Multiple sequence alignment - TraesCS3D01G295500

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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 TraesCS3D01G295500 chr3D 100.000 4232 0 0 1 4232 408314060 408318291 0.000000e+00 7816.0
1 TraesCS3D01G295500 chr3D 86.154 65 6 2 4160 4222 408318142 408318205 2.730000e-07 67.6
2 TraesCS3D01G295500 chr3B 94.915 3127 86 21 553 3631 534190040 534193141 0.000000e+00 4826.0
3 TraesCS3D01G295500 chr3B 91.681 577 15 7 3673 4231 534193482 534194043 0.000000e+00 769.0
4 TraesCS3D01G295500 chr3B 87.812 320 31 5 917 1228 95456169 95456488 6.680000e-98 368.0
5 TraesCS3D01G295500 chr3B 79.265 381 34 13 84 449 534189626 534189976 1.530000e-54 224.0
6 TraesCS3D01G295500 chr3B 96.774 93 3 0 1 93 534189239 534189331 5.670000e-34 156.0
7 TraesCS3D01G295500 chr3A 90.598 3510 178 60 216 3631 543181337 543177886 0.000000e+00 4514.0
8 TraesCS3D01G295500 chr3A 89.695 262 13 4 3631 3887 543177693 543177441 5.280000e-84 322.0
9 TraesCS3D01G295500 chr3A 93.333 105 7 0 3891 3995 543177410 543177306 5.670000e-34 156.0
10 TraesCS3D01G295500 chr3A 93.243 74 4 1 4083 4156 543177152 543177080 1.610000e-19 108.0
11 TraesCS3D01G295500 chr3A 91.549 71 6 0 4010 4080 543177315 543177245 9.680000e-17 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 TraesCS3D01G295500 chr3D 408314060 408318291 4231 False 3941.80 7816 93.07700 1 4232 2 chr3D.!!$F1 4231
1 TraesCS3D01G295500 chr3B 534189239 534194043 4804 False 1493.75 4826 90.65875 1 4231 4 chr3B.!!$F2 4230
2 TraesCS3D01G295500 chr3A 543177080 543181337 4257 True 1039.80 4514 91.68360 216 4156 5 chr3A.!!$R1 3940

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
571 930 0.175760 TCCAACACTAGAGCCGATGC 59.824 55.000 0.0 0.0 37.95 3.91 F
627 987 0.402861 TTTTCTCCCCAGTCCCCACT 60.403 55.000 0.0 0.0 0.00 4.00 F
1926 2343 1.004440 GCTCCCTGGTCTGTGTGTC 60.004 63.158 0.0 0.0 0.00 3.67 F
2419 2836 1.127951 CACGTAAAGCGAATGGGTCAC 59.872 52.381 0.0 0.0 44.77 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2241 1.933051 TCCTCCTCCTCCTCTTCATGA 59.067 52.381 0.0 0.0 0.00 3.07 R
1962 2379 1.978617 CGCCTTGCCACCCTTCATT 60.979 57.895 0.0 0.0 0.00 2.57 R
2732 3149 3.510388 TGGCGATTGTTTTTGTCAACA 57.490 38.095 0.0 0.0 34.76 3.33 R
