Multiple sequence alignment - TraesCS4D01G008400

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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 TraesCS4D01G008400 chr4D 100.000 6987 0 0 1 6987 4127933 4134919 0.000000e+00 12903.0
1 TraesCS4D01G008400 chr4D 92.798 722 28 11 6285 6987 3860117 3859401 0.000000e+00 1024.0
2 TraesCS4D01G008400 chr4D 92.713 494 36 0 1781 2274 465588052 465587559 0.000000e+00 713.0
3 TraesCS4D01G008400 chr4D 94.194 310 17 1 2474 2782 465578614 465578305 8.200000e-129 472.0
4 TraesCS4D01G008400 chr4D 83.466 502 65 9 1291 1786 50353593 50353104 1.070000e-122 451.0
5 TraesCS4D01G008400 chr4D 91.667 312 20 2 6619 6927 3950033 3949725 1.800000e-115 427.0
6 TraesCS4D01G008400 chr4D 82.927 451 59 8 1342 1786 465588531 465588093 2.360000e-104 390.0
7 TraesCS4D01G008400 chr4D 92.925 212 10 4 988 1199 50353794 50353588 3.170000e-78 303.0
8 TraesCS4D01G008400 chr4D 95.588 68 3 0 5892 5959 4133782 4133849 7.410000e-20 110.0
9 TraesCS4D01G008400 chr4D 95.588 68 3 0 5850 5917 4133824 4133891 7.410000e-20 110.0
10 TraesCS4D01G008400 chr4A 97.436 3471 70 6 1781 5243 599888369 599891828 0.000000e+00 5899.0
11 TraesCS4D01G008400 chr4A 92.469 1766 92 21 5243 6987 599891892 599893637 0.000000e+00 2486.0
12 TraesCS4D01G008400 chr4A 87.426 1177 85 21 625 1780 599887181 599888315 0.000000e+00 1295.0
13 TraesCS4D01G008400 chr4A 95.304 362 17 0 6626 6987 599732989 599732628 6.080000e-160 575.0
14 TraesCS4D01G008400 chr4A 93.734 383 20 1 6609 6987 600387004 600387386 7.860000e-159 571.0
15 TraesCS4D01G008400 chr4A 77.960 549 75 18 5376 5897 590380267 590380796 1.140000e-77 302.0
16 TraesCS4D01G008400 chr4A 82.550 149 12 5 5264 5412 590380133 590380267 1.230000e-22 119.0
17 TraesCS4D01G008400 chr4A 90.909 88 8 0 5850 5937 599892538 599892625 1.230000e-22 119.0
18 TraesCS4D01G008400 chr4A 95.588 68 3 0 5892 5959 599892496 599892563 7.410000e-20 110.0
19 TraesCS4D01G008400 chr4B 95.761 3468 91 22 1781 5243 4525585 4522169 0.000000e+00 5539.0
20 TraesCS4D01G008400 chr4B 91.884 1380 72 22 5643 6987 4521391 4520017 0.000000e+00 1892.0
21 TraesCS4D01G008400 chr4B 88.536 724 67 8 916 1624 4526800 4526078 0.000000e+00 863.0
22 TraesCS4D01G008400 chr4B 93.817 372 20 1 6619 6987 4708296 4708667 2.200000e-154 556.0
23 TraesCS4D01G008400 chr4B 92.545 389 19 4 477 863 4527504 4527124 3.680000e-152 549.0
24 TraesCS4D01G008400 chr4B 83.505 485 61 11 5243 5714 4522105 4521627 1.080000e-117 435.0
25 TraesCS4D01G008400 chr4B 79.701 335 45 7 114 427 4528038 4527706 3.280000e-53 220.0
26 TraesCS4D01G008400 chr4B 88.095 168 16 1 5076 5243 22721308 22721471 5.530000e-46 196.0
27 TraesCS4D01G008400 chr4B 92.941 85 6 0 5853 5937 4521138 4521054 2.650000e-24 124.0
28 TraesCS4D01G008400 chr4B 90.541 74 7 0 5895 5968 4521180 4521107 1.600000e-16 99.0
29 TraesCS4D01G008400 chr6B 94.036 1006 53 5 1781 2782 438297802 438298804 0.000000e+00 1519.0
30 TraesCS4D01G008400 chr6B 86.584 805 86 15 988 1786 713143568 713142780 0.000000e+00 869.0
31 TraesCS4D01G008400 chr6B 92.605 595 39 3 1781 2372 713142739 713142147 0.000000e+00 850.0
32 TraesCS4D01G008400 chr6B 85.482 799 90 18 988 1780 438296977 438297755 0.000000e+00 809.0
33 TraesCS4D01G008400 chr6B 82.669 502 67 10 1292 1786 681266323 681265835 1.800000e-115 427.0
34 TraesCS4D01G008400 chr6B 91.827 208 13 2 992 1199 681266522 681266319 3.190000e-73 287.0
35 TraesCS4D01G008400 chr7D 93.738 1006 58 3 1781 2783 39493252 39492249 0.000000e+00 1504.0
36 TraesCS4D01G008400 chr7D 83.673 98 15 1 1 98 1331647 1331743 2.680000e-14 91.6
37 TraesCS4D01G008400 chr3A 86.991 638 68 12 1792 2417 72692358 72692992 0.000000e+00 704.0
38 TraesCS4D01G008400 chr3A 85.826 642 73 15 1792 2420 705927019 705926383 0.000000e+00 665.0
39 TraesCS4D01G008400 chr1D 86.180 644 70 14 1792 2420 481042834 481042195 0.000000e+00 678.0
40 TraesCS4D01G008400 chr5B 91.467 375 18 5 6613 6987 641332771 641333131 2.910000e-138 503.0
41 TraesCS4D01G008400 chr2B 83.501 497 62 10 1291 1780 485754080 485754563 4.970000e-121 446.0
42 TraesCS4D01G008400 chr2B 92.788 208 11 2 992 1199 485753882 485754085 1.470000e-76 298.0
43 TraesCS4D01G008400 chr7A 91.121 214 14 4 988 1201 117675524 117675732 1.150000e-72 285.0
44 TraesCS4D01G008400 chr7A 85.714 98 13 1 1 98 360230143 360230239 1.240000e-17 102.0
45 TraesCS4D01G008400 chrUn 94.444 72 4 0 996 1067 79238796 79238725 2.060000e-20 111.0
46 TraesCS4D01G008400 chr5A 84.783 92 13 1 21 112 413889747 413889657 2.680000e-14 91.6
47 TraesCS4D01G008400 chr7B 88.889 72 8 0 27 98 741477743 741477814 9.650000e-14 89.8


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 TraesCS4D01G008400 chr4D 4127933 4134919 6986 False 4374.333333 12903 97.058667 1 6987 3 chr4D.!!$F1 6986
1 TraesCS4D01G008400 chr4D 3859401 3860117 716 True 1024.000000 1024 92.798000 6285 6987 1 chr4D.!!$R1 702
2 TraesCS4D01G008400 chr4D 465587559 465588531 972 True 551.500000 713 87.820000 1342 2274 2 chr4D.!!$R5 932
