Multiple sequence alignment - TraesCS2D01G269900

Loading Multiple Alignment...

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 TraesCS2D01G269900 chr2D 100.000 5525 0 0 557 6081 332519058 332513534 0.000000e+00 10203.0
1 TraesCS2D01G269900 chr2D 100.000 223 0 0 1 223 332519614 332519392 4.390000e-111 412.0
2 TraesCS2D01G269900 chr2D 80.045 441 69 17 5648 6081 586943382 586943810 5.920000e-80 309.0
3 TraesCS2D01G269900 chr2A 94.885 4790 100 31 565 5311 440930075 440925388 0.000000e+00 7354.0
4 TraesCS2D01G269900 chr2A 87.565 386 44 3 5308 5693 440925201 440924820 1.560000e-120 444.0
5 TraesCS2D01G269900 chr2A 94.248 226 6 4 1 223 440930351 440930130 7.550000e-89 339.0
6 TraesCS2D01G269900 chr2B 94.074 2987 93 36 2385 5312 400625424 400622463 0.000000e+00 4458.0
7 TraesCS2D01G269900 chr2B 96.356 1811 32 11 588 2394 400627355 400625575 0.000000e+00 2948.0
8 TraesCS2D01G269900 chr2B 96.386 1411 51 0 3898 5308 400603850 400605260 0.000000e+00 2324.0
9 TraesCS2D01G269900 chr2B 90.460 587 47 7 5496 6081 400622103 400621525 0.000000e+00 765.0
10 TraesCS2D01G269900 chr2B 94.196 224 4 3 1 223 400627890 400627675 3.510000e-87 333.0
11 TraesCS2D01G269900 chr2B 80.702 342 54 10 5615 5954 196202268 196201937 7.820000e-64 255.0
12 TraesCS2D01G269900 chr2B 100.000 30 0 0 5363 5392 200901029 200901058 8.510000e-04 56.5
13 TraesCS2D01G269900 chr2B 100.000 30 0 0 5363 5392 200901250 200901279 8.510000e-04 56.5
14 TraesCS2D01G269900 chr5A 83.256 430 61 9 5648 6071 92447787 92447363 9.560000e-103 385.0
15 TraesCS2D01G269900 chr5A 76.302 384 64 19 5712 6081 272129041 272128671 4.840000e-41 180.0
16 TraesCS2D01G269900 chr4B 91.489 235 18 1 3228 3460 567379852 567379618 7.600000e-84 322.0
17 TraesCS2D01G269900 chr4B 85.830 247 11 9 2851 3097 567380181 567379959 2.190000e-59 241.0
18 TraesCS2D01G269900 chr3D 80.353 397 64 11 5690 6081 524878573 524878960 7.710000e-74 289.0
19 TraesCS2D01G269900 chr3D 78.230 418 69 13 5673 6076 471580688 471580279 1.310000e-61 248.0
20 TraesCS2D01G269900 chr4D 88.511 235 21 4 3228 3460 454658937 454658707 4.640000e-71 279.0
21 TraesCS2D01G269900 chr4D 86.640 247 9 9 2851 3097 454659266 454659044 1.010000e-62 252.0
22 TraesCS2D01G269900 chr4D 78.138 247 44 10 5609 5852 65102531 65102770 1.370000e-31 148.0
23 TraesCS2D01G269900 chr1B 78.475 223 42 6 5622 5841 374520812 374520593 2.290000e-29 141.0
24 TraesCS2D01G269900 chr7D 83.065 124 20 1 5713 5836 66819856 66819978 1.790000e-20 111.0
25 TraesCS2D01G269900 chr6D 80.000 95 18 1 5303 5396 140649992 140650086 1.090000e-07 69.4
26 TraesCS2D01G269900 chr6A 86.667 60 8 0 5344 5403 607948424 607948483 3.930000e-07 67.6
27 TraesCS2D01G269900 chr3A 94.595 37 1 1 5303 5338 574008672 574008708 8.510000e-04 56.5
