Multiple sequence alignment - TraesCS6B01G362000

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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 TraesCS6B01G362000 chr6B 100.000 3611 0 0 1 3611 633729679 633733289 0.000000e+00 6669.0
1 TraesCS6B01G362000 chr6B 92.081 985 76 1 1638 2622 612744562 612743580 0.000000e+00 1386.0
2 TraesCS6B01G362000 chr6B 90.359 1058 94 3 1656 2705 612270839 612269782 0.000000e+00 1382.0
3 TraesCS6B01G362000 chr6B 95.374 843 27 7 2772 3606 672136840 672136002 0.000000e+00 1330.0
4 TraesCS6B01G362000 chr6B 92.634 543 37 2 993 1535 612745155 612744616 0.000000e+00 778.0
5 TraesCS6B01G362000 chr6B 92.669 532 36 2 999 1530 612271447 612270919 0.000000e+00 763.0
6 TraesCS6B01G362000 chr6B 83.268 257 17 13 618 860 612745620 612745376 2.820000e-51 213.0
7 TraesCS6B01G362000 chr6B 93.333 75 5 0 471 545 77458147 77458221 1.060000e-20 111.0
8 TraesCS6B01G362000 chr6B 79.688 128 18 5 618 744 612271904 612271784 6.420000e-13 86.1
9 TraesCS6B01G362000 chr6B 90.476 63 3 2 796 857 612271681 612271621 2.990000e-11 80.5
10 TraesCS6B01G362000 chr6D 94.428 2046 84 14 707 2739 420569439 420567411 0.000000e+00 3120.0
11 TraesCS6B01G362000 chr6D 94.075 2059 92 12 712 2746 420558956 420561008 0.000000e+00 3099.0
12 TraesCS6B01G362000 chr6D 89.988 1708 150 8 993 2693 408157089 408155396 0.000000e+00 2187.0
13 TraesCS6B01G362000 chr6D 88.889 1719 148 23 999 2705 59089086 59087399 0.000000e+00 2076.0
14 TraesCS6B01G362000 chr6D 90.227 440 40 2 1 438 420570415 420569977 4.040000e-159 571.0
15 TraesCS6B01G362000 chr6D 90.183 438 41 2 3 438 420556269 420556706 1.450000e-158 569.0
16 TraesCS6B01G362000 chr6D 80.620 387 25 19 619 971 408157554 408157184 1.660000e-63 254.0
17 TraesCS6B01G362000 chr6D 81.569 255 21 8 620 858 59089542 59089298 1.710000e-43 187.0
18 TraesCS6B01G362000 chr6D 93.023 43 3 0 663 705 420558890 420558932 3.010000e-06 63.9
19 TraesCS6B01G362000 chr6A 92.562 2178 107 23 618 2746 563484355 563486526 0.000000e+00 3073.0
20 TraesCS6B01G362000 chr6A 88.547 1720 150 25 999 2705 553913299 553911614 0.000000e+00 2041.0
21 TraesCS6B01G362000 chr6A 89.217 1660 136 25 993 2641 553766978 553765351 0.000000e+00 2034.0
22 TraesCS6B01G362000 chr6A 87.443 438 53 2 1 438 563483870 563484305 1.500000e-138 503.0
23 TraesCS6B01G362000 chr6A 76.444 225 20 15 593 789 553767320 553767101 1.380000e-14 91.6
24 TraesCS6B01G362000 chr2B 96.548 840 24 4 2769 3606 731337813 731338649 0.000000e+00 1386.0
25 TraesCS6B01G362000 chr2B 95.853 844 28 6 2764 3606 42269849 42269012 0.000000e+00 1358.0
26 TraesCS6B01G362000 chr1B 96.177 837 28 3 2772 3606 99630752 99631586 0.000000e+00 1365.0
27 TraesCS6B01G362000 chr1B 95.249 842 30 6 2770 3606 664950409 664951245 0.000000e+00 1325.0
28 TraesCS6B01G362000 chr1B 95.775 71 3 0 480 550 72877122 72877052 8.190000e-22 115.0
