Multiple sequence alignment - TraesCS1D01G115800

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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 TraesCS1D01G115800 chr1D 100.000 3777 0 0 1 3777 111607654 111603878 0.000000e+00 6975.0
1 TraesCS1D01G115800 chr1D 96.053 152 5 1 695 846 463344453 463344303 2.910000e-61 246.0
2 TraesCS1D01G115800 chr1D 95.395 152 6 1 695 846 325676900 325676750 1.360000e-59 241.0
3 TraesCS1D01G115800 chr1D 95.395 152 6 1 695 846 367162682 367162532 1.360000e-59 241.0
4 TraesCS1D01G115800 chr1B 94.288 2556 104 18 859 3391 170843992 170841456 0.000000e+00 3873.0
5 TraesCS1D01G115800 chr1B 96.995 366 10 1 3413 3777 170839678 170839313 6.930000e-172 614.0
6 TraesCS1D01G115800 chr1B 91.463 246 19 2 414 658 647545053 647545297 1.680000e-88 337.0
7 TraesCS1D01G115800 chr1B 91.960 199 14 2 3 201 170844473 170844277 1.030000e-70 278.0
8 TraesCS1D01G115800 chr1B 82.456 171 12 10 190 348 170844245 170844081 2.370000e-27 134.0
9 TraesCS1D01G115800 chr1A 92.916 2414 115 23 856 3239 117981730 117979343 0.000000e+00 3459.0
10 TraesCS1D01G115800 chr1A 94.186 258 8 4 3522 3777 117977625 117977373 1.650000e-103 387.0
11 TraesCS1D01G115800 chr1A 92.444 225 14 3 3318 3542 117977873 117977652 6.090000e-83 318.0
12 TraesCS1D01G115800 chr1A 90.643 171 12 3 3019 3188 117978227 117978060 1.370000e-54 224.0
13 TraesCS1D01G115800 chr1A 93.519 108 3 3 244 348 117982154 117982048 1.400000e-34 158.0
14 TraesCS1D01G115800 chr1A 83.077 130 17 4 3255 3382 117978098 117977972 3.080000e-21 113.0
15 TraesCS1D01G115800 chr1A 95.312 64 2 1 3241 3304 117979082 117979020 2.400000e-17 100.0
16 TraesCS1D01G115800 chr5D 91.057 246 20 2 414 658 377354216 377353972 7.820000e-87 331.0
17 TraesCS1D01G115800 chr5D 89.370 254 24 3 406 658 472804732 472804983 2.190000e-82 316.0
18 TraesCS1D01G115800 chr4B 90.650 246 21 2 414 658 645456782 645456538 3.640000e-85 326.0
19 TraesCS1D01G115800 chr2D 90.650 246 21 2 414 658 590101358 590101114 3.640000e-85 326.0
20 TraesCS1D01G115800 chr2D 94.937 158 3 2 695 848 296710111 296709955 3.770000e-60 243.0
21 TraesCS1D01G115800 chr2D 80.328 122 24 0 5 126 595197618 595197739 4.020000e-15 93.5
22 TraesCS1D01G115800 chr6D 90.323 248 22 2 412 658 94757446 94757200 1.310000e-84 324.0
23 TraesCS1D01G115800 chr5B 90.283 247 22 2 413 658 320385901 320385656 4.710000e-84 322.0
24 TraesCS1D01G115800 chr5B 90.283 247 22 2 413 658 508061713 508061958 4.710000e-84 322.0
25 TraesCS1D01G115800 chr4D 89.723 253 23 3 408 658 63811656 63811907 1.690000e-83 320.0
26 TraesCS1D01G115800 chr4D 98.026 152 3 0 695 846 447293661 447293812 8.040000e-67 265.0
27 TraesCS1D01G115800 chr4D 96.078 153 5 1 695 847 351463796 351463645 8.100000e-62 248.0
28 TraesCS1D01G115800 chr3D 96.711 152 4 1 695 846 529127311 529127161 6.260000e-63 252.0
29 TraesCS1D01G115800 chr3D 96.053 152 5 1 695 846 488863429 488863579 2.910000e-61 246.0
30 TraesCS1D01G115800 chrUn 94.839 155 7 1 695 849 64153323 64153170 1.360000e-59 241.0


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 TraesCS1D01G115800 chr1D 111603878 111607654 3776 True 6975.000000 6975 100.000000 1 3777 1 chr1D.!!$R1 3776
1 TraesCS1D01G115800 chr1B 170839313 170844473 5160 True 1224.750000 3873 91.424750 3 3777 4 chr1B.!!$R1 3774
2 TraesCS1D01G115800 chr1A 117977373 117982154 4781 True 679.857143 3459 91.728143 244 3777 7 chr1A.!!$R1 3533

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
669 966 0.179000 ACACATCTCGGGAATCCAGC 59.821 55.0 0.09 0.0 0.00 4.85 F
718 1015 0.251787 AATGAGACCAACCCAAGGGC 60.252 55.0 4.70 0.0 39.32 5.19 F
929 1228 0.263172 ACACCCATCCGATCCTCTCT 59.737 55.0 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2438 0.036388 GGCGTCCTCACCATTCTTGA 60.036 55.000 0.00 0.00 0.0 3.02 R
2137 2440 1.079127 CGGCGTCCTCACCATTCTT 60.079 57.895 0.00 0.00 0.0 2.52 R
2858 3185 1.071502 CAGTACGCCACGCAATATTCG 60.072 52.381 5.96 5.96 0.0 3.34 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
30 31 6.902224 TCATCACAATGTTTACATAGACGG 57.098 37.500 0.00 0.00 35.10 4.79
33 34 7.768582 TCATCACAATGTTTACATAGACGGAAT 59.231 33.333 0.00 0.00 35.10 3.01
49 50 4.710324 ACGGAATTAAAATCATCGGGCTA 58.290 39.130 0.00 0.00 0.00 3.93
60 61 4.764050 TCATCGGGCTAACCTAATCAAA 57.236 40.909 0.00 0.00 36.97 2.69
86 87 0.331616 GGCCAGCCCCTAAAGAAAGA 59.668 55.000 0.00 0.00 0.00 2.52
96 97 4.268359 CCCTAAAGAAAGAGCATGCTTCT 58.732 43.478 23.61 17.90 0.00 2.85
112 113 3.131933 TGCTTCTCTAGATTGTGAGCCTC 59.868 47.826 0.00 0.00 0.00 4.70
126 127 0.610174 AGCCTCAACATTCGAGCTCA 59.390 50.000 15.40 0.00 0.00 4.26
133 134 6.219473 CCTCAACATTCGAGCTCATATACTT 58.781 40.000 15.40 0.00 0.00 2.24
199 241 9.829507 AACAATTTCTCAAATAATTGACAACCA 57.170 25.926 12.85 0.00 41.86 3.67
222 264 0.820891 AATGCGATGCCACCTGGATC 60.821 55.000 0.00 0.00 37.39 3.36
259 301 6.252233 AGATCATCCATTAGTGCTAGAGCTA 58.748 40.000 2.72 0.00 42.66 3.32
260 302 6.896860 AGATCATCCATTAGTGCTAGAGCTAT 59.103 38.462 2.72 0.00 42.66 2.97
373 670 4.850859 TTTGAGACAAACAGTGTGTACG 57.149 40.909 0.00 0.00 41.96 3.67
406 703 1.892474 GCAGCCCAACAACTTCCAATA 59.108 47.619 0.00 0.00 0.00 1.90
