Multiple sequence alignment - TraesCS7D01G091400

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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 TraesCS7D01G091400 chr7D 100.000 4227 0 0 1 4227 54762128 54757902 0.000000e+00 7806
1 TraesCS7D01G091400 chr7D 100.000 445 0 0 4454 4898 54757675 54757231 0.000000e+00 822
2 TraesCS7D01G091400 chr7D 82.500 440 53 9 2202 2641 80714833 80714418 1.000000e-96 364
3 TraesCS7D01G091400 chr7D 80.000 475 65 18 3314 3770 80713670 80713208 1.700000e-84 324
4 TraesCS7D01G091400 chr7A 91.841 2770 156 26 1506 4215 58233688 58236447 0.000000e+00 3799
5 TraesCS7D01G091400 chr7A 92.424 792 48 7 846 1636 58232996 58233776 0.000000e+00 1120
6 TraesCS7D01G091400 chr7A 88.116 690 32 14 1 661 58232087 58232755 0.000000e+00 774
7 TraesCS7D01G091400 chr7A 89.593 442 34 6 4455 4886 58236440 58236879 7.170000e-153 551
8 TraesCS7D01G091400 chr7A 81.602 462 61 11 2180 2641 83298280 83297843 1.300000e-95 361
9 TraesCS7D01G091400 chr7A 78.238 579 87 21 3314 3868 83292205 83291642 7.860000e-88 335
10 TraesCS7D01G091400 chr4A 92.785 2370 126 17 1568 3918 670886800 670889143 0.000000e+00 3387
11 TraesCS7D01G091400 chr4A 91.128 1082 58 16 548 1611 670885827 670886888 0.000000e+00 1432
12 TraesCS7D01G091400 chr4A 86.925 413 51 1 2169 2581 670943329 670943738 1.240000e-125 460
13 TraesCS7D01G091400 chr4A 86.308 409 51 4 1647 2054 670942701 670943105 1.620000e-119 440
14 TraesCS7D01G091400 chr4A 86.738 279 26 7 3946 4215 670925054 670925330 2.870000e-77 300
15 TraesCS7D01G091400 chr4A 92.473 93 6 1 4494 4586 670934722 670934813 1.110000e-26 132
16 TraesCS7D01G091400 chr4A 84.615 117 11 4 445 555 670884527 670884642 5.180000e-20 110
17 TraesCS7D01G091400 chr4A 100.000 40 0 0 4455 4494 670925323 670925362 1.890000e-09 75
18 TraesCS7D01G091400 chr3B 81.716 979 159 17 2198 3171 818315437 818316400 0.000000e+00 798
19 TraesCS7D01G091400 chr6A 90.212 378 34 3 1654 2031 585971745 585972119 1.580000e-134 490
20 TraesCS7D01G091400 chr6A 85.957 470 46 10 1063 1516 585971103 585971568 7.370000e-133 484
21 TraesCS7D01G091400 chr6A 82.510 486 66 13 2221 2701 585972360 585972831 4.560000e-110 409
22 TraesCS7D01G091400 chr6A 76.242 463 68 19 3307 3769 585973437 585973857 1.790000e-49 207
23 TraesCS7D01G091400 chrUn 90.331 362 30 3 1655 2015 108746461 108746818 2.060000e-128 470
24 TraesCS7D01G091400 chrUn 87.371 388 46 1 1654 2041 108800280 108799896 4.500000e-120 442
25 TraesCS7D01G091400 chrUn 83.721 430 62 6 2213 2641 108747117 108747539 2.750000e-107 399
26 TraesCS7D01G091400 chrUn 83.894 416 60 5 2765 3173 108795243 108794828 1.650000e-104 390
27 TraesCS7D01G091400 chrUn 87.213 305 39 0 1213 1517 108746103 108746407 1.010000e-91 348
28 TraesCS7D01G091400 chrUn 77.615 478 72 20 3311 3767 108620533 108620996 1.750000e-64 257
29 TraesCS7D01G091400 chrUn 88.571 140 12 3 1057 1195 108800938 108800802 3.030000e-37 167
30 TraesCS7D01G091400 chrUn 87.943 141 14 2 1057 1197 108745884 108746021 3.920000e-36 163
31 TraesCS7D01G091400 chrUn 87.770 139 14 2 1057 1195 108754667 108754532 5.070000e-35 159
32 TraesCS7D01G091400 chr4B 88.831 385 39 2 1647 2031 665302209 665301829 2.060000e-128 470
33 TraesCS7D01G091400 chr4B 87.382 317 34 5 1204 1517 665302569 665302256 4.660000e-95 359
34 TraesCS7D01G091400 chr4B 88.489 139 13 2 1057 1195 665302770 665302635 1.090000e-36 165
35 TraesCS7D01G091400 chr4B 79.429 175 31 4 3596 3768 665300752 665300581 8.610000e-23 119
36 TraesCS7D01G091400 chr5A 86.935 398 48 2 1647 2044 704975083 704974690 1.250000e-120 444
