Multiple sequence alignment - TraesCS6B01G432300

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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 TraesCS6B01G432300 chr6B 100.000 3297 0 0 1 3297 701663415 701660119 0.000000e+00 6089
1 TraesCS6B01G432300 chr6D 91.263 3285 134 58 127 3297 460575460 460572215 0.000000e+00 4335
2 TraesCS6B01G432300 chr6A 93.064 1139 66 11 2166 3297 606767063 606765931 0.000000e+00 1653
3 TraesCS6B01G432300 chr6A 84.948 1342 94 44 115 1395 606769096 606767802 0.000000e+00 1260
4 TraesCS6B01G432300 chr6A 91.791 804 50 10 1283 2077 606767863 606767067 0.000000e+00 1105
5 TraesCS6B01G432300 chr5D 93.750 96 6 0 2072 2167 561630087 561629992 9.540000e-31 145
6 TraesCS6B01G432300 chr2B 93.000 100 6 1 2065 2164 63783717 63783815 9.540000e-31 145
7 TraesCS6B01G432300 chr1D 89.655 116 7 5 2064 2177 301353492 301353604 3.430000e-30 143
8 TraesCS6B01G432300 chr1D 93.684 95 5 1 2066 2159 295954206 295954300 1.230000e-29 141
9 TraesCS6B01G432300 chr1D 93.548 93 6 0 2067 2159 252473138 252473230 4.440000e-29 139
10 TraesCS6B01G432300 chr2D 92.784 97 5 2 2073 2168 15682986 15682891 4.440000e-29 139
11 TraesCS6B01G432300 chr7A 89.815 108 9 2 2072 2178 485195292 485195186 1.600000e-28 137
12 TraesCS6B01G432300 chr4A 91.919 99 7 1 2069 2167 69329850 69329947 1.600000e-28 137


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 TraesCS6B01G432300 chr6B 701660119 701663415 3296 True 6089.000000 6089 100.000000 1 3297 1 chr6B.!!$R1 3296
1 TraesCS6B01G432300 chr6D 460572215 460575460 3245 True 4335.000000 4335 91.263000 127 3297 1 chr6D.!!$R1 3170
2 TraesCS6B01G432300 chr6A 606765931 606769096 3165 True 1339.333333 1653 89.934333 115 3297 3 chr6A.!!$R1 3182

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
182 186 0.180171 TCCTCTCTCTCTCTCGCCAG 59.820 60.0 0.0 0.0 0.00 4.85 F
1597 1752 0.456312 GGTCGTCGTGAAGAGCGATT 60.456 55.0 0.0 0.0 40.59 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1881 0.109532 TATGTGGGTGTGGGTGTGTG 59.890 55.0 0.00 0.0 0.00 3.82 R
2961 3161 0.316841 GGCGTTCATTGGCCTTTTCA 59.683 50.0 3.32 0.0 45.93 2.69 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
17 18 3.277133 ATCCATTGCCACGTGTGC 58.723 55.556 15.65 17.32 0.00 4.57
18 19 2.689785 ATCCATTGCCACGTGTGCG 61.690 57.895 15.65 0.00 44.93 5.34
19 20 4.403137 CCATTGCCACGTGTGCGG 62.403 66.667 15.65 10.27 43.45 5.69
36 37 3.871395 GCCTGGGCCTGCCTAGAG 61.871 72.222 21.68 12.95 46.11 2.43
37 38 2.366167 CCTGGGCCTGCCTAGAGT 60.366 66.667 21.68 0.00 46.11 3.24
38 39 2.439104 CCTGGGCCTGCCTAGAGTC 61.439 68.421 21.68 0.00 46.11 3.36
39 40 1.687146 CTGGGCCTGCCTAGAGTCA 60.687 63.158 15.81 0.00 46.11 3.41
40 41 1.229496 TGGGCCTGCCTAGAGTCAA 60.229 57.895 4.53 0.00 36.10 3.18
41 42 1.222113 GGGCCTGCCTAGAGTCAAC 59.778 63.158 8.29 0.00 36.10 3.18
42 43 1.268283 GGGCCTGCCTAGAGTCAACT 61.268 60.000 8.29 0.00 36.10 3.16
