Multiple sequence alignment - TraesCS3A01G400000

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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 TraesCS3A01G400000 chr3A 100.000 4182 0 0 1 4182 646811083 646815264 0.000000e+00 7723.0
1 TraesCS3A01G400000 chr3A 88.521 453 32 8 1940 2387 552510858 552510421 7.960000e-147 531.0
2 TraesCS3A01G400000 chr3D 92.114 2346 101 34 410 2719 509228133 509230430 0.000000e+00 3230.0
3 TraesCS3A01G400000 chr3D 88.858 1427 72 46 2752 4128 509230548 509231937 0.000000e+00 1674.0
4 TraesCS3A01G400000 chr3D 90.859 908 57 9 1499 2397 440219603 440218713 0.000000e+00 1194.0
5 TraesCS3A01G400000 chr3D 88.083 386 40 6 1 381 509227588 509227972 1.770000e-123 453.0
6 TraesCS3A01G400000 chr3B 90.029 2397 104 49 392 2719 671995747 671998077 0.000000e+00 2977.0
7 TraesCS3A01G400000 chr3B 92.206 834 37 12 2752 3560 671998195 671999025 0.000000e+00 1155.0
8 TraesCS3A01G400000 chr3B 85.255 373 36 12 3763 4128 671999265 671999625 2.380000e-97 366.0
9 TraesCS3A01G400000 chr3B 82.254 355 46 8 1 350 671881371 671881713 1.470000e-74 291.0
10 TraesCS3A01G400000 chr2D 92.238 1108 60 9 1499 2597 571962960 571964050 0.000000e+00 1546.0
11 TraesCS3A01G400000 chr2D 92.659 722 35 6 1883 2600 29676686 29675979 0.000000e+00 1024.0
12 TraesCS3A01G400000 chr1D 93.490 722 29 7 1883 2600 359550477 359549770 0.000000e+00 1057.0
13 TraesCS3A01G400000 chr5D 93.324 719 30 7 1883 2597 12361315 12362019 0.000000e+00 1046.0
14 TraesCS3A01G400000 chr5D 93.564 404 24 2 997 1399 390573151 390572749 5.980000e-168 601.0
15 TraesCS3A01G400000 chr5D 82.492 594 66 22 2135 2722 390571939 390571378 1.750000e-133 486.0
16 TraesCS3A01G400000 chr5D 80.000 205 39 2 1184 1387 527842124 527841921 2.600000e-32 150.0
17 TraesCS3A01G400000 chr4B 89.847 719 39 17 1883 2597 41177908 41178596 0.000000e+00 893.0
18 TraesCS3A01G400000 chr5B 93.317 404 25 2 997 1399 470978982 470978580 2.780000e-166 595.0
19 TraesCS3A01G400000 chr5B 83.646 587 63 18 2135 2719 470977780 470977225 4.790000e-144 521.0
20 TraesCS3A01G400000 chr5B 79.806 515 67 18 2755 3236 470977122 470976612 1.440000e-89 340.0
21 TraesCS3A01G400000 chr5A 92.822 404 27 2 997 1399 493866891 493866489 6.020000e-163 584.0
22 TraesCS3A01G400000 chr5A 88.811 429 44 4 2296 2722 493865571 493865145 1.330000e-144 523.0
23 TraesCS3A01G400000 chr5A 80.906 508 64 17 2755 3236 493865043 493864543 1.840000e-98 370.0
24 TraesCS3A01G400000 chr2B 88.300 453 33 6 1940 2387 87454006 87454443 3.700000e-145 525.0
25 TraesCS3A01G400000 chr2A 88.300 453 33 7 1940 2387 763539457 763539894 3.700000e-145 525.0
26 TraesCS3A01G400000 chr7A 79.167 192 38 2 1184 1374 459210136 459209946 9.430000e-27 132.0
27 TraesCS3A01G400000 chr7B 78.125 192 40 2 1184 1374 411059978 411059788 2.040000e-23 121.0
28 TraesCS3A01G400000 chr1B 85.714 91 12 1 1270 1359 628218971 628219061 1.240000e-15 95.3


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 TraesCS3A01G400000 chr3A 646811083 646815264 4181 False 7723.000000 7723 100.000000 1 4182 1 chr3A.!!$F1 4181
1 TraesCS3A01G400000 chr3D 509227588 509231937 4349 False 1785.666667 3230 89.685000 1 4128 3 chr3D.!!$F1 4127
2 TraesCS3A01G400000 chr3D 440218713 440219603 890 True 1194.000000 1194 90.859000 1499 2397 1 chr3D.!!$R1 898
3 TraesCS3A01G400000 chr3B 671995747 671999625 3878 False 1499.333333 2977 89.163333 392 4128 3 chr3B.!!$F2 3736
4 TraesCS3A01G400000 chr2D 571962960 571964050 1090 False 1546.000000 1546 92.238000 1499 2597 1 chr2D.!!$F1 1098
5 TraesCS3A01G400000 chr2D 29675979 29676686 707 True 1024.000000 1024 92.659000 1883 2600 1 chr2D.!!$R1 717
6 TraesCS3A01G400000 chr1D 359549770 359550477 707 True 1057.000000 1057 93.490000 1883 2600 1 chr1D.!!$R1 717
7 TraesCS3A01G400000 chr5D 12361315 12362019 704 False 1046.000000 1046 93.324000 1883 2597 1 chr5D.!!$F1 714
8 TraesCS3A01G400000 chr5D 390571378 390573151 1773 True 543.500000 601 88.028000 997 2722 2 chr5D.!!$R2 1725
9 TraesCS3A01G400000 chr4B 41177908 41178596 688 False 893.000000 893 89.847000 1883 2597 1 chr4B.!!$F1 714
10 TraesCS3A01G400000 chr5B 470976612 470978982 2370 True 485.333333 595 85.589667 997 3236 3 chr5B.!!$R1 2239
11 TraesCS3A01G400000 chr5A 493864543 493866891 2348 True 492.333333 584 87.513000 997 3236 3 chr5A.!!$R1 2239

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
314 318 0.035820 TCTCGGCCGGTTTAATGCTT 60.036 50.0 27.83 0.0 0.00 3.91 F
