Multiple sequence alignment - TraesCS5A01G086500

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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 TraesCS5A01G086500 chr5A 100.000 5835 0 0 1691 7525 115093217 115099051 0.000000e+00 10776.0
1 TraesCS5A01G086500 chr5A 100.000 1341 0 0 1 1341 115091527 115092867 0.000000e+00 2477.0
2 TraesCS5A01G086500 chr5A 95.253 653 31 0 1 653 115086819 115087471 0.000000e+00 1035.0
3 TraesCS5A01G086500 chr5A 96.596 617 21 0 6 622 115083325 115083941 0.000000e+00 1024.0
4 TraesCS5A01G086500 chr5A 93.488 215 8 2 768 976 115081156 115081370 1.580000e-81 315.0
5 TraesCS5A01G086500 chr5D 94.443 5777 145 64 1850 7506 112242357 112248077 0.000000e+00 8728.0
6 TraesCS5A01G086500 chr5D 89.255 577 28 17 797 1341 112241529 112242103 0.000000e+00 691.0
7 TraesCS5A01G086500 chr5B 95.634 5428 135 37 1850 7202 121247727 121253127 0.000000e+00 8617.0
8 TraesCS5A01G086500 chr5B 89.009 555 32 13 812 1341 121246588 121247138 0.000000e+00 660.0
9 TraesCS5A01G086500 chr5B 81.503 346 15 15 7202 7506 121255146 121255483 9.760000e-59 239.0
10 TraesCS5A01G086500 chr7A 92.615 650 40 5 6 649 548311919 548312566 0.000000e+00 928.0
11 TraesCS5A01G086500 chrUn 99.274 413 3 0 4675 5087 477434327 477433915 0.000000e+00 747.0
12 TraesCS5A01G086500 chr2B 87.681 552 46 14 89 624 794832316 794831771 2.310000e-174 623.0
13 TraesCS5A01G086500 chr2B 88.235 272 30 1 3590 3861 18809334 18809065 2.620000e-84 324.0
14 TraesCS5A01G086500 chr6B 88.852 305 27 5 89 387 356629644 356629947 1.190000e-97 368.0
15 TraesCS5A01G086500 chr2A 94.043 235 10 2 109 339 772055656 772055890 3.340000e-93 353.0
16 TraesCS5A01G086500 chr2A 94.043 235 10 2 109 339 772095246 772095480 3.340000e-93 353.0
17 TraesCS5A01G086500 chr2A 93.617 235 11 2 109 339 772135346 772135580 1.550000e-91 348.0
18 TraesCS5A01G086500 chr2A 93.277 238 12 2 106 339 772178066 772178303 1.550000e-91 348.0
19 TraesCS5A01G086500 chr3A 89.015 264 25 3 3597 3859 91026755 91026495 2.620000e-84 324.0
20 TraesCS5A01G086500 chr3A 88.390 267 29 2 3595 3861 706867801 706868065 3.390000e-83 320.0
21 TraesCS5A01G086500 chr3D 87.857 280 26 6 3587 3863 532171824 532172098 9.420000e-84 322.0
22 TraesCS5A01G086500 chr3B 88.636 264 28 2 3598 3861 29495453 29495714 3.390000e-83 320.0
23 TraesCS5A01G086500 chr1A 88.235 272 26 3 3593 3861 434422672 434422940 3.390000e-83 320.0
24 TraesCS5A01G086500 chr4A 87.823 271 29 4 3597 3866 165816545 165816278 1.580000e-81 315.0
25 TraesCS5A01G086500 chr1B 90.116 172 15 1 3344 3513 583163765 583163594 9.830000e-54 222.0
26 TraesCS5A01G086500 chr1B 87.387 111 12 1 3405 3513 583204552 583204442 7.930000e-25 126.0
27 TraesCS5A01G086500 chr7D 100.000 28 0 0 729 756 588032526 588032553 1.400000e-02 52.8


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 TraesCS5A01G086500 chr5A 115091527 115099051 7524 False 6626.500000 10776 100.000000 1 7525 2 chr5A.!!$F2 7524
1 TraesCS5A01G086500 chr5A 115081156 115087471 6315 False 791.333333 1035 95.112333 1 976 3 chr5A.!!$F1 975
2 TraesCS5A01G086500 chr5D 112241529 112248077 6548 False 4709.500000 8728 91.849000 797 7506 2 chr5D.!!$F1 6709
3 TraesCS5A01G086500 chr5B 121246588 121255483 8895 False 3172.000000 8617 88.715333 812 7506 3 chr5B.!!$F1 6694
4 TraesCS5A01G086500 chr7A 548311919 548312566 647 False 928.000000 928 92.615000 6 649 1 chr7A.!!$F1 643
5 TraesCS5A01G086500 chr2B 794831771 794832316 545 True 623.000000 623 87.681000 89 624 1 chr2B.!!$R2 535

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
754 2941 0.102481 ACGCACGGCCATTCTACTAG 59.898 55.000 2.24 0.00 0.00 2.57 F
914 3101 1.000993 AGGATCACCGCAGAGTCCT 59.999 57.895 0.00 0.00 41.83 3.85 F
1337 3740 1.146263 CGGGGTATCCTTGGACTGC 59.854 63.158 0.00 0.00 0.00 4.40 F
2172 4733 1.134431 TCTGAACTGTGCTGTGCTGAA 60.134 47.619 0.00 0.00 0.00 3.02 F
3073 5641 3.620374 GCATCACAAGTGAGGAGTACATG 59.380 47.826 17.88 5.59 43.36 3.21 F
3993 6591 1.674322 CCGTGGCGATTTCCAAGGT 60.674 57.895 6.60 0.00 46.44 3.50 F
4244 6842 1.466167 CTGCGGTGGATCAAGTCAAAG 59.534 52.381 0.00 0.00 0.00 2.77 F
5281 7879 3.322369 TGGCAGTGTTGTACATTACTCG 58.678 45.455 8.98 7.09 0.00 4.18 F
6016 9874 0.251653 ACTCCACGAGCCTCACCTTA 60.252 55.000 0.00 0.00 32.04 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 4129 0.031585 TCCGTCGGCAAGATAATCCG 59.968 55.000 6.34 0.00 44.16 4.18 R
1732 4135 0.251916 TGGATTTCCGTCGGCAAGAT 59.748 50.000 6.34 0.00 39.43 2.40 R
2234 4795 2.415893 CCTGCTTTTGCCTAATTCACCG 60.416 50.000 0.00 0.00 46.87 4.94 R
3833 6430 5.399991 TCCCTCCATTCCGTAATATAGTGT 58.600 41.667 0.00 0.00 0.00 3.55 R
4207 6805 2.416202 CGCAGTTCATCAGTGTAATGCA 59.584 45.455 7.89 0.00 43.81 3.96 R
5170 7768 0.677731 GCATGGCACCTTGCTCACTA 60.678 55.000 17.72 0.00 44.28 2.74 R
