Multiple sequence alignment - TraesCS1D01G278900

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 TraesCS1D01G278900 chr1D 100.000 9562 0 0 1 9562 376720922 376730483 0.000000e+00 17658.0
1 TraesCS1D01G278900 chr1D 82.614 903 115 25 7707 8595 376266210 376267084 0.000000e+00 760.0
2 TraesCS1D01G278900 chr1D 79.722 1080 158 32 7601 8654 376255644 376256688 0.000000e+00 725.0
3 TraesCS1D01G278900 chr1D 83.189 809 109 13 7468 8263 376260866 376261660 0.000000e+00 715.0
4 TraesCS1D01G278900 chr1D 80.575 870 126 22 7712 8564 376243545 376244388 1.750000e-176 630.0
5 TraesCS1D01G278900 chr1D 71.757 1565 364 64 3742 5259 245088159 245086626 4.220000e-98 370.0
6 TraesCS1D01G278900 chr1D 86.510 341 41 4 7113 7453 376260434 376260769 4.220000e-98 370.0
7 TraesCS1D01G278900 chr1D 85.088 342 45 6 7113 7452 376240236 376240573 2.560000e-90 344.0
8 TraesCS1D01G278900 chr1D 72.015 1315 314 46 3960 5241 490487237 490488530 3.310000e-89 340.0
9 TraesCS1D01G278900 chr1D 76.407 462 103 5 4775 5233 472192679 472193137 2.670000e-60 244.0
10 TraesCS1D01G278900 chr1D 73.084 535 105 27 5994 6505 349088770 349089288 4.620000e-33 154.0
11 TraesCS1D01G278900 chr1B 96.703 3579 95 12 3883 7453 503467191 503470754 0.000000e+00 5934.0
12 TraesCS1D01G278900 chr1B 94.307 3882 158 29 1 3856 503463052 503466896 0.000000e+00 5886.0
13 TraesCS1D01G278900 chr1B 95.207 1210 43 6 7450 8656 503470827 503472024 0.000000e+00 1899.0
14 TraesCS1D01G278900 chr1B 81.166 1184 166 25 7456 8615 502790391 502791541 0.000000e+00 898.0
15 TraesCS1D01G278900 chr1B 81.494 870 116 22 7712 8564 502793256 502794097 0.000000e+00 673.0
16 TraesCS1D01G278900 chr1B 81.764 839 119 16 7456 8278 502804335 502805155 0.000000e+00 671.0
17 TraesCS1D01G278900 chr1B 81.051 818 113 18 7839 8654 502748610 502749387 1.760000e-171 614.0
18 TraesCS1D01G278900 chr1B 82.688 491 58 12 8099 8578 502866086 502866560 2.490000e-110 411.0
19 TraesCS1D01G278900 chr1B 83.894 416 64 3 66 480 502747075 502747488 2.500000e-105 394.0
20 TraesCS1D01G278900 chr1B 84.503 342 47 5 7113 7453 502803913 502804249 5.530000e-87 333.0
21 TraesCS1D01G278900 chr1B 84.136 353 40 8 7113 7452 502789956 502790305 2.570000e-85 327.0
22 TraesCS1D01G278900 chr1B 81.844 347 57 5 94 440 502754094 502754434 4.370000e-73 287.0
23 TraesCS1D01G278900 chr1B 94.444 36 1 1 1558 1593 494243987 494244021 5.000000e-03 54.7
24 TraesCS1D01G278900 chr1A 94.979 1215 42 9 7450 8656 476980624 476981827 0.000000e+00 1888.0
25 TraesCS1D01G278900 chr1A 90.864 1412 87 20 1 1402 476971577 476972956 0.000000e+00 1855.0
26 TraesCS1D01G278900 chr1A 97.889 1042 21 1 4932 5972 476975937 476976978 0.000000e+00 1801.0
27 TraesCS1D01G278900 chr1A 98.350 909 15 0 3980 4888 476975037 476975945 0.000000e+00 1596.0
28 TraesCS1D01G278900 chr1A 95.982 672 19 5 6785 7453 476979914 476980580 0.000000e+00 1085.0
29 TraesCS1D01G278900 chr1A 81.509 1233 159 31 7461 8654 475484250 475485452 0.000000e+00 950.0
30 TraesCS1D01G278900 chr1A 96.048 582 18 3 2415 2995 476973881 476974458 0.000000e+00 942.0
31 TraesCS1D01G278900 chr1A 81.377 1235 156 34 7461 8654 475458254 475457053 0.000000e+00 939.0
32 TraesCS1D01G278900 chr1A 96.442 534 18 1 5970 6502 476978741 476979274 0.000000e+00 880.0
33 TraesCS1D01G278900 chr1A 93.162 585 40 0 3096 3680 476974455 476975039 0.000000e+00 859.0
34 TraesCS1D01G278900 chr1A 91.333 450 16 12 1386 1834 476973288 476973715 2.300000e-165 593.0
35 TraesCS1D01G278900 chr1A 82.733 666 79 14 8001 8654 475626549 475627190 2.330000e-155 560.0
36 TraesCS1D01G278900 chr1A 95.197 229 8 2 6494 6722 476979662 476979887 9.130000e-95 359.0
37 TraesCS1D01G278900 chr1A 81.549 439 55 13 7495 7920 475623225 475623650 1.190000e-88 339.0
38 TraesCS1D01G278900 chr1A 90.123 162 14 2 2211 2370 476973708 476973869 9.730000e-50 209.0
