Multiple sequence alignment - TraesCS3D01G016500

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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 TraesCS3D01G016500 chr3D 100.000 5749 0 0 1 5749 5789619 5795367 0.000000e+00 10617.0
1 TraesCS3D01G016500 chr3D 83.326 2153 315 28 2701 4842 5735148 5733029 0.000000e+00 1947.0
2 TraesCS3D01G016500 chr3D 95.567 767 10 2 1 744 500513131 500512366 0.000000e+00 1206.0
3 TraesCS3D01G016500 chr3D 95.306 767 13 1 1 744 566367685 566368451 0.000000e+00 1195.0
4 TraesCS3D01G016500 chr3D 95.306 767 10 2 1 744 75653595 75654358 0.000000e+00 1194.0
5 TraesCS3D01G016500 chr3D 95.084 773 11 2 1 746 613106256 613107028 0.000000e+00 1192.0
6 TraesCS3D01G016500 chr3D 89.020 510 44 6 870 1367 5737338 5736829 6.330000e-174 621.0
7 TraesCS3D01G016500 chr3D 77.778 144 22 7 1695 1831 338932126 338931986 4.780000e-11 80.5
8 TraesCS3D01G016500 chr3A 95.027 1830 88 2 2994 4822 12163193 12165020 0.000000e+00 2872.0
9 TraesCS3D01G016500 chr3A 93.878 1470 78 10 745 2211 12160587 12162047 0.000000e+00 2206.0
10 TraesCS3D01G016500 chr3A 85.501 1745 246 5 2941 4684 15464602 15466340 0.000000e+00 1814.0
11 TraesCS3D01G016500 chr3A 89.139 534 32 11 2427 2956 12162682 12163193 4.860000e-180 641.0
12 TraesCS3D01G016500 chr3A 87.363 546 54 6 870 1400 15462248 15462793 3.810000e-171 612.0
13 TraesCS3D01G016500 chr3A 93.939 198 12 0 2231 2428 12162316 12162513 3.370000e-77 300.0
14 TraesCS3D01G016500 chr3A 94.086 186 9 2 4873 5056 12165020 12165205 1.220000e-71 281.0
15 TraesCS3D01G016500 chr3A 95.455 44 2 0 5702 5745 15450958 15450915 2.870000e-08 71.3
16 TraesCS3D01G016500 chrUn 91.348 1988 158 10 2885 4863 28821627 28819645 0.000000e+00 2706.0
17 TraesCS3D01G016500 chrUn 89.421 605 26 10 5151 5749 32302259 32302831 0.000000e+00 728.0
18 TraesCS3D01G016500 chrUn 83.483 557 53 16 899 1450 28813899 28814421 3.110000e-132 483.0
19 TraesCS3D01G016500 chrUn 83.483 557 53 16 899 1450 28825543 28825021 3.110000e-132 483.0
20 TraesCS3D01G016500 chrUn 88.328 317 37 0 3229 3545 349477698 349477382 1.170000e-101 381.0
21 TraesCS3D01G016500 chrUn 88.288 222 24 1 4667 4888 371203375 371203156 1.230000e-66 265.0
22 TraesCS3D01G016500 chrUn 88.288 222 24 1 4667 4888 371315563 371315344 1.230000e-66 265.0
23 TraesCS3D01G016500 chr1B 88.902 1676 181 5 3248 4921 590523541 590521869 0.000000e+00 2060.0
24 TraesCS3D01G016500 chr1B 88.401 1345 152 3 3545 4888 590647133 590645792 0.000000e+00 1616.0
25 TraesCS3D01G016500 chr1B 88.253 1345 154 3 3545 4888 590666895 590665554 0.000000e+00 1605.0
26 TraesCS3D01G016500 chr1B 87.596 911 109 3 3979 4888 590639788 590638881 0.000000e+00 1053.0
27 TraesCS3D01G016500 chr1B 87.463 670 72 8 2885 3545 590649918 590649252 0.000000e+00 761.0
28 TraesCS3D01G016500 chr1B 87.463 670 72 8 2885 3545 590669681 590669015 0.000000e+00 761.0
29 TraesCS3D01G016500 chr1B 87.164 670 72 9 2885 3545 590643596 590642932 0.000000e+00 749.0
30 TraesCS3D01G016500 chr1B 83.514 552 57 15 899 1450 590504627 590505144 8.660000e-133 484.0
31 TraesCS3D01G016500 chr1B 87.770 417 40 7 1035 1450 590506691 590506285 1.450000e-130 477.0
32 TraesCS3D01G016500 chr1B 87.028 424 53 1 4465 4888 590656422 590656001 1.450000e-130 477.0
33 TraesCS3D01G016500 chr1B 92.208 308 24 0 3545 3852 590640613 590640306 2.460000e-118 436.0
34 TraesCS3D01G016500 chr1B 86.737 377 38 8 2885 3252 590632583 590632210 5.360000e-110 409.0
35 TraesCS3D01G016500 chr3B 84.083 2023 291 18 2831 4842 27828337 27830339 0.000000e+00 1923.0
36 TraesCS3D01G016500 chr3B 83.982 2029 295 15 2831 4849 12088450 12086442 0.000000e+00 1919.0
37 TraesCS3D01G016500 chr3B 90.496 484 42 3 887 1367 27826219 27826701 2.260000e-178 636.0
38 TraesCS3D01G016500 chr3B 90.289 484 43 3 887 1367 12090796 12090314 1.050000e-176 630.0
39 TraesCS3D01G016500 chr6D 97.751 756 15 1 1 754 459705395 459704640 0.000000e+00 1301.0
40 TraesCS3D01G016500 chr6D 80.547 1244 231 10 3042 4278 300329035 300327796 0.000000e+00 946.0
41 TraesCS3D01G016500 chr6D 98.944 284 3 0 461 744 446953627 446953910 5.140000e-140 508.0
42 TraesCS3D01G016500 chr6D 85.833 360 49 2 1009 1367 300330445 300330087 1.170000e-101 381.0
43 TraesCS3D01G016500 chr4D 95.613 775 10 2 1 751 105972495 105973269 0.000000e+00 1221.0
44 TraesCS3D01G016500 chr4D 99.351 462 3 0 1 462 464202977 464203438 0.000000e+00 837.0
45 TraesCS3D01G016500 chr1D 95.828 767 9 1 1 744 447842776 447843542 0.000000e+00 1218.0
46 TraesCS3D01G016500 chr1D 95.573 768 9 2 1 745 7746074 7745309 0.000000e+00 1206.0
47 TraesCS3D01G016500 chr1D 97.590 498 6 2 1 498 389332578 389332087 0.000000e+00 848.0
48 TraesCS3D01G016500 chr1D 99.567 462 2 0 1 462 398538739 398538278 0.000000e+00 843.0
49 TraesCS3D01G016500 chr1D 86.567 67 9 0 2602 2668 358223359 358223293 2.220000e-09 75.0
50 TraesCS3D01G016500 chr7D 95.567 767 11 1 1 744 632421455 632422221 0.000000e+00 1206.0
51 TraesCS3D01G016500 chr7D 94.560 772 15 6 1 746 38799939 38799169 0.000000e+00 1170.0
52 TraesCS3D01G016500 chr5D 95.695 604 3 1 1 581 55015052 55015655 0.000000e+00 950.0
53 TraesCS3D01G016500 chr5D 99.567 462 2 0 1 462 554826053 554825592 0.000000e+00 843.0
54 TraesCS3D01G016500 chr6B 80.209 1243 237 8 3042 4278 465150173 465148934 0.000000e+00 924.0
55 TraesCS3D01G016500 chr6B 85.833 360 49 2 1009 1367 465151642 465151284 1.170000e-101 381.0