28 TraesCS2D01G269900 chr7B 87.500 48 5 1 5303 5349 429195968 429195921 3.000000e-03 54.7


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 TraesCS2D01G269900 chr2D 332513534 332519614 6080 True 5307.500000 10203 100.000000 1 6081 2 chr2D.!!$R1 6080
1 TraesCS2D01G269900 chr2A 440924820 440930351 5531 True 2712.333333 7354 92.232667 1 5693 3 chr2A.!!$R1 5692
2 TraesCS2D01G269900 chr2B 400603850 400605260 1410 False 2324.000000 2324 96.386000 3898 5308 1 chr2B.!!$F1 1410
3 TraesCS2D01G269900 chr2B 400621525 400627890 6365 True 2126.000000 4458 93.771500 1 6081 4 chr2B.!!$R2 6080
4 TraesCS2D01G269900 chr4B 567379618 567380181 563 True 281.500000 322 88.659500 2851 3460 2 chr4B.!!$R1 609
5 TraesCS2D01G269900 chr4D 454658707 454659266 559 True 265.500000 279 87.575500 2851 3460 2 chr4D.!!$R1 609

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
21 22 0.179134 GGAGCACGTAGGCAGTAGTG 60.179 60.0 0.36 0.0 37.63 2.74 F
208 213 0.261696 AAGGAGGAGAGAGAGAGGGC 59.738 60.0 0.00 0.0 0.00 5.19 F
1812 2084 0.324943 CGGTCTTGGAGGTGATGGTT 59.675 55.0 0.00 0.0 0.00 3.67 F
2447 2879 0.038251 TGCATGTGTCTCGTGTCCTC 60.038 55.0 0.00 0.0 35.64 3.71 F
2449 2881 0.108615 CATGTGTCTCGTGTCCTCCC 60.109 60.0 0.00 0.0 0.00 4.30 F
2450 2882 0.251832 ATGTGTCTCGTGTCCTCCCT 60.252 55.0 0.00 0.0 0.00 4.20 F
2597 3032 0.392193 CTGCACCACTAGCCCTCAAG 60.392 60.0 0.00 0.0 0.00 3.02 F
2708 3173 0.815734 GCTTGCAGGCTTGATCATGT 59.184 50.0 14.45 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1910 0.382515 GGGACGAAGACGAGGATGAG 59.617 60.000 0.00 0.00 42.66 2.90 R
1818 2090 2.203182 TTGGTCCGTCTCCCCTGT 59.797 61.111 0.00 0.00 0.00 4.00 R
3751 4313 1.961180 AAGAAGGGGAGCACGGATCG 61.961 60.000 0.00 0.00 0.00 3.69 R
3778 4340 2.049627 GAGGTGCAGATAGCCCAGGG 62.050 65.000 0.00 0.00 44.83 4.45 R
4231 4793 2.433318 GAGCCACAGCACGTCTCC 60.433 66.667 0.00 0.00 43.56 3.71 R
4456 5018 7.190501 AGATAATGATGGATCCAGAGAGATCA 58.809 38.462 21.33 17.38 43.79 2.92 R
5061 5629 2.808919 CTCAGTCTACAAGGACCCTGA 58.191 52.381 0.00 0.00 36.95 3.86 R
5294 5862 5.189934 CCTCCTAACCATCCAACTAAGTTCT 59.810 44.000 0.00 0.00 0.00 3.01 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
21 22 0.179134 GGAGCACGTAGGCAGTAGTG 60.179 60.000 0.36 0.00 37.63 2.74
64 69 1.347707 CAGTGGAGTGGTACATGTGGT 59.652 52.381 9.11 0.00 44.52 4.16
206 211 1.756538 GCAAAGGAGGAGAGAGAGAGG 59.243 57.143 0.00 0.00 0.00 3.69
207 212 2.387757 CAAAGGAGGAGAGAGAGAGGG 58.612 57.143 0.00 0.00 0.00 4.30
208 213 0.261696 AAGGAGGAGAGAGAGAGGGC 59.738 60.000 0.00 0.00 0.00 5.19
770 1023 0.386476 CACAAAAGAAGGCAGCAGCA 59.614 50.000 2.65 0.00 44.61 4.41
771 1024 0.672342 ACAAAAGAAGGCAGCAGCAG 59.328 50.000 2.65 0.00 44.61 4.24
