Multiple sequence alignment - TraesCS7A01G163900

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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 TraesCS7A01G163900 chr7A 100.000 3604 0 0 1 3604 120573331 120576934 0.000000e+00 6656.0
1 TraesCS7A01G163900 chr7A 91.692 1962 129 6 497 2456 462252658 462254587 0.000000e+00 2689.0
2 TraesCS7A01G163900 chr7A 91.417 501 41 2 1 501 462165436 462165934 0.000000e+00 686.0
3 TraesCS7A01G163900 chr3D 97.804 2641 56 2 1 2639 67670995 67668355 0.000000e+00 4554.0
4 TraesCS7A01G163900 chr5D 97.572 2636 58 2 1 2635 440951269 440953899 0.000000e+00 4508.0
5 TraesCS7A01G163900 chr6D 97.382 2636 64 2 1 2635 458476690 458474059 0.000000e+00 4481.0
6 TraesCS7A01G163900 chr6D 95.349 43 2 0 2635 2677 116948066 116948024 6.460000e-08 69.4
7 TraesCS7A01G163900 chr7B 95.799 2642 109 2 1 2640 200778960 200776319 0.000000e+00 4263.0
8 TraesCS7A01G163900 chr7B 94.413 877 49 0 1759 2635 809809 810685 0.000000e+00 1349.0
9 TraesCS7A01G163900 chr7B 88.095 252 12 3 2762 3000 75151465 75151711 2.120000e-72 283.0
10 TraesCS7A01G163900 chr3B 94.419 2634 146 1 1 2633 565192961 565195594 0.000000e+00 4048.0
11 TraesCS7A01G163900 chr3B 95.238 42 2 0 2635 2676 755301746 755301705 2.320000e-07 67.6
12 TraesCS7A01G163900 chr5A 96.691 2357 75 3 254 2609 632792930 632795284 0.000000e+00 3917.0
13 TraesCS7A01G163900 chr5A 90.031 642 26 14 3001 3604 60748110 60747469 0.000000e+00 797.0
14 TraesCS7A01G163900 chr5A 88.712 629 31 15 3004 3604 40153766 40154382 0.000000e+00 732.0
15 TraesCS7A01G163900 chr5A 88.169 617 43 18 3001 3604 49516002 49516601 0.000000e+00 708.0
16 TraesCS7A01G163900 chr5A 87.844 617 41 21 3001 3604 49957680 49958275 0.000000e+00 693.0
17 TraesCS7A01G163900 chr5A 96.124 258 10 0 1 258 632777449 632777706 4.300000e-114 422.0
18 TraesCS7A01G163900 chr5A 97.619 42 0 1 2635 2676 601556382 601556422 1.800000e-08 71.3
19 TraesCS7A01G163900 chr1D 96.443 506 17 1 2130 2635 38015253 38015757 0.000000e+00 833.0
20 TraesCS7A01G163900 chr1D 93.182 44 3 0 2635 2678 78979225 78979182 8.350000e-07 65.8
21 TraesCS7A01G163900 chr1D 95.238 42 1 1 2635 2676 361212762 361212802 8.350000e-07 65.8
22 TraesCS7A01G163900 chr3A 88.906 631 31 17 3001 3604 649823765 649823147 0.000000e+00 741.0
23 TraesCS7A01G163900 chr3A 86.328 629 51 23 2998 3604 114433124 114432509 0.000000e+00 652.0
24 TraesCS7A01G163900 chr3A 95.238 42 2 0 2635 2676 708899018 708899059 2.320000e-07 67.6
25 TraesCS7A01G163900 chr4A 88.320 625 37 23 3001 3604 451014136 451013527 0.000000e+00 717.0
26 TraesCS7A01G163900 chr7D 88.198 627 37 20 3001 3604 241941254 241941866 0.000000e+00 713.0
27 TraesCS7A01G163900 chr7D 81.073 354 26 24 2680 3000 116469662 116470007 1.000000e-60 244.0
28 TraesCS7A01G163900 chr7D 73.895 475 100 24 53 515 616192805 616193267 6.190000e-38 169.0
29 TraesCS7A01G163900 chr2A 86.094 640 49 26 2999 3604 179798530 179797897 0.000000e+00 652.0
30 TraesCS7A01G163900 chr2A 82.432 370 34 25 3239 3604 90422609 90422267 9.790000e-76 294.0
31 TraesCS7A01G163900 chr2A 84.553 246 19 17 3371 3604 414957707 414957945 3.620000e-55 226.0
32 TraesCS7A01G163900 chr6B 74.624 1395 329 16 2 1380 38958150 38959535 3.100000e-165 592.0
33 TraesCS7A01G163900 chrUn 78.187 353 65 11 56 402 94641202 94640856 7.840000e-52 215.0
34 TraesCS7A01G163900 chrUn 95.238 42 2 0 2635 2676 325782707 325782748 2.320000e-07 67.6
35 TraesCS7A01G163900 chr5B 95.238 42 2 0 2635 2676 222451888 222451847 2.320000e-07 67.6
36 TraesCS7A01G163900 chr1A 95.238 42 2 0 2635 2676 99311928 99311969 2.320000e-07 67.6


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 TraesCS7A01G163900 chr7A 120573331 120576934 3603 False 6656 6656 100.000 1 3604 1 chr7A.!!$F1 3603
1 TraesCS7A01G163900 chr7A 462252658 462254587 1929 False 2689 2689 91.692 497 2456 1 chr7A.!!$F3 1959
2 TraesCS7A01G163900 chr3D 67668355 67670995 2640 True 4554 4554 97.804 1 2639 1 chr3D.!!$R1 2638
3 TraesCS7A01G163900 chr5D 440951269 440953899 2630 False 4508 4508 97.572 1 2635 1 chr5D.!!$F1 2634
4 TraesCS7A01G163900 chr6D 458474059 458476690 2631 True 4481 4481 97.382 1 2635 1 chr6D.!!$R2 2634
5 TraesCS7A01G163900 chr7B 200776319 200778960 2641 True 4263 4263 95.799 1 2640 1 chr7B.!!$R1 2639
6 TraesCS7A01G163900 chr7B 809809 810685 876 False 1349 1349 94.413 1759 2635 1 chr7B.!!$F1 876
7 TraesCS7A01G163900 chr3B 565192961 565195594 2633 False 4048 4048 94.419 1 2633 1 chr3B.!!$F1 2632
