Multiple sequence alignment - TraesCS6D01G004000

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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 TraesCS6D01G004000 chr6D 100.000 8926 0 0 1 8926 2066079 2075004 0.000000e+00 16484.0
1 TraesCS6D01G004000 chr6D 89.671 4647 319 61 3568 8156 2032328 2036871 0.000000e+00 5773.0
2 TraesCS6D01G004000 chr6D 87.217 884 78 11 1329 2192 2029972 2030840 0.000000e+00 974.0
3 TraesCS6D01G004000 chr6D 86.319 614 62 13 2198 2801 2031034 2031635 0.000000e+00 649.0
4 TraesCS6D01G004000 chr6D 92.986 442 17 10 829 1260 2029504 2029941 4.550000e-177 632.0
5 TraesCS6D01G004000 chr6D 89.552 469 21 8 1 469 2028631 2029071 3.620000e-158 569.0
6 TraesCS6D01G004000 chr6D 90.343 321 22 3 8184 8495 2037173 2037493 6.450000e-111 412.0
7 TraesCS6D01G004000 chr6D 89.451 237 16 3 8611 8844 2037513 2037743 3.150000e-74 291.0
8 TraesCS6D01G004000 chr6D 92.045 176 14 0 3406 3581 2031795 2031970 1.920000e-61 248.0
9 TraesCS6D01G004000 chr6D 90.968 155 10 2 471 622 2029111 2029264 1.170000e-48 206.0
10 TraesCS6D01G004000 chr6D 91.525 59 5 0 1272 1330 425084191 425084249 2.070000e-11 82.4
11 TraesCS6D01G004000 chr6B 93.225 5063 267 43 3078 8113 4795587 4790574 0.000000e+00 7380.0
12 TraesCS6D01G004000 chr6B 88.687 4517 365 66 3631 8097 4536830 4532410 0.000000e+00 5376.0
13 TraesCS6D01G004000 chr6B 89.523 2348 202 22 4059 6372 4583086 4580749 0.000000e+00 2933.0
14 TraesCS6D01G004000 chr6B 89.333 2025 170 26 5182 7198 4556657 4554671 0.000000e+00 2501.0
15 TraesCS6D01G004000 chr6B 91.831 1677 119 10 6450 8111 4580741 4579068 0.000000e+00 2322.0
16 TraesCS6D01G004000 chr6B 89.522 1756 129 25 7195 8926 4554641 4552917 0.000000e+00 2172.0
17 TraesCS6D01G004000 chr6B 85.750 2021 159 37 3167 5150 4558585 4556657 0.000000e+00 2017.0
18 TraesCS6D01G004000 chr6B 93.399 1212 59 12 1348 2558 4797352 4796161 0.000000e+00 1775.0
19 TraesCS6D01G004000 chr6B 88.302 1496 126 25 1329 2805 4560039 4558574 0.000000e+00 1748.0
20 TraesCS6D01G004000 chr6B 87.617 1494 142 23 1329 2805 4585627 4584160 0.000000e+00 1694.0
21 TraesCS6D01G004000 chr6B 86.630 1436 157 19 1329 2754 4538240 4536830 0.000000e+00 1555.0
22 TraesCS6D01G004000 chr6B 93.613 595 10 7 202 784 4561068 4560490 0.000000e+00 863.0
23 TraesCS6D01G004000 chr6B 88.842 717 60 6 3267 3980 4584053 4583354 0.000000e+00 863.0
24 TraesCS6D01G004000 chr6B 88.937 461 22 7 1 460 4798513 4798081 7.880000e-150 542.0
25 TraesCS6D01G004000 chr6B 88.260 477 14 11 2630 3080 4796165 4795705 4.740000e-147 532.0
26 TraesCS6D01G004000 chr6B 91.908 346 21 4 882 1225 4560459 4560119 2.250000e-130 477.0
27 TraesCS6D01G004000 chr6B 88.372 387 33 8 845 1224 4538716 4538335 1.060000e-123 455.0
28 TraesCS6D01G004000 chr6B 88.325 394 20 14 882 1253 4586054 4585665 4.920000e-122 449.0
29 TraesCS6D01G004000 chr6B 88.116 345 31 7 8160 8494 4790570 4790226 1.400000e-107 401.0
30 TraesCS6D01G004000 chr6B 87.719 342 32 7 8165 8502 4579072 4578737 3.020000e-104 390.0
31 TraesCS6D01G004000 chr6B 93.822 259 11 4 882 1139 4797606 4797352 1.410000e-102 385.0
32 TraesCS6D01G004000 chr6B 86.350 337 17 9 472 784 4797981 4797650 3.090000e-89 340.0
33 TraesCS6D01G004000 chr6B 84.444 360 33 12 8175 8511 4526704 4526345 5.160000e-87 333.0
34 TraesCS6D01G004000 chr6B 94.578 166 7 1 288 453 4586514 4586351 1.150000e-63 255.0
35 TraesCS6D01G004000 chr6B 92.571 175 13 0 4 178 4562065 4561891 1.490000e-62 252.0
36 TraesCS6D01G004000 chr6B 92.994 157 11 0 4 160 4586733 4586577 6.970000e-56 230.0
37 TraesCS6D01G004000 chr6B 93.706 143 9 0 513 655 4586325 4586183 1.950000e-51 215.0
38 TraesCS6D01G004000 chr6B 88.722 133 11 3 652 784 4538836 4538708 9.280000e-35 159.0
39 TraesCS6D01G004000 chr6B 95.833 72 3 0 713 784 4586170 4586099 5.660000e-22 117.0
40 TraesCS6D01G004000 chr6B 91.549 71 6 0 778 848 4538805 4538735 2.050000e-16 99.0
41 TraesCS6D01G004000 chr6B 93.103 58 4 0 1273 1330 516473880 516473937 1.600000e-12 86.1
42 TraesCS6D01G004000 chr6A 89.270 4781 361 71 3713 8446 864911 860236 0.000000e+00 5847.0
43 TraesCS6D01G004000 chr6A 92.868 3421 191 25 3291 6688 822954 819564 0.000000e+00 4916.0
44 TraesCS6D01G004000 chr6A 92.907 1424 67 13 6738 8154 819563 818167 0.000000e+00 2039.0
