Multiple sequence alignment - TraesCS6B01G341600

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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 TraesCS6B01G341600 chr6B 100.000 8526 0 0 1 8526 601125362 601133887 0.000000e+00 15745.0
1 TraesCS6B01G341600 chr6B 98.925 651 7 0 7876 8526 698458650 698458000 0.000000e+00 1164.0
2 TraesCS6B01G341600 chr6B 97.059 102 3 0 6422 6523 601131720 601131821 1.140000e-38 172.0
3 TraesCS6B01G341600 chr6B 97.059 102 3 0 6359 6460 601131783 601131884 1.140000e-38 172.0
4 TraesCS6B01G341600 chr6B 97.561 41 1 0 6485 6525 601131720 601131760 4.270000e-08 71.3
5 TraesCS6B01G341600 chr6B 97.561 41 1 0 6359 6399 601131846 601131886 4.270000e-08 71.3
6 TraesCS6B01G341600 chr6D 95.264 5025 172 36 933 5922 401176376 401181369 0.000000e+00 7901.0
7 TraesCS6B01G341600 chr6D 92.356 1439 64 15 6426 7845 401181840 401183251 0.000000e+00 2006.0
8 TraesCS6B01G341600 chr6D 95.413 545 18 2 5917 6460 401181399 401181937 0.000000e+00 861.0
9 TraesCS6B01G341600 chr6D 97.561 41 1 0 6359 6399 401181899 401181939 4.270000e-08 71.3
10 TraesCS6B01G341600 chr6A 94.754 4994 186 37 949 5907 547733088 547738040 0.000000e+00 7701.0
11 TraesCS6B01G341600 chr6A 92.875 786 39 14 7067 7845 547739270 547740045 0.000000e+00 1125.0
12 TraesCS6B01G341600 chr6A 93.553 636 33 6 6422 7056 547738523 547739151 0.000000e+00 941.0
13 TraesCS6B01G341600 chr6A 95.596 545 22 2 5917 6460 547738081 547738624 0.000000e+00 872.0
14 TraesCS6B01G341600 chr6A 97.436 39 1 0 6485 6523 547738523 547738561 5.520000e-07 67.6
15 TraesCS6B01G341600 chr2A 91.686 878 68 4 7 884 135210692 135209820 0.000000e+00 1212.0
16 TraesCS6B01G341600 chr2A 98.925 651 7 0 7876 8526 676076736 676077386 0.000000e+00 1164.0
17 TraesCS6B01G341600 chr2A 95.238 42 2 0 6784 6825 733925465 733925424 5.520000e-07 67.6
18 TraesCS6B01G341600 chr1A 99.078 651 6 0 7876 8526 517048062 517047412 0.000000e+00 1170.0
19 TraesCS6B01G341600 chr5A 98.925 651 7 0 7876 8526 544160764 544161414 0.000000e+00 1164.0
20 TraesCS6B01G341600 chr4B 98.925 651 7 0 7876 8526 5375767 5375117 0.000000e+00 1164.0
21 TraesCS6B01G341600 chr4B 98.925 651 7 0 7876 8526 30597169 30597819 0.000000e+00 1164.0
22 TraesCS6B01G341600 chr4B 97.500 40 1 0 6784 6823 70256670 70256631 1.540000e-07 69.4
23 TraesCS6B01G341600 chr3A 98.925 651 7 0 7876 8526 15350769 15351419 0.000000e+00 1164.0
24 TraesCS6B01G341600 chr3A 78.288 631 97 25 1737 2338 727341412 727340793 3.760000e-98 370.0
25 TraesCS6B01G341600 chr3A 76.267 375 57 15 1295 1666 727341891 727341546 4.090000e-38 171.0
26 TraesCS6B01G341600 chr2B 98.925 651 7 0 7876 8526 311798592 311797942 0.000000e+00 1164.0
27 TraesCS6B01G341600 chr2B 95.122 41 2 0 6782 6822 59217980 59218020 1.990000e-06 65.8
28 TraesCS6B01G341600 chrUn 98.771 651 8 0 7876 8526 1038905 1038255 0.000000e+00 1158.0
29 TraesCS6B01G341600 chr3D 88.269 878 99 4 7 883 414903869 414902995 0.000000e+00 1048.0
30 TraesCS6B01G341600 chr4A 83.427 887 133 13 1 882 741120675 741121552 0.000000e+00 811.0
31 TraesCS6B01G341600 chr2D 88.034 117 14 0 1531 1647 284221480 284221364 1.150000e-28 139.0
32 TraesCS6B01G341600 chr2D 97.500 40 1 0 6784 6823 590238940 590238979 1.540000e-07 69.4
33 TraesCS6B01G341600 chr5D 95.349 43 2 0 6780 6822 381914446 381914488 1.540000e-07 69.4
34 TraesCS6B01G341600 chr7B 93.333 45 3 0 6781 6825 537165929 537165885 5.520000e-07 67.6
35 TraesCS6B01G341600 chr7A 95.238 42 2 0 6781 6822 579340234 579340275 5.520000e-07 67.6


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 TraesCS6B01G341600 chr6B 601125362 601133887 8525 False 3246.320 15745 97.8480 1 8526 5 chr6B.!!$F1 8525
1 TraesCS6B01G341600 chr6B 698458000 698458650 650 True 1164.000 1164 98.9250 7876 8526 1 chr6B.!!$R1 650
2 TraesCS6B01G341600 chr6D 401176376 401183251 6875 False 2709.825 7901 95.1485 933 7845 4 chr6D.!!$F1 6912
3 TraesCS6B01G341600 chr6A 547733088 547740045 6957 False 2141.320 7701 94.8428 949 7845 5 chr6A.!!$F1 6896
4 TraesCS6B01G341600 chr2A 135209820 135210692 872 True 1212.000 1212 91.6860 7 884 1 chr2A.!!$R1 877
5 TraesCS6B01G341600 chr2A 676076736 676077386 650 False 1164.000 1164 98.9250 7876 8526 1 chr2A.!!$F1 650
6 TraesCS6B01G341600 chr1A 517047412 517048062 650 True 1170.000 1170 99.0780 7876 8526 1 chr1A.!!$R1 650
7 TraesCS6B01G341600 chr5A 544160764 544161414 650 False 1164.000 1164 98.9250 7876 8526 1 chr5A.!!$F1 650
8 TraesCS6B01G341600 chr4B 5375117 5375767 650 True 1164.000 1164 98.9250 7876 8526 1 chr4B.!!$R1 650
9 TraesCS6B01G341600 chr4B 30597169 30597819 650 False 1164.000 1164 98.9250 7876 8526 1 chr4B.!!$F1 650
10 TraesCS6B01G341600 chr3A 15350769 15351419 650 False 1164.000 1164 98.9250 7876 8526 1 chr3A.!!$F1 650
11 TraesCS6B01G341600 chr3A 727340793 727341891 1098 True 270.500 370 77.2775 1295 2338 2 chr3A.!!$R1 1043
12 TraesCS6B01G341600 chr2B 311797942 311798592 650 True 1164.000 1164 98.9250 7876 8526 1 chr2B.!!$R1 650
13 TraesCS6B01G341600 chrUn 1038255 1038905 650 True 1158.000 1158 98.7710 7876 8526 1 chrUn.!!$R1 650
14 TraesCS6B01G341600 chr3D 414902995 414903869 874 True 1048.000 1048 88.2690 7 883 1 chr3D.!!$R1 876
15 TraesCS6B01G341600 chr4A 741120675 741121552 877 False 811.000 811 83.4270 1 882 1 chr4A.!!$F1 881

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
941 943 0.035317 ACGCCATGAAGTTGCTCTCA 59.965 50.000 0.00 0.00 0.00 3.27 F
