Multiple sequence alignment - TraesCS3D01G248400

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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 TraesCS3D01G248400 chr3D 100.000 5268 0 0 1 5268 347413442 347418709 0.000000e+00 9729.0
1 TraesCS3D01G248400 chr3D 95.370 648 30 0 4621 5268 347440148 347440795 0.000000e+00 1031.0
2 TraesCS3D01G248400 chr3A 96.212 3300 69 13 1207 4467 466574548 466577830 0.000000e+00 5350.0
3 TraesCS3D01G248400 chr3A 88.869 548 44 8 136 683 466572650 466573180 0.000000e+00 658.0
4 TraesCS3D01G248400 chr3A 96.063 381 11 2 689 1069 466573661 466574037 7.500000e-173 617.0
5 TraesCS3D01G248400 chr3A 88.519 270 29 2 4608 4875 220263254 220262985 5.090000e-85 326.0
6 TraesCS3D01G248400 chr3A 84.431 334 31 8 926 1259 466567387 466567699 5.120000e-80 309.0
7 TraesCS3D01G248400 chr3A 93.617 141 9 0 1 141 466567912 466568052 1.490000e-50 211.0
8 TraesCS3D01G248400 chr3A 95.890 73 3 0 4549 4621 395536376 395536304 9.270000e-23 119.0
9 TraesCS3D01G248400 chr3B 95.522 1764 40 11 748 2501 447228839 447230573 0.000000e+00 2784.0
10 TraesCS3D01G248400 chr3B 93.494 1076 51 11 2498 3570 447230621 447231680 0.000000e+00 1581.0
11 TraesCS3D01G248400 chr3B 94.632 950 43 6 3599 4545 447231895 447232839 0.000000e+00 1465.0
12 TraesCS3D01G248400 chr3B 91.139 79 2 1 683 756 447226093 447226171 9.330000e-18 102.0
13 TraesCS3D01G248400 chr3B 90.789 76 6 1 769 844 447211085 447211159 3.360000e-17 100.0
14 TraesCS3D01G248400 chr2D 90.839 644 55 4 4620 5263 400400964 400401603 0.000000e+00 859.0
15 TraesCS3D01G248400 chr2D 88.092 655 67 10 4622 5268 607722407 607721756 0.000000e+00 767.0
16 TraesCS3D01G248400 chr2D 87.253 659 76 8 4610 5265 358984413 358985066 0.000000e+00 745.0
17 TraesCS3D01G248400 chr2D 94.805 77 4 0 4545 4621 398452585 398452661 2.580000e-23 121.0
18 TraesCS3D01G248400 chr7D 90.123 648 61 3 4621 5268 514562577 514561933 0.000000e+00 839.0
19 TraesCS3D01G248400 chr7D 89.060 649 67 3 4621 5268 514575664 514575019 0.000000e+00 802.0
20 TraesCS3D01G248400 chr7D 94.805 77 4 0 4545 4621 116061128 116061052 2.580000e-23 121.0
21 TraesCS3D01G248400 chr4D 88.073 654 66 12 4622 5268 453573877 453574525 0.000000e+00 765.0
22 TraesCS3D01G248400 chr4D 87.156 654 73 11 4622 5268 453759854 453760503 0.000000e+00 732.0
23 TraesCS3D01G248400 chr6A 87.211 649 73 9 4622 5268 400042055 400042695 0.000000e+00 730.0
24 TraesCS3D01G248400 chr6A 85.824 649 79 12 4622 5268 397503671 397503034 0.000000e+00 676.0
25 TraesCS3D01G248400 chr6A 96.104 77 3 0 4545 4621 263879394 263879318 5.540000e-25 126.0
26 TraesCS3D01G248400 chr6A 94.805 77 4 0 4545 4621 99379196 99379272 2.580000e-23 121.0
27 TraesCS3D01G248400 chr6A 94.737 76 4 0 4546 4621 263883929 263883854 9.270000e-23 119.0
28 TraesCS3D01G248400 chr6A 100.000 28 0 0 2572 2599 563726767 563726794 1.000000e-02 52.8
29 TraesCS3D01G248400 chr1D 81.525 931 91 39 3208 4114 479728139 479729012 0.000000e+00 691.0
30 TraesCS3D01G248400 chr1D 96.203 79 3 0 4543 4621 235664697 235664775 4.280000e-26 130.0
31 TraesCS3D01G248400 chr7B 77.811 676 109 33 4604 5268 135293972 135294617 3.850000e-101 379.0
32 TraesCS3D01G248400 chr7B 77.023 692 109 40 4609 5268 165186425 165185752 8.390000e-93 351.0
33 TraesCS3D01G248400 chr5B 90.076 262 26 0 4622 4883 333603542 333603281 1.820000e-89 340.0
34 TraesCS3D01G248400 chr2B 75.367 682 123 38 4607 5268 100652716 100653372 2.400000e-73 287.0
35 TraesCS3D01G248400 chr1A 96.104 77 3 0 4545 4621 514942487 514942411 5.540000e-25 126.0
36 TraesCS3D01G248400 chr1A 95.833 72 3 0 4550 4621 515199178 515199107 3.330000e-22 117.0
37 TraesCS3D01G248400 chr6D 100.000 28 0 0 667 694 120659113 120659140 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G248400 chr3D 347413442 347418709 5267 False 9729.000000 9729 100.000000 1 5268 1 chr3D.!!$F1 5267
1 TraesCS3D01G248400 chr3D 347440148 347440795 647 False 1031.000000 1031 95.370000 4621 5268 1 chr3D.!!$F2 647
2 TraesCS3D01G248400 chr3A 466572650 466577830 5180 False 2208.333333 5350 93.714667 136 4467 3 chr3A.!!$F2 4331
3 TraesCS3D01G248400 chr3A 466567387 466568052 665 False 260.000000 309 89.024000 1 1259 2 chr3A.!!$F1 1258
4 TraesCS3D01G248400 chr3B 447226093 447232839 6746 False 1483.000000 2784 93.696750 683 4545 4 chr3B.!!$F2 3862
5 TraesCS3D01G248400 chr2D 400400964 400401603 639 False 859.000000 859 90.839000 4620 5263 1 chr2D.!!$F3 643
6 TraesCS3D01G248400 chr2D 607721756 607722407 651 True 767.000000 767 88.092000 4622 5268 1 chr2D.!!$R1 646
7 TraesCS3D01G248400 chr2D 358984413 358985066 653 False 745.000000 745 87.253000 4610 5265 1 chr2D.!!$F1 655
8 TraesCS3D01G248400 chr7D 514561933 514562577 644 True 839.000000 839 90.123000 4621 5268 1 chr7D.!!$R2 647
9 TraesCS3D01G248400 chr7D 514575019 514575664 645 True 802.000000 802 89.060000 4621 5268 1 chr7D.!!$R3 647
10 TraesCS3D01G248400 chr4D 453573877 453574525 648 False 765.000000 765 88.073000 4622 5268 1 chr4D.!!$F1 646
11 TraesCS3D01G248400 chr4D 453759854 453760503 649 False 732.000000 732 87.156000 4622 5268 1 chr4D.!!$F2 646
