Multiple sequence alignment - TraesCS5A01G163900

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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 TraesCS5A01G163900 chr5A 100.000 2864 0 0 1 2864 351473206 351476069 0.000000e+00 5289.0
1 TraesCS5A01G163900 chr5A 92.308 39 3 0 1262 1300 470194386 470194424 3.990000e-04 56.5
2 TraesCS5A01G163900 chr5D 93.416 2886 137 28 1 2864 264794304 264797158 0.000000e+00 4228.0
3 TraesCS5A01G163900 chr5D 94.118 34 2 0 22 55 215424242 215424275 5.000000e-03 52.8
4 TraesCS5A01G163900 chr5B 93.349 2090 90 27 426 2491 297105350 297107414 0.000000e+00 3044.0
5 TraesCS5A01G163900 chr5B 94.723 379 8 4 2484 2862 297112871 297113237 1.910000e-161 579.0
6 TraesCS5A01G163900 chr5B 86.977 430 43 7 2 422 297096886 297097311 3.340000e-129 472.0
7 TraesCS5A01G163900 chr5B 100.000 28 0 0 1273 1300 436257253 436257280 5.000000e-03 52.8
8 TraesCS5A01G163900 chr4D 83.857 446 69 3 67 511 226373444 226373001 3.410000e-114 422.0
9 TraesCS5A01G163900 chr4D 83.705 448 66 7 67 511 226546866 226546423 1.590000e-112 416.0
10 TraesCS5A01G163900 chr4D 83.408 446 71 3 67 511 226452258 226451815 7.390000e-111 411.0
11 TraesCS5A01G163900 chr4D 100.000 28 0 0 28 55 321852676 321852703 5.000000e-03 52.8
12 TraesCS5A01G163900 chr1D 79.741 232 36 9 76 303 56508669 56508893 1.060000e-34 158.0
13 TraesCS5A01G163900 chr2B 78.814 236 32 15 67 295 793312679 793312455 2.970000e-30 143.0
14 TraesCS5A01G163900 chr2B 100.000 29 0 0 27 55 510900763 510900735 1.000000e-03 54.7
15 TraesCS5A01G163900 chr7D 100.000 29 0 0 27 55 146420041 146420069 1.000000e-03 54.7
16 TraesCS5A01G163900 chr7D 96.875 32 1 0 24 55 368928954 368928985 1.000000e-03 54.7
17 TraesCS5A01G163900 chr4B 96.970 33 0 1 28 59 372824811 372824843 1.000000e-03 54.7
18 TraesCS5A01G163900 chrUn 100.000 28 0 0 28 55 111779348 111779375 5.000000e-03 52.8
19 TraesCS5A01G163900 chr1A 96.875 32 0 1 25 55 10244354 10244323 5.000000e-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 TraesCS5A01G163900 chr5A 351473206 351476069 2863 False 5289 5289 100.000 1 2864 1 chr5A.!!$F1 2863
1 TraesCS5A01G163900 chr5D 264794304 264797158 2854 False 4228 4228 93.416 1 2864 1 chr5D.!!$F2 2863
2 TraesCS5A01G163900 chr5B 297105350 297107414 2064 False 3044 3044 93.349 426 2491 1 chr5B.!!$F2 2065

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
196 197 0.168348 TAACACTGCGTCTCGAGCTC 59.832 55.0 7.81 2.73 35.28 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1917 0.602638 TGTTGCCTAGTTGCAGTCGG 60.603 55.0 0.0 0.0 43.21 4.79 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