37 TraesCS7D01G091400 chr5A 82.904 427 65 8 2216 2641 704974426 704974007 1.290000e-100 377
38 TraesCS7D01G091400 chr5A 86.495 311 42 0 1206 1516 705143019 705143329 4.690000e-90 342
39 TraesCS7D01G091400 chr5A 86.164 318 39 4 1201 1517 704975443 704975130 6.070000e-89 339
40 TraesCS7D01G091400 chr5A 78.186 463 82 12 3307 3769 680216871 680216428 1.340000e-70 278
41 TraesCS7D01G091400 chr5A 88.489 139 13 2 1057 1195 704948070 704948205 1.090000e-36 165
42 TraesCS7D01G091400 chr2D 86.375 389 49 4 1647 2035 584758585 584758969 5.860000e-114 422
43 TraesCS7D01G091400 chr2D 83.973 443 58 7 2209 2649 584759222 584759653 3.530000e-111 412
44 TraesCS7D01G091400 chr4D 81.053 475 76 10 2774 3244 499458510 499458046 2.790000e-97 366
45 TraesCS7D01G091400 chr4D 82.270 423 63 1 2219 2641 499459032 499458622 6.030000e-94 355
46 TraesCS7D01G091400 chr4D 86.875 320 37 4 1202 1520 499460245 499459930 2.170000e-93 353
47 TraesCS7D01G091400 chr4D 80.384 469 74 8 3307 3769 499457956 499457500 1.690000e-89 340
48 TraesCS7D01G091400 chr4D 91.034 145 9 3 1057 1200 499460448 499460307 5.000000e-45 193
49 TraesCS7D01G091400 chr7B 86.731 309 39 2 1215 1522 28062590 28062283 4.690000e-90 342
50 TraesCS7D01G091400 chr7B 76.570 653 106 27 3314 3934 28060141 28059504 1.020000e-81 315


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 TraesCS7D01G091400 chr7D 54757231 54762128 4897 True 4314.000000 7806 100.000000 1 4898 2 chr7D.!!$R1 4897
1 TraesCS7D01G091400 chr7D 80713208 80714833 1625 True 344.000000 364 81.250000 2202 3770 2 chr7D.!!$R2 1568
2 TraesCS7D01G091400 chr7A 58232087 58236879 4792 False 1561.000000 3799 90.493500 1 4886 4 chr7A.!!$F1 4885
3 TraesCS7D01G091400 chr7A 83291642 83292205 563 True 335.000000 335 78.238000 3314 3868 1 chr7A.!!$R1 554
4 TraesCS7D01G091400 chr4A 670884527 670889143 4616 False 1643.000000 3387 89.509333 445 3918 3 chr4A.!!$F2 3473
5 TraesCS7D01G091400 chr4A 670942701 670943738 1037 False 450.000000 460 86.616500 1647 2581 2 chr4A.!!$F4 934
6 TraesCS7D01G091400 chr3B 818315437 818316400 963 False 798.000000 798 81.716000 2198 3171 1 chr3B.!!$F1 973
7 TraesCS7D01G091400 chr6A 585971103 585973857 2754 False 397.500000 490 83.730250 1063 3769 4 chr6A.!!$F1 2706
8 TraesCS7D01G091400 chrUn 108745884 108747539 1655 False 345.000000 470 87.302000 1057 2641 4 chrUn.!!$F2 1584
9 TraesCS7D01G091400 chrUn 108799896 108800938 1042 True 304.500000 442 87.971000 1057 2041 2 chrUn.!!$R3 984
10 TraesCS7D01G091400 chr4B 665300581 665302770 2189 True 278.250000 470 86.032750 1057 3768 4 chr4B.!!$R1 2711
11 TraesCS7D01G091400 chr5A 704974007 704975443 1436 True 386.666667 444 85.334333 1201 2641 3 chr5A.!!$R2 1440
12 TraesCS7D01G091400 chr2D 584758585 584759653 1068 False 417.000000 422 85.174000 1647 2649 2 chr2D.!!$F1 1002
13 TraesCS7D01G091400 chr4D 499457500 499460448 2948 True 321.400000 366 84.323200 1057 3769 5 chr4D.!!$R1 2712
14 TraesCS7D01G091400 chr7B 28059504 28062590 3086 True 328.500000 342 81.650500 1215 3934 2 chr7B.!!$R1 2719

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
792 2026 0.106619 GAGCGAGGTAGGAAGGAGGA 60.107 60.0 0.00 0.0 0.00 3.71 F
795 2029 0.395862 CGAGGTAGGAAGGAGGAGCA 60.396 60.0 0.00 0.0 0.00 4.26 F
2707 5221 0.249155 CAACAGGCTTGCACAACTGG 60.249 55.0 13.37 0.0 35.34 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2707 5221 1.375268 GGCTGGCAGAGAGACACAC 60.375 63.158 20.86 0.0 0.00 3.82 R
3105 5781 1.194781 AGATGGAGGTCCGCAGTTGT 61.195 55.000 0.00 0.0 39.43 3.32 R
4546 7350 0.035152 TCATGACCGCCTTGCATTCT 60.035 50.000 0.00 0.0 0.00 2.40 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
