Multiple sequence alignment - TraesCS5D01G226600

Loading Multiple Alignment...

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 TraesCS5D01G226600 chr5D 100.000 7594 0 0 1 7594 334888656 334896249 0.000000e+00 14024.0
1 TraesCS5D01G226600 chr5D 82.339 2146 317 39 1942 4073 49151298 49149201 0.000000e+00 1807.0
2 TraesCS5D01G226600 chr5D 86.209 1356 177 7 1942 3292 370838604 370839954 0.000000e+00 1459.0
3 TraesCS5D01G226600 chr5D 85.851 1357 188 4 1942 3296 370826821 370828175 0.000000e+00 1439.0
4 TraesCS5D01G226600 chr5D 81.039 770 113 24 3365 4123 370839985 370840732 3.950000e-162 582.0
5 TraesCS5D01G226600 chr5D 80.485 743 111 26 3346 4075 370828192 370828913 8.670000e-149 538.0
6 TraesCS5D01G226600 chr5D 83.495 515 69 3 4485 4995 370841235 370841737 4.150000e-127 466.0
7 TraesCS5D01G226600 chr5D 84.829 468 55 10 4532 4995 370829165 370829620 2.500000e-124 457.0
8 TraesCS5D01G226600 chr5D 82.101 514 77 9 4485 4995 49148879 49148378 7.040000e-115 425.0
9 TraesCS5D01G226600 chr5D 78.216 482 89 13 6127 6605 370830371 370830839 2.070000e-75 294.0
10 TraesCS5D01G226600 chr5B 97.012 5757 137 19 1730 7460 391753025 391758772 0.000000e+00 9646.0
11 TraesCS5D01G226600 chr5B 82.665 2221 318 45 1924 4121 440210934 440213110 0.000000e+00 1906.0
12 TraesCS5D01G226600 chr5B 82.051 2145 326 38 1942 4073 51860919 51858821 0.000000e+00 1773.0
13 TraesCS5D01G226600 chr5B 82.975 1533 234 17 1924 3450 440185050 440186561 0.000000e+00 1360.0
14 TraesCS5D01G226600 chr5B 95.455 814 30 5 823 1632 391752205 391753015 0.000000e+00 1291.0
15 TraesCS5D01G226600 chr5B 90.146 893 52 12 1 861 391751317 391752205 0.000000e+00 1129.0
16 TraesCS5D01G226600 chr5B 83.876 614 84 11 2693 3300 440227728 440228332 8.550000e-159 571.0
17 TraesCS5D01G226600 chr5B 80.207 773 109 25 3365 4123 440228354 440229096 2.410000e-149 540.0
18 TraesCS5D01G226600 chr5B 80.837 621 86 22 3520 4122 440186666 440187271 2.500000e-124 457.0
19 TraesCS5D01G226600 chr5B 83.107 515 68 6 4485 4995 440234861 440235360 1.160000e-122 451.0
20 TraesCS5D01G226600 chr5B 82.685 514 74 9 4485 4995 51858500 51857999 6.990000e-120 442.0
21 TraesCS5D01G226600 chr5B 81.042 480 74 7 4518 4992 440213462 440213929 4.330000e-97 366.0
22 TraesCS5D01G226600 chr5B 81.679 131 17 5 123 249 233489659 233489786 1.350000e-17 102.0
23 TraesCS5D01G226600 chr5A 96.569 5596 118 24 1898 7460 436286531 436292085 0.000000e+00 9202.0
24 TraesCS5D01G226600 chr5A 82.471 2145 299 49 1942 4073 38779129 38777049 0.000000e+00 1807.0
25 TraesCS5D01G226600 chr5A 85.693 1356 184 6 1942 3292 473619917 473621267 0.000000e+00 1421.0
26 TraesCS5D01G226600 chr5A 84.593 1350 204 4 1948 3295 473418085 473419432 0.000000e+00 1338.0
27 TraesCS5D01G226600 chr5A 93.908 476 26 2 1386 1858 436286066 436286541 0.000000e+00 715.0
28 TraesCS5D01G226600 chr5A 88.273 631 16 9 763 1372 436284139 436284732 0.000000e+00 702.0
29 TraesCS5D01G226600 chr5A 80.649 770 113 26 3365 4123 473621298 473622042 1.430000e-156 564.0
30 TraesCS5D01G226600 chr5A 81.302 722 105 25 3346 4058 473419450 473420150 6.660000e-155 558.0
31 TraesCS5D01G226600 chr5A 83.883 515 67 3 4485 4995 473622724 473623226 1.920000e-130 477.0
32 TraesCS5D01G226600 chr5A 90.087 343 31 3 1 343 436282977 436283316 6.990000e-120 442.0
33 TraesCS5D01G226600 chr5A 82.752 516 67 16 4485 4995 38776725 38776227 2.520000e-119 440.0
34 TraesCS5D01G226600 chr5A 84.632 475 37 10 315 757 436283607 436284077 2.520000e-119 440.0
35 TraesCS5D01G226600 chr5A 84.188 468 57 11 4532 4995 473429168 473429622 9.050000e-119 438.0
36 TraesCS5D01G226600 chr5A 78.468 483 86 14 6127 6605 473430331 473430799 4.450000e-77 300.0
37 TraesCS5D01G226600 chr5A 94.444 54 2 1 294 347 436283633 436283685 1.760000e-11 82.4
38 TraesCS5D01G226600 chr5A 100.000 33 0 0 7483 7515 609874654 609874686 2.290000e-05 62.1
39 TraesCS5D01G226600 chr5A 94.737 38 2 0 1479 1516 436286108 436286145 8.230000e-05 60.2
40 TraesCS5D01G226600 chr6D 92.424 66 3 2 5256 5319 182993341 182993276 8.110000e-15 93.5
41 TraesCS5D01G226600 chr6A 92.424 66 3 2 5256 5319 578219287 578219222 8.110000e-15 93.5
42 TraesCS5D01G226600 chr6A 92.424 66 3 2 5256 5319 597231518 597231583 8.110000e-15 93.5
43 TraesCS5D01G226600 chr4A 92.424 66 3 2 5256 5319 295266177 295266112 8.110000e-15 93.5
44 TraesCS5D01G226600 chr4A 90.909 44 3 1 4228 4271 534781615 534781573 2.960000e-04 58.4
45 TraesCS5D01G226600 chr3B 92.424 66 3 2 5256 5319 201595210 201595275 8.110000e-15 93.5
46 TraesCS5D01G226600 chr3B 93.182 44 3 0 4228 4271 684251660 684251703 1.770000e-06 65.8
47 TraesCS5D01G226600 chrUn 88.889 72 6 2 5250 5319 282365200 282365271 3.770000e-13 87.9
