Multiple sequence alignment - TraesCS7A01G120000

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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 TraesCS7A01G120000 chr7A 100.000 9108 0 0 1 9108 77205962 77196855 0.000000e+00 16820.0
1 TraesCS7A01G120000 chr7A 98.556 831 9 2 1427 2255 117151439 117152268 0.000000e+00 1465.0
2 TraesCS7A01G120000 chr7A 98.436 831 9 3 1427 2255 665802252 665803080 0.000000e+00 1459.0
3 TraesCS7A01G120000 chr7A 95.736 774 29 3 5909 6682 24387130 24386361 0.000000e+00 1243.0
4 TraesCS7A01G120000 chr7A 95.736 774 29 3 5909 6682 24407752 24406983 0.000000e+00 1243.0
5 TraesCS7A01G120000 chr7A 95.006 781 21 7 5913 6683 491827754 491828526 0.000000e+00 1210.0
6 TraesCS7A01G120000 chr7A 94.317 739 24 6 5913 6641 600552720 600551990 0.000000e+00 1116.0
7 TraesCS7A01G120000 chr7A 89.286 280 18 5 6404 6683 473617960 473618227 3.150000e-89 340.0
8 TraesCS7A01G120000 chr7A 82.895 152 25 1 4352 4502 712101794 712101643 1.600000e-27 135.0
9 TraesCS7A01G120000 chr7A 97.222 36 1 0 8706 8741 77197206 77197171 2.750000e-05 62.1
10 TraesCS7A01G120000 chr7A 97.222 36 1 0 8757 8792 77197257 77197222 2.750000e-05 62.1
11 TraesCS7A01G120000 chr7D 94.209 2953 119 20 2659 5580 73108911 73111842 0.000000e+00 4458.0
12 TraesCS7A01G120000 chr7D 93.123 2065 107 17 601 2651 73106819 73108862 0.000000e+00 2994.0
13 TraesCS7A01G120000 chr7D 90.481 935 56 12 7256 8184 73113594 73114501 0.000000e+00 1203.0
14 TraesCS7A01G120000 chr7D 95.447 615 24 3 1 612 73106066 73106679 0.000000e+00 977.0
15 TraesCS7A01G120000 chr7D 94.035 570 23 6 6683 7244 73112793 73113359 0.000000e+00 854.0
16 TraesCS7A01G120000 chr7D 97.059 374 9 2 208 579 188355937 188356310 6.000000e-176 628.0
17 TraesCS7A01G120000 chr7D 97.938 97 2 0 5770 5866 73111849 73111945 1.570000e-37 169.0
18 TraesCS7A01G120000 chr7D 74.212 539 61 29 8187 8698 73114547 73115034 4.400000e-33 154.0
19 TraesCS7A01G120000 chr7D 92.632 95 7 0 1 95 188355846 188355940 4.440000e-28 137.0
20 TraesCS7A01G120000 chr7D 93.220 59 4 0 8695 8753 73115820 73115878 4.530000e-13 87.9
21 TraesCS7A01G120000 chr7D 100.000 32 0 0 8758 8789 73115832 73115863 9.880000e-05 60.2
22 TraesCS7A01G120000 chr7B 95.200 2125 80 17 3792 5903 15305662 15303547 0.000000e+00 3339.0
23 TraesCS7A01G120000 chr7B 94.375 1760 82 11 2662 4410 15039268 15037515 0.000000e+00 2686.0
24 TraesCS7A01G120000 chr7B 93.178 1158 55 12 2659 3793 15306922 15305766 0.000000e+00 1679.0
25 TraesCS7A01G120000 chr7B 94.863 915 40 4 1718 2632 15307886 15306979 0.000000e+00 1423.0
26 TraesCS7A01G120000 chr7B 93.785 901 45 11 4421 5316 15032523 15031629 0.000000e+00 1343.0
27 TraesCS7A01G120000 chr7B 90.508 906 69 10 824 1719 15308866 15307968 0.000000e+00 1181.0
28 TraesCS7A01G120000 chr7B 94.746 571 22 5 6683 7252 15303518 15302955 0.000000e+00 881.0
29 TraesCS7A01G120000 chr7B 95.376 519 24 0 1824 2342 15052966 15052448 0.000000e+00 826.0
30 TraesCS7A01G120000 chr7B 89.002 591 48 6 7256 7845 15022093 15021519 0.000000e+00 715.0
31 TraesCS7A01G120000 chr7B 88.045 619 50 12 7875 8489 15079606 15079008 0.000000e+00 712.0
32 TraesCS7A01G120000 chr7B 86.645 614 39 14 7256 7845 15302666 15302072 2.770000e-179 640.0
33 TraesCS7A01G120000 chr7B 85.968 620 51 22 7901 8500 15021507 15020904 1.670000e-176 630.0
34 TraesCS7A01G120000 chr7B 93.571 420 20 3 6683 7102 15029158 15028746 3.610000e-173 619.0
35 TraesCS7A01G120000 chr7B 84.489 548 54 20 7976 8501 15292471 15291933 6.310000e-141 512.0
36 TraesCS7A01G120000 chr7B 84.436 559 43 22 7901 8434 15302060 15301521 2.270000e-140 510.0
37 TraesCS7A01G120000 chr7B 94.156 308 15 1 2344 2651 15039624 15039320 4.980000e-127 466.0
38 TraesCS7A01G120000 chr7B 93.060 317 9 6 5589 5903 15029492 15029187 1.390000e-122 451.0
39 TraesCS7A01G120000 chr7B 92.580 283 21 0 8796 9078 15071305 15071023 3.060000e-109 407.0
40 TraesCS7A01G120000 chr7B 92.254 284 21 1 7256 7539 15100682 15100400 1.420000e-107 401.0
41 TraesCS7A01G120000 chr7B 89.899 297 30 0 8796 9092 15019765 15019469 5.160000e-102 383.0
42 TraesCS7A01G120000 chr7B 89.803 304 23 4 8796 9092 15299899 15299597 5.160000e-102 383.0
43 TraesCS7A01G120000 chr7B 84.936 312 35 9 6686 6989 217426876 217426569 1.150000e-78 305.0
44 TraesCS7A01G120000 chr7B 95.276 127 6 0 7581 7707 15100388 15100262 1.550000e-47 202.0
45 TraesCS7A01G120000 chr7B 92.086 139 11 0 5309 5447 15031437 15031299 7.210000e-46 196.0
46 TraesCS7A01G120000 chr7B 80.408 245 37 10 8809 9050 14778490 14778726 9.400000e-40 176.0
47 TraesCS7A01G120000 chr7B 82.500 160 23 5 4353 4508 749477827 749477985 1.600000e-27 135.0
48 TraesCS7A01G120000 chr7B 85.593 118 15 2 6821 6938 312334515 312334630 1.240000e-23 122.0
49 TraesCS7A01G120000 chr7B 88.889 99 10 1 645 743 15318106 15318009 4.470000e-23 121.0
50 TraesCS7A01G120000 chr7B 89.796 49 5 0 8695 8743 15071907 15071859 7.630000e-06 63.9
51 TraesCS7A01G120000 chr6A 98.797 831 6 3 1427 2255 421293089 421292261 0.000000e+00 1476.0
52 TraesCS7A01G120000 chr6A 95.979 373 12 2 208 579 389467737 389468107 3.640000e-168 603.0
53 TraesCS7A01G120000 chr6A 91.579 95 8 0 1 95 389467646 389467740 2.060000e-26 132.0
54 TraesCS7A01G120000 chr6A 83.673 98 14 2 4352 4448 39004769 39004865 3.500000e-14 91.6
55 TraesCS7A01G120000 chr6A 100.000 36 0 0 1345 1380 436834680 436834715 5.900000e-07 67.6
56 TraesCS7A01G120000 chr5A 98.794 829 7 2 1429 2255 409744325 409743498 0.000000e+00 1472.0
57 TraesCS7A01G120000 chr5A 95.519 781 21 4 5913 6683 47459009 47458233 0.000000e+00 1236.0
58 TraesCS7A01G120000 chr5A 95.256 780 26 3 5913 6682 3455539 3456317 0.000000e+00 1225.0
59 TraesCS7A01G120000 chr5A 95.256 780 23 4 5913 6682 299776966 299777741 0.000000e+00 1223.0
60 TraesCS7A01G120000 chr5A 95.924 368 13 2 212 578 281325766 281325400 6.090000e-166 595.0
61 TraesCS7A01G120000 chr5A 82.507 686 75 13 5223 5903 501421071 501420426 2.220000e-155 560.0
62 TraesCS7A01G120000 chr5A 84.643 280 31 9 6718 6989 501413819 501413544 1.510000e-67 268.0
63 TraesCS7A01G120000 chr5A 97.183 142 4 0 212 353 281327562 281327421 3.290000e-59 241.0
64 TraesCS7A01G120000 chr5A 90.476 126 11 1 93 218 649239248 649239372 2.030000e-36 165.0
65 TraesCS7A01G120000 chr5A 82.895 152 25 1 4352 4502 605038450 605038299 1.600000e-27 135.0
66 TraesCS7A01G120000 chr5A 100.000 36 0 0 1345 1380 12738854 12738889 5.900000e-07 67.6
67 TraesCS7A01G120000 chr5A 100.000 36 0 0 1345 1380 497940402 497940437 5.900000e-07 67.6
68 TraesCS7A01G120000 chr5A 100.000 36 0 0 1345 1380 647849669 647849634 5.900000e-07 67.6
69 TraesCS7A01G120000 chr5A 88.636 44 4 1 5344 5387 633752392 633752350 1.700000e-02 52.8
70 TraesCS7A01G120000 chr2A 98.794 829 7 2 1427 2253 149629724 149628897 0.000000e+00 1472.0
71 TraesCS7A01G120000 chr2A 98.676 831 8 2 1427 2255 30680924 30680095 0.000000e+00 1471.0
72 TraesCS7A01G120000 chr2A 98.676 831 8 2 1427 2255 518824568 518823739 0.000000e+00 1471.0
73 TraesCS7A01G120000 chr2A 97.051 373 10 1 208 579 733587981 733588353 2.160000e-175 627.0