8 TraesCS7A01G163900 chr5A 632792930 632795284 2354 False 3917 3917 96.691 254 2609 1 chr5A.!!$F6 2355
9 TraesCS7A01G163900 chr5A 60747469 60748110 641 True 797 797 90.031 3001 3604 1 chr5A.!!$R1 603
10 TraesCS7A01G163900 chr5A 40153766 40154382 616 False 732 732 88.712 3004 3604 1 chr5A.!!$F1 600
11 TraesCS7A01G163900 chr5A 49516002 49516601 599 False 708 708 88.169 3001 3604 1 chr5A.!!$F2 603
12 TraesCS7A01G163900 chr5A 49957680 49958275 595 False 693 693 87.844 3001 3604 1 chr5A.!!$F3 603
13 TraesCS7A01G163900 chr1D 38015253 38015757 504 False 833 833 96.443 2130 2635 1 chr1D.!!$F1 505
14 TraesCS7A01G163900 chr3A 649823147 649823765 618 True 741 741 88.906 3001 3604 1 chr3A.!!$R2 603
15 TraesCS7A01G163900 chr3A 114432509 114433124 615 True 652 652 86.328 2998 3604 1 chr3A.!!$R1 606
16 TraesCS7A01G163900 chr4A 451013527 451014136 609 True 717 717 88.320 3001 3604 1 chr4A.!!$R1 603
17 TraesCS7A01G163900 chr7D 241941254 241941866 612 False 713 713 88.198 3001 3604 1 chr7D.!!$F2 603
18 TraesCS7A01G163900 chr2A 179797897 179798530 633 True 652 652 86.094 2999 3604 1 chr2A.!!$R2 605
19 TraesCS7A01G163900 chr6B 38958150 38959535 1385 False 592 592 74.624 2 1380 1 chr6B.!!$F1 1378

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
638 639 0.248215 GCATGTCGGCAAGGAATTCG 60.248 55.000 0.0 0.0 0.0 3.34 F
1542 1551 1.364171 GCAGTGTGTCGGTGAGTCT 59.636 57.895 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1707 0.387202 CCTCTAGCCCACAGATCGTG 59.613 60.0 9.75 9.75 45.92 4.35 R
2868 2878 0.034059 ACTGGAACTGAACTCGGCTG 59.966 55.0 0.00 0.00 0.00 4.85 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
27 28 2.611971 GGTGAACAGACTGCGTCCATTA 60.612 50.000 1.25 0.00 32.18 1.90
119 120 4.211794 GGTGGCATTTGAATGTTTTCACAG 59.788 41.667 5.68 0.00 41.50 3.66
122 123 5.982516 TGGCATTTGAATGTTTTCACAGTAC 59.017 36.000 5.68 0.00 41.50 2.73
159 160 2.092968 ACAACAAGACTCCTTCTGTGCA 60.093 45.455 0.00 0.00 33.46 4.57
312 313 5.817784 TCCGTAAAATTCAATGGAACCCTA 58.182 37.500 0.00 0.00 35.46 3.53
322 323 4.224147 TCAATGGAACCCTACTTGATTCGA 59.776 41.667 0.00 0.00 0.00 3.71
455 456 6.157994 ACAATAACTCCTCTTAAGGTATGCCA 59.842 38.462 1.54 0.00 43.82 4.92
638 639 0.248215 GCATGTCGGCAAGGAATTCG 60.248 55.000 0.00 0.00 0.00 3.34
914 916 5.729510 TGATTTAACACAGATGATCCGTCA 58.270 37.500 0.00 0.00 39.04 4.35
1011 1020 2.208872 AGAGGTGGTATGGGCTTCAAT 58.791 47.619 0.00 0.00 0.00 2.57
1018 1027 4.646492 GTGGTATGGGCTTCAATGATCTTT 59.354 41.667 0.00 0.00 0.00 2.52
1104 1113 2.343758 GCTCAGGTTCTCCGTGCA 59.656 61.111 0.00 0.00 39.05 4.57
1115 1124 2.522185 TCTCCGTGCAAAGTACTACCT 58.478 47.619 0.00 0.00 0.00 3.08
1405 1414 6.032956 TCCCAATAGACGTCGCAAATATAT 57.967 37.500 10.46 0.00 0.00 0.86
1542 1551 1.364171 GCAGTGTGTCGGTGAGTCT 59.636 57.895 0.00 0.00 0.00 3.24
1656 1665 3.345737 CGAAGCATTAGCCACTCGA 57.654 52.632 0.00 0.00 43.56 4.04
1923 1933 0.108992 GTGGCATGTGCACAATGAGG 60.109 55.000 25.72 12.03 44.36 3.86
2073 2083 3.317711 CCTCAGTGCAAATACCACAACAA 59.682 43.478 0.00 0.00 35.69 2.83
2094 2104 2.691409 AGTTCATACCGTGACCCATG 57.309 50.000 0.00 0.00 36.32 3.66
2328 2338 0.694771 TCTGCATTGGTCTCAAGCCT 59.305 50.000 0.00 0.00 36.19 4.58
2566 2576 3.550974 TCCCCAGGAGATTAGCGC 58.449 61.111 0.00 0.00 0.00 5.92
2656 2666 8.460831 AAAATAAAGCTAAGGTACGCAATTTG 57.539 30.769 0.00 0.00 0.00 2.32
2657 2667 3.487563 AAGCTAAGGTACGCAATTTGC 57.512 42.857 11.42 11.42 40.69 3.68
2667 2677 3.877801 GCAATTTGCGTACTCTCGG 57.122 52.632 5.49 0.00 31.71 4.63
2668 2678 0.373716 GCAATTTGCGTACTCTCGGG 59.626 55.000 5.49 0.00 31.71 5.14
2669 2679 2.004583 CAATTTGCGTACTCTCGGGA 57.995 50.000 0.00 0.00 0.00 5.14
2670 2680 2.343101 CAATTTGCGTACTCTCGGGAA 58.657 47.619 0.00 0.00 0.00 3.97
2671 2681 2.739913 CAATTTGCGTACTCTCGGGAAA 59.260 45.455 0.00 0.00 0.00 3.13
2672 2682 2.529780 TTTGCGTACTCTCGGGAAAA 57.470 45.000 0.00 0.00 0.00 2.29
2673 2683 2.529780 TTGCGTACTCTCGGGAAAAA 57.470 45.000 0.00 0.00 0.00 1.94
2718 2728 4.247380 CAGCCCCCGAGCCTGATC 62.247 72.222 0.00 0.00 0.00 2.92
2719 2729 4.804420 AGCCCCCGAGCCTGATCA 62.804 66.667 0.00 0.00 0.00 2.92
2720 2730 4.247380 GCCCCCGAGCCTGATCAG 62.247 72.222 16.24 16.24 0.00 2.90
2721 2731 2.444706 CCCCCGAGCCTGATCAGA 60.445 66.667 24.62 0.00 0.00 3.27
2722 2732 1.840650 CCCCCGAGCCTGATCAGAT 60.841 63.158 24.62 12.07 0.00 2.90
2723 2733 1.370437 CCCCGAGCCTGATCAGATG 59.630 63.158 24.62 9.41 0.00 2.90
2724 2734 1.301558 CCCGAGCCTGATCAGATGC 60.302 63.158 24.62 18.82 0.00 3.91
