Multiple sequence alignment - TraesCS4B01G033800

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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 TraesCS4B01G033800 chr4B 100.000 7016 0 0 1 7016 24839684 24832669 0.000000e+00 12957.0
1 TraesCS4B01G033800 chr4B 91.021 1381 80 24 3574 4922 25273186 25274554 0.000000e+00 1823.0
2 TraesCS4B01G033800 chr4B 89.907 1189 69 19 5024 6193 25274551 25275707 0.000000e+00 1483.0
3 TraesCS4B01G033800 chr4B 87.094 1170 84 33 1124 2235 25270945 25272105 0.000000e+00 1262.0
4 TraesCS4B01G033800 chr4B 86.578 678 55 21 6364 7016 24770001 24769335 0.000000e+00 715.0
5 TraesCS4B01G033800 chr4B 88.027 451 36 14 3073 3518 25272422 25272859 1.040000e-142 518.0
6 TraesCS4B01G033800 chr4B 89.545 220 19 4 2696 2913 25272113 25272330 6.930000e-70 276.0
7 TraesCS4B01G033800 chr4B 96.753 154 5 0 935 1088 25270016 25270169 2.510000e-64 257.0
8 TraesCS4B01G033800 chr4B 92.308 104 6 2 2298 2399 427495781 427495884 5.670000e-31 147.0
9 TraesCS4B01G033800 chr4B 92.063 63 5 0 6233 6295 25385026 25385088 9.690000e-14 89.8
10 TraesCS4B01G033800 chr3B 94.777 1455 60 13 1108 2555 452549586 452551031 0.000000e+00 2252.0
11 TraesCS4B01G033800 chr3B 97.727 1232 18 2 3701 4922 452552758 452553989 0.000000e+00 2111.0
12 TraesCS4B01G033800 chr3B 93.842 1153 40 12 5024 6174 452553986 452555109 0.000000e+00 1707.0
13 TraesCS4B01G033800 chr3B 98.920 926 10 0 2594 3519 452551459 452552384 0.000000e+00 1655.0
14 TraesCS4B01G033800 chr3B 92.547 644 43 3 292 935 790745645 790745007 0.000000e+00 918.0
15 TraesCS4B01G033800 chr3B 98.635 513 4 1 6505 7014 452563686 452564198 0.000000e+00 905.0
16 TraesCS4B01G033800 chr3B 89.857 700 56 12 233 928 817240479 817241167 0.000000e+00 885.0
17 TraesCS4B01G033800 chr3B 86.471 680 55 18 6364 7016 452696511 452697180 0.000000e+00 712.0
18 TraesCS4B01G033800 chr3B 98.540 274 4 0 6233 6506 452563330 452563603 1.060000e-132 484.0
19 TraesCS4B01G033800 chr3B 89.412 340 34 2 65 402 293749438 293749099 1.810000e-115 427.0
20 TraesCS4B01G033800 chr3B 95.000 160 2 1 935 1088 452548645 452548804 5.440000e-61 246.0
21 TraesCS4B01G033800 chr3B 96.324 136 5 0 767 902 230935532 230935667 2.550000e-54 224.0
22 TraesCS4B01G033800 chr3B 94.898 98 4 1 3545 3642 452552675 452552771 1.220000e-32 152.0
23 TraesCS4B01G033800 chr3B 93.814 97 5 1 2303 2399 672737286 672737191 2.040000e-30 145.0
24 TraesCS4B01G033800 chr4D 90.731 1381 84 20 3574 4922 14995396 14996764 0.000000e+00 1801.0
25 TraesCS4B01G033800 chr4D 90.750 1146 64 12 1122 2235 14991469 14992604 0.000000e+00 1491.0
26 TraesCS4B01G033800 chr4D 90.000 1030 49 21 5024 6036 14996761 14997753 0.000000e+00 1282.0
27 TraesCS4B01G033800 chr4D 90.411 657 51 7 6366 7016 14398922 14399572 0.000000e+00 854.0
28 TraesCS4B01G033800 chr4D 86.680 518 53 10 6233 6749 15149079 15149581 1.710000e-155 560.0
29 TraesCS4B01G033800 chr4D 85.024 414 53 8 1811 2222 448186444 448186038 5.060000e-111 412.0
30 TraesCS4B01G033800 chr4D 86.082 388 47 5 2609 2995 448185474 448185093 1.820000e-110 411.0
31 TraesCS4B01G033800 chr4D 87.279 283 27 2 2696 2978 14992612 14992885 1.470000e-81 315.0
32 TraesCS4B01G033800 chr4D 89.427 227 20 3 3264 3488 14994797 14995021 4.140000e-72 283.0
33 TraesCS4B01G033800 chr4D 97.403 154 4 0 935 1088 14990511 14990664 5.400000e-66 263.0
34 TraesCS4B01G033800 chr4D 93.388 121 8 0 2426 2546 55352438 55352558 5.590000e-41 180.0
35 TraesCS4B01G033800 chr4D 81.618 136 16 9 2289 2420 501331680 501331810 3.460000e-18 104.0
36 TraesCS4B01G033800 chr4A 91.519 1014 44 15 5032 6032 586432783 586431799 0.000000e+00 1358.0
37 TraesCS4B01G033800 chr4A 87.425 1161 88 27 1118 2235 586436803 586435658 0.000000e+00 1282.0
38 TraesCS4B01G033800 chr4A 89.659 822 53 17 3574 4370 586434559 586433745 0.000000e+00 1018.0
39 TraesCS4B01G033800 chr4A 88.473 668 53 14 6364 7016 585693620 585692962 0.000000e+00 785.0
40 TraesCS4B01G033800 chr4A 91.800 561 37 4 4365 4922 586433492 586432938 0.000000e+00 773.0
41 TraesCS4B01G033800 chr4A 86.408 515 50 9 6236 6749 586091548 586091053 4.790000e-151 545.0
42 TraesCS4B01G033800 chr4A 87.082 449 42 9 3074 3518 586435344 586434908 1.760000e-135 494.0
43 TraesCS4B01G033800 chr4A 86.380 279 28 3 2701 2978 586435652 586435383 5.320000e-76 296.0
44 TraesCS4B01G033800 chr4A 97.403 154 4 0 935 1088 586437704 586437551 5.400000e-66 263.0
45 TraesCS4B01G033800 chr4A 93.814 97 6 0 2299 2395 241153027 241152931 5.670000e-31 147.0
46 TraesCS4B01G033800 chr4A 90.090 111 9 1 2277 2387 597739858 597739966 7.340000e-30 143.0
47 TraesCS4B01G033800 chr4A 82.692 156 20 6 1359 1513 538169695 538169844 1.590000e-26 132.0
48 TraesCS4B01G033800 chr4A 93.750 80 5 0 1144 1223 586426385 586426306 3.440000e-23 121.0
49 TraesCS4B01G033800 chr1A 89.306 879 76 4 65 934 22652661 22651792 0.000000e+00 1086.0
50 TraesCS4B01G033800 chr1A 84.334 383 49 7 2609 2986 462128919 462129295 1.440000e-96 364.0
51 TraesCS4B01G033800 chr1A 91.429 105 6 3 2288 2390 566604758 566604655 2.640000e-29 141.0
52 TraesCS4B01G033800 chr7B 87.238 956 92 7 10 935 599340784 599341739 0.000000e+00 1062.0
53 TraesCS4B01G033800 chr7B 90.404 792 69 4 62 847 462244108 462244898 0.000000e+00 1035.0
54 TraesCS4B01G033800 chr7B 89.855 138 12 2 2425 2562 673996225 673996090 7.230000e-40 176.0
55 TraesCS4B01G033800 chr7B 94.681 94 5 0 2299 2392 715360403 715360310 5.670000e-31 147.0
