Multiple sequence alignment - TraesCS1D01G374400

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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 TraesCS1D01G374400 chr1D 100.000 3047 0 0 1 3047 451942170 451939124 0.000000e+00 5627
1 TraesCS1D01G374400 chr1D 77.286 1039 220 15 1043 2072 79115844 79116875 5.620000e-167 597
2 TraesCS1D01G374400 chr1D 81.890 381 66 3 2339 2719 451883913 451883536 4.900000e-83 318
3 TraesCS1D01G374400 chr1D 99.301 143 1 0 2905 3047 445312725 445312867 3.010000e-65 259
4 TraesCS1D01G374400 chr1D 97.333 150 3 1 2899 3047 313387746 313387597 1.400000e-63 254
5 TraesCS1D01G374400 chr1A 93.641 2799 159 10 108 2904 546504570 546501789 0.000000e+00 4165
6 TraesCS1D01G374400 chr1A 80.577 381 68 6 2341 2719 546501080 546500704 3.840000e-74 289
7 TraesCS1D01G374400 chr1A 97.115 104 3 0 1 104 546504736 546504633 3.120000e-40 176
8 TraesCS1D01G374400 chr1B 93.467 2801 173 9 108 2904 621948367 621945573 0.000000e+00 4150
9 TraesCS1D01G374400 chr1B 77.146 1037 225 9 1043 2072 130010148 130011179 2.620000e-165 592
10 TraesCS1D01G374400 chr1B 94.231 104 6 0 1 104 621948533 621948430 3.140000e-35 159
11 TraesCS1D01G374400 chr6D 83.912 634 82 10 1233 1864 361520411 361521026 3.380000e-164 588
12 TraesCS1D01G374400 chr6D 98.639 147 2 0 2901 3047 66297436 66297582 8.380000e-66 261
13 TraesCS1D01G374400 chr6D 97.959 147 3 0 2901 3047 66663005 66663151 3.900000e-64 255
14 TraesCS1D01G374400 chr6D 96.732 153 3 2 2897 3047 109004366 109004214 1.400000e-63 254
15 TraesCS1D01G374400 chr6B 83.728 633 82 8 1233 1864 543213231 543213843 2.040000e-161 579
16 TraesCS1D01G374400 chr6A 82.808 634 89 9 1233 1864 502671532 502672147 1.600000e-152 549
17 TraesCS1D01G374400 chr5D 98.611 144 2 0 2904 3047 318665957 318665814 3.900000e-64 255
18 TraesCS1D01G374400 chr5D 92.857 168 10 2 2882 3047 361942561 361942728 3.040000e-60 243
19 TraesCS1D01G374400 chr4D 97.315 149 4 0 2899 3047 351364784 351364636 1.400000e-63 254
20 TraesCS1D01G374400 chr2D 97.333 150 3 1 2899 3047 282665458 282665607 1.400000e-63 254
21 TraesCS1D01G374400 chr4A 74.172 604 140 10 1455 2056 726576669 726576080 1.410000e-58 237
22 TraesCS1D01G374400 chr7D 72.803 603 144 14 1460 2058 11261491 11262077 1.440000e-43 187
23 TraesCS1D01G374400 chr7A 73.517 472 99 17 1460 1924 10380944 10381396 4.070000e-34 156


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 TraesCS1D01G374400 chr1D 451939124 451942170 3046 True 5627.000000 5627 100.000000 1 3047 1 chr1D.!!$R3 3046
1 TraesCS1D01G374400 chr1D 79115844 79116875 1031 False 597.000000 597 77.286000 1043 2072 1 chr1D.!!$F1 1029
2 TraesCS1D01G374400 chr1A 546500704 546504736 4032 True 1543.333333 4165 90.444333 1 2904 3 chr1A.!!$R1 2903
3 TraesCS1D01G374400 chr1B 621945573 621948533 2960 True 2154.500000 4150 93.849000 1 2904 2 chr1B.!!$R1 2903
