Multiple sequence alignment - TraesCS2D01G332500

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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 TraesCS2D01G332500 chr2D 100.000 7145 0 0 1 7145 425739741 425746885 0.000000e+00 13195.0
1 TraesCS2D01G332500 chr2D 96.125 1084 24 5 3997 5062 276935669 276936752 0.000000e+00 1753.0
2 TraesCS2D01G332500 chr2D 95.056 1072 36 5 4004 5059 285350083 285349013 0.000000e+00 1670.0
3 TraesCS2D01G332500 chr2D 90.795 239 20 2 5920 6158 425757879 425758115 1.160000e-82 318.0
4 TraesCS2D01G332500 chr2D 91.667 96 4 1 5716 5811 296173669 296173760 5.820000e-26 130.0
5 TraesCS2D01G332500 chr2B 93.921 3438 120 33 540 3942 501005943 501009326 0.000000e+00 5108.0
6 TraesCS2D01G332500 chr2B 90.335 807 70 4 5810 6616 501341612 501342410 0.000000e+00 1051.0
7 TraesCS2D01G332500 chr2B 93.614 642 37 4 5086 5724 501009486 501010126 0.000000e+00 955.0
8 TraesCS2D01G332500 chr2B 94.343 548 26 2 1 548 500990378 500990920 0.000000e+00 835.0
9 TraesCS2D01G332500 chr2B 90.075 534 38 6 5810 6339 501010125 501010647 0.000000e+00 678.0
10 TraesCS2D01G332500 chr2B 90.244 533 28 9 6616 7145 501937882 501938393 0.000000e+00 675.0
11 TraesCS2D01G332500 chr2B 85.814 571 72 9 6579 7145 501134705 501135270 1.330000e-166 597.0
12 TraesCS2D01G332500 chr2B 90.875 263 24 0 5340 5602 501341265 501341527 3.170000e-93 353.0
13 TraesCS2D01G332500 chr2B 90.805 87 8 0 5638 5724 501341527 501341613 4.530000e-22 117.0
14 TraesCS2D01G332500 chr2A 93.393 2573 85 21 442 2992 562606100 562603591 0.000000e+00 3731.0
15 TraesCS2D01G332500 chr2A 94.303 1018 56 2 2988 4003 562603544 562602527 0.000000e+00 1557.0
16 TraesCS2D01G332500 chr2A 91.377 777 35 13 6372 7145 562600619 562599872 0.000000e+00 1035.0
17 TraesCS2D01G332500 chr2A 94.590 647 30 3 5086 5730 562602499 562601856 0.000000e+00 996.0
18 TraesCS2D01G332500 chr2A 98.239 568 7 2 5810 6374 562601863 562601296 0.000000e+00 990.0
19 TraesCS2D01G332500 chr2A 95.238 336 16 0 1 336 562607101 562606766 3.790000e-147 532.0
20 TraesCS2D01G332500 chr2A 92.469 239 18 0 5920 6158 562599565 562599327 6.860000e-90 342.0
21 TraesCS2D01G332500 chr2A 88.991 109 7 3 5714 5822 714303010 714302907 5.820000e-26 130.0
22 TraesCS2D01G332500 chr2A 95.833 72 1 2 375 444 562606756 562606685 1.630000e-21 115.0
23 TraesCS2D01G332500 chr7D 94.659 1086 40 6 3995 5065 576643956 576645038 0.000000e+00 1668.0
24 TraesCS2D01G332500 chr7D 94.490 1089 41 4 3996 5065 145918967 145920055 0.000000e+00 1661.0
25 TraesCS2D01G332500 chr7D 94.037 1090 42 8 3997 5066 616464828 616465914 0.000000e+00 1631.0
26 TraesCS2D01G332500 chr7D 92.797 597 24 7 3997 4575 21001734 21002329 0.000000e+00 846.0
27 TraesCS2D01G332500 chr6D 94.182 1100 40 11 4004 5084 446133056 446134150 0.000000e+00 1655.0
28 TraesCS2D01G332500 chr6D 92.831 1088 36 11 3996 5065 464697145 464696082 0.000000e+00 1539.0
29 TraesCS2D01G332500 chr6D 79.183 514 95 11 2285 2792 262268939 262269446 5.310000e-91 346.0
30 TraesCS2D01G332500 chr6D 91.304 92 4 1 5722 5813 65497171 65497084 9.730000e-24 122.0
31 TraesCS2D01G332500 chr6D 90.625 96 4 3 5716 5811 114587708 114587798 9.730000e-24 122.0
32 TraesCS2D01G332500 chr6D 88.889 99 7 2 5713 5811 95294999 95294905 1.260000e-22 119.0
33 TraesCS2D01G332500 chr6D 87.500 104 8 3 5709 5812 88833988 88834086 1.630000e-21 115.0
34 TraesCS2D01G332500 chr6D 91.566 83 6 1 2829 2910 13290766 13290848 5.860000e-21 113.0
35 TraesCS2D01G332500 chr6D 85.000 100 6 3 2829 2926 211444021 211443929 7.630000e-15 93.5
36 TraesCS2D01G332500 chr6D 86.364 88 5 1 2829 2916 211443945 211444025 9.870000e-14 89.8
37 TraesCS2D01G332500 chr6D 85.882 85 8 3 2829 2912 335373916 335373835 3.550000e-13 87.9
38 TraesCS2D01G332500 chr6D 97.561 41 1 0 2872 2912 24231419 24231459 3.580000e-08 71.3
39 TraesCS2D01G332500 chr6B 94.118 1088 43 9 3987 5058 626809160 626810242 0.000000e+00 1635.0
40 TraesCS2D01G332500 chr6B 79.572 514 93 11 2285 2792 348706617 348706110 2.450000e-94 357.0
41 TraesCS2D01G332500 chr3B 93.686 1077 58 8 3996 5069 49155555 49156624 0.000000e+00 1604.0
42 TraesCS2D01G332500 chr3B 91.753 97 6 2 5716 5811 76271905 76271810 4.500000e-27 134.0
43 TraesCS2D01G332500 chr1D 93.560 1087 51 6 3997 5066 467390142 467389058 0.000000e+00 1602.0
44 TraesCS2D01G332500 chr1D 92.391 92 5 2 2826 2915 279101373 279101464 5.820000e-26 130.0
45 TraesCS2D01G332500 chr1D 94.366 71 3 1 2847 2916 22976551 22976621 2.730000e-19 108.0
46 TraesCS2D01G332500 chr1D 87.640 89 8 1 2828 2913 493932303 493932391 4.560000e-17 100.0
47 TraesCS2D01G332500 chr1D 87.209 86 9 2 2829 2913 468830134 468830218 5.900000e-16 97.1
