Multiple sequence alignment - TraesCS6B01G290300

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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 TraesCS6B01G290300 chr6B 100.000 2558 0 0 1 2558 522064532 522061975 0.000000e+00 4724.0
1 TraesCS6B01G290300 chr6B 79.619 525 68 20 139 642 28062017 28062523 8.770000e-90 340.0
2 TraesCS6B01G290300 chr6B 96.117 103 4 0 1 103 622200371 622200269 4.380000e-38 169.0
3 TraesCS6B01G290300 chr6D 94.403 1215 56 7 808 2017 346075596 346074389 0.000000e+00 1857.0
4 TraesCS6B01G290300 chr6D 81.569 765 89 29 87 816 97736606 97737353 3.670000e-163 584.0
5 TraesCS6B01G290300 chr6D 87.940 199 14 4 2337 2530 346074213 346074020 2.560000e-55 226.0
6 TraesCS6B01G290300 chr6D 94.488 127 7 0 2006 2132 305136403 305136529 2.010000e-46 196.0
7 TraesCS6B01G290300 chr6D 96.581 117 4 0 2014 2130 17166754 17166638 7.220000e-46 195.0
8 TraesCS6B01G290300 chr6D 91.509 106 4 2 2247 2348 346074337 346074233 9.540000e-30 141.0
9 TraesCS6B01G290300 chr6D 98.000 50 1 0 2133 2182 346074388 346074339 1.260000e-13 87.9
10 TraesCS6B01G290300 chr6A 94.246 1147 49 8 881 2016 486353723 486352583 0.000000e+00 1736.0
11 TraesCS6B01G290300 chr6A 88.945 199 12 4 2337 2530 486352406 486352213 1.180000e-58 237.0
12 TraesCS6B01G290300 chr6A 100.000 54 0 0 2129 2182 486352585 486352532 1.620000e-17 100.0
13 TraesCS6B01G290300 chr2B 83.841 755 74 21 87 815 143942177 143941445 0.000000e+00 675.0
14 TraesCS6B01G290300 chr2B 94.488 127 6 1 2014 2140 2233732 2233857 7.220000e-46 195.0
15 TraesCS6B01G290300 chr2B 95.798 119 5 0 2012 2130 624544491 624544373 2.600000e-45 193.0
16 TraesCS6B01G290300 chr2B 94.393 107 4 2 1 107 201631825 201631929 2.040000e-36 163.0
17 TraesCS6B01G290300 chr2B 90.244 123 8 4 1 122 31316756 31316637 9.470000e-35 158.0
18 TraesCS6B01G290300 chr2B 97.143 70 2 0 2176 2245 512484327 512484258 4.470000e-23 119.0
19 TraesCS6B01G290300 chr2B 97.143 70 1 1 2177 2245 739542310 739542379 1.610000e-22 117.0
20 TraesCS6B01G290300 chr1B 83.197 732 90 12 101 815 489919311 489918596 7.720000e-180 640.0
21 TraesCS6B01G290300 chr1B 84.390 615 61 14 164 747 20690626 20691236 2.860000e-159 571.0
22 TraesCS6B01G290300 chr1B 98.020 101 0 2 1 101 468985156 468985254 9.410000e-40 174.0
23 TraesCS6B01G290300 chr1B 97.030 101 1 2 1 101 116716 116814 4.380000e-38 169.0
24 TraesCS6B01G290300 chr1B 97.938 97 0 2 1 97 604343222 604343316 1.570000e-37 167.0
25 TraesCS6B01G290300 chr1B 94.495 109 3 2 1 109 480169213 480169318 5.660000e-37 165.0
26 TraesCS6B01G290300 chr1B 100.000 69 0 0 2177 2245 668137121 668137189 7.430000e-26 128.0
27 TraesCS6B01G290300 chr1B 98.529 68 1 0 2178 2245 22196662 22196729 1.240000e-23 121.0
28 TraesCS6B01G290300 chr4B 82.575 769 86 25 87 815 520189618 520188858 3.590000e-178 634.0
29 TraesCS6B01G290300 chr4B 85.505 614 64 8 87 696 596930213 596929621 3.620000e-173 617.0
30 TraesCS6B01G290300 chr4B 86.515 571 51 11 139 697 37315657 37315101 2.820000e-169 604.0
31 TraesCS6B01G290300 chr4B 99.219 128 1 0 1889 2016 656074609 656074736 5.500000e-57 231.0
32 TraesCS6B01G290300 chr4B 94.400 125 7 0 2014 2138 22258903 22258779 2.600000e-45 193.0
33 TraesCS6B01G290300 chr4B 98.020 101 0 2 1 101 132208085 132207987 9.410000e-40 174.0
34 TraesCS6B01G290300 chr4B 97.183 71 2 0 2488 2558 656074877 656074947 1.240000e-23 121.0
35 TraesCS6B01G290300 chr4B 97.101 69 2 0 2176 2244 625876867 625876799 1.610000e-22 117.0
36 TraesCS6B01G290300 chr4B 98.148 54 1 0 2129 2182 656074734 656074787 7.530000e-16 95.3
37 TraesCS6B01G290300 chr4B 93.750 64 3 1 2247 2310 656074789 656074851 7.530000e-16 95.3
38 TraesCS6B01G290300 chr3B 83.768 690 78 16 87 747 33502559 33501875 7.770000e-175 623.0
39 TraesCS6B01G290300 chr3B 84.295 624 71 11 87 696 252810263 252810873 3.670000e-163 584.0
40 TraesCS6B01G290300 chr3B 82.743 678 63 17 87 750 625621786 625621149 2.880000e-154 555.0
41 TraesCS6B01G290300 chr3B 83.025 648 72 15 87 718 418899169 418898544 1.030000e-153 553.0
42 TraesCS6B01G290300 chr3B 85.584 548 49 7 88 608 681023870 681023326 4.810000e-152 547.0
43 TraesCS6B01G290300 chr3B 86.261 444 46 12 315 745 726125359 726124918 3.850000e-128 468.0
44 TraesCS6B01G290300 chr3B 95.200 125 5 1 2007 2130 481619634 481619510 2.010000e-46 196.0
45 TraesCS6B01G290300 chr3B 91.912 136 11 0 1997 2132 564169684 564169819 9.340000e-45 191.0
46 TraesCS6B01G290300 chr7B 86.762 559 55 8 166 708 571565282 571565837 2.820000e-169 604.0
47 TraesCS6B01G290300 chr7B 88.571 315 31 4 454 764 474486086 474485773 6.680000e-101 377.0
48 TraesCS6B01G290300 chr7B 100.000 71 0 0 2488 2558 585075671 585075601 5.740000e-27 132.0
49 TraesCS6B01G290300 chr7B 93.750 64 3 1 2247 2310 585075759 585075697 7.530000e-16 95.3
50 TraesCS6B01G290300 chr3D 83.555 602 66 18 103 681 426949412 426948821 1.350000e-147 532.0
51 TraesCS6B01G290300 chr3D 83.275 574 44 12 89 618 384265702 384265137 4.950000e-132 481.0
52 TraesCS6B01G290300 chr3D 95.868 121 5 0 2013 2133 16531948 16532068 2.010000e-46 196.0
53 TraesCS6B01G290300 chr4D 83.527 601 65 9 178 747 352572252 352572849 4.850000e-147 531.0
54 TraesCS6B01G290300 chr5B 95.312 128 5 1 1889 2016 699687316 699687190 4.320000e-48 202.0
55 TraesCS6B01G290300 chr5B 97.436 117 3 0 2014 2130 539282150 539282034 1.550000e-47 200.0
