Multiple sequence alignment - TraesCS3A01G322700

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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 TraesCS3A01G322700 chr3A 100.000 3356 0 0 1 3356 566318081 566321436 0.000000e+00 6198
1 TraesCS3A01G322700 chr3B 90.497 3399 229 48 1 3356 550805362 550802015 0.000000e+00 4401
2 TraesCS3A01G322700 chr3D 94.206 2123 107 8 735 2857 422660882 422658776 0.000000e+00 3225
3 TraesCS3A01G322700 chr3D 92.434 489 33 2 2868 3356 422658688 422658204 0.000000e+00 695
4 TraesCS3A01G322700 chr3D 86.176 340 34 7 73 400 422661501 422661163 4.120000e-94 355


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 TraesCS3A01G322700 chr3A 566318081 566321436 3355 False 6198 6198 100.000000 1 3356 1 chr3A.!!$F1 3355
1 TraesCS3A01G322700 chr3B 550802015 550805362 3347 True 4401 4401 90.497000 1 3356 1 chr3B.!!$R1 3355
2 TraesCS3A01G322700 chr3D 422658204 422661501 3297 True 1425 3225 90.938667 73 3356 3 chr3D.!!$R1 3283

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
687 746 0.386476 AAAAACGAGAAAACCCGCCC 59.614 50.0 0.0 0.0 0.00 6.13 F
994 1053 0.733150 GTTGCTCCGTTAATCAGGGC 59.267 55.0 0.0 0.0 0.00 5.19 F
1653 1712 0.029834 CCGCAGCAAATCTGGCATAC 59.970 55.0 0.0 0.0 43.06 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1613 0.036306 TCAAGAAAGCCTCCCGGAAC 59.964 55.000 0.73 0.0 0.0 3.62 R
2105 2164 0.111061 TGCACCATGGAGCTGACTTT 59.889 50.000 30.48 0.0 33.0 2.66 R
3036 3176 1.265095 GTGGTGTTGCTCTGTCATGTG 59.735 52.381 0.00 0.0 0.0 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
35 36 6.265876 GGTTGTTGTCCACCCTAAGATTTTAA 59.734 38.462 0.00 0.00 0.00 1.52
36 37 7.039293 GGTTGTTGTCCACCCTAAGATTTTAAT 60.039 37.037 0.00 0.00 0.00 1.40
38 39 9.589461 TTGTTGTCCACCCTAAGATTTTAATTA 57.411 29.630 0.00 0.00 0.00 1.40
40 41 9.457436 GTTGTCCACCCTAAGATTTTAATTAGA 57.543 33.333 0.00 0.00 31.87 2.10
43 44 8.989980 GTCCACCCTAAGATTTTAATTAGATCG 58.010 37.037 0.00 0.00 31.87 3.69
44 45 8.154856 TCCACCCTAAGATTTTAATTAGATCGG 58.845 37.037 0.00 4.40 31.87 4.18
45 46 7.094762 CCACCCTAAGATTTTAATTAGATCGGC 60.095 40.741 0.00 0.00 31.87 5.54
46 47 7.661847 CACCCTAAGATTTTAATTAGATCGGCT 59.338 37.037 0.00 0.00 31.87 5.52
47 48 7.878644 ACCCTAAGATTTTAATTAGATCGGCTC 59.121 37.037 0.00 0.00 31.87 4.70
48 49 7.878127 CCCTAAGATTTTAATTAGATCGGCTCA 59.122 37.037 0.00 0.00 31.87 4.26
49 50 9.442047 CCTAAGATTTTAATTAGATCGGCTCAT 57.558 33.333 0.00 0.00 31.87 2.90
51 52 7.678947 AGATTTTAATTAGATCGGCTCATGG 57.321 36.000 0.00 0.00 0.00 3.66