48 TraesCS5D01G226600 chr1B 89.041 73 5 3 5256 5325 668813366 668813438 3.770000e-13 87.9
49 TraesCS5D01G226600 chr1B 100.000 33 0 0 7483 7515 510601284 510601252 2.290000e-05 62.1
50 TraesCS5D01G226600 chr3D 92.308 52 2 2 5836 5886 266427019 266427069 1.060000e-08 73.1
51 TraesCS5D01G226600 chr3D 100.000 33 0 0 7483 7515 483176040 483176072 2.290000e-05 62.1
52 TraesCS5D01G226600 chr3A 92.308 52 2 2 5836 5886 301143303 301143353 1.060000e-08 73.1
53 TraesCS5D01G226600 chr7D 97.561 41 1 0 5841 5881 141356416 141356376 3.800000e-08 71.3
54 TraesCS5D01G226600 chr7D 89.091 55 3 2 5835 5886 127000927 127000981 1.770000e-06 65.8
55 TraesCS5D01G226600 chr7D 100.000 33 0 0 7483 7515 6817260 6817228 2.290000e-05 62.1
56 TraesCS5D01G226600 chr6B 91.837 49 4 0 4223 4271 664222689 664222737 1.370000e-07 69.4
57 TraesCS5D01G226600 chr6B 87.273 55 7 0 621 675 495430358 495430412 6.360000e-06 63.9
58 TraesCS5D01G226600 chr4B 95.455 44 1 1 4228 4271 91337719 91337761 1.370000e-07 69.4
59 TraesCS5D01G226600 chr4B 97.368 38 1 0 7483 7520 568601656 568601693 1.770000e-06 65.8
60 TraesCS5D01G226600 chr4B 100.000 33 0 0 7483 7515 19987502 19987534 2.290000e-05 62.1
61 TraesCS5D01G226600 chr1D 95.349 43 1 1 5837 5879 22976619 22976578 4.920000e-07 67.6
62 TraesCS5D01G226600 chr2D 93.333 45 2 1 5836 5880 35799968 35800011 1.770000e-06 65.8
63 TraesCS5D01G226600 chr2D 100.000 33 0 0 7483 7515 626409016 626409048 2.290000e-05 62.1
64 TraesCS5D01G226600 chr2B 91.667 48 3 1 5841 5888 775028720 775028674 1.770000e-06 65.8
65 TraesCS5D01G226600 chr4D 93.023 43 3 0 7477 7519 38445387 38445345 6.360000e-06 63.9
66 TraesCS5D01G226600 chr4D 100.000 33 0 0 7483 7515 19442613 19442645 2.290000e-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 TraesCS5D01G226600 chr5D 334888656 334896249 7593 False 14024.000000 14024 100.000000 1 7594 1 chr5D.!!$F1 7593
1 TraesCS5D01G226600 chr5D 49148378 49151298 2920 True 1116.000000 1807 82.220000 1942 4995 2 chr5D.!!$R1 3053
2 TraesCS5D01G226600 chr5D 370838604 370841737 3133 False 835.666667 1459 83.581000 1942 4995 3 chr5D.!!$F3 3053
3 TraesCS5D01G226600 chr5D 370826821 370830839 4018 False 682.000000 1439 82.345250 1942 6605 4 chr5D.!!$F2 4663
4 TraesCS5D01G226600 chr5B 391751317 391758772 7455 False 4022.000000 9646 94.204333 1 7460 3 chr5B.!!$F3 7459
5 TraesCS5D01G226600 chr5B 440210934 440213929 2995 False 1136.000000 1906 81.853500 1924 4992 2 chr5B.!!$F5 3068
6 TraesCS5D01G226600 chr5B 51857999 51860919 2920 True 1107.500000 1773 82.368000 1942 4995 2 chr5B.!!$R1 3053
7 TraesCS5D01G226600 chr5B 440185050 440187271 2221 False 908.500000 1360 81.906000 1924 4122 2 chr5B.!!$F4 2198
8 TraesCS5D01G226600 chr5B 440227728 440229096 1368 False 555.500000 571 82.041500 2693 4123 2 chr5B.!!$F6 1430
9 TraesCS5D01G226600 chr5A 436282977 436292085 9108 False 1663.371429 9202 91.807143 1 7460 7 chr5A.!!$F2 7459
10 TraesCS5D01G226600 chr5A 38776227 38779129 2902 True 1123.500000 1807 82.611500 1942 4995 2 chr5A.!!$R1 3053
11 TraesCS5D01G226600 chr5A 473418085 473420150 2065 False 948.000000 1338 82.947500 1948 4058 2 chr5A.!!$F3 2110
12 TraesCS5D01G226600 chr5A 473619917 473623226 3309 False 820.666667 1421 83.408333 1942 4995 3 chr5A.!!$F5 3053
13 TraesCS5D01G226600 chr5A 473429168 473430799 1631 False 369.000000 438 81.328000 4532 6605 2 chr5A.!!$F4 2073

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
879 1327 1.059264 GTACACGACGAAAGATGCTGC 59.941 52.381 0.00 0.00 0.00 5.25 F
1044 1509 1.173913 ATCTAAAACTTGCGGTGCCC 58.826 50.000 0.00 0.00 0.00 5.36 F
1828 3622 1.129624 GTCACAAGCAACACGAACACA 59.870 47.619 0.00 0.00 0.00 3.72 F
1844 3638 4.726704 CGAACACACAAAAACCTAAACTCG 59.273 41.667 0.00 0.00 0.00 4.18 F
1850 3644 5.047188 CACAAAAACCTAAACTCGCCATTT 58.953 37.500 0.00 0.00 0.00 2.32 F
1895 3689 5.448438 TGTGTTATGATGTTGTTTCTTCGC 58.552 37.500 0.00 0.00 0.00 4.70 F
5056 7390 4.199310 TGAAGTTTGCTAGCAAGTCAAGT 58.801 39.130 27.82 14.77 37.24 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 3600 1.129624 TGTGTTCGTGTTGCTTGTGAC 59.870 47.619 0.00 0.00 0.00 3.67 R
1906 3700 4.514401 AGGAAATTTCGGTCAGATGGTAC 58.486 43.478 11.95 0.00 0.00 3.34 R
3414 5229 4.473444 ACACTGGATGAAAATGTGGAACT 58.527 39.130 0.00 0.00 38.04 3.01 R
4059 5936 2.111756 CGGCGCTTCTTATTTTCATGC 58.888 47.619 7.64 0.00 0.00 4.06 R
5032 7366 5.300286 ACTTGACTTGCTAGCAAACTTCAAT 59.700 36.000 30.22 22.53 35.33 2.57 R
5075 7409 6.070995 ACGTGGTATGTAGAATTGAAGGAGAA 60.071 38.462 0.00 0.00 0.00 2.87 R
7562 10301 0.317160 CGTGCCCTCGAATGCCTATA 59.683 55.000 3.63 0.00 0.00 1.31 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