48 TraesCS2D01G332500 chr1D 84.091 88 10 2 2829 2914 302696422 302696507 1.650000e-11 82.4
49 TraesCS2D01G332500 chr5D 92.692 1081 52 8 3997 5062 432173410 432174478 0.000000e+00 1533.0
50 TraesCS2D01G332500 chr5D 91.765 85 7 0 2829 2913 49761845 49761929 1.260000e-22 119.0
51 TraesCS2D01G332500 chr5D 91.765 85 7 0 2829 2913 50198537 50198621 1.260000e-22 119.0
52 TraesCS2D01G332500 chr5D 90.698 86 7 1 2829 2913 464070864 464070949 5.860000e-21 113.0
53 TraesCS2D01G332500 chr1B 87.683 1023 93 16 4042 5050 596927665 596926662 0.000000e+00 1160.0
54 TraesCS2D01G332500 chr1B 90.323 93 7 2 2822 2913 658497423 658497514 3.500000e-23 121.0
55 TraesCS2D01G332500 chr7B 83.301 1018 98 32 4004 5016 687100549 687101499 0.000000e+00 872.0
56 TraesCS2D01G332500 chr7B 90.909 99 7 2 5715 5811 453550695 453550793 1.620000e-26 132.0
57 TraesCS2D01G332500 chr7B 90.816 98 7 2 5715 5811 49313343 49313247 5.820000e-26 130.0
58 TraesCS2D01G332500 chr7B 95.238 84 1 1 2829 2912 450642196 450642116 5.820000e-26 130.0
59 TraesCS2D01G332500 chr6A 79.767 514 92 11 2285 2792 323000386 322999879 5.270000e-96 363.0
60 TraesCS2D01G332500 chr6A 91.304 92 4 1 5723 5814 604198404 604198317 9.730000e-24 122.0
61 TraesCS2D01G332500 chr6A 88.298 94 7 3 2822 2914 127186110 127186200 7.580000e-20 110.0
62 TraesCS2D01G332500 chr4B 93.548 93 5 1 5719 5811 548345573 548345664 3.480000e-28 137.0
63 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 44018814 44018905 1.620000e-26 132.0
64 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 45004118 45004209 1.620000e-26 132.0
65 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 70768078 70768169 1.620000e-26 132.0
66 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 74144229 74144138 1.620000e-26 132.0
67 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 181288874 181288783 1.620000e-26 132.0
68 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 189886724 189886815 1.620000e-26 132.0
69 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 474779173 474779264 1.620000e-26 132.0
70 TraesCS2D01G332500 chr4B 92.473 93 6 1 5719 5811 505064023 505064114 1.620000e-26 132.0
71 TraesCS2D01G332500 chr4B 89.011 91 7 3 2829 2916 486282367 486282277 7.580000e-20 110.0
72 TraesCS2D01G332500 chr5B 92.553 94 6 1 5719 5812 475346834 475346926 4.500000e-27 134.0
73 TraesCS2D01G332500 chr3D 93.478 92 2 1 5723 5814 92781286 92781373 4.500000e-27 134.0
74 TraesCS2D01G332500 chr3D 94.253 87 4 1 2829 2914 45931417 45931331 1.620000e-26 132.0
75 TraesCS2D01G332500 chr3D 94.048 84 2 2 2829 2912 250931573 250931493 2.710000e-24 124.0
76 TraesCS2D01G332500 chrUn 91.398 93 7 1 5719 5811 265882304 265882395 7.520000e-25 126.0
77 TraesCS2D01G332500 chrUn 91.398 93 7 1 5719 5811 282866090 282866181 7.520000e-25 126.0
78 TraesCS2D01G332500 chrUn 91.398 93 7 1 5719 5811 369927657 369927566 7.520000e-25 126.0
79 TraesCS2D01G332500 chrUn 91.398 93 7 1 5719 5811 423795706 423795615 7.520000e-25 126.0
80 TraesCS2D01G332500 chrUn 91.489 94 3 3 5722 5814 81299913 81300002 2.710000e-24 124.0
81 TraesCS2D01G332500 chrUn 92.135 89 3 1 5723 5811 100223739 100223823 9.730000e-24 122.0
82 TraesCS2D01G332500 chrUn 90.323 93 8 1 5719 5811 56954203 56954112 3.500000e-23 121.0
83 TraesCS2D01G332500 chrUn 91.111 90 4 2 5722 5811 222975769 222975854 1.260000e-22 119.0
84 TraesCS2D01G332500 chrUn 91.111 90 4 2 5722 5811 303647903 303647988 1.260000e-22 119.0
85 TraesCS2D01G332500 chrUn 90.323 93 4 2 5719 5811 142658669 142658582 4.530000e-22 117.0
86 TraesCS2D01G332500 chrUn 88.506 87 6 3 2829 2913 371432434 371432518 1.270000e-17 102.0
87 TraesCS2D01G332500 chrUn 94.643 56 3 0 2857 2912 16904467 16904522 3.550000e-13 87.9
88 TraesCS2D01G332500 chrUn 88.235 68 7 1 2848 2914 478179596 478179663 5.940000e-11 80.5
89 TraesCS2D01G332500 chrUn 100.000 41 0 0 2873 2913 313622390 313622430 7.690000e-10 76.8
90 TraesCS2D01G332500 chrUn 100.000 33 0 0 2880 2912 32098221 32098253 2.150000e-05 62.1
91 TraesCS2D01G332500 chrUn 97.059 34 1 0 2879 2912 295853755 295853722 2.780000e-04 58.4
92 TraesCS2D01G332500 chr1A 92.308 91 3 1 5723 5813 14584423 14584509 7.520000e-25 126.0
93 TraesCS2D01G332500 chr1A 88.000 100 9 3 2822 2920 567969919 567970016 1.630000e-21 115.0
94 TraesCS2D01G332500 chr1A 90.476 84 4 2 2829 2912 501030273 501030194 2.730000e-19 108.0
95 TraesCS2D01G332500 chr4D 89.899 99 5 2 5716 5813 371601305 371601211 9.730000e-24 122.0
96 TraesCS2D01G332500 chr4D 93.750 48 1 1 2865 2912 44749401 44749356 3.580000e-08 71.3
97 TraesCS2D01G332500 chr4D 82.558 86 10 2 2821 2902 509317265 509317181 3.580000e-08 71.3
