Multiple sequence alignment - TraesCS6D01G157200

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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 TraesCS6D01G157200 chr6D 100.000 4624 0 0 1 4624 133230406 133225783 0.000000e+00 8540
1 TraesCS6D01G157200 chr6A 91.037 3559 205 54 825 4354 172134686 172131213 0.000000e+00 4700
2 TraesCS6D01G157200 chr6A 91.213 239 9 3 4386 4624 172130867 172130641 9.660000e-82 315
3 TraesCS6D01G157200 chr6B 95.232 1447 52 11 826 2262 231685855 231684416 0.000000e+00 2274
4 TraesCS6D01G157200 chr6B 95.136 1439 50 11 2314 3744 231684421 231682995 0.000000e+00 2252
5 TraesCS6D01G157200 chr6B 90.079 887 25 23 3769 4624 231682923 231682069 0.000000e+00 1092
6 TraesCS6D01G157200 chr5A 90.488 778 65 8 1 775 55166750 55165979 0.000000e+00 1018
7 TraesCS6D01G157200 chr3A 90.360 778 66 8 1 775 668399976 668399205 0.000000e+00 1013
8 TraesCS6D01G157200 chr1A 90.379 738 67 4 40 775 554768119 554767384 0.000000e+00 966
9 TraesCS6D01G157200 chr7B 88.212 755 81 6 1 752 205381476 205380727 0.000000e+00 894
10 TraesCS6D01G157200 chr7B 76.516 643 143 8 1 640 624241533 624242170 1.230000e-90 344
11 TraesCS6D01G157200 chr7B 74.005 804 172 33 1 776 488708915 488708121 4.530000e-75 292
12 TraesCS6D01G157200 chr1B 75.980 791 163 21 1 775 592966579 592967358 2.610000e-102 383
13 TraesCS6D01G157200 chr2A 76.531 686 129 23 108 775 4397062 4397733 3.420000e-91 346
14 TraesCS6D01G157200 chr7D 73.832 642 154 12 5 640 497903081 497902448 4.620000e-60 243
15 TraesCS6D01G157200 chr2B 73.112 543 137 9 27 564 109154815 109154277 7.900000e-43 185


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 TraesCS6D01G157200 chr6D 133225783 133230406 4623 True 8540.000000 8540 100.000000 1 4624 1 chr6D.!!$R1 4623
1 TraesCS6D01G157200 chr6A 172130641 172134686 4045 True 2507.500000 4700 91.125000 825 4624 2 chr6A.!!$R1 3799
2 TraesCS6D01G157200 chr6B 231682069 231685855 3786 True 1872.666667 2274 93.482333 826 4624 3 chr6B.!!$R1 3798
3 TraesCS6D01G157200 chr5A 55165979 55166750 771 True 1018.000000 1018 90.488000 1 775 1 chr5A.!!$R1 774
4 TraesCS6D01G157200 chr3A 668399205 668399976 771 True 1013.000000 1013 90.360000 1 775 1 chr3A.!!$R1 774
5 TraesCS6D01G157200 chr1A 554767384 554768119 735 True 966.000000 966 90.379000 40 775 1 chr1A.!!$R1 735
6 TraesCS6D01G157200 chr7B 205380727 205381476 749 True 894.000000 894 88.212000 1 752 1 chr7B.!!$R1 751
7 TraesCS6D01G157200 chr7B 624241533 624242170 637 False 344.000000 344 76.516000 1 640 1 chr7B.!!$F1 639
8 TraesCS6D01G157200 chr7B 488708121 488708915 794 True 292.000000 292 74.005000 1 776 1 chr7B.!!$R2 775
9 TraesCS6D01G157200 chr1B 592966579 592967358 779 False 383.000000 383 75.980000 1 775 1 chr1B.!!$F1 774
10 TraesCS6D01G157200 chr2A 4397062 4397733 671 False 346.000000 346 76.531000 108 775 1 chr2A.!!$F1 667
11 TraesCS6D01G157200 chr7D 497902448 497903081 633 True 243.000000 243 73.832000 5 640 1 chr7D.!!$R1 635

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
384 387 0.038744 CCTCTTGCACCAAGTCCCAT 59.961 55.0 5.03 0.00 41.66 4.00 F