52 53 7.453393 AGATTTTAATTAGATCGGCTCATGGA 58.547 34.615 0.00 0.00 0.00 3.41
55 56 8.463930 TTTTAATTAGATCGGCTCATGGAAAT 57.536 30.769 0.00 0.00 0.00 2.17
57 58 9.567776 TTTAATTAGATCGGCTCATGGAAATTA 57.432 29.630 0.00 0.00 0.00 1.40
69 70 4.709397 TCATGGAAATTAAAATGACGGGCT 59.291 37.500 0.00 0.00 0.00 5.19
71 72 3.194542 TGGAAATTAAAATGACGGGCTGG 59.805 43.478 0.00 0.00 0.00 4.85
88 89 4.221482 GGGCTGGATGAGAAAAAGAAATGT 59.779 41.667 0.00 0.00 0.00 2.71
112 113 3.947910 ACAAATCTCGTCCGACCTTAA 57.052 42.857 0.00 0.00 0.00 1.85
113 114 3.582780 ACAAATCTCGTCCGACCTTAAC 58.417 45.455 0.00 0.00 0.00 2.01
134 135 1.142748 CTGGCCCAACAAAAACGCA 59.857 52.632 0.00 0.00 0.00 5.24
213 223 1.891919 GAACCAACTGGCACTCGCA 60.892 57.895 0.00 0.00 41.24 5.10
248 258 3.906846 TGGATTGGCCCAACTATGTTTTT 59.093 39.130 0.00 0.00 34.97 1.94
270 280 3.509575 TGTTAAATCCATTGACTGGTGGC 59.490 43.478 0.00 0.00 46.08 5.01
298 309 2.097036 TCGTTGACCGTCACCTATCAT 58.903 47.619 0.00 0.00 37.94 2.45
309 320 3.199946 GTCACCTATCATCCCTTGACCAA 59.800 47.826 0.00 0.00 37.11 3.67
311 322 3.455910 CACCTATCATCCCTTGACCAAGA 59.544 47.826 11.06 0.00 40.79 3.02
401 414 8.566008 AATTCGTGAATTTGAAAGAAGTTCAG 57.434 30.769 5.50 0.00 46.85 3.02
403 416 7.496529 TCGTGAATTTGAAAGAAGTTCAGAT 57.503 32.000 5.50 0.00 46.85 2.90
648 704 8.396390 GGATAAACGAAAATAAAAGGAGGAGAC 58.604 37.037 0.00 0.00 0.00 3.36
650 706 4.251268 ACGAAAATAAAAGGAGGAGACCG 58.749 43.478 0.00 0.00 34.73 4.79
652 708 4.622220 CGAAAATAAAAGGAGGAGACCGGA 60.622 45.833 9.46 0.00 34.73 5.14
653 709 4.921644 AAATAAAAGGAGGAGACCGGAA 57.078 40.909 9.46 0.00 34.73 4.30
657 713 1.730851 AAGGAGGAGACCGGAAAACT 58.269 50.000 9.46 0.00 34.73 2.66
659 715 0.974383 GGAGGAGACCGGAAAACTCA 59.026 55.000 9.46 0.00 33.00 3.41
668 724 1.533625 CGGAAAACTCATGCTGGGAA 58.466 50.000 0.00 0.00 0.00 3.97
669 725 1.885887 CGGAAAACTCATGCTGGGAAA 59.114 47.619 0.00 0.00 0.00 3.13
670 726 2.295909 CGGAAAACTCATGCTGGGAAAA 59.704 45.455 0.00 0.00 0.00 2.29
671 727 3.243704 CGGAAAACTCATGCTGGGAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
687 746 0.386476 AAAAACGAGAAAACCCGCCC 59.614 50.000 0.00 0.00 0.00 6.13
711 770 0.898326 AAACCGGCAGAATGTTCCCC 60.898 55.000 0.00 0.00 39.31 4.81
762 821 3.256631 GGCTGGCCCATTTTGATATGTAG 59.743 47.826 0.00 0.00 0.00 2.74
768 827 4.339247 GCCCATTTTGATATGTAGTGCTGT 59.661 41.667 0.00 0.00 0.00 4.40
769 828 5.734220 GCCCATTTTGATATGTAGTGCTGTG 60.734 44.000 0.00 0.00 0.00 3.66
771 830 5.589855 CCATTTTGATATGTAGTGCTGTGGA 59.410 40.000 0.00 0.00 0.00 4.02
