Multiple sequence alignment - TraesCS1D01G185600

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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 TraesCS1D01G185600 chr1D 100.000 5012 0 0 1 5012 256778774 256783785 0.000000e+00 9256.0
1 TraesCS1D01G185600 chr1A 94.896 2880 89 15 719 3569 330082679 330085529 0.000000e+00 4451.0
2 TraesCS1D01G185600 chr1A 97.079 719 20 1 3563 4280 330085589 330086307 0.000000e+00 1210.0
3 TraesCS1D01G185600 chr1A 99.034 207 2 0 4751 4957 330086569 330086775 6.130000e-99 372.0
4 TraesCS1D01G185600 chr1A 86.638 232 14 6 4277 4493 330086342 330086571 1.800000e-59 241.0
5 TraesCS1D01G185600 chr1A 100.000 58 0 0 4955 5012 330086797 330086854 1.910000e-19 108.0
6 TraesCS1D01G185600 chr1B 97.308 2266 57 2 1307 3569 356455488 356453224 0.000000e+00 3843.0
7 TraesCS1D01G185600 chr1B 91.176 1428 77 31 3562 4957 356453170 356451760 0.000000e+00 1893.0
8 TraesCS1D01G185600 chr1B 91.032 1037 70 14 211 1232 356456724 356455696 0.000000e+00 1378.0
9 TraesCS1D01G185600 chr1B 95.208 626 18 1 1346 1971 229488952 229489565 0.000000e+00 979.0
10 TraesCS1D01G185600 chr1B 91.525 177 10 3 1 177 356456893 356456722 6.480000e-59 239.0
11 TraesCS1D01G185600 chr6A 96.006 626 25 0 1346 1971 586055283 586055908 0.000000e+00 1018.0
12 TraesCS1D01G185600 chr4B 79.102 646 120 13 2569 3199 673250963 673251608 9.970000e-117 431.0
13 TraesCS1D01G185600 chr4B 92.053 151 12 0 1333 1483 673249000 673249150 3.930000e-51 213.0
14 TraesCS1D01G185600 chrUn 79.019 591 101 18 2927 3503 99825439 99824858 2.830000e-102 383.0
15 TraesCS1D01G185600 chrUn 79.475 419 60 19 1330 1744 99827460 99827064 1.780000e-69 274.0
16 TraesCS1D01G185600 chr3A 90.385 156 15 0 1332 1487 703425203 703425048 6.580000e-49 206.0
17 TraesCS1D01G185600 chr4D 90.789 152 14 0 1332 1483 491381165 491381014 2.370000e-48 204.0
18 TraesCS1D01G185600 chr7A 94.444 36 0 2 4419 4452 650673014 650673049 3.000000e-03 54.7
19 TraesCS1D01G185600 chr7A 100.000 28 0 0 4419 4446 650814608 650814635 9.000000e-03 52.8


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 TraesCS1D01G185600 chr1D 256778774 256783785 5011 False 9256.00 9256 100.00000 1 5012 1 chr1D.!!$F1 5011
1 TraesCS1D01G185600 chr1A 330082679 330086854 4175 False 1276.40 4451 95.52940 719 5012 5 chr1A.!!$F1 4293
2 TraesCS1D01G185600 chr1B 356451760 356456893 5133 True 1838.25 3843 92.76025 1 4957 4 chr1B.!!$R1 4956
3 TraesCS1D01G185600 chr1B 229488952 229489565 613 False 979.00 979 95.20800 1346 1971 1 chr1B.!!$F1 625
4 TraesCS1D01G185600 chr6A 586055283 586055908 625 False 1018.00 1018 96.00600 1346 1971 1 chr6A.!!$F1 625
5 TraesCS1D01G185600 chr4B 673249000 673251608 2608 False 322.00 431 85.57750 1333 3199 2 chr4B.!!$F1 1866
6 TraesCS1D01G185600 chrUn 99824858 99827460 2602 True 328.50 383 79.24700 1330 3503 2 chrUn.!!$R1 2173

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
955 994 0.904649 AGAATGAGATGACACGCCCA 59.095 50.000 0.0 0.0 0.00 5.36 F
1568 1740 0.466739 GAGGGTTTGGGTGGTCGTTT 60.467 55.000 0.0 0.0 0.00 3.60 F
1603 1778 1.079127 GGCGTGCATCACCTACTGT 60.079 57.895 0.0 0.0 0.00 3.55 F
1796 2140 1.279840 GCGTTGTGTTGTCCAGCTC 59.720 57.895 0.0 0.0 0.00 4.09 F
2203 2893 2.763933 CACACATTCTGTCAGCAGTCT 58.236 47.619 0.0 0.0 43.05 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2045 1.279840 GAGCTGGACAACACAACGC 59.720 57.895 0.00 0.00 0.00 4.84 R
