Multiple sequence alignment - TraesCS1B01G446800

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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 TraesCS1B01G446800 chr1B 100.000 2911 0 0 1 2911 666822180 666825090 0.000000e+00 5376.0
1 TraesCS1B01G446800 chr1B 80.749 374 48 16 887 1242 4624367 4624734 1.330000e-68 270.0
2 TraesCS1B01G446800 chr1B 91.736 121 7 3 1156 1276 644448932 644449049 6.450000e-37 165.0
3 TraesCS1B01G446800 chr1B 97.059 34 1 0 88 121 622608709 622608742 1.130000e-04 58.4
4 TraesCS1B01G446800 chr1D 95.192 1248 47 8 896 2140 478816064 478817301 0.000000e+00 1960.0
5 TraesCS1B01G446800 chr1D 85.923 753 48 20 123 847 478815335 478816057 0.000000e+00 750.0
6 TraesCS1B01G446800 chr1D 89.731 409 28 5 2510 2911 478817660 478818061 7.200000e-141 510.0
7 TraesCS1B01G446800 chr1D 84.689 209 16 11 2305 2507 478817364 478817562 8.230000e-46 195.0
8 TraesCS1B01G446800 chr1D 100.000 32 0 0 88 119 219735109 219735078 3.130000e-05 60.2
9 TraesCS1B01G446800 chr1A 95.868 484 18 2 1658 2140 574935361 574935843 0.000000e+00 782.0
10 TraesCS1B01G446800 chr1A 85.000 660 63 14 872 1525 574934460 574935089 3.160000e-179 638.0
11 TraesCS1B01G446800 chr1A 91.111 405 19 9 2510 2904 574936260 574936657 1.540000e-147 532.0
12 TraesCS1B01G446800 chr1A 92.647 204 11 3 2305 2507 574935962 574936162 1.020000e-74 291.0
13 TraesCS1B01G446800 chr1A 82.707 133 5 6 1526 1658 574935167 574935281 5.130000e-18 102.0
14 TraesCS1B01G446800 chr1A 97.059 34 1 0 88 121 547344861 547344894 1.130000e-04 58.4
15 TraesCS1B01G446800 chr7B 79.661 649 74 33 887 1516 3796640 3796031 5.800000e-112 414.0
16 TraesCS1B01G446800 chr7B 80.396 505 55 20 1041 1525 19119420 19119900 7.720000e-91 344.0
17 TraesCS1B01G446800 chr7B 81.081 370 44 18 887 1239 78570819 78571179 3.700000e-69 272.0
18 TraesCS1B01G446800 chr7B 77.433 483 70 25 1625 2086 3795768 3795304 4.820000e-63 252.0
19 TraesCS1B01G446800 chr7B 84.348 230 30 6 872 1099 19119197 19119422 1.360000e-53 220.0
20 TraesCS1B01G446800 chr7B 100.000 52 0 0 1 52 174744127 174744178 2.390000e-16 97.1
21 TraesCS1B01G446800 chr7D 79.904 627 71 27 922 1525 63437187 63436593 2.700000e-110 409.0
22 TraesCS1B01G446800 chr7D 76.832 423 50 25 1693 2094 63436254 63435859 8.230000e-46 195.0
23 TraesCS1B01G446800 chr7D 97.500 40 0 1 88 126 139094253 139094214 1.870000e-07 67.6
24 TraesCS1B01G446800 chr4A 79.500 600 79 23 934 1510 591505886 591505308 1.270000e-103 387.0
25 TraesCS1B01G446800 chr4A 79.534 601 77 24 934 1510 592538005 592538583 1.270000e-103 387.0
26 TraesCS1B01G446800 chr4A 95.789 95 4 0 2134 2228 684976198 684976104 1.400000e-33 154.0
27 TraesCS1B01G446800 chr4A 90.083 121 9 3 1156 1276 742981383 742981500 1.400000e-33 154.0
28 TraesCS1B01G446800 chr4B 90.943 265 16 4 2635 2898 546685106 546685363 1.660000e-92 350.0
29 TraesCS1B01G446800 chr4B 100.000 52 0 0 1 52 1748712 1748661 2.390000e-16 97.1
30 TraesCS1B01G446800 chr4B 100.000 52 0 0 1 52 584953082 584953031 2.390000e-16 97.1
31 TraesCS1B01G446800 chr4B 100.000 34 0 0 88 121 665982630 665982597 2.420000e-06 63.9
32 TraesCS1B01G446800 chr7A 78.063 506 66 29 1041 1525 34140937 34140456 7.940000e-71 278.0
33 TraesCS1B01G446800 chr7A 76.471 493 63 29 1625 2094 66228295 66227833 4.880000e-53 219.0
34 TraesCS1B01G446800 chr7A 100.000 91 0 0 2135 2225 332924648 332924558 4.990000e-38 169.0
35 TraesCS1B01G446800 chr6B 80.811 370 45 18 887 1239 51420126 51419766 1.720000e-67 267.0
36 TraesCS1B01G446800 chr6B 98.889 90 1 0 2132 2221 231315830 231315741 8.350000e-36 161.0
37 TraesCS1B01G446800 chr6B 95.789 95 4 0 2130 2224 476176018 476176112 1.400000e-33 154.0
38 TraesCS1B01G446800 chr6B 100.000 52 0 0 1 52 470924013 470924064 2.390000e-16 97.1
39 TraesCS1B01G446800 chr6B 97.059 34 1 0 88 121 462034253 462034286 1.130000e-04 58.4
40 TraesCS1B01G446800 chr3B 80.707 368 49 14 887 1239 160126856 160126496 1.720000e-67 267.0
41 TraesCS1B01G446800 chr3B 100.000 87 0 0 2137 2223 459409131 459409045 8.350000e-36 161.0
42 TraesCS1B01G446800 chr3B 95.789 95 4 0 2132 2226 556644793 556644699 1.400000e-33 154.0
43 TraesCS1B01G446800 chr3B 100.000 52 0 0 1 52 249987058 249987007 2.390000e-16 97.1
44 TraesCS1B01G446800 chr6D 91.146 192 10 3 2707 2898 445175422 445175238 1.340000e-63 254.0
