Multiple sequence alignment - TraesCS1A01G364100

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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 TraesCS1A01G364100 chr1A 100.000 6394 0 0 1 6394 544193514 544199907 0.000000e+00 11808.0
1 TraesCS1A01G364100 chr1A 87.973 582 24 22 4379 4956 544194200 544194739 0.000000e+00 645.0
2 TraesCS1A01G364100 chr1A 87.973 582 24 22 687 1226 544197892 544198469 0.000000e+00 645.0
3 TraesCS1A01G364100 chr1A 97.436 312 7 1 3193 3504 279824476 279824786 1.220000e-146 531.0
4 TraesCS1A01G364100 chr1A 92.910 268 18 1 2031 2297 405459925 405459658 7.770000e-104 388.0
5 TraesCS1A01G364100 chr1A 91.606 274 22 1 2033 2305 73312158 73312431 1.680000e-100 377.0
6 TraesCS1A01G364100 chr1A 86.420 324 23 13 4967 5290 544194684 544194986 1.030000e-87 335.0
7 TraesCS1A01G364100 chr1A 86.420 324 23 14 1171 1473 544198480 544198803 1.030000e-87 335.0
8 TraesCS1A01G364100 chr1A 93.839 211 13 0 481 691 544193121 544192911 1.030000e-82 318.0
9 TraesCS1A01G364100 chr1A 80.488 410 54 12 4900 5290 544176974 544177376 2.260000e-74 291.0
10 TraesCS1A01G364100 chr1A 87.600 250 27 4 1199 1446 430343146 430342899 2.920000e-73 287.0
11 TraesCS1A01G364100 chr1A 82.609 345 38 9 4963 5290 544318892 544319231 1.050000e-72 285.0
12 TraesCS1A01G364100 chr1A 83.041 171 25 3 1171 1339 544177041 544177209 1.110000e-32 152.0
13 TraesCS1A01G364100 chr1A 89.189 111 4 4 4396 4498 544292704 544292814 1.450000e-26 132.0
14 TraesCS1A01G364100 chr1A 94.444 54 3 0 5321 5374 544319290 544319343 4.110000e-12 84.2
15 TraesCS1A01G364100 chr1B 87.164 966 53 35 4329 5290 614277851 614278749 0.000000e+00 1031.0
16 TraesCS1A01G364100 chr1B 89.982 549 22 16 692 1226 614277907 614278436 0.000000e+00 678.0
17 TraesCS1A01G364100 chr1B 77.545 1336 147 78 4329 5618 614291994 614293222 0.000000e+00 664.0
18 TraesCS1A01G364100 chr1B 84.897 629 45 22 739 1337 614292083 614292691 1.990000e-164 590.0
19 TraesCS1A01G364100 chr1B 98.714 311 4 0 3194 3504 628011118 628010808 2.610000e-153 553.0
20 TraesCS1A01G364100 chr1B 88.218 348 35 6 1200 1544 614183767 614184111 1.660000e-110 411.0
21 TraesCS1A01G364100 chr1B 90.820 305 25 1 1307 1611 614278583 614278884 7.720000e-109 405.0
22 TraesCS1A01G364100 chr1B 83.406 458 38 9 5772 6202 614329626 614330072 2.160000e-104 390.0
23 TraesCS1A01G364100 chr1B 88.424 311 31 3 3939 4246 614290996 614291304 2.820000e-98 370.0
24 TraesCS1A01G364100 chr1B 84.795 342 27 12 1317 1636 614292704 614293042 2.880000e-83 320.0
25 TraesCS1A01G364100 chr1B 93.878 196 5 5 6205 6394 614330242 614330436 8.110000e-74 289.0
26 TraesCS1A01G364100 chr1B 79.333 450 48 18 4963 5374 614442823 614443265 2.270000e-69 274.0
27 TraesCS1A01G364100 chr1B 77.778 441 68 21 4714 5132 614183417 614183849 1.780000e-60 244.0
28 TraesCS1A01G364100 chr1B 77.064 436 74 23 4874 5290 614183612 614184040 1.790000e-55 228.0
29 TraesCS1A01G364100 chr1B 77.667 403 60 15 4908 5290 614425723 614426115 1.080000e-52 219.0
30 TraesCS1A01G364100 chr1B 95.918 98 2 2 4403 4498 614417002 614417099 2.390000e-34 158.0
31 TraesCS1A01G364100 chr1B 74.201 438 72 30 809 1222 614183237 614183657 1.860000e-30 145.0
32 TraesCS1A01G364100 chr1B 90.722 97 7 2 710 805 614442215 614442310 1.870000e-25 128.0
33 TraesCS1A01G364100 chr1B 97.959 49 1 0 2939 2987 212947798 212947846 1.140000e-12 86.1
34 TraesCS1A01G364100 chr2B 95.912 636 23 2 58 691 227683143 227683777 0.000000e+00 1027.0
35 TraesCS1A01G364100 chr2B 93.365 211 14 0 481 691 227681940 227681730 4.810000e-81 313.0
