Multiple sequence alignment - TraesCS1B01G171500

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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 TraesCS1B01G171500 chr1B 100.000 5796 0 0 1 5796 305174568 305168773 0.000000e+00 10704
1 TraesCS1B01G171500 chr1B 88.542 96 10 1 2877 2971 572529218 572529313 1.320000e-21 115
2 TraesCS1B01G171500 chr1A 96.240 3431 98 14 615 4031 267146375 267149788 0.000000e+00 5592
3 TraesCS1B01G171500 chr1A 90.137 1024 75 9 4018 5026 267154769 267155781 0.000000e+00 1308
4 TraesCS1B01G171500 chr1A 96.883 770 23 1 5025 5794 441795415 441796183 0.000000e+00 1288
5 TraesCS1B01G171500 chr1A 94.165 617 25 2 1 617 267145695 267146300 0.000000e+00 929
6 TraesCS1B01G171500 chr1A 87.500 96 11 1 2877 2971 519257535 519257630 6.140000e-20 110
7 TraesCS1B01G171500 chr1D 96.766 2659 71 11 1 2653 211685971 211688620 0.000000e+00 4420
8 TraesCS1B01G171500 chr1D 94.997 1659 56 15 2658 4306 211688917 211690558 0.000000e+00 2579
9 TraesCS1B01G171500 chr1D 91.534 756 43 6 4290 5026 211690579 211691332 0.000000e+00 1022
10 TraesCS1B01G171500 chr1D 88.542 96 10 1 2877 2971 423255686 423255781 1.320000e-21 115
11 TraesCS1B01G171500 chr2B 96.891 772 20 4 5024 5794 479849660 479850428 0.000000e+00 1290
12 TraesCS1B01G171500 chr5B 96.879 769 22 2 5026 5794 308226905 308226139 0.000000e+00 1286
13 TraesCS1B01G171500 chr4B 96.745 768 24 1 5027 5794 519387326 519386560 0.000000e+00 1279
14 TraesCS1B01G171500 chr3A 96.623 770 25 1 5025 5794 499681345 499682113 0.000000e+00 1277
15 TraesCS1B01G171500 chr5A 96.268 777 24 5 5020 5794 668187173 668187946 0.000000e+00 1269
16 TraesCS1B01G171500 chr7B 96.368 771 26 2 5024 5794 18102221 18101453 0.000000e+00 1267
17 TraesCS1B01G171500 chr7B 96.139 777 24 6 5020 5794 37081565 37080793 0.000000e+00 1264
18 TraesCS1B01G171500 chr7B 95.669 785 31 2 5012 5794 477782433 477781650 0.000000e+00 1258


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 TraesCS1B01G171500 chr1B 305168773 305174568 5795 True 10704.000000 10704 100.000000 1 5796 1 chr1B.!!$R1 5795
1 TraesCS1B01G171500 chr1A 267145695 267149788 4093 False 3260.500000 5592 95.202500 1 4031 2 chr1A.!!$F4 4030
2 TraesCS1B01G171500 chr1A 267154769 267155781 1012 False 1308.000000 1308 90.137000 4018 5026 1 chr1A.!!$F1 1008
3 TraesCS1B01G171500 chr1A 441795415 441796183 768 False 1288.000000 1288 96.883000 5025 5794 1 chr1A.!!$F2 769
4 TraesCS1B01G171500 chr1D 211685971 211691332 5361 False 2673.666667 4420 94.432333 1 5026 3 chr1D.!!$F2 5025
5 TraesCS1B01G171500 chr2B 479849660 479850428 768 False 1290.000000 1290 96.891000 5024 5794 1 chr2B.!!$F1 770