56 TraesCS4B01G033800 chr6B 88.041 878 92 9 65 936 133417869 133416999 0.000000e+00 1027.0
57 TraesCS4B01G033800 chr6B 84.247 876 69 19 65 934 144897463 144896651 0.000000e+00 789.0
58 TraesCS4B01G033800 chr6B 85.545 422 31 16 10 402 308582154 308581734 1.410000e-111 414.0
59 TraesCS4B01G033800 chr6B 96.396 111 4 0 4916 5026 1158144 1158254 4.320000e-42 183.0
60 TraesCS4B01G033800 chr6B 86.577 149 20 0 2789 2937 88719806 88719658 1.570000e-36 165.0
61 TraesCS4B01G033800 chr6B 84.848 66 5 4 2346 2411 290718570 290718630 2.110000e-05 62.1
62 TraesCS4B01G033800 chr2B 87.833 863 81 13 56 913 180439015 180438172 0.000000e+00 990.0
63 TraesCS4B01G033800 chr2B 86.364 396 44 5 10 402 407871604 407871216 2.340000e-114 424.0
64 TraesCS4B01G033800 chr2B 96.364 110 4 0 4917 5026 369499451 369499342 1.550000e-41 182.0
65 TraesCS4B01G033800 chr2B 92.800 125 6 3 4908 5031 206676867 206676989 2.010000e-40 178.0
66 TraesCS4B01G033800 chr5B 85.142 949 103 24 10 935 567876964 567876031 0.000000e+00 937.0
67 TraesCS4B01G033800 chr5B 88.295 393 41 1 10 402 497162020 497161633 3.830000e-127 466.0
68 TraesCS4B01G033800 chr5B 89.941 338 34 0 65 402 470018815 470018478 3.000000e-118 436.0
69 TraesCS4B01G033800 chr5B 96.364 110 4 0 4916 5025 665971279 665971388 1.550000e-41 182.0
70 TraesCS4B01G033800 chr5B 93.388 121 8 0 2426 2546 214108401 214108521 5.590000e-41 180.0
71 TraesCS4B01G033800 chr5A 94.343 548 31 0 387 934 313876064 313876611 0.000000e+00 841.0
72 TraesCS4B01G033800 chr5A 88.506 522 46 6 6505 7016 40877895 40877378 2.780000e-173 619.0
73 TraesCS4B01G033800 chr5A 91.071 112 8 1 2294 2403 113720079 113720190 4.380000e-32 150.0
74 TraesCS4B01G033800 chr1D 86.094 791 94 8 6236 7016 320391232 320390448 0.000000e+00 837.0
75 TraesCS4B01G033800 chr3D 93.583 561 34 2 374 934 268944618 268945176 0.000000e+00 835.0
76 TraesCS4B01G033800 chr3D 96.610 118 3 1 4916 5032 33827600 33827483 2.000000e-45 195.0
77 TraesCS4B01G033800 chr3D 97.222 108 3 0 4918 5025 523325665 523325558 4.320000e-42 183.0
78 TraesCS4B01G033800 chr3A 94.161 548 32 0 387 934 746265975 746265428 0.000000e+00 835.0
79 TraesCS4B01G033800 chr3A 93.388 121 8 0 2429 2549 12239979 12239859 5.590000e-41 180.0
80 TraesCS4B01G033800 chr3A 93.388 121 8 0 2429 2549 638983761 638983641 5.590000e-41 180.0
81 TraesCS4B01G033800 chr1B 85.768 794 91 11 6236 7016 433427650 433426866 0.000000e+00 821.0
82 TraesCS4B01G033800 chr1B 90.342 497 45 3 62 555 359443390 359443886 0.000000e+00 649.0
83 TraesCS4B01G033800 chr1B 85.042 361 39 10 2644 2998 326789018 326789369 3.110000e-93 353.0
84 TraesCS4B01G033800 chr2A 88.922 668 50 14 6364 7016 195824730 195824072 0.000000e+00 802.0
85 TraesCS4B01G033800 chr2A 86.232 138 17 2 2411 2546 747602289 747602426 1.580000e-31 148.0
86 TraesCS4B01G033800 chr2A 84.252 127 16 3 2287 2412 107387169 107387292 3.440000e-23 121.0
87 TraesCS4B01G033800 chr5D 99.074 108 1 0 4918 5025 554363515 554363622 2.000000e-45 195.0
88 TraesCS4B01G033800 chr5D 92.800 125 9 0 2427 2551 385720422 385720546 1.550000e-41 182.0
89 TraesCS4B01G033800 chr5D 88.596 114 8 5 2301 2414 525478258 525478150 4.420000e-27 134.0
90 TraesCS4B01G033800 chr2D 97.273 110 3 0 4917 5026 549006367 549006476 3.340000e-43 187.0
91 TraesCS4B01G033800 chr2D 94.167 120 7 0 2427 2546 12692238 12692357 4.320000e-42 183.0
92 TraesCS4B01G033800 chr2D 91.525 118 10 0 2429 2546 586154926 586154809 5.630000e-36 163.0
93 TraesCS4B01G033800 chr2D 89.855 69 6 1 12 80 618312227 618312160 3.490000e-13 87.9
94 TraesCS4B01G033800 chr6A 97.248 109 3 0 4917 5025 612565248 612565356 1.200000e-42 185.0
95 TraesCS4B01G033800 chr7A 93.388 121 8 0 2426 2546 543780215 543780335 5.590000e-41 180.0
96 TraesCS4B01G033800 chrUn 88.793 116 7 6 2274 2387 197752368 197752479 3.410000e-28 137.0
97 TraesCS4B01G033800 chr7D 88.182 110 11 2 2302 2411 22964256 22964363 5.710000e-26 130.0
98 TraesCS4B01G033800 chr6D 88.393 112 7 5 2301 2412 187277362 187277467 5.710000e-26 130.0


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 TraesCS4B01G033800 chr4B 24832669 24839684 7015 True 12957.000000 12957 100.000000 1 7016 1 chr4B.!!$R2 7015
1 TraesCS4B01G033800 chr4B 25270016 25275707 5691 False 936.500000 1823 90.391167 935 6193 6 chr4B.!!$F3 5258
2 TraesCS4B01G033800 chr4B 24769335 24770001 666 True 715.000000 715 86.578000 6364 7016 1 chr4B.!!$R1 652
3 TraesCS4B01G033800 chr3B 452548645 452555109 6464 False 1353.833333 2252 95.860667 935 6174 6 chr3B.!!$F4 5239
4 TraesCS4B01G033800 chr3B 790745007 790745645 638 True 918.000000 918 92.547000 292 935 1 chr3B.!!$R3 643
5 TraesCS4B01G033800 chr3B 817240479 817241167 688 False 885.000000 885 89.857000 233 928 1 chr3B.!!$F3 695
6 TraesCS4B01G033800 chr3B 452696511 452697180 669 False 712.000000 712 86.471000 6364 7016 1 chr3B.!!$F2 652
7 TraesCS4B01G033800 chr3B 452563330 452564198 868 False 694.500000 905 98.587500 6233 7014 2 chr3B.!!$F5 781
8 TraesCS4B01G033800 chr4D 14990511 14997753 7242 False 905.833333 1801 90.931667 935 6036 6 chr4D.!!$F5 5101
9 TraesCS4B01G033800 chr4D 14398922 14399572 650 False 854.000000 854 90.411000 6366 7016 1 chr4D.!!$F1 650
10 TraesCS4B01G033800 chr4D 15149079 15149581 502 False 560.000000 560 86.680000 6233 6749 1 chr4D.!!$F2 516
11 TraesCS4B01G033800 chr4D 448185093 448186444 1351 True 411.500000 412 85.553000 1811 2995 2 chr4D.!!$R1 1184
12 TraesCS4B01G033800 chr4A 585692962 585693620 658 True 785.000000 785 88.473000 6364 7016 1 chr4A.!!$R2 652
