Multiple sequence alignment - TraesCS3B01G435500

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 TraesCS3B01G435500 chr3B 100.000 2716 0 0 1 2716 673848032 673845317 0.000000e+00 5016.0
1 TraesCS3B01G435500 chr3B 100.000 279 0 0 2871 3149 673845162 673844884 1.670000e-142 516.0
2 TraesCS3B01G435500 chr3B 91.667 204 8 1 2513 2716 673840480 673840286 1.110000e-69 274.0
3 TraesCS3B01G435500 chr3B 100.000 35 0 0 428 462 743799306 743799340 7.290000e-07 65.8
4 TraesCS3B01G435500 chr3A 92.018 1992 108 16 509 2465 647690828 647688853 0.000000e+00 2750.0
5 TraesCS3B01G435500 chr3A 95.699 279 12 0 2871 3149 18136222 18136500 1.720000e-122 449.0
6 TraesCS3B01G435500 chr3A 85.284 299 24 6 38 320 647691555 647691261 1.100000e-74 291.0
7 TraesCS3B01G435500 chr3A 89.756 205 17 3 2514 2716 18135969 18136171 3.120000e-65 259.0
8 TraesCS3B01G435500 chr3A 90.698 86 5 1 322 407 647691174 647691092 9.230000e-21 111.0
9 TraesCS3B01G435500 chr7A 81.994 933 140 12 1015 1945 550052079 550052985 0.000000e+00 767.0
10 TraesCS3B01G435500 chr7D 81.886 933 141 12 1015 1945 483877550 483878456 0.000000e+00 761.0
11 TraesCS3B01G435500 chr7D 93.907 279 17 0 2871 3149 27286774 27286496 3.760000e-114 422.0
12 TraesCS3B01G435500 chr7D 86.538 208 15 8 2513 2716 27282087 27281889 1.900000e-52 217.0
13 TraesCS3B01G435500 chr7B 81.458 933 145 12 1015 1945 509512380 509513286 0.000000e+00 739.0
14 TraesCS3B01G435500 chr7B 97.491 279 7 0 2871 3149 735294923 735295201 7.900000e-131 477.0
15 TraesCS3B01G435500 chr7B 94.265 279 16 0 2871 3149 14899626 14899348 8.070000e-116 427.0
16 TraesCS3B01G435500 chr7B 95.567 203 8 1 2515 2716 735294670 735294872 1.090000e-84 324.0
17 TraesCS3B01G435500 chr7B 95.588 204 6 2 2513 2715 735299798 735299999 1.090000e-84 324.0
18 TraesCS3B01G435500 chr7B 91.748 206 13 3 2513 2716 14894952 14894749 1.850000e-72 283.0
19 TraesCS3B01G435500 chr7B 90.686 204 15 3 2515 2716 14899878 14899677 5.180000e-68 268.0
20 TraesCS3B01G435500 chr7B 100.000 29 0 0 431 459 633689129 633689157 2.000000e-03 54.7
21 TraesCS3B01G435500 chr4D 96.774 279 9 0 2871 3149 480981899 480982177 1.710000e-127 466.0
22 TraesCS3B01G435500 chr4D 95.050 202 10 0 2515 2716 480981647 480981848 5.070000e-83 318.0
23 TraesCS3B01G435500 chr1D 96.416 279 10 0 2871 3149 391722311 391722033 7.960000e-126 460.0
24 TraesCS3B01G435500 chr5A 95.699 279 12 0 2871 3149 539016067 539015789 1.720000e-122 449.0
25 TraesCS3B01G435500 chr4B 94.265 279 16 0 2871 3149 624467841 624468119 8.070000e-116 427.0
26 TraesCS3B01G435500 chr4B 88.293 205 19 3 2515 2716 624467588 624467790 1.130000e-59 241.0
27 TraesCS3B01G435500 chr6A 93.907 279 17 0 2871 3149 14399324 14399046 3.760000e-114 422.0
28 TraesCS3B01G435500 chr2A 81.875 160 10 6 96 241 15527447 15527293 1.980000e-22 117.0
29 TraesCS3B01G435500 chr2A 80.380 158 12 6 96 239 15528289 15528441 5.560000e-18 102.0
30 TraesCS3B01G435500 chr2A 93.750 64 4 0 249 312 657530294 657530357 2.590000e-16 97.1
31 TraesCS3B01G435500 chr2A 91.837 49 3 1 410 458 144859207 144859254 2.030000e-07 67.6
32 TraesCS3B01G435500 chr2A 85.075 67 5 5 249 311 144858932 144858997 2.620000e-06 63.9
33 TraesCS3B01G435500 chr3D 87.629 97 6 4 152 247 25107924 25107833 1.190000e-19 108.0
34 TraesCS3B01G435500 chrUn 86.667 90 8 2 152 241 99393005 99393090 2.590000e-16 97.1
35 TraesCS3B01G435500 chrUn 97.436 39 1 0 425 463 42055583 42055621 2.030000e-07 67.6
36 TraesCS3B01G435500 chr6B 86.667 90 8 2 152 241 656201590 656201505 2.590000e-16 97.1
37 TraesCS3B01G435500 chr2B 85.417 96 9 3 151 246 773077535 773077625 9.300000e-16 95.3
38 TraesCS3B01G435500 chr2B 86.207 58 3 4 258 311 212580574 212580518 1.220000e-04 58.4
39 TraesCS3B01G435500 chr2B 100.000 31 0 0 429 459 766052666 766052636 1.220000e-04 58.4
40 TraesCS3B01G435500 chr6D 100.000 34 0 0 426 459 258190308 258190275 2.620000e-06 63.9
41 TraesCS3B01G435500 chr2D 86.207 58 3 4 258 311 155453334 155453278 1.220000e-04 58.4


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 TraesCS3B01G435500 chr3B 673844884 673848032 3148 True 2766.000000 5016 100.000000 1 3149 2 chr3B.!!$R2 3148
1 TraesCS3B01G435500 chr3A 647688853 647691555 2702 True 1050.666667 2750 89.333333 38 2465 3 chr3A.!!$R1 2427
2 TraesCS3B01G435500 chr3A 18135969 18136500 531 False 354.000000 449 92.727500 2514 3149 2 chr3A.!!$F1 635
