Multiple sequence alignment - TraesCS3A01G079900

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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 TraesCS3A01G079900 chr3A 100.000 6676 0 0 1 6676 51774622 51767947 0.000000e+00 12329.0
1 TraesCS3A01G079900 chr3A 88.865 1886 176 22 3469 5330 44354340 44352465 0.000000e+00 2289.0
2 TraesCS3A01G079900 chr3A 93.100 1029 60 5 973 1991 44356523 44355496 0.000000e+00 1496.0
3 TraesCS3A01G079900 chr3A 88.125 800 80 7 2634 3422 44355134 44354339 0.000000e+00 937.0
4 TraesCS3A01G079900 chr3A 74.246 1592 337 55 3779 5325 42798185 42796622 9.580000e-168 601.0
5 TraesCS3A01G079900 chr3A 73.831 1647 349 57 3722 5324 42368008 42366400 4.490000e-161 579.0
6 TraesCS3A01G079900 chr3A 91.720 314 21 2 2226 2538 44355475 44355166 1.330000e-116 431.0
7 TraesCS3A01G079900 chr3A 95.339 236 9 2 674 907 375018281 375018046 2.270000e-99 374.0
8 TraesCS3A01G079900 chr3A 79.361 407 73 10 1571 1973 43292748 43292349 6.590000e-70 276.0
9 TraesCS3A01G079900 chr3A 83.650 263 33 7 5382 5636 44323032 44322772 8.650000e-59 239.0
10 TraesCS3A01G079900 chr3A 84.651 215 29 2 3471 3682 42034296 42034083 1.890000e-50 211.0
11 TraesCS3A01G079900 chr3A 82.627 236 41 0 2255 2490 43292292 43292057 6.780000e-50 209.0
12 TraesCS3A01G079900 chr3A 81.466 232 43 0 2257 2488 42379230 42379461 2.460000e-44 191.0
13 TraesCS3A01G079900 chr3A 83.007 153 18 6 3471 3618 42221596 42221447 1.510000e-26 132.0
14 TraesCS3A01G079900 chr3A 88.462 104 8 3 5618 5718 44322406 44322304 9.090000e-24 122.0
15 TraesCS3A01G079900 chr3A 85.246 122 10 6 3502 3618 42248421 42248303 1.180000e-22 119.0
16 TraesCS3A01G079900 chr3A 88.372 86 8 1 5635 5718 44313426 44313341 1.180000e-17 102.0
17 TraesCS3A01G079900 chr3A 97.368 38 0 1 3435 3472 51771008 51770972 5.590000e-06 63.9
18 TraesCS3A01G079900 chr3A 97.368 38 0 1 3615 3651 51771188 51771151 5.590000e-06 63.9
19 TraesCS3A01G079900 chr3A 96.774 31 1 0 2561 2591 44355165 44355135 1.200000e-02 52.8
20 TraesCS3A01G079900 chr3D 97.664 5778 98 14 906 6676 31432233 31437980 0.000000e+00 9888.0
21 TraesCS3A01G079900 chr3D 89.019 1876 185 12 3469 5330 30985602 30983734 0.000000e+00 2303.0
22 TraesCS3A01G079900 chr3D 92.405 1027 61 7 981 1991 30988174 30987149 0.000000e+00 1448.0
23 TraesCS3A01G079900 chr3D 97.826 690 9 4 1 686 31431434 31432121 0.000000e+00 1186.0
24 TraesCS3A01G079900 chr3D 88.091 613 63 5 2817 3422 30986210 30985601 0.000000e+00 719.0
25 TraesCS3A01G079900 chr3D 75.221 1473 276 71 3878 5316 30428000 30429417 3.420000e-172 616.0
26 TraesCS3A01G079900 chr3D 74.395 1488 314 49 3870 5324 30412335 30410882 5.810000e-160 575.0
27 TraesCS3A01G079900 chr3D 91.954 348 25 3 6330 6676 529009116 529009461 1.010000e-132 484.0
28 TraesCS3A01G079900 chr3D 78.250 800 137 26 1189 1971 30679170 30678391 4.680000e-131 479.0
29 TraesCS3A01G079900 chr3D 77.485 835 147 28 1157 1973 30418464 30417653 4.720000e-126 462.0
30 TraesCS3A01G079900 chr3D 90.536 317 27 3 2204 2517 30987022 30986706 3.720000e-112 416.0
31 TraesCS3A01G079900 chr3D 92.917 240 13 4 671 907 381188800 381189038 4.960000e-91 346.0
32 TraesCS3A01G079900 chr3D 89.961 259 26 0 2552 2810 30986537 30986279 1.070000e-87 335.0
33 TraesCS3A01G079900 chr3D 79.707 409 68 13 1571 1973 30414550 30414151 1.420000e-71 281.0
34 TraesCS3A01G079900 chr3D 76.905 420 79 11 2253 2665 30678310 30677902 8.710000e-54 222.0
35 TraesCS3A01G079900 chr3D 80.075 266 53 0 2257 2522 30425092 30425357 1.470000e-46 198.0
36 TraesCS3A01G079900 chr3D 79.545 220 35 5 3471 3682 30370143 30369926 1.500000e-31 148.0
37 TraesCS3A01G079900 chr3D 100.000 38 0 0 3435 3472 31434946 31434983 3.340000e-08 71.3
38 TraesCS3A01G079900 chr3D 97.368 38 0 1 3615 3651 31434767 31434804 5.590000e-06 63.9
39 TraesCS3A01G079900 chr3B 89.670 1878 172 14 3469 5330 53576298 53574427 0.000000e+00 2374.0
40 TraesCS3A01G079900 chr3B 92.593 1026 67 5 973 1991 53580113 53579090 0.000000e+00 1465.0
41 TraesCS3A01G079900 chr3B 88.926 605 57 6 2825 3422 53576898 53576297 0.000000e+00 737.0
42 TraesCS3A01G079900 chr3B 86.765 612 54 11 2226 2836 53579069 53578484 0.000000e+00 656.0
43 TraesCS3A01G079900 chr3B 73.622 1596 304 84 3779 5324 53219104 53217576 2.150000e-139 507.0
44 TraesCS3A01G079900 chr3B 76.429 420 81 11 2253 2665 53358072 53357664 1.890000e-50 211.0
45 TraesCS3A01G079900 chr3B 90.741 54 3 2 2176 2227 4625049 4624996 3.340000e-08 71.3
46 TraesCS3A01G079900 chr1D 92.529 348 25 1 6329 6676 376968276 376967930 1.290000e-136 497.0