4 TraesCS1D01G374400 chr1B 130010148 130011179 1031 False 592.000000 592 77.146000 1043 2072 1 chr1B.!!$F1 1029
5 TraesCS1D01G374400 chr6D 361520411 361521026 615 False 588.000000 588 83.912000 1233 1864 1 chr6D.!!$F3 631
6 TraesCS1D01G374400 chr6B 543213231 543213843 612 False 579.000000 579 83.728000 1233 1864 1 chr6B.!!$F1 631
7 TraesCS1D01G374400 chr6A 502671532 502672147 615 False 549.000000 549 82.808000 1233 1864 1 chr6A.!!$F1 631
8 TraesCS1D01G374400 chr4A 726576080 726576669 589 True 237.000000 237 74.172000 1455 2056 1 chr4A.!!$R1 601

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
551 623 1.001633 AGCGTGTTTTCGGATACCACT 59.998 47.619 0.00 0.00 0.00 4.00 F
741 814 1.231221 TTTGATTGTGAACCGACCGG 58.769 50.000 6.94 6.94 42.03 5.28 F
804 877 1.704641 AGGCATACTCCATAGTCGCA 58.295 50.000 0.00 0.00 36.46 5.10 F
1140 1213 1.934589 TCGATGTTGGCGGATACTTG 58.065 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1498 0.323178 CTGCCACCTTGGATTCTGCT 60.323 55.000 0.00 0.00 40.96 4.24 R
1574 1650 1.213537 GACCGCATTGCAAGCACAT 59.786 52.632 17.22 5.42 0.00 3.21 R
1634 1710 1.774254 TGTTCATGGTCCACCTTGTCT 59.226 47.619 10.56 0.00 40.77 3.41 R
3016 3093 1.134280 CGGCATTCTCCCTCTTCATGT 60.134 52.381 0.00 0.00 0.00 3.21 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
65 66 9.214957 CCACATACAGTTTCTCTATTGTTACAA 57.785 33.333 0.00 0.00 0.00 2.41
104 105 5.473504 TCAAATTGGCAAGTAGAGAAACTCC 59.526 40.000 5.96 0.00 0.00 3.85
105 106 4.640771 ATTGGCAAGTAGAGAAACTCCA 57.359 40.909 5.96 0.00 0.00 3.86
106 107 4.640771 TTGGCAAGTAGAGAAACTCCAT 57.359 40.909 0.00 0.00 0.00 3.41
141 201 7.993416 AGTGACTCCATTATCATATTTCCCAT 58.007 34.615 0.00 0.00 0.00 4.00
178 238 9.301153 CTATTGGGAAACTTTGGAAATTTATCG 57.699 33.333 0.00 0.00 0.00 2.92
214 274 2.422597 CACTAACTCCAAATCCACGCA 58.577 47.619 0.00 0.00 0.00 5.24
316 376 3.394674 TCGAGACAATGGTAAAGCACA 57.605 42.857 0.00 0.00 0.00 4.57
344 404 2.288152 CCACAAAAATGACCGTTGGGAG 60.288 50.000 0.00 0.00 36.97 4.30
364 436 2.542595 AGTAAAGCGTGTTTTGACCGAG 59.457 45.455 0.00 0.00 0.00 4.63
365 437 1.658994 AAAGCGTGTTTTGACCGAGA 58.341 45.000 0.00 0.00 0.00 4.04
366 438 1.658994 AAGCGTGTTTTGACCGAGAA 58.341 45.000 0.00 0.00 0.00 2.87
367 439 1.878953 AGCGTGTTTTGACCGAGAAT 58.121 45.000 0.00 0.00 0.00 2.40
368 440 2.218603 AGCGTGTTTTGACCGAGAATT 58.781 42.857 0.00 0.00 0.00 2.17
369 441 2.616842 AGCGTGTTTTGACCGAGAATTT 59.383 40.909 0.00 0.00 0.00 1.82
370 442 2.719046 GCGTGTTTTGACCGAGAATTTG 59.281 45.455 0.00 0.00 0.00 2.32
371 443 3.547214 GCGTGTTTTGACCGAGAATTTGA 60.547 43.478 0.00 0.00 0.00 2.69
372 444 3.966218 CGTGTTTTGACCGAGAATTTGAC 59.034 43.478 0.00 0.00 0.00 3.18
373 445 4.287720 GTGTTTTGACCGAGAATTTGACC 58.712 43.478 0.00 0.00 0.00 4.02
374 446 3.002862 TGTTTTGACCGAGAATTTGACCG 59.997 43.478 0.00 0.00 0.00 4.79
375 447 2.823924 TTGACCGAGAATTTGACCGA 57.176 45.000 0.00 0.00 0.00 4.69
