Multiple sequence alignment - TraesCS5B01G338500

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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 TraesCS5B01G338500 chr5B 100.000 9883 0 0 1 9883 522491232 522481350 0.000000e+00 18251.0
1 TraesCS5B01G338500 chr5B 98.666 4949 56 2 3260 8199 158546820 158541873 0.000000e+00 8765.0
2 TraesCS5B01G338500 chr5B 98.343 4949 73 1 3260 8199 287750928 287745980 0.000000e+00 8676.0
3 TraesCS5B01G338500 chr5B 98.974 1072 11 0 1 1072 88747292 88746221 0.000000e+00 1919.0
4 TraesCS5B01G338500 chr5B 96.180 890 29 5 1933 2818 522849390 522850278 0.000000e+00 1450.0
5 TraesCS5B01G338500 chr5B 91.935 744 24 14 8205 8927 522855144 522855872 0.000000e+00 1009.0
6 TraesCS5B01G338500 chr5B 94.695 509 23 4 9377 9883 507931964 507931458 0.000000e+00 787.0
7 TraesCS5B01G338500 chr5B 97.701 435 9 1 2823 3256 522854706 522855140 0.000000e+00 747.0
8 TraesCS5B01G338500 chr5B 86.866 335 29 8 727 1049 710939686 710940017 2.620000e-95 361.0
9 TraesCS5B01G338500 chr5B 88.554 166 11 3 1717 1878 522847303 522847464 2.820000e-45 195.0
10 TraesCS5B01G338500 chr5B 88.312 154 10 3 1076 1222 521276311 521276463 2.840000e-40 178.0
11 TraesCS5B01G338500 chr5B 78.059 237 52 0 8205 8441 137324437 137324201 6.180000e-32 150.0
12 TraesCS5B01G338500 chr5B 90.123 81 8 0 9145 9225 153463047 153463127 1.360000e-18 106.0
13 TraesCS5B01G338500 chr2A 98.768 4950 51 2 3259 8199 43152110 43147162 0.000000e+00 8794.0
14 TraesCS5B01G338500 chr2A 98.646 4949 58 1 3260 8199 758665830 758660882 0.000000e+00 8759.0
15 TraesCS5B01G338500 chr2A 94.898 490 24 1 9395 9883 22156122 22156611 0.000000e+00 765.0
16 TraesCS5B01G338500 chr2B 98.747 4949 52 2 3260 8199 748487835 748482888 0.000000e+00 8787.0
17 TraesCS5B01G338500 chr2B 98.182 4951 64 2 3258 8199 501738989 501734056 0.000000e+00 8621.0
18 TraesCS5B01G338500 chr2B 87.626 695 50 14 405 1066 46235410 46236101 0.000000e+00 774.0
19 TraesCS5B01G338500 chr2B 86.927 436 30 4 1 436 46235065 46235473 1.940000e-126 464.0
20 TraesCS5B01G338500 chr1A 98.747 4949 53 1 3260 8199 72341295 72346243 0.000000e+00 8787.0
21 TraesCS5B01G338500 chr1A 94.549 1064 57 1 1 1064 7828248 7829310 0.000000e+00 1642.0
22 TraesCS5B01G338500 chr1A 93.156 526 33 3 9358 9883 533300835 533300313 0.000000e+00 769.0
23 TraesCS5B01G338500 chr1A 84.444 270 40 2 804 1071 563326321 563326052 2.120000e-66 265.0
24 TraesCS5B01G338500 chr3B 98.687 4949 56 1 3260 8199 191215772 191220720 0.000000e+00 8770.0
25 TraesCS5B01G338500 chr3B 84.441 1806 245 28 3260 5046 615784334 615786122 0.000000e+00 1746.0
26 TraesCS5B01G338500 chr3B 94.183 1083 31 5 4 1076 36016579 36015519 0.000000e+00 1622.0
27 TraesCS5B01G338500 chr3B 100.000 34 0 0 1686 1719 28489199 28489166 8.290000e-06 63.9
28 TraesCS5B01G338500 chr7A 98.589 4962 58 2 3257 8206 20993315 20998276 0.000000e+00 8765.0
29 TraesCS5B01G338500 chr7A 98.666 4949 57 1 3260 8199 570181424 570176476 0.000000e+00 8765.0
30 TraesCS5B01G338500 chr7A 86.409 4959 576 69 3259 8189 646810622 646815510 0.000000e+00 5334.0
31 TraesCS5B01G338500 chr7A 90.183 438 35 6 1 436 12002319 12002750 1.860000e-156 564.0
32 TraesCS5B01G338500 chr7A 89.286 84 9 0 9143 9226 642410584 642410667 1.360000e-18 106.0
33 TraesCS5B01G338500 chr5A 98.609 4959 56 3 3259 8208 657402645 657407599 0.000000e+00 8763.0
34 TraesCS5B01G338500 chr5A 96.915 1329 37 3 1933 3258 546762246 546763573 0.000000e+00 2224.0
35 TraesCS5B01G338500 chr5A 93.413 835 33 8 8205 9023 546845986 546845158 0.000000e+00 1218.0
36 TraesCS5B01G338500 chr5A 90.036 843 51 16 8200 9015 546763570 546764406 0.000000e+00 1061.0
37 TraesCS5B01G338500 chr5A 95.455 572 18 4 2686 3256 546864573 546864009 0.000000e+00 905.0
38 TraesCS5B01G338500 chr5A 90.444 586 40 9 1111 1683 546761486 546762068 0.000000e+00 758.0
39 TraesCS5B01G338500 chr5A 88.774 579 52 7 1110 1681 546880118 546879546 0.000000e+00 697.0
40 TraesCS5B01G338500 chr5A 95.029 342 9 3 1933 2267 546864904 546864564 1.890000e-146 531.0
41 TraesCS5B01G338500 chr5A 92.570 323 15 3 9029 9346 546845106 546844788 1.170000e-123 455.0
42 TraesCS5B01G338500 chr5A 95.631 206 7 1 1715 1918 546762057 546762262 7.400000e-86 329.0
43 TraesCS5B01G338500 chr5A 83.784 259 29 10 1076 1328 680282571 680282822 5.970000e-57 233.0
44 TraesCS5B01G338500 chr5A 92.424 132 6 2 1717 1844 546879553 546879422 1.700000e-42 185.0
