Multiple sequence alignment - TraesCS1D01G443300

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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 TraesCS1D01G443300 chr1D 100.000 7407 0 0 1 7407 487274116 487281522 0.000000e+00 13679.0
1 TraesCS1D01G443300 chr1D 93.076 1242 48 10 4896 6099 8479231 8477990 0.000000e+00 1783.0
2 TraesCS1D01G443300 chr1D 92.512 1242 55 14 4896 6099 8517104 8515863 0.000000e+00 1744.0
3 TraesCS1D01G443300 chr1D 95.468 1015 33 6 4898 5901 233088288 233087276 0.000000e+00 1607.0
4 TraesCS1D01G443300 chr1D 94.938 810 30 4 4899 5697 2678709 2677900 0.000000e+00 1258.0
5 TraesCS1D01G443300 chr1D 81.190 1260 219 11 1834 3088 487288555 487289801 0.000000e+00 998.0
6 TraesCS1D01G443300 chr1D 82.664 1096 178 9 2003 3092 487314938 487316027 0.000000e+00 961.0
7 TraesCS1D01G443300 chr1D 83.654 312 51 0 992 1303 487313733 487314044 2.020000e-75 294.0
8 TraesCS1D01G443300 chr1A 92.551 2913 137 24 711 3603 584846482 584849334 0.000000e+00 4104.0
9 TraesCS1D01G443300 chr1A 92.778 1357 62 8 4890 6211 534170638 534169283 0.000000e+00 1930.0
10 TraesCS1D01G443300 chr1A 92.237 1301 50 20 4896 6159 425262640 425261354 0.000000e+00 1796.0
11 TraesCS1D01G443300 chr1A 93.264 1158 77 1 6250 7407 584862017 584863173 0.000000e+00 1705.0
12 TraesCS1D01G443300 chr1A 89.474 817 78 4 1998 2812 584840187 584840997 0.000000e+00 1026.0
13 TraesCS1D01G443300 chr1A 81.144 1066 189 9 2032 3091 584754900 584755959 0.000000e+00 845.0
14 TraesCS1D01G443300 chr1A 80.984 752 63 29 4153 4896 584861350 584862029 2.370000e-144 523.0
15 TraesCS1D01G443300 chr1A 87.821 312 38 0 992 1303 584753430 584753741 4.220000e-97 366.0
16 TraesCS1D01G443300 chr1A 87.500 312 15 11 3 296 584845662 584845967 9.210000e-89 339.0
17 TraesCS1D01G443300 chr1A 81.330 391 53 11 992 1375 584836280 584836657 4.340000e-77 300.0
18 TraesCS1D01G443300 chr1A 84.520 323 22 8 405 725 584845967 584846263 2.020000e-75 294.0
19 TraesCS1D01G443300 chr1A 91.011 178 16 0 3768 3945 584854711 584854888 2.670000e-59 241.0
20 TraesCS1D01G443300 chr1A 95.370 108 5 0 292 399 35575934 35575827 9.880000e-39 172.0
21 TraesCS1D01G443300 chr1A 94.545 110 6 0 293 402 348850076 348849967 3.550000e-38 171.0
22 TraesCS1D01G443300 chr1A 100.000 38 0 0 4118 4155 584856108 584856145 3.710000e-08 71.3
23 TraesCS1D01G443300 chr1A 91.489 47 2 2 3497 3543 64714374 64714330 6.200000e-06 63.9
24 TraesCS1D01G443300 chr1B 91.761 2925 176 31 736 3634 678606803 678603918 0.000000e+00 4006.0
25 TraesCS1D01G443300 chr1B 91.379 2784 183 26 710 3477 678486789 678484047 0.000000e+00 3759.0
26 TraesCS1D01G443300 chr1B 92.966 2431 126 17 1493 3908 678311781 678314181 0.000000e+00 3500.0
27 TraesCS1D01G443300 chr1B 91.045 2546 159 32 717 3224 641196672 641199186 0.000000e+00 3374.0
28 TraesCS1D01G443300 chr1B 92.917 2033 114 14 1888 3908 678406896 678408910 0.000000e+00 2929.0
29 TraesCS1D01G443300 chr1B 93.089 1939 105 12 1708 3634 678790434 678788513 0.000000e+00 2811.0
30 TraesCS1D01G443300 chr1B 93.209 1826 101 14 2000 3813 678738788 678736974 0.000000e+00 2663.0
31 TraesCS1D01G443300 chr1B 93.270 1798 99 13 1456 3240 678552878 678551090 0.000000e+00 2630.0
32 TraesCS1D01G443300 chr1B 91.028 1828 123 22 2316 4116 641123346 641125159 0.000000e+00 2429.0
33 TraesCS1D01G443300 chr1B 90.391 1686 130 18 2338 3999 678409507 678411184 0.000000e+00 2187.0
34 TraesCS1D01G443300 chr1B 93.273 1427 82 5 2004 3418 678444490 678443066 0.000000e+00 2091.0
35 TraesCS1D01G443300 chr1B 94.492 1162 60 2 6249 7407 678315503 678316663 0.000000e+00 1788.0
36 TraesCS1D01G443300 chr1B 94.392 1159 64 1 6249 7407 678603060 678601903 0.000000e+00 1779.0
37 TraesCS1D01G443300 chr1B 93.529 1159 74 1 6249 7407 678786997 678785840 0.000000e+00 1724.0
38 TraesCS1D01G443300 chr1B 92.487 1158 86 1 6250 7407 678482312 678481156 0.000000e+00 1655.0
39 TraesCS1D01G443300 chr1B 92.062 1159 88 3 6249 7407 641125587 641126741 0.000000e+00 1628.0
40 TraesCS1D01G443300 chr1B 91.509 1166 89 7 1166 2329 641111808 641112965 0.000000e+00 1596.0
41 TraesCS1D01G443300 chr1B 89.560 1159 119 2 6249 7407 678745127 678743971 0.000000e+00 1469.0
42 TraesCS1D01G443300 chr1B 89.215 1159 123 2 6249 7407 678550039 678548883 0.000000e+00 1447.0
43 TraesCS1D01G443300 chr1B 88.803 1161 125 5 6249 7407 641200609 641201766 0.000000e+00 1419.0
44 TraesCS1D01G443300 chr1B 87.024 1025 56 24 3924 4896 678787983 678786984 0.000000e+00 1085.0
45 TraesCS1D01G443300 chr1B 91.436 724 45 5 704 1423 678553585 678552875 0.000000e+00 977.0
46 TraesCS1D01G443300 chr1B 93.323 629 38 2 992 1616 678739824 678739196 0.000000e+00 926.0
47 TraesCS1D01G443300 chr1B 90.808 631 52 4 992 1616 678445538 678444908 0.000000e+00 839.0
48 TraesCS1D01G443300 chr1B 90.837 633 44 4 736 1366 678791093 678790473 0.000000e+00 835.0
49 TraesCS1D01G443300 chr1B 89.172 628 43 9 697 1322 678753343 678752739 0.000000e+00 760.0
50 TraesCS1D01G443300 chr1B 91.636 538 28 8 3941 4467 678721204 678720673 0.000000e+00 728.0
51 TraesCS1D01G443300 chr1B 91.111 540 35 9 3921 4454 678314490 678315022 0.000000e+00 719.0
