Multiple sequence alignment - TraesCS6D01G403400

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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 TraesCS6D01G403400 chr6D 100.000 3690 0 0 1 3690 471569909 471566220 0.000000e+00 6815.0
1 TraesCS6D01G403400 chr6D 93.909 394 24 0 3297 3690 312308890 312309283 2.450000e-166 595.0
2 TraesCS6D01G403400 chr6D 90.968 310 28 0 1411 1720 471568433 471568124 5.700000e-113 418.0
3 TraesCS6D01G403400 chr6D 90.968 310 28 0 1477 1786 471568499 471568190 5.700000e-113 418.0
4 TraesCS6D01G403400 chr6D 90.830 229 21 0 1411 1639 471568367 471568139 1.290000e-79 307.0
5 TraesCS6D01G403400 chr6D 90.830 229 21 0 1543 1771 471568499 471568271 1.290000e-79 307.0
6 TraesCS6D01G403400 chr6D 83.860 285 17 18 2253 2509 471567618 471567335 1.020000e-60 244.0
7 TraesCS6D01G403400 chr6D 83.860 285 17 18 2292 2575 471567657 471567401 1.020000e-60 244.0
8 TraesCS6D01G403400 chr6D 85.870 92 12 1 245 336 16517426 16517336 3.030000e-16 97.1
9 TraesCS6D01G403400 chr6D 98.000 50 1 0 2253 2302 471567540 471567491 1.830000e-13 87.9
10 TraesCS6D01G403400 chr6D 98.000 50 1 0 2370 2419 471567657 471567608 1.830000e-13 87.9
11 TraesCS6D01G403400 chrUn 90.736 1630 106 23 1 1596 62915944 62917562 0.000000e+00 2132.0
12 TraesCS6D01G403400 chrUn 85.445 1381 104 41 2353 3690 62919543 62920869 0.000000e+00 1347.0
13 TraesCS6D01G403400 chrUn 89.379 885 54 20 1630 2509 62918916 62919765 0.000000e+00 1077.0
14 TraesCS6D01G403400 chrUn 94.167 120 7 0 1411 1530 62917443 62917562 2.260000e-42 183.0
15 TraesCS6D01G403400 chr6A 88.940 1085 92 16 1451 2509 616250307 616249225 0.000000e+00 1314.0
16 TraesCS6D01G403400 chr6A 92.927 820 28 7 2292 3103 616249505 616248708 0.000000e+00 1166.0
17 TraesCS6D01G403400 chr6A 93.217 457 18 3 983 1426 616250900 616250444 0.000000e+00 660.0
18 TraesCS6D01G403400 chr6A 91.244 434 29 1 1 434 617999714 618000138 1.910000e-162 582.0
19 TraesCS6D01G403400 chr6A 85.849 318 44 1 1411 1727 616250281 616249964 1.640000e-88 337.0
20 TraesCS6D01G403400 chr1B 85.111 947 88 16 1454 2369 368710205 368709281 0.000000e+00 918.0
21 TraesCS6D01G403400 chr1B 81.818 429 38 18 1015 1413 368710759 368710341 1.280000e-84 324.0
22 TraesCS6D01G403400 chr1B 93.578 218 11 1 2292 2509 368709397 368709183 4.600000e-84 322.0
23 TraesCS6D01G403400 chr1B 77.778 477 39 34 2644 3081 368708628 368708180 7.970000e-57 231.0
24 TraesCS6D01G403400 chr1B 80.195 308 27 22 2331 2636 368709397 368709122 2.250000e-47 200.0
25 TraesCS6D01G403400 chr1B 89.189 74 6 2 14 86 367749613 367749541 1.410000e-14 91.6
26 TraesCS6D01G403400 chr1D 85.919 838 64 13 1534 2341 233930091 233929278 0.000000e+00 845.0
27 TraesCS6D01G403400 chr1D 94.684 395 21 0 3296 3690 293114466 293114860 6.770000e-172 614.0
28 TraesCS6D01G403400 chr1D 94.162 394 23 0 3297 3690 142654146 142654539 5.270000e-168 601.0
29 TraesCS6D01G403400 chr1D 82.093 430 37 13 1015 1413 233930654 233930234 7.640000e-87 331.0
30 TraesCS6D01G403400 chr1D 94.413 179 7 1 2331 2509 233929363 233929188 4.700000e-69 272.0
31 TraesCS6D01G403400 chr1D 78.085 470 46 33 2644 3081 233928620 233928176 1.020000e-60 244.0
32 TraesCS6D01G403400 chr1D 85.043 234 29 6 358 588 489752074 489752304 2.220000e-57 233.0
33 TraesCS6D01G403400 chr1D 92.086 139 9 2 2507 2644 233929256 233929119 1.050000e-45 195.0
34 TraesCS6D01G403400 chr1D 85.135 74 11 0 2436 2509 233929618 233929545 3.950000e-10 76.8
35 TraesCS6D01G403400 chr1A 84.859 852 78 16 1520 2341 313489980 313490810 0.000000e+00 811.0
36 TraesCS6D01G403400 chr1A 82.436 427 43 14 1015 1413 313489433 313489855 9.810000e-91 344.0
37 TraesCS6D01G403400 chr1A 93.956 182 11 0 2328 2509 313490719 313490900 3.630000e-70 276.0
38 TraesCS6D01G403400 chr1A 85.903 227 28 4 363 588 11666371 11666594 4.760000e-59 239.0
39 TraesCS6D01G403400 chr1A 92.806 139 8 2 2507 2644 313490832 313490969 2.250000e-47 200.0
40 TraesCS6D01G403400 chr1A 87.356 87 10 1 1 87 261828334 261828249 8.430000e-17 99.0
41 TraesCS6D01G403400 chr1A 95.652 46 2 0 3206 3251 119845776 119845731 1.420000e-09 75.0
42 TraesCS6D01G403400 chr1A 95.652 46 2 0 3206 3251 162922432 162922387 1.420000e-09 75.0
43 TraesCS6D01G403400 chr7D 94.162 394 23 0 3297 3690 360350426 360350819 5.270000e-168 601.0
44 TraesCS6D01G403400 chr7D 87.336 229 25 4 362 588 16909721 16909495 3.660000e-65 259.0
45 TraesCS6D01G403400 chr7D 87.379 103 11 2 235 336 46993679 46993578 2.330000e-22 117.0
46 TraesCS6D01G403400 chr7D 82.524 103 12 3 234 336 126820781 126820685 6.570000e-13 86.1
47 TraesCS6D01G403400 chr7D 94.000 50 2 1 3206 3254 607410075 607410026 1.420000e-09 75.0