772 831 6.263842 CCATTTTGATATGTAGTGCTGTGGAT 59.736 38.462 0.00 0.00 0.00 3.41
773 832 6.682423 TTTTGATATGTAGTGCTGTGGATG 57.318 37.500 0.00 0.00 0.00 3.51
774 833 5.357742 TTGATATGTAGTGCTGTGGATGT 57.642 39.130 0.00 0.00 0.00 3.06
775 834 6.478512 TTGATATGTAGTGCTGTGGATGTA 57.521 37.500 0.00 0.00 0.00 2.29
776 835 6.478512 TGATATGTAGTGCTGTGGATGTAA 57.521 37.500 0.00 0.00 0.00 2.41
777 836 6.515832 TGATATGTAGTGCTGTGGATGTAAG 58.484 40.000 0.00 0.00 0.00 2.34
778 837 4.826274 ATGTAGTGCTGTGGATGTAAGT 57.174 40.909 0.00 0.00 0.00 2.24
779 838 5.932619 ATGTAGTGCTGTGGATGTAAGTA 57.067 39.130 0.00 0.00 0.00 2.24
780 839 5.324784 TGTAGTGCTGTGGATGTAAGTAG 57.675 43.478 0.00 0.00 0.00 2.57
781 840 3.252974 AGTGCTGTGGATGTAAGTAGC 57.747 47.619 0.00 0.00 0.00 3.58
839 898 2.496341 CTCCGCCGCTTCTGATCA 59.504 61.111 0.00 0.00 0.00 2.92
852 911 2.048312 CTGATCACGACGGCTCGCTA 62.048 60.000 0.00 0.00 44.33 4.26
865 924 3.812019 CGCTACCTGCTCGTCGGT 61.812 66.667 0.00 0.00 40.11 4.69
949 1008 4.530875 CCAGCTGAAATTTCTGATAGGGT 58.469 43.478 24.40 9.06 0.00 4.34
994 1053 0.733150 GTTGCTCCGTTAATCAGGGC 59.267 55.000 0.00 0.00 0.00 5.19
1115 1174 1.925455 CTTCCCTCTCCAGCCCCAA 60.925 63.158 0.00 0.00 0.00 4.12
1236 1295 3.524606 GCGCTCCTTGCATGCCAT 61.525 61.111 16.68 0.00 43.06 4.40
1388 1447 3.499737 CCAGGTTCATGCGCGGAC 61.500 66.667 8.83 0.00 0.00 4.79
1398 1457 3.345808 GCGCGGACAGTTCTTGCA 61.346 61.111 8.83 0.00 0.00 4.08
1554 1613 1.442526 GATGCGTGGAGAATGGCCAG 61.443 60.000 13.05 0.00 35.77 4.85
1579 1638 1.340405 GGGAGGCTTTCTTGATGCTGA 60.340 52.381 0.00 0.00 0.00 4.26
1584 1643 1.340405 GCTTTCTTGATGCTGAGGGGA 60.340 52.381 0.00 0.00 0.00 4.81
1611 1670 4.630644 ACTCAATGGAATCACACTGACT 57.369 40.909 0.00 0.00 0.00 3.41
1653 1712 0.029834 CCGCAGCAAATCTGGCATAC 59.970 55.000 0.00 0.00 43.06 2.39
1668 1727 0.447801 CATACGGCCTTCAAGTGCAC 59.552 55.000 9.40 9.40 0.00 4.57
1795 1854 2.542020 TCGGATGACTTGCAGAAACA 57.458 45.000 0.00 0.00 0.00 2.83
1809 1868 3.319122 GCAGAAACATTGTTTCCTGGTCT 59.681 43.478 29.60 13.96 0.00 3.85
1812 1871 4.762251 AGAAACATTGTTTCCTGGTCTAGC 59.238 41.667 29.60 9.54 0.00 3.42
1870 1929 3.575687 AGAGGCTTTGGATTTGTTTGAGG 59.424 43.478 0.00 0.00 0.00 3.86
1908 1967 2.291800 ACCCATTGTCTTGCCTAATGCT 60.292 45.455 0.00 0.00 42.00 3.79
1981 2040 0.252197 AGGCCGGTCCAAGTTACATC 59.748 55.000 15.92 0.00 37.29 3.06
2096 2155 6.406370 CATGGGATCTCTACTGTTGTTTACA 58.594 40.000 0.00 0.00 34.95 2.41
2103 2162 9.088512 GATCTCTACTGTTGTTTACATTCGAAT 57.911 33.333 4.39 4.39 35.85 3.34
