Multiple sequence alignment - TraesCS7A01G374200

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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 TraesCS7A01G374200 chr7A 100.000 4436 0 0 1 4436 547115139 547110704 0.000000e+00 8192.0
1 TraesCS7A01G374200 chr7A 81.140 2439 407 35 988 3402 720864357 720861948 0.000000e+00 1906.0
2 TraesCS7A01G374200 chr7A 81.874 2284 364 31 1183 3433 720885032 720887298 0.000000e+00 1879.0
3 TraesCS7A01G374200 chr7A 93.869 473 29 0 2530 3002 547102329 547101857 0.000000e+00 713.0
4 TraesCS7A01G374200 chr7D 94.463 3666 159 19 622 4257 448855018 448858669 0.000000e+00 5605.0
5 TraesCS7A01G374200 chr7D 83.412 2544 362 31 1012 3516 625355391 625352869 0.000000e+00 2305.0
6 TraesCS7A01G374200 chr7D 81.991 2421 383 41 1044 3433 625227661 625225263 0.000000e+00 2006.0
7 TraesCS7A01G374200 chr7D 81.658 2437 399 33 988 3399 625250519 625252932 0.000000e+00 1980.0
8 TraesCS7A01G374200 chr7D 89.200 250 20 4 2 250 448854321 448854564 5.570000e-79 305.0
9 TraesCS7A01G374200 chr7D 92.737 179 7 2 4258 4436 448858751 448858923 2.050000e-63 254.0
10 TraesCS7A01G374200 chr7D 83.658 257 21 8 343 586 448854637 448854885 5.780000e-54 222.0
11 TraesCS7A01G374200 chr7D 94.000 50 3 0 312 361 536139599 536139648 4.760000e-10 76.8
12 TraesCS7A01G374200 chr7D 100.000 39 0 0 590 628 448854960 448854998 6.150000e-09 73.1
13 TraesCS7A01G374200 chr7D 100.000 32 0 0 279 310 543628117 543628148 4.790000e-05 60.2
14 TraesCS7A01G374200 chr7D 86.792 53 5 2 4369 4420 531068241 531068292 1.720000e-04 58.4
15 TraesCS7A01G374200 chr7D 86.538 52 5 2 4369 4420 77045876 77045827 6.200000e-04 56.5
16 TraesCS7A01G374200 chr7D 96.875 32 1 0 334 365 57073305 57073336 2.000000e-03 54.7
17 TraesCS7A01G374200 chr7B 89.207 3493 305 38 719 4166 466668621 466672086 0.000000e+00 4296.0
18 TraesCS7A01G374200 chr7B 83.825 2541 359 29 1012 3516 724955925 724953401 0.000000e+00 2368.0
19 TraesCS7A01G374200 chr7B 81.501 2411 393 34 1046 3430 723902909 723900526 0.000000e+00 1932.0
20 TraesCS7A01G374200 chr7B 81.449 2415 399 31 1063 3448 723929236 723931630 0.000000e+00 1932.0
21 TraesCS7A01G374200 chr1B 83.775 2453 368 15 965 3399 623547490 623549930 0.000000e+00 2298.0
22 TraesCS7A01G374200 chr1B 81.130 832 135 14 2873 3697 622964403 622963587 0.000000e+00 647.0
23 TraesCS7A01G374200 chr1B 100.000 30 0 0 332 361 653831814 653831843 6.200000e-04 56.5
24 TraesCS7A01G374200 chr1D 83.333 2460 380 15 965 3406 453113307 453115754 0.000000e+00 2244.0
25 TraesCS7A01G374200 chr1D 100.000 31 0 0 280 310 364506852 364506822 1.720000e-04 58.4
26 TraesCS7A01G374200 chr6A 80.630 2478 424 42 988 3433 608493806 608491353 0.000000e+00 1866.0
27 TraesCS7A01G374200 chr6A 94.286 35 2 0 4379 4413 12076282 12076316 2.000000e-03 54.7
28 TraesCS7A01G374200 chr6A 96.875 32 0 1 309 339 497348829 497348798 8.000000e-03 52.8
29 TraesCS7A01G374200 chr4A 94.340 53 3 0 312 364 46054186 46054134 1.020000e-11 82.4
30 TraesCS7A01G374200 chr4A 100.000 31 0 0 280 310 615041360 615041330 1.720000e-04 58.4
31 TraesCS7A01G374200 chr4A 100.000 29 0 0 337 365 11306860 11306832 2.000000e-03 54.7
32 TraesCS7A01G374200 chr4A 100.000 28 0 0 277 304 589013550 589013577 8.000000e-03 52.8
33 TraesCS7A01G374200 chr4A 100.000 28 0 0 280 307 738150213 738150186 8.000000e-03 52.8
34 TraesCS7A01G374200 chr6B 87.719 57 7 0 308 364 482469233 482469289 2.860000e-07 67.6
35 TraesCS7A01G374200 chr6B 100.000 30 0 0 4383 4412 29238854 29238883 6.200000e-04 56.5
36 TraesCS7A01G374200 chr6B 90.698 43 2 2 323 364 618224281 618224322 6.200000e-04 56.5
