Multiple sequence alignment - TraesCS2B01G154900

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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 TraesCS2B01G154900 chr2B 100.000 3569 0 0 1 3569 122925525 122929093 0.000000e+00 6591.0
1 TraesCS2B01G154900 chr2B 94.314 2691 108 18 674 3363 122992011 122994657 0.000000e+00 4080.0
2 TraesCS2B01G154900 chr2B 78.977 1584 178 71 844 2367 55032861 55031373 0.000000e+00 937.0
3 TraesCS2B01G154900 chr2B 90.463 713 57 5 2652 3364 172722355 172723056 0.000000e+00 929.0
4 TraesCS2B01G154900 chr2B 83.614 830 68 32 859 1666 54787479 54786696 0.000000e+00 717.0
5 TraesCS2B01G154900 chr2B 80.968 909 122 32 888 1779 55203674 55202800 0.000000e+00 673.0
6 TraesCS2B01G154900 chr2B 79.201 726 85 40 897 1616 55699399 55698734 9.090000e-121 444.0
7 TraesCS2B01G154900 chr2B 86.494 385 33 7 858 1241 55227656 55227290 4.290000e-109 405.0
8 TraesCS2B01G154900 chr2B 79.221 385 51 13 3179 3553 54785722 54785357 1.280000e-59 241.0
9 TraesCS2B01G154900 chr2B 86.408 206 11 5 3364 3569 122994748 122994936 3.610000e-50 209.0
10 TraesCS2B01G154900 chr2B 75.890 365 66 18 2830 3180 601733860 601734216 2.200000e-37 167.0
11 TraesCS2B01G154900 chr2B 94.667 75 4 0 2425 2499 172722200 172722274 2.250000e-22 117.0
12 TraesCS2B01G154900 chr2B 92.958 71 5 0 405 475 122991889 122991959 1.750000e-18 104.0
13 TraesCS2B01G154900 chr2B 85.263 95 12 2 2521 2615 55225316 55225224 2.930000e-16 97.1
14 TraesCS2B01G154900 chr2A 92.009 2728 124 29 859 3569 79342308 79344958 0.000000e+00 3744.0
15 TraesCS2B01G154900 chr2A 80.851 846 88 49 854 1671 36392812 36392013 6.600000e-167 597.0
16 TraesCS2B01G154900 chr2A 87.701 374 40 3 34 403 174457507 174457136 7.080000e-117 431.0
17 TraesCS2B01G154900 chr2A 86.632 389 49 1 1231 1616 36202794 36202406 9.160000e-116 427.0
18 TraesCS2B01G154900 chr2A 78.973 623 79 30 1751 2356 36234937 36234350 9.350000e-101 377.0
19 TraesCS2B01G154900 chr2A 82.426 404 51 14 3163 3554 36410258 36409863 5.710000e-88 335.0
20 TraesCS2B01G154900 chr2A 79.830 352 56 5 2076 2417 36399399 36399053 3.560000e-60 243.0
21 TraesCS2B01G154900 chr2A 80.606 330 47 12 2076 2392 36391919 36391594 4.600000e-59 239.0
22 TraesCS2B01G154900 chr2A 97.561 41 1 0 429 469 36401643 36401603 1.780000e-08 71.3
23 TraesCS2B01G154900 chr2D 95.171 1636 64 6 866 2499 79084882 79086504 0.000000e+00 2569.0
24 TraesCS2B01G154900 chr2D 92.308 598 32 5 2971 3568 79086870 79087453 0.000000e+00 837.0
25 TraesCS2B01G154900 chr2D 84.154 833 86 21 858 1671 33315537 33314732 0.000000e+00 765.0
26 TraesCS2B01G154900 chr2D 83.141 866 85 31 844 1672 33165479 33164638 0.000000e+00 734.0
27 TraesCS2B01G154900 chr2D 83.374 812 92 24 888 1671 33374315 33373519 0.000000e+00 712.0
28 TraesCS2B01G154900 chr2D 80.621 676 89 25 1731 2388 33164618 33163967 5.360000e-133 484.0
29 TraesCS2B01G154900 chr2D 86.632 389 49 1 1231 1616 33049299 33048911 9.160000e-116 427.0
30 TraesCS2B01G154900 chr2D 89.320 309 26 6 523 829 79084585 79084888 7.230000e-102 381.0
31 TraesCS2B01G154900 chr2D 87.234 282 26 3 2657 2938 79086596 79086867 2.680000e-81 313.0
32 TraesCS2B01G154900 chr2D 90.476 231 19 3 173 403 79083682 79083909 5.790000e-78 302.0
33 TraesCS2B01G154900 chr2D 81.365 381 56 12 3179 3553 33047172 33046801 2.690000e-76 296.0
34 TraesCS2B01G154900 chr2D 76.896 567 84 33 2076 2606 33314586 33314031 9.760000e-71 278.0
35 TraesCS2B01G154900 chr2D 96.000 75 3 0 401 475 79084401 79084475 4.840000e-24 122.0
36 TraesCS2B01G154900 chr2D 81.102 127 19 4 2491 2615 33371816 33371693 2.930000e-16 97.1
37 TraesCS2B01G154900 chr1B 91.904 457 30 1 2825 3281 67349266 67349715 1.810000e-177 632.0
38 TraesCS2B01G154900 chrUn 92.000 325 18 2 2973 3297 38525037 38524721 1.950000e-122 449.0
39 TraesCS2B01G154900 chr3B 92.000 325 18 2 2973 3297 34594315 34593999 1.950000e-122 449.0
40 TraesCS2B01G154900 chr7A 74.055 1376 215 84 2235 3553 77732665 77733955 1.970000e-117 433.0
41 TraesCS2B01G154900 chr7A 83.459 133 20 2 2481 2612 78389745 78389876 4.840000e-24 122.0
42 TraesCS2B01G154900 chr7A 81.203 133 19 3 2481 2612 78391049 78391176 6.300000e-18 102.0
43 TraesCS2B01G154900 chr6A 76.676 343 55 21 2854 3180 561588652 561588319 2.200000e-37 167.0
44 TraesCS2B01G154900 chr6A 83.626 171 18 9 3368 3533 31881587 31881752 6.170000e-33 152.0
45 TraesCS2B01G154900 chr6D 85.616 146 15 6 3368 3512 30748348 30748488 7.980000e-32 148.0
46 TraesCS2B01G154900 chr7D 83.459 133 20 2 2481 2612 74392883 74393014 4.840000e-24 122.0
47 TraesCS2B01G154900 chr7B 81.818 132 22 2 2481 2611 17508939 17509069 3.770000e-20 110.0
48 TraesCS2B01G154900 chr5D 86.170 94 12 1 2518 2611 214784752 214784844 2.270000e-17 100.0


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 TraesCS2B01G154900 chr2B 122925525 122929093 3568 False 6591.000000 6591 100.000000 1 3569 1 chr2B.!!$F1 3568
1 TraesCS2B01G154900 chr2B 122991889 122994936 3047 False 1464.333333 4080 91.226667 405 3569 3 chr2B.!!$F3 3164
2 TraesCS2B01G154900 chr2B 55031373 55032861 1488 True 937.000000 937 78.977000 844 2367 1 chr2B.!!$R1 1523
3 TraesCS2B01G154900 chr2B 55202800 55203674 874 True 673.000000 673 80.968000 888 1779 1 chr2B.!!$R2 891
4 TraesCS2B01G154900 chr2B 172722200 172723056 856 False 523.000000 929 92.565000 2425 3364 2 chr2B.!!$F4 939