2105 2164 9.917129 TCTCTACTGTTGTTTACATTCGAATAA 57.083 29.630 10.97 0.00 35.85 1.40
2110 2169 9.659830 ACTGTTGTTTACATTCGAATAAAAGTC 57.340 29.630 10.97 4.94 35.85 3.01
2124 2183 0.111061 AAAGTCAGCTCCATGGTGCA 59.889 50.000 33.78 16.57 43.32 4.57
2144 2203 3.011818 CAATCTGTGTGGCTATGCTGAA 58.988 45.455 0.00 0.00 0.00 3.02
2187 2246 1.963515 GTGGCAAGAGGAAACATGGTT 59.036 47.619 0.00 0.00 0.00 3.67
2200 2259 5.067674 GGAAACATGGTTGCTGAGCATATTA 59.932 40.000 8.44 0.00 44.32 0.98
2280 2339 4.503817 GCTGCTGGACAATGGTCTATATCA 60.504 45.833 0.00 0.00 43.77 2.15
2285 2344 6.364568 TGGACAATGGTCTATATCAGATGG 57.635 41.667 0.00 0.00 43.77 3.51
2286 2345 6.084060 TGGACAATGGTCTATATCAGATGGA 58.916 40.000 0.00 0.00 43.77 3.41
2472 2532 7.524717 AACCTACAAATCAATGTTGCTAACT 57.475 32.000 0.00 0.00 34.75 2.24
2482 2542 0.237498 GTTGCTAACTGGTTCGTGGC 59.763 55.000 0.00 0.00 0.00 5.01
2533 2593 0.106268 TGCTTGAACCCAGCCTGAAA 60.106 50.000 0.00 0.00 0.00 2.69
2674 2736 8.422973 TCTGGAATTGTCAAAAATTGTTTCAG 57.577 30.769 0.00 0.00 29.89 3.02
2694 2757 3.126514 CAGCAAAACTCTATCCTGCACAG 59.873 47.826 0.00 0.00 35.44 3.66
2820 2883 6.669591 TCTGCTGGTACATGAATATAGGCTAT 59.330 38.462 12.41 12.41 38.20 2.97
2865 2928 8.795842 TCGTCAAATTTAATATTGGTGGTACT 57.204 30.769 0.00 0.00 0.00 2.73
2890 3030 6.174720 ACTGAAGTACATGTCCTTTTCTGA 57.825 37.500 0.00 0.00 0.00 3.27
2936 3076 5.904362 AATTTGGATCCTAAAGTGCAGTC 57.096 39.130 14.23 0.00 0.00 3.51
2948 3088 6.595326 CCTAAAGTGCAGTCATTTATCTGACA 59.405 38.462 6.95 0.00 46.45 3.58
2949 3089 6.882610 AAAGTGCAGTCATTTATCTGACAA 57.117 33.333 6.95 0.00 46.45 3.18
2959 3099 7.395489 AGTCATTTATCTGACAAAAGCCTCATT 59.605 33.333 6.95 0.00 46.45 2.57
2960 3100 8.031277 GTCATTTATCTGACAAAAGCCTCATTT 58.969 33.333 0.00 0.00 44.03 2.32
2987 3127 0.325671 TTCCCTGGTCCTCCTAGCAG 60.326 60.000 0.00 0.00 43.14 4.24
3017 3157 7.938140 TTACTCCATTTATCCCTTTGTTCAG 57.062 36.000 0.00 0.00 0.00 3.02
3018 3158 6.139679 ACTCCATTTATCCCTTTGTTCAGA 57.860 37.500 0.00 0.00 0.00 3.27
3020 3160 6.434340 ACTCCATTTATCCCTTTGTTCAGAAC 59.566 38.462 6.32 6.32 0.00 3.01
3036 3176 7.359595 TGTTCAGAACAAGCATGTAACAATAC 58.640 34.615 13.90 0.00 39.40 1.89
3058 3198 1.534163 CATGACAGAGCAACACCACAG 59.466 52.381 0.00 0.00 0.00 3.66
3084 3224 6.431234 AGGCTTTAAGTTTCAGGACATGTTAG 59.569 38.462 0.00 0.00 0.00 2.34
3093 3233 9.520515 AGTTTCAGGACATGTTAGTATTTTCAT 57.479 29.630 0.00 0.00 0.00 2.57
3126 3266 4.406069 CATGTGAACCTGTTAAATCAGCG 58.594 43.478 0.00 0.00 34.47 5.18
