Multiple sequence alignment - TraesCS2D01G316900

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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 TraesCS2D01G316900 chr2D 100.000 7263 0 0 1 7263 406204004 406211266 0.000000e+00 13413.0
1 TraesCS2D01G316900 chr2D 92.575 633 24 5 142 770 189689680 189689067 0.000000e+00 887.0
2 TraesCS2D01G316900 chr2A 96.359 3873 82 23 2166 6027 544306958 544310782 0.000000e+00 6316.0
3 TraesCS2D01G316900 chr2A 92.551 792 35 10 1069 1848 544305534 544306313 0.000000e+00 1114.0
4 TraesCS2D01G316900 chr2A 97.512 201 4 1 6321 6521 544310781 544310980 6.980000e-90 342.0
5 TraesCS2D01G316900 chr2A 87.584 298 26 10 775 1064 544305188 544305482 1.170000e-87 335.0
6 TraesCS2D01G316900 chr2A 97.740 177 3 1 1849 2024 544306566 544306742 3.290000e-78 303.0
7 TraesCS2D01G316900 chr2A 97.674 129 2 1 2060 2188 544306740 544306867 3.410000e-53 220.0
8 TraesCS2D01G316900 chr2B 95.531 3737 118 23 2300 6021 481879670 481883372 0.000000e+00 5930.0
9 TraesCS2D01G316900 chr2B 92.238 773 47 11 1530 2293 481878130 481878898 0.000000e+00 1083.0
10 TraesCS2D01G316900 chr2B 94.349 637 31 3 142 774 547098219 547098854 0.000000e+00 972.0
11 TraesCS2D01G316900 chr2B 92.153 497 22 8 953 1436 481877481 481877973 0.000000e+00 686.0
12 TraesCS2D01G316900 chr2B 95.856 362 9 2 6166 6521 481883372 481883733 1.360000e-161 580.0
13 TraesCS2D01G316900 chr2B 91.912 408 25 7 366 768 526460280 526459876 1.370000e-156 564.0
14 TraesCS2D01G316900 chr2B 100.000 28 0 0 1668 1695 776973069 776973096 1.300000e-02 52.8
15 TraesCS2D01G316900 chr7D 97.449 784 13 2 1 778 31108631 31107849 0.000000e+00 1330.0
16 TraesCS2D01G316900 chr7D 82.953 745 111 15 6519 7254 163119897 163120634 0.000000e+00 658.0
17 TraesCS2D01G316900 chr7D 95.801 381 14 1 386 766 552323935 552324313 1.340000e-171 614.0
18 TraesCS2D01G316900 chr3D 97.919 769 15 1 1 769 55366272 55365505 0.000000e+00 1330.0
19 TraesCS2D01G316900 chr3D 95.035 423 17 1 142 560 606928029 606927607 0.000000e+00 662.0
20 TraesCS2D01G316900 chr3D 95.862 145 5 1 1 144 454525966 454525822 4.380000e-57 233.0
21 TraesCS2D01G316900 chr3D 95.862 145 5 1 1 144 580543856 580544000 4.380000e-57 233.0
22 TraesCS2D01G316900 chr5D 96.084 766 19 6 1 765 26524332 26523577 0.000000e+00 1238.0
23 TraesCS2D01G316900 chr5D 77.376 747 153 15 6525 7263 213275678 213274940 5.210000e-116 429.0
24 TraesCS2D01G316900 chr6D 95.613 775 26 5 1 769 49804417 49803645 0.000000e+00 1236.0
25 TraesCS2D01G316900 chr4D 92.405 632 23 13 142 768 472924973 472925584 0.000000e+00 878.0
26 TraesCS2D01G316900 chr4D 92.114 634 28 3 142 771 400894256 400894871 0.000000e+00 874.0
27 TraesCS2D01G316900 chr4D 93.750 48 3 0 1364 1411 344955629 344955582 1.010000e-08 73.1
28 TraesCS2D01G316900 chr4A 86.406 743 98 3 6519 7260 122625880 122625140 0.000000e+00 809.0
29 TraesCS2D01G316900 chr4A 97.183 142 4 0 3 144 701655932 701656073 2.620000e-59 241.0
30 TraesCS2D01G316900 chr4A 91.667 48 4 0 1364 1411 120718416 120718369 4.700000e-07 67.6
31 TraesCS2D01G316900 chr7B 82.361 737 118 11 6523 7255 614645665 614644937 1.330000e-176 630.0
32 TraesCS2D01G316900 chr7B 92.020 401 26 5 367 764 163760783 163761180 6.360000e-155 558.0
33 TraesCS2D01G316900 chr3A 92.010 413 26 6 366 774 112383027 112383436 2.270000e-159 573.0
34 TraesCS2D01G316900 chr4B 77.600 750 155 12 6521 7263 401111915 401112658 6.690000e-120 442.0
35 TraesCS2D01G316900 chr4B 95.139 144 7 0 1 144 486259107 486259250 2.040000e-55 228.0
36 TraesCS2D01G316900 chr3B 81.282 390 66 7 6524 6908 684495912 684495525 7.080000e-80 309.0
37 TraesCS2D01G316900 chr3B 92.683 41 3 0 6711 6751 434666906 434666946 7.870000e-05 60.2
38 TraesCS2D01G316900 chr1B 95.833 144 6 0 1 144 29404970 29405113 4.380000e-57 233.0
39 TraesCS2D01G316900 chr1A 77.931 145 11 11 1605 1747 489183865 489183990 3.640000e-08 71.3
40 TraesCS2D01G316900 chr1D 88.889 45 5 0 1371 1415 18870077 18870033 1.000000e-03 56.5
41 TraesCS2D01G316900 chr5A 88.889 45 2 3 1654 1695 379962725 379962769 1.300000e-02 52.8


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 TraesCS2D01G316900 chr2D 406204004 406211266 7262 False 13413.000000 13413 100.000000 1 7263 1 chr2D.!!$F1 7262
1 TraesCS2D01G316900 chr2D 189689067 189689680 613 True 887.000000 887 92.575000 142 770 1 chr2D.!!$R1 628
2 TraesCS2D01G316900 chr2A 544305188 544310980 5792 False 1438.333333 6316 94.903333 775 6521 6 chr2A.!!$F1 5746
3 TraesCS2D01G316900 chr2B 481877481 481883733 6252 False 2069.750000 5930 93.944500 953 6521 4 chr2B.!!$F3 5568
4 TraesCS2D01G316900 chr2B 547098219 547098854 635 False 972.000000 972 94.349000 142 774 1 chr2B.!!$F1 632
5 TraesCS2D01G316900 chr7D 31107849 31108631 782 True 1330.000000 1330 97.449000 1 778 1 chr7D.!!$R1 777
6 TraesCS2D01G316900 chr7D 163119897 163120634 737 False 658.000000 658 82.953000 6519 7254 1 chr7D.!!$F1 735
7 TraesCS2D01G316900 chr3D 55365505 55366272 767 True 1330.000000 1330 97.919000 1 769 1 chr3D.!!$R1 768
