Multiple sequence alignment - TraesCS2D01G571200

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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 TraesCS2D01G571200 chr2D 100.000 3138 0 0 890 4027 637649854 637652991 0.000000e+00 5795
1 TraesCS2D01G571200 chr2D 100.000 465 0 0 1 465 637648965 637649429 0.000000e+00 859
2 TraesCS2D01G571200 chr2D 95.181 83 4 0 2850 2932 598020597 598020679 9.080000e-27 132
3 TraesCS2D01G571200 chr2D 93.976 83 5 0 2850 2932 598048788 598048870 4.230000e-25 126
4 TraesCS2D01G571200 chr2B 90.562 3221 177 59 890 4027 795062714 795065890 0.000000e+00 4146
5 TraesCS2D01G571200 chr2B 85.535 477 39 18 14 465 795062203 795062674 4.710000e-129 472
6 TraesCS2D01G571200 chr2A 93.339 2417 133 16 1628 4027 762292798 762290393 0.000000e+00 3546
7 TraesCS2D01G571200 chr2A 89.041 730 46 20 890 1600 762293512 762292798 0.000000e+00 874
8 TraesCS2D01G571200 chr2A 95.074 203 8 2 4 206 762299171 762298971 6.490000e-83 318
9 TraesCS2D01G571200 chr2A 85.606 264 8 7 198 447 762293809 762293562 2.400000e-62 250
10 TraesCS2D01G571200 chr7A 74.956 563 101 28 2487 3029 472196569 472197111 5.240000e-54 222
11 TraesCS2D01G571200 chr7A 79.327 208 40 2 3819 4026 472571744 472571948 4.200000e-30 143
12 TraesCS2D01G571200 chr7A 96.104 77 3 0 1037 1113 472195029 472195105 4.230000e-25 126
13 TraesCS2D01G571200 chr7D 74.245 563 113 23 2483 3029 411308162 411308708 1.470000e-49 207
14 TraesCS2D01G571200 chr7D 79.327 208 40 2 3819 4026 411609591 411609795 4.200000e-30 143
15 TraesCS2D01G571200 chr7D 96.104 77 3 0 1037 1113 411306648 411306724 4.230000e-25 126
16 TraesCS2D01G571200 chr7B 80.000 245 49 0 2483 2727 425716934 425717178 8.890000e-42 182
17 TraesCS2D01G571200 chr7B 80.288 208 38 2 3819 4026 426113933 426114137 1.940000e-33 154
18 TraesCS2D01G571200 chr7B 96.104 77 3 0 1037 1113 425714133 425714209 4.230000e-25 126


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 TraesCS2D01G571200 chr2D 637648965 637652991 4026 False 3327.000000 5795 100.000000 1 4027 2 chr2D.!!$F3 4026
1 TraesCS2D01G571200 chr2B 795062203 795065890 3687 False 2309.000000 4146 88.048500 14 4027 2 chr2B.!!$F1 4013
2 TraesCS2D01G571200 chr2A 762290393 762293809 3416 True 1556.666667 3546 89.328667 198 4027 3 chr2A.!!$R2 3829

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
130 133 1.157257 TCATGCGCGTGAGTTGTTGT 61.157 50.000 27.87 0.0 0.00 3.32 F