6 TraesCS1B01G171500 chr5B 308226139 308226905 766 True 1286.000000 1286 96.879000 5026 5794 1 chr5B.!!$R1 768
7 TraesCS1B01G171500 chr4B 519386560 519387326 766 True 1279.000000 1279 96.745000 5027 5794 1 chr4B.!!$R1 767
8 TraesCS1B01G171500 chr3A 499681345 499682113 768 False 1277.000000 1277 96.623000 5025 5794 1 chr3A.!!$F1 769
9 TraesCS1B01G171500 chr5A 668187173 668187946 773 False 1269.000000 1269 96.268000 5020 5794 1 chr5A.!!$F1 774
10 TraesCS1B01G171500 chr7B 18101453 18102221 768 True 1267.000000 1267 96.368000 5024 5794 1 chr7B.!!$R1 770
11 TraesCS1B01G171500 chr7B 37080793 37081565 772 True 1264.000000 1264 96.139000 5020 5794 1 chr7B.!!$R2 774
12 TraesCS1B01G171500 chr7B 477781650 477782433 783 True 1258.000000 1258 95.669000 5012 5794 1 chr7B.!!$R3 782

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
439 440 0.031994 ACGCCAAGCACCATTGTTTC 59.968 50.0 0.00 0.00 0.00 2.78 F
1960 2044 0.876777 CTGGGTGTGCGTTTACGTCA 60.877 55.0 0.00 0.24 42.22 4.35 F
2195 2279 0.617820 AGGCCAGGTTCTATGTCGGT 60.618 55.0 5.01 0.00 0.00 4.69 F
2996 3376 0.339859 TCCAGGCTCCACATCTAGGT 59.660 55.0 0.00 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2207 0.249615 ATGTCATCATGTCGCCTCCG 60.250 55.000 0.00 0.0 32.51 4.63 R
2977 3357 0.339859 ACCTAGATGTGGAGCCTGGA 59.660 55.000 0.00 0.0 0.00 3.86 R
3649 4030 2.412870 GGGAAAAAGCGGTCCAAATTG 58.587 47.619 0.00 0.0 35.44 2.32 R
4843 5284 0.667487 ACAGCACCGACTTGATGACG 60.667 55.000 4.26 0.0 0.00 4.35 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
20 21 0.174617 GGGAGCTCCGAAAGTCTGAG 59.825 60.000 26.36 0.00 36.71 3.35
137 138 8.571336 CACTTGTATTTCTGTCCTGAAAGATTT 58.429 33.333 5.73 0.00 39.01 2.17
215 216 6.089820 CGTTTGAAAACTAGAGCACGGTTATA 59.910 38.462 0.00 0.00 36.77 0.98
315 316 5.299279 ACAGTCGTGAAACCAAGAATGATTT 59.701 36.000 13.62 0.00 39.33 2.17
439 440 0.031994 ACGCCAAGCACCATTGTTTC 59.968 50.000 0.00 0.00 0.00 2.78
521 523 3.102052 AGCAAAGCCACAAAACTCATG 57.898 42.857 0.00 0.00 0.00 3.07
850 930 7.437862 GCAAACAAAATTGTGATCCTAACTTCA 59.562 33.333 1.62 0.00 41.31 3.02
950 1030 0.984230 CTTCCTAGACAAGGGTGCCA 59.016 55.000 0.00 0.00 46.55 4.92
1011 1091 1.067706 CCGTTTGCAATGGATTCTGCA 60.068 47.619 11.80 0.00 46.50 4.41
1152 1232 1.501741 CGCGGCAAAGCAGTACATT 59.498 52.632 0.00 0.00 36.85 2.71
1224 1304 3.069729 GGTAAGTAATGAGGATCCGTGCT 59.930 47.826 5.98 0.00 0.00 4.40
1303 1383 4.281688 GGCCCATGATGTAATATGTTTGCT 59.718 41.667 0.00 0.00 0.00 3.91
1612 1696 2.915349 CTAGCAGATGCCAATGTGTCT 58.085 47.619 0.14 0.00 43.38 3.41
1748 1832 3.356529 AAGGAGCATTTGGTGAGGTAG 57.643 47.619 0.00 0.00 0.00 3.18