1314 1322 0.395311 CACTAGGGTCACGCCTAGGA 60.395 60.000 14.75 0.00 39.98 2.94 F
3224 3343 0.405198 ATGGCACTGTCATGTGGGAA 59.595 50.000 0.00 0.00 38.31 3.97 F
3465 3588 1.005748 TTGGTGCTCGACTGCAGAG 60.006 57.895 23.35 14.08 44.20 3.35 F
5140 5280 0.320771 CAGTTCAGCGTAGGCCACTT 60.321 55.000 5.01 0.00 41.24 3.16 F
5206 5346 1.022451 ACGCCACACAACACGACTTT 61.022 50.000 0.00 0.00 0.00 2.66 F
6834 7027 1.896465 AGGGAGTACTTCAGAGTGTGC 59.104 52.381 2.92 0.00 36.60 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2775 2894 0.102120 TGCTTGCTGTCGTTTTTGGG 59.898 50.000 0.00 0.0 0.00 4.12 R
3258 3377 3.483808 TAACAGTGAACTGGTGATGCA 57.516 42.857 11.28 0.0 44.89 3.96 R
4896 5036 0.173481 GTGGCTATGCACTCTCGTGA 59.827 55.000 0.00 0.0 43.97 4.35 R
5240 5380 0.662619 CAATGTGTGTGCCGAAGTGT 59.337 50.000 0.00 0.0 0.00 3.55 R
6908 7101 1.226746 AAAGAAACGACAAGCCGGAG 58.773 50.000 5.05 0.0 0.00 4.63 R
6967 7162 2.093235 ACAGCTTTCCCTGATCTACAGC 60.093 50.000 0.00 0.0 44.52 4.40 R
7870 8193 0.110486 TCCCTGCCAGAGACCAAAAC 59.890 55.000 0.00 0.0 0.00 2.43 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 3.833559 ATTTGTGGTTCCCTGGATTCT 57.166 42.857 0.00 0.00 0.00 2.40
109 110 2.301346 GTCGATGAAGAATTGGCCCAT 58.699 47.619 0.00 0.00 0.00 4.00
122 123 0.972471 GGCCCATAAACTTGCAGCCT 60.972 55.000 0.00 0.00 33.83 4.58
263 265 7.601508 GCAATTCATGAAGGAATTTTTCAGAGT 59.398 33.333 14.54 0.00 43.13 3.24
275 277 1.951209 TTCAGAGTCCCCATAGCACA 58.049 50.000 0.00 0.00 0.00 4.57
323 325 2.169352 CGAGTTGGAGATGATCAAGGGT 59.831 50.000 0.00 0.00 0.00 4.34
378 380 3.005554 CAAGCGAATCTGAACATCCAGT 58.994 45.455 0.00 0.00 35.71 4.00
397 399 4.531426 ACCAAAAGCCCCGCCACA 62.531 61.111 0.00 0.00 0.00 4.17
428 430 6.624352 TCTAAAATTCATGTAGATGCTGCC 57.376 37.500 0.00 0.00 0.00 4.85
435 437 1.450312 GTAGATGCTGCCTGCCGTT 60.450 57.895 0.00 0.00 42.00 4.44
457 459 2.524394 ACGAGGTGGGTCAGCAGT 60.524 61.111 0.00 0.00 33.95 4.40
504 506 3.500343 ACTATTTTGGGCAGTTCTGCTT 58.500 40.909 21.46 5.76 34.73 3.91
515 517 4.397417 GGCAGTTCTGCTTTAGTGATTCAT 59.603 41.667 21.46 0.00 34.73 2.57
635 637 3.927481 GAAGGAGGTGGTGGCAGCC 62.927 68.421 14.97 3.66 0.00 4.85
645 647 0.458669 GGTGGCAGCCATCAATTCAG 59.541 55.000 20.84 0.00 34.21 3.02
655 657 5.182570 CAGCCATCAATTCAGAAAGTCAAGA 59.817 40.000 0.00 0.00 0.00 3.02
675 677 4.716794 AGAAGAGAATGGAGCCATCATTC 58.283 43.478 1.88 13.24 46.39 2.67
689 691 7.363355 GGAGCCATCATTCGAGAGATTAATAGA 60.363 40.741 0.00 0.00 41.60 1.98
795 797 1.147376 CTGGGTTTGGGACGTCACA 59.853 57.895 18.52 18.52 0.00 3.58
800 802 2.355310 GGGTTTGGGACGTCACATATGA 60.355 50.000 23.39 2.99 0.00 2.15
822 824 4.396357 TTTGACCAATCCCATAACCAGT 57.604 40.909 0.00 0.00 0.00 4.00
867 869 6.200854 GGAGTTTGCTGAATAAAACTTGGTTG 59.799 38.462 2.63 0.00 44.53 3.77
902 904 5.838531 AAAAACGTAAACACCATGAAGGA 57.161 34.783 0.00 0.00 41.22 3.36
903 905 6.399639 AAAAACGTAAACACCATGAAGGAT 57.600 33.333 0.00 0.00 41.22 3.24
904 906 5.371115 AAACGTAAACACCATGAAGGATG 57.629 39.130 0.00 0.00 41.22 3.51
905 907 2.747446 ACGTAAACACCATGAAGGATGC 59.253 45.455 0.00 0.00 41.22 3.91
906 908 3.009723 CGTAAACACCATGAAGGATGCT 58.990 45.455 0.00 0.00 41.22 3.79
907 909 4.188462 CGTAAACACCATGAAGGATGCTA 58.812 43.478 0.00 0.00 41.22 3.49
908 910 4.634004 CGTAAACACCATGAAGGATGCTAA 59.366 41.667 0.00 0.00 41.22 3.09
909 911 5.123186 CGTAAACACCATGAAGGATGCTAAA 59.877 40.000 0.00 0.00 41.22 1.85
910 912 6.348950 CGTAAACACCATGAAGGATGCTAAAA 60.349 38.462 0.00 0.00 41.22 1.52
911 913 6.418057 AAACACCATGAAGGATGCTAAAAA 57.582 33.333 0.00 0.00 41.22 1.94
933 935 3.974871 AAAACGTAAACGCCATGAAGT 57.025 38.095 1.74 0.00 44.43 3.01
934 936 3.974871 AAACGTAAACGCCATGAAGTT 57.025 38.095 1.74 0.00 44.43 2.66
935 937 2.961522 ACGTAAACGCCATGAAGTTG 57.038 45.000 1.74 0.00 44.43 3.16
936 938 1.069500 ACGTAAACGCCATGAAGTTGC 60.069 47.619 1.74 0.00 44.43 4.17
937 939 1.196808 CGTAAACGCCATGAAGTTGCT 59.803 47.619 0.00 0.00 0.00 3.91
938 940 2.724839 CGTAAACGCCATGAAGTTGCTC 60.725 50.000 0.00 0.00 0.00 4.26
939 941 1.609208 AAACGCCATGAAGTTGCTCT 58.391 45.000 0.00 0.00 0.00 4.09
940 942 1.160137 AACGCCATGAAGTTGCTCTC 58.840 50.000 0.00 0.00 0.00 3.20
941 943 0.035317 ACGCCATGAAGTTGCTCTCA 59.965 50.000 0.00 0.00 0.00 3.27
942 944 1.159285 CGCCATGAAGTTGCTCTCAA 58.841 50.000 0.00 0.00 0.00 3.02
943 945 1.536766 CGCCATGAAGTTGCTCTCAAA 59.463 47.619 0.00 0.00 33.37 2.69
944 946 2.163010 CGCCATGAAGTTGCTCTCAAAT 59.837 45.455 0.00 0.00 33.37 2.32
945 947 3.366679 CGCCATGAAGTTGCTCTCAAATT 60.367 43.478 0.00 0.00 42.38 1.82
946 948 4.563061 GCCATGAAGTTGCTCTCAAATTT 58.437 39.130 0.00 0.00 40.14 1.82
947 949 4.992951 GCCATGAAGTTGCTCTCAAATTTT 59.007 37.500 0.00 0.00 40.14 1.82
948 950 6.158598 GCCATGAAGTTGCTCTCAAATTTTA 58.841 36.000 0.00 0.00 40.14 1.52
949 951 6.646240 GCCATGAAGTTGCTCTCAAATTTTAA 59.354 34.615 0.00 0.00 40.14 1.52
950 952 7.171337 GCCATGAAGTTGCTCTCAAATTTTAAA 59.829 33.333 0.00 0.00 40.14 1.52
951 953 9.044150 CCATGAAGTTGCTCTCAAATTTTAAAA 57.956 29.630 2.51 2.51 40.14 1.52
1019 1021 2.492088 TCATGGAGGCGTATATCGGAAG 59.508 50.000 0.00 0.00 40.26 3.46
1260 1268 1.688211 GCCTCCTCTCCAAAAGCCT 59.312 57.895 0.00 0.00 0.00 4.58
1314 1322 0.395311 CACTAGGGTCACGCCTAGGA 60.395 60.000 14.75 0.00 39.98 2.94
1332 1340 1.341209 GGATTCCCCAATGCGAAATCC 59.659 52.381 0.00 0.00 34.14 3.01
1486 1495 1.605753 GGTTTTCGTTCAGGGAGCTT 58.394 50.000 0.00 0.00 0.00 3.74