137 140 1.557443 CGTGAGTTGTTGTCGGCCTC 61.557 60.000 0.00 0.0 0.00 4.70 F
167 170 1.694150 AGCTATTTATGGAGCCGAGCA 59.306 47.619 0.00 0.0 39.65 4.26 F
1296 1340 0.444651 GCAATTGGTAGCAACGCGTA 59.555 50.000 14.46 0.0 0.00 4.42 F
1313 1357 0.548510 GTAGCTCTCCTTGCCCCAAT 59.451 55.000 0.00 0.0 0.00 3.16 F
2636 2746 0.343372 TCATCCTAGGCTCAGGGGTT 59.657 55.000 2.96 0.0 36.26 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1313 0.255890 GCTACCAATTGCTCCCTCCA 59.744 55.000 0.00 0.0 0.00 3.86 R
1275 1319 0.521242 CGCGTTGCTACCAATTGCTC 60.521 55.000 0.00 0.0 34.78 4.26 R
1562 1639 0.821301 TTTGCGGCCAGAACATGACA 60.821 50.000 2.24 0.0 0.00 3.58 R
2564 2674 0.179145 AGAACCAGTCGATTACGCCG 60.179 55.000 0.00 0.0 39.58 6.46 R
2840 2951 1.202806 GCATTCATTGGGGAGATCGGA 60.203 52.381 0.00 0.0 0.00 4.55 R
3723 3854 3.523806 GAAGCCTCAACTTCGAGCT 57.476 52.632 0.00 0.0 36.96 4.09 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
32 33 6.713762 ATTGTTCTTCTCCATGACAAACAA 57.286 33.333 0.00 3.11 40.48 2.83
34 35 6.522625 TGTTCTTCTCCATGACAAACAAAA 57.477 33.333 0.00 0.00 30.85 2.44
52 53 7.856145 AACAAAATGCACAGAAAAATACCAA 57.144 28.000 0.00 0.00 0.00 3.67
53 54 8.449251 AACAAAATGCACAGAAAAATACCAAT 57.551 26.923 0.00 0.00 0.00 3.16
55 56 9.206870 ACAAAATGCACAGAAAAATACCAATAG 57.793 29.630 0.00 0.00 0.00 1.73
84 85 9.968743 CATTTTACCTCTTAATACGACTTTGTC 57.031 33.333 0.00 0.00 0.00 3.18
95 96 1.635663 GACTTTGTCGTGGATGGCCG 61.636 60.000 0.00 0.00 36.79 6.13
96 97 2.359354 TTTGTCGTGGATGGCCGG 60.359 61.111 0.00 0.00 36.79 6.13
114 117 1.160137 GGCGCTTCTGTTGTTCTCAT 58.840 50.000 7.64 0.00 0.00 2.90
130 133 1.157257 TCATGCGCGTGAGTTGTTGT 61.157 50.000 27.87 0.00 0.00 3.32
137 140 1.557443 CGTGAGTTGTTGTCGGCCTC 61.557 60.000 0.00 0.00 0.00 4.70
148 151 2.028190 CGGCCTCGTGCATCCTAG 59.972 66.667 0.00 0.00 43.89 3.02
149 152 2.280457 GGCCTCGTGCATCCTAGC 60.280 66.667 0.00 0.00 43.89 3.42
159 162 4.526650 TCGTGCATCCTAGCTATTTATGGA 59.473 41.667 0.00 0.00 34.99 3.41
162 165 4.195416 GCATCCTAGCTATTTATGGAGCC 58.805 47.826 5.08 0.00 39.65 4.70
166 169 2.464157 AGCTATTTATGGAGCCGAGC 57.536 50.000 0.00 0.00 39.65 5.03
167 170 1.694150 AGCTATTTATGGAGCCGAGCA 59.306 47.619 0.00 0.00 39.65 4.26
168 171 2.104792 AGCTATTTATGGAGCCGAGCAA 59.895 45.455 0.00 0.00 39.65 3.91
178 181 2.037251 GGAGCCGAGCAATATCCACTTA 59.963 50.000 0.00 0.00 0.00 2.24