3420 4833 1.377366 TAGTGCTTCTCGCCTCCTCG 61.377 60.000 0.00 0.00 38.05 4.63 R
3541 4954 5.657826 TTGTTATTGCACTGCATTACCAT 57.342 34.783 4.10 0.00 38.76 3.55 R
3620 5101 0.899717 GGGAAGGCATTCACCTGCAA 60.900 55.000 13.81 0.00 44.12 4.08 R
4086 5568 1.196354 CAAAGCTCTACTGTGCAGTGC 59.804 52.381 8.58 8.58 42.52 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.500559 GGATTAATAAGCTCATCCACTGTTCTT 59.499 37.037 0.00 0.00 36.04 2.52
55 56 5.136828 TGTTCTTAGCAAAACATTCCCTCA 58.863 37.500 0.00 0.00 30.73 3.86
60 61 4.112634 AGCAAAACATTCCCTCACCTTA 57.887 40.909 0.00 0.00 0.00 2.69
67 68 5.520748 ACATTCCCTCACCTTAACTGAAT 57.479 39.130 0.00 0.00 0.00 2.57
68 69 5.501156 ACATTCCCTCACCTTAACTGAATC 58.499 41.667 0.00 0.00 0.00 2.52
69 70 5.014123 ACATTCCCTCACCTTAACTGAATCA 59.986 40.000 0.00 0.00 0.00 2.57
70 71 5.779241 TTCCCTCACCTTAACTGAATCAT 57.221 39.130 0.00 0.00 0.00 2.45
71 72 5.779241 TCCCTCACCTTAACTGAATCATT 57.221 39.130 0.00 0.00 0.00 2.57
74 75 6.012508 TCCCTCACCTTAACTGAATCATTCTT 60.013 38.462 0.00 0.00 0.00 2.52
93 94 2.337359 TGTTGGGCTAGAAGGTACCT 57.663 50.000 9.21 9.21 0.00 3.08
95 96 3.793712 TGTTGGGCTAGAAGGTACCTAA 58.206 45.455 16.67 0.00 0.00 2.69
145 146 2.332063 AATATGCCCACTCCTGAACG 57.668 50.000 0.00 0.00 0.00 3.95
170 171 7.481642 GTTTGAAGACCATCGAAGATACTCTA 58.518 38.462 0.00 0.00 45.12 2.43
177 178 7.724506 AGACCATCGAAGATACTCTACCAAATA 59.275 37.037 0.00 0.00 45.12 1.40
178 179 8.246430 ACCATCGAAGATACTCTACCAAATAA 57.754 34.615 0.00 0.00 45.12 1.40
179 180 8.701895 ACCATCGAAGATACTCTACCAAATAAA 58.298 33.333 0.00 0.00 45.12 1.40
180 181 8.979574 CCATCGAAGATACTCTACCAAATAAAC 58.020 37.037 0.00 0.00 45.12 2.01
181 182 9.529325 CATCGAAGATACTCTACCAAATAAACA 57.471 33.333 0.00 0.00 45.12 2.83
189 190 7.881775 ACTCTACCAAATAAACAATGATCCC 57.118 36.000 0.00 0.00 0.00 3.85
190 191 7.643123 ACTCTACCAAATAAACAATGATCCCT 58.357 34.615 0.00 0.00 0.00 4.20
191 192 8.116026 ACTCTACCAAATAAACAATGATCCCTT 58.884 33.333 0.00 0.00 0.00 3.95
192 193 8.893563 TCTACCAAATAAACAATGATCCCTTT 57.106 30.769 0.00 0.00 0.00 3.11
193 194 9.320295 TCTACCAAATAAACAATGATCCCTTTT 57.680 29.630 0.00 0.00 0.00 2.27
194 195 9.942850 CTACCAAATAAACAATGATCCCTTTTT 57.057 29.630 0.00 0.00 0.00 1.94
233 234 8.571336 CAGAATGTTTCCATCAGAAAAGTACTT 58.429 33.333 1.12 1.12 45.93 2.24
245 246 6.807230 TCAGAAAAGTACTTCGCTCATAAGAC 59.193 38.462 8.95 0.00 0.00 3.01
265 266 4.106197 GACCGTAGCACAAAGAGTATCAG 58.894 47.826 0.00 0.00 37.82 2.90
266 267 2.860735 CCGTAGCACAAAGAGTATCAGC 59.139 50.000 0.00 0.00 37.82 4.26
269 270 5.281727 CGTAGCACAAAGAGTATCAGCATA 58.718 41.667 0.00 0.00 37.82 3.14
312 313 4.952957 TGCTTGGCTAACATGGCTAAATTA 59.047 37.500 0.00 0.00 30.37 1.40
323 324 7.069877 ACATGGCTAAATTAAATGCATGGAT 57.930 32.000 0.00 0.00 0.00 3.41
340 341 3.687045 TGGATATCCCTAAACCCCATGT 58.313 45.455 19.34 0.00 35.38 3.21
341 342 3.655777 TGGATATCCCTAAACCCCATGTC 59.344 47.826 19.34 0.00 35.38 3.06
372 373 4.043310 TCTTTTGGAAGACACATCCTCCAT 59.957 41.667 0.00 0.00 43.66 3.41
377 378 3.308402 GGAAGACACATCCTCCATCCAAA 60.308 47.826 0.00 0.00 35.71 3.28
405 406 5.747197 GCCAATGCATTTTCTTCTACTCATG 59.253 40.000 9.83 0.00 37.47 3.07
406 407 6.626623 GCCAATGCATTTTCTTCTACTCATGT 60.627 38.462 9.83 0.00 37.47 3.21
