Multiple sequence alignment - TraesCS3D01G292900

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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 TraesCS3D01G292900 chr3D 100.000 3986 0 0 1 3986 402782016 402778031 0.000000e+00 7361.0
1 TraesCS3D01G292900 chr3D 82.716 81 11 2 521 598 133088844 133088924 7.150000e-08 69.4
2 TraesCS3D01G292900 chr3B 93.056 3946 167 38 80 3986 528503454 528499577 0.000000e+00 5670.0
3 TraesCS3D01G292900 chr3B 80.682 88 12 5 516 599 828423952 828424038 3.330000e-06 63.9
4 TraesCS3D01G292900 chr3A 95.345 2621 102 9 526 3127 523734064 523731445 0.000000e+00 4146.0
5 TraesCS3D01G292900 chr3A 95.449 835 25 5 3152 3986 523731344 523730523 0.000000e+00 1319.0
6 TraesCS3D01G292900 chr3A 88.333 240 20 7 74 310 523735448 523735214 8.430000e-72 281.0
7 TraesCS3D01G292900 chr5A 82.716 81 9 4 521 598 428815556 428815634 2.570000e-07 67.6
8 TraesCS3D01G292900 chr7B 84.375 64 6 4 553 614 637248975 637248914 4.300000e-05 60.2


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 TraesCS3D01G292900 chr3D 402778031 402782016 3985 True 7361.000000 7361 100.000000 1 3986 1 chr3D.!!$R1 3985
1 TraesCS3D01G292900 chr3B 528499577 528503454 3877 True 5670.000000 5670 93.056000 80 3986 1 chr3B.!!$R1 3906
2 TraesCS3D01G292900 chr3A 523730523 523735448 4925 True 1915.333333 4146 93.042333 74 3986 3 chr3A.!!$R1 3912

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
70 71 0.038310 GCCTTTGCAAGAGGTACCCT 59.962 55.000 21.25 2.33 36.63 4.34 F
852 1995 0.182537 CACCACCTTGTTCCACTCCA 59.817 55.000 0.00 0.00 0.00 3.86 F
897 2040 0.311790 CGCCAACACAGCTCACATTT 59.688 50.000 0.00 0.00 0.00 2.32 F
2700 3843 1.407989 GCTATGGAAGAGGCTGCTGTT 60.408 52.381 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 2335 2.123248 TTGAGGATGAGCGGGTGCAA 62.123 55.000 0.0 0.0 46.23 4.08 R
2373 3516 1.826720 TGCCCCAAAATTCTCATCTGC 59.173 47.619 0.0 0.0 0.00 4.26 R
2799 3942 3.265791 CATCCCAGCTTCAGTTGAGTAC 58.734 50.000 0.0 0.0 0.00 2.73 R
3844 5070 2.859165 TACTCTCCTTTTGCCTGTGG 57.141 50.000 0.0 0.0 0.00 4.17 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
29 30 4.400529 ACATGTAGTGTGTCACTTGTCA 57.599 40.909 7.70 6.25 42.59 3.58
30 31 4.119862 ACATGTAGTGTGTCACTTGTCAC 58.880 43.478 7.70 0.29 42.59 3.67
31 32 3.173668 TGTAGTGTGTCACTTGTCACC 57.826 47.619 7.70 0.00 42.59 4.02
32 33 2.498078 TGTAGTGTGTCACTTGTCACCA 59.502 45.455 7.70 0.00 42.59 4.17
33 34 2.024176 AGTGTGTCACTTGTCACCAC 57.976 50.000 4.27 3.69 42.59 4.16
