Multiple sequence alignment - TraesCS6D01G297200

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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 TraesCS6D01G297200 chr6D 100.000 2924 0 0 1 2924 408215873 408212950 0.000000e+00 5400
1 TraesCS6D01G297200 chr6D 80.623 1445 231 33 1038 2452 408184687 408183262 0.000000e+00 1072
2 TraesCS6D01G297200 chr6D 75.670 448 101 8 1139 1582 420560696 420560253 1.760000e-52 217
3 TraesCS6D01G297200 chr6D 75.056 445 103 7 1139 1579 59087679 59088119 1.780000e-47 200
4 TraesCS6D01G297200 chr6B 91.162 2727 171 31 1 2686 612859820 612857123 0.000000e+00 3637
5 TraesCS6D01G297200 chr6B 80.329 1459 249 29 1025 2452 612849441 612847990 0.000000e+00 1070
6 TraesCS6D01G297200 chr6B 76.577 444 98 6 1139 1579 612743769 612744209 3.770000e-59 239
7 TraesCS6D01G297200 chr6B 87.179 195 16 5 2723 2916 612857130 612856944 2.280000e-51 213
8 TraesCS6D01G297200 chr6A 91.510 2497 138 29 227 2674 554305121 554302650 0.000000e+00 3369
9 TraesCS6D01G297200 chr6A 80.123 1464 240 35 1019 2452 553927432 553925990 0.000000e+00 1044
10 TraesCS6D01G297200 chr6A 90.411 292 26 1 1 292 554305402 554305113 1.640000e-102 383
11 TraesCS6D01G297200 chr6A 75.893 448 100 8 1139 1582 563486208 563485765 3.790000e-54 222
12 TraesCS6D01G297200 chr6A 94.574 129 7 0 2662 2790 553943086 553942958 1.780000e-47 200
13 TraesCS6D01G297200 chr6A 91.667 108 6 1 2662 2766 554302600 554302493 2.350000e-31 147
14 TraesCS6D01G297200 chr2B 73.370 721 168 24 1128 1836 405263712 405263004 2.250000e-61 246
15 TraesCS6D01G297200 chr7A 86.260 131 18 0 2322 2452 26978240 26978370 3.040000e-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 TraesCS6D01G297200 chr6D 408212950 408215873 2923 True 5400.000000 5400 100.0000 1 2924 1 chr6D.!!$R2 2923
1 TraesCS6D01G297200 chr6D 408183262 408184687 1425 True 1072.000000 1072 80.6230 1038 2452 1 chr6D.!!$R1 1414
2 TraesCS6D01G297200 chr6B 612856944 612859820 2876 True 1925.000000 3637 89.1705 1 2916 2 chr6B.!!$R2 2915
3 TraesCS6D01G297200 chr6B 612847990 612849441 1451 True 1070.000000 1070 80.3290 1025 2452 1 chr6B.!!$R1 1427
4 TraesCS6D01G297200 chr6A 554302493 554305402 2909 True 1299.666667 3369 91.1960 1 2766 3 chr6A.!!$R4 2765
5 TraesCS6D01G297200 chr6A 553925990 553927432 1442 True 1044.000000 1044 80.1230 1019 2452 1 chr6A.!!$R1 1433
6 TraesCS6D01G297200 chr2B 405263004 405263712 708 True 246.000000 246 73.3700 1128 1836 1 chr2B.!!$R1 708

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
