Multiple sequence alignment - TraesCS5D01G328700

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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 TraesCS5D01G328700 chr5D 100.000 7284 0 0 1 7284 421139948 421132665 0.000000e+00 13452.0
1 TraesCS5D01G328700 chr5D 96.833 1768 46 8 5522 7282 421160275 421158511 0.000000e+00 2946.0
2 TraesCS5D01G328700 chr5D 92.886 1223 50 14 4159 5361 470223349 470224554 0.000000e+00 1742.0
3 TraesCS5D01G328700 chr5D 90.072 1108 78 21 930 2025 421163671 421162584 0.000000e+00 1408.0
4 TraesCS5D01G328700 chr5D 93.411 774 34 6 3403 4159 421161046 421160273 0.000000e+00 1131.0
5 TraesCS5D01G328700 chr5D 90.983 743 42 15 2672 3404 421162097 421161370 0.000000e+00 977.0
6 TraesCS5D01G328700 chr5D 80.000 920 136 33 1101 2008 421090051 421089168 2.870000e-178 636.0
7 TraesCS5D01G328700 chr5D 80.374 642 104 15 3528 4151 421173102 421172465 1.110000e-127 468.0
8 TraesCS5D01G328700 chr5D 78.834 652 94 28 3518 4143 420969745 420969112 4.090000e-107 399.0
9 TraesCS5D01G328700 chr5D 80.925 519 62 20 1055 1568 420977766 420977280 6.900000e-100 375.0
10 TraesCS5D01G328700 chr5D 98.148 162 3 0 5361 5522 438326454 438326615 4.300000e-72 283.0
11 TraesCS5D01G328700 chr5D 88.172 186 18 3 2175 2356 421162581 421162396 1.230000e-52 219.0
12 TraesCS5D01G328700 chr5D 90.000 130 10 2 2348 2475 421162373 421162245 1.630000e-36 165.0
13 TraesCS5D01G328700 chr5D 81.452 124 19 4 2021 2142 9947779 9947658 1.670000e-16 99.0
14 TraesCS5D01G328700 chr5B 92.857 1708 78 18 871 2558 507187361 507189044 0.000000e+00 2438.0
15 TraesCS5D01G328700 chr5B 92.588 1511 79 13 2672 4159 507189060 507190560 0.000000e+00 2139.0
16 TraesCS5D01G328700 chr5B 89.759 1455 110 24 5604 7040 507191776 507193209 0.000000e+00 1825.0
17 TraesCS5D01G328700 chr5B 82.002 1039 130 32 983 2006 507058792 507059788 0.000000e+00 830.0
18 TraesCS5D01G328700 chr5B 83.933 890 95 23 6 883 591681777 591680924 0.000000e+00 808.0
19 TraesCS5D01G328700 chr5B 79.632 653 108 16 3519 4151 507060513 507061160 5.180000e-121 446.0
20 TraesCS5D01G328700 chr5B 93.694 111 7 0 2 112 507171286 507171396 4.520000e-37 167.0
21 TraesCS5D01G328700 chr5B 95.890 73 2 1 2601 2673 94272523 94272594 4.620000e-22 117.0
22 TraesCS5D01G328700 chr5A 94.590 1294 54 10 2829 4114 534465594 534466879 0.000000e+00 1988.0
23 TraesCS5D01G328700 chr5A 90.597 1223 95 9 927 2135 534463723 534464939 0.000000e+00 1604.0
24 TraesCS5D01G328700 chr5A 94.471 1031 45 5 5522 6547 534466943 534467966 0.000000e+00 1578.0
25 TraesCS5D01G328700 chr5A 90.212 1226 87 12 4156 5360 538526073 538524860 0.000000e+00 1568.0
26 TraesCS5D01G328700 chr5A 89.640 888 64 11 4556 5420 470180428 470181310 0.000000e+00 1105.0
27 TraesCS5D01G328700 chr5A 91.228 627 44 7 6585 7204 534467965 534468587 0.000000e+00 843.0
28 TraesCS5D01G328700 chr5A 80.452 1018 151 26 999 2002 534625495 534626478 0.000000e+00 734.0
29 TraesCS5D01G328700 chr5A 79.847 918 141 30 1098 2005 534569926 534570809 1.330000e-176 630.0
30 TraesCS5D01G328700 chr5A 86.981 530 51 9 2041 2558 534464939 534465462 1.360000e-161 580.0
31 TraesCS5D01G328700 chr5A 79.782 643 106 14 3528 4151 534372409 534373046 5.180000e-121 446.0
32 TraesCS5D01G328700 chr5A 80.366 601 88 17 3515 4101 534627509 534628093 5.220000e-116 429.0
33 TraesCS5D01G328700 chr5A 83.959 293 45 2 1715 2006 534371379 534371670 5.560000e-71 279.0
34 TraesCS5D01G328700 chr5A 100.000 71 0 0 4089 4159 534466875 534466945 1.650000e-26 132.0
35 TraesCS5D01G328700 chr5A 88.679 106 3 2 2672 2777 534465478 534465574 3.570000e-23 121.0
36 TraesCS5D01G328700 chr2D 93.987 1214 38 14 4156 5351 17211309 17212505 0.000000e+00 1805.0
37 TraesCS5D01G328700 chr2D 99.383 162 0 1 5361 5521 394235455 394235616 7.150000e-75 292.0
38 TraesCS5D01G328700 chr2D 98.765 162 2 0 5361 5522 620662568 620662407 9.250000e-74 289.0
39 TraesCS5D01G328700 chr2D 98.765 162 1 1 5361 5521 394234729 394234890 3.330000e-73 287.0
40 TraesCS5D01G328700 chr2D 98.507 67 1 0 2607 2673 2673681 2673615 1.280000e-22 119.0
41 TraesCS5D01G328700 chr2D 97.183 71 1 1 2603 2673 43966321 43966252 1.280000e-22 119.0
42 TraesCS5D01G328700 chr2D 80.769 104 16 3 2024 2126 435205897 435205997 2.180000e-10 78.7
43 TraesCS5D01G328700 chrUn 95.785 1115 39 6 5522 6631 270057902 270056791 0.000000e+00 1792.0
44 TraesCS5D01G328700 chrUn 90.072 1108 78 21 930 2025 270061298 270060211 0.000000e+00 1408.0
45 TraesCS5D01G328700 chrUn 93.411 774 34 6 3403 4159 270058673 270057900 0.000000e+00 1131.0