2725 2735 1.664017 CCGAGCCTGATCAGATGCG 60.664 63.158 24.62 20.66 0.00 4.73
2726 2736 2.308769 CGAGCCTGATCAGATGCGC 61.309 63.158 24.62 18.84 0.00 6.09
2727 2737 1.960250 GAGCCTGATCAGATGCGCC 60.960 63.158 24.62 12.57 0.00 6.53
2728 2738 2.976903 GCCTGATCAGATGCGCCC 60.977 66.667 24.62 0.00 0.00 6.13
2729 2739 2.281345 CCTGATCAGATGCGCCCC 60.281 66.667 24.62 0.00 0.00 5.80
2730 2740 2.664185 CTGATCAGATGCGCCCCG 60.664 66.667 18.34 0.00 0.00 5.73
2731 2741 3.153781 TGATCAGATGCGCCCCGA 61.154 61.111 4.18 0.00 0.00 5.14
2732 2742 2.108976 GATCAGATGCGCCCCGAA 59.891 61.111 4.18 0.00 0.00 4.30
2733 2743 2.203070 ATCAGATGCGCCCCGAAC 60.203 61.111 4.18 0.00 0.00 3.95
2734 2744 2.923426 GATCAGATGCGCCCCGAACA 62.923 60.000 4.18 0.00 0.00 3.18
2735 2745 3.499737 CAGATGCGCCCCGAACAC 61.500 66.667 4.18 0.00 0.00 3.32
2745 2755 3.846754 CCGAACACGACGGTTACC 58.153 61.111 0.00 0.00 44.57 2.85
2756 2766 1.931551 CGGTTACCGCAATCCATCG 59.068 57.895 11.93 0.00 41.17 3.84
2757 2767 1.647084 GGTTACCGCAATCCATCGC 59.353 57.895 0.00 0.00 0.00 4.58
2758 2768 1.647084 GTTACCGCAATCCATCGCC 59.353 57.895 0.00 0.00 0.00 5.54
2759 2769 1.092921 GTTACCGCAATCCATCGCCA 61.093 55.000 0.00 0.00 0.00 5.69
2760 2770 0.179032 TTACCGCAATCCATCGCCAT 60.179 50.000 0.00 0.00 0.00 4.40
2761 2771 0.602638 TACCGCAATCCATCGCCATC 60.603 55.000 0.00 0.00 0.00 3.51
2762 2772 1.598962 CCGCAATCCATCGCCATCT 60.599 57.895 0.00 0.00 0.00 2.90
2763 2773 1.572085 CCGCAATCCATCGCCATCTC 61.572 60.000 0.00 0.00 0.00 2.75
2764 2774 0.881600 CGCAATCCATCGCCATCTCA 60.882 55.000 0.00 0.00 0.00 3.27
2765 2775 1.531423 GCAATCCATCGCCATCTCAT 58.469 50.000 0.00 0.00 0.00 2.90
2766 2776 1.467734 GCAATCCATCGCCATCTCATC 59.532 52.381 0.00 0.00 0.00 2.92
2767 2777 1.730612 CAATCCATCGCCATCTCATCG 59.269 52.381 0.00 0.00 0.00 3.84
2768 2778 0.972134 ATCCATCGCCATCTCATCGT 59.028 50.000 0.00 0.00 0.00 3.73
2769 2779 0.315251 TCCATCGCCATCTCATCGTC 59.685 55.000 0.00 0.00 0.00 4.20
2770 2780 0.668706 CCATCGCCATCTCATCGTCC 60.669 60.000 0.00 0.00 0.00 4.79
2771 2781 0.668706 CATCGCCATCTCATCGTCCC 60.669 60.000 0.00 0.00 0.00 4.46
2772 2782 1.115326 ATCGCCATCTCATCGTCCCA 61.115 55.000 0.00 0.00 0.00 4.37
2773 2783 1.592669 CGCCATCTCATCGTCCCAC 60.593 63.158 0.00 0.00 0.00 4.61
2774 2784 1.227674 GCCATCTCATCGTCCCACC 60.228 63.158 0.00 0.00 0.00 4.61
2775 2785 1.068083 CCATCTCATCGTCCCACCG 59.932 63.158 0.00 0.00 0.00 4.94
2776 2786 1.592669 CATCTCATCGTCCCACCGC 60.593 63.158 0.00 0.00 0.00 5.68
2777 2787 1.758514 ATCTCATCGTCCCACCGCT 60.759 57.895 0.00 0.00 0.00 5.52
2778 2788 0.467474 ATCTCATCGTCCCACCGCTA 60.467 55.000 0.00 0.00 0.00 4.26
2779 2789 1.065928 CTCATCGTCCCACCGCTAC 59.934 63.158 0.00 0.00 0.00 3.58
2780 2790 1.379443 TCATCGTCCCACCGCTACT 60.379 57.895 0.00 0.00 0.00 2.57
2781 2791 1.065928 CATCGTCCCACCGCTACTC 59.934 63.158 0.00 0.00 0.00 2.59
2782 2792 2.125961 ATCGTCCCACCGCTACTCC 61.126 63.158 0.00 0.00 0.00 3.85
2783 2793 2.849096 ATCGTCCCACCGCTACTCCA 62.849 60.000 0.00 0.00 0.00 3.86
2784 2794 2.577593 GTCCCACCGCTACTCCAC 59.422 66.667 0.00 0.00 0.00 4.02
2785 2795 2.682494 TCCCACCGCTACTCCACC 60.682 66.667 0.00 0.00 0.00 4.61
2786 2796 3.782443 CCCACCGCTACTCCACCC 61.782 72.222 0.00 0.00 0.00 4.61
2787 2797 2.683933 CCACCGCTACTCCACCCT 60.684 66.667 0.00 0.00 0.00 4.34
2788 2798 2.579201 CACCGCTACTCCACCCTG 59.421 66.667 0.00 0.00 0.00 4.45
2789 2799 3.391382 ACCGCTACTCCACCCTGC 61.391 66.667 0.00 0.00 0.00 4.85
2790 2800 4.162690 CCGCTACTCCACCCTGCC 62.163 72.222 0.00 0.00 0.00 4.85
2791 2801 4.162690 CGCTACTCCACCCTGCCC 62.163 72.222 0.00 0.00 0.00 5.36
2792 2802 2.689034 GCTACTCCACCCTGCCCT 60.689 66.667 0.00 0.00 0.00 5.19
2793 2803 1.382695 GCTACTCCACCCTGCCCTA 60.383 63.158 0.00 0.00 0.00 3.53
2794 2804 1.687297 GCTACTCCACCCTGCCCTAC 61.687 65.000 0.00 0.00 0.00 3.18
2795 2805 1.002533 TACTCCACCCTGCCCTACC 59.997 63.158 0.00 0.00 0.00 3.18
2796 2806 1.817572 TACTCCACCCTGCCCTACCA 61.818 60.000 0.00 0.00 0.00 3.25
2797 2807 2.285368 TCCACCCTGCCCTACCAG 60.285 66.667 0.00 0.00 0.00 4.00
2806 2816 3.643398 CCCTACCAGGCTACCACC 58.357 66.667 0.00 0.00 32.73 4.61
2807 2817 1.306654 CCCTACCAGGCTACCACCA 60.307 63.158 0.00 0.00 32.73 4.17
2808 2818 1.623542 CCCTACCAGGCTACCACCAC 61.624 65.000 0.00 0.00 32.73 4.16
2809 2819 1.623542 CCTACCAGGCTACCACCACC 61.624 65.000 0.00 0.00 0.00 4.61
2810 2820 0.907704 CTACCAGGCTACCACCACCA 60.908 60.000 0.00 0.00 0.00 4.17
2811 2821 0.252974 TACCAGGCTACCACCACCAT 60.253 55.000 0.00 0.00 0.00 3.55
