Multiple sequence alignment - TraesCS5D01G424800

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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 TraesCS5D01G424800 chr5D 100.000 3122 0 0 1 3122 483770924 483767803 0.000000e+00 5729.0
1 TraesCS5D01G424800 chr5A 93.666 1784 95 10 1346 3122 605245089 605243317 0.000000e+00 2652.0
2 TraesCS5D01G424800 chr5A 94.301 579 25 2 768 1338 605245964 605245386 0.000000e+00 880.0
3 TraesCS5D01G424800 chr5A 83.966 237 20 8 1 220 605246624 605246389 2.420000e-56 230.0
4 TraesCS5D01G424800 chr5B 92.603 1798 107 18 1346 3122 595009605 595007813 0.000000e+00 2560.0
5 TraesCS5D01G424800 chr5B 86.765 1292 68 30 123 1348 595011161 595009907 0.000000e+00 1343.0
6 TraesCS5D01G424800 chr7A 83.125 1120 150 24 1355 2452 566791177 566792279 0.000000e+00 985.0
7 TraesCS5D01G424800 chr7A 84.727 897 109 19 1348 2223 619305506 619306395 0.000000e+00 872.0
8 TraesCS5D01G424800 chr7A 86.364 330 36 6 999 1324 566790507 566790831 4.950000e-93 351.0
9 TraesCS5D01G424800 chr7A 86.943 314 37 1 999 1308 566910406 566910719 1.780000e-92 350.0
10 TraesCS5D01G424800 chr7A 84.765 361 40 9 999 1348 566989681 566990037 6.410000e-92 348.0
11 TraesCS5D01G424800 chr7D 82.420 1132 153 29 1348 2455 500776893 500778002 0.000000e+00 946.0
12 TraesCS5D01G424800 chr7D 83.835 897 118 18 1348 2223 113583715 113584605 0.000000e+00 828.0
13 TraesCS5D01G424800 chr7B 83.864 942 120 19 1348 2264 528876811 528877745 0.000000e+00 869.0
14 TraesCS5D01G424800 chr7B 83.210 947 124 22 1348 2267 664398195 664397257 0.000000e+00 835.0
15 TraesCS5D01G424800 chr7B 79.245 583 76 21 781 1346 664399060 664398506 6.360000e-97 364.0
16 TraesCS5D01G424800 chr3A 83.369 944 125 20 1348 2267 732403865 732402930 0.000000e+00 845.0
17 TraesCS5D01G424800 chr3A 85.955 356 41 6 1001 1348 732404533 732404179 3.800000e-99 372.0
18 TraesCS5D01G424800 chr3D 84.060 596 82 7 1871 2455 598724947 598724354 2.100000e-156 562.0
19 TraesCS5D01G424800 chrUn 84.971 346 45 5 999 1338 86612162 86612506 8.290000e-91 344.0
20 TraesCS5D01G424800 chr3B 84.076 314 45 2 999 1308 810194217 810193905 6.550000e-77 298.0
21 TraesCS5D01G424800 chr1B 93.750 48 1 1 241 288 22180059 22180104 1.550000e-08 71.3
22 TraesCS5D01G424800 chr1B 86.667 60 6 1 241 300 7067649 7067706 7.230000e-07 65.8


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 TraesCS5D01G424800 chr5D 483767803 483770924 3121 True 5729.0 5729 100.000000 1 3122 1 chr5D.!!$R1 3121