3 TraesCS4D01G008400 chr4D 50353104 50353794 690 True 377.000000 451 88.195500 988 1786 2 chr4D.!!$R4 798
4 TraesCS4D01G008400 chr4A 599887181 599893637 6456 False 1981.800000 5899 92.765600 625 6987 5 chr4A.!!$F3 6362
5 TraesCS4D01G008400 chr4A 590380133 590380796 663 False 210.500000 302 80.255000 5264 5897 2 chr4A.!!$F2 633
6 TraesCS4D01G008400 chr4B 4520017 4528038 8021 True 1215.125000 5539 89.426750 114 6987 8 chr4B.!!$R1 6873
7 TraesCS4D01G008400 chr6B 438296977 438298804 1827 False 1164.000000 1519 89.759000 988 2782 2 chr6B.!!$F1 1794
8 TraesCS4D01G008400 chr6B 713142147 713143568 1421 True 859.500000 869 89.594500 988 2372 2 chr6B.!!$R2 1384
9 TraesCS4D01G008400 chr6B 681265835 681266522 687 True 357.000000 427 87.248000 992 1786 2 chr6B.!!$R1 794
10 TraesCS4D01G008400 chr7D 39492249 39493252 1003 True 1504.000000 1504 93.738000 1781 2783 1 chr7D.!!$R1 1002
11 TraesCS4D01G008400 chr3A 72692358 72692992 634 False 704.000000 704 86.991000 1792 2417 1 chr3A.!!$F1 625
12 TraesCS4D01G008400 chr3A 705926383 705927019 636 True 665.000000 665 85.826000 1792 2420 1 chr3A.!!$R1 628
13 TraesCS4D01G008400 chr1D 481042195 481042834 639 True 678.000000 678 86.180000 1792 2420 1 chr1D.!!$R1 628
14 TraesCS4D01G008400 chr2B 485753882 485754563 681 False 372.000000 446 88.144500 992 1780 2 chr2B.!!$F1 788

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
66 67 0.391927 TAGGGGCAATTTCCGTGACG 60.392 55.000 0.00 0.00 0.00 4.35 F
1262 1826 0.311790 GTGCACATCAGTGGGTTGTG 59.688 55.000 13.17 13.91 45.98 3.33 F
1427 2000 0.109272 ACATCAGTGTGTCGTAGCGG 60.109 55.000 0.00 0.00 37.14 5.52 F
1537 2110 0.607112 CTCTGCAGGAGCTTGTGAGA 59.393 55.000 15.13 0.00 42.74 3.27 F
1565 2138 1.246649 TGTCGTTACCGGCTTACAGA 58.753 50.000 0.00 0.00 40.05 3.41 F
1606 2179 1.536766 TCAATTGGTGCTGCTTCTTCG 59.463 47.619 5.42 0.00 0.00 3.79 F
3402 4332 0.397816 AGGAGCTCGGATACAGGCTT 60.398 55.000 7.83 0.00 42.76 4.35 F
4492 5423 0.389556 CGATGATGATGGGCTCCTCG 60.390 60.000 0.00 0.00 0.00 4.63 F
4691 5626 2.616256 CCTCAGTTCACCTTGCTGCATA 60.616 50.000 1.84 0.00 0.00 3.14 F
5672 7040 2.857618 TGCATTCGATTTTAACACGGC 58.142 42.857 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1852 0.462759 AGCTAATGCAGAGAACGGCC 60.463 55.000 0.00 0.00 42.74 6.13 R
2437 3367 3.120792 TCGGCATAAGAAACAGATACGC 58.879 45.455 0.00 0.00 0.00 4.42 R
3336 4266 1.332889 ATCCATCCAGAGAGCACGCA 61.333 55.000 0.00 0.00 0.00 5.24 R
3390 4320 4.038042 TCAGAATCACTAAGCCTGTATCCG 59.962 45.833 0.00 0.00 0.00 4.18 R
3402 4332 9.958180 TTTAATTCATCCAGTTCAGAATCACTA 57.042 29.630 0.00 0.00 30.87 2.74 R
3690 4620 4.038522 GGACTAGATACCCGGGTAACTTTC 59.961 50.000 38.87 32.44 35.72 2.62 R
5294 6298 4.340381 AGGATTTCAGCAAAGCATGATACC 59.660 41.667 0.00 0.00 28.75 2.73 R
5672 7040 1.073216 ATCGAAGAGCGCAACTGACG 61.073 55.000 11.47 16.74 43.63 4.35 R
5980 7364 1.132453 GAAGGGTTTGTTCGCTATGCC 59.868 52.381 0.00 0.00 0.00 4.40 R
6860 8308 2.187946 CTTCGCCGCATTCCTCCT 59.812 61.111 0.00 0.00 0.00 3.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.621629 TTACCAGTTAATAGATAACATTGGTGG 57.378 33.333 16.41 10.31 45.50 4.61
30 31 6.546034 ACCAGTTAATAGATAACATTGGTGGC 59.454 38.462 9.95 0.00 44.84 5.01
31 32 6.772716 CCAGTTAATAGATAACATTGGTGGCT 59.227 38.462 1.68 0.00 45.29 4.75
32 33 7.936847 CCAGTTAATAGATAACATTGGTGGCTA 59.063 37.037 1.68 0.00 45.29 3.93
33 34 9.337396 CAGTTAATAGATAACATTGGTGGCTAA 57.663 33.333 1.68 0.00 45.29 3.09
40 41 8.169977 AGATAACATTGGTGGCTAATATTGTG 57.830 34.615 0.00 0.00 0.00 3.33
41 42 4.654091 ACATTGGTGGCTAATATTGTGC 57.346 40.909 0.00 2.60 0.00 4.57
42 43 4.022603 ACATTGGTGGCTAATATTGTGCA 58.977 39.130 14.35 0.00 0.00 4.57
43 44 4.465660 ACATTGGTGGCTAATATTGTGCAA 59.534 37.500 14.35 3.68 0.00 4.08
44 45 4.448537 TTGGTGGCTAATATTGTGCAAC 57.551 40.909 14.35 13.12 37.35 4.17
45 46 3.696045 TGGTGGCTAATATTGTGCAACT 58.304 40.909 16.92 0.00 38.04 3.16
46 47 4.085733 TGGTGGCTAATATTGTGCAACTT 58.914 39.130 16.92 0.00 38.04 2.66
47 48 4.526262 TGGTGGCTAATATTGTGCAACTTT 59.474 37.500 16.92 0.00 38.04 2.66
48 49 5.712446 TGGTGGCTAATATTGTGCAACTTTA 59.288 36.000 16.92 6.72 38.04 1.85
49 50 6.127758 TGGTGGCTAATATTGTGCAACTTTAG 60.128 38.462 16.92 9.51 38.04 1.85
50 51 6.265577 GTGGCTAATATTGTGCAACTTTAGG 58.734 40.000 14.35 0.00 38.04 2.69
51 52 5.359576 TGGCTAATATTGTGCAACTTTAGGG 59.640 40.000 14.35 0.00 38.04 3.53
52 53 5.221244 GGCTAATATTGTGCAACTTTAGGGG 60.221 44.000 14.35 0.00 38.04 4.79
53 54 4.736126 AATATTGTGCAACTTTAGGGGC 57.264 40.909 0.00 0.00 38.04 5.80
54 55 2.008242 ATTGTGCAACTTTAGGGGCA 57.992 45.000 0.00 0.00 38.04 5.36
55 56 1.781786 TTGTGCAACTTTAGGGGCAA 58.218 45.000 0.00 0.00 38.10 4.52
56 57 2.008242 TGTGCAACTTTAGGGGCAAT 57.992 45.000 0.00 0.00 38.10 3.56
57 58 2.324541 TGTGCAACTTTAGGGGCAATT 58.675 42.857 0.00 0.00 38.10 2.32
58 59 2.703007 TGTGCAACTTTAGGGGCAATTT 59.297 40.909 0.00 0.00 38.10 1.82
59 60 3.244044 TGTGCAACTTTAGGGGCAATTTC 60.244 43.478 0.00 0.00 38.10 2.17
