Multiple sequence alignment - TraesCS4B01G121500

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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 TraesCS4B01G121500 chr4B 100.000 4674 0 0 1 4674 143316700 143312027 0.000000e+00 8632.0
1 TraesCS4B01G121500 chr4A 95.216 2864 72 23 975 3783 475395947 475398800 0.000000e+00 4470.0
2 TraesCS4B01G121500 chr4A 88.069 461 49 6 390 846 475395106 475395564 4.110000e-150 542.0
3 TraesCS4B01G121500 chr4A 90.625 416 21 6 4049 4451 475412990 475413400 1.910000e-148 536.0
4 TraesCS4B01G121500 chr4A 88.976 127 8 3 3933 4059 475404326 475404446 8.100000e-33 152.0
5 TraesCS4B01G121500 chr4A 88.696 115 11 2 4545 4658 475413469 475413582 6.310000e-29 139.0
6 TraesCS4B01G121500 chr4A 74.558 283 59 8 410 689 475395039 475395311 1.370000e-20 111.0
7 TraesCS4B01G121500 chr4A 91.549 71 3 1 3795 3865 475398902 475398969 1.380000e-15 95.3
8 TraesCS4B01G121500 chr4A 100.000 28 0 0 3795 3822 200093532 200093505 8.000000e-03 52.8
9 TraesCS4B01G121500 chr4D 96.768 2073 60 6 1724 3793 100811649 100809581 0.000000e+00 3450.0
10 TraesCS4B01G121500 chr4D 96.186 839 21 5 893 1729 100812517 100811688 0.000000e+00 1362.0
11 TraesCS4B01G121500 chr4D 87.941 539 32 16 4145 4658 100801359 100800829 5.170000e-169 604.0
12 TraesCS4B01G121500 chr4D 80.392 663 90 22 1 653 100813487 100812855 7.080000e-128 468.0
13 TraesCS4B01G121500 chr4D 81.376 596 82 21 232 810 100813133 100812550 4.260000e-125 459.0
14 TraesCS4B01G121500 chr4D 82.338 385 65 3 269 652 100813143 100812761 9.690000e-87 331.0
15 TraesCS4B01G121500 chr4D 79.545 352 63 4 262 605 100813062 100812712 4.670000e-60 243.0
16 TraesCS4B01G121500 chr4D 87.591 137 9 2 3752 3881 100809583 100809448 8.100000e-33 152.0
17 TraesCS4B01G121500 chr4D 100.000 30 0 0 3795 3824 56719309 56719338 6.530000e-04 56.5
18 TraesCS4B01G121500 chr1D 90.789 76 6 1 3823 3897 49592088 49592163 2.980000e-17 100.0
19 TraesCS4B01G121500 chr1D 100.000 30 0 0 3795 3824 49604577 49604548 6.530000e-04 56.5
20 TraesCS4B01G121500 chr7D 92.537 67 5 0 3831 3897 276514136 276514202 3.850000e-16 97.1
21 TraesCS4B01G121500 chr2D 91.176 68 5 1 3831 3897 467062462 467062529 1.790000e-14 91.6
22 TraesCS4B01G121500 chr3D 91.304 46 2 2 3831 3875 488233819 488233775 1.400000e-05 62.1
23 TraesCS4B01G121500 chr7B 100.000 31 0 0 3763 3793 454442005 454442035 1.820000e-04 58.4
24 TraesCS4B01G121500 chr1B 100.000 31 0 0 3763 3793 191709645 191709615 1.820000e-04 58.4
25 TraesCS4B01G121500 chr5D 97.059 34 0 1 3795 3828 437347269 437347301 6.530000e-04 56.5
26 TraesCS4B01G121500 chr5B 97.059 34 0 1 3795 3828 531543607 531543639 6.530000e-04 56.5
27 TraesCS4B01G121500 chr5A 97.059 34 0 1 3795 3828 552528139 552528171 6.530000e-04 56.5


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 TraesCS4B01G121500 chr4B 143312027 143316700 4673 True 8632.000000 8632 100.000000 1 4674 1 chr4B.!!$R1 4673
1 TraesCS4B01G121500 chr4A 475395039 475398969 3930 False 1304.575000 4470 87.348000 390 3865 4 chr4A.!!$F2 3475
2 TraesCS4B01G121500 chr4A 475412990 475413582 592 False 337.500000 536 89.660500 4049 4658 2 chr4A.!!$F3 609
3 TraesCS4B01G121500 chr4D 100809448 100813487 4039 True 923.571429 3450 86.313714 1 3881 7 chr4D.!!$R2 3880
4 TraesCS4B01G121500 chr4D 100800829 100801359 530 True 604.000000 604 87.941000 4145 4658 1 chr4D.!!$R1 513

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
890 1035 0.108041 TAAGCGCCGTTAAGGGAAGG 60.108 55.0 18.31 7.11 41.48 3.46 F
1408 1815 0.035458 CAACTTCCCGAGGTCTGCTT 59.965 55.0 0.00 0.00 0.00 3.91 F
2780 3258 0.248289 ACAGAAGCCATGCCAAATGC 59.752 50.0 0.00 0.00 41.77 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2785 3263 3.895232 ACAATAGGTGCATTCGAGAGT 57.105 42.857 0.00 0.0 0.00 3.24 R
3106 3584 0.391927 CTCTCCTCGAGGACGACTGT 60.392 60.000 30.49 0.0 43.81 3.55 R
4536 5163 0.035056 CAATGAGGGGGCGAGAAACT 60.035 55.000 0.00 0.0 0.00 2.66 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
113 114 9.280174 CCTCTTTGGTTTGTAAGAACTTATACA 57.720 33.333 0.00 0.00 30.55 2.29
135 136 9.802039 ATACATTAGGAAGTTCTTACAAACCAA 57.198 29.630 2.25 0.00 0.00 3.67
136 137 8.528044 ACATTAGGAAGTTCTTACAAACCAAA 57.472 30.769 2.25 0.00 0.00 3.28
137 138 8.630037 ACATTAGGAAGTTCTTACAAACCAAAG 58.370 33.333 2.25 0.00 0.00 2.77
138 139 8.630037 CATTAGGAAGTTCTTACAAACCAAAGT 58.370 33.333 2.25 0.00 0.00 2.66
139 140 6.451064 AGGAAGTTCTTACAAACCAAAGTG 57.549 37.500 2.25 0.00 0.00 3.16
140 141 5.359860 AGGAAGTTCTTACAAACCAAAGTGG 59.640 40.000 2.25 0.00 45.02 4.00
186 187 9.027129 CATGTCATGCTTTAAAAATCCTACATG 57.973 33.333 0.00 11.55 35.08 3.21
247 249 9.994432 GAATAATTCAGAAAGATCAATTGACGT 57.006 29.630 11.07 0.00 0.00 4.34
259 261 3.879892 TCAATTGACGTCACAACCATTGA 59.120 39.130 26.96 26.96 32.50 2.57
266 268 2.306847 GTCACAACCATTGAAGTGGGT 58.693 47.619 0.00 0.00 43.77 4.51
306 399 3.439825 CCGATTGATGTCACAACCATTGA 59.560 43.478 0.00 0.00 32.50 2.57
314 407 4.459331 CAACCATTGACGCGGGCG 62.459 66.667 12.47 12.04 46.03 6.13