4092 4875 2.890311 CAGGTCCATTTTTGCAGTACCA 59.110 45.455 0.0 0.0 0.00 3.25 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
52 53 2.042686 TGTATGCTTGTCTGATGCCC 57.957 50.000 0.00 0.00 0.00 5.36
119 424 5.403246 CCATGGATGCGTACTATAGAGTTC 58.597 45.833 5.56 0.00 37.10 3.01
135 440 2.670414 GAGTTCTTCAGACTCCAATGCG 59.330 50.000 0.00 0.00 0.00 4.73
142 447 1.394917 CAGACTCCAATGCGCACTTAC 59.605 52.381 14.90 0.51 0.00 2.34
143 448 1.276421 AGACTCCAATGCGCACTTACT 59.724 47.619 14.90 3.16 0.00 2.24
145 450 3.056107 AGACTCCAATGCGCACTTACTTA 60.056 43.478 14.90 0.00 0.00 2.24
146 451 3.871594 GACTCCAATGCGCACTTACTTAT 59.128 43.478 14.90 0.00 0.00 1.73
147 452 3.871594 ACTCCAATGCGCACTTACTTATC 59.128 43.478 14.90 0.00 0.00 1.75
148 453 4.122776 CTCCAATGCGCACTTACTTATCT 58.877 43.478 14.90 0.00 0.00 1.98
149 454 4.119862 TCCAATGCGCACTTACTTATCTC 58.880 43.478 14.90 0.00 0.00 2.75
150 455 3.871006 CCAATGCGCACTTACTTATCTCA 59.129 43.478 14.90 0.00 0.00 3.27
151 456 4.512944 CCAATGCGCACTTACTTATCTCAT 59.487 41.667 14.90 0.00 0.00 2.90
152 457 5.696270 CCAATGCGCACTTACTTATCTCATA 59.304 40.000 14.90 0.00 0.00 2.15
153 458 6.128715 CCAATGCGCACTTACTTATCTCATAG 60.129 42.308 14.90 0.00 0.00 2.23
154 459 5.515797 TGCGCACTTACTTATCTCATAGT 57.484 39.130 5.66 0.00 0.00 2.12
155 460 6.628919 TGCGCACTTACTTATCTCATAGTA 57.371 37.500 5.66 0.00 0.00 1.82
156 461 7.215719 TGCGCACTTACTTATCTCATAGTAT 57.784 36.000 5.66 0.00 0.00 2.12
177 482 2.587322 TTTATGAGCCCAGCCCGTCG 62.587 60.000 0.00 0.00 0.00 5.12
183 488 2.202932 CCCAGCCCGTCGATGAAG 60.203 66.667 6.11 0.00 0.00 3.02
189 494 1.084370 GCCCGTCGATGAAGGTTCTG 61.084 60.000 6.11 0.00 29.35 3.02
199 504 5.355071 TCGATGAAGGTTCTGGAATGAATTG 59.645 40.000 0.00 0.00 0.00 2.32
201 506 6.349611 CGATGAAGGTTCTGGAATGAATTGTT 60.350 38.462 0.00 0.00 0.00 2.83
202 507 6.088016 TGAAGGTTCTGGAATGAATTGTTG 57.912 37.500 0.00 0.00 0.00 3.33
203 508 5.010922 TGAAGGTTCTGGAATGAATTGTTGG 59.989 40.000 0.00 0.00 0.00 3.77
204 509 4.739793 AGGTTCTGGAATGAATTGTTGGA 58.260 39.130 0.00 0.00 0.00 3.53
205 510 4.524328 AGGTTCTGGAATGAATTGTTGGAC 59.476 41.667 0.00 0.00 0.00 4.02
206 511 4.524328 GGTTCTGGAATGAATTGTTGGACT 59.476 41.667 0.00 0.00 0.00 3.85
207 512 5.335976 GGTTCTGGAATGAATTGTTGGACTC 60.336 44.000 0.00 0.00 0.00 3.36
208 513 4.335416 TCTGGAATGAATTGTTGGACTCC 58.665 43.478 0.00 0.00 0.00 3.85
