCAATAGAC 59.240 38.462 4.73 0.66 39.31 2.59
2081 2222 1.474879 AGACTCTAAGGAGCTGCGTTC 59.525 52.381 0.00 0.00 42.98 3.95
2111 2252 3.309582 TGGACGGGAATCCAGCTC 58.690 61.111 0.09 0.00 44.14 4.09
2189 2330 1.869767 GTCTTGCATATTGGAGCCTCG 59.130 52.381 0.00 0.00 0.00 4.63
2227 2370 5.766590 TCTGATGATACCAGAGTTAGGTCA 58.233 41.667 0.00 0.00 40.54 4.02
2236 2379 4.954202 ACCAGAGTTAGGTCATGAATACGA 59.046 41.667 0.00 0.00 32.90 3.43
2238 2381 4.979197 CAGAGTTAGGTCATGAATACGAGC 59.021 45.833 0.00 0.00 0.00 5.03
2239 2382 4.645136 AGAGTTAGGTCATGAATACGAGCA 59.355 41.667 0.00 0.00 32.05 4.26
2257 2445 0.248498 CAGCAATGAAGGAGCGCATG 60.248 55.000 11.47 0.00 0.00 4.06
2260 2448 1.268234 GCAATGAAGGAGCGCATGTAC 60.268 52.381 11.47 0.00 0.00 2.90
2272 2460 3.006537 AGCGCATGTACCCGACTTTATAT 59.993 43.478 11.47 0.00 0.00 0.86
2282 2470 4.836736 ACCCGACTTTATATGGCTAGCTAA 59.163 41.667 15.72 3.70 0.00 3.09
2283 2471 5.169295 CCCGACTTTATATGGCTAGCTAAC 58.831 45.833 15.72 0.00 0.00 2.34
2309 2497 3.058224 CCAACTTTAGTACCTGCTTGTGC 60.058 47.826 0.00 0.00 40.20 4.57
2316 2504 1.002468 GTACCTGCTTGTGCTTGTGTG 60.002 52.381 0.00 0.00 40.48 3.82
2319 2507 0.029834 CTGCTTGTGCTTGTGTGGTC 59.970 55.000 0.00 0.00 40.48 4.02
2326 2514 5.528043 TTGTGCTTGTGTGGTCATAAATT 57.472 34.783 0.00 0.00 0.00 1.82
2334 2522 9.289303 GCTTGTGTGGTCATAAATTTATTAGTG 57.711 33.333 8.01 0.00 0.00 2.74
2338 2526 9.931210 GTGTGGTCATAAATTTATTAGTGTAGC 57.069 33.333 8.01 1.70 0.00 3.58
2339 2527 9.116067 TGTGGTCATAAATTTATTAGTGTAGCC 57.884 33.333 8.01 4.89 0.00 3.93
2340 2528 9.338622 GTGGTCATAAATTTATTAGTGTAGCCT 57.661 33.333 8.01 0.00 0.00 4.58
2359 2547 4.347876 AGCCTATATGCAGATGTAACACCA 59.652 41.667 3.54 0.00 0.00 4.17
2366 2554 5.018539 TGCAGATGTAACACCATAGTACC 57.981 43.478 0.00 0.00 0.00 3.34
2383 2571 4.820775 AGTACCTCACCATGGATACTCAT 58.179 43.478 21.47 0.00 37.61 2.90
2456 2644 5.347635 TCTCTGTTTGTGAATAATTCGTCGG 59.652 40.000 0.00 0.00 0.00 4.79
2461 2649 6.089820 TGTTTGTGAATAATTCGTCGGTCTAC 59.910 38.462 0.00 0.00 0.00 2.59
2486 2674 5.862924 ACTTCTGTTTCCGACAATACATG 57.137 39.130 0.00 0.00 37.93 3.21
2498 2686 7.981142 TCCGACAATACATGAAAGGTTATTTC 58.019 34.615 0.00 0.00 28.09 2.17
2519 2707 7.907214 TTTCCTTGTTTGTAATCTCTAGCTC 57.093 36.000 0.00 0.00 0.00 4.09
2523 2711 6.351371 CCTTGTTTGTAATCTCTAGCTCTGGA 60.351 42.308 0.00 0.00 0.00 3.86
2524 2712 6.214191 TGTTTGTAATCTCTAGCTCTGGAG 57.786 41.667 4.14 4.14 39.24 3.86
2573 2761 0.620556 GGACCTGGAATGGAAGAGCA 59.379 55.000 0.00 0.00 0.00 4.26
2588 2776 2.711711 AGCACAAGACTGCTGTTGG 58.288 52.632 0.00 0.00 46.10 3.77
2593 2781 3.491447 GCACAAGACTGCTGTTGGATTTT 60.491 43.478 0.00 0.00 34.06 1.82
2655 2878 1.785041 TTGCCTGCTGAAACTGCGAC 61.785 55.000 0.00 0.00 0.00 5.19
2659 2882 2.076100 CCTGCTGAAACTGCGACATAA 58.924 47.619 0.00 0.00 0.00 1.90