13 TraesCS4B01G033800 chr4A 586431799 586437704 5905 True 783.428571 1358 90.181143 935 6032 7 chr4A.!!$R5 5097
14 TraesCS4B01G033800 chr1A 22651792 22652661 869 True 1086.000000 1086 89.306000 65 934 1 chr1A.!!$R1 869
15 TraesCS4B01G033800 chr7B 599340784 599341739 955 False 1062.000000 1062 87.238000 10 935 1 chr7B.!!$F2 925
16 TraesCS4B01G033800 chr7B 462244108 462244898 790 False 1035.000000 1035 90.404000 62 847 1 chr7B.!!$F1 785
17 TraesCS4B01G033800 chr6B 133416999 133417869 870 True 1027.000000 1027 88.041000 65 936 1 chr6B.!!$R2 871
18 TraesCS4B01G033800 chr6B 144896651 144897463 812 True 789.000000 789 84.247000 65 934 1 chr6B.!!$R3 869
19 TraesCS4B01G033800 chr2B 180438172 180439015 843 True 990.000000 990 87.833000 56 913 1 chr2B.!!$R1 857
20 TraesCS4B01G033800 chr5B 567876031 567876964 933 True 937.000000 937 85.142000 10 935 1 chr5B.!!$R3 925
21 TraesCS4B01G033800 chr5A 313876064 313876611 547 False 841.000000 841 94.343000 387 934 1 chr5A.!!$F2 547
22 TraesCS4B01G033800 chr5A 40877378 40877895 517 True 619.000000 619 88.506000 6505 7016 1 chr5A.!!$R1 511
23 TraesCS4B01G033800 chr1D 320390448 320391232 784 True 837.000000 837 86.094000 6236 7016 1 chr1D.!!$R1 780
24 TraesCS4B01G033800 chr3D 268944618 268945176 558 False 835.000000 835 93.583000 374 934 1 chr3D.!!$F1 560
25 TraesCS4B01G033800 chr3A 746265428 746265975 547 True 835.000000 835 94.161000 387 934 1 chr3A.!!$R3 547
26 TraesCS4B01G033800 chr1B 433426866 433427650 784 True 821.000000 821 85.768000 6236 7016 1 chr1B.!!$R1 780
27 TraesCS4B01G033800 chr2A 195824072 195824730 658 True 802.000000 802 88.922000 6364 7016 1 chr2A.!!$R1 652

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
436 515 0.905337 GCCAGGTATAGCCGGATCCT 60.905 60.0 5.05 0.00 43.70 3.24 F
1063 1154 0.813210 CAAGATCGGGAAGCTGCTCC 60.813 60.0 1.00 6.10 34.41 4.70 F
1694 2655 1.112315 TGGGTGCTGGCGAACATTTT 61.112 50.0 0.00 0.00 0.00 1.82 F
3317 6511 0.896940 GGGAGTACCGTCCTGTCACA 60.897 60.0 1.52 0.00 36.75 3.58 F
4934 8734 0.620556 AACTACTCCCTCCGTACGGA 59.379 55.0 33.55 33.55 42.90 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 2655 3.461061 CAAGCTTTCAGTGACAGTCAGA 58.539 45.455 2.53 0.00 0.00 3.27 R
2589 3748 3.994392 GGTTCAAGCACGAGATAGTTTCA 59.006 43.478 0.00 0.00 0.00 2.69 R
3667 7186 1.737793 GGCATAAACCCTTGAGTGACG 59.262 52.381 0.00 0.00 0.00 4.35 R
5007 8807 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
6215 10211 0.321653 GCATCACTTTCCCGTGTCCT 60.322 55.000 0.00 0.00 36.33 3.85 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
39 40 4.923710 CCGGTGCGATCGATGCGA 62.924 66.667 21.57 0.00 41.13 5.10
41 42 2.026157 GGTGCGATCGATGCGAGA 59.974 61.111 21.57 4.23 39.91 4.04
168 202 3.646976 CGATGGATGGCAGCTGCG 61.647 66.667 31.19 11.96 43.26 5.18
436 515 0.905337 GCCAGGTATAGCCGGATCCT 60.905 60.000 5.05 0.00 43.70 3.24
599 678 1.685765 TGGCTCGGTGTAGATGGCT 60.686 57.895 0.00 0.00 0.00 4.75
625 704 4.612412 GGTGGTGACGGTCGGCAA 62.612 66.667 0.00 0.00 33.39 4.52
643 723 3.781307 CGGAAGCGATGGGGTGGA 61.781 66.667 0.00 0.00 0.00 4.02
675 755 3.724508 ACATGATCGGAACTGAGCTAG 57.275 47.619 0.00 0.00 0.00 3.42
942 1027 1.337074 CGTACTCTAACAACGGCCCAA 60.337 52.381 0.00 0.00 33.13 4.12
1063 1154 0.813210 CAAGATCGGGAAGCTGCTCC 60.813 60.000 1.00 6.10 34.41 4.70
1136 2045 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1379 2339 4.892934 TCTTTTAGCTTGGTTGGTCACAAT 59.107 37.500 0.00 0.00 39.13 2.71
1577 2538 8.790718 CAGCAATACTATGAAAATAGGCTGAAT 58.209 33.333 12.54 0.00 45.69 2.57
1599 2560 4.662468 ATGCTCGATTCTCTTAGAAGCA 57.338 40.909 6.51 6.51 40.41 3.91
1659 2620 3.688049 TCTCCATCCCAGACTATGTGA 57.312 47.619 0.00 0.00 0.00 3.58
1694 2655 1.112315 TGGGTGCTGGCGAACATTTT 61.112 50.000 0.00 0.00 0.00 1.82
1726 2687 2.165030 CTGAAAGCTTGGCTGGTATTGG 59.835 50.000 0.00 0.00 39.62 3.16
1838 2799 2.093764 AGCAAGAGAGTTTCCTCATCCG 60.094 50.000 0.00 0.00 40.40 4.18
1944 2908 8.963725 GGATCAAGATGATGAAATTGGCATATA 58.036 33.333 0.00 0.00 37.20 0.86
1952 2916 7.372714 TGATGAAATTGGCATATAAGATGCAC 58.627 34.615 10.81 1.86 46.21 4.57
1953 2917 6.712179 TGAAATTGGCATATAAGATGCACA 57.288 33.333 10.81 4.19 46.21 4.57
1972 2939 9.423061 GATGCACATTTTTCCATTATAATACCC 57.577 33.333 0.00 0.00 0.00 3.69
2100 3067 1.227823 CAGTGTTGTGAAGCGGGGA 60.228 57.895 0.00 0.00 0.00 4.81
2401 3506 6.464180 CGGAGGGAGTACTTCTACTACTGTAT 60.464 46.154 0.01 0.00 34.48 2.29
2437 3542 2.828877 TGTGTTTGTTGTACTCCCTCG 58.171 47.619 0.00 0.00 0.00 4.63
2557 3662 5.513233 ACGGAGGGAGTAATAGACACTTAA 58.487 41.667 0.00 0.00 0.00 1.85
2946 4444 7.931407 TGATGCCATACTCGTATTACAAGAAAT 59.069 33.333 0.00 0.00 0.00 2.17
3097 4598 9.103861 GCAAACAAATCTACTCTAAGAGCTATT 57.896 33.333 0.00 0.00 32.04 1.73
3172 4673 5.945784 ACATGTGGCATACAGTGTAGAAAAT 59.054 36.000 9.25 0.00 43.80 1.82
3317 6511 0.896940 GGGAGTACCGTCCTGTCACA 60.897 60.000 1.52 0.00 36.75 3.58
3519 6715 9.919416 TTGGATCCATCTATCTCAAATTTAACA 57.081 29.630 17.06 0.00 0.00 2.41
3542 6738 7.607250 ACATCTATTGAGCATACTAGTTAGCC 58.393 38.462 0.00 1.28 0.00 3.93
3543 6739 7.453126 ACATCTATTGAGCATACTAGTTAGCCT 59.547 37.037 0.00 0.00 0.00 4.58
3551 7047 7.724506 TGAGCATACTAGTTAGCCTTATAGTGT 59.275 37.037 0.00 0.00 31.25 3.55
3577 7084 8.217799 TCCAGTAAGGCAGTAATGCTTTAATAT 58.782 33.333 19.39 7.80 37.93 1.28
3634 7152 5.181811 CAGTTATCTTGTTCTTGTGATGCCA 59.818 40.000 0.00 0.00 0.00 4.92