772 1025 0.666577 CAAAAGAAGGCAGCAGCAGC 60.667 55.000 2.65 0.00 44.61 5.25
773 1026 1.111116 AAAAGAAGGCAGCAGCAGCA 61.111 50.000 12.41 0.00 45.49 4.41
774 1027 1.111116 AAAGAAGGCAGCAGCAGCAA 61.111 50.000 12.41 0.00 45.49 3.91
775 1028 1.803366 AAGAAGGCAGCAGCAGCAAC 61.803 55.000 12.41 2.36 45.49 4.17
776 1029 2.520020 AAGGCAGCAGCAGCAACA 60.520 55.556 12.41 0.00 45.49 3.33
777 1030 2.473664 GAAGGCAGCAGCAGCAACAG 62.474 60.000 12.41 0.00 45.49 3.16
778 1031 4.719369 GGCAGCAGCAGCAACAGC 62.719 66.667 12.41 1.57 45.49 4.40
779 1032 3.671411 GCAGCAGCAGCAACAGCT 61.671 61.111 4.63 0.00 45.49 4.24
780 1033 2.330372 GCAGCAGCAGCAACAGCTA 61.330 57.895 4.63 0.00 45.49 3.32
781 1034 1.500844 CAGCAGCAGCAACAGCTAC 59.499 57.895 3.17 0.00 45.49 3.58
782 1035 1.673665 AGCAGCAGCAACAGCTACC 60.674 57.895 3.17 0.00 45.49 3.18
783 1036 2.694760 GCAGCAGCAACAGCTACCC 61.695 63.158 0.00 0.00 41.14 3.69
784 1037 1.302752 CAGCAGCAACAGCTACCCA 60.303 57.895 0.00 0.00 41.14 4.51
785 1038 0.890542 CAGCAGCAACAGCTACCCAA 60.891 55.000 0.00 0.00 41.14 4.12
786 1039 0.607489 AGCAGCAACAGCTACCCAAG 60.607 55.000 0.00 0.00 41.32 3.61
887 1152 4.410743 GCAGCAGCGCCAAAGGAC 62.411 66.667 2.29 0.00 0.00 3.85
907 1172 1.873903 CGAGGTGGTGGTGACAAGAAG 60.874 57.143 0.00 0.00 46.06 2.85
908 1173 1.416401 GAGGTGGTGGTGACAAGAAGA 59.584 52.381 0.00 0.00 46.06 2.87
909 1174 1.843851 AGGTGGTGGTGACAAGAAGAA 59.156 47.619 0.00 0.00 46.06 2.52
933 1198 1.109323 AAGGAGCCACACCAACAAGC 61.109 55.000 0.00 0.00 0.00 4.01
934 1199 1.827789 GGAGCCACACCAACAAGCA 60.828 57.895 0.00 0.00 0.00 3.91
1275 1541 0.964358 AGCTCTGCTTCAATGTGGCC 60.964 55.000 0.00 0.00 33.89 5.36
1812 2084 0.324943 CGGTCTTGGAGGTGATGGTT 59.675 55.000 0.00 0.00 0.00 3.67
1818 2090 1.060729 TGGAGGTGATGGTTCGGAAA 58.939 50.000 0.00 0.00 0.00 3.13
1828 2100 0.321387 GGTTCGGAAACAGGGGAGAC 60.321 60.000 0.00 0.00 37.10 3.36
2070 2342 2.758089 CCTGGTCGTCTACGTCGGG 61.758 68.421 0.00 7.14 40.80 5.14
2447 2879 0.038251 TGCATGTGTCTCGTGTCCTC 60.038 55.000 0.00 0.00 35.64 3.71
2448 2880 0.737715 GCATGTGTCTCGTGTCCTCC 60.738 60.000 0.00 0.00 35.64 4.30
2449 2881 0.108615 CATGTGTCTCGTGTCCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
2450 2882 0.251832 ATGTGTCTCGTGTCCTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
2486 2918 2.353605 CCTTCTCTTCCTGCTCACTGTC 60.354 54.545 0.00 0.00 0.00 3.51
2563 2995 9.657121 GTCAGATGTTTCAAAAACAAAAACAAA 57.343 25.926 9.10 0.00 43.71 2.83
2593 3028 0.978146 CTACCTGCACCACTAGCCCT 60.978 60.000 0.00 0.00 0.00 5.19
2594 3029 0.976073 TACCTGCACCACTAGCCCTC 60.976 60.000 0.00 0.00 0.00 4.30
2596 3031 1.679311 CTGCACCACTAGCCCTCAA 59.321 57.895 0.00 0.00 0.00 3.02