37 38 1.228033 GTTTACCGGGCCACACAGT 60.228 57.895 6.32 0.00 0.00 3.55
42 43 2.111043 CGGGCCACACAGTCAGTT 59.889 61.111 4.39 0.00 0.00 3.16
64 65 2.125269 GGCGCACCAACTATCGGT 60.125 61.111 10.83 0.00 37.16 4.69
93 94 4.875578 ACCAGTAGTAGTCACCATAGGA 57.124 45.455 0.00 0.00 0.00 2.94
98 99 7.175797 CCAGTAGTAGTCACCATAGGATGATA 58.824 42.308 0.00 0.00 0.00 2.15
102 103 4.833478 AGTCACCATAGGATGATATGCC 57.167 45.455 0.00 0.00 32.74 4.40
118 119 8.798859 ATGATATGCCTGATTGGAAGTATTAC 57.201 34.615 0.00 0.00 38.35 1.89
121 122 5.435686 TGCCTGATTGGAAGTATTACACT 57.564 39.130 0.00 0.00 39.82 3.55
236 238 3.189606 TGTGAGAGGGGATTACAATGGT 58.810 45.455 0.00 0.00 0.00 3.55
256 258 9.330063 CAATGGTGAATAGTAAGCTCTATCAAA 57.670 33.333 0.00 0.00 31.24 2.69
307 309 1.961180 CTAGCCCTGACCCCGTCTTG 61.961 65.000 0.00 0.00 33.15 3.02
318 320 1.207329 CCCCGTCTTGTAAAGGAGGAG 59.793 57.143 4.11 0.00 46.24 3.69
413 736 8.500773 TCAGTTGTTAATTCGTAATCTTTGGAC 58.499 33.333 0.00 0.00 0.00 4.02
430 757 7.375053 TCTTTGGACTTTGTATGCCAAAATAC 58.625 34.615 0.00 0.00 46.30 1.89
454 781 3.692791 AACGTCTCAAAAGCAGGAAAC 57.307 42.857 0.00 0.00 0.00 2.78
506 834 2.159382 CGTTTATTGCACAAGTCCCCT 58.841 47.619 0.00 0.00 0.00 4.79
576 930 6.239887 GCCACCCTTATGTAGATTCCTTATCA 60.240 42.308 0.00 0.00 35.59 2.15
622 976 1.561643 TTCTGCTCTCTTCATCCGGT 58.438 50.000 0.00 0.00 0.00 5.28
629 983 6.042093 TCTGCTCTCTTCATCCGGTTTTATAT 59.958 38.462 0.00 0.00 0.00 0.86
646 1000 6.651975 TTTATATGTTGGACACGGGTTTTT 57.348 33.333 0.00 0.00 0.00 1.94
738 1092 2.050351 CGATAGGGGCAGTACGCG 60.050 66.667 3.53 3.53 43.84 6.01
751 1105 1.204941 AGTACGCGATCTTGCTTCCTT 59.795 47.619 15.93 0.00 0.00 3.36
800 1210 6.520061 AACTACTAGTTTATGCAGAGGCAACA 60.520 38.462 0.00 0.00 44.64 3.33
879 1327 1.059264 GTACACGACGAAAGATGCTGC 59.941 52.381 0.00 0.00 0.00 5.25
1034 1499 6.299141 TCTCAGCACCAAAGAATCTAAAACT 58.701 36.000 0.00 0.00 0.00 2.66
1036 1501 6.738114 TCAGCACCAAAGAATCTAAAACTTG 58.262 36.000 0.00 0.00 0.00 3.16
1037 1502 5.403466 CAGCACCAAAGAATCTAAAACTTGC 59.597 40.000 0.00 0.00 0.00 4.01
1038 1503 4.382754 GCACCAAAGAATCTAAAACTTGCG 59.617 41.667 0.00 0.00 0.00 4.85
1039 1504 4.917415 CACCAAAGAATCTAAAACTTGCGG 59.083 41.667 0.00 0.00 0.00 5.69
1040 1505 4.583073 ACCAAAGAATCTAAAACTTGCGGT 59.417 37.500 0.00 0.00 0.00 5.68
1041 1506 4.917415 CCAAAGAATCTAAAACTTGCGGTG 59.083 41.667 0.00 0.00 0.00 4.94
1042 1507 3.831715 AGAATCTAAAACTTGCGGTGC 57.168 42.857 0.00 0.00 0.00 5.01
1044 1509 1.173913 ATCTAAAACTTGCGGTGCCC 58.826 50.000 0.00 0.00 0.00 5.36
1219 1688 1.675641 AGCATTTCACTGGCCGTCC 60.676 57.895 0.00 0.00 0.00 4.79
1287 1756 2.390696 CATTTCAGGGATTCCATGGCA 58.609 47.619 16.80 0.00 34.83 4.92
1412 3201 8.076178 CCATAGTTTGACACCTTAAACAAGAAG 58.924 37.037 0.00 0.00 38.82 2.85
1624 3413 4.348863 TTGGCAATTGCAAACCATAACT 57.651 36.364 30.32 0.00 44.36 2.24
1625 3414 3.661944 TGGCAATTGCAAACCATAACTG 58.338 40.909 30.32 0.00 44.36 3.16
1637 3426 6.620733 GCAAACCATAACTGACATAGTGACAC 60.621 42.308 0.00 0.00 40.26 3.67
1667 3456 4.284234 CCAAATGAGTCAAATCAAACCCCT 59.716 41.667 0.00 0.00 31.76 4.79
1786 3578 1.537202 GCTTAGGCAAACAGGTGTCAG 59.463 52.381 0.00 0.00 38.54 3.51
1808 3600 9.483062 GTCAGATGATCAAGAAAATAGAAAACG 57.517 33.333 0.00 0.00 0.00 3.60
1827 3621 1.810197 GTCACAAGCAACACGAACAC 58.190 50.000 0.00 0.00 0.00 3.32
1828 3622 1.129624 GTCACAAGCAACACGAACACA 59.870 47.619 0.00 0.00 0.00 3.72
1844 3638 4.726704 CGAACACACAAAAACCTAAACTCG 59.273 41.667 0.00 0.00 0.00 4.18
1850 3644 5.047188 CACAAAAACCTAAACTCGCCATTT 58.953 37.500 0.00 0.00 0.00 2.32
1894 3688 9.773328 ATTATGTGTTATGATGTTGTTTCTTCG 57.227 29.630 0.00 0.00 0.00 3.79
1895 3689 5.448438 TGTGTTATGATGTTGTTTCTTCGC 58.552 37.500 0.00 0.00 0.00 4.70
1904 3698 8.094798 TGATGTTGTTTCTTCGCTATTAAACT 57.905 30.769 0.00 0.00 33.89 2.66
1906 3700 9.690434 GATGTTGTTTCTTCGCTATTAAACTAG 57.310 33.333 0.00 0.00 33.89 2.57
4059 5936 6.696198 CATAGACAAAGTATACGTTGCACTG 58.304 40.000 25.39 16.04 38.59 3.66
4417 6730 9.056005 TGATGGTAAGACTTGCATTTATCATAC 57.944 33.333 5.62 0.00 30.46 2.39
5046 7380 7.647907 AAAAATCTGCATTGAAGTTTGCTAG 57.352 32.000 0.00 0.00 39.60 3.42
5056 7390 4.199310 TGAAGTTTGCTAGCAAGTCAAGT 58.801 39.130 27.82 14.77 37.24 3.16
5075 7409 8.796475 AGTCAAGTAAAATGTTATGCTCATGTT 58.204 29.630 0.00 0.00 0.00 2.71
5098 7432 7.606456 TGTTTCTCCTTCAATTCTACATACCAC 59.394 37.037 0.00 0.00 0.00 4.16
5435 8121 3.316029 TGAGCTGATATTTCCATTTGGCG 59.684 43.478 0.00 0.00 34.44 5.69
6173 8861 4.842531 TGATCTCTTTGGTAATCAGGCA 57.157 40.909 0.00 0.00 0.00 4.75
6362 9050 4.041815 GGGTTATTCCTCCTAACTGGGATC 59.958 50.000 0.00 0.00 34.56 3.36
