Multiple sequence alignment - TraesCS5A01G316700

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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 TraesCS5A01G316700 chr5A 100.000 4298 0 0 1 4298 527843579 527847876 0.000000e+00 7938.0
1 TraesCS5A01G316700 chr5D 93.162 2486 105 30 926 3391 415261363 415263803 0.000000e+00 3589.0
2 TraesCS5A01G316700 chr5D 88.987 908 56 18 3432 4298 415263949 415264853 0.000000e+00 1083.0
3 TraesCS5A01G316700 chr5D 84.783 598 64 11 9 586 415259955 415260545 3.730000e-160 575.0
4 TraesCS5A01G316700 chr5D 90.909 297 24 3 610 903 415260532 415260828 3.110000e-106 396.0
5 TraesCS5A01G316700 chr5D 98.507 67 1 0 3370 3436 415263819 415263885 7.550000e-23 119.0
6 TraesCS5A01G316700 chr5B 96.087 920 32 4 926 1844 501237440 501238356 0.000000e+00 1496.0
7 TraesCS5A01G316700 chr5B 89.949 1184 76 20 1926 3089 501238360 501239520 0.000000e+00 1487.0
8 TraesCS5A01G316700 chr5B 94.981 797 31 4 3140 3931 501239543 501240335 0.000000e+00 1242.0
9 TraesCS5A01G316700 chr5B 88.485 330 33 5 338 664 501219153 501219480 1.120000e-105 394.0
10 TraesCS5A01G316700 chr5B 85.450 378 30 16 3928 4298 501240304 501240663 1.890000e-98 370.0
11 TraesCS5A01G316700 chr5B 92.683 41 2 1 3100 3140 501237987 501238026 1.670000e-04 58.4
12 TraesCS5A01G316700 chr3D 80.221 1355 167 59 975 2290 519393224 519391932 0.000000e+00 924.0
13 TraesCS5A01G316700 chr3B 83.814 970 94 39 975 1920 683790285 683789355 0.000000e+00 863.0
14 TraesCS5A01G316700 chr3B 83.386 957 105 37 975 1914 684112214 684111295 0.000000e+00 837.0
15 TraesCS5A01G316700 chr3A 87.645 688 50 16 975 1652 654404977 654404315 0.000000e+00 767.0
16 TraesCS5A01G316700 chr3A 100.000 30 0 0 3491 3520 654396458 654396429 6.000000e-04 56.5
17 TraesCS5A01G316700 chr2B 85.965 57 2 6 562 617 176698244 176698295 6.000000e-04 56.5
18 TraesCS5A01G316700 chr7D 94.444 36 1 1 519 553 166257967 166257932 2.000000e-03 54.7
19 TraesCS5A01G316700 chr7A 94.286 35 2 0 519 553 167827401 167827367 2.000000e-03 54.7
20 TraesCS5A01G316700 chr6D 96.875 32 1 0 1024 1055 8262895 8262864 2.000000e-03 54.7


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 TraesCS5A01G316700 chr5A 527843579 527847876 4297 False 7938.00 7938 100.0000 1 4298 1 chr5A.!!$F1 4297
1 TraesCS5A01G316700 chr5D 415259955 415264853 4898 False 1152.40 3589 91.2696 9 4298 5 chr5D.!!$F1 4289
2 TraesCS5A01G316700 chr5B 501237440 501240663 3223 False 930.68 1496 91.8300 926 4298 5 chr5B.!!$F2 3372
3 TraesCS5A01G316700 chr3D 519391932 519393224 1292 True 924.00 924 80.2210 975 2290 1 chr3D.!!$R1 1315
4 TraesCS5A01G316700 chr3B 683789355 683790285 930 True 863.00 863 83.8140 975 1920 1 chr3B.!!$R1 945
5 TraesCS5A01G316700 chr3B 684111295 684112214 919 True 837.00 837 83.3860 975 1914 1 chr3B.!!$R2 939
6 TraesCS5A01G316700 chr3A 654404315 654404977 662 True 767.00 767 87.6450 975 1652 1 chr3A.!!$R2 677

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
599 619 0.253347 TTGGAGAGGGAGGCCATTCT 60.253 55.0 5.01 1.17 0.00 2.40 F
600 620 0.253347 TGGAGAGGGAGGCCATTCTT 60.253 55.0 5.01 0.00 0.00 2.52 F
1467 2037 0.178921 AGTCTCTGTCTCTTGCCCCA 60.179 55.0 0.00 0.00 0.00 4.96 F
2820 3435 0.181587 TCTGCCAACGGGACAAGAAA 59.818 50.0 0.00 0.00 35.59 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 2024 0.322816 GAGCAATGGGGCAAGAGACA 60.323 55.0 0.00 0.0 35.83 3.41 R
2101 2698 0.391130 TACCAACTGATCGGCTGCAC 60.391 55.0 0.00 0.0 0.00 4.57 R
3114 3741 0.035458 CAAAGTTCAGGCGAGAGGGT 59.965 55.0 0.00 0.0 0.00 4.34 R
3721 4458 0.312416 CTCGAGTCATTCTAGGGGCG 59.688 60.0 3.62 0.0 0.00 6.13 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
88 89 3.854856 AAAAAGCGCTCAAGGCCA 58.145 50.000 12.06 0.00 37.74 5.36
94 95 2.892425 CGCTCAAGGCCATCGGTC 60.892 66.667 5.01 0.00 37.74 4.79
128 129 1.372087 CGATTCTGGGGCTGCTTGAC 61.372 60.000 0.00 0.00 0.00 3.18
138 139 1.525995 CTGCTTGACACGGGGTTGT 60.526 57.895 0.00 0.00 0.00 3.32
139 140 1.785041 CTGCTTGACACGGGGTTGTG 61.785 60.000 0.00 0.00 45.41 3.33
146 147 0.321298 ACACGGGGTTGTGCTACATC 60.321 55.000 0.00 0.00 43.74 3.06
158 159 6.407074 GGTTGTGCTACATCCTCACTATAAGT 60.407 42.308 8.35 0.00 35.58 2.24
193 199 4.115279 CTGGCGCACTCCAGTATG 57.885 61.111 10.83 0.00 46.59 2.39
201 207 1.474143 GCACTCCAGTATGCTTCTCCC 60.474 57.143 0.00 0.00 38.84 4.30
227 233 2.284699 AGCCCCTCAACTAGCGGT 60.285 61.111 0.00 0.00 0.00 5.68
234 240 2.186903 CAACTAGCGGTGGCGGAT 59.813 61.111 0.00 0.00 46.35 4.18
235 241 2.173669 CAACTAGCGGTGGCGGATG 61.174 63.158 0.00 0.00 46.35 3.51
244 250 3.245346 TGGCGGATGACACCACCA 61.245 61.111 0.00 0.00 39.46 4.17