3127 3267 3.472652 TGTGAACCTGTTAAATCAGCGT 58.527 40.909 0.00 0.00 34.47 5.07
3144 3284 3.930229 CAGCGTAAAGGTACATGTGCTAA 59.070 43.478 13.86 0.00 0.00 3.09
3147 3287 4.201685 GCGTAAAGGTACATGTGCTAACAG 60.202 45.833 13.86 3.27 40.39 3.16
3230 3370 5.867174 TCATGACGAGTACACCTTGTATTTG 59.133 40.000 0.00 0.00 37.96 2.32
3232 3372 5.845103 TGACGAGTACACCTTGTATTTGAA 58.155 37.500 0.00 0.00 37.96 2.69
3237 3377 6.254281 AGTACACCTTGTATTTGAACATGC 57.746 37.500 0.00 0.00 35.05 4.06
3249 3389 6.822667 ATTTGAACATGCTGTGAATCACTA 57.177 33.333 14.97 1.75 35.11 2.74
3254 3394 4.759782 ACATGCTGTGAATCACTACCTAC 58.240 43.478 14.97 0.00 35.11 3.18
3262 3402 5.643348 TGTGAATCACTACCTACTTTGCATG 59.357 40.000 14.97 0.00 35.11 4.06
3270 3410 5.877012 ACTACCTACTTTGCATGACAAGATG 59.123 40.000 10.44 5.28 40.06 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.485578 AATTAAAATCTTAGGGTGGACAACAA 57.514 30.769 0.00 0.00 0.00 2.83
13 14 9.238368 CTAATTAAAATCTTAGGGTGGACAACA 57.762 33.333 0.00 0.00 0.00 3.33
35 36 8.463930 TTTTAATTTCCATGAGCCGATCTAAT 57.536 30.769 0.00 0.00 0.00 1.73
36 37 7.873719 TTTTAATTTCCATGAGCCGATCTAA 57.126 32.000 0.00 0.00 0.00 2.10
38 39 6.547141 TCATTTTAATTTCCATGAGCCGATCT 59.453 34.615 0.00 0.00 0.00 2.75
40 41 6.507023 GTCATTTTAATTTCCATGAGCCGAT 58.493 36.000 0.00 0.00 0.00 4.18
41 42 5.448496 CGTCATTTTAATTTCCATGAGCCGA 60.448 40.000 0.00 0.00 0.00 5.54
43 44 5.043248 CCGTCATTTTAATTTCCATGAGCC 58.957 41.667 0.00 0.00 0.00 4.70
44 45 5.043248 CCCGTCATTTTAATTTCCATGAGC 58.957 41.667 0.00 0.00 0.00 4.26
45 46 5.043248 GCCCGTCATTTTAATTTCCATGAG 58.957 41.667 0.00 0.00 0.00 2.90
46 47 4.709397 AGCCCGTCATTTTAATTTCCATGA 59.291 37.500 0.00 0.00 0.00 3.07
47 48 4.805192 CAGCCCGTCATTTTAATTTCCATG 59.195 41.667 0.00 0.00 0.00 3.66
48 49 4.141959 CCAGCCCGTCATTTTAATTTCCAT 60.142 41.667 0.00 0.00 0.00 3.41
49 50 3.194542 CCAGCCCGTCATTTTAATTTCCA 59.805 43.478 0.00 0.00 0.00 3.53
50 51 3.445805 TCCAGCCCGTCATTTTAATTTCC 59.554 43.478 0.00 0.00 0.00 3.13
51 52 4.712122 TCCAGCCCGTCATTTTAATTTC 57.288 40.909 0.00 0.00 0.00 2.17
52 53 4.709397 TCATCCAGCCCGTCATTTTAATTT 59.291 37.500 0.00 0.00 0.00 1.82
55 56 3.054728 TCTCATCCAGCCCGTCATTTTAA 60.055 43.478 0.00 0.00 0.00 1.52
57 58 1.281867 TCTCATCCAGCCCGTCATTTT 59.718 47.619 0.00 0.00 0.00 1.82
69 70 6.262049 TGTTCGACATTTCTTTTTCTCATCCA 59.738 34.615 0.00 0.00 0.00 3.41
71 72 8.560576 TTTGTTCGACATTTCTTTTTCTCATC 57.439 30.769 0.00 0.00 0.00 2.92
88 89 1.401931 GGTCGGACGAGATTTGTTCGA 60.402 52.381 1.43 0.00 44.62 3.71
