Multiple sequence alignment - TraesCS5B01G477100

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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 TraesCS5B01G477100 chr5B 100.000 3266 0 0 1 3266 649452942 649456207 0.000000e+00 6032.0
1 TraesCS5B01G477100 chr5B 78.404 1278 223 31 953 2214 651211059 651212299 0.000000e+00 782.0
2 TraesCS5B01G477100 chr5B 78.228 1185 207 29 953 2122 650983115 650984263 0.000000e+00 712.0
3 TraesCS5B01G477100 chr5B 83.884 726 70 23 1 691 148882943 148883656 0.000000e+00 649.0
4 TraesCS5B01G477100 chr5B 83.707 669 81 19 71 729 293250065 293249415 1.000000e-169 606.0
5 TraesCS5B01G477100 chr5B 78.484 818 135 25 1413 2214 652375835 652376627 6.290000e-137 497.0
6 TraesCS5B01G477100 chr5B 82.569 109 19 0 2772 2880 709330998 709330890 2.680000e-16 97.1
7 TraesCS5B01G477100 chr5B 83.871 93 15 0 2656 2748 684625614 684625522 4.490000e-14 89.8
8 TraesCS5B01G477100 chr5B 97.297 37 1 0 2770 2806 137049692 137049728 2.720000e-06 63.9
9 TraesCS5B01G477100 chr5D 95.625 1440 51 3 883 2319 517046053 517047483 0.000000e+00 2300.0
10 TraesCS5B01G477100 chr5D 78.201 1312 224 36 921 2214 517976283 517975016 0.000000e+00 782.0
11 TraesCS5B01G477100 chr5D 78.092 1310 230 33 921 2214 518755457 518756725 0.000000e+00 776.0
12 TraesCS5B01G477100 chr5D 88.839 448 25 7 2301 2748 517047494 517047916 8.030000e-146 527.0
13 TraesCS5B01G477100 chr5D 83.936 498 63 3 2769 3266 517048169 517048649 8.260000e-126 460.0
14 TraesCS5B01G477100 chr5D 82.051 117 21 0 2769 2885 28996692 28996576 2.070000e-17 100.0
15 TraesCS5B01G477100 chr5A 88.788 1106 78 20 1650 2751 644208727 644209790 0.000000e+00 1314.0
16 TraesCS5B01G477100 chr5A 90.704 753 63 3 906 1652 644176880 644177631 0.000000e+00 996.0
17 TraesCS5B01G477100 chr5A 79.848 526 92 8 1530 2048 644330000 644330518 3.980000e-99 372.0
18 TraesCS5B01G477100 chr6B 86.658 742 76 18 1 728 476337828 476337096 0.000000e+00 800.0
19 TraesCS5B01G477100 chr6B 83.158 95 14 2 2655 2748 562544240 562544333 5.810000e-13 86.1
20 TraesCS5B01G477100 chr6B 75.497 151 28 7 2599 2748 661913191 661913049 7.560000e-07 65.8
21 TraesCS5B01G477100 chr1B 86.912 680 64 15 70 729 268395526 268394852 0.000000e+00 739.0
22 TraesCS5B01G477100 chr1B 83.752 757 90 21 1 728 684622866 684623618 0.000000e+00 686.0
23 TraesCS5B01G477100 chr1B 77.551 196 32 7 2552 2746 681057244 681057428 1.240000e-19 108.0
24 TraesCS5B01G477100 chr2B 84.768 755 72 19 1 734 642971274 642972006 0.000000e+00 717.0
25 TraesCS5B01G477100 chr2B 84.211 114 14 3 2774 2885 18022383 18022494 1.240000e-19 108.0
26 TraesCS5B01G477100 chr1A 83.735 664 80 20 70 716 557944907 557944255 1.300000e-168 603.0
27 TraesCS5B01G477100 chr1A 81.897 116 12 6 2633 2748 404559590 404559696 4.490000e-14 89.8
28 TraesCS5B01G477100 chr1A 87.143 70 9 0 2910 2979 263155392 263155461 2.700000e-11 80.5
29 TraesCS5B01G477100 chr1A 83.333 90 11 4 2660 2748 299179439 299179353 2.700000e-11 80.5
30 TraesCS5B01G477100 chr1A 86.364 66 9 0 2882 2947 121558849 121558914 4.520000e-09 73.1
31 TraesCS5B01G477100 chr1A 93.023 43 3 0 2712 2754 463035586 463035544 2.720000e-06 63.9
32 TraesCS5B01G477100 chr7D 84.603 630 67 20 121 729 204444318 204444938 1.680000e-167 599.0
33 TraesCS5B01G477100 chr7D 81.525 682 89 21 73 726 31600247 31599575 8.030000e-146 527.0
34 TraesCS5B01G477100 chr7D 83.713 571 55 23 180 728 422340446 422339892 3.760000e-139 505.0
35 TraesCS5B01G477100 chr7D 82.456 114 18 2 2773 2885 287897457 287897569 7.460000e-17 99.0
36 TraesCS5B01G477100 chr6A 82.448 678 89 22 70 728 387874941 387875607 1.700000e-157 566.0
37 TraesCS5B01G477100 chr6A 83.636 110 18 0 2769 2878 374426322 374426213 1.600000e-18 104.0
38 TraesCS5B01G477100 chr6A 79.310 145 20 5 2605 2748 16340922 16341057 3.470000e-15 93.5
39 TraesCS5B01G477100 chr3D 78.696 859 131 24 1465 2295 597867947 597868781 2.890000e-145 525.0
40 TraesCS5B01G477100 chr3D 80.242 496 69 19 875 1351 597863791 597864276 2.410000e-91 346.0
41 TraesCS5B01G477100 chr3D 84.444 270 41 1 2880 3148 423849703 423849972 6.950000e-67 265.0
42 TraesCS5B01G477100 chr3D 86.000 100 13 1 2882 2980 449202300 449202399 4.460000e-19 106.0
43 TraesCS5B01G477100 chr3D 84.270 89 12 2 2660 2748 563842219 563842305 5.810000e-13 86.1
44 TraesCS5B01G477100 chr2D 81.669 671 82 29 70 728 426918170 426917529 1.340000e-143 520.0
45 TraesCS5B01G477100 chr2D 84.043 94 15 0 2655 2748 71849295 71849202 1.250000e-14 91.6
46 TraesCS5B01G477100 chr4B 84.018 438 47 13 290 722 14540840 14540421 1.830000e-107 399.0
47 TraesCS5B01G477100 chr4B 75.532 188 35 7 2562 2748 571903926 571904103 7.510000e-12 82.4
48 TraesCS5B01G477100 chr4B 97.297 37 1 0 2712 2748 495353806 495353842 2.720000e-06 63.9
49 TraesCS5B01G477100 chr4D 88.043 92 11 0 2657 2748 495111336 495111427 3.450000e-20 110.0
50 TraesCS5B01G477100 chr4D 81.915 94 17 0 2655 2748 3776946 3777039 2.700000e-11 80.5
51 TraesCS5B01G477100 chr2A 83.621 116 18 1 2769 2884 94203286 94203172 1.240000e-19 108.0
52 TraesCS5B01G477100 chr1D 77.436 195 34 7 2552 2746 488609867 488609683 1.240000e-19 108.0
53 TraesCS5B01G477100 chr1D 83.036 112 19 0 2769 2880 2122459 2122348 5.770000e-18 102.0
54 TraesCS5B01G477100 chr1D 81.416 113 19 2 2769 2880 270024598 270024487 1.250000e-14 91.6
55 TraesCS5B01G477100 chr1D 81.481 108 20 0 2778 2885 445998806 445998913 4.490000e-14 89.8
