Multiple sequence alignment - TraesCS2B01G275100

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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 TraesCS2B01G275100 chr2B 100.000 5317 0 0 1 5317 379784239 379789555 0.000000e+00 9819.0
1 TraesCS2B01G275100 chr2B 94.920 748 27 6 1 739 799410991 799411736 0.000000e+00 1160.0
2 TraesCS2B01G275100 chr2B 83.814 902 104 14 4456 5317 460609906 460609007 0.000000e+00 819.0
3 TraesCS2B01G275100 chr2B 81.618 865 87 17 4481 5315 372238861 372239683 0.000000e+00 651.0
4 TraesCS2B01G275100 chr2D 94.631 1788 67 12 2632 4394 202437578 202439361 0.000000e+00 2743.0
5 TraesCS2B01G275100 chr2D 91.630 1816 73 25 737 2521 202435711 202437478 0.000000e+00 2438.0
6 TraesCS2B01G275100 chr2D 88.568 866 64 11 4481 5317 587269298 587270157 0.000000e+00 1018.0
7 TraesCS2B01G275100 chr2D 86.766 869 79 15 4481 5317 69500494 69499630 0.000000e+00 935.0
8 TraesCS2B01G275100 chr2D 86.490 866 87 8 4481 5317 388514794 388513930 0.000000e+00 924.0
9 TraesCS2B01G275100 chr2D 84.625 813 84 18 4453 5225 303628368 303629179 0.000000e+00 771.0
10 TraesCS2B01G275100 chr2D 85.417 96 9 2 2516 2610 249910657 249910748 1.580000e-15 95.3
11 TraesCS2B01G275100 chr2A 94.180 1615 66 9 739 2333 228853659 228855265 0.000000e+00 2436.0
12 TraesCS2B01G275100 chr2A 91.581 1354 52 28 3433 4763 228857205 228858519 0.000000e+00 1812.0
13 TraesCS2B01G275100 chr2A 95.256 801 32 2 2647 3441 228855432 228856232 0.000000e+00 1264.0
14 TraesCS2B01G275100 chr2A 86.867 731 69 16 17 739 770966563 770967274 0.000000e+00 793.0
15 TraesCS2B01G275100 chr2A 85.567 97 9 3 2514 2609 646556186 646556278 4.380000e-16 97.1
16 TraesCS2B01G275100 chr3B 94.906 746 26 9 1 739 823510206 823510946 0.000000e+00 1157.0
17 TraesCS2B01G275100 chr3B 92.744 758 35 6 1 740 680418910 680419665 0.000000e+00 1077.0
18 TraesCS2B01G275100 chr3B 91.223 752 48 17 1 737 166678601 166679349 0.000000e+00 1007.0
19 TraesCS2B01G275100 chr3B 100.000 30 0 0 2516 2545 434425178 434425149 7.440000e-04 56.5
20 TraesCS2B01G275100 chr1B 94.795 730 27 6 17 739 28491867 28492592 0.000000e+00 1127.0
21 TraesCS2B01G275100 chr1B 92.924 749 41 8 1 739 656573153 656572407 0.000000e+00 1079.0
22 TraesCS2B01G275100 chr4B 93.717 748 36 8 1 740 166768147 166767403 0.000000e+00 1110.0
23 TraesCS2B01G275100 chr4B 84.041 871 97 22 4481 5317 437109632 437110494 0.000000e+00 800.0
24 TraesCS2B01G275100 chr4B 83.006 865 113 12 4481 5317 340863624 340864482 0.000000e+00 752.0
25 TraesCS2B01G275100 chr4B 92.562 121 8 1 4481 4601 560824922 560824803 7.080000e-39 172.0
26 TraesCS2B01G275100 chr5A 92.583 755 45 10 1 745 672025093 672025846 0.000000e+00 1074.0
27 TraesCS2B01G275100 chr5A 86.259 866 89 13 4481 5317 621844561 621845425 0.000000e+00 913.0
28 TraesCS2B01G275100 chr6B 92.112 748 35 12 1 740 130544400 130543669 0.000000e+00 1033.0
29 TraesCS2B01G275100 chr6D 87.875 866 74 13 4481 5317 93632839 93631976 0.000000e+00 989.0
30 TraesCS2B01G275100 chr6D 87.412 850 93 9 4481 5317 59740898 59741746 0.000000e+00 965.0
31 TraesCS2B01G275100 chr6D 85.236 867 94 14 4481 5317 311598437 311599299 0.000000e+00 861.0
32 TraesCS2B01G275100 chr6D 83.991 431 47 8 4481 4891 9177779 9178207 1.390000e-105 394.0
33 TraesCS2B01G275100 chr6D 84.880 291 23 7 4481 4751 451112467 451112756 1.890000e-69 274.0
34 TraesCS2B01G275100 chr4A 90.996 733 52 12 17 739 573894509 573893781 0.000000e+00 976.0
35 TraesCS2B01G275100 chr4A 87.885 454 48 4 4870 5317 176594054 176594506 1.310000e-145 527.0
36 TraesCS2B01G275100 chr1D 86.818 880 82 15 4456 5306 479223746 479222872 0.000000e+00 952.0
37 TraesCS2B01G275100 chr1D 86.239 872 78 21 4476 5317 277993676 277994535 0.000000e+00 907.0
38 TraesCS2B01G275100 chr1D 84.746 649 66 13 4481 5099 465439189 465438544 2.100000e-173 619.0
39 TraesCS2B01G275100 chr1D 83.463 387 40 8 4481 4847 338374360 338373978 6.600000e-89 339.0
40 TraesCS2B01G275100 chr1D 77.019 322 49 15 4497 4797 42626077 42626394 1.530000e-35 161.0
41 TraesCS2B01G275100 chr4D 86.836 866 83 9 4481 5317 353525691 353526554 0.000000e+00 939.0
42 TraesCS2B01G275100 chr4D 85.900 539 59 8 4784 5317 487339705 487340231 4.650000e-155 558.0
43 TraesCS2B01G275100 chr5D 86.736 867 84 15 4481 5317 458000799 458001664 0.000000e+00 935.0