29 TraesCS6B01G362000 chr1B 95.775 71 2 1 480 550 60120532 60120601 2.950000e-21 113.0
30 TraesCS6B01G362000 chr4A 95.390 846 29 7 2763 3604 669838656 669839495 0.000000e+00 1338.0
31 TraesCS6B01G362000 chr7B 95.590 839 27 6 2772 3606 381868306 381867474 0.000000e+00 1336.0
32 TraesCS6B01G362000 chr4B 95.119 840 34 7 2772 3606 638436729 638435892 0.000000e+00 1317.0
33 TraesCS6B01G362000 chr4B 94.084 862 35 12 2751 3606 642451019 642450168 0.000000e+00 1295.0
34 TraesCS6B01G362000 chr5D 97.143 70 1 1 481 550 120391749 120391817 2.280000e-22 117.0
35 TraesCS6B01G362000 chr3D 95.833 72 2 1 480 550 105890063 105889992 8.190000e-22 115.0
36 TraesCS6B01G362000 chr3D 92.105 76 6 0 470 545 613828388 613828463 1.370000e-19 108.0
37 TraesCS6B01G362000 chr3B 96.970 66 2 0 480 545 24003074 24003009 1.060000e-20 111.0
38 TraesCS6B01G362000 chr7D 91.139 79 7 0 480 558 363554611 363554533 1.370000e-19 108.0
39 TraesCS6B01G362000 chr4D 90.361 83 6 2 480 561 424572459 424572378 1.370000e-19 108.0


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 TraesCS6B01G362000 chr6B 633729679 633733289 3610 False 6669.000000 6669 100.000000 1 3611 1 chr6B.!!$F2 3610
1 TraesCS6B01G362000 chr6B 672136002 672136840 838 True 1330.000000 1330 95.374000 2772 3606 1 chr6B.!!$R1 834
2 TraesCS6B01G362000 chr6B 612743580 612745620 2040 True 792.333333 1386 89.327667 618 2622 3 chr6B.!!$R3 2004
3 TraesCS6B01G362000 chr6B 612269782 612271904 2122 True 577.900000 1382 88.298000 618 2705 4 chr6B.!!$R2 2087
4 TraesCS6B01G362000 chr6D 420567411 420570415 3004 True 1845.500000 3120 92.327500 1 2739 2 chr6D.!!$R3 2738
5 TraesCS6B01G362000 chr6D 420556269 420561008 4739 False 1243.966667 3099 92.427000 3 2746 3 chr6D.!!$F1 2743
6 TraesCS6B01G362000 chr6D 408155396 408157554 2158 True 1220.500000 2187 85.304000 619 2693 2 chr6D.!!$R2 2074
7 TraesCS6B01G362000 chr6D 59087399 59089542 2143 True 1131.500000 2076 85.229000 620 2705 2 chr6D.!!$R1 2085
8 TraesCS6B01G362000 chr6A 553911614 553913299 1685 True 2041.000000 2041 88.547000 999 2705 1 chr6A.!!$R1 1706
9 TraesCS6B01G362000 chr6A 563483870 563486526 2656 False 1788.000000 3073 90.002500 1 2746 2 chr6A.!!$F1 2745
10 TraesCS6B01G362000 chr6A 553765351 553767320 1969 True 1062.800000 2034 82.830500 593 2641 2 chr6A.!!$R2 2048
11 TraesCS6B01G362000 chr2B 731337813 731338649 836 False 1386.000000 1386 96.548000 2769 3606 1 chr2B.!!$F1 837
12 TraesCS6B01G362000 chr2B 42269012 42269849 837 True 1358.000000 1358 95.853000 2764 3606 1 chr2B.!!$R1 842
13 TraesCS6B01G362000 chr1B 99630752 99631586 834 False 1365.000000 1365 96.177000 2772 3606 1 chr1B.!!$F2 834
14 TraesCS6B01G362000 chr1B 664950409 664951245 836 False 1325.000000 1325 95.249000 2770 3606 1 chr1B.!!$F3 836
15 TraesCS6B01G362000 chr4A 669838656 669839495 839 False 1338.000000 1338 95.390000 2763 3604 1 chr4A.!!$F1 841