45 TraesCS1B01G446800 chr6D 100.000 37 0 0 88 124 392512746 392512710 5.210000e-08 69.4
46 TraesCS1B01G446800 chr2D 97.895 95 1 1 2129 2223 165009229 165009322 2.320000e-36 163.0
47 TraesCS1B01G446800 chr2D 98.876 89 1 0 2135 2223 188886171 188886083 3.000000e-35 159.0
48 TraesCS1B01G446800 chr3D 95.050 101 4 1 2124 2224 554346213 554346114 1.080000e-34 158.0
49 TraesCS1B01G446800 chr3D 100.000 34 0 0 88 121 569545612 569545645 2.420000e-06 63.9
50 TraesCS1B01G446800 chr3D 93.023 43 3 0 88 130 572461819 572461777 2.420000e-06 63.9
51 TraesCS1B01G446800 chr2B 90.756 119 8 3 1156 1274 465798137 465798252 3.880000e-34 156.0
52 TraesCS1B01G446800 chr5D 100.000 52 0 0 1 52 378335889 378335838 2.390000e-16 97.1
53 TraesCS1B01G446800 chr5B 100.000 52 0 0 1 52 115658564 115658513 2.390000e-16 97.1
54 TraesCS1B01G446800 chr5B 100.000 52 0 0 1 52 115659987 115659936 2.390000e-16 97.1
55 TraesCS1B01G446800 chr5B 100.000 52 0 0 1 52 166318183 166318234 2.390000e-16 97.1


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 TraesCS1B01G446800 chr1B 666822180 666825090 2910 False 5376.00 5376 100.00000 1 2911 1 chr1B.!!$F4 2910
1 TraesCS1B01G446800 chr1D 478815335 478818061 2726 False 853.75 1960 88.88375 123 2911 4 chr1D.!!$F1 2788
2 TraesCS1B01G446800 chr1A 574934460 574936657 2197 False 469.00 782 89.46660 872 2904 5 chr1A.!!$F2 2032
3 TraesCS1B01G446800 chr7B 3795304 3796640 1336 True 333.00 414 78.54700 887 2086 2 chr7B.!!$R1 1199
4 TraesCS1B01G446800 chr7B 19119197 19119900 703 False 282.00 344 82.37200 872 1525 2 chr7B.!!$F3 653
5 TraesCS1B01G446800 chr7D 63435859 63437187 1328 True 302.00 409 78.36800 922 2094 2 chr7D.!!$R2 1172
6 TraesCS1B01G446800 chr4A 591505308 591505886 578 True 387.00 387 79.50000 934 1510 1 chr4A.!!$R1 576
7 TraesCS1B01G446800 chr4A 592538005 592538583 578 False 387.00 387 79.53400 934 1510 1 chr4A.!!$F1 576

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
552 578 0.109597 CTGTCAAACCAATCGGCTGC 60.11 55.0 0.0 0.0 34.57 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2749 0.118346 TCCCTGGGCTGGTAAGAGAA 59.882 55.0 8.22 0.0 0.0 2.87 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
40 41 3.360340 GCCTGCTGCGTGCTTCTT 61.360 61.111 6.02 0.00 43.37 2.52
41 42 2.866028 CCTGCTGCGTGCTTCTTC 59.134 61.111 0.00 0.00 43.37 2.87
42 43 2.684843 CCTGCTGCGTGCTTCTTCC 61.685 63.158 0.00 0.00 43.37 3.46
43 44 1.670406 CTGCTGCGTGCTTCTTCCT 60.670 57.895 0.00 0.00 43.37 3.36
44 45 1.909141 CTGCTGCGTGCTTCTTCCTG 61.909 60.000 0.00 0.00 43.37 3.86
45 46 2.866028 CTGCGTGCTTCTTCCTGC 59.134 61.111 0.00 0.00 0.00 4.85
46 47 1.670406 CTGCGTGCTTCTTCCTGCT 60.670 57.895 0.00 0.00 0.00 4.24
47 48 1.909141 CTGCGTGCTTCTTCCTGCTG 61.909 60.000 0.00 0.00 0.00 4.41
48 49 2.866028 CGTGCTTCTTCCTGCTGC 59.134 61.111 0.00 0.00 0.00 5.25
49 50 1.670406 CGTGCTTCTTCCTGCTGCT 60.670 57.895 0.00 0.00 0.00 4.24
50 51 0.390340 CGTGCTTCTTCCTGCTGCTA 60.390 55.000 0.00 0.00 0.00 3.49
51 52 1.741732 CGTGCTTCTTCCTGCTGCTAT 60.742 52.381 0.00 0.00 0.00 2.97
52 53 2.481969 CGTGCTTCTTCCTGCTGCTATA 60.482 50.000 0.00 0.00 0.00 1.31
53 54 3.737850 GTGCTTCTTCCTGCTGCTATAT 58.262 45.455 0.00 0.00 0.00 0.86
54 55 3.745458 GTGCTTCTTCCTGCTGCTATATC 59.255 47.826 0.00 0.00 0.00 1.63
55 56 3.389002 TGCTTCTTCCTGCTGCTATATCA 59.611 43.478 0.00 0.00 0.00 2.15
56 57 4.141642 TGCTTCTTCCTGCTGCTATATCAA 60.142 41.667 0.00 0.00 0.00 2.57
57 58 4.818546 GCTTCTTCCTGCTGCTATATCAAA 59.181 41.667 0.00 0.00 0.00 2.69
58 59 5.472820 GCTTCTTCCTGCTGCTATATCAAAT 59.527 40.000 0.00 0.00 0.00 2.32
59 60 6.016443 GCTTCTTCCTGCTGCTATATCAAATT 60.016 38.462 0.00 0.00 0.00 1.82
60 61 7.173907 GCTTCTTCCTGCTGCTATATCAAATTA 59.826 37.037 0.00 0.00 0.00 1.40
61 62 8.978874 TTCTTCCTGCTGCTATATCAAATTAA 57.021 30.769 0.00 0.00 0.00 1.40
62 63 8.978874 TCTTCCTGCTGCTATATCAAATTAAA 57.021 30.769 0.00 0.00 0.00 1.52
63 64 9.407380 TCTTCCTGCTGCTATATCAAATTAAAA 57.593 29.630 0.00 0.00 0.00 1.52
64 65 9.674824 CTTCCTGCTGCTATATCAAATTAAAAG 57.325 33.333 0.00 0.00 0.00 2.27
65 66 8.978874 TCCTGCTGCTATATCAAATTAAAAGA 57.021 30.769 0.00 0.00 0.00 2.52
66 67 9.407380 TCCTGCTGCTATATCAAATTAAAAGAA 57.593 29.630 0.00 0.00 0.00 2.52
86 87 9.883142 AAAAGAATGAAAATTACCACTTGACAA 57.117 25.926 0.00 0.00 0.00 3.18
87 88 9.533253 AAAGAATGAAAATTACCACTTGACAAG 57.467 29.630 13.77 13.77 0.00 3.16