56 TraesCS6B01G290300 chr5B 90.984 122 6 5 1 120 52324599 52324481 2.630000e-35 159.0
57 TraesCS6B01G290300 chr5B 97.183 71 2 0 2488 2558 533945924 533945994 1.240000e-23 121.0
58 TraesCS6B01G290300 chr5B 97.183 71 2 0 2488 2558 699687049 699686979 1.240000e-23 121.0
59 TraesCS6B01G290300 chr5B 98.507 67 1 0 2179 2245 250564997 250565063 4.470000e-23 119.0
60 TraesCS6B01G290300 chr5B 95.312 64 2 1 2247 2310 533945836 533945898 1.620000e-17 100.0
61 TraesCS6B01G290300 chr5B 93.617 47 3 0 758 804 572599124 572599078 1.270000e-08 71.3
62 TraesCS6B01G290300 chr3A 98.529 68 1 0 2178 2245 120804775 120804842 1.240000e-23 121.0
63 TraesCS6B01G290300 chr3A 95.833 72 2 1 2174 2245 699764886 699764956 5.780000e-22 115.0
64 TraesCS6B01G290300 chr5A 98.529 68 0 1 2179 2245 39114816 39114749 4.470000e-23 119.0


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 TraesCS6B01G290300 chr6B 522061975 522064532 2557 True 4724.000 4724 100.000 1 2558 1 chr6B.!!$R1 2557
1 TraesCS6B01G290300 chr6B 28062017 28062523 506 False 340.000 340 79.619 139 642 1 chr6B.!!$F1 503
2 TraesCS6B01G290300 chr6D 97736606 97737353 747 False 584.000 584 81.569 87 816 1 chr6D.!!$F1 729
3 TraesCS6B01G290300 chr6D 346074020 346075596 1576 True 577.975 1857 92.963 808 2530 4 chr6D.!!$R2 1722
4 TraesCS6B01G290300 chr6A 486352213 486353723 1510 True 691.000 1736 94.397 881 2530 3 chr6A.!!$R1 1649
5 TraesCS6B01G290300 chr2B 143941445 143942177 732 True 675.000 675 83.841 87 815 1 chr2B.!!$R2 728
6 TraesCS6B01G290300 chr1B 489918596 489919311 715 True 640.000 640 83.197 101 815 1 chr1B.!!$R1 714
7 TraesCS6B01G290300 chr1B 20690626 20691236 610 False 571.000 571 84.390 164 747 1 chr1B.!!$F2 583
8 TraesCS6B01G290300 chr4B 520188858 520189618 760 True 634.000 634 82.575 87 815 1 chr4B.!!$R4 728
9 TraesCS6B01G290300 chr4B 596929621 596930213 592 True 617.000 617 85.505 87 696 1 chr4B.!!$R5 609
10 TraesCS6B01G290300 chr4B 37315101 37315657 556 True 604.000 604 86.515 139 697 1 chr4B.!!$R2 558
11 TraesCS6B01G290300 chr3B 33501875 33502559 684 True 623.000 623 83.768 87 747 1 chr3B.!!$R1 660
12 TraesCS6B01G290300 chr3B 252810263 252810873 610 False 584.000 584 84.295 87 696 1 chr3B.!!$F1 609
13 TraesCS6B01G290300 chr3B 625621149 625621786 637 True 555.000 555 82.743 87 750 1 chr3B.!!$R4 663
14 TraesCS6B01G290300 chr3B 418898544 418899169 625 True 553.000 553 83.025 87 718 1 chr3B.!!$R2 631
15 TraesCS6B01G290300 chr3B 681023326 681023870 544 True 547.000 547 85.584 88 608 1 chr3B.!!$R5 520
16 TraesCS6B01G290300 chr7B 571565282 571565837 555 False 604.000 604 86.762 166 708 1 chr7B.!!$F1 542
17 TraesCS6B01G290300 chr3D 426948821 426949412 591 True 532.000 532 83.555 103 681 1 chr3D.!!$R2 578
18 TraesCS6B01G290300 chr3D 384265137 384265702 565 True 481.000 481 83.275 89 618 1 chr3D.!!$R1 529
19 TraesCS6B01G290300 chr4D 352572252 352572849 597 False 531.000 531 83.527 178 747 1 chr4D.!!$F1 569

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
715 867 0.167908 CATTTTAGCGCGCTGGTGAA 59.832 50.0 41.85 28.08 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2341 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
18 19 3.383162 ATCGTGTCCCTTGTCTCCT 57.617 52.632 0.00 0.00 0.00 3.69
19 20 0.898320 ATCGTGTCCCTTGTCTCCTG 59.102 55.000 0.00 0.00 0.00 3.86
20 21 0.469331 TCGTGTCCCTTGTCTCCTGT 60.469 55.000 0.00 0.00 0.00 4.00
21 22 0.393077 CGTGTCCCTTGTCTCCTGTT 59.607 55.000 0.00 0.00 0.00 3.16
22 23 1.616865 CGTGTCCCTTGTCTCCTGTTA 59.383 52.381 0.00 0.00 0.00 2.41
23 24 2.609737 CGTGTCCCTTGTCTCCTGTTAC 60.610 54.545 0.00 0.00 0.00 2.50
24 25 1.975680 TGTCCCTTGTCTCCTGTTACC 59.024 52.381 0.00 0.00 0.00 2.85
25 26 1.975680 GTCCCTTGTCTCCTGTTACCA 59.024 52.381 0.00 0.00 0.00 3.25
26 27 2.572104 GTCCCTTGTCTCCTGTTACCAT 59.428 50.000 0.00 0.00 0.00 3.55
27 28 2.838202 TCCCTTGTCTCCTGTTACCATC 59.162 50.000 0.00 0.00 0.00 3.51
28 29 2.092914 CCCTTGTCTCCTGTTACCATCC 60.093 54.545 0.00 0.00 0.00 3.51
29 30 2.418746 CCTTGTCTCCTGTTACCATCCG 60.419 54.545 0.00 0.00 0.00 4.18
30 31 0.535335 TGTCTCCTGTTACCATCCGC 59.465 55.000 0.00 0.00 0.00 5.54
31 32 0.179081 GTCTCCTGTTACCATCCGCC 60.179 60.000 0.00 0.00 0.00 6.13
32 33 0.325296 TCTCCTGTTACCATCCGCCT 60.325 55.000 0.00 0.00 0.00 5.52
33 34 1.063492 TCTCCTGTTACCATCCGCCTA 60.063 52.381 0.00 0.00 0.00 3.93
34 35 1.341531 CTCCTGTTACCATCCGCCTAG 59.658 57.143 0.00 0.00 0.00 3.02
35 36 1.063492 TCCTGTTACCATCCGCCTAGA 60.063 52.381 0.00 0.00 0.00 2.43
36 37 1.068741 CCTGTTACCATCCGCCTAGAC 59.931 57.143 0.00 0.00 0.00 2.59
37 38 0.742505 TGTTACCATCCGCCTAGACG 59.257 55.000 0.00 0.00 0.00 4.18
38 39 0.596859 GTTACCATCCGCCTAGACGC 60.597 60.000 0.00 0.00 0.00 5.19
39 40 1.038681 TTACCATCCGCCTAGACGCA 61.039 55.000 0.00 0.00 0.00 5.24
40 41 1.731433 TACCATCCGCCTAGACGCAC 61.731 60.000 0.00 0.00 0.00 5.34
41 42 2.494445 CATCCGCCTAGACGCACA 59.506 61.111 0.00 0.00 0.00 4.57
42 43 1.589993 CATCCGCCTAGACGCACAG 60.590 63.158 0.00 0.00 0.00 3.66
43 44 2.052690 ATCCGCCTAGACGCACAGT 61.053 57.895 0.00 0.00 0.00 3.55
44 45 1.605058 ATCCGCCTAGACGCACAGTT 61.605 55.000 0.00 0.00 0.00 3.16
45 46 1.805945 CCGCCTAGACGCACAGTTC 60.806 63.158 0.00 0.00 0.00 3.01
46 47 2.152699 CGCCTAGACGCACAGTTCG 61.153 63.158 0.00 0.00 0.00 3.95
47 48 1.805945 GCCTAGACGCACAGTTCGG 60.806 63.158 0.00 0.00 0.00 4.30
48 49 1.153823 CCTAGACGCACAGTTCGGG 60.154 63.158 0.00 0.00 0.00 5.14