34 35 0.650512 GTGTGTCACTTGTCACCACG 59.349 55.000 4.27 0.00 34.07 4.94
35 36 0.533032 TGTGTCACTTGTCACCACGA 59.467 50.000 4.27 0.00 34.07 4.35
36 37 1.209128 GTGTCACTTGTCACCACGAG 58.791 55.000 0.00 0.00 39.72 4.18
37 38 1.107945 TGTCACTTGTCACCACGAGA 58.892 50.000 0.00 0.00 37.46 4.04
38 39 1.067060 TGTCACTTGTCACCACGAGAG 59.933 52.381 0.00 0.00 37.46 3.20
39 40 0.673985 TCACTTGTCACCACGAGAGG 59.326 55.000 0.00 0.00 37.46 3.69
40 41 0.673985 CACTTGTCACCACGAGAGGA 59.326 55.000 0.00 0.00 37.46 3.71
41 42 0.962489 ACTTGTCACCACGAGAGGAG 59.038 55.000 0.00 0.00 37.46 3.69
42 43 0.244994 CTTGTCACCACGAGAGGAGG 59.755 60.000 0.00 0.00 36.19 4.30
43 44 0.469331 TTGTCACCACGAGAGGAGGT 60.469 55.000 0.00 0.00 43.13 3.85
46 47 4.425099 ACCACGAGAGGAGGTGAG 57.575 61.111 0.00 0.00 41.22 3.51
47 48 1.768349 ACCACGAGAGGAGGTGAGA 59.232 57.895 0.00 0.00 41.22 3.27
48 49 0.322997 ACCACGAGAGGAGGTGAGAG 60.323 60.000 0.00 0.00 41.22 3.20
49 50 0.322997 CCACGAGAGGAGGTGAGAGT 60.323 60.000 0.00 0.00 36.25 3.24
50 51 0.808125 CACGAGAGGAGGTGAGAGTG 59.192 60.000 0.00 0.00 36.25 3.51
51 52 0.322997 ACGAGAGGAGGTGAGAGTGG 60.323 60.000 0.00 0.00 0.00 4.00
52 53 1.662438 CGAGAGGAGGTGAGAGTGGC 61.662 65.000 0.00 0.00 0.00 5.01
53 54 1.305718 AGAGGAGGTGAGAGTGGCC 60.306 63.158 0.00 0.00 0.00 5.36
54 55 1.305718 GAGGAGGTGAGAGTGGCCT 60.306 63.158 3.32 0.00 34.93 5.19
55 56 0.907230 GAGGAGGTGAGAGTGGCCTT 60.907 60.000 3.32 0.00 31.89 4.35
56 57 0.474660 AGGAGGTGAGAGTGGCCTTT 60.475 55.000 3.32 0.00 31.89 3.11
57 58 0.322008 GGAGGTGAGAGTGGCCTTTG 60.322 60.000 3.32 0.00 31.89 2.77
58 59 0.957888 GAGGTGAGAGTGGCCTTTGC 60.958 60.000 3.32 0.00 31.89 3.68
59 60 1.228245 GGTGAGAGTGGCCTTTGCA 60.228 57.895 3.32 0.00 40.13 4.08
60 61 0.823356 GGTGAGAGTGGCCTTTGCAA 60.823 55.000 3.32 0.00 40.13 4.08
61 62 0.595095 GTGAGAGTGGCCTTTGCAAG 59.405 55.000 3.32 0.00 40.13 4.01
62 63 0.473755 TGAGAGTGGCCTTTGCAAGA 59.526 50.000 3.32 0.00 40.13 3.02
63 64 1.163554 GAGAGTGGCCTTTGCAAGAG 58.836 55.000 3.32 0.45 40.13 2.85
64 65 0.251077 AGAGTGGCCTTTGCAAGAGG 60.251 55.000 18.09 18.09 40.13 3.69
65 66 0.538287 GAGTGGCCTTTGCAAGAGGT 60.538 55.000 21.25 8.18 40.13 3.85
66 67 0.771127 AGTGGCCTTTGCAAGAGGTA 59.229 50.000 21.25 12.60 40.13 3.08
67 68 0.881796 GTGGCCTTTGCAAGAGGTAC 59.118 55.000 21.25 17.64 40.13 3.34
68 69 0.251165 TGGCCTTTGCAAGAGGTACC 60.251 55.000 21.25 2.73 40.13 3.34
69 70 0.965866 GGCCTTTGCAAGAGGTACCC 60.966 60.000 21.25 13.99 40.13 3.69
70 71 0.038310 GCCTTTGCAAGAGGTACCCT 59.962 55.000 21.25 2.33 36.63 4.34