1 TraesCS5D01G424800 chr5A 605243317 605246624 3307 True 1254.0 2652 90.644333 1 3122 3 chr5A.!!$R1 3121
2 TraesCS5D01G424800 chr5B 595007813 595011161 3348 True 1951.5 2560 89.684000 123 3122 2 chr5B.!!$R1 2999
3 TraesCS5D01G424800 chr7A 619305506 619306395 889 False 872.0 872 84.727000 1348 2223 1 chr7A.!!$F3 875
4 TraesCS5D01G424800 chr7A 566790507 566792279 1772 False 668.0 985 84.744500 999 2452 2 chr7A.!!$F4 1453
5 TraesCS5D01G424800 chr7D 500776893 500778002 1109 False 946.0 946 82.420000 1348 2455 1 chr7D.!!$F2 1107
6 TraesCS5D01G424800 chr7D 113583715 113584605 890 False 828.0 828 83.835000 1348 2223 1 chr7D.!!$F1 875
7 TraesCS5D01G424800 chr7B 528876811 528877745 934 False 869.0 869 83.864000 1348 2264 1 chr7B.!!$F1 916
8 TraesCS5D01G424800 chr7B 664397257 664399060 1803 True 599.5 835 81.227500 781 2267 2 chr7B.!!$R1 1486
9 TraesCS5D01G424800 chr3A 732402930 732404533 1603 True 608.5 845 84.662000 1001 2267 2 chr3A.!!$R1 1266
10 TraesCS5D01G424800 chr3D 598724354 598724947 593 True 562.0 562 84.060000 1871 2455 1 chr3D.!!$R1 584

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
747 870 0.109086 CTGGATGAACGACGTCAGCT 60.109 55.0 17.16 0.0 34.32 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 2989 0.763035 ACCCTTAGAACACGTTGCCT 59.237 50.0 0.0 0.0 0.0 4.75 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
35 36 0.773644 AGGTGCCCAATCAGAACAGT 59.226 50.000 0.00 0.00 0.00 3.55
44 45 4.321452 CCCAATCAGAACAGTCACATTTGG 60.321 45.833 0.00 0.00 0.00 3.28
47 48 5.695851 ATCAGAACAGTCACATTTGGAAC 57.304 39.130 0.00 0.00 0.00 3.62
75 76 4.158384 GGCAAGATACAACACGTTGAATG 58.842 43.478 16.48 8.31 42.93 2.67
205 223 7.120285 GGTGGATGTATCTGAATATGGTTGATG 59.880 40.741 0.00 0.00 0.00 3.07
251 276 3.082548 CGATATGATGTACTCCCTCCGT 58.917 50.000 0.00 0.00 0.00 4.69
252 277 3.506455 CGATATGATGTACTCCCTCCGTT 59.494 47.826 0.00 0.00 0.00 4.44
253 278 4.022242 CGATATGATGTACTCCCTCCGTTT 60.022 45.833 0.00 0.00 0.00 3.60
263 288 8.660295 TGTACTCCCTCCGTTTCATAATATAT 57.340 34.615 0.00 0.00 0.00 0.86
264 289 9.758021 TGTACTCCCTCCGTTTCATAATATATA 57.242 33.333 0.00 0.00 0.00 0.86
267 292 9.543231 ACTCCCTCCGTTTCATAATATATAAGA 57.457 33.333 0.00 0.00 0.00 2.10
269 294 8.475639 TCCCTCCGTTTCATAATATATAAGAGC 58.524 37.037 0.00 0.00 0.00 4.09
270 295 7.435488 CCCTCCGTTTCATAATATATAAGAGCG 59.565 40.741 0.00 0.00 0.00 5.03
