Multiple sequence alignment - TraesCS3A01G504600

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 TraesCS3A01G504600 chr3A 100.000 8637 0 0 1 8637 726534971 726543607 0.000000e+00 15950.0
1 TraesCS3A01G504600 chr3A 95.719 841 30 3 1 841 636491268 636492102 0.000000e+00 1349.0
2 TraesCS3A01G504600 chr3A 95.244 841 34 3 1 841 457218485 457219319 0.000000e+00 1327.0
3 TraesCS3A01G504600 chr3A 85.969 898 90 22 2550 3430 726440155 726441033 0.000000e+00 928.0
4 TraesCS3A01G504600 chr3A 86.529 824 100 8 3641 4462 726688625 726689439 0.000000e+00 896.0
5 TraesCS3A01G504600 chr3A 87.445 677 62 8 1952 2618 726686868 726687531 0.000000e+00 758.0
6 TraesCS3A01G504600 chr3A 83.632 837 88 23 2201 3012 726389293 726388481 0.000000e+00 741.0
7 TraesCS3A01G504600 chr3A 85.133 565 59 17 2880 3429 726687683 726688237 9.800000e-154 555.0
8 TraesCS3A01G504600 chr3A 90.998 411 22 5 4680 5088 681554972 681554575 2.740000e-149 540.0
9 TraesCS3A01G504600 chr3A 88.318 428 31 10 6829 7244 681527911 681527491 6.020000e-136 496.0
10 TraesCS3A01G504600 chr3A 97.368 190 4 1 5880 6069 681528572 681528384 1.080000e-83 322.0
11 TraesCS3A01G504600 chr3A 88.281 256 23 5 3641 3890 726441395 726441649 5.070000e-77 300.0
12 TraesCS3A01G504600 chr3A 79.335 421 57 25 7733 8143 726862928 726862528 1.430000e-67 268.0
13 TraesCS3A01G504600 chr3A 78.973 409 51 18 1187 1567 726513738 726514139 6.700000e-61 246.0
14 TraesCS3A01G504600 chr3A 90.503 179 13 1 1773 1951 726390002 726389828 5.210000e-57 233.0
15 TraesCS3A01G504600 chr3A 81.702 235 30 7 7486 7720 726444626 726444847 5.330000e-42 183.0
16 TraesCS3A01G504600 chr3A 81.095 201 8 9 1540 1732 726390612 726390434 5.440000e-27 134.0
17 TraesCS3A01G504600 chr3A 94.737 76 4 0 3499 3574 726441364 726441439 1.520000e-22 119.0
18 TraesCS3A01G504600 chr3A 92.593 81 4 1 3496 3574 726688589 726688669 1.970000e-21 115.0
19 TraesCS3A01G504600 chr3A 100.000 28 0 0 1746 1773 217822263 217822236 1.600000e-02 52.8
20 TraesCS3A01G504600 chr7B 99.781 2742 5 1 4675 7416 630128863 630131603 0.000000e+00 5029.0
21 TraesCS3A01G504600 chr7B 98.605 2151 27 2 4680 6828 607324666 607326815 0.000000e+00 3803.0
22 TraesCS3A01G504600 chr7B 96.271 590 13 4 6829 7409 607327540 607328129 0.000000e+00 959.0
23 TraesCS3A01G504600 chr7B 85.530 774 77 17 4671 5438 288170144 288169400 0.000000e+00 776.0
24 TraesCS3A01G504600 chr7B 79.202 351 36 21 8322 8637 44238129 44238477 8.790000e-50 209.0
25 TraesCS3A01G504600 chr7B 77.647 340 46 22 8322 8637 705531735 705532068 6.890000e-41 180.0
26 TraesCS3A01G504600 chr2B 99.122 2734 19 4 4680 7410 549705169 549707900 0.000000e+00 4911.0
27 TraesCS3A01G504600 chr6A 99.158 2732 13 3 4680 7410 426957314 426960036 0.000000e+00 4909.0
28 TraesCS3A01G504600 chr5B 98.377 2157 26 3 4680 6828 6685585 6683430 0.000000e+00 3781.0
29 TraesCS3A01G504600 chr5B 96.748 492 12 3 6923 7410 6682071 6681580 0.000000e+00 817.0
30 TraesCS3A01G504600 chr2A 97.908 2151 41 3 4680 6828 731338712 731336564 0.000000e+00 3720.0
31 TraesCS3A01G504600 chr2A 95.363 841 33 3 1 841 560769738 560770572 0.000000e+00 1332.0
32 TraesCS3A01G504600 chr2A 95.244 841 36 1 1 841 264895084 264894248 0.000000e+00 1328.0
33 TraesCS3A01G504600 chr2A 95.000 840 38 2 2 841 319899919 319899084 0.000000e+00 1315.0
34 TraesCS3A01G504600 chr2A 94.887 841 38 3 1 841 390815978 390815143 0.000000e+00 1310.0
35 TraesCS3A01G504600 chr2A 92.386 591 22 14 6829 7410 731335792 731335216 0.000000e+00 821.0
36 TraesCS3A01G504600 chr2A 76.812 276 45 14 8336 8609 751499485 751499227 4.200000e-28 137.0
37 TraesCS3A01G504600 chr3D 93.504 1832 72 23 1770 3574 595760665 595762476 0.000000e+00 2680.0
38 TraesCS3A01G504600 chr3D 92.062 1285 36 15 7405 8637 595763474 595764744 0.000000e+00 1748.0
39 TraesCS3A01G504600 chr3D 95.415 1047 41 1 3641 4680 595762432 595763478 0.000000e+00 1661.0
40 TraesCS3A01G504600 chr3D 84.766 1733 158 46 1770 3430 595678879 595680577 0.000000e+00 1640.0
41 TraesCS3A01G504600 chr3D 88.698 991 100 9 3641 4627 595680941 595681923 0.000000e+00 1199.0
42 TraesCS3A01G504600 chr3D 86.282 1006 115 21 3641 4638 595858816 595859806 0.000000e+00 1072.0
43 TraesCS3A01G504600 chr3D 86.660 982 107 18 3643 4614 595711913 595712880 0.000000e+00 1066.0
44 TraesCS3A01G504600 chr3D 83.363 1142 105 35 1770 2852 595276996 595275881 0.000000e+00 977.0
45 TraesCS3A01G504600 chr3D 93.217 575 26 5 935 1500 595759767 595760337 0.000000e+00 833.0
46 TraesCS3A01G504600 chr3D 84.994 833 106 12 3861 4680 595286611 595285785 0.000000e+00 828.0
47 TraesCS3A01G504600 chr3D 84.383 794 81 26 2663 3429 595857643 595858420 0.000000e+00 739.0
48 TraesCS3A01G504600 chr3D 82.753 632 73 20 1770 2387 595855611 595856220 1.650000e-146 531.0
49 TraesCS3A01G504600 chr3D 96.281 242 9 0 1532 1773 595760338 595760579 1.750000e-106 398.0
50 TraesCS3A01G504600 chr3D 75.485 567 87 35 7573 8134 596096126 596095607 6.740000e-56 230.0
51 TraesCS3A01G504600 chr3D 78.607 402 44 17 1771 2134 596113143 596112746 2.430000e-55 228.0
52 TraesCS3A01G504600 chr3D 78.977 352 36 19 8322 8637 506005816 506006165 1.140000e-48 206.0
53 TraesCS3A01G504600 chr3D 76.096 502 47 35 1187 1666 595278155 595277705 2.460000e-45 195.0