44 TraesCS2B01G275100 chr5D 85.797 866 87 13 4481 5315 363190137 363190997 0.000000e+00 885.0
45 TraesCS2B01G275100 chr5D 86.538 572 65 10 4733 5302 490767870 490768431 2.100000e-173 619.0
46 TraesCS2B01G275100 chr5D 85.106 94 9 4 2518 2610 519702211 519702300 2.040000e-14 91.6
47 TraesCS2B01G275100 chr6A 86.374 866 87 12 4481 5317 527530633 527529770 0.000000e+00 917.0
48 TraesCS2B01G275100 chrUn 92.471 611 37 8 1 604 201218486 201219094 0.000000e+00 865.0
49 TraesCS2B01G275100 chr3A 84.589 863 89 11 4481 5315 462328715 462327869 0.000000e+00 817.0
50 TraesCS2B01G275100 chr3A 86.170 94 8 2 2518 2610 739891957 739892046 4.380000e-16 97.1
51 TraesCS2B01G275100 chr3A 97.059 34 1 0 2517 2550 644820392 644820425 2.070000e-04 58.4
52 TraesCS2B01G275100 chr7B 81.766 872 97 23 4478 5317 322491676 322492517 0.000000e+00 673.0
53 TraesCS2B01G275100 chr7B 86.170 94 8 2 2518 2610 107620828 107620917 4.380000e-16 97.1
54 TraesCS2B01G275100 chr5B 84.694 588 88 2 4729 5315 706988298 706987712 2.130000e-163 586.0
55 TraesCS2B01G275100 chr5B 77.061 279 51 11 4481 4751 581245514 581245241 1.190000e-31 148.0
56 TraesCS2B01G275100 chr5B 96.000 50 1 1 2517 2565 561012720 561012671 4.410000e-11 80.5
57 TraesCS2B01G275100 chr3D 88.537 410 41 6 4620 5026 5668602 5668196 4.780000e-135 492.0
58 TraesCS2B01G275100 chr7D 85.106 94 9 2 2518 2610 184039039 184038950 2.040000e-14 91.6
59 TraesCS2B01G275100 chr7D 92.157 51 2 2 2514 2563 242504726 242504677 2.660000e-08 71.3
60 TraesCS2B01G275100 chr1A 96.875 32 0 1 2518 2549 155077310 155077340 1.000000e-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 TraesCS2B01G275100 chr2B 379784239 379789555 5316 False 9819.000000 9819 100.000000 1 5317 1 chr2B.!!$F2 5316
1 TraesCS2B01G275100 chr2B 799410991 799411736 745 False 1160.000000 1160 94.920000 1 739 1 chr2B.!!$F3 738
2 TraesCS2B01G275100 chr2B 460609007 460609906 899 True 819.000000 819 83.814000 4456 5317 1 chr2B.!!$R1 861
3 TraesCS2B01G275100 chr2B 372238861 372239683 822 False 651.000000 651 81.618000 4481 5315 1 chr2B.!!$F1 834
4 TraesCS2B01G275100 chr2D 202435711 202439361 3650 False 2590.500000 2743 93.130500 737 4394 2 chr2D.!!$F4 3657
5 TraesCS2B01G275100 chr2D 587269298 587270157 859 False 1018.000000 1018 88.568000 4481 5317 1 chr2D.!!$F3 836
6 TraesCS2B01G275100 chr2D 69499630 69500494 864 True 935.000000 935 86.766000 4481 5317 1 chr2D.!!$R1 836
7 TraesCS2B01G275100 chr2D 388513930 388514794 864 True 924.000000 924 86.490000 4481 5317 1 chr2D.!!$R2 836
8 TraesCS2B01G275100 chr2D 303628368 303629179 811 False 771.000000 771 84.625000 4453 5225 1 chr2D.!!$F2 772
9 TraesCS2B01G275100 chr2A 228853659 228858519 4860 False 1837.333333 2436 93.672333 739 4763 3 chr2A.!!$F3 4024
10 TraesCS2B01G275100 chr2A 770966563 770967274 711 False 793.000000 793 86.867000 17 739 1 chr2A.!!$F2 722
11 TraesCS2B01G275100 chr3B 823510206 823510946 740 False 1157.000000 1157 94.906000 1 739 1 chr3B.!!$F3 738
12 TraesCS2B01G275100 chr3B 680418910 680419665 755 False 1077.000000 1077 92.744000 1 740 1 chr3B.!!$F2 739
13 TraesCS2B01G275100 chr3B 166678601 166679349 748 False 1007.000000 1007 91.223000 1 737 1 chr3B.!!$F1 736
14 TraesCS2B01G275100 chr1B 28491867 28492592 725 False 1127.000000 1127 94.795000 17 739 1 chr1B.!!$F1 722
15 TraesCS2B01G275100 chr1B 656572407 656573153 746 True 1079.000000 1079 92.924000 1 739 1 chr1B.!!$R1 738
16 TraesCS2B01G275100 chr4B 166767403 166768147 744 True 1110.000000 1110 93.717000 1 740 1 chr4B.!!$R1 739
17 TraesCS2B01G275100 chr4B 437109632 437110494 862 False 800.000000 800 84.041000 4481 5317 1 chr4B.!!$F2 836
18 TraesCS2B01G275100 chr4B 340863624 340864482 858 False 752.000000 752 83.006000 4481 5317 1 chr4B.!!$F1 836
19 TraesCS2B01G275100 chr5A 672025093 672025846 753 False 1074.000000 1074 92.583000 1 745 1 chr5A.!!$F2 744
20 TraesCS2B01G275100 chr5A 621844561 621845425 864 False 913.000000 913 86.259000 4481 5317 1 chr5A.!!$F1 836
21 TraesCS2B01G275100 chr6B 130543669 130544400 731 True 1033.000000 1033 92.112000 1 740 1 chr6B.!!$R1 739
22 TraesCS2B01G275100 chr6D 93631976 93632839 863 True 989.000000 989 87.875000 4481 5317 1 chr6D.!!$R1 836
