Multiple sequence alignment - TraesCS3A01G080500

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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 TraesCS3A01G080500 chr3A 100.000 3602 0 0 1 3602 51949249 51945648 0.000000e+00 6652.0
1 TraesCS3A01G080500 chr3D 98.189 3479 52 5 126 3602 31391342 31394811 0.000000e+00 6065.0
2 TraesCS3A01G080500 chr3D 80.444 900 136 26 282 1158 30625215 30626097 0.000000e+00 651.0
3 TraesCS3A01G080500 chr3B 80.493 892 138 24 295 1163 53243491 53242613 0.000000e+00 651.0
4 TraesCS3A01G080500 chr6D 96.774 62 1 1 3542 3602 216866145 216866206 6.360000e-18 102.0
5 TraesCS3A01G080500 chr6D 95.238 63 3 0 3540 3602 467669443 467669505 2.290000e-17 100.0
6 TraesCS3A01G080500 chr5D 96.721 61 2 0 3542 3602 268345412 268345352 6.360000e-18 102.0
7 TraesCS3A01G080500 chr5D 96.721 61 1 1 3542 3602 75804202 75804261 2.290000e-17 100.0
8 TraesCS3A01G080500 chr4D 96.721 61 2 0 3542 3602 506069558 506069618 6.360000e-18 102.0
9 TraesCS3A01G080500 chr7D 92.754 69 4 1 3530 3597 572205640 572205708 8.230000e-17 99.0
10 TraesCS3A01G080500 chr7D 93.846 65 2 2 3540 3602 133690960 133691024 2.960000e-16 97.1
11 TraesCS3A01G080500 chr2D 96.610 59 2 0 3542 3600 83849725 83849667 8.230000e-17 99.0


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 TraesCS3A01G080500 chr3A 51945648 51949249 3601 True 6652 6652 100.000 1 3602 1 chr3A.!!$R1 3601
1 TraesCS3A01G080500 chr3D 31391342 31394811 3469 False 6065 6065 98.189 126 3602 1 chr3D.!!$F2 3476
2 TraesCS3A01G080500 chr3D 30625215 30626097 882 False 651 651 80.444 282 1158 1 chr3D.!!$F1 876
3 TraesCS3A01G080500 chr3B 53242613 53243491 878 True 651 651 80.493 295 1163 1 chr3B.!!$R1 868

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
27 28 0.179150 GTGCGTGTGTTCTTTGGCAA 60.179 50.0 0.0 0.0 31.53 4.52 F
1180 1207 0.179111 TGCCTCCGTAAGCAATCTCG 60.179 55.0 0.0 0.0 35.69 4.04 F
1724 1751 0.599558 CATGCTTGGTGTGGTGGAAG 59.400 55.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1937 0.544357 ACTTCGTCCTGACATGGGGA 60.544 55.000 0.00 0.0 0.00 4.81 R
2493 2520 0.392998 CCATCTCAACTTGGACCGGG 60.393 60.000 6.32 0.0 34.81 5.73 R
2960 2988 1.400846 CAGGAACAAGCAGCAGCATAG 59.599 52.381 3.17 0.0 45.49 2.23 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
24 25 6.844696 ATATATAGTGCGTGTGTTCTTTGG 57.155 37.500 0.00 0.00 0.00 3.28
25 26 0.941542 TAGTGCGTGTGTTCTTTGGC 59.058 50.000 0.00 0.00 0.00 4.52