2812 2822 1.224592 CCAGGCTACCACCACCATC 59.775 63.158 0.00 0.00 0.00 3.51
2813 2823 1.274703 CCAGGCTACCACCACCATCT 61.275 60.000 0.00 0.00 0.00 2.90
2814 2824 0.179000 CAGGCTACCACCACCATCTC 59.821 60.000 0.00 0.00 0.00 2.75
2815 2825 0.983378 AGGCTACCACCACCATCTCC 60.983 60.000 0.00 0.00 0.00 3.71
2816 2826 1.271840 GGCTACCACCACCATCTCCA 61.272 60.000 0.00 0.00 0.00 3.86
2817 2827 0.107654 GCTACCACCACCATCTCCAC 60.108 60.000 0.00 0.00 0.00 4.02
2818 2828 0.175760 CTACCACCACCATCTCCACG 59.824 60.000 0.00 0.00 0.00 4.94
2819 2829 1.261938 TACCACCACCATCTCCACGG 61.262 60.000 0.00 0.00 0.00 4.94
2820 2830 2.436646 CACCACCATCTCCACGGC 60.437 66.667 0.00 0.00 0.00 5.68
2821 2831 4.082523 ACCACCATCTCCACGGCG 62.083 66.667 4.80 4.80 0.00 6.46
2822 2832 4.838152 CCACCATCTCCACGGCGG 62.838 72.222 13.24 0.00 0.00 6.13
2853 2863 4.699522 GCGGCCCGATACATCCCC 62.700 72.222 7.68 0.00 0.00 4.81
2854 2864 3.238497 CGGCCCGATACATCCCCA 61.238 66.667 0.00 0.00 0.00 4.96
2855 2865 2.430367 GGCCCGATACATCCCCAC 59.570 66.667 0.00 0.00 0.00 4.61
2856 2866 2.030562 GCCCGATACATCCCCACG 59.969 66.667 0.00 0.00 0.00 4.94
2857 2867 2.803817 GCCCGATACATCCCCACGT 61.804 63.158 0.00 0.00 0.00 4.49
2858 2868 1.466025 GCCCGATACATCCCCACGTA 61.466 60.000 0.00 0.00 0.00 3.57
2859 2869 0.316204 CCCGATACATCCCCACGTAC 59.684 60.000 0.00 0.00 0.00 3.67
2860 2870 0.316204 CCGATACATCCCCACGTACC 59.684 60.000 0.00 0.00 0.00 3.34
2861 2871 0.316204 CGATACATCCCCACGTACCC 59.684 60.000 0.00 0.00 0.00 3.69
2862 2872 1.416243 GATACATCCCCACGTACCCA 58.584 55.000 0.00 0.00 0.00 4.51
2863 2873 1.343465 GATACATCCCCACGTACCCAG 59.657 57.143 0.00 0.00 0.00 4.45
2864 2874 0.688418 TACATCCCCACGTACCCAGG 60.688 60.000 0.00 0.00 0.00 4.45
2865 2875 3.087906 ATCCCCACGTACCCAGGC 61.088 66.667 0.00 0.00 0.00 4.85
2870 2880 4.096003 CACGTACCCAGGCCCCAG 62.096 72.222 0.00 0.00 0.00 4.45
2881 2891 4.021925 GCCCCAGCCGAGTTCAGT 62.022 66.667 0.00 0.00 0.00 3.41
2882 2892 2.750350 CCCCAGCCGAGTTCAGTT 59.250 61.111 0.00 0.00 0.00 3.16
2883 2893 1.376037 CCCCAGCCGAGTTCAGTTC 60.376 63.158 0.00 0.00 0.00 3.01
2884 2894 1.376037 CCCAGCCGAGTTCAGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
2885 2895 1.371183 CCAGCCGAGTTCAGTTCCA 59.629 57.895 0.00 0.00 0.00 3.53
2886 2896 0.671781 CCAGCCGAGTTCAGTTCCAG 60.672 60.000 0.00 0.00 0.00 3.86
2887 2897 0.034059 CAGCCGAGTTCAGTTCCAGT 59.966 55.000 0.00 0.00 0.00 4.00
2888 2898 1.272490 CAGCCGAGTTCAGTTCCAGTA 59.728 52.381 0.00 0.00 0.00 2.74
2889 2899 1.272769 AGCCGAGTTCAGTTCCAGTAC 59.727 52.381 0.00 0.00 0.00 2.73
2890 2900 1.672145 GCCGAGTTCAGTTCCAGTACC 60.672 57.143 0.00 0.00 0.00 3.34
2891 2901 1.402456 CCGAGTTCAGTTCCAGTACCG 60.402 57.143 0.00 0.00 0.00 4.02
2892 2902 1.402456 CGAGTTCAGTTCCAGTACCGG 60.402 57.143 0.00 0.00 0.00 5.28
2893 2903 0.320697 AGTTCAGTTCCAGTACCGGC 59.679 55.000 0.00 0.00 0.00 6.13
2894 2904 1.012486 GTTCAGTTCCAGTACCGGCG 61.012 60.000 0.00 0.00 0.00 6.46
2895 2905 2.775032 TTCAGTTCCAGTACCGGCGC 62.775 60.000 0.00 0.00 0.00 6.53
2896 2906 2.995574 AGTTCCAGTACCGGCGCT 60.996 61.111 7.64 0.00 0.00 5.92
2897 2907 2.508663 GTTCCAGTACCGGCGCTC 60.509 66.667 7.64 0.00 0.00 5.03
2898 2908 2.992689 TTCCAGTACCGGCGCTCA 60.993 61.111 7.64 0.00 0.00 4.26
2899 2909 3.291101 TTCCAGTACCGGCGCTCAC 62.291 63.158 7.64 0.00 0.00 3.51
2901 2911 4.111016 CAGTACCGGCGCTCACGA 62.111 66.667 7.64 0.00 43.93 4.35
2902 2912 3.812019 AGTACCGGCGCTCACGAG 61.812 66.667 7.64 0.00 43.93 4.18
2903 2913 3.807538 GTACCGGCGCTCACGAGA 61.808 66.667 7.64 0.00 43.93 4.04
2904 2914 3.807538 TACCGGCGCTCACGAGAC 61.808 66.667 7.64 0.00 43.93 3.36
2926 2936 4.211502 GCCGCATTGCCATCCCAC 62.212 66.667 2.41 0.00 0.00 4.61
2927 2937 3.530260 CCGCATTGCCATCCCACC 61.530 66.667 2.41 0.00 0.00 4.61
2928 2938 2.755064 CGCATTGCCATCCCACCA 60.755 61.111 2.41 0.00 0.00 4.17
2929 2939 2.777972 CGCATTGCCATCCCACCAG 61.778 63.158 2.41 0.00 0.00 4.00
2930 2940 3.085119 GCATTGCCATCCCACCAGC 62.085 63.158 0.00 0.00 0.00 4.85
2931 2941 1.683025 CATTGCCATCCCACCAGCA 60.683 57.895 0.00 0.00 0.00 4.41
2932 2942 2.525075 TTGCCATCCCACCAGCAA 59.475 55.556 0.00 0.00 42.60 3.91
2933 2943 1.259840 ATTGCCATCCCACCAGCAAC 61.260 55.000 0.00 0.00 46.98 4.17
2934 2944 3.443045 GCCATCCCACCAGCAACG 61.443 66.667 0.00 0.00 0.00 4.10
2935 2945 2.350895 CCATCCCACCAGCAACGA 59.649 61.111 0.00 0.00 0.00 3.85
2936 2946 2.040544 CCATCCCACCAGCAACGAC 61.041 63.158 0.00 0.00 0.00 4.34
2937 2947 2.047274 ATCCCACCAGCAACGACG 60.047 61.111 0.00 0.00 0.00 5.12