2597 3032 0.392193 CTGCACCACTAGCCCTCAAG 60.392 60.000 0.00 0.00 0.00 3.02
2598 3033 1.127567 TGCACCACTAGCCCTCAAGT 61.128 55.000 0.00 0.00 0.00 3.16
2599 3034 0.902531 GCACCACTAGCCCTCAAGTA 59.097 55.000 0.00 0.00 0.00 2.24
2600 3035 1.134670 GCACCACTAGCCCTCAAGTAG 60.135 57.143 0.00 0.00 0.00 2.57
2606 3070 4.528920 CACTAGCCCTCAAGTAGAGTAGT 58.471 47.826 0.00 0.00 43.12 2.73
2607 3071 5.397672 CCACTAGCCCTCAAGTAGAGTAGTA 60.398 48.000 0.00 0.00 43.12 1.82
2708 3173 0.815734 GCTTGCAGGCTTGATCATGT 59.184 50.000 14.45 0.00 0.00 3.21
2870 3341 2.399916 AGTCTTCTTCTGATGCAGCC 57.600 50.000 0.00 0.00 0.00 4.85
2871 3342 1.907936 AGTCTTCTTCTGATGCAGCCT 59.092 47.619 0.00 0.00 0.00 4.58
3059 3530 7.093112 ACTCTAGATAGATGGTTTGATATGGCC 60.093 40.741 0.00 0.00 0.00 5.36
3108 3642 2.932614 CTGCTCTACACTGGAAATTCCG 59.067 50.000 7.60 5.05 40.17 4.30
3119 3653 3.745799 TGGAAATTCCGTGAAACTGCTA 58.254 40.909 7.60 0.00 40.17 3.49
3170 3704 3.441496 TTTCTGCTTGCTCCTTTTGTG 57.559 42.857 0.00 0.00 0.00 3.33
3184 3729 6.192234 TCCTTTTGTGCGTGTAAAAACTTA 57.808 33.333 0.00 0.00 0.00 2.24
3216 3761 3.417069 TGGAAACATCGTCATGGTCTT 57.583 42.857 0.00 0.00 33.82 3.01
3220 3765 4.092968 GGAAACATCGTCATGGTCTTGTAC 59.907 45.833 0.00 0.00 33.82 2.90
3221 3766 4.537135 AACATCGTCATGGTCTTGTACT 57.463 40.909 0.00 0.00 33.82 2.73
3222 3767 4.537135 ACATCGTCATGGTCTTGTACTT 57.463 40.909 0.00 0.00 33.82 2.24
3223 3768 4.245660 ACATCGTCATGGTCTTGTACTTG 58.754 43.478 0.00 0.00 33.82 3.16
3224 3769 4.245660 CATCGTCATGGTCTTGTACTTGT 58.754 43.478 0.00 0.00 0.00 3.16
3225 3770 5.047590 ACATCGTCATGGTCTTGTACTTGTA 60.048 40.000 0.00 0.00 33.82 2.41
3226 3771 4.801891 TCGTCATGGTCTTGTACTTGTAC 58.198 43.478 4.14 4.14 0.00 2.90
3233 3778 3.741344 GGTCTTGTACTTGTACACAGCTG 59.259 47.826 13.48 13.48 0.00 4.24
3626 4183 1.133790 CACAGCAAAATCTAGGCCAGC 59.866 52.381 5.01 0.00 0.00 4.85
3778 4340 1.881903 GCTCCCCTTCTTGCTTTGGC 61.882 60.000 0.00 0.00 39.26 4.52
3940 4502 2.293318 ATCGCCTCTGCCTTGTCCA 61.293 57.895 0.00 0.00 0.00 4.02
3960 4522 3.473647 CCTCATGGAGCCGGAGCA 61.474 66.667 5.05 0.00 43.56 4.26
4003 4565 4.101448 CTTGGCACCCTCCTCCCG 62.101 72.222 0.00 0.00 0.00 5.14
4456 5018 1.886542 GACCATTTCGGCCAAGAACTT 59.113 47.619 2.24 0.00 39.03 2.66
5374 6165 4.389077 GCTAAACTTAACACTGATGCTCGT 59.611 41.667 0.00 0.00 0.00 4.18
5421 6212 7.346751 ACTTTTGGTCATGTACTTGTCAATT 57.653 32.000 8.46 0.00 0.00 2.32
5423 6214 8.257306 ACTTTTGGTCATGTACTTGTCAATTTT 58.743 29.630 8.46 1.49 0.00 1.82
5464 6255 2.382882 CCTCTCACAGGTGCTCATAGA 58.617 52.381 0.00 0.00 37.53 1.98
5475 6266 2.621998 GTGCTCATAGAAGTAGGGCGTA 59.378 50.000 0.00 0.00 0.00 4.42
5490 6281 0.101759 GCGTACCTGCGTTCATAGGA 59.898 55.000 0.00 0.00 37.52 2.94