112 113 1.136110 CGTTTTTGTTGGGCCAGAAGT 59.864 47.619 6.23 0.00 0.00 3.01
113 114 1.851658 CGTTTTTGTTGGGCCAGAAG 58.148 50.000 6.23 0.00 0.00 2.85
134 135 0.109781 GGCGCAATGTGATTGTTCGT 60.110 50.000 10.83 0.00 42.20 3.85
213 223 1.670811 CCAATCCATAAGCTTTCGCGT 59.329 47.619 3.20 0.00 42.32 6.01
229 239 4.972751 ACAAAAACATAGTTGGGCCAAT 57.027 36.364 23.95 13.70 0.00 3.16
231 241 5.871396 TTAACAAAAACATAGTTGGGCCA 57.129 34.783 0.00 0.00 0.00 5.36
298 309 3.045634 TCAACTCTTCTTGGTCAAGGGA 58.954 45.455 10.39 8.38 38.88 4.20
309 320 9.832445 TTGTAAAACTCAATAGTCAACTCTTCT 57.168 29.630 0.00 0.00 33.75 2.85
377 390 7.930217 TCTGAACTTCTTTCAAATTCACGAAT 58.070 30.769 0.00 0.00 43.90 3.34
440 494 8.655651 TTTCAAATCTTGTGAACCCATTTTAC 57.344 30.769 0.00 0.00 34.78 2.01
571 627 6.631238 TCGCTTTATTTCGTGAACTTTTCAAG 59.369 34.615 0.00 0.00 42.15 3.02
572 628 6.487960 TCGCTTTATTTCGTGAACTTTTCAA 58.512 32.000 0.00 0.00 42.15 2.69
625 681 6.369615 CGGTCTCCTCCTTTTATTTTCGTTTA 59.630 38.462 0.00 0.00 0.00 2.01
635 691 3.649502 AGTTTTCCGGTCTCCTCCTTTTA 59.350 43.478 0.00 0.00 0.00 1.52
636 692 2.442126 AGTTTTCCGGTCTCCTCCTTTT 59.558 45.455 0.00 0.00 0.00 2.27
648 704 0.322456 TCCCAGCATGAGTTTTCCGG 60.322 55.000 0.00 0.00 39.69 5.14
650 706 4.335400 TTTTTCCCAGCATGAGTTTTCC 57.665 40.909 0.00 0.00 39.69 3.13
668 724 0.386476 GGGCGGGTTTTCTCGTTTTT 59.614 50.000 0.00 0.00 46.75 1.94
669 725 0.752376 TGGGCGGGTTTTCTCGTTTT 60.752 50.000 0.00 0.00 46.75 2.43
670 726 1.152922 TGGGCGGGTTTTCTCGTTT 60.153 52.632 0.00 0.00 46.75 3.60
671 727 1.599797 CTGGGCGGGTTTTCTCGTT 60.600 57.895 0.00 0.00 46.75 3.85
672 728 2.032071 CTGGGCGGGTTTTCTCGT 59.968 61.111 0.00 0.00 46.75 4.18
681 740 3.370231 CCGGTTTTTCTGGGCGGG 61.370 66.667 0.00 0.00 38.86 6.13
687 746 3.308530 GAACATTCTGCCGGTTTTTCTG 58.691 45.455 1.90 0.00 0.00 3.02
718 777 3.188460 CCATGTAGGTCTTTTTGTCACCG 59.812 47.826 0.00 0.00 35.13 4.94
720 779 3.057526 GCCCATGTAGGTCTTTTTGTCAC 60.058 47.826 0.00 0.00 34.66 3.67
721 780 3.153919 GCCCATGTAGGTCTTTTTGTCA 58.846 45.455 0.00 0.00 34.66 3.58
722 781 3.191371 CAGCCCATGTAGGTCTTTTTGTC 59.809 47.826 0.00 0.00 34.66 3.18
730 789 2.193248 GGCCAGCCCATGTAGGTC 59.807 66.667 0.00 0.00 34.66 3.85
762 821 1.927174 CGCTACTTACATCCACAGCAC 59.073 52.381 0.00 0.00 0.00 4.40
768 827 3.802329 GCCTTATGCGCTACTTACATCCA 60.802 47.826 9.73 0.00 0.00 3.41
769 828 2.737252 GCCTTATGCGCTACTTACATCC 59.263 50.000 9.73 0.00 0.00 3.51
949 1008 3.991773 CGACGTAGAGGGTGAAAATTGAA 59.008 43.478 0.00 0.00 0.00 2.69