2662 2885 4.332543 CCTGCTGAAACTGCGACATAATAA 59.667 41.667 0.00 0.00 0.00 1.40
2663 2886 5.469373 TGCTGAAACTGCGACATAATAAG 57.531 39.130 0.00 0.00 0.00 1.73
2664 2887 4.332543 TGCTGAAACTGCGACATAATAAGG 59.667 41.667 0.00 0.00 0.00 2.69
2665 2888 4.332819 GCTGAAACTGCGACATAATAAGGT 59.667 41.667 0.00 0.00 0.00 3.50
2666 2889 5.163754 GCTGAAACTGCGACATAATAAGGTT 60.164 40.000 0.00 0.00 0.00 3.50
2673 2899 9.909644 AACTGCGACATAATAAGGTTATAGTAG 57.090 33.333 0.00 0.00 0.00 2.57
2724 2952 4.183865 TCTGATATGAACTGCCGTTTCAG 58.816 43.478 11.91 11.91 36.38 3.02
2734 2962 0.868406 GCCGTTTCAGTTCACTCTGG 59.132 55.000 0.00 0.00 36.25 3.86
2748 2976 3.964688 TCACTCTGGACCTCAAGTGTTTA 59.035 43.478 16.17 1.50 36.64 2.01
2751 2979 4.177026 CTCTGGACCTCAAGTGTTTATCG 58.823 47.826 0.00 0.00 0.00 2.92
2755 2983 2.930682 GACCTCAAGTGTTTATCGCCTC 59.069 50.000 0.00 0.00 0.00 4.70
2756 2984 1.927174 CCTCAAGTGTTTATCGCCTCG 59.073 52.381 0.00 0.00 0.00 4.63
2757 2985 2.416836 CCTCAAGTGTTTATCGCCTCGA 60.417 50.000 0.00 0.00 41.13 4.04
2758 2986 2.854777 CTCAAGTGTTTATCGCCTCGAG 59.145 50.000 5.13 5.13 39.91 4.04
2759 2987 1.927174 CAAGTGTTTATCGCCTCGAGG 59.073 52.381 27.83 27.83 39.91 4.63
2760 2988 0.460311 AGTGTTTATCGCCTCGAGGG 59.540 55.000 32.06 21.49 39.91 4.30
2761 2989 0.175073 GTGTTTATCGCCTCGAGGGT 59.825 55.000 32.06 14.53 39.91 4.34
2762 2990 0.899720 TGTTTATCGCCTCGAGGGTT 59.100 50.000 32.06 18.40 39.91 4.11
2763 2991 2.101783 TGTTTATCGCCTCGAGGGTTA 58.898 47.619 32.06 17.47 39.91 2.85
2764 2992 2.696707 TGTTTATCGCCTCGAGGGTTAT 59.303 45.455 32.06 14.49 39.91 1.89
2765 2993 3.133362 TGTTTATCGCCTCGAGGGTTATT 59.867 43.478 32.06 11.49 39.91 1.40
2766 2994 3.655276 TTATCGCCTCGAGGGTTATTC 57.345 47.619 32.06 13.63 39.91 1.75
2767 2995 0.314302 ATCGCCTCGAGGGTTATTCG 59.686 55.000 32.06 24.13 39.91 3.34
2768 2996 1.949631 CGCCTCGAGGGTTATTCGC 60.950 63.158 32.06 14.18 37.94 4.70
2769 2997 1.594564 GCCTCGAGGGTTATTCGCC 60.595 63.158 32.06 8.86 37.94 5.54
2770 2998 1.820581 CCTCGAGGGTTATTCGCCA 59.179 57.895 24.62 0.00 37.94 5.69
2771 2999 0.249489 CCTCGAGGGTTATTCGCCAG 60.249 60.000 24.62 0.00 37.94 4.85
2772 3000 0.249489 CTCGAGGGTTATTCGCCAGG 60.249 60.000 3.91 0.00 37.94 4.45
2773 3001 0.974010 TCGAGGGTTATTCGCCAGGT 60.974 55.000 0.00 0.00 37.94 4.00
2774 3002 0.810031 CGAGGGTTATTCGCCAGGTG 60.810 60.000 0.00 0.00 0.00 4.00
2789 3017 4.260784 CGCCAGGTGCAATTTCTAATAGAC 60.261 45.833 0.00 0.00 41.33 2.59
2792 3020 5.235186 CCAGGTGCAATTTCTAATAGACGAG 59.765 44.000 0.00 0.00 0.00 4.18
2795 3023 5.810587 GGTGCAATTTCTAATAGACGAGTCA 59.189 40.000 5.99 0.00 0.00 3.41
2796 3024 6.237861 GGTGCAATTTCTAATAGACGAGTCAC 60.238 42.308 5.99 0.00 0.00 3.67
2800 3028 4.634184 TTCTAATAGACGAGTCACCTGC 57.366 45.455 5.99 0.00 0.00 4.85
2819 3047 4.201891 CCTGCTCAATTAGTTCAGTCATGC 60.202 45.833 0.00 0.00 0.00 4.06