209 514 3.081061 TGGAATGAATTGTTGGACTCCG 58.919 45.455 0.00 0.00 0.00 4.63
210 515 3.244735 TGGAATGAATTGTTGGACTCCGA 60.245 43.478 0.00 0.00 0.00 4.55
211 516 3.756434 GGAATGAATTGTTGGACTCCGAA 59.244 43.478 0.00 0.00 0.00 4.30
212 517 4.142600 GGAATGAATTGTTGGACTCCGAAG 60.143 45.833 0.00 0.00 0.00 3.79
213 518 3.762407 TGAATTGTTGGACTCCGAAGA 57.238 42.857 0.00 0.00 0.00 2.87
214 519 3.664107 TGAATTGTTGGACTCCGAAGAG 58.336 45.455 0.00 0.00 46.36 2.85
239 544 4.389645 CATCGTTTTGCTCGAAGAAGAAG 58.610 43.478 0.00 0.00 40.61 2.85
240 545 3.713288 TCGTTTTGCTCGAAGAAGAAGA 58.287 40.909 0.00 0.00 34.09 2.87
241 546 4.116961 TCGTTTTGCTCGAAGAAGAAGAA 58.883 39.130 0.00 0.00 34.09 2.52
242 547 4.209288 TCGTTTTGCTCGAAGAAGAAGAAG 59.791 41.667 0.00 0.00 34.09 2.85
243 548 4.209288 CGTTTTGCTCGAAGAAGAAGAAGA 59.791 41.667 0.00 0.00 34.09 2.87
244 549 5.276868 CGTTTTGCTCGAAGAAGAAGAAGAA 60.277 40.000 0.00 0.00 34.09 2.52
257 562 8.528044 AGAAGAAGAAGAACGTAGGATAGAAT 57.472 34.615 0.00 0.00 0.00 2.40
259 564 9.240159 GAAGAAGAAGAACGTAGGATAGAATTC 57.760 37.037 0.00 0.00 0.00 2.17
333 644 1.450312 GACCGAACCCTGCTCCATG 60.450 63.158 0.00 0.00 0.00 3.66
386 707 5.249393 ACCAGATTCCTACTCAATTCACACT 59.751 40.000 0.00 0.00 0.00 3.55
388 709 5.518128 CAGATTCCTACTCAATTCACACTCG 59.482 44.000 0.00 0.00 0.00 4.18
394 715 1.866601 CTCAATTCACACTCGCACACA 59.133 47.619 0.00 0.00 0.00 3.72
395 716 2.284190 TCAATTCACACTCGCACACAA 58.716 42.857 0.00 0.00 0.00 3.33
396 717 2.680339 TCAATTCACACTCGCACACAAA 59.320 40.909 0.00 0.00 0.00 2.83
398 719 0.730265 TTCACACTCGCACACAAACC 59.270 50.000 0.00 0.00 0.00 3.27
399 720 0.391793 TCACACTCGCACACAAACCA 60.392 50.000 0.00 0.00 0.00 3.67
400 721 0.449786 CACACTCGCACACAAACCAA 59.550 50.000 0.00 0.00 0.00 3.67
401 722 0.732571 ACACTCGCACACAAACCAAG 59.267 50.000 0.00 0.00 0.00 3.61
429 762 4.408821 CCCGTGCCTGCCTGCTTA 62.409 66.667 0.00 0.00 0.00 3.09
435 773 1.405463 GTGCCTGCCTGCTTAATAACC 59.595 52.381 0.00 0.00 0.00 2.85
436 774 1.032794 GCCTGCCTGCTTAATAACCC 58.967 55.000 0.00 0.00 0.00 4.11
460 798 4.160635 CGATCCCGGCGTGCAAAC 62.161 66.667 6.01 0.00 0.00 2.93
461 799 4.160635 GATCCCGGCGTGCAAACG 62.161 66.667 6.01 0.00 0.00 3.60
485 823 0.317854 TCAGCTCACGTCTGAACACG 60.318 55.000 3.14 0.00 45.65 4.49