5579 6372 6.263392 TGTTTGAAAAAGGACGACAATATGGA 59.737 34.615 0.00 0.00 0.00 3.41
5617 6410 0.037605 CGCCTGGAACGAAGGTTACT 60.038 55.000 0.00 0.00 37.88 2.24
5620 6413 2.809299 GCCTGGAACGAAGGTTACTTGT 60.809 50.000 0.00 0.00 37.88 3.16
5634 6427 4.377124 GGTTACTTGTAAAAGAGCTCGTGC 60.377 45.833 8.37 0.07 40.05 5.34
5649 6442 2.848887 CTCGTGCGTTGTAATGAGAGAG 59.151 50.000 0.00 0.00 32.18 3.20
5651 6444 3.057806 TCGTGCGTTGTAATGAGAGAGAA 60.058 43.478 0.00 0.00 0.00 2.87
5652 6445 3.673338 CGTGCGTTGTAATGAGAGAGAAA 59.327 43.478 0.00 0.00 0.00 2.52
5693 6486 5.456921 ACCCAATAACCATGAGTCAAGAT 57.543 39.130 0.00 0.00 0.00 2.40
5695 6488 5.192522 ACCCAATAACCATGAGTCAAGATCT 59.807 40.000 0.00 0.00 0.00 2.75
5710 6503 7.199766 AGTCAAGATCTCAATAGATTCACGTC 58.800 38.462 0.00 0.00 42.73 4.34
5711 6504 6.975197 GTCAAGATCTCAATAGATTCACGTCA 59.025 38.462 0.00 0.00 42.73 4.35
5727 6520 9.554724 GATTCACGTCATTTATTTAACACATGT 57.445 29.630 0.00 0.00 0.00 3.21
5763 6556 7.027874 TGTTGTCTTTTATCCTCCTTACCAT 57.972 36.000 0.00 0.00 0.00 3.55
5772 6565 1.076559 TCCTTACCATCCTCGCCGA 60.077 57.895 0.00 0.00 0.00 5.54
5774 6567 1.672854 CCTTACCATCCTCGCCGACA 61.673 60.000 0.00 0.00 0.00 4.35
5777 6570 1.663379 TACCATCCTCGCCGACAGTG 61.663 60.000 0.00 0.00 0.00 3.66
5804 6597 1.405105 GTGCTCACACAACCACAATGT 59.595 47.619 0.00 0.00 46.61 2.71
5813 6606 5.392480 CACAACCACAATGTGTTTGAATG 57.608 39.130 26.38 13.59 38.00 2.67
5833 6626 4.002906 TGTTGTCAATCTTAAGGCGTCT 57.997 40.909 1.85 0.00 0.00 4.18
5845 6638 2.101380 GCGTCTCTCTCTCGGCAC 59.899 66.667 0.00 0.00 0.00 5.01
5860 6653 5.377478 TCTCGGCACTAGATGAGAAATCTA 58.623 41.667 0.00 0.00 34.72 1.98
5878 6671 8.166726 AGAAATCTATTCTTTTTCCTGTGAGGT 58.833 33.333 0.00 0.00 36.53 3.85
5887 6680 0.400213 TCCTGTGAGGTTTTGGCGAT 59.600 50.000 0.00 0.00 36.53 4.58
5888 6681 0.523072 CCTGTGAGGTTTTGGCGATG 59.477 55.000 0.00 0.00 0.00 3.84
5889 6682 0.109597 CTGTGAGGTTTTGGCGATGC 60.110 55.000 0.00 0.00 0.00 3.91
5911 6704 3.120095 CGTGCATGCATGGTTATAGATGG 60.120 47.826 28.79 0.00 0.00 3.51
5912 6705 3.192001 GTGCATGCATGGTTATAGATGGG 59.808 47.826 25.64 0.00 0.00 4.00
5913 6706 3.181430 TGCATGCATGGTTATAGATGGGT 60.181 43.478 27.34 0.00 0.00 4.51
5917 6710 6.686126 GCATGCATGGTTATAGATGGGTTTTT 60.686 38.462 27.34 0.00 0.00 1.94
5941 6734 2.489722 GTCTCCAATCCTGGTTTTGCTC 59.510 50.000 0.00 0.00 43.97 4.26
5984 6778 1.939934 TCGGCATCGGCATAAAAGAAG 59.060 47.619 0.00 0.00 43.71 2.85
5987 6781 2.033424 GGCATCGGCATAAAAGAAGGAC 59.967 50.000 0.00 0.00 43.71 3.85
6008 6802 7.386851 AGGACGGATCATTCGTTATTGATTAT 58.613 34.615 0.00 0.00 41.22 1.28
6031 6825 4.530161 TGGTTGCACCCTAAATAGCATTTT 59.470 37.500 0.57 0.00 37.50 1.82