54 TraesCS3A01G504600 chr3D 78.438 320 35 15 8322 8613 515670251 515669938 2.480000e-40 178.0
55 TraesCS3A01G504600 chr3D 79.916 239 34 7 7625 7862 595675419 595675644 6.940000e-36 163.0
56 TraesCS3A01G504600 chr3D 88.073 109 6 1 2379 2480 595857224 595857332 1.180000e-23 122.0
57 TraesCS3A01G504600 chr3D 94.737 76 4 0 3499 3574 595680910 595680985 1.520000e-22 119.0
58 TraesCS3A01G504600 chr3D 94.667 75 4 0 3500 3574 595858786 595858860 5.480000e-22 117.0
59 TraesCS3A01G504600 chr3D 83.471 121 16 2 8024 8140 595304758 595304878 9.170000e-20 110.0
60 TraesCS3A01G504600 chr3D 90.789 76 7 0 3499 3574 595711880 595711955 1.530000e-17 102.0
61 TraesCS3A01G504600 chr3D 90.566 53 5 0 1187 1239 595737388 595737440 4.330000e-08 71.3
62 TraesCS3A01G504600 chr3D 100.000 28 0 0 1748 1775 32951519 32951546 1.600000e-02 52.8
63 TraesCS3A01G504600 chr3D 100.000 28 0 0 1746 1773 170677736 170677763 1.600000e-02 52.8
64 TraesCS3A01G504600 chr3B 93.052 1540 68 24 2840 4362 798952730 798954247 0.000000e+00 2215.0
65 TraesCS3A01G504600 chr3B 92.713 1043 39 8 1772 2814 798951616 798952621 0.000000e+00 1471.0
66 TraesCS3A01G504600 chr3B 86.895 1053 106 21 3644 4680 798639536 798640572 0.000000e+00 1151.0
67 TraesCS3A01G504600 chr3B 85.785 1013 115 19 3641 4638 798992484 798993482 0.000000e+00 1046.0
68 TraesCS3A01G504600 chr3B 100.000 531 0 0 6880 7410 762382412 762382942 0.000000e+00 981.0
69 TraesCS3A01G504600 chr3B 86.989 930 49 25 7742 8633 798967002 798967897 0.000000e+00 981.0
70 TraesCS3A01G504600 chr3B 84.244 787 88 20 2663 3429 798991147 798991917 0.000000e+00 734.0
71 TraesCS3A01G504600 chr3B 94.189 413 23 1 1361 1773 798951117 798951528 5.690000e-176 628.0
72 TraesCS3A01G504600 chr3B 100.000 337 0 0 4680 5016 762380188 762380524 2.650000e-174 623.0
73 TraesCS3A01G504600 chr3B 83.604 677 68 20 1952 2618 798990501 798991144 5.770000e-166 595.0
74 TraesCS3A01G504600 chr3B 84.690 516 53 10 2927 3430 798638603 798639104 7.790000e-135 492.0
75 TraesCS3A01G504600 chr3B 85.270 482 25 16 916 1362 798950431 798950901 1.020000e-123 455.0
76 TraesCS3A01G504600 chr3B 90.741 324 23 1 4364 4680 798966452 798966775 8.010000e-115 425.0
77 TraesCS3A01G504600 chr3B 96.552 232 8 0 7405 7636 798966771 798967002 1.360000e-102 385.0
78 TraesCS3A01G504600 chr3B 78.466 339 41 17 8322 8631 785200427 785200762 8.850000e-45 193.0
79 TraesCS3A01G504600 chr3B 90.826 109 10 0 1770 1878 798660359 798660467 6.990000e-31 147.0
80 TraesCS3A01G504600 chr3B 82.993 147 17 6 7565 7710 799515577 799515438 9.100000e-25 126.0
81 TraesCS3A01G504600 chr3B 94.667 75 4 0 3500 3574 798992454 798992528 5.480000e-22 117.0
82 TraesCS3A01G504600 chr3B 95.455 44 1 1 3501 3543 798953470 798953513 1.560000e-07 69.4
83 TraesCS3A01G504600 chr3B 100.000 28 0 0 1746 1773 447029588 447029615 1.600000e-02 52.8
84 TraesCS3A01G504600 chr7A 95.600 841 33 1 1 841 567566631 567567467 0.000000e+00 1345.0
85 TraesCS3A01G504600 chr7A 96.188 446 17 0 5439 5884 4492789 4493234 0.000000e+00 730.0
86 TraesCS3A01G504600 chr7A 90.157 508 22 11 5880 6362 4493288 4493792 3.400000e-178 636.0
87 TraesCS3A01G504600 chr7A 91.484 411 20 5 4680 5088 4492053 4492450 1.270000e-152 551.0
88 TraesCS3A01G504600 chr7A 90.698 172 13 2 7241 7410 4494380 4494550 8.720000e-55 226.0
89 TraesCS3A01G504600 chr7A 75.465 269 31 22 8382 8632 291813327 291813578 1.980000e-16 99.0
90 TraesCS3A01G504600 chr7A 86.047 86 10 2 8380 8463 688627597 688627512 3.320000e-14 91.6
91 TraesCS3A01G504600 chr5A 95.249 842 36 1 1 842 462964296 462965133 0.000000e+00 1330.0
92 TraesCS3A01G504600 chr1A 94.887 841 39 1 1 841 565947880 565947044 0.000000e+00 1312.0
93 TraesCS3A01G504600 chr1A 85.452 763 79 15 4680 5438 207688128 207687394 0.000000e+00 765.0
94 TraesCS3A01G504600 chr1A 91.566 166 13 1 6659 6824 207680936 207680772 2.430000e-55 228.0
95 TraesCS3A01G504600 chr1A 87.273 110 7 4 1518 1625 37142557 37142661 1.520000e-22 119.0
96 TraesCS3A01G504600 chr1A 87.273 110 7 4 1518 1625 289628573 289628677 1.520000e-22 119.0
97 TraesCS3A01G504600 chr1B 86.065 775 60 14 4675 5438 558778044 558778781 0.000000e+00 789.0
98 TraesCS3A01G504600 chr1B 91.716 169 13 1 6656 6824 558783637 558783804 5.210000e-57 233.0
99 TraesCS3A01G504600 chr6D 90.945 508 17 4 5880 6362 148005913 148005410 0.000000e+00 656.0
100 TraesCS3A01G504600 chr6D 95.696 395 15 2 5439 5832 148006393 148006000 1.220000e-177 634.0
101 TraesCS3A01G504600 chr6D 85.227 616 49 20 6830 7410 148005261 148004653 5.770000e-166 595.0
102 TraesCS3A01G504600 chr2D 90.551 508 17 8 5880 6362 294865311 294865812 2.030000e-180 643.0
103 TraesCS3A01G504600 chr2D 95.949 395 14 2 5439 5832 294864829 294865222 2.630000e-179 640.0
104 TraesCS3A01G504600 chr2D 84.976 619 51 18 6829 7412 294865959 294866570 2.690000e-164 590.0
105 TraesCS3A01G504600 chr2D 81.098 328 30 15 8322 8628 595407051 595407367 5.210000e-57 233.0
106 TraesCS3A01G504600 chr2D 89.216 102 3 5 1521 1620 395318583 395318678 4.230000e-23 121.0
107 TraesCS3A01G504600 chr7D 91.124 169 14 1 6656 6824 498115575 498115742 2.430000e-55 228.0
108 TraesCS3A01G504600 chr4A 79.941 339 44 15 8322 8637 739967283 739967620 2.430000e-55 228.0
109 TraesCS3A01G504600 chr4A 97.059 34 1 0 1742 1775 700445051 700445018 3.370000e-04 58.4