56 TraesCS3D01G016500 chr6B 79.612 103 18 3 2551 2652 32003660 32003560 2.870000e-08 71.3
57 TraesCS3D01G016500 chr6A 80.032 1242 241 6 3042 4278 417444161 417445400 0.000000e+00 913.0
58 TraesCS3D01G016500 chr6A 85.095 369 53 2 1000 1367 417442716 417443083 5.440000e-100 375.0
59 TraesCS3D01G016500 chr6A 83.200 125 17 4 2551 2674 79953883 79953762 1.690000e-20 111.0
60 TraesCS3D01G016500 chr2A 87.740 416 45 4 1035 1450 765249089 765249498 1.120000e-131 481.0
61 TraesCS3D01G016500 chr4B 81.900 558 61 16 899 1450 671720950 671720427 8.850000e-118 435.0
62 TraesCS3D01G016500 chr5A 84.856 416 48 11 1035 1450 709416482 709416882 6.940000e-109 405.0
63 TraesCS3D01G016500 chr5A 85.816 282 31 6 1035 1316 709419253 709418981 2.030000e-74 291.0
64 TraesCS3D01G016500 chr2B 83.193 119 17 3 2551 2668 729806050 729806166 7.880000e-19 106.0
65 TraesCS3D01G016500 chr2D 88.235 51 6 0 2582 2632 650129500 650129450 1.730000e-05 62.1


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 TraesCS3D01G016500 chr3D 5789619 5795367 5748 False 10617.0 10617 100.0000 1 5749 1 chr3D.!!$F1 5748
1 TraesCS3D01G016500 chr3D 5733029 5737338 4309 True 1284.0 1947 86.1730 870 4842 2 chr3D.!!$R3 3972
2 TraesCS3D01G016500 chr3D 500512366 500513131 765 True 1206.0 1206 95.5670 1 744 1 chr3D.!!$R2 743
3 TraesCS3D01G016500 chr3D 566367685 566368451 766 False 1195.0 1195 95.3060 1 744 1 chr3D.!!$F3 743
4 TraesCS3D01G016500 chr3D 75653595 75654358 763 False 1194.0 1194 95.3060 1 744 1 chr3D.!!$F2 743
5 TraesCS3D01G016500 chr3D 613106256 613107028 772 False 1192.0 1192 95.0840 1 746 1 chr3D.!!$F4 745
6 TraesCS3D01G016500 chr3A 12160587 12165205 4618 False 1260.0 2872 93.2138 745 5056 5 chr3A.!!$F1 4311
7 TraesCS3D01G016500 chr3A 15462248 15466340 4092 False 1213.0 1814 86.4320 870 4684 2 chr3A.!!$F2 3814
8 TraesCS3D01G016500 chrUn 28819645 28825543 5898 True 1594.5 2706 87.4155 899 4863 2 chrUn.!!$R4 3964
9 TraesCS3D01G016500 chrUn 32302259 32302831 572 False 728.0 728 89.4210 5151 5749 1 chrUn.!!$F2 598
10 TraesCS3D01G016500 chrUn 28813899 28814421 522 False 483.0 483 83.4830 899 1450 1 chrUn.!!$F1 551
11 TraesCS3D01G016500 chr1B 590521869 590523541 1672 True 2060.0 2060 88.9020 3248 4921 1 chr1B.!!$R2 1673
12 TraesCS3D01G016500 chr1B 590665554 590669681 4127 True 1183.0 1605 87.8580 2885 4888 2 chr1B.!!$R6 2003
13 TraesCS3D01G016500 chr1B 590638881 590649918 11037 True 923.0 1616 88.5664 2885 4888 5 chr1B.!!$R5 2003
14 TraesCS3D01G016500 chr1B 590504627 590505144 517 False 484.0 484 83.5140 899 1450 1 chr1B.!!$F1 551
15 TraesCS3D01G016500 chr3B 27826219 27830339 4120 False 1279.5 1923 87.2895 887 4842 2 chr3B.!!$F1 3955
16 TraesCS3D01G016500 chr3B 12086442 12090796 4354 True 1274.5 1919 87.1355 887 4849 2 chr3B.!!$R1 3962
17 TraesCS3D01G016500 chr6D 459704640 459705395 755 True 1301.0 1301 97.7510 1 754 1 chr6D.!!$R1 753
18 TraesCS3D01G016500 chr6D 300327796 300330445 2649 True 663.5 946 83.1900 1009 4278 2 chr6D.!!$R2 3269
19 TraesCS3D01G016500 chr4D 105972495 105973269 774 False 1221.0 1221 95.6130 1 751 1 chr4D.!!$F1 750
20 TraesCS3D01G016500 chr1D 447842776 447843542 766 False 1218.0 1218 95.8280 1 744 1 chr1D.!!$F1 743
21 TraesCS3D01G016500 chr1D 7745309 7746074 765 True 1206.0 1206 95.5730 1 745 1 chr1D.!!$R1 744
22 TraesCS3D01G016500 chr7D 632421455 632422221 766 False 1206.0 1206 95.5670 1 744 1 chr7D.!!$F1 743
23 TraesCS3D01G016500 chr7D 38799169 38799939 770 True 1170.0 1170 94.5600 1 746 1 chr7D.!!$R1 745
24 TraesCS3D01G016500 chr5D 55015052 55015655 603 False 950.0 950 95.6950 1 581 1 chr5D.!!$F1 580
25 TraesCS3D01G016500 chr6B 465148934 465151642 2708 True 652.5 924 83.0210 1009 4278 2 chr6B.!!$R2 3269
26 TraesCS3D01G016500 chr6A 417442716 417445400 2684 False 644.0 913 82.5635 1000 4278 2 chr6A.!!$F1 3278
27 TraesCS3D01G016500 chr4B 671720427 671720950 523 True 435.0 435 81.9000 899 1450 1 chr4B.!!$R1 551

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
843 892 0.322546 ACCTCGGAGGAAACAATGGC 60.323 55.0 30.13 0.00 37.67 4.40 F
1625 2448 0.865111 CATTCGTGAAAGTCGTGGCA 59.135 50.0 0.00 0.00 0.00 4.92 F
2854 5074 0.663269 TTGCACAGCTCGTACGTGAG 60.663 55.0 20.61 10.38 39.05 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 2510 0.881118 CATTCGTGAAAGTGGTGGGG 59.119 55.0 0.0 0.0 0.0 4.96 R
3087 6748 0.179084 CGTGTAACCTCCGATGGCAT 60.179 55.0 0.0 0.0 0.0 4.40 R
4769 17466 1.078709 CAGACAAGCACACGTATGGG 58.921 55.0 0.0 0.0 0.0 4.00 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
191 192 8.748582 CACATGCATATTTTATCAATGACACAC 58.251 33.333 0.00 0.00 0.00 3.82
682 730 1.676615 CGCGACTAAAGGCCCCTTTTA 60.677 52.381 16.74 0.00 42.93 1.52
740 789 5.292101 CGTATGGAAGCCTCTTTTTCTACTG 59.708 44.000 0.00 0.00 0.00 2.74
747 796 4.001652 GCCTCTTTTTCTACTGGTGGTAC 58.998 47.826 0.00 0.00 0.00 3.34
748 797 4.504340 GCCTCTTTTTCTACTGGTGGTACA 60.504 45.833 0.00 0.00 0.00 2.90
773 822 4.033990 TCTAGCGCTAAGACAATCAGTG 57.966 45.455 19.37 2.02 0.00 3.66
789 838 4.641645 TGAGGCGGCAACCACCTG 62.642 66.667 13.08 0.00 39.67 4.00
800 849 3.052082 CCACCTGGCAGCGTTCTG 61.052 66.667 9.56 0.00 43.16 3.02
843 892 0.322546 ACCTCGGAGGAAACAATGGC 60.323 55.000 30.13 0.00 37.67 4.40
848 897 3.541632 TCGGAGGAAACAATGGCTAATC 58.458 45.455 0.00 0.00 0.00 1.75
860 909 1.837439 TGGCTAATCCACCGTCATCTT 59.163 47.619 0.00 0.00 40.72 2.40