2874 3103 0.322648 TGCATCCTGATATCGCTGGG 59.677 55.000 0.00 0.00 0.00 4.45
2891 3120 4.454678 GCTGGGAAATCATGATCTACACA 58.545 43.478 9.06 9.64 0.00 3.72
2933 3162 5.000591 TCTTATTTGTTTGCTCCACATCGA 58.999 37.500 0.00 0.00 0.00 3.59
2965 3194 4.574892 TGTTTGTCAAATCTATCAGGCGA 58.425 39.130 0.40 0.00 0.00 5.54
2988 3217 6.566079 ACAGTTCAGATTGGATAATGGAGA 57.434 37.500 0.00 0.00 0.00 3.71
3041 3270 3.325293 AGAGTGTCGATTTGCATGAGT 57.675 42.857 0.00 0.00 0.00 3.41
3045 3274 3.928992 AGTGTCGATTTGCATGAGTAGTG 59.071 43.478 0.00 0.00 0.00 2.74
3054 3283 1.134280 GCATGAGTAGTGCACCAGGAT 60.134 52.381 14.63 0.00 42.08 3.24
3055 3284 2.831333 CATGAGTAGTGCACCAGGATC 58.169 52.381 14.63 5.74 0.00 3.36
3056 3285 1.937191 TGAGTAGTGCACCAGGATCA 58.063 50.000 14.63 8.40 0.00 2.92
3057 3286 2.256306 TGAGTAGTGCACCAGGATCAA 58.744 47.619 14.63 0.00 0.00 2.57
3058 3287 2.234661 TGAGTAGTGCACCAGGATCAAG 59.765 50.000 14.63 0.00 0.00 3.02
3059 3288 2.497675 GAGTAGTGCACCAGGATCAAGA 59.502 50.000 14.63 0.00 0.00 3.02
3066 3295 2.093288 GCACCAGGATCAAGATGAGACA 60.093 50.000 0.00 0.00 0.00 3.41
3074 3303 4.436584 GGATCAAGATGAGACAAAGTTGCG 60.437 45.833 0.00 0.00 0.00 4.85
3076 3305 4.318332 TCAAGATGAGACAAAGTTGCGAT 58.682 39.130 0.00 0.00 0.00 4.58
3092 3321 1.514228 GATGACGTCGCTCGAGCAA 60.514 57.895 34.69 17.41 42.86 3.91
3103 3332 1.801395 GCTCGAGCAACGCCTGTTATA 60.801 52.381 31.91 0.00 42.26 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.392165 CGTATTTTAAAATGGGTCGGCTTGA 60.392 40.000 21.19 0.00 0.00 3.02
18 19 4.796312 CGTATTTTAAAATGGGTCGGCTTG 59.204 41.667 21.19 0.00 0.00 4.01
19 20 4.142337 CCGTATTTTAAAATGGGTCGGCTT 60.142 41.667 21.19 0.00 0.00 4.35
20 21 3.379057 CCGTATTTTAAAATGGGTCGGCT 59.621 43.478 21.19 0.00 0.00 5.52
21 22 3.377798 TCCGTATTTTAAAATGGGTCGGC 59.622 43.478 25.56 10.64 33.90 5.54
22 23 4.494526 CGTCCGTATTTTAAAATGGGTCGG 60.495 45.833 26.05 25.53 34.58 4.79
23 24 4.093261 ACGTCCGTATTTTAAAATGGGTCG 59.907 41.667 28.73 28.73 38.90 4.79
24 25 5.326292 CACGTCCGTATTTTAAAATGGGTC 58.674 41.667 21.19 17.14 0.00 4.46
25 26 4.379708 GCACGTCCGTATTTTAAAATGGGT 60.380 41.667 21.19 8.08 0.00 4.51
26 27 4.099824 GCACGTCCGTATTTTAAAATGGG 58.900 43.478 21.19 20.11 0.00 4.00
27 28 4.555747 GTGCACGTCCGTATTTTAAAATGG 59.444 41.667 21.19 15.20 0.00 3.16
28 29 4.258817 CGTGCACGTCCGTATTTTAAAATG 59.741 41.667 30.50 7.36 34.11 2.32
29 30 4.396519 CGTGCACGTCCGTATTTTAAAAT 58.603 39.130 30.50 17.18 34.11 1.82
30 31 3.796783 CGTGCACGTCCGTATTTTAAAA 58.203 40.909 30.50 2.51 34.11 1.52
31 32 3.436817 CGTGCACGTCCGTATTTTAAA 57.563 42.857 30.50 0.00 34.11 1.52
65 66 0.382515 CCGCTTTTTGTCCGTTTGGA 59.617 50.000 0.00 0.00 43.88 3.53
66 67 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
67 68 1.202200 TGTCCGCTTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
