Multiple sequence alignment - TraesCS1A01G244400

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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 TraesCS1A01G244400 chr1A 100.000 5027 0 0 1 5027 432593978 432588952 0.000000e+00 9284.0
1 TraesCS1A01G244400 chr1A 97.115 624 18 0 3595 4218 588987442 588986819 0.000000e+00 1053.0
2 TraesCS1A01G244400 chr1A 96.479 568 20 0 839 1406 532596065 532596632 0.000000e+00 939.0
3 TraesCS1A01G244400 chr1A 90.925 573 47 3 839 1406 532645553 532646125 0.000000e+00 765.0
4 TraesCS1A01G244400 chr1A 96.394 416 13 2 1 416 573880485 573880072 0.000000e+00 684.0
5 TraesCS1A01G244400 chr1A 96.145 415 13 3 2 416 432600803 432600392 0.000000e+00 675.0
6 TraesCS1A01G244400 chr1A 89.911 337 34 0 2967 3303 369497088 369497424 7.730000e-118 435.0
7 TraesCS1A01G244400 chr1A 88.489 278 23 6 1431 1701 532596829 532597104 1.350000e-85 327.0
8 TraesCS1A01G244400 chr1A 88.068 176 14 4 1431 1599 532646321 532646496 8.530000e-48 202.0
9 TraesCS1A01G244400 chr1A 86.331 139 11 1 2414 2552 566609401 566609271 1.460000e-30 145.0
10 TraesCS1A01G244400 chr5D 97.818 3299 59 4 1729 5027 366753034 366756319 0.000000e+00 5681.0
11 TraesCS1A01G244400 chr5D 97.537 2071 51 0 2466 4536 365180427 365182497 0.000000e+00 3542.0
12 TraesCS1A01G244400 chr5D 97.183 781 14 1 1737 2517 365179650 365180422 0.000000e+00 1314.0
13 TraesCS1A01G244400 chr5D 92.121 825 38 12 583 1406 366750379 366751177 0.000000e+00 1138.0
14 TraesCS1A01G244400 chr5D 96.436 505 16 2 4523 5027 365206297 365206799 0.000000e+00 832.0
15 TraesCS1A01G244400 chr5D 94.725 436 23 0 971 1406 365177356 365177791 0.000000e+00 678.0
16 TraesCS1A01G244400 chr5D 95.793 309 12 1 1431 1738 366751374 366751682 9.720000e-137 497.0
17 TraesCS1A01G244400 chr5D 95.793 309 10 2 1431 1738 365177988 365178294 3.500000e-136 496.0
18 TraesCS1A01G244400 chr5D 84.912 285 10 7 611 893 365177104 365177357 1.800000e-64 257.0
19 TraesCS1A01G244400 chr5D 89.011 182 19 1 2644 2824 275428024 275428205 1.820000e-54 224.0
20 TraesCS1A01G244400 chr5B 95.013 782 32 6 3442 4219 433317715 433318493 0.000000e+00 1221.0
21 TraesCS1A01G244400 chr5B 91.395 337 28 1 2967 3303 679584881 679584546 1.280000e-125 460.0
22 TraesCS1A01G244400 chr5B 88.848 269 26 4 411 678 166668353 166668088 1.350000e-85 327.0
23 TraesCS1A01G244400 chr5B 88.603 272 27 4 407 678 697371729 697371996 1.350000e-85 327.0
24 TraesCS1A01G244400 chr5B 88.806 268 26 4 411 678 660350698 660350961 4.850000e-85 326.0
25 TraesCS1A01G244400 chr5B 82.967 182 24 4 2644 2824 312772948 312773123 1.870000e-34 158.0
26 TraesCS1A01G244400 chr5B 96.809 94 3 0 3350 3443 433291936 433292029 1.870000e-34 158.0
27 TraesCS1A01G244400 chr2A 97.600 625 15 0 3595 4219 755718342 755717718 0.000000e+00 1072.0
28 TraesCS1A01G244400 chr2A 95.913 416 15 2 1 416 680305935 680305522 0.000000e+00 673.0
29 TraesCS1A01G244400 chr2A 90.258 349 32 2 4398 4745 55955371 55955718 5.930000e-124 455.0
30 TraesCS1A01G244400 chr2A 94.286 105 6 0 3350 3454 755718439 755718335 1.450000e-35 161.0
31 TraesCS1A01G244400 chr2A 100.000 43 0 0 1694 1736 16578213 16578255 4.170000e-11 80.5
32 TraesCS1A01G244400 chr3A 96.960 625 18 1 3595 4219 514469532 514470155 0.000000e+00 1048.0
