Multiple sequence alignment - TraesCS6A01G103200

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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 TraesCS6A01G103200 chr6A 100.000 6623 0 0 1 6623 72437835 72431213 0.000000e+00 12231.0
1 TraesCS6A01G103200 chr6B 93.456 6326 242 68 184 6435 129276907 129270680 0.000000e+00 9230.0
2 TraesCS6A01G103200 chr6B 85.610 688 67 12 1941 2606 618113042 618113719 0.000000e+00 693.0
3 TraesCS6A01G103200 chr6B 96.503 143 5 0 6434 6576 129270641 129270499 3.090000e-58 237.0
4 TraesCS6A01G103200 chr6B 88.793 116 13 0 1769 1884 618112901 618113016 6.920000e-30 143.0
5 TraesCS6A01G103200 chr6B 100.000 30 0 0 6594 6623 129270502 129270473 1.000000e-03 56.5
6 TraesCS6A01G103200 chr6D 95.665 3645 92 27 3014 6623 57220767 57217154 0.000000e+00 5795.0
7 TraesCS6A01G103200 chr6D 92.170 2848 133 31 184 2978 57223566 57220756 0.000000e+00 3941.0
8 TraesCS6A01G103200 chr6D 93.923 181 10 1 3 183 57223779 57223600 8.460000e-69 272.0
9 TraesCS6A01G103200 chr5A 79.767 2061 313 65 3105 5106 591092308 591090293 0.000000e+00 1400.0
10 TraesCS6A01G103200 chr5A 79.445 613 97 19 1023 1626 591094729 591094137 2.220000e-109 407.0
11 TraesCS6A01G103200 chr5D 81.917 1377 194 33 3764 5106 470386859 470385504 0.000000e+00 1112.0
12 TraesCS6A01G103200 chr5D 80.524 611 96 19 1023 1626 470389829 470389235 1.310000e-121 448.0
13 TraesCS6A01G103200 chr5D 76.362 863 148 32 1731 2564 470389172 470388337 4.780000e-111 412.0
14 TraesCS6A01G103200 chr5D 81.436 404 69 5 3100 3503 470387568 470387171 6.400000e-85 326.0
15 TraesCS6A01G103200 chr5B 81.573 1373 204 30 3764 5106 577695264 577693911 0.000000e+00 1088.0
16 TraesCS6A01G103200 chr5B 76.647 865 142 36 1731 2564 577697443 577696608 2.210000e-114 424.0
17 TraesCS6A01G103200 chr5B 79.445 613 99 18 1023 1626 577698100 577697506 6.180000e-110 409.0
18 TraesCS6A01G103200 chr5B 82.090 402 61 9 3105 3503 577695969 577695576 3.830000e-87 333.0
19 TraesCS6A01G103200 chr4B 85.693 671 57 16 1948 2595 251278206 251278860 0.000000e+00 671.0
20 TraesCS6A01G103200 chr4B 85.693 671 57 16 1948 2595 251664866 251665520 0.000000e+00 671.0
21 TraesCS6A01G103200 chr7D 92.308 91 6 1 3805 3894 270593322 270593232 1.940000e-25 128.0
22 TraesCS6A01G103200 chr7B 92.308 91 6 1 3805 3894 282303475 282303385 1.940000e-25 128.0
23 TraesCS6A01G103200 chr7B 93.878 49 2 1 4002 4049 282303385 282303337 9.210000e-09 73.1
24 TraesCS6A01G103200 chr7A 96.667 60 1 1 3836 3894 62187497 62187556 1.520000e-16 99.0


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 TraesCS6A01G103200 chr6A 72431213 72437835 6622 True 12231.0 12231 100.000000 1 6623 1 chr6A.!!$R1 6622
1 TraesCS6A01G103200 chr6B 129270473 129276907 6434 True 3174.5 9230 96.653000 184 6623 3 chr6B.!!$R1 6439
2 TraesCS6A01G103200 chr6B 618112901 618113719 818 False 418.0 693 87.201500 1769 2606 2 chr6B.!!$F1 837
3 TraesCS6A01G103200 chr6D 57217154 57223779 6625 True 3336.0 5795 93.919333 3 6623 3 chr6D.!!$R1 6620
4 TraesCS6A01G103200 chr5A 591090293 591094729 4436 True 903.5 1400 79.606000 1023 5106 2 chr5A.!!$R1 4083