60 61 2.301583 TGCAACTTTAGGGGCAATTTCC 59.698 45.455 0.00 0.00 32.54 3.13
61 62 2.673893 GCAACTTTAGGGGCAATTTCCG 60.674 50.000 0.00 0.00 0.00 4.30
62 63 2.560981 CAACTTTAGGGGCAATTTCCGT 59.439 45.455 0.00 0.00 0.00 4.69
63 64 2.167662 ACTTTAGGGGCAATTTCCGTG 58.832 47.619 0.00 0.00 0.00 4.94
64 65 2.224917 ACTTTAGGGGCAATTTCCGTGA 60.225 45.455 0.00 0.00 0.00 4.35
65 66 1.828979 TTAGGGGCAATTTCCGTGAC 58.171 50.000 0.00 0.00 0.00 3.67
66 67 0.391927 TAGGGGCAATTTCCGTGACG 60.392 55.000 0.00 0.00 0.00 4.35
67 68 1.969589 GGGGCAATTTCCGTGACGT 60.970 57.895 3.64 0.00 0.00 4.34
68 69 0.674269 GGGGCAATTTCCGTGACGTA 60.674 55.000 3.64 0.00 0.00 3.57
69 70 0.445043 GGGCAATTTCCGTGACGTAC 59.555 55.000 3.64 0.00 0.00 3.67
70 71 0.445043 GGCAATTTCCGTGACGTACC 59.555 55.000 3.64 0.00 0.00 3.34
71 72 1.149987 GCAATTTCCGTGACGTACCA 58.850 50.000 3.64 0.00 0.00 3.25
72 73 1.136169 GCAATTTCCGTGACGTACCAC 60.136 52.381 3.64 0.00 0.00 4.16
73 74 2.409975 CAATTTCCGTGACGTACCACT 58.590 47.619 3.64 0.00 35.02 4.00
74 75 3.577667 CAATTTCCGTGACGTACCACTA 58.422 45.455 3.64 0.00 35.02 2.74
75 76 2.995466 TTTCCGTGACGTACCACTAG 57.005 50.000 3.64 0.00 35.02 2.57
76 77 2.183478 TTCCGTGACGTACCACTAGA 57.817 50.000 3.64 0.63 35.02 2.43
77 78 2.183478 TCCGTGACGTACCACTAGAA 57.817 50.000 3.64 0.00 35.02 2.10
78 79 2.079158 TCCGTGACGTACCACTAGAAG 58.921 52.381 3.64 0.00 35.02 2.85
79 80 1.467035 CCGTGACGTACCACTAGAAGC 60.467 57.143 3.64 0.00 35.02 3.86
80 81 1.198408 CGTGACGTACCACTAGAAGCA 59.802 52.381 0.00 0.00 35.02 3.91
81 82 2.351060 CGTGACGTACCACTAGAAGCAA 60.351 50.000 0.00 0.00 35.02 3.91
82 83 3.672511 CGTGACGTACCACTAGAAGCAAT 60.673 47.826 0.00 0.00 35.02 3.56
83 84 4.437794 CGTGACGTACCACTAGAAGCAATA 60.438 45.833 0.00 0.00 35.02 1.90
84 85 5.035443 GTGACGTACCACTAGAAGCAATAG 58.965 45.833 0.00 0.00 34.38 1.73
85 86 4.043037 ACGTACCACTAGAAGCAATAGC 57.957 45.455 0.00 0.00 42.56 2.97
86 87 3.181478 ACGTACCACTAGAAGCAATAGCC 60.181 47.826 0.00 0.00 43.56 3.93
87 88 3.729966 GTACCACTAGAAGCAATAGCCC 58.270 50.000 0.00 0.00 43.56 5.19
88 89 1.490910 ACCACTAGAAGCAATAGCCCC 59.509 52.381 0.00 0.00 43.56 5.80
89 90 1.771255 CCACTAGAAGCAATAGCCCCT 59.229 52.381 0.00 0.00 43.56 4.79
90 91 2.173569 CCACTAGAAGCAATAGCCCCTT 59.826 50.000 0.00 0.00 43.56 3.95
91 92 3.372025 CCACTAGAAGCAATAGCCCCTTT 60.372 47.826 0.00 0.00 43.56 3.11
92 93 4.141482 CCACTAGAAGCAATAGCCCCTTTA 60.141 45.833 0.00 0.00 43.56 1.85
93 94 5.456763 CCACTAGAAGCAATAGCCCCTTTAT 60.457 44.000 0.00 0.00 43.56 1.40
94 95 6.064717 CACTAGAAGCAATAGCCCCTTTATT 58.935 40.000 0.00 0.00 43.56 1.40
95 96 7.224297 CACTAGAAGCAATAGCCCCTTTATTA 58.776 38.462 0.00 0.00 43.56 0.98
96 97 7.885399 CACTAGAAGCAATAGCCCCTTTATTAT 59.115 37.037 0.00 0.00 43.56 1.28
97 98 8.448816 ACTAGAAGCAATAGCCCCTTTATTATT 58.551 33.333 0.00 0.00 43.56 1.40
98 99 9.301897 CTAGAAGCAATAGCCCCTTTATTATTT 57.698 33.333 0.00 0.00 43.56 1.40
99 100 7.955918 AGAAGCAATAGCCCCTTTATTATTTG 58.044 34.615 0.00 0.00 43.56 2.32
100 101 7.784550 AGAAGCAATAGCCCCTTTATTATTTGA 59.215 33.333 0.00 0.00 43.56 2.69
101 102 8.496534 AAGCAATAGCCCCTTTATTATTTGAT 57.503 30.769 0.00 0.00 43.56 2.57
102 103 9.600432 AAGCAATAGCCCCTTTATTATTTGATA 57.400 29.630 0.00 0.00 43.56 2.15
103 104 9.774071 AGCAATAGCCCCTTTATTATTTGATAT 57.226 29.630 0.00 0.00 43.56 1.63
231 232 9.840427 AATGCGATTAATTAATTAGGCATACAC 57.160 29.630 27.36 9.43 36.88 2.90
232 233 7.812648 TGCGATTAATTAATTAGGCATACACC 58.187 34.615 19.80 3.18 0.00 4.16
245 246 6.561519 AGGCATACACCTAATTAGACTTGT 57.438 37.500 14.28 14.60 38.67 3.16
269 270 9.561069 TGTAGATAATTAGAGATTTTTCCAGCC 57.439 33.333 0.00 0.00 0.00 4.85
270 271 7.736447 AGATAATTAGAGATTTTTCCAGCCG 57.264 36.000 0.00 0.00 0.00 5.52
300 321 7.510675 TCCCTAATAGTCTGATCCACTTTTT 57.489 36.000 0.01 0.00 0.00 1.94
301 322 7.565680 TCCCTAATAGTCTGATCCACTTTTTC 58.434 38.462 0.01 0.00 0.00 2.29
302 323 6.480320 CCCTAATAGTCTGATCCACTTTTTCG 59.520 42.308 0.01 0.00 0.00 3.46
315 336 5.533154 TCCACTTTTTCGGCTATTCTTTTCA 59.467 36.000 0.00 0.00 0.00 2.69
321 342 5.776173 TTCGGCTATTCTTTTCAAAACCA 57.224 34.783 0.00 0.00 0.00 3.67
330 351 9.586435 CTATTCTTTTCAAAACCACCCATAATC 57.414 33.333 0.00 0.00 0.00 1.75
338 359 1.692519 ACCACCCATAATCTACCGCTC 59.307 52.381 0.00 0.00 0.00 5.03
349 370 3.365291 TACCGCTCCACATGCCGTC 62.365 63.158 0.00 0.00 0.00 4.79
357 378 1.959985 TCCACATGCCGTCATTGTTTT 59.040 42.857 0.00 0.00 0.00 2.43
360 381 4.219507 TCCACATGCCGTCATTGTTTTTAT 59.780 37.500 0.00 0.00 0.00 1.40
361 382 4.928615 CCACATGCCGTCATTGTTTTTATT 59.071 37.500 0.00 0.00 0.00 1.40
362 383 5.062058 CCACATGCCGTCATTGTTTTTATTC 59.938 40.000 0.00 0.00 0.00 1.75
371 392 9.410556 CCGTCATTGTTTTTATTCTTTTCATCT 57.589 29.630 0.00 0.00 0.00 2.90
384 405 4.943705 TCTTTTCATCTCATAGCAACCCAC 59.056 41.667 0.00 0.00 0.00 4.61
386 407 1.831106 TCATCTCATAGCAACCCACGT 59.169 47.619 0.00 0.00 0.00 4.49
387 408 1.935873 CATCTCATAGCAACCCACGTG 59.064 52.381 9.08 9.08 0.00 4.49
394 415 5.113383 TCATAGCAACCCACGTGTATTTAG 58.887 41.667 15.65 0.00 0.00 1.85