6455 9143 5.936054 AGCAAAGAAGACGATCAAAATGAG 58.064 37.500 0.00 0.00 0.00 2.90
6611 9305 2.047061 TGACCAGCTACCAGAACAGTT 58.953 47.619 0.00 0.00 0.00 3.16
6616 9310 4.246458 CCAGCTACCAGAACAGTTAGAAC 58.754 47.826 0.00 0.00 0.00 3.01
6676 9370 3.926527 GCAACGTCACTGACTCATATTGA 59.073 43.478 7.58 0.00 0.00 2.57
6681 9375 5.069648 ACGTCACTGACTCATATTGATCCAT 59.930 40.000 7.58 0.00 0.00 3.41
6685 9379 9.499479 GTCACTGACTCATATTGATCCATAAAT 57.501 33.333 1.58 0.00 0.00 1.40
6861 9563 9.573133 CAAAATCAAGTAAAGTTTCAGTCTGTT 57.427 29.630 0.00 0.00 0.00 3.16
6968 9683 8.185505 CACTCCTTGTAGAGACTATTTCTGTAC 58.814 40.741 2.44 2.44 46.74 2.90
7016 9731 0.613777 GAAAGGAGGTGGACGTGGAT 59.386 55.000 0.00 0.00 0.00 3.41
7037 9752 6.652062 TGGATCATCCAATTATCATCACTTCG 59.348 38.462 2.95 0.00 45.00 3.79
7044 9759 5.447144 CCAATTATCATCACTTCGTTTCGCA 60.447 40.000 0.00 0.00 0.00 5.10
7046 9761 2.941891 TCATCACTTCGTTTCGCAAC 57.058 45.000 0.00 0.00 0.00 4.17
7063 9778 2.432444 CAACCTGGAAAATACGAGGCA 58.568 47.619 0.00 0.00 38.94 4.75
7091 9806 1.724582 AACGAACACCTTGGCTGCAC 61.725 55.000 0.50 0.00 0.00 4.57
7102 9817 1.884926 GGCTGCACTATCCGTCTGC 60.885 63.158 0.50 0.00 0.00 4.26
7157 9876 2.163412 TGCAAAATTCCGGTAGCACATC 59.837 45.455 0.00 0.00 0.00 3.06
7177 9896 1.614385 CGCGAACGCATATAGTAGGG 58.386 55.000 18.69 0.00 42.06 3.53
7178 9897 1.731424 CGCGAACGCATATAGTAGGGG 60.731 57.143 18.69 0.00 42.06 4.79
7235 9959 3.058914 AGAGTTCATTTCGGAAGTTTGCG 60.059 43.478 0.00 0.00 43.70 4.85
7271 9995 1.557651 GAATCTCGACGTACCTTGCC 58.442 55.000 0.00 0.00 0.00 4.52
7320 10052 2.833582 GGCTCCTCCATCCGTCGA 60.834 66.667 0.00 0.00 34.01 4.20
7386 10118 3.636231 CGGTGGCAGGTGGAGGAA 61.636 66.667 0.00 0.00 0.00 3.36
7387 10119 2.971598 CGGTGGCAGGTGGAGGAAT 61.972 63.158 0.00 0.00 0.00 3.01
7456 10195 0.392461 GGCCTGGTTCGTCAGCATAA 60.392 55.000 0.00 0.00 33.64 1.90
7468 10207 1.673168 CAGCATAACTGGGAAGGAGC 58.327 55.000 0.00 0.00 43.19 4.70
7469 10208 1.065199 CAGCATAACTGGGAAGGAGCA 60.065 52.381 0.00 0.00 43.19 4.26
7470 10209 1.211457 AGCATAACTGGGAAGGAGCAG 59.789 52.381 0.00 0.00 0.00 4.24
7471 10210 1.748591 GCATAACTGGGAAGGAGCAGG 60.749 57.143 0.00 0.00 0.00 4.85
7472 10211 1.133976 CATAACTGGGAAGGAGCAGGG 60.134 57.143 0.00 0.00 0.00 4.45
7473 10212 0.178873 TAACTGGGAAGGAGCAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
7474 10213 1.783250 AACTGGGAAGGAGCAGGGTG 61.783 60.000 0.00 0.00 0.00 4.61
7475 10214 2.121963 TGGGAAGGAGCAGGGTGT 60.122 61.111 0.00 0.00 0.00 4.16
7476 10215 2.190488 CTGGGAAGGAGCAGGGTGTC 62.190 65.000 0.00 0.00 0.00 3.67
7477 10216 1.920835 GGGAAGGAGCAGGGTGTCT 60.921 63.158 0.00 0.00 0.00 3.41
7478 10217 0.617820 GGGAAGGAGCAGGGTGTCTA 60.618 60.000 0.00 0.00 0.00 2.59
7479 10218 1.276622 GGAAGGAGCAGGGTGTCTAA 58.723 55.000 0.00 0.00 0.00 2.10
7480 10219 1.628846 GGAAGGAGCAGGGTGTCTAAA 59.371 52.381 0.00 0.00 0.00 1.85
7481 10220 2.355209 GGAAGGAGCAGGGTGTCTAAAG 60.355 54.545 0.00 0.00 0.00 1.85
7482 10221 2.031495 AGGAGCAGGGTGTCTAAAGT 57.969 50.000 0.00 0.00 0.00 2.66
7483 10222 1.903183 AGGAGCAGGGTGTCTAAAGTC 59.097 52.381 0.00 0.00 0.00 3.01
7484 10223 1.903183 GGAGCAGGGTGTCTAAAGTCT 59.097 52.381 0.00 0.00 0.00 3.24
7485 10224 3.097614 GGAGCAGGGTGTCTAAAGTCTA 58.902 50.000 0.00 0.00 0.00 2.59
7486 10225 3.514309 GGAGCAGGGTGTCTAAAGTCTAA 59.486 47.826 0.00 0.00 0.00 2.10
7487 10226 4.020485 GGAGCAGGGTGTCTAAAGTCTAAA 60.020 45.833 0.00 0.00 0.00 1.85
7488 10227 4.895961 AGCAGGGTGTCTAAAGTCTAAAC 58.104 43.478 0.00 0.00 0.00 2.01
7489 10228 4.347000 AGCAGGGTGTCTAAAGTCTAAACA 59.653 41.667 0.00 0.00 0.00 2.83
7490 10229 5.013183 AGCAGGGTGTCTAAAGTCTAAACAT 59.987 40.000 0.00 0.00 0.00 2.71
7491 10230 5.705905 GCAGGGTGTCTAAAGTCTAAACATT 59.294 40.000 0.00 0.00 0.00 2.71
7492 10231 6.128254 GCAGGGTGTCTAAAGTCTAAACATTC 60.128 42.308 0.00 0.00 0.00 2.67
7493 10232 7.162082 CAGGGTGTCTAAAGTCTAAACATTCT 58.838 38.462 0.00 0.00 0.00 2.40
7494 10233 7.661847 CAGGGTGTCTAAAGTCTAAACATTCTT 59.338 37.037 0.00 0.00 0.00 2.52
7495 10234 8.877195 AGGGTGTCTAAAGTCTAAACATTCTTA 58.123 33.333 0.00 0.00 0.00 2.10
7496 10235 9.668497 GGGTGTCTAAAGTCTAAACATTCTTAT 57.332 33.333 0.00 0.00 0.00 1.73
7512 10251 8.904099 ACATTCTTATATTTCTTTACGGAGGG 57.096 34.615 0.00 0.00 0.00 4.30
7513 10252 8.711170 ACATTCTTATATTTCTTTACGGAGGGA 58.289 33.333 0.00 0.00 0.00 4.20
7514 10253 9.209175 CATTCTTATATTTCTTTACGGAGGGAG 57.791 37.037 0.00 0.00 0.00 4.30
7515 10254 6.756221 TCTTATATTTCTTTACGGAGGGAGC 58.244 40.000 0.00 0.00 0.00 4.70
7516 10255 6.325545 TCTTATATTTCTTTACGGAGGGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
7517 10256 3.933861 ATTTCTTTACGGAGGGAGCAT 57.066 42.857 0.00 0.00 0.00 3.79