338 432 2.608752 GCTGCATTGAAAGACCAGTTGG 60.609 50.000 0.00 0.00 42.17 3.77
339 433 1.340889 TGCATTGAAAGACCAGTTGGC 59.659 47.619 0.00 0.00 39.32 4.52
371 465 2.048597 TGCGCGGTGTCGAAAGAT 60.049 55.556 8.83 0.00 45.19 2.40
391 485 1.933181 TCGATTGATGTCGCAACCATC 59.067 47.619 0.00 0.00 41.22 3.51
439 533 2.351641 CCAATTGACGTCACACCATTGG 60.352 50.000 30.76 30.76 34.23 3.16
440 534 0.881118 ATTGACGTCACACCATTGGC 59.119 50.000 19.90 0.00 0.00 4.52
441 535 0.179032 TTGACGTCACACCATTGGCT 60.179 50.000 19.90 0.00 0.00 4.75
442 536 0.179032 TGACGTCACACCATTGGCTT 60.179 50.000 15.76 0.00 0.00 4.35
443 537 0.238289 GACGTCACACCATTGGCTTG 59.762 55.000 11.55 0.00 0.00 4.01
472 566 1.611491 GGCACCGAAAGACCAATTGAA 59.389 47.619 7.12 0.00 0.00 2.69
473 567 2.351738 GGCACCGAAAGACCAATTGAAG 60.352 50.000 7.12 0.00 0.00 3.02
474 568 2.293399 GCACCGAAAGACCAATTGAAGT 59.707 45.455 7.12 0.00 0.00 3.01
476 570 2.806244 ACCGAAAGACCAATTGAAGTCG 59.194 45.455 7.12 8.26 38.08 4.18
493 633 2.343387 GCAACCATTGGTGTGGGC 59.657 61.111 9.62 7.62 43.77 5.36
498 638 2.985282 CATTGGTGTGGGCTGCGT 60.985 61.111 0.00 0.00 0.00 5.24
499 639 2.672996 ATTGGTGTGGGCTGCGTC 60.673 61.111 0.00 0.00 0.00 5.19
535 675 2.481289 TGATGTCGCAACCATTGGTA 57.519 45.000 9.20 0.00 33.12 3.25
545 685 1.453745 CCATTGGTATGGGCTGCGT 60.454 57.895 0.00 0.00 46.43 5.24
560 700 3.103911 CGTCGCGCCGAAAGACTT 61.104 61.111 2.03 0.00 37.72 3.01
565 705 0.509499 CGCGCCGAAAGACTTGTTAA 59.491 50.000 0.00 0.00 0.00 2.01
566 706 1.070443 CGCGCCGAAAGACTTGTTAAA 60.070 47.619 0.00 0.00 0.00 1.52
588 728 3.660865 GTCACAAACTATTGACTCGGGT 58.339 45.455 0.00 0.00 39.30 5.28
613 753 4.380023 GCGCCACACTGAAATACCAATTAA 60.380 41.667 0.00 0.00 0.00 1.40
616 756 5.092781 CCACACTGAAATACCAATTAACGC 58.907 41.667 0.00 0.00 0.00 4.84
675 815 1.647084 GTTGCCGTCACAACCACTC 59.353 57.895 0.00 0.00 43.34 3.51
734 877 8.353684 TGAACGTTTTCATAAATTTAGGAAGCA 58.646 29.630 20.75 11.98 36.79 3.91
766 910 9.658799 AAATATAGAGACCGGATTATCAACATG 57.341 33.333 9.46 0.00 0.00 3.21
859 1004 4.282881 GGAAATGCCTGGATGGGG 57.717 61.111 0.00 0.00 36.00 4.96
860 1005 1.458209 GGAAATGCCTGGATGGGGG 60.458 63.158 0.00 0.00 36.00 5.40
861 1006 1.311059 GAAATGCCTGGATGGGGGT 59.689 57.895 0.00 0.00 36.00 4.95
862 1007 1.002017 AAATGCCTGGATGGGGGTG 59.998 57.895 0.00 0.00 36.00 4.61
863 1008 2.534594 AAATGCCTGGATGGGGGTGG 62.535 60.000 0.00 0.00 36.00 4.61
866 1011 4.777546 CCTGGATGGGGGTGGGGA 62.778 72.222 0.00 0.00 0.00 4.81
867 1012 3.099170 CTGGATGGGGGTGGGGAG 61.099 72.222 0.00 0.00 0.00 4.30
868 1013 3.967024 TGGATGGGGGTGGGGAGT 61.967 66.667 0.00 0.00 0.00 3.85
869 1014 2.375173 GGATGGGGGTGGGGAGTA 59.625 66.667 0.00 0.00 0.00 2.59
870 1015 1.308392 GGATGGGGGTGGGGAGTAA 60.308 63.158 0.00 0.00 0.00 2.24
871 1016 0.701310 GGATGGGGGTGGGGAGTAAT 60.701 60.000 0.00 0.00 0.00 1.89
872 1017 1.416907 GGATGGGGGTGGGGAGTAATA 60.417 57.143 0.00 0.00 0.00 0.98
873 1018 2.424793 GATGGGGGTGGGGAGTAATAA 58.575 52.381 0.00 0.00 0.00 1.40
874 1019 1.901648 TGGGGGTGGGGAGTAATAAG 58.098 55.000 0.00 0.00 0.00 1.73
885 1030 2.798847 GGAGTAATAAGCGCCGTTAAGG 59.201 50.000 2.29 0.00 44.97 2.69
888 1033 2.406596 AATAAGCGCCGTTAAGGGAA 57.593 45.000 18.31 0.00 41.48 3.97
889 1034 1.949465 ATAAGCGCCGTTAAGGGAAG 58.051 50.000 18.31 11.34 41.48 3.46
890 1035 0.108041 TAAGCGCCGTTAAGGGAAGG 60.108 55.000 18.31 7.11 41.48 3.46
891 1036 2.814913 AAGCGCCGTTAAGGGAAGGG 62.815 60.000 18.31 4.77 44.57 3.95
892 1037 2.124860 CGCCGTTAAGGGAAGGGG 60.125 66.667 18.31 1.52 42.41 4.79
893 1038 2.662070 CGCCGTTAAGGGAAGGGGA 61.662 63.158 18.31 0.00 42.41 4.81
1075 1478 0.106719 CCTCCTCTCTCCTCGCTTCT 60.107 60.000 0.00 0.00 0.00 2.85
1254 1661 4.305989 TGCGCTTCAGTTTCTTGATTTT 57.694 36.364 9.73 0.00 0.00 1.82
1257 1664 4.557496 GCGCTTCAGTTTCTTGATTTTCCT 60.557 41.667 0.00 0.00 0.00 3.36
1273 1680 2.363306 TCCTTTTTCTGCTCTTGCCA 57.637 45.000 0.00 0.00 38.71 4.92
1275 1682 3.233507 TCCTTTTTCTGCTCTTGCCATT 58.766 40.909 0.00 0.00 38.71 3.16
1279 1686 0.885879 TTCTGCTCTTGCCATTGCTG 59.114 50.000 0.00 0.00 38.71 4.41
1408 1815 0.035458 CAACTTCCCGAGGTCTGCTT 59.965 55.000 0.00 0.00 0.00 3.91
1409 1816 0.321996 AACTTCCCGAGGTCTGCTTC 59.678 55.000 0.00 0.00 0.00 3.86
1410 1817 0.543174 ACTTCCCGAGGTCTGCTTCT 60.543 55.000 0.00 0.00 0.00 2.85
1411 1818 0.610687 CTTCCCGAGGTCTGCTTCTT 59.389 55.000 0.00 0.00 0.00 2.52
1412 1819 0.321671 TTCCCGAGGTCTGCTTCTTG 59.678 55.000 0.00 0.00 0.00 3.02
1413 1820 0.832135 TCCCGAGGTCTGCTTCTTGT 60.832 55.000 0.00 0.00 0.00 3.16
1427 1834 2.559698 TCTTGTTCTTGGCCGATTCA 57.440 45.000 0.00 0.00 0.00 2.57
1449 1856 0.852842 CCATTCCCCCAAGCTCCATA 59.147 55.000 0.00 0.00 0.00 2.74
1578 1985 5.480422 GGGACTGAAATTGGGTGAATTTACT 59.520 40.000 0.00 0.00 43.12 2.24
1606 2013 4.792704 GCGTGTGTTGATCTGGAACATTTT 60.793 41.667 0.94 0.00 38.20 1.82
1734 2191 8.964476 ACTATAGGTGGAGAACATGTTTATTG 57.036 34.615 13.36 8.04 0.00 1.90
2169 2629 5.306678 ACCCAGCAAGACAAATAAAAATCCA 59.693 36.000 0.00 0.00 0.00 3.41
2191 2651 2.128771 AAAGTGTTGGCTCGCCATAT 57.871 45.000 12.00 0.00 46.64 1.78