45 TraesCS6D01G004000 chr6A 86.997 1492 121 37 1340 2805 866527 865083 0.000000e+00 1613.0
46 TraesCS6D01G004000 chr6A 87.594 1330 126 15 882 2182 825217 823898 0.000000e+00 1506.0
47 TraesCS6D01G004000 chr6A 88.462 650 52 15 586 1225 867571 866935 0.000000e+00 763.0
48 TraesCS6D01G004000 chr6A 87.752 596 55 9 2200 2787 823622 823037 0.000000e+00 680.0
49 TraesCS6D01G004000 chr6A 85.059 676 65 13 8198 8852 818172 817512 0.000000e+00 656.0
50 TraesCS6D01G004000 chr6A 92.174 460 30 5 1 459 868519 868065 0.000000e+00 645.0
51 TraesCS6D01G004000 chr6A 89.590 317 29 2 8598 8911 860179 859864 5.020000e-107 399.0
52 TraesCS6D01G004000 chr6A 88.889 144 12 2 482 622 867769 867627 3.310000e-39 174.0
53 TraesCS6D01G004000 chr6A 92.982 114 8 0 59 172 825806 825693 5.540000e-37 167.0
54 TraesCS6D01G004000 chr6A 80.734 218 24 8 585 784 825478 825261 4.320000e-33 154.0
55 TraesCS6D01G004000 chr6A 93.750 48 0 1 2803 2847 268969581 268969628 1.610000e-07 69.4
56 TraesCS6D01G004000 chr2D 83.817 3343 404 67 5136 8436 633681135 633684382 0.000000e+00 3049.0
57 TraesCS6D01G004000 chr2D 82.853 1458 191 37 3512 4941 633678579 633680005 0.000000e+00 1253.0
58 TraesCS6D01G004000 chr2D 84.615 741 97 14 1329 2061 633675429 633676160 0.000000e+00 721.0
59 TraesCS6D01G004000 chr2D 92.000 50 1 1 2800 2846 3952631 3952680 5.780000e-07 67.6
60 TraesCS6D01G004000 chr2D 92.000 50 1 1 2800 2846 4014675 4014724 5.780000e-07 67.6
61 TraesCS6D01G004000 chr3A 83.258 890 127 16 7103 7977 581838652 581837770 0.000000e+00 798.0
62 TraesCS6D01G004000 chr3A 82.175 892 120 27 5188 6056 581615727 581614852 0.000000e+00 730.0
63 TraesCS6D01G004000 chr3A 80.357 896 125 33 5235 6108 581395630 581394764 4.550000e-177 632.0
64 TraesCS6D01G004000 chr3A 81.081 333 58 4 2444 2774 581842830 581842501 2.470000e-65 261.0
65 TraesCS6D01G004000 chr3D 81.099 619 109 7 1352 1966 441180058 441179444 1.040000e-133 488.0
66 TraesCS6D01G004000 chr3D 84.892 278 28 10 3698 3963 441262219 441261944 1.480000e-67 268.0
67 TraesCS6D01G004000 chrUn 77.712 507 95 10 4203 4703 108221388 108220894 2.440000e-75 294.0
68 TraesCS6D01G004000 chrUn 86.719 128 12 4 2803 2928 47241099 47240975 4.350000e-28 137.0
69 TraesCS6D01G004000 chrUn 86.719 128 12 4 2803 2928 47246813 47246689 4.350000e-28 137.0
70 TraesCS6D01G004000 chr3B 78.788 363 65 10 2444 2802 578764525 578764171 5.390000e-57 233.0
71 TraesCS6D01G004000 chr3B 83.432 169 19 5 2801 2966 733453172 733453334 2.010000e-31 148.0
72 TraesCS6D01G004000 chr3B 91.379 58 4 1 1274 1331 783114975 783114919 2.670000e-10 78.7
73 TraesCS6D01G004000 chr4B 86.782 174 20 2 5883 6056 666055723 666055893 3.290000e-44 191.0
74 TraesCS6D01G004000 chr4B 95.652 46 2 0 2801 2846 662686611 662686656 3.460000e-09 75.0
75 TraesCS6D01G004000 chr4A 85.714 189 17 8 2991 3171 710771461 710771647 3.290000e-44 191.0
76 TraesCS6D01G004000 chr4A 89.552 67 4 3 1267 1331 601307495 601307430 2.070000e-11 82.4
77 TraesCS6D01G004000 chr5D 82.474 194 23 9 2993 3177 526764593 526764784 9.280000e-35 159.0
78 TraesCS6D01G004000 chr5D 82.979 188 21 9 2993 3171 526765553 526765738 9.280000e-35 159.0
79 TraesCS6D01G004000 chr5D 94.231 52 3 0 1274 1325 496097751 496097700 7.430000e-11 80.5
80 TraesCS6D01G004000 chr5A 92.941 85 6 0 3087 3171 643313787 643313703 3.380000e-24 124.0
81 TraesCS6D01G004000 chr5A 94.872 78 4 0 3094 3171 690844839 690844762 1.220000e-23 122.0
82 TraesCS6D01G004000 chr5A 91.011 89 8 0 3087 3175 690845913 690845825 4.380000e-23 121.0
83 TraesCS6D01G004000 chr1B 90.667 75 6 1 2983 3056 19539115 19539041 2.050000e-16 99.0
84 TraesCS6D01G004000 chr1B 93.750 64 4 0 2993 3056 19341743 19341680 7.380000e-16 97.1
85 TraesCS6D01G004000 chr1B 93.750 64 4 0 2993 3056 19375675 19375612 7.380000e-16 97.1
86 TraesCS6D01G004000 chr1B 93.750 64 4 0 2993 3056 19440480 19440417 7.380000e-16 97.1
87 TraesCS6D01G004000 chr1B 93.750 64 4 0 2993 3056 19474602 19474539 7.380000e-16 97.1
88 TraesCS6D01G004000 chr7A 88.000 75 8 1 2983 3056 31990531 31990457 4.440000e-13 87.9
89 TraesCS6D01G004000 chr7A 88.000 75 8 1 2983 3056 31998491 31998565 4.440000e-13 87.9
90 TraesCS6D01G004000 chr7A 88.571 70 8 0 2986 3055 32000037 32000106 1.600000e-12 86.1
91 TraesCS6D01G004000 chr2A 93.220 59 3 1 2924 2981 1649994 1649936 1.600000e-12 86.1