2938 2948 3.605749 ATCCCACCAGCAACGACGG 62.606 63.158 0.00 0.00 0.00 4.79
2941 2951 4.012895 CACCAGCAACGACGGCAC 62.013 66.667 0.00 0.00 0.00 5.01
2981 2991 3.017581 GCCCACTCACCCCTCCAT 61.018 66.667 0.00 0.00 0.00 3.41
2982 2992 3.049080 GCCCACTCACCCCTCCATC 62.049 68.421 0.00 0.00 0.00 3.51
2983 2993 1.616327 CCCACTCACCCCTCCATCA 60.616 63.158 0.00 0.00 0.00 3.07
2984 2994 1.207488 CCCACTCACCCCTCCATCAA 61.207 60.000 0.00 0.00 0.00 2.57
2985 2995 0.921896 CCACTCACCCCTCCATCAAT 59.078 55.000 0.00 0.00 0.00 2.57
2986 2996 1.133976 CCACTCACCCCTCCATCAATC 60.134 57.143 0.00 0.00 0.00 2.67
2987 2997 1.561076 CACTCACCCCTCCATCAATCA 59.439 52.381 0.00 0.00 0.00 2.57
2988 2998 2.174210 CACTCACCCCTCCATCAATCAT 59.826 50.000 0.00 0.00 0.00 2.45
2989 2999 2.441001 ACTCACCCCTCCATCAATCATC 59.559 50.000 0.00 0.00 0.00 2.92
2990 3000 2.440627 CTCACCCCTCCATCAATCATCA 59.559 50.000 0.00 0.00 0.00 3.07
2991 3001 2.851821 TCACCCCTCCATCAATCATCAA 59.148 45.455 0.00 0.00 0.00 2.57
2992 3002 3.269118 TCACCCCTCCATCAATCATCAAA 59.731 43.478 0.00 0.00 0.00 2.69
2993 3003 3.635373 CACCCCTCCATCAATCATCAAAG 59.365 47.826 0.00 0.00 0.00 2.77
2994 3004 3.528905 ACCCCTCCATCAATCATCAAAGA 59.471 43.478 0.00 0.00 0.00 2.52
2995 3005 4.169461 ACCCCTCCATCAATCATCAAAGAT 59.831 41.667 0.00 0.00 0.00 2.40
2996 3006 5.145564 CCCCTCCATCAATCATCAAAGATT 58.854 41.667 0.00 0.00 38.72 2.40
3117 3132 8.868522 TTCCCTATATGACATTTCCATTCATC 57.131 34.615 0.00 0.00 32.24 2.92
3327 3367 2.351097 CACACACGCAGCAACACG 60.351 61.111 0.00 0.00 0.00 4.49
3387 3471 1.333308 GCAGCACACACACATACACAA 59.667 47.619 0.00 0.00 0.00 3.33
3388 3472 2.223456 GCAGCACACACACATACACAAA 60.223 45.455 0.00 0.00 0.00 2.83
3389 3473 3.362295 CAGCACACACACATACACAAAC 58.638 45.455 0.00 0.00 0.00 2.93
3390 3474 3.013219 AGCACACACACATACACAAACA 58.987 40.909 0.00 0.00 0.00 2.83
3391 3475 3.105203 GCACACACACATACACAAACAC 58.895 45.455 0.00 0.00 0.00 3.32
3392 3476 3.350043 CACACACACATACACAAACACG 58.650 45.455 0.00 0.00 0.00 4.49
3393 3477 2.223157 ACACACACATACACAAACACGC 60.223 45.455 0.00 0.00 0.00 5.34
3394 3478 2.010497 ACACACATACACAAACACGCA 58.990 42.857 0.00 0.00 0.00 5.24
3395 3479 2.031560 ACACACATACACAAACACGCAG 59.968 45.455 0.00 0.00 0.00 5.18
3396 3480 1.002900 ACACATACACAAACACGCAGC 60.003 47.619 0.00 0.00 0.00 5.25
3397 3481 1.003008 CACATACACAAACACGCAGCA 60.003 47.619 0.00 0.00 0.00 4.41
3398 3482 1.264020 ACATACACAAACACGCAGCAG 59.736 47.619 0.00 0.00 0.00 4.24
3399 3483 0.238289 ATACACAAACACGCAGCAGC 59.762 50.000 0.00 0.00 37.42 5.25
3400 3484 1.092345 TACACAAACACGCAGCAGCA 61.092 50.000 0.82 0.00 42.27 4.41
3401 3485 1.656263 CACAAACACGCAGCAGCAG 60.656 57.895 0.82 0.00 42.27 4.24
3402 3486 2.728383 CAAACACGCAGCAGCAGC 60.728 61.111 0.82 0.00 42.27 5.25
3403 3487 3.211245 AAACACGCAGCAGCAGCA 61.211 55.556 10.77 0.00 45.49 4.41
3404 3488 3.474230 AAACACGCAGCAGCAGCAC 62.474 57.895 10.77 0.00 45.49 4.40
3408 3492 3.733960 CGCAGCAGCAGCACACAT 61.734 61.111 10.77 0.00 45.49 3.21
3456 3558 4.943591 CGCACACACACACGCAGC 62.944 66.667 0.00 0.00 0.00 5.25
3457 3559 4.943591 GCACACACACACGCAGCG 62.944 66.667 14.82 14.82 0.00 5.18
3458 3560 4.297891 CACACACACACGCAGCGG 62.298 66.667 21.15 10.75 0.00 5.52
3580 3736 5.183713 CAGGTGTCATTTAGGCTCAAAATGA 59.816 40.000 17.40 17.40 46.08 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.779241 TTAAGGAGACAATCTCACCCAAT 57.221 39.130 8.06 0.00 45.12 3.16
119 120 4.875544 TGTTTCTTGCAGTGTTCAGTAC 57.124 40.909 0.00 0.00 0.00 2.73
122 123 4.095410 TGTTGTTTCTTGCAGTGTTCAG 57.905 40.909 0.00 0.00 0.00 3.02
159 160 5.312079 GCCTTTGATAGATCCAGCTTGTAT 58.688 41.667 0.00 0.00 0.00 2.29
312 313 4.010349 GAGTTGGGGAAATCGAATCAAGT 58.990 43.478 0.00 0.00 0.00 3.16
322 323 1.657804 AGACCTCGAGTTGGGGAAAT 58.342 50.000 12.31 0.00 0.00 2.17
413 414 1.401761 TGTGCCTTGTGTTGCTTCAT 58.598 45.000 0.00 0.00 0.00 2.57
455 456 1.341531 GTGATATACCTGGTGCTCGCT 59.658 52.381 10.23 0.00 0.00 4.93
638 639 4.223255 GCAAGATACTCCTAATACCCTCCC 59.777 50.000 0.00 0.00 0.00 4.30
914 916 1.207791 CTCTGCTCCCCACCAATACT 58.792 55.000 0.00 0.00 0.00 2.12
1011 1020 9.300681 AGAGATTGATTAAACAACCAAAGATCA 57.699 29.630 0.00 0.00 32.50 2.92
1018 1027 7.446931 TGCTAACAGAGATTGATTAAACAACCA 59.553 33.333 0.00 0.00 32.50 3.67
1104 1113 4.910458 ATTGCCAGACAGGTAGTACTTT 57.090 40.909 0.00 0.00 40.61 2.66
1405 1414 5.774690 ACCACTTAGATGCCTTGATTTTCAA 59.225 36.000 0.00 0.00 34.79 2.69
1426 1435 3.550820 CGATAACATCATCCCCAAACCA 58.449 45.455 0.00 0.00 0.00 3.67