7518 10257 2.691409 TTCTTTACGGAGGGAGCATG 57.309 50.000 0.00 0.00 0.00 4.06
7519 10258 1.568504 TCTTTACGGAGGGAGCATGT 58.431 50.000 0.00 0.00 0.00 3.21
7520 10259 1.480954 TCTTTACGGAGGGAGCATGTC 59.519 52.381 0.00 0.00 0.00 3.06
7521 10260 1.482593 CTTTACGGAGGGAGCATGTCT 59.517 52.381 0.00 0.00 0.00 3.41
7522 10261 1.568504 TTACGGAGGGAGCATGTCTT 58.431 50.000 0.00 0.00 0.00 3.01
7523 10262 2.447408 TACGGAGGGAGCATGTCTTA 57.553 50.000 0.00 0.00 0.00 2.10
7524 10263 1.794714 ACGGAGGGAGCATGTCTTAT 58.205 50.000 0.00 0.00 0.00 1.73
7525 10264 2.119495 ACGGAGGGAGCATGTCTTATT 58.881 47.619 0.00 0.00 0.00 1.40
7526 10265 2.158900 ACGGAGGGAGCATGTCTTATTG 60.159 50.000 0.00 0.00 0.00 1.90
7527 10266 2.103094 CGGAGGGAGCATGTCTTATTGA 59.897 50.000 0.00 0.00 0.00 2.57
7528 10267 3.737850 GGAGGGAGCATGTCTTATTGAG 58.262 50.000 0.00 0.00 0.00 3.02
7529 10268 3.137533 GAGGGAGCATGTCTTATTGAGC 58.862 50.000 0.00 0.00 0.00 4.26
7530 10269 2.158696 AGGGAGCATGTCTTATTGAGCC 60.159 50.000 0.00 0.00 0.00 4.70
7531 10270 2.158696 GGGAGCATGTCTTATTGAGCCT 60.159 50.000 0.00 0.00 0.00 4.58
7532 10271 2.877168 GGAGCATGTCTTATTGAGCCTG 59.123 50.000 0.00 0.00 0.00 4.85
7533 10272 3.539604 GAGCATGTCTTATTGAGCCTGT 58.460 45.455 0.00 0.00 0.00 4.00
7534 10273 3.944015 GAGCATGTCTTATTGAGCCTGTT 59.056 43.478 0.00 0.00 0.00 3.16
7535 10274 5.102953 AGCATGTCTTATTGAGCCTGTTA 57.897 39.130 0.00 0.00 0.00 2.41
7536 10275 5.688807 AGCATGTCTTATTGAGCCTGTTAT 58.311 37.500 0.00 0.00 0.00 1.89
7537 10276 6.125029 AGCATGTCTTATTGAGCCTGTTATT 58.875 36.000 0.00 0.00 0.00 1.40
7538 10277 7.282585 AGCATGTCTTATTGAGCCTGTTATTA 58.717 34.615 0.00 0.00 0.00 0.98
7539 10278 7.941238 AGCATGTCTTATTGAGCCTGTTATTAT 59.059 33.333 0.00 0.00 0.00 1.28
7540 10279 8.571336 GCATGTCTTATTGAGCCTGTTATTATT 58.429 33.333 0.00 0.00 0.00 1.40
7542 10281 9.851686 ATGTCTTATTGAGCCTGTTATTATTCA 57.148 29.630 0.00 0.00 0.00 2.57
7543 10282 9.109393 TGTCTTATTGAGCCTGTTATTATTCAC 57.891 33.333 0.00 0.00 0.00 3.18
7544 10283 9.109393 GTCTTATTGAGCCTGTTATTATTCACA 57.891 33.333 0.00 0.00 0.00 3.58
7545 10284 9.679661 TCTTATTGAGCCTGTTATTATTCACAA 57.320 29.630 0.00 0.00 0.00 3.33
7548 10287 8.986477 ATTGAGCCTGTTATTATTCACAAAAC 57.014 30.769 0.00 0.00 0.00 2.43
7549 10288 7.517614 TGAGCCTGTTATTATTCACAAAACA 57.482 32.000 0.00 0.00 0.00 2.83
7550 10289 7.946207 TGAGCCTGTTATTATTCACAAAACAA 58.054 30.769 0.00 0.00 30.30 2.83
7551 10290 8.584157 TGAGCCTGTTATTATTCACAAAACAAT 58.416 29.630 0.00 0.00 30.30 2.71
7552 10291 8.986477 AGCCTGTTATTATTCACAAAACAATC 57.014 30.769 0.00 0.00 30.30 2.67
7553 10292 8.806146 AGCCTGTTATTATTCACAAAACAATCT 58.194 29.630 0.00 0.00 30.30 2.40
7554 10293 8.863049 GCCTGTTATTATTCACAAAACAATCTG 58.137 33.333 0.00 0.00 30.30 2.90
7555 10294 8.863049 CCTGTTATTATTCACAAAACAATCTGC 58.137 33.333 0.00 0.00 30.30 4.26
7556 10295 8.755696 TGTTATTATTCACAAAACAATCTGCC 57.244 30.769 0.00 0.00 0.00 4.85
7557 10296 8.363390 TGTTATTATTCACAAAACAATCTGCCA 58.637 29.630 0.00 0.00 0.00 4.92
7558 10297 9.202273 GTTATTATTCACAAAACAATCTGCCAA 57.798 29.630 0.00 0.00 0.00 4.52
7559 10298 7.656707 ATTATTCACAAAACAATCTGCCAAC 57.343 32.000 0.00 0.00 0.00 3.77
7560 10299 4.462508 TTCACAAAACAATCTGCCAACA 57.537 36.364 0.00 0.00 0.00 3.33
7561 10300 3.779759 TCACAAAACAATCTGCCAACAC 58.220 40.909 0.00 0.00 0.00 3.32
7562 10301 3.446873 TCACAAAACAATCTGCCAACACT 59.553 39.130 0.00 0.00 0.00 3.55
7563 10302 4.642437 TCACAAAACAATCTGCCAACACTA 59.358 37.500 0.00 0.00 0.00 2.74
7564 10303 5.301551 TCACAAAACAATCTGCCAACACTAT 59.698 36.000 0.00 0.00 0.00 2.12
7565 10304 6.488344 TCACAAAACAATCTGCCAACACTATA 59.512 34.615 0.00 0.00 0.00 1.31
7566 10305 6.803320 CACAAAACAATCTGCCAACACTATAG 59.197 38.462 0.00 0.00 0.00 1.31
7567 10306 6.071952 ACAAAACAATCTGCCAACACTATAGG 60.072 38.462 4.43 0.00 0.00 2.57
7576 10315 3.393800 CCAACACTATAGGCATTCGAGG 58.606 50.000 4.43 0.00 0.00 4.63
7577 10316 3.393800 CAACACTATAGGCATTCGAGGG 58.606 50.000 4.43 0.00 0.00 4.30
7578 10317 1.344763 ACACTATAGGCATTCGAGGGC 59.655 52.381 4.43 4.80 0.00 5.19
7579 10318 1.344438 CACTATAGGCATTCGAGGGCA 59.656 52.381 13.76 2.57 0.00 5.36
7580 10319 1.344763 ACTATAGGCATTCGAGGGCAC 59.655 52.381 13.76 3.90 0.00 5.01
7581 10320 0.317160 TATAGGCATTCGAGGGCACG 59.683 55.000 13.76 0.00 0.00 5.34
7582 10321 1.686325 ATAGGCATTCGAGGGCACGT 61.686 55.000 13.76 0.00 34.70 4.49
7583 10322 1.038681 TAGGCATTCGAGGGCACGTA 61.039 55.000 13.76 0.55 34.70 3.57
7584 10323 1.883084 GGCATTCGAGGGCACGTAG 60.883 63.158 11.73 0.00 34.70 3.51
7585 10324 1.141019 GCATTCGAGGGCACGTAGA 59.859 57.895 5.61 0.00 34.70 2.59
7586 10325 0.459585 GCATTCGAGGGCACGTAGAA 60.460 55.000 5.61 0.00 41.45 2.10
