Multiple sequence alignment - TraesCS6A01G286800

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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 TraesCS6A01G286800 chr6A 100.000 6305 0 0 1 6305 519204403 519210707 0.000000e+00 11644.0
1 TraesCS6A01G286800 chr6A 83.044 519 53 18 5793 6305 449360351 449360840 7.500000e-119 438.0
2 TraesCS6A01G286800 chr6A 79.110 517 58 30 5793 6305 15495352 15494882 1.710000e-80 311.0
3 TraesCS6A01G286800 chr6A 87.500 80 5 4 643 721 488319604 488319679 3.130000e-13 87.9
4 TraesCS6A01G286800 chr6B 94.592 3661 155 23 2053 5682 563996882 564000530 0.000000e+00 5624.0
5 TraesCS6A01G286800 chr6B 95.323 1176 42 6 888 2053 563995662 563996834 0.000000e+00 1855.0
6 TraesCS6A01G286800 chr6B 85.268 448 42 12 3 446 563994830 563995257 2.090000e-119 440.0
7 TraesCS6A01G286800 chr6B 95.833 48 2 0 853 900 563995597 563995644 1.880000e-10 78.7
8 TraesCS6A01G286800 chr6D 94.674 3624 131 26 2100 5682 377544325 377547927 0.000000e+00 5566.0
9 TraesCS6A01G286800 chr6D 93.833 1200 45 8 853 2030 377543132 377544324 0.000000e+00 1779.0
10 TraesCS6A01G286800 chr6D 91.680 649 42 8 1 646 377541137 377541776 0.000000e+00 889.0
11 TraesCS6A01G286800 chr6D 96.209 211 8 0 646 856 377542856 377543066 4.680000e-91 346.0
12 TraesCS6A01G286800 chr6D 97.917 48 0 1 2007 2053 84938453 84938500 1.460000e-11 82.4
13 TraesCS6A01G286800 chr6D 100.000 43 0 0 2011 2053 84938543 84938501 5.240000e-11 80.5
14 TraesCS6A01G286800 chr6D 92.683 41 2 1 695 735 13960331 13960370 2.460000e-04 58.4
15 TraesCS6A01G286800 chr7D 89.362 517 34 12 5793 6305 349949988 349949489 1.150000e-176 630.0
16 TraesCS6A01G286800 chr7D 88.072 503 38 13 5793 6290 499718858 499719343 1.520000e-160 577.0
17 TraesCS6A01G286800 chr7D 92.135 89 6 1 509 597 602187239 602187326 2.390000e-24 124.0
18 TraesCS6A01G286800 chr7D 92.941 85 5 1 513 597 556311132 556311049 8.580000e-24 122.0
19 TraesCS6A01G286800 chr7D 98.039 51 1 0 2027 2077 611705822 611705772 8.710000e-14 89.8
20 TraesCS6A01G286800 chr1D 89.189 518 38 13 5791 6303 320980036 320980540 1.150000e-176 630.0
21 TraesCS6A01G286800 chr1D 86.260 524 43 17 5793 6305 361098999 361099504 5.560000e-150 542.0
22 TraesCS6A01G286800 chr1D 97.297 37 1 0 620 656 465819 465855 5.280000e-06 63.9
23 TraesCS6A01G286800 chr3D 88.247 519 43 11 5791 6305 16130929 16130425 6.990000e-169 604.0
24 TraesCS6A01G286800 chr3D 88.395 517 40 10 5793 6305 580085878 580086378 6.990000e-169 604.0
25 TraesCS6A01G286800 chr3D 87.984 516 46 11 5793 6305 556936763 556937265 4.210000e-166 595.0
26 TraesCS6A01G286800 chr3D 94.340 53 2 1 2011 2062 607096386 607096438 5.240000e-11 80.5
27 TraesCS6A01G286800 chr5D 87.500 520 36 16 5793 6305 325474803 325474306 1.970000e-159 573.0
28 TraesCS6A01G286800 chr4D 87.449 494 44 13 5789 6276 473846274 473845793 2.570000e-153 553.0
29 TraesCS6A01G286800 chr1A 82.852 519 57 18 5787 6296 570121314 570121809 2.700000e-118 436.0
30 TraesCS6A01G286800 chr1A 94.444 90 3 2 506 595 513118099 513118186 3.070000e-28 137.0
31 TraesCS6A01G286800 chr4B 86.634 202 12 10 1816 2012 493764672 493764863 6.410000e-50 209.0
32 TraesCS6A01G286800 chr2A 96.471 85 2 1 511 595 431044670 431044587 8.520000e-29 139.0
33 TraesCS6A01G286800 chr2A 93.103 87 5 1 509 595 714336274 714336359 6.640000e-25 126.0
34 TraesCS6A01G286800 chr7A 92.391 92 5 2 504 595 709389662 709389751 5.130000e-26 130.0
35 TraesCS6A01G286800 chr7A 76.866 134 24 6 604 733 680345935 680345805 1.130000e-07 69.4
36 TraesCS6A01G286800 chr5B 95.062 81 3 1 516 596 13704884 13704963 6.640000e-25 126.0
37 TraesCS6A01G286800 chr2B 93.103 87 5 1 509 595 1266746 1266831 6.640000e-25 126.0
38 TraesCS6A01G286800 chr2B 97.872 47 1 0 2007 2053 749661560 749661606 1.460000e-11 82.4
39 TraesCS6A01G286800 chr2D 92.000 75 3 3 2004 2076 631034908 631034835 1.120000e-17 102.0
40 TraesCS6A01G286800 chrUn 79.839 124 15 9 618 737 71287551 71287434 1.460000e-11 82.4
41 TraesCS6A01G286800 chrUn 92.683 41 2 1 695 735 402795637 402795598 2.460000e-04 58.4
42 TraesCS6A01G286800 chr3B 94.340 53 2 1 2011 2062 816606481 816606533 5.240000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G286800 chr6A 519204403 519210707 6304 False 11644.000 11644 100.000 1 6305 1 chr6A.!!$F3 6304
1 TraesCS6A01G286800 chr6B 563994830 564000530 5700 False 1999.425 5624 92.754 3 5682 4 chr6B.!!$F1 5679
2 TraesCS6A01G286800 chr6D 377541137 377547927 6790 False 2145.000 5566 94.099 1 5682 4 chr6D.!!$F3 5681
3 TraesCS6A01G286800 chr1D 320980036 320980540 504 False 630.000 630 89.189 5791 6303 1 chr1D.!!$F2 512
4 TraesCS6A01G286800 chr1D 361098999 361099504 505 False 542.000 542 86.260 5793 6305 1 chr1D.!!$F3 512