49 50 1.592400 CCTAGACGCACAGTTCGGGA 61.592 60.000 0.00 0.00 0.00 5.14
50 51 0.456312 CTAGACGCACAGTTCGGGAC 60.456 60.000 0.00 0.00 0.00 4.46
51 52 1.870055 TAGACGCACAGTTCGGGACC 61.870 60.000 0.00 0.00 0.00 4.46
52 53 4.309950 ACGCACAGTTCGGGACCC 62.310 66.667 0.00 0.00 0.00 4.46
54 55 4.717313 GCACAGTTCGGGACCCCC 62.717 72.222 4.46 0.00 41.09 5.40
55 56 2.928396 CACAGTTCGGGACCCCCT 60.928 66.667 4.46 0.00 42.67 4.79
56 57 1.611261 CACAGTTCGGGACCCCCTA 60.611 63.158 4.46 0.00 42.67 3.53
57 58 1.611556 ACAGTTCGGGACCCCCTAC 60.612 63.158 4.46 0.29 42.67 3.18
58 59 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
59 60 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
63 64 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
64 65 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
65 66 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
66 67 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
67 68 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
68 69 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
69 70 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
70 71 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
71 72 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
72 73 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
74 75 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
75 76 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
76 77 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
77 78 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
78 79 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
79 80 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
80 81 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
81 82 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
99 100 4.329545 GACAGCGGTGGCCTTGGA 62.330 66.667 20.20 0.00 41.24 3.53
116 123 2.697263 AGGCATGGGAGGCATGGA 60.697 61.111 0.00 0.00 36.37 3.41
127 134 3.908081 GCATGGATGGCCTTGGCG 61.908 66.667 3.32 0.00 39.18 5.69
128 135 3.221389 CATGGATGGCCTTGGCGG 61.221 66.667 3.32 0.00 36.08 6.13
137 171 4.113815 CCTTGGCGGCATGGGAGA 62.114 66.667 29.81 7.28 0.00 3.71
152 186 1.596934 GAGACATGGGTGGCTTCGA 59.403 57.895 0.00 0.00 46.16 3.71
172 206 1.302752 GCTATCATGGGCGGCATGA 60.303 57.895 20.35 20.35 42.41 3.07
269 305 1.152902 CCGTCATGGGTGGCATGAT 60.153 57.895 0.00 0.00 40.62 2.45
360 412 5.276773 GCATGAAGATGTCGTTGAAGATCTC 60.277 44.000 0.00 0.00 31.50 2.75
368 420 2.002586 CGTTGAAGATCTCGCCAACAT 58.997 47.619 23.46 0.00 38.91 2.71
435 487 4.611367 AGGAGGAGGAAGAATCGTCTTAA 58.389 43.478 0.00 0.00 44.42 1.85
442 494 4.098807 AGGAAGAATCGTCTTAAGAGGAGC 59.901 45.833 26.65 21.37 44.42 4.70
444 496 2.696187 AGAATCGTCTTAAGAGGAGCCC 59.304 50.000 26.65 18.95 41.47 5.19
582 687 5.798125 TGTGGGCATGAAATTTTAGTCAA 57.202 34.783 0.00 0.00 0.00 3.18
583 688 6.166984 TGTGGGCATGAAATTTTAGTCAAA 57.833 33.333 0.00 0.00 0.00 2.69
688 840 4.827087 ATGCGTCGGCTGCTCCTG 62.827 66.667 0.00 0.00 40.82 3.86
709 861 2.100991 GCTGCATTTTAGCGCGCT 59.899 55.556 38.01 38.01 37.31 5.92
710 862 2.219562 GCTGCATTTTAGCGCGCTG 61.220 57.895 41.85 26.94 37.31 5.18
711 863 1.584483 CTGCATTTTAGCGCGCTGG 60.584 57.895 41.85 25.13 37.31 4.85
712 864 2.257286 CTGCATTTTAGCGCGCTGGT 62.257 55.000 41.85 20.69 37.31 4.00
713 865 1.869132 GCATTTTAGCGCGCTGGTG 60.869 57.895 41.85 30.89 0.00 4.17
714 866 1.793581 CATTTTAGCGCGCTGGTGA 59.206 52.632 41.85 24.68 0.00 4.02
715 867 0.167908 CATTTTAGCGCGCTGGTGAA 59.832 50.000 41.85 28.08 0.00 3.18
716 868 0.447801 ATTTTAGCGCGCTGGTGAAG 59.552 50.000 41.85 0.00 0.00 3.02
753 942 2.783828 TTTTTCGCGGCTGATGAAAA 57.216 40.000 17.28 17.28 39.18 2.29
756 945 0.947960 TTCGCGGCTGATGAAAACAA 59.052 45.000 6.13 0.00 0.00 2.83
806 1028 2.119484 ATTGGGCGACGGTTGGAGAA 62.119 55.000 0.00 0.00 0.00 2.87
818 1040 2.417515 GGTTGGAGAAGCTCTAAGGTCG 60.418 54.545 0.00 0.00 31.92 4.79
820 1042 2.370349 TGGAGAAGCTCTAAGGTCGAG 58.630 52.381 0.00 0.00 0.00 4.04
821 1043 2.026169 TGGAGAAGCTCTAAGGTCGAGA 60.026 50.000 0.00 0.00 0.00 4.04
822 1044 3.018149 GGAGAAGCTCTAAGGTCGAGAA 58.982 50.000 0.00 0.00 0.00 2.87
838 1060 8.480133 AGGTCGAGAATATAAAGTGGACTTAT 57.520 34.615 0.00 0.00 34.61 1.73
839 1061 8.578151 AGGTCGAGAATATAAAGTGGACTTATC 58.422 37.037 0.00 0.00 34.61 1.75
840 1062 8.578151 GGTCGAGAATATAAAGTGGACTTATCT 58.422 37.037 0.00 0.00 34.61 1.98
920 1142 2.361104 GACGAGCATTTGGGCCCA 60.361 61.111 24.45 24.45 0.00 5.36
924 1146 0.466189 CGAGCATTTGGGCCCAGTAT 60.466 55.000 26.87 19.55 0.00 2.12
943 1165 2.280865 GGATAAGGCGGCCTTCGG 60.281 66.667 35.83 0.00 43.57 4.30
959 1181 0.756903 TCGGCTAGCTAAATCCCCAC 59.243 55.000 15.72 0.00 0.00 4.61
969 1191 0.259938 AAATCCCCACTCCTGCCATC 59.740 55.000 0.00 0.00 0.00 3.51
1069 1291 3.391382 CTTCCTTCCTCCGGCCGT 61.391 66.667 26.12 0.00 0.00 5.68
1073 1295 3.136123 CTTCCTCCGGCCGTCGTA 61.136 66.667 26.12 3.60 37.11 3.43
1171 1393 3.271706 AATCGGCGGTCGTTCGTGA 62.272 57.895 7.21 2.26 40.32 4.35
1395 1617 2.758327 ACGCTGCCGTCCCTCATA 60.758 61.111 0.00 0.00 46.39 2.15
1411 1633 0.735978 CATAGACGACAACGCCTGCA 60.736 55.000 0.00 0.00 43.96 4.41
1455 1677 2.764128 AGGTCCATGGACGCCGAT 60.764 61.111 33.24 16.72 45.41 4.18
1464 1686 2.506217 GACGCCGATGTCTTCGCA 60.506 61.111 0.00 0.00 46.71 5.10
1488 1710 1.739371 GCGTACGAGCCCAAGAAGAAT 60.739 52.381 21.65 0.00 0.00 2.40