74 TraesCS7A01G120000 chr2A 83.495 412 39 13 5223 5632 8159276 8158892 3.130000e-94 357.0
75 TraesCS7A01G120000 chr2A 85.065 154 19 4 3709 3859 550548887 550549039 4.400000e-33 154.0
76 TraesCS7A01G120000 chr2A 92.308 52 4 0 44 95 733587933 733587984 3.530000e-09 75.0
77 TraesCS7A01G120000 chr1A 95.122 779 24 4 5914 6682 251337379 251338153 0.000000e+00 1216.0
78 TraesCS7A01G120000 chr1A 93.990 782 22 7 5913 6683 452758664 452757897 0.000000e+00 1160.0
79 TraesCS7A01G120000 chr1A 90.476 126 9 2 87 212 301777835 301777957 7.320000e-36 163.0
80 TraesCS7A01G120000 chr1A 81.579 152 26 2 3709 3859 201863225 201863375 3.450000e-24 124.0
81 TraesCS7A01G120000 chr1A 100.000 36 0 0 1345 1380 174197949 174197914 5.900000e-07 67.6
82 TraesCS7A01G120000 chr1A 100.000 36 0 0 1345 1380 226709712 226709677 5.900000e-07 67.6
83 TraesCS7A01G120000 chr1A 95.000 40 1 1 1374 1413 574283408 574283446 2.750000e-05 62.1
84 TraesCS7A01G120000 chr5D 95.389 759 21 4 5913 6659 549893106 549893862 0.000000e+00 1195.0
85 TraesCS7A01G120000 chr5D 89.147 129 13 1 84 212 492723162 492723289 9.470000e-35 159.0
86 TraesCS7A01G120000 chr5D 90.000 90 8 1 7442 7531 533991827 533991915 2.080000e-21 115.0
87 TraesCS7A01G120000 chr3D 94.080 777 28 8 5913 6684 338919783 338920546 0.000000e+00 1164.0
88 TraesCS7A01G120000 chr3D 94.638 373 19 1 208 579 601956524 601956152 2.210000e-160 577.0
89 TraesCS7A01G120000 chr3D 83.884 242 30 5 4529 4769 22101887 22102120 1.190000e-53 222.0
90 TraesCS7A01G120000 chr3D 89.474 95 8 1 3 95 601956615 601956521 1.610000e-22 119.0
91 TraesCS7A01G120000 chr5B 93.130 786 27 8 5913 6683 656908521 656907748 0.000000e+00 1127.0
92 TraesCS7A01G120000 chr5B 84.848 297 34 8 293 578 554925461 554925757 1.160000e-73 289.0
93 TraesCS7A01G120000 chr3A 92.902 789 26 10 5913 6683 170979830 170979054 0.000000e+00 1120.0
94 TraesCS7A01G120000 chr3A 84.682 346 45 5 4646 4983 84100480 84100825 1.130000e-88 339.0
95 TraesCS7A01G120000 chr3A 82.484 314 41 8 6686 6989 84092421 84092730 7.010000e-66 263.0
96 TraesCS7A01G120000 chr3A 90.984 122 11 0 91 212 12239859 12239980 2.030000e-36 165.0
97 TraesCS7A01G120000 chr3A 80.000 230 32 7 4984 5210 84100912 84101130 3.400000e-34 158.0
98 TraesCS7A01G120000 chr3A 100.000 36 0 0 1345 1380 201789070 201789035 5.900000e-07 67.6
99 TraesCS7A01G120000 chr3A 95.000 40 1 1 1374 1413 739550528 739550566 2.750000e-05 62.1
100 TraesCS7A01G120000 chr4A 95.430 372 14 3 208 578 163282827 163283196 2.830000e-164 590.0
101 TraesCS7A01G120000 chr4A 92.373 118 9 0 94 211 589013492 589013609 1.570000e-37 169.0
102 TraesCS7A01G120000 chr4A 91.597 119 10 0 93 211 669083960 669084078 2.030000e-36 165.0
103 TraesCS7A01G120000 chr4A 93.684 95 6 0 1 95 163282736 163282830 9.530000e-30 143.0
104 TraesCS7A01G120000 chr4A 86.869 99 10 3 7436 7533 84863698 84863794 3.480000e-19 108.0
105 TraesCS7A01G120000 chr4A 95.000 40 1 1 1374 1413 714762970 714763008 2.750000e-05 62.1
106 TraesCS7A01G120000 chr4D 82.895 684 73 16 5223 5903 95865222 95865864 7.930000e-160 575.0
107 TraesCS7A01G120000 chr4D 84.984 313 33 11 6686 6989 95865896 95866203 1.150000e-78 305.0
108 TraesCS7A01G120000 chr4D 88.462 130 13 1 94 221 93458901 93458772 1.220000e-33 156.0
109 TraesCS7A01G120000 chr4D 82.353 153 24 3 4351 4502 394153595 394153445 7.420000e-26 130.0
110 TraesCS7A01G120000 chr4D 83.036 112 14 3 4403 4509 301777264 301777153 7.530000e-16 97.1
111 TraesCS7A01G120000 chr2D 82.759 667 71 12 5223 5885 643690062 643690688 1.030000e-153 555.0
112 TraesCS7A01G120000 chr2D 79.617 574 60 28 6686 7230 643704500 643705045 8.700000e-95 359.0
113 TraesCS7A01G120000 chr2D 83.117 154 22 4 3709 3859 436379270 436379422 4.440000e-28 137.0
114 TraesCS7A01G120000 chr2D 80.625 160 24 6 4353 4508 560580829 560580673 5.780000e-22 117.0
115 TraesCS7A01G120000 chr2D 95.238 42 2 0 7256 7297 643705323 643705364 5.900000e-07 67.6
116 TraesCS7A01G120000 chr4B 93.566 373 21 3 208 578 658554083 658554454 3.720000e-153 553.0
117 TraesCS7A01G120000 chr2B 91.597 119 10 0 93 211 794534837 794534955 2.030000e-36 165.0
118 TraesCS7A01G120000 chr2B 82.468 154 23 4 3709 3859 514855347 514855195 2.060000e-26 132.0
119 TraesCS7A01G120000 chr6D 85.185 162 21 3 3711 3870 124941258 124941418 7.320000e-36 163.0
120 TraesCS7A01G120000 chr6B 84.516 155 21 3 3711 3863 222680061 222680214 5.700000e-32 150.0
121 TraesCS7A01G120000 chr1B 90.909 88 7 1 7442 7529 4036007 4036093 5.780000e-22 117.0
122 TraesCS7A01G120000 chr1D 90.805 87 6 2 7445 7530 23835772 23835687 2.080000e-21 115.0
123 TraesCS7A01G120000 chr3B 87.500 96 12 0 7437 7532 600979775 600979870 2.690000e-20 111.0
124 TraesCS7A01G120000 chr3B 95.000 40 1 1 1374 1413 262583755 262583717 2.750000e-05 62.1
125 TraesCS7A01G120000 chr3B 95.000 40 1 1 1374 1413 263256484 263256522 2.750000e-05 62.1
126 TraesCS7A01G120000 chr3B 95.000 40 1 1 1374 1413 814178639 814178601 2.750000e-05 62.1
127 TraesCS7A01G120000 chrUn 74.621 264 55 9 8816 9075 84329570 84329825 1.250000e-18 106.0
128 TraesCS7A01G120000 chrUn 95.000 40 1 1 1374 1413 322336394 322336356 2.750000e-05 62.1


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 TraesCS7A01G120000 chr7A 77196855 77205962 9107 True 16820.000000 16820 100.000000 1 9108 1 chr7A.!!$R3 9107
1 TraesCS7A01G120000 chr7A 117151439 117152268 829 False 1465.000000 1465 98.556000 1427 2255 1 chr7A.!!$F1 828
2 TraesCS7A01G120000 chr7A 665802252 665803080 828 False 1459.000000 1459 98.436000 1427 2255 1 chr7A.!!$F4 828
3 TraesCS7A01G120000 chr7A 24386361 24387130 769 True 1243.000000 1243 95.736000 5909 6682 1 chr7A.!!$R1 773
4 TraesCS7A01G120000 chr7A 24406983 24407752 769 True 1243.000000 1243 95.736000 5909 6682 1 chr7A.!!$R2 773
5 TraesCS7A01G120000 chr7A 491827754 491828526 772 False 1210.000000 1210 95.006000 5913 6683 1 chr7A.!!$F3 770
6 TraesCS7A01G120000 chr7A 600551990 600552720 730 True 1116.000000 1116 94.317000 5913 6641 1 chr7A.!!$R4 728
7 TraesCS7A01G120000 chr7D 73106066 73115878 9812 False 1217.455556 4458 92.518333 1 8789 9 chr7D.!!$F1 8788
8 TraesCS7A01G120000 chr7B 15037515 15039624 2109 True 1576.000000 2686 94.265500 2344 4410 2 chr7B.!!$R8 2066
9 TraesCS7A01G120000 chr7B 15299597 15308866 9269 True 1254.500000 3339 91.172375 824 9092 8 chr7B.!!$R11 8268
10 TraesCS7A01G120000 chr7B 15052448 15052966 518 True 826.000000 826 95.376000 1824 2342 1 chr7B.!!$R1 518
11 TraesCS7A01G120000 chr7B 15079008 15079606 598 True 712.000000 712 88.045000 7875 8489 1 chr7B.!!$R2 614
12 TraesCS7A01G120000 chr7B 15028746 15032523 3777 True 652.250000 1343 93.125500 4421 7102 4 chr7B.!!$R7 2681
13 TraesCS7A01G120000 chr7B 15019469 15022093 2624 True 576.000000 715 88.289667 7256 9092 3 chr7B.!!$R6 1836
14 TraesCS7A01G120000 chr7B 15291933 15292471 538 True 512.000000 512 84.489000 7976 8501 1 chr7B.!!$R3 525
15 TraesCS7A01G120000 chr7B 15071023 15071907 884 True 235.450000 407 91.188000 8695 9078 2 chr7B.!!$R9 383
16 TraesCS7A01G120000 chr6A 421292261 421293089 828 True 1476.000000 1476 98.797000 1427 2255 1 chr6A.!!$R1 828