110 TraesCS3A01G504600 chr4D 82.007 289 23 14 8376 8637 490401091 490401377 1.460000e-52 219.0
111 TraesCS3A01G504600 chr4D 81.333 150 16 7 8322 8462 279298572 279298718 2.550000e-20 111.0
112 TraesCS3A01G504600 chrUn 77.011 348 46 21 8322 8636 150140901 150141247 1.490000e-37 169.0
113 TraesCS3A01G504600 chrUn 77.011 348 46 21 8322 8636 321413599 321413945 1.490000e-37 169.0
114 TraesCS3A01G504600 chrUn 76.724 348 47 21 8322 8636 172387216 172386870 6.940000e-36 163.0
115 TraesCS3A01G504600 chrUn 81.982 111 11 4 8322 8424 172394323 172394214 1.540000e-12 86.1
116 TraesCS3A01G504600 chr1D 76.608 342 46 20 8322 8631 474234152 474233813 3.230000e-34 158.0
117 TraesCS3A01G504600 chr5D 86.822 129 8 5 1541 1666 529794473 529794595 1.510000e-27 135.0
118 TraesCS3A01G504600 chr5D 90.000 50 5 0 8323 8372 545696814 545696863 2.010000e-06 65.8
119 TraesCS3A01G504600 chr6B 97.222 36 0 1 1504 1539 359604225 359604191 9.360000e-05 60.2
120 TraesCS3A01G504600 chr6B 100.000 28 0 0 1746 1773 18739920 18739947 1.600000e-02 52.8


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 TraesCS3A01G504600 chr3A 726534971 726543607 8636 False 15950.000000 15950 100.000000 1 8637 1 chr3A.!!$F4 8636
1 TraesCS3A01G504600 chr3A 636491268 636492102 834 False 1349.000000 1349 95.719000 1 841 1 chr3A.!!$F2 840
2 TraesCS3A01G504600 chr3A 457218485 457219319 834 False 1327.000000 1327 95.244000 1 841 1 chr3A.!!$F1 840
3 TraesCS3A01G504600 chr3A 726686868 726689439 2571 False 581.000000 896 87.925000 1952 4462 4 chr3A.!!$F6 2510
4 TraesCS3A01G504600 chr3A 681527491 681528572 1081 True 409.000000 496 92.843000 5880 7244 2 chr3A.!!$R4 1364
5 TraesCS3A01G504600 chr3A 726440155 726444847 4692 False 382.500000 928 87.672250 2550 7720 4 chr3A.!!$F5 5170
6 TraesCS3A01G504600 chr3A 726388481 726390612 2131 True 369.333333 741 85.076667 1540 3012 3 chr3A.!!$R5 1472
7 TraesCS3A01G504600 chr7B 630128863 630131603 2740 False 5029.000000 5029 99.781000 4675 7416 1 chr7B.!!$F2 2741
8 TraesCS3A01G504600 chr7B 607324666 607328129 3463 False 2381.000000 3803 97.438000 4680 7409 2 chr7B.!!$F4 2729
9 TraesCS3A01G504600 chr7B 288169400 288170144 744 True 776.000000 776 85.530000 4671 5438 1 chr7B.!!$R1 767
10 TraesCS3A01G504600 chr2B 549705169 549707900 2731 False 4911.000000 4911 99.122000 4680 7410 1 chr2B.!!$F1 2730
11 TraesCS3A01G504600 chr6A 426957314 426960036 2722 False 4909.000000 4909 99.158000 4680 7410 1 chr6A.!!$F1 2730
12 TraesCS3A01G504600 chr5B 6681580 6685585 4005 True 2299.000000 3781 97.562500 4680 7410 2 chr5B.!!$R1 2730
13 TraesCS3A01G504600 chr2A 731335216 731338712 3496 True 2270.500000 3720 95.147000 4680 7410 2 chr2A.!!$R5 2730
14 TraesCS3A01G504600 chr2A 560769738 560770572 834 False 1332.000000 1332 95.363000 1 841 1 chr2A.!!$F1 840
15 TraesCS3A01G504600 chr2A 264894248 264895084 836 True 1328.000000 1328 95.244000 1 841 1 chr2A.!!$R1 840
16 TraesCS3A01G504600 chr2A 319899084 319899919 835 True 1315.000000 1315 95.000000 2 841 1 chr2A.!!$R2 839
17 TraesCS3A01G504600 chr2A 390815143 390815978 835 True 1310.000000 1310 94.887000 1 841 1 chr2A.!!$R3 840
18 TraesCS3A01G504600 chr3D 595759767 595764744 4977 False 1464.000000 2680 94.095800 935 8637 5 chr3D.!!$F8 7702
19 TraesCS3A01G504600 chr3D 595285785 595286611 826 True 828.000000 828 84.994000 3861 4680 1 chr3D.!!$R2 819
20 TraesCS3A01G504600 chr3D 595675419 595681923 6504 False 780.250000 1640 87.029250 1770 7862 4 chr3D.!!$F6 6092
21 TraesCS3A01G504600 chr3D 595275881 595278155 2274 True 586.000000 977 79.729500 1187 2852 2 chr3D.!!$R5 1665
22 TraesCS3A01G504600 chr3D 595711880 595712880 1000 False 584.000000 1066 88.724500 3499 4614 2 chr3D.!!$F7 1115
23 TraesCS3A01G504600 chr3D 595855611 595859806 4195 False 516.200000 1072 87.231600 1770 4638 5 chr3D.!!$F9 2868
24 TraesCS3A01G504600 chr3D 596095607 596096126 519 True 230.000000 230 75.485000 7573 8134 1 chr3D.!!$R3 561
25 TraesCS3A01G504600 chr3B 798950431 798954247 3816 False 967.680000 2215 92.135800 916 4362 5 chr3B.!!$F6 3446
26 TraesCS3A01G504600 chr3B 798638603 798640572 1969 False 821.500000 1151 85.792500 2927 4680 2 chr3B.!!$F5 1753
27 TraesCS3A01G504600 chr3B 762380188 762382942 2754 False 802.000000 981 100.000000 4680 7410 2 chr3B.!!$F4 2730
28 TraesCS3A01G504600 chr3B 798990501 798993482 2981 False 623.000000 1046 87.075000 1952 4638 4 chr3B.!!$F8 2686
29 TraesCS3A01G504600 chr3B 798966452 798967897 1445 False 597.000000 981 91.427333 4364 8633 3 chr3B.!!$F7 4269
30 TraesCS3A01G504600 chr7A 567566631 567567467 836 False 1345.000000 1345 95.600000 1 841 1 chr7A.!!$F2 840
31 TraesCS3A01G504600 chr7A 4492053 4494550 2497 False 535.750000 730 92.131750 4680 7410 4 chr7A.!!$F3 2730
32 TraesCS3A01G504600 chr5A 462964296 462965133 837 False 1330.000000 1330 95.249000 1 842 1 chr5A.!!$F1 841
33 TraesCS3A01G504600 chr1A 565947044 565947880 836 True 1312.000000 1312 94.887000 1 841 1 chr1A.!!$R3 840
34 TraesCS3A01G504600 chr1A 207687394 207688128 734 True 765.000000 765 85.452000 4680 5438 1 chr1A.!!$R2 758
35 TraesCS3A01G504600 chr1B 558778044 558778781 737 False 789.000000 789 86.065000 4675 5438 1 chr1B.!!$F1 763
36 TraesCS3A01G504600 chr6D 148004653 148006393 1740 True 628.333333 656 90.622667 5439 7410 3 chr6D.!!$R1 1971