407 408 7.318141 CCAATGCATTTTCTTCTACTCATGTT 58.682 34.615 9.83 0.00 0.00 2.71
413 414 6.877611 TTTTCTTCTACTCATGTTTGTCCC 57.122 37.500 0.00 0.00 0.00 4.46
426 427 3.028130 GTTTGTCCCCTCACCAAAAAGA 58.972 45.455 0.00 0.00 30.57 2.52
433 434 3.840078 CCCCTCACCAAAAAGATTCCATT 59.160 43.478 0.00 0.00 0.00 3.16
445 446 8.814235 CAAAAAGATTCCATTGCATCTGTAATC 58.186 33.333 6.87 6.87 29.78 1.75
452 453 5.591472 TCCATTGCATCTGTAATCTCTTTGG 59.409 40.000 0.00 0.00 0.00 3.28
453 454 5.221185 CCATTGCATCTGTAATCTCTTTGGG 60.221 44.000 0.00 0.00 0.00 4.12
454 455 4.842531 TGCATCTGTAATCTCTTTGGGA 57.157 40.909 0.00 0.00 0.00 4.37
455 456 5.378230 TGCATCTGTAATCTCTTTGGGAT 57.622 39.130 0.00 0.00 0.00 3.85
459 460 6.976925 GCATCTGTAATCTCTTTGGGATTTTG 59.023 38.462 0.00 0.00 35.40 2.44
460 461 7.148018 GCATCTGTAATCTCTTTGGGATTTTGA 60.148 37.037 0.00 0.00 35.40 2.69
461 462 8.742777 CATCTGTAATCTCTTTGGGATTTTGAA 58.257 33.333 0.00 0.00 35.40 2.69
462 463 8.704849 TCTGTAATCTCTTTGGGATTTTGAAA 57.295 30.769 0.00 0.00 35.40 2.69
463 464 9.142014 TCTGTAATCTCTTTGGGATTTTGAAAA 57.858 29.630 0.00 0.00 35.40 2.29
464 465 9.196552 CTGTAATCTCTTTGGGATTTTGAAAAC 57.803 33.333 0.00 0.00 35.40 2.43
465 466 8.700051 TGTAATCTCTTTGGGATTTTGAAAACA 58.300 29.630 0.00 0.00 35.40 2.83
466 467 9.541143 GTAATCTCTTTGGGATTTTGAAAACAA 57.459 29.630 0.00 0.00 35.40 2.83
467 468 8.437360 AATCTCTTTGGGATTTTGAAAACAAC 57.563 30.769 0.00 0.00 30.26 3.32
468 469 6.345298 TCTCTTTGGGATTTTGAAAACAACC 58.655 36.000 0.00 0.00 0.00 3.77
471 472 7.796054 TCTTTGGGATTTTGAAAACAACCATA 58.204 30.769 9.58 5.73 0.00 2.74
512 526 6.985653 TTGGATAATGGGTTTCAACAGAAA 57.014 33.333 0.00 0.00 0.00 2.52
522 536 7.796054 TGGGTTTCAACAGAAATTTATTTCCA 58.204 30.769 10.71 0.00 45.52 3.53
523 537 7.713073 TGGGTTTCAACAGAAATTTATTTCCAC 59.287 33.333 10.71 0.00 45.52 4.02
533 547 6.602009 AGAAATTTATTTCCACCCTAAGGACG 59.398 38.462 10.71 0.00 45.52 4.79
539 553 0.974383 CCACCCTAAGGACGTCAACT 59.026 55.000 18.91 2.85 36.73 3.16
548 562 1.856597 AGGACGTCAACTTTTCGTTCG 59.143 47.619 18.91 0.00 38.02 3.95
554 568 3.242188 CGTCAACTTTTCGTTCGAACCTT 60.242 43.478 22.07 2.06 32.27 3.50
571 585 4.073293 ACCTTCAAGTCGATTCACAACT 57.927 40.909 0.00 0.00 0.00 3.16
583 597 5.815222 TCGATTCACAACTCTTTCAACAAGA 59.185 36.000 0.00 0.00 0.00 3.02
585 599 6.794158 CGATTCACAACTCTTTCAACAAGATC 59.206 38.462 0.00 0.00 0.00 2.75
600 614 7.099764 TCAACAAGATCAGAGAAACTATCACC 58.900 38.462 0.00 0.00 0.00 4.02
601 615 6.865834 ACAAGATCAGAGAAACTATCACCT 57.134 37.500 0.00 0.00 0.00 4.00
630 644 7.851387 TCAAACGCACCATAGATAAAATACA 57.149 32.000 0.00 0.00 0.00 2.29
632 646 8.394877 TCAAACGCACCATAGATAAAATACAAG 58.605 33.333 0.00 0.00 0.00 3.16
633 647 8.394877 CAAACGCACCATAGATAAAATACAAGA 58.605 33.333 0.00 0.00 0.00 3.02
634 648 8.677148 AACGCACCATAGATAAAATACAAGAT 57.323 30.769 0.00 0.00 0.00 2.40
635 649 9.772973 AACGCACCATAGATAAAATACAAGATA 57.227 29.630 0.00 0.00 0.00 1.98
636 650 9.424319 ACGCACCATAGATAAAATACAAGATAG 57.576 33.333 0.00 0.00 0.00 2.08
637 651 8.873830 CGCACCATAGATAAAATACAAGATAGG 58.126 37.037 0.00 0.00 0.00 2.57
638 652 9.944376 GCACCATAGATAAAATACAAGATAGGA 57.056 33.333 0.00 0.00 0.00 2.94
674 689 5.707298 CCTCCGCCATTATATTCAGTTTCAT 59.293 40.000 0.00 0.00 0.00 2.57
680 695 7.096353 CGCCATTATATTCAGTTTCATGCAAAG 60.096 37.037 0.00 0.00 0.00 2.77
