Multiple sequence alignment - TraesCS2A01G396900

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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 TraesCS2A01G396900 chr2A 100.000 3490 0 0 1 3490 650629917 650626428 0.000000e+00 6445
1 TraesCS2A01G396900 chr2D 93.265 2539 102 27 972 3478 506145908 506143407 0.000000e+00 3677
2 TraesCS2A01G396900 chr2D 95.948 691 12 3 1 689 506147855 506147179 0.000000e+00 1107
3 TraesCS2A01G396900 chr2D 81.034 290 19 21 691 966 506147106 506146839 7.640000e-47 198
4 TraesCS2A01G396900 chr2B 91.213 2515 134 38 1000 3478 593656716 593654253 0.000000e+00 3339
5 TraesCS2A01G396900 chr2B 91.556 983 40 21 1 966 593658547 593657591 0.000000e+00 1315


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 TraesCS2A01G396900 chr2A 650626428 650629917 3489 True 6445.000000 6445 100.000000 1 3490 1 chr2A.!!$R1 3489
1 TraesCS2A01G396900 chr2D 506143407 506147855 4448 True 1660.666667 3677 90.082333 1 3478 3 chr2D.!!$R1 3477
2 TraesCS2A01G396900 chr2B 593654253 593658547 4294 True 2327.000000 3339 91.384500 1 3478 2 chr2B.!!$R1 3477

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
995 2027 0.317160 AGACGTTCCACGATTCAGCA 59.683 50.0 2.75 0.0 46.05 4.41 F
1827 2879 0.037326 TCAAGGTGCCACTCGATCAC 60.037 55.0 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 3269 0.034896 AGTCCACGAAATGCGAACCT 59.965 50.0 0.0 0.0 44.57 3.50 R
3316 4406 1.167851 CATGCACACGGAAGAATGGT 58.832 50.0 0.0 0.0 0.00 3.55 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
57 58 1.499049 GAGTTCCTCCACGTCACAAC 58.501 55.000 0.00 0.00 0.00 3.32
317 320 8.189119 TGGTAATGGAGTTATTTTTGCTTCTT 57.811 30.769 0.00 0.00 0.00 2.52
486 489 6.802608 TGTGGTTCCTATATAAGTGAACGAG 58.197 40.000 0.00 0.00 36.78 4.18
670 673 6.882656 TGGCTTTATAAATGCATTTGCCTTA 58.117 32.000 33.08 20.93 41.18 2.69
723 802 4.455533 CAGTGCAGCTGTGGAAACTTATTA 59.544 41.667 16.64 0.00 40.27 0.98
758 839 1.507141 GATGCATTCCCCCGTTAGCG 61.507 60.000 0.00 0.00 37.95 4.26
771 852 1.859080 CGTTAGCGGGAACAAGATAGC 59.141 52.381 0.00 0.00 0.00 2.97
772 853 2.737359 CGTTAGCGGGAACAAGATAGCA 60.737 50.000 0.00 0.00 0.00 3.49
773 854 2.866762 GTTAGCGGGAACAAGATAGCAG 59.133 50.000 0.00 0.00 0.00 4.24
774 855 0.462759 AGCGGGAACAAGATAGCAGC 60.463 55.000 0.00 0.00 0.00 5.25
