Multiple sequence alignment - TraesCS5A01G417600

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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 TraesCS5A01G417600 chr5A 100.000 5169 0 0 1 5169 606054020 606048852 0.000000e+00 9546.0
1 TraesCS5A01G417600 chr5A 100.000 1131 0 0 1304 2434 534361815 534362945 0.000000e+00 2089.0
2 TraesCS5A01G417600 chr5A 85.083 724 76 15 18 726 606154113 606153407 0.000000e+00 710.0
3 TraesCS5A01G417600 chr5A 82.983 476 50 16 4622 5072 588413830 588413361 8.060000e-108 401.0
4 TraesCS5A01G417600 chr5A 85.752 379 42 7 2457 2826 605803983 605803608 1.750000e-104 390.0
5 TraesCS5A01G417600 chr5A 84.279 229 27 6 2457 2679 573303163 573303388 1.130000e-51 215.0
6 TraesCS5A01G417600 chr5A 90.361 83 8 0 3950 4032 533281481 533281563 5.470000e-20 110.0
7 TraesCS5A01G417600 chr5A 87.912 91 9 2 1288 1376 17143438 17143528 7.080000e-19 106.0
8 TraesCS5A01G417600 chr5B 92.311 2198 106 39 2435 4573 595624087 595621894 0.000000e+00 3064.0
9 TraesCS5A01G417600 chr5B 86.307 723 68 16 18 726 595653387 595652682 0.000000e+00 758.0
10 TraesCS5A01G417600 chr5B 93.763 481 24 3 280 754 595625149 595624669 0.000000e+00 717.0
11 TraesCS5A01G417600 chr5B 87.825 616 58 10 1303 1913 324964393 324963790 0.000000e+00 706.0
12 TraesCS5A01G417600 chr5B 86.861 548 29 18 739 1280 595624649 595624139 1.610000e-159 573.0
13 TraesCS5A01G417600 chr5B 82.939 592 54 21 4619 5169 374446429 374447014 1.670000e-134 490.0
14 TraesCS5A01G417600 chr5B 86.885 366 39 5 2457 2820 595377714 595377356 8.060000e-108 401.0
15 TraesCS5A01G417600 chr5B 85.600 375 41 8 2454 2826 595469867 595469504 1.050000e-101 381.0
16 TraesCS5A01G417600 chr5B 83.594 384 50 12 2450 2826 595620839 595620462 1.070000e-91 348.0
17 TraesCS5A01G417600 chr5B 83.042 401 29 13 2009 2391 324963756 324963377 1.390000e-85 327.0
18 TraesCS5A01G417600 chr5B 87.983 233 25 3 2596 2826 595377224 595376993 6.600000e-69 272.0
19 TraesCS5A01G417600 chr5B 91.765 85 7 0 3950 4034 505770672 505770756 9.090000e-23 119.0
20 TraesCS5A01G417600 chr5B 96.429 56 2 0 1 56 595625199 595625144 5.510000e-15 93.5
21 TraesCS5A01G417600 chr5D 89.448 2246 145 53 2435 4607 484415107 484412881 0.000000e+00 2750.0
22 TraesCS5A01G417600 chr5D 92.857 1302 71 8 1 1280 484416451 484415150 0.000000e+00 1869.0
23 TraesCS5A01G417600 chr5D 83.333 684 81 18 1785 2438 82951933 82952613 7.410000e-168 601.0
24 TraesCS5A01G417600 chr5D 83.646 587 58 19 4620 5169 563730869 563730284 7.670000e-143 518.0
25 TraesCS5A01G417600 chr5D 88.710 372 40 2 2457 2826 484308155 484307784 2.190000e-123 453.0
26 TraesCS5A01G417600 chr5D 91.398 279 18 2 454 726 484567570 484567292 1.360000e-100 377.0
27 TraesCS5A01G417600 chr5D 86.364 330 45 0 18 347 484568310 484567981 1.370000e-95 361.0
28 TraesCS5A01G417600 chr5D 83.770 382 53 8 2450 2826 484411758 484411381 2.290000e-93 353.0
29 TraesCS5A01G417600 chr5D 90.171 234 22 1 2594 2826 484307659 484307426 2.340000e-78 303.0
30 TraesCS5A01G417600 chr5D 84.375 224 30 3 2457 2679 454119835 454120054 1.130000e-51 215.0
31 TraesCS5A01G417600 chr5D 77.778 234 34 12 3950 4168 418430495 418430725 1.510000e-25 128.0
32 TraesCS5A01G417600 chr2B 99.912 1132 1 0 1303 2434 755626381 755625250 0.000000e+00 2085.0