26 27 1.029408 AGTGCGTGTGTTCTTTGGCA 61.029 50.000 0.00 0.00 0.00 4.92
27 28 0.179150 GTGCGTGTGTTCTTTGGCAA 60.179 50.000 0.00 0.00 31.53 4.52
28 29 0.743688 TGCGTGTGTTCTTTGGCAAT 59.256 45.000 0.00 0.00 0.00 3.56
29 30 1.950216 TGCGTGTGTTCTTTGGCAATA 59.050 42.857 0.00 0.00 0.00 1.90
30 31 2.556189 TGCGTGTGTTCTTTGGCAATAT 59.444 40.909 0.00 0.00 0.00 1.28
31 32 3.171277 GCGTGTGTTCTTTGGCAATATC 58.829 45.455 0.00 0.00 0.00 1.63
32 33 3.119849 GCGTGTGTTCTTTGGCAATATCT 60.120 43.478 0.00 0.00 0.00 1.98
33 34 4.406069 CGTGTGTTCTTTGGCAATATCTG 58.594 43.478 0.00 0.00 0.00 2.90
53 54 7.841282 ATCTGCTAGTAGTATTTTCTAGGCA 57.159 36.000 7.77 0.00 33.81 4.75
54 55 7.655521 TCTGCTAGTAGTATTTTCTAGGCAA 57.344 36.000 7.77 0.00 33.81 4.52
55 56 8.074613 TCTGCTAGTAGTATTTTCTAGGCAAA 57.925 34.615 7.77 0.00 33.81 3.68
56 57 8.198109 TCTGCTAGTAGTATTTTCTAGGCAAAG 58.802 37.037 7.77 0.00 33.81 2.77
57 58 6.761714 TGCTAGTAGTATTTTCTAGGCAAAGC 59.238 38.462 0.00 0.00 33.81 3.51
58 59 6.074249 GCTAGTAGTATTTTCTAGGCAAAGCG 60.074 42.308 0.00 0.00 33.81 4.68
59 60 5.116882 AGTAGTATTTTCTAGGCAAAGCGG 58.883 41.667 0.00 0.00 0.00 5.52
60 61 3.951663 AGTATTTTCTAGGCAAAGCGGT 58.048 40.909 0.00 0.00 0.00 5.68
61 62 3.939592 AGTATTTTCTAGGCAAAGCGGTC 59.060 43.478 0.00 0.00 0.00 4.79
62 63 2.561478 TTTTCTAGGCAAAGCGGTCT 57.439 45.000 0.00 0.00 0.00 3.85
63 64 2.561478 TTTCTAGGCAAAGCGGTCTT 57.439 45.000 0.00 0.00 0.00 3.01
64 65 2.094762 TTCTAGGCAAAGCGGTCTTC 57.905 50.000 0.00 0.00 0.00 2.87
65 66 0.973632 TCTAGGCAAAGCGGTCTTCA 59.026 50.000 0.00 0.00 0.00 3.02
66 67 1.346395 TCTAGGCAAAGCGGTCTTCAA 59.654 47.619 0.00 0.00 0.00 2.69
67 68 2.151202 CTAGGCAAAGCGGTCTTCAAA 58.849 47.619 0.00 0.00 0.00 2.69
68 69 0.668535 AGGCAAAGCGGTCTTCAAAC 59.331 50.000 0.00 0.00 0.00 2.93
69 70 0.383949 GGCAAAGCGGTCTTCAAACA 59.616 50.000 0.00 0.00 0.00 2.83
70 71 1.477105 GCAAAGCGGTCTTCAAACAC 58.523 50.000 0.00 0.00 0.00 3.32
71 72 1.741993 CAAAGCGGTCTTCAAACACG 58.258 50.000 0.00 0.00 0.00 4.49
72 73 1.063469 CAAAGCGGTCTTCAAACACGT 59.937 47.619 0.00 0.00 0.00 4.49
73 74 2.228138 AAGCGGTCTTCAAACACGTA 57.772 45.000 0.00 0.00 0.00 3.57
74 75 1.779569 AGCGGTCTTCAAACACGTAG 58.220 50.000 0.00 0.00 0.00 3.51
75 76 0.788391 GCGGTCTTCAAACACGTAGG 59.212 55.000 0.00 0.00 0.00 3.18
76 77 1.425412 CGGTCTTCAAACACGTAGGG 58.575 55.000 0.00 0.00 0.00 3.53
77 78 1.804601 GGTCTTCAAACACGTAGGGG 58.195 55.000 0.00 0.00 0.00 4.79