37 TraesCS7A01G374200 chr5D 100.000 32 0 0 279 310 480375031 480375062 4.790000e-05 60.2
38 TraesCS7A01G374200 chr3D 97.143 35 1 0 276 310 22931720 22931754 4.790000e-05 60.2
39 TraesCS7A01G374200 chr2D 100.000 32 0 0 279 310 14634779 14634748 4.790000e-05 60.2
40 TraesCS7A01G374200 chr2B 100.000 32 0 0 4385 4416 513590724 513590755 4.790000e-05 60.2
41 TraesCS7A01G374200 chr2B 100.000 31 0 0 279 309 570760206 570760176 1.720000e-04 58.4
42 TraesCS7A01G374200 chr1A 100.000 32 0 0 279 310 364630181 364630150 4.790000e-05 60.2
43 TraesCS7A01G374200 chrUn 97.143 35 0 1 4378 4412 13887340 13887373 1.720000e-04 58.4
44 TraesCS7A01G374200 chr5A 100.000 31 0 0 279 309 602959315 602959285 1.720000e-04 58.4
45 TraesCS7A01G374200 chr2A 100.000 31 0 0 312 342 5707125 5707155 1.720000e-04 58.4
46 TraesCS7A01G374200 chr2A 90.909 44 2 2 323 365 17855749 17855791 1.720000e-04 58.4
47 TraesCS7A01G374200 chr2A 100.000 29 0 0 332 360 16715320 16715292 2.000000e-03 54.7
48 TraesCS7A01G374200 chr4B 100.000 29 0 0 276 304 37572816 37572844 2.000000e-03 54.7
49 TraesCS7A01G374200 chr4B 100.000 28 0 0 4382 4409 642538805 642538778 8.000000e-03 52.8
50 TraesCS7A01G374200 chr3B 96.875 32 1 0 276 307 767620480 767620511 2.000000e-03 54.7
51 TraesCS7A01G374200 chr3B 96.875 32 1 0 276 307 767656839 767656870 2.000000e-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 TraesCS7A01G374200 chr7A 547110704 547115139 4435 True 8192.00 8192 100.0000 1 4436 1 chr7A.!!$R2 4435
1 TraesCS7A01G374200 chr7A 720861948 720864357 2409 True 1906.00 1906 81.1400 988 3402 1 chr7A.!!$R3 2414
2 TraesCS7A01G374200 chr7A 720885032 720887298 2266 False 1879.00 1879 81.8740 1183 3433 1 chr7A.!!$F1 2250
3 TraesCS7A01G374200 chr7D 625352869 625355391 2522 True 2305.00 2305 83.4120 1012 3516 1 chr7D.!!$R3 2504
4 TraesCS7A01G374200 chr7D 625225263 625227661 2398 True 2006.00 2006 81.9910 1044 3433 1 chr7D.!!$R2 2389
5 TraesCS7A01G374200 chr7D 625250519 625252932 2413 False 1980.00 1980 81.6580 988 3399 1 chr7D.!!$F5 2411
6 TraesCS7A01G374200 chr7D 448854321 448858923 4602 False 1291.82 5605 92.0116 2 4436 5 chr7D.!!$F6 4434
7 TraesCS7A01G374200 chr7B 466668621 466672086 3465 False 4296.00 4296 89.2070 719 4166 1 chr7B.!!$F1 3447
8 TraesCS7A01G374200 chr7B 724953401 724955925 2524 True 2368.00 2368 83.8250 1012 3516 1 chr7B.!!$R2 2504
9 TraesCS7A01G374200 chr7B 723900526 723902909 2383 True 1932.00 1932 81.5010 1046 3430 1 chr7B.!!$R1 2384
10 TraesCS7A01G374200 chr7B 723929236 723931630 2394 False 1932.00 1932 81.4490 1063 3448 1 chr7B.!!$F2 2385
11 TraesCS7A01G374200 chr1B 623547490 623549930 2440 False 2298.00 2298 83.7750 965 3399 1 chr1B.!!$F1 2434
12 TraesCS7A01G374200 chr1B 622963587 622964403 816 True 647.00 647 81.1300 2873 3697 1 chr1B.!!$R1 824
13 TraesCS7A01G374200 chr1D 453113307 453115754 2447 False 2244.00 2244 83.3330 965 3406 1 chr1D.!!$F1 2441
14 TraesCS7A01G374200 chr6A 608491353 608493806 2453 True 1866.00 1866 80.6300 988 3433 1 chr6A.!!$R2 2445

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
363 365 0.033796 TCGGACGGAGGGAGTATGTT 60.034 55.0 0.00 0.00 0.0 2.71 F
364 366 0.102481 CGGACGGAGGGAGTATGTTG 59.898 60.0 0.00 0.00 0.0 3.33 F
507 522 0.102844 CATGCGGCCATAAACCCTTG 59.897 55.0 2.24 0.00 0.0 3.61 F
1621 1779 0.172803 GCCAAAGCCTGATCTTGCTG 59.827 55.0 9.80 1.13 38.0 4.41 F
2271 2448 0.180171 TTGGTCCCACATATGCTCCG 59.820 55.0 1.58 0.00 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1675 0.741221 GAAACTGTAGCGCCCAGGAG 60.741 60.000 23.70 8.43 34.16 3.69 R