1487 1496 1.954382 GGTTTTCGTTCAGGGAGCTTT 59.046 47.619 0.00 0.00 0.00 3.51
1688 1716 1.114722 CCCACCCACACAGCACAAAT 61.115 55.000 0.00 0.00 0.00 2.32
1691 1719 2.562298 CCACCCACACAGCACAAATATT 59.438 45.455 0.00 0.00 0.00 1.28
1692 1720 3.367292 CCACCCACACAGCACAAATATTC 60.367 47.826 0.00 0.00 0.00 1.75
1758 1848 4.279922 GTCAGTCTAAGGGCTAGAGGAATC 59.720 50.000 0.00 0.00 37.32 2.52
1911 2015 6.226787 ACGAGAATCAGTCAGTTCAAGAAAT 58.773 36.000 0.00 0.00 33.17 2.17
1919 2023 6.483307 TCAGTCAGTTCAAGAAATAAGTGTGG 59.517 38.462 0.00 0.00 0.00 4.17
1946 2050 1.755380 GTAGTCGGCACAAGGATACCT 59.245 52.381 0.00 0.00 33.87 3.08
2229 2346 1.941975 TCTCGTAACGCATATCGGACA 59.058 47.619 0.00 0.00 43.86 4.02
2331 2449 7.701539 ATTCAGTTTGGTGCAAAGATATGTA 57.298 32.000 0.00 0.00 33.82 2.29
2442 2560 1.728971 GCATTCTCTTGTGTCCTCACG 59.271 52.381 0.00 0.00 46.49 4.35
2512 2631 4.581309 ATTTCTCTCTGCTTGGATTGGA 57.419 40.909 0.00 0.00 0.00 3.53
2524 2643 5.046448 TGCTTGGATTGGAGCAATTGTATTT 60.046 36.000 7.40 0.00 45.19 1.40
2653 2772 5.126222 TCTCATGTAGTCTTCTTACCTGCAG 59.874 44.000 6.78 6.78 0.00 4.41
2702 2821 6.007076 TGTCATAGAAATAGGTGTTGCCAAA 58.993 36.000 0.00 0.00 40.61 3.28
2775 2894 4.035017 CGCGTCAAATAACATTGAATCCC 58.965 43.478 0.00 0.00 40.76 3.85
2863 2982 5.509670 CCACTTGTCGGATCTGAATATGCTA 60.510 44.000 5.62 0.00 0.00 3.49
2975 3094 4.322080 TTGTTGTGTGTACTCTCAGGAG 57.678 45.455 0.00 0.00 44.62 3.69
3224 3343 0.405198 ATGGCACTGTCATGTGGGAA 59.595 50.000 0.00 0.00 38.31 3.97
3236 3355 1.047002 TGTGGGAAAACATTGCTGGG 58.953 50.000 0.00 0.00 0.00 4.45
3258 3377 7.798114 CTGGGTATGAACATCAGAAAAGGTACT 60.798 40.741 0.00 0.00 33.95 2.73
3259 3378 6.316390 GGGTATGAACATCAGAAAAGGTACTG 59.684 42.308 0.00 0.00 40.86 2.74
3300 3421 8.946085 TGTTATTTTTAATCTCGTCAGCAGATT 58.054 29.630 2.25 2.25 42.22 2.40
3375 3496 8.039603 TCGTTCAAGCATAATTACAAACATCT 57.960 30.769 0.00 0.00 0.00 2.90
3395 3516 3.053768 TCTCCCATGCATTGTACCATTCA 60.054 43.478 0.00 0.00 0.00 2.57
3399 3520 5.189342 TCCCATGCATTGTACCATTCATTTT 59.811 36.000 0.00 0.00 0.00 1.82
3409 3530 8.729805 TTGTACCATTCATTTTTGCTTTTCTT 57.270 26.923 0.00 0.00 0.00 2.52
3465 3588 1.005748 TTGGTGCTCGACTGCAGAG 60.006 57.895 23.35 14.08 44.20 3.35
3505 3628 8.770828 TCTTAATAGACAACTGCTTTTGTGTAC 58.229 33.333 8.07 0.00 39.88 2.90
4117 4253 7.538303 AGTAATTTTGTGCAAAAGAAACTGG 57.462 32.000 14.24 0.00 42.72 4.00
4157 4293 7.088905 AGCTTTTCTGCTGATCATTTTACTTG 58.911 34.615 0.00 0.00 42.33 3.16
4271 4407 2.887152 ACTTGCCAACAATCTTCCTGAC 59.113 45.455 0.00 0.00 34.61 3.51
4300 4436 9.670442 AGGTATTATTTTCCTAGATGAGGTACA 57.330 33.333 0.00 0.00 46.76 2.90
4415 4551 7.072030 TGTTTTTGTTGTTGTTCCAAATTTCG 58.928 30.769 0.00 0.00 0.00 3.46
4448 4584 6.040247 GTGTTGTTTGTTTAGGCTTTAAGCT 58.960 36.000 16.89 5.62 41.99 3.74
4531 4670 6.803154 CTCCAAAACAACTTAACTAGGAGG 57.197 41.667 0.00 0.00 37.16 4.30
4538 4677 4.347000 ACAACTTAACTAGGAGGTCTGCAA 59.653 41.667 0.00 0.00 0.00 4.08
4539 4678 5.013183 ACAACTTAACTAGGAGGTCTGCAAT 59.987 40.000 0.00 0.00 0.00 3.56
4540 4679 5.763876 ACTTAACTAGGAGGTCTGCAATT 57.236 39.130 0.00 0.00 0.00 2.32
4541 4680 5.735766 ACTTAACTAGGAGGTCTGCAATTC 58.264 41.667 0.00 0.00 0.00 2.17
4542 4681 5.485708 ACTTAACTAGGAGGTCTGCAATTCT 59.514 40.000 0.00 0.00 0.00 2.40
4543 4682 3.902881 ACTAGGAGGTCTGCAATTCTG 57.097 47.619 0.00 0.00 0.00 3.02
4714 4853 2.938451 TGAAATGCATGAAGCTACTCGG 59.062 45.455 0.00 0.00 45.94 4.63
4788 4927 6.120220 GGGTGTAAGTAATATTGAGTGCCTT 58.880 40.000 0.00 0.00 0.00 4.35
4804 4943 2.819608 TGCCTTTTATCTCTGTTGGTGC 59.180 45.455 0.00 0.00 0.00 5.01
4811 4950 6.801539 TTTATCTCTGTTGGTGCAAGTAAG 57.198 37.500 0.00 0.00 0.00 2.34
4852 4992 3.009363 TCTTTCAATCACTCATCCTGCCA 59.991 43.478 0.00 0.00 0.00 4.92
4931 5071 1.294780 CACGGCTCAAGAGAAGCCT 59.705 57.895 11.99 0.00 45.86 4.58
4933 5073 2.105466 CGGCTCAAGAGAAGCCTGC 61.105 63.158 11.99 0.00 45.86 4.85
4945 5085 3.356290 AGAAGCCTGCGGAACATTAAAT 58.644 40.909 0.00 0.00 0.00 1.40
5097 5237 0.391130 GTCAGCGGTTAGTGCCATGA 60.391 55.000 0.00 0.00 0.00 3.07
5140 5280 0.320771 CAGTTCAGCGTAGGCCACTT 60.321 55.000 5.01 0.00 41.24 3.16
5206 5346 1.022451 ACGCCACACAACACGACTTT 61.022 50.000 0.00 0.00 0.00 2.66
5240 5380 5.384145 TCTACTTTAGCTAGCCCAGTCTA 57.616 43.478 12.13 0.48 0.00 2.59
5394 5534 3.369471 GCATACTTCTAACTGGCAGGACA 60.369 47.826 20.34 2.01 0.00 4.02
5435 5575 8.643324 TGGTTTTTGCTGTGGTTATTTACTTAT 58.357 29.630 0.00 0.00 0.00 1.73
5444 5584 7.598278 TGTGGTTATTTACTTATGCTTTGTGG 58.402 34.615 0.00 0.00 0.00 4.17
5500 5640 7.610865 TCTCCATGTTTTTGGTATCCAATTTC 58.389 34.615 1.97 0.00 43.55 2.17
5587 5727 6.367686 TCATGCTTATTACAATCACTGCAG 57.632 37.500 13.48 13.48 32.65 4.41
5721 5861 2.559440 CCTGCTCTCATCAGGTTTAGC 58.441 52.381 1.07 0.00 44.62 3.09
5758 5898 2.069273 CCTTCTGTGTTCCTGTAAGCG 58.931 52.381 0.00 0.00 0.00 4.68
5766 5906 2.633967 TGTTCCTGTAAGCGGTCCTAAA 59.366 45.455 0.00 0.00 0.00 1.85
5778 5918 5.250200 AGCGGTCCTAAATAATGTTCACAA 58.750 37.500 0.00 0.00 0.00 3.33
5779 5919 5.354234 AGCGGTCCTAAATAATGTTCACAAG 59.646 40.000 0.00 0.00 0.00 3.16
5851 5991 4.414852 CATTTTTCCAAGAGCCGTACATG 58.585 43.478 0.00 0.00 0.00 3.21
5907 6051 8.369424 TGCAATACTGGACTAAACTACTTAACA 58.631 33.333 0.00 0.00 0.00 2.41
5908 6052 8.870879 GCAATACTGGACTAAACTACTTAACAG 58.129 37.037 0.00 0.00 0.00 3.16
5911 6055 6.221659 ACTGGACTAAACTACTTAACAGTGC 58.778 40.000 0.00 0.00 32.31 4.40
