Multiple sequence alignment - TraesCS2B01G285500

Loading Multiple Alignment...

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 TraesCS2B01G285500 chr2B 100.000 2729 0 0 1567 4295 393459502 393462230 0.000000e+00 5040.0
1 TraesCS2B01G285500 chr2B 100.000 1188 0 0 1 1188 393457936 393459123 0.000000e+00 2194.0
2 TraesCS2B01G285500 chr2B 87.945 506 28 5 3277 3760 481633680 481633186 2.240000e-157 566.0
3 TraesCS2B01G285500 chr2B 95.253 316 12 1 1702 2014 481633993 481633678 8.290000e-137 497.0
4 TraesCS2B01G285500 chr2B 94.286 280 15 1 910 1188 481636349 481636070 1.100000e-115 427.0
5 TraesCS2B01G285500 chr2B 94.828 232 11 1 490 720 787047055 787047286 1.140000e-95 361.0
6 TraesCS2B01G285500 chr2B 92.667 150 11 0 1567 1716 481635996 481635847 2.600000e-52 217.0
7 TraesCS2B01G285500 chr3B 98.094 1207 22 1 1567 2772 592331632 592330426 0.000000e+00 2100.0
8 TraesCS2B01G285500 chr3B 97.679 948 16 1 2804 3751 592329922 592328981 0.000000e+00 1624.0
9 TraesCS2B01G285500 chr3B 84.647 964 98 28 2798 3722 816058855 816059807 0.000000e+00 915.0
10 TraesCS2B01G285500 chr3B 96.800 500 15 1 1 500 670194278 670193780 0.000000e+00 833.0
11 TraesCS2B01G285500 chr3B 95.699 279 12 0 910 1188 592332261 592331983 2.360000e-122 449.0
12 TraesCS2B01G285500 chr3B 95.175 228 11 0 493 720 59206642 59206869 1.140000e-95 361.0
13 TraesCS2B01G285500 chr3B 92.095 253 16 4 473 723 670193501 670193251 1.900000e-93 353.0
14 TraesCS2B01G285500 chr5B 95.593 953 30 5 2800 3751 567844683 567843742 0.000000e+00 1517.0
15 TraesCS2B01G285500 chr5B 96.800 500 15 1 1 500 634281312 634281810 0.000000e+00 833.0
16 TraesCS2B01G285500 chr5B 96.600 500 16 1 1 500 134135246 134134748 0.000000e+00 828.0
17 TraesCS2B01G285500 chr5B 96.600 500 16 1 1 500 711262392 711261894 0.000000e+00 828.0
18 TraesCS2B01G285500 chr5B 95.592 431 19 0 1567 1997 567845130 567844700 0.000000e+00 691.0
19 TraesCS2B01G285500 chr5B 94.836 426 16 1 3325 3750 87010955 87011374 0.000000e+00 660.0
20 TraesCS2B01G285500 chr5B 93.750 272 17 0 910 1181 567845879 567845608 4.000000e-110 409.0
21 TraesCS2B01G285500 chr5B 95.238 231 10 1 493 722 220818179 220817949 8.780000e-97 364.0
22 TraesCS2B01G285500 chr5B 94.805 231 12 0 493 723 634282100 634282330 1.140000e-95 361.0
23 TraesCS2B01G285500 chr5B 98.013 151 3 0 718 868 664253284 664253434 3.290000e-66 263.0
24 TraesCS2B01G285500 chr5B 91.573 178 13 2 717 894 419758622 419758797 1.190000e-60 244.0
25 TraesCS2B01G285500 chr7A 92.193 871 62 6 1924 2791 62734721 62735588 0.000000e+00 1227.0
26 TraesCS2B01G285500 chr5D 92.184 870 64 4 1924 2791 538685665 538686532 0.000000e+00 1227.0
27 TraesCS2B01G285500 chr5D 85.550 955 84 29 2798 3722 538687687 538688617 0.000000e+00 950.0
28 TraesCS2B01G285500 chr5D 98.077 52 1 0 1872 1923 538685589 538685640 1.640000e-14 91.6
29 TraesCS2B01G285500 chr1D 92.184 870 64 4 1924 2791 80673204 80674071 0.000000e+00 1227.0
30 TraesCS2B01G285500 chr1D 85.131 955 88 28 2798 3722 80684017 80684947 0.000000e+00 928.0
31 TraesCS2B01G285500 chr1D 83.784 333 45 8 2948 3276 194539692 194539365 1.500000e-79 307.0
32 TraesCS2B01G285500 chr1D 80.720 389 55 13 3340 3722 354506454 354506080 7.030000e-73 285.0
33 TraesCS2B01G285500 chr1D 92.727 165 12 0 1924 2088 354506620 354506456 5.550000e-59 239.0
34 TraesCS2B01G285500 chr1D 92.727 165 10 1 1924 2088 478159779 478159617 2.000000e-58 237.0
35 TraesCS2B01G285500 chr1D 98.077 52 1 0 1872 1923 80673128 80673179 1.640000e-14 91.6
36 TraesCS2B01G285500 chr1D 97.872 47 1 0 1875 1921 354506688 354506642 9.900000e-12 82.4
37 TraesCS2B01G285500 chr4A 92.078 871 62 7 1924 2791 629925230 629926096 0.000000e+00 1219.0
38 TraesCS2B01G285500 chr4A 84.226 989 108 35 2798 3753 117700388 117701361 0.000000e+00 918.0
39 TraesCS2B01G285500 chr4A 84.696 954 93 29 2798 3722 629936187 629937116 0.000000e+00 904.0
40 TraesCS2B01G285500 chr7D 91.609 870 69 4 1924 2791 78507379 78508246 0.000000e+00 1199.0
41 TraesCS2B01G285500 chr7D 84.314 969 95 24 2804 3722 271455498 271456459 0.000000e+00 894.0
42 TraesCS2B01G285500 chr7D 92.690 342 19 1 3418 3759 148128354 148128019 4.990000e-134 488.0
43 TraesCS2B01G285500 chr7D 92.814 334 18 1 3418 3751 112329925 112330252 3.000000e-131 479.0
44 TraesCS2B01G285500 chr7D 91.503 306 16 4 1709 2005 148128666 148128362 3.090000e-111 412.0
45 TraesCS2B01G285500 chr7D 91.892 259 16 4 910 1164 148129138 148128881 1.470000e-94 357.0
46 TraesCS2B01G285500 chr7D 88.968 281 16 5 910 1188 112329046 112329313 2.480000e-87 333.0