271 296 7.974501 CCTCCGTTTCATAATATATAAGAGCGT 59.025 37.037 0.00 0.00 0.00 5.07
272 297 9.999009 CTCCGTTTCATAATATATAAGAGCGTA 57.001 33.333 0.00 0.00 0.00 4.42
351 395 1.767289 AGTTCAGTACAAGACACGCG 58.233 50.000 3.53 3.53 0.00 6.01
383 427 4.803452 AGAACAAACCAGGAAAATCAGGA 58.197 39.130 0.00 0.00 0.00 3.86
544 643 0.728129 TGACGAGCGACATCAACGAC 60.728 55.000 0.00 0.00 0.00 4.34
590 689 1.503818 GAAGAACTTCGCCAACGCCA 61.504 55.000 0.00 0.00 39.84 5.69
616 715 3.310307 GGCACCCACCGGCAAATT 61.310 61.111 0.00 0.00 0.00 1.82
626 749 4.340950 CCCACCGGCAAATTATTTACATCT 59.659 41.667 0.00 0.00 0.00 2.90
627 750 5.533154 CCCACCGGCAAATTATTTACATCTA 59.467 40.000 0.00 0.00 0.00 1.98
628 751 6.435428 CCACCGGCAAATTATTTACATCTAC 58.565 40.000 0.00 0.00 0.00 2.59
629 752 6.262273 CCACCGGCAAATTATTTACATCTACT 59.738 38.462 0.00 0.00 0.00 2.57
630 753 7.132213 CACCGGCAAATTATTTACATCTACTG 58.868 38.462 0.00 0.00 0.00 2.74
631 754 6.142817 CCGGCAAATTATTTACATCTACTGC 58.857 40.000 0.00 0.00 0.00 4.40
632 755 6.238621 CCGGCAAATTATTTACATCTACTGCA 60.239 38.462 0.00 0.00 0.00 4.41
633 756 6.852853 CGGCAAATTATTTACATCTACTGCAG 59.147 38.462 13.48 13.48 0.00 4.41
634 757 6.638468 GGCAAATTATTTACATCTACTGCAGC 59.362 38.462 15.27 0.00 0.00 5.25
635 758 6.358030 GCAAATTATTTACATCTACTGCAGCG 59.642 38.462 15.27 5.33 0.00 5.18
636 759 7.409697 CAAATTATTTACATCTACTGCAGCGT 58.590 34.615 15.27 6.11 0.00 5.07
637 760 6.771188 ATTATTTACATCTACTGCAGCGTC 57.229 37.500 15.27 0.00 0.00 5.19
638 761 3.586100 TTTACATCTACTGCAGCGTCA 57.414 42.857 15.27 0.00 0.00 4.35
639 762 3.586100 TTACATCTACTGCAGCGTCAA 57.414 42.857 15.27 0.00 0.00 3.18
640 763 2.001812 ACATCTACTGCAGCGTCAAG 57.998 50.000 15.27 3.99 0.00 3.02
641 764 1.284657 CATCTACTGCAGCGTCAAGG 58.715 55.000 15.27 0.00 0.00 3.61
642 765 0.898320 ATCTACTGCAGCGTCAAGGT 59.102 50.000 15.27 0.00 0.00 3.50
706 829 2.729882 CCTCCGTGACGTAACTTTTGAG 59.270 50.000 3.64 0.37 0.00 3.02
711 834 4.446385 CCGTGACGTAACTTTTGAGATGAA 59.554 41.667 3.64 0.00 0.00 2.57
718 841 3.409026 ACTTTTGAGATGAAGAGCGGT 57.591 42.857 0.00 0.00 0.00 5.68
735 858 4.032452 TTGGCGCCTGCTGGATGA 62.032 61.111 29.70 0.00 42.25 2.92
736 859 3.565961 TTGGCGCCTGCTGGATGAA 62.566 57.895 29.70 7.02 42.25 2.57
739 862 2.125552 CGCCTGCTGGATGAACGA 60.126 61.111 14.77 0.00 34.57 3.85
740 863 2.456119 CGCCTGCTGGATGAACGAC 61.456 63.158 14.77 0.00 34.57 4.34