282 339 0.037877 ACTCATGGCTTTCTGCTGCT 59.962 50.0 0.0 0.0 42.39 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2047 0.532573 ACTCACTACGTGCTCCATGG 59.467 55.0 4.97 4.97 32.98 3.66 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
42 43 2.680913 CCGTTCTTTCAGCAGCCGG 61.681 63.158 0.00 0.00 0.00 6.13
178 180 9.981114 AGTTTTCAGACCACCAAAATAAATAAG 57.019 29.630 0.00 0.00 0.00 1.73
203 205 4.424061 TTTGCTGTTGTCATACTCATGC 57.576 40.909 0.00 0.00 31.73 4.06
241 243 6.665992 ATAAGCGACTATGTTCCCATCTTA 57.334 37.500 0.00 0.00 32.29 2.10
249 306 7.148738 CGACTATGTTCCCATCTTATTTGATCG 60.149 40.741 0.00 0.00 32.29 3.69
257 314 7.109501 TCCCATCTTATTTGATCGAACTTTGA 58.890 34.615 0.00 0.00 0.00 2.69
270 327 6.539649 TCGAACTTTGAAGTAAACTCATGG 57.460 37.500 0.00 0.00 38.57 3.66
281 338 0.886563 AACTCATGGCTTTCTGCTGC 59.113 50.000 0.00 0.00 42.39 5.25
282 339 0.037877 ACTCATGGCTTTCTGCTGCT 59.962 50.000 0.00 0.00 42.39 4.24
317 374 4.051922 CTCACAACCAACTCAGACAGTAC 58.948 47.826 0.00 0.00 32.30 2.73
319 376 2.223971 ACAACCAACTCAGACAGTACCG 60.224 50.000 0.00 0.00 32.30 4.02
504 561 5.334879 CCAAAATACTCGTTTCTTGACTGGG 60.335 44.000 0.00 0.00 0.00 4.45
607 664 3.440173 CCCATTGTACTGCGAAACTGAAT 59.560 43.478 0.00 0.00 0.00 2.57
608 665 4.082787 CCCATTGTACTGCGAAACTGAATT 60.083 41.667 0.00 0.00 0.00 2.17
686 743 5.008619 AGTCGTCTTCTCTATGTCTACGA 57.991 43.478 0.00 0.00 35.73 3.43
687 744 5.045215 AGTCGTCTTCTCTATGTCTACGAG 58.955 45.833 0.00 0.00 38.41 4.18
695 752 8.994170 TCTTCTCTATGTCTACGAGTATGAATG 58.006 37.037 0.00 0.00 0.00 2.67
696 753 7.674471 TCTCTATGTCTACGAGTATGAATGG 57.326 40.000 0.00 0.00 0.00 3.16
698 755 7.173390 TCTCTATGTCTACGAGTATGAATGGTG 59.827 40.741 0.00 0.00 0.00 4.17
701 758 5.647589 TGTCTACGAGTATGAATGGTGTTC 58.352 41.667 0.00 0.00 0.00 3.18
702 759 5.417894 TGTCTACGAGTATGAATGGTGTTCT 59.582 40.000 0.00 0.00 0.00 3.01
712 769 5.261209 TGAATGGTGTTCTTTTGTTCCTG 57.739 39.130 0.00 0.00 0.00 3.86
723 780 0.596600 TTGTTCCTGCGACACTCGAC 60.597 55.000 0.00 0.00 43.74 4.20
724 781 1.007734 GTTCCTGCGACACTCGACA 60.008 57.895 0.00 0.00 43.74 4.35
725 782 1.007734 TTCCTGCGACACTCGACAC 60.008 57.895 0.00 0.00 43.74 3.67
726 783 1.452953 TTCCTGCGACACTCGACACT 61.453 55.000 0.00 0.00 43.74 3.55
727 784 0.604511 TCCTGCGACACTCGACACTA 60.605 55.000 0.00 0.00 43.74 2.74
728 785 0.452184 CCTGCGACACTCGACACTAT 59.548 55.000 0.00 0.00 43.74 2.12
729 786 1.135373 CCTGCGACACTCGACACTATT 60.135 52.381 0.00 0.00 43.74 1.73
730 787 2.096980 CCTGCGACACTCGACACTATTA 59.903 50.000 0.00 0.00 43.74 0.98