407 704 2.298729 GCAGCCCAACAACTTCCAATAA 59.701 45.455 0.00 0.00 0.00 1.40
408 705 3.244044 GCAGCCCAACAACTTCCAATAAA 60.244 43.478 0.00 0.00 0.00 1.40
410 707 3.006859 AGCCCAACAACTTCCAATAAAGC 59.993 43.478 0.00 0.00 0.00 3.51
411 708 3.864540 GCCCAACAACTTCCAATAAAGCC 60.865 47.826 0.00 0.00 0.00 4.35
413 710 3.578282 CCAACAACTTCCAATAAAGCCCT 59.422 43.478 0.00 0.00 0.00 5.19
415 712 5.336451 CCAACAACTTCCAATAAAGCCCTAC 60.336 44.000 0.00 0.00 0.00 3.18
416 713 5.256806 ACAACTTCCAATAAAGCCCTACT 57.743 39.130 0.00 0.00 0.00 2.57
417 714 5.254115 ACAACTTCCAATAAAGCCCTACTC 58.746 41.667 0.00 0.00 0.00 2.59
418 715 4.505324 ACTTCCAATAAAGCCCTACTCC 57.495 45.455 0.00 0.00 0.00 3.85
419 716 3.202373 ACTTCCAATAAAGCCCTACTCCC 59.798 47.826 0.00 0.00 0.00 4.30
420 717 3.145559 TCCAATAAAGCCCTACTCCCT 57.854 47.619 0.00 0.00 0.00 4.20
421 718 3.046374 TCCAATAAAGCCCTACTCCCTC 58.954 50.000 0.00 0.00 0.00 4.30
422 719 2.106684 CCAATAAAGCCCTACTCCCTCC 59.893 54.545 0.00 0.00 0.00 4.30
423 720 1.718280 ATAAAGCCCTACTCCCTCCG 58.282 55.000 0.00 0.00 0.00 4.63
424 721 0.337428 TAAAGCCCTACTCCCTCCGT 59.663 55.000 0.00 0.00 0.00 4.69
425 722 0.976590 AAAGCCCTACTCCCTCCGTC 60.977 60.000 0.00 0.00 0.00 4.79
426 723 2.838693 GCCCTACTCCCTCCGTCC 60.839 72.222 0.00 0.00 0.00 4.79
427 724 3.017139 CCCTACTCCCTCCGTCCT 58.983 66.667 0.00 0.00 0.00 3.85
428 725 1.310373 CCCTACTCCCTCCGTCCTT 59.690 63.158 0.00 0.00 0.00 3.36
429 726 0.325390 CCCTACTCCCTCCGTCCTTT 60.325 60.000 0.00 0.00 0.00 3.11
430 727 1.063417 CCCTACTCCCTCCGTCCTTTA 60.063 57.143 0.00 0.00 0.00 1.85
431 728 2.625087 CCCTACTCCCTCCGTCCTTTAA 60.625 54.545 0.00 0.00 0.00 1.52
432 729 3.102204 CCTACTCCCTCCGTCCTTTAAA 58.898 50.000 0.00 0.00 0.00 1.52
433 730 3.516700 CCTACTCCCTCCGTCCTTTAAAA 59.483 47.826 0.00 0.00 0.00 1.52
434 731 4.019950 CCTACTCCCTCCGTCCTTTAAAAA 60.020 45.833 0.00 0.00 0.00 1.94
435 732 4.017177 ACTCCCTCCGTCCTTTAAAAAG 57.983 45.455 0.00 0.00 35.79 2.27
436 733 3.393609 ACTCCCTCCGTCCTTTAAAAAGT 59.606 43.478 2.03 0.00 34.20 2.66
437 734 3.746940 TCCCTCCGTCCTTTAAAAAGTG 58.253 45.455 2.03 0.00 34.20 3.16
438 735 3.136992 TCCCTCCGTCCTTTAAAAAGTGT 59.863 43.478 2.03 0.00 34.20 3.55
439 736 4.347583 TCCCTCCGTCCTTTAAAAAGTGTA 59.652 41.667 2.03 0.00 34.20 2.90
440 737 4.453478 CCCTCCGTCCTTTAAAAAGTGTAC 59.547 45.833 2.03 0.00 34.20 2.90
441 738 5.303165 CCTCCGTCCTTTAAAAAGTGTACT 58.697 41.667 0.00 0.00 34.20 2.73
442 739 5.761726 CCTCCGTCCTTTAAAAAGTGTACTT 59.238 40.000 0.00 0.00 37.91 2.24
443 740 6.073385 CCTCCGTCCTTTAAAAAGTGTACTTC 60.073 42.308 0.00 0.00 34.61 3.01
444 741 5.759763 TCCGTCCTTTAAAAAGTGTACTTCC 59.240 40.000 0.00 0.00 34.61 3.46
445 742 5.528320 CCGTCCTTTAAAAAGTGTACTTCCA 59.472 40.000 0.00 0.00 34.61 3.53
446 743 6.038492 CCGTCCTTTAAAAAGTGTACTTCCAA 59.962 38.462 0.00 0.00 34.61 3.53
447 744 6.908820 CGTCCTTTAAAAAGTGTACTTCCAAC 59.091 38.462 0.00 0.00 34.61 3.77
448 745 7.201670 CGTCCTTTAAAAAGTGTACTTCCAACT 60.202 37.037 0.00 0.00 34.61 3.16
449 746 8.464404 GTCCTTTAAAAAGTGTACTTCCAACTT 58.536 33.333 0.00 0.00 34.61 2.66
450 747 9.027202 TCCTTTAAAAAGTGTACTTCCAACTTT 57.973 29.630 3.17 3.17 44.01 2.66
451 748 9.083080 CCTTTAAAAAGTGTACTTCCAACTTTG 57.917 33.333 8.53 0.00 41.93 2.77
452 749 9.634163 CTTTAAAAAGTGTACTTCCAACTTTGT 57.366 29.630 8.53 6.42 41.93 2.83
453 750 9.984190 TTTAAAAAGTGTACTTCCAACTTTGTT 57.016 25.926 8.53 7.96 41.93 2.83
454 751 7.883229 AAAAAGTGTACTTCCAACTTTGTTG 57.117 32.000 8.53 3.69 41.93 3.33
455 752 5.576447 AAGTGTACTTCCAACTTTGTTGG 57.424 39.130 19.97 19.97 40.87 3.77
456 753 4.850680 AGTGTACTTCCAACTTTGTTGGA 58.149 39.130 23.38 23.38 46.08 3.53
464 761 5.730296 TCCAACTTTGTTGGAAAGTCAAA 57.270 34.783 24.52 4.81 44.90 2.69
465 762 5.474825 TCCAACTTTGTTGGAAAGTCAAAC 58.525 37.500 24.52 0.00 44.90 2.93
466 763 5.011125 TCCAACTTTGTTGGAAAGTCAAACA 59.989 36.000 24.52 3.56 44.90 2.83
467 764 5.874261 CCAACTTTGTTGGAAAGTCAAACAT 59.126 36.000 21.06 0.00 42.06 2.71
468 765 6.371271 CCAACTTTGTTGGAAAGTCAAACATT 59.629 34.615 21.06 0.00 42.06 2.71
469 766 7.094848 CCAACTTTGTTGGAAAGTCAAACATTT 60.095 33.333 21.06 0.00 42.06 2.32
470 767 7.977789 ACTTTGTTGGAAAGTCAAACATTTT 57.022 28.000 0.00 0.00 35.76 1.82
471 768 8.389779 ACTTTGTTGGAAAGTCAAACATTTTT 57.610 26.923 0.00 0.00 35.76 1.94
472 769 9.495572 ACTTTGTTGGAAAGTCAAACATTTTTA 57.504 25.926 0.00 0.00 35.76 1.52
524 821 9.577110 ACATCAACAATTATGCTGTCAAATTAG 57.423 29.630 0.00 0.00 0.00 1.73
525 822 9.577110 CATCAACAATTATGCTGTCAAATTAGT 57.423 29.630 0.00 0.00 0.00 2.24
608 905 7.754069 TTGATATATTTTTGCAAAAGCTCGG 57.246 32.000 22.78 0.00 0.00 4.63
609 906 6.862209 TGATATATTTTTGCAAAAGCTCGGT 58.138 32.000 22.78 10.29 0.00 4.69
610 907 7.319646 TGATATATTTTTGCAAAAGCTCGGTT 58.680 30.769 22.78 7.87 0.00 4.44
611 908 8.462811 TGATATATTTTTGCAAAAGCTCGGTTA 58.537 29.630 22.78 7.81 0.00 2.85
612 909 9.296400 GATATATTTTTGCAAAAGCTCGGTTAA 57.704 29.630 22.78 7.11 0.00 2.01
613 910 7.954788 ATATTTTTGCAAAAGCTCGGTTAAA 57.045 28.000 22.78 6.41 0.00 1.52
614 911 5.457650 TTTTTGCAAAAGCTCGGTTAAAC 57.542 34.783 22.78 0.00 0.00 2.01
615 912 4.379339 TTTGCAAAAGCTCGGTTAAACT 57.621 36.364 10.02 0.00 0.00 2.66