5912 6056 6.041751 ACTGGACTAAACTACTTAACAGTGCT 59.958 38.462 0.00 0.00 32.31 4.40
5913 6057 6.220930 TGGACTAAACTACTTAACAGTGCTG 58.779 40.000 0.00 0.00 34.06 4.41
5914 6058 5.120363 GGACTAAACTACTTAACAGTGCTGC 59.880 44.000 0.00 0.00 34.06 5.25
5932 6110 7.795734 CAGTGCTGCAATAAAACTTAGATATCG 59.204 37.037 2.77 0.00 0.00 2.92
5991 6169 4.689612 AACTGTGCTCTTAACTTCTCCA 57.310 40.909 0.00 0.00 0.00 3.86
5993 6171 2.999355 CTGTGCTCTTAACTTCTCCAGC 59.001 50.000 0.00 0.00 0.00 4.85
6101 6279 6.128580 CCAATATGCAAAGCACCTAACAAAAC 60.129 38.462 0.00 0.00 43.04 2.43
6280 6459 3.551485 GCAAAACCACATTGACAGTTCAC 59.449 43.478 0.00 0.00 0.00 3.18
6397 6582 9.880157 AAATAACTTCTGCATGCTTTGATATTT 57.120 25.926 20.33 17.22 0.00 1.40
6424 6609 6.260936 ACACTAAGTTCTTCACAACTCCATTG 59.739 38.462 0.00 0.00 44.60 2.82
6425 6610 6.483307 CACTAAGTTCTTCACAACTCCATTGA 59.517 38.462 0.00 0.00 41.23 2.57
6426 6611 5.757850 AAGTTCTTCACAACTCCATTGAC 57.242 39.130 0.00 0.00 41.23 3.18
6427 6612 4.780815 AGTTCTTCACAACTCCATTGACA 58.219 39.130 0.00 0.00 41.23 3.58
6428 6613 5.380043 AGTTCTTCACAACTCCATTGACAT 58.620 37.500 0.00 0.00 41.23 3.06
6429 6614 6.533730 AGTTCTTCACAACTCCATTGACATA 58.466 36.000 0.00 0.00 41.23 2.29
6430 6615 7.170965 AGTTCTTCACAACTCCATTGACATAT 58.829 34.615 0.00 0.00 41.23 1.78
6431 6616 6.990341 TCTTCACAACTCCATTGACATATG 57.010 37.500 0.00 0.00 41.23 1.78
6432 6617 5.882000 TCTTCACAACTCCATTGACATATGG 59.118 40.000 7.80 9.24 45.34 2.74
6433 6618 5.178096 TCACAACTCCATTGACATATGGT 57.822 39.130 7.80 0.00 44.48 3.55
6434 6619 6.306643 TCACAACTCCATTGACATATGGTA 57.693 37.500 7.80 0.00 44.48 3.25
6435 6620 6.716284 TCACAACTCCATTGACATATGGTAA 58.284 36.000 7.80 2.07 44.48 2.85
6436 6621 7.171653 TCACAACTCCATTGACATATGGTAAA 58.828 34.615 7.80 0.00 44.48 2.01
6437 6622 7.833682 TCACAACTCCATTGACATATGGTAAAT 59.166 33.333 7.80 1.13 44.48 1.40
6438 6623 9.119418 CACAACTCCATTGACATATGGTAAATA 57.881 33.333 7.80 0.00 44.48 1.40
6439 6624 9.693739 ACAACTCCATTGACATATGGTAAATAA 57.306 29.630 7.80 0.00 44.48 1.40
6440 6625 9.950680 CAACTCCATTGACATATGGTAAATAAC 57.049 33.333 7.80 0.00 44.48 1.89
6441 6626 9.920946 AACTCCATTGACATATGGTAAATAACT 57.079 29.630 7.80 0.00 44.48 2.24
6442 6627 9.920946 ACTCCATTGACATATGGTAAATAACTT 57.079 29.630 7.80 0.00 44.48 2.66
6446 6631 9.669353 CATTGACATATGGTAAATAACTTCTGC 57.331 33.333 7.80 0.00 28.87 4.26
6447 6632 8.800370 TTGACATATGGTAAATAACTTCTGCA 57.200 30.769 7.80 0.00 0.00 4.41
6448 6633 8.978874 TGACATATGGTAAATAACTTCTGCAT 57.021 30.769 7.80 0.00 0.00 3.96
6449 6634 8.839343 TGACATATGGTAAATAACTTCTGCATG 58.161 33.333 7.80 0.00 0.00 4.06
6450 6635 7.651808 ACATATGGTAAATAACTTCTGCATGC 58.348 34.615 11.82 11.82 0.00 4.06
6451 6636 7.503566 ACATATGGTAAATAACTTCTGCATGCT 59.496 33.333 20.33 0.00 0.00 3.79
6452 6637 5.818136 TGGTAAATAACTTCTGCATGCTC 57.182 39.130 20.33 0.00 0.00 4.26
6453 6638 5.500234 TGGTAAATAACTTCTGCATGCTCT 58.500 37.500 20.33 0.00 0.00 4.09
6454 6639 5.355071 TGGTAAATAACTTCTGCATGCTCTG 59.645 40.000 20.33 9.28 0.00 3.35
6455 6640 5.586243 GGTAAATAACTTCTGCATGCTCTGA 59.414 40.000 20.33 11.54 0.00 3.27
6456 6641 6.261826 GGTAAATAACTTCTGCATGCTCTGAT 59.738 38.462 20.33 3.58 0.00 2.90
6457 6642 7.442364 GGTAAATAACTTCTGCATGCTCTGATA 59.558 37.037 20.33 5.76 0.00 2.15
6458 6643 8.997323 GTAAATAACTTCTGCATGCTCTGATAT 58.003 33.333 20.33 7.79 0.00 1.63
6459 6644 8.461249 AAATAACTTCTGCATGCTCTGATATT 57.539 30.769 20.33 12.88 0.00 1.28
6460 6645 7.670009 ATAACTTCTGCATGCTCTGATATTC 57.330 36.000 20.33 0.00 0.00 1.75
6461 6646 5.032327 ACTTCTGCATGCTCTGATATTCA 57.968 39.130 20.33 0.00 0.00 2.57
6462 6647 5.434408 ACTTCTGCATGCTCTGATATTCAA 58.566 37.500 20.33 0.00 0.00 2.69
6463 6648 6.062749 ACTTCTGCATGCTCTGATATTCAAT 58.937 36.000 20.33 0.00 0.00 2.57
6464 6649 7.222161 ACTTCTGCATGCTCTGATATTCAATA 58.778 34.615 20.33 0.00 0.00 1.90
6465 6650 7.172875 ACTTCTGCATGCTCTGATATTCAATAC 59.827 37.037 20.33 0.00 0.00 1.89
6466 6651 6.766429 TCTGCATGCTCTGATATTCAATACT 58.234 36.000 20.33 0.00 0.00 2.12
6467 6652 7.899973 TCTGCATGCTCTGATATTCAATACTA 58.100 34.615 20.33 0.00 0.00 1.82
6468 6653 8.370182 TCTGCATGCTCTGATATTCAATACTAA 58.630 33.333 20.33 0.00 0.00 2.24
6469 6654 8.543862 TGCATGCTCTGATATTCAATACTAAG 57.456 34.615 20.33 0.00 0.00 2.18
6470 6655 8.152898 TGCATGCTCTGATATTCAATACTAAGT 58.847 33.333 20.33 0.00 0.00 2.24
6471 6656 8.997323 GCATGCTCTGATATTCAATACTAAGTT 58.003 33.333 11.37 0.00 0.00 2.66
6483 6668 8.603242 TTCAATACTAAGTTCTTCACAACTCC 57.397 34.615 0.00 0.00 35.45 3.85
6484 6669 7.732025 TCAATACTAAGTTCTTCACAACTCCA 58.268 34.615 0.00 0.00 35.45 3.86
6485 6670 8.375506 TCAATACTAAGTTCTTCACAACTCCAT 58.624 33.333 0.00 0.00 35.45 3.41
6486 6671 9.003658 CAATACTAAGTTCTTCACAACTCCATT 57.996 33.333 0.00 0.00 35.45 3.16
6742 6935 9.927668 CACATGTATATATGATCCTTGTGTACA 57.072 33.333 15.59 0.00 0.00 2.90
6820 7013 6.935208 GTCTTACATTTGTTTACAGAGGGAGT 59.065 38.462 0.00 0.00 0.00 3.85
6825 7018 6.935208 ACATTTGTTTACAGAGGGAGTACTTC 59.065 38.462 0.00 0.00 0.00 3.01
6826 7019 6.488769 TTTGTTTACAGAGGGAGTACTTCA 57.511 37.500 2.92 0.00 0.00 3.02
6827 7020 5.723672 TGTTTACAGAGGGAGTACTTCAG 57.276 43.478 2.92 0.00 0.00 3.02
6834 7027 1.896465 AGGGAGTACTTCAGAGTGTGC 59.104 52.381 2.92 0.00 36.60 4.57
6878 7071 5.534207 AAAATGCAAGTCCTGATTCAACA 57.466 34.783 0.00 0.00 0.00 3.33
6890 7083 3.554934 TGATTCAACAACAAGCCTGTCT 58.445 40.909 0.00 0.00 33.45 3.41