12 TraesCS3D01G248400 chr6A 400042055 400042695 640 False 730.000000 730 87.211000 4622 5268 1 chr6A.!!$F2 646
13 TraesCS3D01G248400 chr6A 397503034 397503671 637 True 676.000000 676 85.824000 4622 5268 1 chr6A.!!$R3 646
14 TraesCS3D01G248400 chr1D 479728139 479729012 873 False 691.000000 691 81.525000 3208 4114 1 chr1D.!!$F2 906
15 TraesCS3D01G248400 chr7B 135293972 135294617 645 False 379.000000 379 77.811000 4604 5268 1 chr7B.!!$F1 664
16 TraesCS3D01G248400 chr7B 165185752 165186425 673 True 351.000000 351 77.023000 4609 5268 1 chr7B.!!$R1 659
17 TraesCS3D01G248400 chr2B 100652716 100653372 656 False 287.000000 287 75.367000 4607 5268 1 chr2B.!!$F1 661

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
101 102 0.103208 CCCGCTGTATTTCTCGAGCT 59.897 55.000 7.81 0.0 0.00 4.09 F
148 149 0.394352 GTGTGAACTGGGGGCTATGG 60.394 60.000 0.00 0.0 0.00 2.74 F
1313 4850 0.610232 ATTTGGTCCTCCTGTGCTGC 60.610 55.000 0.00 0.0 34.23 5.25 F
1547 5084 0.785979 GAACGCATTTGGCAGCAAAG 59.214 50.000 0.00 0.0 45.17 2.77 F
2483 6030 1.216930 ACCTAACCTTTTGCCAGTGGT 59.783 47.619 11.74 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 5084 1.538047 TTCATGTTCAGAAGCTGGGC 58.462 50.000 0.00 0.00 31.51 5.36 R
1585 5122 3.337358 CTCACATACACATGCACCAGAA 58.663 45.455 0.00 0.00 35.39 3.02 R
2483 6030 2.193993 GAACCCCCTAACTAAGCTCCA 58.806 52.381 0.00 0.00 0.00 3.86 R
2657 6255 4.750098 ACACTAATCAACTTGAAGTGACCG 59.250 41.667 22.34 4.69 37.39 4.79 R
4479 8290 3.695060 ACTACCATAGAAGACGACACAGG 59.305 47.826 0.00 0.00 0.00 4.00 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
21 22 3.682696 TCTTAGCTCTGTCTGGTTACGA 58.317 45.455 0.00 0.00 0.00 3.43
22 23 3.439476 TCTTAGCTCTGTCTGGTTACGAC 59.561 47.826 0.00 0.00 0.00 4.34
23 24 1.912417 AGCTCTGTCTGGTTACGACT 58.088 50.000 0.00 0.00 32.70 4.18
24 25 1.542030 AGCTCTGTCTGGTTACGACTG 59.458 52.381 0.00 0.00 32.70 3.51
25 26 1.269998 GCTCTGTCTGGTTACGACTGT 59.730 52.381 0.00 0.00 33.64 3.55
26 27 2.486982 GCTCTGTCTGGTTACGACTGTA 59.513 50.000 0.00 0.00 33.64 2.74
27 28 3.426426 GCTCTGTCTGGTTACGACTGTAG 60.426 52.174 0.00 0.00 33.64 2.74
28 29 2.486982 TCTGTCTGGTTACGACTGTAGC 59.513 50.000 0.00 0.00 33.64 3.58
34 35 2.719426 GTTACGACTGTAGCCACTGT 57.281 50.000 0.00 0.00 39.31 3.55
35 36 2.325761 GTTACGACTGTAGCCACTGTG 58.674 52.381 0.00 0.00 37.01 3.66
36 37 1.612676 TACGACTGTAGCCACTGTGT 58.387 50.000 7.08 1.96 37.01 3.72
37 38 0.750850 ACGACTGTAGCCACTGTGTT 59.249 50.000 7.08 0.00 37.01 3.32
38 39 1.139989 CGACTGTAGCCACTGTGTTG 58.860 55.000 7.08 0.00 37.01 3.33
39 40 1.512926 GACTGTAGCCACTGTGTTGG 58.487 55.000 7.08 0.00 37.01 3.77
45 46 2.111043 CCACTGTGTTGGCCTCGT 59.889 61.111 3.32 0.00 0.00 4.18
46 47 1.525995 CCACTGTGTTGGCCTCGTT 60.526 57.895 3.32 0.00 0.00 3.85
47 48 1.648720 CACTGTGTTGGCCTCGTTG 59.351 57.895 3.32 0.00 0.00 4.10
48 49 2.186826 ACTGTGTTGGCCTCGTTGC 61.187 57.895 3.32 0.00 0.00 4.17
49 50 2.124529 TGTGTTGGCCTCGTTGCA 60.125 55.556 3.32 0.00 0.00 4.08
50 51 1.723608 CTGTGTTGGCCTCGTTGCAA 61.724 55.000 3.32 0.00 0.00 4.08
51 52 1.299089 GTGTTGGCCTCGTTGCAAC 60.299 57.895 19.89 19.89 0.00 4.17
52 53 2.335011 GTTGGCCTCGTTGCAACC 59.665 61.111 23.42 9.98 0.00 3.77
53 54 2.909965 TTGGCCTCGTTGCAACCC 60.910 61.111 23.42 18.16 0.00 4.11
54 55 3.429372 TTGGCCTCGTTGCAACCCT 62.429 57.895 23.42 0.00 0.00 4.34
55 56 3.056328 GGCCTCGTTGCAACCCTC 61.056 66.667 23.42 10.10 0.00 4.30
56 57 3.423154 GCCTCGTTGCAACCCTCG 61.423 66.667 23.42 12.22 0.00 4.63
57 58 2.742372 CCTCGTTGCAACCCTCGG 60.742 66.667 23.42 14.04 0.00 4.63
58 59 2.342279 CTCGTTGCAACCCTCGGA 59.658 61.111 23.42 13.16 0.00 4.55
59 60 1.738099 CTCGTTGCAACCCTCGGAG 60.738 63.158 23.42 18.31 0.00 4.63
60 61 2.742372 CGTTGCAACCCTCGGAGG 60.742 66.667 23.42 17.41 34.30 4.30
61 62 2.747686 GTTGCAACCCTCGGAGGA 59.252 61.111 25.60 1.55 37.67 3.71
62 63 1.376037 GTTGCAACCCTCGGAGGAG 60.376 63.158 25.60 16.82 37.67 3.69
63 64 3.254024 TTGCAACCCTCGGAGGAGC 62.254 63.158 25.60 23.10 37.67 4.70
64 65 3.706373 GCAACCCTCGGAGGAGCA 61.706 66.667 25.60 0.00 37.67 4.26
65 66 2.266055 CAACCCTCGGAGGAGCAC 59.734 66.667 25.60 0.00 37.67 4.40
66 67 3.382832 AACCCTCGGAGGAGCACG 61.383 66.667 25.60 10.46 37.67 5.34
67 68 4.680537 ACCCTCGGAGGAGCACGT 62.681 66.667 25.60 11.13 37.67 4.49
68 69 2.439701 CCCTCGGAGGAGCACGTA 60.440 66.667 25.60 0.00 37.67 3.57
69 70 1.828660 CCCTCGGAGGAGCACGTAT 60.829 63.158 25.60 0.00 37.67 3.06
70 71 0.536687 CCCTCGGAGGAGCACGTATA 60.537 60.000 25.60 0.00 37.67 1.47
71 72 0.875728 CCTCGGAGGAGCACGTATAG 59.124 60.000 19.57 0.00 37.67 1.31
72 73 0.875728 CTCGGAGGAGCACGTATAGG 59.124 60.000 0.00 0.00 32.61 2.57
73 74 0.182061 TCGGAGGAGCACGTATAGGT 59.818 55.000 0.00 0.00 0.00 3.08
74 75 1.030457 CGGAGGAGCACGTATAGGTT 58.970 55.000 0.00 0.00 0.00 3.50
75 76 1.269102 CGGAGGAGCACGTATAGGTTG 60.269 57.143 0.00 0.00 0.00 3.77
76 77 1.068741 GGAGGAGCACGTATAGGTTGG 59.931 57.143 0.00 0.00 0.00 3.77
77 78 2.029623 GAGGAGCACGTATAGGTTGGA 58.970 52.381 0.00 0.00 0.00 3.53