396 468 3.658757 TGGGACTAAAGTGCATTTTGC 57.341 42.857 16.66 6.49 45.29 3.68
424 496 1.128507 CTGATTCGCAGCTAAAACGCA 59.871 47.619 0.00 0.00 37.90 5.24
461 533 9.801873 ACACATAACATTAATTCATGGCTAAAC 57.198 29.630 4.70 0.00 0.00 2.01
498 570 6.139679 AGAATCTGACCATTGGGAGTAAAA 57.860 37.500 7.78 0.00 38.05 1.52
547 619 4.386652 TGTCTAAAGCGTGTTTTCGGATAC 59.613 41.667 0.00 0.00 0.00 2.24
551 623 1.001633 AGCGTGTTTTCGGATACCACT 59.998 47.619 0.00 0.00 0.00 4.00
658 731 6.804783 GGTGTAAAGTTTATTTTGGGATGACG 59.195 38.462 0.00 0.00 0.00 4.35
741 814 1.231221 TTTGATTGTGAACCGACCGG 58.769 50.000 6.94 6.94 42.03 5.28
800 873 2.891580 CACGGTAGGCATACTCCATAGT 59.108 50.000 8.63 0.00 39.91 2.12
804 877 1.704641 AGGCATACTCCATAGTCGCA 58.295 50.000 0.00 0.00 36.46 5.10
920 993 3.539604 CCCTACTTTGATGGCTTGAGAG 58.460 50.000 0.00 0.00 0.00 3.20
1020 1093 3.769739 ATGAGGGCGTTAGCATCATTA 57.230 42.857 5.11 0.00 43.98 1.90
1040 1113 2.829384 GCACCCCTTCTGTGGTCCA 61.829 63.158 0.00 0.00 34.27 4.02
1128 1201 4.077184 TCCGCCGCCTTCGATGTT 62.077 61.111 0.00 0.00 38.10 2.71
1140 1213 1.934589 TCGATGTTGGCGGATACTTG 58.065 50.000 0.00 0.00 0.00 3.16
1197 1270 4.870636 AGATGAAAATTGGGGACTATGCA 58.129 39.130 0.00 0.00 0.00 3.96
1371 1447 2.886523 CAAAGACTTCCTGCAACCATCA 59.113 45.455 0.00 0.00 0.00 3.07
1574 1650 3.554934 AGAGTTTCCATGCACACAAGAA 58.445 40.909 0.00 0.00 0.00 2.52
1642 1718 0.321653 GATGGGCGACAAGACAAGGT 60.322 55.000 0.00 0.00 0.00 3.50
1812 1888 1.202746 GCCATGGAGAGGATGAAGGTC 60.203 57.143 18.40 0.00 0.00 3.85
1958 2034 6.406370 CAAATAGAGTACAAGATGTGGTGGA 58.594 40.000 0.00 0.00 0.00 4.02
1967 2043 4.136796 CAAGATGTGGTGGAAAGTGAAGA 58.863 43.478 0.00 0.00 0.00 2.87
2074 2150 8.829373 TGCTCATCCTTGATTAGCTATATAGA 57.171 34.615 14.16 0.00 39.28 1.98
2230 2306 6.045318 TGTGAACATTAATCTCTGCTAGCTC 58.955 40.000 17.23 0.42 0.00 4.09
2453 2529 8.515414 GCAAGAGAGGATTTGTTGTAATTAACT 58.485 33.333 0.00 0.00 0.00 2.24
2491 2567 9.186837 AGATTCAAAGAATCTATGCAAGATGTT 57.813 29.630 17.95 6.56 44.56 2.71
2518 2594 9.739276 TTTGATATTGTCTGATTGAAGTAGGTT 57.261 29.630 0.00 0.00 0.00 3.50
2566 2642 6.377996 CCCAGACCAAAACATTCATCAATAGA 59.622 38.462 0.00 0.00 0.00 1.98
2609 2685 4.406326 TGCCATGCCTCATTAATCACAATT 59.594 37.500 0.00 0.00 0.00 2.32
2642 2718 5.708948 TCAATAGCCAAAACACATAGCAAC 58.291 37.500 0.00 0.00 0.00 4.17
2667 2743 3.719121 CTGGGTCTCCCTGTCTGG 58.281 66.667 6.38 0.00 45.70 3.86
2873 2950 9.258826 CAAAATCAACACTACCATTCAAATCAA 57.741 29.630 0.00 0.00 0.00 2.57
2875 2952 6.325919 TCAACACTACCATTCAAATCAACC 57.674 37.500 0.00 0.00 0.00 3.77
2876 2953 6.068010 TCAACACTACCATTCAAATCAACCT 58.932 36.000 0.00 0.00 0.00 3.50
2877 2954 7.227873 TCAACACTACCATTCAAATCAACCTA 58.772 34.615 0.00 0.00 0.00 3.08
2878 2955 7.174253 TCAACACTACCATTCAAATCAACCTAC 59.826 37.037 0.00 0.00 0.00 3.18