16 TraesCS6B01G362000 chr7B 381867474 381868306 832 True 1336.000000 1336 95.590000 2772 3606 1 chr7B.!!$R1 834
17 TraesCS6B01G362000 chr4B 638435892 638436729 837 True 1317.000000 1317 95.119000 2772 3606 1 chr4B.!!$R1 834
18 TraesCS6B01G362000 chr4B 642450168 642451019 851 True 1295.000000 1295 94.084000 2751 3606 1 chr4B.!!$R2 855


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
442 449 0.107654 GCACCATGTGACCTACTCCC 60.108 60.0 0.00 0.0 35.23 4.30 F
448 455 0.113776 TGTGACCTACTCCCTCCGTT 59.886 55.0 0.00 0.0 0.00 4.44 F
987 3676 0.389948 GCCGTCGACTGGTCTTGATT 60.390 55.0 21.74 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 4337 0.529773 GAGTGCACGTGTTGGAGACA 60.530 55.0 18.38 1.15 39.83 3.41 R
1782 4539 1.019673 GCACTATGTACTCGTCCGGA 58.980 55.0 0.00 0.00 0.00 5.14 R
2730 5500 0.037326 TGCTCTAAGTGGCCTGTTCG 60.037 55.0 3.32 0.00 0.00 3.95 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
95 101 3.370672 TCGGACATTTCATCGAACACATG 59.629 43.478 0.00 0.00 0.00 3.21
116 122 2.087009 GCGCGAGGTGTATATCCGC 61.087 63.158 12.10 0.00 42.11 5.54
117 123 1.284715 CGCGAGGTGTATATCCGCA 59.715 57.895 0.00 0.00 45.32 5.69
135 141 1.489481 CAGGAGCAGGATGTACTGGA 58.511 55.000 0.00 0.00 39.31 3.86
161 167 1.737793 GACCTTGATCGGTTGCGATTT 59.262 47.619 0.00 0.00 37.42 2.17
324 331 3.803162 GGCAAGGAGAGGGGAGGC 61.803 72.222 0.00 0.00 0.00 4.70
325 332 3.803162 GCAAGGAGAGGGGAGGCC 61.803 72.222 0.00 0.00 0.00 5.19
329 336 2.041265 GGAGAGGGGAGGCCTTCA 59.959 66.667 14.70 0.00 0.00 3.02
331 338 1.631071 GGAGAGGGGAGGCCTTCAAG 61.631 65.000 14.70 0.00 0.00 3.02
346 353 0.400213 TCAAGAGAATTGGTGCGGGT 59.600 50.000 0.00 0.00 0.00 5.28
350 357 0.322546 GAGAATTGGTGCGGGTCCTT 60.323 55.000 0.00 0.00 0.00 3.36
357 364 3.751246 TGCGGGTCCTTACGGTCG 61.751 66.667 0.00 0.00 0.00 4.79
358 365 4.503314 GCGGGTCCTTACGGTCGG 62.503 72.222 0.00 0.00 0.00 4.79
370 377 2.106332 GGTCGGTCCTATGTGGCG 59.894 66.667 0.00 0.00 35.26 5.69
378 385 2.188829 CCTATGTGGCGGGCATGTG 61.189 63.158 7.75 0.00 0.00 3.21
411 418 2.415625 GGGCGTTACTATATCTGCCTCG 60.416 54.545 0.69 0.00 42.11 4.63
414 421 3.058432 GCGTTACTATATCTGCCTCGACA 60.058 47.826 0.00 0.00 0.00 4.35
418 425 3.288092 ACTATATCTGCCTCGACACACA 58.712 45.455 0.00 0.00 0.00 3.72
438 445 5.215252 ACATATAGCACCATGTGACCTAC 57.785 43.478 0.00 0.00 35.23 3.18
439 446 4.901849 ACATATAGCACCATGTGACCTACT 59.098 41.667 0.00 0.00 35.23 2.57
440 447 5.011125 ACATATAGCACCATGTGACCTACTC 59.989 44.000 0.00 0.00 35.23 2.59
441 448 0.905357 AGCACCATGTGACCTACTCC 59.095 55.000 0.00 0.00 35.23 3.85
442 449 0.107654 GCACCATGTGACCTACTCCC 60.108 60.000 0.00 0.00 35.23 4.30
443 450 1.573108 CACCATGTGACCTACTCCCT 58.427 55.000 0.00 0.00 35.23 4.20
444 451 1.482593 CACCATGTGACCTACTCCCTC 59.517 57.143 0.00 0.00 35.23 4.30
445 452 1.123928 CCATGTGACCTACTCCCTCC 58.876 60.000 0.00 0.00 0.00 4.30