47 TraesCS2B01G285500 chr7D 98.235 170 2 1 1836 2005 112329749 112329917 3.250000e-76 296.0
48 TraesCS2B01G285500 chr2D 92.028 853 61 6 1924 2774 27770060 27769213 0.000000e+00 1192.0
49 TraesCS2B01G285500 chr2D 97.287 516 12 2 3781 4295 324591765 324592279 0.000000e+00 874.0
50 TraesCS2B01G285500 chr2D 91.917 532 42 1 2804 3334 27769073 27768542 0.000000e+00 743.0
51 TraesCS2B01G285500 chr5A 91.638 861 69 3 1924 2782 78447945 78448804 0.000000e+00 1188.0
52 TraesCS2B01G285500 chr4D 90.690 870 75 5 1924 2791 145380953 145380088 0.000000e+00 1153.0
53 TraesCS2B01G285500 chr4D 85.056 977 86 33 2804 3750 145379518 145378572 0.000000e+00 941.0
54 TraesCS2B01G285500 chr4D 82.883 999 110 30 2804 3753 348040640 348039654 0.000000e+00 841.0
55 TraesCS2B01G285500 chr4D 90.271 442 20 9 1567 2005 405025367 405024946 1.350000e-154 556.0
56 TraesCS2B01G285500 chr4D 84.268 553 73 8 2795 3334 459192413 459192964 1.060000e-145 527.0
57 TraesCS2B01G285500 chr4D 93.195 338 17 1 3418 3755 405024938 405024607 3.860000e-135 492.0
58 TraesCS2B01G285500 chr4D 81.783 258 37 9 3469 3722 154011335 154011586 1.570000e-49 207.0
59 TraesCS2B01G285500 chr6B 92.286 713 27 4 3059 3750 672729952 672730657 0.000000e+00 987.0
60 TraesCS2B01G285500 chr6B 94.182 636 33 2 1596 2231 672728467 672729098 0.000000e+00 966.0
61 TraesCS2B01G285500 chr6B 97.000 500 14 1 1 500 613593751 613593253 0.000000e+00 839.0
62 TraesCS2B01G285500 chr6B 96.400 500 17 1 1 500 188498771 188498273 0.000000e+00 822.0
63 TraesCS2B01G285500 chr6B 86.338 527 65 7 2810 3334 707395038 707394517 6.230000e-158 568.0
64 TraesCS2B01G285500 chr6B 94.231 52 3 0 1872 1923 12328451 12328502 3.560000e-11 80.5
65 TraesCS2B01G285500 chr1A 84.260 953 108 30 2804 3750 80283229 80282313 0.000000e+00 891.0
66 TraesCS2B01G285500 chr1A 87.900 438 33 7 1567 2004 584067648 584067231 8.290000e-137 497.0
67 TraesCS2B01G285500 chr1A 91.279 344 24 1 3418 3761 584067222 584066885 8.410000e-127 464.0
68 TraesCS2B01G285500 chr1A 91.317 334 23 1 3418 3751 508390787 508391114 6.550000e-123 451.0
69 TraesCS2B01G285500 chr1A 91.317 334 23 1 3418 3751 532366299 532366626 6.550000e-123 451.0
70 TraesCS2B01G285500 chr1A 93.214 280 17 2 910 1188 584068006 584067728 1.110000e-110 411.0
71 TraesCS2B01G285500 chr1A 89.577 307 30 2 1940 2246 80284961 80284657 5.210000e-104 388.0
72 TraesCS2B01G285500 chr1A 84.100 239 18 5 1567 1805 532366038 532366256 3.360000e-51 213.0
73 TraesCS2B01G285500 chr1A 83.539 243 20 5 1567 1809 508390525 508390747 4.350000e-50 209.0
74 TraesCS2B01G285500 chr4B 97.000 500 14 1 1 500 221094748 221095246 0.000000e+00 839.0
75 TraesCS2B01G285500 chr4B 82.028 996 116 30 2804 3753 428196319 428195341 0.000000e+00 789.0
76 TraesCS2B01G285500 chr4B 81.982 999 117 37 2798 3752 535286828 535287807 0.000000e+00 789.0
77 TraesCS2B01G285500 chr4B 82.347 946 126 27 2806 3722 449519371 449520304 0.000000e+00 784.0
78 TraesCS2B01G285500 chr4B 84.070 747 72 22 3034 3751 413506962 413506234 0.000000e+00 676.0
79 TraesCS2B01G285500 chr3D 83.061 980 111 31 2804 3751 339817725 339818681 0.000000e+00 839.0
80 TraesCS2B01G285500 chr3D 92.308 351 20 2 3418 3768 275642002 275641659 3.860000e-135 492.0
81 TraesCS2B01G285500 chr3D 92.143 280 20 2 910 1188 275642891 275642613 1.120000e-105 394.0
82 TraesCS2B01G285500 chr7B 96.600 500 16 1 1 500 424535959 424535461 0.000000e+00 828.0
83 TraesCS2B01G285500 chr7B 96.600 500 13 1 1 500 624355216 624355711 0.000000e+00 826.0
84 TraesCS2B01G285500 chr7B 82.347 963 107 34 2807 3717 269096834 269095883 0.000000e+00 778.0
85 TraesCS2B01G285500 chr7B 96.053 228 9 0 493 720 699820843 699821070 5.250000e-99 372.0
86 TraesCS2B01G285500 chr7B 83.667 300 33 11 3461 3756 604371155 604370868 7.080000e-68 268.0
87 TraesCS2B01G285500 chr7B 98.658 149 2 0 718 866 63057682 63057830 9.160000e-67 265.0
88 TraesCS2B01G285500 chr7B 97.959 49 1 0 1872 1920 269180033 269179985 7.650000e-13 86.1
89 TraesCS2B01G285500 chr2A 95.591 499 14 2 3804 4295 394024261 394023764 0.000000e+00 793.0
90 TraesCS2B01G285500 chr1B 88.224 535 61 2 2798 3331 400360022 400360555 4.680000e-179 638.0
91 TraesCS2B01G285500 chr1B 83.640 544 75 8 2804 3334 127025283 127024741 2.310000e-137 499.0
92 TraesCS2B01G285500 chr1B 95.614 228 8 1 493 720 532393293 532393518 8.780000e-97 364.0
93 TraesCS2B01G285500 chr1B 94.444 234 13 0 493 726 353408891 353408658 1.140000e-95 361.0
94 TraesCS2B01G285500 chr1B 94.805 231 10 2 493 723 644568643 644568415 4.080000e-95 359.0