2879 2956 6.539173 ACACTACCATTCAAATCAACCTACA 58.461 36.000 0.00 0.00 0.00 2.74
2881 2958 7.669722 ACACTACCATTCAAATCAACCTACATT 59.330 33.333 0.00 0.00 0.00 2.71
2882 2959 8.522830 CACTACCATTCAAATCAACCTACATTT 58.477 33.333 0.00 0.00 0.00 2.32
2883 2960 9.747898 ACTACCATTCAAATCAACCTACATTTA 57.252 29.630 0.00 0.00 0.00 1.40
2885 2962 8.877864 ACCATTCAAATCAACCTACATTTAGA 57.122 30.769 0.00 0.00 0.00 2.10
2904 2981 4.450305 AGAAATATCAGCCAATGCCTCT 57.550 40.909 0.00 0.00 38.69 3.69
2905 2982 4.142790 AGAAATATCAGCCAATGCCTCTG 58.857 43.478 0.00 0.00 38.69 3.35
2909 2986 2.627515 TCAGCCAATGCCTCTGATAC 57.372 50.000 0.00 0.00 38.69 2.24
2910 2987 1.202568 TCAGCCAATGCCTCTGATACG 60.203 52.381 0.00 0.00 38.69 3.06
2912 2989 1.202580 AGCCAATGCCTCTGATACGTC 60.203 52.381 0.00 0.00 38.69 4.34
2913 2990 1.871080 CCAATGCCTCTGATACGTCC 58.129 55.000 0.00 0.00 0.00 4.79
2915 2992 2.224378 CCAATGCCTCTGATACGTCCAT 60.224 50.000 0.00 0.00 0.00 3.41
2916 2993 3.470709 CAATGCCTCTGATACGTCCATT 58.529 45.455 0.00 0.00 0.00 3.16
2917 2994 3.845781 ATGCCTCTGATACGTCCATTT 57.154 42.857 0.00 0.00 0.00 2.32
2918 2995 3.627395 TGCCTCTGATACGTCCATTTT 57.373 42.857 0.00 0.00 0.00 1.82
2919 2996 3.270027 TGCCTCTGATACGTCCATTTTG 58.730 45.455 0.00 0.00 0.00 2.44
2920 2997 2.032178 GCCTCTGATACGTCCATTTTGC 59.968 50.000 0.00 0.00 0.00 3.68
2921 2998 3.270027 CCTCTGATACGTCCATTTTGCA 58.730 45.455 0.00 0.00 0.00 4.08
2922 2999 3.879295 CCTCTGATACGTCCATTTTGCAT 59.121 43.478 0.00 0.00 0.00 3.96
2923 3000 4.024556 CCTCTGATACGTCCATTTTGCATC 60.025 45.833 0.00 0.00 0.00 3.91
2924 3001 4.512484 TCTGATACGTCCATTTTGCATCA 58.488 39.130 0.00 0.00 0.00 3.07
2925 3002 5.125356 TCTGATACGTCCATTTTGCATCAT 58.875 37.500 0.00 0.00 0.00 2.45
2927 3004 2.282701 ACGTCCATTTTGCATCATGC 57.717 45.000 1.35 1.35 45.29 4.06
2928 3005 1.820519 ACGTCCATTTTGCATCATGCT 59.179 42.857 11.84 0.00 45.31 3.79
2929 3006 2.231964 ACGTCCATTTTGCATCATGCTT 59.768 40.909 11.84 0.00 45.31 3.91
2930 3007 3.255725 CGTCCATTTTGCATCATGCTTT 58.744 40.909 11.84 0.00 45.31 3.51
2931 3008 3.680937 CGTCCATTTTGCATCATGCTTTT 59.319 39.130 11.84 0.00 45.31 2.27
2932 3009 4.863689 CGTCCATTTTGCATCATGCTTTTA 59.136 37.500 11.84 0.00 45.31 1.52
2933 3010 5.521010 CGTCCATTTTGCATCATGCTTTTAT 59.479 36.000 11.84 0.00 45.31 1.40
2935 3012 7.383029 CGTCCATTTTGCATCATGCTTTTATAT 59.617 33.333 11.84 0.00 45.31 0.86
2936 3013 8.706035 GTCCATTTTGCATCATGCTTTTATATC 58.294 33.333 11.84 0.00 45.31 1.63
2937 3014 7.595875 TCCATTTTGCATCATGCTTTTATATCG 59.404 33.333 11.84 0.00 45.31 2.92
2938 3015 7.595875 CCATTTTGCATCATGCTTTTATATCGA 59.404 33.333 11.84 0.00 45.31 3.59
2939 3016 9.135843 CATTTTGCATCATGCTTTTATATCGAT 57.864 29.630 11.84 2.16 45.31 3.59
2959 3036 7.087409 TCGATATTTATTGCATTATGGGCTG 57.913 36.000 0.00 0.00 0.00 4.85
2960 3037 6.658816 TCGATATTTATTGCATTATGGGCTGT 59.341 34.615 0.00 0.00 0.00 4.40