497 835 2.621526 TCTGAACACGAAGCACAGTAGA 59.378 45.455 0.00 0.00 0.00 2.59
498 836 2.983136 CTGAACACGAAGCACAGTAGAG 59.017 50.000 0.00 0.00 0.00 2.43
503 841 3.762288 ACACGAAGCACAGTAGAGGAATA 59.238 43.478 0.00 0.00 0.00 1.75
504 842 4.106197 CACGAAGCACAGTAGAGGAATAC 58.894 47.826 0.00 0.00 0.00 1.89
505 843 4.017808 ACGAAGCACAGTAGAGGAATACT 58.982 43.478 0.00 0.00 36.41 2.12
521 859 7.171630 AGGAATACTCTACCTACACAAACAG 57.828 40.000 0.00 0.00 31.78 3.16
522 860 6.154706 AGGAATACTCTACCTACACAAACAGG 59.845 42.308 0.00 0.00 37.97 4.00
523 861 5.934402 ATACTCTACCTACACAAACAGGG 57.066 43.478 0.00 0.00 36.15 4.45
547 885 3.261250 CAGGGCTGCCATGGATATC 57.739 57.895 24.74 2.17 30.99 1.63
548 886 0.323178 CAGGGCTGCCATGGATATCC 60.323 60.000 24.74 15.39 30.99 2.59
571 930 0.175760 TCCAACACTAGAGCCGATGC 59.824 55.000 0.00 0.00 37.95 3.91
627 987 0.402861 TTTTCTCCCCAGTCCCCACT 60.403 55.000 0.00 0.00 0.00 4.00
671 1048 3.327404 ACCCGTGTCACCATCCCC 61.327 66.667 0.00 0.00 0.00 4.81
807 1184 1.967274 GCCTGCCTCTTCCTCTTCCTA 60.967 57.143 0.00 0.00 0.00 2.94
910 1299 2.509336 CGGCACAGATCCGTCCAC 60.509 66.667 0.00 0.00 41.85 4.02
911 1300 2.125106 GGCACAGATCCGTCCACC 60.125 66.667 0.00 0.00 0.00 4.61
912 1301 2.662596 GCACAGATCCGTCCACCA 59.337 61.111 0.00 0.00 0.00 4.17
913 1302 1.741770 GCACAGATCCGTCCACCAC 60.742 63.158 0.00 0.00 0.00 4.16
914 1303 1.079127 CACAGATCCGTCCACCACC 60.079 63.158 0.00 0.00 0.00 4.61
915 1304 1.535444 ACAGATCCGTCCACCACCA 60.535 57.895 0.00 0.00 0.00 4.17
921 1310 3.867783 CGTCCACCACCACCCACA 61.868 66.667 0.00 0.00 0.00 4.17
975 1364 3.251043 CGAGCGAGCGAGCCTTTC 61.251 66.667 2.87 0.00 38.01 2.62
977 1366 4.803426 AGCGAGCGAGCCTTTCCG 62.803 66.667 2.87 0.00 38.01 4.30
1242 1638 2.044352 GGCGCCAACCCTTACCAT 60.044 61.111 24.80 0.00 0.00 3.55
1777 2194 1.746991 GTGCAGCTCCCTTACCAGC 60.747 63.158 0.00 0.00 35.73 4.85
1824 2241 1.621992 ACTATCCCAGACGCGATGAT 58.378 50.000 15.93 9.32 0.00 2.45
1854 2271 2.316108 GAGGAGGAGGAAGAGGATGAC 58.684 57.143 0.00 0.00 0.00 3.06
1917 2334 1.152756 GTGTGGTTTGCTCCCTGGT 60.153 57.895 0.00 0.00 0.00 4.00
1918 2335 1.150536 TGTGGTTTGCTCCCTGGTC 59.849 57.895 0.00 0.00 0.00 4.02
1926 2343 1.004440 GCTCCCTGGTCTGTGTGTC 60.004 63.158 0.00 0.00 0.00 3.67
1941 2358 3.192422 TGTGTGTCAAAACCTCCTTGTTG 59.808 43.478 0.00 0.00 0.00 3.33