68 69 1.096416 TGTCCGCTTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
69 70 1.096416 TTGTCCGCTTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
70 71 1.064952 CTTTGTCCGCTTTTTGTCCGT 59.935 47.619 0.00 0.00 0.00 4.69
71 72 1.753956 CTTTGTCCGCTTTTTGTCCG 58.246 50.000 0.00 0.00 0.00 4.79
72 73 1.487482 GCTTTGTCCGCTTTTTGTCC 58.513 50.000 0.00 0.00 0.00 4.02
73 74 1.120437 CGCTTTGTCCGCTTTTTGTC 58.880 50.000 0.00 0.00 0.00 3.18
74 75 3.250220 CGCTTTGTCCGCTTTTTGT 57.750 47.368 0.00 0.00 0.00 2.83
86 87 4.659874 AAACGGACGCGCGCTTTG 62.660 61.111 32.58 19.69 0.00 2.77
87 88 4.659874 CAAACGGACGCGCGCTTT 62.660 61.111 32.58 19.12 0.00 3.51
106 107 3.047877 CAACTCCAACGGGGCGAC 61.048 66.667 0.00 0.00 36.21 5.19
109 110 3.056328 GAGCAACTCCAACGGGGC 61.056 66.667 0.00 0.00 36.21 5.80
110 111 0.323629 TAAGAGCAACTCCAACGGGG 59.676 55.000 0.00 0.00 38.37 5.73
111 112 1.275291 TCTAAGAGCAACTCCAACGGG 59.725 52.381 0.00 0.00 0.00 5.28
112 113 2.028930 AGTCTAAGAGCAACTCCAACGG 60.029 50.000 0.00 0.00 0.00 4.44
113 114 3.305398 AGTCTAAGAGCAACTCCAACG 57.695 47.619 0.00 0.00 0.00 4.10
114 115 4.021368 TGGTAGTCTAAGAGCAACTCCAAC 60.021 45.833 0.00 0.00 0.00 3.77
115 116 4.157246 TGGTAGTCTAAGAGCAACTCCAA 58.843 43.478 0.00 0.00 0.00 3.53
116 117 3.774734 TGGTAGTCTAAGAGCAACTCCA 58.225 45.455 0.00 0.00 0.00 3.86
117 118 4.496360 GTTGGTAGTCTAAGAGCAACTCC 58.504 47.826 9.12 0.00 45.89 3.85
121 122 5.801531 TCTTGTTGGTAGTCTAAGAGCAA 57.198 39.130 0.00 0.00 0.00 3.91
122 123 5.801531 TTCTTGTTGGTAGTCTAAGAGCA 57.198 39.130 0.00 0.00 0.00 4.26
123 124 6.456501 TCTTTCTTGTTGGTAGTCTAAGAGC 58.543 40.000 0.00 0.00 0.00 4.09
124 125 8.361139 TCTTCTTTCTTGTTGGTAGTCTAAGAG 58.639 37.037 0.00 0.00 0.00 2.85
125 126 8.142551 GTCTTCTTTCTTGTTGGTAGTCTAAGA 58.857 37.037 0.00 0.00 0.00 2.10
137 138 4.120589 GGTGTCGAGTCTTCTTTCTTGTT 58.879 43.478 0.00 0.00 0.00 2.83
143 144 3.467803 CCTTTGGTGTCGAGTCTTCTTT 58.532 45.455 0.00 0.00 0.00 2.52
155 156 1.456287 GCTGGTCTCCCTTTGGTGT 59.544 57.895 0.00 0.00 0.00 4.16
167 168 4.699522 AAACGAGGCCCGCTGGTC 62.700 66.667 12.78 0.00 43.32 4.02
188 189 2.741092 GGGAACGAGGTGTGAGCA 59.259 61.111 0.00 0.00 0.00 4.26
223 224 4.816984 GACTCGGAGCGGGAGGGA 62.817 72.222 4.58 0.00 35.82 4.20
225 226 2.835431 ATGACTCGGAGCGGGAGG 60.835 66.667 4.58 0.00 35.82 4.30
226 227 2.415010 CATGACTCGGAGCGGGAG 59.585 66.667 4.58 0.96 37.54 4.30
230 231 1.880340 GCTTCCATGACTCGGAGCG 60.880 63.158 4.58 0.00 33.01 5.03
235 236 0.804989 GGTTTGGCTTCCATGACTCG 59.195 55.000 0.00 0.00 31.53 4.18
236 237 2.206576 AGGTTTGGCTTCCATGACTC 57.793 50.000 0.00 0.00 31.53 3.36
237 238 2.290960 GGTAGGTTTGGCTTCCATGACT 60.291 50.000 0.00 0.00 31.53 3.41
238 239 2.092323 GGTAGGTTTGGCTTCCATGAC 58.908 52.381 0.00 0.00 31.53 3.06