52 TraesCS1D01G443300 chr1B 89.910 555 39 8 3924 4467 678442250 678441702 0.000000e+00 699.0
53 TraesCS1D01G443300 chr1B 94.483 435 23 1 3512 3945 678484044 678483610 0.000000e+00 669.0
54 TraesCS1D01G443300 chr1B 89.670 455 23 11 4460 4895 678315066 678315515 6.490000e-155 558.0
55 TraesCS1D01G443300 chr1B 92.581 310 16 4 4161 4467 678483052 678482747 8.820000e-119 438.0
56 TraesCS1D01G443300 chr1B 94.097 288 11 5 3473 3760 678443070 678442789 4.100000e-117 433.0
57 TraesCS1D01G443300 chr1B 93.704 270 15 1 3639 3908 678442789 678442522 3.220000e-108 403.0
58 TraesCS1D01G443300 chr1B 84.864 403 53 4 908 1303 678765785 678765384 4.160000e-107 399.0
59 TraesCS1D01G443300 chr1B 90.541 296 25 2 401 695 678487204 678486911 9.010000e-104 388.0
60 TraesCS1D01G443300 chr1B 95.122 246 12 0 3663 3908 678603917 678603672 9.010000e-104 388.0
61 TraesCS1D01G443300 chr1B 88.253 332 27 6 3915 4236 678409173 678409502 3.240000e-103 387.0
62 TraesCS1D01G443300 chr1B 95.062 243 12 0 3666 3908 678788509 678788267 4.190000e-102 383.0
63 TraesCS1D01G443300 chr1B 89.508 305 24 5 1618 1921 678752507 678752210 5.420000e-101 379.0
64 TraesCS1D01G443300 chr1B 82.774 447 43 13 4463 4896 678482725 678482300 1.170000e-97 368.0
65 TraesCS1D01G443300 chr1B 82.609 437 43 19 4469 4896 678411239 678411651 9.140000e-94 355.0
66 TraesCS1D01G443300 chr1B 90.037 271 17 5 1 264 641110570 641110837 7.120000e-90 342.0
67 TraesCS1D01G443300 chr1B 95.455 176 7 1 4721 4896 678603221 678603047 5.660000e-71 279.0
68 TraesCS1D01G443300 chr1B 93.923 181 11 0 405 585 641110932 641111112 2.630000e-69 274.0
69 TraesCS1D01G443300 chr1B 89.904 208 9 4 775 979 641111608 641111806 2.650000e-64 257.0
70 TraesCS1D01G443300 chr1B 87.336 229 14 9 3944 4162 678483352 678483129 1.600000e-61 248.0
71 TraesCS1D01G443300 chr1B 92.169 166 12 1 130 294 678487368 678487203 4.470000e-57 233.0
72 TraesCS1D01G443300 chr1B 92.903 155 7 1 405 555 678554737 678554583 9.670000e-54 222.0
73 TraesCS1D01G443300 chr1B 91.018 167 9 1 130 296 678753689 678753529 3.480000e-53 220.0
74 TraesCS1D01G443300 chr1B 90.476 168 12 2 130 293 678554906 678554739 1.250000e-52 219.0
75 TraesCS1D01G443300 chr1B 93.289 149 5 2 4136 4284 641125229 641125372 1.620000e-51 215.0
76 TraesCS1D01G443300 chr1B 90.361 166 13 2 132 294 678607140 678606975 1.620000e-51 215.0
77 TraesCS1D01G443300 chr1B 88.136 177 16 3 413 585 678766181 678766006 9.740000e-49 206.0
78 TraesCS1D01G443300 chr1B 96.581 117 4 0 469 585 678791222 678791106 2.110000e-45 195.0
79 TraesCS1D01G443300 chr1B 93.913 115 7 0 405 519 678753529 678753415 2.750000e-39 174.0
80 TraesCS1D01G443300 chr1B 91.270 126 6 1 460 585 678606936 678606816 4.600000e-37 167.0
81 TraesCS1D01G443300 chr1B 95.833 96 4 0 4372 4467 641125410 641125505 9.950000e-34 156.0
82 TraesCS1D01G443300 chr1B 94.000 100 5 1 3901 3999 678314393 678314492 4.630000e-32 150.0
83 TraesCS1D01G443300 chr1B 82.184 174 24 6 3924 4093 678603389 678603219 7.750000e-30 143.0
84 TraesCS1D01G443300 chr1B 96.104 77 3 0 698 774 641111405 641111481 7.800000e-25 126.0
85 TraesCS1D01G443300 chr1B 85.833 120 8 3 130 249 678791614 678791504 1.310000e-22 119.0
86 TraesCS1D01G443300 chr1B 78.523 149 18 10 4529 4677 641200250 641200384 1.320000e-12 86.1
87 TraesCS1D01G443300 chr7D 91.481 1350 61 23 4892 6215 64225111 64226432 0.000000e+00 1807.0
88 TraesCS1D01G443300 chr5B 89.175 1358 104 25 4898 6214 594138699 594140054 0.000000e+00 1653.0
89 TraesCS1D01G443300 chr5B 71.932 823 204 22 2281 3091 665939409 665940216 1.620000e-51 215.0
90 TraesCS1D01G443300 chr5B 70.291 892 217 35 2218 3091 64736857 64735996 1.300000e-27 135.0
91 TraesCS1D01G443300 chr5B 100.000 33 0 0 3510 3542 658562654 658562686 2.230000e-05 62.1
92 TraesCS1D01G443300 chr6D 88.628 1363 103 21 4899 6222 157039612 157038263 0.000000e+00 1611.0
93 TraesCS1D01G443300 chr6D 88.471 850 69 16 5390 6214 24321482 24320637 0.000000e+00 1000.0
94 TraesCS1D01G443300 chr6D 91.803 61 5 0 617 677 127755545 127755605 1.320000e-12 86.1
95 TraesCS1D01G443300 chr3B 88.544 1353 118 24 4896 6214 803061103 803062452 0.000000e+00 1605.0
96 TraesCS1D01G443300 chr3B 91.089 808 59 10 4896 5692 345709826 345710631 0.000000e+00 1081.0
97 TraesCS1D01G443300 chr3B 92.537 67 4 1 621 687 85079028 85078963 2.200000e-15 95.3
98 TraesCS1D01G443300 chr3A 88.187 1346 121 22 4891 6205 179532980 179534318 0.000000e+00 1570.0
99 TraesCS1D01G443300 chr3A 84.762 105 11 5 6092 6194 387293005 387293106 4.730000e-17 100.0
100 TraesCS1D01G443300 chr5A 87.325 1286 119 18 4896 6140 503682599 503683881 0.000000e+00 1432.0
101 TraesCS1D01G443300 chrUn 86.506 1082 108 26 5138 6196 444039605 444040671 0.000000e+00 1155.0
102 TraesCS1D01G443300 chrUn 100.000 34 0 0 6186 6219 209201508 209201541 6.200000e-06 63.9
103 TraesCS1D01G443300 chr2A 88.176 296 29 4 5925 6218 717938215 717937924 1.530000e-91 348.0
104 TraesCS1D01G443300 chr2A 95.536 112 5 0 288 399 759878069 759878180 5.900000e-41 180.0
105 TraesCS1D01G443300 chr2A 95.327 107 5 0 293 399 510433482 510433588 3.550000e-38 171.0