92 TraesCS6D01G004000 chr2A 89.831 59 6 0 1273 1331 10377670 10377728 9.610000e-10 76.8
93 TraesCS6D01G004000 chr2A 100.000 32 0 0 3140 3171 761041336 761041305 9.680000e-05 60.2
94 TraesCS6D01G004000 chr1D 90.476 63 4 2 1269 1330 125125457 125125518 2.070000e-11 82.4
95 TraesCS6D01G004000 chr7B 94.231 52 3 0 1272 1323 572030662 572030611 7.430000e-11 80.5
96 TraesCS6D01G004000 chr7D 97.561 41 1 0 2803 2843 484387297 484387257 4.470000e-08 71.3


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 TraesCS6D01G004000 chr6D 2066079 2075004 8925 False 16484.000000 16484 100.000000 1 8926 1 chr6D.!!$F1 8925
1 TraesCS6D01G004000 chr6D 2028631 2037743 9112 False 1083.777778 5773 89.839111 1 8844 9 chr6D.!!$F3 8843
2 TraesCS6D01G004000 chr6B 4790226 4798513 8287 True 1622.142857 7380 90.301286 1 8494 7 chr6B.!!$R5 8493
3 TraesCS6D01G004000 chr6B 4532410 4538836 6426 True 1528.800000 5376 88.792000 652 8097 5 chr6B.!!$R2 7445
4 TraesCS6D01G004000 chr6B 4552917 4562065 9148 True 1432.857143 2501 90.142714 4 8926 7 chr6B.!!$R3 8922
5 TraesCS6D01G004000 chr6B 4578737 4586733 7996 True 946.800000 2933 91.096800 4 8502 10 chr6B.!!$R4 8498
6 TraesCS6D01G004000 chr6A 859864 868519 8655 True 1573.500000 5847 89.230333 1 8911 6 chr6A.!!$R2 8910
7 TraesCS6D01G004000 chr6A 817512 825806 8294 True 1445.428571 4916 88.556571 59 8852 7 chr6A.!!$R1 8793
8 TraesCS6D01G004000 chr2D 633675429 633684382 8953 False 1674.333333 3049 83.761667 1329 8436 3 chr2D.!!$F3 7107
9 TraesCS6D01G004000 chr3A 581614852 581615727 875 True 730.000000 730 82.175000 5188 6056 1 chr3A.!!$R2 868
10 TraesCS6D01G004000 chr3A 581394764 581395630 866 True 632.000000 632 80.357000 5235 6108 1 chr3A.!!$R1 873
11 TraesCS6D01G004000 chr3A 581837770 581842830 5060 True 529.500000 798 82.169500 2444 7977 2 chr3A.!!$R3 5533
12 TraesCS6D01G004000 chr3D 441179444 441180058 614 True 488.000000 488 81.099000 1352 1966 1 chr3D.!!$R1 614

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
650 1922 0.392336 TTGCATGGTTGGTCAAAGCC 59.608 50.000 0.00 0.00 35.29 4.35 F
1493 3231 1.480212 TTGTCGAGGGTGGCATGAGT 61.480 55.000 0.00 0.00 0.00 3.41 F
2811 5054 0.243365 TTCACATGATTGTTGGCGCC 59.757 50.000 22.73 22.73 32.34 6.53 F
2812 5055 1.514657 CACATGATTGTTGGCGCCG 60.515 57.895 23.90 6.26 32.34 6.46 F
4309 8775 1.396301 CTCTGCGAATGGACTGAAAGC 59.604 52.381 0.00 0.00 37.60 3.51 F
4686 9167 0.734309 TTGCCATGCTCTATTGCACG 59.266 50.000 0.00 0.00 46.33 5.34 F
5374 10911 1.069668 GTGACGGTTCCTGTGGTACTT 59.930 52.381 0.00 0.00 0.00 2.24 F
5772 11315 1.276705 GAGTCAACAGACTTCCTCCCC 59.723 57.143 0.00 0.00 42.48 4.81 F
7544 13659 0.846015 CCCCAGTATTGATGGAGCCA 59.154 55.000 0.00 0.00 40.51 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 3492 1.204941 GTGAGCACCTCGTTCCATAGT 59.795 52.381 0.00 0.0 32.35 2.12 R
3110 5491 1.544246 TGTGAGTCATCTACCCGTGTG 59.456 52.381 0.00 0.0 0.00 3.82 R
4028 8295 2.278330 GGGGGCTTTTGTGGAGCAG 61.278 63.158 0.00 0.0 41.89 4.24 R
4584 9065 3.695816 GAGCTGGTTGTTTGACAAGTTC 58.304 45.455 0.00 0.0 39.00 3.01 R
5780 11323 2.542824 CCACCCATGTTTGTTTCGTGTC 60.543 50.000 0.00 0.0 0.00 3.67 R
6487 12497 1.080569 GCTCCACCAACGCAAATGG 60.081 57.895 0.00 0.0 43.84 3.16 R
6936 12991 6.462487 CCACCACCACCACTATTAGTACTATG 60.462 46.154 2.79 0.0 0.00 2.23 R
7651 13766 1.511768 GCGAGGTCTACCACACTCC 59.488 63.158 1.26 0.0 38.89 3.85 R
8881 15377 0.609131 ACCATGGGCACAGCTTGTAC 60.609 55.000 18.09 0.0 0.00 2.90 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
52 53 6.094186 GGATGAGGAGAAGAAAAATGTACACC 59.906 42.308 0.00 0.00 0.00 4.16
54 55 4.324267 AGGAGAAGAAAAATGTACACCGG 58.676 43.478 0.00 0.00 0.00 5.28
70 71 1.141881 CGGTAGCGTCCAAGCAGAT 59.858 57.895 6.07 0.00 40.15 2.90
218 1018 4.506654 GCTTAGGATCGTTTCTTAATCGCA 59.493 41.667 0.00 0.00 0.00 5.10
508 1673 0.839946 ATTAGCATCGTGGGCTTCCT 59.160 50.000 3.82 0.00 42.62 3.36
648 1920 2.605338 CGAGTTGCATGGTTGGTCAAAG 60.605 50.000 0.00 0.00 0.00 2.77
650 1922 0.392336 TTGCATGGTTGGTCAAAGCC 59.608 50.000 0.00 0.00 35.29 4.35
680 1975 3.052036 CCGGAAAATTGCAAAGACAGTG 58.948 45.455 1.71 0.00 0.00 3.66
681 1976 3.243367 CCGGAAAATTGCAAAGACAGTGA 60.243 43.478 1.71 0.00 0.00 3.41
682 1977 4.358851 CGGAAAATTGCAAAGACAGTGAA 58.641 39.130 1.71 0.00 0.00 3.18