775 856 0.744414 GCGGGAACAAGATAGCAGCA 60.744 55.000 0.00 0.00 0.00 4.41
776 857 1.737838 CGGGAACAAGATAGCAGCAA 58.262 50.000 0.00 0.00 0.00 3.91
777 858 2.292267 CGGGAACAAGATAGCAGCAAT 58.708 47.619 0.00 0.00 0.00 3.56
815 913 2.186903 CTGTACCGCGCCCAATCT 59.813 61.111 0.00 0.00 0.00 2.40
826 924 1.139654 CGCCCAATCTTCTCATCCAGA 59.860 52.381 0.00 0.00 0.00 3.86
828 926 3.746751 CGCCCAATCTTCTCATCCAGATT 60.747 47.826 0.00 0.00 39.83 2.40
869 968 2.700371 TCCTCTTGAAGCAGTCAGACAA 59.300 45.455 2.66 0.00 37.61 3.18
891 990 3.981211 TGACCTTGTCAAACGGTACTAC 58.019 45.455 0.00 0.00 39.78 2.73
894 993 2.030007 CCTTGTCAAACGGTACTACGGA 60.030 50.000 1.00 0.00 38.39 4.69
895 994 3.367703 CCTTGTCAAACGGTACTACGGAT 60.368 47.826 1.00 0.00 38.39 4.18
896 995 4.142403 CCTTGTCAAACGGTACTACGGATA 60.142 45.833 1.00 0.00 38.39 2.59
897 996 4.355543 TGTCAAACGGTACTACGGATAC 57.644 45.455 1.00 0.00 38.39 2.24
923 1022 2.495809 CAGGCACCATAAGCATGCA 58.504 52.632 21.98 0.00 41.27 3.96
924 1023 0.384309 CAGGCACCATAAGCATGCAG 59.616 55.000 21.98 6.47 41.27 4.41
925 1024 1.066918 GGCACCATAAGCATGCAGC 59.933 57.895 21.98 11.12 41.27 5.25
953 1053 4.515404 GCCCAGCGTACGAGAATT 57.485 55.556 21.65 0.00 0.00 2.17
966 1066 6.093404 CGTACGAGAATTGGATATATGCAGT 58.907 40.000 10.44 1.58 0.00 4.40
967 1067 6.251589 CGTACGAGAATTGGATATATGCAGTC 59.748 42.308 10.44 8.96 0.00 3.51
969 1069 5.247110 ACGAGAATTGGATATATGCAGTCCT 59.753 40.000 7.03 0.00 33.15 3.85
977 2009 6.427441 TGGATATATGCAGTCCTACCTAGAG 58.573 44.000 2.31 0.00 33.15 2.43
981 2013 1.281287 TGCAGTCCTACCTAGAGACGT 59.719 52.381 0.00 0.00 35.65 4.34
988 2020 2.625737 CTACCTAGAGACGTTCCACGA 58.374 52.381 2.75 0.00 46.05 4.35
991 2023 2.422832 ACCTAGAGACGTTCCACGATTC 59.577 50.000 2.75 0.56 46.05 2.52
992 2024 2.422479 CCTAGAGACGTTCCACGATTCA 59.578 50.000 2.75 0.00 46.05 2.57
993 2025 2.638556 AGAGACGTTCCACGATTCAG 57.361 50.000 2.75 0.00 46.05 3.02
994 2026 0.992802 GAGACGTTCCACGATTCAGC 59.007 55.000 2.75 0.00 46.05 4.26
995 2027 0.317160 AGACGTTCCACGATTCAGCA 59.683 50.000 2.75 0.00 46.05 4.41
998 2039 2.535984 GACGTTCCACGATTCAGCATAG 59.464 50.000 2.75 0.00 46.05 2.23
1016 2057 4.554036 GATGGCCGTGCTCCCTCC 62.554 72.222 0.00 0.00 0.00 4.30
1057 2098 3.547567 ACAGCAGTGATCTTGCTCC 57.452 52.632 18.47 0.00 36.69 4.70
