Multiple sequence alignment - TraesCS3D01G344600

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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 TraesCS3D01G344600 chr3D 100.000 2642 0 0 1 2642 456533317 456535958 0.000000e+00 4879
1 TraesCS3D01G344600 chr3A 93.926 2239 99 19 65 2281 599325106 599327329 0.000000e+00 3347
2 TraesCS3D01G344600 chr3A 95.066 304 11 2 2340 2642 599327342 599327642 2.380000e-130 475
3 TraesCS3D01G344600 chr3A 83.439 157 23 3 1172 1326 398879702 398879547 2.740000e-30 143
4 TraesCS3D01G344600 chr3B 94.390 1925 72 13 729 2642 602782858 602780959 0.000000e+00 2924
5 TraesCS3D01G344600 chr3B 93.939 66 4 0 679 744 602785131 602785066 1.670000e-17 100
6 TraesCS3D01G344600 chr7A 83.735 166 22 5 1164 1326 258824463 258824626 4.550000e-33 152
7 TraesCS3D01G344600 chr5A 84.076 157 22 3 1172 1326 453519597 453519752 5.890000e-32 148
8 TraesCS3D01G344600 chr7D 83.030 165 25 3 1164 1326 243808148 243808311 2.120000e-31 147
9 TraesCS3D01G344600 chr6A 83.439 157 23 3 1172 1326 116813117 116812962 2.740000e-30 143
10 TraesCS3D01G344600 chr5D 83.439 157 23 3 1172 1326 352454309 352454154 2.740000e-30 143
11 TraesCS3D01G344600 chr5B 83.439 157 23 3 1172 1326 415127618 415127463 2.740000e-30 143


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 TraesCS3D01G344600 chr3D 456533317 456535958 2641 False 4879 4879 100.0000 1 2642 1 chr3D.!!$F1 2641
1 TraesCS3D01G344600 chr3A 599325106 599327642 2536 False 1911 3347 94.4960 65 2642 2 chr3A.!!$F1 2577
2 TraesCS3D01G344600 chr3B 602780959 602785131 4172 True 1512 2924 94.1645 679 2642 2 chr3B.!!$R1 1963

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
20 21 0.60762 TTTTGCTAGTGCCAATGCCC 59.392 50.0 0.0 0.0 38.71 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 4111 0.242825 CTAACTCTGCCGTCCGTGAA 59.757 55.0 0.0 0.0 0.0 3.18 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
19 20 1.713597 GTTTTGCTAGTGCCAATGCC 58.286 50.000 0.00 0.00 38.71 4.40
20 21 0.607620 TTTTGCTAGTGCCAATGCCC 59.392 50.000 0.00 0.00 38.71 5.36
21 22 1.257055 TTTGCTAGTGCCAATGCCCC 61.257 55.000 0.00 0.00 38.71 5.80
22 23 3.211963 GCTAGTGCCAATGCCCCG 61.212 66.667 0.00 0.00 36.33 5.73
23 24 3.211963 CTAGTGCCAATGCCCCGC 61.212 66.667 0.00 0.00 36.33 6.13
24 25 4.813235 TAGTGCCAATGCCCCGCC 62.813 66.667 0.00 0.00 36.33 6.13
28 29 4.758251 GCCAATGCCCCGCCAAAC 62.758 66.667 0.00 0.00 0.00 2.93
29 30 4.081185 CCAATGCCCCGCCAAACC 62.081 66.667 0.00 0.00 0.00 3.27