78 79 1.609841 GGTCTTCAAACACGTAGGGGG 60.610 57.143 0.00 0.00 0.00 5.40
92 93 3.777075 GGGGGAGAGAGAGAGGGA 58.223 66.667 0.00 0.00 0.00 4.20
93 94 1.541672 GGGGGAGAGAGAGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
94 95 1.541672 GGGGAGAGAGAGAGGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
95 96 1.541672 GGGAGAGAGAGAGGGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
96 97 0.996762 GGGAGAGAGAGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
97 98 0.478507 GGAGAGAGAGAGGGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
98 99 1.518367 GAGAGAGAGAGGGAGGGAGA 58.482 60.000 0.00 0.00 0.00 3.71
99 100 1.421646 GAGAGAGAGAGGGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
100 101 1.222567 GAGAGAGAGGGAGGGAGAGT 58.777 60.000 0.00 0.00 0.00 3.24
101 102 0.926293 AGAGAGAGGGAGGGAGAGTG 59.074 60.000 0.00 0.00 0.00 3.51
102 103 0.629058 GAGAGAGGGAGGGAGAGTGT 59.371 60.000 0.00 0.00 0.00 3.55
103 104 1.847737 GAGAGAGGGAGGGAGAGTGTA 59.152 57.143 0.00 0.00 0.00 2.90
104 105 1.850345 AGAGAGGGAGGGAGAGTGTAG 59.150 57.143 0.00 0.00 0.00 2.74
105 106 1.847737 GAGAGGGAGGGAGAGTGTAGA 59.152 57.143 0.00 0.00 0.00 2.59
106 107 2.445525 GAGAGGGAGGGAGAGTGTAGAT 59.554 54.545 0.00 0.00 0.00 1.98
107 108 3.653836 GAGAGGGAGGGAGAGTGTAGATA 59.346 52.174 0.00 0.00 0.00 1.98
108 109 3.655777 AGAGGGAGGGAGAGTGTAGATAG 59.344 52.174 0.00 0.00 0.00 2.08
109 110 2.719705 AGGGAGGGAGAGTGTAGATAGG 59.280 54.545 0.00 0.00 0.00 2.57
110 111 2.447811 GGGAGGGAGAGTGTAGATAGGT 59.552 54.545 0.00 0.00 0.00 3.08
111 112 3.117054 GGGAGGGAGAGTGTAGATAGGTT 60.117 52.174 0.00 0.00 0.00 3.50
112 113 4.146564 GGAGGGAGAGTGTAGATAGGTTC 58.853 52.174 0.00 0.00 0.00 3.62
113 114 4.386536 GGAGGGAGAGTGTAGATAGGTTCA 60.387 50.000 0.00 0.00 0.00 3.18
114 115 5.202004 GAGGGAGAGTGTAGATAGGTTCAA 58.798 45.833 0.00 0.00 0.00 2.69
115 116 5.782925 AGGGAGAGTGTAGATAGGTTCAAT 58.217 41.667 0.00 0.00 0.00 2.57
116 117 6.206042 AGGGAGAGTGTAGATAGGTTCAATT 58.794 40.000 0.00 0.00 0.00 2.32
117 118 6.674419 AGGGAGAGTGTAGATAGGTTCAATTT 59.326 38.462 0.00 0.00 0.00 1.82
118 119 6.763610 GGGAGAGTGTAGATAGGTTCAATTTG 59.236 42.308 0.00 0.00 0.00 2.32
119 120 6.763610 GGAGAGTGTAGATAGGTTCAATTTGG 59.236 42.308 0.00 0.00 0.00 3.28
120 121 7.259088 AGAGTGTAGATAGGTTCAATTTGGT 57.741 36.000 0.00 0.00 0.00 3.67
121 122 8.375493 AGAGTGTAGATAGGTTCAATTTGGTA 57.625 34.615 0.00 0.00 0.00 3.25