6988 7183 2.093235 GCTGTAGATCAGGGAAAGCTGT 60.093 50.000 0.00 0.00 43.78 4.40
6989 7184 3.529533 CTGTAGATCAGGGAAAGCTGTG 58.470 50.000 0.00 0.00 40.23 3.66
6993 7188 0.976641 ATCAGGGAAAGCTGTGTCGA 59.023 50.000 0.00 0.00 0.00 4.20
7057 7252 2.044946 GTGTGCTGTCCCATCCCC 60.045 66.667 0.00 0.00 0.00 4.81
7077 7380 6.251471 TCCCCGTAGTATCTAGGAAATTAGG 58.749 44.000 0.00 0.00 0.00 2.69
7138 7450 3.200593 AGCTACGCATGCTGCTGC 61.201 61.111 22.56 17.33 42.25 5.25
7297 7612 3.725490 GAAGGTATGGTAAACTAGCCCG 58.275 50.000 0.00 0.00 0.00 6.13
7328 7643 2.108250 TCCCCTCTTCTCTTTTTGGGTG 59.892 50.000 0.00 0.00 33.13 4.61
7329 7644 2.158460 CCCCTCTTCTCTTTTTGGGTGT 60.158 50.000 0.00 0.00 33.13 4.16
7330 7645 2.887152 CCCTCTTCTCTTTTTGGGTGTG 59.113 50.000 0.00 0.00 0.00 3.82
7429 7746 0.466124 CCCCTCTTCCTCCAATCGAC 59.534 60.000 0.00 0.00 0.00 4.20
7533 7850 7.040823 ACCTCTGAAATTAGCTTGAAGAAACTG 60.041 37.037 0.00 0.00 0.00 3.16
7608 7927 8.759782 AGGATGTGTATACAGTTAGCTAGTTTT 58.240 33.333 5.62 0.00 40.79 2.43
7689 8010 1.921230 GCTTTCTTTAGACGCGGAGAG 59.079 52.381 12.47 2.34 0.00 3.20
7705 8026 5.362263 GCGGAGAGGGATATAGTAGTCTAG 58.638 50.000 0.00 0.00 0.00 2.43
7729 8050 4.983671 AAGGCGTTCTCAGTTTCTTTTT 57.016 36.364 0.00 0.00 0.00 1.94
7794 8116 3.128068 GGTAATAGTTTGGGCTGAAACCG 59.872 47.826 8.45 0.00 36.63 4.44
7845 8168 2.545731 CTTTGGTTTGGTTGAAACGGG 58.454 47.619 0.00 0.00 44.41 5.28
7846 8169 1.848652 TTGGTTTGGTTGAAACGGGA 58.151 45.000 0.00 0.00 44.41 5.14
7847 8170 2.074729 TGGTTTGGTTGAAACGGGAT 57.925 45.000 0.00 0.00 44.41 3.85
7848 8171 2.389715 TGGTTTGGTTGAAACGGGATT 58.610 42.857 0.00 0.00 44.41 3.01
7849 8172 2.766828 TGGTTTGGTTGAAACGGGATTT 59.233 40.909 0.00 0.00 44.41 2.17
7850 8173 3.958798 TGGTTTGGTTGAAACGGGATTTA 59.041 39.130 0.00 0.00 44.41 1.40
7851 8174 4.404715 TGGTTTGGTTGAAACGGGATTTAA 59.595 37.500 0.00 0.00 44.41 1.52
7852 8175 5.070580 TGGTTTGGTTGAAACGGGATTTAAT 59.929 36.000 0.00 0.00 44.41 1.40
7853 8176 6.267014 TGGTTTGGTTGAAACGGGATTTAATA 59.733 34.615 0.00 0.00 44.41 0.98
7854 8177 7.153315 GGTTTGGTTGAAACGGGATTTAATAA 58.847 34.615 0.00 0.00 44.41 1.40
7855 8178 7.820386 GGTTTGGTTGAAACGGGATTTAATAAT 59.180 33.333 0.00 0.00 44.41 1.28
7856 8179 9.210329 GTTTGGTTGAAACGGGATTTAATAATT 57.790 29.630 0.00 0.00 34.87 1.40
7858 8181 9.857957 TTGGTTGAAACGGGATTTAATAATTAC 57.142 29.630 0.00 0.00 0.00 1.89
7859 8182 9.245481 TGGTTGAAACGGGATTTAATAATTACT 57.755 29.630 0.00 0.00 0.00 2.24
7860 8183 9.511144 GGTTGAAACGGGATTTAATAATTACTG 57.489 33.333 0.00 0.00 0.00 2.74
7861 8184 9.511144 GTTGAAACGGGATTTAATAATTACTGG 57.489 33.333 0.00 0.00 0.00 4.00
7862 8185 8.228035 TGAAACGGGATTTAATAATTACTGGG 57.772 34.615 0.00 0.00 0.00 4.45
7863 8186 7.835181 TGAAACGGGATTTAATAATTACTGGGT 59.165 33.333 0.00 0.00 0.00 4.51
7864 8187 8.598202 AAACGGGATTTAATAATTACTGGGTT 57.402 30.769 0.00 0.00 0.00 4.11
7865 8188 7.576861 ACGGGATTTAATAATTACTGGGTTG 57.423 36.000 0.00 0.00 0.00 3.77
7866 8189 6.548251 ACGGGATTTAATAATTACTGGGTTGG 59.452 38.462 0.00 0.00 0.00 3.77
7867 8190 6.548251 CGGGATTTAATAATTACTGGGTTGGT 59.452 38.462 0.00 0.00 0.00 3.67
7868 8191 7.068962 CGGGATTTAATAATTACTGGGTTGGTT 59.931 37.037 0.00 0.00 0.00 3.67
7869 8192 8.764558 GGGATTTAATAATTACTGGGTTGGTTT 58.235 33.333 0.00 0.00 0.00 3.27
7870 8193 9.594478 GGATTTAATAATTACTGGGTTGGTTTG 57.406 33.333 0.00 0.00 0.00 2.93
7883 8206 3.430236 GGTTGGTTTGTTTTGGTCTCTGG 60.430 47.826 0.00 0.00 0.00 3.86
7926 8249 2.250924 TGATGCAACAGTGAGGAGAGA 58.749 47.619 0.00 0.00 0.00 3.10
8225 8548 1.004745 GGGAAGGCTTGGAAGACATGA 59.995 52.381 3.46 0.00 36.14 3.07
8403 8726 6.260936 GCCTACAACATGATTGTAGCTAACAT 59.739 38.462 26.28 0.00 46.34 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.010617 GGAACCACAAATACCACACAAATCT 59.989 40.000 0.00 0.00 0.00 2.40
5 6 5.227152 GGAACCACAAATACCACACAAATC 58.773 41.667 0.00 0.00 0.00 2.17
53 54 2.559668 ACCTTGACATTGTGCATTCCAG 59.440 45.455 0.00 0.00 0.00 3.86
79 80 3.247056 TTCATCGACCAGCGCCCAA 62.247 57.895 2.29 0.00 40.61 4.12
109 110 5.646360 GGTTCAGTTATAGGCTGCAAGTTTA 59.354 40.000 0.50 0.00 35.30 2.01
177 178 9.453572 AACTGATAGCTTGACAAAAAGATCATA 57.546 29.630 0.00 0.00 0.00 2.15
181 182 7.121315 GGGTAACTGATAGCTTGACAAAAAGAT 59.879 37.037 0.00 0.00 32.48 2.40
306 308 2.239654 GTGGACCCTTGATCATCTCCAA 59.760 50.000 10.97 0.00 29.63 3.53
308 310 1.141858 GGTGGACCCTTGATCATCTCC 59.858 57.143 0.00 0.00 0.00 3.71
323 325 1.915266 CTCCCAGACAGCAGGTGGA 60.915 63.158 4.26 0.00 32.60 4.02
335 337 2.271497 CCTTGCCTCTGCTCCCAG 59.729 66.667 0.00 0.00 40.54 4.45
356 358 2.353889 CTGGATGTTCAGATTCGCTTGG 59.646 50.000 0.00 0.00 36.93 3.61
366 368 3.304928 GCTTTTGGTCACTGGATGTTCAG 60.305 47.826 0.00 0.00 40.40 3.02
378 380 4.211330 TGGCGGGGCTTTTGGTCA 62.211 61.111 0.00 0.00 0.00 4.02
397 399 9.347240 CATCTACATGAATTTTAGAATGACCCT 57.653 33.333 0.00 0.00 30.57 4.34
435 437 1.255667 GCTGACCCACCTCGTCCTTA 61.256 60.000 0.00 0.00 0.00 2.69
457 459 1.206878 ATGGTCTCTGCATACAGCCA 58.793 50.000 0.00 0.00 44.10 4.75
504 506 6.119536 GGTTATCCACACCATGAATCACTAA 58.880 40.000 0.00 0.00 34.04 2.24
515 517 1.136961 TGGCTGGGTTATCCACACCA 61.137 55.000 0.00 0.00 41.77 4.17
635 637 8.320396 TCTCTTCTTGACTTTCTGAATTGATG 57.680 34.615 0.00 0.00 0.00 3.07
645 647 4.394610 GGCTCCATTCTCTTCTTGACTTTC 59.605 45.833 0.00 0.00 0.00 2.62
655 657 3.135348 TCGAATGATGGCTCCATTCTCTT 59.865 43.478 21.13 0.00 44.56 2.85
675 677 7.970384 AGACTCGCTATTCTATTAATCTCTCG 58.030 38.462 0.00 0.00 0.00 4.04