6016 9874 0.111253 CTGGCTCCAAGGGTTTGTCT 59.889 55.000 0.00 0.00 32.21 3.41 R
6306 10170 0.031917 TGATTAGGGGCGGTACCTCA 60.032 55.000 10.90 0.93 44.17 3.86 R
7445 13941 0.036306 GTTGTACCACAGGTCCTGGG 59.964 60.000 23.06 19.25 37.09 4.45 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
28 2193 8.485976 AAATCTCTACTCTTAATTGCACAGTC 57.514 34.615 0.00 0.00 0.00 3.51
29 2194 6.842437 TCTCTACTCTTAATTGCACAGTCT 57.158 37.500 0.00 0.00 0.00 3.24
49 2214 0.661187 GTACGTCGTTGGTTCGCTCA 60.661 55.000 1.78 0.00 0.00 4.26
95 2260 0.251519 ACGTACGTCTCCCCTTCCTT 60.252 55.000 16.72 0.00 0.00 3.36
178 2347 2.639839 CCCCACCTCTTTCTTTCTCTCA 59.360 50.000 0.00 0.00 0.00 3.27
257 2428 3.515502 TGATCAGGGTTTCTCAATCGAGT 59.484 43.478 0.00 0.00 40.44 4.18
287 2461 2.775890 GGATGCACATCTATCTGTGGG 58.224 52.381 10.30 0.00 45.34 4.61
470 2644 1.227823 CGGGCAGGTTGTGTTCAGA 60.228 57.895 0.00 0.00 0.00 3.27
475 2649 1.299541 CAGGTTGTGTTCAGAAGCGT 58.700 50.000 6.31 0.00 0.00 5.07
560 2747 1.575447 GGAACCCCTTCATGGCCTCT 61.575 60.000 3.32 0.00 0.00 3.69
624 2811 2.099831 GCGACAGGTACTCCGACG 59.900 66.667 0.00 0.00 34.60 5.12
625 2812 2.393768 GCGACAGGTACTCCGACGA 61.394 63.158 0.00 0.00 34.60 4.20
626 2813 1.423056 CGACAGGTACTCCGACGAC 59.577 63.158 0.00 0.00 34.60 4.34
627 2814 1.018226 CGACAGGTACTCCGACGACT 61.018 60.000 0.00 0.00 34.60 4.18
628 2815 0.726256 GACAGGTACTCCGACGACTC 59.274 60.000 0.00 0.00 34.60 3.36
629 2816 0.676151 ACAGGTACTCCGACGACTCC 60.676 60.000 0.00 0.00 34.60 3.85
630 2817 0.392729 CAGGTACTCCGACGACTCCT 60.393 60.000 0.00 0.00 34.60 3.69
631 2818 0.107752 AGGTACTCCGACGACTCCTC 60.108 60.000 0.00 0.00 39.05 3.71
632 2819 0.392193 GGTACTCCGACGACTCCTCA 60.392 60.000 0.00 0.00 0.00 3.86
633 2820 0.726256 GTACTCCGACGACTCCTCAC 59.274 60.000 0.00 0.00 0.00 3.51
634 2821 0.392193 TACTCCGACGACTCCTCACC 60.392 60.000 0.00 0.00 0.00 4.02
635 2822 2.360852 TCCGACGACTCCTCACCC 60.361 66.667 0.00 0.00 0.00 4.61
636 2823 2.361357 CCGACGACTCCTCACCCT 60.361 66.667 0.00 0.00 0.00 4.34
637 2824 2.701780 CCGACGACTCCTCACCCTG 61.702 68.421 0.00 0.00 0.00 4.45
638 2825 2.574399 GACGACTCCTCACCCTGC 59.426 66.667 0.00 0.00 0.00 4.85
639 2826 2.997897 ACGACTCCTCACCCTGCC 60.998 66.667 0.00 0.00 0.00 4.85
640 2827 2.997315 CGACTCCTCACCCTGCCA 60.997 66.667 0.00 0.00 0.00 4.92
641 2828 2.665603 GACTCCTCACCCTGCCAC 59.334 66.667 0.00 0.00 0.00 5.01
642 2829 2.930562 ACTCCTCACCCTGCCACC 60.931 66.667 0.00 0.00 0.00 4.61
643 2830 4.087892 CTCCTCACCCTGCCACCG 62.088 72.222 0.00 0.00 0.00 4.94
644 2831 4.954118 TCCTCACCCTGCCACCGT 62.954 66.667 0.00 0.00 0.00 4.83
645 2832 4.704833 CCTCACCCTGCCACCGTG 62.705 72.222 0.00 0.00 0.00 4.94
646 2833 3.625897 CTCACCCTGCCACCGTGA 61.626 66.667 0.00 0.00 35.34 4.35
647 2834 3.883744 CTCACCCTGCCACCGTGAC 62.884 68.421 0.00 0.00 33.18 3.67
678 2865 2.885113 CGCCATCGTGACTCCTCA 59.115 61.111 0.00 0.00 0.00 3.86
679 2866 1.517257 CGCCATCGTGACTCCTCAC 60.517 63.158 0.00 0.00 43.17 3.51
680 2867 1.153549 GCCATCGTGACTCCTCACC 60.154 63.158 0.00 0.00 43.64 4.02
681 2868 1.517832 CCATCGTGACTCCTCACCC 59.482 63.158 0.00 0.00 43.64 4.61
682 2869 1.517832 CATCGTGACTCCTCACCCC 59.482 63.158 0.00 0.00 43.64 4.95
683 2870 2.052690 ATCGTGACTCCTCACCCCG 61.053 63.158 0.00 0.00 43.64 5.73
684 2871 4.436998 CGTGACTCCTCACCCCGC 62.437 72.222 0.00 0.00 43.64 6.13
685 2872 4.083862 GTGACTCCTCACCCCGCC 62.084 72.222 0.00 0.00 41.06 6.13
686 2873 4.631740 TGACTCCTCACCCCGCCA 62.632 66.667 0.00 0.00 0.00 5.69
687 2874 4.083862 GACTCCTCACCCCGCCAC 62.084 72.222 0.00 0.00 0.00 5.01
698 2885 4.436998 CCGCCACCGTGACTCCTC 62.437 72.222 0.00 0.00 0.00 3.71
699 2886 3.680786 CGCCACCGTGACTCCTCA 61.681 66.667 0.00 0.00 0.00 3.86
700 2887 2.048127 GCCACCGTGACTCCTCAC 60.048 66.667 0.00 0.00 43.17 3.51
701 2888 2.657237 CCACCGTGACTCCTCACC 59.343 66.667 0.00 0.00 43.64 4.02
702 2889 2.657237 CACCGTGACTCCTCACCC 59.343 66.667 0.00 0.00 43.64 4.61
703 2890 2.603776 ACCGTGACTCCTCACCCC 60.604 66.667 0.00 0.00 43.64 4.95
704 2891 3.760035 CCGTGACTCCTCACCCCG 61.760 72.222 0.00 0.00 43.64 5.73
705 2892 2.989824 CGTGACTCCTCACCCCGT 60.990 66.667 0.00 0.00 43.64 5.28
706 2893 2.971452 GTGACTCCTCACCCCGTC 59.029 66.667 0.00 0.00 41.06 4.79
707 2894 1.906824 GTGACTCCTCACCCCGTCA 60.907 63.158 0.00 0.00 41.06 4.35
708 2895 1.078528 TGACTCCTCACCCCGTCAT 59.921 57.895 0.00 0.00 32.00 3.06
709 2896 0.970937 TGACTCCTCACCCCGTCATC 60.971 60.000 0.00 0.00 32.00 2.92
710 2897 0.970937 GACTCCTCACCCCGTCATCA 60.971 60.000 0.00 0.00 0.00 3.07
711 2898 0.544357 ACTCCTCACCCCGTCATCAA 60.544 55.000 0.00 0.00 0.00 2.57
712 2899 0.613260 CTCCTCACCCCGTCATCAAA 59.387 55.000 0.00 0.00 0.00 2.69
713 2900 1.003118 CTCCTCACCCCGTCATCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
714 2901 1.422024 TCCTCACCCCGTCATCAAAAA 59.578 47.619 0.00 0.00 0.00 1.94