39 TraesCS1D01G278900 chr1A 87.363 182 20 3 6924 7103 475483544 475483724 1.260000e-48 206.0
40 TraesCS1D01G278900 chr1A 87.791 172 19 2 6934 7103 475458952 475458781 5.860000e-47 200.0
41 TraesCS1D01G278900 chr1A 81.081 111 15 5 7283 7389 475715087 475715195 6.150000e-12 84.2
42 TraesCS1D01G278900 chr4D 96.337 901 33 0 8662 9562 502634220 502635120 0.000000e+00 1482.0
43 TraesCS1D01G278900 chr4D 71.258 1590 384 57 3699 5245 125084611 125083052 4.280000e-88 337.0
44 TraesCS1D01G278900 chr6D 95.833 912 36 2 8652 9562 446091684 446090774 0.000000e+00 1472.0
45 TraesCS1D01G278900 chr6D 95.714 910 36 2 8656 9562 450858742 450857833 0.000000e+00 1461.0
46 TraesCS1D01G278900 chr6D 96.695 696 22 1 8656 9351 469787215 469787909 0.000000e+00 1157.0
47 TraesCS1D01G278900 chr6D 76.327 452 94 12 3899 4343 86765307 86764862 7.470000e-56 230.0
48 TraesCS1D01G278900 chr7D 94.869 916 44 3 8649 9562 58149914 58149000 0.000000e+00 1428.0
49 TraesCS1D01G278900 chr7D 72.806 1971 478 39 3684 5616 540109712 540107762 1.360000e-172 617.0
50 TraesCS1D01G278900 chr7A 93.853 911 55 1 8653 9562 248537913 248538823 0.000000e+00 1371.0
51 TraesCS1D01G278900 chr7A 71.667 600 153 17 5906 6493 729596258 729595664 5.980000e-32 150.0
52 TraesCS1D01G278900 chr7A 73.898 295 59 15 5996 6280 720820262 720819976 1.700000e-17 102.0
53 TraesCS1D01G278900 chr5D 92.223 913 65 3 8656 9562 26903124 26902212 0.000000e+00 1288.0
54 TraesCS1D01G278900 chr5D 85.396 897 124 6 8660 9550 43217676 43218571 0.000000e+00 924.0
55 TraesCS1D01G278900 chr5D 72.051 1560 379 47 3717 5241 31258615 31260152 6.910000e-111 412.0
56 TraesCS1D01G278900 chr5D 75.450 611 128 20 3742 4343 303717074 303716477 2.630000e-70 278.0
57 TraesCS1D01G278900 chr5D 72.963 847 190 36 3822 4650 49278483 49279308 9.530000e-65 259.0
58 TraesCS1D01G278900 chrUn 91.589 856 43 10 1558 2410 232946903 232946074 0.000000e+00 1155.0
59 TraesCS1D01G278900 chrUn 91.589 856 43 10 1558 2410 232957820 232956991 0.000000e+00 1155.0
60 TraesCS1D01G278900 chrUn 96.296 81 3 0 2411 2491 232945007 232944927 6.020000e-27 134.0
61 TraesCS1D01G278900 chrUn 96.296 81 3 0 2411 2491 232956407 232956327 6.020000e-27 134.0
62 TraesCS1D01G278900 chrUn 97.917 48 1 0 1448 1495 232946940 232946893 6.150000e-12 84.2
63 TraesCS1D01G278900 chrUn 97.917 48 1 0 1448 1495 232957857 232957810 6.150000e-12 84.2
64 TraesCS1D01G278900 chr5B 91.005 856 49 9 1558 2410 563739928 563739098 0.000000e+00 1129.0
65 TraesCS1D01G278900 chr5B 90.888 856 50 9 1558 2410 563719993 563719163 0.000000e+00 1123.0
66 TraesCS1D01G278900 chr5B 90.782 857 49 11 1558 2410 563755413 563754583 0.000000e+00 1118.0
67 TraesCS1D01G278900 chr5B 86.184 760 86 9 8652 9394 565542303 565543060 0.000000e+00 804.0
68 TraesCS1D01G278900 chr5B 96.296 81 3 0 2411 2491 563718581 563718501 6.020000e-27 134.0
69 TraesCS1D01G278900 chr5B 95.062 81 4 0 2411 2491 563738517 563738437 2.800000e-25 128.0
70 TraesCS1D01G278900 chr5B 91.026 78 7 0 2411 2488 563685735 563685658 1.310000e-18 106.0
71 TraesCS1D01G278900 chr5B 97.917 48 1 0 1448 1495 563720030 563719983 6.150000e-12 84.2
72 TraesCS1D01G278900 chr5B 97.917 48 1 0 1448 1495 563726944 563726897 6.150000e-12 84.2
73 TraesCS1D01G278900 chr5B 97.917 48 1 0 1448 1495 563739965 563739918 6.150000e-12 84.2
74 TraesCS1D01G278900 chr5B 97.917 48 1 0 1448 1495 563755450 563755403 6.150000e-12 84.2
75 TraesCS1D01G278900 chr5B 97.778 45 1 0 1558 1602 563726907 563726863 2.860000e-10 78.7
76 TraesCS1D01G278900 chr6B 85.049 923 119 12 8656 9562 46792207 46791288 0.000000e+00 922.0
77 TraesCS1D01G278900 chr6B 84.644 267 30 9 1742 1998 690883915 690883650 1.230000e-63 255.0
78 TraesCS1D01G278900 chr6B 70.844 1197 274 59 4117 5266 171984976 171983808 3.500000e-49 207.0
79 TraesCS1D01G278900 chr6B 73.623 345 81 10 5943 6281 624117642 624117982 3.630000e-24 124.0