47 TraesCS3A01G079900 chr1D 91.643 347 28 1 6330 6676 344201053 344201398 4.680000e-131 479.0
48 TraesCS3A01G079900 chr1D 94.468 235 11 2 675 907 194467274 194467508 1.770000e-95 361.0
49 TraesCS3A01G079900 chr1D 92.453 53 1 2 2179 2230 100460908 100460858 9.290000e-09 73.1
50 TraesCS3A01G079900 chr1D 95.122 41 2 0 906 946 193964364 193964404 1.550000e-06 65.8
51 TraesCS3A01G079900 chr1D 97.368 38 1 0 909 946 225419432 225419395 1.550000e-06 65.8
52 TraesCS3A01G079900 chr7B 91.931 347 27 1 6330 6676 198746570 198746225 1.010000e-132 484.0
53 TraesCS3A01G079900 chr7B 90.000 60 5 1 2179 2237 439995711 439995652 7.180000e-10 76.8
54 TraesCS3A01G079900 chr5A 91.908 346 27 1 6330 6675 339286980 339287324 3.620000e-132 483.0
55 TraesCS3A01G079900 chr7D 91.643 347 28 1 6330 6676 242345828 242346173 4.680000e-131 479.0
56 TraesCS3A01G079900 chr7D 91.643 347 27 2 6330 6676 595861057 595860713 4.680000e-131 479.0
57 TraesCS3A01G079900 chr2D 91.643 347 28 1 6330 6676 592417322 592416977 4.680000e-131 479.0
58 TraesCS3A01G079900 chr2D 93.220 236 14 2 674 907 463079839 463079604 4.960000e-91 346.0
59 TraesCS3A01G079900 chr2D 90.566 53 5 0 2192 2244 46469894 46469842 3.340000e-08 71.3
60 TraesCS3A01G079900 chr6D 94.093 237 12 2 673 907 115323557 115323793 6.370000e-95 359.0
61 TraesCS3A01G079900 chr6D 97.368 38 1 0 909 946 450693067 450693030 1.550000e-06 65.8
62 TraesCS3A01G079900 chr6B 93.671 237 12 3 674 907 20231112 20230876 1.070000e-92 351.0
63 TraesCS3A01G079900 chr2A 93.305 239 11 3 671 907 605619463 605619698 1.380000e-91 348.0
64 TraesCS3A01G079900 chr2A 88.136 59 4 3 2189 2246 48407966 48408022 4.320000e-07 67.6
65 TraesCS3A01G079900 chr5D 93.562 233 13 2 671 901 238175829 238176061 4.960000e-91 346.0
66 TraesCS3A01G079900 chr4D 93.220 236 14 2 674 907 313597767 313597532 4.960000e-91 346.0
67 TraesCS3A01G079900 chr4D 95.833 48 1 1 2189 2236 78369311 78369265 7.180000e-10 76.8
68 TraesCS3A01G079900 chr4D 95.122 41 2 0 906 946 505556544 505556584 1.550000e-06 65.8
69 TraesCS3A01G079900 chrUn 80.052 381 69 6 1568 1946 332582489 332582864 6.590000e-70 276.0
70 TraesCS3A01G079900 chrUn 82.627 236 41 0 2255 2490 332582948 332583183 6.780000e-50 209.0
71 TraesCS3A01G079900 chrUn 95.122 41 2 0 906 946 333066059 333066099 1.550000e-06 65.8
72 TraesCS3A01G079900 chrUn 95.122 41 2 0 906 946 477795995 477796035 1.550000e-06 65.8
73 TraesCS3A01G079900 chr1A 97.778 45 1 0 2189 2233 423909820 423909776 2.000000e-10 78.7
74 TraesCS3A01G079900 chr1A 97.368 38 1 0 909 946 508148830 508148793 1.550000e-06 65.8
75 TraesCS3A01G079900 chr5B 90.909 55 3 2 2175 2227 338716757 338716811 9.290000e-09 73.1
76 TraesCS3A01G079900 chr6A 100.000 35 0 0 912 946 176352043 176352009 1.550000e-06 65.8


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 TraesCS3A01G079900 chr3A 51767947 51774622 6675 True 4152.266667 12329 98.245333 1 6676 3 chr3A.!!$R11 6675
1 TraesCS3A01G079900 chr3A 44352465 44356523 4058 True 1041.160000 2289 91.716800 973 5330 5 chr3A.!!$R10 4357
2 TraesCS3A01G079900 chr3A 42796622 42798185 1563 True 601.000000 601 74.246000 3779 5325 1 chr3A.!!$R5 1546
3 TraesCS3A01G079900 chr3A 42366400 42368008 1608 True 579.000000 579 73.831000 3722 5324 1 chr3A.!!$R4 1602
4 TraesCS3A01G079900 chr3A 43292057 43292748 691 True 242.500000 276 80.994000 1571 2490 2 chr3A.!!$R8 919
5 TraesCS3A01G079900 chr3D 31431434 31437980 6546 False 2802.300000 9888 98.214500 1 6676 4 chr3D.!!$F4 6675
6 TraesCS3A01G079900 chr3D 30983734 30988174 4440 True 1044.200000 2303 90.002400 981 5330 5 chr3D.!!$R4 4349
7 TraesCS3A01G079900 chr3D 30410882 30418464 7582 True 439.333333 575 77.195667 1157 5324 3 chr3D.!!$R2 4167
8 TraesCS3A01G079900 chr3D 30425092 30429417 4325 False 407.000000 616 77.648000 2257 5316 2 chr3D.!!$F3 3059
9 TraesCS3A01G079900 chr3D 30677902 30679170 1268 True 350.500000 479 77.577500 1189 2665 2 chr3D.!!$R3 1476
10 TraesCS3A01G079900 chr3B 53574427 53580113 5686 True 1308.000000 2374 89.488500 973 5330 4 chr3B.!!$R4 4357
11 TraesCS3A01G079900 chr3B 53217576 53219104 1528 True 507.000000 507 73.622000 3779 5324 1 chr3B.!!$R2 1545
12 TraesCS3A01G079900 chrUn 332582489 332583183 694 False 242.500000 276 81.339500 1568 2490 2 chrUn.!!$F3 922

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
241 243 0.250901 CCGCTTATGCCCCAGCTAAT 60.251 55.0 0.0 0.0 40.80 1.73 F
813 818 0.744414 GATAGCCAGCTTCCACGCAA 60.744 55.0 0.0 0.0 0.00 4.85 F
886 891 0.898320 ACGGACTCCTCCATGTCAAG 59.102 55.0 0.0 0.0 36.12 3.02 F
914 919 0.927767 ACCCCGATCTCTACAGTCCT 59.072 55.0 0.0 0.0 0.00 3.85 F