88 89 8.463930 AGAATGAAAATTACCACTTGACAAGA 57.536 30.769 21.95 0.00 0.00 3.02
89 90 8.352942 AGAATGAAAATTACCACTTGACAAGAC 58.647 33.333 21.95 1.45 0.00 3.01
90 91 7.581213 ATGAAAATTACCACTTGACAAGACA 57.419 32.000 21.95 0.95 0.00 3.41
91 92 7.397892 TGAAAATTACCACTTGACAAGACAA 57.602 32.000 21.95 9.47 0.00 3.18
93 94 7.338196 TGAAAATTACCACTTGACAAGACAAGA 59.662 33.333 21.95 5.19 46.85 3.02
94 95 6.867662 AATTACCACTTGACAAGACAAGAG 57.132 37.500 21.95 10.07 46.85 2.85
95 96 3.914426 ACCACTTGACAAGACAAGAGT 57.086 42.857 21.95 11.25 46.85 3.24
96 97 3.535561 ACCACTTGACAAGACAAGAGTG 58.464 45.455 21.95 8.09 46.85 3.51
97 98 2.874701 CCACTTGACAAGACAAGAGTGG 59.125 50.000 21.95 13.29 46.85 4.00
98 99 3.535561 CACTTGACAAGACAAGAGTGGT 58.464 45.455 21.95 0.00 46.85 4.16
99 100 4.442893 CCACTTGACAAGACAAGAGTGGTA 60.443 45.833 21.95 0.00 46.85 3.25
100 101 5.116180 CACTTGACAAGACAAGAGTGGTAA 58.884 41.667 21.95 0.00 46.85 2.85
101 102 5.235186 CACTTGACAAGACAAGAGTGGTAAG 59.765 44.000 21.95 0.00 46.85 2.34
102 103 3.728845 TGACAAGACAAGAGTGGTAAGC 58.271 45.455 0.00 0.00 0.00 3.09
103 104 3.388024 TGACAAGACAAGAGTGGTAAGCT 59.612 43.478 0.00 0.00 0.00 3.74
104 105 4.587262 TGACAAGACAAGAGTGGTAAGCTA 59.413 41.667 0.00 0.00 0.00 3.32
105 106 5.246203 TGACAAGACAAGAGTGGTAAGCTAT 59.754 40.000 0.00 0.00 0.00 2.97
106 107 6.436218 TGACAAGACAAGAGTGGTAAGCTATA 59.564 38.462 0.00 0.00 0.00 1.31
107 108 7.124298 TGACAAGACAAGAGTGGTAAGCTATAT 59.876 37.037 0.00 0.00 0.00 0.86
108 109 7.493367 ACAAGACAAGAGTGGTAAGCTATATC 58.507 38.462 0.00 0.00 0.00 1.63
109 110 7.124298 ACAAGACAAGAGTGGTAAGCTATATCA 59.876 37.037 0.00 0.00 0.00 2.15
110 111 7.661536 AGACAAGAGTGGTAAGCTATATCAA 57.338 36.000 0.00 0.00 0.00 2.57
111 112 8.079211 AGACAAGAGTGGTAAGCTATATCAAA 57.921 34.615 0.00 0.00 0.00 2.69
112 113 8.540388 AGACAAGAGTGGTAAGCTATATCAAAA 58.460 33.333 0.00 0.00 0.00 2.44
113 114 9.162764 GACAAGAGTGGTAAGCTATATCAAAAA 57.837 33.333 0.00 0.00 0.00 1.94
114 115 8.947115 ACAAGAGTGGTAAGCTATATCAAAAAC 58.053 33.333 0.00 0.00 0.00 2.43
115 116 8.946085 CAAGAGTGGTAAGCTATATCAAAAACA 58.054 33.333 0.00 0.00 0.00 2.83
116 117 9.686683 AAGAGTGGTAAGCTATATCAAAAACAT 57.313 29.630 0.00 0.00 0.00 2.71
117 118 9.686683 AGAGTGGTAAGCTATATCAAAAACATT 57.313 29.630 0.00 0.00 0.00 2.71
118 119 9.722056 GAGTGGTAAGCTATATCAAAAACATTG 57.278 33.333 0.00 0.00 0.00 2.82
119 120 9.461312 AGTGGTAAGCTATATCAAAAACATTGA 57.539 29.630 0.00 0.00 0.00 2.57
165 166 1.660242 AAGGCCCCTTGATTTTGCAT 58.340 45.000 0.00 0.00 34.60 3.96
172 173 4.370917 CCCCTTGATTTTGCATATTTCGG 58.629 43.478 0.00 0.00 0.00 4.30
173 174 4.141959 CCCCTTGATTTTGCATATTTCGGT 60.142 41.667 0.00 0.00 0.00 4.69
175 176 5.291614 CCCTTGATTTTGCATATTTCGGTTG 59.708 40.000 0.00 0.00 0.00 3.77
180 181 7.995289 TGATTTTGCATATTTCGGTTGTAGAT 58.005 30.769 0.00 0.00 0.00 1.98
202 204 5.833406 TGCTCAAAGTGAGTTGAAATTGA 57.167 34.783 7.08 0.00 45.94 2.57
208 210 8.410030 TCAAAGTGAGTTGAAATTGAAACATG 57.590 30.769 6.35 0.00 34.59 3.21
324 326 0.546747 AGTCGATTCCCCACCTTCCA 60.547 55.000 0.00 0.00 0.00 3.53
350 353 1.544151 GTCCCTCCCCTTTCCCCTT 60.544 63.158 0.00 0.00 0.00 3.95
365 368 2.003548 CCTTCCCCTTCCCCTCCAG 61.004 68.421 0.00 0.00 0.00 3.86
405 408 2.974698 CCGCCGCCTGAATCCATC 60.975 66.667 0.00 0.00 0.00 3.51
448 470 2.410053 CGTTTCTCTTCTTCCTCGCAAG 59.590 50.000 0.00 0.00 0.00 4.01
478 504 0.547954 GGTCTCCTCCCTCCCTTTGT 60.548 60.000 0.00 0.00 0.00 2.83
498 524 4.631131 TGTGGTATGTATGTATGAGCAGC 58.369 43.478 0.00 0.00 0.00 5.25
519 545 0.389948 AGCTAGGTTGTTCCTTCGCG 60.390 55.000 0.00 0.00 45.67 5.87
551 577 1.466167 CTCTGTCAAACCAATCGGCTG 59.534 52.381 0.00 0.00 34.57 4.85
552 578 0.109597 CTGTCAAACCAATCGGCTGC 60.110 55.000 0.00 0.00 34.57 5.25
553 579 0.537143 TGTCAAACCAATCGGCTGCT 60.537 50.000 0.00 0.00 34.57 4.24
554 580 1.271108 TGTCAAACCAATCGGCTGCTA 60.271 47.619 0.00 0.00 34.57 3.49
555 581 1.398390 GTCAAACCAATCGGCTGCTAG 59.602 52.381 0.00 0.00 34.57 3.42
556 582 1.003118 TCAAACCAATCGGCTGCTAGT 59.997 47.619 0.00 0.00 34.57 2.57
593 619 0.704664 GGGACCTTCCAATTCTGGGT 59.295 55.000 0.00 0.00 43.71 4.51
602 628 3.387962 TCCAATTCTGGGTAGATCTGCT 58.612 45.455 10.82 0.00 43.71 4.24
610 636 1.751563 GTAGATCTGCTCCCCCTGC 59.248 63.158 5.18 0.00 0.00 4.85
611 637 1.050988 GTAGATCTGCTCCCCCTGCA 61.051 60.000 5.18 0.00 38.81 4.41