8 TraesCS2D01G316900 chr5D 26523577 26524332 755 True 1238.000000 1238 96.084000 1 765 1 chr5D.!!$R1 764
9 TraesCS2D01G316900 chr5D 213274940 213275678 738 True 429.000000 429 77.376000 6525 7263 1 chr5D.!!$R2 738
10 TraesCS2D01G316900 chr6D 49803645 49804417 772 True 1236.000000 1236 95.613000 1 769 1 chr6D.!!$R1 768
11 TraesCS2D01G316900 chr4D 472924973 472925584 611 False 878.000000 878 92.405000 142 768 1 chr4D.!!$F2 626
12 TraesCS2D01G316900 chr4D 400894256 400894871 615 False 874.000000 874 92.114000 142 771 1 chr4D.!!$F1 629
13 TraesCS2D01G316900 chr4A 122625140 122625880 740 True 809.000000 809 86.406000 6519 7260 1 chr4A.!!$R2 741
14 TraesCS2D01G316900 chr7B 614644937 614645665 728 True 630.000000 630 82.361000 6523 7255 1 chr7B.!!$R1 732
15 TraesCS2D01G316900 chr4B 401111915 401112658 743 False 442.000000 442 77.600000 6521 7263 1 chr4B.!!$F1 742

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
856 886 0.472352 TAACCCCAACCGACCTGTCT 60.472 55.000 0.00 0.0 0.00 3.41 F
1613 1801 1.133025 CCGGCAAAGATAAAGTGCAGG 59.867 52.381 0.00 0.0 45.04 4.85 F
1715 1903 1.428448 GAGCGCACATGTAACACTCA 58.572 50.000 11.47 0.0 0.00 3.41 F
2756 4085 1.699054 AACTGGCACTGGCACTCTGA 61.699 55.000 0.07 0.0 43.71 3.27 F
3416 4756 5.182001 GTGCTTCACAGTTCTCCATATGTTT 59.818 40.000 1.24 0.0 34.08 2.83 F
4386 5729 2.537529 CGATTGCCAGCTATTGTCAACG 60.538 50.000 0.00 0.0 0.00 4.10 F
6029 7376 0.320946 AAATGCCTTGCCATGTGTGC 60.321 50.000 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2734 4057 1.160137 GAGTGCCAGTGCCAGTTAAG 58.840 55.000 0.00 0.0 36.33 1.85 R
2799 4128 1.699634 ACTTCTTAGTTGGCTGGCTCA 59.300 47.619 2.00 0.0 0.00 4.26 R
2947 4276 2.564947 CAGTCTTAGAGAAGCACAGGGT 59.435 50.000 0.00 0.0 32.21 4.34 R
4088 5430 4.113354 GGCACGCTCTTATATGGCTATAC 58.887 47.826 0.00 0.0 34.93 1.47 R
4649 5992 6.408035 TCAAGACAGTTACAGGTTTTACACA 58.592 36.000 0.00 0.0 0.00 3.72 R
6132 7479 0.322187 AGATGTTAACACACCCCGCC 60.322 55.000 11.22 0.0 35.03 6.13 R
6977 8340 0.040157 CACCGTCGTCGTTCCAAGTA 60.040 55.000 0.71 0.0 35.01 2.24 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
46 47 2.388232 GCTGGAACCGGTTGTAGCG 61.388 63.158 27.87 9.33 39.06 4.26
196 199 6.780457 AGATTTTTGCTACAACTGGCATAT 57.220 33.333 0.00 0.00 38.30 1.78
237 240 3.723764 GTCATGTTTTGCTACAACACACG 59.276 43.478 1.73 0.00 36.97 4.49
695 719 0.669318 GAACGGATCTGACGGTGCAA 60.669 55.000 9.00 0.00 35.23 4.08
809 839 9.212641 TCAATTTTCACAAAAGTCAATTGTCAA 57.787 25.926 5.13 0.00 38.90 3.18
856 886 0.472352 TAACCCCAACCGACCTGTCT 60.472 55.000 0.00 0.00 0.00 3.41
857 887 2.052047 AACCCCAACCGACCTGTCTG 62.052 60.000 0.00 0.00 0.00 3.51
859 889 2.738521 CCAACCGACCTGTCTGCG 60.739 66.667 0.00 0.00 0.00 5.18
860 890 2.029073 CAACCGACCTGTCTGCGT 59.971 61.111 0.00 0.00 0.00 5.24
861 891 2.029073 AACCGACCTGTCTGCGTG 59.971 61.111 0.00 0.00 0.00 5.34
862 892 2.792947 AACCGACCTGTCTGCGTGT 61.793 57.895 0.00 0.00 0.00 4.49
863 893 2.734723 CCGACCTGTCTGCGTGTG 60.735 66.667 0.00 0.00 0.00 3.82
864 894 2.335011 CGACCTGTCTGCGTGTGA 59.665 61.111 0.00 0.00 0.00 3.58
865 895 1.730902 CGACCTGTCTGCGTGTGAG 60.731 63.158 0.00 0.00 0.00 3.51
866 896 2.024319 GACCTGTCTGCGTGTGAGC 61.024 63.158 0.00 0.00 37.71 4.26
868 898 3.108289 CTGTCTGCGTGTGAGCGG 61.108 66.667 0.00 0.00 44.50 5.52
1041 1075 3.585862 TCTCGTTTCCATCTTTTCCTCG 58.414 45.455 0.00 0.00 0.00 4.63
1061 1129 5.139435 TCGTCTCTGTTCAGTGAATTCAT 57.861 39.130 12.12 0.00 0.00 2.57
1065 1133 5.406780 GTCTCTGTTCAGTGAATTCATTCGT 59.593 40.000 12.12 0.00 39.62 3.85
1078 1146 7.112984 GTGAATTCATTCGTACAAACCTGAAAC 59.887 37.037 12.12 0.00 39.62 2.78
1080 1148 4.710324 TCATTCGTACAAACCTGAAACCT 58.290 39.130 0.00 0.00 0.00 3.50
1081 1149 4.513692 TCATTCGTACAAACCTGAAACCTG 59.486 41.667 0.00 0.00 0.00 4.00
1250 1328 3.273886 TCCTCCTCTTCCTGGTATGGTTA 59.726 47.826 0.00 0.00 0.00 2.85
1295 1373 2.024868 CCGCCGTGTTCACGAATCA 61.025 57.895 23.84 0.00 34.64 2.57
1321 1399 5.232414 GTCACTTCAGATCCGTAAGTTATGC 59.768 44.000 2.98 0.00 31.21 3.14
1612 1800 1.812571 ACCGGCAAAGATAAAGTGCAG 59.187 47.619 0.00 0.00 40.12 4.41
1613 1801 1.133025 CCGGCAAAGATAAAGTGCAGG 59.867 52.381 0.00 0.00 45.04 4.85
1638 1826 2.685897 GACATAGGTCTGAGCTCGACTT 59.314 50.000 26.46 23.56 40.99 3.01
1715 1903 1.428448 GAGCGCACATGTAACACTCA 58.572 50.000 11.47 0.00 0.00 3.41
1726 1914 7.025365 CACATGTAACACTCATTTTCTCATGG 58.975 38.462 0.00 0.00 35.81 3.66
1791 1979 3.094572 CTCCTGGGGTCGAACTAAACTA 58.905 50.000 0.00 0.00 0.00 2.24
1844 2032 6.761714 GCCTTCGAGATTTATCCAAGACTTAA 59.238 38.462 0.00 0.00 0.00 1.85
2014 2456 4.941873 CCTACAACTAGGGAAAACATGACC 59.058 45.833 0.00 0.00 36.56 4.02
2031 2473 5.481473 ACATGACCCTTGCACATTTCTAAAT 59.519 36.000 0.00 0.00 0.00 1.40
2045 2487 6.649141 ACATTTCTAAATCGTCAACAGCTGTA 59.351 34.615 22.01 3.84 0.00 2.74
2343 3663 2.958355 GCATGCCTTGCCTTTTCCTATA 59.042 45.455 6.36 0.00 46.15 1.31
2404 3724 7.923414 AAGGTTCCTGTGATAGTTGAATTAC 57.077 36.000 0.00 0.00 0.00 1.89
2466 3786 3.825585 TCTTCATTTTGTGCATGTAGGCA 59.174 39.130 0.00 0.00 42.53 4.75