732 734 3.378112 CCATGTGCCTCAACATTAACGAT 59.622 43.478 0.00 0.00 38.75 3.73
795 797 7.304479 TGGTTATGGGATTGGTCAAATCATAT 58.696 34.615 2.33 0.00 45.69 1.78
800 802 4.946646 ACTGGTTATGGGATTGGTCAAAT 58.053 39.130 0.00 0.00 0.00 2.32
884 886 2.747446 GCATCCTTCATGGTGTTTACGT 59.253 45.455 0.00 0.00 37.07 3.57
885 887 3.009723 AGCATCCTTCATGGTGTTTACG 58.990 45.455 0.00 0.00 41.89 3.18
886 888 6.509418 TTTAGCATCCTTCATGGTGTTTAC 57.491 37.500 0.00 0.00 43.36 2.01
887 889 7.531857 TTTTTAGCATCCTTCATGGTGTTTA 57.468 32.000 0.00 0.00 43.36 2.01
888 890 6.418057 TTTTTAGCATCCTTCATGGTGTTT 57.582 33.333 0.00 0.00 43.36 2.83
912 914 4.295857 ACTTCATGGCGTTTACGTTTTT 57.704 36.364 0.00 0.00 42.22 1.94
913 915 3.974871 ACTTCATGGCGTTTACGTTTT 57.025 38.095 0.00 0.00 42.22 2.43
914 916 3.623863 CAACTTCATGGCGTTTACGTTT 58.376 40.909 0.00 0.00 42.22 3.60
915 917 2.603652 GCAACTTCATGGCGTTTACGTT 60.604 45.455 0.00 0.00 42.22 3.99
916 918 1.069500 GCAACTTCATGGCGTTTACGT 60.069 47.619 4.05 0.00 42.22 3.57
917 919 1.196808 AGCAACTTCATGGCGTTTACG 59.803 47.619 0.00 0.00 43.27 3.18
918 920 2.484264 AGAGCAACTTCATGGCGTTTAC 59.516 45.455 0.00 0.00 0.00 2.01
919 921 2.742053 GAGAGCAACTTCATGGCGTTTA 59.258 45.455 0.00 0.00 0.00 2.01
920 922 1.537202 GAGAGCAACTTCATGGCGTTT 59.463 47.619 0.00 0.00 0.00 3.60
921 923 1.160137 GAGAGCAACTTCATGGCGTT 58.840 50.000 0.00 0.00 0.00 4.84
922 924 0.035317 TGAGAGCAACTTCATGGCGT 59.965 50.000 0.00 0.00 0.00 5.68
923 925 1.159285 TTGAGAGCAACTTCATGGCG 58.841 50.000 0.00 0.00 0.00 5.69
924 926 3.863142 ATTTGAGAGCAACTTCATGGC 57.137 42.857 0.00 0.00 32.79 4.40
925 927 8.592105 TTTAAAATTTGAGAGCAACTTCATGG 57.408 30.769 0.00 0.00 32.79 3.66
950 952 3.634283 CCTTCATGGCGTTTACGTTTTT 58.366 40.909 0.00 0.00 42.22 1.94
951 953 3.276882 CCTTCATGGCGTTTACGTTTT 57.723 42.857 0.00 0.00 42.22 2.43
952 954 2.981400 CCTTCATGGCGTTTACGTTT 57.019 45.000 0.00 0.00 42.22 3.60
1011 1013 2.756760 AGAACAAGGCGTACTTCCGATA 59.243 45.455 0.00 0.00 37.29 2.92
1019 1021 2.129607 TCACGAAAGAACAAGGCGTAC 58.870 47.619 0.00 0.00 33.45 3.67
1260 1268 4.357947 GATGCGGAGGCGGCGATA 62.358 66.667 12.98 0.00 44.10 2.92
1275 1283 2.846652 CGTAGAAGGCGAGGCGGAT 61.847 63.158 0.00 0.00 0.00 4.18
1314 1322 1.413118 GGGATTTCGCATTGGGGAAT 58.587 50.000 6.93 6.93 44.27 3.01
1486 1495 8.783093 CCTGTAAACACAGATCAAACTCAATAA 58.217 33.333 6.36 0.00 39.99 1.40
1487 1496 7.390440 CCCTGTAAACACAGATCAAACTCAATA 59.610 37.037 6.36 0.00 39.99 1.90
1688 1716 6.405278 TCAGCAGATAACTCGAATGGAATA 57.595 37.500 0.00 0.00 0.00 1.75
1691 1719 4.081697 TGTTCAGCAGATAACTCGAATGGA 60.082 41.667 0.00 0.00 0.00 3.41
1692 1720 4.183865 TGTTCAGCAGATAACTCGAATGG 58.816 43.478 0.00 0.00 0.00 3.16
1769 1859 0.165944 GCTGACACAATGTACACCGC 59.834 55.000 0.00 0.00 0.00 5.68
1839 1943 3.679980 CAGTTACCACTGTGACATGCTAC 59.320 47.826 9.86 0.00 44.96 3.58
1911 2015 2.440409 GACTACCGAGACCCACACTTA 58.560 52.381 0.00 0.00 0.00 2.24
1919 2023 1.870055 TTGTGCCGACTACCGAGACC 61.870 60.000 0.00 0.00 41.76 3.85
1946 2050 6.491383 ACACTCTACCTAACCTACATCTCAA 58.509 40.000 0.00 0.00 0.00 3.02
2229 2346 2.224606 CAACACACTGTTCTGCCTCAT 58.775 47.619 0.00 0.00 38.77 2.90
2331 2449 4.531732 ACCAAATAACCAGGCAATGACAAT 59.468 37.500 0.00 0.00 0.00 2.71
2524 2643 6.070596 TCCTCTTCAGCTGATCAAACAAGATA 60.071 38.462 19.04 4.12 0.00 1.98
2653 2772 5.584251 TGGAAAAGAAAAACACAAGGCAATC 59.416 36.000 0.00 0.00 0.00 2.67
2775 2894 0.102120 TGCTTGCTGTCGTTTTTGGG 59.898 50.000 0.00 0.00 0.00 4.12
2975 3094 5.125097 ACTGTCAGGCTTGATGAATTCAATC 59.875 40.000 13.09 10.90 43.30 2.67
3224 3343 4.771577 TGATGTTCATACCCAGCAATGTTT 59.228 37.500 0.00 0.00 0.00 2.83
3236 3355 6.371548 TGCAGTACCTTTTCTGATGTTCATAC 59.628 38.462 0.00 0.00 34.02 2.39
3258 3377 3.483808 TAACAGTGAACTGGTGATGCA 57.516 42.857 11.28 0.00 44.89 3.96
3259 3378 5.376854 AAATAACAGTGAACTGGTGATGC 57.623 39.130 11.28 0.00 44.89 3.91
3409 3530 7.993183 ACTGTGAAGGAAAGAAGTCAAATAAGA 59.007 33.333 0.00 0.00 0.00 2.10
3430 3551 1.942657 CCAACCAGAGTGTCAACTGTG 59.057 52.381 0.00 0.00 45.15 3.66
3488 3611 6.288294 TGATAGAGTACACAAAAGCAGTTGT 58.712 36.000 0.00 0.00 42.48 3.32
3868 3998 6.645790 AGAACTGATCTGTTGCAATTTCTT 57.354 33.333 21.13 0.00 36.88 2.52
4117 4253 7.811713 AGCAGAAAAGCTTCAGAAAACATATTC 59.188 33.333 0.00 0.00 43.70 1.75
4300 4436 4.583073 TGTATGCTATACAGATGACGGTGT 59.417 41.667 5.28 0.00 0.00 4.16
4448 4584 6.531923 TCATCATTTGGAAAGGCAAAATTCA 58.468 32.000 0.00 0.00 0.00 2.57
4538 4677 2.243221 AGGCTAAAGGGTCATGCAGAAT 59.757 45.455 0.00 0.00 0.00 2.40
4539 4678 1.635487 AGGCTAAAGGGTCATGCAGAA 59.365 47.619 0.00 0.00 0.00 3.02
4540 4679 1.065199 CAGGCTAAAGGGTCATGCAGA 60.065 52.381 0.00 0.00 0.00 4.26
4541 4680 1.340405 ACAGGCTAAAGGGTCATGCAG 60.340 52.381 0.00 0.00 0.00 4.41
4542 4681 0.698238 ACAGGCTAAAGGGTCATGCA 59.302 50.000 0.00 0.00 0.00 3.96
4543 4682 1.839424 AACAGGCTAAAGGGTCATGC 58.161 50.000 0.00 0.00 0.00 4.06
4544 4683 4.039124 ACAAAAACAGGCTAAAGGGTCATG 59.961 41.667 0.00 0.00 0.00 3.07
4545 4684 4.223144 ACAAAAACAGGCTAAAGGGTCAT 58.777 39.130 0.00 0.00 0.00 3.06
4681 4820 6.094193 TCATGCATTTCACTATCTCGAGAT 57.906 37.500 29.58 29.58 38.51 2.75
4788 4927 5.181245 GCTTACTTGCACCAACAGAGATAAA 59.819 40.000 0.00 0.00 0.00 1.40
4792 4931 2.158827 TGCTTACTTGCACCAACAGAGA 60.159 45.455 0.00 0.00 38.12 3.10
4804 4943 8.630278 AGTATGTATAAACTCGTGCTTACTTG 57.370 34.615 0.00 0.00 0.00 3.16