816 846 0.105593 GGCCTCTCGATGCATGAAGA 59.894 55.0 2.46 5.65 0.00 2.87 F
1694 1741 0.172803 ACGATGAGCGGTACAAGGAC 59.827 55.0 0.00 0.00 46.49 3.85 F
2953 3007 0.615850 GCTAGGAGCAAAGACAGGGT 59.384 55.0 0.00 0.00 41.89 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1498 0.587242 CATCGAAGAAACCATGCGCG 60.587 55.0 0.00 0.00 43.58 6.86 R
2584 2638 1.151777 ATTTGCGTACGGGCTGATCG 61.152 55.0 18.39 5.42 0.00 3.69 R
3251 3306 0.439985 CAATGGAGTTGACACGAGCG 59.560 55.0 0.00 0.00 40.37 5.03 R
4456 4921 0.248661 GCTGCTGCTGAATGCTGATG 60.249 55.0 10.92 0.00 42.27 3.07 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
66 67 2.644299 TGGTGACATCAATTCTGACCCT 59.356 45.455 0.00 0.00 33.30 4.34
209 211 6.470278 TGCATCCAGATGTCTATCTTATTGG 58.530 40.000 9.29 0.00 41.71 3.16
220 222 9.775539 ATGTCTATCTTATTGGGAGCTATAGAA 57.224 33.333 3.21 0.00 0.00 2.10
224 226 9.249053 CTATCTTATTGGGAGCTATAGAAGACA 57.751 37.037 3.21 0.00 0.00 3.41
373 376 1.066858 GTCGGATCTTCACCTCTTGCA 60.067 52.381 0.00 0.00 0.00 4.08
384 387 0.038744 CCTCTTGCACCAAGTCCCAT 59.961 55.000 5.03 0.00 41.66 4.00
419 422 3.573695 TCCTATAGAACCACTACTGGCC 58.426 50.000 0.00 0.00 42.08 5.36
498 501 0.895530 GTTCATCCTCCTCGACCACA 59.104 55.000 0.00 0.00 0.00 4.17
596 601 0.924090 GAAGCGCTGTCGTCCATTAG 59.076 55.000 12.58 0.00 38.14 1.73
597 602 0.530744 AAGCGCTGTCGTCCATTAGA 59.469 50.000 12.58 0.00 38.14 2.10
654 665 1.236282 CCTACCTTCCCGATCCCCT 59.764 63.158 0.00 0.00 0.00 4.79
711 730 3.471806 GAAGGGGAGAGGGGACGC 61.472 72.222 0.00 0.00 0.00 5.19
780 810 3.412237 CCTAACGAGAGGGGAAAACAA 57.588 47.619 0.00 0.00 32.39 2.83
781 811 3.951663 CCTAACGAGAGGGGAAAACAAT 58.048 45.455 0.00 0.00 32.39 2.71
782 812 3.689649 CCTAACGAGAGGGGAAAACAATG 59.310 47.826 0.00 0.00 32.39 2.82
783 813 1.534729 ACGAGAGGGGAAAACAATGC 58.465 50.000 0.00 0.00 0.00 3.56
784 814 1.202879 ACGAGAGGGGAAAACAATGCA 60.203 47.619 0.00 0.00 0.00 3.96
785 815 1.470098 CGAGAGGGGAAAACAATGCAG 59.530 52.381 0.00 0.00 0.00 4.41
786 816 2.519013 GAGAGGGGAAAACAATGCAGT 58.481 47.619 0.00 0.00 0.00 4.40
787 817 3.686016 GAGAGGGGAAAACAATGCAGTA 58.314 45.455 0.00 0.00 0.00 2.74
788 818 4.079253 GAGAGGGGAAAACAATGCAGTAA 58.921 43.478 0.00 0.00 0.00 2.24
789 819 4.479158 AGAGGGGAAAACAATGCAGTAAA 58.521 39.130 0.00 0.00 0.00 2.01
790 820 4.898861 AGAGGGGAAAACAATGCAGTAAAA 59.101 37.500 0.00 0.00 0.00 1.52
791 821 5.543790 AGAGGGGAAAACAATGCAGTAAAAT 59.456 36.000 0.00 0.00 0.00 1.82
792 822 6.723977 AGAGGGGAAAACAATGCAGTAAAATA 59.276 34.615 0.00 0.00 0.00 1.40
793 823 7.234577 AGAGGGGAAAACAATGCAGTAAAATAA 59.765 33.333 0.00 0.00 0.00 1.40
794 824 7.917003 AGGGGAAAACAATGCAGTAAAATAAT 58.083 30.769 0.00 0.00 0.00 1.28
795 825 8.382405 AGGGGAAAACAATGCAGTAAAATAATT 58.618 29.630 0.00 0.00 0.00 1.40
796 826 8.664798 GGGGAAAACAATGCAGTAAAATAATTC 58.335 33.333 0.00 0.00 0.00 2.17
797 827 8.379902 GGGAAAACAATGCAGTAAAATAATTCG 58.620 33.333 0.00 0.00 0.00 3.34
798 828 8.379902 GGAAAACAATGCAGTAAAATAATTCGG 58.620 33.333 0.00 0.00 0.00 4.30