1960 2044 0.876777 CTGGGTGTGCGTTTACGTCA 60.877 55.000 0.00 0.24 42.22 4.35
1965 2049 3.059051 GGGTGTGCGTTTACGTCAAATTA 60.059 43.478 0.00 0.00 42.22 1.40
1974 2058 5.444877 CGTTTACGTCAAATTATTCGCTCCA 60.445 40.000 0.00 0.00 34.11 3.86
1977 2061 3.245284 ACGTCAAATTATTCGCTCCATCG 59.755 43.478 0.00 0.00 0.00 3.84
1988 2072 1.336240 CGCTCCATCGCTGATCATACA 60.336 52.381 0.00 0.00 0.00 2.29
1995 2079 5.187576 TCCATCGCTGATCATACATTGGATA 59.812 40.000 0.00 0.00 0.00 2.59
2078 2162 4.277921 TGCATTGTGAAGCTGTATTGTTCA 59.722 37.500 0.00 0.00 0.00 3.18
2090 2174 8.757982 AGCTGTATTGTTCATTCCAAGATAAT 57.242 30.769 0.00 0.00 0.00 1.28
2123 2207 6.497259 TGTATCTCATAATGGAGTACCTTCCC 59.503 42.308 0.00 0.00 36.35 3.97
2162 2246 4.823442 ACATTGCTGATGAGAAAAGACACA 59.177 37.500 7.50 0.00 39.15 3.72
2180 2264 2.722201 ATTGACCGAGGACGAGGCC 61.722 63.158 0.00 0.00 42.66 5.19
2195 2279 0.617820 AGGCCAGGTTCTATGTCGGT 60.618 55.000 5.01 0.00 0.00 4.69
2201 2285 3.556213 CCAGGTTCTATGTCGGTGAAACA 60.556 47.826 0.00 0.00 39.98 2.83
2227 2311 2.938451 TCGCAATAGAAGCAATCCACAG 59.062 45.455 0.00 0.00 0.00 3.66
2274 2358 4.202284 TGTTCGGCTCCTATAAATGGTACC 60.202 45.833 4.43 4.43 0.00 3.34
2275 2359 3.853207 TCGGCTCCTATAAATGGTACCT 58.147 45.455 14.36 0.00 0.00 3.08
2338 2426 6.423905 TCAGAGATTTTCTTACGAACTTGGTG 59.576 38.462 0.00 0.00 32.41 4.17
2473 2561 3.251479 TGAATGAGAAGGATGTCACGG 57.749 47.619 0.00 0.00 30.73 4.94
2595 2683 6.930068 ACTTTGGTCAGTATTACCTACACT 57.070 37.500 0.00 0.00 37.91 3.55
2737 3117 2.334838 GCTTACTCCACTGTTGGTACG 58.665 52.381 0.00 0.00 44.35 3.67
2811 3191 3.437395 TGCGATTGGTAAGCGTAATTTGT 59.563 39.130 1.20 0.00 43.20 2.83
2940 3320 2.723530 ATCCCCCATTCTACTCGGAT 57.276 50.000 0.00 0.00 0.00 4.18
2974 3354 4.357918 ACTTGCAGAAAGGTAGTCATGT 57.642 40.909 0.00 0.00 40.51 3.21
2975 3355 4.718961 ACTTGCAGAAAGGTAGTCATGTT 58.281 39.130 0.00 0.00 40.51 2.71
2977 3357 5.594317 ACTTGCAGAAAGGTAGTCATGTTTT 59.406 36.000 0.00 0.00 40.51 2.43
2978 3358 5.689383 TGCAGAAAGGTAGTCATGTTTTC 57.311 39.130 0.00 0.00 0.00 2.29
2980 3360 4.518970 GCAGAAAGGTAGTCATGTTTTCCA 59.481 41.667 0.00 0.00 0.00 3.53
2981 3361 5.335191 GCAGAAAGGTAGTCATGTTTTCCAG 60.335 44.000 0.00 0.00 0.00 3.86
2982 3362 5.182001 CAGAAAGGTAGTCATGTTTTCCAGG 59.818 44.000 0.00 0.00 0.00 4.45
2984 3364 2.644798 AGGTAGTCATGTTTTCCAGGCT 59.355 45.455 0.00 0.00 0.00 4.58
2985 3365 3.010420 GGTAGTCATGTTTTCCAGGCTC 58.990 50.000 0.00 0.00 0.00 4.70
2986 3366 2.206576 AGTCATGTTTTCCAGGCTCC 57.793 50.000 0.00 0.00 0.00 4.70
2987 3367 1.425066 AGTCATGTTTTCCAGGCTCCA 59.575 47.619 0.00 0.00 0.00 3.86
