Multiple sequence alignment - TraesCS2B01G461500

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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 TraesCS2B01G461500 chr2B 100.000 4745 0 0 1 4745 655018155 655013411 0.000000e+00 8763.0
1 TraesCS2B01G461500 chr2B 90.833 840 70 3 105 944 5535499 5536331 0.000000e+00 1118.0
2 TraesCS2B01G461500 chr2B 82.086 441 59 10 4309 4743 55229667 55230093 4.510000e-95 359.0
3 TraesCS2B01G461500 chr2B 78.548 606 87 22 4158 4745 800457762 800457182 4.510000e-95 359.0
4 TraesCS2B01G461500 chr2B 87.582 153 19 0 3929 4081 55229276 55229428 1.360000e-40 178.0
5 TraesCS2B01G461500 chr2D 93.680 2927 116 34 944 3850 548086677 548083800 0.000000e+00 4316.0
6 TraesCS2B01G461500 chr2D 91.637 837 68 2 108 943 97083825 97082990 0.000000e+00 1157.0
7 TraesCS2B01G461500 chr2D 85.988 835 68 16 3933 4745 437665018 437665825 0.000000e+00 848.0
8 TraesCS2B01G461500 chr2A 91.340 2448 152 25 1351 3777 690923966 690926374 0.000000e+00 3291.0
9 TraesCS2B01G461500 chr2A 88.564 411 23 9 945 1348 690923531 690923924 1.190000e-130 477.0
10 TraesCS2B01G461500 chr2A 86.525 141 19 0 3927 4067 710764858 710764718 6.360000e-34 156.0
11 TraesCS2B01G461500 chr7B 96.182 943 34 1 1 943 93442809 93441869 0.000000e+00 1541.0
12 TraesCS2B01G461500 chr1B 96.076 943 36 1 1 943 623882533 623883474 0.000000e+00 1535.0
13 TraesCS2B01G461500 chr1B 85.106 141 20 1 3926 4065 661866081 661865941 4.950000e-30 143.0
14 TraesCS2B01G461500 chr5B 96.429 924 33 0 1 924 622525055 622525978 0.000000e+00 1524.0
15 TraesCS2B01G461500 chr5B 94.698 943 35 1 1 943 662870756 662871683 0.000000e+00 1450.0
16 TraesCS2B01G461500 chr3B 95.455 946 42 1 1 946 21766825 21767769 0.000000e+00 1507.0
17 TraesCS2B01G461500 chr4A 93.095 840 55 2 104 943 456588789 456589625 0.000000e+00 1227.0
18 TraesCS2B01G461500 chr4A 88.889 99 8 1 4650 4745 67872329 67872231 8.340000e-23 119.0
19 TraesCS2B01G461500 chr1D 90.442 837 73 4 105 940 471617411 471618241 0.000000e+00 1096.0
20 TraesCS2B01G461500 chr7D 88.591 596 51 8 4158 4745 461239638 461240224 0.000000e+00 708.0
21 TraesCS2B01G461500 chr7D 98.000 50 1 0 4091 4140 461239590 461239639 2.350000e-13 87.9
22 TraesCS2B01G461500 chr6D 86.279 481 55 6 1349 1826 251262180 251261708 3.270000e-141 512.0
23 TraesCS2B01G461500 chr6D 83.673 147 17 5 1209 1349 251262364 251262219 1.070000e-26 132.0
24 TraesCS2B01G461500 chr6D 94.444 72 4 0 1 72 97735798 97735869 1.400000e-20 111.0
25 TraesCS2B01G461500 chr6D 94.444 72 4 0 1 72 115576532 115576461 1.400000e-20 111.0
26 TraesCS2B01G461500 chr6D 94.444 72 4 0 1 72 322578334 322578405 1.400000e-20 111.0
27 TraesCS2B01G461500 chr6D 94.444 54 3 0 1199 1252 447841025 447841078 3.040000e-12 84.2
28 TraesCS2B01G461500 chr4B 78.121 841 106 49 3920 4745 227032035 227032812 3.350000e-126 462.0
29 TraesCS2B01G461500 chr3A 88.554 332 20 7 4418 4745 201477851 201478168 2.070000e-103 387.0
30 TraesCS2B01G461500 chr3A 93.082 159 11 0 3932 4090 201476397 201476555 2.860000e-57 233.0
31 TraesCS2B01G461500 chr3A 92.857 154 9 2 4215 4366 201477856 201477703 6.180000e-54 222.0
32 TraesCS2B01G461500 chr3A 76.880 359 51 17 3926 4259 143139278 143138927 1.760000e-39 174.0
33 TraesCS2B01G461500 chr3A 91.111 90 8 0 4091 4180 201477555 201477644 6.450000e-24 122.0
34 TraesCS2B01G461500 chr3D 81.846 325 30 12 3926 4227 131004968 131004650 3.670000e-61 246.0
35 TraesCS2B01G461500 chr7A 85.621 153 21 1 3929 4081 126019310 126019159 4.910000e-35 159.0
36 TraesCS2B01G461500 chr7A 90.909 99 6 2 4650 4745 539831262 539831164 3.850000e-26 130.0
37 TraesCS2B01G461500 chrUn 88.889 99 8 2 4650 4745 81661845 81661943 8.340000e-23 119.0
38 TraesCS2B01G461500 chr6A 88.889 99 8 1 4650 4745 546925717 546925815 8.340000e-23 119.0
39 TraesCS2B01G461500 chr6A 94.444 54 3 0 1199 1252 594430434 594430487 3.040000e-12 84.2
40 TraesCS2B01G461500 chr4D 94.444 72 4 0 1 72 414600269 414600340 1.400000e-20 111.0
41 TraesCS2B01G461500 chr6B 93.103 58 4 0 1199 1256 678661345 678661402 8.460000e-13 86.1


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 TraesCS2B01G461500 chr2B 655013411 655018155 4744 True 8763.000000 8763 100.000000 1 4745 1 chr2B.!!$R1 4744
1 TraesCS2B01G461500 chr2B 5535499 5536331 832 False 1118.000000 1118 90.833000 105 944 1 chr2B.!!$F1 839
2 TraesCS2B01G461500 chr2B 800457182 800457762 580 True 359.000000 359 78.548000 4158 4745 1 chr2B.!!$R2 587
3 TraesCS2B01G461500 chr2B 55229276 55230093 817 False 268.500000 359 84.834000 3929 4743 2 chr2B.!!$F2 814