5 TraesCS2B01G154900 chr2B 54785357 54787479 2122 True 479.000000 717 81.417500 859 3553 2 chr2B.!!$R4 2694
6 TraesCS2B01G154900 chr2B 55698734 55699399 665 True 444.000000 444 79.201000 897 1616 1 chr2B.!!$R3 719
7 TraesCS2B01G154900 chr2B 55225224 55227656 2432 True 251.050000 405 85.878500 858 2615 2 chr2B.!!$R5 1757
8 TraesCS2B01G154900 chr2A 79342308 79344958 2650 False 3744.000000 3744 92.009000 859 3569 1 chr2A.!!$F1 2710
9 TraesCS2B01G154900 chr2A 36391594 36392812 1218 True 418.000000 597 80.728500 854 2392 2 chr2A.!!$R5 1538
10 TraesCS2B01G154900 chr2A 36234350 36234937 587 True 377.000000 377 78.973000 1751 2356 1 chr2A.!!$R2 605
11 TraesCS2B01G154900 chr2D 79083682 79087453 3771 False 754.000000 2569 91.751500 173 3568 6 chr2D.!!$F1 3395
12 TraesCS2B01G154900 chr2D 33163967 33165479 1512 True 609.000000 734 81.881000 844 2388 2 chr2D.!!$R2 1544
13 TraesCS2B01G154900 chr2D 33314031 33315537 1506 True 521.500000 765 80.525000 858 2606 2 chr2D.!!$R3 1748
14 TraesCS2B01G154900 chr2D 33371693 33374315 2622 True 404.550000 712 82.238000 888 2615 2 chr2D.!!$R4 1727
15 TraesCS2B01G154900 chr2D 33046801 33049299 2498 True 361.500000 427 83.998500 1231 3553 2 chr2D.!!$R1 2322
16 TraesCS2B01G154900 chr7A 77732665 77733955 1290 False 433.000000 433 74.055000 2235 3553 1 chr7A.!!$F1 1318

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
140 141 0.036732 TGGCAGTTGGTCATGGTCTC 59.963 55.000 0.00 0.00 0.00 3.36 F
141 142 0.036732 GGCAGTTGGTCATGGTCTCA 59.963 55.000 0.00 0.00 0.00 3.27 F
846 1416 0.266152 GGAGGAGGAATGGAGGAGGA 59.734 60.000 0.00 0.00 0.00 3.71 F
2364 3404 1.380689 TCGTGGTGAGAGCCTCTCT 59.619 57.895 21.72 10.33 43.73 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 2499 4.039488 TGCTCTCACAAATTTGGCAAGAAT 59.961 37.5 21.74 0.0 0.00 2.40 R
2365 3405 0.394899 GAAGTTGGGGCATGGAGAGG 60.395 60.0 0.00 0.0 0.00 3.69 R
2460 3539 0.097674 GCACAAGCAGATTAGCACCG 59.902 55.0 0.00 0.0 41.58 4.94 R
3483 5560 0.320683 CTGGGTGTCGCAGTTCATCA 60.321 55.0 5.80 0.0 39.17 3.07 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
51 52 8.907222 ATCATATTATTTGCCCATGAAAAACC 57.093 30.769 0.00 0.00 0.00 3.27
52 53 7.855375 TCATATTATTTGCCCATGAAAAACCA 58.145 30.769 0.00 0.00 0.00 3.67
53 54 8.492782 TCATATTATTTGCCCATGAAAAACCAT 58.507 29.630 0.00 0.00 0.00 3.55
54 55 9.122779 CATATTATTTGCCCATGAAAAACCATT 57.877 29.630 0.00 0.00 0.00 3.16
55 56 7.628769 ATTATTTGCCCATGAAAAACCATTC 57.371 32.000 0.00 0.00 0.00 2.67
56 57 4.428294 TTTGCCCATGAAAAACCATTCA 57.572 36.364 0.00 0.00 43.03 2.57
57 58 4.428294 TTGCCCATGAAAAACCATTCAA 57.572 36.364 0.00 0.00 42.22 2.69
58 59 4.637387 TGCCCATGAAAAACCATTCAAT 57.363 36.364 0.00 0.00 42.22 2.57
59 60 5.752036 TGCCCATGAAAAACCATTCAATA 57.248 34.783 0.00 0.00 42.22 1.90
60 61 6.119240 TGCCCATGAAAAACCATTCAATAA 57.881 33.333 0.00 0.00 42.22 1.40
61 62 5.936956 TGCCCATGAAAAACCATTCAATAAC 59.063 36.000 0.00 0.00 42.22 1.89
62 63 6.172630 GCCCATGAAAAACCATTCAATAACT 58.827 36.000 0.00 0.00 42.22 2.24
63 64 7.038729 TGCCCATGAAAAACCATTCAATAACTA 60.039 33.333 0.00 0.00 42.22 2.24
64 65 7.821846 GCCCATGAAAAACCATTCAATAACTAA 59.178 33.333 0.00 0.00 42.22 2.24
65 66 9.369904 CCCATGAAAAACCATTCAATAACTAAG 57.630 33.333 0.00 0.00 42.22 2.18
66 67 9.369904 CCATGAAAAACCATTCAATAACTAAGG 57.630 33.333 0.00 0.00 42.22 2.69
67 68 8.872845 CATGAAAAACCATTCAATAACTAAGGC 58.127 33.333 0.00 0.00 42.22 4.35
68 69 7.957002 TGAAAAACCATTCAATAACTAAGGCA 58.043 30.769 0.00 0.00 36.42 4.75
69 70 8.424918 TGAAAAACCATTCAATAACTAAGGCAA 58.575 29.630 0.00 0.00 36.42 4.52
70 71 8.601845 AAAAACCATTCAATAACTAAGGCAAC 57.398 30.769 0.00 0.00 0.00 4.17
71 72 6.909550 AACCATTCAATAACTAAGGCAACA 57.090 33.333 0.00 0.00 41.41 3.33
72 73 6.267496 ACCATTCAATAACTAAGGCAACAC 57.733 37.500 0.00 0.00 41.41 3.32
73 74 5.185056 ACCATTCAATAACTAAGGCAACACC 59.815 40.000 0.00 0.00 41.41 4.16
74 75 5.184864 CCATTCAATAACTAAGGCAACACCA 59.815 40.000 0.00 0.00 43.14 4.17
75 76 5.699097 TTCAATAACTAAGGCAACACCAC 57.301 39.130 0.00 0.00 43.14 4.16
76 77 3.749088 TCAATAACTAAGGCAACACCACG 59.251 43.478 0.00 0.00 43.14 4.94
77 78 3.688694 ATAACTAAGGCAACACCACGA 57.311 42.857 0.00 0.00 43.14 4.35
78 79 1.878953 AACTAAGGCAACACCACGAG 58.121 50.000 0.00 0.00 43.14 4.18
79 80 1.045407 ACTAAGGCAACACCACGAGA 58.955 50.000 0.00 0.00 43.14 4.04
80 81 1.623811 ACTAAGGCAACACCACGAGAT 59.376 47.619 0.00 0.00 43.14 2.75
81 82 2.002586 CTAAGGCAACACCACGAGATG 58.997 52.381 0.00 0.00 43.14 2.90
82 83 0.396435 AAGGCAACACCACGAGATGA 59.604 50.000 0.00 0.00 43.14 2.92
83 84 0.396435 AGGCAACACCACGAGATGAA 59.604 50.000 0.00 0.00 43.14 2.57
84 85 1.202758 AGGCAACACCACGAGATGAAA 60.203 47.619 0.00 0.00 43.14 2.69
85 86 1.812571 GGCAACACCACGAGATGAAAT 59.187 47.619 0.00 0.00 38.86 2.17
86 87 2.414559 GGCAACACCACGAGATGAAATG 60.415 50.000 0.00 0.00 38.86 2.32
87 88 2.414559 GCAACACCACGAGATGAAATGG 60.415 50.000 0.00 0.00 38.26 3.16
88 89 2.813754 CAACACCACGAGATGAAATGGT 59.186 45.455 0.00 0.00 46.53 3.55
90 91 2.859165 ACCACGAGATGAAATGGTGT 57.141 45.000 0.00 0.00 43.88 4.16
91 92 2.699954 ACCACGAGATGAAATGGTGTC 58.300 47.619 0.00 0.00 43.88 3.67
92 93 2.038426 ACCACGAGATGAAATGGTGTCA 59.962 45.455 0.00 0.00 43.88 3.58
93 94 3.073678 CCACGAGATGAAATGGTGTCAA 58.926 45.455 0.00 0.00 0.00 3.18
94 95 3.125829 CCACGAGATGAAATGGTGTCAAG 59.874 47.826 0.00 0.00 0.00 3.02