33 TraesCS1A01G244400 chr3A 96.145 415 14 2 2 416 121013758 121014170 0.000000e+00 676.0
34 TraesCS1A01G244400 chr3A 93.176 381 20 2 3845 4219 654805290 654805670 5.690000e-154 555.0
35 TraesCS1A01G244400 chr3A 81.600 250 32 9 1436 1678 700203882 700203640 1.430000e-45 195.0
36 TraesCS1A01G244400 chr3A 83.482 224 19 7 1460 1678 700103859 700103649 5.140000e-45 193.0
37 TraesCS1A01G244400 chr3A 95.238 105 5 0 3350 3454 514469435 514469539 3.110000e-37 167.0
38 TraesCS1A01G244400 chr1B 93.310 568 27 3 839 1406 588421866 588422422 0.000000e+00 828.0
39 TraesCS1A01G244400 chr1B 88.316 582 54 11 1 574 476908244 476907669 0.000000e+00 686.0
40 TraesCS1A01G244400 chr1B 94.819 386 19 1 3350 3734 608860546 608860161 7.200000e-168 601.0
41 TraesCS1A01G244400 chr1B 92.285 337 25 1 2967 3303 683420508 683420843 1.270000e-130 477.0
42 TraesCS1A01G244400 chr1B 91.124 338 30 0 2967 3304 398144546 398144883 4.590000e-125 459.0
43 TraesCS1A01G244400 chr1B 88.722 266 26 3 411 676 654683313 654683574 6.280000e-84 322.0
44 TraesCS1A01G244400 chr1B 86.833 281 25 7 1431 1701 588422623 588422901 2.270000e-78 303.0
45 TraesCS1A01G244400 chr1B 80.000 215 20 7 2334 2548 561882258 561882449 2.440000e-28 137.0
46 TraesCS1A01G244400 chr1B 79.452 219 22 6 2334 2552 488713702 488713507 3.160000e-27 134.0
47 TraesCS1A01G244400 chr4B 87.427 684 67 16 1 676 104844137 104844809 0.000000e+00 769.0
48 TraesCS1A01G244400 chr4B 84.104 541 56 13 3702 4219 457412204 457412737 3.500000e-136 496.0
49 TraesCS1A01G244400 chr4B 84.421 475 58 10 1869 2327 535049812 535050286 2.130000e-123 453.0
50 TraesCS1A01G244400 chr4B 88.235 272 27 4 407 678 574594117 574593851 2.260000e-83 320.0
51 TraesCS1A01G244400 chr4B 88.192 271 28 4 408 678 646662237 646662503 2.260000e-83 320.0
52 TraesCS1A01G244400 chr4B 81.959 194 20 4 2359 2552 144928594 144928416 3.140000e-32 150.0
53 TraesCS1A01G244400 chr1D 90.227 573 51 3 839 1406 435044764 435045336 0.000000e+00 743.0
54 TraesCS1A01G244400 chr1D 91.691 337 28 0 2967 3303 296979049 296979385 7.620000e-128 468.0
55 TraesCS1A01G244400 chr1D 88.561 271 27 2 1431 1697 435045536 435045806 4.850000e-85 326.0
56 TraesCS1A01G244400 chr2B 86.522 690 68 20 1 678 654622066 654621390 0.000000e+00 736.0
57 TraesCS1A01G244400 chr5A 96.394 416 13 2 1 416 269293518 269293105 0.000000e+00 684.0
58 TraesCS1A01G244400 chr5A 81.846 325 19 16 2551 2863 548849494 548849790 2.340000e-58 237.0
59 TraesCS1A01G244400 chr7A 95.673 416 16 2 1 416 716951439 716951852 0.000000e+00 667.0
60 TraesCS1A01G244400 chr7A 84.900 649 58 15 1907 2552 11755328 11755939 1.990000e-173 619.0
61 TraesCS1A01G244400 chr6A 95.673 416 16 2 1 416 392630490 392630077 0.000000e+00 667.0
62 TraesCS1A01G244400 chr6A 86.383 470 51 11 1868 2327 272560107 272559641 7.510000e-138 501.0
63 TraesCS1A01G244400 chr6A 86.170 470 52 11 1868 2327 483930358 483930824 3.500000e-136 496.0
64 TraesCS1A01G244400 chr6A 81.514 449 49 15 859 1283 111566623 111566185 6.230000e-89 339.0
65 TraesCS1A01G244400 chr3D 88.247 519 49 10 1 513 459309420 459309932 1.200000e-170 610.0
66 TraesCS1A01G244400 chr3D 95.200 375 17 1 3845 4219 156998775 156999148 4.330000e-165 592.0