2347 2808 2.363711 TAGCATCATGCCGACGGTCC 62.364 60.000 16.73 0.00 46.52 4.46
2433 2901 4.180057 CTGTTAGTCCATCAAGAGACTGC 58.820 47.826 3.00 0.00 43.14 4.40
2780 3258 0.248289 ACAGAAGCCATGCCAAATGC 59.752 50.000 0.00 0.00 41.77 3.56
2989 3467 3.114616 CTGAAGTGCCCTGCGACG 61.115 66.667 0.00 0.00 0.00 5.12
3106 3584 2.836154 GCCCCAGACACCACTGAA 59.164 61.111 0.00 0.00 39.94 3.02
3124 3602 0.036448 AACAGTCGTCCTCGAGGAGA 59.964 55.000 34.41 27.15 46.49 3.71
3183 3661 1.722011 CAGCCGACATTCCTAACGTT 58.278 50.000 5.88 5.88 0.00 3.99
3228 3706 1.334869 GAGCACAACCAACCAACAGAG 59.665 52.381 0.00 0.00 0.00 3.35
3277 3755 1.070601 CAGTGGACAGACACATCACCA 59.929 52.381 0.00 0.00 43.72 4.17
3412 3890 3.610786 TCGAGATGCATCGAGTACTTC 57.389 47.619 20.67 10.03 46.20 3.01
3516 3995 4.286808 TGAAGTTCTGAAGGATCCACATCA 59.713 41.667 15.82 13.85 0.00 3.07
3726 4206 5.932303 TCACTAATGAAGTACTGCAAGGTTC 59.068 40.000 7.88 0.00 34.95 3.62
3784 4264 8.521176 CAACTTACTACCTCTGTACACTAATGT 58.479 37.037 0.00 0.00 43.30 2.71
3793 4273 8.251721 ACCTCTGTACACTAATGTAAGATGTTC 58.748 37.037 0.00 0.00 42.99 3.18
3797 4386 8.234887 TGTACACTAATGTAAGATGTTCAACG 57.765 34.615 0.00 0.00 42.99 4.10
3856 4445 7.504403 ACTCCCTCTGTTCACAATATAAGATG 58.496 38.462 0.00 0.00 0.00 2.90
3881 4470 8.792633 TGTTTTGCATATTTCTATATGGGCTAC 58.207 33.333 7.13 0.00 42.53 3.58
3882 4471 8.792633 GTTTTGCATATTTCTATATGGGCTACA 58.207 33.333 7.13 0.00 42.53 2.74
3883 4472 9.532494 TTTTGCATATTTCTATATGGGCTACAT 57.468 29.630 7.13 0.46 42.53 2.29
3885 4474 9.613428 TTGCATATTTCTATATGGGCTACATAC 57.387 33.333 7.13 0.00 44.41 2.39
3886 4475 8.992349 TGCATATTTCTATATGGGCTACATACT 58.008 33.333 7.13 0.00 44.41 2.12
3887 4476 9.265901 GCATATTTCTATATGGGCTACATACTG 57.734 37.037 7.13 1.98 44.41 2.74
3890 4479 8.671987 ATTTCTATATGGGCTACATACTGACT 57.328 34.615 4.22 0.00 44.41 3.41
3891 4480 7.468141 TTCTATATGGGCTACATACTGACTG 57.532 40.000 4.22 0.00 44.41 3.51
3892 4481 6.790319 TCTATATGGGCTACATACTGACTGA 58.210 40.000 4.22 0.00 44.41 3.41
3893 4482 7.238710 TCTATATGGGCTACATACTGACTGAA 58.761 38.462 4.22 0.00 44.41 3.02
3894 4483 6.747414 ATATGGGCTACATACTGACTGAAA 57.253 37.500 4.22 0.00 44.41 2.69
3895 4484 5.636903 ATGGGCTACATACTGACTGAAAT 57.363 39.130 0.00 0.00 38.26 2.17
3896 4485 4.769688 TGGGCTACATACTGACTGAAATG 58.230 43.478 0.00 0.00 0.00 2.32
3897 4486 4.225042 TGGGCTACATACTGACTGAAATGT 59.775 41.667 8.98 8.98 36.56 2.71
3898 4487 5.423931 TGGGCTACATACTGACTGAAATGTA 59.576 40.000 9.87 9.87 34.54 2.29
3899 4488 5.753921 GGGCTACATACTGACTGAAATGTAC 59.246 44.000 7.61 0.00 34.54 2.90
3900 4489 6.338146 GGCTACATACTGACTGAAATGTACA 58.662 40.000 0.00 0.00 34.54 2.90
3901 4490 6.986817 GGCTACATACTGACTGAAATGTACAT 59.013 38.462 1.41 1.41 34.54 2.29
3902 4491 8.141909 GGCTACATACTGACTGAAATGTACATA 58.858 37.037 9.21 0.00 34.54 2.29
3903 4492 8.969267 GCTACATACTGACTGAAATGTACATAC 58.031 37.037 9.21 7.35 34.54 2.39
3906 4495 9.317936 ACATACTGACTGAAATGTACATACATG 57.682 33.333 9.21 8.37 45.55 3.21
3907 4496 9.317936 CATACTGACTGAAATGTACATACATGT 57.682 33.333 9.21 2.69 45.55 3.21
3908 4497 7.834068 ACTGACTGAAATGTACATACATGTC 57.166 36.000 9.21 17.92 46.42 3.06
3909 4498 7.615403 ACTGACTGAAATGTACATACATGTCT 58.385 34.615 18.69 4.36 46.39 3.41
3910 4499 8.749354 ACTGACTGAAATGTACATACATGTCTA 58.251 33.333 18.69 8.20 46.39 2.59
3911 4500 9.755804 CTGACTGAAATGTACATACATGTCTAT 57.244 33.333 18.69 9.80 46.39 1.98
3964 4553 2.683933 GGCACGAGGGGGAGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
3965 4554 2.291043 GGCACGAGGGGGAGAAGAA 61.291 63.158 0.00 0.00 0.00 2.52
3966 4555 1.627297 GGCACGAGGGGGAGAAGAAT 61.627 60.000 0.00 0.00 0.00 2.40
3967 4556 1.120530 GCACGAGGGGGAGAAGAATA 58.879 55.000 0.00 0.00 0.00 1.75
3968 4557 1.069358 GCACGAGGGGGAGAAGAATAG 59.931 57.143 0.00 0.00 0.00 1.73
3969 4558 1.069358 CACGAGGGGGAGAAGAATAGC 59.931 57.143 0.00 0.00 0.00 2.97
3970 4559 1.062810 ACGAGGGGGAGAAGAATAGCT 60.063 52.381 0.00 0.00 0.00 3.32
3971 4560 1.616374 CGAGGGGGAGAAGAATAGCTC 59.384 57.143 0.00 0.00 0.00 4.09
3972 4561 2.754867 CGAGGGGGAGAAGAATAGCTCT 60.755 54.545 0.00 0.00 35.13 4.09
3984 4573 6.734104 AAGAATAGCTCTTCACAATCACAC 57.266 37.500 13.68 0.00 40.61 3.82
3985 4574 5.181748 AGAATAGCTCTTCACAATCACACC 58.818 41.667 13.68 0.00 0.00 4.16
3986 4575 2.936919 AGCTCTTCACAATCACACCA 57.063 45.000 0.00 0.00 0.00 4.17
3987 4576 3.430042 AGCTCTTCACAATCACACCAT 57.570 42.857 0.00 0.00 0.00 3.55
3988 4577 3.759581 AGCTCTTCACAATCACACCATT 58.240 40.909 0.00 0.00 0.00 3.16
3989 4578 3.755378 AGCTCTTCACAATCACACCATTC 59.245 43.478 0.00 0.00 0.00 2.67
3990 4579 3.425359 GCTCTTCACAATCACACCATTCG 60.425 47.826 0.00 0.00 0.00 3.34
3991 4580 3.996363 CTCTTCACAATCACACCATTCGA 59.004 43.478 0.00 0.00 0.00 3.71
3992 4581 4.384940 TCTTCACAATCACACCATTCGAA 58.615 39.130 0.00 0.00 0.00 3.71
3993 4582 5.003160 TCTTCACAATCACACCATTCGAAT 58.997 37.500 4.39 4.39 0.00 3.34
3994 4583 4.683501 TCACAATCACACCATTCGAATG 57.316 40.909 27.66 27.66 36.17 2.67
3995 4584 4.322567 TCACAATCACACCATTCGAATGA 58.677 39.130 34.21 18.72 38.70 2.57