1533 1691 1.776580 CGCGTCGTCGAAATGGAAA 59.223 52.632 6.17 0.00 39.71 3.13 R
2425 2611 0.322816 TGCTTGCCCTCCAATCTCAC 60.323 55.000 0.00 0.00 31.91 3.51 R
3011 3197 0.317160 TCCATGGATCCGCGATACAC 59.683 55.000 11.44 0.00 35.53 2.90 R
4192 4442 0.521735 GCCCGTTTCTCAAAATCGCT 59.478 50.000 0.00 0.00 0.00 4.93 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
62 63 5.404096 TGCTATCGTCGTGTTAAAATCTCA 58.596 37.500 0.00 0.00 0.00 3.27
90 92 5.104259 TGGGTGCCACTTGTTTTATTTTT 57.896 34.783 0.00 0.00 0.00 1.94
91 93 5.119694 TGGGTGCCACTTGTTTTATTTTTC 58.880 37.500 0.00 0.00 0.00 2.29
97 99 6.978080 TGCCACTTGTTTTATTTTTCTGAGAC 59.022 34.615 0.00 0.00 0.00 3.36
103 105 1.365699 TATTTTTCTGAGACGGCGGC 58.634 50.000 13.24 8.92 0.00 6.53
140 142 4.335315 CAGTCAAGTAAAGTGACAGGCAAA 59.665 41.667 7.26 0.00 46.44 3.68
155 157 0.040067 GCAAAGCAGAAAGTCCCACG 60.040 55.000 0.00 0.00 0.00 4.94
162 164 2.098443 GCAGAAAGTCCCACGTTGAAAA 59.902 45.455 0.00 0.00 0.00 2.29
168 170 3.283751 AGTCCCACGTTGAAAATTGACA 58.716 40.909 0.00 0.00 0.00 3.58
192 194 1.726853 GAGACCCGTCCTTTGTCATG 58.273 55.000 0.00 0.00 0.00 3.07
197 199 0.719465 CCGTCCTTTGTCATGTACGC 59.281 55.000 0.00 0.00 0.00 4.42
201 203 1.070914 TCCTTTGTCATGTACGCACCA 59.929 47.619 0.00 0.00 0.00 4.17
215 217 0.035630 GCACCAGAGGAACAGCATCT 60.036 55.000 0.00 0.00 38.36 2.90
216 218 2.011046 GCACCAGAGGAACAGCATCTC 61.011 57.143 0.00 0.00 34.98 2.75
225 227 3.055530 AGGAACAGCATCTCGACTGAAAT 60.056 43.478 7.68 0.00 37.35 2.17
241 243 5.555017 ACTGAAATGCTTGTCATGTACTCT 58.445 37.500 0.00 0.00 35.13 3.24
246 248 2.164422 TGCTTGTCATGTACTCTCTCCG 59.836 50.000 0.00 0.00 0.00 4.63
250 252 2.290705 TGTCATGTACTCTCTCCGTCCA 60.291 50.000 0.00 0.00 0.00 4.02
252 254 3.192844 GTCATGTACTCTCTCCGTCCAAA 59.807 47.826 0.00 0.00 0.00 3.28
279 281 9.780186 AAAACTTGTCTCTTAAAGTGCTATACT 57.220 29.630 0.00 0.00 42.89 2.12
282 284 9.463902 ACTTGTCTCTTAAAGTGCTATACTAGA 57.536 33.333 0.00 0.00 39.18 2.43
294 296 9.935241 AAGTGCTATACTAGATACATCCATTTG 57.065 33.333 0.00 0.00 39.18 2.32
295 297 9.314133 AGTGCTATACTAGATACATCCATTTGA 57.686 33.333 0.00 0.00 38.04 2.69
296 298 9.579768 GTGCTATACTAGATACATCCATTTGAG 57.420 37.037 0.00 0.00 0.00 3.02
297 299 9.533831 TGCTATACTAGATACATCCATTTGAGA 57.466 33.333 0.00 0.00 0.00 3.27
302 304 8.311395 ACTAGATACATCCATTTGAGAGACAA 57.689 34.615 0.00 0.00 36.65 3.18
303 305 8.420222 ACTAGATACATCCATTTGAGAGACAAG 58.580 37.037 0.00 0.00 39.77 3.16
304 306 7.192852 AGATACATCCATTTGAGAGACAAGT 57.807 36.000 0.00 0.00 39.77 3.16
306 308 8.105829 AGATACATCCATTTGAGAGACAAGTTT 58.894 33.333 0.00 0.00 39.77 2.66
307 309 6.966534 ACATCCATTTGAGAGACAAGTTTT 57.033 33.333 0.00 0.00 39.77 2.43
308 310 7.352079 ACATCCATTTGAGAGACAAGTTTTT 57.648 32.000 0.00 0.00 39.77 1.94
360 362 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
363 365 0.033796 TCGGACGGAGGGAGTATGTT 60.034 55.000 0.00 0.00 0.00 2.71
364 366 0.102481 CGGACGGAGGGAGTATGTTG 59.898 60.000 0.00 0.00 0.00 3.33
377 380 0.391130 TATGTTGCTGACCACTCCGC 60.391 55.000 0.00 0.00 0.00 5.54
393 396 4.560856 GCTCTCCAGCGCGACGAT 62.561 66.667 12.10 0.00 35.39 3.73
405 408 1.006832 GCGACGATGCTAACAATGGT 58.993 50.000 0.00 0.00 0.00 3.55
419 434 6.366061 GCTAACAATGGTCTGGTTTTGATTTC 59.634 38.462 0.00 0.00 0.00 2.17
467 482 1.212455 TTACGTGCGCACACTGACTG 61.212 55.000 37.03 22.26 45.10 3.51
470 485 1.276844 GTGCGCACACTGACTGAAC 59.723 57.895 34.52 2.71 43.85 3.18
475 490 1.597742 GCACACTGACTGAACCATGT 58.402 50.000 0.00 0.00 0.00 3.21
476 491 1.532868 GCACACTGACTGAACCATGTC 59.467 52.381 0.00 0.00 0.00 3.06