250 256 1.065782 CGGATGACACCACCATACCAA 60.066 52.381 0.00 0.00 0.00 3.67
256 262 1.215673 ACACCACCATACCAACACCAA 59.784 47.619 0.00 0.00 0.00 3.67
258 264 1.203001 ACCACCATACCAACACCAAGG 60.203 52.381 0.00 0.00 0.00 3.61
297 303 1.070821 GCGAAAGAAAGCAATTGGCC 58.929 50.000 7.72 0.00 46.50 5.36
300 306 2.289010 CGAAAGAAAGCAATTGGCCCTT 60.289 45.455 7.72 0.00 46.50 3.95
303 309 1.159285 GAAAGCAATTGGCCCTTTGC 58.841 50.000 24.83 24.83 46.68 3.68
312 318 2.203625 GCCCTTTGCCAGACCCAA 60.204 61.111 0.00 0.00 0.00 4.12
313 319 1.610379 GCCCTTTGCCAGACCCAAT 60.610 57.895 0.00 0.00 0.00 3.16
323 329 1.852157 AGACCCAATGACCCAGCCA 60.852 57.895 0.00 0.00 0.00 4.75
328 334 1.000739 CAATGACCCAGCCACCCAT 59.999 57.895 0.00 0.00 0.00 4.00
331 337 2.361610 GACCCAGCCACCCATGTG 60.362 66.667 0.00 0.00 42.39 3.21
336 342 2.937689 AGCCACCCATGTGCCTCT 60.938 61.111 0.00 0.00 41.35 3.69
340 346 1.742880 CACCCATGTGCCTCTGTCG 60.743 63.158 0.00 0.00 35.31 4.35
343 349 1.376424 CCATGTGCCTCTGTCGCTT 60.376 57.895 0.00 0.00 0.00 4.68
346 352 1.830587 ATGTGCCTCTGTCGCTTCCA 61.831 55.000 0.00 0.00 0.00 3.53
347 353 2.029844 GTGCCTCTGTCGCTTCCAC 61.030 63.158 0.00 0.00 0.00 4.02
348 354 2.210013 TGCCTCTGTCGCTTCCACT 61.210 57.895 0.00 0.00 0.00 4.00
362 381 2.356313 CACTCGGTGTCAGCGCTT 60.356 61.111 19.30 5.72 39.21 4.68
367 386 3.286751 GGTGTCAGCGCTTGCCAA 61.287 61.111 7.50 0.00 40.41 4.52
394 413 4.147322 GCACAACGTCCATCCGCG 62.147 66.667 0.00 0.00 0.00 6.46
395 414 4.147322 CACAACGTCCATCCGCGC 62.147 66.667 0.00 0.00 0.00 6.86
397 416 3.195002 CAACGTCCATCCGCGCAT 61.195 61.111 8.75 0.00 0.00 4.73
505 525 2.161012 CCACTGCTGTAATGCACAAGAG 59.839 50.000 0.00 0.00 38.12 2.85
517 537 1.135859 GCACAAGAGCGAATCAACTGG 60.136 52.381 0.00 0.00 0.00 4.00
557 577 7.243604 TGAATACCAAGGAGCAAATTTGAAT 57.756 32.000 22.31 9.13 0.00 2.57
564 584 6.916360 AAGGAGCAAATTTGAATACCTTGA 57.084 33.333 22.31 0.00 35.57 3.02
589 609 9.591792 GATTTCTTTAAATGAAATTGGAGAGGG 57.408 33.333 18.41 0.00 42.17 4.30
590 610 8.719645 TTTCTTTAAATGAAATTGGAGAGGGA 57.280 30.769 8.05 0.00 36.10 4.20
591 611 7.944729 TCTTTAAATGAAATTGGAGAGGGAG 57.055 36.000 0.00 0.00 36.10 4.30
592 612 6.891908 TCTTTAAATGAAATTGGAGAGGGAGG 59.108 38.462 0.00 0.00 36.10 4.30
593 613 2.744352 ATGAAATTGGAGAGGGAGGC 57.256 50.000 0.00 0.00 0.00 4.70
594 614 0.625849 TGAAATTGGAGAGGGAGGCC 59.374 55.000 0.00 0.00 0.00 5.19
595 615 0.625849 GAAATTGGAGAGGGAGGCCA 59.374 55.000 5.01 0.00 0.00 5.36
596 616 1.216427 GAAATTGGAGAGGGAGGCCAT 59.784 52.381 5.01 0.00 0.00 4.40
597 617 1.312884 AATTGGAGAGGGAGGCCATT 58.687 50.000 5.01 0.00 0.00 3.16
598 618 0.849417 ATTGGAGAGGGAGGCCATTC 59.151 55.000 5.01 0.00 0.00 2.67
599 619 0.253347 TTGGAGAGGGAGGCCATTCT 60.253 55.000 5.01 1.17 0.00 2.40
600 620 0.253347 TGGAGAGGGAGGCCATTCTT 60.253 55.000 5.01 0.00 0.00 2.52
601 621 0.922626 GGAGAGGGAGGCCATTCTTT 59.077 55.000 5.01 0.00 0.00 2.52
602 622 1.286257 GGAGAGGGAGGCCATTCTTTT 59.714 52.381 5.01 0.00 0.00 2.27
603 623 2.509964 GGAGAGGGAGGCCATTCTTTTA 59.490 50.000 5.01 0.00 0.00 1.52
604 624 3.139211 GGAGAGGGAGGCCATTCTTTTAT 59.861 47.826 5.01 0.00 0.00 1.40
605 625 4.351111 GGAGAGGGAGGCCATTCTTTTATA 59.649 45.833 5.01 0.00 0.00 0.98
606 626 5.309638 GAGAGGGAGGCCATTCTTTTATAC 58.690 45.833 5.01 0.00 0.00 1.47
607 627 4.104897 AGAGGGAGGCCATTCTTTTATACC 59.895 45.833 5.01 0.00 0.00 2.73
608 628 3.791545 AGGGAGGCCATTCTTTTATACCA 59.208 43.478 5.01 0.00 0.00 3.25
609 629 4.231890 AGGGAGGCCATTCTTTTATACCAA 59.768 41.667 5.01 0.00 0.00 3.67
610 630 4.959839 GGGAGGCCATTCTTTTATACCAAA 59.040 41.667 5.01 0.00 0.00 3.28
611 631 5.423931 GGGAGGCCATTCTTTTATACCAAAA 59.576 40.000 5.01 0.00 0.00 2.44
612 632 6.099701 GGGAGGCCATTCTTTTATACCAAAAT 59.900 38.462 5.01 0.00 0.00 1.82
613 633 7.289084 GGGAGGCCATTCTTTTATACCAAAATA 59.711 37.037 5.01 0.00 0.00 1.40
614 634 8.700973 GGAGGCCATTCTTTTATACCAAAATAA 58.299 33.333 5.01 0.00 0.00 1.40
656 676 2.805671 CGCAAGGTTAGTGTGACATCAA 59.194 45.455 0.00 0.00 0.00 2.57
681 702 7.011499 TGCTAGTCTGTTATTAGTGGGAAAA 57.989 36.000 0.00 0.00 0.00 2.29
682 703 7.630082 TGCTAGTCTGTTATTAGTGGGAAAAT 58.370 34.615 0.00 0.00 0.00 1.82
687 708 8.047310 AGTCTGTTATTAGTGGGAAAATGTAGG 58.953 37.037 0.00 0.00 0.00 3.18
750 771 9.182214 AGCATAGAGTTATGTGAAAATGTTCAT 57.818 29.630 0.61 0.00 45.38 2.57
793 814 4.789012 ATGCTTTCAATGGTCGAAATGT 57.211 36.364 0.00 0.00 32.21 2.71
822 843 2.227089 AAAGACGGCCCAGTAGAGCG 62.227 60.000 0.00 0.00 0.00 5.03
823 844 3.138798 GACGGCCCAGTAGAGCGA 61.139 66.667 0.00 0.00 0.00 4.93
860 881 5.880887 AGTGGGCTACAGTTTATCTTAAAGC 59.119 40.000 3.15 0.00 0.00 3.51