799 829 6.885735 AACAATGCAGTAAAATAATTCGGC 57.114 33.333 0.00 0.00 0.00 5.54
800 830 5.348164 ACAATGCAGTAAAATAATTCGGCC 58.652 37.500 0.00 0.00 0.00 6.13
801 831 5.127031 ACAATGCAGTAAAATAATTCGGCCT 59.873 36.000 0.00 0.00 0.00 5.19
802 832 4.893424 TGCAGTAAAATAATTCGGCCTC 57.107 40.909 0.00 0.00 0.00 4.70
803 833 4.523083 TGCAGTAAAATAATTCGGCCTCT 58.477 39.130 0.00 0.00 0.00 3.69
804 834 4.574828 TGCAGTAAAATAATTCGGCCTCTC 59.425 41.667 0.00 0.00 0.00 3.20
805 835 4.318831 GCAGTAAAATAATTCGGCCTCTCG 60.319 45.833 0.00 0.00 0.00 4.04
806 836 5.047847 CAGTAAAATAATTCGGCCTCTCGA 58.952 41.667 0.00 0.00 37.38 4.04
807 837 5.696724 CAGTAAAATAATTCGGCCTCTCGAT 59.303 40.000 0.00 0.00 39.03 3.59
808 838 5.696724 AGTAAAATAATTCGGCCTCTCGATG 59.303 40.000 0.00 0.00 39.03 3.84
809 839 2.086054 ATAATTCGGCCTCTCGATGC 57.914 50.000 0.00 0.00 39.03 3.91
810 840 0.750249 TAATTCGGCCTCTCGATGCA 59.250 50.000 0.00 0.00 39.03 3.96
811 841 0.107456 AATTCGGCCTCTCGATGCAT 59.893 50.000 0.00 0.00 39.03 3.96
812 842 0.602106 ATTCGGCCTCTCGATGCATG 60.602 55.000 2.46 0.00 39.03 4.06
813 843 1.675720 TTCGGCCTCTCGATGCATGA 61.676 55.000 2.46 0.89 39.03 3.07
814 844 1.227350 CGGCCTCTCGATGCATGAA 60.227 57.895 2.46 0.00 0.00 2.57
815 845 1.220169 CGGCCTCTCGATGCATGAAG 61.220 60.000 2.46 0.55 0.00 3.02
816 846 0.105593 GGCCTCTCGATGCATGAAGA 59.894 55.000 2.46 5.65 0.00 2.87
817 847 1.473965 GGCCTCTCGATGCATGAAGAA 60.474 52.381 2.46 0.00 0.00 2.52
818 848 1.865970 GCCTCTCGATGCATGAAGAAG 59.134 52.381 2.46 1.44 0.00 2.85
819 849 2.482664 GCCTCTCGATGCATGAAGAAGA 60.483 50.000 2.46 0.00 0.00 2.87
820 850 3.790091 CCTCTCGATGCATGAAGAAGAA 58.210 45.455 2.46 0.00 0.00 2.52
821 851 4.378774 CCTCTCGATGCATGAAGAAGAAT 58.621 43.478 2.46 0.00 0.00 2.40
822 852 4.448395 CCTCTCGATGCATGAAGAAGAATC 59.552 45.833 2.46 0.00 0.00 2.52
823 853 5.014808 TCTCGATGCATGAAGAAGAATCA 57.985 39.130 2.46 0.00 0.00 2.57
905 936 3.006967 AGAGCCCAGCCGTTGTATATAAG 59.993 47.826 0.00 0.00 0.00 1.73
912 943 2.551032 GCCGTTGTATATAAGCCAACCC 59.449 50.000 8.38 0.00 36.06 4.11
913 944 3.746432 GCCGTTGTATATAAGCCAACCCT 60.746 47.826 8.38 0.00 36.06 4.34
914 945 3.813166 CCGTTGTATATAAGCCAACCCTG 59.187 47.826 8.38 0.00 36.06 4.45
917 948 1.804748 GTATATAAGCCAACCCTGCGC 59.195 52.381 0.00 0.00 0.00 6.09
1267 1314 4.758165 GGACTTTCGTGGTTCTTGGATTTA 59.242 41.667 0.00 0.00 0.00 1.40
1268 1315 5.239963 GGACTTTCGTGGTTCTTGGATTTAA 59.760 40.000 0.00 0.00 0.00 1.52
1269 1316 6.072119 GGACTTTCGTGGTTCTTGGATTTAAT 60.072 38.462 0.00 0.00 0.00 1.40
1273 1320 6.262193 TCGTGGTTCTTGGATTTAATTTCC 57.738 37.500 0.00 0.00 0.00 3.13
1377 1424 2.208431 CAGGAGGATGATCGAAGCAAC 58.792 52.381 0.00 0.00 0.00 4.17
1396 1443 0.824759 CCGAAGAGTACCAAGGGGAG 59.175 60.000 0.00 0.00 38.05 4.30
1451 1498 1.522900 TGATCCATCCTCCCCTTTCC 58.477 55.000 0.00 0.00 0.00 3.13
1501 1548 1.464997 GGAAACGCTAGCTGGAACTTG 59.535 52.381 13.93 0.00 0.00 3.16
1513 1560 1.214175 TGGAACTTGGGAGTGCAAAGA 59.786 47.619 5.67 0.00 35.91 2.52
1694 1741 0.172803 ACGATGAGCGGTACAAGGAC 59.827 55.000 0.00 0.00 46.49 3.85
1733 1780 7.676004 TCAAAGTGTGGTTAGAATATGTGAGA 58.324 34.615 0.00 0.00 0.00 3.27