30 31 2.996734 CAATGCCCCGCCAAACCT 60.997 61.111 0.00 0.00 0.00 3.50
31 32 2.203773 AATGCCCCGCCAAACCTT 60.204 55.556 0.00 0.00 0.00 3.50
32 33 2.582493 AATGCCCCGCCAAACCTTG 61.582 57.895 0.00 0.00 0.00 3.61
33 34 3.521765 ATGCCCCGCCAAACCTTGA 62.522 57.895 0.00 0.00 0.00 3.02
34 35 3.680786 GCCCCGCCAAACCTTGAC 61.681 66.667 0.00 0.00 0.00 3.18
35 36 2.203422 CCCCGCCAAACCTTGACA 60.203 61.111 0.00 0.00 0.00 3.58
36 37 2.268076 CCCCGCCAAACCTTGACAG 61.268 63.158 0.00 0.00 0.00 3.51
38 39 2.644992 CGCCAAACCTTGACAGGC 59.355 61.111 0.00 0.00 45.56 4.85
39 40 2.919494 CGCCAAACCTTGACAGGCC 61.919 63.158 0.00 0.00 45.56 5.19
40 41 1.832167 GCCAAACCTTGACAGGCCA 60.832 57.895 5.01 0.00 45.56 5.36
41 42 1.398958 GCCAAACCTTGACAGGCCAA 61.399 55.000 5.01 0.00 45.56 4.52
42 43 1.118838 CCAAACCTTGACAGGCCAAA 58.881 50.000 5.01 0.00 45.56 3.28
43 44 1.693606 CCAAACCTTGACAGGCCAAAT 59.306 47.619 5.01 0.00 45.56 2.32
44 45 2.896685 CCAAACCTTGACAGGCCAAATA 59.103 45.455 5.01 0.00 45.56 1.40
45 46 3.323403 CCAAACCTTGACAGGCCAAATAA 59.677 43.478 5.01 0.00 45.56 1.40
46 47 4.306600 CAAACCTTGACAGGCCAAATAAC 58.693 43.478 5.01 0.00 45.56 1.89
47 48 3.525800 ACCTTGACAGGCCAAATAACT 57.474 42.857 5.01 0.00 45.56 2.24
48 49 3.157087 ACCTTGACAGGCCAAATAACTG 58.843 45.455 5.01 0.00 45.56 3.16
49 50 2.493278 CCTTGACAGGCCAAATAACTGG 59.507 50.000 5.01 0.00 39.71 4.00
61 62 5.339990 CCAAATAACTGGCTAACAATTCGG 58.660 41.667 0.00 0.00 0.00 4.30
62 63 5.105917 CCAAATAACTGGCTAACAATTCGGT 60.106 40.000 0.00 0.00 0.00 4.69
63 64 5.813080 AATAACTGGCTAACAATTCGGTC 57.187 39.130 0.00 0.00 0.00 4.79
78 79 5.596836 ATTCGGTCAACATTTTGGCATAT 57.403 34.783 0.00 0.00 39.28 1.78
81 82 6.707440 TCGGTCAACATTTTGGCATATAAT 57.293 33.333 0.00 0.00 39.28 1.28
85 86 7.490725 CGGTCAACATTTTGGCATATAATTGAA 59.509 33.333 0.00 0.00 39.28 2.69
96 97 6.543465 TGGCATATAATTGAACTGAGGAACTG 59.457 38.462 0.00 0.00 41.55 3.16
182 183 0.760945 TTTTTGGACGGGTTGCCCAT 60.761 50.000 4.96 0.00 45.83 4.00
211 214 5.454755 CCGATCCACAACCCTTAAGATACAT 60.455 44.000 3.36 0.00 0.00 2.29
219 222 7.010183 CACAACCCTTAAGATACATGTTAGTCG 59.990 40.741 2.30 0.00 0.00 4.18
220 223 6.158023 ACCCTTAAGATACATGTTAGTCGG 57.842 41.667 2.30 0.03 0.00 4.79
260 263 8.327429 CAAACTTTAAGTGCTACACAATTTTGG 58.673 33.333 0.00 0.00 37.77 3.28
263 266 4.853924 AAGTGCTACACAATTTTGGAGG 57.146 40.909 5.98 0.00 31.06 4.30
267 270 3.056678 TGCTACACAATTTTGGAGGCATG 60.057 43.478 5.98 0.00 0.00 4.06