4 TraesCS2B01G461500 chr2D 548083800 548086677 2877 True 4316.000000 4316 93.680000 944 3850 1 chr2D.!!$R2 2906
5 TraesCS2B01G461500 chr2D 97082990 97083825 835 True 1157.000000 1157 91.637000 108 943 1 chr2D.!!$R1 835
6 TraesCS2B01G461500 chr2D 437665018 437665825 807 False 848.000000 848 85.988000 3933 4745 1 chr2D.!!$F1 812
7 TraesCS2B01G461500 chr2A 690923531 690926374 2843 False 1884.000000 3291 89.952000 945 3777 2 chr2A.!!$F1 2832
8 TraesCS2B01G461500 chr7B 93441869 93442809 940 True 1541.000000 1541 96.182000 1 943 1 chr7B.!!$R1 942
9 TraesCS2B01G461500 chr1B 623882533 623883474 941 False 1535.000000 1535 96.076000 1 943 1 chr1B.!!$F1 942
10 TraesCS2B01G461500 chr5B 622525055 622525978 923 False 1524.000000 1524 96.429000 1 924 1 chr5B.!!$F1 923
11 TraesCS2B01G461500 chr5B 662870756 662871683 927 False 1450.000000 1450 94.698000 1 943 1 chr5B.!!$F2 942
12 TraesCS2B01G461500 chr3B 21766825 21767769 944 False 1507.000000 1507 95.455000 1 946 1 chr3B.!!$F1 945
13 TraesCS2B01G461500 chr4A 456588789 456589625 836 False 1227.000000 1227 93.095000 104 943 1 chr4A.!!$F1 839
14 TraesCS2B01G461500 chr1D 471617411 471618241 830 False 1096.000000 1096 90.442000 105 940 1 chr1D.!!$F1 835
15 TraesCS2B01G461500 chr7D 461239590 461240224 634 False 397.950000 708 93.295500 4091 4745 2 chr7D.!!$F1 654
16 TraesCS2B01G461500 chr6D 251261708 251262364 656 True 322.000000 512 84.976000 1209 1826 2 chr6D.!!$R2 617
17 TraesCS2B01G461500 chr4B 227032035 227032812 777 False 462.000000 462 78.121000 3920 4745 1 chr4B.!!$F1 825
18 TraesCS2B01G461500 chr3A 201476397 201478168 1771 False 247.333333 387 90.915667 3932 4745 3 chr3A.!!$F1 813

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
875 877 0.597637 CGAAACAGTCAGCTCGGTGT 60.598 55.0 0.00 0.0 0.00 4.16 F
1703 1765 1.085091 GTGCACTGAATCAGCTCCAG 58.915 55.0 10.32 0.0 34.37 3.86 F
2848 2920 0.398522 TCAGGCTCCGGTATCCATGT 60.399 55.0 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 2824 0.674581 TCAATTGGACTGCAGCCTCG 60.675 55.0 22.36 11.58 0.00 4.63 R
3530 3608 0.238553 GCAGAGGCACCGAAAGAAAC 59.761 55.0 0.00 0.00 40.72 2.78 R
3858 3953 0.035056 AGATCACCGCCCAAGAAAGG 60.035 55.0 0.00 0.00 0.00 3.11 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
436 438 4.685169 AAGTACACATTATGCAGTGCAC 57.315 40.909 22.44 9.40 43.04 4.57
463 465 2.907634 TGTAGGCTGAAAACACGTCAA 58.092 42.857 0.00 0.00 0.00 3.18
675 677 6.132791 TGCACGGATTAAAAGTTACAACAA 57.867 33.333 0.00 0.00 0.00 2.83
760 762 1.965930 CTAGGCGCTGCACAACCAA 60.966 57.895 7.64 0.00 0.00 3.67
798 800 4.953868 CGTTGGACCGGCGTGTGA 62.954 66.667 6.01 0.00 0.00 3.58
875 877 0.597637 CGAAACAGTCAGCTCGGTGT 60.598 55.000 0.00 0.00 0.00 4.16
1262 1269 3.764466 CAAGGTCCGCCTCGCTCT 61.764 66.667 0.00 0.00 46.33 4.09
1263 1270 2.044252 AAGGTCCGCCTCGCTCTA 60.044 61.111 0.00 0.00 46.33 2.43
1264 1271 2.416432 AAGGTCCGCCTCGCTCTAC 61.416 63.158 0.00 0.00 46.33 2.59
1266 1273 2.416432 GGTCCGCCTCGCTCTACTT 61.416 63.158 0.00 0.00 0.00 2.24
1267 1274 1.099879 GGTCCGCCTCGCTCTACTTA 61.100 60.000 0.00 0.00 0.00 2.24
1269 1276 1.099879 TCCGCCTCGCTCTACTTACC 61.100 60.000 0.00 0.00 0.00 2.85
1272 1279 1.134560 CGCCTCGCTCTACTTACCTTT 59.865 52.381 0.00 0.00 0.00 3.11
1312 1324 2.171840 CCTGGAGCGTGTAGGCTATAT 58.828 52.381 0.00 0.00 44.93 0.86
1596 1657 4.260170 AGAGGATTGCTGTCATTGAGAAC 58.740 43.478 0.00 0.00 0.00 3.01
1661 1722 4.022416 TGCCCAGTCAACATTGTTTGATAC 60.022 41.667 0.00 0.00 37.80 2.24
1703 1765 1.085091 GTGCACTGAATCAGCTCCAG 58.915 55.000 10.32 0.00 34.37 3.86
1723 1785 5.708697 TCCAGTTTAACATGACGAGACTCTA 59.291 40.000 0.00 0.00 0.00 2.43
1724 1786 6.030849 CCAGTTTAACATGACGAGACTCTAG 58.969 44.000 0.00 0.00 0.00 2.43
1725 1787 6.349445 CCAGTTTAACATGACGAGACTCTAGT 60.349 42.308 0.00 0.00 0.00 2.57
1726 1788 6.524933 CAGTTTAACATGACGAGACTCTAGTG 59.475 42.308 0.00 0.00 0.00 2.74
1727 1789 5.562506 TTAACATGACGAGACTCTAGTGG 57.437 43.478 0.00 0.00 0.00 4.00
1728 1790 3.074675 ACATGACGAGACTCTAGTGGT 57.925 47.619 0.00 0.00 0.00 4.16
1733 1795 3.011119 GACGAGACTCTAGTGGTGATGT 58.989 50.000 0.03 0.00 0.00 3.06
1735 1797 4.586884 ACGAGACTCTAGTGGTGATGTTA 58.413 43.478 0.03 0.00 0.00 2.41
1802 1865 4.013728 AGGTGGATATCGATAGCTCACTC 58.986 47.826 26.59 20.52 0.00 3.51
1844 1907 2.094894 CGCTGAAGACATTGTGATGGTC 59.905 50.000 0.00 0.00 37.60 4.02
1981 2044 6.683974 ATCTCATTGGTTCAAAATCTACCG 57.316 37.500 0.00 0.00 34.62 4.02
1984 2047 5.505780 TCATTGGTTCAAAATCTACCGGAT 58.494 37.500 9.46 0.00 34.62 4.18
2035 2098 6.208007 TGGTCTAAAGATGTGTCGAAGTTCTA 59.792 38.462 0.56 0.00 0.00 2.10
2042 2105 4.794278 TGTGTCGAAGTTCTAATGCCTA 57.206 40.909 0.56 0.00 0.00 3.93