3996 4585 4.392754 TCACAATCACACCATTCGAATGAG 59.607 41.667 34.21 27.07 38.70 2.90
3997 4586 4.154737 CACAATCACACCATTCGAATGAGT 59.845 41.667 34.21 27.64 38.70 3.41
3998 4587 4.393062 ACAATCACACCATTCGAATGAGTC 59.607 41.667 34.21 0.00 38.70 3.36
3999 4588 3.961480 TCACACCATTCGAATGAGTCT 57.039 42.857 34.21 17.53 38.70 3.24
4000 4589 5.598416 ATCACACCATTCGAATGAGTCTA 57.402 39.130 34.21 21.68 38.70 2.59
4001 4590 5.598416 TCACACCATTCGAATGAGTCTAT 57.402 39.130 34.21 16.59 38.70 1.98
4002 4591 6.709018 TCACACCATTCGAATGAGTCTATA 57.291 37.500 34.21 15.88 38.70 1.31
4003 4592 6.739112 TCACACCATTCGAATGAGTCTATAG 58.261 40.000 34.21 19.22 38.70 1.31
4004 4593 6.546034 TCACACCATTCGAATGAGTCTATAGA 59.454 38.462 34.21 21.28 38.70 1.98
4005 4594 7.231519 TCACACCATTCGAATGAGTCTATAGAT 59.768 37.037 34.21 10.01 38.70 1.98
4006 4595 7.869937 CACACCATTCGAATGAGTCTATAGATT 59.130 37.037 34.21 0.72 38.70 2.40
4007 4596 8.424918 ACACCATTCGAATGAGTCTATAGATTT 58.575 33.333 34.21 8.03 38.70 2.17
4008 4597 9.914131 CACCATTCGAATGAGTCTATAGATTTA 57.086 33.333 34.21 0.00 38.70 1.40
4014 4603 9.350951 TCGAATGAGTCTATAGATTTAACTCCA 57.649 33.333 5.57 0.00 36.39 3.86
4015 4604 9.619316 CGAATGAGTCTATAGATTTAACTCCAG 57.381 37.037 5.57 0.00 36.39 3.86
4016 4605 9.921637 GAATGAGTCTATAGATTTAACTCCAGG 57.078 37.037 5.57 0.00 36.39 4.45
4017 4606 9.661954 AATGAGTCTATAGATTTAACTCCAGGA 57.338 33.333 5.57 0.00 36.39 3.86
4018 4607 9.661954 ATGAGTCTATAGATTTAACTCCAGGAA 57.338 33.333 5.57 0.00 36.39 3.36
4019 4608 9.137459 TGAGTCTATAGATTTAACTCCAGGAAG 57.863 37.037 5.57 0.00 36.39 3.46
4020 4609 8.485578 AGTCTATAGATTTAACTCCAGGAAGG 57.514 38.462 5.57 0.00 39.47 3.46
4021 4610 8.068733 AGTCTATAGATTTAACTCCAGGAAGGT 58.931 37.037 5.57 0.00 39.02 3.50
4022 4611 9.364653 GTCTATAGATTTAACTCCAGGAAGGTA 57.635 37.037 5.57 0.00 39.02 3.08
4025 4614 6.253946 AGATTTAACTCCAGGAAGGTATGG 57.746 41.667 0.00 0.00 39.02 2.74
4026 4615 3.926058 TTAACTCCAGGAAGGTATGGC 57.074 47.619 0.00 0.00 39.02 4.40
4027 4616 1.668826 AACTCCAGGAAGGTATGGCA 58.331 50.000 0.00 0.00 39.02 4.92
4028 4617 1.898863 ACTCCAGGAAGGTATGGCAT 58.101 50.000 4.88 4.88 39.02 4.40
4029 4618 1.492176 ACTCCAGGAAGGTATGGCATG 59.508 52.381 10.98 0.00 39.02 4.06
4030 4619 0.846015 TCCAGGAAGGTATGGCATGG 59.154 55.000 10.98 1.17 39.02 3.66
4031 4620 0.825010 CCAGGAAGGTATGGCATGGC 60.825 60.000 13.29 13.29 0.00 4.40
4032 4621 0.106569 CAGGAAGGTATGGCATGGCA 60.107 55.000 25.52 25.52 0.00 4.92
4033 4622 0.630673 AGGAAGGTATGGCATGGCAA 59.369 50.000 27.04 12.65 0.00 4.52
4034 4623 1.035139 GGAAGGTATGGCATGGCAAG 58.965 55.000 27.04 0.00 0.00 4.01
4035 4624 1.035139 GAAGGTATGGCATGGCAAGG 58.965 55.000 27.04 0.00 0.00 3.61
4036 4625 1.044790 AAGGTATGGCATGGCAAGGC 61.045 55.000 27.04 17.61 0.00 4.35
4037 4626 1.757731 GGTATGGCATGGCAAGGCA 60.758 57.895 27.04 21.20 45.98 4.75
4038 4627 1.329171 GGTATGGCATGGCAAGGCAA 61.329 55.000 27.04 8.59 45.03 4.52
4039 4628 0.103572 GTATGGCATGGCAAGGCAAG 59.896 55.000 27.04 0.00 45.03 4.01
4040 4629 1.044231 TATGGCATGGCAAGGCAAGG 61.044 55.000 27.04 0.00 45.03 3.61
4041 4630 4.462280 GGCATGGCAAGGCAAGGC 62.462 66.667 15.47 9.40 33.81 4.35
4042 4631 3.697747 GCATGGCAAGGCAAGGCA 61.698 61.111 15.34 7.82 45.98 4.75
4043 4632 3.061752 CATGGCAAGGCAAGGCAA 58.938 55.556 9.31 0.00 45.03 4.52
4044 4633 1.079405 CATGGCAAGGCAAGGCAAG 60.079 57.895 9.31 1.99 45.03 4.01
4045 4634 2.288025 ATGGCAAGGCAAGGCAAGG 61.288 57.895 9.31 0.00 45.03 3.61
4046 4635 4.383861 GGCAAGGCAAGGCAAGGC 62.384 66.667 0.00 0.00 0.00 4.35
4047 4636 3.308705 GCAAGGCAAGGCAAGGCT 61.309 61.111 0.00 0.00 44.54 4.58
4048 4637 2.968206 CAAGGCAAGGCAAGGCTC 59.032 61.111 5.78 0.00 41.47 4.70
4049 4638 1.605738 CAAGGCAAGGCAAGGCTCT 60.606 57.895 5.78 0.00 41.47 4.09
4050 4639 1.154688 AAGGCAAGGCAAGGCTCTT 59.845 52.632 5.78 0.00 41.47 2.85
4051 4640 0.897401 AAGGCAAGGCAAGGCTCTTC 60.897 55.000 5.78 0.00 41.47 2.87
4052 4641 1.604593 GGCAAGGCAAGGCTCTTCA 60.605 57.895 0.00 0.00 0.00 3.02
4053 4642 1.583477 GCAAGGCAAGGCTCTTCAC 59.417 57.895 0.00 0.00 0.00 3.18
4140 4729 1.404583 GCCAACTGCCCATGTCATTTC 60.405 52.381 0.00 0.00 0.00 2.17
4143 4732 3.087031 CAACTGCCCATGTCATTTCTCT 58.913 45.455 0.00 0.00 0.00 3.10
4216 4806 1.320344 CGTCCCGGTTCATCTCCTCA 61.320 60.000 0.00 0.00 0.00 3.86
4245 4835 0.905357 ACTCCATTTCCCTCTCCACG 59.095 55.000 0.00 0.00 0.00 4.94
4250 4840 1.272554 ATTTCCCTCTCCACGTCCCC 61.273 60.000 0.00 0.00 0.00 4.81
4391 5005 2.434185 GATCACCAGGACGCGCAA 60.434 61.111 5.73 0.00 0.00 4.85
4406 5020 1.699656 CGCAAGAGAATGTCGCCCTG 61.700 60.000 0.00 0.00 43.02 4.45
4450 5077 3.390521 CCTACGGGCTGGAGTGCA 61.391 66.667 4.52 0.00 34.04 4.57
4451 5078 2.125512 CTACGGGCTGGAGTGCAC 60.126 66.667 9.40 9.40 34.04 4.57
4465 5092 3.958860 GCACCACAGGCCACCTCT 61.959 66.667 5.01 0.00 0.00 3.69
4519 5146 1.965930 TCTGCCCAATGACGCACAC 60.966 57.895 0.00 0.00 0.00 3.82
4536 5163 0.246360 CACATGCCCTGACACGACTA 59.754 55.000 0.00 0.00 0.00 2.59
4547 5174 0.243095 ACACGACTAGTTTCTCGCCC 59.757 55.000 0.00 0.00 32.98 6.13