862 911 2.420129 GGCTAATCCACCGTCATCTTGT 60.420 50.000 0.00 0.00 34.01 3.16
868 917 1.548719 CCACCGTCATCTTGTAGGTCA 59.451 52.381 0.00 0.00 32.04 4.02
960 1030 1.134580 AGCTCGGTTCATCATCCACTG 60.135 52.381 0.00 0.00 0.00 3.66
1411 1496 6.895898 ACATCTCAACATCATGCGAATATTC 58.104 36.000 5.30 5.30 0.00 1.75
1484 1580 2.599082 GGACGTGATGTTTCTTAGCTCG 59.401 50.000 0.00 0.00 0.00 5.03
1591 2414 9.463443 ACAAATGTTTTGAGTGCTTATAAAGTC 57.537 29.630 6.96 0.00 0.00 3.01
1614 2437 5.703130 TCACACCATGAAATAACATTCGTGA 59.297 36.000 10.07 0.00 45.16 4.35
1616 2439 6.860539 CACACCATGAAATAACATTCGTGAAA 59.139 34.615 10.07 0.00 45.16 2.69
1620 2443 6.465781 CCATGAAATAACATTCGTGAAAGTCG 59.534 38.462 10.07 0.00 45.16 4.18
1621 2444 6.533819 TGAAATAACATTCGTGAAAGTCGT 57.466 33.333 0.00 0.00 31.80 4.34
1625 2448 0.865111 CATTCGTGAAAGTCGTGGCA 59.135 50.000 0.00 0.00 0.00 4.92
1652 2475 6.833342 AAAATATCGATGCTCCAAAAATGC 57.167 33.333 8.54 0.00 0.00 3.56
1657 2480 5.581126 TCGATGCTCCAAAAATGCTATTT 57.419 34.783 0.00 0.00 0.00 1.40
1662 2485 6.542574 TGCTCCAAAAATGCTATTTTTGTG 57.457 33.333 26.88 22.60 43.88 3.33
1707 2530 1.604604 CCCACCACTTTCACGAATGT 58.395 50.000 0.00 0.00 0.00 2.71
1744 2567 3.324556 ACTGTGCAAGCACCCAAAATATT 59.675 39.130 21.19 0.00 45.63 1.28
1745 2568 4.202346 ACTGTGCAAGCACCCAAAATATTT 60.202 37.500 21.19 0.00 45.63 1.40
1755 2578 5.404946 CACCCAAAATATTTGCTCAGAGTG 58.595 41.667 0.39 0.43 0.00 3.51
1758 2581 6.095377 CCCAAAATATTTGCTCAGAGTGTTC 58.905 40.000 0.39 0.00 0.00 3.18
1761 2584 5.886960 AATATTTGCTCAGAGTGTTCCAC 57.113 39.130 0.00 0.00 34.10 4.02
1762 2585 2.708216 TTTGCTCAGAGTGTTCCACA 57.292 45.000 0.00 0.00 36.74 4.17
1824 2648 8.671921 ACTTTACTGTTCATCATAGCTCATTTG 58.328 33.333 0.00 0.00 0.00 2.32
1849 2673 3.206150 TCGCAAGCAAAAGAAGACTTCT 58.794 40.909 12.12 12.12 38.63 2.85
1937 3081 3.878086 TGTGTCGTTCAATCTTTGCTC 57.122 42.857 0.00 0.00 0.00 4.26
1981 3125 5.164606 TCTTTTCTTTGGCAAGTACGTTC 57.835 39.130 0.00 0.00 0.00 3.95
2207 3507 7.984391 TGTGCATAACCACACTTTCTATTATG 58.016 34.615 0.00 0.00 40.55 1.90
2209 3509 7.282224 GTGCATAACCACACTTTCTATTATGGA 59.718 37.037 0.00 0.00 35.80 3.41
2273 3917 7.866898 GCCAACATGAATACAATTGCATATACA 59.133 33.333 5.05 0.97 0.00 2.29
2371 4188 6.128553 ACGCCTGCACAATATTTTATATCTCG 60.129 38.462 0.00 0.00 0.00 4.04
2510 4721 9.770097 GTATGGAAAGTGATAGAATGATCTTGA 57.230 33.333 0.00 0.00 37.10 3.02
2564 4776 1.069358 CTCAATTACTCTCTCCGCCCC 59.931 57.143 0.00 0.00 0.00 5.80
2578 4790 2.424246 TCCGCCCCGAATTATTTTTCAC 59.576 45.455 0.00 0.00 0.00 3.18
2580 4792 2.096174 CGCCCCGAATTATTTTTCACGA 59.904 45.455 0.00 0.00 0.00 4.35
2643 4855 5.928839 GTCTACATACATCCATTTCTGCGAT 59.071 40.000 0.00 0.00 0.00 4.58
2659 4871 4.466567 TGCGATAAATAATTGCGGACAG 57.533 40.909 0.00 0.00 46.67 3.51
2671 4883 1.342076 TGCGGACAGAGGGAGTATTCT 60.342 52.381 0.00 0.00 0.00 2.40
2689 4901 8.848474 AGTATTCTGTAACAGTTATGCAAGTT 57.152 30.769 0.00 0.00 32.61 2.66
2818 5033 6.436218 TCATATATAGCAACACCGTCCATACT 59.564 38.462 0.00 0.00 0.00 2.12
2820 5035 1.808411 AGCAACACCGTCCATACTTG 58.192 50.000 0.00 0.00 0.00 3.16
2854 5074 0.663269 TTGCACAGCTCGTACGTGAG 60.663 55.000 20.61 10.38 39.05 3.51
2873 6242 7.679659 CGTGAGTCGTGATGATATTTTCTAA 57.320 36.000 0.00 0.00 34.52 2.10
2874 6243 8.115491 CGTGAGTCGTGATGATATTTTCTAAA 57.885 34.615 0.00 0.00 34.52 1.85
2937 6306 5.750352 TCCAAGTTATAAAAGACGGGTCT 57.250 39.130 0.00 0.00 42.75 3.85
2952 6321 5.944599 AGACGGGTCTATATGTATGTACCAG 59.055 44.000 0.00 0.00 38.35 4.00
2965 6338 6.406370 TGTATGTACCAGAAATCAGGACTTG 58.594 40.000 0.00 0.00 0.00 3.16
2971 6344 3.251729 CCAGAAATCAGGACTTGTGTGTG 59.748 47.826 0.00 0.00 0.00 3.82
2975 6348 6.091849 CAGAAATCAGGACTTGTGTGTGATAG 59.908 42.308 0.00 0.00 30.52 2.08
3014 6387 1.847798 ATTAGTCTGTTGGCCGGCCA 61.848 55.000 44.23 44.23 45.63 5.36
3077 6735 1.523711 CATATTCGGCACCGGCAGT 60.524 57.895 9.58 0.00 43.71 4.40
3087 6748 3.680786 CCGGCAGTGACCACGAGA 61.681 66.667 0.00 0.00 36.20 4.04
3113 6774 1.288127 GGAGGTTACACGTGCGTCT 59.712 57.895 17.22 8.24 0.00 4.18
3281 6942 0.604243 TTGCTTACATCGCCGGTGTT 60.604 50.000 8.90 3.28 0.00 3.32
3296 6957 3.998672 GTTCTCACCGGACGCCCA 61.999 66.667 9.46 0.00 0.00 5.36
3356 7017 1.097547 CCGCCGAGGCATTCAAGATT 61.098 55.000 15.03 0.00 42.06 2.40
3398 7059 0.850100 TCAAGCTGAACCCCAAGGAA 59.150 50.000 0.00 0.00 36.73 3.36
3410 7071 0.972471 CCAAGGAAGGGTTGGCCATC 60.972 60.000 6.09 5.53 38.23 3.51
3428 7089 2.685829 CGTAAATGGCACGGCTGCA 61.686 57.895 0.50 0.00 46.28 4.41
3452 7113 2.045708 CGCCCTTGCAGCAATGGTA 61.046 57.895 25.32 0.00 37.32 3.25
3602 9383 2.280797 GCCGCGGCTATCATGGAA 60.281 61.111 41.71 0.00 38.26 3.53
4028 16720 4.916293 GAGATCGCCATGGCCGCA 62.916 66.667 30.79 15.44 37.98 5.69
4115 16807 2.155065 CCAGGGGGTGAACTCACTT 58.845 57.895 9.60 0.00 45.73 3.16
4286 16978 1.440938 CCAAAAAGGTGGTCGACGCA 61.441 55.000 9.92 6.05 33.63 5.24
4337 17029 2.873604 CGACCGCGTGGACGTTTTT 61.874 57.895 27.57 1.41 46.22 1.94
4484 17176 1.550072 GAGGAGGAGCTCATGATAGCC 59.450 57.143 17.19 5.44 43.86 3.93
4619 17311 0.032815 TCGGATGCGTGTTTCTGACA 59.967 50.000 6.49 0.00 35.42 3.58
4734 17426 0.322546 GGAATGGAACGGTGAGCCTT 60.323 55.000 0.00 0.00 0.00 4.35
4769 17466 5.684550 AACTCGTGTCAAGGTTTTTATCC 57.315 39.130 0.00 0.00 0.00 2.59
4782 17479 3.637911 TTTTATCCCCATACGTGTGCT 57.362 42.857 6.80 0.00 0.00 4.40
4802 17502 5.909610 GTGCTTGTCTGAATAAGTGAACAAC 59.090 40.000 5.25 0.00 0.00 3.32