2046 2109 5.407387 GTGTCGAAGTTCTAATGCCTAACAA 59.593 40.000 0.56 0.00 0.00 2.83
2312 2375 1.484038 ACAAGGCTCTGGTGCAAAAA 58.516 45.000 0.00 0.00 34.04 1.94
2381 2444 8.454106 AGAATACAGTATAAAAGTGCTTGCTTG 58.546 33.333 0.00 0.00 31.00 4.01
2430 2493 3.425359 GCAGACTGATTTGGTTGATGACG 60.425 47.826 6.65 0.00 0.00 4.35
2523 2587 8.709386 TTTTTGTCAAGTGCAAGCTTATTTTA 57.291 26.923 0.00 0.00 0.00 1.52
2526 2590 8.885494 TTGTCAAGTGCAAGCTTATTTTATTT 57.115 26.923 0.00 0.00 0.00 1.40
2530 2594 7.440556 TCAAGTGCAAGCTTATTTTATTTTGCA 59.559 29.630 0.00 5.68 45.84 4.08
2535 2599 7.226325 TGCAAGCTTATTTTATTTTGCACAAGT 59.774 29.630 0.00 0.00 43.95 3.16
2540 2604 9.928236 GCTTATTTTATTTTGCACAAGTTGAAA 57.072 25.926 10.54 0.00 0.00 2.69
2688 2752 6.767524 TCTTGTGTGTTAAAGAATGTTGGT 57.232 33.333 0.00 0.00 29.59 3.67
2790 2860 7.706179 GTCCAATTGAATGAAAACAAAGAGACA 59.294 33.333 7.12 0.00 0.00 3.41
2791 2861 7.922278 TCCAATTGAATGAAAACAAAGAGACAG 59.078 33.333 7.12 0.00 0.00 3.51
2792 2862 7.170320 CCAATTGAATGAAAACAAAGAGACAGG 59.830 37.037 7.12 0.00 0.00 4.00
2848 2920 0.398522 TCAGGCTCCGGTATCCATGT 60.399 55.000 0.00 0.00 0.00 3.21
2901 2975 9.438228 GCTAACTTTTATATCTAGGGCTTAAGG 57.562 37.037 4.29 0.00 0.00 2.69
3041 3116 9.585099 TCTGTATGCATTCATTTTTATTCAACC 57.415 29.630 3.54 0.00 34.22 3.77
3059 3134 4.140536 CAACCTTCTCCTTTTTCTCAGCT 58.859 43.478 0.00 0.00 0.00 4.24
3060 3135 4.445557 ACCTTCTCCTTTTTCTCAGCTT 57.554 40.909 0.00 0.00 0.00 3.74
3172 3247 7.907389 ACTACTTGATCTTGATGAGGTAAACA 58.093 34.615 0.00 0.00 0.00 2.83
3213 3288 8.415950 TGCTTGAAATATGGTTCTTCCTTTTA 57.584 30.769 0.00 0.00 37.07 1.52
3214 3289 8.522830 TGCTTGAAATATGGTTCTTCCTTTTAG 58.477 33.333 0.00 0.00 37.07 1.85
3215 3290 8.523658 GCTTGAAATATGGTTCTTCCTTTTAGT 58.476 33.333 0.00 0.00 37.07 2.24
3234 3309 4.790718 AGTACCACCAAACTTTTCCTCT 57.209 40.909 0.00 0.00 0.00 3.69
3343 3418 5.046520 AGACCTGTACAGATTAAAGGGTGTC 60.047 44.000 24.68 16.77 31.98 3.67
3388 3463 1.459592 CGCTTCGTGTTTCAGGTTAGG 59.540 52.381 0.00 0.00 0.00 2.69
3425 3500 4.022329 CCTCGGCAAAGAAACCAGTTTATT 60.022 41.667 0.00 0.00 35.75 1.40
3426 3501 5.182380 CCTCGGCAAAGAAACCAGTTTATTA 59.818 40.000 3.77 0.00 33.44 0.98
3427 3502 6.127730 CCTCGGCAAAGAAACCAGTTTATTAT 60.128 38.462 3.77 0.00 33.44 1.28
3455 3530 5.220710 TCTGCTATTCTATCCCTTTGCTC 57.779 43.478 0.00 0.00 0.00 4.26
3491 3566 7.761038 ATCCGTATGATCAGAGTTATGTGTA 57.239 36.000 0.09 0.00 0.00 2.90
3494 3569 6.858478 CCGTATGATCAGAGTTATGTGTAGTG 59.142 42.308 0.09 0.00 0.00 2.74
3505 3583 9.561069 AGAGTTATGTGTAGTGAACTTTTGATT 57.439 29.630 0.00 0.00 32.37 2.57
3520 3598 5.304101 ACTTTTGATTATCCTTGTGTTGCCA 59.696 36.000 0.00 0.00 0.00 4.92
3522 3600 2.746904 TGATTATCCTTGTGTTGCCACG 59.253 45.455 0.00 0.00 44.92 4.94
3529 3607 2.098443 CCTTGTGTTGCCACGTAAAAGT 59.902 45.455 0.00 0.00 44.92 2.66
3530 3608 2.834574 TGTGTTGCCACGTAAAAGTG 57.165 45.000 0.00 0.00 44.92 3.16
3534 3612 3.544682 GTGTTGCCACGTAAAAGTGTTTC 59.455 43.478 0.00 0.00 40.33 2.78
3537 3615 4.705337 TGCCACGTAAAAGTGTTTCTTT 57.295 36.364 0.00 0.00 46.86 2.52
3559 3637 2.359230 GCCTCTGCAGTTTCGCCT 60.359 61.111 14.67 0.00 37.47 5.52
3573 3651 5.351465 CAGTTTCGCCTGTTCTAATGTATGT 59.649 40.000 0.00 0.00 0.00 2.29
3576 3654 5.276461 TCGCCTGTTCTAATGTATGTCAT 57.724 39.130 0.00 0.00 38.57 3.06
3577 3655 5.289595 TCGCCTGTTCTAATGTATGTCATC 58.710 41.667 0.00 0.00 35.48 2.92
3578 3656 4.449068 CGCCTGTTCTAATGTATGTCATCC 59.551 45.833 0.00 0.00 35.48 3.51
3579 3657 4.757149 GCCTGTTCTAATGTATGTCATCCC 59.243 45.833 0.00 0.00 35.48 3.85
3580 3658 4.991056 CCTGTTCTAATGTATGTCATCCCG 59.009 45.833 0.00 0.00 35.48 5.14
3581 3659 4.377021 TGTTCTAATGTATGTCATCCCGC 58.623 43.478 0.00 0.00 35.48 6.13
3582 3660 4.100963 TGTTCTAATGTATGTCATCCCGCT 59.899 41.667 0.00 0.00 35.48 5.52
3583 3661 4.257267 TCTAATGTATGTCATCCCGCTG 57.743 45.455 0.00 0.00 35.48 5.18
3584 3662 1.597742 AATGTATGTCATCCCGCTGC 58.402 50.000 0.00 0.00 35.48 5.25
3585 3663 0.761187 ATGTATGTCATCCCGCTGCT 59.239 50.000 0.00 0.00 29.76 4.24
3586 3664 1.408969 TGTATGTCATCCCGCTGCTA 58.591 50.000 0.00 0.00 0.00 3.49
3587 3665 1.760029 TGTATGTCATCCCGCTGCTAA 59.240 47.619 0.00 0.00 0.00 3.09
3588 3666 2.135933 GTATGTCATCCCGCTGCTAAC 58.864 52.381 0.00 0.00 0.00 2.34
3589 3667 0.833287 ATGTCATCCCGCTGCTAACT 59.167 50.000 0.00 0.00 0.00 2.24
3590 3668 0.175760 TGTCATCCCGCTGCTAACTC 59.824 55.000 0.00 0.00 0.00 3.01
3591 3669 0.530870 GTCATCCCGCTGCTAACTCC 60.531 60.000 0.00 0.00 0.00 3.85
3612 3706 0.878416 GCACGAAATTGCAGGGTGTA 59.122 50.000 0.00 0.00 42.49 2.90