270 273 2.289195 ACACAATTTTGGAGGCATGCAG 60.289 45.455 21.36 0.00 0.00 4.41
350 353 4.280019 GGGTTGGAGGGTGGCGTT 62.280 66.667 0.00 0.00 0.00 4.84
358 361 3.199891 GGGTGGCGTTGCGGTATC 61.200 66.667 0.00 0.00 0.00 2.24
364 367 2.469516 GCGTTGCGGTATCCCCAAG 61.470 63.158 0.00 0.00 0.00 3.61
370 373 1.607612 CGGTATCCCCAAGCCTGTT 59.392 57.895 0.00 0.00 0.00 3.16
373 376 1.477014 GGTATCCCCAAGCCTGTTAGC 60.477 57.143 0.00 0.00 0.00 3.09
380 383 1.234821 CAAGCCTGTTAGCGACCAAA 58.765 50.000 0.00 0.00 38.01 3.28
400 403 1.675483 ACTGCATGTTTGACGCTTTGA 59.325 42.857 0.00 0.00 0.00 2.69
402 405 2.659757 CTGCATGTTTGACGCTTTGATG 59.340 45.455 0.00 0.00 0.00 3.07
408 411 4.930963 TGTTTGACGCTTTGATGTTTCAT 58.069 34.783 0.00 0.00 0.00 2.57
444 447 9.932207 TTATTCTTTCTGTGCATGATGATTTTT 57.068 25.926 0.00 0.00 0.00 1.94
470 473 8.953558 TTATCGATGATAATGAGGCACATGTGC 61.954 40.741 37.29 37.29 40.99 4.57
501 504 3.187227 TCAATCTTGAAGCTTCGCAACTC 59.813 43.478 21.11 0.00 33.55 3.01
521 524 2.923605 CGATCCTATCTTCGGTAGGC 57.076 55.000 0.00 0.00 38.86 3.93
534 537 4.735132 TAGGCGCGGTGTGAGTGC 62.735 66.667 8.83 0.00 43.68 4.40
551 554 3.792047 CGCATGGTGCCGTGAGTG 61.792 66.667 14.13 0.00 41.12 3.51
593 599 9.550811 CATTATAACCGGTGTTTCTAGAAAAAC 57.449 33.333 24.79 24.79 37.70 2.43
630 636 9.173939 CTGAGTGACAATTTTGACAGAAAATAC 57.826 33.333 0.00 0.00 33.83 1.89
761 2990 3.026694 CTGGTTGATCCCTGGAAATTCC 58.973 50.000 4.79 4.79 34.18 3.01
842 3071 8.087982 ACATTCCACATATGTTTATAAGCTCG 57.912 34.615 5.37 0.00 32.48 5.03
871 3100 1.002087 GTGTGGATATCCGATCCCACC 59.998 57.143 17.04 13.37 46.26 4.61
888 3121 7.527196 CGATCCCACCCTCAGTATAAATACAAT 60.527 40.741 3.13 0.00 35.74 2.71
927 3161 2.026262 CACCCCAAACACATAGCTACCT 60.026 50.000 0.00 0.00 0.00 3.08
928 3162 2.238898 ACCCCAAACACATAGCTACCTC 59.761 50.000 0.00 0.00 0.00 3.85
929 3163 2.505819 CCCCAAACACATAGCTACCTCT 59.494 50.000 0.00 0.00 0.00 3.69
930 3164 3.709653 CCCCAAACACATAGCTACCTCTA 59.290 47.826 0.00 0.00 0.00 2.43
965 3199 1.002468 CAGCAGCACACAGTGGTTTAC 60.002 52.381 5.31 0.00 41.72 2.01
980 3214 2.551032 GGTTTACACAACACCTAGCCAC 59.449 50.000 0.00 0.00 0.00 5.01
988 3222 1.227380 CACCTAGCCACGCATCCTC 60.227 63.158 0.00 0.00 0.00 3.71
1390 3624 1.971167 GTTGGCCATGGCGAGTTCA 60.971 57.895 29.90 18.86 43.06 3.18
1631 3865 3.611792 GATCGCTCACGCTCACGC 61.612 66.667 0.00 0.00 45.53 5.34
1737 3971 4.045104 CCAAGTATGTATGTCAGACGCTC 58.955 47.826 0.00 0.00 42.35 5.03
1759 3993 3.505680 CAGATCCGTAGCTGCTATCTCTT 59.494 47.826 13.20 0.00 31.30 2.85