938 1135 0.338120 CCACCCTCTCTCTCCCTCTT 59.662 60.0 0.00 0.0 0.00 2.85 F
1954 2188 0.107831 GGCCGGCCAAGTATGATACA 59.892 55.0 40.73 0.0 35.81 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1748 0.446616 GAAACCGGGCGAAGATTCAC 59.553 55.0 6.32 0.0 0.0 3.18 R
2874 3573 0.802222 CACCAGCACCTGTCGTATCG 60.802 60.0 0.00 0.0 0.0 2.92 R
3706 4545 0.610232 AGCAACCATCCACTTCAGGC 60.610 55.0 0.00 0.0 0.0 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 1.528586 GCTTGATGTACTAGCCATGCG 59.471 52.381 0.49 0.00 40.43 4.73
32 34 1.202521 TGATGTACTAGCCATGCGGTG 60.203 52.381 0.49 0.00 33.28 4.94
65 68 1.220206 CAAGAGCTCTCGCCCATGT 59.780 57.895 18.55 0.00 36.60 3.21
90 93 0.807496 GACGTCGTGGGCTAAGTAGT 59.193 55.000 0.63 0.00 0.00 2.73
122 125 1.068741 GTGTCGAGTCCCTCAGTTGTT 59.931 52.381 0.00 0.00 0.00 2.83
124 127 1.340248 GTCGAGTCCCTCAGTTGTTCA 59.660 52.381 0.00 0.00 0.00 3.18
129 132 1.068741 GTCCCTCAGTTGTTCACGTCT 59.931 52.381 0.00 0.00 0.00 4.18
145 148 1.155390 TCTGTGACCTCGGGGAAGT 59.845 57.895 9.33 0.00 36.25 3.01
150 153 0.841289 TGACCTCGGGGAAGTTTTGT 59.159 50.000 9.33 0.00 36.25 2.83
159 162 2.160205 GGGAAGTTTTGTAGGAGGCAC 58.840 52.381 0.00 0.00 0.00 5.01
160 163 2.488347 GGGAAGTTTTGTAGGAGGCACA 60.488 50.000 0.00 0.00 0.00 4.57
170 173 0.540923 AGGAGGCACATCTTCTCTGC 59.459 55.000 0.00 0.00 0.00 4.26
198 201 1.696884 GAGATTGGGAGAGATGGGGTC 59.303 57.143 0.00 0.00 0.00 4.46
230 233 0.537143 TGCTTTGCGGTGACCAGATT 60.537 50.000 1.11 0.00 0.00 2.40
232 235 1.522668 CTTTGCGGTGACCAGATTGA 58.477 50.000 1.11 0.00 0.00 2.57
263 266 1.489230 GGTTAGGGGATCGATTGGTGT 59.511 52.381 0.00 0.00 0.00 4.16
267 270 1.354368 AGGGGATCGATTGGTGTGTTT 59.646 47.619 0.00 0.00 0.00 2.83
269 272 1.472480 GGGATCGATTGGTGTGTTTGG 59.528 52.381 0.00 0.00 0.00 3.28
285 289 2.103340 GGGAGAGAGAAGCGCGAC 59.897 66.667 12.10 0.04 0.00 5.19
286 290 2.411504 GGGAGAGAGAAGCGCGACT 61.412 63.158 12.10 5.27 0.00 4.18
287 291 1.509004 GGAGAGAGAAGCGCGACTT 59.491 57.895 12.10 13.42 42.98 3.01
289 293 0.169230 GAGAGAGAAGCGCGACTTGA 59.831 55.000 12.10 0.00 39.29 3.02
290 294 0.109504 AGAGAGAAGCGCGACTTGAC 60.110 55.000 12.10 8.91 39.29 3.18
300 304 2.182030 GACTTGACGGGCTCTCGG 59.818 66.667 0.00 0.00 0.00 4.63
310 314 4.534401 GCTCTCGGCCGGTTTAAT 57.466 55.556 27.83 0.00 34.27 1.40
314 318 0.035820 TCTCGGCCGGTTTAATGCTT 60.036 50.000 27.83 0.00 0.00 3.91
341 347 4.167597 GGTGAAAACCCGAGGCAA 57.832 55.556 0.00 0.00 0.00 4.52
350 356 1.984570 CCCGAGGCAAGAGAGGACA 60.985 63.158 0.00 0.00 0.00 4.02
353 359 1.446966 GAGGCAAGAGAGGACACGC 60.447 63.158 0.00 0.00 0.00 5.34
365 371 1.445582 GACACGCCGAGAACCGATT 60.446 57.895 0.00 0.00 41.76 3.34
379 385 3.733236 CGATTGTGGCTCGGAGTAA 57.267 52.632 6.90 0.00 32.58 2.24
381 387 1.134367 CGATTGTGGCTCGGAGTAAGA 59.866 52.381 6.90 0.00 32.58 2.10
382 388 2.541556 GATTGTGGCTCGGAGTAAGAC 58.458 52.381 6.90 0.00 0.00 3.01
383 389 1.334160 TTGTGGCTCGGAGTAAGACA 58.666 50.000 6.90 2.19 0.00 3.41
384 390 1.334160 TGTGGCTCGGAGTAAGACAA 58.666 50.000 6.90 0.00 32.36 3.18
385 391 1.272490 TGTGGCTCGGAGTAAGACAAG 59.728 52.381 6.90 0.00 32.36 3.16
386 392 1.544691 GTGGCTCGGAGTAAGACAAGA 59.455 52.381 6.90 0.00 32.36 3.02
388 394 2.093106 GGCTCGGAGTAAGACAAGAGA 58.907 52.381 6.90 0.00 0.00 3.10
389 395 2.159352 GGCTCGGAGTAAGACAAGAGAC 60.159 54.545 6.90 0.00 0.00 3.36
415 552 7.946655 AAACCTTGCATTCTTTTTAAGTAGC 57.053 32.000 0.00 0.00 0.00 3.58
459 601 9.822185 ATTTTCTTCTTCATTTATTACCATGGC 57.178 29.630 13.04 0.00 0.00 4.40
461 603 8.593945 TTCTTCTTCATTTATTACCATGGCTT 57.406 30.769 13.04 0.00 0.00 4.35
462 604 9.693739 TTCTTCTTCATTTATTACCATGGCTTA 57.306 29.630 13.04 0.00 0.00 3.09
507 649 8.596380 CGTAACAAGAAGATCCAACTCTATTTC 58.404 37.037 0.00 0.00 0.00 2.17
562 704 0.528470 GAGACTGTTCTCTCACCCCG 59.472 60.000 0.00 0.00 44.54 5.73
566 708 1.075050 ACTGTTCTCTCACCCCGTCTA 59.925 52.381 0.00 0.00 0.00 2.59
577 719 1.494721 ACCCCGTCTACCTTATCCGTA 59.505 52.381 0.00 0.00 0.00 4.02
603 745 3.343941 ACCCTATTTTTAGTGCTCGCA 57.656 42.857 0.00 0.00 0.00 5.10
647 789 5.480642 TGGAGAGAAATCCATATCTCAGC 57.519 43.478 5.67 0.00 44.56 4.26
648 790 4.285517 TGGAGAGAAATCCATATCTCAGCC 59.714 45.833 5.67 6.65 44.56 4.85
649 791 4.493547 GAGAGAAATCCATATCTCAGCCG 58.506 47.826 5.67 0.00 43.62 5.52
717 866 3.040147 TCCGAGTTTTGACTAGGCAAG 57.960 47.619 11.68 0.00 33.33 4.01
886 1068 1.235281 GCCACCTCACCGGAAGAAAC 61.235 60.000 9.46 0.00 36.31 2.78