67 TraesCS1A01G244400 chr3D 80.658 243 22 12 1440 1676 565688291 565688068 1.120000e-36 165.0
68 TraesCS1A01G244400 chr7D 94.652 374 19 1 4655 5027 130226461 130226834 3.370000e-161 579.0
69 TraesCS1A01G244400 chr7D 89.504 343 32 3 2966 3307 168798372 168798033 1.000000e-116 431.0
70 TraesCS1A01G244400 chr7D 89.937 318 31 1 1907 2223 12306157 12306474 4.680000e-110 409.0
71 TraesCS1A01G244400 chr7D 86.842 304 28 5 2251 2552 12306476 12306769 3.750000e-86 329.0
72 TraesCS1A01G244400 chr4A 94.293 368 21 0 3845 4212 443426564 443426931 9.450000e-157 564.0
73 TraesCS1A01G244400 chr4A 85.954 477 48 13 1869 2328 36372862 36373336 4.520000e-135 492.0
74 TraesCS1A01G244400 chr4A 88.889 117 11 1 1729 1845 380152750 380152636 5.250000e-30 143.0
75 TraesCS1A01G244400 chr4A 97.826 46 1 0 1693 1738 642918077 642918122 4.170000e-11 80.5
76 TraesCS1A01G244400 chr4A 97.778 45 1 0 1694 1738 658152625 658152581 1.500000e-10 78.7
77 TraesCS1A01G244400 chrUn 92.835 321 20 3 4655 4974 64133725 64134043 3.550000e-126 462.0
78 TraesCS1A01G244400 chr2D 86.047 430 49 8 2131 2552 559179083 559179509 7.670000e-123 451.0
79 TraesCS1A01G244400 chr2D 89.766 342 32 2 2966 3307 36503693 36503355 7.730000e-118 435.0
80 TraesCS1A01G244400 chr2D 97.778 45 1 0 1694 1738 559294980 559294936 1.500000e-10 78.7
81 TraesCS1A01G244400 chr6D 80.873 481 47 19 839 1283 91849104 91848633 2.240000e-88 337.0
82 TraesCS1A01G244400 chr6B 89.179 268 25 4 411 678 179454368 179454105 1.040000e-86 331.0
83 TraesCS1A01G244400 chr6B 97.778 45 1 0 1694 1738 52458327 52458283 1.500000e-10 78.7
84 TraesCS1A01G244400 chr4D 91.489 94 4 3 1738 1829 438379143 438379234 5.280000e-25 126.0
85 TraesCS1A01G244400 chr7B 97.826 46 1 0 1693 1738 479759335 479759290 4.170000e-11 80.5
86 TraesCS1A01G244400 chr3B 100.000 36 0 0 3699 3734 729972832 729972867 3.250000e-07 67.6


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 TraesCS1A01G244400 chr1A 432588952 432593978 5026 True 9284.000000 9284 100.0000 1 5027 1 chr1A.!!$R1 5026
1 TraesCS1A01G244400 chr1A 588986819 588987442 623 True 1053.000000 1053 97.1150 3595 4218 1 chr1A.!!$R5 623
2 TraesCS1A01G244400 chr1A 532596065 532597104 1039 False 633.000000 939 92.4840 839 1701 2 chr1A.!!$F2 862
3 TraesCS1A01G244400 chr1A 532645553 532646496 943 False 483.500000 765 89.4965 839 1599 2 chr1A.!!$F3 760
4 TraesCS1A01G244400 chr5D 366750379 366756319 5940 False 2438.666667 5681 95.2440 583 5027 3 chr5D.!!$F4 4444
5 TraesCS1A01G244400 chr5D 365177104 365182497 5393 False 1257.400000 3542 94.0300 611 4536 5 chr5D.!!$F3 3925
6 TraesCS1A01G244400 chr5D 365206297 365206799 502 False 832.000000 832 96.4360 4523 5027 1 chr5D.!!$F2 504
7 TraesCS1A01G244400 chr5B 433317715 433318493 778 False 1221.000000 1221 95.0130 3442 4219 1 chr5B.!!$F3 777
8 TraesCS1A01G244400 chr2A 755717718 755718439 721 True 616.500000 1072 95.9430 3350 4219 2 chr2A.!!$R2 869
9 TraesCS1A01G244400 chr3A 514469435 514470155 720 False 607.500000 1048 96.0990 3350 4219 2 chr3A.!!$F3 869
10 TraesCS1A01G244400 chr1B 476907669 476908244 575 True 686.000000 686 88.3160 1 574 1 chr1B.!!$R1 573
11 TraesCS1A01G244400 chr1B 588421866 588422901 1035 False 565.500000 828 90.0715 839 1701 2 chr1B.!!$F5 862