56 TraesCS5B01G477100 chr1D 92.982 57 4 0 2689 2745 307665387 307665443 2.090000e-12 84.2
57 TraesCS5B01G477100 chr3A 82.677 127 15 5 2882 3005 591600604 591600726 4.460000e-19 106.0
58 TraesCS5B01G477100 chr7A 82.759 116 20 0 2766 2881 393325549 393325664 1.600000e-18 104.0
59 TraesCS5B01G477100 chr7A 81.553 103 19 0 2769 2871 558758275 558758173 5.810000e-13 86.1
60 TraesCS5B01G477100 chr7B 90.541 74 7 0 2675 2748 687299919 687299992 7.460000e-17 99.0
61 TraesCS5B01G477100 chr7B 87.500 80 8 1 2669 2748 424011724 424011647 1.250000e-14 91.6
62 TraesCS5B01G477100 chr7B 76.923 182 29 6 2570 2748 687678294 687678123 1.250000e-14 91.6
63 TraesCS5B01G477100 chr7B 78.261 115 24 1 2771 2885 513819862 513819975 4.520000e-09 73.1
64 TraesCS5B01G477100 chrUn 87.838 74 7 2 2673 2745 62652877 62652949 5.810000e-13 86.1
65 TraesCS5B01G477100 chr4A 82.979 94 15 1 2655 2748 628628601 628628693 2.090000e-12 84.2
66 TraesCS5B01G477100 chr3B 82.796 93 14 2 2884 2974 624809009 624809101 7.510000e-12 82.4
67 TraesCS5B01G477100 chr6D 78.761 113 23 1 2769 2881 380821043 380820932 1.260000e-09 75.0
68 TraesCS5B01G477100 chr6D 79.439 107 16 2 2778 2884 156427086 156426986 1.630000e-08 71.3
69 TraesCS5B01G477100 chr6D 78.723 94 20 0 2655 2748 57878017 57878110 2.720000e-06 63.9


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 TraesCS5B01G477100 chr5B 649452942 649456207 3265 False 6032.000000 6032 100.000000 1 3266 1 chr5B.!!$F3 3265
1 TraesCS5B01G477100 chr5B 651211059 651212299 1240 False 782.000000 782 78.404000 953 2214 1 chr5B.!!$F5 1261
2 TraesCS5B01G477100 chr5B 650983115 650984263 1148 False 712.000000 712 78.228000 953 2122 1 chr5B.!!$F4 1169
3 TraesCS5B01G477100 chr5B 148882943 148883656 713 False 649.000000 649 83.884000 1 691 1 chr5B.!!$F2 690
4 TraesCS5B01G477100 chr5B 293249415 293250065 650 True 606.000000 606 83.707000 71 729 1 chr5B.!!$R1 658
5 TraesCS5B01G477100 chr5B 652375835 652376627 792 False 497.000000 497 78.484000 1413 2214 1 chr5B.!!$F6 801
6 TraesCS5B01G477100 chr5D 517046053 517048649 2596 False 1095.666667 2300 89.466667 883 3266 3 chr5D.!!$F2 2383
7 TraesCS5B01G477100 chr5D 517975016 517976283 1267 True 782.000000 782 78.201000 921 2214 1 chr5D.!!$R2 1293
8 TraesCS5B01G477100 chr5D 518755457 518756725 1268 False 776.000000 776 78.092000 921 2214 1 chr5D.!!$F1 1293
9 TraesCS5B01G477100 chr5A 644208727 644209790 1063 False 1314.000000 1314 88.788000 1650 2751 1 chr5A.!!$F2 1101
10 TraesCS5B01G477100 chr5A 644176880 644177631 751 False 996.000000 996 90.704000 906 1652 1 chr5A.!!$F1 746
11 TraesCS5B01G477100 chr5A 644330000 644330518 518 False 372.000000 372 79.848000 1530 2048 1 chr5A.!!$F3 518
12 TraesCS5B01G477100 chr6B 476337096 476337828 732 True 800.000000 800 86.658000 1 728 1 chr6B.!!$R1 727
13 TraesCS5B01G477100 chr1B 268394852 268395526 674 True 739.000000 739 86.912000 70 729 1 chr1B.!!$R1 659
14 TraesCS5B01G477100 chr1B 684622866 684623618 752 False 686.000000 686 83.752000 1 728 1 chr1B.!!$F2 727
15 TraesCS5B01G477100 chr2B 642971274 642972006 732 False 717.000000 717 84.768000 1 734 1 chr2B.!!$F2 733
16 TraesCS5B01G477100 chr1A 557944255 557944907 652 True 603.000000 603 83.735000 70 716 1 chr1A.!!$R3 646
17 TraesCS5B01G477100 chr7D 204444318 204444938 620 False 599.000000 599 84.603000 121 729 1 chr7D.!!$F1 608
18 TraesCS5B01G477100 chr7D 31599575 31600247 672 True 527.000000 527 81.525000 73 726 1 chr7D.!!$R1 653
19 TraesCS5B01G477100 chr7D 422339892 422340446 554 True 505.000000 505 83.713000 180 728 1 chr7D.!!$R2 548
20 TraesCS5B01G477100 chr6A 387874941 387875607 666 False 566.000000 566 82.448000 70 728 1 chr6A.!!$F2 658
21 TraesCS5B01G477100 chr3D 597863791 597868781 4990 False 435.500000 525 79.469000 875 2295 2 chr3D.!!$F4 1420
22 TraesCS5B01G477100 chr2D 426917529 426918170 641 True 520.000000 520 81.669000 70 728 1 chr2D.!!$R2 658

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
821 1023 0.026803 GCGACCATTGAGCGCTTAAG 59.973 55.0 19.88 9.89 46.53 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 6905 0.106894 CTTATCGCCCCTTCCTCACC 59.893 60.0 0.0 0.0 0.0 4.02 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
131 150 0.396435 AATCACAACCGTGCCTCTCA 59.604 50.000 0.00 0.00 43.28 3.27
153 172 0.668535 GAAGCAAAACCGTGCCTCTT 59.331 50.000 0.00 0.00 46.14 2.85
338 490 2.288213 TGACTCTCGCGAAATCACAACT 60.288 45.455 11.33 0.00 0.00 3.16
344 496 0.387239 GCGAAATCACAACTGTGCCC 60.387 55.000 4.92 0.00 45.25 5.36
349 501 1.768684 ATCACAACTGTGCCCCTCGT 61.769 55.000 4.92 0.00 45.25 4.18
362 514 0.821711 CCCTCGTGGAAGCAAAACCA 60.822 55.000 4.76 0.00 35.39 3.67
384 537 2.552315 TGCCTCTCGCGAAAAGAAAAAT 59.448 40.909 11.33 0.00 42.08 1.82
385 538 3.749088 TGCCTCTCGCGAAAAGAAAAATA 59.251 39.130 11.33 0.00 42.08 1.40
388 541 5.800438 GCCTCTCGCGAAAAGAAAAATAAAT 59.200 36.000 11.33 0.00 0.00 1.40
558 743 1.073098 AGGGAAGACCGGTGGAAAAT 58.927 50.000 14.63 0.00 46.96 1.82
617 807 0.112904 CGAAAACGCGTGCGAAAAAC 60.113 50.000 22.32 7.11 42.83 2.43
623 825 1.327292 CGCGTGCGAAAAACATCCAC 61.327 55.000 8.89 0.00 42.83 4.02
729 931 3.309954 GCTCGTTAATTAGTTGCTCCCAG 59.690 47.826 0.00 0.00 0.00 4.45
730 932 3.267483 TCGTTAATTAGTTGCTCCCAGC 58.733 45.455 0.00 0.00 42.82 4.85
731 933 2.030457 CGTTAATTAGTTGCTCCCAGCG 59.970 50.000 0.00 0.00 46.26 5.18
