Multiple sequence alignment - TraesCS7D01G476000

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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 TraesCS7D01G476000 chr7D 100.000 5699 0 0 1 5699 587832078 587837776 0.000000e+00 10525.0
1 TraesCS7D01G476000 chr7D 77.075 253 33 17 5238 5473 412652550 412652794 7.750000e-24 122.0
2 TraesCS7D01G476000 chr7B 94.227 3655 145 18 788 4401 659258271 659261900 0.000000e+00 5520.0
3 TraesCS7D01G476000 chr7B 94.571 1271 38 8 4430 5699 659261898 659263138 0.000000e+00 1936.0
4 TraesCS7D01G476000 chr7B 83.611 720 52 27 1 691 659257575 659258257 2.920000e-172 616.0
5 TraesCS7D01G476000 chr7B 97.727 88 2 0 689 776 334323975 334323888 9.890000e-33 152.0
6 TraesCS7D01G476000 chr7B 86.765 68 5 4 5241 5305 669524701 669524635 7.920000e-09 73.1
7 TraesCS7D01G476000 chr7A 91.176 2278 120 44 3462 5697 679763608 679765846 0.000000e+00 3018.0
8 TraesCS7D01G476000 chr7A 92.409 2121 112 15 1382 3464 679761462 679763571 0.000000e+00 2979.0
9 TraesCS7D01G476000 chr7A 96.849 603 19 0 788 1390 679760606 679761208 0.000000e+00 1009.0
10 TraesCS7D01G476000 chr7A 84.549 699 54 30 15 692 679759930 679760595 1.340000e-180 643.0
11 TraesCS7D01G476000 chr7A 94.792 96 4 1 689 784 238816495 238816401 1.280000e-31 148.0
12 TraesCS7D01G476000 chrUn 86.177 463 19 12 236 692 68602056 68602479 5.200000e-125 459.0
13 TraesCS7D01G476000 chr6D 78.249 377 76 5 987 1360 114239182 114238809 2.650000e-58 237.0
14 TraesCS7D01G476000 chr6A 78.022 364 73 5 987 1348 142790099 142789741 7.430000e-54 222.0
15 TraesCS7D01G476000 chr6B 77.394 376 79 5 987 1359 203931048 203930676 9.610000e-53 219.0
16 TraesCS7D01G476000 chr2B 96.667 90 3 0 689 778 540926316 540926405 3.560000e-32 150.0
17 TraesCS7D01G476000 chr5D 95.699 93 3 1 688 780 253048862 253048771 1.280000e-31 148.0
18 TraesCS7D01G476000 chr5B 93.137 102 5 2 689 788 550925177 550925076 1.280000e-31 148.0
19 TraesCS7D01G476000 chr2A 94.792 96 3 1 689 784 622029673 622029580 1.280000e-31 148.0
20 TraesCS7D01G476000 chr1B 93.878 98 6 0 677 774 255504002 255503905 1.280000e-31 148.0
21 TraesCS7D01G476000 chr3B 94.737 95 4 1 689 783 689513372 689513465 4.600000e-31 147.0
22 TraesCS7D01G476000 chr3A 91.509 106 7 2 670 775 646126932 646126829 1.650000e-30 145.0
23 TraesCS7D01G476000 chr5A 73.305 236 45 16 5378 5605 512038761 512038986 2.850000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G476000 chr7D 587832078 587837776 5698 False 10525.000000 10525 100.00000 1 5699 1 chr7D.!!$F2 5698
1 TraesCS7D01G476000 chr7B 659257575 659263138 5563 False 2690.666667 5520 90.80300 1 5699 3 chr7B.!!$F1 5698
2 TraesCS7D01G476000 chr7A 679759930 679765846 5916 False 1912.250000 3018 91.24575 15 5697 4 chr7A.!!$F1 5682

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
669 713 0.104855 CCGATTCTTCCAGATCGCCA 59.895 55.0 0.56 0.0 35.45 5.69 F
777 821 0.113776 TGGAACCGAGGGAGTACTGT 59.886 55.0 0.00 0.0 0.00 3.55 F
2373 2700 0.038801 GCAAGTTGAGGAGCTTTGCC 60.039 55.0 7.16 0.0 0.00 4.52 F
2987 3368 0.404040 CAGAAAGGGTGCCCAGGTAA 59.596 55.0 10.26 0.0 38.92 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 2685 2.884639 TGTAAAGGCAAAGCTCCTCAAC 59.115 45.455 0.0 0.0 32.45 3.18 R
2748 3129 2.760650 CACTAATTCCCCTTTGCTTCCC 59.239 50.000 0.0 0.0 0.00 3.97 R
3936 4373 1.542472 TGGCTGCAAATCACATGACAG 59.458 47.619 0.0 0.0 0.00 3.51 R
4886 5344 0.665670 CGAGGGCAGTATCATCGCTG 60.666 60.000 0.0 0.0 35.93 5.18 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
26 27 3.124088 CCTCCCCTCCTCCCTCTT 58.876 66.667 0.00 0.00 0.00 2.85
40 41 0.389948 CCTCTTCCAGTTCCGTTCCG 60.390 60.000 0.00 0.00 0.00 4.30
46 47 1.007336 CCAGTTCCGTTCCGTTCGAG 61.007 60.000 0.00 0.00 0.00 4.04
52 53 1.663702 CGTTCCGTTCGAGCCAAGT 60.664 57.895 0.00 0.00 0.00 3.16
53 54 1.219522 CGTTCCGTTCGAGCCAAGTT 61.220 55.000 0.00 0.00 0.00 2.66
57 58 2.861006 GTTCGAGCCAAGTTCGCC 59.139 61.111 0.00 0.00 36.29 5.54
141 150 4.135493 GCTCGGCGCGTCTGTTTC 62.135 66.667 9.90 0.00 0.00 2.78
160 170 0.296056 CGAGTTCGAATTCTGCTCGC 59.704 55.000 18.28 0.00 41.62 5.03
232 252 4.404098 CCGGGGGAGTCGGTTTGG 62.404 72.222 0.00 0.00 42.33 3.28
233 253 3.633116 CGGGGGAGTCGGTTTGGT 61.633 66.667 0.00 0.00 0.00 3.67