715 2902 2.041081 TCCTCACCCCGTCATCAAAAAT 59.959 45.455 0.00 0.00 0.00 1.82
716 2903 3.264706 TCCTCACCCCGTCATCAAAAATA 59.735 43.478 0.00 0.00 0.00 1.40
717 2904 4.080015 TCCTCACCCCGTCATCAAAAATAT 60.080 41.667 0.00 0.00 0.00 1.28
718 2905 4.644685 CCTCACCCCGTCATCAAAAATATT 59.355 41.667 0.00 0.00 0.00 1.28
719 2906 5.127031 CCTCACCCCGTCATCAAAAATATTT 59.873 40.000 0.00 0.00 0.00 1.40
720 2907 6.202516 TCACCCCGTCATCAAAAATATTTC 57.797 37.500 0.10 0.00 0.00 2.17
721 2908 5.712446 TCACCCCGTCATCAAAAATATTTCA 59.288 36.000 0.10 0.00 0.00 2.69
722 2909 6.209589 TCACCCCGTCATCAAAAATATTTCAA 59.790 34.615 0.10 0.00 0.00 2.69
723 2910 6.870965 CACCCCGTCATCAAAAATATTTCAAA 59.129 34.615 0.10 0.00 0.00 2.69
724 2911 7.386299 CACCCCGTCATCAAAAATATTTCAAAA 59.614 33.333 0.10 0.00 0.00 2.44
725 2912 8.100164 ACCCCGTCATCAAAAATATTTCAAAAT 58.900 29.630 0.10 0.00 0.00 1.82
726 2913 8.603181 CCCCGTCATCAAAAATATTTCAAAATC 58.397 33.333 0.10 0.00 0.00 2.17
727 2914 9.369904 CCCGTCATCAAAAATATTTCAAAATCT 57.630 29.630 0.10 0.00 0.00 2.40
738 2925 7.740519 ATATTTCAAAATCTTGTAGCAACGC 57.259 32.000 0.00 0.00 33.94 4.84
739 2926 4.560136 TTCAAAATCTTGTAGCAACGCA 57.440 36.364 0.00 0.00 33.94 5.24
740 2927 3.884169 TCAAAATCTTGTAGCAACGCAC 58.116 40.909 0.00 0.00 33.94 5.34
741 2928 2.594529 AAATCTTGTAGCAACGCACG 57.405 45.000 0.00 0.00 0.00 5.34
742 2929 0.796312 AATCTTGTAGCAACGCACGG 59.204 50.000 0.00 0.00 0.00 4.94
743 2930 1.635663 ATCTTGTAGCAACGCACGGC 61.636 55.000 0.00 0.00 0.00 5.68
744 2931 3.308878 CTTGTAGCAACGCACGGCC 62.309 63.158 0.00 0.00 0.00 6.13
745 2932 4.610714 TGTAGCAACGCACGGCCA 62.611 61.111 2.24 0.00 0.00 5.36
746 2933 3.124921 GTAGCAACGCACGGCCAT 61.125 61.111 2.24 0.00 0.00 4.40
747 2934 2.359354 TAGCAACGCACGGCCATT 60.359 55.556 2.24 0.00 0.00 3.16
748 2935 2.395360 TAGCAACGCACGGCCATTC 61.395 57.895 2.24 0.00 0.00 2.67
749 2936 2.796483 TAGCAACGCACGGCCATTCT 62.796 55.000 2.24 0.00 0.00 2.40
750 2937 2.395360 GCAACGCACGGCCATTCTA 61.395 57.895 2.24 0.00 0.00 2.10
751 2938 1.423845 CAACGCACGGCCATTCTAC 59.576 57.895 2.24 0.00 0.00 2.59
752 2939 1.019278 CAACGCACGGCCATTCTACT 61.019 55.000 2.24 0.00 0.00 2.57
753 2940 0.533491 AACGCACGGCCATTCTACTA 59.467 50.000 2.24 0.00 0.00 1.82
754 2941 0.102481 ACGCACGGCCATTCTACTAG 59.898 55.000 2.24 0.00 0.00 2.57
755 2942 0.102481 CGCACGGCCATTCTACTAGT 59.898 55.000 2.24 0.00 0.00 2.57
756 2943 1.335810 CGCACGGCCATTCTACTAGTA 59.664 52.381 2.24 1.89 0.00 1.82
757 2944 2.030185 CGCACGGCCATTCTACTAGTAT 60.030 50.000 2.24 0.00 0.00 2.12
758 2945 3.318017 GCACGGCCATTCTACTAGTATG 58.682 50.000 2.24 0.00 0.00 2.39
759 2946 3.005472 GCACGGCCATTCTACTAGTATGA 59.995 47.826 2.24 0.78 0.00 2.15
760 2947 4.322049 GCACGGCCATTCTACTAGTATGAT 60.322 45.833 2.24 0.00 0.00 2.45
761 2948 5.784177 CACGGCCATTCTACTAGTATGATT 58.216 41.667 2.24 0.00 0.00 2.57
762 2949 6.571731 GCACGGCCATTCTACTAGTATGATTA 60.572 42.308 2.24 0.00 0.00 1.75
763 2950 6.807230 CACGGCCATTCTACTAGTATGATTAC 59.193 42.308 2.24 0.00 0.00 1.89
764 2951 6.720288 ACGGCCATTCTACTAGTATGATTACT 59.280 38.462 2.24 0.00 41.57 2.24
765 2952 7.886970 ACGGCCATTCTACTAGTATGATTACTA 59.113 37.037 2.24 0.00 39.42 1.82
794 2981 7.579589 TCAATCAAAATAAAACATGCTTCCG 57.420 32.000 0.00 0.00 0.00 4.30
795 2982 6.090628 TCAATCAAAATAAAACATGCTTCCGC 59.909 34.615 0.00 0.00 0.00 5.54
830 3017 3.982576 ACTTTGAACATGAACCGAACC 57.017 42.857 0.00 0.00 0.00 3.62
914 3101 1.000993 AGGATCACCGCAGAGTCCT 59.999 57.895 0.00 0.00 41.83 3.85
933 3125 1.481363 CTAGGGTCTCCGGGAAAAGAC 59.519 57.143 11.63 11.63 40.96 3.01
974 3168 3.100207 AGAAGACTCAGGAGAGGGAAG 57.900 52.381 2.79 0.00 46.44 3.46
1105 3498 1.298667 CGGGATCCCCTTCGTGTTT 59.701 57.895 25.73 0.00 42.67 2.83
1198 3591 5.103290 TCGCCGAAGATTATTAATTTGCC 57.897 39.130 0.00 0.00 0.00 4.52
1250 3648 4.927782 TGCTCACCAAAGGCGCGT 62.928 61.111 8.43 0.00 0.00 6.01
1272 3670 1.847818 TTGTTCTCGACCTTGTCACG 58.152 50.000 0.00 0.00 32.09 4.35
1323 3726 2.125350 GAGAAGCAGCTGACGGGG 60.125 66.667 20.43 0.00 0.00 5.73
1337 3740 1.146263 CGGGGTATCCTTGGACTGC 59.854 63.158 0.00 0.00 0.00 4.40
1714 4117 5.810080 AGGTGATTATCTAGGTAAGTGCC 57.190 43.478 1.28 3.41 0.00 5.01
1715 4118 5.468658 AGGTGATTATCTAGGTAAGTGCCT 58.531 41.667 1.28 5.49 42.43 4.75
1716 4119 5.905913 AGGTGATTATCTAGGTAAGTGCCTT 59.094 40.000 1.28 0.00 39.94 4.35
1717 4120 7.073854 AGGTGATTATCTAGGTAAGTGCCTTA 58.926 38.462 1.28 0.00 39.94 2.69
1718 4121 7.233757 AGGTGATTATCTAGGTAAGTGCCTTAG 59.766 40.741 1.28 0.00 39.94 2.18
1719 4122 7.015389 GGTGATTATCTAGGTAAGTGCCTTAGT 59.985 40.741 1.28 0.00 39.94 2.24
1720 4123 8.422566 GTGATTATCTAGGTAAGTGCCTTAGTT 58.577 37.037 1.28 0.00 39.94 2.24
1721 4124 8.989131 TGATTATCTAGGTAAGTGCCTTAGTTT 58.011 33.333 1.28 0.00 39.94 2.66
1722 4125 9.478768 GATTATCTAGGTAAGTGCCTTAGTTTC 57.521 37.037 1.28 0.00 39.94 2.78