5 TraesCS6A01G103200 chr5D 470385504 470389829 4325 True 574.5 1112 80.059750 1023 5106 4 chr5D.!!$R1 4083
6 TraesCS6A01G103200 chr5B 577693911 577698100 4189 True 563.5 1088 79.938750 1023 5106 4 chr5B.!!$R1 4083
7 TraesCS6A01G103200 chr4B 251278206 251278860 654 False 671.0 671 85.693000 1948 2595 1 chr4B.!!$F1 647
8 TraesCS6A01G103200 chr4B 251664866 251665520 654 False 671.0 671 85.693000 1948 2595 1 chr4B.!!$F2 647

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
442 483 0.106419 TGGGCGGTCCTTTTGTTTCT 60.106 50.000 0.00 0.0 36.20 2.52 F
491 532 0.465460 TGATTAGGCGGCATGGGAAC 60.465 55.000 13.08 0.0 0.00 3.62 F
907 961 1.196012 GGTGTCCCTTCCCAGACTAG 58.804 60.000 0.00 0.0 34.02 2.57 F
1480 1566 1.529865 GCTTGGTTGTAGTGGAACGTC 59.470 52.381 0.00 0.0 45.86 4.34 F
2375 2517 3.004734 GCTTACTTTGCTGCTTTTGGAGA 59.995 43.478 0.00 0.0 40.61 3.71 F
3076 3690 1.751351 TCTAGTGAGAACAGGCCATCG 59.249 52.381 5.01 0.0 0.00 3.84 F
3851 4557 0.034059 AGACCAGAAAGTGCCTCACG 59.966 55.000 0.00 0.0 39.64 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1746 1.085091 CAGATCTGCACAACTGAGCC 58.915 55.000 10.38 0.0 33.48 4.70 R
2352 2488 2.692557 TCCAAAAGCAGCAAAGTAAGCA 59.307 40.909 0.00 0.0 0.00 3.91 R
2375 2517 6.435277 GGATTGACCATAATCAGCATACCATT 59.565 38.462 0.00 0.0 38.51 3.16 R
2926 3540 5.351458 AGCCACTTCTGAAACATGAAAAAC 58.649 37.500 0.00 0.0 0.00 2.43 R
3600 4266 2.933495 CCATCTGCATGGTTGTTGAG 57.067 50.000 0.00 0.0 44.46 3.02 R
4509 5248 0.684479 ACTGAGCTGGATCGCCTGTA 60.684 55.000 0.00 0.0 35.68 2.74 R
5649 6392 1.006998 CTTGGTGAATCCCATCCCCAA 59.993 52.381 0.00 0.0 33.60 4.12 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
106 107 2.236223 ATCGCTGCTCTGGTGAGTGG 62.236 60.000 0.00 0.00 42.13 4.00
112 113 2.300152 CTGCTCTGGTGAGTGGTTTCTA 59.700 50.000 0.00 0.00 42.13 2.10
121 122 1.891150 GAGTGGTTTCTACCCTCGTGA 59.109 52.381 0.00 0.00 44.35 4.35
128 129 2.753043 TACCCTCGTGACGGAGCC 60.753 66.667 4.70 0.00 32.57 4.70
129 130 3.278072 TACCCTCGTGACGGAGCCT 62.278 63.158 4.70 0.00 32.57 4.58
130 131 4.135153 CCCTCGTGACGGAGCCTG 62.135 72.222 4.70 0.00 32.57 4.85
131 132 3.062466 CCTCGTGACGGAGCCTGA 61.062 66.667 4.70 0.00 32.57 3.86
134 135 4.436998 CGTGACGGAGCCTGACCC 62.437 72.222 0.00 0.00 0.00 4.46
146 147 1.302033 CTGACCCGCAGCAGACTTT 60.302 57.895 0.00 0.00 37.90 2.66
166 167 2.046285 CCCCCAATTCGTCTGTGCC 61.046 63.158 0.00 0.00 0.00 5.01
296 334 4.892965 AACAAGTGGCTGCCGGCA 62.893 61.111 30.59 30.59 44.01 5.69
359 397 1.111277 AGTTGCCGGAAGTGCTTTTT 58.889 45.000 5.05 0.00 0.00 1.94
360 398 1.202405 AGTTGCCGGAAGTGCTTTTTG 60.202 47.619 5.05 0.00 0.00 2.44
373 411 8.088365 GGAAGTGCTTTTTGGTTTCTGTATAAT 58.912 33.333 0.00 0.00 0.00 1.28
377 415 8.860128 GTGCTTTTTGGTTTCTGTATAATAAGC 58.140 33.333 0.00 0.00 36.51 3.09
378 416 7.753132 TGCTTTTTGGTTTCTGTATAATAAGCG 59.247 33.333 0.00 0.00 37.79 4.68
379 417 7.753580 GCTTTTTGGTTTCTGTATAATAAGCGT 59.246 33.333 0.00 0.00 30.16 5.07
382 420 9.439500 TTTTGGTTTCTGTATAATAAGCGTAGT 57.561 29.630 0.00 0.00 0.00 2.73
383 421 7.997107 TGGTTTCTGTATAATAAGCGTAGTG 57.003 36.000 0.00 0.00 0.00 2.74
433 474 2.355115 GGTTGATTGGGCGGTCCT 59.645 61.111 0.00 0.00 36.20 3.85