1062 2103 2.157738 GCAGTGATCTTGCTCCTGTTT 58.842 47.619 13.39 0.00 0.00 2.83
1063 2104 2.161211 GCAGTGATCTTGCTCCTGTTTC 59.839 50.000 13.39 0.00 0.00 2.78
1065 2106 1.129437 GTGATCTTGCTCCTGTTTCGC 59.871 52.381 0.00 0.00 0.00 4.70
1248 2289 1.064463 AGGACCATTGCGGATGTCATT 60.064 47.619 0.00 0.00 38.63 2.57
1384 2428 1.562672 TTGCTCCTCCCTACTTGGCC 61.563 60.000 0.00 0.00 0.00 5.36
1468 2512 1.154073 CGACGAGACCGGTTCCTTC 60.154 63.158 9.42 6.07 40.78 3.46
1471 2515 2.022934 GACGAGACCGGTTCCTTCTAT 58.977 52.381 9.42 0.00 40.78 1.98
1475 2519 3.379372 CGAGACCGGTTCCTTCTATGTAA 59.621 47.826 9.42 0.00 0.00 2.41
1485 2529 8.175716 CGGTTCCTTCTATGTAAGTGATTTTTC 58.824 37.037 0.00 0.00 0.00 2.29
1486 2530 9.232473 GGTTCCTTCTATGTAAGTGATTTTTCT 57.768 33.333 0.00 0.00 0.00 2.52
1519 2566 5.885912 TGTATACTTCCCTTGGCTTGATTTC 59.114 40.000 4.17 0.00 0.00 2.17
1520 2567 3.532641 ACTTCCCTTGGCTTGATTTCT 57.467 42.857 0.00 0.00 0.00 2.52
1521 2568 3.160269 ACTTCCCTTGGCTTGATTTCTG 58.840 45.455 0.00 0.00 0.00 3.02
1522 2569 2.978156 TCCCTTGGCTTGATTTCTGT 57.022 45.000 0.00 0.00 0.00 3.41
1523 2570 2.795329 TCCCTTGGCTTGATTTCTGTC 58.205 47.619 0.00 0.00 0.00 3.51
1524 2571 2.376518 TCCCTTGGCTTGATTTCTGTCT 59.623 45.455 0.00 0.00 0.00 3.41
1525 2572 2.490903 CCCTTGGCTTGATTTCTGTCTG 59.509 50.000 0.00 0.00 0.00 3.51
1526 2573 3.152341 CCTTGGCTTGATTTCTGTCTGT 58.848 45.455 0.00 0.00 0.00 3.41
1527 2574 3.190118 CCTTGGCTTGATTTCTGTCTGTC 59.810 47.826 0.00 0.00 0.00 3.51
1528 2575 3.777106 TGGCTTGATTTCTGTCTGTCT 57.223 42.857 0.00 0.00 0.00 3.41
1627 2679 1.554836 TGAGAAGACCAGAGCTCAGG 58.445 55.000 22.70 22.70 32.85 3.86
1650 2702 0.046242 TGGAGACCATGGGGGAGAAT 59.954 55.000 18.09 0.00 41.15 2.40
1672 2724 3.702048 CGGCCGACTTCTTGGGGA 61.702 66.667 24.07 0.00 0.00 4.81
1674 2726 1.674651 GGCCGACTTCTTGGGGAAC 60.675 63.158 0.00 0.00 0.00 3.62
1743 2795 0.242825 CACCTGCAGTGCCATTCTTG 59.757 55.000 13.72 0.00 40.28 3.02
1755 2807 2.778299 CCATTCTTGGGACGACAGAAA 58.222 47.619 0.00 0.00 39.56 2.52
1769 2821 0.109342 CAGAAACCTGACCCTGCAGT 59.891 55.000 13.81 0.00 34.06 4.40
1773 2825 1.692411 AACCTGACCCTGCAGTTTTC 58.308 50.000 13.81 6.25 34.06 2.29
1822 2874 0.247460 TCATCTCAAGGTGCCACTCG 59.753 55.000 0.00 0.00 0.00 4.18