3656 3750 2.190578 GAAGCCGTGGGAGGATGG 59.809 66.667 0.00 0.00 0.00 3.51
3702 3796 3.136443 TGTTTATCGGCAGGAATCTGGAT 59.864 43.478 0.00 0.00 41.19 3.41
3741 3835 1.909700 CCTTCAAAGGTTGCCTGCTA 58.090 50.000 0.32 0.00 41.41 3.49
3750 3844 1.331756 GGTTGCCTGCTATGATGAACG 59.668 52.381 0.00 0.00 0.00 3.95
3767 3861 3.433274 TGAACGCTCTGATCATGTGTTTC 59.567 43.478 20.94 16.12 35.03 2.78
3770 3864 2.606725 CGCTCTGATCATGTGTTTCTCC 59.393 50.000 0.00 0.00 0.00 3.71
3771 3865 3.678252 CGCTCTGATCATGTGTTTCTCCT 60.678 47.826 0.00 0.00 0.00 3.69
3772 3866 4.260170 GCTCTGATCATGTGTTTCTCCTT 58.740 43.478 0.00 0.00 0.00 3.36
3773 3867 4.094590 GCTCTGATCATGTGTTTCTCCTTG 59.905 45.833 0.00 0.00 0.00 3.61
3774 3868 4.582869 TCTGATCATGTGTTTCTCCTTGG 58.417 43.478 0.00 0.00 0.00 3.61
3776 3870 3.330405 TGATCATGTGTTTCTCCTTGGGA 59.670 43.478 0.00 0.00 0.00 4.37
3785 3879 3.011517 TCCTTGGGAGGCTGAGGC 61.012 66.667 0.00 0.00 43.21 4.70
3786 3880 3.013932 CCTTGGGAGGCTGAGGCT 61.014 66.667 8.79 8.79 42.48 4.58
3788 3882 2.203983 TTGGGAGGCTGAGGCTGA 60.204 61.111 15.18 0.00 38.98 4.26
3789 3883 1.617536 TTGGGAGGCTGAGGCTGAT 60.618 57.895 15.18 0.00 38.98 2.90
3790 3884 0.326522 TTGGGAGGCTGAGGCTGATA 60.327 55.000 15.18 0.00 38.98 2.15
3791 3885 0.326522 TGGGAGGCTGAGGCTGATAA 60.327 55.000 15.18 0.00 38.98 1.75
3792 3886 0.839946 GGGAGGCTGAGGCTGATAAA 59.160 55.000 15.18 0.00 38.98 1.40
3795 3889 2.171448 GGAGGCTGAGGCTGATAAAGAA 59.829 50.000 15.18 0.00 38.98 2.52
3796 3890 3.465871 GAGGCTGAGGCTGATAAAGAAG 58.534 50.000 15.18 0.00 38.98 2.85
3797 3891 2.843113 AGGCTGAGGCTGATAAAGAAGT 59.157 45.455 8.08 0.00 36.97 3.01
3798 3892 4.033709 AGGCTGAGGCTGATAAAGAAGTA 58.966 43.478 8.08 0.00 36.97 2.24
3799 3893 4.657969 AGGCTGAGGCTGATAAAGAAGTAT 59.342 41.667 8.08 0.00 36.97 2.12
3800 3894 4.754114 GGCTGAGGCTGATAAAGAAGTATG 59.246 45.833 0.00 0.00 38.73 2.39
3805 3900 9.632807 CTGAGGCTGATAAAGAAGTATGTATAC 57.367 37.037 0.00 0.00 0.00 1.47
3827 3922 4.419522 GCAAGTAAATCAGGCGAAAGAA 57.580 40.909 0.00 0.00 0.00 2.52
3828 3923 4.159120 GCAAGTAAATCAGGCGAAAGAAC 58.841 43.478 0.00 0.00 0.00 3.01
3829 3924 4.320202 GCAAGTAAATCAGGCGAAAGAACA 60.320 41.667 0.00 0.00 0.00 3.18
3830 3925 5.757886 CAAGTAAATCAGGCGAAAGAACAA 58.242 37.500 0.00 0.00 0.00 2.83
3831 3926 6.205784 CAAGTAAATCAGGCGAAAGAACAAA 58.794 36.000 0.00 0.00 0.00 2.83
3836 3931 6.385649 AATCAGGCGAAAGAACAAAAAGTA 57.614 33.333 0.00 0.00 0.00 2.24
3850 3945 4.522789 ACAAAAAGTACAAGGCCCTATGTG 59.477 41.667 14.81 2.18 0.00 3.21
3851 3946 3.366052 AAAGTACAAGGCCCTATGTGG 57.634 47.619 14.81 0.00 0.00 4.17
3862 3957 3.864789 CCCTATGTGGCTATGTCCTTT 57.135 47.619 0.00 0.00 0.00 3.11
3863 3958 3.744660 CCCTATGTGGCTATGTCCTTTC 58.255 50.000 0.00 0.00 0.00 2.62
3864 3959 3.392616 CCCTATGTGGCTATGTCCTTTCT 59.607 47.826 0.00 0.00 0.00 2.52
3865 3960 4.141390 CCCTATGTGGCTATGTCCTTTCTT 60.141 45.833 0.00 0.00 0.00 2.52
3866 3961 4.818546 CCTATGTGGCTATGTCCTTTCTTG 59.181 45.833 0.00 0.00 0.00 3.02
3867 3962 3.071874 TGTGGCTATGTCCTTTCTTGG 57.928 47.619 0.00 0.00 0.00 3.61
3868 3963 2.290896 TGTGGCTATGTCCTTTCTTGGG 60.291 50.000 0.00 0.00 0.00 4.12
3869 3964 1.340991 TGGCTATGTCCTTTCTTGGGC 60.341 52.381 0.00 0.00 0.00 5.36
3870 3965 1.017387 GCTATGTCCTTTCTTGGGCG 58.983 55.000 0.00 0.00 33.69 6.13
3871 3966 1.668419 CTATGTCCTTTCTTGGGCGG 58.332 55.000 0.00 0.00 33.69 6.13
3872 3967 0.988832 TATGTCCTTTCTTGGGCGGT 59.011 50.000 0.00 0.00 33.69 5.68
3873 3968 0.609131 ATGTCCTTTCTTGGGCGGTG 60.609 55.000 0.00 0.00 33.69 4.94
3874 3969 1.072505 GTCCTTTCTTGGGCGGTGA 59.927 57.895 0.00 0.00 0.00 4.02
3875 3970 0.322546 GTCCTTTCTTGGGCGGTGAT 60.323 55.000 0.00 0.00 0.00 3.06
3876 3971 0.035439 TCCTTTCTTGGGCGGTGATC 60.035 55.000 0.00 0.00 0.00 2.92
3877 3972 0.035056 CCTTTCTTGGGCGGTGATCT 60.035 55.000 0.00 0.00 0.00 2.75
3878 3973 1.614317 CCTTTCTTGGGCGGTGATCTT 60.614 52.381 0.00 0.00 0.00 2.40
3879 3974 2.162681 CTTTCTTGGGCGGTGATCTTT 58.837 47.619 0.00 0.00 0.00 2.52
3880 3975 2.286365 TTCTTGGGCGGTGATCTTTT 57.714 45.000 0.00 0.00 0.00 2.27
3881 3976 2.286365 TCTTGGGCGGTGATCTTTTT 57.714 45.000 0.00 0.00 0.00 1.94
3882 3977 1.885887 TCTTGGGCGGTGATCTTTTTG 59.114 47.619 0.00 0.00 0.00 2.44
3883 3978 0.316841 TTGGGCGGTGATCTTTTTGC 59.683 50.000 0.00 0.00 0.00 3.68
3884 3979 1.215382 GGGCGGTGATCTTTTTGCC 59.785 57.895 0.00 0.42 41.72 4.52
3885 3980 1.250840 GGGCGGTGATCTTTTTGCCT 61.251 55.000 12.43 0.00 42.11 4.75
3886 3981 0.171231 GGCGGTGATCTTTTTGCCTC 59.829 55.000 0.00 0.00 39.38 4.70
3887 3982 0.179189 GCGGTGATCTTTTTGCCTCG 60.179 55.000 0.00 0.00 0.00 4.63
3888 3983 1.156736 CGGTGATCTTTTTGCCTCGT 58.843 50.000 0.00 0.00 0.00 4.18