37 TraesCS3A01G504600 chr2D 294864829 294866570 1741 False 624.333333 643 90.492000 5439 7412 3 chr2D.!!$F3 1973

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
890 893 0.401738 ACTCATGTCTTGGTGTGGGG 59.598 55.0 0.00 0.00 0.00 4.96 F
894 897 0.620556 ATGTCTTGGTGTGGGGCTAG 59.379 55.0 0.00 0.00 0.00 3.42 F
1235 1254 0.760567 AGGCTACCGAGATGCATCCA 60.761 55.0 23.06 3.02 0.00 3.41 F
1390 1645 0.839946 ACTGATTTCCATCCCTCGGG 59.160 55.0 0.00 0.00 0.00 5.14 F
2978 6436 0.801251 CTGCACACAAAGCTAGCCTC 59.199 55.0 12.13 0.00 0.00 4.70 F
3575 7722 0.249489 ACAGAACTGAGTGACACCGC 60.249 55.0 8.87 0.00 0.00 5.68 F
3604 7751 0.394352 GGGGAGATGCCGACATTTGT 60.394 55.0 0.00 0.00 36.35 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 3634 0.977627 TGCATCGTCCTCACCATCCT 60.978 55.000 0.00 0.00 0.00 3.24 R
2098 3847 1.228094 TTGGCACCGTCAATCTGCA 60.228 52.632 0.00 0.00 32.20 4.41 R
2819 6193 2.232239 GCAGAAAGCACACATGTACG 57.768 50.000 0.00 0.00 44.79 3.67 R
3305 6788 2.169769 TGGAAACAAGACTCTTGTCCGT 59.830 45.455 22.07 12.17 38.72 4.69 R
4643 10889 1.203994 ACTGATAACGCGCCACTACTT 59.796 47.619 5.73 0.00 0.00 2.24 R
5016 11369 1.227943 GGAGCTGCTGGTGTGTGAA 60.228 57.895 7.01 0.00 0.00 3.18 R
7672 15517 9.545105 GAAATTAATTGCAATGGGTATGAATGA 57.455 29.630 13.82 0.00 0.00 2.57 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
239 240 0.604578 TTCGGGTCGGAAAAGATCGT 59.395 50.000 0.00 0.00 0.00 3.73
320 322 7.774157 TGGTTCTAAGTCTGATAGTAGTGTAGG 59.226 40.741 0.00 0.00 0.00 3.18
353 356 3.639094 TGGAGAGGCAAGATCTTAGCTAC 59.361 47.826 21.34 16.80 0.00 3.58
392 395 2.104281 ACAAGGTTTACGAGTTCAGGCT 59.896 45.455 0.00 0.00 0.00 4.58
496 499 1.000486 CCCTTGTCTCGGAGGAGGA 60.000 63.158 18.40 0.00 40.85 3.71
634 637 9.948964 ACCATAAAAACTACTTAATAACCGACT 57.051 29.630 0.00 0.00 0.00 4.18
663 666 1.187087 CGGAGTGCCTTTAGGTCTCT 58.813 55.000 16.43 8.06 37.91 3.10
828 831 4.046360 GGTCCATACCCCTACCCTAGATAA 59.954 50.000 0.00 0.00 40.21 1.75
842 845 9.814899 CTACCCTAGATAAATAGCTTCATCATG 57.185 37.037 0.00 0.00 0.00 3.07
844 847 7.459125 ACCCTAGATAAATAGCTTCATCATGGA 59.541 37.037 0.00 0.00 0.00 3.41
846 849 9.545105 CCTAGATAAATAGCTTCATCATGGATC 57.455 37.037 0.00 0.00 0.00 3.36
849 852 9.976776 AGATAAATAGCTTCATCATGGATCAAT 57.023 29.630 0.00 0.00 0.00 2.57
851 854 9.749340 ATAAATAGCTTCATCATGGATCAATGA 57.251 29.630 15.25 15.25 40.73 2.57
852 855 7.450124 AATAGCTTCATCATGGATCAATGAC 57.550 36.000 15.21 2.40 39.32 3.06
853 856 4.788679 AGCTTCATCATGGATCAATGACA 58.211 39.130 15.21 2.30 39.32 3.58
854 857 5.198207 AGCTTCATCATGGATCAATGACAA 58.802 37.500 15.21 9.94 39.32 3.18
855 858 5.833667 AGCTTCATCATGGATCAATGACAAT 59.166 36.000 15.21 0.00 39.32 2.71
856 859 7.002276 AGCTTCATCATGGATCAATGACAATA 58.998 34.615 15.21 1.10 39.32 1.90
857 860 7.670140 AGCTTCATCATGGATCAATGACAATAT 59.330 33.333 15.21 0.00 39.32 1.28
858 861 8.304596 GCTTCATCATGGATCAATGACAATATT 58.695 33.333 15.21 0.00 39.32 1.28
860 863 9.582648 TTCATCATGGATCAATGACAATATTCT 57.417 29.630 15.21 0.00 39.32 2.40
861 864 9.227777 TCATCATGGATCAATGACAATATTCTC 57.772 33.333 15.21 0.00 39.32 2.87
885 888 6.038603 TCAAAAAGAGAACTCATGTCTTGGTG 59.961 38.462 4.64 0.00 40.54 4.17
886 889 4.696479 AAGAGAACTCATGTCTTGGTGT 57.304 40.909 4.64 0.00 39.97 4.16
887 890 4.000331 AGAGAACTCATGTCTTGGTGTG 58.000 45.455 4.64 0.00 0.00 3.82
888 891 3.070018 GAGAACTCATGTCTTGGTGTGG 58.930 50.000 0.00 0.00 0.00 4.17
889 892 2.154462 GAACTCATGTCTTGGTGTGGG 58.846 52.381 0.00 0.00 0.00 4.61
890 893 0.401738 ACTCATGTCTTGGTGTGGGG 59.598 55.000 0.00 0.00 0.00 4.96
891 894 0.962356 CTCATGTCTTGGTGTGGGGC 60.962 60.000 0.00 0.00 0.00 5.80
892 895 1.075482 CATGTCTTGGTGTGGGGCT 59.925 57.895 0.00 0.00 0.00 5.19
894 897 0.620556 ATGTCTTGGTGTGGGGCTAG 59.379 55.000 0.00 0.00 0.00 3.42
895 898 1.299976 GTCTTGGTGTGGGGCTAGG 59.700 63.158 0.00 0.00 0.00 3.02
896 899 1.923395 TCTTGGTGTGGGGCTAGGG 60.923 63.158 0.00 0.00 0.00 3.53
907 910 2.508663 GCTAGGGCCAACGTCGTC 60.509 66.667 6.18 0.00 0.00 4.20
911 914 2.149803 TAGGGCCAACGTCGTCAGTG 62.150 60.000 6.18 0.00 0.00 3.66
914 917 1.590525 GCCAACGTCGTCAGTGACA 60.591 57.895 22.66 7.60 38.84 3.58
1131 1150 2.421248 GCTCCCTCTCCCTTTCATCTTG 60.421 54.545 0.00 0.00 0.00 3.02
1176 1195 4.794439 TCTCCGTGTGCATCCGCG 62.794 66.667 0.00 0.00 42.97 6.46
1235 1254 0.760567 AGGCTACCGAGATGCATCCA 60.761 55.000 23.06 3.02 0.00 3.41
1390 1645 0.839946 ACTGATTTCCATCCCTCGGG 59.160 55.000 0.00 0.00 0.00 5.14
1455 1710 7.390013 TTTAGCCTCTCTAGATCCTACAGTA 57.610 40.000 0.00 0.00 0.00 2.74
1487 1742 1.676006 GGATTACATTGGAGGGTTGCG 59.324 52.381 0.00 0.00 0.00 4.85
1492 1747 1.152830 ATTGGAGGGTTGCGTGGTT 59.847 52.632 0.00 0.00 0.00 3.67
1851 3545 1.298859 GAATGCCACCGAAGAAGCGT 61.299 55.000 0.00 0.00 0.00 5.07
1912 3606 1.299321 GAGGAAGCTGCTCCTGCTT 59.701 57.895 20.45 8.73 46.33 3.91
2098 3847 3.055719 CGGTGGCAGCCATTCGTT 61.056 61.111 19.75 0.00 35.28 3.85
2115 3864 1.228094 TTGCAGATTGACGGTGCCA 60.228 52.632 0.00 0.00 36.31 4.92
2145 3894 3.127203 CGAGTAAGTGATCGGAGTTCTGT 59.873 47.826 0.00 0.00 35.33 3.41
2146 3895 4.379603 CGAGTAAGTGATCGGAGTTCTGTT 60.380 45.833 0.00 0.00 35.33 3.16
2147 3896 5.470047 AGTAAGTGATCGGAGTTCTGTTT 57.530 39.130 0.00 0.00 0.00 2.83
