Multiple sequence alignment - TraesCS6D01G080400

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 TraesCS6D01G080400 chr6D 100.000 7655 0 0 1 7655 46020926 46013272 0.000000e+00 14137.0
1 TraesCS6D01G080400 chr6A 95.553 5127 135 25 832 5940 60173712 60168661 0.000000e+00 8118.0
2 TraesCS6D01G080400 chr6A 93.566 715 38 5 5983 6691 60168515 60167803 0.000000e+00 1059.0
3 TraesCS6D01G080400 chr6A 88.731 843 69 12 3 824 60189609 60188772 0.000000e+00 1007.0
4 TraesCS6D01G080400 chr6A 86.730 422 24 23 6927 7332 60167509 60167104 2.540000e-119 440.0
5 TraesCS6D01G080400 chr6A 86.127 173 12 7 7345 7506 60167051 60166880 7.890000e-40 176.0
6 TraesCS6D01G080400 chr6A 91.589 107 5 3 6809 6915 60167595 60167493 2.230000e-30 145.0
7 TraesCS6D01G080400 chr6A 81.421 183 16 8 7151 7333 59825093 59825257 4.820000e-27 134.0
8 TraesCS6D01G080400 chr6A 98.305 59 1 0 7597 7655 60164585 60164527 3.780000e-18 104.0
9 TraesCS6D01G080400 chr6B 95.689 3271 94 16 2153 5405 114371459 114368218 0.000000e+00 5216.0
10 TraesCS6D01G080400 chr6B 94.440 1313 58 8 822 2121 114372765 114371455 0.000000e+00 2006.0
11 TraesCS6D01G080400 chr6B 91.819 819 45 12 5983 6782 114367682 114366867 0.000000e+00 1122.0
12 TraesCS6D01G080400 chr6B 86.410 780 81 17 1 758 560790007 560790783 0.000000e+00 830.0
13 TraesCS6D01G080400 chr6B 96.094 256 7 2 5688 5942 114368079 114367826 1.540000e-111 414.0
14 TraesCS6D01G080400 chr6B 96.753 154 4 1 5424 5577 114368232 114368080 9.860000e-64 255.0
15 TraesCS6D01G080400 chr6B 93.069 101 4 3 6816 6915 114366421 114366323 2.230000e-30 145.0
16 TraesCS6D01G080400 chr6B 76.577 333 26 19 7345 7655 114334293 114333991 1.340000e-27 135.0
17 TraesCS6D01G080400 chr6B 82.609 115 11 5 6967 7075 114366278 114366167 8.180000e-15 93.5
18 TraesCS6D01G080400 chr6B 96.429 56 1 1 7158 7213 114032484 114032538 2.940000e-14 91.6
19 TraesCS6D01G080400 chr6B 100.000 28 0 0 6781 6808 114366738 114366711 1.400000e-02 52.8
20 TraesCS6D01G080400 chr7B 87.320 765 71 13 1 741 640720445 640721207 0.000000e+00 852.0
21 TraesCS6D01G080400 chr7B 82.857 700 95 13 54 729 743876357 743877055 8.500000e-169 604.0
22 TraesCS6D01G080400 chr4D 85.509 835 92 21 5970 6797 163805854 163806666 0.000000e+00 845.0
23 TraesCS6D01G080400 chr4D 85.238 840 92 23 5967 6797 163883452 163884268 0.000000e+00 835.0
24 TraesCS6D01G080400 chr3D 87.601 742 68 14 1 720 380179984 380180723 0.000000e+00 839.0
25 TraesCS6D01G080400 chr3D 87.160 662 60 13 1 639 433443404 433444063 0.000000e+00 728.0
26 TraesCS6D01G080400 chr5B 86.312 789 80 18 1 764 356369274 356370059 0.000000e+00 833.0
27 TraesCS6D01G080400 chr2D 86.277 787 77 17 1 765 649052225 649053002 0.000000e+00 826.0
28 TraesCS6D01G080400 chr3B 86.800 750 83 11 5967 6711 437966277 437967015 0.000000e+00 822.0
29 TraesCS6D01G080400 chr3B 85.786 795 74 23 1 765 698233729 698234514 0.000000e+00 806.0
30 TraesCS6D01G080400 chr1B 86.649 764 77 12 1 742 544763492 544764252 0.000000e+00 822.0
31 TraesCS6D01G080400 chr1B 84.547 673 89 9 54 717 402069460 402070126 0.000000e+00 652.0
32 TraesCS6D01G080400 chr4B 83.620 757 94 22 5967 6717 655411378 655410646 0.000000e+00 684.0
33 TraesCS6D01G080400 chr5A 86.855 601 55 8 152 730 17820316 17820914 0.000000e+00 651.0
34 TraesCS6D01G080400 chr7D 81.532 444 62 9 343 767 45802029 45802471 1.580000e-91 348.0
35 TraesCS6D01G080400 chr7D 85.946 185 26 0 561 745 123370824 123371008 1.680000e-46 198.0
36 TraesCS6D01G080400 chr1D 83.000 400 46 9 4814 5205 179139314 179139699 7.360000e-90 342.0


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 TraesCS6D01G080400 chr6D 46013272 46020926 7654 True 14137.000000 14137 100.000000 1 7655 1 chr6D.!!$R1 7654
1 TraesCS6D01G080400 chr6A 60164527 60173712 9185 True 1673.666667 8118 91.978333 832 7655 6 chr6A.!!$R2 6823
2 TraesCS6D01G080400 chr6A 60188772 60189609 837 True 1007.000000 1007 88.731000 3 824 1 chr6A.!!$R1 821
3 TraesCS6D01G080400 chr6B 114366167 114372765 6598 True 1163.037500 5216 93.809125 822 7075 8 chr6B.!!$R2 6253
4 TraesCS6D01G080400 chr6B 560790007 560790783 776 False 830.000000 830 86.410000 1 758 1 chr6B.!!$F2 757
5 TraesCS6D01G080400 chr7B 640720445 640721207 762 False 852.000000 852 87.320000 1 741 1 chr7B.!!$F1 740
6 TraesCS6D01G080400 chr7B 743876357 743877055 698 False 604.000000 604 82.857000 54 729 1 chr7B.!!$F2 675
7 TraesCS6D01G080400 chr4D 163805854 163806666 812 False 845.000000 845 85.509000 5970 6797 1 chr4D.!!$F1 827
8 TraesCS6D01G080400 chr4D 163883452 163884268 816 False 835.000000 835 85.238000 5967 6797 1 chr4D.!!$F2 830