741 864 2.456119 GCCTGCTGGATGAACGACG 61.456 63.158 14.77 0.00 34.57 5.12
742 865 1.079819 CCTGCTGGATGAACGACGT 60.080 57.895 2.92 0.00 34.57 4.34
743 866 1.078759 CCTGCTGGATGAACGACGTC 61.079 60.000 5.18 5.18 34.57 4.34
744 867 0.388520 CTGCTGGATGAACGACGTCA 60.389 55.000 17.16 1.51 36.34 4.35
745 868 0.388520 TGCTGGATGAACGACGTCAG 60.389 55.000 17.16 10.90 36.34 3.51
746 869 1.687494 GCTGGATGAACGACGTCAGC 61.687 60.000 18.87 18.87 36.34 4.26
747 870 0.109086 CTGGATGAACGACGTCAGCT 60.109 55.000 17.16 0.00 34.32 4.24
748 871 0.109272 TGGATGAACGACGTCAGCTC 60.109 55.000 17.16 8.83 34.32 4.09
749 872 0.802607 GGATGAACGACGTCAGCTCC 60.803 60.000 17.16 9.76 34.32 4.70
750 873 0.109272 GATGAACGACGTCAGCTCCA 60.109 55.000 17.16 6.01 34.88 3.86
751 874 0.109086 ATGAACGACGTCAGCTCCAG 60.109 55.000 17.16 0.00 0.00 3.86
752 875 2.049063 AACGACGTCAGCTCCAGC 60.049 61.111 17.16 0.00 42.49 4.85
753 876 3.575351 AACGACGTCAGCTCCAGCC 62.575 63.158 17.16 0.00 43.38 4.85
757 880 3.385384 CGTCAGCTCCAGCCTCCA 61.385 66.667 0.00 0.00 43.38 3.86
884 1024 5.871396 TCTATAAATTGAAGCGAGAGGGT 57.129 39.130 0.00 0.00 0.00 4.34
977 1141 3.741476 CAGCCGCAGAAACCAGCC 61.741 66.667 0.00 0.00 0.00 4.85
994 1158 1.878775 CCGTTCTCGTACGACCCTT 59.121 57.895 15.28 0.00 43.99 3.95
1042 1209 2.750637 GCCTCGTCGTCCTCCTCA 60.751 66.667 0.00 0.00 0.00 3.86
1063 1230 7.505923 TCCTCATCCTCGTTCTAAATCTCAATA 59.494 37.037 0.00 0.00 0.00 1.90
1113 1280 1.079503 GCCATCAGAACAAGTCGTCC 58.920 55.000 0.00 0.00 0.00 4.79
1279 1454 2.032528 TGGCCGCTTCTCCAACTG 59.967 61.111 0.00 0.00 0.00 3.16
1301 1476 6.014840 ACTGCAAAATCCAGTCAGATTTCATT 60.015 34.615 0.36 0.00 43.90 2.57
1358 1852 7.408132 AGTACTGTTATATTATGCAAGCACG 57.592 36.000 0.00 0.00 0.00 5.34
1512 2048 6.840780 ATATTGGAAAGGTGACAAAAGAGG 57.159 37.500 0.00 0.00 0.00 3.69
1706 2243 6.875726 TCATGACAGTAAAGAAGAATGTCCAG 59.124 38.462 0.00 0.00 39.58 3.86
1725 2262 4.082845 CCAGATCATCGACCTATACACCT 58.917 47.826 0.00 0.00 0.00 4.00
1771 2308 4.884744 TGCGCCAGGTATGTATGTATTTTT 59.115 37.500 4.18 0.00 0.00 1.94
1923 2466 1.774639 AGCAATTCAAGCGCAAACTG 58.225 45.000 11.47 1.90 37.01 3.16
2313 2873 7.977789 TGTATACCATATGCCACATTTACAG 57.022 36.000 0.00 0.00 0.00 2.74
2364 2927 5.710567 TGAGTACTTGCATATATACGGCTCT 59.289 40.000 0.00 2.16 0.00 4.09
2456 3028 4.308458 TGACGGGTGCCTTGTCGG 62.308 66.667 8.69 0.00 35.40 4.79
2485 3057 0.976641 TTGTTCGGTCATCCAGAGCT 59.023 50.000 0.00 0.00 42.56 4.09
