Multiple sequence alignment - TraesCS2A01G386200

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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 TraesCS2A01G386200 chr2A 100.000 3879 0 0 1 3879 631970326 631966448 0.000000e+00 7164
1 TraesCS2A01G386200 chr2D 89.316 3407 147 66 1 3292 486958516 486955212 0.000000e+00 4074
2 TraesCS2A01G386200 chr2D 86.990 784 53 15 1851 2619 643637237 643636488 0.000000e+00 837
3 TraesCS2A01G386200 chr2B 91.711 2449 88 51 971 3341 571533522 571531111 0.000000e+00 3291
4 TraesCS2A01G386200 chr2B 84.680 953 41 22 1 895 571534768 571533863 0.000000e+00 854
5 TraesCS2A01G386200 chr2B 87.153 288 24 6 3585 3872 571531090 571530816 8.090000e-82 315
6 TraesCS2A01G386200 chr7A 87.758 776 60 13 1852 2619 176279531 176278783 0.000000e+00 874
7 TraesCS2A01G386200 chr7A 87.629 776 61 13 1852 2619 670564404 670563656 0.000000e+00 869
8 TraesCS2A01G386200 chr7A 87.215 219 25 3 3348 3564 5906631 5906414 2.990000e-61 246
9 TraesCS2A01G386200 chr5D 87.758 776 55 21 1852 2619 365088058 365088801 0.000000e+00 870
10 TraesCS2A01G386200 chr5D 87.671 219 24 3 3348 3564 51685257 51685040 6.430000e-63 252
11 TraesCS2A01G386200 chr3A 87.371 776 60 15 1852 2619 693453535 693452790 0.000000e+00 856
12 TraesCS2A01G386200 chrUn 87.084 782 55 19 1852 2614 116830638 116831392 0.000000e+00 843
13 TraesCS2A01G386200 chr3B 88.841 233 20 4 1832 2061 32282286 32282057 8.210000e-72 281
14 TraesCS2A01G386200 chr3B 83.163 196 18 7 2105 2298 32280465 32280283 8.620000e-37 165
15 TraesCS2A01G386200 chr1D 87.215 219 26 2 3348 3564 410459769 410459551 8.320000e-62 248
16 TraesCS2A01G386200 chr1D 86.758 219 27 2 3348 3564 470941372 470941590 3.870000e-60 243
17 TraesCS2A01G386200 chr6D 86.463 229 26 5 3341 3566 16776300 16776074 2.990000e-61 246
18 TraesCS2A01G386200 chr6D 88.393 112 13 0 1228 1339 310523083 310522972 6.760000e-28 135
19 TraesCS2A01G386200 chr6A 87.215 219 25 3 3348 3564 76520721 76520938 2.990000e-61 246
20 TraesCS2A01G386200 chr3D 87.215 219 25 3 3348 3564 83428753 83428536 2.990000e-61 246
21 TraesCS2A01G386200 chr4A 86.818 220 26 3 3348 3565 599341249 599341467 3.870000e-60 243
22 TraesCS2A01G386200 chr4A 85.590 229 29 3 3348 3575 622287898 622287673 1.800000e-58 237
23 TraesCS2A01G386200 chr6B 88.679 106 11 1 1225 1330 478753293 478753397 1.130000e-25 128


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 TraesCS2A01G386200 chr2A 631966448 631970326 3878 True 7164.000000 7164 100.000 1 3879 1 chr2A.!!$R1 3878
1 TraesCS2A01G386200 chr2D 486955212 486958516 3304 True 4074.000000 4074 89.316 1 3292 1 chr2D.!!$R1 3291
2 TraesCS2A01G386200 chr2D 643636488 643637237 749 True 837.000000 837 86.990 1851 2619 1 chr2D.!!$R2 768
3 TraesCS2A01G386200 chr2B 571530816 571534768 3952 True 1486.666667 3291 87.848 1 3872 3 chr2B.!!$R1 3871
4 TraesCS2A01G386200 chr7A 176278783 176279531 748 True 874.000000 874 87.758 1852 2619 1 chr7A.!!$R2 767
5 TraesCS2A01G386200 chr7A 670563656 670564404 748 True 869.000000 869 87.629 1852 2619 1 chr7A.!!$R3 767
6 TraesCS2A01G386200 chr5D 365088058 365088801 743 False 870.000000 870 87.758 1852 2619 1 chr5D.!!$F1 767
7 TraesCS2A01G386200 chr3A 693452790 693453535 745 True 856.000000 856 87.371 1852 2619 1 chr3A.!!$R1 767
8 TraesCS2A01G386200 chrUn 116830638 116831392 754 False 843.000000 843 87.084 1852 2614 1 chrUn.!!$F1 762
9 TraesCS2A01G386200 chr3B 32280283 32282286 2003 True 223.000000 281 86.002 1832 2298 2 chr3B.!!$R1 466

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
913 985 0.107993 CCTCTCCTGATCAAAGCGCA 60.108 55.0 11.47 0.0 0.0 6.09 F
1188 1553 0.108567 GCTCGTTTCCACCCTCTCTC 60.109 60.0 0.00 0.0 0.0 3.20 F
1783 2178 0.041833 CCTGGGACTGGGAGAAGAGA 59.958 60.0 0.00 0.0 44.2 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2117 0.108138 AGCTAGTACGTACGACCGGT 60.108 55.000 24.41 6.92 0.00 5.28 R
2113 4087 0.185175 GGCCCATTTGGTACCCCTAG 59.815 60.000 10.07 0.00 36.04 3.02 R
3779 5793 1.000955 ACACGTGACTTAGCTCCTTGG 59.999 52.381 25.01 0.00 0.00 3.61 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