43 44 1.486211 GGCCTGCCTAGAGTCAACTA 58.514 55.000 0.00 0.00 0.00 2.24
44 45 1.410882 GGCCTGCCTAGAGTCAACTAG 59.589 57.143 0.00 0.00 39.40 2.57
55 56 7.229581 CTAGAGTCAACTAGGGTTAACAACT 57.770 40.000 8.10 7.55 36.98 3.16
56 57 6.496144 AGAGTCAACTAGGGTTAACAACTT 57.504 37.500 8.10 0.00 33.88 2.66
57 58 6.522946 AGAGTCAACTAGGGTTAACAACTTC 58.477 40.000 8.10 0.00 33.88 3.01
58 59 6.099269 AGAGTCAACTAGGGTTAACAACTTCA 59.901 38.462 8.10 0.00 33.88 3.02
59 60 6.053650 AGTCAACTAGGGTTAACAACTTCAC 58.946 40.000 8.10 0.00 33.88 3.18
60 61 5.237996 GTCAACTAGGGTTAACAACTTCACC 59.762 44.000 8.10 0.00 33.88 4.02
61 62 5.104444 TCAACTAGGGTTAACAACTTCACCA 60.104 40.000 8.10 0.00 33.88 4.17
62 63 4.711399 ACTAGGGTTAACAACTTCACCAC 58.289 43.478 8.10 0.00 0.00 4.16
63 64 2.567985 AGGGTTAACAACTTCACCACG 58.432 47.619 8.10 0.00 0.00 4.94
64 65 2.092807 AGGGTTAACAACTTCACCACGT 60.093 45.455 8.10 0.00 0.00 4.49
65 66 2.684374 GGGTTAACAACTTCACCACGTT 59.316 45.455 8.10 0.00 0.00 3.99
66 67 3.876320 GGGTTAACAACTTCACCACGTTA 59.124 43.478 8.10 0.00 0.00 3.18
67 68 4.516321 GGGTTAACAACTTCACCACGTTAT 59.484 41.667 8.10 0.00 0.00 1.89
68 69 5.008911 GGGTTAACAACTTCACCACGTTATT 59.991 40.000 8.10 0.00 0.00 1.40
69 70 5.910723 GGTTAACAACTTCACCACGTTATTG 59.089 40.000 8.10 0.00 0.00 1.90
70 71 4.561735 AACAACTTCACCACGTTATTGG 57.438 40.909 0.00 0.00 43.04 3.16
71 72 2.882137 ACAACTTCACCACGTTATTGGG 59.118 45.455 0.00 0.00 41.49 4.12
72 73 1.530323 ACTTCACCACGTTATTGGGC 58.470 50.000 0.00 0.00 41.49 5.36
73 74 1.073284 ACTTCACCACGTTATTGGGCT 59.927 47.619 0.00 0.00 41.49 5.19
74 75 2.159382 CTTCACCACGTTATTGGGCTT 58.841 47.619 0.00 0.00 41.49 4.35
75 76 1.529226 TCACCACGTTATTGGGCTTG 58.471 50.000 0.00 0.00 41.49 4.01
76 77 1.072489 TCACCACGTTATTGGGCTTGA 59.928 47.619 0.00 0.00 41.49 3.02
77 78 1.883275 CACCACGTTATTGGGCTTGAA 59.117 47.619 0.00 0.00 41.49 2.69
78 79 2.095263 CACCACGTTATTGGGCTTGAAG 60.095 50.000 0.00 0.00 41.49 3.02
79 80 1.472480 CCACGTTATTGGGCTTGAAGG 59.528 52.381 0.00 0.00 32.35 3.46
80 81 1.135402 CACGTTATTGGGCTTGAAGGC 60.135 52.381 10.64 10.64 40.51 4.35
87 88 3.070576 GGCTTGAAGGCCCGCAAT 61.071 61.111 7.63 0.00 45.92 3.56
88 89 2.491621 GCTTGAAGGCCCGCAATC 59.508 61.111 0.00 0.00 0.00 2.67
89 90 3.068729 GCTTGAAGGCCCGCAATCC 62.069 63.158 0.00 0.00 0.00 3.01
90 91 1.678635 CTTGAAGGCCCGCAATCCA 60.679 57.895 0.00 0.00 0.00 3.41
91 92 1.937546 CTTGAAGGCCCGCAATCCAC 61.938 60.000 0.00 0.00 0.00 4.02
92 93 3.508840 GAAGGCCCGCAATCCACG 61.509 66.667 0.00 0.00 0.00 4.94
93 94 3.969250 GAAGGCCCGCAATCCACGA 62.969 63.158 0.00 0.00 0.00 4.35
94 95 3.976701 AAGGCCCGCAATCCACGAG 62.977 63.158 0.00 0.00 0.00 4.18
97 98 3.197790 CCCGCAATCCACGAGCTG 61.198 66.667 0.00 0.00 0.00 4.24
98 99 3.869272 CCGCAATCCACGAGCTGC 61.869 66.667 0.00 0.00 0.00 5.25
99 100 3.120385 CGCAATCCACGAGCTGCA 61.120 61.111 1.02 0.00 34.39 4.41