2312 5876 0.602638 TTGTGTGCTTACCTGAGCGG 60.603 55.0 0.0 0.0 45.64 5.52 F
2682 6669 2.680339 GTGGTCTCTTGCTCTTTATGCC 59.320 50.0 0.0 0.0 0.00 4.40 F
3176 8956 2.936919 TGCATCCATATCACCTGTCC 57.063 50.0 0.0 0.0 0.00 4.02 F
4864 11792 1.843992 TGTCGCTGTCATCATCATCG 58.156 50.0 0.0 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 5382 2.698803 TCCCATTGTCAGTCAACATCG 58.301 47.619 0.00 0.00 38.97 3.84 R
2303 5867 1.279271 AGAATAAAGTGCCGCTCAGGT 59.721 47.619 0.00 0.00 43.70 4.00 R
2312 5876 6.149474 TCCAGTCTAGCAAAAGAATAAAGTGC 59.851 38.462 0.00 0.00 35.41 4.40 R
2682 6669 8.982685 AGAGTGTATGATACAAATTTATCTGCG 58.017 33.333 6.89 0.00 40.93 5.18 R
3176 8956 1.487976 ACTGTATGATGGGCCTGACAG 59.512 52.381 4.53 12.83 40.09 3.51 R
4050 10955 6.712998 GCAGACTCTCTAGTAATGTATCCTCA 59.287 42.308 0.00 0.00 35.56 3.86 R
4928 11856 2.490903 ACACGCCCTATAGCTAATACCG 59.509 50.000 0.00 0.10 0.00 4.02 R
6096 13026 1.048601 ACGGAGAAAACCTGCTCTGA 58.951 50.000 0.00 0.00 39.36 3.27 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
241 243 0.250901 CCGCTTATGCCCCAGCTAAT 60.251 55.000 0.00 0.00 40.80 1.73
245 247 2.508526 CTTATGCCCCAGCTAATCCAC 58.491 52.381 0.00 0.00 40.80 4.02
272 274 8.294577 CCAAGTTTTACTGGGTTGTTAGTTATC 58.705 37.037 0.00 0.00 34.47 1.75
461 466 2.493030 CCGCCGACCACGTCTATT 59.507 61.111 0.00 0.00 37.88 1.73
528 533 4.500116 GGCGCCTCCTGTCTCGAC 62.500 72.222 22.15 0.00 0.00 4.20
563 568 3.681835 GTCGTCCGGCTCACCACT 61.682 66.667 0.00 0.00 34.57 4.00
659 664 9.305555 TCTACCAACTTCTATAGTGTTTGTACT 57.694 33.333 14.68 0.00 37.12 2.73
661 666 6.649557 ACCAACTTCTATAGTGTTTGTACTGC 59.350 38.462 12.56 0.00 37.12 4.40
672 677 6.467677 AGTGTTTGTACTGCTAATGATGACT 58.532 36.000 0.00 0.00 0.00 3.41
678 683 6.930731 TGTACTGCTAATGATGACTACAACA 58.069 36.000 0.00 0.00 33.64 3.33
679 684 7.382898 TGTACTGCTAATGATGACTACAACAA 58.617 34.615 0.00 0.00 32.91 2.83
680 685 6.727824 ACTGCTAATGATGACTACAACAAC 57.272 37.500 0.00 0.00 32.91 3.32
681 686 6.230472 ACTGCTAATGATGACTACAACAACA 58.770 36.000 0.00 0.00 32.91 3.33
682 687 6.710295 ACTGCTAATGATGACTACAACAACAA 59.290 34.615 0.00 0.00 32.91 2.83
683 688 6.898041 TGCTAATGATGACTACAACAACAAC 58.102 36.000 0.00 0.00 32.91 3.32
684 689 6.484977 TGCTAATGATGACTACAACAACAACA 59.515 34.615 0.00 0.00 32.91 3.33
685 690 7.012799 TGCTAATGATGACTACAACAACAACAA 59.987 33.333 0.00 0.00 32.91 2.83
686 691 7.323656 GCTAATGATGACTACAACAACAACAAC 59.676 37.037 0.00 0.00 32.91 3.32
687 692 6.691754 ATGATGACTACAACAACAACAACA 57.308 33.333 0.00 0.00 32.91 3.33
688 693 6.502136 TGATGACTACAACAACAACAACAA 57.498 33.333 0.00 0.00 0.00 2.83
689 694 6.318628 TGATGACTACAACAACAACAACAAC 58.681 36.000 0.00 0.00 0.00 3.32
690 695 5.690997 TGACTACAACAACAACAACAACA 57.309 34.783 0.00 0.00 0.00 3.33
691 696 6.073327 TGACTACAACAACAACAACAACAA 57.927 33.333 0.00 0.00 0.00 2.83
692 697 5.915758 TGACTACAACAACAACAACAACAAC 59.084 36.000 0.00 0.00 0.00 3.32
693 698 5.833082 ACTACAACAACAACAACAACAACA 58.167 33.333 0.00 0.00 0.00 3.33
694 699 6.273825 ACTACAACAACAACAACAACAACAA 58.726 32.000 0.00 0.00 0.00 2.83
695 700 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
696 701 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
697 702 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
698 703 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
699 704 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
700 705 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
701 706 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
702 707 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
703 708 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
704 709 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
705 710 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
706 711 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
707 712 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
708 713 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
709 714 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
710 715 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
711 716 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
712 717 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
713 718 6.128282 ACAACAACAACAACAACAACAACAAA 60.128 30.769 0.00 0.00 0.00 2.83
714 719 6.042144 ACAACAACAACAACAACAACAAAG 57.958 33.333 0.00 0.00 0.00 2.77
715 720 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
716 721 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
717 722 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