4811 4950 8.181487 TGAAAGAAGTATGTATAAACTCGTGC 57.819 34.615 0.00 0.00 0.00 5.34
4852 4992 2.023791 GTCTCTCCTTCCCTCCCTAACT 60.024 54.545 0.00 0.00 0.00 2.24
4896 5036 0.173481 GTGGCTATGCACTCTCGTGA 59.827 55.000 0.00 0.00 43.97 4.35
4931 5071 6.561737 TGTAACTTCATTTAATGTTCCGCA 57.438 33.333 4.77 0.00 0.00 5.69
4945 5085 9.665719 TCTACATGCAAAGATTATGTAACTTCA 57.334 29.630 0.00 0.00 36.99 3.02
5097 5237 1.308998 CTGTTCCAAGCACGAAAGGT 58.691 50.000 0.00 0.00 0.00 3.50
5140 5280 2.816087 GTTCTGCAAATTCTGAGGAGCA 59.184 45.455 0.00 0.00 0.00 4.26
5206 5346 4.467795 AGCTAAAGTAGATTGCTCTGGTGA 59.532 41.667 0.00 0.00 32.66 4.02
5240 5380 0.662619 CAATGTGTGTGCCGAAGTGT 59.337 50.000 0.00 0.00 0.00 3.55
5394 5534 6.716173 AGCAAAAACCAGGCATGAAATAAAAT 59.284 30.769 0.00 0.00 0.00 1.82
5444 5584 2.294512 GGGGCTTACATGCTAATGCTTC 59.705 50.000 0.00 0.00 40.48 3.86
5500 5640 5.446143 AACTGAGAGGTATCAAGCTATCG 57.554 43.478 0.00 0.00 42.93 2.92
5587 5727 1.268539 GGCAATAATACACACGGCAGC 60.269 52.381 0.00 0.00 0.00 5.25
5637 5777 1.112113 GTCTATCCTGCTCGAACCCA 58.888 55.000 0.00 0.00 0.00 4.51
5758 5898 6.884836 AGACCTTGTGAACATTATTTAGGACC 59.115 38.462 4.09 0.00 0.00 4.46
5766 5906 7.246171 ACTCACTAGACCTTGTGAACATTAT 57.754 36.000 13.49 0.00 42.75 1.28
5778 5918 5.883180 AGAACTTCAGTACTCACTAGACCT 58.117 41.667 0.00 0.00 32.21 3.85
5779 5919 5.706369 TGAGAACTTCAGTACTCACTAGACC 59.294 44.000 0.00 0.00 35.01 3.85
5819 5959 1.714541 TGGAAAAATGCAGGAAGCCA 58.285 45.000 0.00 0.00 44.83 4.75
5907 6051 7.495934 ACGATATCTAAGTTTTATTGCAGCACT 59.504 33.333 0.00 0.00 0.00 4.40
5908 6052 7.584123 CACGATATCTAAGTTTTATTGCAGCAC 59.416 37.037 0.00 0.00 0.00 4.40
5912 6056 9.541143 TGATCACGATATCTAAGTTTTATTGCA 57.459 29.630 0.34 0.00 0.00 4.08
5976 6154 3.055458 AGGAAGCTGGAGAAGTTAAGAGC 60.055 47.826 0.00 0.00 0.00 4.09
5991 6169 4.309933 GCTGCAAATTAACAAAGGAAGCT 58.690 39.130 0.00 0.00 0.00 3.74
5993 6171 3.674753 CGGCTGCAAATTAACAAAGGAAG 59.325 43.478 0.50 0.00 0.00 3.46
6101 6279 1.607148 GGAAAACTGAACCAACTCGGG 59.393 52.381 0.00 0.00 40.22 5.14
6248 6427 1.929836 TGTGGTTTTGCAAACATTCGC 59.070 42.857 12.39 8.77 30.24 4.70
6280 6459 3.049708 TGTGACAGCATCTTCTTCCAG 57.950 47.619 0.00 0.00 0.00 3.86
6358 6537 9.407380 TGCAGAAGTTATTTACCATATGTCAAT 57.593 29.630 1.24 0.00 0.00 2.57
6359 6538 8.800370 TGCAGAAGTTATTTACCATATGTCAA 57.200 30.769 1.24 0.00 0.00 3.18
6360 6539 8.839343 CATGCAGAAGTTATTTACCATATGTCA 58.161 33.333 1.24 0.00 0.00 3.58
6361 6540 7.805071 GCATGCAGAAGTTATTTACCATATGTC 59.195 37.037 14.21 0.00 0.00 3.06
6397 6582 6.880484 TGGAGTTGTGAAGAACTTAGTGTTA 58.120 36.000 0.00 0.00 39.30 2.41
6424 6609 7.805071 GCATGCAGAAGTTATTTACCATATGTC 59.195 37.037 14.21 0.00 0.00 3.06
6425 6610 7.503566 AGCATGCAGAAGTTATTTACCATATGT 59.496 33.333 21.98 0.00 0.00 2.29
6426 6611 7.879070 AGCATGCAGAAGTTATTTACCATATG 58.121 34.615 21.98 0.00 0.00 1.78
6427 6612 7.941238 AGAGCATGCAGAAGTTATTTACCATAT 59.059 33.333 21.98 0.00 0.00 1.78
6428 6613 7.227314 CAGAGCATGCAGAAGTTATTTACCATA 59.773 37.037 21.98 0.00 0.00 2.74
6429 6614 6.039047 CAGAGCATGCAGAAGTTATTTACCAT 59.961 38.462 21.98 0.00 0.00 3.55
6430 6615 5.355071 CAGAGCATGCAGAAGTTATTTACCA 59.645 40.000 21.98 0.00 0.00 3.25
6431 6616 5.586243 TCAGAGCATGCAGAAGTTATTTACC 59.414 40.000 21.98 0.00 0.00 2.85
6432 6617 6.668541 TCAGAGCATGCAGAAGTTATTTAC 57.331 37.500 21.98 0.00 0.00 2.01
6433 6618 9.565090 AATATCAGAGCATGCAGAAGTTATTTA 57.435 29.630 21.98 2.95 0.00 1.40
6434 6619 8.461249 AATATCAGAGCATGCAGAAGTTATTT 57.539 30.769 21.98 0.00 0.00 1.40
6435 6620 7.718314 TGAATATCAGAGCATGCAGAAGTTATT 59.282 33.333 21.98 14.46 0.00 1.40
6436 6621 7.222161 TGAATATCAGAGCATGCAGAAGTTAT 58.778 34.615 21.98 6.83 0.00 1.89
6437 6622 6.585416 TGAATATCAGAGCATGCAGAAGTTA 58.415 36.000 21.98 4.66 0.00 2.24
6438 6623 5.434408 TGAATATCAGAGCATGCAGAAGTT 58.566 37.500 21.98 12.67 0.00 2.66
6439 6624 5.032327 TGAATATCAGAGCATGCAGAAGT 57.968 39.130 21.98 5.30 0.00 3.01
6440 6625 6.561737 ATTGAATATCAGAGCATGCAGAAG 57.438 37.500 21.98 6.79 0.00 2.85
6441 6626 7.222161 AGTATTGAATATCAGAGCATGCAGAA 58.778 34.615 21.98 2.22 0.00 3.02
6442 6627 6.766429 AGTATTGAATATCAGAGCATGCAGA 58.234 36.000 21.98 14.88 0.00 4.26
6443 6628 8.543862 TTAGTATTGAATATCAGAGCATGCAG 57.456 34.615 21.98 9.51 0.00 4.41
6444 6629 8.152898 ACTTAGTATTGAATATCAGAGCATGCA 58.847 33.333 21.98 0.00 0.00 3.96
6445 6630 8.545229 ACTTAGTATTGAATATCAGAGCATGC 57.455 34.615 10.51 10.51 0.00 4.06
6457 6642 9.220767 GGAGTTGTGAAGAACTTAGTATTGAAT 57.779 33.333 0.00 0.00 36.27 2.57
6458 6643 8.208224 TGGAGTTGTGAAGAACTTAGTATTGAA 58.792 33.333 0.00 0.00 36.27 2.69
6459 6644 7.732025 TGGAGTTGTGAAGAACTTAGTATTGA 58.268 34.615 0.00 0.00 36.27 2.57
6460 6645 7.962964 TGGAGTTGTGAAGAACTTAGTATTG 57.037 36.000 0.00 0.00 36.27 1.90
6461 6646 9.003658 CAATGGAGTTGTGAAGAACTTAGTATT 57.996 33.333 0.00 0.00 36.27 1.89
6462 6647 8.375506 TCAATGGAGTTGTGAAGAACTTAGTAT 58.624 33.333 0.00 0.00 36.27 2.12
6463 6648 7.656137 GTCAATGGAGTTGTGAAGAACTTAGTA 59.344 37.037 0.00 0.00 36.27 1.82
6464 6649 6.483640 GTCAATGGAGTTGTGAAGAACTTAGT 59.516 38.462 0.00 0.00 36.27 2.24
6465 6650 6.483307 TGTCAATGGAGTTGTGAAGAACTTAG 59.517 38.462 0.00 0.00 36.27 2.18
6466 6651 6.353323 TGTCAATGGAGTTGTGAAGAACTTA 58.647 36.000 0.00 0.00 36.27 2.24
6467 6652 5.192927 TGTCAATGGAGTTGTGAAGAACTT 58.807 37.500 0.00 0.00 36.27 2.66
6468 6653 4.780815 TGTCAATGGAGTTGTGAAGAACT 58.219 39.130 0.00 0.00 38.94 3.01