98 TraesCS2D01G332500 chr3A 92.941 85 5 1 2829 2912 151644768 151644684 9.730000e-24 122.0
99 TraesCS2D01G332500 chr3A 91.954 87 6 1 2828 2913 491189425 491189511 3.500000e-23 121.0


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 TraesCS2D01G332500 chr2D 425739741 425746885 7144 False 13195.00 13195 100.000000 1 7145 1 chr2D.!!$F3 7144
1 TraesCS2D01G332500 chr2D 276935669 276936752 1083 False 1753.00 1753 96.125000 3997 5062 1 chr2D.!!$F1 1065
2 TraesCS2D01G332500 chr2D 285349013 285350083 1070 True 1670.00 1670 95.056000 4004 5059 1 chr2D.!!$R1 1055
3 TraesCS2D01G332500 chr2B 501005943 501010647 4704 False 2247.00 5108 92.536667 540 6339 3 chr2B.!!$F4 5799
4 TraesCS2D01G332500 chr2B 500990378 500990920 542 False 835.00 835 94.343000 1 548 1 chr2B.!!$F1 547
5 TraesCS2D01G332500 chr2B 501937882 501938393 511 False 675.00 675 90.244000 6616 7145 1 chr2B.!!$F3 529
6 TraesCS2D01G332500 chr2B 501134705 501135270 565 False 597.00 597 85.814000 6579 7145 1 chr2B.!!$F2 566
7 TraesCS2D01G332500 chr2B 501341265 501342410 1145 False 507.00 1051 90.671667 5340 6616 3 chr2B.!!$F5 1276
8 TraesCS2D01G332500 chr2A 562599327 562607101 7774 True 1162.25 3731 94.430250 1 7145 8 chr2A.!!$R2 7144
9 TraesCS2D01G332500 chr7D 576643956 576645038 1082 False 1668.00 1668 94.659000 3995 5065 1 chr7D.!!$F3 1070
10 TraesCS2D01G332500 chr7D 145918967 145920055 1088 False 1661.00 1661 94.490000 3996 5065 1 chr7D.!!$F2 1069
11 TraesCS2D01G332500 chr7D 616464828 616465914 1086 False 1631.00 1631 94.037000 3997 5066 1 chr7D.!!$F4 1069
12 TraesCS2D01G332500 chr7D 21001734 21002329 595 False 846.00 846 92.797000 3997 4575 1 chr7D.!!$F1 578
13 TraesCS2D01G332500 chr6D 446133056 446134150 1094 False 1655.00 1655 94.182000 4004 5084 1 chr6D.!!$F7 1080
14 TraesCS2D01G332500 chr6D 464696082 464697145 1063 True 1539.00 1539 92.831000 3996 5065 1 chr6D.!!$R5 1069
15 TraesCS2D01G332500 chr6D 262268939 262269446 507 False 346.00 346 79.183000 2285 2792 1 chr6D.!!$F6 507
16 TraesCS2D01G332500 chr6B 626809160 626810242 1082 False 1635.00 1635 94.118000 3987 5058 1 chr6B.!!$F1 1071
17 TraesCS2D01G332500 chr6B 348706110 348706617 507 True 357.00 357 79.572000 2285 2792 1 chr6B.!!$R1 507
18 TraesCS2D01G332500 chr3B 49155555 49156624 1069 False 1604.00 1604 93.686000 3996 5069 1 chr3B.!!$F1 1073
19 TraesCS2D01G332500 chr1D 467389058 467390142 1084 True 1602.00 1602 93.560000 3997 5066 1 chr1D.!!$R1 1069
20 TraesCS2D01G332500 chr5D 432173410 432174478 1068 False 1533.00 1533 92.692000 3997 5062 1 chr5D.!!$F3 1065
21 TraesCS2D01G332500 chr1B 596926662 596927665 1003 True 1160.00 1160 87.683000 4042 5050 1 chr1B.!!$R1 1008
22 TraesCS2D01G332500 chr7B 687100549 687101499 950 False 872.00 872 83.301000 4004 5016 1 chr7B.!!$F2 1012
23 TraesCS2D01G332500 chr6A 322999879 323000386 507 True 363.00 363 79.767000 2285 2792 1 chr6A.!!$R1 507

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
637 1240 0.110104 GAGGAGAGGCATCAATGGGG 59.890 60.0 0.00 0.0 0.00 4.96 F
640 1243 0.110104 GAGAGGCATCAATGGGGGAG 59.890 60.0 0.00 0.0 0.00 4.30 F
763 1371 0.326618 TCCCCTCCACCATTCCTCTC 60.327 60.0 0.00 0.0 0.00 3.20 F
1413 2036 1.111715 GCTGGATTGGAAGATGGGGC 61.112 60.0 0.00 0.0 0.00 5.80 F
2781 3408 0.389948 CCGTTACGCCTTCAGAAGCT 60.390 55.0 4.41 0.0 0.00 3.74 F
3308 4007 0.253044 GAGATTACCCAGGCTGCACA 59.747 55.0 9.56 0.0 0.00 4.57 F
4309 5071 0.038892 CTGCCAGTTGCCATGTGTTC 60.039 55.0 0.00 0.0 40.16 3.18 F
5740 6572 0.561184 ATACTCCCTCCGTCCCATGA 59.439 55.0 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2605 0.259938 GCCCCCTTCCTCATCACAAT 59.740 55.000 0.00 0.00 0.00 2.71 R
1979 2606 1.139498 TGCCCCCTTCCTCATCACAA 61.139 55.000 0.00 0.00 0.00 3.33 R
2749 3376 2.268298 CGTAACGGGGAAATCAGTCAG 58.732 52.381 0.00 0.00 0.00 3.51 R
3281 3980 1.207791 CTGGGTAATCTCCACTGGCT 58.792 55.000 0.00 0.00 0.00 4.75 R
4309 5071 1.198408 CAGTTGCCATGTACACTGCAG 59.802 52.381 13.48 13.48 34.81 4.41 R
5034 5857 1.466192 CGACGATAACTGCCACACGTA 60.466 52.381 0.00 0.00 34.26 3.57 R
5797 6629 0.033306 AGGAACTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 46.81 4.79 R
6754 8275 1.291877 GCCGTGAGCCAGTGTTGTAG 61.292 60.000 0.00 0.00 34.35 2.74 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
153 159 1.513160 GCGCGTCTGTCTCTCTCAC 60.513 63.158 8.43 0.00 0.00 3.51
166 172 3.706373 CTCACTGACGGGTGGGGG 61.706 72.222 5.80 0.00 37.75 5.40
197 203 0.682209 ACCTGTCGGCGTACTACCAT 60.682 55.000 6.85 0.00 0.00 3.55
320 326 2.004808 CTACTGCCGCCGTCTCATCA 62.005 60.000 0.00 0.00 0.00 3.07
460 1054 9.961265 ACTAGTTTTATTCAAGGTAAAAAGTGC 57.039 29.630 0.00 0.00 34.05 4.40
461 1055 9.406828 CTAGTTTTATTCAAGGTAAAAAGTGCC 57.593 33.333 0.00 0.00 34.05 5.01