71 72 1.547901 GCCTTTGCAAGAGGTACCCTT 60.548 52.381 21.25 9.01 36.63 3.95
72 73 2.290705 GCCTTTGCAAGAGGTACCCTTA 60.291 50.000 21.25 0.00 36.63 2.69
73 74 3.812882 GCCTTTGCAAGAGGTACCCTTAA 60.813 47.826 21.25 1.73 36.63 1.85
74 75 4.403734 CCTTTGCAAGAGGTACCCTTAAA 58.596 43.478 8.74 9.00 31.76 1.52
75 76 4.830600 CCTTTGCAAGAGGTACCCTTAAAA 59.169 41.667 8.74 13.23 31.76 1.52
76 77 5.480422 CCTTTGCAAGAGGTACCCTTAAAAT 59.520 40.000 8.74 0.00 31.76 1.82
77 78 6.014584 CCTTTGCAAGAGGTACCCTTAAAATT 60.015 38.462 8.74 0.00 31.76 1.82
78 79 7.177744 CCTTTGCAAGAGGTACCCTTAAAATTA 59.822 37.037 8.74 0.00 31.76 1.40
166 168 1.248486 GGCCTCCAAAGTCCAAAGAC 58.752 55.000 0.00 0.00 43.89 3.01
200 202 2.125512 GATGGCGGTTCTGCGAGT 60.126 61.111 0.00 0.00 35.06 4.18
222 224 1.745087 CCTGTTTGATGCTTATGGCGT 59.255 47.619 0.00 0.00 45.43 5.68
223 225 2.164219 CCTGTTTGATGCTTATGGCGTT 59.836 45.455 0.00 0.00 45.43 4.84
271 273 2.173569 GCCTCTCCACCCAACAGATAAT 59.826 50.000 0.00 0.00 0.00 1.28
273 275 4.860022 CCTCTCCACCCAACAGATAATTT 58.140 43.478 0.00 0.00 0.00 1.82
384 1485 6.920569 TTAAAAAGGTGCGCCAAAATTTTA 57.079 29.167 20.59 18.74 37.19 1.52
389 1490 6.384258 AAGGTGCGCCAAAATTTTAAAAAT 57.616 29.167 20.59 0.00 37.19 1.82
513 1620 7.801315 TCCACGAATTTCTAAAAATGTTCGAAG 59.199 33.333 11.59 4.55 38.34 3.79
514 1621 7.801315 CCACGAATTTCTAAAAATGTTCGAAGA 59.199 33.333 11.59 0.00 38.34 2.87
555 1662 9.834628 TGAATTTGAAAATAGTTCCACGTATTC 57.165 29.630 0.00 0.00 0.00 1.75
632 1773 9.581289 TGAGATTTCCTTAAAGGTCATGTTTTA 57.419 29.630 0.00 0.00 36.53 1.52
728 1871 2.054363 CCATAGCTCTGCGTACGAATG 58.946 52.381 21.65 5.71 0.00 2.67
737 1880 1.269569 TGCGTACGAATGGAGCTATGG 60.270 52.381 21.65 0.00 0.00 2.74
749 1892 0.463833 AGCTATGGTTGGCGCCTTAC 60.464 55.000 29.70 23.98 33.93 2.34
763 1906 1.395608 GCCTTACGCGTCAAATAGCAA 59.604 47.619 18.63 0.00 0.00 3.91
776 1919 2.684001 ATAGCAATTTCCGACGGTCA 57.316 45.000 14.79 1.63 0.00 4.02
852 1995 0.182537 CACCACCTTGTTCCACTCCA 59.817 55.000 0.00 0.00 0.00 3.86
855 1998 1.071471 ACCTTGTTCCACTCCAGCG 59.929 57.895 0.00 0.00 0.00 5.18
873 2016 1.150536 GAGCCACAGTTGAACCCCA 59.849 57.895 0.00 0.00 0.00 4.96
892 2035 2.395988 ATCCACGCCAACACAGCTCA 62.396 55.000 0.00 0.00 0.00 4.26
897 2040 0.311790 CGCCAACACAGCTCACATTT 59.688 50.000 0.00 0.00 0.00 2.32
937 2080 2.513204 CCGACTCCCGCTCGACTA 60.513 66.667 0.00 0.00 36.84 2.59
961 2104 2.716244 CTCGGTCGATCGGTCCTG 59.284 66.667 19.53 13.44 0.00 3.86
1095 2238 4.189188 GCCGACGCCTTCTCGCTA 62.189 66.667 0.00 0.00 0.00 4.26