731 788 3.099362 CTGCGACACTCGACACTATTAC 58.901 50.000 0.00 0.00 43.74 1.89
746 803 8.068977 CGACACTATTACTGTTACAGGATAGAC 58.931 40.741 28.23 20.78 36.34 2.59
760 817 7.009179 ACAGGATAGACAAATGTTCTTCAGA 57.991 36.000 0.00 0.00 0.00 3.27
762 819 7.939039 ACAGGATAGACAAATGTTCTTCAGAAA 59.061 33.333 0.00 0.00 35.58 2.52
766 823 6.625873 AGACAAATGTTCTTCAGAAAGACC 57.374 37.500 0.00 0.00 41.23 3.85
774 831 4.145365 TCTTCAGAAAGACCGGTGAAAA 57.855 40.909 14.63 0.00 36.59 2.29
783 842 3.841643 AGACCGGTGAAAATACGTACAG 58.158 45.455 14.63 0.00 0.00 2.74
796 855 1.202440 ACGTACAGCACCGAGAAAACA 60.202 47.619 0.00 0.00 0.00 2.83
801 860 2.687935 ACAGCACCGAGAAAACAACATT 59.312 40.909 0.00 0.00 0.00 2.71
807 866 5.504994 GCACCGAGAAAACAACATTGTAGAA 60.505 40.000 0.00 0.00 41.31 2.10
860 948 2.113289 CGCACAACGGTTTTAAACAGG 58.887 47.619 12.09 5.02 38.44 4.00
884 972 6.409925 GGGGGAAATGGTTACATCATACTGTA 60.410 42.308 0.00 0.00 35.94 2.74
911 999 3.486383 CAACCCCATATACCCATCACAC 58.514 50.000 0.00 0.00 0.00 3.82
934 1022 0.329261 TCAGGGGGCTGATTCAACAG 59.671 55.000 0.00 0.00 40.43 3.16
1272 1360 2.915659 AGCGTCGAGTTCCACCCA 60.916 61.111 0.00 0.00 0.00 4.51
1727 1824 2.607187 GTCGAACGTGTTGAGGATGAT 58.393 47.619 0.00 0.00 0.00 2.45
1787 1884 1.792949 GAAGTTGAGCATGACGTCGTT 59.207 47.619 7.76 0.00 0.00 3.85
1888 1985 1.202268 CGAGGTATCCGTTGGTCAGAC 60.202 57.143 0.00 0.00 0.00 3.51
1914 2011 1.733416 CGTCTACGACATGTGCAGCG 61.733 60.000 1.15 2.53 43.02 5.18
1931 2034 2.785477 CAGCGCAGTTATAATTTGCAGC 59.215 45.455 11.47 19.77 37.69 5.25
1933 2036 2.375110 CGCAGTTATAATTTGCAGCCG 58.625 47.619 18.93 5.14 37.69 5.52
1940 2043 5.356751 AGTTATAATTTGCAGCCGATCACAA 59.643 36.000 0.00 0.00 0.00 3.33
1944 2047 0.874390 TTGCAGCCGATCACAAACTC 59.126 50.000 0.00 0.00 0.00 3.01
1953 2067 2.715046 GATCACAAACTCCATGGAGCA 58.285 47.619 36.78 16.92 45.54 4.26
1959 2073 1.267121 AACTCCATGGAGCACGTAGT 58.733 50.000 36.78 17.24 45.54 2.73
2254 2395 4.873129 TTCTCGATCGGCGGCAGC 62.873 66.667 16.41 0.00 41.33 5.25
2276 2417 1.000019 TCCGGGATGGTCTCGAACT 60.000 57.895 0.00 0.00 44.60 3.01
2368 2509 3.255149 AGTTGACGAAGGTGACGTAGAAT 59.745 43.478 0.00 0.00 43.97 2.40
2537 2696 6.040616 CCGGGACAAGAGGGTGATATATATAC 59.959 46.154 0.00 0.00 0.00 1.47
2556 2717 9.772973 ATATATACAGCCGTTCTTGATTTTACA 57.227 29.630 0.00 0.00 0.00 2.41
2660 2831 0.034574 ATGCAAACCTGATACGCCCA 60.035 50.000 0.00 0.00 0.00 5.36
2668 2839 2.290641 ACCTGATACGCCCATCAAACAA 60.291 45.455 0.00 0.00 34.59 2.83