718 723 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
719 724 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
720 725 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
721 726 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
722 727 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
723 728 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
812 817 1.153369 GATAGCCAGCTTCCACGCA 60.153 57.895 0.00 0.00 0.00 5.24
813 818 0.744414 GATAGCCAGCTTCCACGCAA 60.744 55.000 0.00 0.00 0.00 4.85
842 847 3.643320 CCATGGCTAGTTCTCTGGTGATA 59.357 47.826 0.00 0.00 0.00 2.15
854 859 3.810310 CTGGTGATACTCCAGTCCTTC 57.190 52.381 10.50 0.00 45.09 3.46
855 860 3.099905 CTGGTGATACTCCAGTCCTTCA 58.900 50.000 10.50 0.00 45.09 3.02
856 861 3.099905 TGGTGATACTCCAGTCCTTCAG 58.900 50.000 0.00 0.00 0.00 3.02
857 862 3.245622 TGGTGATACTCCAGTCCTTCAGA 60.246 47.826 0.00 0.00 0.00 3.27
858 863 3.964031 GGTGATACTCCAGTCCTTCAGAT 59.036 47.826 0.00 0.00 0.00 2.90
859 864 4.038642 GGTGATACTCCAGTCCTTCAGATC 59.961 50.000 0.00 0.00 0.00 2.75
860 865 4.038642 GTGATACTCCAGTCCTTCAGATCC 59.961 50.000 0.00 0.00 0.00 3.36
861 866 1.872773 ACTCCAGTCCTTCAGATCCC 58.127 55.000 0.00 0.00 0.00 3.85
862 867 1.364328 ACTCCAGTCCTTCAGATCCCT 59.636 52.381 0.00 0.00 0.00 4.20
863 868 2.038659 CTCCAGTCCTTCAGATCCCTC 58.961 57.143 0.00 0.00 0.00 4.30
864 869 1.648568 TCCAGTCCTTCAGATCCCTCT 59.351 52.381 0.00 0.00 0.00 3.69
865 870 2.045047 TCCAGTCCTTCAGATCCCTCTT 59.955 50.000 0.00 0.00 0.00 2.85
866 871 2.843113 CCAGTCCTTCAGATCCCTCTTT 59.157 50.000 0.00 0.00 0.00 2.52
867 872 4.033709 CCAGTCCTTCAGATCCCTCTTTA 58.966 47.826 0.00 0.00 0.00 1.85
868 873 4.141824 CCAGTCCTTCAGATCCCTCTTTAC 60.142 50.000 0.00 0.00 0.00 2.01
869 874 3.702045 AGTCCTTCAGATCCCTCTTTACG 59.298 47.826 0.00 0.00 0.00 3.18
870 875 3.031736 TCCTTCAGATCCCTCTTTACGG 58.968 50.000 0.00 0.00 0.00 4.02
871 876 3.031736 CCTTCAGATCCCTCTTTACGGA 58.968 50.000 0.00 0.00 0.00 4.69
872 877 3.181474 CCTTCAGATCCCTCTTTACGGAC 60.181 52.174 0.00 0.00 0.00 4.79
873 878 3.383698 TCAGATCCCTCTTTACGGACT 57.616 47.619 0.00 0.00 0.00 3.85
874 879 3.288964 TCAGATCCCTCTTTACGGACTC 58.711 50.000 0.00 0.00 0.00 3.36
875 880 2.362717 CAGATCCCTCTTTACGGACTCC 59.637 54.545 0.00 0.00 0.00 3.85
876 881 2.245287 AGATCCCTCTTTACGGACTCCT 59.755 50.000 0.00 0.00 0.00 3.69
877 882 2.140839 TCCCTCTTTACGGACTCCTC 57.859 55.000 0.00 0.00 0.00 3.71
878 883 1.112950 CCCTCTTTACGGACTCCTCC 58.887 60.000 0.00 0.00 0.00 4.30
879 884 1.618888 CCCTCTTTACGGACTCCTCCA 60.619 57.143 0.00 0.00 36.12 3.86
880 885 2.389715 CCTCTTTACGGACTCCTCCAT 58.610 52.381 0.00 0.00 36.12 3.41
881 886 2.101582 CCTCTTTACGGACTCCTCCATG 59.898 54.545 0.00 0.00 36.12 3.66
882 887 2.761208 CTCTTTACGGACTCCTCCATGT 59.239 50.000 0.00 0.00 36.12 3.21
883 888 2.758979 TCTTTACGGACTCCTCCATGTC 59.241 50.000 0.00 0.00 36.12 3.06
884 889 2.225382 TTACGGACTCCTCCATGTCA 57.775 50.000 0.00 0.00 36.12 3.58
885 890 2.225382 TACGGACTCCTCCATGTCAA 57.775 50.000 0.00 0.00 36.12 3.18
886 891 0.898320 ACGGACTCCTCCATGTCAAG 59.102 55.000 0.00 0.00 36.12 3.02
887 892 0.898320 CGGACTCCTCCATGTCAAGT 59.102 55.000 0.00 0.00 36.12 3.16
888 893 1.276421 CGGACTCCTCCATGTCAAGTT 59.724 52.381 0.00 0.00 36.12 2.66
889 894 2.675317 CGGACTCCTCCATGTCAAGTTC 60.675 54.545 0.00 0.00 36.12 3.01
890 895 2.611518 GACTCCTCCATGTCAAGTTCG 58.388 52.381 0.00 0.00 33.75 3.95
891 896 1.276421 ACTCCTCCATGTCAAGTTCGG 59.724 52.381 0.00 0.00 0.00 4.30
892 897 1.276421 CTCCTCCATGTCAAGTTCGGT 59.724 52.381 0.00 0.00 0.00 4.69
893 898 1.275291 TCCTCCATGTCAAGTTCGGTC 59.725 52.381 0.00 0.00 0.00 4.79
894 899 1.276421 CCTCCATGTCAAGTTCGGTCT 59.724 52.381 0.00 0.00 0.00 3.85
895 900 2.496070 CCTCCATGTCAAGTTCGGTCTA 59.504 50.000 0.00 0.00 0.00 2.59
896 901 3.512680 CTCCATGTCAAGTTCGGTCTAC 58.487 50.000 0.00 0.00 0.00 2.59
897 902 2.232941 TCCATGTCAAGTTCGGTCTACC 59.767 50.000 0.00 0.00 0.00 3.18
898 903 2.618053 CATGTCAAGTTCGGTCTACCC 58.382 52.381 0.00 0.00 0.00 3.69
899 904 0.971386 TGTCAAGTTCGGTCTACCCC 59.029 55.000 0.00 0.00 0.00 4.95
909 914 2.653234 GGTCTACCCCGATCTCTACA 57.347 55.000 0.00 0.00 0.00 2.74
910 915 2.506444 GGTCTACCCCGATCTCTACAG 58.494 57.143 0.00 0.00 0.00 2.74
911 916 2.158638 GGTCTACCCCGATCTCTACAGT 60.159 54.545 0.00 0.00 0.00 3.55
912 917 3.140623 GTCTACCCCGATCTCTACAGTC 58.859 54.545 0.00 0.00 0.00 3.51
913 918 2.106166 TCTACCCCGATCTCTACAGTCC 59.894 54.545 0.00 0.00 0.00 3.85
914 919 0.927767 ACCCCGATCTCTACAGTCCT 59.072 55.000 0.00 0.00 0.00 3.85
915 920 1.288335 ACCCCGATCTCTACAGTCCTT 59.712 52.381 0.00 0.00 0.00 3.36