179 182 3.321497 GAGCCGAGCAATATCCACTTAG 58.679 50.000 0.00 0.00 0.00 2.18
191 194 8.190784 GCAATATCCACTTAGTGCTACATTTTT 58.809 33.333 6.88 0.00 39.43 1.94
376 402 2.230660 TCAGAGCGAGACAAAGACAGA 58.769 47.619 0.00 0.00 0.00 3.41
377 403 2.030717 TCAGAGCGAGACAAAGACAGAC 60.031 50.000 0.00 0.00 0.00 3.51
401 427 4.847444 GCGGCAGCTTCCTCCCTC 62.847 72.222 0.00 0.00 41.01 4.30
1210 1254 4.016706 GGGTCGGGACACCACCAG 62.017 72.222 0.00 0.00 38.76 4.00
1233 1277 1.883926 CCCGTTTTCCGACCTGATTTT 59.116 47.619 0.00 0.00 39.56 1.82
1234 1278 2.295070 CCCGTTTTCCGACCTGATTTTT 59.705 45.455 0.00 0.00 39.56 1.94
1269 1313 2.839098 CCACACCCACAAGGAGCT 59.161 61.111 0.00 0.00 39.89 4.09
1275 1319 2.673523 CCACAAGGAGCTGGAGGG 59.326 66.667 0.00 0.00 36.89 4.30
1296 1340 0.444651 GCAATTGGTAGCAACGCGTA 59.555 50.000 14.46 0.00 0.00 4.42
1311 1355 2.359169 CGTAGCTCTCCTTGCCCCA 61.359 63.158 0.00 0.00 0.00 4.96
1313 1357 0.548510 GTAGCTCTCCTTGCCCCAAT 59.451 55.000 0.00 0.00 0.00 3.16
1342 1388 2.436824 GACCTCCCTTTCTGCGGC 60.437 66.667 0.00 0.00 0.00 6.53
1459 1519 5.485353 AGTGGTCCAGTCTGATTTTGAGATA 59.515 40.000 0.00 0.00 0.00 1.98
1460 1520 6.157645 AGTGGTCCAGTCTGATTTTGAGATAT 59.842 38.462 0.00 0.00 0.00 1.63
1486 1546 1.339824 CCCTTCAGCACTTCAGCTCAT 60.340 52.381 0.00 0.00 44.54 2.90
1498 1571 1.139654 TCAGCTCATCCACCTGTATGC 59.860 52.381 0.00 0.00 0.00 3.14
1506 1579 3.737559 TCCACCTGTATGCAATCCTTT 57.262 42.857 0.00 0.00 0.00 3.11
1530 1607 4.766404 AGTAGTAATGTTTTGCACCTGC 57.234 40.909 0.00 0.00 42.50 4.85
1566 1643 3.838244 AGCTCTTGGTTTACAGTGTCA 57.162 42.857 0.00 0.00 0.00 3.58
1573 1650 5.527214 TCTTGGTTTACAGTGTCATGTTCTG 59.473 40.000 0.00 10.95 34.56 3.02
1579 1656 1.965930 GTGTCATGTTCTGGCCGCA 60.966 57.895 0.00 0.00 0.00 5.69
1599 1676 6.533367 GCCGCAAAAATGGAATGAACTATTAA 59.467 34.615 0.00 0.00 0.00 1.40
1600 1677 7.224557 GCCGCAAAAATGGAATGAACTATTAAT 59.775 33.333 0.00 0.00 0.00 1.40
1601 1678 9.097257 CCGCAAAAATGGAATGAACTATTAATT 57.903 29.630 0.00 0.00 0.00 1.40
1646 1739 2.108075 TGAGAACAATGGCCTCCTTTCA 59.892 45.455 3.32 0.00 0.00 2.69
1721 1821 2.728007 CTGGATTTCAAGTTCCCCCTC 58.272 52.381 0.00 0.00 0.00 4.30
1724 1824 2.225017 GGATTTCAAGTTCCCCCTCACA 60.225 50.000 0.00 0.00 0.00 3.58
1767 1867 1.076559 TCCTCGATCGGGGCTTACA 60.077 57.895 29.84 8.93 35.22 2.41
1850 1950 2.511637 GAGGATCTTCCCCATGTCCTTT 59.488 50.000 0.75 0.00 39.32 3.11