2148 3897 5.855045 AGTAAGTGATCGGAGTTCTGTTTT 58.145 37.500 0.00 0.00 0.00 2.43
2149 3898 6.289064 AGTAAGTGATCGGAGTTCTGTTTTT 58.711 36.000 0.00 0.00 0.00 1.94
2150 3899 7.439381 AGTAAGTGATCGGAGTTCTGTTTTTA 58.561 34.615 0.00 0.00 0.00 1.52
2151 3900 6.541111 AAGTGATCGGAGTTCTGTTTTTAC 57.459 37.500 0.00 0.00 0.00 2.01
2253 4292 4.191544 TGCTGTTAGGATCAGTGCAATAC 58.808 43.478 0.00 0.00 35.60 1.89
2573 5811 7.147976 GTGATTTTCATGTTAGTCAAGGCTTT 58.852 34.615 0.00 0.00 0.00 3.51
2703 5985 8.531982 GCTTATGTCTATGTGTTATATCCTGGA 58.468 37.037 0.00 0.00 0.00 3.86
2709 5991 7.868415 GTCTATGTGTTATATCCTGGACAGAAC 59.132 40.741 5.55 5.55 0.00 3.01
2715 5998 7.985184 GTGTTATATCCTGGACAGAACATTACA 59.015 37.037 17.15 4.00 0.00 2.41
2728 6012 8.858003 ACAGAACATTACATCGTTATACTGAG 57.142 34.615 0.00 0.00 0.00 3.35
2775 6079 8.768957 TCACAATGAAAAACATTTGTCAGAAA 57.231 26.923 3.72 0.00 45.60 2.52
2814 6188 6.110707 GGTCGATTGGACTAAAACCAGATAA 58.889 40.000 0.00 0.00 45.35 1.75
2894 6351 9.677567 GTTGATTGCTTAGAAAAAGAACATACA 57.322 29.630 0.00 0.00 0.00 2.29
2978 6436 0.801251 CTGCACACAAAGCTAGCCTC 59.199 55.000 12.13 0.00 0.00 4.70
3038 6498 4.089923 GCCATGCAAATTCGTTAAAGTGTC 59.910 41.667 0.00 0.00 0.00 3.67
3039 6507 5.218885 CCATGCAAATTCGTTAAAGTGTCA 58.781 37.500 0.00 0.00 0.00 3.58
3081 6551 8.745464 TTGTTTGTAGTTGTACCTTTGTTTTC 57.255 30.769 0.00 0.00 0.00 2.29
3166 6640 7.101700 TCACCTCATGCACATCTAATGATATC 58.898 38.462 0.00 0.00 30.31 1.63
3305 6788 2.481969 GCTGAAGGCGAGTCATCATACA 60.482 50.000 0.00 0.00 0.00 2.29
3306 6789 3.119291 CTGAAGGCGAGTCATCATACAC 58.881 50.000 0.00 0.00 0.00 2.90
3310 6793 1.478137 GCGAGTCATCATACACGGAC 58.522 55.000 0.00 0.00 34.58 4.79
3439 6923 1.889545 TGACACCATCGATTGTTGCA 58.110 45.000 4.31 1.42 0.00 4.08
3440 6924 1.535028 TGACACCATCGATTGTTGCAC 59.465 47.619 4.31 0.00 0.00 4.57
3441 6925 1.535028 GACACCATCGATTGTTGCACA 59.465 47.619 4.31 0.00 0.00 4.57
3447 6942 3.794564 CCATCGATTGTTGCACATTGATG 59.205 43.478 16.63 16.63 32.91 3.07
3452 6947 5.356470 TCGATTGTTGCACATTGATGGATAA 59.644 36.000 0.00 0.00 0.00 1.75
3472 6987 3.364441 GCTGGGCACGCACATGAA 61.364 61.111 0.00 0.00 0.00 2.57
3474 6989 1.659233 CTGGGCACGCACATGAAAA 59.341 52.632 0.00 0.00 0.00 2.29
3570 7717 8.462811 TCTCTTCAATATACAGAACTGAGTGAC 58.537 37.037 8.87 0.00 0.00 3.67
3571 7718 8.122472 TCTTCAATATACAGAACTGAGTGACA 57.878 34.615 8.87 0.00 0.00 3.58
3572 7719 8.029522 TCTTCAATATACAGAACTGAGTGACAC 58.970 37.037 8.87 0.00 0.00 3.67
3573 7720 6.631016 TCAATATACAGAACTGAGTGACACC 58.369 40.000 8.87 0.00 0.00 4.16
3574 7721 3.577649 ATACAGAACTGAGTGACACCG 57.422 47.619 8.87 0.00 0.00 4.94
3575 7722 0.249489 ACAGAACTGAGTGACACCGC 60.249 55.000 8.87 0.00 0.00 5.68
3576 7723 1.007271 AGAACTGAGTGACACCGCG 60.007 57.895 0.00 0.00 0.00 6.46
3577 7724 2.022129 GAACTGAGTGACACCGCGG 61.022 63.158 26.86 26.86 0.00 6.46
3578 7725 3.515316 AACTGAGTGACACCGCGGG 62.515 63.158 31.76 20.69 0.00 6.13
3579 7726 4.742201 CTGAGTGACACCGCGGGG 62.742 72.222 29.60 29.60 40.11 5.73
3601 7748 2.919043 GGGGGAGATGCCGACATT 59.081 61.111 0.00 0.00 36.35 2.71
3602 7749 1.227383 GGGGGAGATGCCGACATTT 59.773 57.895 0.00 0.00 36.35 2.32
3603 7750 1.103398 GGGGGAGATGCCGACATTTG 61.103 60.000 0.00 0.00 36.35 2.32
3604 7751 0.394352 GGGGAGATGCCGACATTTGT 60.394 55.000 0.00 0.00 36.35 2.83
3605 7752 1.463674 GGGAGATGCCGACATTTGTT 58.536 50.000 0.00 0.00 36.35 2.83
3606 7753 1.133025 GGGAGATGCCGACATTTGTTG 59.867 52.381 0.00 0.00 36.35 3.33
3607 7754 1.468054 GGAGATGCCGACATTTGTTGC 60.468 52.381 0.00 0.00 36.35 4.17
3608 7755 1.470098 GAGATGCCGACATTTGTTGCT 59.530 47.619 7.41 0.00 36.35 3.91
3609 7756 2.677836 GAGATGCCGACATTTGTTGCTA 59.322 45.455 7.41 0.00 36.35 3.49
3610 7757 2.420022 AGATGCCGACATTTGTTGCTAC 59.580 45.455 7.41 0.00 36.35 3.58
3611 7758 1.598882 TGCCGACATTTGTTGCTACA 58.401 45.000 0.00 0.00 0.00 2.74
3612 7759 1.265635 TGCCGACATTTGTTGCTACAC 59.734 47.619 0.00 0.00 32.98 2.90
3613 7760 1.724654 GCCGACATTTGTTGCTACACG 60.725 52.381 0.00 0.86 32.98 4.49
3614 7761 1.136085 CCGACATTTGTTGCTACACGG 60.136 52.381 11.53 11.53 34.13 4.94
3615 7762 1.136085 CGACATTTGTTGCTACACGGG 60.136 52.381 0.00 0.00 32.98 5.28
3616 7763 1.199097 GACATTTGTTGCTACACGGGG 59.801 52.381 0.00 0.00 32.98 5.73
3617 7764 1.243902 CATTTGTTGCTACACGGGGT 58.756 50.000 0.00 0.00 32.98 4.95
3618 7765 1.611491 CATTTGTTGCTACACGGGGTT 59.389 47.619 0.00 0.00 32.98 4.11
3619 7766 2.634815 TTTGTTGCTACACGGGGTTA 57.365 45.000 0.00 0.00 32.98 2.85
3620 7767 2.863132 TTGTTGCTACACGGGGTTAT 57.137 45.000 0.00 0.00 32.98 1.89
3621 7768 3.977134 TTGTTGCTACACGGGGTTATA 57.023 42.857 0.00 0.00 32.98 0.98
3622 7769 3.977134 TGTTGCTACACGGGGTTATAA 57.023 42.857 0.00 0.00 0.00 0.98
3623 7770 3.598299 TGTTGCTACACGGGGTTATAAC 58.402 45.455 7.09 7.09 0.00 1.89
3624 7771 3.261390 TGTTGCTACACGGGGTTATAACT 59.739 43.478 15.05 0.00 0.00 2.24
3625 7772 4.465660 TGTTGCTACACGGGGTTATAACTA 59.534 41.667 15.05 0.00 0.00 2.24
3626 7773 5.129155 TGTTGCTACACGGGGTTATAACTAT 59.871 40.000 15.05 0.00 0.00 2.12
3627 7774 6.323482 TGTTGCTACACGGGGTTATAACTATA 59.677 38.462 15.05 0.00 0.00 1.31
3628 7775 7.015487 TGTTGCTACACGGGGTTATAACTATAT 59.985 37.037 15.05 0.00 0.00 0.86
3629 7776 8.522830 GTTGCTACACGGGGTTATAACTATATA 58.477 37.037 15.05 1.39 0.00 0.86