33 34 4.460034 TCACAATCACCATTGGAATCACTG 59.540 41.667 10.37 0.00 43.47 3.66
65 66 5.355350 AGCTAGCAGTATTTGAAACATGACC 59.645 40.000 18.83 0.00 0.00 4.02
66 67 5.355350 GCTAGCAGTATTTGAAACATGACCT 59.645 40.000 10.63 0.00 0.00 3.85
93 94 4.274950 CGTGAGTACATGGTCCTTGTTTTT 59.725 41.667 15.10 2.65 0.00 1.94
183 188 9.574458 TCGTCTTTTTAGAAATATCTGTCTCTG 57.426 33.333 0.00 0.00 37.10 3.35
204 228 4.929479 TGAGGGGCACTACATGTAATTTT 58.071 39.130 7.06 0.00 0.00 1.82
251 275 0.961019 TTGCACTGGCCAAACAGATC 59.039 50.000 7.01 0.00 40.97 2.75
271 296 6.312426 CAGATCGTCTAAAGCAAGATTCTTGT 59.688 38.462 23.66 9.99 0.00 3.16
274 299 5.635280 TCGTCTAAAGCAAGATTCTTGTCAG 59.365 40.000 23.66 16.01 0.00 3.51
311 336 9.809096 ATGAGATGTTAATATATACTGCCTTCG 57.191 33.333 0.00 0.00 0.00 3.79
312 337 8.803235 TGAGATGTTAATATATACTGCCTTCGT 58.197 33.333 0.00 0.00 0.00 3.85
313 338 9.291664 GAGATGTTAATATATACTGCCTTCGTC 57.708 37.037 0.00 0.00 0.00 4.20
314 339 9.026121 AGATGTTAATATATACTGCCTTCGTCT 57.974 33.333 0.00 0.00 0.00 4.18
315 340 9.640963 GATGTTAATATATACTGCCTTCGTCTT 57.359 33.333 0.00 0.00 0.00 3.01
333 358 6.513180 TCGTCTTCAAATAAGTGTCTCAACT 58.487 36.000 0.00 0.00 0.00 3.16
336 361 8.122952 CGTCTTCAAATAAGTGTCTCAACTTTT 58.877 33.333 0.00 0.00 40.77 2.27
399 426 6.763715 TGCCATCCTCCAACTATAATAACT 57.236 37.500 0.00 0.00 0.00 2.24
400 427 6.533730 TGCCATCCTCCAACTATAATAACTG 58.466 40.000 0.00 0.00 0.00 3.16
403 430 7.819900 GCCATCCTCCAACTATAATAACTGTAG 59.180 40.741 0.00 0.00 0.00 2.74
420 447 7.412137 AACTGTAGTTACAACCGTTACAATC 57.588 36.000 0.00 0.00 36.32 2.67
433 460 5.106317 ACCGTTACAATCCAATGATGTGTTC 60.106 40.000 0.00 0.00 0.00 3.18
512 542 6.649973 CCAATCTTCCATGTGCATTTTGTTTA 59.350 34.615 0.00 0.00 0.00 2.01
524 556 9.545105 TGTGCATTTTGTTTAGATCTTTTTCAT 57.455 25.926 0.00 0.00 0.00 2.57
570 1794 6.145534 CGTTAGTGCACTGAAGAATACTTTGA 59.854 38.462 29.57 0.28 36.39 2.69
713 1946 2.506438 GTACGTCTGCCTGCCGTC 60.506 66.667 0.00 0.00 36.12 4.79
728 1961 4.389374 CTGCCGTCCACCAATATTTATCT 58.611 43.478 0.00 0.00 0.00 1.98
734 1967 6.467677 CGTCCACCAATATTTATCTGGATCT 58.532 40.000 0.00 0.00 34.16 2.75
735 1968 6.936900 CGTCCACCAATATTTATCTGGATCTT 59.063 38.462 0.00 0.00 34.16 2.40
736 1969 7.095060 CGTCCACCAATATTTATCTGGATCTTG 60.095 40.741 0.00 0.00 34.16 3.02
737 1970 7.175641 GTCCACCAATATTTATCTGGATCTTGG 59.824 40.741 0.00 0.00 38.26 3.61
738 1971 6.071728 CCACCAATATTTATCTGGATCTTGGC 60.072 42.308 0.00 0.00 36.26 4.52
739 1972 6.718454 CACCAATATTTATCTGGATCTTGGCT 59.282 38.462 0.00 0.00 36.26 4.75
740 1973 6.718454 ACCAATATTTATCTGGATCTTGGCTG 59.282 38.462 0.00 0.00 36.26 4.85
741 1974 6.718454 CCAATATTTATCTGGATCTTGGCTGT 59.282 38.462 0.00 0.00 31.38 4.40
743 1976 4.842531 TTTATCTGGATCTTGGCTGTCA 57.157 40.909 0.00 0.00 0.00 3.58
744 1977 2.706339 ATCTGGATCTTGGCTGTCAC 57.294 50.000 0.00 0.00 0.00 3.67
745 1978 0.247460 TCTGGATCTTGGCTGTCACG 59.753 55.000 0.00 0.00 0.00 4.35
746 1979 0.247460 CTGGATCTTGGCTGTCACGA 59.753 55.000 0.00 0.00 0.00 4.35
747 1980 0.247460 TGGATCTTGGCTGTCACGAG 59.753 55.000 0.00 0.00 0.00 4.18
771 2005 1.280457 GCCAGAGAAGGGAGAAGGAA 58.720 55.000 0.00 0.00 0.00 3.36
788 2022 1.069358 GGAATGAGCGAGGTAGGAAGG 59.931 57.143 0.00 0.00 0.00 3.46
789 2023 2.032620 GAATGAGCGAGGTAGGAAGGA 58.967 52.381 0.00 0.00 0.00 3.36
791 2025 0.395862 TGAGCGAGGTAGGAAGGAGG 60.396 60.000 0.00 0.00 0.00 4.30
792 2026 0.106619 GAGCGAGGTAGGAAGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
794 2028 1.740332 GCGAGGTAGGAAGGAGGAGC 61.740 65.000 0.00 0.00 0.00 4.70