9 TraesCS6D01G080400 chr3D 380179984 380180723 739 False 839.000000 839 87.601000 1 720 1 chr3D.!!$F1 719
10 TraesCS6D01G080400 chr3D 433443404 433444063 659 False 728.000000 728 87.160000 1 639 1 chr3D.!!$F2 638
11 TraesCS6D01G080400 chr5B 356369274 356370059 785 False 833.000000 833 86.312000 1 764 1 chr5B.!!$F1 763
12 TraesCS6D01G080400 chr2D 649052225 649053002 777 False 826.000000 826 86.277000 1 765 1 chr2D.!!$F1 764
13 TraesCS6D01G080400 chr3B 437966277 437967015 738 False 822.000000 822 86.800000 5967 6711 1 chr3B.!!$F1 744
14 TraesCS6D01G080400 chr3B 698233729 698234514 785 False 806.000000 806 85.786000 1 765 1 chr3B.!!$F2 764
15 TraesCS6D01G080400 chr1B 544763492 544764252 760 False 822.000000 822 86.649000 1 742 1 chr1B.!!$F2 741
16 TraesCS6D01G080400 chr1B 402069460 402070126 666 False 652.000000 652 84.547000 54 717 1 chr1B.!!$F1 663
17 TraesCS6D01G080400 chr4B 655410646 655411378 732 True 684.000000 684 83.620000 5967 6717 1 chr4B.!!$R1 750
18 TraesCS6D01G080400 chr5A 17820316 17820914 598 False 651.000000 651 86.855000 152 730 1 chr5A.!!$F1 578

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
623 655 0.393820 ACCCTAACGACAAAGCGGAA 59.606 50.000 0.00 0.0 35.12 4.30 F
1642 1702 0.108585 TTCTGGCAGAGTTGGTGTCC 59.891 55.000 17.91 0.0 0.00 4.02 F
2484 2589 1.212688 CTGATGGTGCTTGGTCCCATA 59.787 52.381 0.00 0.0 39.06 2.74 F
3079 3190 2.907634 GCTAACAAGCCCTCTCTAACC 58.092 52.381 0.00 0.0 0.00 2.85 F
3635 3752 2.415512 GGAGCGTGCTCGTAAAAAGAAT 59.584 45.455 15.13 0.0 43.59 2.40 F
5364 5487 0.465097 AGCGGATGAGGGATTGCTTG 60.465 55.000 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1808 0.033504 TGACAGTCAAAGGAGTCGGC 59.966 55.000 0.00 0.00 33.83 5.54 R
3134 3245 0.632835 ACCACCAGCCCATGATTCAT 59.367 50.000 0.00 0.00 0.00 2.57 R
3397 3508 2.360801 TGGTACCTTTCAAAAGCAGTGC 59.639 45.455 14.36 7.13 34.69 4.40 R
4427 4549 2.639839 ACCAATCCTTATGCGCTCCTAT 59.360 45.455 9.73 0.00 0.00 2.57 R
5543 5666 1.602888 CCTGCAGCTTGCCACTCTT 60.603 57.895 8.66 0.00 44.23 2.85 R
6836 7505 0.034337 GTACTGACCGGCCTGTTTGA 59.966 55.000 5.47 0.00 0.00 2.69 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
74 79 4.892934 GGAGACATATCACCTCTTCACTCT 59.107 45.833 0.00 0.00 33.05 3.24
98 103 2.103538 GACGCGGCTCCATCGTTA 59.896 61.111 12.47 0.00 36.50 3.18
106 111 2.675844 CGGCTCCATCGTTAATCAACAA 59.324 45.455 0.00 0.00 34.05 2.83
267 276 0.606673 GAACTGTCAGCCTCCAACCC 60.607 60.000 0.00 0.00 0.00 4.11
348 361 3.848975 ACTCCTGGATGACAAAATCTCCT 59.151 43.478 0.00 0.00 0.00 3.69
371 384 0.896479 TCCACCATGACGTCGGAGAA 60.896 55.000 15.42 0.00 39.69 2.87
396 409 3.059982 CAGCAACGGGGACAGAGA 58.940 61.111 0.00 0.00 0.00 3.10
477 491 0.806102 TAACGCTGCCGATCTGAAGC 60.806 55.000 7.04 7.04 38.29 3.86
559 574 3.006247 GAGGGTGAAGTTGAAGCAGATC 58.994 50.000 0.00 0.00 0.00 2.75
566 595 1.824230 AGTTGAAGCAGATCTCGCTCT 59.176 47.619 16.64 9.12 39.29 4.09
573 602 1.102154 CAGATCTCGCTCTCACCACT 58.898 55.000 0.00 0.00 0.00 4.00
579 611 1.112916 TCGCTCTCACCACTCCAACA 61.113 55.000 0.00 0.00 0.00 3.33
623 655 0.393820 ACCCTAACGACAAAGCGGAA 59.606 50.000 0.00 0.00 35.12 4.30
730 769 1.133419 GGAGATCCCTTCCCTAGTCGT 60.133 57.143 0.00 0.00 0.00 4.34
1049 1107 1.802069 AGGAAGCAGCTTTCGACTTC 58.198 50.000 9.62 3.30 38.22 3.01
1085 1143 2.440796 ATCGGAAGCGACCCCGTA 60.441 61.111 9.08 0.00 45.48 4.02
1088 1146 2.806237 GGAAGCGACCCCGTAGAG 59.194 66.667 0.00 0.00 38.24 2.43
1369 1429 4.873129 CCGTCGGTGCCTGATCCG 62.873 72.222 2.08 0.00 46.93 4.18
1581 1641 4.253685 TCTGAGATAAGCAAAGGGTTTCG 58.746 43.478 0.00 0.00 35.99 3.46
1642 1702 0.108585 TTCTGGCAGAGTTGGTGTCC 59.891 55.000 17.91 0.00 0.00 4.02
1748 1808 5.936372 TCCGGTATGTATATAGCTATAGCCG 59.064 44.000 21.17 19.51 43.38 5.52
1750 1810 5.391736 CGGTATGTATATAGCTATAGCCGCC 60.392 48.000 21.17 13.17 43.38 6.13
1778 1838 4.330074 CCTTTGACTGTCATGTTATCGGTC 59.670 45.833 11.86 4.17 37.80 4.79
1835 1895 9.289782 GATAATAAGATCATTTTACTGTGGCCT 57.710 33.333 3.32 0.00 0.00 5.19
1979 2045 8.995027 ATACTATTGGTTCTGAATGGCATAAA 57.005 30.769 0.00 0.00 0.00 1.40
2088 2154 6.388689 ACAGGGGTGATAATACTGAATAACCA 59.611 38.462 0.00 0.00 33.57 3.67
2151 2217 5.551760 ATTTCTTAAAGATGACAGTGGCG 57.448 39.130 0.00 0.00 0.00 5.69
2286 2390 7.935338 GCAGCTGCAAATTAATACATAATGT 57.065 32.000 33.36 0.00 41.59 2.71
2484 2589 1.212688 CTGATGGTGCTTGGTCCCATA 59.787 52.381 0.00 0.00 39.06 2.74
2501 2606 8.228206 TGGTCCCATATTTGCCAATAAGTATTA 58.772 33.333 0.00 0.00 33.48 0.98
2627 2732 9.519191 TTAATTCATATGAATGTATGAGGGTGG 57.481 33.333 27.46 0.00 43.41 4.61
2726 2831 7.412891 GCATGCAACATTTAAGGGATTTTGTAC 60.413 37.037 14.21 0.00 0.00 2.90