887 1069 0.605589 CCACCTCACCGGAAGAAACC 60.606 60.000 9.46 0.00 36.31 3.27
933 1130 1.382009 GTCCCCACCCTCTCTCTCC 60.382 68.421 0.00 0.00 0.00 3.71
934 1131 2.041405 CCCCACCCTCTCTCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
935 1132 2.641746 CCCCACCCTCTCTCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
936 1133 1.075600 CCCACCCTCTCTCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
937 1134 1.589399 CCCACCCTCTCTCTCCCTCT 61.589 65.000 0.00 0.00 0.00 3.69
938 1135 0.338120 CCACCCTCTCTCTCCCTCTT 59.662 60.000 0.00 0.00 0.00 2.85
939 1136 1.687996 CCACCCTCTCTCTCCCTCTTC 60.688 61.905 0.00 0.00 0.00 2.87
940 1137 0.634465 ACCCTCTCTCTCCCTCTTCC 59.366 60.000 0.00 0.00 0.00 3.46
945 1142 1.850345 TCTCTCTCCCTCTTCCTCTCC 59.150 57.143 0.00 0.00 0.00 3.71
959 1156 3.827898 CTCCCTCCGTCCGTCTGC 61.828 72.222 0.00 0.00 0.00 4.26
1419 1625 2.189257 CGCCCCGAATCACCATCA 59.811 61.111 0.00 0.00 0.00 3.07
1420 1626 2.180204 CGCCCCGAATCACCATCAC 61.180 63.158 0.00 0.00 0.00 3.06
1476 1685 1.976474 TCATGCCGTTTCTTGCCCC 60.976 57.895 0.00 0.00 0.00 5.80
1477 1686 3.061848 ATGCCGTTTCTTGCCCCG 61.062 61.111 0.00 0.00 0.00 5.73
1534 1748 2.758089 CCCGTCGACCGTAGTGGAG 61.758 68.421 10.58 0.00 42.00 3.86
1794 2024 3.146847 CCTTCTGGTTGGTACTTGTTCC 58.853 50.000 0.00 0.00 0.00 3.62
1814 2044 2.293677 CCTTTGCTGGATCTGATCATGC 59.706 50.000 18.64 19.41 0.00 4.06
1869 2103 4.202151 GGGGTGGCAAAATAGCTAATCTTG 60.202 45.833 0.00 3.09 34.17 3.02
1873 2107 5.302823 GTGGCAAAATAGCTAATCTTGGGAT 59.697 40.000 0.00 0.00 34.17 3.85
1874 2108 5.302568 TGGCAAAATAGCTAATCTTGGGATG 59.697 40.000 0.00 0.00 31.47 3.51
1880 2114 1.750682 GCTAATCTTGGGATGGCCGTT 60.751 52.381 0.00 0.00 33.83 4.44
1881 2115 2.486548 GCTAATCTTGGGATGGCCGTTA 60.487 50.000 0.00 0.00 33.83 3.18
1954 2188 0.107831 GGCCGGCCAAGTATGATACA 59.892 55.000 40.73 0.00 35.81 2.29
1958 2192 3.435671 GCCGGCCAAGTATGATACATTAC 59.564 47.826 18.11 0.00 0.00 1.89
2031 2361 7.607250 AGATCAGTTCTTGTCTTGGTTAGTAG 58.393 38.462 0.00 0.00 0.00 2.57
2040 2370 9.085645 TCTTGTCTTGGTTAGTAGAACTTATGA 57.914 33.333 0.00 0.00 0.00 2.15
2194 2788 4.202461 TGGTGGAGCTAGATGTTTCAACTT 60.202 41.667 0.00 0.00 0.00 2.66
2256 2852 5.632034 AGAAAGTGTTCCAACTCTAACCT 57.368 39.130 0.00 0.00 33.92 3.50
2257 2853 6.742559 AGAAAGTGTTCCAACTCTAACCTA 57.257 37.500 0.00 0.00 33.92 3.08
2260 2856 7.508296 AGAAAGTGTTCCAACTCTAACCTAGTA 59.492 37.037 0.00 0.00 33.92 1.82
2270 2866 7.552687 CCAACTCTAACCTAGTATCAATTTGCA 59.447 37.037 0.00 0.00 0.00 4.08
2278 2874 6.039047 ACCTAGTATCAATTTGCATTGCAGAG 59.961 38.462 11.76 3.71 40.61 3.35
2635 3233 1.313812 ACTCGGTGGAGGACGATGTC 61.314 60.000 0.00 0.00 44.93 3.06
2720 3343 6.812998 TGCAAGTACTATACCAAGGTATGTC 58.187 40.000 19.50 8.61 40.98 3.06
2732 3355 5.044919 ACCAAGGTATGTCTGATGAAATCCA 60.045 40.000 0.00 0.00 44.73 3.41
2734 3357 6.016527 CCAAGGTATGTCTGATGAAATCCATG 60.017 42.308 0.00 0.00 44.73 3.66
2737 3360 7.121382 AGGTATGTCTGATGAAATCCATGTTT 58.879 34.615 0.00 0.00 44.73 2.83
2739 3362 7.703621 GGTATGTCTGATGAAATCCATGTTTTG 59.296 37.037 0.00 0.00 44.73 2.44
2745 3368 6.990798 TGATGAAATCCATGTTTTGTTGCTA 58.009 32.000 0.00 0.00 44.73 3.49
2746 3369 7.613585 TGATGAAATCCATGTTTTGTTGCTAT 58.386 30.769 0.00 0.00 44.73 2.97
2747 3370 7.546316 TGATGAAATCCATGTTTTGTTGCTATG 59.454 33.333 0.00 0.00 44.73 2.23
2749 3372 7.215789 TGAAATCCATGTTTTGTTGCTATGTT 58.784 30.769 0.00 0.00 0.00 2.71
2750 3373 7.384660 TGAAATCCATGTTTTGTTGCTATGTTC 59.615 33.333 0.00 0.00 0.00 3.18
2775 3466 8.296713 TCTAGAACTTTTGCACAATTACCATTC 58.703 33.333 0.00 0.00 0.00 2.67
2820 3511 6.917477 TGTAATTGACACTTGATCTTTGTTGC 59.083 34.615 0.00 0.00 31.20 4.17
2874 3573 3.955650 TCCTACAAGGTACAGCAAGTC 57.044 47.619 0.00 0.00 36.53 3.01
2974 3675 1.076412 TTGCCTGCAAACACCTCCA 60.076 52.632 1.31 0.00 32.44 3.86
3243 3981 7.944729 AATTGTATTGTAAGCTGTTCTGGAT 57.055 32.000 0.00 0.00 0.00 3.41
3244 3982 6.985188 TTGTATTGTAAGCTGTTCTGGATC 57.015 37.500 0.00 0.00 0.00 3.36
3305 4043 4.615588 TTTTGTTTGCTCCCCTTTATGG 57.384 40.909 0.00 0.00 0.00 2.74
3362 4100 7.719633 TGAATAAGCAGGTCCTTCAATATTACC 59.280 37.037 0.00 0.00 0.00 2.85
3521 4261 2.539688 ACGCATGTACAACGCTGATATG 59.460 45.455 18.36 2.75 0.00 1.78
3525 4265 4.212004 GCATGTACAACGCTGATATGTGAT 59.788 41.667 12.16 0.00 0.00 3.06
3526 4266 5.277490 GCATGTACAACGCTGATATGTGATT 60.277 40.000 12.16 0.00 0.00 2.57
3527 4267 6.718388 CATGTACAACGCTGATATGTGATTT 58.282 36.000 0.00 0.00 0.00 2.17