234 254 2.841317 GGGGGAGTCGGTTTGGTT 59.159 61.111 0.00 0.00 0.00 3.67
239 259 0.949397 GGAGTCGGTTTGGTTGGTTC 59.051 55.000 0.00 0.00 0.00 3.62
262 282 4.581648 GAGCTCGAAATGCGGCGC 62.582 66.667 27.44 27.44 39.89 6.53
302 324 2.750888 GGCGGCGATTTGGTCAGAC 61.751 63.158 12.98 0.00 0.00 3.51
380 403 1.827315 TTTTTCTCGCGCGTGTGGAG 61.827 55.000 30.98 19.37 0.00 3.86
382 405 3.891586 TTCTCGCGCGTGTGGAGTC 62.892 63.158 30.98 0.00 0.00 3.36
393 416 1.066430 GTGTGGAGTCCGCCTGATTTA 60.066 52.381 20.03 0.00 32.22 1.40
405 428 3.209410 GCCTGATTTAGACTGGTGGATG 58.791 50.000 0.00 0.00 0.00 3.51
406 429 3.813443 CCTGATTTAGACTGGTGGATGG 58.187 50.000 0.00 0.00 0.00 3.51
407 430 3.455910 CCTGATTTAGACTGGTGGATGGA 59.544 47.826 0.00 0.00 0.00 3.41
408 431 4.103785 CCTGATTTAGACTGGTGGATGGAT 59.896 45.833 0.00 0.00 0.00 3.41
523 553 0.179040 TTTGCTTTCCTCGGGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
525 555 0.601841 TGCTTTCCTCGGGTCGTTTC 60.602 55.000 0.00 0.00 0.00 2.78
526 556 0.601841 GCTTTCCTCGGGTCGTTTCA 60.602 55.000 0.00 0.00 0.00 2.69
527 557 1.145803 CTTTCCTCGGGTCGTTTCAC 58.854 55.000 0.00 0.00 0.00 3.18
528 558 0.249996 TTTCCTCGGGTCGTTTCACC 60.250 55.000 0.00 0.00 35.42 4.02
605 641 2.889503 GGCTGCAGTGCTAGAGCG 60.890 66.667 17.60 0.00 45.83 5.03
625 666 4.742201 CGTCAGGTGACCGGGCTG 62.742 72.222 9.82 0.00 41.86 4.85
626 667 4.394712 GTCAGGTGACCGGGCTGG 62.395 72.222 9.82 11.83 46.41 4.85
660 701 1.964933 CTCTAGGACCCCGATTCTTCC 59.035 57.143 0.00 0.00 0.00 3.46
669 713 0.104855 CCGATTCTTCCAGATCGCCA 59.895 55.000 0.56 0.00 35.45 5.69
692 736 6.647895 CCATTCAGCTTGCTTGATTTTTACTT 59.352 34.615 0.00 0.00 0.00 2.24
694 738 5.772521 TCAGCTTGCTTGATTTTTACTTCC 58.227 37.500 0.00 0.00 0.00 3.46
697 741 4.853743 GCTTGCTTGATTTTTACTTCCTCG 59.146 41.667 0.00 0.00 0.00 4.63
698 742 5.371115 TTGCTTGATTTTTACTTCCTCGG 57.629 39.130 0.00 0.00 0.00 4.63
699 743 4.394729 TGCTTGATTTTTACTTCCTCGGT 58.605 39.130 0.00 0.00 0.00 4.69
701 745 5.048991 TGCTTGATTTTTACTTCCTCGGTTC 60.049 40.000 0.00 0.00 0.00 3.62
702 746 5.619309 GCTTGATTTTTACTTCCTCGGTTCC 60.619 44.000 0.00 0.00 0.00 3.62
704 748 5.378332 TGATTTTTACTTCCTCGGTTCCAA 58.622 37.500 0.00 0.00 0.00 3.53
705 749 5.828859 TGATTTTTACTTCCTCGGTTCCAAA 59.171 36.000 0.00 0.00 0.00 3.28
706 750 6.321690 TGATTTTTACTTCCTCGGTTCCAAAA 59.678 34.615 0.00 0.00 0.00 2.44
707 751 6.718522 TTTTTACTTCCTCGGTTCCAAAAT 57.281 33.333 0.00 0.00 0.00 1.82
708 752 7.820578 TTTTTACTTCCTCGGTTCCAAAATA 57.179 32.000 0.00 0.00 0.00 1.40
709 753 7.443259 TTTTACTTCCTCGGTTCCAAAATAG 57.557 36.000 0.00 0.00 0.00 1.73
710 754 4.903045 ACTTCCTCGGTTCCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
711 755 5.437191 ACTTCCTCGGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
712 756 5.186198 ACTTCCTCGGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
713 757 5.045869 ACTTCCTCGGTTCCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
714 758 4.766375 TCCTCGGTTCCAAAATAGATGAC 58.234 43.478 0.00 0.00 0.00 3.06
715 759 3.877508 CCTCGGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
716 760 3.877508 CTCGGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
717 761 3.264706 TCGGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
718 762 4.013728 CGGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
719 763 4.142469 CGGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
720 764 5.016831 GGTTCCAAAATAGATGACCCAACT 58.983 41.667 0.00 0.00 0.00 3.16
721 765 5.480422 GGTTCCAAAATAGATGACCCAACTT 59.520 40.000 0.00 0.00 0.00 2.66
722 766 6.014584 GGTTCCAAAATAGATGACCCAACTTT 60.015 38.462 0.00 0.00 0.00 2.66
723 767 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
724 768 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
725 769 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
726 770 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
727 771 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
728 772 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
729 773 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
730 774 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
731 775 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