616 913 4.379339 TTGCAAAAGCTCGGTTAAACTT 57.621 36.364 0.00 0.00 0.00 2.66
617 914 4.379339 TGCAAAAGCTCGGTTAAACTTT 57.621 36.364 0.00 0.00 33.92 2.66
618 915 5.502153 TGCAAAAGCTCGGTTAAACTTTA 57.498 34.783 0.00 0.00 32.28 1.85
619 916 5.892568 TGCAAAAGCTCGGTTAAACTTTAA 58.107 33.333 0.00 0.00 32.28 1.52
620 917 5.974751 TGCAAAAGCTCGGTTAAACTTTAAG 59.025 36.000 0.00 0.00 32.28 1.85
621 918 6.183360 TGCAAAAGCTCGGTTAAACTTTAAGA 60.183 34.615 0.00 0.00 32.28 2.10
622 919 6.861572 GCAAAAGCTCGGTTAAACTTTAAGAT 59.138 34.615 0.00 0.00 32.28 2.40
623 920 8.019094 GCAAAAGCTCGGTTAAACTTTAAGATA 58.981 33.333 0.00 0.00 32.28 1.98
624 921 9.543018 CAAAAGCTCGGTTAAACTTTAAGATAG 57.457 33.333 0.00 0.00 32.28 2.08
625 922 8.843885 AAAGCTCGGTTAAACTTTAAGATAGT 57.156 30.769 0.00 0.00 30.84 2.12
626 923 8.843885 AAGCTCGGTTAAACTTTAAGATAGTT 57.156 30.769 0.00 0.00 37.43 2.24
627 924 8.843885 AGCTCGGTTAAACTTTAAGATAGTTT 57.156 30.769 0.00 8.43 45.19 2.66
628 925 8.718734 AGCTCGGTTAAACTTTAAGATAGTTTG 58.281 33.333 12.12 0.00 43.58 2.93
629 926 7.480855 GCTCGGTTAAACTTTAAGATAGTTTGC 59.519 37.037 12.12 4.49 43.58 3.68
630 927 7.809665 TCGGTTAAACTTTAAGATAGTTTGCC 58.190 34.615 12.12 12.14 43.58 4.52
631 928 7.025365 CGGTTAAACTTTAAGATAGTTTGCCC 58.975 38.462 12.12 10.42 43.58 5.36
632 929 7.094506 CGGTTAAACTTTAAGATAGTTTGCCCT 60.095 37.037 12.12 0.00 43.58 5.19
633 930 8.582437 GGTTAAACTTTAAGATAGTTTGCCCTT 58.418 33.333 12.12 0.00 43.58 3.95
634 931 9.622004 GTTAAACTTTAAGATAGTTTGCCCTTC 57.378 33.333 12.12 0.00 43.58 3.46
635 932 7.833285 AAACTTTAAGATAGTTTGCCCTTCA 57.167 32.000 0.00 0.00 42.54 3.02
636 933 7.833285 AACTTTAAGATAGTTTGCCCTTCAA 57.167 32.000 0.00 0.00 32.06 2.69
637 934 7.215719 ACTTTAAGATAGTTTGCCCTTCAAC 57.784 36.000 0.00 0.00 33.73 3.18
638 935 6.775629 ACTTTAAGATAGTTTGCCCTTCAACA 59.224 34.615 0.00 0.00 33.73 3.33
639 936 7.286775 ACTTTAAGATAGTTTGCCCTTCAACAA 59.713 33.333 0.00 0.00 33.73 2.83
640 937 7.589958 TTAAGATAGTTTGCCCTTCAACAAA 57.410 32.000 0.00 0.00 33.73 2.83
641 938 5.712152 AGATAGTTTGCCCTTCAACAAAG 57.288 39.130 0.00 0.00 36.50 2.77
642 939 5.140454 AGATAGTTTGCCCTTCAACAAAGT 58.860 37.500 0.00 0.00 41.20 2.66
643 940 5.598417 AGATAGTTTGCCCTTCAACAAAGTT 59.402 36.000 0.00 0.00 39.50 2.66
644 941 3.860641 AGTTTGCCCTTCAACAAAGTTG 58.139 40.909 3.58 3.58 36.30 3.16
645 942 2.935849 GTTTGCCCTTCAACAAAGTTGG 59.064 45.455 9.72 0.00 36.50 3.77
646 943 2.151502 TGCCCTTCAACAAAGTTGGA 57.848 45.000 9.72 0.48 32.69 3.53
647 944 2.461695 TGCCCTTCAACAAAGTTGGAA 58.538 42.857 9.72 3.27 32.69 3.53
648 945 2.430332 TGCCCTTCAACAAAGTTGGAAG 59.570 45.455 9.72 10.85 37.18 3.46
652 949 4.981806 CTTCAACAAAGTTGGAAGGACA 57.018 40.909 9.72 0.00 34.54 4.02
653 950 4.672409 CTTCAACAAAGTTGGAAGGACAC 58.328 43.478 9.72 0.00 34.54 3.67
654 951 3.691575 TCAACAAAGTTGGAAGGACACA 58.308 40.909 9.72 0.00 0.00 3.72
655 952 4.277476 TCAACAAAGTTGGAAGGACACAT 58.723 39.130 9.72 0.00 0.00 3.21
656 953 4.338118 TCAACAAAGTTGGAAGGACACATC 59.662 41.667 9.72 0.00 0.00 3.06
657 954 4.170468 ACAAAGTTGGAAGGACACATCT 57.830 40.909 0.00 0.00 0.00 2.90
658 955 4.137543 ACAAAGTTGGAAGGACACATCTC 58.862 43.478 0.00 0.00 0.00 2.75
659 956 2.751166 AGTTGGAAGGACACATCTCG 57.249 50.000 0.00 0.00 0.00 4.04
660 957 1.276421 AGTTGGAAGGACACATCTCGG 59.724 52.381 0.00 0.00 0.00 4.63
661 958 0.613260 TTGGAAGGACACATCTCGGG 59.387 55.000 0.00 0.00 0.00 5.14
662 959 0.252057 TGGAAGGACACATCTCGGGA 60.252 55.000 0.00 0.00 0.00 5.14
663 960 0.902531 GGAAGGACACATCTCGGGAA 59.097 55.000 0.00 0.00 0.00 3.97
664 961 1.486726 GGAAGGACACATCTCGGGAAT 59.513 52.381 0.00 0.00 0.00 3.01
665 962 2.483889 GGAAGGACACATCTCGGGAATC 60.484 54.545 0.00 0.00 0.00 2.52
666 963 1.123928 AGGACACATCTCGGGAATCC 58.876 55.000 0.00 0.00 0.00 3.01
667 964 0.830648 GGACACATCTCGGGAATCCA 59.169 55.000 0.09 0.00 0.00 3.41
668 965 1.202580 GGACACATCTCGGGAATCCAG 60.203 57.143 0.09 0.00 0.00 3.86
669 966 0.179000 ACACATCTCGGGAATCCAGC 59.821 55.000 0.09 0.00 0.00 4.85
670 967 0.877649 CACATCTCGGGAATCCAGCG 60.878 60.000 0.09 0.00 0.00 5.18
671 968 1.330655 ACATCTCGGGAATCCAGCGT 61.331 55.000 0.09 0.00 0.00 5.07
680 977 1.593006 GGAATCCAGCGTCGTATGTTG 59.407 52.381 0.00 0.00 0.00 3.33
697 994 2.522193 GGGCCCGAACACCCAAAA 60.522 61.111 5.69 0.00 46.22 2.44
698 995 2.134933 GGGCCCGAACACCCAAAAA 61.135 57.895 5.69 0.00 46.22 1.94
717 1014 2.309136 AAATGAGACCAACCCAAGGG 57.691 50.000 2.91 2.91 42.03 3.95
718 1015 0.251787 AATGAGACCAACCCAAGGGC 60.252 55.000 4.70 0.00 39.32 5.19
720 1017 4.681624 AGACCAACCCAAGGGCTA 57.318 55.556 4.70 0.00 44.68 3.93
721 1018 2.877150 AGACCAACCCAAGGGCTAA 58.123 52.632 4.70 0.00 44.68 3.09
722 1019 0.404426 AGACCAACCCAAGGGCTAAC 59.596 55.000 4.70 0.00 44.68 2.34
723 1020 0.404426 GACCAACCCAAGGGCTAACT 59.596 55.000 4.70 0.00 39.32 2.24
724 1021 0.404426 ACCAACCCAAGGGCTAACTC 59.596 55.000 4.70 0.00 39.32 3.01
725 1022 0.698818 CCAACCCAAGGGCTAACTCT 59.301 55.000 4.70 0.00 39.32 3.24
726 1023 1.340114 CCAACCCAAGGGCTAACTCTC 60.340 57.143 4.70 0.00 39.32 3.20
727 1024 0.613777 AACCCAAGGGCTAACTCTCG 59.386 55.000 4.70 0.00 39.32 4.04
728 1025 0.544595 ACCCAAGGGCTAACTCTCGT 60.545 55.000 4.70 0.00 39.32 4.18