4823 17523 3.003897 ACACTGTTGTTCACGTGTGTTTT 59.996 39.130 16.51 0.00 40.59 2.43
4856 17556 3.951037 TGTGTGTACATGCACCTCTTTTT 59.049 39.130 12.58 0.00 38.52 1.94
4863 17563 5.633830 ACATGCACCTCTTTTTATGTCTG 57.366 39.130 0.00 0.00 0.00 3.51
4866 17566 6.040842 ACATGCACCTCTTTTTATGTCTGTTT 59.959 34.615 0.00 0.00 0.00 2.83
4889 17590 7.846644 TTGACAATCAGCTGTTTTTCATTTT 57.153 28.000 21.17 4.93 0.00 1.82
4894 17595 8.603181 ACAATCAGCTGTTTTTCATTTTGTAAC 58.397 29.630 14.67 0.00 0.00 2.50
4904 17605 7.444558 TTTTCATTTTGTAACTCGAACTTGC 57.555 32.000 0.00 0.00 0.00 4.01
4974 17676 1.538047 TCTTGCCCATCTTTGTCTGC 58.462 50.000 0.00 0.00 0.00 4.26
4995 17697 3.574614 CTTTTAATTTGGGCCACAGTCG 58.425 45.455 5.23 0.00 0.00 4.18
5002 17704 0.106918 TGGGCCACAGTCGAAAAAGT 60.107 50.000 0.00 0.00 0.00 2.66
5020 17722 2.192175 CCCCCACGCATTAGACCC 59.808 66.667 0.00 0.00 0.00 4.46
5025 17727 1.379527 CCACGCATTAGACCCTTTCC 58.620 55.000 0.00 0.00 0.00 3.13
5056 17758 3.632189 CAGCTAAAACAAGCCAGACAAC 58.368 45.455 0.00 0.00 43.86 3.32
5057 17759 3.066621 CAGCTAAAACAAGCCAGACAACA 59.933 43.478 0.00 0.00 43.86 3.33
5058 17760 3.891366 AGCTAAAACAAGCCAGACAACAT 59.109 39.130 0.00 0.00 43.86 2.71
5059 17761 5.048782 CAGCTAAAACAAGCCAGACAACATA 60.049 40.000 0.00 0.00 43.86 2.29
5060 17762 5.711976 AGCTAAAACAAGCCAGACAACATAT 59.288 36.000 0.00 0.00 43.86 1.78
5061 17763 6.030228 GCTAAAACAAGCCAGACAACATATC 58.970 40.000 0.00 0.00 36.45 1.63
5062 17764 5.391312 AAAACAAGCCAGACAACATATCC 57.609 39.130 0.00 0.00 0.00 2.59
5063 17765 3.004752 ACAAGCCAGACAACATATCCC 57.995 47.619 0.00 0.00 0.00 3.85
5064 17766 2.301346 CAAGCCAGACAACATATCCCC 58.699 52.381 0.00 0.00 0.00 4.81
5065 17767 1.898863 AGCCAGACAACATATCCCCT 58.101 50.000 0.00 0.00 0.00 4.79
5066 17768 1.771255 AGCCAGACAACATATCCCCTC 59.229 52.381 0.00 0.00 0.00 4.30
5067 17769 1.771255 GCCAGACAACATATCCCCTCT 59.229 52.381 0.00 0.00 0.00 3.69
5068 17770 2.224402 GCCAGACAACATATCCCCTCTC 60.224 54.545 0.00 0.00 0.00 3.20
5069 17771 3.041211 CCAGACAACATATCCCCTCTCA 58.959 50.000 0.00 0.00 0.00 3.27
5070 17772 3.649981 CCAGACAACATATCCCCTCTCAT 59.350 47.826 0.00 0.00 0.00 2.90
5071 17773 4.103785 CCAGACAACATATCCCCTCTCATT 59.896 45.833 0.00 0.00 0.00 2.57
5072 17774 5.303971 CAGACAACATATCCCCTCTCATTC 58.696 45.833 0.00 0.00 0.00 2.67
5073 17775 5.071519 CAGACAACATATCCCCTCTCATTCT 59.928 44.000 0.00 0.00 0.00 2.40
5074 17776 6.268617 CAGACAACATATCCCCTCTCATTCTA 59.731 42.308 0.00 0.00 0.00 2.10
5075 17777 7.021873 AGACAACATATCCCCTCTCATTCTAT 58.978 38.462 0.00 0.00 0.00 1.98
5076 17778 7.515514 AGACAACATATCCCCTCTCATTCTATT 59.484 37.037 0.00 0.00 0.00 1.73
5077 17779 8.050316 ACAACATATCCCCTCTCATTCTATTT 57.950 34.615 0.00 0.00 0.00 1.40
5078 17780 8.506083 ACAACATATCCCCTCTCATTCTATTTT 58.494 33.333 0.00 0.00 0.00 1.82
5079 17781 8.790718 CAACATATCCCCTCTCATTCTATTTTG 58.209 37.037 0.00 0.00 0.00 2.44
5080 17782 7.465116 ACATATCCCCTCTCATTCTATTTTGG 58.535 38.462 0.00 0.00 0.00 3.28
5081 17783 4.170468 TCCCCTCTCATTCTATTTTGGC 57.830 45.455 0.00 0.00 0.00 4.52
5082 17784 3.788142 TCCCCTCTCATTCTATTTTGGCT 59.212 43.478 0.00 0.00 0.00 4.75
5083 17785 4.230502 TCCCCTCTCATTCTATTTTGGCTT 59.769 41.667 0.00 0.00 0.00 4.35
5084 17786 4.958581 CCCCTCTCATTCTATTTTGGCTTT 59.041 41.667 0.00 0.00 0.00 3.51
5085 17787 5.423290 CCCCTCTCATTCTATTTTGGCTTTT 59.577 40.000 0.00 0.00 0.00 2.27
5086 17788 6.335777 CCCTCTCATTCTATTTTGGCTTTTG 58.664 40.000 0.00 0.00 0.00 2.44
5087 17789 5.809051 CCTCTCATTCTATTTTGGCTTTTGC 59.191 40.000 0.00 0.00 46.64 3.68
5088 17790 6.350780 CCTCTCATTCTATTTTGGCTTTTGCT 60.351 38.462 0.00 0.00 46.54 3.91
5089 17791 6.996509 TCTCATTCTATTTTGGCTTTTGCTT 58.003 32.000 0.00 0.00 46.54 3.91
5090 17792 6.869913 TCTCATTCTATTTTGGCTTTTGCTTG 59.130 34.615 0.00 0.00 46.54 4.01
5091 17793 5.409214 TCATTCTATTTTGGCTTTTGCTTGC 59.591 36.000 0.00 0.00 46.54 4.01
5092 17794 4.605640 TCTATTTTGGCTTTTGCTTGCT 57.394 36.364 0.00 0.00 46.54 3.91
5093 17795 4.309099 TCTATTTTGGCTTTTGCTTGCTG 58.691 39.130 0.00 0.00 46.54 4.41
5094 17796 1.666054 TTTTGGCTTTTGCTTGCTGG 58.334 45.000 0.00 0.00 46.54 4.85
5095 17797 0.829333 TTTGGCTTTTGCTTGCTGGA 59.171 45.000 0.00 0.00 46.54 3.86
5096 17798 1.050204 TTGGCTTTTGCTTGCTGGAT 58.950 45.000 0.00 0.00 46.54 3.41
5097 17799 0.604578 TGGCTTTTGCTTGCTGGATC 59.395 50.000 0.00 0.00 46.54 3.36
5098 17800 0.604578 GGCTTTTGCTTGCTGGATCA 59.395 50.000 0.00 0.00 46.54 2.92
5099 17801 1.670967 GGCTTTTGCTTGCTGGATCAC 60.671 52.381 0.00 0.00 46.54 3.06
5100 17802 1.973138 CTTTTGCTTGCTGGATCACG 58.027 50.000 0.00 0.00 0.00 4.35
5101 17803 1.267806 CTTTTGCTTGCTGGATCACGT 59.732 47.619 0.00 0.00 0.00 4.49
5102 17804 2.177394 TTTGCTTGCTGGATCACGTA 57.823 45.000 0.00 0.00 0.00 3.57
5103 17805 2.177394 TTGCTTGCTGGATCACGTAA 57.823 45.000 0.00 0.00 0.00 3.18
5104 17806 2.401583 TGCTTGCTGGATCACGTAAT 57.598 45.000 0.00 0.00 0.00 1.89
5105 17807 2.009051 TGCTTGCTGGATCACGTAATG 58.991 47.619 0.00 0.00 0.00 1.90
5106 17808 2.009774 GCTTGCTGGATCACGTAATGT 58.990 47.619 0.00 0.00 0.00 2.71
5107 17809 2.030946 GCTTGCTGGATCACGTAATGTC 59.969 50.000 0.00 0.00 0.00 3.06
5108 17810 3.261580 CTTGCTGGATCACGTAATGTCA 58.738 45.455 0.00 0.00 0.00 3.58
5109 17811 3.326836 TGCTGGATCACGTAATGTCAA 57.673 42.857 0.00 0.00 0.00 3.18
5110 17812 3.261580 TGCTGGATCACGTAATGTCAAG 58.738 45.455 0.00 0.00 0.00 3.02