78 79 1.755380 AGGAGCACGTATAGGTTGGAC 59.245 52.381 0.00 0.00 0.00 4.02
79 80 1.202498 GGAGCACGTATAGGTTGGACC 60.202 57.143 0.00 0.00 38.99 4.46
80 81 1.479323 GAGCACGTATAGGTTGGACCA 59.521 52.381 0.00 0.00 41.95 4.02
81 82 1.903860 AGCACGTATAGGTTGGACCAA 59.096 47.619 1.69 1.69 41.95 3.67
82 83 2.004733 GCACGTATAGGTTGGACCAAC 58.995 52.381 26.49 26.49 41.95 3.77
89 90 2.203294 GTTGGACCAACCCGCTGT 60.203 61.111 24.53 0.00 38.30 4.40
90 91 1.071814 GTTGGACCAACCCGCTGTA 59.928 57.895 24.53 0.00 38.30 2.74
91 92 0.322187 GTTGGACCAACCCGCTGTAT 60.322 55.000 24.53 0.00 38.30 2.29
92 93 0.402504 TTGGACCAACCCGCTGTATT 59.597 50.000 1.69 0.00 38.00 1.89
93 94 0.402504 TGGACCAACCCGCTGTATTT 59.597 50.000 0.00 0.00 38.00 1.40
94 95 1.092348 GGACCAACCCGCTGTATTTC 58.908 55.000 0.00 0.00 0.00 2.17
95 96 1.339727 GGACCAACCCGCTGTATTTCT 60.340 52.381 0.00 0.00 0.00 2.52
96 97 2.007608 GACCAACCCGCTGTATTTCTC 58.992 52.381 0.00 0.00 0.00 2.87
97 98 1.006832 CCAACCCGCTGTATTTCTCG 58.993 55.000 0.00 0.00 0.00 4.04
98 99 1.404986 CCAACCCGCTGTATTTCTCGA 60.405 52.381 0.00 0.00 0.00 4.04
99 100 1.927174 CAACCCGCTGTATTTCTCGAG 59.073 52.381 5.93 5.93 0.00 4.04
100 101 0.179108 ACCCGCTGTATTTCTCGAGC 60.179 55.000 7.81 0.00 0.00 5.03
101 102 0.103208 CCCGCTGTATTTCTCGAGCT 59.897 55.000 7.81 0.00 0.00 4.09
102 103 1.482278 CCGCTGTATTTCTCGAGCTC 58.518 55.000 7.81 2.73 0.00 4.09
103 104 1.202302 CCGCTGTATTTCTCGAGCTCA 60.202 52.381 15.40 0.00 0.00 4.26
104 105 2.115595 CGCTGTATTTCTCGAGCTCAG 58.884 52.381 15.40 10.41 0.00 3.35
105 106 1.857837 GCTGTATTTCTCGAGCTCAGC 59.142 52.381 15.40 21.04 39.55 4.26
106 107 2.736719 GCTGTATTTCTCGAGCTCAGCA 60.737 50.000 25.81 15.35 43.83 4.41
107 108 3.515630 CTGTATTTCTCGAGCTCAGCAA 58.484 45.455 15.40 7.53 0.00 3.91
108 109 3.515630 TGTATTTCTCGAGCTCAGCAAG 58.484 45.455 15.40 5.36 0.00 4.01
109 110 3.193479 TGTATTTCTCGAGCTCAGCAAGA 59.807 43.478 15.40 7.70 0.00 3.02
110 111 3.540314 ATTTCTCGAGCTCAGCAAGAT 57.460 42.857 15.40 0.00 0.00 2.40
111 112 4.662468 ATTTCTCGAGCTCAGCAAGATA 57.338 40.909 15.40 6.32 0.00 1.98
112 113 4.662468 TTTCTCGAGCTCAGCAAGATAT 57.338 40.909 15.40 0.00 0.00 1.63
113 114 3.913548 TCTCGAGCTCAGCAAGATATC 57.086 47.619 15.40 0.00 0.00 1.63
114 115 3.485394 TCTCGAGCTCAGCAAGATATCT 58.515 45.455 15.40 0.00 0.00 1.98
115 116 3.501828 TCTCGAGCTCAGCAAGATATCTC 59.498 47.826 15.40 0.00 0.00 2.75
116 117 2.556189 TCGAGCTCAGCAAGATATCTCC 59.444 50.000 15.40 0.43 0.00 3.71
117 118 2.557924 CGAGCTCAGCAAGATATCTCCT 59.442 50.000 15.40 2.92 0.00 3.69
118 119 3.612241 CGAGCTCAGCAAGATATCTCCTG 60.612 52.174 15.40 19.77 0.00 3.86
119 120 3.573538 GAGCTCAGCAAGATATCTCCTGA 59.426 47.826 23.79 23.79 0.00 3.86
120 121 4.161876 AGCTCAGCAAGATATCTCCTGAT 58.838 43.478 24.76 11.44 32.69 2.90
121 122 5.331906 AGCTCAGCAAGATATCTCCTGATA 58.668 41.667 24.76 12.22 39.25 2.15
122 123 5.779260 AGCTCAGCAAGATATCTCCTGATAA 59.221 40.000 24.76 11.74 38.50 1.75
123 124 6.269538 AGCTCAGCAAGATATCTCCTGATAAA 59.730 38.462 24.76 11.49 38.50 1.40
124 125 6.368516 GCTCAGCAAGATATCTCCTGATAAAC 59.631 42.308 24.76 16.00 38.50 2.01
125 126 7.365497 TCAGCAAGATATCTCCTGATAAACA 57.635 36.000 22.51 8.19 38.50 2.83
126 127 7.971201 TCAGCAAGATATCTCCTGATAAACAT 58.029 34.615 22.51 0.00 38.50 2.71
127 128 7.876582 TCAGCAAGATATCTCCTGATAAACATG 59.123 37.037 22.51 9.16 38.50 3.21
128 129 7.660617 CAGCAAGATATCTCCTGATAAACATGT 59.339 37.037 20.62 0.00 38.50 3.21
129 130 7.660617 AGCAAGATATCTCCTGATAAACATGTG 59.339 37.037 5.51 0.00 38.50 3.21
130 131 7.443575 GCAAGATATCTCCTGATAAACATGTGT 59.556 37.037 5.51 0.00 38.50 3.72
131 132 8.771766 CAAGATATCTCCTGATAAACATGTGTG 58.228 37.037 5.51 0.00 38.50 3.82
132 133 8.027524 AGATATCTCCTGATAAACATGTGTGT 57.972 34.615 0.00 0.00 38.50 3.72
133 134 7.930325 AGATATCTCCTGATAAACATGTGTGTG 59.070 37.037 0.00 0.00 38.50 3.82
134 135 5.482163 TCTCCTGATAAACATGTGTGTGA 57.518 39.130 0.00 0.00 38.92 3.58
137 138 5.620206 TCCTGATAAACATGTGTGTGAACT 58.380 37.500 0.00 0.00 38.92 3.01
148 149 0.394352 GTGTGAACTGGGGGCTATGG 60.394 60.000 0.00 0.00 0.00 2.74
154 155 0.853530 ACTGGGGGCTATGGAATTCC 59.146 55.000 18.17 18.17 0.00 3.01
173 174 1.328439 CTCCTAATGTATCGCGCGAC 58.672 55.000 37.37 24.72 0.00 5.19
189 190 1.740285 GACGTCGAGCCCACCATAT 59.260 57.895 0.00 0.00 0.00 1.78
191 192 1.040893 ACGTCGAGCCCACCATATCA 61.041 55.000 0.00 0.00 0.00 2.15
194 195 1.071471 CGAGCCCACCATATCACCC 59.929 63.158 0.00 0.00 0.00 4.61
196 197 0.773644 GAGCCCACCATATCACCCAT 59.226 55.000 0.00 0.00 0.00 4.00
207 208 4.020751 CCATATCACCCATAGAGTCACCAG 60.021 50.000 0.00 0.00 0.00 4.00
209 210 2.179427 TCACCCATAGAGTCACCAGTG 58.821 52.381 0.00 0.00 0.00 3.66
221 222 1.453015 ACCAGTGCTTCCACGCAAA 60.453 52.632 0.00 0.00 46.62 3.68
307 308 1.945387 AGAGTGGTATTGCTGCATCG 58.055 50.000 1.84 0.00 0.00 3.84
313 314 0.855349 GTATTGCTGCATCGTCCTCG 59.145 55.000 1.84 0.00 38.55 4.63
322 323 1.828832 CATCGTCCTCGCTAAGTGAC 58.171 55.000 0.00 0.00 36.96 3.67
327 328 1.135344 GTCCTCGCTAAGTGACCAGAC 60.135 57.143 0.00 0.00 0.00 3.51
343 344 3.440173 ACCAGACACTTTTCGCCATATTG 59.560 43.478 0.00 0.00 0.00 1.90