2748 2856 6.544038 ACAAAAAGCTTTAATTGGATGTGC 57.456 33.333 21.71 0.00 0.00 4.57
2909 3017 4.640201 TGCTTGCTTGACTTAGTTTTGTCT 59.360 37.500 0.00 0.00 34.57 3.41
2932 3040 7.976734 GTCTACTGAGCATCTATTAACAGTGTT 59.023 37.037 14.05 14.05 38.68 3.32
2933 3041 8.191446 TCTACTGAGCATCTATTAACAGTGTTC 58.809 37.037 12.82 0.00 38.68 3.18
2934 3042 6.701340 ACTGAGCATCTATTAACAGTGTTCA 58.299 36.000 12.82 1.20 37.24 3.18
2935 3043 7.161404 ACTGAGCATCTATTAACAGTGTTCAA 58.839 34.615 12.82 6.12 37.24 2.69
2936 3044 7.826252 ACTGAGCATCTATTAACAGTGTTCAAT 59.174 33.333 12.82 12.51 37.24 2.57
2937 3045 7.977904 TGAGCATCTATTAACAGTGTTCAATG 58.022 34.615 12.82 10.78 34.92 2.82
2938 3046 7.066163 TGAGCATCTATTAACAGTGTTCAATGG 59.934 37.037 12.82 12.06 34.92 3.16
3079 3190 2.907634 GCTAACAAGCCCTCTCTAACC 58.092 52.381 0.00 0.00 0.00 2.85
3106 3217 5.584251 GGAAGAGAAGAAGATTAAGGCACAG 59.416 44.000 0.00 0.00 0.00 3.66
3134 3245 6.350110 GCTGAGGTGCTTTTATAAACCATTCA 60.350 38.462 6.79 9.35 35.01 2.57
3415 3526 3.287222 ACAGCACTGCTTTTGAAAGGTA 58.713 40.909 0.00 0.00 36.40 3.08
3426 3537 5.010617 GCTTTTGAAAGGTACCATTTCTCCA 59.989 40.000 24.68 10.21 37.51 3.86
3437 3548 5.587388 ACCATTTCTCCATAATTGTGCAG 57.413 39.130 0.00 0.00 0.00 4.41
3635 3752 2.415512 GGAGCGTGCTCGTAAAAAGAAT 59.584 45.455 15.13 0.00 43.59 2.40
3706 3823 5.364778 ACTTTCATTTGCCCCTGTAAAAAC 58.635 37.500 0.00 0.00 29.67 2.43
3996 4116 9.830975 ACAAAAGCTTACTATGGTTTTCATTTT 57.169 25.926 0.00 0.00 41.30 1.82
4030 4150 8.617290 TTTAACCTCTAGTCTCAAATTTGTCC 57.383 34.615 17.47 7.14 0.00 4.02
4141 4261 5.956563 TGTTTGTTGGAGGTTTTTAGGGTAA 59.043 36.000 0.00 0.00 0.00 2.85
4363 4484 6.183361 TGGCCTTAGCATACTATTTCTTAGCA 60.183 38.462 3.32 0.00 42.56 3.49
4868 4990 9.733556 TTAAGCCTCAAACAGTTTCTCATATTA 57.266 29.630 0.00 0.00 0.00 0.98
5029 5152 3.084039 TGATCCAGATTTTGTGCACCTC 58.916 45.455 15.69 6.07 0.00 3.85
5227 5350 0.683504 GGCCCTCTAGAACCGTCTGA 60.684 60.000 0.00 0.00 35.12 3.27
5253 5376 4.079253 GGCCAGAGTTCATTTTACCTTCA 58.921 43.478 0.00 0.00 0.00 3.02
5364 5487 0.465097 AGCGGATGAGGGATTGCTTG 60.465 55.000 0.00 0.00 0.00 4.01
5616 5739 4.288366 TGTATGTTCCCTCTGACCAAATCA 59.712 41.667 0.00 0.00 35.45 2.57
5617 5740 3.874383 TGTTCCCTCTGACCAAATCAA 57.126 42.857 0.00 0.00 36.69 2.57
5618 5741 3.754965 TGTTCCCTCTGACCAAATCAAG 58.245 45.455 0.00 0.00 36.69 3.02
5619 5742 3.394274 TGTTCCCTCTGACCAAATCAAGA 59.606 43.478 0.00 0.00 36.69 3.02
5620 5743 4.141274 TGTTCCCTCTGACCAAATCAAGAA 60.141 41.667 0.00 0.00 36.69 2.52
5621 5744 4.292186 TCCCTCTGACCAAATCAAGAAG 57.708 45.455 0.00 0.00 36.69 2.85
5622 5745 3.652869 TCCCTCTGACCAAATCAAGAAGT 59.347 43.478 0.00 0.00 36.69 3.01
5623 5746 4.104738 TCCCTCTGACCAAATCAAGAAGTT 59.895 41.667 0.00 0.00 36.69 2.66
5624 5747 5.309543 TCCCTCTGACCAAATCAAGAAGTTA 59.690 40.000 0.00 0.00 36.69 2.24
5625 5748 5.412904 CCCTCTGACCAAATCAAGAAGTTAC 59.587 44.000 0.00 0.00 36.69 2.50
5626 5749 6.234177 CCTCTGACCAAATCAAGAAGTTACT 58.766 40.000 0.00 0.00 36.69 2.24
5627 5750 6.370166 CCTCTGACCAAATCAAGAAGTTACTC 59.630 42.308 0.00 0.00 36.69 2.59
5628 5751 7.067496 TCTGACCAAATCAAGAAGTTACTCT 57.933 36.000 0.00 0.00 36.69 3.24
5629 5752 6.931281 TCTGACCAAATCAAGAAGTTACTCTG 59.069 38.462 0.00 0.00 36.69 3.35
5630 5753 6.826668 TGACCAAATCAAGAAGTTACTCTGA 58.173 36.000 0.00 0.00 33.02 3.27
5631 5754 6.706270 TGACCAAATCAAGAAGTTACTCTGAC 59.294 38.462 0.00 0.00 33.02 3.51
5632 5755 5.998363 ACCAAATCAAGAAGTTACTCTGACC 59.002 40.000 0.00 0.00 0.00 4.02
5633 5756 5.997746 CCAAATCAAGAAGTTACTCTGACCA 59.002 40.000 0.00 0.00 0.00 4.02
5634 5757 6.486657 CCAAATCAAGAAGTTACTCTGACCAA 59.513 38.462 0.00 0.00 0.00 3.67
5635 5758 7.013274 CCAAATCAAGAAGTTACTCTGACCAAA 59.987 37.037 0.00 0.00 0.00 3.28
5636 5759 8.571336 CAAATCAAGAAGTTACTCTGACCAAAT 58.429 33.333 0.00 0.00 0.00 2.32
5637 5760 7.913674 ATCAAGAAGTTACTCTGACCAAATC 57.086 36.000 0.00 0.00 0.00 2.17
5766 5889 6.382859 ACCCAAATATCCATTTCTTAACCCAC 59.617 38.462 0.00 0.00 31.82 4.61
5837 5961 4.445448 GCACAGTTGGGATCTCCTGATATT 60.445 45.833 5.92 0.00 36.20 1.28
5872 5996 2.490903 CCAGTTTCTCTTTGATGCCTGG 59.509 50.000 0.00 0.00 32.07 4.45
5920 6044 6.263344 TGTCTCGAGTGTATTTGCATACTAC 58.737 40.000 13.13 0.00 36.87 2.73
5930 6054 6.720748 TGTATTTGCATACTACCGGGACTATA 59.279 38.462 6.32 0.00 36.87 1.31
5931 6055 6.869206 ATTTGCATACTACCGGGACTATAT 57.131 37.500 6.32 0.00 0.00 0.86
5932 6056 5.654603 TTGCATACTACCGGGACTATATG 57.345 43.478 6.32 4.93 0.00 1.78
5935 6059 6.665695 TGCATACTACCGGGACTATATGATA 58.334 40.000 6.32 0.00 0.00 2.15
5937 6061 7.783119 TGCATACTACCGGGACTATATGATATT 59.217 37.037 6.32 0.00 0.00 1.28