446 453 0.747255 CATGTGACCTACTCCCTCCG 59.253 60.000 0.00 0.00 0.00 4.63
447 454 0.335361 ATGTGACCTACTCCCTCCGT 59.665 55.000 0.00 0.00 0.00 4.69
448 455 0.113776 TGTGACCTACTCCCTCCGTT 59.886 55.000 0.00 0.00 0.00 4.44
449 456 1.355381 TGTGACCTACTCCCTCCGTTA 59.645 52.381 0.00 0.00 0.00 3.18
450 457 1.747924 GTGACCTACTCCCTCCGTTAC 59.252 57.143 0.00 0.00 0.00 2.50
451 458 1.637553 TGACCTACTCCCTCCGTTACT 59.362 52.381 0.00 0.00 0.00 2.24
452 459 2.846206 TGACCTACTCCCTCCGTTACTA 59.154 50.000 0.00 0.00 0.00 1.82
453 460 3.461085 TGACCTACTCCCTCCGTTACTAT 59.539 47.826 0.00 0.00 0.00 2.12
454 461 4.660303 TGACCTACTCCCTCCGTTACTATA 59.340 45.833 0.00 0.00 0.00 1.31
455 462 5.311649 TGACCTACTCCCTCCGTTACTATAT 59.688 44.000 0.00 0.00 0.00 0.86
456 463 5.814481 ACCTACTCCCTCCGTTACTATATC 58.186 45.833 0.00 0.00 0.00 1.63
457 464 5.551189 ACCTACTCCCTCCGTTACTATATCT 59.449 44.000 0.00 0.00 0.00 1.98
458 465 5.881443 CCTACTCCCTCCGTTACTATATCTG 59.119 48.000 0.00 0.00 0.00 2.90
459 466 4.080687 ACTCCCTCCGTTACTATATCTGC 58.919 47.826 0.00 0.00 0.00 4.26
460 467 3.428532 TCCCTCCGTTACTATATCTGCC 58.571 50.000 0.00 0.00 0.00 4.85
461 468 3.075582 TCCCTCCGTTACTATATCTGCCT 59.924 47.826 0.00 0.00 0.00 4.75
462 469 3.444388 CCCTCCGTTACTATATCTGCCTC 59.556 52.174 0.00 0.00 0.00 4.70
463 470 4.079970 CCTCCGTTACTATATCTGCCTCA 58.920 47.826 0.00 0.00 0.00 3.86
464 471 4.523173 CCTCCGTTACTATATCTGCCTCAA 59.477 45.833 0.00 0.00 0.00 3.02
465 472 5.449107 TCCGTTACTATATCTGCCTCAAC 57.551 43.478 0.00 0.00 0.00 3.18
466 473 4.023450 TCCGTTACTATATCTGCCTCAACG 60.023 45.833 0.00 0.00 37.76 4.10
467 474 4.261489 CCGTTACTATATCTGCCTCAACGT 60.261 45.833 0.00 0.00 36.65 3.99
468 475 5.049198 CCGTTACTATATCTGCCTCAACGTA 60.049 44.000 0.00 0.00 36.65 3.57
469 476 5.850128 CGTTACTATATCTGCCTCAACGTAC 59.150 44.000 0.00 0.00 34.44 3.67
470 477 6.512253 CGTTACTATATCTGCCTCAACGTACA 60.512 42.308 0.00 0.00 34.44 2.90
471 478 7.368833 GTTACTATATCTGCCTCAACGTACAT 58.631 38.462 0.00 0.00 0.00 2.29
472 479 8.509690 GTTACTATATCTGCCTCAACGTACATA 58.490 37.037 0.00 0.00 0.00 2.29
473 480 7.704578 ACTATATCTGCCTCAACGTACATAT 57.295 36.000 0.00 0.00 0.00 1.78
474 481 8.803397 ACTATATCTGCCTCAACGTACATATA 57.197 34.615 0.00 0.00 0.00 0.86
475 482 9.409918 ACTATATCTGCCTCAACGTACATATAT 57.590 33.333 0.00 0.00 0.00 0.86
508 515 9.778741 ACATCCGTATGTGATTTATAGTGAAAT 57.221 29.630 0.00 0.00 44.79 2.17
511 518 9.692749 TCCGTATGTGATTTATAGTGAAATCTC 57.307 33.333 9.56 7.06 43.40 2.75
512 519 9.698309 CCGTATGTGATTTATAGTGAAATCTCT 57.302 33.333 9.56 0.00 43.40 3.10
540 547 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
541 548 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
542 549 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
543 550 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
544 551 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