33 TraesCS5A01G417600 chr2B 87.199 1164 94 21 1302 2434 718963893 718962754 0.000000e+00 1273.0
34 TraesCS5A01G417600 chr2B 87.067 549 60 11 3299 3844 250070711 250070171 1.230000e-170 610.0
35 TraesCS5A01G417600 chr2B 82.403 591 60 17 4620 5169 468657633 468657046 4.680000e-130 475.0
36 TraesCS5A01G417600 chr2B 80.732 519 66 21 3840 4332 250070139 250069629 1.760000e-99 374.0
37 TraesCS5A01G417600 chr2B 81.050 438 57 15 4622 5039 787136548 787136117 4.990000e-85 326.0
38 TraesCS5A01G417600 chr6D 94.526 1151 42 9 1303 2434 90876351 90875203 0.000000e+00 1757.0
39 TraesCS5A01G417600 chr6D 91.616 1157 69 16 1304 2434 152188782 152189936 0.000000e+00 1574.0
40 TraesCS5A01G417600 chr6D 83.673 588 52 17 4622 5169 394561089 394561672 9.930000e-142 514.0
41 TraesCS5A01G417600 chr6D 81.839 435 49 16 1848 2256 452312446 452312016 6.410000e-89 339.0
42 TraesCS5A01G417600 chr6D 94.286 35 2 0 44 78 36124455 36124489 3.000000e-03 54.7
43 TraesCS5A01G417600 chr6A 95.573 655 17 4 1303 1955 612997115 612997759 0.000000e+00 1038.0
44 TraesCS5A01G417600 chr6A 95.573 655 16 5 1303 1955 613042331 613042974 0.000000e+00 1037.0
45 TraesCS5A01G417600 chr2D 88.175 778 72 11 1296 2061 32177229 32177998 0.000000e+00 909.0
46 TraesCS5A01G417600 chr2D 87.091 550 62 8 3299 3844 194192176 194191632 9.510000e-172 614.0
47 TraesCS5A01G417600 chr2D 83.249 591 51 19 4621 5169 316326766 316327350 2.780000e-137 499.0
48 TraesCS5A01G417600 chr2D 87.027 370 25 7 2084 2434 32178329 32178694 3.750000e-106 396.0
49 TraesCS5A01G417600 chr2D 80.688 523 63 24 3840 4332 194191600 194191086 6.320000e-99 372.0
50 TraesCS5A01G417600 chr2D 85.437 206 28 2 2230 2434 95179686 95179482 4.050000e-51 213.0
51 TraesCS5A01G417600 chr4D 86.735 588 36 13 4622 5169 111559403 111559988 2.640000e-172 616.0
52 TraesCS5A01G417600 chr4D 80.275 218 27 13 2455 2668 226256400 226256195 3.220000e-32 150.0
53 TraesCS5A01G417600 chr7D 84.890 589 44 15 4622 5169 607220935 607220351 2.100000e-153 553.0
54 TraesCS5A01G417600 chr7D 83.333 588 53 18 4622 5169 59383155 59382573 7.730000e-138 501.0
55 TraesCS5A01G417600 chr7D 83.051 295 30 9 1788 2063 195306243 195305950 3.090000e-62 250.0
56 TraesCS5A01G417600 chr7D 78.017 232 36 11 3950 4168 564534699 564534928 1.170000e-26 132.0
57 TraesCS5A01G417600 chr7D 90.110 91 7 2 2455 2543 575582517 575582427 3.270000e-22 117.0
58 TraesCS5A01G417600 chr3D 83.784 592 44 24 4622 5169 519671547 519670964 9.930000e-142 514.0
59 TraesCS5A01G417600 chr3D 83.249 591 54 18 4620 5169 574731621 574732207 7.730000e-138 501.0
60 TraesCS5A01G417600 chr3D 83.636 110 16 2 1288 1397 11415621 11415728 9.160000e-18 102.0
61 TraesCS5A01G417600 chr4A 83.275 574 67 13 4622 5169 104698143 104697573 7.730000e-138 501.0
62 TraesCS5A01G417600 chr7B 82.823 588 59 13 4622 5169 111898950 111898365 6.020000e-134 488.0
63 TraesCS5A01G417600 chr7B 80.803 573 68 22 4622 5169 380731472 380732027 1.340000e-110 411.0
64 TraesCS5A01G417600 chr7B 77.922 231 37 10 3950 4168 614294188 614293960 1.170000e-26 132.0
65 TraesCS5A01G417600 chr3B 82.770 592 56 19 4619 5169 41618192 41618778 2.160000e-133 486.0
66 TraesCS5A01G417600 chr3B 84.138 435 49 11 4619 5039 661752558 661752130 2.240000e-108 403.0