1900 1948 6.048073 TGTTTTCTACATTCGCTATGCATC 57.952 37.500 0.19 0.00 37.81 3.91
1979 2027 8.085909 GGAATAGCTAGGTGAGATTCTTCTTAC 58.914 40.741 4.27 0.00 37.66 2.34
1984 2032 6.183360 GCTAGGTGAGATTCTTCTTACGAGAA 60.183 42.308 0.00 0.00 38.92 2.87
1989 2037 7.085116 GTGAGATTCTTCTTACGAGAAACTGA 58.915 38.462 2.06 0.00 41.19 3.41
2004 2052 6.399039 CGAGAAACTGACACTTCTATGTTTCG 60.399 42.308 0.00 0.00 44.29 3.46
2045 2093 6.599638 GGGATTACTTTGTAGATTCAAGCACT 59.400 38.462 0.00 0.00 0.00 4.40
2062 2110 8.766000 TCAAGCACTCGTAAAAATATGTCTTA 57.234 30.769 0.00 0.00 0.00 2.10
2110 2160 8.798153 CCAATTGCTGATTTCGTCTAAAAATAC 58.202 33.333 0.00 0.00 0.00 1.89
2159 2209 6.927416 AGTGTCGGTGTAGATATTTGTTACA 58.073 36.000 0.00 0.00 0.00 2.41
2199 2249 5.470098 TGCAAGCGATCTATCCTAAATTTCC 59.530 40.000 0.00 0.00 0.00 3.13
2262 2312 5.230323 TGCACCATTACACACTTTACCTA 57.770 39.130 0.00 0.00 0.00 3.08
2322 2374 9.927081 AAGGAATTGTCTTATGATTACCTCATT 57.073 29.630 0.00 0.00 42.07 2.57
2584 2638 2.205074 CAGGATGATACCGCAAGTGAC 58.795 52.381 0.00 0.00 39.69 3.67
2683 2737 3.562973 CAGCATCAACTTCAAGTGACTGT 59.437 43.478 0.00 0.00 0.00 3.55
2906 2960 8.576442 ACACCGATTTCAATTTACAAAGAGAAT 58.424 29.630 0.00 0.00 0.00 2.40
2953 3007 0.615850 GCTAGGAGCAAAGACAGGGT 59.384 55.000 0.00 0.00 41.89 4.34
3070 3124 9.658799 CCACTAGAATTCTTCAAAGAACAGATA 57.341 33.333 14.36 0.00 46.80 1.98
3110 3164 8.035394 GTGATAGTGATACTTTTCTGAAGGACA 58.965 37.037 0.00 0.00 0.00 4.02
3166 3220 2.215942 TGGAAGAGAGACCGTCATGA 57.784 50.000 0.40 0.00 0.00 3.07
3247 3302 3.946201 AGCACGGCCAGCAGTTCT 61.946 61.111 18.34 0.00 0.00 3.01
3262 3317 3.158537 TTCTGCCCGCTCGTGTCAA 62.159 57.895 0.00 0.00 0.00 3.18
3333 3388 8.617290 ACGACATCCTTAAGTTATCAGTTTTT 57.383 30.769 0.97 0.00 0.00 1.94
3432 3487 2.627699 GCCAAAGAGTCCAAAACCATCA 59.372 45.455 0.00 0.00 0.00 3.07
3736 3801 1.017387 GGCTCGATTGTTGTGATCCC 58.983 55.000 0.00 0.00 0.00 3.85
3763 3888 5.547465 ACACGAATTGTTGAGGATCTTGTA 58.453 37.500 0.00 0.00 33.09 2.41
3764 3889 5.408604 ACACGAATTGTTGAGGATCTTGTAC 59.591 40.000 0.00 0.00 33.09 2.90
3765 3890 5.408299 CACGAATTGTTGAGGATCTTGTACA 59.592 40.000 0.00 0.00 34.92 2.90
3766 3891 6.092670 CACGAATTGTTGAGGATCTTGTACAT 59.907 38.462 0.00 0.00 34.92 2.29
3767 3892 6.655003 ACGAATTGTTGAGGATCTTGTACATT 59.345 34.615 0.00 0.00 34.92 2.71
3768 3893 6.963242 CGAATTGTTGAGGATCTTGTACATTG 59.037 38.462 0.00 0.00 34.92 2.82
3769 3894 7.148423 CGAATTGTTGAGGATCTTGTACATTGA 60.148 37.037 0.00 0.00 34.92 2.57
3770 3895 8.585471 AATTGTTGAGGATCTTGTACATTGAT 57.415 30.769 10.46 10.46 34.92 2.57
3771 3896 8.585471 ATTGTTGAGGATCTTGTACATTGATT 57.415 30.769 11.55 0.26 34.92 2.57
3772 3897 8.408043 TTGTTGAGGATCTTGTACATTGATTT 57.592 30.769 11.55 5.63 34.92 2.17
3773 3898 8.408043 TGTTGAGGATCTTGTACATTGATTTT 57.592 30.769 11.55 5.37 34.92 1.82
3774 3899 8.298854 TGTTGAGGATCTTGTACATTGATTTTG 58.701 33.333 11.55 0.00 34.92 2.44
3775 3900 8.299570 GTTGAGGATCTTGTACATTGATTTTGT 58.700 33.333 11.55 0.00 34.92 2.83
3806 3931 4.452455 GGATGTCCGTAAATTGCATAGAGG 59.548 45.833 0.00 0.00 0.00 3.69