5111 17813 3.262420 GCTGGATCACGTAATGTCAAGT 58.738 45.455 0.00 0.00 0.00 3.16
5112 17814 3.062639 GCTGGATCACGTAATGTCAAGTG 59.937 47.826 0.00 0.00 36.06 3.16
5113 17815 4.494484 CTGGATCACGTAATGTCAAGTGA 58.506 43.478 0.00 0.00 45.93 3.41
5114 17816 4.888917 TGGATCACGTAATGTCAAGTGAA 58.111 39.130 1.19 0.00 45.17 3.18
5115 17817 5.301555 TGGATCACGTAATGTCAAGTGAAA 58.698 37.500 1.19 0.00 45.17 2.69
5116 17818 5.937540 TGGATCACGTAATGTCAAGTGAAAT 59.062 36.000 1.19 0.00 45.17 2.17
5117 17819 6.128309 TGGATCACGTAATGTCAAGTGAAATG 60.128 38.462 1.19 0.00 45.17 2.32
5118 17820 5.029650 TCACGTAATGTCAAGTGAAATGC 57.970 39.130 0.00 0.00 40.19 3.56
5119 17821 4.083537 TCACGTAATGTCAAGTGAAATGCC 60.084 41.667 0.00 0.00 40.19 4.40
5120 17822 4.072131 ACGTAATGTCAAGTGAAATGCCT 58.928 39.130 0.00 0.00 0.00 4.75
5121 17823 4.518970 ACGTAATGTCAAGTGAAATGCCTT 59.481 37.500 0.00 0.00 0.00 4.35
5122 17824 5.703592 ACGTAATGTCAAGTGAAATGCCTTA 59.296 36.000 0.00 0.00 0.00 2.69
5123 17825 6.205853 ACGTAATGTCAAGTGAAATGCCTTAA 59.794 34.615 0.00 0.00 0.00 1.85
5124 17826 6.742718 CGTAATGTCAAGTGAAATGCCTTAAG 59.257 38.462 0.00 0.00 0.00 1.85
5125 17827 4.503741 TGTCAAGTGAAATGCCTTAAGC 57.496 40.909 0.00 0.00 44.14 3.09
5126 17828 4.144297 TGTCAAGTGAAATGCCTTAAGCT 58.856 39.130 0.00 0.00 44.23 3.74
5127 17829 4.584325 TGTCAAGTGAAATGCCTTAAGCTT 59.416 37.500 3.48 3.48 44.23 3.74
5128 17830 5.157067 GTCAAGTGAAATGCCTTAAGCTTC 58.843 41.667 0.00 0.00 44.23 3.86
5129 17831 5.048434 GTCAAGTGAAATGCCTTAAGCTTCT 60.048 40.000 0.00 0.00 44.23 2.85
5130 17832 5.182001 TCAAGTGAAATGCCTTAAGCTTCTC 59.818 40.000 0.00 0.00 44.23 2.87
5131 17833 4.013050 AGTGAAATGCCTTAAGCTTCTCC 58.987 43.478 0.00 0.00 44.23 3.71
5132 17834 4.013050 GTGAAATGCCTTAAGCTTCTCCT 58.987 43.478 0.00 0.00 44.23 3.69
5133 17835 4.012374 TGAAATGCCTTAAGCTTCTCCTG 58.988 43.478 0.00 0.00 44.23 3.86
5134 17836 4.263462 TGAAATGCCTTAAGCTTCTCCTGA 60.263 41.667 0.00 0.00 44.23 3.86
5135 17837 4.516652 AATGCCTTAAGCTTCTCCTGAT 57.483 40.909 0.00 0.00 44.23 2.90
5136 17838 5.636903 AATGCCTTAAGCTTCTCCTGATA 57.363 39.130 0.00 0.00 44.23 2.15
5137 17839 5.636903 ATGCCTTAAGCTTCTCCTGATAA 57.363 39.130 0.00 0.00 44.23 1.75
5138 17840 5.435686 TGCCTTAAGCTTCTCCTGATAAA 57.564 39.130 0.00 0.00 44.23 1.40
5139 17841 5.815581 TGCCTTAAGCTTCTCCTGATAAAA 58.184 37.500 0.00 0.00 44.23 1.52
5140 17842 5.882557 TGCCTTAAGCTTCTCCTGATAAAAG 59.117 40.000 0.00 0.00 44.23 2.27
5141 17843 5.883115 GCCTTAAGCTTCTCCTGATAAAAGT 59.117 40.000 0.00 0.00 38.99 2.66
5142 17844 6.183360 GCCTTAAGCTTCTCCTGATAAAAGTG 60.183 42.308 0.00 0.00 38.99 3.16
5143 17845 7.106239 CCTTAAGCTTCTCCTGATAAAAGTGA 58.894 38.462 0.00 0.00 0.00 3.41
5144 17846 7.279758 CCTTAAGCTTCTCCTGATAAAAGTGAG 59.720 40.741 0.00 0.00 0.00 3.51
5145 17847 5.753721 AGCTTCTCCTGATAAAAGTGAGT 57.246 39.130 0.00 0.00 0.00 3.41
5146 17848 6.120507 AGCTTCTCCTGATAAAAGTGAGTT 57.879 37.500 0.00 0.00 0.00 3.01
5147 17849 6.169800 AGCTTCTCCTGATAAAAGTGAGTTC 58.830 40.000 0.00 0.00 0.00 3.01
5148 17850 5.934625 GCTTCTCCTGATAAAAGTGAGTTCA 59.065 40.000 0.00 0.00 0.00 3.18
5149 17851 6.128418 GCTTCTCCTGATAAAAGTGAGTTCAC 60.128 42.308 4.09 4.09 46.77 3.18
5167 17869 8.777413 TGAGTTCACATATTCTCAAAAAGAGTG 58.223 33.333 0.00 0.00 44.98 3.51
5271 17973 8.690203 ATATCGAAACCACAAATATGAATGGA 57.310 30.769 6.43 0.00 36.04 3.41
5307 18009 7.066887 GGAAAAACAAAACCCAAAATGAGACAT 59.933 33.333 0.00 0.00 0.00 3.06
5354 18056 9.959749 TCAAACAATGAACTTCCTTAAATACAC 57.040 29.630 0.00 0.00 34.30 2.90
5386 18088 7.458409 AATTTTGAGATATGCAGTGAACACT 57.542 32.000 1.32 1.32 43.61 3.55
5387 18089 6.882610 TTTTGAGATATGCAGTGAACACTT 57.117 33.333 4.63 0.00 40.20 3.16
5388 18090 6.882610 TTTGAGATATGCAGTGAACACTTT 57.117 33.333 4.63 0.00 40.20 2.66
5389 18091 6.882610 TTGAGATATGCAGTGAACACTTTT 57.117 33.333 4.63 0.00 40.20 2.27
5390 18092 6.245115 TGAGATATGCAGTGAACACTTTTG 57.755 37.500 4.63 0.00 40.20 2.44
5391 18093 5.051891 AGATATGCAGTGAACACTTTTGC 57.948 39.130 4.63 7.57 40.20 3.68
5392 18094 4.763793 AGATATGCAGTGAACACTTTTGCT 59.236 37.500 15.01 6.88 40.20 3.91
5393 18095 5.939883 AGATATGCAGTGAACACTTTTGCTA 59.060 36.000 15.01 8.24 40.20 3.49
5394 18096 6.600822 AGATATGCAGTGAACACTTTTGCTAT 59.399 34.615 15.01 11.16 40.20 2.97
5395 18097 7.770433 AGATATGCAGTGAACACTTTTGCTATA 59.230 33.333 15.01 11.93 40.20 1.31
5396 18098 6.764308 ATGCAGTGAACACTTTTGCTATAT 57.236 33.333 15.01 2.87 40.20 0.86
5397 18099 5.941733 TGCAGTGAACACTTTTGCTATATG 58.058 37.500 15.01 1.09 40.20 1.78
5398 18100 5.473162 TGCAGTGAACACTTTTGCTATATGT 59.527 36.000 15.01 0.00 40.20 2.29
5399 18101 5.796935 GCAGTGAACACTTTTGCTATATGTG 59.203 40.000 4.63 0.00 40.20 3.21
5400 18102 6.568462 GCAGTGAACACTTTTGCTATATGTGT 60.568 38.462 4.63 0.00 42.68 3.72
5406 18108 7.270757 ACACTTTTGCTATATGTGTTGAACA 57.729 32.000 0.00 0.00 44.79 3.18
5545 18248 9.936759 AAAAATTACTGGAAGACAAAACAGAAA 57.063 25.926 0.00 0.00 37.43 2.52
5553 18256 6.042777 GGAAGACAAAACAGAAAGGAAAAGG 58.957 40.000 0.00 0.00 0.00 3.11
5560 18263 7.336679 ACAAAACAGAAAGGAAAAGGAAAATGG 59.663 33.333 0.00 0.00 0.00 3.16
5564 18267 7.726216 ACAGAAAGGAAAAGGAAAATGGTAAG 58.274 34.615 0.00 0.00 0.00 2.34
5647 18350 9.841880 AAAAGTAAAAGAACAGAACAGAGAAAC 57.158 29.630 0.00 0.00 0.00 2.78
5732 18440 5.108385 AGCGTACACATGGAAAAGAAAAG 57.892 39.130 0.00 0.00 0.00 2.27