2596 3916 6.164876 TCAAATGTTTGCCATACTGAATTGG 58.835 36.000 0.66 0.00 38.05 3.16
2756 4085 1.699054 AACTGGCACTGGCACTCTGA 61.699 55.000 0.07 0.00 43.71 3.27
2947 4276 6.921486 TGATACCTGTGACAACCTTAGTTA 57.079 37.500 0.00 0.00 33.27 2.24
3416 4756 5.182001 GTGCTTCACAGTTCTCCATATGTTT 59.818 40.000 1.24 0.00 34.08 2.83
3565 4905 8.982685 GTTATCTTGTCGAACATGATATGTGAT 58.017 33.333 16.63 0.00 44.07 3.06
3575 4915 8.592998 CGAACATGATATGTGATATGATCTGTG 58.407 37.037 0.00 0.00 44.07 3.66
3600 4940 9.219603 TGTCGAATCTGATCAACTTAAATCTTT 57.780 29.630 0.00 0.00 0.00 2.52
3792 5133 5.710099 GGTTAATGACAGATCAGTTGGGAAA 59.290 40.000 0.00 0.00 38.57 3.13
4088 5430 7.171630 AGTATTACGCTCTAATGGGAATAGG 57.828 40.000 0.00 0.00 0.00 2.57
4386 5729 2.537529 CGATTGCCAGCTATTGTCAACG 60.538 50.000 0.00 0.00 0.00 4.10
4447 5790 3.249091 CATGGAGTTCTTGTCTGTCTCG 58.751 50.000 0.00 0.00 0.00 4.04
4577 5920 8.897752 GCAGTTCATGTCCTTAAAGAATATCTT 58.102 33.333 0.00 0.00 38.59 2.40
4626 5969 3.563223 TCTAGGGAGGTAGTGTATGTGC 58.437 50.000 0.00 0.00 0.00 4.57
4640 5983 6.684686 AGTGTATGTGCGTAAGAAGAACTTA 58.315 36.000 0.00 0.00 39.72 2.24
4644 5987 4.695396 TGTGCGTAAGAAGAACTTAACCA 58.305 39.130 0.00 0.00 41.87 3.67
4645 5988 4.748102 TGTGCGTAAGAAGAACTTAACCAG 59.252 41.667 0.00 0.00 41.87 4.00
4646 5989 4.986659 GTGCGTAAGAAGAACTTAACCAGA 59.013 41.667 0.00 0.00 41.87 3.86
4648 5991 6.018507 GTGCGTAAGAAGAACTTAACCAGAAA 60.019 38.462 0.00 0.00 41.87 2.52
4649 5992 6.708949 TGCGTAAGAAGAACTTAACCAGAAAT 59.291 34.615 0.00 0.00 41.87 2.17
4650 5993 7.015877 GCGTAAGAAGAACTTAACCAGAAATG 58.984 38.462 0.00 0.00 41.87 2.32
4651 5994 7.307811 GCGTAAGAAGAACTTAACCAGAAATGT 60.308 37.037 0.00 0.00 41.87 2.71
4652 5995 8.009974 CGTAAGAAGAACTTAACCAGAAATGTG 58.990 37.037 0.00 0.00 41.87 3.21
4653 5996 7.881775 AAGAAGAACTTAACCAGAAATGTGT 57.118 32.000 0.00 0.00 37.03 3.72
4694 6037 9.176460 TCTTGAAAATGATGTGCTATATGTTGA 57.824 29.630 0.00 0.00 0.00 3.18
4697 6040 8.738106 TGAAAATGATGTGCTATATGTTGAACA 58.262 29.630 0.00 0.00 0.00 3.18
4741 6084 9.480053 CATGAATGAACTTTTGACTTTGGTTAT 57.520 29.630 0.00 0.00 0.00 1.89
5250 6595 9.692749 CAAGTATCTCACACTTAGTTTACTGAA 57.307 33.333 0.00 0.00 34.50 3.02
5370 6716 2.765122 GAGCATCTGGTTAGCCTCATC 58.235 52.381 0.00 0.00 35.27 2.92
5528 6874 9.624697 TTACATTTTTGCAGATAAGCTTTACTG 57.375 29.630 20.72 20.72 34.99 2.74
5622 6968 1.817099 GCATCGGTGAAGCTGAGGG 60.817 63.158 0.00 0.00 35.02 4.30
5909 7256 5.033589 AGGAGATGAAGAATCATTTCGCT 57.966 39.130 4.04 1.15 46.30 4.93
5914 7261 6.549952 AGATGAAGAATCATTTCGCTTTGAC 58.450 36.000 0.00 0.00 46.30 3.18
5999 7346 6.403746 GCATCTTCAAAAGGAGGCTTAGTTAC 60.404 42.308 0.00 0.00 36.51 2.50
6008 7355 4.660771 AGGAGGCTTAGTTACCATTGCTAT 59.339 41.667 0.00 0.00 0.00 2.97
6021 7368 4.060205 CCATTGCTATTAAATGCCTTGCC 58.940 43.478 1.47 0.00 34.35 4.52
6022 7369 4.443175 CCATTGCTATTAAATGCCTTGCCA 60.443 41.667 1.47 0.00 34.35 4.92
6023 7370 5.302360 CATTGCTATTAAATGCCTTGCCAT 58.698 37.500 1.47 0.00 0.00 4.40
6024 7371 4.325028 TGCTATTAAATGCCTTGCCATG 57.675 40.909 1.47 0.00 0.00 3.66
6025 7372 3.705579 TGCTATTAAATGCCTTGCCATGT 59.294 39.130 0.00 0.00 0.00 3.21
6026 7373 4.053295 GCTATTAAATGCCTTGCCATGTG 58.947 43.478 0.00 0.00 0.00 3.21
6027 7374 4.441913 GCTATTAAATGCCTTGCCATGTGT 60.442 41.667 0.00 0.00 0.00 3.72
6028 7375 3.316071 TTAAATGCCTTGCCATGTGTG 57.684 42.857 0.00 0.00 0.00 3.82
6029 7376 0.320946 AAATGCCTTGCCATGTGTGC 60.321 50.000 0.00 0.00 0.00 4.57
6030 7377 1.189524 AATGCCTTGCCATGTGTGCT 61.190 50.000 0.00 0.00 0.00 4.40
6031 7378 1.189524 ATGCCTTGCCATGTGTGCTT 61.190 50.000 0.00 0.00 0.00 3.91
6032 7379 0.539207 TGCCTTGCCATGTGTGCTTA 60.539 50.000 0.00 0.00 0.00 3.09
6033 7380 0.602562 GCCTTGCCATGTGTGCTTAA 59.397 50.000 0.00 0.00 0.00 1.85
6034 7381 1.205417 GCCTTGCCATGTGTGCTTAAT 59.795 47.619 0.00 0.00 0.00 1.40
6035 7382 2.354003 GCCTTGCCATGTGTGCTTAATT 60.354 45.455 0.00 0.00 0.00 1.40
6036 7383 3.865684 GCCTTGCCATGTGTGCTTAATTT 60.866 43.478 0.00 0.00 0.00 1.82
6037 7384 3.928375 CCTTGCCATGTGTGCTTAATTTC 59.072 43.478 0.00 0.00 0.00 2.17
6038 7385 3.591196 TGCCATGTGTGCTTAATTTCC 57.409 42.857 0.00 0.00 0.00 3.13
6039 7386 2.896044 TGCCATGTGTGCTTAATTTCCA 59.104 40.909 0.00 0.00 0.00 3.53
6040 7387 3.514706 TGCCATGTGTGCTTAATTTCCAT 59.485 39.130 0.00 0.00 0.00 3.41
6041 7388 4.114794 GCCATGTGTGCTTAATTTCCATC 58.885 43.478 0.00 0.00 0.00 3.51
6042 7389 4.685924 CCATGTGTGCTTAATTTCCATCC 58.314 43.478 0.00 0.00 0.00 3.51
6043 7390 4.160065 CCATGTGTGCTTAATTTCCATCCA 59.840 41.667 0.00 0.00 0.00 3.41
6044 7391 4.782019 TGTGTGCTTAATTTCCATCCAC 57.218 40.909 0.00 0.00 0.00 4.02
6045 7392 4.406456 TGTGTGCTTAATTTCCATCCACT 58.594 39.130 0.00 0.00 0.00 4.00
6046 7393 4.458989 TGTGTGCTTAATTTCCATCCACTC 59.541 41.667 0.00 0.00 0.00 3.51
6047 7394 4.016444 TGTGCTTAATTTCCATCCACTCC 58.984 43.478 0.00 0.00 0.00 3.85
6048 7395 4.263905 TGTGCTTAATTTCCATCCACTCCT 60.264 41.667 0.00 0.00 0.00 3.69
6049 7396 4.096984 GTGCTTAATTTCCATCCACTCCTG 59.903 45.833 0.00 0.00 0.00 3.86
6050 7397 3.067320 GCTTAATTTCCATCCACTCCTGC 59.933 47.826 0.00 0.00 0.00 4.85