3889 3984 1.135972 CGGTGATCTTTTTGCCTCGTG 60.136 52.381 0.00 0.00 0.00 4.35
3890 3985 1.880027 GGTGATCTTTTTGCCTCGTGT 59.120 47.619 0.00 0.00 0.00 4.49
3891 3986 2.293399 GGTGATCTTTTTGCCTCGTGTT 59.707 45.455 0.00 0.00 0.00 3.32
3892 3987 3.555518 GTGATCTTTTTGCCTCGTGTTC 58.444 45.455 0.00 0.00 0.00 3.18
3893 3988 3.003275 GTGATCTTTTTGCCTCGTGTTCA 59.997 43.478 0.00 0.00 0.00 3.18
3894 3989 3.003275 TGATCTTTTTGCCTCGTGTTCAC 59.997 43.478 0.00 0.00 0.00 3.18
3895 3990 2.639065 TCTTTTTGCCTCGTGTTCACT 58.361 42.857 1.53 0.00 0.00 3.41
3896 3991 2.354510 TCTTTTTGCCTCGTGTTCACTG 59.645 45.455 1.53 0.00 0.00 3.66
3897 3992 2.031258 TTTTGCCTCGTGTTCACTGA 57.969 45.000 1.53 0.61 0.00 3.41
3898 3993 1.581934 TTTGCCTCGTGTTCACTGAG 58.418 50.000 13.48 13.48 0.00 3.35
3899 3994 0.750249 TTGCCTCGTGTTCACTGAGA 59.250 50.000 18.48 3.76 31.31 3.27
3900 3995 0.750249 TGCCTCGTGTTCACTGAGAA 59.250 50.000 18.48 9.32 31.31 2.87
3901 3996 1.138069 TGCCTCGTGTTCACTGAGAAA 59.862 47.619 18.48 9.09 38.13 2.52
3902 3997 1.527311 GCCTCGTGTTCACTGAGAAAC 59.473 52.381 18.48 0.00 38.13 2.78
3903 3998 2.821546 CCTCGTGTTCACTGAGAAACA 58.178 47.619 18.48 2.05 38.13 2.83
3904 3999 3.393800 CCTCGTGTTCACTGAGAAACAT 58.606 45.455 18.48 0.00 38.13 2.71
3905 4000 3.185188 CCTCGTGTTCACTGAGAAACATG 59.815 47.826 18.48 14.24 38.13 3.21
3906 4001 4.051237 CTCGTGTTCACTGAGAAACATGA 58.949 43.478 18.79 18.79 38.13 3.07
3907 4002 4.051237 TCGTGTTCACTGAGAAACATGAG 58.949 43.478 17.15 9.45 38.13 2.90
3908 4003 3.363378 CGTGTTCACTGAGAAACATGAGC 60.363 47.826 14.88 0.00 38.13 4.26
3909 4004 3.561310 GTGTTCACTGAGAAACATGAGCA 59.439 43.478 0.00 0.00 38.13 4.26
3910 4005 4.214971 GTGTTCACTGAGAAACATGAGCAT 59.785 41.667 0.00 0.00 38.13 3.79
3911 4006 4.823442 TGTTCACTGAGAAACATGAGCATT 59.177 37.500 0.00 0.00 38.13 3.56
3912 4007 5.152097 GTTCACTGAGAAACATGAGCATTG 58.848 41.667 0.00 0.00 38.13 2.82
3913 4008 4.392047 TCACTGAGAAACATGAGCATTGT 58.608 39.130 0.00 0.00 0.00 2.71
3914 4009 4.823442 TCACTGAGAAACATGAGCATTGTT 59.177 37.500 0.00 0.00 0.00 2.83
3915 4010 4.915667 CACTGAGAAACATGAGCATTGTTG 59.084 41.667 0.00 0.00 0.00 3.33
4083 4178 2.332654 CCGCGGGCAAAAAGCTAGT 61.333 57.895 20.10 0.00 44.79 2.57
4146 5240 0.456312 GACCGAAACGAGCGTCATCT 60.456 55.000 0.00 0.00 0.00 2.90
4165 5259 2.919856 CCCATCCCCGCTCGAGAT 60.920 66.667 18.75 0.00 0.00 2.75
4317 5559 0.752054 GAGCAGTCCCCTCTCATCTG 59.248 60.000 0.00 0.00 0.00 2.90
4341 5585 3.173151 TCTTCTGTGCATCCTAGGTTGA 58.827 45.455 21.80 6.06 0.00 3.18
4360 5604 4.371624 TGAGGATCCTGTTCACACAATT 57.628 40.909 22.02 0.00 30.36 2.32
4390 5634 2.889503 GCTGCTCGCCTGCTACTG 60.890 66.667 0.00 0.00 35.71 2.74
4571 5828 1.880819 GAGGTCAACGTTCGCCCCTA 61.881 60.000 12.51 0.00 0.00 3.53
4593 5850 1.070758 GGGCGCTCATGAAGGAGATAA 59.929 52.381 7.64 0.00 37.05 1.75
4601 5858 5.454471 GCTCATGAAGGAGATAACAGTCCAT 60.454 44.000 0.00 0.00 37.05 3.41
4602 5859 6.166984 TCATGAAGGAGATAACAGTCCATC 57.833 41.667 0.00 0.00 35.02 3.51
4603 5860 5.901853 TCATGAAGGAGATAACAGTCCATCT 59.098 40.000 0.00 0.00 35.02 2.90
4604 5861 5.860941 TGAAGGAGATAACAGTCCATCTC 57.139 43.478 13.42 13.42 44.26 2.75
4605 5862 5.272402 TGAAGGAGATAACAGTCCATCTCA 58.728 41.667 19.61 4.89 45.97 3.27
4606 5863 5.901853 TGAAGGAGATAACAGTCCATCTCAT 59.098 40.000 19.61 13.60 45.97 2.90
4607 5864 5.804944 AGGAGATAACAGTCCATCTCATG 57.195 43.478 19.61 0.00 45.97 3.07
4608 5865 5.462240 AGGAGATAACAGTCCATCTCATGA 58.538 41.667 19.61 0.00 45.97 3.07
4687 5948 5.678132 TCATGCATTCAACCTCAATATCG 57.322 39.130 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.381801 GCCGCCCACTTATGACAATG 59.618 55.000 0.00 0.00 0.00 2.82
43 44 1.021968 GGTTCAACTTGTCAACCGCT 58.978 50.000 0.00 0.00 30.63 5.52
436 438 4.611355 CGTGTTTTCAGCCTACATGAGTTG 60.611 45.833 0.00 0.00 31.94 3.16
463 465 6.214208 TGATGATAGCCATTCACCTATAGCTT 59.786 38.462 0.00 0.00 35.17 3.74
1261 1268 5.866207 ACTTCACAAGGGAAAGGTAAGTAG 58.134 41.667 0.00 0.00 0.00 2.57
1262 1269 5.899631 ACTTCACAAGGGAAAGGTAAGTA 57.100 39.130 0.00 0.00 0.00 2.24
1263 1270 4.790718 ACTTCACAAGGGAAAGGTAAGT 57.209 40.909 0.00 0.00 0.00 2.24
1264 1271 5.239525 CAGAACTTCACAAGGGAAAGGTAAG 59.760 44.000 0.00 0.00 0.00 2.34
1266 1273 4.714632 CAGAACTTCACAAGGGAAAGGTA 58.285 43.478 0.00 0.00 0.00 3.08
1267 1274 3.555966 CAGAACTTCACAAGGGAAAGGT 58.444 45.455 0.00 0.00 0.00 3.50
1269 1276 3.217626 AGCAGAACTTCACAAGGGAAAG 58.782 45.455 0.00 0.00 0.00 2.62
1272 1279 2.038557 GGTAGCAGAACTTCACAAGGGA 59.961 50.000 0.00 0.00 0.00 4.20
1596 1657 4.822026 ACAAGGATCTTCAGTTAACCTCG 58.178 43.478 0.88 0.00 0.00 4.63