3531 4271 3.323729 ACGCTGATATGTGATTTTGCG 57.676 42.857 0.00 0.00 46.21 4.85
3570 4409 4.207165 TCCTGGCAAGTAATATTTCAGCC 58.793 43.478 16.49 16.49 40.93 4.85
3597 4436 4.913924 GCGGATGATATTTGAATCAACTGC 59.086 41.667 10.77 10.77 46.81 4.40
3612 4451 7.825761 TGAATCAACTGCTCTGAAATCTTGATA 59.174 33.333 0.00 0.00 0.00 2.15
3633 4472 7.771183 TGATAAGTAAATTCTGTTGATTGGCC 58.229 34.615 0.00 0.00 0.00 5.36
3659 4498 5.745312 TCTCTGTTCCATTTCTGAGCTTA 57.255 39.130 0.00 0.00 32.38 3.09
3674 4513 5.711506 TCTGAGCTTATTTTGGATGCTGAAA 59.288 36.000 0.00 0.00 33.83 2.69
3690 4529 8.243426 GGATGCTGAAAATGTGTTATCTTGTAA 58.757 33.333 0.00 0.00 0.00 2.41
3691 4530 8.970691 ATGCTGAAAATGTGTTATCTTGTAAC 57.029 30.769 0.00 0.00 0.00 2.50
3692 4531 7.367285 TGCTGAAAATGTGTTATCTTGTAACC 58.633 34.615 0.00 0.00 0.00 2.85
3693 4532 7.230510 TGCTGAAAATGTGTTATCTTGTAACCT 59.769 33.333 0.00 0.00 0.00 3.50
3699 4538 9.569122 AAATGTGTTATCTTGTAACCTTACTGT 57.431 29.630 0.00 0.00 34.77 3.55
3700 4539 7.956420 TGTGTTATCTTGTAACCTTACTGTG 57.044 36.000 0.00 0.00 34.77 3.66
3701 4540 6.425721 TGTGTTATCTTGTAACCTTACTGTGC 59.574 38.462 0.00 0.00 34.77 4.57
3702 4541 6.649557 GTGTTATCTTGTAACCTTACTGTGCT 59.350 38.462 0.00 0.00 34.77 4.40
3703 4542 7.816031 GTGTTATCTTGTAACCTTACTGTGCTA 59.184 37.037 0.00 0.00 34.77 3.49
3704 4543 8.537016 TGTTATCTTGTAACCTTACTGTGCTAT 58.463 33.333 0.00 0.00 34.77 2.97
3705 4544 9.379791 GTTATCTTGTAACCTTACTGTGCTATT 57.620 33.333 0.00 0.00 34.77 1.73
3706 4545 7.849804 ATCTTGTAACCTTACTGTGCTATTG 57.150 36.000 0.00 0.00 34.77 1.90
3707 4546 5.642063 TCTTGTAACCTTACTGTGCTATTGC 59.358 40.000 0.00 0.00 35.78 3.56
3708 4547 4.258543 TGTAACCTTACTGTGCTATTGCC 58.741 43.478 0.00 0.00 35.01 4.52
3709 4548 3.721087 AACCTTACTGTGCTATTGCCT 57.279 42.857 0.00 0.00 38.71 4.75
3710 4549 2.991250 ACCTTACTGTGCTATTGCCTG 58.009 47.619 0.00 0.00 38.71 4.85
3711 4550 2.571653 ACCTTACTGTGCTATTGCCTGA 59.428 45.455 0.00 0.00 38.71 3.86
3712 4551 3.009033 ACCTTACTGTGCTATTGCCTGAA 59.991 43.478 0.00 0.00 38.71 3.02
3713 4552 3.624861 CCTTACTGTGCTATTGCCTGAAG 59.375 47.826 0.00 0.00 38.71 3.02
3714 4553 2.867109 ACTGTGCTATTGCCTGAAGT 57.133 45.000 0.00 0.00 38.71 3.01
3715 4554 2.430465 ACTGTGCTATTGCCTGAAGTG 58.570 47.619 0.00 0.00 38.71 3.16
3716 4555 1.741706 CTGTGCTATTGCCTGAAGTGG 59.258 52.381 0.00 0.00 38.71 4.00
3717 4556 1.350684 TGTGCTATTGCCTGAAGTGGA 59.649 47.619 0.00 0.00 38.71 4.02
3718 4557 2.025981 TGTGCTATTGCCTGAAGTGGAT 60.026 45.455 0.00 0.00 38.71 3.41
3719 4558 2.357009 GTGCTATTGCCTGAAGTGGATG 59.643 50.000 0.00 0.00 38.71 3.51
3730 4569 0.610232 AAGTGGATGGTTGCTGAGGC 60.610 55.000 0.00 0.00 39.26 4.70
3753 4592 0.539207 TGTGCTGTATTTGCTGGGCA 60.539 50.000 0.00 0.00 36.47 5.36
3757 4596 2.302445 TGCTGTATTTGCTGGGCATTTT 59.698 40.909 0.00 0.00 38.76 1.82
3761 4600 5.681954 GCTGTATTTGCTGGGCATTTTCATA 60.682 40.000 0.00 0.00 38.76 2.15
3762 4601 6.482898 TGTATTTGCTGGGCATTTTCATAT 57.517 33.333 0.00 0.00 38.76 1.78
3763 4602 6.282167 TGTATTTGCTGGGCATTTTCATATG 58.718 36.000 0.00 0.00 38.76 1.78
3764 4603 3.823281 TTGCTGGGCATTTTCATATGG 57.177 42.857 2.13 0.00 38.76 2.74
3926 4765 9.052759 GCTATAGGCTGCTTTAACTTTACATTA 57.947 33.333 0.00 0.00 38.06 1.90
3970 4823 9.504710 CGCTGCTTGTATAGTATATACTTTAGG 57.495 37.037 20.21 10.61 37.73 2.69
3992 4845 6.702329 AGGTAGGTGTTTTGACTGATTAGAG 58.298 40.000 0.00 0.00 0.00 2.43
4020 4876 4.474394 TCATGTTGTTTTGGACCATACCA 58.526 39.130 0.00 0.00 38.24 3.25
4029 4885 0.107165 GGACCATACCACTTCCAGGC 60.107 60.000 0.00 0.00 0.00 4.85
4043 4899 0.757935 CCAGGCATTGATTCCAGGGG 60.758 60.000 0.00 0.00 0.00 4.79
4064 4926 6.553100 AGGGGACAAGATCTATAGTTCTGAAG 59.447 42.308 12.99 9.33 0.00 3.02
4068 4930 7.651704 GGACAAGATCTATAGTTCTGAAGAAGC 59.348 40.741 12.99 1.69 34.27 3.86
4074 4936 7.891183 TCTATAGTTCTGAAGAAGCAAACAC 57.109 36.000 0.00 0.00 34.27 3.32
4080 4942 3.742882 TCTGAAGAAGCAAACACTCGATG 59.257 43.478 0.00 0.00 0.00 3.84
4087 4949 1.470098 GCAAACACTCGATGGATGCTT 59.530 47.619 14.06 0.00 39.58 3.91
4098 4960 5.879237 TCGATGGATGCTTGTATGTTTTTC 58.121 37.500 0.00 0.00 0.00 2.29
4128 4992 9.736023 CCTATTTAAGCTGATTTATTGACCAAC 57.264 33.333 0.00 0.00 0.00 3.77
4129 4993 9.438291 CTATTTAAGCTGATTTATTGACCAACG 57.562 33.333 0.00 0.00 0.00 4.10
4130 4994 7.441890 TTTAAGCTGATTTATTGACCAACGA 57.558 32.000 0.00 0.00 0.00 3.85
4131 4995 5.957842 AAGCTGATTTATTGACCAACGAA 57.042 34.783 0.00 0.00 0.00 3.85
4132 4996 5.957842 AGCTGATTTATTGACCAACGAAA 57.042 34.783 0.00 0.00 0.00 3.46