3 TraesCS3B01G435500 chr7A 550052079 550052985 906 False 767.000000 767 81.994000 1015 1945 1 chr7A.!!$F1 930
4 TraesCS3B01G435500 chr7D 483877550 483878456 906 False 761.000000 761 81.886000 1015 1945 1 chr7D.!!$F1 930
5 TraesCS3B01G435500 chr7B 509512380 509513286 906 False 739.000000 739 81.458000 1015 1945 1 chr7B.!!$F1 930
6 TraesCS3B01G435500 chr7B 735294670 735295201 531 False 400.500000 477 96.529000 2515 3149 2 chr7B.!!$F4 634
7 TraesCS3B01G435500 chr7B 14899348 14899878 530 True 347.500000 427 92.475500 2515 3149 2 chr7B.!!$R2 634
8 TraesCS3B01G435500 chr4D 480981647 480982177 530 False 392.000000 466 95.912000 2515 3149 2 chr4D.!!$F1 634
9 TraesCS3B01G435500 chr4B 624467588 624468119 531 False 334.000000 427 91.279000 2515 3149 2 chr4B.!!$F1 634

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
405 507 0.103572 ATGCAATCAATTCCCGCAGC 59.896 50.0 0.00 0.0 35.79 5.25 F
889 1197 0.108585 AAAGGCAGAGAAACGGCAGA 59.891 50.0 0.00 0.0 41.24 4.26 F
1858 2181 0.030235 CGAACGTATCCGAGGATGCA 59.970 55.0 17.94 0.0 37.12 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2143 0.169009 GTGTCAAGCGCTTCCATTCC 59.831 55.000 22.21 4.8 0.00 3.01 R
2033 2357 0.179124 GAACGTTGGGCACTGCAAAA 60.179 50.000 5.00 0.0 0.00 2.44 R
2951 3287 1.136224 GTAGCTCGCAAACTGCTTGAC 60.136 52.381 0.00 0.0 42.25 3.18 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
31 32 8.268850 TCATTTCTTTCTCTGTATTTACTGCC 57.731 34.615 0.00 0.00 0.00 4.85
32 33 7.882791 TCATTTCTTTCTCTGTATTTACTGCCA 59.117 33.333 0.00 0.00 0.00 4.92
33 34 8.680903 CATTTCTTTCTCTGTATTTACTGCCAT 58.319 33.333 0.00 0.00 0.00 4.40
34 35 8.635765 TTTCTTTCTCTGTATTTACTGCCATT 57.364 30.769 0.00 0.00 0.00 3.16
35 36 8.635765 TTCTTTCTCTGTATTTACTGCCATTT 57.364 30.769 0.00 0.00 0.00 2.32
36 37 8.635765 TCTTTCTCTGTATTTACTGCCATTTT 57.364 30.769 0.00 0.00 0.00 1.82
65 66 9.691362 TTTCTTTCCTTTTCCTCATTTTATTCG 57.309 29.630 0.00 0.00 0.00 3.34
74 75 3.387699 CCTCATTTTATTCGGGGCCAAAT 59.612 43.478 4.39 7.26 0.00 2.32
75 76 4.501400 CCTCATTTTATTCGGGGCCAAATC 60.501 45.833 4.39 0.00 0.00 2.17
78 79 0.256464 TTATTCGGGGCCAAATCCGT 59.744 50.000 16.44 2.79 45.79 4.69
79 80 0.256464 TATTCGGGGCCAAATCCGTT 59.744 50.000 16.44 9.11 45.79 4.44
92 93 6.199393 GCCAAATCCGTTGATCTGTATTTAC 58.801 40.000 0.00 0.00 39.87 2.01
97 98 4.081365 TCCGTTGATCTGTATTTACTGCCA 60.081 41.667 0.00 0.00 0.00 4.92
98 99 4.034048 CCGTTGATCTGTATTTACTGCCAC 59.966 45.833 0.00 0.00 0.00 5.01
106 108 4.260985 TGTATTTACTGCCACCTGTCATG 58.739 43.478 0.00 0.00 0.00 3.07
120 122 5.178252 CACCTGTCATGAACTCACTTAACAG 59.822 44.000 0.00 0.00 0.00 3.16
122 124 4.641396 TGTCATGAACTCACTTAACAGGG 58.359 43.478 0.00 0.00 0.00 4.45
123 125 3.437049 GTCATGAACTCACTTAACAGGGC 59.563 47.826 0.00 0.00 0.00 5.19
125 127 2.054799 TGAACTCACTTAACAGGGCCT 58.945 47.619 0.00 0.00 0.00 5.19
149 151 0.591170 CGCCGATCAGTGGTTTTTGT 59.409 50.000 0.00 0.00 0.00 2.83
225 239 4.134563 TCTAGCCTTCAAAGTGGTGTTTC 58.865 43.478 0.00 0.00 0.00 2.78
240 257 6.756542 AGTGGTGTTTCTTTTGCAATTTACTC 59.243 34.615 0.00 0.00 0.00 2.59
278 295 8.970691 ACTTATATTTCTTTCAACATGCACAC 57.029 30.769 0.00 0.00 0.00 3.82
293 310 0.329261 CACACATCCCACCTCACCAT 59.671 55.000 0.00 0.00 0.00 3.55
299 316 0.546122 TCCCACCTCACCATACATGC 59.454 55.000 0.00 0.00 0.00 4.06
313 330 4.342951 CCATACATGCCACCTCATCAAATT 59.657 41.667 0.00 0.00 0.00 1.82
320 337 6.000246 TGCCACCTCATCAAATTCACTATA 58.000 37.500 0.00 0.00 0.00 1.31
401 503 8.815141 TCAAAATATAATGCAATCAATTCCCG 57.185 30.769 0.00 0.00 0.00 5.14
402 504 7.384660 TCAAAATATAATGCAATCAATTCCCGC 59.615 33.333 0.00 0.00 0.00 6.13
403 505 5.981088 ATATAATGCAATCAATTCCCGCA 57.019 34.783 0.00 0.00 36.95 5.69
404 506 2.589798 AATGCAATCAATTCCCGCAG 57.410 45.000 0.00 0.00 35.79 5.18
405 507 0.103572 ATGCAATCAATTCCCGCAGC 59.896 50.000 0.00 0.00 35.79 5.25
406 508 1.249469 TGCAATCAATTCCCGCAGCA 61.249 50.000 0.00 0.00 0.00 4.41
407 509 0.803380 GCAATCAATTCCCGCAGCAC 60.803 55.000 0.00 0.00 0.00 4.40
408 510 0.527113 CAATCAATTCCCGCAGCACA 59.473 50.000 0.00 0.00 0.00 4.57
409 511 1.067706 CAATCAATTCCCGCAGCACAA 60.068 47.619 0.00 0.00 0.00 3.33
410 512 1.255882 ATCAATTCCCGCAGCACAAA 58.744 45.000 0.00 0.00 0.00 2.83
411 513 1.035923 TCAATTCCCGCAGCACAAAA 58.964 45.000 0.00 0.00 0.00 2.44