395 416 3.412237 AGCAACCCACGTGTATTTAGT 57.588 42.857 15.65 0.00 0.00 2.24
398 419 4.933400 AGCAACCCACGTGTATTTAGTTAG 59.067 41.667 15.65 0.00 0.00 2.34
424 445 9.836076 GTTGGTTACAAAGTTATCTTACCAATC 57.164 33.333 16.33 9.95 43.87 2.67
427 448 9.185680 GGTTACAAAGTTATCTTACCAATCCAT 57.814 33.333 0.00 0.00 32.10 3.41
434 617 9.533831 AAGTTATCTTACCAATCCATGAAAAGT 57.466 29.630 0.00 0.00 31.46 2.66
438 621 5.774690 TCTTACCAATCCATGAAAAGTTGCT 59.225 36.000 0.00 0.00 0.00 3.91
459 642 4.382754 GCTAATTTTTGGCAAGTCTTGTCG 59.617 41.667 12.39 0.00 38.34 4.35
460 643 4.647424 AATTTTTGGCAAGTCTTGTCGA 57.353 36.364 12.39 7.87 38.34 4.20
462 645 4.442375 TTTTTGGCAAGTCTTGTCGAAA 57.558 36.364 23.10 23.10 44.51 3.46
463 646 4.442375 TTTTGGCAAGTCTTGTCGAAAA 57.558 36.364 24.21 19.99 43.56 2.29
465 648 4.647424 TTGGCAAGTCTTGTCGAAAAAT 57.353 36.364 12.39 0.00 38.34 1.82
466 649 4.647424 TGGCAAGTCTTGTCGAAAAATT 57.353 36.364 12.39 0.00 38.34 1.82
467 650 4.358851 TGGCAAGTCTTGTCGAAAAATTG 58.641 39.130 12.39 0.00 38.34 2.32
468 651 4.142271 TGGCAAGTCTTGTCGAAAAATTGT 60.142 37.500 12.39 0.00 38.34 2.71
469 652 4.803613 GGCAAGTCTTGTCGAAAAATTGTT 59.196 37.500 14.03 0.00 0.00 2.83
470 653 5.276348 GGCAAGTCTTGTCGAAAAATTGTTG 60.276 40.000 14.03 3.50 0.00 3.33
471 654 5.276348 GCAAGTCTTGTCGAAAAATTGTTGG 60.276 40.000 14.03 0.00 0.00 3.77
472 655 4.359706 AGTCTTGTCGAAAAATTGTTGGC 58.640 39.130 0.00 0.00 0.00 4.52
473 656 4.109050 GTCTTGTCGAAAAATTGTTGGCA 58.891 39.130 0.00 0.00 0.00 4.92
474 657 4.564769 GTCTTGTCGAAAAATTGTTGGCAA 59.435 37.500 0.00 0.00 39.16 4.52
475 658 4.564769 TCTTGTCGAAAAATTGTTGGCAAC 59.435 37.500 23.12 23.12 37.44 4.17
492 675 2.297033 GCAACACCAATGTCTCCATGTT 59.703 45.455 0.00 0.00 38.45 2.71
504 687 4.458989 TGTCTCCATGTTAAATTGGCAGTC 59.541 41.667 0.00 0.31 32.80 3.51
505 688 4.016444 TCTCCATGTTAAATTGGCAGTCC 58.984 43.478 0.00 0.00 32.80 3.85
521 704 1.649100 AGTCCCCTCTAGAAGCTTCCT 59.351 52.381 22.81 12.48 0.00 3.36
526 709 2.882137 CCCTCTAGAAGCTTCCTAGTCG 59.118 54.545 22.81 15.83 36.06 4.18
551 734 1.750193 CACAACACCTCACACAACCT 58.250 50.000 0.00 0.00 0.00 3.50
558 741 1.134098 ACCTCACACAACCTCCACAAG 60.134 52.381 0.00 0.00 0.00 3.16
573 756 2.290641 CCACAAGGCACCTACCAATACA 60.291 50.000 0.00 0.00 0.00 2.29
574 757 3.417101 CACAAGGCACCTACCAATACAA 58.583 45.455 0.00 0.00 0.00 2.41
575 758 3.190535 CACAAGGCACCTACCAATACAAC 59.809 47.826 0.00 0.00 0.00 3.32
576 759 3.073946 ACAAGGCACCTACCAATACAACT 59.926 43.478 0.00 0.00 0.00 3.16
577 760 4.287585 ACAAGGCACCTACCAATACAACTA 59.712 41.667 0.00 0.00 0.00 2.24
578 761 4.482952 AGGCACCTACCAATACAACTAC 57.517 45.455 0.00 0.00 0.00 2.73
597 780 1.536766 ACAACACATCGGATGCTTGTG 59.463 47.619 23.58 16.72 44.85 3.33
619 802 3.989817 GGATGAATGCAAAGGACACAAAC 59.010 43.478 0.00 0.00 0.00 2.93
620 803 3.077229 TGAATGCAAAGGACACAAACG 57.923 42.857 0.00 0.00 0.00 3.60
623 806 2.842208 TGCAAAGGACACAAACGAAG 57.158 45.000 0.00 0.00 0.00 3.79
702 887 6.240665 TGTTTCAATTCTTCGATTCGATTCG 58.759 36.000 20.58 20.58 40.46 3.34
969 1425 1.677552 GCTTGACGAAGAAGGGGGA 59.322 57.895 0.00 0.00 0.00 4.81
974 1437 3.702048 CGAAGAAGGGGGACGGCA 61.702 66.667 0.00 0.00 0.00 5.69
1210 1675 2.358737 AGTTCTTTCCAGCGGCGG 60.359 61.111 9.78 4.77 0.00 6.13
1256 1820 3.346315 TGGAAATAGTGCACATCAGTGG 58.654 45.455 21.04 0.00 45.98 4.00
1258 1822 3.347216 GAAATAGTGCACATCAGTGGGT 58.653 45.455 21.04 0.00 45.98 4.51
1262 1826 0.311790 GTGCACATCAGTGGGTTGTG 59.688 55.000 13.17 13.91 45.98 3.33
1287 1852 2.437850 GCCATTGCTCGTTTTGCAG 58.562 52.632 0.00 0.00 41.71 4.41
1319 1884 2.621338 CATTAGCTTGCGAGGTTCAGA 58.379 47.619 11.69 0.00 34.88 3.27
1331 1898 2.470821 AGGTTCAGAGTTGTCGTTTCG 58.529 47.619 0.00 0.00 0.00 3.46
1333 1900 2.199236 GTTCAGAGTTGTCGTTTCGGT 58.801 47.619 0.00 0.00 0.00 4.69
1377 1950 5.221322 GCTCAGTTCTTTCCAGAATTTTGGT 60.221 40.000 14.30 0.00 41.26 3.67
1384 1957 4.320608 TTCCAGAATTTTGGTGTTGAGC 57.679 40.909 14.30 0.00 39.35 4.26
1399 1972 2.675348 GTTGAGCTCAAGTGTAGATGGC 59.325 50.000 29.13 9.80 36.39 4.40
1409 1982 6.338146 TCAAGTGTAGATGGCAATAGTACAC 58.662 40.000 14.58 14.58 42.45 2.90
1427 2000 0.109272 ACATCAGTGTGTCGTAGCGG 60.109 55.000 0.00 0.00 37.14 5.52
1443 2016 2.094675 AGCGGCTATTGTTGCTCATTT 58.905 42.857 0.00 0.00 30.37 2.32
1444 2017 2.159338 AGCGGCTATTGTTGCTCATTTG 60.159 45.455 0.00 0.00 30.37 2.32
1456 2029 5.643348 TGTTGCTCATTTGATATGTCGTTCT 59.357 36.000 0.00 0.00 0.00 3.01
1462 2035 4.661993 TTTGATATGTCGTTCTGTGCAC 57.338 40.909 10.75 10.75 0.00 4.57
1463 2036 2.258755 TGATATGTCGTTCTGTGCACG 58.741 47.619 13.13 7.36 39.08 5.34
1467 2040 4.816990 TCGTTCTGTGCACGAACA 57.183 50.000 33.03 24.11 43.52 3.18
1468 2041 2.293765 TCGTTCTGTGCACGAACAC 58.706 52.632 33.03 20.32 43.52 3.32
1481 2054 1.129326 CGAACACGTGAGGTTCAGTC 58.871 55.000 25.01 5.08 43.70 3.51
1496 2069 2.241160 TCAGTCTTGTAGCGGTAACCA 58.759 47.619 0.00 0.00 0.00 3.67
1515 2088 6.751514 AACCATTGCTCGTTTTATATGTCA 57.248 33.333 0.00 0.00 0.00 3.58