6051 7398 2.905415 AATTTCCATCCACTCCTGCA 57.095 45.000 0.00 0.00 0.00 4.41
6052 7399 2.905415 ATTTCCATCCACTCCTGCAA 57.095 45.000 0.00 0.00 0.00 4.08
6053 7400 2.205022 TTTCCATCCACTCCTGCAAG 57.795 50.000 0.00 0.00 0.00 4.01
6054 7401 1.067295 TTCCATCCACTCCTGCAAGT 58.933 50.000 0.00 0.00 0.00 3.16
6055 7402 1.067295 TCCATCCACTCCTGCAAGTT 58.933 50.000 0.00 0.00 0.00 2.66
6056 7403 1.003580 TCCATCCACTCCTGCAAGTTC 59.996 52.381 0.00 0.00 0.00 3.01
6057 7404 1.004044 CCATCCACTCCTGCAAGTTCT 59.996 52.381 0.00 0.00 0.00 3.01
6058 7405 2.354259 CATCCACTCCTGCAAGTTCTC 58.646 52.381 0.00 0.00 0.00 2.87
6059 7406 1.722034 TCCACTCCTGCAAGTTCTCT 58.278 50.000 0.00 0.00 0.00 3.10
6060 7407 1.620819 TCCACTCCTGCAAGTTCTCTC 59.379 52.381 0.00 0.00 0.00 3.20
6061 7408 1.338579 CCACTCCTGCAAGTTCTCTCC 60.339 57.143 0.00 0.00 0.00 3.71
6062 7409 0.980423 ACTCCTGCAAGTTCTCTCCC 59.020 55.000 0.00 0.00 0.00 4.30
6063 7410 1.274712 CTCCTGCAAGTTCTCTCCCT 58.725 55.000 0.00 0.00 0.00 4.20
6064 7411 1.627834 CTCCTGCAAGTTCTCTCCCTT 59.372 52.381 0.00 0.00 0.00 3.95
6065 7412 2.039613 CTCCTGCAAGTTCTCTCCCTTT 59.960 50.000 0.00 0.00 0.00 3.11
6066 7413 2.443255 TCCTGCAAGTTCTCTCCCTTTT 59.557 45.455 0.00 0.00 0.00 2.27
6067 7414 3.117512 TCCTGCAAGTTCTCTCCCTTTTT 60.118 43.478 0.00 0.00 0.00 1.94
6085 7432 3.883997 TTTTTGCGCATTCCACTCC 57.116 47.368 12.75 0.00 0.00 3.85
6086 7433 1.327303 TTTTTGCGCATTCCACTCCT 58.673 45.000 12.75 0.00 0.00 3.69
6087 7434 0.597568 TTTTGCGCATTCCACTCCTG 59.402 50.000 12.75 0.00 0.00 3.86
6088 7435 1.865788 TTTGCGCATTCCACTCCTGC 61.866 55.000 12.75 0.00 0.00 4.85
6089 7436 2.747460 GCGCATTCCACTCCTGCA 60.747 61.111 0.30 0.00 35.64 4.41
6090 7437 2.334946 GCGCATTCCACTCCTGCAA 61.335 57.895 0.30 0.00 35.64 4.08
6091 7438 1.798735 CGCATTCCACTCCTGCAAG 59.201 57.895 0.00 0.00 35.64 4.01
6092 7439 0.957395 CGCATTCCACTCCTGCAAGT 60.957 55.000 0.00 0.00 35.64 3.16
6093 7440 1.251251 GCATTCCACTCCTGCAAGTT 58.749 50.000 0.00 0.00 35.96 2.66
6094 7441 1.200948 GCATTCCACTCCTGCAAGTTC 59.799 52.381 0.00 0.00 35.96 3.01
6095 7442 2.507484 CATTCCACTCCTGCAAGTTCA 58.493 47.619 0.00 0.00 0.00 3.18
6096 7443 2.727123 TTCCACTCCTGCAAGTTCAA 57.273 45.000 0.00 0.00 0.00 2.69
6097 7444 2.727123 TCCACTCCTGCAAGTTCAAA 57.273 45.000 0.00 0.00 0.00 2.69
6098 7445 3.228188 TCCACTCCTGCAAGTTCAAAT 57.772 42.857 0.00 0.00 0.00 2.32
6099 7446 4.365514 TCCACTCCTGCAAGTTCAAATA 57.634 40.909 0.00 0.00 0.00 1.40
6100 7447 4.326826 TCCACTCCTGCAAGTTCAAATAG 58.673 43.478 0.00 0.00 0.00 1.73
6101 7448 4.041567 TCCACTCCTGCAAGTTCAAATAGA 59.958 41.667 0.00 0.00 0.00 1.98
6102 7449 4.394300 CCACTCCTGCAAGTTCAAATAGAG 59.606 45.833 0.00 0.00 0.00 2.43
6103 7450 5.240891 CACTCCTGCAAGTTCAAATAGAGA 58.759 41.667 0.00 0.00 0.00 3.10
6104 7451 5.702670 CACTCCTGCAAGTTCAAATAGAGAA 59.297 40.000 0.00 0.00 0.00 2.87
6105 7452 6.205464 CACTCCTGCAAGTTCAAATAGAGAAA 59.795 38.462 0.00 0.00 0.00 2.52
6106 7453 6.944862 ACTCCTGCAAGTTCAAATAGAGAAAT 59.055 34.615 0.00 0.00 0.00 2.17
6107 7454 7.449704 ACTCCTGCAAGTTCAAATAGAGAAATT 59.550 33.333 0.00 0.00 34.06 1.82
6108 7455 8.862325 TCCTGCAAGTTCAAATAGAGAAATTA 57.138 30.769 0.00 0.00 32.28 1.40
6109 7456 9.466497 TCCTGCAAGTTCAAATAGAGAAATTAT 57.534 29.630 0.00 0.00 32.28 1.28
6110 7457 9.727627 CCTGCAAGTTCAAATAGAGAAATTATC 57.272 33.333 0.00 0.00 32.28 1.75
6116 7463 9.896645 AGTTCAAATAGAGAAATTATCTGAGCA 57.103 29.630 0.00 0.00 38.96 4.26
6119 7466 9.499479 TCAAATAGAGAAATTATCTGAGCATCC 57.501 33.333 0.00 0.00 38.96 3.51
6120 7467 9.504708 CAAATAGAGAAATTATCTGAGCATCCT 57.495 33.333 0.00 0.00 38.96 3.24
6121 7468 9.723601 AAATAGAGAAATTATCTGAGCATCCTC 57.276 33.333 0.00 0.00 38.96 3.71
6122 7469 6.999705 AGAGAAATTATCTGAGCATCCTCT 57.000 37.500 0.00 0.00 38.96 3.69
6123 7470 6.761312 AGAGAAATTATCTGAGCATCCTCTG 58.239 40.000 0.00 0.00 38.96 3.35
6124 7471 6.327104 AGAGAAATTATCTGAGCATCCTCTGT 59.673 38.462 0.00 0.00 38.96 3.41
6125 7472 6.289834 AGAAATTATCTGAGCATCCTCTGTG 58.710 40.000 0.00 0.00 38.93 3.66
6126 7473 5.627182 AATTATCTGAGCATCCTCTGTGT 57.373 39.130 0.00 0.00 38.93 3.72
6127 7474 6.737720 AATTATCTGAGCATCCTCTGTGTA 57.262 37.500 0.00 0.00 38.93 2.90
6128 7475 6.737720 ATTATCTGAGCATCCTCTGTGTAA 57.262 37.500 0.00 0.00 38.93 2.41
6129 7476 4.669206 ATCTGAGCATCCTCTGTGTAAG 57.331 45.455 0.00 0.00 38.93 2.34
6130 7477 2.762887 TCTGAGCATCCTCTGTGTAAGG 59.237 50.000 0.00 0.00 38.93 2.69
6131 7478 2.499289 CTGAGCATCCTCTGTGTAAGGT 59.501 50.000 0.00 0.00 38.93 3.50
6132 7479 2.234661 TGAGCATCCTCTGTGTAAGGTG 59.765 50.000 0.00 0.00 38.93 4.00
6133 7480 1.556911 AGCATCCTCTGTGTAAGGTGG 59.443 52.381 0.00 0.00 35.29 4.61
6134 7481 2.014068 GCATCCTCTGTGTAAGGTGGC 61.014 57.143 0.00 0.00 35.29 5.01
6135 7482 0.537188 ATCCTCTGTGTAAGGTGGCG 59.463 55.000 0.00 0.00 35.29 5.69
6136 7483 1.079127 CCTCTGTGTAAGGTGGCGG 60.079 63.158 0.00 0.00 0.00 6.13
6137 7484 1.079127 CTCTGTGTAAGGTGGCGGG 60.079 63.158 0.00 0.00 0.00 6.13
6138 7485 2.046314 CTGTGTAAGGTGGCGGGG 60.046 66.667 0.00 0.00 0.00 5.73