45 TraesCS5B01G338500 chr5A 100.000 52 0 0 9029 9080 546764468 546764519 8.170000e-16 97.1
46 TraesCS5B01G338500 chr5A 96.552 58 1 1 1836 1893 546871055 546870999 2.940000e-15 95.3
47 TraesCS5B01G338500 chr5A 100.000 42 0 0 3213 3254 546853875 546853834 2.960000e-10 78.7
48 TraesCS5B01G338500 chr5A 100.000 31 0 0 1076 1106 546880140 546880110 3.860000e-04 58.4
49 TraesCS5B01G338500 chr5A 100.000 30 0 0 1889 1918 546864917 546864888 1.000000e-03 56.5
50 TraesCS5B01G338500 chr2D 86.378 2819 360 13 3360 6173 3955871 3958670 0.000000e+00 3057.0
51 TraesCS5B01G338500 chr2D 89.639 1081 63 15 4 1083 15370416 15369384 0.000000e+00 1330.0
52 TraesCS5B01G338500 chr2D 92.776 526 36 1 9358 9883 592736527 592736004 0.000000e+00 760.0
53 TraesCS5B01G338500 chr5D 93.932 1549 62 21 1717 3258 431789457 431787934 0.000000e+00 2311.0
54 TraesCS5B01G338500 chr5D 93.730 1547 65 21 1717 3258 513316940 513315421 0.000000e+00 2290.0
55 TraesCS5B01G338500 chr5D 96.093 1331 46 6 1933 3258 433676657 433677986 0.000000e+00 2165.0
56 TraesCS5B01G338500 chr5D 92.800 750 28 11 8200 8927 513315424 513314679 0.000000e+00 1062.0
57 TraesCS5B01G338500 chr5D 92.602 757 23 15 8200 8927 431787937 431787185 0.000000e+00 1057.0
58 TraesCS5B01G338500 chr5D 92.091 746 22 16 8200 8927 433677983 433678709 0.000000e+00 1016.0
59 TraesCS5B01G338500 chr5D 83.145 884 104 15 2010 2876 124541886 124541031 0.000000e+00 765.0
60 TraesCS5B01G338500 chr5D 87.912 455 25 11 1 454 551735314 551735739 8.860000e-140 508.0
61 TraesCS5B01G338500 chr5D 88.747 391 43 1 2865 3254 124506235 124505845 2.500000e-130 477.0
62 TraesCS5B01G338500 chr5D 93.651 126 4 1 1717 1842 433676491 433676612 1.700000e-42 185.0
63 TraesCS5B01G338500 chr5D 93.590 78 5 0 1215 1292 513317303 513317226 6.270000e-22 117.0
64 TraesCS5B01G338500 chr5D 80.000 115 23 0 9140 9254 496276995 496277109 1.770000e-12 86.1
65 TraesCS5B01G338500 chr1B 89.030 1659 173 8 3258 4911 651443405 651445059 0.000000e+00 2047.0
66 TraesCS5B01G338500 chr1B 79.639 388 72 6 2866 3249 671225887 671226271 1.260000e-68 272.0
67 TraesCS5B01G338500 chr1B 87.069 232 23 5 1391 1615 58253060 58253291 1.270000e-63 255.0
68 TraesCS5B01G338500 chr1B 86.638 232 24 5 1391 1615 252161659 252161890 5.930000e-62 250.0
69 TraesCS5B01G338500 chr1B 86.638 232 24 5 1391 1615 505094476 505094245 5.930000e-62 250.0
70 TraesCS5B01G338500 chr1B 100.000 34 0 0 1686 1719 622626373 622626406 8.290000e-06 63.9
71 TraesCS5B01G338500 chr7D 86.169 1822 228 15 3274 5085 528047786 528049593 0.000000e+00 1947.0
72 TraesCS5B01G338500 chr7B 98.794 1078 11 1 1 1076 657320251 657319174 0.000000e+00 1917.0
73 TraesCS5B01G338500 chr7B 94.095 779 23 4 4 781 684762138 684761382 0.000000e+00 1162.0
74 TraesCS5B01G338500 chr7B 100.000 34 0 0 1686 1719 251316112 251316145 8.290000e-06 63.9
75 TraesCS5B01G338500 chr3D 91.489 1081 58 4 5 1076 18128029 18126974 0.000000e+00 1456.0
76 TraesCS5B01G338500 chr4A 83.225 1079 115 31 6 1072 731499687 731498663 0.000000e+00 929.0
77 TraesCS5B01G338500 chr4A 95.066 527 23 3 9358 9883 605028774 605029298 0.000000e+00 826.0
78 TraesCS5B01G338500 chr4A 90.588 85 8 0 9141 9225 744432969 744432885 8.110000e-21 113.0
79 TraesCS5B01G338500 chr4A 100.000 34 0 0 1686 1719 3118327 3118294 8.290000e-06 63.9
80 TraesCS5B01G338500 chr6B 96.395 527 19 0 9357 9883 101662231 101662757 0.000000e+00 869.0
81 TraesCS5B01G338500 chr6B 86.957 230 23 5 1392 1615 604083298 604083526 1.650000e-62 252.0
82 TraesCS5B01G338500 chr6B 86.383 235 25 5 1388 1615 290212536 290212302 5.930000e-62 250.0
83 TraesCS5B01G338500 chr6B 93.478 46 3 0 1674 1719 527580144 527580189 1.780000e-07 69.4
84 TraesCS5B01G338500 chr6D 95.652 529 23 0 9355 9883 428955267 428954739 0.000000e+00 850.0
85 TraesCS5B01G338500 chr6D 79.646 113 23 0 9142 9254 170566571 170566683 2.290000e-11 82.4
86 TraesCS5B01G338500 chr6D 79.646 113 23 0 9142 9254 455779342 455779454 2.290000e-11 82.4
87 TraesCS5B01G338500 chr6A 95.247 526 24 1 9358 9883 573037610 573038134 0.000000e+00 832.0
88 TraesCS5B01G338500 chr6A 98.182 165 2 1 8039 8203 40587384 40587221 4.520000e-73 287.0
89 TraesCS5B01G338500 chr3A 94.707 529 23 4 9358 9883 742922012 742921486 0.000000e+00 817.0
90 TraesCS5B01G338500 chr3A 87.013 231 23 3 1392 1615 12408996 12408766 4.580000e-63 254.0