6469 6654 5.695851 ATGTCAATGGAGTTGTGAAGAAC 57.304 39.130 0.00 0.00 38.95 3.01
6470 6655 7.381766 CATATGTCAATGGAGTTGTGAAGAA 57.618 36.000 0.00 0.00 38.95 2.52
6471 6656 6.990341 CATATGTCAATGGAGTTGTGAAGA 57.010 37.500 0.00 0.00 38.95 2.87
6483 6668 9.669353 GCAGAAGTTATTTACCATATGTCAATG 57.331 33.333 1.24 0.00 0.00 2.82
6484 6669 9.407380 TGCAGAAGTTATTTACCATATGTCAAT 57.593 29.630 1.24 0.00 0.00 2.57
6485 6670 8.800370 TGCAGAAGTTATTTACCATATGTCAA 57.200 30.769 1.24 0.00 0.00 3.18
6486 6671 8.839343 CATGCAGAAGTTATTTACCATATGTCA 58.161 33.333 1.24 0.00 0.00 3.58
6661 6846 5.067283 ACGGCACTGAGTTTAGAAACATTTT 59.933 36.000 7.82 0.00 41.30 1.82
6742 6935 1.386533 CATCTCTTTGCCGCTTCCAT 58.613 50.000 0.00 0.00 0.00 3.41
6820 7013 6.288294 ACAAAATGTAGCACACTCTGAAGTA 58.712 36.000 0.00 0.00 33.25 2.24
6825 7018 6.299023 TGTTACAAAATGTAGCACACTCTG 57.701 37.500 3.37 0.00 38.77 3.35
6858 7051 4.341806 TGTTGTTGAATCAGGACTTGCATT 59.658 37.500 0.00 0.00 0.00 3.56
6908 7101 1.226746 AAAGAAACGACAAGCCGGAG 58.773 50.000 5.05 0.00 0.00 4.63
6967 7162 2.093235 ACAGCTTTCCCTGATCTACAGC 60.093 50.000 0.00 0.00 44.52 4.40
6988 7183 9.430623 TCACAAATAGACAAATAAGAATCGACA 57.569 29.630 0.00 0.00 0.00 4.35
6989 7184 9.690434 GTCACAAATAGACAAATAAGAATCGAC 57.310 33.333 0.00 0.00 36.06 4.20
7057 7252 7.041508 ACACGACCTAATTTCCTAGATACTACG 60.042 40.741 0.00 0.00 0.00 3.51
7077 7380 7.917720 AAAACATAAAACATTGGTACACGAC 57.082 32.000 0.00 0.00 39.29 4.34
7095 7398 4.763793 CCAGACTGTCCAGATGAAAAACAT 59.236 41.667 3.76 0.00 42.47 2.71
7136 7448 8.077991 CAGTTTGTCTTGAATGATCTTTTAGCA 58.922 33.333 0.00 0.00 0.00 3.49
7137 7449 8.078596 ACAGTTTGTCTTGAATGATCTTTTAGC 58.921 33.333 0.00 0.00 0.00 3.09
7138 7450 9.390795 CACAGTTTGTCTTGAATGATCTTTTAG 57.609 33.333 0.00 0.00 0.00 1.85
7297 7612 4.786425 AGAGAAGAGGGGAAATAACATGC 58.214 43.478 0.00 0.00 0.00 4.06
7328 7643 1.202698 ACCAAGTGAGAAGCTGACCAC 60.203 52.381 0.00 0.00 0.00 4.16
7329 7644 1.070758 GACCAAGTGAGAAGCTGACCA 59.929 52.381 0.00 0.00 0.00 4.02
7330 7645 1.070758 TGACCAAGTGAGAAGCTGACC 59.929 52.381 0.00 0.00 0.00 4.02
7429 7746 1.811217 CGGCACATGCGACATACTCG 61.811 60.000 0.00 0.00 45.97 4.18
7608 7927 7.754851 TCAGATAACTACAGAACCGCATATA 57.245 36.000 0.00 0.00 0.00 0.86
7612 7931 4.794278 TTCAGATAACTACAGAACCGCA 57.206 40.909 0.00 0.00 0.00 5.69
7614 7933 8.251750 TCAAAATTCAGATAACTACAGAACCG 57.748 34.615 0.00 0.00 0.00 4.44
7628 7949 8.301720 CCATGTTTTCTCATCTCAAAATTCAGA 58.698 33.333 0.00 0.00 0.00 3.27
7689 8010 6.883756 ACGCCTTTACTAGACTACTATATCCC 59.116 42.308 0.00 0.00 0.00 3.85
7705 8026 5.419760 AAAGAAACTGAGAACGCCTTTAC 57.580 39.130 0.00 0.00 0.00 2.01
7729 8050 6.027131 CGAGAAAAGTCAAACATTGTCACAA 58.973 36.000 0.00 0.00 0.00 3.33
7733 8054 3.975035 GCCGAGAAAAGTCAAACATTGTC 59.025 43.478 0.00 0.00 0.00 3.18
7794 8116 8.807581 CCAAAATGAAAACTGAACTGAAACTAC 58.192 33.333 0.00 0.00 0.00 2.73
7806 8128 3.116079 AGCAGCCCAAAATGAAAACTG 57.884 42.857 0.00 0.00 0.00 3.16
7807 8129 3.843893 AAGCAGCCCAAAATGAAAACT 57.156 38.095 0.00 0.00 0.00 2.66
7849 8172 9.765795 CAAAACAAACCAACCCAGTAATTATTA 57.234 29.630 0.00 0.00 0.00 0.98
7850 8173 7.717436 CCAAAACAAACCAACCCAGTAATTATT 59.283 33.333 0.00 0.00 0.00 1.40
7851 8174 7.147461 ACCAAAACAAACCAACCCAGTAATTAT 60.147 33.333 0.00 0.00 0.00 1.28
7852 8175 6.156429 ACCAAAACAAACCAACCCAGTAATTA 59.844 34.615 0.00 0.00 0.00 1.40
7853 8176 5.045505 ACCAAAACAAACCAACCCAGTAATT 60.046 36.000 0.00 0.00 0.00 1.40
7854 8177 4.471747 ACCAAAACAAACCAACCCAGTAAT 59.528 37.500 0.00 0.00 0.00 1.89
7855 8178 3.838903 ACCAAAACAAACCAACCCAGTAA 59.161 39.130 0.00 0.00 0.00 2.24
7856 8179 3.442076 ACCAAAACAAACCAACCCAGTA 58.558 40.909 0.00 0.00 0.00 2.74
7857 8180 2.235155 GACCAAAACAAACCAACCCAGT 59.765 45.455 0.00 0.00 0.00 4.00
7858 8181 2.499693 AGACCAAAACAAACCAACCCAG 59.500 45.455 0.00 0.00 0.00 4.45
7859 8182 2.498078 GAGACCAAAACAAACCAACCCA 59.502 45.455 0.00 0.00 0.00 4.51
7860 8183 2.764010 AGAGACCAAAACAAACCAACCC 59.236 45.455 0.00 0.00 0.00 4.11
7861 8184 3.430236 CCAGAGACCAAAACAAACCAACC 60.430 47.826 0.00 0.00 0.00 3.77
7862 8185 3.780902 CCAGAGACCAAAACAAACCAAC 58.219 45.455 0.00 0.00 0.00 3.77
7863 8186 2.167487 GCCAGAGACCAAAACAAACCAA 59.833 45.455 0.00 0.00 0.00 3.67
7864 8187 1.754226 GCCAGAGACCAAAACAAACCA 59.246 47.619 0.00 0.00 0.00 3.67
7865 8188 1.754226 TGCCAGAGACCAAAACAAACC 59.246 47.619 0.00 0.00 0.00 3.27
7866 8189 2.223805 CCTGCCAGAGACCAAAACAAAC 60.224 50.000 0.00 0.00 0.00 2.93
7867 8190 2.031120 CCTGCCAGAGACCAAAACAAA 58.969 47.619 0.00 0.00 0.00 2.83
7868 8191 1.691196 CCTGCCAGAGACCAAAACAA 58.309 50.000 0.00 0.00 0.00 2.83
7869 8192 0.178992 CCCTGCCAGAGACCAAAACA 60.179 55.000 0.00 0.00 0.00 2.83
7870 8193 0.110486 TCCCTGCCAGAGACCAAAAC 59.890 55.000 0.00 0.00 0.00 2.43
7871 8194 0.850100 TTCCCTGCCAGAGACCAAAA 59.150 50.000 0.00 0.00 0.00 2.44
7872 8195 0.401738 CTTCCCTGCCAGAGACCAAA 59.598 55.000 0.00 0.00 0.00 3.28
7873 8196 2.069776 CTTCCCTGCCAGAGACCAA 58.930 57.895 0.00 0.00 0.00 3.67
7874 8197 2.596851 GCTTCCCTGCCAGAGACCA 61.597 63.158 0.00 0.00 0.00 4.02
7883 8206 2.124942 CTCCCGAAGCTTCCCTGC 60.125 66.667 20.62 0.00 0.00 4.85
7926 8249 3.884895 TGGACGCAAAGGATATCAACAT 58.115 40.909 4.83 0.00 0.00 2.71
8225 8548 4.028131 TCACCAATCGGTACACTCCTAAT 58.972 43.478 0.00 0.00 46.94 1.73


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

AutoCloner maintained by Alex Coulton.