1009 1015 5.772672 TCTCTAGGTAGAAAGATGCAGATCC 59.227 44.000 0.00 0.00 0.00 3.36
1852 5382 2.416202 GCAAATTAATGGCCACAACTGC 59.584 45.455 8.16 13.94 0.00 4.40
1931 5461 2.680841 TGAAATTACTATGGTGCACCGC 59.319 45.455 30.07 8.85 39.43 5.68
2121 5678 2.022240 TTTGTTCTGTTTGGCCCGCC 62.022 55.000 0.00 0.00 0.00 6.13
2228 5785 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
2232 5790 1.320507 GGACGGAGGGAGTATGTCTC 58.679 60.000 0.00 0.00 42.07 3.36
2303 5867 6.380995 CAGCATCACTAAATTTGTGTGCTTA 58.619 36.000 25.43 13.06 43.23 3.09
2312 5876 0.602638 TTGTGTGCTTACCTGAGCGG 60.603 55.000 0.00 0.00 45.64 5.52
2682 6669 2.680339 GTGGTCTCTTGCTCTTTATGCC 59.320 50.000 0.00 0.00 0.00 4.40
3176 8956 2.936919 TGCATCCATATCACCTGTCC 57.063 50.000 0.00 0.00 0.00 4.02
3614 10394 5.116882 CAAGTCCGATTTAGAAGGTAAGGG 58.883 45.833 0.00 0.00 0.00 3.95
3988 10887 9.589461 TTAATTCAGGTTGGGTCACTTTTAATA 57.411 29.630 0.00 0.00 0.00 0.98
4050 10955 3.314693 TCACCCTTTGACACTAGGACTT 58.685 45.455 4.66 0.00 33.13 3.01
4604 11528 4.817318 TGCACAGGTGTATTCATAGACA 57.183 40.909 0.91 0.00 0.00 3.41
4864 11792 1.843992 TGTCGCTGTCATCATCATCG 58.156 50.000 0.00 0.00 0.00 3.84
5332 12262 9.872684 AAAGGGTATGTTTTCTATCATCATCAT 57.127 29.630 0.00 0.00 0.00 2.45
5333 12263 9.512588 AAGGGTATGTTTTCTATCATCATCATC 57.487 33.333 0.00 0.00 0.00 2.92
5334 12264 8.663167 AGGGTATGTTTTCTATCATCATCATCA 58.337 33.333 0.00 0.00 0.00 3.07
5335 12265 9.458727 GGGTATGTTTTCTATCATCATCATCAT 57.541 33.333 0.00 0.00 0.00 2.45
5340 12270 9.787435 TGTTTTCTATCATCATCATCATCATCA 57.213 29.630 0.00 0.00 0.00 3.07
5346 12276 9.823647 CTATCATCATCATCATCATCATCTTCA 57.176 33.333 0.00 0.00 0.00 3.02
5379 12309 8.229253 TCGCCTCTTGTCTTACATATTAACTA 57.771 34.615 0.00 0.00 0.00 2.24
5435 12365 4.280929 ACTGCTGATTTTACCAAAGTTCCC 59.719 41.667 0.00 0.00 0.00 3.97
5491 12421 6.349944 GCATTCAACAAGACCTTGATTCAGAT 60.350 38.462 15.84 1.10 42.93 2.90
5616 12546 4.023707 AGACTTGCTGGAATTTCTTGAACG 60.024 41.667 0.00 0.00 0.00 3.95
5787 12717 3.912496 ATATGTTGTGCCAGCTAGTCA 57.088 42.857 0.00 0.00 0.00 3.41
5824 12754 4.718961 AGACCTCTTGTTGCTTTATGTGT 58.281 39.130 0.00 0.00 0.00 3.72
5942 12872 8.528917 AAGTTAAAACCAAAAGAATTATCGCC 57.471 30.769 0.00 0.00 0.00 5.54
5967 12897 7.385752 CCTTTGTGCATCATGTGTCTTTTTAAT 59.614 33.333 0.00 0.00 0.00 1.40
6053 12983 3.282885 AGCTAACCAATAAGCCTGCTTC 58.717 45.455 7.81 0.00 39.64 3.86
6085 13015 1.881591 AGTAGTAGGATCGCGACCTC 58.118 55.000 26.39 15.83 38.76 3.85
6097 13027 3.780357 GACCTCCTAGGGGCGATC 58.220 66.667 9.46 0.00 40.58 3.69
6098 13028 1.152525 GACCTCCTAGGGGCGATCA 60.153 63.158 9.46 0.00 40.58 2.92
6101 13031 0.897863 CCTCCTAGGGGCGATCAGAG 60.898 65.000 9.46 0.00 0.00 3.35
6113 13043 2.275318 CGATCAGAGCAGGTTTTCTCC 58.725 52.381 0.00 0.00 0.00 3.71
6129 13059 5.925506 TTTCTCCGTTTTCTTTCCCTTTT 57.074 34.783 0.00 0.00 0.00 2.27
6130 13060 5.509716 TTCTCCGTTTTCTTTCCCTTTTC 57.490 39.130 0.00 0.00 0.00 2.29
6131 13061 4.788679 TCTCCGTTTTCTTTCCCTTTTCT 58.211 39.130 0.00 0.00 0.00 2.52
6132 13062 5.198207 TCTCCGTTTTCTTTCCCTTTTCTT 58.802 37.500 0.00 0.00 0.00 2.52
6133 13063 5.298527 TCTCCGTTTTCTTTCCCTTTTCTTC 59.701 40.000 0.00 0.00 0.00 2.87
6134 13064 5.198207 TCCGTTTTCTTTCCCTTTTCTTCT 58.802 37.500 0.00 0.00 0.00 2.85
6135 13065 5.298527 TCCGTTTTCTTTCCCTTTTCTTCTC 59.701 40.000 0.00 0.00 0.00 2.87
6136 13066 5.067283 CCGTTTTCTTTCCCTTTTCTTCTCA 59.933 40.000 0.00 0.00 0.00 3.27
6137 13067 6.202226 CGTTTTCTTTCCCTTTTCTTCTCAG 58.798 40.000 0.00 0.00 0.00 3.35
6138 13068 6.038271 CGTTTTCTTTCCCTTTTCTTCTCAGA 59.962 38.462 0.00 0.00 0.00 3.27
6139 13069 7.255277 CGTTTTCTTTCCCTTTTCTTCTCAGAT 60.255 37.037 0.00 0.00 0.00 2.90
6351 13283 8.749026 TCAAATACTTGGTGTTAAGGTTTGTA 57.251 30.769 0.29 0.00 37.91 2.41
6357 13289 6.837048 ACTTGGTGTTAAGGTTTGTAATTCCT 59.163 34.615 0.00 0.00 31.94 3.36
6361 13293 8.798402 TGGTGTTAAGGTTTGTAATTCCTTATG 58.202 33.333 4.02 0.00 41.49 1.90
6390 13322 5.872635 ACGAAAGTCAATAGTCATGCAATG 58.127 37.500 0.00 0.00 44.77 2.82
6391 13323 5.412594 ACGAAAGTCAATAGTCATGCAATGT 59.587 36.000 0.00 0.00 43.90 2.71
6392 13324 5.735892 CGAAAGTCAATAGTCATGCAATGTG 59.264 40.000 0.00 0.00 46.80 3.21
6408 13340 6.179756 TGCAATGTGATTACATCCTACTTGT 58.820 36.000 3.26 0.00 46.54 3.16
6410 13342 6.316140 GCAATGTGATTACATCCTACTTGTGA 59.684 38.462 3.26 0.00 46.54 3.58
6417 13349 8.210265 TGATTACATCCTACTTGTGATGCATTA 58.790 33.333 0.00 0.00 41.63 1.90
6452 13384 7.855545 AGTTATGCTTAATGCTCGTTAATGAG 58.144 34.615 18.69 18.69 43.37 2.90
6481 13413 3.706698 GTTTCTTGGTTGGTTGCTTCTC 58.293 45.455 0.00 0.00 0.00 2.87