91 TraesCS5B01G338500 chr4B 85.714 252 28 7 1080 1327 502241781 502241534 9.850000e-65 259.0
92 TraesCS5B01G338500 chr4B 97.297 37 1 0 1683 1719 490653877 490653913 8.290000e-06 63.9
93 TraesCS5B01G338500 chr1D 87.446 231 22 4 1392 1615 408713681 408713911 9.850000e-65 259.0
94 TraesCS5B01G338500 chr1D 75.350 357 69 10 2867 3208 481168821 481168469 4.780000e-33 154.0
95 TraesCS5B01G338500 chr4D 86.555 119 16 0 9146 9264 493933618 493933500 2.240000e-26 132.0
96 TraesCS5B01G338500 chrUn 79.310 116 24 0 9142 9257 10940567 10940452 2.290000e-11 82.4


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 TraesCS5B01G338500 chr5B 522481350 522491232 9882 True 18251.000000 18251 100.000000 1 9883 1 chr5B.!!$R6 9882
1 TraesCS5B01G338500 chr5B 158541873 158546820 4947 True 8765.000000 8765 98.666000 3260 8199 1 chr5B.!!$R3 4939
2 TraesCS5B01G338500 chr5B 287745980 287750928 4948 True 8676.000000 8676 98.343000 3260 8199 1 chr5B.!!$R4 4939
3 TraesCS5B01G338500 chr5B 88746221 88747292 1071 True 1919.000000 1919 98.974000 1 1072 1 chr5B.!!$R1 1071
4 TraesCS5B01G338500 chr5B 522854706 522855872 1166 False 878.000000 1009 94.818000 2823 8927 2 chr5B.!!$F5 6104
5 TraesCS5B01G338500 chr5B 522847303 522850278 2975 False 822.500000 1450 92.367000 1717 2818 2 chr5B.!!$F4 1101
6 TraesCS5B01G338500 chr5B 507931458 507931964 506 True 787.000000 787 94.695000 9377 9883 1 chr5B.!!$R5 506
7 TraesCS5B01G338500 chr2A 43147162 43152110 4948 True 8794.000000 8794 98.768000 3259 8199 1 chr2A.!!$R1 4940
8 TraesCS5B01G338500 chr2A 758660882 758665830 4948 True 8759.000000 8759 98.646000 3260 8199 1 chr2A.!!$R2 4939
9 TraesCS5B01G338500 chr2B 748482888 748487835 4947 True 8787.000000 8787 98.747000 3260 8199 1 chr2B.!!$R2 4939
10 TraesCS5B01G338500 chr2B 501734056 501738989 4933 True 8621.000000 8621 98.182000 3258 8199 1 chr2B.!!$R1 4941
11 TraesCS5B01G338500 chr2B 46235065 46236101 1036 False 619.000000 774 87.276500 1 1066 2 chr2B.!!$F1 1065
12 TraesCS5B01G338500 chr1A 72341295 72346243 4948 False 8787.000000 8787 98.747000 3260 8199 1 chr1A.!!$F2 4939
13 TraesCS5B01G338500 chr1A 7828248 7829310 1062 False 1642.000000 1642 94.549000 1 1064 1 chr1A.!!$F1 1063
14 TraesCS5B01G338500 chr1A 533300313 533300835 522 True 769.000000 769 93.156000 9358 9883 1 chr1A.!!$R1 525
15 TraesCS5B01G338500 chr3B 191215772 191220720 4948 False 8770.000000 8770 98.687000 3260 8199 1 chr3B.!!$F1 4939
16 TraesCS5B01G338500 chr3B 615784334 615786122 1788 False 1746.000000 1746 84.441000 3260 5046 1 chr3B.!!$F2 1786
17 TraesCS5B01G338500 chr3B 36015519 36016579 1060 True 1622.000000 1622 94.183000 4 1076 1 chr3B.!!$R2 1072
18 TraesCS5B01G338500 chr7A 20993315 20998276 4961 False 8765.000000 8765 98.589000 3257 8206 1 chr7A.!!$F2 4949
19 TraesCS5B01G338500 chr7A 570176476 570181424 4948 True 8765.000000 8765 98.666000 3260 8199 1 chr7A.!!$R1 4939
20 TraesCS5B01G338500 chr7A 646810622 646815510 4888 False 5334.000000 5334 86.409000 3259 8189 1 chr7A.!!$F4 4930
21 TraesCS5B01G338500 chr5A 657402645 657407599 4954 False 8763.000000 8763 98.609000 3259 8208 1 chr5A.!!$F1 4949
22 TraesCS5B01G338500 chr5A 546761486 546764519 3033 False 893.820000 2224 94.605200 1111 9080 5 chr5A.!!$F3 7969
23 TraesCS5B01G338500 chr5A 546844788 546845986 1198 True 836.500000 1218 92.991500 8205 9346 2 chr5A.!!$R3 1141
24 TraesCS5B01G338500 chr5A 546864009 546864917 908 True 497.500000 905 96.828000 1889 3256 3 chr5A.!!$R4 1367
25 TraesCS5B01G338500 chr5A 546879422 546880140 718 True 313.466667 697 93.732667 1076 1844 3 chr5A.!!$R5 768
26 TraesCS5B01G338500 chr2D 3955871 3958670 2799 False 3057.000000 3057 86.378000 3360 6173 1 chr2D.!!$F1 2813
27 TraesCS5B01G338500 chr2D 15369384 15370416 1032 True 1330.000000 1330 89.639000 4 1083 1 chr2D.!!$R1 1079
28 TraesCS5B01G338500 chr2D 592736004 592736527 523 True 760.000000 760 92.776000 9358 9883 1 chr2D.!!$R2 525
29 TraesCS5B01G338500 chr5D 431787185 431789457 2272 True 1684.000000 2311 93.267000 1717 8927 2 chr5D.!!$R3 7210
30 TraesCS5B01G338500 chr5D 513314679 513317303 2624 True 1156.333333 2290 93.373333 1215 8927 3 chr5D.!!$R4 7712
31 TraesCS5B01G338500 chr5D 433676491 433678709 2218 False 1122.000000 2165 93.945000 1717 8927 3 chr5D.!!$F3 7210
32 TraesCS5B01G338500 chr5D 124541031 124541886 855 True 765.000000 765 83.145000 2010 2876 1 chr5D.!!$R2 866