861 882 5.066117 GTGGGCTACAGTTTATCTTAAAGCC 59.934 44.000 0.00 1.40 37.93 4.35
862 883 5.752892 GGCTACAGTTTATCTTAAAGCCC 57.247 43.478 0.00 0.00 33.07 5.19
863 884 4.579340 GGCTACAGTTTATCTTAAAGCCCC 59.421 45.833 0.00 0.00 33.07 5.80
864 885 5.437946 GCTACAGTTTATCTTAAAGCCCCT 58.562 41.667 0.00 0.00 0.00 4.79
892 913 1.372501 AGGCCCAGTAATCTGTTGGT 58.627 50.000 0.00 0.00 39.82 3.67
906 961 0.608308 GTTGGTCAGTTGGGCCTACC 60.608 60.000 14.63 9.60 40.81 3.18
917 972 2.185387 TGGGCCTACCAGAAGAACTAC 58.815 52.381 4.53 0.00 46.80 2.73
918 973 2.185387 GGGCCTACCAGAAGAACTACA 58.815 52.381 0.84 0.00 39.85 2.74
919 974 2.772515 GGGCCTACCAGAAGAACTACAT 59.227 50.000 0.84 0.00 39.85 2.29
920 975 3.200165 GGGCCTACCAGAAGAACTACATT 59.800 47.826 0.84 0.00 39.85 2.71
922 977 5.254115 GGCCTACCAGAAGAACTACATTTT 58.746 41.667 0.00 0.00 35.26 1.82
923 978 5.354513 GGCCTACCAGAAGAACTACATTTTC 59.645 44.000 0.00 0.00 35.26 2.29
983 1517 2.758770 TTCCGTTCGGCCGTCTTCTG 62.759 60.000 27.15 10.27 0.00 3.02
1400 1970 1.811266 GATGCAGAAGCTCGCCGAA 60.811 57.895 0.00 0.00 42.74 4.30
1454 2024 5.391097 CGTCAAGTGAGATCGTTTAGTCTCT 60.391 44.000 4.29 0.00 41.10 3.10
1467 2037 0.178921 AGTCTCTGTCTCTTGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
1524 2095 1.872952 TGTGTCTTTCTGATTGGTGCG 59.127 47.619 0.00 0.00 0.00 5.34
1573 2144 0.392595 GAACCCCGATGAGTTCACCC 60.393 60.000 0.00 0.00 41.62 4.61
1682 2253 6.748333 TGTTCAAAATGTGCCAAAATTTCA 57.252 29.167 0.00 0.00 0.00 2.69
1750 2321 5.636903 AGCATGGTAGAGTACAATGGATT 57.363 39.130 0.00 0.00 39.89 3.01
1831 2408 3.671008 TTGGTACAGCTGTTCGTGTAT 57.329 42.857 27.06 0.00 42.39 2.29
1839 2416 7.064253 GGTACAGCTGTTCGTGTATAAAAGAAT 59.936 37.037 27.06 0.00 31.95 2.40
1840 2417 6.831769 ACAGCTGTTCGTGTATAAAAGAATG 58.168 36.000 15.25 0.00 0.00 2.67
1847 2425 6.106877 TCGTGTATAAAAGAATGCTGCTTC 57.893 37.500 0.00 2.59 0.00 3.86
1861 2440 8.322828 AGAATGCTGCTTCTGATATAAGATGAT 58.677 33.333 7.09 0.00 34.22 2.45
1887 2472 8.622572 ATTGGTTATTTGAAGGGGATACATTT 57.377 30.769 0.00 0.00 39.74 2.32
1917 2502 2.100749 CCCTGTGAAAAGGAACCAACAC 59.899 50.000 0.00 0.00 40.02 3.32
1981 2568 3.791245 TCCAACCACAAATCAAGCAAAC 58.209 40.909 0.00 0.00 0.00 2.93
2003 2590 7.703298 AACACATGTTGTCTTTCATGAATTG 57.297 32.000 9.40 5.84 42.52 2.32
2020 2614 4.161942 TGAATTGGGCCTTCATTTATGTGG 59.838 41.667 4.53 0.00 0.00 4.17
2025 2619 4.464597 TGGGCCTTCATTTATGTGGTTTAC 59.535 41.667 4.53 0.00 0.00 2.01
2033 2627 8.693120 TTCATTTATGTGGTTTACTTACACCA 57.307 30.769 0.00 0.00 40.98 4.17
2042 2636 4.057432 GTTTACTTACACCACGGCAACTA 58.943 43.478 0.00 0.00 0.00 2.24
2043 2637 2.159327 ACTTACACCACGGCAACTAC 57.841 50.000 0.00 0.00 0.00 2.73
2048 2642 0.250124 CACCACGGCAACTACCAAGA 60.250 55.000 0.00 0.00 0.00 3.02
2109 2708 0.459899 TGGTATACAGAGTGCAGCCG 59.540 55.000 5.01 0.00 0.00 5.52
2176 2781 4.532126 TGTTACTCCCATTGACTGTCATCT 59.468 41.667 11.86 0.00 0.00 2.90
2652 3264 8.585018 TCATACATCTGTTTGTTTCAGAGTCTA 58.415 33.333 0.00 0.00 43.66 2.59
2700 3312 5.829924 TGAAGAAGCTTTTCCTGAAGACATT 59.170 36.000 0.00 0.00 0.00 2.71
2743 3355 2.263077 CTACTTCTGCCGCTGTAAGTG 58.737 52.381 17.36 9.28 46.11 3.16
2760 3372 6.107343 TGTAAGTGTAAATATGCCTGCGTTA 58.893 36.000 0.00 0.00 0.00 3.18
2770 3382 6.835819 ATATGCCTGCGTTAGTAAGATAGA 57.164 37.500 0.00 0.00 0.00 1.98
2772 3384 3.242969 TGCCTGCGTTAGTAAGATAGACG 60.243 47.826 0.00 0.00 36.85 4.18
2816 3431 0.893270 CCAATCTGCCAACGGGACAA 60.893 55.000 0.00 0.00 35.59 3.18
2820 3435 0.181587 TCTGCCAACGGGACAAGAAA 59.818 50.000 0.00 0.00 35.59 2.52
2821 3436 1.028905 CTGCCAACGGGACAAGAAAA 58.971 50.000 0.00 0.00 35.59 2.29
2832 3447 5.163457 ACGGGACAAGAAAACAATGTGAATT 60.163 36.000 0.00 0.00 0.00 2.17
2906 3521 4.011966 TGTCACAATGCTCAGTTCATCT 57.988 40.909 0.00 0.00 0.00 2.90
2948 3565 6.586844 GTGTTAGCTTAAGTTGGTGAGACTAG 59.413 42.308 4.02 0.00 0.00 2.57
2969 3588 9.764363 GACTAGAACCATGATATATGTGTTTGA 57.236 33.333 0.00 0.00 0.00 2.69
2993 3620 9.944376 TGATTAGAATCTGCTACTTAAAACACT 57.056 29.630 4.02 0.00 36.39 3.55
3038 3665 6.932356 TTTATCTGAGGACATCATTTGCTC 57.068 37.500 0.00 0.00 37.28 4.26
3097 3724 6.532365 GCTATGGCTCTTGTGTTATTAGTC 57.468 41.667 0.00 0.00 35.22 2.59
3099 3726 6.422400 GCTATGGCTCTTGTGTTATTAGTCTC 59.578 42.308 0.00 0.00 35.22 3.36
3100 3727 5.086104 TGGCTCTTGTGTTATTAGTCTCC 57.914 43.478 0.00 0.00 0.00 3.71
3101 3728 4.113354 GGCTCTTGTGTTATTAGTCTCCG 58.887 47.826 0.00 0.00 0.00 4.63
3104 3731 5.062308 GCTCTTGTGTTATTAGTCTCCGTTG 59.938 44.000 0.00 0.00 0.00 4.10
3105 3732 4.927425 TCTTGTGTTATTAGTCTCCGTTGC 59.073 41.667 0.00 0.00 0.00 4.17