6485 13417 3.960102 TCTTGGTTGGTTGCTTCTCAATT 59.040 39.130 0.00 0.00 36.99 2.32
6508 13440 5.432885 TTTTTGCTAGCCTTCACTTGTAC 57.567 39.130 13.29 0.00 0.00 2.90
6571 13503 4.032960 AGTTTTGCCATATGAGTCCACA 57.967 40.909 3.65 0.00 0.00 4.17
6595 13527 8.599792 ACAATACCTACCTATATGCGGTATTTT 58.400 33.333 14.34 9.31 44.33 1.82
6596 13528 9.444600 CAATACCTACCTATATGCGGTATTTTT 57.555 33.333 14.34 0.88 44.33 1.94
6597 13529 9.444600 AATACCTACCTATATGCGGTATTTTTG 57.555 33.333 12.54 0.00 44.33 2.44
6600 13532 5.432885 ACCTATATGCGGTATTTTTGTGC 57.567 39.130 0.00 0.00 31.69 4.57
6601 13533 4.277423 ACCTATATGCGGTATTTTTGTGCC 59.723 41.667 0.00 0.00 31.69 5.01
6617 13549 7.687005 TTTTGTGCCGTTCTAAGTAAATTTG 57.313 32.000 0.00 0.00 0.00 2.32
6624 13556 7.173562 TGCCGTTCTAAGTAAATTTGTATGTGT 59.826 33.333 0.00 0.00 0.00 3.72
6669 13601 2.563702 TCCTTTTTGTGTGTCCGTACC 58.436 47.619 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 243 1.854280 ACCCAGTAAAACTTGGGTGGA 59.146 47.619 14.07 0.00 43.40 4.02
245 247 4.891168 ACTAACAACCCAGTAAAACTTGGG 59.109 41.667 7.98 7.98 40.28 4.12
272 274 4.261994 CCAAAGTTTGGTGGGTGATAAGTG 60.262 45.833 24.17 0.00 45.93 3.16
461 466 0.972983 GTCAGCTGGGTAGGAGCTCA 60.973 60.000 17.19 0.00 45.24 4.26
528 533 2.182030 GGCGAGACAGGAACGAGG 59.818 66.667 0.00 0.00 0.00 4.63
563 568 6.795590 AGGCCTCTTATATAGAAGCTAGTCA 58.204 40.000 0.00 0.00 39.76 3.41
659 664 6.484977 TGTTGTTGTTGTAGTCATCATTAGCA 59.515 34.615 0.00 0.00 0.00 3.49
661 666 8.341903 TGTTGTTGTTGTTGTAGTCATCATTAG 58.658 33.333 0.00 0.00 0.00 1.73
672 677 6.040247 TGTTGTTGTTGTTGTTGTTGTTGTA 58.960 32.000 0.00 0.00 0.00 2.41
678 683 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
679 684 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
680 685 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
681 686 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
682 687 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
683 688 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
684 689 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
685 690 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
686 691 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
687 692 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
688 693 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
689 694 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
690 695 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
691 696 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
692 697 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
693 698 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
694 699 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
695 700 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
696 701 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
697 702 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
698 703 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
699 704 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
700 705 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
701 706 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
702 707 4.464597 TGGACTAAAGGCTTTGTTGTTGTT 59.535 37.500 22.32 0.00 0.00 2.83
703 708 4.020543 TGGACTAAAGGCTTTGTTGTTGT 58.979 39.130 22.32 10.58 0.00 3.32
704 709 4.647424 TGGACTAAAGGCTTTGTTGTTG 57.353 40.909 22.32 7.79 0.00 3.33
705 710 5.046950 TGTTTGGACTAAAGGCTTTGTTGTT 60.047 36.000 22.32 1.84 0.00 2.83
706 711 4.464597 TGTTTGGACTAAAGGCTTTGTTGT 59.535 37.500 22.32 16.69 0.00 3.32
707 712 5.004922 TGTTTGGACTAAAGGCTTTGTTG 57.995 39.130 22.32 13.85 0.00 3.33
708 713 5.660460 CTTGTTTGGACTAAAGGCTTTGTT 58.340 37.500 22.32 8.73 0.00 2.83
709 714 4.441495 GCTTGTTTGGACTAAAGGCTTTGT 60.441 41.667 22.32 16.86 0.00 2.83
710 715 4.051237 GCTTGTTTGGACTAAAGGCTTTG 58.949 43.478 22.32 13.97 0.00 2.77
711 716 3.960755 AGCTTGTTTGGACTAAAGGCTTT 59.039 39.130 17.76 17.76 30.73 3.51
712 717 3.319122 CAGCTTGTTTGGACTAAAGGCTT 59.681 43.478 0.00 0.00 31.76 4.35
713 718 2.887152 CAGCTTGTTTGGACTAAAGGCT 59.113 45.455 0.00 0.00 33.23 4.58
714 719 2.029918 CCAGCTTGTTTGGACTAAAGGC 60.030 50.000 0.00 0.00 37.96 4.35
715 720 2.558359 CCCAGCTTGTTTGGACTAAAGG 59.442 50.000 0.00 0.00 37.96 3.11
716 721 2.558359 CCCCAGCTTGTTTGGACTAAAG 59.442 50.000 0.00 0.00 37.96 1.85
717 722 2.091555 ACCCCAGCTTGTTTGGACTAAA 60.092 45.455 0.00 0.00 37.96 1.85
718 723 1.497286 ACCCCAGCTTGTTTGGACTAA 59.503 47.619 0.00 0.00 37.96 2.24
719 724 1.145571 ACCCCAGCTTGTTTGGACTA 58.854 50.000 0.00 0.00 37.96 2.59