1244 2387 4.849329 CAGCGACCCGTACTCCGC 62.849 72.222 0.00 0.00 47.00 5.54
1305 2448 2.048127 GAGGCGCTCGACCTGTTT 60.048 61.111 7.64 0.00 37.77 2.83
1461 2604 4.389576 GTTGCGGTCTTGCCTGCG 62.390 66.667 0.00 0.00 38.82 5.18
1562 2705 4.151689 GCTGAATTGTTACTGTACTTGCGA 59.848 41.667 0.00 0.00 0.00 5.10
1954 3097 6.097412 TGCTCTGCTTTCTATCAAGTCAGATA 59.903 38.462 7.54 0.00 36.84 1.98
1980 3123 8.734386 AGTGATTTTCCAACTCTGTTTATGATC 58.266 33.333 0.00 0.00 0.00 2.92
1993 3136 7.609960 TCTGTTTATGATCCTGAGAGATATGC 58.390 38.462 0.00 0.00 0.00 3.14
1997 3140 2.230750 TGATCCTGAGAGATATGCTGCG 59.769 50.000 0.00 0.00 0.00 5.18
2150 3293 9.760926 TGCTATTATATCTTCCTATGTCTCACT 57.239 33.333 0.00 0.00 0.00 3.41
2168 3311 3.953612 TCACTTGGCTTTGTTTCTGATGT 59.046 39.130 0.00 0.00 0.00 3.06
2208 3351 4.080863 ACATTGGATCCTGACTCCTGTAAC 60.081 45.833 14.23 0.00 33.69 2.50
2300 3443 8.531982 ACTCTTACATCAGCAAACTAGTGATAA 58.468 33.333 0.00 0.00 29.64 1.75
2373 3516 4.614946 CTGAAGCTTTTGGACTTTTCAGG 58.385 43.478 0.00 0.00 38.41 3.86
2700 3843 1.407989 GCTATGGAAGAGGCTGCTGTT 60.408 52.381 0.00 0.00 0.00 3.16
2799 3942 6.703607 AGATATTCAAACGTATGGAAGCTGAG 59.296 38.462 0.00 0.00 0.00 3.35
2928 4071 3.801293 GCCCGAGTACTATTATTTGGCGT 60.801 47.826 0.00 0.00 0.00 5.68
3006 4149 6.821665 GCTAGTGATGGTCTTGGTAAACAATA 59.178 38.462 0.00 0.00 38.65 1.90
3036 4179 4.919754 GGTGTTTTCTCACATGAATTCAGC 59.080 41.667 14.54 0.00 39.76 4.26
3067 4210 9.869757 GGTTGTTGCCAAATTAATATTTAGACT 57.130 29.630 0.00 0.00 32.75 3.24
3119 4262 8.329203 TGCACATAGTGTTGATATTGTTACAA 57.671 30.769 0.00 0.00 35.75 2.41
3121 4264 9.787532 GCACATAGTGTTGATATTGTTACAATT 57.212 29.630 16.08 4.40 35.75 2.32
3186 4412 6.919775 ACCTAGTAATGGAGGATATGTGAC 57.080 41.667 0.00 0.00 0.00 3.67
3328 4554 0.179189 GTCGGCATTTCTTTGCTCCG 60.179 55.000 0.00 0.00 42.38 4.63
3333 4559 1.729149 GCATTTCTTTGCTCCGTTCCG 60.729 52.381 0.00 0.00 39.57 4.30
3440 4666 0.874390 TGCAAACTAGCAAAGAGGCG 59.126 50.000 0.00 0.00 42.46 5.52
3442 4668 1.266989 GCAAACTAGCAAAGAGGCGTT 59.733 47.619 0.00 0.00 39.27 4.84
3444 4670 1.809684 AACTAGCAAAGAGGCGTTCC 58.190 50.000 0.00 0.00 39.27 3.62
3445 4671 0.389948 ACTAGCAAAGAGGCGTTCCG 60.390 55.000 0.00 0.00 39.27 4.30
3446 4672 0.389948 CTAGCAAAGAGGCGTTCCGT 60.390 55.000 0.00 0.00 39.27 4.69
3447 4673 0.669318 TAGCAAAGAGGCGTTCCGTG 60.669 55.000 0.00 0.00 39.27 4.94
3448 4674 2.251642 GCAAAGAGGCGTTCCGTGT 61.252 57.895 0.00 0.00 37.47 4.49
3449 4675 1.860078 CAAAGAGGCGTTCCGTGTC 59.140 57.895 0.00 0.00 37.47 3.67