48 TraesCS6D01G403400 chr2D 93.516 401 24 2 3292 3690 150931583 150931983 2.450000e-166 595.0
49 TraesCS6D01G403400 chr2D 93.893 393 24 0 3297 3689 12607087 12606695 8.820000e-166 593.0
50 TraesCS6D01G403400 chr2D 86.344 227 29 2 362 588 74135677 74135901 2.850000e-61 246.0
51 TraesCS6D01G403400 chr2D 86.522 230 24 7 362 588 565153445 565153670 2.850000e-61 246.0
52 TraesCS6D01G403400 chr2D 85.366 82 11 1 1 82 494635935 494635855 2.360000e-12 84.2
53 TraesCS6D01G403400 chr5D 93.655 394 25 0 3297 3690 499298263 499297870 1.140000e-164 590.0
54 TraesCS6D01G403400 chr5D 85.526 228 33 0 361 588 103631871 103632098 4.760000e-59 239.0
55 TraesCS6D01G403400 chr3D 93.655 394 25 0 3297 3690 239313154 239313547 1.140000e-164 590.0
56 TraesCS6D01G403400 chr3D 93.655 394 23 1 3297 3690 308295317 308294926 4.110000e-164 588.0
57 TraesCS6D01G403400 chr3D 95.652 46 2 0 3206 3251 203309242 203309197 1.420000e-09 75.0
58 TraesCS6D01G403400 chr6B 90.657 396 35 1 1 396 719267743 719268136 3.260000e-145 525.0
59 TraesCS6D01G403400 chr6B 83.529 85 14 0 1 85 146845627 146845543 3.050000e-11 80.5
60 TraesCS6D01G403400 chr5A 86.842 228 22 7 364 588 315263376 315263598 7.910000e-62 248.0
61 TraesCS6D01G403400 chr5A 89.655 87 9 0 1 87 600044142 600044056 1.080000e-20 111.0
62 TraesCS6D01G403400 chr5A 85.057 87 6 7 243 326 626220990 626220908 8.490000e-12 82.4
63 TraesCS6D01G403400 chr7A 85.841 226 29 3 362 586 630485310 630485087 1.710000e-58 237.0
64 TraesCS6D01G403400 chr7A 85.437 103 13 2 234 336 313682324 313682224 5.040000e-19 106.0
65 TraesCS6D01G403400 chr5B 86.207 87 11 1 1 87 589344345 589344260 3.920000e-15 93.5
66 TraesCS6D01G403400 chr5B 95.652 46 2 0 3206 3251 84208559 84208604 1.420000e-09 75.0
67 TraesCS6D01G403400 chr5B 95.652 46 2 0 3206 3251 492225483 492225528 1.420000e-09 75.0
68 TraesCS6D01G403400 chr2B 87.179 78 8 2 234 311 10767476 10767401 1.830000e-13 87.9
69 TraesCS6D01G403400 chr2B 95.652 46 2 0 3206 3251 180174195 180174240 1.420000e-09 75.0
70 TraesCS6D01G403400 chr7B 95.652 46 2 0 3206 3251 446509795 446509750 1.420000e-09 75.0
71 TraesCS6D01G403400 chr3B 93.023 43 1 2 588 628 440112676 440112634 1.110000e-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 TraesCS6D01G403400 chr6D 471566220 471569909 3689 True 992.088889 6815 91.92400 1 3690 9 chr6D.!!$R2 3689
1 TraesCS6D01G403400 chrUn 62915944 62920869 4925 False 1184.750000 2132 89.93175 1 3690 4 chrUn.!!$F1 3689
2 TraesCS6D01G403400 chr6A 616248708 616250900 2192 True 869.250000 1314 90.23325 983 3103 4 chr6A.!!$R1 2120
3 TraesCS6D01G403400 chr1B 368708180 368710759 2579 True 399.000000 918 83.69600 1015 3081 5 chr1B.!!$R2 2066
4 TraesCS6D01G403400 chr1D 233928176 233930654 2478 True 327.300000 845 86.28850 1015 3081 6 chr1D.!!$R1 2066
5 TraesCS6D01G403400 chr1A 313489433 313490969 1536 False 407.750000 811 88.51425 1015 2644 4 chr1A.!!$F2 1629

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
580 586 0.036294 TCGGCTCAGTCTCTCGAAGA 60.036 55.0 0.00 0.0 0.0 2.87 F
2058 3804 0.601046 CTCAAGAACACGGCAGCTGA 60.601 55.0 20.43 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 3946 1.000612 GTCGAGGTCCCTCTTCCCT 59.999 63.158 11.41 0.0 40.69 4.20 R
3396 5930 1.000955 AGGTGTGTCGGTCATGTCTTC 59.999 52.381 0.00 0.0 0.00 2.87 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
25 26 4.863131 CGTGTCCCTAGTTCATCTTGTTAC 59.137 45.833 0.00 0.00 0.00 2.50
35 36 5.189736 AGTTCATCTTGTTACCATCTAGCCA 59.810 40.000 0.00 0.00 0.00 4.75
48 49 1.483827 TCTAGCCAAGATCACCAGCTG 59.516 52.381 6.78 6.78 35.03 4.24
69 70 1.697082 GGACCCCCTTCCCGAGATTC 61.697 65.000 0.00 0.00 0.00 2.52
82 83 2.470821 CGAGATTCGCCGGATTTAACT 58.529 47.619 5.05 0.00 31.14 2.24
209 210 4.585879 TGGTCAACCAGATTTAAGCTACC 58.414 43.478 0.00 0.00 42.01 3.18
210 211 4.288626 TGGTCAACCAGATTTAAGCTACCT 59.711 41.667 0.00 0.00 42.01 3.08
213 214 6.127140 GGTCAACCAGATTTAAGCTACCTAGA 60.127 42.308 0.00 0.00 35.64 2.43
373 375 0.370273 GAGTAGCGCGAACCAACATG 59.630 55.000 12.10 0.00 0.00 3.21
396 398 2.092914 GGTTGGATGGTTAGGAGGACAG 60.093 54.545 0.00 0.00 0.00 3.51
403 405 3.798515 TGGTTAGGAGGACAGTGGTATT 58.201 45.455 0.00 0.00 0.00 1.89
406 408 2.950990 AGGAGGACAGTGGTATTCCT 57.049 50.000 0.00 0.00 42.79 3.36
417 419 2.039084 GTGGTATTCCTAGCCCATCAGG 59.961 54.545 0.00 0.00 34.73 3.86
420 422 3.198853 GGTATTCCTAGCCCATCAGGATC 59.801 52.174 0.00 0.00 40.62 3.36
423 425 1.133167 TCCTAGCCCATCAGGATCGAA 60.133 52.381 0.00 0.00 35.99 3.71
424 426 1.274728 CCTAGCCCATCAGGATCGAAG 59.725 57.143 0.00 0.00 38.24 3.79