67 TraesCS5A01G417600 chr3B 77.344 256 48 8 1704 1954 29495714 29495464 5.400000e-30 143.0
68 TraesCS5A01G417600 chr1D 82.069 580 66 23 4622 5169 184475900 184476473 1.310000e-125 460.0
69 TraesCS5A01G417600 chr1D 89.091 165 15 3 4636 4798 450578468 450578305 8.780000e-48 202.0
70 TraesCS5A01G417600 chr1D 76.050 238 49 7 1703 1936 163132922 163133155 3.270000e-22 117.0
71 TraesCS5A01G417600 chr2A 84.096 459 56 9 3299 3756 208151335 208150893 1.330000e-115 427.0
72 TraesCS5A01G417600 chr2A 86.911 191 8 4 4996 5169 689601888 689602078 1.140000e-46 198.0
73 TraesCS5A01G417600 chr2A 81.579 114 19 2 1290 1403 19372672 19372783 5.510000e-15 93.5
74 TraesCS5A01G417600 chr7A 79.526 591 74 19 4620 5169 526544128 526544712 1.360000e-100 377.0
75 TraesCS5A01G417600 chr7A 79.060 234 30 12 3950 4168 649477707 649477478 5.400000e-30 143.0
76 TraesCS5A01G417600 chr7A 77.350 234 34 12 3950 4168 649799441 649799212 2.530000e-23 121.0
77 TraesCS5A01G417600 chr1B 85.437 206 28 2 2230 2434 563621561 563621765 4.050000e-51 213.0
78 TraesCS5A01G417600 chr1A 78.063 351 61 13 3864 4208 545893531 545893191 1.890000e-49 207.0
79 TraesCS5A01G417600 chr3A 89.655 58 4 2 1288 1344 741658020 741658076 7.180000e-09 73.1
80 TraesCS5A01G417600 chr6B 94.286 35 2 0 44 78 75670519 75670553 3.000000e-03 54.7


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 TraesCS5A01G417600 chr5A 606048852 606054020 5168 True 9546.000000 9546 100.000000 1 5169 1 chr5A.!!$R3 5168
1 TraesCS5A01G417600 chr5A 534361815 534362945 1130 False 2089.000000 2089 100.000000 1304 2434 1 chr5A.!!$F3 1130
2 TraesCS5A01G417600 chr5A 606153407 606154113 706 True 710.000000 710 85.083000 18 726 1 chr5A.!!$R4 708
3 TraesCS5A01G417600 chr5B 595620462 595625199 4737 True 959.100000 3064 90.591600 1 4573 5 chr5B.!!$R5 4572
4 TraesCS5A01G417600 chr5B 595652682 595653387 705 True 758.000000 758 86.307000 18 726 1 chr5B.!!$R2 708
5 TraesCS5A01G417600 chr5B 324963377 324964393 1016 True 516.500000 706 85.433500 1303 2391 2 chr5B.!!$R3 1088
6 TraesCS5A01G417600 chr5B 374446429 374447014 585 False 490.000000 490 82.939000 4619 5169 1 chr5B.!!$F1 550
7 TraesCS5A01G417600 chr5B 595376993 595377714 721 True 336.500000 401 87.434000 2457 2826 2 chr5B.!!$R4 369
8 TraesCS5A01G417600 chr5D 484411381 484416451 5070 True 1657.333333 2750 88.691667 1 4607 3 chr5D.!!$R3 4606
9 TraesCS5A01G417600 chr5D 82951933 82952613 680 False 601.000000 601 83.333000 1785 2438 1 chr5D.!!$F1 653
10 TraesCS5A01G417600 chr5D 563730284 563730869 585 True 518.000000 518 83.646000 4620 5169 1 chr5D.!!$R1 549
11 TraesCS5A01G417600 chr5D 484307426 484308155 729 True 378.000000 453 89.440500 2457 2826 2 chr5D.!!$R2 369
12 TraesCS5A01G417600 chr5D 484567292 484568310 1018 True 369.000000 377 88.881000 18 726 2 chr5D.!!$R4 708
13 TraesCS5A01G417600 chr2B 755625250 755626381 1131 True 2085.000000 2085 99.912000 1303 2434 1 chr2B.!!$R3 1131
14 TraesCS5A01G417600 chr2B 718962754 718963893 1139 True 1273.000000 1273 87.199000 1302 2434 1 chr2B.!!$R2 1132
15 TraesCS5A01G417600 chr2B 250069629 250070711 1082 True 492.000000 610 83.899500 3299 4332 2 chr2B.!!$R5 1033
16 TraesCS5A01G417600 chr2B 468657046 468657633 587 True 475.000000 475 82.403000 4620 5169 1 chr2B.!!$R1 549