95 TraesCS2B01G285500 chr1B 82.161 398 50 12 3340 3722 313099006 313099397 5.360000e-84 322.0
96 TraesCS2B01G285500 chr1B 98.658 149 2 0 718 866 532393545 532393693 9.160000e-67 265.0
97 TraesCS2B01G285500 chr1B 97.403 154 3 1 717 869 358167353 358167200 1.180000e-65 261.0
98 TraesCS2B01G285500 chr1B 81.639 305 43 10 3459 3760 400360729 400361023 1.540000e-59 241.0
99 TraesCS2B01G285500 chr1B 82.403 233 19 11 1872 2082 313098766 313098998 2.640000e-42 183.0
100 TraesCS2B01G285500 chr1B 93.878 49 3 0 1872 1920 419975101 419975149 1.660000e-09 75.0
101 TraesCS2B01G285500 chr6A 87.638 542 61 3 2798 3334 571575344 571575884 3.650000e-175 625.0
102 TraesCS2B01G285500 chr6A 88.613 483 28 8 1573 2055 551183476 551183021 2.900000e-156 562.0
103 TraesCS2B01G285500 chr6A 93.333 375 19 3 3377 3751 551182377 551182009 2.260000e-152 549.0
104 TraesCS2B01G285500 chr6A 87.797 295 35 1 1924 2218 373064857 373064564 1.140000e-90 344.0
105 TraesCS2B01G285500 chr6A 89.416 274 23 4 910 1182 551184069 551183801 1.480000e-89 340.0
106 TraesCS2B01G285500 chr6D 89.391 443 23 9 1567 2005 2295062 2295484 1.760000e-148 536.0
107 TraesCS2B01G285500 chr6D 93.393 333 16 1 3418 3750 2295492 2295818 4.990000e-134 488.0
108 TraesCS2B01G285500 chr6D 91.818 110 9 0 3613 3722 175749282 175749173 2.070000e-33 154.0
109 TraesCS2B01G285500 chr3A 87.321 489 36 10 1567 2055 388412403 388411941 1.760000e-148 536.0
110 TraesCS2B01G285500 chr3A 91.349 393 27 2 3359 3751 388411942 388411557 8.180000e-147 531.0
111 TraesCS2B01G285500 chrUn 80.759 369 48 15 3390 3750 47391626 47391979 2.550000e-67 267.0
112 TraesCS2B01G285500 chrUn 97.419 155 4 0 718 872 4345728 4345574 9.160000e-67 265.0
113 TraesCS2B01G285500 chrUn 98.026 152 3 0 718 869 131818724 131818875 9.160000e-67 265.0
114 TraesCS2B01G285500 chrUn 97.419 155 4 0 718 872 378240068 378239914 9.160000e-67 265.0
115 TraesCS2B01G285500 chrUn 97.386 153 4 0 720 872 123974851 123974699 1.180000e-65 261.0
116 TraesCS2B01G285500 chrUn 85.377 212 25 5 3514 3722 96554853 96555061 9.350000e-52 215.0
117 TraesCS2B01G285500 chrUn 80.743 296 38 12 3459 3752 108495095 108494817 3.360000e-51 213.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G285500 chr2B 393457936 393462230 4294 False 3617.000000 5040 100.000000 1 4295 2 chr2B.!!$F2 4294
1 TraesCS2B01G285500 chr2B 481633186 481636349 3163 True 426.750000 566 92.537750 910 3760 4 chr2B.!!$R1 2850
2 TraesCS2B01G285500 chr3B 592328981 592332261 3280 True 1391.000000 2100 97.157333 910 3751 3 chr3B.!!$R1 2841
3 TraesCS2B01G285500 chr3B 816058855 816059807 952 False 915.000000 915 84.647000 2798 3722 1 chr3B.!!$F2 924
4 TraesCS2B01G285500 chr3B 670193251 670194278 1027 True 593.000000 833 94.447500 1 723 2 chr3B.!!$R2 722
5 TraesCS2B01G285500 chr5B 567843742 567845879 2137 True 872.333333 1517 94.978333 910 3751 3 chr5B.!!$R4 2841
6 TraesCS2B01G285500 chr5B 634281312 634282330 1018 False 597.000000 833 95.802500 1 723 2 chr5B.!!$F4 722
7 TraesCS2B01G285500 chr7A 62734721 62735588 867 False 1227.000000 1227 92.193000 1924 2791 1 chr7A.!!$F1 867
8 TraesCS2B01G285500 chr5D 538685589 538688617 3028 False 756.200000 1227 91.937000 1872 3722 3 chr5D.!!$F1 1850
9 TraesCS2B01G285500 chr1D 80684017 80684947 930 False 928.000000 928 85.131000 2798 3722 1 chr1D.!!$F1 924
10 TraesCS2B01G285500 chr1D 80673128 80674071 943 False 659.300000 1227 95.130500 1872 2791 2 chr1D.!!$F2 919
11 TraesCS2B01G285500 chr1D 354506080 354506688 608 True 202.133333 285 90.439667 1875 3722 3 chr1D.!!$R3 1847
12 TraesCS2B01G285500 chr4A 629925230 629926096 866 False 1219.000000 1219 92.078000 1924 2791 1 chr4A.!!$F2 867
13 TraesCS2B01G285500 chr4A 117700388 117701361 973 False 918.000000 918 84.226000 2798 3753 1 chr4A.!!$F1 955
14 TraesCS2B01G285500 chr4A 629936187 629937116 929 False 904.000000 904 84.696000 2798 3722 1 chr4A.!!$F3 924
15 TraesCS2B01G285500 chr7D 78507379 78508246 867 False 1199.000000 1199 91.609000 1924 2791 1 chr7D.!!$F1 867
16 TraesCS2B01G285500 chr7D 271455498 271456459 961 False 894.000000 894 84.314000 2804 3722 1 chr7D.!!$F2 918
17 TraesCS2B01G285500 chr7D 148128019 148129138 1119 True 419.000000 488 92.028333 910 3759 3 chr7D.!!$R1 2849
18 TraesCS2B01G285500 chr7D 112329046 112330252 1206 False 369.333333 479 93.339000 910 3751 3 chr7D.!!$F3 2841
19 TraesCS2B01G285500 chr2D 27768542 27770060 1518 True 967.500000 1192 91.972500 1924 3334 2 chr2D.!!$R1 1410