122 123 8.822805 AGAGTGTAGATAGGTTCAATTTGGTAA 58.177 33.333 0.00 0.00 0.00 2.85
123 124 9.614792 GAGTGTAGATAGGTTCAATTTGGTAAT 57.385 33.333 0.00 0.00 0.00 1.89
124 125 9.975218 AGTGTAGATAGGTTCAATTTGGTAATT 57.025 29.630 0.00 0.00 34.29 1.40
452 465 2.615447 CTGTTTCACAGCAGCTTCTCAA 59.385 45.455 0.00 0.00 39.62 3.02
537 550 6.208599 TGGTGGTTGAAATTGAGATTAGGAAC 59.791 38.462 0.00 0.00 0.00 3.62
663 684 2.416202 TGTGTTATCGCTGTGAATGCTG 59.584 45.455 0.00 0.00 0.00 4.41
787 809 1.003233 GGAGGTTCCTGTGACCAGC 60.003 63.158 0.00 0.00 39.71 4.85
915 941 6.590292 GCTAAAGCTACATTGTACTTCTGTGA 59.410 38.462 10.20 0.00 38.21 3.58
974 1000 5.047731 CCATTTTGAGGAAAGGAGGAAAGAC 60.048 44.000 0.00 0.00 30.82 3.01
1144 1171 5.276584 CGAGAGTCAGGAATTTTTAGCATCG 60.277 44.000 0.00 0.00 0.00 3.84
1180 1207 0.179111 TGCCTCCGTAAGCAATCTCG 60.179 55.000 0.00 0.00 35.69 4.04
1189 1216 2.859273 AAGCAATCTCGCTCCACCCG 62.859 60.000 0.00 0.00 42.89 5.28
1413 1440 7.232941 GGAAGAGTTAGATAGGCTGTATAACCA 59.767 40.741 20.56 0.00 0.00 3.67
1414 1441 8.548880 AAGAGTTAGATAGGCTGTATAACCAA 57.451 34.615 20.56 0.00 0.00 3.67
1417 1444 9.075678 GAGTTAGATAGGCTGTATAACCAAGTA 57.924 37.037 20.56 0.00 0.00 2.24
1528 1555 5.368145 AGAGCATTGATTGGCGTAGATAAA 58.632 37.500 0.00 0.00 34.54 1.40
1724 1751 0.599558 CATGCTTGGTGTGGTGGAAG 59.400 55.000 0.00 0.00 0.00 3.46
1874 1901 3.217626 CTGTTGATAGGGCAAGGAATCC 58.782 50.000 0.00 0.00 0.00 3.01
1902 1929 2.094700 TCGAAGCGAGAGTACATTTGCT 60.095 45.455 5.74 5.74 0.00 3.91
1910 1937 4.449068 CGAGAGTACATTTGCTGTGAGTTT 59.551 41.667 0.00 0.00 38.92 2.66
1954 1981 4.521256 TGGTTCCAAACGATAAGGAAAAGG 59.479 41.667 0.00 0.00 42.59 3.11
2493 2520 2.742589 GCAGCTAAGGTTACACAAGTCC 59.257 50.000 0.00 0.00 0.00 3.85
2498 2525 0.765519 AGGTTACACAAGTCCCCGGT 60.766 55.000 0.00 0.00 0.00 5.28
2600 2627 3.560226 GGAGGAGCTCCCCATCTTA 57.440 57.895 29.54 0.00 44.36 2.10
2704 2731 6.636454 AGGTAGACCATTTGACCTAAATCA 57.364 37.500 0.66 0.00 40.59 2.57
2949 2977 0.615331 TGCTTAAGGGAGCCTGAGTG 59.385 55.000 4.29 0.00 42.01 3.51
2960 2988 4.767255 CTGAGTGCTGGCCCGTCC 62.767 72.222 0.00 0.00 0.00 4.79
3069 3097 2.376518 AGAATCTCCAGCTGGTTTCCAA 59.623 45.455 31.58 11.07 36.34 3.53
3070 3098 3.011032 AGAATCTCCAGCTGGTTTCCAAT 59.989 43.478 31.58 14.03 36.34 3.16
3093 3121 0.183492 TGTGCCAACTTGCTCTCCTT 59.817 50.000 0.00 0.00 0.00 3.36
3252 3280 9.862371 AGCAAGATATATAAGGTGAGTTATTCG 57.138 33.333 0.00 0.00 0.00 3.34