720 725 1.073923 CTACCCCAGCTTGTTTGGACT 59.926 52.381 0.00 0.00 37.96 3.85
721 726 1.534729 CTACCCCAGCTTGTTTGGAC 58.465 55.000 0.00 0.00 37.96 4.02
722 727 0.404040 CCTACCCCAGCTTGTTTGGA 59.596 55.000 0.00 0.00 37.96 3.53
723 728 1.250840 GCCTACCCCAGCTTGTTTGG 61.251 60.000 0.00 0.00 35.41 3.28
800 805 2.281761 AGGGTTGCGTGGAAGCTG 60.282 61.111 3.41 0.00 38.13 4.24
812 817 1.282157 GAACTAGCCATGGACAGGGTT 59.718 52.381 18.40 11.85 38.04 4.11
813 818 0.912486 GAACTAGCCATGGACAGGGT 59.088 55.000 18.40 0.00 40.53 4.34
842 847 1.364328 AGGGATCTGAAGGACTGGAGT 59.636 52.381 0.00 0.00 0.00 3.85
854 859 2.362717 GGAGTCCGTAAAGAGGGATCTG 59.637 54.545 0.00 0.00 41.58 2.90
855 860 2.245287 AGGAGTCCGTAAAGAGGGATCT 59.755 50.000 2.76 0.00 41.58 2.75
856 861 2.624364 GAGGAGTCCGTAAAGAGGGATC 59.376 54.545 2.76 0.00 41.58 3.36
857 862 2.668625 GAGGAGTCCGTAAAGAGGGAT 58.331 52.381 2.76 0.00 41.58 3.85
858 863 1.341778 GGAGGAGTCCGTAAAGAGGGA 60.342 57.143 2.76 0.00 37.28 4.20
859 864 1.112950 GGAGGAGTCCGTAAAGAGGG 58.887 60.000 2.76 0.00 31.37 4.30
869 874 2.675317 CGAACTTGACATGGAGGAGTCC 60.675 54.545 0.00 0.00 44.24 3.85
870 875 2.611518 CGAACTTGACATGGAGGAGTC 58.388 52.381 0.00 0.00 35.37 3.36
871 876 1.276421 CCGAACTTGACATGGAGGAGT 59.724 52.381 0.00 0.00 0.00 3.85
872 877 1.276421 ACCGAACTTGACATGGAGGAG 59.724 52.381 0.00 0.00 0.00 3.69
873 878 1.275291 GACCGAACTTGACATGGAGGA 59.725 52.381 0.00 0.00 0.00 3.71
874 879 1.276421 AGACCGAACTTGACATGGAGG 59.724 52.381 0.00 0.00 0.00 4.30
875 880 2.751166 AGACCGAACTTGACATGGAG 57.249 50.000 0.00 0.00 0.00 3.86
876 881 2.232941 GGTAGACCGAACTTGACATGGA 59.767 50.000 0.00 0.00 0.00 3.41
877 882 2.618053 GGTAGACCGAACTTGACATGG 58.382 52.381 0.00 0.00 0.00 3.66
878 883 2.618053 GGGTAGACCGAACTTGACATG 58.382 52.381 0.00 0.00 36.71 3.21
879 884 1.553704 GGGGTAGACCGAACTTGACAT 59.446 52.381 0.00 0.00 41.60 3.06
880 885 0.971386 GGGGTAGACCGAACTTGACA 59.029 55.000 0.00 0.00 41.60 3.58
881 886 3.828657 GGGGTAGACCGAACTTGAC 57.171 57.895 0.00 0.00 41.60 3.18
890 895 2.158638 ACTGTAGAGATCGGGGTAGACC 60.159 54.545 0.00 0.00 39.11 3.85
891 896 3.140623 GACTGTAGAGATCGGGGTAGAC 58.859 54.545 0.00 0.00 0.00 2.59
892 897 2.106166 GGACTGTAGAGATCGGGGTAGA 59.894 54.545 0.00 0.00 0.00 2.59
893 898 2.106857 AGGACTGTAGAGATCGGGGTAG 59.893 54.545 0.00 0.00 0.00 3.18
894 899 2.133520 AGGACTGTAGAGATCGGGGTA 58.866 52.381 0.00 0.00 0.00 3.69
895 900 0.927767 AGGACTGTAGAGATCGGGGT 59.072 55.000 0.00 0.00 0.00 4.95
896 901 2.074729 AAGGACTGTAGAGATCGGGG 57.925 55.000 0.00 0.00 0.00 5.73
897 902 4.462133 TCTTAAGGACTGTAGAGATCGGG 58.538 47.826 1.85 0.00 0.00 5.14
898 903 5.182380 GGATCTTAAGGACTGTAGAGATCGG 59.818 48.000 1.85 0.00 40.05 4.18
899 904 5.182380 GGGATCTTAAGGACTGTAGAGATCG 59.818 48.000 1.85 0.00 40.05 3.69
900 905 6.311735 AGGGATCTTAAGGACTGTAGAGATC 58.688 44.000 1.85 0.00 39.01 2.75
901 906 6.104094 AGAGGGATCTTAAGGACTGTAGAGAT 59.896 42.308 1.85 0.00 0.00 2.75
902 907 5.433712 AGAGGGATCTTAAGGACTGTAGAGA 59.566 44.000 1.85 0.00 0.00 3.10
903 908 5.701224 AGAGGGATCTTAAGGACTGTAGAG 58.299 45.833 1.85 0.00 0.00 2.43
904 909 5.735733 AGAGGGATCTTAAGGACTGTAGA 57.264 43.478 1.85 0.00 0.00 2.59
905 910 6.800072 AAAGAGGGATCTTAAGGACTGTAG 57.200 41.667 1.85 0.00 0.00 2.74
906 911 6.320672 CGTAAAGAGGGATCTTAAGGACTGTA 59.679 42.308 1.85 0.00 0.00 2.74
907 912 5.127356 CGTAAAGAGGGATCTTAAGGACTGT 59.873 44.000 1.85 0.00 0.00 3.55
908 913 5.452077 CCGTAAAGAGGGATCTTAAGGACTG 60.452 48.000 1.85 0.00 31.81 3.51
909 914 4.650131 CCGTAAAGAGGGATCTTAAGGACT 59.350 45.833 1.85 0.00 31.81 3.85
910 915 4.648307 TCCGTAAAGAGGGATCTTAAGGAC 59.352 45.833 1.85 0.00 34.63 3.85
911 916 4.648307 GTCCGTAAAGAGGGATCTTAAGGA 59.352 45.833 1.85 3.31 41.58 3.36
912 917 4.650131 AGTCCGTAAAGAGGGATCTTAAGG 59.350 45.833 1.85 0.00 41.58 2.69
913 918 5.221283 GGAGTCCGTAAAGAGGGATCTTAAG 60.221 48.000 0.00 0.00 41.58 1.85
914 919 4.648307 GGAGTCCGTAAAGAGGGATCTTAA 59.352 45.833 0.00 0.00 41.58 1.85
915 920 4.079327 AGGAGTCCGTAAAGAGGGATCTTA 60.079 45.833 2.76 0.00 41.58 2.10
1009 1015 1.026718 GGTTGAACATCCCCTCGCTG 61.027 60.000 0.00 0.00 0.00 5.18
1852 5382 2.698803 TCCCATTGTCAGTCAACATCG 58.301 47.619 0.00 0.00 38.97 3.84
1931 5461 8.092521 TGCAGAAAAGTAAAGAGAGAAATCAG 57.907 34.615 0.00 0.00 0.00 2.90
2228 5785 3.073274 ACATTTAGTGCCCCAAGAGAC 57.927 47.619 0.00 0.00 0.00 3.36
2232 5790 3.715628 GCATACATTTAGTGCCCCAAG 57.284 47.619 0.00 0.00 32.88 3.61
2303 5867 1.279271 AGAATAAAGTGCCGCTCAGGT 59.721 47.619 0.00 0.00 43.70 4.00
2312 5876 6.149474 TCCAGTCTAGCAAAAGAATAAAGTGC 59.851 38.462 0.00 0.00 35.41 4.40