732 776 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
733 777 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
734 778 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
735 779 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
736 780 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
737 781 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
750 794 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
751 795 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
752 796 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
753 797 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
754 798 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
755 799 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
756 800 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
757 801 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
758 802 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
759 803 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
760 804 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
761 805 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
762 806 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
763 807 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
764 808 5.016831 AGTTGGGTCATCTATTTTGGAACC 58.983 41.667 0.00 0.00 37.64 3.62
765 809 3.616219 TGGGTCATCTATTTTGGAACCG 58.384 45.455 0.00 0.00 40.06 4.44
766 810 3.264706 TGGGTCATCTATTTTGGAACCGA 59.735 43.478 0.00 0.00 40.06 4.69
767 811 3.877508 GGGTCATCTATTTTGGAACCGAG 59.122 47.826 0.00 0.00 0.00 4.63
768 812 3.877508 GGTCATCTATTTTGGAACCGAGG 59.122 47.826 0.00 0.00 0.00 4.63
769 813 3.877508 GTCATCTATTTTGGAACCGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
770 814 3.778075 TCATCTATTTTGGAACCGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
771 815 3.906720 TCTATTTTGGAACCGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
772 816 3.178865 TCTATTTTGGAACCGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
773 817 4.355549 TCTATTTTGGAACCGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
774 818 2.845363 TTTTGGAACCGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
775 819 2.019807 TTTGGAACCGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
776 820 1.263356 TTGGAACCGAGGGAGTACTG 58.737 55.000 0.00 0.00 0.00 2.74
777 821 0.113776 TGGAACCGAGGGAGTACTGT 59.886 55.000 0.00 0.00 0.00 3.55
778 822 1.355381 TGGAACCGAGGGAGTACTGTA 59.645 52.381 0.00 0.00 0.00 2.74
779 823 1.747924 GGAACCGAGGGAGTACTGTAC 59.252 57.143 9.93 9.93 0.00 2.90
780 824 2.620108 GGAACCGAGGGAGTACTGTACT 60.620 54.545 19.79 19.79 42.86 2.73
781 825 3.370953 GGAACCGAGGGAGTACTGTACTA 60.371 52.174 19.73 0.00 39.59 1.82
782 826 3.274095 ACCGAGGGAGTACTGTACTAC 57.726 52.381 19.80 19.80 39.59 2.73
783 827 2.843113 ACCGAGGGAGTACTGTACTACT 59.157 50.000 25.19 21.80 39.66 2.57
784 828 3.265479 ACCGAGGGAGTACTGTACTACTT 59.735 47.826 25.19 20.08 39.66 2.24
785 829 3.876320 CCGAGGGAGTACTGTACTACTTC 59.124 52.174 24.82 24.82 41.08 3.01
806 850 2.221286 CGTCATGATCTCTTGCATCAGC 59.779 50.000 0.00 0.00 42.57 4.26
825 869 2.092882 GCCGTGCTTACCTCGTGTC 61.093 63.158 0.00 0.00 0.00 3.67
830 874 1.792949 GTGCTTACCTCGTGTCTTGTG 59.207 52.381 0.00 0.00 0.00 3.33
865 913 2.125188 GAGGAGTCAGCTGCCTGC 60.125 66.667 15.25 12.17 39.00 4.85
905 953 3.188786 GTGTAGCAGCGGCCTTCG 61.189 66.667 4.82 0.00 42.56 3.79
919 967 1.388065 CCTTCGCACCCAAACAACCA 61.388 55.000 0.00 0.00 0.00 3.67
1155 1203 1.742831 CTCTCTGCTTCTAGCGTCTGT 59.257 52.381 0.00 0.00 46.26 3.41
1248 1296 5.869579 GCTGTTATCAGGGATATTCTTGGA 58.130 41.667 3.05 0.00 41.57 3.53
1284 1332 3.485877 CGTCGAAGAATCCAAAGATTGCC 60.486 47.826 0.00 0.00 42.93 4.52
1394 1704 6.985188 TGTGCAATTTGAAGGAGTATAGTC 57.015 37.500 0.00 0.00 0.00 2.59
1496 1806 5.010012 ACAACTATTTGGGTTGCTGAGAAAG 59.990 40.000 6.51 0.00 45.34 2.62
1508 1818 6.374578 GTTGCTGAGAAAGAATTTAGTGGTC 58.625 40.000 0.00 0.00 39.27 4.02
1513 1823 5.694910 TGAGAAAGAATTTAGTGGTCGACAC 59.305 40.000 18.91 13.33 44.82 3.67
1713 2039 4.344102 TGTACCTCCATGCTACTAACCATC 59.656 45.833 0.00 0.00 0.00 3.51
1714 2040 3.658725 ACCTCCATGCTACTAACCATCT 58.341 45.455 0.00 0.00 0.00 2.90