5 TraesCS6A01G286800 chr3D 16130425 16130929 504 True 604.000 604 88.247 5791 6305 1 chr3D.!!$R1 514
6 TraesCS6A01G286800 chr3D 580085878 580086378 500 False 604.000 604 88.395 5793 6305 1 chr3D.!!$F2 512
7 TraesCS6A01G286800 chr3D 556936763 556937265 502 False 595.000 595 87.984 5793 6305 1 chr3D.!!$F1 512

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
173 176 0.896923 TTGGCATGGGAAATGAGTGC 59.103 50.000 0.00 0.0 35.17 4.40 F
867 2035 1.278637 CGTTCGTCACAACAAGCCC 59.721 57.895 0.00 0.0 0.00 5.19 F
1668 2889 0.179012 CCCCACGGTTACTGTTGGTT 60.179 55.000 12.58 0.0 0.00 3.67 F
1812 3033 1.094785 ACGGGCAATTTCAAGGATCG 58.905 50.000 0.00 0.0 0.00 3.69 F
2794 4081 1.069022 CACAGCAAGTCCCACATTTCG 60.069 52.381 0.00 0.0 0.00 3.46 F
4002 5303 0.037326 GGTGCTGACATCCTCGTTGA 60.037 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 2714 0.253113 TCATCACATCCCCCACCTCA 60.253 55.000 0.00 0.0 0.00 3.86 R
1963 3184 0.618458 TCTCGGGGAACAAATCTGGG 59.382 55.000 0.00 0.0 0.00 4.45 R
2654 3939 2.441750 AGGAACTAGTGCAACCTTTCCA 59.558 45.455 16.62 0.0 40.27 3.53 R
3087 4375 2.768527 TGGATGAGGAGTGATGGACTTC 59.231 50.000 0.00 0.0 33.83 3.01 R
4182 5485 2.035321 TCGTTGCCCTTTTGGACAAATC 59.965 45.455 0.00 0.0 44.07 2.17 R
5732 7050 0.033504 ACTGGACACGAAGCACGAAT 59.966 50.000 10.05 0.0 45.77 3.34 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
173 176 0.896923 TTGGCATGGGAAATGAGTGC 59.103 50.000 0.00 0.00 35.17 4.40
232 235 1.668294 CAAGGCGTCACTGAGGAGT 59.332 57.895 2.83 0.00 0.00 3.85
446 451 5.739752 AGGTGTACCTAAAAACGTTTCAC 57.260 39.130 15.01 14.90 46.48 3.18
455 460 8.161699 ACCTAAAAACGTTTCACATGTCTTAT 57.838 30.769 15.01 0.00 0.00 1.73
457 462 9.113876 CCTAAAAACGTTTCACATGTCTTATTC 57.886 33.333 15.01 0.00 0.00 1.75
461 466 9.581099 AAAACGTTTCACATGTCTTATTCTTTT 57.419 25.926 15.01 0.00 0.00 2.27
543 550 2.561569 CGAAATACTTGTAGCTGGGGG 58.438 52.381 0.00 0.00 0.00 5.40
685 1772 6.060028 TGAGTACAAAAGAATGTTCAGTGC 57.940 37.500 0.00 0.00 34.75 4.40
783 1871 8.795842 AATTAAAACCAATGCACATCATGAAT 57.204 26.923 0.00 0.00 35.13 2.57
831 1919 7.437862 TGAAATCTTTTCAAAACCGATGAAAGG 59.562 33.333 0.37 5.16 44.83 3.11
867 2035 1.278637 CGTTCGTCACAACAAGCCC 59.721 57.895 0.00 0.00 0.00 5.19
928 2127 3.361281 AGAGAAACGGATAAAACCCCC 57.639 47.619 0.00 0.00 0.00 5.40
1441 2658 4.562552 CCCCATTAACGGCATTCAGTTTTT 60.563 41.667 0.00 0.00 0.00 1.94
1447 2664 7.861176 TTAACGGCATTCAGTTTTTACAATC 57.139 32.000 0.00 0.00 0.00 2.67
1493 2714 0.981183 TGTAGGAATGGAGCAACCGT 59.019 50.000 0.00 0.00 42.61 4.83
1588 2809 1.005394 GCTTGGAGGGTTCGTCGAA 60.005 57.895 2.90 2.90 0.00 3.71
1595 2816 0.538977 AGGGTTCGTCGAAGTGGAGA 60.539 55.000 8.18 0.00 0.00 3.71
1601 2822 2.366533 TCGTCGAAGTGGAGAAGCTAT 58.633 47.619 0.00 0.00 0.00 2.97
1668 2889 0.179012 CCCCACGGTTACTGTTGGTT 60.179 55.000 12.58 0.00 0.00 3.67
1677 2898 1.956297 TACTGTTGGTTTGACACCCG 58.044 50.000 0.00 0.00 46.68 5.28
1812 3033 1.094785 ACGGGCAATTTCAAGGATCG 58.905 50.000 0.00 0.00 0.00 3.69
1870 3091 8.570068 TTTTTGTCCTAGTCATTTACCATACC 57.430 34.615 0.00 0.00 0.00 2.73
2045 3266 6.939132 TCCAAAATACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 0.00 1.52
2047 3268 6.543100 TCCAAAATACTTGTCGTGGTTTTAGT 59.457 34.615 0.00 0.00 0.00 2.24
2053 3274 6.256912 ACTTGTCGTGGTTTTAGTTCAAAA 57.743 33.333 0.00 0.00 33.66 2.44
2054 3275 6.319399 ACTTGTCGTGGTTTTAGTTCAAAAG 58.681 36.000 0.00 0.00 36.79 2.27
2055 3276 5.883503 TGTCGTGGTTTTAGTTCAAAAGT 57.116 34.783 0.00 0.00 36.79 2.66
2057 3278 7.375106 TGTCGTGGTTTTAGTTCAAAAGTAA 57.625 32.000 0.00 0.00 36.79 2.24
2067 3336 8.859517 TTTAGTTCAAAAGTAATTTGGAACGG 57.140 30.769 23.26 0.00 46.85 4.44
2142 3411 2.275089 CATGGGGCATTCACGGGA 59.725 61.111 0.00 0.00 0.00 5.14
2160 3429 7.846066 TCACGGGAATTCCATTTTATTTCAAT 58.154 30.769 25.67 0.00 37.91 2.57
2214 3485 2.813474 CGGAATTCGTCGCAGCCA 60.813 61.111 0.00 0.00 0.00 4.75
2333 3616 8.656849 GTTTGACTATCACTATGAAAACATCGT 58.343 33.333 0.00 0.00 0.00 3.73
2410 3693 8.776470 CATTAATTGATTTTTGAGTTTGGTGCT 58.224 29.630 0.00 0.00 0.00 4.40
2431 3714 7.244192 GTGCTGCTACTTTCTTATTTTAGGTG 58.756 38.462 0.00 0.00 0.00 4.00
2607 3892 4.700213 TGCCCTTTTCTGCTATAAGAACAC 59.300 41.667 0.00 0.00 35.92 3.32
2654 3939 5.066505 GCAGGTTCGTTTAGAATCAATGGAT 59.933 40.000 0.00 0.00 42.37 3.41
2722 4007 8.506196 AGCCCTGAGGTATTACATTTTCTATA 57.494 34.615 0.00 0.00 34.57 1.31
2723 4008 9.117223 AGCCCTGAGGTATTACATTTTCTATAT 57.883 33.333 0.00 0.00 34.57 0.86
2794 4081 1.069022 CACAGCAAGTCCCACATTTCG 60.069 52.381 0.00 0.00 0.00 3.46
2845 4133 2.083774 TGCTGAATTCCTTAAGCACCG 58.916 47.619 12.73 0.00 42.83 4.94