17 TraesCS5A01G417600 chr6D 90875203 90876351 1148 True 1757.000000 1757 94.526000 1303 2434 1 chr6D.!!$R1 1131
18 TraesCS5A01G417600 chr6D 152188782 152189936 1154 False 1574.000000 1574 91.616000 1304 2434 1 chr6D.!!$F2 1130
19 TraesCS5A01G417600 chr6D 394561089 394561672 583 False 514.000000 514 83.673000 4622 5169 1 chr6D.!!$F3 547
20 TraesCS5A01G417600 chr6A 612997115 612997759 644 False 1038.000000 1038 95.573000 1303 1955 1 chr6A.!!$F1 652
21 TraesCS5A01G417600 chr6A 613042331 613042974 643 False 1037.000000 1037 95.573000 1303 1955 1 chr6A.!!$F2 652
22 TraesCS5A01G417600 chr2D 32177229 32178694 1465 False 652.500000 909 87.601000 1296 2434 2 chr2D.!!$F2 1138
23 TraesCS5A01G417600 chr2D 316326766 316327350 584 False 499.000000 499 83.249000 4621 5169 1 chr2D.!!$F1 548
24 TraesCS5A01G417600 chr2D 194191086 194192176 1090 True 493.000000 614 83.889500 3299 4332 2 chr2D.!!$R2 1033
25 TraesCS5A01G417600 chr4D 111559403 111559988 585 False 616.000000 616 86.735000 4622 5169 1 chr4D.!!$F1 547
26 TraesCS5A01G417600 chr7D 607220351 607220935 584 True 553.000000 553 84.890000 4622 5169 1 chr7D.!!$R4 547
27 TraesCS5A01G417600 chr7D 59382573 59383155 582 True 501.000000 501 83.333000 4622 5169 1 chr7D.!!$R1 547
28 TraesCS5A01G417600 chr3D 519670964 519671547 583 True 514.000000 514 83.784000 4622 5169 1 chr3D.!!$R1 547
29 TraesCS5A01G417600 chr3D 574731621 574732207 586 False 501.000000 501 83.249000 4620 5169 1 chr3D.!!$F2 549
30 TraesCS5A01G417600 chr4A 104697573 104698143 570 True 501.000000 501 83.275000 4622 5169 1 chr4A.!!$R1 547
31 TraesCS5A01G417600 chr7B 111898365 111898950 585 True 488.000000 488 82.823000 4622 5169 1 chr7B.!!$R1 547
32 TraesCS5A01G417600 chr7B 380731472 380732027 555 False 411.000000 411 80.803000 4622 5169 1 chr7B.!!$F1 547
33 TraesCS5A01G417600 chr3B 41618192 41618778 586 False 486.000000 486 82.770000 4619 5169 1 chr3B.!!$F1 550
34 TraesCS5A01G417600 chr1D 184475900 184476473 573 False 460.000000 460 82.069000 4622 5169 1 chr1D.!!$F2 547
35 TraesCS5A01G417600 chr7A 526544128 526544712 584 False 377.000000 377 79.526000 4620 5169 1 chr7A.!!$F1 549

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
747 1085 1.040646 AGAACAGACCAAGTCGAGCA 58.959 50.000 0.00 0.00 37.67 4.26 F
1157 1542 0.109342 CTGGTGCTTGTGGGTTCTCT 59.891 55.000 0.00 0.00 0.00 3.10 F
2585 3400 2.430332 CCTTTGCTCACTTTTTCCACCA 59.570 45.455 0.00 0.00 0.00 4.17 F
2864 3721 0.390866 ATTCTCTCTGTGCACGCTGG 60.391 55.000 13.13 2.53 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 3420 0.256752 CCTTCCTCATCATGCCACCA 59.743 55.000 0.00 0.0 0.00 4.17 R
2605 3422 0.394762 TGCCTTCCTCATCATGCCAC 60.395 55.000 0.00 0.0 0.00 5.01 R
3937 4852 1.593196 TGCCTGAAGAAAAGGTCACG 58.407 50.000 0.00 0.0 37.13 4.35 R
4793 6294 1.375013 GTTAAAGTCGGAGCGGCCA 60.375 57.895 2.24 0.0 35.94 5.36 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
114 115 3.103911 CTGTCGACGCCGGTCAAC 61.104 66.667 11.62 0.00 43.61 3.18
579 899 3.500642 CAGACGAGAGAGGCGCGA 61.501 66.667 12.10 0.00 42.77 5.87
718 1056 3.346426 CCCAACAAACTCCTCTGGG 57.654 57.895 0.00 0.00 40.85 4.45
736 1074 2.347731 GGGAAACCGATCAGAACAGAC 58.652 52.381 0.00 0.00 43.64 3.51