42 43 8.357402 ACAAAACAAAAACCGAAGCTAGATAAT 58.643 29.630 0.00 0.00 0.00 1.28
43 44 8.850452 CAAAACAAAAACCGAAGCTAGATAATC 58.150 33.333 0.00 0.00 0.00 1.75
60 61 5.540337 AGATAATCGGAGAAGCCAGTCAATA 59.460 40.000 0.00 0.00 43.58 1.90
142 150 4.090057 GCTGTCCGCTTTGACCGC 62.090 66.667 0.00 0.00 38.11 5.68
162 170 4.554036 GAGGCCCGCCAGATCACC 62.554 72.222 8.74 0.00 38.92 4.02
186 194 4.321718 AGATTCACACAGTGATGGACAAG 58.678 43.478 7.81 0.00 42.40 3.16
200 208 2.279451 CAAGCGATCATCGGCCGA 60.279 61.111 33.12 33.12 40.84 5.54
268 277 2.033141 GAGCTGCCACCAGAGCAA 59.967 61.111 0.00 0.00 41.77 3.91
282 291 1.303155 AGCAAAGCAGGCCAGAGAC 60.303 57.895 5.01 0.00 0.00 3.36
283 292 2.684843 GCAAAGCAGGCCAGAGACG 61.685 63.158 5.01 0.00 0.00 4.18
289 298 3.063084 AGGCCAGAGACGACGTCC 61.063 66.667 23.76 15.12 32.18 4.79
413 440 1.898154 CTAGCTACCGGGCACTGTT 59.102 57.895 6.32 0.00 34.17 3.16
435 462 1.136329 AGCCACTGTTCCCTGTCCAT 61.136 55.000 0.00 0.00 0.00 3.41
504 549 0.332632 CTTTCCCAATCTGCCCCTCA 59.667 55.000 0.00 0.00 0.00 3.86
508 553 1.565390 CCCAATCTGCCCCTCACTCA 61.565 60.000 0.00 0.00 0.00 3.41
511 556 0.908198 AATCTGCCCCTCACTCACTC 59.092 55.000 0.00 0.00 0.00 3.51
526 571 3.541713 CTCGCCCTGCTACCTCCC 61.542 72.222 0.00 0.00 0.00 4.30
623 668 1.522668 TCAAATCACCAGAGGCAACG 58.477 50.000 0.00 0.00 46.39 4.10
646 691 2.849007 GACGACGACGACGACAGA 59.151 61.111 25.15 0.00 42.66 3.41
647 692 1.506686 GACGACGACGACGACAGAC 60.507 63.158 25.15 7.94 42.66 3.51
648 693 3.273748 ACGACGACGACGACAGACG 62.274 63.158 25.15 12.64 44.35 4.18
675 720 2.979130 GAGGCTTTCTCGAATCGGG 58.021 57.895 1.76 0.00 32.18 5.14
693 738 1.478105 GGGCAGGTCAATCAAATCCAC 59.522 52.381 0.00 0.00 0.00 4.02
771 821 4.974368 AGACTAGAGTATATGCGCATCC 57.026 45.455 29.11 15.98 0.00 3.51
772 822 4.336280 AGACTAGAGTATATGCGCATCCA 58.664 43.478 29.11 11.39 0.00 3.41
773 823 4.952957 AGACTAGAGTATATGCGCATCCAT 59.047 41.667 29.11 18.46 0.00 3.41
774 824 5.420421 AGACTAGAGTATATGCGCATCCATT 59.580 40.000 29.11 12.56 0.00 3.16
778 828 5.114780 AGAGTATATGCGCATCCATTCATC 58.885 41.667 29.11 16.02 0.00 2.92
842 892 2.606587 ATCCCCACCACTGCTCACC 61.607 63.158 0.00 0.00 0.00 4.02
845 895 3.252284 CCACCACTGCTCACCCCT 61.252 66.667 0.00 0.00 0.00 4.79
846 896 2.348998 CACCACTGCTCACCCCTC 59.651 66.667 0.00 0.00 0.00 4.30
847 897 2.205462 ACCACTGCTCACCCCTCT 59.795 61.111 0.00 0.00 0.00 3.69
848 898 1.915769 ACCACTGCTCACCCCTCTC 60.916 63.158 0.00 0.00 0.00 3.20
850 900 1.611851 CACTGCTCACCCCTCTCCT 60.612 63.158 0.00 0.00 0.00 3.69
851 901 1.305718 ACTGCTCACCCCTCTCCTC 60.306 63.158 0.00 0.00 0.00 3.71
852 902 1.001503 CTGCTCACCCCTCTCCTCT 59.998 63.158 0.00 0.00 0.00 3.69
854 904 1.760480 GCTCACCCCTCTCCTCTCC 60.760 68.421 0.00 0.00 0.00 3.71
857 907 0.553862 TCACCCCTCTCCTCTCCTCT 60.554 60.000 0.00 0.00 0.00 3.69
911 983 0.179062 CCCCTCTCCTGATCAAAGCG 60.179 60.000 0.00 0.00 0.00 4.68
913 985 0.107993 CCTCTCCTGATCAAAGCGCA 60.108 55.000 11.47 0.00 0.00 6.09
933 1024 1.953642 GCCGAGCAAGCTAGCTAGC 60.954 63.158 33.96 33.96 46.75 3.42
943 1034 2.596776 CTAGCTAGCAGGTGGTGGT 58.403 57.895 18.83 0.00 40.92 4.16
945 1036 1.264749 TAGCTAGCAGGTGGTGGTGG 61.265 60.000 18.83 0.00 37.49 4.61
947 1038 3.628646 CTAGCAGGTGGTGGTGGGC 62.629 68.421 0.00 0.00 37.49 5.36
953 1044 3.131478 GTGGTGGTGGGCGCATAC 61.131 66.667 10.83 9.54 0.00 2.39
961 1052 1.885388 TGGGCGCATACACATACGC 60.885 57.895 10.83 0.00 44.60 4.42
990 1327 2.427410 GACGCGGCTTTGCTTGTG 60.427 61.111 12.47 0.00 0.00 3.33
995 1332 2.029518 GGCTTTGCTTGTGGCCAC 59.970 61.111 29.67 29.67 43.59 5.01
1163 1528 2.288518 GCCTCCGTTAGATTAGCTCCTG 60.289 54.545 0.00 0.00 0.00 3.86
1187 1552 1.878656 CGCTCGTTTCCACCCTCTCT 61.879 60.000 0.00 0.00 0.00 3.10
1188 1553 0.108567 GCTCGTTTCCACCCTCTCTC 60.109 60.000 0.00 0.00 0.00 3.20
1201 1566 2.757868 CCCTCTCTCGTCTCACAATCTT 59.242 50.000 0.00 0.00 0.00 2.40
1202 1567 3.428725 CCCTCTCTCGTCTCACAATCTTG 60.429 52.174 0.00 0.00 0.00 3.02
1204 1569 4.321601 CCTCTCTCGTCTCACAATCTTGTT 60.322 45.833 0.00 0.00 39.91 2.83
1206 1571 3.565516 TCTCGTCTCACAATCTTGTTCG 58.434 45.455 0.00 0.00 39.91 3.95