348 349 3.119849 ACACTTTTCGCCATATTGCAGTC 60.120 43.478 0.00 0.00 0.00 3.51
354 355 4.505313 TCGCCATATTGCAGTCTAGTAG 57.495 45.455 0.00 0.00 0.00 2.57
365 366 3.004315 GCAGTCTAGTAGAGCATGTCTCC 59.996 52.174 0.00 0.00 42.90 3.71
378 379 3.427233 GCATGTCTCCAAGAATCAACAGC 60.427 47.826 0.00 0.00 0.00 4.40
381 382 1.347707 TCTCCAAGAATCAACAGCCGT 59.652 47.619 0.00 0.00 0.00 5.68
382 383 1.466167 CTCCAAGAATCAACAGCCGTG 59.534 52.381 0.00 0.00 0.00 4.94
472 473 1.669115 CCTCACAAGCCTCCACACG 60.669 63.158 0.00 0.00 0.00 4.49
487 488 2.946990 CCACACGAACACCCTAAGTTTT 59.053 45.455 0.00 0.00 0.00 2.43
489 490 2.356695 ACACGAACACCCTAAGTTTTGC 59.643 45.455 0.00 0.00 0.00 3.68
497 498 2.177016 ACCCTAAGTTTTGCTGGGACTT 59.823 45.455 3.13 0.00 40.23 3.01
537 538 5.741011 ACGCCAATTATTCTCCTCAACTTA 58.259 37.500 0.00 0.00 0.00 2.24
540 541 6.260936 CGCCAATTATTCTCCTCAACTTATGT 59.739 38.462 0.00 0.00 0.00 2.29
565 566 3.908103 TGGAGCTCCAAACCTAAACTACT 59.092 43.478 33.41 0.00 44.35 2.57
570 571 5.071923 AGCTCCAAACCTAAACTACTGAAGT 59.928 40.000 0.00 0.00 41.49 3.01
571 572 6.269307 AGCTCCAAACCTAAACTACTGAAGTA 59.731 38.462 0.00 0.00 37.50 2.24
573 574 7.607615 TCCAAACCTAAACTACTGAAGTACT 57.392 36.000 0.00 0.00 37.50 2.73
574 575 8.026396 TCCAAACCTAAACTACTGAAGTACTT 57.974 34.615 8.13 8.13 37.50 2.24
575 576 8.146412 TCCAAACCTAAACTACTGAAGTACTTC 58.854 37.037 25.73 25.73 37.50 3.01
578 579 7.465353 ACCTAAACTACTGAAGTACTTCCTC 57.535 40.000 28.43 9.42 37.50 3.71
579 580 7.240167 ACCTAAACTACTGAAGTACTTCCTCT 58.760 38.462 28.43 15.19 37.50 3.69
580 581 7.729431 ACCTAAACTACTGAAGTACTTCCTCTT 59.271 37.037 28.43 16.40 37.50 2.85
581 582 8.586744 CCTAAACTACTGAAGTACTTCCTCTTT 58.413 37.037 28.43 19.72 37.50 2.52
619 620 6.461640 AGCGTTAAGGTCATTAAAGTAGTGT 58.538 36.000 5.14 0.00 35.86 3.55
907 4059 2.774234 CACCTCCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
908 4060 3.041946 ACCTCCTCTCTCTCTCTCTCTC 58.958 54.545 0.00 0.00 0.00 3.20
1311 4848 1.004044 CTGATTTGGTCCTCCTGTGCT 59.996 52.381 0.00 0.00 34.23 4.40
1312 4849 1.271543 TGATTTGGTCCTCCTGTGCTG 60.272 52.381 0.00 0.00 34.23 4.41
1313 4850 0.610232 ATTTGGTCCTCCTGTGCTGC 60.610 55.000 0.00 0.00 34.23 5.25
1547 5084 0.785979 GAACGCATTTGGCAGCAAAG 59.214 50.000 0.00 0.00 45.17 2.77
1585 5122 7.439381 ACATGAATTTTGTGCTGAAAATCTCT 58.561 30.769 0.00 0.00 35.01 3.10
1892 5429 2.098117 GCTGTTGTAATCACATCTGGGC 59.902 50.000 0.00 0.00 33.76 5.36
1973 5510 1.474143 GCATTCTACAGAGGGGCAGAC 60.474 57.143 0.00 0.00 0.00 3.51
2177 5720 6.170846 TGAGATGACAGCTTGATATGATGT 57.829 37.500 0.00 0.00 36.71 3.06
2192 5735 7.660112 TGATATGATGTTGCCATTATGTTTCC 58.340 34.615 0.00 0.00 30.62 3.13
2457 6004 2.733026 GCAATTGAGCAATGAAAGCGTT 59.267 40.909 10.34 0.00 37.01 4.84
2483 6030 1.216930 ACCTAACCTTTTGCCAGTGGT 59.783 47.619 11.74 0.00 0.00 4.16
2555 6153 3.287222 TGGGTCCTCAACTTTGTTCAAG 58.713 45.455 0.00 0.00 38.64 3.02
2657 6255 2.554893 TGTAAATTCCGGCAAGGTGAAC 59.445 45.455 0.00 0.00 41.99 3.18
2680 6278 4.750098 CGGTCACTTCAAGTTGATTAGTGT 59.250 41.667 26.04 11.56 36.86 3.55
2826 6424 6.904463 ATAAATATCTGGATGTGCAATGCA 57.096 33.333 2.72 2.72 35.60 3.96
2895 6493 4.400251 CCTACAATGTTGGTTGATGCAGAT 59.600 41.667 5.70 0.00 33.37 2.90
2976 6574 2.916934 TGGTGGGCTATCAGGTTAACTT 59.083 45.455 5.42 0.00 0.00 2.66
2977 6575 3.054655 TGGTGGGCTATCAGGTTAACTTC 60.055 47.826 5.42 0.00 0.00 3.01
3680 7483 3.126000 GCTTCTGTTCATACTTGTCCAGC 59.874 47.826 0.00 0.00 0.00 4.85
3727 7530 4.509230 CGCTAAGACTATCAATGTGCATGT 59.491 41.667 0.00 0.00 0.00 3.21
3736 7539 3.644823 TCAATGTGCATGTCAGCTTTTG 58.355 40.909 0.00 0.00 34.99 2.44
3814 7620 4.018484 GAGATTGCTCCTAAGATGGCAT 57.982 45.455 0.00 0.00 35.01 4.40
4298 8109 4.843728 ACACTTTGGGATATATATGGCCG 58.156 43.478 0.00 0.00 0.00 6.13
4363 8174 0.454452 GCGTTGATTTTGGTCGAGGC 60.454 55.000 0.00 0.00 36.56 4.70
4463 8274 7.781056 TCTTTCTTTGTTTAAGGAGCAACATT 58.219 30.769 0.00 0.00 32.96 2.71
4545 8356 6.252995 TGAAATTTCAACCCTGGCTAATAGT 58.747 36.000 18.45 0.00 33.55 2.12
4546 8357 6.152661 TGAAATTTCAACCCTGGCTAATAGTG 59.847 38.462 18.45 0.00 33.55 2.74
4547 8358 4.650972 TTTCAACCCTGGCTAATAGTGT 57.349 40.909 0.00 0.00 0.00 3.55
4548 8359 4.650972 TTCAACCCTGGCTAATAGTGTT 57.349 40.909 0.00 0.00 0.00 3.32
4549 8360 3.950397 TCAACCCTGGCTAATAGTGTTG 58.050 45.455 0.00 0.00 34.45 3.33
4550 8361 3.585289 TCAACCCTGGCTAATAGTGTTGA 59.415 43.478 6.75 6.75 38.50 3.18
4551 8362 3.914426 ACCCTGGCTAATAGTGTTGAG 57.086 47.619 0.00 0.00 0.00 3.02
4552 8363 3.182152 ACCCTGGCTAATAGTGTTGAGT 58.818 45.455 0.00 0.00 0.00 3.41
4553 8364 4.359105 ACCCTGGCTAATAGTGTTGAGTA 58.641 43.478 0.00 0.00 0.00 2.59
4554 8365 4.969359 ACCCTGGCTAATAGTGTTGAGTAT 59.031 41.667 0.00 0.00 0.00 2.12
4555 8366 6.141083 ACCCTGGCTAATAGTGTTGAGTATA 58.859 40.000 0.00 0.00 0.00 1.47
4556 8367 6.787957 ACCCTGGCTAATAGTGTTGAGTATAT 59.212 38.462 0.00 0.00 0.00 0.86
4557 8368 7.099764 CCCTGGCTAATAGTGTTGAGTATATG 58.900 42.308 0.00 0.00 0.00 1.78
4558 8369 7.256332 CCCTGGCTAATAGTGTTGAGTATATGT 60.256 40.741 0.00 0.00 0.00 2.29