747 1085 1.040646 AGAACAGACCAAGTCGAGCA 58.959 50.000 0.00 0.00 37.67 4.26
762 1145 4.036262 AGTCGAGCAGTCATCTCATCTTAC 59.964 45.833 0.00 0.00 0.00 2.34
766 1149 3.119291 GCAGTCATCTCATCTTACGTGG 58.881 50.000 0.00 0.00 0.00 4.94
855 1238 2.418777 CAGCGGCCGATCTGATCA 59.581 61.111 33.48 0.00 32.26 2.92
882 1265 4.335647 ACCTCCGCAGCACCCAAG 62.336 66.667 0.00 0.00 0.00 3.61
894 1277 2.092375 AGCACCCAAGCCCTATAAGAAC 60.092 50.000 0.00 0.00 34.23 3.01
1012 1397 3.402681 CCGCCATGGTCTGTCCCT 61.403 66.667 14.67 0.00 34.77 4.20
1125 1510 4.202253 ACCAATTGTTGCCTCTTTTTCTCC 60.202 41.667 4.43 0.00 0.00 3.71
1157 1542 0.109342 CTGGTGCTTGTGGGTTCTCT 59.891 55.000 0.00 0.00 0.00 3.10
1192 1577 2.470821 CGATTAGATGTCCGACCCAAC 58.529 52.381 0.00 0.00 0.00 3.77
1200 1585 2.437716 CCGACCCAACCCATTCCG 60.438 66.667 0.00 0.00 0.00 4.30
1266 1651 5.105351 ACTGGTTCTGTTTTTCTTTTCCCTG 60.105 40.000 0.00 0.00 0.00 4.45
1267 1652 4.775253 TGGTTCTGTTTTTCTTTTCCCTGT 59.225 37.500 0.00 0.00 0.00 4.00
1268 1653 5.105513 TGGTTCTGTTTTTCTTTTCCCTGTC 60.106 40.000 0.00 0.00 0.00 3.51
1269 1654 5.105513 GGTTCTGTTTTTCTTTTCCCTGTCA 60.106 40.000 0.00 0.00 0.00 3.58
1299 1712 5.412640 TGCTTGAATTCCATGTGCTTATTG 58.587 37.500 2.27 0.00 0.00 1.90
2438 3248 9.211410 TGGTGTACTATAGTAGTAGAGAAGAGT 57.789 37.037 12.99 0.00 41.59 3.24
2445 3255 9.635520 CTATAGTAGTAGAGAAGAGTAGAGTGC 57.364 40.741 0.00 0.00 0.00 4.40
2446 3256 6.555463 AGTAGTAGAGAAGAGTAGAGTGCT 57.445 41.667 0.00 0.00 0.00 4.40
2447 3257 7.664552 AGTAGTAGAGAAGAGTAGAGTGCTA 57.335 40.000 0.00 0.00 0.00 3.49
2453 3263 7.710676 AGAGAAGAGTAGAGTGCTATTTTGA 57.289 36.000 0.00 0.00 0.00 2.69
2493 3303 8.850156 TGATGAAAATAGATGACGAGTCTGATA 58.150 33.333 4.78 0.00 0.00 2.15
2524 3335 5.241403 TCAGTTACACCATGTGGAAATCT 57.759 39.130 5.96 0.00 38.17 2.40
2574 3385 3.674410 GCTTAGCCATTTCCTTTGCTCAC 60.674 47.826 0.00 0.00 35.34 3.51
2578 3393 3.389002 AGCCATTTCCTTTGCTCACTTTT 59.611 39.130 0.00 0.00 0.00 2.27
2584 3399 2.693074 TCCTTTGCTCACTTTTTCCACC 59.307 45.455 0.00 0.00 0.00 4.61
2585 3400 2.430332 CCTTTGCTCACTTTTTCCACCA 59.570 45.455 0.00 0.00 0.00 4.17
2603 3420 6.692486 TCCACCATTTTTGTATAATTGCGTT 58.308 32.000 0.00 0.00 0.00 4.84
2605 3422 6.183360 CCACCATTTTTGTATAATTGCGTTGG 60.183 38.462 0.00 0.00 0.00 3.77
2628 3445 2.035576 GGCATGATGAGGAAGGCAATTC 59.964 50.000 0.00 0.00 37.17 2.17
2792 3621 4.872124 GGGAAATGATGAAGAACAATTGGC 59.128 41.667 10.83 1.25 0.00 4.52
2860 3717 7.468922 TTGAATTATATTCTCTCTGTGCACG 57.531 36.000 13.13 7.36 0.00 5.34
2864 3721 0.390866 ATTCTCTCTGTGCACGCTGG 60.391 55.000 13.13 2.53 0.00 4.85
2877 3734 1.032014 ACGCTGGATTTTTGTGCACT 58.968 45.000 19.41 0.00 0.00 4.40
2894 3751 5.352293 TGTGCACTGATGAGCTGTATTTTAG 59.648 40.000 19.41 0.00 0.00 1.85
2960 3817 9.645059 TGAGATGTGCTTTAGATATGTATAAGC 57.355 33.333 14.40 14.40 41.10 3.09
2961 3818 9.868277 GAGATGTGCTTTAGATATGTATAAGCT 57.132 33.333 18.51 0.00 41.25 3.74
2962 3819 9.650539 AGATGTGCTTTAGATATGTATAAGCTG 57.349 33.333 18.51 0.00 41.25 4.24
2988 3845 4.656112 ACTAGTTTATATCAGGCAGCTGGT 59.344 41.667 17.12 0.00 0.00 4.00
3014 3871 6.975196 TTTTTCAAAGATGGAATGGACTGA 57.025 33.333 0.00 0.00 0.00 3.41
3037 3895 2.216488 CGTCGTGTCAGAAACAAGTCTG 59.784 50.000 0.00 0.00 45.44 3.51