732 934 3.267483 GTTAATTAGTTGCTCCCAGCGA 58.733 45.455 0.00 0.00 46.26 4.93
733 935 2.029838 AATTAGTTGCTCCCAGCGAG 57.970 50.000 0.00 0.00 46.26 5.03
734 936 0.905357 ATTAGTTGCTCCCAGCGAGT 59.095 50.000 0.00 0.00 46.26 4.18
735 937 0.037326 TTAGTTGCTCCCAGCGAGTG 60.037 55.000 3.66 0.00 46.26 3.51
736 938 2.507110 TAGTTGCTCCCAGCGAGTGC 62.507 60.000 3.66 0.00 46.26 4.40
737 939 4.704833 TTGCTCCCAGCGAGTGCC 62.705 66.667 0.00 0.00 46.26 5.01
742 944 4.063967 CCCAGCGAGTGCCACGTA 62.064 66.667 0.00 0.00 44.31 3.57
743 945 2.048597 CCAGCGAGTGCCACGTAA 60.049 61.111 0.00 0.00 44.31 3.18
744 946 1.666553 CCAGCGAGTGCCACGTAAA 60.667 57.895 0.00 0.00 44.31 2.01
745 947 1.225376 CCAGCGAGTGCCACGTAAAA 61.225 55.000 0.00 0.00 44.31 1.52
746 948 0.584396 CAGCGAGTGCCACGTAAAAA 59.416 50.000 0.00 0.00 44.31 1.94
747 949 1.196808 CAGCGAGTGCCACGTAAAAAT 59.803 47.619 0.00 0.00 44.31 1.82
748 950 2.413796 CAGCGAGTGCCACGTAAAAATA 59.586 45.455 0.00 0.00 44.31 1.40
749 951 3.068560 AGCGAGTGCCACGTAAAAATAA 58.931 40.909 0.00 0.00 44.31 1.40
750 952 3.687698 AGCGAGTGCCACGTAAAAATAAT 59.312 39.130 0.00 0.00 44.31 1.28
751 953 4.871557 AGCGAGTGCCACGTAAAAATAATA 59.128 37.500 0.00 0.00 44.31 0.98
752 954 5.352016 AGCGAGTGCCACGTAAAAATAATAA 59.648 36.000 0.00 0.00 44.31 1.40
753 955 6.037830 AGCGAGTGCCACGTAAAAATAATAAT 59.962 34.615 0.00 0.00 44.31 1.28
754 956 6.356190 GCGAGTGCCACGTAAAAATAATAATC 59.644 38.462 0.00 0.00 33.98 1.75
755 957 6.568601 CGAGTGCCACGTAAAAATAATAATCG 59.431 38.462 0.00 0.00 0.00 3.34
756 958 7.311364 AGTGCCACGTAAAAATAATAATCGT 57.689 32.000 0.00 0.00 0.00 3.73
757 959 8.422973 AGTGCCACGTAAAAATAATAATCGTA 57.577 30.769 0.00 0.00 0.00 3.43
758 960 8.545420 AGTGCCACGTAAAAATAATAATCGTAG 58.455 33.333 0.00 0.00 0.00 3.51
759 961 7.319615 GTGCCACGTAAAAATAATAATCGTAGC 59.680 37.037 0.00 0.00 35.77 3.58
760 962 6.513991 GCCACGTAAAAATAATAATCGTAGCG 59.486 38.462 0.00 0.00 0.00 4.26
761 963 7.567409 GCCACGTAAAAATAATAATCGTAGCGA 60.567 37.037 0.00 0.00 41.13 4.93
762 964 7.943065 CCACGTAAAAATAATAATCGTAGCGAG 59.057 37.037 0.00 0.00 39.91 5.03
763 965 7.943065 CACGTAAAAATAATAATCGTAGCGAGG 59.057 37.037 0.00 0.00 39.91 4.63
764 966 7.649306 ACGTAAAAATAATAATCGTAGCGAGGT 59.351 33.333 0.00 0.00 39.91 3.85
765 967 7.943065 CGTAAAAATAATAATCGTAGCGAGGTG 59.057 37.037 0.00 0.00 39.91 4.00
766 968 8.971321 GTAAAAATAATAATCGTAGCGAGGTGA 58.029 33.333 0.00 0.00 39.91 4.02
767 969 7.639162 AAAATAATAATCGTAGCGAGGTGAG 57.361 36.000 0.00 0.00 39.91 3.51
768 970 2.708386 ATAATCGTAGCGAGGTGAGC 57.292 50.000 0.00 0.00 39.91 4.26
769 971 0.306840 TAATCGTAGCGAGGTGAGCG 59.693 55.000 0.00 0.00 39.91 5.03
770 972 1.374343 AATCGTAGCGAGGTGAGCGA 61.374 55.000 0.00 0.00 39.91 4.93
771 973 2.049475 ATCGTAGCGAGGTGAGCGAC 62.049 60.000 0.00 0.00 39.91 5.19
772 974 2.277373 GTAGCGAGGTGAGCGACG 60.277 66.667 0.00 0.00 40.04 5.12
775 977 4.175489 GCGAGGTGAGCGACGCTA 62.175 66.667 24.55 8.61 46.06 4.26
776 978 2.716244 CGAGGTGAGCGACGCTAT 59.284 61.111 24.55 9.25 39.88 2.97
777 979 1.064296 CGAGGTGAGCGACGCTATT 59.936 57.895 24.55 8.47 39.88 1.73
778 980 0.525668 CGAGGTGAGCGACGCTATTT 60.526 55.000 24.55 8.85 39.88 1.40
779 981 0.924090 GAGGTGAGCGACGCTATTTG 59.076 55.000 24.55 0.00 39.88 2.32
780 982 0.460284 AGGTGAGCGACGCTATTTGG 60.460 55.000 24.55 0.00 39.88 3.28
781 983 1.348594 GTGAGCGACGCTATTTGGC 59.651 57.895 24.55 9.79 39.88 4.52
782 984 1.813753 TGAGCGACGCTATTTGGCC 60.814 57.895 24.55 8.99 39.88 5.36
783 985 2.513897 AGCGACGCTATTTGGCCC 60.514 61.111 23.15 0.00 36.99 5.80
784 986 3.937062 GCGACGCTATTTGGCCCG 61.937 66.667 13.73 0.00 0.00 6.13
785 987 3.269347 CGACGCTATTTGGCCCGG 61.269 66.667 0.00 0.00 0.00 5.73
786 988 3.583086 GACGCTATTTGGCCCGGC 61.583 66.667 0.00 0.00 0.00 6.13
798 1000 4.483243 CCCGGCCCATAGCGTGTT 62.483 66.667 0.00 0.00 45.17 3.32
799 1001 2.895372 CCGGCCCATAGCGTGTTC 60.895 66.667 0.00 0.00 45.17 3.18
800 1002 2.186903 CGGCCCATAGCGTGTTCT 59.813 61.111 0.00 0.00 45.17 3.01
801 1003 2.173669 CGGCCCATAGCGTGTTCTG 61.174 63.158 0.00 0.00 45.17 3.02
802 1004 1.819632 GGCCCATAGCGTGTTCTGG 60.820 63.158 0.00 0.00 45.17 3.86
803 1005 2.472909 GCCCATAGCGTGTTCTGGC 61.473 63.158 0.00 0.00 0.00 4.85
804 1006 2.173669 CCCATAGCGTGTTCTGGCG 61.174 63.158 0.00 0.00 0.00 5.69
805 1007 1.153647 CCATAGCGTGTTCTGGCGA 60.154 57.895 0.00 0.00 0.00 5.54
806 1008 1.421410 CCATAGCGTGTTCTGGCGAC 61.421 60.000 0.00 0.00 0.00 5.19
807 1009 1.153628 ATAGCGTGTTCTGGCGACC 60.154 57.895 0.00 0.00 0.00 4.79
808 1010 1.884075 ATAGCGTGTTCTGGCGACCA 61.884 55.000 0.00 0.00 0.00 4.02
809 1011 1.884075 TAGCGTGTTCTGGCGACCAT 61.884 55.000 0.00 0.00 30.82 3.55
810 1012 2.325082 GCGTGTTCTGGCGACCATT 61.325 57.895 0.00 0.00 30.82 3.16
811 1013 1.497278 CGTGTTCTGGCGACCATTG 59.503 57.895 0.00 0.00 30.82 2.82
812 1014 0.948623 CGTGTTCTGGCGACCATTGA 60.949 55.000 0.00 0.00 30.82 2.57
813 1015 0.798776 GTGTTCTGGCGACCATTGAG 59.201 55.000 0.00 0.00 30.82 3.02
814 1016 0.955428 TGTTCTGGCGACCATTGAGC 60.955 55.000 0.00 0.00 30.82 4.26
815 1017 1.741401 TTCTGGCGACCATTGAGCG 60.741 57.895 0.00 0.00 30.82 5.03
819 1021 3.794270 GCGACCATTGAGCGCTTA 58.206 55.556 13.26 3.74 46.53 3.09
820 1022 2.086510 GCGACCATTGAGCGCTTAA 58.913 52.632 17.56 17.56 46.53 1.85
821 1023 0.026803 GCGACCATTGAGCGCTTAAG 59.973 55.000 19.88 9.89 46.53 1.85
822 1024 0.652592 CGACCATTGAGCGCTTAAGG 59.347 55.000 19.88 19.13 0.00 2.69