704 719 4.773323 AAGCTTTAACCTCAGCATTCAC 57.227 40.909 0.00 0.00 38.61 3.18
737 752 7.822822 GCTGAAAAAGATACTACACTTCCCTTA 59.177 37.037 0.00 0.00 0.00 2.69
753 769 3.655777 TCCCTTAACTCACCAATTGTCCT 59.344 43.478 4.43 0.00 0.00 3.85
756 772 4.697352 CCTTAACTCACCAATTGTCCTGAG 59.303 45.833 17.36 17.36 36.90 3.35
765 781 1.531423 ATTGTCCTGAGCTTGCACAG 58.469 50.000 12.01 12.01 0.00 3.66
778 794 5.647589 AGCTTGCACAGTATTCATTCAATG 58.352 37.500 0.00 0.00 0.00 2.82
924 963 1.074775 TGCCCACTGCTCCGAAATT 59.925 52.632 0.00 0.00 42.00 1.82
934 973 1.560923 CTCCGAAATTCGACGCAGAT 58.439 50.000 17.75 0.00 43.74 2.90
935 974 1.256376 CTCCGAAATTCGACGCAGATG 59.744 52.381 17.75 0.00 43.74 2.90
936 975 1.135228 TCCGAAATTCGACGCAGATGA 60.135 47.619 17.75 0.00 43.74 2.92
937 976 1.256376 CCGAAATTCGACGCAGATGAG 59.744 52.381 17.75 0.00 43.74 2.90
938 977 2.185262 CGAAATTCGACGCAGATGAGA 58.815 47.619 10.18 0.00 43.74 3.27
939 978 2.598637 CGAAATTCGACGCAGATGAGAA 59.401 45.455 10.18 0.00 43.74 2.87
955 994 0.904649 AGAATGAGATGACACGCCCA 59.095 50.000 0.00 0.00 0.00 5.36
980 1019 3.810373 CTGCGCGTATAAAATCCATTCC 58.190 45.455 8.43 0.00 0.00 3.01
1305 1345 3.017442 TCGTCTCTCGATTTCCTGATGT 58.983 45.455 0.00 0.00 44.01 3.06
1568 1740 0.466739 GAGGGTTTGGGTGGTCGTTT 60.467 55.000 0.00 0.00 0.00 3.60
1603 1778 1.079127 GGCGTGCATCACCTACTGT 60.079 57.895 0.00 0.00 0.00 3.55
1778 2045 3.304996 CCAGATCTACGTGCCTATCAGTG 60.305 52.174 0.00 0.00 0.00 3.66
1796 2140 1.279840 GCGTTGTGTTGTCCAGCTC 59.720 57.895 0.00 0.00 0.00 4.09
2203 2893 2.763933 CACACATTCTGTCAGCAGTCT 58.236 47.619 0.00 0.00 43.05 3.24
2340 3033 4.525024 TCGAAGTTTTTCAGGGTAAACCA 58.475 39.130 0.81 0.00 43.89 3.67
2387 3080 5.028375 GGAAACTAATTGATGCGTACAAGC 58.972 41.667 0.00 0.00 37.71 4.01
2424 3121 5.189928 TGTTGTGTCCTGTTCAGTACAATT 58.810 37.500 13.30 0.00 36.02 2.32
2430 3127 4.065088 TCCTGTTCAGTACAATTCACTGC 58.935 43.478 10.59 1.46 42.58 4.40
2475 3350 4.976864 ACCTTTTGTGATTAACCTACCGT 58.023 39.130 0.00 0.00 0.00 4.83
3145 4553 5.552870 AGGTCGAAGGTTATATGCAGATT 57.447 39.130 0.00 0.00 0.00 2.40
3324 4737 2.797177 AAGGTGGAAGCATCTCCTTC 57.203 50.000 11.16 0.00 40.33 3.46
3420 4833 8.316497 TGAAGATGAGATCTCAATATATCCCC 57.684 38.462 28.40 14.86 43.58 4.81
3537 4950 5.630121 TCAATTCCAACTCTCTGGCTTTAA 58.370 37.500 0.00 0.00 36.32 1.52
3541 4954 8.522830 CAATTCCAACTCTCTGGCTTTAATTTA 58.477 33.333 0.00 0.00 36.32 1.40
3581 5060 4.782019 ACAAAACAAGCTGAAGTGTCAA 57.218 36.364 0.00 0.00 31.88 3.18
3620 5101 7.865706 AATGCTCTTCCTACGAATGTTATTT 57.134 32.000 0.00 0.00 0.00 1.40
3621 5102 7.865706 ATGCTCTTCCTACGAATGTTATTTT 57.134 32.000 0.00 0.00 0.00 1.82
3711 5192 2.894387 GCAGAGGCGGCTGATGTC 60.894 66.667 19.63 0.48 38.14 3.06
3750 5231 8.367911 TCACAGATCAACTAGTATGTTGTCTTT 58.632 33.333 0.00 1.90 45.26 2.52
3804 5285 6.601217 GCCATTTTCTCTCTTGGAATTAGACT 59.399 38.462 0.00 0.00 0.00 3.24
3930 5411 2.359354 TGAACCGGGCATGGAACG 60.359 61.111 6.32 0.00 0.00 3.95
4086 5568 5.464722 GGCTCGGCATGTATTGAGATATATG 59.535 44.000 8.99 0.00 39.20 1.78
4163 5645 7.946655 TCTTACGTTTGCTAATAGGATGATG 57.053 36.000 0.00 0.00 0.00 3.07
4292 5814 4.744570 TGCCGTCTTAGTGATTTGTCTAG 58.255 43.478 0.00 0.00 0.00 2.43
4293 5815 4.219944 TGCCGTCTTAGTGATTTGTCTAGT 59.780 41.667 0.00 0.00 0.00 2.57
4312 5836 9.314321 TGTCTAGTTTTCTTGTCTCTACAAAAG 57.686 33.333 0.00 0.00 44.79 2.27