2513 3085 9.126151 TCGATGTATTTATTTTATTTGGGCTGA 57.874 29.630 0.00 0.00 0.00 4.26
2526 3098 5.913137 TTTGGGCTGATTTGTACTAATGG 57.087 39.130 7.29 2.09 0.00 3.16
2540 3112 9.452287 TTTGTACTAATGGTGAACCTTATAACC 57.548 33.333 0.37 0.00 36.82 2.85
2559 3131 5.845391 AACCGATCAAAGTCCTTTTTCAA 57.155 34.783 0.00 0.00 0.00 2.69
2697 3269 7.919690 TCGGCATTTAATTAGTTCATCAGAAG 58.080 34.615 0.00 0.00 33.63 2.85
2788 3360 6.147864 AGATGCTTGTTTGCTTTTAAGACA 57.852 33.333 0.00 0.00 0.00 3.41
2861 3435 8.818057 CAGTAGACTTCCGAATTAAATAACTGG 58.182 37.037 0.00 0.00 0.00 4.00
2900 3474 3.437049 GCAACTTGACAATAGACTCCACC 59.563 47.826 0.00 0.00 0.00 4.61
2920 3494 3.506067 ACCCCATCAAAATTGTCGACTTC 59.494 43.478 17.92 0.00 0.00 3.01
2948 3523 4.875536 GCATTGTGACACTGTACATGGATA 59.124 41.667 7.20 0.00 0.00 2.59
2983 3558 3.882888 TCAACGCTTTTCTTGATTCAGGT 59.117 39.130 0.00 0.00 0.00 4.00
3061 3636 3.347216 GGTGCACAAGTACTTCCATGAT 58.653 45.455 20.43 0.00 0.00 2.45
3086 3661 0.036765 AGCCGGCAATCGAGTGTAAA 60.037 50.000 31.54 0.00 42.43 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.107378 TGCCCAGTAGTTCCAAATGTGA 59.893 45.455 0.00 0.00 0.00 3.58
44 45 4.392138 GTGTTGTATCTTGCCCAGTAGTTC 59.608 45.833 0.00 0.00 0.00 3.01
47 48 2.930040 CGTGTTGTATCTTGCCCAGTAG 59.070 50.000 0.00 0.00 0.00 2.57
75 76 7.043454 TGTTATTGCGTAATTTGTTTGCATC 57.957 32.000 3.47 0.00 35.20 3.91
132 150 3.190535 CCAGGTGTCCTTTTTATGGTTCG 59.809 47.826 0.00 0.00 0.00 3.95
205 223 9.210426 CGATGTGTGCTATAAACAAAATAACTC 57.790 33.333 0.00 0.00 0.00 3.01
214 232 8.243289 CATCATATCGATGTGTGCTATAAACA 57.757 34.615 19.92 0.00 45.61 2.83
351 395 0.031585 GGTTTGTTCTTCCGGTTGCC 59.968 55.000 0.00 0.00 0.00 4.52
383 427 0.321653 GTGTCGGGCACTTGGATCTT 60.322 55.000 5.29 0.00 44.41 2.40
402 446 1.308069 CCATCTTGGCCTCGGTGTTG 61.308 60.000 3.32 0.00 0.00 3.33
450 528 0.815615 GAGGATGCTTAACCGGCTGG 60.816 60.000 11.02 11.02 42.84 4.85
590 689 1.303317 GGTGGGTGCCGTCTTTGAT 60.303 57.895 0.00 0.00 0.00 2.57
616 715 5.257082 TGACGCTGCAGTAGATGTAAATA 57.743 39.130 16.64 0.00 0.00 1.40
626 749 1.667830 GCACCTTGACGCTGCAGTA 60.668 57.895 16.64 0.00 0.00 2.74
627 750 2.974698 GCACCTTGACGCTGCAGT 60.975 61.111 16.64 0.00 0.00 4.40
628 751 4.081030 CGCACCTTGACGCTGCAG 62.081 66.667 10.11 10.11 0.00 4.41
635 758 4.030452 GTGGCTGCGCACCTTGAC 62.030 66.667 23.38 11.28 0.00 3.18
636 759 4.254709 AGTGGCTGCGCACCTTGA 62.255 61.111 23.38 6.91 0.00 3.02