241 242 1.710809 ACAGGTAGGTTTGGCTTCCAT 59.289 47.619 0.00 0.00 31.53 3.41
269 270 2.026879 GCTCCTCACGCGATCCTC 59.973 66.667 15.93 0.00 0.00 3.71
278 279 0.250513 ATTCCTCGTTGGCTCCTCAC 59.749 55.000 0.00 0.00 35.26 3.51
279 280 0.537188 GATTCCTCGTTGGCTCCTCA 59.463 55.000 0.00 0.00 35.26 3.86
297 298 4.222145 ACTTGCCTCCTATTCTTTACACGA 59.778 41.667 0.00 0.00 0.00 4.35
352 353 2.124570 GGATGTCATGGCGGCAGT 60.125 61.111 19.29 2.72 0.00 4.40
374 375 9.832445 GATAGATTTGGGAACTAGTATGTTCAA 57.168 33.333 0.00 0.00 45.74 2.69
400 401 6.508563 CGACTTGTTCATTCCTATTGTCGATG 60.509 42.308 0.00 0.00 44.72 3.84
407 408 6.934645 TCTTTGACGACTTGTTCATTCCTATT 59.065 34.615 0.00 0.00 0.00 1.73
412 413 6.287107 TCTTCTTTGACGACTTGTTCATTC 57.713 37.500 0.00 0.00 0.00 2.67
420 421 5.215252 TCCAGATTCTTCTTTGACGACTT 57.785 39.130 0.00 0.00 0.00 3.01
422 423 3.369451 GCTCCAGATTCTTCTTTGACGAC 59.631 47.826 0.00 0.00 0.00 4.34
428 429 1.680249 GGCGGCTCCAGATTCTTCTTT 60.680 52.381 0.00 0.00 34.01 2.52
445 446 4.404654 GTCTTGGCTTTGGCGGCG 62.405 66.667 0.51 0.51 39.81 6.46
446 447 4.404654 CGTCTTGGCTTTGGCGGC 62.405 66.667 0.00 0.00 39.81 6.53
448 449 4.404654 GGCGTCTTGGCTTTGGCG 62.405 66.667 0.00 0.00 40.72 5.69
449 450 4.404654 CGGCGTCTTGGCTTTGGC 62.405 66.667 0.00 0.00 42.02 4.52
450 451 2.258013 TTCGGCGTCTTGGCTTTGG 61.258 57.895 6.85 0.00 42.02 3.28
454 473 3.986006 TCGTTCGGCGTCTTGGCT 61.986 61.111 6.85 0.00 42.02 4.75
460 479 2.246042 TTTTGGGTCGTTCGGCGTC 61.246 57.895 6.85 0.36 42.13 5.19
464 483 1.802365 CTTAGGTTTTGGGTCGTTCGG 59.198 52.381 0.00 0.00 0.00 4.30
469 488 3.329929 AGTAGCTTAGGTTTTGGGTCG 57.670 47.619 0.00 0.00 0.00 4.79
470 489 4.383880 CCCTAGTAGCTTAGGTTTTGGGTC 60.384 50.000 10.05 0.00 38.86 4.46
490 509 1.214217 GCTTTAGGTTCTAGGGCCCT 58.786 55.000 31.35 31.35 0.00 5.19
515 534 2.591715 CCCCACGCATTCGGATCC 60.592 66.667 0.00 0.00 40.69 3.36
579 598 2.022240 CTGTCTTCTAGCGGCTCCCC 62.022 65.000 5.39 0.00 0.00 4.81
580 599 1.439644 CTGTCTTCTAGCGGCTCCC 59.560 63.158 5.39 0.00 0.00 4.30
588 607 2.750166 TCCTTCTGTCGCTGTCTTCTAG 59.250 50.000 0.00 0.00 0.00 2.43
590 609 1.621992 TCCTTCTGTCGCTGTCTTCT 58.378 50.000 0.00 0.00 0.00 2.85
593 612 1.476085 CTGATCCTTCTGTCGCTGTCT 59.524 52.381 0.00 0.00 0.00 3.41
601 620 2.109774 CAGGAGAGCTGATCCTTCTGT 58.890 52.381 13.37 0.00 45.13 3.41
642 670 2.412089 CGTTTTTCTCTTAGGTGAGCGG 59.588 50.000 0.00 0.00 34.29 5.52
649 677 5.392057 GCTTGGGAATCGTTTTTCTCTTAGG 60.392 44.000 0.00 0.00 0.00 2.69
653 681 3.756117 AGCTTGGGAATCGTTTTTCTCT 58.244 40.909 0.00 0.00 0.00 3.10
663 691 2.807676 TCCCTTTGAAGCTTGGGAATC 58.192 47.619 17.72 0.00 44.89 2.52
692 720 6.683861 GCAGTCCCTTGAAAGTTCTCAAAAAT 60.684 38.462 0.00 0.00 34.96 1.82
723 752 3.105203 CGAGCTTTTGTTTTTCGAAGCA 58.895 40.909 9.28 0.00 33.38 3.91
827 856 0.737715 CAGTAGCGAGTTGGAGGCAC 60.738 60.000 0.00 0.00 0.00 5.01