106 TraesCS1D01G443300 chr2A 94.545 110 6 0 291 400 555342332 555342223 3.550000e-38 171.0
107 TraesCS1D01G443300 chr7A 93.966 116 6 1 293 408 635205175 635205289 2.750000e-39 174.0
108 TraesCS1D01G443300 chr7A 91.803 122 9 1 291 411 269960318 269960439 1.280000e-37 169.0
109 TraesCS1D01G443300 chr7A 93.694 111 7 0 292 402 572868076 572867966 4.600000e-37 167.0
110 TraesCS1D01G443300 chr7A 86.458 96 4 4 598 685 129877026 129876932 6.120000e-16 97.1
111 TraesCS1D01G443300 chr6B 92.982 114 8 0 286 399 693130458 693130571 4.600000e-37 167.0
112 TraesCS1D01G443300 chr2B 89.412 85 2 5 600 677 296066644 296066728 4.730000e-17 100.0
113 TraesCS1D01G443300 chr2B 95.161 62 3 0 620 681 434185027 434185088 1.700000e-16 99.0
114 TraesCS1D01G443300 chr7B 93.846 65 3 1 620 684 312542122 312542185 6.120000e-16 97.1
115 TraesCS1D01G443300 chr7B 88.158 76 8 1 620 695 131183291 131183217 1.020000e-13 89.8
116 TraesCS1D01G443300 chr5D 85.542 83 11 1 600 681 76906044 76905962 1.320000e-12 86.1
117 TraesCS1D01G443300 chr5D 85.526 76 9 2 3017 3091 27321614 27321540 2.220000e-10 78.7


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 TraesCS1D01G443300 chr1D 487274116 487281522 7406 False 13679.000000 13679 100.000000 1 7407 1 chr1D.!!$F1 7406
1 TraesCS1D01G443300 chr1D 8477990 8479231 1241 True 1783.000000 1783 93.076000 4896 6099 1 chr1D.!!$R2 1203
2 TraesCS1D01G443300 chr1D 8515863 8517104 1241 True 1744.000000 1744 92.512000 4896 6099 1 chr1D.!!$R3 1203
3 TraesCS1D01G443300 chr1D 233087276 233088288 1012 True 1607.000000 1607 95.468000 4898 5901 1 chr1D.!!$R4 1003
4 TraesCS1D01G443300 chr1D 2677900 2678709 809 True 1258.000000 1258 94.938000 4899 5697 1 chr1D.!!$R1 798
5 TraesCS1D01G443300 chr1D 487288555 487289801 1246 False 998.000000 998 81.190000 1834 3088 1 chr1D.!!$F2 1254
6 TraesCS1D01G443300 chr1D 487313733 487316027 2294 False 627.500000 961 83.159000 992 3092 2 chr1D.!!$F3 2100
7 TraesCS1D01G443300 chr1A 534169283 534170638 1355 True 1930.000000 1930 92.778000 4890 6211 1 chr1A.!!$R5 1321
8 TraesCS1D01G443300 chr1A 425261354 425262640 1286 True 1796.000000 1796 92.237000 4896 6159 1 chr1A.!!$R4 1263
9 TraesCS1D01G443300 chr1A 584845662 584849334 3672 False 1579.000000 4104 88.190333 3 3603 3 chr1A.!!$F3 3600
10 TraesCS1D01G443300 chr1A 584861350 584863173 1823 False 1114.000000 1705 87.124000 4153 7407 2 chr1A.!!$F5 3254
11 TraesCS1D01G443300 chr1A 584836280 584840997 4717 False 663.000000 1026 85.402000 992 2812 2 chr1A.!!$F2 1820
12 TraesCS1D01G443300 chr1A 584753430 584755959 2529 False 605.500000 845 84.482500 992 3091 2 chr1A.!!$F1 2099
13 TraesCS1D01G443300 chr1B 678736974 678739824 2850 True 1794.500000 2663 93.266000 992 3813 2 chr1B.!!$R7 2821
14 TraesCS1D01G443300 chr1B 641196672 641201766 5094 False 1626.366667 3374 86.123667 717 7407 3 chr1B.!!$F3 6690
15 TraesCS1D01G443300 chr1B 678743971 678745127 1156 True 1469.000000 1469 89.560000 6249 7407 1 chr1B.!!$R2 1158
16 TraesCS1D01G443300 chr1B 678406896 678411651 4755 False 1464.500000 2929 88.542500 1888 4896 4 chr1B.!!$F5 3008
17 TraesCS1D01G443300 chr1B 678311781 678316663 4882 False 1343.000000 3500 92.447800 1493 7407 5 chr1B.!!$F4 5914
18 TraesCS1D01G443300 chr1B 641123346 641126741 3395 False 1107.000000 2429 93.053000 2316 7407 4 chr1B.!!$F2 5091
19 TraesCS1D01G443300 chr1B 678548883 678554906 6023 True 1099.000000 2630 91.460000 130 7407 5 chr1B.!!$R5 7277
20 TraesCS1D01G443300 chr1B 678785840 678791614 5774 True 1021.714286 2811 91.707857 130 7407 7 chr1B.!!$R10 7277
21 TraesCS1D01G443300 chr1B 678601903 678607140 5237 True 996.714286 4006 91.506429 132 7407 7 chr1B.!!$R6 7275
22 TraesCS1D01G443300 chr1B 678481156 678487368 6212 True 969.750000 3759 90.468750 130 7407 8 chr1B.!!$R4 7277
23 TraesCS1D01G443300 chr1B 678441702 678445538 3836 True 893.000000 2091 92.358400 992 4467 5 chr1B.!!$R3 3475
24 TraesCS1D01G443300 chr1B 678720673 678721204 531 True 728.000000 728 91.636000 3941 4467 1 chr1B.!!$R1 526
25 TraesCS1D01G443300 chr1B 641110570 641112965 2395 False 519.000000 1596 92.295400 1 2329 5 chr1B.!!$F1 2328
26 TraesCS1D01G443300 chr1B 678752210 678753689 1479 True 383.250000 760 90.902750 130 1921 4 chr1B.!!$R8 1791
27 TraesCS1D01G443300 chr1B 678765384 678766181 797 True 302.500000 399 86.500000 413 1303 2 chr1B.!!$R9 890
28 TraesCS1D01G443300 chr7D 64225111 64226432 1321 False 1807.000000 1807 91.481000 4892 6215 1 chr7D.!!$F1 1323
29 TraesCS1D01G443300 chr5B 594138699 594140054 1355 False 1653.000000 1653 89.175000 4898 6214 1 chr5B.!!$F1 1316
30 TraesCS1D01G443300 chr5B 665939409 665940216 807 False 215.000000 215 71.932000 2281 3091 1 chr5B.!!$F3 810
31 TraesCS1D01G443300 chr6D 157038263 157039612 1349 True 1611.000000 1611 88.628000 4899 6222 1 chr6D.!!$R2 1323
32 TraesCS1D01G443300 chr6D 24320637 24321482 845 True 1000.000000 1000 88.471000 5390 6214 1 chr6D.!!$R1 824
33 TraesCS1D01G443300 chr3B 803061103 803062452 1349 False 1605.000000 1605 88.544000 4896 6214 1 chr3B.!!$F2 1318