12 TraesCS1A01G244400 chr4B 104844137 104844809 672 False 769.000000 769 87.4270 1 676 1 chr4B.!!$F1 675
13 TraesCS1A01G244400 chr4B 457412204 457412737 533 False 496.000000 496 84.1040 3702 4219 1 chr4B.!!$F2 517
14 TraesCS1A01G244400 chr1D 435044764 435045806 1042 False 534.500000 743 89.3940 839 1697 2 chr1D.!!$F2 858
15 TraesCS1A01G244400 chr2B 654621390 654622066 676 True 736.000000 736 86.5220 1 678 1 chr2B.!!$R1 677
16 TraesCS1A01G244400 chr7A 11755328 11755939 611 False 619.000000 619 84.9000 1907 2552 1 chr7A.!!$F1 645
17 TraesCS1A01G244400 chr3D 459309420 459309932 512 False 610.000000 610 88.2470 1 513 1 chr3D.!!$F2 512
18 TraesCS1A01G244400 chr7D 12306157 12306769 612 False 369.000000 409 88.3895 1907 2552 2 chr7D.!!$F2 645

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
355 362 0.178861 AAGGAGCAAAGGGAGGAGGA 60.179 55.000 0.00 0.0 0.00 3.71 F
1214 1227 0.178990 GGCAAGGTCCTGTTCCAACT 60.179 55.000 0.00 0.0 0.00 3.16 F
1860 3428 0.868602 CGCCACGGTTAGATGGTACG 60.869 60.000 0.00 0.0 38.34 3.67 F
2244 3813 1.210478 CAGGACTCGTGGGATTGGAAT 59.790 52.381 0.00 0.0 0.00 3.01 F
3155 4782 2.792947 GGATGTAGAGCGCCGGGAA 61.793 63.158 2.29 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1891 0.039180 TGCCTTCTACAGTCTCGGGA 59.961 55.000 0.0 0.0 0.0 5.14 R
2332 3901 5.306937 TGGTCTACTCTTTCCATTGACTTGA 59.693 40.000 0.0 0.0 0.0 3.02 R
3264 4891 0.842030 TCCTCCTGGCCACAATCACT 60.842 55.000 0.0 0.0 0.0 3.41 R
3270 4897 1.306141 CCTACTCCTCCTGGCCACA 60.306 63.158 0.0 0.0 0.0 4.17 R
4772 6696 2.282701 ACAAACAACACAGCAGCAAG 57.717 45.000 0.0 0.0 0.0 4.01 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
80 82 1.011968 CGACCGATCAAGCACCGAAA 61.012 55.000 0.00 0.00 0.00 3.46
81 83 0.442699 GACCGATCAAGCACCGAAAC 59.557 55.000 0.00 0.00 0.00 2.78
119 121 0.312729 TAGCACACGTTCAGCTCGAA 59.687 50.000 9.17 0.00 39.68 3.71
132 134 2.273123 TCGAAGACGATCCCCGGA 59.727 61.111 0.73 0.00 43.81 5.14
149 151 0.250513 GGACTCCGATCCAGCAAAGT 59.749 55.000 0.00 0.00 38.77 2.66
150 152 1.363744 GACTCCGATCCAGCAAAGTG 58.636 55.000 0.00 0.00 0.00 3.16
155 157 0.389817 CGATCCAGCAAAGTGTCGGA 60.390 55.000 0.00 0.00 0.00 4.55
156 158 1.808411 GATCCAGCAAAGTGTCGGAA 58.192 50.000 0.00 0.00 0.00 4.30
158 160 2.045561 TCCAGCAAAGTGTCGGAAAA 57.954 45.000 0.00 0.00 0.00 2.29
206 208 3.442625 TGACGATCTTGATGTTCTACCGT 59.557 43.478 0.00 0.00 0.00 4.83
231 233 4.606071 CTTCGCCTAAGCACTGCT 57.394 55.556 0.00 0.00 42.56 4.24
234 236 0.606096 TTCGCCTAAGCACTGCTACA 59.394 50.000 3.33 0.00 38.25 2.74
237 239 1.328680 CGCCTAAGCACTGCTACAATG 59.671 52.381 3.33 0.00 38.25 2.82
239 241 2.749621 GCCTAAGCACTGCTACAATGTT 59.250 45.455 3.33 0.00 38.25 2.71
241 243 4.576463 GCCTAAGCACTGCTACAATGTTAT 59.424 41.667 3.33 0.00 38.25 1.89
248 253 5.292765 CACTGCTACAATGTTATCGAGGAT 58.707 41.667 0.00 0.00 0.00 3.24
260 265 2.767644 TCGAGGATTATGGTGGAGGA 57.232 50.000 0.00 0.00 0.00 3.71
286 291 2.423926 CGCACACGGCTAATAGATCT 57.576 50.000 0.00 0.00 41.67 2.75
287 292 2.320367 CGCACACGGCTAATAGATCTC 58.680 52.381 0.00 0.00 41.67 2.75
288 293 2.287608 CGCACACGGCTAATAGATCTCA 60.288 50.000 0.00 0.00 41.67 3.27