1525 2098 7.468922 TCGTTTTATATGTCATTCTCTGCAG 57.531 36.000 7.63 7.63 0.00 4.41
1526 2099 6.479990 TCGTTTTATATGTCATTCTCTGCAGG 59.520 38.462 15.13 4.77 0.00 4.85
1537 2110 0.607112 CTCTGCAGGAGCTTGTGAGA 59.393 55.000 15.13 0.00 42.74 3.27
1553 2126 4.939271 TGTGAGATTCAGTGTTGTCGTTA 58.061 39.130 0.00 0.00 0.00 3.18
1565 2138 1.246649 TGTCGTTACCGGCTTACAGA 58.753 50.000 0.00 0.00 40.05 3.41
1566 2139 1.820519 TGTCGTTACCGGCTTACAGAT 59.179 47.619 0.00 0.00 40.05 2.90
1606 2179 1.536766 TCAATTGGTGCTGCTTCTTCG 59.463 47.619 5.42 0.00 0.00 3.79
1639 2496 7.926555 TCCTTGACTGAAGTTAGTTTCTGTTAG 59.073 37.037 0.91 2.66 38.73 2.34
1644 2501 9.182933 GACTGAAGTTAGTTTCTGTTAGTAGTG 57.817 37.037 0.00 0.00 38.73 2.74
1659 2516 6.480981 TGTTAGTAGTGTTAGGAACTTGTTGC 59.519 38.462 0.00 0.00 41.75 4.17
1664 2521 6.803154 AGTGTTAGGAACTTGTTGCTATTC 57.197 37.500 13.85 11.10 41.75 1.75
1668 2525 4.546829 AGGAACTTGTTGCTATTCGGTA 57.453 40.909 5.74 0.00 27.25 4.02
1692 2549 1.946768 CACTCCGGTCAAGCTTGAAAA 59.053 47.619 29.99 14.47 39.21 2.29
1693 2550 2.357637 CACTCCGGTCAAGCTTGAAAAA 59.642 45.455 29.99 14.79 39.21 1.94
1732 2590 7.015877 AGCCTACCGTTCTTATGATGGTAATTA 59.984 37.037 9.92 0.00 34.96 1.40
1735 2593 9.760077 CTACCGTTCTTATGATGGTAATTAAGT 57.240 33.333 9.92 0.00 34.96 2.24
1737 2595 8.483758 ACCGTTCTTATGATGGTAATTAAGTCT 58.516 33.333 2.32 0.00 31.97 3.24
1796 2707 7.542130 GCTTATGGTTTAGGATGTTTGTTTGAG 59.458 37.037 0.00 0.00 0.00 3.02
1836 2747 3.890756 TGGATTCTGCAGTGTTGATGTTT 59.109 39.130 14.67 0.00 0.00 2.83
1853 2773 8.704234 GTTGATGTTTTTAACTTGTTGTGTCAA 58.296 29.630 0.00 0.00 0.00 3.18
1868 2788 7.093354 TGTTGTGTCAAACTGCAAGAATTTTA 58.907 30.769 0.00 0.00 37.43 1.52
1956 2878 2.751806 CTCCATCTGTTTGCCTTCTTCC 59.248 50.000 0.00 0.00 0.00 3.46
2268 3190 3.565307 TCTGCCAAAATTTCAGTCCAGT 58.435 40.909 5.55 0.00 0.00 4.00
2393 3323 9.159254 AGGTAGATCTGAATGTGGTAATTATCA 57.841 33.333 5.18 0.00 0.00 2.15
2405 3335 8.133024 TGTGGTAATTATCAGCCAAAATTTCT 57.867 30.769 0.00 0.00 32.26 2.52
3044 3974 7.707035 CGTAAGAATTTAGCTACTGGTCAAGAT 59.293 37.037 0.00 0.00 43.02 2.40
3336 4266 5.086621 AGCCCTGATGGTTATTCACTTTTT 58.913 37.500 0.00 0.00 36.04 1.94
3402 4332 0.397816 AGGAGCTCGGATACAGGCTT 60.398 55.000 7.83 0.00 42.76 4.35
3690 4620 2.842394 AAGCGGCTGATGACACCTCG 62.842 60.000 1.81 0.00 0.00 4.63
3732 4662 8.832735 TCTAGTCCAGTAAAACAAAGGGAATAT 58.167 33.333 0.00 0.00 0.00 1.28
3852 4782 4.882671 TTTTTCATCCTTAGATCAGCGC 57.117 40.909 0.00 0.00 0.00 5.92
3985 4915 8.686334 AGAGTCTTGTTATTCAAAAAGCTTCAA 58.314 29.630 0.00 0.00 35.48 2.69
4331 5262 4.202367 CCTGCAGGTAGAAATAACCCCTAG 60.202 50.000 25.53 0.00 37.77 3.02
4333 5264 5.531198 TGCAGGTAGAAATAACCCCTAGTA 58.469 41.667 0.00 0.00 37.77 1.82
4492 5423 0.389556 CGATGATGATGGGCTCCTCG 60.390 60.000 0.00 0.00 0.00 4.63
4691 5626 2.616256 CCTCAGTTCACCTTGCTGCATA 60.616 50.000 1.84 0.00 0.00 3.14
5294 6298 6.484643 TGGTTGAGAGATTTCTTCTTGAAGTG 59.515 38.462 9.80 0.00 35.89 3.16
5323 6327 4.624015 TGCTTTGCTGAAATCCTTCTTTG 58.376 39.130 0.00 0.00 32.33 2.77
5464 6504 6.348868 CCTGATGTTCTTGTAAGGCTCTTTTC 60.349 42.308 0.00 0.00 0.00 2.29
5534 6583 7.548967 AGACTGGTAGTTTCTATTAGTTGCTC 58.451 38.462 0.00 0.00 0.00 4.26
5553 6602 3.954904 GCTCTAGTCCATCCTGTTACAGA 59.045 47.826 14.66 0.42 32.44 3.41
5572 6623 8.410141 GTTACAGATACTAGCTTCACAGAAGAT 58.590 37.037 10.72 6.84 0.00 2.40
5573 6624 6.804677 ACAGATACTAGCTTCACAGAAGATG 58.195 40.000 10.72 2.77 0.00 2.90
5672 7040 2.857618 TGCATTCGATTTTAACACGGC 58.142 42.857 0.00 0.00 0.00 5.68
5980 7364 3.423154 GAAGCCAAGGACACCGCG 61.423 66.667 0.00 0.00 0.00 6.46
6158 7543 2.737376 GTGTGACCTCGGCGGAAC 60.737 66.667 7.21 0.00 36.31 3.62
6292 7683 4.243383 GCGCAATGCCGTTTCTTT 57.757 50.000 0.30 0.00 37.76 2.52
6347 7738 4.215399 CCTTTTCTGAAGCGAAATGGTGTA 59.785 41.667 8.99 0.00 40.54 2.90
6364 7771 4.202060 TGGTGTATTCTCTTCTCGCTCATC 60.202 45.833 0.00 0.00 0.00 2.92
6409 7842 4.856664 TCGCTTACATCGATCTTTACTCC 58.143 43.478 0.00 0.00 0.00 3.85
6431 7864 5.298527 TCCGAATAGAGTAGCGAATTTCAGA 59.701 40.000 0.00 0.00 0.00 3.27
6436 7869 9.464714 GAATAGAGTAGCGAATTTCAGATGTTA 57.535 33.333 0.00 0.00 0.00 2.41
6455 7888 1.734655 AGAGGCAAGTGGAGGAGAAA 58.265 50.000 0.00 0.00 0.00 2.52
6458 7891 1.072965 AGGCAAGTGGAGGAGAAACAG 59.927 52.381 0.00 0.00 0.00 3.16
6461 7894 3.006247 GCAAGTGGAGGAGAAACAGATC 58.994 50.000 0.00 0.00 0.00 2.75
6464 7897 2.757868 AGTGGAGGAGAAACAGATCGAG 59.242 50.000 0.00 0.00 0.00 4.04
6860 8308 1.202428 TGTCACCATTGTTGTCGTCGA 60.202 47.619 0.00 0.00 0.00 4.20
6861 8309 1.455786 GTCACCATTGTTGTCGTCGAG 59.544 52.381 0.00 0.00 0.00 4.04
6867 8315 1.034356 TTGTTGTCGTCGAGGAGGAA 58.966 50.000 8.30 1.82 0.00 3.36
6868 8316 1.254026 TGTTGTCGTCGAGGAGGAAT 58.746 50.000 8.30 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.621629 CCACCAATGTTATCTATTAACTGGTAA 57.378 33.333 8.31 0.00 42.82 2.85
4 5 7.717875 GCCACCAATGTTATCTATTAACTGGTA 59.282 37.037 8.31 0.00 42.82 3.25
5 6 6.546034 GCCACCAATGTTATCTATTAACTGGT 59.454 38.462 4.48 4.48 44.28 4.00