34 TraesCS1D01G443300 chr3B 345709826 345710631 805 False 1081.000000 1081 91.089000 4896 5692 1 chr3B.!!$F1 796
35 TraesCS1D01G443300 chr3A 179532980 179534318 1338 False 1570.000000 1570 88.187000 4891 6205 1 chr3A.!!$F1 1314
36 TraesCS1D01G443300 chr5A 503682599 503683881 1282 False 1432.000000 1432 87.325000 4896 6140 1 chr5A.!!$F1 1244
37 TraesCS1D01G443300 chrUn 444039605 444040671 1066 False 1155.000000 1155 86.506000 5138 6196 1 chrUn.!!$F2 1058

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
885 2515 0.460987 CAAGGTCCGATCCAGCAGAC 60.461 60.000 0.00 0.00 0.00 3.51 F
888 2518 1.142748 GTCCGATCCAGCAGACCAG 59.857 63.158 0.00 0.00 0.00 4.00 F
922 2552 2.013563 GCAAGCAAGATCCCATCACGA 61.014 52.381 0.00 0.00 0.00 4.35 F
1657 6559 2.634940 ACACACTCTGCCTGTTCATAGT 59.365 45.455 0.00 0.00 0.00 2.12 F
1891 7312 3.393278 TGGTCTTAACCTTGGCAGTTACT 59.607 43.478 0.00 0.00 46.60 2.24 F
2893 8850 5.374921 CTGAAATCTATGAAGCCTGGTCAT 58.625 41.667 5.29 5.29 39.12 3.06 F
4430 11379 0.249826 AAAATTGTGGTTGCTGCCGG 60.250 50.000 0.00 0.00 0.00 6.13 F
4743 13150 0.303493 GACGCTGACGCAAAAGAACA 59.697 50.000 0.00 0.00 45.53 3.18 F
5599 14050 0.033920 CCCCAAACAAGCTCCTTTGC 59.966 55.000 9.57 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 7884 1.155859 AAAATGGCCAGCACCCAGA 59.844 52.632 13.05 0.0 35.48 3.86 R
2283 8235 7.122138 TCTGTCATGCTCTCAGATAAAGAAT 57.878 36.000 0.00 0.0 34.00 2.40 R
2893 8850 7.921041 ATTACTATCTCTCACTGATTCCCAA 57.079 36.000 0.00 0.0 0.00 4.12 R
3510 9516 3.572682 TCGGATCCATATTACTTGTCGCT 59.427 43.478 13.41 0.0 0.00 4.93 R
3511 9517 3.909430 TCGGATCCATATTACTTGTCGC 58.091 45.455 13.41 0.0 0.00 5.19 R
4483 12843 0.458543 CTGTTCATCGTCTCCCACCG 60.459 60.000 0.00 0.0 0.00 4.94 R
5375 13821 0.325765 TGGGTATGATGGTCGGTGGA 60.326 55.000 0.00 0.0 0.00 4.02 R
5765 14225 1.949847 GCGGCTCCTCTTGTGCTCTA 61.950 60.000 0.00 0.0 33.94 2.43 R
7039 15572 1.748879 GCAGTTTGGATAGGCCGCA 60.749 57.895 0.00 0.0 40.66 5.69 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
52 58 1.592223 GACTCGCTTAGGCAGGTGT 59.408 57.895 0.00 0.00 38.60 4.16
59 65 1.739067 CTTAGGCAGGTGTTGGTAGC 58.261 55.000 0.00 0.00 0.00 3.58
60 66 1.279271 CTTAGGCAGGTGTTGGTAGCT 59.721 52.381 0.00 0.00 0.00 3.32
61 67 2.241281 TAGGCAGGTGTTGGTAGCTA 57.759 50.000 0.00 0.00 0.00 3.32
63 69 0.613777 GGCAGGTGTTGGTAGCTAGT 59.386 55.000 0.00 0.00 0.00 2.57
64 70 1.829222 GGCAGGTGTTGGTAGCTAGTA 59.171 52.381 0.00 0.00 0.00 1.82
66 72 3.458189 GCAGGTGTTGGTAGCTAGTATG 58.542 50.000 0.00 0.00 0.00 2.39
99 114 9.688091 TCCTATCATCTTGTATGTATCTACCTC 57.312 37.037 0.00 0.00 0.00 3.85
100 115 9.693739 CCTATCATCTTGTATGTATCTACCTCT 57.306 37.037 0.00 0.00 0.00 3.69
103 118 8.865420 TCATCTTGTATGTATCTACCTCTACC 57.135 38.462 0.00 0.00 0.00 3.18
104 119 8.670490 TCATCTTGTATGTATCTACCTCTACCT 58.330 37.037 0.00 0.00 0.00 3.08
117 132 1.833630 CTCTACCTGTGATGGCTTCCA 59.166 52.381 0.00 0.00 38.19 3.53
119 134 0.618458 TACCTGTGATGGCTTCCACC 59.382 55.000 0.00 0.00 35.80 4.61
250 280 5.888724 TCCTAGCTAGACACCATATATCTGC 59.111 44.000 22.70 0.00 0.00 4.26
299 329 6.402981 AAAAATGGATAACACCTACTCCCT 57.597 37.500 0.00 0.00 0.00 4.20
300 330 5.632034 AAATGGATAACACCTACTCCCTC 57.368 43.478 0.00 0.00 0.00 4.30
301 331 3.042059 TGGATAACACCTACTCCCTCC 57.958 52.381 0.00 0.00 0.00 4.30
302 332 1.962100 GGATAACACCTACTCCCTCCG 59.038 57.143 0.00 0.00 0.00 4.63
303 333 2.664015 GATAACACCTACTCCCTCCGT 58.336 52.381 0.00 0.00 0.00 4.69
304 334 2.610438 TAACACCTACTCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
305 335 1.264295 AACACCTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
306 336 0.614134 ACACCTACTCCCTCCGTTCC 60.614 60.000 0.00 0.00 0.00 3.62
307 337 1.379576 ACCTACTCCCTCCGTTCCG 60.380 63.158 0.00 0.00 0.00 4.30
308 338 1.077212 CCTACTCCCTCCGTTCCGA 60.077 63.158 0.00 0.00 0.00 4.55
309 339 0.682209 CCTACTCCCTCCGTTCCGAA 60.682 60.000 0.00 0.00 0.00 4.30
310 340 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
311 341 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
312 342 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
313 343 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
314 344 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
315 345 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
316 346 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
317 347 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
318 348 2.671396 CCTCCGTTCCGAATTACTTGTG 59.329 50.000 0.00 0.00 0.00 3.33
319 349 2.671396 CTCCGTTCCGAATTACTTGTGG 59.329 50.000 0.00 0.00 0.00 4.17
320 350 1.129811 CCGTTCCGAATTACTTGTGGC 59.870 52.381 0.00 0.00 0.00 5.01
321 351 1.801771 CGTTCCGAATTACTTGTGGCA 59.198 47.619 0.00 0.00 0.00 4.92
322 352 2.159707 CGTTCCGAATTACTTGTGGCAG 60.160 50.000 0.00 0.00 0.00 4.85
323 353 2.107950 TCCGAATTACTTGTGGCAGG 57.892 50.000 0.00 0.00 0.00 4.85
324 354 1.349688 TCCGAATTACTTGTGGCAGGT 59.650 47.619 0.00 0.00 0.00 4.00
338 368 4.528206 TGTGGCAGGTATGGATGTATCTAG 59.472 45.833 0.00 0.00 0.00 2.43
340 370 5.423610 GTGGCAGGTATGGATGTATCTAGAT 59.576 44.000 10.73 10.73 0.00 1.98