1670 1731 4.314961 TCAGTGCACTATCGATTTGTTGT 58.685 39.130 21.20 0.00 0.00 3.32
1703 1765 5.800941 CCACTAGAGTCTCGTCATGTTAAAC 59.199 44.000 0.00 0.00 0.00 2.01
1724 1786 8.979574 GCTTATTCTACATAGTAACATCACCAC 58.020 37.037 0.00 0.00 0.00 4.16
1725 1787 8.148351 GGCTTATTCTACATAGTAACATCACCA 58.852 37.037 0.00 0.00 0.00 4.17
1726 1788 8.148351 TGGCTTATTCTACATAGTAACATCACC 58.852 37.037 0.00 0.00 0.00 4.02
1727 1789 9.712305 ATGGCTTATTCTACATAGTAACATCAC 57.288 33.333 0.00 0.00 0.00 3.06
1733 1795 9.667107 GGCAATATGGCTTATTCTACATAGTAA 57.333 33.333 1.19 0.00 40.14 2.24
1735 1797 7.037297 AGGGCAATATGGCTTATTCTACATAGT 60.037 37.037 1.19 0.00 43.20 2.12
1802 1865 0.852777 CGGATGAATGGTTAGCGACG 59.147 55.000 0.00 0.00 0.00 5.12
1844 1907 2.536365 CAGCACAAGCAGCCATTATTG 58.464 47.619 0.00 0.00 45.49 1.90
1919 1982 7.548780 TCAATGACGATATGATCAAACTTGTCA 59.451 33.333 19.66 19.66 38.10 3.58
2007 2070 5.696724 ACTTCGACACATCTTTAGACCAAAG 59.303 40.000 0.00 0.00 44.36 2.77
2011 2074 5.471257 AGAACTTCGACACATCTTTAGACC 58.529 41.667 0.00 0.00 0.00 3.85
2035 2098 7.014230 ACAGTGACATTAGTTTTGTTAGGCATT 59.986 33.333 0.00 0.00 0.00 3.56
2042 2105 7.280356 ACCTAGACAGTGACATTAGTTTTGTT 58.720 34.615 0.00 0.00 0.00 2.83
2046 2109 6.919775 AGACCTAGACAGTGACATTAGTTT 57.080 37.500 0.00 0.00 0.00 2.66
2289 2352 1.639722 TGCACCAGAGCCTTGTAGTA 58.360 50.000 0.00 0.00 0.00 1.82
2290 2353 0.764890 TTGCACCAGAGCCTTGTAGT 59.235 50.000 0.00 0.00 0.00 2.73
2291 2354 1.896220 TTTGCACCAGAGCCTTGTAG 58.104 50.000 0.00 0.00 0.00 2.74
2405 2468 4.768448 TCATCAACCAAATCAGTCTGCATT 59.232 37.500 0.00 0.00 0.00 3.56
2430 2493 2.687935 TGGTCAAAACCTCAAGTTCTGC 59.312 45.455 0.00 0.00 46.60 4.26
2523 2587 8.098220 AGAAAACTTTTCAACTTGTGCAAAAT 57.902 26.923 15.17 0.00 0.00 1.82
2526 2590 5.344665 CGAGAAAACTTTTCAACTTGTGCAA 59.655 36.000 15.17 0.00 0.00 4.08
2530 2594 5.344933 GCAACGAGAAAACTTTTCAACTTGT 59.655 36.000 15.17 3.78 0.00 3.16
2535 2599 3.857093 GCTGCAACGAGAAAACTTTTCAA 59.143 39.130 15.17 0.00 0.00 2.69
2540 2604 2.288666 TGAGCTGCAACGAGAAAACTT 58.711 42.857 1.02 0.00 0.00 2.66
2592 2656 6.363167 AAATCCATGTCAACATCACCAAAT 57.637 33.333 0.00 0.00 33.61 2.32
2661 2725 8.930760 CCAACATTCTTTAACACACAAGAAAAA 58.069 29.630 0.00 0.00 41.28 1.94
2688 2752 5.264395 TGACATCTGACTCAGGATTACAGA 58.736 41.667 6.20 0.00 40.88 3.41
2741 2811 1.549620 CAGCCTCGATCCTGCAGATAT 59.450 52.381 17.39 8.37 34.42 1.63
2742 2812 0.964700 CAGCCTCGATCCTGCAGATA 59.035 55.000 17.39 2.75 34.42 1.98
2743 2813 1.747145 CAGCCTCGATCCTGCAGAT 59.253 57.895 17.39 6.84 38.17 2.90
2744 2814 3.214253 CAGCCTCGATCCTGCAGA 58.786 61.111 17.39 1.21 0.00 4.26
2754 2824 0.674581 TCAATTGGACTGCAGCCTCG 60.675 55.000 22.36 11.58 0.00 4.63
2848 2920 6.157820 TGTCTAATATGGTGGGATTCAGAACA 59.842 38.462 0.00 0.00 0.00 3.18
2901 2975 1.467920 AGGAAGCCACTAAATGCTGC 58.532 50.000 0.00 0.00 38.00 5.25
2941 3016 9.807649 GCATTTATATGTCTCCAACAGAATTTT 57.192 29.630 0.00 0.00 42.37 1.82
3041 3116 5.764487 AACAAGCTGAGAAAAAGGAGAAG 57.236 39.130 0.00 0.00 0.00 2.85
3059 3134 6.451393 ACAAGTCAGCAAAGTAAACAAACAA 58.549 32.000 0.00 0.00 0.00 2.83
3060 3135 6.019779 ACAAGTCAGCAAAGTAAACAAACA 57.980 33.333 0.00 0.00 0.00 2.83
3213 3288 4.461198 CAGAGGAAAAGTTTGGTGGTACT 58.539 43.478 0.00 0.00 0.00 2.73
3214 3289 3.004419 GCAGAGGAAAAGTTTGGTGGTAC 59.996 47.826 0.00 0.00 0.00 3.34
3215 3290 3.219281 GCAGAGGAAAAGTTTGGTGGTA 58.781 45.455 0.00 0.00 0.00 3.25
3343 3418 3.547868 CAGTTGACTCGTTGACGGATATG 59.452 47.826 3.48 0.00 40.29 1.78
3388 3463 1.581447 CGAGGAAAGGTTTGGCTGC 59.419 57.895 0.00 0.00 0.00 5.25
3425 3500 8.907829 AAGGGATAGAATAGCAGAAGATGATA 57.092 34.615 0.00 0.00 33.51 2.15
3426 3501 7.811482 AAGGGATAGAATAGCAGAAGATGAT 57.189 36.000 0.00 0.00 0.00 2.45
3427 3502 7.448420 CAAAGGGATAGAATAGCAGAAGATGA 58.552 38.462 0.00 0.00 0.00 2.92
3441 3516 2.097036 TCGTTCGAGCAAAGGGATAGA 58.903 47.619 0.00 0.00 0.00 1.98
3455 3530 3.431856 TCATACGGATCAACTTCGTTCG 58.568 45.455 0.00 0.00 38.19 3.95
3473 3548 8.072321 AGTTCACTACACATAACTCTGATCAT 57.928 34.615 0.00 0.00 0.00 2.45
3491 3566 7.823745 ACACAAGGATAATCAAAAGTTCACT 57.176 32.000 0.00 0.00 0.00 3.41
3494 3569 6.366061 GGCAACACAAGGATAATCAAAAGTTC 59.634 38.462 0.00 0.00 0.00 3.01
3529 3607 1.593196 CAGAGGCACCGAAAGAAACA 58.407 50.000 0.00 0.00 0.00 2.83
3530 3608 0.238553 GCAGAGGCACCGAAAGAAAC 59.761 55.000 0.00 0.00 40.72 2.78
3559 3637 4.100963 AGCGGGATGACATACATTAGAACA 59.899 41.667 0.00 0.00 39.56 3.18
3573 3651 0.687757 AGGAGTTAGCAGCGGGATGA 60.688 55.000 0.00 0.00 0.00 2.92
3576 3654 3.019003 GCAGGAGTTAGCAGCGGGA 62.019 63.158 0.00 0.00 0.00 5.14