434 475 1.304134 GGTTGATTGGGCGGTCCTT 60.304 57.895 0.00 0.00 36.20 3.36
436 477 0.966179 GTTGATTGGGCGGTCCTTTT 59.034 50.000 0.00 0.00 36.20 2.27
437 478 0.965439 TTGATTGGGCGGTCCTTTTG 59.035 50.000 0.00 0.00 36.20 2.44
438 479 0.178975 TGATTGGGCGGTCCTTTTGT 60.179 50.000 0.00 0.00 36.20 2.83
439 480 0.966179 GATTGGGCGGTCCTTTTGTT 59.034 50.000 0.00 0.00 36.20 2.83
442 483 0.106419 TGGGCGGTCCTTTTGTTTCT 60.106 50.000 0.00 0.00 36.20 2.52
445 486 1.407618 GGCGGTCCTTTTGTTTCTGTT 59.592 47.619 0.00 0.00 0.00 3.16
446 487 2.159156 GGCGGTCCTTTTGTTTCTGTTT 60.159 45.455 0.00 0.00 0.00 2.83
447 488 3.067040 GGCGGTCCTTTTGTTTCTGTTTA 59.933 43.478 0.00 0.00 0.00 2.01
449 490 5.286438 GCGGTCCTTTTGTTTCTGTTTAAT 58.714 37.500 0.00 0.00 0.00 1.40
450 491 6.440436 GCGGTCCTTTTGTTTCTGTTTAATA 58.560 36.000 0.00 0.00 0.00 0.98
451 492 6.919115 GCGGTCCTTTTGTTTCTGTTTAATAA 59.081 34.615 0.00 0.00 0.00 1.40
452 493 7.096353 GCGGTCCTTTTGTTTCTGTTTAATAAC 60.096 37.037 0.00 0.00 34.75 1.89
453 494 7.380333 CGGTCCTTTTGTTTCTGTTTAATAACC 59.620 37.037 0.00 0.00 33.15 2.85
454 495 8.198778 GGTCCTTTTGTTTCTGTTTAATAACCA 58.801 33.333 0.00 0.00 33.15 3.67
455 496 9.027129 GTCCTTTTGTTTCTGTTTAATAACCAC 57.973 33.333 0.00 0.00 33.15 4.16
456 497 7.916450 TCCTTTTGTTTCTGTTTAATAACCACG 59.084 33.333 0.00 0.00 33.15 4.94
457 498 7.916450 CCTTTTGTTTCTGTTTAATAACCACGA 59.084 33.333 0.00 0.00 33.15 4.35
458 499 8.617761 TTTTGTTTCTGTTTAATAACCACGAC 57.382 30.769 0.00 0.00 33.15 4.34
459 500 5.976586 TGTTTCTGTTTAATAACCACGACG 58.023 37.500 0.00 0.00 33.15 5.12
460 501 5.050227 TGTTTCTGTTTAATAACCACGACGG 60.050 40.000 0.00 0.00 42.50 4.79
461 502 4.517952 TCTGTTTAATAACCACGACGGA 57.482 40.909 0.00 0.00 38.63 4.69
462 503 5.075858 TCTGTTTAATAACCACGACGGAT 57.924 39.130 0.00 0.00 38.63 4.18
463 504 5.481105 TCTGTTTAATAACCACGACGGATT 58.519 37.500 0.00 0.00 38.63 3.01
464 505 5.349270 TCTGTTTAATAACCACGACGGATTG 59.651 40.000 0.00 0.00 38.63 2.67
465 506 4.392445 TGTTTAATAACCACGACGGATTGG 59.608 41.667 0.00 0.00 38.63 3.16
466 507 2.032680 AATAACCACGACGGATTGGG 57.967 50.000 7.76 0.05 37.18 4.12
467 508 0.906775 ATAACCACGACGGATTGGGT 59.093 50.000 7.76 3.58 37.18 4.51
477 518 3.874543 CGACGGATTGGGTGATTTGATTA 59.125 43.478 0.00 0.00 0.00 1.75
480 521 3.004734 CGGATTGGGTGATTTGATTAGGC 59.995 47.826 0.00 0.00 0.00 3.93
491 532 0.465460 TGATTAGGCGGCATGGGAAC 60.465 55.000 13.08 0.00 0.00 3.62
522 563 1.735559 GTGCGACGTGGTTAGGACC 60.736 63.158 0.00 0.00 46.71 4.46
657 704 2.352814 CCCTTTCGAACGATCAGACACT 60.353 50.000 2.75 0.00 0.00 3.55
658 705 3.318017 CCTTTCGAACGATCAGACACTT 58.682 45.455 2.75 0.00 0.00 3.16
775 822 5.990996 TCTTCAATTTCCTTGGCAATTTGTC 59.009 36.000 0.00 0.00 35.43 3.18
779 826 6.205076 TCAATTTCCTTGGCAATTTGTCAATG 59.795 34.615 16.20 13.60 41.56 2.82
783 830 5.435291 TCCTTGGCAATTTGTCAATGTTTT 58.565 33.333 16.20 0.00 41.56 2.43
826 879 6.381481 TGAGCTGCCACTTCATTTTATATG 57.619 37.500 0.00 0.00 0.00 1.78
865 919 5.576563 TCTAGGAATTTTGAACCTGACCA 57.423 39.130 0.00 0.00 35.52 4.02
878 932 2.699846 ACCTGACCATTGTTGCATTGTT 59.300 40.909 0.00 0.00 0.00 2.83