1577 1799 1.623811 GGCAAGTTCCAGTGTAGGAGA 59.376 52.381 0.00 0.00 39.25 3.71
1595 1817 6.867662 AGGAGAAGAAACAGTTGTTATGTG 57.132 37.500 0.00 0.00 37.25 3.21
1596 1818 5.765182 AGGAGAAGAAACAGTTGTTATGTGG 59.235 40.000 0.00 0.00 37.25 4.17
1597 1819 5.763204 GGAGAAGAAACAGTTGTTATGTGGA 59.237 40.000 0.00 0.00 37.25 4.02
1700 1929 3.193267 TCTGCTGTGCTGTTTGTCTTTTT 59.807 39.130 0.00 0.00 0.00 1.94
1726 1955 8.876275 ATATTGGTGTTGCAATGCTATTTTAG 57.124 30.769 6.82 0.00 0.00 1.85
1769 1998 2.749621 CCTTGGTTAGATTGTCCAGTGC 59.250 50.000 0.00 0.00 32.63 4.40
1771 2000 0.727398 GGTTAGATTGTCCAGTGCGC 59.273 55.000 0.00 0.00 0.00 6.09
1783 2014 3.684788 GTCCAGTGCGCAATATTATAGGG 59.315 47.826 14.00 6.74 0.00 3.53
1801 2035 9.801873 ATTATAGGGAAATGTTCATTGAAAACG 57.198 29.630 0.00 0.00 0.00 3.60
1832 2066 5.391312 ACCCAGTTGACTAAATGCAAATC 57.609 39.130 0.00 0.00 30.87 2.17
1872 2106 6.963242 CGATTTTGTCAAGTCTAATGTGGATG 59.037 38.462 0.00 0.00 0.00 3.51
1880 2114 2.092968 GTCTAATGTGGATGTGGGCAGA 60.093 50.000 0.00 0.00 0.00 4.26
1893 2127 7.448161 TGGATGTGGGCAGATAATAACATTAAG 59.552 37.037 0.00 0.00 0.00 1.85
1896 2130 6.262944 TGTGGGCAGATAATAACATTAAGCAG 59.737 38.462 0.00 0.00 0.00 4.24
2023 2257 9.404848 TGTTACTCATATTATATACTCCCTCCG 57.595 37.037 0.00 0.00 0.00 4.63
2024 2258 9.406113 GTTACTCATATTATATACTCCCTCCGT 57.594 37.037 0.00 0.00 0.00 4.69
2025 2259 9.624373 TTACTCATATTATATACTCCCTCCGTC 57.376 37.037 0.00 0.00 0.00 4.79
2026 2260 7.061688 ACTCATATTATATACTCCCTCCGTCC 58.938 42.308 0.00 0.00 0.00 4.79
2027 2261 6.371278 TCATATTATATACTCCCTCCGTCCC 58.629 44.000 0.00 0.00 0.00 4.46
2028 2262 2.795231 TATATACTCCCTCCGTCCCG 57.205 55.000 0.00 0.00 0.00 5.14
2029 2263 1.070604 ATATACTCCCTCCGTCCCGA 58.929 55.000 0.00 0.00 0.00 5.14
2030 2264 0.846015 TATACTCCCTCCGTCCCGAA 59.154 55.000 0.00 0.00 0.00 4.30
2031 2265 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
2032 2266 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
2033 2267 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
2034 2268 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
2035 2269 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
2036 2270 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
2037 2271 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
2038 2272 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
2039 2273 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
2040 2274 1.135315 TCCGTCCCGAAATACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
2049 2283 4.045104 CGAAATACTTGTCGGAGAGATGG 58.955 47.826 0.00 0.00 36.95 3.51
2050 2284 4.202020 CGAAATACTTGTCGGAGAGATGGA 60.202 45.833 0.00 0.00 36.95 3.41
2051 2285 5.508153 CGAAATACTTGTCGGAGAGATGGAT 60.508 44.000 0.00 0.00 36.95 3.41
2052 2286 6.294010 CGAAATACTTGTCGGAGAGATGGATA 60.294 42.308 0.00 0.00 36.95 2.59
2053 2287 6.978674 AATACTTGTCGGAGAGATGGATAA 57.021 37.500 0.00 0.00 36.95 1.75
2054 2288 6.978674 ATACTTGTCGGAGAGATGGATAAA 57.021 37.500 0.00 0.00 36.95 1.40
2055 2289 5.677319 ACTTGTCGGAGAGATGGATAAAA 57.323 39.130 0.00 0.00 36.95 1.52
2056 2290 6.240549 ACTTGTCGGAGAGATGGATAAAAT 57.759 37.500 0.00 0.00 36.95 1.82
2057 2291 6.653989 ACTTGTCGGAGAGATGGATAAAATT 58.346 36.000 0.00 0.00 36.95 1.82
2058 2292 6.540189 ACTTGTCGGAGAGATGGATAAAATTG 59.460 38.462 0.00 0.00 36.95 2.32
2059 2293 5.368145 TGTCGGAGAGATGGATAAAATTGG 58.632 41.667 0.00 0.00 36.95 3.16
2060 2294 5.130311 TGTCGGAGAGATGGATAAAATTGGA 59.870 40.000 0.00 0.00 36.95 3.53
2061 2295 6.183361 TGTCGGAGAGATGGATAAAATTGGAT 60.183 38.462 0.00 0.00 36.95 3.41
2062 2296 6.148480 GTCGGAGAGATGGATAAAATTGGATG 59.852 42.308 0.00 0.00 36.95 3.51
2063 2297 5.106396 CGGAGAGATGGATAAAATTGGATGC 60.106 44.000 0.00 0.00 0.00 3.91
2064 2298 5.771666 GGAGAGATGGATAAAATTGGATGCA 59.228 40.000 0.00 0.00 0.00 3.96
2065 2299 6.436532 GGAGAGATGGATAAAATTGGATGCAT 59.563 38.462 0.00 0.00 36.89 3.96
2066 2300 7.362747 GGAGAGATGGATAAAATTGGATGCATC 60.363 40.741 18.81 18.81 45.93 3.91
2073 2307 9.812347 TGGATAAAATTGGATGCATCTATAACT 57.188 29.630 25.28 9.77 0.00 2.24
2082 2316 9.772973 TTGGATGCATCTATAACTAAAATACGT 57.227 29.630 25.28 0.00 0.00 3.57
2083 2317 9.419297 TGGATGCATCTATAACTAAAATACGTC 57.581 33.333 25.28 3.59 0.00 4.34
2084 2318 9.640963 GGATGCATCTATAACTAAAATACGTCT 57.359 33.333 25.28 0.00 0.00 4.18
2119 2353 4.996062 TTTTCGACAAGTATTTCCGGAC 57.004 40.909 1.83 0.00 0.00 4.79
2120 2354 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
2121 2355 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
2122 2356 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2123 2357 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2124 2358 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2125 2359 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2126 2360 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2127 2361 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2128 2362 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2129 2363 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2130 2364 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
2182 2416 6.595716 AGGAAATTAGAGATGCACACAAGTAC 59.404 38.462 0.00 0.00 0.00 2.73
2183 2417 6.595716 GGAAATTAGAGATGCACACAAGTACT 59.404 38.462 0.00 0.00 0.00 2.73
2184 2418 7.201565 GGAAATTAGAGATGCACACAAGTACTC 60.202 40.741 0.00 0.00 0.00 2.59