80 TraesCS1D01G278900 chr2D 86.475 451 44 8 1556 1998 455309018 455309459 6.720000e-131 479.0
81 TraesCS1D01G278900 chr2D 83.019 212 29 5 2680 2884 572679656 572679445 1.640000e-42 185.0
82 TraesCS1D01G278900 chr2D 70.783 575 142 22 5947 6504 647230276 647230841 3.650000e-19 108.0
83 TraesCS1D01G278900 chr2D 87.342 79 9 1 2411 2489 544872365 544872442 1.320000e-13 89.8
84 TraesCS1D01G278900 chr7B 85.138 471 56 5 1577 2040 130580044 130580507 4.040000e-128 470.0
85 TraesCS1D01G278900 chr7B 74.194 403 93 10 5989 6382 139793745 139793345 3.570000e-34 158.0
86 TraesCS1D01G278900 chr7B 94.286 35 2 0 4809 4843 617795105 617795071 5.000000e-03 54.7
87 TraesCS1D01G278900 chr4A 71.273 1650 427 34 3985 5600 588601940 588603576 2.520000e-100 377.0
88 TraesCS1D01G278900 chr2A 70.063 2375 625 65 3960 6280 779593283 779595625 1.520000e-97 368.0
89 TraesCS1D01G278900 chr2A 73.768 568 145 4 4760 5325 531918126 531918691 4.500000e-53 220.0
90 TraesCS1D01G278900 chr2A 71.722 778 182 32 3822 4581 779486987 779487744 5.900000e-42 183.0
91 TraesCS1D01G278900 chr2A 72.414 580 135 21 5942 6505 779489124 779489694 2.760000e-35 161.0
92 TraesCS1D01G278900 chr2B 71.043 1668 406 57 3983 5600 31412293 31410653 5.530000e-87 333.0
93 TraesCS1D01G278900 chr6A 90.789 76 4 2 2411 2485 120871023 120870950 2.200000e-16 99.0
94 TraesCS1D01G278900 chr3B 88.333 60 7 0 4784 4843 187568292 187568233 1.330000e-08 73.1
95 TraesCS1D01G278900 chr4B 94.444 36 2 0 4808 4843 429716110 429716075 1.000000e-03 56.5


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 TraesCS1D01G278900 chr1D 376720922 376730483 9561 False 17658.000000 17658 100.000000 1 9562 1 chr1D.!!$F3 9561
1 TraesCS1D01G278900 chr1D 376266210 376267084 874 False 760.000000 760 82.614000 7707 8595 1 chr1D.!!$F2 888
2 TraesCS1D01G278900 chr1D 376255644 376261660 6016 False 603.333333 725 83.140333 7113 8654 3 chr1D.!!$F7 1541
3 TraesCS1D01G278900 chr1D 376240236 376244388 4152 False 487.000000 630 82.831500 7113 8564 2 chr1D.!!$F6 1451
4 TraesCS1D01G278900 chr1D 245086626 245088159 1533 True 370.000000 370 71.757000 3742 5259 1 chr1D.!!$R1 1517
5 TraesCS1D01G278900 chr1D 490487237 490488530 1293 False 340.000000 340 72.015000 3960 5241 1 chr1D.!!$F5 1281
6 TraesCS1D01G278900 chr1B 503463052 503472024 8972 False 4573.000000 5934 95.405667 1 8656 3 chr1B.!!$F7 8655
7 TraesCS1D01G278900 chr1B 502789956 502794097 4141 False 632.666667 898 82.265333 7113 8615 3 chr1B.!!$F5 1502
8 TraesCS1D01G278900 chr1B 502747075 502749387 2312 False 504.000000 614 82.472500 66 8654 2 chr1B.!!$F4 8588
9 TraesCS1D01G278900 chr1B 502803913 502805155 1242 False 502.000000 671 83.133500 7113 8278 2 chr1B.!!$F6 1165
10 TraesCS1D01G278900 chr1A 476971577 476981827 10250 False 1097.000000 1888 94.579000 1 8656 11 chr1A.!!$F4 8655
11 TraesCS1D01G278900 chr1A 475483544 475485452 1908 False 578.000000 950 84.436000 6924 8654 2 chr1A.!!$F2 1730
12 TraesCS1D01G278900 chr1A 475457053 475458952 1899 True 569.500000 939 84.584000 6934 8654 2 chr1A.!!$R1 1720
13 TraesCS1D01G278900 chr1A 475623225 475627190 3965 False 449.500000 560 82.141000 7495 8654 2 chr1A.!!$F3 1159
14 TraesCS1D01G278900 chr4D 502634220 502635120 900 False 1482.000000 1482 96.337000 8662 9562 1 chr4D.!!$F1 900
15 TraesCS1D01G278900 chr4D 125083052 125084611 1559 True 337.000000 337 71.258000 3699 5245 1 chr4D.!!$R1 1546
16 TraesCS1D01G278900 chr6D 446090774 446091684 910 True 1472.000000 1472 95.833000 8652 9562 1 chr6D.!!$R2 910
17 TraesCS1D01G278900 chr6D 450857833 450858742 909 True 1461.000000 1461 95.714000 8656 9562 1 chr6D.!!$R3 906
18 TraesCS1D01G278900 chr6D 469787215 469787909 694 False 1157.000000 1157 96.695000 8656 9351 1 chr6D.!!$F1 695
19 TraesCS1D01G278900 chr7D 58149000 58149914 914 True 1428.000000 1428 94.869000 8649 9562 1 chr7D.!!$R1 913