100 101 2.466982 CGCAATCCACGAGCTGCAT 61.467 57.895 1.02 0.00 34.39 3.96
101 102 1.354506 GCAATCCACGAGCTGCATC 59.645 57.895 1.02 0.00 34.87 3.91
171 175 1.659794 GAGCGCTGGATCCTCTCTC 59.340 63.158 18.48 10.55 0.00 3.20
172 176 0.823356 GAGCGCTGGATCCTCTCTCT 60.823 60.000 18.48 3.64 0.00 3.10
176 180 1.202806 CGCTGGATCCTCTCTCTCTCT 60.203 57.143 14.23 0.00 0.00 3.10
178 182 2.771089 CTGGATCCTCTCTCTCTCTCG 58.229 57.143 14.23 0.00 0.00 4.04
180 184 1.523758 GATCCTCTCTCTCTCTCGCC 58.476 60.000 0.00 0.00 0.00 5.54
181 185 0.843309 ATCCTCTCTCTCTCTCGCCA 59.157 55.000 0.00 0.00 0.00 5.69
182 186 0.180171 TCCTCTCTCTCTCTCGCCAG 59.820 60.000 0.00 0.00 0.00 4.85
183 187 1.447317 CCTCTCTCTCTCTCGCCAGC 61.447 65.000 0.00 0.00 0.00 4.85
184 188 0.464373 CTCTCTCTCTCTCGCCAGCT 60.464 60.000 0.00 0.00 0.00 4.24
255 266 2.581354 GCTCCGACAGGTCAGCAT 59.419 61.111 6.82 0.00 37.34 3.79
351 362 3.695022 CTCTCCGCCAACCGTACCG 62.695 68.421 0.00 0.00 34.38 4.02
553 564 2.066999 GGACCAGAGATTCCGGGCT 61.067 63.158 0.00 0.00 0.00 5.19
561 572 1.001393 GATTCCGGGCTGGGACAAA 60.001 57.895 13.58 0.00 38.70 2.83
564 575 1.110518 TTCCGGGCTGGGACAAAAAC 61.111 55.000 13.58 0.00 38.70 2.43
565 576 1.830408 CCGGGCTGGGACAAAAACA 60.830 57.895 3.77 0.00 38.70 2.83
566 577 1.362355 CGGGCTGGGACAAAAACAC 59.638 57.895 0.00 0.00 38.70 3.32
567 578 1.362355 GGGCTGGGACAAAAACACG 59.638 57.895 0.00 0.00 38.70 4.49
568 579 1.299850 GGCTGGGACAAAAACACGC 60.300 57.895 0.00 0.00 38.70 5.34
569 580 1.299850 GCTGGGACAAAAACACGCC 60.300 57.895 0.00 0.00 38.70 5.68
570 581 1.362355 CTGGGACAAAAACACGCCC 59.638 57.895 0.00 0.00 38.70 6.13
571 582 1.379977 TGGGACAAAAACACGCCCA 60.380 52.632 0.00 0.00 46.10 5.36
572 583 1.362355 GGGACAAAAACACGCCCAG 59.638 57.895 0.00 0.00 38.68 4.45
573 584 1.388837 GGGACAAAAACACGCCCAGT 61.389 55.000 0.00 0.00 38.68 4.00
604 615 5.106791 CCAACTTGTCATCACATTCAGAGTC 60.107 44.000 0.00 0.00 30.55 3.36
695 744 3.092301 CCTTTCTCCCAAGGAATTCACC 58.908 50.000 7.93 0.00 45.79 4.02
815 888 2.203082 AGCACCAGTCGCTCACTCA 61.203 57.895 0.00 0.00 33.35 3.41
817 890 1.373497 CACCAGTCGCTCACTCACC 60.373 63.158 0.00 0.00 30.26 4.02
898 982 2.664185 CATGGAGCGATCCCAGCG 60.664 66.667 18.75 0.00 37.08 5.18
973 1057 2.146342 CACAGTCAGACAACATCCACC 58.854 52.381 2.66 0.00 0.00 4.61
978 1062 0.867746 CAGACAACATCCACCACACG 59.132 55.000 0.00 0.00 0.00 4.49
990 1074 1.068588 CACCACACGAGACAAGGAAGA 59.931 52.381 0.00 0.00 0.00 2.87
991 1075 1.341531 ACCACACGAGACAAGGAAGAG 59.658 52.381 0.00 0.00 0.00 2.85
1051 1154 0.609662 CATGTTCAAAGGGGCCAAGG 59.390 55.000 4.39 0.00 0.00 3.61
1173 1276 2.663188 GACGCCATCATCTCCGGC 60.663 66.667 0.00 0.00 42.64 6.13
1248 1351 4.717313 TCCCAGCAGCAGCAGCAG 62.717 66.667 12.92 3.65 45.49 4.24
1266 1369 2.674380 CAGCAGCCACCTTCCCAC 60.674 66.667 0.00 0.00 0.00 4.61
1269 1372 4.335647 CAGCCACCTTCCCACGCT 62.336 66.667 0.00 0.00 0.00 5.07