2962 3039 8.458052 CGATATTTATTGCATTATGGGCTGTTA 58.542 33.333 0.00 0.00 0.00 2.41
2966 3043 9.927668 ATTTATTGCATTATGGGCTGTTATTAC 57.072 29.630 0.00 0.00 0.00 1.89
2968 3045 5.766150 TGCATTATGGGCTGTTATTACAC 57.234 39.130 0.00 0.00 0.00 2.90
2969 3046 4.274705 TGCATTATGGGCTGTTATTACACG 59.725 41.667 0.00 0.00 0.00 4.49
2970 3047 4.274950 GCATTATGGGCTGTTATTACACGT 59.725 41.667 0.00 0.00 0.00 4.49
2972 3049 6.017770 GCATTATGGGCTGTTATTACACGTTA 60.018 38.462 0.00 0.00 0.00 3.18
2974 3051 7.485418 TTATGGGCTGTTATTACACGTTATG 57.515 36.000 0.00 0.00 0.00 1.90
2976 3053 4.871557 TGGGCTGTTATTACACGTTATGTC 59.128 41.667 0.00 0.00 42.09 3.06
2980 3057 5.444877 GCTGTTATTACACGTTATGTCGCAA 60.445 40.000 0.00 0.00 42.09 4.85
2981 3058 6.650239 TGTTATTACACGTTATGTCGCAAT 57.350 33.333 0.00 0.00 42.09 3.56
2983 3060 7.611387 TGTTATTACACGTTATGTCGCAATAC 58.389 34.615 0.00 0.00 42.09 1.89
2984 3061 7.488792 TGTTATTACACGTTATGTCGCAATACT 59.511 33.333 0.00 0.00 42.09 2.12
2985 3062 6.897259 ATTACACGTTATGTCGCAATACTT 57.103 33.333 0.00 0.00 42.09 2.24
2987 3064 7.990541 TTACACGTTATGTCGCAATACTTAT 57.009 32.000 0.00 0.00 42.09 1.73
2988 3065 6.268797 ACACGTTATGTCGCAATACTTATG 57.731 37.500 0.00 0.00 36.54 1.90
2989 3066 5.130519 CACGTTATGTCGCAATACTTATGC 58.869 41.667 0.00 0.00 40.41 3.14
2990 3067 4.210537 ACGTTATGTCGCAATACTTATGCC 59.789 41.667 0.00 0.00 40.72 4.40
2991 3068 4.447724 CGTTATGTCGCAATACTTATGCCT 59.552 41.667 0.00 0.00 40.72 4.75
2994 3071 7.148639 CGTTATGTCGCAATACTTATGCCTATT 60.149 37.037 0.00 0.00 40.72 1.73
2995 3072 6.727824 ATGTCGCAATACTTATGCCTATTC 57.272 37.500 0.00 0.00 40.72 1.75
2996 3073 5.853936 TGTCGCAATACTTATGCCTATTCT 58.146 37.500 0.00 0.00 40.72 2.40
2997 3074 5.926542 TGTCGCAATACTTATGCCTATTCTC 59.073 40.000 0.00 0.00 40.72 2.87
3000 3077 6.209589 TCGCAATACTTATGCCTATTCTCTCT 59.790 38.462 0.00 0.00 40.72 3.10
3002 3079 7.148672 CGCAATACTTATGCCTATTCTCTCTTG 60.149 40.741 0.00 0.00 40.72 3.02
3003 3080 7.659390 GCAATACTTATGCCTATTCTCTCTTGT 59.341 37.037 0.00 0.00 37.85 3.16
3026 3103 7.936584 TGTTTTACAAGGTTTACATGAAGAGG 58.063 34.615 0.00 0.00 0.00 3.69
3029 3106 4.911390 ACAAGGTTTACATGAAGAGGGAG 58.089 43.478 0.00 0.00 0.00 4.30
3031 3108 5.073144 ACAAGGTTTACATGAAGAGGGAGAA 59.927 40.000 0.00 0.00 0.00 2.87
3033 3110 5.749462 AGGTTTACATGAAGAGGGAGAATG 58.251 41.667 0.00 0.00 0.00 2.67
3034 3111 4.336713 GGTTTACATGAAGAGGGAGAATGC 59.663 45.833 0.00 0.00 0.00 3.56
3042 3119 4.496336 GGGAGAATGCCGGCAGCT 62.496 66.667 35.36 31.54 44.23 4.24
3044 3121 3.207669 GAGAATGCCGGCAGCTGG 61.208 66.667 35.36 17.00 44.23 4.85
3046 3123 2.751436 GAATGCCGGCAGCTGGAA 60.751 61.111 35.36 15.43 44.23 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 6.174049 GCCAATTTGAGAGTTACTCTTAGGT 58.826 40.000 16.60 2.34 41.35 3.08
214 274 9.520204 CTTGTGATTGTTTCTTGTAATTCACTT 57.480 29.630 0.00 0.00 0.00 3.16
316 376 3.576550 ACGGTCATTTTTGTGGCCTAAAT 59.423 39.130 3.32 2.15 41.76 1.40