43 44 5.030147 ACACAAATACTACCTCCATCCTGA 58.970 41.667 0.00 0.00 0.00 3.86
52 53 5.672194 ACTACCTCCATCCTGATTTATTGGT 59.328 40.000 0.00 0.00 0.00 3.67
58 59 4.997395 CCATCCTGATTTATTGGTCCGTAG 59.003 45.833 0.00 0.00 0.00 3.51
63 64 2.012937 TTTATTGGTCCGTAGCGTGG 57.987 50.000 0.00 0.00 0.00 4.94
65 66 0.683828 TATTGGTCCGTAGCGTGGGA 60.684 55.000 0.00 0.00 0.00 4.37
78 79 0.818296 CGTGGGAGGGAGTTACTCTG 59.182 60.000 12.41 0.00 35.34 3.35
82 83 2.104170 GGGAGGGAGTTACTCTGACAG 58.896 57.143 12.41 0.00 35.34 3.51
83 84 2.291670 GGGAGGGAGTTACTCTGACAGA 60.292 54.545 12.41 4.78 35.34 3.41
121 122 2.996631 ACAAGGGCTAGATCAAGCAAG 58.003 47.619 0.00 0.00 44.64 4.01
124 125 0.548510 GGGCTAGATCAAGCAAGGGT 59.451 55.000 0.00 0.00 44.64 4.34
148 149 1.877443 AGCGTGACACATGGGTTTTAC 59.123 47.619 0.00 1.35 0.00 2.01
159 160 1.270252 TGGGTTTTACGAGTTCGGACC 60.270 52.381 6.48 7.96 44.95 4.46
184 185 3.952323 TCTCGGAGGAGGTAATAACACTG 59.048 47.826 4.96 0.00 40.85 3.66
194 195 1.630148 AATAACACTGCGTCTCGAGC 58.370 50.000 7.81 1.89 0.00 5.03
196 197 0.168348 TAACACTGCGTCTCGAGCTC 59.832 55.000 7.81 2.73 35.28 4.09
200 201 3.408501 CTGCGTCTCGAGCTCTGGG 62.409 68.421 12.85 5.62 35.28 4.45
225 227 5.069781 AGCTGTGTTTTCTTCTCTAGTGTCT 59.930 40.000 0.00 0.00 0.00 3.41
226 228 5.176590 GCTGTGTTTTCTTCTCTAGTGTCTG 59.823 44.000 0.00 0.00 0.00 3.51
243 245 5.530171 AGTGTCTGATGATTACAATGGATGC 59.470 40.000 0.00 0.00 0.00 3.91
247 249 5.237127 TCTGATGATTACAATGGATGCGAAC 59.763 40.000 0.00 0.00 0.00 3.95
248 250 4.275689 TGATGATTACAATGGATGCGAACC 59.724 41.667 0.00 0.00 0.00 3.62
271 273 1.940883 CTTACTGTGCTACGGGGCGA 61.941 60.000 0.00 0.00 34.52 5.54
283 285 3.151912 ACGGGGCGACTTATATAGAGT 57.848 47.619 0.00 0.00 0.00 3.24
285 287 2.415625 CGGGGCGACTTATATAGAGTGC 60.416 54.545 0.00 6.62 0.00 4.40
286 288 2.561419 GGGGCGACTTATATAGAGTGCA 59.439 50.000 0.00 0.00 0.00 4.57
303 305 2.038975 ACCGCCCCTTGAGCTAGA 59.961 61.111 0.00 0.00 0.00 2.43
323 325 6.641723 GCTAGATACGTTACAAAGAGGGATTC 59.358 42.308 0.00 0.00 0.00 2.52
373 375 4.811024 ACGCATGGTAACTGATGTATTGAG 59.189 41.667 0.00 0.00 37.61 3.02
408 420 3.188786 GGCGTGCACCTCTTAGCG 61.189 66.667 12.15 0.00 0.00 4.26
412 424 1.291877 CGTGCACCTCTTAGCGCTTT 61.292 55.000 18.68 0.00 39.01 3.51
418 430 3.326747 CACCTCTTAGCGCTTTAGTGTT 58.673 45.455 18.68 0.00 0.00 3.32
419 431 3.368236 CACCTCTTAGCGCTTTAGTGTTC 59.632 47.826 18.68 0.00 0.00 3.18
455 467 2.241430 TCTCCCTCTGACCGAATCACTA 59.759 50.000 0.00 0.00 32.37 2.74
458 470 2.959030 CCCTCTGACCGAATCACTATGA 59.041 50.000 0.00 0.00 32.37 2.15
466 478 3.387050 ACCGAATCACTATGAGGTAACCC 59.613 47.826 0.00 0.00 37.17 4.11