1823 2875 0.247460 CATCTCAAGGTGCCACTCGA 59.753 55.000 0.00 0.00 0.00 4.04
1824 2876 1.134580 CATCTCAAGGTGCCACTCGAT 60.135 52.381 0.00 0.00 0.00 3.59
1826 2878 0.247460 CTCAAGGTGCCACTCGATCA 59.753 55.000 0.00 0.00 0.00 2.92
1827 2879 0.037326 TCAAGGTGCCACTCGATCAC 60.037 55.000 0.00 0.00 0.00 3.06
1829 2881 2.982130 GGTGCCACTCGATCACCT 59.018 61.111 14.94 0.00 45.04 4.00
1832 2884 1.103803 GTGCCACTCGATCACCTCTA 58.896 55.000 0.00 0.00 0.00 2.43
1837 2889 2.032302 CCACTCGATCACCTCTAACTCG 59.968 54.545 0.00 0.00 0.00 4.18
1863 2923 4.757149 AGTCACCAGCACTGTAATTTTCTC 59.243 41.667 0.00 0.00 0.00 2.87
1876 2936 1.238439 TTTTCTCTGCTTTGCTCCCG 58.762 50.000 0.00 0.00 0.00 5.14
1899 2959 2.026542 TCTGAGCTCACCATCTTGCAAT 60.027 45.455 13.74 0.00 0.00 3.56
1988 3048 1.881252 GGGCTGCATACCGTACGTG 60.881 63.158 15.21 7.27 0.00 4.49
2038 3098 2.664851 TTCGGCGGCTGTGAACAG 60.665 61.111 7.21 6.08 46.40 3.16
2059 3119 1.354040 CTCTGCGAAGGCTACAACAG 58.646 55.000 0.00 0.00 40.82 3.16
2309 3370 3.197790 CCGCCGTTCCTCTGCATG 61.198 66.667 0.00 0.00 0.00 4.06
2538 3618 1.592223 GCGGAATATCTCCTCCCCG 59.408 63.158 0.00 0.00 42.85 5.73
2561 3642 0.316442 CAACACTTGCTGCACGTCTG 60.316 55.000 8.97 6.20 0.00 3.51
2633 3716 9.823647 AATTTTCTTTTCTTTTTCCTTCTCTCC 57.176 29.630 0.00 0.00 0.00 3.71
2638 3721 2.368875 TCTTTTTCCTTCTCTCCGCTGT 59.631 45.455 0.00 0.00 0.00 4.40
2695 3778 0.234884 CGCTGTTGTCGAAAGGAACC 59.765 55.000 0.00 0.00 0.00 3.62
2703 3786 2.000447 GTCGAAAGGAACCATTCGGAG 59.000 52.381 23.91 4.33 44.59 4.63
2817 3904 1.504359 TTTTACGGGACTGTTCTGCG 58.496 50.000 0.00 0.00 0.00 5.18
2901 3988 2.954753 GCGCAACACTTGGACTCGG 61.955 63.158 0.30 0.00 0.00 4.63
3157 4247 3.775654 CTGGTCCTCCTCGGCACC 61.776 72.222 0.00 0.00 35.05 5.01
3316 4406 1.003118 AGTTGCTTCACCTGCCGAATA 59.997 47.619 0.00 0.00 0.00 1.75
3330 4420 2.901249 CCGAATACCATTCTTCCGTGT 58.099 47.619 0.00 0.00 0.00 4.49
3352 4442 3.269178 GCATGCAGTAGCTTCTCTTCTT 58.731 45.455 14.21 0.00 42.74 2.52
3365 4455 1.642843 CTCTTCTTTCGACACGTACGC 59.357 52.381 16.72 0.00 0.00 4.42
3372 4462 3.170585 GACACGTACGCGCCTGTC 61.171 66.667 16.72 17.18 42.83 3.51
3443 4533 2.093288 CAGACCAGATGTACACAGCCAT 60.093 50.000 0.00 0.00 31.57 4.40
3444 4534 3.132824 CAGACCAGATGTACACAGCCATA 59.867 47.826 0.00 0.00 31.57 2.74