2670 2841 3.192422 CCTGATACGCCCATCAAACAAAA 59.808 43.478 0.00 0.00 34.59 2.44
2691 2924 9.353431 ACAAAATTTGAAAAGCATAATTCCCTT 57.647 25.926 13.19 0.00 0.00 3.95
2704 2937 7.503902 AGCATAATTCCCTTGGAAGATAAAGAC 59.496 37.037 1.64 0.00 45.48 3.01
2709 2942 4.079787 TCCCTTGGAAGATAAAGACATGGG 60.080 45.833 0.00 0.00 43.90 4.00
2800 3036 4.844349 ATACCTTGCCAGTATTGTCACT 57.156 40.909 0.00 0.00 0.00 3.41
2808 3044 3.129287 GCCAGTATTGTCACTTGGATTGG 59.871 47.826 0.00 0.00 0.00 3.16
2810 3046 5.195940 CCAGTATTGTCACTTGGATTGGAT 58.804 41.667 0.00 0.00 0.00 3.41
2811 3047 5.066893 CCAGTATTGTCACTTGGATTGGATG 59.933 44.000 0.00 0.00 0.00 3.51
2812 3048 5.066893 CAGTATTGTCACTTGGATTGGATGG 59.933 44.000 0.00 0.00 0.00 3.51
2814 3050 3.805066 TGTCACTTGGATTGGATGGAA 57.195 42.857 0.00 0.00 0.00 3.53
2815 3051 3.420893 TGTCACTTGGATTGGATGGAAC 58.579 45.455 0.00 0.00 0.00 3.62
2816 3052 3.074390 TGTCACTTGGATTGGATGGAACT 59.926 43.478 0.00 0.00 0.00 3.01
2817 3053 4.288366 TGTCACTTGGATTGGATGGAACTA 59.712 41.667 0.00 0.00 0.00 2.24
2818 3054 5.222027 TGTCACTTGGATTGGATGGAACTAA 60.222 40.000 0.00 0.00 0.00 2.24
2819 3055 5.888161 GTCACTTGGATTGGATGGAACTAAT 59.112 40.000 0.00 0.00 0.00 1.73
2820 3056 6.378280 GTCACTTGGATTGGATGGAACTAATT 59.622 38.462 0.00 0.00 0.00 1.40
2821 3057 7.556275 GTCACTTGGATTGGATGGAACTAATTA 59.444 37.037 0.00 0.00 0.00 1.40
2822 3058 7.556275 TCACTTGGATTGGATGGAACTAATTAC 59.444 37.037 0.00 0.00 0.00 1.89
2828 3064 8.143835 GGATTGGATGGAACTAATTACCATTTG 58.856 37.037 7.35 0.00 43.30 2.32
2835 3071 8.600449 TGGAACTAATTACCATTTGCTTTTTG 57.400 30.769 0.00 0.00 0.00 2.44
2851 3087 4.093261 GCTTTTTGATTGTGTTGTTGCTGT 59.907 37.500 0.00 0.00 0.00 4.40
2852 3088 5.724769 GCTTTTTGATTGTGTTGTTGCTGTC 60.725 40.000 0.00 0.00 0.00 3.51
2853 3089 4.717233 TTTGATTGTGTTGTTGCTGTCT 57.283 36.364 0.00 0.00 0.00 3.41
2864 3100 1.734465 GTTGCTGTCTATGTGTCTGCC 59.266 52.381 0.00 0.00 0.00 4.85
2872 3108 4.020307 TGTCTATGTGTCTGCCATTTCAGA 60.020 41.667 0.00 0.00 40.50 3.27
2874 3110 5.007430 GTCTATGTGTCTGCCATTTCAGATG 59.993 44.000 0.00 0.00 44.04 2.90
2880 3116 3.317430 GTCTGCCATTTCAGATGATTCCC 59.683 47.826 0.00 0.00 44.04 3.97
2902 3138 5.008217 CCCCAGCATGCATAAATTTCATTTG 59.992 40.000 21.98 4.05 31.56 2.32
2904 3140 6.485313 CCCAGCATGCATAAATTTCATTTGAT 59.515 34.615 21.98 0.00 31.56 2.57
2906 3142 9.214957 CCAGCATGCATAAATTTCATTTGATAT 57.785 29.630 21.98 0.00 31.56 1.63
2922 3158 8.963725 TCATTTGATATTCAGATAATGGATGCC 58.036 33.333 0.00 0.00 28.39 4.40