506 518 1.843832 TGGATGGGTGGTGTCCGAA 60.844 57.895 0.00 0.00 34.72 4.30
528 540 2.087646 GGAAGGAACCTTGACTGATGC 58.912 52.381 11.02 0.00 36.26 3.91
549 561 2.423373 CCCGAATGGATTTGAGACCCAT 60.423 50.000 0.00 0.00 42.08 4.00
550 562 3.181445 CCCGAATGGATTTGAGACCCATA 60.181 47.826 0.00 0.00 39.58 2.74
551 563 4.507335 CCCGAATGGATTTGAGACCCATAT 60.507 45.833 0.00 0.00 39.58 1.78
554 566 3.228188 TGGATTTGAGACCCATATGCC 57.772 47.619 0.00 0.00 0.00 4.40
555 567 2.785269 TGGATTTGAGACCCATATGCCT 59.215 45.455 0.00 0.00 0.00 4.75
556 568 3.181440 TGGATTTGAGACCCATATGCCTC 60.181 47.826 0.00 4.37 0.00 4.70
558 570 3.565764 TTTGAGACCCATATGCCTCAG 57.434 47.619 15.44 0.00 37.04 3.35
571 583 2.320587 CCTCAGTGTCTGGCGTTGC 61.321 63.158 0.00 0.00 31.51 4.17
588 600 1.145377 GCGGGTCCCACGTATGATT 59.855 57.895 9.12 0.00 0.00 2.57
606 618 8.568794 CGTATGATTCAGAATGTACCTCTCTTA 58.431 37.037 0.00 0.00 37.40 2.10
625 637 9.369672 CTCTCTTAACTCTACCTATAATGGGTT 57.630 37.037 0.00 0.00 38.19 4.11
654 666 8.026607 CCCAATAGTTCGTTTGTATTTTGTGAT 58.973 33.333 0.00 0.00 0.00 3.06
668 680 8.310382 TGTATTTTGTGATAAATTTGGACCAGG 58.690 33.333 0.00 0.00 0.00 4.45
680 692 8.499288 AAATTTGGACCAGGGATTTAACTAAA 57.501 30.769 9.52 0.00 0.00 1.85
722 734 8.424731 GTCACGAAAAATTACATTGTTGGATTC 58.575 33.333 0.00 0.00 0.00 2.52
900 936 3.430098 CCTGTTGCAAAACCAGCTAAACA 60.430 43.478 0.00 0.00 0.00 2.83
975 1011 3.381333 CTACCGCCGAAGTTCCCCC 62.381 68.421 0.00 0.00 0.00 5.40
1113 1149 2.257676 GACCCGAACGACGAGCTT 59.742 61.111 0.00 0.00 45.77 3.74
1132 1168 4.154347 GCCTGTCGAGCCTCCAGG 62.154 72.222 13.31 13.31 46.91 4.45
1164 1200 2.317609 CCGCAACTGGACCAAGTCG 61.318 63.158 0.00 0.00 32.65 4.18
1794 1830 2.202987 GTCTGCATCTGGCTCCGG 60.203 66.667 0.00 0.00 45.15 5.14
1864 1910 1.522092 CTCATGCCGGCCTACTGAA 59.478 57.895 26.77 2.60 0.00 3.02
1865 1911 0.811616 CTCATGCCGGCCTACTGAAC 60.812 60.000 26.77 0.00 0.00 3.18
1866 1912 1.221840 CATGCCGGCCTACTGAACT 59.778 57.895 26.77 0.00 0.00 3.01
1867 1913 0.811616 CATGCCGGCCTACTGAACTC 60.812 60.000 26.77 0.00 0.00 3.01
1868 1914 1.264749 ATGCCGGCCTACTGAACTCA 61.265 55.000 26.77 0.00 0.00 3.41
1935 1981 2.262471 GATGCAACCAGCTCCTTGCG 62.262 60.000 16.48 0.00 44.84 4.85
2100 2148 1.514553 CAGAGCAGCCGTCATCAGA 59.485 57.895 0.00 0.00 0.00 3.27
2101 2149 0.528033 CAGAGCAGCCGTCATCAGAG 60.528 60.000 0.00 0.00 0.00 3.35
2119 2167 4.159321 TCAGAGTGTCAGAAGCTAATCCAG 59.841 45.833 0.00 0.00 0.00 3.86
2211 2266 3.340814 TTTAGTACGACCCTCTCGAGT 57.659 47.619 13.13 0.00 46.14 4.18
2278 2333 4.816385 CCACCTGTGCTTGTATATTGGTAG 59.184 45.833 0.00 0.00 0.00 3.18
