Multiple sequence alignment - TraesCS5A01G274900

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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 TraesCS5A01G274900 chr5A 100.000 5414 0 0 1 5414 484445847 484440434 0.000000e+00 9998.0
1 TraesCS5A01G274900 chr5A 100.000 3633 0 0 5684 9316 484440164 484436532 0.000000e+00 6709.0
2 TraesCS5A01G274900 chr5A 95.182 1536 71 2 1812 3347 484441966 484440434 0.000000e+00 2423.0
3 TraesCS5A01G274900 chr5A 95.182 1536 71 2 3882 5414 484444036 484442501 0.000000e+00 2423.0
4 TraesCS5A01G274900 chr5A 78.442 1271 232 36 7076 8325 509126134 509124885 0.000000e+00 791.0
5 TraesCS5A01G274900 chr5A 87.934 663 67 11 5684 6338 680852284 680851627 0.000000e+00 769.0
6 TraesCS5A01G274900 chr5A 75.155 805 179 19 7076 7867 484839988 484840784 8.890000e-95 359.0
7 TraesCS5A01G274900 chr5A 98.507 67 1 0 7010 7076 484438805 484438739 1.640000e-22 119.0
8 TraesCS5A01G274900 chr5A 100.000 28 0 0 1525 1552 484587574 484587601 1.700000e-02 52.8
9 TraesCS5A01G274900 chr1A 91.639 3624 255 19 1829 5414 13781326 13777713 0.000000e+00 4970.0
10 TraesCS5A01G274900 chr1A 92.205 1655 113 12 1829 3473 13779225 13777577 0.000000e+00 2327.0
11 TraesCS5A01G274900 chr1A 93.647 850 51 3 5686 6533 13779740 13778892 0.000000e+00 1267.0
12 TraesCS5A01G274900 chr1A 89.281 737 62 8 3513 4234 103630057 103630791 0.000000e+00 907.0
13 TraesCS5A01G274900 chr1A 85.039 127 17 2 6706 6831 531664264 531664139 2.730000e-25 128.0
14 TraesCS5A01G274900 chr1A 85.039 127 17 2 6706 6831 531680316 531680191 2.730000e-25 128.0
15 TraesCS5A01G274900 chr5D 96.255 2804 77 8 6535 9316 384019771 384016974 0.000000e+00 4571.0
16 TraesCS5A01G274900 chr5D 93.685 1536 95 1 3881 5414 111604048 111605583 0.000000e+00 2298.0
17 TraesCS5A01G274900 chr5D 93.555 1536 97 1 3881 5414 302886751 302888286 0.000000e+00 2287.0
18 TraesCS5A01G274900 chr5D 93.490 1536 97 2 3882 5414 382351917 382353452 0.000000e+00 2279.0
19 TraesCS5A01G274900 chr5D 91.953 1367 46 18 485 1812 384021107 384019766 0.000000e+00 1857.0
20 TraesCS5A01G274900 chr5D 87.787 827 81 15 3423 4234 111606020 111606841 0.000000e+00 950.0
21 TraesCS5A01G274900 chr5D 77.628 1265 254 25 7076 8325 384154203 384155453 0.000000e+00 741.0
22 TraesCS5A01G274900 chr5D 78.276 1183 211 39 7076 8235 404881337 404882496 0.000000e+00 719.0
23 TraesCS5A01G274900 chr5D 98.507 67 1 0 7043 7109 384019282 384019216 1.640000e-22 119.0
24 TraesCS5A01G274900 chr5D 97.015 67 2 0 7010 7076 384019249 384019183 7.650000e-21 113.0
25 TraesCS5A01G274900 chr5D 100.000 34 0 0 7076 7109 384019282 384019249 7.810000e-06 63.9
26 TraesCS5A01G274900 chr5D 100.000 28 0 0 1525 1552 384141336 384141363 1.700000e-02 52.8
27 TraesCS5A01G274900 chr5B 92.631 2334 124 27 7010 9316 460495008 460492696 0.000000e+00 3314.0
28 TraesCS5A01G274900 chr5B 96.058 1319 23 8 514 1812 460496834 460495525 0.000000e+00 2121.0
29 TraesCS5A01G274900 chr5B 96.435 589 7 1 6535 7109 460495530 460494942 0.000000e+00 959.0
30 TraesCS5A01G274900 chr5B 77.312 1265 258 25 7076 8325 460942996 460944246 0.000000e+00 719.0
31 TraesCS5A01G274900 chr5B 81.458 631 107 5 7674 8297 460660494 460661121 8.350000e-140 508.0
32 TraesCS5A01G274900 chr5B 92.857 336 10 3 83 418 460497657 460497336 8.460000e-130 475.0
33 TraesCS5A01G274900 chr5B 100.000 67 0 0 7043 7109 460495041 460494975 3.530000e-24 124.0
34 TraesCS5A01G274900 chr5B 98.507 67 1 0 7010 7076 460494975 460494909 1.640000e-22 119.0
35 TraesCS5A01G274900 chr5B 98.182 55 1 0 1492 1546 460498205 460498151 7.700000e-16 97.1
36 TraesCS5A01G274900 chr3D 90.648 2438 195 27 1812 4234 604894231 604896650 0.000000e+00 3208.0
37 TraesCS5A01G274900 chr3D 91.604 1989 149 15 1810 3786 178653546 178655528 0.000000e+00 2732.0
38 TraesCS5A01G274900 chr3D 90.035 1997 180 15 1812 3798 551011205 551013192 0.000000e+00 2567.0
39 TraesCS5A01G274900 chr3D 89.392 2008 179 26 1802 3798 400454587 400452603 0.000000e+00 2497.0
40 TraesCS5A01G274900 chr3D 93.681 1535 94 2 3882 5414 178653548 178655081 0.000000e+00 2294.0
41 TraesCS5A01G274900 chr3D 93.390 1528 99 1 3882 5407 549650796 549649269 0.000000e+00 2261.0
42 TraesCS5A01G274900 chr3D 91.270 630 43 12 5684 6306 647390 646766 0.000000e+00 848.0
43 TraesCS5A01G274900 chr3D 82.640 553 65 17 672 1205 163120421 163120961 2.370000e-125 460.0
44 TraesCS5A01G274900 chr4D 88.049 2460 222 47 1812 4234 121543070 121540646 0.000000e+00 2848.0
45 TraesCS5A01G274900 chr4D 91.315 852 54 13 5694 6532 103954195 103955039 0.000000e+00 1146.0
46 TraesCS5A01G274900 chr4D 93.023 602 37 5 5684 6282 301751524 301750925 0.000000e+00 874.0
47 TraesCS5A01G274900 chr7D 92.631 1737 113 10 1810 3534 7543397 7541664 0.000000e+00 2484.0
48 TraesCS5A01G274900 chr7D 85.242 393 50 7 712 1097 575142902 575143293 1.880000e-106 398.0
49 TraesCS5A01G274900 chr7D 85.185 189 25 2 1204 1391 575143627 575143813 3.430000e-44 191.0