2851 4139 4.515191 TGAATTCCTTAAGCACCGCATATC 59.485 41.667 2.27 0.00 0.00 1.63
3087 4375 9.667107 TTTCTCCATACCAAGTTAGTTATCAAG 57.333 33.333 0.00 0.00 0.00 3.02
3098 4386 8.660373 CAAGTTAGTTATCAAGAAGTCCATCAC 58.340 37.037 0.00 0.00 0.00 3.06
3116 4404 4.487714 TCACTCCTCATCCATTGGTAAC 57.512 45.455 1.86 0.00 0.00 2.50
3119 4407 3.209410 CTCCTCATCCATTGGTAACTGC 58.791 50.000 1.86 0.00 37.61 4.40
3180 4468 1.669795 GCTTGTTTTCGGAAGGCCATG 60.670 52.381 5.01 0.00 0.00 3.66
3267 4555 5.897377 ATATTGTGCACCCTTTTCTGTAC 57.103 39.130 15.69 0.00 0.00 2.90
3378 4674 6.529220 AGAGTATACTTGATTTCAGATGGGC 58.471 40.000 6.88 0.00 0.00 5.36
3379 4675 5.625150 AGTATACTTGATTTCAGATGGGCC 58.375 41.667 0.00 0.00 0.00 5.80
3380 4676 2.905415 ACTTGATTTCAGATGGGCCA 57.095 45.000 9.61 9.61 0.00 5.36
3976 5277 4.155826 GTCGATGGTGTTGATCCATTTGAA 59.844 41.667 0.00 0.00 44.52 2.69
3989 5290 3.256383 TCCATTTGAATGTCTTGGTGCTG 59.744 43.478 3.30 0.00 34.60 4.41
4002 5303 0.037326 GGTGCTGACATCCTCGTTGA 60.037 55.000 0.00 0.00 0.00 3.18
4037 5338 8.390921 TCTCTCTCCCAATAAAATGGTAAAGTT 58.609 33.333 0.00 0.00 38.91 2.66
4133 5435 4.575885 TGGGTAATGGAAGAGAAAACTCG 58.424 43.478 0.00 0.00 0.00 4.18
4378 5683 2.167075 GCATGTTCTCTGGGGAAAATGG 59.833 50.000 13.38 0.00 39.83 3.16
4643 5948 5.863935 GGCACCAATTATTTTCAGAACTGTC 59.136 40.000 1.73 0.00 0.00 3.51
4850 6155 4.277476 CCTAGAGGTGAGATCTTGTCTGT 58.723 47.826 0.00 0.00 37.29 3.41
4893 6199 2.806945 TCCCCATGTGATTTCAGACC 57.193 50.000 0.00 0.00 0.00 3.85
4895 6201 1.340017 CCCCATGTGATTTCAGACCGT 60.340 52.381 0.00 0.00 0.00 4.83
4910 6216 2.769663 AGACCGTGCCATTCCTGTTATA 59.230 45.455 0.00 0.00 0.00 0.98
4913 6219 3.054655 ACCGTGCCATTCCTGTTATAAGT 60.055 43.478 0.00 0.00 0.00 2.24
4951 6258 6.325919 TCATTCGGCACCAATATTATTTCC 57.674 37.500 0.00 0.00 0.00 3.13
4954 6261 6.385649 TTCGGCACCAATATTATTTCCTTC 57.614 37.500 0.00 0.00 0.00 3.46
4976 6283 9.364989 CCTTCAAATGTCAGTTTTTAAGTCAAA 57.635 29.630 0.00 0.00 0.00 2.69
5017 6324 0.832135 AGGGTTCTGCGGAAGTCTCA 60.832 55.000 8.61 0.00 31.46 3.27
5056 6363 4.003648 CCAACAGGACCTTGCTACTAAAG 58.996 47.826 0.00 0.00 0.00 1.85
5153 6460 1.901085 AGCCTAGCTGGTTCCTTCG 59.099 57.895 0.00 0.00 37.57 3.79
5157 6464 0.820871 CTAGCTGGTTCCTTCGCTCT 59.179 55.000 0.00 0.00 34.14 4.09
5160 6467 1.004560 CTGGTTCCTTCGCTCTGCA 60.005 57.895 0.00 0.00 0.00 4.41
5168 6475 1.690283 CTTCGCTCTGCACGTCATGG 61.690 60.000 0.00 0.00 0.00 3.66
5184 6491 0.755327 ATGGGGTTATTCCTTGGCGC 60.755 55.000 0.00 0.00 36.25 6.53
5206 6513 3.118408 CCTCACATTTCCTCCCGTTGATA 60.118 47.826 0.00 0.00 0.00 2.15
5292 6599 6.875726 TGTCACTATTCAATGGTCTCAGAAAG 59.124 38.462 0.00 0.00 0.00 2.62
5320 6627 9.507329 TCTTCAAATAAACAGATGGGCTATATC 57.493 33.333 0.00 0.00 0.00 1.63
5426 6741 3.176661 TCGTCGTCGAATGCCGTA 58.823 55.556 1.37 0.00 43.34 4.02
5427 6742 1.723273 TCGTCGTCGAATGCCGTAT 59.277 52.632 1.37 0.00 43.34 3.06
5456 6771 2.957680 TGAACACCACATGATGCAGTTT 59.042 40.909 0.00 0.00 0.00 2.66
5467 6782 2.229792 GATGCAGTTTCAGTTCCACCA 58.770 47.619 0.00 0.00 0.00 4.17
5471 6786 0.923358 AGTTTCAGTTCCACCACCCA 59.077 50.000 0.00 0.00 0.00 4.51
5472 6787 1.286553 AGTTTCAGTTCCACCACCCAA 59.713 47.619 0.00 0.00 0.00 4.12
5497 6812 0.536006 GGTGAGCTCAGGTGTTTGCT 60.536 55.000 18.89 0.00 38.59 3.91
5539 6857 0.813210 CAGGCCAAGATCTTCGGAGC 60.813 60.000 21.24 14.66 0.00 4.70
5555 6873 2.860735 CGGAGCTGCAACTGAATAGTAC 59.139 50.000 5.91 0.00 35.69 2.73
5556 6874 2.860735 GGAGCTGCAACTGAATAGTACG 59.139 50.000 0.00 0.00 35.69 3.67
5557 6875 3.512680 GAGCTGCAACTGAATAGTACGT 58.487 45.455 1.02 0.00 35.69 3.57
5558 6876 4.439700 GGAGCTGCAACTGAATAGTACGTA 60.440 45.833 0.00 0.00 35.69 3.57
5561 6879 4.360563 CTGCAACTGAATAGTACGTAGGG 58.639 47.826 0.00 0.00 35.69 3.53
5568 6886 7.237209 ACTGAATAGTACGTAGGGAAAACTT 57.763 36.000 0.00 0.00 34.74 2.66
5569 6887 8.353423 ACTGAATAGTACGTAGGGAAAACTTA 57.647 34.615 0.00 0.00 34.74 2.24
5570 6888 8.465201 ACTGAATAGTACGTAGGGAAAACTTAG 58.535 37.037 0.00 0.00 34.74 2.18
5576 6894 7.157347 AGTACGTAGGGAAAACTTAGAAAAGG 58.843 38.462 0.00 0.00 37.01 3.11
5609 6927 2.094894 CCAAGAATAGCTGCGAGTTGTG 59.905 50.000 0.00 0.00 0.00 3.33
5682 7000 4.346129 CAGCGCATCTGTTTATCTTTTCC 58.654 43.478 11.47 0.00 38.02 3.13
5683 7001 4.095483 CAGCGCATCTGTTTATCTTTTCCT 59.905 41.667 11.47 0.00 38.02 3.36
5684 7002 5.294306 CAGCGCATCTGTTTATCTTTTCCTA 59.706 40.000 11.47 0.00 38.02 2.94
5685 7003 5.294552 AGCGCATCTGTTTATCTTTTCCTAC 59.705 40.000 11.47 0.00 0.00 3.18
5686 7004 5.064707 GCGCATCTGTTTATCTTTTCCTACA 59.935 40.000 0.30 0.00 0.00 2.74
5687 7005 6.478588 CGCATCTGTTTATCTTTTCCTACAC 58.521 40.000 0.00 0.00 0.00 2.90