3577 3655 2.512515 GCAGGAGTTAGCAGCGGG 60.513 66.667 0.00 0.00 0.00 6.13
3578 3656 2.103042 GTGCAGGAGTTAGCAGCGG 61.103 63.158 0.00 0.00 42.14 5.52
3579 3657 2.447887 CGTGCAGGAGTTAGCAGCG 61.448 63.158 0.00 0.00 42.14 5.18
3580 3658 0.670546 TTCGTGCAGGAGTTAGCAGC 60.671 55.000 9.34 0.00 42.14 5.25
3581 3659 1.795768 TTTCGTGCAGGAGTTAGCAG 58.204 50.000 9.34 0.00 42.14 4.24
3582 3660 2.472695 ATTTCGTGCAGGAGTTAGCA 57.527 45.000 9.34 0.00 38.65 3.49
3583 3661 2.729156 GCAATTTCGTGCAGGAGTTAGC 60.729 50.000 9.34 9.25 44.29 3.09
3584 3662 3.122937 GCAATTTCGTGCAGGAGTTAG 57.877 47.619 9.34 3.34 44.29 2.34
3612 3706 3.412386 GCAACCTTCCAACATAGAGTGT 58.588 45.455 0.00 0.00 44.84 3.55
3656 3750 2.093553 AGCTTGCTGATCCTCTTCTCAC 60.094 50.000 0.00 0.00 0.00 3.51
3702 3796 1.447838 CTTCCTTAGCGCGGCTTCA 60.448 57.895 8.83 0.00 40.44 3.02
3741 3835 3.808174 CACATGATCAGAGCGTTCATCAT 59.192 43.478 0.00 8.63 36.59 2.45
3750 3844 3.871485 AGGAGAAACACATGATCAGAGC 58.129 45.455 0.00 0.00 0.00 4.09
3767 3861 3.041469 GCCTCAGCCTCCCAAGGAG 62.041 68.421 3.51 3.51 46.67 3.69
3770 3864 1.633915 ATCAGCCTCAGCCTCCCAAG 61.634 60.000 0.00 0.00 41.25 3.61
3771 3865 0.326522 TATCAGCCTCAGCCTCCCAA 60.327 55.000 0.00 0.00 41.25 4.12
3772 3866 0.326522 TTATCAGCCTCAGCCTCCCA 60.327 55.000 0.00 0.00 41.25 4.37
3773 3867 0.839946 TTTATCAGCCTCAGCCTCCC 59.160 55.000 0.00 0.00 41.25 4.30
3774 3868 1.765314 TCTTTATCAGCCTCAGCCTCC 59.235 52.381 0.00 0.00 41.25 4.30
3776 3870 2.843113 ACTTCTTTATCAGCCTCAGCCT 59.157 45.455 0.00 0.00 41.25 4.58
3778 3872 5.363939 ACATACTTCTTTATCAGCCTCAGC 58.636 41.667 0.00 0.00 40.32 4.26
3779 3873 9.632807 GTATACATACTTCTTTATCAGCCTCAG 57.367 37.037 0.00 0.00 0.00 3.35
3780 3874 8.297426 CGTATACATACTTCTTTATCAGCCTCA 58.703 37.037 3.32 0.00 0.00 3.86
3782 3876 7.091443 GCGTATACATACTTCTTTATCAGCCT 58.909 38.462 3.32 0.00 0.00 4.58
3785 3879 9.464714 ACTTGCGTATACATACTTCTTTATCAG 57.535 33.333 3.32 0.00 0.00 2.90
3791 3885 9.811995 TGATTTACTTGCGTATACATACTTCTT 57.188 29.630 3.32 0.00 0.00 2.52
3792 3886 9.464714 CTGATTTACTTGCGTATACATACTTCT 57.535 33.333 3.32 0.00 0.00 2.85
3795 3889 6.645415 GCCTGATTTACTTGCGTATACATACT 59.355 38.462 3.32 0.00 0.00 2.12
3796 3890 6.399669 CGCCTGATTTACTTGCGTATACATAC 60.400 42.308 3.32 0.00 40.33 2.39
3797 3891 5.631929 CGCCTGATTTACTTGCGTATACATA 59.368 40.000 3.32 0.00 40.33 2.29
3798 3892 4.447724 CGCCTGATTTACTTGCGTATACAT 59.552 41.667 3.32 0.00 40.33 2.29
3799 3893 3.799963 CGCCTGATTTACTTGCGTATACA 59.200 43.478 3.32 0.00 40.33 2.29
3800 3894 4.046462 TCGCCTGATTTACTTGCGTATAC 58.954 43.478 0.00 0.00 45.06 1.47
3805 3900 2.415168 TCTTTCGCCTGATTTACTTGCG 59.585 45.455 0.00 0.00 46.09 4.85
3825 3920 5.243060 ACATAGGGCCTTGTACTTTTTGTTC 59.757 40.000 13.45 0.00 0.00 3.18
3826 3921 5.010617 CACATAGGGCCTTGTACTTTTTGTT 59.989 40.000 13.45 0.00 0.00 2.83
3827 3922 4.522789 CACATAGGGCCTTGTACTTTTTGT 59.477 41.667 13.45 0.00 0.00 2.83
3828 3923 4.082245 CCACATAGGGCCTTGTACTTTTTG 60.082 45.833 13.45 2.74 0.00 2.44
3829 3924 4.086457 CCACATAGGGCCTTGTACTTTTT 58.914 43.478 13.45 0.00 0.00 1.94
3830 3925 3.697166 CCACATAGGGCCTTGTACTTTT 58.303 45.455 13.45 0.00 0.00 2.27
3831 3926 3.366052 CCACATAGGGCCTTGTACTTT 57.634 47.619 13.45 0.00 0.00 2.66
3850 3945 1.393603 GCCCAAGAAAGGACATAGCC 58.606 55.000 0.00 0.00 0.00 3.93
3851 3946 1.017387 CGCCCAAGAAAGGACATAGC 58.983 55.000 0.00 0.00 0.00 2.97
3852 3947 1.065418 ACCGCCCAAGAAAGGACATAG 60.065 52.381 0.00 0.00 0.00 2.23
3853 3948 0.988832 ACCGCCCAAGAAAGGACATA 59.011 50.000 0.00 0.00 0.00 2.29
3854 3949 0.609131 CACCGCCCAAGAAAGGACAT 60.609 55.000 0.00 0.00 0.00 3.06
3855 3950 1.228124 CACCGCCCAAGAAAGGACA 60.228 57.895 0.00 0.00 0.00 4.02
3856 3951 0.322546 ATCACCGCCCAAGAAAGGAC 60.323 55.000 0.00 0.00 0.00 3.85
3857 3952 0.035439 GATCACCGCCCAAGAAAGGA 60.035 55.000 0.00 0.00 0.00 3.36
3858 3953 0.035056 AGATCACCGCCCAAGAAAGG 60.035 55.000 0.00 0.00 0.00 3.11
3859 3954 1.826385 AAGATCACCGCCCAAGAAAG 58.174 50.000 0.00 0.00 0.00 2.62
3860 3955 2.286365 AAAGATCACCGCCCAAGAAA 57.714 45.000 0.00 0.00 0.00 2.52
3861 3956 2.286365 AAAAGATCACCGCCCAAGAA 57.714 45.000 0.00 0.00 0.00 2.52
3862 3957 1.885887 CAAAAAGATCACCGCCCAAGA 59.114 47.619 0.00 0.00 0.00 3.02
3863 3958 1.669795 GCAAAAAGATCACCGCCCAAG 60.670 52.381 0.00 0.00 0.00 3.61
3864 3959 0.316841 GCAAAAAGATCACCGCCCAA 59.683 50.000 0.00 0.00 0.00 4.12
3865 3960 1.531739 GGCAAAAAGATCACCGCCCA 61.532 55.000 0.00 0.00 33.31 5.36
3866 3961 1.215382 GGCAAAAAGATCACCGCCC 59.785 57.895 0.00 0.00 33.31 6.13
3867 3962 0.171231 GAGGCAAAAAGATCACCGCC 59.829 55.000 0.00 0.00 39.90 6.13