477 492 1.794701 CACACTGACTGAACCATGTCG 59.205 52.381 0.00 0.00 36.10 4.35
478 493 1.412710 ACACTGACTGAACCATGTCGT 59.587 47.619 0.00 0.00 36.10 4.34
504 519 2.417097 GCATGCGGCCATAAACCC 59.583 61.111 0.00 0.00 36.11 4.11
507 522 0.102844 CATGCGGCCATAAACCCTTG 59.897 55.000 2.24 0.00 0.00 3.61
513 528 2.560981 CGGCCATAAACCCTTGTTTTCT 59.439 45.455 2.24 0.00 41.92 2.52
514 529 3.006430 CGGCCATAAACCCTTGTTTTCTT 59.994 43.478 2.24 0.00 41.92 2.52
515 530 4.314961 GGCCATAAACCCTTGTTTTCTTG 58.685 43.478 0.00 0.00 41.92 3.02
516 531 4.202315 GGCCATAAACCCTTGTTTTCTTGT 60.202 41.667 0.00 0.00 41.92 3.16
517 532 5.011227 GGCCATAAACCCTTGTTTTCTTGTA 59.989 40.000 0.00 0.00 41.92 2.41
556 571 9.128107 CATTCAACGCTTACATTTTCTTGTAAT 57.872 29.630 0.00 0.00 40.34 1.89
557 572 9.691362 ATTCAACGCTTACATTTTCTTGTAATT 57.309 25.926 0.00 0.00 40.34 1.40
586 601 3.828451 ACTGGTCCCATGTCATTTTCTTG 59.172 43.478 0.00 0.00 0.00 3.02
587 602 3.828451 CTGGTCCCATGTCATTTTCTTGT 59.172 43.478 0.00 0.00 0.00 3.16
634 720 4.234530 CTGAAAGCCTGAAACCTGAAAG 57.765 45.455 0.00 0.00 0.00 2.62
686 798 6.540551 TGTTGCTGACTGAATACAACAAGTTA 59.459 34.615 4.52 0.00 45.38 2.24
700 812 5.423931 ACAACAAGTTACCACCAAAGGAAAT 59.576 36.000 0.00 0.00 0.00 2.17
706 818 2.504367 ACCACCAAAGGAAATGACGAG 58.496 47.619 0.00 0.00 0.00 4.18
709 821 3.557054 CCACCAAAGGAAATGACGAGAGA 60.557 47.826 0.00 0.00 0.00 3.10
710 822 4.065088 CACCAAAGGAAATGACGAGAGAA 58.935 43.478 0.00 0.00 0.00 2.87
711 823 4.153117 CACCAAAGGAAATGACGAGAGAAG 59.847 45.833 0.00 0.00 0.00 2.85
712 824 3.686726 CCAAAGGAAATGACGAGAGAAGG 59.313 47.826 0.00 0.00 0.00 3.46
715 827 1.066143 GGAAATGACGAGAGAAGGCCA 60.066 52.381 5.01 0.00 0.00 5.36
716 828 2.420687 GGAAATGACGAGAGAAGGCCAT 60.421 50.000 5.01 0.00 0.00 4.40
792 936 6.511767 CGGCAGCCTTTGTATACTAATGAAAG 60.512 42.308 10.54 5.22 0.00 2.62
793 937 6.542370 GGCAGCCTTTGTATACTAATGAAAGA 59.458 38.462 3.29 0.00 0.00 2.52
794 938 7.067008 GGCAGCCTTTGTATACTAATGAAAGAA 59.933 37.037 3.29 0.00 0.00 2.52
795 939 8.458843 GCAGCCTTTGTATACTAATGAAAGAAA 58.541 33.333 12.05 0.00 0.00 2.52
815 959 5.821470 AGAAATACATCACAGCTTGAGGATG 59.179 40.000 14.52 12.49 38.35 3.51
830 974 6.419484 TTGAGGATGAAGACTTCACAACTA 57.581 37.500 19.96 4.83 43.48 2.24
831 975 6.419484 TGAGGATGAAGACTTCACAACTAA 57.581 37.500 19.96 8.90 43.48 2.24
870 1014 2.036862 ACCAGAACCTAACACTTCCGTC 59.963 50.000 0.00 0.00 0.00 4.79
872 1016 3.244112 CCAGAACCTAACACTTCCGTCTT 60.244 47.826 0.00 0.00 0.00 3.01
873 1017 3.988517 CAGAACCTAACACTTCCGTCTTC 59.011 47.826 0.00 0.00 0.00 2.87
874 1018 3.640029 AGAACCTAACACTTCCGTCTTCA 59.360 43.478 0.00 0.00 0.00 3.02
886 1031 7.331193 ACACTTCCGTCTTCATCATTAAACTAC 59.669 37.037 0.00 0.00 0.00 2.73
896 1041 9.760660 CTTCATCATTAAACTACAGCAGTAAAC 57.239 33.333 0.00 0.00 36.04 2.01
959 1104 3.066342 CAGCATTCACCTGTGATCATTCC 59.934 47.826 0.00 0.00 39.64 3.01
980 1125 4.844085 TCCAAGGAAAGATCAACCTGAGTA 59.156 41.667 0.00 0.00 34.03 2.59
985 1130 4.383226 GGAAAGATCAACCTGAGTACCTCC 60.383 50.000 0.00 0.00 0.00 4.30
1004 1149 1.909781 AGCCTGCAACCAACATGGG 60.910 57.895 0.00 0.00 43.37 4.00
1005 1150 2.658422 CCTGCAACCAACATGGGC 59.342 61.111 0.00 0.00 43.37 5.36
1037 1185 2.167487 CCTCCCTGCTTCTACTGACTTC 59.833 54.545 0.00 0.00 0.00 3.01
1053 1201 3.243670 TGACTTCGATGATCCATCTGCTC 60.244 47.826 5.16 0.00 38.59 4.26
1095 1243 3.898509 CTCTCGCCAGGCTCCTCG 61.899 72.222 10.54 0.00 0.00 4.63
1110 1258 2.750637 TCGCTCTCCACCGAGGAC 60.751 66.667 0.00 0.00 43.07 3.85
1205 1353 4.796231 CTCCGTCTGGTTCGCCGG 62.796 72.222 0.00 0.00 45.14 6.13