5688 7006 6.092122 CGCATCTGTTTATCTTTTCCTACACA 59.908 38.462 0.00 0.00 0.00 3.72
5689 7007 7.467623 GCATCTGTTTATCTTTTCCTACACAG 58.532 38.462 0.00 0.00 33.19 3.66
5690 7008 7.334421 GCATCTGTTTATCTTTTCCTACACAGA 59.666 37.037 0.00 0.00 42.58 3.41
5691 7009 8.877779 CATCTGTTTATCTTTTCCTACACAGAG 58.122 37.037 0.00 0.00 41.90 3.35
5692 7010 6.874134 TCTGTTTATCTTTTCCTACACAGAGC 59.126 38.462 0.00 0.00 35.59 4.09
5693 7011 6.769512 TGTTTATCTTTTCCTACACAGAGCT 58.230 36.000 0.00 0.00 0.00 4.09
5694 7012 6.874134 TGTTTATCTTTTCCTACACAGAGCTC 59.126 38.462 5.27 5.27 0.00 4.09
5695 7013 6.859112 TTATCTTTTCCTACACAGAGCTCT 57.141 37.500 11.45 11.45 0.00 4.09
5696 7014 5.753721 ATCTTTTCCTACACAGAGCTCTT 57.246 39.130 15.27 1.93 0.00 2.85
5697 7015 5.552870 TCTTTTCCTACACAGAGCTCTTT 57.447 39.130 15.27 4.62 0.00 2.52
5698 7016 5.930135 TCTTTTCCTACACAGAGCTCTTTT 58.070 37.500 15.27 0.21 0.00 2.27
5699 7017 6.357367 TCTTTTCCTACACAGAGCTCTTTTT 58.643 36.000 15.27 3.21 0.00 1.94
5700 7018 6.260936 TCTTTTCCTACACAGAGCTCTTTTTG 59.739 38.462 15.27 13.89 0.00 2.44
5701 7019 4.008074 TCCTACACAGAGCTCTTTTTGG 57.992 45.455 15.27 12.72 0.00 3.28
5702 7020 3.077359 CCTACACAGAGCTCTTTTTGGG 58.923 50.000 15.27 8.89 0.00 4.12
5703 7021 1.986882 ACACAGAGCTCTTTTTGGGG 58.013 50.000 15.27 6.06 0.00 4.96
5704 7022 1.215423 ACACAGAGCTCTTTTTGGGGT 59.785 47.619 15.27 6.81 0.00 4.95
5705 7023 1.882623 CACAGAGCTCTTTTTGGGGTC 59.117 52.381 15.27 0.00 0.00 4.46
5706 7024 1.160137 CAGAGCTCTTTTTGGGGTCG 58.840 55.000 15.27 0.00 33.42 4.79
5707 7025 0.606673 AGAGCTCTTTTTGGGGTCGC 60.607 55.000 11.45 0.00 33.42 5.19
5708 7026 1.587043 GAGCTCTTTTTGGGGTCGCC 61.587 60.000 6.43 0.00 0.00 5.54
5709 7027 1.603739 GCTCTTTTTGGGGTCGCCT 60.604 57.895 7.55 0.00 0.00 5.52
5710 7028 1.866853 GCTCTTTTTGGGGTCGCCTG 61.867 60.000 7.55 0.00 0.00 4.85
5711 7029 0.537371 CTCTTTTTGGGGTCGCCTGT 60.537 55.000 7.55 0.00 0.00 4.00
5712 7030 0.766131 TCTTTTTGGGGTCGCCTGTA 59.234 50.000 7.55 0.00 0.00 2.74
5713 7031 0.879090 CTTTTTGGGGTCGCCTGTAC 59.121 55.000 7.55 0.00 0.00 2.90
5714 7032 0.475044 TTTTTGGGGTCGCCTGTACT 59.525 50.000 7.55 0.00 0.00 2.73
5715 7033 0.035739 TTTTGGGGTCGCCTGTACTC 59.964 55.000 7.55 0.00 0.00 2.59
5716 7034 1.833787 TTTGGGGTCGCCTGTACTCC 61.834 60.000 7.55 0.00 38.05 3.85
5717 7035 3.468140 GGGGTCGCCTGTACTCCC 61.468 72.222 0.00 0.00 37.59 4.30
5718 7036 2.682494 GGGTCGCCTGTACTCCCA 60.682 66.667 0.00 0.00 38.15 4.37
5719 7037 2.288025 GGGTCGCCTGTACTCCCAA 61.288 63.158 0.00 0.00 38.15 4.12
5720 7038 1.675219 GGTCGCCTGTACTCCCAAA 59.325 57.895 0.00 0.00 0.00 3.28
5721 7039 0.391263 GGTCGCCTGTACTCCCAAAG 60.391 60.000 0.00 0.00 0.00 2.77
5722 7040 0.606604 GTCGCCTGTACTCCCAAAGA 59.393 55.000 0.00 0.00 0.00 2.52
5723 7041 0.606604 TCGCCTGTACTCCCAAAGAC 59.393 55.000 0.00 0.00 0.00 3.01
5724 7042 0.736325 CGCCTGTACTCCCAAAGACG 60.736 60.000 0.00 0.00 0.00 4.18
5725 7043 1.019805 GCCTGTACTCCCAAAGACGC 61.020 60.000 0.00 0.00 0.00 5.19
5726 7044 0.391263 CCTGTACTCCCAAAGACGCC 60.391 60.000 0.00 0.00 0.00 5.68
5727 7045 0.320374 CTGTACTCCCAAAGACGCCA 59.680 55.000 0.00 0.00 0.00 5.69
5728 7046 0.320374 TGTACTCCCAAAGACGCCAG 59.680 55.000 0.00 0.00 0.00 4.85
5729 7047 0.606604 GTACTCCCAAAGACGCCAGA 59.393 55.000 0.00 0.00 0.00 3.86
5730 7048 0.895530 TACTCCCAAAGACGCCAGAG 59.104 55.000 0.00 0.00 0.00 3.35
5731 7049 1.743252 CTCCCAAAGACGCCAGAGC 60.743 63.158 0.00 0.00 0.00 4.09
5732 7050 2.032528 CCCAAAGACGCCAGAGCA 59.967 61.111 0.00 0.00 39.83 4.26
5733 7051 1.377725 CCCAAAGACGCCAGAGCAT 60.378 57.895 0.00 0.00 39.83 3.79
5734 7052 0.962356 CCCAAAGACGCCAGAGCATT 60.962 55.000 0.00 0.00 39.83 3.56
5735 7053 0.449388 CCAAAGACGCCAGAGCATTC 59.551 55.000 0.00 0.00 39.83 2.67
5736 7054 0.095935 CAAAGACGCCAGAGCATTCG 59.904 55.000 0.00 0.00 39.83 3.34
5737 7055 0.320771 AAAGACGCCAGAGCATTCGT 60.321 50.000 0.00 0.00 39.83 3.85
5738 7056 1.016130 AAGACGCCAGAGCATTCGTG 61.016 55.000 0.00 0.00 39.83 4.35
5739 7057 3.088500 GACGCCAGAGCATTCGTGC 62.089 63.158 0.00 0.00 39.83 5.34
5741 7059 2.393768 CGCCAGAGCATTCGTGCTT 61.394 57.895 4.24 0.00 46.36 3.91
5742 7060 1.427020 GCCAGAGCATTCGTGCTTC 59.573 57.895 4.24 0.00 46.36 3.86
5743 7061 1.712081 CCAGAGCATTCGTGCTTCG 59.288 57.895 4.24 0.00 46.36 3.79
5744 7062 1.016130 CCAGAGCATTCGTGCTTCGT 61.016 55.000 4.24 0.00 46.36 3.85
5745 7063 0.094216 CAGAGCATTCGTGCTTCGTG 59.906 55.000 4.24 0.09 46.36 4.35
5746 7064 0.319900 AGAGCATTCGTGCTTCGTGT 60.320 50.000 4.24 0.00 46.36 4.49
5747 7065 0.093705 GAGCATTCGTGCTTCGTGTC 59.906 55.000 4.24 0.00 46.36 3.67
5748 7066 1.132640 GCATTCGTGCTTCGTGTCC 59.867 57.895 0.00 0.00 40.80 4.02