823 1025 0.378610 GACCATTGAGCGCTTAAGGC 59.621 55.000 19.72 6.18 37.64 4.35
824 1026 0.035056 ACCATTGAGCGCTTAAGGCT 60.035 50.000 19.72 15.62 45.00 4.58
829 1031 3.713650 AGCGCTTAAGGCTCCTGA 58.286 55.556 2.64 0.00 35.37 3.86
830 1032 1.983224 AGCGCTTAAGGCTCCTGAA 59.017 52.632 2.64 0.00 35.37 3.02
831 1033 0.543749 AGCGCTTAAGGCTCCTGAAT 59.456 50.000 2.64 0.00 35.37 2.57
832 1034 0.940833 GCGCTTAAGGCTCCTGAATC 59.059 55.000 0.00 0.00 39.13 2.52
833 1035 1.474143 GCGCTTAAGGCTCCTGAATCT 60.474 52.381 0.00 0.00 39.13 2.40
834 1036 2.478831 CGCTTAAGGCTCCTGAATCTC 58.521 52.381 4.29 0.00 39.13 2.75
835 1037 2.804933 CGCTTAAGGCTCCTGAATCTCC 60.805 54.545 4.29 0.00 39.13 3.71
836 1038 2.171448 GCTTAAGGCTCCTGAATCTCCA 59.829 50.000 4.29 0.00 38.06 3.86
837 1039 3.802866 CTTAAGGCTCCTGAATCTCCAC 58.197 50.000 0.00 0.00 0.00 4.02
838 1040 0.539051 AAGGCTCCTGAATCTCCACG 59.461 55.000 0.00 0.00 0.00 4.94
839 1041 1.144936 GGCTCCTGAATCTCCACGG 59.855 63.158 0.00 0.00 0.00 4.94
840 1042 1.617947 GGCTCCTGAATCTCCACGGT 61.618 60.000 0.00 0.00 0.00 4.83
841 1043 0.179097 GCTCCTGAATCTCCACGGTC 60.179 60.000 0.00 0.00 0.00 4.79
842 1044 0.461961 CTCCTGAATCTCCACGGTCC 59.538 60.000 0.00 0.00 0.00 4.46
843 1045 0.252057 TCCTGAATCTCCACGGTCCA 60.252 55.000 0.00 0.00 0.00 4.02
844 1046 0.176680 CCTGAATCTCCACGGTCCAG 59.823 60.000 0.00 0.00 0.00 3.86
845 1047 0.176680 CTGAATCTCCACGGTCCAGG 59.823 60.000 0.00 0.00 0.00 4.45
846 1048 0.544357 TGAATCTCCACGGTCCAGGT 60.544 55.000 0.00 0.00 0.00 4.00
847 1049 0.613777 GAATCTCCACGGTCCAGGTT 59.386 55.000 0.00 0.00 0.00 3.50
848 1050 1.829222 GAATCTCCACGGTCCAGGTTA 59.171 52.381 0.00 0.00 0.00 2.85
849 1051 1.192428 ATCTCCACGGTCCAGGTTAC 58.808 55.000 0.00 0.00 0.00 2.50
850 1052 0.113776 TCTCCACGGTCCAGGTTACT 59.886 55.000 0.00 0.00 0.00 2.24
851 1053 0.531200 CTCCACGGTCCAGGTTACTC 59.469 60.000 0.00 0.00 0.00 2.59
852 1054 0.901580 TCCACGGTCCAGGTTACTCC 60.902 60.000 0.00 0.00 0.00 3.85
853 1055 1.214589 CACGGTCCAGGTTACTCCG 59.785 63.158 0.00 0.00 45.53 4.63
854 1056 2.183555 CGGTCCAGGTTACTCCGC 59.816 66.667 0.00 0.00 41.99 5.54
855 1057 2.642254 CGGTCCAGGTTACTCCGCA 61.642 63.158 0.00 0.00 41.99 5.69
856 1058 1.905512 GGTCCAGGTTACTCCGCAT 59.094 57.895 0.00 0.00 41.99 4.73
857 1059 0.179081 GGTCCAGGTTACTCCGCATC 60.179 60.000 0.00 0.00 41.99 3.91
858 1060 0.824759 GTCCAGGTTACTCCGCATCT 59.175 55.000 0.00 0.00 41.99 2.90
859 1061 0.824109 TCCAGGTTACTCCGCATCTG 59.176 55.000 0.00 0.00 41.99 2.90
860 1062 0.811616 CCAGGTTACTCCGCATCTGC 60.812 60.000 0.00 0.00 41.99 4.26
861 1063 0.108186 CAGGTTACTCCGCATCTGCA 60.108 55.000 2.72 0.00 42.21 4.41
862 1064 0.108138 AGGTTACTCCGCATCTGCAC 60.108 55.000 2.72 0.00 42.21 4.57
863 1065 0.108138 GGTTACTCCGCATCTGCACT 60.108 55.000 2.72 0.00 42.21 4.40
864 1066 1.281899 GTTACTCCGCATCTGCACTC 58.718 55.000 2.72 0.00 42.21 3.51
865 1067 0.894835 TTACTCCGCATCTGCACTCA 59.105 50.000 2.72 0.00 42.21 3.41
866 1068 0.894835 TACTCCGCATCTGCACTCAA 59.105 50.000 2.72 0.00 42.21 3.02
867 1069 0.035317 ACTCCGCATCTGCACTCAAA 59.965 50.000 2.72 0.00 42.21 2.69
868 1070 1.159285 CTCCGCATCTGCACTCAAAA 58.841 50.000 2.72 0.00 42.21 2.44
869 1071 1.129998 CTCCGCATCTGCACTCAAAAG 59.870 52.381 2.72 0.00 42.21 2.27
870 1072 0.169672 CCGCATCTGCACTCAAAAGG 59.830 55.000 2.72 0.00 42.21 3.11
871 1073 1.159285 CGCATCTGCACTCAAAAGGA 58.841 50.000 2.72 0.00 42.21 3.36
872 1074 1.536766 CGCATCTGCACTCAAAAGGAA 59.463 47.619 2.72 0.00 42.21 3.36
873 1075 2.030893 CGCATCTGCACTCAAAAGGAAA 60.031 45.455 2.72 0.00 42.21 3.13
874 1076 3.550639 CGCATCTGCACTCAAAAGGAAAA 60.551 43.478 2.72 0.00 42.21 2.29
875 1077 3.985925 GCATCTGCACTCAAAAGGAAAAG 59.014 43.478 0.00 0.00 41.59 2.27
876 1078 4.500375 GCATCTGCACTCAAAAGGAAAAGT 60.500 41.667 0.00 0.00 41.59 2.66
995 1211 1.153823 CACGTCTCCGGCGATCTTT 60.154 57.895 9.30 0.00 38.78 2.52
1131 1347 4.778143 GCGGGCGTCAAGGATGGT 62.778 66.667 0.00 0.00 0.00 3.55
1149 1365 0.253327 GTTCCTGGATCCTGGACCAC 59.747 60.000 33.61 26.60 42.45 4.16
1335 1554 1.731613 CGACGGCGCTAAGAACACA 60.732 57.895 6.90 0.00 0.00 3.72
1397 4876 1.573607 TTCATGGCCTGCCTCATGGA 61.574 55.000 9.97 0.00 40.63 3.41
1440 5229 4.821589 GAACTCCTGGAGCGGCCG 62.822 72.222 24.05 24.05 40.66 6.13
1941 5753 4.702081 GACGTCGTGCTGCGGAGT 62.702 66.667 0.63 2.79 41.72 3.85
2006 5818 4.704833 GGAGCTGCCCTTGACGCA 62.705 66.667 0.00 0.00 34.41 5.24
2146 5961 0.035458 CAAGAGAAGAAGGCCACGGT 59.965 55.000 5.01 0.00 0.00 4.83
2194 6012 1.089112 CATCAACATGCGCAGGAAGA 58.911 50.000 30.79 24.06 0.00 2.87
2415 6281 8.466617 TCTTTTAAGTATTTGGCAACCAAGTA 57.533 30.769 0.00 0.00 44.84 2.24
2417 6283 8.874744 TTTTAAGTATTTGGCAACCAAGTAAC 57.125 30.769 0.00 2.46 44.84 2.50
2491 6357 6.323996 CCATGGGTAGAGAACTGTATAAGACA 59.676 42.308 2.85 0.00 36.35 3.41
2493 6359 7.973048 TGGGTAGAGAACTGTATAAGACATT 57.027 36.000 0.00 0.00 37.45 2.71
2494 6360 8.375493 TGGGTAGAGAACTGTATAAGACATTT 57.625 34.615 0.00 0.00 37.45 2.32
2496 6362 9.668497 GGGTAGAGAACTGTATAAGACATTTTT 57.332 33.333 0.00 0.00 37.45 1.94
2558 6424 5.416952 GGAACACAAGATCATGTCCTTCATT 59.583 40.000 15.11 1.04 34.09 2.57
2748 6614 4.993029 TGAGTTTTGTTAGGGTTTGTGG 57.007 40.909 0.00 0.00 0.00 4.17
2751 6617 4.345854 AGTTTTGTTAGGGTTTGTGGACA 58.654 39.130 0.00 0.00 0.00 4.02
2752 6618 4.401202 AGTTTTGTTAGGGTTTGTGGACAG 59.599 41.667 0.00 0.00 0.00 3.51