3638 7156 5.534207 TCTTGTTCTTGTGATGCCATTTT 57.466 34.783 0.00 0.00 0.00 1.82
3639 7157 5.291178 TCTTGTTCTTGTGATGCCATTTTG 58.709 37.500 0.00 0.00 0.00 2.44
3678 7197 3.374058 AGTTTGTGTTTCGTCACTCAAGG 59.626 43.478 8.80 0.00 38.90 3.61
3680 7199 1.208535 TGTGTTTCGTCACTCAAGGGT 59.791 47.619 8.80 0.00 38.90 4.34
3685 7204 4.513692 TGTTTCGTCACTCAAGGGTTTATG 59.486 41.667 0.00 0.00 0.00 1.90
3686 7205 2.695359 TCGTCACTCAAGGGTTTATGC 58.305 47.619 0.00 0.00 0.00 3.14
3698 7220 6.948886 TCAAGGGTTTATGCCTGTGTTAAATA 59.051 34.615 0.00 0.00 0.00 1.40
3700 7222 7.971368 AGGGTTTATGCCTGTGTTAAATATT 57.029 32.000 0.00 0.00 0.00 1.28
3703 7225 8.421002 GGGTTTATGCCTGTGTTAAATATTGAT 58.579 33.333 0.00 0.00 0.00 2.57
3915 7441 4.883585 GTCCTGAACCATTATGCATTCTCA 59.116 41.667 3.54 0.00 0.00 3.27
4538 8337 1.848652 TGGAGCTGACTGGTAGTACC 58.151 55.000 12.80 12.80 39.22 3.34
4563 8362 6.016360 CAGGATAAAATACCATGCGAATGGAA 60.016 38.462 29.99 7.07 44.39 3.53
4697 8497 1.282875 GTTCGCTCACTTGGGTTGC 59.717 57.895 0.00 0.00 0.00 4.17
4700 8500 0.884704 TCGCTCACTTGGGTTGCTTC 60.885 55.000 0.00 0.00 0.00 3.86
4808 8608 3.518590 CGACGAGGCTAACAAATACCTT 58.481 45.455 0.00 0.00 30.95 3.50
4811 8611 3.006940 CGAGGCTAACAAATACCTTGCA 58.993 45.455 0.00 0.00 38.75 4.08
4891 8691 5.163426 TGCTTGACAAGGTTTCATTCATGTT 60.163 36.000 16.80 0.00 0.00 2.71
4922 8722 2.354203 CCAGCCTCTGTTGGAACTACTC 60.354 54.545 0.00 0.00 45.12 2.59
4923 8723 1.903183 AGCCTCTGTTGGAACTACTCC 59.097 52.381 0.00 0.00 45.64 3.85
4924 8724 1.066071 GCCTCTGTTGGAACTACTCCC 60.066 57.143 0.00 0.00 44.69 4.30
4925 8725 2.541466 CCTCTGTTGGAACTACTCCCT 58.459 52.381 0.00 0.00 44.69 4.20
4926 8726 2.498078 CCTCTGTTGGAACTACTCCCTC 59.502 54.545 0.00 0.00 44.69 4.30
4927 8727 2.498078 CTCTGTTGGAACTACTCCCTCC 59.502 54.545 0.00 0.00 44.69 4.30
4928 8728 1.204941 CTGTTGGAACTACTCCCTCCG 59.795 57.143 0.00 0.00 44.69 4.63
4929 8729 1.264295 GTTGGAACTACTCCCTCCGT 58.736 55.000 0.00 0.00 44.69 4.69
4930 8730 2.225091 TGTTGGAACTACTCCCTCCGTA 60.225 50.000 0.00 0.00 44.69 4.02
4931 8731 2.134789 TGGAACTACTCCCTCCGTAC 57.865 55.000 0.00 0.00 44.69 3.67
4932 8732 1.020437 GGAACTACTCCCTCCGTACG 58.980 60.000 8.69 8.69 38.44 3.67
4933 8733 1.020437 GAACTACTCCCTCCGTACGG 58.980 60.000 28.66 28.66 0.00 4.02
4934 8734 0.620556 AACTACTCCCTCCGTACGGA 59.379 55.000 33.55 33.55 42.90 4.69
4935 8735 0.620556 ACTACTCCCTCCGTACGGAA 59.379 55.000 34.77 21.09 44.66 4.30
4936 8736 1.213926 ACTACTCCCTCCGTACGGAAT 59.786 52.381 34.77 20.47 44.66 3.01
4937 8737 2.305009 CTACTCCCTCCGTACGGAATT 58.695 52.381 34.77 18.48 44.66 2.17
4938 8738 2.442236 ACTCCCTCCGTACGGAATTA 57.558 50.000 34.77 21.70 44.66 1.40
4939 8739 2.027385 ACTCCCTCCGTACGGAATTAC 58.973 52.381 34.77 0.00 44.66 1.89
4940 8740 2.305009 CTCCCTCCGTACGGAATTACT 58.695 52.381 34.77 0.00 44.66 2.24
4941 8741 2.692041 CTCCCTCCGTACGGAATTACTT 59.308 50.000 34.77 0.00 44.66 2.24
4942 8742 2.428171 TCCCTCCGTACGGAATTACTTG 59.572 50.000 34.77 21.77 44.66 3.16
4943 8743 2.167075 CCCTCCGTACGGAATTACTTGT 59.833 50.000 34.77 0.00 44.66 3.16
4944 8744 3.442100 CCTCCGTACGGAATTACTTGTC 58.558 50.000 34.77 0.00 44.66 3.18
4945 8745 3.119388 CCTCCGTACGGAATTACTTGTCA 60.119 47.826 34.77 10.83 44.66 3.58
4946 8746 3.836949 TCCGTACGGAATTACTTGTCAC 58.163 45.455 33.96 0.00 42.05 3.67
4947 8747 2.925563 CCGTACGGAATTACTTGTCACC 59.074 50.000 30.64 0.00 37.50 4.02
4948 8748 3.577667 CGTACGGAATTACTTGTCACCA 58.422 45.455 7.57 0.00 0.00 4.17
4949 8749 3.989167 CGTACGGAATTACTTGTCACCAA 59.011 43.478 7.57 0.00 0.00 3.67
4950 8750 4.448395 CGTACGGAATTACTTGTCACCAAA 59.552 41.667 7.57 0.00 0.00 3.28
4951 8751 5.050227 CGTACGGAATTACTTGTCACCAAAA 60.050 40.000 7.57 0.00 0.00 2.44
4952 8752 6.347888 CGTACGGAATTACTTGTCACCAAAAT 60.348 38.462 7.57 0.00 0.00 1.82
4953 8753 5.768317 ACGGAATTACTTGTCACCAAAATG 58.232 37.500 0.00 0.00 0.00 2.32
4954 8754 5.160641 CGGAATTACTTGTCACCAAAATGG 58.839 41.667 0.00 0.00 45.02 3.16
4955 8755 5.048364 CGGAATTACTTGTCACCAAAATGGA 60.048 40.000 2.85 0.00 40.96 3.41
4956 8756 6.350110 CGGAATTACTTGTCACCAAAATGGAT 60.350 38.462 2.85 0.00 40.96 3.41
4957 8757 6.813152 GGAATTACTTGTCACCAAAATGGATG 59.187 38.462 2.85 0.00 40.96 3.51
4958 8758 6.916360 ATTACTTGTCACCAAAATGGATGT 57.084 33.333 2.85 0.00 40.96 3.06
4959 8759 8.415950 AATTACTTGTCACCAAAATGGATGTA 57.584 30.769 2.85 0.00 40.96 2.29
4960 8760 8.593945 ATTACTTGTCACCAAAATGGATGTAT 57.406 30.769 2.85 0.00 40.96 2.29
4961 8761 6.515272 ACTTGTCACCAAAATGGATGTATC 57.485 37.500 2.85 0.00 40.96 2.24
4962 8762 6.248433 ACTTGTCACCAAAATGGATGTATCT 58.752 36.000 2.85 0.00 40.96 1.98
4963 8763 7.402054 ACTTGTCACCAAAATGGATGTATCTA 58.598 34.615 2.85 0.00 40.96 1.98
4964 8764 7.554118 ACTTGTCACCAAAATGGATGTATCTAG 59.446 37.037 2.85 0.00 40.96 2.43
4965 8765 7.194112 TGTCACCAAAATGGATGTATCTAGA 57.806 36.000 2.85 0.00 40.96 2.43
4966 8766 7.629157 TGTCACCAAAATGGATGTATCTAGAA 58.371 34.615 2.85 0.00 40.96 2.10
4967 8767 7.552687 TGTCACCAAAATGGATGTATCTAGAAC 59.447 37.037 2.85 0.00 40.96 3.01
4968 8768 7.770897 GTCACCAAAATGGATGTATCTAGAACT 59.229 37.037 2.85 0.00 40.96 3.01
4969 8769 8.988060 TCACCAAAATGGATGTATCTAGAACTA 58.012 33.333 2.85 0.00 40.96 2.24
4970 8770 9.613428 CACCAAAATGGATGTATCTAGAACTAA 57.387 33.333 2.85 0.00 40.96 2.24
5000 8800 9.499479 ACATCTAGATACATCCATTTCAATGAC 57.501 33.333 4.54 0.00 38.70 3.06
5001 8801 8.654215 CATCTAGATACATCCATTTCAATGACG 58.346 37.037 4.54 0.00 38.70 4.35