795 2029 0.395862 CGAGGTAGGAAGGAGGAGCA 60.396 60.000 0.00 0.00 0.00 4.26
803 2041 0.467804 GAAGGAGGAGCAGTGGGATC 59.532 60.000 0.00 0.00 0.00 3.36
807 2045 1.743321 GAGGAGCAGTGGGATCGAGG 61.743 65.000 0.00 0.00 30.89 4.63
818 2056 1.033574 GGATCGAGGGGAGTACAGTG 58.966 60.000 0.00 0.00 0.00 3.66
825 2063 3.171528 GAGGGGAGTACAGTGTAAAGGT 58.828 50.000 4.11 0.00 0.00 3.50
847 2137 4.065088 TCACACACTGTTGAGCTTTATCC 58.935 43.478 0.00 0.00 0.00 2.59
855 2145 2.533266 TGAGCTTTATCCGAGCATCC 57.467 50.000 0.00 0.00 42.56 3.51
859 2149 1.808945 GCTTTATCCGAGCATCCATGG 59.191 52.381 4.97 4.97 39.89 3.66
860 2150 2.430465 CTTTATCCGAGCATCCATGGG 58.570 52.381 13.02 0.00 0.00 4.00
861 2151 0.692476 TTATCCGAGCATCCATGGGG 59.308 55.000 13.02 5.90 0.00 4.96
1015 2313 5.494632 TCACTGTATGTCACTATACCACG 57.505 43.478 0.00 0.00 33.56 4.94
1338 2729 2.355108 CCTGGTCGTCATCATGTTCCTT 60.355 50.000 0.00 0.00 0.00 3.36
1347 2738 1.541379 TCATGTTCCTTCTCGACCGA 58.459 50.000 0.00 0.00 0.00 4.69
1368 2759 1.351430 GCATCAGCGACAACAGCGTA 61.351 55.000 0.00 0.00 40.04 4.42
1504 2896 1.729484 CTCGTCTTCGCTTGCGTCA 60.729 57.895 14.70 2.57 36.96 4.35
1615 3168 4.426313 CCCCCTCGGACAAAGCCC 62.426 72.222 0.00 0.00 0.00 5.19
1619 3172 4.778143 CTCGGACAAAGCCCGGGG 62.778 72.222 25.28 9.31 43.61 5.73
1621 3174 4.778143 CGGACAAAGCCCGGGGAG 62.778 72.222 25.28 5.44 43.05 4.30
1622 3175 3.327404 GGACAAAGCCCGGGGAGA 61.327 66.667 25.28 0.00 0.00 3.71
2127 4141 1.376466 GGAGCCAGAACAAGAGCCA 59.624 57.895 0.00 0.00 0.00 4.75
2526 5034 3.356290 GGCCATGATACTGAACCTGTTT 58.644 45.455 0.00 0.00 0.00 2.83
2707 5221 0.249155 CAACAGGCTTGCACAACTGG 60.249 55.000 13.37 0.00 35.34 4.00
3264 5952 1.210413 CCTAGGATCATCGCCGTCG 59.790 63.158 1.05 0.00 0.00 5.12
3268 5956 2.104331 GATCATCGCCGTCGTGGT 59.896 61.111 0.00 0.00 41.21 4.16
3303 6033 4.894784 ACAAAGGTGATGACGAACAGTAT 58.105 39.130 0.00 0.00 0.00 2.12
3312 6042 1.058695 GACGAACAGTATGCGAAACGG 59.941 52.381 0.00 0.00 42.53 4.44
3476 6227 1.683917 CCCGATCCTACTTCACTCCAG 59.316 57.143 0.00 0.00 0.00 3.86
3580 6334 3.120321 ACACCGTGAAGAAGCAATACA 57.880 42.857 5.28 0.00 0.00 2.29
3591 6345 4.385825 AGAAGCAATACACCGTGAAGAAA 58.614 39.130 5.28 0.00 0.00 2.52
3654 6417 2.359169 CCTGTTCGGCCTGCTAGGA 61.359 63.158 0.00 0.00 37.67 2.94
3696 6459 3.371063 GACTGGGAGACGTCCGCA 61.371 66.667 13.01 16.24 45.05 5.69
3717 6480 4.831307 GTCATCGCGCTCGTCGGT 62.831 66.667 5.56 0.00 38.94 4.69
3747 6510 2.538939 CGTCTTCATCACGATCTACGCA 60.539 50.000 0.00 0.00 46.94 5.24
3785 6548 4.475135 GCGAGGGAGGGTGAAGGC 62.475 72.222 0.00 0.00 0.00 4.35
3786 6549 3.003173 CGAGGGAGGGTGAAGGCA 61.003 66.667 0.00 0.00 0.00 4.75
3787 6550 2.592993 CGAGGGAGGGTGAAGGCAA 61.593 63.158 0.00 0.00 0.00 4.52
3813 6576 4.510340 ACGGTGTGCAAGTACTTTTCTAAG 59.490 41.667 5.07 0.00 37.40 2.18
3835 6598 2.315176 TGATGGAAAAACAGGTGTGGG 58.685 47.619 0.00 0.00 0.00 4.61
3875 6638 5.123936 CAATGGTGATGATGATCAGTCAGT 58.876 41.667 0.09 0.00 39.36 3.41
3878 6641 3.181482 GGTGATGATGATCAGTCAGTCGT 60.181 47.826 0.09 0.00 39.36 4.34
4016 6790 7.726216 TCATGTTACATCTAATGTAGTCCTGG 58.274 38.462 0.00 0.00 45.58 4.45
4042 6816 3.782889 AGACAAACCAAAACAGAGCAC 57.217 42.857 0.00 0.00 0.00 4.40
4046 6820 3.181504 ACAAACCAAAACAGAGCACGTAC 60.182 43.478 0.00 0.00 0.00 3.67
4048 6822 3.738830 ACCAAAACAGAGCACGTACTA 57.261 42.857 0.00 0.00 0.00 1.82
4050 6824 3.994392 ACCAAAACAGAGCACGTACTATG 59.006 43.478 8.86 8.86 35.02 2.23
4051 6825 3.181520 CCAAAACAGAGCACGTACTATGC 60.182 47.826 10.30 10.21 43.74 3.14
4053 6827 1.182667 ACAGAGCACGTACTATGCCA 58.817 50.000 10.30 0.00 44.53 4.92