17 TraesCS7A01G120000 chr5A 409743498 409744325 827 True 1472.000000 1472 98.794000 1429 2255 1 chr5A.!!$R2 826
18 TraesCS7A01G120000 chr5A 47458233 47459009 776 True 1236.000000 1236 95.519000 5913 6683 1 chr5A.!!$R1 770
19 TraesCS7A01G120000 chr5A 3455539 3456317 778 False 1225.000000 1225 95.256000 5913 6682 1 chr5A.!!$F1 769
20 TraesCS7A01G120000 chr5A 299776966 299777741 775 False 1223.000000 1223 95.256000 5913 6682 1 chr5A.!!$F3 769
21 TraesCS7A01G120000 chr5A 501420426 501421071 645 True 560.000000 560 82.507000 5223 5903 1 chr5A.!!$R4 680
22 TraesCS7A01G120000 chr5A 281325400 281327562 2162 True 418.000000 595 96.553500 212 578 2 chr5A.!!$R8 366
23 TraesCS7A01G120000 chr2A 149628897 149629724 827 True 1472.000000 1472 98.794000 1427 2253 1 chr2A.!!$R3 826
24 TraesCS7A01G120000 chr2A 30680095 30680924 829 True 1471.000000 1471 98.676000 1427 2255 1 chr2A.!!$R2 828
25 TraesCS7A01G120000 chr2A 518823739 518824568 829 True 1471.000000 1471 98.676000 1427 2255 1 chr2A.!!$R4 828
26 TraesCS7A01G120000 chr1A 251337379 251338153 774 False 1216.000000 1216 95.122000 5914 6682 1 chr1A.!!$F2 768
27 TraesCS7A01G120000 chr1A 452757897 452758664 767 True 1160.000000 1160 93.990000 5913 6683 1 chr1A.!!$R3 770
28 TraesCS7A01G120000 chr5D 549893106 549893862 756 False 1195.000000 1195 95.389000 5913 6659 1 chr5D.!!$F3 746
29 TraesCS7A01G120000 chr3D 338919783 338920546 763 False 1164.000000 1164 94.080000 5913 6684 1 chr3D.!!$F2 771
30 TraesCS7A01G120000 chr5B 656907748 656908521 773 True 1127.000000 1127 93.130000 5913 6683 1 chr5B.!!$R1 770
31 TraesCS7A01G120000 chr3A 170979054 170979830 776 True 1120.000000 1120 92.902000 5913 6683 1 chr3A.!!$R1 770
32 TraesCS7A01G120000 chr3A 84100480 84101130 650 False 248.500000 339 82.341000 4646 5210 2 chr3A.!!$F4 564
33 TraesCS7A01G120000 chr4D 95865222 95866203 981 False 440.000000 575 83.939500 5223 6989 2 chr4D.!!$F1 1766
34 TraesCS7A01G120000 chr2D 643690062 643690688 626 False 555.000000 555 82.759000 5223 5885 1 chr2D.!!$F2 662
35 TraesCS7A01G120000 chr2D 643704500 643705364 864 False 213.300000 359 87.427500 6686 7297 2 chr2D.!!$F3 611

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
836 2788 1.362717 CGCCTGGGTCCGTGTATAG 59.637 63.158 0.00 0.0 0.00 1.31 F
2314 4370 0.107361 TCATACGGTCAGCGAGGAGA 60.107 55.000 1.65 0.0 0.00 3.71 F
2765 4862 1.039856 CCAGTTTTGTGGGTTCCCTG 58.960 55.000 9.43 0.0 33.46 4.45 F
3646 5769 0.456221 ACTGAAGTCCGTGCTATCCG 59.544 55.000 0.00 0.0 0.00 4.18 F
3650 5773 0.892755 AAGTCCGTGCTATCCGTTGA 59.107 50.000 0.00 0.0 0.00 3.18 F
4370 6602 1.760192 AACTAGACGATACCCTGCGT 58.240 50.000 0.00 0.0 44.33 5.24 F
5618 9857 3.330701 GGCATATTATGAGGTTGGAGGGA 59.669 47.826 7.87 0.0 0.00 4.20 F
7146 12252 0.035725 CATGTGCTGGAGAGGCTTGA 60.036 55.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 4828 0.689055 ACTGGTGAAGCATGCTCTCA 59.311 50.000 22.93 21.85 0.00 3.27 R
3628 5751 0.456221 ACGGATAGCACGGACTTCAG 59.544 55.000 0.00 0.00 35.23 3.02 R
4370 6602 1.135141 GCATAAATTCCTGCCGCAACA 60.135 47.619 0.00 0.00 32.15 3.33 R
4864 7106 1.281867 TGAATTGGAGGGCGAGAACAT 59.718 47.619 0.00 0.00 0.00 2.71 R
4951 7194 3.955551 GTGTGAACCCTCTTTACCCAAAA 59.044 43.478 0.00 0.00 0.00 2.44 R
6019 11055 1.160137 GCAGGACAAATTGACGCTCT 58.840 50.000 0.00 0.00 0.00 4.09 R
7546 12941 0.312102 CACACACACAGCGAGAGAGA 59.688 55.000 0.00 0.00 0.00 3.10 R
8823 15702 0.387239 GCGATGTTGCCCTTCACAAC 60.387 55.000 0.00 0.00 46.05 3.32 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
41 42 9.715121 ATTGCAAATCAGTTCTGATATTTTGTT 57.285 25.926 19.37 8.36 0.00 2.83
79 80 5.940470 CAGTTAGCCATTCTTTTACTCACCT 59.060 40.000 0.00 0.00 0.00 4.00
80 81 5.940470 AGTTAGCCATTCTTTTACTCACCTG 59.060 40.000 0.00 0.00 0.00 4.00
99 100 6.435277 TCACCTGTCGTAAAAATAGTACTCCT 59.565 38.462 0.00 0.00 0.00 3.69
103 104 6.324819 TGTCGTAAAAATAGTACTCCTTCCG 58.675 40.000 0.00 0.00 0.00 4.30
128 130 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
150 152 9.461312 AAATGAATGTATCTAGCACCAAGTTAA 57.539 29.630 0.00 0.00 0.00 2.01
153 155 7.333423 TGAATGTATCTAGCACCAAGTTAACAC 59.667 37.037 8.61 0.00 0.00 3.32
157 159 5.401531 TCTAGCACCAAGTTAACACTAGG 57.598 43.478 8.61 6.27 30.68 3.02
179 181 6.653989 AGGTACATCCATTTGAAAGACTAGG 58.346 40.000 0.00 0.00 39.02 3.02
227 229 7.202139 GGAGGGAGTAGATATTTCAAGTCCAAT 60.202 40.741 0.00 0.00 0.00 3.16
247 249 2.214376 TTCTATGGGCAAAGTGGTGG 57.786 50.000 0.00 0.00 0.00 4.61
304 2102 1.906574 TGTCCACTGTAGGCCTAAAGG 59.093 52.381 29.94 20.74 38.53 3.11
556 2356 1.460273 AAAAAGACGGGTGCGGCAAT 61.460 50.000 3.23 0.00 0.00 3.56
834 2786 4.157120 GCGCCTGGGTCCGTGTAT 62.157 66.667 0.00 0.00 0.00 2.29
836 2788 1.362717 CGCCTGGGTCCGTGTATAG 59.637 63.158 0.00 0.00 0.00 1.31
1218 3175 1.226323 GTCGTCGTCCTCCACATCG 60.226 63.158 0.00 0.00 0.00 3.84
1255 3212 3.055530 CCTTCACTCTGTACTGCTTGGAT 60.056 47.826 0.00 0.00 0.00 3.41
1299 3256 0.322187 GTTGGTGGGCTGTTCGGTAT 60.322 55.000 0.00 0.00 0.00 2.73
1337 3295 0.317938 CGTGCTGTATCGAGTAGGGC 60.318 60.000 0.00 0.00 0.00 5.19
1424 3382 8.764524 TCTTAGTTGAGTTCTGATTTAAGAGC 57.235 34.615 0.00 0.00 0.00 4.09
1453 3411 6.775142 TGAGTGGAAAGTGGAATTGAACAATA 59.225 34.615 0.37 0.00 0.00 1.90
2276 4332 5.756347 TGTGCTAGAAATGTACAAACGAGTT 59.244 36.000 0.00 0.00 0.00 3.01
2314 4370 0.107361 TCATACGGTCAGCGAGGAGA 60.107 55.000 1.65 0.00 0.00 3.71
2338 4394 3.674423 GCTTTAGCTGTCAATTAGTGCG 58.326 45.455 0.00 0.00 38.21 5.34
2396 4452 8.171337 AGTGGTTTATCCTTTTTATCCTAGGT 57.829 34.615 9.08 0.00 37.07 3.08
2511 4567 5.059833 CCATTCCATCCTTAGCAGACTAAC 58.940 45.833 0.00 0.00 34.62 2.34
2543 4599 4.471386 AGATGGTGTAGCTTGTTCCATACT 59.529 41.667 10.76 8.22 38.74 2.12
2544 4600 3.937814 TGGTGTAGCTTGTTCCATACTG 58.062 45.455 0.00 0.00 0.00 2.74
2545 4601 3.580895 TGGTGTAGCTTGTTCCATACTGA 59.419 43.478 0.00 0.00 0.00 3.41
2651 4707 7.152645 TGTTATGGTTCACAGTAGAAGAACTC 58.847 38.462 0.00 0.00 40.97 3.01
2652 4708 5.808366 ATGGTTCACAGTAGAAGAACTCA 57.192 39.130 0.00 0.00 40.97 3.41
2653 4709 5.808366 TGGTTCACAGTAGAAGAACTCAT 57.192 39.130 0.00 0.00 40.97 2.90
2654 4710 5.784177 TGGTTCACAGTAGAAGAACTCATC 58.216 41.667 0.00 0.00 40.97 2.92
2655 4711 5.172205 GGTTCACAGTAGAAGAACTCATCC 58.828 45.833 0.00 0.00 40.97 3.51
2656 4712 5.046950 GGTTCACAGTAGAAGAACTCATCCT 60.047 44.000 0.00 0.00 40.97 3.24
2657 4713 6.153000 GGTTCACAGTAGAAGAACTCATCCTA 59.847 42.308 0.00 0.00 40.97 2.94
2688 4785 8.999431 TGTTGTAACTATTTCAGACTTTGATCC 58.001 33.333 0.00 0.00 35.27 3.36
2741 4838 4.498682 GGGTTGAAATGTATGAGAGCATGC 60.499 45.833 10.51 10.51 37.60 4.06
2765 4862 1.039856 CCAGTTTTGTGGGTTCCCTG 58.960 55.000 9.43 0.00 33.46 4.45
2807 4904 5.698741 TCATTTTCTAGAGAAGCATCCCA 57.301 39.130 1.86 0.00 35.21 4.37
2886 5007 4.196193 CCCTCACAGCGTTTGGATAATTA 58.804 43.478 0.00 0.00 0.00 1.40
3062 5184 4.927782 GCAGACGCCACCACCACA 62.928 66.667 0.00 0.00 0.00 4.17
3065 5187 2.515057 GACGCCACCACCACAACA 60.515 61.111 0.00 0.00 0.00 3.33
3248 5370 2.826128 CAGTCTGGTCTAGCAACACCTA 59.174 50.000 0.51 0.00 33.36 3.08