617 643 4.416738 GCTCCCCCTGCAGTGTCC 62.417 72.222 13.81 0.00 0.00 4.02
618 644 2.930019 CTCCCCCTGCAGTGTCCA 60.930 66.667 13.81 0.00 0.00 4.02
619 645 2.204136 TCCCCCTGCAGTGTCCAT 60.204 61.111 13.81 0.00 0.00 3.41
620 646 2.044650 CCCCCTGCAGTGTCCATG 60.045 66.667 13.81 0.00 0.00 3.66
621 647 2.044650 CCCCTGCAGTGTCCATGG 60.045 66.667 13.81 4.97 0.00 3.66
622 648 2.753043 CCCTGCAGTGTCCATGGC 60.753 66.667 13.81 2.72 0.00 4.40
623 649 3.129502 CCTGCAGTGTCCATGGCG 61.130 66.667 13.81 0.00 0.00 5.69
624 650 3.129502 CTGCAGTGTCCATGGCGG 61.130 66.667 6.96 0.00 0.00 6.13
627 653 3.129502 CAGTGTCCATGGCGGCAG 61.130 66.667 19.29 9.56 33.14 4.85
628 654 4.415150 AGTGTCCATGGCGGCAGG 62.415 66.667 19.29 18.40 33.14 4.85
645 671 2.511600 GGCGTGTTCCTGGATCCG 60.512 66.667 7.39 4.44 0.00 4.18
664 693 3.127548 TCCGAGTTTGTGGATACGAGTAC 59.872 47.826 0.00 0.00 42.51 2.73
684 713 2.061773 CGATTGGTCTGCGGATGATAC 58.938 52.381 0.00 0.00 0.00 2.24
703 732 5.350640 TGATACGATCTATATCTTGCGTCGT 59.649 40.000 12.53 0.00 42.55 4.34
726 755 9.119329 TCGTTACAAATTTCGGTTGATTTTATG 57.881 29.630 0.00 0.00 0.00 1.90
756 785 9.974980 TTTATTAGTACAAGATGATGCGTGATA 57.025 29.630 0.00 0.00 0.00 2.15
760 789 3.801698 ACAAGATGATGCGTGATAGCTT 58.198 40.909 0.00 0.00 38.13 3.74
831 860 3.973206 TGGATACCCTTGTGTGTACAG 57.027 47.619 0.00 0.00 38.23 2.74
838 867 2.806244 CCCTTGTGTGTACAGTTACTGC 59.194 50.000 12.80 0.00 38.23 4.40
847 876 7.170828 TGTGTGTACAGTTACTGCATCTTTTAG 59.829 37.037 12.80 0.00 34.37 1.85
848 877 6.649141 TGTGTACAGTTACTGCATCTTTTAGG 59.351 38.462 12.80 0.00 34.37 2.69
849 878 6.649557 GTGTACAGTTACTGCATCTTTTAGGT 59.350 38.462 12.80 0.00 34.37 3.08
852 881 9.211485 GTACAGTTACTGCATCTTTTAGGTTAA 57.789 33.333 12.80 0.00 34.37 2.01
853 882 8.685838 ACAGTTACTGCATCTTTTAGGTTAAA 57.314 30.769 12.80 0.00 34.37 1.52
854 883 9.297037 ACAGTTACTGCATCTTTTAGGTTAAAT 57.703 29.630 12.80 0.00 34.37 1.40
876 905 8.894768 AAATATACTCTGCACTTGGAGTATTC 57.105 34.615 23.58 0.00 46.98 1.75
881 910 5.246203 ACTCTGCACTTGGAGTATTCAGTAA 59.754 40.000 4.62 0.00 40.49 2.24
900 929 5.971792 CAGTAATGATTTCTTCGCGACTAGA 59.028 40.000 9.15 7.51 0.00 2.43
902 931 7.168302 CAGTAATGATTTCTTCGCGACTAGAAT 59.832 37.037 20.59 13.24 31.00 2.40
903 932 8.350722 AGTAATGATTTCTTCGCGACTAGAATA 58.649 33.333 20.59 13.28 31.00 1.75
918 947 7.133513 CGACTAGAATATCCAGTAGTGTGTTC 58.866 42.308 0.00 0.00 0.00 3.18
997 1033 3.611970 TGAAGTAAGGAGAGAGGTCGAG 58.388 50.000 0.00 0.00 0.00 4.04
1101 1193 2.045926 AACCATGGGAGCAGCGTC 60.046 61.111 18.09 0.00 0.00 5.19
1135 1227 7.707035 GGATGTTAGTACTATCTTCACCTGTTG 59.293 40.741 20.21 0.00 0.00 3.33
1289 1406 7.798516 GCAAATGGTATGTATGAATTAGACACG 59.201 37.037 0.00 0.00 32.53 4.49
1417 1538 6.814644 TCTCAACCAAATGATTGATTGATTGC 59.185 34.615 0.00 0.00 45.76 3.56
1607 1834 2.719739 ACCTGCATTCATCAGAACTGG 58.280 47.619 1.93 0.00 36.39 4.00
1621 1848 7.290948 TCATCAGAACTGGACCTGTATGATAAT 59.709 37.037 21.68 7.91 30.09 1.28
1622 1849 6.820335 TCAGAACTGGACCTGTATGATAATG 58.180 40.000 4.21 0.00 0.00 1.90
1623 1850 6.384015 TCAGAACTGGACCTGTATGATAATGT 59.616 38.462 4.21 0.00 0.00 2.71
1711 2034 9.862371 TCTCAGAATTGTACTAATTCTCTGTTC 57.138 33.333 20.81 3.71 43.08 3.18
1950 2296 4.256920 ACTCTATGACCTCAATGTGTTGC 58.743 43.478 0.00 0.00 35.26 4.17
1953 2299 0.953727 TGACCTCAATGTGTTGCTGC 59.046 50.000 0.00 0.00 35.26 5.25
2063 2410 6.033619 GTGCTTAATACACGACCGATGATATC 59.966 42.308 0.00 0.00 0.00 1.63
2129 2476 3.262405 ACCTAATCTCGGTACCTGCAAAA 59.738 43.478 10.90 0.00 31.69 2.44
2151 2498 6.564709 AAAATTTGTACTCCCTCCGTAAAC 57.435 37.500 0.00 0.00 0.00 2.01
2152 2499 4.895668 ATTTGTACTCCCTCCGTAAACA 57.104 40.909 0.00 0.00 0.00 2.83
2153 2500 4.686191 TTTGTACTCCCTCCGTAAACAA 57.314 40.909 0.00 0.00 0.00 2.83
2154 2501 4.686191 TTGTACTCCCTCCGTAAACAAA 57.314 40.909 0.00 0.00 0.00 2.83
2155 2502 4.895668 TGTACTCCCTCCGTAAACAAAT 57.104 40.909 0.00 0.00 0.00 2.32
2156 2503 5.999205 TGTACTCCCTCCGTAAACAAATA 57.001 39.130 0.00 0.00 0.00 1.40
2157 2504 6.549433 TGTACTCCCTCCGTAAACAAATAT 57.451 37.500 0.00 0.00 0.00 1.28
2158 2505 7.658525 TGTACTCCCTCCGTAAACAAATATA 57.341 36.000 0.00 0.00 0.00 0.86
2159 2506 8.076910 TGTACTCCCTCCGTAAACAAATATAA 57.923 34.615 0.00 0.00 0.00 0.98
2160 2507 8.199449 TGTACTCCCTCCGTAAACAAATATAAG 58.801 37.037 0.00 0.00 0.00 1.73