5002 8802 7.951591 TCTAGATACATCCATTTCAATGACGA 58.048 34.615 0.81 0.00 38.70 4.20
5003 8803 8.084684 TCTAGATACATCCATTTCAATGACGAG 58.915 37.037 0.81 0.00 38.70 4.18
5004 8804 6.586344 AGATACATCCATTTCAATGACGAGT 58.414 36.000 0.81 0.00 38.70 4.18
5005 8805 7.726216 AGATACATCCATTTCAATGACGAGTA 58.274 34.615 0.81 0.37 38.70 2.59
5006 8806 8.370940 AGATACATCCATTTCAATGACGAGTAT 58.629 33.333 0.81 4.50 38.70 2.12
5007 8807 8.908786 ATACATCCATTTCAATGACGAGTATT 57.091 30.769 0.81 0.00 38.70 1.89
5008 8808 7.630242 ACATCCATTTCAATGACGAGTATTT 57.370 32.000 0.81 0.00 38.70 1.40
5009 8809 7.697691 ACATCCATTTCAATGACGAGTATTTC 58.302 34.615 0.81 0.00 38.70 2.17
5010 8810 6.677781 TCCATTTCAATGACGAGTATTTCC 57.322 37.500 0.81 0.00 38.70 3.13
5011 8811 5.293324 TCCATTTCAATGACGAGTATTTCCG 59.707 40.000 0.81 0.00 38.70 4.30
5012 8812 5.293324 CCATTTCAATGACGAGTATTTCCGA 59.707 40.000 0.81 0.00 38.70 4.55
5013 8813 6.183360 CCATTTCAATGACGAGTATTTCCGAA 60.183 38.462 0.81 0.00 38.70 4.30
5014 8814 5.773239 TTCAATGACGAGTATTTCCGAAC 57.227 39.130 0.00 0.00 0.00 3.95
5015 8815 3.855379 TCAATGACGAGTATTTCCGAACG 59.145 43.478 0.00 0.00 0.00 3.95
5016 8816 2.267188 TGACGAGTATTTCCGAACGG 57.733 50.000 6.94 6.94 0.00 4.44
5017 8817 1.811965 TGACGAGTATTTCCGAACGGA 59.188 47.619 12.04 12.04 43.52 4.69
5018 8818 2.159476 TGACGAGTATTTCCGAACGGAG 60.159 50.000 15.34 5.60 46.06 4.63
5019 8819 1.133790 ACGAGTATTTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
5020 8820 1.535437 CGAGTATTTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
5021 8821 1.753073 GAGTATTTCCGAACGGAGGGA 59.247 52.381 15.34 7.17 46.06 4.20
5022 8822 1.755380 AGTATTTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5023 8823 1.479730 GTATTTCCGAACGGAGGGAGT 59.520 52.381 15.34 1.96 46.06 3.85
5024 8824 1.856629 ATTTCCGAACGGAGGGAGTA 58.143 50.000 15.34 0.00 46.06 2.59
5025 8825 0.890683 TTTCCGAACGGAGGGAGTAC 59.109 55.000 15.34 0.00 46.06 2.73
5026 8826 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
5080 9035 7.509141 TGCAACTTATGATTTCTCTGTTGAA 57.491 32.000 0.00 0.00 36.43 2.69
5350 9305 3.430790 GCTGCACATTTCCCCCTAATTTC 60.431 47.826 0.00 0.00 0.00 2.17
5364 9319 6.293244 CCCCCTAATTTCTAAAGCGTAATTCG 60.293 42.308 0.00 0.00 43.12 3.34
5365 9320 6.293244 CCCCTAATTTCTAAAGCGTAATTCGG 60.293 42.308 0.00 0.00 40.26 4.30
5374 9329 2.325509 GCGTAATTCGGTGCTTTTGT 57.674 45.000 0.00 0.00 40.26 2.83
5375 9330 2.657184 GCGTAATTCGGTGCTTTTGTT 58.343 42.857 0.00 0.00 40.26 2.83
5376 9331 3.047093 GCGTAATTCGGTGCTTTTGTTT 58.953 40.909 0.00 0.00 40.26 2.83
5377 9332 3.487942 GCGTAATTCGGTGCTTTTGTTTT 59.512 39.130 0.00 0.00 40.26 2.43
5378 9333 4.026393 GCGTAATTCGGTGCTTTTGTTTTT 60.026 37.500 0.00 0.00 40.26 1.94
5379 9334 5.419530 CGTAATTCGGTGCTTTTGTTTTTG 58.580 37.500 0.00 0.00 35.71 2.44
5380 9335 5.004916 CGTAATTCGGTGCTTTTGTTTTTGT 59.995 36.000 0.00 0.00 35.71 2.83
5381 9336 6.196724 CGTAATTCGGTGCTTTTGTTTTTGTA 59.803 34.615 0.00 0.00 35.71 2.41
5382 9337 6.969828 AATTCGGTGCTTTTGTTTTTGTAA 57.030 29.167 0.00 0.00 0.00 2.41
5383 9338 7.546778 AATTCGGTGCTTTTGTTTTTGTAAT 57.453 28.000 0.00 0.00 0.00 1.89
5384 9339 6.576551 TTCGGTGCTTTTGTTTTTGTAATC 57.423 33.333 0.00 0.00 0.00 1.75
5385 9340 5.044558 TCGGTGCTTTTGTTTTTGTAATCC 58.955 37.500 0.00 0.00 0.00 3.01
5457 9412 2.821378 TGATCCATTGGTGCAAAGACAG 59.179 45.455 1.86 0.00 0.00 3.51
5523 9478 3.535561 TGCTGCTGAAACCTTCTATAGC 58.464 45.455 0.00 0.00 33.32 2.97
5528 9483 5.348986 TGCTGAAACCTTCTATAGCTTACG 58.651 41.667 0.00 0.00 30.19 3.18
5565 9522 1.008538 CTGAAAACCTGCGTGCCAC 60.009 57.895 0.00 0.00 0.00 5.01
5571 9528 1.754380 AACCTGCGTGCCACTCTGTA 61.754 55.000 0.00 0.00 0.00 2.74
5585 9542 2.076863 CTCTGTAAAACCTTGCTCCCG 58.923 52.381 0.00 0.00 0.00 5.14
5731 9688 0.388520 TGACGGACTCGCAGAACATG 60.389 55.000 0.00 0.00 40.63 3.21
5734 9691 0.716108 CGGACTCGCAGAACATGAAC 59.284 55.000 0.00 0.00 34.09 3.18
5922 9894 4.497291 AGAGGGACAACAAACAACAGTA 57.503 40.909 0.00 0.00 0.00 2.74
5923 9895 5.048846 AGAGGGACAACAAACAACAGTAT 57.951 39.130 0.00 0.00 0.00 2.12
5924 9896 5.445964 AGAGGGACAACAAACAACAGTATT 58.554 37.500 0.00 0.00 0.00 1.89
5925 9897 6.597562 AGAGGGACAACAAACAACAGTATTA 58.402 36.000 0.00 0.00 0.00 0.98
5998 9980 5.929697 TCATTGTTGAAGACTGCTACTTG 57.070 39.130 0.00 0.00 0.00 3.16
6193 10189 1.278302 TTGCAGCCACCCAGCCTATA 61.278 55.000 0.00 0.00 0.00 1.31
6194 10190 1.278302 TGCAGCCACCCAGCCTATAA 61.278 55.000 0.00 0.00 0.00 0.98
6195 10191 0.106719 GCAGCCACCCAGCCTATAAA 60.107 55.000 0.00 0.00 0.00 1.40
6196 10192 1.680338 CAGCCACCCAGCCTATAAAC 58.320 55.000 0.00 0.00 0.00 2.01
6197 10193 1.212935 CAGCCACCCAGCCTATAAACT 59.787 52.381 0.00 0.00 0.00 2.66
6198 10194 1.923148 AGCCACCCAGCCTATAAACTT 59.077 47.619 0.00 0.00 0.00 2.66
6199 10195 3.118038 CAGCCACCCAGCCTATAAACTTA 60.118 47.826 0.00 0.00 0.00 2.24
6200 10196 3.722101 AGCCACCCAGCCTATAAACTTAT 59.278 43.478 0.00 0.00 0.00 1.73
6201 10197 4.911522 AGCCACCCAGCCTATAAACTTATA 59.088 41.667 0.00 0.00 0.00 0.98
6202 10198 5.551977 AGCCACCCAGCCTATAAACTTATAT 59.448 40.000 0.00 0.00 0.00 0.86
6203 10199 5.648092 GCCACCCAGCCTATAAACTTATATG 59.352 44.000 0.00 0.00 0.00 1.78
6204 10200 5.648092 CCACCCAGCCTATAAACTTATATGC 59.352 44.000 8.06 8.06 37.45 3.14
6205 10201 6.237901 CACCCAGCCTATAAACTTATATGCA 58.762 40.000 14.99 0.00 38.74 3.96
6206 10202 6.886459 CACCCAGCCTATAAACTTATATGCAT 59.114 38.462 3.79 3.79 38.74 3.96
6207 10203 8.046708 CACCCAGCCTATAAACTTATATGCATA 58.953 37.037 9.27 9.27 38.74 3.14