5749 7067 1.565156 GCATTCGTGCTTCGTGTCCA 61.565 55.000 0.00 0.00 40.80 4.02
5750 7068 0.439985 CATTCGTGCTTCGTGTCCAG 59.560 55.000 2.39 0.00 40.80 3.86
5751 7069 0.033504 ATTCGTGCTTCGTGTCCAGT 59.966 50.000 2.39 0.00 40.80 4.00
5752 7070 0.179094 TTCGTGCTTCGTGTCCAGTT 60.179 50.000 2.39 0.00 40.80 3.16
5753 7071 0.596600 TCGTGCTTCGTGTCCAGTTC 60.597 55.000 2.39 0.00 40.80 3.01
5754 7072 0.597637 CGTGCTTCGTGTCCAGTTCT 60.598 55.000 0.00 0.00 34.52 3.01
5755 7073 1.335597 CGTGCTTCGTGTCCAGTTCTA 60.336 52.381 0.00 0.00 34.52 2.10
5756 7074 2.059541 GTGCTTCGTGTCCAGTTCTAC 58.940 52.381 0.00 0.00 0.00 2.59
5757 7075 1.000506 TGCTTCGTGTCCAGTTCTACC 59.999 52.381 0.00 0.00 0.00 3.18
5758 7076 1.978542 CTTCGTGTCCAGTTCTACCG 58.021 55.000 0.00 0.00 0.00 4.02
5759 7077 0.599558 TTCGTGTCCAGTTCTACCGG 59.400 55.000 0.00 0.00 0.00 5.28
5760 7078 0.538057 TCGTGTCCAGTTCTACCGGT 60.538 55.000 13.98 13.98 0.00 5.28
5761 7079 0.388134 CGTGTCCAGTTCTACCGGTG 60.388 60.000 19.93 7.59 0.00 4.94
5762 7080 0.669625 GTGTCCAGTTCTACCGGTGC 60.670 60.000 19.93 4.69 0.00 5.01
5763 7081 1.116536 TGTCCAGTTCTACCGGTGCA 61.117 55.000 19.93 0.00 0.00 4.57
5764 7082 0.389948 GTCCAGTTCTACCGGTGCAG 60.390 60.000 19.93 7.88 0.00 4.41
5765 7083 1.741770 CCAGTTCTACCGGTGCAGC 60.742 63.158 19.93 5.64 0.00 5.25
5766 7084 1.293498 CAGTTCTACCGGTGCAGCT 59.707 57.895 19.93 7.81 0.00 4.24
5767 7085 0.737715 CAGTTCTACCGGTGCAGCTC 60.738 60.000 19.93 4.07 0.00 4.09
5768 7086 1.805945 GTTCTACCGGTGCAGCTCG 60.806 63.158 19.93 6.32 0.00 5.03
5778 7096 4.530857 GCAGCTCGGTGGCGGTAT 62.531 66.667 0.00 0.00 37.29 2.73
5779 7097 2.186903 CAGCTCGGTGGCGGTATT 59.813 61.111 0.00 0.00 37.29 1.89
5780 7098 2.173669 CAGCTCGGTGGCGGTATTG 61.174 63.158 0.00 0.00 37.29 1.90
5781 7099 2.125269 GCTCGGTGGCGGTATTGT 60.125 61.111 0.00 0.00 0.00 2.71
5782 7100 2.461110 GCTCGGTGGCGGTATTGTG 61.461 63.158 0.00 0.00 0.00 3.33
5783 7101 1.079405 CTCGGTGGCGGTATTGTGT 60.079 57.895 0.00 0.00 0.00 3.72
5784 7102 1.358725 CTCGGTGGCGGTATTGTGTG 61.359 60.000 0.00 0.00 0.00 3.82
5785 7103 1.374885 CGGTGGCGGTATTGTGTGA 60.375 57.895 0.00 0.00 0.00 3.58
5786 7104 1.632046 CGGTGGCGGTATTGTGTGAC 61.632 60.000 0.00 0.00 0.00 3.67
5787 7105 0.321298 GGTGGCGGTATTGTGTGACT 60.321 55.000 0.00 0.00 0.00 3.41
5788 7106 0.796312 GTGGCGGTATTGTGTGACTG 59.204 55.000 0.00 0.00 0.00 3.51
5789 7107 0.394938 TGGCGGTATTGTGTGACTGT 59.605 50.000 0.00 0.00 0.00 3.55
5851 7172 3.016971 CCATCTGGGGGTGAGCCA 61.017 66.667 1.97 0.00 36.17 4.75
5923 7246 2.328099 GCTCCCAGGCACGTTCAAG 61.328 63.158 0.00 0.00 0.00 3.02
6018 7343 8.766994 AACTTGGGCATATATTAGACATGTTT 57.233 30.769 0.00 0.00 0.00 2.83
6037 7362 8.031864 ACATGTTTGCGGATTTTCATTACATAA 58.968 29.630 0.00 0.00 0.00 1.90
6128 7456 2.095282 CGTCGTCGTCATCGTCGT 59.905 61.111 7.05 0.00 45.27 4.34
6135 7463 1.662629 GTCGTCATCGTCGTCCTTCTA 59.337 52.381 0.00 0.00 38.33 2.10
6147 7475 1.544691 GTCCTTCTACTCCTTGACGCA 59.455 52.381 0.00 0.00 0.00 5.24
6195 7523 2.897350 GCTATGGCGACTGGTGGC 60.897 66.667 0.00 0.00 0.00 5.01
6196 7524 2.586079 CTATGGCGACTGGTGGCG 60.586 66.667 0.00 0.00 35.01 5.69
6197 7525 4.155733 TATGGCGACTGGTGGCGG 62.156 66.667 0.00 0.00 35.01 6.13
6267 7601 4.796231 CCTCCTTCGTCGTGGCCG 62.796 72.222 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 6.268387 ACTCATGATGGAGTTGTTGGATTTTT 59.732 34.615 0.00 0.00 45.59 1.94
88 90 4.085619 GCAAGTGCACAAAATTTAGTCGTG 60.086 41.667 21.04 0.00 41.59 4.35
90 92 4.613570 GCAAGTGCACAAAATTTAGTCG 57.386 40.909 21.04 0.00 41.59 4.18
224 227 3.691575 TCACTAACCTCAGACTCCTCAG 58.308 50.000 0.00 0.00 0.00 3.35
232 235 5.237996 CGTATAACCGATCACTAACCTCAGA 59.762 44.000 0.00 0.00 0.00 3.27
520 527 3.133362 CCCCAGCTACAAGTATTTCGGTA 59.867 47.826 0.00 0.00 0.00 4.02
673 1760 3.441163 TCCGTATACGCACTGAACATTC 58.559 45.455 19.86 0.00 38.18 2.67
685 1772 5.060816 ACACGTTGTACATTTTCCGTATACG 59.939 40.000 18.40 18.40 36.57 3.06
831 1919 4.317069 CGAACGGTTTTGCAAAGATGAAAC 60.317 41.667 12.41 6.43 0.00 2.78
867 2035 0.041312 CGTTTTCGTGGGCTTGACAG 60.041 55.000 0.00 0.00 38.65 3.51
999 2198 2.203625 GTGGTGGTGGTGGCCATT 60.204 61.111 9.72 0.00 41.08 3.16
1077 2282 2.367512 GAGGAGGAGGGGCATGGT 60.368 66.667 0.00 0.00 0.00 3.55
1080 2285 2.040043 CTGGAGGAGGAGGGGCAT 60.040 66.667 0.00 0.00 0.00 4.40
1085 2290 3.151022 GGACGCTGGAGGAGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
1441 2658 5.368145 AGCACAAGAAAGACAGTGATTGTA 58.632 37.500 0.00 0.00 41.05 2.41
1447 2664 2.033407 CACGAGCACAAGAAAGACAGTG 60.033 50.000 0.00 0.00 35.19 3.66
1493 2714 0.253113 TCATCACATCCCCCACCTCA 60.253 55.000 0.00 0.00 0.00 3.86
1499 2720 1.216990 ACCTCTTCATCACATCCCCC 58.783 55.000 0.00 0.00 0.00 5.40