1454 1463 0.889186 ACGCCCATGTTTGTCTGGTC 60.889 55.000 0.00 0.00 0.00 4.02
1503 1512 4.142071 TGCCGAGCCATGATATTATCTCTC 60.142 45.833 5.33 5.80 0.00 3.20
1521 1530 3.207547 CTCACCGACACACTGCCGA 62.208 63.158 0.00 0.00 0.00 5.54
1542 1551 3.519107 TGAATCCATCAGGTCTTGTGCTA 59.481 43.478 0.00 0.00 35.89 3.49
1656 1665 1.926511 GCCTACGCTGCATGTTGCTT 61.927 55.000 0.00 4.06 45.31 3.91
1698 1707 0.387202 CCTCTAGCCCACAGATCGTG 59.613 60.000 9.75 9.75 45.92 4.35
1923 1933 4.764679 TCAATGGCTTGTCATGTGTTAC 57.235 40.909 0.00 0.00 33.87 2.50
2073 2083 3.494398 GCATGGGTCACGGTATGAACTAT 60.494 47.826 0.00 0.00 46.59 2.12
2094 2104 5.208463 TCCCATTTAACTTCAGGTTTTGC 57.792 39.130 0.00 0.00 39.17 3.68
2219 2229 4.551702 TCTGCAGGCAGTAAAGATAACA 57.448 40.909 19.75 0.00 43.96 2.41
2246 2256 0.395724 GGGGTCCCTCGCAATCAAAT 60.396 55.000 8.15 0.00 0.00 2.32
2328 2338 1.176619 TCCGTCTCAACCTGAAGCGA 61.177 55.000 0.00 0.00 0.00 4.93
2635 2645 4.976987 GCAAATTGCGTACCTTAGCTTTA 58.023 39.130 0.90 0.00 31.71 1.85
2649 2659 0.373716 CCCGAGAGTACGCAAATTGC 59.626 55.000 8.09 8.09 40.69 3.56
2650 2660 2.004583 TCCCGAGAGTACGCAAATTG 57.995 50.000 0.00 0.00 0.00 2.32
2651 2661 2.754946 TTCCCGAGAGTACGCAAATT 57.245 45.000 0.00 0.00 0.00 1.82
2652 2662 2.754946 TTTCCCGAGAGTACGCAAAT 57.245 45.000 0.00 0.00 0.00 2.32
2653 2663 2.529780 TTTTCCCGAGAGTACGCAAA 57.470 45.000 0.00 0.00 0.00 3.68
2654 2664 2.529780 TTTTTCCCGAGAGTACGCAA 57.470 45.000 0.00 0.00 0.00 4.85
2703 2713 4.247380 CTGATCAGGCTCGGGGGC 62.247 72.222 15.38 0.00 41.20 5.80
2704 2714 1.840650 ATCTGATCAGGCTCGGGGG 60.841 63.158 22.42 0.00 0.00 5.40
2705 2715 1.370437 CATCTGATCAGGCTCGGGG 59.630 63.158 22.42 0.00 0.00 5.73
2706 2716 1.301558 GCATCTGATCAGGCTCGGG 60.302 63.158 22.42 7.24 0.00 5.14
2707 2717 1.664017 CGCATCTGATCAGGCTCGG 60.664 63.158 22.42 8.85 0.00 4.63
2708 2718 2.308769 GCGCATCTGATCAGGCTCG 61.309 63.158 22.42 20.73 0.00 5.03
2709 2719 1.960250 GGCGCATCTGATCAGGCTC 60.960 63.158 22.42 13.24 0.00 4.70
2710 2720 2.110627 GGCGCATCTGATCAGGCT 59.889 61.111 22.42 7.83 0.00 4.58
2711 2721 2.976903 GGGCGCATCTGATCAGGC 60.977 66.667 22.42 16.99 0.00 4.85
2712 2722 2.281345 GGGGCGCATCTGATCAGG 60.281 66.667 22.42 8.67 0.00 3.86
2713 2723 2.649245 TTCGGGGCGCATCTGATCAG 62.649 60.000 17.07 17.07 0.00 2.90
2714 2724 2.730524 TTCGGGGCGCATCTGATCA 61.731 57.895 10.83 0.00 0.00 2.92
2715 2725 2.108976 TTCGGGGCGCATCTGATC 59.891 61.111 10.83 0.00 0.00 2.92
2716 2726 2.203070 GTTCGGGGCGCATCTGAT 60.203 61.111 10.83 0.00 0.00 2.90
2717 2727 3.700970 TGTTCGGGGCGCATCTGA 61.701 61.111 10.83 8.71 0.00 3.27
2718 2728 3.499737 GTGTTCGGGGCGCATCTG 61.500 66.667 10.83 6.06 0.00 2.90
2729 2739 3.440267 CGGTAACCGTCGTGTTCG 58.560 61.111 0.00 0.00 42.73 3.95
2739 2749 1.647084 GCGATGGATTGCGGTAACC 59.353 57.895 0.00 0.00 0.00 2.85
2740 2750 1.092921 TGGCGATGGATTGCGGTAAC 61.093 55.000 0.00 0.00 38.09 2.50
2741 2751 0.179032 ATGGCGATGGATTGCGGTAA 60.179 50.000 0.00 0.00 38.09 2.85
2742 2752 0.602638 GATGGCGATGGATTGCGGTA 60.603 55.000 0.00 0.00 38.09 4.02
2743 2753 1.893808 GATGGCGATGGATTGCGGT 60.894 57.895 0.00 0.00 38.09 5.68
2744 2754 1.572085 GAGATGGCGATGGATTGCGG 61.572 60.000 0.00 0.00 38.09 5.69
2745 2755 0.881600 TGAGATGGCGATGGATTGCG 60.882 55.000 0.00 0.00 38.09 4.85
2746 2756 1.467734 GATGAGATGGCGATGGATTGC 59.532 52.381 0.00 0.00 36.44 3.56
2747 2757 1.730612 CGATGAGATGGCGATGGATTG 59.269 52.381 0.00 0.00 0.00 2.67
2748 2758 1.345741 ACGATGAGATGGCGATGGATT 59.654 47.619 0.00 0.00 0.00 3.01
2749 2759 0.972134 ACGATGAGATGGCGATGGAT 59.028 50.000 0.00 0.00 0.00 3.41
2750 2760 0.315251 GACGATGAGATGGCGATGGA 59.685 55.000 0.00 0.00 0.00 3.41
2751 2761 0.668706 GGACGATGAGATGGCGATGG 60.669 60.000 0.00 0.00 0.00 3.51
2752 2762 0.668706 GGGACGATGAGATGGCGATG 60.669 60.000 0.00 0.00 0.00 3.84
2753 2763 1.115326 TGGGACGATGAGATGGCGAT 61.115 55.000 0.00 0.00 0.00 4.58
2754 2764 1.756561 TGGGACGATGAGATGGCGA 60.757 57.895 0.00 0.00 0.00 5.54
2755 2765 1.592669 GTGGGACGATGAGATGGCG 60.593 63.158 0.00 0.00 0.00 5.69
2756 2766 1.227674 GGTGGGACGATGAGATGGC 60.228 63.158 0.00 0.00 0.00 4.40
2757 2767 1.068083 CGGTGGGACGATGAGATGG 59.932 63.158 0.00 0.00 35.47 3.51
2758 2768 1.592669 GCGGTGGGACGATGAGATG 60.593 63.158 0.00 0.00 35.47 2.90
2759 2769 0.467474 TAGCGGTGGGACGATGAGAT 60.467 55.000 0.00 0.00 35.47 2.75
2760 2770 1.077285 TAGCGGTGGGACGATGAGA 60.077 57.895 0.00 0.00 35.47 3.27
2761 2771 1.065928 GTAGCGGTGGGACGATGAG 59.934 63.158 0.00 0.00 35.47 2.90