5941 6065 8.896722 ACTACCGGGACTATATGATATTTCTT 57.103 34.615 6.32 0.00 0.00 2.52
6204 6431 9.442047 GGAGAAATTCAGAAAGATCAGACTTAA 57.558 33.333 0.00 0.00 0.00 1.85
6233 6460 3.701664 ACATTCCAGGTGAATTCCCTTC 58.298 45.455 11.53 0.00 41.85 3.46
6242 6469 2.511637 GTGAATTCCCTTCTCCCTGGAT 59.488 50.000 2.27 0.00 34.75 3.41
6260 6489 1.536331 GATTGGTAAAAACGACGCCCA 59.464 47.619 0.00 0.00 0.00 5.36
6321 6550 0.676151 CCTTGCAGGAGAGAGTTGGC 60.676 60.000 0.00 0.00 37.67 4.52
6546 6775 0.180171 TGAATCGGGAATGTGGCGAT 59.820 50.000 0.00 0.00 0.00 4.58
6628 6862 2.894765 CGGGGAAATTTTTACACAGGGT 59.105 45.455 0.00 0.00 0.00 4.34
6648 6882 4.412528 GGGTAACTGGTCCTATCCAAAGAT 59.587 45.833 0.00 0.00 37.01 2.40
6649 6883 5.454897 GGGTAACTGGTCCTATCCAAAGATC 60.455 48.000 0.00 0.00 37.01 2.75
6650 6884 5.367060 GGTAACTGGTCCTATCCAAAGATCT 59.633 44.000 0.00 0.00 37.01 2.75
6653 6889 5.995446 ACTGGTCCTATCCAAAGATCTTTC 58.005 41.667 17.91 4.40 37.01 2.62
6655 6891 4.788075 TGGTCCTATCCAAAGATCTTTCCA 59.212 41.667 17.91 15.59 34.24 3.53
6671 6907 4.351111 TCTTTCCAAAAGTCTAGGCTTCCT 59.649 41.667 10.65 0.00 37.71 3.36
6674 6910 3.910627 TCCAAAAGTCTAGGCTTCCTCTT 59.089 43.478 10.65 0.00 34.61 2.85
6675 6911 4.351111 TCCAAAAGTCTAGGCTTCCTCTTT 59.649 41.667 10.65 0.00 34.61 2.52
6676 6912 5.073428 CCAAAAGTCTAGGCTTCCTCTTTT 58.927 41.667 10.65 0.00 36.37 2.27
6719 6958 5.139435 GCAAAATAGAAGTCCTTTGCCTT 57.861 39.130 7.04 0.00 44.98 4.35
6720 6959 4.925646 GCAAAATAGAAGTCCTTTGCCTTG 59.074 41.667 7.04 0.00 44.98 3.61
6746 6985 1.537889 ACCTCCAACGTGGGGATCA 60.538 57.895 9.71 0.00 41.85 2.92
6747 6986 1.221840 CCTCCAACGTGGGGATCAG 59.778 63.158 9.71 0.00 41.85 2.90
6814 7201 4.248691 ACAAATTTCTGCTGCTTCTTCC 57.751 40.909 0.00 0.00 0.00 3.46
6903 7573 1.517242 GCCTTGACCTCACAACAGAG 58.483 55.000 0.00 0.00 35.39 3.35
6904 7574 1.070758 GCCTTGACCTCACAACAGAGA 59.929 52.381 0.00 0.00 37.87 3.10
6905 7575 2.760374 CCTTGACCTCACAACAGAGAC 58.240 52.381 0.00 0.00 37.87 3.36
6906 7576 2.103094 CCTTGACCTCACAACAGAGACA 59.897 50.000 0.00 0.00 37.87 3.41
6907 7577 3.432186 CCTTGACCTCACAACAGAGACAA 60.432 47.826 0.00 0.00 37.87 3.18
6908 7578 3.904800 TGACCTCACAACAGAGACAAA 57.095 42.857 0.00 0.00 37.87 2.83
6909 7579 3.531538 TGACCTCACAACAGAGACAAAC 58.468 45.455 0.00 0.00 37.87 2.93
6910 7580 2.540101 GACCTCACAACAGAGACAAACG 59.460 50.000 0.00 0.00 37.87 3.60
6911 7581 1.867233 CCTCACAACAGAGACAAACGG 59.133 52.381 0.00 0.00 37.87 4.44
6912 7582 2.483013 CCTCACAACAGAGACAAACGGA 60.483 50.000 0.00 0.00 37.87 4.69
6913 7583 3.393800 CTCACAACAGAGACAAACGGAT 58.606 45.455 0.00 0.00 37.87 4.18
6914 7584 3.804036 TCACAACAGAGACAAACGGATT 58.196 40.909 0.00 0.00 0.00 3.01
6915 7585 4.196193 TCACAACAGAGACAAACGGATTT 58.804 39.130 0.00 0.00 0.00 2.17
6916 7586 8.635542 CCTCACAACAGAGACAAACGGATTTG 62.636 46.154 0.00 0.00 40.59 2.32
6929 7599 7.979115 CAAACGGATTTGTCTAAGAAAAACA 57.021 32.000 0.00 0.00 40.39 2.83
6930 7600 8.574196 CAAACGGATTTGTCTAAGAAAAACAT 57.426 30.769 0.00 0.00 40.39 2.71
6931 7601 9.672086 CAAACGGATTTGTCTAAGAAAAACATA 57.328 29.630 0.00 0.00 40.39 2.29
6961 7631 0.177141 TACCGGAAGTGTAGCATGCC 59.823 55.000 15.66 0.00 0.00 4.40
6962 7632 1.819632 CCGGAAGTGTAGCATGCCC 60.820 63.158 15.66 5.99 0.00 5.36
6963 7633 1.221840 CGGAAGTGTAGCATGCCCT 59.778 57.895 15.66 2.26 0.00 5.19
6964 7634 1.091771 CGGAAGTGTAGCATGCCCTG 61.092 60.000 15.66 0.00 0.00 4.45
6978 7669 0.737219 GCCCTGCATGAAGCTACTTG 59.263 55.000 0.00 0.00 45.94 3.16
7004 7696 4.918588 ACTCAAAAATAACGACCCCTCAT 58.081 39.130 0.00 0.00 0.00 2.90
7005 7697 4.941873 ACTCAAAAATAACGACCCCTCATC 59.058 41.667 0.00 0.00 0.00 2.92
7006 7698 4.912586 TCAAAAATAACGACCCCTCATCA 58.087 39.130 0.00 0.00 0.00 3.07
7045 7737 4.342352 AAAGTTAACGCAAGCTAGCATC 57.658 40.909 18.83 4.14 45.62 3.91
7048 7740 4.113354 AGTTAACGCAAGCTAGCATCTAC 58.887 43.478 18.83 3.86 45.62 2.59
7049 7741 2.672961 AACGCAAGCTAGCATCTACA 57.327 45.000 18.83 0.00 45.62 2.74
7050 7742 1.927895 ACGCAAGCTAGCATCTACAC 58.072 50.000 18.83 0.00 45.62 2.90
7052 7744 2.093973 ACGCAAGCTAGCATCTACACTT 60.094 45.455 18.83 0.00 45.62 3.16
7080 7776 0.314302 GCGTCTACATGCTACCGGAT 59.686 55.000 9.46 0.00 0.00 4.18
7082 7778 1.784525 GTCTACATGCTACCGGATGC 58.215 55.000 9.46 12.83 42.11 3.91
7087 7783 1.340991 ACATGCTACCGGATGCCTTTT 60.341 47.619 9.46 0.00 42.11 2.27
7088 7784 1.066002 CATGCTACCGGATGCCTTTTG 59.934 52.381 9.46 3.75 32.11 2.44
7089 7785 0.326595 TGCTACCGGATGCCTTTTGA 59.673 50.000 9.46 0.00 0.00 2.69
7090 7786 1.064758 TGCTACCGGATGCCTTTTGAT 60.065 47.619 9.46 0.00 0.00 2.57
7092 7788 2.808543 GCTACCGGATGCCTTTTGATAG 59.191 50.000 9.46 0.00 0.00 2.08