928 957 1.017387 GAACTTGATGATGGGACCGC 58.983 55.000 0.00 0.00 0.00 5.68
931 960 4.273480 CGGTAATGAACTTGATGATGGGAC 59.727 45.833 0.00 0.00 0.00 4.46
1185 1237 1.404391 GCGAGGGTCGACTGAGAAATA 59.596 52.381 16.46 0.00 43.74 1.40
1186 1238 0.173708 GCGAGGGTCGACTGAGAAAT 59.826 55.000 16.46 0.00 43.74 2.17
1312 1409 7.439655 GTCCAATATGTCTAGTTTCTCACATCC 59.560 40.741 0.00 0.00 31.83 3.51
1317 1414 6.155221 AGCAGTCCAATATGTCTAGTTTCTCA 59.845 38.462 0.00 0.00 0.00 3.27
1466 1575 1.370414 CCCAAGCGAACTTTGCACG 60.370 57.895 3.77 0.00 32.29 5.34
1538 1647 2.370189 CTCTTATCCCCATCCCAGACAC 59.630 54.545 0.00 0.00 0.00 3.67
1709 1818 2.599973 GTCGCAACCAAATCATCATTGC 59.400 45.455 0.00 0.00 41.74 3.56
1784 1893 7.093814 ACACATAAACATCATAAGCACCACATT 60.094 33.333 0.00 0.00 0.00 2.71
1785 1894 6.377996 ACACATAAACATCATAAGCACCACAT 59.622 34.615 0.00 0.00 0.00 3.21
1809 1918 1.470051 AATACAAATGGCCCCGTGAC 58.530 50.000 0.00 0.00 0.00 3.67
1835 1944 8.922058 AATTGATATTTCAGAAGCATCACAAC 57.078 30.769 7.82 0.00 32.27 3.32
1860 1969 8.789762 GCAGTACTAAAATCTTCTAAAACCCAA 58.210 33.333 0.00 0.00 0.00 4.12
1942 2051 4.464951 ACAACAATGATCATCATGGCTTGT 59.535 37.500 9.06 13.26 37.15 3.16
2057 2198 3.067461 ACGCAGCTCCTTAGAGTCTATTG 59.933 47.826 0.00 0.00 42.59 1.90
2061 2202 1.474879 GAACGCAGCTCCTTAGAGTCT 59.525 52.381 0.00 0.00 42.59 3.24
2064 2205 0.452184 TCGAACGCAGCTCCTTAGAG 59.548 55.000 0.00 0.00 43.57 2.43
2081 2222 2.296190 TCCCGTCCAAGATCACATATCG 59.704 50.000 0.00 0.00 0.00 2.92
2111 2252 6.206180 AGGGAACATATGAAAGATAAGGGG 57.794 41.667 10.38 0.00 0.00 4.79
2215 2358 4.979197 GCTCGTATTCATGACCTAACTCTG 59.021 45.833 0.00 0.00 0.00 3.35
2223 2366 1.939974 TGCTGCTCGTATTCATGACC 58.060 50.000 0.00 0.00 0.00 4.02
2227 2370 3.562973 CCTTCATTGCTGCTCGTATTCAT 59.437 43.478 0.00 0.00 0.00 2.57
2236 2379 2.404995 GCGCTCCTTCATTGCTGCT 61.405 57.895 0.00 0.00 0.00 4.24
2238 2381 0.248498 CATGCGCTCCTTCATTGCTG 60.248 55.000 9.73 0.00 0.00 4.41
2239 2382 0.679002 ACATGCGCTCCTTCATTGCT 60.679 50.000 9.73 0.00 0.00 3.91
2257 2445 4.220163 AGCTAGCCATATAAAGTCGGGTAC 59.780 45.833 12.13 0.00 0.00 3.34
2260 2448 3.963428 AGCTAGCCATATAAAGTCGGG 57.037 47.619 12.13 0.00 0.00 5.14
2282 2470 2.552373 GCAGGTACTAAAGTTGGCTGGT 60.552 50.000 0.00 0.00 36.02 4.00
2283 2471 2.084546 GCAGGTACTAAAGTTGGCTGG 58.915 52.381 0.00 0.00 36.02 4.85
2287 2475 3.058224 GCACAAGCAGGTACTAAAGTTGG 60.058 47.826 0.00 0.00 41.58 3.77
2292 2480 3.563808 CACAAGCACAAGCAGGTACTAAA 59.436 43.478 0.00 0.00 45.49 1.85
2293 2481 3.138304 CACAAGCACAAGCAGGTACTAA 58.862 45.455 0.00 0.00 45.49 2.24
2326 2514 9.035890 ACATCTGCATATAGGCTACACTAATAA 57.964 33.333 11.14 0.00 34.04 1.40
2334 2522 5.869888 GGTGTTACATCTGCATATAGGCTAC 59.130 44.000 11.14 0.00 34.04 3.58
2335 2523 5.542251 TGGTGTTACATCTGCATATAGGCTA 59.458 40.000 11.14 0.00 34.04 3.93