6032 6826 5.717178 TGGTTGCACCCTAAATAGCATTTTA 59.283 36.000 0.57 0.00 37.50 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.949631 GCGCTGCGATGGTACTACC 60.950 63.158 28.07 0.00 39.22 3.18
64 69 2.256306 TCAACCAGGAGCAGTGACATA 58.744 47.619 0.00 0.00 0.00 2.29
556 561 2.548057 CCGCTCTCATACACTCTCTCTC 59.452 54.545 0.00 0.00 0.00 3.20
557 562 2.171659 TCCGCTCTCATACACTCTCTCT 59.828 50.000 0.00 0.00 0.00 3.10
558 563 2.548057 CTCCGCTCTCATACACTCTCTC 59.452 54.545 0.00 0.00 0.00 3.20
559 564 2.571212 CTCCGCTCTCATACACTCTCT 58.429 52.381 0.00 0.00 0.00 3.10
560 565 1.606668 CCTCCGCTCTCATACACTCTC 59.393 57.143 0.00 0.00 0.00 3.20
561 566 1.686355 CCTCCGCTCTCATACACTCT 58.314 55.000 0.00 0.00 0.00 3.24
562 567 0.671251 CCCTCCGCTCTCATACACTC 59.329 60.000 0.00 0.00 0.00 3.51
563 568 0.259065 TCCCTCCGCTCTCATACACT 59.741 55.000 0.00 0.00 0.00 3.55
682 935 2.760092 GGATAGATAGCCTGAGCCTGAG 59.240 54.545 0.00 0.00 41.25 3.35
683 936 2.813907 GGATAGATAGCCTGAGCCTGA 58.186 52.381 0.00 0.00 41.25 3.86
684 937 1.476085 CGGATAGATAGCCTGAGCCTG 59.524 57.143 0.00 0.00 41.25 4.85
685 938 1.618345 CCGGATAGATAGCCTGAGCCT 60.618 57.143 0.00 0.00 41.25 4.58
686 939 0.820871 CCGGATAGATAGCCTGAGCC 59.179 60.000 0.00 0.00 41.25 4.70
687 940 1.474879 GACCGGATAGATAGCCTGAGC 59.525 57.143 9.46 0.00 40.32 4.26
688 941 2.096248 GGACCGGATAGATAGCCTGAG 58.904 57.143 9.46 0.00 0.00 3.35
689 942 1.427753 TGGACCGGATAGATAGCCTGA 59.572 52.381 9.46 0.00 0.00 3.86
778 1031 0.957395 CACTGTGGCAGCTTGGGTAG 60.957 60.000 0.00 0.00 34.37 3.18
779 1032 1.073025 CACTGTGGCAGCTTGGGTA 59.927 57.895 0.00 0.00 34.37 3.69
780 1033 2.072874 ATCACTGTGGCAGCTTGGGT 62.073 55.000 8.11 0.00 34.37 4.51
781 1034 1.303888 ATCACTGTGGCAGCTTGGG 60.304 57.895 8.11 0.00 34.37 4.12
782 1035 0.607217 TGATCACTGTGGCAGCTTGG 60.607 55.000 8.11 0.00 34.37 3.61
783 1036 0.520404 GTGATCACTGTGGCAGCTTG 59.480 55.000 18.83 0.00 34.37 4.01
784 1037 0.952497 CGTGATCACTGTGGCAGCTT 60.952 55.000 22.95 0.00 34.37 3.74
785 1038 1.375140 CGTGATCACTGTGGCAGCT 60.375 57.895 22.95 0.00 34.37 4.24
786 1039 3.031964 GCGTGATCACTGTGGCAGC 62.032 63.158 22.95 13.24 34.37 5.25
787 1040 2.393768 GGCGTGATCACTGTGGCAG 61.394 63.158 22.95 7.23 37.52 4.85
788 1041 1.540435 TAGGCGTGATCACTGTGGCA 61.540 55.000 22.95 8.53 0.00 4.92
789 1042 1.084370 GTAGGCGTGATCACTGTGGC 61.084 60.000 22.95 18.66 0.00 5.01
887 1152 0.105964 TTCTTGTCACCACCACCTCG 59.894 55.000 0.00 0.00 0.00 4.63
907 1172 1.072331 TGGTGTGGCTCCTTCTTCTTC 59.928 52.381 0.00 0.00 0.00 2.87
908 1173 1.140312 TGGTGTGGCTCCTTCTTCTT 58.860 50.000 0.00 0.00 0.00 2.52
909 1174 1.140312 TTGGTGTGGCTCCTTCTTCT 58.860 50.000 0.00 0.00 0.00 2.85
933 1198 0.620121 AGAAGCTCCTCCCCCTCTTG 60.620 60.000 0.00 0.00 0.00 3.02
934 1199 0.120172 AAGAAGCTCCTCCCCCTCTT 59.880 55.000 0.00 0.00 0.00 2.85