412 514 1.617850 TCAATTCCCGCAGCACAAAAT 59.382 42.857 0.00 0.00 0.00 1.82
413 515 2.822561 TCAATTCCCGCAGCACAAAATA 59.177 40.909 0.00 0.00 0.00 1.40
440 542 1.067706 CAATCAATTCCCGCAGCAACA 60.068 47.619 0.00 0.00 0.00 3.33
452 554 0.321210 CAGCAACACGTGGGGTATCA 60.321 55.000 21.57 0.00 0.00 2.15
463 565 4.771054 ACGTGGGGTATCATCTAGTATTCC 59.229 45.833 0.00 0.00 0.00 3.01
464 566 4.159879 CGTGGGGTATCATCTAGTATTCCC 59.840 50.000 7.95 7.95 0.00 3.97
489 591 0.319813 AAGGCATTGAAAAGTGGCGC 60.320 50.000 0.00 0.00 44.68 6.53
495 597 3.729462 GCATTGAAAAGTGGCGCGTTATA 60.729 43.478 8.43 0.00 0.00 0.98
505 607 1.599419 GGCGCGTTATATTGGCAAAGG 60.599 52.381 8.43 0.00 0.00 3.11
565 861 2.012673 GAATAGAAGGCAGCACACCTG 58.987 52.381 0.00 0.00 44.67 4.00
597 893 5.119694 GGTGTGTTATTTTGGCAAAGGAAA 58.880 37.500 13.04 6.23 0.00 3.13
598 894 5.586643 GGTGTGTTATTTTGGCAAAGGAAAA 59.413 36.000 13.04 3.96 0.00 2.29
599 895 6.262049 GGTGTGTTATTTTGGCAAAGGAAAAT 59.738 34.615 13.04 6.08 36.14 1.82
632 928 2.270352 ATGAAGCAAACGTGGAGGAA 57.730 45.000 0.00 0.00 0.00 3.36
712 1008 3.128589 GTGGCAATCATCGGTGTGTTATT 59.871 43.478 0.00 0.00 0.00 1.40
775 1073 6.725246 AGAGGAAAGTTGTGTTATTTTGTCG 58.275 36.000 0.00 0.00 0.00 4.35
783 1081 7.360361 AGTTGTGTTATTTTGTCGAAATCCTC 58.640 34.615 1.05 0.00 38.80 3.71
845 1153 2.748605 TGCGTTATTTTGGCAAAGGTG 58.251 42.857 13.04 4.39 33.01 4.00
850 1158 4.709250 GTTATTTTGGCAAAGGTGGGAAA 58.291 39.130 13.04 0.00 0.00 3.13
889 1197 0.108585 AAAGGCAGAGAAACGGCAGA 59.891 50.000 0.00 0.00 41.24 4.26
896 1204 3.684788 GCAGAGAAACGGCAGAGAAAATA 59.315 43.478 0.00 0.00 39.38 1.40
932 1240 2.250939 ACGCCCACACAATGACACG 61.251 57.895 0.00 0.00 0.00 4.49
945 1253 6.646653 ACACAATGACACGATCCATACATATC 59.353 38.462 0.00 0.00 0.00 1.63
949 1257 6.013842 TGACACGATCCATACATATCTGTC 57.986 41.667 0.00 0.00 36.79 3.51
1009 1317 5.958955 TGTCTAGTCTCATCACATTCACAG 58.041 41.667 0.00 0.00 0.00 3.66
1010 1318 5.105595 TGTCTAGTCTCATCACATTCACAGG 60.106 44.000 0.00 0.00 0.00 4.00
1023 1331 0.610174 TCACAGGCTCCTAGCACAAG 59.390 55.000 0.78 0.00 44.75 3.16
1084 1401 2.649742 TCCTCAAGACCTCATTCCCT 57.350 50.000 0.00 0.00 0.00 4.20
1170 1487 0.907486 TGCAACTCCATCTCCTCCTG 59.093 55.000 0.00 0.00 0.00 3.86
1222 1539 3.011032 AGTTCAGCCCCATGAAAGAATCT 59.989 43.478 0.00 0.00 40.72 2.40
1234 1551 1.258445 AAGAATCTGTCGCCTCCCGT 61.258 55.000 0.00 0.00 38.35 5.28
1246 1563 0.823769 CCTCCCGTGAGATGATCCGA 60.824 60.000 0.00 0.00 41.42 4.55
1351 1668 1.985116 GCTCTCCAAGGACCCGTCT 60.985 63.158 0.00 0.00 0.00 4.18
1354 1671 0.471211 TCTCCAAGGACCCGTCTGTT 60.471 55.000 0.00 0.00 0.00 3.16
1356 1673 1.621814 CTCCAAGGACCCGTCTGTTAA 59.378 52.381 0.00 0.00 0.00 2.01
1370 1687 3.248602 GTCTGTTAACATCGCCATCATCC 59.751 47.826 9.13 0.00 0.00 3.51
1372 1689 3.615155 TGTTAACATCGCCATCATCCAA 58.385 40.909 3.59 0.00 0.00 3.53
1462 1779 2.496817 GCGCACCTCTTCCTCGAT 59.503 61.111 0.30 0.00 0.00 3.59
1465 1782 0.173481 CGCACCTCTTCCTCGATGAA 59.827 55.000 3.05 3.05 0.00 2.57
1516 1833 0.321919 ACGTGGTCATCAAGCATGCT 60.322 50.000 16.30 16.30 44.57 3.79
1576 1893 1.172812 GGCCCAACGTGAAGCTCTTT 61.173 55.000 0.00 0.00 0.00 2.52
1598 1915 2.254651 GCGTCGTCGTGGAAGACT 59.745 61.111 3.66 0.00 38.52 3.24
1601 1918 1.002250 CGTCGTCGTGGAAGACTTGG 61.002 60.000 9.38 0.00 38.52 3.61
1603 1920 0.748450 TCGTCGTGGAAGACTTGGTT 59.252 50.000 0.00 0.00 38.90 3.67
1615 1932 3.825328 AGACTTGGTTGTCAAAGAGCAT 58.175 40.909 0.00 0.00 39.27 3.79
1622 1939 0.319469 TGTCAAAGAGCATCGCGTCA 60.319 50.000 5.77 0.00 42.67 4.35
1627 1944 4.796231 GAGCATCGCGTCACCGGT 62.796 66.667 0.00 0.00 33.68 5.28
1678 2001 0.908910 ACCAGGACACACACTCACAA 59.091 50.000 0.00 0.00 0.00 3.33
1679 2002 1.280710 ACCAGGACACACACTCACAAA 59.719 47.619 0.00 0.00 0.00 2.83
1687 2010 3.755905 ACACACACTCACAAACACAATCA 59.244 39.130 0.00 0.00 0.00 2.57
1723 2046 2.481276 CGTCATGGAAGCCAAGATCGTA 60.481 50.000 0.00 0.00 36.95 3.43
1765 2088 3.153024 GCTATTCAGTGCCAACGGA 57.847 52.632 0.00 0.00 0.00 4.69
1814 2137 0.394352 AATGATCAAGACGGTGCCCC 60.394 55.000 0.00 0.00 0.00 5.80
1844 2167 1.154836 GAAGCGCTTGACACGAACG 60.155 57.895 30.47 0.00 0.00 3.95
1846 2169 0.595567 AAGCGCTTGACACGAACGTA 60.596 50.000 24.40 0.00 0.00 3.57
1858 2181 0.030235 CGAACGTATCCGAGGATGCA 59.970 55.000 17.94 0.00 37.12 3.96
1864 2187 2.872245 CGTATCCGAGGATGCAATTGTT 59.128 45.455 17.94 0.00 37.12 2.83