1317 1468 2.806608 TGGTTGTGGAAGACTACGAC 57.193 50.000 0.00 0.00 39.94 4.34
1321 1472 1.513586 GTGGAAGACTACGACGGCG 60.514 63.158 10.39 10.39 44.79 6.46
1417 1575 2.046023 TCAGCGGCCAAGGTGATG 60.046 61.111 2.24 0.00 42.80 3.07
1517 1675 2.202566 GTCCGCTCATAGGTTACTTGC 58.797 52.381 0.00 0.00 0.00 4.01
1533 1691 3.775654 GCTCCTGGGCGCTACAGT 61.776 66.667 23.89 0.00 34.16 3.55
1548 1706 3.181533 GCTACAGTTTCCATTTCGACGAC 60.182 47.826 0.00 0.00 0.00 4.34
1563 1721 2.020559 GACGCGCATTTGCTCTCG 59.979 61.111 5.73 4.43 39.32 4.04
1579 1737 2.274437 TCTCGCTGTTTGATGATGAGC 58.726 47.619 0.00 0.00 0.00 4.26
1621 1779 0.172803 GCCAAAGCCTGATCTTGCTG 59.827 55.000 9.80 1.13 38.00 4.41
1850 2017 1.287815 CCTGCTTCGTACACGGTCA 59.712 57.895 1.39 0.00 40.29 4.02
1896 2063 0.181350 ATACACCTAGGCCTGCTTGC 59.819 55.000 17.99 0.00 0.00 4.01
1947 2114 1.600916 AAGTGACCGGAGCAAAGGC 60.601 57.895 9.46 0.00 41.61 4.35
2157 2331 1.273327 CCAAAGTCATCCCTTGTTGGC 59.727 52.381 0.00 0.00 0.00 4.52
2160 2334 2.046285 GTCATCCCTTGTTGGCGGG 61.046 63.158 0.00 0.00 42.05 6.13
2271 2448 0.180171 TTGGTCCCACATATGCTCCG 59.820 55.000 1.58 0.00 0.00 4.63
2382 2568 9.507329 TTCTATGGGTTCTTATCAGCAATATTC 57.493 33.333 0.00 0.00 0.00 1.75
2549 2735 2.213499 AGCAACTCGGAAGTTCAAGTG 58.787 47.619 5.01 2.10 43.99 3.16
2688 2874 5.702670 TGAACTGAGTGTGATTGGAAAGATC 59.297 40.000 0.00 0.00 0.00 2.75
2766 2952 8.316214 AGGATATTGGTTTTAGAGTACGTTGAA 58.684 33.333 0.00 0.00 0.00 2.69
2781 2967 4.678622 ACGTTGAAAATGGTTCTTTGGAC 58.321 39.130 0.00 0.00 37.08 4.02
2787 2973 5.578727 TGAAAATGGTTCTTTGGACAAAACG 59.421 36.000 0.00 0.00 0.00 3.60
2890 3076 3.501445 GGCTTATCTTCATCATGAGTGCC 59.499 47.826 0.09 0.85 0.00 5.01
2942 3128 4.194640 CCTGAGAACATACTGTTGGATGG 58.805 47.826 0.00 0.00 41.28 3.51
3011 3197 2.309136 AGGGGTGGATCCAACAAAAG 57.691 50.000 30.61 0.00 38.11 2.27
3165 3351 2.362760 TGGGCGCCAAATGCTGAT 60.363 55.556 30.85 0.00 38.05 2.90
3251 3443 4.439057 GGTAGCAAACAGTTATGGATCGA 58.561 43.478 0.00 0.00 0.00 3.59
3273 3465 5.624509 CGATGACTTCATTGACTCCAGGTTA 60.625 44.000 0.60 0.00 39.56 2.85
3384 3576 2.527100 GAAAATGCTGTGCAGATGCTC 58.473 47.619 6.35 3.06 43.65 4.26
3444 3648 5.948992 ATTCTACCAACTGAACAAAGAGC 57.051 39.130 0.00 0.00 0.00 4.09
3467 3671 6.260936 AGCTTGGTGTTTGATATAGCATACAC 59.739 38.462 26.64 26.64 44.59 2.90
3475 3679 7.877612 TGTTTGATATAGCATACACCATCGATT 59.122 33.333 9.76 0.00 0.00 3.34
3483 3687 7.834068 AGCATACACCATCGATTATTATCAC 57.166 36.000 0.00 0.00 0.00 3.06
3510 3715 9.919416 TGGATCCAAAACAAGATATCTATGAAA 57.081 29.630 13.46 0.00 0.00 2.69
3528 3733 9.112725 TCTATGAAATGTGTCCATGTAAATCAG 57.887 33.333 0.00 0.00 0.00 2.90
3646 3858 8.504005 GTTATGCTAGTTTGTGTTGTAACAGAT 58.496 33.333 0.00 0.00 40.05 2.90
3705 3921 4.742659 GCACAATATTTTCACGTTTGTGGT 59.257 37.500 21.85 0.00 46.42 4.16
3708 3924 7.115663 GCACAATATTTTCACGTTTGTGGTATT 59.884 33.333 21.85 6.23 46.42 1.89
3710 3926 9.187455 ACAATATTTTCACGTTTGTGGTATTTC 57.813 29.630 0.00 0.00 46.42 2.17
3819 4065 2.606725 TGTTTGCAAGCAAATTCCGTTG 59.393 40.909 21.43 0.00 45.90 4.10
3858 4104 1.180029 CCAGGAGGCAAGGTCAATTG 58.820 55.000 0.00 0.00 0.00 2.32
3913 4159 9.877178 CTAACAATACATAGTTCAGTCCTTTCT 57.123 33.333 0.00 0.00 0.00 2.52
3916 4162 4.828072 ACATAGTTCAGTCCTTTCTCCC 57.172 45.455 0.00 0.00 0.00 4.30
4039 4288 7.598869 TCCATTGTTGATAGAGTAATATGCGTC 59.401 37.037 0.00 0.00 0.00 5.19
4210 4460 4.413495 TTTAGCGATTTTGAGAAACGGG 57.587 40.909 0.00 0.00 0.00 5.28
4215 4465 2.979813 CGATTTTGAGAAACGGGCAAAG 59.020 45.455 0.00 0.00 33.60 2.77
4234 4484 5.528870 CAAAGAAATAACACAGGGACCAAC 58.471 41.667 0.00 0.00 0.00 3.77