1823 4057 1.471684 CACTGGCAGCAATTTCCTCTC 59.528 52.381 15.89 0.00 0.00 3.20
1876 4110 4.518590 TGTTGGTCGATCAATGTGATTGTT 59.481 37.500 15.35 0.00 37.20 2.83
1877 4111 5.009510 TGTTGGTCGATCAATGTGATTGTTT 59.990 36.000 15.35 0.00 37.20 2.83
1887 4121 2.309898 GTGATTGTTTTCACGGACGG 57.690 50.000 0.00 0.00 36.93 4.79
1892 4126 0.878523 TGTTTTCACGGACGGCAGAG 60.879 55.000 0.00 0.00 0.00 3.35
1924 4158 2.497273 GCCTCCATGTTTACTGCCATTT 59.503 45.455 0.00 0.00 0.00 2.32
1940 4174 3.181476 GCCATTTTTATTCGCCCAGTCAT 60.181 43.478 0.00 0.00 0.00 3.06
1942 4176 5.762045 CCATTTTTATTCGCCCAGTCATAG 58.238 41.667 0.00 0.00 0.00 2.23
2008 4256 2.165167 TCGTCCTCCACTTTATCGTGT 58.835 47.619 0.00 0.00 33.07 4.49
2009 4257 2.094906 TCGTCCTCCACTTTATCGTGTG 60.095 50.000 0.00 0.00 33.07 3.82
2010 4258 2.000447 GTCCTCCACTTTATCGTGTGC 59.000 52.381 0.00 0.00 33.07 4.57
2011 4259 1.621317 TCCTCCACTTTATCGTGTGCA 59.379 47.619 0.00 0.00 33.07 4.57
2012 4260 2.002586 CCTCCACTTTATCGTGTGCAG 58.997 52.381 0.00 0.00 33.07 4.41
2013 4261 1.394917 CTCCACTTTATCGTGTGCAGC 59.605 52.381 0.00 0.00 33.07 5.25
2014 4262 1.001974 TCCACTTTATCGTGTGCAGCT 59.998 47.619 0.00 0.00 33.07 4.24
2060 4317 7.916914 TTTCTAGCTATTTGGGTGTTTAGTC 57.083 36.000 0.00 0.00 0.00 2.59
2066 4323 5.447279 GCTATTTGGGTGTTTAGTCGACATG 60.447 44.000 19.50 0.00 0.00 3.21
2173 4430 2.182825 CAGGACGACGTGCTGTATAAC 58.817 52.381 33.40 5.26 44.86 1.89
2379 4636 6.596106 GGAAACTAGGAAGAGAACCAGATTTC 59.404 42.308 0.00 0.00 0.00 2.17
2386 4643 5.337975 GGAAGAGAACCAGATTTCTAGTGCT 60.338 44.000 0.00 0.00 35.90 4.40
2448 4706 4.672587 ACTATTTTGCTCGGCAGATCTA 57.327 40.909 0.00 0.00 40.61 1.98
2457 4715 1.756538 TCGGCAGATCTACATGCTCAA 59.243 47.619 0.00 0.00 42.19 3.02
2458 4716 1.863454 CGGCAGATCTACATGCTCAAC 59.137 52.381 0.00 0.00 42.19 3.18
2459 4717 2.216898 GGCAGATCTACATGCTCAACC 58.783 52.381 0.00 0.00 42.19 3.77
2492 4750 8.218441 TCAAGAACGAAAATATGTCTAACAACG 58.782 33.333 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.672737 GGGCATTGGCACTAGCAAAAC 60.673 52.381 12.70 0.00 41.45 2.43
3 4 1.682005 GGGGCATTGGCACTAGCAA 60.682 57.895 12.70 0.00 45.12 3.91
7 8 4.813235 GGCGGGGCATTGGCACTA 62.813 66.667 11.04 0.00 45.12 2.74
11 12 4.758251 GTTTGGCGGGGCATTGGC 62.758 66.667 0.70 0.70 40.13 4.52
12 13 4.081185 GGTTTGGCGGGGCATTGG 62.081 66.667 0.00 0.00 0.00 3.16
13 14 2.582493 AAGGTTTGGCGGGGCATTG 61.582 57.895 0.00 0.00 0.00 2.82
14 15 2.203773 AAGGTTTGGCGGGGCATT 60.204 55.556 0.00 0.00 0.00 3.56