50 TraesCS5A01G274900 chr2D 94.061 1566 90 3 1812 3376 115586181 115584618 0.000000e+00 2374.0
51 TraesCS5A01G274900 chr2D 93.876 1535 91 2 3882 5414 115586181 115584648 0.000000e+00 2311.0
52 TraesCS5A01G274900 chr2D 89.498 638 53 13 5710 6338 186637580 186636948 0.000000e+00 795.0
53 TraesCS5A01G274900 chr1D 90.028 1795 147 20 2467 4234 357320756 357322545 0.000000e+00 2303.0
54 TraesCS5A01G274900 chr1D 93.628 1538 96 1 3879 5414 314434009 314435546 0.000000e+00 2296.0
55 TraesCS5A01G274900 chr1D 90.177 621 51 9 5726 6339 31325401 31324784 0.000000e+00 800.0
56 TraesCS5A01G274900 chr1D 89.302 645 57 11 5702 6338 476251593 476252233 0.000000e+00 798.0
57 TraesCS5A01G274900 chr1D 83.214 560 61 16 672 1205 439133078 439133630 5.060000e-132 483.0
58 TraesCS5A01G274900 chr1D 85.039 127 17 2 6706 6831 433267680 433267555 2.730000e-25 128.0
59 TraesCS5A01G274900 chr7A 93.705 826 51 1 3410 4234 287474938 287474113 0.000000e+00 1236.0
60 TraesCS5A01G274900 chr7A 88.451 736 70 7 3513 4234 17842361 17843095 0.000000e+00 874.0
61 TraesCS5A01G274900 chr3A 92.308 663 48 3 3426 4086 535186912 535187573 0.000000e+00 939.0
62 TraesCS5A01G274900 chr3A 91.376 603 44 8 5684 6282 594025050 594024452 0.000000e+00 819.0
63 TraesCS5A01G274900 chr3A 95.170 352 17 0 6182 6533 654394108 654393757 2.940000e-154 556.0
64 TraesCS5A01G274900 chr3A 95.170 352 15 2 6182 6533 301138039 301138388 1.060000e-153 555.0
65 TraesCS5A01G274900 chr3A 93.370 362 24 0 6172 6533 654392283 654391922 3.830000e-148 536.0
66 TraesCS5A01G274900 chr3A 90.634 363 21 5 6182 6533 697504672 697504312 3.940000e-128 470.0
67 TraesCS5A01G274900 chr3A 86.313 358 31 11 6191 6533 331478989 331478635 3.180000e-99 374.0
68 TraesCS5A01G274900 chr6D 86.036 888 98 17 3360 4234 375032756 375033630 0.000000e+00 929.0
69 TraesCS5A01G274900 chr4A 93.466 352 23 0 6182 6533 716524943 716525294 2.980000e-144 523.0
70 TraesCS5A01G274900 chr4A 93.134 335 22 1 6199 6533 547296242 547295909 3.020000e-134 490.0
71 TraesCS5A01G274900 chr2B 82.609 552 65 15 673 1205 405748754 405748215 8.520000e-125 459.0
72 TraesCS5A01G274900 chr1B 85.039 127 17 2 6706 6831 585241641 585241516 2.730000e-25 128.0


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 TraesCS5A01G274900 chr5A 484436532 484445847 9315 True 5608.666667 9998 99.502333 1 9316 3 chr5A.!!$R3 9315
1 TraesCS5A01G274900 chr5A 484440434 484444036 3602 True 2423.000000 2423 95.182000 1812 5414 2 chr5A.!!$R4 3602
2 TraesCS5A01G274900 chr5A 509124885 509126134 1249 True 791.000000 791 78.442000 7076 8325 1 chr5A.!!$R1 1249
3 TraesCS5A01G274900 chr5A 680851627 680852284 657 True 769.000000 769 87.934000 5684 6338 1 chr5A.!!$R2 654
4 TraesCS5A01G274900 chr5A 484839988 484840784 796 False 359.000000 359 75.155000 7076 7867 1 chr5A.!!$F2 791
5 TraesCS5A01G274900 chr1A 13777577 13781326 3749 True 2854.666667 4970 92.497000 1829 6533 3 chr1A.!!$R3 4704
6 TraesCS5A01G274900 chr1A 103630057 103630791 734 False 907.000000 907 89.281000 3513 4234 1 chr1A.!!$F1 721
7 TraesCS5A01G274900 chr5D 302886751 302888286 1535 False 2287.000000 2287 93.555000 3881 5414 1 chr5D.!!$F1 1533
8 TraesCS5A01G274900 chr5D 382351917 382353452 1535 False 2279.000000 2279 93.490000 3882 5414 1 chr5D.!!$F2 1532
9 TraesCS5A01G274900 chr5D 111604048 111606841 2793 False 1624.000000 2298 90.736000 3423 5414 2 chr5D.!!$F6 1991
10 TraesCS5A01G274900 chr5D 384016974 384021107 4133 True 1344.780000 4571 96.746000 485 9316 5 chr5D.!!$R1 8831
11 TraesCS5A01G274900 chr5D 384154203 384155453 1250 False 741.000000 741 77.628000 7076 8325 1 chr5D.!!$F4 1249
12 TraesCS5A01G274900 chr5D 404881337 404882496 1159 False 719.000000 719 78.276000 7076 8235 1 chr5D.!!$F5 1159
13 TraesCS5A01G274900 chr5B 460492696 460498205 5509 True 1029.871429 3314 96.381429 83 9316 7 chr5B.!!$R1 9233
14 TraesCS5A01G274900 chr5B 460942996 460944246 1250 False 719.000000 719 77.312000 7076 8325 1 chr5B.!!$F2 1249
15 TraesCS5A01G274900 chr5B 460660494 460661121 627 False 508.000000 508 81.458000 7674 8297 1 chr5B.!!$F1 623
16 TraesCS5A01G274900 chr3D 604894231 604896650 2419 False 3208.000000 3208 90.648000 1812 4234 1 chr3D.!!$F3 2422
17 TraesCS5A01G274900 chr3D 551011205 551013192 1987 False 2567.000000 2567 90.035000 1812 3798 1 chr3D.!!$F2 1986
18 TraesCS5A01G274900 chr3D 178653546 178655528 1982 False 2513.000000 2732 92.642500 1810 5414 2 chr3D.!!$F4 3604
19 TraesCS5A01G274900 chr3D 400452603 400454587 1984 True 2497.000000 2497 89.392000 1802 3798 1 chr3D.!!$R2 1996
20 TraesCS5A01G274900 chr3D 549649269 549650796 1527 True 2261.000000 2261 93.390000 3882 5407 1 chr3D.!!$R3 1525
21 TraesCS5A01G274900 chr3D 646766 647390 624 True 848.000000 848 91.270000 5684 6306 1 chr3D.!!$R1 622
22 TraesCS5A01G274900 chr3D 163120421 163120961 540 False 460.000000 460 82.640000 672 1205 1 chr3D.!!$F1 533