904 958 3.900888 TGGTGTCCCTTCCCAGAC 58.099 61.111 0.00 0.00 0.00 3.51
905 959 1.238938 TGGTGTCCCTTCCCAGACT 59.761 57.895 0.00 0.00 34.02 3.24
907 961 1.196012 GGTGTCCCTTCCCAGACTAG 58.804 60.000 0.00 0.00 34.02 2.57
917 972 4.323104 CCTTCCCAGACTAGTTTCTTGAGG 60.323 50.000 0.00 0.00 0.00 3.86
986 1041 3.386768 TTGAAGACTTGAAGGACCTCG 57.613 47.619 0.00 0.00 0.00 4.63
1317 1402 6.751157 TGTATCGTAAAAGTGACCTTCTGAA 58.249 36.000 0.00 0.00 0.00 3.02
1322 1407 6.647895 TCGTAAAAGTGACCTTCTGAATAACC 59.352 38.462 0.00 0.00 0.00 2.85
1327 1412 7.454260 AAGTGACCTTCTGAATAACCAATTC 57.546 36.000 0.00 0.00 43.77 2.17
1341 1427 9.566432 GAATAACCAATTCATTCCTGTATCTCT 57.434 33.333 0.00 0.00 43.10 3.10
1480 1566 1.529865 GCTTGGTTGTAGTGGAACGTC 59.470 52.381 0.00 0.00 45.86 4.34
1616 1702 4.838642 CGTGACATTTACAAACACATCGAC 59.161 41.667 0.00 0.00 0.00 4.20
1619 1705 6.140108 GTGACATTTACAAACACATCGACAAC 59.860 38.462 0.00 0.00 0.00 3.32
1656 1762 5.627499 TTTTTATAGGCTCAGTTGTGCAG 57.373 39.130 8.25 0.00 36.36 4.41
2375 2517 3.004734 GCTTACTTTGCTGCTTTTGGAGA 59.995 43.478 0.00 0.00 40.61 3.71
2395 2541 5.645497 GGAGAATGGTATGCTGATTATGGTC 59.355 44.000 0.00 0.00 0.00 4.02
2629 2786 9.119329 GATCAGATGTATTTACTGTTAGTAGCG 57.881 37.037 0.00 0.00 31.47 4.26
2817 2976 6.093082 TGAACTGCATCAGACAGAACATATTG 59.907 38.462 0.29 0.00 38.55 1.90
2831 2990 8.258007 ACAGAACATATTGTTGCTAAGCTACTA 58.742 33.333 0.00 0.00 41.28 1.82
2926 3540 8.996271 TGAACATATTCTTGCTAAGCAGATATG 58.004 33.333 16.23 16.23 40.13 1.78
3031 3645 6.732531 AGTATTGCATGTCATTGATATCGG 57.267 37.500 0.00 0.00 0.00 4.18
3076 3690 1.751351 TCTAGTGAGAACAGGCCATCG 59.249 52.381 5.01 0.00 0.00 3.84
3406 4047 3.290948 TTGCCCATACAGGTTGTATCC 57.709 47.619 0.00 0.00 41.28 2.59
3547 4203 4.553330 GTCTCTGACCAAGGGTGAAATA 57.447 45.455 0.00 0.00 35.25 1.40
3600 4266 8.281212 AGAACATTATCATTTGTAACTGGTCC 57.719 34.615 0.00 0.00 0.00 4.46
3601 4267 8.109634 AGAACATTATCATTTGTAACTGGTCCT 58.890 33.333 0.00 0.00 0.00 3.85
3602 4268 7.865706 ACATTATCATTTGTAACTGGTCCTC 57.134 36.000 0.00 0.00 0.00 3.71
3851 4557 0.034059 AGACCAGAAAGTGCCTCACG 59.966 55.000 0.00 0.00 39.64 4.35
4223 4935 6.507023 ACTTGAGGCAAAACTAGAAAATGTG 58.493 36.000 0.00 0.00 0.00 3.21
4306 5033 5.411053 CCAACAGATCAAAGAAGAAGAGGAC 59.589 44.000 0.00 0.00 0.00 3.85
4493 5229 2.549754 CACTGGGGATTTATCATCACGC 59.450 50.000 0.00 0.00 0.00 5.34
4509 5248 2.094659 CGCGATGAAACTCCACGCT 61.095 57.895 0.00 0.00 45.64 5.07
4510 5249 0.800683 CGCGATGAAACTCCACGCTA 60.801 55.000 0.00 0.00 45.64 4.26
4511 5250 0.645868 GCGATGAAACTCCACGCTAC 59.354 55.000 0.00 0.00 44.67 3.58
4565 5304 3.256558 GCAGAAGATGTTCCAAAATGCC 58.743 45.455 0.00 0.00 32.48 4.40
4835 5576 5.126707 GGATGAAGATCCAGTTGAAAATGCT 59.873 40.000 0.00 0.00 46.93 3.79
5078 5819 0.250858 CTGCACTTGGTGATGACCCA 60.251 55.000 0.00 0.00 42.34 4.51
5106 5847 7.492994 CAGTTTCTCTAGCCTCAAGGTAAATAC 59.507 40.741 0.00 0.00 37.57 1.89
5115 5856 5.353123 GCCTCAAGGTAAATACGATGACAAA 59.647 40.000 0.00 0.00 37.57 2.83
5118 5859 5.349270 TCAAGGTAAATACGATGACAAACCG 59.651 40.000 0.00 0.00 0.00 4.44
5126 5867 1.464608 CGATGACAAACCGACATGCTT 59.535 47.619 0.00 0.00 29.73 3.91