1901 2001 3.083349 AGCCTGCGCTACATCCCA 61.083 61.111 9.73 0.00 46.08 4.37
1922 2022 4.141756 CCAGTCTCCTTCATGCAGACTATT 60.142 45.833 13.06 0.00 44.15 1.73
1928 2028 7.172361 GTCTCCTTCATGCAGACTATTAAATCC 59.828 40.741 0.00 0.00 34.79 3.01
1997 2106 3.904136 ATTCCTGTTCACAAAGAAGCG 57.096 42.857 0.00 0.00 36.78 4.68
2044 2153 7.898309 CCTATTAACAACTTTTCTGACGATTCG 59.102 37.037 4.14 4.14 0.00 3.34
2147 2256 1.403687 GGGGGATCCTCTTGACCTCG 61.404 65.000 12.53 0.00 0.00 4.63
2177 2286 2.477754 GCTCAGCTTCAACATTTTTGGC 59.522 45.455 0.00 0.00 0.00 4.52
2195 2304 1.671979 GCTTCTGTGCTGCCATGATA 58.328 50.000 0.00 0.00 0.00 2.15
2332 2441 2.380084 TGTCTGGCATCCGTAAGTTC 57.620 50.000 0.00 0.00 0.00 3.01
2452 2562 4.287067 TCAGTCCTGTAATTTCTTGCCTCT 59.713 41.667 0.00 0.00 0.00 3.69
2564 2674 2.358939 CAATGTTGCTTGAAGGAGGC 57.641 50.000 0.00 0.00 0.00 4.70
2603 2713 2.493713 ACACACACGACTCTGTCTTC 57.506 50.000 0.00 0.00 0.00 2.87
2636 2746 0.343372 TCATCCTAGGCTCAGGGGTT 59.657 55.000 2.96 0.00 36.26 4.11
2681 2791 3.983988 CCATCTTCTACGTGATCCATTCG 59.016 47.826 0.00 0.00 0.00 3.34
2687 2797 2.288013 CGTGATCCATTCGACCACG 58.712 57.895 0.00 0.00 43.24 4.94
2742 2852 6.487299 AAGTAAGACCATTCTGGACTATCC 57.513 41.667 0.00 0.00 41.50 2.59
2778 2888 6.162777 CCTCAAGTTTCTCCTCTGTTTCTAG 58.837 44.000 0.00 0.00 0.00 2.43
2804 2915 2.200373 ACATTCCACTGTAGGTTGCC 57.800 50.000 0.00 0.00 0.00 4.52
2840 2951 1.770658 TCATGGCTGATCTTCCGGAAT 59.229 47.619 19.21 3.02 0.00 3.01
3118 3229 2.581354 CTGAGTTGAGGGAGGCCG 59.419 66.667 0.00 0.00 0.00 6.13
3222 3334 3.828875 AGTTCTCATAGGGTTGCTAGC 57.171 47.619 8.10 8.10 0.00 3.42
3224 3336 3.133721 AGTTCTCATAGGGTTGCTAGCTG 59.866 47.826 17.23 3.79 0.00 4.24
3233 3345 3.003480 GGGTTGCTAGCTGTCAACTTAG 58.997 50.000 23.22 2.84 41.53 2.18
3273 3385 0.821517 TCGTGCGATTAGGATGGTGT 59.178 50.000 0.00 0.00 0.00 4.16
3274 3386 1.202371 TCGTGCGATTAGGATGGTGTC 60.202 52.381 0.00 0.00 0.00 3.67
3275 3387 1.470805 CGTGCGATTAGGATGGTGTCA 60.471 52.381 0.00 0.00 0.00 3.58
3276 3388 2.627945 GTGCGATTAGGATGGTGTCAA 58.372 47.619 0.00 0.00 0.00 3.18
3286 3398 5.304686 AGGATGGTGTCAACTTCTGTTTA 57.695 39.130 3.97 0.00 33.52 2.01
3354 3466 9.447157 TGAATATTGATGCCATTATGATACGAA 57.553 29.630 0.00 0.00 0.00 3.85
3402 3532 4.409570 CGCATTGTCTCTGATTGGAAAAG 58.590 43.478 0.00 0.00 0.00 2.27
3419 3549 4.944317 GGAAAAGAGGGACTTAGGAACATG 59.056 45.833 0.00 0.00 41.55 3.21