3136 3994 3.848019 GCTTCATGCAACTTCACATTACG 59.152 43.478 0.00 0.00 42.31 3.18
3159 4017 4.941263 GTGATACATCTAAAACCCACTGCA 59.059 41.667 0.00 0.00 0.00 4.41
3213 4072 1.877637 TGGTGTGTTTGACATCCGAG 58.122 50.000 0.00 0.00 34.37 4.63
3220 4079 4.576873 TGTGTTTGACATCCGAGCTTTTTA 59.423 37.500 0.00 0.00 0.00 1.52
3222 4081 6.149633 GTGTTTGACATCCGAGCTTTTTATT 58.850 36.000 0.00 0.00 0.00 1.40
3312 4180 9.474313 TGCCATTAATTACTTCTTTCTTACCAT 57.526 29.630 0.00 0.00 0.00 3.55
3397 4270 7.595819 TTGCTATTTTAATTATGGGGTCCTG 57.404 36.000 0.00 0.00 0.00 3.86
3464 4337 4.521146 ACCATAAGCATGTTTCTGAGGAG 58.479 43.478 8.90 0.00 0.00 3.69
3605 4479 8.008513 TGCAAACCCTGTTTTAACATTAGTTA 57.991 30.769 0.00 0.00 38.41 2.24
3887 4797 4.697514 CCATCTACTTATGGTGTGTCTGG 58.302 47.826 0.00 0.00 41.38 3.86
3937 4852 4.402474 AGCCAGTTGGGAAATGCTAATTAC 59.598 41.667 0.00 0.00 40.01 1.89
4103 5023 5.489792 TGCTCAGTCTGTCTTTATTCCTT 57.510 39.130 0.00 0.00 0.00 3.36
4192 5121 5.738619 TTGCTTTCACCTATCTGTAGTCA 57.261 39.130 0.00 0.00 0.00 3.41
4221 5150 8.636843 GTGTTCAAGAACTATTACTACTTGTCG 58.363 37.037 13.49 0.00 41.67 4.35
4487 5432 1.337260 CCTAGTGTGGACAGTGTCAGC 60.337 57.143 24.20 15.80 33.68 4.26
4583 5532 7.391833 GGAGTTTCAGATATGTGAGGTTTTCTT 59.608 37.037 2.46 0.00 0.00 2.52
4585 5534 9.136323 AGTTTCAGATATGTGAGGTTTTCTTTT 57.864 29.630 2.46 0.00 0.00 2.27
4587 5536 7.452880 TCAGATATGTGAGGTTTTCTTTTGG 57.547 36.000 0.00 0.00 0.00 3.28
4588 5537 6.071952 TCAGATATGTGAGGTTTTCTTTTGGC 60.072 38.462 0.00 0.00 0.00 4.52
4589 5538 2.861462 TGTGAGGTTTTCTTTTGGCG 57.139 45.000 0.00 0.00 0.00 5.69
4590 5539 2.370349 TGTGAGGTTTTCTTTTGGCGA 58.630 42.857 0.00 0.00 0.00 5.54
4591 5540 2.357637 TGTGAGGTTTTCTTTTGGCGAG 59.642 45.455 0.00 0.00 0.00 5.03
4593 5542 3.020984 TGAGGTTTTCTTTTGGCGAGTT 58.979 40.909 0.00 0.00 0.00 3.01
4594 5543 3.066203 TGAGGTTTTCTTTTGGCGAGTTC 59.934 43.478 0.00 0.00 0.00 3.01
4607 5556 7.946655 TTTGGCGAGTTCTTATGTCTATATG 57.053 36.000 0.00 0.00 0.00 1.78
4609 5558 7.050970 TGGCGAGTTCTTATGTCTATATGTT 57.949 36.000 0.00 0.00 0.00 2.71
4611 5560 7.438160 TGGCGAGTTCTTATGTCTATATGTTTG 59.562 37.037 0.00 0.00 0.00 2.93
4612 5561 7.438459 GGCGAGTTCTTATGTCTATATGTTTGT 59.562 37.037 0.00 0.00 0.00 2.83
4613 5562 8.480853 GCGAGTTCTTATGTCTATATGTTTGTC 58.519 37.037 0.00 0.00 0.00 3.18
4615 5564 8.873215 AGTTCTTATGTCTATATGTTTGTCCG 57.127 34.615 0.00 0.00 0.00 4.79
4616 5565 8.692710 AGTTCTTATGTCTATATGTTTGTCCGA 58.307 33.333 0.00 0.00 0.00 4.55
4618 5567 8.234136 TCTTATGTCTATATGTTTGTCCGAGT 57.766 34.615 0.00 0.00 0.00 4.18
4738 6204 2.539081 AAGGACCAAGCCCACTCCC 61.539 63.158 0.00 0.00 0.00 4.30
4752 6218 1.002888 CACTCCCAGAGACAAGCACAT 59.997 52.381 0.00 0.00 33.32 3.21
4797 6308 1.302511 AACATGTCGACCTGTGGCC 60.303 57.895 24.32 0.00 0.00 5.36
4807 6318 4.379243 CTGTGGCCGCTCCGACTT 62.379 66.667 18.96 0.00 37.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 4.323477 TTCCGGTTCCAGGCGGTG 62.323 66.667 0.00 0.00 0.00 4.94
240 241 4.675029 GTGTGGGACCCCGTCACG 62.675 72.222 8.45 0.00 39.08 4.35
459 779 1.153745 CGGCTTCTTCGAGGAGGTG 60.154 63.158 8.45 0.00 0.00 4.00
557 877 0.667487 CGCCTCTCTCGTCTGCAAAA 60.667 55.000 0.00 0.00 0.00 2.44