2161 2508 7.427989 ACTCCCTCCGTAAACAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
2162 2509 7.498443 ACTCCCTCCGTAAACAAATATAAGAG 58.502 38.462 0.00 0.00 0.00 2.85
2163 2510 6.285990 TCCCTCCGTAAACAAATATAAGAGC 58.714 40.000 0.00 0.00 0.00 4.09
2164 2511 5.176958 CCCTCCGTAAACAAATATAAGAGCG 59.823 44.000 0.00 0.00 0.00 5.03
2165 2512 5.751990 CCTCCGTAAACAAATATAAGAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
2166 2513 6.257193 CCTCCGTAAACAAATATAAGAGCGTT 59.743 38.462 0.00 0.00 0.00 4.84
2167 2514 7.201582 CCTCCGTAAACAAATATAAGAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
2168 2515 8.700722 TCCGTAAACAAATATAAGAGCGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
2169 2516 8.810427 TCCGTAAACAAATATAAGAGCGTTTAG 58.190 33.333 0.00 0.00 31.53 1.85
2170 2517 8.810427 CCGTAAACAAATATAAGAGCGTTTAGA 58.190 33.333 0.00 0.00 31.53 2.10
2175 2522 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
2182 2529 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2183 2530 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2184 2531 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2185 2532 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
2186 2533 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
2187 2534 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
2188 2535 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
2217 2564 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
2232 2579 2.763448 AGAGGGAGTACTTGAGACATGC 59.237 50.000 0.00 0.00 0.00 4.06
2233 2580 1.834263 AGGGAGTACTTGAGACATGCC 59.166 52.381 0.00 0.00 0.00 4.40
2239 2586 1.238439 ACTTGAGACATGCCGTTTGG 58.762 50.000 0.00 0.00 38.77 3.28
2244 2591 1.002624 GACATGCCGTTTGGGAGGA 60.003 57.895 0.00 0.00 40.16 3.71
2257 2604 2.054021 TGGGAGGATGTTCTGTGAACA 58.946 47.619 14.29 14.29 34.31 3.18
2260 2607 3.496870 GGGAGGATGTTCTGTGAACAGTT 60.497 47.826 16.50 3.37 44.12 3.16
2275 2622 9.651718 CTGTGAACAGTTAAGTCAAGAATTTAC 57.348 33.333 2.14 0.00 39.09 2.01
2303 2650 3.324268 TGGTACGGTGGTTGTTTGATAGA 59.676 43.478 0.00 0.00 0.00 1.98
2322 2706 3.589988 AGACCATGAACTGTGAATCGTC 58.410 45.455 0.00 0.00 0.00 4.20
2350 2734 2.806434 TGCTACTTTTGGGATGTGCAT 58.194 42.857 0.00 0.00 0.00 3.96
2387 2773 1.198759 TCTTACCAGCCCAGGGACAC 61.199 60.000 10.89 0.00 0.00 3.67
2388 2774 1.151899 TTACCAGCCCAGGGACACT 60.152 57.895 10.89 0.00 0.00 3.55
2389 2775 0.117541 TTACCAGCCCAGGGACACTA 59.882 55.000 10.89 0.00 0.00 2.74
2453 2841 7.656707 AACTTCGTAAACATGTATAAACCGT 57.343 32.000 0.00 0.00 0.00 4.83
2507 2897 7.956943 AGCAATTTTTCAAAGAAAAACAAGACG 59.043 29.630 16.97 6.38 32.75 4.18
2523 3008 1.195448 AGACGATGCTTTCAAGTTGCG 59.805 47.619 0.00 0.00 0.00 4.85
2583 3068 6.436261 CAGACTTGATTTTATGCTATGCTGG 58.564 40.000 0.00 0.00 0.00 4.85
2633 3118 0.251165 TTGCCTTGTAAGGGTCCTGC 60.251 55.000 12.32 0.00 46.56 4.85
2706 3193 0.325933 TGCAGCCACTCTAACAGCAT 59.674 50.000 0.00 0.00 0.00 3.79
2727 3214 1.615392 GCTGCACTTGTTTTCCAGGAT 59.385 47.619 0.00 0.00 0.00 3.24
2728 3215 2.608752 GCTGCACTTGTTTTCCAGGATG 60.609 50.000 0.00 0.00 0.00 3.51
2784 3271 1.023513 GGTGTGCAGCAGAGCTTAGG 61.024 60.000 14.27 0.00 36.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.866028 CAGGAAGAAGCACGCAGC 59.134 61.111 0.00 0.00 46.19 5.25
28 29 1.670406 AGCAGGAAGAAGCACGCAG 60.670 57.895 0.00 0.00 0.00 5.18
29 30 1.962822 CAGCAGGAAGAAGCACGCA 60.963 57.895 0.00 0.00 0.00 5.24
30 31 2.866028 CAGCAGGAAGAAGCACGC 59.134 61.111 0.00 0.00 0.00 5.34
31 32 0.390340 TAGCAGCAGGAAGAAGCACG 60.390 55.000 0.00 0.00 0.00 5.34
32 33 2.035530 ATAGCAGCAGGAAGAAGCAC 57.964 50.000 0.00 0.00 0.00 4.40
33 34 3.389002 TGATATAGCAGCAGGAAGAAGCA 59.611 43.478 0.00 0.00 0.00 3.91
34 35 4.000331 TGATATAGCAGCAGGAAGAAGC 58.000 45.455 0.00 0.00 0.00 3.86
35 36 7.507733 AATTTGATATAGCAGCAGGAAGAAG 57.492 36.000 0.00 0.00 0.00 2.85
36 37 8.978874 TTAATTTGATATAGCAGCAGGAAGAA 57.021 30.769 0.00 0.00 0.00 2.52
37 38 8.978874 TTTAATTTGATATAGCAGCAGGAAGA 57.021 30.769 0.00 0.00 0.00 2.87
38 39 9.674824 CTTTTAATTTGATATAGCAGCAGGAAG 57.325 33.333 0.00 0.00 0.00 3.46
39 40 9.407380 TCTTTTAATTTGATATAGCAGCAGGAA 57.593 29.630 0.00 0.00 0.00 3.36
40 41 8.978874 TCTTTTAATTTGATATAGCAGCAGGA 57.021 30.769 0.00 0.00 0.00 3.86
60 61 9.883142 TTGTCAAGTGGTAATTTTCATTCTTTT 57.117 25.926 0.00 0.00 0.00 2.27