1962 2379 5.823861 TGCTACTGAATCCAATGCCTATA 57.176 39.130 0.00 0.00 0.00 1.31
2149 2566 5.698089 TCAGAGTTATGTTGCTTCTTGACAG 59.302 40.000 0.00 0.00 0.00 3.51
2419 2836 1.127951 CACGTAAAGCGAATGGGTCAC 59.872 52.381 0.00 0.00 44.77 3.67
2732 3149 9.334947 CATAGTGGAAGTTCAAGACAATGATAT 57.665 33.333 5.01 0.00 0.00 1.63
2808 3225 4.933400 GGAAACGCAGGATCAGTAAAACTA 59.067 41.667 0.00 0.00 0.00 2.24
3040 3457 4.682714 AAGCTCCCTGGGCCTCCA 62.683 66.667 8.22 0.00 41.58 3.86
3342 3774 4.320494 CCCTGTTTTGCTGTTGTAGTGATC 60.320 45.833 0.00 0.00 0.00 2.92
3991 4774 3.012518 GGACACTGCTGATGCTGTTATT 58.987 45.455 0.00 0.00 46.76 1.40
4003 4786 5.769662 TGATGCTGTTATTTTGGTTGAGACT 59.230 36.000 0.00 0.00 0.00 3.24
4089 4872 7.857734 CTTAGAGAGCAGATAGATATTCCGA 57.142 40.000 0.00 0.00 0.00 4.55
4090 4873 8.275015 CTTAGAGAGCAGATAGATATTCCGAA 57.725 38.462 0.00 0.00 0.00 4.30
4092 4875 6.245408 AGAGAGCAGATAGATATTCCGAACT 58.755 40.000 0.00 0.00 0.00 3.01
4093 4876 6.150976 AGAGAGCAGATAGATATTCCGAACTG 59.849 42.308 0.00 0.00 0.00 3.16
4094 4877 5.184864 AGAGCAGATAGATATTCCGAACTGG 59.815 44.000 0.00 0.00 40.09 4.00
4095 4878 4.835615 AGCAGATAGATATTCCGAACTGGT 59.164 41.667 0.00 0.00 39.52 4.00
4099 4882 7.309177 CAGATAGATATTCCGAACTGGTACTG 58.691 42.308 0.00 0.00 39.52 2.74
4100 4883 4.323553 AGATATTCCGAACTGGTACTGC 57.676 45.455 0.00 0.00 39.52 4.40
4101 4884 3.704566 AGATATTCCGAACTGGTACTGCA 59.295 43.478 0.00 0.00 39.52 4.41
4107 4890 3.252215 TCCGAACTGGTACTGCAAAAATG 59.748 43.478 0.00 0.00 39.52 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 393 1.009335 CGCATCCATGGCATGTTCG 60.009 57.895 24.80 17.19 0.00 3.95
119 424 0.445436 GTGCGCATTGGAGTCTGAAG 59.555 55.000 15.91 0.00 0.00 3.02
148 453 6.003950 GGCTGGGCTCATAAAAATACTATGA 58.996 40.000 0.00 0.00 35.13 2.15
149 454 5.183904 GGGCTGGGCTCATAAAAATACTATG 59.816 44.000 0.00 0.00 0.00 2.23
150 455 5.325239 GGGCTGGGCTCATAAAAATACTAT 58.675 41.667 0.00 0.00 0.00 2.12
151 456 4.725490 GGGCTGGGCTCATAAAAATACTA 58.275 43.478 0.00 0.00 0.00 1.82
152 457 3.566351 GGGCTGGGCTCATAAAAATACT 58.434 45.455 0.00 0.00 0.00 2.12
153 458 2.293399 CGGGCTGGGCTCATAAAAATAC 59.707 50.000 0.00 0.00 0.00 1.89
154 459 2.092103 ACGGGCTGGGCTCATAAAAATA 60.092 45.455 0.00 0.00 0.00 1.40
155 460 1.341976 ACGGGCTGGGCTCATAAAAAT 60.342 47.619 0.00 0.00 0.00 1.82