548 555 5.767277 TTTAGGAACGGAGGGAGTAATTT 57.233 39.130 0.00 0.00 0.00 1.82
575 779 1.081242 CAACGCATGTGACCTTGCC 60.081 57.895 14.43 0.00 38.23 4.52
591 795 2.203070 CCGATTCGGCCCCTTCAG 60.203 66.667 12.95 0.00 41.17 3.02
608 812 3.984765 GCGCGCACGTATAGCACC 61.985 66.667 29.10 0.00 42.83 5.01
675 2981 1.685765 CCGACCTCAGGATGACCCA 60.686 63.158 0.00 0.00 42.56 4.51
775 3331 4.345854 ACAAACAGTTTACTCACCCCAAA 58.654 39.130 0.00 0.00 0.00 3.28
896 3537 2.289694 CCTGCCTATAAATACAGCCGCT 60.290 50.000 0.00 0.00 0.00 5.52
987 3676 0.389948 GCCGTCGACTGGTCTTGATT 60.390 55.000 21.74 0.00 0.00 2.57
1011 3734 1.681793 TCGGAGAAGATGGGTTCGATC 59.318 52.381 0.00 0.00 0.00 3.69
1012 3735 1.409064 CGGAGAAGATGGGTTCGATCA 59.591 52.381 0.00 0.00 0.00 2.92
1013 3736 2.036475 CGGAGAAGATGGGTTCGATCAT 59.964 50.000 0.00 0.00 0.00 2.45
1014 3737 3.397482 GGAGAAGATGGGTTCGATCATG 58.603 50.000 0.00 0.00 0.00 3.07
1015 3738 3.070159 GGAGAAGATGGGTTCGATCATGA 59.930 47.826 0.00 0.00 0.00 3.07
1016 3739 4.054671 GAGAAGATGGGTTCGATCATGAC 58.945 47.826 0.00 0.00 0.00 3.06
1152 3883 2.132762 GTCAACACCGAGTACAACCAG 58.867 52.381 0.00 0.00 0.00 4.00
1224 3955 4.473520 CGCTTCGCCACCATCCCT 62.474 66.667 0.00 0.00 0.00 4.20
1602 4345 2.530497 GCGCACGTTGTGTCTCCAA 61.530 57.895 0.30 0.00 35.75 3.53
1612 4355 1.520192 TGTCTCCAACACGTGCACT 59.480 52.632 17.22 0.00 31.20 4.40
1620 4363 2.740055 CACGTGCACTCTCTGCCC 60.740 66.667 16.19 0.00 46.51 5.36
1636 4387 2.620115 CTGCCCATTATCAGCGTTGATT 59.380 45.455 20.20 0.00 41.24 2.57
1654 4405 7.678218 GCGTTGATTGAAGCTCTTATCTGAATT 60.678 37.037 0.00 0.00 0.00 2.17
1701 4458 0.747255 AGCAGCTGACGAACGGATAT 59.253 50.000 20.43 0.00 0.00 1.63
1872 4629 1.080093 CAACAGCTTCGCCGACCTA 60.080 57.895 0.00 0.00 0.00 3.08
1926 4683 1.761174 CCTGCCCAAGGTGTACACT 59.239 57.895 24.55 8.86 41.74 3.55
2152 4909 2.618816 GGGAAGCAGTTCATGTGGATCA 60.619 50.000 0.00 0.00 33.93 2.92
2175 4932 2.283966 CGAGACCTGGTGAGGGGT 60.284 66.667 2.82 0.00 44.84 4.95
2364 5121 2.042259 CAGCTGGCCATTCTTCGCA 61.042 57.895 5.51 0.00 0.00 5.10
2521 5278 3.760035 GAGCGGCGGAGTGGAAGA 61.760 66.667 9.78 0.00 0.00 2.87
2574 5331 1.148310 CGTCTCACCGCAACTTTGAT 58.852 50.000 0.00 0.00 0.00 2.57
2585 5342 2.879756 GCAACTTTGATGGGCTGGTCTA 60.880 50.000 0.00 0.00 0.00 2.59
2600 5357 1.674651 TCTACGACGTGCTCCTGCT 60.675 57.895 11.56 0.00 40.48 4.24
2611 5368 2.028567 GTGCTCCTGCTCAAGAACTAGT 60.029 50.000 0.00 0.00 40.48 2.57
2613 5370 2.999355 GCTCCTGCTCAAGAACTAGTTG 59.001 50.000 14.14 0.00 36.03 3.16
2682 5450 8.083462 TGTTTGTTAAGAAGGTTCGTTTCTTTT 58.917 29.630 5.66 0.00 40.92 2.27
2688 5456 4.273724 AGAAGGTTCGTTTCTTTTGAGAGC 59.726 41.667 0.00 0.00 30.98 4.09
2730 5500 5.004821 CAGTGTGATTGTGTAGAACGATAGC 59.995 44.000 0.00 0.00 42.67 2.97
2746 5516 1.552578 TAGCGAACAGGCCACTTAGA 58.447 50.000 5.01 0.00 0.00 2.10