3630 7777 8.284945 TGCTACACGGGGTTATAACTATATAG 57.715 38.462 15.05 8.27 0.00 1.31
3631 7778 7.890127 TGCTACACGGGGTTATAACTATATAGT 59.110 37.037 15.05 9.71 38.39 2.12
3632 7779 8.401709 GCTACACGGGGTTATAACTATATAGTC 58.598 40.741 15.72 3.19 34.99 2.59
3633 7780 9.453572 CTACACGGGGTTATAACTATATAGTCA 57.546 37.037 15.72 1.52 34.99 3.41
3634 7781 8.710749 ACACGGGGTTATAACTATATAGTCAA 57.289 34.615 15.72 7.94 34.99 3.18
3635 7782 9.146586 ACACGGGGTTATAACTATATAGTCAAA 57.853 33.333 15.72 7.88 34.99 2.69
3636 7783 9.985730 CACGGGGTTATAACTATATAGTCAAAA 57.014 33.333 15.72 7.56 34.99 2.44
3674 7821 7.906199 ACTAGCCTCTTCAATATACAGAACT 57.094 36.000 0.00 0.00 0.00 3.01
3675 7822 7.721402 ACTAGCCTCTTCAATATACAGAACTG 58.279 38.462 0.00 0.00 0.00 3.16
3676 7823 6.798427 AGCCTCTTCAATATACAGAACTGA 57.202 37.500 8.87 0.00 0.00 3.41
3677 7824 6.815089 AGCCTCTTCAATATACAGAACTGAG 58.185 40.000 8.87 0.00 0.00 3.35
3678 7825 6.382570 AGCCTCTTCAATATACAGAACTGAGT 59.617 38.462 8.87 0.00 0.00 3.41
3679 7826 6.478344 GCCTCTTCAATATACAGAACTGAGTG 59.522 42.308 8.87 0.00 0.00 3.51
3680 7827 7.631594 GCCTCTTCAATATACAGAACTGAGTGA 60.632 40.741 8.87 0.00 0.00 3.41
3845 8011 8.893219 TTATAGTATCTGCTGGAATTGTTGAG 57.107 34.615 0.00 0.00 0.00 3.02
3846 8012 5.171339 AGTATCTGCTGGAATTGTTGAGT 57.829 39.130 0.00 0.00 0.00 3.41
4085 8373 5.717078 ACATTGGCTGATTATGGCATAAG 57.283 39.130 23.01 12.24 39.67 1.73
4327 10560 1.896465 CGAAAGGGTCCACTCTTCTCT 59.104 52.381 0.00 0.00 0.00 3.10
4352 10585 2.683933 CCTCCCGTGTAGGCCAGT 60.684 66.667 5.01 0.00 39.21 4.00
4375 10608 8.206867 CAGTAGAAAGTAGGATGATCCAAATCA 58.793 37.037 14.90 0.00 45.73 2.57
4568 10804 4.640771 TTCTGAGCAATTCTACCCTTGT 57.359 40.909 0.00 0.00 0.00 3.16
4643 10889 4.159377 CAGTTTTATTTTGCTGGAGCGA 57.841 40.909 0.00 0.00 45.83 4.93
5465 11855 6.391227 AAGCCAAATAAAGATATTGACCCG 57.609 37.500 0.00 0.00 32.06 5.28
6878 14140 1.336517 CCTGGTTCGCGTTTCTGAGTA 60.337 52.381 5.77 0.00 0.00 2.59
7894 15739 1.079127 CTCGTCCTTGCCGTTGGAT 60.079 57.895 0.00 0.00 34.58 3.41
7895 15740 0.673644 CTCGTCCTTGCCGTTGGATT 60.674 55.000 0.00 0.00 34.58 3.01
7920 15765 3.998672 GGAGGACGGTGGCGTGAA 61.999 66.667 0.00 0.00 0.00 3.18
7949 15794 4.468689 GGCGTGGTGTAGGAGCCC 62.469 72.222 0.00 0.00 41.81 5.19
8017 15865 0.848735 ATGGAGCACTGGTGGCATAT 59.151 50.000 2.84 0.00 0.00 1.78
8018 15866 1.506025 TGGAGCACTGGTGGCATATA 58.494 50.000 2.84 0.00 0.00 0.86
8019 15867 2.057140 TGGAGCACTGGTGGCATATAT 58.943 47.619 2.84 0.00 0.00 0.86
8020 15868 3.247162 TGGAGCACTGGTGGCATATATA 58.753 45.455 2.84 0.00 0.00 0.86
8103 15975 3.287222 CTTGAAGGCGGATTGGGATTTA 58.713 45.455 0.00 0.00 0.00 1.40
8308 16181 6.072618 GGAAGGGCTACTTGACTTTTAACTTC 60.073 42.308 0.00 0.00 40.21 3.01
8319 16192 5.884792 TGACTTTTAACTTCCAAACCGGTTA 59.115 36.000 22.60 1.22 35.57 2.85
8332 16205 1.339727 ACCGGTTAGTCAAATGCTCCC 60.340 52.381 0.00 0.00 0.00 4.30
8444 16327 1.237533 AGCACAAATGACATGCGTGA 58.762 45.000 14.17 0.00 44.25 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.050351 CTCGACGTGGACGCACTT 60.050 61.111 0.00 0.00 44.43 3.16
239 240 3.202829 AGCGTTTTGTTGGAGGAGTTA 57.797 42.857 0.00 0.00 0.00 2.24
320 322 2.062636 TGCCTCTCCATAATTACCCCC 58.937 52.381 0.00 0.00 0.00 5.40
353 356 2.479837 TGTGTGCTTACAACTTCTCCG 58.520 47.619 0.00 0.00 0.00 4.63
392 395 3.890147 GGCTATTACTTCCTCCGAGAAGA 59.110 47.826 14.27 0.00 45.08 2.87
496 499 2.563179 CGCACTCTATATAAGCCACCCT 59.437 50.000 0.00 0.00 0.00 4.34
634 637 1.745115 GGCACTCCGCATGCTAACA 60.745 57.895 17.13 0.00 45.17 2.41
663 666 0.249868 CCAAGCCACTCGACAGTCAA 60.250 55.000 0.41 0.00 0.00 3.18
727 730 0.877071 TAGGTGTTCCACTCGACGTC 59.123 55.000 5.18 5.18 34.40 4.34
728 731 0.595095 GTAGGTGTTCCACTCGACGT 59.405 55.000 0.00 0.00 34.40 4.34
729 732 0.594602 TGTAGGTGTTCCACTCGACG 59.405 55.000 0.00 0.00 34.40 5.12
746 749 7.678947 AGAAATCATCTTTCAATCGACTTGT 57.321 32.000 0.00 0.00 33.39 3.16
812 815 5.635133 AGCTATTTATCTAGGGTAGGGGT 57.365 43.478 0.00 0.00 0.00 4.95
828 831 7.002276 TGTCATTGATCCATGATGAAGCTATT 58.998 34.615 12.25 0.00 32.14 1.73
860 863 6.038603 CACCAAGACATGAGTTCTCTTTTTGA 59.961 38.462 0.00 0.00 0.00 2.69
861 864 6.183360 ACACCAAGACATGAGTTCTCTTTTTG 60.183 38.462 0.00 0.01 0.00 2.44
865 868 4.384056 CACACCAAGACATGAGTTCTCTT 58.616 43.478 0.00 0.00 0.00 2.85
867 870 3.070018 CCACACCAAGACATGAGTTCTC 58.930 50.000 0.00 0.00 0.00 2.87
868 871 2.224621 CCCACACCAAGACATGAGTTCT 60.225 50.000 0.00 0.00 0.00 3.01
869 872 2.154462 CCCACACCAAGACATGAGTTC 58.846 52.381 0.00 0.00 0.00 3.01
872 875 0.962356 GCCCCACACCAAGACATGAG 60.962 60.000 0.00 0.00 0.00 2.90
873 876 1.074775 GCCCCACACCAAGACATGA 59.925 57.895 0.00 0.00 0.00 3.07
874 877 0.327924 TAGCCCCACACCAAGACATG 59.672 55.000 0.00 0.00 0.00 3.21
875 878 0.620556 CTAGCCCCACACCAAGACAT 59.379 55.000 0.00 0.00 0.00 3.06
877 880 1.299976 CCTAGCCCCACACCAAGAC 59.700 63.158 0.00 0.00 0.00 3.01
878 881 1.923395 CCCTAGCCCCACACCAAGA 60.923 63.158 0.00 0.00 0.00 3.02
879 882 2.677228 CCCTAGCCCCACACCAAG 59.323 66.667 0.00 0.00 0.00 3.61
880 883 3.657350 GCCCTAGCCCCACACCAA 61.657 66.667 0.00 0.00 0.00 3.67
890 893 2.508663 GACGACGTTGGCCCTAGC 60.509 66.667 7.90 0.00 38.76 3.42
891 894 1.153823 CTGACGACGTTGGCCCTAG 60.154 63.158 6.08 0.00 0.00 3.02