2988 3368 1.541588 GTCATGTTTTCCAGGCTCCAC 59.458 52.381 0.00 0.00 0.00 4.02
2990 3370 2.173519 CATGTTTTCCAGGCTCCACAT 58.826 47.619 0.00 0.00 0.00 3.21
2991 3371 1.909700 TGTTTTCCAGGCTCCACATC 58.090 50.000 0.00 0.00 0.00 3.06
2992 3372 1.425066 TGTTTTCCAGGCTCCACATCT 59.575 47.619 0.00 0.00 0.00 2.90
2993 3373 2.642311 TGTTTTCCAGGCTCCACATCTA 59.358 45.455 0.00 0.00 0.00 1.98
2995 3375 1.500474 TTCCAGGCTCCACATCTAGG 58.500 55.000 0.00 0.00 0.00 3.02
2996 3376 0.339859 TCCAGGCTCCACATCTAGGT 59.660 55.000 0.00 0.00 0.00 3.08
2997 3377 0.467384 CCAGGCTCCACATCTAGGTG 59.533 60.000 0.04 0.04 38.52 4.00
2998 3378 1.489481 CAGGCTCCACATCTAGGTGA 58.511 55.000 10.76 0.00 41.32 4.02
2999 3379 2.045524 CAGGCTCCACATCTAGGTGAT 58.954 52.381 10.76 0.00 41.32 3.06
3010 3390 6.127897 CCACATCTAGGTGATTTTCCAAGTTC 60.128 42.308 10.76 0.00 41.32 3.01
3051 3431 7.243487 TCATCTTATGCAATTTTGTTCTCGTC 58.757 34.615 0.00 0.00 0.00 4.20
3247 3627 1.243342 TGCCTTGAAACATGCCTCCG 61.243 55.000 0.00 0.00 0.00 4.63
3252 3632 2.028420 TGAAACATGCCTCCGATCAG 57.972 50.000 0.00 0.00 0.00 2.90
3306 3687 7.690952 AATTGGTGCTACTACCGAATTTTTA 57.309 32.000 0.00 0.00 43.87 1.52
3649 4030 9.632807 TTACAAATTTCAACCTATGTATGCAAC 57.367 29.630 0.00 0.00 0.00 4.17
3662 4043 0.968405 ATGCAACAATTTGGACCGCT 59.032 45.000 0.78 0.00 35.65 5.52
3754 4136 9.813080 CTATACTTACAAGAACTTTGAACTTGC 57.187 33.333 0.00 0.00 42.93 4.01
3806 4188 6.345920 ACTGTGTACTTTCGACTTTCTTTG 57.654 37.500 0.00 0.00 0.00 2.77
3873 4255 9.750125 TGTTATAGCCGATTATATAAGCAGATG 57.250 33.333 11.08 0.00 0.00 2.90
4104 4486 5.602561 ACCCTAATCTGGCTTTGAAAAGTTT 59.397 36.000 4.80 0.00 38.28 2.66
4181 4570 8.532977 AATTAAAAATCACAAACATTCCTCCG 57.467 30.769 0.00 0.00 0.00 4.63
4185 4574 5.982890 AATCACAAACATTCCTCCGAATT 57.017 34.783 0.00 0.00 36.54 2.17
4194 4583 3.866883 TTCCTCCGAATTTTGGAATGC 57.133 42.857 6.82 0.00 34.44 3.56
4247 4636 5.106752 TGTGTGTGTGGAATACAAATGATCG 60.107 40.000 0.00 0.00 40.53 3.69
4249 4638 5.106752 TGTGTGTGGAATACAAATGATCGTG 60.107 40.000 0.00 0.00 40.53 4.35
4268 4657 5.823353 TCGTGTTAGTTGAATTTGTTTCCC 58.177 37.500 0.00 0.00 33.04 3.97
4359 4785 1.873591 CAACCCTTCAAGACTTGACCG 59.126 52.381 17.52 11.27 39.87 4.79
4404 4838 6.830912 TGAATCTTCAGAGTTTCAGGAAAGA 58.169 36.000 0.00 0.00 36.93 2.52
4405 4839 7.282585 TGAATCTTCAGAGTTTCAGGAAAGAA 58.717 34.615 0.00 0.00 36.93 2.52
4408 4842 5.471456 TCTTCAGAGTTTCAGGAAAGAATGC 59.529 40.000 0.00 0.00 0.00 3.56
4437 4871 2.151202 ACGAACAGCCATAAACAGTGG 58.849 47.619 0.00 0.00 39.80 4.00
4461 4895 4.886247 TGCTATACCGTTACCATTTTGC 57.114 40.909 0.00 0.00 0.00 3.68