729 1026 0.613777 CCCAAGGGCTAACTCTCGTT 59.386 55.000 0.00 0.00 37.15 3.85
730 1027 1.676014 CCCAAGGGCTAACTCTCGTTG 60.676 57.143 0.00 0.00 34.59 4.10
731 1028 1.676014 CCAAGGGCTAACTCTCGTTGG 60.676 57.143 0.00 0.00 39.15 3.77
740 1037 5.674933 CTAACTCTCGTTGGCTTTTCTTT 57.325 39.130 0.00 0.00 34.59 2.52
741 1038 6.780706 CTAACTCTCGTTGGCTTTTCTTTA 57.219 37.500 0.00 0.00 34.59 1.85
742 1039 7.365840 CTAACTCTCGTTGGCTTTTCTTTAT 57.634 36.000 0.00 0.00 34.59 1.40
743 1040 8.475331 CTAACTCTCGTTGGCTTTTCTTTATA 57.525 34.615 0.00 0.00 34.59 0.98
744 1041 6.969828 ACTCTCGTTGGCTTTTCTTTATAG 57.030 37.500 0.00 0.00 0.00 1.31
745 1042 5.875359 ACTCTCGTTGGCTTTTCTTTATAGG 59.125 40.000 0.00 0.00 0.00 2.57
746 1043 6.045072 TCTCGTTGGCTTTTCTTTATAGGA 57.955 37.500 0.00 0.00 0.00 2.94
747 1044 6.106673 TCTCGTTGGCTTTTCTTTATAGGAG 58.893 40.000 0.00 0.00 0.00 3.69
748 1045 6.045072 TCGTTGGCTTTTCTTTATAGGAGA 57.955 37.500 0.00 0.00 0.00 3.71
749 1046 6.469410 TCGTTGGCTTTTCTTTATAGGAGAA 58.531 36.000 0.00 0.00 0.00 2.87
750 1047 6.938030 TCGTTGGCTTTTCTTTATAGGAGAAA 59.062 34.615 8.49 8.49 40.36 2.52
751 1048 7.446013 TCGTTGGCTTTTCTTTATAGGAGAAAA 59.554 33.333 17.84 17.84 45.70 2.29
752 1049 7.537649 CGTTGGCTTTTCTTTATAGGAGAAAAC 59.462 37.037 16.17 13.74 44.06 2.43
753 1050 8.577296 GTTGGCTTTTCTTTATAGGAGAAAACT 58.423 33.333 16.17 0.00 44.06 2.66
754 1051 8.336801 TGGCTTTTCTTTATAGGAGAAAACTC 57.663 34.615 16.17 12.95 44.06 3.01
755 1052 7.393515 TGGCTTTTCTTTATAGGAGAAAACTCC 59.606 37.037 16.17 17.63 44.06 3.85
762 1059 3.606886 GGAGAAAACTCCGTGAGCA 57.393 52.632 0.00 0.00 33.39 4.26
763 1060 1.149148 GGAGAAAACTCCGTGAGCAC 58.851 55.000 0.00 0.00 33.39 4.40
764 1061 1.149148 GAGAAAACTCCGTGAGCACC 58.851 55.000 1.36 0.00 32.04 5.01
765 1062 0.600255 AGAAAACTCCGTGAGCACCG 60.600 55.000 1.36 0.00 32.04 4.94
766 1063 2.171489 GAAAACTCCGTGAGCACCGC 62.171 60.000 1.36 0.00 32.04 5.68
788 1085 4.143333 CCGTGCCGGGACTCGAAT 62.143 66.667 24.50 0.00 44.15 3.34
789 1086 2.125673 CGTGCCGGGACTCGAATT 60.126 61.111 24.50 0.00 42.43 2.17
790 1087 2.165301 CGTGCCGGGACTCGAATTC 61.165 63.158 24.50 0.00 42.43 2.17
791 1088 2.165301 GTGCCGGGACTCGAATTCG 61.165 63.158 21.78 21.78 42.43 3.34
792 1089 2.585247 GCCGGGACTCGAATTCGG 60.585 66.667 26.47 18.95 42.43 4.30
799 1096 2.584608 CTCGAATTCGGGTGGGCT 59.415 61.111 26.47 0.00 40.29 5.19
800 1097 1.815421 CTCGAATTCGGGTGGGCTG 60.815 63.158 26.47 4.74 40.29 4.85
801 1098 2.824041 CGAATTCGGGTGGGCTGG 60.824 66.667 20.16 0.00 35.37 4.85
802 1099 3.140814 GAATTCGGGTGGGCTGGC 61.141 66.667 0.00 0.00 0.00 4.85
803 1100 3.936772 GAATTCGGGTGGGCTGGCA 62.937 63.158 2.88 0.00 0.00 4.92
804 1101 3.944250 AATTCGGGTGGGCTGGCAG 62.944 63.158 10.94 10.94 0.00 4.85
810 1107 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
811 1108 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
812 1109 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
813 1110 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
814 1111 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
815 1112 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
820 1117 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
821 1118 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
835 1132 2.819595 CCAGCCAATGGGTCGACG 60.820 66.667 9.92 0.00 46.36 5.12
836 1133 3.499737 CAGCCAATGGGTCGACGC 61.500 66.667 24.41 24.41 36.17 5.19
837 1134 4.778143 AGCCAATGGGTCGACGCC 62.778 66.667 27.39 20.43 36.17 5.68
856 1153 4.452733 CGTCCTCTTGGGCCCGAC 62.453 72.222 19.37 16.71 33.53 4.79
857 1154 4.097361 GTCCTCTTGGGCCCGACC 62.097 72.222 19.37 0.00 37.93 4.79
926 1225 1.341531 CTACACACCCATCCGATCCTC 59.658 57.143 0.00 0.00 0.00 3.71
927 1226 0.325671 ACACACCCATCCGATCCTCT 60.326 55.000 0.00 0.00 0.00 3.69
928 1227 0.390860 CACACCCATCCGATCCTCTC 59.609 60.000 0.00 0.00 0.00 3.20
929 1228 0.263172 ACACCCATCCGATCCTCTCT 59.737 55.000 0.00 0.00 0.00 3.10
930 1229 0.965439 CACCCATCCGATCCTCTCTC 59.035 60.000 0.00 0.00 0.00 3.20
931 1230 0.856982 ACCCATCCGATCCTCTCTCT 59.143 55.000 0.00 0.00 0.00 3.10
1423 1726 3.636231 CGGAGCAGTGGTTCCCCA 61.636 66.667 0.00 0.00 41.05 4.96
1431 1734 1.201429 AGTGGTTCCCCATCTTCGCT 61.201 55.000 0.00 0.00 44.35 4.93
1541 1844 1.340017 GGTTTGGCTATCCTGCAGACA 60.340 52.381 17.39 0.66 34.04 3.41
1764 2067 4.248842 CAGGCCACGACACCACCA 62.249 66.667 5.01 0.00 0.00 4.17
2135 2438 2.635915 TGTTCGTACCTTTCCAGTGGAT 59.364 45.455 14.00 0.00 0.00 3.41
2137 2440 2.531771 TCGTACCTTTCCAGTGGATCA 58.468 47.619 14.00 1.72 0.00 2.92
2138 2441 2.901192 TCGTACCTTTCCAGTGGATCAA 59.099 45.455 14.00 4.24 0.00 2.57
2140 2443 3.056107 CGTACCTTTCCAGTGGATCAAGA 60.056 47.826 20.76 0.95 0.00 3.02
2142 2445 4.664688 ACCTTTCCAGTGGATCAAGAAT 57.335 40.909 20.76 9.03 0.00 2.40
2144 2447 3.698040 CCTTTCCAGTGGATCAAGAATGG 59.302 47.826 20.76 10.08 0.00 3.16
2153 2456 1.936547 GATCAAGAATGGTGAGGACGC 59.063 52.381 0.00 0.00 0.00 5.19
2297 2600 4.082523 CCGAGGCCACGACACCAT 62.083 66.667 24.92 0.00 35.09 3.55
2323 2626 1.511305 GCCACGAACGAGATGGAGA 59.489 57.895 0.14 0.00 35.33 3.71
2331 2634 2.414994 ACGAGATGGAGAGTTCGGTA 57.585 50.000 0.00 0.00 37.38 4.02