6139 7486 2.850130 TGTGTAAGGTGGCGGGGT 60.850 61.111 0.00 0.00 0.00 4.95
6140 7487 2.359478 GTGTAAGGTGGCGGGGTG 60.359 66.667 0.00 0.00 0.00 4.61
6141 7488 2.850130 TGTAAGGTGGCGGGGTGT 60.850 61.111 0.00 0.00 0.00 4.16
6142 7489 2.359478 GTAAGGTGGCGGGGTGTG 60.359 66.667 0.00 0.00 0.00 3.82
6143 7490 2.850130 TAAGGTGGCGGGGTGTGT 60.850 61.111 0.00 0.00 0.00 3.72
6144 7491 2.453812 TAAGGTGGCGGGGTGTGTT 61.454 57.895 0.00 0.00 0.00 3.32
6145 7492 1.126329 TAAGGTGGCGGGGTGTGTTA 61.126 55.000 0.00 0.00 0.00 2.41
6146 7493 1.997256 AAGGTGGCGGGGTGTGTTAA 61.997 55.000 0.00 0.00 0.00 2.01
6147 7494 2.263021 GGTGGCGGGGTGTGTTAAC 61.263 63.158 0.00 0.00 0.00 2.01
6148 7495 1.526455 GTGGCGGGGTGTGTTAACA 60.526 57.895 3.59 3.59 0.00 2.41
6149 7496 0.891904 GTGGCGGGGTGTGTTAACAT 60.892 55.000 12.26 0.00 38.92 2.71
6150 7497 0.606944 TGGCGGGGTGTGTTAACATC 60.607 55.000 12.26 8.24 38.92 3.06
6151 7498 0.322187 GGCGGGGTGTGTTAACATCT 60.322 55.000 12.26 0.00 37.58 2.90
6152 7499 1.084289 GCGGGGTGTGTTAACATCTC 58.916 55.000 12.26 8.19 37.58 2.75
6153 7500 1.609580 GCGGGGTGTGTTAACATCTCA 60.610 52.381 12.26 2.23 37.83 3.27
6154 7501 2.939640 GCGGGGTGTGTTAACATCTCAT 60.940 50.000 12.26 0.00 37.83 2.90
6155 7502 2.677836 CGGGGTGTGTTAACATCTCATG 59.322 50.000 12.26 1.94 37.83 3.07
6156 7503 2.423538 GGGGTGTGTTAACATCTCATGC 59.576 50.000 12.26 0.00 37.88 4.06
6157 7504 3.081061 GGGTGTGTTAACATCTCATGCA 58.919 45.455 12.26 0.00 37.58 3.96
6158 7505 3.127548 GGGTGTGTTAACATCTCATGCAG 59.872 47.826 12.26 0.00 37.58 4.41
6159 7506 3.753272 GGTGTGTTAACATCTCATGCAGT 59.247 43.478 12.26 0.00 38.92 4.40
6160 7507 4.216257 GGTGTGTTAACATCTCATGCAGTT 59.784 41.667 12.26 0.00 38.92 3.16
6161 7508 5.385617 GTGTGTTAACATCTCATGCAGTTC 58.614 41.667 12.26 0.00 38.92 3.01
6162 7509 5.049474 GTGTGTTAACATCTCATGCAGTTCA 60.049 40.000 12.26 0.00 38.92 3.18
6163 7510 5.049474 TGTGTTAACATCTCATGCAGTTCAC 60.049 40.000 12.26 0.00 0.00 3.18
6164 7511 5.180117 GTGTTAACATCTCATGCAGTTCACT 59.820 40.000 12.26 0.00 0.00 3.41
6165 7512 5.409520 TGTTAACATCTCATGCAGTTCACTC 59.590 40.000 3.59 0.00 0.00 3.51
6263 7610 1.783031 GAGGATGCGAGCCAATGCAG 61.783 60.000 0.00 0.00 45.52 4.41
6265 7612 3.480225 GATGCGAGCCAATGCAGCC 62.480 63.158 0.00 0.00 45.52 4.85
6275 7622 3.705579 AGCCAATGCAGCCATATTTTGTA 59.294 39.130 0.00 0.00 41.13 2.41
6304 7651 6.645790 ATTGAAACTCAAGCTCAATCAAGT 57.354 33.333 0.00 0.00 40.05 3.16
6423 7771 0.402504 AAAACCATCCCGTGTGCCTA 59.597 50.000 0.00 0.00 0.00 3.93
6510 7863 6.423302 GCTTGACCTGTGATAACTAGATGATG 59.577 42.308 0.00 0.00 0.00 3.07
6575 7930 1.769026 TCATAAGCAGGAGAGAGCGT 58.231 50.000 0.00 0.00 35.48 5.07
6629 7988 5.860941 TGGAAAGAAAATTACACAGCCAA 57.139 34.783 0.00 0.00 0.00 4.52
6716 8079 1.512230 GCAATGCATTTGGCTCCGA 59.488 52.632 9.83 0.00 45.15 4.55
6741 8104 0.745486 CTCCATTGCTCCATGTCGCA 60.745 55.000 2.38 2.38 0.00 5.10
6832 8195 0.904649 TAGATGTGCCAGACCACCAG 59.095 55.000 0.00 0.00 34.85 4.00
6977 8340 1.688197 CAAGTTGCCACCTTGTTCCAT 59.312 47.619 0.00 0.00 35.63 3.41
7074 8437 2.109126 GCTGTTGACCCATCCTCGC 61.109 63.158 0.00 0.00 0.00 5.03
7098 8461 1.142667 TGGAGTCTGTCATTGCACCAA 59.857 47.619 0.00 0.00 0.00 3.67
7124 8487 0.465287 TCGAGATGCAGCAGCCATAA 59.535 50.000 7.13 0.00 41.13 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.597663 CTACCACCGGCGATTGAATTC 59.402 52.381 9.30 0.00 0.00 2.17
219 222 1.202200 GCCGTGTGTTGTAGCAAAACA 60.202 47.619 1.13 1.13 35.22 2.83
695 719 2.060980 GCCGTCAGATCTGGTCCCT 61.061 63.158 22.42 0.00 0.00 4.20
778 808 9.603921 AATTGACTTTTGTGAAAATTGAGTGAT 57.396 25.926 0.00 0.00 0.00 3.06
779 809 8.871862 CAATTGACTTTTGTGAAAATTGAGTGA 58.128 29.630 0.00 0.00 36.95 3.41
780 810 8.658609 ACAATTGACTTTTGTGAAAATTGAGTG 58.341 29.630 13.59 0.00 37.54 3.51
781 811 8.776376 ACAATTGACTTTTGTGAAAATTGAGT 57.224 26.923 13.59 0.00 37.54 3.41
782 812 8.871862 TGACAATTGACTTTTGTGAAAATTGAG 58.128 29.630 13.59 0.00 37.43 3.02
783 813 8.768957 TGACAATTGACTTTTGTGAAAATTGA 57.231 26.923 13.59 0.00 37.43 2.57
809 839 2.819608 CAATTCTTGACCGGTTGACCAT 59.180 45.455 9.42 0.00 35.14 3.55
849 879 2.029666 GCTCACACGCAGACAGGT 59.970 61.111 0.00 0.00 0.00 4.00
861 891 4.681978 AACTCGTGGGCCGCTCAC 62.682 66.667 13.79 13.79 36.19 3.51
862 892 4.680237 CAACTCGTGGGCCGCTCA 62.680 66.667 16.24 0.00 36.19 4.26
863 893 4.681978 ACAACTCGTGGGCCGCTC 62.682 66.667 16.24 0.00 36.19 5.03
864 894 4.988598 CACAACTCGTGGGCCGCT 62.989 66.667 16.24 0.00 42.34 5.52
874 904 4.077188 GAGCCACGCGCACAACTC 62.077 66.667 5.73 4.87 41.38 3.01
878 908 2.867793 ATTATGGAGCCACGCGCACA 62.868 55.000 5.73 0.00 41.38 4.57
880 910 2.179547 CATTATGGAGCCACGCGCA 61.180 57.895 5.73 0.00 41.38 6.09
881 911 2.633657 CATTATGGAGCCACGCGC 59.366 61.111 5.73 0.00 37.98 6.86
882 912 2.253758 CCCATTATGGAGCCACGCG 61.254 63.158 13.63 3.53 40.96 6.01
883 913 2.555547 GCCCATTATGGAGCCACGC 61.556 63.158 13.63 2.36 40.96 5.34
885 915 1.898574 CCGCCCATTATGGAGCCAC 60.899 63.158 13.63 0.00 40.96 5.01
886 916 2.515398 CCGCCCATTATGGAGCCA 59.485 61.111 13.63 0.00 40.96 4.75