3450 4676 0.878523 CAAAGAGGCGTTCCGTGTCA 60.879 55.000 0.00 0.00 37.47 3.58
3451 4677 0.179067 AAAGAGGCGTTCCGTGTCAA 60.179 50.000 0.00 0.00 37.47 3.18
3452 4678 0.179067 AAGAGGCGTTCCGTGTCAAA 60.179 50.000 0.00 0.00 37.47 2.69
3453 4679 0.179067 AGAGGCGTTCCGTGTCAAAA 60.179 50.000 0.00 0.00 37.47 2.44
3454 4680 0.872388 GAGGCGTTCCGTGTCAAAAT 59.128 50.000 0.00 0.00 37.47 1.82
3455 4681 1.265905 GAGGCGTTCCGTGTCAAAATT 59.734 47.619 0.00 0.00 37.47 1.82
3456 4682 1.001815 AGGCGTTCCGTGTCAAAATTG 60.002 47.619 0.00 0.00 37.47 2.32
3457 4683 1.002251 GGCGTTCCGTGTCAAAATTGA 60.002 47.619 0.00 0.00 34.20 2.57
3503 4729 0.322816 TTCTGCAACATGGAGGAGGC 60.323 55.000 0.00 0.00 36.40 4.70
3558 4784 2.806945 TGTGGCCCTTAAAGATCCAG 57.193 50.000 0.00 0.00 0.00 3.86
3600 4826 4.893424 TGTTCACTTTGGCAGTTAGAAC 57.107 40.909 14.14 14.14 38.25 3.01
3781 5007 8.618702 AGATGATCTCATGGCATAAAGTTTAG 57.381 34.615 0.00 0.00 36.57 1.85
3982 5209 6.459923 CCCTCCTATTTACTATGCTTGACTC 58.540 44.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.119862 GTGACAAGTGACACACTACATGT 58.880 43.478 8.59 2.69 44.62 3.21
9 10 3.494626 GGTGACAAGTGACACACTACATG 59.505 47.826 8.59 0.00 44.62 3.21
10 11 3.133901 TGGTGACAAGTGACACACTACAT 59.866 43.478 8.59 0.00 44.62 2.29
11 12 2.498078 TGGTGACAAGTGACACACTACA 59.502 45.455 8.59 0.21 44.62 2.74
12 13 2.864343 GTGGTGACAAGTGACACACTAC 59.136 50.000 8.59 10.67 44.62 2.73
13 14 2.480587 CGTGGTGACAAGTGACACACTA 60.481 50.000 8.59 3.98 44.62 2.74
15 16 0.650512 CGTGGTGACAAGTGACACAC 59.349 55.000 8.59 9.87 46.06 3.82
16 17 0.533032 TCGTGGTGACAAGTGACACA 59.467 50.000 8.59 0.69 46.06 3.72
17 18 1.202371 TCTCGTGGTGACAAGTGACAC 60.202 52.381 0.00 0.00 46.06 3.67
18 19 1.067060 CTCTCGTGGTGACAAGTGACA 59.933 52.381 0.00 0.00 46.06 3.58
19 20 1.603172 CCTCTCGTGGTGACAAGTGAC 60.603 57.143 0.00 0.00 46.06 3.67
20 21 0.673985 CCTCTCGTGGTGACAAGTGA 59.326 55.000 0.00 0.00 46.06 3.41
21 22 0.673985 TCCTCTCGTGGTGACAAGTG 59.326 55.000 0.00 0.00 46.06 3.16
22 23 0.962489 CTCCTCTCGTGGTGACAAGT 59.038 55.000 0.00 0.00 46.06 3.16
23 24 0.244994 CCTCCTCTCGTGGTGACAAG 59.755 60.000 0.00 0.00 46.06 3.16
24 25 0.469331 ACCTCCTCTCGTGGTGACAA 60.469 55.000 0.00 0.00 46.06 3.18
25 26 1.153061 ACCTCCTCTCGTGGTGACA 59.847 57.895 0.00 0.00 36.97 3.58
26 27 4.098847 ACCTCCTCTCGTGGTGAC 57.901 61.111 0.00 0.00 36.97 3.67
29 30 0.322997 CTCTCACCTCCTCTCGTGGT 60.323 60.000 0.00 0.00 38.96 4.16
30 31 0.322997 ACTCTCACCTCCTCTCGTGG 60.323 60.000 0.00 0.00 0.00 4.94
31 32 0.808125 CACTCTCACCTCCTCTCGTG 59.192 60.000 0.00 0.00 0.00 4.35