3868 3963 0.179189 CGAGGCAAAAAGATCACCGC 60.179 55.000 0.00 0.00 0.00 5.68
3869 3964 1.135972 CACGAGGCAAAAAGATCACCG 60.136 52.381 0.00 0.00 0.00 4.94
3870 3965 1.880027 ACACGAGGCAAAAAGATCACC 59.120 47.619 0.00 0.00 0.00 4.02
3871 3966 3.003275 TGAACACGAGGCAAAAAGATCAC 59.997 43.478 0.00 0.00 0.00 3.06
3872 3967 3.003275 GTGAACACGAGGCAAAAAGATCA 59.997 43.478 0.00 0.00 0.00 2.92
3873 3968 3.251004 AGTGAACACGAGGCAAAAAGATC 59.749 43.478 0.00 0.00 36.20 2.75
3874 3969 3.003689 CAGTGAACACGAGGCAAAAAGAT 59.996 43.478 0.00 0.00 36.20 2.40
3875 3970 2.354510 CAGTGAACACGAGGCAAAAAGA 59.645 45.455 0.00 0.00 36.20 2.52
3876 3971 2.354510 TCAGTGAACACGAGGCAAAAAG 59.645 45.455 0.00 0.00 36.20 2.27
3877 3972 2.354510 CTCAGTGAACACGAGGCAAAAA 59.645 45.455 14.15 0.00 36.20 1.94
3878 3973 1.939934 CTCAGTGAACACGAGGCAAAA 59.060 47.619 14.15 0.00 36.20 2.44
3879 3974 1.138069 TCTCAGTGAACACGAGGCAAA 59.862 47.619 18.42 5.24 34.83 3.68
3880 3975 0.750249 TCTCAGTGAACACGAGGCAA 59.250 50.000 18.42 5.47 34.83 4.52
3881 3976 0.750249 TTCTCAGTGAACACGAGGCA 59.250 50.000 18.42 9.29 34.83 4.75
3882 3977 1.527311 GTTTCTCAGTGAACACGAGGC 59.473 52.381 18.42 10.70 34.83 4.70
3883 3978 2.821546 TGTTTCTCAGTGAACACGAGG 58.178 47.619 18.42 7.19 34.83 4.63
3884 3979 4.051237 TCATGTTTCTCAGTGAACACGAG 58.949 43.478 15.12 15.12 33.88 4.18
3885 3980 4.051237 CTCATGTTTCTCAGTGAACACGA 58.949 43.478 0.00 0.00 33.88 4.35
3886 3981 3.363378 GCTCATGTTTCTCAGTGAACACG 60.363 47.826 0.00 0.00 33.88 4.49
3887 3982 3.561310 TGCTCATGTTTCTCAGTGAACAC 59.439 43.478 0.00 0.00 33.88 3.32
3888 3983 3.807553 TGCTCATGTTTCTCAGTGAACA 58.192 40.909 0.00 0.00 33.88 3.18
3889 3984 5.152097 CAATGCTCATGTTTCTCAGTGAAC 58.848 41.667 0.00 0.00 33.88 3.18
3890 3985 4.823442 ACAATGCTCATGTTTCTCAGTGAA 59.177 37.500 0.00 0.00 0.00 3.18
3891 3986 4.392047 ACAATGCTCATGTTTCTCAGTGA 58.608 39.130 0.00 0.00 0.00 3.41
3892 3987 4.761235 ACAATGCTCATGTTTCTCAGTG 57.239 40.909 0.00 0.00 0.00 3.66
3893 3988 5.117355 CAACAATGCTCATGTTTCTCAGT 57.883 39.130 0.00 0.00 38.90 3.41
3911 4006 3.058293 CAGCGTAAGAGATTTTGGCAACA 60.058 43.478 0.00 0.00 45.37 3.33
3912 4007 3.058224 ACAGCGTAAGAGATTTTGGCAAC 60.058 43.478 0.00 0.00 43.02 4.17
3913 4008 3.058293 CACAGCGTAAGAGATTTTGGCAA 60.058 43.478 0.00 0.00 43.02 4.52
3914 4009 2.483877 CACAGCGTAAGAGATTTTGGCA 59.516 45.455 0.00 0.00 43.02 4.92
3915 4010 2.484264 ACACAGCGTAAGAGATTTTGGC 59.516 45.455 0.00 0.00 43.02 4.52
3916 4011 4.749245 AACACAGCGTAAGAGATTTTGG 57.251 40.909 0.00 0.00 43.02 3.28
3917 4012 4.911610 CCAAACACAGCGTAAGAGATTTTG 59.088 41.667 0.00 0.00 43.02 2.44
3918 4013 4.819630 TCCAAACACAGCGTAAGAGATTTT 59.180 37.500 0.00 0.00 43.02 1.82
3919 4014 4.385825 TCCAAACACAGCGTAAGAGATTT 58.614 39.130 0.00 0.00 43.02 2.17
3920 4015 4.002906 TCCAAACACAGCGTAAGAGATT 57.997 40.909 0.00 0.00 43.02 2.40
3921 4016 3.678056 TCCAAACACAGCGTAAGAGAT 57.322 42.857 0.00 0.00 43.02 2.75
3927 4022 2.287308 GCAAACATCCAAACACAGCGTA 60.287 45.455 0.00 0.00 0.00 4.42
4018 4113 0.540133 TGCCAGAGCTGAATGCCAAA 60.540 50.000 0.00 0.00 44.23 3.28
4083 4178 0.684479 ACTCAGCGATGTCTGGGCTA 60.684 55.000 0.00 0.00 38.10 3.93
4146 5240 2.946988 ATCTCGAGCGGGGATGGGAA 62.947 60.000 7.81 0.00 0.00 3.97
4221 5316 4.097361 GGACAAGAGGGGCGGGAC 62.097 72.222 0.00 0.00 0.00 4.46
4317 5559 2.763448 ACCTAGGATGCACAGAAGAGAC 59.237 50.000 17.98 0.00 0.00 3.36
4341 5585 3.074390 TCCAATTGTGTGAACAGGATCCT 59.926 43.478 9.02 9.02 0.00 3.24
4360 5604 1.969200 GAGCAGCTGCAGGATCTCCA 61.969 60.000 38.24 0.00 45.16 3.86
4383 5627 2.138179 GGATACGGCCCCAGTAGCA 61.138 63.158 0.00 0.00 32.66 3.49
4483 5729 0.895530 TCTTCCTTGCAGTACCGGAG 59.104 55.000 9.46 0.00 0.00 4.63
4571 5828 2.688666 TCCTTCATGAGCGCCCCT 60.689 61.111 2.29 0.00 0.00 4.79
4593 5850 5.149239 AGATGAGATCATGAGATGGACTGT 58.851 41.667 0.09 0.00 36.57 3.55
4601 5858 6.603224 TGAAGAGAGAGATGAGATCATGAGA 58.397 40.000 0.09 0.00 36.57 3.27
4602 5859 6.569801 GCTGAAGAGAGAGATGAGATCATGAG 60.570 46.154 0.09 0.00 36.57 2.90
4603 5860 5.242171 GCTGAAGAGAGAGATGAGATCATGA 59.758 44.000 0.00 0.00 36.57 3.07
4604 5861 5.466819 GCTGAAGAGAGAGATGAGATCATG 58.533 45.833 0.00 0.00 36.57 3.07
4605 5862 4.216902 CGCTGAAGAGAGAGATGAGATCAT 59.783 45.833 0.00 0.00 39.70 2.45
4606 5863 3.565063 CGCTGAAGAGAGAGATGAGATCA 59.435 47.826 0.00 0.00 0.00 2.92
4607 5864 3.814842 TCGCTGAAGAGAGAGATGAGATC 59.185 47.826 0.00 0.00 0.00 2.75
4608 5865 3.565482 GTCGCTGAAGAGAGAGATGAGAT 59.435 47.826 0.00 0.00 0.00 2.75
4687 5948 5.934402 TTAGGTATTCAGAACAGAGACCC 57.066 43.478 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.