1715 2041 3.643792 ACCTCCATGCTACTAACCATCTC 59.356 47.826 0.00 0.00 0.00 2.75
1716 2042 3.900601 CCTCCATGCTACTAACCATCTCT 59.099 47.826 0.00 0.00 0.00 3.10
1717 2043 4.262377 CCTCCATGCTACTAACCATCTCTG 60.262 50.000 0.00 0.00 0.00 3.35
1718 2044 3.070159 TCCATGCTACTAACCATCTCTGC 59.930 47.826 0.00 0.00 0.00 4.26
1719 2045 3.181462 CCATGCTACTAACCATCTCTGCA 60.181 47.826 0.00 0.00 0.00 4.41
1720 2046 4.504514 CCATGCTACTAACCATCTCTGCAT 60.505 45.833 0.00 0.00 39.99 3.96
1721 2047 4.063998 TGCTACTAACCATCTCTGCATG 57.936 45.455 0.00 0.00 0.00 4.06
1722 2048 3.452264 TGCTACTAACCATCTCTGCATGT 59.548 43.478 0.00 0.00 0.00 3.21
1723 2049 4.054671 GCTACTAACCATCTCTGCATGTC 58.945 47.826 0.00 0.00 0.00 3.06
1724 2050 4.202202 GCTACTAACCATCTCTGCATGTCT 60.202 45.833 0.00 0.00 0.00 3.41
1725 2051 5.010112 GCTACTAACCATCTCTGCATGTCTA 59.990 44.000 0.00 0.00 0.00 2.59
1726 2052 5.269505 ACTAACCATCTCTGCATGTCTAC 57.730 43.478 0.00 0.00 0.00 2.59
1727 2053 4.711846 ACTAACCATCTCTGCATGTCTACA 59.288 41.667 0.00 0.00 0.00 2.74
1728 2054 4.767578 AACCATCTCTGCATGTCTACAT 57.232 40.909 0.00 0.00 36.96 2.29
1800 2126 7.448748 AAATAACTTTGATACACAGGGTCAC 57.551 36.000 0.00 0.00 0.00 3.67
2049 2375 4.767578 TCTCCCTCTCAATGAATGAAGG 57.232 45.455 0.00 0.00 37.67 3.46
2087 2413 7.591421 TCAACTGATTGATATTGATGCCATT 57.409 32.000 0.00 0.00 40.01 3.16
2280 2606 4.441634 GGCCAGTCTTAGTATCATGACGTT 60.442 45.833 0.00 0.00 34.92 3.99
2344 2670 4.882671 TGAGATGCCGAAAAATCTTAGC 57.117 40.909 0.00 0.00 33.26 3.09
2358 2685 9.508567 GAAAAATCTTAGCCTACTAATTGCAAG 57.491 33.333 4.94 0.00 37.73 4.01
2360 2687 8.581253 AAATCTTAGCCTACTAATTGCAAGTT 57.419 30.769 4.05 2.06 37.73 2.66
2372 2699 0.670162 TGCAAGTTGAGGAGCTTTGC 59.330 50.000 7.16 9.56 0.00 3.68
2373 2700 0.038801 GCAAGTTGAGGAGCTTTGCC 60.039 55.000 7.16 0.00 0.00 4.52
2374 2701 1.613836 CAAGTTGAGGAGCTTTGCCT 58.386 50.000 0.00 0.00 38.81 4.75
2383 2711 5.509498 TGAGGAGCTTTGCCTTTACATATT 58.491 37.500 0.00 0.00 35.44 1.28
2555 2935 4.761739 TGTCTTGCTTTCTGATAGGTTTGG 59.238 41.667 0.00 0.00 0.00 3.28
2563 2943 6.387192 TTTCTGATAGGTTTGGATTCCTGA 57.613 37.500 3.95 0.00 35.51 3.86
2594 2974 8.508883 AATGATTTCCTTCTTGAGAGATTCTG 57.491 34.615 0.00 0.00 0.00 3.02
2595 2975 5.879223 TGATTTCCTTCTTGAGAGATTCTGC 59.121 40.000 0.00 0.00 0.00 4.26
2600 2980 2.259917 TCTTGAGAGATTCTGCCACCA 58.740 47.619 0.00 0.00 0.00 4.17
2641 3021 1.005748 CTCTCGCAGCTGTGTTCCA 60.006 57.895 25.68 6.69 0.00 3.53
2665 3045 7.230222 CACTTCATTCATTTGACTACGTCTTC 58.770 38.462 0.00 0.00 33.15 2.87
2718 3098 6.640518 TCATTGATTGGTAAGAGTACTGGAC 58.359 40.000 0.00 0.00 0.00 4.02
2719 3099 6.212589 TCATTGATTGGTAAGAGTACTGGACA 59.787 38.462 0.00 0.00 0.00 4.02
2754 3135 8.840833 TTACCATTTTGAAAAATAAGGGAAGC 57.159 30.769 9.25 0.00 36.52 3.86
2802 3183 0.774276 TGGCCAATACCACAAGGACA 59.226 50.000 0.61 0.00 36.65 4.02
2804 3185 2.024414 GGCCAATACCACAAGGACATC 58.976 52.381 0.00 0.00 38.69 3.06
2805 3186 2.620367 GGCCAATACCACAAGGACATCA 60.620 50.000 0.00 0.00 38.69 3.07
2874 3255 2.035704 TGCATGTTGATTTTTGTCCGCT 59.964 40.909 0.00 0.00 0.00 5.52
2899 3280 8.964476 TTTTATTGCCATTTTGTAGTTTCCAA 57.036 26.923 0.00 0.00 0.00 3.53
2987 3368 0.404040 CAGAAAGGGTGCCCAGGTAA 59.596 55.000 10.26 0.00 38.92 2.85
3019 3400 9.757227 TTTGTGAAGTTGTTTCCTTATTATTGG 57.243 29.630 0.00 0.00 34.77 3.16
3026 3407 8.357402 AGTTGTTTCCTTATTATTGGTGTTGTC 58.643 33.333 0.00 0.00 0.00 3.18
3041 3422 4.457603 GGTGTTGTCCTTGCAATGTGTATA 59.542 41.667 0.00 0.00 0.00 1.47
3095 3476 7.419204 CAAATTCATGCTTTGACCAACAATTT 58.581 30.769 12.62 2.36 38.36 1.82
3099 3480 6.815089 TCATGCTTTGACCAACAATTTACTT 58.185 32.000 0.00 0.00 38.36 2.24
3152 3539 4.588106 AGACACCATCAGATCAGTATCCAG 59.412 45.833 0.00 0.00 31.98 3.86
3245 3633 5.187967 TGTGGGTCCACTGTTTGTTATTTTT 59.812 36.000 19.44 0.00 46.30 1.94
3659 4087 8.884323 AGGCCATAATGAACTGAAGAATAGATA 58.116 33.333 5.01 0.00 0.00 1.98
3692 4127 6.774354 AAACAGCAGAAAATTAATGTGCAG 57.226 33.333 13.50 9.16 36.57 4.41
3709 4144 3.133691 TGCAGACTCTGTTGCAAAGTAG 58.866 45.455 0.00 0.81 46.42 2.57
3710 4145 3.134458 GCAGACTCTGTTGCAAAGTAGT 58.866 45.455 0.00 4.49 40.02 2.73
3711 4146 3.185391 GCAGACTCTGTTGCAAAGTAGTC 59.815 47.826 20.55 20.55 40.02 2.59