156 461 0.039035 ACGGGCTGGGCTCATAAAAA 59.961 50.000 0.00 0.00 0.00 1.94
169 474 1.218316 GAACCTTCATCGACGGGCT 59.782 57.895 0.00 0.00 0.00 5.19
177 482 6.521151 ACAATTCATTCCAGAACCTTCATC 57.479 37.500 0.00 0.00 0.00 2.92
178 483 6.295462 CCAACAATTCATTCCAGAACCTTCAT 60.295 38.462 0.00 0.00 0.00 2.57
183 488 4.524328 AGTCCAACAATTCATTCCAGAACC 59.476 41.667 0.00 0.00 0.00 3.62
189 494 3.343617 TCGGAGTCCAACAATTCATTCC 58.656 45.455 10.49 0.00 0.00 3.01
205 510 1.714794 AAACGATGCACTCTTCGGAG 58.285 50.000 11.73 0.00 46.82 4.63
206 511 1.798223 CAAAACGATGCACTCTTCGGA 59.202 47.619 11.73 0.00 42.15 4.55
207 512 1.725931 GCAAAACGATGCACTCTTCGG 60.726 52.381 11.73 0.00 45.70 4.30
208 513 1.595609 GCAAAACGATGCACTCTTCG 58.404 50.000 5.91 5.91 45.70 3.79
220 525 4.209288 TCTTCTTCTTCTTCGAGCAAAACG 59.791 41.667 0.00 0.00 0.00 3.60
266 571 7.770366 ACCGTTCATAAACTTTTTCCCTAAT 57.230 32.000 0.00 0.00 32.95 1.73
267 572 8.156165 TCTACCGTTCATAAACTTTTTCCCTAA 58.844 33.333 0.00 0.00 32.95 2.69
268 573 7.678837 TCTACCGTTCATAAACTTTTTCCCTA 58.321 34.615 0.00 0.00 32.95 3.53
271 576 9.687210 ATTTTCTACCGTTCATAAACTTTTTCC 57.313 29.630 0.00 0.00 32.95 3.13
307 618 0.107848 CAGGGTTCGGTCGGCTAATT 60.108 55.000 0.00 0.00 0.00 1.40
308 619 1.520666 CAGGGTTCGGTCGGCTAAT 59.479 57.895 0.00 0.00 0.00 1.73
309 620 2.975536 CAGGGTTCGGTCGGCTAA 59.024 61.111 0.00 0.00 0.00 3.09
313 624 4.452733 GGAGCAGGGTTCGGTCGG 62.453 72.222 0.00 0.00 0.00 4.79
333 644 6.238648 TCTCTCCCTTGGTTTGTTTAATCTC 58.761 40.000 0.00 0.00 0.00 2.75
386 707 0.817634 CTCCCTTGGTTTGTGTGCGA 60.818 55.000 0.00 0.00 0.00 5.10
388 709 0.385390 CACTCCCTTGGTTTGTGTGC 59.615 55.000 0.00 0.00 0.00 4.57
394 715 0.759060 GGTTGCCACTCCCTTGGTTT 60.759 55.000 0.00 0.00 39.09 3.27
395 716 1.152546 GGTTGCCACTCCCTTGGTT 60.153 57.895 0.00 0.00 39.09 3.67
396 717 2.520968 GGTTGCCACTCCCTTGGT 59.479 61.111 0.00 0.00 39.09 3.67
398 719 2.672996 CGGGTTGCCACTCCCTTG 60.673 66.667 3.18 0.00 41.40 3.61
399 720 3.175710 ACGGGTTGCCACTCCCTT 61.176 61.111 3.18 0.00 41.40 3.95
400 721 3.953775 CACGGGTTGCCACTCCCT 61.954 66.667 3.18 0.00 41.40 4.20
444 782 4.160635 CGTTTGCACGCCGGGATC 62.161 66.667 2.18 0.00 40.18 3.36
455 793 0.179205 GTGAGCTGATCTGCGTTTGC 60.179 55.000 17.62 7.86 43.20 3.68
456 794 0.094216 CGTGAGCTGATCTGCGTTTG 59.906 55.000 17.62 7.13 38.13 2.93