36 TraesCS1A01G364100 chr2B 100.000 38 0 0 1 38 227682331 227682368 3.200000e-08 71.3
37 TraesCS1A01G364100 chr2B 85.484 62 4 3 3869 3925 29129220 29129281 6.920000e-05 60.2
38 TraesCS1A01G364100 chr2A 95.440 636 19 5 58 691 737478497 737479124 0.000000e+00 1005.0
39 TraesCS1A01G364100 chr2A 97.097 310 9 0 3193 3502 526340997 526340688 2.040000e-144 523.0
40 TraesCS1A01G364100 chr2A 96.440 309 11 0 3197 3505 652480585 652480277 1.590000e-140 510.0
41 TraesCS1A01G364100 chr2A 93.839 211 13 0 481 691 737477376 737477166 1.030000e-82 318.0
42 TraesCS1A01G364100 chr1D 86.089 992 70 35 691 1627 448376487 448377465 0.000000e+00 1005.0
43 TraesCS1A01G364100 chr1D 81.846 1300 100 59 4329 5576 448423803 448425018 0.000000e+00 968.0
44 TraesCS1A01G364100 chr1D 83.861 979 71 39 4329 5290 448388600 448389508 0.000000e+00 852.0
45 TraesCS1A01G364100 chr1D 86.136 678 47 21 5754 6394 448428264 448428931 0.000000e+00 688.0
46 TraesCS1A01G364100 chr1D 86.156 679 38 25 4335 4997 448376438 448377076 0.000000e+00 682.0
47 TraesCS1A01G364100 chr1D 84.097 698 49 29 692 1339 448388656 448389341 9.110000e-173 617.0
48 TraesCS1A01G364100 chr1D 83.618 702 63 27 692 1351 448423859 448424550 4.240000e-171 612.0
49 TraesCS1A01G364100 chr1D 89.216 306 33 0 1226 1531 448640195 448640500 3.620000e-102 383.0
50 TraesCS1A01G364100 chr1D 78.444 617 72 41 4945 5538 448376991 448377569 4.750000e-91 346.0
51 TraesCS1A01G364100 chr1D 84.659 352 29 10 1307 1636 448424539 448424887 1.720000e-85 327.0
52 TraesCS1A01G364100 chr1D 84.969 326 33 10 1317 1636 448389352 448389667 3.720000e-82 316.0
53 TraesCS1A01G364100 chr1D 81.220 410 51 12 4900 5290 448283482 448283884 2.240000e-79 307.0
54 TraesCS1A01G364100 chr1D 81.690 355 40 12 1307 1636 448283718 448284072 8.170000e-69 272.0
55 TraesCS1A01G364100 chr1D 85.944 249 33 2 1199 1446 332703527 332703280 1.370000e-66 265.0
56 TraesCS1A01G364100 chr1D 81.587 315 42 13 4714 5022 448283234 448283538 4.950000e-61 246.0
57 TraesCS1A01G364100 chr1D 86.875 160 19 2 3038 3197 75102785 75102628 1.830000e-40 178.0
58 TraesCS1A01G364100 chr1D 94.792 96 5 0 710 805 448639480 448639575 3.990000e-32 150.0
59 TraesCS1A01G364100 chr1D 92.424 66 4 1 4272 4336 448423695 448423760 6.830000e-15 93.5
60 TraesCS1A01G364100 chr1D 83.516 91 9 2 4252 4336 448376310 448376400 5.310000e-11 80.5
61 TraesCS1A01G364100 chr1D 95.556 45 1 1 5613 5657 448425018 448425061 3.200000e-08 71.3
62 TraesCS1A01G364100 chr1D 97.222 36 1 0 4288 4323 448388520 448388555 1.920000e-05 62.1
63 TraesCS1A01G364100 chr5A 98.052 308 5 1 3195 3502 197207066 197206760 9.440000e-148 534.0
64 TraesCS1A01G364100 chr5A 93.156 263 16 2 2035 2295 104621188 104620926 1.010000e-102 385.0
65 TraesCS1A01G364100 chr5A 96.552 58 1 1 2938 2994 643192247 643192304 1.900000e-15 95.3
66 TraesCS1A01G364100 chr7D 90.141 426 19 9 58 468 592858073 592858490 3.390000e-147 532.0
67 TraesCS1A01G364100 chr7D 80.135 297 35 14 70 359 592634115 592633836 3.910000e-47 200.0
68 TraesCS1A01G364100 chr7D 92.727 55 2 2 2939 2991 407024212 407024266 1.910000e-10 78.7
69 TraesCS1A01G364100 chr7D 94.872 39 1 1 1 38 592857245 592857283 6.920000e-05 60.2
70 TraesCS1A01G364100 chr6A 97.386 306 8 0 3196 3501 550062378 550062683 7.350000e-144 521.0
71 TraesCS1A01G364100 chr6A 96.463 311 11 0 3194 3504 484569342 484569032 1.230000e-141 514.0
72 TraesCS1A01G364100 chr6A 93.704 270 16 1 2033 2302 524227665 524227933 2.780000e-108 403.0
73 TraesCS1A01G364100 chr6A 93.704 270 16 1 2033 2302 524253152 524252884 2.780000e-108 403.0