4056 6830 2.348666 CAGAGCACGTACTATGCCAAAC 59.651 50.000 13.62 5.58 44.53 2.93
4057 6831 1.323534 GAGCACGTACTATGCCAAACG 59.676 52.381 13.62 0.00 44.53 3.60
4058 6832 1.067425 AGCACGTACTATGCCAAACGA 60.067 47.619 13.62 0.00 44.53 3.85
4088 6864 5.748402 TCACTGGAAACAATATGCTGAGAT 58.252 37.500 0.00 0.00 42.06 2.75
4089 6865 6.888105 TCACTGGAAACAATATGCTGAGATA 58.112 36.000 0.00 0.00 42.06 1.98
4090 6866 6.988580 TCACTGGAAACAATATGCTGAGATAG 59.011 38.462 0.00 0.00 42.06 2.08
4154 6957 2.464796 ATCAATGGGTGCATCCATGT 57.535 45.000 31.98 18.43 46.05 3.21
4182 6985 2.387757 ACCCAATTGAACAACTGCACT 58.612 42.857 7.12 0.00 0.00 4.40
4191 6994 3.193267 TGAACAACTGCACTGCTCTTTTT 59.807 39.130 1.98 0.00 0.00 1.94
4199 7002 2.229792 CACTGCTCTTTTTACCCTGCA 58.770 47.619 0.00 0.00 0.00 4.41
4226 7029 3.124686 GGTGCTCACCCGCAAAAA 58.875 55.556 7.82 0.00 45.68 1.94
4480 7283 2.289569 GCTAGAAGGCCATCCATCTCAG 60.290 54.545 5.01 0.00 39.48 3.35
4481 7284 2.187239 AGAAGGCCATCCATCTCAGA 57.813 50.000 5.01 0.00 35.65 3.27
4482 7285 2.703947 AGAAGGCCATCCATCTCAGAT 58.296 47.619 5.01 0.00 35.65 2.90
4505 7308 9.688091 AGATCTCACTAGTCAGTAGAACAATAA 57.312 33.333 0.00 0.00 32.21 1.40
4570 7374 1.725665 CAAGGCGGTCATGATGCTG 59.274 57.895 18.67 9.35 0.00 4.41
4575 7379 1.512996 GCGGTCATGATGCTGGGATG 61.513 60.000 13.81 0.00 0.00 3.51
4586 7390 3.017048 TGCTGGGATGGAAGTAATTGG 57.983 47.619 0.00 0.00 0.00 3.16
4605 7409 1.977293 GCAAACCAAACAGGCCCCAA 61.977 55.000 0.00 0.00 43.14 4.12
4629 7433 2.280186 CCCTCCTAATGCGACGGC 60.280 66.667 0.00 0.00 40.52 5.68
4652 7456 3.254892 GCAGTCTGGCAGAACTAACTAC 58.745 50.000 20.62 4.58 0.00 2.73
4653 7457 3.851098 CAGTCTGGCAGAACTAACTACC 58.149 50.000 20.62 3.15 0.00 3.18
4654 7458 3.258372 CAGTCTGGCAGAACTAACTACCA 59.742 47.826 20.62 0.00 33.01 3.25
4655 7459 3.901844 AGTCTGGCAGAACTAACTACCAA 59.098 43.478 20.62 0.00 33.56 3.67
4656 7460 4.021016 AGTCTGGCAGAACTAACTACCAAG 60.021 45.833 20.62 0.00 33.56 3.61
4657 7461 3.901844 TCTGGCAGAACTAACTACCAAGT 59.098 43.478 16.28 0.00 33.56 3.16
4658 7462 4.021368 TCTGGCAGAACTAACTACCAAGTC 60.021 45.833 16.28 0.00 33.56 3.01
4700 7506 9.935241 CACTAATAATGCATAACAGGAGATAGT 57.065 33.333 0.00 0.00 0.00 2.12
4741 7553 4.217118 CAGCCTGGAGATTATTTATGCCAC 59.783 45.833 0.00 0.00 0.00 5.01
4742 7554 4.141181 AGCCTGGAGATTATTTATGCCACA 60.141 41.667 0.00 0.00 0.00 4.17
4743 7555 4.768968 GCCTGGAGATTATTTATGCCACAT 59.231 41.667 0.00 0.00 0.00 3.21
4752 7564 9.283768 AGATTATTTATGCCACATATGTTCGAA 57.716 29.630 5.37 0.00 0.00 3.71
4857 7670 8.630054 TGAGTATGTTTACATTTTAAGGCTGT 57.370 30.769 0.02 0.00 37.76 4.40
4865 7678 5.782893 ACATTTTAAGGCTGTAAGTTGCA 57.217 34.783 0.00 0.00 35.30 4.08
4871 7684 4.766404 AAGGCTGTAAGTTGCAACATAC 57.234 40.909 29.11 29.11 34.61 2.39
4877 7690 6.316390 GGCTGTAAGTTGCAACATACTTCTAT 59.684 38.462 32.82 10.65 34.97 1.98
4896 7709 9.771534 ACTTCTATATAAGAATCAAAGCTCCAC 57.228 33.333 4.97 0.00 43.32 4.02
4897 7710 9.995003 CTTCTATATAAGAATCAAAGCTCCACT 57.005 33.333 0.00 0.00 43.32 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.755655 AGGACCATGTACTCACGAGAAG 59.244 50.000 0.00 0.00 0.00 2.85
66 67 2.803956 AGGACCATGTACTCACGAGAA 58.196 47.619 0.00 0.00 0.00 2.87
93 94 9.040939 GCCTACAGAAAAATAAAGCAAGAAAAA 57.959 29.630 0.00 0.00 0.00 1.94
158 163 9.574458 TCAGAGACAGATATTTCTAAAAAGACG 57.426 33.333 0.00 0.00 0.00 4.18
181 186 3.845781 ATTACATGTAGTGCCCCTCAG 57.154 47.619 5.56 0.00 0.00 3.35
183 188 5.193679 AGAAAATTACATGTAGTGCCCCTC 58.806 41.667 5.56 0.00 0.00 4.30
251 275 5.635280 TCTGACAAGAATCTTGCTTTAGACG 59.365 40.000 21.69 3.73 0.00 4.18