4352 5876 7.117667 CACAGATTTTACAATTAAAAGGGCCAC 59.882 37.037 6.18 0.00 39.89 5.01
4471 6022 7.651808 TGCAAAAACCTTCTCTTCTCTAATTG 58.348 34.615 0.00 0.00 0.00 2.32
4504 6055 1.688197 CCCATGTTGCACAACCTCTTT 59.312 47.619 10.82 0.00 40.46 2.52
4510 6061 6.449698 CATGTTGCACAACCTCTTTTCTAAT 58.550 36.000 10.82 0.00 40.46 1.73
4522 6073 8.424274 ACCTCTTTTCTAATTTTTGCAACAAG 57.576 30.769 0.00 0.00 0.00 3.16
4573 6127 3.186409 TGTCGCATCTAACTTTCTGCAAC 59.814 43.478 0.00 0.00 34.29 4.17
4583 6137 2.287188 ACTTTCTGCAACAAGACGCATG 60.287 45.455 10.77 0.00 37.54 4.06
4591 6145 2.798976 ACAAGACGCATGTTGCAAAT 57.201 40.000 0.00 0.00 45.36 2.32
4592 6146 2.396601 ACAAGACGCATGTTGCAAATG 58.603 42.857 0.00 8.83 45.36 2.32
4593 6147 1.722464 CAAGACGCATGTTGCAAATGG 59.278 47.619 17.53 12.30 45.36 3.16
4594 6148 0.388907 AGACGCATGTTGCAAATGGC 60.389 50.000 17.53 13.01 45.36 4.40
4611 6181 3.425713 CGCATCACGCACCTTGCT 61.426 61.111 0.00 0.00 42.25 3.91
4612 6182 2.177531 GCATCACGCACCTTGCTG 59.822 61.111 0.00 0.00 42.25 4.41
4614 6184 1.855213 GCATCACGCACCTTGCTGAA 61.855 55.000 0.00 0.00 42.25 3.02
4625 6195 2.421424 ACCTTGCTGAATCATCTTTCGC 59.579 45.455 0.00 0.00 0.00 4.70
4628 6198 1.399440 TGCTGAATCATCTTTCGCTGC 59.601 47.619 0.00 0.00 0.00 5.25
4629 6199 1.268437 GCTGAATCATCTTTCGCTGCC 60.268 52.381 0.00 0.00 0.00 4.85
4630 6200 2.011947 CTGAATCATCTTTCGCTGCCA 58.988 47.619 0.00 0.00 0.00 4.92
4632 6202 2.012673 GAATCATCTTTCGCTGCCACT 58.987 47.619 0.00 0.00 0.00 4.00
4633 6203 1.376543 ATCATCTTTCGCTGCCACTG 58.623 50.000 0.00 0.00 0.00 3.66
4634 6204 0.035317 TCATCTTTCGCTGCCACTGT 59.965 50.000 0.00 0.00 0.00 3.55
4635 6205 0.877071 CATCTTTCGCTGCCACTGTT 59.123 50.000 0.00 0.00 0.00 3.16
4636 6206 2.076100 CATCTTTCGCTGCCACTGTTA 58.924 47.619 0.00 0.00 0.00 2.41
4637 6207 2.472695 TCTTTCGCTGCCACTGTTAT 57.527 45.000 0.00 0.00 0.00 1.89
4638 6208 2.076100 TCTTTCGCTGCCACTGTTATG 58.924 47.619 0.00 0.00 0.00 1.90
4639 6209 0.521291 TTTCGCTGCCACTGTTATGC 59.479 50.000 0.00 0.00 0.00 3.14
4640 6210 0.605050 TTCGCTGCCACTGTTATGCA 60.605 50.000 0.00 0.00 0.00 3.96
4641 6211 0.605050 TCGCTGCCACTGTTATGCAA 60.605 50.000 0.00 0.00 34.06 4.08
4642 6212 0.454957 CGCTGCCACTGTTATGCAAC 60.455 55.000 0.00 0.00 34.06 4.17
4643 6213 0.597568 GCTGCCACTGTTATGCAACA 59.402 50.000 0.00 0.00 42.39 3.33
4644 6214 1.000385 GCTGCCACTGTTATGCAACAA 60.000 47.619 0.00 0.00 43.92 2.83
4645 6215 2.664916 CTGCCACTGTTATGCAACAAC 58.335 47.619 7.43 7.43 43.92 3.32
4646 6216 2.027385 TGCCACTGTTATGCAACAACA 58.973 42.857 14.43 14.43 43.92 3.33
4647 6217 2.627221 TGCCACTGTTATGCAACAACAT 59.373 40.909 15.27 5.95 43.92 2.71
4648 6218 3.244976 GCCACTGTTATGCAACAACATC 58.755 45.455 15.27 4.86 43.92 3.06
4649 6219 3.491356 CCACTGTTATGCAACAACATCG 58.509 45.455 15.27 9.07 43.92 3.84
4650 6220 3.058293 CCACTGTTATGCAACAACATCGT 60.058 43.478 15.27 9.58 43.92 3.73
4651 6221 4.536065 CACTGTTATGCAACAACATCGTT 58.464 39.130 15.27 1.74 43.92 3.85
4652 6222 4.379498 CACTGTTATGCAACAACATCGTTG 59.621 41.667 15.27 5.34 43.92 4.10
4653 6223 4.036262 ACTGTTATGCAACAACATCGTTGT 59.964 37.500 15.27 6.68 46.47 3.32
4654 6224 4.926244 TGTTATGCAACAACATCGTTGTT 58.074 34.783 17.21 17.21 46.47 2.83
4681 6251 2.977772 AAAGATGAGGAAGAGAGCCG 57.022 50.000 0.00 0.00 0.00 5.52