23 TraesCS5A01G274900 chr4D 121540646 121543070 2424 True 2848.000000 2848 88.049000 1812 4234 1 chr4D.!!$R1 2422
24 TraesCS5A01G274900 chr4D 103954195 103955039 844 False 1146.000000 1146 91.315000 5694 6532 1 chr4D.!!$F1 838
25 TraesCS5A01G274900 chr4D 301750925 301751524 599 True 874.000000 874 93.023000 5684 6282 1 chr4D.!!$R2 598
26 TraesCS5A01G274900 chr7D 7541664 7543397 1733 True 2484.000000 2484 92.631000 1810 3534 1 chr7D.!!$R1 1724
27 TraesCS5A01G274900 chr7D 575142902 575143813 911 False 294.500000 398 85.213500 712 1391 2 chr7D.!!$F1 679
28 TraesCS5A01G274900 chr2D 115584618 115586181 1563 True 2342.500000 2374 93.968500 1812 5414 2 chr2D.!!$R2 3602
29 TraesCS5A01G274900 chr2D 186636948 186637580 632 True 795.000000 795 89.498000 5710 6338 1 chr2D.!!$R1 628
30 TraesCS5A01G274900 chr1D 357320756 357322545 1789 False 2303.000000 2303 90.028000 2467 4234 1 chr1D.!!$F2 1767
31 TraesCS5A01G274900 chr1D 314434009 314435546 1537 False 2296.000000 2296 93.628000 3879 5414 1 chr1D.!!$F1 1535
32 TraesCS5A01G274900 chr1D 31324784 31325401 617 True 800.000000 800 90.177000 5726 6339 1 chr1D.!!$R1 613
33 TraesCS5A01G274900 chr1D 476251593 476252233 640 False 798.000000 798 89.302000 5702 6338 1 chr1D.!!$F4 636
34 TraesCS5A01G274900 chr1D 439133078 439133630 552 False 483.000000 483 83.214000 672 1205 1 chr1D.!!$F3 533
35 TraesCS5A01G274900 chr7A 287474113 287474938 825 True 1236.000000 1236 93.705000 3410 4234 1 chr7A.!!$R1 824
36 TraesCS5A01G274900 chr7A 17842361 17843095 734 False 874.000000 874 88.451000 3513 4234 1 chr7A.!!$F1 721
37 TraesCS5A01G274900 chr3A 535186912 535187573 661 False 939.000000 939 92.308000 3426 4086 1 chr3A.!!$F2 660
38 TraesCS5A01G274900 chr3A 594024452 594025050 598 True 819.000000 819 91.376000 5684 6282 1 chr3A.!!$R2 598
39 TraesCS5A01G274900 chr3A 654391922 654394108 2186 True 546.000000 556 94.270000 6172 6533 2 chr3A.!!$R4 361
40 TraesCS5A01G274900 chr6D 375032756 375033630 874 False 929.000000 929 86.036000 3360 4234 1 chr6D.!!$F1 874
41 TraesCS5A01G274900 chr2B 405748215 405748754 539 True 459.000000 459 82.609000 673 1205 1 chr2B.!!$R1 532

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
381 848 0.239879 CCCCGTGTGATTTTGTTCCG 59.760 55.000 0.00 0.0 0.00 4.30 F
500 967 1.374758 GTGTCCTCCAGTTCAGGCG 60.375 63.158 0.00 0.0 0.00 5.52 F
1275 2397 1.404583 GCCAAGGTGCATCATGTTTCC 60.405 52.381 0.00 0.0 0.00 3.13 F
1432 2554 0.332632 CACTGTGGGGATTGGGTGAT 59.667 55.000 0.00 0.0 0.00 3.06 F
1433 2555 0.332632 ACTGTGGGGATTGGGTGATG 59.667 55.000 0.00 0.0 0.00 3.07 F
1450 2572 0.409092 ATGGCAGTGGATCAACCCAA 59.591 50.000 2.67 0.0 38.06 4.12 F
3724 5259 1.222936 CAGGGTGCTGGTCATCTCC 59.777 63.158 0.00 0.0 0.00 3.71 F
4331 5867 0.107410 ACCAGCGTCAAACACCTTCA 60.107 50.000 0.00 0.0 0.00 3.02 F
5090 6628 0.107703 TGGCGAAATCGATCTTGGCT 60.108 50.000 13.22 0.0 43.02 4.75 F
5342 6880 0.616111 AGACCTGCTGGATCGGAAGT 60.616 55.000 17.64 0.0 37.04 3.01 F
6533 12241 0.320421 CCCCTATGCCGGTCATAACG 60.320 60.000 16.10 10.7 37.22 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 2536 0.332632 CATCACCCAATCCCCACAGT 59.667 55.000 0.00 0.00 0.00 3.55 R
1432 2554 0.409092 ATTGGGTTGATCCACTGCCA 59.591 50.000 0.00 0.00 36.38 4.92 R
3581 5113 1.934956 CGATCCAGAACGCGTCGAG 60.935 63.158 14.44 4.84 34.46 4.04 R
3710 5245 1.142748 CGGAGGAGATGACCAGCAC 59.857 63.158 0.00 0.00 0.00 4.40 R
3724 5259 3.744719 TCCGTCTTCACGCCGGAG 61.745 66.667 5.05 3.72 45.20 4.63 R
3786 5322 2.819595 CGAATGACCACTGCCGGG 60.820 66.667 2.18 0.00 0.00 5.73 R
5243 6781 0.040646 TGTACACAGAGGTCGGGGAT 59.959 55.000 0.00 0.00 0.00 3.85 R
6533 12241 1.501582 AGCAGGGGATCTAACACTCC 58.498 55.000 0.00 0.00 0.00 3.85 R
6534 12242 2.365941 GGTAGCAGGGGATCTAACACTC 59.634 54.545 0.00 0.00 0.00 3.51 R
6535 12243 2.399580 GGTAGCAGGGGATCTAACACT 58.600 52.381 0.00 0.00 0.00 3.55 R
8833 14623 0.179150 CGGCCTTCGAGAGAACTGAG 60.179 60.000 0.00 0.00 46.92 3.35 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
29 30 3.924238 AAAAACGTCTGCTGTGCTG 57.076 47.368 0.00 0.00 0.00 4.41
30 31 0.248621 AAAAACGTCTGCTGTGCTGC 60.249 50.000 0.00 0.00 0.00 5.25
31 32 2.063541 AAAACGTCTGCTGTGCTGCC 62.064 55.000 0.00 0.00 0.00 4.85
32 33 4.996434 ACGTCTGCTGTGCTGCCC 62.996 66.667 0.00 0.00 0.00 5.36
34 35 4.341783 GTCTGCTGTGCTGCCCCT 62.342 66.667 0.00 0.00 0.00 4.79
35 36 4.025858 TCTGCTGTGCTGCCCCTC 62.026 66.667 0.00 0.00 0.00 4.30
39 40 2.752358 CTGTGCTGCCCCTCTGAA 59.248 61.111 0.00 0.00 0.00 3.02
48 49 4.821589 CCCTCTGAAGGCGACGGC 62.822 72.222 14.41 14.41 41.85 5.68
59 60 2.127383 CGACGGCGCAAGAAAACC 60.127 61.111 10.83 0.00 43.02 3.27
60 61 2.254350 GACGGCGCAAGAAAACCC 59.746 61.111 10.83 0.00 43.02 4.11
61 62 2.203294 ACGGCGCAAGAAAACCCT 60.203 55.556 10.83 0.00 43.02 4.34
64 65 1.880894 GGCGCAAGAAAACCCTACC 59.119 57.895 10.83 0.00 43.02 3.18