1865 2188 3.303329 CGTATCCGAGGATGCAATTGTTG 60.303 47.826 17.94 0.00 37.12 3.33
1903 2226 4.592192 CCCGGCATGATCGTCGCT 62.592 66.667 0.00 0.00 31.09 4.93
1915 2238 2.034879 CGTCGCTGGCATTGAGGTT 61.035 57.895 0.00 0.00 0.00 3.50
1960 2283 9.107177 CAGAGGATGGTGAGAAATATATAATGC 57.893 37.037 0.00 0.00 0.00 3.56
1961 2284 7.984050 AGAGGATGGTGAGAAATATATAATGCG 59.016 37.037 0.00 0.00 0.00 4.73
1964 2287 8.730680 GGATGGTGAGAAATATATAATGCGTTT 58.269 33.333 0.00 0.00 0.00 3.60
1965 2288 9.760660 GATGGTGAGAAATATATAATGCGTTTC 57.239 33.333 0.00 0.00 0.00 2.78
1987 2310 3.319137 TCACAGGAGTTCTTGGAATCG 57.681 47.619 0.00 0.00 0.00 3.34
1988 2311 2.897326 TCACAGGAGTTCTTGGAATCGA 59.103 45.455 0.00 0.00 0.00 3.59
2015 2339 0.599204 TCTCTCACCGCGTTTTGGTC 60.599 55.000 4.92 0.00 37.72 4.02
2033 2357 2.420129 GGTCTGTCTTGTCTTGTGGTGT 60.420 50.000 0.00 0.00 0.00 4.16
2034 2358 3.270877 GTCTGTCTTGTCTTGTGGTGTT 58.729 45.455 0.00 0.00 0.00 3.32
2099 2423 4.254709 AGCGCACCTGGCACTCAA 62.255 61.111 11.47 0.00 45.17 3.02
2128 2452 2.181021 GTCCGAACGGCATCGACT 59.819 61.111 8.48 0.00 45.48 4.18
2202 2526 1.228657 GGAGGTGACACCAAAGCGTC 61.229 60.000 26.30 13.35 41.95 5.19
2218 2542 1.875963 GTCCGCTGGTGTTTGATGG 59.124 57.895 0.00 0.00 0.00 3.51
2238 2562 2.610727 GGAACAGAGGAGACTTTGGACG 60.611 54.545 0.00 0.00 46.41 4.79
2279 2603 7.064728 GTCATCTGTCTACTTGTGTTTAATCCC 59.935 40.741 0.00 0.00 0.00 3.85
2281 2605 5.546499 TCTGTCTACTTGTGTTTAATCCCCT 59.454 40.000 0.00 0.00 0.00 4.79
2294 2618 7.610305 GTGTTTAATCCCCTTGTTCATCTCTAA 59.390 37.037 0.00 0.00 0.00 2.10
2297 2621 9.847224 TTTAATCCCCTTGTTCATCTCTAATAC 57.153 33.333 0.00 0.00 0.00 1.89
2300 2624 7.598759 TCCCCTTGTTCATCTCTAATACTAC 57.401 40.000 0.00 0.00 0.00 2.73
2301 2625 7.363031 TCCCCTTGTTCATCTCTAATACTACT 58.637 38.462 0.00 0.00 0.00 2.57
2304 2628 9.357161 CCCTTGTTCATCTCTAATACTACTAGT 57.643 37.037 0.00 0.00 0.00 2.57
2314 2638 6.757237 TCTAATACTACTAGTAGCAGCGTCT 58.243 40.000 26.54 10.35 33.66 4.18
2319 2643 3.219052 ACTAGTAGCAGCGTCTTGTTC 57.781 47.619 0.00 0.00 0.00 3.18
2333 2657 1.305219 TTGTTCATAGCACTGCCGCC 61.305 55.000 0.00 0.00 0.00 6.13
2336 2660 3.566853 CATAGCACTGCCGCCGTG 61.567 66.667 10.34 10.34 35.53 4.94
2352 2676 3.948719 TGTGCCCTTCCCCGTGAC 61.949 66.667 0.00 0.00 0.00 3.67
2371 2695 0.533755 CGGCAACTCCATGGATCCTC 60.534 60.000 16.63 5.32 34.01 3.71
2434 2764 1.514014 GCGCGCGTTGAATTTCCAT 60.514 52.632 32.35 0.00 0.00 3.41
2441 2771 4.663889 GCGCGTTGAATTTCCATTTCTTTG 60.664 41.667 8.43 0.00 0.00 2.77
2445 2775 6.128729 CGTTGAATTTCCATTTCTTTGTTGC 58.871 36.000 0.00 0.00 0.00 4.17
2465 2795 2.659291 GCTGTATGCGCACGCTATTTAC 60.659 50.000 14.90 10.42 42.51 2.01
2466 2796 2.794910 CTGTATGCGCACGCTATTTACT 59.205 45.455 14.90 0.00 42.51 2.24
2467 2797 2.792674 TGTATGCGCACGCTATTTACTC 59.207 45.455 14.90 0.00 42.51 2.59
2468 2798 1.217882 ATGCGCACGCTATTTACTCC 58.782 50.000 14.90 0.00 42.51 3.85
2469 2799 0.108567 TGCGCACGCTATTTACTCCA 60.109 50.000 16.77 0.00 42.51 3.86
2470 2800 1.217882 GCGCACGCTATTTACTCCAT 58.782 50.000 7.96 0.00 38.26 3.41
2471 2801 1.070577 GCGCACGCTATTTACTCCATG 60.071 52.381 7.96 0.00 38.26 3.66
2472 2802 1.526887 CGCACGCTATTTACTCCATGG 59.473 52.381 4.97 4.97 0.00 3.66
2473 2803 2.801699 CGCACGCTATTTACTCCATGGA 60.802 50.000 15.27 15.27 0.00 3.41
2474 2804 3.403038 GCACGCTATTTACTCCATGGAT 58.597 45.455 16.63 8.36 0.00 3.41
2475 2805 4.566004 GCACGCTATTTACTCCATGGATA 58.434 43.478 16.63 7.32 0.00 2.59
2476 2806 4.994852 GCACGCTATTTACTCCATGGATAA 59.005 41.667 16.63 12.88 0.00 1.75
2477 2807 5.468746 GCACGCTATTTACTCCATGGATAAA 59.531 40.000 16.63 19.87 0.00 1.40
2478 2808 6.347725 GCACGCTATTTACTCCATGGATAAAG 60.348 42.308 16.63 5.99 0.00 1.85
2479 2809 5.701290 ACGCTATTTACTCCATGGATAAAGC 59.299 40.000 16.63 18.15 0.00 3.51
2480 2810 5.122396 CGCTATTTACTCCATGGATAAAGCC 59.878 44.000 16.63 12.02 0.00 4.35
2481 2811 6.241645 GCTATTTACTCCATGGATAAAGCCT 58.758 40.000 16.63 9.75 0.00 4.58
2482 2812 6.372937 GCTATTTACTCCATGGATAAAGCCTC 59.627 42.308 16.63 9.06 0.00 4.70
2483 2813 4.706842 TTACTCCATGGATAAAGCCTCC 57.293 45.455 16.63 0.00 0.00 4.30
2484 2814 1.417890 ACTCCATGGATAAAGCCTCCG 59.582 52.381 16.63 1.50 35.41 4.63
2485 2815 1.694150 CTCCATGGATAAAGCCTCCGA 59.306 52.381 16.63 0.00 35.41 4.55
2486 2816 1.416401 TCCATGGATAAAGCCTCCGAC 59.584 52.381 11.44 0.00 35.41 4.79