2762 2772 1.379443 AGTAGCGGTGGGACGATGA 60.379 57.895 0.00 0.00 35.47 2.92
2763 2773 1.065928 GAGTAGCGGTGGGACGATG 59.934 63.158 0.00 0.00 35.47 3.84
2764 2774 2.125961 GGAGTAGCGGTGGGACGAT 61.126 63.158 0.00 0.00 35.47 3.73
2765 2775 2.753043 GGAGTAGCGGTGGGACGA 60.753 66.667 0.00 0.00 35.47 4.20
2766 2776 3.066190 TGGAGTAGCGGTGGGACG 61.066 66.667 0.00 0.00 0.00 4.79
2767 2777 2.577593 GTGGAGTAGCGGTGGGAC 59.422 66.667 0.00 0.00 0.00 4.46
2768 2778 2.682494 GGTGGAGTAGCGGTGGGA 60.682 66.667 0.00 0.00 0.00 4.37
2769 2779 3.782443 GGGTGGAGTAGCGGTGGG 61.782 72.222 0.00 0.00 0.00 4.61
2770 2780 2.683933 AGGGTGGAGTAGCGGTGG 60.684 66.667 0.00 0.00 0.00 4.61
2771 2781 2.579201 CAGGGTGGAGTAGCGGTG 59.421 66.667 0.00 0.00 0.00 4.94
2772 2782 3.391382 GCAGGGTGGAGTAGCGGT 61.391 66.667 0.00 0.00 0.00 5.68
2773 2783 4.162690 GGCAGGGTGGAGTAGCGG 62.163 72.222 0.00 0.00 0.00 5.52
2774 2784 4.162690 GGGCAGGGTGGAGTAGCG 62.163 72.222 0.00 0.00 0.00 4.26
2775 2785 1.382695 TAGGGCAGGGTGGAGTAGC 60.383 63.158 0.00 0.00 0.00 3.58
2776 2786 1.049289 GGTAGGGCAGGGTGGAGTAG 61.049 65.000 0.00 0.00 0.00 2.57
2777 2787 1.002533 GGTAGGGCAGGGTGGAGTA 59.997 63.158 0.00 0.00 0.00 2.59
2778 2788 2.285442 GGTAGGGCAGGGTGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
2779 2789 2.285368 TGGTAGGGCAGGGTGGAG 60.285 66.667 0.00 0.00 0.00 3.86
2780 2790 2.285368 CTGGTAGGGCAGGGTGGA 60.285 66.667 0.00 0.00 0.00 4.02
2781 2791 3.411517 CCTGGTAGGGCAGGGTGG 61.412 72.222 0.00 0.00 35.04 4.61
2789 2799 1.306654 TGGTGGTAGCCTGGTAGGG 60.307 63.158 0.00 0.00 35.37 3.53
2790 2800 1.623542 GGTGGTGGTAGCCTGGTAGG 61.624 65.000 0.00 0.00 38.80 3.18
2791 2801 0.907704 TGGTGGTGGTAGCCTGGTAG 60.908 60.000 0.00 0.00 0.00 3.18
2792 2802 0.252974 ATGGTGGTGGTAGCCTGGTA 60.253 55.000 0.00 0.00 0.00 3.25
2793 2803 1.541368 ATGGTGGTGGTAGCCTGGT 60.541 57.895 0.00 0.00 0.00 4.00
2794 2804 1.224592 GATGGTGGTGGTAGCCTGG 59.775 63.158 0.00 0.00 0.00 4.45
2795 2805 0.179000 GAGATGGTGGTGGTAGCCTG 59.821 60.000 0.00 0.00 0.00 4.85
2796 2806 0.983378 GGAGATGGTGGTGGTAGCCT 60.983 60.000 0.00 0.00 0.00 4.58
2797 2807 1.271840 TGGAGATGGTGGTGGTAGCC 61.272 60.000 0.00 0.00 0.00 3.93
2798 2808 0.107654 GTGGAGATGGTGGTGGTAGC 60.108 60.000 0.00 0.00 0.00 3.58
2799 2809 0.175760 CGTGGAGATGGTGGTGGTAG 59.824 60.000 0.00 0.00 0.00 3.18
2800 2810 1.261938 CCGTGGAGATGGTGGTGGTA 61.262 60.000 0.00 0.00 0.00 3.25
2801 2811 2.592993 CCGTGGAGATGGTGGTGGT 61.593 63.158 0.00 0.00 0.00 4.16
2802 2812 2.268920 CCGTGGAGATGGTGGTGG 59.731 66.667 0.00 0.00 0.00 4.61
2803 2813 2.436646 GCCGTGGAGATGGTGGTG 60.437 66.667 0.00 0.00 0.00 4.17
2804 2814 4.082523 CGCCGTGGAGATGGTGGT 62.083 66.667 0.00 0.00 35.38 4.16
2836 2846 4.699522 GGGGATGTATCGGGCCGC 62.700 72.222 23.83 8.26 0.00 6.53
2837 2847 3.238497 TGGGGATGTATCGGGCCG 61.238 66.667 22.51 22.51 0.00 6.13
2838 2848 2.430367 GTGGGGATGTATCGGGCC 59.570 66.667 0.00 0.00 0.00 5.80
2839 2849 1.466025 TACGTGGGGATGTATCGGGC 61.466 60.000 0.00 0.00 0.00 6.13
2840 2850 0.316204 GTACGTGGGGATGTATCGGG 59.684 60.000 0.00 0.00 0.00 5.14
2841 2851 0.316204 GGTACGTGGGGATGTATCGG 59.684 60.000 0.00 0.00 0.00 4.18
2842 2852 0.316204 GGGTACGTGGGGATGTATCG 59.684 60.000 0.00 0.00 0.00 2.92
2843 2853 1.343465 CTGGGTACGTGGGGATGTATC 59.657 57.143 0.00 0.00 0.00 2.24
2844 2854 1.420430 CTGGGTACGTGGGGATGTAT 58.580 55.000 0.00 0.00 0.00 2.29
2845 2855 0.688418 CCTGGGTACGTGGGGATGTA 60.688 60.000 0.00 0.00 0.00 2.29
2846 2856 1.993391 CCTGGGTACGTGGGGATGT 60.993 63.158 0.00 0.00 0.00 3.06
2847 2857 2.908015 CCTGGGTACGTGGGGATG 59.092 66.667 0.00 0.00 0.00 3.51
2848 2858 3.087906 GCCTGGGTACGTGGGGAT 61.088 66.667 0.00 0.00 0.00 3.85
2853 2863 4.096003 CTGGGGCCTGGGTACGTG 62.096 72.222 0.84 0.00 0.00 4.49
2864 2874 3.553095 AACTGAACTCGGCTGGGGC 62.553 63.158 0.00 0.00 37.82 5.80
2865 2875 1.376037 GAACTGAACTCGGCTGGGG 60.376 63.158 0.00 0.00 0.00 4.96
2866 2876 1.376037 GGAACTGAACTCGGCTGGG 60.376 63.158 0.00 0.00 0.00 4.45
2867 2877 0.671781 CTGGAACTGAACTCGGCTGG 60.672 60.000 0.00 0.00 0.00 4.85
2868 2878 0.034059 ACTGGAACTGAACTCGGCTG 59.966 55.000 0.00 0.00 0.00 4.85
2869 2879 1.272769 GTACTGGAACTGAACTCGGCT 59.727 52.381 0.00 0.00 0.00 5.52
2870 2880 1.672145 GGTACTGGAACTGAACTCGGC 60.672 57.143 0.00 0.00 0.00 5.54
2871 2881 1.402456 CGGTACTGGAACTGAACTCGG 60.402 57.143 0.00 0.00 0.00 4.63
2872 2882 1.402456 CCGGTACTGGAACTGAACTCG 60.402 57.143 16.40 0.00 0.00 4.18
2873 2883 1.672145 GCCGGTACTGGAACTGAACTC 60.672 57.143 25.59 0.00 0.00 3.01