1496 1869 7.553881 TGGCAGATATTTGCTAACTTAACTC 57.446 36.000 16.93 0.00 43.57 3.01
1687 2060 3.349481 GAGGAAGAGCGCTGCGTCT 62.349 63.158 18.48 19.87 32.82 4.18
1707 2080 0.804933 GGGACTAAGCGTAAGTGCCG 60.805 60.000 10.05 0.00 44.19 5.69
1722 2117 1.250840 TGCCGAGCTCAGTTCTGCTA 61.251 55.000 15.40 0.00 39.91 3.49
1741 2136 0.108138 ACCGGTCGTACGTACTAGCT 60.108 55.000 22.55 4.94 0.00 3.32
1759 2154 4.195225 AGCTACTAGTCAAAGCACCTTC 57.805 45.455 16.49 0.00 38.75 3.46
1770 2165 3.089838 CACCTTCATGCCCTGGGA 58.910 61.111 19.27 1.59 0.00 4.37
1772 2167 1.542375 ACCTTCATGCCCTGGGACT 60.542 57.895 19.27 0.00 0.00 3.85
1781 2176 4.896979 CCTGGGACTGGGAGAAGA 57.103 61.111 0.00 0.00 44.20 2.87
1783 2178 0.041833 CCTGGGACTGGGAGAAGAGA 59.958 60.000 0.00 0.00 44.20 3.10
1785 2180 0.616111 TGGGACTGGGAGAAGAGAGC 60.616 60.000 0.00 0.00 0.00 4.09
1904 2300 2.159382 GATTCTTTCTGGGCGGTCAAA 58.841 47.619 0.00 0.00 0.00 2.69
1913 2309 1.037493 GGGCGGTCAAAGGAGTTTTT 58.963 50.000 0.00 0.00 0.00 1.94
1930 2326 1.125093 TTTGAGTGGAAGAGGCCGGA 61.125 55.000 5.05 0.00 0.00 5.14
1948 2348 2.614057 CGGATGAATAGTTTGCTCACCC 59.386 50.000 0.00 0.00 0.00 4.61
1978 2379 0.549469 ACCTTTTGTCCGTGGAGGTT 59.451 50.000 0.00 0.00 37.44 3.50
2090 4053 7.806960 GCATTAGGAATCAGAAACATAATCAGC 59.193 37.037 0.00 0.00 0.00 4.26
2094 4057 6.991531 AGGAATCAGAAACATAATCAGCTCTC 59.008 38.462 0.00 0.00 0.00 3.20
2113 4087 6.930722 AGCTCTCTAAGTTAGGTATACGACTC 59.069 42.308 10.02 0.00 0.00 3.36
2144 4118 3.349304 TGGGCCACCAGGATGCAT 61.349 61.111 0.00 0.00 43.37 3.96
2155 4129 2.621998 CCAGGATGCATTTGTCTGATCC 59.378 50.000 16.52 5.69 33.97 3.36
2298 4280 4.269603 CCGATTCATCAAGTGAGTGATCAC 59.730 45.833 18.47 18.47 36.04 3.06
2331 4313 2.235402 TGGTTCATTCTAGTTCCCCGTC 59.765 50.000 0.00 0.00 0.00 4.79
2392 4387 4.104579 TGATGCATGGGTTCCTATGTATGT 59.895 41.667 19.26 2.24 31.22 2.29
2393 4388 5.309282 TGATGCATGGGTTCCTATGTATGTA 59.691 40.000 19.26 8.72 31.22 2.29
2482 4477 2.793585 CGCAGCTGCCAAGAATGTAATG 60.794 50.000 32.07 9.98 37.91 1.90
2483 4478 2.805845 CAGCTGCCAAGAATGTAATGC 58.194 47.619 0.00 0.00 0.00 3.56
2507 4508 8.045507 TGCACTTCATCTTCTCTATTTCTCAAT 58.954 33.333 0.00 0.00 0.00 2.57
2526 4527 6.483307 TCTCAATACACATTTTGATCGGATCC 59.517 38.462 15.06 0.00 31.83 3.36
2564 4565 8.763356 TGATTTGTTCAATGCTTTGTGTATTTC 58.237 29.630 11.67 5.54 34.32 2.17
2579 4580 5.163652 TGTGTATTTCTCATCGATCGTCTGT 60.164 40.000 15.94 0.00 0.00 3.41
2704 4705 6.447409 GGAGGCCCTAAAACCTAATCCTATAT 59.553 42.308 0.00 0.00 36.05 0.86
2705 4706 7.626487 GGAGGCCCTAAAACCTAATCCTATATA 59.374 40.741 0.00 0.00 36.05 0.86
2706 4707 9.226879 GAGGCCCTAAAACCTAATCCTATATAT 57.773 37.037 0.00 0.00 36.05 0.86
2832 4836 2.275134 TGCATGCTCTTCAAGGACAA 57.725 45.000 20.33 0.00 0.00 3.18
3034 5044 4.095932 AGTTTTCGTTGTTTCTTCCTGTCC 59.904 41.667 0.00 0.00 0.00 4.02
3137 5147 8.589338 ACATAAAATAGATCGATCTAGTTGCCT 58.411 33.333 35.57 26.26 44.14 4.75
3230 5244 3.761218 TGAATAATTGAACATGTGCGGGT 59.239 39.130 0.00 0.00 0.00 5.28
3322 5336 8.812329 CAACATGACACTAGTAATAAAGAGCTC 58.188 37.037 5.27 5.27 0.00 4.09
3341 5355 5.999044 AGCTCAAATCATACTCACTCCATT 58.001 37.500 0.00 0.00 0.00 3.16
3342 5356 6.421485 AGCTCAAATCATACTCACTCCATTT 58.579 36.000 0.00 0.00 0.00 2.32
3343 5357 6.888632 AGCTCAAATCATACTCACTCCATTTT 59.111 34.615 0.00 0.00 0.00 1.82
3344 5358 7.395489 AGCTCAAATCATACTCACTCCATTTTT 59.605 33.333 0.00 0.00 0.00 1.94
3377 5391 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
3378 5392 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
3448 5462 8.800231 TGAAAATATATTTCACAATGCATCCG 57.200 30.769 11.08 0.00 33.90 4.18
3449 5463 8.628280 TGAAAATATATTTCACAATGCATCCGA 58.372 29.630 11.08 0.00 33.90 4.55
3450 5464 9.630098 GAAAATATATTTCACAATGCATCCGAT 57.370 29.630 11.08 0.00 0.00 4.18
3457 5471 8.975410 ATTTCACAATGCATCCGATAATATTG 57.025 30.769 0.00 0.00 0.00 1.90
3458 5472 7.742556 TTCACAATGCATCCGATAATATTGA 57.257 32.000 0.00 0.00 31.79 2.57
3459 5473 7.132694 TCACAATGCATCCGATAATATTGAC 57.867 36.000 0.00 0.00 31.79 3.18
3460 5474 6.936335 TCACAATGCATCCGATAATATTGACT 59.064 34.615 0.00 0.00 31.79 3.41