7093 7789 3.494398 GCTACCGGATGCCTTTTGATAGA 60.494 47.826 9.46 0.00 0.00 1.98
7127 7823 0.320771 AACTGCATCTGTGGACGACC 60.321 55.000 0.00 0.00 0.00 4.79
7147 7843 2.171870 CCGGCCTAGGGAAATAAAGTGA 59.828 50.000 11.72 0.00 0.00 3.41
7230 7926 4.530857 CCCGGCCGGAGCAAGTAG 62.531 72.222 45.44 22.17 42.56 2.57
7232 7928 2.577059 CGGCCGGAGCAAGTAGAA 59.423 61.111 20.10 0.00 42.56 2.10
7235 7931 1.087501 GGCCGGAGCAAGTAGAAAAG 58.912 55.000 5.05 0.00 42.56 2.27
7237 7933 2.423577 GCCGGAGCAAGTAGAAAAGAA 58.576 47.619 5.05 0.00 39.53 2.52
7238 7934 3.010420 GCCGGAGCAAGTAGAAAAGAAT 58.990 45.455 5.05 0.00 39.53 2.40
7274 7972 0.512518 GCCGCTGCAAAATCAAAACC 59.487 50.000 0.00 0.00 37.47 3.27
7276 7974 2.208431 CCGCTGCAAAATCAAAACCAA 58.792 42.857 0.00 0.00 0.00 3.67
7277 7975 2.807392 CCGCTGCAAAATCAAAACCAAT 59.193 40.909 0.00 0.00 0.00 3.16
7279 7977 4.456914 CGCTGCAAAATCAAAACCAATTC 58.543 39.130 0.00 0.00 0.00 2.17
7281 7979 5.445845 GCTGCAAAATCAAAACCAATTCTG 58.554 37.500 0.00 0.00 0.00 3.02
7290 7988 5.124645 TCAAAACCAATTCTGCATTTTGCT 58.875 33.333 12.43 0.00 45.31 3.91
7315 8013 2.386661 AGTCTGTAGGAACAATGCCG 57.613 50.000 0.00 0.00 34.49 5.69
7316 8014 0.727398 GTCTGTAGGAACAATGCCGC 59.273 55.000 0.00 0.00 34.49 6.53
7332 8030 2.581354 GCGAGCATCTGTCCAGGT 59.419 61.111 0.00 0.00 0.00 4.00
7356 8094 4.827284 TGGTCTGAATTTTCTTTCTGTCCC 59.173 41.667 0.00 0.00 34.34 4.46
7369 8107 2.048503 GTCCCGTCCCGTCAAGTG 60.049 66.667 0.00 0.00 0.00 3.16
7370 8108 3.998672 TCCCGTCCCGTCAAGTGC 61.999 66.667 0.00 0.00 0.00 4.40
7374 8112 3.050275 GTCCCGTCAAGTGCAGGC 61.050 66.667 0.00 0.00 0.00 4.85
7428 8175 4.398358 ACAGACAGCATGGAATTCAGATTG 59.602 41.667 7.93 1.68 43.62 2.67
7429 8176 4.398358 CAGACAGCATGGAATTCAGATTGT 59.602 41.667 7.93 4.84 43.62 2.71
7430 8177 4.398358 AGACAGCATGGAATTCAGATTGTG 59.602 41.667 7.93 0.03 43.62 3.33
7431 8178 3.119245 ACAGCATGGAATTCAGATTGTGC 60.119 43.478 7.93 7.63 43.62 4.57
7440 8187 1.372582 TCAGATTGTGCGGATTCAGC 58.627 50.000 1.49 1.49 0.00 4.26
7441 8188 0.027194 CAGATTGTGCGGATTCAGCG 59.973 55.000 4.35 0.00 37.44 5.18
7442 8189 1.297893 GATTGTGCGGATTCAGCGC 60.298 57.895 14.31 14.31 44.57 5.92
7468 8215 3.766051 GGGATTGATGGGCATCTAATTCC 59.234 47.826 0.00 0.00 38.60 3.01
7472 8219 4.362470 TGATGGGCATCTAATTCCAGAG 57.638 45.455 0.00 0.00 38.60 3.35
7477 8224 2.411904 GCATCTAATTCCAGAGGCTCG 58.588 52.381 9.22 4.13 46.22 5.03
7514 10460 4.383602 GCGCGCGCTTTCCTCAAA 62.384 61.111 44.38 0.00 38.26 2.69
7515 10461 2.202222 CGCGCGCTTTCCTCAAAG 60.202 61.111 30.48 5.07 41.92 2.77
7549 10495 3.188011 TCGCAGAGGACGCACTAG 58.812 61.111 0.00 0.00 0.00 2.57
7550 10496 1.376812 TCGCAGAGGACGCACTAGA 60.377 57.895 0.00 0.00 0.00 2.43
7551 10497 1.063327 CGCAGAGGACGCACTAGAG 59.937 63.158 0.00 0.00 0.00 2.43
7552 10498 1.435515 GCAGAGGACGCACTAGAGG 59.564 63.158 0.00 0.00 0.00 3.69
7553 10499 1.435515 CAGAGGACGCACTAGAGGC 59.564 63.158 0.00 0.00 0.00 4.70
7554 10500 1.034838 CAGAGGACGCACTAGAGGCT 61.035 60.000 0.00 0.00 0.00 4.58
7555 10501 0.750182 AGAGGACGCACTAGAGGCTC 60.750 60.000 6.34 6.34 0.00 4.70
7595 10541 3.550842 GCTTTTGGAAAGCAACGTCTGAT 60.551 43.478 17.78 0.00 42.56 2.90
7629 10593 3.539604 CTTTGCCCTGACTTGGAGATAG 58.460 50.000 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 29 2.297698 TAGTGGAGAGGGACAAACGA 57.702 50.000 0.00 0.00 0.00 3.85
28 33 5.456186 CCTTTTTCTTAGTGGAGAGGGACAA 60.456 44.000 0.00 0.00 0.00 3.18
98 103 4.070009 GGAGGTCCGTAAAGTTGTTGATT 58.930 43.478 0.00 0.00 0.00 2.57
106 111 3.899980 ACTACTTTGGAGGTCCGTAAAGT 59.100 43.478 18.64 18.64 41.87 2.66
188 193 1.390463 GTTCTGAAGTTCGATGGCGTC 59.610 52.381 0.00 0.00 38.98 5.19
267 276 1.411977 TGCATCTTGTGTTGGGTTTGG 59.588 47.619 0.00 0.00 0.00 3.28
348 361 1.374125 CGACGTCATGGTGGAGCAA 60.374 57.895 17.16 0.00 0.00 3.91
396 409 3.772025 CCATAGGTGTGTCTCTCCTTCTT 59.228 47.826 1.13 0.00 40.14 2.52
477 491 1.609932 GCATCGTGTGTTTGCTGATG 58.390 50.000 0.00 0.00 39.47 3.07
559 574 0.389166 GTTGGAGTGGTGAGAGCGAG 60.389 60.000 0.00 0.00 0.00 5.03
566 595 1.885388 CGCGTTGTTGGAGTGGTGA 60.885 57.895 0.00 0.00 0.00 4.02
573 602 4.893601 TCGTGGCGCGTTGTTGGA 62.894 61.111 20.88 0.00 42.13 3.53
579 611 2.974935 TTTGTAGGTCGTGGCGCGTT 62.975 55.000 20.88 9.89 42.13 4.84
623 655 2.039137 GAGGAGGGACCCCGTTCT 59.961 66.667 7.00 0.00 41.95 3.01
697 734 2.043227 GGATCTCCTTCCACCGATCTT 58.957 52.381 0.00 0.00 35.72 2.40
719 756 1.030488 CGAGCCAGACGACTAGGGAA 61.030 60.000 0.00 0.00 0.00 3.97
749 791 2.265589 AACCACGTTTTCCTACCCTG 57.734 50.000 0.00 0.00 0.00 4.45
784 826 6.403878 ACAGCAGTAAGGTACGTATCAAATT 58.596 36.000 8.86 0.00 0.00 1.82