2398 2453 7.032580 ACGATAATGCTACTCTAATCATCAGC 58.967 38.462 0.00 0.00 0.00 4.26
2549 2607 0.318955 AAAATTGCGTGAGTGGCAGC 60.319 50.000 0.00 0.00 42.12 5.25
2551 2609 3.557903 ATTGCGTGAGTGGCAGCCT 62.558 57.895 14.15 0.00 42.12 4.58
2552 2610 4.994471 TGCGTGAGTGGCAGCCTG 62.994 66.667 14.15 0.00 35.04 4.85
2594 2652 2.504026 GCGCGCTTTGCTTTACCC 60.504 61.111 26.67 0.00 43.27 3.69
2723 2781 1.597027 CTTCCGTGTGGGTGTGGAC 60.597 63.158 0.00 0.00 37.00 4.02
2724 2782 2.318519 CTTCCGTGTGGGTGTGGACA 62.319 60.000 0.00 0.00 37.00 4.02
2725 2783 1.701031 TTCCGTGTGGGTGTGGACAT 61.701 55.000 0.00 0.00 37.00 3.06
2726 2784 1.965930 CCGTGTGGGTGTGGACATG 60.966 63.158 0.00 0.00 0.00 3.21
2829 2887 3.319122 GTGTGAAGTTCCCATCAGCTTTT 59.681 43.478 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.871125 AGGATGGAGGTAGTATTTGTGTTATAG 58.129 37.037 0.00 0.00 0.00 1.31
17 18 7.347222 TCAGGATGGAGGTAGTATTTGTGTTAT 59.653 37.037 0.00 0.00 36.16 1.89
18 19 6.670464 TCAGGATGGAGGTAGTATTTGTGTTA 59.330 38.462 0.00 0.00 36.16 2.41
43 44 2.557317 CCACGCTACGGACCAATAAAT 58.443 47.619 0.00 0.00 0.00 1.40
52 53 4.051167 TCCCTCCCACGCTACGGA 62.051 66.667 0.00 0.00 0.00 4.69
58 59 0.971447 AGAGTAACTCCCTCCCACGC 60.971 60.000 0.00 0.00 0.00 5.34
63 64 3.020984 CTCTGTCAGAGTAACTCCCTCC 58.979 54.545 20.06 0.00 37.57 4.30
65 66 3.963129 CTCTCTGTCAGAGTAACTCCCT 58.037 50.000 25.68 0.00 43.61 4.20
78 79 6.550108 TGTTCATACCCCTAATACTCTCTGTC 59.450 42.308 0.00 0.00 0.00 3.51
82 83 6.239629 CCCTTGTTCATACCCCTAATACTCTC 60.240 46.154 0.00 0.00 0.00 3.20
83 84 5.607171 CCCTTGTTCATACCCCTAATACTCT 59.393 44.000 0.00 0.00 0.00 3.24
84 85 5.745181 GCCCTTGTTCATACCCCTAATACTC 60.745 48.000 0.00 0.00 0.00 2.59
89 90 2.568979 AGCCCTTGTTCATACCCCTAA 58.431 47.619 0.00 0.00 0.00 2.69
94 95 4.689612 TGATCTAGCCCTTGTTCATACC 57.310 45.455 0.00 0.00 0.00 2.73
121 122 2.260869 ATGTGTCACGCTTGCACCC 61.261 57.895 12.68 0.00 32.13 4.61
124 125 2.260154 CCCATGTGTCACGCTTGCA 61.260 57.895 0.00 0.00 0.00 4.08
130 131 2.136728 TCGTAAAACCCATGTGTCACG 58.863 47.619 0.00 4.47 0.00 4.35
148 149 2.762234 CGAGAGGGGTCCGAACTCG 61.762 68.421 13.03 13.03 38.83 4.18
184 185 3.119709 CTCCCAGAGCTCGAGACGC 62.120 68.421 18.75 9.51 0.00 5.19
194 195 2.557920 AGAAAACACAGCTCCCAGAG 57.442 50.000 0.00 0.00 0.00 3.35
196 197 2.810852 GAGAAGAAAACACAGCTCCCAG 59.189 50.000 0.00 0.00 0.00 4.45
200 201 5.293560 ACACTAGAGAAGAAAACACAGCTC 58.706 41.667 0.00 0.00 0.00 4.09
205 206 7.148641 TCATCAGACACTAGAGAAGAAAACAC 58.851 38.462 0.00 0.00 0.00 3.32
211 213 8.581253 TTGTAATCATCAGACACTAGAGAAGA 57.419 34.615 0.00 0.00 0.00 2.87
212 214 9.247126 CATTGTAATCATCAGACACTAGAGAAG 57.753 37.037 0.00 0.00 0.00 2.85