3461 5475 7.445096 TCACAATGCATCCGATAATATTGACTT 59.555 33.333 0.00 0.00 31.79 3.01
3462 5476 7.747799 CACAATGCATCCGATAATATTGACTTC 59.252 37.037 0.00 0.00 31.79 3.01
3463 5477 7.445096 ACAATGCATCCGATAATATTGACTTCA 59.555 33.333 0.00 0.00 31.79 3.02
3464 5478 8.456471 CAATGCATCCGATAATATTGACTTCAT 58.544 33.333 0.00 0.00 0.00 2.57
3465 5479 9.671279 AATGCATCCGATAATATTGACTTCATA 57.329 29.630 0.00 0.00 0.00 2.15
3466 5480 9.842775 ATGCATCCGATAATATTGACTTCATAT 57.157 29.630 0.00 0.00 0.00 1.78
3467 5481 9.671279 TGCATCCGATAATATTGACTTCATATT 57.329 29.630 0.00 0.00 0.00 1.28
3468 5482 9.926751 GCATCCGATAATATTGACTTCATATTG 57.073 33.333 0.00 0.00 0.00 1.90
3515 5529 7.689953 TGAAGTTAGTCAGAGTTTACGAAAC 57.310 36.000 0.00 0.00 41.69 2.78
3531 5545 9.712359 GTTTACGAAACTTGACTTTGACTAAAT 57.288 29.630 0.00 0.00 38.35 1.40
3556 5570 8.873215 TTTATATGCAAACCAAAAAGAAACGA 57.127 26.923 0.00 0.00 0.00 3.85
3557 5571 8.514136 TTATATGCAAACCAAAAAGAAACGAG 57.486 30.769 0.00 0.00 0.00 4.18
3558 5572 3.516615 TGCAAACCAAAAAGAAACGAGG 58.483 40.909 0.00 0.00 0.00 4.63
3559 5573 2.863740 GCAAACCAAAAAGAAACGAGGG 59.136 45.455 0.00 0.00 0.00 4.30
3560 5574 3.429684 GCAAACCAAAAAGAAACGAGGGA 60.430 43.478 0.00 0.00 0.00 4.20
3561 5575 4.359706 CAAACCAAAAAGAAACGAGGGAG 58.640 43.478 0.00 0.00 0.00 4.30
3562 5576 3.292492 ACCAAAAAGAAACGAGGGAGT 57.708 42.857 0.00 0.00 0.00 3.85
3563 5577 4.426736 ACCAAAAAGAAACGAGGGAGTA 57.573 40.909 0.00 0.00 0.00 2.59
3564 5578 4.981812 ACCAAAAAGAAACGAGGGAGTAT 58.018 39.130 0.00 0.00 0.00 2.12
3565 5579 5.382616 ACCAAAAAGAAACGAGGGAGTATT 58.617 37.500 0.00 0.00 0.00 1.89
3566 5580 6.536447 ACCAAAAAGAAACGAGGGAGTATTA 58.464 36.000 0.00 0.00 0.00 0.98
3567 5581 6.429078 ACCAAAAAGAAACGAGGGAGTATTAC 59.571 38.462 0.00 0.00 0.00 1.89
3568 5582 6.128090 CCAAAAAGAAACGAGGGAGTATTACC 60.128 42.308 0.00 0.00 0.00 2.85
3569 5583 6.370186 AAAAGAAACGAGGGAGTATTACCT 57.630 37.500 0.00 0.00 40.54 3.08
3578 5592 2.941480 GGAGTATTACCTCCGTCCTGA 58.059 52.381 0.00 0.00 41.58 3.86
3579 5593 3.294214 GGAGTATTACCTCCGTCCTGAA 58.706 50.000 0.00 0.00 41.58 3.02
3580 5594 3.703052 GGAGTATTACCTCCGTCCTGAAA 59.297 47.826 0.00 0.00 41.58 2.69
3581 5595 4.161001 GGAGTATTACCTCCGTCCTGAAAA 59.839 45.833 0.00 0.00 41.58 2.29
3582 5596 5.337813 GGAGTATTACCTCCGTCCTGAAAAA 60.338 44.000 0.00 0.00 41.58 1.94
3583 5597 5.731591 AGTATTACCTCCGTCCTGAAAAAG 58.268 41.667 0.00 0.00 0.00 2.27
3584 5598 4.635699 ATTACCTCCGTCCTGAAAAAGT 57.364 40.909 0.00 0.00 0.00 2.66
3585 5599 4.426736 TTACCTCCGTCCTGAAAAAGTT 57.573 40.909 0.00 0.00 0.00 2.66
3586 5600 2.572290 ACCTCCGTCCTGAAAAAGTTG 58.428 47.619 0.00 0.00 0.00 3.16
3587 5601 2.092592 ACCTCCGTCCTGAAAAAGTTGT 60.093 45.455 0.00 0.00 0.00 3.32
3588 5602 2.548480 CCTCCGTCCTGAAAAAGTTGTC 59.452 50.000 0.00 0.00 0.00 3.18
3589 5603 3.467803 CTCCGTCCTGAAAAAGTTGTCT 58.532 45.455 0.00 0.00 0.00 3.41
3596 5610 7.549488 CCGTCCTGAAAAAGTTGTCTTAGATAT 59.451 37.037 0.00 0.00 33.09 1.63
3624 5638 4.726035 ATCTAGACAATAGACCGAGGGA 57.274 45.455 0.00 0.00 0.00 4.20
3629 5643 4.145807 AGACAATAGACCGAGGGAGTATG 58.854 47.826 0.00 0.00 0.00 2.39
3644 5658 5.015178 AGGGAGTATGAAATTTGAGGAACCA 59.985 40.000 0.00 0.00 0.00 3.67
3667 5681 8.993121 ACCAATAGAATTGTATAATGAAGAGCG 58.007 33.333 0.00 0.00 0.00 5.03
3682 5696 8.545229 AATGAAGAGCGAAAATCATATAGGAG 57.455 34.615 0.00 0.00 32.47 3.69
3715 5729 6.903883 TGTCCGAGAATTTCTATTGCTAAC 57.096 37.500 0.00 0.00 0.00 2.34
3775 5789 9.959749 AAAAGTTGTTGTATTGTACATAAGTGG 57.040 29.630 0.00 0.00 38.68 4.00
3779 5793 6.904498 TGTTGTATTGTACATAAGTGGTTGC 58.096 36.000 0.00 0.00 38.68 4.17
3786 5800 2.795329 ACATAAGTGGTTGCCAAGGAG 58.205 47.619 0.00 0.00 34.18 3.69
3802 5816 3.470645 AGGAGCTAAGTCACGTGTTTT 57.529 42.857 16.51 13.19 0.00 2.43
3803 5817 3.391049 AGGAGCTAAGTCACGTGTTTTC 58.609 45.455 16.51 6.36 0.00 2.29
3804 5818 2.155155 GGAGCTAAGTCACGTGTTTTCG 59.845 50.000 16.51 8.42 0.00 3.46
3835 5849 2.472695 TGGAGGCACACTTATCACAC 57.527 50.000 0.00 0.00 0.00 3.82
3859 5873 7.337436 CACGGTTGGGTAAATTAATCCTCTAAA 59.663 37.037 0.00 0.00 0.00 1.85