289 294 3.717707 GCACACGGCTAATAGATCTCAA 58.282 45.455 0.00 0.00 40.25 3.02
307 314 5.624159 TCTCAAGGATCAATTGTTGTGTCT 58.376 37.500 5.13 0.00 0.00 3.41
308 315 6.064060 TCTCAAGGATCAATTGTTGTGTCTT 58.936 36.000 5.13 0.36 0.00 3.01
316 323 0.820871 TTGTTGTGTCTTTGGGGTGC 59.179 50.000 0.00 0.00 0.00 5.01
342 349 4.265073 CCTGCACCCATATATAAAGGAGC 58.735 47.826 13.53 13.53 0.00 4.70
345 352 5.700183 TGCACCCATATATAAAGGAGCAAA 58.300 37.500 18.12 3.31 32.84 3.68
349 356 5.615261 ACCCATATATAAAGGAGCAAAGGGA 59.385 40.000 0.00 0.00 35.43 4.20
355 362 0.178861 AAGGAGCAAAGGGAGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
444 451 0.892358 TCTCAGTTGGTAGGTCGCGT 60.892 55.000 5.77 0.00 0.00 6.01
446 453 0.390124 TCAGTTGGTAGGTCGCGTTT 59.610 50.000 5.77 0.00 0.00 3.60
450 457 1.804396 TTGGTAGGTCGCGTTTCGGA 61.804 55.000 5.77 0.00 39.05 4.55
469 476 3.440872 CGGATTTTATTTTCGTCCCACCA 59.559 43.478 0.00 0.00 0.00 4.17
473 480 2.188062 TATTTTCGTCCCACCACACC 57.812 50.000 0.00 0.00 0.00 4.16
478 485 3.881104 GTCCCACCACACCCGGTT 61.881 66.667 0.00 0.00 37.07 4.44
512 519 3.323775 TCTTTGGTACTTTCTCCCACCT 58.676 45.455 0.00 0.00 32.04 4.00
517 524 1.281287 GTACTTTCTCCCACCTTCCCC 59.719 57.143 0.00 0.00 0.00 4.81
523 530 3.732849 CCCACCTTCCCCTCAGCC 61.733 72.222 0.00 0.00 0.00 4.85
524 531 2.935481 CCACCTTCCCCTCAGCCA 60.935 66.667 0.00 0.00 0.00 4.75
532 539 0.536460 TCCCCTCAGCCACGAAAAAC 60.536 55.000 0.00 0.00 0.00 2.43
556 563 1.419107 GAAAACCCCGCGATCGAGTC 61.419 60.000 21.57 4.10 38.10 3.36
574 581 4.025401 CCGCACACGCCCAAACTC 62.025 66.667 0.00 0.00 38.22 3.01
575 582 2.972505 CGCACACGCCCAAACTCT 60.973 61.111 0.00 0.00 33.11 3.24
576 583 2.946762 GCACACGCCCAAACTCTC 59.053 61.111 0.00 0.00 0.00 3.20
577 584 2.954753 GCACACGCCCAAACTCTCG 61.955 63.158 0.00 0.00 0.00 4.04
578 585 1.594293 CACACGCCCAAACTCTCGT 60.594 57.895 0.00 0.00 35.35 4.18
579 586 1.300697 ACACGCCCAAACTCTCGTC 60.301 57.895 0.00 0.00 32.38 4.20
580 587 2.049433 ACGCCCAAACTCTCGTCG 60.049 61.111 0.00 0.00 0.00 5.12
581 588 2.049433 CGCCCAAACTCTCGTCGT 60.049 61.111 0.00 0.00 0.00 4.34
592 599 5.721876 AACTCTCGTCGTTATCTCTACTG 57.278 43.478 0.00 0.00 0.00 2.74
593 600 4.757594 ACTCTCGTCGTTATCTCTACTGT 58.242 43.478 0.00 0.00 0.00 3.55
615 622 6.455647 TGTTAATGTCTCAGTTGGTAGTCTG 58.544 40.000 0.00 0.00 0.00 3.51
624 631 1.180456 TTGGTAGTCTGCGTTCCGGA 61.180 55.000 0.00 0.00 0.00 5.14
715 728 1.478654 GCTCTCTGTTGGTTTTCCCCA 60.479 52.381 0.00 0.00 39.73 4.96
718 731 2.171003 CTCTGTTGGTTTTCCCCATCC 58.829 52.381 0.00 0.00 39.73 3.51
763 776 3.522731 CCCTCGGTCTCGCCTCTG 61.523 72.222 0.00 0.00 36.13 3.35
854 867 0.267356 CCCTCCCTCTCCATCTCCTT 59.733 60.000 0.00 0.00 0.00 3.36
953 966 3.745803 GCCCTTCTCCGACGACGT 61.746 66.667 0.00 0.00 37.88 4.34
1107 1120 1.128188 AGAGGTTCTTGCCGGACCTT 61.128 55.000 12.72 1.65 0.00 3.50
1214 1227 0.178990 GGCAAGGTCCTGTTCCAACT 60.179 55.000 0.00 0.00 0.00 3.16
1334 1352 1.336440 CTTTTGTGTTGGTGGATCGCA 59.664 47.619 0.00 0.00 0.00 5.10
1342 1360 2.711922 GGTGGATCGCACGTCTCCT 61.712 63.158 12.97 0.00 0.00 3.69
1424 1531 4.357918 AAAGAGCACTACCATGTCAAGT 57.642 40.909 0.00 0.00 0.00 3.16
1426 1533 3.931578 AGAGCACTACCATGTCAAGTTC 58.068 45.455 0.00 0.00 0.00 3.01