3254 3282 9.088512 CAAGATATATAAGGTGAGTTATTCGGC 57.911 37.037 0.00 0.00 0.00 5.54
3326 3354 8.235226 GTCATAGGCATGATGATAAAAGATGTG 58.765 37.037 0.00 0.00 43.03 3.21
3357 3385 5.356751 TGATTACAAATGCGAATACCAGCTT 59.643 36.000 0.00 0.00 0.00 3.74
3383 3411 6.633500 TCTTGAAACCACAATCCTTGTTAG 57.367 37.500 0.00 0.00 43.23 2.34
3455 3483 7.692460 ATTGTGAGCTAAATTCTTGTCATCA 57.308 32.000 0.00 0.00 0.00 3.07
3589 3617 7.016661 TGAGGAATAGTTATTCTTCATCCCCTC 59.983 40.741 17.60 11.36 46.85 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.238374 GCCAAAGAACACACGCACTATATATT 60.238 38.462 0.00 0.00 0.00 1.28
1 2 5.236478 GCCAAAGAACACACGCACTATATAT 59.764 40.000 0.00 0.00 0.00 0.86
2 3 4.569162 GCCAAAGAACACACGCACTATATA 59.431 41.667 0.00 0.00 0.00 0.86
3 4 3.374058 GCCAAAGAACACACGCACTATAT 59.626 43.478 0.00 0.00 0.00 0.86
4 5 2.739913 GCCAAAGAACACACGCACTATA 59.260 45.455 0.00 0.00 0.00 1.31
5 6 1.535462 GCCAAAGAACACACGCACTAT 59.465 47.619 0.00 0.00 0.00 2.12
6 7 0.941542 GCCAAAGAACACACGCACTA 59.058 50.000 0.00 0.00 0.00 2.74
7 8 1.029408 TGCCAAAGAACACACGCACT 61.029 50.000 0.00 0.00 0.00 4.40
8 9 0.179150 TTGCCAAAGAACACACGCAC 60.179 50.000 0.00 0.00 0.00 5.34
9 10 0.743688 ATTGCCAAAGAACACACGCA 59.256 45.000 0.00 0.00 0.00 5.24
10 11 2.697431 TATTGCCAAAGAACACACGC 57.303 45.000 0.00 0.00 0.00 5.34
11 12 4.406069 CAGATATTGCCAAAGAACACACG 58.594 43.478 0.00 0.00 0.00 4.49
27 28 9.535170 TGCCTAGAAAATACTACTAGCAGATAT 57.465 33.333 0.00 0.00 34.21 1.63
28 29 8.935614 TGCCTAGAAAATACTACTAGCAGATA 57.064 34.615 0.00 0.00 34.21 1.98
29 30 7.841282 TGCCTAGAAAATACTACTAGCAGAT 57.159 36.000 0.00 0.00 34.21 2.90
30 31 7.655521 TTGCCTAGAAAATACTACTAGCAGA 57.344 36.000 0.00 0.00 34.21 4.26
31 32 7.042389 GCTTTGCCTAGAAAATACTACTAGCAG 60.042 40.741 0.00 0.00 34.21 4.24
32 33 6.761714 GCTTTGCCTAGAAAATACTACTAGCA 59.238 38.462 0.00 0.00 34.21 3.49
33 34 6.074249 CGCTTTGCCTAGAAAATACTACTAGC 60.074 42.308 0.00 0.00 34.21 3.42
34 35 6.421202 CCGCTTTGCCTAGAAAATACTACTAG 59.579 42.308 0.00 0.00 35.00 2.57
35 36 6.127253 ACCGCTTTGCCTAGAAAATACTACTA 60.127 38.462 0.00 0.00 0.00 1.82
36 37 5.116882 CCGCTTTGCCTAGAAAATACTACT 58.883 41.667 0.00 0.00 0.00 2.57
37 38 4.874396 ACCGCTTTGCCTAGAAAATACTAC 59.126 41.667 0.00 0.00 0.00 2.73
38 39 5.093849 ACCGCTTTGCCTAGAAAATACTA 57.906 39.130 0.00 0.00 0.00 1.82
39 40 3.939592 GACCGCTTTGCCTAGAAAATACT 59.060 43.478 0.00 0.00 0.00 2.12
40 41 3.939592 AGACCGCTTTGCCTAGAAAATAC 59.060 43.478 0.00 0.00 0.00 1.89