95 96 3.125829 CACGAGATGAAATGGTGTCAAGG 59.874 47.826 0.00 0.00 0.00 3.61
96 97 3.244561 ACGAGATGAAATGGTGTCAAGGT 60.245 43.478 0.00 0.00 0.00 3.50
97 98 3.753272 CGAGATGAAATGGTGTCAAGGTT 59.247 43.478 0.00 0.00 0.00 3.50
98 99 4.378770 CGAGATGAAATGGTGTCAAGGTTG 60.379 45.833 0.00 0.00 0.00 3.77
99 100 3.828451 AGATGAAATGGTGTCAAGGTTGG 59.172 43.478 0.00 0.00 0.00 3.77
100 101 3.304911 TGAAATGGTGTCAAGGTTGGA 57.695 42.857 0.00 0.00 0.00 3.53
101 102 2.955660 TGAAATGGTGTCAAGGTTGGAC 59.044 45.455 0.00 0.00 35.83 4.02
102 103 2.746279 AATGGTGTCAAGGTTGGACA 57.254 45.000 0.00 0.00 42.62 4.02
103 104 2.746279 ATGGTGTCAAGGTTGGACAA 57.254 45.000 0.00 0.00 45.96 3.18
104 105 2.746279 TGGTGTCAAGGTTGGACAAT 57.254 45.000 0.00 0.00 45.96 2.71
105 106 2.582052 TGGTGTCAAGGTTGGACAATC 58.418 47.619 0.00 0.00 45.96 2.67
106 107 1.886542 GGTGTCAAGGTTGGACAATCC 59.113 52.381 0.00 0.00 45.96 3.01
107 108 2.582052 GTGTCAAGGTTGGACAATCCA 58.418 47.619 0.00 0.00 46.61 3.41
117 118 3.931907 TGGACAATCCAATCCTCGATT 57.068 42.857 0.00 0.00 45.00 3.34
118 119 3.808728 TGGACAATCCAATCCTCGATTC 58.191 45.455 0.00 0.00 45.00 2.52
119 120 3.199727 TGGACAATCCAATCCTCGATTCA 59.800 43.478 0.00 0.00 45.00 2.57
120 121 3.812053 GGACAATCCAATCCTCGATTCAG 59.188 47.826 0.00 0.00 36.28 3.02
121 122 4.446371 GACAATCCAATCCTCGATTCAGT 58.554 43.478 0.00 0.00 28.87 3.41
122 123 4.194640 ACAATCCAATCCTCGATTCAGTG 58.805 43.478 0.00 0.00 28.87 3.66
123 124 2.988010 TCCAATCCTCGATTCAGTGG 57.012 50.000 0.00 0.00 28.87 4.00
124 125 1.134401 TCCAATCCTCGATTCAGTGGC 60.134 52.381 0.00 0.00 28.87 5.01
125 126 1.407299 CCAATCCTCGATTCAGTGGCA 60.407 52.381 0.00 0.00 28.87 4.92
126 127 1.938577 CAATCCTCGATTCAGTGGCAG 59.061 52.381 0.00 0.00 28.87 4.85
127 128 1.198713 ATCCTCGATTCAGTGGCAGT 58.801 50.000 0.00 0.00 0.00 4.40
128 129 0.976641 TCCTCGATTCAGTGGCAGTT 59.023 50.000 0.00 0.00 0.00 3.16
129 130 1.081892 CCTCGATTCAGTGGCAGTTG 58.918 55.000 0.00 0.00 0.00 3.16
130 131 1.081892 CTCGATTCAGTGGCAGTTGG 58.918 55.000 0.00 0.00 0.00 3.77
131 132 0.396435 TCGATTCAGTGGCAGTTGGT 59.604 50.000 0.00 0.00 0.00 3.67
132 133 0.798776 CGATTCAGTGGCAGTTGGTC 59.201 55.000 0.00 0.00 0.00 4.02
133 134 1.877680 CGATTCAGTGGCAGTTGGTCA 60.878 52.381 0.00 0.00 0.00 4.02
134 135 2.440409 GATTCAGTGGCAGTTGGTCAT 58.560 47.619 0.00 0.00 30.93 3.06
135 136 1.608055 TTCAGTGGCAGTTGGTCATG 58.392 50.000 0.00 0.00 30.93 3.07
136 137 0.250858 TCAGTGGCAGTTGGTCATGG 60.251 55.000 0.00 0.00 30.93 3.66
137 138 0.538057 CAGTGGCAGTTGGTCATGGT 60.538 55.000 0.00 0.00 30.93 3.55
138 139 0.250901 AGTGGCAGTTGGTCATGGTC 60.251 55.000 0.00 0.00 30.93 4.02
139 140 0.250901 GTGGCAGTTGGTCATGGTCT 60.251 55.000 0.00 0.00 30.93 3.85
140 141 0.036732 TGGCAGTTGGTCATGGTCTC 59.963 55.000 0.00 0.00 0.00 3.36
141 142 0.036732 GGCAGTTGGTCATGGTCTCA 59.963 55.000 0.00 0.00 0.00 3.27
142 143 1.160137 GCAGTTGGTCATGGTCTCAC 58.840 55.000 0.00 0.00 0.00 3.51
143 144 1.543208 GCAGTTGGTCATGGTCTCACA 60.543 52.381 0.00 0.00 0.00 3.58
144 145 2.849942 CAGTTGGTCATGGTCTCACAA 58.150 47.619 0.00 0.00 0.00 3.33
145 146 2.810274 CAGTTGGTCATGGTCTCACAAG 59.190 50.000 0.00 0.00 0.00 3.16
146 147 2.154462 GTTGGTCATGGTCTCACAAGG 58.846 52.381 0.00 0.00 0.00 3.61
147 148 1.728323 TGGTCATGGTCTCACAAGGA 58.272 50.000 0.00 0.00 0.00 3.36
148 149 1.347707 TGGTCATGGTCTCACAAGGAC 59.652 52.381 0.00 0.00 0.00 3.85
149 150 1.347707 GGTCATGGTCTCACAAGGACA 59.652 52.381 0.00 0.00 35.61 4.02
150 151 2.224523 GGTCATGGTCTCACAAGGACAA 60.225 50.000 0.00 0.00 35.61 3.18
151 152 3.560025 GGTCATGGTCTCACAAGGACAAT 60.560 47.826 0.00 0.00 35.61 2.71
152 153 4.074970 GTCATGGTCTCACAAGGACAATT 58.925 43.478 0.00 0.00 35.61 2.32
153 154 4.154918 GTCATGGTCTCACAAGGACAATTC 59.845 45.833 0.00 0.00 35.61 2.17
154 155 3.855255 TGGTCTCACAAGGACAATTCA 57.145 42.857 0.00 0.00 35.61 2.57
155 156 4.163441 TGGTCTCACAAGGACAATTCAA 57.837 40.909 0.00 0.00 35.61 2.69
156 157 4.728772 TGGTCTCACAAGGACAATTCAAT 58.271 39.130 0.00 0.00 35.61 2.57
157 158 4.761739 TGGTCTCACAAGGACAATTCAATC 59.238 41.667 0.00 0.00 35.61 2.67
158 159 4.156739 GGTCTCACAAGGACAATTCAATCC 59.843 45.833 0.00 0.00 35.61 3.01
160 161 5.123027 GTCTCACAAGGACAATTCAATCCTC 59.877 44.000 3.45 0.00 44.97 3.71
161 162 4.002982 TCACAAGGACAATTCAATCCTCG 58.997 43.478 3.45 0.00 44.97 4.63
162 163 4.002982 CACAAGGACAATTCAATCCTCGA 58.997 43.478 3.45 0.00 44.97 4.04
163 164 4.637534 CACAAGGACAATTCAATCCTCGAT 59.362 41.667 3.45 0.00 44.97 3.59
164 165 5.124457 CACAAGGACAATTCAATCCTCGATT 59.876 40.000 3.45 0.00 44.97 3.34
165 166 5.711976 ACAAGGACAATTCAATCCTCGATTT 59.288 36.000 3.45 0.00 44.97 2.17
166 167 5.824904 AGGACAATTCAATCCTCGATTTG 57.175 39.130 0.00 0.00 41.83 2.32
167 168 4.641989 AGGACAATTCAATCCTCGATTTGG 59.358 41.667 0.00 0.00 41.83 3.28
168 169 4.354587 GACAATTCAATCCTCGATTTGGC 58.645 43.478 0.00 0.00 31.26 4.52
169 170 3.181497 ACAATTCAATCCTCGATTTGGCG 60.181 43.478 0.00 0.00 31.26 5.69
170 171 0.732571 TTCAATCCTCGATTTGGCGC 59.267 50.000 0.00 0.00 28.87 6.53
171 172 1.095228 TCAATCCTCGATTTGGCGCC 61.095 55.000 22.73 22.73 28.87 6.53
179 180 1.803289 GATTTGGCGCCAGTTCCTC 59.197 57.895 30.75 17.96 0.00 3.71
185 186 2.125552 CGCCAGTTCCTCGATGCA 60.126 61.111 0.00 0.00 0.00 3.96
186 187 1.741401 CGCCAGTTCCTCGATGCAA 60.741 57.895 0.00 0.00 0.00 4.08