6 7 6.772716 AGCCACCAATGTTATCTATTAACTGG 59.227 38.462 0.00 0.00 39.94 4.00
7 8 7.807977 AGCCACCAATGTTATCTATTAACTG 57.192 36.000 0.00 0.00 40.77 3.16
14 15 9.283768 CACAATATTAGCCACCAATGTTATCTA 57.716 33.333 0.00 0.00 0.00 1.98
15 16 7.255590 GCACAATATTAGCCACCAATGTTATCT 60.256 37.037 1.60 0.00 0.00 1.98
16 17 6.863126 GCACAATATTAGCCACCAATGTTATC 59.137 38.462 1.60 0.00 0.00 1.75
17 18 6.323482 TGCACAATATTAGCCACCAATGTTAT 59.677 34.615 8.95 0.00 0.00 1.89
18 19 5.654209 TGCACAATATTAGCCACCAATGTTA 59.346 36.000 8.95 0.00 0.00 2.41
19 20 4.465660 TGCACAATATTAGCCACCAATGTT 59.534 37.500 8.95 0.00 0.00 2.71
20 21 4.022603 TGCACAATATTAGCCACCAATGT 58.977 39.130 8.95 0.00 0.00 2.71
21 22 4.652421 TGCACAATATTAGCCACCAATG 57.348 40.909 8.95 0.00 0.00 2.82
22 23 4.711355 AGTTGCACAATATTAGCCACCAAT 59.289 37.500 10.70 0.00 0.00 3.16
23 24 4.085733 AGTTGCACAATATTAGCCACCAA 58.914 39.130 10.70 0.00 0.00 3.67
24 25 3.696045 AGTTGCACAATATTAGCCACCA 58.304 40.909 10.70 0.00 0.00 4.17
25 26 4.718940 AAGTTGCACAATATTAGCCACC 57.281 40.909 10.70 1.14 0.00 4.61
26 27 6.265577 CCTAAAGTTGCACAATATTAGCCAC 58.734 40.000 8.95 8.30 0.00 5.01
27 28 5.359576 CCCTAAAGTTGCACAATATTAGCCA 59.640 40.000 8.95 0.00 0.00 4.75
28 29 5.221244 CCCCTAAAGTTGCACAATATTAGCC 60.221 44.000 8.95 0.00 0.00 3.93
29 30 5.736207 GCCCCTAAAGTTGCACAATATTAGC 60.736 44.000 5.38 5.38 0.00 3.09
30 31 5.359576 TGCCCCTAAAGTTGCACAATATTAG 59.640 40.000 0.00 9.45 0.00 1.73
31 32 5.265191 TGCCCCTAAAGTTGCACAATATTA 58.735 37.500 0.00 0.00 0.00 0.98
32 33 4.093011 TGCCCCTAAAGTTGCACAATATT 58.907 39.130 0.00 0.00 0.00 1.28
33 34 3.707316 TGCCCCTAAAGTTGCACAATAT 58.293 40.909 0.00 0.00 0.00 1.28
34 35 3.162147 TGCCCCTAAAGTTGCACAATA 57.838 42.857 0.00 0.00 0.00 1.90
35 36 2.008242 TGCCCCTAAAGTTGCACAAT 57.992 45.000 0.00 0.00 0.00 2.71
36 37 1.781786 TTGCCCCTAAAGTTGCACAA 58.218 45.000 0.00 0.00 32.63 3.33
37 38 2.008242 ATTGCCCCTAAAGTTGCACA 57.992 45.000 0.00 0.00 32.63 4.57
38 39 3.325870 GAAATTGCCCCTAAAGTTGCAC 58.674 45.455 0.00 0.00 32.63 4.57
39 40 2.301583 GGAAATTGCCCCTAAAGTTGCA 59.698 45.455 0.00 0.00 0.00 4.08
40 41 2.673893 CGGAAATTGCCCCTAAAGTTGC 60.674 50.000 0.00 0.00 0.00 4.17
41 42 2.560981 ACGGAAATTGCCCCTAAAGTTG 59.439 45.455 0.00 0.00 0.00 3.16
42 43 2.560981 CACGGAAATTGCCCCTAAAGTT 59.439 45.455 0.00 0.00 0.00 2.66
43 44 2.167662 CACGGAAATTGCCCCTAAAGT 58.832 47.619 0.00 0.00 0.00 2.66
44 45 2.163613 GTCACGGAAATTGCCCCTAAAG 59.836 50.000 0.00 0.00 0.00 1.85
45 46 2.164338 GTCACGGAAATTGCCCCTAAA 58.836 47.619 0.00 0.00 0.00 1.85
46 47 1.828979 GTCACGGAAATTGCCCCTAA 58.171 50.000 0.00 0.00 0.00 2.69
47 48 0.391927 CGTCACGGAAATTGCCCCTA 60.392 55.000 0.00 0.00 0.00 3.53
48 49 1.674322 CGTCACGGAAATTGCCCCT 60.674 57.895 0.00 0.00 0.00 4.79
49 50 0.674269 TACGTCACGGAAATTGCCCC 60.674 55.000 0.35 0.00 0.00 5.80
50 51 0.445043 GTACGTCACGGAAATTGCCC 59.555 55.000 0.35 0.00 0.00 5.36
51 52 0.445043 GGTACGTCACGGAAATTGCC 59.555 55.000 0.35 0.00 0.00 4.52
52 53 1.136169 GTGGTACGTCACGGAAATTGC 60.136 52.381 0.35 0.00 0.00 3.56
53 54 2.409975 AGTGGTACGTCACGGAAATTG 58.590 47.619 0.35 0.00 42.10 2.32
54 55 2.825861 AGTGGTACGTCACGGAAATT 57.174 45.000 0.35 0.00 42.10 1.82
55 56 3.084039 TCTAGTGGTACGTCACGGAAAT 58.916 45.455 0.35 0.00 42.10 2.17
56 57 2.503331 TCTAGTGGTACGTCACGGAAA 58.497 47.619 0.35 0.00 42.10 3.13
57 58 2.183478 TCTAGTGGTACGTCACGGAA 57.817 50.000 0.35 0.00 42.10 4.30
58 59 2.079158 CTTCTAGTGGTACGTCACGGA 58.921 52.381 0.35 0.00 42.10 4.69
59 60 1.467035 GCTTCTAGTGGTACGTCACGG 60.467 57.143 0.35 0.00 42.10 4.94
60 61 1.198408 TGCTTCTAGTGGTACGTCACG 59.802 52.381 0.00 0.00 42.10 4.35
61 62 3.293311 TTGCTTCTAGTGGTACGTCAC 57.707 47.619 0.00 0.00 37.89 3.67
62 63 4.439700 GCTATTGCTTCTAGTGGTACGTCA 60.440 45.833 0.00 0.00 36.03 4.35
63 64 4.043073 GCTATTGCTTCTAGTGGTACGTC 58.957 47.826 0.00 0.00 36.03 4.34
64 65 3.181478 GGCTATTGCTTCTAGTGGTACGT 60.181 47.826 0.00 0.00 39.59 3.57
65 66 3.381949 GGCTATTGCTTCTAGTGGTACG 58.618 50.000 0.00 0.00 39.59 3.67
66 67 3.494573 GGGGCTATTGCTTCTAGTGGTAC 60.495 52.174 0.00 0.00 39.59 3.34
67 68 2.704065 GGGGCTATTGCTTCTAGTGGTA 59.296 50.000 0.00 0.00 39.59 3.25
68 69 1.490910 GGGGCTATTGCTTCTAGTGGT 59.509 52.381 0.00 0.00 39.59 4.16
69 70 1.771255 AGGGGCTATTGCTTCTAGTGG 59.229 52.381 0.00 0.00 39.59 4.00
70 71 3.567478 AAGGGGCTATTGCTTCTAGTG 57.433 47.619 0.00 0.00 39.59 2.74
71 72 5.913946 ATAAAGGGGCTATTGCTTCTAGT 57.086 39.130 0.00 0.00 39.59 2.57
72 73 8.870075 AATAATAAAGGGGCTATTGCTTCTAG 57.130 34.615 0.00 0.00 39.59 2.43
73 74 9.077885 CAAATAATAAAGGGGCTATTGCTTCTA 57.922 33.333 0.00 0.00 39.59 2.10
74 75 7.784550 TCAAATAATAAAGGGGCTATTGCTTCT 59.215 33.333 0.00 0.00 39.59 2.85
75 76 7.951591 TCAAATAATAAAGGGGCTATTGCTTC 58.048 34.615 0.00 0.00 39.59 3.86
76 77 7.912778 TCAAATAATAAAGGGGCTATTGCTT 57.087 32.000 0.00 0.00 39.59 3.91
77 78 9.774071 ATATCAAATAATAAAGGGGCTATTGCT 57.226 29.630 0.00 0.00 39.59 3.91