5127 5868 2.474526 CGATGACAAACCGACATGCTTC 60.475 50.000 0.00 0.00 29.73 3.86
5128 5869 2.254546 TGACAAACCGACATGCTTCT 57.745 45.000 0.00 0.00 0.00 2.85
5130 5871 3.325870 TGACAAACCGACATGCTTCTAG 58.674 45.455 0.00 0.00 0.00 2.43
5131 5872 3.244078 TGACAAACCGACATGCTTCTAGT 60.244 43.478 0.00 0.00 0.00 2.57
5132 5873 3.067106 ACAAACCGACATGCTTCTAGTG 58.933 45.455 0.00 0.00 0.00 2.74
5133 5874 3.067106 CAAACCGACATGCTTCTAGTGT 58.933 45.455 0.00 0.00 0.00 3.55
5149 5892 7.119846 GCTTCTAGTGTCTTTTGGTGATATTGT 59.880 37.037 0.00 0.00 0.00 2.71
5150 5893 8.918202 TTCTAGTGTCTTTTGGTGATATTGTT 57.082 30.769 0.00 0.00 0.00 2.83
5167 5910 5.959618 ATTGTTCTACCCTGCTTTGTTAC 57.040 39.130 0.00 0.00 0.00 2.50
5170 5913 4.594062 TGTTCTACCCTGCTTTGTTACCTA 59.406 41.667 0.00 0.00 0.00 3.08
5189 5932 2.010145 ACATCATTCAACTCGTCCCG 57.990 50.000 0.00 0.00 0.00 5.14
5211 5954 4.992319 CGTGTAGGTGTTATTTGTCTCCAA 59.008 41.667 0.00 0.00 0.00 3.53
5439 6182 0.660488 ACGACAAAGCGCACATTGAA 59.340 45.000 22.11 0.00 33.86 2.69
5532 6275 1.177895 TCAATTTTGCGCTCCCTGCA 61.178 50.000 9.73 0.00 43.06 4.41
5604 6347 1.531578 GAGAAAACTCGCCAGTTGGTC 59.468 52.381 0.00 0.00 42.45 4.02
5640 6383 5.045286 ACAGTGAGGAAAAAGGAGCTGATAT 60.045 40.000 0.00 0.00 0.00 1.63
5695 6438 5.422012 TGAACTGGCACTGAGATGTTCTATA 59.578 40.000 12.72 0.00 35.99 1.31
5865 6608 8.725148 AGAATGTTCATAACTTGTCAGTGATTC 58.275 33.333 0.00 0.00 31.60 2.52
5883 6626 8.733458 CAGTGATTCTTGGATGAAAATAACTCA 58.267 33.333 0.00 0.00 0.00 3.41
6032 6779 4.541085 TCTGCATTTGCTATTGTCATCG 57.459 40.909 3.94 0.00 42.66 3.84
6047 6794 3.252944 TGTCATCGAATGCAACACACAAT 59.747 39.130 0.00 0.00 0.00 2.71
6077 6824 0.179048 TGGCAGAGTGGAGTGTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
6291 7058 3.216800 GCATGGAAGCTGGATGAACATA 58.783 45.455 0.00 0.00 0.00 2.29
6393 7169 3.507162 TGTGTCATTCTCCCAACACAT 57.493 42.857 3.24 0.00 45.05 3.21
6476 7305 4.537135 TTCACCTCCTACAACATGTCTC 57.463 45.455 0.00 0.00 0.00 3.36
6495 7324 1.398041 TCGCTGAAATATGCTGCACAC 59.602 47.619 3.57 0.00 0.00 3.82
6513 7342 5.068591 TGCACACGGACATATATAGTGAAGT 59.931 40.000 13.30 0.00 36.71 3.01
6577 7406 8.625651 CGAGTACTATATCTAGCCAGCATATTT 58.374 37.037 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 0.883833 TCCGTCACGAGGGTAGAAAC 59.116 55.000 0.00 0.00 37.60 2.78
112 113 4.680537 AGGCTCCGTCACGAGGGT 62.681 66.667 0.00 0.00 37.60 4.34
128 129 1.294659 GAAAGTCTGCTGCGGGTCAG 61.295 60.000 8.89 0.00 45.62 3.51
129 130 1.301716 GAAAGTCTGCTGCGGGTCA 60.302 57.895 8.89 0.00 0.00 4.02
130 131 2.035442 GGAAAGTCTGCTGCGGGTC 61.035 63.158 8.89 2.72 0.00 4.46
131 132 2.032681 GGAAAGTCTGCTGCGGGT 59.967 61.111 8.89 0.00 0.00 5.28
134 135 2.747855 GGGGGAAAGTCTGCTGCG 60.748 66.667 0.00 0.00 0.00 5.18
166 167 3.207669 GCGCAGAAGCCAGATGGG 61.208 66.667 0.30 0.00 37.52 4.00
195 229 2.381445 CCTCAAGAGGGCTCCACTT 58.619 57.895 8.28 0.00 44.87 3.16
196 230 4.143740 CCTCAAGAGGGCTCCACT 57.856 61.111 8.28 0.00 44.87 4.00
359 397 7.490079 CACACTACGCTTATTATACAGAAACCA 59.510 37.037 0.00 0.00 0.00 3.67
360 398 7.516312 GCACACTACGCTTATTATACAGAAACC 60.516 40.741 0.00 0.00 0.00 3.27