32 33 0.322997 CCACTCTCACCTCCTCTCGT 60.323 60.000 0.00 0.00 0.00 4.18
33 34 1.662438 GCCACTCTCACCTCCTCTCG 61.662 65.000 0.00 0.00 0.00 4.04
34 35 1.326951 GGCCACTCTCACCTCCTCTC 61.327 65.000 0.00 0.00 0.00 3.20
35 36 1.305718 GGCCACTCTCACCTCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
36 37 0.907230 AAGGCCACTCTCACCTCCTC 60.907 60.000 5.01 0.00 31.86 3.71
37 38 0.474660 AAAGGCCACTCTCACCTCCT 60.475 55.000 5.01 0.00 31.86 3.69
38 39 0.322008 CAAAGGCCACTCTCACCTCC 60.322 60.000 5.01 0.00 31.86 4.30
39 40 0.957888 GCAAAGGCCACTCTCACCTC 60.958 60.000 5.01 0.00 31.86 3.85
40 41 1.073897 GCAAAGGCCACTCTCACCT 59.926 57.895 5.01 0.00 34.45 4.00
41 42 0.823356 TTGCAAAGGCCACTCTCACC 60.823 55.000 5.01 0.00 40.13 4.02
42 43 0.595095 CTTGCAAAGGCCACTCTCAC 59.405 55.000 5.01 0.00 41.27 3.51
43 44 0.473755 TCTTGCAAAGGCCACTCTCA 59.526 50.000 5.01 0.00 46.24 3.27
44 45 1.163554 CTCTTGCAAAGGCCACTCTC 58.836 55.000 5.01 0.00 46.24 3.20
45 46 0.251077 CCTCTTGCAAAGGCCACTCT 60.251 55.000 5.01 0.00 46.24 3.24
46 47 0.538287 ACCTCTTGCAAAGGCCACTC 60.538 55.000 20.76 0.00 46.24 3.51
47 48 0.771127 TACCTCTTGCAAAGGCCACT 59.229 50.000 20.76 9.35 46.24 4.00
48 49 0.881796 GTACCTCTTGCAAAGGCCAC 59.118 55.000 20.76 16.41 46.24 5.01
49 50 0.251165 GGTACCTCTTGCAAAGGCCA 60.251 55.000 20.76 10.93 46.24 5.36
50 51 2.568003 GGTACCTCTTGCAAAGGCC 58.432 57.895 20.76 14.06 46.24 5.19
72 73 8.038351 CCGTGGACCCAATTTCTTTATAATTTT 58.962 33.333 0.00 0.00 0.00 1.82
73 74 7.552459 CCGTGGACCCAATTTCTTTATAATTT 58.448 34.615 0.00 0.00 0.00 1.82
74 75 6.406512 GCCGTGGACCCAATTTCTTTATAATT 60.407 38.462 0.00 0.00 0.00 1.40
75 76 5.068591 GCCGTGGACCCAATTTCTTTATAAT 59.931 40.000 0.00 0.00 0.00 1.28
76 77 4.399934 GCCGTGGACCCAATTTCTTTATAA 59.600 41.667 0.00 0.00 0.00 0.98
77 78 3.949113 GCCGTGGACCCAATTTCTTTATA 59.051 43.478 0.00 0.00 0.00 0.98
78 79 2.758423 GCCGTGGACCCAATTTCTTTAT 59.242 45.455 0.00 0.00 0.00 1.40
166 168 3.216800 CCATCCCAATGACTATGGTGTG 58.783 50.000 0.00 0.00 36.14 3.82
200 202 2.423185 CGCCATAAGCATCAAACAGGAA 59.577 45.455 0.00 0.00 44.04 3.36
358 1459 4.601621 TTTTGGCGCACCTTTTTAAAAC 57.398 36.364 10.83 0.00 36.63 2.43
360 1461 5.819825 AAATTTTGGCGCACCTTTTTAAA 57.180 30.435 10.83 0.00 36.63 1.52
361 1462 5.819825 AAAATTTTGGCGCACCTTTTTAA 57.180 30.435 10.83 0.00 36.63 1.52
362 1463 6.920569 TTAAAATTTTGGCGCACCTTTTTA 57.079 29.167 10.83 9.71 36.63 1.52
363 1464 5.819825 TTAAAATTTTGGCGCACCTTTTT 57.180 30.435 10.83 10.68 36.63 1.94