20 TraesCS2B01G285500 chr2D 324591765 324592279 514 False 874.000000 874 97.287000 3781 4295 1 chr2D.!!$F1 514
21 TraesCS2B01G285500 chr5A 78447945 78448804 859 False 1188.000000 1188 91.638000 1924 2782 1 chr5A.!!$F1 858
22 TraesCS2B01G285500 chr4D 145378572 145380953 2381 True 1047.000000 1153 87.873000 1924 3750 2 chr4D.!!$R2 1826
23 TraesCS2B01G285500 chr4D 348039654 348040640 986 True 841.000000 841 82.883000 2804 3753 1 chr4D.!!$R1 949
24 TraesCS2B01G285500 chr4D 459192413 459192964 551 False 527.000000 527 84.268000 2795 3334 1 chr4D.!!$F2 539
25 TraesCS2B01G285500 chr4D 405024607 405025367 760 True 524.000000 556 91.733000 1567 3755 2 chr4D.!!$R3 2188
26 TraesCS2B01G285500 chr6B 672728467 672730657 2190 False 976.500000 987 93.234000 1596 3750 2 chr6B.!!$F2 2154
27 TraesCS2B01G285500 chr6B 707394517 707395038 521 True 568.000000 568 86.338000 2810 3334 1 chr6B.!!$R3 524
28 TraesCS2B01G285500 chr1A 80282313 80284961 2648 True 639.500000 891 86.918500 1940 3750 2 chr1A.!!$R1 1810
29 TraesCS2B01G285500 chr1A 584066885 584068006 1121 True 457.333333 497 90.797667 910 3761 3 chr1A.!!$R2 2851
30 TraesCS2B01G285500 chr1A 532366038 532366626 588 False 332.000000 451 87.708500 1567 3751 2 chr1A.!!$F2 2184
31 TraesCS2B01G285500 chr1A 508390525 508391114 589 False 330.000000 451 87.428000 1567 3751 2 chr1A.!!$F1 2184
32 TraesCS2B01G285500 chr4B 428195341 428196319 978 True 789.000000 789 82.028000 2804 3753 1 chr4B.!!$R2 949
33 TraesCS2B01G285500 chr4B 535286828 535287807 979 False 789.000000 789 81.982000 2798 3752 1 chr4B.!!$F3 954
34 TraesCS2B01G285500 chr4B 449519371 449520304 933 False 784.000000 784 82.347000 2806 3722 1 chr4B.!!$F2 916
35 TraesCS2B01G285500 chr4B 413506234 413506962 728 True 676.000000 676 84.070000 3034 3751 1 chr4B.!!$R1 717
36 TraesCS2B01G285500 chr3D 339817725 339818681 956 False 839.000000 839 83.061000 2804 3751 1 chr3D.!!$F1 947
37 TraesCS2B01G285500 chr3D 275641659 275642891 1232 True 443.000000 492 92.225500 910 3768 2 chr3D.!!$R1 2858
38 TraesCS2B01G285500 chr7B 269095883 269096834 951 True 778.000000 778 82.347000 2807 3717 1 chr7B.!!$R1 910
39 TraesCS2B01G285500 chr1B 127024741 127025283 542 True 499.000000 499 83.640000 2804 3334 1 chr1B.!!$R1 530
40 TraesCS2B01G285500 chr1B 400360022 400361023 1001 False 439.500000 638 84.931500 2798 3760 2 chr1B.!!$F3 962
41 TraesCS2B01G285500 chr1B 313098766 313099397 631 False 252.500000 322 82.282000 1872 3722 2 chr1B.!!$F2 1850
42 TraesCS2B01G285500 chr6A 571575344 571575884 540 False 625.000000 625 87.638000 2798 3334 1 chr6A.!!$F1 536
43 TraesCS2B01G285500 chr6A 551182009 551184069 2060 True 483.666667 562 90.454000 910 3751 3 chr6A.!!$R2 2841
44 TraesCS2B01G285500 chr6D 2295062 2295818 756 False 512.000000 536 91.392000 1567 3750 2 chr6D.!!$F1 2183
45 TraesCS2B01G285500 chr3A 388411557 388412403 846 True 533.500000 536 89.335000 1567 3751 2 chr3A.!!$R1 2184

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
726 1033 0.101579 AAAACAGTTTGCCGGGTTCG 59.898 50.0 2.18 0.0 0.00 3.95 F
893 1200 0.109039 AGCTCGTTTCGCTTCCTCTC 60.109 55.0 0.00 0.0 32.98 3.20 F
895 1202 0.528470 CTCGTTTCGCTTCCTCTCCT 59.472 55.0 0.00 0.0 0.00 3.69 F
896 1203 0.966920 TCGTTTCGCTTCCTCTCCTT 59.033 50.0 0.00 0.0 0.00 3.36 F
897 1204 1.071605 CGTTTCGCTTCCTCTCCTTG 58.928 55.0 0.00 0.0 0.00 3.61 F
900 1207 1.338107 TTCGCTTCCTCTCCTTGTGA 58.662 50.0 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 2357 1.342174 GGATAGGAAACGACCGGCATA 59.658 52.381 0.00 0.0 34.73 3.14 R
2538 5242 1.404986 GGTAACACCAGCTCGCACATA 60.405 52.381 0.00 0.0 38.42 2.29 R
2802 6754 1.549037 GGGGCATCAACTTTGTGGGTA 60.549 52.381 0.00 0.0 0.00 3.69 R
3129 7102 2.233922 AGACACTACATCCCAAAGGTCG 59.766 50.000 0.00 0.0 0.00 4.79 R
3259 7249 5.308497 TCTTCACATACCTACTCACCCAAAA 59.692 40.000 0.00 0.0 0.00 2.44 R
3454 7497 5.528043 TTTCAACAAGGTGCACATACAAT 57.472 34.783 20.43 0.0 0.00 2.71 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
158 159 4.077180 ACGAGGAGGAGGACCCCC 62.077 72.222 0.00 0.00 36.73 5.40
178 179 3.838271 GGTCTCCATGCGCCTCGA 61.838 66.667 4.18 0.00 0.00 4.04
527 834 4.924187 CGAGGGAGGGCGAGGGAT 62.924 72.222 0.00 0.00 0.00 3.85
632 939 0.535328 TTGATTCGCCGTGGGAAACA 60.535 50.000 7.31 8.02 37.97 2.83
704 1011 3.259930 GCCTGCGGCTTTTTCGTA 58.740 55.556 11.61 0.00 46.69 3.43
723 1030 0.973496 ACCAAAACAGTTTGCCGGGT 60.973 50.000 2.18 3.01 42.44 5.28
724 1031 0.176910 CCAAAACAGTTTGCCGGGTT 59.823 50.000 2.18 0.00 42.44 4.11
725 1032 1.566404 CAAAACAGTTTGCCGGGTTC 58.434 50.000 2.18 0.00 37.89 3.62