507 1103 1.734047 GCACTAGCTCTCACTTCACCG 60.734 57.143 0.00 0.00 37.91 4.94
581 1184 2.236223 CTGACTGGGATCGCAGCTGT 62.236 60.000 32.93 19.00 0.00 4.40
627 1230 2.730524 GCCAGTCCTGAGGAGAGGC 61.731 68.421 23.35 23.35 42.70 4.70
635 1238 1.202782 CCTGAGGAGAGGCATCAATGG 60.203 57.143 0.00 0.00 36.79 3.16
636 1239 0.841961 TGAGGAGAGGCATCAATGGG 59.158 55.000 0.00 0.00 33.80 4.00
637 1240 0.110104 GAGGAGAGGCATCAATGGGG 59.890 60.000 0.00 0.00 0.00 4.96
638 1241 1.152368 GGAGAGGCATCAATGGGGG 59.848 63.158 0.00 0.00 0.00 5.40
639 1242 1.355718 GGAGAGGCATCAATGGGGGA 61.356 60.000 0.00 0.00 0.00 4.81
640 1243 0.110104 GAGAGGCATCAATGGGGGAG 59.890 60.000 0.00 0.00 0.00 4.30
763 1371 0.326618 TCCCCTCCACCATTCCTCTC 60.327 60.000 0.00 0.00 0.00 3.20
1051 1673 2.029073 CCGTCGTGTTGCTCTGGT 59.971 61.111 0.00 0.00 0.00 4.00
1161 1783 1.775039 TTTGTGCGTGCTCTGTCTGC 61.775 55.000 0.00 0.00 0.00 4.26
1373 1996 5.237048 TCATTTTTGCACTCATTTTAGGCC 58.763 37.500 0.00 0.00 0.00 5.19
1413 2036 1.111715 GCTGGATTGGAAGATGGGGC 61.112 60.000 0.00 0.00 0.00 5.80
1439 2062 3.937814 CCAAATTAGCTTTTTGGGGGTC 58.062 45.455 23.57 0.00 46.12 4.46
1521 2144 3.710677 AGCTTCTGGAGATCAAGCAGTAT 59.289 43.478 14.90 0.00 44.24 2.12
1528 2151 8.568676 TCTGGAGATCAAGCAGTATATACTAC 57.431 38.462 15.03 9.92 34.13 2.73
1529 2152 7.334671 TCTGGAGATCAAGCAGTATATACTACG 59.665 40.741 15.03 5.55 34.13 3.51
1531 2154 8.098912 TGGAGATCAAGCAGTATATACTACGTA 58.901 37.037 15.03 0.00 34.13 3.57
1538 2161 9.222916 CAAGCAGTATATACTACGTATATGTGC 57.777 37.037 15.03 21.15 43.55 4.57
1601 2224 4.778213 TTATGATCTGGTCCTTCCAAGG 57.222 45.455 0.00 0.00 46.59 3.61
1607 2230 2.039879 TCTGGTCCTTCCAAGGCTAAAC 59.960 50.000 0.00 0.00 46.59 2.01
1874 2498 2.584143 GGCGTATCGACAACGGGG 60.584 66.667 19.98 0.00 40.64 5.73
1935 2562 4.569943 AGTGTCTTGTAAGTGCTACCATG 58.430 43.478 0.00 0.00 0.00 3.66
1959 2586 7.977904 TGCTGTGATAATGTTACTGAAGATTG 58.022 34.615 0.00 0.00 31.41 2.67
1960 2587 7.066163 TGCTGTGATAATGTTACTGAAGATTGG 59.934 37.037 0.00 0.00 31.41 3.16
1961 2588 7.280876 GCTGTGATAATGTTACTGAAGATTGGA 59.719 37.037 0.00 0.00 31.41 3.53
1962 2589 9.334947 CTGTGATAATGTTACTGAAGATTGGAT 57.665 33.333 0.00 0.00 31.41 3.41
1963 2590 9.330063 TGTGATAATGTTACTGAAGATTGGATC 57.670 33.333 0.00 0.00 31.41 3.36
1964 2591 9.553064 GTGATAATGTTACTGAAGATTGGATCT 57.447 33.333 0.00 0.00 42.61 2.75
1976 2603 5.171339 AGATTGGATCTTGTAGTGCTTGT 57.829 39.130 0.00 0.00 35.76 3.16
1977 2604 5.564550 AGATTGGATCTTGTAGTGCTTGTT 58.435 37.500 0.00 0.00 35.76 2.83
1978 2605 6.711277 AGATTGGATCTTGTAGTGCTTGTTA 58.289 36.000 0.00 0.00 35.76 2.41
1979 2606 7.341805 AGATTGGATCTTGTAGTGCTTGTTAT 58.658 34.615 0.00 0.00 35.76 1.89
2505 3132 7.378181 AGACATATGGTTCCATGTTGAAAAAC 58.622 34.615 13.86 0.00 35.55 2.43
2556 3183 4.680702 GGATACTTGTCCCGAAGAAGTAC 58.319 47.826 8.86 0.00 35.54 2.73
2749 3376 4.563976 GTGCATTTTCTGTTGATGGCATAC 59.436 41.667 0.00 0.00 0.00 2.39
2781 3408 0.389948 CCGTTACGCCTTCAGAAGCT 60.390 55.000 4.41 0.00 0.00 3.74
2826 3453 5.233476 GCCATATTGACAATGATGCAAACTG 59.767 40.000 11.05 0.00 0.00 3.16
3099 3788 7.797038 TGTCTGATGGATTATGTTTCTCATG 57.203 36.000 0.00 0.00 37.91 3.07
3117 3806 7.839680 TCTCATGCCACTCTGTTCTATATTA 57.160 36.000 0.00 0.00 0.00 0.98
3185 3876 9.293404 CAGATCATGGTATGTATCATTCCTTTT 57.707 33.333 0.00 0.00 0.00 2.27
3281 3980 9.753674 AAACCTCTAATTATTTCTCACAATGGA 57.246 29.630 0.00 0.00 0.00 3.41
3308 4007 0.253044 GAGATTACCCAGGCTGCACA 59.747 55.000 9.56 0.00 0.00 4.57
3777 4477 4.248859 GCTGCAGACTGATTTCTCTACAA 58.751 43.478 20.43 0.00 0.00 2.41
3928 4628 7.675619 TCAGGAATCATGATTAGCATAGAGGTA 59.324 37.037 20.75 0.00 34.82 3.08
4309 5071 0.038892 CTGCCAGTTGCCATGTGTTC 60.039 55.000 0.00 0.00 40.16 3.18
4342 5104 1.301677 GCAACTGCCCTAGTGTGCTC 61.302 60.000 0.00 0.00 40.26 4.26
4468 5242 4.527038 ACTCTCTCTTTTACCCGAACATGA 59.473 41.667 0.00 0.00 0.00 3.07
4544 5332 4.886579 AGGTTTTCAAATCATGGCAACTC 58.113 39.130 0.00 0.00 37.61 3.01
4634 5422 6.308015 TCATGGCAACTATAGTAAACCAGT 57.692 37.500 20.08 10.40 31.05 4.00
5034 5857 1.607612 CAGACCCCTTAACGCCCAT 59.392 57.895 0.00 0.00 0.00 4.00
5073 5896 8.889849 ATCGTCGTCCTAAATTATTTGTTTTG 57.110 30.769 0.00 0.00 0.00 2.44
5074 5897 7.863666 TCGTCGTCCTAAATTATTTGTTTTGT 58.136 30.769 0.00 0.00 0.00 2.83
5142 5974 8.256611 TCTAAAATGCATGTTCTTACTGAGTC 57.743 34.615 5.08 0.00 0.00 3.36
5162 5994 5.688807 AGTCCCAGAAATAGGATCATGTTG 58.311 41.667 0.00 0.00 0.00 3.33
5332 6164 0.868406 GCTCGGTTCTGGTGAAGTTG 59.132 55.000 0.00 0.00 32.15 3.16
5350 6182 5.520376 AGTTGAAGCAGCAAACAAAGTAT 57.480 34.783 0.00 0.00 0.00 2.12
5356 6188 3.254166 AGCAGCAAACAAAGTATGACCTG 59.746 43.478 0.00 0.00 0.00 4.00