4585 5212 0.109272 ATATGATGTCCGCTACGCCG 60.109 55.000 0.00 0.00 0.00 6.46
4590 5217 2.278989 GTCCGCTACGCCGCATAA 60.279 61.111 0.00 0.00 0.00 1.90
4602 5230 0.104304 CCGCATAAGCCTAGGTCGTT 59.896 55.000 11.31 4.59 37.52 3.85
4604 5232 1.202371 CGCATAAGCCTAGGTCGTTCA 60.202 52.381 11.31 0.00 37.52 3.18
4621 5249 3.057337 ACCCCGGTGAAGTCTTCG 58.943 61.111 8.06 0.00 0.00 3.79
4658 5286 1.079127 AATCGTTGGCGGTGGAGAG 60.079 57.895 0.00 0.00 38.89 3.20
4659 5287 2.521958 AATCGTTGGCGGTGGAGAGG 62.522 60.000 0.00 0.00 38.89 3.69
4660 5288 3.691342 CGTTGGCGGTGGAGAGGA 61.691 66.667 0.00 0.00 0.00 3.71
4661 5289 2.266055 GTTGGCGGTGGAGAGGAG 59.734 66.667 0.00 0.00 0.00 3.69
4662 5290 3.706373 TTGGCGGTGGAGAGGAGC 61.706 66.667 0.00 0.00 0.00 4.70
4664 5292 3.474570 GGCGGTGGAGAGGAGCAT 61.475 66.667 0.00 0.00 0.00 3.79
4665 5293 2.202987 GCGGTGGAGAGGAGCATG 60.203 66.667 0.00 0.00 0.00 4.06
4666 5294 2.202987 CGGTGGAGAGGAGCATGC 60.203 66.667 10.51 10.51 0.00 4.06
4667 5295 2.191641 GGTGGAGAGGAGCATGCC 59.808 66.667 15.66 5.80 0.00 4.40
4668 5296 2.673200 GGTGGAGAGGAGCATGCCA 61.673 63.158 15.66 0.00 0.00 4.92
4669 5297 1.530771 GTGGAGAGGAGCATGCCAT 59.469 57.895 15.66 3.19 0.00 4.40
4670 5298 0.106819 GTGGAGAGGAGCATGCCATT 60.107 55.000 15.66 0.00 0.00 3.16
4671 5299 0.627451 TGGAGAGGAGCATGCCATTT 59.373 50.000 15.66 0.00 0.00 2.32
4672 5300 1.030457 GGAGAGGAGCATGCCATTTG 58.970 55.000 15.66 0.00 0.00 2.32
4673 5301 1.030457 GAGAGGAGCATGCCATTTGG 58.970 55.000 15.66 0.00 38.53 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.540914 TGGTTAACTTTGGTTTAGTCTGACAG 59.459 38.462 10.88 0.00 36.92 3.51
23 24 9.758651 ATTTTGATGGTTAACTTTGGTTTAGTC 57.241 29.630 5.42 0.00 36.92 2.59
109 110 9.802039 TTGGTTTGTAAGAACTTCCTAATGTAT 57.198 29.630 0.00 0.00 0.00 2.29
110 111 9.629878 TTTGGTTTGTAAGAACTTCCTAATGTA 57.370 29.630 0.00 0.00 0.00 2.29
111 112 8.528044 TTTGGTTTGTAAGAACTTCCTAATGT 57.472 30.769 0.00 0.00 0.00 2.71
112 113 8.630037 ACTTTGGTTTGTAAGAACTTCCTAATG 58.370 33.333 0.00 0.00 0.00 1.90
113 114 8.630037 CACTTTGGTTTGTAAGAACTTCCTAAT 58.370 33.333 0.00 0.00 0.00 1.73
115 116 6.544564 CCACTTTGGTTTGTAAGAACTTCCTA 59.455 38.462 0.00 0.00 31.35 2.94
116 117 5.359860 CCACTTTGGTTTGTAAGAACTTCCT 59.640 40.000 0.00 0.00 31.35 3.36
117 118 5.588240 CCACTTTGGTTTGTAAGAACTTCC 58.412 41.667 0.00 0.00 31.35 3.46
132 133 6.445357 ACTTGTAACTTGTAACCACTTTGG 57.555 37.500 0.00 0.00 45.02 3.28
135 136 9.398538 TGATAAACTTGTAACTTGTAACCACTT 57.601 29.630 0.00 0.00 0.00 3.16
136 137 8.967664 TGATAAACTTGTAACTTGTAACCACT 57.032 30.769 0.00 0.00 0.00 4.00
137 138 9.607285 CATGATAAACTTGTAACTTGTAACCAC 57.393 33.333 0.00 0.00 0.00 4.16
138 139 9.344772 ACATGATAAACTTGTAACTTGTAACCA 57.655 29.630 0.00 0.00 35.57 3.67
139 140 9.821662 GACATGATAAACTTGTAACTTGTAACC 57.178 33.333 0.00 0.00 37.08 2.85
143 144 8.023128 GCATGACATGATAAACTTGTAACTTGT 58.977 33.333 19.76 0.00 37.08 3.16
144 145 8.239314 AGCATGACATGATAAACTTGTAACTTG 58.761 33.333 19.76 0.00 37.08 3.16
145 146 8.340618 AGCATGACATGATAAACTTGTAACTT 57.659 30.769 19.76 0.00 37.08 2.66
146 147 7.928307 AGCATGACATGATAAACTTGTAACT 57.072 32.000 19.76 0.00 37.08 2.24
147 148 8.970691 AAAGCATGACATGATAAACTTGTAAC 57.029 30.769 19.76 0.00 37.08 2.50
221 222 9.994432 ACGTCAATTGATCTTTCTGAATTATTC 57.006 29.630 12.12 0.00 0.00 1.75
222 223 9.994432 GACGTCAATTGATCTTTCTGAATTATT 57.006 29.630 12.12 0.00 0.00 1.40
224 225 8.443160 GTGACGTCAATTGATCTTTCTGAATTA 58.557 33.333 21.95 0.00 0.00 1.40
225 226 7.041167 TGTGACGTCAATTGATCTTTCTGAATT 60.041 33.333 21.95 0.00 0.00 2.17
227 228 5.757808 TGTGACGTCAATTGATCTTTCTGAA 59.242 36.000 21.95 0.00 0.00 3.02
228 229 5.296748 TGTGACGTCAATTGATCTTTCTGA 58.703 37.500 21.95 0.00 0.00 3.27
234 236 3.738982 TGGTTGTGACGTCAATTGATCT 58.261 40.909 21.95 0.00 0.00 2.75
247 249 2.746279 ACCCACTTCAATGGTTGTGA 57.254 45.000 0.00 0.00 38.16 3.58
266 268 1.081509 GTCTTTTGATGCGGCGCAA 60.082 52.632 39.46 21.57 43.62 4.85
278 371 4.023193 GGTTGTGACATCAATCGGTCTTTT 60.023 41.667 0.00 0.00 35.11 2.27
314 407 1.153958 GGTCTTTCAATGCAGCGCC 60.154 57.895 2.29 0.00 0.00 6.53
319 412 1.340889 GCCAACTGGTCTTTCAATGCA 59.659 47.619 0.00 0.00 37.57 3.96
320 413 1.666888 CGCCAACTGGTCTTTCAATGC 60.667 52.381 0.00 0.00 37.57 3.56
323 416 2.623878 TACGCCAACTGGTCTTTCAA 57.376 45.000 0.00 0.00 37.57 2.69
324 417 2.811431 CAATACGCCAACTGGTCTTTCA 59.189 45.455 0.00 0.00 37.57 2.69
338 432 3.051392 GCAGCCCACACCAATACGC 62.051 63.158 0.00 0.00 0.00 4.42
339 433 2.749865 CGCAGCCCACACCAATACG 61.750 63.158 0.00 0.00 0.00 3.06
371 465 1.933181 GATGGTTGCGACATCAATCGA 59.067 47.619 6.39 0.00 45.13 3.59
466 560 2.627699 ACCAATGGTTGCGACTTCAATT 59.372 40.909 0.00 0.00 27.29 2.32
472 566 1.172180 CCACACCAATGGTTGCGACT 61.172 55.000 0.16 0.00 34.77 4.18
473 567 1.285641 CCACACCAATGGTTGCGAC 59.714 57.895 0.16 0.00 34.77 5.19
474 568 1.900981 CCCACACCAATGGTTGCGA 60.901 57.895 0.16 0.00 38.16 5.10
476 570 2.209315 AGCCCACACCAATGGTTGC 61.209 57.895 0.16 3.43 38.16 4.17