1588 2809 2.226912 GCGTCGATATAGCTTCTCCACT 59.773 50.000 0.00 0.00 0.00 4.00
1595 2816 2.069273 GGCAATGCGTCGATATAGCTT 58.931 47.619 0.00 0.00 0.00 3.74
1601 2822 0.319555 GCCTAGGCAATGCGTCGATA 60.320 55.000 29.33 0.00 41.49 2.92
1668 2889 2.094906 CGTCTTATCACTCGGGTGTCAA 60.095 50.000 16.53 9.61 43.41 3.18
1677 2898 5.694910 TCAAAAACCACTCGTCTTATCACTC 59.305 40.000 0.00 0.00 0.00 3.51
1812 3033 2.684001 TACGTCCCAATCACATCACC 57.316 50.000 0.00 0.00 0.00 4.02
1849 3070 6.442564 ACTTGGTATGGTAAATGACTAGGACA 59.557 38.462 0.00 0.00 0.00 4.02
1870 3091 4.734695 GCACCAAACAGAGGAGAAAACTTG 60.735 45.833 0.00 0.00 0.00 3.16
1963 3184 0.618458 TCTCGGGGAACAAATCTGGG 59.382 55.000 0.00 0.00 0.00 4.45
2045 3266 6.544564 TCTCCGTTCCAAATTACTTTTGAACT 59.455 34.615 15.78 0.00 46.36 3.01
2047 3268 6.768861 TCTCTCCGTTCCAAATTACTTTTGAA 59.231 34.615 0.00 0.00 46.36 2.69
2053 3274 5.715753 ACTACTCTCTCCGTTCCAAATTACT 59.284 40.000 0.00 0.00 0.00 2.24
2054 3275 5.963594 ACTACTCTCTCCGTTCCAAATTAC 58.036 41.667 0.00 0.00 0.00 1.89
2055 3276 6.600882 AACTACTCTCTCCGTTCCAAATTA 57.399 37.500 0.00 0.00 0.00 1.40
2057 3278 5.485209 AAACTACTCTCTCCGTTCCAAAT 57.515 39.130 0.00 0.00 0.00 2.32
2067 3336 9.646427 ATGTTCATCAGTTTAAACTACTCTCTC 57.354 33.333 20.15 9.28 37.08 3.20
2214 3485 4.263727 TGTGTATAGAAATTGGGTGGCACT 60.264 41.667 18.45 0.00 0.00 4.40
2257 3528 6.037172 AGTCATGCTGTATTCGGAACATTTAC 59.963 38.462 0.00 0.00 0.00 2.01
2387 3670 6.202570 GCAGCACCAAACTCAAAAATCAATTA 59.797 34.615 0.00 0.00 0.00 1.40
2410 3693 9.781633 TTGTACACCTAAAATAAGAAAGTAGCA 57.218 29.630 0.00 0.00 0.00 3.49
2431 3714 6.879458 ACCATCTAAAGTTCTCCATGTTGTAC 59.121 38.462 0.00 0.00 0.00 2.90
2489 3772 7.518161 TCATATTTTAGCTTCACGACACTTTG 58.482 34.615 0.00 0.00 0.00 2.77
2497 3780 6.197096 GGTTTGCATCATATTTTAGCTTCACG 59.803 38.462 0.00 0.00 0.00 4.35
2498 3781 7.260603 AGGTTTGCATCATATTTTAGCTTCAC 58.739 34.615 0.00 0.00 0.00 3.18
2586 3871 4.201822 GCGTGTTCTTATAGCAGAAAAGGG 60.202 45.833 0.00 0.00 34.50 3.95
2654 3939 2.441750 AGGAACTAGTGCAACCTTTCCA 59.558 45.455 16.62 0.00 40.27 3.53
2794 4081 7.707774 TGCTAAAAATTCTTTGTAAACAGGC 57.292 32.000 0.00 0.00 0.00 4.85
2845 4133 3.632145 AGGTGGAAAATTGTCCGATATGC 59.368 43.478 10.19 0.00 40.96 3.14
2851 4139 4.055360 GGAAAAAGGTGGAAAATTGTCCG 58.945 43.478 10.19 0.00 40.96 4.79
3087 4375 2.768527 TGGATGAGGAGTGATGGACTTC 59.231 50.000 0.00 0.00 33.83 3.01
3098 4386 3.209410 GCAGTTACCAATGGATGAGGAG 58.791 50.000 6.16 0.00 0.00 3.69
3180 4468 5.596845 TGTAAAACCAAAAGAAGATGCCAC 58.403 37.500 0.00 0.00 0.00 5.01
3267 4555 6.537301 TCGTACTTTAAATGCCAGTCTATTGG 59.463 38.462 0.00 0.00 41.35 3.16
3378 4674 7.535139 CCACAATAAAATAAGTACAGTGGTGG 58.465 38.462 0.00 0.00 39.21 4.61
3379 4675 7.027161 GCCACAATAAAATAAGTACAGTGGTG 58.973 38.462 0.00 0.00 44.30 4.17
3380 4676 6.152154 GGCCACAATAAAATAAGTACAGTGGT 59.848 38.462 0.00 0.00 44.30 4.16
3783 5080 6.386635 AGAATATGCCAACAAATACCCCAATT 59.613 34.615 0.00 0.00 0.00 2.32
3785 5082 5.276440 AGAATATGCCAACAAATACCCCAA 58.724 37.500 0.00 0.00 0.00 4.12
3845 5142 8.068977 TCATTGCACAAACAAAATGCTATTTTC 58.931 29.630 0.00 0.00 40.13 2.29
3852 5149 4.799419 ACTCATTGCACAAACAAAATGC 57.201 36.364 0.00 0.00 39.88 3.56
3989 5290 3.448686 ACATCGAATCAACGAGGATGTC 58.551 45.455 9.49 0.00 42.86 3.06
4002 5303 6.485830 TTATTGGGAGAGAGAACATCGAAT 57.514 37.500 0.00 0.00 0.00 3.34
4037 5338 2.045561 TTTCCAAAACGTGAGCAGGA 57.954 45.000 0.00 0.00 0.00 3.86
4182 5485 2.035321 TCGTTGCCCTTTTGGACAAATC 59.965 45.455 0.00 0.00 44.07 2.17
4378 5683 2.673368 GCACATACTACTGAACTGGTGC 59.327 50.000 0.00 0.00 42.73 5.01
4460 5765 4.563140 TCCACCCTTGTCAATACTAACC 57.437 45.455 0.00 0.00 0.00 2.85
4464 5769 3.200825 CCAGATCCACCCTTGTCAATACT 59.799 47.826 0.00 0.00 0.00 2.12
4643 5948 5.300752 CACCCTTGTTATAGCTGTATGGAG 58.699 45.833 0.00 0.00 0.00 3.86
4678 5983 8.972458 TCTGCACAAATAAGTTATATAGGCAA 57.028 30.769 11.13 3.81 0.00 4.52
4888 6193 0.606401 AACAGGAATGGCACGGTCTG 60.606 55.000 0.00 0.00 0.00 3.51
4893 6199 5.583061 TGTAACTTATAACAGGAATGGCACG 59.417 40.000 0.00 0.00 0.00 5.34
4895 6201 6.477253 TGTGTAACTTATAACAGGAATGGCA 58.523 36.000 0.00 0.00 38.04 4.92
4910 6216 7.915397 GCCGAATGATTATGATTTGTGTAACTT 59.085 33.333 0.00 0.00 38.04 2.66
4913 6219 7.192913 GTGCCGAATGATTATGATTTGTGTAA 58.807 34.615 0.00 0.00 0.00 2.41
4976 6283 3.561143 TGGCGCCCTGAAATATTATTGT 58.439 40.909 26.77 0.00 0.00 2.71
5017 6324 3.577848 TGTTGGCCTGCTTTGTATTGATT 59.422 39.130 3.32 0.00 0.00 2.57
5056 6363 2.203401 CACAGATCTCTTGCTAGCTGC 58.797 52.381 17.23 0.00 43.25 5.25
5148 6455 1.446792 ATGACGTGCAGAGCGAAGG 60.447 57.895 0.00 0.00 0.00 3.46