7587 10326 2.004583 CATTCGAGGGCACGTAGAAA 57.995 50.000 0.00 0.00 40.70 2.52
7588 10327 2.550978 CATTCGAGGGCACGTAGAAAT 58.449 47.619 0.00 0.00 40.70 2.17
7589 10328 2.004583 TTCGAGGGCACGTAGAAATG 57.995 50.000 0.00 0.00 35.17 2.32
7590 10329 1.179152 TCGAGGGCACGTAGAAATGA 58.821 50.000 0.00 0.00 34.70 2.57
7591 10330 1.546923 TCGAGGGCACGTAGAAATGAA 59.453 47.619 0.00 0.00 34.70 2.57
7592 10331 2.028839 TCGAGGGCACGTAGAAATGAAA 60.029 45.455 0.00 0.00 34.70 2.69
7593 10332 2.739913 CGAGGGCACGTAGAAATGAAAA 59.260 45.455 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.252072 GATAGTTGGTGCGCCAGGGA 62.252 60.000 20.15 8.79 46.91 4.20
64 65 5.776208 TGGTGACTACTACTGGTTTCATACA 59.224 40.000 0.00 0.00 0.00 2.29
93 94 8.385491 TGTAATACTTCCAATCAGGCATATCAT 58.615 33.333 0.00 0.00 37.29 2.45
98 99 6.006275 AGTGTAATACTTCCAATCAGGCAT 57.994 37.500 0.00 0.00 35.67 4.40
102 103 7.361457 TCCCTAGTGTAATACTTCCAATCAG 57.639 40.000 0.00 0.00 40.89 2.90
118 119 0.888619 TCTTCGTGTGCTCCCTAGTG 59.111 55.000 0.00 0.00 0.00 2.74
121 122 3.695830 AAAATCTTCGTGTGCTCCCTA 57.304 42.857 0.00 0.00 0.00 3.53
165 167 7.597228 CCAAGCAGGAGTAAGGTATTACCTCT 61.597 46.154 15.73 9.54 44.76 3.69
256 258 7.343316 AGACACCTTGCATCTAATCTAGTACTT 59.657 37.037 0.00 0.00 0.00 2.24
261 263 6.403866 AGAGACACCTTGCATCTAATCTAG 57.596 41.667 0.00 0.00 0.00 2.43
268 270 1.484240 GCCTAGAGACACCTTGCATCT 59.516 52.381 0.00 0.00 0.00 2.90
307 309 2.635427 CCTAGGCATCCTCCTCCTTTAC 59.365 54.545 0.00 0.00 37.66 2.01
318 320 2.036089 CTCTTCGTAACCCTAGGCATCC 59.964 54.545 2.05 0.00 0.00 3.51
400 723 5.123186 TGGCATACAAAGTCCAAAGATTACG 59.877 40.000 0.00 0.00 0.00 3.18
430 757 5.418310 TTCCTGCTTTTGAGACGTTAAAG 57.582 39.130 0.00 0.00 33.19 1.85
454 781 3.740044 ATATTTTGTGGAGCGTTGACG 57.260 42.857 0.00 0.00 43.27 4.35
547 901 1.855295 TCTACATAAGGGTGGCGTGA 58.145 50.000 0.00 0.00 0.00 4.35
622 976 6.651975 AAAACCCGTGTCCAACATATAAAA 57.348 33.333 0.00 0.00 0.00 1.52
629 983 2.299521 CCTAAAAACCCGTGTCCAACA 58.700 47.619 0.00 0.00 0.00 3.33
646 1000 7.825270 TGTTTTGTTAGTCAAACTGAAGACCTA 59.175 33.333 0.00 0.00 44.39 3.08
674 1028 9.575702 GGTTTTTAGATTTTTAATTTGACACGC 57.424 29.630 0.00 0.00 0.00 5.34
738 1092 9.860898 ATATAAACAAACAAAGGAAGCAAGATC 57.139 29.630 0.00 0.00 0.00 2.75
751 1105 6.971602 TCGCCAAGAACATATAAACAAACAA 58.028 32.000 0.00 0.00 0.00 2.83
804 1214 6.151144 GCAGCTAAATTACCGGGAATATCAAT 59.849 38.462 13.68 0.00 0.00 2.57
879 1327 8.194104 AGCTGTGACAGATTAGTTGTCTATTAG 58.806 37.037 18.18 2.28 44.08 1.73
1219 1688 0.242825 TGGACCGCGTAGAAGTCTTG 59.757 55.000 4.92 0.00 32.71 3.02
1260 1729 3.282885 GGAATCCCTGAAATGGAGTGTC 58.717 50.000 0.00 0.00 32.81 3.67
1261 1730 2.649312 TGGAATCCCTGAAATGGAGTGT 59.351 45.455 0.00 0.00 32.81 3.55
1262 1731 3.370840 TGGAATCCCTGAAATGGAGTG 57.629 47.619 0.00 0.00 32.81 3.51
1263 1732 3.373438 CCATGGAATCCCTGAAATGGAGT 60.373 47.826 5.56 0.00 35.40 3.85
1287 1756 3.689347 TGATGCAGCCTTTACATCACTT 58.311 40.909 0.00 0.00 43.85 3.16
1468 3257 4.702131 AGGTGTCAAATGCTTGATAACTCC 59.298 41.667 0.00 0.00 44.78 3.85
1606 3395 4.305769 TGTCAGTTATGGTTTGCAATTGC 58.694 39.130 23.69 23.69 42.50 3.56
1624 3413 5.482163 TGGAGAATTGTGTCACTATGTCA 57.518 39.130 4.27 0.00 0.00 3.58
1625 3414 6.801539 TTTGGAGAATTGTGTCACTATGTC 57.198 37.500 4.27 3.50 0.00 3.06
1700 3489 9.283768 TGAAATGATAACACACTCTGTTTACAT 57.716 29.630 0.00 0.00 40.45 2.29
1786 3578 9.267096 GTGACGTTTTCTATTTTCTTGATCATC 57.733 33.333 0.00 0.00 0.00 2.92
1808 3600 1.129624 TGTGTTCGTGTTGCTTGTGAC 59.870 47.619 0.00 0.00 0.00 3.67
1827 3621 3.701532 TGGCGAGTTTAGGTTTTTGTG 57.298 42.857 0.00 0.00 0.00 3.33
1828 3622 4.929819 AATGGCGAGTTTAGGTTTTTGT 57.070 36.364 0.00 0.00 0.00 2.83
1868 3662 9.773328 CGAAGAAACAACATCATAACACATAAT 57.227 29.630 0.00 0.00 0.00 1.28
1892 3686 7.255381 GGTCAGATGGTACTAGTTTAATAGCGA 60.255 40.741 0.00 0.00 0.00 4.93
1894 3688 6.862090 CGGTCAGATGGTACTAGTTTAATAGC 59.138 42.308 0.00 0.00 0.00 2.97
1895 3689 8.162878 TCGGTCAGATGGTACTAGTTTAATAG 57.837 38.462 0.00 0.00 0.00 1.73
1904 3698 5.424252 AGGAAATTTCGGTCAGATGGTACTA 59.576 40.000 11.95 0.00 0.00 1.82
1906 3700 4.514401 AGGAAATTTCGGTCAGATGGTAC 58.486 43.478 11.95 0.00 0.00 3.34
2228 4022 5.479306 TCTTGAAGTGCACTAATGAGGTAC 58.521 41.667 22.01 4.22 0.00 3.34
3414 5229 4.473444 ACACTGGATGAAAATGTGGAACT 58.527 39.130 0.00 0.00 38.04 3.01
4059 5936 2.111756 CGGCGCTTCTTATTTTCATGC 58.888 47.619 7.64 0.00 0.00 4.06
5032 7366 5.300286 ACTTGACTTGCTAGCAAACTTCAAT 59.700 36.000 30.22 22.53 35.33 2.57
5046 7380 7.083858 TGAGCATAACATTTTACTTGACTTGC 58.916 34.615 0.00 0.00 0.00 4.01
5056 7390 8.579850 AGGAGAAACATGAGCATAACATTTTA 57.420 30.769 0.00 0.00 0.00 1.52