341 371 6.607600 GTGGCAGGTATGGATGTATCTAGATA 59.392 42.308 8.44 8.44 0.00 1.98
344 374 9.540538 GGCAGGTATGGATGTATCTAGATATAT 57.459 37.037 18.82 18.82 0.00 0.86
380 410 9.121658 AGATACATCTATTTCTGTGACGAGTAA 57.878 33.333 0.00 0.00 34.85 2.24
389 419 6.922980 TTCTGTGACGAGTAATTTAGAACG 57.077 37.500 0.00 0.00 0.00 3.95
390 420 6.245115 TCTGTGACGAGTAATTTAGAACGA 57.755 37.500 0.00 0.00 0.00 3.85
399 429 7.067981 ACGAGTAATTTAGAACGAAGGGAGTAT 59.932 37.037 0.00 0.00 0.00 2.12
569 734 1.745115 GCACTGAGGCGGCACATTA 60.745 57.895 13.08 0.00 0.00 1.90
581 746 2.352388 GGCACATTAGCCGAAACTACA 58.648 47.619 0.00 0.00 46.12 2.74
585 750 2.991190 ACATTAGCCGAAACTACACACG 59.009 45.455 0.00 0.00 0.00 4.49
586 751 2.798976 TTAGCCGAAACTACACACGT 57.201 45.000 0.00 0.00 0.00 4.49
591 760 0.704551 CGAAACTACACACGTACGCC 59.295 55.000 16.72 0.00 0.00 5.68
609 778 1.485480 GCCTTGGTAACTACTCCCTCC 59.515 57.143 0.00 0.00 37.61 4.30
881 2511 0.539986 TTACCAAGGTCCGATCCAGC 59.460 55.000 0.00 0.00 0.00 4.85
882 2512 0.616395 TACCAAGGTCCGATCCAGCA 60.616 55.000 0.00 0.00 0.00 4.41
883 2513 1.153289 CCAAGGTCCGATCCAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
884 2514 1.617018 CCAAGGTCCGATCCAGCAGA 61.617 60.000 0.00 0.00 0.00 4.26
885 2515 0.460987 CAAGGTCCGATCCAGCAGAC 60.461 60.000 0.00 0.00 0.00 3.51
886 2516 2.501610 GGTCCGATCCAGCAGACC 59.498 66.667 0.00 0.00 41.87 3.85
887 2517 2.359169 GGTCCGATCCAGCAGACCA 61.359 63.158 3.21 0.00 46.61 4.02
888 2518 1.142748 GTCCGATCCAGCAGACCAG 59.857 63.158 0.00 0.00 0.00 4.00
922 2552 2.013563 GCAAGCAAGATCCCATCACGA 61.014 52.381 0.00 0.00 0.00 4.35
931 2562 2.885644 CCATCACGAACCTCGCCG 60.886 66.667 0.00 0.00 45.12 6.46
1599 6435 7.696755 TCACAAATGATGGATTTTATCGACTG 58.303 34.615 0.00 0.00 31.41 3.51
1657 6559 2.634940 ACACACTCTGCCTGTTCATAGT 59.365 45.455 0.00 0.00 0.00 2.12
1719 6688 9.826574 TTACAATACTTGGTATCTGTTATCCAC 57.173 33.333 0.00 0.00 34.12 4.02
1820 7123 7.937942 GGCTGAGCATATGAAATATCTCCATAT 59.062 37.037 6.82 0.00 37.44 1.78
1821 7124 9.993454 GCTGAGCATATGAAATATCTCCATATA 57.007 33.333 6.97 0.00 37.44 0.86
1891 7312 3.393278 TGGTCTTAACCTTGGCAGTTACT 59.607 43.478 0.00 0.00 46.60 2.24
1974 7869 6.964807 TGGCTGAATGCATTTGTAATATCT 57.035 33.333 14.33 0.00 45.15 1.98
2283 8235 9.693739 GACTGAGGAGAGAGATATAATATTGGA 57.306 37.037 0.00 0.00 0.00 3.53
2438 8391 6.299604 GTTTACGTGTCTCAGACATTTGATG 58.700 40.000 11.62 0.00 44.63 3.07
2597 8550 5.488911 ACCTGTGGGAAGACAACATGTCTA 61.489 45.833 12.98 0.00 45.39 2.59
2893 8850 5.374921 CTGAAATCTATGAAGCCTGGTCAT 58.625 41.667 5.29 5.29 39.12 3.06
3226 9195 6.633500 TTCTTTTGGAACTGGTGTAAGATG 57.367 37.500 0.00 0.00 0.00 2.90
3480 9486 7.878547 AGTACACATTAGTAAGTACTCCCTC 57.121 40.000 0.00 0.00 42.38 4.30
3559 9565 3.382083 ACTAAGGCCATCGGGAAAATT 57.618 42.857 5.01 0.00 35.59 1.82
3612 9627 3.596214 GAGGTCTTTAGTTCGCATCCAA 58.404 45.455 0.00 0.00 0.00 3.53
3655 9670 8.094548 TGCATAAACACAGTCTCTTACTTACAT 58.905 33.333 0.00 0.00 35.76 2.29
3675 9807 5.694995 ACATATGCTATTGGGCTTACTGTT 58.305 37.500 1.58 0.00 0.00 3.16
3944 10587 6.901300 AGACATACTCCCTCCACAACTTAATA 59.099 38.462 0.00 0.00 0.00 0.98
3994 10654 9.481800 GTGCCAAAAACGTCTTATATTAAGTAC 57.518 33.333 0.00 0.00 0.00 2.73
3995 10655 8.382130 TGCCAAAAACGTCTTATATTAAGTACG 58.618 33.333 13.00 13.00 36.48 3.67
4001 10661 6.299141 ACGTCTTATATTAAGTACGGAGGGA 58.701 40.000 16.21 0.00 34.81 4.20
4002 10662 6.429385 ACGTCTTATATTAAGTACGGAGGGAG 59.571 42.308 16.21 0.00 34.81 4.30
4003 10663 6.429385 CGTCTTATATTAAGTACGGAGGGAGT 59.571 42.308 0.00 0.00 0.00 3.85
4004 10664 7.604164 CGTCTTATATTAAGTACGGAGGGAGTA 59.396 40.741 0.00 0.00 0.00 2.59
4005 10665 8.945057 GTCTTATATTAAGTACGGAGGGAGTAG 58.055 40.741 0.00 0.00 0.00 2.57
4006 10666 8.664079 TCTTATATTAAGTACGGAGGGAGTAGT 58.336 37.037 0.00 0.00 0.00 2.73
4085 10745 1.935300 GCTAACACACGTGGACAGAGG 60.935 57.143 21.57 4.81 34.19 3.69
4307 11117 7.789273 AAGCATATCTTCTGAAATCAGTGAG 57.211 36.000 10.06 9.44 44.12 3.51
4430 11379 0.249826 AAAATTGTGGTTGCTGCCGG 60.250 50.000 0.00 0.00 0.00 6.13
4506 12868 1.278985 TGGGAGACGATGAACAGCAAT 59.721 47.619 0.00 0.00 0.00 3.56
4620 12990 7.656412 TGTATTTTTGTGCTTCTCTATTGCAA 58.344 30.769 0.00 0.00 38.50 4.08
4634 13004 2.967459 TTGCAATAGTGTTCGCAGTG 57.033 45.000 0.00 0.00 35.47 3.66
4731 13138 0.394938 TTTAAGTGGGCAGACGCTGA 59.605 50.000 10.46 0.00 38.60 4.26
4743 13150 0.303493 GACGCTGACGCAAAAGAACA 59.697 50.000 0.00 0.00 45.53 3.18
4807 13223 1.847328 TCGTATGGGCTTGAGACTCA 58.153 50.000 0.00 0.00 0.00 3.41
4868 13308 7.122650 CCAAATCTAAACTTGGGAAATAGCAGA 59.877 37.037 0.00 0.00 38.77 4.26
4869 13309 8.689972 CAAATCTAAACTTGGGAAATAGCAGAT 58.310 33.333 0.00 0.00 0.00 2.90
4882 13322 8.257306 GGGAAATAGCAGATGACCAAAAATAAA 58.743 33.333 0.00 0.00 0.00 1.40
4883 13323 9.651913 GGAAATAGCAGATGACCAAAAATAAAA 57.348 29.630 0.00 0.00 0.00 1.52
4911 13351 7.520451 AGTATTTAACCGAAAAAGGCTTTCT 57.480 32.000 13.76 0.00 33.69 2.52
5055 13500 4.938575 TCTACAGGAAGGAAGAGAGAGT 57.061 45.455 0.00 0.00 0.00 3.24
5108 13553 4.116961 TGAACGAATCACAACGAAGAGTT 58.883 39.130 0.00 0.00 36.94 3.01