2336 2524 4.347876 TGGTGTTACATCTGCATATAGGCT 59.652 41.667 11.14 0.00 34.04 4.58
2337 2525 4.641396 TGGTGTTACATCTGCATATAGGC 58.359 43.478 1.55 1.55 0.00 3.93
2338 2526 7.615403 ACTATGGTGTTACATCTGCATATAGG 58.385 38.462 0.00 0.00 32.39 2.57
2339 2527 9.574458 GTACTATGGTGTTACATCTGCATATAG 57.426 37.037 0.00 0.00 32.39 1.31
2340 2528 8.528643 GGTACTATGGTGTTACATCTGCATATA 58.471 37.037 0.00 0.00 32.39 0.86
2341 2529 7.235606 AGGTACTATGGTGTTACATCTGCATAT 59.764 37.037 0.00 0.00 36.02 1.78
2359 2547 5.965486 TGAGTATCCATGGTGAGGTACTAT 58.035 41.667 12.58 0.00 41.55 2.12
2366 2554 8.347771 CAAAACAATATGAGTATCCATGGTGAG 58.652 37.037 12.58 0.00 0.00 3.51
2435 2623 5.120208 AGACCGACGAATTATTCACAAACAG 59.880 40.000 5.76 0.00 0.00 3.16
2439 2627 5.104374 GGTAGACCGACGAATTATTCACAA 58.896 41.667 5.76 0.00 0.00 3.33
2456 2644 3.739810 GTCGGAAACAGAAGTTGGTAGAC 59.260 47.826 0.00 0.00 38.17 2.59
2461 2649 4.513692 TGTATTGTCGGAAACAGAAGTTGG 59.486 41.667 0.00 0.00 39.58 3.77
2498 2686 5.814705 CCAGAGCTAGAGATTACAAACAAGG 59.185 44.000 0.00 0.00 0.00 3.61
2519 2707 6.533367 GCAAGATCTTCAGTTAGTTACTCCAG 59.467 42.308 4.57 0.00 33.85 3.86
2523 2711 6.998802 ACAGCAAGATCTTCAGTTAGTTACT 58.001 36.000 4.57 0.00 37.68 2.24
2524 2712 7.659652 AACAGCAAGATCTTCAGTTAGTTAC 57.340 36.000 4.57 0.00 0.00 2.50
2593 2781 5.651387 TGGAATGACAAACAGACACAAAA 57.349 34.783 0.00 0.00 0.00 2.44
2595 2783 5.850557 AATGGAATGACAAACAGACACAA 57.149 34.783 0.00 0.00 0.00 3.33
2597 2785 6.534793 ACAAAAATGGAATGACAAACAGACAC 59.465 34.615 0.00 0.00 0.00 3.67
2633 2856 0.670162 GCAGTTTCAGCAGGCAAGAA 59.330 50.000 0.00 0.00 0.00 2.52
2634 2857 1.509644 CGCAGTTTCAGCAGGCAAGA 61.510 55.000 0.00 0.00 0.00 3.02
2663 2886 9.374960 CGATCGTGTTAAACTACTACTATAACC 57.625 37.037 7.03 0.00 0.00 2.85
2664 2887 9.922305 ACGATCGTGTTAAACTACTACTATAAC 57.078 33.333 22.06 0.00 0.00 1.89
2666 2889 8.480066 CGACGATCGTGTTAAACTACTACTATA 58.520 37.037 28.12 0.00 34.72 1.31
2673 2899 3.166657 AGCGACGATCGTGTTAAACTAC 58.833 45.455 28.12 6.61 42.81 2.73
2691 2917 5.050499 CAGTTCATATCAGAAAGCCTTAGCG 60.050 44.000 0.00 0.00 46.67 4.26
2724 2952 2.103263 ACACTTGAGGTCCAGAGTGAAC 59.897 50.000 19.94 0.00 41.46 3.18
2727 2955 2.918712 AACACTTGAGGTCCAGAGTG 57.081 50.000 14.33 14.33 43.81 3.51
2734 2962 2.930682 GAGGCGATAAACACTTGAGGTC 59.069 50.000 0.00 0.00 0.00 3.85
2748 2976 0.314302 CGAATAACCCTCGAGGCGAT 59.686 55.000 26.87 14.84 40.58 4.58
2751 2979 1.594564 GGCGAATAACCCTCGAGGC 60.595 63.158 26.87 11.61 40.58 4.70
2755 2983 0.810031 CACCTGGCGAATAACCCTCG 60.810 60.000 0.00 0.00 39.33 4.63
2756 2984 1.095807 GCACCTGGCGAATAACCCTC 61.096 60.000 0.00 0.00 0.00 4.30
2757 2985 1.077716 GCACCTGGCGAATAACCCT 60.078 57.895 0.00 0.00 0.00 4.34
2758 2986 3.509659 GCACCTGGCGAATAACCC 58.490 61.111 0.00 0.00 0.00 4.11