66 67 0.803117 GCGCAAGAAAACCCTACCTC 59.197 55.000 0.30 0.00 43.02 3.85
67 68 1.880646 GCGCAAGAAAACCCTACCTCA 60.881 52.381 0.30 0.00 43.02 3.86
71 72 4.698304 CGCAAGAAAACCCTACCTCAATTA 59.302 41.667 0.00 0.00 43.02 1.40
72 73 5.182380 CGCAAGAAAACCCTACCTCAATTAA 59.818 40.000 0.00 0.00 43.02 1.40
73 74 6.294286 CGCAAGAAAACCCTACCTCAATTAAA 60.294 38.462 0.00 0.00 43.02 1.52
74 75 7.438564 GCAAGAAAACCCTACCTCAATTAAAA 58.561 34.615 0.00 0.00 0.00 1.52
75 76 7.929245 GCAAGAAAACCCTACCTCAATTAAAAA 59.071 33.333 0.00 0.00 0.00 1.94
222 689 1.899437 GCTCATCCGGTTGGTCTCCA 61.899 60.000 12.54 0.00 36.30 3.86
274 741 2.355007 CCAAAATGCTCCATTGTTCCCC 60.355 50.000 0.00 0.00 34.04 4.81
324 791 2.808906 AAGCTCCCCAAATCACCTAC 57.191 50.000 0.00 0.00 0.00 3.18
344 811 1.987855 CCTCCTGGTTCCTACGCCA 60.988 63.158 0.00 0.00 0.00 5.69
351 818 3.149005 TGGTTCCTACGCCAGATTTTT 57.851 42.857 0.00 0.00 0.00 1.94
355 822 1.810151 TCCTACGCCAGATTTTTGTGC 59.190 47.619 0.00 0.00 0.00 4.57
381 848 0.239879 CCCCGTGTGATTTTGTTCCG 59.760 55.000 0.00 0.00 0.00 4.30
404 871 2.543031 GCTGTGTTCGTTCTTTTTCCCC 60.543 50.000 0.00 0.00 0.00 4.81
418 885 2.203126 CCCCTGGAGCTGCGAATC 60.203 66.667 0.00 0.00 0.00 2.52
419 886 2.203126 CCCTGGAGCTGCGAATCC 60.203 66.667 0.00 0.00 36.05 3.01
420 887 2.739996 CCCTGGAGCTGCGAATCCT 61.740 63.158 0.00 0.00 36.50 3.24
421 888 1.523258 CCTGGAGCTGCGAATCCTG 60.523 63.158 0.00 7.04 36.50 3.86
422 889 1.523258 CTGGAGCTGCGAATCCTGG 60.523 63.158 0.00 0.00 36.50 4.45
423 890 2.249413 CTGGAGCTGCGAATCCTGGT 62.249 60.000 0.00 0.00 36.50 4.00
424 891 1.817099 GGAGCTGCGAATCCTGGTG 60.817 63.158 0.00 0.00 32.51 4.17
425 892 1.817099 GAGCTGCGAATCCTGGTGG 60.817 63.158 0.00 0.00 0.00 4.61
427 894 1.377202 GCTGCGAATCCTGGTGGAA 60.377 57.895 0.00 0.00 46.80 3.53
428 895 1.648467 GCTGCGAATCCTGGTGGAAC 61.648 60.000 0.00 0.00 46.80 3.62
443 910 4.600012 GTGGAACCTTCAACGTATCATG 57.400 45.455 0.00 0.00 0.00 3.07
444 911 3.006940 TGGAACCTTCAACGTATCATGC 58.993 45.455 0.00 0.00 0.00 4.06
445 912 3.006940 GGAACCTTCAACGTATCATGCA 58.993 45.455 0.00 0.00 0.00 3.96
446 913 3.627577 GGAACCTTCAACGTATCATGCAT 59.372 43.478 0.00 0.00 0.00 3.96
447 914 4.814234 GGAACCTTCAACGTATCATGCATA 59.186 41.667 0.00 0.00 0.00 3.14
448 915 5.470098 GGAACCTTCAACGTATCATGCATAT 59.530 40.000 0.00 0.00 0.00 1.78
449 916 5.929697 ACCTTCAACGTATCATGCATATG 57.070 39.130 0.00 0.00 35.57 1.78
452 919 5.237127 CCTTCAACGTATCATGCATATGTGT 59.763 40.000 0.00 0.00 37.29 3.72
453 920 5.655893 TCAACGTATCATGCATATGTGTG 57.344 39.130 0.00 4.03 37.29 3.82
455 922 3.732212 ACGTATCATGCATATGTGTGCT 58.268 40.909 0.00 0.00 45.27 4.40
456 923 3.495753 ACGTATCATGCATATGTGTGCTG 59.504 43.478 0.00 0.45 45.27 4.41
457 924 3.495753 CGTATCATGCATATGTGTGCTGT 59.504 43.478 0.00 0.00 45.27 4.40
459 926 4.563337 ATCATGCATATGTGTGCTGTTC 57.437 40.909 0.00 0.00 45.27 3.18
461 928 4.011698 TCATGCATATGTGTGCTGTTCTT 58.988 39.130 0.00 0.00 45.27 2.52
462 929 3.835378 TGCATATGTGTGCTGTTCTTG 57.165 42.857 4.29 0.00 45.27 3.02
465 932 4.759183 TGCATATGTGTGCTGTTCTTGTTA 59.241 37.500 4.29 0.00 45.27 2.41
466 933 5.106594 TGCATATGTGTGCTGTTCTTGTTAG 60.107 40.000 4.29 0.00 45.27 2.34
467 934 5.106555 GCATATGTGTGCTGTTCTTGTTAGT 60.107 40.000 4.29 0.00 41.82 2.24
468 935 6.092122 GCATATGTGTGCTGTTCTTGTTAGTA 59.908 38.462 4.29 0.00 41.82 1.82
471 938 6.151663 TGTGTGCTGTTCTTGTTAGTACTA 57.848 37.500 0.00 0.00 0.00 1.82
472 939 5.981315 TGTGTGCTGTTCTTGTTAGTACTAC 59.019 40.000 0.91 0.00 0.00 2.73
473 940 6.183360 TGTGTGCTGTTCTTGTTAGTACTACT 60.183 38.462 0.91 0.00 0.00 2.57
475 942 6.921857 TGTGCTGTTCTTGTTAGTACTACTTC 59.078 38.462 0.91 0.00 0.00 3.01
476 943 7.146648 GTGCTGTTCTTGTTAGTACTACTTCT 58.853 38.462 0.91 0.00 0.00 2.85
477 944 7.652507 GTGCTGTTCTTGTTAGTACTACTTCTT 59.347 37.037 0.91 0.00 0.00 2.52
478 945 8.853126 TGCTGTTCTTGTTAGTACTACTTCTTA 58.147 33.333 0.91 0.00 0.00 2.10
479 946 9.688592 GCTGTTCTTGTTAGTACTACTTCTTAA 57.311 33.333 0.91 0.00 0.00 1.85
481 948 9.669353 TGTTCTTGTTAGTACTACTTCTTAACG 57.331 33.333 0.91 0.00 0.00 3.18
482 949 9.122613 GTTCTTGTTAGTACTACTTCTTAACGG 57.877 37.037 0.91 0.00 0.00 4.44
483 950 8.396272 TCTTGTTAGTACTACTTCTTAACGGT 57.604 34.615 0.91 0.00 0.00 4.83
500 967 1.374758 GTGTCCTCCAGTTCAGGCG 60.375 63.158 0.00 0.00 0.00 5.52
506 973 2.358737 CCAGTTCAGGCGGTGTCC 60.359 66.667 0.00 0.00 0.00 4.02
507 974 2.743718 CAGTTCAGGCGGTGTCCT 59.256 61.111 0.00 0.00 36.78 3.85
543 1416 6.093633 GGACCATGTTTCCTGTAATCTTGTAC 59.906 42.308 3.75 0.00 0.00 2.90
544 1417 6.779860 ACCATGTTTCCTGTAATCTTGTACT 58.220 36.000 0.00 0.00 0.00 2.73
545 1418 7.231467 ACCATGTTTCCTGTAATCTTGTACTT 58.769 34.615 0.00 0.00 0.00 2.24
546 1419 8.380099 ACCATGTTTCCTGTAATCTTGTACTTA 58.620 33.333 0.00 0.00 0.00 2.24
550 1423 7.602644 TGTTTCCTGTAATCTTGTACTTAGCTG 59.397 37.037 0.00 0.00 0.00 4.24
741 1614 7.122501 TGCTGCTTCTTAATGTTGGATAATTGA 59.877 33.333 0.00 0.00 0.00 2.57