33 TraesCS5B01G338500 chr1B 651443405 651445059 1654 False 2047.000000 2047 89.030000 3258 4911 1 chr1B.!!$F4 1653
34 TraesCS5B01G338500 chr7D 528047786 528049593 1807 False 1947.000000 1947 86.169000 3274 5085 1 chr7D.!!$F1 1811
35 TraesCS5B01G338500 chr7B 657319174 657320251 1077 True 1917.000000 1917 98.794000 1 1076 1 chr7B.!!$R1 1075
36 TraesCS5B01G338500 chr7B 684761382 684762138 756 True 1162.000000 1162 94.095000 4 781 1 chr7B.!!$R2 777
37 TraesCS5B01G338500 chr3D 18126974 18128029 1055 True 1456.000000 1456 91.489000 5 1076 1 chr3D.!!$R1 1071
38 TraesCS5B01G338500 chr4A 731498663 731499687 1024 True 929.000000 929 83.225000 6 1072 1 chr4A.!!$R2 1066
39 TraesCS5B01G338500 chr4A 605028774 605029298 524 False 826.000000 826 95.066000 9358 9883 1 chr4A.!!$F1 525
40 TraesCS5B01G338500 chr6B 101662231 101662757 526 False 869.000000 869 96.395000 9357 9883 1 chr6B.!!$F1 526
41 TraesCS5B01G338500 chr6D 428954739 428955267 528 True 850.000000 850 95.652000 9355 9883 1 chr6D.!!$R1 528
42 TraesCS5B01G338500 chr6A 573037610 573038134 524 False 832.000000 832 95.247000 9358 9883 1 chr6A.!!$F1 525
43 TraesCS5B01G338500 chr3A 742921486 742922012 526 True 817.000000 817 94.707000 9358 9883 1 chr3A.!!$R2 525

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
887 951 2.503061 CCTACCTCGCTGCTGCAT 59.497 61.111 16.29 0.47 39.64 3.96 F
1415 1489 1.411216 CCCTCCGCCCTTAAGAGAGTA 60.411 57.143 3.36 0.00 0.00 2.59 F
1706 1869 1.352352 ACTTGGCATGAGTGGTAAGCT 59.648 47.619 7.45 0.00 0.00 3.74 F
2986 5086 0.246635 CCGTCATCCAGGACTCGTTT 59.753 55.000 0.00 0.00 35.63 3.60 F
3504 5628 1.134280 CATCGTCTCCATGGCTTCCTT 60.134 52.381 6.96 0.00 0.00 3.36 F
5095 7247 1.673168 GGCCAGCTCCTATTTCAGTG 58.327 55.000 0.00 0.00 0.00 3.66 F
5382 7534 3.782046 AGCACCGTCACATAGTTGATAC 58.218 45.455 0.00 0.00 0.00 2.24 F
6302 8475 1.827789 GCCACACCAGAAGCCACAA 60.828 57.895 0.00 0.00 0.00 3.33 F
6322 8495 0.035317 GATCCCCTGCGCATATGACA 59.965 55.000 12.24 2.70 0.00 3.58 F
6675 8851 1.466856 GCAGATGGCTCCATTGACAA 58.533 50.000 2.53 0.00 40.25 3.18 F
6720 8896 3.681593 AGGGCTTTAAGCAACGTTATGA 58.318 40.909 19.10 0.00 44.75 2.15 F
8651 10854 1.285023 GAGCAACAGCAGCAACAGG 59.715 57.895 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1852 1.905894 TGTAGCTTACCACTCATGCCA 59.094 47.619 0.00 0.00 0.00 4.92 R
2759 4858 2.882927 ACAGCGTGTAGTTGTCTTGA 57.117 45.000 0.00 0.00 40.36 3.02 R
3616 5740 1.302832 GGTGTTGTCCAGGAGCCTG 60.303 63.158 9.59 9.59 43.26 4.85 R
4524 6657 1.482593 CTCCATTGTACTTCTCCCGCT 59.517 52.381 0.00 0.00 0.00 5.52 R
5382 7534 2.700773 GCTAACAAGGCAAGCCCCG 61.701 63.158 7.62 1.40 36.58 5.73 R
6302 8475 0.322975 GTCATATGCGCAGGGGATCT 59.677 55.000 18.32 0.00 0.00 2.75 R
6322 8495 3.489355 TGATGCAGTGGACTGATTTGTT 58.511 40.909 11.06 0.00 46.59 2.83 R
8179 10372 4.259970 CCACTGAAAGATATGAAGCGTTCG 60.260 45.833 0.00 0.00 37.43 3.95 R
8482 10684 2.274760 CGTACTCCCTCCGGTCCT 59.725 66.667 0.00 0.00 0.00 3.85 R
8647 10850 2.203252 CTGTGCCTGTGTGCCTGT 60.203 61.111 0.00 0.00 0.00 4.00 R
8742 10961 4.275443 AGACGTAGAAATCGGTGGTATCTC 59.725 45.833 0.00 0.00 0.00 2.75 R
9572 11851 2.240918 ACCAGGGCCACATCCATGT 61.241 57.895 6.18 0.00 42.84 3.21 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
887 951 2.503061 CCTACCTCGCTGCTGCAT 59.497 61.111 16.29 0.47 39.64 3.96
1110 1183 7.294676 TGCAATGCACGTCTAATCATATATC 57.705 36.000 2.72 0.00 31.71 1.63
1111 1184 7.099120 TGCAATGCACGTCTAATCATATATCT 58.901 34.615 2.72 0.00 31.71 1.98
1112 1185 8.250332 TGCAATGCACGTCTAATCATATATCTA 58.750 33.333 2.72 0.00 31.71 1.98
1113 1186 9.087424 GCAATGCACGTCTAATCATATATCTAA 57.913 33.333 0.00 0.00 0.00 2.10
1180 1253 2.026641 CCCCAACCTGAACATATGCTG 58.973 52.381 1.58 0.00 0.00 4.41
1189 1262 5.070981 ACCTGAACATATGCTGCTACAGTAT 59.929 40.000 1.58 3.69 39.84 2.12
1241 1315 6.793478 AGAGCCATTTATATGCCCAAATCTA 58.207 36.000 0.00 0.00 0.00 1.98
1351 1425 3.284617 TGCAAGACTTGATGGATCATGG 58.715 45.455 19.51 0.00 36.56 3.66
1357 1431 4.291513 AGACTTGATGGATCATGGGCATAT 59.708 41.667 0.00 0.00 36.56 1.78
1415 1489 1.411216 CCCTCCGCCCTTAAGAGAGTA 60.411 57.143 3.36 0.00 0.00 2.59
1550 1706 9.890629 AGTCTAATGCTACTAATTTGATGTCAA 57.109 29.630 0.00 0.00 0.00 3.18
1677 1840 9.975218 AGTATAACTCCCTAACAATCAACAAAT 57.025 29.630 0.00 0.00 0.00 2.32
1693 1856 9.941325 AATCAACAAATTATTTATCACTTGGCA 57.059 25.926 0.00 0.00 0.00 4.92