203 204 1.299976 AAAGGTCGCCCCTGTGATC 59.700 57.895 0.00 0.00 45.47 2.92
216 217 3.399181 TGATCGCCCCTCCGCTTT 61.399 61.111 0.00 0.00 0.00 3.51
253 254 3.010584 ACCCTCTGTGCTCCAAAATGTAT 59.989 43.478 0.00 0.00 0.00 2.29
256 257 4.885907 CCTCTGTGCTCCAAAATGTATCAT 59.114 41.667 0.00 0.00 0.00 2.45
261 262 4.646492 GTGCTCCAAAATGTATCATCCCTT 59.354 41.667 0.00 0.00 0.00 3.95
262 263 4.889409 TGCTCCAAAATGTATCATCCCTTC 59.111 41.667 0.00 0.00 0.00 3.46
287 288 9.842775 TCTCTTAGAATCATTAAAGTCATGCAT 57.157 29.630 0.00 0.00 0.00 3.96
289 290 8.843262 TCTTAGAATCATTAAAGTCATGCATGG 58.157 33.333 25.97 7.85 0.00 3.66
307 308 4.310769 CATGGTAATCTTCATCCTCGTCC 58.689 47.826 0.00 0.00 0.00 4.79
313 314 0.818296 CTTCATCCTCGTCCCGACTT 59.182 55.000 0.00 0.00 0.00 3.01
356 357 0.874390 GCATCTCTGCCACGTGAAAA 59.126 50.000 19.30 0.43 42.88 2.29
358 359 2.918131 GCATCTCTGCCACGTGAAAAAC 60.918 50.000 19.30 1.25 42.88 2.43
364 365 0.958822 GCCACGTGAAAAACCCTCAT 59.041 50.000 19.30 0.00 0.00 2.90
389 390 5.258841 TCAAAGATGATGCCAACTGAAGAT 58.741 37.500 0.00 0.00 0.00 2.40
411 906 6.825721 AGATTGAAGAACCATAGGACACAATC 59.174 38.462 0.00 0.00 40.33 2.67
475 970 7.038799 AGGCAAAGTGAAATATCAAAAGGATGT 60.039 33.333 0.00 0.00 37.30 3.06
478 973 9.132521 CAAAGTGAAATATCAAAAGGATGTGTC 57.867 33.333 0.00 0.00 37.30 3.67
479 974 8.408043 AAGTGAAATATCAAAAGGATGTGTCA 57.592 30.769 0.00 0.00 38.58 3.58
481 976 6.742718 GTGAAATATCAAAAGGATGTGTCACG 59.257 38.462 8.11 0.00 46.11 4.35
482 977 4.882671 ATATCAAAAGGATGTGTCACGC 57.117 40.909 0.00 0.00 36.72 5.34
483 978 0.865111 TCAAAAGGATGTGTCACGCG 59.135 50.000 3.53 3.53 0.00 6.01
484 979 0.865111 CAAAAGGATGTGTCACGCGA 59.135 50.000 15.93 0.00 0.00 5.87
485 980 1.136252 CAAAAGGATGTGTCACGCGAG 60.136 52.381 15.93 4.59 0.00 5.03
486 981 1.291877 AAAGGATGTGTCACGCGAGC 61.292 55.000 15.93 1.51 0.00 5.03
487 982 3.545481 GGATGTGTCACGCGAGCG 61.545 66.667 15.93 16.38 46.03 5.03
488 983 3.545481 GATGTGTCACGCGAGCGG 61.545 66.667 21.69 10.56 44.69 5.52
489 984 3.964221 GATGTGTCACGCGAGCGGA 62.964 63.158 21.69 12.66 44.69 5.54
490 985 4.994201 TGTGTCACGCGAGCGGAC 62.994 66.667 21.69 22.23 44.69 4.79
491 986 4.994201 GTGTCACGCGAGCGGACA 62.994 66.667 25.78 25.78 42.54 4.02
513 1062 0.317603 GAGCAGCACAGCAAACACAG 60.318 55.000 0.00 0.00 36.85 3.66
518 1067 2.008268 GCACAGCAAACACAGCAGGT 62.008 55.000 0.00 0.00 0.00 4.00
552 1121 3.364441 GCGAGCAATGCACACCCA 61.364 61.111 8.35 0.00 0.00 4.51
553 1122 2.872557 CGAGCAATGCACACCCAG 59.127 61.111 8.35 0.00 0.00 4.45
554 1123 1.968017 CGAGCAATGCACACCCAGT 60.968 57.895 8.35 0.00 0.00 4.00
555 1124 0.673333 CGAGCAATGCACACCCAGTA 60.673 55.000 8.35 0.00 0.00 2.74
572 1142 2.020720 AGTAGTCTCGCTGATCTGGTG 58.979 52.381 1.46 0.00 0.00 4.17
581 1151 0.962356 CTGATCTGGTGGTGGTTGCC 60.962 60.000 0.00 0.00 0.00 4.52
606 1176 3.432588 CGCTCCTCACCGTCGTCT 61.433 66.667 0.00 0.00 0.00 4.18
684 1254 1.311651 GCAAGCCTGGAAAGGAGAGC 61.312 60.000 0.00 0.00 0.00 4.09
687 1257 0.980231 AGCCTGGAAAGGAGAGCGAT 60.980 55.000 0.00 0.00 0.00 4.58
808 1378 1.827399 GCGTCTGTTCAGGGAAGGGA 61.827 60.000 0.00 0.00 0.00 4.20
812 1382 1.150135 TCTGTTCAGGGAAGGGACTCT 59.850 52.381 0.00 0.00 38.49 3.24
842 1412 2.812619 GCGGGAGGAGGAATGGAGG 61.813 68.421 0.00 0.00 0.00 4.30
843 1413 1.075226 CGGGAGGAGGAATGGAGGA 60.075 63.158 0.00 0.00 0.00 3.71
844 1414 1.118356 CGGGAGGAGGAATGGAGGAG 61.118 65.000 0.00 0.00 0.00 3.69
845 1415 0.766288 GGGAGGAGGAATGGAGGAGG 60.766 65.000 0.00 0.00 0.00 4.30
846 1416 0.266152 GGAGGAGGAATGGAGGAGGA 59.734 60.000 0.00 0.00 0.00 3.71
847 1417 1.419381 GAGGAGGAATGGAGGAGGAC 58.581 60.000 0.00 0.00 0.00 3.85
877 1448 4.715523 CGATTGTGTGGGCCGGGT 62.716 66.667 2.18 0.00 0.00 5.28
1700 2499 2.294233 CAGGCTTTCAGCTGCAGTTTTA 59.706 45.455 16.64 0.00 41.99 1.52
2363 3403 4.004348 TCGTGGTGAGAGCCTCTC 57.996 61.111 14.98 14.98 43.65 3.20
2364 3404 1.380689 TCGTGGTGAGAGCCTCTCT 59.619 57.895 21.72 10.33 43.73 3.10
2460 3539 5.416083 GTCTATTGGGGTTTATTTTGGTGC 58.584 41.667 0.00 0.00 0.00 5.01
2488 3676 4.595762 AATCTGCTTGTGCTTGAAACAT 57.404 36.364 0.00 0.00 40.48 2.71
2489 3677 4.595762 ATCTGCTTGTGCTTGAAACATT 57.404 36.364 0.00 0.00 40.48 2.71
2490 3678 4.389890 TCTGCTTGTGCTTGAAACATTT 57.610 36.364 0.00 0.00 40.48 2.32
2491 3679 4.757594 TCTGCTTGTGCTTGAAACATTTT 58.242 34.783 0.00 0.00 40.48 1.82
2492 3680 5.900425 TCTGCTTGTGCTTGAAACATTTTA 58.100 33.333 0.00 0.00 40.48 1.52
2493 3681 5.748152 TCTGCTTGTGCTTGAAACATTTTAC 59.252 36.000 0.00 0.00 40.48 2.01
2494 3682 5.659463 TGCTTGTGCTTGAAACATTTTACT 58.341 33.333 0.00 0.00 40.48 2.24
2495 3683 5.519566 TGCTTGTGCTTGAAACATTTTACTG 59.480 36.000 0.00 0.00 40.48 2.74
2496 3684 5.748152 GCTTGTGCTTGAAACATTTTACTGA 59.252 36.000 0.00 0.00 36.03 3.41
2497 3685 6.255453 GCTTGTGCTTGAAACATTTTACTGAA 59.745 34.615 0.00 0.00 36.03 3.02
2498 3686 7.201513 GCTTGTGCTTGAAACATTTTACTGAAA 60.202 33.333 0.00 0.00 36.03 2.69
2499 3687 7.518731 TGTGCTTGAAACATTTTACTGAAAC 57.481 32.000 0.00 0.00 0.00 2.78
2500 3688 7.319646 TGTGCTTGAAACATTTTACTGAAACT 58.680 30.769 0.00 0.00 0.00 2.66
2501 3689 7.816995 TGTGCTTGAAACATTTTACTGAAACTT 59.183 29.630 0.00 0.00 0.00 2.66
2502 3690 8.321005 GTGCTTGAAACATTTTACTGAAACTTC 58.679 33.333 0.00 0.00 0.00 3.01
2503 3691 8.250332 TGCTTGAAACATTTTACTGAAACTTCT 58.750 29.630 0.00 0.00 0.00 2.85