4559 8370 7.600375 CCTGGCTAATAGTGTTGAGTATATGTG 59.400 40.741 0.00 0.00 0.00 3.21
4560 8371 6.929049 TGGCTAATAGTGTTGAGTATATGTGC 59.071 38.462 0.00 0.00 0.00 4.57
4561 8372 7.155328 GGCTAATAGTGTTGAGTATATGTGCT 58.845 38.462 0.00 0.00 0.00 4.40
4562 8373 8.304596 GGCTAATAGTGTTGAGTATATGTGCTA 58.695 37.037 0.00 0.00 0.00 3.49
4563 8374 9.862371 GCTAATAGTGTTGAGTATATGTGCTAT 57.138 33.333 0.00 0.00 0.00 2.97
4566 8377 9.481340 AATAGTGTTGAGTATATGTGCTATGTG 57.519 33.333 0.00 0.00 0.00 3.21
4567 8378 5.755375 AGTGTTGAGTATATGTGCTATGTGC 59.245 40.000 0.00 0.00 43.25 4.57
4583 8394 6.546395 GCTATGTGCATATTGTGTATTAGGC 58.454 40.000 0.00 0.00 42.31 3.93
4584 8395 5.964958 ATGTGCATATTGTGTATTAGGCC 57.035 39.130 0.00 0.00 0.00 5.19
4585 8396 4.141287 TGTGCATATTGTGTATTAGGCCC 58.859 43.478 0.00 0.00 0.00 5.80
4586 8397 3.188460 GTGCATATTGTGTATTAGGCCCG 59.812 47.826 0.00 0.00 0.00 6.13
4587 8398 2.161609 GCATATTGTGTATTAGGCCCGC 59.838 50.000 0.00 0.00 0.00 6.13
4588 8399 2.554370 TATTGTGTATTAGGCCCGCC 57.446 50.000 0.00 0.00 0.00 6.13
4590 8401 0.179468 TTGTGTATTAGGCCCGCCTC 59.821 55.000 12.53 0.00 44.43 4.70
4591 8402 1.070957 GTGTATTAGGCCCGCCTCC 59.929 63.158 12.53 0.00 44.43 4.30
4592 8403 1.074775 TGTATTAGGCCCGCCTCCT 60.075 57.895 12.53 3.34 44.43 3.69
4593 8404 0.189080 TGTATTAGGCCCGCCTCCTA 59.811 55.000 12.53 2.32 44.43 2.94
4594 8405 1.345063 GTATTAGGCCCGCCTCCTAA 58.655 55.000 12.53 1.28 44.43 2.69
4595 8406 3.182105 ATTAGGCCCGCCTCCTAAT 57.818 52.632 12.53 3.90 46.38 1.73
4596 8407 2.939780 TTAGGCCCGCCTCCTAATT 58.060 52.632 12.53 0.00 44.43 1.40
4597 8408 1.218844 TTAGGCCCGCCTCCTAATTT 58.781 50.000 12.53 0.00 44.43 1.82
4598 8409 0.763035 TAGGCCCGCCTCCTAATTTC 59.237 55.000 12.53 0.00 44.43 2.17
4599 8410 0.988678 AGGCCCGCCTCCTAATTTCT 60.989 55.000 1.26 0.00 44.43 2.52
4600 8411 0.106669 GGCCCGCCTCCTAATTTCTT 60.107 55.000 0.00 0.00 0.00 2.52
4601 8412 1.025041 GCCCGCCTCCTAATTTCTTG 58.975 55.000 0.00 0.00 0.00 3.02
4602 8413 1.682087 GCCCGCCTCCTAATTTCTTGT 60.682 52.381 0.00 0.00 0.00 3.16
4603 8414 2.420967 GCCCGCCTCCTAATTTCTTGTA 60.421 50.000 0.00 0.00 0.00 2.41
4604 8415 3.747708 GCCCGCCTCCTAATTTCTTGTAT 60.748 47.826 0.00 0.00 0.00 2.29
4605 8416 4.504340 GCCCGCCTCCTAATTTCTTGTATA 60.504 45.833 0.00 0.00 0.00 1.47
4606 8417 5.238583 CCCGCCTCCTAATTTCTTGTATAG 58.761 45.833 0.00 0.00 0.00 1.31
4607 8418 5.221661 CCCGCCTCCTAATTTCTTGTATAGT 60.222 44.000 0.00 0.00 0.00 2.12
4608 8419 6.289064 CCGCCTCCTAATTTCTTGTATAGTT 58.711 40.000 0.00 0.00 0.00 2.24
4609 8420 6.202954 CCGCCTCCTAATTTCTTGTATAGTTG 59.797 42.308 0.00 0.00 0.00 3.16
4610 8421 6.984474 CGCCTCCTAATTTCTTGTATAGTTGA 59.016 38.462 0.00 0.00 0.00 3.18
4611 8422 7.169982 CGCCTCCTAATTTCTTGTATAGTTGAG 59.830 40.741 0.00 0.00 0.00 3.02
4612 8423 7.442666 GCCTCCTAATTTCTTGTATAGTTGAGG 59.557 40.741 0.00 0.00 36.95 3.86
4613 8424 8.487028 CCTCCTAATTTCTTGTATAGTTGAGGT 58.513 37.037 0.00 0.00 0.00 3.85
4616 8427 7.438459 CCTAATTTCTTGTATAGTTGAGGTCCG 59.562 40.741 0.00 0.00 0.00 4.79
4686 8497 2.442272 GGAGGCTCGAGGGCACTA 60.442 66.667 15.58 0.00 43.56 2.74
4755 8566 0.337428 TACCTAGGTTCGGGGCTCTT 59.663 55.000 22.11 0.00 0.00 2.85
4804 8616 7.718525 TGCCGAGTGTAGTTGATATGTATTAA 58.281 34.615 0.00 0.00 0.00 1.40
4971 8913 2.439156 GTGTGCATGAGGGCTCCC 60.439 66.667 0.00 0.00 34.04 4.30
5048 8993 4.681978 GCCGGGTTGTCAGCGTCT 62.682 66.667 2.18 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.542030 CAGTCGTAACCAGACAGAGCT 59.458 52.381 0.00 0.00 40.84 4.09
5 6 1.269998 ACAGTCGTAACCAGACAGAGC 59.730 52.381 0.00 0.00 40.84 4.09
6 7 3.426426 GCTACAGTCGTAACCAGACAGAG 60.426 52.174 0.00 0.00 40.84 3.35
8 9 2.415625 GGCTACAGTCGTAACCAGACAG 60.416 54.545 0.00 0.00 40.84 3.51
9 10 1.542915 GGCTACAGTCGTAACCAGACA 59.457 52.381 0.00 0.00 40.84 3.41
10 11 1.542915 TGGCTACAGTCGTAACCAGAC 59.457 52.381 0.00 0.00 38.63 3.51
13 14 1.271379 CAGTGGCTACAGTCGTAACCA 59.729 52.381 2.02 0.00 40.74 3.67
16 17 1.958579 ACACAGTGGCTACAGTCGTAA 59.041 47.619 5.31 0.00 0.00 3.18
17 18 1.612676 ACACAGTGGCTACAGTCGTA 58.387 50.000 5.31 0.00 0.00 3.43
18 19 0.750850 AACACAGTGGCTACAGTCGT 59.249 50.000 5.31 0.00 0.00 4.34
19 20 1.139989 CAACACAGTGGCTACAGTCG 58.860 55.000 5.31 0.00 0.00 4.18
20 21 1.512926 CCAACACAGTGGCTACAGTC 58.487 55.000 5.31 0.00 0.00 3.51
21 22 3.706055 CCAACACAGTGGCTACAGT 57.294 52.632 5.31 0.00 0.00 3.55
28 29 1.525995 AACGAGGCCAACACAGTGG 60.526 57.895 5.01 0.00 42.05 4.00
29 30 1.648720 CAACGAGGCCAACACAGTG 59.351 57.895 5.01 0.00 0.00 3.66
30 31 2.186826 GCAACGAGGCCAACACAGT 61.187 57.895 5.01 0.00 0.00 3.55
31 32 1.723608 TTGCAACGAGGCCAACACAG 61.724 55.000 5.01 0.00 0.00 3.66
32 33 1.750780 TTGCAACGAGGCCAACACA 60.751 52.632 5.01 0.00 0.00 3.72
33 34 1.299089 GTTGCAACGAGGCCAACAC 60.299 57.895 14.90 0.00 0.00 3.32
34 35 2.485795 GGTTGCAACGAGGCCAACA 61.486 57.895 22.67 0.00 31.14 3.33
35 36 2.335011 GGTTGCAACGAGGCCAAC 59.665 61.111 22.67 3.03 0.00 3.77
36 37 2.909965 GGGTTGCAACGAGGCCAA 60.910 61.111 22.67 0.00 0.00 4.52
37 38 3.842925 GAGGGTTGCAACGAGGCCA 62.843 63.158 22.67 0.00 0.00 5.36