5736 18444 7.174253 AGCGTACACATGGAAAAGAAAAGATTA 59.826 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 192 3.606153 CGGTTAGCAACTTGAACCTTTCG 60.606 47.826 9.56 0.00 40.46 3.46
740 789 1.134788 AGCGCTAGATGTTGTACCACC 60.135 52.381 8.99 0.00 0.00 4.61
747 796 4.805719 TGATTGTCTTAGCGCTAGATGTTG 59.194 41.667 17.98 5.43 0.00 3.33
748 797 5.011090 TGATTGTCTTAGCGCTAGATGTT 57.989 39.130 17.98 2.50 0.00 2.71
789 838 0.445436 CATCTGAACAGAACGCTGCC 59.555 55.000 8.59 0.00 46.26 4.85
794 843 2.807967 TCAAAGGCATCTGAACAGAACG 59.192 45.455 8.59 4.74 41.36 3.95
800 849 4.741342 CAAGGAATCAAAGGCATCTGAAC 58.259 43.478 0.00 0.00 0.00 3.18
843 892 4.099573 ACCTACAAGATGACGGTGGATTAG 59.900 45.833 0.00 0.00 0.00 1.73
848 897 1.548719 TGACCTACAAGATGACGGTGG 59.451 52.381 0.00 0.00 0.00 4.61
860 909 0.682292 TGCATCACCGTTGACCTACA 59.318 50.000 0.00 0.00 33.38 2.74
862 911 1.609580 GGTTGCATCACCGTTGACCTA 60.610 52.381 0.00 0.00 33.38 3.08
868 917 0.965363 GGATGGGTTGCATCACCGTT 60.965 55.000 1.48 0.00 37.76 4.44
960 1030 1.002624 TGGTTGATCGGTTGAGGGC 60.003 57.895 0.00 0.00 0.00 5.19
1380 1465 8.207521 TCGCATGATGTTGAGATGTAAAATTA 57.792 30.769 0.00 0.00 0.00 1.40
1381 1466 7.087409 TCGCATGATGTTGAGATGTAAAATT 57.913 32.000 0.00 0.00 0.00 1.82
1411 1496 3.058293 TGCCAAAATTGCAAGACTACTCG 60.058 43.478 4.94 0.00 35.40 4.18
1417 1502 3.981211 TCTTCTGCCAAAATTGCAAGAC 58.019 40.909 4.94 0.00 38.46 3.01
1484 1580 5.582665 ACTTTCATCCGAACTATTTGAGCTC 59.417 40.000 6.82 6.82 0.00 4.09
1591 2414 5.937187 TCACGAATGTTATTTCATGGTGTG 58.063 37.500 0.00 0.00 35.97 3.82
1633 2456 6.882610 AATAGCATTTTTGGAGCATCGATA 57.117 33.333 0.00 0.00 34.37 2.92
1652 2475 6.128742 GCACCTCAAAATGCTCACAAAAATAG 60.129 38.462 0.00 0.00 38.84 1.73
1657 2480 3.096489 GCACCTCAAAATGCTCACAAA 57.904 42.857 0.00 0.00 38.84 2.83
1687 2510 0.881118 CATTCGTGAAAGTGGTGGGG 59.119 55.000 0.00 0.00 0.00 4.96
1688 2511 1.535462 GACATTCGTGAAAGTGGTGGG 59.465 52.381 0.00 0.00 0.00 4.61
1693 2516 4.747540 TGGAATGACATTCGTGAAAGTG 57.252 40.909 19.43 0.00 40.17 3.16
1799 2623 8.886719 TCAAATGAGCTATGATGAACAGTAAAG 58.113 33.333 0.00 0.00 0.00 1.85
1849 2673 0.956902 TAGTAGCAGCGTGACCGTCA 60.957 55.000 0.00 0.00 36.15 4.35
1909 2881 7.962918 GCAAAGATTGAACGACACAAATATACT 59.037 33.333 0.00 0.00 0.00 2.12
1937 3081 3.329929 AAACCTACTACTTTGAGGCCG 57.670 47.619 0.00 0.00 33.28 6.13
2119 3341 2.535012 TTGTACCACATCTTGCGACA 57.465 45.000 0.00 0.00 0.00 4.35
2121 3343 3.326836 TCATTGTACCACATCTTGCGA 57.673 42.857 0.00 0.00 0.00 5.10
2169 3442 7.990314 TGTGGTTATGCACATGTATACATTACT 59.010 33.333 15.85 0.00 33.61 2.24
2247 3809 7.866898 TGTATATGCAATTGTATTCATGTTGGC 59.133 33.333 14.47 0.00 0.00 4.52
2371 4188 7.065085 TGCTCTCAACTAAATTAGCAAGATGTC 59.935 37.037 0.00 0.00 37.05 3.06
2433 4475 4.003648 GTGGTGGTGGCAAGCTATATATC 58.996 47.826 0.00 0.00 0.00 1.63
2434 4476 3.394274 TGTGGTGGTGGCAAGCTATATAT 59.606 43.478 0.00 0.00 0.00 0.86
2510 4721 5.906772 AGGAAATTGGGTTCGTATAGGAT 57.093 39.130 0.00 0.00 0.00 3.24
2556 4768 2.685897 TGAAAAATAATTCGGGGCGGAG 59.314 45.455 0.00 0.00 31.80 4.63
2643 4855 4.163458 ACTCCCTCTGTCCGCAATTATTTA 59.837 41.667 0.00 0.00 0.00 1.40
2652 4864 1.067821 CAGAATACTCCCTCTGTCCGC 59.932 57.143 0.00 0.00 35.38 5.54
2659 4871 6.702282 GCATAACTGTTACAGAATACTCCCTC 59.298 42.308 20.07 0.00 35.18 4.30
2671 4883 9.845740 ATCCATATAACTTGCATAACTGTTACA 57.154 29.630 1.73 0.00 0.00 2.41
2870 5090 4.759516 TTAGCCTTGCCGTTTTCTTTAG 57.240 40.909 0.00 0.00 0.00 1.85
2873 6242 4.600692 AATTTAGCCTTGCCGTTTTCTT 57.399 36.364 0.00 0.00 0.00 2.52
2874 6243 4.202212 ACAAATTTAGCCTTGCCGTTTTCT 60.202 37.500 0.00 0.00 0.00 2.52
2879 6248 2.625790 TCAACAAATTTAGCCTTGCCGT 59.374 40.909 0.00 0.00 0.00 5.68
2880 6249 3.296322 TCAACAAATTTAGCCTTGCCG 57.704 42.857 0.00 0.00 0.00 5.69
2937 6306 9.601810 AGTCCTGATTTCTGGTACATACATATA 57.398 33.333 0.00 0.00 38.20 0.86
2952 6321 6.166279 TCTATCACACACAAGTCCTGATTTC 58.834 40.000 0.00 0.00 0.00 2.17
3014 6387 4.516698 GCATGGACGAATAAGGTCAATGAT 59.483 41.667 12.27 0.00 44.92 2.45
3077 6735 1.141665 CGATGGCATCTCGTGGTCA 59.858 57.895 23.97 0.00 0.00 4.02
3087 6748 0.179084 CGTGTAACCTCCGATGGCAT 60.179 55.000 0.00 0.00 0.00 4.40
3281 6942 3.235481 TTTGGGCGTCCGGTGAGA 61.235 61.111 0.00 0.00 35.24 3.27
3296 6957 0.601057 GGGTAATTGCCTGTGCGTTT 59.399 50.000 12.66 0.00 41.78 3.60
3356 7017 2.818169 GCCACCATCTATCCCGGCA 61.818 63.158 0.00 0.00 39.38 5.69
3398 7059 1.684869 CCATTTACGATGGCCAACCCT 60.685 52.381 10.96 0.00 33.59 4.34
3410 7071 2.100216 GCAGCCGTGCCATTTACG 59.900 61.111 0.00 0.00 44.72 3.18
3446 7107 3.818210 TGTTGCAATCGAACAGTACCATT 59.182 39.130 0.59 0.00 0.00 3.16
3452 7113 3.120546 CGAAGATGTTGCAATCGAACAGT 60.121 43.478 12.82 0.00 36.77 3.55
3497 7158 1.960417 TCACCTCACAAAACATCGCA 58.040 45.000 0.00 0.00 0.00 5.10
3602 9383 3.165606 GCTGCTAGCCAGAATGTGT 57.834 52.632 13.29 0.00 44.64 3.72
3615 9396 2.045926 GACCATGAACGGGCTGCT 60.046 61.111 0.00 0.00 0.00 4.24
4028 16720 1.418334 ATTGGAGCTCCGAGCAGTAT 58.582 50.000 26.79 7.27 45.56 2.12
4203 16895 2.342279 CAGGTGGCGAAGGTCGAA 59.658 61.111 1.05 0.00 43.74 3.71
4271 16963 1.890510 GGTTGCGTCGACCACCTTT 60.891 57.895 10.58 0.00 37.82 3.11
4286 16978 3.471680 GAGCTTCTTCTCAACACTGGTT 58.528 45.455 0.00 0.00 37.87 3.67
4337 17029 3.896133 GGGTCGTCGGCATAGCGA 61.896 66.667 0.00 0.00 0.00 4.93
4476 17168 2.822637 CCCGTGGCAGGGCTATCAT 61.823 63.158 20.57 0.00 45.72 2.45
4643 17335 3.531538 GAACACCTTGTCACACTCTTCA 58.468 45.455 0.00 0.00 0.00 3.02