2368 2671 3.249687 AGGGACTCGTTTTGCATCC 57.750 52.632 0.00 0.00 0.00 3.51
2400 2703 2.047844 TTCTGCTCCGAGCTGTGC 60.048 61.111 20.87 0.00 42.97 4.57
2524 2827 1.000019 TTCGGGGACATCGAGGTCT 60.000 57.895 27.24 0.00 37.93 3.85
2786 3111 2.836262 TCGACTTCTAGGAGATCGACC 58.164 52.381 16.82 4.22 36.92 4.79
2841 3168 2.036256 AGTGGTGATTGCCTGGCC 59.964 61.111 17.53 0.00 0.00 5.36
2858 3185 5.426504 CCTGGCCATTACATCTATGATCTC 58.573 45.833 5.51 0.00 0.00 2.75
2923 3254 2.101917 TCGAGGAACTTCGGAACTGTTT 59.898 45.455 6.50 0.00 41.55 2.83
2936 3267 3.372822 GGAACTGTTTGAAAGTGTCGTCA 59.627 43.478 0.00 0.00 0.00 4.35
2975 3306 6.978659 CGTGTCTACTTTGAAATGCCTAGATA 59.021 38.462 0.00 0.00 0.00 1.98
3015 3346 7.158021 CCATTTTTACATGTGGTTGTGGTTAT 58.842 34.615 9.11 0.00 0.00 1.89
3021 3352 2.591923 TGTGGTTGTGGTTATGCATGT 58.408 42.857 10.16 0.00 0.00 3.21
3184 4849 4.786507 CATCCGTGCATGTTATGGTATTG 58.213 43.478 4.96 4.42 0.00 1.90
3212 4877 1.478916 GAGGTGCTTCAGTAGGAGGTC 59.521 57.143 0.00 0.00 0.00 3.85
3222 4887 1.995626 TAGGAGGTCTGGGGCTTGC 60.996 63.158 0.00 0.00 0.00 4.01
3253 4918 9.368674 CTGATTTTGGTTCATGCATTGTTATTA 57.631 29.630 0.00 0.00 0.00 0.98
3320 4985 5.707298 ACAAATTCTGGGTGATTCAGTAGTG 59.293 40.000 0.00 0.00 34.15 2.74
3342 5169 4.201910 TGCTTACTTGCTCTGTTCACAAAC 60.202 41.667 0.00 0.00 35.85 2.93
3354 5181 8.482429 GCTCTGTTCACAAACATAAGATTTTTG 58.518 33.333 0.00 0.00 44.18 2.44
3355 5182 8.351495 TCTGTTCACAAACATAAGATTTTTGC 57.649 30.769 0.00 0.00 44.18 3.68
3356 5183 7.159437 TGTTCACAAACATAAGATTTTTGCG 57.841 32.000 0.00 0.00 40.45 4.85
3392 5220 5.086104 ACTACATGCGGACAGAAATAAGT 57.914 39.130 0.00 0.00 0.00 2.24
3400 5228 4.909880 GCGGACAGAAATAAGTGAACAAAC 59.090 41.667 0.00 0.00 0.00 2.93
3415 6999 4.934001 TGAACAAACACACTAAACCGTGTA 59.066 37.500 0.00 0.00 45.74 2.90
3573 7204 5.581874 CAGTGGAAGTGAATTTTGTTTGCTT 59.418 36.000 0.00 0.00 40.62 3.91
3689 7326 5.567430 ACTTTAGTGGGTCAAAAGGGTATC 58.433 41.667 0.00 0.00 35.09 2.24
3717 7354 9.629878 TTGGAGTTAAGTGACTAAATTAAACCA 57.370 29.630 0.00 0.00 31.48 3.67
3726 7363 9.349713 AGTGACTAAATTAAACCATCTCAACAA 57.650 29.630 0.00 0.00 0.00 2.83
3741 7378 9.778993 CCATCTCAACAAGTTTAGTGATTATTG 57.221 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.984764 CCGATGATTTTAATTCCGTCTATGTAA 58.015 33.333 0.00 0.00 0.00 2.41
22 23 6.620733 GCCCGATGATTTTAATTCCGTCTATG 60.621 42.308 0.00 0.00 0.00 2.23
25 26 3.564225 GCCCGATGATTTTAATTCCGTCT 59.436 43.478 0.00 0.00 0.00 4.18
30 31 6.635030 AGGTTAGCCCGATGATTTTAATTC 57.365 37.500 0.00 0.00 38.74 2.17
33 34 7.284074 TGATTAGGTTAGCCCGATGATTTTAA 58.716 34.615 0.00 0.00 38.74 1.52
37 38 4.974645 TGATTAGGTTAGCCCGATGATT 57.025 40.909 0.00 0.00 38.74 2.57
42 43 3.985019 TGTTTGATTAGGTTAGCCCGA 57.015 42.857 0.00 0.00 38.74 5.14
49 50 1.476488 GCCGCCATGTTTGATTAGGTT 59.524 47.619 0.00 0.00 0.00 3.50
86 87 4.695396 CTCACAATCTAGAGAAGCATGCT 58.305 43.478 16.30 16.30 33.74 3.79
96 97 5.423015 GAATGTTGAGGCTCACAATCTAGA 58.577 41.667 18.55 0.00 0.00 2.43
199 241 1.755395 AGGTGGCATCGCATTGCAT 60.755 52.632 9.69 0.00 44.59 3.96
288 333 4.907269 TGGGATCCTCTGCAATTATCTACA 59.093 41.667 12.58 0.00 0.00 2.74
350 405 5.623335 CGTACACACTGTTTGTCTCAAAAA 58.377 37.500 2.38 0.00 35.67 1.94
352 407 3.062909 GCGTACACACTGTTTGTCTCAAA 59.937 43.478 2.38 0.00 35.67 2.69
353 408 2.605818 GCGTACACACTGTTTGTCTCAA 59.394 45.455 2.38 0.00 35.67 3.02
355 410 2.218759 CAGCGTACACACTGTTTGTCTC 59.781 50.000 2.38 0.00 35.67 3.36
356 411 2.201732 CAGCGTACACACTGTTTGTCT 58.798 47.619 2.38 0.00 35.67 3.41
357 412 1.332904 GCAGCGTACACACTGTTTGTC 60.333 52.381 2.38 0.00 35.67 3.18
358 413 0.655733 GCAGCGTACACACTGTTTGT 59.344 50.000 4.85 4.85 39.97 2.83
360 415 0.937304 CTGCAGCGTACACACTGTTT 59.063 50.000 0.00 0.00 36.26 2.83
361 416 0.179084 ACTGCAGCGTACACACTGTT 60.179 50.000 15.27 0.00 36.26 3.16
362 417 0.875908 CACTGCAGCGTACACACTGT 60.876 55.000 15.27 0.00 36.26 3.55
366 663 2.664851 GGCACTGCAGCGTACACA 60.665 61.111 15.27 0.00 34.64 3.72
368 665 3.914605 CTCGGCACTGCAGCGTACA 62.915 63.158 15.27 0.00 34.64 2.90
406 703 0.976590 GACGGAGGGAGTAGGGCTTT 60.977 60.000 0.00 0.00 0.00 3.51
407 704 1.381463 GACGGAGGGAGTAGGGCTT 60.381 63.158 0.00 0.00 0.00 4.35
408 705 2.279408 GACGGAGGGAGTAGGGCT 59.721 66.667 0.00 0.00 0.00 5.19
410 707 0.325390 AAAGGACGGAGGGAGTAGGG 60.325 60.000 0.00 0.00 0.00 3.53
411 708 2.449137 TAAAGGACGGAGGGAGTAGG 57.551 55.000 0.00 0.00 0.00 3.18
413 710 4.594491 ACTTTTTAAAGGACGGAGGGAGTA 59.406 41.667 7.12 0.00 40.31 2.59
415 712 3.751698 CACTTTTTAAAGGACGGAGGGAG 59.248 47.826 7.12 0.00 40.31 4.30
416 713 3.136992 ACACTTTTTAAAGGACGGAGGGA 59.863 43.478 7.12 0.00 40.31 4.20
417 714 3.483421 ACACTTTTTAAAGGACGGAGGG 58.517 45.455 7.12 0.00 40.31 4.30
418 715 5.303165 AGTACACTTTTTAAAGGACGGAGG 58.697 41.667 7.12 0.00 40.31 4.30
419 716 6.073385 GGAAGTACACTTTTTAAAGGACGGAG 60.073 42.308 7.12 0.00 40.31 4.63
420 717 5.759763 GGAAGTACACTTTTTAAAGGACGGA 59.240 40.000 7.12 0.00 40.31 4.69
421 718 5.528320 TGGAAGTACACTTTTTAAAGGACGG 59.472 40.000 7.12 0.00 40.31 4.79
422 719 6.607735 TGGAAGTACACTTTTTAAAGGACG 57.392 37.500 7.12 0.00 40.31 4.79