46 TraesCS5D01G328700 chrUn 90.983 743 42 15 2672 3404 270059724 270058997 0.000000e+00 977.0
47 TraesCS5D01G328700 chrUn 81.713 1039 133 32 983 2006 325469252 325468256 0.000000e+00 813.0
48 TraesCS5D01G328700 chrUn 83.759 665 78 22 1057 1705 396803143 396802493 2.910000e-168 603.0
49 TraesCS5D01G328700 chrUn 88.172 186 18 3 2175 2356 270060208 270060023 1.230000e-52 219.0
50 TraesCS5D01G328700 chrUn 90.000 130 10 2 2348 2475 270060000 270059872 1.630000e-36 165.0
51 TraesCS5D01G328700 chrUn 97.222 72 1 1 2602 2673 111028706 111028776 3.570000e-23 121.0
52 TraesCS5D01G328700 chr1D 92.641 1223 53 15 4160 5361 30883731 30884937 0.000000e+00 1725.0
53 TraesCS5D01G328700 chr1D 97.222 72 2 0 2602 2673 108802274 108802345 9.920000e-24 122.0
54 TraesCS5D01G328700 chr1D 97.143 70 1 1 2604 2673 454511838 454511770 4.620000e-22 117.0
55 TraesCS5D01G328700 chr1D 88.636 88 5 4 2019 2104 112766081 112766165 1.290000e-17 102.0
56 TraesCS5D01G328700 chr7A 89.485 1398 94 22 4160 5519 651432269 651430887 0.000000e+00 1718.0
57 TraesCS5D01G328700 chr7A 88.785 1391 81 28 4160 5521 111859007 111857663 0.000000e+00 1635.0
58 TraesCS5D01G328700 chr7A 91.237 1221 74 12 4160 5361 646201345 646202551 0.000000e+00 1631.0
59 TraesCS5D01G328700 chr7A 90.385 1196 81 13 4160 5334 725047434 725046252 0.000000e+00 1541.0
60 TraesCS5D01G328700 chr7A 89.478 1226 95 15 4160 5361 103620118 103618903 0.000000e+00 1519.0
61 TraesCS5D01G328700 chr7A 97.183 71 1 1 2603 2673 6486673 6486742 1.280000e-22 119.0
62 TraesCS5D01G328700 chr7A 93.506 77 5 0 2597 2673 29442757 29442833 1.660000e-21 115.0
63 TraesCS5D01G328700 chr7A 88.710 62 5 1 2382 2443 158841261 158841320 2.820000e-09 75.0
64 TraesCS5D01G328700 chr4D 92.935 1104 29 9 4298 5360 497398805 497397710 0.000000e+00 1561.0
65 TraesCS5D01G328700 chr3B 91.887 1097 55 16 4154 5237 573118236 573117161 0.000000e+00 1502.0
66 TraesCS5D01G328700 chr3B 88.929 840 54 12 4714 5523 756442838 756442008 0.000000e+00 1000.0
67 TraesCS5D01G328700 chr3B 84.729 884 104 16 4 883 775360451 775359595 0.000000e+00 856.0
68 TraesCS5D01G328700 chr3B 82.418 819 129 9 66 880 829311907 829312714 0.000000e+00 701.0
69 TraesCS5D01G328700 chr1A 89.819 992 74 12 4551 5522 289504800 289503816 0.000000e+00 1247.0
70 TraesCS5D01G328700 chr1A 85.185 864 110 9 4 866 561376796 561377642 0.000000e+00 870.0
71 TraesCS5D01G328700 chr6D 93.070 837 19 9 4542 5361 464256757 464255943 0.000000e+00 1188.0
72 TraesCS5D01G328700 chr6D 84.073 879 118 12 4 880 17885453 17886311 0.000000e+00 828.0
73 TraesCS5D01G328700 chr6D 85.139 794 109 7 2 792 343620033 343620820 0.000000e+00 804.0
74 TraesCS5D01G328700 chr6D 80.866 878 148 16 1 873 309920850 309919988 0.000000e+00 673.0
75 TraesCS5D01G328700 chr6D 98.148 162 3 0 5361 5522 13001332 13001493 4.300000e-72 283.0
76 TraesCS5D01G328700 chr6D 86.486 111 15 0 2025 2135 31087688 31087578 9.920000e-24 122.0
77 TraesCS5D01G328700 chr7D 91.092 797 22 6 4601 5361 23661636 23662419 0.000000e+00 1033.0
78 TraesCS5D01G328700 chr7D 98.758 161 2 0 5361 5521 78678844 78679004 3.330000e-73 287.0
79 TraesCS5D01G328700 chr1B 83.893 894 122 15 4 889 593246886 593246007 0.000000e+00 833.0
80 TraesCS5D01G328700 chr1B 95.000 80 3 1 2594 2673 680978891 680978969 2.760000e-24 124.0
81 TraesCS5D01G328700 chr1B 80.000 125 21 3 2018 2140 83204677 83204799 1.010000e-13 89.8
82 TraesCS5D01G328700 chr3D 92.101 595 17 5 4785 5363 612056956 612056376 0.000000e+00 811.0
83 TraesCS5D01G328700 chr3D 86.358 755 64 10 4741 5462 585913073 585913821 0.000000e+00 787.0
84 TraesCS5D01G328700 chr3D 84.483 116 18 0 2023 2138 347446764 347446879 1.660000e-21 115.0
85 TraesCS5D01G328700 chr2B 82.991 876 129 15 4 874 24351748 24350888 0.000000e+00 774.0
86 TraesCS5D01G328700 chr2B 82.688 878 131 16 4 876 24323573 24322712 0.000000e+00 760.0
87 TraesCS5D01G328700 chr2B 80.328 122 19 5 2326 2443 675210784 675210664 3.620000e-13 87.9
88 TraesCS5D01G328700 chr3A 83.049 879 107 17 4 880 728326436 728327274 0.000000e+00 760.0
89 TraesCS5D01G328700 chr4B 86.667 105 9 4 2035 2137 116221575 116221676 2.150000e-20 111.0
90 TraesCS5D01G328700 chr4B 93.750 64 3 1 2380 2443 372670292 372670230 2.160000e-15 95.3
91 TraesCS5D01G328700 chr2A 87.143 70 3 2 2380 2443 106591532 106591463 2.820000e-09 75.0
92 TraesCS5D01G328700 chr6B 93.182 44 2 1 2399 2441 25974765 25974808 6.100000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G328700 chr5D 421132665 421139948 7283 True 13452.000000 13452 100.000000 1 7284 1 chr5D.!!$R5 7283