38 39 3.056328 GAGGGTTGCAACGAGGCC 61.056 66.667 22.67 17.50 0.00 5.19
39 40 3.423154 CGAGGGTTGCAACGAGGC 61.423 66.667 22.67 9.12 0.00 4.70
40 41 2.742372 CCGAGGGTTGCAACGAGG 60.742 66.667 22.67 17.68 0.00 4.63
41 42 1.738099 CTCCGAGGGTTGCAACGAG 60.738 63.158 22.67 18.01 0.00 4.18
42 43 2.342279 CTCCGAGGGTTGCAACGA 59.658 61.111 22.67 12.89 0.00 3.85
43 44 2.742372 CCTCCGAGGGTTGCAACG 60.742 66.667 22.67 11.59 0.00 4.10
44 45 1.376037 CTCCTCCGAGGGTTGCAAC 60.376 63.158 21.59 21.59 35.59 4.17
45 46 3.068881 CTCCTCCGAGGGTTGCAA 58.931 61.111 14.76 0.00 35.59 4.08
46 47 3.706373 GCTCCTCCGAGGGTTGCA 61.706 66.667 14.76 0.00 35.59 4.08
47 48 3.706373 TGCTCCTCCGAGGGTTGC 61.706 66.667 14.76 15.58 35.59 4.17
48 49 2.266055 GTGCTCCTCCGAGGGTTG 59.734 66.667 14.76 6.62 35.59 3.77
49 50 2.776370 TACGTGCTCCTCCGAGGGTT 62.776 60.000 14.76 0.00 35.59 4.11
50 51 2.569218 ATACGTGCTCCTCCGAGGGT 62.569 60.000 14.76 6.56 35.59 4.34
51 52 0.536687 TATACGTGCTCCTCCGAGGG 60.537 60.000 14.76 6.58 35.59 4.30
52 53 0.875728 CTATACGTGCTCCTCCGAGG 59.124 60.000 8.30 8.30 36.55 4.63
53 54 0.875728 CCTATACGTGCTCCTCCGAG 59.124 60.000 0.00 0.00 39.33 4.63
54 55 0.182061 ACCTATACGTGCTCCTCCGA 59.818 55.000 0.00 0.00 0.00 4.55
55 56 1.030457 AACCTATACGTGCTCCTCCG 58.970 55.000 0.00 0.00 0.00 4.63
56 57 1.068741 CCAACCTATACGTGCTCCTCC 59.931 57.143 0.00 0.00 0.00 4.30
57 58 2.029623 TCCAACCTATACGTGCTCCTC 58.970 52.381 0.00 0.00 0.00 3.71
58 59 1.755380 GTCCAACCTATACGTGCTCCT 59.245 52.381 0.00 0.00 0.00 3.69
59 60 1.202498 GGTCCAACCTATACGTGCTCC 60.202 57.143 0.00 0.00 34.73 4.70
60 61 1.479323 TGGTCCAACCTATACGTGCTC 59.521 52.381 0.00 0.00 39.58 4.26
61 62 1.563924 TGGTCCAACCTATACGTGCT 58.436 50.000 0.00 0.00 39.58 4.40
62 63 2.004733 GTTGGTCCAACCTATACGTGC 58.995 52.381 22.30 0.00 39.58 5.34
72 73 0.322187 ATACAGCGGGTTGGTCCAAC 60.322 55.000 24.34 24.34 42.89 3.77
73 74 0.402504 AATACAGCGGGTTGGTCCAA 59.597 50.000 0.00 0.00 38.11 3.53
74 75 0.402504 AAATACAGCGGGTTGGTCCA 59.597 50.000 0.00 0.00 38.11 4.02
75 76 1.092348 GAAATACAGCGGGTTGGTCC 58.908 55.000 0.00 0.00 0.00 4.46
76 77 2.007608 GAGAAATACAGCGGGTTGGTC 58.992 52.381 0.00 0.00 0.00 4.02
77 78 1.674817 CGAGAAATACAGCGGGTTGGT 60.675 52.381 0.00 0.00 0.00 3.67
78 79 1.006832 CGAGAAATACAGCGGGTTGG 58.993 55.000 0.00 0.00 0.00 3.77
79 80 1.927174 CTCGAGAAATACAGCGGGTTG 59.073 52.381 6.58 0.00 0.00 3.77
80 81 1.739371 GCTCGAGAAATACAGCGGGTT 60.739 52.381 18.75 0.00 0.00 4.11
81 82 0.179108 GCTCGAGAAATACAGCGGGT 60.179 55.000 18.75 0.00 0.00 5.28
82 83 0.103208 AGCTCGAGAAATACAGCGGG 59.897 55.000 18.75 0.00 36.95 6.13
83 84 1.202302 TGAGCTCGAGAAATACAGCGG 60.202 52.381 18.75 0.00 36.95 5.52
84 85 2.115595 CTGAGCTCGAGAAATACAGCG 58.884 52.381 18.75 0.00 36.95 5.18
85 86 1.857837 GCTGAGCTCGAGAAATACAGC 59.142 52.381 18.75 21.38 41.33 4.40
86 87 3.156511 TGCTGAGCTCGAGAAATACAG 57.843 47.619 18.75 16.37 0.00 2.74
87 88 3.193479 TCTTGCTGAGCTCGAGAAATACA 59.807 43.478 18.75 5.15 0.00 2.29
88 89 3.775202 TCTTGCTGAGCTCGAGAAATAC 58.225 45.455 18.75 2.23 0.00 1.89
89 90 4.662468 ATCTTGCTGAGCTCGAGAAATA 57.338 40.909 18.75 2.31 0.00 1.40
90 91 3.540314 ATCTTGCTGAGCTCGAGAAAT 57.460 42.857 18.75 0.00 0.00 2.17
91 92 4.340666 AGATATCTTGCTGAGCTCGAGAAA 59.659 41.667 18.75 7.71 0.00 2.52
92 93 3.888323 AGATATCTTGCTGAGCTCGAGAA 59.112 43.478 18.75 0.00 0.00 2.87
93 94 3.485394 AGATATCTTGCTGAGCTCGAGA 58.515 45.455 18.75 9.96 0.00 4.04
94 95 3.366273 GGAGATATCTTGCTGAGCTCGAG 60.366 52.174 8.45 8.45 0.00 4.04
95 96 2.556189 GGAGATATCTTGCTGAGCTCGA 59.444 50.000 9.64 2.06 0.00 4.04
96 97 2.557924 AGGAGATATCTTGCTGAGCTCG 59.442 50.000 9.64 5.21 0.00 5.03
97 98 3.573538 TCAGGAGATATCTTGCTGAGCTC 59.426 47.826 16.65 6.82 37.98 4.09
98 99 3.574749 TCAGGAGATATCTTGCTGAGCT 58.425 45.455 16.65 0.00 37.98 4.09
99 100 4.540359 ATCAGGAGATATCTTGCTGAGC 57.460 45.455 21.54 0.00 44.49 4.26
100 101 7.440198 TGTTTATCAGGAGATATCTTGCTGAG 58.560 38.462 21.54 7.12 44.49 3.35
101 102 7.365497 TGTTTATCAGGAGATATCTTGCTGA 57.635 36.000 20.29 20.29 45.18 4.26
102 103 7.660617 ACATGTTTATCAGGAGATATCTTGCTG 59.339 37.037 6.70 11.18 36.65 4.41
103 104 7.660617 CACATGTTTATCAGGAGATATCTTGCT 59.339 37.037 6.70 0.00 36.65 3.91
104 105 7.443575 ACACATGTTTATCAGGAGATATCTTGC 59.556 37.037 6.70 0.00 36.65 4.01
105 106 8.771766 CACACATGTTTATCAGGAGATATCTTG 58.228 37.037 6.70 2.24 36.65 3.02
106 107 8.489489 ACACACATGTTTATCAGGAGATATCTT 58.511 33.333 6.70 0.00 34.46 2.40
107 108 7.930325 CACACACATGTTTATCAGGAGATATCT 59.070 37.037 4.47 4.47 36.72 1.98
108 109 7.928167 TCACACACATGTTTATCAGGAGATATC 59.072 37.037 0.00 0.00 36.72 1.63
109 110 7.795047 TCACACACATGTTTATCAGGAGATAT 58.205 34.615 0.00 0.00 36.72 1.63
110 111 7.181569 TCACACACATGTTTATCAGGAGATA 57.818 36.000 0.00 0.00 36.72 1.98
111 112 6.053632 TCACACACATGTTTATCAGGAGAT 57.946 37.500 0.00 0.00 36.72 2.75
112 113 5.482163 TCACACACATGTTTATCAGGAGA 57.518 39.130 0.00 0.00 36.72 3.71
113 114 5.702670 AGTTCACACACATGTTTATCAGGAG 59.297 40.000 0.00 0.00 36.72 3.69
114 115 5.469760 CAGTTCACACACATGTTTATCAGGA 59.530 40.000 0.00 0.00 36.72 3.86