41 42 4.216411 AGACCGCTTTGCCTAGAAAATA 57.784 40.909 0.00 0.00 0.00 1.40
42 43 3.073274 AGACCGCTTTGCCTAGAAAAT 57.927 42.857 0.00 0.00 0.00 1.82
43 44 2.561478 AGACCGCTTTGCCTAGAAAA 57.439 45.000 0.00 0.00 0.00 2.29
44 45 2.224426 TGAAGACCGCTTTGCCTAGAAA 60.224 45.455 0.00 0.00 33.61 2.52
45 46 1.346395 TGAAGACCGCTTTGCCTAGAA 59.654 47.619 0.00 0.00 33.61 2.10
46 47 0.973632 TGAAGACCGCTTTGCCTAGA 59.026 50.000 0.00 0.00 33.61 2.43
47 48 1.808411 TTGAAGACCGCTTTGCCTAG 58.192 50.000 0.00 0.00 33.61 3.02
48 49 1.877443 GTTTGAAGACCGCTTTGCCTA 59.123 47.619 0.00 0.00 33.61 3.93
49 50 0.668535 GTTTGAAGACCGCTTTGCCT 59.331 50.000 0.00 0.00 33.61 4.75
50 51 0.383949 TGTTTGAAGACCGCTTTGCC 59.616 50.000 0.00 0.00 33.61 4.52
51 52 1.477105 GTGTTTGAAGACCGCTTTGC 58.523 50.000 0.00 0.00 33.61 3.68
52 53 1.063469 ACGTGTTTGAAGACCGCTTTG 59.937 47.619 0.00 0.00 33.61 2.77
53 54 1.375551 ACGTGTTTGAAGACCGCTTT 58.624 45.000 0.00 0.00 33.61 3.51
54 55 2.132762 CTACGTGTTTGAAGACCGCTT 58.867 47.619 0.00 0.00 36.96 4.68
55 56 1.604693 CCTACGTGTTTGAAGACCGCT 60.605 52.381 0.00 0.00 0.00 5.52
56 57 0.788391 CCTACGTGTTTGAAGACCGC 59.212 55.000 0.00 0.00 0.00 5.68
57 58 1.425412 CCCTACGTGTTTGAAGACCG 58.575 55.000 0.00 0.00 0.00 4.79
58 59 1.609841 CCCCCTACGTGTTTGAAGACC 60.610 57.143 0.00 0.00 0.00 3.85
59 60 1.804601 CCCCCTACGTGTTTGAAGAC 58.195 55.000 0.00 0.00 0.00 3.01
75 76 1.541672 CTCCCTCTCTCTCTCCCCC 59.458 68.421 0.00 0.00 0.00 5.40
76 77 1.541672 CCTCCCTCTCTCTCTCCCC 59.458 68.421 0.00 0.00 0.00 4.81
77 78 0.996762 TCCCTCCCTCTCTCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
78 79 0.478507 CTCCCTCCCTCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
79 80 1.421646 CTCTCCCTCCCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
80 81 1.275002 ACTCTCCCTCCCTCTCTCTCT 60.275 57.143 0.00 0.00 0.00 3.10
81 82 1.133792 CACTCTCCCTCCCTCTCTCTC 60.134 61.905 0.00 0.00 0.00 3.20
82 83 0.926293 CACTCTCCCTCCCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
83 84 0.629058 ACACTCTCCCTCCCTCTCTC 59.371 60.000 0.00 0.00 0.00 3.20
84 85 1.850345 CTACACTCTCCCTCCCTCTCT 59.150 57.143 0.00 0.00 0.00 3.10
85 86 1.847737 TCTACACTCTCCCTCCCTCTC 59.152 57.143 0.00 0.00 0.00 3.20
86 87 1.988539 TCTACACTCTCCCTCCCTCT 58.011 55.000 0.00 0.00 0.00 3.69
87 88 3.245122 CCTATCTACACTCTCCCTCCCTC 60.245 56.522 0.00 0.00 0.00 4.30
88 89 2.719705 CCTATCTACACTCTCCCTCCCT 59.280 54.545 0.00 0.00 0.00 4.20