3346 5469 7.701539 TTTGCTTGGATTTTCTATTAGCTCA 57.298 32.000 0.00 0.00 0.00 4.26
3613 5736 7.151976 AGAAAATTATGTTGTTAAGCCCACAC 58.848 34.615 0.00 0.00 0.00 3.82
3628 5751 3.943381 GCCCACACCCTTAAGTTATGTAC 59.057 47.826 0.97 0.00 0.00 2.90
3646 5769 0.456221 ACTGAAGTCCGTGCTATCCG 59.544 55.000 0.00 0.00 0.00 4.18
3650 5773 0.892755 AAGTCCGTGCTATCCGTTGA 59.107 50.000 0.00 0.00 0.00 3.18
3678 5801 3.835978 TGCTACCAAGGTTCTGCTACTTA 59.164 43.478 0.00 0.00 0.00 2.24
3892 6123 7.986889 TGTTGCAGATATTAGCACATTTCTCTA 59.013 33.333 2.87 0.00 41.05 2.43
3915 6146 8.948145 TCTATAGTCTATTTTATGACTCCGCTC 58.052 37.037 0.00 0.00 41.92 5.03
4230 6461 9.430838 CTTTAGCAATACTTTCTTTCATCATCG 57.569 33.333 0.00 0.00 0.00 3.84
4370 6602 1.760192 AACTAGACGATACCCTGCGT 58.240 50.000 0.00 0.00 44.33 5.24
4517 6750 3.822167 GTGTTTCGACCATTAAGGGGAAA 59.178 43.478 11.49 8.59 43.89 3.13
4622 6855 9.045223 TCAATTTCGTAATATCATCTCAACCAG 57.955 33.333 0.00 0.00 0.00 4.00
4694 6928 8.298854 TCACACATTTACAGATTTCCTGAATTG 58.701 33.333 0.00 0.00 45.78 2.32
4958 7201 7.539034 AAATGCTATCAGTAACTTTTTGGGT 57.461 32.000 0.00 0.00 0.00 4.51
4967 7210 5.831525 CAGTAACTTTTTGGGTAAAGAGGGT 59.168 40.000 0.00 0.00 38.27 4.34
5034 7365 9.723601 AAAACAATGTGCAAATAATAGACCATT 57.276 25.926 0.00 0.00 0.00 3.16
5181 7514 8.044060 TGCAGAAAATCTAGGAAAGTAACATG 57.956 34.615 0.00 0.00 0.00 3.21
5412 7947 9.020813 GCCTATCGAAATAAAGAAAATGAAACC 57.979 33.333 0.00 0.00 0.00 3.27
5413 7948 9.221775 CCTATCGAAATAAAGAAAATGAAACCG 57.778 33.333 0.00 0.00 0.00 4.44
5425 7961 7.654568 AGAAAATGAAACCGTACCTTTTTAGG 58.345 34.615 0.00 0.00 0.00 2.69
5472 8009 9.412460 TCAGAATATATTTCCAAGTGAAGCAAT 57.588 29.630 0.00 0.00 33.63 3.56
5576 8113 9.076596 GCAAAACAAAGGCATAGAAACTATTAG 57.923 33.333 0.00 0.00 0.00 1.73
5580 8117 9.969001 AACAAAGGCATAGAAACTATTAGGTTA 57.031 29.630 0.00 0.00 0.00 2.85
5581 8118 9.969001 ACAAAGGCATAGAAACTATTAGGTTAA 57.031 29.630 0.00 0.00 0.00 2.01
5618 9857 3.330701 GGCATATTATGAGGTTGGAGGGA 59.669 47.826 7.87 0.00 0.00 4.20
5619 9858 4.327680 GCATATTATGAGGTTGGAGGGAC 58.672 47.826 7.87 0.00 0.00 4.46
5620 9859 4.202461 GCATATTATGAGGTTGGAGGGACA 60.202 45.833 7.87 0.00 0.00 4.02
5622 9861 6.546484 CATATTATGAGGTTGGAGGGACAAT 58.454 40.000 0.00 0.00 32.24 2.71
5623 9862 7.689299 CATATTATGAGGTTGGAGGGACAATA 58.311 38.462 0.00 0.00 32.24 1.90
5624 9863 5.630415 TTATGAGGTTGGAGGGACAATAG 57.370 43.478 0.00 0.00 32.24 1.73
5686 9933 8.837389 GTTAGTTTGTTTGTACTCTTGGAAGAT 58.163 33.333 0.00 0.00 33.93 2.40
5880 10913 4.193240 ACACTTACCTTTGTGGGGAATT 57.807 40.909 0.00 0.00 41.11 2.17
5903 10936 7.428282 TTCTTCATAGTTTCACACGCATTAA 57.572 32.000 0.00 0.00 0.00 1.40
5904 10937 7.609760 TCTTCATAGTTTCACACGCATTAAT 57.390 32.000 0.00 0.00 0.00 1.40
5907 10940 8.446489 TTCATAGTTTCACACGCATTAATTTG 57.554 30.769 0.00 0.00 0.00 2.32
5911 10944 7.617533 AGTTTCACACGCATTAATTTGTAAC 57.382 32.000 0.00 0.00 0.00 2.50
6066 11102 4.808042 AGGCCAGTAAGCATATTTCCATT 58.192 39.130 5.01 0.00 0.00 3.16
6139 11175 1.077644 CTCATTGGCCTGAGCTGCT 60.078 57.895 8.93 0.00 36.53 4.24
6159 11195 4.333649 TGCTGCTGCTGAATACAATACTTC 59.666 41.667 17.00 0.00 40.48 3.01
6255 11291 1.006639 GAGGGCAGGGGGTAAAAATCA 59.993 52.381 0.00 0.00 0.00 2.57
6414 11456 1.754234 CAATGGAGGGAAAGGGCCG 60.754 63.158 0.00 0.00 0.00 6.13
6458 11501 2.653234 AGAGCATAAGCAATGGAGGG 57.347 50.000 0.00 0.00 45.49 4.30
6461 11504 3.053395 AGAGCATAAGCAATGGAGGGAAA 60.053 43.478 0.00 0.00 45.49 3.13
6465 11508 0.041684 AAGCAATGGAGGGAAAGGGG 59.958 55.000 0.00 0.00 0.00 4.79
6466 11509 1.381735 GCAATGGAGGGAAAGGGGG 60.382 63.158 0.00 0.00 0.00 5.40
6470 11513 1.848835 ATGGAGGGAAAGGGGGAGGA 61.849 60.000 0.00 0.00 0.00 3.71
6575 11634 2.748532 CGACTAGTCCTTCGACTCCTTT 59.251 50.000 17.23 0.00 46.90 3.11
6790 11853 4.037446 CCAGCTAACCAAGTTTTGCACTTA 59.963 41.667 0.00 0.00 44.60 2.24
6970 12040 2.502538 CCCCTACTTTGGTTACCATCGA 59.497 50.000 4.38 0.00 31.53 3.59
6997 12095 1.817447 GTAGAGACAGGTTAGGCACGT 59.183 52.381 0.00 0.00 0.00 4.49
7083 12189 2.000048 AGAGGCTCCAATTGGGGTTAA 59.000 47.619 25.33 4.40 38.19 2.01
7125 12231 4.101448 GTGCAGGTGGGCGGATCT 62.101 66.667 0.00 0.00 36.28 2.75
7131 12237 2.124570 GTGGGCGGATCTGCATGT 60.125 61.111 27.26 0.00 36.28 3.21
7142 12248 2.045634 TGCATGTGCTGGAGAGGC 60.046 61.111 6.55 0.00 42.66 4.70
7144 12250 1.378250 GCATGTGCTGGAGAGGCTT 60.378 57.895 0.00 0.00 38.21 4.35
7145 12251 1.654954 GCATGTGCTGGAGAGGCTTG 61.655 60.000 0.00 0.00 38.21 4.01
7146 12252 0.035725 CATGTGCTGGAGAGGCTTGA 60.036 55.000 0.00 0.00 0.00 3.02
7148 12254 1.739562 GTGCTGGAGAGGCTTGACG 60.740 63.158 0.00 0.00 0.00 4.35
7149 12255 2.817396 GCTGGAGAGGCTTGACGC 60.817 66.667 0.00 0.00 38.13 5.19
7239 12345 0.623723 GGTGGGGTCCATATGTGTGT 59.376 55.000 1.24 0.00 35.28 3.72
7252 12358 0.104120 TGTGTGTGTTGGTCCTCTCG 59.896 55.000 0.00 0.00 0.00 4.04
7298 12693 5.169032 GGTCGATCATTTTATTTTCGTTCGC 59.831 40.000 0.00 0.00 0.00 4.70
7299 12694 5.730802 GTCGATCATTTTATTTTCGTTCGCA 59.269 36.000 0.00 0.00 0.00 5.10
7364 12759 5.581126 TGGTATTCGTCGGTTATGTACTT 57.419 39.130 0.00 0.00 0.00 2.24
7377 12772 2.319136 TGTACTTGTTGTCGCTGGTT 57.681 45.000 0.00 0.00 0.00 3.67
7397 12792 2.142220 TGGAACACACTGAGGGGAC 58.858 57.895 0.00 0.00 0.00 4.46
7476 12871 2.045926 GCTGATGTGGACGGGCTT 60.046 61.111 0.00 0.00 0.00 4.35
7547 12942 8.744568 ATAAATTTGGTCCATTTCTCTCTCTC 57.255 34.615 0.00 0.00 0.00 3.20
7548 12943 6.385766 AATTTGGTCCATTTCTCTCTCTCT 57.614 37.500 0.00 0.00 0.00 3.10
7549 12944 5.413309 TTTGGTCCATTTCTCTCTCTCTC 57.587 43.478 0.00 0.00 0.00 3.20
7550 12945 4.329638 TGGTCCATTTCTCTCTCTCTCT 57.670 45.455 0.00 0.00 0.00 3.10
7551 12946 4.277476 TGGTCCATTTCTCTCTCTCTCTC 58.723 47.826 0.00 0.00 0.00 3.20
7552 12947 4.017591 TGGTCCATTTCTCTCTCTCTCTCT 60.018 45.833 0.00 0.00 0.00 3.10
7553 12948 4.580580 GGTCCATTTCTCTCTCTCTCTCTC 59.419 50.000 0.00 0.00 0.00 3.20
7554 12949 4.273480 GTCCATTTCTCTCTCTCTCTCTCG 59.727 50.000 0.00 0.00 0.00 4.04
7555 12950 3.003689 CCATTTCTCTCTCTCTCTCTCGC 59.996 52.174 0.00 0.00 0.00 5.03
7556 12951 3.627395 TTTCTCTCTCTCTCTCTCGCT 57.373 47.619 0.00 0.00 0.00 4.93
7557 12952 2.602257 TCTCTCTCTCTCTCTCGCTG 57.398 55.000 0.00 0.00 0.00 5.18
7567 12962 1.592400 CTCTCGCTGTGTGTGTGCA 60.592 57.895 0.00 0.00 0.00 4.57
7568 12963 1.825285 CTCTCGCTGTGTGTGTGCAC 61.825 60.000 10.75 10.75 45.44 4.57
7602 12997 4.033358 CACACTAATCGATTGGAGAACTGC 59.967 45.833 26.04 0.00 0.00 4.40
7733 13151 7.916552 ACGTGGACAGTTATAAAATAATGAGC 58.083 34.615 0.00 0.00 0.00 4.26
7756 13174 3.132467 AGAATACTTCCCGTTCTGGCTAC 59.868 47.826 0.00 0.00 35.87 3.58
7771 13189 3.334691 TGGCTACAGCTGTAAATCACAC 58.665 45.455 25.95 12.01 41.70 3.82
7782 13200 6.259167 AGCTGTAAATCACACAGTTTAACGAA 59.741 34.615 4.57 0.00 44.30 3.85
7792 13212 5.019498 CACAGTTTAACGAACAACAGTCAC 58.981 41.667 0.00 0.00 40.84 3.67
7845 13266 7.556996 TGTGTATGTCCATCATTCATTCAATCA 59.443 33.333 0.00 0.00 36.51 2.57
7847 13268 8.407832 TGTATGTCCATCATTCATTCAATCAAC 58.592 33.333 0.00 0.00 37.91 3.18