3807 3932 4.481368 TGTCCGTAAATTGCATAGAGGT 57.519 40.909 0.00 0.00 0.00 3.85
3886 4011 6.612863 TCTGAATATCCAGAGAGGTCAAATCA 59.387 38.462 0.00 0.00 38.18 2.57
3937 4062 5.246883 AGCAAATAAAGAACCTTGAAGGCAT 59.753 36.000 11.96 0.00 39.63 4.40
4075 4204 1.001378 GCATGACCTTTGTTTGCTCGT 60.001 47.619 0.00 0.00 33.52 4.18
4076 4205 2.225491 GCATGACCTTTGTTTGCTCGTA 59.775 45.455 0.00 0.00 33.52 3.43
4179 4308 5.123227 CACAACAGGGTACAGAAGAAGAAA 58.877 41.667 0.00 0.00 0.00 2.52
4275 4415 1.197721 CAGATCAGGCGTGTCAAAACC 59.802 52.381 6.26 0.00 0.00 3.27
4280 4420 0.681564 AGGCGTGTCAAAACCCACAA 60.682 50.000 0.00 0.00 0.00 3.33
4311 4462 6.922957 AGATTTTGAATAATTTGTGTGCGTGT 59.077 30.769 0.00 0.00 0.00 4.49
4312 4463 5.879948 TTTGAATAATTTGTGTGCGTGTG 57.120 34.783 0.00 0.00 0.00 3.82
4313 4464 3.304257 TGAATAATTTGTGTGCGTGTGC 58.696 40.909 0.00 0.00 43.20 4.57
4375 4555 3.616956 TTGTACTCTCCATCTTGCTGG 57.383 47.619 0.00 0.00 37.66 4.85
4391 4856 5.181245 TCTTGCTGGATTAACTAACAAGCAC 59.819 40.000 0.00 0.00 34.48 4.40
4458 4923 0.726827 CGGTGCAATCTACAACGCAT 59.273 50.000 0.00 0.00 41.89 4.73
4459 4924 1.267532 CGGTGCAATCTACAACGCATC 60.268 52.381 0.00 0.00 41.89 3.91
4461 4926 2.223112 GGTGCAATCTACAACGCATCAG 60.223 50.000 0.00 0.00 35.54 2.90
4462 4927 1.398041 TGCAATCTACAACGCATCAGC 59.602 47.619 0.00 0.00 37.42 4.26
4463 4928 1.398041 GCAATCTACAACGCATCAGCA 59.602 47.619 0.00 0.00 42.27 4.41
4464 4929 2.032550 GCAATCTACAACGCATCAGCAT 59.967 45.455 0.00 0.00 42.27 3.79
4500 4972 1.450312 CACGACAGGATCAAGGGCC 60.450 63.158 0.00 0.00 0.00 5.80
4556 5028 3.121688 AGAGGATGGAGCCAAGAGAAAT 58.878 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.485313 CCCTTAAGAATGTTGTGTCACTTGTA 59.515 38.462 3.36 0.00 0.00 2.41
209 211 2.554893 CCCGACTGTCTTCTATAGCTCC 59.445 54.545 6.21 0.00 0.00 4.70
220 222 1.194781 ATGGCTTCACCCGACTGTCT 61.195 55.000 6.21 0.00 37.83 3.41
224 226 1.496060 TATGATGGCTTCACCCGACT 58.504 50.000 5.09 0.00 37.11 4.18
373 376 0.773644 AGAGTTGCATGGGACTTGGT 59.226 50.000 0.00 0.00 0.00 3.67
384 387 6.544928 TTCTATAGGAACATGAGAGTTGCA 57.455 37.500 0.00 0.00 41.61 4.08
411 414 2.467566 ACAAAGGTTACGGCCAGTAG 57.532 50.000 2.24 0.00 36.56 2.57
419 422 2.849473 GTGCACACAAACAAAGGTTACG 59.151 45.455 13.17 0.00 35.82 3.18
447 450 1.674962 GCAACAAGATGGATGGCTCTC 59.325 52.381 0.00 0.00 0.00 3.20
570 573 1.153765 CGACAGCGCTTCAGGATCA 60.154 57.895 7.50 0.00 0.00 2.92
654 665 0.251165 GGTAACCCTGGCTTGCAAGA 60.251 55.000 30.39 9.22 0.00 3.02
711 730 0.100682 CCACCACCGTAGAGACATCG 59.899 60.000 0.00 0.00 0.00 3.84
776 806 5.810074 GGCCGAATTATTTTACTGCATTGTT 59.190 36.000 0.00 0.00 0.00 2.83
777 807 5.127031 AGGCCGAATTATTTTACTGCATTGT 59.873 36.000 0.00 0.00 0.00 2.71
778 808 5.591099 AGGCCGAATTATTTTACTGCATTG 58.409 37.500 0.00 0.00 0.00 2.82
779 809 5.594317 AGAGGCCGAATTATTTTACTGCATT 59.406 36.000 0.00 0.00 0.00 3.56
780 810 5.133221 AGAGGCCGAATTATTTTACTGCAT 58.867 37.500 0.00 0.00 0.00 3.96
781 811 4.523083 AGAGGCCGAATTATTTTACTGCA 58.477 39.130 0.00 0.00 0.00 4.41