174 175 9.796120 ACTTGATTTTTAAATTGACTGTTTCGA 57.204 25.926 0.00 0.00 0.00 3.71
208 209 8.040716 AGGTGTATGCCTAATTAATTAATCGC 57.959 34.615 11.08 12.73 37.04 4.58
245 246 8.429641 ACGGCTGGAAAAATCTCTAATTATCTA 58.570 33.333 0.00 0.00 0.00 1.98
256 257 4.159693 GGGAAAATACGGCTGGAAAAATCT 59.840 41.667 0.00 0.00 0.00 2.40
263 264 4.657039 ACTATTAGGGAAAATACGGCTGGA 59.343 41.667 0.00 0.00 0.00 3.86
265 266 5.696724 CAGACTATTAGGGAAAATACGGCTG 59.303 44.000 0.00 0.00 0.00 4.85
267 268 5.850614 TCAGACTATTAGGGAAAATACGGC 58.149 41.667 0.00 0.00 0.00 5.68
268 269 7.097834 GGATCAGACTATTAGGGAAAATACGG 58.902 42.308 0.00 0.00 0.00 4.02
269 270 7.599245 GTGGATCAGACTATTAGGGAAAATACG 59.401 40.741 0.00 0.00 0.00 3.06
270 271 8.652290 AGTGGATCAGACTATTAGGGAAAATAC 58.348 37.037 0.00 0.00 0.00 1.89
300 321 4.022676 GGTGGTTTTGAAAAGAATAGCCGA 60.023 41.667 0.00 0.00 0.00 5.54
301 322 4.234574 GGTGGTTTTGAAAAGAATAGCCG 58.765 43.478 0.00 0.00 0.00 5.52
302 323 4.039852 TGGGTGGTTTTGAAAAGAATAGCC 59.960 41.667 0.00 0.00 0.00 3.93
315 336 3.053917 AGCGGTAGATTATGGGTGGTTTT 60.054 43.478 0.00 0.00 0.00 2.43
321 342 1.692519 GTGGAGCGGTAGATTATGGGT 59.307 52.381 0.00 0.00 0.00 4.51
330 351 2.586079 CGGCATGTGGAGCGGTAG 60.586 66.667 0.00 0.00 0.00 3.18
338 359 2.437200 AAAACAATGACGGCATGTGG 57.563 45.000 3.39 0.00 34.26 4.17
357 378 7.833682 TGGGTTGCTATGAGATGAAAAGAATAA 59.166 33.333 0.00 0.00 0.00 1.40
360 381 5.415701 GTGGGTTGCTATGAGATGAAAAGAA 59.584 40.000 0.00 0.00 0.00 2.52
361 382 4.943705 GTGGGTTGCTATGAGATGAAAAGA 59.056 41.667 0.00 0.00 0.00 2.52
362 383 4.201851 CGTGGGTTGCTATGAGATGAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
371 392 3.620427 AATACACGTGGGTTGCTATGA 57.380 42.857 21.57 0.00 0.00 2.15
381 402 6.790285 AACCAACTAACTAAATACACGTGG 57.210 37.500 21.57 2.84 0.00 4.94
384 405 9.801714 CTTTGTAACCAACTAACTAAATACACG 57.198 33.333 0.00 0.00 0.00 4.49
398 419 9.836076 GATTGGTAAGATAACTTTGTAACCAAC 57.164 33.333 15.94 9.34 45.49 3.77
418 439 6.610075 ATTAGCAACTTTTCATGGATTGGT 57.390 33.333 0.00 0.00 35.37 3.67
424 445 6.017275 TGCCAAAAATTAGCAACTTTTCATGG 60.017 34.615 0.00 0.00 32.56 3.66
427 448 6.597280 ACTTGCCAAAAATTAGCAACTTTTCA 59.403 30.769 0.00 0.00 41.35 2.69
428 449 7.011389 AGACTTGCCAAAAATTAGCAACTTTTC 59.989 33.333 0.00 0.00 41.35 2.29
434 617 5.669477 ACAAGACTTGCCAAAAATTAGCAA 58.331 33.333 15.24 0.00 43.83 3.91
438 621 5.759506 TCGACAAGACTTGCCAAAAATTA 57.240 34.783 15.24 0.00 0.00 1.40
469 652 0.184692 TGGAGACATTGGTGTTGCCA 59.815 50.000 0.00 0.00 40.14 4.92
470 653 3.034924 TGGAGACATTGGTGTTGCC 57.965 52.632 0.00 0.00 39.09 4.52
487 670 3.099141 AGGGGACTGCCAATTTAACATG 58.901 45.455 0.00 0.00 41.13 3.21
492 675 3.731431 TCTAGAGGGGACTGCCAATTTA 58.269 45.455 0.00 0.00 44.43 1.40
504 687 3.227614 GACTAGGAAGCTTCTAGAGGGG 58.772 54.545 25.05 11.20 38.02 4.79
505 688 2.882137 CGACTAGGAAGCTTCTAGAGGG 59.118 54.545 25.05 12.11 38.02 4.30
521 704 0.871722 GGTGTTGTGCAATGCGACTA 59.128 50.000 0.00 0.00 0.00 2.59
526 709 0.385029 TGTGAGGTGTTGTGCAATGC 59.615 50.000 0.00 0.00 0.00 3.56
551 734 1.072266 ATTGGTAGGTGCCTTGTGGA 58.928 50.000 0.00 0.00 34.57 4.02
558 741 4.210724 TGTAGTTGTATTGGTAGGTGCC 57.789 45.455 0.00 0.00 0.00 5.01
573 756 3.334583 AGCATCCGATGTGTTGTAGTT 57.665 42.857 10.10 0.00 0.00 2.24
574 757 3.002791 CAAGCATCCGATGTGTTGTAGT 58.997 45.455 10.10 0.00 0.00 2.73
575 758 3.002791 ACAAGCATCCGATGTGTTGTAG 58.997 45.455 20.87 5.86 37.61 2.74
576 759 2.741517 CACAAGCATCCGATGTGTTGTA 59.258 45.455 21.39 0.00 39.60 2.41
577 760 1.536766 CACAAGCATCCGATGTGTTGT 59.463 47.619 18.40 18.40 39.60 3.32
578 761 1.135603 CCACAAGCATCCGATGTGTTG 60.136 52.381 17.49 17.49 42.17 3.33
597 780 3.940209 TTGTGTCCTTTGCATTCATCC 57.060 42.857 0.00 0.00 0.00 3.51
619 802 1.070821 TTGAGATTCGTGCTGCTTCG 58.929 50.000 0.00 6.34 0.00 3.79
620 803 2.727298 GCTTTGAGATTCGTGCTGCTTC 60.727 50.000 0.00 0.00 0.00 3.86
623 806 0.518636 TGCTTTGAGATTCGTGCTGC 59.481 50.000 0.00 0.00 0.00 5.25
824 1009 3.800833 GGGGGCGATTTACGGGGT 61.801 66.667 0.00 0.00 42.83 4.95
901 1086 1.610554 CGAAAACCCTAGCTCCGGGA 61.611 60.000 23.90 0.00 44.90 5.14
1210 1675 1.586564 CTGAACCTCGACGCCGATC 60.587 63.158 0.00 0.00 44.62 3.69
1256 1820 0.887933 CAATGGCTACCACCACAACC 59.112 55.000 0.00 0.00 44.17 3.77
1258 1822 2.652313 GCAATGGCTACCACCACAA 58.348 52.632 0.00 0.00 44.17 3.33
1285 1850 1.293924 CTAATGCAGAGAACGGCCTG 58.706 55.000 0.00 0.00 36.45 4.85
1287 1852 0.462759 AGCTAATGCAGAGAACGGCC 60.463 55.000 0.00 0.00 42.74 6.13
1319 1884 2.288640 CCCTAAGACCGAAACGACAACT 60.289 50.000 0.00 0.00 0.00 3.16
1331 1898 1.121378 GGCACTACTCCCCTAAGACC 58.879 60.000 0.00 0.00 0.00 3.85
1333 1900 2.467880 CTTGGCACTACTCCCCTAAGA 58.532 52.381 0.00 0.00 0.00 2.10
1377 1950 3.866066 GCCATCTACACTTGAGCTCAACA 60.866 47.826 25.16 6.48 0.00 3.33
1384 1957 6.477033 GTGTACTATTGCCATCTACACTTGAG 59.523 42.308 9.69 0.00 36.05 3.02
1409 1982 1.413767 GCCGCTACGACACACTGATG 61.414 60.000 0.00 0.00 0.00 3.07
1427 2000 6.576313 CGACATATCAAATGAGCAACAATAGC 59.424 38.462 0.00 0.00 0.00 2.97