892 895 1.904865 ACTGACGACGTTGGCCCTA 60.905 57.895 6.08 0.00 0.00 3.53
894 897 3.041940 CACTGACGACGTTGGCCC 61.042 66.667 6.08 0.00 0.00 5.80
895 898 2.028484 TCACTGACGACGTTGGCC 59.972 61.111 6.08 0.00 0.00 5.36
896 899 1.149361 TTGTCACTGACGACGTTGGC 61.149 55.000 7.90 4.29 38.84 4.52
898 901 1.006391 GTGTTGTCACTGACGACGTTG 60.006 52.381 20.24 0.00 46.65 4.10
902 905 1.067212 AGAGGTGTTGTCACTGACGAC 59.933 52.381 19.24 19.24 44.65 4.34
903 906 1.337071 GAGAGGTGTTGTCACTGACGA 59.663 52.381 4.71 0.00 43.41 4.20
905 908 1.689273 AGGAGAGGTGTTGTCACTGAC 59.311 52.381 1.86 1.86 43.41 3.51
906 909 2.088104 AGGAGAGGTGTTGTCACTGA 57.912 50.000 0.00 0.00 43.41 3.41
907 910 2.918712 AAGGAGAGGTGTTGTCACTG 57.081 50.000 0.00 0.00 43.41 3.66
946 949 2.172679 GAGAGGAGAAGAAAGACGGGT 58.827 52.381 0.00 0.00 0.00 5.28
1001 1006 1.859302 GAGAGAGGCAGAAAGAGGGA 58.141 55.000 0.00 0.00 0.00 4.20
1092 1109 1.751349 GCGGATTAGGGCCTACCGAA 61.751 60.000 34.39 16.42 46.96 4.30
1176 1195 2.232452 TCTCAAGAACACTAGAGCAGCC 59.768 50.000 0.00 0.00 0.00 4.85
1235 1254 0.823356 ATCGCAGCAAACACAAGGGT 60.823 50.000 0.00 0.00 0.00 4.34
1390 1645 1.094785 ACAATTGCATGGCGGTAGAC 58.905 50.000 5.05 0.00 0.00 2.59
1455 1710 4.382685 CCAATGTAATCCTACCTGACACGT 60.383 45.833 0.00 0.00 0.00 4.49
1487 1742 4.379652 AGCAACAAATTCCATGAAACCAC 58.620 39.130 0.00 0.00 0.00 4.16
1492 1747 5.538053 TGAGGTTAGCAACAAATTCCATGAA 59.462 36.000 0.00 0.00 0.00 2.57
1543 1798 9.986157 AGCAATGATGGACAATTATAATCCTAT 57.014 29.630 0.00 0.00 33.34 2.57
1912 3606 2.604912 TCTGTGCCAGAGGTAGAGAA 57.395 50.000 0.00 0.00 35.10 2.87
1940 3634 0.977627 TGCATCGTCCTCACCATCCT 60.978 55.000 0.00 0.00 0.00 3.24
2067 3813 1.366366 CACCGTCTTCGTTGTCCCT 59.634 57.895 0.00 0.00 35.01 4.20
2098 3847 1.228094 TTGGCACCGTCAATCTGCA 60.228 52.632 0.00 0.00 32.20 4.41
2115 3864 3.428999 CCGATCACTTACTCGTCCATGTT 60.429 47.826 0.00 0.00 33.11 2.71
2176 3926 4.566545 TTAACTGCAGGAAACACACATG 57.433 40.909 19.93 0.00 0.00 3.21
2253 4292 4.871933 ACAAAATGCTTTCCTAACAGGG 57.128 40.909 0.00 0.00 35.59 4.45
2689 5964 7.985184 TGTAATGTTCTGTCCAGGATATAACAC 59.015 37.037 16.47 7.59 0.00 3.32
2690 5965 8.084985 TGTAATGTTCTGTCCAGGATATAACA 57.915 34.615 16.47 16.47 0.00 2.41
2694 5969 6.042093 ACGATGTAATGTTCTGTCCAGGATAT 59.958 38.462 0.00 0.00 0.00 1.63
2695 5970 5.362717 ACGATGTAATGTTCTGTCCAGGATA 59.637 40.000 0.00 0.00 0.00 2.59
2696 5971 4.162320 ACGATGTAATGTTCTGTCCAGGAT 59.838 41.667 0.00 0.00 0.00 3.24
2697 5972 3.513912 ACGATGTAATGTTCTGTCCAGGA 59.486 43.478 0.00 0.00 0.00 3.86
2698 5973 3.861840 ACGATGTAATGTTCTGTCCAGG 58.138 45.455 0.00 0.00 0.00 4.45
2699 5974 7.921214 AGTATAACGATGTAATGTTCTGTCCAG 59.079 37.037 0.00 0.00 0.00 3.86
2703 5985 7.435488 GCTCAGTATAACGATGTAATGTTCTGT 59.565 37.037 0.00 0.00 0.00 3.41
2709 5991 8.076781 ACTACAGCTCAGTATAACGATGTAATG 58.923 37.037 0.00 0.00 0.00 1.90
2715 5998 7.096884 TGAAACTACAGCTCAGTATAACGAT 57.903 36.000 0.00 0.00 0.00 3.73
2728 6012 6.853362 GTGAACAGAAAAGATGAAACTACAGC 59.147 38.462 0.00 0.00 0.00 4.40
2775 6079 5.460646 CAATCGACCAACTATTGCTTGTTT 58.539 37.500 0.00 0.00 0.00 2.83
2814 6188 2.543777 AAGCACACATGTACGAACCT 57.456 45.000 0.00 0.00 0.00 3.50
2819 6193 2.232239 GCAGAAAGCACACATGTACG 57.768 50.000 0.00 0.00 44.79 3.67
2950 6408 3.132646 AGCTTTGTGTGCAGATTTGGAAA 59.867 39.130 0.00 0.00 0.00 3.13
2978 6436 4.164822 AGAACAATCATGGCGAAAACAG 57.835 40.909 0.00 0.00 0.00 3.16
3038 6498 7.697691 ACAAACAAAGACAACTCACTAATCTG 58.302 34.615 0.00 0.00 0.00 2.90
3039 6507 7.865706 ACAAACAAAGACAACTCACTAATCT 57.134 32.000 0.00 0.00 0.00 2.40
3166 6640 7.172019 TCTCATCACAATTGTATTCGATGATGG 59.828 37.037 26.75 20.10 38.73 3.51
3305 6788 2.169769 TGGAAACAAGACTCTTGTCCGT 59.830 45.455 22.07 12.17 38.72 4.69
3306 6789 2.544267 GTGGAAACAAGACTCTTGTCCG 59.456 50.000 22.07 0.00 46.06 4.79
3310 6793 2.291741 GGCAGTGGAAACAAGACTCTTG 59.708 50.000 16.01 16.01 46.06 3.02
3439 6923 3.322828 GCCCAGCAATTATCCATCAATGT 59.677 43.478 0.00 0.00 0.00 2.71
3440 6924 3.322541 TGCCCAGCAATTATCCATCAATG 59.677 43.478 0.00 0.00 34.76 2.82
3441 6925 3.322828 GTGCCCAGCAATTATCCATCAAT 59.677 43.478 0.00 0.00 41.47 2.57
3447 6942 1.360192 GCGTGCCCAGCAATTATCC 59.640 57.895 0.00 0.00 41.47 2.59
3452 6947 2.677524 ATGTGCGTGCCCAGCAAT 60.678 55.556 0.00 0.00 46.97 3.56
3472 6987 7.721402 TGTTCTTAACCATGTAGCAACAATTT 58.279 30.769 0.00 0.00 39.58 1.82
3474 6989 6.892658 TGTTCTTAACCATGTAGCAACAAT 57.107 33.333 0.00 0.00 39.58 2.71
3503 7556 7.706607 TCATCAAGTGATACTTCTATTCGGTTG 59.293 37.037 0.00 0.00 36.03 3.77
3584 7731 1.103398 CAAATGTCGGCATCTCCCCC 61.103 60.000 1.37 0.00 33.50 5.40
3585 7732 0.394352 ACAAATGTCGGCATCTCCCC 60.394 55.000 1.37 0.00 33.50 4.81
3586 7733 1.133025 CAACAAATGTCGGCATCTCCC 59.867 52.381 1.37 0.00 33.50 4.30
3587 7734 1.468054 GCAACAAATGTCGGCATCTCC 60.468 52.381 1.37 0.00 33.50 3.71
3588 7735 1.470098 AGCAACAAATGTCGGCATCTC 59.530 47.619 1.37 0.00 33.50 2.75
3589 7736 1.538047 AGCAACAAATGTCGGCATCT 58.462 45.000 1.37 0.00 33.50 2.90
3590 7737 2.161410 TGTAGCAACAAATGTCGGCATC 59.839 45.455 1.37 0.00 33.50 3.91
3591 7738 2.095263 GTGTAGCAACAAATGTCGGCAT 60.095 45.455 0.00 0.00 37.36 4.40
3592 7739 1.265635 GTGTAGCAACAAATGTCGGCA 59.734 47.619 0.00 0.00 37.36 5.69
3593 7740 1.724654 CGTGTAGCAACAAATGTCGGC 60.725 52.381 2.90 2.90 37.36 5.54