2504 3692 9.730420 GCTTGAAACATTTTACTGAAACTTCTA 57.270 29.630 0.00 0.00 0.00 2.10
2510 3698 9.614792 AACATTTTACTGAAACTTCTACAGTCT 57.385 29.630 0.00 0.00 42.65 3.24
2511 3699 9.262358 ACATTTTACTGAAACTTCTACAGTCTC 57.738 33.333 0.00 0.00 42.65 3.36
2512 3700 9.261180 CATTTTACTGAAACTTCTACAGTCTCA 57.739 33.333 0.00 0.00 42.65 3.27
2515 3703 5.713792 CTGAAACTTCTACAGTCTCAGGA 57.286 43.478 0.00 0.00 44.24 3.86
2516 3704 6.279513 CTGAAACTTCTACAGTCTCAGGAT 57.720 41.667 0.00 0.00 44.24 3.24
2517 3705 7.397892 CTGAAACTTCTACAGTCTCAGGATA 57.602 40.000 0.00 0.00 44.24 2.59
2615 3851 3.124578 TGTCTGCAGCTGTTGTAATCA 57.875 42.857 16.64 1.46 0.00 2.57
2625 4239 6.676456 GCAGCTGTTGTAATCAGTTATTGGAG 60.676 42.308 16.64 0.00 35.60 3.86
2627 4241 6.595716 AGCTGTTGTAATCAGTTATTGGAGTC 59.404 38.462 0.00 0.00 35.60 3.36
2628 4242 6.183360 GCTGTTGTAATCAGTTATTGGAGTCC 60.183 42.308 0.73 0.73 35.60 3.85
2640 4254 1.361204 TGGAGTCCAAATCAGCTGGA 58.639 50.000 15.13 0.00 40.77 3.86
2643 4257 2.290577 GGAGTCCAAATCAGCTGGAACT 60.291 50.000 15.13 8.38 44.55 3.01
2647 4261 5.385198 AGTCCAAATCAGCTGGAACTTAAA 58.615 37.500 15.13 0.00 44.55 1.52
2680 4336 6.084326 TGGAACTTAAAACTCCAAATCAGC 57.916 37.500 0.00 0.00 36.30 4.26
2683 4339 5.712152 ACTTAAAACTCCAAATCAGCTGG 57.288 39.130 15.13 0.00 35.05 4.85
2710 4366 5.552870 TCTCTTTTCAGCCTTAACAGAGT 57.447 39.130 2.64 0.00 0.00 3.24
2716 4372 3.173151 TCAGCCTTAACAGAGTGGATGA 58.827 45.455 0.00 0.00 41.83 2.92
2726 4383 8.718158 TTAACAGAGTGGATGATGAGATATCT 57.282 34.615 4.47 4.47 0.00 1.98
2983 4916 4.522722 TTTTGCTGCATGAACATGATGA 57.477 36.364 17.40 1.33 41.20 2.92
2989 4922 4.676986 GCTGCATGAACATGATGATTGTGT 60.677 41.667 17.40 0.00 41.20 3.72
3021 4967 3.449018 AGTGGAGTGCTAATCTGATCGTT 59.551 43.478 0.00 0.00 0.00 3.85
3025 4971 5.359860 TGGAGTGCTAATCTGATCGTTCTTA 59.640 40.000 0.00 0.00 0.00 2.10
3126 5072 7.563924 AGAGTAGTTGGATGTAAATAGTAGGCA 59.436 37.037 0.00 0.00 0.00 4.75
3149 5103 6.427853 GCAGCATGTGGATTTATCACTATGTA 59.572 38.462 0.00 0.00 39.31 2.29
3150 5104 7.571983 GCAGCATGTGGATTTATCACTATGTAC 60.572 40.741 0.00 0.00 39.31 2.90
3151 5105 7.442062 CAGCATGTGGATTTATCACTATGTACA 59.558 37.037 0.00 0.00 36.21 2.90
3152 5106 7.442364 AGCATGTGGATTTATCACTATGTACAC 59.558 37.037 0.00 0.00 36.21 2.90
3153 5107 7.226523 GCATGTGGATTTATCACTATGTACACA 59.773 37.037 0.00 0.00 39.12 3.72
3154 5108 9.276590 CATGTGGATTTATCACTATGTACACAT 57.723 33.333 0.00 0.00 43.97 3.21
3195 5149 5.827797 TGGACTGAAGCTAGTTGAACATTTT 59.172 36.000 0.00 0.00 0.00 1.82
3248 5212 1.003851 TCGTAACATTTGCCGCTAGC 58.996 50.000 4.06 4.06 44.14 3.42
3276 5241 9.546428 GAAATTATGCAAGTTATAGGCCAAATT 57.454 29.630 5.01 0.00 0.00 1.82
3434 5511 8.070034 TGCCTTCTTGATCATGTTATTGATTT 57.930 30.769 8.33 0.00 36.48 2.17
3446 5523 1.696988 ATTGATTTTTGACGTGCCGC 58.303 45.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.995003 GGTTTTTCATGGGCAAATAATATGATA 57.005 29.630 0.00 0.00 0.00 2.15
26 27 8.492782 TGGTTTTTCATGGGCAAATAATATGAT 58.507 29.630 0.00 0.00 0.00 2.45
27 28 7.855375 TGGTTTTTCATGGGCAAATAATATGA 58.145 30.769 0.00 0.00 0.00 2.15
28 29 8.680039 ATGGTTTTTCATGGGCAAATAATATG 57.320 30.769 0.00 0.00 0.00 1.78
29 30 9.341078 GAATGGTTTTTCATGGGCAAATAATAT 57.659 29.630 0.00 0.00 0.00 1.28
30 31 8.324306 TGAATGGTTTTTCATGGGCAAATAATA 58.676 29.630 0.00 0.00 30.82 0.98
31 32 7.173722 TGAATGGTTTTTCATGGGCAAATAAT 58.826 30.769 0.00 0.00 30.82 1.28
32 33 6.537355 TGAATGGTTTTTCATGGGCAAATAA 58.463 32.000 0.00 0.00 30.82 1.40
33 34 6.119240 TGAATGGTTTTTCATGGGCAAATA 57.881 33.333 0.00 0.00 30.82 1.40
34 35 4.983053 TGAATGGTTTTTCATGGGCAAAT 58.017 34.783 0.00 0.00 30.82 2.32
35 36 4.428294 TGAATGGTTTTTCATGGGCAAA 57.572 36.364 0.00 0.00 30.82 3.68
36 37 4.428294 TTGAATGGTTTTTCATGGGCAA 57.572 36.364 0.00 0.00 35.64 4.52
37 38 4.637387 ATTGAATGGTTTTTCATGGGCA 57.363 36.364 0.00 0.00 35.64 5.36
38 39 6.172630 AGTTATTGAATGGTTTTTCATGGGC 58.827 36.000 0.00 0.00 35.64 5.36
39 40 9.369904 CTTAGTTATTGAATGGTTTTTCATGGG 57.630 33.333 0.00 0.00 35.64 4.00
40 41 9.369904 CCTTAGTTATTGAATGGTTTTTCATGG 57.630 33.333 0.00 0.00 35.64 3.66
41 42 8.872845 GCCTTAGTTATTGAATGGTTTTTCATG 58.127 33.333 0.00 0.00 35.64 3.07
42 43 8.592809 TGCCTTAGTTATTGAATGGTTTTTCAT 58.407 29.630 0.00 0.00 35.64 2.57
43 44 7.957002 TGCCTTAGTTATTGAATGGTTTTTCA 58.043 30.769 0.00 0.00 33.89 2.69
44 45 8.708742 GTTGCCTTAGTTATTGAATGGTTTTTC 58.291 33.333 0.00 0.00 0.00 2.29
45 46 8.207545 TGTTGCCTTAGTTATTGAATGGTTTTT 58.792 29.630 0.00 0.00 0.00 1.94
46 47 7.655732 GTGTTGCCTTAGTTATTGAATGGTTTT 59.344 33.333 0.00 0.00 0.00 2.43
47 48 7.151976 GTGTTGCCTTAGTTATTGAATGGTTT 58.848 34.615 0.00 0.00 0.00 3.27
48 49 6.295067 GGTGTTGCCTTAGTTATTGAATGGTT 60.295 38.462 0.00 0.00 0.00 3.67
49 50 5.185056 GGTGTTGCCTTAGTTATTGAATGGT 59.815 40.000 0.00 0.00 0.00 3.55
50 51 5.184864 TGGTGTTGCCTTAGTTATTGAATGG 59.815 40.000 0.00 0.00 38.35 3.16
51 52 6.092748 GTGGTGTTGCCTTAGTTATTGAATG 58.907 40.000 0.00 0.00 38.35 2.67
52 53 5.106317 CGTGGTGTTGCCTTAGTTATTGAAT 60.106 40.000 0.00 0.00 38.35 2.57
53 54 4.214545 CGTGGTGTTGCCTTAGTTATTGAA 59.785 41.667 0.00 0.00 38.35 2.69
54 55 3.749088 CGTGGTGTTGCCTTAGTTATTGA 59.251 43.478 0.00 0.00 38.35 2.57
55 56 3.749088 TCGTGGTGTTGCCTTAGTTATTG 59.251 43.478 0.00 0.00 38.35 1.90
56 57 4.000988 CTCGTGGTGTTGCCTTAGTTATT 58.999 43.478 0.00 0.00 38.35 1.40