5443 6275 1.361668 CCGATGCCGTTTCTGTGGAG 61.362 60.000 0.00 0.00 0.00 3.86
5533 6365 2.196925 CGCCGGGCTCTCAGTCTAT 61.197 63.158 18.34 0.00 0.00 1.98
5541 6373 2.035321 GGCTCTCAGTCTATGCCTACAC 59.965 54.545 0.00 0.00 40.36 2.90
5542 6374 2.955660 GCTCTCAGTCTATGCCTACACT 59.044 50.000 0.00 0.00 0.00 3.55
5561 6393 4.271049 ACACTCTCATGAACGAGTTTGTTG 59.729 41.667 13.45 6.47 38.37 3.33
5716 6548 2.274542 TCCTTGCATTGTCCCTCCTAA 58.725 47.619 0.00 0.00 0.00 2.69
5722 6554 5.912149 TGCATTGTCCCTCCTAAATAGAT 57.088 39.130 0.00 0.00 0.00 1.98
5723 6555 7.387265 TTGCATTGTCCCTCCTAAATAGATA 57.613 36.000 0.00 0.00 0.00 1.98
5724 6556 6.769512 TGCATTGTCCCTCCTAAATAGATAC 58.230 40.000 0.00 0.00 0.00 2.24
5725 6557 6.558775 TGCATTGTCCCTCCTAAATAGATACT 59.441 38.462 0.00 0.00 0.00 2.12
5726 6558 7.100409 GCATTGTCCCTCCTAAATAGATACTC 58.900 42.308 0.00 0.00 0.00 2.59
5727 6559 7.616313 CATTGTCCCTCCTAAATAGATACTCC 58.384 42.308 0.00 0.00 0.00 3.85
5728 6560 5.652324 TGTCCCTCCTAAATAGATACTCCC 58.348 45.833 0.00 0.00 0.00 4.30
5729 6561 5.378985 TGTCCCTCCTAAATAGATACTCCCT 59.621 44.000 0.00 0.00 0.00 4.20
5730 6562 5.953548 GTCCCTCCTAAATAGATACTCCCTC 59.046 48.000 0.00 0.00 0.00 4.30
5731 6563 5.016459 TCCCTCCTAAATAGATACTCCCTCC 59.984 48.000 0.00 0.00 0.00 4.30
5732 6564 4.951094 CCTCCTAAATAGATACTCCCTCCG 59.049 50.000 0.00 0.00 0.00 4.63
5733 6565 5.516945 CCTCCTAAATAGATACTCCCTCCGT 60.517 48.000 0.00 0.00 0.00 4.69
5734 6566 5.568392 TCCTAAATAGATACTCCCTCCGTC 58.432 45.833 0.00 0.00 0.00 4.79
5735 6567 4.705991 CCTAAATAGATACTCCCTCCGTCC 59.294 50.000 0.00 0.00 0.00 4.79
5736 6568 2.903375 ATAGATACTCCCTCCGTCCC 57.097 55.000 0.00 0.00 0.00 4.46
5737 6569 1.526315 TAGATACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
5738 6570 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
5739 6571 0.969894 GATACTCCCTCCGTCCCATG 59.030 60.000 0.00 0.00 0.00 3.66
5740 6572 0.561184 ATACTCCCTCCGTCCCATGA 59.439 55.000 0.00 0.00 0.00 3.07
5741 6573 0.561184 TACTCCCTCCGTCCCATGAT 59.439 55.000 0.00 0.00 0.00 2.45
5742 6574 0.561184 ACTCCCTCCGTCCCATGATA 59.439 55.000 0.00 0.00 0.00 2.15
5743 6575 1.150135 ACTCCCTCCGTCCCATGATAT 59.850 52.381 0.00 0.00 0.00 1.63
5744 6576 2.382305 ACTCCCTCCGTCCCATGATATA 59.618 50.000 0.00 0.00 0.00 0.86
5745 6577 3.181410 ACTCCCTCCGTCCCATGATATAA 60.181 47.826 0.00 0.00 0.00 0.98
5746 6578 3.441101 TCCCTCCGTCCCATGATATAAG 58.559 50.000 0.00 0.00 0.00 1.73
5747 6579 3.076937 TCCCTCCGTCCCATGATATAAGA 59.923 47.826 0.00 0.00 0.00 2.10
5748 6580 3.838317 CCCTCCGTCCCATGATATAAGAA 59.162 47.826 0.00 0.00 0.00 2.52
5749 6581 4.322801 CCCTCCGTCCCATGATATAAGAAC 60.323 50.000 0.00 0.00 0.00 3.01
5750 6582 4.486090 CTCCGTCCCATGATATAAGAACG 58.514 47.826 0.00 0.00 0.00 3.95
5751 6583 3.893200 TCCGTCCCATGATATAAGAACGT 59.107 43.478 0.00 0.00 0.00 3.99
5752 6584 4.342951 TCCGTCCCATGATATAAGAACGTT 59.657 41.667 0.00 0.00 0.00 3.99
5753 6585 5.054477 CCGTCCCATGATATAAGAACGTTT 58.946 41.667 0.46 0.00 0.00 3.60
5754 6586 5.526111 CCGTCCCATGATATAAGAACGTTTT 59.474 40.000 0.46 0.00 0.00 2.43
5755 6587 6.037830 CCGTCCCATGATATAAGAACGTTTTT 59.962 38.462 9.22 9.22 0.00 1.94
5756 6588 6.905076 CGTCCCATGATATAAGAACGTTTTTG 59.095 38.462 13.87 0.00 0.00 2.44
5757 6589 7.201574 CGTCCCATGATATAAGAACGTTTTTGA 60.202 37.037 13.87 2.81 0.00 2.69
5758 6590 7.908601 GTCCCATGATATAAGAACGTTTTTGAC 59.091 37.037 13.87 5.89 0.00 3.18
5759 6591 7.608376 TCCCATGATATAAGAACGTTTTTGACA 59.392 33.333 13.87 8.67 0.00 3.58
5760 6592 7.696453 CCCATGATATAAGAACGTTTTTGACAC 59.304 37.037 13.87 4.54 0.00 3.67
5761 6593 8.450964 CCATGATATAAGAACGTTTTTGACACT 58.549 33.333 13.87 0.00 0.00 3.55
5764 6596 9.478768 TGATATAAGAACGTTTTTGACACTACA 57.521 29.630 13.87 3.34 0.00 2.74
5765 6597 9.737025 GATATAAGAACGTTTTTGACACTACAC 57.263 33.333 13.87 0.00 0.00 2.90
5766 6598 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
5767 6599 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
5768 6600 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
5769 6601 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
5770 6602 6.815142 AGAACGTTTTTGACACTACACTAGTT 59.185 34.615 0.46 0.00 36.76 2.24
5771 6603 7.975616 AGAACGTTTTTGACACTACACTAGTTA 59.024 33.333 0.46 0.00 36.76 2.24
5772 6604 7.689953 ACGTTTTTGACACTACACTAGTTAG 57.310 36.000 0.00 1.76 36.76 2.34
5773 6605 7.260603 ACGTTTTTGACACTACACTAGTTAGT 58.739 34.615 10.24 10.24 36.76 2.24
5788 6620 8.663771 CACTAGTTAGTGTCAAAAACGTTTTT 57.336 30.769 28.62 28.62 46.51 1.94
5789 6621 9.757859 CACTAGTTAGTGTCAAAAACGTTTTTA 57.242 29.630 32.12 18.43 46.51 1.52
5797 6629 9.405587 AGTGTCAAAAACGTTTTTATATCATGG 57.594 29.630 32.12 19.85 38.23 3.66