433 435 2.933573 TCAGGATCGAAGTCCTAGACC 58.066 52.381 7.26 0.00 46.85 3.85
441 443 4.087182 TCGAAGTCCTAGACCTGACATTT 58.913 43.478 0.00 0.00 33.89 2.32
457 459 6.183360 CCTGACATTTGTGCTTGCATTATTTC 60.183 38.462 0.00 0.00 0.00 2.17
497 499 1.635663 GGCGATGTTCGTTCAGTGGG 61.636 60.000 0.00 0.00 42.81 4.61
500 502 1.726853 GATGTTCGTTCAGTGGGAGG 58.273 55.000 0.00 0.00 0.00 4.30
504 506 0.966920 TTCGTTCAGTGGGAGGAGAC 59.033 55.000 0.00 0.00 0.00 3.36
520 526 2.050351 ACGTTCCTGTCGACTGCG 60.050 61.111 17.92 16.49 39.35 5.18
530 536 4.430423 CGACTGCGAGGCGTTTGC 62.430 66.667 3.57 0.00 42.99 3.68
567 573 4.244425 TCTTAAGATGCTATGTCGGCTC 57.756 45.455 0.00 0.00 0.00 4.70
580 586 0.036294 TCGGCTCAGTCTCTCGAAGA 60.036 55.000 0.00 0.00 0.00 2.87
586 592 2.682352 CTCAGTCTCTCGAAGATGCTCA 59.318 50.000 0.00 0.00 36.11 4.26
600 606 6.089150 CGAAGATGCTCATGTATGTGAGTATG 59.911 42.308 11.30 0.00 46.87 2.39
630 636 6.561902 CGACTTCGATTGTACCGTGTTAAAAA 60.562 38.462 0.00 0.00 43.02 1.94
701 711 4.699522 AGAGGCAAACCCCGACGC 62.700 66.667 0.00 0.00 36.11 5.19
707 717 3.669344 AAACCCCGACGCGACGTA 61.669 61.111 27.23 0.00 41.37 3.57
708 718 2.993471 AAACCCCGACGCGACGTAT 61.993 57.895 27.23 11.11 41.37 3.06
709 719 2.872337 AAACCCCGACGCGACGTATC 62.872 60.000 27.23 6.91 41.37 2.24
710 720 3.879682 CCCCGACGCGACGTATCA 61.880 66.667 27.23 0.00 41.37 2.15
711 721 2.649975 CCCGACGCGACGTATCAC 60.650 66.667 27.23 1.60 41.37 3.06
712 722 2.649975 CCGACGCGACGTATCACC 60.650 66.667 27.23 0.00 41.37 4.02
713 723 3.009599 CGACGCGACGTATCACCG 61.010 66.667 22.21 3.07 41.37 4.94
714 724 2.649975 GACGCGACGTATCACCGG 60.650 66.667 15.93 0.00 41.37 5.28
715 725 4.842091 ACGCGACGTATCACCGGC 62.842 66.667 15.93 0.00 38.73 6.13
717 727 4.501714 GCGACGTATCACCGGCCA 62.502 66.667 0.00 0.00 29.99 5.36
718 728 2.182284 CGACGTATCACCGGCCAA 59.818 61.111 0.00 0.00 29.99 4.52
719 729 1.446445 CGACGTATCACCGGCCAAA 60.446 57.895 0.00 0.00 29.99 3.28
720 730 1.015085 CGACGTATCACCGGCCAAAA 61.015 55.000 0.00 0.00 29.99 2.44
721 731 1.375551 GACGTATCACCGGCCAAAAT 58.624 50.000 0.00 0.00 0.00 1.82
722 732 2.553086 GACGTATCACCGGCCAAAATA 58.447 47.619 0.00 0.00 0.00 1.40
723 733 3.135994 GACGTATCACCGGCCAAAATAT 58.864 45.455 0.00 0.00 0.00 1.28
724 734 3.135994 ACGTATCACCGGCCAAAATATC 58.864 45.455 0.00 0.00 0.00 1.63
725 735 2.482721 CGTATCACCGGCCAAAATATCC 59.517 50.000 0.00 0.00 0.00 2.59
726 736 3.751518 GTATCACCGGCCAAAATATCCT 58.248 45.455 0.00 0.00 0.00 3.24
727 737 2.051334 TCACCGGCCAAAATATCCTG 57.949 50.000 0.00 0.00 0.00 3.86
728 738 1.032014 CACCGGCCAAAATATCCTGG 58.968 55.000 0.00 0.00 35.67 4.45
729 739 0.923358 ACCGGCCAAAATATCCTGGA 59.077 50.000 0.00 0.00 34.35 3.86
730 740 1.318576 CCGGCCAAAATATCCTGGAC 58.681 55.000 2.24 3.45 37.38 4.02
732 742 2.341846 GGCCAAAATATCCTGGACGA 57.658 50.000 0.00 0.00 34.35 4.20
733 743 2.222027 GGCCAAAATATCCTGGACGAG 58.778 52.381 0.00 0.00 34.35 4.18
747 757 4.409588 CGAGTTTGGCACGACGCG 62.410 66.667 3.53 3.53 43.84 6.01
750 760 1.941476 GAGTTTGGCACGACGCGTAG 61.941 60.000 13.97 16.40 43.84 3.51
762 772 4.752879 GCGTAGGTCGGCTGGCAA 62.753 66.667 0.00 0.00 40.26 4.52
763 773 2.509336 CGTAGGTCGGCTGGCAAG 60.509 66.667 0.00 0.00 35.71 4.01
771 824 2.173669 CGGCTGGCAAGTATGGTCG 61.174 63.158 1.08 0.00 0.00 4.79
775 828 1.369091 CTGGCAAGTATGGTCGGCAC 61.369 60.000 0.00 0.00 0.00 5.01
793 846 0.877071 ACAGCAATTTCAGTCGGCAG 59.123 50.000 0.00 0.00 0.00 4.85
859 912 4.016706 CTCCACCCACCCCACGTC 62.017 72.222 0.00 0.00 0.00 4.34
870 923 4.602259 CCACGTCCACCTGTGCGT 62.602 66.667 0.00 0.00 38.14 5.24
872 925 4.640855 ACGTCCACCTGTGCGTCG 62.641 66.667 0.00 0.00 31.54 5.12
874 927 2.430921 GTCCACCTGTGCGTCGAG 60.431 66.667 0.00 0.00 0.00 4.04
875 928 3.680786 TCCACCTGTGCGTCGAGG 61.681 66.667 0.00 0.00 35.26 4.63
876 929 3.991051 CCACCTGTGCGTCGAGGT 61.991 66.667 7.01 0.00 43.79 3.85
878 931 4.664677 ACCTGTGCGTCGAGGTGC 62.665 66.667 7.01 2.05 41.27 5.01
902 955 4.069232 CTCCCGCGTTCTGCTCCA 62.069 66.667 4.92 0.00 43.27 3.86
906 959 2.671177 CCGCGTTCTGCTCCACTTG 61.671 63.158 4.92 0.00 43.27 3.16
937 990 7.822161 ATCTATCCATCCTCGATTGATCTAG 57.178 40.000 0.00 0.00 29.77 2.43
952 1005 0.809385 TCTAGGCTTTCACCGTCTCG 59.191 55.000 0.00 0.00 33.69 4.04
964 1017 1.730902 CGTCTCGCACACACAGAGG 60.731 63.158 0.00 0.00 33.16 3.69
967 1020 1.112916 TCTCGCACACACAGAGGGAA 61.113 55.000 0.00 0.00 33.16 3.97
1090 1144 4.794241 GCACGTCGTCGCCATTGC 62.794 66.667 0.99 0.65 41.18 3.56
1103 1157 4.630069 GTCGCCATTGCTATATCCGTTATT 59.370 41.667 0.00 0.00 34.43 1.40
1104 1158 4.629634 TCGCCATTGCTATATCCGTTATTG 59.370 41.667 0.00 0.00 34.43 1.90