782 812 4.318831 CGAGAGGCCGAATTATTTTACTGC 60.319 45.833 0.00 0.00 0.00 4.40
783 813 5.047847 TCGAGAGGCCGAATTATTTTACTG 58.952 41.667 0.00 0.00 35.42 2.74
784 814 5.272283 TCGAGAGGCCGAATTATTTTACT 57.728 39.130 0.00 0.00 35.42 2.24
785 815 5.614887 GCATCGAGAGGCCGAATTATTTTAC 60.615 44.000 0.00 0.00 42.22 2.01
786 816 4.451096 GCATCGAGAGGCCGAATTATTTTA 59.549 41.667 0.00 0.00 42.22 1.52
787 817 3.251004 GCATCGAGAGGCCGAATTATTTT 59.749 43.478 0.00 0.00 42.22 1.82
788 818 2.808543 GCATCGAGAGGCCGAATTATTT 59.191 45.455 0.00 0.00 42.22 1.40
789 819 2.224281 TGCATCGAGAGGCCGAATTATT 60.224 45.455 7.29 0.00 42.22 1.40
790 820 1.344438 TGCATCGAGAGGCCGAATTAT 59.656 47.619 7.29 0.00 42.22 1.28
791 821 0.750249 TGCATCGAGAGGCCGAATTA 59.250 50.000 7.29 0.00 42.22 1.40
792 822 0.107456 ATGCATCGAGAGGCCGAATT 59.893 50.000 7.29 0.00 42.22 2.17
793 823 0.602106 CATGCATCGAGAGGCCGAAT 60.602 55.000 7.29 0.00 42.22 3.34
794 824 1.227350 CATGCATCGAGAGGCCGAA 60.227 57.895 7.29 0.00 42.22 4.30
795 825 1.675720 TTCATGCATCGAGAGGCCGA 61.676 55.000 7.29 1.47 43.16 5.54
796 826 1.220169 CTTCATGCATCGAGAGGCCG 61.220 60.000 7.29 0.00 37.30 6.13
797 827 0.105593 TCTTCATGCATCGAGAGGCC 59.894 55.000 7.29 0.00 37.30 5.19
798 828 1.865970 CTTCTTCATGCATCGAGAGGC 59.134 52.381 0.00 2.50 38.80 4.70
799 829 3.449528 TCTTCTTCATGCATCGAGAGG 57.550 47.619 0.00 3.93 0.00 3.69
800 830 5.048507 TGATTCTTCTTCATGCATCGAGAG 58.951 41.667 0.00 0.00 0.00 3.20
801 831 5.014808 TGATTCTTCTTCATGCATCGAGA 57.985 39.130 0.00 0.00 0.00 4.04
802 832 5.926214 ATGATTCTTCTTCATGCATCGAG 57.074 39.130 0.00 0.00 32.67 4.04
803 833 5.698089 GGTATGATTCTTCTTCATGCATCGA 59.302 40.000 0.00 0.00 37.77 3.59
804 834 5.467735 TGGTATGATTCTTCTTCATGCATCG 59.532 40.000 0.00 0.00 37.77 3.84
805 835 6.872628 TGGTATGATTCTTCTTCATGCATC 57.127 37.500 0.00 0.00 37.77 3.91
806 836 7.940688 TGTATGGTATGATTCTTCTTCATGCAT 59.059 33.333 0.00 0.00 37.77 3.96
807 837 7.281841 TGTATGGTATGATTCTTCTTCATGCA 58.718 34.615 0.00 0.00 37.77 3.96
808 838 7.734924 TGTATGGTATGATTCTTCTTCATGC 57.265 36.000 0.00 0.00 35.50 4.06
809 839 9.498176 TGATGTATGGTATGATTCTTCTTCATG 57.502 33.333 0.00 0.00 35.50 3.07
810 840 9.722184 CTGATGTATGGTATGATTCTTCTTCAT 57.278 33.333 0.00 0.00 37.56 2.57
811 841 8.152898 CCTGATGTATGGTATGATTCTTCTTCA 58.847 37.037 0.00 0.00 0.00 3.02
812 842 8.153550 ACCTGATGTATGGTATGATTCTTCTTC 58.846 37.037 0.00 0.00 34.36 2.87
813 843 7.935755 CACCTGATGTATGGTATGATTCTTCTT 59.064 37.037 0.00 0.00 34.79 2.52
814 844 7.448420 CACCTGATGTATGGTATGATTCTTCT 58.552 38.462 0.00 0.00 34.79 2.85
815 845 6.652481 CCACCTGATGTATGGTATGATTCTTC 59.348 42.308 0.00 0.00 34.79 2.87
816 846 6.466326 CCCACCTGATGTATGGTATGATTCTT 60.466 42.308 0.00 0.00 34.79 2.52
817 847 5.013495 CCCACCTGATGTATGGTATGATTCT 59.987 44.000 0.00 0.00 34.79 2.40
818 848 5.248640 CCCACCTGATGTATGGTATGATTC 58.751 45.833 0.00 0.00 34.79 2.52
819 849 4.507335 GCCCACCTGATGTATGGTATGATT 60.507 45.833 0.00 0.00 34.79 2.57
820 850 3.009473 GCCCACCTGATGTATGGTATGAT 59.991 47.826 0.00 0.00 34.79 2.45
821 851 2.371841 GCCCACCTGATGTATGGTATGA 59.628 50.000 0.00 0.00 34.79 2.15