373 411 7.719483 ACCTAATTAATAGCACACTACGCTTA 58.281 34.615 0.00 0.00 40.96 3.09
374 412 6.579865 ACCTAATTAATAGCACACTACGCTT 58.420 36.000 0.00 0.00 40.96 4.68
375 413 6.158023 ACCTAATTAATAGCACACTACGCT 57.842 37.500 0.00 0.00 43.62 5.07
376 414 6.839820 AACCTAATTAATAGCACACTACGC 57.160 37.500 0.00 0.00 0.00 4.42
377 415 7.709613 AGGAAACCTAATTAATAGCACACTACG 59.290 37.037 0.00 0.00 28.47 3.51
378 416 8.959705 AGGAAACCTAATTAATAGCACACTAC 57.040 34.615 0.00 0.00 28.47 2.73
379 417 9.969001 AAAGGAAACCTAATTAATAGCACACTA 57.031 29.630 0.00 0.00 31.13 2.74
380 418 8.879427 AAAGGAAACCTAATTAATAGCACACT 57.121 30.769 0.00 0.00 31.13 3.55
381 419 9.569167 GAAAAGGAAACCTAATTAATAGCACAC 57.431 33.333 0.00 0.00 31.13 3.82
382 420 8.745590 GGAAAAGGAAACCTAATTAATAGCACA 58.254 33.333 0.00 0.00 31.13 4.57
383 421 8.195436 GGGAAAAGGAAACCTAATTAATAGCAC 58.805 37.037 0.00 0.00 31.13 4.40
412 453 3.439540 CCGCCCAATCAACCACCG 61.440 66.667 0.00 0.00 0.00 4.94
417 458 0.966179 AAAAGGACCGCCCAATCAAC 59.034 50.000 0.00 0.00 37.41 3.18
433 474 7.428761 CGTCGTGGTTATTAAACAGAAACAAAA 59.571 33.333 0.00 0.00 37.34 2.44
434 475 6.906143 CGTCGTGGTTATTAAACAGAAACAAA 59.094 34.615 0.00 0.00 37.34 2.83
436 477 5.050227 CCGTCGTGGTTATTAAACAGAAACA 60.050 40.000 0.00 0.00 37.34 2.83
437 478 5.177327 TCCGTCGTGGTTATTAAACAGAAAC 59.823 40.000 0.00 0.00 37.34 2.78
438 479 5.295950 TCCGTCGTGGTTATTAAACAGAAA 58.704 37.500 0.00 0.00 37.34 2.52
439 480 4.880759 TCCGTCGTGGTTATTAAACAGAA 58.119 39.130 0.00 0.00 37.34 3.02
442 483 4.392445 CCAATCCGTCGTGGTTATTAAACA 59.608 41.667 0.00 0.00 37.34 2.83
445 486 3.055240 ACCCAATCCGTCGTGGTTATTAA 60.055 43.478 0.31 0.00 39.52 1.40
446 487 2.500910 ACCCAATCCGTCGTGGTTATTA 59.499 45.455 0.31 0.00 39.52 0.98
447 488 1.279846 ACCCAATCCGTCGTGGTTATT 59.720 47.619 0.31 0.00 39.52 1.40
449 490 0.037139 CACCCAATCCGTCGTGGTTA 60.037 55.000 0.31 0.00 39.52 2.85
450 491 1.302192 CACCCAATCCGTCGTGGTT 60.302 57.895 0.31 0.00 39.52 3.67
451 492 1.550130 ATCACCCAATCCGTCGTGGT 61.550 55.000 0.31 0.00 39.52 4.16
452 493 0.392461 AATCACCCAATCCGTCGTGG 60.392 55.000 0.00 0.00 40.09 4.94
453 494 1.130373 CAAATCACCCAATCCGTCGTG 59.870 52.381 0.00 0.00 0.00 4.35
454 495 1.002659 TCAAATCACCCAATCCGTCGT 59.997 47.619 0.00 0.00 0.00 4.34
455 496 1.732941 TCAAATCACCCAATCCGTCG 58.267 50.000 0.00 0.00 0.00 5.12
456 497 4.275936 CCTAATCAAATCACCCAATCCGTC 59.724 45.833 0.00 0.00 0.00 4.79
457 498 4.207165 CCTAATCAAATCACCCAATCCGT 58.793 43.478 0.00 0.00 0.00 4.69
458 499 3.004734 GCCTAATCAAATCACCCAATCCG 59.995 47.826 0.00 0.00 0.00 4.18
459 500 3.004734 CGCCTAATCAAATCACCCAATCC 59.995 47.826 0.00 0.00 0.00 3.01
460 501 3.004734 CCGCCTAATCAAATCACCCAATC 59.995 47.826 0.00 0.00 0.00 2.67
461 502 2.958355 CCGCCTAATCAAATCACCCAAT 59.042 45.455 0.00 0.00 0.00 3.16
462 503 2.374184 CCGCCTAATCAAATCACCCAA 58.626 47.619 0.00 0.00 0.00 4.12
463 504 2.021723 GCCGCCTAATCAAATCACCCA 61.022 52.381 0.00 0.00 0.00 4.51
464 505 0.668535 GCCGCCTAATCAAATCACCC 59.331 55.000 0.00 0.00 0.00 4.61
465 506 1.388547 TGCCGCCTAATCAAATCACC 58.611 50.000 0.00 0.00 0.00 4.02
466 507 2.287788 CCATGCCGCCTAATCAAATCAC 60.288 50.000 0.00 0.00 0.00 3.06