5132 13577 1.674611 CTGTGCACGACGAACCGATC 61.675 60.000 13.13 0.00 0.00 3.69
5245 13691 2.434359 GAAGAGGAACCACGGCGG 60.434 66.667 13.24 0.00 42.50 6.13
5321 13767 2.846193 CCAGAAAGAGTTTTCACCCGA 58.154 47.619 3.21 0.00 44.14 5.14
5375 13821 2.281070 CACGCTGCAGAACCACCT 60.281 61.111 20.43 0.00 0.00 4.00
5568 14017 0.823356 GTGAAGGGGCAGCAAAGACA 60.823 55.000 0.00 0.00 0.00 3.41
5599 14050 0.033920 CCCCAAACAAGCTCCTTTGC 59.966 55.000 9.57 0.00 0.00 3.68
5634 14093 2.750237 GGCAGGGAAAACGCCGAT 60.750 61.111 0.00 0.00 35.79 4.18
5947 14456 2.595463 CCAGGCACACACCACCAG 60.595 66.667 0.00 0.00 0.00 4.00
6069 14589 2.764128 GAGGACGAGGATGCCCCA 60.764 66.667 0.00 0.00 37.41 4.96
6231 14760 3.159347 GGGTCGGGCGGGACTTAT 61.159 66.667 7.17 0.00 37.12 1.73
6232 14761 2.420466 GGTCGGGCGGGACTTATC 59.580 66.667 7.17 0.00 37.12 1.75
6233 14762 2.428925 GGTCGGGCGGGACTTATCA 61.429 63.158 7.17 0.00 37.12 2.15
6234 14763 1.227176 GTCGGGCGGGACTTATCAC 60.227 63.158 0.62 0.00 34.09 3.06
6235 14764 1.683025 TCGGGCGGGACTTATCACA 60.683 57.895 0.00 0.00 0.00 3.58
6236 14765 1.046472 TCGGGCGGGACTTATCACAT 61.046 55.000 0.00 0.00 0.00 3.21
6237 14766 0.179056 CGGGCGGGACTTATCACATT 60.179 55.000 0.00 0.00 0.00 2.71
6238 14767 1.745827 CGGGCGGGACTTATCACATTT 60.746 52.381 0.00 0.00 0.00 2.32
6239 14768 1.676006 GGGCGGGACTTATCACATTTG 59.324 52.381 0.00 0.00 0.00 2.32
6240 14769 1.065551 GGCGGGACTTATCACATTTGC 59.934 52.381 0.00 0.00 0.00 3.68
6241 14770 2.017049 GCGGGACTTATCACATTTGCT 58.983 47.619 0.00 0.00 0.00 3.91
6242 14771 2.032178 GCGGGACTTATCACATTTGCTC 59.968 50.000 0.00 0.00 0.00 4.26
6243 14772 2.614057 CGGGACTTATCACATTTGCTCC 59.386 50.000 0.00 0.00 0.00 4.70
6244 14773 2.614057 GGGACTTATCACATTTGCTCCG 59.386 50.000 0.00 0.00 0.00 4.63
6245 14774 3.531538 GGACTTATCACATTTGCTCCGA 58.468 45.455 0.00 0.00 0.00 4.55
6246 14775 3.309954 GGACTTATCACATTTGCTCCGAC 59.690 47.826 0.00 0.00 0.00 4.79
6247 14776 3.270877 ACTTATCACATTTGCTCCGACC 58.729 45.455 0.00 0.00 0.00 4.79
6361 14894 5.411831 AGTCTGACACTGCTGAATGATTA 57.588 39.130 10.88 0.00 32.26 1.75
6818 15351 5.746990 ACAATCTTAGCACTACCAGAGTT 57.253 39.130 0.00 0.00 35.64 3.01
6860 15393 8.956426 GGGTCTAATGTATCTTGATTTGTCAAA 58.044 33.333 0.00 0.00 0.00 2.69
6904 15437 3.434167 GCCAGAATCATTCAGGAGGCTAA 60.434 47.826 12.94 0.00 38.51 3.09
6943 15476 7.857734 TTGGATTTATCAAATTGCTCGTCTA 57.142 32.000 0.00 0.00 0.00 2.59
6961 15494 4.386049 CGTCTATTGAAGGAATATCGGTGC 59.614 45.833 0.00 0.00 0.00 5.01
6963 15496 5.992217 GTCTATTGAAGGAATATCGGTGCTT 59.008 40.000 0.00 0.00 0.00 3.91
7039 15572 2.103263 GGAGACACACCAGAAGTTCTGT 59.897 50.000 27.07 14.95 42.80 3.41
7081 15614 7.748683 TGCAGTATTTAAACTTATCAAACAGCG 59.251 33.333 0.00 0.00 0.00 5.18
7099 15632 2.615447 AGCGCATATCTTCAATGTGGTG 59.385 45.455 11.47 0.00 42.25 4.17
7307 15840 5.995282 TCCATCTTGACTTATCACGTTGTTT 59.005 36.000 0.00 0.00 33.38 2.83
7324 15857 6.016693 ACGTTGTTTGATGATTGATGGTGTAA 60.017 34.615 0.00 0.00 0.00 2.41
7383 15916 9.838975 CATTTGAATTTACAACATACACAGCTA 57.161 29.630 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 58 2.090719 AGGGAGGCATACTAGCTACCAA 60.091 50.000 0.00 0.00 33.76 3.67
59 65 4.323569 TGATAGGAGGGAGGCATACTAG 57.676 50.000 0.00 0.00 0.00 2.57
60 66 4.546195 AGATGATAGGAGGGAGGCATACTA 59.454 45.833 0.00 0.00 0.00 1.82
61 67 3.339436 AGATGATAGGAGGGAGGCATACT 59.661 47.826 0.00 0.00 0.00 2.12
63 69 4.099633 CAAGATGATAGGAGGGAGGCATA 58.900 47.826 0.00 0.00 0.00 3.14
64 70 2.911636 CAAGATGATAGGAGGGAGGCAT 59.088 50.000 0.00 0.00 0.00 4.40
66 72 2.334023 ACAAGATGATAGGAGGGAGGC 58.666 52.381 0.00 0.00 0.00 4.70
99 114 1.407437 GGTGGAAGCCATCACAGGTAG 60.407 57.143 0.00 0.00 34.21 3.18
100 115 0.618458 GGTGGAAGCCATCACAGGTA 59.382 55.000 0.00 0.00 34.21 3.08
101 116 1.380302 GGTGGAAGCCATCACAGGT 59.620 57.895 0.00 0.00 34.21 4.00
102 117 1.746615 CGGTGGAAGCCATCACAGG 60.747 63.158 0.00 0.00 33.50 4.00
103 118 1.746615 CCGGTGGAAGCCATCACAG 60.747 63.158 0.00 0.00 33.50 3.66
104 119 2.184020 CTCCGGTGGAAGCCATCACA 62.184 60.000 0.00 0.00 33.50 3.58
117 132 3.296709 AAACGCTCATCGCTCCGGT 62.297 57.895 0.00 0.00 43.23 5.28
119 134 1.475441 GAGAAACGCTCATCGCTCCG 61.475 60.000 0.00 0.00 43.38 4.63
281 311 2.688817 CGGAGGGAGTAGGTGTTATCCA 60.689 54.545 0.00 0.00 33.24 3.41
283 313 2.664015 ACGGAGGGAGTAGGTGTTATC 58.336 52.381 0.00 0.00 0.00 1.75
284 314 2.842645 ACGGAGGGAGTAGGTGTTAT 57.157 50.000 0.00 0.00 0.00 1.89
285 315 2.450476 GAACGGAGGGAGTAGGTGTTA 58.550 52.381 0.00 0.00 0.00 2.41
286 316 1.264295 GAACGGAGGGAGTAGGTGTT 58.736 55.000 0.00 0.00 0.00 3.32
287 317 0.614134 GGAACGGAGGGAGTAGGTGT 60.614 60.000 0.00 0.00 0.00 4.16
288 318 2.200052 GGAACGGAGGGAGTAGGTG 58.800 63.158 0.00 0.00 0.00 4.00
289 319 4.781264 GGAACGGAGGGAGTAGGT 57.219 61.111 0.00 0.00 0.00 3.08
302 332 2.161609 CCTGCCACAAGTAATTCGGAAC 59.838 50.000 0.00 0.00 0.00 3.62
303 333 2.224670 ACCTGCCACAAGTAATTCGGAA 60.225 45.455 0.00 0.00 0.00 4.30
304 334 1.349688 ACCTGCCACAAGTAATTCGGA 59.650 47.619 0.00 0.00 0.00 4.55
305 335 1.821216 ACCTGCCACAAGTAATTCGG 58.179 50.000 0.00 0.00 0.00 4.30