5153 6460 2.821366 CCCCATGACGTGCAGAGC 60.821 66.667 0.00 0.00 0.00 4.09
5157 6464 1.680555 GGAATAACCCCATGACGTGCA 60.681 52.381 0.00 0.00 0.00 4.57
5160 6467 2.356741 CCAAGGAATAACCCCATGACGT 60.357 50.000 0.00 0.00 40.05 4.34
5168 6475 1.076995 AGGCGCCAAGGAATAACCC 60.077 57.895 31.54 0.00 40.05 4.11
5184 6491 1.003118 TCAACGGGAGGAAATGTGAGG 59.997 52.381 0.00 0.00 0.00 3.86
5292 6599 4.400567 AGCCCATCTGTTTATTTGAAGAGC 59.599 41.667 0.00 0.00 0.00 4.09
5320 6627 2.373224 GAAATCTTCAGGGGGCAGAAG 58.627 52.381 0.00 0.00 41.95 2.85
5420 6735 3.003897 GGTGTTCAGTGAAAAATACGGCA 59.996 43.478 7.25 0.00 0.00 5.69
5421 6736 3.003897 TGGTGTTCAGTGAAAAATACGGC 59.996 43.478 7.25 0.00 0.00 5.68
5422 6737 4.035792 TGTGGTGTTCAGTGAAAAATACGG 59.964 41.667 7.25 0.00 0.00 4.02
5424 6739 6.734137 TCATGTGGTGTTCAGTGAAAAATAC 58.266 36.000 7.25 5.65 0.00 1.89
5425 6740 6.951062 TCATGTGGTGTTCAGTGAAAAATA 57.049 33.333 7.25 0.00 0.00 1.40
5426 6741 5.850557 TCATGTGGTGTTCAGTGAAAAAT 57.149 34.783 7.25 0.00 0.00 1.82
5427 6742 5.590145 CATCATGTGGTGTTCAGTGAAAAA 58.410 37.500 7.25 0.00 0.00 1.94
5456 6771 1.993956 CAATTGGGTGGTGGAACTGA 58.006 50.000 0.00 0.00 36.74 3.41
5525 6840 1.396301 GTTGCAGCTCCGAAGATCTTG 59.604 52.381 14.00 5.36 0.00 3.02
5539 6857 4.097437 TCCCTACGTACTATTCAGTTGCAG 59.903 45.833 0.00 0.00 36.14 4.41
5555 6873 6.484308 TCAACCTTTTCTAAGTTTTCCCTACG 59.516 38.462 0.00 0.00 0.00 3.51
5556 6874 7.812690 TCAACCTTTTCTAAGTTTTCCCTAC 57.187 36.000 0.00 0.00 0.00 3.18
5557 6875 8.002459 ACATCAACCTTTTCTAAGTTTTCCCTA 58.998 33.333 0.00 0.00 0.00 3.53
5558 6876 6.839134 ACATCAACCTTTTCTAAGTTTTCCCT 59.161 34.615 0.00 0.00 0.00 4.20
5561 6879 9.581099 TTTCACATCAACCTTTTCTAAGTTTTC 57.419 29.630 0.00 0.00 0.00 2.29
5568 6886 6.831353 TCTTGGTTTCACATCAACCTTTTCTA 59.169 34.615 3.60 0.00 43.75 2.10
5569 6887 5.656416 TCTTGGTTTCACATCAACCTTTTCT 59.344 36.000 3.60 0.00 43.75 2.52
5570 6888 5.901552 TCTTGGTTTCACATCAACCTTTTC 58.098 37.500 3.60 0.00 43.75 2.29
5576 6894 6.088824 CAGCTATTCTTGGTTTCACATCAAC 58.911 40.000 0.00 0.00 0.00 3.18
5592 6910 3.618594 TCAATCACAACTCGCAGCTATTC 59.381 43.478 0.00 0.00 0.00 1.75
5682 7000 3.077359 CCCCAAAAAGAGCTCTGTGTAG 58.923 50.000 19.06 0.00 0.00 2.74
5683 7001 2.441750 ACCCCAAAAAGAGCTCTGTGTA 59.558 45.455 19.06 0.00 0.00 2.90
5684 7002 1.215423 ACCCCAAAAAGAGCTCTGTGT 59.785 47.619 19.06 3.09 0.00 3.72
5685 7003 1.882623 GACCCCAAAAAGAGCTCTGTG 59.117 52.381 19.06 15.34 0.00 3.66
5686 7004 1.543429 CGACCCCAAAAAGAGCTCTGT 60.543 52.381 19.06 9.37 0.00 3.41
5687 7005 1.160137 CGACCCCAAAAAGAGCTCTG 58.840 55.000 19.06 5.25 0.00 3.35
5688 7006 0.606673 GCGACCCCAAAAAGAGCTCT 60.607 55.000 11.45 11.45 0.00 4.09
5689 7007 1.587043 GGCGACCCCAAAAAGAGCTC 61.587 60.000 5.27 5.27 0.00 4.09
5690 7008 1.603739 GGCGACCCCAAAAAGAGCT 60.604 57.895 0.00 0.00 0.00 4.09
5691 7009 1.603739 AGGCGACCCCAAAAAGAGC 60.604 57.895 0.00 0.00 35.39 4.09
5692 7010 0.537371 ACAGGCGACCCCAAAAAGAG 60.537 55.000 0.00 0.00 35.39 2.85
5693 7011 0.766131 TACAGGCGACCCCAAAAAGA 59.234 50.000 0.00 0.00 35.39 2.52
5694 7012 0.879090 GTACAGGCGACCCCAAAAAG 59.121 55.000 0.00 0.00 35.39 2.27
5695 7013 0.475044 AGTACAGGCGACCCCAAAAA 59.525 50.000 0.00 0.00 35.39 1.94
5696 7014 0.035739 GAGTACAGGCGACCCCAAAA 59.964 55.000 0.00 0.00 35.39 2.44
5697 7015 1.675219 GAGTACAGGCGACCCCAAA 59.325 57.895 0.00 0.00 35.39 3.28
5698 7016 2.288025 GGAGTACAGGCGACCCCAA 61.288 63.158 0.00 0.00 35.39 4.12
5699 7017 2.682494 GGAGTACAGGCGACCCCA 60.682 66.667 0.00 0.00 35.39 4.96
5700 7018 3.468140 GGGAGTACAGGCGACCCC 61.468 72.222 0.00 0.00 35.00 4.95
5701 7019 1.833787 TTTGGGAGTACAGGCGACCC 61.834 60.000 0.00 0.00 40.79 4.46
5702 7020 0.391263 CTTTGGGAGTACAGGCGACC 60.391 60.000 0.00 0.00 0.00 4.79
5703 7021 0.606604 TCTTTGGGAGTACAGGCGAC 59.393 55.000 0.00 0.00 0.00 5.19
5704 7022 0.606604 GTCTTTGGGAGTACAGGCGA 59.393 55.000 0.00 0.00 0.00 5.54
5705 7023 0.736325 CGTCTTTGGGAGTACAGGCG 60.736 60.000 0.00 0.00 0.00 5.52
5706 7024 1.019805 GCGTCTTTGGGAGTACAGGC 61.020 60.000 0.00 0.00 0.00 4.85
5707 7025 0.391263 GGCGTCTTTGGGAGTACAGG 60.391 60.000 0.00 0.00 0.00 4.00
5708 7026 0.320374 TGGCGTCTTTGGGAGTACAG 59.680 55.000 0.00 0.00 0.00 2.74
5709 7027 0.320374 CTGGCGTCTTTGGGAGTACA 59.680 55.000 0.00 0.00 0.00 2.90
5710 7028 0.606604 TCTGGCGTCTTTGGGAGTAC 59.393 55.000 0.00 0.00 0.00 2.73
5711 7029 0.895530 CTCTGGCGTCTTTGGGAGTA 59.104 55.000 0.00 0.00 0.00 2.59
5712 7030 1.674057 CTCTGGCGTCTTTGGGAGT 59.326 57.895 0.00 0.00 0.00 3.85
5713 7031 1.743252 GCTCTGGCGTCTTTGGGAG 60.743 63.158 0.00 0.00 0.00 4.30
5714 7032 1.841302 ATGCTCTGGCGTCTTTGGGA 61.841 55.000 0.00 0.00 42.25 4.37