467 508 1.955778 CCATGCCGCCTAATCAAATCA 59.044 47.619 0.00 0.00 0.00 2.57
480 521 3.124921 GGTCACGTTCCCATGCCG 61.125 66.667 0.00 0.00 0.00 5.69
522 563 7.744715 AGAAACGAACTAATTTACAAGCAATCG 59.255 33.333 0.00 0.00 0.00 3.34
699 746 5.263968 CTTCCGGAAGTAGTATGACACAT 57.736 43.478 32.16 0.00 33.87 3.21
726 773 1.285078 GTTGGGGGCCTGAGAAATACT 59.715 52.381 0.84 0.00 0.00 2.12
854 908 2.064434 TGCAACAATGGTCAGGTTCA 57.936 45.000 0.00 0.00 0.00 3.18
878 932 0.842030 AAGGGACACCAGGATCTGCA 60.842 55.000 0.00 0.00 40.13 4.41
890 944 2.715763 AACTAGTCTGGGAAGGGACA 57.284 50.000 0.00 0.00 35.18 4.02
904 958 4.543590 TCCAGCTTCCTCAAGAAACTAG 57.456 45.455 0.00 0.00 32.88 2.57
905 959 6.620877 TTATCCAGCTTCCTCAAGAAACTA 57.379 37.500 0.00 0.00 32.88 2.24
907 961 6.558909 CAATTATCCAGCTTCCTCAAGAAAC 58.441 40.000 0.00 0.00 32.88 2.78
917 972 6.275335 TGCAAAATAGCAATTATCCAGCTTC 58.725 36.000 0.00 0.00 42.46 3.86
972 1027 0.252742 ATCCCCGAGGTCCTTCAAGT 60.253 55.000 0.00 0.00 0.00 3.16
986 1041 7.066525 TCGATGTACTCATTTTGTAAAATCCCC 59.933 37.037 0.00 0.00 36.52 4.81
1086 1167 0.399806 GGATCTTCTCCTCCTGGGCT 60.400 60.000 0.00 0.00 41.29 5.19
1239 1320 4.699637 TGGACAGTGTACCAAAAGTGTAG 58.300 43.478 2.17 0.00 32.93 2.74
1317 1402 9.927081 AAAGAGATACAGGAATGAATTGGTTAT 57.073 29.630 0.00 0.00 0.00 1.89
1322 1407 7.066645 TCTGCAAAGAGATACAGGAATGAATTG 59.933 37.037 0.00 0.00 0.00 2.32
1327 1412 7.172875 CCTTATCTGCAAAGAGATACAGGAATG 59.827 40.741 11.96 0.00 36.51 2.67
1330 1415 5.663106 ACCTTATCTGCAAAGAGATACAGGA 59.337 40.000 18.27 0.00 37.08 3.86
1341 1427 2.298729 GCCCAAACACCTTATCTGCAAA 59.701 45.455 0.00 0.00 0.00 3.68
1376 1462 5.045286 AGCTCCATCTTCATAAACCAAGTCT 60.045 40.000 0.00 0.00 0.00 3.24
1480 1566 2.611518 GAAAGGGTCACTCACAGATCG 58.388 52.381 0.00 0.00 0.00 3.69
1642 1746 1.085091 CAGATCTGCACAACTGAGCC 58.915 55.000 10.38 0.00 33.48 4.70
1656 1762 6.317088 TCAAAATGATTTGCTTCGACAGATC 58.683 36.000 0.00 0.00 44.52 2.75
2352 2488 2.692557 TCCAAAAGCAGCAAAGTAAGCA 59.307 40.909 0.00 0.00 0.00 3.91
2375 2517 6.435277 GGATTGACCATAATCAGCATACCATT 59.565 38.462 0.00 0.00 38.51 3.16
2395 2541 7.406799 AGCAAAAGTTAATTTGAACGGATTG 57.593 32.000 5.85 0.00 41.73 2.67
2550 2702 9.726438 TTTGTTTTTGAGAAATCCAAACCTTAA 57.274 25.926 0.00 0.00 33.74 1.85
2629 2786 6.760298 TCATTTCATGATAGTGCAGAGAAGAC 59.240 38.462 0.00 0.00 33.59 3.01
2831 2990 9.093970 GCAAAACCTTAGTGTTTCACTTAAAAT 57.906 29.630 7.70 0.00 42.59 1.82
2926 3540 5.351458 AGCCACTTCTGAAACATGAAAAAC 58.649 37.500 0.00 0.00 0.00 2.43
3406 4047 6.111768 AGATGCTTAACAAGTTGCTTATCG 57.888 37.500 1.81 0.00 0.00 2.92
3579 4245 7.864108 TGAGGACCAGTTACAAATGATAATG 57.136 36.000 0.00 0.00 0.00 1.90
3580 4246 7.888021 TGTTGAGGACCAGTTACAAATGATAAT 59.112 33.333 0.00 0.00 0.00 1.28
3581 4247 7.227873 TGTTGAGGACCAGTTACAAATGATAA 58.772 34.615 0.00 0.00 0.00 1.75
3583 4249 5.630121 TGTTGAGGACCAGTTACAAATGAT 58.370 37.500 0.00 0.00 0.00 2.45
3584 4250 5.042463 TGTTGAGGACCAGTTACAAATGA 57.958 39.130 0.00 0.00 0.00 2.57
3585 4251 5.507315 GGTTGTTGAGGACCAGTTACAAATG 60.507 44.000 0.00 0.00 35.95 2.32
3586 4252 4.583073 GGTTGTTGAGGACCAGTTACAAAT 59.417 41.667 0.00 0.00 35.95 2.32