1723 4126 6.869206 ATCTAGGTAAGTGCCTTAGTTTCA 57.131 37.500 0.00 0.00 39.94 2.69
1724 4127 6.675413 TCTAGGTAAGTGCCTTAGTTTCAA 57.325 37.500 0.00 0.00 39.94 2.69
1725 4128 7.253905 TCTAGGTAAGTGCCTTAGTTTCAAT 57.746 36.000 0.00 0.00 39.94 2.57
1726 4129 7.328737 TCTAGGTAAGTGCCTTAGTTTCAATC 58.671 38.462 0.00 0.00 39.94 2.67
1727 4130 4.935808 AGGTAAGTGCCTTAGTTTCAATCG 59.064 41.667 0.00 0.00 34.71 3.34
1728 4131 4.094442 GGTAAGTGCCTTAGTTTCAATCGG 59.906 45.833 0.00 0.00 0.00 4.18
1729 4132 3.695830 AGTGCCTTAGTTTCAATCGGA 57.304 42.857 0.00 0.00 0.00 4.55
1730 4133 4.222124 AGTGCCTTAGTTTCAATCGGAT 57.778 40.909 0.00 0.00 0.00 4.18
1731 4134 4.589908 AGTGCCTTAGTTTCAATCGGATT 58.410 39.130 0.00 0.00 0.00 3.01
1732 4135 5.741011 AGTGCCTTAGTTTCAATCGGATTA 58.259 37.500 2.35 0.00 0.00 1.75
1733 4136 6.357367 AGTGCCTTAGTTTCAATCGGATTAT 58.643 36.000 2.35 0.00 0.00 1.28
1734 4137 6.483640 AGTGCCTTAGTTTCAATCGGATTATC 59.516 38.462 2.35 0.00 0.00 1.75
1735 4138 6.483640 GTGCCTTAGTTTCAATCGGATTATCT 59.516 38.462 2.35 2.90 0.00 1.98
1736 4139 7.012421 GTGCCTTAGTTTCAATCGGATTATCTT 59.988 37.037 2.35 0.00 0.00 2.40
1737 4140 7.012327 TGCCTTAGTTTCAATCGGATTATCTTG 59.988 37.037 2.35 0.00 0.00 3.02
1738 4141 7.355778 CCTTAGTTTCAATCGGATTATCTTGC 58.644 38.462 2.35 0.00 0.00 4.01
1739 4142 5.757850 AGTTTCAATCGGATTATCTTGCC 57.242 39.130 2.35 0.00 0.00 4.52
1740 4143 4.273480 AGTTTCAATCGGATTATCTTGCCG 59.727 41.667 2.35 0.00 46.08 5.69
1745 4148 3.980583 GGATTATCTTGCCGACGGA 57.019 52.632 20.50 0.00 0.00 4.69
1746 4149 2.234300 GGATTATCTTGCCGACGGAA 57.766 50.000 20.50 3.25 0.00 4.30
1747 4150 2.557317 GGATTATCTTGCCGACGGAAA 58.443 47.619 20.50 13.68 0.00 3.13
1748 4151 3.139077 GGATTATCTTGCCGACGGAAAT 58.861 45.455 20.50 1.27 0.00 2.17
1749 4152 3.186613 GGATTATCTTGCCGACGGAAATC 59.813 47.826 20.50 14.21 0.00 2.17
1750 4153 2.234300 TATCTTGCCGACGGAAATCC 57.766 50.000 20.50 0.00 0.00 3.01
1817 4371 8.809066 TCATGGAAGTGATGAATTCTTTCAATT 58.191 29.630 18.15 18.15 44.70 2.32
1818 4372 8.869897 CATGGAAGTGATGAATTCTTTCAATTG 58.130 33.333 21.13 0.00 44.70 2.32
1819 4373 8.180706 TGGAAGTGATGAATTCTTTCAATTGA 57.819 30.769 21.13 3.38 44.70 2.57
1820 4374 8.809066 TGGAAGTGATGAATTCTTTCAATTGAT 58.191 29.630 21.13 0.00 44.70 2.57
1821 4375 9.084164 GGAAGTGATGAATTCTTTCAATTGATG 57.916 33.333 21.13 5.84 44.70 3.07
1822 4376 9.850628 GAAGTGATGAATTCTTTCAATTGATGA 57.149 29.630 21.13 8.17 44.70 2.92
1980 4541 6.298361 TCTGAGTGTTGGATTCTGATTCAAA 58.702 36.000 2.40 0.00 32.59 2.69
2067 4628 1.268625 CGTGCTGCATATACTACCGGA 59.731 52.381 9.46 0.00 0.00 5.14
2116 4677 3.456277 ACCCAAATCTCATCCTGAGGTAC 59.544 47.826 0.00 0.00 44.39 3.34
2172 4733 1.134431 TCTGAACTGTGCTGTGCTGAA 60.134 47.619 0.00 0.00 0.00 3.02
2234 4795 4.359706 CAGAAAAGGCTGGTTACACAAAC 58.640 43.478 0.00 0.00 37.36 2.93
2342 4903 6.215845 AGTTTACAGCCATGCTAACTTTTTG 58.784 36.000 0.00 0.00 36.40 2.44
2398 4959 5.163683 GCGTACTTACCTAGTGTTCATCTCA 60.164 44.000 0.00 0.00 37.73 3.27
2510 5071 5.240844 ACTTTGTACATTACTTGTTGCCTCC 59.759 40.000 0.00 0.00 39.87 4.30
2723 5287 4.085733 CACATGTGGAAGGTTGGGATTTA 58.914 43.478 18.51 0.00 0.00 1.40
2774 5338 4.804597 AGAAATAAGCCTAATTCACCCCC 58.195 43.478 0.00 0.00 0.00 5.40
3073 5641 3.620374 GCATCACAAGTGAGGAGTACATG 59.380 47.826 17.88 5.59 43.36 3.21
3516 6104 5.454966 CCCTGGGCACTAATTATTACCTTT 58.545 41.667 0.00 0.00 0.00 3.11
3828 6425 8.479313 ACAAAGTTTGACTTTTCAGAAAATCC 57.521 30.769 22.23 4.93 45.38 3.01
3833 6430 8.912988 AGTTTGACTTTTCAGAAAATCCATACA 58.087 29.630 20.23 10.28 31.71 2.29
3993 6591 1.674322 CCGTGGCGATTTCCAAGGT 60.674 57.895 6.60 0.00 46.44 3.50
4065 6663 6.015688 ACAGAATGCTTCTCAATTGACACAAT 60.016 34.615 3.38 0.00 42.53 2.71
4244 6842 1.466167 CTGCGGTGGATCAAGTCAAAG 59.534 52.381 0.00 0.00 0.00 2.77
4329 6927 4.350346 TCTGTTGTTTTCTTCACGCATTG 58.650 39.130 0.00 0.00 0.00 2.82
4437 7035 6.800072 AAAACATTGGTCCCAAACTCTTAA 57.200 33.333 2.32 0.00 39.55 1.85
5131 7729 5.880332 TGGTAGAATAAGTTTGCAGTGATCC 59.120 40.000 0.00 0.00 0.00 3.36
5281 7879 3.322369 TGGCAGTGTTGTACATTACTCG 58.678 45.455 8.98 7.09 0.00 4.18
5543 8141 9.106070 GATATACTTGTATCCAACCGAAAAAGT 57.894 33.333 0.00 0.00 0.00 2.66
5568 8166 6.014327 TGGTAATTTTGGACTTACGAGTACCT 60.014 38.462 0.00 0.00 35.73 3.08
5569 8167 6.312180 GGTAATTTTGGACTTACGAGTACCTG 59.688 42.308 0.00 0.00 35.73 4.00
6016 9874 0.251653 ACTCCACGAGCCTCACCTTA 60.252 55.000 0.00 0.00 32.04 2.69
6047 9905 0.605589 GGAGCCAGGCGTTGTAAGTT 60.606 55.000 5.55 0.00 0.00 2.66
6076 9934 1.757731 AGCTGGCTTTTGTGCACCA 60.758 52.632 15.69 0.00 34.04 4.17
6118 9981 3.759581 AGCGCATCTCCCAATTATCATT 58.240 40.909 11.47 0.00 0.00 2.57
6120 9983 3.503363 GCGCATCTCCCAATTATCATTCA 59.497 43.478 0.30 0.00 0.00 2.57
6237 10101 2.361438 GGTCCCGATACTCAACGAGAAT 59.639 50.000 0.00 0.00 33.32 2.40