4763 6338 6.883744 ACTAAAGCTTTTTGAATCAAACCCA 58.116 32.000 18.47 0.00 32.79 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.718454 CAGTGGATGAGCTTATTAATCCCATT 59.282 38.462 0.00 0.00 38.25 3.16
38 39 3.806949 AGGTGAGGGAATGTTTTGCTA 57.193 42.857 0.00 0.00 0.00 3.49
55 56 6.209391 CCCAACAAGAATGATTCAGTTAAGGT 59.791 38.462 8.03 0.00 31.77 3.50
60 61 4.154942 AGCCCAACAAGAATGATTCAGTT 58.845 39.130 8.03 8.78 32.70 3.16
67 68 3.330701 ACCTTCTAGCCCAACAAGAATGA 59.669 43.478 0.00 0.00 0.00 2.57
68 69 3.690460 ACCTTCTAGCCCAACAAGAATG 58.310 45.455 0.00 0.00 0.00 2.67
69 70 4.324331 GGTACCTTCTAGCCCAACAAGAAT 60.324 45.833 4.06 0.00 0.00 2.40
70 71 3.008704 GGTACCTTCTAGCCCAACAAGAA 59.991 47.826 4.06 0.00 0.00 2.52
71 72 2.570302 GGTACCTTCTAGCCCAACAAGA 59.430 50.000 4.06 0.00 0.00 3.02
74 75 2.337359 AGGTACCTTCTAGCCCAACA 57.663 50.000 9.21 0.00 0.00 3.33
111 112 6.980397 GTGGGCATATTTGGTGAGAAAATAAG 59.020 38.462 0.00 0.00 34.18 1.73
145 146 6.576551 GAGTATCTTCGATGGTCTTCAAAC 57.423 41.667 0.00 0.00 0.00 2.93
191 192 4.527816 ACATTCTGAAGGCATGGCTAAAAA 59.472 37.500 23.63 14.36 0.00 1.94
192 193 4.088634 ACATTCTGAAGGCATGGCTAAAA 58.911 39.130 23.63 14.02 0.00 1.52
193 194 3.700538 ACATTCTGAAGGCATGGCTAAA 58.299 40.909 23.63 14.37 0.00 1.85
194 195 3.370840 ACATTCTGAAGGCATGGCTAA 57.629 42.857 23.63 13.39 0.00 3.09
195 196 3.370840 AACATTCTGAAGGCATGGCTA 57.629 42.857 23.63 6.68 0.00 3.93
196 197 2.226962 AACATTCTGAAGGCATGGCT 57.773 45.000 17.44 17.44 0.00 4.75
197 198 2.417787 GGAAACATTCTGAAGGCATGGC 60.418 50.000 12.14 12.14 0.00 4.40
198 199 2.827322 TGGAAACATTCTGAAGGCATGG 59.173 45.455 1.41 0.00 33.40 3.66
245 246 2.860735 GCTGATACTCTTTGTGCTACGG 59.139 50.000 0.00 0.00 0.00 4.02
265 266 8.014517 GCAAAGCTAGAGAATGATAACTTATGC 58.985 37.037 0.00 0.00 0.00 3.14
266 267 9.270640 AGCAAAGCTAGAGAATGATAACTTATG 57.729 33.333 0.00 0.00 36.99 1.90
269 270 7.066766 CCAAGCAAAGCTAGAGAATGATAACTT 59.933 37.037 0.00 0.00 38.25 2.66
312 313 5.086621 GGGTTTAGGGATATCCATGCATTT 58.913 41.667 23.27 2.47 38.24 2.32
323 324 3.323775 GGAGACATGGGGTTTAGGGATA 58.676 50.000 0.00 0.00 0.00 2.59
362 363 2.173569 GGCTAGTTTGGATGGAGGATGT 59.826 50.000 0.00 0.00 0.00 3.06
372 373 4.527816 AGAAAATGCATTGGCTAGTTTGGA 59.472 37.500 13.82 0.00 41.91 3.53
377 378 6.183347 AGTAGAAGAAAATGCATTGGCTAGT 58.817 36.000 13.82 9.96 41.91 2.57
405 406 3.028130 TCTTTTTGGTGAGGGGACAAAC 58.972 45.455 0.00 0.00 34.21 2.93
406 407 3.390175 TCTTTTTGGTGAGGGGACAAA 57.610 42.857 0.00 0.00 32.77 2.83
407 408 3.611025 ATCTTTTTGGTGAGGGGACAA 57.389 42.857 0.00 0.00 0.00 3.18
413 414 4.248058 GCAATGGAATCTTTTTGGTGAGG 58.752 43.478 0.00 0.00 0.00 3.86
426 427 7.201884 CCAAAGAGATTACAGATGCAATGGAAT 60.202 37.037 11.48 11.48 33.80 3.01
433 434 4.842531 TCCCAAAGAGATTACAGATGCA 57.157 40.909 0.00 0.00 0.00 3.96
445 446 6.112058 TGGTTGTTTTCAAAATCCCAAAGAG 58.888 36.000 0.00 0.00 41.76 2.85
452 453 9.921637 TGTATTCTATGGTTGTTTTCAAAATCC 57.078 29.630 0.00 0.00 41.76 3.01
482 496 9.928618 TGTTGAAACCCATTATCCAATCTATTA 57.071 29.630 0.00 0.00 0.00 0.98
489 503 6.985653 TTTCTGTTGAAACCCATTATCCAA 57.014 33.333 0.00 0.00 37.27 3.53
502 516 7.610580 AGGGTGGAAATAAATTTCTGTTGAA 57.389 32.000 13.57 0.00 44.21 2.69
507 521 7.415206 CGTCCTTAGGGTGGAAATAAATTTCTG 60.415 40.741 13.57 0.00 44.21 3.02
512 526 5.045432 TGACGTCCTTAGGGTGGAAATAAAT 60.045 40.000 14.12 0.00 35.10 1.40