15 16 2.996734 CAAGGTTTGGCGGGGCAT 60.997 61.111 0.00 0.00 0.00 4.40
16 17 4.211330 TCAAGGTTTGGCGGGGCA 62.211 61.111 0.00 0.00 0.00 5.36
17 18 3.680786 GTCAAGGTTTGGCGGGGC 61.681 66.667 0.00 0.00 0.00 5.80
18 19 2.203422 TGTCAAGGTTTGGCGGGG 60.203 61.111 0.00 0.00 38.34 5.73
19 20 3.354678 CTGTCAAGGTTTGGCGGG 58.645 61.111 0.00 0.00 37.98 6.13
20 21 2.919494 GCCTGTCAAGGTTTGGCGG 61.919 63.158 0.00 0.00 46.43 6.13
21 22 2.644992 GCCTGTCAAGGTTTGGCG 59.355 61.111 0.00 0.00 46.43 5.69
22 23 1.398958 TTGGCCTGTCAAGGTTTGGC 61.399 55.000 3.32 0.00 46.43 4.52
23 24 1.118838 TTTGGCCTGTCAAGGTTTGG 58.881 50.000 3.32 0.00 46.43 3.28
24 25 4.039124 AGTTATTTGGCCTGTCAAGGTTTG 59.961 41.667 3.32 0.00 46.43 2.93
25 26 4.039124 CAGTTATTTGGCCTGTCAAGGTTT 59.961 41.667 3.32 0.00 46.43 3.27
26 27 3.573967 CAGTTATTTGGCCTGTCAAGGTT 59.426 43.478 3.32 0.00 46.43 3.50
27 28 3.157087 CAGTTATTTGGCCTGTCAAGGT 58.843 45.455 3.32 0.00 46.43 3.50
29 30 3.855689 CCAGTTATTTGGCCTGTCAAG 57.144 47.619 3.32 0.00 0.00 3.02
38 39 5.105917 ACCGAATTGTTAGCCAGTTATTTGG 60.106 40.000 0.00 0.00 41.35 3.28
39 40 5.949735 ACCGAATTGTTAGCCAGTTATTTG 58.050 37.500 0.00 0.00 0.00 2.32
40 41 5.708230 TGACCGAATTGTTAGCCAGTTATTT 59.292 36.000 0.00 0.00 0.00 1.40
41 42 5.250200 TGACCGAATTGTTAGCCAGTTATT 58.750 37.500 0.00 0.00 0.00 1.40
42 43 4.839121 TGACCGAATTGTTAGCCAGTTAT 58.161 39.130 0.00 0.00 0.00 1.89
43 44 4.274602 TGACCGAATTGTTAGCCAGTTA 57.725 40.909 0.00 0.00 0.00 2.24
44 45 3.134574 TGACCGAATTGTTAGCCAGTT 57.865 42.857 0.00 0.00 0.00 3.16
45 46 2.812011 GTTGACCGAATTGTTAGCCAGT 59.188 45.455 0.00 0.00 0.00 4.00
46 47 2.811431 TGTTGACCGAATTGTTAGCCAG 59.189 45.455 0.00 0.00 0.00 4.85
47 48 2.852449 TGTTGACCGAATTGTTAGCCA 58.148 42.857 0.00 0.00 0.00 4.75
48 49 4.434713 AATGTTGACCGAATTGTTAGCC 57.565 40.909 0.00 0.00 0.00 3.93
49 50 5.118510 CCAAAATGTTGACCGAATTGTTAGC 59.881 40.000 0.00 0.00 36.83 3.09
50 51 5.118510 GCCAAAATGTTGACCGAATTGTTAG 59.881 40.000 0.00 0.00 36.83 2.34
51 52 4.985409 GCCAAAATGTTGACCGAATTGTTA 59.015 37.500 0.00 0.00 36.83 2.41
52 53 3.807071 GCCAAAATGTTGACCGAATTGTT 59.193 39.130 0.00 0.00 36.83 2.83
53 54 3.181471 TGCCAAAATGTTGACCGAATTGT 60.181 39.130 0.00 0.00 36.83 2.71
54 55 3.388308 TGCCAAAATGTTGACCGAATTG 58.612 40.909 0.00 0.00 36.83 2.32
55 56 3.742433 TGCCAAAATGTTGACCGAATT 57.258 38.095 0.00 0.00 36.83 2.17
56 57 3.959535 ATGCCAAAATGTTGACCGAAT 57.040 38.095 0.00 0.00 36.83 3.34