637 760 4.034258 CAGTGGCTGCGCACCTTG 62.034 66.667 23.38 18.45 0.00 3.61
646 769 3.914605 TACGACGCTGCAGTGGCTG 62.915 63.158 29.51 23.72 41.91 4.85
647 770 3.220999 TTACGACGCTGCAGTGGCT 62.221 57.895 29.51 18.78 41.91 4.75
648 771 2.730672 CTTACGACGCTGCAGTGGC 61.731 63.158 29.60 26.87 41.68 5.01
649 772 2.730672 GCTTACGACGCTGCAGTGG 61.731 63.158 29.60 17.48 0.00 4.00
672 795 2.597903 GGAGGGACCAATGGAGCC 59.402 66.667 6.16 6.85 38.79 4.70
680 803 1.228521 TTACGTCACGGAGGGACCA 60.229 57.895 0.35 0.00 38.90 4.02
706 829 3.093278 CGCCAACCGCTCTTCATC 58.907 61.111 0.00 0.00 34.21 2.92
718 841 3.565961 TTCATCCAGCAGGCGCCAA 62.566 57.895 31.54 7.70 39.83 4.52
733 856 1.285950 CTGGAGCTGACGTCGTTCA 59.714 57.895 19.43 9.06 0.00 3.18
735 858 2.049063 GCTGGAGCTGACGTCGTT 60.049 61.111 11.62 3.73 38.21 3.85
736 859 4.057428 GGCTGGAGCTGACGTCGT 62.057 66.667 11.62 0.00 41.70 4.34
739 862 3.386237 GGAGGCTGGAGCTGACGT 61.386 66.667 0.00 0.00 41.70 4.34
740 863 2.729479 ATGGAGGCTGGAGCTGACG 61.729 63.158 0.00 0.00 41.70 4.35
741 864 1.153208 CATGGAGGCTGGAGCTGAC 60.153 63.158 0.00 0.00 41.70 3.51
742 865 1.306397 TCATGGAGGCTGGAGCTGA 60.306 57.895 0.00 0.00 41.70 4.26
743 866 1.153208 GTCATGGAGGCTGGAGCTG 60.153 63.158 0.00 0.00 41.70 4.24
744 867 2.729479 CGTCATGGAGGCTGGAGCT 61.729 63.158 0.00 0.00 41.70 4.09
745 868 2.202987 CGTCATGGAGGCTGGAGC 60.203 66.667 0.00 0.00 41.14 4.70
746 869 2.202987 GCGTCATGGAGGCTGGAG 60.203 66.667 0.00 0.00 39.86 3.86
747 870 1.048160 TATGCGTCATGGAGGCTGGA 61.048 55.000 11.54 0.00 42.87 3.86
748 871 0.035881 ATATGCGTCATGGAGGCTGG 59.964 55.000 11.54 0.00 42.87 4.85
749 872 1.436600 GATATGCGTCATGGAGGCTG 58.563 55.000 11.54 0.00 42.87 4.85
750 873 0.322975 GGATATGCGTCATGGAGGCT 59.677 55.000 11.54 0.00 42.87 4.58
751 874 1.016130 CGGATATGCGTCATGGAGGC 61.016 60.000 8.66 4.12 42.76 4.70
752 875 0.318441 ACGGATATGCGTCATGGAGG 59.682 55.000 17.18 0.00 0.00 4.30
753 876 1.269778 ACACGGATATGCGTCATGGAG 60.270 52.381 20.08 9.94 0.00 3.86
757 880 0.318699 CGGACACGGATATGCGTCAT 60.319 55.000 20.08 10.96 36.18 3.06
884 1024 3.387091 ACGTACGCCATGGCCTGA 61.387 61.111 30.79 13.41 37.98 3.86
977 1141 0.179179 GGAAGGGTCGTACGAGAACG 60.179 60.000 20.18 0.00 44.19 3.95
994 1158 1.404181 CGGAAGAAGCTTCATCGTGGA 60.404 52.381 27.57 0.00 0.00 4.02
1042 1209 7.923344 CACACTATTGAGATTTAGAACGAGGAT 59.077 37.037 0.00 0.00 0.00 3.24
1104 1271 0.532862 AGGTGTTGCTGGACGACTTG 60.533 55.000 0.00 0.00 33.33 3.16