807 1691 6.371548 TCAACAAGTATGAAGAAGCACATACC 59.628 38.462 0.00 0.00 45.46 2.73
821 1708 5.491982 AGCACATACCTCTTTCCAGTTTAG 58.508 41.667 0.00 0.00 0.00 1.85
1127 2177 3.865446 TGTTCTGCCAGATATCAGTGTG 58.135 45.455 5.32 0.00 0.00 3.82
1129 2179 4.466015 TGTTCTGCCAGATATCAGTGTGTA 59.534 41.667 5.32 0.00 0.00 2.90
1206 2264 3.765381 TGGAGAATCAGTTTGGATGCAA 58.235 40.909 0.00 0.00 36.25 4.08
1275 2397 1.404583 GCCAAGGTGCATCATGTTTCC 60.405 52.381 0.00 0.00 0.00 3.13
1414 2536 4.111577 AGGTAGTTGGAAGGGATTGATCA 58.888 43.478 0.00 0.00 0.00 2.92
1432 2554 0.332632 CACTGTGGGGATTGGGTGAT 59.667 55.000 0.00 0.00 0.00 3.06
1433 2555 0.332632 ACTGTGGGGATTGGGTGATG 59.667 55.000 0.00 0.00 0.00 3.07
1450 2572 0.409092 ATGGCAGTGGATCAACCCAA 59.591 50.000 2.67 0.00 38.06 4.12
1575 2713 4.941263 TCGATTAGTTCATGGGTTGAAAGG 59.059 41.667 0.00 0.00 45.71 3.11
1600 2738 3.596214 GGCGAAAGAACAGAATACTCCA 58.404 45.455 0.00 0.00 0.00 3.86
1613 2751 1.729586 TACTCCAGGCCACAACTTCT 58.270 50.000 5.01 0.00 0.00 2.85
1808 2966 3.120408 CGAAGAAGAATGCCTGTTGTGAG 60.120 47.826 0.00 0.00 0.00 3.51
1809 2967 3.498774 AGAAGAATGCCTGTTGTGAGT 57.501 42.857 0.00 0.00 0.00 3.41
1810 2968 3.144506 AGAAGAATGCCTGTTGTGAGTG 58.855 45.455 0.00 0.00 0.00 3.51
3596 5128 4.415332 GGCTCGACGCGTTCTGGA 62.415 66.667 15.53 8.14 40.44 3.86
3597 5129 2.202623 GCTCGACGCGTTCTGGAT 60.203 61.111 15.53 0.00 0.00 3.41
3672 5207 4.708386 CGGGCCGGCCAAGTACAA 62.708 66.667 44.46 0.00 37.98 2.41
3673 5208 2.750237 GGGCCGGCCAAGTACAAG 60.750 66.667 44.46 0.00 37.98 3.16
3674 5209 2.750237 GGCCGGCCAAGTACAAGG 60.750 66.667 40.73 0.00 35.81 3.61
3675 5210 2.349755 GCCGGCCAAGTACAAGGA 59.650 61.111 18.11 0.00 0.00 3.36
3708 5243 4.778415 CGTCACGAGGTCCCGCAG 62.778 72.222 0.00 0.00 0.00 5.18
3721 5256 2.821366 CGCAGGGTGCTGGTCATC 60.821 66.667 0.00 0.00 42.25 2.92
3724 5259 1.222936 CAGGGTGCTGGTCATCTCC 59.777 63.158 0.00 0.00 0.00 3.71
3736 5271 1.227089 CATCTCCTCCGGCGTGAAG 60.227 63.158 6.01 0.00 0.00 3.02
3802 5338 2.351276 ACCCGGCAGTGGTCATTC 59.649 61.111 0.00 0.00 0.00 2.67
3804 5340 2.819595 CCGGCAGTGGTCATTCGG 60.820 66.667 0.00 0.00 0.00 4.30
3819 5355 2.867793 TTCGGGCGGTGGTGATGATG 62.868 60.000 0.00 0.00 0.00 3.07
3843 5379 2.748647 GGCGGCGTGGGTGTTAAT 60.749 61.111 9.37 0.00 0.00 1.40
3846 5382 1.791662 CGGCGTGGGTGTTAATGAC 59.208 57.895 0.00 0.00 0.00 3.06
3947 5483 2.687566 GGAAGGGGAAGGGCGAGA 60.688 66.667 0.00 0.00 0.00 4.04
3948 5484 2.298661 GGAAGGGGAAGGGCGAGAA 61.299 63.158 0.00 0.00 0.00 2.87
4044 5580 0.976590 GTTTAGGTCTCCCGGCTCCT 60.977 60.000 0.00 2.93 35.12 3.69
4141 5677 6.543735 AGGTTTACTTGACTCCTAAGCAAAT 58.456 36.000 0.00 0.00 0.00 2.32
4265 5801 0.463654 TGCACAAACAGCTCGTCCTT 60.464 50.000 0.00 0.00 0.00 3.36
4331 5867 0.107410 ACCAGCGTCAAACACCTTCA 60.107 50.000 0.00 0.00 0.00 3.02
4339 5875 0.307760 CAAACACCTTCACGACAGCC 59.692 55.000 0.00 0.00 0.00 4.85
4660 6196 2.812499 CGGGCGTAGTACATGGCT 59.188 61.111 0.00 0.00 38.74 4.75
4665 6201 1.679680 GGCGTAGTACATGGCTGTCTA 59.320 52.381 0.00 0.00 36.79 2.59
4682 6218 1.358103 TCTAGATATCCTGGGGTCCCG 59.642 57.143 0.48 0.00 39.42 5.14
4723 6259 1.221021 GTGATCCGGAAGTCCACCC 59.779 63.158 9.01 0.00 35.14 4.61
4755 6291 2.412323 CCTGCTGTTGCGCCATCAT 61.412 57.895 4.18 0.00 43.34 2.45
5058 6596 0.546747 CCAGTTAGGTGGGTCCTCCA 60.547 60.000 10.33 0.00 44.42 3.86
5090 6628 0.107703 TGGCGAAATCGATCTTGGCT 60.108 50.000 13.22 0.00 43.02 4.75
5255 6793 2.041819 GGTGGATCCCCGACCTCT 60.042 66.667 9.90 0.00 33.54 3.69
5261 6799 0.745468 GATCCCCGACCTCTGTGTAC 59.255 60.000 0.00 0.00 0.00 2.90
5264 6802 1.590147 CCCGACCTCTGTGTACACC 59.410 63.158 22.91 5.63 0.00 4.16
5294 6832 3.712907 GTCCCGGTTAGCCAGGCA 61.713 66.667 15.80 0.00 32.21 4.75
5339 6877 3.621225 CAGACCTGCTGGATCGGA 58.379 61.111 17.64 0.00 41.07 4.55
5342 6880 0.616111 AGACCTGCTGGATCGGAAGT 60.616 55.000 17.64 0.00 37.04 3.01
5883 9705 2.109126 GTTCTGGATCGGCCACTGC 61.109 63.158 2.24 0.00 43.33 4.40
5884 9706 3.664025 TTCTGGATCGGCCACTGCG 62.664 63.158 2.24 0.00 43.33 5.18
6533 12241 0.320421 CCCCTATGCCGGTCATAACG 60.320 60.000 16.10 10.70 37.22 3.18
7018 12740 2.316108 TCAGACAGCTGTTACACCTGA 58.684 47.619 23.92 23.92 42.84 3.86
7232 12987 1.234821 CCAGCGTTGAACTTGGCTTA 58.765 50.000 0.00 0.00 32.46 3.09
7810 13574 6.522946 TCTCTCATATCCTTCTTTGATGCTG 58.477 40.000 0.00 0.00 0.00 4.41
7824 13588 0.924823 ATGCTGCTCCTTCCTTGGAT 59.075 50.000 0.00 0.00 35.30 3.41
7853 13618 9.607988 TTTCTTCTTGAATGTAAGTCACTGTTA 57.392 29.630 0.00 0.00 42.58 2.41
7886 13652 7.523293 AAGATGTCACATTAAACAATGGTGA 57.477 32.000 0.00 0.00 34.56 4.02
8030 13804 9.255304 GATAACCTTAAGACAGTGAAGATCATC 57.745 37.037 3.36 0.00 0.00 2.92
8269 14049 2.941720 CCTCCAGAGTCAAGCTAAATGC 59.058 50.000 0.00 0.00 43.29 3.56
8333 14113 4.685165 CCATGATCTCAAACTCTAGATGCG 59.315 45.833 0.00 0.00 32.60 4.73