423 720 7.993101 AGTTGGAAGTACACTTTTTAAAGGAC 58.007 34.615 7.12 2.67 40.31 3.85
424 721 8.584063 AAGTTGGAAGTACACTTTTTAAAGGA 57.416 30.769 7.12 0.00 40.31 3.36
425 722 9.083080 CAAAGTTGGAAGTACACTTTTTAAAGG 57.917 33.333 5.73 0.00 40.31 3.11
426 723 9.634163 ACAAAGTTGGAAGTACACTTTTTAAAG 57.366 29.630 5.73 0.80 41.73 1.85
427 724 9.984190 AACAAAGTTGGAAGTACACTTTTTAAA 57.016 25.926 5.73 0.00 36.11 1.52
428 725 9.413048 CAACAAAGTTGGAAGTACACTTTTTAA 57.587 29.630 5.73 0.00 36.11 1.52
429 726 8.030106 CCAACAAAGTTGGAAGTACACTTTTTA 58.970 33.333 21.24 0.00 42.06 1.52
430 727 6.871492 CCAACAAAGTTGGAAGTACACTTTTT 59.129 34.615 21.24 0.00 42.06 1.94
431 728 6.209788 TCCAACAAAGTTGGAAGTACACTTTT 59.790 34.615 24.83 0.00 44.90 2.27
432 729 5.712917 TCCAACAAAGTTGGAAGTACACTTT 59.287 36.000 24.83 0.00 44.90 2.66
433 730 5.258051 TCCAACAAAGTTGGAAGTACACTT 58.742 37.500 24.83 0.00 44.90 3.16
434 731 4.850680 TCCAACAAAGTTGGAAGTACACT 58.149 39.130 24.83 0.00 44.90 3.55
442 739 5.011125 TGTTTGACTTTCCAACAAAGTTGGA 59.989 36.000 23.64 23.64 46.08 3.53
443 740 5.233988 TGTTTGACTTTCCAACAAAGTTGG 58.766 37.500 20.09 20.09 40.27 3.77
444 741 6.966435 ATGTTTGACTTTCCAACAAAGTTG 57.034 33.333 3.00 3.00 40.27 3.16
445 742 7.977789 AAATGTTTGACTTTCCAACAAAGTT 57.022 28.000 1.44 0.00 40.27 2.66
446 743 7.977789 AAAATGTTTGACTTTCCAACAAAGT 57.022 28.000 0.00 0.00 42.62 2.66
498 795 9.577110 CTAATTTGACAGCATAATTGTTGATGT 57.423 29.630 12.22 12.22 45.62 3.06
499 796 9.577110 ACTAATTTGACAGCATAATTGTTGATG 57.423 29.630 6.85 6.85 37.49 3.07
598 895 9.543018 CTATCTTAAAGTTTAACCGAGCTTTTG 57.457 33.333 3.88 0.00 33.78 2.44
599 896 9.281371 ACTATCTTAAAGTTTAACCGAGCTTTT 57.719 29.630 3.88 0.00 33.78 2.27
600 897 8.843885 ACTATCTTAAAGTTTAACCGAGCTTT 57.156 30.769 3.88 0.00 35.62 3.51
601 898 8.843885 AACTATCTTAAAGTTTAACCGAGCTT 57.156 30.769 3.88 0.00 33.39 3.74
602 899 8.718734 CAAACTATCTTAAAGTTTAACCGAGCT 58.281 33.333 3.88 0.00 43.52 4.09
603 900 7.480855 GCAAACTATCTTAAAGTTTAACCGAGC 59.519 37.037 3.88 0.38 43.52 5.03
604 901 7.961283 GGCAAACTATCTTAAAGTTTAACCGAG 59.039 37.037 3.88 4.55 43.52 4.63
605 902 7.094677 GGGCAAACTATCTTAAAGTTTAACCGA 60.095 37.037 3.88 2.35 43.52 4.69
606 903 7.025365 GGGCAAACTATCTTAAAGTTTAACCG 58.975 38.462 3.88 0.00 43.52 4.44
607 904 8.118976 AGGGCAAACTATCTTAAAGTTTAACC 57.881 34.615 3.88 8.51 43.52 2.85
608 905 9.622004 GAAGGGCAAACTATCTTAAAGTTTAAC 57.378 33.333 3.88 0.00 43.52 2.01
609 906 9.357161 TGAAGGGCAAACTATCTTAAAGTTTAA 57.643 29.630 7.80 7.80 43.52 1.52
610 907 8.927675 TGAAGGGCAAACTATCTTAAAGTTTA 57.072 30.769 3.96 0.00 43.52 2.01
611 908 7.833285 TGAAGGGCAAACTATCTTAAAGTTT 57.167 32.000 0.00 0.00 45.64 2.66
612 909 7.286775 TGTTGAAGGGCAAACTATCTTAAAGTT 59.713 33.333 0.00 0.00 38.44 2.66
613 910 6.775629 TGTTGAAGGGCAAACTATCTTAAAGT 59.224 34.615 0.00 0.00 38.44 2.66
614 911 7.214467 TGTTGAAGGGCAAACTATCTTAAAG 57.786 36.000 0.00 0.00 38.44 1.85
615 912 7.589958 TTGTTGAAGGGCAAACTATCTTAAA 57.410 32.000 0.00 0.00 38.44 1.52
616 913 7.286775 ACTTTGTTGAAGGGCAAACTATCTTAA 59.713 33.333 0.00 0.00 39.79 1.85
617 914 6.775629 ACTTTGTTGAAGGGCAAACTATCTTA 59.224 34.615 0.00 0.00 39.79 2.10
618 915 5.598417 ACTTTGTTGAAGGGCAAACTATCTT 59.402 36.000 0.00 0.00 39.79 2.40
619 916 5.140454 ACTTTGTTGAAGGGCAAACTATCT 58.860 37.500 0.00 0.00 39.79 1.98
620 917 5.453567 ACTTTGTTGAAGGGCAAACTATC 57.546 39.130 0.00 0.00 39.79 2.08
621 918 5.453198 CCAACTTTGTTGAAGGGCAAACTAT 60.453 40.000 11.47 0.00 39.79 2.12
622 919 4.142049 CCAACTTTGTTGAAGGGCAAACTA 60.142 41.667 11.47 0.00 39.79 2.24
623 920 3.369366 CCAACTTTGTTGAAGGGCAAACT 60.369 43.478 11.47 0.00 39.79 2.66
624 921 2.935849 CCAACTTTGTTGAAGGGCAAAC 59.064 45.455 11.47 0.00 39.79 2.93
625 922 2.834549 TCCAACTTTGTTGAAGGGCAAA 59.165 40.909 11.47 0.00 39.79 3.68
626 923 2.461695 TCCAACTTTGTTGAAGGGCAA 58.538 42.857 11.47 0.00 39.79 4.52
627 924 2.151502 TCCAACTTTGTTGAAGGGCA 57.848 45.000 11.47 0.00 39.79 5.36
628 925 2.224042 CCTTCCAACTTTGTTGAAGGGC 60.224 50.000 20.76 0.00 39.79 5.19
629 926 3.068165 GTCCTTCCAACTTTGTTGAAGGG 59.932 47.826 24.11 13.24 39.79 3.95
630 927 3.699038 TGTCCTTCCAACTTTGTTGAAGG 59.301 43.478 21.59 21.59 39.79 3.46
631 928 4.157656 TGTGTCCTTCCAACTTTGTTGAAG 59.842 41.667 11.47 11.65 41.32 3.02
632 929 4.082845 TGTGTCCTTCCAACTTTGTTGAA 58.917 39.130 11.47 4.30 0.00 2.69
633 930 3.691575 TGTGTCCTTCCAACTTTGTTGA 58.308 40.909 11.47 0.00 0.00 3.18
634 931 4.339247 AGATGTGTCCTTCCAACTTTGTTG 59.661 41.667 3.69 3.69 0.00 3.33
635 932 4.536765 AGATGTGTCCTTCCAACTTTGTT 58.463 39.130 0.00 0.00 0.00 2.83
636 933 4.137543 GAGATGTGTCCTTCCAACTTTGT 58.862 43.478 0.00 0.00 0.00 2.83
637 934 3.187227 CGAGATGTGTCCTTCCAACTTTG 59.813 47.826 0.00 0.00 0.00 2.77
638 935 3.403038 CGAGATGTGTCCTTCCAACTTT 58.597 45.455 0.00 0.00 0.00 2.66
639 936 2.289694 CCGAGATGTGTCCTTCCAACTT 60.290 50.000 0.00 0.00 0.00 2.66
640 937 1.276421 CCGAGATGTGTCCTTCCAACT 59.724 52.381 0.00 0.00 0.00 3.16
641 938 1.676014 CCCGAGATGTGTCCTTCCAAC 60.676 57.143 0.00 0.00 0.00 3.77
642 939 0.613260 CCCGAGATGTGTCCTTCCAA 59.387 55.000 0.00 0.00 0.00 3.53
643 940 0.252057 TCCCGAGATGTGTCCTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