89 90 2.447811 ACCTATCTACACTCTCCCTCCC 59.552 54.545 0.00 0.00 0.00 4.30
90 91 3.887916 ACCTATCTACACTCTCCCTCC 57.112 52.381 0.00 0.00 0.00 4.30
91 92 4.794334 TGAACCTATCTACACTCTCCCTC 58.206 47.826 0.00 0.00 0.00 4.30
92 93 4.883021 TGAACCTATCTACACTCTCCCT 57.117 45.455 0.00 0.00 0.00 4.20
93 94 6.487299 AATTGAACCTATCTACACTCTCCC 57.513 41.667 0.00 0.00 0.00 4.30
94 95 6.763610 CCAAATTGAACCTATCTACACTCTCC 59.236 42.308 0.00 0.00 0.00 3.71
95 96 7.331791 ACCAAATTGAACCTATCTACACTCTC 58.668 38.462 0.00 0.00 0.00 3.20
96 97 7.259088 ACCAAATTGAACCTATCTACACTCT 57.741 36.000 0.00 0.00 0.00 3.24
97 98 9.614792 ATTACCAAATTGAACCTATCTACACTC 57.385 33.333 0.00 0.00 0.00 3.51
98 99 9.975218 AATTACCAAATTGAACCTATCTACACT 57.025 29.630 0.00 0.00 33.97 3.55
113 114 6.001460 TCCGAGACAGAACAATTACCAAATT 58.999 36.000 0.00 0.00 35.65 1.82
114 115 5.556915 TCCGAGACAGAACAATTACCAAAT 58.443 37.500 0.00 0.00 0.00 2.32
115 116 4.963373 TCCGAGACAGAACAATTACCAAA 58.037 39.130 0.00 0.00 0.00 3.28
116 117 4.610605 TCCGAGACAGAACAATTACCAA 57.389 40.909 0.00 0.00 0.00 3.67
117 118 4.610605 TTCCGAGACAGAACAATTACCA 57.389 40.909 0.00 0.00 0.00 3.25
118 119 4.142881 GCTTTCCGAGACAGAACAATTACC 60.143 45.833 0.00 0.00 0.00 2.85
119 120 4.451096 TGCTTTCCGAGACAGAACAATTAC 59.549 41.667 0.00 0.00 0.00 1.89
120 121 4.637276 TGCTTTCCGAGACAGAACAATTA 58.363 39.130 0.00 0.00 0.00 1.40
121 122 3.476552 TGCTTTCCGAGACAGAACAATT 58.523 40.909 0.00 0.00 0.00 2.32
122 123 3.126001 TGCTTTCCGAGACAGAACAAT 57.874 42.857 0.00 0.00 0.00 2.71
123 124 2.613026 TGCTTTCCGAGACAGAACAA 57.387 45.000 0.00 0.00 0.00 2.83
124 125 2.416747 CATGCTTTCCGAGACAGAACA 58.583 47.619 0.00 0.00 0.00 3.18
537 550 2.605338 CCAGAACAAAATGAGTGCACCG 60.605 50.000 14.63 0.00 0.00 4.94
713 734 3.743521 TCAGCCCATATAACTGCATGAC 58.256 45.455 0.00 0.00 0.00 3.06
915 941 3.019799 TGACTAGGAGGCTCGAATCTT 57.980 47.619 8.69 0.00 0.00 2.40
1144 1171 2.893489 AGGCATTCAAAGACTGGAAACC 59.107 45.455 0.00 0.00 0.00 3.27
1180 1207 2.434359 GTGTACAGCGGGTGGAGC 60.434 66.667 12.33 1.94 0.00 4.70
1307 1334 2.684001 ACATTCAATACGGAAGCGGA 57.316 45.000 0.00 0.00 0.00 5.54
1308 1335 3.713288 TCTACATTCAATACGGAAGCGG 58.287 45.455 0.00 0.00 0.00 5.52
1413 1440 3.093057 AGAACGACAGATCCAGCTACTT 58.907 45.455 0.00 0.00 0.00 2.24
1414 1441 2.729194 AGAACGACAGATCCAGCTACT 58.271 47.619 0.00 0.00 0.00 2.57
1417 1444 2.729194 AGTAGAACGACAGATCCAGCT 58.271 47.619 0.00 0.00 0.00 4.24