994 1053 2.753966 CCGTGCGAGCCATTTCCTG 61.754 63.158 0.00 0.00 0.00 3.86
1056 1115 2.938798 AATGCGGGGGAGTGGGAA 60.939 61.111 0.00 0.00 0.00 3.97
1134 1193 3.879159 GCTTTTGCGTAGGCGGTA 58.121 55.556 2.53 0.00 44.10 4.02
1182 1241 3.418913 CGCACGGGCATTTCGTCA 61.419 61.111 11.77 0.00 41.24 4.35
1227 1286 2.039974 GTGACGGACATGGCATGCA 61.040 57.895 26.70 13.47 0.00 3.96
1257 1316 1.372997 GAAGACTTCAGCGACGGCA 60.373 57.895 10.42 0.00 43.41 5.69
1374 1433 2.240612 GAACTGTCCGCGCATGAACC 62.241 60.000 8.75 0.00 0.00 3.62
1377 1436 1.005037 AAGAACTGTCCGCGCATGA 60.005 52.632 8.75 0.00 0.00 3.07
1380 1439 3.345808 GCAAGAACTGTCCGCGCA 61.346 61.111 8.75 0.00 0.00 6.09
1388 1447 1.210931 CCGTGGCATGCAAGAACTG 59.789 57.895 21.36 4.69 0.00 3.16
1422 1481 5.065704 TGTAGAGATCAACAAGAGCTGTC 57.934 43.478 0.00 0.00 44.50 3.51
1554 1613 0.036306 TCAAGAAAGCCTCCCGGAAC 59.964 55.000 0.73 0.00 0.00 3.62
1579 1638 4.402616 TTCCATTGAGTTCAATTCCCCT 57.597 40.909 4.66 0.00 43.48 4.79
1584 1643 6.491062 TCAGTGTGATTCCATTGAGTTCAATT 59.509 34.615 4.66 0.00 43.48 2.32
1653 1712 2.949106 CAGTGCACTTGAAGGCCG 59.051 61.111 18.94 0.00 0.00 6.13
1668 1727 1.699656 CGCATCGGAGAACCTTGCAG 61.700 60.000 0.00 0.00 43.58 4.41
1795 1854 4.574674 TCATGCTAGACCAGGAAACAAT 57.425 40.909 0.00 0.00 0.00 2.71
1809 1868 5.869344 GCGACTATAACCATCAATCATGCTA 59.131 40.000 0.00 0.00 0.00 3.49
1812 1871 4.996758 TGGCGACTATAACCATCAATCATG 59.003 41.667 0.00 0.00 0.00 3.07
1870 1929 1.134068 GGGTACAGCTTTCTCCATCCC 60.134 57.143 0.00 0.00 0.00 3.85
1908 1967 8.484641 CTGAGAGAACAGCAAGAAATGTAATA 57.515 34.615 0.00 0.00 0.00 0.98
1981 2040 8.975410 TCAATTGCATACTTTCTTTTCATCAG 57.025 30.769 0.00 0.00 0.00 2.90
2096 2155 5.297776 CCATGGAGCTGACTTTTATTCGAAT 59.702 40.000 16.15 16.15 0.00 3.34
2103 2162 2.224744 TGCACCATGGAGCTGACTTTTA 60.225 45.455 30.48 8.87 33.00 1.52
2105 2164 0.111061 TGCACCATGGAGCTGACTTT 59.889 50.000 30.48 0.00 33.00 2.66
2110 2169 0.738975 CAGATTGCACCATGGAGCTG 59.261 55.000 30.48 18.65 33.00 4.24
2124 2183 3.354948 TTCAGCATAGCCACACAGATT 57.645 42.857 0.00 0.00 0.00 2.40
2187 2246 4.102996 TCAACCTCCATAATATGCTCAGCA 59.897 41.667 0.00 0.00 44.86 4.41
2200 2259 3.117738 GGATTCTGTGGATCAACCTCCAT 60.118 47.826 0.00 0.00 46.67 3.41
2280 2339 7.295672 TCCATTATAACCTTCCTTGATCCATCT 59.704 37.037 0.00 0.00 0.00 2.90
2285 2344 7.229506 CCTTGTCCATTATAACCTTCCTTGATC 59.770 40.741 0.00 0.00 0.00 2.92
2286 2345 7.062957 CCTTGTCCATTATAACCTTCCTTGAT 58.937 38.462 0.00 0.00 0.00 2.57
2365 2424 6.121776 TGAACTGTACCTCCATATTTGTGT 57.878 37.500 0.00 0.00 0.00 3.72