683 1978 4.803088 CGGAAAATTGCAAAGACAGTGAAA 59.197 37.500 1.71 0.00 0.00 2.69
789 2090 5.125417 CACCTACCGATGAACAAAATTCCAT 59.875 40.000 0.00 0.00 0.00 3.41
798 2099 4.815308 TGAACAAAATTCCATGGCAAGTTG 59.185 37.500 6.96 11.19 0.00 3.16
799 2100 3.140623 ACAAAATTCCATGGCAAGTTGC 58.859 40.909 19.87 19.87 44.08 4.17
812 2113 4.088823 GCAAGTTGCAGTTCCTCTATTG 57.911 45.455 22.90 0.00 44.26 1.90
813 2114 3.753272 GCAAGTTGCAGTTCCTCTATTGA 59.247 43.478 22.90 0.00 44.26 2.57
814 2115 4.397417 GCAAGTTGCAGTTCCTCTATTGAT 59.603 41.667 22.90 0.00 44.26 2.57
815 2116 5.105997 GCAAGTTGCAGTTCCTCTATTGATT 60.106 40.000 22.90 0.00 44.26 2.57
816 2117 6.549952 CAAGTTGCAGTTCCTCTATTGATTC 58.450 40.000 0.00 0.00 0.00 2.52
817 2118 5.189180 AGTTGCAGTTCCTCTATTGATTCC 58.811 41.667 0.00 0.00 0.00 3.01
818 2119 4.842531 TGCAGTTCCTCTATTGATTCCA 57.157 40.909 0.00 0.00 0.00 3.53
819 2120 5.378230 TGCAGTTCCTCTATTGATTCCAT 57.622 39.130 0.00 0.00 0.00 3.41
820 2121 6.499106 TGCAGTTCCTCTATTGATTCCATA 57.501 37.500 0.00 0.00 0.00 2.74
821 2122 6.528321 TGCAGTTCCTCTATTGATTCCATAG 58.472 40.000 0.00 0.00 0.00 2.23
822 2123 6.327365 TGCAGTTCCTCTATTGATTCCATAGA 59.673 38.462 7.14 7.14 0.00 1.98
823 2124 7.016957 TGCAGTTCCTCTATTGATTCCATAGAT 59.983 37.037 7.67 0.00 0.00 1.98
824 2125 7.882271 GCAGTTCCTCTATTGATTCCATAGATT 59.118 37.037 7.67 0.00 0.00 2.40
829 2130 9.896645 TCCTCTATTGATTCCATAGATTAATGC 57.103 33.333 7.67 0.00 0.00 3.56
830 2131 9.676861 CCTCTATTGATTCCATAGATTAATGCA 57.323 33.333 7.67 0.00 0.00 3.96
875 2244 4.022676 ACTTTTGTTTTCTTCACACCGTGT 60.023 37.500 0.00 0.00 34.79 4.49
1198 2587 5.926542 TCTGCATGTAGTACAGTTCTGTTTC 59.073 40.000 10.80 5.49 33.12 2.78
1204 2594 6.880484 TGTAGTACAGTTCTGTTTCCTTCAA 58.120 36.000 10.74 0.00 0.00 2.69
1219 2626 6.707440 TTCCTTCAACATGCAACTTAAAGA 57.293 33.333 0.00 0.00 0.00 2.52
1255 2662 7.851228 TCCATACATTATTATCGGCTTCTCAT 58.149 34.615 0.00 0.00 0.00 2.90
1320 3046 8.768019 TCTTGCGTATCATTTCATTGATAGAAG 58.232 33.333 0.00 0.00 38.83 2.85
1323 3049 7.714813 TGCGTATCATTTCATTGATAGAAGGAA 59.285 33.333 0.00 0.00 38.83 3.36
1493 3231 1.480212 TTGTCGAGGGTGGCATGAGT 61.480 55.000 0.00 0.00 0.00 3.41
1754 3492 4.020039 ACAAATTGGGACCACACGAGTATA 60.020 41.667 0.00 0.00 0.00 1.47
1755 3493 3.814005 ATTGGGACCACACGAGTATAC 57.186 47.619 0.00 0.00 0.00 1.47
1862 3600 1.635487 TCATTGGAGCTAAGGCCACTT 59.365 47.619 5.01 0.00 40.74 3.16
1949 3687 4.465632 TGGCAACGTCACTGACTATATT 57.534 40.909 7.58 0.00 42.51 1.28
2013 3762 1.604604 TCTAAGTTGTGCCTGCCAAC 58.395 50.000 12.59 12.59 41.94 3.77
2071 3840 9.249053 TGCATATAATGTGTTTCCTCCTTTTTA 57.751 29.630 0.00 0.00 0.00 1.52
2138 3909 4.464069 AAGTCTCAAGGTGATGAGTAGC 57.536 45.455 4.41 0.00 45.65 3.58
2190 4152 6.864360 AAGTAAATGCAAAACTGTACCGTA 57.136 33.333 0.00 0.00 0.00 4.02
2192 4154 5.759273 AGTAAATGCAAAACTGTACCGTACA 59.241 36.000 10.92 10.92 37.13 2.90
2194 4156 5.502153 AATGCAAAACTGTACCGTACAAA 57.498 34.783 12.39 0.00 38.38 2.83
2195 4157 5.699097 ATGCAAAACTGTACCGTACAAAT 57.301 34.783 12.39 1.58 38.38 2.32
2196 4158 5.502153 TGCAAAACTGTACCGTACAAATT 57.498 34.783 12.39 7.30 38.38 1.82
2615 4847 1.353804 GTCGTTTCTTGCGCAACCA 59.646 52.632 21.02 5.75 0.00 3.67
2806 5049 9.874215 GTATATGACAGATTCACATGATTGTTG 57.126 33.333 0.00 0.00 36.92 3.33
2807 5050 5.632244 TGACAGATTCACATGATTGTTGG 57.368 39.130 0.00 0.00 32.34 3.77
2808 5051 4.082625 TGACAGATTCACATGATTGTTGGC 60.083 41.667 0.00 0.00 32.34 4.52
2809 5052 3.119743 ACAGATTCACATGATTGTTGGCG 60.120 43.478 0.00 0.00 32.34 5.69
2810 5053 2.159338 AGATTCACATGATTGTTGGCGC 60.159 45.455 0.00 0.00 32.34 6.53
2811 5054 0.243365 TTCACATGATTGTTGGCGCC 59.757 50.000 22.73 22.73 32.34 6.53
2812 5055 1.514657 CACATGATTGTTGGCGCCG 60.515 57.895 23.90 6.26 32.34 6.46
2813 5056 2.580326 CATGATTGTTGGCGCCGC 60.580 61.111 23.90 17.91 0.00 6.53
2865 5108 4.081030 CGCTGCCTCGCACAACTG 62.081 66.667 0.00 0.00 33.79 3.16
2866 5109 2.974698 GCTGCCTCGCACAACTGT 60.975 61.111 0.00 0.00 33.79 3.55
2909 5152 2.545742 CCTCTCACGAACACACACATGA 60.546 50.000 0.00 0.00 0.00 3.07
3030 5292 8.912787 ATCAACTTAAATAGTCTGTACGAGTG 57.087 34.615 0.00 0.00 35.54 3.51
3064 5326 3.118408 GGCCACTAACTCACATATGGACA 60.118 47.826 7.80 0.00 35.16 4.02
3066 5328 4.512944 GCCACTAACTCACATATGGACATG 59.487 45.833 7.80 0.00 0.00 3.21