3445 4535 3.133003 AGACCAGATGTACACAGCCATAC 59.867 47.826 0.00 0.00 31.57 2.39
3458 4548 6.049149 ACACAGCCATACTACATATGTTCAC 58.951 40.000 14.77 0.00 39.36 3.18
3478 4568 4.518970 TCACCTTTTGTTTCTATGTCCAGC 59.481 41.667 0.00 0.00 0.00 4.85
3479 4569 3.826729 ACCTTTTGTTTCTATGTCCAGCC 59.173 43.478 0.00 0.00 0.00 4.85
3480 4570 3.119849 CCTTTTGTTTCTATGTCCAGCCG 60.120 47.826 0.00 0.00 0.00 5.52
3481 4571 2.851263 TTGTTTCTATGTCCAGCCGT 57.149 45.000 0.00 0.00 0.00 5.68
3482 4572 2.380084 TGTTTCTATGTCCAGCCGTC 57.620 50.000 0.00 0.00 0.00 4.79
3483 4573 1.066430 TGTTTCTATGTCCAGCCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
3484 4574 1.066430 GTTTCTATGTCCAGCCGTCCA 60.066 52.381 0.00 0.00 0.00 4.02
3485 4575 0.824109 TTCTATGTCCAGCCGTCCAG 59.176 55.000 0.00 0.00 0.00 3.86
3486 4576 1.043116 TCTATGTCCAGCCGTCCAGG 61.043 60.000 0.00 0.00 44.97 4.45
3487 4577 1.001120 TATGTCCAGCCGTCCAGGA 59.999 57.895 0.00 0.00 45.00 3.86
3488 4578 0.398522 TATGTCCAGCCGTCCAGGAT 60.399 55.000 0.00 0.00 45.00 3.24
3489 4579 1.690219 ATGTCCAGCCGTCCAGGATC 61.690 60.000 0.00 0.00 45.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.591659 TCACTCGGCTATTCGGATCG 59.408 55.000 0.00 0.00 0.00 3.69
171 172 3.057734 GGACCTACTCAACTGAAACACG 58.942 50.000 0.00 0.00 0.00 4.49
486 489 4.226113 AGTCGAAGTTCACTGTGACTAC 57.774 45.455 10.56 7.25 38.60 2.73
570 573 4.418013 TTGCTGATAACGTTCCACAATG 57.582 40.909 2.82 0.00 0.00 2.82
580 583 4.818534 ATACTGCCATTTGCTGATAACG 57.181 40.909 0.00 0.00 41.11 3.18
670 673 0.761187 ATGGCAGATGCATCCGTACT 59.239 50.000 23.06 0.84 44.36 2.73
723 802 8.416329 GGGAATGCATCTGTCTTACAAAATAAT 58.584 33.333 0.00 0.00 0.00 1.28
731 812 2.576615 GGGGGAATGCATCTGTCTTAC 58.423 52.381 0.00 0.00 0.00 2.34
758 839 4.261363 GCTAATTGCTGCTATCTTGTTCCC 60.261 45.833 0.00 0.00 38.95 3.97
760 841 5.490139 TGCTAATTGCTGCTATCTTGTTC 57.510 39.130 0.00 0.00 43.37 3.18
762 843 4.885907 ACATGCTAATTGCTGCTATCTTGT 59.114 37.500 0.00 0.00 43.37 3.16
763 844 5.238868 AGACATGCTAATTGCTGCTATCTTG 59.761 40.000 0.00 0.00 43.37 3.02
765 846 4.755629 CAGACATGCTAATTGCTGCTATCT 59.244 41.667 0.00 0.00 43.37 1.98
766 847 4.753610 TCAGACATGCTAATTGCTGCTATC 59.246 41.667 0.00 0.00 43.37 2.08
767 848 4.514441 GTCAGACATGCTAATTGCTGCTAT 59.486 41.667 0.00 0.00 43.37 2.97