2747 5517 0.247736 AGCGAACAGGCCACTTAGAG 59.752 55.000 5.01 0.00 0.00 2.43
2748 5518 1.362406 GCGAACAGGCCACTTAGAGC 61.362 60.000 5.01 0.00 0.00 4.09
2749 5519 0.037326 CGAACAGGCCACTTAGAGCA 60.037 55.000 5.01 0.00 0.00 4.26
2750 5520 1.406069 CGAACAGGCCACTTAGAGCAT 60.406 52.381 5.01 0.00 0.00 3.79
2751 5521 2.284190 GAACAGGCCACTTAGAGCATC 58.716 52.381 5.01 0.00 0.00 3.91
2767 5537 1.579698 CATCTCAACAGCTGCGCTAT 58.420 50.000 15.27 0.00 36.40 2.97
2790 5560 3.512516 GGCATCTCCAGCCGTTGC 61.513 66.667 0.00 0.00 43.15 4.17
2921 5694 1.298041 CACGGCGCAAAAACGACTT 60.298 52.632 10.83 0.00 39.56 3.01
3083 5859 2.050350 CGAGGAGGCGGTAGAACCA 61.050 63.158 0.00 0.00 38.47 3.67
3089 5865 2.025418 GGCGGTAGAACCACGTGTG 61.025 63.158 15.65 8.62 38.47 3.82
3582 6374 4.475135 GTCCAGGAGCTTCCCCGC 62.475 72.222 0.00 0.00 37.19 6.13
3606 6398 1.160870 TGAGAAGGAAGGGGGAGCA 59.839 57.895 0.00 0.00 0.00 4.26
3607 6399 0.253347 TGAGAAGGAAGGGGGAGCAT 60.253 55.000 0.00 0.00 0.00 3.79
3608 6400 0.182299 GAGAAGGAAGGGGGAGCATG 59.818 60.000 0.00 0.00 0.00 4.06
3609 6401 1.228510 GAAGGAAGGGGGAGCATGG 59.771 63.158 0.00 0.00 0.00 3.66
3610 6402 1.544917 AAGGAAGGGGGAGCATGGT 60.545 57.895 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 101 0.666577 GGATATACACCTCGCGCACC 60.667 60.000 8.75 0.00 0.00 5.01
116 122 1.489481 TCCAGTACATCCTGCTCCTG 58.511 55.000 0.00 0.00 0.00 3.86
117 123 1.834263 GTTCCAGTACATCCTGCTCCT 59.166 52.381 0.00 0.00 0.00 3.69
122 128 1.471287 TCGTCGTTCCAGTACATCCTG 59.529 52.381 0.00 0.00 0.00 3.86
135 141 0.316204 AACCGATCAAGGTCGTCGTT 59.684 50.000 1.77 0.00 45.21 3.85
190 197 0.812412 ATACGCCATAACGCCACCAC 60.812 55.000 0.00 0.00 36.19 4.16
201 208 1.547675 CCCAGCCCATAAATACGCCAT 60.548 52.381 0.00 0.00 0.00 4.40
269 276 3.761752 CTCTTCTCCTTTCTTCCTCGTCT 59.238 47.826 0.00 0.00 0.00 4.18
324 331 1.470098 CCGCACCAATTCTCTTGAAGG 59.530 52.381 0.00 0.00 35.44 3.46
325 332 1.470098 CCCGCACCAATTCTCTTGAAG 59.530 52.381 0.00 0.00 35.44 3.02
329 336 0.322546 GGACCCGCACCAATTCTCTT 60.323 55.000 0.00 0.00 0.00 2.85
331 338 0.322546 AAGGACCCGCACCAATTCTC 60.323 55.000 0.00 0.00 0.00 2.87
350 357 1.386525 GCCACATAGGACCGACCGTA 61.387 60.000 0.00 0.00 44.74 4.02
357 364 3.120086 ATGCCCGCCACATAGGACC 62.120 63.158 0.00 0.00 41.22 4.46
358 365 1.893808 CATGCCCGCCACATAGGAC 60.894 63.158 0.00 0.00 41.22 3.85
370 377 2.751436 ATGCGTCCACACATGCCC 60.751 61.111 0.00 0.00 0.00 5.36
386 393 2.165845 GCAGATATAGTAACGCCCGGAT 59.834 50.000 0.73 0.00 0.00 4.18
396 403 4.457466 TGTGTGTCGAGGCAGATATAGTA 58.543 43.478 0.00 0.00 0.00 1.82
397 404 3.288092 TGTGTGTCGAGGCAGATATAGT 58.712 45.455 0.00 0.00 0.00 2.12
411 418 4.801147 CACATGGTGCTATATGTGTGTC 57.199 45.455 15.15 0.00 45.58 3.67
418 425 4.528596 GGAGTAGGTCACATGGTGCTATAT 59.471 45.833 0.00 0.00 32.98 0.86
438 445 3.444388 GGCAGATATAGTAACGGAGGGAG 59.556 52.174 0.00 0.00 0.00 4.30