1427 1534 2.668457 GAGCACTACCATGTCAAGTTCG 59.332 50.000 0.00 0.00 0.00 3.95
1428 1535 2.037251 AGCACTACCATGTCAAGTTCGT 59.963 45.455 0.00 0.00 0.00 3.85
1467 1661 1.619654 TGGTTTCCAGCATGTCTTGG 58.380 50.000 6.68 6.68 0.00 3.61
1517 1716 1.270571 TGCAATCGACAAGGTGTGCTA 60.271 47.619 0.00 0.00 33.19 3.49
1519 1718 2.225491 GCAATCGACAAGGTGTGCTAAA 59.775 45.455 0.00 0.00 0.00 1.85
1583 1788 5.987347 TCACAGTTACTTTTAGCACTACCAC 59.013 40.000 0.00 0.00 0.00 4.16
1653 1860 7.940688 AGTATGAAATATCAGGATTGTGCATGA 59.059 33.333 0.00 0.00 39.39 3.07
1684 1891 6.464222 TCTTTTACGACTGACAATGGAGAAT 58.536 36.000 0.00 0.00 0.00 2.40
1860 3428 0.868602 CGCCACGGTTAGATGGTACG 60.869 60.000 0.00 0.00 38.34 3.67
2244 3813 1.210478 CAGGACTCGTGGGATTGGAAT 59.790 52.381 0.00 0.00 0.00 3.01
2356 3925 5.306937 TCAAGTCAATGGAAAGAGTAGACCA 59.693 40.000 0.00 0.00 36.83 4.02
2357 3926 5.153950 AGTCAATGGAAAGAGTAGACCAC 57.846 43.478 0.00 0.00 35.19 4.16
2358 3927 4.841246 AGTCAATGGAAAGAGTAGACCACT 59.159 41.667 0.00 0.00 41.47 4.00
2359 3928 6.017192 AGTCAATGGAAAGAGTAGACCACTA 58.983 40.000 0.00 0.00 37.72 2.74
2360 3929 6.153680 AGTCAATGGAAAGAGTAGACCACTAG 59.846 42.308 0.00 0.00 37.72 2.57
2361 3930 6.153000 GTCAATGGAAAGAGTAGACCACTAGA 59.847 42.308 0.00 0.00 37.72 2.43
2362 3931 6.153000 TCAATGGAAAGAGTAGACCACTAGAC 59.847 42.308 0.00 0.00 37.72 2.59
2363 3932 4.342359 TGGAAAGAGTAGACCACTAGACC 58.658 47.826 0.00 0.00 37.72 3.85
2895 4522 4.054359 TGGGGCATACATTAGTTGGTTT 57.946 40.909 0.00 0.00 0.00 3.27
3155 4782 2.792947 GGATGTAGAGCGCCGGGAA 61.793 63.158 2.29 0.00 0.00 3.97
3270 4897 2.690778 GCGCTGCGGGAAAGTGATT 61.691 57.895 24.61 0.00 0.00 2.57
3543 5170 0.308684 CACATGCTGCGTTCTGTGTT 59.691 50.000 13.07 0.00 35.42 3.32
3559 5187 7.148423 CGTTCTGTGTTGATATGGATGAGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
3952 5683 5.586243 GCTGCTGTAGAACAGGATTTTATCA 59.414 40.000 8.99 0.00 45.46 2.15
4287 6211 2.153645 TGTGACATCAGCACATCCAAC 58.846 47.619 0.00 0.00 41.00 3.77
4429 6353 1.826385 ACTTGAGCAAGGTATGTGGC 58.174 50.000 14.14 0.00 42.53 5.01
4587 6511 6.632219 GCAGCATCCCTAGAGAATATATTGCT 60.632 42.308 1.78 2.95 37.19 3.91
4588 6512 6.985645 CAGCATCCCTAGAGAATATATTGCTC 59.014 42.308 1.78 9.23 34.72 4.26
4589 6513 6.671340 AGCATCCCTAGAGAATATATTGCTCA 59.329 38.462 18.80 9.77 31.54 4.26
4591 6515 6.537453 TCCCTAGAGAATATATTGCTCAGC 57.463 41.667 18.80 0.00 0.00 4.26
4749 6673 7.787725 AGTTTACATTTTCTTATAGGGCTCG 57.212 36.000 0.00 0.00 0.00 5.03
4772 6696 3.798202 ACCGAATAAAGTCTGATCAGGC 58.202 45.455 19.90 19.90 0.00 4.85
4830 6754 4.647564 AATTGTGGAGGAGTGAGTCATT 57.352 40.909 0.00 0.00 0.00 2.57
4831 6755 3.685139 TTGTGGAGGAGTGAGTCATTC 57.315 47.619 7.09 7.09 0.00 2.67
4852 6778 3.094572 CTCTCATGGGGATTTGTTTGCT 58.905 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.941542 TGTGCTAACGCTTTCGCTTT 59.058 45.000 1.22 0.00 39.84 3.51
59 60 2.511600 GGTGCTTGATCGGTCGGG 60.512 66.667 0.00 0.00 0.00 5.14
100 102 0.312729 TTCGAGCTGAACGTGTGCTA 59.687 50.000 9.63 0.00 37.16 3.49
119 121 2.123812 GGAGTCCGGGGATCGTCT 60.124 66.667 0.00 0.00 37.11 4.18
132 134 0.687354 ACACTTTGCTGGATCGGAGT 59.313 50.000 0.00 0.00 0.00 3.85
155 157 1.202486 TCGTGCTGACGGAACTCTTTT 60.202 47.619 0.00 0.00 46.11 2.27