20 TraesCS1D01G278900 chr7D 540107762 540109712 1950 True 617.000000 617 72.806000 3684 5616 1 chr7D.!!$R2 1932
21 TraesCS1D01G278900 chr7A 248537913 248538823 910 False 1371.000000 1371 93.853000 8653 9562 1 chr7A.!!$F1 909
22 TraesCS1D01G278900 chr5D 26902212 26903124 912 True 1288.000000 1288 92.223000 8656 9562 1 chr5D.!!$R1 906
23 TraesCS1D01G278900 chr5D 43217676 43218571 895 False 924.000000 924 85.396000 8660 9550 1 chr5D.!!$F2 890
24 TraesCS1D01G278900 chr5D 31258615 31260152 1537 False 412.000000 412 72.051000 3717 5241 1 chr5D.!!$F1 1524
25 TraesCS1D01G278900 chr5D 303716477 303717074 597 True 278.000000 278 75.450000 3742 4343 1 chr5D.!!$R2 601
26 TraesCS1D01G278900 chr5D 49278483 49279308 825 False 259.000000 259 72.963000 3822 4650 1 chr5D.!!$F3 828
27 TraesCS1D01G278900 chrUn 232944927 232946940 2013 True 457.733333 1155 95.267333 1448 2491 3 chrUn.!!$R1 1043
28 TraesCS1D01G278900 chrUn 232956327 232957857 1530 True 457.733333 1155 95.267333 1448 2491 3 chrUn.!!$R2 1043
29 TraesCS1D01G278900 chr5B 565542303 565543060 757 False 804.000000 804 86.184000 8652 9394 1 chr5B.!!$F1 742
30 TraesCS1D01G278900 chr5B 563754583 563755450 867 True 601.100000 1118 94.349500 1448 2410 2 chr5B.!!$R5 962
31 TraesCS1D01G278900 chr5B 563718501 563720030 1529 True 447.066667 1123 95.033667 1448 2491 3 chr5B.!!$R2 1043
32 TraesCS1D01G278900 chr5B 563738437 563739965 1528 True 447.066667 1129 94.661333 1448 2491 3 chr5B.!!$R4 1043
33 TraesCS1D01G278900 chr6B 46791288 46792207 919 True 922.000000 922 85.049000 8656 9562 1 chr6B.!!$R1 906
34 TraesCS1D01G278900 chr6B 171983808 171984976 1168 True 207.000000 207 70.844000 4117 5266 1 chr6B.!!$R2 1149
35 TraesCS1D01G278900 chr4A 588601940 588603576 1636 False 377.000000 377 71.273000 3985 5600 1 chr4A.!!$F1 1615
36 TraesCS1D01G278900 chr2A 779593283 779595625 2342 False 368.000000 368 70.063000 3960 6280 1 chr2A.!!$F2 2320
37 TraesCS1D01G278900 chr2A 531918126 531918691 565 False 220.000000 220 73.768000 4760 5325 1 chr2A.!!$F1 565
38 TraesCS1D01G278900 chr2B 31410653 31412293 1640 True 333.000000 333 71.043000 3983 5600 1 chr2B.!!$R1 1617

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
651 664 0.321653 AGATCGCGTTTCAGGCCTTT 60.322 50.000 0.00 0.0 0.00 3.11 F
1042 1067 1.079127 GGCATGCTGTACCACGAGT 60.079 57.895 18.92 0.0 0.00 4.18 F
1841 2297 1.679153 TGCATGCAGTATGATTGCTGG 59.321 47.619 18.46 0.0 43.26 4.85 F
3334 4879 0.242825 CCTGCCTTAGTTCGACGACA 59.757 55.000 0.00 0.0 0.00 4.35 F
3476 5021 0.923358 ATGGTTTCGGCCTCCCAATA 59.077 50.000 0.00 0.0 0.00 1.90 F
5308 7151 2.989840 GTTCATCTCTTCTGTGACCACG 59.010 50.000 0.00 0.0 0.00 4.94 F
5779 7625 0.250467 GTCCATGGTCGGCTGCATAT 60.250 55.000 12.58 0.0 0.00 1.78 F
5800 7646 1.176619 ATGCATCCATGACCATGCCG 61.177 55.000 16.85 0.0 44.15 5.69 F
7981 16922 0.035630 ACTGCCTTCATCTGCCACTC 60.036 55.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2675 1.473965 GCTAGCTGCTGCCACTGATTA 60.474 52.381 13.43 0.00 40.80 1.75 R
2760 4305 1.072173 TGAGCTTCTTAGTTGCCAGCA 59.928 47.619 0.00 0.00 32.58 4.41 R
3463 5008 0.467290 GGCAAATATTGGGAGGCCGA 60.467 55.000 0.00 0.00 0.00 5.54 R
5308 7151 1.009222 GCTGCAGCATATTGACGGC 60.009 57.895 33.36 1.56 41.59 5.68 R
5779 7625 1.324383 GCATGGTCATGGATGCATGA 58.676 50.000 24.29 24.29 43.75 3.07 R
6170 9784 0.462581 ATCTACCATGGCTGTGTGCG 60.463 55.000 13.04 0.00 44.05 5.34 R
6726 10738 1.648504 GCCACCATTCGTAGTGTACC 58.351 55.000 0.00 0.00 31.88 3.34 R
8084 17039 2.356125 CCCCCTCATGTTGTCAAGGTAG 60.356 54.545 0.00 0.00 0.00 3.18 R
9324 18329 0.234884 GGACGCTGACAAACCTTTCG 59.765 55.000 0.00 0.00 0.00 3.46 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
54 55 1.064979 ACAACTTTGGACGTGGAAGGT 60.065 47.619 0.00 0.00 37.85 3.50