822 852 2.553028 GGCCCACCTGATGTATGGTATG 60.553 54.545 0.00 0.00 34.79 2.39
823 853 1.705186 GGCCCACCTGATGTATGGTAT 59.295 52.381 0.00 0.00 34.79 2.73
894 925 3.250040 CGCAGGGTTGGCTTATATACAAC 59.750 47.826 6.27 6.27 42.70 3.32
1035 1071 4.838486 GCCAGAGTCTCCGCGTCG 62.838 72.222 4.92 0.00 0.00 5.12
1268 1315 9.502091 GGCCAGAAAGTAAAATAAAAAGGAAAT 57.498 29.630 0.00 0.00 0.00 2.17
1269 1316 7.934665 GGGCCAGAAAGTAAAATAAAAAGGAAA 59.065 33.333 4.39 0.00 0.00 3.13
1273 1320 5.867174 CCGGGCCAGAAAGTAAAATAAAAAG 59.133 40.000 4.39 0.00 0.00 2.27
1377 1424 0.824759 CTCCCCTTGGTACTCTTCGG 59.175 60.000 0.00 0.00 0.00 4.30
1396 1443 3.839353 CCATGGCTGGAGCGGATCC 62.839 68.421 5.08 5.08 46.37 3.36
1451 1498 0.587242 CATCGAAGAAACCATGCGCG 60.587 55.000 0.00 0.00 43.58 6.86
1527 1574 2.346803 GCACCGAGCTTGTAGAAATCA 58.653 47.619 0.00 0.00 41.15 2.57
1583 1630 2.165030 CTCCTGAACCCATTTGATGCAC 59.835 50.000 0.00 0.00 0.00 4.57
1694 1741 1.749634 ACTTTGAGGTACCGGAGATCG 59.250 52.381 9.46 0.00 38.88 3.69
1733 1780 1.741706 CAAGCCGAATTCAGTCAGCAT 59.258 47.619 6.22 0.00 0.00 3.79
1900 1948 2.876091 TGTTCTTCGACTCCATTAGCG 58.124 47.619 0.00 0.00 0.00 4.26
1979 2027 6.399039 CGAAACATAGAAGTGTCAGTTTCTCG 60.399 42.308 12.25 0.16 38.63 4.04
1984 2032 5.696724 CCTTCGAAACATAGAAGTGTCAGTT 59.303 40.000 0.00 0.00 41.51 3.16
1989 2037 5.855045 AGAACCTTCGAAACATAGAAGTGT 58.145 37.500 0.00 0.64 41.51 3.55
2004 2052 5.952347 AGTAATCCCAAATCCAAGAACCTTC 59.048 40.000 0.00 0.00 0.00 3.46
2159 2209 4.572389 CGCTTGCAGACTGGAAACTAATAT 59.428 41.667 10.82 0.00 0.00 1.28
2199 2249 6.702329 AGAACAGTAAAATACAGGACTCCAG 58.298 40.000 0.00 0.00 0.00 3.86
2236 2286 5.413213 GGTAAAGTGTGTAATGGTGCATACA 59.587 40.000 0.00 0.00 34.57 2.29
2262 2312 4.310022 AGAGAGGCAAGTAGTACTCTGT 57.690 45.455 2.58 0.00 40.19 3.41
2322 2374 7.119699 CACAATTGCATAGTTAGTGGAAGAGAA 59.880 37.037 5.05 0.00 30.42 2.87
2363 2415 4.383010 CCCAAGGATAAAATTTCACCAGCC 60.383 45.833 0.00 0.00 0.00 4.85
2584 2638 1.151777 ATTTGCGTACGGGCTGATCG 61.152 55.000 18.39 5.42 0.00 3.69
2665 2719 4.384056 CCAGACAGTCACTTGAAGTTGAT 58.616 43.478 2.66 0.00 0.00 2.57
2683 2737 8.792633 CAAATTCAAGATTAGTTTACACCCAGA 58.207 33.333 0.00 0.00 0.00 3.86
2953 3007 0.626382 TGTTCCAAGGGTGTTCCACA 59.374 50.000 0.00 0.00 35.86 4.17
3080 3134 9.814899 CTTCAGAAAAGTATCACTATCACAGAT 57.185 33.333 0.00 0.00 0.00 2.90
3081 3135 8.253810 CCTTCAGAAAAGTATCACTATCACAGA 58.746 37.037 0.00 0.00 0.00 3.41
3083 3137 8.035394 GTCCTTCAGAAAAGTATCACTATCACA 58.965 37.037 0.00 0.00 0.00 3.58
3159 3213 1.067846 TGAACGGAAGAGGTCATGACG 60.068 52.381 19.33 8.79 0.00 4.35
3166 3220 6.356186 AGTTTATAACTGAACGGAAGAGGT 57.644 37.500 0.00 0.00 41.01 3.85
3198 3253 5.476599 TCGGTGGAATCTGTTCAATGAAATT 59.523 36.000 0.00 0.00 36.63 1.82
3247 3302 3.858868 GAGTTGACACGAGCGGGCA 62.859 63.158 0.00 0.00 0.00 5.36
3251 3306 0.439985 CAATGGAGTTGACACGAGCG 59.560 55.000 0.00 0.00 40.37 5.03
3262 3317 3.698289 TCTACGAAGACCTCAATGGAGT 58.302 45.455 0.00 0.00 39.64 3.85
3278 3333 2.791560 CTCGGCACATTCTTCATCTACG 59.208 50.000 0.00 0.00 0.00 3.51