2185 2419 3.601443 AGAGATGCACACAAGTACTCC 57.399 47.619 0.00 0.00 0.00 3.85
2186 2420 2.234908 AGAGATGCACACAAGTACTCCC 59.765 50.000 0.00 0.00 0.00 4.30
2187 2421 2.234908 GAGATGCACACAAGTACTCCCT 59.765 50.000 0.00 0.00 0.00 4.20
2188 2422 2.234908 AGATGCACACAAGTACTCCCTC 59.765 50.000 0.00 0.00 0.00 4.30
2189 2423 0.685097 TGCACACAAGTACTCCCTCC 59.315 55.000 0.00 0.00 0.00 4.30
2190 2424 0.389948 GCACACAAGTACTCCCTCCG 60.390 60.000 0.00 0.00 0.00 4.63
2191 2425 0.966920 CACACAAGTACTCCCTCCGT 59.033 55.000 0.00 0.00 0.00 4.69
2192 2426 1.067776 CACACAAGTACTCCCTCCGTC 60.068 57.143 0.00 0.00 0.00 4.79
2193 2427 0.531200 CACAAGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
2194 2428 0.964358 ACAAGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
2195 2429 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
2196 2430 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
2197 2431 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2198 2432 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2199 2433 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2200 2434 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2201 2435 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2202 2436 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2203 2437 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2204 2438 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2205 2439 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2206 2440 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2207 2441 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2208 2442 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
2209 2443 2.537401 CGTCCGGAAATACTTGTCCTC 58.463 52.381 5.23 0.00 0.00 3.71
2210 2444 2.094390 CGTCCGGAAATACTTGTCCTCA 60.094 50.000 5.23 0.00 0.00 3.86
2211 2445 3.615592 CGTCCGGAAATACTTGTCCTCAA 60.616 47.826 5.23 0.00 0.00 3.02
2212 2446 4.320870 GTCCGGAAATACTTGTCCTCAAA 58.679 43.478 5.23 0.00 32.87 2.69
2213 2447 4.758165 GTCCGGAAATACTTGTCCTCAAAA 59.242 41.667 5.23 0.00 32.87 2.44
2214 2448 5.414765 GTCCGGAAATACTTGTCCTCAAAAT 59.585 40.000 5.23 0.00 32.87 1.82
2215 2449 5.414454 TCCGGAAATACTTGTCCTCAAAATG 59.586 40.000 0.00 0.00 32.87 2.32
2216 2450 5.393027 CCGGAAATACTTGTCCTCAAAATGG 60.393 44.000 0.00 0.00 32.87 3.16
2217 2451 5.414454 CGGAAATACTTGTCCTCAAAATGGA 59.586 40.000 0.00 0.00 32.87 3.41
2218 2452 6.095440 CGGAAATACTTGTCCTCAAAATGGAT 59.905 38.462 0.00 0.00 35.87 3.41
2219 2453 7.282224 CGGAAATACTTGTCCTCAAAATGGATA 59.718 37.037 0.00 0.00 35.87 2.59
2220 2454 8.966868 GGAAATACTTGTCCTCAAAATGGATAA 58.033 33.333 0.00 0.00 35.87 1.75
2225 2459 8.421249 ACTTGTCCTCAAAATGGATAAAATGA 57.579 30.769 0.00 0.00 34.98 2.57
2226 2460 8.869109 ACTTGTCCTCAAAATGGATAAAATGAA 58.131 29.630 0.00 0.00 34.98 2.57
2227 2461 9.880157 CTTGTCCTCAAAATGGATAAAATGAAT 57.120 29.630 0.00 0.00 34.98 2.57
2228 2462 9.656040 TTGTCCTCAAAATGGATAAAATGAATG 57.344 29.630 0.00 0.00 35.87 2.67
2229 2463 8.814931 TGTCCTCAAAATGGATAAAATGAATGT 58.185 29.630 0.00 0.00 35.87 2.71
2273 2507 7.064728 GGCTTAGTAAGGTTGTATGTCTTTCAG 59.935 40.741 11.84 0.00 0.00 3.02
2278 2512 8.154856 AGTAAGGTTGTATGTCTTTCAGCTTTA 58.845 33.333 0.00 0.00 0.00 1.85
2279 2513 8.947115 GTAAGGTTGTATGTCTTTCAGCTTTAT 58.053 33.333 0.00 0.00 0.00 1.40
2334 2572 8.428063 TCCATTGTTGTTTATGGTCTTCAAATT 58.572 29.630 0.00 0.00 41.65 1.82
2365 2634 6.483307 TGAATGATTCAGACGTTGAGAGTTTT 59.517 34.615 3.29 0.00 37.07 2.43
2367 2636 8.553459 AATGATTCAGACGTTGAGAGTTTTAT 57.447 30.769 0.00 0.00 37.07 1.40
2372 2641 5.050363 TCAGACGTTGAGAGTTTTATTGCAC 60.050 40.000 0.00 0.00 0.00 4.57
2375 2644 3.234386 GTTGAGAGTTTTATTGCACGGC 58.766 45.455 0.00 0.00 0.00 5.68
2406 2676 2.031682 CACTGTTGGTTAGCTGAAGTGC 60.032 50.000 0.00 0.00 0.00 4.40
2467 2741 6.260936 CTGGAAGAAAGCGTATGGAACAATAT 59.739 38.462 0.00 0.00 38.23 1.28
2483 2757 7.284261 TGGAACAATATGAAATTATCGAAGGCA 59.716 33.333 0.00 0.00 31.92 4.75
2484 2758 8.134895 GGAACAATATGAAATTATCGAAGGCAA 58.865 33.333 0.00 0.00 0.00 4.52
2495 2769 0.040958 CGAAGGCAATGATAAGGCGC 60.041 55.000 0.00 0.00 35.18 6.53
2496 2770 1.312815 GAAGGCAATGATAAGGCGCT 58.687 50.000 7.64 0.00 35.18 5.92
2497 2771 1.265365 GAAGGCAATGATAAGGCGCTC 59.735 52.381 7.64 0.00 35.18 5.03
2530 2804 8.778059 TCTATATGAAACAAATGGTAGGTCCTT 58.222 33.333 0.00 0.00 37.07 3.36
2532 2806 8.747538 ATATGAAACAAATGGTAGGTCCTTAC 57.252 34.615 0.00 0.00 37.07 2.34
2533 2807 6.195600 TGAAACAAATGGTAGGTCCTTACT 57.804 37.500 0.00 0.00 37.07 2.24
2534 2808 7.319052 TGAAACAAATGGTAGGTCCTTACTA 57.681 36.000 0.00 0.00 37.07 1.82
2535 2809 7.924541 TGAAACAAATGGTAGGTCCTTACTAT 58.075 34.615 0.00 0.00 37.07 2.12
2536 2810 7.827236 TGAAACAAATGGTAGGTCCTTACTATG 59.173 37.037 0.00 0.00 37.07 2.23
2537 2811 5.681639 ACAAATGGTAGGTCCTTACTATGC 58.318 41.667 0.00 0.00 37.07 3.14
2538 2812 5.428783 ACAAATGGTAGGTCCTTACTATGCT 59.571 40.000 0.00 0.00 37.07 3.79
2539 2813 6.614087 ACAAATGGTAGGTCCTTACTATGCTA 59.386 38.462 0.00 0.00 37.07 3.49
2540 2814 6.919775 AATGGTAGGTCCTTACTATGCTAG 57.080 41.667 0.00 0.00 37.07 3.42
2541 2815 5.399052 TGGTAGGTCCTTACTATGCTAGT 57.601 43.478 0.00 2.19 38.74 2.57
2542 2816 6.520021 TGGTAGGTCCTTACTATGCTAGTA 57.480 41.667 0.00 0.00 39.38 1.82
2543 2817 6.302269 TGGTAGGTCCTTACTATGCTAGTAC 58.698 44.000 0.00 0.00 40.74 2.73