5075 7409 6.070995 ACGTGGTATGTAGAATTGAAGGAGAA 60.071 38.462 0.00 0.00 0.00 2.87
5098 7432 6.525578 TGTATATAGCAATCTTAGGGGACG 57.474 41.667 0.00 0.00 0.00 4.79
5185 7520 8.690203 TTTTCATTCAGTCAACTGGAAGATAA 57.310 30.769 10.13 3.43 43.91 1.75
5435 8121 8.954350 AGATTATTTATCATAATCCACTGCAGC 58.046 33.333 15.27 0.00 40.21 5.25
5531 8218 1.341383 GGCTCCTGGAAATGTGACCAT 60.341 52.381 0.00 0.00 35.54 3.55
5980 8668 4.569943 CAGCAGTACCATACTTTCACACT 58.430 43.478 0.00 0.00 36.76 3.55
6173 8861 1.145738 AGTGGTGATTGCTTGGGAAGT 59.854 47.619 0.00 0.00 0.00 3.01
6362 9050 0.944386 CAAGGGAACAGGTTGTCACG 59.056 55.000 0.00 0.00 0.00 4.35
6455 9143 0.381801 CTTGTTGCCTGTGTCCACAC 59.618 55.000 2.69 2.69 46.59 3.82
6465 9153 3.160269 CTCCATTTTCTCCTTGTTGCCT 58.840 45.455 0.00 0.00 0.00 4.75
6611 9305 5.427157 TCCACAGCCTATATTGTTGGTTCTA 59.573 40.000 0.00 0.00 0.00 2.10
6616 9310 5.009010 GTGAATCCACAGCCTATATTGTTGG 59.991 44.000 0.00 0.00 42.72 3.77
6676 9370 3.074390 TCCCCTGCGAATGATTTATGGAT 59.926 43.478 0.00 0.00 0.00 3.41
6681 9375 2.503765 TGTCTCCCCTGCGAATGATTTA 59.496 45.455 0.00 0.00 0.00 1.40
6685 9379 0.690192 TTTGTCTCCCCTGCGAATGA 59.310 50.000 0.00 0.00 0.00 2.57
6691 9385 3.418684 TTCTACTTTTGTCTCCCCTGC 57.581 47.619 0.00 0.00 0.00 4.85
6976 9691 6.730960 TTCCGTGTGAAAACCTGAATATAC 57.269 37.500 0.00 0.00 0.00 1.47
6979 9694 4.517453 CCTTTCCGTGTGAAAACCTGAATA 59.483 41.667 0.00 0.00 42.25 1.75
7016 9731 7.254421 CGAAACGAAGTGATGATAATTGGATGA 60.254 37.037 0.00 0.00 45.00 2.92
7037 9752 3.058777 TCGTATTTTCCAGGTTGCGAAAC 60.059 43.478 0.00 0.00 0.00 2.78
7044 9759 2.618045 CCTGCCTCGTATTTTCCAGGTT 60.618 50.000 0.00 0.00 36.10 3.50
7046 9761 1.668419 CCTGCCTCGTATTTTCCAGG 58.332 55.000 0.00 0.00 34.54 4.45
7063 9778 3.074412 CAAGGTGTTCGTTAGAATGCCT 58.926 45.455 0.00 0.00 41.62 4.75
7091 9806 1.348064 TTATGGGGGCAGACGGATAG 58.652 55.000 0.00 0.00 0.00 2.08
7102 9817 4.029520 TGATGTGTTGGAATTTATGGGGG 58.970 43.478 0.00 0.00 0.00 5.40
7157 9876 1.614385 CCTACTATATGCGTTCGCGG 58.386 55.000 6.13 1.44 41.67 6.46
7235 9959 0.458543 TTCGATCAGTTCTGCCGAGC 60.459 55.000 13.21 0.00 0.00 5.03
7408 10147 2.190488 GACACCCTGCTCCTTCCCAG 62.190 65.000 0.00 0.00 0.00 4.45
7409 10148 2.121963 ACACCCTGCTCCTTCCCA 60.122 61.111 0.00 0.00 0.00 4.37
7456 10195 2.208349 ACCCTGCTCCTTCCCAGT 59.792 61.111 0.00 0.00 0.00 4.00
7460 10199 1.276622 TTAGACACCCTGCTCCTTCC 58.723 55.000 0.00 0.00 0.00 3.46
7461 10200 2.303311 ACTTTAGACACCCTGCTCCTTC 59.697 50.000 0.00 0.00 0.00 3.46
7462 10201 2.303311 GACTTTAGACACCCTGCTCCTT 59.697 50.000 0.00 0.00 0.00 3.36
7463 10202 1.903183 GACTTTAGACACCCTGCTCCT 59.097 52.381 0.00 0.00 0.00 3.69
7464 10203 1.903183 AGACTTTAGACACCCTGCTCC 59.097 52.381 0.00 0.00 0.00 4.70
7465 10204 4.803098 TTAGACTTTAGACACCCTGCTC 57.197 45.455 0.00 0.00 0.00 4.26
7466 10205 4.347000 TGTTTAGACTTTAGACACCCTGCT 59.653 41.667 0.00 0.00 0.00 4.24
7467 10206 4.638304 TGTTTAGACTTTAGACACCCTGC 58.362 43.478 0.00 0.00 0.00 4.85
7468 10207 7.162082 AGAATGTTTAGACTTTAGACACCCTG 58.838 38.462 0.00 0.00 0.00 4.45
7469 10208 7.317722 AGAATGTTTAGACTTTAGACACCCT 57.682 36.000 0.00 0.00 0.00 4.34
7470 10209 7.981102 AAGAATGTTTAGACTTTAGACACCC 57.019 36.000 0.00 0.00 0.00 4.61
7486 10225 9.338622 CCCTCCGTAAAGAAATATAAGAATGTT 57.661 33.333 0.00 0.00 0.00 2.71
7487 10226 8.711170 TCCCTCCGTAAAGAAATATAAGAATGT 58.289 33.333 0.00 0.00 0.00 2.71
7488 10227 9.209175 CTCCCTCCGTAAAGAAATATAAGAATG 57.791 37.037 0.00 0.00 0.00 2.67
7489 10228 7.878644 GCTCCCTCCGTAAAGAAATATAAGAAT 59.121 37.037 0.00 0.00 0.00 2.40
7490 10229 7.147620 TGCTCCCTCCGTAAAGAAATATAAGAA 60.148 37.037 0.00 0.00 0.00 2.52
7491 10230 6.325545 TGCTCCCTCCGTAAAGAAATATAAGA 59.674 38.462 0.00 0.00 0.00 2.10
7492 10231 6.522054 TGCTCCCTCCGTAAAGAAATATAAG 58.478 40.000 0.00 0.00 0.00 1.73
7493 10232 6.488769 TGCTCCCTCCGTAAAGAAATATAA 57.511 37.500 0.00 0.00 0.00 0.98
7494 10233 6.042781 ACATGCTCCCTCCGTAAAGAAATATA 59.957 38.462 0.00 0.00 0.00 0.86
7495 10234 5.163195 ACATGCTCCCTCCGTAAAGAAATAT 60.163 40.000 0.00 0.00 0.00 1.28
7496 10235 4.163458 ACATGCTCCCTCCGTAAAGAAATA 59.837 41.667 0.00 0.00 0.00 1.40
7497 10236 3.054361 ACATGCTCCCTCCGTAAAGAAAT 60.054 43.478 0.00 0.00 0.00 2.17
7498 10237 2.304761 ACATGCTCCCTCCGTAAAGAAA 59.695 45.455 0.00 0.00 0.00 2.52
7499 10238 1.906574 ACATGCTCCCTCCGTAAAGAA 59.093 47.619 0.00 0.00 0.00 2.52
7500 10239 1.480954 GACATGCTCCCTCCGTAAAGA 59.519 52.381 0.00 0.00 0.00 2.52
7501 10240 1.482593 AGACATGCTCCCTCCGTAAAG 59.517 52.381 0.00 0.00 0.00 1.85
7502 10241 1.568504 AGACATGCTCCCTCCGTAAA 58.431 50.000 0.00 0.00 0.00 2.01
7503 10242 1.568504 AAGACATGCTCCCTCCGTAA 58.431 50.000 0.00 0.00 0.00 3.18