3515 3645 8.128582 TGTGATTTCACTTTACTCATTGTGAAC 58.871 33.333 11.67 0.00 45.32 3.18
3585 3715 3.977326 TCCCCCAAAAGTTTGCCTAAAAT 59.023 39.130 0.00 0.00 36.86 1.82
3621 3752 8.525290 AGGATAACTTTAAAGGTGAATCCATG 57.475 34.615 26.38 0.78 39.02 3.66
3625 3756 5.079643 ACTTTAAAGGTGAATCCATGCACT 58.920 37.500 19.14 0.00 39.02 4.40
3626 3757 5.539955 ACTTTAAAGGTGAATCCATGCACTT 59.460 36.000 19.14 0.00 39.02 3.16
3642 3773 5.276461 TGCACTTATCCTATGTACACTGG 57.724 43.478 0.00 3.43 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.553064 GTCATGGAGAAGAACAATACATCTTAT 57.447 33.333 0.00 0.00 36.08 1.73
1 2 8.539544 TGTCATGGAGAAGAACAATACATCTTA 58.460 33.333 0.00 0.00 36.08 2.10
2 3 7.397221 TGTCATGGAGAAGAACAATACATCTT 58.603 34.615 0.00 0.00 38.56 2.40
3 4 6.950842 TGTCATGGAGAAGAACAATACATCT 58.049 36.000 0.00 0.00 0.00 2.90
4 5 7.615582 TTGTCATGGAGAAGAACAATACATC 57.384 36.000 0.00 0.00 0.00 3.06
5 6 7.448161 TGTTTGTCATGGAGAAGAACAATACAT 59.552 33.333 0.00 0.00 33.18 2.29
6 7 6.770303 TGTTTGTCATGGAGAAGAACAATACA 59.230 34.615 0.00 0.23 33.18 2.29
7 8 7.202016 TGTTTGTCATGGAGAAGAACAATAC 57.798 36.000 0.00 0.00 33.18 1.89
8 9 7.815840 TTGTTTGTCATGGAGAAGAACAATA 57.184 32.000 0.00 0.00 37.88 1.90
9 10 6.713762 TTGTTTGTCATGGAGAAGAACAAT 57.286 33.333 0.00 0.00 37.88 2.71
10 11 6.522625 TTTGTTTGTCATGGAGAAGAACAA 57.477 33.333 0.00 0.00 39.49 2.83
11 12 6.522625 TTTTGTTTGTCATGGAGAAGAACA 57.477 33.333 0.00 0.00 33.84 3.18
12 13 6.074142 GCATTTTGTTTGTCATGGAGAAGAAC 60.074 38.462 0.00 0.00 0.00 3.01
15 16 5.176223 GTGCATTTTGTTTGTCATGGAGAAG 59.824 40.000 0.00 0.00 0.00 2.85
21 22 5.970140 TTCTGTGCATTTTGTTTGTCATG 57.030 34.783 0.00 0.00 0.00 3.07
22 23 6.981762 TTTTCTGTGCATTTTGTTTGTCAT 57.018 29.167 0.00 0.00 0.00 3.06
32 33 9.423061 GAACTATTGGTATTTTTCTGTGCATTT 57.577 29.630 0.00 0.00 0.00 2.32
34 35 8.121305 TGAACTATTGGTATTTTTCTGTGCAT 57.879 30.769 0.00 0.00 0.00 3.96
93 94 1.901650 GAGAACAACAGAAGCGCCGG 61.902 60.000 2.29 0.00 0.00 6.13
95 96 1.135859 CATGAGAACAACAGAAGCGCC 60.136 52.381 2.29 0.00 0.00 6.53
96 97 1.727213 GCATGAGAACAACAGAAGCGC 60.727 52.381 0.00 0.00 0.00 5.92
97 98 1.463034 CGCATGAGAACAACAGAAGCG 60.463 52.381 0.00 0.00 36.62 4.68
98 99 1.727213 GCGCATGAGAACAACAGAAGC 60.727 52.381 0.30 0.00 0.00 3.86
99 100 1.463034 CGCGCATGAGAACAACAGAAG 60.463 52.381 8.75 0.00 0.00 2.85
102 103 0.451628 CACGCGCATGAGAACAACAG 60.452 55.000 5.73 0.00 0.00 3.16