5798 6630 8.643752 GTGTCAAAAACGTTTTTATATCATGGG 58.356 33.333 32.12 19.25 38.23 4.00
5799 6631 8.577296 TGTCAAAAACGTTTTTATATCATGGGA 58.423 29.630 32.12 20.87 38.23 4.37
5800 6632 8.856247 GTCAAAAACGTTTTTATATCATGGGAC 58.144 33.333 32.12 25.97 38.23 4.46
5801 6633 7.751348 TCAAAAACGTTTTTATATCATGGGACG 59.249 33.333 32.12 18.06 38.23 4.79
5802 6634 5.744666 AACGTTTTTATATCATGGGACGG 57.255 39.130 0.00 0.00 33.95 4.79
5803 6635 5.026038 ACGTTTTTATATCATGGGACGGA 57.974 39.130 0.00 0.00 33.95 4.69
5804 6636 5.054477 ACGTTTTTATATCATGGGACGGAG 58.946 41.667 0.00 0.00 33.95 4.63
5805 6637 4.451096 CGTTTTTATATCATGGGACGGAGG 59.549 45.833 0.00 0.00 0.00 4.30
5806 6638 4.634012 TTTTATATCATGGGACGGAGGG 57.366 45.455 0.00 0.00 0.00 4.30
5807 6639 3.553375 TTATATCATGGGACGGAGGGA 57.447 47.619 0.00 0.00 0.00 4.20
5808 6640 1.944177 ATATCATGGGACGGAGGGAG 58.056 55.000 0.00 0.00 0.00 4.30
5840 6672 2.957402 TCCCAGCAGTTTTGAGTCAT 57.043 45.000 0.00 0.00 0.00 3.06
6128 6960 0.673644 ACCTTAGCGATGCTTTGCGT 60.674 50.000 6.20 0.00 40.44 5.24
6339 7175 2.758979 TCCTCTTATGTTCTGGACCGAC 59.241 50.000 0.00 0.00 0.00 4.79
6432 7947 9.817809 ATAAGATCGAACTTCTGCAATAAACTA 57.182 29.630 11.58 0.00 0.00 2.24
6433 7948 7.527084 AGATCGAACTTCTGCAATAAACTAC 57.473 36.000 0.00 0.00 0.00 2.73
6434 7949 7.097192 AGATCGAACTTCTGCAATAAACTACA 58.903 34.615 0.00 0.00 0.00 2.74
6435 7950 7.602644 AGATCGAACTTCTGCAATAAACTACAA 59.397 33.333 0.00 0.00 0.00 2.41
6436 7951 7.667043 TCGAACTTCTGCAATAAACTACAAT 57.333 32.000 0.00 0.00 0.00 2.71
6437 7952 7.518161 TCGAACTTCTGCAATAAACTACAATG 58.482 34.615 0.00 0.00 0.00 2.82
6516 8031 7.124573 AGTATTCCTTTGCAAGTTTTTCCTT 57.875 32.000 0.00 0.00 0.00 3.36
6809 8330 0.394352 CGGAGACTGGATTTTGGGGG 60.394 60.000 0.00 0.00 0.00 5.40
7011 8532 8.630054 TTTAGGAGCTTATTTAAACTTGCTCA 57.370 30.769 25.63 13.08 45.87 4.26
7012 8533 8.807948 TTAGGAGCTTATTTAAACTTGCTCAT 57.192 30.769 25.63 23.20 45.87 2.90
7068 8589 6.607019 ACCAAAGTTTAGGATTGGAGTTACA 58.393 36.000 10.50 0.00 45.14 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.848886 AAATCCCACTCCCACCCGAC 61.849 60.000 0.00 0.00 0.00 4.79
37 38 1.540367 AAATCCCACTCCCACCCGA 60.540 57.895 0.00 0.00 0.00 5.14
38 39 1.077716 GAAATCCCACTCCCACCCG 60.078 63.158 0.00 0.00 0.00 5.28
197 203 0.036765 GTGATTACAGCGGTCACCCA 60.037 55.000 0.00 0.00 37.00 4.51
368 374 0.861837 CCACTTGACGAGCAACAGTC 59.138 55.000 0.00 0.00 37.85 3.51
460 1054 1.421410 CCTCCTTTTCGCGACGATGG 61.421 60.000 9.15 12.55 35.23 3.51
461 1055 1.421410 CCCTCCTTTTCGCGACGATG 61.421 60.000 9.15 2.79 35.23 3.84
507 1103 0.531974 TGTCAGGTTCGTTCAGCCAC 60.532 55.000 0.00 0.00 0.00 5.01
627 1230 1.701024 TCCCCCTCCCCCATTGATG 60.701 63.158 0.00 0.00 0.00 3.07
635 1238 4.862823 CTCTCCGTCCCCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
636 1239 4.862823 CCTCTCCGTCCCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
638 1241 4.779733 TGCCTCTCCGTCCCCCTC 62.780 72.222 0.00 0.00 0.00 4.30
639 1242 4.787280 CTGCCTCTCCGTCCCCCT 62.787 72.222 0.00 0.00 0.00 4.79
829 1437 0.393808 GTGCTGGATTTAAGCCCCGA 60.394 55.000 0.00 0.00 40.06 5.14
1107 1729 4.111053 GAGGGAGCCCGGGGAAAC 62.111 72.222 25.28 4.90 41.95 2.78
1161 1783 3.624900 TCTGTAAATAATCGACGCGGAG 58.375 45.455 12.47 3.43 0.00 4.63
1373 1996 1.277557 ACTCCTGAGGCACTGCTAAAG 59.722 52.381 0.00 0.00 41.55 1.85
1439 2062 3.976942 GCTGAAAACAGCAACTGTATGTG 59.023 43.478 15.78 0.00 44.62 3.21
1538 2161 3.130869 AGAGATGTGTAGAGCTGCTCAAG 59.869 47.826 29.49 0.00 32.06 3.02
1601 2224 6.620678 TGAAACATCAAGCCTATTGTTTAGC 58.379 36.000 5.68 0.00 41.10 3.09
1607 2230 3.444742 TGCCTGAAACATCAAGCCTATTG 59.555 43.478 0.00 0.00 0.00 1.90
1715 2339 0.667792 GGATTGTATCGGGCGAGCTC 60.668 60.000 2.73 2.73 0.00 4.09
1739 2363 4.693532 GTCAGCCGGACATCACAA 57.306 55.556 5.05 0.00 46.19 3.33
1781 2405 2.325583 TGTCCATCTTAATGTCCGGC 57.674 50.000 0.00 0.00 0.00 6.13
1874 2498 0.963962 TGTAGTCCACGGAGAACCAC 59.036 55.000 0.00 0.00 35.59 4.16
1935 2562 7.280876 TCCAATCTTCAGTAACATTATCACAGC 59.719 37.037 0.00 0.00 0.00 4.40
1959 2586 6.371548 TCACAATAACAAGCACTACAAGATCC 59.628 38.462 0.00 0.00 0.00 3.36
1960 2587 7.364522 TCACAATAACAAGCACTACAAGATC 57.635 36.000 0.00 0.00 0.00 2.75
1961 2588 7.607607 TCATCACAATAACAAGCACTACAAGAT 59.392 33.333 0.00 0.00 0.00 2.40
1962 2589 6.934083 TCATCACAATAACAAGCACTACAAGA 59.066 34.615 0.00 0.00 0.00 3.02
1963 2590 7.132694 TCATCACAATAACAAGCACTACAAG 57.867 36.000 0.00 0.00 0.00 3.16
1964 2591 6.149308 CCTCATCACAATAACAAGCACTACAA 59.851 38.462 0.00 0.00 0.00 2.41
1965 2592 5.643348 CCTCATCACAATAACAAGCACTACA 59.357 40.000 0.00 0.00 0.00 2.74
1966 2593 5.874810 TCCTCATCACAATAACAAGCACTAC 59.125 40.000 0.00 0.00 0.00 2.73