6318 10182 4.564110 GGCCATGAGGTACCGCCC 62.564 72.222 13.56 3.01 38.26 6.13
6530 10920 2.217590 GCTGCTTGCAACTGAGGATCA 61.218 52.381 0.00 0.00 42.41 2.92
6594 10984 4.198530 TCATGTGGCATCGACATTACATT 58.801 39.130 0.00 0.00 31.46 2.71
6602 10992 6.486320 TGGCATCGACATTACATTCATTACAT 59.514 34.615 0.00 0.00 0.00 2.29
6691 11082 3.882888 TCTGAAAAGTTTCGCCAGTTCAT 59.117 39.130 10.46 0.00 40.01 2.57
6733 11126 9.787532 CTGTTAGGGTTTGTAATATGTTCATTG 57.212 33.333 0.00 0.00 0.00 2.82
6756 11149 5.188751 TGGACAAAGTTTTGGGTCTTCATTT 59.811 36.000 9.22 0.00 42.34 2.32
6759 11152 7.201609 GGACAAAGTTTTGGGTCTTCATTTTTC 60.202 37.037 9.22 0.00 42.34 2.29
6763 11156 8.862325 AAGTTTTGGGTCTTCATTTTTCTTTT 57.138 26.923 0.00 0.00 0.00 2.27
6819 11212 7.182817 TGGTGTAATAACTGTAGCTGAAGAT 57.817 36.000 0.00 0.00 0.00 2.40
6821 11214 7.093509 TGGTGTAATAACTGTAGCTGAAGATGA 60.094 37.037 0.00 0.00 0.00 2.92
6830 11223 3.051081 AGCTGAAGATGACTGTTGTCC 57.949 47.619 0.00 0.00 42.28 4.02
6852 11245 1.405933 GCAATCAATGGTGAAAGGGCC 60.406 52.381 0.00 0.00 37.30 5.80
6866 11280 1.452108 GGGCCTTTCATCAGACGGG 60.452 63.158 0.84 0.00 0.00 5.28
6982 11403 0.964358 GCATCAGGCTTGTGCTCCTT 60.964 55.000 12.32 0.00 40.25 3.36
6986 11407 3.376918 GGCTTGTGCTCCTTGGCC 61.377 66.667 0.00 0.00 39.59 5.36
7084 11510 2.513897 GGAACGGAAGGGCGATGG 60.514 66.667 0.00 0.00 0.00 3.51
7107 11533 2.986534 ATCATGGGAATGGGATGGAC 57.013 50.000 0.00 0.00 0.00 4.02
7133 11559 3.545481 CGTCATCGCTGTCGTGGC 61.545 66.667 0.00 0.00 36.96 5.01
7180 11616 4.918129 GCAGCCATGAATGCGCGG 62.918 66.667 8.83 0.00 31.87 6.46
7181 11617 3.511595 CAGCCATGAATGCGCGGT 61.512 61.111 8.83 0.00 0.00 5.68
7214 13670 0.114954 TAGGTGGTGGTAGGTTCGGT 59.885 55.000 0.00 0.00 0.00 4.69
7265 13731 2.040464 ATGGACGGATGGAGGCCT 60.040 61.111 3.86 3.86 0.00 5.19
7266 13732 2.388890 GATGGACGGATGGAGGCCTG 62.389 65.000 12.00 0.00 0.00 4.85
7267 13733 4.554036 GGACGGATGGAGGCCTGC 62.554 72.222 18.95 18.95 0.00 4.85
7268 13734 4.899239 GACGGATGGAGGCCTGCG 62.899 72.222 20.39 11.07 0.00 5.18
7306 13772 3.382832 CGTCCTTCGGTCCTGCCT 61.383 66.667 0.00 0.00 35.71 4.75
7307 13773 2.579738 GTCCTTCGGTCCTGCCTC 59.420 66.667 0.00 0.00 34.25 4.70
7349 13823 2.170273 GAAACGCGTTGTCCGAGC 59.830 61.111 27.34 5.53 40.31 5.03
7412 13886 0.236187 TGAAACGTTTGAATCGCCCG 59.764 50.000 20.10 0.00 0.00 6.13
7413 13887 0.236449 GAAACGTTTGAATCGCCCGT 59.764 50.000 20.10 0.00 0.00 5.28
7414 13888 0.664224 AAACGTTTGAATCGCCCGTT 59.336 45.000 13.81 0.00 42.86 4.44
7415 13889 0.664224 AACGTTTGAATCGCCCGTTT 59.336 45.000 0.00 0.00 38.46 3.60
7416 13890 0.040781 ACGTTTGAATCGCCCGTTTG 60.041 50.000 0.00 0.00 0.00 2.93
7417 13891 0.727793 CGTTTGAATCGCCCGTTTGG 60.728 55.000 0.00 0.00 37.09 3.28
7448 13944 3.245087 TGGAATTCCAGTTCGATTTCCCA 60.245 43.478 23.63 0.00 42.01 4.37
7452 13948 1.278127 TCCAGTTCGATTTCCCAGGAC 59.722 52.381 0.00 0.00 0.00 3.85
7479 13975 4.395854 TGGTACAACATGATGCATCTTCAC 59.604 41.667 26.32 13.76 31.92 3.18
7483 13979 5.224888 ACAACATGATGCATCTTCACAAAC 58.775 37.500 26.32 0.00 0.00 2.93
7491 13987 3.004629 TGCATCTTCACAAACTTCGCAAT 59.995 39.130 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.587772 GACTGTGCAATTAAGAGTAGAGATTTA 57.412 33.333 0.00 0.00 0.00 1.40
15 2180 3.671459 CGACGTACAGACTGTGCAATTAA 59.329 43.478 21.45 0.00 32.27 1.40
28 2193 0.662374 AGCGAACCAACGACGTACAG 60.662 55.000 0.00 0.00 35.09 2.74
29 2194 0.661187 GAGCGAACCAACGACGTACA 60.661 55.000 0.00 0.00 35.09 2.90
124 2289 2.031012 CGCAGCTGGTGGAGAACA 59.969 61.111 17.12 0.00 0.00 3.18
178 2347 5.297278 GCATCGATCTAGGAATCCTATACGT 59.703 44.000 9.80 0.00 35.36 3.57
287 2461 1.197721 CCATTGTTGCGGAGAAGTCAC 59.802 52.381 0.00 0.00 0.00 3.67
457 2631 1.583054 GACGCTTCTGAACACAACCT 58.417 50.000 0.00 0.00 0.00 3.50
560 2747 2.168521 GTCGGAGGAATCCTTCATGTCA 59.831 50.000 8.55 0.00 31.76 3.58
624 2811 2.665603 GTGGCAGGGTGAGGAGTC 59.334 66.667 0.00 0.00 0.00 3.36
625 2812 2.930562 GGTGGCAGGGTGAGGAGT 60.931 66.667 0.00 0.00 0.00 3.85
626 2813 4.087892 CGGTGGCAGGGTGAGGAG 62.088 72.222 0.00 0.00 0.00 3.69
627 2814 4.954118 ACGGTGGCAGGGTGAGGA 62.954 66.667 0.00 0.00 0.00 3.71
628 2815 4.704833 CACGGTGGCAGGGTGAGG 62.705 72.222 11.34 0.00 33.58 3.86
629 2816 3.625897 TCACGGTGGCAGGGTGAG 61.626 66.667 14.53 0.00 35.89 3.51
630 2817 3.936203 GTCACGGTGGCAGGGTGA 61.936 66.667 14.53 14.53 38.29 4.02
661 2848 1.517257 GTGAGGAGTCACGATGGCG 60.517 63.158 0.00 0.00 43.75 5.69
662 2849 4.504132 GTGAGGAGTCACGATGGC 57.496 61.111 0.00 0.00 43.75 4.40
669 2856 4.631740 TGGCGGGGTGAGGAGTCA 62.632 66.667 0.00 0.00 0.00 3.41
670 2857 4.083862 GTGGCGGGGTGAGGAGTC 62.084 72.222 0.00 0.00 0.00 3.36
681 2868 4.436998 GAGGAGTCACGGTGGCGG 62.437 72.222 7.14 0.00 0.00 6.13
682 2869 3.680786 TGAGGAGTCACGGTGGCG 61.681 66.667 7.14 0.00 0.00 5.69
683 2870 2.048127 GTGAGGAGTCACGGTGGC 60.048 66.667 4.16 4.16 43.75 5.01