2487 2817 1.140852 CCATGGATAAAGCCTCCGACA 59.859 52.381 5.56 0.00 35.41 4.35
2488 2818 2.421388 CCATGGATAAAGCCTCCGACAA 60.421 50.000 5.56 0.00 35.41 3.18
2489 2819 2.691409 TGGATAAAGCCTCCGACAAG 57.309 50.000 0.00 0.00 35.41 3.16
2490 2820 1.300481 GGATAAAGCCTCCGACAAGC 58.700 55.000 0.00 0.00 0.00 4.01
2491 2821 0.931005 GATAAAGCCTCCGACAAGCG 59.069 55.000 0.00 0.00 40.47 4.68
2502 2832 2.279582 CGACAAGCGGTAGTTGATCT 57.720 50.000 0.00 0.00 36.03 2.75
2503 2833 2.607187 CGACAAGCGGTAGTTGATCTT 58.393 47.619 0.00 0.00 36.03 2.40
2504 2834 2.345641 CGACAAGCGGTAGTTGATCTTG 59.654 50.000 0.00 0.00 39.79 3.02
2505 2835 2.076863 ACAAGCGGTAGTTGATCTTGC 58.923 47.619 0.00 0.00 38.06 4.01
2506 2836 1.061131 CAAGCGGTAGTTGATCTTGCG 59.939 52.381 0.00 0.00 0.00 4.85
2507 2837 1.084370 AGCGGTAGTTGATCTTGCGC 61.084 55.000 0.00 0.00 0.00 6.09
2508 2838 1.358725 GCGGTAGTTGATCTTGCGCA 61.359 55.000 5.66 5.66 0.00 6.09
2509 2839 1.075542 CGGTAGTTGATCTTGCGCAA 58.924 50.000 23.48 23.48 0.00 4.85
2510 2840 1.201921 CGGTAGTTGATCTTGCGCAAC 60.202 52.381 21.02 10.74 43.48 4.17
2511 2841 1.201921 GGTAGTTGATCTTGCGCAACG 60.202 52.381 21.02 15.44 46.65 4.10
2687 3021 4.039852 AGTTTGAACAGAAGAGTCCTCTCC 59.960 45.833 0.00 0.00 41.26 3.71
3016 3352 8.877864 AAATCAACCTCAATATGTTTAGTCCA 57.122 30.769 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.730680 GGCAGTAAATACAGAGAAAGAAATGAA 58.269 33.333 0.00 0.00 0.00 2.57
6 7 7.882791 TGGCAGTAAATACAGAGAAAGAAATGA 59.117 33.333 0.00 0.00 0.00 2.57
7 8 8.044060 TGGCAGTAAATACAGAGAAAGAAATG 57.956 34.615 0.00 0.00 0.00 2.32
8 9 8.814038 ATGGCAGTAAATACAGAGAAAGAAAT 57.186 30.769 0.00 0.00 0.00 2.17
9 10 8.635765 AATGGCAGTAAATACAGAGAAAGAAA 57.364 30.769 0.00 0.00 0.00 2.52
10 11 8.635765 AAATGGCAGTAAATACAGAGAAAGAA 57.364 30.769 0.00 0.00 0.00 2.52
11 12 8.635765 AAAATGGCAGTAAATACAGAGAAAGA 57.364 30.769 0.00 0.00 0.00 2.52
12 13 9.132521 CAAAAATGGCAGTAAATACAGAGAAAG 57.867 33.333 0.00 0.00 0.00 2.62
13 14 8.637986 ACAAAAATGGCAGTAAATACAGAGAAA 58.362 29.630 0.00 0.00 0.00 2.52
14 15 8.177119 ACAAAAATGGCAGTAAATACAGAGAA 57.823 30.769 0.00 0.00 0.00 2.87
15 16 7.759489 ACAAAAATGGCAGTAAATACAGAGA 57.241 32.000 0.00 0.00 0.00 3.10
16 17 8.816640 AAACAAAAATGGCAGTAAATACAGAG 57.183 30.769 0.00 0.00 0.00 3.35
17 18 8.637986 AGAAACAAAAATGGCAGTAAATACAGA 58.362 29.630 0.00 0.00 0.00 3.41
18 19 8.816640 AGAAACAAAAATGGCAGTAAATACAG 57.183 30.769 0.00 0.00 0.00 2.74
19 20 9.606631 AAAGAAACAAAAATGGCAGTAAATACA 57.393 25.926 0.00 0.00 0.00 2.29
21 22 9.267084 GGAAAGAAACAAAAATGGCAGTAAATA 57.733 29.630 0.00 0.00 0.00 1.40
22 23 7.992608 AGGAAAGAAACAAAAATGGCAGTAAAT 59.007 29.630 0.00 0.00 0.00 1.40
23 24 7.334858 AGGAAAGAAACAAAAATGGCAGTAAA 58.665 30.769 0.00 0.00 0.00 2.01
24 25 6.883744 AGGAAAGAAACAAAAATGGCAGTAA 58.116 32.000 0.00 0.00 0.00 2.24
25 26 6.478512 AGGAAAGAAACAAAAATGGCAGTA 57.521 33.333 0.00 0.00 0.00 2.74
26 27 5.357742 AGGAAAGAAACAAAAATGGCAGT 57.642 34.783 0.00 0.00 0.00 4.40
27 28 6.682423 AAAGGAAAGAAACAAAAATGGCAG 57.318 33.333 0.00 0.00 0.00 4.85
28 29 6.094742 GGAAAAGGAAAGAAACAAAAATGGCA 59.905 34.615 0.00 0.00 0.00 4.92
29 30 6.318648 AGGAAAAGGAAAGAAACAAAAATGGC 59.681 34.615 0.00 0.00 0.00 4.40
30 31 7.552330 TGAGGAAAAGGAAAGAAACAAAAATGG 59.448 33.333 0.00 0.00 0.00 3.16
31 32 8.491331 TGAGGAAAAGGAAAGAAACAAAAATG 57.509 30.769 0.00 0.00 0.00 2.32
32 33 9.685276 AATGAGGAAAAGGAAAGAAACAAAAAT 57.315 25.926 0.00 0.00 0.00 1.82
33 34 9.513906 AAATGAGGAAAAGGAAAGAAACAAAAA 57.486 25.926 0.00 0.00 0.00 1.94
34 35 9.513906 AAAATGAGGAAAAGGAAAGAAACAAAA 57.486 25.926 0.00 0.00 0.00 2.44
65 66 0.395724 AGATCAACGGATTTGGCCCC 60.396 55.000 0.00 0.00 35.69 5.80
74 75 4.081365 TGGCAGTAAATACAGATCAACGGA 60.081 41.667 0.00 0.00 0.00 4.69
75 76 4.034048 GTGGCAGTAAATACAGATCAACGG 59.966 45.833 0.00 0.00 0.00 4.44
78 79 5.185454 CAGGTGGCAGTAAATACAGATCAA 58.815 41.667 0.00 0.00 0.00 2.57
79 80 4.225042 ACAGGTGGCAGTAAATACAGATCA 59.775 41.667 0.00 0.00 0.00 2.92
92 93 1.271001 TGAGTTCATGACAGGTGGCAG 60.271 52.381 0.00 0.00 35.91 4.85
97 98 5.290493 TGTTAAGTGAGTTCATGACAGGT 57.710 39.130 0.00 0.00 0.00 4.00
98 99 4.692625 CCTGTTAAGTGAGTTCATGACAGG 59.307 45.833 10.45 10.45 35.68 4.00
106 108 2.861147 AGGCCCTGTTAAGTGAGTTC 57.139 50.000 0.00 0.00 0.00 3.01
122 124 0.946221 CACTGATCGGCGGATTAGGC 60.946 60.000 23.92 7.22 39.82 3.93