57 58 3.259876 TCTCGTGGTGTTGCCTTAGTTAT 59.740 43.478 0.00 0.00 38.35 1.89
58 59 2.629137 TCTCGTGGTGTTGCCTTAGTTA 59.371 45.455 0.00 0.00 38.35 2.24
59 60 1.414919 TCTCGTGGTGTTGCCTTAGTT 59.585 47.619 0.00 0.00 38.35 2.24
60 61 1.045407 TCTCGTGGTGTTGCCTTAGT 58.955 50.000 0.00 0.00 38.35 2.24
61 62 2.002586 CATCTCGTGGTGTTGCCTTAG 58.997 52.381 0.00 0.00 38.35 2.18
62 63 1.621317 TCATCTCGTGGTGTTGCCTTA 59.379 47.619 0.00 0.00 38.35 2.69
63 64 0.396435 TCATCTCGTGGTGTTGCCTT 59.604 50.000 0.00 0.00 38.35 4.35
64 65 0.396435 TTCATCTCGTGGTGTTGCCT 59.604 50.000 0.00 0.00 38.35 4.75
65 66 1.234821 TTTCATCTCGTGGTGTTGCC 58.765 50.000 0.00 0.00 37.90 4.52
66 67 2.414559 CCATTTCATCTCGTGGTGTTGC 60.415 50.000 0.00 0.00 0.00 4.17
67 68 2.813754 ACCATTTCATCTCGTGGTGTTG 59.186 45.455 0.00 0.00 43.02 3.33
68 69 3.140325 ACCATTTCATCTCGTGGTGTT 57.860 42.857 0.00 0.00 43.02 3.32
69 70 2.859165 ACCATTTCATCTCGTGGTGT 57.141 45.000 0.00 0.00 43.02 4.16
71 72 2.038426 TGACACCATTTCATCTCGTGGT 59.962 45.455 0.00 0.00 45.41 4.16
72 73 2.698803 TGACACCATTTCATCTCGTGG 58.301 47.619 0.00 0.00 37.74 4.94
73 74 3.125829 CCTTGACACCATTTCATCTCGTG 59.874 47.826 0.00 0.00 0.00 4.35
74 75 3.244561 ACCTTGACACCATTTCATCTCGT 60.245 43.478 0.00 0.00 0.00 4.18
75 76 3.338249 ACCTTGACACCATTTCATCTCG 58.662 45.455 0.00 0.00 0.00 4.04
76 77 4.082571 CCAACCTTGACACCATTTCATCTC 60.083 45.833 0.00 0.00 0.00 2.75
77 78 3.828451 CCAACCTTGACACCATTTCATCT 59.172 43.478 0.00 0.00 0.00 2.90
78 79 3.826157 TCCAACCTTGACACCATTTCATC 59.174 43.478 0.00 0.00 0.00 2.92
79 80 3.573967 GTCCAACCTTGACACCATTTCAT 59.426 43.478 0.00 0.00 0.00 2.57
80 81 2.955660 GTCCAACCTTGACACCATTTCA 59.044 45.455 0.00 0.00 0.00 2.69
81 82 2.955660 TGTCCAACCTTGACACCATTTC 59.044 45.455 0.00 0.00 0.00 2.17
82 83 3.025322 TGTCCAACCTTGACACCATTT 57.975 42.857 0.00 0.00 0.00 2.32
83 84 2.746279 TGTCCAACCTTGACACCATT 57.254 45.000 0.00 0.00 0.00 3.16
84 85 2.746279 TTGTCCAACCTTGACACCAT 57.254 45.000 0.00 0.00 0.00 3.55
85 86 2.582052 GATTGTCCAACCTTGACACCA 58.418 47.619 0.00 0.00 0.00 4.17
86 87 1.886542 GGATTGTCCAACCTTGACACC 59.113 52.381 0.00 0.00 36.28 4.16
87 88 2.582052 TGGATTGTCCAACCTTGACAC 58.418 47.619 0.00 0.00 45.00 3.67
97 98 3.199727 TGAATCGAGGATTGGATTGTCCA 59.800 43.478 0.00 0.00 46.61 4.02
98 99 3.808728 TGAATCGAGGATTGGATTGTCC 58.191 45.455 0.00 0.00 32.68 4.02
99 100 4.272018 CACTGAATCGAGGATTGGATTGTC 59.728 45.833 0.00 0.00 32.68 3.18
100 101 4.194640 CACTGAATCGAGGATTGGATTGT 58.805 43.478 0.00 0.00 32.68 2.71
101 102 3.562973 CCACTGAATCGAGGATTGGATTG 59.437 47.826 0.00 0.00 32.68 2.67
102 103 3.813443 CCACTGAATCGAGGATTGGATT 58.187 45.455 0.00 0.00 34.87 3.01
103 104 2.486191 GCCACTGAATCGAGGATTGGAT 60.486 50.000 6.96 0.00 31.89 3.41
104 105 1.134401 GCCACTGAATCGAGGATTGGA 60.134 52.381 6.96 0.00 31.89 3.53
105 106 1.303309 GCCACTGAATCGAGGATTGG 58.697 55.000 0.00 0.00 31.89 3.16
106 107 1.938577 CTGCCACTGAATCGAGGATTG 59.061 52.381 0.00 0.00 31.89 2.67
107 108 1.556911 ACTGCCACTGAATCGAGGATT 59.443 47.619 0.00 0.00 34.71 3.01
108 109 1.198713 ACTGCCACTGAATCGAGGAT 58.801 50.000 0.00 0.00 0.00 3.24
109 110 0.976641 AACTGCCACTGAATCGAGGA 59.023 50.000 0.00 0.00 0.00 3.71
110 111 1.081892 CAACTGCCACTGAATCGAGG 58.918 55.000 0.00 0.00 0.00 4.63
111 112 1.081892 CCAACTGCCACTGAATCGAG 58.918 55.000 0.00 0.00 0.00 4.04
112 113 0.396435 ACCAACTGCCACTGAATCGA 59.604 50.000 0.00 0.00 0.00 3.59
113 114 0.798776 GACCAACTGCCACTGAATCG 59.201 55.000 0.00 0.00 0.00 3.34
114 115 1.896220 TGACCAACTGCCACTGAATC 58.104 50.000 0.00 0.00 0.00 2.52
115 116 2.165167 CATGACCAACTGCCACTGAAT 58.835 47.619 0.00 0.00 0.00 2.57
116 117 1.608055 CATGACCAACTGCCACTGAA 58.392 50.000 0.00 0.00 0.00 3.02
117 118 0.250858 CCATGACCAACTGCCACTGA 60.251 55.000 0.00 0.00 0.00 3.41
118 119 0.538057 ACCATGACCAACTGCCACTG 60.538 55.000 0.00 0.00 0.00 3.66
119 120 0.250901 GACCATGACCAACTGCCACT 60.251 55.000 0.00 0.00 0.00 4.00
120 121 0.250901 AGACCATGACCAACTGCCAC 60.251 55.000 0.00 0.00 0.00 5.01
121 122 0.036732 GAGACCATGACCAACTGCCA 59.963 55.000 0.00 0.00 0.00 4.92
122 123 0.036732 TGAGACCATGACCAACTGCC 59.963 55.000 0.00 0.00 0.00 4.85
123 124 1.160137 GTGAGACCATGACCAACTGC 58.840 55.000 0.00 0.00 0.00 4.40
124 125 2.549064 TGTGAGACCATGACCAACTG 57.451 50.000 0.00 0.00 0.00 3.16
125 126 2.224621 CCTTGTGAGACCATGACCAACT 60.225 50.000 0.00 0.00 0.00 3.16
126 127 2.154462 CCTTGTGAGACCATGACCAAC 58.846 52.381 0.00 0.00 0.00 3.77
127 128 2.054021 TCCTTGTGAGACCATGACCAA 58.946 47.619 0.00 0.00 0.00 3.67
128 129 1.347707 GTCCTTGTGAGACCATGACCA 59.652 52.381 0.00 0.00 0.00 4.02
129 130 1.347707 TGTCCTTGTGAGACCATGACC 59.652 52.381 0.00 0.00 33.09 4.02
130 131 2.839486 TGTCCTTGTGAGACCATGAC 57.161 50.000 0.00 0.00 33.09 3.06
131 132 4.202451 TGAATTGTCCTTGTGAGACCATGA 60.202 41.667 0.00 0.00 33.09 3.07
132 133 4.074259 TGAATTGTCCTTGTGAGACCATG 58.926 43.478 0.00 0.00 33.09 3.66
133 134 4.371624 TGAATTGTCCTTGTGAGACCAT 57.628 40.909 0.00 0.00 33.09 3.55
134 135 3.855255 TGAATTGTCCTTGTGAGACCA 57.145 42.857 0.00 0.00 33.09 4.02
135 136 4.156739 GGATTGAATTGTCCTTGTGAGACC 59.843 45.833 0.00 0.00 33.09 3.85
136 137 5.006386 AGGATTGAATTGTCCTTGTGAGAC 58.994 41.667 0.00 0.00 42.09 3.36
137 138 5.246981 AGGATTGAATTGTCCTTGTGAGA 57.753 39.130 0.00 0.00 42.09 3.27
138 139 4.093998 CGAGGATTGAATTGTCCTTGTGAG 59.906 45.833 5.40 0.00 44.70 3.51