768 849 3.873361 GTCAGACATGCTAATTGCTGCTA 59.127 43.478 0.00 0.00 43.37 3.49
769 850 2.681848 GTCAGACATGCTAATTGCTGCT 59.318 45.455 0.00 0.00 43.37 4.24
770 851 2.421073 TGTCAGACATGCTAATTGCTGC 59.579 45.455 0.00 0.00 43.37 5.25
771 852 3.487042 GCTGTCAGACATGCTAATTGCTG 60.487 47.826 2.97 0.00 43.37 4.41
772 853 2.681848 GCTGTCAGACATGCTAATTGCT 59.318 45.455 2.97 0.00 43.37 3.91
773 854 2.681848 AGCTGTCAGACATGCTAATTGC 59.318 45.455 19.88 11.06 43.25 3.56
774 855 3.001026 CGAGCTGTCAGACATGCTAATTG 59.999 47.826 20.79 11.55 34.43 2.32
775 856 3.193263 CGAGCTGTCAGACATGCTAATT 58.807 45.455 20.79 6.05 34.43 1.40
776 857 2.819115 CGAGCTGTCAGACATGCTAAT 58.181 47.619 20.79 6.32 34.43 1.73
777 858 1.737029 GCGAGCTGTCAGACATGCTAA 60.737 52.381 20.79 0.00 34.43 3.09
804 895 1.502163 GGATGAGAAGATTGGGCGCG 61.502 60.000 0.00 0.00 0.00 6.86
815 913 3.845992 TCCCAACTGAATCTGGATGAGAA 59.154 43.478 0.00 0.00 34.35 2.87
826 924 4.990526 AGATTGAACTGTCCCAACTGAAT 58.009 39.130 0.00 0.00 0.00 2.57
828 926 3.244561 GGAGATTGAACTGTCCCAACTGA 60.245 47.826 0.00 0.00 0.00 3.41
869 968 3.764237 AGTACCGTTTGACAAGGTCAT 57.236 42.857 2.53 0.00 42.40 3.06
875 974 3.940209 ATCCGTAGTACCGTTTGACAA 57.060 42.857 0.00 0.00 0.00 3.18
891 990 2.313172 GCCTGCTGCATCGTATCCG 61.313 63.158 1.31 0.00 40.77 4.18
912 1011 0.387565 TGCCATGCTGCATGCTTATG 59.612 50.000 31.84 20.61 40.20 1.90
942 1042 6.093404 ACTGCATATATCCAATTCTCGTACG 58.907 40.000 9.53 9.53 0.00 3.67
950 1050 6.959606 AGGTAGGACTGCATATATCCAATT 57.040 37.500 8.62 0.00 34.73 2.32
953 1053 6.217693 TCTCTAGGTAGGACTGCATATATCCA 59.782 42.308 8.62 0.00 34.73 3.41
966 1066 2.996631 GTGGAACGTCTCTAGGTAGGA 58.003 52.381 0.00 0.00 0.00 2.94
981 2013 3.494924 CCATCCTATGCTGAATCGTGGAA 60.495 47.826 0.00 0.00 0.00 3.53
988 2020 0.767375 ACGGCCATCCTATGCTGAAT 59.233 50.000 2.24 0.00 37.31 2.57
991 2023 2.256591 GCACGGCCATCCTATGCTG 61.257 63.158 2.24 0.00 38.43 4.41
992 2024 2.111878 GCACGGCCATCCTATGCT 59.888 61.111 2.24 0.00 38.43 3.79
993 2025 1.963338 GAGCACGGCCATCCTATGC 60.963 63.158 2.24 2.06 40.47 3.14
994 2026 1.302033 GGAGCACGGCCATCCTATG 60.302 63.158 2.24 0.00 0.00 2.23
995 2027 2.520536 GGGAGCACGGCCATCCTAT 61.521 63.158 2.24 0.00 33.40 2.57
998 2039 4.554036 GAGGGAGCACGGCCATCC 62.554 72.222 2.24 3.96 30.30 3.51