1 TraesCS5D01G328700 chr5D 470223349 470224554 1205 False 1742.000000 1742 92.886000 4159 5361 1 chr5D.!!$F2 1202
2 TraesCS5D01G328700 chr5D 421158511 421163671 5160 True 1141.000000 2946 91.578500 930 7282 6 chr5D.!!$R7 6352
3 TraesCS5D01G328700 chr5D 421089168 421090051 883 True 636.000000 636 80.000000 1101 2008 1 chr5D.!!$R4 907
4 TraesCS5D01G328700 chr5D 421172465 421173102 637 True 468.000000 468 80.374000 3528 4151 1 chr5D.!!$R6 623
5 TraesCS5D01G328700 chr5D 420969112 420969745 633 True 399.000000 399 78.834000 3518 4143 1 chr5D.!!$R2 625
6 TraesCS5D01G328700 chr5B 507187361 507193209 5848 False 2134.000000 2438 91.734667 871 7040 3 chr5B.!!$F4 6169
7 TraesCS5D01G328700 chr5B 591680924 591681777 853 True 808.000000 808 83.933000 6 883 1 chr5B.!!$R1 877
8 TraesCS5D01G328700 chr5B 507058792 507061160 2368 False 638.000000 830 80.817000 983 4151 2 chr5B.!!$F3 3168
9 TraesCS5D01G328700 chr5A 538524860 538526073 1213 True 1568.000000 1568 90.212000 4156 5360 1 chr5A.!!$R1 1204
10 TraesCS5D01G328700 chr5A 470180428 470181310 882 False 1105.000000 1105 89.640000 4556 5420 1 chr5A.!!$F1 864
11 TraesCS5D01G328700 chr5A 534463723 534468587 4864 False 978.000000 1988 92.363714 927 7204 7 chr5A.!!$F4 6277
12 TraesCS5D01G328700 chr5A 534569926 534570809 883 False 630.000000 630 79.847000 1098 2005 1 chr5A.!!$F2 907
13 TraesCS5D01G328700 chr5A 534625495 534628093 2598 False 581.500000 734 80.409000 999 4101 2 chr5A.!!$F5 3102
14 TraesCS5D01G328700 chr5A 534371379 534373046 1667 False 362.500000 446 81.870500 1715 4151 2 chr5A.!!$F3 2436
15 TraesCS5D01G328700 chr2D 17211309 17212505 1196 False 1805.000000 1805 93.987000 4156 5351 1 chr2D.!!$F1 1195
16 TraesCS5D01G328700 chr2D 394234729 394235616 887 False 289.500000 292 99.074000 5361 5521 2 chr2D.!!$F3 160
17 TraesCS5D01G328700 chrUn 270056791 270061298 4507 True 948.666667 1792 91.403833 930 6631 6 chrUn.!!$R3 5701
18 TraesCS5D01G328700 chrUn 325468256 325469252 996 True 813.000000 813 81.713000 983 2006 1 chrUn.!!$R1 1023
19 TraesCS5D01G328700 chrUn 396802493 396803143 650 True 603.000000 603 83.759000 1057 1705 1 chrUn.!!$R2 648
20 TraesCS5D01G328700 chr1D 30883731 30884937 1206 False 1725.000000 1725 92.641000 4160 5361 1 chr1D.!!$F1 1201
21 TraesCS5D01G328700 chr7A 651430887 651432269 1382 True 1718.000000 1718 89.485000 4160 5519 1 chr7A.!!$R3 1359
22 TraesCS5D01G328700 chr7A 111857663 111859007 1344 True 1635.000000 1635 88.785000 4160 5521 1 chr7A.!!$R2 1361
23 TraesCS5D01G328700 chr7A 646201345 646202551 1206 False 1631.000000 1631 91.237000 4160 5361 1 chr7A.!!$F4 1201
24 TraesCS5D01G328700 chr7A 725046252 725047434 1182 True 1541.000000 1541 90.385000 4160 5334 1 chr7A.!!$R4 1174
25 TraesCS5D01G328700 chr7A 103618903 103620118 1215 True 1519.000000 1519 89.478000 4160 5361 1 chr7A.!!$R1 1201
26 TraesCS5D01G328700 chr4D 497397710 497398805 1095 True 1561.000000 1561 92.935000 4298 5360 1 chr4D.!!$R1 1062
27 TraesCS5D01G328700 chr3B 573117161 573118236 1075 True 1502.000000 1502 91.887000 4154 5237 1 chr3B.!!$R1 1083
28 TraesCS5D01G328700 chr3B 756442008 756442838 830 True 1000.000000 1000 88.929000 4714 5523 1 chr3B.!!$R2 809
29 TraesCS5D01G328700 chr3B 775359595 775360451 856 True 856.000000 856 84.729000 4 883 1 chr3B.!!$R3 879
30 TraesCS5D01G328700 chr3B 829311907 829312714 807 False 701.000000 701 82.418000 66 880 1 chr3B.!!$F1 814
31 TraesCS5D01G328700 chr1A 289503816 289504800 984 True 1247.000000 1247 89.819000 4551 5522 1 chr1A.!!$R1 971
32 TraesCS5D01G328700 chr1A 561376796 561377642 846 False 870.000000 870 85.185000 4 866 1 chr1A.!!$F1 862
33 TraesCS5D01G328700 chr6D 464255943 464256757 814 True 1188.000000 1188 93.070000 4542 5361 1 chr6D.!!$R3 819
34 TraesCS5D01G328700 chr6D 17885453 17886311 858 False 828.000000 828 84.073000 4 880 1 chr6D.!!$F2 876
35 TraesCS5D01G328700 chr6D 343620033 343620820 787 False 804.000000 804 85.139000 2 792 1 chr6D.!!$F3 790
36 TraesCS5D01G328700 chr6D 309919988 309920850 862 True 673.000000 673 80.866000 1 873 1 chr6D.!!$R2 872
37 TraesCS5D01G328700 chr7D 23661636 23662419 783 False 1033.000000 1033 91.092000 4601 5361 1 chr7D.!!$F1 760
38 TraesCS5D01G328700 chr1B 593246007 593246886 879 True 833.000000 833 83.893000 4 889 1 chr1B.!!$R1 885
39 TraesCS5D01G328700 chr3D 612056376 612056956 580 True 811.000000 811 92.101000 4785 5363 1 chr3D.!!$R1 578
40 TraesCS5D01G328700 chr3D 585913073 585913821 748 False 787.000000 787 86.358000 4741 5462 1 chr3D.!!$F2 721