2682 6669 8.982685 AGAGTGTATGATACAAATTTATCTGCG 58.017 33.333 6.89 0.00 40.93 5.18
2994 8758 5.297527 CCATCATATTAGCACACACACACAT 59.702 40.000 0.00 0.00 0.00 3.21
3176 8956 1.487976 ACTGTATGATGGGCCTGACAG 59.512 52.381 4.53 12.83 40.09 3.51
4050 10955 6.712998 GCAGACTCTCTAGTAATGTATCCTCA 59.287 42.308 0.00 0.00 35.56 3.86
4289 11198 7.362662 TGAAAAGAGTAGTCAAATGTGCAATC 58.637 34.615 0.00 0.00 0.00 2.67
4864 11792 3.054878 TCCGAGTACAGCGAAGTTTTTC 58.945 45.455 9.37 0.00 0.00 2.29
4928 11856 2.490903 ACACGCCCTATAGCTAATACCG 59.509 50.000 0.00 0.10 0.00 4.02
5131 12060 7.880195 AGTAGAAAGAACATGATGCTTGTAAGT 59.120 33.333 0.00 0.00 0.00 2.24
5332 12262 8.077991 GGCGAAATTTATTGAAGATGATGATGA 58.922 33.333 0.00 0.00 0.00 2.92
5333 12263 8.080417 AGGCGAAATTTATTGAAGATGATGATG 58.920 33.333 0.00 0.00 0.00 3.07
5334 12264 8.174733 AGGCGAAATTTATTGAAGATGATGAT 57.825 30.769 0.00 0.00 0.00 2.45
5335 12265 7.500227 AGAGGCGAAATTTATTGAAGATGATGA 59.500 33.333 0.00 0.00 0.00 2.92
5336 12266 7.646314 AGAGGCGAAATTTATTGAAGATGATG 58.354 34.615 0.00 0.00 0.00 3.07
5337 12267 7.814264 AGAGGCGAAATTTATTGAAGATGAT 57.186 32.000 0.00 0.00 0.00 2.45
5338 12268 7.121168 ACAAGAGGCGAAATTTATTGAAGATGA 59.879 33.333 0.00 0.00 0.00 2.92
5339 12269 7.253422 ACAAGAGGCGAAATTTATTGAAGATG 58.747 34.615 0.00 0.00 0.00 2.90
5340 12270 7.337942 AGACAAGAGGCGAAATTTATTGAAGAT 59.662 33.333 0.00 0.00 0.00 2.40
5341 12271 6.655003 AGACAAGAGGCGAAATTTATTGAAGA 59.345 34.615 0.00 0.00 0.00 2.87
5342 12272 6.846350 AGACAAGAGGCGAAATTTATTGAAG 58.154 36.000 0.00 0.00 0.00 3.02
5343 12273 6.817765 AGACAAGAGGCGAAATTTATTGAA 57.182 33.333 0.00 0.00 0.00 2.69
5344 12274 6.817765 AAGACAAGAGGCGAAATTTATTGA 57.182 33.333 0.00 0.00 0.00 2.57
5345 12275 7.526608 TGTAAGACAAGAGGCGAAATTTATTG 58.473 34.615 0.00 0.00 0.00 1.90
5346 12276 7.681939 TGTAAGACAAGAGGCGAAATTTATT 57.318 32.000 0.00 0.00 0.00 1.40
5491 12421 9.710900 CATAAGTAAGTCCATGAATAGTGCATA 57.289 33.333 0.00 0.00 0.00 3.14
5616 12546 7.700322 TCACATTAGTCATAGCGAAATTCTC 57.300 36.000 0.00 0.00 0.00 2.87
5787 12717 3.136626 AGAGGTCTTTGTGTAAGTGCCTT 59.863 43.478 0.00 0.00 39.01 4.35
5802 12732 4.718961 ACACATAAAGCAACAAGAGGTCT 58.281 39.130 0.00 0.00 0.00 3.85
5824 12754 9.621629 CCACCTTATAGATTACATGTGGTTTAA 57.378 33.333 9.11 0.00 37.74 1.52
5863 12793 4.496341 CGGCAACTAGTGATTTGGCTAATG 60.496 45.833 14.66 0.00 44.08 1.90
5919 12849 8.528917 AAGGCGATAATTCTTTTGGTTTTAAC 57.471 30.769 0.00 0.00 0.00 2.01
5925 12855 5.469479 CACAAAGGCGATAATTCTTTTGGT 58.531 37.500 0.00 0.00 0.00 3.67
5942 12872 7.697352 TTAAAAAGACACATGATGCACAAAG 57.303 32.000 0.00 0.00 0.00 2.77
6085 13015 1.814772 CTGCTCTGATCGCCCCTAGG 61.815 65.000 0.06 0.06 0.00 3.02
6094 13024 2.275318 CGGAGAAAACCTGCTCTGATC 58.725 52.381 0.00 0.00 39.36 2.92
6095 13025 1.625818 ACGGAGAAAACCTGCTCTGAT 59.374 47.619 0.00 0.00 39.36 2.90
6096 13026 1.048601 ACGGAGAAAACCTGCTCTGA 58.951 50.000 0.00 0.00 39.36 3.27
6097 13027 1.884235 AACGGAGAAAACCTGCTCTG 58.116 50.000 0.00 0.00 42.02 3.35
6098 13028 2.640316 AAACGGAGAAAACCTGCTCT 57.360 45.000 0.00 0.00 0.00 4.09
6101 13031 3.710326 AAGAAAACGGAGAAAACCTGC 57.290 42.857 0.00 0.00 0.00 4.85
6113 13043 6.038271 TCTGAGAAGAAAAGGGAAAGAAAACG 59.962 38.462 0.00 0.00 0.00 3.60
6351 13283 4.218417 ACTTTCGTGCTTGCATAAGGAATT 59.782 37.500 14.62 0.00 35.94 2.17
6357 13289 4.764679 ATTGACTTTCGTGCTTGCATAA 57.235 36.364 0.00 0.00 0.00 1.90
6361 13293 3.186409 TGACTATTGACTTTCGTGCTTGC 59.814 43.478 0.00 0.00 0.00 4.01
6392 13324 7.502120 AATGCATCACAAGTAGGATGTAATC 57.498 36.000 0.00 0.00 42.22 1.75
6408 13340 7.519809 GCATAACTAACACCGAATAATGCATCA 60.520 37.037 0.00 0.00 37.67 3.07
6410 13342 6.486657 AGCATAACTAACACCGAATAATGCAT 59.513 34.615 0.00 0.00 39.63 3.96
6417 13349 6.725246 GCATTAAGCATAACTAACACCGAAT 58.275 36.000 0.00 0.00 44.79 3.34
6452 13384 5.501736 GCAACCAACCAAGAAACGAAAATTC 60.502 40.000 0.00 0.00 0.00 2.17
6533 13465 8.581578 TGGCAAAACTAGGTTTAAGGATTTTAG 58.418 33.333 5.20 0.00 34.43 1.85
6534 13466 8.480133 TGGCAAAACTAGGTTTAAGGATTTTA 57.520 30.769 5.20 0.00 34.43 1.52
6541 13473 8.281212 ACTCATATGGCAAAACTAGGTTTAAG 57.719 34.615 5.20 0.00 34.43 1.85
6549 13481 5.172687 TGTGGACTCATATGGCAAAACTA 57.827 39.130 2.13 0.00 0.00 2.24
6595 13527 6.380095 ACAAATTTACTTAGAACGGCACAA 57.620 33.333 0.00 0.00 0.00 3.33
6596 13528 7.173562 ACATACAAATTTACTTAGAACGGCACA 59.826 33.333 0.00 0.00 0.00 4.57
6597 13529 7.480542 CACATACAAATTTACTTAGAACGGCAC 59.519 37.037 0.00 0.00 0.00 5.01
6600 13532 8.714179 TGACACATACAAATTTACTTAGAACGG 58.286 33.333 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.