74 TraesCS1A01G364100 chr6A 96.078 51 1 1 2939 2988 521740848 521740898 1.480000e-11 82.4
75 TraesCS1A01G364100 chr4A 96.226 318 10 1 3194 3509 96276662 96276345 2.640000e-143 520.0
76 TraesCS1A01G364100 chr4A 93.511 262 16 1 2034 2294 396575434 396575173 7.770000e-104 388.0
77 TraesCS1A01G364100 chr4A 93.487 261 16 1 2035 2294 641546265 641546525 2.800000e-103 387.0
78 TraesCS1A01G364100 chr3A 95.584 317 14 0 3191 3507 29033369 29033685 5.720000e-140 508.0
79 TraesCS1A01G364100 chr3A 95.349 215 10 0 481 695 593341384 593341170 6.140000e-90 342.0
80 TraesCS1A01G364100 chr3A 93.868 212 13 0 481 692 7892939 7893150 2.880000e-83 320.0
81 TraesCS1A01G364100 chr3A 92.130 216 17 0 481 696 101906763 101906548 8.050000e-79 305.0
82 TraesCS1A01G364100 chr3A 91.667 48 4 0 3883 3930 574453007 574452960 4.140000e-07 67.6
83 TraesCS1A01G364100 chr7A 87.736 424 33 12 59 468 685228250 685228668 1.610000e-130 477.0
84 TraesCS1A01G364100 chr7A 93.893 262 15 1 2034 2295 344583631 344583371 1.670000e-105 394.0
85 TraesCS1A01G364100 chr7A 93.182 264 17 1 2033 2295 653720679 653720942 2.800000e-103 387.0
86 TraesCS1A01G364100 chr7A 81.000 300 36 11 70 363 685214590 685214306 1.080000e-52 219.0
87 TraesCS1A01G364100 chr7A 79.791 287 41 9 70 354 685095717 685095446 6.540000e-45 193.0
88 TraesCS1A01G364100 chr7A 97.297 37 1 0 2 38 685227519 685227555 5.350000e-06 63.9
89 TraesCS1A01G364100 chr6B 98.419 253 1 1 58 310 265822451 265822700 5.880000e-120 442.0
90 TraesCS1A01G364100 chr6B 93.426 289 19 0 407 695 265822699 265822987 4.580000e-116 429.0
91 TraesCS1A01G364100 chr6B 96.154 52 1 1 2939 2989 451110476 451110527 4.110000e-12 84.2
92 TraesCS1A01G364100 chr6B 97.368 38 1 0 1 38 265821681 265821718 1.490000e-06 65.8
93 TraesCS1A01G364100 chr7B 85.748 428 35 15 58 471 668914558 668914143 4.580000e-116 429.0
94 TraesCS1A01G364100 chr7B 94.340 53 2 1 2939 2990 534557319 534557371 5.310000e-11 80.5
95 TraesCS1A01G364100 chr7B 97.368 38 1 0 1 38 668915302 668915265 1.490000e-06 65.8
96 TraesCS1A01G364100 chr6D 88.125 160 17 2 3038 3197 82504026 82503869 8.460000e-44 189.0
97 TraesCS1A01G364100 chr6D 87.273 55 6 1 3873 3926 271737309 271737255 1.920000e-05 62.1
98 TraesCS1A01G364100 chr4D 94.118 51 3 0 2938 2988 171045115 171045165 1.910000e-10 78.7
99 TraesCS1A01G364100 chr4D 94.000 50 3 0 2939 2988 250692083 250692034 6.870000e-10 76.8
100 TraesCS1A01G364100 chr4D 95.745 47 1 1 2944 2989 53460442 53460488 2.470000e-09 75.0
101 TraesCS1A01G364100 chr4D 90.000 50 5 0 3876 3925 30420773 30420822 1.490000e-06 65.8
102 TraesCS1A01G364100 chr3D 97.561 41 1 0 3885 3925 304711025 304710985 3.200000e-08 71.3
103 TraesCS1A01G364100 chr4B 97.500 40 1 0 3887 3926 48680172 48680211 1.150000e-07 69.4
104 TraesCS1A01G364100 chrUn 91.489 47 4 0 3879 3925 320347995 320348041 1.490000e-06 65.8
105 TraesCS1A01G364100 chr5D 88.889 54 4 1 3891 3942 538568889 538568836 1.490000e-06 65.8
106 TraesCS1A01G364100 chr5D 100.000 30 0 0 1971 2000 463402824 463402853 8.960000e-04 56.5
107 TraesCS1A01G364100 chr2D 87.719 57 3 2 3891 3943 190218747 190218691 5.350000e-06 63.9


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 TraesCS1A01G364100 chr1A 544193514 544199907 6393 False 11808.000000 11808 100.000000 1 6394 1 chr1A.!!$F3 6393
1 TraesCS1A01G364100 chr1A 544194200 544198803 4603 False 490.000000 645 87.196500 687 5290 4 chr1A.!!$F6 4603
2 TraesCS1A01G364100 chr1B 614277851 614278884 1033 False 704.666667 1031 89.322000 692 5290 3 chr1B.!!$F5 4598