114 117 2.866010 CGACAACAACTCACGCGCA 61.866 57.895 5.73 0.00 0.00 6.09
130 133 2.441348 TAGGATGCACGAGGCCGA 60.441 61.111 0.00 0.00 43.89 5.54
137 140 4.820897 TCCATAAATAGCTAGGATGCACG 58.179 43.478 0.00 0.00 34.99 5.34
148 151 2.169832 TGCTCGGCTCCATAAATAGC 57.830 50.000 0.00 0.00 38.03 2.97
149 152 5.525378 GGATATTGCTCGGCTCCATAAATAG 59.475 44.000 0.00 0.00 0.00 1.73
159 162 2.700897 ACTAAGTGGATATTGCTCGGCT 59.299 45.455 0.00 0.00 0.00 5.52
162 165 3.722147 AGCACTAAGTGGATATTGCTCG 58.278 45.455 0.00 0.00 37.24 5.03
401 427 2.374170 GAGTAGGAGAGAGTAGGGAGGG 59.626 59.091 0.00 0.00 0.00 4.30
907 935 1.281899 GCCGCAGTTAGTAGCTGAAG 58.718 55.000 17.31 9.85 36.12 3.02
1118 1151 3.010226 CGAGAGGGGGAGAAGGGGA 62.010 68.421 0.00 0.00 0.00 4.81
1165 1206 2.908940 GCAATGGAGATGGGCGGG 60.909 66.667 0.00 0.00 0.00 6.13
1172 1216 1.270732 GCAGATCCGAGCAATGGAGAT 60.271 52.381 0.00 0.00 39.30 2.75
1205 1249 2.989253 GGAAAACGGGGCCTGGTG 60.989 66.667 18.49 0.41 0.00 4.17
1206 1250 4.653888 CGGAAAACGGGGCCTGGT 62.654 66.667 18.49 7.39 39.42 4.00
1210 1254 4.340246 AGGTCGGAAAACGGGGCC 62.340 66.667 0.00 0.00 44.45 5.80
1217 1261 3.383185 AGCACAAAAATCAGGTCGGAAAA 59.617 39.130 0.00 0.00 0.00 2.29
1245 1289 3.372422 TTGTGGGTGTGGCTGCCTT 62.372 57.895 21.03 0.00 0.00 4.35
1250 1294 2.839098 CTCCTTGTGGGTGTGGCT 59.161 61.111 0.00 0.00 36.25 4.75
1269 1313 0.255890 GCTACCAATTGCTCCCTCCA 59.744 55.000 0.00 0.00 0.00 3.86
1275 1319 0.521242 CGCGTTGCTACCAATTGCTC 60.521 55.000 0.00 0.00 34.78 4.26
1296 1340 1.305623 CATTGGGGCAAGGAGAGCT 59.694 57.895 0.00 0.00 0.00 4.09
1311 1355 1.078823 GGAGGTCCTTTTTCCCCCATT 59.921 52.381 0.00 0.00 0.00 3.16
1313 1357 1.440362 GGGAGGTCCTTTTTCCCCCA 61.440 60.000 6.25 0.00 43.98 4.96
1441 1501 7.201767 GGGACAAATATCTCAAAATCAGACTGG 60.202 40.741 1.81 0.00 0.00 4.00
1459 1519 2.158475 TGAAGTGCTGAAGGGGACAAAT 60.158 45.455 0.00 0.00 0.00 2.32
1460 1520 1.214175 TGAAGTGCTGAAGGGGACAAA 59.786 47.619 0.00 0.00 0.00 2.83
1486 1546 3.245229 ACAAAGGATTGCATACAGGTGGA 60.245 43.478 0.00 0.00 40.34 4.02
1498 1571 9.341899 GCAAAACATTACTACTACAAAGGATTG 57.658 33.333 0.00 0.00 42.46 2.67
1506 1579 5.180492 GCAGGTGCAAAACATTACTACTACA 59.820 40.000 0.00 0.00 41.59 2.74
1530 1607 2.106844 GCTAATTGAGCCCCGGTTG 58.893 57.895 0.00 0.00 46.41 3.77
1542 1619 6.296026 TGACACTGTAAACCAAGAGCTAATT 58.704 36.000 0.00 0.00 0.00 1.40