498 638 3.636313 AATCGGTCTTTCGGCGCGA 62.636 57.895 12.10 4.50 0.00 5.87
499 639 3.186047 AATCGGTCTTTCGGCGCG 61.186 61.111 0.00 0.00 0.00 6.86
545 685 0.318869 TAACAAGTCTTTCGGCGCGA 60.319 50.000 12.10 0.00 0.00 5.87
576 716 1.448893 GGCGCAACCCGAGTCAATA 60.449 57.895 10.83 0.00 40.02 1.90
588 728 0.878416 GGTATTTCAGTGTGGCGCAA 59.122 50.000 10.83 0.00 0.00 4.85
616 756 1.065600 CCGCGCCAATGGTTTATGG 59.934 57.895 0.00 0.00 39.80 2.74
687 827 1.244019 AATCTGGTGTTTCGGGCAGC 61.244 55.000 0.00 0.00 35.19 5.25
689 829 2.026729 TCATAATCTGGTGTTTCGGGCA 60.027 45.455 0.00 0.00 0.00 5.36
796 941 8.698210 TCTTCCAAGAGTGTACTACTTTTGTTA 58.302 33.333 18.45 9.89 45.33 2.41
855 1000 1.901648 CTTATTACTCCCCACCCCCA 58.098 55.000 0.00 0.00 0.00 4.96
856 1001 0.477204 GCTTATTACTCCCCACCCCC 59.523 60.000 0.00 0.00 0.00 5.40
857 1002 0.108019 CGCTTATTACTCCCCACCCC 59.892 60.000 0.00 0.00 0.00 4.95
858 1003 0.534427 GCGCTTATTACTCCCCACCC 60.534 60.000 0.00 0.00 0.00 4.61
859 1004 0.534427 GGCGCTTATTACTCCCCACC 60.534 60.000 7.64 0.00 0.00 4.61
860 1005 0.878961 CGGCGCTTATTACTCCCCAC 60.879 60.000 7.64 0.00 0.00 4.61
861 1006 1.332144 ACGGCGCTTATTACTCCCCA 61.332 55.000 6.90 0.00 0.00 4.96
862 1007 0.179065 AACGGCGCTTATTACTCCCC 60.179 55.000 6.90 0.00 0.00 4.81
863 1008 2.514205 TAACGGCGCTTATTACTCCC 57.486 50.000 6.90 0.00 0.00 4.30
864 1009 2.798847 CCTTAACGGCGCTTATTACTCC 59.201 50.000 6.90 0.00 0.00 3.85
865 1010 2.798847 CCCTTAACGGCGCTTATTACTC 59.201 50.000 6.90 0.00 0.00 2.59
866 1011 2.431782 TCCCTTAACGGCGCTTATTACT 59.568 45.455 6.90 0.00 0.00 2.24
867 1012 2.825205 TCCCTTAACGGCGCTTATTAC 58.175 47.619 6.90 0.00 0.00 1.89
868 1013 3.460103 CTTCCCTTAACGGCGCTTATTA 58.540 45.455 6.90 0.51 0.00 0.98
869 1014 2.285977 CTTCCCTTAACGGCGCTTATT 58.714 47.619 6.90 1.60 0.00 1.40
870 1015 1.474498 CCTTCCCTTAACGGCGCTTAT 60.474 52.381 6.90 0.00 0.00 1.73
871 1016 0.108041 CCTTCCCTTAACGGCGCTTA 60.108 55.000 6.90 2.03 0.00 3.09
872 1017 1.376812 CCTTCCCTTAACGGCGCTT 60.377 57.895 6.90 3.13 0.00 4.68
873 1018 2.267961 CCTTCCCTTAACGGCGCT 59.732 61.111 6.90 0.00 0.00 5.92
874 1019 2.822701 CCCTTCCCTTAACGGCGC 60.823 66.667 6.90 0.00 0.00 6.53
885 1030 1.228510 CTCCCATGCTTCCCCTTCC 59.771 63.158 0.00 0.00 0.00 3.46
888 1033 1.695597 CCTCTCCCATGCTTCCCCT 60.696 63.158 0.00 0.00 0.00 4.79
889 1034 2.761465 CCCTCTCCCATGCTTCCCC 61.761 68.421 0.00 0.00 0.00 4.81
890 1035 2.761465 CCCCTCTCCCATGCTTCCC 61.761 68.421 0.00 0.00 0.00 3.97
891 1036 2.761465 CCCCCTCTCCCATGCTTCC 61.761 68.421 0.00 0.00 0.00 3.46
892 1037 2.922234 CCCCCTCTCCCATGCTTC 59.078 66.667 0.00 0.00 0.00 3.86
893 1038 3.424105 GCCCCCTCTCCCATGCTT 61.424 66.667 0.00 0.00 0.00 3.91
1075 1478 0.327259 TCGGTCGGAGAAGGAGAAGA 59.673 55.000 0.00 0.00 39.69 2.87
1192 1599 2.749621 CGAGAAATTAGCAGGGCAAACT 59.250 45.455 0.00 0.00 0.00 2.66
1254 1661 2.363306 TGGCAAGAGCAGAAAAAGGA 57.637 45.000 0.00 0.00 44.61 3.36
1257 1664 2.366266 AGCAATGGCAAGAGCAGAAAAA 59.634 40.909 10.95 0.00 44.61 1.94
1273 1680 3.726517 GTCGCCACGCACAGCAAT 61.727 61.111 0.00 0.00 0.00 3.56
1287 1694 3.068691 TCCTCCTTCCTGGCGTCG 61.069 66.667 0.00 0.00 35.26 5.12
1350 1757 1.592400 CGCCGTACTTCCTCCACTGA 61.592 60.000 0.00 0.00 0.00 3.41
1408 1815 2.151202 GTGAATCGGCCAAGAACAAGA 58.849 47.619 2.24 0.00 0.00 3.02
1409 1816 2.154462 AGTGAATCGGCCAAGAACAAG 58.846 47.619 2.24 0.00 0.00 3.16
1410 1817 2.151202 GAGTGAATCGGCCAAGAACAA 58.849 47.619 2.24 0.00 0.00 2.83
1411 1818 1.610624 GGAGTGAATCGGCCAAGAACA 60.611 52.381 2.24 0.00 0.00 3.18
1412 1819 1.087501 GGAGTGAATCGGCCAAGAAC 58.912 55.000 2.24 0.00 0.00 3.01
1413 1820 0.690192 TGGAGTGAATCGGCCAAGAA 59.310 50.000 2.24 0.00 0.00 2.52
1427 1834 1.575447 GGAGCTTGGGGGAATGGAGT 61.575 60.000 0.00 0.00 0.00 3.85
1449 1856 4.709397 TGCATGAACGGGAATAGGAAAAAT 59.291 37.500 0.00 0.00 0.00 1.82
1569 1976 2.224426 ACACACGCCCTCAGTAAATTCA 60.224 45.455 0.00 0.00 0.00 2.57
1578 1985 0.320683 CAGATCAACACACGCCCTCA 60.321 55.000 0.00 0.00 0.00 3.86
1613 2020 2.535836 AGGAGTAGAAGGTCCAGGAC 57.464 55.000 11.70 11.70 35.02 3.85
1614 2021 3.562108 AAAGGAGTAGAAGGTCCAGGA 57.438 47.619 0.00 0.00 35.02 3.86
1778 2235 5.344128 CACAAGCTGCATACAAAGAAATGTC 59.656 40.000 1.02 0.00 34.75 3.06
1858 2318 6.714356 TGATGTGATTTGTGGTACTGATGAAA 59.286 34.615 0.00 0.00 0.00 2.69
2347 2808 8.669243 CAAGGAAGTAAAAGAAGTATTAGCTGG 58.331 37.037 0.00 0.00 0.00 4.85
2647 3125 7.025963 GCCTTATTCTTCTTCACATTTGAGTG 58.974 38.462 0.00 0.00 40.85 3.51
2785 3263 3.895232 ACAATAGGTGCATTCGAGAGT 57.105 42.857 0.00 0.00 0.00 3.24
2898 3376 5.480422 AGATTTAAATTTCCAAGCCCGAAGT 59.520 36.000 1.43 0.00 0.00 3.01
2989 3467 2.851195 TCCTTCTGCTGGACTTGTTTC 58.149 47.619 0.00 0.00 0.00 2.78
3106 3584 0.391927 CTCTCCTCGAGGACGACTGT 60.392 60.000 30.49 0.00 43.81 3.55
3202 3680 1.891919 GTTGGTTGTGCTCGCTGGA 60.892 57.895 0.00 0.00 0.00 3.86
3319 3797 1.664649 CGAAGCGTCTGTTCCAGCA 60.665 57.895 0.00 0.00 0.00 4.41
3355 3833 0.528017 GTGTCCTCGACAGAGCATGA 59.472 55.000 0.00 0.00 43.57 3.07
3412 3890 3.251729 CACACTTCCATCACAAGAACTGG 59.748 47.826 0.00 0.00 0.00 4.00