61 62 9.533253 CTTGTCAAGTGGTAATTTTCATTCTTT 57.467 29.630 4.27 0.00 0.00 2.52
62 63 8.912988 TCTTGTCAAGTGGTAATTTTCATTCTT 58.087 29.630 12.30 0.00 0.00 2.52
63 64 8.352942 GTCTTGTCAAGTGGTAATTTTCATTCT 58.647 33.333 12.30 0.00 0.00 2.40
64 65 8.134895 TGTCTTGTCAAGTGGTAATTTTCATTC 58.865 33.333 12.30 0.00 0.00 2.67
65 66 8.006298 TGTCTTGTCAAGTGGTAATTTTCATT 57.994 30.769 12.30 0.00 0.00 2.57
66 67 7.581213 TGTCTTGTCAAGTGGTAATTTTCAT 57.419 32.000 12.30 0.00 0.00 2.57
67 68 7.338196 TCTTGTCTTGTCAAGTGGTAATTTTCA 59.662 33.333 12.30 0.00 43.44 2.69
68 69 7.703328 TCTTGTCTTGTCAAGTGGTAATTTTC 58.297 34.615 12.30 0.00 43.44 2.29
69 70 7.339466 ACTCTTGTCTTGTCAAGTGGTAATTTT 59.661 33.333 12.30 0.00 43.44 1.82
70 71 6.828785 ACTCTTGTCTTGTCAAGTGGTAATTT 59.171 34.615 12.30 0.00 43.44 1.82
71 72 6.260936 CACTCTTGTCTTGTCAAGTGGTAATT 59.739 38.462 12.30 0.00 43.44 1.40
72 73 5.760253 CACTCTTGTCTTGTCAAGTGGTAAT 59.240 40.000 12.30 0.00 43.44 1.89
73 74 5.116180 CACTCTTGTCTTGTCAAGTGGTAA 58.884 41.667 12.30 3.68 43.44 2.85
74 75 4.442893 CCACTCTTGTCTTGTCAAGTGGTA 60.443 45.833 12.30 0.00 43.44 3.25
75 76 3.535561 CACTCTTGTCTTGTCAAGTGGT 58.464 45.455 12.30 1.93 43.44 4.16
76 77 2.874701 CCACTCTTGTCTTGTCAAGTGG 59.125 50.000 12.30 7.72 43.44 4.00
77 78 3.535561 ACCACTCTTGTCTTGTCAAGTG 58.464 45.455 12.30 2.36 43.44 3.16
78 79 3.914426 ACCACTCTTGTCTTGTCAAGT 57.086 42.857 12.30 0.00 43.44 3.16
79 80 4.212214 GCTTACCACTCTTGTCTTGTCAAG 59.788 45.833 6.21 6.21 44.08 3.02
80 81 4.127171 GCTTACCACTCTTGTCTTGTCAA 58.873 43.478 0.00 0.00 0.00 3.18
81 82 3.388024 AGCTTACCACTCTTGTCTTGTCA 59.612 43.478 0.00 0.00 0.00 3.58
82 83 3.996480 AGCTTACCACTCTTGTCTTGTC 58.004 45.455 0.00 0.00 0.00 3.18
83 84 5.746990 ATAGCTTACCACTCTTGTCTTGT 57.253 39.130 0.00 0.00 0.00 3.16
84 85 7.492524 TGATATAGCTTACCACTCTTGTCTTG 58.507 38.462 0.00 0.00 0.00 3.02
85 86 7.661536 TGATATAGCTTACCACTCTTGTCTT 57.338 36.000 0.00 0.00 0.00 3.01
86 87 7.661536 TTGATATAGCTTACCACTCTTGTCT 57.338 36.000 0.00 0.00 0.00 3.41
87 88 8.718102 TTTTGATATAGCTTACCACTCTTGTC 57.282 34.615 0.00 0.00 0.00 3.18
88 89 8.947115 GTTTTTGATATAGCTTACCACTCTTGT 58.053 33.333 0.00 0.00 0.00 3.16
89 90 8.946085 TGTTTTTGATATAGCTTACCACTCTTG 58.054 33.333 0.00 0.00 0.00 3.02
90 91 9.686683 ATGTTTTTGATATAGCTTACCACTCTT 57.313 29.630 0.00 0.00 0.00 2.85
91 92 9.686683 AATGTTTTTGATATAGCTTACCACTCT 57.313 29.630 0.00 0.00 0.00 3.24
92 93 9.722056 CAATGTTTTTGATATAGCTTACCACTC 57.278 33.333 0.00 0.00 0.00 3.51
93 94 9.461312 TCAATGTTTTTGATATAGCTTACCACT 57.539 29.630 0.00 0.00 0.00 4.00
121 122 3.996363 GCTCCGCATTTTCCATTCTTTTT 59.004 39.130 0.00 0.00 0.00 1.94
124 125 1.478105 GGCTCCGCATTTTCCATTCTT 59.522 47.619 0.00 0.00 0.00 2.52
165 166 6.092122 CACTTTGAGCATCTACAACCGAAATA 59.908 38.462 0.00 0.00 34.92 1.40
220 222 4.027556 CGCAATCGTCGTTGTTTATCAAAC 59.972 41.667 8.60 0.00 41.73 2.93
301 303 1.497161 AGGTGGGGAATCGACTAAGG 58.503 55.000 0.00 0.00 0.00 2.69
302 304 2.158943 GGAAGGTGGGGAATCGACTAAG 60.159 54.545 0.00 0.00 0.00 2.18
305 307 0.546747 TGGAAGGTGGGGAATCGACT 60.547 55.000 0.00 0.00 0.00 4.18
424 446 1.351153 GAGGAAGAAGAGAAACGGCG 58.649 55.000 4.80 4.80 0.00 6.46
433 455 0.036952 CCTGCTTGCGAGGAAGAAGA 60.037 55.000 13.12 0.00 30.78 2.87
448 470 1.893919 GAGGAGACCTGGTGACCTGC 61.894 65.000 21.13 10.85 31.76 4.85
478 504 5.336770 GCTAGCTGCTCATACATACATACCA 60.337 44.000 4.91 0.00 38.95 3.25
512 538 1.552348 GAGAATCGATGCCGCGAAGG 61.552 60.000 8.23 0.00 44.22 3.46
519 545 2.879002 TGACAGAGAGAATCGATGCC 57.121 50.000 0.00 0.00 42.67 4.40
551 577 0.960286 CCTACCCTAGCGGAACTAGC 59.040 60.000 4.45 0.00 46.17 3.42
552 578 1.144503 TCCCTACCCTAGCGGAACTAG 59.855 57.143 4.45 0.00 46.95 2.57
553 579 1.133668 GTCCCTACCCTAGCGGAACTA 60.134 57.143 4.45 0.00 34.64 2.24
554 580 0.396835 GTCCCTACCCTAGCGGAACT 60.397 60.000 4.45 0.00 34.64 3.01
555 581 1.732417 CGTCCCTACCCTAGCGGAAC 61.732 65.000 4.45 0.00 34.64 3.62
556 582 1.454479 CGTCCCTACCCTAGCGGAA 60.454 63.158 4.45 0.00 34.64 4.30
593 619 1.314518 TGCAGGGGGAGCAGATCTA 59.685 57.895 0.00 0.00 37.02 1.98
602 628 2.204136 ATGGACACTGCAGGGGGA 60.204 61.111 22.46 3.30 0.00 4.81
610 636 3.129502 CTGCCGCCATGGACACTG 61.130 66.667 18.40 3.34 42.00 3.66
611 637 4.415150 CCTGCCGCCATGGACACT 62.415 66.667 18.40 0.00 42.00 3.55