933 967 1.863155 TTTAAGCAGCAGGGAGGGGG 61.863 60.000 0.00 0.00 0.00 5.40
934 968 0.394899 CTTTAAGCAGCAGGGAGGGG 60.395 60.000 0.00 0.00 0.00 4.79
944 978 3.190878 CCGGCAGGCTTTAAGCAG 58.809 61.111 19.10 11.33 44.75 4.24
1041 1075 5.406780 ACGAATGAATTCACTGAACAGAGAC 59.593 40.000 11.07 0.00 36.61 3.36
1061 1129 4.139859 TCAGGTTTCAGGTTTGTACGAA 57.860 40.909 0.00 0.00 0.00 3.85
1065 1133 4.601084 TGGTTTCAGGTTTCAGGTTTGTA 58.399 39.130 0.00 0.00 0.00 2.41
1078 1146 1.002366 CGCTCGATCTTGGTTTCAGG 58.998 55.000 0.00 0.00 0.00 3.86
1080 1148 0.606096 TCCGCTCGATCTTGGTTTCA 59.394 50.000 0.00 0.00 0.00 2.69
1081 1149 1.661112 CTTCCGCTCGATCTTGGTTTC 59.339 52.381 0.00 0.00 0.00 2.78
1250 1328 3.787001 GGGCGAAGTGGCTAGGCT 61.787 66.667 18.18 0.00 44.11 4.58
1295 1373 5.470047 AACTTACGGATCTGAAGTGACTT 57.530 39.130 9.00 0.00 33.75 3.01
1321 1399 1.270968 CTAGTCAATCAAGCGCGCG 59.729 57.895 28.44 28.44 0.00 6.86
1447 1542 6.584954 CACTCGCATGATTAGCTTACAATAC 58.415 40.000 0.00 0.00 0.00 1.89
1571 1758 7.011016 GCCGGTTGAAAAAGGATAATTAATTGG 59.989 37.037 11.05 0.00 0.00 3.16
1576 1763 6.591750 TTGCCGGTTGAAAAAGGATAATTA 57.408 33.333 1.90 0.00 0.00 1.40
1594 1782 1.468054 GCCTGCACTTTATCTTTGCCG 60.468 52.381 0.00 0.00 35.26 5.69
1612 1800 1.415659 AGCTCAGACCTATGTCATGCC 59.584 52.381 0.81 0.00 44.33 4.40
1613 1801 2.753296 GAGCTCAGACCTATGTCATGC 58.247 52.381 9.40 2.27 44.33 4.06
1638 1826 0.231024 CGCATCGTGTTTCGTGAACA 59.769 50.000 3.59 3.59 45.70 3.18
1702 1890 6.716628 ACCATGAGAAAATGAGTGTTACATGT 59.283 34.615 2.69 2.69 33.29 3.21
1726 1914 4.081198 ACTCTCTTCCACATCTCATTGGAC 60.081 45.833 0.00 0.00 41.79 4.02
1791 1979 1.203038 TGCTTTCATGACATGGTGGGT 60.203 47.619 15.37 0.00 0.00 4.51
2014 2456 5.295431 TGACGATTTAGAAATGTGCAAGG 57.705 39.130 0.00 0.00 0.00 3.61
2031 2473 4.310357 TGTAGTTTACAGCTGTTGACGA 57.690 40.909 27.06 16.57 34.06 4.20
2045 2487 4.644685 CCATTCGATGGGGAAATGTAGTTT 59.355 41.667 6.11 0.00 46.86 2.66
2343 3663 7.362401 GCAAGAGATGGTGAATTTAACACAGAT 60.362 37.037 0.00 0.00 39.65 2.90
2360 3680 5.048224 ACCTTTCAAATGTCAGCAAGAGATG 60.048 40.000 0.00 0.00 29.38 2.90
2404 3724 3.842732 TGAAATGCATTCAGTCTGCTG 57.157 42.857 13.38 0.00 43.08 4.41
2466 3786 2.223711 GGCAAGTGAATCAAACGGTTGT 60.224 45.455 13.90 0.00 36.07 3.32
2629 3949 3.733337 AGACGTTGCACTTCTTTGAGAT 58.267 40.909 0.00 0.00 0.00 2.75
2734 4057 1.160137 GAGTGCCAGTGCCAGTTAAG 58.840 55.000 0.00 0.00 36.33 1.85
2799 4128 1.699634 ACTTCTTAGTTGGCTGGCTCA 59.300 47.619 2.00 0.00 0.00 4.26
2947 4276 2.564947 CAGTCTTAGAGAAGCACAGGGT 59.435 50.000 0.00 0.00 32.21 4.34
3549 4889 8.592998 CACAGATCATATCACATATCATGTTCG 58.407 37.037 0.00 0.00 42.70 3.95
3560 4900 6.039717 TCAGATTCGACACAGATCATATCACA 59.960 38.462 0.00 0.00 0.00 3.58
3565 4905 6.639632 TGATCAGATTCGACACAGATCATA 57.360 37.500 16.36 2.65 37.53 2.15
3575 4915 9.483062 CAAAGATTTAAGTTGATCAGATTCGAC 57.517 33.333 0.00 0.00 0.00 4.20
3946 5288 5.894393 AGAAGCAGCTCTAGTTACCTTATCA 59.106 40.000 0.00 0.00 0.00 2.15
4088 5430 4.113354 GGCACGCTCTTATATGGCTATAC 58.887 47.826 0.00 0.00 34.93 1.47
4626 5969 8.009974 CACATTTCTGGTTAAGTTCTTCTTACG 58.990 37.037 0.00 0.00 38.22 3.18
4640 5983 7.340999 AGTTACAGGTTTTACACATTTCTGGTT 59.659 33.333 0.00 0.00 0.00 3.67
4644 5987 7.773690 AGACAGTTACAGGTTTTACACATTTCT 59.226 33.333 0.00 0.00 0.00 2.52
4645 5988 7.927048 AGACAGTTACAGGTTTTACACATTTC 58.073 34.615 0.00 0.00 0.00 2.17
4646 5989 7.875327 AGACAGTTACAGGTTTTACACATTT 57.125 32.000 0.00 0.00 0.00 2.32
4648 5991 7.051623 TCAAGACAGTTACAGGTTTTACACAT 58.948 34.615 0.00 0.00 0.00 3.21
4649 5992 6.408035 TCAAGACAGTTACAGGTTTTACACA 58.592 36.000 0.00 0.00 0.00 3.72
4650 5993 6.913873 TCAAGACAGTTACAGGTTTTACAC 57.086 37.500 0.00 0.00 0.00 2.90
4651 5994 7.925043 TTTCAAGACAGTTACAGGTTTTACA 57.075 32.000 0.00 0.00 0.00 2.41
4652 5995 9.233232 CATTTTCAAGACAGTTACAGGTTTTAC 57.767 33.333 0.00 0.00 0.00 2.01
4653 5996 9.179909 TCATTTTCAAGACAGTTACAGGTTTTA 57.820 29.630 0.00 0.00 0.00 1.52
4741 6084 6.832520 ACATTATATTGCACCACAACTTCA 57.167 33.333 0.00 0.00 42.27 3.02
4796 6141 6.618811 TCGAGAAGGTGACTCATAACTTTAC 58.381 40.000 0.00 0.00 42.68 2.01
4955 6300 8.609176 GTTAACGGTTAGATATGAAGAAATGCA 58.391 33.333 0.33 0.00 0.00 3.96
5370 6716 8.557864 AGATTTGCGAATATCTCAAGAATTCAG 58.442 33.333 8.44 0.00 31.37 3.02
5909 7256 5.034852 TCACCTCTGTTCAATCTGTCAAA 57.965 39.130 0.00 0.00 0.00 2.69
5914 7261 3.607741 AGCATCACCTCTGTTCAATCTG 58.392 45.455 0.00 0.00 0.00 2.90
5999 7346 4.060205 GGCAAGGCATTTAATAGCAATGG 58.940 43.478 2.61 0.00 32.98 3.16
6008 7355 2.612471 GCACACATGGCAAGGCATTTAA 60.612 45.455 6.36 0.00 0.00 1.52
6021 7368 5.104374 GTGGATGGAAATTAAGCACACATG 58.896 41.667 0.00 0.00 0.00 3.21
6022 7369 5.018809 AGTGGATGGAAATTAAGCACACAT 58.981 37.500 0.00 0.00 0.00 3.21
6023 7370 4.406456 AGTGGATGGAAATTAAGCACACA 58.594 39.130 0.00 0.00 0.00 3.72
6024 7371 4.142381 GGAGTGGATGGAAATTAAGCACAC 60.142 45.833 0.00 0.00 0.00 3.82
6025 7372 4.016444 GGAGTGGATGGAAATTAAGCACA 58.984 43.478 0.00 0.00 0.00 4.57
6026 7373 4.096984 CAGGAGTGGATGGAAATTAAGCAC 59.903 45.833 0.00 0.00 0.00 4.40