3516 3995 0.539051 AGCAGCGGCAGTAATCTCTT 59.461 50.000 12.44 0.00 44.61 2.85
3741 4221 1.784283 GTTGCATAAACCAACACACGC 59.216 47.619 0.00 0.00 41.58 5.34
3784 4264 9.135843 CACTAATGTAAGACGTTGAACATCTTA 57.864 33.333 9.51 9.51 34.55 2.10
3793 4273 6.527023 CCTCTGTACACTAATGTAAGACGTTG 59.473 42.308 0.00 0.00 42.99 4.10
3797 4386 8.278729 ACTACCTCTGTACACTAATGTAAGAC 57.721 38.462 0.00 0.00 42.99 3.01
3856 4445 8.792633 TGTAGCCCATATAGAAATATGCAAAAC 58.207 33.333 0.00 0.00 42.48 2.43
3868 4457 6.790319 TCAGTCAGTATGTAGCCCATATAGA 58.210 40.000 0.00 0.00 38.29 1.98
3870 4459 7.849322 TTTCAGTCAGTATGTAGCCCATATA 57.151 36.000 0.00 0.00 38.29 0.86
3881 4470 9.317936 ACATGTATGTACATTTCAGTCAGTATG 57.682 33.333 14.77 9.36 43.99 2.39
3882 4471 9.534565 GACATGTATGTACATTTCAGTCAGTAT 57.465 33.333 14.77 0.00 43.99 2.12
3883 4472 8.749354 AGACATGTATGTACATTTCAGTCAGTA 58.251 33.333 14.77 0.00 43.99 2.74
3884 4473 7.615403 AGACATGTATGTACATTTCAGTCAGT 58.385 34.615 14.77 10.72 43.99 3.41
3885 4474 9.755804 ATAGACATGTATGTACATTTCAGTCAG 57.244 33.333 14.77 8.16 43.99 3.51
3938 4527 2.258013 CCCTCGTGCCGCTGAAAAA 61.258 57.895 0.00 0.00 0.00 1.94
3939 4528 2.668212 CCCTCGTGCCGCTGAAAA 60.668 61.111 0.00 0.00 0.00 2.29
3940 4529 4.697756 CCCCTCGTGCCGCTGAAA 62.698 66.667 0.00 0.00 0.00 2.69
3946 4535 4.148825 CTTCTCCCCCTCGTGCCG 62.149 72.222 0.00 0.00 0.00 5.69
3947 4536 1.627297 ATTCTTCTCCCCCTCGTGCC 61.627 60.000 0.00 0.00 0.00 5.01
3948 4537 1.069358 CTATTCTTCTCCCCCTCGTGC 59.931 57.143 0.00 0.00 0.00 5.34
3949 4538 1.069358 GCTATTCTTCTCCCCCTCGTG 59.931 57.143 0.00 0.00 0.00 4.35
3950 4539 1.062810 AGCTATTCTTCTCCCCCTCGT 60.063 52.381 0.00 0.00 0.00 4.18
3951 4540 1.616374 GAGCTATTCTTCTCCCCCTCG 59.384 57.143 0.00 0.00 0.00 4.63
3952 4541 2.970987 AGAGCTATTCTTCTCCCCCTC 58.029 52.381 0.00 0.00 29.61 4.30
3953 4542 3.429736 AAGAGCTATTCTTCTCCCCCT 57.570 47.619 0.00 0.00 42.54 4.79
3962 4551 5.181748 GGTGTGATTGTGAAGAGCTATTCT 58.818 41.667 20.95 1.41 37.93 2.40
3963 4552 4.937620 TGGTGTGATTGTGAAGAGCTATTC 59.062 41.667 14.21 14.21 0.00 1.75
3964 4553 4.910195 TGGTGTGATTGTGAAGAGCTATT 58.090 39.130 0.00 0.00 0.00 1.73
3965 4554 4.558226 TGGTGTGATTGTGAAGAGCTAT 57.442 40.909 0.00 0.00 0.00 2.97
3966 4555 4.558226 ATGGTGTGATTGTGAAGAGCTA 57.442 40.909 0.00 0.00 0.00 3.32
3967 4556 2.936919 TGGTGTGATTGTGAAGAGCT 57.063 45.000 0.00 0.00 0.00 4.09
3968 4557 3.425359 CGAATGGTGTGATTGTGAAGAGC 60.425 47.826 0.00 0.00 0.00 4.09
3969 4558 3.996363 TCGAATGGTGTGATTGTGAAGAG 59.004 43.478 0.00 0.00 0.00 2.85
3970 4559 4.001618 TCGAATGGTGTGATTGTGAAGA 57.998 40.909 0.00 0.00 0.00 2.87
3971 4560 4.747540 TTCGAATGGTGTGATTGTGAAG 57.252 40.909 0.00 0.00 0.00 3.02
3972 4561 4.759183 TCATTCGAATGGTGTGATTGTGAA 59.241 37.500 32.03 10.19 37.03 3.18
3973 4562 4.322567 TCATTCGAATGGTGTGATTGTGA 58.677 39.130 32.03 11.30 37.03 3.58
3974 4563 4.154737 ACTCATTCGAATGGTGTGATTGTG 59.845 41.667 32.03 12.73 37.03 3.33
3975 4564 4.326826 ACTCATTCGAATGGTGTGATTGT 58.673 39.130 32.03 16.97 37.03 2.71
3976 4565 4.633126 AGACTCATTCGAATGGTGTGATTG 59.367 41.667 32.03 16.47 37.03 2.67
3977 4566 4.836825 AGACTCATTCGAATGGTGTGATT 58.163 39.130 32.03 12.38 37.03 2.57
3978 4567 4.478206 AGACTCATTCGAATGGTGTGAT 57.522 40.909 32.03 19.55 37.03 3.06
3979 4568 3.961480 AGACTCATTCGAATGGTGTGA 57.039 42.857 32.03 16.52 37.03 3.58
3980 4569 6.739112 TCTATAGACTCATTCGAATGGTGTG 58.261 40.000 32.03 22.26 37.03 3.82
3981 4570 6.961360 TCTATAGACTCATTCGAATGGTGT 57.039 37.500 32.03 28.65 37.03 4.16
3982 4571 8.824159 AAATCTATAGACTCATTCGAATGGTG 57.176 34.615 32.03 26.25 37.03 4.17
3988 4577 9.350951 TGGAGTTAAATCTATAGACTCATTCGA 57.649 33.333 16.25 0.00 38.72 3.71
3989 4578 9.619316 CTGGAGTTAAATCTATAGACTCATTCG 57.381 37.037 16.25 2.94 38.72 3.34
3990 4579 9.921637 CCTGGAGTTAAATCTATAGACTCATTC 57.078 37.037 16.25 6.99 38.72 2.67
3991 4580 9.661954 TCCTGGAGTTAAATCTATAGACTCATT 57.338 33.333 16.25 8.29 38.72 2.57
3992 4581 9.661954 TTCCTGGAGTTAAATCTATAGACTCAT 57.338 33.333 16.25 3.34 38.72 2.90
3993 4582 9.137459 CTTCCTGGAGTTAAATCTATAGACTCA 57.863 37.037 16.25 6.01 38.72 3.41
3994 4583 8.581578 CCTTCCTGGAGTTAAATCTATAGACTC 58.418 40.741 4.10 7.24 38.35 3.36
3995 4584 8.068733 ACCTTCCTGGAGTTAAATCTATAGACT 58.931 37.037 4.10 0.00 39.71 3.24
3996 4585 8.252624 ACCTTCCTGGAGTTAAATCTATAGAC 57.747 38.462 4.10 0.00 39.71 2.59
3999 4588 9.101325 CCATACCTTCCTGGAGTTAAATCTATA 57.899 37.037 2.56 0.00 39.71 1.31
4000 4589 7.474936 GCCATACCTTCCTGGAGTTAAATCTAT 60.475 40.741 2.56 0.00 39.71 1.98
4001 4590 6.183361 GCCATACCTTCCTGGAGTTAAATCTA 60.183 42.308 2.56 0.00 39.71 1.98
4002 4591 5.398012 GCCATACCTTCCTGGAGTTAAATCT 60.398 44.000 2.56 0.00 39.71 2.40
4003 4592 4.822350 GCCATACCTTCCTGGAGTTAAATC 59.178 45.833 0.00 0.00 39.71 2.17
4004 4593 4.229582 TGCCATACCTTCCTGGAGTTAAAT 59.770 41.667 0.00 0.00 39.71 1.40
4005 4594 3.589735 TGCCATACCTTCCTGGAGTTAAA 59.410 43.478 0.00 0.00 39.71 1.52
4006 4595 3.186283 TGCCATACCTTCCTGGAGTTAA 58.814 45.455 0.00 0.00 39.71 2.01