1298 1401 2.305343 AGGTGCTTCTTCTTGCTGATCT 59.695 45.455 0.00 0.00 0.00 2.75
1311 1414 4.462508 TGCTGATCTTTGTAGTCTCTGG 57.537 45.455 0.00 0.00 0.00 3.86
1316 1419 3.616956 TCTTTGTAGTCTCTGGCCATG 57.383 47.619 5.51 2.03 0.00 3.66
1332 1435 2.562635 CCATGTCCTCTCTTGATGCTG 58.437 52.381 0.00 0.00 0.00 4.41
1379 1534 3.959449 TCTGTCATCTCCTCTCTTGATGG 59.041 47.826 0.00 0.00 38.38 3.51
1396 1551 4.914983 TGATGGTGCTTCTTCTTCTTGAT 58.085 39.130 0.00 0.00 0.00 2.57
1413 1568 3.507162 TGATCCCTTGCTTGACTTTGA 57.493 42.857 0.00 0.00 0.00 2.69
1416 1571 2.306847 TCCCTTGCTTGACTTTGAACC 58.693 47.619 0.00 0.00 0.00 3.62
1417 1572 2.091885 TCCCTTGCTTGACTTTGAACCT 60.092 45.455 0.00 0.00 0.00 3.50
1418 1573 2.695147 CCCTTGCTTGACTTTGAACCTT 59.305 45.455 0.00 0.00 0.00 3.50
1419 1574 3.491447 CCCTTGCTTGACTTTGAACCTTG 60.491 47.826 0.00 0.00 0.00 3.61
1423 1578 2.860136 GCTTGACTTTGAACCTTGTTGC 59.140 45.455 0.00 0.00 0.00 4.17
1428 1583 2.831526 ACTTTGAACCTTGTTGCTTGGT 59.168 40.909 0.00 0.00 35.29 3.67
1597 1752 0.456312 GGTCGTCGTGAAGAGCGATT 60.456 55.000 0.00 0.00 40.59 3.34
1718 1881 9.847706 AGAAGAAGAAAAAGACAGAAAAAGAAC 57.152 29.630 0.00 0.00 0.00 3.01
1738 1901 0.109723 ACACACCCACACCCACATAC 59.890 55.000 0.00 0.00 0.00 2.39
1755 1918 4.754618 CACATACACAAGTTGCTACCTCAA 59.245 41.667 1.81 0.00 0.00 3.02
1786 1949 7.119846 ACCATCTTGTGTTTGCTAATCTAGTTC 59.880 37.037 0.00 0.00 0.00 3.01
1900 2063 7.951530 ATTGTTGTTTCCACTCATCATTTTC 57.048 32.000 0.00 0.00 0.00 2.29
1901 2064 5.841810 TGTTGTTTCCACTCATCATTTTCC 58.158 37.500 0.00 0.00 0.00 3.13
1902 2065 5.221422 TGTTGTTTCCACTCATCATTTTCCC 60.221 40.000 0.00 0.00 0.00 3.97
1910 2074 6.103946 TCCACTCATCATTTTCCCCCATATTA 59.896 38.462 0.00 0.00 0.00 0.98
1973 2140 1.449070 CCGCAGCTCTGATGCTCAA 60.449 57.895 6.25 0.00 41.98 3.02
2066 2258 5.442391 ACAAAACCAGCAGTAAAGGACTTA 58.558 37.500 0.00 0.00 35.64 2.24
2137 2329 8.995220 ACTAATGTAATGTCAAAAACGCTCTTA 58.005 29.630 0.00 0.00 0.00 2.10
2183 2375 6.789457 AGATCTGTATCATCCCCTTAACATCA 59.211 38.462 0.00 0.00 34.28 3.07
2197 2389 7.124147 CCCCTTAACATCAACTATTGTTTGGAT 59.876 37.037 0.00 0.00 37.29 3.41
2353 2546 1.083489 AAATATGTGTGTCCGCGGTG 58.917 50.000 27.15 0.00 0.00 4.94
2553 2749 5.707298 ACTTCCACATTCCACAGTAAGATTG 59.293 40.000 0.00 0.00 0.00 2.67
2601 2797 4.931661 AGAATGGAGGCAATATGCTTTG 57.068 40.909 2.00 0.00 44.28 2.77
2688 2885 7.446769 ACAATGATGGTATAGCATACGGTTTA 58.553 34.615 17.08 0.00 33.46 2.01
2788 2985 4.948608 TTAACAACGAGAAGTGCAAACA 57.051 36.364 0.00 0.00 0.00 2.83
2887 3087 7.255451 CGGTGCCTTTATTTATTGGACATACAT 60.255 37.037 0.00 0.00 0.00 2.29
2961 3161 3.416156 GACAATGCAAGAGAAAGGAGGT 58.584 45.455 0.00 0.00 0.00 3.85
2977 3177 2.029020 GGAGGTGAAAAGGCCAATGAAC 60.029 50.000 5.01 0.00 0.00 3.18
3153 3353 1.348064 TGTTGACCTTCTCCGGATGT 58.652 50.000 3.57 0.00 0.00 3.06