6208 10204 8.047310 ACCCAGCCTATAAACTTATATGCATAC 58.953 37.037 8.99 0.00 38.74 2.39
6209 10205 8.267894 CCCAGCCTATAAACTTATATGCATACT 58.732 37.037 8.99 1.39 38.74 2.12
6210 10206 9.102757 CCAGCCTATAAACTTATATGCATACTG 57.897 37.037 8.99 6.83 38.74 2.74
6211 10207 8.607459 CAGCCTATAAACTTATATGCATACTGC 58.393 37.037 8.99 0.00 45.29 4.40
6212 10208 8.543774 AGCCTATAAACTTATATGCATACTGCT 58.456 33.333 8.99 0.00 45.31 4.24
6213 10209 9.167311 GCCTATAAACTTATATGCATACTGCTT 57.833 33.333 8.99 2.93 45.31 3.91
6219 10215 8.608844 AACTTATATGCATACTGCTTAAGGAC 57.391 34.615 20.35 0.00 45.31 3.85
6220 10216 7.735917 ACTTATATGCATACTGCTTAAGGACA 58.264 34.615 20.35 0.00 45.31 4.02
6221 10217 7.657761 ACTTATATGCATACTGCTTAAGGACAC 59.342 37.037 20.35 0.00 45.31 3.67
6222 10218 2.616960 TGCATACTGCTTAAGGACACG 58.383 47.619 4.29 0.00 45.31 4.49
6223 10219 1.933853 GCATACTGCTTAAGGACACGG 59.066 52.381 4.29 0.00 40.96 4.94
6224 10220 2.550978 CATACTGCTTAAGGACACGGG 58.449 52.381 4.29 0.00 0.00 5.28
6225 10221 1.927487 TACTGCTTAAGGACACGGGA 58.073 50.000 4.29 0.00 0.00 5.14
6226 10222 1.053424 ACTGCTTAAGGACACGGGAA 58.947 50.000 4.29 0.00 0.00 3.97
6227 10223 1.418637 ACTGCTTAAGGACACGGGAAA 59.581 47.619 4.29 0.00 0.00 3.13
6228 10224 2.076863 CTGCTTAAGGACACGGGAAAG 58.923 52.381 4.29 0.00 0.00 2.62
6229 10225 1.418637 TGCTTAAGGACACGGGAAAGT 59.581 47.619 4.29 0.00 0.00 2.66
6230 10226 1.804748 GCTTAAGGACACGGGAAAGTG 59.195 52.381 4.29 0.00 46.83 3.16
6231 10227 2.549349 GCTTAAGGACACGGGAAAGTGA 60.549 50.000 4.29 0.00 44.43 3.41
6232 10228 3.868754 GCTTAAGGACACGGGAAAGTGAT 60.869 47.826 4.29 0.00 44.43 3.06
6233 10229 2.185004 AAGGACACGGGAAAGTGATG 57.815 50.000 0.00 0.00 44.43 3.07
6234 10230 0.321653 AGGACACGGGAAAGTGATGC 60.322 55.000 0.00 0.00 44.43 3.91
6361 10363 2.094803 CCATGTTTATGCGCAGACCAAA 60.095 45.455 18.32 10.51 32.79 3.28
6433 10435 5.294552 GGCTTGTAACACTGATCTCCAATAC 59.705 44.000 0.00 0.00 0.00 1.89
6492 10494 4.289672 TCCTTGGCCTACTTTCTTTCTCAT 59.710 41.667 3.32 0.00 0.00 2.90
6537 10626 4.878397 GGGGTACATCATGAAAAGACAGAG 59.122 45.833 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.125961 GGAGTCCCGCTGGATACGT 61.126 63.158 0.00 0.00 44.28 3.57
2 3 2.728817 GGAGTCCCGCTGGATACG 59.271 66.667 0.00 0.00 44.28 3.06
30 31 3.034878 CTCCGGTCTCGCATCGAT 58.965 61.111 0.00 0.00 34.61 3.59
436 515 2.596338 TCGTCACAGCCGTCCAGA 60.596 61.111 0.00 0.00 0.00 3.86
585 664 1.452953 CCGCTAGCCATCTACACCGA 61.453 60.000 9.66 0.00 0.00 4.69
599 678 4.367023 GTCACCACCACGCCGCTA 62.367 66.667 0.00 0.00 0.00 4.26
625 704 4.096003 CCACCCCATCGCTTCCGT 62.096 66.667 0.00 0.00 35.54 4.69
643 723 1.977594 GATCATGTTTTCGCCGCCGT 61.978 55.000 0.00 0.00 35.54 5.68
654 734 3.739519 GCTAGCTCAGTTCCGATCATGTT 60.740 47.826 7.70 0.00 0.00 2.71
675 755 7.017645 CAGCGTCATAATAATTTGGTATCAGC 58.982 38.462 0.00 0.00 0.00 4.26
747 829 3.721706 CTTCCCTCTTGCCCGGCT 61.722 66.667 11.61 0.00 0.00 5.52
822 907 4.351874 CTTGGGAGTCAAGTAAACCTCA 57.648 45.455 0.00 0.00 45.81 3.86
853 938 2.429478 GTCGCTTGCTTAGGGGTTAAA 58.571 47.619 4.21 0.00 37.41 1.52
856 941 1.002502 GGTCGCTTGCTTAGGGGTT 60.003 57.895 4.21 0.00 37.41 4.11
942 1027 1.626356 CCGATGGGGTGTGGATGACT 61.626 60.000 0.00 0.00 0.00 3.41
1088 1179 1.506718 CAGCTGCTGCATCAACAGG 59.493 57.895 17.73 0.00 42.74 4.00
1136 2045 3.883549 GCTCCATCTGCCTCCCCC 61.884 72.222 0.00 0.00 0.00 5.40
1388 2348 8.010105 CCCCAGCTAGATCCTATAAGAAGATAT 58.990 40.741 0.00 0.00 0.00 1.63
1481 2442 4.574674 TCTTACTGCTGATGGTTTGGAT 57.425 40.909 0.00 0.00 0.00 3.41
1528 2489 3.979495 CAGCAAGAAACAGAATCAGCAAC 59.021 43.478 0.00 0.00 0.00 4.17
1577 2538 5.524284 GTGCTTCTAAGAGAATCGAGCATA 58.476 41.667 4.41 0.00 42.67 3.14
1694 2655 3.461061 CAAGCTTTCAGTGACAGTCAGA 58.539 45.455 2.53 0.00 0.00 3.27
1726 2687 5.123344 ACAGTTACTTCCACACAGAAACAAC 59.877 40.000 0.00 0.00 0.00 3.32
1838 2799 8.987890 GCCATAGAGATCATAAAAGAAGAGTTC 58.012 37.037 0.00 0.00 0.00 3.01
1972 2939 6.923928 TGGAAGCAAAATGAAAAAGGAAAG 57.076 33.333 0.00 0.00 0.00 2.62
2013 2980 9.866655 ACAGAGAGATAAGAGACTAGAAATCAT 57.133 33.333 0.00 0.00 0.00 2.45
2582 3741 9.764363 TCAAGCACGAGATAGTTTCATAAATAT 57.236 29.630 0.00 0.00 0.00 1.28
2583 3742 9.594478 TTCAAGCACGAGATAGTTTCATAAATA 57.406 29.630 0.00 0.00 0.00 1.40
2584 3743 8.391106 GTTCAAGCACGAGATAGTTTCATAAAT 58.609 33.333 0.00 0.00 0.00 1.40
2585 3744 7.148474 GGTTCAAGCACGAGATAGTTTCATAAA 60.148 37.037 0.00 0.00 0.00 1.40
2586 3745 6.312918 GGTTCAAGCACGAGATAGTTTCATAA 59.687 38.462 0.00 0.00 0.00 1.90
2587 3746 5.810587 GGTTCAAGCACGAGATAGTTTCATA 59.189 40.000 0.00 0.00 0.00 2.15
2588 3747 4.631813 GGTTCAAGCACGAGATAGTTTCAT 59.368 41.667 0.00 0.00 0.00 2.57
2589 3748 3.994392 GGTTCAAGCACGAGATAGTTTCA 59.006 43.478 0.00 0.00 0.00 2.69
2590 3749 4.246458 AGGTTCAAGCACGAGATAGTTTC 58.754 43.478 0.00 0.00 0.00 2.78
2591 3750 4.273148 AGGTTCAAGCACGAGATAGTTT 57.727 40.909 0.00 0.00 0.00 2.66
2899 4394 7.555195 GCATCATAACATGGATCAGGAATATCA 59.445 37.037 0.00 0.00 0.00 2.15
3002 4501 6.536941 GCTCTGGTTTGGTTGTTTATTTTCAA 59.463 34.615 0.00 0.00 0.00 2.69
3172 4673 5.129634 TGGGAGCAATTTCGCTAATAATGA 58.870 37.500 0.00 0.00 44.01 2.57
3519 6715 8.429237 AAGGCTAACTAGTATGCTCAATAGAT 57.571 34.615 16.28 0.00 0.00 1.98
3523 6719 9.315363 ACTATAAGGCTAACTAGTATGCTCAAT 57.685 33.333 16.28 10.87 0.00 2.57
3525 6721 7.724506 ACACTATAAGGCTAACTAGTATGCTCA 59.275 37.037 16.28 5.91 0.00 4.26