344 404 2.540931 TCTCGGTCAAAACACGCTTTAC 59.459 45.455 0.00 0.00 0.00 2.01
364 436 4.941873 ACTTTAGTCCCATCGGTCAAATTC 59.058 41.667 0.00 0.00 0.00 2.17
365 437 4.700213 CACTTTAGTCCCATCGGTCAAATT 59.300 41.667 0.00 0.00 0.00 1.82
366 438 4.261801 CACTTTAGTCCCATCGGTCAAAT 58.738 43.478 0.00 0.00 0.00 2.32
367 439 3.670625 CACTTTAGTCCCATCGGTCAAA 58.329 45.455 0.00 0.00 0.00 2.69
368 440 2.614481 GCACTTTAGTCCCATCGGTCAA 60.614 50.000 0.00 0.00 0.00 3.18
369 441 1.066430 GCACTTTAGTCCCATCGGTCA 60.066 52.381 0.00 0.00 0.00 4.02
370 442 1.066430 TGCACTTTAGTCCCATCGGTC 60.066 52.381 0.00 0.00 0.00 4.79
371 443 0.981183 TGCACTTTAGTCCCATCGGT 59.019 50.000 0.00 0.00 0.00 4.69
372 444 2.332063 ATGCACTTTAGTCCCATCGG 57.668 50.000 0.00 0.00 0.00 4.18
373 445 4.414852 CAAAATGCACTTTAGTCCCATCG 58.585 43.478 0.00 0.00 0.00 3.84
374 446 4.176271 GCAAAATGCACTTTAGTCCCATC 58.824 43.478 0.00 0.00 44.26 3.51
375 447 3.367292 CGCAAAATGCACTTTAGTCCCAT 60.367 43.478 0.00 0.00 45.36 4.00
396 468 2.196749 AGCTGCGAATCAGTGTTATCG 58.803 47.619 9.51 9.51 44.66 2.92
404 476 1.128507 TGCGTTTTAGCTGCGAATCAG 59.871 47.619 0.00 0.00 45.62 2.90
461 533 2.157668 CAGATTCTCGGTCAAAACACGG 59.842 50.000 0.00 0.00 0.00 4.94
498 570 9.874205 ACGAATCAATGTTATCCAAAAATGAAT 57.126 25.926 0.00 0.00 0.00 2.57
547 619 5.587388 AGCCATGAATCAATGTTAAGTGG 57.413 39.130 0.00 0.00 0.00 4.00
551 623 5.221028 CGCCTTAGCCATGAATCAATGTTAA 60.221 40.000 0.00 0.00 34.57 2.01
658 731 2.095768 TGCGCTTTAGCTGTCAATCAAC 60.096 45.455 9.73 0.00 39.32 3.18
741 814 5.412286 CCTATTTAGGGCTCTCGAGTACTAC 59.588 48.000 13.13 0.72 39.86 2.73
773 846 0.104304 GTATGCCTACCGTGGTCCAG 59.896 60.000 0.00 0.00 0.00 3.86
800 873 2.204461 TGAGGGAAAGGACGTGCGA 61.204 57.895 0.00 0.00 0.00 5.10
804 877 0.826672 ACTCGTGAGGGAAAGGACGT 60.827 55.000 1.43 0.00 33.92 4.34
855 928 2.094675 GAGGGGTTGATGGTGATGTTG 58.905 52.381 0.00 0.00 0.00 3.33
920 993 0.620556 TTCTGGATGGGGAGAACTGC 59.379 55.000 0.00 0.00 0.00 4.40
1020 1093 1.380302 GACCACAGAAGGGGTGCAT 59.620 57.895 0.00 0.00 37.57 3.96
1040 1113 5.679638 GCAATCTTGAAAGTGTGTGTTCCTT 60.680 40.000 0.00 0.00 0.00 3.36
1128 1201 2.125310 CGCCACAAGTATCCGCCA 60.125 61.111 0.00 0.00 0.00 5.69
1140 1213 1.287425 GGTAGTACTCAATGCGCCAC 58.713 55.000 4.18 0.00 0.00 5.01
1197 1270 5.595952 GCTCACAAAATCTAGGGAAATGGAT 59.404 40.000 0.00 0.00 0.00 3.41
1371 1447 3.347216 GTTGTCATCCTGCAGGTACAAT 58.653 45.455 33.12 20.91 36.56 2.71
1422 1498 0.323178 CTGCCACCTTGGATTCTGCT 60.323 55.000 0.00 0.00 40.96 4.24
1574 1650 1.213537 GACCGCATTGCAAGCACAT 59.786 52.632 17.22 5.42 0.00 3.21
1634 1710 1.774254 TGTTCATGGTCCACCTTGTCT 59.226 47.619 10.56 0.00 40.77 3.41
1642 1718 6.613679 TGTATACCTTCTATGTTCATGGTCCA 59.386 38.462 0.00 0.00 0.00 4.02
1958 2034 8.677148 TTTGAGTTTAGCATACTCTTCACTTT 57.323 30.769 12.24 0.00 41.99 2.66