726 1033 0.101579 AAAACAGTTTGCCGGGTTCG 59.898 50.000 2.18 0.00 0.00 3.95
750 1057 3.660111 GTCCGCCAGCGCTGTTTT 61.660 61.111 33.75 0.00 38.24 2.43
751 1058 3.353836 TCCGCCAGCGCTGTTTTC 61.354 61.111 33.75 18.84 38.24 2.29
752 1059 4.741781 CCGCCAGCGCTGTTTTCG 62.742 66.667 33.75 27.32 38.24 3.46
753 1060 4.741781 CGCCAGCGCTGTTTTCGG 62.742 66.667 33.75 19.86 0.00 4.30
760 1067 2.049156 GCTGTTTTCGGCCCAAGC 60.049 61.111 0.00 0.00 45.68 4.01
770 1077 3.758931 GCCCAAGCCGGCGAAAAT 61.759 61.111 23.20 0.00 39.64 1.82
771 1078 2.489751 CCCAAGCCGGCGAAAATC 59.510 61.111 23.20 0.00 0.00 2.17
772 1079 2.100216 CCAAGCCGGCGAAAATCG 59.900 61.111 23.20 5.28 43.89 3.34
774 1081 3.131478 AAGCCGGCGAAAATCGGG 61.131 61.111 23.20 0.00 45.75 5.14
777 1084 3.573491 CCGGCGAAAATCGGGCTC 61.573 66.667 9.30 0.00 42.32 4.70
778 1085 3.573491 CGGCGAAAATCGGGCTCC 61.573 66.667 0.00 0.00 40.84 4.70
779 1086 2.124695 GGCGAAAATCGGGCTCCT 60.125 61.111 1.64 0.00 40.84 3.69
780 1087 2.472909 GGCGAAAATCGGGCTCCTG 61.473 63.158 1.64 0.00 40.84 3.86
781 1088 2.472909 GCGAAAATCGGGCTCCTGG 61.473 63.158 1.64 0.00 40.84 4.45
782 1089 1.819632 CGAAAATCGGGCTCCTGGG 60.820 63.158 0.00 0.00 36.00 4.45
783 1090 1.453928 GAAAATCGGGCTCCTGGGG 60.454 63.158 0.00 0.00 0.00 4.96
784 1091 2.911221 GAAAATCGGGCTCCTGGGGG 62.911 65.000 0.00 0.00 0.00 5.40
802 1109 2.961768 CGCGACTGGGCCATTTTT 59.038 55.556 6.72 0.00 0.00 1.94
843 1150 3.415087 CCTGGGGAGGCCTTCCTG 61.415 72.222 30.10 23.65 44.46 3.86
844 1151 3.415087 CTGGGGAGGCCTTCCTGG 61.415 72.222 30.10 18.11 44.46 4.45
870 1177 2.777832 GGCTGGAGATGCCCTAATAG 57.222 55.000 0.00 0.00 44.32 1.73
871 1178 2.260822 GGCTGGAGATGCCCTAATAGA 58.739 52.381 0.00 0.00 44.32 1.98
872 1179 2.027653 GGCTGGAGATGCCCTAATAGAC 60.028 54.545 0.00 0.00 44.32 2.59
873 1180 2.903135 GCTGGAGATGCCCTAATAGACT 59.097 50.000 0.00 0.00 34.97 3.24
874 1181 4.090090 GCTGGAGATGCCCTAATAGACTA 58.910 47.826 0.00 0.00 34.97 2.59
875 1182 4.159506 GCTGGAGATGCCCTAATAGACTAG 59.840 50.000 0.00 0.00 34.97 2.57
876 1183 4.090090 TGGAGATGCCCTAATAGACTAGC 58.910 47.826 0.00 0.00 34.97 3.42
877 1184 4.202727 TGGAGATGCCCTAATAGACTAGCT 60.203 45.833 0.00 0.00 34.97 3.32
878 1185 4.401202 GGAGATGCCCTAATAGACTAGCTC 59.599 50.000 0.00 0.00 0.00 4.09
879 1186 4.013728 AGATGCCCTAATAGACTAGCTCG 58.986 47.826 0.00 0.00 0.00 5.03
880 1187 3.225177 TGCCCTAATAGACTAGCTCGT 57.775 47.619 0.00 0.00 0.00 4.18
881 1188 3.563223 TGCCCTAATAGACTAGCTCGTT 58.437 45.455 0.00 0.00 0.00 3.85
882 1189 3.958798 TGCCCTAATAGACTAGCTCGTTT 59.041 43.478 0.00 0.00 0.00 3.60
883 1190 4.037684 TGCCCTAATAGACTAGCTCGTTTC 59.962 45.833 0.00 0.00 0.00 2.78
884 1191 4.785417 CCCTAATAGACTAGCTCGTTTCG 58.215 47.826 0.00 0.00 0.00 3.46
885 1192 4.220572 CCTAATAGACTAGCTCGTTTCGC 58.779 47.826 0.00 0.00 0.00 4.70
886 1193 4.023878 CCTAATAGACTAGCTCGTTTCGCT 60.024 45.833 0.00 0.00 41.35 4.93
887 1194 4.373348 AATAGACTAGCTCGTTTCGCTT 57.627 40.909 0.00 0.00 38.86 4.68
888 1195 2.265647 AGACTAGCTCGTTTCGCTTC 57.734 50.000 0.00 0.00 38.86 3.86
889 1196 1.135344 AGACTAGCTCGTTTCGCTTCC 60.135 52.381 0.00 0.00 38.86 3.46
890 1197 0.889306 ACTAGCTCGTTTCGCTTCCT 59.111 50.000 0.00 0.00 38.86 3.36
891 1198 1.135344 ACTAGCTCGTTTCGCTTCCTC 60.135 52.381 0.00 0.00 38.86 3.71
892 1199 1.133407 CTAGCTCGTTTCGCTTCCTCT 59.867 52.381 0.00 0.00 38.86 3.69
893 1200 0.109039 AGCTCGTTTCGCTTCCTCTC 60.109 55.000 0.00 0.00 32.98 3.20
894 1201 1.079317 GCTCGTTTCGCTTCCTCTCC 61.079 60.000 0.00 0.00 0.00 3.71
895 1202 0.528470 CTCGTTTCGCTTCCTCTCCT 59.472 55.000 0.00 0.00 0.00 3.69
896 1203 0.966920 TCGTTTCGCTTCCTCTCCTT 59.033 50.000 0.00 0.00 0.00 3.36
897 1204 1.071605 CGTTTCGCTTCCTCTCCTTG 58.928 55.000 0.00 0.00 0.00 3.61
898 1205 1.605712 CGTTTCGCTTCCTCTCCTTGT 60.606 52.381 0.00 0.00 0.00 3.16
899 1206 1.801178 GTTTCGCTTCCTCTCCTTGTG 59.199 52.381 0.00 0.00 0.00 3.33
900 1207 1.338107 TTCGCTTCCTCTCCTTGTGA 58.662 50.000 0.00 0.00 0.00 3.58
901 1208 1.561643 TCGCTTCCTCTCCTTGTGAT 58.438 50.000 0.00 0.00 0.00 3.06
902 1209 1.478510 TCGCTTCCTCTCCTTGTGATC 59.521 52.381 0.00 0.00 0.00 2.92
903 1210 1.480137 CGCTTCCTCTCCTTGTGATCT 59.520 52.381 0.00 0.00 0.00 2.75
904 1211 2.093764 CGCTTCCTCTCCTTGTGATCTT 60.094 50.000 0.00 0.00 0.00 2.40
905 1212 3.530535 GCTTCCTCTCCTTGTGATCTTC 58.469 50.000 0.00 0.00 0.00 2.87
906 1213 3.197549 GCTTCCTCTCCTTGTGATCTTCT 59.802 47.826 0.00 0.00 0.00 2.85
907 1214 4.323409 GCTTCCTCTCCTTGTGATCTTCTT 60.323 45.833 0.00 0.00 0.00 2.52