4133 4997 6.325919 AGCTGATTTATTGACCAACGAAAA 57.674 33.333 0.00 0.00 0.00 2.29
4134 4998 6.744112 AGCTGATTTATTGACCAACGAAAAA 58.256 32.000 0.00 0.00 0.00 1.94
4135 4999 7.378181 AGCTGATTTATTGACCAACGAAAAAT 58.622 30.769 0.00 0.00 0.00 1.82
4136 5000 7.872483 AGCTGATTTATTGACCAACGAAAAATT 59.128 29.630 0.00 0.00 0.00 1.82
4137 5001 9.134734 GCTGATTTATTGACCAACGAAAAATTA 57.865 29.630 0.00 0.00 0.00 1.40
4142 5006 9.849166 TTTATTGACCAACGAAAAATTATCTCC 57.151 29.630 0.00 0.00 0.00 3.71
4143 5007 7.703058 ATTGACCAACGAAAAATTATCTCCT 57.297 32.000 0.00 0.00 0.00 3.69
4144 5008 6.737254 TGACCAACGAAAAATTATCTCCTC 57.263 37.500 0.00 0.00 0.00 3.71
4145 5009 6.472887 TGACCAACGAAAAATTATCTCCTCT 58.527 36.000 0.00 0.00 0.00 3.69
4146 5010 7.617225 TGACCAACGAAAAATTATCTCCTCTA 58.383 34.615 0.00 0.00 0.00 2.43
4147 5011 7.548075 TGACCAACGAAAAATTATCTCCTCTAC 59.452 37.037 0.00 0.00 0.00 2.59
4148 5012 7.391620 ACCAACGAAAAATTATCTCCTCTACA 58.608 34.615 0.00 0.00 0.00 2.74
4149 5013 8.047310 ACCAACGAAAAATTATCTCCTCTACAT 58.953 33.333 0.00 0.00 0.00 2.29
4150 5014 9.542462 CCAACGAAAAATTATCTCCTCTACATA 57.458 33.333 0.00 0.00 0.00 2.29
4152 5016 8.798748 ACGAAAAATTATCTCCTCTACATACG 57.201 34.615 0.00 0.00 0.00 3.06
4153 5017 8.627403 ACGAAAAATTATCTCCTCTACATACGA 58.373 33.333 0.00 0.00 0.00 3.43
4154 5018 9.459640 CGAAAAATTATCTCCTCTACATACGAA 57.540 33.333 0.00 0.00 0.00 3.85
4156 5020 9.543783 AAAAATTATCTCCTCTACATACGAACC 57.456 33.333 0.00 0.00 0.00 3.62
4157 5021 7.834881 AATTATCTCCTCTACATACGAACCA 57.165 36.000 0.00 0.00 0.00 3.67
4158 5022 7.834881 ATTATCTCCTCTACATACGAACCAA 57.165 36.000 0.00 0.00 0.00 3.67
4159 5023 7.834881 TTATCTCCTCTACATACGAACCAAT 57.165 36.000 0.00 0.00 0.00 3.16
4160 5024 8.929260 TTATCTCCTCTACATACGAACCAATA 57.071 34.615 0.00 0.00 0.00 1.90
4161 5025 6.879276 TCTCCTCTACATACGAACCAATAG 57.121 41.667 0.00 0.00 0.00 1.73
4162 5026 6.598503 TCTCCTCTACATACGAACCAATAGA 58.401 40.000 0.00 0.00 0.00 1.98
4163 5027 7.058525 TCTCCTCTACATACGAACCAATAGAA 58.941 38.462 0.00 0.00 0.00 2.10
4164 5028 7.558807 TCTCCTCTACATACGAACCAATAGAAA 59.441 37.037 0.00 0.00 0.00 2.52
4165 5029 8.070034 TCCTCTACATACGAACCAATAGAAAA 57.930 34.615 0.00 0.00 0.00 2.29
4166 5030 7.977853 TCCTCTACATACGAACCAATAGAAAAC 59.022 37.037 0.00 0.00 0.00 2.43
4167 5031 7.762615 CCTCTACATACGAACCAATAGAAAACA 59.237 37.037 0.00 0.00 0.00 2.83
4168 5032 8.697846 TCTACATACGAACCAATAGAAAACAG 57.302 34.615 0.00 0.00 0.00 3.16
4169 5033 6.737254 ACATACGAACCAATAGAAAACAGG 57.263 37.500 0.00 0.00 0.00 4.00
4170 5034 5.123344 ACATACGAACCAATAGAAAACAGGC 59.877 40.000 0.00 0.00 0.00 4.85
4171 5035 3.751518 ACGAACCAATAGAAAACAGGCT 58.248 40.909 0.00 0.00 0.00 4.58
4172 5036 4.901868 ACGAACCAATAGAAAACAGGCTA 58.098 39.130 0.00 0.00 0.00 3.93
4173 5037 5.497474 ACGAACCAATAGAAAACAGGCTAT 58.503 37.500 0.00 0.00 0.00 2.97
4174 5038 5.354234 ACGAACCAATAGAAAACAGGCTATG 59.646 40.000 0.00 0.00 0.00 2.23
4175 5039 5.354234 CGAACCAATAGAAAACAGGCTATGT 59.646 40.000 0.00 0.00 46.97 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.804572 CGCATGGCTAGTACATCAAGCT 60.805 50.000 0.00 0.00 36.48 3.74
36 38 4.103103 GCTCTTGCGTTTCGGGGC 62.103 66.667 0.00 0.00 0.00 5.80
83 86 0.535335 CTGCCGCCTGGAACTACTTA 59.465 55.000 0.00 0.00 37.49 2.24
90 93 4.680237 CGACACTGCCGCCTGGAA 62.680 66.667 0.00 0.00 37.49 3.53
124 127 2.989173 TTCCCCGAGGTCACAGACGT 62.989 60.000 0.00 0.00 32.65 4.34
129 132 0.841289 AAAACTTCCCCGAGGTCACA 59.159 50.000 0.00 0.00 0.00 3.58
132 135 2.614734 CCTACAAAACTTCCCCGAGGTC 60.615 54.545 0.00 0.00 0.00 3.85
139 142 2.160205 GTGCCTCCTACAAAACTTCCC 58.840 52.381 0.00 0.00 0.00 3.97
145 148 4.287067 AGAGAAGATGTGCCTCCTACAAAA 59.713 41.667 0.00 0.00 0.00 2.44
150 153 1.759445 GCAGAGAAGATGTGCCTCCTA 59.241 52.381 0.00 0.00 42.29 2.94
159 162 1.135170 TCGTGAGCAGCAGAGAAGATG 60.135 52.381 0.00 0.00 0.00 2.90
160 163 1.134753 CTCGTGAGCAGCAGAGAAGAT 59.865 52.381 0.00 0.00 32.84 2.40
170 173 0.820226 TCTCCCAATCTCGTGAGCAG 59.180 55.000 0.00 0.00 0.00 4.24
207 210 1.154225 GGTCACCGCAAAGCATTCG 60.154 57.895 0.00 0.00 0.00 3.34
230 233 2.024273 CCCCTAACCCTACTCACTCTCA 60.024 54.545 0.00 0.00 0.00 3.27
232 235 2.295143 TCCCCTAACCCTACTCACTCT 58.705 52.381 0.00 0.00 0.00 3.24
263 266 0.320771 GCGCTTCTCTCTCCCAAACA 60.321 55.000 0.00 0.00 0.00 2.83
267 270 2.361230 TCGCGCTTCTCTCTCCCA 60.361 61.111 5.56 0.00 0.00 4.37
269 272 0.800300 CAAGTCGCGCTTCTCTCTCC 60.800 60.000 5.56 0.00 34.69 3.71