368 1469 6.693113 TGAAATTTTTAAAATTTTGGCGCACC 59.307 30.769 23.64 12.39 30.68 5.01
389 1490 7.645735 TCGTCGACATTTTTCAAATTCATGAAA 59.354 29.630 17.16 1.91 45.07 2.69
484 1591 9.716507 CGAACATTTTTAGAAATTCGTGGATAT 57.283 29.630 6.40 0.00 34.75 1.63
498 1605 8.810652 TTTTCCCAATCTTCGAACATTTTTAG 57.189 30.769 0.00 0.00 0.00 1.85
501 1608 6.816136 ACTTTTCCCAATCTTCGAACATTTT 58.184 32.000 0.00 0.00 0.00 1.82
509 1616 5.689383 TCAAGAACTTTTCCCAATCTTCG 57.311 39.130 0.00 0.00 0.00 3.79
513 1620 8.661352 TTCAAATTCAAGAACTTTTCCCAATC 57.339 30.769 0.00 0.00 0.00 2.67
514 1621 9.460019 TTTTCAAATTCAAGAACTTTTCCCAAT 57.540 25.926 0.00 0.00 0.00 3.16
601 1727 8.910944 CATGACCTTTAAGGAAATCTCATGAAT 58.089 33.333 24.98 2.51 38.82 2.57
694 1837 1.540267 CTATGGGCCGGTTTTGTTCA 58.460 50.000 1.90 0.00 0.00 3.18
728 1871 2.893682 AAGGCGCCAACCATAGCTCC 62.894 60.000 31.54 0.00 33.97 4.70
749 1892 2.101125 CGGAAATTGCTATTTGACGCG 58.899 47.619 10.91 3.53 34.16 6.01
763 1906 0.981277 AGGGGATGACCGTCGGAAAT 60.981 55.000 20.51 10.76 41.60 2.17
852 1995 1.598130 GGTTCAACTGTGGCTCGCT 60.598 57.895 0.00 0.00 0.00 4.93
855 1998 0.251341 ATGGGGTTCAACTGTGGCTC 60.251 55.000 0.00 0.00 0.00 4.70
873 2016 1.672356 GAGCTGTGTTGGCGTGGAT 60.672 57.895 0.00 0.00 34.52 3.41
892 2035 1.714899 GCGGCTGCGATGGTAAATGT 61.715 55.000 0.00 0.00 0.00 2.71
931 2074 2.513204 CCGAGGCCGTCTAGTCGA 60.513 66.667 11.05 0.00 34.28 4.20
937 2080 3.210528 GATCGACCGAGGCCGTCT 61.211 66.667 0.00 0.00 0.00 4.18
1192 2335 2.123248 TTGAGGATGAGCGGGTGCAA 62.123 55.000 0.00 0.00 46.23 4.08
1202 2345 4.838152 GGCCGCGCTTGAGGATGA 62.838 66.667 5.56 0.00 33.84 2.92
1378 2521 3.423154 CCAAAGCACGGCGTCCTC 61.423 66.667 10.85 1.93 0.00 3.71
1461 2604 2.668550 GGGTCCGGTGACACAAGC 60.669 66.667 8.08 1.99 44.73 4.01
1954 3097 8.641498 ATCATAAACAGAGTTGGAAAATCACT 57.359 30.769 0.00 0.00 44.66 3.41
1980 3123 2.230750 TGATCGCAGCATATCTCTCAGG 59.769 50.000 6.35 0.00 0.00 3.86
1993 3136 3.223661 GGCTAATCCCTGATCGCAG 57.776 57.895 0.00 0.00 41.93 5.18
2045 3188 2.553602 TGCACATCCAACAGTGATGAAC 59.446 45.455 1.27 1.21 41.72 3.18
2047 3190 2.565046 TGCACATCCAACAGTGATGA 57.435 45.000 1.27 0.00 41.72 2.92
2150 3293 3.318839 CAGGACATCAGAAACAAAGCCAA 59.681 43.478 0.00 0.00 0.00 4.52
2168 3311 4.385199 CCAATGTAACTCCATAAGCCAGGA 60.385 45.833 0.00 0.00 0.00 3.86
2208 3351 4.201851 CCAGCTAAAACATTCATGGAGACG 60.202 45.833 0.00 0.00 0.00 4.18
2373 3516 1.826720 TGCCCCAAAATTCTCATCTGC 59.173 47.619 0.00 0.00 0.00 4.26
2799 3942 3.265791 CATCCCAGCTTCAGTTGAGTAC 58.734 50.000 0.00 0.00 0.00 2.73