4734 17426 2.224426 ACACGAGTTAGTTGATGGGCAA 60.224 45.455 0.00 0.00 0.00 4.52
4769 17466 1.078709 CAGACAAGCACACGTATGGG 58.921 55.000 0.00 0.00 0.00 4.00
4802 17502 2.892373 AACACACGTGAACAACAGTG 57.108 45.000 25.01 9.85 39.27 3.66
4863 17563 6.833342 ATGAAAAACAGCTGATTGTCAAAC 57.167 33.333 27.39 5.26 29.68 2.93
4866 17566 6.817641 ACAAAATGAAAAACAGCTGATTGTCA 59.182 30.769 26.28 26.28 30.29 3.58
4889 17590 1.338973 ACGAGGCAAGTTCGAGTTACA 59.661 47.619 0.61 0.00 40.36 2.41
4894 17595 0.318699 TGACACGAGGCAAGTTCGAG 60.319 55.000 0.61 0.00 40.36 4.04
4904 17605 3.739300 ACGAGTTACAAAATGACACGAGG 59.261 43.478 0.00 0.00 35.05 4.63
4974 17676 3.254657 TCGACTGTGGCCCAAATTAAAAG 59.745 43.478 0.00 0.00 0.00 2.27
4995 17697 0.966179 AATGCGTGGGGGACTTTTTC 59.034 50.000 0.00 0.00 0.00 2.29
5002 17704 2.372074 GGGTCTAATGCGTGGGGGA 61.372 63.158 0.00 0.00 0.00 4.81
5020 17722 0.392193 AGCTGCGAGTCATGGGAAAG 60.392 55.000 0.00 0.00 0.00 2.62
5025 17727 2.076100 TGTTTTAGCTGCGAGTCATGG 58.924 47.619 0.00 0.00 0.00 3.66
5056 17758 6.376581 GCCAAAATAGAATGAGAGGGGATATG 59.623 42.308 0.00 0.00 0.00 1.78
5057 17759 6.276568 AGCCAAAATAGAATGAGAGGGGATAT 59.723 38.462 0.00 0.00 0.00 1.63
5058 17760 5.612688 AGCCAAAATAGAATGAGAGGGGATA 59.387 40.000 0.00 0.00 0.00 2.59
5059 17761 4.418190 AGCCAAAATAGAATGAGAGGGGAT 59.582 41.667 0.00 0.00 0.00 3.85
5060 17762 3.788142 AGCCAAAATAGAATGAGAGGGGA 59.212 43.478 0.00 0.00 0.00 4.81
5061 17763 4.176120 AGCCAAAATAGAATGAGAGGGG 57.824 45.455 0.00 0.00 0.00 4.79
5062 17764 6.335777 CAAAAGCCAAAATAGAATGAGAGGG 58.664 40.000 0.00 0.00 0.00 4.30
5063 17765 5.809051 GCAAAAGCCAAAATAGAATGAGAGG 59.191 40.000 0.00 0.00 0.00 3.69
5064 17766 6.628185 AGCAAAAGCCAAAATAGAATGAGAG 58.372 36.000 0.00 0.00 0.00 3.20
5065 17767 6.594788 AGCAAAAGCCAAAATAGAATGAGA 57.405 33.333 0.00 0.00 0.00 3.27
5066 17768 6.401796 GCAAGCAAAAGCCAAAATAGAATGAG 60.402 38.462 0.00 0.00 0.00 2.90
5067 17769 5.409214 GCAAGCAAAAGCCAAAATAGAATGA 59.591 36.000 0.00 0.00 0.00 2.57
5068 17770 5.410439 AGCAAGCAAAAGCCAAAATAGAATG 59.590 36.000 0.00 0.00 0.00 2.67
5069 17771 5.410439 CAGCAAGCAAAAGCCAAAATAGAAT 59.590 36.000 0.00 0.00 0.00 2.40
5070 17772 4.751098 CAGCAAGCAAAAGCCAAAATAGAA 59.249 37.500 0.00 0.00 0.00 2.10
5071 17773 4.309099 CAGCAAGCAAAAGCCAAAATAGA 58.691 39.130 0.00 0.00 0.00 1.98
5072 17774 3.434299 CCAGCAAGCAAAAGCCAAAATAG 59.566 43.478 0.00 0.00 0.00 1.73
5073 17775 3.070734 TCCAGCAAGCAAAAGCCAAAATA 59.929 39.130 0.00 0.00 0.00 1.40
5074 17776 2.158784 TCCAGCAAGCAAAAGCCAAAAT 60.159 40.909 0.00 0.00 0.00 1.82
5075 17777 1.209019 TCCAGCAAGCAAAAGCCAAAA 59.791 42.857 0.00 0.00 0.00 2.44
5076 17778 0.829333 TCCAGCAAGCAAAAGCCAAA 59.171 45.000 0.00 0.00 0.00 3.28
5077 17779 1.001181 GATCCAGCAAGCAAAAGCCAA 59.999 47.619 0.00 0.00 0.00 4.52
5078 17780 0.604578 GATCCAGCAAGCAAAAGCCA 59.395 50.000 0.00 0.00 0.00 4.75
5079 17781 0.604578 TGATCCAGCAAGCAAAAGCC 59.395 50.000 0.00 0.00 0.00 4.35
5080 17782 1.706443 GTGATCCAGCAAGCAAAAGC 58.294 50.000 0.00 0.00 0.00 3.51
5081 17783 1.267806 ACGTGATCCAGCAAGCAAAAG 59.732 47.619 0.00 0.00 0.00 2.27
5082 17784 1.317613 ACGTGATCCAGCAAGCAAAA 58.682 45.000 0.00 0.00 0.00 2.44
5083 17785 2.177394 TACGTGATCCAGCAAGCAAA 57.823 45.000 0.00 0.00 0.00 3.68
5084 17786 2.177394 TTACGTGATCCAGCAAGCAA 57.823 45.000 0.00 0.00 0.00 3.91
5085 17787 2.009051 CATTACGTGATCCAGCAAGCA 58.991 47.619 0.00 0.00 0.00 3.91
5086 17788 2.009774 ACATTACGTGATCCAGCAAGC 58.990 47.619 0.00 0.00 0.00 4.01
5087 17789 3.261580 TGACATTACGTGATCCAGCAAG 58.738 45.455 0.00 0.00 0.00 4.01
5088 17790 3.326836 TGACATTACGTGATCCAGCAA 57.673 42.857 0.00 0.00 0.00 3.91
5089 17791 3.261580 CTTGACATTACGTGATCCAGCA 58.738 45.455 0.00 0.00 0.00 4.41
5090 17792 3.062639 CACTTGACATTACGTGATCCAGC 59.937 47.826 0.00 0.00 0.00 4.85
5091 17793 4.494484 TCACTTGACATTACGTGATCCAG 58.506 43.478 0.00 0.00 32.00 3.86
5092 17794 4.529109 TCACTTGACATTACGTGATCCA 57.471 40.909 0.00 0.00 32.00 3.41
5093 17795 5.856126 TTTCACTTGACATTACGTGATCC 57.144 39.130 0.00 0.00 36.41 3.36
5094 17796 5.734498 GCATTTCACTTGACATTACGTGATC 59.266 40.000 0.00 0.00 36.41 2.92
5095 17797 5.391950 GGCATTTCACTTGACATTACGTGAT 60.392 40.000 0.00 0.00 36.41 3.06
5096 17798 4.083537 GGCATTTCACTTGACATTACGTGA 60.084 41.667 0.00 0.00 34.85 4.35
5097 17799 4.083324 AGGCATTTCACTTGACATTACGTG 60.083 41.667 0.00 0.00 0.00 4.49
5098 17800 4.072131 AGGCATTTCACTTGACATTACGT 58.928 39.130 0.00 0.00 0.00 3.57
5099 17801 4.685169 AGGCATTTCACTTGACATTACG 57.315 40.909 0.00 0.00 0.00 3.18
5100 17802 6.528072 GCTTAAGGCATTTCACTTGACATTAC 59.472 38.462 4.29 0.00 41.35 1.89
5101 17803 6.434028 AGCTTAAGGCATTTCACTTGACATTA 59.566 34.615 4.29 0.00 44.79 1.90
5102 17804 5.244626 AGCTTAAGGCATTTCACTTGACATT 59.755 36.000 4.29 0.00 44.79 2.71
5103 17805 4.768968 AGCTTAAGGCATTTCACTTGACAT 59.231 37.500 4.29 0.00 44.79 3.06
5104 17806 4.144297 AGCTTAAGGCATTTCACTTGACA 58.856 39.130 4.29 0.00 44.79 3.58
5105 17807 4.773323 AGCTTAAGGCATTTCACTTGAC 57.227 40.909 4.29 0.00 44.79 3.18
5106 17808 5.072741 AGAAGCTTAAGGCATTTCACTTGA 58.927 37.500 0.00 0.00 44.79 3.02
5107 17809 5.382618 AGAAGCTTAAGGCATTTCACTTG 57.617 39.130 0.00 0.00 44.79 3.16
5108 17810 4.460731 GGAGAAGCTTAAGGCATTTCACTT 59.539 41.667 0.00 0.00 44.79 3.16
5109 17811 4.013050 GGAGAAGCTTAAGGCATTTCACT 58.987 43.478 0.00 0.00 44.79 3.41