1695 1858 9.368674 TCAACAAATTATTTATCACTTGGCATG 57.631 29.630 0.00 0.00 0.00 4.06
1696 1859 9.368674 CAACAAATTATTTATCACTTGGCATGA 57.631 29.630 7.45 0.00 0.00 3.07
1697 1860 9.590451 AACAAATTATTTATCACTTGGCATGAG 57.410 29.630 7.45 0.00 0.00 2.90
1698 1861 8.752187 ACAAATTATTTATCACTTGGCATGAGT 58.248 29.630 7.45 0.00 0.00 3.41
1699 1862 9.027129 CAAATTATTTATCACTTGGCATGAGTG 57.973 33.333 12.16 12.16 44.54 3.51
1700 1863 6.698008 TTATTTATCACTTGGCATGAGTGG 57.302 37.500 16.96 2.09 43.61 4.00
1701 1864 3.719268 TTATCACTTGGCATGAGTGGT 57.281 42.857 16.96 13.52 43.61 4.16
1702 1865 4.835284 TTATCACTTGGCATGAGTGGTA 57.165 40.909 16.96 12.60 43.61 3.25
1703 1866 3.719268 ATCACTTGGCATGAGTGGTAA 57.281 42.857 16.96 1.45 43.61 2.85
1704 1867 3.057969 TCACTTGGCATGAGTGGTAAG 57.942 47.619 16.96 0.00 43.61 2.34
1705 1868 1.470098 CACTTGGCATGAGTGGTAAGC 59.530 52.381 10.79 0.00 40.58 3.09
1706 1869 1.352352 ACTTGGCATGAGTGGTAAGCT 59.648 47.619 7.45 0.00 0.00 3.74
1707 1870 2.571653 ACTTGGCATGAGTGGTAAGCTA 59.428 45.455 7.45 0.00 0.00 3.32
1708 1871 2.691409 TGGCATGAGTGGTAAGCTAC 57.309 50.000 0.00 0.00 0.00 3.58
1709 1872 1.905894 TGGCATGAGTGGTAAGCTACA 59.094 47.619 0.00 0.00 0.00 2.74
1710 1873 2.505407 TGGCATGAGTGGTAAGCTACAT 59.495 45.455 0.00 0.00 0.00 2.29
1711 1874 3.134458 GGCATGAGTGGTAAGCTACATC 58.866 50.000 0.00 0.00 0.00 3.06
1712 1875 3.432186 GGCATGAGTGGTAAGCTACATCA 60.432 47.826 0.00 0.00 0.00 3.07
1713 1876 4.191544 GCATGAGTGGTAAGCTACATCAA 58.808 43.478 0.00 0.00 0.00 2.57
1714 1877 4.635765 GCATGAGTGGTAAGCTACATCAAA 59.364 41.667 0.00 0.00 0.00 2.69
1715 1878 5.123820 GCATGAGTGGTAAGCTACATCAAAA 59.876 40.000 0.00 0.00 0.00 2.44
1883 2059 2.722188 GCACGCACGCACAAAGTC 60.722 61.111 0.00 0.00 0.00 3.01
1918 3992 7.426929 ACTAATTAATCATGATTCGGTGCTC 57.573 36.000 23.95 0.00 32.50 4.26
1919 3993 6.992123 ACTAATTAATCATGATTCGGTGCTCA 59.008 34.615 23.95 1.65 32.50 4.26
1920 3994 5.936686 ATTAATCATGATTCGGTGCTCAG 57.063 39.130 23.95 0.00 32.50 3.35
1921 3995 2.996249 ATCATGATTCGGTGCTCAGT 57.004 45.000 1.18 0.00 0.00 3.41
1922 3996 2.768253 TCATGATTCGGTGCTCAGTT 57.232 45.000 0.00 0.00 0.00 3.16
1923 3997 2.621338 TCATGATTCGGTGCTCAGTTC 58.379 47.619 0.00 0.00 0.00 3.01
1924 3998 2.028203 TCATGATTCGGTGCTCAGTTCA 60.028 45.455 0.00 0.00 0.00 3.18
1925 3999 2.542020 TGATTCGGTGCTCAGTTCAA 57.458 45.000 0.00 0.00 0.00 2.69
1926 4000 2.844946 TGATTCGGTGCTCAGTTCAAA 58.155 42.857 0.00 0.00 0.00 2.69
1927 4001 3.210227 TGATTCGGTGCTCAGTTCAAAA 58.790 40.909 0.00 0.00 0.00 2.44
1928 4002 3.629855 TGATTCGGTGCTCAGTTCAAAAA 59.370 39.130 0.00 0.00 0.00 1.94
1959 4035 8.185003 TCATGATTCGGTGCTATATTAAATCG 57.815 34.615 0.00 0.00 0.00 3.34
1964 4040 6.525578 TCGGTGCTATATTAAATCGGATCT 57.474 37.500 0.00 0.00 0.00 2.75
2032 4115 1.661112 CATCGGAGAAAGAAGGCGAAC 59.339 52.381 0.00 0.00 43.58 3.95
2759 4858 2.043852 ATCCTGCTCTCCGACGGT 60.044 61.111 14.79 0.00 0.00 4.83
2986 5086 0.246635 CCGTCATCCAGGACTCGTTT 59.753 55.000 0.00 0.00 35.63 3.60
3504 5628 1.134280 CATCGTCTCCATGGCTTCCTT 60.134 52.381 6.96 0.00 0.00 3.36
3945 6069 3.738982 TGGCGAAGATGAAAAGTCTTGA 58.261 40.909 0.00 0.00 36.13 3.02
4814 6951 4.735369 AGGACTCTACCCACTCATATCAG 58.265 47.826 0.00 0.00 0.00 2.90
4885 7037 4.471386 ACCAAGCTATCTACATCAAGGTGT 59.529 41.667 0.00 0.00 36.13 4.16
5095 7247 1.673168 GGCCAGCTCCTATTTCAGTG 58.327 55.000 0.00 0.00 0.00 3.66
5283 7435 9.016438 GGGTGGTGAGTATGAAAAACTAAATTA 57.984 33.333 0.00 0.00 0.00 1.40
5382 7534 3.782046 AGCACCGTCACATAGTTGATAC 58.218 45.455 0.00 0.00 0.00 2.24
5841 7993 6.128227 GGCGACAACAATTGTACTAACCAATA 60.128 38.462 12.39 0.00 45.52 1.90
6302 8475 1.827789 GCCACACCAGAAGCCACAA 60.828 57.895 0.00 0.00 0.00 3.33
6322 8495 0.035317 GATCCCCTGCGCATATGACA 59.965 55.000 12.24 2.70 0.00 3.58
6418 8594 1.614903 TCTTCACGTGTTATGACCCGT 59.385 47.619 16.51 0.00 40.52 5.28
6675 8851 1.466856 GCAGATGGCTCCATTGACAA 58.533 50.000 2.53 0.00 40.25 3.18
6720 8896 3.681593 AGGGCTTTAAGCAACGTTATGA 58.318 40.909 19.10 0.00 44.75 2.15
7234 9410 9.295825 ACTCAAGATGGTATTGTGTTAAATCAA 57.704 29.630 0.00 0.00 32.14 2.57
7760 9936 7.890127 AGATCATTTGGGTTGAATCACTTCTTA 59.110 33.333 0.00 0.00 32.29 2.10
8200 10393 4.495422 ACGAACGCTTCATATCTTTCAGT 58.505 39.130 0.00 0.00 0.00 3.41
8647 10850 1.501337 CTCGTGAGCAACAGCAGCAA 61.501 55.000 0.00 0.00 0.00 3.91
8651 10854 1.285023 GAGCAACAGCAGCAACAGG 59.715 57.895 0.00 0.00 0.00 4.00