517 531 1.719529 TGACGTCCTTAGGGTGGAAA 58.280 50.000 14.12 0.00 35.10 3.13
519 533 0.971386 GTTGACGTCCTTAGGGTGGA 59.029 55.000 14.12 0.00 0.00 4.02
522 536 3.736720 GAAAAGTTGACGTCCTTAGGGT 58.263 45.455 14.12 0.00 0.00 4.34
523 537 2.735134 CGAAAAGTTGACGTCCTTAGGG 59.265 50.000 14.12 0.00 0.00 3.53
533 547 3.938778 AGGTTCGAACGAAAAGTTGAC 57.061 42.857 21.34 4.16 44.35 3.18
539 553 3.000523 CGACTTGAAGGTTCGAACGAAAA 59.999 43.478 21.34 11.97 35.75 2.29
548 562 4.511826 AGTTGTGAATCGACTTGAAGGTTC 59.488 41.667 0.00 0.00 37.49 3.62
554 568 5.356426 TGAAAGAGTTGTGAATCGACTTGA 58.644 37.500 0.00 0.00 40.56 3.02
571 585 9.429359 GATAGTTTCTCTGATCTTGTTGAAAGA 57.571 33.333 0.00 0.00 0.00 2.52
583 597 4.282496 ACCGAGGTGATAGTTTCTCTGAT 58.718 43.478 0.00 0.00 0.00 2.90
585 599 4.082190 TGAACCGAGGTGATAGTTTCTCTG 60.082 45.833 0.00 0.00 0.00 3.35
630 644 4.043596 AGGCCAATTCTGACTCCTATCTT 58.956 43.478 5.01 0.00 0.00 2.40
632 646 3.244387 GGAGGCCAATTCTGACTCCTATC 60.244 52.174 16.21 0.00 40.54 2.08
633 647 2.708325 GGAGGCCAATTCTGACTCCTAT 59.292 50.000 16.21 0.00 40.54 2.57
634 648 2.119495 GGAGGCCAATTCTGACTCCTA 58.881 52.381 16.21 0.00 40.54 2.94
635 649 0.915364 GGAGGCCAATTCTGACTCCT 59.085 55.000 16.21 0.00 40.54 3.69
636 650 0.462759 CGGAGGCCAATTCTGACTCC 60.463 60.000 14.20 14.20 40.42 3.85
637 651 1.092345 GCGGAGGCCAATTCTGACTC 61.092 60.000 5.01 0.00 0.00 3.36
638 652 1.078143 GCGGAGGCCAATTCTGACT 60.078 57.895 5.01 0.00 0.00 3.41
639 653 3.502572 GCGGAGGCCAATTCTGAC 58.497 61.111 5.01 0.00 0.00 3.51
663 678 5.047519 AGCTTAGCTTTGCATGAAACTGAAT 60.048 36.000 0.00 0.00 33.89 2.57
691 706 2.028748 GCCAAAATGTGAATGCTGAGGT 60.029 45.455 0.00 0.00 0.00 3.85
697 712 5.236911 TCTTTTTCAGCCAAAATGTGAATGC 59.763 36.000 0.00 0.00 33.82 3.56
704 719 8.299570 AGTGTAGTATCTTTTTCAGCCAAAATG 58.700 33.333 0.00 0.00 33.82 2.32
715 730 9.722184 GAGTTAAGGGAAGTGTAGTATCTTTTT 57.278 33.333 0.00 0.00 0.00 1.94
737 752 2.107204 AGCTCAGGACAATTGGTGAGTT 59.893 45.455 24.27 19.58 38.96 3.01
753 769 4.325972 TGAATGAATACTGTGCAAGCTCA 58.674 39.130 0.00 0.00 0.00 4.26
756 772 4.266976 GCATTGAATGAATACTGTGCAAGC 59.733 41.667 9.76 0.00 0.00 4.01
778 794 5.632347 CCAAGAAATCACAATTGAGACAAGC 59.368 40.000 13.59 1.05 34.35 4.01
916 955 1.135228 TCATCTGCGTCGAATTTCGGA 60.135 47.619 18.02 7.89 40.88 4.55
924 963 2.017049 TCTCATTCTCATCTGCGTCGA 58.983 47.619 0.00 0.00 0.00 4.20
934 973 1.134699 GGGCGTGTCATCTCATTCTCA 60.135 52.381 0.00 0.00 0.00 3.27
935 974 1.134699 TGGGCGTGTCATCTCATTCTC 60.135 52.381 0.00 0.00 0.00 2.87
936 975 0.904649 TGGGCGTGTCATCTCATTCT 59.095 50.000 0.00 0.00 0.00 2.40
937 976 1.009829 GTGGGCGTGTCATCTCATTC 58.990 55.000 0.00 0.00 0.00 2.67
938 977 0.392998 GGTGGGCGTGTCATCTCATT 60.393 55.000 0.00 0.00 0.00 2.57
939 978 1.221840 GGTGGGCGTGTCATCTCAT 59.778 57.895 0.00 0.00 0.00 2.90
980 1019 3.353370 TTGGGTCGGTTTGTTATAGGG 57.647 47.619 0.00 0.00 0.00 3.53
1250 1290 2.190578 CCGGGTTCAGATCTGGGC 59.809 66.667 22.42 14.54 0.00 5.36
1298 1338 0.926155 CGCACGATTCAGACATCAGG 59.074 55.000 0.00 0.00 0.00 3.86
1305 1345 1.737735 CACCAGCGCACGATTCAGA 60.738 57.895 11.47 0.00 0.00 3.27
1543 1715 0.698238 CCACCCAAACCCTCATCAGA 59.302 55.000 0.00 0.00 0.00 3.27
1568 1740 1.925455 CCCTCTTCCTTCCCCTGCA 60.925 63.158 0.00 0.00 0.00 4.41
1603 1778 2.630098 GCAGCTGAGGATGTAGGTGATA 59.370 50.000 20.43 0.00 43.20 2.15