3217 3417 3.074412 GCTTCCTTCTGAATCGGAAACA 58.926 45.455 5.96 0.00 36.47 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.689785 CGCACACGTGGCAATGGAT 61.690 57.895 21.57 0.00 33.53 3.41
1 2 3.353029 CGCACACGTGGCAATGGA 61.353 61.111 21.57 0.00 33.53 3.41
2 3 4.403137 CCGCACACGTGGCAATGG 62.403 66.667 21.57 12.63 35.59 3.16
19 20 3.871395 CTCTAGGCAGGCCCAGGC 61.871 72.222 6.70 10.99 41.06 4.85
20 21 2.366167 ACTCTAGGCAGGCCCAGG 60.366 66.667 6.70 0.01 36.58 4.45
21 22 1.267574 TTGACTCTAGGCAGGCCCAG 61.268 60.000 6.70 2.57 36.58 4.45
22 23 1.229496 TTGACTCTAGGCAGGCCCA 60.229 57.895 6.70 0.00 36.58 5.36
23 24 1.222113 GTTGACTCTAGGCAGGCCC 59.778 63.158 6.70 0.00 36.58 5.80
24 25 1.410882 CTAGTTGACTCTAGGCAGGCC 59.589 57.143 0.97 0.97 35.20 5.19
25 26 1.410882 CCTAGTTGACTCTAGGCAGGC 59.589 57.143 6.81 0.00 46.71 4.85
31 32 7.229581 AGTTGTTAACCCTAGTTGACTCTAG 57.770 40.000 2.48 0.00 41.71 2.43
32 33 7.288389 TGAAGTTGTTAACCCTAGTTGACTCTA 59.712 37.037 2.48 0.00 41.71 2.43
33 34 6.099269 TGAAGTTGTTAACCCTAGTTGACTCT 59.901 38.462 2.48 0.10 41.71 3.24
34 35 6.202379 GTGAAGTTGTTAACCCTAGTTGACTC 59.798 42.308 2.48 0.00 41.71 3.36
35 36 6.053650 GTGAAGTTGTTAACCCTAGTTGACT 58.946 40.000 2.48 0.00 41.71 3.41
36 37 5.237996 GGTGAAGTTGTTAACCCTAGTTGAC 59.762 44.000 2.48 2.80 41.58 3.18
37 38 5.104444 TGGTGAAGTTGTTAACCCTAGTTGA 60.104 40.000 2.48 0.00 36.39 3.18
38 39 5.008316 GTGGTGAAGTTGTTAACCCTAGTTG 59.992 44.000 2.48 0.00 36.39 3.16
39 40 5.128205 GTGGTGAAGTTGTTAACCCTAGTT 58.872 41.667 2.48 0.00 36.39 2.24
40 41 4.711399 GTGGTGAAGTTGTTAACCCTAGT 58.289 43.478 2.48 0.00 36.39 2.57
41 42 3.744426 CGTGGTGAAGTTGTTAACCCTAG 59.256 47.826 2.48 0.00 36.39 3.02
42 43 3.134442 ACGTGGTGAAGTTGTTAACCCTA 59.866 43.478 2.48 0.00 36.39 3.53
43 44 2.092807 ACGTGGTGAAGTTGTTAACCCT 60.093 45.455 2.48 0.00 36.39 4.34
44 45 2.291365 ACGTGGTGAAGTTGTTAACCC 58.709 47.619 2.48 0.00 36.39 4.11
45 46 5.678132 ATAACGTGGTGAAGTTGTTAACC 57.322 39.130 2.48 0.00 37.68 2.85
46 47 5.910723 CCAATAACGTGGTGAAGTTGTTAAC 59.089 40.000 0.00 0.00 31.98 2.01
47 48 5.008811 CCCAATAACGTGGTGAAGTTGTTAA 59.991 40.000 0.00 0.00 36.90 2.01
48 49 4.515944 CCCAATAACGTGGTGAAGTTGTTA 59.484 41.667 0.00 0.00 36.90 2.41
49 50 3.316868 CCCAATAACGTGGTGAAGTTGTT 59.683 43.478 0.00 0.00 36.90 2.83
50 51 2.882137 CCCAATAACGTGGTGAAGTTGT 59.118 45.455 0.00 0.00 36.90 3.32
51 52 2.351350 GCCCAATAACGTGGTGAAGTTG 60.351 50.000 0.00 0.00 36.90 3.16
52 53 1.883926 GCCCAATAACGTGGTGAAGTT 59.116 47.619 0.00 0.00 36.90 2.66
53 54 1.073284 AGCCCAATAACGTGGTGAAGT 59.927 47.619 0.00 0.00 36.90 3.01
54 55 1.821216 AGCCCAATAACGTGGTGAAG 58.179 50.000 0.00 0.00 36.90 3.02
55 56 1.883275 CAAGCCCAATAACGTGGTGAA 59.117 47.619 0.00 0.00 36.90 3.18
56 57 1.072489 TCAAGCCCAATAACGTGGTGA 59.928 47.619 0.00 0.00 36.90 4.02
57 58 1.529226 TCAAGCCCAATAACGTGGTG 58.471 50.000 0.00 0.00 36.90 4.17
58 59 2.159382 CTTCAAGCCCAATAACGTGGT 58.841 47.619 0.00 0.00 36.90 4.16