225 227 4.275689 GGTTCGCATCCATTGTAATCATCA 59.724 41.667 0.00 0.00 0.00 3.07
226 228 4.320494 GGGTTCGCATCCATTGTAATCATC 60.320 45.833 0.00 0.00 0.00 2.92
243 245 0.608640 AGCACAGTAAGAGGGGTTCG 59.391 55.000 0.00 0.00 0.00 3.95
247 249 0.460311 CCGTAGCACAGTAAGAGGGG 59.540 60.000 0.00 0.00 0.00 4.79
248 250 0.460311 CCCGTAGCACAGTAAGAGGG 59.540 60.000 0.00 0.00 0.00 4.30
271 273 2.299297 GGGCGGTGCACTCTATATAAGT 59.701 50.000 17.98 0.00 0.00 2.24
285 287 1.690219 ATCTAGCTCAAGGGGCGGTG 61.690 60.000 0.00 0.00 34.52 4.94
286 288 0.105658 TATCTAGCTCAAGGGGCGGT 60.106 55.000 0.00 0.00 34.52 5.68
303 305 5.587388 TCGAATCCCTCTTTGTAACGTAT 57.413 39.130 0.00 0.00 0.00 3.06
352 354 5.504665 GCACTCAATACATCAGTTACCATGC 60.505 44.000 0.00 0.00 0.00 4.06
389 401 1.376037 GCTAAGAGGTGCACGCCTT 60.376 57.895 20.91 20.91 39.34 4.35
408 420 0.714439 GTCCGAGCGAACACTAAAGC 59.286 55.000 0.00 0.00 0.00 3.51
412 424 1.915614 GACGGTCCGAGCGAACACTA 61.916 60.000 25.67 0.00 42.41 2.74
418 430 0.879400 GAGATAGACGGTCCGAGCGA 60.879 60.000 25.67 6.23 42.41 4.93
419 431 1.570475 GAGATAGACGGTCCGAGCG 59.430 63.158 20.51 18.03 45.69 5.03
422 434 0.108207 GAGGGAGATAGACGGTCCGA 59.892 60.000 20.51 0.00 0.00 4.55
455 467 4.475016 ACTAAGCTCATTGGGTTACCTCAT 59.525 41.667 0.00 0.00 37.76 2.90
458 470 3.622455 GCACTAAGCTCATTGGGTTACCT 60.622 47.826 0.00 0.00 41.15 3.08
466 478 1.456296 TGGCTGCACTAAGCTCATTG 58.544 50.000 0.50 0.00 45.94 2.82
506 518 3.875369 GCATCAGTCAAGGTTCCTTCCAT 60.875 47.826 0.60 0.00 0.00 3.41
511 523 0.329596 GGGCATCAGTCAAGGTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
528 540 1.064758 TGGGTCTCAAATCCATTCGGG 60.065 52.381 0.00 0.00 38.37 5.14
554 566 2.661566 CGCAACGCCAGACACTGAG 61.662 63.158 0.00 0.00 32.44 3.35
555 567 2.661537 CGCAACGCCAGACACTGA 60.662 61.111 0.00 0.00 32.44 3.41
556 568 3.716006 CCGCAACGCCAGACACTG 61.716 66.667 0.00 0.00 0.00 3.66
571 583 0.462375 TGAATCATACGTGGGACCCG 59.538 55.000 5.91 0.00 0.00 5.28
580 592 6.976088 AGAGAGGTACATTCTGAATCATACG 58.024 40.000 0.00 0.00 0.00 3.06
588 600 7.556996 GGTAGAGTTAAGAGAGGTACATTCTGA 59.443 40.741 4.08 0.00 0.00 3.27
625 637 7.447853 ACAAAATACAAACGAACTATTGGGGTA 59.552 33.333 0.00 0.00 0.00 3.69
637 649 9.967346 TCCAAATTTATCACAAAATACAAACGA 57.033 25.926 0.00 0.00 0.00 3.85
654 666 9.603189 TTTAGTTAAATCCCTGGTCCAAATTTA 57.397 29.630 0.00 1.85 0.00 1.40
685 697 9.737427 TGTAATTTTTCGTGACACACATTAATT 57.263 25.926 6.37 7.04 33.40 1.40
686 698 9.906660 ATGTAATTTTTCGTGACACACATTAAT 57.093 25.926 6.37 0.00 33.40 1.40
693 705 6.473778 CCAACAATGTAATTTTTCGTGACACA 59.526 34.615 6.37 0.00 31.22 3.72