4466 4900 1.960689 ACCGTTACCATTTTGCTGCTT 59.039 42.857 0.00 0.00 0.00 3.91
4470 4904 4.158384 CGTTACCATTTTGCTGCTTACTG 58.842 43.478 0.00 0.00 0.00 2.74
4483 4917 3.221771 TGCTTACTGACAATGCCTTGTT 58.778 40.909 8.84 0.00 45.57 2.83
4591 5026 3.429543 CCGTTTGGTGCTCAAATTTGATG 59.570 43.478 20.76 15.17 45.79 3.07
4596 5031 4.619973 TGGTGCTCAAATTTGATGTGTTC 58.380 39.130 20.76 9.58 36.46 3.18
4655 5090 0.975040 TGAGCCTGAAGGAGAGGAGC 60.975 60.000 0.00 0.00 37.39 4.70
4800 5241 2.599973 CCTTACCAACGGATTAACGACG 59.400 50.000 0.00 0.00 37.61 5.12
4843 5284 3.441572 TGTACTCTGGACCTTTACGCTAC 59.558 47.826 0.00 0.00 0.00 3.58
4944 5390 1.766496 CCGGATTAGCTGAAGGGGTTA 59.234 52.381 0.00 0.00 0.00 2.85
4954 5400 3.279434 CTGAAGGGGTTAATACTGCACC 58.721 50.000 0.00 0.00 0.00 5.01
4984 5430 3.773119 ACGATTGGAAAAGCTACCTAGGA 59.227 43.478 17.98 0.00 0.00 2.94
4996 5442 2.146920 ACCTAGGAGTCTTCGGAAGG 57.853 55.000 17.98 2.38 0.00 3.46
5012 5458 4.717778 TCGGAAGGAAGGATAAACATGGTA 59.282 41.667 0.00 0.00 0.00 3.25
5129 5575 1.025812 CACCTACGTGTGGGCAAAAA 58.974 50.000 12.88 0.00 35.10 1.94
5147 5593 4.953940 AAAACAACTAATGCCCACACAT 57.046 36.364 0.00 0.00 0.00 3.21
5171 5618 2.242495 TTTTTCCCTCCCGAACCCA 58.758 52.632 0.00 0.00 0.00 4.51
5232 5679 2.279517 CCGTATGTCAGGCCTCGC 60.280 66.667 0.00 0.00 0.00 5.03
5364 5811 1.609580 GGTTGCCATGTCGGACAACTA 60.610 52.381 15.72 2.39 44.53 2.24
5367 5814 1.070914 TGCCATGTCGGACAACTACAA 59.929 47.619 15.72 0.00 36.56 2.41
5441 5888 7.707893 GCAGTTGCCATGATTTCATAACTTTAT 59.292 33.333 0.00 0.00 33.04 1.40
5492 5939 1.085091 GAGAGTTGCCATGTGCTCAG 58.915 55.000 7.54 0.00 42.00 3.35
5527 5974 4.376146 GCAGTTGCCATGTAAAAAGGAAA 58.624 39.130 0.00 0.00 34.31 3.13
5644 6091 4.327680 GGTAAAAGAGAGTTGCCATCTGT 58.672 43.478 0.00 0.00 31.59 3.41
5794 6243 1.610624 GCAACTAGCAGCTTGGGTGTA 60.611 52.381 0.00 0.00 44.79 2.90
5795 6244 2.350522 CAACTAGCAGCTTGGGTGTAG 58.649 52.381 0.00 0.00 33.19 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.884836 ACCCACACTTCTATTCAGGAAAATAC 59.115 38.462 0.00 0.00 0.00 1.89
137 138 5.120208 GCTTTTCGCATAAACAGTACTCTCA 59.880 40.000 0.00 0.00 38.92 3.27
162 163 7.188834 TCTTCGCAAATGATAGCATAAAACAG 58.811 34.615 0.00 0.00 33.44 3.16
197 198 7.822822 AGAACAAATATAACCGTGCTCTAGTTT 59.177 33.333 0.00 0.00 0.00 2.66
215 216 2.676839 CAGATCAGCGCAGAGAACAAAT 59.323 45.455 11.47 0.00 0.00 2.32
521 523 4.742438 TTGAAGCTGTGATACCGTTTTC 57.258 40.909 0.00 0.00 0.00 2.29
850 930 1.076024 ACATGTGAATGAACTGCCCCT 59.924 47.619 0.00 0.00 0.00 4.79
950 1030 6.720112 ACAATCAAATGCATAAGCCTATGT 57.280 33.333 0.00 0.00 41.13 2.29
1011 1091 1.133668 AGCTTGTTGAACCAGCTCCTT 60.134 47.619 17.07 0.00 0.00 3.36