690 2877 0.970937 GATGACGGGGTGAGGAGTCA 60.971 60.000 0.00 0.00 45.93 3.41
691 2878 0.970937 TGATGACGGGGTGAGGAGTC 60.971 60.000 0.00 0.00 0.00 3.36
692 2879 0.544357 TTGATGACGGGGTGAGGAGT 60.544 55.000 0.00 0.00 0.00 3.85
693 2880 0.613260 TTTGATGACGGGGTGAGGAG 59.387 55.000 0.00 0.00 0.00 3.69
694 2881 1.060729 TTTTGATGACGGGGTGAGGA 58.939 50.000 0.00 0.00 0.00 3.71
695 2882 1.904287 TTTTTGATGACGGGGTGAGG 58.096 50.000 0.00 0.00 0.00 3.86
696 2883 5.835113 AATATTTTTGATGACGGGGTGAG 57.165 39.130 0.00 0.00 0.00 3.51
697 2884 5.712446 TGAAATATTTTTGATGACGGGGTGA 59.288 36.000 1.43 0.00 0.00 4.02
698 2885 5.960113 TGAAATATTTTTGATGACGGGGTG 58.040 37.500 1.43 0.00 0.00 4.61
699 2886 6.597832 TTGAAATATTTTTGATGACGGGGT 57.402 33.333 1.43 0.00 0.00 4.95
700 2887 7.897575 TTTTGAAATATTTTTGATGACGGGG 57.102 32.000 1.43 0.00 0.00 5.73
701 2888 9.369904 AGATTTTGAAATATTTTTGATGACGGG 57.630 29.630 1.43 0.00 0.00 5.28
712 2899 8.647226 GCGTTGCTACAAGATTTTGAAATATTT 58.353 29.630 0.00 0.00 37.73 1.40
713 2900 7.812191 TGCGTTGCTACAAGATTTTGAAATATT 59.188 29.630 2.48 0.00 37.73 1.28
714 2901 7.273381 GTGCGTTGCTACAAGATTTTGAAATAT 59.727 33.333 2.48 0.00 37.73 1.28
715 2902 6.580791 GTGCGTTGCTACAAGATTTTGAAATA 59.419 34.615 2.48 0.00 37.73 1.40
716 2903 5.402270 GTGCGTTGCTACAAGATTTTGAAAT 59.598 36.000 2.48 0.00 37.73 2.17
717 2904 4.737765 GTGCGTTGCTACAAGATTTTGAAA 59.262 37.500 2.48 0.00 37.73 2.69
718 2905 4.286910 GTGCGTTGCTACAAGATTTTGAA 58.713 39.130 2.48 0.00 37.73 2.69
719 2906 3.605922 CGTGCGTTGCTACAAGATTTTGA 60.606 43.478 2.48 0.00 37.73 2.69
720 2907 2.651703 CGTGCGTTGCTACAAGATTTTG 59.348 45.455 0.00 0.00 40.24 2.44
721 2908 2.350388 CCGTGCGTTGCTACAAGATTTT 60.350 45.455 0.00 0.00 0.00 1.82
722 2909 1.196808 CCGTGCGTTGCTACAAGATTT 59.803 47.619 0.00 0.00 0.00 2.17
723 2910 0.796312 CCGTGCGTTGCTACAAGATT 59.204 50.000 0.00 0.00 0.00 2.40
724 2911 1.635663 GCCGTGCGTTGCTACAAGAT 61.636 55.000 0.00 0.00 0.00 2.40
725 2912 2.314647 GCCGTGCGTTGCTACAAGA 61.315 57.895 0.00 0.00 0.00 3.02
726 2913 2.173382 GCCGTGCGTTGCTACAAG 59.827 61.111 0.00 0.00 0.00 3.16
727 2914 3.350612 GGCCGTGCGTTGCTACAA 61.351 61.111 0.00 0.00 0.00 2.41
728 2915 3.892740 ATGGCCGTGCGTTGCTACA 62.893 57.895 0.00 0.00 0.00 2.74
729 2916 2.577763 GAATGGCCGTGCGTTGCTAC 62.578 60.000 0.00 0.00 0.00 3.58
730 2917 2.359354 AATGGCCGTGCGTTGCTA 60.359 55.556 0.00 0.00 0.00 3.49
731 2918 2.796483 TAGAATGGCCGTGCGTTGCT 62.796 55.000 0.00 0.00 0.00 3.91
732 2919 2.395360 TAGAATGGCCGTGCGTTGC 61.395 57.895 0.00 0.00 0.00 4.17
733 2920 1.019278 AGTAGAATGGCCGTGCGTTG 61.019 55.000 0.00 0.00 0.00 4.10
734 2921 0.533491 TAGTAGAATGGCCGTGCGTT 59.467 50.000 0.00 0.00 0.00 4.84
735 2922 0.102481 CTAGTAGAATGGCCGTGCGT 59.898 55.000 0.00 0.00 0.00 5.24
736 2923 0.102481 ACTAGTAGAATGGCCGTGCG 59.898 55.000 3.59 0.00 0.00 5.34
737 2924 3.005472 TCATACTAGTAGAATGGCCGTGC 59.995 47.826 8.85 0.00 0.00 5.34
738 2925 4.848562 TCATACTAGTAGAATGGCCGTG 57.151 45.455 8.85 0.00 0.00 4.94
739 2926 6.720288 AGTAATCATACTAGTAGAATGGCCGT 59.280 38.462 8.85 0.00 40.62 5.68
740 2927 7.159322 AGTAATCATACTAGTAGAATGGCCG 57.841 40.000 8.85 0.00 40.62 6.13
768 2955 9.299963 CGGAAGCATGTTTTATTTTGATTGATA 57.700 29.630 0.00 0.00 0.00 2.15
769 2956 8.188531 CGGAAGCATGTTTTATTTTGATTGAT 57.811 30.769 0.00 0.00 0.00 2.57
770 2957 7.579589 CGGAAGCATGTTTTATTTTGATTGA 57.420 32.000 0.00 0.00 0.00 2.57
800 2987 8.652463 CGGTTCATGTTCAAAGTTTTTACTTTT 58.348 29.630 0.77 0.00 37.80 2.27
801 2988 8.030106 TCGGTTCATGTTCAAAGTTTTTACTTT 58.970 29.630 0.00 0.00 40.22 2.66
802 2989 7.540299 TCGGTTCATGTTCAAAGTTTTTACTT 58.460 30.769 0.00 0.00 0.00 2.24
803 2990 7.090953 TCGGTTCATGTTCAAAGTTTTTACT 57.909 32.000 0.00 0.00 0.00 2.24
804 2991 7.253850 GGTTCGGTTCATGTTCAAAGTTTTTAC 60.254 37.037 0.00 0.00 0.00 2.01
805 2992 6.752815 GGTTCGGTTCATGTTCAAAGTTTTTA 59.247 34.615 0.00 0.00 0.00 1.52
830 3017 2.858344 CCGTCACTAATCCTAAAGCGTG 59.142 50.000 0.00 0.00 0.00 5.34
914 3101 1.565067 GTCTTTTCCCGGAGACCCTA 58.435 55.000 0.73 0.00 37.02 3.53
933 3125 4.101448 CCCCTCCACCAGCCTTCG 62.101 72.222 0.00 0.00 0.00 3.79
974 3168 3.436924 CTGCGGCGTTAAACCCCC 61.437 66.667 9.37 0.00 0.00 5.40
1035 3410 1.226717 GAGTACCTCGCTTGCTCGG 60.227 63.158 0.00 0.00 0.00 4.63
1092 3470 0.178897 TAGGGGAAACACGAAGGGGA 60.179 55.000 0.00 0.00 40.46 4.81
1095 3488 3.343941 TGATTAGGGGAAACACGAAGG 57.656 47.619 0.00 0.00 40.46 3.46
1105 3498 8.220559 CAGAAAATCCTAAGAATGATTAGGGGA 58.779 37.037 13.62 0.00 0.00 4.81
1250 3648 3.454375 GTGACAAGGTCGAGAACAAAGA 58.546 45.455 0.00 0.00 34.95 2.52
1690 4093 6.722129 AGGCACTTACCTAGATAATCACCTAG 59.278 42.308 0.00 0.00 38.67 3.02
1691 4094 6.621394 AGGCACTTACCTAGATAATCACCTA 58.379 40.000 0.00 0.00 38.67 3.08
1692 4095 5.468658 AGGCACTTACCTAGATAATCACCT 58.531 41.667 0.00 0.00 38.67 4.00