1562 1639 0.821301 TTTGCGGCCAGAACATGACA 60.821 50.000 2.24 0.00 0.00 3.58
1566 1643 1.338011 CCATTTTTGCGGCCAGAACAT 60.338 47.619 2.24 0.00 0.00 2.71
1573 1650 1.731709 GTTCATTCCATTTTTGCGGCC 59.268 47.619 0.00 0.00 0.00 6.13
1599 1676 5.564651 GCCATATGGTTTATGCAGCGTAAAT 60.565 40.000 22.79 9.37 37.57 1.40
1600 1677 4.261405 GCCATATGGTTTATGCAGCGTAAA 60.261 41.667 22.79 14.75 37.57 2.01
1601 1678 3.252215 GCCATATGGTTTATGCAGCGTAA 59.748 43.478 22.79 2.68 37.57 3.18
1602 1679 2.811431 GCCATATGGTTTATGCAGCGTA 59.189 45.455 22.79 0.00 37.57 4.42
1604 1681 1.608109 TGCCATATGGTTTATGCAGCG 59.392 47.619 22.79 0.00 37.57 5.18
1646 1739 3.701040 ACCAAACAAACACATTGCTCTCT 59.299 39.130 0.00 0.00 43.13 3.10
1684 1783 1.731160 CCAGCTTCTGCGAGAGAAAAG 59.269 52.381 0.00 0.00 40.33 2.27
1691 1791 1.730501 TGAAATCCAGCTTCTGCGAG 58.269 50.000 0.00 0.00 45.42 5.03
1692 1792 2.079158 CTTGAAATCCAGCTTCTGCGA 58.921 47.619 0.00 0.00 45.42 5.10
1693 1793 1.808945 ACTTGAAATCCAGCTTCTGCG 59.191 47.619 0.00 0.00 45.42 5.18
1724 1824 1.367840 GAAGTGGACGCAGGACACT 59.632 57.895 0.00 0.00 46.59 3.55
1767 1867 2.278857 GAGCACGTGGATCGCGAT 60.279 61.111 23.97 23.97 44.19 4.58
1790 1890 1.021390 CGACCTGAATCAGCGGCTTT 61.021 55.000 4.40 0.00 0.00 3.51
1814 1914 1.984570 CCTCTTCCAGCGGTCCTCA 60.985 63.158 0.00 0.00 0.00 3.86
1922 2022 2.556559 GGTTGCAGGGGTGAAGGATTTA 60.557 50.000 0.00 0.00 0.00 1.40
1928 2028 1.152777 TGTGGTTGCAGGGGTGAAG 60.153 57.895 0.00 0.00 0.00 3.02
1952 2052 1.226888 GGCAGTAAGAGCGGGTACG 60.227 63.158 0.00 0.00 44.63 3.67
1958 2058 1.939974 TAATGCAGGCAGTAAGAGCG 58.060 50.000 0.00 0.00 0.00 5.03
1997 2106 1.873591 CAGCAACACCACAACTCTACC 59.126 52.381 0.00 0.00 0.00 3.18
2139 2248 1.550327 AGCTCTGTCATCGAGGTCAA 58.450 50.000 0.00 0.00 34.39 3.18
2147 2256 2.669300 TGAAGCTGAGCTCTGTCATC 57.331 50.000 20.24 15.65 38.25 2.92
2177 2286 2.219458 CCTATCATGGCAGCACAGAAG 58.781 52.381 0.00 0.00 0.00 2.85
2246 2355 6.486248 CATGTACCTGTCAAATTTGTATCCG 58.514 40.000 17.47 5.92 0.00 4.18
2377 2486 9.354673 ACTAAATCTTTTGATCCTTGAACTCAA 57.645 29.630 0.00 0.00 38.40 3.02
2441 2551 4.564782 ATCATCTGACAGAGGCAAGAAA 57.435 40.909 12.26 0.00 0.00 2.52
2564 2674 0.179145 AGAACCAGTCGATTACGCCG 60.179 55.000 0.00 0.00 39.58 6.46
2603 2713 5.649557 CCTAGGATGATAATCAGCGAAGAG 58.350 45.833 1.05 0.00 32.73 2.85
2636 2746 1.388547 AGTTGAGGCAAAACGCAAGA 58.611 45.000 0.00 0.00 45.17 3.02