2754 6620 0.872388 GTTAGGGTTTGTGGACAGCG 59.128 55.000 0.00 0.00 0.00 5.18
2755 6621 0.759959 TTAGGGTTTGTGGACAGCGA 59.240 50.000 0.00 0.00 0.00 4.93
2756 6622 0.320374 TAGGGTTTGTGGACAGCGAG 59.680 55.000 0.00 0.00 0.00 5.03
2757 6623 1.070786 GGGTTTGTGGACAGCGAGA 59.929 57.895 0.00 0.00 0.00 4.04
2758 6624 0.321653 GGGTTTGTGGACAGCGAGAT 60.322 55.000 0.00 0.00 0.00 2.75
2759 6625 1.523758 GGTTTGTGGACAGCGAGATT 58.476 50.000 0.00 0.00 0.00 2.40
2760 6626 1.464997 GGTTTGTGGACAGCGAGATTC 59.535 52.381 0.00 0.00 0.00 2.52
2761 6627 2.417719 GTTTGTGGACAGCGAGATTCT 58.582 47.619 0.00 0.00 0.00 2.40
2762 6628 2.370281 TTGTGGACAGCGAGATTCTC 57.630 50.000 3.43 3.43 0.00 2.87
2763 6629 1.550327 TGTGGACAGCGAGATTCTCT 58.450 50.000 11.75 0.00 0.00 3.10
2764 6630 1.474478 TGTGGACAGCGAGATTCTCTC 59.526 52.381 11.75 3.85 40.06 3.20
2765 6631 1.107114 TGGACAGCGAGATTCTCTCC 58.893 55.000 11.75 11.39 40.34 3.71
2766 6632 0.030101 GGACAGCGAGATTCTCTCCG 59.970 60.000 11.75 0.81 40.34 4.63
2767 6633 0.593773 GACAGCGAGATTCTCTCCGC 60.594 60.000 11.75 10.56 40.34 5.54
2775 6873 1.381327 ATTCTCTCCGCCTTCCCGA 60.381 57.895 0.00 0.00 0.00 5.14
2782 6880 0.685131 TCCGCCTTCCCGATTGTCTA 60.685 55.000 0.00 0.00 0.00 2.59
2783 6881 0.393077 CCGCCTTCCCGATTGTCTAT 59.607 55.000 0.00 0.00 0.00 1.98
2801 6899 5.151389 GTCTATTACAACAAGTTTTGCCCG 58.849 41.667 0.00 0.00 0.00 6.13
2802 6900 2.873133 TTACAACAAGTTTTGCCCGG 57.127 45.000 0.00 0.00 0.00 5.73
2806 6904 1.040339 AACAAGTTTTGCCCGGCTCA 61.040 50.000 11.61 0.00 0.00 4.26
2807 6905 1.286880 CAAGTTTTGCCCGGCTCAG 59.713 57.895 11.61 0.00 0.00 3.35
2808 6906 1.903404 AAGTTTTGCCCGGCTCAGG 60.903 57.895 11.61 0.00 0.00 3.86
2821 6919 3.003173 TCAGGTGAGGAAGGGGCG 61.003 66.667 0.00 0.00 0.00 6.13
2826 6924 0.106894 GGTGAGGAAGGGGCGATAAG 59.893 60.000 0.00 0.00 0.00 1.73
2827 6925 1.120530 GTGAGGAAGGGGCGATAAGA 58.879 55.000 0.00 0.00 0.00 2.10
2829 6927 1.343075 TGAGGAAGGGGCGATAAGAGT 60.343 52.381 0.00 0.00 0.00 3.24
2831 6929 1.486726 AGGAAGGGGCGATAAGAGTTG 59.513 52.381 0.00 0.00 0.00 3.16
2833 6931 0.462047 AAGGGGCGATAAGAGTTGCG 60.462 55.000 0.00 0.00 0.00 4.85
2838 6936 1.878522 CGATAAGAGTTGCGCGCCT 60.879 57.895 30.77 19.99 0.00 5.52
2840 6938 0.301987 GATAAGAGTTGCGCGCCTTC 59.698 55.000 30.77 22.11 0.00 3.46
2856 6954 2.680805 GCCTTCGGATCACTTCAATGGA 60.681 50.000 0.00 0.00 0.00 3.41
2869 6967 1.749063 TCAATGGATGTAGTCGTCGCT 59.251 47.619 0.00 0.00 0.00 4.93
2887 6985 2.802816 CGCTAAATGGTCTACTGATGGC 59.197 50.000 0.00 0.00 0.00 4.40
2892 6990 0.909133 TGGTCTACTGATGGCCTGCA 60.909 55.000 3.32 0.34 0.00 4.41
2894 6992 1.661341 GTCTACTGATGGCCTGCAAG 58.339 55.000 3.32 0.00 0.00 4.01
2943 7041 6.785337 TCAAAGTAAGAGTATCGATCCCAA 57.215 37.500 0.00 0.00 42.67 4.12
2964 7062 1.530771 GGAGCACATGGATCAGCCT 59.469 57.895 0.00 0.00 37.63 4.58
2965 7063 0.106819 GGAGCACATGGATCAGCCTT 60.107 55.000 0.00 0.00 37.63 4.35
2966 7064 1.684248 GGAGCACATGGATCAGCCTTT 60.684 52.381 0.00 0.00 37.63 3.11
2967 7065 2.097825 GAGCACATGGATCAGCCTTTT 58.902 47.619 0.00 0.00 37.63 2.27
2968 7066 1.822990 AGCACATGGATCAGCCTTTTG 59.177 47.619 0.00 0.00 37.63 2.44
2969 7067 1.547372 GCACATGGATCAGCCTTTTGT 59.453 47.619 0.00 0.00 37.63 2.83
2970 7068 2.416431 GCACATGGATCAGCCTTTTGTC 60.416 50.000 0.00 0.00 37.63 3.18
2971 7069 3.087031 CACATGGATCAGCCTTTTGTCT 58.913 45.455 0.00 0.00 37.63 3.41
2972 7070 3.128242 CACATGGATCAGCCTTTTGTCTC 59.872 47.826 0.00 0.00 37.63 3.36
2973 7071 3.009916 ACATGGATCAGCCTTTTGTCTCT 59.990 43.478 0.00 0.00 37.63 3.10
2974 7072 3.795688 TGGATCAGCCTTTTGTCTCTT 57.204 42.857 0.00 0.00 37.63 2.85
2975 7073 3.415212 TGGATCAGCCTTTTGTCTCTTG 58.585 45.455 0.00 0.00 37.63 3.02
2976 7074 3.181440 TGGATCAGCCTTTTGTCTCTTGT 60.181 43.478 0.00 0.00 37.63 3.16
2977 7075 4.041567 TGGATCAGCCTTTTGTCTCTTGTA 59.958 41.667 0.00 0.00 37.63 2.41
2978 7076 4.633565 GGATCAGCCTTTTGTCTCTTGTAG 59.366 45.833 0.00 0.00 0.00 2.74
2979 7077 4.008074 TCAGCCTTTTGTCTCTTGTAGG 57.992 45.455 0.00 0.00 0.00 3.18
2980 7078 3.077359 CAGCCTTTTGTCTCTTGTAGGG 58.923 50.000 0.00 0.00 0.00 3.53
2985 7083 4.757149 CCTTTTGTCTCTTGTAGGGTTCAG 59.243 45.833 0.00 0.00 0.00 3.02
2986 7084 4.351874 TTTGTCTCTTGTAGGGTTCAGG 57.648 45.455 0.00 0.00 0.00 3.86
2994 7092 5.027460 TCTTGTAGGGTTCAGGTAGCAATA 58.973 41.667 0.00 0.00 0.00 1.90
2995 7093 5.665812 TCTTGTAGGGTTCAGGTAGCAATAT 59.334 40.000 0.00 0.00 0.00 1.28
3020 7118 6.321181 TCTGCAAGTTTAGTGAAATCCAAAGT 59.679 34.615 0.00 0.00 33.76 2.66
3049 7147 6.720288 AGTAGTATCAGTGAAAGTGGTGTAGT 59.280 38.462 0.00 0.00 38.01 2.73
3068 7166 8.546244 GGTGTAGTGAACAAAGAAGTAAAGTAC 58.454 37.037 0.00 0.00 40.63 2.73
3114 7212 7.707104 AGAGACGTGAATGAAAGTTTTTGAAT 58.293 30.769 0.00 0.00 0.00 2.57
3136 7234 1.406539 TGATAGGACTAACGCGTTCCC 59.593 52.381 30.28 25.49 0.00 3.97
3179 7277 1.518774 TCGTCCCCGAGCAAATACC 59.481 57.895 0.00 0.00 38.40 2.73
3180 7278 1.219664 CGTCCCCGAGCAAATACCA 59.780 57.895 0.00 0.00 35.63 3.25
3184 7282 1.376609 CCCCGAGCAAATACCACAGC 61.377 60.000 0.00 0.00 0.00 4.40
3219 7317 7.036829 AGAGATCATCTTGATTATGAGATGCG 58.963 38.462 8.15 0.00 45.59 4.73
3226 7324 6.758254 TCTTGATTATGAGATGCGGATAACA 58.242 36.000 0.00 0.00 0.00 2.41
3235 7333 7.099266 TGAGATGCGGATAACAAAAATGAAT 57.901 32.000 0.00 0.00 0.00 2.57