644 941 0.902531 TTCCCGAGATGTGTCCTTCC 59.097 55.000 0.00 0.00 0.00 3.46
645 942 2.483889 GGATTCCCGAGATGTGTCCTTC 60.484 54.545 0.00 0.00 0.00 3.46
646 943 1.486726 GGATTCCCGAGATGTGTCCTT 59.513 52.381 0.00 0.00 0.00 3.36
647 944 1.123928 GGATTCCCGAGATGTGTCCT 58.876 55.000 0.00 0.00 0.00 3.85
648 945 0.830648 TGGATTCCCGAGATGTGTCC 59.169 55.000 0.00 0.00 34.29 4.02
649 946 1.808133 GCTGGATTCCCGAGATGTGTC 60.808 57.143 0.00 0.00 34.29 3.67
650 947 0.179000 GCTGGATTCCCGAGATGTGT 59.821 55.000 0.00 0.00 34.29 3.72
651 948 0.877649 CGCTGGATTCCCGAGATGTG 60.878 60.000 0.00 0.00 34.29 3.21
652 949 1.330655 ACGCTGGATTCCCGAGATGT 61.331 55.000 8.15 0.00 34.29 3.06
653 950 0.598680 GACGCTGGATTCCCGAGATG 60.599 60.000 8.15 0.00 34.29 2.90
654 951 1.742768 GACGCTGGATTCCCGAGAT 59.257 57.895 8.15 0.00 34.29 2.75
655 952 2.771639 CGACGCTGGATTCCCGAGA 61.772 63.158 8.15 0.00 34.29 4.04
656 953 1.721664 TACGACGCTGGATTCCCGAG 61.722 60.000 8.15 2.63 34.29 4.63
657 954 1.105167 ATACGACGCTGGATTCCCGA 61.105 55.000 8.15 0.00 34.29 5.14
658 955 0.939577 CATACGACGCTGGATTCCCG 60.940 60.000 0.00 0.00 34.29 5.14
659 956 0.104304 ACATACGACGCTGGATTCCC 59.896 55.000 0.00 0.00 0.00 3.97
660 957 1.593006 CAACATACGACGCTGGATTCC 59.407 52.381 0.00 0.00 0.00 3.01
661 958 1.593006 CCAACATACGACGCTGGATTC 59.407 52.381 0.00 0.00 0.00 2.52
662 959 1.651987 CCAACATACGACGCTGGATT 58.348 50.000 0.00 0.00 0.00 3.01
663 960 0.179084 CCCAACATACGACGCTGGAT 60.179 55.000 0.00 0.00 0.00 3.41
664 961 1.216977 CCCAACATACGACGCTGGA 59.783 57.895 0.00 0.00 0.00 3.86
665 962 2.461110 GCCCAACATACGACGCTGG 61.461 63.158 0.00 0.00 0.00 4.85
666 963 2.461110 GGCCCAACATACGACGCTG 61.461 63.158 0.00 0.00 0.00 5.18
667 964 2.125269 GGCCCAACATACGACGCT 60.125 61.111 0.00 0.00 0.00 5.07
668 965 3.199891 GGGCCCAACATACGACGC 61.200 66.667 19.95 0.00 0.00 5.19
669 966 2.839043 TTCGGGCCCAACATACGACG 62.839 60.000 24.92 3.10 32.85 5.12
670 967 1.078988 TTCGGGCCCAACATACGAC 60.079 57.895 24.92 0.00 32.85 4.34
671 968 1.078988 GTTCGGGCCCAACATACGA 60.079 57.895 24.92 8.43 0.00 3.43
680 977 2.134933 TTTTTGGGTGTTCGGGCCC 61.135 57.895 13.57 13.57 45.04 5.80
696 993 2.972021 CCCTTGGGTTGGTCTCATTTTT 59.028 45.455 0.00 0.00 0.00 1.94
697 994 2.608623 CCCTTGGGTTGGTCTCATTTT 58.391 47.619 0.00 0.00 0.00 1.82
698 995 1.827245 GCCCTTGGGTTGGTCTCATTT 60.827 52.381 7.61 0.00 0.00 2.32
699 996 0.251787 GCCCTTGGGTTGGTCTCATT 60.252 55.000 7.61 0.00 0.00 2.57
700 997 1.142688 AGCCCTTGGGTTGGTCTCAT 61.143 55.000 7.61 0.00 0.00 2.90
702 999 0.696501 TTAGCCCTTGGGTTGGTCTC 59.303 55.000 7.61 0.00 34.28 3.36
703 1000 0.404426 GTTAGCCCTTGGGTTGGTCT 59.596 55.000 7.61 0.00 34.28 3.85
704 1001 0.404426 AGTTAGCCCTTGGGTTGGTC 59.596 55.000 7.61 0.00 34.28 4.02
705 1002 0.404426 GAGTTAGCCCTTGGGTTGGT 59.596 55.000 7.61 0.00 34.28 3.67
706 1003 0.698818 AGAGTTAGCCCTTGGGTTGG 59.301 55.000 7.61 0.00 34.28 3.77
707 1004 1.676014 CGAGAGTTAGCCCTTGGGTTG 60.676 57.143 7.61 0.00 34.28 3.77
708 1005 0.613777 CGAGAGTTAGCCCTTGGGTT 59.386 55.000 7.61 3.76 34.28 4.11
710 1007 2.287829 ACGAGAGTTAGCCCTTGGG 58.712 57.895 0.32 0.32 46.40 4.12
722 1019 6.106673 TCCTATAAAGAAAAGCCAACGAGAG 58.893 40.000 0.00 0.00 0.00 3.20
723 1020 6.045072 TCCTATAAAGAAAAGCCAACGAGA 57.955 37.500 0.00 0.00 0.00 4.04
724 1021 6.106673 TCTCCTATAAAGAAAAGCCAACGAG 58.893 40.000 0.00 0.00 0.00 4.18
725 1022 6.045072 TCTCCTATAAAGAAAAGCCAACGA 57.955 37.500 0.00 0.00 0.00 3.85
726 1023 6.737254 TTCTCCTATAAAGAAAAGCCAACG 57.263 37.500 0.00 0.00 30.00 4.10
745 1042 1.149148 GGTGCTCACGGAGTTTTCTC 58.851 55.000 3.38 0.00 41.61 2.87
746 1043 0.600255 CGGTGCTCACGGAGTTTTCT 60.600 55.000 1.90 0.00 41.61 2.52
747 1044 1.860078 CGGTGCTCACGGAGTTTTC 59.140 57.895 1.90 0.00 41.61 2.29
748 1045 2.251642 GCGGTGCTCACGGAGTTTT 61.252 57.895 11.07 0.00 41.61 2.43
749 1046 2.665185 GCGGTGCTCACGGAGTTT 60.665 61.111 11.07 0.00 41.61 2.66
773 1070 2.165301 CGAATTCGAGTCCCGGCAC 61.165 63.158 23.29 0.00 43.02 5.01
774 1071 2.183300 CGAATTCGAGTCCCGGCA 59.817 61.111 23.29 0.00 43.02 5.69
775 1072 2.585247 CCGAATTCGAGTCCCGGC 60.585 66.667 28.76 0.00 43.02 6.13
776 1073 2.106332 CCCGAATTCGAGTCCCGG 59.894 66.667 28.76 15.89 43.02 5.73
777 1074 1.518572 CACCCGAATTCGAGTCCCG 60.519 63.158 28.76 10.72 43.02 5.14
778 1075 1.153429 CCACCCGAATTCGAGTCCC 60.153 63.158 28.76 0.00 43.02 4.46
779 1076 1.153429 CCCACCCGAATTCGAGTCC 60.153 63.158 28.76 0.00 43.02 3.85
780 1077 1.814169 GCCCACCCGAATTCGAGTC 60.814 63.158 28.76 6.67 43.02 3.36
781 1078 2.267961 GCCCACCCGAATTCGAGT 59.732 61.111 28.76 19.65 43.02 4.18
782 1079 1.815421 CAGCCCACCCGAATTCGAG 60.815 63.158 28.76 18.89 43.02 4.04
783 1080 2.267642 CAGCCCACCCGAATTCGA 59.732 61.111 28.76 0.00 43.02 3.71
784 1081 2.824041 CCAGCCCACCCGAATTCG 60.824 66.667 20.92 20.92 39.44 3.34
785 1082 3.140814 GCCAGCCCACCCGAATTC 61.141 66.667 0.00 0.00 0.00 2.17
786 1083 3.944250 CTGCCAGCCCACCCGAATT 62.944 63.158 0.00 0.00 0.00 2.17
787 1084 4.431131 CTGCCAGCCCACCCGAAT 62.431 66.667 0.00 0.00 0.00 3.34
793 1090 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
794 1091 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