2544 2818 6.102321 TGGTAGGTCCTTACTATGCTAGTACT 59.898 42.308 0.00 0.00 40.74 2.73
2545 2819 7.003482 GGTAGGTCCTTACTATGCTAGTACTT 58.997 42.308 0.00 0.00 40.74 2.24
2546 2820 7.505248 GGTAGGTCCTTACTATGCTAGTACTTT 59.495 40.741 0.00 0.00 40.74 2.66
2547 2821 7.974730 AGGTCCTTACTATGCTAGTACTTTT 57.025 36.000 0.00 0.00 40.74 2.27
2548 2822 8.376803 AGGTCCTTACTATGCTAGTACTTTTT 57.623 34.615 0.00 0.00 40.74 1.94
2549 2823 8.258708 AGGTCCTTACTATGCTAGTACTTTTTG 58.741 37.037 0.00 0.00 40.74 2.44
2550 2824 8.255905 GGTCCTTACTATGCTAGTACTTTTTGA 58.744 37.037 0.00 0.00 40.74 2.69
2551 2825 9.085250 GTCCTTACTATGCTAGTACTTTTTGAC 57.915 37.037 0.00 0.00 40.74 3.18
2552 2826 9.032624 TCCTTACTATGCTAGTACTTTTTGACT 57.967 33.333 0.00 0.00 40.74 3.41
2553 2827 9.088512 CCTTACTATGCTAGTACTTTTTGACTG 57.911 37.037 0.00 0.00 40.74 3.51
2554 2828 6.969828 ACTATGCTAGTACTTTTTGACTGC 57.030 37.500 0.00 0.00 37.23 4.40
2555 2829 5.875359 ACTATGCTAGTACTTTTTGACTGCC 59.125 40.000 0.00 0.00 37.23 4.85
2556 2830 4.351874 TGCTAGTACTTTTTGACTGCCT 57.648 40.909 0.00 0.00 0.00 4.75
2557 2831 5.477607 TGCTAGTACTTTTTGACTGCCTA 57.522 39.130 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.898320 CAGGAGACAAGGGACACGAT 59.102 55.000 0.00 0.00 0.00 3.73
1 2 0.469331 ACAGGAGACAAGGGACACGA 60.469 55.000 0.00 0.00 0.00 4.35
2 3 0.393077 AACAGGAGACAAGGGACACG 59.607 55.000 0.00 0.00 0.00 4.49
3 4 2.289506 GGTAACAGGAGACAAGGGACAC 60.290 54.545 0.00 0.00 0.00 3.67
4 5 1.975680 GGTAACAGGAGACAAGGGACA 59.024 52.381 0.00 0.00 0.00 4.02
5 6 1.975680 TGGTAACAGGAGACAAGGGAC 59.024 52.381 0.00 0.00 46.17 4.46
6 7 2.409064 TGGTAACAGGAGACAAGGGA 57.591 50.000 0.00 0.00 46.17 4.20
19 20 0.596859 GCGTCTAGGCGGATGGTAAC 60.597 60.000 19.86 0.00 0.00 2.50
20 21 1.038681 TGCGTCTAGGCGGATGGTAA 61.039 55.000 19.86 0.00 35.06 2.85
21 22 1.454295 TGCGTCTAGGCGGATGGTA 60.454 57.895 19.86 0.00 35.06 3.25
22 23 2.758327 TGCGTCTAGGCGGATGGT 60.758 61.111 19.86 0.00 35.06 3.55
23 24 2.279517 GTGCGTCTAGGCGGATGG 60.280 66.667 19.86 0.00 34.24 3.51
24 25 1.589993 CTGTGCGTCTAGGCGGATG 60.590 63.158 19.86 9.25 34.24 3.51
25 26 1.605058 AACTGTGCGTCTAGGCGGAT 61.605 55.000 19.86 0.00 34.24 4.18
26 27 2.209064 GAACTGTGCGTCTAGGCGGA 62.209 60.000 19.86 14.02 35.06 5.54
27 28 1.805945 GAACTGTGCGTCTAGGCGG 60.806 63.158 19.86 3.85 35.06 6.13
28 29 2.152699 CGAACTGTGCGTCTAGGCG 61.153 63.158 13.55 13.55 35.06 5.52
29 30 1.805945 CCGAACTGTGCGTCTAGGC 60.806 63.158 7.51 0.00 0.00 3.93
30 31 1.153823 CCCGAACTGTGCGTCTAGG 60.154 63.158 7.51 0.00 0.00 3.02
31 32 0.456312 GTCCCGAACTGTGCGTCTAG 60.456 60.000 7.51 0.00 0.00 2.43
32 33 1.582968 GTCCCGAACTGTGCGTCTA 59.417 57.895 7.51 0.00 0.00 2.59
33 34 2.338984 GTCCCGAACTGTGCGTCT 59.661 61.111 7.51 0.00 0.00 4.18
34 35 2.737376 GGTCCCGAACTGTGCGTC 60.737 66.667 7.51 0.00 0.00 5.19
35 36 4.309950 GGGTCCCGAACTGTGCGT 62.310 66.667 7.51 0.00 0.00 5.24
37 38 4.717313 GGGGGTCCCGAACTGTGC 62.717 72.222 0.48 0.00 36.85 4.57
46 47 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
47 48 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
48 49 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
49 50 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
50 51 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
51 52 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
52 53 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
53 54 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
54 55 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
59 60 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
60 61 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
61 62 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
62 63 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
63 64 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
64 65 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
70 71 1.278637 CGCTGTCGGTGTCAAAACC 59.721 57.895 0.00 0.00 36.82 3.27
71 72 4.893241 CGCTGTCGGTGTCAAAAC 57.107 55.556 0.00 0.00 0.00 2.43
82 83 4.329545 TCCAAGGCCACCGCTGTC 62.330 66.667 5.01 0.00 34.44 3.51
83 84 4.335647 CTCCAAGGCCACCGCTGT 62.336 66.667 5.01 0.00 34.44 4.40
137 171 1.675641 GCTTCGAAGCCACCCATGT 60.676 57.895 34.88 0.00 46.20 3.21
152 186 1.457604 ATGCCGCCCATGATAGCTT 59.542 52.632 0.00 0.00 31.48 3.74
172 206 0.540365 CCAAAGTCACCCATGGCACT 60.540 55.000 6.09 4.75 30.46 4.40
269 305 2.813754 CCTCCAATGAGAGACGCAAAAA 59.186 45.455 1.20 0.00 41.42 1.94
360 412 1.396301 GAAGCTCAGAAGATGTTGGCG 59.604 52.381 0.00 0.00 0.00 5.69
368 420 2.558359 TCATCACGTGAAGCTCAGAAGA 59.442 45.455 24.13 6.63 32.78 2.87
435 487 2.363147 GACTCACCGGGCTCCTCT 60.363 66.667 6.32 0.00 0.00 3.69
444 496 1.507174 GTCTTCCTCCGACTCACCG 59.493 63.158 0.00 0.00 0.00 4.94
456 526 1.596895 AAGCCTCGTCCTCGTCTTCC 61.597 60.000 0.00 0.00 38.33 3.46
692 844 2.100991 AGCGCGCTAAAATGCAGC 59.899 55.556 35.79 0.00 36.80 5.25
693 845 1.584483 CCAGCGCGCTAAAATGCAG 60.584 57.895 36.02 18.66 0.00 4.41
694 846 2.331893 ACCAGCGCGCTAAAATGCA 61.332 52.632 36.02 0.00 0.00 3.96
695 847 1.869132 CACCAGCGCGCTAAAATGC 60.869 57.895 36.02 0.00 0.00 3.56
696 848 0.167908 TTCACCAGCGCGCTAAAATG 59.832 50.000 36.02 26.63 0.00 2.32
697 849 0.447801 CTTCACCAGCGCGCTAAAAT 59.552 50.000 36.02 16.58 0.00 1.82
698 850 1.866237 CTTCACCAGCGCGCTAAAA 59.134 52.632 36.02 22.36 0.00 1.52
699 851 2.677003 GCTTCACCAGCGCGCTAAA 61.677 57.895 36.02 22.70 39.29 1.85