1152 1232 1.970640 TGCTCCTTGTAGTGCTTCTCA 59.029 47.619 0.00 0.00 0.00 3.27
1224 1304 0.322366 TGACAATCGGCCAAGATGCA 60.322 50.000 2.24 0.00 0.00 3.96
1316 1396 5.763204 ACACGTGAAAGGTCTCACAATTATT 59.237 36.000 25.01 0.00 45.03 1.40
1612 1696 1.423584 TGTTGTTCTGCTCCTCCTCA 58.576 50.000 0.00 0.00 0.00 3.86
1748 1832 3.445096 AGCCTACATTTGCATGGAAGTTC 59.555 43.478 0.00 0.00 34.27 3.01
1960 2044 3.466836 TCAGCGATGGAGCGAATAATTT 58.533 40.909 0.00 0.00 43.00 1.82
1965 2049 0.390492 TGATCAGCGATGGAGCGAAT 59.610 50.000 0.00 0.00 43.00 3.34
1974 2058 6.760298 GTGATATCCAATGTATGATCAGCGAT 59.240 38.462 0.09 0.00 0.00 4.58
1977 2061 6.652062 TGTGTGATATCCAATGTATGATCAGC 59.348 38.462 0.09 0.00 0.00 4.26
1988 2072 4.202441 GCTCAACCTGTGTGATATCCAAT 58.798 43.478 0.00 0.00 0.00 3.16
1995 2079 2.224597 TGACATGCTCAACCTGTGTGAT 60.225 45.455 0.00 0.00 0.00 3.06
2123 2207 0.249615 ATGTCATCATGTCGCCTCCG 60.250 55.000 0.00 0.00 32.51 4.63
2162 2246 2.722201 GGCCTCGTCCTCGGTCAAT 61.722 63.158 0.00 0.00 37.69 2.57
2180 2264 3.659786 TGTTTCACCGACATAGAACCTG 58.340 45.455 0.00 0.00 0.00 4.00
2195 2279 4.152402 GCTTCTATTGCGAGAACTGTTTCA 59.848 41.667 0.00 0.00 33.72 2.69
2201 2285 3.873952 GGATTGCTTCTATTGCGAGAACT 59.126 43.478 0.00 0.00 32.05 3.01
2227 2311 1.271379 ACCTGTGGATGTAGTTGTGCC 60.271 52.381 0.00 0.00 0.00 5.01
2328 2416 2.160417 GGAAGATCAAGCACCAAGTTCG 59.840 50.000 0.00 0.00 0.00 3.95
2473 2561 4.560128 TGAGCCGATGATGTTCTATTAGC 58.440 43.478 0.00 0.00 0.00 3.09
2653 2741 3.641986 GCGGCCGAACGAACAACA 61.642 61.111 33.48 0.00 35.47 3.33
2702 3082 5.125417 TGGAGTAAGCCTGCAATCATTTAAC 59.875 40.000 0.00 0.00 38.74 2.01
2737 3117 0.811616 CTGGAGCAATGTAGTCGGGC 60.812 60.000 0.00 0.00 0.00 6.13
2940 3320 4.350368 TCTGCAAGTTGTCATAGGTTCA 57.650 40.909 4.48 0.00 33.76 3.18
2974 3354 2.239654 CCTAGATGTGGAGCCTGGAAAA 59.760 50.000 0.00 0.00 0.00 2.29
2975 3355 1.839994 CCTAGATGTGGAGCCTGGAAA 59.160 52.381 0.00 0.00 0.00 3.13
2977 3357 0.339859 ACCTAGATGTGGAGCCTGGA 59.660 55.000 0.00 0.00 0.00 3.86
2978 3358 0.467384 CACCTAGATGTGGAGCCTGG 59.533 60.000 0.00 0.00 32.50 4.45
2980 3360 2.485966 ATCACCTAGATGTGGAGCCT 57.514 50.000 0.00 0.00 36.87 4.58
2981 3361 3.567478 AAATCACCTAGATGTGGAGCC 57.433 47.619 0.00 0.00 36.96 4.70
2982 3362 3.879892 GGAAAATCACCTAGATGTGGAGC 59.120 47.826 0.00 0.00 36.96 4.70
2984 3364 5.014123 ACTTGGAAAATCACCTAGATGTGGA 59.986 40.000 0.00 0.00 36.96 4.02
2985 3365 5.256474 ACTTGGAAAATCACCTAGATGTGG 58.744 41.667 0.00 0.00 36.96 4.17
2986 3366 6.656693 AGAACTTGGAAAATCACCTAGATGTG 59.343 38.462 0.00 0.00 36.96 3.21