123 125 0.319900 CCACTGATCGGCGGATTAGG 60.320 60.000 23.92 15.14 39.82 2.69
125 127 0.828022 AACCACTGATCGGCGGATTA 59.172 50.000 15.67 3.36 31.51 1.75
149 151 4.713553 TCTGCAGAAAACACCACATCTTA 58.286 39.130 15.67 0.00 0.00 2.10
199 213 4.520492 ACACCACTTTGAAGGCTAGATTTG 59.480 41.667 0.00 0.00 0.00 2.32
203 217 3.857157 AACACCACTTTGAAGGCTAGA 57.143 42.857 0.00 0.00 0.00 2.43
208 222 4.329801 GCAAAAGAAACACCACTTTGAAGG 59.670 41.667 0.00 0.00 36.62 3.46
225 239 8.872845 GTGGAATTATGGAGTAAATTGCAAAAG 58.127 33.333 1.71 0.00 42.54 2.27
265 282 1.612950 GTGGGATGTGTGCATGTTGAA 59.387 47.619 0.00 0.00 35.07 2.69
278 295 2.854963 CATGTATGGTGAGGTGGGATG 58.145 52.381 0.00 0.00 0.00 3.51
293 310 4.398988 GTGAATTTGATGAGGTGGCATGTA 59.601 41.667 0.00 0.00 0.00 2.29
378 480 7.215789 TGCGGGAATTGATTGCATTATATTTT 58.784 30.769 0.00 0.00 0.00 1.82
383 485 3.553508 GCTGCGGGAATTGATTGCATTAT 60.554 43.478 0.00 0.00 34.66 1.28
384 486 2.223782 GCTGCGGGAATTGATTGCATTA 60.224 45.455 0.00 0.00 34.66 1.90
385 487 1.472026 GCTGCGGGAATTGATTGCATT 60.472 47.619 0.00 0.00 34.66 3.56
386 488 0.103572 GCTGCGGGAATTGATTGCAT 59.896 50.000 0.00 0.00 34.66 3.96
387 489 1.249469 TGCTGCGGGAATTGATTGCA 61.249 50.000 0.00 0.00 0.00 4.08
388 490 0.803380 GTGCTGCGGGAATTGATTGC 60.803 55.000 0.00 0.00 0.00 3.56
389 491 0.527113 TGTGCTGCGGGAATTGATTG 59.473 50.000 0.00 0.00 0.00 2.67
390 492 1.255882 TTGTGCTGCGGGAATTGATT 58.744 45.000 0.00 0.00 0.00 2.57
391 493 1.255882 TTTGTGCTGCGGGAATTGAT 58.744 45.000 0.00 0.00 0.00 2.57
392 494 1.035923 TTTTGTGCTGCGGGAATTGA 58.964 45.000 0.00 0.00 0.00 2.57
393 495 2.083167 ATTTTGTGCTGCGGGAATTG 57.917 45.000 0.00 0.00 0.00 2.32
394 496 3.951775 TTATTTTGTGCTGCGGGAATT 57.048 38.095 0.00 0.00 0.00 2.17
395 497 5.590530 TTATTATTTTGTGCTGCGGGAAT 57.409 34.783 0.00 0.00 0.00 3.01
396 498 5.347342 CATTATTATTTTGTGCTGCGGGAA 58.653 37.500 0.00 0.00 0.00 3.97
397 499 4.736168 GCATTATTATTTTGTGCTGCGGGA 60.736 41.667 0.00 0.00 33.25 5.14
398 500 3.490526 GCATTATTATTTTGTGCTGCGGG 59.509 43.478 0.00 0.00 33.25 6.13
399 501 4.111198 TGCATTATTATTTTGTGCTGCGG 58.889 39.130 0.00 0.00 36.78 5.69
400 502 5.699438 TTGCATTATTATTTTGTGCTGCG 57.301 34.783 0.00 0.00 36.78 5.18
401 503 7.236674 TGATTGCATTATTATTTTGTGCTGC 57.763 32.000 0.00 0.00 36.78 5.25
404 506 9.654417 GGAATTGATTGCATTATTATTTTGTGC 57.346 29.630 0.00 0.00 36.39 4.57
406 508 9.044150 CGGGAATTGATTGCATTATTATTTTGT 57.956 29.630 0.00 0.00 0.00 2.83
407 509 8.011106 GCGGGAATTGATTGCATTATTATTTTG 58.989 33.333 0.00 0.00 0.00 2.44
408 510 7.714377 TGCGGGAATTGATTGCATTATTATTTT 59.286 29.630 0.00 0.00 0.00 1.82
409 511 7.215789 TGCGGGAATTGATTGCATTATTATTT 58.784 30.769 0.00 0.00 0.00 1.40
410 512 6.757237 TGCGGGAATTGATTGCATTATTATT 58.243 32.000 0.00 0.00 0.00 1.40
411 513 6.343716 TGCGGGAATTGATTGCATTATTAT 57.656 33.333 0.00 0.00 0.00 1.28
412 514 5.771469 CTGCGGGAATTGATTGCATTATTA 58.229 37.500 0.00 0.00 34.66 0.98
413 515 4.624015 CTGCGGGAATTGATTGCATTATT 58.376 39.130 0.00 0.00 34.66 1.40
440 542 4.771054 GGAATACTAGATGATACCCCACGT 59.229 45.833 0.00 0.00 0.00 4.49
471 573 1.290009 GCGCCACTTTTCAATGCCT 59.710 52.632 0.00 0.00 0.00 4.75
473 575 0.939106 AACGCGCCACTTTTCAATGC 60.939 50.000 5.73 0.00 0.00 3.56
474 576 2.323939 TAACGCGCCACTTTTCAATG 57.676 45.000 5.73 0.00 0.00 2.82
475 577 4.893424 ATATAACGCGCCACTTTTCAAT 57.107 36.364 5.73 0.00 0.00 2.57
476 578 4.407818 CAATATAACGCGCCACTTTTCAA 58.592 39.130 5.73 0.00 0.00 2.69
479 581 2.478879 GCCAATATAACGCGCCACTTTT 60.479 45.455 5.73 0.00 0.00 2.27
487 589 3.684103 TTCCTTTGCCAATATAACGCG 57.316 42.857 3.53 3.53 0.00 6.01
520 816 5.809719 TTGCCAAACATTGTTTTCCTTTC 57.190 34.783 12.02 0.15 0.00 2.62
565 861 1.241315 AATAACACACCACTGCCGCC 61.241 55.000 0.00 0.00 0.00 6.13
567 863 2.606795 CCAAAATAACACACCACTGCCG 60.607 50.000 0.00 0.00 0.00 5.69
575 871 6.670077 TTTTCCTTTGCCAAAATAACACAC 57.330 33.333 0.00 0.00 0.00 3.82
599 895 9.522804 ACGTTTGCTTCATAAGAAAAACATTTA 57.477 25.926 13.85 0.00 37.76 1.40
605 901 6.137794 TCCACGTTTGCTTCATAAGAAAAA 57.862 33.333 0.00 0.00 37.76 1.94
632 928 9.860898 GAGGATTTTGACAAAATAACATAGCTT 57.139 29.630 22.85 8.01 40.97 3.74
668 964 4.395231 ACTTAGCCAAATAGCCGTTTTCTC 59.605 41.667 0.00 0.00 0.00 2.87
702 998 5.523438 TTCCTTCACCAAAATAACACACC 57.477 39.130 0.00 0.00 0.00 4.16