558 878 1.080501 CGCCTCTCTCGTCTGCAAA 60.081 57.895 0.00 0.00 0.00 3.68
682 1020 4.193334 CGAGATGACCTGCGGCGA 62.193 66.667 12.98 0.00 0.00 5.54
718 1056 3.040147 TGGTCTGTTCTGATCGGTTTC 57.960 47.619 0.42 0.00 0.00 2.78
733 1071 1.203523 GATGACTGCTCGACTTGGTCT 59.796 52.381 0.00 0.00 0.00 3.85
736 1074 1.203287 TGAGATGACTGCTCGACTTGG 59.797 52.381 0.00 0.00 35.15 3.61
747 1085 2.101582 GCCCACGTAAGATGAGATGACT 59.898 50.000 0.00 0.00 43.62 3.41
882 1265 0.672342 TCGCCTCGTTCTTATAGGGC 59.328 55.000 0.00 0.00 36.60 5.19
907 1290 4.794648 TGGAAGATTGGCGGCGGG 62.795 66.667 9.78 0.00 0.00 6.13
944 1327 3.656243 TTAGCGTCGTCGTCGGCAG 62.656 63.158 13.43 1.10 42.21 4.85
945 1328 3.725459 TTAGCGTCGTCGTCGGCA 61.725 61.111 13.43 0.00 42.21 5.69
947 1330 2.575262 GGTTAGCGTCGTCGTCGG 60.575 66.667 13.43 0.00 39.49 4.79
1157 1542 5.337578 TCTAATCGGTGTTGATCATCACA 57.662 39.130 29.08 15.79 36.43 3.58
1192 1577 2.869233 CCATGTTTTAGCGGAATGGG 57.131 50.000 0.00 0.00 35.22 4.00
1200 1585 3.004944 TCGTTTTGTCCCCATGTTTTAGC 59.995 43.478 0.00 0.00 0.00 3.09
1249 1634 4.746611 GCATGACAGGGAAAAGAAAAACAG 59.253 41.667 0.00 0.00 0.00 3.16
1254 1639 2.297033 GCAGCATGACAGGGAAAAGAAA 59.703 45.455 0.00 0.00 39.69 2.52
1256 1641 1.074405 AGCAGCATGACAGGGAAAAGA 59.926 47.619 0.00 0.00 39.69 2.52
1262 1647 1.677966 AAGCAGCAGCATGACAGGG 60.678 57.895 3.17 0.00 45.49 4.45
1266 1651 2.527100 GAATTCAAGCAGCAGCATGAC 58.473 47.619 8.62 0.00 46.88 3.06
1267 1652 1.475280 GGAATTCAAGCAGCAGCATGA 59.525 47.619 4.80 4.80 45.72 3.07
1268 1653 1.203758 TGGAATTCAAGCAGCAGCATG 59.796 47.619 7.93 1.05 45.49 4.06
1269 1654 1.552578 TGGAATTCAAGCAGCAGCAT 58.447 45.000 7.93 0.00 45.49 3.79
1299 1712 7.572502 AAGCACGTACAAATTACTAGTACAC 57.427 36.000 0.91 0.00 38.35 2.90
2434 3244 9.196139 AGAACTATCAAAATAGCACTCTACTCT 57.804 33.333 0.00 0.00 38.81 3.24
2435 3245 9.458374 GAGAACTATCAAAATAGCACTCTACTC 57.542 37.037 0.00 0.00 38.81 2.59
2436 3246 9.196139 AGAGAACTATCAAAATAGCACTCTACT 57.804 33.333 14.53 0.00 42.63 2.57
2437 3247 9.243637 CAGAGAACTATCAAAATAGCACTCTAC 57.756 37.037 15.17 0.00 42.60 2.59
2438 3248 8.972127 ACAGAGAACTATCAAAATAGCACTCTA 58.028 33.333 15.17 0.00 42.60 2.43
2439 3249 7.763528 CACAGAGAACTATCAAAATAGCACTCT 59.236 37.037 12.20 12.20 43.77 3.24
2440 3250 7.761704 TCACAGAGAACTATCAAAATAGCACTC 59.238 37.037 0.00 0.00 38.81 3.51
2441 3251 7.615403 TCACAGAGAACTATCAAAATAGCACT 58.385 34.615 0.00 0.00 38.81 4.40
2442 3252 7.834068 TCACAGAGAACTATCAAAATAGCAC 57.166 36.000 0.00 0.00 38.81 4.40
2443 3253 8.260114 TCATCACAGAGAACTATCAAAATAGCA 58.740 33.333 0.00 0.00 38.81 3.49
2444 3254 8.654230 TCATCACAGAGAACTATCAAAATAGC 57.346 34.615 0.00 0.00 38.81 2.97
2447 3257 9.676861 TTCATCATCACAGAGAACTATCAAAAT 57.323 29.630 0.00 0.00 0.00 1.82
2493 3303 6.547141 CCACATGGTGTAACTGAATGGATTAT 59.453 38.462 0.00 0.00 36.74 1.28
2524 3335 2.833943 TGCTCTCTCAGACAAATGCCTA 59.166 45.455 0.00 0.00 0.00 3.93
2574 3385 9.824534 GCAATTATACAAAAATGGTGGAAAAAG 57.175 29.630 0.00 0.00 0.00 2.27
2578 3393 6.692486 ACGCAATTATACAAAAATGGTGGAA 58.308 32.000 0.00 0.00 0.00 3.53
2584 3399 6.671879 GCCACCAACGCAATTATACAAAAATG 60.672 38.462 0.00 0.00 0.00 2.32
2585 3400 5.350091 GCCACCAACGCAATTATACAAAAAT 59.650 36.000 0.00 0.00 0.00 1.82