439 446 3.075582 AGGCAGATATAGTAACGGAGGGA 59.924 47.826 0.00 0.00 0.00 4.20
440 447 3.432378 AGGCAGATATAGTAACGGAGGG 58.568 50.000 0.00 0.00 0.00 4.30
441 448 4.079970 TGAGGCAGATATAGTAACGGAGG 58.920 47.826 0.00 0.00 0.00 4.30
442 449 5.462405 GTTGAGGCAGATATAGTAACGGAG 58.538 45.833 0.00 0.00 0.00 4.63
443 450 4.023450 CGTTGAGGCAGATATAGTAACGGA 60.023 45.833 0.00 0.00 36.85 4.69
444 451 4.227538 CGTTGAGGCAGATATAGTAACGG 58.772 47.826 0.00 0.00 36.85 4.44
445 452 4.856664 ACGTTGAGGCAGATATAGTAACG 58.143 43.478 0.00 0.00 43.48 3.18
446 453 6.732154 TGTACGTTGAGGCAGATATAGTAAC 58.268 40.000 0.00 0.00 0.00 2.50
447 454 6.947644 TGTACGTTGAGGCAGATATAGTAA 57.052 37.500 0.00 0.00 0.00 2.24
448 455 8.803397 ATATGTACGTTGAGGCAGATATAGTA 57.197 34.615 0.00 0.00 0.00 1.82
449 456 7.704578 ATATGTACGTTGAGGCAGATATAGT 57.295 36.000 0.00 0.00 0.00 2.12
485 492 9.692749 GAGATTTCACTATAAATCACATACGGA 57.307 33.333 10.86 0.00 44.70 4.69
486 493 9.698309 AGAGATTTCACTATAAATCACATACGG 57.302 33.333 10.86 0.00 44.70 4.02
514 521 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
515 522 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
516 523 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
517 524 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
518 525 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
519 526 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
520 527 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
521 528 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
522 529 8.731591 AATTACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
523 530 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
524 531 7.277396 CAAATTACTCCCTCCGTTCCTAAATA 58.723 38.462 0.00 0.00 0.00 1.40
525 532 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
526 533 5.493809 CAAATTACTCCCTCCGTTCCTAAA 58.506 41.667 0.00 0.00 0.00 1.85
527 534 4.080751 CCAAATTACTCCCTCCGTTCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
528 535 3.453353 CCAAATTACTCCCTCCGTTCCTA 59.547 47.826 0.00 0.00 0.00 2.94
529 536 2.238898 CCAAATTACTCCCTCCGTTCCT 59.761 50.000 0.00 0.00 0.00 3.36
530 537 2.026542 ACCAAATTACTCCCTCCGTTCC 60.027 50.000 0.00 0.00 0.00 3.62
531 538 3.007635 CACCAAATTACTCCCTCCGTTC 58.992 50.000 0.00 0.00 0.00 3.95
532 539 2.374170 ACACCAAATTACTCCCTCCGTT 59.626 45.455 0.00 0.00 0.00 4.44
533 540 1.982958 ACACCAAATTACTCCCTCCGT 59.017 47.619 0.00 0.00 0.00 4.69
534 541 2.781681 ACACCAAATTACTCCCTCCG 57.218 50.000 0.00 0.00 0.00 4.63
535 542 3.756963 GTGAACACCAAATTACTCCCTCC 59.243 47.826 0.00 0.00 0.00 4.30
536 543 4.394729 TGTGAACACCAAATTACTCCCTC 58.605 43.478 2.46 0.00 0.00 4.30
537 544 4.447138 TGTGAACACCAAATTACTCCCT 57.553 40.909 2.46 0.00 0.00 4.20
538 545 4.555906 CGTTGTGAACACCAAATTACTCCC 60.556 45.833 2.46 0.00 0.00 4.30
539 546 4.533222 CGTTGTGAACACCAAATTACTCC 58.467 43.478 2.46 0.00 0.00 3.85