23 TraesCS2B01G275100 chr6D 59740898 59741746 848 False 965.000000 965 87.412000 4481 5317 1 chr6D.!!$F2 836
24 TraesCS2B01G275100 chr6D 311598437 311599299 862 False 861.000000 861 85.236000 4481 5317 1 chr6D.!!$F3 836
25 TraesCS2B01G275100 chr4A 573893781 573894509 728 True 976.000000 976 90.996000 17 739 1 chr4A.!!$R1 722
26 TraesCS2B01G275100 chr1D 479222872 479223746 874 True 952.000000 952 86.818000 4456 5306 1 chr1D.!!$R3 850
27 TraesCS2B01G275100 chr1D 277993676 277994535 859 False 907.000000 907 86.239000 4476 5317 1 chr1D.!!$F2 841
28 TraesCS2B01G275100 chr1D 465438544 465439189 645 True 619.000000 619 84.746000 4481 5099 1 chr1D.!!$R2 618
29 TraesCS2B01G275100 chr4D 353525691 353526554 863 False 939.000000 939 86.836000 4481 5317 1 chr4D.!!$F1 836
30 TraesCS2B01G275100 chr4D 487339705 487340231 526 False 558.000000 558 85.900000 4784 5317 1 chr4D.!!$F2 533
31 TraesCS2B01G275100 chr5D 458000799 458001664 865 False 935.000000 935 86.736000 4481 5317 1 chr5D.!!$F2 836
32 TraesCS2B01G275100 chr5D 363190137 363190997 860 False 885.000000 885 85.797000 4481 5315 1 chr5D.!!$F1 834
33 TraesCS2B01G275100 chr5D 490767870 490768431 561 False 619.000000 619 86.538000 4733 5302 1 chr5D.!!$F3 569
34 TraesCS2B01G275100 chr6A 527529770 527530633 863 True 917.000000 917 86.374000 4481 5317 1 chr6A.!!$R1 836
35 TraesCS2B01G275100 chrUn 201218486 201219094 608 False 865.000000 865 92.471000 1 604 1 chrUn.!!$F1 603
36 TraesCS2B01G275100 chr3A 462327869 462328715 846 True 817.000000 817 84.589000 4481 5315 1 chr3A.!!$R1 834
37 TraesCS2B01G275100 chr7B 322491676 322492517 841 False 673.000000 673 81.766000 4478 5317 1 chr7B.!!$F2 839
38 TraesCS2B01G275100 chr5B 706987712 706988298 586 True 586.000000 586 84.694000 4729 5315 1 chr5B.!!$R3 586

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
694 725 0.179040 TGTTTTCAGACCGGGGTCAC 60.179 55.000 19.38 9.08 46.76 3.67 F
889 948 0.683504 GGAACCCTCTCACGGCTCTA 60.684 60.000 0.00 0.00 0.00 2.43 F
2538 2620 1.071857 ACTCCCTCCGTCTGGAAAAAC 59.928 52.381 0.00 0.00 45.87 2.43 F
3371 3518 0.995024 ATGCTCAAGTAAGTGCCCCT 59.005 50.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 2603 1.880027 CAAGTTTTTCCAGACGGAGGG 59.120 52.381 0.00 0.0 44.10 4.30 R
2752 2899 1.333931 AGCTTCGCGTATTCGATGAGA 59.666 47.619 5.77 0.0 38.37 3.27 R
3657 4791 0.037605 GACGGGTGAGGTTGACGATT 60.038 55.000 0.00 0.0 0.00 3.34 R
4424 5574 0.108804 CCGATAACTGGCGTGTGACT 60.109 55.000 0.00 0.0 0.00 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.068636 AGCATCCAATACTTGCATCTTAGG 58.931 41.667 0.00 0.00 38.84 2.69
203 215 8.787818 TCAACCTAAATCAATCCTAGGGTTAAT 58.212 33.333 7.05 0.00 37.17 1.40
502 526 3.278072 TACCGCCGGAGACTCTGGT 62.278 63.158 27.63 18.94 44.85 4.00
526 550 0.320697 GGTTCAGACAACCTACCGCT 59.679 55.000 0.00 0.00 37.34 5.52
529 553 0.541063 TCAGACAACCTACCGCTGGA 60.541 55.000 1.50 0.00 0.00 3.86
592 623 2.223711 GGTGCTGACGTGGAAAAATTGT 60.224 45.455 0.00 0.00 0.00 2.71
624 655 1.521450 GCTCGGCGGTAGGCTATACA 61.521 60.000 7.21 0.00 42.94 2.29
627 658 1.965643 TCGGCGGTAGGCTATACAATT 59.034 47.619 7.21 0.00 42.94 2.32
642 673 2.676265 AATTCTACCGCCGGGCCTT 61.676 57.895 14.55 2.50 36.48 4.35
686 717 4.783764 AATCCCGAAATGTTTTCAGACC 57.216 40.909 1.40 0.00 0.00 3.85
694 725 0.179040 TGTTTTCAGACCGGGGTCAC 60.179 55.000 19.38 9.08 46.76 3.67
696 727 0.179040 TTTTCAGACCGGGGTCACAC 60.179 55.000 19.38 0.00 46.76 3.82
716 748 6.054295 CACACCTCAATTTGATTTCCCAAAA 58.946 36.000 0.00 0.00 39.20 2.44
742 774 4.208047 TCAAAACACGAAATTTTGCCGATG 59.792 37.500 5.27 0.00 43.62 3.84
782 820 2.184322 CCGATCCACCTCACCACG 59.816 66.667 0.00 0.00 0.00 4.94
889 948 0.683504 GGAACCCTCTCACGGCTCTA 60.684 60.000 0.00 0.00 0.00 2.43
959 1018 2.353406 CCGTCCAGATACAACGAACCTT 60.353 50.000 0.00 0.00 38.65 3.50
1076 1135 1.275666 TCCCTGCGAATTTGAGAGGA 58.724 50.000 11.25 4.01 0.00 3.71
1099 1158 2.196245 GGGATTCATTCAGCGGCCC 61.196 63.158 0.00 0.00 0.00 5.80
1186 1245 2.159819 GAGCCTGCTGTCCGAGTTCA 62.160 60.000 0.00 0.00 0.00 3.18
1187 1246 1.078848 GCCTGCTGTCCGAGTTCAT 60.079 57.895 0.00 0.00 0.00 2.57
1214 1273 5.523552 CCTGTTTTGAATTCAGGGTTTTGTC 59.476 40.000 8.41 0.00 43.30 3.18
1215 1274 5.423886 TGTTTTGAATTCAGGGTTTTGTCC 58.576 37.500 8.41 0.00 0.00 4.02