41 TraesCS5D01G328700 chr2B 24350888 24351748 860 True 774.000000 774 82.991000 4 874 1 chr2B.!!$R2 870
42 TraesCS5D01G328700 chr2B 24322712 24323573 861 True 760.000000 760 82.688000 4 876 1 chr2B.!!$R1 872
43 TraesCS5D01G328700 chr3A 728326436 728327274 838 False 760.000000 760 83.049000 4 880 1 chr3A.!!$F1 876

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
196 220 0.250640 CAGCAGACAAGGCAAGGAGT 60.251 55.000 0.00 0.00 0.00 3.85 F
551 581 0.383590 CTCGCACGACCAGATCTGAT 59.616 55.000 24.62 6.85 0.00 2.90 F
794 829 1.080434 GAGCATATCCTCGCCGGTC 60.080 63.158 1.90 0.00 0.00 4.79 F
2645 3101 0.110486 AAGAAGAGCCCGGCTTTGAA 59.890 50.000 14.70 0.00 39.88 2.69 F
2668 3124 0.037590 ACAAAGCTATCAACCGGCCA 59.962 50.000 0.00 0.00 0.00 5.36 F
2669 3125 0.734889 CAAAGCTATCAACCGGCCAG 59.265 55.000 0.00 0.00 0.00 4.85 F
2698 3154 0.771127 ACATGTGTGGCCTTAGTGGT 59.229 50.000 3.32 0.00 38.35 4.16 F
2699 3155 1.144913 ACATGTGTGGCCTTAGTGGTT 59.855 47.619 3.32 0.00 38.35 3.67 F
3308 3838 1.193650 TCAGAACGATTTTCAACGCCG 59.806 47.619 0.00 0.00 0.00 6.46 F
4430 5384 1.375013 GTACCGGTTCGTGCCATGT 60.375 57.895 15.04 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1995 1.007734 AGTCGTCGCAGCGAAGAAA 60.008 52.632 30.93 11.22 44.48 2.52 R
2236 2606 1.274596 GAATGCCGTACGTACACAGG 58.725 55.000 24.50 18.04 0.00 4.00 R
2649 3105 0.037590 TGGCCGGTTGATAGCTTTGT 59.962 50.000 1.90 0.00 0.00 2.83 R
3896 4821 0.179034 CCTGCCTGCTAGGATTGTCC 60.179 60.000 6.40 0.00 37.67 4.02 R
4517 5472 0.401738 AATGGCGATACATGGGAGGG 59.598 55.000 0.00 0.00 0.00 4.30 R
4520 5475 2.172505 ACTGAAATGGCGATACATGGGA 59.827 45.455 0.00 0.00 0.00 4.37 R
4749 5707 4.963953 CAGTCAAAATCGTATGCGGATTTC 59.036 41.667 2.62 0.00 38.89 2.17 R
5180 6254 4.499758 CACGCTTAACTTCGGAGTTCTATC 59.500 45.833 13.67 0.35 44.75 2.08 R
5358 6448 1.146041 TGAGCTCGCACTGTGGTTT 59.854 52.632 9.64 0.00 0.00 3.27 R
6626 8960 0.550147 ATGGGCACAGAGTACCCCTT 60.550 55.000 0.00 0.00 38.32 3.95 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
28 30 0.515564 CCACCCGACGACAACAATTC 59.484 55.000 0.00 0.00 0.00 2.17
56 58 2.766263 ACATGAAGATCCAGACCGCTTA 59.234 45.455 0.00 0.00 0.00 3.09
140 155 0.320683 CCATTCGTCCAGACTGTGCA 60.321 55.000 0.93 0.00 0.00 4.57
142 157 2.079158 CATTCGTCCAGACTGTGCAAT 58.921 47.619 0.93 0.00 0.00 3.56
143 158 3.261580 CATTCGTCCAGACTGTGCAATA 58.738 45.455 0.93 0.00 0.00 1.90
144 159 2.363788 TCGTCCAGACTGTGCAATAC 57.636 50.000 0.93 0.00 0.00 1.89
145 160 1.616374 TCGTCCAGACTGTGCAATACA 59.384 47.619 0.93 0.00 37.78 2.29
196 220 0.250640 CAGCAGACAAGGCAAGGAGT 60.251 55.000 0.00 0.00 0.00 3.85
239 265 1.065418 CAGACACCACCTCCAATACCC 60.065 57.143 0.00 0.00 0.00 3.69
418 446 3.082055 GGGAGGAGGGGGACGAAC 61.082 72.222 0.00 0.00 0.00 3.95
537 567 3.716195 CACCACCCCATCCTCGCA 61.716 66.667 0.00 0.00 0.00 5.10
540 570 3.770040 CACCCCATCCTCGCACGA 61.770 66.667 0.00 0.00 0.00 4.35
551 581 0.383590 CTCGCACGACCAGATCTGAT 59.616 55.000 24.62 6.85 0.00 2.90
646 678 4.749310 CAGCAAGACCTCGCCGCT 62.749 66.667 0.00 0.00 0.00 5.52
733 768 2.597340 CCGCCATCTCCACCCAAT 59.403 61.111 0.00 0.00 0.00 3.16
792 827 2.262915 GGAGCATATCCTCGCCGG 59.737 66.667 0.00 0.00 45.64 6.13
793 828 2.574955 GGAGCATATCCTCGCCGGT 61.575 63.158 1.90 0.00 45.64 5.28
794 829 1.080434 GAGCATATCCTCGCCGGTC 60.080 63.158 1.90 0.00 0.00 4.79
795 830 2.430921 GCATATCCTCGCCGGTCG 60.431 66.667 1.90 7.73 40.15 4.79
1576 1727 2.444421 GGAGTTCCACTTCCTCGACTA 58.556 52.381 0.00 0.00 35.64 2.59
1844 1995 1.371183 CACCATGGTGGACGTGAGT 59.629 57.895 33.56 0.00 40.96 3.41
1904 2055 2.342279 CCCTTCAGACGTGCGGAA 59.658 61.111 0.00 0.00 0.00 4.30
2037 2188 4.922471 AGCTATCTACTCCCTTCGTTTC 57.078 45.455 0.00 0.00 0.00 2.78
2171 2536 8.584063 AAAGCCTTATATTTAAAAACGGAGGA 57.416 30.769 10.42 0.00 0.00 3.71
2236 2606 8.983724 GTTCTAAAATCCTCATCTACACTATGC 58.016 37.037 0.00 0.00 0.00 3.14
2297 2668 8.888579 AATAGTTGTATAATTAGTTCGCAGCT 57.111 30.769 0.00 0.00 0.00 4.24
2303 2675 8.443898 TGTATAATTAGTTCGCAGCTTATACG 57.556 34.615 11.16 0.00 35.95 3.06
2372 2775 5.928839 ACTACTTCTATGACACTTTGCACTG 59.071 40.000 0.00 0.00 0.00 3.66
2490 2946 6.885922 ACCTTGATATGAGGTTACCAGTTAC 58.114 40.000 3.51 0.00 45.06 2.50
2548 3004 9.911788 ATAGAATGTCTTTAATCTCACAACCAT 57.088 29.630 0.00 0.00 0.00 3.55
2549 3005 8.273780 AGAATGTCTTTAATCTCACAACCATC 57.726 34.615 0.00 0.00 0.00 3.51
2550 3006 8.105829 AGAATGTCTTTAATCTCACAACCATCT 58.894 33.333 0.00 0.00 0.00 2.90
2551 3007 8.641498 AATGTCTTTAATCTCACAACCATCTT 57.359 30.769 0.00 0.00 0.00 2.40