908 1215 5.802821 GCTTCCTCTCCTTGTGATCTTCTTT 60.803 44.000 0.00 0.00 0.00 2.52
1682 2357 3.728373 GGCCGGTTCCACCCATCT 61.728 66.667 1.90 0.00 33.75 2.90
2787 5492 7.118723 TGTCCATTTGTTATTGCCTCTAGAAT 58.881 34.615 0.00 0.00 0.00 2.40
2788 5493 8.271458 TGTCCATTTGTTATTGCCTCTAGAATA 58.729 33.333 0.00 0.00 0.00 1.75
2790 5495 7.719633 TCCATTTGTTATTGCCTCTAGAATACC 59.280 37.037 0.00 0.00 0.00 2.73
2791 5496 7.040409 CCATTTGTTATTGCCTCTAGAATACCC 60.040 40.741 0.00 0.00 0.00 3.69
2792 5497 5.562298 TGTTATTGCCTCTAGAATACCCC 57.438 43.478 0.00 0.00 0.00 4.95
2793 5498 4.349930 TGTTATTGCCTCTAGAATACCCCC 59.650 45.833 0.00 0.00 0.00 5.40
2796 5501 2.690840 TGCCTCTAGAATACCCCCTTC 58.309 52.381 0.00 0.00 0.00 3.46
2800 6752 4.557705 CCTCTAGAATACCCCCTTCTTGA 58.442 47.826 0.00 0.00 34.81 3.02
2802 6754 5.608860 CCTCTAGAATACCCCCTTCTTGAAT 59.391 44.000 0.00 0.00 35.23 2.57
3129 7102 5.360999 TGGAGATGATGATGATATACCCGAC 59.639 44.000 0.00 0.00 0.00 4.79
3259 7249 7.123547 TGAAACTTACCCAAATCAACAAGTCTT 59.876 33.333 0.00 0.00 0.00 3.01
3454 7497 6.293735 GGGAATTTCGTTTGTGAACTGTATGA 60.294 38.462 0.00 0.00 33.51 2.15
3623 7700 1.134175 CGTGCTTCCAACCAAACACTT 59.866 47.619 0.00 0.00 0.00 3.16
3722 7800 4.419282 ACCATTCCATTCCATGACAGTTT 58.581 39.130 0.00 0.00 0.00 2.66
3723 7801 4.221262 ACCATTCCATTCCATGACAGTTTG 59.779 41.667 0.00 0.00 0.00 2.93
3724 7802 4.382254 CCATTCCATTCCATGACAGTTTGG 60.382 45.833 0.00 0.00 0.00 3.28
3725 7803 2.806434 TCCATTCCATGACAGTTTGGG 58.194 47.619 0.00 0.00 33.62 4.12
3726 7804 2.378208 TCCATTCCATGACAGTTTGGGA 59.622 45.455 0.00 0.00 33.62 4.37
3727 7805 3.011595 TCCATTCCATGACAGTTTGGGAT 59.988 43.478 0.00 0.00 30.89 3.85
3763 7841 3.917300 ACACACCCTTTGTATCCCAAAA 58.083 40.909 0.00 0.00 42.31 2.44
3768 7846 5.011635 ACACCCTTTGTATCCCAAAATGAAC 59.988 40.000 0.00 0.00 42.31 3.18
3769 7847 5.011533 CACCCTTTGTATCCCAAAATGAACA 59.988 40.000 0.00 0.00 42.31 3.18
3770 7848 5.784906 ACCCTTTGTATCCCAAAATGAACAT 59.215 36.000 0.00 0.00 42.31 2.71
3771 7849 6.070824 ACCCTTTGTATCCCAAAATGAACATC 60.071 38.462 0.00 0.00 42.31 3.06
3772 7850 6.035843 CCTTTGTATCCCAAAATGAACATCG 58.964 40.000 0.00 0.00 42.31 3.84
3773 7851 6.350110 CCTTTGTATCCCAAAATGAACATCGT 60.350 38.462 0.00 0.00 42.31 3.73
3774 7852 6.582677 TTGTATCCCAAAATGAACATCGTT 57.417 33.333 0.00 0.00 0.00 3.85
3775 7853 7.689446 TTGTATCCCAAAATGAACATCGTTA 57.311 32.000 0.00 0.00 0.00 3.18
3776 7854 7.079182 TGTATCCCAAAATGAACATCGTTAC 57.921 36.000 0.00 0.00 0.00 2.50
3777 7855 6.655425 TGTATCCCAAAATGAACATCGTTACA 59.345 34.615 0.00 0.00 0.00 2.41
3778 7856 6.773976 ATCCCAAAATGAACATCGTTACAT 57.226 33.333 0.00 0.00 0.00 2.29
3779 7857 6.582677 TCCCAAAATGAACATCGTTACATT 57.417 33.333 0.00 0.00 34.99 2.71
3783 7861 9.364989 CCCAAAATGAACATCGTTACATTAAAT 57.635 29.630 0.00 0.00 33.50 1.40
3790 7868 9.982291 TGAACATCGTTACATTAAATAAAGAGC 57.018 29.630 5.28 0.00 0.00 4.09
3792 7870 7.123830 ACATCGTTACATTAAATAAAGAGCGC 58.876 34.615 0.00 0.00 0.00 5.92
3837 7916 6.016777 TGTGAAAAGGAGAAAAATCTGAGAGC 60.017 38.462 0.00 0.00 0.00 4.09
3840 7919 4.219264 AGGAGAAAAATCTGAGAGCCTG 57.781 45.455 0.00 0.00 0.00 4.85
3845 7924 1.831580 AAATCTGAGAGCCTGGCAAC 58.168 50.000 22.65 14.26 0.00 4.17
3886 7965 0.250597 ACGTAGCAAACACTTCCCCC 60.251 55.000 0.00 0.00 0.00 5.40
3999 8078 2.781595 TTTGCTTCCTCCGCTCCGTC 62.782 60.000 0.00 0.00 0.00 4.79
4066 8145 2.368011 CCCCCGTCCCTTCTTCTCC 61.368 68.421 0.00 0.00 0.00 3.71
4125 8204 5.480205 CCAGTTAGGGTTGAGTCTTACTTC 58.520 45.833 0.00 0.00 0.00 3.01
4162 8241 1.468520 CCATGGCGAATTCGTGTCTTT 59.531 47.619 27.24 5.98 42.22 2.52
4177 8256 9.825972 ATTCGTGTCTTTATTTTGTAATGTCAG 57.174 29.630 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.087892 AGCTCTGGCGTCCGCATT 62.088 61.111 14.19 0.00 44.37 3.56
178 179 2.285743 GGGGAAGCTCCTGGACCT 60.286 66.667 0.00 0.00 36.57 3.85
199 200 2.294078 CCCCCTTCCTTCTCACGCT 61.294 63.158 0.00 0.00 0.00 5.07
240 241 1.966901 TACATCGAGGGCGGCAACAT 61.967 55.000 12.47 0.00 38.28 2.71
564 871 1.180029 GTCAGCCTGCACCATTGATT 58.820 50.000 0.00 0.00 0.00 2.57
601 908 1.403249 GCGAATCAATGCCAAAGCTGT 60.403 47.619 0.00 0.00 40.80 4.40
624 931 0.322456 CCTCATCGCCTTGTTTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
632 939 1.592400 TTCGTCGTCCTCATCGCCTT 61.592 55.000 0.00 0.00 0.00 4.35
690 997 1.022735 TTTGGTACGAAAAAGCCGCA 58.977 45.000 0.00 0.00 0.00 5.69
703 1010 1.033574 CCCGGCAAACTGTTTTGGTA 58.966 50.000 2.41 0.00 42.22 3.25
704 1011 0.973496 ACCCGGCAAACTGTTTTGGT 60.973 50.000 2.41 5.53 42.22 3.67