3106 3733 3.592059 TGTGTTATTAGTCTCCGTTGCC 58.408 45.455 0.00 0.00 0.00 4.52
3108 3735 2.231964 TGTTATTAGTCTCCGTTGCCGT 59.768 45.455 0.00 0.00 0.00 5.68
3109 3736 3.256558 GTTATTAGTCTCCGTTGCCGTT 58.743 45.455 0.00 0.00 0.00 4.44
3110 3737 1.722011 ATTAGTCTCCGTTGCCGTTG 58.278 50.000 0.00 0.00 0.00 4.10
3111 3738 0.390124 TTAGTCTCCGTTGCCGTTGT 59.610 50.000 0.00 0.00 0.00 3.32
3112 3739 0.390124 TAGTCTCCGTTGCCGTTGTT 59.610 50.000 0.00 0.00 0.00 2.83
3113 3740 1.157870 AGTCTCCGTTGCCGTTGTTG 61.158 55.000 0.00 0.00 0.00 3.33
3114 3741 1.144276 TCTCCGTTGCCGTTGTTGA 59.856 52.632 0.00 0.00 0.00 3.18
3115 3742 1.155424 TCTCCGTTGCCGTTGTTGAC 61.155 55.000 0.00 0.00 0.00 3.18
3116 3743 2.113131 CTCCGTTGCCGTTGTTGACC 62.113 60.000 0.00 0.00 0.00 4.02
3117 3744 2.330041 CGTTGCCGTTGTTGACCC 59.670 61.111 0.00 0.00 0.00 4.46
3118 3745 2.184167 CGTTGCCGTTGTTGACCCT 61.184 57.895 0.00 0.00 0.00 4.34
3119 3746 1.652563 GTTGCCGTTGTTGACCCTC 59.347 57.895 0.00 0.00 0.00 4.30
3120 3747 0.818040 GTTGCCGTTGTTGACCCTCT 60.818 55.000 0.00 0.00 0.00 3.69
3121 3748 0.534203 TTGCCGTTGTTGACCCTCTC 60.534 55.000 0.00 0.00 0.00 3.20
3122 3749 2.027625 GCCGTTGTTGACCCTCTCG 61.028 63.158 0.00 0.00 0.00 4.04
3123 3750 2.027625 CCGTTGTTGACCCTCTCGC 61.028 63.158 0.00 0.00 0.00 5.03
3124 3751 2.027625 CGTTGTTGACCCTCTCGCC 61.028 63.158 0.00 0.00 0.00 5.54
3125 3752 1.371558 GTTGTTGACCCTCTCGCCT 59.628 57.895 0.00 0.00 0.00 5.52
3126 3753 0.951040 GTTGTTGACCCTCTCGCCTG 60.951 60.000 0.00 0.00 0.00 4.85
3127 3754 1.118965 TTGTTGACCCTCTCGCCTGA 61.119 55.000 0.00 0.00 0.00 3.86
3128 3755 1.118965 TGTTGACCCTCTCGCCTGAA 61.119 55.000 0.00 0.00 0.00 3.02
3129 3756 0.670854 GTTGACCCTCTCGCCTGAAC 60.671 60.000 0.00 0.00 0.00 3.18
3130 3757 0.832135 TTGACCCTCTCGCCTGAACT 60.832 55.000 0.00 0.00 0.00 3.01
3131 3758 0.832135 TGACCCTCTCGCCTGAACTT 60.832 55.000 0.00 0.00 0.00 2.66
3132 3759 0.321996 GACCCTCTCGCCTGAACTTT 59.678 55.000 0.00 0.00 0.00 2.66
3133 3760 0.035458 ACCCTCTCGCCTGAACTTTG 59.965 55.000 0.00 0.00 0.00 2.77
3134 3761 0.035458 CCCTCTCGCCTGAACTTTGT 59.965 55.000 0.00 0.00 0.00 2.83
3135 3762 1.433534 CCTCTCGCCTGAACTTTGTC 58.566 55.000 0.00 0.00 0.00 3.18
3136 3763 1.270305 CCTCTCGCCTGAACTTTGTCA 60.270 52.381 0.00 0.00 0.00 3.58
3137 3764 2.613977 CCTCTCGCCTGAACTTTGTCAT 60.614 50.000 0.00 0.00 0.00 3.06
3307 3934 2.534298 CTGAGCACTGACATAAGGACG 58.466 52.381 0.00 0.00 0.00 4.79
3316 3943 2.106074 CATAAGGACGCAAGCCGCA 61.106 57.895 0.00 0.00 42.60 5.69
3543 4280 1.415289 TGTAGCCATCATCAGCCAGAG 59.585 52.381 0.00 0.00 0.00 3.35
3553 4290 4.517285 TCATCAGCCAGAGTTGGTAATTC 58.483 43.478 0.00 0.00 46.80 2.17
3558 4295 2.356135 CCAGAGTTGGTAATTCGGGTG 58.644 52.381 0.00 0.00 39.79 4.61
3613 4350 4.733887 CAGTCGCGTAGTAAGTTAATCTGG 59.266 45.833 5.77 0.00 0.00 3.86
3637 4374 3.866883 TGAGCTCATCATCGTGTGTTA 57.133 42.857 13.74 0.00 31.12 2.41
3644 4381 5.063944 GCTCATCATCGTGTGTTAGTTTGAT 59.936 40.000 0.00 0.00 0.00 2.57
3645 4382 6.255670 GCTCATCATCGTGTGTTAGTTTGATA 59.744 38.462 0.00 0.00 0.00 2.15
3646 4383 7.515841 GCTCATCATCGTGTGTTAGTTTGATAG 60.516 40.741 0.00 0.00 0.00 2.08
3721 4458 4.423625 AATACTAATCCTGTGGGCTGTC 57.576 45.455 0.00 0.00 0.00 3.51
3773 4510 5.198602 AGGTTGCCTCTTGGAGATATTTT 57.801 39.130 0.00 0.00 34.57 1.82
3824 4561 2.544267 GGCCGTCACTATGATAAGTTGC 59.456 50.000 0.00 0.00 0.00 4.17
3869 4606 5.104735 GGAGGTCATCTAGGTGAAGTGATTT 60.105 44.000 7.42 0.00 0.00 2.17
3912 4649 0.806868 TGCCGGTCGTCAGTACTAAG 59.193 55.000 1.90 0.00 0.00 2.18
3913 4650 1.089920 GCCGGTCGTCAGTACTAAGA 58.910 55.000 1.90 0.00 0.00 2.10
3914 4651 1.470098 GCCGGTCGTCAGTACTAAGAA 59.530 52.381 1.90 0.00 0.00 2.52
3915 4652 2.730402 GCCGGTCGTCAGTACTAAGAAC 60.730 54.545 1.90 0.00 0.00 3.01
3916 4653 2.485426 CCGGTCGTCAGTACTAAGAACA 59.515 50.000 0.00 0.00 0.00 3.18
3917 4654 3.425892 CCGGTCGTCAGTACTAAGAACAG 60.426 52.174 0.00 0.00 0.00 3.16
3918 4655 3.434641 CGGTCGTCAGTACTAAGAACAGA 59.565 47.826 0.00 0.00 0.00 3.41
3919 4656 4.435784 CGGTCGTCAGTACTAAGAACAGAG 60.436 50.000 0.00 0.00 0.00 3.35
3920 4657 4.455190 GGTCGTCAGTACTAAGAACAGAGT 59.545 45.833 0.00 0.00 0.00 3.24
3921 4658 5.383958 GTCGTCAGTACTAAGAACAGAGTG 58.616 45.833 0.00 0.00 0.00 3.51
3922 4659 4.083431 TCGTCAGTACTAAGAACAGAGTGC 60.083 45.833 0.00 0.00 0.00 4.40
3923 4660 4.320275 CGTCAGTACTAAGAACAGAGTGCA 60.320 45.833 0.00 0.00 31.39 4.57
3924 4661 4.918583 GTCAGTACTAAGAACAGAGTGCAC 59.081 45.833 9.40 9.40 31.39 4.57
3925 4662 4.583073 TCAGTACTAAGAACAGAGTGCACA 59.417 41.667 21.04 0.00 31.39 4.57
3926 4663 5.243954 TCAGTACTAAGAACAGAGTGCACAT 59.756 40.000 21.04 3.86 31.39 3.21