1275 1334 9.152327 TGTTTATGATTTGGGGCAAATGATATA 57.848 29.630 0.00 0.00 43.05 0.86
1318 1377 4.982295 CCTCCAAAATTTCGACAGGTTTTC 59.018 41.667 0.00 0.00 0.00 2.29
1323 1382 6.399626 CAAAATTTCGACAGGTTTTCGTTTC 58.600 36.000 0.00 0.00 37.73 2.78
1433 1497 6.241385 CGTGAGAACAATCCGTCTAAATTTC 58.759 40.000 0.00 0.00 0.00 2.17
1588 1652 3.019003 GCCAGCGAGGAAGCCAGTA 62.019 63.158 2.12 0.00 41.22 2.74
1816 1881 3.670625 TGTTTTCGATGAGGTTTCCGAT 58.329 40.909 0.00 0.00 0.00 4.18
1837 1902 5.124138 CGATCCTAGCGTACTGGATTAGAAT 59.876 44.000 0.00 0.00 40.33 2.40
1838 1903 6.315642 CGATCCTAGCGTACTGGATTAGAATA 59.684 42.308 0.00 0.00 40.33 1.75
1839 1904 7.466185 CGATCCTAGCGTACTGGATTAGAATAG 60.466 44.444 0.00 0.00 40.33 1.73
1840 1905 6.776744 TCCTAGCGTACTGGATTAGAATAGA 58.223 40.000 0.00 0.00 0.00 1.98
1841 1906 7.403671 TCCTAGCGTACTGGATTAGAATAGAT 58.596 38.462 0.00 0.00 0.00 1.98
1946 2011 1.294138 CATTGCCAAGCCAACCTGG 59.706 57.895 0.00 0.00 41.55 4.45
2056 2127 7.859325 AAGCTTGTGTTTTCAAAGTACTCTA 57.141 32.000 0.00 0.00 0.00 2.43
2091 2164 5.545063 TTATCATGAGGTTTGAGGCGATA 57.455 39.130 0.09 0.00 0.00 2.92
2092 2165 4.630644 ATCATGAGGTTTGAGGCGATAT 57.369 40.909 0.09 0.00 0.00 1.63
2093 2166 4.422073 TCATGAGGTTTGAGGCGATATT 57.578 40.909 0.00 0.00 0.00 1.28
2094 2167 5.545063 TCATGAGGTTTGAGGCGATATTA 57.455 39.130 0.00 0.00 0.00 0.98
2203 2281 1.076923 GACTGGGAGGGCGTCTAGA 60.077 63.158 15.26 0.00 0.00 2.43
2251 2329 3.454082 CTCCTTGGACCAGAGCTAGAATT 59.546 47.826 0.00 0.00 0.00 2.17
2273 2351 3.286751 CCCACCAACCACGCACAG 61.287 66.667 0.00 0.00 0.00 3.66
2363 2445 4.233005 GGCCTAATAGATTCCGTTACGTC 58.767 47.826 3.52 0.00 0.00 4.34
2367 2449 6.622462 GCCTAATAGATTCCGTTACGTCCTAG 60.622 46.154 3.52 0.00 0.00 3.02
2368 2450 5.702349 AATAGATTCCGTTACGTCCTAGG 57.298 43.478 0.82 0.82 0.00 3.02
2369 2451 3.287867 AGATTCCGTTACGTCCTAGGA 57.712 47.619 7.62 7.62 0.00 2.94
2370 2452 3.212685 AGATTCCGTTACGTCCTAGGAG 58.787 50.000 13.15 9.15 32.03 3.69
2386 2468 7.099120 GTCCTAGGAGTAGTAGTATAGCACTC 58.901 46.154 13.15 0.00 38.80 3.51
2405 2487 8.763049 AGCACTCTTTTTCATTTAATAAAGCC 57.237 30.769 0.00 0.00 0.00 4.35
2406 2488 8.367156 AGCACTCTTTTTCATTTAATAAAGCCA 58.633 29.630 0.00 0.00 0.00 4.75
2407 2489 8.435430 GCACTCTTTTTCATTTAATAAAGCCAC 58.565 33.333 0.00 0.00 0.00 5.01
2409 2491 9.476202 ACTCTTTTTCATTTAATAAAGCCACAC 57.524 29.630 0.00 0.00 0.00 3.82
2410 2492 8.514136 TCTTTTTCATTTAATAAAGCCACACG 57.486 30.769 0.00 0.00 0.00 4.49
2412 2494 9.400638 CTTTTTCATTTAATAAAGCCACACGTA 57.599 29.630 0.00 0.00 0.00 3.57
2413 2495 8.730970 TTTTCATTTAATAAAGCCACACGTAC 57.269 30.769 0.00 0.00 0.00 3.67
2414 2496 7.675962 TTCATTTAATAAAGCCACACGTACT 57.324 32.000 0.00 0.00 0.00 2.73
2415 2497 7.298507 TCATTTAATAAAGCCACACGTACTC 57.701 36.000 0.00 0.00 0.00 2.59
2416 2498 5.766702 TTTAATAAAGCCACACGTACTCG 57.233 39.130 0.00 0.00 43.34 4.18
2429 2511 2.924903 CGTACTCGTTCACAGCTAACA 58.075 47.619 0.00 0.00 0.00 2.41
2430 2512 3.499048 CGTACTCGTTCACAGCTAACAT 58.501 45.455 0.00 0.00 0.00 2.71
2431 2513 3.300853 CGTACTCGTTCACAGCTAACATG 59.699 47.826 0.00 0.00 0.00 3.21
2432 2514 3.386768 ACTCGTTCACAGCTAACATGT 57.613 42.857 0.00 0.00 0.00 3.21
2433 2515 3.728845 ACTCGTTCACAGCTAACATGTT 58.271 40.909 16.68 16.68 0.00 2.71
2504 2586 5.525378 AGTGTAAGTAGCAGCAATTCTATGC 59.475 40.000 0.00 0.00 46.78 3.14
2523 2605 2.839975 GCAGGATTGCTAAGTACTCCC 58.160 52.381 0.00 0.00 46.95 4.30
2524 2606 2.436173 GCAGGATTGCTAAGTACTCCCT 59.564 50.000 0.00 0.00 46.95 4.20
2526 2608 3.070302 CAGGATTGCTAAGTACTCCCTCC 59.930 52.174 0.00 0.00 0.00 4.30
2527 2609 2.036089 GGATTGCTAAGTACTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
2528 2610 2.226962 TTGCTAAGTACTCCCTCCGT 57.773 50.000 0.00 0.00 0.00 4.69
2529 2611 1.760192 TGCTAAGTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
2530 2612 1.284198 TGCTAAGTACTCCCTCCGTCT 59.716 52.381 0.00 0.00 0.00 4.18
2531 2613 1.677052 GCTAAGTACTCCCTCCGTCTG 59.323 57.143 0.00 0.00 0.00 3.51
2532 2614 2.299521 CTAAGTACTCCCTCCGTCTGG 58.700 57.143 0.00 0.00 0.00 3.86
2535 2617 1.076677 AGTACTCCCTCCGTCTGGAAA 59.923 52.381 0.00 0.00 45.87 3.13
2536 2618 1.897802 GTACTCCCTCCGTCTGGAAAA 59.102 52.381 0.00 0.00 45.87 2.29
2538 2620 1.071857 ACTCCCTCCGTCTGGAAAAAC 59.928 52.381 0.00 0.00 45.87 2.43