3712 4147 3.743396 CAGACTCTGTTGCAAAGTAGTCC 59.257 47.826 22.80 11.85 35.13 3.85
3831 4268 1.990563 GCATTTGAGTGATGTGCTTGC 59.009 47.619 0.00 0.00 33.25 4.01
3873 4310 6.223852 TGAAGTCTCAACCAATACTTGAGTC 58.776 40.000 7.78 3.45 43.51 3.36
3983 4425 0.179189 GGCGCAACTGTATTGCTGAC 60.179 55.000 10.83 2.49 42.87 3.51
4078 4523 7.988599 TCCTTGAGTTACTTGCTAACTAACAAA 59.011 33.333 0.00 0.00 44.45 2.83
4130 4575 4.385199 CCAGGTGGAATAGCTAATTGGTCA 60.385 45.833 0.00 0.00 34.81 4.02
4171 4616 1.078490 TGAGGGGAAATGGCATCCAAA 59.922 47.619 9.25 0.00 36.95 3.28
4296 4741 8.428186 TTTCTATTTAGTGCATAACCCTTACG 57.572 34.615 0.00 0.00 0.00 3.18
4303 4748 2.680841 TGCATAACCCTTACGTTGATGC 59.319 45.455 0.00 0.00 35.55 3.91
4368 4813 5.065602 CCATCCATGTAACAAGTGATGACAG 59.934 44.000 6.05 0.00 0.00 3.51
4388 4833 3.888930 CAGGGTATGGGCAATAATTTCGT 59.111 43.478 0.00 0.00 0.00 3.85
4405 4850 7.687941 AATTTCGTCATCAGTATTTTGACCT 57.312 32.000 0.00 0.00 37.13 3.85
4409 4854 6.227522 TCGTCATCAGTATTTTGACCTTCAA 58.772 36.000 0.00 0.00 37.13 2.69
4478 4936 6.758886 ACTTTTCCTTCGATTATCTGCTAGTG 59.241 38.462 0.00 0.00 0.00 2.74
4575 5033 4.657814 TCTATCCCCTTTGCAGAAACTT 57.342 40.909 0.00 0.00 0.00 2.66
4886 5344 0.320771 AGGGATGCGGCGATATTGAC 60.321 55.000 12.98 0.00 0.00 3.18
4960 5425 0.623723 AGTCCTTCGCCTCTCTCTCT 59.376 55.000 0.00 0.00 0.00 3.10
4961 5426 1.021968 GTCCTTCGCCTCTCTCTCTC 58.978 60.000 0.00 0.00 0.00 3.20
4962 5427 0.916086 TCCTTCGCCTCTCTCTCTCT 59.084 55.000 0.00 0.00 0.00 3.10
4963 5428 1.134220 TCCTTCGCCTCTCTCTCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
4964 5429 1.134098 CCTTCGCCTCTCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
4965 5430 2.213499 CTTCGCCTCTCTCTCTCTCTC 58.787 57.143 0.00 0.00 0.00 3.20
4966 5431 1.496060 TCGCCTCTCTCTCTCTCTCT 58.504 55.000 0.00 0.00 0.00 3.10
4967 5432 1.412710 TCGCCTCTCTCTCTCTCTCTC 59.587 57.143 0.00 0.00 0.00 3.20
4978 5443 6.980577 TCTCTCTCTCTCTCCCTCTTTAATT 58.019 40.000 0.00 0.00 0.00 1.40
5010 5475 3.802866 CCTCATTAGTTCCTGGCTCTTC 58.197 50.000 0.00 0.00 0.00 2.87
5087 5555 7.857734 TTGTAGACACAAAGAAATGAGTGAA 57.142 32.000 0.00 0.00 41.69 3.18
5238 5708 1.826096 AGTTACTCGGAAAGGAGCTCC 59.174 52.381 26.22 26.22 37.57 4.70
5414 5890 3.968649 CTGTTTAGCACATGCACTGTTT 58.031 40.909 6.64 0.00 45.16 2.83
5416 5892 3.379688 TGTTTAGCACATGCACTGTTTGA 59.620 39.130 6.64 0.00 45.16 2.69
5418 5894 5.240403 TGTTTAGCACATGCACTGTTTGATA 59.760 36.000 6.64 0.00 45.16 2.15
5478 5955 5.170270 GCAATTCGAGTTATTTCATTGCGAG 59.830 40.000 10.41 0.00 37.75 5.03
5489 5966 2.932498 TCATTGCGAGATTTTGCACAC 58.068 42.857 0.00 0.00 43.38 3.82
5613 6090 6.013379 TGTCCTCCAAAATGCCTTAACATTA 58.987 36.000 0.00 0.00 39.32 1.90
5614 6091 6.667414 TGTCCTCCAAAATGCCTTAACATTAT 59.333 34.615 0.00 0.00 39.32 1.28
5615 6092 7.836685 TGTCCTCCAAAATGCCTTAACATTATA 59.163 33.333 0.00 0.00 39.32 0.98
5616 6093 8.860088 GTCCTCCAAAATGCCTTAACATTATAT 58.140 33.333 0.00 0.00 39.32 0.86
5617 6094 9.077885 TCCTCCAAAATGCCTTAACATTATATC 57.922 33.333 0.00 0.00 39.32 1.63
5618 6095 8.859090 CCTCCAAAATGCCTTAACATTATATCA 58.141 33.333 0.00 0.00 39.32 2.15
5626 6103 8.339344 TGCCTTAACATTATATCATCATGTGG 57.661 34.615 0.00 0.00 31.37 4.17
5627 6104 8.162746 TGCCTTAACATTATATCATCATGTGGA 58.837 33.333 0.00 0.00 31.37 4.02
5628 6105 9.013229 GCCTTAACATTATATCATCATGTGGAA 57.987 33.333 0.00 0.00 31.37 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.861006 GGCGAACTTGGCTCGAAC 59.139 61.111 0.00 0.00 38.61 3.95
230 250 1.079405 GCTCGATCCGAACCAACCA 60.079 57.895 0.00 0.00 34.74 3.67
231 251 0.806492 GAGCTCGATCCGAACCAACC 60.806 60.000 0.00 0.00 34.74 3.77
232 252 1.140407 CGAGCTCGATCCGAACCAAC 61.140 60.000 32.06 0.00 43.02 3.77
233 253 1.138883 CGAGCTCGATCCGAACCAA 59.861 57.895 32.06 0.00 43.02 3.67
234 254 1.747745 TCGAGCTCGATCCGAACCA 60.748 57.895 33.84 9.60 44.22 3.67
302 324 2.893489 CTGGGGAGGGAAAAAGTCAAAG 59.107 50.000 0.00 0.00 0.00 2.77
380 403 1.207329 ACCAGTCTAAATCAGGCGGAC 59.793 52.381 0.00 0.00 32.51 4.79
382 405 1.656652 CACCAGTCTAAATCAGGCGG 58.343 55.000 0.00 0.00 32.51 6.13
405 428 3.557290 GGCCGGGGTAGGTGATCC 61.557 72.222 2.18 0.00 0.00 3.36
406 429 3.557290 GGGCCGGGGTAGGTGATC 61.557 72.222 2.18 0.00 0.00 2.92