1105 1159 4.629634 CGCCATTGCTATATCCGTTATTGA 59.370 41.667 0.00 0.00 34.43 2.57
1106 1160 5.294306 CGCCATTGCTATATCCGTTATTGAT 59.706 40.000 0.00 0.00 34.43 2.57
1110 1177 9.345517 CCATTGCTATATCCGTTATTGATTTTG 57.654 33.333 0.00 0.00 0.00 2.44
1118 1185 4.683781 TCCGTTATTGATTTTGCTTGCAAC 59.316 37.500 7.60 0.00 0.00 4.17
1282 1385 3.991051 CACGAGCAGGACACCGGT 61.991 66.667 0.00 0.00 0.00 5.28
1415 1679 3.343788 GACTCCAGTCCCGAGCACG 62.344 68.421 0.00 0.00 39.07 5.34
1513 1777 2.594592 GTGCGGCTTGGTGACCTT 60.595 61.111 2.11 0.00 0.00 3.50
1518 1782 4.043200 GCTTGGTGACCTTGGCGC 62.043 66.667 2.11 0.00 0.00 6.53
1611 1875 2.125350 GGAGCAGGAGGTGAAGCG 60.125 66.667 0.00 0.00 0.00 4.68
1652 1916 3.850098 CTTGGTGACCTTGGCGCCT 62.850 63.158 29.70 6.86 42.67 5.52
1790 3506 3.695606 GTCTCGGCAGCCCTGTCA 61.696 66.667 5.63 0.00 34.22 3.58
2058 3804 0.601046 CTCAAGAACACGGCAGCTGA 60.601 55.000 20.43 0.00 0.00 4.26
2269 4111 4.785453 GGCACGGAGGGGCTGAAG 62.785 72.222 0.00 0.00 32.57 3.02
2270 4112 3.706373 GCACGGAGGGGCTGAAGA 61.706 66.667 0.00 0.00 0.00 2.87
2271 4113 3.068881 CACGGAGGGGCTGAAGAA 58.931 61.111 0.00 0.00 0.00 2.52
2272 4114 1.376037 CACGGAGGGGCTGAAGAAC 60.376 63.158 0.00 0.00 0.00 3.01
2273 4115 2.125512 CGGAGGGGCTGAAGAACG 60.126 66.667 0.00 0.00 0.00 3.95
2274 4116 2.436824 GGAGGGGCTGAAGAACGC 60.437 66.667 0.00 0.00 0.00 4.84
2275 4117 2.815647 GAGGGGCTGAAGAACGCG 60.816 66.667 3.53 3.53 0.00 6.01
2276 4118 4.394712 AGGGGCTGAAGAACGCGG 62.395 66.667 12.47 0.00 0.00 6.46
2280 4122 4.090057 GCTGAAGAACGCGGCCAC 62.090 66.667 12.47 0.00 0.00 5.01
2281 4123 3.777925 CTGAAGAACGCGGCCACG 61.778 66.667 12.53 12.53 44.63 4.94
2308 4150 4.785453 GGCACGGAGGGGCTGAAG 62.785 72.222 0.00 0.00 32.57 3.02
2309 4151 3.706373 GCACGGAGGGGCTGAAGA 61.706 66.667 0.00 0.00 0.00 2.87
2310 4152 3.068881 CACGGAGGGGCTGAAGAA 58.931 61.111 0.00 0.00 0.00 2.52
2311 4153 1.376037 CACGGAGGGGCTGAAGAAC 60.376 63.158 0.00 0.00 0.00 3.01
2312 4154 2.125512 CGGAGGGGCTGAAGAACG 60.126 66.667 0.00 0.00 0.00 3.95
2313 4155 2.436824 GGAGGGGCTGAAGAACGC 60.437 66.667 0.00 0.00 0.00 4.84
2314 4156 2.815647 GAGGGGCTGAAGAACGCG 60.816 66.667 3.53 3.53 0.00 6.01
2315 4157 4.394712 AGGGGCTGAAGAACGCGG 62.395 66.667 12.47 0.00 0.00 6.46
2319 4161 4.090057 GCTGAAGAACGCGGCCAC 62.090 66.667 12.47 0.00 0.00 5.01
2320 4162 3.777925 CTGAAGAACGCGGCCACG 61.778 66.667 12.53 12.53 44.63 4.94
2347 4189 4.785453 GGCACGGAGGGGCTGAAG 62.785 72.222 0.00 0.00 32.57 3.02
2348 4190 3.706373 GCACGGAGGGGCTGAAGA 61.706 66.667 0.00 0.00 0.00 2.87
2349 4191 3.068881 CACGGAGGGGCTGAAGAA 58.931 61.111 0.00 0.00 0.00 2.52
2350 4192 1.376037 CACGGAGGGGCTGAAGAAC 60.376 63.158 0.00 0.00 0.00 3.01
2351 4193 2.125512 CGGAGGGGCTGAAGAACG 60.126 66.667 0.00 0.00 0.00 3.95
2352 4194 2.436824 GGAGGGGCTGAAGAACGC 60.437 66.667 0.00 0.00 0.00 4.84
2704 5126 0.532640 TGTGAAGTGCAGCGTGTGAT 60.533 50.000 0.00 0.00 0.00 3.06
2727 5156 4.796231 AGTGCGCCGTGGTCGATC 62.796 66.667 4.18 0.00 39.71 3.69
2733 5162 3.445687 CCGTGGTCGATCGTGGGA 61.446 66.667 15.94 0.00 39.71 4.37
2734 5163 2.782222 CCGTGGTCGATCGTGGGAT 61.782 63.158 15.94 0.00 39.71 3.85
2899 5377 5.633601 CGTGTGTATGTACATGTTTCTGTCT 59.366 40.000 18.81 0.00 38.63 3.41
2900 5378 6.399986 CGTGTGTATGTACATGTTTCTGTCTG 60.400 42.308 18.81 0.00 38.63 3.51
2901 5379 6.423905 GTGTGTATGTACATGTTTCTGTCTGT 59.576 38.462 18.81 0.00 38.63 3.41
2902 5380 6.645003 TGTGTATGTACATGTTTCTGTCTGTC 59.355 38.462 18.81 0.00 38.63 3.51
2903 5381 6.868864 GTGTATGTACATGTTTCTGTCTGTCT 59.131 38.462 18.81 0.00 38.63 3.41
2904 5382 6.868339 TGTATGTACATGTTTCTGTCTGTCTG 59.132 38.462 18.81 0.00 0.00 3.51
2905 5383 5.276461 TGTACATGTTTCTGTCTGTCTGT 57.724 39.130 2.30 0.00 0.00 3.41
2906 5384 5.289595 TGTACATGTTTCTGTCTGTCTGTC 58.710 41.667 2.30 0.00 0.00 3.51
2907 5385 4.679373 ACATGTTTCTGTCTGTCTGTCT 57.321 40.909 0.00 0.00 0.00 3.41
2908 5386 4.375272 ACATGTTTCTGTCTGTCTGTCTG 58.625 43.478 0.00 0.00 0.00 3.51
2910 5388 4.046938 TGTTTCTGTCTGTCTGTCTGTC 57.953 45.455 0.00 0.00 0.00 3.51
2916 5394 2.620585 TGTCTGTCTGTCTGTCTGTCTG 59.379 50.000 0.00 0.00 0.00 3.51
2918 5396 2.881513 TCTGTCTGTCTGTCTGTCTGTC 59.118 50.000 0.00 0.00 0.00 3.51
3003 5492 2.049156 TGCTCGTCGTTGCCAGAG 60.049 61.111 9.61 0.00 0.00 3.35
3008 5507 0.320374 TCGTCGTTGCCAGAGGATTT 59.680 50.000 0.00 0.00 0.00 2.17
3009 5508 0.443869 CGTCGTTGCCAGAGGATTTG 59.556 55.000 0.00 0.00 0.00 2.32
3010 5509 1.523758 GTCGTTGCCAGAGGATTTGT 58.476 50.000 0.00 0.00 0.00 2.83
3011 5510 1.197721 GTCGTTGCCAGAGGATTTGTG 59.802 52.381 0.00 0.00 0.00 3.33
3012 5511 1.071542 TCGTTGCCAGAGGATTTGTGA 59.928 47.619 0.00 0.00 0.00 3.58