3006 4149 1.843851 TGTGAGAAAACACCCACCTCT 59.156 47.619 0.00 0.00 39.69 3.69
3144 4370 5.217978 AGGTTGTTCAAACATACTCCGTA 57.782 39.130 3.43 0.00 38.95 4.02
3145 4371 4.081322 AGGTTGTTCAAACATACTCCGT 57.919 40.909 3.43 0.00 38.95 4.69
3146 4372 5.235516 ACTAGGTTGTTCAAACATACTCCG 58.764 41.667 3.43 0.00 38.95 4.63
3147 4373 8.665685 CATTACTAGGTTGTTCAAACATACTCC 58.334 37.037 3.43 0.00 38.95 3.85
3148 4374 8.665685 CCATTACTAGGTTGTTCAAACATACTC 58.334 37.037 3.43 0.00 38.95 2.59
3149 4375 8.380099 TCCATTACTAGGTTGTTCAAACATACT 58.620 33.333 3.43 1.50 38.95 2.12
3150 4376 8.556213 TCCATTACTAGGTTGTTCAAACATAC 57.444 34.615 3.43 0.00 38.95 2.39
3186 4412 1.838112 TGATAAAGGTGCCCAGCAAG 58.162 50.000 0.00 0.00 41.47 4.01
3328 4554 3.004002 CCAAACCAAAGGAACTACGGAAC 59.996 47.826 0.00 0.00 38.49 3.62
3333 4559 4.142026 ACAAAGCCAAACCAAAGGAACTAC 60.142 41.667 0.00 0.00 38.49 2.73
3435 4661 5.140124 TCAATTTTGACACGGAACGCCTC 62.140 47.826 0.00 0.00 44.80 4.70
3436 4662 3.324587 TCAATTTTGACACGGAACGCCT 61.325 45.455 0.00 0.00 44.80 5.52
3438 4664 2.392933 TCAATTTTGACACGGAACGC 57.607 45.000 0.00 0.00 44.80 4.84
3448 4674 6.723298 AGGTAACAACATGGTCAATTTTGA 57.277 33.333 0.00 0.00 41.41 2.69
3449 4675 6.983307 TGAAGGTAACAACATGGTCAATTTTG 59.017 34.615 0.00 0.00 41.41 2.44
3450 4676 7.118496 TGAAGGTAACAACATGGTCAATTTT 57.882 32.000 0.00 0.00 41.41 1.82
3451 4677 6.723298 TGAAGGTAACAACATGGTCAATTT 57.277 33.333 0.00 0.00 41.41 1.82
3452 4678 6.690530 CATGAAGGTAACAACATGGTCAATT 58.309 36.000 0.00 0.00 43.55 2.32
3453 4679 6.271488 CATGAAGGTAACAACATGGTCAAT 57.729 37.500 0.00 0.00 43.55 2.57
3454 4680 5.703978 CATGAAGGTAACAACATGGTCAA 57.296 39.130 0.00 0.00 43.55 3.18
3486 4712 2.110967 CGCCTCCTCCATGTTGCAG 61.111 63.158 0.00 0.00 0.00 4.41
3503 4729 4.199310 TGGAATAGAAGCCATCCTTTTCG 58.801 43.478 0.00 0.00 32.78 3.46
3558 4784 4.586001 ACATTTCATTGACCATATGGAGGC 59.414 41.667 28.77 16.26 38.94 4.70
3600 4826 5.207768 CAAAGAATGACGACCAGTTTCAAG 58.792 41.667 0.00 0.00 0.00 3.02
3664 4890 5.836024 TTCCAACTAGGTACACATTTCCT 57.164 39.130 0.00 0.00 39.02 3.36
3683 4909 9.674824 CTGTGCAATATTTCTTCAGATATTTCC 57.325 33.333 0.00 0.00 0.00 3.13
3705 4931 5.640783 TGAATAGCTGAATTCAGTCACTGTG 59.359 40.000 30.88 9.58 45.45 3.66
3781 5007 4.101741 ACCCAGTAGATTCCTAATGCTCAC 59.898 45.833 0.00 0.00 39.05 3.51
3840 5066 3.330701 ACTCTCCTTTTGCCTGTGGATTA 59.669 43.478 0.00 0.00 0.00 1.75
3844 5070 2.859165 TACTCTCCTTTTGCCTGTGG 57.141 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.