8349 14129 4.697514 AGATGCGACAAGTTGCTATGTAT 58.302 39.130 13.19 0.00 40.60 2.29
8365 14145 2.422597 TGTATGGTCAGAAGCAAACCG 58.577 47.619 0.00 0.00 36.29 4.44
8386 14168 3.003689 CGTTGCCAATGTTCAGAAAGACT 59.996 43.478 0.00 0.00 0.00 3.24
8406 14188 2.717639 AGTGTGTTGTTCCAAGAGCT 57.282 45.000 0.00 0.00 0.00 4.09
8449 14233 2.802247 TCTTGTTGCTCGACTGAACATG 59.198 45.455 0.00 0.00 30.00 3.21
8453 14237 3.814842 TGTTGCTCGACTGAACATGAAAT 59.185 39.130 0.00 0.00 0.00 2.17
8548 14332 1.811266 CATTCTGGTGGGCGTCTCG 60.811 63.158 0.00 0.00 0.00 4.04
8568 14352 4.065088 TCGTGAATTCAGGAAGAACTTGG 58.935 43.478 24.56 0.00 39.49 3.61
8584 14368 8.667592 AAGAACTTGGGAGTTACTATTACTCT 57.332 34.615 0.00 0.00 45.88 3.24
8808 14598 9.974980 AATAAAATTATAAACAGCCCATAACGG 57.025 29.630 0.00 0.00 0.00 4.44
8833 14623 0.761187 TCATGCATACTCCTGCCTCC 59.239 55.000 0.00 0.00 41.58 4.30
8834 14624 0.763652 CATGCATACTCCTGCCTCCT 59.236 55.000 0.00 0.00 41.58 3.69
8835 14625 1.055040 ATGCATACTCCTGCCTCCTC 58.945 55.000 0.00 0.00 41.58 3.71
8945 14738 0.387367 CCGACGATGATCCGATGGTC 60.387 60.000 0.00 0.00 0.00 4.02
8959 14752 0.904865 ATGGTCAGGAGGTTCGAGCA 60.905 55.000 0.53 0.00 41.00 4.26
9201 15397 2.597510 AGAACTTTGCCCCCGTGC 60.598 61.111 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.248621 GCAGCACAGCAGACGTTTTT 60.249 50.000 0.00 0.00 0.00 1.94
13 14 2.546494 GGCAGCACAGCAGACGTTT 61.546 57.895 0.00 0.00 35.83 3.60
14 15 2.974698 GGCAGCACAGCAGACGTT 60.975 61.111 0.00 0.00 35.83 3.99
15 16 4.996434 GGGCAGCACAGCAGACGT 62.996 66.667 0.00 0.00 35.83 4.34
17 18 4.341783 AGGGGCAGCACAGCAGAC 62.342 66.667 0.00 0.00 35.83 3.51
18 19 4.025858 GAGGGGCAGCACAGCAGA 62.026 66.667 0.00 0.00 35.83 4.26
19 20 4.031129 AGAGGGGCAGCACAGCAG 62.031 66.667 0.00 0.00 35.83 4.24
20 21 4.340246 CAGAGGGGCAGCACAGCA 62.340 66.667 0.00 0.00 35.83 4.41
21 22 3.557903 TTCAGAGGGGCAGCACAGC 62.558 63.158 0.00 0.00 0.00 4.40
23 24 2.752358 CTTCAGAGGGGCAGCACA 59.248 61.111 0.00 0.00 0.00 4.57
31 32 4.821589 GCCGTCGCCTTCAGAGGG 62.822 72.222 0.00 0.00 43.75 4.30
42 43 2.127383 GGTTTTCTTGCGCCGTCG 60.127 61.111 4.18 0.00 39.07 5.12
43 44 0.952010 TAGGGTTTTCTTGCGCCGTC 60.952 55.000 4.18 0.00 0.00 4.79
44 45 1.071814 TAGGGTTTTCTTGCGCCGT 59.928 52.632 4.18 0.00 0.00 5.68
45 46 1.500396 GTAGGGTTTTCTTGCGCCG 59.500 57.895 4.18 0.00 0.00 6.46
48 49 2.178912 TGAGGTAGGGTTTTCTTGCG 57.821 50.000 0.00 0.00 0.00 4.85
75 76 1.966451 CTGCCCTCGCCTCGTTTTT 60.966 57.895 0.00 0.00 0.00 1.94
76 77 2.358737 CTGCCCTCGCCTCGTTTT 60.359 61.111 0.00 0.00 0.00 2.43
178 645 3.308035 TCCAGCGGAGATAGAACCTTA 57.692 47.619 0.00 0.00 0.00 2.69
292 759 3.140225 GAGCTTACCGGAGCCGAGG 62.140 68.421 9.46 0.00 43.74 4.63
324 791 2.494918 CGTAGGAACCAGGAGGCG 59.505 66.667 0.00 0.00 39.06 5.52
344 811 4.818417 CGCGTCGCACAAAAATCT 57.182 50.000 18.75 0.00 0.00 2.40
358 825 3.732892 AAAATCACACGGGGCGCG 61.733 61.111 23.00 23.00 0.00 6.86
381 848 2.543031 GGAAAAAGAACGAACACAGCCC 60.543 50.000 0.00 0.00 0.00 5.19
404 871 1.523258 CCAGGATTCGCAGCTCCAG 60.523 63.158 2.18 0.00 32.55 3.86
418 885 0.179029 ACGTTGAAGGTTCCACCAGG 60.179 55.000 0.00 0.00 41.95 4.45
419 886 2.536761 TACGTTGAAGGTTCCACCAG 57.463 50.000 0.00 0.00 41.95 4.00
420 887 2.369203 TGATACGTTGAAGGTTCCACCA 59.631 45.455 0.00 0.00 41.95 4.17
421 888 3.048337 TGATACGTTGAAGGTTCCACC 57.952 47.619 0.00 0.00 38.99 4.61
422 889 3.181510 GCATGATACGTTGAAGGTTCCAC 60.182 47.826 0.00 0.00 0.00 4.02
423 890 3.006940 GCATGATACGTTGAAGGTTCCA 58.993 45.455 0.00 0.00 0.00 3.53
424 891 3.006940 TGCATGATACGTTGAAGGTTCC 58.993 45.455 0.00 0.00 0.00 3.62
425 892 4.882671 ATGCATGATACGTTGAAGGTTC 57.117 40.909 0.00 0.00 0.00 3.62
426 893 5.822519 ACATATGCATGATACGTTGAAGGTT 59.177 36.000 10.16 0.00 35.96 3.50
427 894 5.237127 CACATATGCATGATACGTTGAAGGT 59.763 40.000 10.16 0.00 35.96 3.50
428 895 5.237127 ACACATATGCATGATACGTTGAAGG 59.763 40.000 10.16 0.00 35.96 3.46
429 896 6.131389 CACACATATGCATGATACGTTGAAG 58.869 40.000 10.16 0.00 35.96 3.02
432 899 4.213674 GCACACATATGCATGATACGTTG 58.786 43.478 10.16 0.00 45.39 4.10
433 900 4.472691 GCACACATATGCATGATACGTT 57.527 40.909 10.16 0.00 45.39 3.99
443 910 3.837213 ACAAGAACAGCACACATATGC 57.163 42.857 1.58 0.00 46.50 3.14
444 911 6.486253 ACTAACAAGAACAGCACACATATG 57.514 37.500 0.00 0.00 0.00 1.78
445 912 7.386851 AGTACTAACAAGAACAGCACACATAT 58.613 34.615 0.00 0.00 0.00 1.78
446 913 6.755206 AGTACTAACAAGAACAGCACACATA 58.245 36.000 0.00 0.00 0.00 2.29
447 914 5.611374 AGTACTAACAAGAACAGCACACAT 58.389 37.500 0.00 0.00 0.00 3.21
448 915 5.018539 AGTACTAACAAGAACAGCACACA 57.981 39.130 0.00 0.00 0.00 3.72
449 916 6.214399 AGTAGTACTAACAAGAACAGCACAC 58.786 40.000 3.61 0.00 0.00 3.82
452 919 7.286215 AGAAGTAGTACTAACAAGAACAGCA 57.714 36.000 3.61 0.00 0.00 4.41
453 920 9.688592 TTAAGAAGTAGTACTAACAAGAACAGC 57.311 33.333 3.61 0.00 0.00 4.40
455 922 9.669353 CGTTAAGAAGTAGTACTAACAAGAACA 57.331 33.333 3.61 0.00 0.00 3.18