59 60 1.472480 CCTTCAAGCCCAATAACGTGG 59.528 52.381 0.00 0.00 38.51 4.94
60 61 1.135402 GCCTTCAAGCCCAATAACGTG 60.135 52.381 0.00 0.00 0.00 4.49
61 62 1.173913 GCCTTCAAGCCCAATAACGT 58.826 50.000 0.00 0.00 0.00 3.99
71 72 2.491621 GATTGCGGGCCTTCAAGC 59.508 61.111 0.84 6.35 0.00 4.01
72 73 1.678635 TGGATTGCGGGCCTTCAAG 60.679 57.895 0.84 0.00 0.00 3.02
73 74 1.976474 GTGGATTGCGGGCCTTCAA 60.976 57.895 0.84 7.74 0.00 2.69
74 75 2.361104 GTGGATTGCGGGCCTTCA 60.361 61.111 0.84 0.00 0.00 3.02
75 76 3.508840 CGTGGATTGCGGGCCTTC 61.509 66.667 0.84 0.00 0.00 3.46
76 77 3.976701 CTCGTGGATTGCGGGCCTT 62.977 63.158 0.84 0.00 0.00 4.35
77 78 4.473520 CTCGTGGATTGCGGGCCT 62.474 66.667 0.84 0.00 0.00 5.19
80 81 3.197790 CAGCTCGTGGATTGCGGG 61.198 66.667 0.00 0.00 0.00 6.13
81 82 3.869272 GCAGCTCGTGGATTGCGG 61.869 66.667 0.00 0.00 0.00 5.69
82 83 2.370824 GATGCAGCTCGTGGATTGCG 62.371 60.000 0.00 0.00 37.34 4.85
83 84 1.354506 GATGCAGCTCGTGGATTGC 59.645 57.895 0.00 0.00 37.34 3.56
84 85 1.640069 CGATGCAGCTCGTGGATTG 59.360 57.895 0.00 0.00 37.34 2.67
85 86 4.115279 CGATGCAGCTCGTGGATT 57.885 55.556 0.00 0.00 37.34 3.01
98 99 1.825191 CCCATCCCTGGCAACGATG 60.825 63.158 13.82 13.82 41.64 3.84
99 100 1.987807 CTCCCATCCCTGGCAACGAT 61.988 60.000 0.00 0.00 41.64 3.73
100 101 2.609299 TCCCATCCCTGGCAACGA 60.609 61.111 0.00 0.00 41.64 3.85
101 102 1.987807 ATCTCCCATCCCTGGCAACG 61.988 60.000 0.00 0.00 41.64 4.10
102 103 0.259938 AATCTCCCATCCCTGGCAAC 59.740 55.000 0.00 0.00 41.64 4.17
103 104 0.552848 GAATCTCCCATCCCTGGCAA 59.447 55.000 0.00 0.00 41.64 4.52
104 105 0.327867 AGAATCTCCCATCCCTGGCA 60.328 55.000 0.00 0.00 41.64 4.92
105 106 0.110104 CAGAATCTCCCATCCCTGGC 59.890 60.000 0.00 0.00 41.64 4.85
106 107 0.110104 GCAGAATCTCCCATCCCTGG 59.890 60.000 0.00 0.00 42.73 4.45
107 108 0.250209 CGCAGAATCTCCCATCCCTG 60.250 60.000 0.00 0.00 0.00 4.45
108 109 2.049627 GCGCAGAATCTCCCATCCCT 62.050 60.000 0.30 0.00 0.00 4.20
109 110 1.599240 GCGCAGAATCTCCCATCCC 60.599 63.158 0.30 0.00 0.00 3.85
110 111 0.883814 CTGCGCAGAATCTCCCATCC 60.884 60.000 33.66 0.00 0.00 3.51
111 112 1.505477 GCTGCGCAGAATCTCCCATC 61.505 60.000 40.21 14.87 0.00 3.51
112 113 1.525535 GCTGCGCAGAATCTCCCAT 60.526 57.895 40.21 0.00 0.00 4.00
113 114 2.124983 GCTGCGCAGAATCTCCCA 60.125 61.111 40.21 0.00 0.00 4.37
171 175 2.103934 CGGAAGCTGGCGAGAGAG 59.896 66.667 0.00 0.00 0.00 3.20
183 187 0.305922 GAATGAATCTGCGGCGGAAG 59.694 55.000 16.55 0.00 0.00 3.46
184 188 0.392327 TGAATGAATCTGCGGCGGAA 60.392 50.000 16.55 0.00 0.00 4.30
191 198 2.169179 GTTTCGCGTGAATGAATCTGC 58.831 47.619 12.94 0.00 33.20 4.26
214 225 1.595382 GGGACGATGAATGAGCCCG 60.595 63.158 0.00 0.00 0.00 6.13
351 362 3.787001 CCTTCACTCCCTCCGGCC 61.787 72.222 0.00 0.00 0.00 6.13
352 363 3.787001 CCCTTCACTCCCTCCGGC 61.787 72.222 0.00 0.00 0.00 6.13
353 364 2.284699 ACCCTTCACTCCCTCCGG 60.285 66.667 0.00 0.00 0.00 5.14
354 365 2.711922 CGACCCTTCACTCCCTCCG 61.712 68.421 0.00 0.00 0.00 4.63