152 153 3.535561 ACTCAATGCCCTGTCTAATTCG 58.464 45.455 0.00 0.00 0.00 3.34
162 163 4.344102 CCCTGTCTAATTCGGATCCTAACA 59.656 45.833 10.75 0.00 0.00 2.41
269 274 9.650539 TTCATAACCAAAATGAAATACATGGTG 57.349 29.630 0.00 0.00 39.70 4.17
287 292 4.130857 TGGTGTAGAAGTTGCATTCGAAA 58.869 39.130 0.00 0.00 34.27 3.46
320 325 7.010460 GTGTTCTATTGGCTTGCAAATATTTCC 59.990 37.037 0.00 0.00 0.00 3.13
321 326 6.160576 TCTATTGGCTTGCAAATATTTCCC 57.839 37.500 0.00 0.00 0.00 3.97
325 330 2.235898 GGCTTGCAAATATTTCCCCACA 59.764 45.455 0.00 0.00 0.00 4.17
336 341 9.359653 CAAATATTTCCCCACATCTCTAAGATT 57.640 33.333 0.00 0.00 31.32 2.40
367 372 3.316029 TGAATATTTCTCGCCCAATGCAG 59.684 43.478 0.00 0.00 41.33 4.41
402 414 1.647346 TTACGCCAATCATCCGACAC 58.353 50.000 0.00 0.00 0.00 3.67
528 540 9.238368 TCTTTTAGGTGAAGAAGAAAGAAACAA 57.762 29.630 0.00 0.00 32.15 2.83
544 556 1.303236 CAAATGGGGTCGCCACTGA 60.303 57.895 11.42 0.00 0.00 3.41
651 664 0.321653 AGATCGCGTTTCAGGCCTTT 60.322 50.000 0.00 0.00 0.00 3.11
729 748 1.527380 GGAACAAGGTGTGGCGGAA 60.527 57.895 0.00 0.00 0.00 4.30
965 990 1.224592 CTGTCAAATCGGGGAGGGG 59.775 63.158 0.00 0.00 0.00 4.79
991 1016 2.171840 CGGAGTTCTTCTGAAGGAGGA 58.828 52.381 16.83 0.00 33.75 3.71
1042 1067 1.079127 GGCATGCTGTACCACGAGT 60.079 57.895 18.92 0.00 0.00 4.18
1661 2117 7.928908 TTGAGCATTTCATCAAACAAAGTAC 57.071 32.000 0.00 0.00 35.27 2.73
1662 2118 7.275888 TGAGCATTTCATCAAACAAAGTACT 57.724 32.000 0.00 0.00 0.00 2.73
1664 2120 6.681777 AGCATTTCATCAAACAAAGTACTCC 58.318 36.000 0.00 0.00 0.00 3.85
1776 2232 7.118496 TGGAGTTTTCTTCTTGCCAATAAAA 57.882 32.000 0.00 0.00 0.00 1.52
1841 2297 1.679153 TGCATGCAGTATGATTGCTGG 59.321 47.619 18.46 0.00 43.26 4.85
1959 2418 8.250332 GGTTTTCATTTAATAGTTGGCAGATGA 58.750 33.333 0.00 0.00 0.00 2.92
2088 2549 6.418101 AGTAGCAATCAGTGGTAATGTCATT 58.582 36.000 3.06 3.06 41.75 2.57
2098 2559 7.014134 TCAGTGGTAATGTCATTGACAAACATT 59.986 33.333 22.44 17.85 45.96 2.71
2114 2588 9.605275 TGACAAACATTTAAATTTCATCAACCA 57.395 25.926 0.00 0.00 0.00 3.67
2251 2725 4.390556 AGCCGAGCAGGGGAGAGT 62.391 66.667 0.34 0.00 41.48 3.24
2563 4106 3.456277 CCCTCTCTAGCTAACAAATGGGT 59.544 47.826 0.00 0.00 0.00 4.51
2695 4240 2.920647 GCTCGTTTAACATTGCCACCAC 60.921 50.000 0.00 0.00 0.00 4.16
2696 4241 2.292016 CTCGTTTAACATTGCCACCACA 59.708 45.455 0.00 0.00 0.00 4.17
2829 4374 1.926426 GAAGTAGCAGGCACCCCCAT 61.926 60.000 0.00 0.00 35.39 4.00
3002 4547 1.026718 CCTTCACCGACTGCCATTCC 61.027 60.000 0.00 0.00 0.00 3.01
3020 4565 1.486310 TCCTGCATGTAGTGGATCACC 59.514 52.381 10.09 0.00 34.49 4.02
3021 4566 1.575244 CTGCATGTAGTGGATCACCG 58.425 55.000 2.12 0.00 39.42 4.94
3022 4567 1.136891 CTGCATGTAGTGGATCACCGA 59.863 52.381 2.12 0.00 39.42 4.69
3044 4589 4.670606 GCAATAACCTGCGCTTCG 57.329 55.556 9.73 0.00 31.50 3.79
3080 4625 4.706476 CCCTTCTATGTTTCATTCCTTGCA 59.294 41.667 0.00 0.00 0.00 4.08
3124 4669 0.246635 ACCATCGTTGCTCTAGCGTT 59.753 50.000 0.00 0.00 45.83 4.84
3174 4719 1.001158 GCCACGTAGATAGAGCACTCC 60.001 57.143 0.00 0.00 0.00 3.85
3324 4869 2.887152 ACACAAAAAGCTCCTGCCTTAG 59.113 45.455 0.00 0.00 40.80 2.18
3334 4879 0.242825 CCTGCCTTAGTTCGACGACA 59.757 55.000 0.00 0.00 0.00 4.35
3361 4906 3.322466 AGCACCAACCGCTAGCCT 61.322 61.111 9.66 0.00 38.15 4.58
3409 4954 9.869757 ATGGATTTTAGCTTTATTTGGTGTAAC 57.130 29.630 0.00 0.00 0.00 2.50
3439 4984 4.118584 GCCCAGCCATCCTTTGTT 57.881 55.556 0.00 0.00 0.00 2.83
3463 5008 2.930826 AAGACTGTGGACGATGGTTT 57.069 45.000 0.00 0.00 0.00 3.27
3476 5021 0.923358 ATGGTTTCGGCCTCCCAATA 59.077 50.000 0.00 0.00 0.00 1.90
4455 6272 4.308458 TGACCCAACGCCACCTCG 62.308 66.667 0.00 0.00 0.00 4.63
4715 6554 6.152154 CCCATTAAGATTTACCGAAAACCTGT 59.848 38.462 0.00 0.00 0.00 4.00
5060 6901 3.799432 ACTGAGATAGTAGCTCCGGAT 57.201 47.619 12.74 0.00 38.04 4.18
5308 7151 2.989840 GTTCATCTCTTCTGTGACCACG 59.010 50.000 0.00 0.00 0.00 4.94