3261 7359 7.398047 TGAGTCCATCCAATGATTCAAGAATTT 59.602 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 348 1.275471 TTGTGCTTTCGCGAGAGTCG 61.275 55.000 25.34 4.35 43.69 4.18
243 383 0.668535 GAGAGGCACGGTTTTGCTTT 59.331 50.000 0.00 0.00 42.56 3.51
338 490 4.329545 GCTTCCACGAGGGGCACA 62.330 66.667 11.29 0.00 37.22 4.57
344 496 1.068333 CATGGTTTTGCTTCCACGAGG 60.068 52.381 0.00 0.00 36.50 4.63
349 501 0.968405 GAGGCATGGTTTTGCTTCCA 59.032 50.000 0.00 0.00 41.44 3.53
362 514 1.808411 TTTCTTTTCGCGAGAGGCAT 58.192 45.000 9.59 0.00 43.84 4.40
617 807 2.187946 GGACGCTCCCTGTGGATG 59.812 66.667 0.00 0.00 40.80 3.51
623 825 2.125912 CGTTCTGGACGCTCCCTG 60.126 66.667 0.00 0.00 45.86 4.45
706 908 3.267483 GGGAGCAACTAATTAACGAGCA 58.733 45.455 0.00 0.00 0.00 4.26
731 933 7.404203 ACGATTATTATTTTTACGTGGCACTC 58.596 34.615 16.72 0.00 0.00 3.51
732 934 7.311364 ACGATTATTATTTTTACGTGGCACT 57.689 32.000 16.72 5.47 0.00 4.40
733 935 8.689737 CTACGATTATTATTTTTACGTGGCAC 57.310 34.615 7.79 7.79 34.52 5.01
735 937 6.513991 CGCTACGATTATTATTTTTACGTGGC 59.486 38.462 0.00 0.00 46.77 5.01
736 938 7.776464 TCGCTACGATTATTATTTTTACGTGG 58.224 34.615 0.00 0.00 34.52 4.94
737 939 7.943065 CCTCGCTACGATTATTATTTTTACGTG 59.057 37.037 0.00 0.00 34.61 4.49
738 940 7.649306 ACCTCGCTACGATTATTATTTTTACGT 59.351 33.333 0.00 0.00 34.61 3.57
739 941 7.943065 CACCTCGCTACGATTATTATTTTTACG 59.057 37.037 0.00 0.00 34.61 3.18
740 942 8.971321 TCACCTCGCTACGATTATTATTTTTAC 58.029 33.333 0.00 0.00 34.61 2.01
741 943 9.188588 CTCACCTCGCTACGATTATTATTTTTA 57.811 33.333 0.00 0.00 34.61 1.52
742 944 7.307219 GCTCACCTCGCTACGATTATTATTTTT 60.307 37.037 0.00 0.00 34.61 1.94
743 945 6.145696 GCTCACCTCGCTACGATTATTATTTT 59.854 38.462 0.00 0.00 34.61 1.82
744 946 5.634020 GCTCACCTCGCTACGATTATTATTT 59.366 40.000 0.00 0.00 34.61 1.40
745 947 5.162075 GCTCACCTCGCTACGATTATTATT 58.838 41.667 0.00 0.00 34.61 1.40
746 948 4.672024 CGCTCACCTCGCTACGATTATTAT 60.672 45.833 0.00 0.00 34.61 1.28
747 949 3.364664 CGCTCACCTCGCTACGATTATTA 60.365 47.826 0.00 0.00 34.61 0.98
748 950 2.604855 CGCTCACCTCGCTACGATTATT 60.605 50.000 0.00 0.00 34.61 1.40
749 951 1.069159 CGCTCACCTCGCTACGATTAT 60.069 52.381 0.00 0.00 34.61 1.28
750 952 0.306840 CGCTCACCTCGCTACGATTA 59.693 55.000 0.00 0.00 34.61 1.75
751 953 1.064296 CGCTCACCTCGCTACGATT 59.936 57.895 0.00 0.00 34.61 3.34
752 954 1.818363 TCGCTCACCTCGCTACGAT 60.818 57.895 0.00 0.00 34.61 3.73
753 955 2.435410 TCGCTCACCTCGCTACGA 60.435 61.111 0.00 0.00 0.00 3.43
754 956 2.277373 GTCGCTCACCTCGCTACG 60.277 66.667 0.00 0.00 0.00 3.51
755 957 2.277373 CGTCGCTCACCTCGCTAC 60.277 66.667 0.00 0.00 0.00 3.58
756 958 4.175489 GCGTCGCTCACCTCGCTA 62.175 66.667 10.68 0.00 44.28 4.26
759 961 0.525668 AAATAGCGTCGCTCACCTCG 60.526 55.000 25.50 0.00 40.44 4.63
760 962 0.924090 CAAATAGCGTCGCTCACCTC 59.076 55.000 25.50 0.00 40.44 3.85
761 963 0.460284 CCAAATAGCGTCGCTCACCT 60.460 55.000 25.50 1.33 40.44 4.00
762 964 2.006772 CCAAATAGCGTCGCTCACC 58.993 57.895 25.50 0.00 40.44 4.02
763 965 1.348594 GCCAAATAGCGTCGCTCAC 59.651 57.895 25.50 4.20 40.44 3.51
764 966 1.813753 GGCCAAATAGCGTCGCTCA 60.814 57.895 25.50 10.82 40.44 4.26
765 967 2.534903 GGGCCAAATAGCGTCGCTC 61.535 63.158 25.50 7.99 40.44 5.03
766 968 2.513897 GGGCCAAATAGCGTCGCT 60.514 61.111 25.08 25.08 43.41 4.93
767 969 3.937062 CGGGCCAAATAGCGTCGC 61.937 66.667 9.80 9.80 0.00 5.19
768 970 3.269347 CCGGGCCAAATAGCGTCG 61.269 66.667 4.39 0.00 0.00 5.12
769 971 3.583086 GCCGGGCCAAATAGCGTC 61.583 66.667 8.12 0.00 0.00 5.19
781 983 4.483243 AACACGCTATGGGCCGGG 62.483 66.667 2.18 0.00 37.74 5.73
782 984 2.895372 GAACACGCTATGGGCCGG 60.895 66.667 0.00 0.00 37.74 6.13
783 985 2.173669 CAGAACACGCTATGGGCCG 61.174 63.158 0.00 0.00 37.74 6.13
784 986 1.819632 CCAGAACACGCTATGGGCC 60.820 63.158 0.00 0.00 37.74 5.80
785 987 2.472909 GCCAGAACACGCTATGGGC 61.473 63.158 0.00 0.00 33.23 5.36
786 988 2.173669 CGCCAGAACACGCTATGGG 61.174 63.158 0.00 0.00 33.23 4.00
787 989 1.153647 TCGCCAGAACACGCTATGG 60.154 57.895 0.00 0.00 35.84 2.74
788 990 1.421410 GGTCGCCAGAACACGCTATG 61.421 60.000 0.00 0.00 33.32 2.23
789 991 1.153628 GGTCGCCAGAACACGCTAT 60.154 57.895 0.00 0.00 33.32 2.97
790 992 2.260434 GGTCGCCAGAACACGCTA 59.740 61.111 0.00 0.00 33.32 4.26
791 993 3.923864 TGGTCGCCAGAACACGCT 61.924 61.111 0.00 0.00 39.55 5.07
796 998 1.796796 GCTCAATGGTCGCCAGAAC 59.203 57.895 4.90 0.00 36.75 3.01
797 999 1.741401 CGCTCAATGGTCGCCAGAA 60.741 57.895 4.90 0.00 36.75 3.02
798 1000 2.125552 CGCTCAATGGTCGCCAGA 60.126 61.111 4.90 0.00 36.75 3.86
799 1001 3.869272 GCGCTCAATGGTCGCCAG 61.869 66.667 0.00 0.00 42.71 4.85
803 1005 0.652592 CCTTAAGCGCTCAATGGTCG 59.347 55.000 12.06 0.00 0.00 4.79
804 1006 0.378610 GCCTTAAGCGCTCAATGGTC 59.621 55.000 12.06 6.81 0.00 4.02
805 1007 2.482326 GCCTTAAGCGCTCAATGGT 58.518 52.632 12.06 0.00 0.00 3.55
815 1017 2.171448 TGGAGATTCAGGAGCCTTAAGC 59.829 50.000 0.00 0.00 44.25 3.09
816 1018 3.739519 CGTGGAGATTCAGGAGCCTTAAG 60.740 52.174 0.00 0.00 0.00 1.85
817 1019 2.168521 CGTGGAGATTCAGGAGCCTTAA 59.831 50.000 0.00 0.00 0.00 1.85
818 1020 1.757118 CGTGGAGATTCAGGAGCCTTA 59.243 52.381 0.00 0.00 0.00 2.69
819 1021 0.539051 CGTGGAGATTCAGGAGCCTT 59.461 55.000 0.00 0.00 0.00 4.35
820 1022 1.333636 CCGTGGAGATTCAGGAGCCT 61.334 60.000 0.00 0.00 0.00 4.58
821 1023 1.144936 CCGTGGAGATTCAGGAGCC 59.855 63.158 0.00 0.00 0.00 4.70
822 1024 0.179097 GACCGTGGAGATTCAGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