3927 4664 5.928839 CAGTACTAAGAACAGAGTGCACATT 59.071 40.000 21.04 7.50 31.39 2.71
3928 4665 6.425114 CAGTACTAAGAACAGAGTGCACATTT 59.575 38.462 21.04 5.78 31.39 2.32
3929 4666 5.679734 ACTAAGAACAGAGTGCACATTTG 57.320 39.130 21.04 15.71 0.00 2.32
3930 4667 5.126067 ACTAAGAACAGAGTGCACATTTGT 58.874 37.500 21.04 16.37 0.00 2.83
3931 4668 4.558538 AAGAACAGAGTGCACATTTGTC 57.441 40.909 21.04 7.31 0.00 3.18
3932 4669 3.544684 AGAACAGAGTGCACATTTGTCA 58.455 40.909 21.04 0.00 0.00 3.58
3933 4670 3.562973 AGAACAGAGTGCACATTTGTCAG 59.437 43.478 21.04 6.75 0.00 3.51
3934 4671 2.923121 ACAGAGTGCACATTTGTCAGT 58.077 42.857 21.04 7.43 0.00 3.41
3935 4672 4.071961 ACAGAGTGCACATTTGTCAGTA 57.928 40.909 21.04 0.00 0.00 2.74
3936 4673 3.809832 ACAGAGTGCACATTTGTCAGTAC 59.190 43.478 21.04 0.00 0.00 2.73
3937 4674 4.060900 CAGAGTGCACATTTGTCAGTACT 58.939 43.478 21.04 0.00 0.00 2.73
3938 4675 5.221441 ACAGAGTGCACATTTGTCAGTACTA 60.221 40.000 21.04 0.00 0.00 1.82
3939 4676 5.696270 CAGAGTGCACATTTGTCAGTACTAA 59.304 40.000 21.04 0.00 0.00 2.24
3954 4691 5.048643 TCAGTACTAAGAACAGAGAGCACAC 60.049 44.000 0.00 0.00 0.00 3.82
3990 4762 2.048444 TTGATGAGCCCTTGAGATGC 57.952 50.000 0.00 0.00 0.00 3.91
4017 4789 3.615155 TCACAGTGACAACCATGAAACA 58.385 40.909 0.00 0.00 0.00 2.83
4094 4869 1.945355 GCCCAAGGCGCAAAATTCATT 60.945 47.619 10.83 0.00 39.62 2.57
4095 4870 2.001872 CCCAAGGCGCAAAATTCATTC 58.998 47.619 10.83 0.00 0.00 2.67
4096 4871 2.612471 CCCAAGGCGCAAAATTCATTCA 60.612 45.455 10.83 0.00 0.00 2.57
4097 4872 3.065655 CCAAGGCGCAAAATTCATTCAA 58.934 40.909 10.83 0.00 0.00 2.69
4099 4874 3.665745 AGGCGCAAAATTCATTCAACT 57.334 38.095 10.83 0.00 0.00 3.16
4103 4886 6.862209 AGGCGCAAAATTCATTCAACTATAA 58.138 32.000 10.83 0.00 0.00 0.98
4115 4898 8.962884 TCATTCAACTATAATGTACAGCATGT 57.037 30.769 0.33 0.00 41.77 3.21
4149 4932 8.080363 ACCCTGTAGATTTAAGGTAGAAAGAG 57.920 38.462 0.00 0.00 0.00 2.85
4158 4941 9.541143 GATTTAAGGTAGAAAGAGGAGAGATTG 57.459 37.037 0.00 0.00 0.00 2.67
4159 4942 8.437274 TTTAAGGTAGAAAGAGGAGAGATTGT 57.563 34.615 0.00 0.00 0.00 2.71
4160 4943 6.538945 AAGGTAGAAAGAGGAGAGATTGTC 57.461 41.667 0.00 0.00 0.00 3.18
4162 4945 4.399934 GGTAGAAAGAGGAGAGATTGTCGT 59.600 45.833 0.00 0.00 0.00 4.34
4192 4996 5.346281 CGAAACAGCTAAAGACAGGTTCTAG 59.654 44.000 0.00 0.00 32.51 2.43
4194 4998 6.613153 AACAGCTAAAGACAGGTTCTAGAT 57.387 37.500 0.00 0.00 32.51 1.98
4234 5038 4.686972 TGAGCTACATTGTGAGCAGATAC 58.313 43.478 15.73 0.00 41.36 2.24
4255 5059 4.474113 ACGAAACATCTACGACTGAAGAC 58.526 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.162690 AGAATCGGTCGGGCCAGC 62.163 66.667 4.39 0.00 36.97 4.85
102 103 4.547367 CCCCAGAATCGGTCGGGC 62.547 72.222 0.00 0.00 40.09 6.13
103 104 4.547367 GCCCCAGAATCGGTCGGG 62.547 72.222 0.00 0.00 41.04 5.14
108 109 2.117156 CAAGCAGCCCCAGAATCGG 61.117 63.158 0.00 0.00 0.00 4.18
110 111 0.322816 TGTCAAGCAGCCCCAGAATC 60.323 55.000 0.00 0.00 0.00 2.52
128 129 1.024579 GGATGTAGCACAACCCCGTG 61.025 60.000 4.84 0.00 35.27 4.94
158 159 2.731571 GGGGCGCCACTATGTCTCA 61.732 63.158 30.85 0.00 0.00 3.27
192 198 3.393970 CGGGAGCAGGGAGAAGCA 61.394 66.667 0.00 0.00 0.00 3.91
193 199 3.077556 TCGGGAGCAGGGAGAAGC 61.078 66.667 0.00 0.00 0.00 3.86
234 240 1.202830 GGTGTTGGTATGGTGGTGTCA 60.203 52.381 0.00 0.00 0.00 3.58
235 241 1.202830 TGGTGTTGGTATGGTGGTGTC 60.203 52.381 0.00 0.00 0.00 3.67
240 246 0.887933 GCCTTGGTGTTGGTATGGTG 59.112 55.000 0.00 0.00 0.00 4.17
241 247 0.480690 TGCCTTGGTGTTGGTATGGT 59.519 50.000 0.00 0.00 0.00 3.55
243 249 0.887933 GGTGCCTTGGTGTTGGTATG 59.112 55.000 0.00 0.00 0.00 2.39
244 250 0.608035 CGGTGCCTTGGTGTTGGTAT 60.608 55.000 0.00 0.00 0.00 2.73
266 272 3.879351 CTTTCGCAACGCCACTGCC 62.879 63.158 0.00 0.00 36.40 4.85
268 274 0.028770 TTTCTTTCGCAACGCCACTG 59.971 50.000 0.00 0.00 0.00 3.66
277 283 1.605202 GGCCAATTGCTTTCTTTCGCA 60.605 47.619 0.00 0.00 40.92 5.10
297 303 0.890683 GTCATTGGGTCTGGCAAAGG 59.109 55.000 0.00 0.00 0.00 3.11
300 306 1.076549 GGGTCATTGGGTCTGGCAA 59.923 57.895 0.00 0.00 0.00 4.52
303 309 1.379044 GCTGGGTCATTGGGTCTGG 60.379 63.158 0.00 0.00 0.00 3.86
305 311 1.852157 TGGCTGGGTCATTGGGTCT 60.852 57.895 0.00 0.00 0.00 3.85
307 313 2.440599 GTGGCTGGGTCATTGGGT 59.559 61.111 0.00 0.00 0.00 4.51
312 318 2.240918 ACATGGGTGGCTGGGTCAT 61.241 57.895 0.00 0.00 0.00 3.06
313 319 2.858476 ACATGGGTGGCTGGGTCA 60.858 61.111 0.00 0.00 0.00 4.02
323 329 2.665000 CGACAGAGGCACATGGGT 59.335 61.111 0.00 0.00 0.00 4.51
328 334 2.343758 GGAAGCGACAGAGGCACA 59.656 61.111 0.00 0.00 0.00 4.57