271 296 9.745018 ATTAACATCTCATTTCCTTCTTTCTGA 57.255 29.630 0.00 0.00 0.00 3.27
300 325 6.313905 CACTTATTTGAAGACGAAGGCAGTAT 59.686 38.462 0.00 0.00 0.00 2.12
301 326 5.637810 CACTTATTTGAAGACGAAGGCAGTA 59.362 40.000 0.00 0.00 0.00 2.74
302 327 4.452455 CACTTATTTGAAGACGAAGGCAGT 59.548 41.667 0.00 0.00 0.00 4.40
303 328 4.452455 ACACTTATTTGAAGACGAAGGCAG 59.548 41.667 0.00 0.00 0.00 4.85
304 329 4.385825 ACACTTATTTGAAGACGAAGGCA 58.614 39.130 0.00 0.00 0.00 4.75
305 330 4.691216 AGACACTTATTTGAAGACGAAGGC 59.309 41.667 0.00 0.00 0.00 4.35
306 331 5.926542 TGAGACACTTATTTGAAGACGAAGG 59.073 40.000 0.00 0.00 0.00 3.46
307 332 7.169982 AGTTGAGACACTTATTTGAAGACGAAG 59.830 37.037 0.00 0.00 0.00 3.79
308 333 6.984474 AGTTGAGACACTTATTTGAAGACGAA 59.016 34.615 0.00 0.00 0.00 3.85
309 334 6.513180 AGTTGAGACACTTATTTGAAGACGA 58.487 36.000 0.00 0.00 0.00 4.20
310 335 6.771188 AGTTGAGACACTTATTTGAAGACG 57.229 37.500 0.00 0.00 0.00 4.18
338 363 9.765295 ATCTTCTACACCCGGTATAAGTTATAT 57.235 33.333 5.90 0.00 37.42 0.86
339 364 9.592196 AATCTTCTACACCCGGTATAAGTTATA 57.408 33.333 0.00 0.00 37.42 0.98
340 365 8.488308 AATCTTCTACACCCGGTATAAGTTAT 57.512 34.615 0.00 0.17 37.42 1.89
341 366 7.902920 AATCTTCTACACCCGGTATAAGTTA 57.097 36.000 0.00 0.00 37.42 2.24
343 368 6.015603 GCTAATCTTCTACACCCGGTATAAGT 60.016 42.308 0.00 0.00 37.42 2.24
344 369 6.208994 AGCTAATCTTCTACACCCGGTATAAG 59.791 42.308 0.00 0.00 37.46 1.73
361 386 3.484407 GATGGCATGGACAAGCTAATCT 58.516 45.455 3.81 0.00 0.00 2.40
399 426 5.851720 TGGATTGTAACGGTTGTAACTACA 58.148 37.500 3.07 0.00 0.00 2.74
400 427 6.783892 TTGGATTGTAACGGTTGTAACTAC 57.216 37.500 3.07 0.00 0.00 2.73
403 430 6.243811 TCATTGGATTGTAACGGTTGTAAC 57.756 37.500 3.07 0.00 0.00 2.50
410 437 4.963276 ACACATCATTGGATTGTAACGG 57.037 40.909 0.00 0.00 0.00 4.44
411 438 5.937187 TGAACACATCATTGGATTGTAACG 58.063 37.500 0.00 0.00 31.50 3.18
420 447 8.601476 CGATCATCTATATGAACACATCATTGG 58.399 37.037 0.00 0.00 46.85 3.16
524 556 4.588951 ACGCAATCCATAGGATAGAAGTCA 59.411 41.667 0.00 0.00 42.27 3.41
532 564 3.181455 TGCACTAACGCAATCCATAGGAT 60.181 43.478 0.00 0.00 45.46 3.24
570 1794 0.259938 GATGGCAAGGAGAATGGGGT 59.740 55.000 0.00 0.00 0.00 4.95
619 1851 3.077359 AGAAAGAGAACGGAATGGCTTG 58.923 45.455 0.00 0.00 0.00 4.01
692 1925 4.735132 GCAGGCAGACGTACGGCA 62.735 66.667 25.52 0.00 41.24 5.69
702 1935 2.535485 TATTGGTGGACGGCAGGCAG 62.535 60.000 0.00 0.00 0.00 4.85
713 1946 6.071728 GCCAAGATCCAGATAAATATTGGTGG 60.072 42.308 9.67 0.00 38.53 4.61
728 1961 0.247460 CTCGTGACAGCCAAGATCCA 59.753 55.000 0.00 0.00 32.98 3.41
734 1967 0.390340 GCATCTCTCGTGACAGCCAA 60.390 55.000 0.00 0.00 0.00 4.52
735 1968 1.216444 GCATCTCTCGTGACAGCCA 59.784 57.895 0.00 0.00 0.00 4.75
736 1969 1.520342 GGCATCTCTCGTGACAGCC 60.520 63.158 4.86 4.86 34.75 4.85
737 1970 0.805322 CTGGCATCTCTCGTGACAGC 60.805 60.000 0.00 0.00 44.97 4.40
738 1971 3.342395 CTGGCATCTCTCGTGACAG 57.658 57.895 0.00 0.00 45.46 3.51
739 1972 0.813821 CTCTGGCATCTCTCGTGACA 59.186 55.000 0.00 0.00 32.68 3.58
740 1973 1.098869 TCTCTGGCATCTCTCGTGAC 58.901 55.000 0.00 0.00 0.00 3.67
741 1974 1.747924 CTTCTCTGGCATCTCTCGTGA 59.252 52.381 0.00 0.00 0.00 4.35
743 1976 1.110442 CCTTCTCTGGCATCTCTCGT 58.890 55.000 0.00 0.00 0.00 4.18
744 1977 0.388659 CCCTTCTCTGGCATCTCTCG 59.611 60.000 0.00 0.00 0.00 4.04
745 1978 1.688197 CTCCCTTCTCTGGCATCTCTC 59.312 57.143 0.00 0.00 0.00 3.20
746 1979 1.290431 TCTCCCTTCTCTGGCATCTCT 59.710 52.381 0.00 0.00 0.00 3.10
747 1980 1.786937 TCTCCCTTCTCTGGCATCTC 58.213 55.000 0.00 0.00 0.00 2.75