626 652 2.670148 GGATCCAGGAACACGCCCT 61.670 63.158 6.95 0.00 0.00 5.19
627 653 2.124695 GGATCCAGGAACACGCCC 60.125 66.667 6.95 0.00 0.00 6.13
628 654 2.511600 CGGATCCAGGAACACGCC 60.512 66.667 13.41 0.00 0.00 5.68
645 671 4.346734 TCGTACTCGTATCCACAAACTC 57.653 45.455 0.00 0.00 38.33 3.01
664 693 2.061773 GTATCATCCGCAGACCAATCG 58.938 52.381 0.00 0.00 0.00 3.34
684 713 5.379827 TGTAACGACGCAAGATATAGATCG 58.620 41.667 0.00 0.00 43.62 3.69
728 757 9.157104 TCACGCATCATCTTGTACTAATAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
729 758 8.710835 TCACGCATCATCTTGTACTAATAAAA 57.289 30.769 0.00 0.00 0.00 1.52
730 759 8.887036 ATCACGCATCATCTTGTACTAATAAA 57.113 30.769 0.00 0.00 0.00 1.40
731 760 9.626045 CTATCACGCATCATCTTGTACTAATAA 57.374 33.333 0.00 0.00 0.00 1.40
732 761 7.755373 GCTATCACGCATCATCTTGTACTAATA 59.245 37.037 0.00 0.00 0.00 0.98
733 762 6.587990 GCTATCACGCATCATCTTGTACTAAT 59.412 38.462 0.00 0.00 0.00 1.73
734 763 5.920840 GCTATCACGCATCATCTTGTACTAA 59.079 40.000 0.00 0.00 0.00 2.24
735 764 5.241728 AGCTATCACGCATCATCTTGTACTA 59.758 40.000 0.00 0.00 0.00 1.82
736 765 4.038522 AGCTATCACGCATCATCTTGTACT 59.961 41.667 0.00 0.00 0.00 2.73
737 766 4.302455 AGCTATCACGCATCATCTTGTAC 58.698 43.478 0.00 0.00 0.00 2.90
738 767 4.590850 AGCTATCACGCATCATCTTGTA 57.409 40.909 0.00 0.00 0.00 2.41
739 768 3.465742 AGCTATCACGCATCATCTTGT 57.534 42.857 0.00 0.00 0.00 3.16
740 769 3.805971 TCAAGCTATCACGCATCATCTTG 59.194 43.478 0.00 0.00 0.00 3.02
741 770 4.063998 TCAAGCTATCACGCATCATCTT 57.936 40.909 0.00 0.00 0.00 2.40
742 771 3.740631 TCAAGCTATCACGCATCATCT 57.259 42.857 0.00 0.00 0.00 2.90
799 828 2.766828 AGGGTATCCAAGTGCAGAGTAC 59.233 50.000 0.00 0.00 34.83 2.73
810 839 3.649023 ACTGTACACACAAGGGTATCCAA 59.351 43.478 0.00 0.00 33.22 3.53
847 876 7.048512 ACTCCAAGTGCAGAGTATATTTAACC 58.951 38.462 4.62 0.00 41.51 2.85
856 885 4.772624 ACTGAATACTCCAAGTGCAGAGTA 59.227 41.667 13.95 13.95 46.61 2.59
857 886 3.580458 ACTGAATACTCCAAGTGCAGAGT 59.420 43.478 10.74 10.74 45.20 3.24
858 887 4.199432 ACTGAATACTCCAAGTGCAGAG 57.801 45.455 0.00 0.00 36.16 3.35
859 888 5.738619 TTACTGAATACTCCAAGTGCAGA 57.261 39.130 0.00 0.00 31.88 4.26
860 889 6.108687 TCATTACTGAATACTCCAAGTGCAG 58.891 40.000 0.00 0.00 32.91 4.41
861 890 6.048732 TCATTACTGAATACTCCAAGTGCA 57.951 37.500 0.00 0.00 0.00 4.57
862 891 7.559590 AATCATTACTGAATACTCCAAGTGC 57.440 36.000 0.00 0.00 34.37 4.40
863 892 9.388506 AGAAATCATTACTGAATACTCCAAGTG 57.611 33.333 0.00 0.00 34.37 3.16
867 896 7.224753 GCGAAGAAATCATTACTGAATACTCCA 59.775 37.037 0.00 0.00 34.37 3.86
876 905 5.971792 TCTAGTCGCGAAGAAATCATTACTG 59.028 40.000 12.06 0.00 0.00 2.74
881 910 6.809196 GGATATTCTAGTCGCGAAGAAATCAT 59.191 38.462 22.96 16.81 35.47 2.45
900 929 8.540507 AGACATAGAACACACTACTGGATATT 57.459 34.615 0.00 0.00 0.00 1.28
902 931 7.956328 AAGACATAGAACACACTACTGGATA 57.044 36.000 0.00 0.00 0.00 2.59
903 932 6.859112 AAGACATAGAACACACTACTGGAT 57.141 37.500 0.00 0.00 0.00 3.41
997 1033 1.228510 CCTTCCTCTTCCCCATGGC 59.771 63.158 6.09 0.00 0.00 4.40
1101 1193 3.093717 AGTACTAACATCCGGCATTCG 57.906 47.619 0.00 0.00 38.88 3.34
1135 1227 7.285401 TGGATAGCCATTCCAAATTAAGAAGAC 59.715 37.037 0.00 0.00 40.29 3.01
1289 1406 2.550487 TGGTACAATCTGCGGTTGC 58.450 52.632 0.00 0.00 37.11 4.17
1358 1476 4.074259 CAATGAGATGTCTGGTGTGGAAA 58.926 43.478 0.00 0.00 0.00 3.13
1417 1538 3.679389 ACCATGTTCCTAGAGTTGCAAG 58.321 45.455 0.00 0.00 0.00 4.01
1711 2034 1.962822 TCAGCGCTGCACCAAAGAG 60.963 57.895 32.44 5.01 0.00 2.85
1953 2299 1.086696 CTGACGGTGGCAGTAAATGG 58.913 55.000 0.00 0.00 0.00 3.16
2063 2410 6.424509 TCAAGGTTTACAAATACAGGTACACG 59.575 38.462 0.00 0.00 0.00 4.49
2129 2476 5.623169 TGTTTACGGAGGGAGTACAAATTT 58.377 37.500 0.00 0.00 0.00 1.82
2133 2480 4.686191 TTTGTTTACGGAGGGAGTACAA 57.314 40.909 0.00 0.00 0.00 2.41
2135 2482 8.416329 TCTTATATTTGTTTACGGAGGGAGTAC 58.584 37.037 0.00 0.00 0.00 2.73
2136 2483 8.537728 TCTTATATTTGTTTACGGAGGGAGTA 57.462 34.615 0.00 0.00 0.00 2.59
2137 2484 7.427989 TCTTATATTTGTTTACGGAGGGAGT 57.572 36.000 0.00 0.00 0.00 3.85
2138 2485 6.424207 GCTCTTATATTTGTTTACGGAGGGAG 59.576 42.308 0.00 0.00 0.00 4.30
2139 2486 6.285990 GCTCTTATATTTGTTTACGGAGGGA 58.714 40.000 0.00 0.00 0.00 4.20
2140 2487 5.176958 CGCTCTTATATTTGTTTACGGAGGG 59.823 44.000 0.00 0.00 0.00 4.30