1029 2070 3.529252 CACTGCTGTGAAGAGGGAG 57.471 57.895 18.08 0.00 46.55 4.30
1051 2092 0.960364 GATGGGCGAAACAGGAGCAA 60.960 55.000 0.00 0.00 0.00 3.91
1057 2098 1.815421 CCGGAGATGGGCGAAACAG 60.815 63.158 0.00 0.00 0.00 3.16
1065 2106 4.996434 GGCGATGCCGGAGATGGG 62.996 72.222 5.05 0.00 39.62 4.00
1248 2289 9.595823 GAAAACTCATACTTGCTACTATTACCA 57.404 33.333 0.00 0.00 0.00 3.25
1384 2428 3.070018 CACTTCAGCACTAGAGTTTGGG 58.930 50.000 0.00 0.00 0.00 4.12
1471 2515 8.519526 ACAAGTTGAACAGAAAAATCACTTACA 58.480 29.630 10.54 0.00 0.00 2.41
1485 2529 6.149474 CCAAGGGAAGTATACAAGTTGAACAG 59.851 42.308 10.54 0.00 0.00 3.16
1486 2530 6.001460 CCAAGGGAAGTATACAAGTTGAACA 58.999 40.000 10.54 0.00 0.00 3.18
1487 2531 5.106277 GCCAAGGGAAGTATACAAGTTGAAC 60.106 44.000 10.54 4.88 0.00 3.18
1490 2534 4.589908 AGCCAAGGGAAGTATACAAGTTG 58.410 43.478 5.50 0.00 0.00 3.16
1519 2566 3.396560 TGCAATTCAGACAGACAGACAG 58.603 45.455 0.00 0.00 0.00 3.51
1520 2567 3.473923 TGCAATTCAGACAGACAGACA 57.526 42.857 0.00 0.00 0.00 3.41
1521 2568 5.152097 CAATTGCAATTCAGACAGACAGAC 58.848 41.667 21.70 0.00 0.00 3.51
1522 2569 4.823442 ACAATTGCAATTCAGACAGACAGA 59.177 37.500 21.70 0.00 0.00 3.41
1523 2570 4.915667 CACAATTGCAATTCAGACAGACAG 59.084 41.667 21.70 9.15 0.00 3.51
1524 2571 4.338964 ACACAATTGCAATTCAGACAGACA 59.661 37.500 21.70 0.00 0.00 3.41
1525 2572 4.678287 CACACAATTGCAATTCAGACAGAC 59.322 41.667 21.70 0.00 0.00 3.51
1526 2573 4.579753 TCACACAATTGCAATTCAGACAGA 59.420 37.500 21.70 11.91 0.00 3.41
1527 2574 4.862350 TCACACAATTGCAATTCAGACAG 58.138 39.130 21.70 11.92 0.00 3.51
1528 2575 4.915158 TCACACAATTGCAATTCAGACA 57.085 36.364 21.70 3.83 0.00 3.41
1627 2679 0.326238 TCCCCCATGGTCTCCAGTAC 60.326 60.000 11.73 0.00 36.75 2.73
1650 2702 3.936203 AAGAAGTCGGCCGTGGCA 61.936 61.111 27.15 1.49 44.11 4.92
1654 2706 4.016706 CCCCAAGAAGTCGGCCGT 62.017 66.667 27.15 5.51 0.00 5.68
1743 2795 0.320508 GGTCAGGTTTCTGTCGTCCC 60.321 60.000 0.00 0.00 41.59 4.46
1755 2807 0.178990 GGAAAACTGCAGGGTCAGGT 60.179 55.000 19.93 0.00 38.36 4.00
1769 2821 0.106419 AACCAAGGCGTCCTGGAAAA 60.106 50.000 12.63 0.00 32.13 2.29
1773 2825 3.365265 GCAACCAAGGCGTCCTGG 61.365 66.667 2.27 2.27 32.13 4.45
1809 2861 1.021390 GGTGATCGAGTGGCACCTTG 61.021 60.000 15.27 4.41 46.56 3.61