407 430 3.954740 TTGGGCCGGGGTAGGTGAT 62.955 63.158 2.18 0.00 0.00 3.06
408 431 3.954740 ATTGGGCCGGGGTAGGTGA 62.955 63.158 2.18 0.00 0.00 4.02
523 553 2.130821 TATGGCAAGCGGTGGGTGAA 62.131 55.000 0.00 0.00 0.00 3.18
525 555 1.447317 GATATGGCAAGCGGTGGGTG 61.447 60.000 0.00 0.00 0.00 4.61
526 556 1.152963 GATATGGCAAGCGGTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
527 557 1.149174 AGATATGGCAAGCGGTGGG 59.851 57.895 0.00 0.00 0.00 4.61
528 558 0.179048 TCAGATATGGCAAGCGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
626 667 2.866085 CTAGAGGCCAGCACCAGCAC 62.866 65.000 5.01 0.00 45.49 4.40
627 668 2.607442 TAGAGGCCAGCACCAGCA 60.607 61.111 5.01 0.00 45.49 4.41
628 669 2.188994 CTAGAGGCCAGCACCAGC 59.811 66.667 5.01 0.00 42.56 4.85
629 670 1.687146 TCCTAGAGGCCAGCACCAG 60.687 63.158 5.01 0.00 34.44 4.00
642 683 1.689273 CTGGAAGAATCGGGGTCCTAG 59.311 57.143 0.00 0.00 34.07 3.02
660 701 0.029035 GCAAGCTGAATGGCGATCTG 59.971 55.000 0.00 0.00 37.29 2.90
669 713 6.870439 GGAAGTAAAAATCAAGCAAGCTGAAT 59.130 34.615 0.00 0.00 0.00 2.57
692 736 4.383770 GGTCATCTATTTTGGAACCGAGGA 60.384 45.833 0.00 0.00 0.00 3.71
694 738 3.877508 GGGTCATCTATTTTGGAACCGAG 59.122 47.826 0.00 0.00 0.00 4.63
697 741 5.016831 AGTTGGGTCATCTATTTTGGAACC 58.983 41.667 0.00 0.00 37.64 3.62
698 742 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
699 743 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
701 745 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
702 746 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
704 748 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
705 749 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
706 750 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
707 751 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
708 752 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
709 753 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
710 754 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
711 755 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
724 768 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
725 769 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
726 770 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
727 771 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
729 773 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
730 774 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
731 775 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
732 776 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
733 777 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
734 778 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
735 779 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
736 780 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
737 781 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
738 782 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
739 783 6.014584 GGTTCCAAAATAGATGACCCAACTTT 60.015 38.462 0.00 0.00 0.00 2.66
740 784 5.480422 GGTTCCAAAATAGATGACCCAACTT 59.520 40.000 0.00 0.00 0.00 2.66
741 785 5.016831 GGTTCCAAAATAGATGACCCAACT 58.983 41.667 0.00 0.00 0.00 3.16
742 786 4.142469 CGGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
743 787 4.013728 CGGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
744 788 3.264706 TCGGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
745 789 3.877508 CTCGGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
746 790 3.877508 CCTCGGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
747 791 3.877508 CCCTCGGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
748 792 3.778075 TCCCTCGGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
749 793 4.130118 CTCCCTCGGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
750 794 3.780850 ACTCCCTCGGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
751 795 3.178865 ACTCCCTCGGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
752 796 3.629142 ACTCCCTCGGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
753 797 4.081309 CAGTACTCCCTCGGTTCCAAAATA 60.081 45.833 0.00 0.00 0.00 1.40
754 798 2.910977 AGTACTCCCTCGGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