2874 2884 0.320697 GCCGGTACTGGAACTGAACT 59.679 55.000 25.59 0.00 0.00 3.01
2875 2885 1.012486 CGCCGGTACTGGAACTGAAC 61.012 60.000 25.59 3.53 0.00 3.18
2876 2886 1.290955 CGCCGGTACTGGAACTGAA 59.709 57.895 25.59 0.00 0.00 3.02
2877 2887 2.967397 CGCCGGTACTGGAACTGA 59.033 61.111 25.59 0.00 0.00 3.41
2878 2888 2.813908 GCGCCGGTACTGGAACTG 60.814 66.667 25.59 11.16 0.00 3.16
2879 2889 2.995574 AGCGCCGGTACTGGAACT 60.996 61.111 25.59 16.71 0.00 3.01
2880 2890 2.508663 GAGCGCCGGTACTGGAAC 60.509 66.667 25.59 14.63 0.00 3.62
2881 2891 2.992689 TGAGCGCCGGTACTGGAA 60.993 61.111 25.59 0.72 0.00 3.53
2882 2892 3.755628 GTGAGCGCCGGTACTGGA 61.756 66.667 25.59 0.00 0.00 3.86
2884 2894 4.111016 TCGTGAGCGCCGGTACTG 62.111 66.667 2.29 0.00 38.14 2.74
2885 2895 3.812019 CTCGTGAGCGCCGGTACT 61.812 66.667 2.29 0.00 38.14 2.73
2886 2896 3.807538 TCTCGTGAGCGCCGGTAC 61.808 66.667 2.29 0.00 38.14 3.34
2887 2897 3.807538 GTCTCGTGAGCGCCGGTA 61.808 66.667 2.29 0.00 38.14 4.02
2909 2919 4.211502 GTGGGATGGCAATGCGGC 62.212 66.667 0.00 0.00 41.67 6.53
2910 2920 3.530260 GGTGGGATGGCAATGCGG 61.530 66.667 0.00 0.00 0.00 5.69
2911 2921 2.755064 TGGTGGGATGGCAATGCG 60.755 61.111 0.00 0.00 0.00 4.73
2912 2922 3.085119 GCTGGTGGGATGGCAATGC 62.085 63.158 0.00 0.00 0.00 3.56
2913 2923 1.259142 TTGCTGGTGGGATGGCAATG 61.259 55.000 0.00 0.00 39.33 2.82
2914 2924 1.078891 TTGCTGGTGGGATGGCAAT 59.921 52.632 0.00 0.00 39.33 3.56
2915 2925 1.907807 GTTGCTGGTGGGATGGCAA 60.908 57.895 0.00 0.00 41.47 4.52
2916 2926 2.283101 GTTGCTGGTGGGATGGCA 60.283 61.111 0.00 0.00 0.00 4.92
2917 2927 3.443045 CGTTGCTGGTGGGATGGC 61.443 66.667 0.00 0.00 0.00 4.40
2918 2928 2.040544 GTCGTTGCTGGTGGGATGG 61.041 63.158 0.00 0.00 0.00 3.51
2919 2929 2.390599 CGTCGTTGCTGGTGGGATG 61.391 63.158 0.00 0.00 0.00 3.51
2920 2930 2.047274 CGTCGTTGCTGGTGGGAT 60.047 61.111 0.00 0.00 0.00 3.85
2921 2931 4.308458 CCGTCGTTGCTGGTGGGA 62.308 66.667 0.00 0.00 0.00 4.37
2924 2934 4.012895 GTGCCGTCGTTGCTGGTG 62.013 66.667 0.00 0.00 0.00 4.17
2964 2974 3.017581 ATGGAGGGGTGAGTGGGC 61.018 66.667 0.00 0.00 0.00 5.36
2965 2975 1.207488 TTGATGGAGGGGTGAGTGGG 61.207 60.000 0.00 0.00 0.00 4.61
2966 2976 0.921896 ATTGATGGAGGGGTGAGTGG 59.078 55.000 0.00 0.00 0.00 4.00
2967 2977 1.561076 TGATTGATGGAGGGGTGAGTG 59.439 52.381 0.00 0.00 0.00 3.51
2968 2978 1.971149 TGATTGATGGAGGGGTGAGT 58.029 50.000 0.00 0.00 0.00 3.41
2969 2979 2.440627 TGATGATTGATGGAGGGGTGAG 59.559 50.000 0.00 0.00 0.00 3.51
2970 2980 2.490961 TGATGATTGATGGAGGGGTGA 58.509 47.619 0.00 0.00 0.00 4.02
2971 2981 3.301794 TTGATGATTGATGGAGGGGTG 57.698 47.619 0.00 0.00 0.00 4.61
2972 2982 3.528905 TCTTTGATGATTGATGGAGGGGT 59.471 43.478 0.00 0.00 0.00 4.95
2973 2983 4.174704 TCTTTGATGATTGATGGAGGGG 57.825 45.455 0.00 0.00 0.00 4.79
2974 2984 5.831525 TGAATCTTTGATGATTGATGGAGGG 59.168 40.000 0.00 0.00 36.86 4.30
2975 2985 6.954487 TGAATCTTTGATGATTGATGGAGG 57.046 37.500 0.00 0.00 36.86 4.30
2976 2986 8.166422 TCATGAATCTTTGATGATTGATGGAG 57.834 34.615 13.57 0.00 43.37 3.86
2977 2987 7.996644 TCTCATGAATCTTTGATGATTGATGGA 59.003 33.333 13.57 8.94 43.37 3.41
2978 2988 8.166422 TCTCATGAATCTTTGATGATTGATGG 57.834 34.615 13.57 7.39 43.37 3.51
2985 2995 9.251440 AGGAATTTTCTCATGAATCTTTGATGA 57.749 29.630 0.00 0.00 31.56 2.92
2986 2996 9.871238 AAGGAATTTTCTCATGAATCTTTGATG 57.129 29.630 0.00 0.00 31.56 3.07
2995 3005 9.912634 GTGTCAAATAAGGAATTTTCTCATGAA 57.087 29.630 0.00 0.00 35.54 2.57
2996 3006 9.300681 AGTGTCAAATAAGGAATTTTCTCATGA 57.699 29.630 0.00 0.00 35.54 3.07
3117 3132 6.748333 TTTCAGATGTCATTTAGGCTCAAG 57.252 37.500 0.00 0.00 0.00 3.02
3207 3223 0.546122 TTGTGTGTGCTCCTGTCCTT 59.454 50.000 0.00 0.00 0.00 3.36
3262 3284 2.099254 TGTTGTTGCGTGTGTGCG 59.901 55.556 0.00 0.00 37.81 5.34
3347 3389 1.798234 ATGCGTGTGTGTTGCTGCAT 61.798 50.000 1.84 0.00 38.16 3.96
3348 3390 2.479750 ATGCGTGTGTGTTGCTGCA 61.480 52.632 0.00 0.00 36.69 4.41
3387 3471 3.957535 GTGCTGCTGCTGCGTGTT 61.958 61.111 23.38 0.00 43.34 3.32
3389 3473 4.678269 GTGTGCTGCTGCTGCGTG 62.678 66.667 23.38 7.48 43.34 5.34
3391 3475 3.733960 ATGTGTGCTGCTGCTGCG 61.734 61.111 23.38 7.03 43.34 5.18
3392 3476 2.126463 CATGTGTGCTGCTGCTGC 60.126 61.111 22.51 22.51 40.48 5.25
3440 3538 4.943591 CGCTGCGTGTGTGTGTGC 62.944 66.667 14.93 0.00 0.00 4.57
3580 3736 5.831702 ATTCTCTATACGACACTTCCGTT 57.168 39.130 0.00 0.00 40.95 4.44


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

AutoCloner maintained by Alex Coulton.