2552 3008 8.641498 ATGTCTTTAATCTCACAACCATCTTT 57.359 30.769 0.00 0.00 0.00 2.52
2553 3009 9.739276 ATGTCTTTAATCTCACAACCATCTTTA 57.261 29.630 0.00 0.00 0.00 1.85
2554 3010 9.567776 TGTCTTTAATCTCACAACCATCTTTAA 57.432 29.630 0.00 0.00 0.00 1.52
2563 3019 9.354673 TCTCACAACCATCTTTAATCTTTTTCT 57.645 29.630 0.00 0.00 0.00 2.52
2564 3020 9.971922 CTCACAACCATCTTTAATCTTTTTCTT 57.028 29.630 0.00 0.00 0.00 2.52
2567 3023 9.045223 ACAACCATCTTTAATCTTTTTCTTTGC 57.955 29.630 0.00 0.00 0.00 3.68
2568 3024 7.873739 ACCATCTTTAATCTTTTTCTTTGCG 57.126 32.000 0.00 0.00 0.00 4.85
2569 3025 6.868339 ACCATCTTTAATCTTTTTCTTTGCGG 59.132 34.615 0.00 0.00 0.00 5.69
2570 3026 6.311200 CCATCTTTAATCTTTTTCTTTGCGGG 59.689 38.462 0.00 0.00 0.00 6.13
2571 3027 5.778862 TCTTTAATCTTTTTCTTTGCGGGG 58.221 37.500 0.00 0.00 0.00 5.73
2572 3028 5.536916 TCTTTAATCTTTTTCTTTGCGGGGA 59.463 36.000 0.00 0.00 0.00 4.81
2584 3040 2.588464 TGCGGGGAAAAACCATCTTA 57.412 45.000 0.00 0.00 41.20 2.10
2628 3084 3.708563 TTTTTGGAACGAAGGCTCAAG 57.291 42.857 0.00 0.00 0.00 3.02
2629 3085 2.631160 TTTGGAACGAAGGCTCAAGA 57.369 45.000 0.00 0.00 0.00 3.02
2630 3086 2.631160 TTGGAACGAAGGCTCAAGAA 57.369 45.000 0.00 0.00 0.00 2.52
2631 3087 2.169832 TGGAACGAAGGCTCAAGAAG 57.830 50.000 0.00 0.00 0.00 2.85
2632 3088 1.691976 TGGAACGAAGGCTCAAGAAGA 59.308 47.619 0.00 0.00 0.00 2.87
2640 3096 2.985456 CTCAAGAAGAGCCCGGCT 59.015 61.111 13.16 13.16 43.88 5.52
2641 3097 1.298014 CTCAAGAAGAGCCCGGCTT 59.702 57.895 14.70 0.00 39.88 4.35
2642 3098 0.322008 CTCAAGAAGAGCCCGGCTTT 60.322 55.000 14.70 4.65 39.88 3.51
2643 3099 0.606401 TCAAGAAGAGCCCGGCTTTG 60.606 55.000 14.70 13.91 39.88 2.77
2644 3100 0.606401 CAAGAAGAGCCCGGCTTTGA 60.606 55.000 14.70 0.00 39.88 2.69
2645 3101 0.110486 AAGAAGAGCCCGGCTTTGAA 59.890 50.000 14.70 0.00 39.88 2.69
2646 3102 0.329596 AGAAGAGCCCGGCTTTGAAT 59.670 50.000 14.70 0.00 39.88 2.57
2647 3103 1.177401 GAAGAGCCCGGCTTTGAATT 58.823 50.000 14.70 4.04 39.88 2.17
2648 3104 2.026262 AGAAGAGCCCGGCTTTGAATTA 60.026 45.455 14.70 0.00 39.88 1.40
2649 3105 2.507407 AGAGCCCGGCTTTGAATTAA 57.493 45.000 14.70 0.00 39.88 1.40
2650 3106 2.092323 AGAGCCCGGCTTTGAATTAAC 58.908 47.619 14.70 0.00 39.88 2.01
2651 3107 1.816224 GAGCCCGGCTTTGAATTAACA 59.184 47.619 14.70 0.00 39.88 2.41
2652 3108 2.230266 GAGCCCGGCTTTGAATTAACAA 59.770 45.455 14.70 0.00 39.88 2.83
2653 3109 2.630580 AGCCCGGCTTTGAATTAACAAA 59.369 40.909 5.94 0.00 33.89 2.83
2664 3120 8.161754 CTTTGAATTAACAAAGCTATCAACCG 57.838 34.615 6.67 0.00 46.05 4.44
2665 3121 6.189677 TGAATTAACAAAGCTATCAACCGG 57.810 37.500 0.00 0.00 0.00 5.28
2666 3122 4.632538 ATTAACAAAGCTATCAACCGGC 57.367 40.909 0.00 0.00 0.00 6.13
2667 3123 1.173913 AACAAAGCTATCAACCGGCC 58.826 50.000 0.00 0.00 0.00 6.13
2668 3124 0.037590 ACAAAGCTATCAACCGGCCA 59.962 50.000 0.00 0.00 0.00 5.36
2669 3125 0.734889 CAAAGCTATCAACCGGCCAG 59.265 55.000 0.00 0.00 0.00 4.85
2695 3151 2.371841 TCTTGACATGTGTGGCCTTAGT 59.628 45.455 1.15 0.00 29.75 2.24
2698 3154 0.771127 ACATGTGTGGCCTTAGTGGT 59.229 50.000 3.32 0.00 38.35 4.16
2699 3155 1.144913 ACATGTGTGGCCTTAGTGGTT 59.855 47.619 3.32 0.00 38.35 3.67
2700 3156 2.373836 ACATGTGTGGCCTTAGTGGTTA 59.626 45.455 3.32 0.00 38.35 2.85
2701 3157 3.010138 ACATGTGTGGCCTTAGTGGTTAT 59.990 43.478 3.32 0.00 38.35 1.89
2702 3158 4.226394 ACATGTGTGGCCTTAGTGGTTATA 59.774 41.667 3.32 0.00 38.35 0.98
2703 3159 4.912317 TGTGTGGCCTTAGTGGTTATAA 57.088 40.909 3.32 0.00 38.35 0.98
2704 3160 5.244189 TGTGTGGCCTTAGTGGTTATAAA 57.756 39.130 3.32 0.00 38.35 1.40
2705 3161 5.822204 TGTGTGGCCTTAGTGGTTATAAAT 58.178 37.500 3.32 0.00 38.35 1.40
2808 3265 1.632046 CCCGAACATTAACGCGCAGT 61.632 55.000 5.73 3.19 0.00 4.40
2980 3451 5.121105 GGTAAGTAATGTAAGCCGGACAAT 58.879 41.667 5.05 0.00 0.00 2.71
3069 3543 4.497291 TCTTCAACTTGTGTTAGGTGGT 57.503 40.909 0.00 0.00 33.57 4.16
3307 3837 2.032377 TGTCAGAACGATTTTCAACGCC 60.032 45.455 0.00 0.00 0.00 5.68
3308 3838 1.193650 TCAGAACGATTTTCAACGCCG 59.806 47.619 0.00 0.00 0.00 6.46
3334 3865 7.917003 AGTTTTGGCCCATTACTTTTCATATT 58.083 30.769 0.00 0.00 0.00 1.28
3429 4303 7.798596 ATGCACACCTGAAGAATCTAATTAG 57.201 36.000 6.11 6.11 0.00 1.73
3464 4354 6.573434 TCATACTAGTAGTTTGACTGCATGG 58.427 40.000 16.65 0.00 32.54 3.66
3523 4427 9.217278 AGATCATCTCATTACAAAGCATATCAC 57.783 33.333 0.00 0.00 0.00 3.06
3637 4541 1.889829 CTAGGCTACATCCTCCTTCCG 59.110 57.143 0.00 0.00 37.66 4.30
3941 4866 4.395959 TTTATCTTCCGCCGTATGTTCT 57.604 40.909 0.00 0.00 0.00 3.01