5779 7625 0.250467 GTCCATGGTCGGCTGCATAT 60.250 55.000 12.58 0.00 0.00 1.78
5800 7646 1.176619 ATGCATCCATGACCATGCCG 61.177 55.000 16.85 0.00 44.15 5.69
5953 7800 4.408921 TGATCAACAATAGTCTCCGGGAAT 59.591 41.667 0.00 0.00 0.00 3.01
6109 9721 1.988107 TCCCTGAAAGCTTCCATCTGT 59.012 47.619 0.00 0.00 0.00 3.41
6126 9740 5.394663 CCATCTGTGTAACTTCTCGGATTCT 60.395 44.000 0.00 0.00 38.04 2.40
6216 9830 4.365514 TGGGCTCTAAGAAATCACAACA 57.634 40.909 0.00 0.00 0.00 3.33
6405 10020 1.795170 AACTCACCGCAACACCATGC 61.795 55.000 0.00 0.00 42.94 4.06
6419 10034 1.593265 CATGCCTGAAACCCAAGCC 59.407 57.895 0.00 0.00 31.22 4.35
6551 10562 5.016831 AGATGGCTTTTCTAATTTTCCCGT 58.983 37.500 0.00 0.00 0.00 5.28
6705 10717 9.336171 AGAAGCTTATAAGATGGCTTTTCTAAG 57.664 33.333 16.85 0.00 43.74 2.18
6748 10762 2.125269 ACTACGAATGGTGGCGGC 60.125 61.111 0.00 0.00 0.00 6.53
6753 10767 2.746277 GAATGGTGGCGGCGTTCT 60.746 61.111 9.37 0.00 0.00 3.01
6803 10817 6.097554 ACTCATGTGTTGGTTAATTTTGTCCA 59.902 34.615 0.00 0.00 0.00 4.02
7654 11865 5.844301 AGAAATTTGCCAAGTTTATTGCG 57.156 34.783 0.00 0.00 0.00 4.85
7981 16922 0.035630 ACTGCCTTCATCTGCCACTC 60.036 55.000 0.00 0.00 0.00 3.51
8084 17039 4.331968 TCTCTCAGTTTCTCCTCTCAGAC 58.668 47.826 0.00 0.00 0.00 3.51
8213 17171 2.103094 TGAGGAAGCCAGGATCATTACG 59.897 50.000 0.00 0.00 0.00 3.18
8230 17188 0.884704 ACGCATTCACGCTTCAAGGT 60.885 50.000 0.00 0.00 36.19 3.50
8363 17321 3.097614 AGTACCTCGTCAGCAACCTTAT 58.902 45.455 0.00 0.00 0.00 1.73
8389 17364 1.154197 CAGGGCATGACTATGATGCG 58.846 55.000 0.00 0.00 46.05 4.73
8399 17374 2.487762 GACTATGATGCGAGAGGAGAGG 59.512 54.545 0.00 0.00 32.19 3.69
8508 17487 1.522668 TTTGATCAGCAAGGACACCG 58.477 50.000 0.00 0.00 37.87 4.94
8578 17564 6.257994 AGATTAGGATGCCATCTTTCTTCA 57.742 37.500 4.41 0.00 0.00 3.02
8580 17566 7.982252 AGATTAGGATGCCATCTTTCTTCATA 58.018 34.615 4.41 0.00 0.00 2.15
8595 17581 8.300286 TCTTTCTTCATAATCTACATAGGAGCG 58.700 37.037 0.00 0.00 0.00 5.03
8785 17788 5.533528 GGGAATAAAATTACATGTAGCGGGT 59.466 40.000 5.56 0.00 0.00 5.28
8977 17980 4.878397 CGCTTCCAGATATTCCAAAGAACT 59.122 41.667 0.00 0.00 33.97 3.01
9235 18240 0.452585 GCCAGAGGTAGAGTCGACAC 59.547 60.000 19.50 12.15 0.00 3.67
9291 18296 1.971167 GCGTGTCCATGGGCTTTGA 60.971 57.895 19.09 0.00 0.00 2.69
9298 18303 0.682209 CCATGGGCTTTGACCTCCAG 60.682 60.000 2.85 0.00 32.30 3.86
9324 18329 1.227292 GGTAGGCGAGCTTAGTGGC 60.227 63.158 0.00 0.00 0.00 5.01
9334 18339 1.880027 AGCTTAGTGGCGAAAGGTTTG 59.120 47.619 0.00 0.00 37.29 2.93
9356 18361 0.526662 AGCGTCCCTTGTAGTTCTCG 59.473 55.000 0.00 0.00 0.00 4.04
9403 18408 1.569493 CGTGGCCAATATAGTGCGC 59.431 57.895 7.24 0.00 0.00 6.09
9493 18498 2.509336 ATAGCGCGTGCCACTGAC 60.509 61.111 19.02 0.00 44.31 3.51
9494 18499 3.295304 ATAGCGCGTGCCACTGACA 62.295 57.895 19.02 0.00 44.31 3.58
9553 18558 1.916273 TCGGGCTAGGGTTTGAGCA 60.916 57.895 0.00 0.00 40.64 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.363680 CTGCTTAGATCCGACAGTCCAT 59.636 50.000 0.00 0.00 0.00 3.41
54 55 7.335924 GCAGACATTTTAGGGTTAGTCAATACA 59.664 37.037 0.00 0.00 0.00 2.29
152 153 5.163301 TGAAGCCTAAGTCATGTTAGGATCC 60.163 44.000 20.88 2.48 46.00 3.36
235 240 7.881643 TTCATTTTGGTTATGAATTCGTTGG 57.118 32.000 5.29 0.00 37.15 3.77
269 274 5.854157 TCGAATTTCGAATGCAACTTCTAC 58.146 37.500 18.56 0.00 46.90 2.59
287 292 3.247006 AGCCAATAGAACACGTCGAAT 57.753 42.857 0.00 0.00 0.00 3.34
320 325 7.814264 AAGCATTTAATCTTAGAGATGTGGG 57.186 36.000 0.00 0.00 34.65 4.61
321 326 8.896744 TCAAAGCATTTAATCTTAGAGATGTGG 58.103 33.333 0.00 0.00 35.03 4.17
336 341 6.096141 TGGGCGAGAAATATTCAAAGCATTTA 59.904 34.615 0.00 0.00 35.03 1.40
367 372 1.588404 CGTAATGACTCGATGGTGTGC 59.412 52.381 0.00 0.00 0.00 4.57
402 414 1.135083 AGGTCGAATCGTGCAGTAAGG 60.135 52.381 1.52 0.00 0.00 2.69