1693 4096 5.810080 AGGCACTTACCTAGATAATCACC 57.190 43.478 0.00 0.00 38.67 4.02
1710 4113 4.965119 AATCCGATTGAAACTAAGGCAC 57.035 40.909 0.00 0.00 0.00 5.01
1711 4114 6.591935 AGATAATCCGATTGAAACTAAGGCA 58.408 36.000 3.73 0.00 0.00 4.75
1712 4115 7.355778 CAAGATAATCCGATTGAAACTAAGGC 58.644 38.462 3.73 0.00 0.00 4.35
1713 4116 7.355778 GCAAGATAATCCGATTGAAACTAAGG 58.644 38.462 3.73 0.00 0.00 2.69
1714 4117 7.355778 GGCAAGATAATCCGATTGAAACTAAG 58.644 38.462 3.73 0.00 0.00 2.18
1715 4118 6.018262 CGGCAAGATAATCCGATTGAAACTAA 60.018 38.462 3.73 0.00 45.53 2.24
1716 4119 5.465390 CGGCAAGATAATCCGATTGAAACTA 59.535 40.000 3.73 0.00 45.53 2.24
1717 4120 4.273480 CGGCAAGATAATCCGATTGAAACT 59.727 41.667 3.73 0.00 45.53 2.66
1718 4121 4.272504 TCGGCAAGATAATCCGATTGAAAC 59.727 41.667 3.73 0.00 46.12 2.78
1719 4122 4.447290 TCGGCAAGATAATCCGATTGAAA 58.553 39.130 3.73 0.00 46.12 2.69
1720 4123 4.066646 TCGGCAAGATAATCCGATTGAA 57.933 40.909 3.73 0.00 46.12 2.69
1721 4124 3.744238 TCGGCAAGATAATCCGATTGA 57.256 42.857 3.73 0.00 46.12 2.57
1726 4129 0.031585 TCCGTCGGCAAGATAATCCG 59.968 55.000 6.34 0.00 44.16 4.18
1727 4130 2.234300 TTCCGTCGGCAAGATAATCC 57.766 50.000 6.34 0.00 0.00 3.01
1728 4131 3.186613 GGATTTCCGTCGGCAAGATAATC 59.813 47.826 6.34 8.11 0.00 1.75
1729 4132 3.139077 GGATTTCCGTCGGCAAGATAAT 58.861 45.455 6.34 0.00 0.00 1.28
1730 4133 2.093394 TGGATTTCCGTCGGCAAGATAA 60.093 45.455 6.34 0.00 39.43 1.75
1731 4134 1.483004 TGGATTTCCGTCGGCAAGATA 59.517 47.619 6.34 0.00 39.43 1.98
1732 4135 0.251916 TGGATTTCCGTCGGCAAGAT 59.748 50.000 6.34 0.00 39.43 2.40
1733 4136 0.251916 ATGGATTTCCGTCGGCAAGA 59.748 50.000 6.34 0.00 39.43 3.02
1734 4137 0.657840 GATGGATTTCCGTCGGCAAG 59.342 55.000 6.34 0.00 41.68 4.01
1735 4138 2.775351 GATGGATTTCCGTCGGCAA 58.225 52.632 6.34 1.58 41.68 4.52
1736 4139 4.532490 GATGGATTTCCGTCGGCA 57.468 55.556 6.34 0.00 41.68 5.69
1740 4143 2.218953 TAGCACGATGGATTTCCGTC 57.781 50.000 8.52 8.52 46.19 4.79
1741 4144 2.684001 TTAGCACGATGGATTTCCGT 57.316 45.000 0.00 0.00 39.43 4.69
1742 4145 3.303990 CCATTTAGCACGATGGATTTCCG 60.304 47.826 6.43 0.00 44.49 4.30
1743 4146 3.882888 TCCATTTAGCACGATGGATTTCC 59.117 43.478 9.95 0.00 45.14 3.13
1749 4152 6.427853 TGAAAGATATCCATTTAGCACGATGG 59.572 38.462 0.00 6.04 43.36 3.51
1750 4153 7.172190 ACTGAAAGATATCCATTTAGCACGATG 59.828 37.037 0.00 0.00 37.43 3.84
1768 4171 8.317891 TGATAAAAGCGAACATTACTGAAAGA 57.682 30.769 0.00 0.00 37.43 2.52
1769 4172 9.003112 CATGATAAAAGCGAACATTACTGAAAG 57.997 33.333 0.00 0.00 42.29 2.62
1838 4392 6.723298 ATATAATTCATCACCCCGCAAAAA 57.277 33.333 0.00 0.00 0.00 1.94
1839 4393 6.322456 TGAATATAATTCATCACCCCGCAAAA 59.678 34.615 0.00 0.00 0.00 2.44
1840 4394 5.830457 TGAATATAATTCATCACCCCGCAAA 59.170 36.000 0.00 0.00 0.00 3.68
1841 4395 5.380900 TGAATATAATTCATCACCCCGCAA 58.619 37.500 0.00 0.00 0.00 4.85
1842 4396 4.979335 TGAATATAATTCATCACCCCGCA 58.021 39.130 0.00 0.00 0.00 5.69
1843 4397 5.957842 TTGAATATAATTCATCACCCCGC 57.042 39.130 3.34 0.00 0.00 6.13
1844 4398 6.886459 AGGATTGAATATAATTCATCACCCCG 59.114 38.462 3.34 0.00 0.00 5.73
1845 4399 8.655935 AAGGATTGAATATAATTCATCACCCC 57.344 34.615 3.34 2.21 0.00 4.95
1980 4541 1.225855 TGCAGAATTCGAACAACGCT 58.774 45.000 0.00 0.00 42.26 5.07
2058 4619 6.989155 ACATCAATTATTCCTCCGGTAGTA 57.011 37.500 0.00 0.00 0.00 1.82
2067 4628 4.162131 GGTTGGCCAACATCAATTATTCCT 59.838 41.667 41.33 0.00 42.85 3.36
2116 4677 4.808364 GCACACTGAGCCTAAAAGAGATAG 59.192 45.833 0.00 0.00 0.00 2.08
2172 4733 8.635765 TTTCCACAGCAGATTATAAAAGAAGT 57.364 30.769 0.00 0.00 0.00 3.01
2228 4789 3.634568 TTGCCTAATTCACCGTTTGTG 57.365 42.857 0.00 0.00 46.88 3.33
2234 4795 2.415893 CCTGCTTTTGCCTAATTCACCG 60.416 50.000 0.00 0.00 46.87 4.94
2278 4839 4.009675 TGCAGCAATAAACCAGTAAGGAG 58.990 43.478 0.00 0.00 41.22 3.69
2375 4936 6.128090 TGTGAGATGAACACTAGGTAAGTACG 60.128 42.308 0.00 0.00 35.76 3.67
2398 4959 5.520751 AGAACTAGCTATCACCTACCTTGT 58.479 41.667 0.00 0.00 0.00 3.16
2723 5287 9.951866 AGATAATGGGGTAAATTCAGGTAAAAT 57.048 29.630 0.00 0.00 0.00 1.82
2966 5533 6.563422 TGAAAAGAATCACTTTGACAACCAG 58.437 36.000 0.00 0.00 46.55 4.00
3232 5800 9.687210 CATAAACCAGTTTCCTTACTTAAAACC 57.313 33.333 0.00 0.00 34.23 3.27
3644 6232 5.913137 TGTCAAAGTTTGTGAGGTTTGAT 57.087 34.783 15.08 0.00 40.16 2.57
3828 6425 7.759886 CCTCCATTCCGTAATATAGTGTGTATG 59.240 40.741 0.00 0.00 0.00 2.39
3833 6430 5.399991 TCCCTCCATTCCGTAATATAGTGT 58.600 41.667 0.00 0.00 0.00 3.55
3993 6591 5.917462 TCTCTGATCACAAAAAGAGTGTCA 58.083 37.500 7.14 0.00 37.88 3.58
4207 6805 2.416202 CGCAGTTCATCAGTGTAATGCA 59.584 45.455 7.89 0.00 43.81 3.96
4244 6842 3.375299 CCCTCATCAACTTGATTTCCGAC 59.625 47.826 1.17 0.00 34.28 4.79
4329 6927 6.991938 AGCATCAGACTCAATATCTCCTAAC 58.008 40.000 0.00 0.00 0.00 2.34