2923 3159 8.745590 CATTTGATATTCAGATAATGGATGCCA 58.254 33.333 0.00 0.00 38.19 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.377333 CCTGGAAAGAACCCTCGGC 60.377 63.158 0.00 0.00 0.00 5.54
178 180 4.797471 TGAGTATGACAACAGCAAAATGC 58.203 39.130 0.00 0.00 45.46 3.56
191 193 7.970614 TCGACATATGAATAGCATGAGTATGAC 59.029 37.037 10.38 0.00 37.87 3.06
241 243 8.836413 TGAGTTTACTTCAAAGTTCGATCAAAT 58.164 29.630 0.00 0.00 40.37 2.32
249 306 6.319141 AGCCATGAGTTTACTTCAAAGTTC 57.681 37.500 0.00 0.00 40.37 3.01
257 314 4.773323 GCAGAAAGCCATGAGTTTACTT 57.227 40.909 0.00 0.00 37.23 2.24
270 327 3.065786 TGCAACATATAGCAGCAGAAAGC 59.934 43.478 0.00 0.00 46.19 3.51
281 338 3.313526 GGTTGTGAGCCTGCAACATATAG 59.686 47.826 14.09 0.00 44.70 1.31
282 339 3.278574 GGTTGTGAGCCTGCAACATATA 58.721 45.455 14.09 0.00 44.70 0.86
295 352 3.185246 ACTGTCTGAGTTGGTTGTGAG 57.815 47.619 0.00 0.00 0.00 3.51
317 374 1.899437 TTTGTAGCCTCAGCCTCCGG 61.899 60.000 0.00 0.00 41.25 5.14
319 376 0.324943 TGTTTGTAGCCTCAGCCTCC 59.675 55.000 0.00 0.00 41.25 4.30
397 454 2.140065 TCAGTTCAGCGAGTCAGTTG 57.860 50.000 0.00 0.00 0.00 3.16
607 664 4.555262 GAATTCCATTTTCTGGCGTGAAA 58.445 39.130 0.00 2.10 45.52 2.69
608 665 3.365868 CGAATTCCATTTTCTGGCGTGAA 60.366 43.478 0.00 0.00 45.52 3.18
653 710 0.528470 AAGACGACTACCAGCAGAGC 59.472 55.000 0.00 0.00 0.00 4.09
654 711 2.088423 AGAAGACGACTACCAGCAGAG 58.912 52.381 0.00 0.00 0.00 3.35
655 712 2.085320 GAGAAGACGACTACCAGCAGA 58.915 52.381 0.00 0.00 0.00 4.26
661 718 5.175491 CGTAGACATAGAGAAGACGACTACC 59.825 48.000 0.00 0.00 0.00 3.18
686 743 6.777580 AGGAACAAAAGAACACCATTCATACT 59.222 34.615 0.00 0.00 0.00 2.12
687 744 6.863126 CAGGAACAAAAGAACACCATTCATAC 59.137 38.462 0.00 0.00 0.00 2.39
695 752 1.673920 TCGCAGGAACAAAAGAACACC 59.326 47.619 0.00 0.00 0.00 4.16
696 753 2.096819 TGTCGCAGGAACAAAAGAACAC 59.903 45.455 0.00 0.00 0.00 3.32
698 755 2.354821 AGTGTCGCAGGAACAAAAGAAC 59.645 45.455 0.00 0.00 0.00 3.01
701 758 1.070577 CGAGTGTCGCAGGAACAAAAG 60.071 52.381 0.00 0.00 31.14 2.27
702 759 0.934496 CGAGTGTCGCAGGAACAAAA 59.066 50.000 0.00 0.00 31.14 2.44
712 769 3.099362 CAGTAATAGTGTCGAGTGTCGC 58.901 50.000 0.00 0.00 40.21 5.19
727 784 9.959721 AACATTTGTCTATCCTGTAACAGTAAT 57.040 29.630 0.00 0.00 0.00 1.89
728 785 9.431887 GAACATTTGTCTATCCTGTAACAGTAA 57.568 33.333 0.00 0.00 0.00 2.24
729 786 8.812972 AGAACATTTGTCTATCCTGTAACAGTA 58.187 33.333 0.00 0.00 0.00 2.74
730 787 7.680730 AGAACATTTGTCTATCCTGTAACAGT 58.319 34.615 0.00 0.00 0.00 3.55
731 788 8.553459 AAGAACATTTGTCTATCCTGTAACAG 57.447 34.615 0.00 0.00 0.00 3.16