3013 5512 2.086869 CGTTGCCAGAGGATTTGTGAT 58.913 47.619 0.00 0.00 0.00 3.06
3014 5513 2.096496 CGTTGCCAGAGGATTTGTGATC 59.904 50.000 0.00 0.00 0.00 2.92
3015 5514 2.424956 GTTGCCAGAGGATTTGTGATCC 59.575 50.000 0.00 0.00 38.47 3.36
3016 5515 1.634973 TGCCAGAGGATTTGTGATCCA 59.365 47.619 7.71 0.00 40.61 3.41
3017 5516 2.019984 GCCAGAGGATTTGTGATCCAC 58.980 52.381 7.71 1.57 40.61 4.02
3045 5553 3.248602 CAGCTAACACGCTCAACTTCTTT 59.751 43.478 0.00 0.00 38.41 2.52
3074 5582 1.339247 TGTACTGCAACCGTATTGGGG 60.339 52.381 0.00 0.00 44.64 4.96
3131 5639 1.134491 CACGGTATCTCCAAGTTCCCC 60.134 57.143 0.00 0.00 35.57 4.81
3133 5641 1.557832 CGGTATCTCCAAGTTCCCCAA 59.442 52.381 0.00 0.00 35.57 4.12
3136 5644 4.412843 GGTATCTCCAAGTTCCCCAAAAA 58.587 43.478 0.00 0.00 35.97 1.94
3162 5670 3.884037 AGGTGGAATTGGAGAAGTTGT 57.116 42.857 0.00 0.00 0.00 3.32
3194 5716 1.979155 GAAAACAGCCCAGCTCCCC 60.979 63.158 0.00 0.00 36.40 4.81
3200 5722 1.059006 CAGCCCAGCTCCCCTTCTAT 61.059 60.000 0.00 0.00 36.40 1.98
3201 5723 0.568192 AGCCCAGCTCCCCTTCTATA 59.432 55.000 0.00 0.00 30.62 1.31
3203 5725 1.988846 GCCCAGCTCCCCTTCTATAAT 59.011 52.381 0.00 0.00 0.00 1.28
3220 5742 9.075678 CTTCTATAATGCCTCTTCCAATGAAAT 57.924 33.333 0.00 0.00 0.00 2.17
3229 5751 5.163581 CCTCTTCCAATGAAATGGTGCTTAG 60.164 44.000 0.00 0.00 41.46 2.18
3260 5782 5.118286 GCTAAATGCATTAAGGCCATGTTT 58.882 37.500 13.39 8.08 42.31 2.83
3267 5789 4.640364 CATTAAGGCCATGTTTGTTTGGT 58.360 39.130 5.01 0.00 35.34 3.67
3275 5797 3.937706 CCATGTTTGTTTGGTCTTTTGCA 59.062 39.130 0.00 0.00 0.00 4.08
3276 5798 4.034279 CCATGTTTGTTTGGTCTTTTGCAG 59.966 41.667 0.00 0.00 0.00 4.41
3285 5819 4.405116 TGGTCTTTTGCAGCTTTTTCAT 57.595 36.364 0.00 0.00 0.00 2.57
3288 5822 6.344500 TGGTCTTTTGCAGCTTTTTCATTTA 58.656 32.000 0.00 0.00 0.00 1.40
3290 5824 7.041916 TGGTCTTTTGCAGCTTTTTCATTTATG 60.042 33.333 0.00 0.00 0.00 1.90
3301 5835 6.427853 GCTTTTTCATTTATGCTTTTGGGACT 59.572 34.615 0.00 0.00 0.00 3.85
3304 5838 4.671831 TCATTTATGCTTTTGGGACTCCA 58.328 39.130 0.00 0.00 42.25 3.86
3316 5850 1.165270 GGACTCCAAACAACATCCGG 58.835 55.000 0.00 0.00 0.00 5.14
3320 5854 2.224769 ACTCCAAACAACATCCGGTCAT 60.225 45.455 0.00 0.00 0.00 3.06
3375 5909 0.247145 CGAATGTTAAGCGTGCGGAC 60.247 55.000 0.00 0.00 31.54 4.79
3395 5929 1.403323 CCCTACGGGTTCGAGAACTAC 59.597 57.143 14.62 8.11 40.94 2.73
3396 5930 1.063174 CCTACGGGTTCGAGAACTACG 59.937 57.143 21.75 21.75 42.53 3.51
3397 5931 2.002586 CTACGGGTTCGAGAACTACGA 58.997 52.381 26.45 15.76 40.88 3.43
3419 5953 0.603569 ACATGACCGACACACCTCTC 59.396 55.000 0.00 0.00 0.00 3.20
3421 5955 1.595993 ATGACCGACACACCTCTCCG 61.596 60.000 0.00 0.00 0.00 4.63
3422 5956 2.989824 ACCGACACACCTCTCCGG 60.990 66.667 0.00 0.00 45.09 5.14
3430 5964 2.028385 ACACACCTCTCCGGTCAATAAC 60.028 50.000 0.00 0.00 44.93 1.89
3450 5984 9.252962 CAATAACCAATAAAGAAATCTGGATGC 57.747 33.333 0.00 0.00 0.00 3.91
3482 6016 8.362464 TGGCTCCTACATATTATACGAAGATT 57.638 34.615 0.00 0.00 0.00 2.40
3513 6047 3.853103 TCGAACCGTTATGACAACATACG 59.147 43.478 0.00 0.00 38.50 3.06
3519 6053 7.225523 ACCGTTATGACAACATACGTAATTC 57.774 36.000 0.00 0.00 38.50 2.17
3544 6078 5.064707 CCTTTGTCCATCGGTATGTTACTTG 59.935 44.000 0.00 0.00 0.00 3.16
3571 6105 3.433957 AGATTCGATCGTCGGTATCTCTG 59.566 47.826 15.94 0.00 40.88 3.35
3601 6135 1.659098 CAATCTCGTTACCGGCAAGTC 59.341 52.381 0.00 0.00 33.95 3.01
3616 6150 3.554337 GGCAAGTCTCTTTACTCGTTCCA 60.554 47.826 0.00 0.00 0.00 3.53
3630 6164 6.235231 ACTCGTTCCATAATACATCACCTT 57.765 37.500 0.00 0.00 0.00 3.50
3634 6168 5.815222 CGTTCCATAATACATCACCTTGTGA 59.185 40.000 0.00 0.00 46.90 3.58
3680 6214 6.118852 TGCAAGCTTATGATGTGTATTACCA 58.881 36.000 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.809665 GCTGGTGATCTTGGCTAGATGG 60.810 54.545 16.10 3.01 43.75 3.51
35 36 1.566298 GGTCCCCAGCTGGTGATCTT 61.566 60.000 30.63 0.00 0.00 2.40
59 60 1.682451 AAATCCGGCGAATCTCGGGA 61.682 55.000 9.30 6.97 45.69 5.14
82 83 2.844362 CAGCCTGCCCCTATCGGA 60.844 66.667 0.00 0.00 0.00 4.55
119 120 2.738521 CGTTGACCACCGCCTCAG 60.739 66.667 0.00 0.00 0.00 3.35
153 154 3.805307 CTGCTCTCGCGACTCCGT 61.805 66.667 3.71 0.00 39.65 4.69
373 375 1.913419 TCCTCCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
387 389 2.950990 AGGAATACCACTGTCCTCCT 57.049 50.000 0.00 0.00 37.15 3.69
396 398 2.039084 CCTGATGGGCTAGGAATACCAC 59.961 54.545 0.00 0.00 38.94 4.16
403 405 0.482887 TCGATCCTGATGGGCTAGGA 59.517 55.000 0.00 0.00 46.43 2.94
406 408 1.964223 GACTTCGATCCTGATGGGCTA 59.036 52.381 0.00 0.00 34.39 3.93
417 419 3.280295 TGTCAGGTCTAGGACTTCGATC 58.720 50.000 0.00 0.00 35.11 3.69