3085 5347 4.015406 CTGGCCGGCCACTACACA 62.015 66.667 44.23 22.02 41.89 3.72
3094 5475 2.572290 GGCCACTACACATAATGACCC 58.428 52.381 0.00 0.00 0.00 4.46
3097 5478 2.210116 CACTACACATAATGACCCGGC 58.790 52.381 0.00 0.00 0.00 6.13
3110 5491 2.428171 TGACCCGGCTAACTACACATAC 59.572 50.000 0.00 0.00 0.00 2.39
3116 5497 3.184541 GGCTAACTACACATACACACGG 58.815 50.000 0.00 0.00 0.00 4.94
3117 5498 3.184541 GCTAACTACACATACACACGGG 58.815 50.000 0.00 0.00 0.00 5.28
3130 5511 1.544246 CACACGGGTAGATGACTCACA 59.456 52.381 0.00 0.00 0.00 3.58
3194 5575 7.975058 ACAATGATCGTGATGCAATTTATTCAA 59.025 29.630 0.00 0.00 0.00 2.69
3248 5629 4.679197 TGCATGCGTTTACAAAGAAATGTC 59.321 37.500 14.09 0.00 34.75 3.06
3285 5666 1.811965 TGACTCCATTTGGCATTGTCG 59.188 47.619 0.00 0.00 34.44 4.35
3378 5790 8.451908 AGTATGCCAGAATATAAAGGTCAAAC 57.548 34.615 0.00 0.00 0.00 2.93
3531 7373 2.067365 TGGAGATGCTTCGGCTAGTA 57.933 50.000 0.00 0.00 42.37 1.82
3545 7387 5.202004 TCGGCTAGTAAAAGGAGAGAGATT 58.798 41.667 0.00 0.00 0.00 2.40
3909 8151 1.850345 TCCTGGGAAGGTTTGACTTGT 59.150 47.619 0.00 0.00 0.00 3.16
4065 8517 5.076873 CCCCCTCTTGATTTAAGTGTTTCA 58.923 41.667 0.00 0.00 37.65 2.69
4309 8775 1.396301 CTCTGCGAATGGACTGAAAGC 59.604 52.381 0.00 0.00 37.60 3.51
4686 9167 0.734309 TTGCCATGCTCTATTGCACG 59.266 50.000 0.00 0.00 46.33 5.34
4707 9188 9.154847 TGCACGATTCCTTGATATATTTCTATG 57.845 33.333 0.00 0.00 0.00 2.23
4881 9422 7.667557 AGCTACACATGTTCACTTTCTACTTA 58.332 34.615 0.00 0.00 0.00 2.24
5062 9673 2.369860 TGTGAGCCTTCAACATGAGAGT 59.630 45.455 0.00 0.00 34.49 3.24
5112 9725 3.244976 CGATTTGAAAACCATGCAGTCC 58.755 45.455 0.00 0.00 0.00 3.85
5141 10676 5.695424 AAAGAGGTTGGAGGTCCTTATAC 57.305 43.478 0.00 0.00 36.82 1.47
5142 10677 4.348020 AGAGGTTGGAGGTCCTTATACA 57.652 45.455 0.00 0.00 36.82 2.29
5374 10911 1.069668 GTGACGGTTCCTGTGGTACTT 59.930 52.381 0.00 0.00 0.00 2.24
5409 10946 5.945310 AGTATTGATGTGCATAACCTGGAT 58.055 37.500 0.00 0.00 0.00 3.41
5772 11315 1.276705 GAGTCAACAGACTTCCTCCCC 59.723 57.143 0.00 0.00 42.48 4.81
5798 11341 3.641437 ATGACACGAAACAAACATGGG 57.359 42.857 0.00 0.00 0.00 4.00
5801 11365 1.407258 ACACGAAACAAACATGGGTGG 59.593 47.619 0.00 0.00 0.00 4.61
5893 11562 9.478768 CATATGCAATAAATACAATTGGCTTGA 57.521 29.630 10.83 0.00 35.34 3.02
6056 11725 6.928348 TCAACAACTCATAAGAGGAGGTTA 57.072 37.500 0.00 0.00 46.44 2.85
6198 11905 9.528489 AGCCAAACCTAAAATCTGTAAAATCTA 57.472 29.630 0.00 0.00 0.00 1.98
6239 11946 9.506018 CAAATTCAAGGTTTTAATTCCTCCAAT 57.494 29.630 0.42 0.63 33.09 3.16
6407 12401 6.456501 TCTAAAGTCAAAGTAGTCCAGCTTC 58.543 40.000 0.00 0.00 0.00 3.86
6588 12616 7.717436 TCTTGAAGTCACAACCATGTAATGTTA 59.283 33.333 0.00 0.00 44.81 2.41
6649 12681 6.069963 AGGAAAGCATAGTCACACTCCTAAAT 60.070 38.462 0.00 0.00 30.24 1.40
6683 12731 9.865321 CATGACATGGAATTGTAAGAATCTTTT 57.135 29.630 7.60 0.00 0.00 2.27
6839 12888 8.492673 TCGAATATCAAAGCTCAGTTTTATGT 57.507 30.769 0.00 0.00 0.00 2.29
6969 13025 2.453812 GGTGGTGGTGGTGGTGGTA 61.454 63.158 0.00 0.00 0.00 3.25
6985 13047 6.352222 GGTGGTGGTAGTAGTAGTAGTAGTGA 60.352 46.154 3.00 0.00 0.00 3.41
6988 13050 8.992349 TGGTGGTAGTAGTAGTAGTAGTGATAA 58.008 37.037 3.00 0.00 0.00 1.75
7013 13075 5.192176 AGTGGTGGTAGAAGTAGTAGTAGC 58.808 45.833 0.00 0.00 0.00 3.58
7181 13260 2.223340 GCTGCACAAGGTCCATATTTCG 60.223 50.000 0.00 0.00 0.00 3.46
7544 13659 0.846015 CCCCAGTATTGATGGAGCCA 59.154 55.000 0.00 0.00 40.51 4.75
7613 13728 4.456911 GGCAATATTCATGACATCGTGGAT 59.543 41.667 0.00 0.59 35.38 3.41
7651 13766 0.172578 TACGATGCCAGTTCACTCCG 59.827 55.000 0.00 0.00 0.00 4.63
8138 14274 3.065095 GGAAGCATCTTCTTCATGTCAGC 59.935 47.826 6.54 0.00 43.14 4.26
8156 14292 7.739498 TGTCAGCACTCGTGATATATTACTA 57.261 36.000 6.13 0.00 0.00 1.82
8157 14293 7.807680 TGTCAGCACTCGTGATATATTACTAG 58.192 38.462 7.41 7.41 0.00 2.57
8158 14294 7.094762 TGTCAGCACTCGTGATATATTACTAGG 60.095 40.741 12.11 4.60 0.00 3.02
8159 14295 7.119407 GTCAGCACTCGTGATATATTACTAGGA 59.881 40.741 12.11 0.61 0.00 2.94
8160 14296 7.829706 TCAGCACTCGTGATATATTACTAGGAT 59.170 37.037 12.11 0.61 0.00 3.24
8161 14297 8.462811 CAGCACTCGTGATATATTACTAGGATT 58.537 37.037 12.11 0.00 0.00 3.01
8162 14298 9.026121 AGCACTCGTGATATATTACTAGGATTT 57.974 33.333 12.11 0.00 0.00 2.17
8163 14299 9.291664 GCACTCGTGATATATTACTAGGATTTC 57.708 37.037 12.11 0.00 0.00 2.17