139 140 4.002982 CGAGGATTGAATTGTCCTTGTGA 58.997 43.478 5.40 0.00 44.70 3.58
140 141 4.002982 TCGAGGATTGAATTGTCCTTGTG 58.997 43.478 13.95 5.88 44.70 3.33
141 142 4.286297 TCGAGGATTGAATTGTCCTTGT 57.714 40.909 13.95 0.00 44.70 3.16
142 143 5.824904 AATCGAGGATTGAATTGTCCTTG 57.175 39.130 10.28 10.28 44.70 3.61
143 144 5.126061 CCAAATCGAGGATTGAATTGTCCTT 59.874 40.000 9.27 0.00 44.70 3.36
145 146 4.734695 GCCAAATCGAGGATTGAATTGTCC 60.735 45.833 9.27 0.00 37.63 4.02
146 147 4.354587 GCCAAATCGAGGATTGAATTGTC 58.645 43.478 9.27 0.00 37.63 3.18
147 148 3.181497 CGCCAAATCGAGGATTGAATTGT 60.181 43.478 9.27 0.00 37.63 2.71
148 149 3.365832 CGCCAAATCGAGGATTGAATTG 58.634 45.455 9.27 0.00 38.78 2.32
149 150 2.223572 GCGCCAAATCGAGGATTGAATT 60.224 45.455 0.00 0.00 32.14 2.17
150 151 1.334869 GCGCCAAATCGAGGATTGAAT 59.665 47.619 0.00 0.00 32.14 2.57
151 152 0.732571 GCGCCAAATCGAGGATTGAA 59.267 50.000 0.00 0.00 32.14 2.69
152 153 1.095228 GGCGCCAAATCGAGGATTGA 61.095 55.000 24.80 0.00 32.14 2.57
153 154 1.356624 GGCGCCAAATCGAGGATTG 59.643 57.895 24.80 0.00 32.14 2.67
154 155 1.077787 TGGCGCCAAATCGAGGATT 60.078 52.632 30.74 0.00 33.25 3.01
155 156 1.524621 CTGGCGCCAAATCGAGGAT 60.525 57.895 32.09 0.00 0.00 3.24
156 157 2.125147 CTGGCGCCAAATCGAGGA 60.125 61.111 32.09 3.44 0.00 3.71
157 158 1.982073 GAACTGGCGCCAAATCGAGG 61.982 60.000 32.09 19.23 0.00 4.63
158 159 1.425428 GAACTGGCGCCAAATCGAG 59.575 57.895 32.09 20.02 0.00 4.04
159 160 2.038269 GGAACTGGCGCCAAATCGA 61.038 57.895 32.09 6.08 0.00 3.59
160 161 1.982073 GAGGAACTGGCGCCAAATCG 61.982 60.000 32.09 21.22 41.55 3.34
161 162 1.803289 GAGGAACTGGCGCCAAATC 59.197 57.895 32.09 28.22 41.55 2.17
162 163 2.040544 CGAGGAACTGGCGCCAAAT 61.041 57.895 32.09 22.12 41.55 2.32
163 164 2.463589 ATCGAGGAACTGGCGCCAAA 62.464 55.000 32.09 8.76 41.55 3.28
164 165 2.954684 ATCGAGGAACTGGCGCCAA 61.955 57.895 32.09 13.75 41.55 4.52
165 166 3.390521 ATCGAGGAACTGGCGCCA 61.391 61.111 30.59 30.59 41.55 5.69
166 167 2.892425 CATCGAGGAACTGGCGCC 60.892 66.667 22.73 22.73 41.55 6.53
167 168 3.567797 GCATCGAGGAACTGGCGC 61.568 66.667 0.00 0.00 41.55 6.53
168 169 1.298157 TTTGCATCGAGGAACTGGCG 61.298 55.000 0.00 0.00 41.55 5.69
169 170 0.449388 CTTTGCATCGAGGAACTGGC 59.551 55.000 0.00 0.00 41.55 4.85
170 171 1.089920 CCTTTGCATCGAGGAACTGG 58.910 55.000 0.00 0.00 41.55 4.00
171 172 1.734465 GACCTTTGCATCGAGGAACTG 59.266 52.381 15.77 0.00 41.55 3.16
216 217 2.346597 GGGTTGACATGCCCGAAAA 58.653 52.632 0.00 0.00 34.90 2.29
221 222 0.962356 CACAGAGGGTTGACATGCCC 60.962 60.000 7.36 7.36 45.16 5.36
256 257 9.046846 TGACTTTAATGATTCTAAGAGAAGGGA 57.953 33.333 6.88 0.00 37.69 4.20
261 262 9.842775 ATGCATGACTTTAATGATTCTAAGAGA 57.157 29.630 0.00 0.00 0.00 3.10
262 263 9.880064 CATGCATGACTTTAATGATTCTAAGAG 57.120 33.333 22.59 0.00 0.00 2.85
287 288 2.698797 GGGACGAGGATGAAGATTACCA 59.301 50.000 0.00 0.00 0.00 3.25
307 308 3.850740 GCTTGTTTCGGGTTAAAAGTCGG 60.851 47.826 0.00 0.00 0.00 4.79
313 314 1.957877 CCCTGCTTGTTTCGGGTTAAA 59.042 47.619 0.00 0.00 31.89 1.52
333 334 1.078848 ACGTGGCAGAGATGCTTCC 60.079 57.895 0.00 0.00 34.73 3.46
349 350 6.494893 TCTTTGATATGAGGGTTTTTCACG 57.505 37.500 0.00 0.00 0.00 4.35
350 351 8.055279 TCATCTTTGATATGAGGGTTTTTCAC 57.945 34.615 0.00 0.00 0.00 3.18
356 357 5.075493 GGCATCATCTTTGATATGAGGGTT 58.925 41.667 0.00 0.00 40.70 4.11
358 359 4.659115 TGGCATCATCTTTGATATGAGGG 58.341 43.478 0.00 0.00 40.70 4.30
364 365 6.417258 TCTTCAGTTGGCATCATCTTTGATA 58.583 36.000 0.00 0.00 40.70 2.15
389 390 6.126863 AGATTGTGTCCTATGGTTCTTCAA 57.873 37.500 0.00 0.00 0.00 2.69
411 906 8.939929 ACTGTGTGATATACAGATTGTTTGAAG 58.060 33.333 10.44 0.00 46.52 3.02
475 970 4.700365 CTGTCCGCTCGCGTGACA 62.700 66.667 23.67 23.67 42.54 3.58
487 982 3.117171 CTGTGCTGCTCGCTGTCC 61.117 66.667 0.00 0.00 40.11 4.02
488 983 3.786586 GCTGTGCTGCTCGCTGTC 61.787 66.667 0.00 0.00 40.11 3.51
489 984 4.614112 TGCTGTGCTGCTCGCTGT 62.614 61.111 15.37 0.00 40.11 4.40
490 985 2.900167 TTTGCTGTGCTGCTCGCTG 61.900 57.895 15.37 6.20 40.11 5.18
491 986 2.592574 TTTGCTGTGCTGCTCGCT 60.593 55.556 15.37 0.00 40.11 4.93
493 988 1.369689 GTGTTTGCTGTGCTGCTCG 60.370 57.895 0.00 0.00 0.00 5.03
497 1046 0.594028 CTGCTGTGTTTGCTGTGCTG 60.594 55.000 0.00 0.00 0.00 4.41
513 1062 3.512516 GGCTTGCCGATGACCTGC 61.513 66.667 0.00 0.00 0.00 4.85
543 1112 1.964448 CGAGACTACTGGGTGTGCA 59.036 57.895 0.00 0.00 0.00 4.57
552 1121 2.020720 CACCAGATCAGCGAGACTACT 58.979 52.381 0.00 0.00 0.00 2.57
553 1122 1.066303 CCACCAGATCAGCGAGACTAC 59.934 57.143 0.00 0.00 0.00 2.73
554 1123 1.341089 ACCACCAGATCAGCGAGACTA 60.341 52.381 0.00 0.00 0.00 2.59
555 1124 0.613292 ACCACCAGATCAGCGAGACT 60.613 55.000 0.00 0.00 0.00 3.24
590 1160 2.486042 GAGACGACGGTGAGGAGC 59.514 66.667 0.00 0.00 0.00 4.70
666 1236 1.023513 CGCTCTCCTTTCCAGGCTTG 61.024 60.000 0.00 0.00 40.58 4.01
667 1237 1.194781 TCGCTCTCCTTTCCAGGCTT 61.195 55.000 0.00 0.00 40.58 4.35
672 1242 2.036475 GCATAGATCGCTCTCCTTTCCA 59.964 50.000 0.00 0.00 32.66 3.53
675 1245 1.000283 CGGCATAGATCGCTCTCCTTT 60.000 52.381 0.00 0.00 32.66 3.11
684 1254 2.740055 GGCTGGCGGCATAGATCG 60.740 66.667 21.68 0.00 44.01 3.69
687 1257 4.221422 GACGGCTGGCGGCATAGA 62.221 66.667 25.53 0.00 44.01 1.98
783 1353 3.767230 CTGAACAGACGCGCGGTG 61.767 66.667 35.22 30.41 0.00 4.94
799 1369 2.294078 CCGCAAGAGTCCCTTCCCT 61.294 63.158 0.00 0.00 43.02 4.20