420 422 4.177026 CAAATGTCAGGTCTAGGACTTCG 58.823 47.826 0.00 0.00 35.11 3.79
423 425 3.307059 GCACAAATGTCAGGTCTAGGACT 60.307 47.826 0.00 0.00 35.11 3.85
424 426 3.003480 GCACAAATGTCAGGTCTAGGAC 58.997 50.000 0.00 0.00 34.63 3.85
433 435 6.588756 AGAAATAATGCAAGCACAAATGTCAG 59.411 34.615 0.00 0.00 0.00 3.51
441 443 5.664294 AATCCAGAAATAATGCAAGCACA 57.336 34.783 0.00 0.00 0.00 4.57
457 459 4.734695 GCCGAAAGCCTGAAATAAATCCAG 60.735 45.833 0.00 0.00 34.35 3.86
476 478 1.006825 CACTGAACGAACATCGCCGA 61.007 55.000 0.00 0.00 45.12 5.54
500 502 0.729816 GCAGTCGACAGGAACGTCTC 60.730 60.000 19.50 0.00 33.54 3.36
504 506 1.797933 CTCGCAGTCGACAGGAACG 60.798 63.158 19.50 13.10 40.21 3.95
510 512 3.493830 AAACGCCTCGCAGTCGACA 62.494 57.895 19.50 0.00 40.21 4.35
511 513 2.733593 AAACGCCTCGCAGTCGAC 60.734 61.111 7.70 7.70 40.21 4.20
520 526 0.517316 AAAGTCATCGCAAACGCCTC 59.483 50.000 0.00 0.00 39.84 4.70
523 529 2.587612 TACAAAGTCATCGCAAACGC 57.412 45.000 0.00 0.00 39.84 4.84
527 533 8.779303 TCTTAAGATTTTACAAAGTCATCGCAA 58.221 29.630 0.00 0.00 0.00 4.85
530 536 9.214953 GCATCTTAAGATTTTACAAAGTCATCG 57.785 33.333 15.49 0.19 31.21 3.84
567 573 3.181488 ACATGAGCATCTTCGAGAGACTG 60.181 47.826 0.00 2.81 41.84 3.51
586 592 4.645136 AGTCGGTCACATACTCACATACAT 59.355 41.667 0.00 0.00 0.00 2.29
600 606 2.257034 GGTACAATCGAAGTCGGTCAC 58.743 52.381 0.11 0.00 40.29 3.67
671 677 1.371558 GCCTCTTTGGTCGGTGTCT 59.628 57.895 0.00 0.00 38.35 3.41
672 678 0.534203 TTGCCTCTTTGGTCGGTGTC 60.534 55.000 0.00 0.00 38.35 3.67
701 711 1.015085 TTTTGGCCGGTGATACGTCG 61.015 55.000 1.90 0.00 0.00 5.12
702 712 1.375551 ATTTTGGCCGGTGATACGTC 58.624 50.000 1.90 0.00 0.00 4.34
703 713 2.695127 TATTTTGGCCGGTGATACGT 57.305 45.000 1.90 0.00 0.00 3.57
704 714 2.482721 GGATATTTTGGCCGGTGATACG 59.517 50.000 1.90 0.00 0.00 3.06
705 715 3.502211 CAGGATATTTTGGCCGGTGATAC 59.498 47.826 1.90 0.00 0.00 2.24
706 716 3.497763 CCAGGATATTTTGGCCGGTGATA 60.498 47.826 1.90 0.00 0.00 2.15
707 717 2.586425 CAGGATATTTTGGCCGGTGAT 58.414 47.619 1.90 0.00 0.00 3.06
708 718 1.409521 CCAGGATATTTTGGCCGGTGA 60.410 52.381 1.90 0.00 0.00 4.02
709 719 1.032014 CCAGGATATTTTGGCCGGTG 58.968 55.000 1.90 0.00 0.00 4.94
710 720 0.923358 TCCAGGATATTTTGGCCGGT 59.077 50.000 1.90 0.00 34.38 5.28
711 721 1.318576 GTCCAGGATATTTTGGCCGG 58.681 55.000 0.00 0.00 34.38 6.13
712 722 0.944386 CGTCCAGGATATTTTGGCCG 59.056 55.000 0.00 0.00 34.38 6.13
713 723 2.222027 CTCGTCCAGGATATTTTGGCC 58.778 52.381 0.00 0.00 34.38 5.36
714 724 2.919228 ACTCGTCCAGGATATTTTGGC 58.081 47.619 0.00 0.00 34.38 4.52
715 725 4.096382 CCAAACTCGTCCAGGATATTTTGG 59.904 45.833 16.17 16.17 35.74 3.28
716 726 4.438744 GCCAAACTCGTCCAGGATATTTTG 60.439 45.833 0.00 1.92 0.00 2.44
717 727 3.694566 GCCAAACTCGTCCAGGATATTTT 59.305 43.478 0.00 0.00 0.00 1.82
718 728 3.279434 GCCAAACTCGTCCAGGATATTT 58.721 45.455 0.00 0.00 0.00 1.40
719 729 2.238646 TGCCAAACTCGTCCAGGATATT 59.761 45.455 0.00 0.00 0.00 1.28
720 730 1.837439 TGCCAAACTCGTCCAGGATAT 59.163 47.619 0.00 0.00 0.00 1.63
721 731 1.066430 GTGCCAAACTCGTCCAGGATA 60.066 52.381 0.00 0.00 0.00 2.59
722 732 0.321653 GTGCCAAACTCGTCCAGGAT 60.322 55.000 0.00 0.00 0.00 3.24
723 733 1.070786 GTGCCAAACTCGTCCAGGA 59.929 57.895 0.00 0.00 0.00 3.86
724 734 2.317609 CGTGCCAAACTCGTCCAGG 61.318 63.158 0.00 0.00 0.00 4.45
725 735 1.300620 TCGTGCCAAACTCGTCCAG 60.301 57.895 0.00 0.00 36.65 3.86
726 736 1.593209 GTCGTGCCAAACTCGTCCA 60.593 57.895 0.00 0.00 36.65 4.02
727 737 2.654912 CGTCGTGCCAAACTCGTCC 61.655 63.158 0.00 0.00 36.65 4.79
728 738 2.844146 CGTCGTGCCAAACTCGTC 59.156 61.111 0.00 0.00 36.65 4.20
729 739 3.335534 GCGTCGTGCCAAACTCGT 61.336 61.111 0.00 0.00 37.76 4.18
730 740 4.409588 CGCGTCGTGCCAAACTCG 62.410 66.667 0.00 0.00 42.08 4.18
731 741 1.941476 CTACGCGTCGTGCCAAACTC 61.941 60.000 18.63 0.00 41.39 3.01
732 742 2.019951 CTACGCGTCGTGCCAAACT 61.020 57.895 18.63 0.00 41.39 2.66
733 743 2.468532 CTACGCGTCGTGCCAAAC 59.531 61.111 18.63 0.00 41.39 2.93
747 757 0.464452 ATACTTGCCAGCCGACCTAC 59.536 55.000 0.00 0.00 0.00 3.18
750 760 1.819632 CCATACTTGCCAGCCGACC 60.820 63.158 0.00 0.00 0.00 4.79
762 772 0.253044 ATTGCTGTGCCGACCATACT 59.747 50.000 0.00 0.00 0.00 2.12
763 773 1.094785 AATTGCTGTGCCGACCATAC 58.905 50.000 0.00 0.00 0.00 2.39
771 824 0.109597 CCGACTGAAATTGCTGTGCC 60.110 55.000 0.00 0.00 0.00 5.01
775 828 0.169672 CCTGCCGACTGAAATTGCTG 59.830 55.000 0.00 0.00 0.00 4.41
793 846 3.448660 ACTGGATTTAATTTGCTGCTCCC 59.551 43.478 0.00 0.00 0.00 4.30
805 858 0.609151 TCCGTGCCGACTGGATTTAA 59.391 50.000 0.00 0.00 37.49 1.52
859 912 3.991051 ACCTCGACGCACAGGTGG 61.991 66.667 5.96 0.00 41.79 4.61