4057 4982 2.103432 TGGAGTTCCGCAAGTAAGTCAA 59.897 45.455 0.00 0.00 39.43 3.18
4071 4997 7.360101 GCAAGTAAGTCAACACGATCTTATGTT 60.360 37.037 0.00 2.09 39.63 2.71
4292 5245 4.628963 ATGTTGAACCTTTAGTACCGGT 57.371 40.909 13.98 13.98 0.00 5.28
4293 5246 4.420522 TGTTGAACCTTTAGTACCGGTT 57.579 40.909 15.04 0.00 43.32 4.44
4296 5249 3.303881 GAACCTTTAGTACCGGTTCGT 57.696 47.619 15.04 0.00 44.86 3.85
4337 5290 4.675303 AGGGGTGGTGGCAGGCTA 62.675 66.667 0.00 0.00 0.00 3.93
4430 5384 1.375013 GTACCGGTTCGTGCCATGT 60.375 57.895 15.04 0.00 0.00 3.21
4474 5428 2.176247 ATAGTCCCGGTTGGAGACAT 57.824 50.000 9.96 0.46 46.38 3.06
4876 5851 7.691213 TGGTTAAATCTGGTCAAACTATGGTA 58.309 34.615 0.00 0.00 0.00 3.25
5523 6705 3.988517 AGCTTCGTTTTCTACTAGTGTGC 59.011 43.478 5.39 0.00 0.00 4.57
5532 6714 5.924475 TTCTACTAGTGTGCTTTGCTTTC 57.076 39.130 5.39 0.00 0.00 2.62
5538 6720 2.358898 AGTGTGCTTTGCTTTCGAACAT 59.641 40.909 0.00 0.00 0.00 2.71
5570 6756 9.277565 CACTCAATCTAAATTATCAAAACCACG 57.722 33.333 0.00 0.00 0.00 4.94
5594 6780 7.968405 ACGCATTTGATCTACTTTGGTTTATTC 59.032 33.333 0.00 0.00 0.00 1.75
5597 6783 6.995511 TTGATCTACTTTGGTTTATTCGGG 57.004 37.500 0.00 0.00 0.00 5.14
5814 8139 7.933577 TGAGATAGTTAGGAGTATTTGCATTGG 59.066 37.037 0.00 0.00 0.00 3.16
6246 8577 4.030913 TCCTTCGGACTCATTAAGGATGT 58.969 43.478 0.00 0.00 41.94 3.06
7144 9490 0.108804 ACTAGTCCATTCCGTGCACG 60.109 55.000 31.77 31.77 39.44 5.34
7146 9492 2.845752 TAGTCCATTCCGTGCACGCC 62.846 60.000 33.17 13.32 38.18 5.68
7147 9493 4.015406 TCCATTCCGTGCACGCCT 62.015 61.111 33.17 16.47 38.18 5.52
7148 9494 3.803082 CCATTCCGTGCACGCCTG 61.803 66.667 33.17 25.55 38.18 4.85
7149 9495 4.465512 CATTCCGTGCACGCCTGC 62.466 66.667 33.17 0.19 44.52 4.85
7231 9577 6.886307 TGTTTTCTGTTTGTTTTCTTTGCTG 58.114 32.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 0.541392 TGGATCTTCATGTCCACGGG 59.459 55.000 0.00 0.00 39.51 5.28
56 58 1.804748 GCGGAGTCGATGTTTTCCTTT 59.195 47.619 0.00 0.00 39.00 3.11
140 155 1.010419 GGTTGTCGTCCGCGTGTATT 61.010 55.000 4.92 0.00 39.49 1.89
142 157 2.050168 GGTTGTCGTCCGCGTGTA 60.050 61.111 4.92 0.00 39.49 2.90
143 158 4.210093 TGGTTGTCGTCCGCGTGT 62.210 61.111 4.92 0.00 39.49 4.49
144 159 3.698463 GTGGTTGTCGTCCGCGTG 61.698 66.667 4.92 0.00 39.49 5.34
145 160 4.955774 GGTGGTTGTCGTCCGCGT 62.956 66.667 4.92 0.00 39.49 6.01
239 265 0.889186 CTCGGTTTCCCCTGGTTGTG 60.889 60.000 0.00 0.00 0.00 3.33
418 446 2.356667 GGGGGTCAAGCTTCCAGG 59.643 66.667 0.00 0.00 0.00 4.45
537 567 1.333177 GGCCTATCAGATCTGGTCGT 58.667 55.000 22.42 9.06 0.00 4.34
540 570 1.055040 GCTGGCCTATCAGATCTGGT 58.945 55.000 22.42 18.48 36.93 4.00
551 581 2.434843 CGATCTGGTGGCTGGCCTA 61.435 63.158 13.05 0.00 36.94 3.93
702 736 3.219928 GCGGCCTCGATCTCTCCA 61.220 66.667 0.00 0.00 39.00 3.86
773 808 2.574018 CGGCGAGGATATGCTCCCA 61.574 63.158 22.50 0.00 46.27 4.37
776 811 1.080434 GACCGGCGAGGATATGCTC 60.080 63.158 13.90 13.90 45.00 4.26
857 903 2.197324 CTCTCCTCCCTCCTCCCG 59.803 72.222 0.00 0.00 0.00 5.14
923 969 9.191479 GCTTGATCTGTAGGTGTAGGTATATAT 57.809 37.037 0.00 0.00 0.00 0.86
1844 1995 1.007734 AGTCGTCGCAGCGAAGAAA 60.008 52.632 30.93 11.22 44.48 2.52
1904 2055 1.947642 GTTGAACGTGACGTCGCCT 60.948 57.895 22.62 10.63 39.99 5.52
2171 2536 1.406069 CCATCGAACAGGCAGCTACTT 60.406 52.381 0.00 0.00 0.00 2.24
2210 2578 8.983724 GCATAGTGTAGATGAGGATTTTAGAAC 58.016 37.037 0.00 0.00 0.00 3.01
2236 2606 1.274596 GAATGCCGTACGTACACAGG 58.725 55.000 24.50 18.04 0.00 4.00
2297 2668 4.754618 CCTTCATACATGCCAAGCGTATAA 59.245 41.667 0.00 0.00 0.00 0.98
2303 2675 3.545703 ACTACCTTCATACATGCCAAGC 58.454 45.455 0.00 0.00 0.00 4.01
2345 2717 8.314751 AGTGCAAAGTGTCATAGAAGTAGTATT 58.685 33.333 0.00 0.00 0.00 1.89
2537 2993 9.354673 AGAAAAAGATTAAAGATGGTTGTGAGA 57.645 29.630 0.00 0.00 0.00 3.27
2538 2994 9.971922 AAGAAAAAGATTAAAGATGGTTGTGAG 57.028 29.630 0.00 0.00 0.00 3.51
2541 2997 9.045223 GCAAAGAAAAAGATTAAAGATGGTTGT 57.955 29.630 0.00 0.00 0.00 3.32
2542 2998 8.216453 CGCAAAGAAAAAGATTAAAGATGGTTG 58.784 33.333 0.00 0.00 0.00 3.77
2543 2999 7.384932 CCGCAAAGAAAAAGATTAAAGATGGTT 59.615 33.333 0.00 0.00 0.00 3.67
2544 3000 6.868339 CCGCAAAGAAAAAGATTAAAGATGGT 59.132 34.615 0.00 0.00 0.00 3.55
2545 3001 6.311200 CCCGCAAAGAAAAAGATTAAAGATGG 59.689 38.462 0.00 0.00 0.00 3.51
2546 3002 6.311200 CCCCGCAAAGAAAAAGATTAAAGATG 59.689 38.462 0.00 0.00 0.00 2.90
2547 3003 6.210584 TCCCCGCAAAGAAAAAGATTAAAGAT 59.789 34.615 0.00 0.00 0.00 2.40
2548 3004 5.536916 TCCCCGCAAAGAAAAAGATTAAAGA 59.463 36.000 0.00 0.00 0.00 2.52