7915 13339 5.519722 ACAATTTTGTCCTGACGTTTCATC 58.480 37.500 0.00 0.00 36.50 2.92
7923 13347 3.256383 TCCTGACGTTTCATCTTCGGTTA 59.744 43.478 0.00 0.00 0.00 2.85
7950 13375 2.558359 GCAAAGCATAAACCTGGACTGT 59.442 45.455 0.00 0.00 0.00 3.55
7956 13381 3.486383 CATAAACCTGGACTGTGTGGTT 58.514 45.455 0.00 0.00 43.73 3.67
7971 13396 2.166664 TGTGGTTTGTTTACCTTGTGGC 59.833 45.455 0.00 0.00 39.04 5.01
8029 13454 1.141881 CGAGATGGGGTTCACCTCG 59.858 63.158 0.00 0.00 40.19 4.63
8032 13457 3.310860 GATGGGGTTCACCTCGCGT 62.311 63.158 5.77 0.00 40.19 6.01
8113 13538 2.789092 GCTCAGCACGACATAACATTGC 60.789 50.000 0.00 0.00 0.00 3.56
8158 13583 2.997897 AGTGAGACAGGTCCCGCC 60.998 66.667 0.00 0.00 37.58 6.13
8160 13585 2.680352 TGAGACAGGTCCCGCCTC 60.680 66.667 0.00 0.00 46.96 4.70
8161 13586 2.363147 GAGACAGGTCCCGCCTCT 60.363 66.667 0.00 0.00 46.96 3.69
8162 13587 1.076923 GAGACAGGTCCCGCCTCTA 60.077 63.158 0.00 0.00 46.96 2.43
8163 13588 0.683504 GAGACAGGTCCCGCCTCTAA 60.684 60.000 0.00 0.00 46.96 2.10
8184 13609 7.615403 TCTAATCTAGCCAACATTATGCCTAG 58.385 38.462 0.00 0.00 0.00 3.02
8249 13721 3.233980 TCTGTCAGCTGCGGGTGT 61.234 61.111 23.32 0.00 41.24 4.16
8294 13774 0.464036 TGGCGTGTCACAGTCTTTCT 59.536 50.000 3.42 0.00 0.00 2.52
8312 13792 8.355169 AGTCTTTCTACACAGTACGTTATTTCA 58.645 33.333 0.00 0.00 0.00 2.69
8327 13822 7.461107 ACGTTATTTCAGTTATGTGTGTATGC 58.539 34.615 0.00 0.00 0.00 3.14
8328 13823 6.623353 CGTTATTTCAGTTATGTGTGTATGCG 59.377 38.462 0.00 0.00 0.00 4.73
8333 13828 2.093625 AGTTATGTGTGTATGCGTTGCG 59.906 45.455 0.00 0.00 0.00 4.85
8403 13908 3.357079 CCACCGTGCAGCTCCAAC 61.357 66.667 0.00 0.00 0.00 3.77
8431 13936 1.224592 GGACCCAGGGCTACATGTG 59.775 63.158 9.11 0.00 0.00 3.21
8433 13938 0.107654 GACCCAGGGCTACATGTGTC 60.108 60.000 9.11 0.48 0.00 3.67
8434 13939 0.840288 ACCCAGGGCTACATGTGTCA 60.840 55.000 9.11 0.00 0.00 3.58
8435 13940 0.548031 CCCAGGGCTACATGTGTCAT 59.452 55.000 9.11 0.00 0.00 3.06
8436 13941 1.671979 CCAGGGCTACATGTGTCATG 58.328 55.000 9.11 7.99 0.00 3.07
8441 13946 3.455910 AGGGCTACATGTGTCATGTATGT 59.544 43.478 18.60 11.29 38.48 2.29
8442 13947 4.653801 AGGGCTACATGTGTCATGTATGTA 59.346 41.667 18.60 11.69 36.52 2.29
8443 13948 5.307976 AGGGCTACATGTGTCATGTATGTAT 59.692 40.000 18.60 7.23 36.87 2.29
8445 13950 5.991606 GGCTACATGTGTCATGTATGTATGT 59.008 40.000 18.60 10.59 36.87 2.29
8446 13951 6.073602 GGCTACATGTGTCATGTATGTATGTG 60.074 42.308 18.60 9.53 36.87 3.21
8447 13952 6.479990 GCTACATGTGTCATGTATGTATGTGT 59.520 38.462 18.60 0.00 36.87 3.72
8448 13953 6.908870 ACATGTGTCATGTATGTATGTGTC 57.091 37.500 12.74 0.00 33.57 3.67
8450 13955 5.413309 TGTGTCATGTATGTATGTGTCCA 57.587 39.130 0.00 0.00 0.00 4.02
8451 13956 5.988287 TGTGTCATGTATGTATGTGTCCAT 58.012 37.500 0.00 0.00 34.97 3.41
8458 13963 7.992608 TCATGTATGTATGTGTCCATTTAGCTT 59.007 33.333 0.00 0.00 32.29 3.74
8462 13967 6.494893 TGTATGTGTCCATTTAGCTTGTTC 57.505 37.500 0.00 0.00 32.29 3.18
8505 14010 1.325640 CAGAACTGCACCATCGAATCG 59.674 52.381 0.00 0.00 0.00 3.34
8506 14011 0.026803 GAACTGCACCATCGAATCGC 59.973 55.000 0.00 0.00 0.00 4.58
8529 14035 0.478072 TGGCCTAACCATATGCCCAG 59.522 55.000 3.32 0.00 46.36 4.45
8530 14036 0.895559 GGCCTAACCATATGCCCAGC 60.896 60.000 0.00 0.00 36.97 4.85
8548 14054 4.070552 ACGGGCCAAGCGAGAGAC 62.071 66.667 4.39 0.00 0.00 3.36
8549 14055 4.069232 CGGGCCAAGCGAGAGACA 62.069 66.667 4.39 0.00 0.00 3.41
8551 14057 1.743252 GGGCCAAGCGAGAGACAAG 60.743 63.158 4.39 0.00 0.00 3.16
8552 14058 2.394563 GGCCAAGCGAGAGACAAGC 61.395 63.158 0.00 0.00 0.00 4.01
8554 14060 1.230635 GCCAAGCGAGAGACAAGCAA 61.231 55.000 0.00 0.00 0.00 3.91
8555 14061 1.229428 CCAAGCGAGAGACAAGCAAA 58.771 50.000 0.00 0.00 0.00 3.68
8558 14064 3.063180 CCAAGCGAGAGACAAGCAAATAG 59.937 47.826 0.00 0.00 0.00 1.73
8560 14066 4.720649 AGCGAGAGACAAGCAAATAGTA 57.279 40.909 0.00 0.00 0.00 1.82
8561 14067 5.269505 AGCGAGAGACAAGCAAATAGTAT 57.730 39.130 0.00 0.00 0.00 2.12
8562 14068 5.285651 AGCGAGAGACAAGCAAATAGTATC 58.714 41.667 0.00 0.00 0.00 2.24
8565 14071 5.174761 CGAGAGACAAGCAAATAGTATCTGC 59.825 44.000 0.00 0.00 34.33 4.26
8566 14072 5.046529 AGAGACAAGCAAATAGTATCTGCG 58.953 41.667 2.82 0.00 41.05 5.18
8567 14073 4.122776 AGACAAGCAAATAGTATCTGCGG 58.877 43.478 2.82 2.77 41.05 5.69
8568 14074 4.119862 GACAAGCAAATAGTATCTGCGGA 58.880 43.478 0.00 0.00 41.05 5.54
8573 14079 4.100189 AGCAAATAGTATCTGCGGAGAACT 59.900 41.667 11.77 16.94 41.05 3.01
8574 14080 4.210120 GCAAATAGTATCTGCGGAGAACTG 59.790 45.833 22.45 13.00 0.00 3.16
8576 14082 2.145397 AGTATCTGCGGAGAACTGGA 57.855 50.000 11.77 0.00 0.00 3.86
8577 14083 2.028130 AGTATCTGCGGAGAACTGGAG 58.972 52.381 11.77 0.00 41.27 3.86
8578 14084 4.843624 TCTGCGGAGAACTGGAGA 57.156 55.556 3.28 0.00 45.19 3.71
8580 14086 2.437085 TCTGCGGAGAACTGGAGATA 57.563 50.000 3.28 0.00 43.16 1.98
8582 14088 4.100279 TCTGCGGAGAACTGGAGATATA 57.900 45.455 3.28 0.00 43.16 0.86
8584 14090 5.816682 TCTGCGGAGAACTGGAGATATATA 58.183 41.667 3.28 0.00 43.16 0.86
8585 14091 6.246163 TCTGCGGAGAACTGGAGATATATAA 58.754 40.000 3.28 0.00 43.16 0.98
8588 14094 6.437477 TGCGGAGAACTGGAGATATATAACAT 59.563 38.462 0.00 0.00 0.00 2.71
8589 14095 7.614192 TGCGGAGAACTGGAGATATATAACATA 59.386 37.037 0.00 0.00 0.00 2.29
8590 14096 7.916450 GCGGAGAACTGGAGATATATAACATAC 59.084 40.741 0.00 0.00 0.00 2.39
8591 14097 8.957466 CGGAGAACTGGAGATATATAACATACA 58.043 37.037 0.00 0.00 0.00 2.29
8593 14099 9.796120 GAGAACTGGAGATATATAACATACAGC 57.204 37.037 4.96 0.00 0.00 4.40
8594 14100 9.540538 AGAACTGGAGATATATAACATACAGCT 57.459 33.333 4.96 0.00 0.00 4.24
8650 14156 4.038361 CAGATTGAACTCGATCAGTACGG 58.962 47.826 9.19 0.00 38.86 4.02
8651 14157 2.273370 TTGAACTCGATCAGTACGGC 57.727 50.000 0.00 0.00 32.30 5.68
8652 14158 0.454600 TGAACTCGATCAGTACGGCC 59.545 55.000 0.00 0.00 32.30 6.13
8653 14159 0.739561 GAACTCGATCAGTACGGCCT 59.260 55.000 0.00 0.00 32.30 5.19
8654 14160 0.739561 AACTCGATCAGTACGGCCTC 59.260 55.000 0.00 0.00 32.30 4.70
8657 14163 1.101635 TCGATCAGTACGGCCTCCAG 61.102 60.000 0.00 0.00 0.00 3.86
8744 15114 7.033791 TCTCACAGACGATACAGGTAATTTTC 58.966 38.462 0.00 0.00 0.00 2.29
8747 15117 5.581085 ACAGACGATACAGGTAATTTTCTGC 59.419 40.000 7.40 0.00 34.57 4.26
8753 15123 6.292381 CGATACAGGTAATTTTCTGCAGTAGC 60.292 42.308 14.67 7.95 42.57 3.58
8766 15136 1.943340 GCAGTAGCAAGGTTATCAGCC 59.057 52.381 0.00 0.00 41.58 4.85
8767 15137 2.680805 GCAGTAGCAAGGTTATCAGCCA 60.681 50.000 0.00 0.00 41.58 4.75
8769 15139 3.107601 AGTAGCAAGGTTATCAGCCAGA 58.892 45.455 0.00 0.00 0.00 3.86
8771 15141 3.205784 AGCAAGGTTATCAGCCAGATC 57.794 47.619 0.00 0.00 38.19 2.75
8772 15142 2.776536 AGCAAGGTTATCAGCCAGATCT 59.223 45.455 0.00 0.00 38.19 2.75
8773 15143 3.137533 GCAAGGTTATCAGCCAGATCTC 58.862 50.000 0.00 0.00 38.19 2.75
8774 15144 3.432749 GCAAGGTTATCAGCCAGATCTCA 60.433 47.826 0.00 0.00 38.19 3.27
8775 15145 4.125703 CAAGGTTATCAGCCAGATCTCAC 58.874 47.826 0.00 0.00 38.19 3.51
8776 15146 3.378512 AGGTTATCAGCCAGATCTCACA 58.621 45.455 0.00 0.00 38.19 3.58
8780 15150 0.813821 TCAGCCAGATCTCACAGACG 59.186 55.000 0.00 0.00 0.00 4.18