2539 2621 1.348036 CTCCCTCCGTCTGGAAAAACT 59.652 52.381 0.00 0.00 45.87 2.66
2540 2622 1.772453 TCCCTCCGTCTGGAAAAACTT 59.228 47.619 0.00 0.00 45.87 2.66
2541 2623 1.880027 CCCTCCGTCTGGAAAAACTTG 59.120 52.381 0.00 0.00 45.87 3.16
2542 2624 2.572290 CCTCCGTCTGGAAAAACTTGT 58.428 47.619 0.00 0.00 45.87 3.16
2543 2625 2.548480 CCTCCGTCTGGAAAAACTTGTC 59.452 50.000 0.00 0.00 45.87 3.18
2546 2628 2.548480 CCGTCTGGAAAAACTTGTCCTC 59.452 50.000 0.41 0.00 37.49 3.71
2548 2630 3.625764 CGTCTGGAAAAACTTGTCCTCAA 59.374 43.478 0.41 0.00 34.77 3.02
2549 2631 4.095782 CGTCTGGAAAAACTTGTCCTCAAA 59.904 41.667 0.41 0.00 34.77 2.69
2551 2633 5.979517 GTCTGGAAAAACTTGTCCTCAAATG 59.020 40.000 0.41 0.00 34.77 2.32
2552 2634 5.068987 TCTGGAAAAACTTGTCCTCAAATGG 59.931 40.000 0.41 0.00 34.77 3.16
2553 2635 4.959210 TGGAAAAACTTGTCCTCAAATGGA 59.041 37.500 0.41 0.00 34.77 3.41
2554 2636 5.602145 TGGAAAAACTTGTCCTCAAATGGAT 59.398 36.000 0.41 0.00 38.52 3.41
2555 2637 6.099557 TGGAAAAACTTGTCCTCAAATGGATT 59.900 34.615 0.41 0.00 38.52 3.01
2556 2638 6.992123 GGAAAAACTTGTCCTCAAATGGATTT 59.008 34.615 0.00 0.00 38.52 2.17
2557 2639 8.147704 GGAAAAACTTGTCCTCAAATGGATTTA 58.852 33.333 0.00 0.00 38.52 1.40
2559 2641 9.710900 AAAAACTTGTCCTCAAATGGATTTATC 57.289 29.630 0.00 0.00 38.52 1.75
2560 2642 8.655935 AAACTTGTCCTCAAATGGATTTATCT 57.344 30.769 0.00 0.00 38.52 1.98
2561 2643 9.753674 AAACTTGTCCTCAAATGGATTTATCTA 57.246 29.630 0.00 0.00 38.52 1.98
2562 2644 8.970859 ACTTGTCCTCAAATGGATTTATCTAG 57.029 34.615 0.00 0.00 38.52 2.43
2563 2645 7.500559 ACTTGTCCTCAAATGGATTTATCTAGC 59.499 37.037 0.00 0.00 38.52 3.42
2564 2646 6.899089 TGTCCTCAAATGGATTTATCTAGCA 58.101 36.000 0.00 0.00 38.52 3.49
2566 2648 8.659527 TGTCCTCAAATGGATTTATCTAGCATA 58.340 33.333 0.00 0.00 38.52 3.14
2567 2649 9.507329 GTCCTCAAATGGATTTATCTAGCATAA 57.493 33.333 0.00 0.00 38.52 1.90
2576 2658 9.273016 TGGATTTATCTAGCATAAAGTTAGTGC 57.727 33.333 4.65 4.65 39.10 4.40
2612 2694 9.434420 ACATTCATTTGAAAGACAAGTTTGAAA 57.566 25.926 2.82 0.00 39.77 2.69
2641 2723 2.675844 CGACTTGCATTATGGGACGAAA 59.324 45.455 0.00 0.00 0.00 3.46
2731 2878 3.072915 TGTGGATTCACTCTGGATTGTGT 59.927 43.478 5.55 0.00 43.94 3.72
2770 2917 1.711298 GCTCTCATCGAATACGCGAAG 59.289 52.381 15.93 0.00 44.22 3.79
2809 2956 1.507141 GGGTGTTCAGCCTTGACACG 61.507 60.000 12.97 0.00 36.78 4.49
2834 2981 1.134371 GGCTGAACCCAGAGACATACC 60.134 57.143 0.00 0.00 43.02 2.73
2989 3136 2.434359 GTGAGGAAGGTTCGGCCG 60.434 66.667 22.12 22.12 43.70 6.13
3137 3284 6.529125 CACCTGCATTTTTCAGTATCAATCAC 59.471 38.462 0.00 0.00 0.00 3.06
3371 3518 0.995024 ATGCTCAAGTAAGTGCCCCT 59.005 50.000 0.00 0.00 0.00 4.79
3403 3550 4.127171 AGGTGTAATACGGACATGCAATC 58.873 43.478 0.00 0.00 0.00 2.67
3407 3554 2.260844 ATACGGACATGCAATCTGGG 57.739 50.000 13.22 2.08 0.00 4.45
3410 3557 1.271871 ACGGACATGCAATCTGGGAAA 60.272 47.619 13.22 0.00 0.00 3.13
3414 3561 3.703052 GGACATGCAATCTGGGAAATTCT 59.297 43.478 0.00 0.00 0.00 2.40
3415 3562 4.161001 GGACATGCAATCTGGGAAATTCTT 59.839 41.667 0.00 0.00 0.00 2.52
3416 3563 5.334724 ACATGCAATCTGGGAAATTCTTC 57.665 39.130 0.00 0.00 0.00 2.87
3657 4791 1.203441 ACATCTTCCAGAGCCAGGCA 61.203 55.000 15.80 0.00 0.00 4.75
3702 4836 2.125350 GAGAACCTCCTGCGGCTG 60.125 66.667 0.00 0.00 0.00 4.85
3805 4950 2.614983 GTTGCCAACTACGTTCAGGAAA 59.385 45.455 0.00 0.00 0.00 3.13
3838 4983 0.950836 TGCTGAAACGATTGTGGTGG 59.049 50.000 0.00 0.00 0.00 4.61
3900 5045 2.202864 GAGAAGCTGAGCGGCTCC 60.203 66.667 26.00 12.41 42.24 4.70
3924 5069 1.528309 CAAGGTGGCCAAGTTCCGT 60.528 57.895 7.24 0.00 0.00 4.69
4125 5270 3.118261 ACCATCGTTCTCTGCATTGGTAT 60.118 43.478 0.00 0.00 34.37 2.73
4375 5525 4.363138 TGTATTCTATGCGCTCTGTCTTG 58.637 43.478 9.73 0.00 0.00 3.02
4377 5527 2.568696 TCTATGCGCTCTGTCTTGTC 57.431 50.000 9.73 0.00 0.00 3.18
4387 5537 1.674441 TCTGTCTTGTCGTTCACTCGT 59.326 47.619 0.00 0.00 0.00 4.18
4394 5544 1.941975 TGTCGTTCACTCGTAGTCACA 59.058 47.619 0.00 0.00 0.00 3.58
4395 5545 2.032290 TGTCGTTCACTCGTAGTCACAG 60.032 50.000 0.00 0.00 0.00 3.66
4396 5546 1.534163 TCGTTCACTCGTAGTCACAGG 59.466 52.381 0.00 0.00 0.00 4.00
4397 5547 1.266175 CGTTCACTCGTAGTCACAGGT 59.734 52.381 0.00 0.00 0.00 4.00
4442 5594 2.159421 AGTAGTCACACGCCAGTTATCG 60.159 50.000 0.00 0.00 0.00 2.92