2549 3005 5.778862 TCCCCGCAAAGAAAAAGATTAAAG 58.221 37.500 0.00 0.00 0.00 1.85
2550 3006 5.793030 TCCCCGCAAAGAAAAAGATTAAA 57.207 34.783 0.00 0.00 0.00 1.52
2551 3007 5.793030 TTCCCCGCAAAGAAAAAGATTAA 57.207 34.783 0.00 0.00 0.00 1.40
2552 3008 5.793030 TTTCCCCGCAAAGAAAAAGATTA 57.207 34.783 0.00 0.00 0.00 1.75
2553 3009 4.681074 TTTCCCCGCAAAGAAAAAGATT 57.319 36.364 0.00 0.00 0.00 2.40
2554 3010 4.681074 TTTTCCCCGCAAAGAAAAAGAT 57.319 36.364 3.12 0.00 38.63 2.40
2555 3011 4.185394 GTTTTTCCCCGCAAAGAAAAAGA 58.815 39.130 14.35 0.00 46.82 2.52
2556 3012 3.311322 GGTTTTTCCCCGCAAAGAAAAAG 59.689 43.478 14.35 0.00 46.82 2.27
2557 3013 3.271729 GGTTTTTCCCCGCAAAGAAAAA 58.728 40.909 11.39 11.39 45.12 1.94
2558 3014 2.236395 TGGTTTTTCCCCGCAAAGAAAA 59.764 40.909 1.76 1.76 39.54 2.29
2559 3015 1.831736 TGGTTTTTCCCCGCAAAGAAA 59.168 42.857 0.00 0.00 34.77 2.52
2560 3016 1.486211 TGGTTTTTCCCCGCAAAGAA 58.514 45.000 0.00 0.00 34.77 2.52
2561 3017 1.616374 GATGGTTTTTCCCCGCAAAGA 59.384 47.619 0.00 0.00 34.77 2.52
2562 3018 1.618343 AGATGGTTTTTCCCCGCAAAG 59.382 47.619 0.00 0.00 34.77 2.77
2563 3019 1.710816 AGATGGTTTTTCCCCGCAAA 58.289 45.000 0.00 0.00 34.77 3.68
2564 3020 1.710816 AAGATGGTTTTTCCCCGCAA 58.289 45.000 0.00 0.00 34.77 4.85
2565 3021 2.588464 TAAGATGGTTTTTCCCCGCA 57.412 45.000 0.00 0.00 34.77 5.69
2566 3022 3.945981 TTTAAGATGGTTTTTCCCCGC 57.054 42.857 0.00 0.00 34.77 6.13
2567 3023 5.417580 TGAGATTTAAGATGGTTTTTCCCCG 59.582 40.000 0.00 0.00 34.77 5.73
2568 3024 6.850752 TGAGATTTAAGATGGTTTTTCCCC 57.149 37.500 0.00 0.00 34.77 4.81
2608 3064 3.283751 TCTTGAGCCTTCGTTCCAAAAA 58.716 40.909 0.00 0.00 0.00 1.94
2609 3065 2.925724 TCTTGAGCCTTCGTTCCAAAA 58.074 42.857 0.00 0.00 0.00 2.44
2610 3066 2.631160 TCTTGAGCCTTCGTTCCAAA 57.369 45.000 0.00 0.00 0.00 3.28
2611 3067 2.104111 TCTTCTTGAGCCTTCGTTCCAA 59.896 45.455 0.00 0.00 0.00 3.53
2612 3068 1.691976 TCTTCTTGAGCCTTCGTTCCA 59.308 47.619 0.00 0.00 0.00 3.53
2613 3069 2.342179 CTCTTCTTGAGCCTTCGTTCC 58.658 52.381 0.00 0.00 35.84 3.62
2623 3079 0.322008 AAAGCCGGGCTCTTCTTGAG 60.322 55.000 24.08 0.00 45.33 3.02
2624 3080 0.606401 CAAAGCCGGGCTCTTCTTGA 60.606 55.000 24.08 0.00 38.25 3.02
2625 3081 0.606401 TCAAAGCCGGGCTCTTCTTG 60.606 55.000 24.08 21.74 38.25 3.02
2626 3082 0.110486 TTCAAAGCCGGGCTCTTCTT 59.890 50.000 24.08 10.16 38.25 2.52
2627 3083 0.329596 ATTCAAAGCCGGGCTCTTCT 59.670 50.000 24.08 2.98 38.25 2.85
2628 3084 1.177401 AATTCAAAGCCGGGCTCTTC 58.823 50.000 24.08 0.00 38.25 2.87
2629 3085 2.492088 GTTAATTCAAAGCCGGGCTCTT 59.508 45.455 24.08 15.43 38.25 2.85
2630 3086 2.092323 GTTAATTCAAAGCCGGGCTCT 58.908 47.619 24.08 5.15 38.25 4.09
2631 3087 1.816224 TGTTAATTCAAAGCCGGGCTC 59.184 47.619 24.08 6.82 38.25 4.70
2632 3088 1.917872 TGTTAATTCAAAGCCGGGCT 58.082 45.000 17.69 17.69 42.56 5.19
2633 3089 2.734276 TTGTTAATTCAAAGCCGGGC 57.266 45.000 12.11 12.11 0.00 6.13
2640 3096 7.087639 CCGGTTGATAGCTTTGTTAATTCAAA 58.912 34.615 0.00 0.00 36.18 2.69
2641 3097 6.616947 CCGGTTGATAGCTTTGTTAATTCAA 58.383 36.000 0.00 0.00 0.00 2.69
2642 3098 5.392595 GCCGGTTGATAGCTTTGTTAATTCA 60.393 40.000 1.90 0.00 0.00 2.57
2643 3099 5.034797 GCCGGTTGATAGCTTTGTTAATTC 58.965 41.667 1.90 0.00 0.00 2.17
2644 3100 4.142249 GGCCGGTTGATAGCTTTGTTAATT 60.142 41.667 1.90 0.00 0.00 1.40
2645 3101 3.380320 GGCCGGTTGATAGCTTTGTTAAT 59.620 43.478 1.90 0.00 0.00 1.40
2646 3102 2.750712 GGCCGGTTGATAGCTTTGTTAA 59.249 45.455 1.90 0.00 0.00 2.01
2647 3103 2.290387 TGGCCGGTTGATAGCTTTGTTA 60.290 45.455 1.90 0.00 0.00 2.41
2648 3104 1.173913 GGCCGGTTGATAGCTTTGTT 58.826 50.000 1.90 0.00 0.00 2.83
2649 3105 0.037590 TGGCCGGTTGATAGCTTTGT 59.962 50.000 1.90 0.00 0.00 2.83
2650 3106 0.734889 CTGGCCGGTTGATAGCTTTG 59.265 55.000 2.29 0.00 0.00 2.77
2651 3107 0.394352 CCTGGCCGGTTGATAGCTTT 60.394 55.000 11.58 0.00 0.00 3.51
2652 3108 1.224592 CCTGGCCGGTTGATAGCTT 59.775 57.895 11.58 0.00 0.00 3.74
2653 3109 1.056700 ATCCTGGCCGGTTGATAGCT 61.057 55.000 11.58 0.00 0.00 3.32
2654 3110 0.603975 GATCCTGGCCGGTTGATAGC 60.604 60.000 11.58 0.00 0.00 2.97
2655 3111 1.001406 GAGATCCTGGCCGGTTGATAG 59.999 57.143 11.58 0.00 0.00 2.08
2656 3112 1.048601 GAGATCCTGGCCGGTTGATA 58.951 55.000 11.58 0.00 0.00 2.15
2657 3113 0.692419 AGAGATCCTGGCCGGTTGAT 60.692 55.000 11.58 6.95 0.00 2.57
2658 3114 0.909610 AAGAGATCCTGGCCGGTTGA 60.910 55.000 11.58 1.27 0.00 3.18
2659 3115 0.745845 CAAGAGATCCTGGCCGGTTG 60.746 60.000 11.58 3.24 0.00 3.77
2660 3116 0.909610 TCAAGAGATCCTGGCCGGTT 60.910 55.000 11.58 3.79 0.00 4.44