540 547 3.972502 GCGTTGTGAACACCAAATTACTC 59.027 43.478 2.46 0.00 0.00 2.59
541 548 3.378742 TGCGTTGTGAACACCAAATTACT 59.621 39.130 2.46 0.00 0.00 2.24
542 549 3.696898 TGCGTTGTGAACACCAAATTAC 58.303 40.909 2.46 0.00 0.00 1.89
543 550 4.202060 ACATGCGTTGTGAACACCAAATTA 60.202 37.500 0.00 0.00 37.11 1.40
544 551 2.949451 TGCGTTGTGAACACCAAATT 57.051 40.000 2.46 0.00 0.00 1.82
548 555 2.787191 ACATGCGTTGTGAACACCA 58.213 47.368 0.00 0.00 37.11 4.17
575 779 2.897350 GCTGAAGGGGCCGAATCG 60.897 66.667 0.00 0.00 0.00 3.34
591 795 3.984765 GGTGCTATACGTGCGCGC 61.985 66.667 27.26 27.26 42.83 6.86
675 2981 0.104855 AGCCGCGTGTGATCATGTAT 59.895 50.000 4.92 0.00 33.51 2.29
769 3320 2.483014 TAGGATCGTGTTGTTTGGGG 57.517 50.000 0.00 0.00 0.00 4.96
770 3321 4.033587 CGTATTAGGATCGTGTTGTTTGGG 59.966 45.833 0.00 0.00 0.00 4.12
775 3331 4.707030 TGACGTATTAGGATCGTGTTGT 57.293 40.909 0.00 0.00 37.92 3.32
979 3667 3.914312 TCTTCTCCGACACAATCAAGAC 58.086 45.455 0.00 0.00 0.00 3.01
987 3676 1.275291 GAACCCATCTTCTCCGACACA 59.725 52.381 0.00 0.00 0.00 3.72
1594 4337 0.529773 GAGTGCACGTGTTGGAGACA 60.530 55.000 18.38 1.15 39.83 3.41
1612 4355 1.123077 ACGCTGATAATGGGCAGAGA 58.877 50.000 0.00 0.00 35.80 3.10
1620 4363 5.007430 AGAGCTTCAATCAACGCTGATAATG 59.993 40.000 0.94 0.00 41.66 1.90
1654 4405 2.539688 CTGCATGCGCGTAAAGATAGAA 59.460 45.455 14.09 0.00 42.97 2.10
1701 4458 2.709125 CTTCCACCGGCGTGTCAAGA 62.709 60.000 6.01 0.00 38.41 3.02
1782 4539 1.019673 GCACTATGTACTCGTCCGGA 58.980 55.000 0.00 0.00 0.00 5.14
2152 4909 3.461773 CACCAGGTCTCGGCGGAT 61.462 66.667 7.21 0.00 0.00 4.18
2409 5166 3.466836 GTTGTTATCGATCTCCATGCCA 58.533 45.455 0.00 0.00 0.00 4.92
2585 5342 2.755542 CTTGAGCAGGAGCACGTCGT 62.756 60.000 0.00 0.00 45.49 4.34
2600 5357 5.410746 ACGTCGATCTACAACTAGTTCTTGA 59.589 40.000 4.77 1.02 0.00 3.02
2611 5368 3.861276 ACAATGGACGTCGATCTACAA 57.139 42.857 13.75 0.00 0.00 2.41
2613 5370 4.918037 AGTTACAATGGACGTCGATCTAC 58.082 43.478 13.75 9.22 0.00 2.59
2688 5456 3.391665 GACCACTCAGGGCCCATCG 62.392 68.421 27.56 13.83 40.85 3.84
2713 5483 4.740268 TGTTCGCTATCGTTCTACACAAT 58.260 39.130 0.00 0.00 36.96 2.71
2730 5500 0.037326 TGCTCTAAGTGGCCTGTTCG 60.037 55.000 3.32 0.00 0.00 3.95
2759 5529 3.452474 GAGATGCCCTTATATAGCGCAG 58.548 50.000 11.47 0.00 40.77 5.18
2760 5530 2.168521 GGAGATGCCCTTATATAGCGCA 59.831 50.000 11.47 0.00 41.62 6.09
2761 5531 2.168521 TGGAGATGCCCTTATATAGCGC 59.831 50.000 0.00 0.00 34.97 5.92
2921 5694 3.846896 CGCCGATGTTTGCGTTAAATTTA 59.153 39.130 0.00 0.00 45.43 1.40
3046 5822 1.447140 GCATGTAGAACCGCGTGGA 60.447 57.895 24.59 0.00 39.21 4.02
3140 5916 2.611800 AGGGATGCAGCAGGGACA 60.612 61.111 3.51 0.00 0.00 4.02
3582 6374 2.125512 CCTTCCTTCTCACGCCGG 60.126 66.667 0.00 0.00 0.00 6.13



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

AutoCloner maintained by Alex Coulton.