712 1008 6.105333 CACACATTTCTTTTCCTTCACCAAA 58.895 36.000 0.00 0.00 0.00 3.28
802 1110 7.600375 CGCATACTGGATTGACACTATAATCTT 59.400 37.037 0.00 0.00 34.52 2.40
824 1132 3.324993 CACCTTTGCCAAAATAACGCAT 58.675 40.909 0.00 0.00 31.44 4.73
864 1172 0.670162 GTTTCTCTGCCTTTGCTGCA 59.330 50.000 0.00 0.00 38.71 4.41
868 1176 1.081175 GCCGTTTCTCTGCCTTTGC 60.081 57.895 0.00 0.00 38.26 3.68
889 1197 5.992217 GCCGTCAGATATTGAGGTATTTTCT 59.008 40.000 6.76 0.00 39.49 2.52
896 1204 1.202417 CGTGCCGTCAGATATTGAGGT 60.202 52.381 6.76 0.00 39.49 3.85
918 1226 1.807139 TGGATCGTGTCATTGTGTGG 58.193 50.000 0.00 0.00 0.00 4.17
932 1240 4.407296 GGAGGGGACAGATATGTATGGATC 59.593 50.000 0.00 0.00 0.00 3.36
945 1253 0.323908 AGAAGACGAGGAGGGGACAG 60.324 60.000 0.00 0.00 0.00 3.51
949 1257 3.975168 TTTAAAGAAGACGAGGAGGGG 57.025 47.619 0.00 0.00 0.00 4.79
1010 1318 2.111582 GCTGGCTTGTGCTAGGAGC 61.112 63.158 3.77 0.00 46.16 4.70
1084 1401 4.049640 GCCGGAATGCAAACGCCA 62.050 61.111 5.05 0.00 0.00 5.69
1170 1487 0.980423 GAGATCATAGGGAGGGGTGC 59.020 60.000 0.00 0.00 0.00 5.01
1222 1539 2.362503 ATCTCACGGGAGGCGACA 60.363 61.111 16.20 0.00 41.69 4.35
1234 1551 2.047002 TGTACCGTCGGATCATCTCA 57.953 50.000 20.51 3.29 0.00 3.27
1273 1590 2.829741 TGATGACATCGGTGTTGACA 57.170 45.000 1.13 0.00 39.09 3.58
1315 1632 2.675423 TCGTAGGCGCAGGACAGT 60.675 61.111 10.83 0.00 38.14 3.55
1351 1668 3.274095 TGGATGATGGCGATGTTAACA 57.726 42.857 11.41 11.41 0.00 2.41
1354 1671 2.209273 CGTTGGATGATGGCGATGTTA 58.791 47.619 0.00 0.00 0.00 2.41
1356 1673 0.815213 CCGTTGGATGATGGCGATGT 60.815 55.000 0.00 0.00 0.00 3.06
1372 1689 3.633116 CCAGGGGAAACGGACCGT 61.633 66.667 15.37 15.37 43.97 4.83
1462 1779 3.666111 CGTCGTACTCGATGTTGAGTTCA 60.666 47.826 8.14 0.00 46.85 3.18
1516 1833 2.343758 GTGGAGGTGAAGAGCGCA 59.656 61.111 11.47 0.00 0.00 6.09
1598 1915 1.266718 GCGATGCTCTTTGACAACCAA 59.733 47.619 0.00 0.00 0.00 3.67
1601 1918 0.512952 ACGCGATGCTCTTTGACAAC 59.487 50.000 15.93 0.00 0.00 3.32
1603 1920 0.319469 TGACGCGATGCTCTTTGACA 60.319 50.000 15.93 0.00 0.00 3.58
1627 1944 2.194597 GCCCAGTTGGTGACCACA 59.805 61.111 2.46 0.00 36.04 4.17
1678 2001 1.266718 GCGTCCATGTGTGATTGTGTT 59.733 47.619 0.00 0.00 0.00 3.32
1679 2002 0.874390 GCGTCCATGTGTGATTGTGT 59.126 50.000 0.00 0.00 0.00 3.72
1723 2046 0.391661 CGTGGCCACATGAGCTTACT 60.392 55.000 34.16 0.00 35.58 2.24
1750 2073 1.247567 CCTTTCCGTTGGCACTGAAT 58.752 50.000 0.00 0.00 0.00 2.57
1765 2088 0.602905 CGAGCCGTTTGACTCCCTTT 60.603 55.000 0.00 0.00 0.00 3.11
1814 2137 3.089784 CGCTTCCATTCCGGTTCG 58.910 61.111 0.00 0.00 35.57 3.95
1818 2141 1.745115 TCAAGCGCTTCCATTCCGG 60.745 57.895 22.21 6.60 0.00 5.14
1819 2142 1.298157 TGTCAAGCGCTTCCATTCCG 61.298 55.000 22.21 7.42 0.00 4.30
1820 2143 0.169009 GTGTCAAGCGCTTCCATTCC 59.831 55.000 22.21 4.80 0.00 3.01
1821 2144 0.179215 CGTGTCAAGCGCTTCCATTC 60.179 55.000 22.21 9.39 0.00 2.67
1822 2145 0.602638 TCGTGTCAAGCGCTTCCATT 60.603 50.000 22.21 0.00 0.00 3.16
1823 2146 0.602638 TTCGTGTCAAGCGCTTCCAT 60.603 50.000 22.21 0.00 0.00 3.41
1828 2151 0.388134 ATACGTTCGTGTCAAGCGCT 60.388 50.000 2.64 2.64 0.00 5.92
1844 2167 3.003689 CCAACAATTGCATCCTCGGATAC 59.996 47.826 5.05 0.00 32.93 2.24
1846 2169 2.026641 CCAACAATTGCATCCTCGGAT 58.973 47.619 5.05 0.00 34.81 4.18
1858 2181 0.242555 CGCGGGTTAAGCCAACAATT 59.757 50.000 22.89 0.00 39.04 2.32
1955 2278 4.002906 ACTCCTGTGAAGAAACGCATTA 57.997 40.909 0.00 0.00 0.00 1.90
1956 2279 2.851195 ACTCCTGTGAAGAAACGCATT 58.149 42.857 0.00 0.00 0.00 3.56
1957 2280 2.550830 ACTCCTGTGAAGAAACGCAT 57.449 45.000 0.00 0.00 0.00 4.73
1958 2281 2.158957 AGAACTCCTGTGAAGAAACGCA 60.159 45.455 0.00 0.00 0.00 5.24
1960 2283 3.248602 CCAAGAACTCCTGTGAAGAAACG 59.751 47.826 0.00 0.00 0.00 3.60
1961 2284 4.451900 TCCAAGAACTCCTGTGAAGAAAC 58.548 43.478 0.00 0.00 0.00 2.78
1964 2287 4.561530 CGATTCCAAGAACTCCTGTGAAGA 60.562 45.833 0.00 0.00 0.00 2.87
1965 2288 3.681897 CGATTCCAAGAACTCCTGTGAAG 59.318 47.826 0.00 0.00 0.00 3.02
1987 2310 2.123342 CGCGGTGAGAGAAATGAGATC 58.877 52.381 0.00 0.00 0.00 2.75
1988 2311 1.478510 ACGCGGTGAGAGAAATGAGAT 59.521 47.619 12.47 0.00 0.00 2.75
2015 2339 4.414852 CAAAACACCACAAGACAAGACAG 58.585 43.478 0.00 0.00 0.00 3.51
2033 2357 0.179124 GAACGTTGGGCACTGCAAAA 60.179 50.000 5.00 0.00 0.00 2.44
2034 2358 1.435515 GAACGTTGGGCACTGCAAA 59.564 52.632 5.00 0.00 0.00 3.68