5110 17812 4.013050 AGGAGAAGCTTAAGGCATTTCAC 58.987 43.478 0.00 0.00 44.79 3.18
5111 17813 4.012374 CAGGAGAAGCTTAAGGCATTTCA 58.988 43.478 0.00 0.00 44.79 2.69
5112 17814 4.265073 TCAGGAGAAGCTTAAGGCATTTC 58.735 43.478 0.00 0.00 44.79 2.17
5113 17815 4.307032 TCAGGAGAAGCTTAAGGCATTT 57.693 40.909 0.00 0.00 44.79 2.32
5114 17816 4.516652 ATCAGGAGAAGCTTAAGGCATT 57.483 40.909 0.00 0.00 44.79 3.56
5115 17817 5.636903 TTATCAGGAGAAGCTTAAGGCAT 57.363 39.130 0.00 0.00 44.79 4.40
5116 17818 5.435686 TTTATCAGGAGAAGCTTAAGGCA 57.564 39.130 0.00 0.00 44.79 4.75
5117 17819 5.883115 ACTTTTATCAGGAGAAGCTTAAGGC 59.117 40.000 0.00 0.00 42.19 4.35
5118 17820 7.106239 TCACTTTTATCAGGAGAAGCTTAAGG 58.894 38.462 0.00 0.00 0.00 2.69
5119 17821 7.821846 ACTCACTTTTATCAGGAGAAGCTTAAG 59.178 37.037 0.00 0.00 0.00 1.85
5120 17822 7.680730 ACTCACTTTTATCAGGAGAAGCTTAA 58.319 34.615 0.00 0.00 0.00 1.85
5121 17823 7.246171 ACTCACTTTTATCAGGAGAAGCTTA 57.754 36.000 0.00 0.00 0.00 3.09
5122 17824 6.120507 ACTCACTTTTATCAGGAGAAGCTT 57.879 37.500 0.00 0.00 0.00 3.74
5123 17825 5.753721 ACTCACTTTTATCAGGAGAAGCT 57.246 39.130 0.00 0.00 0.00 3.74
5124 17826 5.934625 TGAACTCACTTTTATCAGGAGAAGC 59.065 40.000 0.00 0.00 0.00 3.86
5125 17827 6.931281 TGTGAACTCACTTTTATCAGGAGAAG 59.069 38.462 10.99 0.00 46.55 2.85
5126 17828 6.826668 TGTGAACTCACTTTTATCAGGAGAA 58.173 36.000 10.99 0.00 46.55 2.87
5127 17829 6.419484 TGTGAACTCACTTTTATCAGGAGA 57.581 37.500 10.99 0.00 46.55 3.71
5128 17830 8.954950 ATATGTGAACTCACTTTTATCAGGAG 57.045 34.615 10.99 0.00 46.55 3.69
5129 17831 9.383519 GAATATGTGAACTCACTTTTATCAGGA 57.616 33.333 10.99 0.00 46.55 3.86
5130 17832 9.388506 AGAATATGTGAACTCACTTTTATCAGG 57.611 33.333 10.99 0.00 46.55 3.86
5132 17834 9.942850 TGAGAATATGTGAACTCACTTTTATCA 57.057 29.630 10.99 10.66 46.55 2.15
5137 17839 9.956720 CTTTTTGAGAATATGTGAACTCACTTT 57.043 29.630 10.99 2.94 46.55 2.66
5138 17840 9.342308 TCTTTTTGAGAATATGTGAACTCACTT 57.658 29.630 10.99 7.34 46.55 3.16
5139 17841 8.908786 TCTTTTTGAGAATATGTGAACTCACT 57.091 30.769 10.99 0.32 46.55 3.41
5140 17842 8.778358 ACTCTTTTTGAGAATATGTGAACTCAC 58.222 33.333 2.78 2.78 45.39 3.51
5141 17843 8.777413 CACTCTTTTTGAGAATATGTGAACTCA 58.223 33.333 0.00 0.00 45.39 3.41
5142 17844 8.993121 TCACTCTTTTTGAGAATATGTGAACTC 58.007 33.333 0.00 0.00 45.39 3.01
5143 17845 8.908786 TCACTCTTTTTGAGAATATGTGAACT 57.091 30.769 0.00 0.00 45.39 3.01
5144 17846 8.778358 ACTCACTCTTTTTGAGAATATGTGAAC 58.222 33.333 6.37 0.00 45.39 3.18
5145 17847 8.908786 ACTCACTCTTTTTGAGAATATGTGAA 57.091 30.769 6.37 0.00 45.39 3.18
5146 17848 8.908786 AACTCACTCTTTTTGAGAATATGTGA 57.091 30.769 6.37 0.00 45.39 3.58
5147 17849 8.777413 TGAACTCACTCTTTTTGAGAATATGTG 58.223 33.333 6.37 0.00 45.39 3.21
5148 17850 8.778358 GTGAACTCACTCTTTTTGAGAATATGT 58.222 33.333 6.37 0.00 45.39 2.29
5149 17851 8.777413 TGTGAACTCACTCTTTTTGAGAATATG 58.223 33.333 10.99 0.00 46.55 1.78
5150 17852 8.908786 TGTGAACTCACTCTTTTTGAGAATAT 57.091 30.769 10.99 0.00 46.55 1.28
5151 17853 8.908786 ATGTGAACTCACTCTTTTTGAGAATA 57.091 30.769 10.99 0.00 46.55 1.75
5152 17854 7.814264 ATGTGAACTCACTCTTTTTGAGAAT 57.186 32.000 10.99 0.00 46.55 2.40
5153 17855 8.908786 ATATGTGAACTCACTCTTTTTGAGAA 57.091 30.769 10.99 0.00 46.55 2.87
5154 17856 8.908786 AATATGTGAACTCACTCTTTTTGAGA 57.091 30.769 10.99 0.00 46.55 3.27
5155 17857 8.997323 AGAATATGTGAACTCACTCTTTTTGAG 58.003 33.333 10.99 0.00 46.55 3.02
5156 17858 8.908786 AGAATATGTGAACTCACTCTTTTTGA 57.091 30.769 10.99 0.00 46.55 2.69
5157 17859 8.777413 TGAGAATATGTGAACTCACTCTTTTTG 58.223 33.333 10.99 0.00 46.55 2.44
5158 17860 8.908786 TGAGAATATGTGAACTCACTCTTTTT 57.091 30.769 10.99 0.00 46.55 1.94
5159 17861 8.908786 TTGAGAATATGTGAACTCACTCTTTT 57.091 30.769 10.99 1.24 46.55 2.27
5160 17862 8.908786 TTTGAGAATATGTGAACTCACTCTTT 57.091 30.769 10.99 2.32 46.55 2.52
5161 17863 8.908786 TTTTGAGAATATGTGAACTCACTCTT 57.091 30.769 10.99 2.47 46.55 2.85
5162 17864 8.908786 TTTTTGAGAATATGTGAACTCACTCT 57.091 30.769 10.99 5.41 46.55 3.24
5250 17952 7.881643 TTTTCCATTCATATTTGTGGTTTCG 57.118 32.000 0.00 0.00 33.47 3.46
5271 17973 6.262496 TGGGTTTTGTTTTTCCGTTTCTTTTT 59.738 30.769 0.00 0.00 0.00 1.94
5376 18078 6.902341 ACACATATAGCAAAAGTGTTCACTG 58.098 36.000 6.22 0.00 40.20 3.66
5387 18089 9.979578 AGAAAAATGTTCAACACATATAGCAAA 57.020 25.926 0.00 0.00 46.23 3.68
5388 18090 9.409312 CAGAAAAATGTTCAACACATATAGCAA 57.591 29.630 0.00 0.00 46.23 3.91
5389 18091 8.791675 TCAGAAAAATGTTCAACACATATAGCA 58.208 29.630 0.00 0.00 46.23 3.49
5390 18092 9.624697 TTCAGAAAAATGTTCAACACATATAGC 57.375 29.630 0.00 0.00 46.23 2.97
5396 18098 9.814899 AACATATTCAGAAAAATGTTCAACACA 57.185 25.926 16.28 0.00 37.91 3.72
5540 18243 7.951591 TCTTACCATTTTCCTTTTCCTTTCTG 58.048 34.615 0.00 0.00 0.00 3.02
5541 18244 8.547481 TTCTTACCATTTTCCTTTTCCTTTCT 57.453 30.769 0.00 0.00 0.00 2.52
5542 18245 9.607988 TTTTCTTACCATTTTCCTTTTCCTTTC 57.392 29.630 0.00 0.00 0.00 2.62
5592 18295 5.862678 TTTCCTTTTCATTTCGGTTTCCT 57.137 34.783 0.00 0.00 0.00 3.36
5625 18328 7.118088 GTCGTTTCTCTGTTCTGTTCTTTTAC 58.882 38.462 0.00 0.00 0.00 2.01
5643 18346 3.303760 GCTATCAGGTCTTTCGTCGTTTC 59.696 47.826 0.00 0.00 0.00 2.78
5647 18350 2.561733 TGCTATCAGGTCTTTCGTCG 57.438 50.000 0.00 0.00 0.00 5.12
5687 18395 3.371965 ACCTCGGGTGTAGTTGATATGT 58.628 45.455 0.00 0.00 32.98 2.29


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

AutoCloner maintained by Alex Coulton.