755 799 2.038033 CAGTACTCCCTCGGTTCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
756 800 1.621814 CAGTACTCCCTCGGTTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
757 801 1.263356 CAGTACTCCCTCGGTTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
758 802 0.113776 ACAGTACTCCCTCGGTTCCA 59.886 55.000 0.00 0.00 0.00 3.53
759 803 1.747924 GTACAGTACTCCCTCGGTTCC 59.252 57.143 3.19 0.00 0.00 3.62
760 804 2.720915 AGTACAGTACTCCCTCGGTTC 58.279 52.381 7.48 0.00 32.47 3.62
761 805 2.895242 AGTACAGTACTCCCTCGGTT 57.105 50.000 7.48 0.00 32.47 4.44
762 806 2.843113 AGTAGTACAGTACTCCCTCGGT 59.157 50.000 16.91 0.00 40.14 4.69
763 807 3.557228 AGTAGTACAGTACTCCCTCGG 57.443 52.381 16.91 0.00 40.14 4.63
764 808 3.555139 CGAAGTAGTACAGTACTCCCTCG 59.445 52.174 16.91 17.13 40.14 4.63
765 809 4.512484 ACGAAGTAGTACAGTACTCCCTC 58.488 47.826 16.91 10.32 41.94 4.30
766 810 4.566426 ACGAAGTAGTACAGTACTCCCT 57.434 45.455 16.91 11.12 41.94 4.20
782 826 4.117685 TGATGCAAGAGATCATGACGAAG 58.882 43.478 0.00 0.00 0.00 3.79
783 827 4.117685 CTGATGCAAGAGATCATGACGAA 58.882 43.478 0.00 0.00 0.00 3.85
784 828 3.714391 CTGATGCAAGAGATCATGACGA 58.286 45.455 0.00 0.00 0.00 4.20
785 829 2.221286 GCTGATGCAAGAGATCATGACG 59.779 50.000 0.00 0.00 39.41 4.35
786 830 2.221286 CGCTGATGCAAGAGATCATGAC 59.779 50.000 0.00 0.00 39.64 3.06
806 850 3.179265 CACGAGGTAAGCACGGCG 61.179 66.667 4.80 4.80 0.00 6.46
825 869 1.180029 CCTTCCCCTGCATTCACAAG 58.820 55.000 0.00 0.00 0.00 3.16
830 874 1.380380 CACCCCTTCCCCTGCATTC 60.380 63.158 0.00 0.00 0.00 2.67
865 913 0.032813 ACCAGGGCCTGATGAAATGG 60.033 55.000 34.84 18.47 32.44 3.16
905 953 1.109323 AGCTCTGGTTGTTTGGGTGC 61.109 55.000 0.00 0.00 0.00 5.01
907 955 2.159179 AAAGCTCTGGTTGTTTGGGT 57.841 45.000 0.00 0.00 0.00 4.51
908 956 3.888930 TCTAAAAGCTCTGGTTGTTTGGG 59.111 43.478 0.00 0.00 0.00 4.12
910 958 6.317789 TCATCTAAAAGCTCTGGTTGTTTG 57.682 37.500 0.00 0.00 0.00 2.93
919 967 6.771749 CCATCTTTGGATCATCTAAAAGCTCT 59.228 38.462 0.00 0.00 46.92 4.09
1155 1203 1.022451 GCCAATCCTTGAACGGCGTA 61.022 55.000 15.20 0.00 32.14 4.42
1248 1296 1.745115 CGACGTGGACATGGGCATT 60.745 57.895 0.00 0.00 0.00 3.56
1284 1332 4.074970 AGCCAGGTGTCAAGAACATAAAG 58.925 43.478 0.00 0.00 40.80 1.85
1421 1731 3.388024 TGATACCTAGGCACCATCAGTTC 59.612 47.826 9.30 0.00 0.00 3.01
1800 2126 5.013547 ACATAGATGGAGTATCTTCCCTCG 58.986 45.833 0.00 0.00 43.68 4.63
2049 2375 5.824904 ATCAGTTGAGCCATTAACACATC 57.175 39.130 0.00 0.00 0.00 3.06
2280 2606 6.270000 TGGTCTTTAGAAGTCAGAAGATCCAA 59.730 38.462 0.00 0.00 32.06 3.53
2344 2670 4.333926 GCTCCTCAACTTGCAATTAGTAGG 59.666 45.833 0.00 4.19 0.00 3.18
2358 2685 2.884639 TGTAAAGGCAAAGCTCCTCAAC 59.115 45.455 0.00 0.00 32.45 3.18
2360 2687 2.949177 TGTAAAGGCAAAGCTCCTCA 57.051 45.000 0.00 0.00 32.45 3.86
2689 3069 9.653287 CAGTACTCTTACCAATCAATGAAACTA 57.347 33.333 0.00 0.00 0.00 2.24
2710 3090 7.624360 TGGTAATGAAATCAATGTCCAGTAC 57.376 36.000 0.00 0.00 0.00 2.73
2748 3129 2.760650 CACTAATTCCCCTTTGCTTCCC 59.239 50.000 0.00 0.00 0.00 3.97
2754 3135 6.215845 CACTTGTTTCACTAATTCCCCTTTG 58.784 40.000 0.00 0.00 0.00 2.77
2819 3200 7.148137 GGACACCTATAAGTGGTAAAACAATGG 60.148 40.741 6.44 0.00 42.28 3.16
2830 3211 3.454447 TGGACATGGACACCTATAAGTGG 59.546 47.826 6.44 0.00 42.28 4.00
2874 3255 8.964476 TTGGAAACTACAAAATGGCAATAAAA 57.036 26.923 0.00 0.00 0.00 1.52
2899 3280 1.971149 TTCCATGTGGACCAGGATCT 58.029 50.000 0.15 0.00 45.39 2.75
3019 3400 2.869233 ACACATTGCAAGGACAACAC 57.131 45.000 19.41 0.00 31.03 3.32
3026 3407 5.713025 AGCAAACTTATACACATTGCAAGG 58.287 37.500 10.01 10.01 46.59 3.61
3062 3443 6.161381 GTCAAAGCATGAATTTGGAACAGAT 58.839 36.000 18.33 0.00 39.09 2.90
3126 3513 6.435591 TGGATACTGATCTGATGGTGTCTATC 59.564 42.308 6.60 1.26 37.61 2.08
3152 3539 8.922058 AAATCACAATCATATGAAAGTGCTTC 57.078 30.769 24.89 0.00 34.78 3.86
3274 3662 5.979993 TGAACAAGTCCGCTTTATACCATA 58.020 37.500 0.00 0.00 31.49 2.74
3287 3675 7.142680 TCAATAACCGATTTTTGAACAAGTCC 58.857 34.615 0.00 0.00 34.18 3.85
3555 3982 7.831193 ACAACTCCAGCTTCATATTAGAACATT 59.169 33.333 0.00 0.00 0.00 2.71
3659 4087 6.655078 ATTTTCTGCTGTTTATGGAAGTGT 57.345 33.333 0.00 0.00 0.00 3.55