733 1040 3.595108 GAAAACAGCGCTGGCGGAC 62.595 63.158 38.27 21.80 46.35 4.79
734 1041 3.353836 GAAAACAGCGCTGGCGGA 61.354 61.111 38.27 0.00 46.35 5.54
735 1042 4.741781 CGAAAACAGCGCTGGCGG 62.742 66.667 38.27 19.79 46.35 6.13
736 1043 4.741781 CCGAAAACAGCGCTGGCG 62.742 66.667 38.27 31.28 46.35 5.69
738 1045 4.404654 GGCCGAAAACAGCGCTGG 62.405 66.667 38.27 22.37 34.19 4.85
739 1046 4.404654 GGGCCGAAAACAGCGCTG 62.405 66.667 34.89 34.89 38.77 5.18
740 1047 4.947147 TGGGCCGAAAACAGCGCT 62.947 61.111 2.64 2.64 42.05 5.92
741 1048 3.896863 CTTGGGCCGAAAACAGCGC 62.897 63.158 0.00 0.00 41.90 5.92
742 1049 2.255252 CTTGGGCCGAAAACAGCG 59.745 61.111 0.54 0.00 0.00 5.18
743 1050 2.049156 GCTTGGGCCGAAAACAGC 60.049 61.111 0.54 0.00 0.00 4.40
754 1061 2.489751 GATTTTCGCCGGCTTGGG 59.510 61.111 26.68 9.07 38.63 4.12
755 1062 2.100216 CGATTTTCGCCGGCTTGG 59.900 61.111 26.68 9.50 42.50 3.61
756 1063 2.100216 CCGATTTTCGCCGGCTTG 59.900 61.111 26.68 10.37 38.82 4.01
757 1064 3.131478 CCCGATTTTCGCCGGCTT 61.131 61.111 26.68 3.40 44.07 4.35
760 1067 3.573491 GAGCCCGATTTTCGCCGG 61.573 66.667 0.00 0.00 44.94 6.13
761 1068 3.573491 GGAGCCCGATTTTCGCCG 61.573 66.667 0.00 0.00 38.82 6.46
762 1069 2.124695 AGGAGCCCGATTTTCGCC 60.125 61.111 0.00 0.00 38.82 5.54
763 1070 2.472909 CCAGGAGCCCGATTTTCGC 61.473 63.158 0.00 0.00 38.82 4.70
764 1071 1.819632 CCCAGGAGCCCGATTTTCG 60.820 63.158 0.00 0.00 40.07 3.46
765 1072 1.453928 CCCCAGGAGCCCGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
766 1073 2.683475 CCCCAGGAGCCCGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
767 1074 3.420482 CCCCCAGGAGCCCGATTT 61.420 66.667 0.00 0.00 33.47 2.17
784 1091 3.281359 AAAAATGGCCCAGTCGCGC 62.281 57.895 0.00 0.00 0.00 6.86
785 1092 2.961768 AAAAATGGCCCAGTCGCG 59.038 55.556 0.00 0.00 0.00 5.87
826 1133 3.415087 CAGGAAGGCCTCCCCAGG 61.415 72.222 22.02 12.25 46.81 4.45
827 1134 3.415087 CCAGGAAGGCCTCCCCAG 61.415 72.222 22.02 15.58 46.81 4.45
852 1159 2.903135 AGTCTATTAGGGCATCTCCAGC 59.097 50.000 0.00 0.00 36.21 4.85
853 1160 4.159506 GCTAGTCTATTAGGGCATCTCCAG 59.840 50.000 0.00 0.00 36.21 3.86
854 1161 4.090090 GCTAGTCTATTAGGGCATCTCCA 58.910 47.826 0.00 0.00 36.21 3.86
855 1162 4.349365 AGCTAGTCTATTAGGGCATCTCC 58.651 47.826 0.00 0.00 0.00 3.71
856 1163 4.095782 CGAGCTAGTCTATTAGGGCATCTC 59.904 50.000 0.00 0.00 0.00 2.75
857 1164 4.013728 CGAGCTAGTCTATTAGGGCATCT 58.986 47.826 0.00 0.00 0.00 2.90
858 1165 3.759618 ACGAGCTAGTCTATTAGGGCATC 59.240 47.826 0.00 0.00 0.00 3.91
859 1166 3.768878 ACGAGCTAGTCTATTAGGGCAT 58.231 45.455 0.00 0.00 0.00 4.40
860 1167 3.225177 ACGAGCTAGTCTATTAGGGCA 57.775 47.619 0.00 0.00 0.00 5.36
861 1168 4.548494 GAAACGAGCTAGTCTATTAGGGC 58.452 47.826 0.00 0.00 0.00 5.19
862 1169 4.785417 CGAAACGAGCTAGTCTATTAGGG 58.215 47.826 0.00 0.00 0.00 3.53
863 1170 4.023878 AGCGAAACGAGCTAGTCTATTAGG 60.024 45.833 0.00 0.00 44.05 2.69
864 1171 5.098218 AGCGAAACGAGCTAGTCTATTAG 57.902 43.478 0.00 0.00 44.05 1.73
865 1172 5.496133 AAGCGAAACGAGCTAGTCTATTA 57.504 39.130 0.00 0.00 45.31 0.98
866 1173 4.352887 GAAGCGAAACGAGCTAGTCTATT 58.647 43.478 0.00 0.00 45.31 1.73
867 1174 3.243134 GGAAGCGAAACGAGCTAGTCTAT 60.243 47.826 0.00 0.00 45.31 1.98
868 1175 2.097142 GGAAGCGAAACGAGCTAGTCTA 59.903 50.000 0.00 0.00 45.31 2.59
869 1176 1.135344 GGAAGCGAAACGAGCTAGTCT 60.135 52.381 0.00 0.00 45.31 3.24
870 1177 1.135344 AGGAAGCGAAACGAGCTAGTC 60.135 52.381 0.00 0.00 45.31 2.59
871 1178 0.889306 AGGAAGCGAAACGAGCTAGT 59.111 50.000 0.00 0.00 45.31 2.57
872 1179 1.133407 AGAGGAAGCGAAACGAGCTAG 59.867 52.381 0.00 0.00 45.31 3.42
873 1180 1.132643 GAGAGGAAGCGAAACGAGCTA 59.867 52.381 0.00 0.00 45.31 3.32
875 1182 1.079317 GGAGAGGAAGCGAAACGAGC 61.079 60.000 0.00 0.00 0.00 5.03
876 1183 0.528470 AGGAGAGGAAGCGAAACGAG 59.472 55.000 0.00 0.00 0.00 4.18
877 1184 0.966920 AAGGAGAGGAAGCGAAACGA 59.033 50.000 0.00 0.00 0.00 3.85
878 1185 1.071605 CAAGGAGAGGAAGCGAAACG 58.928 55.000 0.00 0.00 0.00 3.60
879 1186 1.801178 CACAAGGAGAGGAAGCGAAAC 59.199 52.381 0.00 0.00 0.00 2.78
880 1187 1.691976 TCACAAGGAGAGGAAGCGAAA 59.308 47.619 0.00 0.00 0.00 3.46
881 1188 1.338107 TCACAAGGAGAGGAAGCGAA 58.662 50.000 0.00 0.00 0.00 4.70
882 1189 1.478510 GATCACAAGGAGAGGAAGCGA 59.521 52.381 0.00 0.00 0.00 4.93
883 1190 1.480137 AGATCACAAGGAGAGGAAGCG 59.520 52.381 0.00 0.00 0.00 4.68
884 1191 3.197549 AGAAGATCACAAGGAGAGGAAGC 59.802 47.826 0.00 0.00 0.00 3.86
885 1192 5.419239 AAGAAGATCACAAGGAGAGGAAG 57.581 43.478 0.00 0.00 0.00 3.46
886 1193 5.513788 CCAAAGAAGATCACAAGGAGAGGAA 60.514 44.000 0.00 0.00 0.00 3.36