2987 3367 6.784031 AGAACTTGGAAAATCACCTAGATGT 58.216 36.000 0.00 0.00 36.96 3.06
2988 3368 8.970859 ATAGAACTTGGAAAATCACCTAGATG 57.029 34.615 0.00 0.00 36.96 2.90
2990 3370 8.383175 ACAATAGAACTTGGAAAATCACCTAGA 58.617 33.333 0.00 0.00 35.09 2.43
2991 3371 8.567285 ACAATAGAACTTGGAAAATCACCTAG 57.433 34.615 0.00 0.00 36.60 3.02
2992 3372 8.934023 AACAATAGAACTTGGAAAATCACCTA 57.066 30.769 0.00 0.00 0.00 3.08
2993 3373 7.725844 AGAACAATAGAACTTGGAAAATCACCT 59.274 33.333 0.00 0.00 0.00 4.00
2995 3375 8.787852 AGAGAACAATAGAACTTGGAAAATCAC 58.212 33.333 0.00 0.00 0.00 3.06
2996 3376 8.786898 CAGAGAACAATAGAACTTGGAAAATCA 58.213 33.333 0.00 0.00 0.00 2.57
2997 3377 7.752686 GCAGAGAACAATAGAACTTGGAAAATC 59.247 37.037 0.00 0.00 0.00 2.17
2998 3378 7.449704 AGCAGAGAACAATAGAACTTGGAAAAT 59.550 33.333 0.00 0.00 0.00 1.82
2999 3379 6.772716 AGCAGAGAACAATAGAACTTGGAAAA 59.227 34.615 0.00 0.00 0.00 2.29
3010 3390 8.068977 GCATAAGATGAAAGCAGAGAACAATAG 58.931 37.037 0.00 0.00 0.00 1.73
3051 3431 2.979676 ATGGCCCACATATGCGCG 60.980 61.111 0.00 0.00 38.26 6.86
3068 3448 4.101585 AGTTCTCCAGTTCACAATCTGTCA 59.898 41.667 0.00 0.00 0.00 3.58
3252 3632 9.877178 TCTGTTCTTTTAAAGGACTCAGATATC 57.123 33.333 20.31 0.00 37.90 1.63
3284 3665 7.390996 TGAATAAAAATTCGGTAGTAGCACCAA 59.609 33.333 0.00 0.00 38.61 3.67
3374 3755 6.639632 AAATATGCAGCTTCGGTTTCATAT 57.360 33.333 0.00 0.00 0.00 1.78
3481 3862 8.815565 TGTACTGACTTCTAGAGATGAAGAAT 57.184 34.615 10.00 0.00 42.37 2.40
3519 3900 8.394877 CCGAAGACTGCAAATACAACATAAATA 58.605 33.333 0.00 0.00 0.00 1.40
3649 4030 2.412870 GGGAAAAAGCGGTCCAAATTG 58.587 47.619 0.00 0.00 35.44 2.32
3662 4043 7.579339 GCAAATGACAGAATAGATGGGGAAAAA 60.579 37.037 0.00 0.00 0.00 1.94
3754 4136 7.431376 CCATTTCAAGAACTTCATCATCATTCG 59.569 37.037 0.00 0.00 0.00 3.34
3806 4188 7.573968 ATGGAAGAGGCAAACATAGTTATTC 57.426 36.000 0.00 0.00 0.00 1.75
3873 4255 4.242475 TCACACAGTTCGAATCATGGTAC 58.758 43.478 0.00 0.00 0.00 3.34
4165 4554 5.508825 CCAAAATTCGGAGGAATGTTTGTGA 60.509 40.000 15.17 0.00 41.99 3.58
4181 4570 6.422776 TCTCTCGTAAGCATTCCAAAATTC 57.577 37.500 0.00 0.00 37.18 2.17
4185 4574 4.876107 GGATTCTCTCGTAAGCATTCCAAA 59.124 41.667 0.00 0.00 37.18 3.28
4216 4605 1.160989 TTCCACACACACACACACAC 58.839 50.000 0.00 0.00 0.00 3.82
4218 4607 2.939756 TGTATTCCACACACACACACAC 59.060 45.455 0.00 0.00 30.04 3.82
4219 4608 3.268023 TGTATTCCACACACACACACA 57.732 42.857 0.00 0.00 30.04 3.72
4220 4609 4.624336 TTTGTATTCCACACACACACAC 57.376 40.909 0.00 0.00 36.69 3.82
4221 4610 4.884164 TCATTTGTATTCCACACACACACA 59.116 37.500 0.00 0.00 36.69 3.72
4222 4611 5.431420 TCATTTGTATTCCACACACACAC 57.569 39.130 0.00 0.00 36.69 3.82