457 795 0.319900 ACGTGAGCTGATCTGCGTTT 60.320 50.000 17.62 1.86 37.07 3.60
458 796 0.734253 GACGTGAGCTGATCTGCGTT 60.734 55.000 17.62 2.58 39.21 4.84
459 797 1.153939 GACGTGAGCTGATCTGCGT 60.154 57.895 17.62 13.64 40.81 5.24
460 798 1.138459 AGACGTGAGCTGATCTGCG 59.862 57.895 17.62 7.21 38.13 5.18
461 799 0.172127 TCAGACGTGAGCTGATCTGC 59.828 55.000 16.18 16.18 38.62 4.26
462 800 2.257894 GTTCAGACGTGAGCTGATCTG 58.742 52.381 6.30 0.00 41.45 2.90
463 801 1.889170 TGTTCAGACGTGAGCTGATCT 59.111 47.619 6.30 0.00 41.45 2.75
468 806 0.384309 TTCGTGTTCAGACGTGAGCT 59.616 50.000 0.00 0.00 40.34 4.09
497 835 6.154706 CCTGTTTGTGTAGGTAGAGTATTCCT 59.845 42.308 0.00 0.00 35.60 3.36
498 836 6.338937 CCTGTTTGTGTAGGTAGAGTATTCC 58.661 44.000 0.00 0.00 0.00 3.01
503 841 2.302157 GCCCTGTTTGTGTAGGTAGAGT 59.698 50.000 0.00 0.00 31.99 3.24
504 842 2.301870 TGCCCTGTTTGTGTAGGTAGAG 59.698 50.000 0.00 0.00 31.99 2.43
505 843 2.301870 CTGCCCTGTTTGTGTAGGTAGA 59.698 50.000 0.00 0.00 31.99 2.59
510 848 1.244019 GCCCTGCCCTGTTTGTGTAG 61.244 60.000 0.00 0.00 0.00 2.74
511 849 1.228429 GCCCTGCCCTGTTTGTGTA 60.228 57.895 0.00 0.00 0.00 2.90
512 850 2.521708 GCCCTGCCCTGTTTGTGT 60.522 61.111 0.00 0.00 0.00 3.72
513 851 2.521465 TGCCCTGCCCTGTTTGTG 60.521 61.111 0.00 0.00 0.00 3.33
515 853 2.993264 CCTGCCCTGCCCTGTTTG 60.993 66.667 0.00 0.00 0.00 2.93
545 883 2.237392 GGCTCTAGTGTTGGACTTGGAT 59.763 50.000 0.00 0.00 35.96 3.41
546 884 1.623811 GGCTCTAGTGTTGGACTTGGA 59.376 52.381 0.00 0.00 35.96 3.53
547 885 1.673033 CGGCTCTAGTGTTGGACTTGG 60.673 57.143 0.00 0.00 35.96 3.61
548 886 1.272490 TCGGCTCTAGTGTTGGACTTG 59.728 52.381 0.00 0.00 35.96 3.16
549 887 1.629043 TCGGCTCTAGTGTTGGACTT 58.371 50.000 0.00 0.00 35.96 3.01
550 888 1.478510 CATCGGCTCTAGTGTTGGACT 59.521 52.381 0.00 0.00 38.88 3.85
571 930 2.165030 CCTAAAAAGGTGATGCCAGCAG 59.835 50.000 0.00 0.00 42.91 4.24
905 1294 2.203294 GTGTGGGTGGTGGTGGAC 60.203 66.667 0.00 0.00 0.00 4.02
906 1295 2.367648 AGTGTGGGTGGTGGTGGA 60.368 61.111 0.00 0.00 0.00 4.02
907 1296 2.113139 GAGTGTGGGTGGTGGTGG 59.887 66.667 0.00 0.00 0.00 4.61
908 1297 2.113139 GGAGTGTGGGTGGTGGTG 59.887 66.667 0.00 0.00 0.00 4.17
909 1298 3.175710 GGGAGTGTGGGTGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
910 1299 3.966543 GGGGAGTGTGGGTGGTGG 61.967 72.222 0.00 0.00 0.00 4.61