3874 5888 5.990668 TCCTCTAAAGACCTCCTAAAATGC 58.009 41.667 0.00 0.00 0.00 3.56
3875 5889 5.487488 TCCTCTAAAGACCTCCTAAAATGCA 59.513 40.000 0.00 0.00 0.00 3.96
3876 5890 6.158695 TCCTCTAAAGACCTCCTAAAATGCAT 59.841 38.462 0.00 0.00 0.00 3.96
3877 5891 6.830838 CCTCTAAAGACCTCCTAAAATGCATT 59.169 38.462 5.99 5.99 0.00 3.56
3878 5892 7.993183 CCTCTAAAGACCTCCTAAAATGCATTA 59.007 37.037 13.39 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.843541 GCTTCGGTTTTTGTTTTGTTTGC 59.156 39.130 0.00 0.00 0.00 3.68
42 43 3.973206 TTTATTGACTGGCTTCTCCGA 57.027 42.857 0.00 0.00 37.80 4.55
43 44 4.191544 TGATTTATTGACTGGCTTCTCCG 58.808 43.478 0.00 0.00 37.80 4.63
70 71 0.108520 CGCAGAGGCCATGCATTTTT 60.109 50.000 26.72 0.00 44.05 1.94
115 123 1.951631 GCGGACAGCGATTCTAGCC 60.952 63.158 0.00 0.00 35.41 3.93
162 170 4.067192 TGTCCATCACTGTGTGAATCTTG 58.933 43.478 7.79 0.00 45.96 3.02
186 194 2.720758 CGAATCGGCCGATGATCGC 61.721 63.158 35.75 24.06 38.82 4.58
200 208 2.509336 CCTGTTCCGCGCTCGAAT 60.509 61.111 5.56 0.00 38.10 3.34
211 219 0.886490 CAGTGCCCACAGTCCTGTTC 60.886 60.000 0.00 0.00 42.83 3.18
258 267 2.633509 GGCCTGCTTTGCTCTGGTG 61.634 63.158 0.00 0.00 0.00 4.17
265 274 2.684843 CGTCTCTGGCCTGCTTTGC 61.685 63.158 3.32 0.00 0.00 3.68
268 277 2.659610 GTCGTCTCTGGCCTGCTT 59.340 61.111 3.32 0.00 0.00 3.91
413 440 2.113774 CAGGGAACAGTGGCTGCA 59.886 61.111 0.50 0.00 34.37 4.41
416 443 1.136329 ATGGACAGGGAACAGTGGCT 61.136 55.000 0.00 0.00 0.00 4.75
435 462 2.277072 CCCGCTCTCTCCTCTCCA 59.723 66.667 0.00 0.00 0.00 3.86
504 549 2.352032 GGTAGCAGGGCGAGTGAGT 61.352 63.158 0.00 0.00 0.00 3.41
508 553 2.760385 GGAGGTAGCAGGGCGAGT 60.760 66.667 0.00 0.00 0.00 4.18
511 556 3.541713 GAGGGAGGTAGCAGGGCG 61.542 72.222 0.00 0.00 0.00 6.13
526 571 1.063417 AGGCAAGGAATGGGAATGGAG 60.063 52.381 0.00 0.00 0.00 3.86
589 634 1.794885 TTTGAAAGCCGGGATCCCCA 61.795 55.000 25.73 13.06 45.83 4.96
623 668 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
636 681 0.443088 GATCTGTCGTCTGTCGTCGT 59.557 55.000 0.00 0.00 40.80 4.34
637 682 0.247735 GGATCTGTCGTCTGTCGTCG 60.248 60.000 0.00 0.00 40.80 5.12
638 683 0.247735 CGGATCTGTCGTCTGTCGTC 60.248 60.000 0.00 0.00 40.80 4.20
639 684 0.672711 TCGGATCTGTCGTCTGTCGT 60.673 55.000 0.42 0.00 40.80 4.34
640 685 0.026933 CTCGGATCTGTCGTCTGTCG 59.973 60.000 0.42 0.00 41.41 4.35
641 686 0.378962 CCTCGGATCTGTCGTCTGTC 59.621 60.000 0.42 0.00 0.00 3.51
642 687 1.658686 GCCTCGGATCTGTCGTCTGT 61.659 60.000 0.42 0.00 0.00 3.41
643 688 1.064946 GCCTCGGATCTGTCGTCTG 59.935 63.158 0.42 0.00 0.00 3.51
644 689 0.681564 AAGCCTCGGATCTGTCGTCT 60.682 55.000 0.42 0.00 0.00 4.18
645 690 0.173708 AAAGCCTCGGATCTGTCGTC 59.826 55.000 0.42 0.00 0.00 4.20
646 691 0.173708 GAAAGCCTCGGATCTGTCGT 59.826 55.000 0.42 0.00 0.00 4.34
647 692 0.457851 AGAAAGCCTCGGATCTGTCG 59.542 55.000 0.42 0.00 0.00 4.35
648 693 2.217429 GAGAAAGCCTCGGATCTGTC 57.783 55.000 0.42 0.00 31.32 3.51
675 720 2.165030 CTGGTGGATTTGATTGACCTGC 59.835 50.000 0.00 0.00 0.00 4.85
693 738 1.341285 TGATTTGATGGGCACTCCTGG 60.341 52.381 0.00 0.00 36.20 4.45
771 821 2.109480 AGTGGGGATGGATGGATGAATG 59.891 50.000 0.00 0.00 0.00 2.67
772 822 2.109480 CAGTGGGGATGGATGGATGAAT 59.891 50.000 0.00 0.00 0.00 2.57
773 823 1.496001 CAGTGGGGATGGATGGATGAA 59.504 52.381 0.00 0.00 0.00 2.57
774 824 1.142936 CAGTGGGGATGGATGGATGA 58.857 55.000 0.00 0.00 0.00 2.92
778 828 2.196776 GGCAGTGGGGATGGATGG 59.803 66.667 0.00 0.00 0.00 3.51
842 892 0.478507 GAGGAGAGGAGAGGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
845 895 1.010793 AGGAGAGGAGAGGAGAGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
846 896 1.421646 GAGGAGAGGAGAGGAGAGGAG 59.578 61.905 0.00 0.00 0.00 3.69
847 897 1.010793 AGAGGAGAGGAGAGGAGAGGA 59.989 57.143 0.00 0.00 0.00 3.71
848 898 1.421646 GAGAGGAGAGGAGAGGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
850 900 1.010793 AGGAGAGGAGAGGAGAGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
851 901 1.421646 GAGGAGAGGAGAGGAGAGGAG 59.578 61.905 0.00 0.00 0.00 3.69
852 902 1.518367 GAGGAGAGGAGAGGAGAGGA 58.482 60.000 0.00 0.00 0.00 3.71