793 808 9.310449 GATTAGTCCCTCTGTATTTAGGTCATA 57.690 37.037 0.00 0.00 0.00 2.15
798 813 7.147549 TGGTTGATTAGTCCCTCTGTATTTAGG 60.148 40.741 0.00 0.00 0.00 2.69
800 815 7.147549 CCTGGTTGATTAGTCCCTCTGTATTTA 60.148 40.741 0.00 0.00 0.00 1.40
806 821 2.171448 CCCTGGTTGATTAGTCCCTCTG 59.829 54.545 0.00 0.00 0.00 3.35
900 936 3.560636 AATGTTATAAGGCGGCTGTCT 57.439 42.857 14.21 0.00 0.00 3.41
975 1011 0.676782 GACGATGGGGGTGGTGAAAG 60.677 60.000 0.00 0.00 0.00 2.62
1164 1200 0.602905 CACAGGGGTCGGTGAAGAAC 60.603 60.000 0.00 0.00 40.69 3.01
1707 1743 4.457496 ACGATGGCCAGCACGGAG 62.457 66.667 22.95 6.54 36.56 4.63
1821 1857 2.688666 ATCTTGCCCTCCTCGCCA 60.689 61.111 0.00 0.00 0.00 5.69
1868 1914 2.982130 CCTAGTTGCAGTCGGGCT 59.018 61.111 0.00 0.00 34.04 5.19
1869 1915 2.820037 GCCTAGTTGCAGTCGGGC 60.820 66.667 6.99 6.99 0.00 6.13
1870 1916 1.003839 TTGCCTAGTTGCAGTCGGG 60.004 57.895 0.00 0.00 43.21 5.14
1871 1917 0.602638 TGTTGCCTAGTTGCAGTCGG 60.603 55.000 0.00 0.00 43.21 4.79
1872 1918 1.129251 CATGTTGCCTAGTTGCAGTCG 59.871 52.381 0.00 0.00 43.21 4.18
1873 1919 1.135575 GCATGTTGCCTAGTTGCAGTC 60.136 52.381 0.00 0.00 43.21 3.51
1894 1940 0.671796 TGATAGTACCACCGGCATCG 59.328 55.000 0.00 0.00 0.00 3.84
1910 1956 1.681166 GGAGCTGGTTGCATCTGTGAT 60.681 52.381 0.00 0.00 45.94 3.06
1935 1981 2.921754 CAAATCCGTACTCCAACTCGAC 59.078 50.000 0.00 0.00 0.00 4.20
2100 2148 4.564406 CCAACTGGATTAGCTTCTGACACT 60.564 45.833 0.00 0.00 37.39 3.55
2101 2149 3.686726 CCAACTGGATTAGCTTCTGACAC 59.313 47.826 0.00 0.00 37.39 3.67
2119 2167 4.881920 ACAATGCACCAATTAACTCCAAC 58.118 39.130 0.00 0.00 0.00 3.77
2193 2248 3.340814 AAACTCGAGAGGGTCGTACTA 57.659 47.619 21.68 0.00 46.10 1.82
2207 2262 3.082548 TCTCCCTCACTCACTAAACTCG 58.917 50.000 0.00 0.00 0.00 4.18
2211 2266 2.382305 TCCCTCTCCCTCACTCACTAAA 59.618 50.000 0.00 0.00 0.00 1.85
2278 2333 7.550906 AGTGAAGTGGAATAAATTCTCTACTGC 59.449 37.037 2.91 5.06 37.00 4.40
2525 2583 3.181515 TGCCACTCACGCAATTTTATACG 60.182 43.478 0.00 0.00 32.05 3.06
2594 2652 3.825012 ACATGATGATGTTGCCGGAACG 61.825 50.000 5.05 0.00 46.89 3.95
2675 2733 1.003851 ACGATGATTTTACGTGGGCG 58.996 50.000 0.00 0.00 44.93 6.13
2723 2781 5.918576 ACTTGCGCATTCATATTTCATCATG 59.081 36.000 12.75 0.00 0.00 3.07
2724 2782 5.918576 CACTTGCGCATTCATATTTCATCAT 59.081 36.000 12.75 0.00 0.00 2.45
2725 2783 5.275494 CACTTGCGCATTCATATTTCATCA 58.725 37.500 12.75 0.00 0.00 3.07
2726 2784 4.678287 CCACTTGCGCATTCATATTTCATC 59.322 41.667 12.75 0.00 0.00 2.92
2829 2887 3.187313 TCCTCGGTGGAAGGGAGA 58.813 61.111 0.00 0.00 42.94 3.71


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

AutoCloner maintained by Alex Coulton.