4708 7306 7.175104 TGGCAACTTGAGGTAAAATTCTAGAT 58.825 34.615 0.00 0.00 37.61 1.98
4874 7472 4.079253 AGAGACTGGACAGAAAGAGAGAC 58.921 47.826 6.29 0.00 0.00 3.36
5131 7729 8.438676 AGTTCCTTAATTTATGGATCTCAACG 57.561 34.615 10.83 0.00 30.49 4.10
5162 7760 4.429108 GCACCTTGCTCACTAAACAAAAA 58.571 39.130 0.00 0.00 40.96 1.94
5170 7768 0.677731 GCATGGCACCTTGCTCACTA 60.678 55.000 17.72 0.00 44.28 2.74
5281 7879 9.092876 CTCTGTTGTACCTTCTTATCATTTCTC 57.907 37.037 0.00 0.00 0.00 2.87
5359 7957 2.159212 TCTGTCAAACGACTCAAACGGA 60.159 45.455 0.00 0.00 34.31 4.69
5543 8141 6.014327 AGGTACTCGTAAGTCCAAAATTACCA 60.014 38.462 0.00 0.00 36.92 3.25
5746 8442 5.046878 TGGAGATTAGAGCGTGGACTTTTTA 60.047 40.000 0.00 0.00 0.00 1.52
5875 8572 7.589958 TCTAATCAAGAGACAGGTAGATTCC 57.410 40.000 0.00 0.00 0.00 3.01
5992 9850 0.900182 TGAGGCTCGTGGAGTCATGT 60.900 55.000 10.42 0.00 36.65 3.21
6016 9874 0.111253 CTGGCTCCAAGGGTTTGTCT 59.889 55.000 0.00 0.00 32.21 3.41
6076 9934 6.526674 GCGCTAAATTTGCTAGTGTAAAATGT 59.473 34.615 0.00 0.00 31.96 2.71
6118 9981 7.855375 ACAACTCAGATTTCCATAGAAGATGA 58.145 34.615 0.00 0.00 32.35 2.92
6120 9983 9.606631 GTTACAACTCAGATTTCCATAGAAGAT 57.393 33.333 0.00 0.00 32.35 2.40
6214 10078 1.065701 CTCGTTGAGTATCGGGACCTG 59.934 57.143 0.00 0.00 38.61 4.00
6215 10079 1.064906 TCTCGTTGAGTATCGGGACCT 60.065 52.381 0.00 0.00 38.61 3.85
6306 10170 0.031917 TGATTAGGGGCGGTACCTCA 60.032 55.000 10.90 0.93 44.17 3.86
6318 10182 3.994392 CGGTACCGGATGAAATGATTAGG 59.006 47.826 27.00 0.00 35.56 2.69
6541 10931 2.440539 AAGGATATCATCGTGTCGCC 57.559 50.000 4.83 0.00 0.00 5.54
6614 11005 6.454318 CGATTTCTACATCTTTGACAGGAACG 60.454 42.308 0.00 0.00 0.00 3.95
6671 11062 3.243367 CCATGAACTGGCGAAACTTTTCA 60.243 43.478 0.00 0.00 38.47 2.69
6733 11126 4.937201 ATGAAGACCCAAAACTTTGTCC 57.063 40.909 1.76 0.00 36.45 4.02
6763 11156 3.216187 TCCAATTCCCTCGACAACAAA 57.784 42.857 0.00 0.00 0.00 2.83
6771 11164 4.641989 ACAAATGAAGATCCAATTCCCTCG 59.358 41.667 0.00 0.00 0.00 4.63
6819 11212 0.107643 TGATTGCCGGACAACAGTCA 59.892 50.000 5.05 7.42 42.27 3.41
6821 11214 1.541147 CATTGATTGCCGGACAACAGT 59.459 47.619 5.05 4.80 42.27 3.55
6830 11223 1.135024 CCCTTTCACCATTGATTGCCG 60.135 52.381 0.00 0.00 0.00 5.69
6866 11280 2.439701 GCTTAAACCCGGCTCCCC 60.440 66.667 0.00 0.00 0.00 4.81
6872 11286 1.667212 GGTCGTAATGCTTAAACCCGG 59.333 52.381 0.00 0.00 0.00 5.73
7069 11490 1.546589 TACACCATCGCCCTTCCGTT 61.547 55.000 0.00 0.00 0.00 4.44
7076 11502 0.606401 CCCATGATACACCATCGCCC 60.606 60.000 0.00 0.00 36.33 6.13
7084 11510 3.074390 TCCATCCCATTCCCATGATACAC 59.926 47.826 0.00 0.00 31.07 2.90
7116 11542 3.545481 GCCACGACAGCGATGACG 61.545 66.667 22.71 22.71 41.64 4.35
7138 11564 4.323477 TTTCCCTCACCCGCCACG 62.323 66.667 0.00 0.00 0.00 4.94
7139 11565 2.671963 GTTTCCCTCACCCGCCAC 60.672 66.667 0.00 0.00 0.00 5.01
7180 11616 2.100989 CACCTACCTCCTACCACAGAC 58.899 57.143 0.00 0.00 0.00 3.51
7181 11617 1.006758 CCACCTACCTCCTACCACAGA 59.993 57.143 0.00 0.00 0.00 3.41
7241 13707 2.246469 CTCCATCCGTCCATCATCTCT 58.754 52.381 0.00 0.00 0.00 3.10
7242 13708 1.274728 CCTCCATCCGTCCATCATCTC 59.725 57.143 0.00 0.00 0.00 2.75
7265 13731 1.745115 GTTATCAGGCAGGCACGCA 60.745 57.895 0.00 0.00 0.00 5.24
7266 13732 2.813179 CGTTATCAGGCAGGCACGC 61.813 63.158 0.00 0.00 0.00 5.34
7267 13733 2.813179 GCGTTATCAGGCAGGCACG 61.813 63.158 0.00 0.00 33.72 5.34
7268 13734 1.450312 AGCGTTATCAGGCAGGCAC 60.450 57.895 0.00 0.00 36.16 5.01
7305 13771 1.583054 CGAGATTTAAAGCCGGGGAG 58.417 55.000 2.18 0.00 0.00 4.30
7306 13772 0.463116 GCGAGATTTAAAGCCGGGGA 60.463 55.000 2.18 0.00 0.00 4.81
7307 13773 0.746563 TGCGAGATTTAAAGCCGGGG 60.747 55.000 2.18 0.00 0.00 5.73
7412 13886 4.058124 GGAATTCCACTTTTGAGCCAAAC 58.942 43.478 20.04 0.00 32.65 2.93
7413 13887 3.708631 TGGAATTCCACTTTTGAGCCAAA 59.291 39.130 23.63 0.00 42.01 3.28
7414 13888 3.303938 TGGAATTCCACTTTTGAGCCAA 58.696 40.909 23.63 0.00 42.01 4.52
7415 13889 2.892852 CTGGAATTCCACTTTTGAGCCA 59.107 45.455 23.63 0.00 42.01 4.75
7416 13890 2.893489 ACTGGAATTCCACTTTTGAGCC 59.107 45.455 23.63 0.00 42.01 4.70
7417 13891 4.550422 GAACTGGAATTCCACTTTTGAGC 58.450 43.478 23.63 5.14 42.01 4.26
7418 13892 4.515191 TCGAACTGGAATTCCACTTTTGAG 59.485 41.667 23.63 13.90 42.01 3.02
7419 13893 4.456535 TCGAACTGGAATTCCACTTTTGA 58.543 39.130 23.63 21.95 42.01 2.69
7421 13895 6.405278 AAATCGAACTGGAATTCCACTTTT 57.595 33.333 23.63 15.73 42.01 2.27
7440 13936 0.698818 ACCACAGGTCCTGGGAAATC 59.301 55.000 23.64 0.00 36.97 2.17
7445 13941 0.036306 GTTGTACCACAGGTCCTGGG 59.964 60.000 23.06 19.25 37.09 4.45
7448 13944 2.334977 TCATGTTGTACCACAGGTCCT 58.665 47.619 11.00 0.00 37.09 3.85
7452 13948 2.435422 TGCATCATGTTGTACCACAGG 58.565 47.619 5.44 5.44 0.00 4.00


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

AutoCloner maintained by Alex Coulton.