331 337 1.446966 GAGTGGAAGCGACAGAGGC 60.447 63.158 0.00 0.00 0.00 4.70
336 342 2.338620 CACCGAGTGGAAGCGACA 59.661 61.111 0.00 0.00 39.21 4.35
340 346 2.029844 GCTGACACCGAGTGGAAGC 61.030 63.158 13.32 13.32 38.31 3.86
343 349 4.357947 GCGCTGACACCGAGTGGA 62.358 66.667 0.00 0.00 37.94 4.02
346 352 2.356313 CAAGCGCTGACACCGAGT 60.356 61.111 12.58 0.00 0.00 4.18
347 353 3.782244 GCAAGCGCTGACACCGAG 61.782 66.667 12.58 0.00 34.30 4.63
365 384 1.003262 CGTTGTGCCTTTCGCCATTG 61.003 55.000 0.00 0.00 36.24 2.82
367 386 1.852067 GACGTTGTGCCTTTCGCCAT 61.852 55.000 0.00 0.00 36.24 4.40
372 391 0.521735 GGATGGACGTTGTGCCTTTC 59.478 55.000 0.00 0.00 0.00 2.62
375 394 2.047274 CGGATGGACGTTGTGCCT 60.047 61.111 0.00 0.00 0.00 4.75
376 395 3.799755 GCGGATGGACGTTGTGCC 61.800 66.667 0.00 0.00 35.98 5.01
383 402 4.889856 TGGATGCGCGGATGGACG 62.890 66.667 20.78 0.00 0.00 4.79
384 403 2.513666 TTGGATGCGCGGATGGAC 60.514 61.111 20.78 8.76 0.00 4.02
394 413 6.515272 TGAGAAGAAATTTACCTTGGATGC 57.485 37.500 0.00 0.00 0.00 3.91
395 414 9.933723 AATTTGAGAAGAAATTTACCTTGGATG 57.066 29.630 0.00 0.00 32.70 3.51
462 482 4.147479 GGCATGGAAAAACGTTTTAGTTCG 59.853 41.667 25.44 15.22 32.43 3.95
464 484 4.806775 GTGGCATGGAAAAACGTTTTAGTT 59.193 37.500 25.44 11.27 35.59 2.24
472 492 0.314935 AGCAGTGGCATGGAAAAACG 59.685 50.000 0.00 0.00 44.61 3.60
505 525 5.905480 AAAACAAATTCCAGTTGATTCGC 57.095 34.783 0.00 0.00 0.00 4.70
564 584 9.325248 TCCCTCTCCAATTTCATTTAAAGAAAT 57.675 29.630 14.60 14.60 45.01 2.17
586 606 3.791545 TGGTATAAAAGAATGGCCTCCCT 59.208 43.478 3.32 0.00 0.00 4.20
587 607 4.178956 TGGTATAAAAGAATGGCCTCCC 57.821 45.455 3.32 0.00 0.00 4.30
588 608 6.538945 TTTTGGTATAAAAGAATGGCCTCC 57.461 37.500 3.32 0.00 0.00 4.30
602 622 8.745590 GGACTTTGCTCCTTTTATTTTGGTATA 58.254 33.333 0.00 0.00 0.00 1.47
603 623 7.454694 AGGACTTTGCTCCTTTTATTTTGGTAT 59.545 33.333 0.00 0.00 37.37 2.73
604 624 6.780522 AGGACTTTGCTCCTTTTATTTTGGTA 59.219 34.615 0.00 0.00 37.37 3.25
605 625 5.602561 AGGACTTTGCTCCTTTTATTTTGGT 59.397 36.000 0.00 0.00 37.37 3.67
606 626 5.928264 CAGGACTTTGCTCCTTTTATTTTGG 59.072 40.000 0.00 0.00 38.77 3.28
607 627 5.928264 CCAGGACTTTGCTCCTTTTATTTTG 59.072 40.000 0.00 0.00 38.77 2.44
608 628 5.511373 GCCAGGACTTTGCTCCTTTTATTTT 60.511 40.000 0.00 0.00 38.77 1.82
609 629 4.021104 GCCAGGACTTTGCTCCTTTTATTT 60.021 41.667 0.00 0.00 38.77 1.40
610 630 3.511540 GCCAGGACTTTGCTCCTTTTATT 59.488 43.478 0.00 0.00 38.77 1.40
611 631 3.092301 GCCAGGACTTTGCTCCTTTTAT 58.908 45.455 0.00 0.00 38.77 1.40
612 632 2.108250 AGCCAGGACTTTGCTCCTTTTA 59.892 45.455 0.00 0.00 38.77 1.52
613 633 1.133356 AGCCAGGACTTTGCTCCTTTT 60.133 47.619 0.00 0.00 38.77 2.27
614 634 0.480252 AGCCAGGACTTTGCTCCTTT 59.520 50.000 0.00 0.00 38.77 3.11
615 635 0.037447 GAGCCAGGACTTTGCTCCTT 59.963 55.000 8.65 0.00 44.45 3.36
616 636 1.682257 GAGCCAGGACTTTGCTCCT 59.318 57.895 8.65 0.00 44.45 3.69
617 637 4.310288 GAGCCAGGACTTTGCTCC 57.690 61.111 8.65 0.00 44.45 4.70
619 639 2.348998 CGGAGCCAGGACTTTGCT 59.651 61.111 0.00 0.00 38.24 3.91
656 676 6.808321 TTCCCACTAATAACAGACTAGCAT 57.192 37.500 0.00 0.00 0.00 3.79
698 719 9.972106 TTAGGGATAAAAGTCCGGTAAATTTTA 57.028 29.630 9.94 9.94 39.26 1.52
757 778 5.708948 TGAAAGCATTACTACATTTGCACC 58.291 37.500 0.00 0.00 37.56 5.01
771 792 5.138125 ACATTTCGACCATTGAAAGCATT 57.862 34.783 0.00 0.00 38.60 3.56
808 829 2.105128 CTTCGCTCTACTGGGCCG 59.895 66.667 0.00 0.00 0.00 6.13
809 830 2.359967 ACCTTCGCTCTACTGGGCC 61.360 63.158 0.00 0.00 0.00 5.80
822 843 2.320587 CCACTCACTGCGCACCTTC 61.321 63.158 5.66 0.00 0.00 3.46
823 844 2.281070 CCACTCACTGCGCACCTT 60.281 61.111 5.66 0.00 0.00 3.50
860 881 0.399949 TGGGCCTACAGTATCAGGGG 60.400 60.000 4.53 0.00 32.15 4.79
861 882 1.051812 CTGGGCCTACAGTATCAGGG 58.948 60.000 4.53 0.00 33.81 4.45
892 913 0.984230 CTTCTGGTAGGCCCAACTGA 59.016 55.000 0.00 0.00 44.65 3.41
973 1507 4.475135 GGAGGGGCAGAAGACGGC 62.475 72.222 0.00 0.00 36.54 5.68
983 1517 3.774599 ATGGCGAAATCGGAGGGGC 62.775 63.158 4.84 0.00 40.23 5.80
1083 1630 3.697747 CGGTCGCCCCCTTGTACA 61.698 66.667 0.00 0.00 0.00 2.90
1104 1660 3.358076 CTGCTTCGACGGGTCCTCC 62.358 68.421 0.00 0.00 0.00 4.30
1291 1848 1.122019 AGAATAAGCCGCGGGAGGAT 61.122 55.000 29.38 0.00 0.00 3.24
1400 1970 1.075482 CACCTGGATGTTGCACCCT 59.925 57.895 0.00 0.00 0.00 4.34
1454 2024 0.322816 GAGCAATGGGGCAAGAGACA 60.323 55.000 0.00 0.00 35.83 3.41
1467 2037 2.694628 TCAACAACAGCAAAGGAGCAAT 59.305 40.909 0.00 0.00 36.85 3.56
1524 2095 6.071463 GTCATCGATCAAACTAACAACACAC 58.929 40.000 0.00 0.00 0.00 3.82
1573 2144 3.414700 GCTGTTGAGCACGTCCCG 61.415 66.667 0.00 0.00 45.46 5.14