456 923 9.122613 CCGTTAAGAAGTAGTACTAACAAGAAC 57.877 37.037 3.61 4.80 0.00 3.01
457 924 8.850156 ACCGTTAAGAAGTAGTACTAACAAGAA 58.150 33.333 3.61 0.00 0.00 2.52
459 926 8.078596 ACACCGTTAAGAAGTAGTACTAACAAG 58.921 37.037 3.61 2.02 0.00 3.16
461 928 7.308589 GGACACCGTTAAGAAGTAGTACTAACA 60.309 40.741 3.61 0.00 0.00 2.41
462 929 7.024171 GGACACCGTTAAGAAGTAGTACTAAC 58.976 42.308 3.61 3.59 0.00 2.34
465 932 5.320277 AGGACACCGTTAAGAAGTAGTACT 58.680 41.667 0.00 0.00 0.00 2.73
466 933 5.392487 GGAGGACACCGTTAAGAAGTAGTAC 60.392 48.000 0.00 0.00 0.00 2.73
467 934 4.702131 GGAGGACACCGTTAAGAAGTAGTA 59.298 45.833 0.00 0.00 0.00 1.82
468 935 3.509184 GGAGGACACCGTTAAGAAGTAGT 59.491 47.826 0.00 0.00 0.00 2.73
471 938 2.299297 CTGGAGGACACCGTTAAGAAGT 59.701 50.000 0.00 0.00 0.00 3.01
472 939 2.299297 ACTGGAGGACACCGTTAAGAAG 59.701 50.000 0.00 0.00 0.00 2.85
473 940 2.322658 ACTGGAGGACACCGTTAAGAA 58.677 47.619 0.00 0.00 0.00 2.52
475 942 2.036733 TGAACTGGAGGACACCGTTAAG 59.963 50.000 0.00 0.00 31.20 1.85
476 943 2.036733 CTGAACTGGAGGACACCGTTAA 59.963 50.000 0.00 0.00 31.20 2.01
477 944 1.616865 CTGAACTGGAGGACACCGTTA 59.383 52.381 0.00 0.00 31.20 3.18
478 945 0.393077 CTGAACTGGAGGACACCGTT 59.607 55.000 0.00 0.00 32.68 4.44
479 946 1.472662 CCTGAACTGGAGGACACCGT 61.473 60.000 0.00 0.00 31.48 4.83
481 948 1.003233 GCCTGAACTGGAGGACACC 60.003 63.158 2.01 0.00 31.48 4.16
482 949 1.374758 CGCCTGAACTGGAGGACAC 60.375 63.158 2.01 0.00 31.48 3.67
483 950 3.059982 CGCCTGAACTGGAGGACA 58.940 61.111 2.01 0.00 31.48 4.02
500 967 3.595691 CTGACAGTGACAGGACACC 57.404 57.895 13.93 0.00 41.12 4.16
506 973 1.345741 ACATGGTCCTGACAGTGACAG 59.654 52.381 14.67 14.67 33.09 3.51
507 974 1.423584 ACATGGTCCTGACAGTGACA 58.576 50.000 19.39 8.79 33.09 3.58
508 975 2.550830 AACATGGTCCTGACAGTGAC 57.449 50.000 12.94 12.94 0.00 3.67
509 976 2.224523 GGAAACATGGTCCTGACAGTGA 60.225 50.000 9.82 0.00 31.94 3.41
510 977 2.154462 GGAAACATGGTCCTGACAGTG 58.846 52.381 9.82 0.00 31.94 3.66
511 978 2.057922 AGGAAACATGGTCCTGACAGT 58.942 47.619 17.08 0.00 44.14 3.55
543 1416 8.887717 AGCAATTAAGACAAGATAACAGCTAAG 58.112 33.333 0.00 0.00 0.00 2.18
544 1417 8.668353 CAGCAATTAAGACAAGATAACAGCTAA 58.332 33.333 0.00 0.00 0.00 3.09
545 1418 7.824289 ACAGCAATTAAGACAAGATAACAGCTA 59.176 33.333 0.00 0.00 0.00 3.32
546 1419 6.656693 ACAGCAATTAAGACAAGATAACAGCT 59.343 34.615 0.00 0.00 0.00 4.24
624 1497 5.010012 CACCTTACCAAGTCAATCAAAAGCT 59.990 40.000 0.00 0.00 0.00 3.74
626 1499 6.633500 TCACCTTACCAAGTCAATCAAAAG 57.367 37.500 0.00 0.00 0.00 2.27
807 1691 4.326826 TGCCATGACTAAACTGGAAAGAG 58.673 43.478 0.00 0.00 31.38 2.85
821 1708 2.456577 ACAGGGGTAAATTGCCATGAC 58.543 47.619 10.52 0.00 0.00 3.06
1206 2264 9.764870 GAAAACTTTAAGTACACTCTCGTTTTT 57.235 29.630 0.00 0.00 33.71 1.94
1275 2397 4.097135 TGGGTAAATGACATATTTGGCGTG 59.903 41.667 0.00 0.00 31.31 5.34
1414 2536 0.332632 CATCACCCAATCCCCACAGT 59.667 55.000 0.00 0.00 0.00 3.55
1432 2554 0.409092 ATTGGGTTGATCCACTGCCA 59.591 50.000 0.00 0.00 36.38 4.92
1433 2555 1.106285 GATTGGGTTGATCCACTGCC 58.894 55.000 0.00 0.00 36.38 4.85
1575 2713 2.115343 ATTCTGTTCTTTCGCCCTCC 57.885 50.000 0.00 0.00 0.00 4.30
1600 2738 1.062488 ACCTCCAGAAGTTGTGGCCT 61.062 55.000 14.20 0.00 34.77 5.19
1613 2751 1.067142 GCATCTCACAACGTACCTCCA 60.067 52.381 0.00 0.00 0.00 3.86
1808 2966 4.886496 AGAACCCTAGTTTCTACCACAC 57.114 45.455 2.67 0.00 35.94 3.82
1809 2967 4.774200 GGTAGAACCCTAGTTTCTACCACA 59.226 45.833 32.40 9.61 45.01 4.17
1810 2968 5.336150 GGTAGAACCCTAGTTTCTACCAC 57.664 47.826 32.40 19.04 45.01 4.16
3579 5111 3.701604 ATCCAGAACGCGTCGAGCC 62.702 63.158 14.44 0.00 44.76 4.70
3580 5112 2.202623 ATCCAGAACGCGTCGAGC 60.203 61.111 14.44 2.33 43.95 5.03
3581 5113 1.934956 CGATCCAGAACGCGTCGAG 60.935 63.158 14.44 4.84 34.46 4.04
3582 5114 2.099638 CGATCCAGAACGCGTCGA 59.900 61.111 14.44 6.47 34.46 4.20
3583 5115 2.949678 CCGATCCAGAACGCGTCG 60.950 66.667 14.44 10.05 0.00 5.12
3585 5117 4.814294 GGCCGATCCAGAACGCGT 62.814 66.667 5.58 5.58 34.01 6.01
3658 5193 1.745489 CTCCTTGTACTTGGCCGGC 60.745 63.158 21.18 21.18 0.00 6.13
3666 5201 1.207791 CCAGGGCATCTCCTTGTACT 58.792 55.000 0.00 0.00 40.11 2.73
3672 5207 2.765807 CCGTCCAGGGCATCTCCT 60.766 66.667 0.00 0.00 37.71 3.69
3708 5243 1.524482 GAGGAGATGACCAGCACCC 59.476 63.158 0.00 0.00 0.00 4.61
3710 5245 1.142748 CGGAGGAGATGACCAGCAC 59.857 63.158 0.00 0.00 0.00 4.40
3724 5259 3.744719 TCCGTCTTCACGCCGGAG 61.745 66.667 5.05 3.72 45.20 4.63
3786 5322 2.819595 CGAATGACCACTGCCGGG 60.820 66.667 2.18 0.00 0.00 5.73
3792 5328 3.319198 ACCGCCCGAATGACCACT 61.319 61.111 0.00 0.00 0.00 4.00
3800 5336 2.665089 ATCATCACCACCGCCCGAA 61.665 57.895 0.00 0.00 0.00 4.30
3801 5337 3.080765 ATCATCACCACCGCCCGA 61.081 61.111 0.00 0.00 0.00 5.14
3802 5338 2.896854 CATCATCACCACCGCCCG 60.897 66.667 0.00 0.00 0.00 6.13