8781 15151 0.813821 CAGCCAGATCTCACAGACGA 59.186 55.000 0.00 0.00 0.00 4.20
8784 15154 2.621055 AGCCAGATCTCACAGACGATAC 59.379 50.000 0.00 0.00 0.00 2.24
8786 15156 3.549827 GCCAGATCTCACAGACGATACAG 60.550 52.174 0.00 0.00 0.00 2.74
8788 15158 3.629855 CAGATCTCACAGACGATACAGGT 59.370 47.826 0.00 0.00 0.00 4.00
8790 15160 5.297029 CAGATCTCACAGACGATACAGGTTA 59.703 44.000 0.00 0.00 0.00 2.85
8791 15161 6.016693 CAGATCTCACAGACGATACAGGTTAT 60.017 42.308 0.00 0.00 0.00 1.89
8792 15162 5.752892 TCTCACAGACGATACAGGTTATC 57.247 43.478 0.00 0.00 0.00 1.75
8794 15164 5.297029 TCTCACAGACGATACAGGTTATCAG 59.703 44.000 0.00 0.00 0.00 2.90
8823 15702 1.073025 TACTGTGGCACCAGCAAGG 59.927 57.895 16.26 0.00 44.61 3.61
8840 15719 1.620822 AGGTTGTGAAGGGCAACATC 58.379 50.000 9.83 0.00 45.64 3.06
8843 15722 0.821301 TTGTGAAGGGCAACATCGCA 60.821 50.000 0.00 0.00 41.04 5.10
8894 15773 0.620556 ACGTGAGCTGGGATGGAATT 59.379 50.000 0.00 0.00 0.00 2.17
8927 15806 4.478843 AGCTGCAAACAATATCATAGCG 57.521 40.909 1.02 0.00 35.25 4.26
8946 15825 3.190849 CTGCGGTGATGAGTGGCG 61.191 66.667 0.00 0.00 0.00 5.69
8968 15847 2.563179 CCTACTCATATCCACCTTCCGG 59.437 54.545 0.00 0.00 0.00 5.14
9015 15901 1.073444 CCCATAGCCTGATCACAGCAT 59.927 52.381 13.91 4.62 42.25 3.79
9036 15922 7.168972 CAGCATAAGTTTACTCAGAGATACTGC 59.831 40.741 3.79 5.46 45.38 4.40
9081 15967 2.736721 TGTCAGATAACAGCGCAAGTTC 59.263 45.455 19.42 8.65 41.68 3.01
9089 15975 0.510359 CAGCGCAAGTTCAGTCAGAC 59.490 55.000 11.47 0.00 41.68 3.51
9092 15978 0.861837 CGCAAGTTCAGTCAGACACC 59.138 55.000 2.66 0.00 0.00 4.16
9093 15979 1.806247 CGCAAGTTCAGTCAGACACCA 60.806 52.381 2.66 0.00 0.00 4.17
9094 15980 2.288666 GCAAGTTCAGTCAGACACCAA 58.711 47.619 2.66 0.00 0.00 3.67
9095 15981 2.682856 GCAAGTTCAGTCAGACACCAAA 59.317 45.455 2.66 0.00 0.00 3.28
9096 15982 3.316308 GCAAGTTCAGTCAGACACCAAAT 59.684 43.478 2.66 0.00 0.00 2.32
9097 15983 4.202050 GCAAGTTCAGTCAGACACCAAATT 60.202 41.667 2.66 0.00 0.00 1.82
9098 15984 5.008613 GCAAGTTCAGTCAGACACCAAATTA 59.991 40.000 2.66 0.00 0.00 1.40
9099 15985 6.430451 CAAGTTCAGTCAGACACCAAATTAC 58.570 40.000 2.66 0.00 0.00 1.89
9100 15986 5.930135 AGTTCAGTCAGACACCAAATTACT 58.070 37.500 2.66 0.00 0.00 2.24
9101 15987 5.992217 AGTTCAGTCAGACACCAAATTACTC 59.008 40.000 2.66 0.00 0.00 2.59
9102 15988 5.545063 TCAGTCAGACACCAAATTACTCA 57.455 39.130 2.66 0.00 0.00 3.41
9103 15989 6.114187 TCAGTCAGACACCAAATTACTCAT 57.886 37.500 2.66 0.00 0.00 2.90
9104 15990 6.533730 TCAGTCAGACACCAAATTACTCATT 58.466 36.000 2.66 0.00 0.00 2.57
9105 15991 6.650807 TCAGTCAGACACCAAATTACTCATTC 59.349 38.462 2.66 0.00 0.00 2.67
9106 15992 6.652481 CAGTCAGACACCAAATTACTCATTCT 59.348 38.462 2.66 0.00 0.00 2.40
9107 15993 6.652481 AGTCAGACACCAAATTACTCATTCTG 59.348 38.462 2.66 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.312895 TGGCTAACTGCAAACAAGAAGATA 58.687 37.500 0.00 0.00 45.15 1.98
47 48 4.510038 AGAATGGCTAACTGCAAACAAG 57.490 40.909 0.00 0.00 45.15 3.16
79 80 6.071952 ACGGAAGGAGTACTATTTTTACGACA 60.072 38.462 15.46 0.00 0.00 4.35
80 81 6.325596 ACGGAAGGAGTACTATTTTTACGAC 58.674 40.000 15.46 0.00 0.00 4.34
99 100 1.600485 GACAAGCTTTTTCGGACGGAA 59.400 47.619 0.00 0.00 0.00 4.30
103 104 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
128 130 7.549488 AGTGTTAACTTGGTGCTAGATACATTC 59.451 37.037 7.22 0.00 30.14 2.67
150 152 6.879458 GTCTTTCAAATGGATGTACCTAGTGT 59.121 38.462 0.00 0.00 39.86 3.55
153 155 7.928706 CCTAGTCTTTCAAATGGATGTACCTAG 59.071 40.741 0.00 0.00 39.86 3.02
157 159 7.148239 CCAACCTAGTCTTTCAAATGGATGTAC 60.148 40.741 0.00 0.00 0.00 2.90
197 199 5.063017 TGAAATATCTACTCCCTCCGTCT 57.937 43.478 0.00 0.00 0.00 4.18
227 229 2.158385 ACCACCACTTTGCCCATAGAAA 60.158 45.455 0.00 0.00 0.00 2.52
556 2356 2.621371 TAGATCATCGTTGGCGCGCA 62.621 55.000 34.42 16.55 38.14 6.09
598 2398 1.363080 GAGCGGACGGGACTATTCC 59.637 63.158 0.00 0.00 41.95 3.01
681 2632 0.033504 CCGTAGCGAGCCCATAACAT 59.966 55.000 0.00 0.00 0.00 2.71
731 2682 2.677979 GCGACGTTTCTCTTGCCCC 61.678 63.158 0.00 0.00 0.00 5.80
783 2735 2.843912 AAAGGGCGGCTCATCAAGGG 62.844 60.000 9.56 0.00 0.00 3.95
784 2736 0.107214 TAAAGGGCGGCTCATCAAGG 60.107 55.000 9.56 0.00 0.00 3.61
792 2744 3.310860 CTGACGGTAAAGGGCGGCT 62.311 63.158 9.56 0.00 0.00 5.52
798 2750 2.388232 GCGGTGCTGACGGTAAAGG 61.388 63.158 0.00 0.00 0.00 3.11
851 2806 1.922545 GTGTACACGGAATTACGGCTC 59.077 52.381 15.86 2.66 38.39 4.70
1152 3109 3.138798 GACGAGGGAGCTGCGGTA 61.139 66.667 0.00 0.00 0.00 4.02
1194 3151 2.462782 GGAGGACGACGACGAGGAG 61.463 68.421 15.32 0.00 42.66 3.69
1200 3157 1.226323 CGATGTGGAGGACGACGAC 60.226 63.158 0.00 0.00 0.00 4.34
1218 3175 2.701423 GTGAAGGGAGAGGGGATTACTC 59.299 54.545 0.00 0.00 35.20 2.59
1337 3295 3.320733 TCGAACGAAAGATCTAGCGAG 57.679 47.619 20.00 12.20 0.00 5.03
1340 3298 3.874706 TCGATCGAACGAAAGATCTAGC 58.125 45.455 16.99 0.00 40.65 3.42
1424 3382 0.107831 TTCCACTTTCCACTCACGGG 59.892 55.000 0.00 0.00 0.00 5.28
1453 3411 3.177228 ACTGCCTCAGTTTCAGGTCTAT 58.823 45.455 0.00 0.00 42.59 1.98
2276 4332 7.170828 CCGTATGATGCTAAGTTGCTAACAATA 59.829 37.037 0.00 0.00 38.27 1.90
2511 4567 7.383102 ACAAGCTACACCATCTATTTTTCAG 57.617 36.000 0.00 0.00 0.00 3.02
2517 4573 5.435686 TGGAACAAGCTACACCATCTATT 57.564 39.130 0.00 0.00 31.92 1.73
2543 4599 5.999600 CCAGTGTTTAGATATGCCATCATCA 59.000 40.000 0.00 0.00 34.22 3.07
2544 4600 6.233434 TCCAGTGTTTAGATATGCCATCATC 58.767 40.000 0.00 0.00 34.22 2.92
2545 4601 6.191657 TCCAGTGTTTAGATATGCCATCAT 57.808 37.500 0.00 0.00 36.73 2.45
2651 4707 8.892723 TGAAATAGTTACAACAGCAATAGGATG 58.107 33.333 0.00 0.00 39.32 3.51
2652 4708 9.113838 CTGAAATAGTTACAACAGCAATAGGAT 57.886 33.333 0.00 0.00 0.00 3.24
2653 4709 8.318412 TCTGAAATAGTTACAACAGCAATAGGA 58.682 33.333 0.00 0.00 0.00 2.94
2654 4710 8.391106 GTCTGAAATAGTTACAACAGCAATAGG 58.609 37.037 0.00 0.00 0.00 2.57
2655 4711 9.155975 AGTCTGAAATAGTTACAACAGCAATAG 57.844 33.333 0.00 0.00 0.00 1.73
2656 4712 9.502091 AAGTCTGAAATAGTTACAACAGCAATA 57.498 29.630 0.00 0.00 0.00 1.90
2657 4713 7.986085 AGTCTGAAATAGTTACAACAGCAAT 57.014 32.000 0.00 0.00 0.00 3.56
2731 4828 0.689055 ACTGGTGAAGCATGCTCTCA 59.311 50.000 22.93 21.85 0.00 3.27
2735 4832 2.034124 ACAAAACTGGTGAAGCATGCT 58.966 42.857 16.30 16.30 0.00 3.79
2741 4838 2.100749 GGAACCCACAAAACTGGTGAAG 59.899 50.000 0.00 0.00 38.54 3.02
2807 4904 2.095263 GCATACACGTTTGCAGAATGGT 60.095 45.455 7.60 0.00 37.46 3.55
2840 4937 5.279256 GGAAGGGTAAATAAAAAGCAGCACA 60.279 40.000 0.00 0.00 0.00 4.57
2841 4938 5.168569 GGAAGGGTAAATAAAAAGCAGCAC 58.831 41.667 0.00 0.00 0.00 4.40
2842 4939 4.221924 GGGAAGGGTAAATAAAAAGCAGCA 59.778 41.667 0.00 0.00 0.00 4.41
2886 5007 8.417273 AACATAACACTAATTAAAAGGGTGCT 57.583 30.769 0.00 0.00 28.89 4.40
3062 5184 5.220681 GGTTGTTGTTGTTGTTGTTGTTGTT 60.221 36.000 0.00 0.00 0.00 2.83
3065 5187 4.271291 GTGGTTGTTGTTGTTGTTGTTGTT 59.729 37.500 0.00 0.00 0.00 2.83
3261 5383 8.395605 TGGGTCTAACAGAAAAGGGTATAAAAT 58.604 33.333 0.00 0.00 0.00 1.82
3268 5390 3.462205 AGTTGGGTCTAACAGAAAAGGGT 59.538 43.478 0.38 0.00 33.02 4.34