890 943 1.726853 ATACAAGTGGAGCAGAACGC 58.273 50.000 0.00 0.00 42.91 4.84
902 955 9.922477 TCGAGGATGGATAGATATAATACAAGT 57.078 33.333 0.00 0.00 0.00 3.16
930 983 2.427453 GAGACGGTGAAAGCCTAGATCA 59.573 50.000 0.00 0.00 0.00 2.92
937 990 2.357034 TGCGAGACGGTGAAAGCC 60.357 61.111 0.00 0.00 0.00 4.35
952 1005 0.819259 TGCTTTCCCTCTGTGTGTGC 60.819 55.000 0.00 0.00 0.00 4.57
964 1017 1.671054 TACGGTGCAGCTGCTTTCC 60.671 57.895 36.61 30.57 42.66 3.13
967 1020 2.358737 GGTACGGTGCAGCTGCTT 60.359 61.111 36.61 21.13 42.66 3.91
1090 1144 8.075574 TGCAAGCAAAATCAATAACGGATATAG 58.924 33.333 0.00 0.00 0.00 1.31
1103 1157 3.188492 CACACAGTTGCAAGCAAAATCA 58.812 40.909 9.32 0.00 37.70 2.57
1104 1158 3.000523 CACACACAGTTGCAAGCAAAATC 59.999 43.478 9.32 0.00 37.70 2.17
1105 1159 2.931325 CACACACAGTTGCAAGCAAAAT 59.069 40.909 9.32 0.00 37.70 1.82
1106 1160 2.335752 CACACACAGTTGCAAGCAAAA 58.664 42.857 9.32 0.00 37.70 2.44
1110 1177 1.589727 GGCACACACAGTTGCAAGC 60.590 57.895 0.00 0.00 0.00 4.01
1118 1185 2.593725 AGCTGCAGGCACACACAG 60.594 61.111 17.12 0.00 44.79 3.66
1282 1385 1.745115 GCTGTTGCTATCACCGCCA 60.745 57.895 0.00 0.00 36.03 5.69
1435 1699 2.594592 GCGCCAAGGTCACCAAGT 60.595 61.111 0.00 0.00 0.00 3.16
1524 1788 2.177594 CTTCACCTCCTGCTCCGCTT 62.178 60.000 0.00 0.00 0.00 4.68
1525 1789 2.604686 TTCACCTCCTGCTCCGCT 60.605 61.111 0.00 0.00 0.00 5.52
1526 1790 2.125350 CTTCACCTCCTGCTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
1530 1794 4.749310 CGCGCTTCACCTCCTGCT 62.749 66.667 5.56 0.00 0.00 4.24
1532 1796 2.811317 GTCGCGCTTCACCTCCTG 60.811 66.667 5.56 0.00 0.00 3.86
1596 1860 4.749310 CGCGCTTCACCTCCTGCT 62.749 66.667 5.56 0.00 0.00 4.24
1598 1862 2.811317 GTCGCGCTTCACCTCCTG 60.811 66.667 5.56 0.00 0.00 3.86
1773 3489 2.914777 GATGACAGGGCTGCCGAGAC 62.915 65.000 13.40 8.42 0.00 3.36
1865 3581 1.030457 ATCGCCTCGAAGTTACGGAT 58.970 50.000 0.00 0.00 39.99 4.18
2021 3737 3.680786 CCTGTCCGTGTCGCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
2058 3804 2.034305 GCGACCTTCTCATATACCGTGT 59.966 50.000 0.00 0.00 0.00 4.49
2200 3946 1.000612 GTCGAGGTCCCTCTTCCCT 59.999 63.158 11.41 0.00 40.69 4.20
2257 4099 2.436824 GCGTTCTTCAGCCCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
2258 4100 2.815647 CGCGTTCTTCAGCCCCTC 60.816 66.667 0.00 0.00 0.00 4.30
2259 4101 4.394712 CCGCGTTCTTCAGCCCCT 62.395 66.667 4.92 0.00 0.00 4.79
2263 4105 4.090057 GTGGCCGCGTTCTTCAGC 62.090 66.667 4.92 0.00 0.00 4.26
2264 4106 3.777925 CGTGGCCGCGTTCTTCAG 61.778 66.667 30.21 0.00 0.00 3.02
2291 4133 4.785453 CTTCAGCCCCTCCGTGCC 62.785 72.222 0.00 0.00 0.00 5.01
2292 4134 3.254024 TTCTTCAGCCCCTCCGTGC 62.254 63.158 0.00 0.00 0.00 5.34
2293 4135 1.376037 GTTCTTCAGCCCCTCCGTG 60.376 63.158 0.00 0.00 0.00 4.94
2294 4136 2.943978 CGTTCTTCAGCCCCTCCGT 61.944 63.158 0.00 0.00 0.00 4.69
2295 4137 2.125512 CGTTCTTCAGCCCCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
2296 4138 2.436824 GCGTTCTTCAGCCCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
2297 4139 2.815647 CGCGTTCTTCAGCCCCTC 60.816 66.667 0.00 0.00 0.00 4.30
2298 4140 4.394712 CCGCGTTCTTCAGCCCCT 62.395 66.667 4.92 0.00 0.00 4.79
2302 4144 4.090057 GTGGCCGCGTTCTTCAGC 62.090 66.667 4.92 0.00 0.00 4.26
2303 4145 3.777925 CGTGGCCGCGTTCTTCAG 61.778 66.667 30.21 0.00 0.00 3.02
2330 4172 4.785453 CTTCAGCCCCTCCGTGCC 62.785 72.222 0.00 0.00 0.00 5.01
2331 4173 3.254024 TTCTTCAGCCCCTCCGTGC 62.254 63.158 0.00 0.00 0.00 5.34
2332 4174 1.376037 GTTCTTCAGCCCCTCCGTG 60.376 63.158 0.00 0.00 0.00 4.94
2333 4175 2.943978 CGTTCTTCAGCCCCTCCGT 61.944 63.158 0.00 0.00 0.00 4.69
2334 4176 2.125512 CGTTCTTCAGCCCCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
2335 4177 2.436824 GCGTTCTTCAGCCCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
2336 4178 2.815647 CGCGTTCTTCAGCCCCTC 60.816 66.667 0.00 0.00 0.00 4.30
2337 4179 4.394712 CCGCGTTCTTCAGCCCCT 62.395 66.667 4.92 0.00 0.00 4.79
2341 4183 4.090057 GTGGCCGCGTTCTTCAGC 62.090 66.667 4.92 0.00 0.00 4.26
2342 4184 3.777925 CGTGGCCGCGTTCTTCAG 61.778 66.667 30.21 0.00 0.00 3.02
2704 5126 4.794439 CCACGGCGCACTGATCGA 62.794 66.667 10.83 0.00 0.00 3.59
2726 5155 2.721859 CAGCGATCGATCCCACGA 59.278 61.111 21.57 0.00 46.04 4.35
2727 5156 2.349969 TTCCAGCGATCGATCCCACG 62.350 60.000 21.57 9.72 0.00 4.94
2728 5157 0.034059 ATTCCAGCGATCGATCCCAC 59.966 55.000 21.57 9.45 0.00 4.61
2729 5158 1.627864 TATTCCAGCGATCGATCCCA 58.372 50.000 21.57 0.00 0.00 4.37
2731 5160 3.246619 GACTTATTCCAGCGATCGATCC 58.753 50.000 21.57 12.11 0.00 3.36
2732 5161 2.911723 CGACTTATTCCAGCGATCGATC 59.088 50.000 21.57 15.68 0.00 3.69