3528 6724 7.039923 TGGACACTATAAGGCTAACTAGTATGC 60.040 40.741 10.49 10.49 0.00 3.14
3533 6729 6.963083 ACTGGACACTATAAGGCTAACTAG 57.037 41.667 0.00 0.00 0.00 2.57
3534 6730 7.504911 CCTTACTGGACACTATAAGGCTAACTA 59.495 40.741 0.00 0.00 37.84 2.24
3537 6733 6.726490 CCTTACTGGACACTATAAGGCTAA 57.274 41.667 0.00 0.00 37.84 3.09
3541 6737 4.406003 ACTGCCTTACTGGACACTATAAGG 59.594 45.833 4.80 4.80 44.43 2.69
3542 6738 5.599999 ACTGCCTTACTGGACACTATAAG 57.400 43.478 0.00 0.00 38.35 1.73
3543 6739 7.497595 CATTACTGCCTTACTGGACACTATAA 58.502 38.462 0.00 0.00 38.35 0.98
3577 7084 4.589798 CCCCAGCAATTGATGATATGGAAA 59.410 41.667 24.73 0.00 33.05 3.13
3651 7170 3.749088 AGTGACGAAACACAAACTGTTCA 59.251 39.130 12.49 0.00 42.70 3.18
3667 7186 1.737793 GGCATAAACCCTTGAGTGACG 59.262 52.381 0.00 0.00 0.00 4.35
3678 7197 9.463443 GATCAATATTTAACACAGGCATAAACC 57.537 33.333 0.00 0.00 0.00 3.27
3685 7204 8.986477 AAAACTGATCAATATTTAACACAGGC 57.014 30.769 0.00 0.00 0.00 4.85
4505 8304 1.487976 AGCTCCATCACCATACCTGTG 59.512 52.381 0.00 0.00 35.01 3.66
4538 8337 5.702865 CCATTCGCATGGTATTTTATCCTG 58.297 41.667 5.85 0.00 44.81 3.86
4563 8362 4.834406 TCTCTATGGGAGGGTTATCAGT 57.166 45.455 0.00 0.00 42.10 3.41
4697 8497 7.987268 TCTACAATAACATAGAAGCACGAAG 57.013 36.000 0.00 0.00 0.00 3.79
4808 8608 1.971481 ACTTCTCACATGTTGCTGCA 58.029 45.000 0.00 0.00 0.00 4.41
4811 8611 4.558226 TCCATACTTCTCACATGTTGCT 57.442 40.909 0.00 0.00 0.00 3.91
4922 8722 2.167075 ACAAGTAATTCCGTACGGAGGG 59.833 50.000 33.67 20.89 46.06 4.30
4923 8723 3.119388 TGACAAGTAATTCCGTACGGAGG 60.119 47.826 33.67 20.29 46.06 4.30
4924 8724 3.855950 GTGACAAGTAATTCCGTACGGAG 59.144 47.826 33.67 23.26 46.06 4.63
4925 8725 3.367292 GGTGACAAGTAATTCCGTACGGA 60.367 47.826 32.61 32.61 43.52 4.69
4926 8726 2.925563 GGTGACAAGTAATTCCGTACGG 59.074 50.000 28.66 28.66 0.00 4.02
4927 8727 3.577667 TGGTGACAAGTAATTCCGTACG 58.422 45.455 8.69 8.69 37.44 3.67
4941 8741 7.194112 TCTAGATACATCCATTTTGGTGACA 57.806 36.000 0.00 0.00 39.03 3.58
4942 8742 7.770897 AGTTCTAGATACATCCATTTTGGTGAC 59.229 37.037 0.00 0.00 39.03 3.67
4943 8743 7.861629 AGTTCTAGATACATCCATTTTGGTGA 58.138 34.615 0.00 0.00 39.03 4.02
4944 8744 9.613428 TTAGTTCTAGATACATCCATTTTGGTG 57.387 33.333 0.00 0.00 39.03 4.17
4974 8774 9.499479 GTCATTGAAATGGATGTATCTAGATGT 57.501 33.333 15.79 1.25 37.03 3.06
4975 8775 8.654215 CGTCATTGAAATGGATGTATCTAGATG 58.346 37.037 15.79 0.00 37.03 2.90
4976 8776 8.588472 TCGTCATTGAAATGGATGTATCTAGAT 58.412 33.333 10.73 10.73 37.03 1.98
4977 8777 7.951591 TCGTCATTGAAATGGATGTATCTAGA 58.048 34.615 0.00 0.00 37.03 2.43
4978 8778 7.869937 ACTCGTCATTGAAATGGATGTATCTAG 59.130 37.037 3.31 0.00 37.03 2.43
4979 8779 7.726216 ACTCGTCATTGAAATGGATGTATCTA 58.274 34.615 3.31 0.00 37.03 1.98
4980 8780 6.586344 ACTCGTCATTGAAATGGATGTATCT 58.414 36.000 3.31 0.00 37.03 1.98
4981 8781 6.851222 ACTCGTCATTGAAATGGATGTATC 57.149 37.500 3.31 0.00 37.03 2.24
4982 8782 8.908786 AATACTCGTCATTGAAATGGATGTAT 57.091 30.769 3.31 5.20 37.03 2.29
4983 8783 8.731275 AAATACTCGTCATTGAAATGGATGTA 57.269 30.769 3.31 3.46 37.03 2.29
4984 8784 7.201732 GGAAATACTCGTCATTGAAATGGATGT 60.202 37.037 3.31 1.66 37.03 3.06
4985 8785 7.134815 GGAAATACTCGTCATTGAAATGGATG 58.865 38.462 3.31 0.00 37.03 3.51
4986 8786 6.017934 CGGAAATACTCGTCATTGAAATGGAT 60.018 38.462 3.31 0.00 37.03 3.41
4987 8787 5.293324 CGGAAATACTCGTCATTGAAATGGA 59.707 40.000 3.31 0.00 37.03 3.41
4988 8788 5.293324 TCGGAAATACTCGTCATTGAAATGG 59.707 40.000 3.31 0.00 37.03 3.16
4989 8789 6.344572 TCGGAAATACTCGTCATTGAAATG 57.655 37.500 0.00 0.00 37.75 2.32
4990 8790 6.455113 CGTTCGGAAATACTCGTCATTGAAAT 60.455 38.462 0.00 0.00 0.00 2.17
4991 8791 5.164031 CGTTCGGAAATACTCGTCATTGAAA 60.164 40.000 0.00 0.00 0.00 2.69
4992 8792 4.325204 CGTTCGGAAATACTCGTCATTGAA 59.675 41.667 0.00 0.00 0.00 2.69
4993 8793 3.855379 CGTTCGGAAATACTCGTCATTGA 59.145 43.478 0.00 0.00 0.00 2.57
4994 8794 3.000078 CCGTTCGGAAATACTCGTCATTG 60.000 47.826 5.19 0.00 0.00 2.82
4995 8795 3.119388 TCCGTTCGGAAATACTCGTCATT 60.119 43.478 11.66 0.00 0.00 2.57
4996 8796 2.424601 TCCGTTCGGAAATACTCGTCAT 59.575 45.455 11.66 0.00 0.00 3.06
4997 8797 1.811965 TCCGTTCGGAAATACTCGTCA 59.188 47.619 11.66 0.00 0.00 4.35
4998 8798 2.448219 CTCCGTTCGGAAATACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
4999 8799 1.133790 CCTCCGTTCGGAAATACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
5000 8800 1.535437 CCCTCCGTTCGGAAATACTCG 60.535 57.143 14.79 1.97 33.41 4.18
5001 8801 1.753073 TCCCTCCGTTCGGAAATACTC 59.247 52.381 14.79 0.00 33.41 2.59
5002 8802 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
5003 8803 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
5004 8804 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
5005 8805 1.479730 GTACTCCCTCCGTTCGGAAAT 59.520 52.381 14.79 2.39 33.41 2.17
5006 8806 0.890683 GTACTCCCTCCGTTCGGAAA 59.109 55.000 14.79 3.49 33.41 3.13
5007 8807 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
5008 8808 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
5009 8809 0.172803 CAAGTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
5010 8810 0.886563 ACAAGTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
5011 8811 4.525912 TTAACAAGTACTCCCTCCGTTC 57.474 45.455 0.00 0.00 0.00 3.95
5012 8812 4.961438 TTTAACAAGTACTCCCTCCGTT 57.039 40.909 0.00 0.00 0.00 4.44
5013 8813 4.346127 AGTTTTAACAAGTACTCCCTCCGT 59.654 41.667 0.00 0.00 0.00 4.69