355 366 2.359967 CCGACCCTTCACTCCCTCC 61.360 68.421 0.00 0.00 0.00 4.30
356 367 3.020237 GCCGACCCTTCACTCCCTC 62.020 68.421 0.00 0.00 0.00 4.30
357 368 3.003763 GCCGACCCTTCACTCCCT 61.004 66.667 0.00 0.00 0.00 4.20
358 369 3.319198 TGCCGACCCTTCACTCCC 61.319 66.667 0.00 0.00 0.00 4.30
363 374 2.203788 AGGAGTGCCGACCCTTCA 60.204 61.111 0.00 0.00 39.96 3.02
489 500 4.980805 GGACACGCGGTGCTTCCA 62.981 66.667 12.47 0.00 36.98 3.53
553 564 1.379977 TGGGCGTGTTTTTGTCCCA 60.380 52.632 0.00 0.00 44.16 4.37
561 572 0.321653 GATCTGGACTGGGCGTGTTT 60.322 55.000 0.00 0.00 0.00 2.83
564 575 2.184020 TTGGATCTGGACTGGGCGTG 62.184 60.000 0.00 0.00 0.00 5.34
565 576 1.918293 TTGGATCTGGACTGGGCGT 60.918 57.895 0.00 0.00 0.00 5.68
566 577 1.450312 GTTGGATCTGGACTGGGCG 60.450 63.158 0.00 0.00 0.00 6.13
567 578 0.329596 AAGTTGGATCTGGACTGGGC 59.670 55.000 0.00 0.00 0.00 5.36
568 579 1.352352 ACAAGTTGGATCTGGACTGGG 59.648 52.381 7.96 0.00 0.00 4.45
569 580 2.038952 TGACAAGTTGGATCTGGACTGG 59.961 50.000 7.96 0.00 0.00 4.00
570 581 3.407424 TGACAAGTTGGATCTGGACTG 57.593 47.619 7.96 0.00 0.00 3.51
571 582 3.584406 TGATGACAAGTTGGATCTGGACT 59.416 43.478 7.96 0.00 0.00 3.85
572 583 3.686726 GTGATGACAAGTTGGATCTGGAC 59.313 47.826 7.96 0.24 0.00 4.02
573 584 3.327464 TGTGATGACAAGTTGGATCTGGA 59.673 43.478 7.96 0.00 0.00 3.86
604 615 0.545171 AGGATCTGGATGTGCACCTG 59.455 55.000 15.69 3.23 0.00 4.00
695 744 3.056749 GGTAGGTAGGTAGAATCATGGCG 60.057 52.174 0.00 0.00 0.00 5.69
831 904 2.123982 GCTTGCATGGGGAGGGAG 60.124 66.667 1.34 0.00 0.00 4.30
878 961 3.839353 CTGGGATCGCTCCATGCCC 62.839 68.421 7.74 0.00 44.08 5.36
898 982 0.978146 TAGGGAGTGAAGCTGGAGGC 60.978 60.000 0.00 0.00 42.19 4.70
973 1057 2.802787 ACTCTTCCTTGTCTCGTGTG 57.197 50.000 0.00 0.00 0.00 3.82
978 1062 3.449018 TGGATGCTACTCTTCCTTGTCTC 59.551 47.826 0.00 0.00 39.19 3.36
990 1074 1.524621 GCACGCCATGGATGCTACT 60.525 57.895 26.24 0.00 36.40 2.57
991 1075 1.168407 ATGCACGCCATGGATGCTAC 61.168 55.000 30.52 11.53 38.09 3.58
1051 1154 4.811364 GCCCCTTCTGGCCTCAGC 62.811 72.222 3.32 0.00 46.11 4.26
1082 1185 4.785453 GGCACCCGAAGCTCCCTG 62.785 72.222 0.00 0.00 0.00 4.45
1173 1276 1.446272 GAAGTTCTCGGGCCACTCG 60.446 63.158 4.39 0.00 0.00 4.18
1221 1324 1.965754 GCTGCTGGGACTGGAGGTAG 61.966 65.000 0.00 0.00 45.06 3.18
1248 1351 4.666253 TGGGAAGGTGGCTGCTGC 62.666 66.667 7.10 7.10 38.76 5.25
1266 1369 4.827087 AGCACCTGATCGGCAGCG 62.827 66.667 9.82 0.00 43.50 5.18
1269 1372 0.391661 GAAGAAGCACCTGATCGGCA 60.392 55.000 0.00 0.00 35.61 5.69
1271 1374 2.005451 CAAGAAGAAGCACCTGATCGG 58.995 52.381 0.00 0.00 39.35 4.18
1298 1401 2.027192 GGACATGGCCAGAGACTACAAA 60.027 50.000 14.59 0.00 0.00 2.83
1311 1414 1.134159 AGCATCAAGAGAGGACATGGC 60.134 52.381 0.00 0.00 0.00 4.40
1316 1419 2.093553 AGAAGCAGCATCAAGAGAGGAC 60.094 50.000 0.00 0.00 0.00 3.85