1275 1541 4.659172 TTGGGCAGGCGGTTGAGG 62.659 66.667 0.00 0.00 0.00 3.86
1638 1910 0.382515 GGGACGAAGACGAGGATGAG 59.617 60.000 0.00 0.00 42.66 2.90
1812 2084 2.280552 CCGTCTCCCCTGTTTCCGA 61.281 63.158 0.00 0.00 0.00 4.55
1818 2090 2.203182 TTGGTCCGTCTCCCCTGT 59.797 61.111 0.00 0.00 0.00 4.00
2142 2414 3.064324 GCCACCATGTGCTCCACC 61.064 66.667 0.00 0.00 32.73 4.61
2344 2616 4.568592 GGAAGAATGGAGATTGTTGAGGGT 60.569 45.833 0.00 0.00 0.00 4.34
2447 2879 1.304464 GCAACAAGGGAAGGGAGGG 60.304 63.158 0.00 0.00 0.00 4.30
2448 2880 1.304464 GGCAACAAGGGAAGGGAGG 60.304 63.158 0.00 0.00 0.00 4.30
2449 2881 0.113190 AAGGCAACAAGGGAAGGGAG 59.887 55.000 0.00 0.00 41.41 4.30
2450 2882 0.112412 GAAGGCAACAAGGGAAGGGA 59.888 55.000 0.00 0.00 41.41 4.20
2563 2995 1.550976 GTGCAGGTAGTAGAGCTTGGT 59.449 52.381 0.00 0.00 31.94 3.67
2623 3087 7.195646 TCATTAATGTCGAAAGATGAAATGGC 58.804 34.615 14.97 0.00 45.19 4.40
2994 3465 5.890049 ACCATCCCCATCTACTAGTACTAC 58.110 45.833 0.00 0.00 0.00 2.73
2996 3467 5.374753 TGTACCATCCCCATCTACTAGTACT 59.625 44.000 0.00 0.00 0.00 2.73
3000 3471 6.494666 TTTTGTACCATCCCCATCTACTAG 57.505 41.667 0.00 0.00 0.00 2.57
3145 3679 4.516365 AAAGGAGCAAGCAGAAAAGATG 57.484 40.909 0.00 0.00 0.00 2.90
3184 3729 7.881142 TGACGATGTTTCCATCAAGTTATTTT 58.119 30.769 0.00 0.00 46.54 1.82
3191 3736 3.691118 ACCATGACGATGTTTCCATCAAG 59.309 43.478 0.00 0.00 46.54 3.02
3203 3748 4.537135 ACAAGTACAAGACCATGACGAT 57.463 40.909 0.00 0.00 0.00 3.73
3205 3750 4.384846 GTGTACAAGTACAAGACCATGACG 59.615 45.833 14.08 0.00 46.33 4.35
3216 3761 3.106242 CACCAGCTGTGTACAAGTACA 57.894 47.619 13.81 8.88 43.14 2.90
3233 3778 2.203972 ATGTCAAGCACATGCGCACC 62.204 55.000 14.90 0.89 44.70 5.01
3556 4106 6.541641 GCATTAGAATGTCCTGTTTGATCTCT 59.458 38.462 4.27 0.00 38.65 3.10
3626 4183 4.653341 AGGAGATAAGACATCCAACTCCAG 59.347 45.833 0.00 0.00 43.06 3.86
3751 4313 1.961180 AAGAAGGGGAGCACGGATCG 61.961 60.000 0.00 0.00 0.00 3.69
3778 4340 2.049627 GAGGTGCAGATAGCCCAGGG 62.050 65.000 0.00 0.00 44.83 4.45
3960 4522 2.595463 TCGTCTTCACGTCCGGGT 60.595 61.111 0.00 0.00 46.76 5.28
4231 4793 2.433318 GAGCCACAGCACGTCTCC 60.433 66.667 0.00 0.00 43.56 3.71
4456 5018 7.190501 AGATAATGATGGATCCAGAGAGATCA 58.809 38.462 21.33 17.38 43.79 2.92
5061 5629 2.808919 CTCAGTCTACAAGGACCCTGA 58.191 52.381 0.00 0.00 36.95 3.86
5294 5862 5.189934 CCTCCTAACCATCCAACTAAGTTCT 59.810 44.000 0.00 0.00 0.00 3.01
5301 5869 2.572104 GTGTCCTCCTAACCATCCAACT 59.428 50.000 0.00 0.00 0.00 3.16
5351 6142 4.389077 ACGAGCATCAGTGTTAAGTTTAGC 59.611 41.667 0.00 0.00 33.17 3.09
5402 6193 8.684386 TCTTAAAATTGACAAGTACATGACCA 57.316 30.769 4.87 0.00 0.00 4.02
5421 6212 4.183865 CTGAGCCGACACATCATCTTAAA 58.816 43.478 0.00 0.00 0.00 1.52