854 904 0.108585 CGGAGGAGAGGAGAGGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
898 970 2.390599 GCGTGCGCTTTGATCAGGA 61.391 57.895 9.73 0.00 38.26 3.86
911 983 3.558411 CTAGCTTGCTCGGCGTGC 61.558 66.667 25.31 25.31 34.52 5.34
913 985 2.343163 CTAGCTAGCTTGCTCGGCGT 62.343 60.000 25.94 4.23 42.97 5.68
942 1033 1.931551 CGTATGTGTATGCGCCCAC 59.068 57.895 4.18 10.04 35.71 4.61
943 1034 4.429213 CGTATGTGTATGCGCCCA 57.571 55.556 4.18 0.00 35.71 5.36
947 1038 3.113322 ACAGTAAGCGTATGTGTATGCG 58.887 45.455 0.00 0.00 45.50 4.73
950 1041 4.285292 GCGTACAGTAAGCGTATGTGTAT 58.715 43.478 2.52 0.00 0.00 2.29
951 1042 3.683989 GCGTACAGTAAGCGTATGTGTA 58.316 45.455 2.52 2.19 0.00 2.90
990 1327 2.114670 CGACATCATGGTGGTGGCC 61.115 63.158 11.45 0.00 31.12 5.36
995 1332 2.173669 GGCGACGACATCATGGTGG 61.174 63.158 11.45 0.00 0.00 4.61
1151 1516 2.360801 GAGCGAACTCAGGAGCTAATCT 59.639 50.000 0.00 0.00 42.93 2.40
1156 1521 1.528292 AACGAGCGAACTCAGGAGCT 61.528 55.000 0.00 0.00 43.66 4.09
1159 1524 0.038526 GGAAACGAGCGAACTCAGGA 60.039 55.000 0.00 0.00 43.66 3.86
1163 1528 1.289800 GGGTGGAAACGAGCGAACTC 61.290 60.000 0.00 0.00 39.75 3.01
1187 1552 3.305964 GACGAACAAGATTGTGAGACGA 58.694 45.455 15.80 0.00 41.31 4.20
1188 1553 2.089121 CGACGAACAAGATTGTGAGACG 59.911 50.000 0.00 5.33 41.31 4.18
1428 1793 7.250569 ACAAGTTAAGAATCCAACGCATAATG 58.749 34.615 0.00 0.00 0.00 1.90
1661 2034 3.394836 GCTCTTCCTCTGCGGGGT 61.395 66.667 0.00 0.00 0.00 4.95
1670 2043 3.377759 AGACGCAGCGCTCTTCCT 61.378 61.111 16.61 0.00 0.00 3.36
1687 2060 0.248289 GGCACTTACGCTTAGTCCCA 59.752 55.000 0.00 0.00 0.00 4.37
1693 2066 0.179145 GAGCTCGGCACTTACGCTTA 60.179 55.000 0.00 0.00 0.00 3.09
1707 2080 0.179124 CCGGTAGCAGAACTGAGCTC 60.179 60.000 6.82 6.82 42.05 4.09
1722 2117 0.108138 AGCTAGTACGTACGACCGGT 60.108 55.000 24.41 6.92 0.00 5.28
1741 2136 4.253685 GCATGAAGGTGCTTTGACTAGTA 58.746 43.478 0.00 0.00 41.82 1.82
1759 2154 3.016971 TCCCAGTCCCAGGGCATG 61.017 66.667 0.00 1.20 46.36 4.06
1770 2165 0.682855 CGGAGCTCTCTTCTCCCAGT 60.683 60.000 14.64 0.00 45.66 4.00
1772 2167 1.380515 CCGGAGCTCTCTTCTCCCA 60.381 63.158 14.64 0.00 45.66 4.37
1774 2169 2.791868 GCCCGGAGCTCTCTTCTCC 61.792 68.421 14.64 0.00 45.12 3.71
1777 2172 4.882396 GCGCCCGGAGCTCTCTTC 62.882 72.222 14.64 0.00 40.39 2.87
1904 2300 3.748989 GCCTCTTCCACTCAAAAACTCCT 60.749 47.826 0.00 0.00 0.00 3.69
1913 2309 1.306141 ATCCGGCCTCTTCCACTCA 60.306 57.895 0.00 0.00 0.00 3.41
1930 2326 2.017049 GCGGGTGAGCAAACTATTCAT 58.983 47.619 0.00 0.00 37.05 2.57
1948 2348 3.306166 CGGACAAAAGGTACTATTGAGCG 59.694 47.826 11.10 0.00 38.49 5.03
1978 2379 3.363627 ACGTTGGAGTTTGGGGTAAAAA 58.636 40.909 0.00 0.00 0.00 1.94
2090 4053 9.630098 CTAGAGTCGTATACCTAACTTAGAGAG 57.370 40.741 0.00 0.00 0.00 3.20
2094 4057 6.878389 CCCCTAGAGTCGTATACCTAACTTAG 59.122 46.154 0.00 4.50 0.00 2.18
2113 4087 0.185175 GGCCCATTTGGTACCCCTAG 59.815 60.000 10.07 0.00 36.04 3.02
2144 4118 5.338708 GGATCAAGGAGAAGGATCAGACAAA 60.339 44.000 0.00 0.00 39.30 2.83
2155 4129 1.066573 ACAGCACGGATCAAGGAGAAG 60.067 52.381 0.00 0.00 0.00 2.85
2298 4280 3.945921 AGAATGAACCATGCACTGATCAG 59.054 43.478 21.37 21.37 0.00 2.90
2299 4281 3.959293 AGAATGAACCATGCACTGATCA 58.041 40.909 0.00 0.00 0.00 2.92
2300 4282 5.121811 ACTAGAATGAACCATGCACTGATC 58.878 41.667 0.00 0.00 0.00 2.92
2301 4283 5.108187 ACTAGAATGAACCATGCACTGAT 57.892 39.130 0.00 0.00 0.00 2.90
2302 4284 4.558226 ACTAGAATGAACCATGCACTGA 57.442 40.909 0.00 0.00 0.00 3.41
2303 4285 4.095483 GGAACTAGAATGAACCATGCACTG 59.905 45.833 0.00 0.00 0.00 3.66
2304 4286 4.265073 GGAACTAGAATGAACCATGCACT 58.735 43.478 0.00 0.00 0.00 4.40
2305 4287 3.378427 GGGAACTAGAATGAACCATGCAC 59.622 47.826 0.00 0.00 0.00 4.57
2306 4288 3.620488 GGGAACTAGAATGAACCATGCA 58.380 45.455 0.00 0.00 0.00 3.96
2307 4289 2.952310 GGGGAACTAGAATGAACCATGC 59.048 50.000 0.00 0.00 0.00 4.06
2308 4290 3.206150 CGGGGAACTAGAATGAACCATG 58.794 50.000 0.00 0.00 0.00 3.66
2309 4291 2.844348 ACGGGGAACTAGAATGAACCAT 59.156 45.455 0.00 0.00 0.00 3.55
2331 4313 4.121317 CCAGAGAGAAGATGCAAGCTAAG 58.879 47.826 0.00 0.00 0.00 2.18