8742 10961 0.895530 TCGCTAAGAACCTGGTGAGG 59.104 55.000 0.00 0.00 46.21 3.86
8862 11082 3.873529 GTGAACTTGCACGGTCTTTTAG 58.126 45.455 9.89 0.00 0.00 1.85
8866 11086 5.992829 TGAACTTGCACGGTCTTTTAGATTA 59.007 36.000 9.89 0.00 0.00 1.75
8940 11167 8.809066 AGGTTTACAGTTTGGTTCTAAAAGTTT 58.191 29.630 0.00 0.00 0.00 2.66
9023 11252 8.792831 ATTACTACTGTATTTATGGAACGTCG 57.207 34.615 0.00 0.00 0.00 5.12
9024 11253 6.199937 ACTACTGTATTTATGGAACGTCGT 57.800 37.500 0.00 0.00 0.00 4.34
9027 11256 5.338365 ACTGTATTTATGGAACGTCGTCTC 58.662 41.667 0.00 0.00 0.00 3.36
9083 11358 3.657956 CTCACCGAGAGCCTCAATC 57.342 57.895 0.00 0.00 37.59 2.67
9084 11359 0.820226 CTCACCGAGAGCCTCAATCA 59.180 55.000 0.00 0.00 37.59 2.57
9085 11360 1.205655 CTCACCGAGAGCCTCAATCAA 59.794 52.381 0.00 0.00 37.59 2.57
9141 11416 0.179081 GGCGGCTAGGGTAACTCTTG 60.179 60.000 0.00 0.00 0.00 3.02
9164 11439 6.243148 TGGAGTAAAGTCTGAAATAAACCCC 58.757 40.000 0.00 0.00 0.00 4.95
9165 11440 6.183361 TGGAGTAAAGTCTGAAATAAACCCCA 60.183 38.462 0.00 0.00 0.00 4.96
9182 11457 1.439679 CCAACTTTGTAGAGGCCGAC 58.560 55.000 0.00 0.00 0.00 4.79
9183 11458 1.270625 CCAACTTTGTAGAGGCCGACA 60.271 52.381 0.00 0.00 0.00 4.35
9184 11459 1.798813 CAACTTTGTAGAGGCCGACAC 59.201 52.381 7.58 2.55 0.00 3.67
9202 11477 3.636764 GACACAAATGAACCCTCACCTTT 59.363 43.478 0.00 0.00 33.30 3.11
9239 11514 2.350863 ACCCTGACCTCTTTGATCCT 57.649 50.000 0.00 0.00 0.00 3.24
9258 11533 8.195165 TGATCCTGGTCTATTCTAACCTTATG 57.805 38.462 0.00 0.00 36.47 1.90
9273 11548 0.887247 TTATGCATGTTTGGCGCACT 59.113 45.000 10.83 0.00 38.73 4.40
9277 11552 1.659233 CATGTTTGGCGCACTGGAA 59.341 52.632 10.83 0.00 0.00 3.53
9304 11583 1.818674 ACAATTCAAGGCGGGTTCATC 59.181 47.619 0.00 0.00 0.00 2.92
9328 11607 3.464907 CTGCTCTCACTGACATTATGGG 58.535 50.000 0.00 0.00 0.00 4.00
9343 11622 4.563140 TTATGGGTCCACAAGTTAGTCC 57.437 45.455 0.00 0.00 0.00 3.85
9344 11623 2.112279 TGGGTCCACAAGTTAGTCCT 57.888 50.000 0.00 0.00 0.00 3.85
9345 11624 1.975680 TGGGTCCACAAGTTAGTCCTC 59.024 52.381 0.00 0.00 0.00 3.71
9347 11626 2.258109 GGTCCACAAGTTAGTCCTCCT 58.742 52.381 0.00 0.00 0.00 3.69
9348 11627 2.234168 GGTCCACAAGTTAGTCCTCCTC 59.766 54.545 0.00 0.00 0.00 3.71
9349 11628 3.166679 GTCCACAAGTTAGTCCTCCTCT 58.833 50.000 0.00 0.00 0.00 3.69
9350 11629 4.342359 GTCCACAAGTTAGTCCTCCTCTA 58.658 47.826 0.00 0.00 0.00 2.43
9351 11630 4.957327 GTCCACAAGTTAGTCCTCCTCTAT 59.043 45.833 0.00 0.00 0.00 1.98
9352 11631 5.068067 GTCCACAAGTTAGTCCTCCTCTATC 59.932 48.000 0.00 0.00 0.00 2.08
9353 11632 4.342665 CCACAAGTTAGTCCTCCTCTATCC 59.657 50.000 0.00 0.00 0.00 2.59
9365 11644 3.315596 TCCTCTATCCTCTCACTACCGA 58.684 50.000 0.00 0.00 0.00 4.69
9572 11851 2.048444 AGGCATAGTTAGGTCGTCGA 57.952 50.000 0.00 0.00 0.00 4.20
9576 11855 3.043586 GCATAGTTAGGTCGTCGACATG 58.956 50.000 25.64 18.99 33.68 3.21
9617 11896 3.291101 GACAGACGGCGGGCTAACA 62.291 63.158 13.24 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1112 1185 9.970395 ATGCGTTTTCACATATGATTAATGATT 57.030 25.926 10.38 0.00 33.85 2.57
1113 1186 9.401873 CATGCGTTTTCACATATGATTAATGAT 57.598 29.630 10.38 0.00 33.85 2.45
1114 1187 8.404765 ACATGCGTTTTCACATATGATTAATGA 58.595 29.630 10.38 0.00 33.85 2.57
1115 1188 8.564648 ACATGCGTTTTCACATATGATTAATG 57.435 30.769 10.38 4.90 33.85 1.90
1330 1404 3.284617 CCATGATCCATCAAGTCTTGCA 58.715 45.455 7.78 0.00 40.69 4.08
1332 1406 2.621998 GCCCATGATCCATCAAGTCTTG 59.378 50.000 6.21 6.21 40.69 3.02
1351 1425 3.625764 TCTTTACAACGAAGCCATATGCC 59.374 43.478 0.00 0.00 42.71 4.40
1357 1431 3.311322 CACAGTTCTTTACAACGAAGCCA 59.689 43.478 0.00 0.00 0.00 4.75
1443 1517 6.650807 ACAAACTCGATCAAGCTTTGAGATAA 59.349 34.615 17.12 2.33 43.98 1.75
1673 1836 9.027129 CACTCATGCCAAGTGATAAATAATTTG 57.973 33.333 7.13 0.00 45.64 2.32
1674 1837 8.199449 CCACTCATGCCAAGTGATAAATAATTT 58.801 33.333 13.20 0.00 45.64 1.82
1675 1838 7.342799 ACCACTCATGCCAAGTGATAAATAATT 59.657 33.333 13.20 0.00 45.64 1.40
1676 1839 6.835488 ACCACTCATGCCAAGTGATAAATAAT 59.165 34.615 13.20 0.00 45.64 1.28
1677 1840 6.186957 ACCACTCATGCCAAGTGATAAATAA 58.813 36.000 13.20 0.00 45.64 1.40
1678 1841 5.754782 ACCACTCATGCCAAGTGATAAATA 58.245 37.500 13.20 0.00 45.64 1.40
1679 1842 4.603131 ACCACTCATGCCAAGTGATAAAT 58.397 39.130 13.20 0.00 45.64 1.40
1680 1843 4.032960 ACCACTCATGCCAAGTGATAAA 57.967 40.909 13.20 0.00 45.64 1.40