3 TraesCS1A01G364100 chr1B 614290996 614293222 2226 False 486.000000 664 83.915250 739 5618 4 chr1B.!!$F6 4879
4 TraesCS1A01G364100 chr1B 614329626 614330436 810 False 339.500000 390 88.642000 5772 6394 2 chr1B.!!$F7 622
5 TraesCS1A01G364100 chr1B 614183237 614184111 874 False 257.000000 411 79.315250 809 5290 4 chr1B.!!$F4 4481
6 TraesCS1A01G364100 chr1B 614442215 614443265 1050 False 201.000000 274 85.027500 710 5374 2 chr1B.!!$F8 4664
7 TraesCS1A01G364100 chr2B 227682331 227683777 1446 False 549.150000 1027 97.956000 1 691 2 chr2B.!!$F2 690
8 TraesCS1A01G364100 chr2A 737478497 737479124 627 False 1005.000000 1005 95.440000 58 691 1 chr2A.!!$F1 633
9 TraesCS1A01G364100 chr1D 448376310 448377569 1259 False 528.375000 1005 83.551250 691 5538 4 chr1D.!!$F2 4847
10 TraesCS1A01G364100 chr1D 448388520 448389667 1147 False 461.775000 852 87.537250 692 5290 4 chr1D.!!$F3 4598
11 TraesCS1A01G364100 chr1D 448423695 448428931 5236 False 459.966667 968 87.373167 692 6394 6 chr1D.!!$F4 5702
12 TraesCS1A01G364100 chr1D 448283234 448284072 838 False 275.000000 307 81.499000 1307 5290 3 chr1D.!!$F1 3983
13 TraesCS1A01G364100 chr1D 448639480 448640500 1020 False 266.500000 383 92.004000 710 1531 2 chr1D.!!$F5 821
14 TraesCS1A01G364100 chr7D 592857245 592858490 1245 False 296.100000 532 92.506500 1 468 2 chr7D.!!$F2 467
15 TraesCS1A01G364100 chr7A 685227519 685228668 1149 False 270.450000 477 92.516500 2 468 2 chr7A.!!$F2 466
16 TraesCS1A01G364100 chr6B 265821681 265822987 1306 False 312.266667 442 96.404333 1 695 3 chr6B.!!$F2 694
17 TraesCS1A01G364100 chr7B 668914143 668915302 1159 True 247.400000 429 91.558000 1 471 2 chr7B.!!$R1 470

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
448 1392 1.135315 GGTGCGTGCATGTTAGCTG 59.865 57.895 7.93 0.0 34.99 4.24 F
5310 7396 0.179045 GAACACGCTAGGCATGGGAT 60.179 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5316 7415 2.594303 TGTCCTTTGTGGCGCCAG 60.594 61.111 33.73 18.75 35.26 4.85 R
6144 11439 1.349627 CCACGCTTTATGCTGCTCG 59.650 57.895 0.00 0.00 40.11 5.03 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
38 40 4.207165 CATGGTCCAACCCTTCGAATTAT 58.793 43.478 0.00 0.00 37.50 1.28
39 41 3.616219 TGGTCCAACCCTTCGAATTATG 58.384 45.455 0.00 0.00 37.50 1.90
40 42 2.949644 GGTCCAACCCTTCGAATTATGG 59.050 50.000 0.00 5.73 30.04 2.74
42 44 3.377172 GTCCAACCCTTCGAATTATGGTG 59.623 47.826 14.97 6.79 0.00 4.17
44 46 4.080015 TCCAACCCTTCGAATTATGGTGAT 60.080 41.667 14.97 0.00 0.00 3.06
45 47 4.275936 CCAACCCTTCGAATTATGGTGATC 59.724 45.833 0.00 0.00 0.00 2.92
48 50 4.080582 ACCCTTCGAATTATGGTGATCACA 60.081 41.667 26.47 13.45 0.00 3.58
49 51 4.273480 CCCTTCGAATTATGGTGATCACAC 59.727 45.833 26.47 16.16 45.27 3.82
411 1355 1.203052 GGTGATCAATTGCACTGGGTG 59.797 52.381 13.65 0.00 35.43 4.61
448 1392 1.135315 GGTGCGTGCATGTTAGCTG 59.865 57.895 7.93 0.00 34.99 4.24
479 1423 1.957186 GTTGTCGCCGTGCTTACCA 60.957 57.895 0.00 0.00 0.00 3.25
609 1553 4.133820 CACATAGGGTGTCAAGTTTGTGA 58.866 43.478 0.00 0.00 42.75 3.58
628 1572 5.924356 TGTGAAGTCCTCAGTCACATTTTA 58.076 37.500 1.74 0.00 45.02 1.52
635 1579 6.483640 AGTCCTCAGTCACATTTTACAAGTTC 59.516 38.462 0.00 0.00 0.00 3.01
673 1617 1.686355 TCGGTGCAAGTTTGTGGATT 58.314 45.000 0.00 0.00 0.00 3.01
675 1619 3.215151 TCGGTGCAAGTTTGTGGATTTA 58.785 40.909 0.00 0.00 0.00 1.40
676 1620 3.632604 TCGGTGCAAGTTTGTGGATTTAA 59.367 39.130 0.00 0.00 0.00 1.52
5309 7395 1.220749 GAACACGCTAGGCATGGGA 59.779 57.895 0.00 0.00 0.00 4.37