6027 7374 4.272489 CAGGAGTGGATGGAAATTAAGCA 58.728 43.478 0.00 0.00 0.00 3.91
6028 7375 3.067320 GCAGGAGTGGATGGAAATTAAGC 59.933 47.826 0.00 0.00 0.00 3.09
6029 7376 4.272489 TGCAGGAGTGGATGGAAATTAAG 58.728 43.478 0.00 0.00 0.00 1.85
6030 7377 4.314522 TGCAGGAGTGGATGGAAATTAA 57.685 40.909 0.00 0.00 0.00 1.40
6031 7378 4.263905 ACTTGCAGGAGTGGATGGAAATTA 60.264 41.667 1.40 0.00 0.00 1.40
6032 7379 2.905415 TGCAGGAGTGGATGGAAATT 57.095 45.000 0.00 0.00 0.00 1.82
6033 7380 2.042162 ACTTGCAGGAGTGGATGGAAAT 59.958 45.455 1.40 0.00 0.00 2.17
6034 7381 1.425066 ACTTGCAGGAGTGGATGGAAA 59.575 47.619 1.40 0.00 0.00 3.13
6035 7382 1.067295 ACTTGCAGGAGTGGATGGAA 58.933 50.000 1.40 0.00 0.00 3.53
6036 7383 1.003580 GAACTTGCAGGAGTGGATGGA 59.996 52.381 1.40 0.00 0.00 3.41
6037 7384 1.004044 AGAACTTGCAGGAGTGGATGG 59.996 52.381 1.40 0.00 0.00 3.51
6038 7385 2.027377 AGAGAACTTGCAGGAGTGGATG 60.027 50.000 1.40 0.00 0.00 3.51
6039 7386 2.235898 GAGAGAACTTGCAGGAGTGGAT 59.764 50.000 1.40 0.00 0.00 3.41
6040 7387 1.620819 GAGAGAACTTGCAGGAGTGGA 59.379 52.381 1.40 0.00 0.00 4.02
6041 7388 1.338579 GGAGAGAACTTGCAGGAGTGG 60.339 57.143 1.40 0.00 0.00 4.00
6042 7389 1.338579 GGGAGAGAACTTGCAGGAGTG 60.339 57.143 1.40 0.00 0.00 3.51
6043 7390 0.980423 GGGAGAGAACTTGCAGGAGT 59.020 55.000 1.40 0.00 0.00 3.85
6044 7391 1.274712 AGGGAGAGAACTTGCAGGAG 58.725 55.000 1.40 0.00 0.00 3.69
6045 7392 1.734655 AAGGGAGAGAACTTGCAGGA 58.265 50.000 1.40 0.00 0.00 3.86
6046 7393 2.575805 AAAGGGAGAGAACTTGCAGG 57.424 50.000 0.00 0.00 0.00 4.85
6067 7414 1.000385 CAGGAGTGGAATGCGCAAAAA 60.000 47.619 17.11 0.00 0.00 1.94
6068 7415 0.597568 CAGGAGTGGAATGCGCAAAA 59.402 50.000 17.11 0.00 0.00 2.44
6069 7416 1.865788 GCAGGAGTGGAATGCGCAAA 61.866 55.000 17.11 0.00 0.00 3.68
6070 7417 2.334946 GCAGGAGTGGAATGCGCAA 61.335 57.895 17.11 0.00 0.00 4.85
6071 7418 2.747460 GCAGGAGTGGAATGCGCA 60.747 61.111 14.96 14.96 0.00 6.09
6072 7419 2.262471 CTTGCAGGAGTGGAATGCGC 62.262 60.000 0.00 0.00 42.92 6.09
6073 7420 0.957395 ACTTGCAGGAGTGGAATGCG 60.957 55.000 1.40 0.00 42.92 4.73
6074 7421 1.200948 GAACTTGCAGGAGTGGAATGC 59.799 52.381 1.40 0.00 40.40 3.56
6075 7422 2.507484 TGAACTTGCAGGAGTGGAATG 58.493 47.619 1.40 0.00 32.93 2.67
6076 7423 2.957402 TGAACTTGCAGGAGTGGAAT 57.043 45.000 1.40 0.00 32.93 3.01
6077 7424 2.727123 TTGAACTTGCAGGAGTGGAA 57.273 45.000 1.40 0.00 32.33 3.53
6078 7425 2.727123 TTTGAACTTGCAGGAGTGGA 57.273 45.000 1.40 0.00 0.00 4.02
6079 7426 4.326826 TCTATTTGAACTTGCAGGAGTGG 58.673 43.478 1.40 0.00 0.00 4.00
6080 7427 5.240891 TCTCTATTTGAACTTGCAGGAGTG 58.759 41.667 1.40 0.00 0.00 3.51
6081 7428 5.489792 TCTCTATTTGAACTTGCAGGAGT 57.510 39.130 1.40 0.00 0.00 3.85
6082 7429 6.808008 TTTCTCTATTTGAACTTGCAGGAG 57.192 37.500 1.40 0.00 0.00 3.69
6083 7430 7.765695 AATTTCTCTATTTGAACTTGCAGGA 57.234 32.000 1.40 0.00 0.00 3.86
6084 7431 9.727627 GATAATTTCTCTATTTGAACTTGCAGG 57.272 33.333 0.00 0.00 0.00 4.85
6090 7437 9.896645 TGCTCAGATAATTTCTCTATTTGAACT 57.103 29.630 0.00 0.00 29.93 3.01
6093 7440 9.499479 GGATGCTCAGATAATTTCTCTATTTGA 57.501 33.333 0.00 0.00 29.93 2.69
6094 7441 9.504708 AGGATGCTCAGATAATTTCTCTATTTG 57.495 33.333 0.00 0.00 29.93 2.32
6095 7442 9.723601 GAGGATGCTCAGATAATTTCTCTATTT 57.276 33.333 9.69 0.00 29.93 1.40
6096 7443 9.103582 AGAGGATGCTCAGATAATTTCTCTATT 57.896 33.333 17.24 0.00 29.93 1.73
6097 7444 8.533657 CAGAGGATGCTCAGATAATTTCTCTAT 58.466 37.037 17.24 0.00 29.93 1.98
6098 7445 7.508636 ACAGAGGATGCTCAGATAATTTCTCTA 59.491 37.037 17.24 0.00 29.93 2.43
6099 7446 6.327104 ACAGAGGATGCTCAGATAATTTCTCT 59.673 38.462 17.24 0.00 29.93 3.10
6100 7447 6.424509 CACAGAGGATGCTCAGATAATTTCTC 59.575 42.308 17.24 0.00 29.93 2.87
6101 7448 6.126825 ACACAGAGGATGCTCAGATAATTTCT 60.127 38.462 17.24 0.00 33.90 2.52
6102 7449 6.054295 ACACAGAGGATGCTCAGATAATTTC 58.946 40.000 17.24 0.00 0.00 2.17
6103 7450 5.999044 ACACAGAGGATGCTCAGATAATTT 58.001 37.500 17.24 0.00 0.00 1.82
6104 7451 5.627182 ACACAGAGGATGCTCAGATAATT 57.373 39.130 17.24 0.00 0.00 1.40
6105 7452 6.239543 CCTTACACAGAGGATGCTCAGATAAT 60.240 42.308 17.24 0.00 36.33 1.28
6106 7453 5.069648 CCTTACACAGAGGATGCTCAGATAA 59.930 44.000 17.24 11.18 36.33 1.75
6107 7454 4.586421 CCTTACACAGAGGATGCTCAGATA 59.414 45.833 17.24 4.42 36.33 1.98
6108 7455 3.387374 CCTTACACAGAGGATGCTCAGAT 59.613 47.826 17.24 5.35 36.33 2.90
6109 7456 2.762887 CCTTACACAGAGGATGCTCAGA 59.237 50.000 17.24 0.00 36.33 3.27
6110 7457 2.499289 ACCTTACACAGAGGATGCTCAG 59.501 50.000 17.24 11.15 37.72 3.35
6111 7458 2.234661 CACCTTACACAGAGGATGCTCA 59.765 50.000 17.24 0.00 37.72 4.26
6112 7459 2.419297 CCACCTTACACAGAGGATGCTC 60.419 54.545 6.03 6.03 37.72 4.26
6113 7460 1.556911 CCACCTTACACAGAGGATGCT 59.443 52.381 0.00 0.00 37.72 3.79
6114 7461 2.014068 GCCACCTTACACAGAGGATGC 61.014 57.143 0.00 0.00 37.72 3.91
6115 7462 1.740380 CGCCACCTTACACAGAGGATG 60.740 57.143 0.00 0.00 37.72 3.51
6116 7463 0.537188 CGCCACCTTACACAGAGGAT 59.463 55.000 0.00 0.00 37.72 3.24
6117 7464 1.541310 CCGCCACCTTACACAGAGGA 61.541 60.000 0.00 0.00 37.72 3.71