4443 5595 0.108804 AGTCACACGCCAGTTATCGG 60.109 55.000 0.00 0.00 0.00 4.18
4454 5606 1.860950 CAGTTATCGGATTCTGGTGCG 59.139 52.381 0.00 0.00 0.00 5.34
4479 5642 3.315596 TGATGCTCAATCAGATCCTCCT 58.684 45.455 0.00 0.00 40.50 3.69
4610 5777 1.147824 CGGCAGCATCCCTTCATCT 59.852 57.895 0.00 0.00 0.00 2.90
4615 5798 2.208431 CAGCATCCCTTCATCTTCGAC 58.792 52.381 0.00 0.00 0.00 4.20
4719 5909 2.222227 AGAACTTCAAATGCCCTCCC 57.778 50.000 0.00 0.00 0.00 4.30
4734 5924 2.436173 CCCTCCCTGACATCCTTTCTAC 59.564 54.545 0.00 0.00 0.00 2.59
4780 5973 2.354109 GCCTTTTTCTGGCTAACTGC 57.646 50.000 0.00 0.00 46.38 4.40
4794 5987 1.967319 AACTGCGTTTGAGATGGTGT 58.033 45.000 0.00 0.00 0.00 4.16
4813 6006 2.377193 TGTTGGTAAAGGTAGCCCATGT 59.623 45.455 0.00 0.00 0.00 3.21
4891 6086 0.905357 TAGTGGCAAGGAGGAGCTTC 59.095 55.000 0.00 0.00 0.00 3.86
4904 6099 3.625649 GGAGCTTCTCCTTCAATCAGT 57.374 47.619 5.65 0.00 46.41 3.41
4937 6132 0.373370 GCGATCGTTGCAGCACATTA 59.627 50.000 17.81 0.00 0.00 1.90
4943 6138 2.159720 TCGTTGCAGCACATTAATGTCG 60.160 45.455 18.25 15.84 39.39 4.35
4945 6140 3.163594 GTTGCAGCACATTAATGTCGTC 58.836 45.455 18.25 10.35 39.39 4.20
4955 6150 5.884255 ACATTAATGTCGTCGTGAGACCCT 61.884 45.833 15.47 0.00 46.14 4.34
4971 6170 0.906775 CCCTGGCATGCCAAAGAAAT 59.093 50.000 37.47 0.00 46.63 2.17
5084 6295 2.808523 TCCATTTTCAATGCACGCAA 57.191 40.000 0.00 0.00 0.00 4.85
5176 6392 5.892119 CCATAGTTGGTTCTCTCAGGTACTA 59.108 44.000 0.00 0.00 38.30 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.250982 TGATGGATGATGCATGTTCCTATC 58.749 41.667 19.99 18.99 0.00 2.08
71 73 9.479549 ACCCTAGTTCATAATTGATTTGAATGT 57.520 29.630 0.00 0.00 32.48 2.71
624 655 2.206182 AAAGGCCCGGCGGTAGAATT 62.206 55.000 26.32 10.15 0.00 2.17
627 658 3.324108 AAAAGGCCCGGCGGTAGA 61.324 61.111 26.32 0.00 0.00 2.59
642 673 1.182385 CCCTTTTGCCTACCGCCAAA 61.182 55.000 0.00 0.00 36.24 3.28
686 717 0.881118 CAAATTGAGGTGTGACCCCG 59.119 55.000 0.00 0.00 39.75 5.73
694 725 5.702209 CCTTTTGGGAAATCAAATTGAGGTG 59.298 40.000 1.10 0.00 36.63 4.00
696 727 5.868454 ACCTTTTGGGAAATCAAATTGAGG 58.132 37.500 1.10 0.00 46.08 3.86
716 748 3.868661 GGCAAAATTTCGTGTTTTGACCT 59.131 39.130 19.19 0.00 44.81 3.85
742 774 2.514824 GGCCGTCTTCATGCCTCC 60.515 66.667 0.00 0.00 42.01 4.30
767 805 1.218316 GGACGTGGTGAGGTGGATC 59.782 63.158 0.00 0.00 0.00 3.36
795 834 1.601759 GGTGCCACATGACTGCAGT 60.602 57.895 21.88 21.88 35.33 4.40
889 948 1.726853 GTGTCGTGCTTCTATTGGCT 58.273 50.000 0.00 0.00 0.00 4.75
931 990 2.225382 TGTATCTGGACGGGTTCTGA 57.775 50.000 0.00 0.00 0.00 3.27
1076 1135 1.133976 CCGCTGAATGAATCCCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
1214 1273 3.204827 CGCCAAGGCTGATTCCGG 61.205 66.667 9.73 0.00 39.32 5.14
1215 1274 3.880846 GCGCCAAGGCTGATTCCG 61.881 66.667 9.73 0.00 39.32 4.30
1275 1334 0.605319 AAATGCGACCGTGTGACCAT 60.605 50.000 0.00 0.00 0.00 3.55
1276 1335 1.225376 GAAATGCGACCGTGTGACCA 61.225 55.000 0.00 0.00 0.00 4.02
1318 1377 5.297314 GCGCAAAATACTCAAATTGAAACG 58.703 37.500 0.30 0.00 0.00 3.60
1323 1382 5.005012 CAGATGGCGCAAAATACTCAAATTG 59.995 40.000 10.83 0.00 0.00 2.32
1433 1497 0.451783 CGGGCGAAAAATCAGGGAAG 59.548 55.000 0.00 0.00 0.00 3.46
1460 1524 1.949847 CTCACGGCTCCAATCCTCGT 61.950 60.000 0.00 0.00 34.19 4.18
1787 1851 3.264450 ACCTCATCGAAAACAAGGGATCT 59.736 43.478 0.00 0.00 0.00 2.75
1816 1881 6.776744 TCTATTCTAATCCAGTACGCTAGGA 58.223 40.000 0.00 2.65 35.59 2.94
2071 2142 4.630644 ATATCGCCTCAAACCTCATGAT 57.369 40.909 0.00 0.00 0.00 2.45
2104 2177 7.178983 ACCGATCCGACCCATTTACTATATTTA 59.821 37.037 0.00 0.00 0.00 1.40
2231 2309 3.922171 AATTCTAGCTCTGGTCCAAGG 57.078 47.619 0.00 0.00 0.00 3.61
2251 2329 2.353189 CGTGGTTGGTGGGCCATA 59.647 61.111 10.70 0.00 45.56 2.74
2273 2351 2.682856 TCAAGCAAATATTCTGTCCGCC 59.317 45.455 0.00 0.00 0.00 6.13
2363 2445 7.248743 AGAGTGCTATACTACTACTCCTAGG 57.751 44.000 0.82 0.82 40.53 3.02
2367 2449 8.684520 TGAAAAAGAGTGCTATACTACTACTCC 58.315 37.037 0.00 0.00 40.53 3.85
2386 2468 8.293114 ACGTGTGGCTTTATTAAATGAAAAAG 57.707 30.769 0.00 0.00 33.15 2.27
2409 2491 2.924903 TGTTAGCTGTGAACGAGTACG 58.075 47.619 0.00 0.00 45.75 3.67
2410 2492 4.235360 ACATGTTAGCTGTGAACGAGTAC 58.765 43.478 0.00 0.00 0.00 2.73