339 345 1.153939 CTCGGCGTGTCCTCTCTTG 60.154 63.158 6.85 0.00 0.00 3.02
341 347 1.303398 TTCTCGGCGTGTCCTCTCT 60.303 57.895 6.85 0.00 0.00 3.10
350 356 1.736645 CACAATCGGTTCTCGGCGT 60.737 57.895 6.85 0.00 39.77 5.68
353 359 1.079127 AGCCACAATCGGTTCTCGG 60.079 57.895 0.00 0.00 39.77 4.63
365 371 1.272490 CTTGTCTTACTCCGAGCCACA 59.728 52.381 0.00 0.00 0.00 4.17
377 383 5.189928 TGCAAGGTTTTGTCTCTTGTCTTA 58.810 37.500 0.00 0.00 39.80 2.10
379 385 3.620488 TGCAAGGTTTTGTCTCTTGTCT 58.380 40.909 0.00 0.00 39.80 3.41
381 387 4.646492 AGAATGCAAGGTTTTGTCTCTTGT 59.354 37.500 0.00 0.00 39.80 3.16
382 388 5.192327 AGAATGCAAGGTTTTGTCTCTTG 57.808 39.130 0.00 0.00 40.38 3.02
383 389 5.859205 AAGAATGCAAGGTTTTGTCTCTT 57.141 34.783 0.00 0.00 36.65 2.85
384 390 5.859205 AAAGAATGCAAGGTTTTGTCTCT 57.141 34.783 0.00 0.00 36.65 3.10
385 391 6.908870 AAAAAGAATGCAAGGTTTTGTCTC 57.091 33.333 0.00 0.00 36.65 3.36
386 392 8.040727 ACTTAAAAAGAATGCAAGGTTTTGTCT 58.959 29.630 0.00 0.00 36.65 3.41
388 394 9.313118 CTACTTAAAAAGAATGCAAGGTTTTGT 57.687 29.630 0.00 0.00 36.65 2.83
389 395 8.275632 GCTACTTAAAAAGAATGCAAGGTTTTG 58.724 33.333 0.00 0.00 37.36 2.44
444 585 8.454106 GCTCAGTATAAGCCATGGTAATAAATG 58.546 37.037 14.67 6.62 33.53 2.32
458 600 5.392595 CGGATAAGAGAGGCTCAGTATAAGC 60.393 48.000 18.26 0.00 39.09 3.09
459 601 5.708230 ACGGATAAGAGAGGCTCAGTATAAG 59.292 44.000 18.26 9.94 32.06 1.73
461 603 5.244189 ACGGATAAGAGAGGCTCAGTATA 57.756 43.478 18.26 4.63 32.06 1.47
462 604 4.107127 ACGGATAAGAGAGGCTCAGTAT 57.893 45.455 18.26 10.46 32.06 2.12
464 606 2.445682 ACGGATAAGAGAGGCTCAGT 57.554 50.000 18.26 3.51 32.06 3.41
465 607 3.632604 TGTTACGGATAAGAGAGGCTCAG 59.367 47.826 18.26 0.06 32.06 3.35
466 608 3.628008 TGTTACGGATAAGAGAGGCTCA 58.372 45.455 18.26 0.00 32.06 4.26
467 609 4.338682 TCTTGTTACGGATAAGAGAGGCTC 59.661 45.833 6.34 6.34 31.43 4.70
507 649 3.274288 GGTAAGAACAGCCTCATCCTTG 58.726 50.000 0.00 0.00 0.00 3.61
600 742 6.092748 AGACAAATGTTTTAGGCTAATTGCG 58.907 36.000 7.96 0.00 44.05 4.85
603 745 8.189119 TCCAAGACAAATGTTTTAGGCTAATT 57.811 30.769 7.96 0.00 0.00 1.40
655 797 2.414994 ACTGAATCTGATGGCCTGTG 57.585 50.000 3.32 0.00 0.00 3.66
656 798 3.350833 GAAACTGAATCTGATGGCCTGT 58.649 45.455 3.32 0.00 0.00 4.00
657 799 2.686915 GGAAACTGAATCTGATGGCCTG 59.313 50.000 3.32 0.00 0.00 4.85
700 849 3.434984 CAGCTCTTGCCTAGTCAAAACTC 59.565 47.826 0.00 0.00 40.80 3.01
717 866 1.302993 TTGGCCCGTTAACCAGCTC 60.303 57.895 0.00 5.63 37.24 4.09
933 1130 0.753848 GACGGAGGGAGAGGAAGAGG 60.754 65.000 0.00 0.00 0.00 3.69
934 1131 0.753848 GGACGGAGGGAGAGGAAGAG 60.754 65.000 0.00 0.00 0.00 2.85
935 1132 1.306970 GGACGGAGGGAGAGGAAGA 59.693 63.158 0.00 0.00 0.00 2.87
936 1133 2.122167 CGGACGGAGGGAGAGGAAG 61.122 68.421 0.00 0.00 0.00 3.46
937 1134 2.044252 CGGACGGAGGGAGAGGAA 60.044 66.667 0.00 0.00 0.00 3.36
938 1135 3.336568 ACGGACGGAGGGAGAGGA 61.337 66.667 0.00 0.00 0.00 3.71
939 1136 2.829458 GACGGACGGAGGGAGAGG 60.829 72.222 0.00 0.00 0.00 3.69
940 1137 2.115911 CAGACGGACGGAGGGAGAG 61.116 68.421 0.00 0.00 0.00 3.20
976 1173 2.429930 CCTCCCCAAGAACGCACA 59.570 61.111 0.00 0.00 0.00 4.57
977 1174 2.359975 CCCTCCCCAAGAACGCAC 60.360 66.667 0.00 0.00 0.00 5.34
1214 1411 3.554692 CGTTGTCGCGGAGGATGC 61.555 66.667 6.13 0.00 0.00 3.91
1402 1608 2.180204 GTGATGGTGATTCGGGGCG 61.180 63.158 0.00 0.00 0.00 6.13
1534 1748 0.446616 GAAACCGGGCGAAGATTCAC 59.553 55.000 6.32 0.00 0.00 3.18
1693 1914 1.594862 GATTCCACGGAAGATTCAGCG 59.405 52.381 4.58 0.00 37.56 5.18
1794 2024 2.031944 CGCATGATCAGATCCAGCAAAG 60.032 50.000 18.88 4.83 0.00 2.77
1814 2044 1.807165 CGTCAGTGAGGGTGCATCG 60.807 63.158 4.87 0.00 0.00 3.84
1850 2084 4.865905 TCCCAAGATTAGCTATTTTGCCA 58.134 39.130 0.00 0.00 29.28 4.92
1852 2086 5.776744 CCATCCCAAGATTAGCTATTTTGC 58.223 41.667 0.00 0.00 29.28 3.68
1869 2103 5.250200 TGTTTCATATATAACGGCCATCCC 58.750 41.667 2.24 0.00 0.00 3.85
1873 2107 7.809546 TGATTTGTTTCATATATAACGGCCA 57.190 32.000 2.24 0.00 0.00 5.36
1874 2108 9.691362 AAATGATTTGTTTCATATATAACGGCC 57.309 29.630 0.00 0.00 35.29 6.13
2194 2788 7.712639 TGCAGAGCACAAATTTACCAATAAAAA 59.287 29.630 0.00 0.00 31.62 1.94
2203 2797 3.577667 TGCATGCAGAGCACAAATTTAC 58.422 40.909 18.46 0.00 43.04 2.01
2256 2852 6.825213 AGACTCTGCAATGCAAATTGATACTA 59.175 34.615 9.92 0.00 38.41 1.82
2257 2853 5.651139 AGACTCTGCAATGCAAATTGATACT 59.349 36.000 9.92 2.98 38.41 2.12
2260 2856 4.219944 ACAGACTCTGCAATGCAAATTGAT 59.780 37.500 9.92 0.00 38.41 2.57