771 2005 1.698506 CTCCTTCCTACCTCGCTCAT 58.301 55.000 0.00 0.00 0.00 2.90
788 2022 1.739049 CTCGATCCCACTGCTCCTC 59.261 63.158 0.00 0.00 0.00 3.71
789 2023 1.760086 CCTCGATCCCACTGCTCCT 60.760 63.158 0.00 0.00 0.00 3.69
791 2025 2.801631 CCCCTCGATCCCACTGCTC 61.802 68.421 0.00 0.00 0.00 4.26
792 2026 2.765807 CCCCTCGATCCCACTGCT 60.766 66.667 0.00 0.00 0.00 4.24
794 2028 0.106167 TACTCCCCTCGATCCCACTG 60.106 60.000 0.00 0.00 0.00 3.66
795 2029 0.106116 GTACTCCCCTCGATCCCACT 60.106 60.000 0.00 0.00 0.00 4.00
803 2041 2.165845 CCTTTACACTGTACTCCCCTCG 59.834 54.545 0.00 0.00 0.00 4.63
807 2045 3.322828 TGTGACCTTTACACTGTACTCCC 59.677 47.826 0.00 0.00 38.81 4.30
818 2056 3.002348 GCTCAACAGTGTGTGACCTTTAC 59.998 47.826 0.00 0.00 0.00 2.01
825 2063 4.065088 GGATAAAGCTCAACAGTGTGTGA 58.935 43.478 0.00 2.35 0.00 3.58
847 2137 2.429058 CCTCCCCATGGATGCTCG 59.571 66.667 15.22 0.00 40.80 5.03
855 2145 2.449322 CCTCCCTCCCTCCCCATG 60.449 72.222 0.00 0.00 0.00 3.66
859 2149 2.040359 CCTTCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
860 2150 0.692756 CTTCCTTCCTCCCTCCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
861 2151 1.341913 GCTTCCTTCCTCCCTCCCTC 61.342 65.000 0.00 0.00 0.00 4.30
862 2152 1.307430 GCTTCCTTCCTCCCTCCCT 60.307 63.158 0.00 0.00 0.00 4.20
863 2153 1.208165 TTGCTTCCTTCCTCCCTCCC 61.208 60.000 0.00 0.00 0.00 4.30
864 2154 0.254462 CTTGCTTCCTTCCTCCCTCC 59.746 60.000 0.00 0.00 0.00 4.30
865 2155 0.393673 GCTTGCTTCCTTCCTCCCTC 60.394 60.000 0.00 0.00 0.00 4.30
866 2156 1.136329 TGCTTGCTTCCTTCCTCCCT 61.136 55.000 0.00 0.00 0.00 4.20
936 2230 2.357517 GGCGACTGTGGGAGTGTG 60.358 66.667 0.00 0.00 33.83 3.82
937 2231 2.172483 GATGGCGACTGTGGGAGTGT 62.172 60.000 0.00 0.00 33.83 3.55
938 2232 1.448540 GATGGCGACTGTGGGAGTG 60.449 63.158 0.00 0.00 33.83 3.51
939 2233 1.267574 ATGATGGCGACTGTGGGAGT 61.268 55.000 0.00 0.00 37.76 3.85
940 2234 0.531532 GATGATGGCGACTGTGGGAG 60.532 60.000 0.00 0.00 0.00 4.30
941 2235 1.522092 GATGATGGCGACTGTGGGA 59.478 57.895 0.00 0.00 0.00 4.37
942 2236 1.524621 GGATGATGGCGACTGTGGG 60.525 63.158 0.00 0.00 0.00 4.61
943 2237 0.531532 GAGGATGATGGCGACTGTGG 60.532 60.000 0.00 0.00 0.00 4.17
944 2238 0.873312 CGAGGATGATGGCGACTGTG 60.873 60.000 0.00 0.00 0.00 3.66
945 2239 1.439228 CGAGGATGATGGCGACTGT 59.561 57.895 0.00 0.00 0.00 3.55
1338 2729 2.791927 CTGATGCGTCGGTCGAGA 59.208 61.111 6.59 0.00 42.86 4.04
1563 2956 1.229529 TTCTCCCCGGGCTTTCTCT 60.230 57.895 17.73 0.00 0.00 3.10
1597 3150 3.327404 GGCTTTGTCCGAGGGGGA 61.327 66.667 0.00 0.00 44.68 4.81
2493 5001 4.393155 ATGGCCGTCTTGAGCGCA 62.393 61.111 11.47 0.00 0.00 6.09
2707 5221 1.375268 GGCTGGCAGAGAGACACAC 60.375 63.158 20.86 0.00 0.00 3.82
3105 5781 1.194781 AGATGGAGGTCCGCAGTTGT 61.195 55.000 0.00 0.00 39.43 3.32
3268 5956 2.621055 CACCTTTGTTTCGGATGGACAA 59.379 45.455 0.00 0.00 0.00 3.18
3303 6033 0.675083 TCAGGTACTTCCGTTTCGCA 59.325 50.000 0.00 0.00 41.99 5.10
3312 6042 1.565305 CGAGCAGCATCAGGTACTTC 58.435 55.000 0.00 0.00 34.60 3.01
3420 6150 3.861797 GATGGGGACGGCGATGGT 61.862 66.667 16.62 0.00 0.00 3.55
3580 6334 2.604174 CGGCGCTTTTCTTCACGGT 61.604 57.895 7.64 0.00 0.00 4.83
3747 6510 2.729862 GCGTCGAACGACAGCAGT 60.730 61.111 25.37 0.00 46.05 4.40
3776 6539 1.303317 ACCGTGATTGCCTTCACCC 60.303 57.895 9.73 0.00 42.46 4.61
3785 6548 2.143122 AGTACTTGCACACCGTGATTG 58.857 47.619 5.28 0.00 35.23 2.67
3786 6549 2.543777 AGTACTTGCACACCGTGATT 57.456 45.000 5.28 0.00 35.23 2.57
3787 6550 2.543777 AAGTACTTGCACACCGTGAT 57.456 45.000 7.48 0.00 35.23 3.06
3813 6576 3.056607 CCCACACCTGTTTTTCCATCATC 60.057 47.826 0.00 0.00 0.00 2.92