57 58 6.516739 TTATATGCCAAAATGTTGACCGAA 57.483 33.333 0.00 0.00 36.83 4.30
58 59 6.707440 ATTATATGCCAAAATGTTGACCGA 57.293 33.333 0.00 0.00 36.83 4.69
59 60 6.977502 TCAATTATATGCCAAAATGTTGACCG 59.022 34.615 0.00 0.00 36.83 4.79
60 61 8.603181 GTTCAATTATATGCCAAAATGTTGACC 58.397 33.333 0.00 0.00 36.83 4.02
61 62 9.369904 AGTTCAATTATATGCCAAAATGTTGAC 57.630 29.630 0.00 0.00 36.83 3.18
62 63 9.368674 CAGTTCAATTATATGCCAAAATGTTGA 57.631 29.630 0.00 0.00 36.83 3.18
63 64 9.368674 TCAGTTCAATTATATGCCAAAATGTTG 57.631 29.630 0.00 0.00 34.25 3.33
78 79 6.039270 CACCAAACAGTTCCTCAGTTCAATTA 59.961 38.462 0.00 0.00 0.00 1.40
81 82 3.694072 CACCAAACAGTTCCTCAGTTCAA 59.306 43.478 0.00 0.00 0.00 2.69
85 86 2.026262 ACACACCAAACAGTTCCTCAGT 60.026 45.455 0.00 0.00 0.00 3.41
182 183 2.668632 GGTTGTGGATCGGAGCCA 59.331 61.111 11.64 11.64 0.00 4.75
232 235 8.856490 AAATTGTGTAGCACTTAAAGTTTGAG 57.144 30.769 5.88 5.88 35.11 3.02
237 240 7.341445 TCCAAAATTGTGTAGCACTTAAAGT 57.659 32.000 0.00 0.00 35.11 2.66
238 241 6.863126 CCTCCAAAATTGTGTAGCACTTAAAG 59.137 38.462 0.00 0.00 35.11 1.85
248 251 2.896044 TGCATGCCTCCAAAATTGTGTA 59.104 40.909 16.68 0.00 0.00 2.90
358 361 1.745489 GTCGCTAACAGGCTTGGGG 60.745 63.158 0.00 0.00 0.00 4.96
364 367 0.517316 CAGTTTGGTCGCTAACAGGC 59.483 55.000 0.00 0.00 0.00 4.85
370 373 1.890876 AACATGCAGTTTGGTCGCTA 58.109 45.000 0.00 0.00 37.03 4.26
380 383 1.675483 TCAAAGCGTCAAACATGCAGT 59.325 42.857 0.00 0.00 39.85 4.40
442 445 7.445096 ACATGTGCCTCATTATCATCGATAAAA 59.555 33.333 0.00 0.00 37.92 1.52
444 447 6.369615 CACATGTGCCTCATTATCATCGATAA 59.630 38.462 13.94 0.00 38.61 1.75
474 477 3.983666 CGAAGCTTCAAGATTGACGAAG 58.016 45.455 25.47 1.22 39.32 3.79
517 520 4.735132 GCACTCACACCGCGCCTA 62.735 66.667 0.00 0.00 0.00 3.93
534 537 3.792047 CACTCACGGCACCATGCG 61.792 66.667 0.00 0.00 46.21 4.73
536 539 2.327343 CCACACTCACGGCACCATG 61.327 63.158 0.00 0.00 0.00 3.66
549 552 1.292061 TGTAAACTCACACGCCACAC 58.708 50.000 0.00 0.00 0.00 3.82
551 554 4.939509 ATAATGTAAACTCACACGCCAC 57.060 40.909 0.00 0.00 0.00 5.01
598 604 8.367911 TCTGTCAAAATTGTCACTCAGTATACT 58.632 33.333 0.00 0.00 0.00 2.12
604 610 9.173939 GTATTTTCTGTCAAAATTGTCACTCAG 57.826 33.333 0.00 0.00 32.64 3.35
672 678 1.081242 GGGCTCACACAATTGCACG 60.081 57.895 5.05 0.00 0.00 5.34
871 3100 7.680730 AGGGTGCTATTGTATTTATACTGAGG 58.319 38.462 1.95 0.00 34.41 3.86
965 3199 0.955428 ATGCGTGGCTAGGTGTTGTG 60.955 55.000 0.00 0.00 0.00 3.33
980 3214 1.596477 GCAAGCTAGGGAGGATGCG 60.596 63.158 0.00 0.00 0.00 4.73