1049 1107 3.518068 GAGCGAATTTGGGGGCGG 61.518 66.667 0.00 0.00 0.00 6.13
1085 1143 2.124819 CCGCCATTGCTGCTCTCT 60.125 61.111 0.00 0.00 34.43 3.10
1317 1376 1.289109 ACGCAGGATCAACGAAACCG 61.289 55.000 8.06 0.00 0.00 4.44
1369 1429 2.165301 CGAATCGACAGGCGGAACC 61.165 63.158 0.00 0.00 41.33 3.62
1642 1702 1.352083 TCTCCTTGTTCACCTCTGGG 58.648 55.000 0.00 0.00 38.88 4.45
1748 1808 0.033504 TGACAGTCAAAGGAGTCGGC 59.966 55.000 0.00 0.00 33.83 5.54
1750 1810 3.032017 ACATGACAGTCAAAGGAGTCG 57.968 47.619 7.50 0.00 33.83 4.18
1979 2045 9.920946 TTTTCCTTGGCTAAGTAATCTGATATT 57.079 29.630 9.16 0.00 31.80 1.28
2125 2191 8.184192 CGCCACTGTCATCTTTAAGAAATTTAT 58.816 33.333 0.00 0.00 0.00 1.40
2126 2192 7.174253 ACGCCACTGTCATCTTTAAGAAATTTA 59.826 33.333 0.00 0.00 0.00 1.40
2127 2193 6.016276 ACGCCACTGTCATCTTTAAGAAATTT 60.016 34.615 0.00 0.00 0.00 1.82
2128 2194 5.473504 ACGCCACTGTCATCTTTAAGAAATT 59.526 36.000 0.00 0.00 0.00 1.82
2129 2195 5.003804 ACGCCACTGTCATCTTTAAGAAAT 58.996 37.500 0.00 0.00 0.00 2.17
2130 2196 4.385825 ACGCCACTGTCATCTTTAAGAAA 58.614 39.130 0.00 0.00 0.00 2.52
2131 2197 3.994392 GACGCCACTGTCATCTTTAAGAA 59.006 43.478 0.00 0.00 38.75 2.52
2132 2198 3.006430 TGACGCCACTGTCATCTTTAAGA 59.994 43.478 0.00 0.00 43.62 2.10
2133 2199 3.325870 TGACGCCACTGTCATCTTTAAG 58.674 45.455 0.00 0.00 43.62 1.85
2134 2200 3.394674 TGACGCCACTGTCATCTTTAA 57.605 42.857 0.00 0.00 43.62 1.52
2141 2207 3.120321 AGTTATTTGACGCCACTGTCA 57.880 42.857 0.00 0.00 46.63 3.58
2142 2208 5.600908 TTTAGTTATTTGACGCCACTGTC 57.399 39.130 0.00 0.00 39.37 3.51
2143 2209 6.569179 AATTTAGTTATTTGACGCCACTGT 57.431 33.333 0.00 0.00 0.00 3.55
2144 2210 6.964934 GGTAATTTAGTTATTTGACGCCACTG 59.035 38.462 0.00 0.00 0.00 3.66
2145 2211 6.882678 AGGTAATTTAGTTATTTGACGCCACT 59.117 34.615 0.00 0.00 0.00 4.00
2146 2212 6.964934 CAGGTAATTTAGTTATTTGACGCCAC 59.035 38.462 0.00 0.00 0.00 5.01
2147 2213 6.879993 TCAGGTAATTTAGTTATTTGACGCCA 59.120 34.615 0.00 0.00 0.00 5.69
2148 2214 7.311364 TCAGGTAATTTAGTTATTTGACGCC 57.689 36.000 0.00 0.00 0.00 5.68
2149 2215 9.221775 CATTCAGGTAATTTAGTTATTTGACGC 57.778 33.333 0.00 0.00 0.00 5.19
2150 2216 9.716507 CCATTCAGGTAATTTAGTTATTTGACG 57.283 33.333 0.00 0.00 0.00 4.35
2158 2260 7.630082 TGCTAGTCCATTCAGGTAATTTAGTT 58.370 34.615 0.00 0.00 39.02 2.24
2501 2606 7.823745 ACTGTGATGAAAAGACTACCAAAAT 57.176 32.000 0.00 0.00 0.00 1.82
2603 2708 7.449395 CACCACCCTCATACATTCATATGAATT 59.551 37.037 25.16 18.56 42.41 2.17
2627 2732 5.010617 ACCATGTCATTTGGGAAAAGTACAC 59.989 40.000 0.00 0.00 38.64 2.90
2726 2831 6.424509 TGAGCACATCCAATTAAAGCTTTTTG 59.575 34.615 18.47 15.90 0.00 2.44
2748 2856 6.992063 AGTAGCATTTCACCATAAAGTGAG 57.008 37.500 0.00 0.00 46.90 3.51
2909 3017 7.836842 TGAACACTGTTAATAGATGCTCAGTA 58.163 34.615 6.19 0.00 34.95 2.74
2932 3040 4.524802 AACATCTATTCAGCCCCATTGA 57.475 40.909 0.00 0.00 0.00 2.57
2933 3041 5.240183 CAGTAACATCTATTCAGCCCCATTG 59.760 44.000 0.00 0.00 0.00 2.82
2934 3042 5.132648 TCAGTAACATCTATTCAGCCCCATT 59.867 40.000 0.00 0.00 0.00 3.16
2935 3043 4.660303 TCAGTAACATCTATTCAGCCCCAT 59.340 41.667 0.00 0.00 0.00 4.00
2936 3044 4.037222 TCAGTAACATCTATTCAGCCCCA 58.963 43.478 0.00 0.00 0.00 4.96
2937 3045 4.141711 TGTCAGTAACATCTATTCAGCCCC 60.142 45.833 0.00 0.00 31.20 5.80
2938 3046 4.811557 GTGTCAGTAACATCTATTCAGCCC 59.188 45.833 0.00 0.00 40.80 5.19
3079 3190 5.047188 GCCTTAATCTTCTTCTCTTCCTCG 58.953 45.833 0.00 0.00 0.00 4.63
3106 3217 4.096532 GGTTTATAAAAGCACCTCAGCTCC 59.903 45.833 0.00 0.00 45.89 4.70
3134 3245 0.632835 ACCACCAGCCCATGATTCAT 59.367 50.000 0.00 0.00 0.00 2.57
3303 3414 9.801873 GTTCACAAAAGTATAAATGCACCATAT 57.198 29.630 0.00 0.00 0.00 1.78
3312 3423 7.329226 GCACTGCATGTTCACAAAAGTATAAAT 59.671 33.333 0.00 0.00 0.00 1.40
3397 3508 2.360801 TGGTACCTTTCAAAAGCAGTGC 59.639 45.455 14.36 7.13 34.69 4.40
3415 3526 5.263599 TCTGCACAATTATGGAGAAATGGT 58.736 37.500 5.36 0.00 43.26 3.55
3426 3537 8.404000 CAAGCTCTAAGATTTCTGCACAATTAT 58.596 33.333 0.00 0.00 0.00 1.28
3437 3548 7.856145 TCTGAATTCCAAGCTCTAAGATTTC 57.144 36.000 2.27 0.00 0.00 2.17
3505 3619 9.507329 ACAAGTGCTCTTTATCTCTGAAATTTA 57.493 29.630 0.00 0.00 0.00 1.40
3513 3627 6.352016 TCAAGACAAGTGCTCTTTATCTCT 57.648 37.500 10.85 2.32 30.63 3.10
3792 3911 3.334583 ACAGGTTATGCTGATGTCGTT 57.665 42.857 0.00 0.00 0.00 3.85
3941 4061 9.787435 TGAAATATTAACATAAAGGGCTATCGT 57.213 29.630 0.00 0.00 0.00 3.73
4030 4150 3.165890 CACTTGCAAATACACATCAGCG 58.834 45.455 0.00 0.00 0.00 5.18
4427 4549 2.639839 ACCAATCCTTATGCGCTCCTAT 59.360 45.455 9.73 0.00 0.00 2.57
4542 4664 8.469309 AGCAAAACTTGATATTACCAGCATAT 57.531 30.769 0.00 0.00 0.00 1.78