1750 2321 5.163561 CCAGCAAACTTTCTCACTGGTTTTA 60.164 40.000 0.00 0.00 39.85 1.52
1818 2395 5.643777 AGCATTCTTTTATACACGAACAGCT 59.356 36.000 0.00 2.81 0.00 4.24
1831 2408 9.836864 TCTTATATCAGAAGCAGCATTCTTTTA 57.163 29.630 0.00 0.00 37.43 1.52
1839 2416 9.379791 CAATATCATCTTATATCAGAAGCAGCA 57.620 33.333 0.00 0.00 0.00 4.41
1840 2417 8.828644 CCAATATCATCTTATATCAGAAGCAGC 58.171 37.037 0.00 0.00 0.00 5.25
1861 2440 9.722317 AAATGTATCCCCTTCAAATAACCAATA 57.278 29.630 0.00 0.00 0.00 1.90
1887 2472 4.219115 TCCTTTTCACAGGGCATACAAAA 58.781 39.130 0.00 0.00 34.24 2.44
1981 2568 5.636121 CCCAATTCATGAAAGACAACATGTG 59.364 40.000 13.09 0.00 42.75 3.21
2003 2590 4.709886 AGTAAACCACATAAATGAAGGCCC 59.290 41.667 0.00 0.00 32.50 5.80
2020 2614 2.874086 AGTTGCCGTGGTGTAAGTAAAC 59.126 45.455 0.00 0.00 0.00 2.01
2025 2619 1.270412 TGGTAGTTGCCGTGGTGTAAG 60.270 52.381 0.00 0.00 0.00 2.34
2066 2662 7.506938 CCATAACCAATTTAAGTGGATGGAGAT 59.493 37.037 20.55 0.00 40.55 2.75
2101 2698 0.391130 TACCAACTGATCGGCTGCAC 60.391 55.000 0.00 0.00 0.00 4.57
2321 2930 2.245582 AGTAGGCCTTACAGACAACGT 58.754 47.619 12.58 0.00 34.56 3.99
2630 3242 6.708054 CCTTAGACTCTGAAACAAACAGATGT 59.292 38.462 0.00 0.00 42.32 3.06
2631 3243 6.931281 TCCTTAGACTCTGAAACAAACAGATG 59.069 38.462 0.00 0.00 42.32 2.90
2652 3264 3.387699 GCTCCTCTAGAAGATGCTTCCTT 59.612 47.826 3.71 0.00 0.00 3.36
2700 3312 2.430694 ACGTATCTGCCTGTATGCTTCA 59.569 45.455 0.00 0.00 0.00 3.02
2743 3355 7.653767 ATCTTACTAACGCAGGCATATTTAC 57.346 36.000 0.00 0.00 0.00 2.01
2795 3410 0.035820 GTCCCGTTGGCAGATTGGTA 60.036 55.000 0.00 0.00 0.00 3.25
2798 3413 0.523072 CTTGTCCCGTTGGCAGATTG 59.477 55.000 0.00 0.00 0.00 2.67
2836 3451 7.903145 TCAAGCTCCTTACTAATGTAGTCAAA 58.097 34.615 0.00 0.00 40.14 2.69
2857 3472 6.757947 AGAAACATGAAACCACATTGTTCAAG 59.242 34.615 0.00 0.00 0.00 3.02
2906 3521 3.297134 ACACTTCCAGAAGGCAAAGAA 57.703 42.857 11.87 0.00 42.53 2.52
2969 3588 9.944376 TCAGTGTTTTAAGTAGCAGATTCTAAT 57.056 29.630 0.00 0.00 0.00 1.73
3036 3663 7.362662 ACAAACAATGCATTACTAACACAGAG 58.637 34.615 12.53 0.00 0.00 3.35
3038 3665 9.457110 TTTACAAACAATGCATTACTAACACAG 57.543 29.630 12.53 0.00 0.00 3.66
3085 3712 3.592059 GGCAACGGAGACTAATAACACA 58.408 45.455 0.00 0.00 0.00 3.72
3101 3728 0.818040 AGAGGGTCAACAACGGCAAC 60.818 55.000 0.00 0.00 0.00 4.17
3104 3731 2.027625 CGAGAGGGTCAACAACGGC 61.028 63.158 0.00 0.00 0.00 5.68
3105 3732 2.027625 GCGAGAGGGTCAACAACGG 61.028 63.158 0.00 0.00 0.00 4.44
3106 3733 2.027625 GGCGAGAGGGTCAACAACG 61.028 63.158 0.00 0.00 0.00 4.10
3108 3735 1.118965 TCAGGCGAGAGGGTCAACAA 61.119 55.000 0.00 0.00 0.00 2.83
3109 3736 1.118965 TTCAGGCGAGAGGGTCAACA 61.119 55.000 0.00 0.00 0.00 3.33
3110 3737 0.670854 GTTCAGGCGAGAGGGTCAAC 60.671 60.000 0.00 0.00 0.00 3.18
3111 3738 0.832135 AGTTCAGGCGAGAGGGTCAA 60.832 55.000 0.00 0.00 0.00 3.18
3112 3739 0.832135 AAGTTCAGGCGAGAGGGTCA 60.832 55.000 0.00 0.00 0.00 4.02
3113 3740 0.321996 AAAGTTCAGGCGAGAGGGTC 59.678 55.000 0.00 0.00 0.00 4.46
3114 3741 0.035458 CAAAGTTCAGGCGAGAGGGT 59.965 55.000 0.00 0.00 0.00 4.34
3115 3742 0.035458 ACAAAGTTCAGGCGAGAGGG 59.965 55.000 0.00 0.00 0.00 4.30
3116 3743 1.270305 TGACAAAGTTCAGGCGAGAGG 60.270 52.381 0.00 0.00 0.00 3.69
3117 3744 2.154854 TGACAAAGTTCAGGCGAGAG 57.845 50.000 0.00 0.00 0.00 3.20
3118 3745 2.839486 ATGACAAAGTTCAGGCGAGA 57.161 45.000 0.00 0.00 0.00 4.04
3119 3746 3.558505 CAAATGACAAAGTTCAGGCGAG 58.441 45.455 0.00 0.00 0.00 5.03
3120 3747 2.293122 CCAAATGACAAAGTTCAGGCGA 59.707 45.455 0.00 0.00 0.00 5.54
3121 3748 2.607771 CCCAAATGACAAAGTTCAGGCG 60.608 50.000 0.00 0.00 0.00 5.52
3122 3749 2.867647 GCCCAAATGACAAAGTTCAGGC 60.868 50.000 0.00 0.00 0.00 4.85
3123 3750 2.629617 AGCCCAAATGACAAAGTTCAGG 59.370 45.455 0.00 0.00 0.00 3.86
3124 3751 3.068590 ACAGCCCAAATGACAAAGTTCAG 59.931 43.478 0.00 0.00 0.00 3.02
3125 3752 3.030291 ACAGCCCAAATGACAAAGTTCA 58.970 40.909 0.00 0.00 0.00 3.18
3126 3753 3.552890 GGACAGCCCAAATGACAAAGTTC 60.553 47.826 0.00 0.00 34.14 3.01
3127 3754 2.365293 GGACAGCCCAAATGACAAAGTT 59.635 45.455 0.00 0.00 34.14 2.66
3128 3755 1.963515 GGACAGCCCAAATGACAAAGT 59.036 47.619 0.00 0.00 34.14 2.66
3129 3756 1.962807 TGGACAGCCCAAATGACAAAG 59.037 47.619 0.00 0.00 43.29 2.77
3130 3757 2.079170 TGGACAGCCCAAATGACAAA 57.921 45.000 0.00 0.00 43.29 2.83
3131 3758 3.837893 TGGACAGCCCAAATGACAA 57.162 47.368 0.00 0.00 43.29 3.18
3307 3934 1.731969 CTTGCTCTTTGCGGCTTGC 60.732 57.895 0.00 0.00 46.63 4.01
3330 3957 3.891977 TGTAAGCATAGGAGAGCTACAGG 59.108 47.826 0.00 0.00 40.90 4.00
3543 4280 1.092348 GAGGCACCCGAATTACCAAC 58.908 55.000 0.00 0.00 0.00 3.77