2141 2488 5.751990 ACGCTCTTATATTTGTTTACGGAGG 59.248 40.000 0.00 0.00 0.00 4.30
2142 2489 6.823678 ACGCTCTTATATTTGTTTACGGAG 57.176 37.500 0.00 0.00 0.00 4.63
2143 2490 7.599630 AAACGCTCTTATATTTGTTTACGGA 57.400 32.000 0.00 0.00 0.00 4.69
2144 2491 8.810427 TCTAAACGCTCTTATATTTGTTTACGG 58.190 33.333 0.00 0.00 32.41 4.02
2149 2496 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
2156 2503 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2157 2504 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2158 2505 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2159 2506 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2160 2507 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2161 2508 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
2191 2538 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
2192 2539 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2193 2540 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2199 2546 9.710818 TCAAGTACTCCCTCTGTAAACTAATAT 57.289 33.333 0.00 0.00 0.00 1.28
2200 2547 9.186837 CTCAAGTACTCCCTCTGTAAACTAATA 57.813 37.037 0.00 0.00 0.00 0.98
2201 2548 7.894364 TCTCAAGTACTCCCTCTGTAAACTAAT 59.106 37.037 0.00 0.00 0.00 1.73
2202 2549 7.176340 GTCTCAAGTACTCCCTCTGTAAACTAA 59.824 40.741 0.00 0.00 0.00 2.24
2203 2550 6.658391 GTCTCAAGTACTCCCTCTGTAAACTA 59.342 42.308 0.00 0.00 0.00 2.24
2204 2551 5.477637 GTCTCAAGTACTCCCTCTGTAAACT 59.522 44.000 0.00 0.00 0.00 2.66
2205 2552 5.243283 TGTCTCAAGTACTCCCTCTGTAAAC 59.757 44.000 0.00 0.00 0.00 2.01
2206 2553 5.391256 TGTCTCAAGTACTCCCTCTGTAAA 58.609 41.667 0.00 0.00 0.00 2.01
2207 2554 4.994282 TGTCTCAAGTACTCCCTCTGTAA 58.006 43.478 0.00 0.00 0.00 2.41
2208 2555 4.652679 TGTCTCAAGTACTCCCTCTGTA 57.347 45.455 0.00 0.00 0.00 2.74
2209 2556 3.527507 TGTCTCAAGTACTCCCTCTGT 57.472 47.619 0.00 0.00 0.00 3.41
2210 2557 3.430098 GCATGTCTCAAGTACTCCCTCTG 60.430 52.174 0.00 0.00 0.00 3.35
2211 2558 2.763448 GCATGTCTCAAGTACTCCCTCT 59.237 50.000 0.00 0.00 0.00 3.69
2212 2559 2.159028 GGCATGTCTCAAGTACTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
2213 2560 1.834263 GGCATGTCTCAAGTACTCCCT 59.166 52.381 0.00 0.00 0.00 4.20
2214 2561 1.471676 CGGCATGTCTCAAGTACTCCC 60.472 57.143 0.00 0.00 0.00 4.30
2215 2562 1.204941 ACGGCATGTCTCAAGTACTCC 59.795 52.381 0.00 0.00 0.00 3.85
2216 2563 2.656560 ACGGCATGTCTCAAGTACTC 57.343 50.000 0.00 0.00 0.00 2.59
2217 2564 3.067106 CAAACGGCATGTCTCAAGTACT 58.933 45.455 0.00 0.00 0.00 2.73
2232 2579 1.271379 ACAGAACATCCTCCCAAACGG 60.271 52.381 0.00 0.00 0.00 4.44
2233 2580 1.806542 CACAGAACATCCTCCCAAACG 59.193 52.381 0.00 0.00 0.00 3.60
2239 2586 3.409026 ACTGTTCACAGAACATCCTCC 57.591 47.619 14.00 0.00 46.59 4.30
2244 2591 7.047891 TCTTGACTTAACTGTTCACAGAACAT 58.952 34.615 14.00 2.71 46.59 2.71
2275 2622 3.048337 ACAACCACCGTACCATAAGTG 57.952 47.619 0.00 0.00 0.00 3.16
2286 2633 2.773487 TGGTCTATCAAACAACCACCG 58.227 47.619 0.00 0.00 36.88 4.94
2303 2650 2.029380 TCGACGATTCACAGTTCATGGT 60.029 45.455 0.00 0.00 0.00 3.55
2322 2706 5.296780 ACATCCCAAAAGTAGCATACATTCG 59.703 40.000 0.00 0.00 46.26 3.34
2350 2734 5.885912 GGTAAGAGAATTTTCCATACTGGCA 59.114 40.000 8.52 0.00 37.47 4.92
2360 2744 3.696548 CCTGGGCTGGTAAGAGAATTTTC 59.303 47.826 0.00 0.00 0.00 2.29
2365 2749 0.118346 TCCCTGGGCTGGTAAGAGAA 59.882 55.000 8.22 0.00 0.00 2.87
2387 2773 8.818141 ACCACATGACATACTTCGAAATATAG 57.182 34.615 0.00 0.00 0.00 1.31
2388 2774 9.256477 GAACCACATGACATACTTCGAAATATA 57.744 33.333 0.00 0.00 0.00 0.86
2389 2775 7.768582 TGAACCACATGACATACTTCGAAATAT 59.231 33.333 0.00 0.00 0.00 1.28
2453 2841 9.555727 AGAACAGCTAACAAGTTAACAAATCTA 57.444 29.630 8.61 0.00 0.00 1.98
2507 2897 2.686558 TCACGCAACTTGAAAGCATC 57.313 45.000 0.00 0.00 0.00 3.91
2620 3105 5.636123 TGAAATTAAAGCAGGACCCTTACA 58.364 37.500 0.00 0.00 0.00 2.41
2706 3193 0.746063 CCTGGAAAACAAGTGCAGCA 59.254 50.000 0.00 0.00 33.43 4.41
2728 3215 9.495572 CCTTTTGAAGTTATCTATCCAGTATCC 57.504 37.037 0.00 0.00 0.00 2.59
2732 3219 9.981460 AATTCCTTTTGAAGTTATCTATCCAGT 57.019 29.630 0.00 0.00 36.14 4.00
2743 3230 7.145323 CACCGTGATAAATTCCTTTTGAAGTT 58.855 34.615 0.00 0.00 43.23 2.66
2763 3250 2.099652 TAAGCTCTGCTGCACACCGT 62.100 55.000 0.00 0.00 39.62 4.83
2875 3369 5.567430 ACTTCTGAAACCCCAAATACTACC 58.433 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.