3827 6590 3.260100 CCAAGGGCTCCCACACCT 61.260 66.667 7.82 0.00 38.92 4.00
3835 6598 0.328258 TTGCTAACTCCCAAGGGCTC 59.672 55.000 0.00 0.00 34.68 4.70
3875 6638 0.248336 CACGCTGCTACCGATTACGA 60.248 55.000 0.00 0.00 42.66 3.43
3878 6641 3.067040 TGATTACACGCTGCTACCGATTA 59.933 43.478 0.00 0.00 0.00 1.75
4016 6790 7.378728 GTGCTCTGTTTTGGTTTGTCTATTTAC 59.621 37.037 0.00 0.00 0.00 2.01
4042 6816 5.961395 AACTATTCGTTTGGCATAGTACG 57.039 39.130 0.00 0.00 33.44 3.67
4089 6865 9.511272 TGTGCTATTTCATTCATATCTAATGCT 57.489 29.630 3.40 0.00 34.89 3.79
4116 6919 8.319881 CCATTGATATCTGTGAGGATTGTATCT 58.680 37.037 3.98 0.00 0.00 1.98
4166 6969 2.954318 AGAGCAGTGCAGTTGTTCAATT 59.046 40.909 19.20 0.00 0.00 2.32
4182 6985 2.158682 TGTCTGCAGGGTAAAAAGAGCA 60.159 45.455 15.13 0.00 0.00 4.26
4191 6994 1.260538 CCAGCTCTGTCTGCAGGGTA 61.261 60.000 15.13 0.00 44.91 3.69
4453 7256 0.543749 GATGGCCTTCTAGCACCAGT 59.456 55.000 11.34 0.00 35.20 4.00
4454 7257 0.179034 GGATGGCCTTCTAGCACCAG 60.179 60.000 17.48 0.00 35.20 4.00
4455 7258 0.913934 TGGATGGCCTTCTAGCACCA 60.914 55.000 17.48 4.64 36.43 4.17
4456 7259 0.475906 ATGGATGGCCTTCTAGCACC 59.524 55.000 17.48 2.01 34.31 5.01
4457 7260 1.419387 AGATGGATGGCCTTCTAGCAC 59.581 52.381 19.97 9.75 44.40 4.40
4458 7261 1.696336 GAGATGGATGGCCTTCTAGCA 59.304 52.381 19.97 10.07 45.74 3.49
4459 7262 1.696336 TGAGATGGATGGCCTTCTAGC 59.304 52.381 17.48 14.61 45.74 3.42
4460 7263 3.237746 TCTGAGATGGATGGCCTTCTAG 58.762 50.000 17.48 7.58 45.74 2.43
4461 7264 3.334910 TCTGAGATGGATGGCCTTCTA 57.665 47.619 17.48 12.64 45.74 2.10
4545 7349 0.813184 CATGACCGCCTTGCATTCTT 59.187 50.000 0.00 0.00 0.00 2.52
4546 7350 0.035152 TCATGACCGCCTTGCATTCT 60.035 50.000 0.00 0.00 0.00 2.40
4557 7361 0.887836 CCATCCCAGCATCATGACCG 60.888 60.000 0.00 0.00 0.00 4.79
4561 7365 2.359981 ACTTCCATCCCAGCATCATG 57.640 50.000 0.00 0.00 0.00 3.07
4570 7374 3.118775 GGTTTGCCAATTACTTCCATCCC 60.119 47.826 0.00 0.00 34.09 3.85
4586 7390 1.977293 TTGGGGCCTGTTTGGTTTGC 61.977 55.000 0.84 0.00 38.35 3.68
4600 7404 4.568592 GCATTAGGAGGGAGATTATTGGGG 60.569 50.000 0.00 0.00 0.00 4.96
4605 7409 3.193691 CGTCGCATTAGGAGGGAGATTAT 59.806 47.826 0.00 0.00 0.00 1.28
4629 7433 0.037326 TTAGTTCTGCCAGACTGCCG 60.037 55.000 0.00 0.00 0.00 5.69
4652 7456 4.142622 TGCTTCATATTTCTTGCGACTTGG 60.143 41.667 0.00 0.00 0.00 3.61
4653 7457 4.790140 GTGCTTCATATTTCTTGCGACTTG 59.210 41.667 0.00 0.00 0.00 3.16
4654 7458 4.697352 AGTGCTTCATATTTCTTGCGACTT 59.303 37.500 0.00 0.00 0.00 3.01
4655 7459 4.256920 AGTGCTTCATATTTCTTGCGACT 58.743 39.130 0.00 0.00 0.00 4.18
4656 7460 4.606457 AGTGCTTCATATTTCTTGCGAC 57.394 40.909 0.00 0.00 0.00 5.19
4657 7461 6.925610 ATTAGTGCTTCATATTTCTTGCGA 57.074 33.333 0.00 0.00 0.00 5.10
4658 7462 9.110617 CATTATTAGTGCTTCATATTTCTTGCG 57.889 33.333 0.00 0.00 0.00 4.85
4700 7506 0.682292 TGCGTGTGTGAAGGGTGATA 59.318 50.000 0.00 0.00 0.00 2.15
4701 7507 0.603707 CTGCGTGTGTGAAGGGTGAT 60.604 55.000 0.00 0.00 0.00 3.06
4741 7553 5.718649 AGAAATGTCGGTTCGAACATATG 57.281 39.130 28.24 15.08 37.72 1.78
4742 7554 6.737254 AAAGAAATGTCGGTTCGAACATAT 57.263 33.333 28.24 13.80 37.72 1.78
4743 7555 6.869913 ACTAAAGAAATGTCGGTTCGAACATA 59.130 34.615 28.24 13.58 37.72 2.29
4752 7564 5.591067 TCCACAAAACTAAAGAAATGTCGGT 59.409 36.000 0.00 0.00 0.00 4.69
4852 7665 4.455877 AGAAGTATGTTGCAACTTACAGCC 59.544 41.667 36.93 28.51 40.20 4.85
4871 7684 9.995003 AGTGGAGCTTTGATTCTTATATAGAAG 57.005 33.333 0.41 0.41 45.69 2.85


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

AutoCloner maintained by Alex Coulton.