1967 2043 5.817816 CGGGATCTTTTGAGTTTAGCATACT 59.182 40.000 0.00 0.00 0.00 2.12
2207 2283 5.174761 CGAGCTAGCAGAGATTAATGTTCAC 59.825 44.000 18.83 0.00 0.00 3.18
2420 2496 5.033589 ACAAATCCTCTCTTGCTCCTATG 57.966 43.478 0.00 0.00 0.00 2.23
2453 2529 9.144298 AGATTCTTTGAATCTACCGGTCTTATA 57.856 33.333 12.40 0.00 35.39 0.98
2491 2567 9.739276 ACCTACTTCAATCAGACAATATCAAAA 57.261 29.630 0.00 0.00 0.00 2.44
2518 2594 7.463941 TGGGATATCCTATTGTCCAATATTCCA 59.536 37.037 21.18 1.82 36.19 3.53
2566 2642 9.051679 CATGGCATGATGATGAAACAAAAATAT 57.948 29.630 22.91 0.00 0.00 1.28
2569 2645 5.122554 GCATGGCATGATGATGAAACAAAAA 59.877 36.000 30.69 0.00 0.00 1.94
2667 2743 2.604046 ATCACACGTAAGAGATGGGC 57.396 50.000 0.00 0.00 43.62 5.36
2873 2950 9.071276 CATTGGCTGATATTTCTAAATGTAGGT 57.929 33.333 0.00 0.00 0.00 3.08
2875 2952 8.025445 GGCATTGGCTGATATTTCTAAATGTAG 58.975 37.037 2.42 0.00 40.87 2.74
2876 2953 7.725397 AGGCATTGGCTGATATTTCTAAATGTA 59.275 33.333 12.53 0.00 40.87 2.29
2877 2954 6.552350 AGGCATTGGCTGATATTTCTAAATGT 59.448 34.615 12.53 0.00 40.87 2.71
2878 2955 6.989659 AGGCATTGGCTGATATTTCTAAATG 58.010 36.000 12.53 0.00 40.87 2.32
2879 2956 7.008941 AGAGGCATTGGCTGATATTTCTAAAT 58.991 34.615 18.51 0.00 38.98 1.40
2881 2958 5.766670 CAGAGGCATTGGCTGATATTTCTAA 59.233 40.000 18.51 0.00 38.98 2.10
2882 2959 5.072193 TCAGAGGCATTGGCTGATATTTCTA 59.928 40.000 18.51 0.00 38.98 2.10
2883 2960 4.141321 TCAGAGGCATTGGCTGATATTTCT 60.141 41.667 18.51 3.80 38.98 2.52
2884 2961 4.139786 TCAGAGGCATTGGCTGATATTTC 58.860 43.478 18.51 1.32 38.98 2.17
2885 2962 4.174704 TCAGAGGCATTGGCTGATATTT 57.825 40.909 18.51 0.00 38.98 1.40
2904 2981 4.497842 GCATGATGCAAAATGGACGTATCA 60.498 41.667 13.36 0.00 44.26 2.15
2905 2982 3.976942 GCATGATGCAAAATGGACGTATC 59.023 43.478 13.36 0.00 44.26 2.24
2908 2985 2.282701 GCATGATGCAAAATGGACGT 57.717 45.000 13.36 0.00 44.26 4.34
2932 3009 9.578576 AGCCCATAATGCAATAAATATCGATAT 57.421 29.630 12.25 12.25 0.00 1.63
2933 3010 8.839343 CAGCCCATAATGCAATAAATATCGATA 58.161 33.333 7.75 7.75 0.00 2.92
2935 3012 6.658816 ACAGCCCATAATGCAATAAATATCGA 59.341 34.615 0.00 0.00 0.00 3.59
2936 3013 6.855836 ACAGCCCATAATGCAATAAATATCG 58.144 36.000 0.00 0.00 0.00 2.92
2941 3018 8.918116 TGTAATAACAGCCCATAATGCAATAAA 58.082 29.630 0.00 0.00 0.00 1.40
2942 3019 8.356657 GTGTAATAACAGCCCATAATGCAATAA 58.643 33.333 0.00 0.00 35.91 1.40
2943 3020 7.308288 CGTGTAATAACAGCCCATAATGCAATA 60.308 37.037 0.00 0.00 35.91 1.90
2944 3021 6.514870 CGTGTAATAACAGCCCATAATGCAAT 60.515 38.462 0.00 0.00 35.91 3.56
2945 3022 5.220951 CGTGTAATAACAGCCCATAATGCAA 60.221 40.000 0.00 0.00 35.91 4.08
2947 3024 4.274950 ACGTGTAATAACAGCCCATAATGC 59.725 41.667 0.00 0.00 35.91 3.56
2948 3025 6.371809 AACGTGTAATAACAGCCCATAATG 57.628 37.500 0.00 0.00 35.91 1.90
2949 3026 7.717875 ACATAACGTGTAATAACAGCCCATAAT 59.282 33.333 0.00 0.00 39.91 1.28