115 116 5.335113 CCAGTTCACACACATGTTTATCAGG 60.335 44.000 0.00 0.00 36.72 3.86
116 117 5.335113 CCCAGTTCACACACATGTTTATCAG 60.335 44.000 0.00 0.00 36.72 2.90
117 118 4.518590 CCCAGTTCACACACATGTTTATCA 59.481 41.667 0.00 0.00 36.72 2.15
118 119 4.082787 CCCCAGTTCACACACATGTTTATC 60.083 45.833 0.00 0.00 36.72 1.75
119 120 3.826157 CCCCAGTTCACACACATGTTTAT 59.174 43.478 0.00 0.00 36.72 1.40
120 121 3.218453 CCCCAGTTCACACACATGTTTA 58.782 45.455 0.00 0.00 36.72 2.01
121 122 2.031120 CCCCAGTTCACACACATGTTT 58.969 47.619 0.00 0.00 36.72 2.83
122 123 1.691196 CCCCAGTTCACACACATGTT 58.309 50.000 0.00 0.00 36.72 2.71
123 124 0.178992 CCCCCAGTTCACACACATGT 60.179 55.000 0.00 0.00 40.80 3.21
124 125 1.526575 GCCCCCAGTTCACACACATG 61.527 60.000 0.00 0.00 0.00 3.21
125 126 1.228552 GCCCCCAGTTCACACACAT 60.229 57.895 0.00 0.00 0.00 3.21
126 127 1.057275 TAGCCCCCAGTTCACACACA 61.057 55.000 0.00 0.00 0.00 3.72
127 128 0.328258 ATAGCCCCCAGTTCACACAC 59.672 55.000 0.00 0.00 0.00 3.82
128 129 0.327924 CATAGCCCCCAGTTCACACA 59.672 55.000 0.00 0.00 0.00 3.72
129 130 0.394352 CCATAGCCCCCAGTTCACAC 60.394 60.000 0.00 0.00 0.00 3.82
130 131 0.548926 TCCATAGCCCCCAGTTCACA 60.549 55.000 0.00 0.00 0.00 3.58
131 132 0.623723 TTCCATAGCCCCCAGTTCAC 59.376 55.000 0.00 0.00 0.00 3.18
132 133 1.607225 ATTCCATAGCCCCCAGTTCA 58.393 50.000 0.00 0.00 0.00 3.18
133 134 2.587522 GAATTCCATAGCCCCCAGTTC 58.412 52.381 0.00 0.00 0.00 3.01
134 135 1.217942 GGAATTCCATAGCCCCCAGTT 59.782 52.381 20.04 0.00 35.64 3.16
137 138 1.149101 GAGGAATTCCATAGCCCCCA 58.851 55.000 26.22 0.00 38.89 4.96
148 149 3.368236 GCGCGATACATTAGGAGGAATTC 59.632 47.826 12.10 0.00 0.00 2.17
154 155 1.328439 GTCGCGCGATACATTAGGAG 58.672 55.000 37.03 0.00 0.00 3.69
173 174 0.597637 GTGATATGGTGGGCTCGACG 60.598 60.000 0.00 0.00 0.00 5.12
189 190 2.179427 CACTGGTGACTCTATGGGTGA 58.821 52.381 0.00 0.00 0.00 4.02
191 192 0.905357 GCACTGGTGACTCTATGGGT 59.095 55.000 4.79 0.00 0.00 4.51
194 195 2.234661 TGGAAGCACTGGTGACTCTATG 59.765 50.000 4.79 0.00 0.00 2.23
196 197 1.618837 GTGGAAGCACTGGTGACTCTA 59.381 52.381 4.79 0.00 0.00 2.43
209 210 4.096732 AGAAACATATTTGCGTGGAAGC 57.903 40.909 0.00 0.00 37.71 3.86
221 222 8.470805 CCTGAGTACAACACTAGAGAAACATAT 58.529 37.037 0.00 0.00 37.72 1.78
271 272 2.632996 ACTCTTCGGAGATGAAACACCA 59.367 45.455 0.00 0.00 44.41 4.17
307 308 1.135344 GTCTGGTCACTTAGCGAGGAC 60.135 57.143 0.00 0.00 0.00 3.85
322 323 3.731867 GCAATATGGCGAAAAGTGTCTGG 60.732 47.826 0.00 0.00 0.00 3.86
327 328 3.127548 AGACTGCAATATGGCGAAAAGTG 59.872 43.478 0.00 0.00 36.28 3.16
334 335 4.480541 CTCTACTAGACTGCAATATGGCG 58.519 47.826 0.00 0.00 36.28 5.69
343 344 3.004315 GGAGACATGCTCTACTAGACTGC 59.996 52.174 14.20 0.00 43.43 4.40
348 349 5.843673 TTCTTGGAGACATGCTCTACTAG 57.156 43.478 14.20 12.25 43.43 2.57
354 355 4.005650 TGTTGATTCTTGGAGACATGCTC 58.994 43.478 8.20 8.20 42.32 4.26
378 379 2.223479 GCATGCCCTATTTACAACACGG 60.223 50.000 6.36 0.00 0.00 4.94
404 405 7.652105 TCGAAAGTACCATAACATAGCAGATTC 59.348 37.037 0.00 0.00 0.00 2.52
407 408 6.459670 TCGAAAGTACCATAACATAGCAGA 57.540 37.500 0.00 0.00 0.00 4.26
472 473 2.296190 CCCAGCAAAACTTAGGGTGTTC 59.704 50.000 0.00 0.00 34.75 3.18
487 488 3.586470 TGGAAAGTTAAAGTCCCAGCA 57.414 42.857 0.00 0.00 0.00 4.41
489 490 5.581085 CGACTATGGAAAGTTAAAGTCCCAG 59.419 44.000 0.00 0.00 31.74 4.45
497 498 3.056678 TGGCGTCGACTATGGAAAGTTAA 60.057 43.478 14.70 0.00 0.00 2.01
590 591 9.530633 CTACTTTAATGACCTTAACGCTCTTAT 57.469 33.333 0.00 0.00 0.00 1.73
591 592 8.526147 ACTACTTTAATGACCTTAACGCTCTTA 58.474 33.333 0.00 0.00 0.00 2.10
592 593 7.331193 CACTACTTTAATGACCTTAACGCTCTT 59.669 37.037 0.00 0.00 0.00 2.85
593 594 6.812160 CACTACTTTAATGACCTTAACGCTCT 59.188 38.462 0.00 0.00 0.00 4.09
594 595 6.589139 ACACTACTTTAATGACCTTAACGCTC 59.411 38.462 0.00 0.00 0.00 5.03
595 596 6.461640 ACACTACTTTAATGACCTTAACGCT 58.538 36.000 0.00 0.00 0.00 5.07
596 597 6.716898 ACACTACTTTAATGACCTTAACGC 57.283 37.500 0.00 0.00 0.00 4.84
597 598 8.530269 AGAACACTACTTTAATGACCTTAACG 57.470 34.615 0.00 0.00 0.00 3.18
601 602 8.985805 CGTTTAGAACACTACTTTAATGACCTT 58.014 33.333 0.00 0.00 0.00 3.50
602 603 7.117379 GCGTTTAGAACACTACTTTAATGACCT 59.883 37.037 0.00 0.00 0.00 3.85
603 604 7.232300 GCGTTTAGAACACTACTTTAATGACC 58.768 38.462 0.00 0.00 0.00 4.02
604 605 6.946584 CGCGTTTAGAACACTACTTTAATGAC 59.053 38.462 0.00 0.00 0.00 3.06
907 4059 1.622607 GGATGACCGTGGTGGATGGA 61.623 60.000 0.00 0.00 42.00 3.41
908 4060 1.153168 GGATGACCGTGGTGGATGG 60.153 63.158 0.00 0.00 42.00 3.51
1311 4848 3.691342 CGTCTTCCCGACCCTGCA 61.691 66.667 0.00 0.00 39.56 4.41
1312 4849 3.644399 GACGTCTTCCCGACCCTGC 62.644 68.421 8.70 0.00 39.56 4.85
1313 4850 2.572284 GACGTCTTCCCGACCCTG 59.428 66.667 8.70 0.00 39.56 4.45
1547 5084 1.538047 TTCATGTTCAGAAGCTGGGC 58.462 50.000 0.00 0.00 31.51 5.36
1585 5122 3.337358 CTCACATACACATGCACCAGAA 58.663 45.455 0.00 0.00 35.39 3.02
1892 5429 4.161189 TCCCAGATCTAGAAACAGAGCAAG 59.839 45.833 0.00 0.00 33.31 4.01
1973 5510 5.522456 ACATCATAAACAAGCACACAACAG 58.478 37.500 0.00 0.00 0.00 3.16