2379 4365 7.698550 CGTCTCTGCATATACATACATAGGAAC 59.301 40.741 0.00 0.00 0.00 3.62
2392 4387 4.378874 CGCTGAATCTCGTCTCTGCATATA 60.379 45.833 0.00 0.00 36.59 0.86
2393 4388 3.611293 CGCTGAATCTCGTCTCTGCATAT 60.611 47.826 0.00 0.00 36.59 1.78
2482 4477 7.840342 TTGAGAAATAGAGAAGATGAAGTGC 57.160 36.000 0.00 0.00 0.00 4.40
2507 4508 3.118555 ACCGGATCCGATCAAAATGTGTA 60.119 43.478 35.42 0.00 42.83 2.90
2526 4527 5.029650 TGAACAAATCAAAGATCGAACCG 57.970 39.130 0.00 0.00 34.30 4.44
2564 4565 3.273919 TGCATACAGACGATCGATGAG 57.726 47.619 24.34 14.77 0.00 2.90
2579 4580 3.301794 AAATGAGCCCACTGATGCATA 57.698 42.857 0.00 0.00 0.00 3.14
2704 4705 7.610305 TGATTCTGCACGGACATAGATACTATA 59.390 37.037 0.00 0.00 0.00 1.31
2705 4706 6.434340 TGATTCTGCACGGACATAGATACTAT 59.566 38.462 0.00 0.00 0.00 2.12
2706 4707 5.768164 TGATTCTGCACGGACATAGATACTA 59.232 40.000 0.00 0.00 0.00 1.82
2707 4708 4.584743 TGATTCTGCACGGACATAGATACT 59.415 41.667 0.00 0.00 0.00 2.12
2708 4709 4.871513 TGATTCTGCACGGACATAGATAC 58.128 43.478 0.00 0.00 0.00 2.24
2709 4710 4.827284 TCTGATTCTGCACGGACATAGATA 59.173 41.667 0.00 0.00 0.00 1.98
2710 4711 3.638627 TCTGATTCTGCACGGACATAGAT 59.361 43.478 0.00 0.00 0.00 1.98
2711 4712 3.023832 TCTGATTCTGCACGGACATAGA 58.976 45.455 0.00 0.00 0.00 1.98
2777 4781 2.066262 CTACGTACACAGCACAAAGGG 58.934 52.381 0.00 0.00 0.00 3.95
2960 4965 9.667989 CGATACATCTCAAGATCTCATATGATC 57.332 37.037 5.72 1.86 42.18 2.92
2961 4966 9.187996 ACGATACATCTCAAGATCTCATATGAT 57.812 33.333 5.72 0.00 31.21 2.45
2962 4967 8.572855 ACGATACATCTCAAGATCTCATATGA 57.427 34.615 5.07 5.07 31.21 2.15
2965 4970 8.821894 CGATACGATACATCTCAAGATCTCATA 58.178 37.037 0.00 0.00 31.21 2.15
3007 5017 6.258068 ACAGGAAGAAACAACGAAAACTAGAG 59.742 38.462 0.00 0.00 0.00 2.43
3034 5044 1.636003 AGGACTAGGGAAAGGGCAAAG 59.364 52.381 0.00 0.00 0.00 2.77
3288 5302 8.723942 ATTACTAGTGTCATGTTGAAAGATCC 57.276 34.615 5.39 0.00 0.00 3.36
3352 5366 8.840833 AAATTTGGTCAAACTTTGTGTAGTTT 57.159 26.923 1.44 0.00 46.42 2.66
3395 5409 9.971922 ACTACGTAGTTTTAGTTTTGTAGATGT 57.028 29.630 22.45 0.00 37.78 3.06
3422 5436 9.414295 CGGATGCATTGTGAAATATATTTTCAT 57.586 29.630 11.92 7.27 40.12 2.57
3423 5437 8.628280 TCGGATGCATTGTGAAATATATTTTCA 58.372 29.630 11.92 11.23 36.21 2.69
3424 5438 9.630098 ATCGGATGCATTGTGAAATATATTTTC 57.370 29.630 11.92 9.09 0.00 2.29
3432 5446 8.795513 TCAATATTATCGGATGCATTGTGAAAT 58.204 29.630 0.00 1.95 0.00 2.17
3433 5447 8.075574 GTCAATATTATCGGATGCATTGTGAAA 58.924 33.333 0.00 0.00 0.00 2.69
3434 5448 7.445096 AGTCAATATTATCGGATGCATTGTGAA 59.555 33.333 0.00 0.00 0.00 3.18
3435 5449 6.936335 AGTCAATATTATCGGATGCATTGTGA 59.064 34.615 0.00 0.00 0.00 3.58
3436 5450 7.137490 AGTCAATATTATCGGATGCATTGTG 57.863 36.000 0.00 0.00 0.00 3.33
3437 5451 7.445096 TGAAGTCAATATTATCGGATGCATTGT 59.555 33.333 0.00 0.00 0.00 2.71
3438 5452 7.809665 TGAAGTCAATATTATCGGATGCATTG 58.190 34.615 0.00 7.52 0.00 2.82
3439 5453 7.984422 TGAAGTCAATATTATCGGATGCATT 57.016 32.000 0.00 0.00 0.00 3.56
3440 5454 9.842775 ATATGAAGTCAATATTATCGGATGCAT 57.157 29.630 0.00 0.00 0.00 3.96
3441 5455 9.671279 AATATGAAGTCAATATTATCGGATGCA 57.329 29.630 0.00 0.00 0.00 3.96
3442 5456 9.926751 CAATATGAAGTCAATATTATCGGATGC 57.073 33.333 0.00 0.00 0.00 3.91
3489 5503 9.403110 GTTTCGTAAACTCTGACTAACTTCATA 57.597 33.333 0.00 0.00 38.35 2.15
3490 5504 8.295569 GTTTCGTAAACTCTGACTAACTTCAT 57.704 34.615 0.00 0.00 38.35 2.57
3491 5505 7.689953 GTTTCGTAAACTCTGACTAACTTCA 57.310 36.000 0.00 0.00 38.35 3.02
3505 5519 9.712359 ATTTAGTCAAAGTCAAGTTTCGTAAAC 57.288 29.630 3.26 3.26 41.69 2.01
3530 5544 9.482627 TCGTTTCTTTTTGGTTTGCATATAAAT 57.517 25.926 0.00 0.00 0.00 1.40
3531 5545 8.873215 TCGTTTCTTTTTGGTTTGCATATAAA 57.127 26.923 0.00 0.00 0.00 1.40
3532 5546 7.596995 CCTCGTTTCTTTTTGGTTTGCATATAA 59.403 33.333 0.00 0.00 0.00 0.98
3533 5547 7.087639 CCTCGTTTCTTTTTGGTTTGCATATA 58.912 34.615 0.00 0.00 0.00 0.86
3534 5548 5.925969 CCTCGTTTCTTTTTGGTTTGCATAT 59.074 36.000 0.00 0.00 0.00 1.78
3535 5549 5.285651 CCTCGTTTCTTTTTGGTTTGCATA 58.714 37.500 0.00 0.00 0.00 3.14
3536 5550 4.119136 CCTCGTTTCTTTTTGGTTTGCAT 58.881 39.130 0.00 0.00 0.00 3.96