5310 7396 0.179045 GAACACGCTAGGCATGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
5313 7412 0.882042 CACGCTAGGCATGGGATCAC 60.882 60.000 0.00 0.00 0.00 3.06
5326 7425 3.899981 GATCACCACTGGCGCCACA 62.900 63.158 29.03 5.41 0.00 4.17
5388 7511 2.032054 CGCATGCATACGTCCAATCTTT 59.968 45.455 19.57 0.00 0.00 2.52
5407 7530 6.594788 TCTTTGCTGATTTGCTTCCTTTAT 57.405 33.333 0.00 0.00 0.00 1.40
5409 7532 8.121305 TCTTTGCTGATTTGCTTCCTTTATTA 57.879 30.769 0.00 0.00 0.00 0.98
5411 7534 7.466746 TTGCTGATTTGCTTCCTTTATTACT 57.533 32.000 0.00 0.00 0.00 2.24
5412 7535 7.088589 TGCTGATTTGCTTCCTTTATTACTC 57.911 36.000 0.00 0.00 0.00 2.59
5419 7552 5.310451 TGCTTCCTTTATTACTCGTTTGGT 58.690 37.500 0.00 0.00 0.00 3.67
5432 7565 6.980051 ACTCGTTTGGTCCTTTTACATATC 57.020 37.500 0.00 0.00 0.00 1.63
5457 7593 6.303054 TGTATGTTTCCCTCTTGTGATTTCA 58.697 36.000 0.00 0.00 0.00 2.69
5462 7598 2.005451 CCCTCTTGTGATTTCAGCTCG 58.995 52.381 0.00 0.00 0.00 5.03
5473 7609 6.480651 TGTGATTTCAGCTCGTTTAGTGTAAA 59.519 34.615 0.00 0.00 0.00 2.01
5490 7626 6.381801 AGTGTAAATTTGCCTTCGATTTGAG 58.618 36.000 0.00 0.00 0.00 3.02
5524 7662 5.416947 GTGTCCGGTTCTGTAATGAGTTAT 58.583 41.667 0.00 0.00 0.00 1.89
5525 7663 6.567050 GTGTCCGGTTCTGTAATGAGTTATA 58.433 40.000 0.00 0.00 0.00 0.98
5526 7664 7.037438 GTGTCCGGTTCTGTAATGAGTTATAA 58.963 38.462 0.00 0.00 0.00 0.98
5527 7665 7.709613 GTGTCCGGTTCTGTAATGAGTTATAAT 59.290 37.037 0.00 0.00 0.00 1.28
5528 7666 7.924412 TGTCCGGTTCTGTAATGAGTTATAATC 59.076 37.037 0.00 0.00 0.00 1.75
5529 7667 7.384387 GTCCGGTTCTGTAATGAGTTATAATCC 59.616 40.741 0.00 0.00 0.00 3.01
5531 7669 7.878127 CCGGTTCTGTAATGAGTTATAATCCAT 59.122 37.037 0.00 0.00 0.00 3.41
5532 7670 8.712363 CGGTTCTGTAATGAGTTATAATCCATG 58.288 37.037 4.10 0.00 0.00 3.66
5576 7723 1.213013 CGAGGACAGTCGAAGGTGG 59.787 63.158 0.00 0.00 42.85 4.61
5583 7730 3.270877 GACAGTCGAAGGTGGCAATAAT 58.729 45.455 0.00 0.00 0.00 1.28
5584 7731 4.439057 GACAGTCGAAGGTGGCAATAATA 58.561 43.478 0.00 0.00 0.00 0.98
5587 7734 6.588204 ACAGTCGAAGGTGGCAATAATATTA 58.412 36.000 0.00 0.00 0.00 0.98
5588 7735 6.706270 ACAGTCGAAGGTGGCAATAATATTAG 59.294 38.462 1.02 0.00 0.00 1.73
5593 7740 9.048446 TCGAAGGTGGCAATAATATTAGTTTAC 57.952 33.333 1.02 0.00 0.00 2.01
5594 7741 8.007716 CGAAGGTGGCAATAATATTAGTTTACG 58.992 37.037 1.02 0.00 0.00 3.18
5595 7742 7.739498 AGGTGGCAATAATATTAGTTTACGG 57.261 36.000 1.02 0.00 0.00 4.02
5596 7743 7.511268 AGGTGGCAATAATATTAGTTTACGGA 58.489 34.615 1.02 0.00 0.00 4.69
5598 7745 7.658575 GGTGGCAATAATATTAGTTTACGGAGA 59.341 37.037 1.02 0.00 0.00 3.71
5599 7746 8.709646 GTGGCAATAATATTAGTTTACGGAGAG 58.290 37.037 1.02 0.00 0.00 3.20
5601 7748 9.141400 GGCAATAATATTAGTTTACGGAGAGAG 57.859 37.037 1.02 0.00 0.00 3.20
5657 7804 6.660887 GAAGCTTTCTTCACTTCCTATCTG 57.339 41.667 0.00 0.00 46.14 2.90
5659 7806 5.486526 AGCTTTCTTCACTTCCTATCTGTG 58.513 41.667 0.00 0.00 0.00 3.66
5660 7807 4.094146 GCTTTCTTCACTTCCTATCTGTGC 59.906 45.833 0.00 0.00 0.00 4.57
5661 7808 3.510388 TCTTCACTTCCTATCTGTGCG 57.490 47.619 0.00 0.00 0.00 5.34
5684 10876 4.040755 AGTCCCAAACAGGCTCTACATAT 58.959 43.478 0.00 0.00 35.39 1.78
5695 10887 5.529060 CAGGCTCTACATATTGGTTTCCTTC 59.471 44.000 0.00 0.00 0.00 3.46
5701 10893 9.231297 CTCTACATATTGGTTTCCTTCTGAAAA 57.769 33.333 0.00 0.00 44.30 2.29
5705 10897 5.549742 ATTGGTTTCCTTCTGAAAATGCA 57.450 34.783 0.00 0.00 44.30 3.96
5706 10898 5.350504 TTGGTTTCCTTCTGAAAATGCAA 57.649 34.783 0.00 0.00 44.30 4.08
5707 10899 5.549742 TGGTTTCCTTCTGAAAATGCAAT 57.450 34.783 0.00 0.00 44.30 3.56