3337 3392 9.502091 AACACTTTCTGTTTATATAGTGCTTCA 57.498 29.630 0.00 0.00 40.45 3.02
3355 3410 7.645402 TCGAAAGGGAATTTAGAAACACTTTC 58.355 34.615 0.00 0.00 39.21 2.62
3403 3458 1.768275 TGGACTCTTTGGCACTTGAGA 59.232 47.619 14.75 3.94 0.00 3.27
3736 3801 5.171476 AGATCCTCAACAATTCGTGTACAG 58.829 41.667 0.00 0.00 40.60 2.74
3763 3888 8.278729 ACATCCAAACAAAACAAAATCAATGT 57.721 26.923 0.00 0.00 0.00 2.71
3764 3889 7.856894 GGACATCCAAACAAAACAAAATCAATG 59.143 33.333 0.00 0.00 35.64 2.82
3765 3890 7.254727 CGGACATCCAAACAAAACAAAATCAAT 60.255 33.333 0.00 0.00 35.14 2.57
3766 3891 6.036517 CGGACATCCAAACAAAACAAAATCAA 59.963 34.615 0.00 0.00 35.14 2.57
3767 3892 5.521735 CGGACATCCAAACAAAACAAAATCA 59.478 36.000 0.00 0.00 35.14 2.57
3768 3893 5.522097 ACGGACATCCAAACAAAACAAAATC 59.478 36.000 0.00 0.00 35.14 2.17
3769 3894 5.423886 ACGGACATCCAAACAAAACAAAAT 58.576 33.333 0.00 0.00 35.14 1.82
3770 3895 4.822026 ACGGACATCCAAACAAAACAAAA 58.178 34.783 0.00 0.00 35.14 2.44
3771 3896 4.457834 ACGGACATCCAAACAAAACAAA 57.542 36.364 0.00 0.00 35.14 2.83
3772 3897 5.578005 TTACGGACATCCAAACAAAACAA 57.422 34.783 0.00 0.00 35.14 2.83
3773 3898 5.578005 TTTACGGACATCCAAACAAAACA 57.422 34.783 0.00 0.00 35.14 2.83
3774 3899 6.563196 GCAATTTACGGACATCCAAACAAAAC 60.563 38.462 0.00 0.00 35.14 2.43
3775 3900 5.463724 GCAATTTACGGACATCCAAACAAAA 59.536 36.000 0.00 0.00 35.14 2.44
3782 3907 5.029807 TCTATGCAATTTACGGACATCCA 57.970 39.130 0.00 0.00 35.14 3.41
3806 3931 6.922957 TGGCAAGATCAAATTACTTTGTGAAC 59.077 34.615 5.56 0.00 42.02 3.18
3807 3932 7.048629 TGGCAAGATCAAATTACTTTGTGAA 57.951 32.000 5.56 0.00 42.02 3.18
3886 4011 0.537188 AATCGGGCTGTCTCGACATT 59.463 50.000 0.00 0.00 41.01 2.71
4179 4308 0.601841 ATGGCTTCGGTTTCGTCGTT 60.602 50.000 0.00 0.00 37.69 3.85
4221 4353 2.108075 TGCATCAAGACCCTTCAGGAAA 59.892 45.455 0.00 0.00 39.89 3.13
4275 4415 3.749665 TTCAAAATCTTGGGCTTGTGG 57.250 42.857 0.00 0.00 33.01 4.17
4280 4420 7.388500 CACACAAATTATTCAAAATCTTGGGCT 59.612 33.333 0.00 0.00 33.01 5.19
4375 4555 5.505165 TCGTTCGTGCTTGTTAGTTAATC 57.495 39.130 0.00 0.00 0.00 1.75
4427 4892 2.689553 TTGCACCGCTATCTGAATCA 57.310 45.000 0.00 0.00 0.00 2.57
4456 4921 0.248661 GCTGCTGCTGAATGCTGATG 60.249 55.000 10.92 0.00 42.27 3.07
4458 4923 2.044555 GGCTGCTGCTGAATGCTGA 61.045 57.895 15.64 0.00 42.27 4.26
4459 4924 2.046864 AGGCTGCTGCTGAATGCTG 61.047 57.895 15.64 0.00 43.37 4.41
4461 4926 2.490217 CAGGCTGCTGCTGAATGC 59.510 61.111 15.64 2.61 43.25 3.56
4462 4927 1.677966 ACCAGGCTGCTGCTGAATG 60.678 57.895 15.64 9.09 39.59 2.67
4463 4928 1.677966 CACCAGGCTGCTGCTGAAT 60.678 57.895 15.64 0.00 39.59 2.57
4464 4929 2.281970 CACCAGGCTGCTGCTGAA 60.282 61.111 15.64 0.00 39.59 3.02
4481 4953 2.109126 GCCCTTGATCCTGTCGTGC 61.109 63.158 0.00 0.00 0.00 5.34
4500 4972 1.059838 CGTCATGTCATGCTGTGCG 59.940 57.895 8.03 4.08 0.00 5.34
4544 5016 2.564504 GCCTGGAAAATTTCTCTTGGCT 59.435 45.455 17.15 0.00 35.44 4.75
4556 5028 3.687698 GCATAAACTACTCGCCTGGAAAA 59.312 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.