3594 7741 1.136085 CCGTGTAGCAACAAATGTCGG 60.136 52.381 0.00 0.00 37.36 4.79
3595 7742 1.136085 CCCGTGTAGCAACAAATGTCG 60.136 52.381 0.00 0.00 37.36 4.35
3596 7743 1.199097 CCCCGTGTAGCAACAAATGTC 59.801 52.381 0.00 0.00 37.36 3.06
3597 7744 1.243902 CCCCGTGTAGCAACAAATGT 58.756 50.000 0.00 0.00 37.36 2.71
3598 7745 1.243902 ACCCCGTGTAGCAACAAATG 58.756 50.000 0.00 0.00 37.36 2.32
3599 7746 1.989706 AACCCCGTGTAGCAACAAAT 58.010 45.000 0.00 0.00 37.36 2.32
3600 7747 2.634815 TAACCCCGTGTAGCAACAAA 57.365 45.000 0.00 0.00 37.36 2.83
3601 7748 2.863132 ATAACCCCGTGTAGCAACAA 57.137 45.000 0.00 0.00 37.36 2.83
3602 7749 3.261390 AGTTATAACCCCGTGTAGCAACA 59.739 43.478 12.05 0.00 0.00 3.33
3603 7750 3.865446 AGTTATAACCCCGTGTAGCAAC 58.135 45.455 12.05 0.00 0.00 4.17
3604 7751 5.874897 ATAGTTATAACCCCGTGTAGCAA 57.125 39.130 12.05 0.00 0.00 3.91
3605 7752 7.890127 ACTATATAGTTATAACCCCGTGTAGCA 59.110 37.037 9.71 0.00 31.13 3.49
3606 7753 8.286191 ACTATATAGTTATAACCCCGTGTAGC 57.714 38.462 9.71 0.00 31.13 3.58
3607 7754 9.453572 TGACTATATAGTTATAACCCCGTGTAG 57.546 37.037 16.46 9.49 36.50 2.74
3608 7755 9.806448 TTGACTATATAGTTATAACCCCGTGTA 57.194 33.333 16.46 0.00 36.50 2.90
3609 7756 8.710749 TTGACTATATAGTTATAACCCCGTGT 57.289 34.615 16.46 4.99 36.50 4.49
3610 7757 9.985730 TTTTGACTATATAGTTATAACCCCGTG 57.014 33.333 16.46 2.02 36.50 4.94
3648 7795 9.422681 AGTTCTGTATATTGAAGAGGCTAGTTA 57.577 33.333 0.00 0.00 0.00 2.24
3649 7796 8.200792 CAGTTCTGTATATTGAAGAGGCTAGTT 58.799 37.037 0.00 0.00 0.00 2.24
3650 7797 7.561722 TCAGTTCTGTATATTGAAGAGGCTAGT 59.438 37.037 0.00 0.00 0.00 2.57
3651 7798 7.946207 TCAGTTCTGTATATTGAAGAGGCTAG 58.054 38.462 0.00 0.00 0.00 3.42
3652 7799 7.561722 ACTCAGTTCTGTATATTGAAGAGGCTA 59.438 37.037 0.00 0.00 0.00 3.93
3653 7800 6.382570 ACTCAGTTCTGTATATTGAAGAGGCT 59.617 38.462 0.00 0.00 0.00 4.58
3654 7801 6.478344 CACTCAGTTCTGTATATTGAAGAGGC 59.522 42.308 0.00 0.00 0.00 4.70
3655 7802 7.776107 TCACTCAGTTCTGTATATTGAAGAGG 58.224 38.462 0.00 0.00 0.00 3.69
3658 7805 9.469807 GGTATCACTCAGTTCTGTATATTGAAG 57.530 37.037 0.00 0.00 0.00 3.02
3659 7806 8.977412 TGGTATCACTCAGTTCTGTATATTGAA 58.023 33.333 0.00 0.00 0.00 2.69
3660 7807 8.533569 TGGTATCACTCAGTTCTGTATATTGA 57.466 34.615 0.00 0.00 0.00 2.57
3661 7808 9.201127 CATGGTATCACTCAGTTCTGTATATTG 57.799 37.037 0.00 0.00 0.00 1.90
3662 7809 8.928448 ACATGGTATCACTCAGTTCTGTATATT 58.072 33.333 0.00 0.00 0.00 1.28
3663 7810 8.363390 CACATGGTATCACTCAGTTCTGTATAT 58.637 37.037 0.00 0.00 0.00 0.86
3664 7811 7.342026 ACACATGGTATCACTCAGTTCTGTATA 59.658 37.037 0.00 0.00 0.00 1.47
3665 7812 6.155221 ACACATGGTATCACTCAGTTCTGTAT 59.845 38.462 0.00 0.00 0.00 2.29
3666 7813 5.480422 ACACATGGTATCACTCAGTTCTGTA 59.520 40.000 0.00 0.00 0.00 2.74
3667 7814 4.284490 ACACATGGTATCACTCAGTTCTGT 59.716 41.667 0.00 0.00 0.00 3.41
3668 7815 4.825422 ACACATGGTATCACTCAGTTCTG 58.175 43.478 0.00 0.00 0.00 3.02
3669 7816 6.798427 ATACACATGGTATCACTCAGTTCT 57.202 37.500 0.00 0.00 38.30 3.01
3670 7817 7.849804 AAATACACATGGTATCACTCAGTTC 57.150 36.000 0.00 0.00 41.87 3.01
3671 7818 8.635765 AAAAATACACATGGTATCACTCAGTT 57.364 30.769 0.00 0.00 41.87 3.16
3672 7819 9.905713 ATAAAAATACACATGGTATCACTCAGT 57.094 29.630 0.00 0.00 41.87 3.41
3674 7821 9.119418 CCATAAAAATACACATGGTATCACTCA 57.881 33.333 0.00 0.00 41.87 3.41
3811 7977 7.295340 TCCAGCAGATACTATAAGGAAGTGTA 58.705 38.462 0.00 0.00 0.00 2.90
4327 10560 2.662866 CCTACACGGGAGGAGTATGAA 58.337 52.381 0.00 0.00 35.99 2.57
4568 10804 1.600636 CAAAGCCGGAGCACCAGAA 60.601 57.895 5.05 0.00 43.56 3.02
4642 10888 1.852895 CTGATAACGCGCCACTACTTC 59.147 52.381 5.73 0.00 0.00 3.01
4643 10889 1.203994 ACTGATAACGCGCCACTACTT 59.796 47.619 5.73 0.00 0.00 2.24
5016 11369 1.227943 GGAGCTGCTGGTGTGTGAA 60.228 57.895 7.01 0.00 0.00 3.18
7672 15517 9.545105 GAAATTAATTGCAATGGGTATGAATGA 57.455 29.630 13.82 0.00 0.00 2.57
7721 15566 7.465379 CGTCACTTCAACTTTTAACTGTGATGA 60.465 37.037 0.00 0.00 40.52 2.92
7810 15655 5.531634 GTCAATGTGACATTCATGTGGTTT 58.468 37.500 8.03 0.00 46.22 3.27
7894 15739 1.618888 CCACCGTCCTCCTCCTTCTAA 60.619 57.143 0.00 0.00 0.00 2.10
7895 15740 0.033405 CCACCGTCCTCCTCCTTCTA 60.033 60.000 0.00 0.00 0.00 2.10
7920 15765 2.047274 CACGCCCCATCGTTGTCT 60.047 61.111 0.00 0.00 41.21 3.41
7949 15794 1.190643 GTCTCCTTGTCCTCCTCCAG 58.809 60.000 0.00 0.00 0.00 3.86
8017 15865 4.844085 CCATGGTCCACATAAGGTCCTATA 59.156 45.833 2.57 0.00 37.84 1.31
8018 15866 3.652869 CCATGGTCCACATAAGGTCCTAT 59.347 47.826 2.57 0.00 37.84 2.57
8019 15867 3.045634 CCATGGTCCACATAAGGTCCTA 58.954 50.000 2.57 0.00 37.84 2.94
8020 15868 1.846439 CCATGGTCCACATAAGGTCCT 59.154 52.381 2.57 0.00 37.84 3.85
8164 16037 2.760634 TCTAAAAGAGCACGCATGGA 57.239 45.000 0.00 0.00 0.00 3.41
8278 16151 2.185387 GTCAAGTAGCCCTTCCCTACA 58.815 52.381 0.00 0.00 38.07 2.74
8308 16181 2.556622 AGCATTTGACTAACCGGTTTGG 59.443 45.455 27.64 20.29 46.41 3.28
8319 16192 1.002069 TCATGGGGGAGCATTTGACT 58.998 50.000 0.00 0.00 0.00 3.41
8424 16307 2.421619 TCACGCATGTCATTTGTGCTA 58.578 42.857 8.65 0.00 36.74 3.49
8461 16359 8.611757 GTTCCAAAAATGCTAGTTTGAAAACAT 58.388 29.630 8.53 0.00 41.30 2.71


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

AutoCloner maintained by Alex Coulton.