823 1025 0.461961 GGACCGTGGAGATTCAGGAG 59.538 60.000 0.00 0.00 0.00 3.69
824 1026 0.252057 TGGACCGTGGAGATTCAGGA 60.252 55.000 0.00 0.00 0.00 3.86
825 1027 0.176680 CTGGACCGTGGAGATTCAGG 59.823 60.000 0.00 0.00 0.00 3.86
826 1028 0.176680 CCTGGACCGTGGAGATTCAG 59.823 60.000 0.00 0.00 0.00 3.02
827 1029 0.544357 ACCTGGACCGTGGAGATTCA 60.544 55.000 0.00 0.00 0.00 2.57
828 1030 0.613777 AACCTGGACCGTGGAGATTC 59.386 55.000 0.00 0.00 0.00 2.52
829 1031 1.553704 GTAACCTGGACCGTGGAGATT 59.446 52.381 0.00 0.00 0.00 2.40
830 1032 1.192428 GTAACCTGGACCGTGGAGAT 58.808 55.000 0.00 0.06 0.00 2.75
831 1033 0.113776 AGTAACCTGGACCGTGGAGA 59.886 55.000 0.00 0.00 0.00 3.71
832 1034 0.531200 GAGTAACCTGGACCGTGGAG 59.469 60.000 0.00 0.00 0.00 3.86
833 1035 0.901580 GGAGTAACCTGGACCGTGGA 60.902 60.000 0.00 0.00 35.41 4.02
834 1036 1.595357 GGAGTAACCTGGACCGTGG 59.405 63.158 0.00 2.14 35.41 4.94
835 1037 1.214589 CGGAGTAACCTGGACCGTG 59.785 63.158 0.00 0.00 38.97 4.94
836 1038 2.643232 GCGGAGTAACCTGGACCGT 61.643 63.158 0.00 0.00 44.48 4.83
837 1039 1.956629 ATGCGGAGTAACCTGGACCG 61.957 60.000 0.00 8.48 45.26 4.79
838 1040 0.179081 GATGCGGAGTAACCTGGACC 60.179 60.000 0.00 0.00 36.31 4.46
839 1041 0.824759 AGATGCGGAGTAACCTGGAC 59.175 55.000 0.00 0.00 36.31 4.02
840 1042 0.824109 CAGATGCGGAGTAACCTGGA 59.176 55.000 0.00 0.00 36.31 3.86
841 1043 0.811616 GCAGATGCGGAGTAACCTGG 60.812 60.000 0.00 0.00 36.31 4.45
842 1044 0.108186 TGCAGATGCGGAGTAACCTG 60.108 55.000 0.00 0.00 45.83 4.00
843 1045 0.108138 GTGCAGATGCGGAGTAACCT 60.108 55.000 0.00 0.00 45.83 3.50
844 1046 0.108138 AGTGCAGATGCGGAGTAACC 60.108 55.000 0.00 0.00 45.83 2.85
845 1047 1.281899 GAGTGCAGATGCGGAGTAAC 58.718 55.000 0.00 0.00 45.83 2.50
846 1048 0.894835 TGAGTGCAGATGCGGAGTAA 59.105 50.000 0.00 0.00 45.83 2.24
847 1049 0.894835 TTGAGTGCAGATGCGGAGTA 59.105 50.000 0.00 0.00 45.83 2.59
848 1050 0.035317 TTTGAGTGCAGATGCGGAGT 59.965 50.000 0.00 0.00 45.83 3.85
849 1051 1.129998 CTTTTGAGTGCAGATGCGGAG 59.870 52.381 0.00 0.00 45.83 4.63
850 1052 1.159285 CTTTTGAGTGCAGATGCGGA 58.841 50.000 0.00 0.00 45.83 5.54
851 1053 0.169672 CCTTTTGAGTGCAGATGCGG 59.830 55.000 0.00 0.00 45.83 5.69
852 1054 1.159285 TCCTTTTGAGTGCAGATGCG 58.841 50.000 0.00 0.00 45.83 4.73
853 1055 3.648339 TTTCCTTTTGAGTGCAGATGC 57.352 42.857 0.00 0.00 42.50 3.91
854 1056 5.192327 ACTTTTCCTTTTGAGTGCAGATG 57.808 39.130 0.00 0.00 0.00 2.90
855 1057 5.859205 AACTTTTCCTTTTGAGTGCAGAT 57.141 34.783 0.00 0.00 0.00 2.90
856 1058 5.659440 AAACTTTTCCTTTTGAGTGCAGA 57.341 34.783 0.00 0.00 0.00 4.26
857 1059 5.455525 CGTAAACTTTTCCTTTTGAGTGCAG 59.544 40.000 0.00 0.00 0.00 4.41
858 1060 5.336744 CGTAAACTTTTCCTTTTGAGTGCA 58.663 37.500 0.00 0.00 0.00 4.57
859 1061 4.206404 GCGTAAACTTTTCCTTTTGAGTGC 59.794 41.667 0.00 0.00 0.00 4.40
860 1062 4.738252 GGCGTAAACTTTTCCTTTTGAGTG 59.262 41.667 0.00 0.00 0.00 3.51
861 1063 4.496840 CGGCGTAAACTTTTCCTTTTGAGT 60.497 41.667 0.00 0.00 0.00 3.41
862 1064 3.972502 CGGCGTAAACTTTTCCTTTTGAG 59.027 43.478 0.00 0.00 0.00 3.02
863 1065 3.792794 GCGGCGTAAACTTTTCCTTTTGA 60.793 43.478 9.37 0.00 0.00 2.69
864 1066 2.469886 GCGGCGTAAACTTTTCCTTTTG 59.530 45.455 9.37 0.00 0.00 2.44
865 1067 2.099427 TGCGGCGTAAACTTTTCCTTTT 59.901 40.909 9.37 0.00 0.00 2.27
866 1068 1.677052 TGCGGCGTAAACTTTTCCTTT 59.323 42.857 9.37 0.00 0.00 3.11
867 1069 1.310904 TGCGGCGTAAACTTTTCCTT 58.689 45.000 9.37 0.00 0.00 3.36
868 1070 1.467342 GATGCGGCGTAAACTTTTCCT 59.533 47.619 9.37 0.00 0.00 3.36
869 1071 1.467342 AGATGCGGCGTAAACTTTTCC 59.533 47.619 9.37 0.00 0.00 3.13
870 1072 2.158841 TCAGATGCGGCGTAAACTTTTC 59.841 45.455 9.37 0.00 0.00 2.29
871 1073 2.095919 GTCAGATGCGGCGTAAACTTTT 60.096 45.455 9.37 0.00 0.00 2.27
872 1074 1.463444 GTCAGATGCGGCGTAAACTTT 59.537 47.619 9.37 0.00 0.00 2.66
873 1075 1.076332 GTCAGATGCGGCGTAAACTT 58.924 50.000 9.37 0.00 0.00 2.66
874 1076 0.739813 GGTCAGATGCGGCGTAAACT 60.740 55.000 9.37 5.46 0.00 2.66
875 1077 0.739813 AGGTCAGATGCGGCGTAAAC 60.740 55.000 9.37 2.91 0.00 2.01
876 1078 0.036765 AAGGTCAGATGCGGCGTAAA 60.037 50.000 9.37 0.00 0.00 2.01
995 1211 0.103026 CCTCGATGAAGACATGCCGA 59.897 55.000 0.00 0.00 36.82 5.54
1131 1347 0.119155 AGTGGTCCAGGATCCAGGAA 59.881 55.000 26.31 10.38 33.39 3.36
1149 1365 4.116328 TGCGCGTCGAGGGAGAAG 62.116 66.667 8.43 0.00 34.27 2.85
1201 1417 1.741401 CCTCGATCTTGGCACGCAA 60.741 57.895 0.00 0.00 0.00 4.85
1263 1479 1.066573 AGCGTCATGAGGAGGAAGTTG 60.067 52.381 19.26 0.00 33.18 3.16
1326 1545 1.613925 AGCAGCGAGAGTGTGTTCTTA 59.386 47.619 0.00 0.00 0.00 2.10
1397 4876 2.147387 ACAGGAAAGACCGTGGGCT 61.147 57.895 0.00 0.00 44.74 5.19
2146 5961 6.413892 TCACATACTCAACCTTCATGCATAA 58.586 36.000 0.00 0.00 0.00 1.90
2194 6012 1.915769 GGCTGTGGGACAGGAGAGT 60.916 63.158 5.90 0.00 46.01 3.24
2299 6133 9.219603 TGTGCTTAAATAACATCATATAGGAGC 57.780 33.333 0.00 0.00 0.00 4.70
2380 6246 7.910683 GCCAAATACTTAAAAGATGAGCTACAC 59.089 37.037 0.00 0.00 0.00 2.90
2522 6388 1.303643 GTGTTCCCCTCAAGCCCTG 60.304 63.158 0.00 0.00 0.00 4.45
2558 6424 0.256464 GAGGAGAGACGAAGGGGAGA 59.744 60.000 0.00 0.00 0.00 3.71
2667 6533 2.047655 GAATCCACCACGCGTCCA 60.048 61.111 9.86 0.00 0.00 4.02
2668 6534 2.818274 GGAATCCACCACGCGTCC 60.818 66.667 9.86 0.00 0.00 4.79
2669 6535 3.186047 CGGAATCCACCACGCGTC 61.186 66.667 9.86 0.00 0.00 5.19