3346 5469 4.142038 AGGTTAAAAGTGGCATCGAGTTT 58.858 39.130 0.00 0.00 0.00 2.66
3437 5560 6.428771 ACCCTCATGATTTTCTTGCAATTTTG 59.571 34.615 0.00 0.00 0.00 2.44
3498 5621 5.948162 AGAATGGATAGAACAACAAGCACAT 59.052 36.000 0.00 0.00 0.00 3.21
3613 5736 6.040878 CGGACTTCAGTACATAACTTAAGGG 58.959 44.000 7.53 0.00 41.73 3.95
3628 5751 0.456221 ACGGATAGCACGGACTTCAG 59.544 55.000 0.00 0.00 35.23 3.02
3646 5769 1.537202 CCTTGGTAGCAAGCTGTCAAC 59.463 52.381 25.82 0.00 0.00 3.18
3650 5773 1.421646 AGAACCTTGGTAGCAAGCTGT 59.578 47.619 25.82 17.45 0.00 4.40
3713 5836 8.049721 AGGACTTAGAATAATTTGGAACAGAGG 58.950 37.037 0.00 0.00 42.39 3.69
3892 6123 6.430308 TCGAGCGGAGTCATAAAATAGACTAT 59.570 38.462 0.00 0.00 44.61 2.12
4217 6448 9.958234 TTTTTGTAATTGACGATGATGAAAGAA 57.042 25.926 0.00 0.00 0.00 2.52
4358 6590 2.798501 CGCAACACGCAGGGTATCG 61.799 63.158 0.00 0.00 42.60 2.92
4370 6602 1.135141 GCATAAATTCCTGCCGCAACA 60.135 47.619 0.00 0.00 32.15 3.33
4559 6792 6.636454 AACCTCAGGTATGAATAGGAAACA 57.364 37.500 0.00 0.00 33.12 2.83
4567 6800 6.824958 TTTAGCCTAACCTCAGGTATGAAT 57.175 37.500 0.00 0.00 38.05 2.57
4622 6855 8.534333 TGTAACATCTTCTGTGAACATCTAAC 57.466 34.615 0.00 0.00 38.39 2.34
4758 6995 9.042008 TGTACTTCAGAAAGAACATTTAGTGAC 57.958 33.333 0.00 0.00 36.30 3.67
4794 7031 9.988350 GTCACGTCTATGTTATTCAATTTTGAT 57.012 29.630 0.00 0.00 37.00 2.57
4800 7038 8.716646 TTCATGTCACGTCTATGTTATTCAAT 57.283 30.769 0.00 0.00 0.00 2.57
4846 7088 7.277981 CGAGAACATACTTGGTATGCTAAGTTT 59.722 37.037 17.09 7.45 46.76 2.66
4864 7106 1.281867 TGAATTGGAGGGCGAGAACAT 59.718 47.619 0.00 0.00 0.00 2.71
4951 7194 3.955551 GTGTGAACCCTCTTTACCCAAAA 59.044 43.478 0.00 0.00 0.00 2.44
4958 7201 4.407621 TGTCTCAAGTGTGAACCCTCTTTA 59.592 41.667 0.00 0.00 31.88 1.85
5425 7961 4.522789 TGAATTGGTTGAGCCTACCTTTTC 59.477 41.667 7.18 9.24 36.60 2.29
5472 8009 8.363390 TGTTTTGTGATCTTAACCAAATGCATA 58.637 29.630 0.00 0.00 0.00 3.14
5525 8062 7.707893 GCATTGCTTTGTGTTCTATTATTGGAT 59.292 33.333 0.16 0.00 0.00 3.41
5576 8113 4.526650 TGCCCTTCTCTCCAAAATTTAACC 59.473 41.667 0.00 0.00 0.00 2.85
5580 8117 8.645110 CATAATATGCCCTTCTCTCCAAAATTT 58.355 33.333 0.00 0.00 0.00 1.82
5581 8118 8.006564 TCATAATATGCCCTTCTCTCCAAAATT 58.993 33.333 0.00 0.00 0.00 1.82
5686 9933 2.567615 GGAGCAGAAAACCTGAGGAGTA 59.432 50.000 4.99 0.00 45.78 2.59
5880 10913 7.609760 ATTAATGCGTGTGAAACTATGAAGA 57.390 32.000 0.00 0.00 38.04 2.87
5903 10936 5.720041 TCCAGCAGTAGTCTAGGTTACAAAT 59.280 40.000 7.14 0.00 0.00 2.32
5904 10937 5.047519 GTCCAGCAGTAGTCTAGGTTACAAA 60.048 44.000 7.14 0.00 0.00 2.83
5907 10940 4.271661 AGTCCAGCAGTAGTCTAGGTTAC 58.728 47.826 0.00 0.00 0.00 2.50
5911 10944 4.159244 ACTAGTCCAGCAGTAGTCTAGG 57.841 50.000 0.00 0.00 36.64 3.02
6008 11044 7.820648 ACAAATTGACGCTCTAATGATCTTTT 58.179 30.769 0.00 0.00 0.00 2.27
6013 11049 5.295292 CAGGACAAATTGACGCTCTAATGAT 59.705 40.000 0.00 0.00 0.00 2.45
6014 11050 4.631377 CAGGACAAATTGACGCTCTAATGA 59.369 41.667 0.00 0.00 0.00 2.57
6019 11055 1.160137 GCAGGACAAATTGACGCTCT 58.840 50.000 0.00 0.00 0.00 4.09
6066 11102 3.308402 CCAACTAGGAGCAAGGATCCAAA 60.308 47.826 15.82 0.00 41.08 3.28
6159 11195 5.391310 GCAATGTCTATGCCGGAAATATCTG 60.391 44.000 5.05 0.00 37.85 2.90
6255 11291 6.718912 CCTTCTCTTCTTCCCTTCTTTGATTT 59.281 38.462 0.00 0.00 0.00 2.17
6414 11456 0.104671 GATCTGCACTCCTCTGCTCC 59.895 60.000 0.00 0.00 38.07 4.70
6458 11501 1.228510 CAGCCATCCTCCCCCTTTC 59.771 63.158 0.00 0.00 0.00 2.62
6465 11508 1.919600 AAGTGAGCCAGCCATCCTCC 61.920 60.000 0.00 0.00 0.00 4.30
6466 11509 0.833287 TAAGTGAGCCAGCCATCCTC 59.167 55.000 0.00 0.00 0.00 3.71
6470 11513 0.475906 GGGATAAGTGAGCCAGCCAT 59.524 55.000 0.00 0.00 34.10 4.40
6529 11578 1.542030 CTAGTCGTGCACCTTGAGTCT 59.458 52.381 12.15 2.58 0.00 3.24
6575 11634 2.005451 GTAGACTAGTTCGCCGAGTCA 58.995 52.381 14.24 2.59 41.73 3.41
6790 11853 2.025321 ACTATGGTTTTCCCTTCCGCAT 60.025 45.455 0.00 0.00 39.73 4.73
6970 12040 4.857679 CCTAACCTGTCTCTACCTACAGT 58.142 47.826 0.00 0.00 41.25 3.55
6997 12095 1.211703 TCCTGAAGGTGCTGTCACAAA 59.788 47.619 0.00 0.00 44.87 2.83
7083 12189 1.919600 GATGGAGGCTTGGCTCCTGT 61.920 60.000 33.09 24.76 40.28 4.00
7125 12231 2.045634 GCCTCTCCAGCACATGCA 60.046 61.111 6.64 0.00 45.16 3.96
7131 12237 2.659016 CGTCAAGCCTCTCCAGCA 59.341 61.111 0.00 0.00 0.00 4.41
7167 12273 4.498520 ACCTCCATGCGCGACGAG 62.499 66.667 12.10 7.77 0.00 4.18
7239 12345 3.134081 AGAAAAAGACGAGAGGACCAACA 59.866 43.478 0.00 0.00 0.00 3.33
7252 12358 1.740025 CCATCTCCGCCAGAAAAAGAC 59.260 52.381 0.00 0.00 33.62 3.01
7298 12693 1.584724 AACCACTGACCCTCCCTATG 58.415 55.000 0.00 0.00 0.00 2.23
7299 12694 2.361085 AAACCACTGACCCTCCCTAT 57.639 50.000 0.00 0.00 0.00 2.57
7364 12759 2.147958 GTTCCATAACCAGCGACAACA 58.852 47.619 0.00 0.00 0.00 3.33
7377 12772 1.906574 GTCCCCTCAGTGTGTTCCATA 59.093 52.381 0.00 0.00 0.00 2.74
7385 12780 1.544825 CCATGTCGTCCCCTCAGTGT 61.545 60.000 0.00 0.00 0.00 3.55
7476 12871 8.206867 CCCACTATCTTATTTCTCTTCACATGA 58.793 37.037 0.00 0.00 0.00 3.07
7525 12920 6.215227 AGAGAGAGAGAGAAATGGACCAAATT 59.785 38.462 0.00 0.00 0.00 1.82
7539 12934 1.935873 CACAGCGAGAGAGAGAGAGAG 59.064 57.143 0.00 0.00 0.00 3.20
7541 12936 1.398041 CACACAGCGAGAGAGAGAGAG 59.602 57.143 0.00 0.00 0.00 3.20
7543 12938 1.135717 CACACACAGCGAGAGAGAGAG 60.136 57.143 0.00 0.00 0.00 3.20
7544 12939 0.877743 CACACACAGCGAGAGAGAGA 59.122 55.000 0.00 0.00 0.00 3.10
7545 12940 0.595588 ACACACACAGCGAGAGAGAG 59.404 55.000 0.00 0.00 0.00 3.20
7546 12941 0.312102 CACACACACAGCGAGAGAGA 59.688 55.000 0.00 0.00 0.00 3.10
7547 12942 1.280886 GCACACACACAGCGAGAGAG 61.281 60.000 0.00 0.00 0.00 3.20
7548 12943 1.300156 GCACACACACAGCGAGAGA 60.300 57.895 0.00 0.00 0.00 3.10
7549 12944 1.592400 TGCACACACACAGCGAGAG 60.592 57.895 0.00 0.00 0.00 3.20
7550 12945 1.882625 GTGCACACACACAGCGAGA 60.883 57.895 13.17 0.00 46.61 4.04
7551 12946 2.628106 GTGCACACACACAGCGAG 59.372 61.111 13.17 0.00 46.61 5.03
7602 12997 2.668457 GGATAGAACGACAAGCACAGTG 59.332 50.000 0.00 0.00 0.00 3.66
7709 13127 7.915508 TGCTCATTATTTTATAACTGTCCACG 58.084 34.615 0.00 0.00 0.00 4.94
7733 13151 2.093447 AGCCAGAACGGGAAGTATTCTG 60.093 50.000 6.29 6.29 46.56 3.02
7743 13161 1.448540 CAGCTGTAGCCAGAACGGG 60.449 63.158 5.25 0.00 41.50 5.28
7771 13189 5.464965 AGTGACTGTTGTTCGTTAAACTG 57.535 39.130 0.00 0.00 38.76 3.16
7792 13212 6.163476 TGCACACTATTGTTCCACTACTAAG 58.837 40.000 0.00 0.00 31.66 2.18
7801 13221 4.870363 ACACAAATGCACACTATTGTTCC 58.130 39.130 0.00 0.00 33.97 3.62
7812 13232 4.700268 TGATGGACATACACAAATGCAC 57.300 40.909 0.00 0.00 0.00 4.57
7845 13266 2.332514 GCACACATGCGCACTGTT 59.667 55.556 14.90 6.98 43.33 3.16
7866 13287 5.116084 TGCATACAGAAGATAAAAGGGCT 57.884 39.130 0.00 0.00 0.00 5.19
7915 13339 1.135402 GCTTTGCCACCATAACCGAAG 60.135 52.381 0.00 0.00 0.00 3.79
7923 13347 2.234414 CAGGTTTATGCTTTGCCACCAT 59.766 45.455 0.00 0.00 0.00 3.55
7950 13375 2.166664 GCCACAAGGTAAACAAACCACA 59.833 45.455 0.00 0.00 42.40 4.17
7956 13381 0.665835 CTGCGCCACAAGGTAAACAA 59.334 50.000 4.18 0.00 37.19 2.83