5715 7033 0.962356 AATGCTCTGGCGTCTTTGGG 60.962 55.000 0.00 0.00 42.25 4.12
5716 7034 0.449388 GAATGCTCTGGCGTCTTTGG 59.551 55.000 0.00 0.00 42.25 3.28
5717 7035 0.095935 CGAATGCTCTGGCGTCTTTG 59.904 55.000 0.00 0.00 42.25 2.77
5718 7036 0.320771 ACGAATGCTCTGGCGTCTTT 60.321 50.000 0.00 0.00 42.25 2.52
5719 7037 1.016130 CACGAATGCTCTGGCGTCTT 61.016 55.000 0.00 0.00 42.25 3.01
5720 7038 1.446792 CACGAATGCTCTGGCGTCT 60.447 57.895 0.00 0.00 42.25 4.18
5721 7039 3.084579 CACGAATGCTCTGGCGTC 58.915 61.111 0.00 0.00 42.25 5.19
5731 7049 0.439985 CTGGACACGAAGCACGAATG 59.560 55.000 10.05 2.14 45.77 2.67
5732 7050 0.033504 ACTGGACACGAAGCACGAAT 59.966 50.000 10.05 0.00 45.77 3.34
5733 7051 0.179094 AACTGGACACGAAGCACGAA 60.179 50.000 10.05 0.00 45.77 3.85
5734 7052 0.596600 GAACTGGACACGAAGCACGA 60.597 55.000 10.05 0.00 45.77 4.35
5736 7054 2.059541 GTAGAACTGGACACGAAGCAC 58.940 52.381 0.00 0.00 0.00 4.40
5737 7055 1.000506 GGTAGAACTGGACACGAAGCA 59.999 52.381 0.00 0.00 0.00 3.91
5738 7056 1.711206 GGTAGAACTGGACACGAAGC 58.289 55.000 0.00 0.00 0.00 3.86
5739 7057 1.978542 CGGTAGAACTGGACACGAAG 58.021 55.000 0.00 0.00 0.00 3.79
5748 7066 0.737715 GAGCTGCACCGGTAGAACTG 60.738 60.000 6.87 2.62 0.00 3.16
5749 7067 1.592223 GAGCTGCACCGGTAGAACT 59.408 57.895 6.87 2.30 0.00 3.01
5750 7068 1.805945 CGAGCTGCACCGGTAGAAC 60.806 63.158 6.87 0.00 0.00 3.01
5751 7069 2.571757 CGAGCTGCACCGGTAGAA 59.428 61.111 6.87 0.00 0.00 2.10
5752 7070 3.449227 CCGAGCTGCACCGGTAGA 61.449 66.667 20.41 0.00 40.78 2.59
5761 7079 4.530857 ATACCGCCACCGAGCTGC 62.531 66.667 0.00 0.00 36.29 5.25
5762 7080 2.173669 CAATACCGCCACCGAGCTG 61.174 63.158 0.00 0.00 36.29 4.24
5763 7081 2.186903 CAATACCGCCACCGAGCT 59.813 61.111 0.00 0.00 36.29 4.09
5764 7082 2.125269 ACAATACCGCCACCGAGC 60.125 61.111 0.00 0.00 36.29 5.03
5765 7083 1.079405 ACACAATACCGCCACCGAG 60.079 57.895 0.00 0.00 36.29 4.63
5766 7084 1.374885 CACACAATACCGCCACCGA 60.375 57.895 0.00 0.00 36.29 4.69
5767 7085 1.374885 TCACACAATACCGCCACCG 60.375 57.895 0.00 0.00 0.00 4.94
5768 7086 0.321298 AGTCACACAATACCGCCACC 60.321 55.000 0.00 0.00 0.00 4.61
5769 7087 0.796312 CAGTCACACAATACCGCCAC 59.204 55.000 0.00 0.00 0.00 5.01
5770 7088 0.394938 ACAGTCACACAATACCGCCA 59.605 50.000 0.00 0.00 0.00 5.69
5771 7089 1.519408 AACAGTCACACAATACCGCC 58.481 50.000 0.00 0.00 0.00 6.13
5772 7090 3.991773 TCTAAACAGTCACACAATACCGC 59.008 43.478 0.00 0.00 0.00 5.68
5773 7091 4.091509 GCTCTAAACAGTCACACAATACCG 59.908 45.833 0.00 0.00 0.00 4.02
5774 7092 4.994852 TGCTCTAAACAGTCACACAATACC 59.005 41.667 0.00 0.00 0.00 2.73
5775 7093 6.591834 AGATGCTCTAAACAGTCACACAATAC 59.408 38.462 0.00 0.00 0.00 1.89
5776 7094 6.701340 AGATGCTCTAAACAGTCACACAATA 58.299 36.000 0.00 0.00 0.00 1.90
5777 7095 5.555017 AGATGCTCTAAACAGTCACACAAT 58.445 37.500 0.00 0.00 0.00 2.71
5778 7096 4.960938 AGATGCTCTAAACAGTCACACAA 58.039 39.130 0.00 0.00 0.00 3.33
5779 7097 4.560128 GAGATGCTCTAAACAGTCACACA 58.440 43.478 0.00 0.00 0.00 3.72
5780 7098 3.929610 GGAGATGCTCTAAACAGTCACAC 59.070 47.826 0.00 0.00 0.00 3.82
5781 7099 3.578282 TGGAGATGCTCTAAACAGTCACA 59.422 43.478 0.00 0.00 0.00 3.58
5782 7100 4.180057 CTGGAGATGCTCTAAACAGTCAC 58.820 47.826 0.00 0.00 0.00 3.67
5783 7101 3.368843 GCTGGAGATGCTCTAAACAGTCA 60.369 47.826 0.00 0.00 30.39 3.41
5784 7102 3.194062 GCTGGAGATGCTCTAAACAGTC 58.806 50.000 0.00 0.00 30.39 3.51
5785 7103 2.093235 GGCTGGAGATGCTCTAAACAGT 60.093 50.000 0.00 0.00 30.39 3.55
5786 7104 2.559440 GGCTGGAGATGCTCTAAACAG 58.441 52.381 0.00 0.00 0.00 3.16
5787 7105 1.134699 CGGCTGGAGATGCTCTAAACA 60.135 52.381 0.00 0.00 0.00 2.83
5788 7106 1.134670 ACGGCTGGAGATGCTCTAAAC 60.135 52.381 0.00 0.00 0.00 2.01
5789 7107 1.195115 ACGGCTGGAGATGCTCTAAA 58.805 50.000 0.00 0.00 0.00 1.85
5824 7144 1.142870 CCCCCAGATGGCGATTTTAGA 59.857 52.381 0.00 0.00 0.00 2.10
5907 7230 0.181587 TTTCTTGAACGTGCCTGGGA 59.818 50.000 0.00 0.00 0.00 4.37
6018 7343 8.994429 ATTTTGTTATGTAATGAAAATCCGCA 57.006 26.923 0.00 0.00 0.00 5.69
6058 7383 2.857748 GGCGTTCAACCAGTTTCTTTTG 59.142 45.455 0.00 0.00 0.00 2.44
6071 7396 1.443194 GCGACTACTCGGCGTTCAA 60.443 57.895 6.85 0.00 40.53 2.69
6128 7456 1.819288 CTGCGTCAAGGAGTAGAAGGA 59.181 52.381 0.00 0.00 33.20 3.36
6180 7508 4.155733 CCGCCACCAGTCGCCATA 62.156 66.667 0.00 0.00 0.00 2.74
6229 7560 2.202311 CGTCGTCATCGTCGCTGT 60.202 61.111 0.00 0.00 40.72 4.40
6231 7562 2.097918 GTCGTCGTCATCGTCGCT 59.902 61.111 0.00 0.00 44.86 4.93
6232 7563 1.928769 GAGTCGTCGTCATCGTCGC 60.929 63.158 0.00 0.01 44.86 5.19
6235 7569 1.367599 GGAGGAGTCGTCGTCATCGT 61.368 60.000 6.74 0.00 39.03 3.73


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

AutoCloner maintained by Alex Coulton.