501 513 9.238368 TGTTTCTTTCTTCTTCACCTAAAAGAA 57.762 29.630 4.47 4.47 39.59 2.52
502 514 8.801882 TGTTTCTTTCTTCTTCACCTAAAAGA 57.198 30.769 0.00 0.00 32.54 2.52
505 517 9.801873 CATTTGTTTCTTTCTTCTTCACCTAAA 57.198 29.630 0.00 0.00 0.00 1.85
506 518 8.413229 CCATTTGTTTCTTTCTTCTTCACCTAA 58.587 33.333 0.00 0.00 0.00 2.69
507 519 7.014230 CCCATTTGTTTCTTTCTTCTTCACCTA 59.986 37.037 0.00 0.00 0.00 3.08
509 521 5.985530 CCCATTTGTTTCTTTCTTCTTCACC 59.014 40.000 0.00 0.00 0.00 4.02
510 522 5.985530 CCCCATTTGTTTCTTTCTTCTTCAC 59.014 40.000 0.00 0.00 0.00 3.18
512 524 6.161855 ACCCCATTTGTTTCTTTCTTCTTC 57.838 37.500 0.00 0.00 0.00 2.87
513 525 5.221244 CGACCCCATTTGTTTCTTTCTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
514 526 4.278419 CGACCCCATTTGTTTCTTTCTTCT 59.722 41.667 0.00 0.00 0.00 2.85
515 527 4.546570 CGACCCCATTTGTTTCTTTCTTC 58.453 43.478 0.00 0.00 0.00 2.87
518 530 2.609491 GGCGACCCCATTTGTTTCTTTC 60.609 50.000 0.00 0.00 0.00 2.62
544 556 2.558554 CTAGCCGGCGTTGCTACTGT 62.559 60.000 23.20 0.95 40.23 3.55
809 830 3.839432 CGGGAAGGAGGGAGCGAC 61.839 72.222 0.00 0.00 0.00 5.19
965 990 4.083862 AGAAGAACTCCGGCGGCC 62.084 66.667 23.83 9.54 0.00 6.13
1275 1300 2.813754 CGAGCCAGAGAGATAGAGAAGG 59.186 54.545 0.00 0.00 0.00 3.46
1277 1302 2.158682 AGCGAGCCAGAGAGATAGAGAA 60.159 50.000 0.00 0.00 0.00 2.87
1638 2094 7.275888 AGTACTTTGTTTGATGAAATGCTCA 57.724 32.000 0.00 0.00 38.81 4.26
1660 2116 4.878397 GCATTAGCAACTGATTACTGGAGT 59.122 41.667 0.00 0.00 41.58 3.85
1661 2117 5.415415 GCATTAGCAACTGATTACTGGAG 57.585 43.478 0.00 0.00 41.58 3.86
1776 2232 9.018582 TCAAAATCAAACAAACCCAAGAATTTT 57.981 25.926 0.00 0.00 0.00 1.82
1779 2235 7.563906 TCTCAAAATCAAACAAACCCAAGAAT 58.436 30.769 0.00 0.00 0.00 2.40
1795 2251 8.025445 AGCTGTGTATTGTTCAATCTCAAAATC 58.975 33.333 1.11 0.00 0.00 2.17
1959 2418 5.009631 TGTCGATGGTTCATGAATCCTTTT 58.990 37.500 16.06 6.79 0.00 2.27
2088 2549 9.605275 TGGTTGATGAAATTTAAATGTTTGTCA 57.395 25.926 0.39 2.05 0.00 3.58
2201 2675 1.473965 GCTAGCTGCTGCCACTGATTA 60.474 52.381 13.43 0.00 40.80 1.75
2251 2725 2.739943 CAGGATCCAGACTCCAGTACA 58.260 52.381 15.82 0.00 35.08 2.90
2695 4240 6.488344 TCATATGGAGCTAGACTGTAAGACTG 59.512 42.308 2.13 0.00 39.80 3.51
2696 4241 6.606069 TCATATGGAGCTAGACTGTAAGACT 58.394 40.000 2.13 0.00 42.73 3.24
2760 4305 1.072173 TGAGCTTCTTAGTTGCCAGCA 59.928 47.619 0.00 0.00 32.58 4.41
2829 4374 4.438255 CCACCATGGTGCATTCCA 57.562 55.556 35.34 0.00 44.16 3.53
3002 4547 1.136891 TCGGTGATCCACTACATGCAG 59.863 52.381 0.00 0.00 34.40 4.41
3020 4565 2.287915 AGCGCAGGTTATTGCTAAATCG 59.712 45.455 11.47 0.00 41.90 3.34
3021 4566 3.971032 AGCGCAGGTTATTGCTAAATC 57.029 42.857 11.47 0.00 41.90 2.17
3044 4589 7.929941 AACATAGAAGGGAAAGAGAATTGAC 57.070 36.000 0.00 0.00 0.00 3.18
3080 4625 1.065854 GGAGTCTATGTGCTGTGGCTT 60.066 52.381 0.00 0.00 39.59 4.35
3124 4669 0.944311 GTTCGCAGAAGCTTCGGACA 60.944 55.000 27.75 11.59 45.90 4.02
3174 4719 1.512156 CCGGACTGTTTTGGTTCCCG 61.512 60.000 0.00 0.00 35.68 5.14
3324 4869 3.181543 GCTGAACTACATTGTCGTCGAAC 60.182 47.826 0.00 0.00 0.00 3.95
3334 4879 2.151202 CGGTTGGTGCTGAACTACATT 58.849 47.619 0.00 0.00 0.00 2.71
3409 4954 4.659172 TGGGCCTTTGGGACTGCG 62.659 66.667 4.53 0.00 41.42 5.18
3439 4984 2.353704 CCATCGTCCACAGTCTTTAGCA 60.354 50.000 0.00 0.00 0.00 3.49
3463 5008 0.467290 GGCAAATATTGGGAGGCCGA 60.467 55.000 0.00 0.00 0.00 5.54
3797 5342 2.499693 TCGTTGAAGGACTCATATGGCA 59.500 45.455 2.13 0.00 32.78 4.92
4455 6272 5.496133 TGCGAACTATTCTACAGGACTAC 57.504 43.478 0.00 0.00 0.00 2.73
4715 6554 2.238942 ATGTGTTGCGTCACTTCAGA 57.761 45.000 11.32 0.00 38.90 3.27
5060 6901 8.877864 ATTGTCATGATCCCAAAAGTTAACTA 57.122 30.769 8.92 0.00 0.00 2.24
5308 7151 1.009222 GCTGCAGCATATTGACGGC 60.009 57.895 33.36 1.56 41.59 5.68
5779 7625 1.324383 GCATGGTCATGGATGCATGA 58.676 50.000 24.29 24.29 43.75 3.07