6118 7465 1.079127 CCGCCACCTTACACAGAGG 60.079 63.158 0.00 0.00 40.24 3.69
6119 7466 1.079127 CCCGCCACCTTACACAGAG 60.079 63.158 0.00 0.00 0.00 3.35
6120 7467 2.589157 CCCCGCCACCTTACACAGA 61.589 63.158 0.00 0.00 0.00 3.41
6121 7468 2.046314 CCCCGCCACCTTACACAG 60.046 66.667 0.00 0.00 0.00 3.66
6122 7469 2.850130 ACCCCGCCACCTTACACA 60.850 61.111 0.00 0.00 0.00 3.72
6123 7470 2.359478 CACCCCGCCACCTTACAC 60.359 66.667 0.00 0.00 0.00 2.90
6124 7471 2.850130 ACACCCCGCCACCTTACA 60.850 61.111 0.00 0.00 0.00 2.41
6125 7472 2.359478 CACACCCCGCCACCTTAC 60.359 66.667 0.00 0.00 0.00 2.34
6126 7473 1.126329 TAACACACCCCGCCACCTTA 61.126 55.000 0.00 0.00 0.00 2.69
6127 7474 1.997256 TTAACACACCCCGCCACCTT 61.997 55.000 0.00 0.00 0.00 3.50
6128 7475 2.453812 TTAACACACCCCGCCACCT 61.454 57.895 0.00 0.00 0.00 4.00
6129 7476 2.113562 TTAACACACCCCGCCACC 59.886 61.111 0.00 0.00 0.00 4.61
6130 7477 0.891904 ATGTTAACACACCCCGCCAC 60.892 55.000 11.22 0.00 35.03 5.01
6131 7478 0.606944 GATGTTAACACACCCCGCCA 60.607 55.000 11.22 0.00 35.03 5.69
6132 7479 0.322187 AGATGTTAACACACCCCGCC 60.322 55.000 11.22 0.00 35.03 6.13
6133 7480 1.084289 GAGATGTTAACACACCCCGC 58.916 55.000 11.22 0.00 35.03 6.13
6134 7481 2.465860 TGAGATGTTAACACACCCCG 57.534 50.000 11.22 0.00 35.03 5.73
6135 7482 2.423538 GCATGAGATGTTAACACACCCC 59.576 50.000 11.22 4.48 35.03 4.95
6136 7483 3.081061 TGCATGAGATGTTAACACACCC 58.919 45.455 11.22 0.00 35.03 4.61
6137 7484 3.753272 ACTGCATGAGATGTTAACACACC 59.247 43.478 11.22 3.47 35.03 4.16
6138 7485 5.049474 TGAACTGCATGAGATGTTAACACAC 60.049 40.000 11.22 8.39 35.03 3.82
6139 7486 5.049474 GTGAACTGCATGAGATGTTAACACA 60.049 40.000 11.22 5.09 37.31 3.72
6140 7487 5.180117 AGTGAACTGCATGAGATGTTAACAC 59.820 40.000 11.22 5.31 0.00 3.32
6141 7488 5.308014 AGTGAACTGCATGAGATGTTAACA 58.692 37.500 11.41 11.41 0.00 2.41
6142 7489 5.409520 TGAGTGAACTGCATGAGATGTTAAC 59.590 40.000 0.00 0.00 0.00 2.01
6143 7490 5.550290 TGAGTGAACTGCATGAGATGTTAA 58.450 37.500 0.00 0.00 0.00 2.01
6144 7491 5.151297 TGAGTGAACTGCATGAGATGTTA 57.849 39.130 0.00 0.00 0.00 2.41
6145 7492 4.011966 TGAGTGAACTGCATGAGATGTT 57.988 40.909 0.00 0.00 0.00 2.71
6146 7493 3.690475 TGAGTGAACTGCATGAGATGT 57.310 42.857 0.00 0.00 0.00 3.06
6147 7494 3.181509 GCTTGAGTGAACTGCATGAGATG 60.182 47.826 0.00 0.00 0.00 2.90
6148 7495 3.008330 GCTTGAGTGAACTGCATGAGAT 58.992 45.455 0.00 0.00 0.00 2.75
6149 7496 2.224354 TGCTTGAGTGAACTGCATGAGA 60.224 45.455 0.00 0.00 0.00 3.27
6150 7497 2.148768 TGCTTGAGTGAACTGCATGAG 58.851 47.619 0.00 0.00 0.00 2.90
6151 7498 2.259266 TGCTTGAGTGAACTGCATGA 57.741 45.000 0.00 0.00 0.00 3.07
6152 7499 3.358707 TTTGCTTGAGTGAACTGCATG 57.641 42.857 0.00 0.00 33.50 4.06
6153 7500 4.595762 AATTTGCTTGAGTGAACTGCAT 57.404 36.364 0.00 0.00 33.50 3.96
6154 7501 4.362279 GAAATTTGCTTGAGTGAACTGCA 58.638 39.130 0.00 0.00 0.00 4.41
6155 7502 3.423206 CGAAATTTGCTTGAGTGAACTGC 59.577 43.478 0.00 0.00 0.00 4.40
6156 7503 3.423206 GCGAAATTTGCTTGAGTGAACTG 59.577 43.478 0.00 0.00 0.00 3.16
6157 7504 3.066621 TGCGAAATTTGCTTGAGTGAACT 59.933 39.130 6.77 0.00 0.00 3.01
6158 7505 3.371168 TGCGAAATTTGCTTGAGTGAAC 58.629 40.909 6.77 0.00 0.00 3.18
6159 7506 3.706802 TGCGAAATTTGCTTGAGTGAA 57.293 38.095 6.77 0.00 0.00 3.18
6160 7507 3.314913 TCTTGCGAAATTTGCTTGAGTGA 59.685 39.130 6.77 0.00 0.00 3.41
6161 7508 3.631144 TCTTGCGAAATTTGCTTGAGTG 58.369 40.909 6.77 0.00 0.00 3.51
6162 7509 3.988379 TCTTGCGAAATTTGCTTGAGT 57.012 38.095 6.77 0.00 0.00 3.41
6163 7510 5.834239 AAATCTTGCGAAATTTGCTTGAG 57.166 34.783 6.77 2.72 0.00 3.02
6164 7511 5.976586 CAAAATCTTGCGAAATTTGCTTGA 58.023 33.333 6.77 5.17 0.00 3.02
6263 7610 9.423061 AGTTTCAATCAAAGTACAAAATATGGC 57.577 29.630 0.00 0.00 0.00 4.40
6275 7622 6.455360 TTGAGCTTGAGTTTCAATCAAAGT 57.545 33.333 5.73 0.00 34.39 2.66
6304 7651 3.211045 GGGTCAACTAGTGCAGTTTTGA 58.789 45.455 12.15 12.15 45.54 2.69
6423 7771 3.776969 ACATAGAGTGACCCACATGTCAT 59.223 43.478 0.00 0.00 46.20 3.06
6651 8013 5.074377 TGAAATATAGCAATCAGGCCCCTTA 59.926 40.000 0.00 0.00 0.00 2.69
6716 8079 1.135094 ATGGAGCAATGGAGGATCGT 58.865 50.000 0.00 0.00 34.37 3.73
6752 8115 3.031964 GCGCTCGCAGCATCACTTT 62.032 57.895 9.59 0.00 42.58 2.66
6753 8116 3.494336 GCGCTCGCAGCATCACTT 61.494 61.111 9.59 0.00 42.58 3.16
6813 8176 0.904649 CTGGTGGTCTGGCACATCTA 59.095 55.000 0.00 0.00 38.20 1.98
6977 8340 0.040157 CACCGTCGTCGTTCCAAGTA 60.040 55.000 0.71 0.00 35.01 2.24
6985 8348 4.338539 GGAGTGCACCGTCGTCGT 62.339 66.667 14.63 0.00 35.01 4.34
6988 8351 3.991051 CTGGGAGTGCACCGTCGT 61.991 66.667 14.63 0.00 0.00 4.34
6989 8352 3.220999 TTCTGGGAGTGCACCGTCG 62.221 63.158 14.63 0.00 0.00 5.12
7033 8396 0.106268 TTCTGCCAACTTTGCCTCCA 60.106 50.000 0.00 0.00 0.00 3.86
7074 8437 1.277273 TGCAATGACAGACTCCAGAGG 59.723 52.381 0.00 0.00 0.00 3.69
7098 8461 0.755079 TGCTGCATCTCGATAGGCTT 59.245 50.000 8.90 0.00 0.00 4.35
7124 8487 1.203052 CGGGCAAGATGAAAATGCTGT 59.797 47.619 0.00 0.00 39.94 4.40


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

AutoCloner maintained by Alex Coulton.