887 1194 4.019860 CCAAAGAAGATCACAAGGAGAGGA 60.020 45.833 0.00 0.00 0.00 3.71
888 1195 4.260170 CCAAAGAAGATCACAAGGAGAGG 58.740 47.826 0.00 0.00 0.00 3.69
889 1196 4.694509 CACCAAAGAAGATCACAAGGAGAG 59.305 45.833 0.00 0.00 0.00 3.20
890 1197 4.103153 ACACCAAAGAAGATCACAAGGAGA 59.897 41.667 0.00 0.00 0.00 3.71
891 1198 4.214971 CACACCAAAGAAGATCACAAGGAG 59.785 45.833 0.00 0.00 0.00 3.69
892 1199 4.136796 CACACCAAAGAAGATCACAAGGA 58.863 43.478 0.00 0.00 0.00 3.36
893 1200 3.885297 ACACACCAAAGAAGATCACAAGG 59.115 43.478 0.00 0.00 0.00 3.61
894 1201 5.066375 TGAACACACCAAAGAAGATCACAAG 59.934 40.000 0.00 0.00 0.00 3.16
895 1202 4.946772 TGAACACACCAAAGAAGATCACAA 59.053 37.500 0.00 0.00 0.00 3.33
896 1203 4.522114 TGAACACACCAAAGAAGATCACA 58.478 39.130 0.00 0.00 0.00 3.58
897 1204 4.576463 ACTGAACACACCAAAGAAGATCAC 59.424 41.667 0.00 0.00 0.00 3.06
898 1205 4.780815 ACTGAACACACCAAAGAAGATCA 58.219 39.130 0.00 0.00 0.00 2.92
899 1206 5.296780 TCAACTGAACACACCAAAGAAGATC 59.703 40.000 0.00 0.00 0.00 2.75
900 1207 5.192927 TCAACTGAACACACCAAAGAAGAT 58.807 37.500 0.00 0.00 0.00 2.40
901 1208 4.584874 TCAACTGAACACACCAAAGAAGA 58.415 39.130 0.00 0.00 0.00 2.87
902 1209 4.963276 TCAACTGAACACACCAAAGAAG 57.037 40.909 0.00 0.00 0.00 2.85
903 1210 4.157656 CCTTCAACTGAACACACCAAAGAA 59.842 41.667 0.00 0.00 0.00 2.52
904 1211 3.694072 CCTTCAACTGAACACACCAAAGA 59.306 43.478 0.00 0.00 0.00 2.52
905 1212 3.181487 CCCTTCAACTGAACACACCAAAG 60.181 47.826 0.00 0.00 0.00 2.77
906 1213 2.757868 CCCTTCAACTGAACACACCAAA 59.242 45.455 0.00 0.00 0.00 3.28
907 1214 2.025793 TCCCTTCAACTGAACACACCAA 60.026 45.455 0.00 0.00 0.00 3.67
908 1215 1.562008 TCCCTTCAACTGAACACACCA 59.438 47.619 0.00 0.00 0.00 4.17
1078 1388 4.394712 CGAGGGAGGCAGCCGTTT 62.395 66.667 5.55 0.00 0.00 3.60
1682 2357 1.342174 GGATAGGAAACGACCGGCATA 59.658 52.381 0.00 0.00 34.73 3.14
2448 5152 9.086758 GCCTACATACCTAAGGAATAGTTTCTA 57.913 37.037 0.00 0.00 31.64 2.10
2538 5242 1.404986 GGTAACACCAGCTCGCACATA 60.405 52.381 0.00 0.00 38.42 2.29
2787 5492 2.848071 GTGGGTATTCAAGAAGGGGGTA 59.152 50.000 0.00 0.00 0.00 3.69
2788 5493 1.639108 GTGGGTATTCAAGAAGGGGGT 59.361 52.381 0.00 0.00 0.00 4.95
2790 5495 3.449746 TTGTGGGTATTCAAGAAGGGG 57.550 47.619 0.00 0.00 0.00 4.79
2791 5496 4.407365 ACTTTGTGGGTATTCAAGAAGGG 58.593 43.478 0.00 0.00 0.00 3.95
2792 5497 5.534654 TCAACTTTGTGGGTATTCAAGAAGG 59.465 40.000 0.00 0.00 0.00 3.46
2793 5498 6.633500 TCAACTTTGTGGGTATTCAAGAAG 57.367 37.500 0.00 0.00 0.00 2.85
2796 5501 5.163513 GCATCAACTTTGTGGGTATTCAAG 58.836 41.667 0.00 0.00 0.00 3.02
2800 6752 2.831526 GGGCATCAACTTTGTGGGTATT 59.168 45.455 0.00 0.00 0.00 1.89
2802 6754 1.549037 GGGGCATCAACTTTGTGGGTA 60.549 52.381 0.00 0.00 0.00 3.69
3129 7102 2.233922 AGACACTACATCCCAAAGGTCG 59.766 50.000 0.00 0.00 0.00 4.79
3259 7249 5.308497 TCTTCACATACCTACTCACCCAAAA 59.692 40.000 0.00 0.00 0.00 2.44
3454 7497 5.528043 TTTCAACAAGGTGCACATACAAT 57.472 34.783 20.43 0.00 0.00 2.71
3768 7846 6.297641 CGCGCTCTTTATTTAATGTAACGATG 59.702 38.462 5.56 0.00 0.00 3.84
3769 7847 6.352526 CGCGCTCTTTATTTAATGTAACGAT 58.647 36.000 5.56 0.00 0.00 3.73
3770 7848 5.276489 CCGCGCTCTTTATTTAATGTAACGA 60.276 40.000 5.56 0.00 0.00 3.85
3771 7849 4.896238 CCGCGCTCTTTATTTAATGTAACG 59.104 41.667 5.56 0.00 0.00 3.18
3772 7850 5.803118 ACCGCGCTCTTTATTTAATGTAAC 58.197 37.500 5.56 0.00 0.00 2.50
3773 7851 6.092396 TGAACCGCGCTCTTTATTTAATGTAA 59.908 34.615 5.56 0.00 0.00 2.41
3774 7852 5.581479 TGAACCGCGCTCTTTATTTAATGTA 59.419 36.000 5.56 0.00 0.00 2.29
3775 7853 4.393680 TGAACCGCGCTCTTTATTTAATGT 59.606 37.500 5.56 0.00 0.00 2.71
3776 7854 4.904116 TGAACCGCGCTCTTTATTTAATG 58.096 39.130 5.56 0.00 0.00 1.90
3777 7855 5.123344 AGTTGAACCGCGCTCTTTATTTAAT 59.877 36.000 5.56 0.00 0.00 1.40
3778 7856 4.453136 AGTTGAACCGCGCTCTTTATTTAA 59.547 37.500 5.56 0.00 0.00 1.52
3779 7857 3.998341 AGTTGAACCGCGCTCTTTATTTA 59.002 39.130 5.56 0.00 0.00 1.40
3783 7861 2.728690 TAGTTGAACCGCGCTCTTTA 57.271 45.000 5.56 0.00 0.00 1.85
3785 7863 1.873698 TTTAGTTGAACCGCGCTCTT 58.126 45.000 5.56 0.00 0.00 2.85
3999 8078 2.481854 CGGATTTCCTGCAGAGATGAG 58.518 52.381 17.39 0.00 0.00 2.90
4125 8204 1.004918 GGCGGGACTATCCAATCCG 60.005 63.158 0.00 0.00 38.64 4.18
4162 8241 8.768397 ACTGGATCCTACTGACATTACAAAATA 58.232 33.333 14.23 0.00 0.00 1.40
4177 8256 6.570692 TGTAATCGAAGAAACTGGATCCTAC 58.429 40.000 14.23 2.81 43.58 3.18


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

AutoCloner maintained by Alex Coulton.