2950 3027 7.049133 ACATAACGTGTAATAACAGCCCATAA 58.951 34.615 0.00 0.00 39.91 1.90
2954 3031 4.026310 CGACATAACGTGTAATAACAGCCC 60.026 45.833 0.00 0.00 42.36 5.19
2955 3032 4.549489 GCGACATAACGTGTAATAACAGCC 60.549 45.833 0.00 0.00 42.36 4.85
2956 3033 4.031991 TGCGACATAACGTGTAATAACAGC 59.968 41.667 0.00 0.00 42.36 4.40
2957 3034 5.689927 TGCGACATAACGTGTAATAACAG 57.310 39.130 0.00 0.00 42.36 3.16
2959 3036 7.834529 AGTATTGCGACATAACGTGTAATAAC 58.165 34.615 0.00 0.00 42.36 1.89
2960 3037 7.990541 AGTATTGCGACATAACGTGTAATAA 57.009 32.000 0.00 0.00 42.36 1.40
2962 3039 6.897259 AAGTATTGCGACATAACGTGTAAT 57.103 33.333 0.00 0.00 42.36 1.89
2965 3042 5.276678 GCATAAGTATTGCGACATAACGTGT 60.277 40.000 0.00 0.00 45.83 4.49
2966 3043 5.130519 GCATAAGTATTGCGACATAACGTG 58.869 41.667 0.00 0.00 35.59 4.49
2968 3045 4.447724 AGGCATAAGTATTGCGACATAACG 59.552 41.667 0.00 0.00 41.07 3.18
2969 3046 5.924475 AGGCATAAGTATTGCGACATAAC 57.076 39.130 0.00 0.00 41.07 1.89
2970 3047 8.094548 AGAATAGGCATAAGTATTGCGACATAA 58.905 33.333 0.00 0.00 41.07 1.90
2972 3049 6.467677 AGAATAGGCATAAGTATTGCGACAT 58.532 36.000 0.00 0.00 41.07 3.06
2974 3051 6.159988 AGAGAATAGGCATAAGTATTGCGAC 58.840 40.000 0.00 0.00 41.07 5.19
2976 3053 6.393990 AGAGAGAATAGGCATAAGTATTGCG 58.606 40.000 0.00 0.00 41.07 4.85
2983 3060 9.383519 TGTAAAACAAGAGAGAATAGGCATAAG 57.616 33.333 0.00 0.00 0.00 1.73
2984 3061 9.733556 TTGTAAAACAAGAGAGAATAGGCATAA 57.266 29.630 0.00 0.00 32.34 1.90
3000 3077 8.410141 CCTCTTCATGTAAACCTTGTAAAACAA 58.590 33.333 0.00 0.00 36.54 2.83
3002 3079 7.229907 TCCCTCTTCATGTAAACCTTGTAAAAC 59.770 37.037 0.00 0.00 0.00 2.43
3003 3080 7.291566 TCCCTCTTCATGTAAACCTTGTAAAA 58.708 34.615 0.00 0.00 0.00 1.52
3006 3083 5.783360 TCTCCCTCTTCATGTAAACCTTGTA 59.217 40.000 0.00 0.00 0.00 2.41
3007 3084 4.597507 TCTCCCTCTTCATGTAAACCTTGT 59.402 41.667 0.00 0.00 0.00 3.16
3011 3088 4.336713 GCATTCTCCCTCTTCATGTAAACC 59.663 45.833 0.00 0.00 0.00 3.27
3012 3089 4.336713 GGCATTCTCCCTCTTCATGTAAAC 59.663 45.833 0.00 0.00 0.00 2.01
3014 3091 3.432186 CGGCATTCTCCCTCTTCATGTAA 60.432 47.826 0.00 0.00 0.00 2.41
3015 3092 2.103094 CGGCATTCTCCCTCTTCATGTA 59.897 50.000 0.00 0.00 0.00 2.29
3016 3093 1.134280 CGGCATTCTCCCTCTTCATGT 60.134 52.381 0.00 0.00 0.00 3.21
3017 3094 1.590932 CGGCATTCTCCCTCTTCATG 58.409 55.000 0.00 0.00 0.00 3.07
3019 3096 1.907739 CCGGCATTCTCCCTCTTCA 59.092 57.895 0.00 0.00 0.00 3.02
3021 3098 2.262774 CTGCCGGCATTCTCCCTCTT 62.263 60.000 32.87 0.00 0.00 2.85
3022 3099 2.688666 TGCCGGCATTCTCCCTCT 60.689 61.111 29.03 0.00 0.00 3.69
3024 3101 4.496336 GCTGCCGGCATTCTCCCT 62.496 66.667 32.87 0.00 41.35 4.20
3026 3103 3.207669 CAGCTGCCGGCATTCTCC 61.208 66.667 32.87 15.69 44.79 3.71
3029 3106 2.751436 TTCCAGCTGCCGGCATTC 60.751 61.111 32.87 24.20 44.79 2.67


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

AutoCloner maintained by Alex Coulton.