2670 6536 4.752879 CCGGAATCCACCACGCGT 62.753 66.667 5.58 5.58 0.00 6.01
2674 6540 3.282374 AAGGGCCGGAATCCACCAC 62.282 63.158 5.05 0.00 0.00 4.16
2675 6541 2.938798 AAGGGCCGGAATCCACCA 60.939 61.111 5.05 0.00 0.00 4.17
2727 6593 4.399934 GTCCACAAACCCTAACAAAACTCA 59.600 41.667 0.00 0.00 0.00 3.41
2756 6622 1.068250 CGGGAAGGCGGAGAGAATC 59.932 63.158 0.00 0.00 0.00 2.52
2757 6623 0.760945 ATCGGGAAGGCGGAGAGAAT 60.761 55.000 0.00 0.00 0.00 2.40
2758 6624 0.976073 AATCGGGAAGGCGGAGAGAA 60.976 55.000 0.00 0.00 0.00 2.87
2759 6625 1.381327 AATCGGGAAGGCGGAGAGA 60.381 57.895 0.00 0.00 0.00 3.10
2760 6626 1.227380 CAATCGGGAAGGCGGAGAG 60.227 63.158 0.00 0.00 0.00 3.20
2761 6627 1.956629 GACAATCGGGAAGGCGGAGA 61.957 60.000 0.00 0.00 0.00 3.71
2762 6628 1.521681 GACAATCGGGAAGGCGGAG 60.522 63.158 0.00 0.00 0.00 4.63
2763 6629 0.685131 TAGACAATCGGGAAGGCGGA 60.685 55.000 0.00 0.00 0.00 5.54
2764 6630 0.393077 ATAGACAATCGGGAAGGCGG 59.607 55.000 0.00 0.00 0.00 6.13
2765 6631 2.240493 AATAGACAATCGGGAAGGCG 57.760 50.000 0.00 0.00 0.00 5.52
2766 6632 4.067972 TGTAATAGACAATCGGGAAGGC 57.932 45.455 0.00 0.00 34.15 4.35
2782 6880 2.547007 GCCGGGCAAAACTTGTTGTAAT 60.547 45.455 15.62 0.00 0.00 1.89
2783 6881 1.202428 GCCGGGCAAAACTTGTTGTAA 60.202 47.619 15.62 0.00 0.00 2.41
2801 6899 2.674220 CCCCTTCCTCACCTGAGCC 61.674 68.421 0.00 0.00 40.75 4.70
2802 6900 2.993853 CCCCTTCCTCACCTGAGC 59.006 66.667 0.00 0.00 40.75 4.26
2806 6904 0.326238 TTATCGCCCCTTCCTCACCT 60.326 55.000 0.00 0.00 0.00 4.00
2807 6905 0.106894 CTTATCGCCCCTTCCTCACC 59.893 60.000 0.00 0.00 0.00 4.02
2808 6906 1.069358 CTCTTATCGCCCCTTCCTCAC 59.931 57.143 0.00 0.00 0.00 3.51
2813 6911 1.300481 GCAACTCTTATCGCCCCTTC 58.700 55.000 0.00 0.00 0.00 3.46
2814 6912 0.462047 CGCAACTCTTATCGCCCCTT 60.462 55.000 0.00 0.00 0.00 3.95
2821 6919 0.301987 GAAGGCGCGCAACTCTTATC 59.698 55.000 34.42 12.03 0.00 1.75
2838 6936 4.220693 ACATCCATTGAAGTGATCCGAA 57.779 40.909 0.00 0.00 0.00 4.30
2840 6938 4.697514 ACTACATCCATTGAAGTGATCCG 58.302 43.478 0.00 0.00 0.00 4.18
2856 6954 3.380637 AGACCATTTAGCGACGACTACAT 59.619 43.478 0.00 0.00 0.00 2.29
2869 6967 3.433598 GCAGGCCATCAGTAGACCATTTA 60.434 47.826 5.01 0.00 0.00 1.40
2887 6985 1.995376 AAACCTTGTACCCTTGCAGG 58.005 50.000 0.00 0.00 34.30 4.85
2914 7012 8.604890 GGATCGATACTCTTACTTTGAAAAAGG 58.395 37.037 0.00 0.00 0.00 3.11
2920 7018 6.785337 TTGGGATCGATACTCTTACTTTGA 57.215 37.500 7.75 0.00 0.00 2.69
2922 7020 6.583562 CCTTTGGGATCGATACTCTTACTTT 58.416 40.000 7.75 0.00 33.58 2.66
2943 7041 0.106819 GCTGATCCATGTGCTCCCTT 60.107 55.000 0.00 0.00 0.00 3.95
2950 7048 3.087031 AGACAAAAGGCTGATCCATGTG 58.913 45.455 0.00 0.00 37.29 3.21
2954 7052 3.181440 ACAAGAGACAAAAGGCTGATCCA 60.181 43.478 0.00 0.00 37.29 3.41
2956 7054 4.633565 CCTACAAGAGACAAAAGGCTGATC 59.366 45.833 0.00 0.00 0.00 2.92
2964 7062 4.165372 ACCTGAACCCTACAAGAGACAAAA 59.835 41.667 0.00 0.00 0.00 2.44
2965 7063 3.714798 ACCTGAACCCTACAAGAGACAAA 59.285 43.478 0.00 0.00 0.00 2.83
2966 7064 3.314693 ACCTGAACCCTACAAGAGACAA 58.685 45.455 0.00 0.00 0.00 3.18
2967 7065 2.972348 ACCTGAACCCTACAAGAGACA 58.028 47.619 0.00 0.00 0.00 3.41
2968 7066 3.119065 GCTACCTGAACCCTACAAGAGAC 60.119 52.174 0.00 0.00 0.00 3.36
2969 7067 3.097614 GCTACCTGAACCCTACAAGAGA 58.902 50.000 0.00 0.00 0.00 3.10
2970 7068 2.832129 TGCTACCTGAACCCTACAAGAG 59.168 50.000 0.00 0.00 0.00 2.85
2971 7069 2.897350 TGCTACCTGAACCCTACAAGA 58.103 47.619 0.00 0.00 0.00 3.02
2972 7070 3.695830 TTGCTACCTGAACCCTACAAG 57.304 47.619 0.00 0.00 0.00 3.16
2973 7071 5.665812 AGATATTGCTACCTGAACCCTACAA 59.334 40.000 0.00 0.00 0.00 2.41
2974 7072 5.070446 CAGATATTGCTACCTGAACCCTACA 59.930 44.000 0.00 0.00 0.00 2.74
2975 7073 5.542779 CAGATATTGCTACCTGAACCCTAC 58.457 45.833 0.00 0.00 0.00 3.18
2976 7074 5.808366 CAGATATTGCTACCTGAACCCTA 57.192 43.478 0.00 0.00 0.00 3.53
2977 7075 4.696479 CAGATATTGCTACCTGAACCCT 57.304 45.455 0.00 0.00 0.00 4.34
2994 7092 6.899393 TTGGATTTCACTAAACTTGCAGAT 57.101 33.333 0.00 0.00 0.00 2.90
2995 7093 6.321181 ACTTTGGATTTCACTAAACTTGCAGA 59.679 34.615 0.00 0.00 0.00 4.26
3020 7118 9.251440 ACACCACTTTCACTGATACTACTATTA 57.749 33.333 0.00 0.00 0.00 0.98
3032 7130 4.188462 TGTTCACTACACCACTTTCACTG 58.812 43.478 0.00 0.00 0.00 3.66
3033 7131 4.481368 TGTTCACTACACCACTTTCACT 57.519 40.909 0.00 0.00 0.00 3.41
3078 7176 6.931838 TCATTCACGTCTCTTGTTACCTTAT 58.068 36.000 0.00 0.00 0.00 1.73
3082 7180 5.465724 ACTTTCATTCACGTCTCTTGTTACC 59.534 40.000 0.00 0.00 0.00 2.85
3114 7212 3.514645 GGAACGCGTTAGTCCTATCAAA 58.485 45.455 26.68 0.00 0.00 2.69
3128 7226 1.738099 CTGACTCCTTGGGAACGCG 60.738 63.158 3.53 3.53 0.00 6.01
3136 7234 2.183679 ACCTCTAAGCCTGACTCCTTG 58.816 52.381 0.00 0.00 0.00 3.61
3179 7277 8.484453 AAGATGATCTCTTTCTCACAAGCTGTG 61.484 40.741 0.00 9.27 44.38 3.66
3180 7278 4.613925 TGATCTCTTTCTCACAAGCTGT 57.386 40.909 0.00 0.00 0.00 4.40
3184 7282 8.495361 AATCAAGATGATCTCTTTCTCACAAG 57.505 34.615 0.00 0.00 41.60 3.16
3211 7309 6.507958 TTCATTTTTGTTATCCGCATCTCA 57.492 33.333 0.00 0.00 0.00 3.27
3219 7317 7.922811 GGATGGACTCATTCATTTTTGTTATCC 59.077 37.037 0.00 0.00 32.98 2.59
3226 7324 7.484993 TCATTGGATGGACTCATTCATTTTT 57.515 32.000 0.00 0.00 38.58 1.94
3235 7333 5.440207 TCTTGAATCATTGGATGGACTCA 57.560 39.130 0.00 0.00 32.92 3.41


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

AutoCloner maintained by Alex Coulton.