1528 1555 3.135348 TCTCGCCATCCTTGATTTGAGAT 59.865 43.478 0.00 0.00 0.00 2.75
1724 1751 4.008074 TCAAACCAAGTGTCTCATCCTC 57.992 45.455 0.00 0.00 0.00 3.71
1874 1901 8.420945 CAAATGTACTCTCGCTTCGATAAATAG 58.579 37.037 0.00 0.00 34.61 1.73
1910 1937 0.544357 ACTTCGTCCTGACATGGGGA 60.544 55.000 0.00 0.00 0.00 4.81
1954 1981 6.071952 TGCATAATCTCCTTGGTTTCTTCAAC 60.072 38.462 0.00 0.00 34.18 3.18
1976 2003 1.512230 GGCGCTCCAATCAATTGCA 59.488 52.632 7.64 0.00 36.48 4.08
2158 2185 6.991938 ACTGCCATTTCTTTTAGCATAACAA 58.008 32.000 0.00 0.00 32.11 2.83
2159 2186 6.588719 ACTGCCATTTCTTTTAGCATAACA 57.411 33.333 0.00 0.00 32.11 2.41
2493 2520 0.392998 CCATCTCAACTTGGACCGGG 60.393 60.000 6.32 0.00 34.81 5.73
2498 2525 4.996793 TCCAAAATCCATCTCAACTTGGA 58.003 39.130 0.00 0.00 45.69 3.53
2600 2627 6.094048 CAGGAAACGAATGACAATACCTGATT 59.906 38.462 0.00 0.00 43.12 2.57
2704 2731 4.019860 AGGATCAGAGCACTTAACACACAT 60.020 41.667 0.00 0.00 0.00 3.21
2949 2977 3.866582 AGCATAGGACGGGCCAGC 61.867 66.667 4.39 2.82 40.02 4.85
2960 2988 1.400846 CAGGAACAAGCAGCAGCATAG 59.599 52.381 3.17 0.00 45.49 2.23
3069 3097 3.077359 GAGAGCAAGTTGGCACACTAAT 58.923 45.455 4.75 0.00 39.29 1.73
3070 3098 2.494059 GAGAGCAAGTTGGCACACTAA 58.506 47.619 4.75 0.00 39.29 2.24
3093 3121 4.824479 TCATTACAGGAGACATGCAAGA 57.176 40.909 0.00 0.00 0.00 3.02
3127 3155 9.315525 CCCTTTCCGTTAATTTCTTAACAAAAA 57.684 29.630 8.47 6.83 44.59 1.94
3128 3156 7.927092 CCCCTTTCCGTTAATTTCTTAACAAAA 59.073 33.333 8.47 7.09 44.59 2.44
3129 3157 7.435305 CCCCTTTCCGTTAATTTCTTAACAAA 58.565 34.615 8.47 2.88 44.59 2.83
3130 3158 6.015265 CCCCCTTTCCGTTAATTTCTTAACAA 60.015 38.462 8.47 0.00 44.59 2.83
3131 3159 5.477637 CCCCCTTTCCGTTAATTTCTTAACA 59.522 40.000 8.47 0.00 44.59 2.41
3252 3280 2.861147 ACCAGGAACTAAGAACAGCC 57.139 50.000 0.00 0.00 36.02 4.85
3254 3282 5.470437 GGAAAGAACCAGGAACTAAGAACAG 59.530 44.000 0.00 0.00 36.02 3.16
3306 3334 5.190992 TGCACATCTTTTATCATCATGCC 57.809 39.130 0.00 0.00 0.00 4.40
3326 3354 7.323656 GGTATTCGCATTTGTAATCATAGTTGC 59.676 37.037 0.00 0.00 0.00 4.17
3343 3371 2.472695 AGAACAAGCTGGTATTCGCA 57.527 45.000 0.00 0.00 0.00 5.10
3357 3385 5.261209 CAAGGATTGTGGTTTCAAGAACA 57.739 39.130 0.00 0.00 42.34 3.18
3383 3411 6.171213 AGGCTAACATACTTGGTGTAACTTC 58.829 40.000 0.00 0.00 36.74 3.01
3455 3483 7.092668 ACCTTAATTACTCTTCCATCTCAAGCT 60.093 37.037 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.