2661 3117 1.306141 TCAAGAGATCCTGGCCGGT 60.306 57.895 11.58 0.00 0.00 5.28
2662 3118 1.144936 GTCAAGAGATCCTGGCCGG 59.855 63.158 3.88 3.88 0.00 6.13
2663 3119 0.467384 ATGTCAAGAGATCCTGGCCG 59.533 55.000 0.00 0.00 0.00 6.13
2664 3120 1.211457 ACATGTCAAGAGATCCTGGCC 59.789 52.381 0.00 0.00 0.00 5.36
2665 3121 2.286872 CACATGTCAAGAGATCCTGGC 58.713 52.381 0.00 0.00 0.00 4.85
2666 3122 3.268330 CACACATGTCAAGAGATCCTGG 58.732 50.000 0.00 0.00 0.00 4.45
2667 3123 3.268330 CCACACATGTCAAGAGATCCTG 58.732 50.000 0.00 0.00 0.00 3.86
2668 3124 2.355513 GCCACACATGTCAAGAGATCCT 60.356 50.000 0.00 0.00 0.00 3.24
2669 3125 2.012673 GCCACACATGTCAAGAGATCC 58.987 52.381 0.00 0.00 0.00 3.36
2670 3126 2.012673 GGCCACACATGTCAAGAGATC 58.987 52.381 0.00 0.00 0.00 2.75
2702 3158 9.236691 CGCACACAGAAGCATAATTATAAATTT 57.763 29.630 0.00 0.00 0.00 1.82
2703 3159 8.405531 ACGCACACAGAAGCATAATTATAAATT 58.594 29.630 0.00 0.00 0.00 1.82
2704 3160 7.930217 ACGCACACAGAAGCATAATTATAAAT 58.070 30.769 0.00 0.00 0.00 1.40
2705 3161 7.279981 AGACGCACACAGAAGCATAATTATAAA 59.720 33.333 0.00 0.00 0.00 1.40
2770 3227 1.265365 GGCACAACTCACTTCAAGCTC 59.735 52.381 0.00 0.00 0.00 4.09
2851 3311 8.716646 AACACAGGCAAAATTAATTATTAGCC 57.283 30.769 18.15 18.15 43.04 3.93
2980 3451 3.773119 GTGGGAGAAACTGTATACCCTCA 59.227 47.826 0.00 0.00 38.28 3.86
3069 3543 4.228824 ACCAGGTTCTGTAGGTGTTAGAA 58.771 43.478 0.00 0.00 32.04 2.10
3087 3561 0.460987 GGAGGACAGATCGCAACCAG 60.461 60.000 0.00 0.00 0.00 4.00
3223 3730 4.323417 TCGGAGTGCAGAAACACAAATAT 58.677 39.130 0.00 0.00 43.23 1.28
3224 3731 3.734463 TCGGAGTGCAGAAACACAAATA 58.266 40.909 0.00 0.00 43.23 1.40
3229 3736 2.096218 GTCATTCGGAGTGCAGAAACAC 60.096 50.000 0.00 0.00 41.02 3.32
3307 3837 3.934457 AAAGTAATGGGCCAAAACTCG 57.066 42.857 20.56 0.00 0.00 4.18
3308 3838 5.208463 TGAAAAGTAATGGGCCAAAACTC 57.792 39.130 20.56 11.64 0.00 3.01
3395 3944 8.782339 TTCTTCAGGTGTGCATATATGATATG 57.218 34.615 17.10 5.83 0.00 1.78
3429 4303 9.517609 CAAACTACTAGTATGATACACTGGAAC 57.482 37.037 2.33 0.00 0.00 3.62
3464 4354 8.973835 TCCGAAATAATTTACATTTCAACACC 57.026 30.769 11.05 0.00 40.76 4.16
3637 4541 3.383546 TCGTGCATCGCTAAATGAAAC 57.616 42.857 0.00 0.00 39.67 2.78
3752 4656 5.519927 CCTTCAGACCAAACATTTTGACAAC 59.480 40.000 0.09 0.00 0.00 3.32
3896 4821 0.179034 CCTGCCTGCTAGGATTGTCC 60.179 60.000 6.40 0.00 37.67 4.02
4057 4982 8.783093 TGAAGATTTTTCAACATAAGATCGTGT 58.217 29.630 0.00 0.00 0.00 4.49
4270 5223 5.743636 ACCGGTACTAAAGGTTCAACATA 57.256 39.130 4.49 0.00 33.96 2.29
4351 5305 2.547826 GTACTAAAGGTGATCGTGGGC 58.452 52.381 0.00 0.00 0.00 5.36
4430 5384 0.712380 AGACCCCTTTAGTCCCGGTA 59.288 55.000 0.00 0.00 34.67 4.02
4474 5428 2.475339 TGCCCTATAGTCCCGGTTTA 57.525 50.000 0.00 0.00 0.00 2.01
4517 5472 0.401738 AATGGCGATACATGGGAGGG 59.598 55.000 0.00 0.00 0.00 4.30
4520 5475 2.172505 ACTGAAATGGCGATACATGGGA 59.827 45.455 0.00 0.00 0.00 4.37
4749 5707 4.963953 CAGTCAAAATCGTATGCGGATTTC 59.036 41.667 2.62 0.00 38.89 2.17
5180 6254 4.499758 CACGCTTAACTTCGGAGTTCTATC 59.500 45.833 13.67 0.35 44.75 2.08
5211 6285 2.136878 CCATCCTCTCACTCCCCCG 61.137 68.421 0.00 0.00 0.00 5.73
5358 6448 1.146041 TGAGCTCGCACTGTGGTTT 59.854 52.632 9.64 0.00 0.00 3.27
5359 6449 1.595382 GTGAGCTCGCACTGTGGTT 60.595 57.895 22.25 0.00 35.91 3.67
5532 6714 6.662414 TTAGATTGAGTGGCTTTATGTTCG 57.338 37.500 0.00 0.00 0.00 3.95
5570 6756 7.432252 CCGAATAAACCAAAGTAGATCAAATGC 59.568 37.037 0.00 0.00 0.00 3.56
5665 7985 8.900983 AGTTTCTCCTTCTTGCATCTATAATC 57.099 34.615 0.00 0.00 0.00 1.75
5814 8139 3.425659 AGAAGAGGAGGGAAAAATGCAC 58.574 45.455 0.00 0.00 0.00 4.57
5822 8147 5.368523 TCACTTACAAAAGAAGAGGAGGGAA 59.631 40.000 0.00 0.00 36.50 3.97
5823 8148 4.905456 TCACTTACAAAAGAAGAGGAGGGA 59.095 41.667 0.00 0.00 36.50 4.20
6246 8577 2.363306 TTCTGAAAGCCTTGAAGCCA 57.637 45.000 0.00 0.00 0.00 4.75
6626 8960 0.550147 ATGGGCACAGAGTACCCCTT 60.550 55.000 0.00 0.00 38.32 3.95
6815 9150 2.204463 TGGAGGGGCAAGATAATGTCA 58.796 47.619 0.00 0.00 0.00 3.58
7144 9490 0.312102 GGCAAATAGGATTCGCAGGC 59.688 55.000 0.00 0.00 0.00 4.85
7146 9492 0.040958 GCGGCAAATAGGATTCGCAG 60.041 55.000 0.00 0.00 42.27 5.18
7147 9493 2.021722 GCGGCAAATAGGATTCGCA 58.978 52.632 0.00 0.00 42.27 5.10
7148 9494 0.593128 ATGCGGCAAATAGGATTCGC 59.407 50.000 6.82 0.00 42.90 4.70
7149 9495 4.466828 CTTAATGCGGCAAATAGGATTCG 58.533 43.478 6.82 0.00 31.11 3.34
7150 9496 4.229876 GCTTAATGCGGCAAATAGGATTC 58.770 43.478 6.82 0.00 31.11 2.52


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

AutoCloner maintained by Alex Coulton.