7504 10243 2.447408 TAAGACATGCTCCCTCCGTA 57.553 50.000 0.00 0.00 0.00 4.02
7505 10244 1.794714 ATAAGACATGCTCCCTCCGT 58.205 50.000 0.00 0.00 0.00 4.69
7506 10245 2.103094 TCAATAAGACATGCTCCCTCCG 59.897 50.000 0.00 0.00 0.00 4.63
7507 10246 3.737850 CTCAATAAGACATGCTCCCTCC 58.262 50.000 0.00 0.00 0.00 4.30
7508 10247 3.137533 GCTCAATAAGACATGCTCCCTC 58.862 50.000 0.00 0.00 0.00 4.30
7509 10248 2.158696 GGCTCAATAAGACATGCTCCCT 60.159 50.000 0.00 0.00 30.88 4.20
7510 10249 2.158696 AGGCTCAATAAGACATGCTCCC 60.159 50.000 0.00 0.00 34.25 4.30
7511 10250 2.877168 CAGGCTCAATAAGACATGCTCC 59.123 50.000 0.00 0.00 34.25 4.70
7512 10251 3.539604 ACAGGCTCAATAAGACATGCTC 58.460 45.455 0.00 0.00 34.25 4.26
7513 10252 3.641434 ACAGGCTCAATAAGACATGCT 57.359 42.857 0.00 0.00 34.25 3.79
7514 10253 6.382869 AATAACAGGCTCAATAAGACATGC 57.617 37.500 0.00 0.00 34.25 4.06
7516 10255 9.851686 TGAATAATAACAGGCTCAATAAGACAT 57.148 29.630 0.00 0.00 34.25 3.06
7517 10256 9.109393 GTGAATAATAACAGGCTCAATAAGACA 57.891 33.333 0.00 0.00 34.25 3.41
7518 10257 9.109393 TGTGAATAATAACAGGCTCAATAAGAC 57.891 33.333 0.00 0.00 0.00 3.01
7519 10258 9.679661 TTGTGAATAATAACAGGCTCAATAAGA 57.320 29.630 0.00 0.00 0.00 2.10
7523 10262 8.584157 TGTTTTGTGAATAATAACAGGCTCAAT 58.416 29.630 0.00 0.00 0.00 2.57
7524 10263 7.946207 TGTTTTGTGAATAATAACAGGCTCAA 58.054 30.769 0.00 0.00 0.00 3.02
7525 10264 7.517614 TGTTTTGTGAATAATAACAGGCTCA 57.482 32.000 0.00 0.00 0.00 4.26
7526 10265 8.986477 ATTGTTTTGTGAATAATAACAGGCTC 57.014 30.769 0.00 0.00 31.19 4.70
7527 10266 8.806146 AGATTGTTTTGTGAATAATAACAGGCT 58.194 29.630 0.00 0.00 31.19 4.58
7528 10267 8.863049 CAGATTGTTTTGTGAATAATAACAGGC 58.137 33.333 0.00 0.00 31.19 4.85
7529 10268 8.863049 GCAGATTGTTTTGTGAATAATAACAGG 58.137 33.333 0.00 0.00 31.19 4.00
7530 10269 8.863049 GGCAGATTGTTTTGTGAATAATAACAG 58.137 33.333 0.00 0.00 31.19 3.16
7531 10270 8.363390 TGGCAGATTGTTTTGTGAATAATAACA 58.637 29.630 0.00 0.00 0.00 2.41
7532 10271 8.755696 TGGCAGATTGTTTTGTGAATAATAAC 57.244 30.769 0.00 0.00 0.00 1.89
7533 10272 9.202273 GTTGGCAGATTGTTTTGTGAATAATAA 57.798 29.630 0.00 0.00 0.00 1.40
7534 10273 8.363390 TGTTGGCAGATTGTTTTGTGAATAATA 58.637 29.630 0.00 0.00 0.00 0.98
7535 10274 7.171337 GTGTTGGCAGATTGTTTTGTGAATAAT 59.829 33.333 0.00 0.00 0.00 1.28
7536 10275 6.478344 GTGTTGGCAGATTGTTTTGTGAATAA 59.522 34.615 0.00 0.00 0.00 1.40
7537 10276 5.982516 GTGTTGGCAGATTGTTTTGTGAATA 59.017 36.000 0.00 0.00 0.00 1.75
7538 10277 4.810491 GTGTTGGCAGATTGTTTTGTGAAT 59.190 37.500 0.00 0.00 0.00 2.57
7539 10278 4.081752 AGTGTTGGCAGATTGTTTTGTGAA 60.082 37.500 0.00 0.00 0.00 3.18
7540 10279 3.446873 AGTGTTGGCAGATTGTTTTGTGA 59.553 39.130 0.00 0.00 0.00 3.58
7541 10280 3.784338 AGTGTTGGCAGATTGTTTTGTG 58.216 40.909 0.00 0.00 0.00 3.33
7542 10281 5.789643 ATAGTGTTGGCAGATTGTTTTGT 57.210 34.783 0.00 0.00 0.00 2.83
7543 10282 6.324819 CCTATAGTGTTGGCAGATTGTTTTG 58.675 40.000 0.00 0.00 0.00 2.44
7544 10283 5.105756 GCCTATAGTGTTGGCAGATTGTTTT 60.106 40.000 7.45 0.00 46.41 2.43
7545 10284 4.399303 GCCTATAGTGTTGGCAGATTGTTT 59.601 41.667 7.45 0.00 46.41 2.83
7546 10285 3.947834 GCCTATAGTGTTGGCAGATTGTT 59.052 43.478 7.45 0.00 46.41 2.83
7547 10286 3.545703 GCCTATAGTGTTGGCAGATTGT 58.454 45.455 7.45 0.00 46.41 2.71
7555 10294 3.393800 CCTCGAATGCCTATAGTGTTGG 58.606 50.000 0.00 0.00 0.00 3.77
7556 10295 3.393800 CCCTCGAATGCCTATAGTGTTG 58.606 50.000 0.00 0.00 0.00 3.33
7557 10296 2.224305 GCCCTCGAATGCCTATAGTGTT 60.224 50.000 0.00 0.00 0.00 3.32
7558 10297 1.344763 GCCCTCGAATGCCTATAGTGT 59.655 52.381 0.00 0.00 0.00 3.55
7559 10298 1.344438 TGCCCTCGAATGCCTATAGTG 59.656 52.381 0.00 0.00 0.00 2.74
7560 10299 1.344763 GTGCCCTCGAATGCCTATAGT 59.655 52.381 0.00 0.00 0.00 2.12
7561 10300 1.670087 CGTGCCCTCGAATGCCTATAG 60.670 57.143 3.63 0.00 0.00 1.31
7562 10301 0.317160 CGTGCCCTCGAATGCCTATA 59.683 55.000 3.63 0.00 0.00 1.31
7563 10302 1.069765 CGTGCCCTCGAATGCCTAT 59.930 57.895 3.63 0.00 0.00 2.57
7564 10303 1.038681 TACGTGCCCTCGAATGCCTA 61.039 55.000 0.00 0.00 34.70 3.93
7565 10304 2.298158 CTACGTGCCCTCGAATGCCT 62.298 60.000 0.00 0.00 34.70 4.75
7566 10305 1.883084 CTACGTGCCCTCGAATGCC 60.883 63.158 0.00 0.00 34.70 4.40
7567 10306 0.459585 TTCTACGTGCCCTCGAATGC 60.460 55.000 0.00 0.00 34.70 3.56
7568 10307 2.004583 TTTCTACGTGCCCTCGAATG 57.995 50.000 0.00 0.00 34.70 2.67
7569 10308 2.167693 TCATTTCTACGTGCCCTCGAAT 59.832 45.455 0.00 0.00 34.70 3.34
7570 10309 1.546923 TCATTTCTACGTGCCCTCGAA 59.453 47.619 0.00 0.00 34.70 3.71
7571 10310 1.179152 TCATTTCTACGTGCCCTCGA 58.821 50.000 0.00 0.00 34.70 4.04
7572 10311 2.004583 TTCATTTCTACGTGCCCTCG 57.995 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.