8272 14714 3.138304 TCCCTAATATGTCACGCAATGC 58.862 45.455 0.00 0.00 0.00 3.56
8332 14782 4.472108 ACCCTATGAACATTTCCCGAGTTA 59.528 41.667 0.00 0.00 0.00 2.24
8333 14783 5.132144 ACCCTATGAACATTTCCCGAGTTAT 59.868 40.000 0.00 0.00 0.00 1.89
8334 14784 5.470098 CCCTATGAACATTTCCCGAGTTATG 59.530 44.000 0.00 0.00 0.00 1.90
8353 14820 7.823665 AGTTATGGACAGAATTATACGCGATA 58.176 34.615 15.93 3.36 0.00 2.92
8476 14943 1.137872 CTGCAGCGTCTAATCCTCCTT 59.862 52.381 0.00 0.00 0.00 3.36
8478 14945 1.137086 GCAGCGTCTAATCCTCCTTCA 59.863 52.381 0.00 0.00 0.00 3.02
8479 14946 2.224161 GCAGCGTCTAATCCTCCTTCAT 60.224 50.000 0.00 0.00 0.00 2.57
8511 14978 1.086696 CTGTTGTGGCCTTGTATCCG 58.913 55.000 3.32 0.00 0.00 4.18
8520 14987 1.622607 CCTTGTATCCGGACAGCCCA 61.623 60.000 6.12 0.00 34.14 5.36
8563 15036 2.572149 TAACGGGCTGCACGTACCA 61.572 57.895 31.59 15.95 44.83 3.25
8669 15150 2.543641 TCTCACACATAGCTGCATTCG 58.456 47.619 1.02 0.00 0.00 3.34
8679 15160 1.400846 AGCTGCATTCGCTCAAAGATG 59.599 47.619 1.02 0.00 39.64 2.90
8688 15170 6.359087 GCATTCGCTCAAAGATGAAATATCAC 59.641 38.462 0.00 0.00 34.87 3.06
8724 15206 2.073056 CAGTACAAGCGTGTATGCCAA 58.927 47.619 15.58 0.00 42.18 4.52
8779 15267 1.066573 GCCACCGATATCCTGGATGAG 60.067 57.143 19.42 9.69 0.00 2.90
8878 15374 7.706607 GCTGCAGTCATACCGATGAATTATATA 59.293 37.037 16.64 0.00 43.77 0.86
8879 15375 8.926715 TGCAGTCATACCGATGAATTATATAC 57.073 34.615 0.00 0.00 43.77 1.47
8881 15377 7.167635 GCAGTCATACCGATGAATTATATACCG 59.832 40.741 0.00 0.00 43.77 4.02
8922 15422 2.032528 CAGGCTCAGGCGACCAAA 59.967 61.111 0.00 0.00 39.81 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.340337 GACGCTACCGGTGTACATTTT 58.660 47.619 19.93 0.00 38.95 1.82
52 53 0.460284 AATCTGCTTGGACGCTACCG 60.460 55.000 0.00 0.00 41.14 4.02
54 55 0.375106 GCAATCTGCTTGGACGCTAC 59.625 55.000 0.00 0.00 40.96 3.58
70 71 4.142315 GCTTTGGCTCTCATGAATTAGCAA 60.142 41.667 20.06 10.68 36.68 3.91
83 84 1.845809 CGACGCTTTGCTTTGGCTCT 61.846 55.000 0.00 0.00 39.59 4.09
189 190 4.744795 AGAAACGATCCTAAGCAGACAT 57.255 40.909 0.00 0.00 0.00 3.06
190 191 4.537135 AAGAAACGATCCTAAGCAGACA 57.463 40.909 0.00 0.00 0.00 3.41
218 1018 4.137543 GGATCGTTTCTTAATCAGCCCAT 58.862 43.478 0.00 0.00 0.00 4.00
650 1922 2.635443 AATTTTCCGGCCAGCGTGG 61.635 57.895 2.24 0.00 41.55 4.94
660 1944 3.963665 TCACTGTCTTTGCAATTTTCCG 58.036 40.909 0.00 0.00 0.00 4.30
680 1975 6.090223 ACTTGACGTGGAATTTTGTTTGTTTC 59.910 34.615 0.00 0.00 0.00 2.78
681 1976 5.929415 ACTTGACGTGGAATTTTGTTTGTTT 59.071 32.000 0.00 0.00 0.00 2.83
682 1977 5.474825 ACTTGACGTGGAATTTTGTTTGTT 58.525 33.333 0.00 0.00 0.00 2.83
683 1978 5.066968 ACTTGACGTGGAATTTTGTTTGT 57.933 34.783 0.00 0.00 0.00 2.83
754 2055 3.380479 TCGGTAGGTGAACTTGTCTTG 57.620 47.619 0.00 0.00 0.00 3.02
789 2090 0.183492 AGAGGAACTGCAACTTGCCA 59.817 50.000 11.29 0.00 44.23 4.92
798 2099 6.763355 TCTATGGAATCAATAGAGGAACTGC 58.237 40.000 3.28 0.00 41.55 4.40
803 2104 9.896645 GCATTAATCTATGGAATCAATAGAGGA 57.103 33.333 12.45 1.34 31.35 3.71
804 2105 9.676861 TGCATTAATCTATGGAATCAATAGAGG 57.323 33.333 12.45 2.45 31.35 3.69
809 2110 9.976511 CAACTTGCATTAATCTATGGAATCAAT 57.023 29.630 0.00 0.00 35.67 2.57
810 2111 7.922278 GCAACTTGCATTAATCTATGGAATCAA 59.078 33.333 8.97 0.00 44.26 2.57
811 2112 7.428020 GCAACTTGCATTAATCTATGGAATCA 58.572 34.615 8.97 0.00 44.26 2.57
812 2113 7.864307 GCAACTTGCATTAATCTATGGAATC 57.136 36.000 8.97 0.00 44.26 2.52
827 2128 9.420677 GTTTGGTTCAAAGAAATGCAACTTGCA 62.421 37.037 18.60 18.60 44.98 4.08
828 2129 3.870419 TGGTTCAAAGAAATGCAACTTGC 59.130 39.130 6.82 6.82 45.29 4.01
829 2130 6.092533 AGTTTGGTTCAAAGAAATGCAACTTG 59.907 34.615 0.00 0.00 33.82 3.16
830 2131 6.172630 AGTTTGGTTCAAAGAAATGCAACTT 58.827 32.000 0.00 0.00 33.82 2.66
831 2132 5.733676 AGTTTGGTTCAAAGAAATGCAACT 58.266 33.333 0.00 0.00 33.82 3.16
832 2133 6.421377 AAGTTTGGTTCAAAGAAATGCAAC 57.579 33.333 0.00 0.00 33.82 4.17
833 2134 7.040823 ACAAAAGTTTGGTTCAAAGAAATGCAA 60.041 29.630 8.55 0.00 42.34 4.08
834 2135 6.429385 ACAAAAGTTTGGTTCAAAGAAATGCA 59.571 30.769 8.55 0.00 42.34 3.96
875 2244 0.681887 CATGACTTGGCCTCCATGCA 60.682 55.000 3.32 0.00 32.73 3.96
1182 2571 6.880484 TGTTGAAGGAAACAGAACTGTACTA 58.120 36.000 7.90 0.00 44.13 1.82
1198 2587 7.869429 AGATTTCTTTAAGTTGCATGTTGAAGG 59.131 33.333 11.08 0.00 0.00 3.46