5708 10900 5.927819 TGGTTTCCTTCTGAAAATGCAATT 58.072 33.333 0.00 0.00 44.30 2.32
5709 10901 5.990996 TGGTTTCCTTCTGAAAATGCAATTC 59.009 36.000 8.29 8.29 44.30 2.17
5710 10902 5.990996 GGTTTCCTTCTGAAAATGCAATTCA 59.009 36.000 15.13 15.13 44.30 2.57
5711 10903 6.073602 GGTTTCCTTCTGAAAATGCAATTCAC 60.074 38.462 12.72 0.55 44.30 3.18
5712 10904 4.797471 TCCTTCTGAAAATGCAATTCACG 58.203 39.130 12.72 9.92 33.67 4.35
5713 10905 4.278170 TCCTTCTGAAAATGCAATTCACGT 59.722 37.500 12.72 0.00 33.67 4.49
5714 10906 4.984161 CCTTCTGAAAATGCAATTCACGTT 59.016 37.500 12.72 0.00 33.67 3.99
5715 10907 5.463061 CCTTCTGAAAATGCAATTCACGTTT 59.537 36.000 12.72 0.00 33.67 3.60
5721 10913 8.586570 TGAAAATGCAATTCACGTTTAATCTT 57.413 26.923 12.72 0.00 33.67 2.40
5735 10927 8.285394 CACGTTTAATCTTATTGATAGCTGCAT 58.715 33.333 1.02 0.00 34.45 3.96
5755 10947 6.866179 GCATTTCTTCATGCTTGAAACTAG 57.134 37.500 15.12 4.86 45.35 2.57
5756 10948 6.615088 GCATTTCTTCATGCTTGAAACTAGA 58.385 36.000 15.12 6.98 45.35 2.43
5757 10949 7.086376 GCATTTCTTCATGCTTGAAACTAGAA 58.914 34.615 15.12 11.94 45.35 2.10
5758 10950 7.596248 GCATTTCTTCATGCTTGAAACTAGAAA 59.404 33.333 20.55 20.55 45.35 2.52
5759 10951 9.125906 CATTTCTTCATGCTTGAAACTAGAAAG 57.874 33.333 21.76 14.62 41.22 2.62
5760 10952 6.808008 TCTTCATGCTTGAAACTAGAAAGG 57.192 37.500 15.12 2.20 41.22 3.11
5761 10953 6.299141 TCTTCATGCTTGAAACTAGAAAGGT 58.701 36.000 15.12 0.00 41.22 3.50
5762 10954 7.450074 TCTTCATGCTTGAAACTAGAAAGGTA 58.550 34.615 15.12 0.00 41.22 3.08
5764 10956 5.643777 TCATGCTTGAAACTAGAAAGGTAGC 59.356 40.000 0.00 0.00 0.00 3.58
5765 10957 4.968259 TGCTTGAAACTAGAAAGGTAGCA 58.032 39.130 0.00 1.52 34.10 3.49
5766 10958 5.373222 TGCTTGAAACTAGAAAGGTAGCAA 58.627 37.500 0.00 0.00 33.63 3.91
5783 11049 2.887152 AGCAACCTGTCAAACCTTCATC 59.113 45.455 0.00 0.00 0.00 2.92
5793 11059 7.252612 TGTCAAACCTTCATCTCACCTTATA 57.747 36.000 0.00 0.00 0.00 0.98
5794 11060 7.861629 TGTCAAACCTTCATCTCACCTTATAT 58.138 34.615 0.00 0.00 0.00 0.86
5795 11061 8.988060 TGTCAAACCTTCATCTCACCTTATATA 58.012 33.333 0.00 0.00 0.00 0.86
5821 11087 9.745880 ATTCTTTCTTATATGCTTCAATGCAAG 57.254 29.630 0.00 0.00 46.61 4.01
5824 11090 9.577110 CTTTCTTATATGCTTCAATGCAAGAAA 57.423 29.630 11.18 11.18 46.61 2.52
5834 11100 5.034554 TCAATGCAAGAAAGAATGTCGAC 57.965 39.130 9.11 9.11 0.00 4.20
5918 11184 6.844696 ACCATGCTTAGTTATACATCAACG 57.155 37.500 0.00 0.00 0.00 4.10
5941 11207 5.207033 GTTTTGCATTTTGAAGTCATTGCC 58.793 37.500 0.00 0.00 0.00 4.52
5947 11213 5.220265 GCATTTTGAAGTCATTGCCATAACG 60.220 40.000 0.00 0.00 0.00 3.18
6034 11303 9.710900 ATTTCAAGACTGGGAAAAATAATTGAC 57.289 29.630 6.64 0.00 36.67 3.18
6040 11309 8.390921 AGACTGGGAAAAATAATTGACTAGGAA 58.609 33.333 0.00 0.00 0.00 3.36
6042 11311 9.547279 ACTGGGAAAAATAATTGACTAGGAATT 57.453 29.630 0.00 1.08 0.00 2.17
6091 11360 2.483876 TGAGAAAAGGCTGAACTGACG 58.516 47.619 0.00 0.00 0.00 4.35
6099 11368 1.583054 GCTGAACTGACGGTCTGTTT 58.417 50.000 26.99 15.21 38.41 2.83
6100 11369 2.547218 GGCTGAACTGACGGTCTGTTTA 60.547 50.000 26.99 22.96 38.41 2.01
6102 11371 3.746492 GCTGAACTGACGGTCTGTTTATT 59.254 43.478 26.99 11.21 38.41 1.40
6103 11372 4.213482 GCTGAACTGACGGTCTGTTTATTT 59.787 41.667 26.99 10.89 38.41 1.40
6144 11439 2.250646 TGCACATCAGCAGCAGAAC 58.749 52.632 0.00 0.00 40.11 3.01
6268 11735 5.803967 CAGCTGAGGAAAAATAACTGAATGC 59.196 40.000 8.42 0.00 0.00 3.56
6339 11806 2.184448 CATAATTTGCGGCCAAGAACG 58.816 47.619 2.24 0.00 31.52 3.95
6348 11815 1.165270 GGCCAAGAACGCTGTACAAT 58.835 50.000 0.00 0.00 0.00 2.71