5423 6214 2.481969 GCTGAGCCGACACATCATCTTA 60.482 50.000 0.00 0.00 0.00 2.10
5451 6242 2.224161 GCCCTACTTCTATGAGCACCTG 60.224 54.545 0.00 0.00 0.00 4.00
5464 6255 1.538687 AACGCAGGTACGCCCTACTT 61.539 55.000 0.00 0.00 43.86 2.24
5475 6266 1.557099 TCAGTCCTATGAACGCAGGT 58.443 50.000 0.00 0.00 33.37 4.00
5479 6270 5.050490 ACATACATTCAGTCCTATGAACGC 58.950 41.667 0.00 0.00 41.76 4.84
5551 6344 4.768130 TGTCGTCCTTTTTCAAACACAA 57.232 36.364 0.00 0.00 0.00 3.33
5552 6345 4.768130 TTGTCGTCCTTTTTCAAACACA 57.232 36.364 0.00 0.00 0.00 3.72
5553 6346 6.362283 CCATATTGTCGTCCTTTTTCAAACAC 59.638 38.462 0.00 0.00 0.00 3.32
5554 6347 6.263392 TCCATATTGTCGTCCTTTTTCAAACA 59.737 34.615 0.00 0.00 0.00 2.83
5579 6372 2.480416 GCGGATCAAGATCTGACGTTCT 60.480 50.000 20.21 0.00 44.92 3.01
5606 6399 5.608449 AGCTCTTTTACAAGTAACCTTCGT 58.392 37.500 0.00 0.00 0.00 3.85
5617 6410 1.860676 ACGCACGAGCTCTTTTACAA 58.139 45.000 12.85 0.00 39.10 2.41
5620 6413 1.860676 ACAACGCACGAGCTCTTTTA 58.139 45.000 12.85 0.00 39.10 1.52
5651 6444 4.698780 GGGTTAGAGAAGCGTGGTATTTTT 59.301 41.667 0.00 0.00 33.67 1.94
5652 6445 4.259356 GGGTTAGAGAAGCGTGGTATTTT 58.741 43.478 0.00 0.00 33.67 1.82
5715 6508 9.842775 ACATAGATGAGATGACATGTGTTAAAT 57.157 29.630 1.15 0.00 0.00 1.40
5723 6516 8.434733 AAAGACAACATAGATGAGATGACATG 57.565 34.615 0.00 0.00 0.00 3.21
5727 6520 9.770097 GGATAAAAGACAACATAGATGAGATGA 57.230 33.333 0.00 0.00 0.00 2.92
5772 6565 2.142761 TGAGCACTGAGGCCACTGT 61.143 57.895 5.01 6.12 0.00 3.55
5774 6567 2.142761 TGTGAGCACTGAGGCCACT 61.143 57.895 5.01 0.00 36.53 4.00
5777 6570 1.227943 TTGTGTGAGCACTGAGGCC 60.228 57.895 0.00 0.00 45.44 5.19
5804 6597 6.922957 GCCTTAAGATTGACAACATTCAAACA 59.077 34.615 3.36 0.00 38.95 2.83
5805 6598 6.088085 CGCCTTAAGATTGACAACATTCAAAC 59.912 38.462 3.36 0.00 38.95 2.93
5813 6606 4.246458 AGAGACGCCTTAAGATTGACAAC 58.754 43.478 3.36 0.00 0.00 3.32
5833 6626 2.436173 TCTCATCTAGTGCCGAGAGAGA 59.564 50.000 0.00 0.00 31.11 3.10
5860 6653 5.684813 GCCAAAACCTCACAGGAAAAAGAAT 60.685 40.000 0.00 0.00 37.67 2.40
5878 6671 1.444042 CATGCACGCATCGCCAAAA 60.444 52.632 0.44 0.00 33.90 2.44
5888 6681 1.872952 TCTATAACCATGCATGCACGC 59.127 47.619 25.37 0.00 0.00 5.34
5889 6682 3.120095 CCATCTATAACCATGCATGCACG 60.120 47.826 25.37 16.18 0.00 5.34
5941 6734 0.100503 GGATTGGAAATGAACGCCCG 59.899 55.000 0.00 0.00 0.00 6.13
5970 6764 1.551430 TCCGTCCTTCTTTTATGCCGA 59.449 47.619 0.00 0.00 0.00 5.54
5984 6778 5.924475 AATCAATAACGAATGATCCGTCC 57.076 39.130 0.00 0.00 39.57 4.79
5987 6781 7.364522 ACCATAATCAATAACGAATGATCCG 57.635 36.000 0.00 0.00 35.29 4.18


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

AutoCloner maintained by Alex Coulton.