1204 2594 7.715657 TGTTCAGATTTCTTTAAGTTGCATGT 58.284 30.769 0.00 0.00 0.00 3.21
1293 3019 8.837788 TCTATCAATGAAATGATACGCAAGAT 57.162 30.769 0.00 0.00 40.44 2.40
1294 3020 8.661352 TTCTATCAATGAAATGATACGCAAGA 57.339 30.769 0.00 0.00 40.44 3.02
1299 3025 8.226448 GCTTCCTTCTATCAATGAAATGATACG 58.774 37.037 0.00 0.00 40.44 3.06
1320 3046 2.987232 ACGGTTTAGGATTCTGCTTCC 58.013 47.619 0.00 0.00 0.00 3.46
1323 3049 2.304761 TCCAACGGTTTAGGATTCTGCT 59.695 45.455 0.00 0.00 0.00 4.24
1333 3059 2.156098 GCTCCAACATCCAACGGTTTA 58.844 47.619 0.00 0.00 0.00 2.01
1754 3492 1.204941 GTGAGCACCTCGTTCCATAGT 59.795 52.381 0.00 0.00 32.35 2.12
1755 3493 1.927895 GTGAGCACCTCGTTCCATAG 58.072 55.000 0.00 0.00 32.35 2.23
1862 3600 6.711194 TGACAAAAGGGTACATCGTATTTTCA 59.289 34.615 0.00 0.00 0.00 2.69
1949 3687 1.822990 GACCCGTCATCTCACCTTGTA 59.177 52.381 0.00 0.00 0.00 2.41
1980 3728 7.414540 GGCACAACTTAGATCTACTCCAAAATG 60.415 40.741 0.67 0.00 0.00 2.32
2035 3790 7.759489 AACACATTATATGCATTACGGGATT 57.241 32.000 3.54 0.00 0.00 3.01
2036 3791 7.094377 GGAAACACATTATATGCATTACGGGAT 60.094 37.037 3.54 0.00 0.00 3.85
2037 3792 6.205853 GGAAACACATTATATGCATTACGGGA 59.794 38.462 3.54 0.00 0.00 5.14
2038 3793 6.206634 AGGAAACACATTATATGCATTACGGG 59.793 38.462 3.54 0.00 0.00 5.28
2039 3794 7.202016 AGGAAACACATTATATGCATTACGG 57.798 36.000 3.54 0.00 0.00 4.02
2040 3795 7.173218 AGGAGGAAACACATTATATGCATTACG 59.827 37.037 3.54 0.00 0.00 3.18
2138 3909 1.338136 ACGGGATCTAGCAACCCTGG 61.338 60.000 13.84 0.00 41.28 4.45
2262 4488 1.774110 TGGAGTTGCTTTGCCAGAAA 58.226 45.000 0.00 0.00 0.00 2.52
2505 4737 3.576982 TGTAGATGTCGAACCTCCTGTTT 59.423 43.478 0.00 0.00 37.29 2.83
2615 4847 4.166725 TGTTCAGGAGGAAGGATGCATTAT 59.833 41.667 0.00 0.00 35.82 1.28
2819 5062 4.803426 AAGAAGAGGCGCCGCGAG 62.803 66.667 24.88 1.54 0.00 5.03
2820 5063 4.796231 GAAGAAGAGGCGCCGCGA 62.796 66.667 24.88 0.00 0.00 5.87
2821 5064 4.803426 AGAAGAAGAGGCGCCGCG 62.803 66.667 24.88 8.83 0.00 6.46
2865 5108 4.086457 AGAGAAGAGAGAAACCTCAGGAC 58.914 47.826 0.00 0.00 35.68 3.85
2866 5109 4.340617 GAGAGAAGAGAGAAACCTCAGGA 58.659 47.826 0.00 0.00 35.68 3.86
2909 5152 4.686091 CGTTGTGTGTGTAGAGTTCATCAT 59.314 41.667 0.00 0.00 0.00 2.45
2973 5216 3.562176 GGAAAAATGAGGCCTCAGGAAGA 60.562 47.826 37.03 15.98 43.61 2.87
2974 5217 2.757314 GGAAAAATGAGGCCTCAGGAAG 59.243 50.000 37.03 0.00 43.61 3.46
2975 5218 2.109834 TGGAAAAATGAGGCCTCAGGAA 59.890 45.455 37.03 17.15 43.61 3.36
2976 5219 1.710244 TGGAAAAATGAGGCCTCAGGA 59.290 47.619 37.03 17.54 43.61 3.86
2977 5220 2.220653 TGGAAAAATGAGGCCTCAGG 57.779 50.000 37.03 0.00 43.61 3.86
2980 5223 4.648307 AGATGAATGGAAAAATGAGGCCTC 59.352 41.667 26.78 26.78 0.00 4.70
3077 5339 2.158957 AGCCGGGTCATTATGTGTAGTG 60.159 50.000 0.00 0.00 0.00 2.74
3078 5340 2.116238 AGCCGGGTCATTATGTGTAGT 58.884 47.619 0.00 0.00 0.00 2.73
3079 5341 2.910688 AGCCGGGTCATTATGTGTAG 57.089 50.000 0.00 0.00 0.00 2.74
3080 5342 3.707611 AGTTAGCCGGGTCATTATGTGTA 59.292 43.478 10.79 0.00 0.00 2.90
3081 5343 2.504175 AGTTAGCCGGGTCATTATGTGT 59.496 45.455 10.79 0.00 0.00 3.72
3083 5345 3.707611 TGTAGTTAGCCGGGTCATTATGT 59.292 43.478 10.79 0.00 0.00 2.29
3084 5346 4.056050 GTGTAGTTAGCCGGGTCATTATG 58.944 47.826 10.79 0.00 0.00 1.90
3085 5347 3.707611 TGTGTAGTTAGCCGGGTCATTAT 59.292 43.478 10.79 0.00 0.00 1.28
3094 5475 2.850060 CGTGTGTATGTGTAGTTAGCCG 59.150 50.000 0.00 0.00 0.00 5.52
3097 5478 4.445452 ACCCGTGTGTATGTGTAGTTAG 57.555 45.455 0.00 0.00 0.00 2.34
3110 5491 1.544246 TGTGAGTCATCTACCCGTGTG 59.456 52.381 0.00 0.00 0.00 3.82
3116 5497 2.093500 TGCATGGTGTGAGTCATCTACC 60.093 50.000 14.04 14.04 35.32 3.18
3117 5498 3.251479 TGCATGGTGTGAGTCATCTAC 57.749 47.619 0.00 0.00 0.00 2.59
3130 5511 8.009622 TGTCATATTGATTGTATTTGCATGGT 57.990 30.769 0.00 0.00 0.00 3.55
3248 5629 4.248859 GAGTCATGATATCCCGGTCATTG 58.751 47.826 0.00 0.00 32.98 2.82
3285 5666 8.483758 TGTTTCTACTACTTTAATGAGGATCCC 58.516 37.037 8.55 0.11 0.00 3.85
3357 5769 5.125417 GCAGTTTGACCTTTATATTCTGGCA 59.875 40.000 0.00 0.00 0.00 4.92
3397 5809 8.455903 AATTCATTCCTCAACTATATGGTGTG 57.544 34.615 0.00 0.00 34.34 3.82
3531 7373 8.052141 CCTAAATTCTCCAATCTCTCTCCTTTT 58.948 37.037 0.00 0.00 0.00 2.27
3545 7387 9.725206 ATACTAGAAGTTACCCTAAATTCTCCA 57.275 33.333 7.73 0.00 46.43 3.86