2733 5162 2.922758 GCGACTTATTCCAGCGATCGAT 60.923 50.000 21.57 10.64 0.00 3.59
2734 5163 1.599667 GCGACTTATTCCAGCGATCGA 60.600 52.381 21.57 0.00 0.00 3.59
2899 5377 2.937519 AGACAGACAGACAGACAGACA 58.062 47.619 0.00 0.00 0.00 3.41
2900 5378 5.440234 TTTAGACAGACAGACAGACAGAC 57.560 43.478 0.00 0.00 0.00 3.51
2901 5379 6.491745 AGAATTTAGACAGACAGACAGACAGA 59.508 38.462 0.00 0.00 0.00 3.41
2902 5380 6.686630 AGAATTTAGACAGACAGACAGACAG 58.313 40.000 0.00 0.00 0.00 3.51
2903 5381 6.656632 AGAATTTAGACAGACAGACAGACA 57.343 37.500 0.00 0.00 0.00 3.41
2904 5382 7.954788 AAAGAATTTAGACAGACAGACAGAC 57.045 36.000 0.00 0.00 35.86 3.51
2905 5383 8.204160 TGAAAAGAATTTAGACAGACAGACAGA 58.796 33.333 0.00 0.00 37.28 3.41
2906 5384 8.370493 TGAAAAGAATTTAGACAGACAGACAG 57.630 34.615 0.00 0.00 37.28 3.51
2907 5385 8.612619 GTTGAAAAGAATTTAGACAGACAGACA 58.387 33.333 0.00 0.00 37.28 3.41
2908 5386 8.831550 AGTTGAAAAGAATTTAGACAGACAGAC 58.168 33.333 0.00 0.00 37.28 3.51
2910 5388 9.657121 GAAGTTGAAAAGAATTTAGACAGACAG 57.343 33.333 0.00 0.00 37.28 3.51
2916 5394 7.908601 ACACGTGAAGTTGAAAAGAATTTAGAC 59.091 33.333 25.01 0.00 37.28 2.59
2918 5396 7.696453 ACACACGTGAAGTTGAAAAGAATTTAG 59.304 33.333 25.01 0.00 37.28 1.85
3012 5511 2.159043 CGTGTTAGCTGATCAGGTGGAT 60.159 50.000 32.43 6.68 39.78 3.41
3013 5512 1.204704 CGTGTTAGCTGATCAGGTGGA 59.795 52.381 32.43 19.99 39.78 4.02
3014 5513 1.645034 CGTGTTAGCTGATCAGGTGG 58.355 55.000 32.43 15.02 39.78 4.61
3015 5514 1.002366 GCGTGTTAGCTGATCAGGTG 58.998 55.000 32.43 18.70 39.78 4.00
3016 5515 3.442996 GCGTGTTAGCTGATCAGGT 57.557 52.632 28.82 28.82 42.47 4.00
3063 5571 2.640826 TGAAGAACTTCCCCAATACGGT 59.359 45.455 11.30 0.00 38.77 4.83
3074 5582 3.627577 TCACCAAGTTGCTGAAGAACTTC 59.372 43.478 7.51 7.51 40.83 3.01
3104 5612 5.934402 ACTTGGAGATACCGTGAACTTAT 57.066 39.130 0.00 0.00 42.61 1.73
3113 5621 1.200519 TGGGGAACTTGGAGATACCG 58.799 55.000 0.00 0.00 42.61 4.02
3114 5622 3.732048 TTTGGGGAACTTGGAGATACC 57.268 47.619 0.00 0.00 39.54 2.73
3136 5644 5.397360 ACTTCTCCAATTCCACCTTCATTT 58.603 37.500 0.00 0.00 0.00 2.32
3162 5670 2.364970 CTGTTTTCAAGATGTTGGGGCA 59.635 45.455 2.33 0.00 34.09 5.36
3194 5716 8.455903 TTTCATTGGAAGAGGCATTATAGAAG 57.544 34.615 0.00 0.00 33.82 2.85
3200 5722 5.127519 CACCATTTCATTGGAAGAGGCATTA 59.872 40.000 0.00 0.00 39.25 1.90
3201 5723 4.081309 CACCATTTCATTGGAAGAGGCATT 60.081 41.667 0.00 0.00 39.25 3.56
3203 5725 2.827322 CACCATTTCATTGGAAGAGGCA 59.173 45.455 0.00 0.00 39.25 4.75
3220 5742 4.551702 TTAGCAACTCATCTAAGCACCA 57.448 40.909 0.00 0.00 0.00 4.17
3255 5777 3.622612 GCTGCAAAAGACCAAACAAACAT 59.377 39.130 0.00 0.00 0.00 2.71
3260 5782 3.608316 AAAGCTGCAAAAGACCAAACA 57.392 38.095 1.02 0.00 0.00 2.83
3267 5789 6.707161 AGCATAAATGAAAAAGCTGCAAAAGA 59.293 30.769 1.02 0.00 0.00 2.52
3275 5797 6.427853 GTCCCAAAAGCATAAATGAAAAAGCT 59.572 34.615 0.00 0.00 0.00 3.74
3276 5798 6.427853 AGTCCCAAAAGCATAAATGAAAAAGC 59.572 34.615 0.00 0.00 0.00 3.51
3301 5835 2.224646 TGATGACCGGATGTTGTTTGGA 60.225 45.455 9.46 0.00 0.00 3.53
3304 5838 4.522405 TGATTTGATGACCGGATGTTGTTT 59.478 37.500 9.46 0.00 0.00 2.83
3307 5841 3.439825 TGTGATTTGATGACCGGATGTTG 59.560 43.478 9.46 0.00 0.00 3.33
3310 5844 5.528690 AGTTATGTGATTTGATGACCGGATG 59.471 40.000 9.46 0.00 0.00 3.51
3313 5847 4.875536 TGAGTTATGTGATTTGATGACCGG 59.124 41.667 0.00 0.00 0.00 5.28
3360 5894 1.534336 TAGGGTCCGCACGCTTAACA 61.534 55.000 0.00 0.00 43.11 2.41
3382 5916 3.549299 TGTCTTCGTAGTTCTCGAACC 57.451 47.619 6.20 0.00 41.33 3.62
3395 5929 1.060713 GTGTGTCGGTCATGTCTTCG 58.939 55.000 0.00 0.00 0.00 3.79
3396 5930 1.000955 AGGTGTGTCGGTCATGTCTTC 59.999 52.381 0.00 0.00 0.00 2.87
3397 5931 1.000955 GAGGTGTGTCGGTCATGTCTT 59.999 52.381 0.00 0.00 0.00 3.01
3430 5964 4.650588 TGGGCATCCAGATTTCTTTATTGG 59.349 41.667 0.00 0.00 38.32 3.16
3450 5984 7.872993 CGTATAATATGTAGGAGCCAATATGGG 59.127 40.741 0.00 0.00 38.19 4.00
3472 6006 6.199719 GGTTCGACCGATAAAAATCTTCGTAT 59.800 38.462 0.00 0.00 0.00 3.06
3504 6038 5.413523 GGACAAAGGGAATTACGTATGTTGT 59.586 40.000 0.00 0.00 0.00 3.32
3513 6047 3.617284 ACCGATGGACAAAGGGAATTAC 58.383 45.455 0.00 0.00 0.00 1.89
3519 6053 2.710096 ACATACCGATGGACAAAGGG 57.290 50.000 0.00 0.00 37.39 3.95
3544 6078 1.215655 CCGACGATCGAATCTTGGGC 61.216 60.000 24.34 0.00 43.74 5.36
3601 6135 8.969267 GTGATGTATTATGGAACGAGTAAAGAG 58.031 37.037 0.00 0.00 0.00 2.85
3616 6150 8.204836 GGAGTTAGTCACAAGGTGATGTATTAT 58.795 37.037 2.02 0.00 44.63 1.28
3670 6204 2.343484 GGGCCCTCTTGGTAATACAC 57.657 55.000 17.04 0.00 36.04 2.90


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

AutoCloner maintained by Alex Coulton.