760 817 4.630111 TGTACGTATTTTCACCGGTCTTT 58.370 39.130 2.59 0.00 0.00 2.52
762 819 3.841643 CTGTACGTATTTTCACCGGTCT 58.158 45.455 2.59 0.00 0.00 3.85
766 823 2.093152 GGTGCTGTACGTATTTTCACCG 59.907 50.000 17.31 0.00 34.08 4.94
774 831 3.248266 GTTTTCTCGGTGCTGTACGTAT 58.752 45.455 0.00 0.00 0.00 3.06
783 842 3.078594 ACAATGTTGTTTTCTCGGTGC 57.921 42.857 0.00 0.00 38.47 5.01
801 860 9.261180 GTATGCAAGATAAACTATGCTTCTACA 57.739 33.333 0.00 0.00 39.49 2.74
807 866 7.770433 TCAACAGTATGCAAGATAAACTATGCT 59.230 33.333 0.00 0.00 42.53 3.79
817 876 5.698089 CGTCCATATCAACAGTATGCAAGAT 59.302 40.000 0.00 0.00 42.53 2.40
860 948 5.445964 ACAGTATGATGTAACCATTTCCCC 58.554 41.667 0.00 0.00 39.69 4.81
934 1022 2.844122 AGCTGAAAACGTTGTTGTCC 57.156 45.000 0.00 0.00 0.00 4.02
1039 1127 0.909610 ATGTGGAAGGAGAAGGCCGA 60.910 55.000 0.00 0.00 0.00 5.54
1272 1360 1.005630 GCTGTTCCTGACGCACTCT 60.006 57.895 0.00 0.00 0.00 3.24
1854 1951 4.538283 CTCGACACGGCGCTCGAT 62.538 66.667 24.69 11.22 42.43 3.59
1914 2011 3.691049 TCGGCTGCAAATTATAACTGC 57.309 42.857 12.44 12.44 36.60 4.40
1931 2034 2.283298 CTCCATGGAGTTTGTGATCGG 58.717 52.381 30.55 4.24 37.47 4.18
1933 2036 2.421424 GTGCTCCATGGAGTTTGTGATC 59.579 50.000 36.32 20.74 43.70 2.92
1940 2043 1.066858 CACTACGTGCTCCATGGAGTT 60.067 52.381 36.32 22.74 41.28 3.01
1944 2047 0.532573 ACTCACTACGTGCTCCATGG 59.467 55.000 4.97 4.97 32.98 3.66
1953 2067 2.283145 AGGTACCACACTCACTACGT 57.717 50.000 15.94 0.00 0.00 3.57
1959 2073 2.104111 CCACTCAAAGGTACCACACTCA 59.896 50.000 15.94 0.00 0.00 3.41
1961 2075 1.202770 GCCACTCAAAGGTACCACACT 60.203 52.381 15.94 0.00 0.00 3.55
2194 2329 3.044305 GCGCTCTGCACGTCCTTT 61.044 61.111 0.00 0.00 45.45 3.11
2276 2417 3.744719 CGGCCTCGACGACTTCCA 61.745 66.667 0.00 0.00 35.20 3.53
2368 2509 3.640407 GTGCTGCACTCCAGGGGA 61.640 66.667 24.68 0.00 42.03 4.81
2477 2635 3.244284 ACGACACATAAACCTTGTAGCCA 60.244 43.478 0.00 0.00 0.00 4.75
2482 2640 1.877443 GCCACGACACATAAACCTTGT 59.123 47.619 0.00 0.00 0.00 3.16
2537 2696 4.749245 ACTGTAAAATCAAGAACGGCTG 57.251 40.909 0.00 0.00 0.00 4.85
2554 2715 9.273016 GCCAACTTATATGTTGACATATACTGT 57.727 33.333 25.36 16.94 45.98 3.55
2555 2716 8.721478 GGCCAACTTATATGTTGACATATACTG 58.279 37.037 25.36 16.49 45.98 2.74
2556 2717 8.436778 TGGCCAACTTATATGTTGACATATACT 58.563 33.333 25.36 8.28 45.98 2.12
2592 2761 5.531659 TCTTCAGTCCTCACGGAATACTATC 59.468 44.000 0.00 0.00 42.08 2.08
2638 2807 2.094234 GGGCGTATCAGGTTTGCATTTT 60.094 45.455 0.00 0.00 0.00 1.82