1822 2874 3.878103 TGACTAGCGAGTTAGAGGTGATC 59.122 47.826 0.00 0.00 35.45 2.92
1823 2875 3.628487 GTGACTAGCGAGTTAGAGGTGAT 59.372 47.826 0.00 0.00 35.45 3.06
1824 2876 3.008330 GTGACTAGCGAGTTAGAGGTGA 58.992 50.000 0.00 0.00 35.45 4.02
1826 2878 2.290768 TGGTGACTAGCGAGTTAGAGGT 60.291 50.000 0.00 0.00 35.45 3.85
1827 2879 2.356382 CTGGTGACTAGCGAGTTAGAGG 59.644 54.545 0.00 0.00 35.45 3.69
1828 2880 2.223386 GCTGGTGACTAGCGAGTTAGAG 60.223 54.545 4.89 0.00 35.45 2.43
1829 2881 1.743958 GCTGGTGACTAGCGAGTTAGA 59.256 52.381 4.89 0.00 35.45 2.10
1832 2884 0.038159 GTGCTGGTGACTAGCGAGTT 60.038 55.000 16.13 0.00 44.01 3.01
1837 2889 2.743636 TTACAGTGCTGGTGACTAGC 57.256 50.000 14.42 14.42 41.49 3.42
1863 2923 0.603707 TCAGAACGGGAGCAAAGCAG 60.604 55.000 0.00 0.00 0.00 4.24
1876 2936 1.736681 GCAAGATGGTGAGCTCAGAAC 59.263 52.381 18.89 11.29 0.00 3.01
2038 3098 1.079127 TTGTAGCCTTCGCAGAGCC 60.079 57.895 0.00 0.00 38.43 4.70
2059 3119 1.000731 CGATCATCCTCTTCAGCCTCC 59.999 57.143 0.00 0.00 0.00 4.30
2209 3269 0.034896 AGTCCACGAAATGCGAACCT 59.965 50.000 0.00 0.00 44.57 3.50
2583 3664 1.300697 GCGTCAAAGTCACCGTCCT 60.301 57.895 0.00 0.00 0.00 3.85
2584 3665 2.654912 CGCGTCAAAGTCACCGTCC 61.655 63.158 0.00 0.00 0.00 4.79
2728 3814 4.757354 TACACCGCACGTACGCCG 62.757 66.667 16.72 17.76 44.03 6.46
2865 3952 2.660944 CGCATATATACCCGCGTGG 58.339 57.895 8.42 8.42 42.66 4.94
2901 3988 3.103911 CGGCCGTCGTCAACAGAC 61.104 66.667 19.50 0.00 35.41 3.51
3279 4369 2.800544 CAACTGCAAGCTACGTACAAGT 59.199 45.455 0.00 0.00 37.60 3.16
3281 4371 1.529438 GCAACTGCAAGCTACGTACAA 59.471 47.619 0.00 0.00 41.59 2.41
3316 4406 1.167851 CATGCACACGGAAGAATGGT 58.832 50.000 0.00 0.00 0.00 3.55
3330 4420 2.235650 AGAAGAGAAGCTACTGCATGCA 59.764 45.455 21.29 21.29 42.74 3.96
3352 4442 4.029186 AGGCGCGTACGTGTCGAA 62.029 61.111 27.72 0.00 42.83 3.71
3365 4455 4.033358 CAGAGCAAACTAATTAGACAGGCG 59.967 45.833 19.38 2.79 0.00 5.52
3372 4462 5.353678 AGAAGCAGCAGAGCAAACTAATTAG 59.646 40.000 11.05 11.05 36.85 1.73
3443 4533 9.787435 AGAAACAAAAGGTGAACATATGTAGTA 57.213 29.630 9.21 0.00 0.00 1.82
3444 4534 8.691661 AGAAACAAAAGGTGAACATATGTAGT 57.308 30.769 9.21 0.00 0.00 2.73
3458 4548 3.119849 CGGCTGGACATAGAAACAAAAGG 60.120 47.826 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.