1681 1844 3.719268 ACCACTCATGCCAAGTGATAA 57.281 42.857 13.20 0.00 45.64 1.75
1682 1845 4.769688 CTTACCACTCATGCCAAGTGATA 58.230 43.478 13.20 0.00 45.64 2.15
1683 1846 3.614092 CTTACCACTCATGCCAAGTGAT 58.386 45.455 13.20 0.37 45.64 3.06
1684 1847 2.875672 GCTTACCACTCATGCCAAGTGA 60.876 50.000 13.20 0.00 45.64 3.41
1685 1848 1.470098 GCTTACCACTCATGCCAAGTG 59.530 52.381 6.14 6.14 43.04 3.16
1686 1849 1.352352 AGCTTACCACTCATGCCAAGT 59.648 47.619 0.00 0.00 0.00 3.16
1687 1850 2.119801 AGCTTACCACTCATGCCAAG 57.880 50.000 0.00 0.00 0.00 3.61
1688 1851 2.304470 TGTAGCTTACCACTCATGCCAA 59.696 45.455 0.00 0.00 0.00 4.52
1689 1852 1.905894 TGTAGCTTACCACTCATGCCA 59.094 47.619 0.00 0.00 0.00 4.92
1690 1853 2.691409 TGTAGCTTACCACTCATGCC 57.309 50.000 0.00 0.00 0.00 4.40
1691 1854 3.797039 TGATGTAGCTTACCACTCATGC 58.203 45.455 0.00 0.00 0.00 4.06
1692 1855 6.149308 TGTTTTGATGTAGCTTACCACTCATG 59.851 38.462 0.00 0.00 0.00 3.07
1693 1856 6.237901 TGTTTTGATGTAGCTTACCACTCAT 58.762 36.000 0.00 0.00 0.00 2.90
1694 1857 5.616270 TGTTTTGATGTAGCTTACCACTCA 58.384 37.500 0.00 0.00 0.00 3.41
1695 1858 6.554334 TTGTTTTGATGTAGCTTACCACTC 57.446 37.500 0.00 0.00 0.00 3.51
1696 1859 6.952773 TTTGTTTTGATGTAGCTTACCACT 57.047 33.333 0.00 0.00 0.00 4.00
1697 1860 9.855021 ATAATTTGTTTTGATGTAGCTTACCAC 57.145 29.630 0.00 0.00 0.00 4.16
1702 1865 9.995003 TGGAAATAATTTGTTTTGATGTAGCTT 57.005 25.926 0.00 0.00 0.00 3.74
1703 1866 9.423061 GTGGAAATAATTTGTTTTGATGTAGCT 57.577 29.630 0.00 0.00 0.00 3.32
1704 1867 8.372521 CGTGGAAATAATTTGTTTTGATGTAGC 58.627 33.333 0.00 0.00 0.00 3.58
1705 1868 8.859156 CCGTGGAAATAATTTGTTTTGATGTAG 58.141 33.333 0.00 0.00 0.00 2.74
1706 1869 8.361139 ACCGTGGAAATAATTTGTTTTGATGTA 58.639 29.630 0.00 0.00 0.00 2.29
1707 1870 7.170658 CACCGTGGAAATAATTTGTTTTGATGT 59.829 33.333 0.00 0.00 0.00 3.06
1708 1871 7.359933 CCACCGTGGAAATAATTTGTTTTGATG 60.360 37.037 12.68 0.00 40.96 3.07
1709 1872 6.648725 CCACCGTGGAAATAATTTGTTTTGAT 59.351 34.615 12.68 0.00 40.96 2.57
1710 1873 5.986135 CCACCGTGGAAATAATTTGTTTTGA 59.014 36.000 12.68 0.00 40.96 2.69
1711 1874 5.986135 TCCACCGTGGAAATAATTTGTTTTG 59.014 36.000 18.34 0.00 45.00 2.44
1712 1875 6.163135 TCCACCGTGGAAATAATTTGTTTT 57.837 33.333 18.34 0.00 45.00 2.43
1713 1876 5.793030 TCCACCGTGGAAATAATTTGTTT 57.207 34.783 18.34 0.00 45.00 2.83
1933 4007 8.820933 CGATTTAATATAGCACCGAATCATGAT 58.179 33.333 1.18 1.18 0.00 2.45
1934 4008 7.277760 CCGATTTAATATAGCACCGAATCATGA 59.722 37.037 0.00 0.00 0.00 3.07
1935 4009 7.277760 TCCGATTTAATATAGCACCGAATCATG 59.722 37.037 0.00 0.00 0.00 3.07
1936 4010 7.327975 TCCGATTTAATATAGCACCGAATCAT 58.672 34.615 0.00 0.00 0.00 2.45
1937 4011 6.693466 TCCGATTTAATATAGCACCGAATCA 58.307 36.000 0.00 0.00 0.00 2.57
1938 4012 7.707035 AGATCCGATTTAATATAGCACCGAATC 59.293 37.037 0.00 0.00 0.00 2.52
1939 4013 7.556844 AGATCCGATTTAATATAGCACCGAAT 58.443 34.615 0.00 0.00 0.00 3.34
1940 4014 6.931838 AGATCCGATTTAATATAGCACCGAA 58.068 36.000 0.00 0.00 0.00 4.30
1941 4015 6.152154 TGAGATCCGATTTAATATAGCACCGA 59.848 38.462 0.00 0.00 0.00 4.69
1942 4016 6.253727 GTGAGATCCGATTTAATATAGCACCG 59.746 42.308 0.00 0.00 0.00 4.94
1943 4017 7.097192 TGTGAGATCCGATTTAATATAGCACC 58.903 38.462 0.00 0.00 0.00 5.01
1944 4018 7.201478 GCTGTGAGATCCGATTTAATATAGCAC 60.201 40.741 0.00 0.00 0.00 4.40
1945 4019 6.813649 GCTGTGAGATCCGATTTAATATAGCA 59.186 38.462 0.00 0.00 0.00 3.49
1946 4020 7.009999 CAGCTGTGAGATCCGATTTAATATAGC 59.990 40.741 5.25 0.00 0.00 2.97
1947 4021 8.031864 ACAGCTGTGAGATCCGATTTAATATAG 58.968 37.037 20.97 0.00 0.00 1.31
1948 4022 7.896811 ACAGCTGTGAGATCCGATTTAATATA 58.103 34.615 20.97 0.00 0.00 0.86
1959 4035 3.876274 TCTACAACAGCTGTGAGATCC 57.124 47.619 22.49 0.00 39.20 3.36
1964 4040 4.256110 CAATGGATCTACAACAGCTGTGA 58.744 43.478 22.49 13.79 39.20 3.58
2032 4115 6.081872 GATTAATCATCCAAAGCTCTTGGG 57.918 41.667 20.54 10.63 39.96 4.12
2330 4428 4.476752 TTGGCGATGGCGGGGTAC 62.477 66.667 0.00 0.00 41.24 3.34
2759 4858 2.882927 ACAGCGTGTAGTTGTCTTGA 57.117 45.000 0.00 0.00 40.36 3.02
3616 5740 1.302832 GGTGTTGTCCAGGAGCCTG 60.303 63.158 9.59 9.59 43.26 4.85
3617 5741 2.883828 CGGTGTTGTCCAGGAGCCT 61.884 63.158 0.00 0.00 0.00 4.58
3945 6069 2.355513 CCTGCAACAGCTAGTTCATCCT 60.356 50.000 0.00 0.00 38.74 3.24
4524 6657 1.482593 CTCCATTGTACTTCTCCCGCT 59.517 52.381 0.00 0.00 0.00 5.52