4240 4490 7.507616 AGAAATAACACAGGGACCAACAATTAA 59.492 33.333 0.00 0.00 0.00 1.40
4331 4663 2.467826 GGAAGCATGAGGACTGCGC 61.468 63.158 0.00 0.00 44.38 6.09
4332 4664 1.449246 GAAGCATGAGGACTGCGCT 60.449 57.895 9.73 0.00 44.38 5.92
4333 4665 1.703438 GAAGCATGAGGACTGCGCTG 61.703 60.000 13.23 13.23 44.38 5.18
4334 4666 3.873883 GCATGAGGACTGCGCTGC 61.874 66.667 14.80 6.20 0.00 5.25
4335 4667 3.561213 CATGAGGACTGCGCTGCG 61.561 66.667 19.17 19.17 0.00 5.18
4357 4689 8.581057 TGCGTCTCTTTAAATTTGCAATTTTA 57.419 26.923 18.08 18.08 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.455113 CCAAGGTATGAGATTTTAACACGACG 60.455 42.308 0.00 0.00 0.00 5.12
46 47 6.183360 CCCAAGGTATGAGATTTTAACACGAC 60.183 42.308 0.00 0.00 0.00 4.34
47 48 5.878116 CCCAAGGTATGAGATTTTAACACGA 59.122 40.000 0.00 0.00 0.00 4.35
48 49 5.646360 ACCCAAGGTATGAGATTTTAACACG 59.354 40.000 0.00 0.00 32.11 4.49
62 63 0.777446 ACAAGTGGCACCCAAGGTAT 59.223 50.000 15.27 0.00 34.18 2.73
97 99 2.726691 CTAACAAGTGACGCCGCCG 61.727 63.158 0.00 0.00 41.14 6.46
103 105 2.148916 TGACTGCCTAACAAGTGACG 57.851 50.000 0.00 0.00 0.00 4.35
140 142 0.468226 TCAACGTGGGACTTTCTGCT 59.532 50.000 0.00 0.00 0.00 4.24
155 157 2.032377 TCTCGCCGTGTCAATTTTCAAC 60.032 45.455 0.00 0.00 0.00 3.18
162 164 2.264794 GGGTCTCGCCGTGTCAAT 59.735 61.111 0.00 0.00 38.44 2.57
192 194 1.014564 GCTGTTCCTCTGGTGCGTAC 61.015 60.000 0.00 0.00 0.00 3.67
197 199 1.738365 CGAGATGCTGTTCCTCTGGTG 60.738 57.143 0.00 0.00 0.00 4.17
201 203 1.476085 CAGTCGAGATGCTGTTCCTCT 59.524 52.381 0.00 0.00 0.00 3.69
215 217 3.402110 ACATGACAAGCATTTCAGTCGA 58.598 40.909 0.00 0.00 34.15 4.20
216 218 3.818961 ACATGACAAGCATTTCAGTCG 57.181 42.857 0.00 0.00 34.15 4.18
225 227 2.164422 CGGAGAGAGTACATGACAAGCA 59.836 50.000 0.00 0.00 0.00 3.91
268 270 9.935241 CAAATGGATGTATCTAGTATAGCACTT 57.065 33.333 0.00 0.00 38.99 3.16
269 271 9.314133 TCAAATGGATGTATCTAGTATAGCACT 57.686 33.333 0.00 0.00 38.99 4.40
271 273 9.533831 TCTCAAATGGATGTATCTAGTATAGCA 57.466 33.333 0.00 0.00 38.99 3.49
275 277 9.593565 TGTCTCTCAAATGGATGTATCTAGTAT 57.406 33.333 0.00 0.00 0.00 2.12
276 278 8.996651 TGTCTCTCAAATGGATGTATCTAGTA 57.003 34.615 0.00 0.00 0.00 1.82
277 279 7.904558 TGTCTCTCAAATGGATGTATCTAGT 57.095 36.000 0.00 0.00 0.00 2.57
278 280 8.420222 ACTTGTCTCTCAAATGGATGTATCTAG 58.580 37.037 0.00 0.00 35.48 2.43
279 281 8.311395 ACTTGTCTCTCAAATGGATGTATCTA 57.689 34.615 0.00 0.00 35.48 1.98
280 282 7.192852 ACTTGTCTCTCAAATGGATGTATCT 57.807 36.000 0.00 0.00 35.48 1.98
281 283 7.856145 AACTTGTCTCTCAAATGGATGTATC 57.144 36.000 0.00 0.00 35.48 2.24
282 284 8.641498 AAAACTTGTCTCTCAAATGGATGTAT 57.359 30.769 0.00 0.00 35.48 2.29
284 286 6.966534 AAAACTTGTCTCTCAAATGGATGT 57.033 33.333 0.00 0.00 35.48 3.06
340 342 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
341 343 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
344 346 0.033796 AACATACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
347 349 0.824759 AGCAACATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
351 353 1.555075 TGGTCAGCAACATACTCCCTC 59.445 52.381 0.00 0.00 0.00 4.30
360 362 2.280797 GCGGAGTGGTCAGCAACA 60.281 61.111 0.00 0.00 42.88 3.33
377 380 2.653448 CATCGTCGCGCTGGAGAG 60.653 66.667 5.56 0.00 0.00 3.20
387 390 2.282555 CAGACCATTGTTAGCATCGTCG 59.717 50.000 0.00 0.00 0.00 5.12
393 396 4.211125 TCAAAACCAGACCATTGTTAGCA 58.789 39.130 0.00 0.00 0.00 3.49
405 408 8.748412 TCTTTTTCTTCAGAAATCAAAACCAGA 58.252 29.630 2.83 0.00 42.83 3.86
419 434 7.862873 GTCTACCCATTGTTTCTTTTTCTTCAG 59.137 37.037 0.00 0.00 0.00 3.02