911 1300 3.966543 GGGGGAGTGTGGGTGGTG 61.967 72.222 0.00 0.00 0.00 4.17
1031 1421 2.202932 CCAGGTCGATCCGCTTGG 60.203 66.667 0.00 0.00 41.99 3.61
1077 1467 4.147135 AGGTCGGCCTTGTGGTAT 57.853 55.556 0.35 0.00 44.18 2.73
1221 1617 2.670251 TAAGGGTTGGCGCCGTTG 60.670 61.111 23.90 0.00 37.23 4.10
1232 1628 1.615424 AGGGCGTCATGGTAAGGGT 60.615 57.895 0.00 0.00 0.00 4.34
1777 2194 4.891756 AGACAAATAATTGGGAGGCAGATG 59.108 41.667 0.00 0.00 41.01 2.90
1824 2241 1.933051 TCCTCCTCCTCCTCTTCATGA 59.067 52.381 0.00 0.00 0.00 3.07
1917 2334 3.278574 CAAGGAGGTTTTGACACACAGA 58.721 45.455 0.00 0.00 0.00 3.41
1918 2335 3.016736 ACAAGGAGGTTTTGACACACAG 58.983 45.455 0.00 0.00 0.00 3.66
1926 2343 3.882888 TCAGTAGCAACAAGGAGGTTTTG 59.117 43.478 0.00 0.00 0.00 2.44
1941 2358 6.881065 TCATTATAGGCATTGGATTCAGTAGC 59.119 38.462 0.00 0.00 0.00 3.58
1962 2379 1.978617 CGCCTTGCCACCCTTCATT 60.979 57.895 0.00 0.00 0.00 2.57
1985 2402 4.101077 CCCTGCCTCTCCCTCCCT 62.101 72.222 0.00 0.00 0.00 4.20
2149 2566 6.285990 TGTTTAGAACTACCACTCCTGAAAC 58.714 40.000 0.00 0.00 0.00 2.78
2409 2826 5.794894 TCTCTTACTTCAAGTGACCCATTC 58.205 41.667 0.00 0.00 33.02 2.67
2732 3149 3.510388 TGGCGATTGTTTTTGTCAACA 57.490 38.095 0.00 0.00 34.76 3.33
3040 3457 5.447778 AGATCATTCTCCTTTGGATGTGT 57.552 39.130 0.00 0.00 0.00 3.72
3284 3716 4.349503 ATTGGGCGCTGGCAGTCA 62.350 61.111 17.16 7.08 42.47 3.41
3342 3774 4.926207 GGTAAGTGGTACCCAGCG 57.074 61.111 10.07 0.00 46.03 5.18
3834 4572 3.764885 ACACAAAACAAGAGTGCAGAC 57.235 42.857 0.00 0.00 36.76 3.51
4040 4823 3.314913 TGTTCGAATCAAGAGCAGCAAAA 59.685 39.130 0.00 0.00 0.00 2.44
4089 4872 3.320826 GGTCCATTTTTGCAGTACCAGTT 59.679 43.478 0.00 0.00 0.00 3.16
4090 4873 2.890945 GGTCCATTTTTGCAGTACCAGT 59.109 45.455 0.00 0.00 0.00 4.00
4092 4875 2.890311 CAGGTCCATTTTTGCAGTACCA 59.110 45.455 0.00 0.00 0.00 3.25
4093 4876 2.890945 ACAGGTCCATTTTTGCAGTACC 59.109 45.455 0.00 0.00 0.00 3.34
4094 4877 5.183140 ACATACAGGTCCATTTTTGCAGTAC 59.817 40.000 0.00 0.00 0.00 2.73
4095 4878 5.182950 CACATACAGGTCCATTTTTGCAGTA 59.817 40.000 0.00 0.00 0.00 2.74
4099 4882 4.519540 ACACATACAGGTCCATTTTTGC 57.480 40.909 0.00 0.00 0.00 3.68
4100 4883 8.879342 TTTTAACACATACAGGTCCATTTTTG 57.121 30.769 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.