6367 11837 8.095792 TGTACAATCATGCCTTTTCAATTTCAT 58.904 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 5.898911 CGTCTATCGTCGGTGTGATCACC 62.899 56.522 22.85 13.66 45.56 4.02
40 42 2.717530 GTCTATCGTCGGTGTGATCAC 58.282 52.381 19.27 19.27 43.19 3.06
42 44 1.333881 CCGTCTATCGTCGGTGTGATC 60.334 57.143 0.00 0.00 41.58 2.92
44 46 2.092374 CCGTCTATCGTCGGTGTGA 58.908 57.895 0.00 0.00 41.58 3.58
45 47 4.684265 CCGTCTATCGTCGGTGTG 57.316 61.111 0.00 0.00 41.58 3.82
51 53 1.588139 CGGGTTGCCGTCTATCGTC 60.588 63.158 0.00 0.00 37.94 4.20
52 54 2.493030 CGGGTTGCCGTCTATCGT 59.507 61.111 0.00 0.00 37.94 3.73
382 1319 7.201848 CCAGTGCAATTGATCACCATTAACTAT 60.202 37.037 10.34 0.00 33.90 2.12
411 1355 2.027837 ACCTTTGCTTCATTTGCATCCC 60.028 45.455 0.00 0.00 40.34 3.85
448 1392 1.125566 GCGACAACAACGGTAAGCTAC 59.874 52.381 0.00 0.00 0.00 3.58
457 1401 1.823260 TAAGCACGGCGACAACAACG 61.823 55.000 16.62 0.00 0.00 4.10
479 1423 2.002586 CTGGCGTTCACTCGATTCAAT 58.997 47.619 0.00 0.00 0.00 2.57
609 1553 6.357367 ACTTGTAAAATGTGACTGAGGACTT 58.643 36.000 0.00 0.00 0.00 3.01
635 1579 6.907212 GCACCGAATATGATGTTTTAGTTCAG 59.093 38.462 0.00 0.00 0.00 3.02
651 1595 2.852449 TCCACAAACTTGCACCGAATA 58.148 42.857 0.00 0.00 0.00 1.75
5309 7395 2.974692 TTTGTGGCGCCAGTGGTGAT 62.975 55.000 33.73 0.00 34.74 3.06
5310 7396 3.705934 TTTGTGGCGCCAGTGGTGA 62.706 57.895 33.73 10.20 34.74 4.02
5313 7412 3.673484 CCTTTGTGGCGCCAGTGG 61.673 66.667 33.73 24.23 0.00 4.00
5316 7415 2.594303 TGTCCTTTGTGGCGCCAG 60.594 61.111 33.73 18.75 35.26 4.85
5317 7416 2.594303 CTGTCCTTTGTGGCGCCA 60.594 61.111 29.03 29.03 35.26 5.69
5319 7418 3.286751 TGCTGTCCTTTGTGGCGC 61.287 61.111 0.00 0.00 35.26 6.53
5326 7425 1.071471 CTCGGTGGTGCTGTCCTTT 59.929 57.895 0.00 0.00 0.00 3.11
5388 7511 6.183360 CGAGTAATAAAGGAAGCAAATCAGCA 60.183 38.462 0.00 0.00 36.85 4.41
5407 7530 8.316214 AGATATGTAAAAGGACCAAACGAGTAA 58.684 33.333 0.00 0.00 0.00 2.24
5409 7532 6.594159 CAGATATGTAAAAGGACCAAACGAGT 59.406 38.462 0.00 0.00 0.00 4.18
5411 7534 6.469410 ACAGATATGTAAAAGGACCAAACGA 58.531 36.000 0.00 0.00 0.00 3.85
5412 7535 6.737254 ACAGATATGTAAAAGGACCAAACG 57.263 37.500 0.00 0.00 0.00 3.60
5432 7565 6.430925 TGAAATCACAAGAGGGAAACATACAG 59.569 38.462 0.00 0.00 0.00 2.74
5457 7593 4.760204 AGGCAAATTTACACTAAACGAGCT 59.240 37.500 0.00 0.00 0.00 4.09
5462 7598 8.424731 CAAATCGAAGGCAAATTTACACTAAAC 58.575 33.333 0.00 0.00 0.00 2.01
5473 7609 4.589908 AGTACCTCAAATCGAAGGCAAAT 58.410 39.130 0.60 0.00 0.00 2.32
5490 7626 1.354506 CCGGACACGATCGAGTACC 59.645 63.158 24.34 19.98 44.60 3.34
5495 7631 1.239296 ACAGAACCGGACACGATCGA 61.239 55.000 24.34 0.00 44.60 3.59
5496 7632 0.448990 TACAGAACCGGACACGATCG 59.551 55.000 14.88 14.88 44.60 3.69
5498 7634 2.494471 TCATTACAGAACCGGACACGAT 59.506 45.455 9.46 0.00 44.60 3.73
5528 7666 6.773976 ATCCATTTACACCAAAGTACATGG 57.226 37.500 14.31 14.31 46.45 3.66
5529 7667 8.902806 ACATATCCATTTACACCAAAGTACATG 58.097 33.333 0.00 0.00 33.86 3.21
5531 7669 9.961264 TTACATATCCATTTACACCAAAGTACA 57.039 29.630 0.00 0.00 0.00 2.90
5551 7698 3.376234 CCTTCGACTGTCCTCGTTACATA 59.624 47.826 1.55 0.00 35.10 2.29
5552 7699 2.163815 CCTTCGACTGTCCTCGTTACAT 59.836 50.000 1.55 0.00 35.10 2.29
5553 7700 1.538512 CCTTCGACTGTCCTCGTTACA 59.461 52.381 1.55 0.00 35.10 2.41
5554 7701 1.538950 ACCTTCGACTGTCCTCGTTAC 59.461 52.381 1.55 0.00 35.10 2.50
5576 7723 9.694137 ACTCTCTCCGTAAACTAATATTATTGC 57.306 33.333 0.00 0.00 0.00 3.56
5587 7734 7.921745 GCTTCAATAATACTCTCTCCGTAAACT 59.078 37.037 0.00 0.00 0.00 2.66