1967 2594 6.048732 TCCTCATCACAATAACAAGCACTA 57.951 37.500 0.00 0.00 0.00 2.74
1968 2595 4.910195 TCCTCATCACAATAACAAGCACT 58.090 39.130 0.00 0.00 0.00 4.40
1969 2596 5.392380 CCTTCCTCATCACAATAACAAGCAC 60.392 44.000 0.00 0.00 0.00 4.40
1970 2597 4.701651 CCTTCCTCATCACAATAACAAGCA 59.298 41.667 0.00 0.00 0.00 3.91
1971 2598 4.096984 CCCTTCCTCATCACAATAACAAGC 59.903 45.833 0.00 0.00 0.00 4.01
1972 2599 4.641989 CCCCTTCCTCATCACAATAACAAG 59.358 45.833 0.00 0.00 0.00 3.16
1973 2600 4.569653 CCCCCTTCCTCATCACAATAACAA 60.570 45.833 0.00 0.00 0.00 2.83
1974 2601 3.053693 CCCCCTTCCTCATCACAATAACA 60.054 47.826 0.00 0.00 0.00 2.41
1975 2602 3.555966 CCCCCTTCCTCATCACAATAAC 58.444 50.000 0.00 0.00 0.00 1.89
1976 2603 2.091885 GCCCCCTTCCTCATCACAATAA 60.092 50.000 0.00 0.00 0.00 1.40
1977 2604 1.494721 GCCCCCTTCCTCATCACAATA 59.505 52.381 0.00 0.00 0.00 1.90
1978 2605 0.259938 GCCCCCTTCCTCATCACAAT 59.740 55.000 0.00 0.00 0.00 2.71
1979 2606 1.139498 TGCCCCCTTCCTCATCACAA 61.139 55.000 0.00 0.00 0.00 3.33
2005 2632 2.959465 AGAGGGGTCAAACAAGAAGG 57.041 50.000 0.00 0.00 0.00 3.46
2505 3132 9.241317 GATGCAAATGTCTTGATAAATGTAAGG 57.759 33.333 0.00 0.00 0.00 2.69
2556 3183 3.344703 TGGTGAAACAGGCCAGATG 57.655 52.632 5.01 0.00 39.98 2.90
2749 3376 2.268298 CGTAACGGGGAAATCAGTCAG 58.732 52.381 0.00 0.00 0.00 3.51
2826 3453 4.684484 ATTTTGATACGGAGGGAGTACC 57.316 45.455 0.00 0.00 40.67 3.34
2945 3582 2.781174 ACCAACTCCAGTACCAAAGGAA 59.219 45.455 0.00 0.00 0.00 3.36
3034 3723 9.382275 AGAATTAAACACAAAATGAAGTTTGCT 57.618 25.926 3.32 0.00 41.33 3.91
3099 3788 8.768955 CAAAGACATAATATAGAACAGAGTGGC 58.231 37.037 0.00 0.00 0.00 5.01
3117 3806 2.804212 GCAAAACAGCCTGCAAAGACAT 60.804 45.455 0.00 0.00 38.48 3.06
3185 3876 9.480053 GAACATGAAGAATGAAAAAGATGGAAA 57.520 29.630 0.00 0.00 38.72 3.13
3281 3980 1.207791 CTGGGTAATCTCCACTGGCT 58.792 55.000 0.00 0.00 0.00 4.75
3642 4342 5.010112 TGAGCCGATTTAGAGTCAGATAAGG 59.990 44.000 0.00 0.00 0.00 2.69
3777 4477 3.181450 GGTAGATATCTTGGCTGCAAGGT 60.181 47.826 11.25 2.54 33.26 3.50
3960 4711 3.503363 ACACGCAATCTCATCACAATGTT 59.497 39.130 0.00 0.00 34.32 2.71
3961 4712 3.076621 ACACGCAATCTCATCACAATGT 58.923 40.909 0.00 0.00 34.32 2.71
3973 4725 5.942325 AACACAAGTAAAAACACGCAATC 57.058 34.783 0.00 0.00 0.00 2.67
4309 5071 1.198408 CAGTTGCCATGTACACTGCAG 59.802 52.381 13.48 13.48 34.81 4.41
4342 5104 2.015736 AGAGTTGCCATCTGCTTACG 57.984 50.000 0.00 0.00 42.00 3.18
4468 5242 1.796459 CCGTGTAGCGCTACAAAAAGT 59.204 47.619 42.80 8.61 46.33 2.66
4567 5355 6.103997 GCCACATACTAACACTAAGCAGTTA 58.896 40.000 0.00 0.00 30.46 2.24
5034 5857 1.466192 CGACGATAACTGCCACACGTA 60.466 52.381 0.00 0.00 34.26 3.57
5086 5909 5.049474 TCGTTAGATGGCATGCAATACATTC 60.049 40.000 21.36 1.80 36.64 2.67
5087 5910 4.821260 TCGTTAGATGGCATGCAATACATT 59.179 37.500 21.36 3.21 36.64 2.71
5088 5911 4.388485 TCGTTAGATGGCATGCAATACAT 58.612 39.130 21.36 13.41 40.66 2.29
5090 5913 4.811555 TTCGTTAGATGGCATGCAATAC 57.188 40.909 21.36 8.21 0.00 1.89
5142 5974 5.439721 TGACAACATGATCCTATTTCTGGG 58.560 41.667 0.00 0.00 0.00 4.45
5332 6164 4.022849 AGGTCATACTTTGTTTGCTGCTTC 60.023 41.667 0.00 0.00 0.00 3.86
5350 6182 4.224818 TCATTGATCATGTACACCAGGTCA 59.775 41.667 0.00 0.25 34.06 4.02
5356 6188 6.539826 TGACATCTTCATTGATCATGTACACC 59.460 38.462 0.00 0.00 34.06 4.16
5443 6275 1.072331 TCAGGGAAAACAGAGCTGGTC 59.928 52.381 0.00 0.00 34.19 4.02
5527 6359 4.797743 TCATGAGAGTGTAGGCATAGACT 58.202 43.478 8.03 8.03 38.18 3.24
5533 6365 2.164422 CTCGTTCATGAGAGTGTAGGCA 59.836 50.000 0.00 0.00 38.28 4.75
5541 6373 3.496130 AGCAACAAACTCGTTCATGAGAG 59.504 43.478 9.77 9.77 39.35 3.20
5542 6374 3.466836 AGCAACAAACTCGTTCATGAGA 58.533 40.909 2.93 0.00 39.35 3.27
5561 6393 2.159170 AGAAGAAGTCGTATGGCTGAGC 60.159 50.000 0.00 0.00 0.00 4.26
5597 6429 4.070716 CCCTGAACATAGGCAATGATCTC 58.929 47.826 5.38 0.86 38.03 2.75
5716 6548 2.449730 TGGGACGGAGGGAGTATCTATT 59.550 50.000 0.00 0.00 33.73 1.73
5722 6554 0.561184 ATCATGGGACGGAGGGAGTA 59.439 55.000 0.00 0.00 0.00 2.59
5723 6555 0.561184 TATCATGGGACGGAGGGAGT 59.439 55.000 0.00 0.00 0.00 3.85
5724 6556 1.944177 ATATCATGGGACGGAGGGAG 58.056 55.000 0.00 0.00 0.00 4.30
5725 6557 3.076937 TCTTATATCATGGGACGGAGGGA 59.923 47.826 0.00 0.00 0.00 4.20
5726 6558 3.441101 TCTTATATCATGGGACGGAGGG 58.559 50.000 0.00 0.00 0.00 4.30
5727 6559 4.618460 CGTTCTTATATCATGGGACGGAGG 60.618 50.000 0.00 0.00 0.00 4.30
5728 6560 4.022242 ACGTTCTTATATCATGGGACGGAG 60.022 45.833 3.74 0.00 0.00 4.63
5729 6561 3.893200 ACGTTCTTATATCATGGGACGGA 59.107 43.478 3.74 0.00 0.00 4.69
5730 6562 4.252971 ACGTTCTTATATCATGGGACGG 57.747 45.455 3.74 0.00 0.00 4.79