1443 2016 2.094957 TCGTGCACAGAACGACATATCA 60.095 45.455 18.64 0.00 44.58 2.15
1444 2017 2.526077 TCGTGCACAGAACGACATATC 58.474 47.619 18.64 0.00 44.58 1.63
1462 2035 1.129326 GACTGAACCTCACGTGTTCG 58.871 55.000 16.51 10.59 43.95 3.95
1463 2036 2.510768 AGACTGAACCTCACGTGTTC 57.489 50.000 16.51 12.59 41.91 3.18
1465 2038 1.480954 ACAAGACTGAACCTCACGTGT 59.519 47.619 16.51 0.00 0.00 4.49
1467 2040 2.288273 GCTACAAGACTGAACCTCACGT 60.288 50.000 0.00 0.00 0.00 4.49
1468 2041 2.329379 GCTACAAGACTGAACCTCACG 58.671 52.381 0.00 0.00 0.00 4.35
1481 2054 2.351726 GAGCAATGGTTACCGCTACAAG 59.648 50.000 2.38 0.00 34.12 3.16
1496 2069 8.554528 CAGAGAATGACATATAAAACGAGCAAT 58.445 33.333 0.00 0.00 0.00 3.56
1515 2088 1.627329 TCACAAGCTCCTGCAGAGAAT 59.373 47.619 17.39 0.00 46.50 2.40
1525 2098 3.051081 ACACTGAATCTCACAAGCTCC 57.949 47.619 0.00 0.00 0.00 4.70
1526 2099 3.812053 ACAACACTGAATCTCACAAGCTC 59.188 43.478 0.00 0.00 0.00 4.09
1553 2126 1.000163 CGCAGATATCTGTAAGCCGGT 60.000 52.381 28.92 0.00 45.45 5.28
1565 2138 2.028112 AGACACACAACCACGCAGATAT 60.028 45.455 0.00 0.00 0.00 1.63
1566 2139 1.343142 AGACACACAACCACGCAGATA 59.657 47.619 0.00 0.00 0.00 1.98
1606 2179 4.965119 AACTTCAGTCAAGGACAACAAC 57.035 40.909 0.00 0.00 36.26 3.32
1639 2496 7.411588 CGAATAGCAACAAGTTCCTAACACTAC 60.412 40.741 0.00 0.00 0.00 2.73
1644 2501 4.694037 ACCGAATAGCAACAAGTTCCTAAC 59.306 41.667 0.00 0.00 0.00 2.34
1664 2521 2.149803 TTGACCGGAGTGTGCTACCG 62.150 60.000 9.46 0.00 45.24 4.02
1668 2525 2.031163 GCTTGACCGGAGTGTGCT 59.969 61.111 9.46 0.00 0.00 4.40
1673 2530 2.341846 TTTTCAAGCTTGACCGGAGT 57.658 45.000 28.46 0.00 36.83 3.85
1750 2608 5.873146 AGCTTCTATTAGTTACCTCCCAC 57.127 43.478 0.00 0.00 0.00 4.61
1754 2612 9.833917 AAACCATAAGCTTCTATTAGTTACCTC 57.166 33.333 0.00 0.00 0.00 3.85
1770 2628 7.375053 TCAAACAAACATCCTAAACCATAAGC 58.625 34.615 0.00 0.00 0.00 3.09
1771 2629 8.792633 TCTCAAACAAACATCCTAAACCATAAG 58.207 33.333 0.00 0.00 0.00 1.73
1796 2707 6.491403 AGAATCCAACCAATATACCAGCATTC 59.509 38.462 0.00 0.00 0.00 2.67
1836 2747 5.773575 TGCAGTTTGACACAACAAGTTAAA 58.226 33.333 0.00 0.00 0.00 1.52
1853 2773 7.945134 AGAGTTGATGTAAAATTCTTGCAGTT 58.055 30.769 0.00 0.00 0.00 3.16
1956 2878 6.130298 TGTTCCATATGCGAACCTATTTTG 57.870 37.500 23.15 0.00 39.10 2.44
2393 3323 3.494332 AGACAGCTCAGAAATTTTGGCT 58.506 40.909 0.00 0.00 0.00 4.75
2405 3335 5.880332 ACAAAAGACTAACAAAGACAGCTCA 59.120 36.000 0.00 0.00 0.00 4.26
2437 3367 3.120792 TCGGCATAAGAAACAGATACGC 58.879 45.455 0.00 0.00 0.00 4.42
3044 3974 3.286751 GCTGGTGCCGTCTTTGCA 61.287 61.111 0.00 0.00 36.12 4.08
3336 4266 1.332889 ATCCATCCAGAGAGCACGCA 61.333 55.000 0.00 0.00 0.00 5.24
3390 4320 4.038042 TCAGAATCACTAAGCCTGTATCCG 59.962 45.833 0.00 0.00 0.00 4.18
3402 4332 9.958180 TTTAATTCATCCAGTTCAGAATCACTA 57.042 29.630 0.00 0.00 30.87 2.74
3690 4620 4.038522 GGACTAGATACCCGGGTAACTTTC 59.961 50.000 38.87 32.44 35.72 2.62
3732 4662 3.822192 CGACCATCAGGACGCCGA 61.822 66.667 0.00 0.00 45.21 5.54
3852 4782 3.426309 ATTCTCCCCAGGGCGCATG 62.426 63.158 10.83 7.39 34.68 4.06
3864 4794 7.038659 CGTAGGATGATCTTATTCCATTCTCC 58.961 42.308 0.00 0.00 29.58 3.71
3985 4915 1.274703 CCATCCCTGCCAGTACCAGT 61.275 60.000 0.00 0.00 0.00 4.00
4391 5322 5.523883 TGGGTAGTTTAGGGCTAACATTT 57.476 39.130 0.00 0.00 0.00 2.32
4492 5423 7.912250 CAGTCATCACAATCTATAAAAACAGCC 59.088 37.037 0.00 0.00 0.00 4.85
4691 5626 4.953667 ACATGCATCAGACACTAATCGAT 58.046 39.130 0.00 0.00 0.00 3.59
5294 6298 4.340381 AGGATTTCAGCAAAGCATGATACC 59.660 41.667 0.00 0.00 28.75 2.73
5464 6504 4.717877 TGTATGCCATGGAATCTAACAGG 58.282 43.478 18.40 0.00 0.00 4.00
5534 6583 7.094549 GCTAGTATCTGTAACAGGATGGACTAG 60.095 44.444 13.15 13.15 43.62 2.57
5553 6602 6.992664 ATCCATCTTCTGTGAAGCTAGTAT 57.007 37.500 2.71 0.00 0.00 2.12
5654 7021 3.088552 GACGCCGTGTTAAAATCGAATG 58.911 45.455 0.00 0.00 0.00 2.67
5664 7031 2.304401 CGCAACTGACGCCGTGTTA 61.304 57.895 0.00 0.00 0.00 2.41
5672 7040 1.073216 ATCGAAGAGCGCAACTGACG 61.073 55.000 11.47 16.74 43.63 4.35
5712 7082 5.104982 TGTTTCTTCATTCCCTGCAAAAGTT 60.105 36.000 0.00 0.00 0.00 2.66
5980 7364 1.132453 GAAGGGTTTGTTCGCTATGCC 59.868 52.381 0.00 0.00 0.00 4.40
6158 7543 2.132762 ACAGCGAACAGGTTAAAGTCG 58.867 47.619 0.00 0.00 0.00 4.18
6224 7612 7.618137 ACCTACGGATAAAACTGTTACAGAAT 58.382 34.615 20.07 4.51 35.18 2.40
6292 7683 1.580942 GTGCATCCTGCTCGCAAAA 59.419 52.632 0.00 0.00 45.31 2.44
6347 7738 2.028130 ACGGATGAGCGAGAAGAGAAT 58.972 47.619 0.00 0.00 0.00 2.40
6364 7771 2.950877 GAGCATCGAACTCTGACGG 58.049 57.895 10.67 0.00 0.00 4.79
6409 7842 6.638873 ACATCTGAAATTCGCTACTCTATTCG 59.361 38.462 0.00 0.00 0.00 3.34
6431 7864 2.503356 CTCCTCCACTTGCCTCTAACAT 59.497 50.000 0.00 0.00 0.00 2.71
6436 7869 1.349357 GTTTCTCCTCCACTTGCCTCT 59.651 52.381 0.00 0.00 0.00 3.69
6860 8308 2.187946 CTTCGCCGCATTCCTCCT 59.812 61.111 0.00 0.00 0.00 3.69
6861 8309 2.897350 CCTTCGCCGCATTCCTCC 60.897 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.