306 336 3.312421 CCATACCTGCCACAAGTAATTCG 59.688 47.826 0.00 0.00 0.00 3.34
307 337 4.523083 TCCATACCTGCCACAAGTAATTC 58.477 43.478 0.00 0.00 0.00 2.17
308 338 4.584638 TCCATACCTGCCACAAGTAATT 57.415 40.909 0.00 0.00 0.00 1.40
309 339 4.079787 ACATCCATACCTGCCACAAGTAAT 60.080 41.667 0.00 0.00 0.00 1.89
310 340 3.265737 ACATCCATACCTGCCACAAGTAA 59.734 43.478 0.00 0.00 0.00 2.24
311 341 2.843730 ACATCCATACCTGCCACAAGTA 59.156 45.455 0.00 0.00 0.00 2.24
312 342 1.635487 ACATCCATACCTGCCACAAGT 59.365 47.619 0.00 0.00 0.00 3.16
313 343 2.425143 ACATCCATACCTGCCACAAG 57.575 50.000 0.00 0.00 0.00 3.16
314 344 3.716353 AGATACATCCATACCTGCCACAA 59.284 43.478 0.00 0.00 0.00 3.33
315 345 3.317406 AGATACATCCATACCTGCCACA 58.683 45.455 0.00 0.00 0.00 4.17
316 346 4.772624 TCTAGATACATCCATACCTGCCAC 59.227 45.833 0.00 0.00 0.00 5.01
317 347 5.010708 TCTAGATACATCCATACCTGCCA 57.989 43.478 0.00 0.00 0.00 4.92
318 348 7.847711 ATATCTAGATACATCCATACCTGCC 57.152 40.000 14.71 0.00 0.00 4.85
350 380 9.338622 TCGTCACAGAAATAGATGTATCTAGAA 57.661 33.333 0.00 0.00 42.20 2.10
364 394 7.811236 TCGTTCTAAATTACTCGTCACAGAAAT 59.189 33.333 0.00 0.00 0.00 2.17
370 400 5.287992 CCCTTCGTTCTAAATTACTCGTCAC 59.712 44.000 0.00 0.00 0.00 3.67
371 401 5.183713 TCCCTTCGTTCTAAATTACTCGTCA 59.816 40.000 0.00 0.00 0.00 4.35
373 403 5.184671 ACTCCCTTCGTTCTAAATTACTCGT 59.815 40.000 0.00 0.00 0.00 4.18
399 429 9.865321 GTAATCAAACCGCTGGAGTATATATAA 57.135 33.333 1.50 0.00 0.00 0.98
401 431 8.035394 CAGTAATCAAACCGCTGGAGTATATAT 58.965 37.037 1.50 0.00 0.00 0.86
402 432 7.231925 TCAGTAATCAAACCGCTGGAGTATATA 59.768 37.037 1.50 0.00 0.00 0.86
403 433 6.041637 TCAGTAATCAAACCGCTGGAGTATAT 59.958 38.462 1.50 0.00 0.00 0.86
569 734 1.664016 CGTACGTGTGTAGTTTCGGCT 60.664 52.381 7.22 0.00 0.00 5.52
581 746 0.675633 AGTTACCAAGGCGTACGTGT 59.324 50.000 17.90 9.07 0.00 4.49
585 750 2.159184 GGGAGTAGTTACCAAGGCGTAC 60.159 54.545 0.00 0.00 0.00 3.67
586 751 2.102578 GGGAGTAGTTACCAAGGCGTA 58.897 52.381 0.00 0.00 0.00 4.42
591 760 3.032459 GGAGGAGGGAGTAGTTACCAAG 58.968 54.545 0.00 0.00 0.00 3.61
663 1781 7.049754 TGGGTATTAATTTACTCCCTTCGTTC 58.950 38.462 0.00 0.00 36.23 3.95
695 1920 7.652727 CAGCTCTATATGCACTTGAGTTAGTA 58.347 38.462 9.99 0.00 0.00 1.82
696 1921 6.511416 CAGCTCTATATGCACTTGAGTTAGT 58.489 40.000 9.99 0.00 0.00 2.24
815 2425 2.027653 TCAGTCCTTGTGTGTGTGTTCA 60.028 45.455 0.00 0.00 0.00 3.18
816 2426 2.609459 CTCAGTCCTTGTGTGTGTGTTC 59.391 50.000 0.00 0.00 0.00 3.18
817 2427 2.632377 CTCAGTCCTTGTGTGTGTGTT 58.368 47.619 0.00 0.00 0.00 3.32
818 2428 1.743772 GCTCAGTCCTTGTGTGTGTGT 60.744 52.381 0.00 0.00 0.00 3.72
819 2429 0.940126 GCTCAGTCCTTGTGTGTGTG 59.060 55.000 0.00 0.00 0.00 3.82
881 2511 0.954452 GAAGTTTGGGTGCTGGTCTG 59.046 55.000 0.00 0.00 0.00 3.51
882 2512 0.550914 TGAAGTTTGGGTGCTGGTCT 59.449 50.000 0.00 0.00 0.00 3.85
883 2513 0.954452 CTGAAGTTTGGGTGCTGGTC 59.046 55.000 0.00 0.00 0.00 4.02
884 2514 1.109323 GCTGAAGTTTGGGTGCTGGT 61.109 55.000 0.00 0.00 0.00 4.00
885 2515 1.108727 TGCTGAAGTTTGGGTGCTGG 61.109 55.000 0.00 0.00 0.00 4.85
886 2516 0.746063 TTGCTGAAGTTTGGGTGCTG 59.254 50.000 0.00 0.00 0.00 4.41
887 2517 1.035139 CTTGCTGAAGTTTGGGTGCT 58.965 50.000 0.00 0.00 0.00 4.40
888 2518 0.598419 GCTTGCTGAAGTTTGGGTGC 60.598 55.000 0.00 0.00 0.00 5.01
922 2552 4.719369 GCAGACGACGGCGAGGTT 62.719 66.667 22.49 0.00 41.64 3.50
931 2562 0.824759 AGAATGGTAGGGCAGACGAC 59.175 55.000 0.00 0.00 0.00 4.34
1599 6435 6.321717 TGTGTCCGCTTGATATTTCATTTTC 58.678 36.000 0.00 0.00 0.00 2.29
1657 6559 7.445707 TGTGTTTATTAGTTGTGTGCATCCTAA 59.554 33.333 0.00 0.00 0.00 2.69
1719 6688 8.299570 GTGCCCAAATTATTATTATGTGGAGAG 58.700 37.037 2.22 0.00 0.00 3.20
1820 7123 6.775629 AGAACTGGAGCTAAAACAAAATGGTA 59.224 34.615 0.00 0.00 0.00 3.25
1821 7124 5.598417 AGAACTGGAGCTAAAACAAAATGGT 59.402 36.000 0.00 0.00 0.00 3.55
1823 7126 6.738114 TGAGAACTGGAGCTAAAACAAAATG 58.262 36.000 0.00 0.00 0.00 2.32
1824 7127 6.772716 TCTGAGAACTGGAGCTAAAACAAAAT 59.227 34.615 0.00 0.00 0.00 1.82
1891 7312 6.349243 TGTTATTTCTAAGAACCTCCGACA 57.651 37.500 0.00 0.00 0.00 4.35
1974 7869 7.364408 CCAGCACCCAGAAGTTTAGTATAGTAA 60.364 40.741 0.00 0.00 0.00 2.24
1989 7884 1.155859 AAAATGGCCAGCACCCAGA 59.844 52.632 13.05 0.00 35.48 3.86
2283 8235 7.122138 TCTGTCATGCTCTCAGATAAAGAAT 57.878 36.000 0.00 0.00 34.00 2.40
2893 8850 7.921041 ATTACTATCTCTCACTGATTCCCAA 57.079 36.000 0.00 0.00 0.00 4.12
3510 9516 3.572682 TCGGATCCATATTACTTGTCGCT 59.427 43.478 13.41 0.00 0.00 4.93
3511 9517 3.909430 TCGGATCCATATTACTTGTCGC 58.091 45.455 13.41 0.00 0.00 5.19
3559 9565 6.072175 GGCATTTCTTACAACAGGACATTACA 60.072 38.462 0.00 0.00 0.00 2.41
3655 9670 6.494666 AGTAACAGTAAGCCCAATAGCATA 57.505 37.500 0.00 0.00 34.23 3.14
3675 9807 4.098807 TCGCACCAAGTAATCATGCTAGTA 59.901 41.667 0.00 0.00 34.06 1.82
3994 10654 6.002704 AGTATAATGTACACTACTCCCTCCG 58.997 44.000 0.00 0.00 0.00 4.63
3995 10655 7.121020 GCTAGTATAATGTACACTACTCCCTCC 59.879 44.444 14.54 2.25 0.00 4.30
3998 10658 6.128063 CCGCTAGTATAATGTACACTACTCCC 60.128 46.154 14.54 8.63 0.00 4.30
4001 10661 7.814264 AACCGCTAGTATAATGTACACTACT 57.186 36.000 15.16 15.16 0.00 2.57