4007 4596 2.840511 TGCCATACCTTCCTGGAGTTA 58.159 47.619 0.00 0.00 39.71 2.24
4008 4597 1.668826 TGCCATACCTTCCTGGAGTT 58.331 50.000 0.00 0.00 39.71 3.01
4009 4598 1.492176 CATGCCATACCTTCCTGGAGT 59.508 52.381 0.00 0.00 39.71 3.85
4010 4599 1.202855 CCATGCCATACCTTCCTGGAG 60.203 57.143 0.00 0.00 39.71 3.86
4011 4600 0.846015 CCATGCCATACCTTCCTGGA 59.154 55.000 0.00 0.00 39.71 3.86
4012 4601 0.825010 GCCATGCCATACCTTCCTGG 60.825 60.000 0.00 0.00 42.93 4.45
4013 4602 0.106569 TGCCATGCCATACCTTCCTG 60.107 55.000 0.00 0.00 0.00 3.86
4014 4603 0.630673 TTGCCATGCCATACCTTCCT 59.369 50.000 0.00 0.00 0.00 3.36
4015 4604 1.035139 CTTGCCATGCCATACCTTCC 58.965 55.000 0.00 0.00 0.00 3.46
4016 4605 1.035139 CCTTGCCATGCCATACCTTC 58.965 55.000 0.00 0.00 0.00 3.46
4017 4606 1.044790 GCCTTGCCATGCCATACCTT 61.045 55.000 0.00 0.00 0.00 3.50
4018 4607 1.456331 GCCTTGCCATGCCATACCT 60.456 57.895 0.00 0.00 0.00 3.08
4019 4608 1.329171 TTGCCTTGCCATGCCATACC 61.329 55.000 0.00 0.00 0.00 2.73
4020 4609 0.103572 CTTGCCTTGCCATGCCATAC 59.896 55.000 0.00 0.00 0.00 2.39
4021 4610 1.044231 CCTTGCCTTGCCATGCCATA 61.044 55.000 0.00 0.00 0.00 2.74
4022 4611 2.363975 CCTTGCCTTGCCATGCCAT 61.364 57.895 0.00 0.00 0.00 4.40
4023 4612 2.998480 CCTTGCCTTGCCATGCCA 60.998 61.111 0.00 0.00 0.00 4.92
4024 4613 4.462280 GCCTTGCCTTGCCATGCC 62.462 66.667 0.00 0.00 0.00 4.40
4025 4614 3.242897 TTGCCTTGCCTTGCCATGC 62.243 57.895 0.00 0.00 0.00 4.06
4026 4615 1.079405 CTTGCCTTGCCTTGCCATG 60.079 57.895 0.00 0.00 0.00 3.66
4027 4616 2.288025 CCTTGCCTTGCCTTGCCAT 61.288 57.895 0.00 0.00 0.00 4.40
4028 4617 2.918802 CCTTGCCTTGCCTTGCCA 60.919 61.111 0.00 0.00 0.00 4.92
4029 4618 4.383861 GCCTTGCCTTGCCTTGCC 62.384 66.667 0.00 0.00 0.00 4.52
4030 4619 3.292500 GAGCCTTGCCTTGCCTTGC 62.293 63.158 0.00 0.00 0.00 4.01
4031 4620 1.183676 AAGAGCCTTGCCTTGCCTTG 61.184 55.000 0.00 0.00 0.00 3.61
4032 4621 0.897401 GAAGAGCCTTGCCTTGCCTT 60.897 55.000 0.00 0.00 0.00 4.35
4033 4622 1.303970 GAAGAGCCTTGCCTTGCCT 60.304 57.895 0.00 0.00 0.00 4.75
4034 4623 1.604593 TGAAGAGCCTTGCCTTGCC 60.605 57.895 0.00 0.00 0.00 4.52
4035 4624 1.174712 TGTGAAGAGCCTTGCCTTGC 61.175 55.000 0.00 0.00 0.00 4.01
4036 4625 1.321474 TTGTGAAGAGCCTTGCCTTG 58.679 50.000 0.00 0.00 0.00 3.61
4037 4626 2.165998 GATTGTGAAGAGCCTTGCCTT 58.834 47.619 0.00 0.00 0.00 4.35
4038 4627 1.074405 TGATTGTGAAGAGCCTTGCCT 59.926 47.619 0.00 0.00 0.00 4.75
4039 4628 1.200948 GTGATTGTGAAGAGCCTTGCC 59.799 52.381 0.00 0.00 0.00 4.52
4040 4629 1.881973 TGTGATTGTGAAGAGCCTTGC 59.118 47.619 0.00 0.00 0.00 4.01
4041 4630 2.227388 GGTGTGATTGTGAAGAGCCTTG 59.773 50.000 0.00 0.00 0.00 3.61
4042 4631 2.158623 TGGTGTGATTGTGAAGAGCCTT 60.159 45.455 0.00 0.00 0.00 4.35
4043 4632 1.421268 TGGTGTGATTGTGAAGAGCCT 59.579 47.619 0.00 0.00 0.00 4.58
4044 4633 1.896220 TGGTGTGATTGTGAAGAGCC 58.104 50.000 0.00 0.00 0.00 4.70
4045 4634 3.503363 TGAATGGTGTGATTGTGAAGAGC 59.497 43.478 0.00 0.00 0.00 4.09
4046 4635 5.694231 TTGAATGGTGTGATTGTGAAGAG 57.306 39.130 0.00 0.00 0.00 2.85
4047 4636 5.827267 TCTTTGAATGGTGTGATTGTGAAGA 59.173 36.000 0.00 0.00 0.00 2.87
4048 4637 6.075762 TCTTTGAATGGTGTGATTGTGAAG 57.924 37.500 0.00 0.00 0.00 3.02
4049 4638 6.461370 CCTTCTTTGAATGGTGTGATTGTGAA 60.461 38.462 0.00 0.00 0.00 3.18
4050 4639 5.009911 CCTTCTTTGAATGGTGTGATTGTGA 59.990 40.000 0.00 0.00 0.00 3.58
4051 4640 5.224888 CCTTCTTTGAATGGTGTGATTGTG 58.775 41.667 0.00 0.00 0.00 3.33
4052 4641 4.262164 GCCTTCTTTGAATGGTGTGATTGT 60.262 41.667 0.00 0.00 0.00 2.71
4053 4642 4.021719 AGCCTTCTTTGAATGGTGTGATTG 60.022 41.667 0.00 0.00 0.00 2.67
4128 4717 1.747355 GTGGCAGAGAAATGACATGGG 59.253 52.381 0.00 0.00 41.20 4.00
4216 4806 1.620822 GAAATGGAGTTGTGGGCAGT 58.379 50.000 0.00 0.00 0.00 4.40
4245 4835 3.403558 GTGGAGCCAGAGGGGGAC 61.404 72.222 0.00 0.00 37.04 4.46
4250 4840 3.086600 GGGGAGTGGAGCCAGAGG 61.087 72.222 0.00 0.00 0.00 3.69
4381 4971 0.737715 GACATTCTCTTGCGCGTCCT 60.738 55.000 8.43 0.00 0.00 3.85
4391 5005 1.617947 GGACCAGGGCGACATTCTCT 61.618 60.000 0.00 0.00 0.00 3.10
4450 5077 2.839098 CAAGAGGTGGCCTGTGGT 59.161 61.111 3.32 0.00 31.76 4.16
4451 5078 2.674380 GCAAGAGGTGGCCTGTGG 60.674 66.667 3.32 0.00 31.76 4.17
4465 5092 1.746615 GCGATCTTCAGGCTGGCAA 60.747 57.895 15.73 1.15 0.00 4.52
4519 5146 0.532573 ACTAGTCGTGTCAGGGCATG 59.467 55.000 0.00 0.00 0.00 4.06
4529 5156 0.458025 GGGGCGAGAAACTAGTCGTG 60.458 60.000 0.00 0.00 38.48 4.35
4530 5157 1.602327 GGGGGCGAGAAACTAGTCGT 61.602 60.000 0.00 0.00 38.48 4.34
4536 5163 0.035056 CAATGAGGGGGCGAGAAACT 60.035 55.000 0.00 0.00 0.00 2.66
4547 5174 2.806945 TGCCTCCTTAACAATGAGGG 57.193 50.000 10.89 0.00 44.77 4.30
4585 5212 2.202566 GTGAACGACCTAGGCTTATGC 58.797 52.381 9.30 0.00 38.76 3.14
4590 5217 1.988406 GGGGTGAACGACCTAGGCT 60.988 63.158 9.30 0.00 45.33 4.58
4604 5232 1.532316 TCGAAGACTTCACCGGGGT 60.532 57.895 15.36 0.00 0.00 4.95
4621 5249 1.226717 GCACGATGACGGTCTCCTC 60.227 63.158 9.88 3.21 44.46 3.71


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

AutoCloner maintained by Alex Coulton.