2412 2494 3.386768 ACATGTTAGCTGTGAACGAGT 57.613 42.857 0.00 0.00 0.00 4.18
2413 2495 3.123621 GGAACATGTTAGCTGTGAACGAG 59.876 47.826 11.95 0.00 0.00 4.18
2414 2496 3.064207 GGAACATGTTAGCTGTGAACGA 58.936 45.455 11.95 0.00 0.00 3.85
2415 2497 2.805671 TGGAACATGTTAGCTGTGAACG 59.194 45.455 11.95 0.00 0.00 3.95
2416 2498 4.829064 TTGGAACATGTTAGCTGTGAAC 57.171 40.909 11.95 0.00 39.30 3.18
2417 2499 4.260990 CGTTTGGAACATGTTAGCTGTGAA 60.261 41.667 11.95 0.00 39.30 3.18
2418 2500 3.249799 CGTTTGGAACATGTTAGCTGTGA 59.750 43.478 11.95 0.00 39.30 3.58
2419 2501 3.554524 CGTTTGGAACATGTTAGCTGTG 58.445 45.455 11.95 0.00 39.30 3.66
2420 2502 2.552315 CCGTTTGGAACATGTTAGCTGT 59.448 45.455 11.95 0.00 39.30 4.40
2421 2503 2.811431 TCCGTTTGGAACATGTTAGCTG 59.189 45.455 11.95 0.00 42.85 4.24
2422 2504 3.074412 CTCCGTTTGGAACATGTTAGCT 58.926 45.455 11.95 0.00 45.87 3.32
2423 2505 3.071479 TCTCCGTTTGGAACATGTTAGC 58.929 45.455 11.95 0.00 45.87 3.09
2424 2506 4.513692 TGTTCTCCGTTTGGAACATGTTAG 59.486 41.667 11.95 2.65 45.87 2.34
2425 2507 4.452825 TGTTCTCCGTTTGGAACATGTTA 58.547 39.130 11.95 0.00 45.87 2.41
2426 2508 3.283751 TGTTCTCCGTTTGGAACATGTT 58.716 40.909 11.78 11.78 45.87 2.71
2427 2509 2.878406 CTGTTCTCCGTTTGGAACATGT 59.122 45.455 8.60 0.00 46.69 3.21
2428 2510 3.138304 TCTGTTCTCCGTTTGGAACATG 58.862 45.455 8.60 0.00 46.69 3.21
2429 2511 3.485463 TCTGTTCTCCGTTTGGAACAT 57.515 42.857 8.60 0.00 46.69 2.71
2430 2512 2.992124 TCTGTTCTCCGTTTGGAACA 57.008 45.000 8.00 8.00 45.87 3.18
2431 2513 3.247886 GTCTTCTGTTCTCCGTTTGGAAC 59.752 47.826 0.00 0.00 45.87 3.62
2432 2514 3.134081 AGTCTTCTGTTCTCCGTTTGGAA 59.866 43.478 0.00 0.00 45.87 3.53
2433 2515 2.698797 AGTCTTCTGTTCTCCGTTTGGA 59.301 45.455 0.00 0.00 43.88 3.53
2504 2586 3.070302 GGAGGGAGTACTTAGCAATCCTG 59.930 52.174 0.00 0.00 0.00 3.86
2521 2603 1.880027 CAAGTTTTTCCAGACGGAGGG 59.120 52.381 0.00 0.00 44.10 4.30
2522 2604 2.548480 GACAAGTTTTTCCAGACGGAGG 59.452 50.000 0.00 0.00 44.10 4.30
2523 2605 2.548480 GGACAAGTTTTTCCAGACGGAG 59.452 50.000 0.00 0.00 44.10 4.63
2524 2606 2.171870 AGGACAAGTTTTTCCAGACGGA 59.828 45.455 3.58 0.00 40.60 4.69
2526 2608 3.202906 TGAGGACAAGTTTTTCCAGACG 58.797 45.455 3.58 0.00 33.92 4.18
2527 2609 5.576447 TTTGAGGACAAGTTTTTCCAGAC 57.424 39.130 3.58 0.00 37.32 3.51
2528 2610 5.068987 CCATTTGAGGACAAGTTTTTCCAGA 59.931 40.000 3.58 0.00 37.32 3.86
2529 2611 5.068987 TCCATTTGAGGACAAGTTTTTCCAG 59.931 40.000 3.58 0.00 37.32 3.86
2530 2612 4.959210 TCCATTTGAGGACAAGTTTTTCCA 59.041 37.500 3.58 0.00 37.32 3.53
2531 2613 5.529581 TCCATTTGAGGACAAGTTTTTCC 57.470 39.130 0.00 0.00 37.32 3.13
2532 2614 9.710900 ATAAATCCATTTGAGGACAAGTTTTTC 57.289 29.630 0.00 0.00 41.30 2.29
2535 2617 8.655935 AGATAAATCCATTTGAGGACAAGTTT 57.344 30.769 0.00 0.00 41.30 2.66
2536 2618 9.401058 CTAGATAAATCCATTTGAGGACAAGTT 57.599 33.333 0.00 0.00 41.30 2.66
2538 2620 7.500227 TGCTAGATAAATCCATTTGAGGACAAG 59.500 37.037 0.00 0.00 41.30 3.16
2539 2621 7.345691 TGCTAGATAAATCCATTTGAGGACAA 58.654 34.615 0.00 0.00 41.30 3.18
2540 2622 6.899089 TGCTAGATAAATCCATTTGAGGACA 58.101 36.000 0.00 0.00 41.30 4.02
2541 2623 7.992754 ATGCTAGATAAATCCATTTGAGGAC 57.007 36.000 0.00 0.00 41.30 3.85
2586 2668 9.434420 TTTCAAACTTGTCTTTCAAATGAATGT 57.566 25.926 8.37 0.00 35.36 2.71
2617 2699 2.418628 CGTCCCATAATGCAAGTCGTTT 59.581 45.455 0.00 0.00 0.00 3.60
2618 2700 2.006888 CGTCCCATAATGCAAGTCGTT 58.993 47.619 0.00 0.00 0.00 3.85
2620 2702 1.934589 TCGTCCCATAATGCAAGTCG 58.065 50.000 0.00 0.00 0.00 4.18
2622 2704 3.016736 CCTTTCGTCCCATAATGCAAGT 58.983 45.455 0.00 0.00 0.00 3.16
2623 2705 3.278574 TCCTTTCGTCCCATAATGCAAG 58.721 45.455 0.00 0.00 0.00 4.01
2625 2707 2.238646 ACTCCTTTCGTCCCATAATGCA 59.761 45.455 0.00 0.00 0.00 3.96
2626 2708 2.919228 ACTCCTTTCGTCCCATAATGC 58.081 47.619 0.00 0.00 0.00 3.56
2627 2709 7.761704 CAGATATACTCCTTTCGTCCCATAATG 59.238 40.741 0.00 0.00 0.00 1.90
2628 2710 7.674348 TCAGATATACTCCTTTCGTCCCATAAT 59.326 37.037 0.00 0.00 0.00 1.28
2629 2711 7.008332 TCAGATATACTCCTTTCGTCCCATAA 58.992 38.462 0.00 0.00 0.00 1.90
2630 2712 6.549242 TCAGATATACTCCTTTCGTCCCATA 58.451 40.000 0.00 0.00 0.00 2.74
2641 2723 7.661536 TTGCAAGTACTTCAGATATACTCCT 57.338 36.000 4.77 0.00 0.00 3.69
2731 2878 2.282674 ACGTCCTCGGCACCACTA 60.283 61.111 0.00 0.00 41.85 2.74