7971 13396 0.588252 CACAAACTCCTTCACCTGCG 59.412 55.000 0.00 0.00 0.00 5.18
8158 13583 6.734104 GGCATAATGTTGGCTAGATTAGAG 57.266 41.667 0.00 2.12 39.00 2.43
8184 13609 7.488471 CCATTACAAGTTACAGCTAGTACAGTC 59.512 40.741 0.00 0.00 30.91 3.51
8271 13749 0.681733 AGACTGTGACACGCCAATCT 59.318 50.000 0.22 0.00 0.00 2.40
8294 13774 9.131416 CACATAACTGAAATAACGTACTGTGTA 57.869 33.333 0.00 0.00 0.00 2.90
8312 13792 2.093625 CGCAACGCATACACACATAACT 59.906 45.455 0.00 0.00 0.00 2.24
8327 13822 0.732880 ACGAGATCTTCACCGCAACG 60.733 55.000 0.00 0.00 0.00 4.10
8328 13823 0.992802 GACGAGATCTTCACCGCAAC 59.007 55.000 0.00 0.00 0.00 4.17
8333 13828 2.494073 AGTTCCAGACGAGATCTTCACC 59.506 50.000 0.00 0.00 34.41 4.02
8403 13908 2.017113 GCCCTGGGTCCTAACATTTCG 61.017 57.143 15.56 0.00 0.00 3.46
8431 13936 7.442364 AGCTAAATGGACACATACATACATGAC 59.558 37.037 0.00 0.00 35.94 3.06
8433 13938 7.734924 AGCTAAATGGACACATACATACATG 57.265 36.000 0.00 0.00 35.94 3.21
8434 13939 7.775093 ACAAGCTAAATGGACACATACATACAT 59.225 33.333 0.00 0.00 35.94 2.29
8435 13940 7.109501 ACAAGCTAAATGGACACATACATACA 58.890 34.615 0.00 0.00 35.94 2.29
8436 13941 7.553881 ACAAGCTAAATGGACACATACATAC 57.446 36.000 0.00 0.00 35.94 2.39
8441 13946 5.121611 CACGAACAAGCTAAATGGACACATA 59.878 40.000 0.00 0.00 35.94 2.29
8442 13947 4.072131 ACGAACAAGCTAAATGGACACAT 58.928 39.130 0.00 0.00 39.54 3.21
8443 13948 3.249799 CACGAACAAGCTAAATGGACACA 59.750 43.478 0.00 0.00 0.00 3.72
8445 13950 2.225491 GCACGAACAAGCTAAATGGACA 59.775 45.455 0.00 0.00 0.00 4.02
8446 13951 2.225491 TGCACGAACAAGCTAAATGGAC 59.775 45.455 0.00 0.00 0.00 4.02
8447 13952 2.483877 CTGCACGAACAAGCTAAATGGA 59.516 45.455 0.00 0.00 0.00 3.41
8448 13953 2.855180 CTGCACGAACAAGCTAAATGG 58.145 47.619 0.00 0.00 0.00 3.16
8450 13955 2.619013 GCTGCACGAACAAGCTAAAT 57.381 45.000 0.00 0.00 0.00 1.40
8530 14036 4.069232 TCTCTCGCTTGGCCCGTG 62.069 66.667 0.00 0.00 0.00 4.94
8535 14041 1.230635 TTGCTTGTCTCTCGCTTGGC 61.231 55.000 0.00 0.00 0.00 4.52
8546 14052 4.119862 TCCGCAGATACTATTTGCTTGTC 58.880 43.478 9.29 0.00 35.73 3.18
8548 14054 4.371786 TCTCCGCAGATACTATTTGCTTG 58.628 43.478 9.29 2.23 35.73 4.01
8549 14055 4.672587 TCTCCGCAGATACTATTTGCTT 57.327 40.909 9.29 0.00 35.73 3.91
8551 14057 4.210120 CAGTTCTCCGCAGATACTATTTGC 59.790 45.833 2.11 2.11 34.58 3.68
8552 14058 4.747108 CCAGTTCTCCGCAGATACTATTTG 59.253 45.833 0.00 0.00 0.00 2.32
8554 14060 4.215908 TCCAGTTCTCCGCAGATACTATT 58.784 43.478 0.00 0.00 0.00 1.73
8555 14061 3.823873 CTCCAGTTCTCCGCAGATACTAT 59.176 47.826 0.00 0.00 0.00 2.12
8558 14064 2.025155 TCTCCAGTTCTCCGCAGATAC 58.975 52.381 0.00 0.00 0.00 2.24
8560 14066 1.786937 ATCTCCAGTTCTCCGCAGAT 58.213 50.000 0.00 0.00 0.00 2.90
8561 14067 2.437085 TATCTCCAGTTCTCCGCAGA 57.563 50.000 0.00 0.00 0.00 4.26
8562 14068 6.071896 TGTTATATATCTCCAGTTCTCCGCAG 60.072 42.308 0.00 0.00 0.00 5.18
8565 14071 8.957466 TGTATGTTATATATCTCCAGTTCTCCG 58.043 37.037 0.00 0.00 0.00 4.63
8567 14073 9.796120 GCTGTATGTTATATATCTCCAGTTCTC 57.204 37.037 0.00 0.00 0.00 2.87
8568 14074 9.540538 AGCTGTATGTTATATATCTCCAGTTCT 57.459 33.333 0.00 0.00 0.00 3.01
8596 14102 8.678199 CGTCACTGTAGATATATATCACCACAT 58.322 37.037 21.95 5.53 35.17 3.21
8597 14103 7.881232 TCGTCACTGTAGATATATATCACCACA 59.119 37.037 21.95 19.15 35.17 4.17
8598 14104 8.265165 TCGTCACTGTAGATATATATCACCAC 57.735 38.462 21.95 16.38 35.17 4.16
8599 14105 8.857694 TTCGTCACTGTAGATATATATCACCA 57.142 34.615 21.95 16.23 35.17 4.17
8602 14108 9.788960 GCATTTCGTCACTGTAGATATATATCA 57.211 33.333 21.95 7.84 35.17 2.15
8607 14113 7.272037 TCTGCATTTCGTCACTGTAGATATA 57.728 36.000 0.00 0.00 28.52 0.86
8614 14120 3.402110 TCAATCTGCATTTCGTCACTGT 58.598 40.909 0.00 0.00 0.00 3.55
8619 14125 3.367932 TCGAGTTCAATCTGCATTTCGTC 59.632 43.478 0.00 0.00 0.00 4.20
8620 14126 3.325870 TCGAGTTCAATCTGCATTTCGT 58.674 40.909 0.00 0.00 0.00 3.85
8626 14132 3.599730 ACTGATCGAGTTCAATCTGCA 57.400 42.857 0.00 0.00 0.00 4.41
8747 15117 3.118629 TCTGGCTGATAACCTTGCTACTG 60.119 47.826 0.00 0.00 0.00 2.74
8753 15123 4.125703 GTGAGATCTGGCTGATAACCTTG 58.874 47.826 0.00 0.00 35.14 3.61
8756 15126 3.386078 TCTGTGAGATCTGGCTGATAACC 59.614 47.826 0.00 0.87 35.14 2.85
8757 15127 4.367450 GTCTGTGAGATCTGGCTGATAAC 58.633 47.826 0.00 7.03 35.14 1.89
8759 15129 2.620585 CGTCTGTGAGATCTGGCTGATA 59.379 50.000 0.00 0.00 35.14 2.15
8760 15130 1.408340 CGTCTGTGAGATCTGGCTGAT 59.592 52.381 0.00 6.58 38.27 2.90
8761 15131 0.813821 CGTCTGTGAGATCTGGCTGA 59.186 55.000 0.00 0.00 0.00 4.26
8762 15132 0.813821 TCGTCTGTGAGATCTGGCTG 59.186 55.000 0.00 0.00 0.00 4.85
8764 15134 2.359214 TGTATCGTCTGTGAGATCTGGC 59.641 50.000 0.00 0.00 0.00 4.85
8765 15135 3.004210 CCTGTATCGTCTGTGAGATCTGG 59.996 52.174 0.00 0.00 0.00 3.86
8766 15136 3.629855 ACCTGTATCGTCTGTGAGATCTG 59.370 47.826 0.00 0.00 0.00 2.90
8767 15137 3.892284 ACCTGTATCGTCTGTGAGATCT 58.108 45.455 0.00 0.00 0.00 2.75
8769 15139 5.828328 TGATAACCTGTATCGTCTGTGAGAT 59.172 40.000 0.00 0.00 0.00 2.75
8771 15141 5.500645 TGATAACCTGTATCGTCTGTGAG 57.499 43.478 0.00 0.00 0.00 3.51
8772 15142 4.202020 GCTGATAACCTGTATCGTCTGTGA 60.202 45.833 0.00 0.00 0.00 3.58
8773 15143 4.045104 GCTGATAACCTGTATCGTCTGTG 58.955 47.826 0.00 0.00 0.00 3.66
8774 15144 3.068307 GGCTGATAACCTGTATCGTCTGT 59.932 47.826 0.00 0.00 0.00 3.41
8775 15145 3.553096 GGGCTGATAACCTGTATCGTCTG 60.553 52.174 0.00 0.00 0.00 3.51
8776 15146 2.628657 GGGCTGATAACCTGTATCGTCT 59.371 50.000 0.00 0.00 0.00 4.18
8780 15150 4.530161 AGATCTGGGCTGATAACCTGTATC 59.470 45.833 0.00 0.00 0.00 2.24
8781 15151 4.285517 CAGATCTGGGCTGATAACCTGTAT 59.714 45.833 15.38 0.00 35.39 2.29
8784 15154 2.437281 ACAGATCTGGGCTGATAACCTG 59.563 50.000 26.08 0.00 36.86 4.00
8786 15156 3.643792 AGTACAGATCTGGGCTGATAACC 59.356 47.826 26.08 0.00 36.86 2.85
8788 15158 4.100035 CACAGTACAGATCTGGGCTGATAA 59.900 45.833 34.91 10.71 38.69 1.75
8790 15160 2.433604 CACAGTACAGATCTGGGCTGAT 59.566 50.000 34.91 23.72 38.69 2.90
8791 15161 1.827344 CACAGTACAGATCTGGGCTGA 59.173 52.381 34.91 14.43 38.69 4.26
8792 15162 1.134580 CCACAGTACAGATCTGGGCTG 60.135 57.143 30.44 30.44 40.06 4.85
8794 15164 0.462759 GCCACAGTACAGATCTGGGC 60.463 60.000 26.08 22.00 39.76 5.36
8823 15702 0.387239 GCGATGTTGCCCTTCACAAC 60.387 55.000 0.00 0.00 46.05 3.32
8843 15722 4.988598 CCACAGGCCGTCGCACTT 62.989 66.667 0.00 0.00 36.38 3.16
8858 15737 1.592400 CGTAGTTCTGCGGGTCTCCA 61.592 60.000 2.60 0.00 0.00 3.86
8894 15773 2.747460 GCAGCTTCGGTGGCATGA 60.747 61.111 0.00 0.00 0.00 3.07
8903 15782 4.908156 GCTATGATATTGTTTGCAGCTTCG 59.092 41.667 0.00 0.00 0.00 3.79
8927 15806 2.103042 GCCACTCATCACCGCAGAC 61.103 63.158 0.00 0.00 0.00 3.51
8933 15812 1.521681 GTAGGCGCCACTCATCACC 60.522 63.158 31.54 0.00 0.00 4.02
8946 15825 2.028930 CGGAAGGTGGATATGAGTAGGC 60.029 54.545 0.00 0.00 0.00 3.93
8968 15847 2.866156 GGCTGGCAAAGTTTTGAAAGAC 59.134 45.455 8.70 3.47 40.55 3.01
9015 15901 7.036220 GCAAGCAGTATCTCTGAGTAAACTTA 58.964 38.462 4.32 0.00 46.27 2.24
9081 15967 6.652481 AGAATGAGTAATTTGGTGTCTGACTG 59.348 38.462 9.51 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.