826 1396 0.766288 CCTCCTCCATTCCTCCTCCC 60.766 65.000 0.00 0.00 0.00 4.30
842 1412 3.404141 GAGCGCCGTCTCTGTCCTC 62.404 68.421 2.29 0.00 0.00 3.71
843 1413 3.444805 GAGCGCCGTCTCTGTCCT 61.445 66.667 2.29 0.00 0.00 3.85
844 1414 4.838486 CGAGCGCCGTCTCTGTCC 62.838 72.222 2.29 0.00 0.00 4.02
845 1415 2.600122 AATCGAGCGCCGTCTCTGTC 62.600 60.000 16.00 0.00 39.75 3.51
846 1416 2.701780 AATCGAGCGCCGTCTCTGT 61.702 57.895 16.00 0.00 39.75 3.41
847 1417 2.103143 AATCGAGCGCCGTCTCTG 59.897 61.111 16.00 0.30 39.75 3.35
877 1448 3.776347 TTGCGGGCCGTTTCCTTGA 62.776 57.895 28.82 1.76 0.00 3.02
929 1500 1.396996 CAACGCGAGGTATTTCAAGGG 59.603 52.381 15.93 0.00 0.00 3.95
1700 2499 4.039488 TGCTCTCACAAATTTGGCAAGAAT 59.961 37.500 21.74 0.00 0.00 2.40
2362 3402 1.082766 TTGGGGCATGGAGAGGAGA 59.917 57.895 0.00 0.00 0.00 3.71
2363 3403 1.225704 GTTGGGGCATGGAGAGGAG 59.774 63.158 0.00 0.00 0.00 3.69
2364 3404 0.846427 AAGTTGGGGCATGGAGAGGA 60.846 55.000 0.00 0.00 0.00 3.71
2365 3405 0.394899 GAAGTTGGGGCATGGAGAGG 60.395 60.000 0.00 0.00 0.00 3.69
2366 3406 0.394899 GGAAGTTGGGGCATGGAGAG 60.395 60.000 0.00 0.00 0.00 3.20
2460 3539 0.097674 GCACAAGCAGATTAGCACCG 59.902 55.000 0.00 0.00 41.58 4.94
2494 3682 6.948886 ACTATCCTGAGACTGTAGAAGTTTCA 59.051 38.462 0.00 0.00 45.24 2.69
2495 3683 7.399245 ACTATCCTGAGACTGTAGAAGTTTC 57.601 40.000 0.00 0.00 40.07 2.78
2496 3684 7.784470 AACTATCCTGAGACTGTAGAAGTTT 57.216 36.000 0.00 0.00 40.07 2.66
2497 3685 7.784470 AAACTATCCTGAGACTGTAGAAGTT 57.216 36.000 0.00 0.00 40.07 2.66
2498 3686 8.110908 AGTAAACTATCCTGAGACTGTAGAAGT 58.889 37.037 0.00 0.00 43.85 3.01
2499 3687 8.402472 CAGTAAACTATCCTGAGACTGTAGAAG 58.598 40.741 0.00 0.00 0.00 2.85
2500 3688 8.107729 TCAGTAAACTATCCTGAGACTGTAGAA 58.892 37.037 0.00 0.00 35.46 2.10
2501 3689 7.631007 TCAGTAAACTATCCTGAGACTGTAGA 58.369 38.462 0.00 0.00 35.46 2.59
2502 3690 7.867305 TCAGTAAACTATCCTGAGACTGTAG 57.133 40.000 0.00 0.00 35.46 2.74
2503 3691 8.645814 TTTCAGTAAACTATCCTGAGACTGTA 57.354 34.615 0.00 0.00 36.64 2.74
2504 3692 7.233757 ACTTTCAGTAAACTATCCTGAGACTGT 59.766 37.037 0.00 0.00 36.64 3.55
2505 3693 7.543868 CACTTTCAGTAAACTATCCTGAGACTG 59.456 40.741 0.00 0.00 36.64 3.51
2506 3694 7.233757 ACACTTTCAGTAAACTATCCTGAGACT 59.766 37.037 0.00 0.00 36.64 3.24
2507 3695 7.379750 ACACTTTCAGTAAACTATCCTGAGAC 58.620 38.462 0.00 0.00 36.64 3.36
2508 3696 7.540474 ACACTTTCAGTAAACTATCCTGAGA 57.460 36.000 0.00 0.00 36.64 3.27
2509 3697 9.877178 ATAACACTTTCAGTAAACTATCCTGAG 57.123 33.333 0.00 0.00 36.64 3.35
2510 3698 9.871238 GATAACACTTTCAGTAAACTATCCTGA 57.129 33.333 0.00 0.00 33.59 3.86
2511 3699 8.808529 CGATAACACTTTCAGTAAACTATCCTG 58.191 37.037 0.00 0.00 0.00 3.86
2512 3700 8.529476 ACGATAACACTTTCAGTAAACTATCCT 58.471 33.333 0.00 0.00 0.00 3.24
2513 3701 8.699283 ACGATAACACTTTCAGTAAACTATCC 57.301 34.615 0.00 0.00 0.00 2.59
2514 3702 9.570488 AGACGATAACACTTTCAGTAAACTATC 57.430 33.333 0.00 0.00 0.00 2.08
2515 3703 9.355215 CAGACGATAACACTTTCAGTAAACTAT 57.645 33.333 0.00 0.00 0.00 2.12
2516 3704 8.570488 TCAGACGATAACACTTTCAGTAAACTA 58.430 33.333 0.00 0.00 0.00 2.24
2517 3705 7.431249 TCAGACGATAACACTTTCAGTAAACT 58.569 34.615 0.00 0.00 0.00 2.66
2615 3851 4.946157 CAGCTGATTTGGACTCCAATAACT 59.054 41.667 8.42 3.04 43.55 2.24
2625 4239 5.705609 TTTAAGTTCCAGCTGATTTGGAC 57.294 39.130 17.39 2.78 44.13 4.02
2647 4261 9.362151 TGGAGTTTTAAGTTCCATAGTGATTTT 57.638 29.630 1.75 0.00 36.13 1.82
2680 4336 3.683802 AGGCTGAAAAGAGATGAACCAG 58.316 45.455 0.00 0.00 0.00 4.00
2683 4339 6.428159 TCTGTTAAGGCTGAAAAGAGATGAAC 59.572 38.462 0.00 0.00 0.00 3.18
2716 4372 7.520798 TGGGCTAAATCAAACAGATATCTCAT 58.479 34.615 1.03 0.00 35.39 2.90
2726 4383 6.207810 ACGAGTAAAATGGGCTAAATCAAACA 59.792 34.615 0.00 0.00 0.00 2.83
2838 4519 1.603802 CTCAGAGCCTTGCGAAACAAA 59.396 47.619 0.00 0.00 37.96 2.83
2841 4522 1.731720 ATCTCAGAGCCTTGCGAAAC 58.268 50.000 0.00 0.00 0.00 2.78
2845 4526 4.889832 ATTTAAATCTCAGAGCCTTGCG 57.110 40.909 0.00 0.00 0.00 4.85
2983 4916 6.204882 GCACTCCACTAAAGTAAGAACACAAT 59.795 38.462 0.19 0.00 0.00 2.71
2989 4922 8.035394 CAGATTAGCACTCCACTAAAGTAAGAA 58.965 37.037 0.00 0.00 33.54 2.52
3126 5072 7.442364 GTGTACATAGTGATAAATCCACATGCT 59.558 37.037 0.00 0.00 37.01 3.79
3149 5103 6.945435 TCCATCTTTTACCATGTGTTATGTGT 59.055 34.615 0.00 0.00 0.00 3.72
3150 5104 7.121168 AGTCCATCTTTTACCATGTGTTATGTG 59.879 37.037 0.00 0.00 0.00 3.21
3151 5105 7.121168 CAGTCCATCTTTTACCATGTGTTATGT 59.879 37.037 0.00 0.00 0.00 2.29
3152 5106 7.336679 TCAGTCCATCTTTTACCATGTGTTATG 59.663 37.037 0.00 0.00 0.00 1.90
3153 5107 7.402054 TCAGTCCATCTTTTACCATGTGTTAT 58.598 34.615 0.00 0.00 0.00 1.89
3154 5108 6.774673 TCAGTCCATCTTTTACCATGTGTTA 58.225 36.000 0.00 0.00 0.00 2.41
3155 5109 5.630121 TCAGTCCATCTTTTACCATGTGTT 58.370 37.500 0.00 0.00 0.00 3.32
3195 5149 6.537355 ACTGAATCTTCTGAATCAAGGACAA 58.463 36.000 4.12 0.00 32.38 3.18
3248 5212 7.275888 TGGCCTATAACTTGCATAATTTCTG 57.724 36.000 3.32 0.00 0.00 3.02
3276 5241 9.219603 CAAAGGTGAATAAGATGACTGAACTTA 57.780 33.333 0.00 0.00 0.00 2.24
3370 5442 4.773323 ATGTGCAAGGAACTAAGCTTTC 57.227 40.909 3.20 0.00 38.49 2.62
3483 5560 0.320683 CTGGGTGTCGCAGTTCATCA 60.321 55.000 5.80 0.00 39.17 3.07


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

AutoCloner maintained by Alex Coulton.