5731 6563 6.598753 AAAACGTTCTTATATCATGGGACG 57.401 37.500 0.00 0.00 0.00 4.79
5732 6564 7.908601 GTCAAAAACGTTCTTATATCATGGGAC 59.091 37.037 0.00 0.00 0.00 4.46
5733 6565 7.608376 TGTCAAAAACGTTCTTATATCATGGGA 59.392 33.333 0.00 0.00 0.00 4.37
5734 6566 7.696453 GTGTCAAAAACGTTCTTATATCATGGG 59.304 37.037 0.00 0.00 0.00 4.00
5735 6567 8.450964 AGTGTCAAAAACGTTCTTATATCATGG 58.549 33.333 0.00 0.00 0.00 3.66
5738 6570 9.478768 TGTAGTGTCAAAAACGTTCTTATATCA 57.521 29.630 0.00 0.00 0.00 2.15
5739 6571 9.737025 GTGTAGTGTCAAAAACGTTCTTATATC 57.263 33.333 0.00 0.00 0.00 1.63
5740 6572 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
5741 6573 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
5742 6574 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
5743 6575 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
5744 6576 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
5745 6577 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
5746 6578 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
5747 6579 6.973229 AACTAGTGTAGTGTCAAAAACGTT 57.027 33.333 0.00 0.00 39.39 3.99
5748 6580 7.221452 CACTAACTAGTGTAGTGTCAAAAACGT 59.779 37.037 23.28 0.00 46.51 3.99
5749 6581 7.553034 CACTAACTAGTGTAGTGTCAAAAACG 58.447 38.462 23.28 7.45 46.51 3.60
5763 6595 8.663771 AAAAACGTTTTTGACACTAACTAGTG 57.336 30.769 32.14 14.06 46.15 2.74
5771 6603 9.405587 CCATGATATAAAAACGTTTTTGACACT 57.594 29.630 36.92 21.88 40.33 3.55
5772 6604 8.643752 CCCATGATATAAAAACGTTTTTGACAC 58.356 33.333 36.92 26.78 40.33 3.67
5773 6605 8.577296 TCCCATGATATAAAAACGTTTTTGACA 58.423 29.630 36.92 29.42 40.33 3.58
5774 6606 8.856247 GTCCCATGATATAAAAACGTTTTTGAC 58.144 33.333 36.92 28.43 40.33 3.18
5775 6607 7.751348 CGTCCCATGATATAAAAACGTTTTTGA 59.249 33.333 36.92 27.73 40.33 2.69
5776 6608 7.008810 CCGTCCCATGATATAAAAACGTTTTTG 59.991 37.037 36.92 24.07 40.33 2.44
5777 6609 7.030768 CCGTCCCATGATATAAAAACGTTTTT 58.969 34.615 33.94 33.94 42.51 1.94
5778 6610 6.374894 TCCGTCCCATGATATAAAAACGTTTT 59.625 34.615 20.26 20.26 0.00 2.43
5779 6611 5.881443 TCCGTCCCATGATATAAAAACGTTT 59.119 36.000 7.96 7.96 0.00 3.60
5780 6612 5.430007 TCCGTCCCATGATATAAAAACGTT 58.570 37.500 0.00 0.00 0.00 3.99
5781 6613 5.026038 TCCGTCCCATGATATAAAAACGT 57.974 39.130 0.00 0.00 0.00 3.99
5782 6614 4.451096 CCTCCGTCCCATGATATAAAAACG 59.549 45.833 0.00 0.00 0.00 3.60
5783 6615 4.760204 CCCTCCGTCCCATGATATAAAAAC 59.240 45.833 0.00 0.00 0.00 2.43
5784 6616 4.661240 TCCCTCCGTCCCATGATATAAAAA 59.339 41.667 0.00 0.00 0.00 1.94
5785 6617 4.236195 TCCCTCCGTCCCATGATATAAAA 58.764 43.478 0.00 0.00 0.00 1.52
5786 6618 3.838317 CTCCCTCCGTCCCATGATATAAA 59.162 47.826 0.00 0.00 0.00 1.40
5787 6619 3.181410 ACTCCCTCCGTCCCATGATATAA 60.181 47.826 0.00 0.00 0.00 0.98
5788 6620 2.382305 ACTCCCTCCGTCCCATGATATA 59.618 50.000 0.00 0.00 0.00 0.86
5789 6621 1.150135 ACTCCCTCCGTCCCATGATAT 59.850 52.381 0.00 0.00 0.00 1.63
5790 6622 0.561184 ACTCCCTCCGTCCCATGATA 59.439 55.000 0.00 0.00 0.00 2.15
5791 6623 0.561184 TACTCCCTCCGTCCCATGAT 59.439 55.000 0.00 0.00 0.00 2.45
5792 6624 0.106167 CTACTCCCTCCGTCCCATGA 60.106 60.000 0.00 0.00 0.00 3.07
5793 6625 0.397254 ACTACTCCCTCCGTCCCATG 60.397 60.000 0.00 0.00 0.00 3.66
5794 6626 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
5795 6627 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
5796 6628 1.042003 GGAACTACTCCCTCCGTCCC 61.042 65.000 0.00 0.00 38.44 4.46
5797 6629 0.033306 AGGAACTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 46.81 4.79
5798 6630 2.725221 TAGGAACTACTCCCTCCGTC 57.275 55.000 0.00 0.00 46.81 4.79
5840 6672 2.093816 TGCAACCACAATGTCAGCAAAA 60.094 40.909 0.00 0.00 0.00 2.44
6128 6960 2.997315 CTCAGACCGTGGCCCAGA 60.997 66.667 0.00 0.00 0.00 3.86
6339 7175 7.528307 CCTCAGAAATTCAGATTGTTGAGAAG 58.472 38.462 7.46 0.00 38.02 2.85
6432 7947 3.230134 TCTTTTGGTAGGCTTGCATTGT 58.770 40.909 0.00 0.00 0.00 2.71
6433 7948 3.940209 TCTTTTGGTAGGCTTGCATTG 57.060 42.857 0.00 0.00 0.00 2.82
6434 7949 3.897505 ACTTCTTTTGGTAGGCTTGCATT 59.102 39.130 0.00 0.00 0.00 3.56
6435 7950 3.500343 ACTTCTTTTGGTAGGCTTGCAT 58.500 40.909 0.00 0.00 0.00 3.96
6436 7951 2.944129 ACTTCTTTTGGTAGGCTTGCA 58.056 42.857 0.00 0.00 0.00 4.08
6437 7952 3.190744 GGTACTTCTTTTGGTAGGCTTGC 59.809 47.826 0.00 0.00 0.00 4.01
6516 8031 9.558396 AAAAACATAATGAAATCTTGCAAAGGA 57.442 25.926 0.00 0.00 46.24 3.36
6553 8068 4.508124 CGAAGAATACTGCCACATAGTTCC 59.492 45.833 0.00 0.00 0.00 3.62
6754 8275 1.291877 GCCGTGAGCCAGTGTTGTAG 61.292 60.000 0.00 0.00 34.35 2.74
7042 8563 7.562088 TGTAACTCCAATCCTAAACTTTGGTTT 59.438 33.333 0.00 0.00 46.06 3.27


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

AutoCloner maintained by Alex Coulton.