988 3222 0.251077 GGATCCATGGCAAGCTAGGG 60.251 60.000 6.96 2.49 0.00 3.53
1251 3485 2.048603 GGTGTCCATCTTGCTGCCC 61.049 63.158 0.00 0.00 0.00 5.36
1374 3608 2.359850 GTGAACTCGCCATGGCCA 60.360 61.111 30.79 18.42 37.98 5.36
1631 3865 9.944376 TGGCTAAATAACTAGGCTAATAAGATG 57.056 33.333 0.00 0.00 43.20 2.90
1665 3899 6.739112 TCAGTACTACTGCATGCAATACTAG 58.261 40.000 22.88 17.97 45.54 2.57
1737 3971 3.081061 AGAGATAGCAGCTACGGATCTG 58.919 50.000 9.74 0.00 0.00 2.90
1876 4110 0.675083 TAACTCTGCCGTCCGTGAAA 59.325 50.000 0.00 0.00 0.00 2.69
1877 4111 0.242825 CTAACTCTGCCGTCCGTGAA 59.757 55.000 0.00 0.00 0.00 3.18
1887 4121 2.744741 GGAGGCAAGAAACTAACTCTGC 59.255 50.000 0.00 0.00 0.00 4.26
1892 4126 5.453567 AAACATGGAGGCAAGAAACTAAC 57.546 39.130 0.00 0.00 0.00 2.34
1924 4158 3.838244 AGCTATGACTGGGCGAATAAA 57.162 42.857 0.00 0.00 0.00 1.40
1942 4176 9.282569 AGTTGGATCAGAATATGAAGATAAAGC 57.717 33.333 0.00 0.00 42.53 3.51
2008 4256 5.581605 CAAGTGAAAAAGAGTAAAGCTGCA 58.418 37.500 1.02 0.00 0.00 4.41
2009 4257 4.442403 GCAAGTGAAAAAGAGTAAAGCTGC 59.558 41.667 0.00 0.00 0.00 5.25
2010 4258 4.978580 GGCAAGTGAAAAAGAGTAAAGCTG 59.021 41.667 0.00 0.00 0.00 4.24
2011 4259 4.889995 AGGCAAGTGAAAAAGAGTAAAGCT 59.110 37.500 0.00 0.00 0.00 3.74
2012 4260 5.188327 AGGCAAGTGAAAAAGAGTAAAGC 57.812 39.130 0.00 0.00 0.00 3.51
2013 4261 8.479313 AAAAAGGCAAGTGAAAAAGAGTAAAG 57.521 30.769 0.00 0.00 0.00 1.85
2014 4262 8.311109 AGAAAAAGGCAAGTGAAAAAGAGTAAA 58.689 29.630 0.00 0.00 0.00 2.01
2060 4317 0.940126 GCATACAGCTTCCCATGTCG 59.060 55.000 0.00 0.00 41.15 4.35
2173 4430 7.839907 TGGAGTTGAAATGAAATAAATGGGAG 58.160 34.615 0.00 0.00 0.00 4.30
2287 4544 9.410556 GAAAGAAATGTTTTGTGCTATGTATGT 57.589 29.630 0.00 0.00 0.00 2.29
2297 4554 7.775397 ACAGAATGGAAAGAAATGTTTTGTG 57.225 32.000 0.00 0.00 43.62 3.33
2335 4592 1.002468 CCAAGTGGAGTTGCGTTTGAG 60.002 52.381 0.00 0.00 37.39 3.02
2379 4636 1.151668 GTGAACAGCACCAGCACTAG 58.848 55.000 0.00 0.00 45.49 2.57
2448 4706 0.323725 GATGGGGTGGTTGAGCATGT 60.324 55.000 0.00 0.00 0.00 3.21
2457 4715 0.768622 TTCGTTCTTGATGGGGTGGT 59.231 50.000 0.00 0.00 0.00 4.16
2458 4716 1.904287 TTTCGTTCTTGATGGGGTGG 58.096 50.000 0.00 0.00 0.00 4.61
2459 4717 5.125417 ACATATTTTCGTTCTTGATGGGGTG 59.875 40.000 0.00 0.00 0.00 4.61
2492 4750 1.882912 TATGGAGATGCATGTTCGCC 58.117 50.000 2.46 2.13 34.05 5.54


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

AutoCloner maintained by Alex Coulton.