3600 4266 2.933495 CCATCTGCATGGTTGTTGAG 57.067 50.000 0.00 0.00 44.46 3.02
3851 4557 9.771534 ATCTTATTATTACTTGGCTCAGAGAAC 57.228 33.333 0.00 0.00 0.00 3.01
4223 4935 8.613060 TCACCAATTTATCAATAGATCTCTGC 57.387 34.615 0.00 0.00 35.67 4.26
4306 5033 3.458189 CTTATACCCAGTGGAAGAAGCG 58.542 50.000 11.95 0.00 34.81 4.68
4493 5229 1.920574 CTGTAGCGTGGAGTTTCATCG 59.079 52.381 0.00 0.00 0.00 3.84
4509 5248 0.684479 ACTGAGCTGGATCGCCTGTA 60.684 55.000 0.00 0.00 35.68 2.74
4510 5249 1.986757 ACTGAGCTGGATCGCCTGT 60.987 57.895 0.00 0.00 35.68 4.00
4511 5250 1.521010 CACTGAGCTGGATCGCCTG 60.521 63.158 0.00 0.00 36.29 4.85
4565 5304 0.856641 TTCTCACGTTTTCTTCGGCG 59.143 50.000 0.00 0.00 0.00 6.46
4835 5576 1.839994 GGACCATCCTGTTGAGATCCA 59.160 52.381 0.00 0.00 32.53 3.41
5078 5819 2.235898 CCTTGAGGCTAGAGAAACTGCT 59.764 50.000 0.00 0.00 0.00 4.24
5106 5847 1.078709 AGCATGTCGGTTTGTCATCG 58.921 50.000 0.00 0.00 0.00 3.84
5115 5856 2.171840 AGACACTAGAAGCATGTCGGT 58.828 47.619 0.00 0.00 45.97 4.69
5118 5859 4.757149 ACCAAAAGACACTAGAAGCATGTC 59.243 41.667 0.00 0.00 42.54 3.06
5126 5867 8.375506 AGAACAATATCACCAAAAGACACTAGA 58.624 33.333 0.00 0.00 0.00 2.43
5127 5868 8.553459 AGAACAATATCACCAAAAGACACTAG 57.447 34.615 0.00 0.00 0.00 2.57
5128 5869 9.431887 GTAGAACAATATCACCAAAAGACACTA 57.568 33.333 0.00 0.00 0.00 2.74
5130 5871 7.361799 GGGTAGAACAATATCACCAAAAGACAC 60.362 40.741 0.00 0.00 0.00 3.67
5131 5872 6.657541 GGGTAGAACAATATCACCAAAAGACA 59.342 38.462 0.00 0.00 0.00 3.41
5132 5873 6.884836 AGGGTAGAACAATATCACCAAAAGAC 59.115 38.462 0.00 0.00 0.00 3.01
5133 5874 6.884295 CAGGGTAGAACAATATCACCAAAAGA 59.116 38.462 0.00 0.00 0.00 2.52
5149 5892 4.594062 TGTAGGTAACAAAGCAGGGTAGAA 59.406 41.667 0.00 0.00 34.29 2.10
5150 5893 4.161876 TGTAGGTAACAAAGCAGGGTAGA 58.838 43.478 0.00 0.00 34.29 2.59
5167 5910 3.458189 GGGACGAGTTGAATGATGTAGG 58.542 50.000 0.00 0.00 0.00 3.18
5262 6005 2.353889 CTCATTCCTCAACGCCTTCATG 59.646 50.000 0.00 0.00 0.00 3.07
5439 6182 1.729470 CCACTATGTCGGCGCTCTCT 61.729 60.000 7.64 0.00 0.00 3.10
5604 6347 3.017442 TCCTCACTGTAATGGAGTCGAG 58.983 50.000 0.00 0.00 0.00 4.04
5640 6383 6.953520 GTGAATCCCATCCCCAATATGAAATA 59.046 38.462 0.00 0.00 0.00 1.40
5649 6392 1.006998 CTTGGTGAATCCCATCCCCAA 59.993 52.381 0.00 0.00 33.60 4.12
5695 6438 7.939784 TGAGCTATCTACGTATATCACCAAT 57.060 36.000 0.00 0.00 0.00 3.16
5865 6608 6.151648 TGCCTCTTGAGTTATTTTCATCCAAG 59.848 38.462 0.00 0.00 0.00 3.61
5883 6626 0.250901 AGCACCGACAATTGCCTCTT 60.251 50.000 5.05 0.00 39.75 2.85
6002 6749 5.927281 ATAGCAAATGCAGAAGTTCCAAT 57.073 34.783 8.28 0.00 45.16 3.16
6047 6794 6.206634 CACTCCACTCTGCCAAAAGTATTAAA 59.793 38.462 0.00 0.00 0.00 1.52
6077 6824 2.421424 CACTCTGATTTTAGGCTGGCAC 59.579 50.000 3.38 0.00 0.00 5.01
6203 6950 4.986054 TTCAGTGTTTATGTGGGGTACT 57.014 40.909 0.00 0.00 0.00 2.73
6291 7058 2.322355 ACAATATGCTTCTGCTCGCT 57.678 45.000 0.00 0.00 40.48 4.93
6476 7305 1.818850 GTGTGCAGCATATTTCAGCG 58.181 50.000 0.00 0.00 35.48 5.18
6577 7406 5.280164 GGAGGATATACAAGATGGTGATGCA 60.280 44.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.