2270 2866 4.039730 ACAGTTCAGTACAGACTCTGCAAT 59.960 41.667 5.92 0.00 34.37 3.56
2278 2874 8.395633 ACAACAAATTAACAGTTCAGTACAGAC 58.604 33.333 0.00 0.00 0.00 3.51
2720 3343 5.929992 AGCAACAAAACATGGATTTCATCAG 59.070 36.000 0.00 0.00 32.92 2.90
2732 3355 8.396272 AGTTCTAGAACATAGCAACAAAACAT 57.604 30.769 31.80 7.56 43.47 2.71
2734 3357 9.516314 AAAAGTTCTAGAACATAGCAACAAAAC 57.484 29.630 31.80 5.93 43.47 2.43
2737 3360 7.138736 GCAAAAGTTCTAGAACATAGCAACAA 58.861 34.615 31.80 0.00 43.47 2.83
2739 3362 6.578919 GTGCAAAAGTTCTAGAACATAGCAAC 59.421 38.462 31.80 22.91 43.47 4.17
2745 3368 8.082242 GGTAATTGTGCAAAAGTTCTAGAACAT 58.918 33.333 31.80 21.04 43.47 2.71
2746 3369 7.067615 TGGTAATTGTGCAAAAGTTCTAGAACA 59.932 33.333 31.80 11.98 43.47 3.18
2747 3370 7.422399 TGGTAATTGTGCAAAAGTTCTAGAAC 58.578 34.615 25.24 25.24 41.45 3.01
2749 3372 7.759489 ATGGTAATTGTGCAAAAGTTCTAGA 57.241 32.000 0.00 0.00 0.00 2.43
2750 3373 8.081633 TGAATGGTAATTGTGCAAAAGTTCTAG 58.918 33.333 0.00 0.00 0.00 2.43
2811 3502 6.647334 TCCTACAATCAAATGCAACAAAGA 57.353 33.333 0.00 0.00 0.00 2.52
2820 3511 5.356751 TCCACGGAAATCCTACAATCAAATG 59.643 40.000 0.00 0.00 0.00 2.32
2874 3573 0.802222 CACCAGCACCTGTCGTATCG 60.802 60.000 0.00 0.00 0.00 2.92
3243 3981 2.171840 GAGTACACCTTGCTCCTGAGA 58.828 52.381 0.00 0.00 30.89 3.27
3244 3982 2.663826 GAGTACACCTTGCTCCTGAG 57.336 55.000 0.00 0.00 30.89 3.35
3305 4043 7.624360 AAGAATTCCAAAACAAAAACCCTTC 57.376 32.000 0.65 0.00 0.00 3.46
3362 4100 3.432252 GGACTTGGTACAGAAATGACACG 59.568 47.826 0.00 0.00 42.39 4.49
3420 4159 6.394809 CCAATACAGTTGGAACCCAAATAAC 58.605 40.000 0.52 0.00 45.73 1.89
3521 4261 4.560819 TCACAACACTTTTCGCAAAATCAC 59.439 37.500 0.00 0.00 0.00 3.06
3525 4265 3.305629 GCATCACAACACTTTTCGCAAAA 59.694 39.130 0.00 0.00 0.00 2.44
3526 4266 2.857152 GCATCACAACACTTTTCGCAAA 59.143 40.909 0.00 0.00 0.00 3.68
3527 4267 2.098934 AGCATCACAACACTTTTCGCAA 59.901 40.909 0.00 0.00 0.00 4.85
3531 4271 3.304928 CCAGGAGCATCACAACACTTTTC 60.305 47.826 0.00 0.00 36.25 2.29
3560 4300 2.147374 CATCCGCCACGGCTGAAATAT 61.147 52.381 6.26 0.00 44.57 1.28
3570 4409 3.498018 TGATTCAAATATCATCCGCCACG 59.502 43.478 0.00 0.00 29.82 4.94
3576 4415 7.228108 TCAGAGCAGTTGATTCAAATATCATCC 59.772 37.037 0.00 0.00 34.67 3.51
3612 4451 4.618227 GCGGCCAATCAACAGAATTTACTT 60.618 41.667 2.24 0.00 0.00 2.24
3659 4498 8.316214 AGATAACACATTTTCAGCATCCAAAAT 58.684 29.630 0.00 0.00 33.37 1.82
3674 4513 8.999431 CACAGTAAGGTTACAAGATAACACATT 58.001 33.333 2.83 0.00 36.12 2.71
3690 4529 2.571653 TCAGGCAATAGCACAGTAAGGT 59.428 45.455 0.00 0.00 44.61 3.50
3691 4530 3.266510 TCAGGCAATAGCACAGTAAGG 57.733 47.619 0.00 0.00 44.61 2.69
3692 4531 4.093998 CACTTCAGGCAATAGCACAGTAAG 59.906 45.833 0.00 0.00 44.61 2.34
3693 4532 4.002982 CACTTCAGGCAATAGCACAGTAA 58.997 43.478 0.00 0.00 44.61 2.24
3696 4535 1.741706 CCACTTCAGGCAATAGCACAG 59.258 52.381 0.00 0.00 44.61 3.66
3697 4536 1.350684 TCCACTTCAGGCAATAGCACA 59.649 47.619 0.00 0.00 44.61 4.57
3698 4537 2.113860 TCCACTTCAGGCAATAGCAC 57.886 50.000 0.00 0.00 44.61 4.40
3699 4538 2.646930 CATCCACTTCAGGCAATAGCA 58.353 47.619 0.00 0.00 44.61 3.49
3700 4539 1.952296 CCATCCACTTCAGGCAATAGC 59.048 52.381 0.00 0.00 41.10 2.97
3701 4540 3.287867 ACCATCCACTTCAGGCAATAG 57.712 47.619 0.00 0.00 0.00 1.73
3702 4541 3.355378 CAACCATCCACTTCAGGCAATA 58.645 45.455 0.00 0.00 0.00 1.90
3703 4542 2.173519 CAACCATCCACTTCAGGCAAT 58.826 47.619 0.00 0.00 0.00 3.56
3704 4543 1.619654 CAACCATCCACTTCAGGCAA 58.380 50.000 0.00 0.00 0.00 4.52
3705 4544 0.895100 GCAACCATCCACTTCAGGCA 60.895 55.000 0.00 0.00 0.00 4.75
3706 4545 0.610232 AGCAACCATCCACTTCAGGC 60.610 55.000 0.00 0.00 0.00 4.85
3707 4546 1.171308 CAGCAACCATCCACTTCAGG 58.829 55.000 0.00 0.00 0.00 3.86
3708 4547 2.082231 CTCAGCAACCATCCACTTCAG 58.918 52.381 0.00 0.00 0.00 3.02
3709 4548 1.271543 CCTCAGCAACCATCCACTTCA 60.272 52.381 0.00 0.00 0.00 3.02
3710 4549 1.457346 CCTCAGCAACCATCCACTTC 58.543 55.000 0.00 0.00 0.00 3.01
3711 4550 0.610232 GCCTCAGCAACCATCCACTT 60.610 55.000 0.00 0.00 39.53 3.16
3712 4551 1.001641 GCCTCAGCAACCATCCACT 60.002 57.895 0.00 0.00 39.53 4.00
3713 4552 3.595819 GCCTCAGCAACCATCCAC 58.404 61.111 0.00 0.00 39.53 4.02
3730 4569 3.551454 GCCCAGCAAATACAGCACATATG 60.551 47.826 0.00 0.00 0.00 1.78
3733 4572 0.819582 GCCCAGCAAATACAGCACAT 59.180 50.000 0.00 0.00 0.00 3.21
3753 4592 8.907222 AAACAAGAAAGCAACCATATGAAAAT 57.093 26.923 3.65 0.00 0.00 1.82