455 470 0.514255 CATGGTTCAGTCAGTGTGCG 59.486 55.000 0.00 0.00 0.00 5.34
467 482 0.385974 GCTGCAACACGACATGGTTC 60.386 55.000 0.00 0.00 0.00 3.62
470 485 2.174107 CGCTGCAACACGACATGG 59.826 61.111 0.00 0.00 0.00 3.66
492 507 2.560981 AGAAAACAAGGGTTTATGGCCG 59.439 45.455 0.00 0.00 46.20 6.13
513 528 7.696035 GCGTTGAATGTTGATTCATACATACAA 59.304 33.333 12.02 0.00 45.91 2.41
514 529 7.065683 AGCGTTGAATGTTGATTCATACATACA 59.934 33.333 12.02 3.60 45.91 2.29
515 530 7.409697 AGCGTTGAATGTTGATTCATACATAC 58.590 34.615 12.02 8.10 45.91 2.39
516 531 7.552458 AGCGTTGAATGTTGATTCATACATA 57.448 32.000 12.02 0.58 45.91 2.29
517 532 6.441093 AGCGTTGAATGTTGATTCATACAT 57.559 33.333 0.00 7.99 45.91 2.29
565 580 3.828451 ACAAGAAAATGACATGGGACCAG 59.172 43.478 0.00 0.00 0.00 4.00
586 601 5.758784 GGCTGGTGTATAGTCCTGAAATTAC 59.241 44.000 4.83 0.00 0.00 1.89
587 602 5.427157 TGGCTGGTGTATAGTCCTGAAATTA 59.573 40.000 4.83 0.00 0.00 1.40
628 714 3.388308 CTGTGTGGTCTCTGTCTTTCAG 58.612 50.000 0.00 0.00 44.85 3.02
629 715 2.103094 CCTGTGTGGTCTCTGTCTTTCA 59.897 50.000 0.00 0.00 0.00 2.69
631 717 2.398588 TCCTGTGTGGTCTCTGTCTTT 58.601 47.619 0.00 0.00 37.07 2.52
632 718 2.088104 TCCTGTGTGGTCTCTGTCTT 57.912 50.000 0.00 0.00 37.07 3.01
634 720 3.093057 ACTATCCTGTGTGGTCTCTGTC 58.907 50.000 0.00 0.00 37.07 3.51
686 798 2.105821 TCTCGTCATTTCCTTTGGTGGT 59.894 45.455 0.00 0.00 0.00 4.16
700 812 0.532573 GACATGGCCTTCTCTCGTCA 59.467 55.000 3.32 0.00 0.00 4.35
706 818 0.106819 AGCATGGACATGGCCTTCTC 60.107 55.000 21.02 6.65 39.16 2.87
709 821 2.056223 GCAGCATGGACATGGCCTT 61.056 57.895 21.02 10.26 39.16 4.35
710 822 2.441532 GCAGCATGGACATGGCCT 60.442 61.111 21.02 0.63 39.16 5.19
711 823 1.890625 TTTGCAGCATGGACATGGCC 61.891 55.000 12.04 12.04 34.66 5.36
712 824 0.459585 CTTTGCAGCATGGACATGGC 60.460 55.000 13.63 9.82 34.66 4.40
792 936 5.819379 TCATCCTCAAGCTGTGATGTATTTC 59.181 40.000 12.15 0.00 36.75 2.17
793 937 5.748402 TCATCCTCAAGCTGTGATGTATTT 58.252 37.500 12.15 0.00 36.75 1.40
794 938 5.363562 TCATCCTCAAGCTGTGATGTATT 57.636 39.130 12.15 0.00 36.75 1.89
795 939 5.129980 TCTTCATCCTCAAGCTGTGATGTAT 59.870 40.000 12.15 1.18 36.75 2.29
800 944 2.902486 AGTCTTCATCCTCAAGCTGTGA 59.098 45.455 0.00 0.00 34.17 3.58
830 974 6.542821 TCTGGTCAGTTCCATGAATAGTTTT 58.457 36.000 0.00 0.00 36.84 2.43
831 975 6.126863 TCTGGTCAGTTCCATGAATAGTTT 57.873 37.500 0.00 0.00 36.84 2.66
870 1014 9.760660 GTTTACTGCTGTAGTTTAATGATGAAG 57.239 33.333 3.17 0.00 40.89 3.02
872 1016 7.064134 CGGTTTACTGCTGTAGTTTAATGATGA 59.936 37.037 3.17 0.00 40.89 2.92
873 1017 7.180079 CGGTTTACTGCTGTAGTTTAATGATG 58.820 38.462 3.17 0.00 40.89 3.07
874 1018 6.183360 GCGGTTTACTGCTGTAGTTTAATGAT 60.183 38.462 3.17 0.00 44.58 2.45
913 1058 3.499737 GAATCCACCGGCAGTGCG 61.500 66.667 9.45 4.48 45.83 5.34
921 1066 3.469008 TGCTGTTATAGGAATCCACCG 57.531 47.619 0.61 0.00 34.73 4.94
959 1104 4.938226 GGTACTCAGGTTGATCTTTCCTTG 59.062 45.833 0.00 0.00 0.00 3.61
980 1125 2.766925 TTGGTTGCAGGCTGGAGGT 61.767 57.895 17.64 0.00 0.00 3.85
985 1130 1.290955 CCATGTTGGTTGCAGGCTG 59.709 57.895 10.94 10.94 31.35 4.85
1037 1185 1.979897 CGAGAGCAGATGGATCATCG 58.020 55.000 0.00 0.00 44.67 3.84
1287 1438 2.112928 ACAACCATGCTGCCGTCA 59.887 55.556 0.00 0.00 0.00 4.35
1296 1447 2.993899 GTCGTAGTCTTCCACAACCATG 59.006 50.000 0.00 0.00 0.00 3.66
1341 1492 1.649664 CCTTTGATGAGGAGCTGACG 58.350 55.000 0.00 0.00 39.25 4.35
1417 1575 3.054878 CAAAGCTTTGCCACAGAATGAC 58.945 45.455 25.26 0.00 39.69 3.06
1488 1646 2.271800 CTATGAGCGGACACCAACTTC 58.728 52.381 0.00 0.00 0.00 3.01