3553 4290 2.884639 CCCATTTATAAAGAGGCACCCG 59.115 50.000 12.00 0.00 0.00 5.28
3558 4295 6.516693 GCACCATAACCCATTTATAAAGAGGC 60.517 42.308 13.64 0.98 0.00 4.70
3596 4333 6.418226 GCTCATCACCAGATTAACTTACTACG 59.582 42.308 0.00 0.00 30.20 3.51
3644 4381 8.049117 GCCCATGATGAGGAATGATTATTACTA 58.951 37.037 0.00 0.00 37.60 1.82
3645 4382 6.888632 GCCCATGATGAGGAATGATTATTACT 59.111 38.462 0.00 0.00 40.24 2.24
3646 4383 6.096001 GGCCCATGATGAGGAATGATTATTAC 59.904 42.308 0.00 0.00 0.00 1.89
3721 4458 0.312416 CTCGAGTCATTCTAGGGGCG 59.688 60.000 3.62 0.00 0.00 6.13
3773 4510 7.921787 TCAGTTAAACTATTCGAAACAAAGCA 58.078 30.769 0.00 0.00 0.00 3.91
3824 4561 3.380142 CAAAAGGAAATCAACCACCACG 58.620 45.455 0.00 0.00 0.00 4.94
3869 4606 2.038952 CACACATGGAAGTTCCCTCTCA 59.961 50.000 19.42 0.00 35.03 3.27
3912 4649 3.313526 ACTGACAAATGTGCACTCTGTTC 59.686 43.478 19.41 9.59 0.00 3.18
3913 4650 3.282021 ACTGACAAATGTGCACTCTGTT 58.718 40.909 19.41 5.04 0.00 3.16
3914 4651 2.923121 ACTGACAAATGTGCACTCTGT 58.077 42.857 19.41 17.26 0.00 3.41
3915 4652 4.060900 AGTACTGACAAATGTGCACTCTG 58.939 43.478 19.41 14.21 0.00 3.35
3916 4653 4.342862 AGTACTGACAAATGTGCACTCT 57.657 40.909 19.41 2.18 0.00 3.24
3917 4654 5.926542 TCTTAGTACTGACAAATGTGCACTC 59.073 40.000 19.41 7.26 0.00 3.51
3918 4655 5.853936 TCTTAGTACTGACAAATGTGCACT 58.146 37.500 19.41 0.15 0.00 4.40
3919 4656 6.018262 TGTTCTTAGTACTGACAAATGTGCAC 60.018 38.462 10.75 10.75 0.00 4.57
3920 4657 6.052360 TGTTCTTAGTACTGACAAATGTGCA 58.948 36.000 5.39 0.00 0.00 4.57
3921 4658 6.423905 TCTGTTCTTAGTACTGACAAATGTGC 59.576 38.462 5.39 0.00 0.00 4.57
3922 4659 7.867909 TCTCTGTTCTTAGTACTGACAAATGTG 59.132 37.037 5.39 0.00 0.00 3.21
3923 4660 7.952671 TCTCTGTTCTTAGTACTGACAAATGT 58.047 34.615 5.39 0.00 0.00 2.71
3924 4661 7.062839 GCTCTCTGTTCTTAGTACTGACAAATG 59.937 40.741 5.39 0.00 0.00 2.32
3925 4662 7.093992 GCTCTCTGTTCTTAGTACTGACAAAT 58.906 38.462 5.39 0.00 0.00 2.32
3926 4663 6.040504 TGCTCTCTGTTCTTAGTACTGACAAA 59.959 38.462 5.39 0.00 0.00 2.83
3927 4664 5.535030 TGCTCTCTGTTCTTAGTACTGACAA 59.465 40.000 5.39 0.00 0.00 3.18
3928 4665 5.048643 GTGCTCTCTGTTCTTAGTACTGACA 60.049 44.000 5.39 4.54 0.00 3.58
3929 4666 5.048643 TGTGCTCTCTGTTCTTAGTACTGAC 60.049 44.000 5.39 0.00 0.00 3.51
3930 4667 5.048643 GTGTGCTCTCTGTTCTTAGTACTGA 60.049 44.000 5.39 0.00 0.00 3.41
3931 4668 5.048364 AGTGTGCTCTCTGTTCTTAGTACTG 60.048 44.000 5.39 0.00 0.00 2.74
3932 4669 5.074115 AGTGTGCTCTCTGTTCTTAGTACT 58.926 41.667 0.00 0.00 0.00 2.73
3933 4670 5.379732 AGTGTGCTCTCTGTTCTTAGTAC 57.620 43.478 0.00 0.00 0.00 2.73
3934 4671 5.302059 ACAAGTGTGCTCTCTGTTCTTAGTA 59.698 40.000 0.00 0.00 0.00 1.82
3935 4672 4.100189 ACAAGTGTGCTCTCTGTTCTTAGT 59.900 41.667 0.00 0.00 0.00 2.24
3936 4673 4.626042 ACAAGTGTGCTCTCTGTTCTTAG 58.374 43.478 0.00 0.00 0.00 2.18
3937 4674 4.672587 ACAAGTGTGCTCTCTGTTCTTA 57.327 40.909 0.00 0.00 0.00 2.10
3938 4675 3.550437 ACAAGTGTGCTCTCTGTTCTT 57.450 42.857 0.00 0.00 0.00 2.52
3939 4676 3.550437 AACAAGTGTGCTCTCTGTTCT 57.450 42.857 0.00 0.00 0.00 3.01
3990 4762 2.816689 TGGTTGTCACTGTGAAGTACG 58.183 47.619 12.81 0.00 0.00 3.67
4094 4869 9.961265 GTACTACATGCTGTACATTATAGTTGA 57.039 33.333 18.27 0.00 38.34 3.18
4095 4870 9.744468 TGTACTACATGCTGTACATTATAGTTG 57.256 33.333 20.60 0.00 42.49 3.16
4096 4871 9.967346 CTGTACTACATGCTGTACATTATAGTT 57.033 33.333 23.07 0.00 45.05 2.24
4097 4872 9.350951 TCTGTACTACATGCTGTACATTATAGT 57.649 33.333 23.07 10.00 45.05 2.12
4099 4874 9.961265 GTTCTGTACTACATGCTGTACATTATA 57.039 33.333 23.07 12.10 45.05 0.98
4103 4886 5.395324 GGGTTCTGTACTACATGCTGTACAT 60.395 44.000 23.07 0.00 45.05 2.29
4149 4932 1.993370 CGGTTCAACGACAATCTCTCC 59.007 52.381 0.00 0.00 35.47 3.71
4158 4941 0.935196 AGCTGTTTCGGTTCAACGAC 59.065 50.000 0.00 0.00 43.37 4.34
4159 4942 2.512485 TAGCTGTTTCGGTTCAACGA 57.488 45.000 0.00 0.00 41.76 3.85
4160 4943 3.246699 TCTTTAGCTGTTTCGGTTCAACG 59.753 43.478 0.00 0.00 0.00 4.10
4162 4945 4.193090 TGTCTTTAGCTGTTTCGGTTCAA 58.807 39.130 0.00 0.00 0.00 2.69
4192 4996 6.603201 AGCTCATGAGGCTCTAAGTAGATATC 59.397 42.308 23.89 0.00 34.70 1.63
4194 4998 5.886609 AGCTCATGAGGCTCTAAGTAGATA 58.113 41.667 23.89 0.00 34.70 1.98
4204 5008 2.871022 CACAATGTAGCTCATGAGGCTC 59.129 50.000 23.89 7.79 40.74 4.70
4206 5010 2.871022 CTCACAATGTAGCTCATGAGGC 59.129 50.000 23.89 15.58 36.81 4.70
4234 5038 4.555360 CAGTCTTCAGTCGTAGATGTTTCG 59.445 45.833 0.00 0.00 40.67 3.46
4255 5059 1.460504 TACTACAGGTCCAGCGACAG 58.539 55.000 0.00 0.00 41.13 3.51


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

AutoCloner maintained by Alex Coulton.