5588 7735 7.921745 AGCTTCAATAATACTCTCTCCGTAAAC 59.078 37.037 0.00 0.00 0.00 2.01
5593 7740 6.507900 TGAAGCTTCAATAATACTCTCTCCG 58.492 40.000 26.61 0.00 33.55 4.63
5618 7765 1.882352 GCTTCTGACAACCAACGGGAT 60.882 52.381 0.00 0.00 38.05 3.85
5619 7766 0.534203 GCTTCTGACAACCAACGGGA 60.534 55.000 0.00 0.00 38.05 5.14
5620 7767 0.535102 AGCTTCTGACAACCAACGGG 60.535 55.000 0.00 0.00 41.29 5.28
5651 7798 2.271800 GTTTGGGACTCGCACAGATAG 58.728 52.381 0.00 0.00 0.00 2.08
5657 7804 2.617274 GCCTGTTTGGGACTCGCAC 61.617 63.158 0.00 0.00 36.00 5.34
5659 7806 2.032681 AGCCTGTTTGGGACTCGC 59.967 61.111 0.00 0.00 36.00 5.03
5660 7807 0.895530 TAGAGCCTGTTTGGGACTCG 59.104 55.000 0.00 0.00 35.89 4.18
5661 7808 1.623811 TGTAGAGCCTGTTTGGGACTC 59.376 52.381 0.00 0.00 36.00 3.36
5684 10876 5.350504 TTGCATTTTCAGAAGGAAACCAA 57.649 34.783 0.00 0.00 44.89 3.67
5695 10887 8.231304 AGATTAAACGTGAATTGCATTTTCAG 57.769 30.769 11.65 9.13 33.95 3.02
5707 10899 8.335356 GCAGCTATCAATAAGATTAAACGTGAA 58.665 33.333 0.00 0.00 38.19 3.18
5708 10900 7.494298 TGCAGCTATCAATAAGATTAAACGTGA 59.506 33.333 0.00 0.00 38.19 4.35
5709 10901 7.630026 TGCAGCTATCAATAAGATTAAACGTG 58.370 34.615 0.00 0.00 38.19 4.49
5710 10902 7.786178 TGCAGCTATCAATAAGATTAAACGT 57.214 32.000 0.00 0.00 38.19 3.99
5711 10903 9.669353 AAATGCAGCTATCAATAAGATTAAACG 57.331 29.630 0.00 0.00 38.19 3.60
5735 10927 7.285401 ACCTTTCTAGTTTCAAGCATGAAGAAA 59.715 33.333 13.13 13.13 45.82 2.52
5759 10951 2.271944 AGGTTTGACAGGTTGCTACC 57.728 50.000 9.54 9.54 45.39 3.18
5760 10952 3.211045 TGAAGGTTTGACAGGTTGCTAC 58.789 45.455 0.00 0.00 0.00 3.58
5761 10953 3.569194 TGAAGGTTTGACAGGTTGCTA 57.431 42.857 0.00 0.00 0.00 3.49
5762 10954 2.435372 TGAAGGTTTGACAGGTTGCT 57.565 45.000 0.00 0.00 0.00 3.91
5764 10956 4.023707 GTGAGATGAAGGTTTGACAGGTTG 60.024 45.833 0.00 0.00 0.00 3.77
5765 10957 4.137543 GTGAGATGAAGGTTTGACAGGTT 58.862 43.478 0.00 0.00 0.00 3.50
5766 10958 3.496870 GGTGAGATGAAGGTTTGACAGGT 60.497 47.826 0.00 0.00 0.00 4.00
5795 11061 9.745880 CTTGCATTGAAGCATATAAGAAAGAAT 57.254 29.630 0.00 0.00 45.19 2.40
5796 11062 8.959548 TCTTGCATTGAAGCATATAAGAAAGAA 58.040 29.630 0.00 0.00 45.19 2.52
5802 11068 9.745880 ATTCTTTCTTGCATTGAAGCATATAAG 57.254 29.630 0.00 0.00 45.19 1.73
5821 11087 2.532973 CGATGCACGTCGACATTCTTTC 60.533 50.000 17.16 4.05 44.06 2.62
5824 11090 1.413767 GCGATGCACGTCGACATTCT 61.414 55.000 17.16 0.00 44.06 2.40
5834 11100 3.853330 CAACGAGGGCGATGCACG 61.853 66.667 0.00 0.00 45.66 5.34
5905 11171 8.695284 TCAAAATGCAAAACGTTGATGTATAAC 58.305 29.630 15.02 1.84 36.83 1.89
5918 11184 5.207033 GGCAATGACTTCAAAATGCAAAAC 58.793 37.500 13.63 0.00 36.42 2.43
6034 11303 8.483758 ACACACCCTATACACTTAAATTCCTAG 58.516 37.037 0.00 0.00 0.00 3.02
6040 11309 6.382919 ACCACACACCCTATACACTTAAAT 57.617 37.500 0.00 0.00 0.00 1.40
6042 11311 5.829062 AACCACACACCCTATACACTTAA 57.171 39.130 0.00 0.00 0.00 1.85
6053 11322 4.331968 TCTCATGAATAAACCACACACCC 58.668 43.478 0.00 0.00 0.00 4.61
6103 11372 9.990360 TGCATACGTAGGAAATAAATAAGATGA 57.010 29.630 12.12 0.00 0.00 2.92
6133 11428 3.024782 GCTGCTCGTTCTGCTGCTG 62.025 63.158 0.00 0.00 46.79 4.41
6144 11439 1.349627 CCACGCTTTATGCTGCTCG 59.650 57.895 0.00 0.00 40.11 5.03
6268 11735 2.026641 CTCCATTTAGCACATGGGTGG 58.973 52.381 0.00 0.00 45.38 4.61
6339 11806 4.439305 TGAAAAGGCATGATTGTACAGC 57.561 40.909 0.00 0.00 0.00 4.40
6348 11815 7.669427 ACTTACATGAAATTGAAAAGGCATGA 58.331 30.769 0.00 0.00 36.60 3.07


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

AutoCloner maintained by Alex Coulton.