1517 1675 0.741221 GAAACTGTAGCGCCCAGGAG 60.741 60.000 23.70 8.43 34.16 3.69
1533 1691 1.776580 CGCGTCGTCGAAATGGAAA 59.223 52.632 6.17 0.00 39.71 3.13
1563 1721 2.097142 GTCCTGCTCATCATCAAACAGC 59.903 50.000 0.00 0.00 0.00 4.40
1579 1737 5.988561 GCCAGTAGATAAAAGAGATGTCCTG 59.011 44.000 0.00 0.00 0.00 3.86
1850 2017 6.543465 CACACATATTCCATTCATACCACACT 59.457 38.462 0.00 0.00 0.00 3.55
1947 2114 4.697756 TTGAACCTCGGCCGGCAG 62.698 66.667 30.85 26.21 0.00 4.85
2175 2349 7.232534 AGCTTGAGATAGATAGAACCAGGTAAG 59.767 40.741 0.00 0.00 0.00 2.34
2271 2448 9.463443 AAATATTTGTTCTTTGCACTACAGTTC 57.537 29.630 0.00 0.00 0.00 3.01
2382 2568 4.096382 GCCACAAATATTACCTCCACACAG 59.904 45.833 0.00 0.00 0.00 3.66
2425 2611 0.322816 TGCTTGCCCTCCAATCTCAC 60.323 55.000 0.00 0.00 31.91 3.51
2549 2735 2.190578 CGCCCCTCCCAATCTGAC 59.809 66.667 0.00 0.00 0.00 3.51
2766 2952 3.868661 GCGTTTTGTCCAAAGAACCATTT 59.131 39.130 0.00 0.00 0.00 2.32
2781 2967 4.041723 CCTTTCCACTAAACAGCGTTTTG 58.958 43.478 10.96 11.29 0.00 2.44
2787 2973 1.813178 GAGGCCTTTCCACTAAACAGC 59.187 52.381 6.77 0.00 37.29 4.40
2942 3128 2.489722 GTGATCTTTGGCTCCAAGTTCC 59.510 50.000 1.26 0.00 37.24 3.62
3011 3197 0.317160 TCCATGGATCCGCGATACAC 59.683 55.000 11.44 0.00 35.53 2.90
3251 3443 4.647564 AACCTGGAGTCAATGAAGTCAT 57.352 40.909 0.00 0.00 38.41 3.06
3273 3465 0.958822 GGTCATTGAACTGGCGGTTT 59.041 50.000 13.88 0.00 38.41 3.27
3384 3576 3.057736 CACTGGCTTCATCAACTGAAAGG 60.058 47.826 0.00 0.00 43.20 3.11
3467 3671 6.643388 TGGATCCAGTGATAATAATCGATGG 58.357 40.000 11.44 0.00 39.78 3.51
3483 3687 9.565090 TTCATAGATATCTTGTTTTGGATCCAG 57.435 33.333 15.53 1.98 0.00 3.86
3510 3715 4.860802 TCCCTGATTTACATGGACACAT 57.139 40.909 0.00 0.00 38.14 3.21
3528 3733 0.610232 AAGTGGCTCATGCAGTTCCC 60.610 55.000 0.00 0.00 41.91 3.97
3616 3828 6.165659 ACAACACAAACTAGCATAACGATC 57.834 37.500 0.00 0.00 0.00 3.69
3646 3858 4.454161 CCACATGGTCACACGAAATCTTAA 59.546 41.667 0.00 0.00 0.00 1.85
3708 3924 8.306038 CCATGAACATGTATTCTCAAAAAGGAA 58.694 33.333 12.74 0.00 37.11 3.36
3710 3926 7.037438 CCCATGAACATGTATTCTCAAAAAGG 58.963 38.462 12.74 1.29 37.11 3.11
3794 4040 3.551863 CGGAATTTGCTTGCAAACAGGTA 60.552 43.478 20.87 0.60 0.00 3.08
3819 4065 5.357032 CCTGGATATAACCAAAACAGGTGTC 59.643 44.000 3.04 0.00 42.25 3.67
3913 4159 2.704065 ACTCTGAACTTCCTTTTCGGGA 59.296 45.455 0.00 0.00 31.26 5.14
3916 4162 4.621991 TCTGACTCTGAACTTCCTTTTCG 58.378 43.478 0.00 0.00 0.00 3.46
4039 4288 9.855021 CTTTACTTTCCCCAAATGTTTATGTAG 57.145 33.333 0.00 0.00 0.00 2.74
4192 4442 0.521735 GCCCGTTTCTCAAAATCGCT 59.478 50.000 0.00 0.00 0.00 4.93
4210 4460 3.572255 TGGTCCCTGTGTTATTTCTTTGC 59.428 43.478 0.00 0.00 0.00 3.68
4215 4465 5.722021 ATTGTTGGTCCCTGTGTTATTTC 57.278 39.130 0.00 0.00 0.00 2.17
4331 4663 6.695292 AATTGCAAATTTAAAGAGACGCAG 57.305 33.333 1.71 0.00 0.00 5.18
4332 4664 7.475771 AAAATTGCAAATTTAAAGAGACGCA 57.524 28.000 10.75 0.00 0.00 5.24
4333 4665 7.684083 GCTAAAATTGCAAATTTAAAGAGACGC 59.316 33.333 17.91 12.85 0.00 5.19
4334 4666 8.915654 AGCTAAAATTGCAAATTTAAAGAGACG 58.084 29.630 17.91 8.00 0.00 4.18
4357 4689 4.650972 TTGGGTCAAAATGTAGGTAGCT 57.349 40.909 0.00 0.00 0.00 3.32
4362 4694 3.306019 GCTGGTTTGGGTCAAAATGTAGG 60.306 47.826 0.00 0.00 35.03 3.18
4366 4698 2.548493 CCTGCTGGTTTGGGTCAAAATG 60.548 50.000 0.51 0.00 35.03 2.32
4367 4699 1.693606 CCTGCTGGTTTGGGTCAAAAT 59.306 47.619 0.51 0.00 35.03 1.82
4412 4744 2.434359 CTGCGTCTCGTTTCCCCC 60.434 66.667 0.00 0.00 0.00 5.40
4413 4745 2.434359 CCTGCGTCTCGTTTCCCC 60.434 66.667 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.