3765 8002 7.559897 ACACAGAAAAATATGAACCGGGAATAT 59.440 33.333 6.32 3.07 0.00 1.28
3909 8151 3.641436 TCTGGTTGCTCTTTGAGTAGTCA 59.359 43.478 0.00 0.00 31.39 3.41
4028 8295 2.278330 GGGGGCTTTTGTGGAGCAG 61.278 63.158 0.00 0.00 41.89 4.24
4261 8726 5.029650 TCTGCAAAAGCAACTATGTTACG 57.970 39.130 0.00 0.00 0.00 3.18
4309 8775 5.482006 TCATGAATGATACGGCTAATCCAG 58.518 41.667 0.00 0.00 34.01 3.86
4584 9065 3.695816 GAGCTGGTTGTTTGACAAGTTC 58.304 45.455 0.00 0.00 39.00 3.01
4734 9251 6.037610 GTGATAATGAACCTTGTGTGGAGATC 59.962 42.308 0.00 0.00 0.00 2.75
4736 9253 5.221823 TGTGATAATGAACCTTGTGTGGAGA 60.222 40.000 0.00 0.00 0.00 3.71
4740 9257 6.558771 TTCTGTGATAATGAACCTTGTGTG 57.441 37.500 0.00 0.00 0.00 3.82
4881 9422 1.624336 ATGGAAGTGTGTTGCTGCAT 58.376 45.000 1.84 0.00 0.00 3.96
5062 9673 9.337714 TCCCATCATGAATAGGTCATTATCTTA 57.662 33.333 0.00 0.00 45.13 2.10
5112 9725 4.492611 GACCTCCAACCTCTTTACTAACG 58.507 47.826 0.00 0.00 0.00 3.18
5141 10676 6.628185 ACACGACTAACCCTCTAATAGTTTG 58.372 40.000 0.00 0.00 30.33 2.93
5142 10677 6.847421 ACACGACTAACCCTCTAATAGTTT 57.153 37.500 0.00 0.00 30.33 2.66
5207 10742 8.591940 TCATCTCTCAAGCATATTAGCTACAAT 58.408 33.333 0.00 0.00 45.89 2.71
5374 10911 5.246203 GCACATCAATACTAGGAGGGATACA 59.754 44.000 0.00 0.00 39.74 2.29
5454 10991 5.707411 AATTTTATTGCAGCGATGAAAGC 57.293 34.783 15.75 0.00 0.00 3.51
5772 11315 3.491639 TGTTTGTTTCGTGTCATACCTCG 59.508 43.478 0.00 0.00 0.00 4.63
5780 11323 2.542824 CCACCCATGTTTGTTTCGTGTC 60.543 50.000 0.00 0.00 0.00 3.67
5798 11341 6.599244 TGTCTATTGAAGAAACCATGATCCAC 59.401 38.462 0.00 0.00 35.47 4.02
5801 11365 7.856145 ACTGTCTATTGAAGAAACCATGATC 57.144 36.000 0.00 0.00 35.47 2.92
5866 11511 9.478768 CAAGCCAATTGTATTTATTGCATATGA 57.521 29.630 6.97 0.00 33.95 2.15
5881 11542 4.420522 ACCAAACATTCAAGCCAATTGT 57.579 36.364 4.43 0.00 40.05 2.71
5893 11562 9.280174 CGGGAATACATATAGTTACCAAACATT 57.720 33.333 0.00 0.00 38.12 2.71
6198 11905 5.831702 TGAATTTGCCAACTTGCATTTTT 57.168 30.435 0.00 0.00 41.70 1.94
6239 11946 6.767524 AGGTGTCTGTTTTGATTGTTTGTA 57.232 33.333 0.00 0.00 0.00 2.41
6487 12497 1.080569 GCTCCACCAACGCAAATGG 60.081 57.895 0.00 0.00 43.84 3.16
6683 12731 6.772716 AGTTGATTTCTTTCTTACTGGCTTCA 59.227 34.615 0.00 0.00 0.00 3.02
6936 12991 6.462487 CCACCACCACCACTATTAGTACTATG 60.462 46.154 2.79 0.00 0.00 2.23
6988 13050 6.997476 GCTACTACTACTTCTACCACCACTAT 59.003 42.308 0.00 0.00 0.00 2.12
7544 13659 5.301805 CCAGTTTGGTAGATGAAAGGTTTGT 59.698 40.000 0.00 0.00 31.35 2.83
7613 13728 4.768448 TCGTACTGATCCAACAACCTCTTA 59.232 41.667 0.00 0.00 0.00 2.10
7651 13766 1.511768 GCGAGGTCTACCACACTCC 59.488 63.158 1.26 0.00 38.89 3.85
7913 14037 0.395312 TTCCCTTTCACCGTCCAGAC 59.605 55.000 0.00 0.00 0.00 3.51
8156 14292 5.032327 GTGGGTAACGGATAAGAAATCCT 57.968 43.478 2.75 0.00 36.07 3.24
8292 14739 4.173290 AGGGTTTGGTAAAAGTAGCACA 57.827 40.909 0.00 0.00 37.45 4.57
8332 14782 6.151312 ACTCTATCGCGTATAATTCTGTCCAT 59.849 38.462 5.77 0.00 0.00 3.41
8333 14783 5.472478 ACTCTATCGCGTATAATTCTGTCCA 59.528 40.000 5.77 0.00 0.00 4.02
8334 14784 5.940595 ACTCTATCGCGTATAATTCTGTCC 58.059 41.667 5.77 0.00 0.00 4.02
8454 14921 0.878086 GAGGATTAGACGCTGCAGCC 60.878 60.000 32.07 19.42 37.91 4.85
8467 14934 4.728772 TGTGTTCAACATGAAGGAGGATT 58.271 39.130 0.00 0.00 37.00 3.01
8511 14978 4.937431 GGCGGCTATGGGCTGTCC 62.937 72.222 0.00 0.00 45.48 4.02
8542 15011 2.572149 TACGTGCAGCCCGTTACCA 61.572 57.895 8.61 0.00 39.60 3.25
8587 15068 1.526917 GCTGTTGATGCCGGCCTAT 60.527 57.895 26.77 12.32 0.00 2.57
8669 15150 4.274459 AGCCGTGATATTTCATCTTTGAGC 59.726 41.667 0.00 0.00 33.56 4.26
8679 15160 1.668419 ACCTGCAGCCGTGATATTTC 58.332 50.000 8.66 0.00 0.00 2.17
8688 15170 2.024176 ACTGTTATAACCTGCAGCCG 57.976 50.000 8.66 0.00 32.65 5.52
8724 15206 1.202879 TGAACTGAAAGCGTCCCCAAT 60.203 47.619 0.00 0.00 37.60 3.16
8779 15267 9.227777 AGTTTGTACTTGGTTAGGATGAATTAC 57.772 33.333 0.00 0.00 0.00 1.89
8810 15305 9.547753 TGCAGGTTATATCTATTTTTCACTCTC 57.452 33.333 0.00 0.00 0.00 3.20
8878 15374 2.032071 GGGCACAGCTTGTACGGT 59.968 61.111 0.00 0.00 0.00 4.83
8879 15375 1.377202 ATGGGCACAGCTTGTACGG 60.377 57.895 0.00 0.00 0.00 4.02
8881 15377 0.609131 ACCATGGGCACAGCTTGTAC 60.609 55.000 18.09 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.