4672 6806 4.062293 TGAATCGATGAACGGAAACAAGT 58.938 39.130 0.00 0.00 42.82 3.16
4814 6951 5.416013 ACCATGAAGATGATGATGATGATGC 59.584 40.000 0.00 0.00 0.00 3.91
4885 7037 5.833667 AGATGGATGACCTAAACGACTATGA 59.166 40.000 0.00 0.00 37.04 2.15
5283 7435 7.332678 GTGATATGCCAAGCTTTTGAAAGAAAT 59.667 33.333 7.63 0.00 38.28 2.17
5382 7534 2.700773 GCTAACAAGGCAAGCCCCG 61.701 63.158 7.62 1.40 36.58 5.73
5841 7993 6.728164 ACTAGTACCAGCAGGAATATCATCAT 59.272 38.462 0.35 0.00 38.69 2.45
6302 8475 0.322975 GTCATATGCGCAGGGGATCT 59.677 55.000 18.32 0.00 0.00 2.75
6322 8495 3.489355 TGATGCAGTGGACTGATTTGTT 58.511 40.909 11.06 0.00 46.59 2.83
6418 8594 6.371278 AGGATTCCGTATACCTTTCTGTAGA 58.629 40.000 0.00 0.00 0.00 2.59
6675 8851 5.018539 TGCAACTAGACGTGCCTTATATT 57.981 39.130 0.00 0.00 0.00 1.28
6720 8896 5.505181 AAAGGTGTCCTCATAGTCAATGT 57.495 39.130 0.00 0.00 36.89 2.71
7234 9410 8.401490 ACAGAAGCTCAAGAATGTATTTTTCT 57.599 30.769 0.00 0.00 34.95 2.52
7760 9936 6.096001 CGATTCTTCTTGATTCCCAATTCCTT 59.904 38.462 0.00 0.00 33.68 3.36
8179 10372 4.259970 CCACTGAAAGATATGAAGCGTTCG 60.260 45.833 0.00 0.00 37.43 3.95
8482 10684 2.274760 CGTACTCCCTCCGGTCCT 59.725 66.667 0.00 0.00 0.00 3.85
8647 10850 2.203252 CTGTGCCTGTGTGCCTGT 60.203 61.111 0.00 0.00 0.00 4.00
8742 10961 4.275443 AGACGTAGAAATCGGTGGTATCTC 59.725 45.833 0.00 0.00 0.00 2.75
8825 11045 7.806014 TGCAAGTTCACGTCTTAATTATTTTCC 59.194 33.333 0.00 0.00 0.00 3.13
8883 11104 7.223260 ACAAGATTGATGAATGCAAAGAGAA 57.777 32.000 0.00 0.00 0.00 2.87
8940 11167 7.798710 AACCAGCCTATTATTATCTGCTAGA 57.201 36.000 0.00 0.00 0.00 2.43
9004 11231 5.125097 AGAGACGACGTTCCATAAATACAGT 59.875 40.000 0.13 0.00 0.00 3.55
9005 11232 5.579718 AGAGACGACGTTCCATAAATACAG 58.420 41.667 0.13 0.00 0.00 2.74
9006 11233 5.356190 AGAGAGACGACGTTCCATAAATACA 59.644 40.000 0.13 0.00 0.00 2.29
9023 11252 2.777832 ATCCCAGCAAACAGAGAGAC 57.222 50.000 0.00 0.00 0.00 3.36
9024 11253 4.908601 TTAATCCCAGCAAACAGAGAGA 57.091 40.909 0.00 0.00 0.00 3.10
9027 11256 4.907879 GGATTAATCCCAGCAAACAGAG 57.092 45.455 22.09 0.00 41.20 3.35
9082 11357 5.933463 ACCCGTGTCGTTTTATTATTCTTGA 59.067 36.000 0.00 0.00 0.00 3.02
9083 11358 6.173191 ACCCGTGTCGTTTTATTATTCTTG 57.827 37.500 0.00 0.00 0.00 3.02
9084 11359 6.413018 GACCCGTGTCGTTTTATTATTCTT 57.587 37.500 0.00 0.00 0.00 2.52
9120 11395 1.043673 AGAGTTACCCTAGCCGCCAG 61.044 60.000 0.00 0.00 0.00 4.85
9141 11416 6.243148 TGGGGTTTATTTCAGACTTTACTCC 58.757 40.000 0.00 0.00 0.00 3.85
9164 11439 1.798813 GTGTCGGCCTCTACAAAGTTG 59.201 52.381 0.00 0.00 0.00 3.16
9165 11440 1.414919 TGTGTCGGCCTCTACAAAGTT 59.585 47.619 0.00 0.00 0.00 2.66
9182 11457 5.782893 TTAAAGGTGAGGGTTCATTTGTG 57.217 39.130 0.00 0.00 35.39 3.33
9183 11458 6.014584 GGATTTAAAGGTGAGGGTTCATTTGT 60.015 38.462 0.00 0.00 35.39 2.83
9184 11459 6.398095 GGATTTAAAGGTGAGGGTTCATTTG 58.602 40.000 0.00 0.00 35.39 2.32
9239 11514 7.136822 ACATGCATAAGGTTAGAATAGACCA 57.863 36.000 0.00 0.00 38.42 4.02
9258 11533 2.419057 TTCCAGTGCGCCAAACATGC 62.419 55.000 4.18 0.00 0.00 4.06
9273 11548 5.336372 CCGCCTTGAATTGTTTCTATTTCCA 60.336 40.000 0.00 0.00 32.78 3.53
9277 11552 4.086457 ACCCGCCTTGAATTGTTTCTATT 58.914 39.130 0.00 0.00 32.78 1.73
9304 11583 0.390866 AATGTCAGTGAGAGCAGCGG 60.391 55.000 0.00 0.00 0.00 5.52
9328 11607 3.166679 AGAGGAGGACTAACTTGTGGAC 58.833 50.000 0.00 0.00 0.00 4.02
9343 11622 3.325425 TCGGTAGTGAGAGGATAGAGGAG 59.675 52.174 0.00 0.00 0.00 3.69
9344 11623 3.315596 TCGGTAGTGAGAGGATAGAGGA 58.684 50.000 0.00 0.00 0.00 3.71
9345 11624 3.773418 TCGGTAGTGAGAGGATAGAGG 57.227 52.381 0.00 0.00 0.00 3.69
9347 11626 6.489361 GGTTATTTCGGTAGTGAGAGGATAGA 59.511 42.308 0.00 0.00 0.00 1.98
9348 11627 6.490721 AGGTTATTTCGGTAGTGAGAGGATAG 59.509 42.308 0.00 0.00 0.00 2.08
9349 11628 6.371278 AGGTTATTTCGGTAGTGAGAGGATA 58.629 40.000 0.00 0.00 0.00 2.59
9350 11629 5.209659 AGGTTATTTCGGTAGTGAGAGGAT 58.790 41.667 0.00 0.00 0.00 3.24
9351 11630 4.607239 AGGTTATTTCGGTAGTGAGAGGA 58.393 43.478 0.00 0.00 0.00 3.71
9352 11631 5.340439 AAGGTTATTTCGGTAGTGAGAGG 57.660 43.478 0.00 0.00 0.00 3.69
9353 11632 9.627395 CATATAAGGTTATTTCGGTAGTGAGAG 57.373 37.037 0.00 0.00 0.00 3.20
9517 11796 4.096732 CATAGATCGATGTATGCCGACA 57.903 45.455 24.50 0.00 37.64 4.35
9572 11851 2.240918 ACCAGGGCCACATCCATGT 61.241 57.895 6.18 0.00 42.84 3.21


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

AutoCloner maintained by Alex Coulton.