5014 8814 4.891260 AGTTTTAACAAGTACTCCCTCCG 58.109 43.478 0.00 0.00 0.00 4.63
5015 8815 5.472478 CCAAGTTTTAACAAGTACTCCCTCC 59.528 44.000 0.00 0.00 0.00 4.30
5016 8816 5.048921 GCCAAGTTTTAACAAGTACTCCCTC 60.049 44.000 0.00 0.00 0.00 4.30
5017 8817 4.825634 GCCAAGTTTTAACAAGTACTCCCT 59.174 41.667 0.00 0.00 0.00 4.20
5018 8818 4.825634 AGCCAAGTTTTAACAAGTACTCCC 59.174 41.667 0.00 0.00 0.00 4.30
5019 8819 6.183360 ACAAGCCAAGTTTTAACAAGTACTCC 60.183 38.462 0.00 0.00 0.00 3.85
5020 8820 6.792326 ACAAGCCAAGTTTTAACAAGTACTC 58.208 36.000 0.00 0.00 0.00 2.59
5021 8821 6.769134 ACAAGCCAAGTTTTAACAAGTACT 57.231 33.333 0.00 0.00 0.00 2.73
5022 8822 7.821595 AAACAAGCCAAGTTTTAACAAGTAC 57.178 32.000 0.00 0.00 35.81 2.73
5023 8823 9.356433 GTTAAACAAGCCAAGTTTTAACAAGTA 57.644 29.630 9.75 0.00 39.65 2.24
5024 8824 8.092068 AGTTAAACAAGCCAAGTTTTAACAAGT 58.908 29.630 14.80 2.52 39.65 3.16
5025 8825 8.474006 AGTTAAACAAGCCAAGTTTTAACAAG 57.526 30.769 14.80 0.00 39.65 3.16
5026 8826 8.834749 AAGTTAAACAAGCCAAGTTTTAACAA 57.165 26.923 14.80 0.27 39.65 2.83
5187 9142 8.899427 TCTCTGGATGATTGATGATAAAAGTC 57.101 34.615 0.00 0.00 0.00 3.01
5364 9319 4.210328 CCGGATTACAAAAACAAAAGCACC 59.790 41.667 0.00 0.00 0.00 5.01
5365 9320 4.806775 ACCGGATTACAAAAACAAAAGCAC 59.193 37.500 9.46 0.00 0.00 4.40
5366 9321 4.806247 CACCGGATTACAAAAACAAAAGCA 59.194 37.500 9.46 0.00 0.00 3.91
5367 9322 4.318475 GCACCGGATTACAAAAACAAAAGC 60.318 41.667 9.46 0.00 0.00 3.51
5368 9323 5.047188 AGCACCGGATTACAAAAACAAAAG 58.953 37.500 9.46 0.00 0.00 2.27
5369 9324 5.012328 AGCACCGGATTACAAAAACAAAA 57.988 34.783 9.46 0.00 0.00 2.44
5370 9325 4.657436 AGCACCGGATTACAAAAACAAA 57.343 36.364 9.46 0.00 0.00 2.83
5371 9326 4.339814 AGAAGCACCGGATTACAAAAACAA 59.660 37.500 9.46 0.00 0.00 2.83
5372 9327 3.886505 AGAAGCACCGGATTACAAAAACA 59.113 39.130 9.46 0.00 0.00 2.83
5373 9328 4.226761 CAGAAGCACCGGATTACAAAAAC 58.773 43.478 9.46 0.00 0.00 2.43
5374 9329 3.886505 ACAGAAGCACCGGATTACAAAAA 59.113 39.130 9.46 0.00 0.00 1.94
5375 9330 3.482436 ACAGAAGCACCGGATTACAAAA 58.518 40.909 9.46 0.00 0.00 2.44
5376 9331 3.134574 ACAGAAGCACCGGATTACAAA 57.865 42.857 9.46 0.00 0.00 2.83
5377 9332 2.851263 ACAGAAGCACCGGATTACAA 57.149 45.000 9.46 0.00 0.00 2.41
5378 9333 3.181469 GGATACAGAAGCACCGGATTACA 60.181 47.826 9.46 0.00 0.00 2.41
5379 9334 3.069729 AGGATACAGAAGCACCGGATTAC 59.930 47.826 9.46 0.00 41.41 1.89
5380 9335 3.305720 AGGATACAGAAGCACCGGATTA 58.694 45.455 9.46 0.00 41.41 1.75
5381 9336 2.103263 GAGGATACAGAAGCACCGGATT 59.897 50.000 9.46 0.00 41.41 3.01
5382 9337 1.689273 GAGGATACAGAAGCACCGGAT 59.311 52.381 9.46 0.00 41.41 4.18
5383 9338 1.112113 GAGGATACAGAAGCACCGGA 58.888 55.000 9.46 0.00 41.41 5.14
5384 9339 0.105039 GGAGGATACAGAAGCACCGG 59.895 60.000 0.00 0.00 41.41 5.28
5385 9340 1.115467 AGGAGGATACAGAAGCACCG 58.885 55.000 0.00 0.00 41.41 4.94
5457 9412 1.062294 CTCAGCTGCTCTTCAAATCGC 59.938 52.381 9.47 0.00 0.00 4.58
5493 9448 0.667993 TTTCAGCAGCAAGTTTCGGG 59.332 50.000 0.00 0.00 0.00 5.14
5528 9483 6.476243 TTCAGAAAACGTGGCTATAGAAAC 57.524 37.500 3.21 0.00 0.00 2.78
5565 9522 2.076863 CGGGAGCAAGGTTTTACAGAG 58.923 52.381 0.00 0.00 0.00 3.35
5731 9688 0.526739 GGGGTGTTGCACAAACGTTC 60.527 55.000 0.00 0.00 42.10 3.95
5734 9691 1.949847 TTGGGGGTGTTGCACAAACG 61.950 55.000 1.61 0.00 42.10 3.60
5884 9856 2.352960 CCTCTTCAGTTGAAATAGCGGC 59.647 50.000 0.00 0.00 33.07 6.53
5998 9980 6.530019 AATCCACAAATATCAAACACTCCC 57.470 37.500 0.00 0.00 0.00 4.30
6204 10200 2.167693 TCCCGTGTCCTTAAGCAGTATG 59.832 50.000 0.00 0.00 40.87 2.39
6205 10201 2.463752 TCCCGTGTCCTTAAGCAGTAT 58.536 47.619 0.00 0.00 0.00 2.12
6206 10202 1.927487 TCCCGTGTCCTTAAGCAGTA 58.073 50.000 0.00 0.00 0.00 2.74
6207 10203 1.053424 TTCCCGTGTCCTTAAGCAGT 58.947 50.000 0.00 0.00 0.00 4.40
6208 10204 2.076863 CTTTCCCGTGTCCTTAAGCAG 58.923 52.381 0.00 0.00 0.00 4.24
6209 10205 1.418637 ACTTTCCCGTGTCCTTAAGCA 59.581 47.619 0.00 0.00 0.00 3.91
6210 10206 1.804748 CACTTTCCCGTGTCCTTAAGC 59.195 52.381 0.00 0.00 0.00 3.09
6211 10207 3.396260 TCACTTTCCCGTGTCCTTAAG 57.604 47.619 0.00 0.00 36.33 1.85
6212 10208 3.670625 CATCACTTTCCCGTGTCCTTAA 58.329 45.455 0.00 0.00 36.33 1.85
6213 10209 2.614481 GCATCACTTTCCCGTGTCCTTA 60.614 50.000 0.00 0.00 36.33 2.69
6214 10210 1.882352 GCATCACTTTCCCGTGTCCTT 60.882 52.381 0.00 0.00 36.33 3.36
6215 10211 0.321653 GCATCACTTTCCCGTGTCCT 60.322 55.000 0.00 0.00 36.33 3.85
6216 10212 0.321653 AGCATCACTTTCCCGTGTCC 60.322 55.000 0.00 0.00 36.33 4.02
6217 10213 1.523758 AAGCATCACTTTCCCGTGTC 58.476 50.000 0.00 0.00 33.71 3.67
6218 10214 2.851263 TAAGCATCACTTTCCCGTGT 57.149 45.000 0.00 0.00 39.97 4.49
6219 10215 3.731867 GCAATAAGCATCACTTTCCCGTG 60.732 47.826 0.00 0.00 44.79 4.94
6220 10216 2.423538 GCAATAAGCATCACTTTCCCGT 59.576 45.455 0.00 0.00 44.79 5.28
6221 10217 3.070429 GCAATAAGCATCACTTTCCCG 57.930 47.619 0.00 0.00 44.79 5.14
6233 10229 2.418628 TCGCCACTTACAAGCAATAAGC 59.581 45.455 0.00 0.00 46.19 3.09
6234 10230 3.932710 TCTCGCCACTTACAAGCAATAAG 59.067 43.478 0.00 0.00 36.01 1.73
6361 10363 2.950309 CAGCCTATGCAAGCTCAGATTT 59.050 45.455 6.30 0.00 41.13 2.17
6433 10435 3.380320 ACACAAAGAGAAGTTTTTCCCCG 59.620 43.478 0.00 0.00 33.64 5.73
6492 10494 6.326583 CCCCTAGTGAAATATGTGAGAGGTTA 59.673 42.308 0.00 0.00 0.00 2.85
6537 10626 2.843701 CTGGCTGGAAGTATGGATGTC 58.156 52.381 0.00 0.00 35.30 3.06


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

AutoCloner maintained by Alex Coulton.