3804 5340 2.516930 CCCATCATCACCACCGCC 60.517 66.667 0.00 0.00 0.00 6.13
3830 5366 0.441145 GTCGTCATTAACACCCACGC 59.559 55.000 0.00 0.00 0.00 5.34
3834 5370 3.245284 CGATCATGTCGTCATTAACACCC 59.755 47.826 8.84 0.00 45.19 4.61
3858 5394 0.629596 TGGTATCCAGAGACTCGGGT 59.370 55.000 19.53 11.85 33.27 5.28
3896 5432 1.454479 CGCCCTAGACCGGGTAGAA 60.454 63.158 6.32 0.00 46.47 2.10
3897 5433 1.344953 TACGCCCTAGACCGGGTAGA 61.345 60.000 6.32 0.00 46.47 2.59
3918 5454 0.919710 CCCCTTCCTTCCCTTACAGG 59.080 60.000 0.00 0.00 34.30 4.00
3919 5455 1.966845 TCCCCTTCCTTCCCTTACAG 58.033 55.000 0.00 0.00 0.00 2.74
3924 5460 1.230314 CCCTTCCCCTTCCTTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
3933 5469 2.122954 AGTTCTCGCCCTTCCCCT 59.877 61.111 0.00 0.00 0.00 4.79
4008 5544 2.366167 CCCTAGCCACCTCCTGCT 60.366 66.667 0.00 0.00 41.57 4.24
4017 5553 1.875488 GGAGACCTAAACCCTAGCCA 58.125 55.000 0.00 0.00 0.00 4.75
4044 5580 2.507407 ATTTGCTCGGCTTCCCTTAA 57.493 45.000 0.00 0.00 0.00 1.85
4265 5801 0.984230 CTTCCCCACCTTACAGCTCA 59.016 55.000 0.00 0.00 0.00 4.26
4564 6100 1.768077 GCTACCCTGGCCAGATCCT 60.768 63.158 34.91 14.71 0.00 3.24
4603 6139 2.811317 GCCGTCCAGCAAGAGTCG 60.811 66.667 0.00 0.00 0.00 4.18
4660 6196 2.111972 GGGACCCCAGGATATCTAGACA 59.888 54.545 0.00 0.00 35.81 3.41
4665 6201 1.158705 CCGGGACCCCAGGATATCT 59.841 63.158 4.46 0.00 35.37 1.98
4682 6218 2.432628 CGTGGACGTGGAGCTTCC 60.433 66.667 0.00 0.00 36.18 3.46
4723 6259 2.328099 GCAGGCCGACCTCTTTGTG 61.328 63.158 0.00 0.00 46.34 3.33
4744 6280 4.792804 TCGGGCATGATGGCGCAA 62.793 61.111 10.83 0.00 46.02 4.85
4857 6393 4.715523 TTCGCTTTGGGCCTCCGG 62.716 66.667 4.53 0.00 37.74 5.14
4861 6397 2.352805 CTCCTTCGCTTTGGGCCT 59.647 61.111 4.53 0.00 37.74 5.19
4870 6406 2.202864 GAGCTCTGCCTCCTTCGC 60.203 66.667 6.43 0.00 0.00 4.70
5009 6547 0.317854 GTGAGCAGTTTTTCCGTGGC 60.318 55.000 0.00 0.00 0.00 5.01
5058 6596 0.107897 TTCGCCACTTATGACGGCAT 60.108 50.000 9.70 9.70 46.60 4.40
5078 6616 1.202533 CCACGGTTAGCCAAGATCGAT 60.203 52.381 0.00 0.00 34.09 3.59
5243 6781 0.040646 TGTACACAGAGGTCGGGGAT 59.959 55.000 0.00 0.00 0.00 3.85
5250 6788 2.927580 CGCCGGTGTACACAGAGGT 61.928 63.158 26.51 0.00 0.00 3.85
5294 6832 4.070265 TCACCGTCCCCGATCCCT 62.070 66.667 0.00 0.00 35.63 4.20
6156 10004 2.108970 GGTATCCAGAGACTCGGGTTT 58.891 52.381 19.53 11.86 33.27 3.27
6533 12241 1.501582 AGCAGGGGATCTAACACTCC 58.498 55.000 0.00 0.00 0.00 3.85
6534 12242 2.365941 GGTAGCAGGGGATCTAACACTC 59.634 54.545 0.00 0.00 0.00 3.51
6535 12243 2.399580 GGTAGCAGGGGATCTAACACT 58.600 52.381 0.00 0.00 0.00 3.55
7238 12993 8.246180 ACATAACACAAATCAATCCTTGTCATC 58.754 33.333 0.00 0.00 33.51 2.92
7248 13003 9.230122 TGTGATACAGACATAACACAAATCAAT 57.770 29.630 0.00 0.00 35.60 2.57
7810 13574 4.495690 AGAAAGTATCCAAGGAAGGAGC 57.504 45.455 0.00 0.00 41.90 4.70
7824 13588 9.261180 CAGTGACTTACATTCAAGAAGAAAGTA 57.739 33.333 7.01 0.00 38.87 2.24
7853 13618 6.839124 TTAATGTGACATCTTTGCAGGATT 57.161 33.333 0.00 0.00 0.00 3.01
7886 13652 7.300658 AGCCAAGATACTTGGATTAATGGATT 58.699 34.615 27.71 3.51 42.06 3.01
8030 13804 1.805945 CTTCGCCGAGGAGAAACCG 60.806 63.158 9.45 0.00 44.74 4.44
8117 13891 1.450312 CCAAGGATGCCCTCGTGTC 60.450 63.158 0.00 0.00 43.48 3.67
8186 13966 1.153353 TACGAGCTTCCGCCAAAAAG 58.847 50.000 0.00 0.00 36.60 2.27
8333 14113 5.419542 TCTGACCATACATAGCAACTTGTC 58.580 41.667 0.00 0.00 0.00 3.18
8349 14129 1.021202 CAACGGTTTGCTTCTGACCA 58.979 50.000 0.00 0.00 32.95 4.02
8365 14145 4.574599 AGTCTTTCTGAACATTGGCAAC 57.425 40.909 0.00 0.00 0.00 4.17
8406 14188 7.222000 AGAAACGGCATTAAGGAAAAATACA 57.778 32.000 0.00 0.00 0.00 2.29
8453 14237 7.829211 GGGAATAAAGGCTAGAATGCATATGTA 59.171 37.037 0.00 0.00 34.04 2.29
8548 14332 4.398319 TCCCAAGTTCTTCCTGAATTCAC 58.602 43.478 3.38 0.00 36.99 3.18
8568 14352 7.378966 TGCATGCATAGAGTAATAGTAACTCC 58.621 38.462 18.46 0.00 43.64 3.85
8584 14368 3.055602 AGAGTCAGTGAACTGCATGCATA 60.056 43.478 22.97 5.39 43.46 3.14
8833 14623 0.179150 CGGCCTTCGAGAGAACTGAG 60.179 60.000 0.00 0.00 46.92 3.35
8834 14624 0.608308 TCGGCCTTCGAGAGAACTGA 60.608 55.000 0.00 0.00 46.92 3.41
8835 14625 1.883732 TCGGCCTTCGAGAGAACTG 59.116 57.895 0.00 0.00 46.92 3.16
8854 14644 1.225426 CTGGCCATTGCTGGAGCTA 59.775 57.895 5.51 0.00 46.37 3.32
8882 14675 0.897863 AGACGAGCAGCAGGAGAAGT 60.898 55.000 0.00 0.00 0.00 3.01
8919 14712 1.638467 GATCATCGTCGGCAACAGC 59.362 57.895 0.00 0.00 0.00 4.40
8921 14714 1.518352 CGGATCATCGTCGGCAACA 60.518 57.895 0.00 0.00 0.00 3.33
8924 14717 1.007387 CATCGGATCATCGTCGGCA 60.007 57.895 0.00 0.00 0.00 5.69
8945 14738 1.079543 CCACTGCTCGAACCTCCTG 60.080 63.158 0.00 0.00 0.00 3.86
8959 14752 2.360350 CGTGCTTGCCCATCCACT 60.360 61.111 0.00 0.00 0.00 4.00
9201 15397 3.245797 TCGAGAGAAGAAAGCATTCACG 58.754 45.455 4.27 0.91 37.03 4.35


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

AutoCloner maintained by Alex Coulton.