5800 7646 5.368145 TGGACTAGGCATGAATTGTATGAC 58.632 41.667 0.00 1.13 33.65 3.06
5842 7688 0.181114 GCAGTAGGATGCACATGGGA 59.819 55.000 0.00 0.00 45.77 4.37
5987 9599 4.192317 GAGAACATACAAGTTAGGCTGGG 58.808 47.826 0.00 0.00 0.00 4.45
6109 9721 4.087182 AGGTGAGAATCCGAGAAGTTACA 58.913 43.478 0.00 0.00 0.00 2.41
6126 9740 3.360867 TCCAAGCAGAACAAAAAGGTGA 58.639 40.909 0.00 0.00 0.00 4.02
6170 9784 0.462581 ATCTACCATGGCTGTGTGCG 60.463 55.000 13.04 0.00 44.05 5.34
6216 9830 2.372172 AGAGGATGAAAACTTGGGACGT 59.628 45.455 0.00 0.00 0.00 4.34
6331 9946 1.274728 GAGAGACAGTGTGCAGGTGAT 59.725 52.381 0.00 0.00 0.00 3.06
6405 10020 1.908299 GTGGGGCTTGGGTTTCAGG 60.908 63.158 0.00 0.00 0.00 3.86
6483 10098 5.084519 ACAGACCTGATACAGTCCTACAAA 58.915 41.667 3.76 0.00 0.00 2.83
6710 10722 9.502145 CGTAGTGTACCATTCGTTAAATACTAA 57.498 33.333 0.00 0.00 0.00 2.24
6711 10723 8.888716 TCGTAGTGTACCATTCGTTAAATACTA 58.111 33.333 0.00 0.00 0.00 1.82
6712 10724 7.761409 TCGTAGTGTACCATTCGTTAAATACT 58.239 34.615 0.00 0.00 0.00 2.12
6713 10725 7.969387 TCGTAGTGTACCATTCGTTAAATAC 57.031 36.000 0.00 0.00 0.00 1.89
6715 10727 7.010738 CCATTCGTAGTGTACCATTCGTTAAAT 59.989 37.037 0.00 0.00 0.00 1.40
6717 10729 5.806502 CCATTCGTAGTGTACCATTCGTTAA 59.193 40.000 0.00 0.00 0.00 2.01
6718 10730 5.105797 ACCATTCGTAGTGTACCATTCGTTA 60.106 40.000 0.00 0.00 0.00 3.18
6719 10731 4.178540 CCATTCGTAGTGTACCATTCGTT 58.821 43.478 0.00 0.00 0.00 3.85
6720 10732 3.194116 ACCATTCGTAGTGTACCATTCGT 59.806 43.478 0.00 0.00 0.00 3.85
6721 10733 3.550275 CACCATTCGTAGTGTACCATTCG 59.450 47.826 0.00 0.00 0.00 3.34
6722 10734 3.869246 CCACCATTCGTAGTGTACCATTC 59.131 47.826 0.00 0.00 31.88 2.67
6726 10738 1.648504 GCCACCATTCGTAGTGTACC 58.351 55.000 0.00 0.00 31.88 3.34
6863 10877 7.178451 CAGAACCCCATTAACAATTACTTCCTT 59.822 37.037 0.00 0.00 0.00 3.36
6864 10878 6.663523 CAGAACCCCATTAACAATTACTTCCT 59.336 38.462 0.00 0.00 0.00 3.36
6915 10931 5.923204 AGAACTACTTCATGATGGTCCATC 58.077 41.667 23.06 23.06 40.88 3.51
7147 11258 9.959749 TCAAAAGCGAAAACTAAAGTATGAAAT 57.040 25.926 0.00 0.00 0.00 2.17
7628 11839 7.111870 CGCAATAAACTTGGCAAATTTCTTTTG 59.888 33.333 10.22 13.06 46.22 2.44
7654 11865 6.144078 ACACACAAACCAAAAGGAAGATAC 57.856 37.500 0.00 0.00 0.00 2.24
8084 17039 2.356125 CCCCCTCATGTTGTCAAGGTAG 60.356 54.545 0.00 0.00 0.00 3.18
8213 17171 0.730494 GCACCTTGAAGCGTGAATGC 60.730 55.000 15.01 2.28 31.36 3.56
8230 17188 1.174712 GCTCCCTTGTTTCTGCTGCA 61.175 55.000 0.88 0.88 0.00 4.41
8363 17321 3.008923 TCATAGTCATGCCCTGTTGTTCA 59.991 43.478 0.00 0.00 31.73 3.18
8389 17364 1.604604 CTCGTCATCCCTCTCCTCTC 58.395 60.000 0.00 0.00 0.00 3.20
8399 17374 1.880340 CGCCTTCAGCTCGTCATCC 60.880 63.158 0.00 0.00 40.39 3.51
8508 17487 2.440980 GCCAGGTTCCTCCATGGC 60.441 66.667 6.96 0.78 45.60 4.40
8578 17564 9.694137 GTTTAAGAACGCTCCTATGTAGATTAT 57.306 33.333 0.00 0.00 0.00 1.28
8785 17788 0.329931 TTGCCGGGAGAATTTAGCCA 59.670 50.000 2.18 0.00 0.00 4.75
8863 17866 2.173143 TCTTAAACTTTGGTCCCACCGT 59.827 45.455 0.00 0.00 42.58 4.83
8903 17906 0.670546 CTTGGGCTTCATGACGTCGT 60.671 55.000 11.62 7.97 0.00 4.34
8905 17908 1.667724 CATCTTGGGCTTCATGACGTC 59.332 52.381 9.11 9.11 33.23 4.34
8908 17911 1.466856 TGCATCTTGGGCTTCATGAC 58.533 50.000 0.00 0.00 33.23 3.06
9235 18240 1.937899 CGGAACTACGCCCCAAATAAG 59.062 52.381 0.00 0.00 0.00 1.73
9291 18296 1.229082 TACCAAGCGGTCTGGAGGT 60.229 57.895 18.46 10.53 44.71 3.85
9324 18329 0.234884 GGACGCTGACAAACCTTTCG 59.765 55.000 0.00 0.00 0.00 3.46
9334 18339 1.272769 AGAACTACAAGGGACGCTGAC 59.727 52.381 0.00 0.00 0.00 3.51
9356 18361 3.855689 AAATATGCAGGTTGCTGACAC 57.144 42.857 2.48 0.00 45.31 3.67
9403 18408 2.591148 CGAATGCGAACTGCTTGAATTG 59.409 45.455 0.00 0.00 46.63 2.32


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

AutoCloner maintained by Alex Coulton.