3757 4596 7.759489 ACTAAACAAGAAAGCAACCATATGA 57.241 32.000 3.65 0.00 0.00 2.15
3761 4600 6.273071 GTCAACTAAACAAGAAAGCAACCAT 58.727 36.000 0.00 0.00 0.00 3.55
3762 4601 5.646606 GTCAACTAAACAAGAAAGCAACCA 58.353 37.500 0.00 0.00 0.00 3.67
3763 4602 4.733405 CGTCAACTAAACAAGAAAGCAACC 59.267 41.667 0.00 0.00 0.00 3.77
3764 4603 4.204370 GCGTCAACTAAACAAGAAAGCAAC 59.796 41.667 0.00 0.00 0.00 4.17
3926 4765 9.999009 CAAGCAGCGAATAAATAATCATCATAT 57.001 29.630 0.00 0.00 0.00 1.78
3928 4767 7.879070 ACAAGCAGCGAATAAATAATCATCAT 58.121 30.769 0.00 0.00 0.00 2.45
3929 4768 7.263100 ACAAGCAGCGAATAAATAATCATCA 57.737 32.000 0.00 0.00 0.00 3.07
3932 4771 9.489084 ACTATACAAGCAGCGAATAAATAATCA 57.511 29.630 0.00 0.00 0.00 2.57
3962 4815 7.364149 TCAGTCAAAACACCTACCTAAAGTA 57.636 36.000 0.00 0.00 0.00 2.24
3963 4816 6.243216 TCAGTCAAAACACCTACCTAAAGT 57.757 37.500 0.00 0.00 0.00 2.66
3964 4817 7.745620 AATCAGTCAAAACACCTACCTAAAG 57.254 36.000 0.00 0.00 0.00 1.85
3965 4818 8.653191 TCTAATCAGTCAAAACACCTACCTAAA 58.347 33.333 0.00 0.00 0.00 1.85
3968 4821 6.295916 CCTCTAATCAGTCAAAACACCTACCT 60.296 42.308 0.00 0.00 0.00 3.08
3969 4822 5.875359 CCTCTAATCAGTCAAAACACCTACC 59.125 44.000 0.00 0.00 0.00 3.18
3970 4823 6.698380 TCCTCTAATCAGTCAAAACACCTAC 58.302 40.000 0.00 0.00 0.00 3.18
3971 4824 6.928348 TCCTCTAATCAGTCAAAACACCTA 57.072 37.500 0.00 0.00 0.00 3.08
3972 4825 5.825593 TCCTCTAATCAGTCAAAACACCT 57.174 39.130 0.00 0.00 0.00 4.00
3973 4826 8.738645 ATAATCCTCTAATCAGTCAAAACACC 57.261 34.615 0.00 0.00 0.00 4.16
3992 4845 6.279513 TGGTCCAAAACAACATGATAATCC 57.720 37.500 0.00 0.00 0.00 3.01
4020 4876 2.622452 CCTGGAATCAATGCCTGGAAGT 60.622 50.000 7.06 0.00 43.70 3.01
4029 4885 3.370840 TCTTGTCCCCTGGAATCAATG 57.629 47.619 0.00 0.00 31.38 2.82
4043 4899 8.194104 TGCTTCTTCAGAACTATAGATCTTGTC 58.806 37.037 9.67 0.00 0.00 3.18
4064 4926 2.476854 GCATCCATCGAGTGTTTGCTTC 60.477 50.000 0.00 0.00 33.44 3.86
4068 4930 2.485426 ACAAGCATCCATCGAGTGTTTG 59.515 45.455 13.70 13.70 39.15 2.93
4074 4936 5.490139 AAAACATACAAGCATCCATCGAG 57.510 39.130 0.00 0.00 0.00 4.04
4080 4942 4.857037 GGAACGAAAAACATACAAGCATCC 59.143 41.667 0.00 0.00 0.00 3.51
4087 4949 9.005777 AGCTTAAATAGGAACGAAAAACATACA 57.994 29.630 0.00 0.00 0.00 2.29
4098 4960 9.651718 GTCAATAAATCAGCTTAAATAGGAACG 57.348 33.333 0.00 0.00 0.00 3.95
4122 4986 6.986904 AGAGGAGATAATTTTTCGTTGGTC 57.013 37.500 0.00 0.00 0.00 4.02
4128 4992 9.459640 TTCGTATGTAGAGGAGATAATTTTTCG 57.540 33.333 0.00 0.00 0.00 3.46
4130 4994 9.543783 GGTTCGTATGTAGAGGAGATAATTTTT 57.456 33.333 0.00 0.00 0.00 1.94
4131 4995 8.701895 TGGTTCGTATGTAGAGGAGATAATTTT 58.298 33.333 0.00 0.00 0.00 1.82
4132 4996 8.246430 TGGTTCGTATGTAGAGGAGATAATTT 57.754 34.615 0.00 0.00 0.00 1.82
4133 4997 7.834881 TGGTTCGTATGTAGAGGAGATAATT 57.165 36.000 0.00 0.00 0.00 1.40
4134 4998 7.834881 TTGGTTCGTATGTAGAGGAGATAAT 57.165 36.000 0.00 0.00 0.00 1.28
4135 4999 7.834881 ATTGGTTCGTATGTAGAGGAGATAA 57.165 36.000 0.00 0.00 0.00 1.75
4136 5000 8.380867 TCTATTGGTTCGTATGTAGAGGAGATA 58.619 37.037 0.00 0.00 0.00 1.98
4137 5001 7.232188 TCTATTGGTTCGTATGTAGAGGAGAT 58.768 38.462 0.00 0.00 0.00 2.75
4138 5002 6.598503 TCTATTGGTTCGTATGTAGAGGAGA 58.401 40.000 0.00 0.00 0.00 3.71
4139 5003 6.879276 TCTATTGGTTCGTATGTAGAGGAG 57.121 41.667 0.00 0.00 0.00 3.69
4140 5004 7.649533 TTTCTATTGGTTCGTATGTAGAGGA 57.350 36.000 0.00 0.00 0.00 3.71
4141 5005 7.762615 TGTTTTCTATTGGTTCGTATGTAGAGG 59.237 37.037 0.00 0.00 0.00 3.69
4142 5006 8.697846 TGTTTTCTATTGGTTCGTATGTAGAG 57.302 34.615 0.00 0.00 0.00 2.43
4143 5007 7.762615 CCTGTTTTCTATTGGTTCGTATGTAGA 59.237 37.037 0.00 0.00 0.00 2.59
4144 5008 7.465513 GCCTGTTTTCTATTGGTTCGTATGTAG 60.466 40.741 0.00 0.00 0.00 2.74
4145 5009 6.314400 GCCTGTTTTCTATTGGTTCGTATGTA 59.686 38.462 0.00 0.00 0.00 2.29
4146 5010 5.123344 GCCTGTTTTCTATTGGTTCGTATGT 59.877 40.000 0.00 0.00 0.00 2.29
4147 5011 5.354234 AGCCTGTTTTCTATTGGTTCGTATG 59.646 40.000 0.00 0.00 0.00 2.39
4148 5012 5.497474 AGCCTGTTTTCTATTGGTTCGTAT 58.503 37.500 0.00 0.00 0.00 3.06
4149 5013 4.901868 AGCCTGTTTTCTATTGGTTCGTA 58.098 39.130 0.00 0.00 0.00 3.43
4150 5014 3.751518 AGCCTGTTTTCTATTGGTTCGT 58.248 40.909 0.00 0.00 0.00 3.85
4151 5015 5.354234 ACATAGCCTGTTTTCTATTGGTTCG 59.646 40.000 0.00 0.00 32.90 3.95
4152 5016 6.759497 ACATAGCCTGTTTTCTATTGGTTC 57.241 37.500 0.00 0.00 32.90 3.62


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

AutoCloner maintained by Alex Coulton.