795 1092 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
796 1093 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
797 1094 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
798 1095 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
803 1100 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
804 1101 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
818 1115 2.819595 CGTCGACCCATTGGCTGG 60.820 66.667 10.58 0.00 45.51 4.85
819 1116 3.499737 GCGTCGACCCATTGGCTG 61.500 66.667 10.58 0.00 33.59 4.85
820 1117 4.778143 GGCGTCGACCCATTGGCT 62.778 66.667 10.58 0.00 33.59 4.75
841 1138 4.649705 TGGTCGGGCCCAAGAGGA 62.650 66.667 24.92 7.53 38.24 3.71
842 1139 4.410400 GTGGTCGGGCCCAAGAGG 62.410 72.222 24.92 4.63 35.92 3.69
843 1140 3.316573 GAGTGGTCGGGCCCAAGAG 62.317 68.421 24.92 5.09 35.92 2.85
844 1141 3.319198 GAGTGGTCGGGCCCAAGA 61.319 66.667 24.92 9.31 35.92 3.02
845 1142 4.760047 CGAGTGGTCGGGCCCAAG 62.760 72.222 24.92 6.44 42.87 3.61
853 1150 0.966920 ATATAAGGCCCGAGTGGTCG 59.033 55.000 0.00 0.00 46.38 4.79
854 1151 4.566987 CTTTATATAAGGCCCGAGTGGTC 58.433 47.826 0.00 0.00 39.93 4.02
855 1152 3.244457 GCTTTATATAAGGCCCGAGTGGT 60.244 47.826 16.62 0.00 32.80 4.16
856 1153 3.335579 GCTTTATATAAGGCCCGAGTGG 58.664 50.000 16.62 0.00 32.80 4.00
926 1225 4.235079 TCTGAAGGGAAGAGAGAGAGAG 57.765 50.000 0.00 0.00 0.00 3.20
927 1226 4.290985 TCTTCTGAAGGGAAGAGAGAGAGA 59.709 45.833 16.83 0.00 44.37 3.10
928 1227 4.599041 TCTTCTGAAGGGAAGAGAGAGAG 58.401 47.826 16.83 0.00 44.37 3.20
929 1228 4.666412 TCTTCTGAAGGGAAGAGAGAGA 57.334 45.455 16.83 0.00 44.37 3.10
1423 1726 2.185350 CTGGACGCCAGCGAAGAT 59.815 61.111 20.32 0.00 45.13 2.40
1431 1734 3.311110 GTGGAGACCTGGACGCCA 61.311 66.667 16.54 16.54 35.08 5.69
1541 1844 1.299976 GCCCTCGTTGTCCTGGAAT 59.700 57.895 0.00 0.00 0.00 3.01
1739 2042 4.408821 TCGTGGCCTGGATGGTGC 62.409 66.667 3.32 0.00 38.35 5.01
1745 2048 3.936203 GTGGTGTCGTGGCCTGGA 61.936 66.667 3.32 0.00 0.00 3.86
1998 2301 0.863799 CGGCATGGTTGATCGATCAG 59.136 55.000 25.95 16.14 38.19 2.90
2135 2438 0.036388 GGCGTCCTCACCATTCTTGA 60.036 55.000 0.00 0.00 0.00 3.02
2137 2440 1.079127 CGGCGTCCTCACCATTCTT 60.079 57.895 0.00 0.00 0.00 2.52
2138 2441 1.949847 CTCGGCGTCCTCACCATTCT 61.950 60.000 6.85 0.00 0.00 2.40
2140 2443 2.579201 CTCGGCGTCCTCACCATT 59.421 61.111 6.85 0.00 0.00 3.16
2142 2445 4.671590 TCCTCGGCGTCCTCACCA 62.672 66.667 6.85 0.00 0.00 4.17
2144 2447 2.637383 AACTCCTCGGCGTCCTCAC 61.637 63.158 6.85 0.00 0.00 3.51
2311 2614 1.546961 ACCGAACTCTCCATCTCGTT 58.453 50.000 0.00 0.00 0.00 3.85
2318 2621 1.255667 GGGTGCTACCGAACTCTCCA 61.256 60.000 0.00 0.00 39.83 3.86
2421 2724 2.427753 GGGATGATCTCGTGGCCC 59.572 66.667 0.00 0.00 0.00 5.80
2511 2814 1.798079 GCGTTACAGACCTCGATGTCC 60.798 57.143 16.07 1.37 35.83 4.02
2785 3110 3.797353 CACCCTCACCCCCATCGG 61.797 72.222 0.00 0.00 0.00 4.18
2786 3111 2.687200 TCACCCTCACCCCCATCG 60.687 66.667 0.00 0.00 0.00 3.84
2806 3133 3.181495 CCACTCCTTCACTAGCTAACGAG 60.181 52.174 0.00 0.00 0.00 4.18
2858 3185 1.071502 CAGTACGCCACGCAATATTCG 60.072 52.381 5.96 5.96 0.00 3.34
2923 3254 2.971660 TCCAACTGACGACACTTTCA 57.028 45.000 0.00 0.00 0.00 2.69
2936 3267 6.282199 AGTAGACACGAAATGTATCCAACT 57.718 37.500 0.00 0.00 43.56 3.16
2975 3306 2.898729 AATGGCTCGACGATCTCAAT 57.101 45.000 0.00 0.00 0.00 2.57
3015 3346 3.058293 GGTTCGACATTCTTTCACATGCA 60.058 43.478 0.00 0.00 0.00 3.96
3021 3352 4.862574 CGTAGATGGTTCGACATTCTTTCA 59.137 41.667 0.00 0.00 0.00 2.69
3184 4849 0.954452 CTGAAGCACCTCAACAACCC 59.046 55.000 0.00 0.00 0.00 4.11
3212 4877 1.327690 ATCAGCATTGCAAGCCCCAG 61.328 55.000 11.91 0.63 0.00 4.45
3222 4887 3.997681 TGCATGAACCAAAATCAGCATTG 59.002 39.130 0.00 0.00 31.04 2.82
3253 4918 3.319122 CAGGGAAGCTAACAAAAGCAAGT 59.681 43.478 0.00 0.00 45.30 3.16
3320 4985 4.201910 TGTTTGTGAACAGAGCAAGTAAGC 60.202 41.667 0.00 0.00 40.71 3.09
3354 5181 7.384124 CGCATGTAGTCTATATTGAAATACGC 58.616 38.462 0.00 0.00 0.00 4.42
3355 5182 7.753580 TCCGCATGTAGTCTATATTGAAATACG 59.246 37.037 0.00 0.00 0.00 3.06
3356 5183 8.861101 GTCCGCATGTAGTCTATATTGAAATAC 58.139 37.037 0.00 0.00 0.00 1.89
3392 5220 4.343811 CACGGTTTAGTGTGTTTGTTCA 57.656 40.909 0.00 0.00 37.35 3.18
3633 7265 3.334583 TTGGCTTGCTAGACTAGGTTG 57.665 47.619 11.48 0.00 0.00 3.77
3634 7266 4.576330 ATTTGGCTTGCTAGACTAGGTT 57.424 40.909 11.48 0.00 0.00 3.50
3635 7267 5.693769 TTATTTGGCTTGCTAGACTAGGT 57.306 39.130 11.48 0.00 0.00 3.08
3636 7268 7.283127 TGAATTTATTTGGCTTGCTAGACTAGG 59.717 37.037 11.48 0.00 0.00 3.02
3637 7269 8.213518 TGAATTTATTTGGCTTGCTAGACTAG 57.786 34.615 1.86 5.03 0.00 2.57
3638 7270 8.458843 GTTGAATTTATTTGGCTTGCTAGACTA 58.541 33.333 1.86 0.00 0.00 2.59
3689 7326 9.590088 GTTTAATTTAGTCACTTAACTCCAACG 57.410 33.333 0.00 0.00 0.00 4.10
3717 7354 8.462016 GCCAATAATCACTAAACTTGTTGAGAT 58.538 33.333 4.97 0.00 0.00 2.75
3726 7363 3.886123 AGGCGCCAATAATCACTAAACT 58.114 40.909 31.54 0.00 0.00 2.66
3741 7378 0.728129 GCAACTTACGAAAAGGCGCC 60.728 55.000 21.89 21.89 33.86 6.53


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

AutoCloner maintained by Alex Coulton.