2767 2995 4.260784 CGTCTATTAGAAATTGCACCTGGC 60.261 45.833 0.00 0.00 45.13 4.85
2768 2996 5.116180 TCGTCTATTAGAAATTGCACCTGG 58.884 41.667 0.00 0.00 0.00 4.45
2769 2997 5.812642 ACTCGTCTATTAGAAATTGCACCTG 59.187 40.000 0.00 0.00 0.00 4.00
2770 2998 5.978814 ACTCGTCTATTAGAAATTGCACCT 58.021 37.500 0.00 0.00 0.00 4.00
2771 2999 5.810587 TGACTCGTCTATTAGAAATTGCACC 59.189 40.000 0.00 0.00 0.00 5.01
2772 3000 6.237861 GGTGACTCGTCTATTAGAAATTGCAC 60.238 42.308 0.00 2.64 0.00 4.57
2773 3001 5.810587 GGTGACTCGTCTATTAGAAATTGCA 59.189 40.000 0.00 0.00 0.00 4.08
2774 3002 6.019479 CAGGTGACTCGTCTATTAGAAATTGC 60.019 42.308 0.00 0.00 40.21 3.56
2789 3017 3.238108 ACTAATTGAGCAGGTGACTCG 57.762 47.619 0.00 0.00 40.21 4.18
2792 3020 4.319177 ACTGAACTAATTGAGCAGGTGAC 58.681 43.478 0.00 0.00 0.00 3.67
2795 3023 4.623932 TGACTGAACTAATTGAGCAGGT 57.376 40.909 0.00 0.00 0.00 4.00
2796 3024 4.201891 GCATGACTGAACTAATTGAGCAGG 60.202 45.833 0.00 0.00 0.00 4.85
2800 3028 4.033358 GGACGCATGACTGAACTAATTGAG 59.967 45.833 0.00 0.00 0.00 3.02
2819 3047 1.254284 ACTTCTGAGCAGGAGGGACG 61.254 60.000 10.40 0.00 38.40 4.79
2863 3092 5.426504 AGATCATGATTTCCCAGCGATATC 58.573 41.667 10.14 0.00 31.53 1.63
2865 3094 4.897509 AGATCATGATTTCCCAGCGATA 57.102 40.909 10.14 0.00 0.00 2.92
2869 3098 4.454678 TGTGTAGATCATGATTTCCCAGC 58.545 43.478 10.14 0.00 0.00 4.85
2874 3103 5.065602 TGCAAGCTGTGTAGATCATGATTTC 59.934 40.000 10.14 0.00 0.00 2.17
2891 3120 3.549794 AGAAGTTTCTCTGTTGCAAGCT 58.450 40.909 0.00 0.00 29.94 3.74
2933 3162 6.645790 AGATTTGACAAACAATCAGAAGCT 57.354 33.333 1.94 0.00 38.36 3.74
2965 3194 6.566079 TCTCCATTATCCAATCTGAACTGT 57.434 37.500 0.00 0.00 0.00 3.55
2988 3217 1.967319 ACGTGTGCAGTCCAGATTTT 58.033 45.000 0.00 0.00 0.00 1.82
3041 3270 3.106827 TCATCTTGATCCTGGTGCACTA 58.893 45.455 17.98 10.29 0.00 2.74
3045 3274 2.093288 TGTCTCATCTTGATCCTGGTGC 60.093 50.000 0.00 0.00 0.00 5.01
3054 3283 3.727726 TCGCAACTTTGTCTCATCTTGA 58.272 40.909 0.00 0.00 0.00 3.02
3055 3284 4.152938 TCATCGCAACTTTGTCTCATCTTG 59.847 41.667 0.00 0.00 0.00 3.02
3056 3285 4.153117 GTCATCGCAACTTTGTCTCATCTT 59.847 41.667 0.00 0.00 0.00 2.40
3057 3286 3.681897 GTCATCGCAACTTTGTCTCATCT 59.318 43.478 0.00 0.00 0.00 2.90
3058 3287 3.482598 CGTCATCGCAACTTTGTCTCATC 60.483 47.826 0.00 0.00 0.00 2.92
3059 3288 2.413112 CGTCATCGCAACTTTGTCTCAT 59.587 45.455 0.00 0.00 0.00 2.90
3074 3303 1.514228 TTGCTCGAGCGACGTCATC 60.514 57.895 30.75 11.76 45.83 2.92
3076 3305 2.428569 GTTGCTCGAGCGACGTCA 60.429 61.111 35.41 14.99 44.53 4.35
3092 3321 2.613595 TCGACACGTATATAACAGGCGT 59.386 45.455 0.00 0.00 36.12 5.68
3103 3332 9.702726 CAGAAAATTAATCAAATCGACACGTAT 57.297 29.630 0.00 0.00 0.00 3.06
3140 3370 1.688197 ACTTGCAAATTGGGTCACAGG 59.312 47.619 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.