3674 4109 5.798934 CAGAGTCTGCACATTAATTTTCTGC 59.201 40.000 7.33 0.00 0.00 4.26
3692 4127 3.996480 AGGACTACTTTGCAACAGAGTC 58.004 45.455 18.87 18.87 31.33 3.36
3831 4268 4.098654 ACTTCAGGAATGATGACTACCGAG 59.901 45.833 0.00 0.00 0.00 4.63
3873 4310 5.989777 TCGGAGAAAACTAGAAAAGTGGAAG 59.010 40.000 0.00 0.00 38.88 3.46
3932 4369 4.096833 GGCTGCAAATCACATGACAGATAA 59.903 41.667 0.00 0.00 0.00 1.75
3933 4370 3.628942 GGCTGCAAATCACATGACAGATA 59.371 43.478 0.00 0.00 0.00 1.98
3934 4371 2.426024 GGCTGCAAATCACATGACAGAT 59.574 45.455 0.00 0.00 0.00 2.90
3936 4373 1.542472 TGGCTGCAAATCACATGACAG 59.458 47.619 0.00 0.00 0.00 3.51
3992 4434 3.763360 TGACATTGAATAGGGTTGGCAAG 59.237 43.478 0.00 0.00 0.00 4.01
4078 4523 5.129485 ACCATCTGATGTTTCGTAGAAGGAT 59.871 40.000 15.95 0.00 45.90 3.24
4130 4575 4.041567 TCAGACCAATCCACATGTGTAACT 59.958 41.667 23.79 10.22 38.04 2.24
4296 4741 7.798516 CGGTAATGTACATTAGAATGCATCAAC 59.201 37.037 25.18 13.17 40.04 3.18
4303 4748 5.460748 TGCGACGGTAATGTACATTAGAATG 59.539 40.000 25.18 17.42 42.10 2.67
4368 4813 3.886505 TGACGAAATTATTGCCCATACCC 59.113 43.478 0.00 0.00 0.00 3.69
4388 4833 8.567948 GTTCTTTGAAGGTCAAAATACTGATGA 58.432 33.333 5.06 0.00 44.69 2.92
4446 4900 9.982651 CAGATAATCGAAGGAAAAGTAATAGGA 57.017 33.333 0.00 0.00 0.00 2.94
4509 4967 2.234908 AGTTGTAGCAGATCACTGGGAC 59.765 50.000 0.00 0.00 43.62 4.46
4575 5033 2.346766 AACATGGCTTCTGTGTCACA 57.653 45.000 5.36 5.36 0.00 3.58
4771 5229 9.653287 TCTAAGTATCGATTGACTTCACAAATT 57.347 29.630 15.19 0.00 37.16 1.82
4772 5230 9.823647 ATCTAAGTATCGATTGACTTCACAAAT 57.176 29.630 15.19 3.52 37.16 2.32
4773 5231 9.302345 GATCTAAGTATCGATTGACTTCACAAA 57.698 33.333 15.19 0.00 37.16 2.83
4886 5344 0.665670 CGAGGGCAGTATCATCGCTG 60.666 60.000 0.00 0.00 35.93 5.18
4960 5425 6.155393 GGACAGAAATTAAAGAGGGAGAGAGA 59.845 42.308 0.00 0.00 0.00 3.10
4961 5426 6.156083 AGGACAGAAATTAAAGAGGGAGAGAG 59.844 42.308 0.00 0.00 0.00 3.20
4962 5427 6.026186 AGGACAGAAATTAAAGAGGGAGAGA 58.974 40.000 0.00 0.00 0.00 3.10
4963 5428 6.306643 AGGACAGAAATTAAAGAGGGAGAG 57.693 41.667 0.00 0.00 0.00 3.20
4964 5429 6.127026 GCTAGGACAGAAATTAAAGAGGGAGA 60.127 42.308 0.00 0.00 0.00 3.71
4965 5430 6.052360 GCTAGGACAGAAATTAAAGAGGGAG 58.948 44.000 0.00 0.00 0.00 4.30
4966 5431 5.104485 GGCTAGGACAGAAATTAAAGAGGGA 60.104 44.000 0.00 0.00 0.00 4.20
4967 5432 5.104318 AGGCTAGGACAGAAATTAAAGAGGG 60.104 44.000 0.00 0.00 0.00 4.30
4978 5443 4.406003 GGAACTAATGAGGCTAGGACAGAA 59.594 45.833 0.00 0.00 0.00 3.02
5010 5475 7.307493 TGACAAAAATATGATCTCCAACTCG 57.693 36.000 0.00 0.00 0.00 4.18
5047 5512 9.112725 TGTGTCTACAAAAGAATGGATCATATG 57.887 33.333 0.00 0.00 35.47 1.78
5461 5938 6.527722 TGCAAAATCTCGCAATGAAATAACTC 59.472 34.615 0.00 0.00 34.59 3.01
5478 5955 7.483307 AGGATGTAATGTATGTGTGCAAAATC 58.517 34.615 0.00 0.00 0.00 2.17
5613 6090 6.893554 CCATGGGTATTTCCACATGATGATAT 59.106 38.462 2.85 0.00 42.29 1.63
5614 6091 6.247676 CCATGGGTATTTCCACATGATGATA 58.752 40.000 2.85 0.00 42.29 2.15
5615 6092 5.081728 CCATGGGTATTTCCACATGATGAT 58.918 41.667 2.85 0.00 42.29 2.45
5616 6093 4.472496 CCATGGGTATTTCCACATGATGA 58.528 43.478 2.85 0.00 42.29 2.92
5617 6094 3.006110 GCCATGGGTATTTCCACATGATG 59.994 47.826 15.13 0.00 42.29 3.07
5618 6095 3.117016 AGCCATGGGTATTTCCACATGAT 60.117 43.478 16.58 0.00 42.29 2.45
5619 6096 2.244510 AGCCATGGGTATTTCCACATGA 59.755 45.455 16.58 0.00 42.29 3.07
5620 6097 2.363038 CAGCCATGGGTATTTCCACATG 59.637 50.000 17.80 0.00 39.97 3.21
5621 6098 2.244510 TCAGCCATGGGTATTTCCACAT 59.755 45.455 17.80 0.00 39.97 3.21
5622 6099 1.638070 TCAGCCATGGGTATTTCCACA 59.362 47.619 17.80 0.00 39.97 4.17
5623 6100 2.435372 TCAGCCATGGGTATTTCCAC 57.565 50.000 17.80 0.00 39.97 4.02
5624 6101 3.298619 CATTCAGCCATGGGTATTTCCA 58.701 45.455 17.80 0.00 41.60 3.53
5625 6102 3.068590 CACATTCAGCCATGGGTATTTCC 59.931 47.826 17.80 0.00 0.00 3.13
5626 6103 3.701040 ACACATTCAGCCATGGGTATTTC 59.299 43.478 17.80 0.00 39.13 2.17
5627 6104 3.711863 ACACATTCAGCCATGGGTATTT 58.288 40.909 17.80 0.64 39.13 1.40
5628 6105 3.386932 ACACATTCAGCCATGGGTATT 57.613 42.857 17.80 1.04 39.13 1.89


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

AutoCloner maintained by Alex Coulton.