2177 5720 3.172339 AGCCTTGGAAACATAATGGCAA 58.828 40.909 0.00 0.00 41.82 4.52
2457 6004 5.242838 CACTGGCAAAAGGTTAGGTATTGAA 59.757 40.000 0.00 0.00 0.00 2.69
2483 6030 2.193993 GAACCCCCTAACTAAGCTCCA 58.806 52.381 0.00 0.00 0.00 3.86
2657 6255 4.750098 ACACTAATCAACTTGAAGTGACCG 59.250 41.667 22.34 4.69 37.39 4.79
2997 6595 9.407380 TCTGTTTGTATGATTAAACATATGCCT 57.593 29.630 8.48 0.00 43.44 4.75
3439 7044 8.495148 GCTTAATCCATGTTAAACAAAACCTTG 58.505 33.333 0.00 0.00 38.61 3.61
3727 7530 4.156455 ACAGAGTTTCCTCAAAAGCTGA 57.844 40.909 0.00 0.00 40.40 4.26
3736 7539 6.625873 AGATCAACAAAACAGAGTTTCCTC 57.374 37.500 0.00 0.00 38.04 3.71
4279 8090 4.576463 GCTTCGGCCATATATATCCCAAAG 59.424 45.833 2.24 7.23 34.32 2.77
4298 8109 6.072064 AGCTGCATGAATATAATTGAGGCTTC 60.072 38.462 1.02 0.00 0.00 3.86
4363 8174 6.697019 CCAAACATTTAGAAGAATTATGCCCG 59.303 38.462 0.00 0.00 0.00 6.13
4439 8250 7.492344 ACAATGTTGCTCCTTAAACAAAGAAAG 59.508 33.333 0.00 0.00 39.57 2.62
4479 8290 3.695060 ACTACCATAGAAGACGACACAGG 59.305 47.826 0.00 0.00 0.00 4.00
4559 8370 6.403636 GGCCTAATACACAATATGCACATAGC 60.404 42.308 0.00 0.00 45.96 2.97
4560 8371 6.094048 GGGCCTAATACACAATATGCACATAG 59.906 42.308 0.84 0.00 0.00 2.23
4561 8372 5.943416 GGGCCTAATACACAATATGCACATA 59.057 40.000 0.84 0.00 0.00 2.29
4562 8373 4.766891 GGGCCTAATACACAATATGCACAT 59.233 41.667 0.84 0.00 0.00 3.21
4563 8374 4.141287 GGGCCTAATACACAATATGCACA 58.859 43.478 0.84 0.00 0.00 4.57
4564 8375 3.188460 CGGGCCTAATACACAATATGCAC 59.812 47.826 0.84 0.00 0.00 4.57
4565 8376 3.407698 CGGGCCTAATACACAATATGCA 58.592 45.455 0.84 0.00 0.00 3.96
4566 8377 2.161609 GCGGGCCTAATACACAATATGC 59.838 50.000 0.84 0.00 0.00 3.14
4567 8378 2.747446 GGCGGGCCTAATACACAATATG 59.253 50.000 0.84 0.00 0.00 1.78
4568 8379 2.642807 AGGCGGGCCTAATACACAATAT 59.357 45.455 11.22 0.00 46.14 1.28
4569 8380 2.051692 AGGCGGGCCTAATACACAATA 58.948 47.619 11.22 0.00 46.14 1.90
4570 8381 0.843984 AGGCGGGCCTAATACACAAT 59.156 50.000 11.22 0.00 46.14 2.71
4571 8382 2.303043 AGGCGGGCCTAATACACAA 58.697 52.632 11.22 0.00 46.14 3.33
4572 8383 4.060065 AGGCGGGCCTAATACACA 57.940 55.556 11.22 0.00 46.14 3.72
4581 8392 0.106669 AAGAAATTAGGAGGCGGGCC 60.107 55.000 0.18 0.18 0.00 5.80
4582 8393 1.025041 CAAGAAATTAGGAGGCGGGC 58.975 55.000 0.00 0.00 0.00 6.13
4583 8394 2.420058 ACAAGAAATTAGGAGGCGGG 57.580 50.000 0.00 0.00 0.00 6.13
4584 8395 5.855045 ACTATACAAGAAATTAGGAGGCGG 58.145 41.667 0.00 0.00 0.00 6.13
4585 8396 6.984474 TCAACTATACAAGAAATTAGGAGGCG 59.016 38.462 0.00 0.00 0.00 5.52
4586 8397 7.442666 CCTCAACTATACAAGAAATTAGGAGGC 59.557 40.741 0.00 0.00 30.55 4.70
4587 8398 8.487028 ACCTCAACTATACAAGAAATTAGGAGG 58.513 37.037 0.00 0.00 41.01 4.30
4588 8399 9.535878 GACCTCAACTATACAAGAAATTAGGAG 57.464 37.037 0.00 0.00 0.00 3.69
4589 8400 8.483758 GGACCTCAACTATACAAGAAATTAGGA 58.516 37.037 0.00 0.00 0.00 2.94
4590 8401 7.438459 CGGACCTCAACTATACAAGAAATTAGG 59.562 40.741 0.00 0.00 0.00 2.69
4591 8402 7.980099 ACGGACCTCAACTATACAAGAAATTAG 59.020 37.037 0.00 0.00 0.00 1.73
4592 8403 7.762615 CACGGACCTCAACTATACAAGAAATTA 59.237 37.037 0.00 0.00 0.00 1.40
4593 8404 6.594159 CACGGACCTCAACTATACAAGAAATT 59.406 38.462 0.00 0.00 0.00 1.82
4594 8405 6.106673 CACGGACCTCAACTATACAAGAAAT 58.893 40.000 0.00 0.00 0.00 2.17
4595 8406 5.475719 CACGGACCTCAACTATACAAGAAA 58.524 41.667 0.00 0.00 0.00 2.52
4596 8407 4.081862 CCACGGACCTCAACTATACAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
4597 8408 3.446161 CCACGGACCTCAACTATACAAGA 59.554 47.826 0.00 0.00 0.00 3.02
4598 8409 3.782046 CCACGGACCTCAACTATACAAG 58.218 50.000 0.00 0.00 0.00 3.16
4599 8410 2.093869 GCCACGGACCTCAACTATACAA 60.094 50.000 0.00 0.00 0.00 2.41
4600 8411 1.479323 GCCACGGACCTCAACTATACA 59.521 52.381 0.00 0.00 0.00 2.29
4601 8412 1.755380 AGCCACGGACCTCAACTATAC 59.245 52.381 0.00 0.00 0.00 1.47
4602 8413 1.754803 CAGCCACGGACCTCAACTATA 59.245 52.381 0.00 0.00 0.00 1.31
4603 8414 0.537188 CAGCCACGGACCTCAACTAT 59.463 55.000 0.00 0.00 0.00 2.12
4604 8415 0.830444 ACAGCCACGGACCTCAACTA 60.830 55.000 0.00 0.00 0.00 2.24
4605 8416 2.100879 GACAGCCACGGACCTCAACT 62.101 60.000 0.00 0.00 0.00 3.16
4606 8417 1.668151 GACAGCCACGGACCTCAAC 60.668 63.158 0.00 0.00 0.00 3.18
4607 8418 2.741092 GACAGCCACGGACCTCAA 59.259 61.111 0.00 0.00 0.00 3.02
4608 8419 3.680786 CGACAGCCACGGACCTCA 61.681 66.667 0.00 0.00 0.00 3.86
4609 8420 3.681835 ACGACAGCCACGGACCTC 61.682 66.667 0.00 0.00 34.93 3.85
4610 8421 3.991051 CACGACAGCCACGGACCT 61.991 66.667 0.00 0.00 34.93 3.85
4612 8423 4.295119 ACCACGACAGCCACGGAC 62.295 66.667 0.00 0.00 34.93 4.79
4613 8424 4.293648 CACCACGACAGCCACGGA 62.294 66.667 0.00 0.00 34.93 4.69
4686 8497 4.704103 TCGCCTCTGGAGCCCACT 62.704 66.667 0.00 0.00 0.00 4.00
4755 8566 4.213513 GACTAGGGGTTTTATCTCTCCGA 58.786 47.826 0.00 0.00 0.00 4.55
4767 8578 1.686110 CTCGGCAGGACTAGGGGTT 60.686 63.158 0.00 0.00 0.00 4.11
5048 8993 3.727258 CCCAGCATCGGGTTCCCA 61.727 66.667 8.70 0.00 41.83 4.37


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

AutoCloner maintained by Alex Coulton.