4223 4612 5.106752 CGATCATTTGTATTCCACACACACA 60.107 40.000 0.00 0.00 36.69 3.72
4224 4613 5.106712 ACGATCATTTGTATTCCACACACAC 60.107 40.000 0.00 0.00 36.69 3.82
4247 4636 7.039270 ACAAGGGAAACAAATTCAACTAACAC 58.961 34.615 0.00 0.00 39.98 3.32
4249 4638 7.979537 AGAACAAGGGAAACAAATTCAACTAAC 59.020 33.333 0.00 0.00 39.98 2.34
4268 4657 6.017275 GGATGGAGAATGCTATGAAGAACAAG 60.017 42.308 0.00 0.00 0.00 3.16
4403 4837 3.542310 GCTGTTCGTAAATTTCCGCATTC 59.458 43.478 0.00 0.00 0.00 2.67
4404 4838 3.498082 GCTGTTCGTAAATTTCCGCATT 58.502 40.909 0.00 0.00 0.00 3.56
4405 4839 2.159435 GGCTGTTCGTAAATTTCCGCAT 60.159 45.455 0.00 0.00 0.00 4.73
4408 4842 3.757745 ATGGCTGTTCGTAAATTTCCG 57.242 42.857 0.00 0.00 0.00 4.30
4437 4871 5.212194 CAAAATGGTAACGGTATAGCATGC 58.788 41.667 10.51 10.51 41.72 4.06
4461 4895 2.816087 ACAAGGCATTGTCAGTAAGCAG 59.184 45.455 11.64 0.00 46.90 4.24
4483 4917 3.718097 CGCGCGCAGTGGGTTAAA 61.718 61.111 32.61 0.00 46.11 1.52
4574 5008 4.501229 GGAACACATCAAATTTGAGCACCA 60.501 41.667 24.17 2.38 41.08 4.17
4575 5009 3.989817 GGAACACATCAAATTTGAGCACC 59.010 43.478 24.17 16.54 41.08 5.01
4591 5026 2.872858 AGCTTTTCGTCAAGAGGAACAC 59.127 45.455 4.83 0.00 35.28 3.32
4596 5031 4.008539 GCATAAGCTTTTCGTCAAGAGG 57.991 45.455 3.20 0.00 37.91 3.69
4770 5211 1.003718 GTTGGTAAGGCGAGGCTGT 60.004 57.895 0.00 0.00 0.00 4.40
4800 5241 1.135286 CAAAGGGAAAGAAGCGATGCC 60.135 52.381 0.00 0.00 0.00 4.40
4843 5284 0.667487 ACAGCACCGACTTGATGACG 60.667 55.000 4.26 0.00 0.00 4.35
4954 5400 3.803778 AGCTTTTCCAATCGTTTTTGCAG 59.196 39.130 0.00 0.00 0.00 4.41
5129 5575 3.009473 AGAGATGTGTGGGCATTAGTTGT 59.991 43.478 0.00 0.00 0.00 3.32
5158 5604 2.606519 TGAGTGGGTTCGGGAGGG 60.607 66.667 0.00 0.00 0.00 4.30
5193 5640 1.533731 CGTGTGGGCGTTATCAACTTT 59.466 47.619 0.00 0.00 0.00 2.66
5276 5723 2.672996 GGACCATGGCAACTGCGT 60.673 61.111 13.04 0.00 43.26 5.24
5364 5811 1.340088 TGAGCAACCATGGCAATTGT 58.660 45.000 13.04 0.35 0.00 2.71
5367 5814 1.274167 CAGTTGAGCAACCATGGCAAT 59.726 47.619 13.04 0.00 42.06 3.56
5416 5863 9.027129 CATAAAGTTATGAAATCATGGCAACTG 57.973 33.333 6.17 0.00 42.38 3.16
5441 5888 6.462487 GCCTAGTGTTAGTATATGGCAACTCA 60.462 42.308 0.00 0.00 38.99 3.41
5451 5898 7.344134 TCTCTCAACTGCCTAGTGTTAGTATA 58.656 38.462 0.00 0.00 37.19 1.47
5644 6091 1.069513 ACTGCCTAGTGTGCACGTAAA 59.930 47.619 13.13 0.00 35.34 2.01
5676 6123 2.935201 GAGTTGCCATGTGTTTTTGCAA 59.065 40.909 0.00 0.00 39.42 4.08
5759 6208 1.135915 AGTTGCCATGTGTTTTCGCAA 59.864 42.857 0.00 0.00 43.76 4.85


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

AutoCloner maintained by Alex Coulton.