700 852 3.118454 GCTTCACCAGCGCGCTAA 61.118 61.111 36.02 23.21 39.29 3.09
738 927 0.237235 GTTGTTTTCATCAGCCGCGA 59.763 50.000 8.23 0.00 0.00 5.87
747 936 3.163630 AGTTTGCAGCGTTGTTTTCAT 57.836 38.095 0.00 0.00 0.00 2.57
752 941 3.775661 AAACTAGTTTGCAGCGTTGTT 57.224 38.095 19.94 0.00 0.00 2.83
753 942 3.775661 AAAACTAGTTTGCAGCGTTGT 57.224 38.095 21.22 0.00 32.36 3.32
756 945 3.606153 CGCTAAAAACTAGTTTGCAGCGT 60.606 43.478 37.91 19.38 46.70 5.07
787 1009 2.046314 CTCCAACCGTCGCCCAAT 60.046 61.111 0.00 0.00 0.00 3.16
795 1017 1.550976 CCTTAGAGCTTCTCCAACCGT 59.449 52.381 0.00 0.00 0.00 4.83
806 1028 7.255660 CCACTTTATATTCTCGACCTTAGAGCT 60.256 40.741 0.00 0.00 35.79 4.09
838 1060 3.186409 CCTCAACTTCGCAATTTTCGAGA 59.814 43.478 0.00 0.00 37.26 4.04
839 1061 3.058914 ACCTCAACTTCGCAATTTTCGAG 60.059 43.478 0.69 0.00 37.26 4.04
840 1062 2.875933 ACCTCAACTTCGCAATTTTCGA 59.124 40.909 0.00 0.00 0.00 3.71
920 1142 1.435256 AGGCCGCCTTATCCAATACT 58.565 50.000 5.94 0.00 0.00 2.12
924 1146 1.153249 CGAAGGCCGCCTTATCCAA 60.153 57.895 24.89 0.00 44.82 3.53
943 1165 2.050918 AGGAGTGGGGATTTAGCTAGC 58.949 52.381 6.62 6.62 0.00 3.42
944 1166 2.224402 GCAGGAGTGGGGATTTAGCTAG 60.224 54.545 0.00 0.00 0.00 3.42
945 1167 1.768870 GCAGGAGTGGGGATTTAGCTA 59.231 52.381 0.00 0.00 0.00 3.32
946 1168 0.548510 GCAGGAGTGGGGATTTAGCT 59.451 55.000 0.00 0.00 0.00 3.32
1069 1291 3.672293 GGACCACGACAGGTACGA 58.328 61.111 0.00 0.00 43.38 3.43
1171 1393 4.514577 CGTCCAAGCCGCTCGGAT 62.515 66.667 13.11 2.04 37.50 4.18
1425 1647 0.551396 TGGACCTCTCGGCTATGAGA 59.449 55.000 0.00 4.29 42.56 3.27
1488 1710 0.757188 GCTTCCCCTCGATCCTCTCA 60.757 60.000 0.00 0.00 0.00 3.27
1577 1799 8.691661 AATACTCCACATAACAACTGTTTCTT 57.308 30.769 0.00 0.00 39.31 2.52
1595 1817 9.178758 ACATGGATCAAACTAAAGAAATACTCC 57.821 33.333 0.00 0.00 0.00 3.85
1649 1875 8.065473 AGCTATTACTAGATCATCACCATCAG 57.935 38.462 0.00 0.00 0.00 2.90
1700 1929 9.964303 CTAAAATAGCATTGCAACACCAATATA 57.036 29.630 11.91 0.00 33.86 0.86
1769 1998 9.345517 CAATGAACATTTCCCTATAATATTGCG 57.654 33.333 0.00 0.00 0.00 4.85
1783 2014 8.722342 TTACTAGCGTTTTCAATGAACATTTC 57.278 30.769 0.00 0.00 0.00 2.17
1797 2031 4.274214 GTCAACTGGGTTTTACTAGCGTTT 59.726 41.667 0.00 0.00 0.00 3.60
1801 2035 7.527457 CATTTAGTCAACTGGGTTTTACTAGC 58.473 38.462 0.00 0.00 29.29 3.42
1832 2066 2.540265 AATCGGATAGCTCCAGCAAG 57.460 50.000 0.48 0.00 42.19 4.01
1848 2082 7.752239 CACATCCACATTAGACTTGACAAAATC 59.248 37.037 0.00 0.00 0.00 2.17
1872 2106 6.486657 TCTGCTTAATGTTATTATCTGCCCAC 59.513 38.462 0.00 0.00 0.00 4.61
1893 2127 6.292381 CCATAACTTGCTCGTTATAGTTCTGC 60.292 42.308 9.74 0.00 37.84 4.26
1896 2130 7.868415 AGATCCATAACTTGCTCGTTATAGTTC 59.132 37.037 9.74 8.13 37.84 3.01
2027 2261 4.045104 CCATCTCTCCGACAAGTATTTCG 58.955 47.826 0.00 0.00 34.93 3.46
2028 2262 5.263968 TCCATCTCTCCGACAAGTATTTC 57.736 43.478 0.00 0.00 0.00 2.17
2029 2263 5.878406 ATCCATCTCTCCGACAAGTATTT 57.122 39.130 0.00 0.00 0.00 1.40
2030 2264 6.978674 TTATCCATCTCTCCGACAAGTATT 57.021 37.500 0.00 0.00 0.00 1.89
2031 2265 6.978674 TTTATCCATCTCTCCGACAAGTAT 57.021 37.500 0.00 0.00 0.00 2.12
2032 2266 6.785337 TTTTATCCATCTCTCCGACAAGTA 57.215 37.500 0.00 0.00 0.00 2.24
2033 2267 5.677319 TTTTATCCATCTCTCCGACAAGT 57.323 39.130 0.00 0.00 0.00 3.16
2034 2268 6.017605 CCAATTTTATCCATCTCTCCGACAAG 60.018 42.308 0.00 0.00 0.00 3.16
2035 2269 5.822519 CCAATTTTATCCATCTCTCCGACAA 59.177 40.000 0.00 0.00 0.00 3.18
2036 2270 5.130311 TCCAATTTTATCCATCTCTCCGACA 59.870 40.000 0.00 0.00 0.00 4.35
2037 2271 5.611374 TCCAATTTTATCCATCTCTCCGAC 58.389 41.667 0.00 0.00 0.00 4.79
2038 2272 5.887214 TCCAATTTTATCCATCTCTCCGA 57.113 39.130 0.00 0.00 0.00 4.55
2039 2273 5.106396 GCATCCAATTTTATCCATCTCTCCG 60.106 44.000 0.00 0.00 0.00 4.63
2040 2274 5.771666 TGCATCCAATTTTATCCATCTCTCC 59.228 40.000 0.00 0.00 0.00 3.71
2041 2275 6.889301 TGCATCCAATTTTATCCATCTCTC 57.111 37.500 0.00 0.00 0.00 3.20
2042 2276 7.239438 AGATGCATCCAATTTTATCCATCTCT 58.761 34.615 23.06 0.00 34.70 3.10
2043 2277 7.463961 AGATGCATCCAATTTTATCCATCTC 57.536 36.000 23.06 0.00 34.70 2.75
2047 2281 9.812347 AGTTATAGATGCATCCAATTTTATCCA 57.188 29.630 23.06 1.94 0.00 3.41
2056 2290 9.772973 ACGTATTTTAGTTATAGATGCATCCAA 57.227 29.630 23.06 12.25 0.00 3.53
2057 2291 9.419297 GACGTATTTTAGTTATAGATGCATCCA 57.581 33.333 23.06 10.57 0.00 3.41
2058 2292 9.640963 AGACGTATTTTAGTTATAGATGCATCC 57.359 33.333 23.06 7.42 0.00 3.51
2097 2331 4.084433 CGTCCGGAAATACTTGTCGAAAAA 60.084 41.667 5.23 0.00 0.00 1.94
2098 2332 3.429543 CGTCCGGAAATACTTGTCGAAAA 59.570 43.478 5.23 0.00 0.00 2.29
2099 2333 2.988493 CGTCCGGAAATACTTGTCGAAA 59.012 45.455 5.23 0.00 0.00 3.46
2100 2334 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
2101 2335 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
2102 2336 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2103 2337 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2104 2338 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2105 2339 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2106 2340 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2107 2341 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2108 2342 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2109 2343 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2110 2344 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2111 2345 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2112 2346 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2113 2347 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