3537 5551 3.516615 CCTCGTTTCTTTTTGGTTTGCA 58.483 40.909 0.00 0.00 0.00 4.08
3538 5552 2.863740 CCCTCGTTTCTTTTTGGTTTGC 59.136 45.455 0.00 0.00 0.00 3.68
3539 5553 4.142249 ACTCCCTCGTTTCTTTTTGGTTTG 60.142 41.667 0.00 0.00 0.00 2.93
3540 5554 4.021229 ACTCCCTCGTTTCTTTTTGGTTT 58.979 39.130 0.00 0.00 0.00 3.27
3541 5555 3.628008 ACTCCCTCGTTTCTTTTTGGTT 58.372 40.909 0.00 0.00 0.00 3.67
3542 5556 3.292492 ACTCCCTCGTTTCTTTTTGGT 57.708 42.857 0.00 0.00 0.00 3.67
3543 5557 5.959618 AATACTCCCTCGTTTCTTTTTGG 57.040 39.130 0.00 0.00 0.00 3.28
3544 5558 6.653740 AGGTAATACTCCCTCGTTTCTTTTTG 59.346 38.462 0.00 0.00 0.00 2.44
3545 5559 6.776744 AGGTAATACTCCCTCGTTTCTTTTT 58.223 36.000 0.00 0.00 0.00 1.94
3546 5560 6.370186 AGGTAATACTCCCTCGTTTCTTTT 57.630 37.500 0.00 0.00 0.00 2.27
3547 5561 5.975282 GAGGTAATACTCCCTCGTTTCTTT 58.025 41.667 0.00 0.00 38.06 2.52
3548 5562 5.595257 GAGGTAATACTCCCTCGTTTCTT 57.405 43.478 0.00 0.00 38.06 2.52
3559 5573 4.996788 TTTCAGGACGGAGGTAATACTC 57.003 45.455 0.00 0.00 36.76 2.59
3560 5574 5.247792 ACTTTTTCAGGACGGAGGTAATACT 59.752 40.000 0.00 0.00 0.00 2.12
3561 5575 5.485620 ACTTTTTCAGGACGGAGGTAATAC 58.514 41.667 0.00 0.00 0.00 1.89
3562 5576 5.750352 ACTTTTTCAGGACGGAGGTAATA 57.250 39.130 0.00 0.00 0.00 0.98
3563 5577 4.635699 ACTTTTTCAGGACGGAGGTAAT 57.364 40.909 0.00 0.00 0.00 1.89
3564 5578 4.131596 CAACTTTTTCAGGACGGAGGTAA 58.868 43.478 0.00 0.00 0.00 2.85
3565 5579 3.135167 ACAACTTTTTCAGGACGGAGGTA 59.865 43.478 0.00 0.00 0.00 3.08
3566 5580 2.092592 ACAACTTTTTCAGGACGGAGGT 60.093 45.455 0.00 0.00 0.00 3.85
3567 5581 2.548480 GACAACTTTTTCAGGACGGAGG 59.452 50.000 0.00 0.00 0.00 4.30
3568 5582 3.467803 AGACAACTTTTTCAGGACGGAG 58.532 45.455 0.00 0.00 0.00 4.63
3569 5583 3.553828 AGACAACTTTTTCAGGACGGA 57.446 42.857 0.00 0.00 0.00 4.69
3570 5584 5.054477 TCTAAGACAACTTTTTCAGGACGG 58.946 41.667 0.00 0.00 37.53 4.79
3571 5585 6.787085 ATCTAAGACAACTTTTTCAGGACG 57.213 37.500 0.00 0.00 37.53 4.79
3572 5586 8.669243 CCATATCTAAGACAACTTTTTCAGGAC 58.331 37.037 0.00 0.00 37.53 3.85
3573 5587 8.602424 TCCATATCTAAGACAACTTTTTCAGGA 58.398 33.333 0.00 0.00 37.53 3.86
3574 5588 8.792830 TCCATATCTAAGACAACTTTTTCAGG 57.207 34.615 0.00 0.00 37.53 3.86
3576 5590 9.739276 ACATCCATATCTAAGACAACTTTTTCA 57.261 29.630 0.00 0.00 37.53 2.69
3596 5610 6.540083 TCGGTCTATTGTCTAGATACATCCA 58.460 40.000 0.00 0.00 0.00 3.41
3612 5626 6.326583 TCAAATTTCATACTCCCTCGGTCTAT 59.673 38.462 0.00 0.00 0.00 1.98
3613 5627 5.659525 TCAAATTTCATACTCCCTCGGTCTA 59.340 40.000 0.00 0.00 0.00 2.59
3618 5632 5.023533 TCCTCAAATTTCATACTCCCTCG 57.976 43.478 0.00 0.00 0.00 4.63
3624 5638 9.753674 TTCTATTGGTTCCTCAAATTTCATACT 57.246 29.630 0.00 0.00 0.00 2.12
3676 5690 9.756571 ATTCTCGGACATAACTATTACTCCTAT 57.243 33.333 0.00 0.00 0.00 2.57
3677 5691 9.584008 AATTCTCGGACATAACTATTACTCCTA 57.416 33.333 0.00 0.00 0.00 2.94
3678 5692 8.480133 AATTCTCGGACATAACTATTACTCCT 57.520 34.615 0.00 0.00 0.00 3.69
3679 5693 9.194271 GAAATTCTCGGACATAACTATTACTCC 57.806 37.037 0.00 0.00 0.00 3.85
3680 5694 9.968870 AGAAATTCTCGGACATAACTATTACTC 57.031 33.333 0.00 0.00 0.00 2.59
3687 5701 7.275920 AGCAATAGAAATTCTCGGACATAACT 58.724 34.615 0.00 0.00 0.00 2.24
3752 5766 8.564574 CAACCACTTATGTACAATACAACAACT 58.435 33.333 0.00 0.00 42.76 3.16
3755 5769 6.072397 GGCAACCACTTATGTACAATACAACA 60.072 38.462 0.00 0.00 42.76 3.33
3756 5770 6.072397 TGGCAACCACTTATGTACAATACAAC 60.072 38.462 0.00 0.00 42.76 3.32
3767 5781 1.474077 GCTCCTTGGCAACCACTTATG 59.526 52.381 0.00 0.00 30.78 1.90
3775 5789 1.807142 GTGACTTAGCTCCTTGGCAAC 59.193 52.381 0.00 0.00 34.17 4.17
3779 5793 1.000955 ACACGTGACTTAGCTCCTTGG 59.999 52.381 25.01 0.00 0.00 3.61
3786 5800 3.847037 TTCGAAAACACGTGACTTAGC 57.153 42.857 25.01 9.58 34.70 3.09
3802 5816 1.613255 GCCTCCAACCCTGAATTTCGA 60.613 52.381 0.00 0.00 0.00 3.71
3803 5817 0.811281 GCCTCCAACCCTGAATTTCG 59.189 55.000 0.00 0.00 0.00 3.46
3804 5818 1.546029 GTGCCTCCAACCCTGAATTTC 59.454 52.381 0.00 0.00 0.00 2.17
3835 5849 7.771826 TCTTTAGAGGATTAATTTACCCAACCG 59.228 37.037 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.