2645 2816 2.752903 GTTTGATGGGCGTATCAGGTTT 59.247 45.455 3.77 0.00 38.25 3.27
2668 2839 8.162746 TCCAAGGGAATTATGCTTTTCAAATTT 58.837 29.630 0.00 0.00 0.00 1.82
2670 2841 7.256494 TCCAAGGGAATTATGCTTTTCAAAT 57.744 32.000 0.00 0.00 0.00 2.32
2686 2919 4.079787 CCCATGTCTTTATCTTCCAAGGGA 60.080 45.833 0.00 0.00 36.40 4.20
2691 2924 4.567537 CCACACCCATGTCTTTATCTTCCA 60.568 45.833 0.00 0.00 36.72 3.53
2704 2937 2.824936 TGCTGAATTAACCACACCCATG 59.175 45.455 0.00 0.00 0.00 3.66
2709 2942 5.649557 TGCATTATGCTGAATTAACCACAC 58.350 37.500 18.44 0.00 45.31 3.82
2790 3026 5.192927 TCCATCCAATCCAAGTGACAATAC 58.807 41.667 0.00 0.00 0.00 1.89
2791 3027 5.449297 TCCATCCAATCCAAGTGACAATA 57.551 39.130 0.00 0.00 0.00 1.90
2800 3036 6.736581 TGGTAATTAGTTCCATCCAATCCAA 58.263 36.000 0.00 0.00 0.00 3.53
2808 3044 9.435688 AAAAAGCAAATGGTAATTAGTTCCATC 57.564 29.630 6.56 0.00 40.52 3.51
2810 3046 8.424918 TCAAAAAGCAAATGGTAATTAGTTCCA 58.575 29.630 0.00 0.00 35.64 3.53
2811 3047 8.825667 TCAAAAAGCAAATGGTAATTAGTTCC 57.174 30.769 0.00 0.00 0.00 3.62
2814 3050 9.777297 ACAATCAAAAAGCAAATGGTAATTAGT 57.223 25.926 0.00 0.00 0.00 2.24
2816 3052 9.553064 ACACAATCAAAAAGCAAATGGTAATTA 57.447 25.926 0.00 0.00 0.00 1.40
2817 3053 8.449251 ACACAATCAAAAAGCAAATGGTAATT 57.551 26.923 0.00 0.00 0.00 1.40
2818 3054 8.344098 CAACACAATCAAAAAGCAAATGGTAAT 58.656 29.630 0.00 0.00 0.00 1.89
2819 3055 7.335422 ACAACACAATCAAAAAGCAAATGGTAA 59.665 29.630 0.00 0.00 0.00 2.85
2820 3056 6.820656 ACAACACAATCAAAAAGCAAATGGTA 59.179 30.769 0.00 0.00 0.00 3.25
2821 3057 5.647225 ACAACACAATCAAAAAGCAAATGGT 59.353 32.000 0.00 0.00 0.00 3.55
2822 3058 6.121613 ACAACACAATCAAAAAGCAAATGG 57.878 33.333 0.00 0.00 0.00 3.16
2828 3064 4.093261 ACAGCAACAACACAATCAAAAAGC 59.907 37.500 0.00 0.00 0.00 3.51
2835 3071 5.149273 CACATAGACAGCAACAACACAATC 58.851 41.667 0.00 0.00 0.00 2.67
2851 3087 4.824479 TCTGAAATGGCAGACACATAGA 57.176 40.909 0.00 0.00 39.84 1.98
2852 3088 5.121105 TCATCTGAAATGGCAGACACATAG 58.879 41.667 0.00 0.00 46.72 2.23
2853 3089 5.101648 TCATCTGAAATGGCAGACACATA 57.898 39.130 0.00 0.00 46.72 2.29
2864 3100 3.293337 TGCTGGGGAATCATCTGAAATG 58.707 45.455 0.00 0.00 0.00 2.32
2872 3108 2.984435 TATGCATGCTGGGGAATCAT 57.016 45.000 20.33 2.82 0.00 2.45
2874 3110 4.612264 AATTTATGCATGCTGGGGAATC 57.388 40.909 20.33 0.00 0.00 2.52
2880 3116 6.912203 TCAAATGAAATTTATGCATGCTGG 57.088 33.333 20.33 0.00 46.64 4.85


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

AutoCloner maintained by Alex Coulton.