1778 2045 1.279840 GAGCTGGACAACACAACGC 59.720 57.895 0.00 0.00 0.00 4.84
2051 2717 3.735746 CACGAAGCTTCCATTTTCCAAAC 59.264 43.478 20.62 0.00 0.00 2.93
2387 3080 4.867047 GGACACAACAGAGTACTCATGATG 59.133 45.833 24.44 22.03 0.00 3.07
2424 3121 6.875948 TGTTTAAGCAAAATAGAGCAGTGA 57.124 33.333 0.00 0.00 0.00 3.41
3145 4553 6.233434 AGTGAAAGCTGATATTGAGAACACA 58.767 36.000 0.00 0.00 0.00 3.72
3387 4800 8.840833 ATTGAGATCTCATCTTCATGATTGAG 57.159 34.615 25.64 18.10 40.38 3.02
3420 4833 1.377366 TAGTGCTTCTCGCCTCCTCG 61.377 60.000 0.00 0.00 38.05 4.63
3537 4950 7.780064 TGTTATTGCACTGCATTACCATAAAT 58.220 30.769 4.10 0.00 38.76 1.40
3541 4954 5.657826 TTGTTATTGCACTGCATTACCAT 57.342 34.783 4.10 0.00 38.76 3.55
3581 5060 6.460103 AAGAGCATTATTGGGGATGAGTAT 57.540 37.500 0.00 0.00 0.00 2.12
3620 5101 0.899717 GGGAAGGCATTCACCTGCAA 60.900 55.000 13.81 0.00 44.12 4.08
3621 5102 1.304381 GGGAAGGCATTCACCTGCA 60.304 57.895 13.81 0.00 44.12 4.41
3711 5192 1.372997 CTGTGAAGGTCGGACACGG 60.373 63.158 10.76 0.79 41.39 4.94
3750 5231 6.644181 TGCTTGCATCAAAATTGAAACGAATA 59.356 30.769 0.00 0.00 41.13 1.75
3755 5236 6.129300 GCATTTGCTTGCATCAAAATTGAAAC 60.129 34.615 15.57 0.00 42.31 2.78
3804 5285 5.049267 GTGGTTAGCAATTTGTTAAGTCGGA 60.049 40.000 6.01 0.00 0.00 4.55
3930 5411 2.777832 AGCAGATGAAGTTGGAGACC 57.222 50.000 0.00 0.00 0.00 3.85
4086 5568 1.196354 CAAAGCTCTACTGTGCAGTGC 59.804 52.381 8.58 8.58 42.52 4.40
4163 5645 9.797556 GACTGGTTGGATTTAAATACAAATACC 57.202 33.333 24.25 21.72 40.72 2.73
4292 5814 6.967199 CACACCTTTTGTAGAGACAAGAAAAC 59.033 38.462 0.00 0.00 46.11 2.43
4293 5815 6.404293 GCACACCTTTTGTAGAGACAAGAAAA 60.404 38.462 0.00 0.00 46.11 2.29
4368 5892 1.365699 GCGAGGCGTAAAAAGATCCA 58.634 50.000 0.00 0.00 0.00 3.41
4471 6022 1.181098 ACATGGGTCTTGTTGCAGGC 61.181 55.000 0.00 0.00 0.00 4.85
4510 6061 6.783892 GCAATAAGGATCTTGTTGCAAAAA 57.216 33.333 25.92 0.00 43.18 1.94
4547 6098 4.738124 CAGAAAGTTAGATGCGACAGAGA 58.262 43.478 0.00 0.00 0.00 3.10
4549 6100 3.254060 GCAGAAAGTTAGATGCGACAGA 58.746 45.455 0.00 0.00 0.00 3.41
4551 6102 3.038788 TGCAGAAAGTTAGATGCGACA 57.961 42.857 0.00 0.00 41.58 4.35
4552 6103 3.737305 GTTGCAGAAAGTTAGATGCGAC 58.263 45.455 10.01 10.01 43.62 5.19
4553 6104 3.398406 TGTTGCAGAAAGTTAGATGCGA 58.602 40.909 0.00 0.00 41.58 5.10
4583 6137 1.676438 CGTGATGCGCCATTTGCAAC 61.676 55.000 4.18 0.00 46.87 4.17
4602 6156 3.730061 CGAAAGATGATTCAGCAAGGTGC 60.730 47.826 4.52 0.00 45.46 5.01
4603 6157 3.730061 GCGAAAGATGATTCAGCAAGGTG 60.730 47.826 4.52 0.00 32.75 4.00
4604 6158 2.421424 GCGAAAGATGATTCAGCAAGGT 59.579 45.455 4.52 0.00 32.75 3.50
4605 6159 2.681848 AGCGAAAGATGATTCAGCAAGG 59.318 45.455 4.52 0.00 33.97 3.61
4625 6195 2.034432 TGTTGTTGCATAACAGTGGCAG 59.966 45.455 11.66 0.00 46.63 4.85
4628 6198 3.058293 ACGATGTTGTTGCATAACAGTGG 60.058 43.478 18.20 13.13 46.63 4.00
4629 6199 4.145876 ACGATGTTGTTGCATAACAGTG 57.854 40.909 18.20 15.28 46.63 3.66
4630 6200 4.536065 CAACGATGTTGTTGCATAACAGT 58.464 39.130 18.20 11.22 46.63 3.55
4665 6235 0.529555 GCACGGCTCTCTTCCTCATC 60.530 60.000 0.00 0.00 0.00 2.92
4705 6279 5.985911 TCAAAACCGTTTTAATTGGGGAAA 58.014 33.333 8.90 0.00 0.00 3.13
4708 6282 5.992217 TGATTCAAAACCGTTTTAATTGGGG 59.008 36.000 8.90 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.