2752 2899 1.333931 AGCTTCGCGTATTCGATGAGA 59.666 47.619 5.77 0.00 38.37 3.27
2770 2917 3.959991 GAAGGGGCGTCCAGTCAGC 62.960 68.421 9.07 0.00 38.24 4.26
2834 2981 2.035961 TCTCCACCTTGTCGAAGAGTTG 59.964 50.000 0.00 0.00 36.95 3.16
2908 3055 3.239861 CTTGCTCCTCACAAGGTCC 57.760 57.895 0.00 0.00 43.82 4.46
2929 3076 3.933955 CGTCCTCGTAGAAAGAGAAGAGA 59.066 47.826 0.00 0.00 37.93 3.10
3073 3220 5.692204 GGAGTATCATCATACCTGAACAACG 59.308 44.000 0.00 0.00 36.26 4.10
3146 3293 8.928733 GTTCAAGACACAATATCAAAATGCATT 58.071 29.630 5.99 5.99 0.00 3.56
3371 3518 2.416296 CGTATTACACCTCTGCAACCGA 60.416 50.000 0.00 0.00 0.00 4.69
3403 3550 3.751175 TGCGTGTAAGAAGAATTTCCCAG 59.249 43.478 0.00 0.00 33.64 4.45
3407 3554 5.985781 TCAAGTGCGTGTAAGAAGAATTTC 58.014 37.500 0.00 0.00 0.00 2.17
3410 3557 5.057149 AGTTCAAGTGCGTGTAAGAAGAAT 58.943 37.500 0.00 0.00 0.00 2.40
3414 3561 4.393680 ACAAAGTTCAAGTGCGTGTAAGAA 59.606 37.500 0.00 0.00 0.00 2.52
3415 3562 3.936453 ACAAAGTTCAAGTGCGTGTAAGA 59.064 39.130 0.00 0.00 0.00 2.10
3416 3563 4.028383 CACAAAGTTCAAGTGCGTGTAAG 58.972 43.478 0.00 0.00 0.00 2.34
3657 4791 0.037605 GACGGGTGAGGTTGACGATT 60.038 55.000 0.00 0.00 0.00 3.34
3805 4950 4.557296 CGTTTCAGCAAACCATGTTCTGAT 60.557 41.667 0.00 0.00 39.07 2.90
3838 4983 4.961511 TGCCTGCACGACACGACC 62.962 66.667 0.00 0.00 0.00 4.79
3924 5069 1.005748 CTTCTGCTCACCGTCTGCA 60.006 57.895 0.00 0.00 35.30 4.41
3933 5078 2.102438 CGCGAATGGCTTCTGCTCA 61.102 57.895 0.00 0.00 40.44 4.26
3969 5114 1.092345 GGATCGTTGGGAAGCTCTGC 61.092 60.000 0.00 0.00 0.00 4.26
3981 5126 1.043673 CGGGGAAGAGGAGGATCGTT 61.044 60.000 0.00 0.00 34.37 3.85
4125 5270 2.825075 TAGTGCCTAGACACCGCCGA 62.825 60.000 5.46 0.00 41.67 5.54
4313 5463 5.786311 TGAAGCCTTGGATCAAAATTTCAG 58.214 37.500 0.00 0.00 0.00 3.02
4375 5525 2.572243 CTGTGACTACGAGTGAACGAC 58.428 52.381 0.00 0.00 37.03 4.34
4377 5527 1.266175 ACCTGTGACTACGAGTGAACG 59.734 52.381 0.00 0.00 39.31 3.95
4396 5546 4.823790 TTTTCTTTTTCGGGTAGCTGAC 57.176 40.909 2.11 0.00 0.00 3.51
4420 5570 3.064408 CGATAACTGGCGTGTGACTACTA 59.936 47.826 0.00 0.00 0.00 1.82
4422 5572 2.182825 CGATAACTGGCGTGTGACTAC 58.817 52.381 0.00 0.00 0.00 2.73
4423 5573 1.133598 CCGATAACTGGCGTGTGACTA 59.866 52.381 0.00 0.00 0.00 2.59
4424 5574 0.108804 CCGATAACTGGCGTGTGACT 60.109 55.000 0.00 0.00 0.00 3.41
4425 5575 0.108992 TCCGATAACTGGCGTGTGAC 60.109 55.000 0.00 0.00 0.00 3.67
4426 5576 0.821517 ATCCGATAACTGGCGTGTGA 59.178 50.000 0.00 0.00 0.00 3.58
4427 5577 1.593006 GAATCCGATAACTGGCGTGTG 59.407 52.381 0.00 0.00 0.00 3.82
4428 5578 1.480954 AGAATCCGATAACTGGCGTGT 59.519 47.619 0.00 0.00 0.00 4.49
4442 5594 0.745845 ATCAGTGCGCACCAGAATCC 60.746 55.000 35.51 9.76 0.00 3.01
4443 5595 0.376152 CATCAGTGCGCACCAGAATC 59.624 55.000 35.51 10.59 0.00 2.52
4610 5777 4.739195 TGACATGTTATGTGATCGTCGAA 58.261 39.130 0.00 0.00 45.03 3.71
4719 5909 3.902881 AGCAGGTAGAAAGGATGTCAG 57.097 47.619 0.00 0.00 0.00 3.51
4734 5924 5.529060 ACTTTACTCAAAGACAAGAAGCAGG 59.471 40.000 4.23 0.00 43.32 4.85
4780 5973 4.320202 CCTTTACCAACACCATCTCAAACG 60.320 45.833 0.00 0.00 0.00 3.60
4794 5987 3.201266 CCTACATGGGCTACCTTTACCAA 59.799 47.826 0.00 0.00 36.44 3.67
4813 6006 8.268605 ACTATCTGATTGACGCTATCTATCCTA 58.731 37.037 6.11 0.00 38.41 2.94
4891 6086 4.276678 TGTTTGCAAGACTGATTGAAGGAG 59.723 41.667 0.00 0.00 31.55 3.69
4899 6094 1.001378 GCCGTTGTTTGCAAGACTGAT 60.001 47.619 0.00 0.00 34.94 2.90
4904 6099 0.237235 GATCGCCGTTGTTTGCAAGA 59.763 50.000 0.00 0.00 34.94 3.02
4937 6132 0.243907 CAGGGTCTCACGACGACATT 59.756 55.000 0.00 0.00 41.16 2.71
4943 6138 1.448540 CATGCCAGGGTCTCACGAC 60.449 63.158 0.00 0.00 39.49 4.34
4945 6140 2.821366 GCATGCCAGGGTCTCACG 60.821 66.667 6.36 0.00 0.00 4.35
4955 6150 3.254470 CATGATTTCTTTGGCATGCCA 57.746 42.857 35.59 35.59 45.63 4.92
4971 6170 4.158949 CACAGGATCTTTGGATTTGCATGA 59.841 41.667 0.00 0.00 31.46 3.07
5012 6215 0.251341 AAGGTCAAGCCCACCATCAC 60.251 55.000 0.00 0.00 36.23 3.06
5084 6295 4.015084 CAGGTTTGCTTGGATCTCTTGAT 58.985 43.478 0.00 0.00 35.26 2.57
5214 6432 2.596631 ATGCGGAGATGCCATGGC 60.597 61.111 30.54 30.54 42.35 4.40
5279 6501 0.473755 TCCGGATGCTTGCATATGGT 59.526 50.000 18.71 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.