2138 2462 2.997315 CTGGTCCTCACGCTGGGA 60.997 66.667 0.00 0.00 0.00 4.37
2166 2490 4.129737 CGTCGTCCAGGCGTCCAT 62.130 66.667 3.62 0.00 44.05 3.41
2202 2526 0.240945 GTTCCATCAAACACCAGCGG 59.759 55.000 0.00 0.00 0.00 5.52
2218 2542 2.296471 TCGTCCAAAGTCTCCTCTGTTC 59.704 50.000 0.00 0.00 0.00 3.18
2294 2618 5.124645 ACAAGACGCTGCTACTAGTAGTAT 58.875 41.667 26.76 11.29 35.65 2.12
2297 2621 4.142665 TGAACAAGACGCTGCTACTAGTAG 60.143 45.833 23.25 23.25 36.29 2.57
2300 2624 3.217599 TGAACAAGACGCTGCTACTAG 57.782 47.619 0.00 0.00 0.00 2.57
2301 2625 3.868757 ATGAACAAGACGCTGCTACTA 57.131 42.857 0.00 0.00 0.00 1.82
2304 2628 2.094234 TGCTATGAACAAGACGCTGCTA 60.094 45.455 0.00 0.00 0.00 3.49
2307 2631 2.093310 CAGTGCTATGAACAAGACGCTG 59.907 50.000 0.00 0.00 0.00 5.18
2308 2632 2.341257 CAGTGCTATGAACAAGACGCT 58.659 47.619 0.00 0.00 0.00 5.07
2314 2638 1.305219 GGCGGCAGTGCTATGAACAA 61.305 55.000 16.11 0.00 34.52 2.83
2319 2643 3.566853 CACGGCGGCAGTGCTATG 61.567 66.667 19.63 6.63 32.52 2.23
2352 2676 0.533755 GAGGATCCATGGAGTTGCCG 60.534 60.000 21.33 0.00 40.66 5.69
2371 2695 7.452880 TTTTATTCTGTCATCTTGTTCCAGG 57.547 36.000 0.00 0.00 0.00 4.45
2434 2764 2.033927 TGCGCATACAGCAACAAAGAAA 59.966 40.909 5.66 0.00 46.13 2.52
2441 2771 1.692148 TAGCGTGCGCATACAGCAAC 61.692 55.000 15.91 0.00 46.97 4.17
2445 2775 2.794910 AGTAAATAGCGTGCGCATACAG 59.205 45.455 15.91 7.09 44.88 2.74
2465 2795 1.694150 TCGGAGGCTTTATCCATGGAG 59.306 52.381 21.33 7.50 36.57 3.86
2466 2796 1.416401 GTCGGAGGCTTTATCCATGGA 59.584 52.381 18.88 18.88 36.57 3.41
2467 2797 1.140852 TGTCGGAGGCTTTATCCATGG 59.859 52.381 4.97 4.97 36.57 3.66
2468 2798 2.620251 TGTCGGAGGCTTTATCCATG 57.380 50.000 0.00 0.00 36.57 3.66
2469 2799 2.746472 GCTTGTCGGAGGCTTTATCCAT 60.746 50.000 0.00 0.00 36.57 3.41
2470 2800 1.406887 GCTTGTCGGAGGCTTTATCCA 60.407 52.381 0.00 0.00 36.57 3.41
2471 2801 1.300481 GCTTGTCGGAGGCTTTATCC 58.700 55.000 0.00 0.00 0.00 2.59
2472 2802 0.931005 CGCTTGTCGGAGGCTTTATC 59.069 55.000 0.00 0.00 33.78 1.75
2473 2803 3.065575 CGCTTGTCGGAGGCTTTAT 57.934 52.632 0.00 0.00 33.78 1.40
2474 2804 4.590487 CGCTTGTCGGAGGCTTTA 57.410 55.556 0.00 0.00 33.78 1.85
2483 2813 2.279582 AGATCAACTACCGCTTGTCG 57.720 50.000 0.00 0.00 38.08 4.35
2484 2814 2.094417 GCAAGATCAACTACCGCTTGTC 59.906 50.000 0.00 0.00 38.48 3.18
2485 2815 2.076863 GCAAGATCAACTACCGCTTGT 58.923 47.619 0.00 0.00 38.48 3.16
2486 2816 1.061131 CGCAAGATCAACTACCGCTTG 59.939 52.381 0.00 0.00 43.02 4.01
2487 2817 1.359848 CGCAAGATCAACTACCGCTT 58.640 50.000 0.00 0.00 43.02 4.68
2488 2818 1.084370 GCGCAAGATCAACTACCGCT 61.084 55.000 0.30 0.00 41.53 5.52
2489 2819 1.348594 GCGCAAGATCAACTACCGC 59.651 57.895 0.30 0.00 39.54 5.68
2490 2820 1.075542 TTGCGCAAGATCAACTACCG 58.924 50.000 21.02 0.00 43.02 4.02
2491 2821 1.201921 CGTTGCGCAAGATCAACTACC 60.202 52.381 25.78 6.53 40.12 3.18
2492 2822 2.145053 CGTTGCGCAAGATCAACTAC 57.855 50.000 25.78 8.15 40.12 2.73
2505 2835 4.026968 CCCAATAATTTTACATGCGTTGCG 60.027 41.667 0.00 0.00 0.00 4.85
2506 2836 5.105752 TCCCAATAATTTTACATGCGTTGC 58.894 37.500 0.00 0.00 0.00 4.17
2507 2837 6.237808 GCTTCCCAATAATTTTACATGCGTTG 60.238 38.462 0.00 0.00 0.00 4.10
2508 2838 5.810074 GCTTCCCAATAATTTTACATGCGTT 59.190 36.000 0.00 0.00 0.00 4.84
2509 2839 5.348164 GCTTCCCAATAATTTTACATGCGT 58.652 37.500 0.00 0.00 0.00 5.24
2510 2840 4.440758 CGCTTCCCAATAATTTTACATGCG 59.559 41.667 0.00 0.00 0.00 4.73
2511 2841 5.348164 ACGCTTCCCAATAATTTTACATGC 58.652 37.500 0.00 0.00 0.00 4.06
2512 2842 8.918961 TTAACGCTTCCCAATAATTTTACATG 57.081 30.769 0.00 0.00 0.00 3.21
2519 2849 5.020795 AGGGTTTAACGCTTCCCAATAATT 58.979 37.500 8.90 0.00 38.28 1.40
2552 2883 6.685527 TTGCCAATATAAATACAAGTGCGA 57.314 33.333 0.00 0.00 0.00 5.10
2669 3002 2.815158 AGGGAGAGGACTCTTCTGTTC 58.185 52.381 7.52 0.00 40.61 3.18
2951 3287 1.136224 GTAGCTCGCAAACTGCTTGAC 60.136 52.381 0.00 0.00 42.25 3.18
2980 3316 5.371115 TGAGGTTGATTTCCATTTCGTTC 57.629 39.130 0.00 0.00 0.00 3.95
3016 3352 2.362077 GCTAATCCCGTTTTCCATGCAT 59.638 45.455 0.00 0.00 0.00 3.96
3029 3365 4.200092 CAACCTACCTTTCAGCTAATCCC 58.800 47.826 0.00 0.00 0.00 3.85
3054 3390 6.863126 GCAAGGTTATGGTGTGATAATATTGC 59.137 38.462 0.00 0.00 36.28 3.56


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

AutoCloner maintained by Alex Coulton.