156 158 0.387929 TCGTGCTGACGGAACTCTTT 59.612 50.000 0.00 0.00 46.11 2.52
158 160 1.286260 GTCGTGCTGACGGAACTCT 59.714 57.895 0.00 0.00 46.11 3.24
183 185 4.098044 ACGGTAGAACATCAAGATCGTCAT 59.902 41.667 0.00 0.00 0.00 3.06
191 193 1.920574 CTGCGACGGTAGAACATCAAG 59.079 52.381 0.00 0.00 0.00 3.02
192 194 1.403647 CCTGCGACGGTAGAACATCAA 60.404 52.381 0.00 0.00 0.00 2.57
224 226 3.246226 CCTCGATAACATTGTAGCAGTGC 59.754 47.826 7.13 7.13 0.00 4.40
226 228 5.537300 ATCCTCGATAACATTGTAGCAGT 57.463 39.130 0.00 0.00 0.00 4.40
228 230 6.873605 CCATAATCCTCGATAACATTGTAGCA 59.126 38.462 0.00 0.00 0.00 3.49
231 233 7.015779 TCCACCATAATCCTCGATAACATTGTA 59.984 37.037 0.00 0.00 0.00 2.41
234 236 6.433847 TCCACCATAATCCTCGATAACATT 57.566 37.500 0.00 0.00 0.00 2.71
237 239 4.527038 TCCTCCACCATAATCCTCGATAAC 59.473 45.833 0.00 0.00 0.00 1.89
239 241 4.344978 CTCCTCCACCATAATCCTCGATA 58.655 47.826 0.00 0.00 0.00 2.92
241 243 2.598565 CTCCTCCACCATAATCCTCGA 58.401 52.381 0.00 0.00 0.00 4.04
248 253 2.307153 GTGCCCTCCTCCACCATAA 58.693 57.895 0.00 0.00 0.00 1.90
284 289 5.624159 AGACACAACAATTGATCCTTGAGA 58.376 37.500 13.59 0.00 0.00 3.27
285 290 5.954296 AGACACAACAATTGATCCTTGAG 57.046 39.130 13.59 7.35 0.00 3.02
286 291 6.461370 CCAAAGACACAACAATTGATCCTTGA 60.461 38.462 13.59 0.00 29.92 3.02
287 292 5.693104 CCAAAGACACAACAATTGATCCTTG 59.307 40.000 13.59 8.64 0.00 3.61
288 293 5.221501 CCCAAAGACACAACAATTGATCCTT 60.222 40.000 13.59 3.85 0.00 3.36
289 294 4.281688 CCCAAAGACACAACAATTGATCCT 59.718 41.667 13.59 0.00 0.00 3.24
297 304 0.820871 GCACCCCAAAGACACAACAA 59.179 50.000 0.00 0.00 0.00 2.83
299 306 1.739667 GGCACCCCAAAGACACAAC 59.260 57.895 0.00 0.00 0.00 3.32
300 307 4.268720 GGCACCCCAAAGACACAA 57.731 55.556 0.00 0.00 0.00 3.33
325 332 5.615261 TCCCTTTGCTCCTTTATATATGGGT 59.385 40.000 0.00 0.00 0.00 4.51
329 336 6.216456 CCTCCTCCCTTTGCTCCTTTATATAT 59.784 42.308 0.00 0.00 0.00 0.86
342 349 3.002371 GGCCTCCTCCTCCCTTTG 58.998 66.667 0.00 0.00 0.00 2.77
444 451 5.335819 GGTGGGACGAAAATAAAATCCGAAA 60.336 40.000 0.00 0.00 0.00 3.46
446 453 3.690628 GGTGGGACGAAAATAAAATCCGA 59.309 43.478 0.00 0.00 0.00 4.55
450 457 4.021807 GGTGTGGTGGGACGAAAATAAAAT 60.022 41.667 0.00 0.00 0.00 1.82
497 504 1.281287 GGGGAAGGTGGGAGAAAGTAC 59.719 57.143 0.00 0.00 0.00 2.73
512 519 0.183971 TTTTTCGTGGCTGAGGGGAA 59.816 50.000 0.00 0.00 0.00 3.97
517 524 2.357637 TCTTTGGTTTTTCGTGGCTGAG 59.642 45.455 0.00 0.00 0.00 3.35
523 530 3.619483 GGGGTTTTCTTTGGTTTTTCGTG 59.381 43.478 0.00 0.00 0.00 4.35
524 531 3.676598 CGGGGTTTTCTTTGGTTTTTCGT 60.677 43.478 0.00 0.00 0.00 3.85
532 539 0.170339 GATCGCGGGGTTTTCTTTGG 59.830 55.000 6.13 0.00 0.00 3.28
574 581 7.408123 ACATTAACAGTAGAGATAACGACGAG 58.592 38.462 0.00 0.00 0.00 4.18
575 582 7.279536 AGACATTAACAGTAGAGATAACGACGA 59.720 37.037 0.00 0.00 0.00 4.20
576 583 7.408123 AGACATTAACAGTAGAGATAACGACG 58.592 38.462 0.00 0.00 0.00 5.12
577 584 8.396390 TGAGACATTAACAGTAGAGATAACGAC 58.604 37.037 0.00 0.00 0.00 4.34
578 585 8.502105 TGAGACATTAACAGTAGAGATAACGA 57.498 34.615 0.00 0.00 0.00 3.85
579 586 8.399425 ACTGAGACATTAACAGTAGAGATAACG 58.601 37.037 0.00 0.00 42.01 3.18
592 599 5.348997 GCAGACTACCAACTGAGACATTAAC 59.651 44.000 0.00 0.00 36.38 2.01