4868 4990 5.854010 TCTACGTTCAGCCTGAGAATAAT 57.146 39.130 0.00 0.00 0.00 1.28
5029 5152 8.067784 AGTGTAATGTCGTGTTTAAATTGACAG 58.932 33.333 18.59 4.56 42.23 3.51
5227 5350 4.043435 AGGTAAAATGAACTCTGGCCTCTT 59.957 41.667 3.32 0.00 0.00 2.85
5364 5487 3.181507 TGTTCTGCTGCTTGATATTTCGC 60.182 43.478 0.00 0.00 0.00 4.70
5398 5521 4.142469 CCGTGACTTCCATGGGAAAATTAC 60.142 45.833 13.02 0.00 46.09 1.89
5543 5666 1.602888 CCTGCAGCTTGCCACTCTT 60.603 57.895 8.66 0.00 44.23 2.85
5616 5739 7.509546 TCTTGATTTGGTCAGAGTAACTTCTT 58.490 34.615 0.00 0.00 38.29 2.52
5617 5740 7.067496 TCTTGATTTGGTCAGAGTAACTTCT 57.933 36.000 0.00 0.00 38.29 2.85
5618 5741 7.442666 ACTTCTTGATTTGGTCAGAGTAACTTC 59.557 37.037 0.00 0.00 38.29 3.01
5619 5742 7.283329 ACTTCTTGATTTGGTCAGAGTAACTT 58.717 34.615 0.00 0.00 38.29 2.66
5620 5743 6.831976 ACTTCTTGATTTGGTCAGAGTAACT 58.168 36.000 0.00 0.00 38.29 2.24
5621 5744 7.497925 AACTTCTTGATTTGGTCAGAGTAAC 57.502 36.000 0.00 0.00 38.29 2.50
5622 5745 8.647796 TCTAACTTCTTGATTTGGTCAGAGTAA 58.352 33.333 0.00 0.00 38.29 2.24
5623 5746 8.190326 TCTAACTTCTTGATTTGGTCAGAGTA 57.810 34.615 0.00 0.00 38.29 2.59
5624 5747 7.067496 TCTAACTTCTTGATTTGGTCAGAGT 57.933 36.000 0.00 0.00 38.29 3.24
5625 5748 8.558973 AATCTAACTTCTTGATTTGGTCAGAG 57.441 34.615 0.00 0.00 38.29 3.35
5626 5749 8.786898 CAAATCTAACTTCTTGATTTGGTCAGA 58.213 33.333 15.65 0.00 46.20 3.27
5627 5750 8.961294 CAAATCTAACTTCTTGATTTGGTCAG 57.039 34.615 15.65 0.00 46.20 3.51
5633 5756 7.288810 TGGCACAAATCTAACTTCTTGATTT 57.711 32.000 0.00 0.00 39.93 2.17
5634 5757 6.899393 TGGCACAAATCTAACTTCTTGATT 57.101 33.333 0.00 0.00 31.92 2.57
5759 5882 0.391130 GTGCAGATGAGCGTGGGTTA 60.391 55.000 0.00 0.00 37.31 2.85
5761 5884 2.046892 GTGCAGATGAGCGTGGGT 60.047 61.111 0.00 0.00 37.31 4.51
5766 5889 4.457496 ACCGGGTGCAGATGAGCG 62.457 66.667 6.32 0.00 37.31 5.03
5837 5961 3.953612 AGAAACTGGACACAAAGCAATGA 59.046 39.130 0.00 0.00 0.00 2.57
5872 5996 2.472695 TGACCCTGCACAAGTCATAC 57.527 50.000 4.93 0.00 35.67 2.39
5955 6079 8.564574 GGTTTGTGAATACACTCAAGACAAATA 58.435 33.333 0.00 0.00 46.07 1.40
5956 6080 7.285401 AGGTTTGTGAATACACTCAAGACAAAT 59.715 33.333 0.00 0.00 46.07 2.32
5958 6082 6.119536 AGGTTTGTGAATACACTCAAGACAA 58.880 36.000 0.00 0.00 46.07 3.18
5960 6084 6.619801 AAGGTTTGTGAATACACTCAAGAC 57.380 37.500 0.00 0.00 46.07 3.01
5961 6085 8.918202 ATTAAGGTTTGTGAATACACTCAAGA 57.082 30.769 0.00 0.00 46.07 3.02
6059 6286 6.990349 CCCGTGTAGGTAAGTATGATCAAATT 59.010 38.462 0.00 0.00 38.74 1.82
6204 6431 6.491403 GGAATTCACCTGGAATGTAGCATTAT 59.509 38.462 7.93 0.00 45.46 1.28
6205 6432 5.827797 GGAATTCACCTGGAATGTAGCATTA 59.172 40.000 7.93 0.00 45.46 1.90
6233 6460 3.439129 GTCGTTTTTACCAATCCAGGGAG 59.561 47.826 0.00 0.00 0.00 4.30
6242 6469 1.386533 TTGGGCGTCGTTTTTACCAA 58.613 45.000 0.00 0.00 35.78 3.67
6260 6489 2.304761 TCTCAGGTTATTCGGCAGGTTT 59.695 45.455 0.00 0.00 0.00 3.27
6592 6822 3.536956 TCCCCGTGTTGTCTGATATTC 57.463 47.619 0.00 0.00 0.00 1.75
6628 6862 7.365652 GGAAAGATCTTTGGATAGGACCAGTTA 60.366 40.741 25.12 0.00 41.19 2.24
6648 6882 4.351111 AGGAAGCCTAGACTTTTGGAAAGA 59.649 41.667 7.37 0.00 28.47 2.52
6649 6883 4.657013 AGGAAGCCTAGACTTTTGGAAAG 58.343 43.478 0.00 0.00 28.47 2.62
6650 6884 4.351111 AGAGGAAGCCTAGACTTTTGGAAA 59.649 41.667 0.00 0.00 31.76 3.13
6653 6889 3.990959 AGAGGAAGCCTAGACTTTTGG 57.009 47.619 0.00 0.00 31.76 3.28
6674 6910 7.773149 TGCTGGCAGTAAAGTTAAACTAAAAA 58.227 30.769 17.16 0.00 0.00 1.94
6675 6911 7.336161 TGCTGGCAGTAAAGTTAAACTAAAA 57.664 32.000 17.16 0.00 0.00 1.52
6676 6912 6.945938 TGCTGGCAGTAAAGTTAAACTAAA 57.054 33.333 17.16 0.00 0.00 1.85
6719 6958 2.484065 CCACGTTGGAGGTCTTTACACA 60.484 50.000 0.00 0.00 40.96 3.72
6720 6959 2.140717 CCACGTTGGAGGTCTTTACAC 58.859 52.381 0.00 0.00 40.96 2.90
6746 6985 8.787852 GCTACTTTTATTTTGCTGGATATAGCT 58.212 33.333 0.00 0.00 44.01 3.32
6747 6986 8.023706 GGCTACTTTTATTTTGCTGGATATAGC 58.976 37.037 0.00 0.00 43.95 2.97
6836 7505 0.034337 GTACTGACCGGCCTGTTTGA 59.966 55.000 5.47 0.00 0.00 2.69
6908 7578 9.673454 GTTTATGTTTTTCTTAGACAAATCCGT 57.327 29.630 0.00 0.00 0.00 4.69
6909 7579 9.672086 TGTTTATGTTTTTCTTAGACAAATCCG 57.328 29.630 0.00 0.00 0.00 4.18
6913 7583 9.291664 CCGTTGTTTATGTTTTTCTTAGACAAA 57.708 29.630 0.00 0.00 34.83 2.83
6914 7584 8.675504 TCCGTTGTTTATGTTTTTCTTAGACAA 58.324 29.630 0.00 0.00 32.53 3.18
6915 7585 8.211116 TCCGTTGTTTATGTTTTTCTTAGACA 57.789 30.769 0.00 0.00 0.00 3.41
6916 7586 9.673454 AATCCGTTGTTTATGTTTTTCTTAGAC 57.327 29.630 0.00 0.00 0.00 2.59
6919 7589 9.896263 GGTAATCCGTTGTTTATGTTTTTCTTA 57.104 29.630 0.00 0.00 0.00 2.10