2681 2791 1.668151 GAAGGTCACTGCCGTGGTC 60.668 63.158 8.50 2.61 41.53 4.02
2687 2797 1.336240 GCAACATTGAAGGTCACTGCC 60.336 52.381 0.00 0.00 31.15 4.85
2742 2852 4.522022 AGAAACTTGAGGGAAGAAAGCATG 59.478 41.667 0.00 0.00 35.42 4.06
2778 2888 4.642429 ACCTACAGTGGAATGTTCAGTTC 58.358 43.478 0.00 0.00 34.56 3.01
2804 2915 1.462283 CATGAGACCAAGACTGCAACG 59.538 52.381 0.00 0.00 0.00 4.10
2813 2924 3.204526 GAAGATCAGCCATGAGACCAAG 58.795 50.000 0.00 0.00 39.29 3.61
2840 2951 1.202806 GCATTCATTGGGGAGATCGGA 60.203 52.381 0.00 0.00 0.00 4.55
3080 3191 2.095567 GCATCTGTGTGCCAAACTGTAG 60.096 50.000 0.00 0.00 39.18 2.74
3184 3296 3.487120 ACTAGTGACTGAACAAACCCC 57.513 47.619 0.00 0.00 0.00 4.95
3222 3334 4.010349 GGGGGATTTGACTAAGTTGACAG 58.990 47.826 0.00 0.00 0.00 3.51
3273 3385 6.806249 CAGCAAAACAAGTAAACAGAAGTTGA 59.194 34.615 0.00 0.00 38.17 3.18
3274 3386 6.454186 GCAGCAAAACAAGTAAACAGAAGTTG 60.454 38.462 0.00 0.00 38.17 3.16
3275 3387 5.576774 GCAGCAAAACAAGTAAACAGAAGTT 59.423 36.000 0.00 0.00 40.40 2.66
3276 3388 5.102313 GCAGCAAAACAAGTAAACAGAAGT 58.898 37.500 0.00 0.00 0.00 3.01
3286 3398 4.605640 AACATATGGCAGCAAAACAAGT 57.394 36.364 7.80 0.00 0.00 3.16
3354 3466 3.190327 TGGAATTTCGATGCAAACACGAT 59.810 39.130 0.00 0.00 36.02 3.73
3402 3532 3.519913 ACCTTCATGTTCCTAAGTCCCTC 59.480 47.826 0.00 0.00 0.00 4.30
3419 3549 4.929819 TTTTGGAAGTGGCTTAACCTTC 57.070 40.909 0.00 0.00 40.22 3.46
3540 3670 6.093633 GGAAGTGAGGTCCAAAATACATGTAC 59.906 42.308 7.96 0.00 35.05 2.90
3596 3726 7.068716 GCATGGATTCACCTTTAAAGTTATCCT 59.931 37.037 22.31 13.08 39.86 3.24
3608 3738 4.079558 AGGATAAGTGCATGGATTCACCTT 60.080 41.667 0.00 0.00 39.86 3.50
3610 3740 3.825328 AGGATAAGTGCATGGATTCACC 58.175 45.455 0.00 0.00 39.54 4.02
3617 3748 5.698089 CAGTGTACATAGGATAAGTGCATGG 59.302 44.000 0.00 0.00 37.24 3.66
3621 3752 5.277857 ACCAGTGTACATAGGATAAGTGC 57.722 43.478 19.74 0.00 0.00 4.40
3625 3756 5.685520 TGCAACCAGTGTACATAGGATAA 57.314 39.130 19.74 1.88 0.00 1.75
3626 3757 5.685520 TTGCAACCAGTGTACATAGGATA 57.314 39.130 19.74 4.09 0.00 2.59
3661 3792 5.643421 ATGGAGTTCATCTTCCAGCTTAT 57.357 39.130 0.00 0.00 35.54 1.73
3723 3854 3.523806 GAAGCCTCAACTTCGAGCT 57.476 52.632 0.00 0.00 36.96 4.09
3780 3911 6.215636 AGAGTTCAGGGACCTGTAAATATTGT 59.784 38.462 17.34 0.00 43.96 2.71


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

AutoCloner maintained by Alex Coulton.