4002 10662 8.749499 CAAAACCGCTAGTATAATGTACACTAC 58.251 37.037 0.00 0.76 0.00 2.73
4003 10663 7.436080 GCAAAACCGCTAGTATAATGTACACTA 59.564 37.037 0.00 0.00 0.00 2.74
4004 10664 6.257193 GCAAAACCGCTAGTATAATGTACACT 59.743 38.462 0.00 0.00 0.00 3.55
4005 10665 6.416514 GCAAAACCGCTAGTATAATGTACAC 58.583 40.000 0.00 0.00 0.00 2.90
4006 10666 5.524646 GGCAAAACCGCTAGTATAATGTACA 59.475 40.000 0.00 0.00 0.00 2.90
4085 10745 0.887933 ATGTGTTCATTGGCGGGTTC 59.112 50.000 0.00 0.00 0.00 3.62
4307 11117 4.768968 CCATGGTCCATTAAAGATGGGATC 59.231 45.833 2.57 0.00 39.60 3.36
4430 11379 0.608582 GCCTGCATCATCAGATCCCC 60.609 60.000 0.00 0.00 36.19 4.81
4483 12843 0.458543 CTGTTCATCGTCTCCCACCG 60.459 60.000 0.00 0.00 0.00 4.94
4506 12868 2.501261 TCAACGAGAAAGACGAGGAGA 58.499 47.619 0.00 0.00 34.70 3.71
4598 12968 8.526147 ACTATTGCAATAGAGAAGCACAAAAAT 58.474 29.630 40.04 18.31 40.63 1.82
4614 12984 2.813754 ACACTGCGAACACTATTGCAAT 59.186 40.909 17.56 17.56 39.18 3.56
4731 13138 2.331451 GCGGCTGTTCTTTTGCGT 59.669 55.556 0.00 0.00 0.00 5.24
4743 13150 2.238942 TCATATTTGATGACGCGGCT 57.761 45.000 15.80 0.00 0.00 5.52
4884 13324 9.681692 GAAAGCCTTTTTCGGTTAAATACTAAA 57.318 29.630 0.00 0.00 0.00 1.85
4885 13325 9.070179 AGAAAGCCTTTTTCGGTTAAATACTAA 57.930 29.630 0.00 0.00 33.86 2.24
4886 13326 8.625786 AGAAAGCCTTTTTCGGTTAAATACTA 57.374 30.769 0.00 0.00 33.86 1.82
4887 13327 7.309012 GGAGAAAGCCTTTTTCGGTTAAATACT 60.309 37.037 2.06 0.00 33.86 2.12
4888 13328 6.805271 GGAGAAAGCCTTTTTCGGTTAAATAC 59.195 38.462 2.06 0.00 33.86 1.89
4889 13329 6.071784 GGGAGAAAGCCTTTTTCGGTTAAATA 60.072 38.462 2.06 0.00 33.86 1.40
4890 13330 5.279306 GGGAGAAAGCCTTTTTCGGTTAAAT 60.279 40.000 2.06 0.00 33.86 1.40
4891 13331 4.038282 GGGAGAAAGCCTTTTTCGGTTAAA 59.962 41.667 2.06 0.00 33.86 1.52
4892 13332 3.570975 GGGAGAAAGCCTTTTTCGGTTAA 59.429 43.478 2.06 0.00 33.86 2.01
4893 13333 3.151554 GGGAGAAAGCCTTTTTCGGTTA 58.848 45.455 2.06 0.00 33.86 2.85
4894 13334 1.961394 GGGAGAAAGCCTTTTTCGGTT 59.039 47.619 2.06 0.00 33.86 4.44
5099 13544 0.601311 GCACAGCTCCAACTCTTCGT 60.601 55.000 0.00 0.00 0.00 3.85
5108 13553 3.145422 TTCGTCGTGCACAGCTCCA 62.145 57.895 18.64 0.00 0.00 3.86
5245 13691 0.931005 CGTATCCTTCTTGAAGGCGC 59.069 55.000 21.16 0.00 39.80 6.53
5321 13767 2.665603 GAGGCGAAGAGGGCTTGT 59.334 61.111 0.00 0.00 43.66 3.16
5375 13821 0.325765 TGGGTATGATGGTCGGTGGA 60.326 55.000 0.00 0.00 0.00 4.02
5568 14017 2.466186 TTTGGGGCGGAAAGAGGGT 61.466 57.895 0.00 0.00 0.00 4.34
5765 14225 1.949847 GCGGCTCCTCTTGTGCTCTA 61.950 60.000 0.00 0.00 33.94 2.43
6222 14751 2.614057 GGAGCAAATGTGATAAGTCCCG 59.386 50.000 0.00 0.00 0.00 5.14
6223 14752 2.614057 CGGAGCAAATGTGATAAGTCCC 59.386 50.000 0.00 0.00 0.00 4.46
6224 14753 3.309954 GTCGGAGCAAATGTGATAAGTCC 59.690 47.826 0.00 0.00 0.00 3.85
6225 14754 3.309954 GGTCGGAGCAAATGTGATAAGTC 59.690 47.826 1.64 0.00 0.00 3.01
6226 14755 3.270877 GGTCGGAGCAAATGTGATAAGT 58.729 45.455 1.64 0.00 0.00 2.24
6227 14756 3.270027 TGGTCGGAGCAAATGTGATAAG 58.730 45.455 7.54 0.00 0.00 1.73
6228 14757 3.342377 TGGTCGGAGCAAATGTGATAA 57.658 42.857 7.54 0.00 0.00 1.75
6229 14758 3.342377 TTGGTCGGAGCAAATGTGATA 57.658 42.857 19.32 0.00 32.03 2.15
6230 14759 2.198827 TTGGTCGGAGCAAATGTGAT 57.801 45.000 19.32 0.00 32.03 3.06
6231 14760 2.198827 ATTGGTCGGAGCAAATGTGA 57.801 45.000 24.39 3.16 39.20 3.58
6232 14761 3.302365 AAATTGGTCGGAGCAAATGTG 57.698 42.857 24.39 0.00 39.20 3.21
6233 14762 4.079253 ACTAAATTGGTCGGAGCAAATGT 58.921 39.130 24.39 16.90 39.20 2.71
6234 14763 4.701956 ACTAAATTGGTCGGAGCAAATG 57.298 40.909 24.39 16.38 39.20 2.32
6235 14764 7.404671 AAATACTAAATTGGTCGGAGCAAAT 57.595 32.000 24.39 15.00 39.20 2.32
6236 14765 6.827586 AAATACTAAATTGGTCGGAGCAAA 57.172 33.333 24.39 9.16 39.20 3.68
6237 14766 7.925043 TTAAATACTAAATTGGTCGGAGCAA 57.075 32.000 23.09 23.09 40.12 3.91
6238 14767 9.616156 TTATTAAATACTAAATTGGTCGGAGCA 57.384 29.630 5.66 5.66 0.00 4.26
6283 14812 9.354673 TGACTTCCTTCTTCAAATCTAAAACAT 57.645 29.630 0.00 0.00 0.00 2.71
6361 14894 6.825213 TCATATAGCTCAAAAGTCTGCAACAT 59.175 34.615 0.00 0.00 0.00 2.71
6532 15065 2.912295 TGGACAAGTCTGATCCCAATGA 59.088 45.455 0.00 0.00 0.00 2.57
6818 15351 8.336235 ACATTAGACCCTCAATTTCTCCAATTA 58.664 33.333 0.00 0.00 32.90 1.40
6860 15393 5.227152 GCAGTTTTGTAATTCCGGAACAAT 58.773 37.500 21.56 11.58 33.44 2.71
6943 15476 5.163519 CCAAAAGCACCGATATTCCTTCAAT 60.164 40.000 0.00 0.00 0.00 2.57
6961 15494 4.446371 AGTTGTGTGAGACTCTCCAAAAG 58.554 43.478 3.68 0.00 0.00 2.27
6963 15496 4.893524 TCTAGTTGTGTGAGACTCTCCAAA 59.106 41.667 3.68 0.00 0.00 3.28
7039 15572 1.748879 GCAGTTTGGATAGGCCGCA 60.749 57.895 0.00 0.00 40.66 5.69
7099 15632 3.742882 GCACCCAAAAATTCTGCTTCTTC 59.257 43.478 0.00 0.00 0.00 2.87
7307 15840 6.604396 AGCTTCATTTACACCATCAATCATCA 59.396 34.615 0.00 0.00 0.00 3.07
7324 15857 2.568623 AGACCGACCAAAGCTTCATT 57.431 45.000 0.00 0.00 0.00 2.57
7383 15916 2.753452 CAGATCATCTGGCAGCAAACTT 59.247 45.455 10.34 0.00 40.71 2.66


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

AutoCloner maintained by Alex Coulton.