2114 2348 1.664321 CTTGTACTCCCTCCGTCCGG 61.664 65.000 0.00 0.00 0.00 5.14
2115 2349 0.964358 ACTTGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
2116 2350 2.134789 TACTTGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
2117 2351 4.277921 CCTTATACTTGTACTCCCTCCGTC 59.722 50.000 0.00 0.00 0.00 4.79
2118 2352 4.079558 TCCTTATACTTGTACTCCCTCCGT 60.080 45.833 0.00 0.00 0.00 4.69
2119 2353 4.467769 TCCTTATACTTGTACTCCCTCCG 58.532 47.826 0.00 0.00 0.00 4.63
2120 2354 5.659971 TGTTCCTTATACTTGTACTCCCTCC 59.340 44.000 0.00 0.00 0.00 4.30
2121 2355 6.786967 TGTTCCTTATACTTGTACTCCCTC 57.213 41.667 0.00 0.00 0.00 4.30
2122 2356 6.672657 ACATGTTCCTTATACTTGTACTCCCT 59.327 38.462 0.00 0.00 33.65 4.20
2123 2357 6.761714 CACATGTTCCTTATACTTGTACTCCC 59.238 42.308 0.00 0.00 33.65 4.30
2124 2358 6.761714 CCACATGTTCCTTATACTTGTACTCC 59.238 42.308 0.00 0.00 33.65 3.85
2125 2359 7.553334 TCCACATGTTCCTTATACTTGTACTC 58.447 38.462 0.00 0.00 33.65 2.59
2126 2360 7.490657 TCCACATGTTCCTTATACTTGTACT 57.509 36.000 0.00 0.00 33.65 2.73
2127 2361 8.732746 AATCCACATGTTCCTTATACTTGTAC 57.267 34.615 0.00 0.00 33.65 2.90
2128 2362 9.173021 CAAATCCACATGTTCCTTATACTTGTA 57.827 33.333 0.00 0.00 33.65 2.41
2129 2363 7.362920 GCAAATCCACATGTTCCTTATACTTGT 60.363 37.037 0.00 0.00 35.15 3.16
2130 2364 6.974622 GCAAATCCACATGTTCCTTATACTTG 59.025 38.462 0.00 0.00 0.00 3.16
2182 2416 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2183 2417 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2184 2418 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2185 2419 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2186 2420 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2187 2421 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2188 2422 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
2189 2423 2.094390 TGAGGACAAGTATTTCCGGACG 60.094 50.000 1.83 0.00 36.95 4.79
2190 2424 3.604875 TGAGGACAAGTATTTCCGGAC 57.395 47.619 1.83 0.00 36.95 4.79
2191 2425 4.627284 TTTGAGGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 36.95 5.14
2192 2426 5.393027 CCATTTTGAGGACAAGTATTTCCGG 60.393 44.000 0.00 0.00 36.95 5.14
2193 2427 5.414454 TCCATTTTGAGGACAAGTATTTCCG 59.586 40.000 0.00 0.00 36.95 4.30
2194 2428 6.834168 TCCATTTTGAGGACAAGTATTTCC 57.166 37.500 0.00 0.00 37.32 3.13
2199 2433 9.527157 TCATTTTATCCATTTTGAGGACAAGTA 57.473 29.630 0.00 0.00 38.13 2.24
2200 2434 8.421249 TCATTTTATCCATTTTGAGGACAAGT 57.579 30.769 0.00 0.00 38.13 3.16
2201 2435 9.880157 ATTCATTTTATCCATTTTGAGGACAAG 57.120 29.630 0.00 0.00 38.13 3.16
2202 2436 9.656040 CATTCATTTTATCCATTTTGAGGACAA 57.344 29.630 0.00 0.00 38.13 3.18
2203 2437 8.814931 ACATTCATTTTATCCATTTTGAGGACA 58.185 29.630 0.00 0.00 38.13 4.02
2234 2468 9.749340 AACCTTACTAAGCCACATTTTAGTTAT 57.251 29.630 2.66 0.00 39.89 1.89
2235 2469 9.005777 CAACCTTACTAAGCCACATTTTAGTTA 57.994 33.333 2.66 0.00 39.89 2.24
2236 2470 7.504574 ACAACCTTACTAAGCCACATTTTAGTT 59.495 33.333 2.66 0.00 39.89 2.24
2237 2471 7.002276 ACAACCTTACTAAGCCACATTTTAGT 58.998 34.615 2.88 2.88 41.57 2.24
2238 2472 7.448748 ACAACCTTACTAAGCCACATTTTAG 57.551 36.000 0.00 0.00 33.98 1.85
2239 2473 8.952278 CATACAACCTTACTAAGCCACATTTTA 58.048 33.333 0.00 0.00 0.00 1.52
2240 2474 7.450323 ACATACAACCTTACTAAGCCACATTTT 59.550 33.333 0.00 0.00 0.00 1.82
2241 2475 6.946009 ACATACAACCTTACTAAGCCACATTT 59.054 34.615 0.00 0.00 0.00 2.32
2242 2476 6.481643 ACATACAACCTTACTAAGCCACATT 58.518 36.000 0.00 0.00 0.00 2.71
2243 2477 6.062258 ACATACAACCTTACTAAGCCACAT 57.938 37.500 0.00 0.00 0.00 3.21
2244 2478 5.247564 AGACATACAACCTTACTAAGCCACA 59.752 40.000 0.00 0.00 0.00 4.17
2245 2479 5.731591 AGACATACAACCTTACTAAGCCAC 58.268 41.667 0.00 0.00 0.00 5.01
2279 2513 9.443323 TCATTCACCGATTTTCTGATAACTAAA 57.557 29.630 0.00 0.00 0.00 1.85
2352 2621 3.059188 CCGTGCAATAAAACTCTCAACGT 60.059 43.478 0.00 0.00 0.00 3.99
2367 2636 1.265635 GTGAACATAGTTGCCGTGCAA 59.734 47.619 7.15 7.15 46.80 4.08
2372 2641 2.095768 CCAACAGTGAACATAGTTGCCG 60.096 50.000 0.00 0.00 39.86 5.69
2375 2644 5.470098 AGCTAACCAACAGTGAACATAGTTG 59.530 40.000 0.00 12.12 40.63 3.16
2378 2647 5.237815 TCAGCTAACCAACAGTGAACATAG 58.762 41.667 0.00 0.00 0.00 2.23
2406 2676 5.852738 ATTTTGATGAACACGAGAGACAG 57.147 39.130 0.00 0.00 0.00 3.51
2467 2741 7.522073 GCCTTATCATTGCCTTCGATAATTTCA 60.522 37.037 0.00 0.00 32.66 2.69
2473 2747 3.325870 CGCCTTATCATTGCCTTCGATA 58.674 45.455 0.00 0.00 0.00 2.92
2474 2748 2.146342 CGCCTTATCATTGCCTTCGAT 58.854 47.619 0.00 0.00 0.00 3.59
2495 2769 7.443575 CCATTTGTTTCATATAGACAGGAGGAG 59.556 40.741 0.00 0.00 0.00 3.69
2496 2770 7.092444 ACCATTTGTTTCATATAGACAGGAGGA 60.092 37.037 0.00 0.00 0.00 3.71
2497 2771 7.056635 ACCATTTGTTTCATATAGACAGGAGG 58.943 38.462 0.00 0.00 0.00 4.30
2532 2806 6.109359 AGGCAGTCAAAAAGTACTAGCATAG 58.891 40.000 0.00 0.00 46.50 2.23
2533 2807 6.049955 AGGCAGTCAAAAAGTACTAGCATA 57.950 37.500 0.00 0.00 0.00 3.14
2534 2808 4.911390 AGGCAGTCAAAAAGTACTAGCAT 58.089 39.130 0.00 0.00 0.00 3.79
2535 2809 4.351874 AGGCAGTCAAAAAGTACTAGCA 57.648 40.909 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.