6920 7590 8.806177 GGTAATCCGTTGTTTATGTTTTTCTT 57.194 30.769 0.00 0.00 0.00 2.52
6961 7631 1.662629 CGTCAAGTAGCTTCATGCAGG 59.337 52.381 0.00 0.00 45.94 4.85
6962 7632 2.346847 GTCGTCAAGTAGCTTCATGCAG 59.653 50.000 0.00 0.00 45.94 4.41
6963 7633 2.029020 AGTCGTCAAGTAGCTTCATGCA 60.029 45.455 0.00 0.00 45.94 3.96
6964 7634 2.600867 GAGTCGTCAAGTAGCTTCATGC 59.399 50.000 0.00 0.00 43.29 4.06
6978 7669 3.124128 GGGGTCGTTATTTTTGAGTCGTC 59.876 47.826 0.00 0.00 0.00 4.20
7022 7714 4.141855 TGCTAGCTTGCGTTAACTTTTC 57.858 40.909 17.23 0.00 35.36 2.29
7027 7719 3.863424 TGTAGATGCTAGCTTGCGTTAAC 59.137 43.478 17.23 15.94 35.36 2.01
7034 7726 6.486253 TTTTGAAGTGTAGATGCTAGCTTG 57.514 37.500 17.23 0.00 0.00 4.01
7080 7776 4.094887 GCGACTTTCATCTATCAAAAGGCA 59.905 41.667 0.00 0.00 37.80 4.75
7082 7778 4.878397 AGGCGACTTTCATCTATCAAAAGG 59.122 41.667 0.00 0.00 37.44 3.11
7087 7783 2.168313 TGCAGGCGACTTTCATCTATCA 59.832 45.455 0.00 0.00 40.21 2.15
7088 7784 2.826428 TGCAGGCGACTTTCATCTATC 58.174 47.619 0.00 0.00 40.21 2.08
7089 7785 2.939103 GTTGCAGGCGACTTTCATCTAT 59.061 45.455 4.39 0.00 40.21 1.98
7090 7786 2.028112 AGTTGCAGGCGACTTTCATCTA 60.028 45.455 8.36 0.00 40.21 1.98
7092 7788 1.135859 CAGTTGCAGGCGACTTTCATC 60.136 52.381 11.41 0.00 40.21 2.92
7093 7789 0.877071 CAGTTGCAGGCGACTTTCAT 59.123 50.000 11.41 0.00 40.21 2.57
7127 7823 3.118371 AGTCACTTTATTTCCCTAGGCCG 60.118 47.826 2.05 0.00 0.00 6.13
7147 7843 9.883142 CAGAGATCTTTATTTACCTCTCAAAGT 57.117 33.333 0.00 0.00 33.27 2.66
7213 7909 4.530857 CTACTTGCTCCGGCCGGG 62.531 72.222 42.36 32.16 37.74 5.73
7214 7910 2.515996 TTTCTACTTGCTCCGGCCGG 62.516 60.000 39.13 39.13 37.74 6.13
7216 7912 1.087501 CTTTTCTACTTGCTCCGGCC 58.912 55.000 0.00 0.00 37.74 6.13
7217 7913 2.094762 TCTTTTCTACTTGCTCCGGC 57.905 50.000 0.00 0.00 39.26 6.13
7223 7919 4.725790 ATGGCCATTCTTTTCTACTTGC 57.274 40.909 14.09 0.00 0.00 4.01
7225 7921 6.466812 CCAAAATGGCCATTCTTTTCTACTT 58.533 36.000 30.74 15.11 0.00 2.24
7226 7922 6.041423 CCAAAATGGCCATTCTTTTCTACT 57.959 37.500 30.74 9.56 0.00 2.57
7251 7949 2.577911 GATTTTGCAGCGGCGCTC 60.578 61.111 34.22 25.42 45.35 5.03
7257 7955 4.211794 AGAATTGGTTTTGATTTTGCAGCG 59.788 37.500 0.00 0.00 0.00 5.18
7295 7993 2.418197 GCGGCATTGTTCCTACAGACTA 60.418 50.000 0.00 0.00 35.28 2.59
7315 8013 1.078848 AACCTGGACAGATGCTCGC 60.079 57.895 0.00 0.00 0.00 5.03
7316 8014 0.742281 CCAACCTGGACAGATGCTCG 60.742 60.000 0.00 0.00 40.96 5.03
7325 8023 4.145052 AGAAAATTCAGACCAACCTGGAC 58.855 43.478 0.00 0.00 40.96 4.02
7332 8030 5.301805 GGGACAGAAAGAAAATTCAGACCAA 59.698 40.000 0.00 0.00 34.19 3.67
7369 8107 0.955178 TGAGCTAGATAGACGCCTGC 59.045 55.000 0.00 0.00 0.00 4.85
7370 8108 2.881513 TCTTGAGCTAGATAGACGCCTG 59.118 50.000 0.00 0.00 0.00 4.85
7374 8112 6.975197 TGTCAATTTCTTGAGCTAGATAGACG 59.025 38.462 0.00 0.00 41.96 4.18
7431 8178 2.930385 ATCCCACAGCGCTGAATCCG 62.930 60.000 42.03 22.86 0.00 4.18
7440 8187 2.484062 GCCCATCAATCCCACAGCG 61.484 63.158 0.00 0.00 0.00 5.18
7441 8188 0.757935 ATGCCCATCAATCCCACAGC 60.758 55.000 0.00 0.00 0.00 4.40
7442 8189 1.133575 AGATGCCCATCAATCCCACAG 60.134 52.381 10.58 0.00 40.22 3.66
7535 10481 1.034838 AGCCTCTAGTGCGTCCTCTG 61.035 60.000 0.00 0.00 0.00 3.35
7536 10482 0.750182 GAGCCTCTAGTGCGTCCTCT 60.750 60.000 0.00 0.00 0.00 3.69
7539 10485 1.435515 CTGAGCCTCTAGTGCGTCC 59.564 63.158 0.00 0.00 0.00 4.79
7540 10486 1.435515 CCTGAGCCTCTAGTGCGTC 59.564 63.158 0.00 0.00 0.00 5.19
7541 10487 2.716017 GCCTGAGCCTCTAGTGCGT 61.716 63.158 0.00 0.00 0.00 5.24
7542 10488 2.105930 GCCTGAGCCTCTAGTGCG 59.894 66.667 0.00 0.00 0.00 5.34
7543 10489 1.441311 GAGCCTGAGCCTCTAGTGC 59.559 63.158 0.00 0.00 41.25 4.40
7544 10490 1.733402 CGGAGCCTGAGCCTCTAGTG 61.733 65.000 0.00 0.00 41.25 2.74
7545 10491 1.454847 CGGAGCCTGAGCCTCTAGT 60.455 63.158 0.00 0.00 41.25 2.57
7546 10492 2.199652 CCGGAGCCTGAGCCTCTAG 61.200 68.421 0.00 0.00 41.25 2.43
7547 10493 1.642513 TACCGGAGCCTGAGCCTCTA 61.643 60.000 9.46 0.00 41.25 2.43
7548 10494 2.920076 CTACCGGAGCCTGAGCCTCT 62.920 65.000 9.46 0.00 41.25 3.69
7549 10495 2.442272 TACCGGAGCCTGAGCCTC 60.442 66.667 9.46 0.00 41.25 4.70
7550 10496 2.443016 CTACCGGAGCCTGAGCCT 60.443 66.667 9.46 0.00 41.25 4.58
7551 10497 4.228567 GCTACCGGAGCCTGAGCC 62.229 72.222 9.46 0.00 46.41 4.70
7580 10526 3.063997 CCCATACATCAGACGTTGCTTTC 59.936 47.826 0.00 0.00 0.00 2.62
7595 10541 2.446666 AGGGCAAAGCATATCCCATACA 59.553 45.455 6.85 0.00 41.22 2.29
7629 10593 1.592669 CGGTGCATCCATCCGTCTC 60.593 63.158 4.61 0.00 39.51 3.36


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

AutoCloner maintained by Alex Coulton.