2603 3420 0.256752 CCTTCCTCATCATGCCACCA 59.743 55.000 0.00 0.00 0.00 4.17
2605 3422 0.394762 TGCCTTCCTCATCATGCCAC 60.395 55.000 0.00 0.00 0.00 5.01
2792 3621 2.360801 ACATGGTTTTCAGAAACACGGG 59.639 45.455 0.00 0.00 45.52 5.28
2860 3717 2.798976 TCAGTGCACAAAAATCCAGC 57.201 45.000 21.04 0.00 0.00 4.85
2864 3721 3.918591 CAGCTCATCAGTGCACAAAAATC 59.081 43.478 21.04 2.27 36.73 2.17
2894 3751 6.453926 ACCTAGAGCAGTACTAAAGTAAGC 57.546 41.667 0.00 7.42 35.39 3.09
2899 3756 8.283699 ACTAGAAACCTAGAGCAGTACTAAAG 57.716 38.462 0.00 0.00 37.61 1.85
2956 3813 7.507956 TGCCTGATATAAACTAGTACCAGCTTA 59.492 37.037 0.00 0.00 0.00 3.09
2958 3815 5.839063 TGCCTGATATAAACTAGTACCAGCT 59.161 40.000 0.00 0.00 0.00 4.24
2959 3816 6.097915 TGCCTGATATAAACTAGTACCAGC 57.902 41.667 0.00 0.00 0.00 4.85
2960 3817 6.015010 AGCTGCCTGATATAAACTAGTACCAG 60.015 42.308 0.00 0.00 0.00 4.00
2961 3818 5.839063 AGCTGCCTGATATAAACTAGTACCA 59.161 40.000 0.00 0.00 0.00 3.25
2962 3819 6.159988 CAGCTGCCTGATATAAACTAGTACC 58.840 44.000 0.00 0.00 41.77 3.34
3011 3868 2.661594 TGTTTCTGACACGACGATCAG 58.338 47.619 20.65 20.65 43.16 2.90
3012 3869 2.785713 TGTTTCTGACACGACGATCA 57.214 45.000 0.00 4.05 32.00 2.92
3014 3871 3.050619 GACTTGTTTCTGACACGACGAT 58.949 45.455 0.00 0.00 38.18 3.73
3136 3994 4.941263 TGCAGTGGGTTTTAGATGTATCAC 59.059 41.667 0.00 0.00 0.00 3.06
3397 4270 5.338365 GTCTCAAAGATTTCATGCCATCAC 58.662 41.667 6.70 0.00 0.00 3.06
3464 4337 8.209917 AGCCACTAGTACAATAAACAATTAGC 57.790 34.615 0.00 0.00 0.00 3.09
3605 4479 4.881273 TCACCTATTTAGCATTCGCAACAT 59.119 37.500 0.00 0.00 42.27 2.71
3937 4852 1.593196 TGCCTGAAGAAAAGGTCACG 58.407 50.000 0.00 0.00 37.13 4.35
4075 4995 2.855209 AGACAGACTGAGCAAAGCAT 57.145 45.000 10.08 0.00 0.00 3.79
4402 5344 2.033299 CCAACAGCATATAAACAGCGGG 59.967 50.000 0.00 0.00 0.00 6.13
4404 5346 3.002656 CCTCCAACAGCATATAAACAGCG 59.997 47.826 0.00 0.00 0.00 5.18
4457 5400 6.369065 CACTGTCCACACTAGGATTTTTCTAC 59.631 42.308 0.00 0.00 40.42 2.59
4487 5432 7.095313 CCTCAGGATTAATCACAAATCATCTCG 60.095 40.741 17.07 0.00 35.46 4.04
4583 5532 7.497595 ACATATAGACATAAGAACTCGCCAAA 58.502 34.615 0.00 0.00 0.00 3.28
4585 5534 6.650427 ACATATAGACATAAGAACTCGCCA 57.350 37.500 0.00 0.00 0.00 5.69
4587 5536 8.354011 ACAAACATATAGACATAAGAACTCGC 57.646 34.615 0.00 0.00 0.00 5.03
4588 5537 8.969267 GGACAAACATATAGACATAAGAACTCG 58.031 37.037 0.00 0.00 0.00 4.18
4589 5538 8.969267 CGGACAAACATATAGACATAAGAACTC 58.031 37.037 0.00 0.00 0.00 3.01
4590 5539 8.692710 TCGGACAAACATATAGACATAAGAACT 58.307 33.333 0.00 0.00 0.00 3.01
4591 5540 8.867112 TCGGACAAACATATAGACATAAGAAC 57.133 34.615 0.00 0.00 0.00 3.01
4593 5542 8.234136 ACTCGGACAAACATATAGACATAAGA 57.766 34.615 0.00 0.00 0.00 2.10
4594 5543 8.873215 AACTCGGACAAACATATAGACATAAG 57.127 34.615 0.00 0.00 0.00 1.73
4738 6204 2.082231 CCCTGAATGTGCTTGTCTCTG 58.918 52.381 0.00 0.00 0.00 3.35
4763 6264 3.454447 ACATGTTGTCGATTAGGATGGGA 59.546 43.478 0.00 0.00 0.00 4.37
4793 6294 1.375013 GTTAAAGTCGGAGCGGCCA 60.375 57.895 2.24 0.00 35.94 5.36
4807 6318 8.606602 GTTTTGTTCTTCTAAGTTCTCCGTTAA 58.393 33.333 0.00 0.00 0.00 2.01
4952 6476 1.064458 GTAGTCGGCTCTTCTCCGC 59.936 63.158 0.00 0.00 46.05 5.54


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

AutoCloner maintained by Alex Coulton.