1332 1435 2.709213 ACAAGATCAGCAGGAAGAAGC 58.291 47.619 0.00 0.00 0.00 3.86
1379 1534 3.949132 AGGGATCAAGAAGAAGAAGCAC 58.051 45.455 0.00 0.00 0.00 4.40
1396 1551 2.091885 AGGTTCAAAGTCAAGCAAGGGA 60.092 45.455 0.00 0.00 0.00 4.20
1413 1568 1.567357 ACCAACCAAGCAACAAGGTT 58.433 45.000 0.00 0.00 46.03 3.50
1416 1571 1.289276 GCAACCAACCAAGCAACAAG 58.711 50.000 0.00 0.00 0.00 3.16
1417 1572 0.610174 TGCAACCAACCAAGCAACAA 59.390 45.000 0.00 0.00 33.48 2.83
1418 1573 0.175302 CTGCAACCAACCAAGCAACA 59.825 50.000 0.00 0.00 36.44 3.33
1419 1574 1.153597 GCTGCAACCAACCAAGCAAC 61.154 55.000 0.00 0.00 36.44 4.17
1423 1578 1.300388 GCTGCTGCAACCAACCAAG 60.300 57.895 11.11 0.00 39.41 3.61
1597 1752 4.393155 ATGTGAAGCCCTCGCGCA 62.393 61.111 8.75 0.00 41.18 6.09
1601 1756 2.124570 CCCCATGTGAAGCCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
1690 1850 9.846248 TCTTTTTCTGTCTTTTTCTTCTTCTTG 57.154 29.630 0.00 0.00 0.00 3.02
1718 1881 0.109532 TATGTGGGTGTGGGTGTGTG 59.890 55.000 0.00 0.00 0.00 3.82
1738 1901 5.065218 GGTGATATTGAGGTAGCAACTTGTG 59.935 44.000 0.00 0.00 0.00 3.33
1755 1918 7.776969 AGATTAGCAAACACAAGATGGTGATAT 59.223 33.333 0.00 0.00 41.32 1.63
1786 1949 6.149633 GTCTTTGGCTGTTACAACAAATAGG 58.850 40.000 12.85 5.14 38.66 2.57
1900 2063 9.649316 TTAATTAACTGGAAACTAATATGGGGG 57.351 33.333 0.00 0.00 0.00 5.40
1910 2074 6.991531 TGTGTACGGTTAATTAACTGGAAACT 59.008 34.615 30.40 18.01 41.98 2.66
1973 2140 4.956700 TCGGTAATCTGTGGATCTTCTTCT 59.043 41.667 0.00 0.00 0.00 2.85
2120 2312 8.567948 CCCATAATATAAGAGCGTTTTTGACAT 58.432 33.333 0.00 0.00 0.00 3.06
2125 2317 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2137 2329 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2257 2449 3.749373 AACGCGCGAAGAACGTCG 61.749 61.111 39.36 3.06 44.60 5.12
2353 2546 1.813513 TCTGCCTGCTACTCAAAAGC 58.186 50.000 0.00 0.00 40.50 3.51
2473 2669 5.511234 ACCAGATACGGTACATAACAGAC 57.489 43.478 0.00 0.00 37.57 3.51
2574 2770 4.765856 GCATATTGCCTCCATTCTTCTGAT 59.234 41.667 0.00 0.00 37.42 2.90
2601 2797 7.378181 TGATCAATTTAGGCAAGTCCTTTTTC 58.622 34.615 0.00 0.00 44.75 2.29
2688 2885 6.765989 TGATAAAACTGTTGTACTGCTTCTGT 59.234 34.615 0.00 0.00 0.00 3.41
2862 3061 7.341445 TGTATGTCCAATAAATAAAGGCACC 57.659 36.000 0.00 0.00 0.00 5.01
2887 3087 3.777106 ACCTGAAGTGCTCAAAGATGA 57.223 42.857 0.00 0.00 32.17 2.92
2921 3121 5.648178 TGTCCTGCTGTAGTTTTCGTATA 57.352 39.130 0.00 0.00 0.00 1.47
2961 3161 0.316841 GGCGTTCATTGGCCTTTTCA 59.683 50.000 3.32 0.00 45.93 2.69
2977 3177 4.020573 TGGTTATATTCTCTGGTATGGGCG 60.021 45.833 0.00 0.00 0.00 6.13
3029 3229 8.690203 TCATCTCAGTTCAACTTGGAAATTTA 57.310 30.769 0.00 0.00 0.00 1.40
3042 3242 4.760204 TGAGTACGTTCTCATCTCAGTTCA 59.240 41.667 19.53 0.00 39.20 3.18
3153 3353 6.380274 AGTGGCTGTTTCTACTGCTAGTATTA 59.620 38.462 7.02 0.00 45.44 0.98


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

AutoCloner maintained by Alex Coulton.