2452 2511 6.892658 ACCAGTTAGCAACATTGATTTGTA 57.107 33.333 0.00 0.00 0.00 2.41
2533 2593 9.574516 ACTTAAGAACCAAGATAAACTGAATGT 57.425 29.630 10.09 0.00 0.00 2.71
2674 2736 3.338249 TCTGTGCAGGATAGAGTTTTGC 58.662 45.455 0.00 0.00 35.42 3.68
2731 2794 8.661352 AAATTGGTTATTTCACCTCTGTTTTG 57.339 30.769 0.00 0.00 37.75 2.44
2764 2827 2.618816 CCAGGAACCATCAAGCTAAGCA 60.619 50.000 0.00 0.00 0.00 3.91
2820 2883 8.996024 TGACGATTAATTTCAGAATACTGTCA 57.004 30.769 0.00 0.00 43.81 3.58
2854 2917 6.675413 TGTACTTCAGTTAGTACCACCAAT 57.325 37.500 10.45 0.00 46.37 3.16
2857 2920 6.034161 ACATGTACTTCAGTTAGTACCACC 57.966 41.667 0.00 0.00 46.37 4.61
2858 2921 6.071503 AGGACATGTACTTCAGTTAGTACCAC 60.072 42.308 4.17 0.00 46.37 4.16
2862 2925 8.867097 AGAAAAGGACATGTACTTCAGTTAGTA 58.133 33.333 23.60 0.00 31.17 1.82
2865 2928 7.732025 TCAGAAAAGGACATGTACTTCAGTTA 58.268 34.615 23.60 7.33 31.17 2.24
2936 3076 8.767478 AAAATGAGGCTTTTGTCAGATAAATG 57.233 30.769 0.00 0.00 0.00 2.32
2948 3088 6.099701 AGGGAAACTTGTAAAATGAGGCTTTT 59.900 34.615 0.00 0.00 33.17 2.27
2949 3089 5.602561 AGGGAAACTTGTAAAATGAGGCTTT 59.397 36.000 0.00 0.00 0.00 3.51
2959 3099 3.181437 GGAGGACCAGGGAAACTTGTAAA 60.181 47.826 0.00 0.00 35.23 2.01
2960 3100 2.374170 GGAGGACCAGGGAAACTTGTAA 59.626 50.000 0.00 0.00 35.23 2.41
3017 3157 7.496704 CATGTGTATTGTTACATGCTTGTTC 57.503 36.000 10.85 5.74 45.09 3.18
3036 3176 1.265095 GTGGTGTTGCTCTGTCATGTG 59.735 52.381 0.00 0.00 0.00 3.21
3041 3181 1.506493 CTCTGTGGTGTTGCTCTGTC 58.494 55.000 0.00 0.00 0.00 3.51
3058 3198 4.762251 ACATGTCCTGAAACTTAAAGCCTC 59.238 41.667 0.00 0.00 0.00 4.70
3084 3224 7.661437 TCACATGCACCCTATCTATGAAAATAC 59.339 37.037 0.00 0.00 0.00 1.89
3093 3233 3.134623 CAGGTTCACATGCACCCTATCTA 59.865 47.826 5.83 0.00 31.42 1.98
3126 3266 5.243207 ACCTGTTAGCACATGTACCTTTAC 58.757 41.667 0.00 1.61 30.60 2.01
3127 3267 5.492855 ACCTGTTAGCACATGTACCTTTA 57.507 39.130 0.00 0.00 30.60 1.85
3144 3284 2.047061 TCAACCAAGCTCACTACCTGT 58.953 47.619 0.00 0.00 0.00 4.00
3147 3287 6.759497 ATTATTTCAACCAAGCTCACTACC 57.241 37.500 0.00 0.00 0.00 3.18
3155 3295 8.691661 TCTATAGGGAATTATTTCAACCAAGC 57.308 34.615 0.00 0.00 33.23 4.01
3237 3377 5.237815 TGCAAAGTAGGTAGTGATTCACAG 58.762 41.667 18.57 0.00 36.74 3.66
3249 3389 4.910195 TCATCTTGTCATGCAAAGTAGGT 58.090 39.130 0.00 0.00 36.53 3.08
3254 3394 7.811236 ACAATTAGTTCATCTTGTCATGCAAAG 59.189 33.333 0.00 0.00 36.53 2.77


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

AutoCloner maintained by Alex Coulton.