1113 1280 1.871080 AGACGAAGAAGGTGTTGCTG 58.129 50.000 0.00 0.00 0.00 4.41
1172 1343 1.292223 CGACATCTTGGTGACGGGT 59.708 57.895 0.00 0.00 34.51 5.28
1279 1454 5.579511 CCAATGAAATCTGACTGGATTTTGC 59.420 40.000 4.34 0.00 43.36 3.68
1358 1852 2.474816 CTACTTAGGCCAATCACGCTC 58.525 52.381 5.01 0.00 0.00 5.03
1512 2048 1.305219 TGCTCCACATTAGCCGCAAC 61.305 55.000 0.00 0.00 39.30 4.17
1706 2243 5.906113 ATGAGGTGTATAGGTCGATGATC 57.094 43.478 0.00 0.00 0.00 2.92
1725 2262 7.384932 CGCATGATCCACAATACTAGTAAATGA 59.615 37.037 20.07 8.88 0.00 2.57
1771 2308 9.230122 TCTAAAATAATGAGACACTTTGCATGA 57.770 29.630 0.00 0.00 0.00 3.07
1893 2436 5.390356 GCGCTTGAATTGCTTAGATAGATCC 60.390 44.000 0.00 0.00 0.00 3.36
2295 2851 7.566760 TCTTTACTGTAAATGTGGCATATGG 57.433 36.000 12.95 0.00 0.00 2.74
2313 2873 9.804758 ACTTGTATAGCTAGAACACATCTTTAC 57.195 33.333 10.42 0.00 39.71 2.01
2340 2900 5.710567 AGAGCCGTATATATGCAAGTACTCA 59.289 40.000 0.00 0.00 0.00 3.41
2364 2927 3.120792 GTGGAATCGCGTTGAGCTTATA 58.879 45.455 5.77 0.00 45.59 0.98
2378 2941 5.390613 ACAAAAATCAATCGACGTGGAATC 58.609 37.500 3.81 0.00 0.00 2.52
2417 2986 1.336517 CCTTAGAACACGTTGCCTCGA 60.337 52.381 4.73 0.00 34.70 4.04
2420 2989 0.763035 ACCCTTAGAACACGTTGCCT 59.237 50.000 0.00 0.00 0.00 4.75
2456 3028 1.287041 GACCGAACAACCACTACCGC 61.287 60.000 0.00 0.00 0.00 5.68
2485 3057 9.349713 AGCCCAAATAAAATAAATACATCGAGA 57.650 29.630 0.00 0.00 0.00 4.04
2522 3094 5.996644 TGATCGGTTATAAGGTTCACCATT 58.003 37.500 0.00 0.00 38.89 3.16
2526 3098 6.036844 GGACTTTGATCGGTTATAAGGTTCAC 59.963 42.308 0.00 0.00 0.00 3.18
2539 3111 5.181690 TGTTGAAAAAGGACTTTGATCGG 57.818 39.130 0.00 0.00 32.36 4.18
2540 3112 7.518731 TTTTGTTGAAAAAGGACTTTGATCG 57.481 32.000 0.00 0.00 32.36 3.69
2666 3238 8.682936 ATGAACTAATTAAATGCCGAAGATCT 57.317 30.769 0.00 0.00 0.00 2.75
2697 3269 7.681065 GCATAAAGGTGTATTTGGATGGTGTAC 60.681 40.741 0.00 0.00 0.00 2.90
2759 3331 0.109597 GCAAACAAGCATCTCGGTGG 60.110 55.000 0.00 0.00 0.00 4.61
2900 3474 3.747193 CGAAGTCGACAATTTTGATGGG 58.253 45.455 19.50 0.00 43.02 4.00
2920 3494 0.239082 ACAGTGTCACAATGCATGCG 59.761 50.000 14.09 0.76 32.35 4.73
2948 3523 1.151668 GCGTTGACTGCACAAGAGAT 58.848 50.000 0.00 0.00 0.00 2.75
3061 3636 4.812476 CGATTGCCGGCTGGACGA 62.812 66.667 29.70 7.10 37.49 4.20


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

AutoCloner maintained by Alex Coulton.