593 600 5.479306 GCAGACTACCAACTGAGACATTAA 58.521 41.667 0.00 0.00 36.38 1.40
624 631 6.096695 CGAAAATGGTGGGACGAAAATAAAT 58.903 36.000 0.00 0.00 0.00 1.40
715 728 2.087462 TTGGATCGAGCGATGCGGAT 62.087 55.000 17.27 0.00 44.35 4.18
718 731 1.543941 GAGTTGGATCGAGCGATGCG 61.544 60.000 17.27 0.00 44.35 4.73
953 966 0.173481 CTCGAGGCGGACAGATTCAA 59.827 55.000 3.91 0.00 0.00 2.69
1107 1120 0.249155 CCTTCTCCGCCGCGTATAAA 60.249 55.000 12.58 0.00 0.00 1.40
1214 1227 3.119459 GGACGCATAGAAGAAGACTCACA 60.119 47.826 0.00 0.00 0.00 3.58
1312 1330 1.662876 CGATCCACCAACACAAAAGCG 60.663 52.381 0.00 0.00 0.00 4.68
1424 1531 0.934496 CTGCTTGTCGACCAAACGAA 59.066 50.000 14.12 0.00 43.75 3.85
1426 1533 1.569493 CCTGCTTGTCGACCAAACG 59.431 57.895 14.12 0.00 31.20 3.60
1427 1534 0.534203 TCCCTGCTTGTCGACCAAAC 60.534 55.000 14.12 3.87 31.20 2.93
1428 1535 0.181587 TTCCCTGCTTGTCGACCAAA 59.818 50.000 14.12 0.04 31.20 3.28
1457 1651 2.029649 ACAGTGCATTTCCAAGACATGC 60.030 45.455 8.43 8.43 43.47 4.06
1458 1652 3.571571 CACAGTGCATTTCCAAGACATG 58.428 45.455 0.00 0.00 0.00 3.21
1517 1716 3.445096 GTGCAGGAAAGGATAGCATGTTT 59.555 43.478 0.00 0.00 37.56 2.83
1519 1718 2.025981 TGTGCAGGAAAGGATAGCATGT 60.026 45.455 0.00 0.00 37.56 3.21
1630 1837 7.776618 ATCATGCACAATCCTGATATTTCAT 57.223 32.000 0.00 0.00 0.00 2.57
1653 1860 9.840427 CCATTGTCAGTCGTAAAAGAATAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
1684 1891 0.039180 TGCCTTCTACAGTCTCGGGA 59.961 55.000 0.00 0.00 0.00 5.14
1860 3428 2.167861 GGTGTTCGGCATCGAGCTC 61.168 63.158 2.73 2.73 46.75 4.09
2119 3687 6.547510 GCAATTATCAAACTTCCCTGTAGGAT 59.452 38.462 0.00 0.00 46.94 3.24
2244 3813 6.101734 AGGGATGCTAGATCCTTGTGAATTTA 59.898 38.462 16.17 0.00 38.26 1.40
2332 3901 5.306937 TGGTCTACTCTTTCCATTGACTTGA 59.693 40.000 0.00 0.00 0.00 3.02
2379 3948 5.869753 ATGCAAGCAGTAACTGAAACTAG 57.130 39.130 0.00 0.00 32.44 2.57
2598 4225 9.885934 CGTATCTAAGAATATGGGAGAATATCG 57.114 37.037 0.00 0.00 0.00 2.92
3264 4891 0.842030 TCCTCCTGGCCACAATCACT 60.842 55.000 0.00 0.00 0.00 3.41
3270 4897 1.306141 CCTACTCCTCCTGGCCACA 60.306 63.158 0.00 0.00 0.00 4.17
3543 5170 5.239306 GCACGGAATTTTCTCATCCATATCA 59.761 40.000 0.00 0.00 32.58 2.15
3559 5187 5.417580 ACAAATAATGTTGTAGGCACGGAAT 59.582 36.000 0.00 0.00 40.06 3.01
3952 5683 6.627087 TTCAAGAACCTTCTCTGGATATGT 57.373 37.500 0.00 0.00 36.28 2.29
4287 6211 5.794894 ACAAATGAGGGACTACAGTTACAG 58.205 41.667 0.00 0.00 41.55 2.74
4429 6353 7.716998 ACTGTATGCAAGGATTAAGTTAGATGG 59.283 37.037 0.00 0.00 0.00 3.51
4587 6511 8.418662 AGATGTTTATTAGGTACATAACGCTGA 58.581 33.333 1.42 0.00 32.94 4.26
4588 6512 8.487970 CAGATGTTTATTAGGTACATAACGCTG 58.512 37.037 1.42 1.63 32.94 5.18
4589 6513 8.418662 TCAGATGTTTATTAGGTACATAACGCT 58.581 33.333 1.42 0.00 32.94 5.07
4749 6673 4.372656 CCTGATCAGACTTTATTCGGTCC 58.627 47.826 24.62 0.00 33.39 4.46
4772 6696 2.282701 ACAAACAACACAGCAGCAAG 57.717 45.000 0.00 0.00 0.00 4.01
4830 6754 3.091545 GCAAACAAATCCCCATGAGAGA 58.908 45.455 0.00 0.00 0.00 3.10
4831 6755 3.094572 AGCAAACAAATCCCCATGAGAG 58.905 45.455 0.00 0.00 0.00 3.20
4884 6810 5.249163 TGGGAGTATGTAAGCTGCATCATAT 59.751 40.000 1.02 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.