Multiple sequence alignment - TraesCS5D01G270100

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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 TraesCS5D01G270100 chr5D 100.000 3062 0 0 1 3062 373777524 373774463 0.000000e+00 5655
1 TraesCS5D01G270100 chr5A 94.066 2292 95 13 798 3062 475635439 475633162 0.000000e+00 3441
2 TraesCS5D01G270100 chr5A 83.238 698 48 34 165 809 475636977 475636296 7.360000e-161 577
3 TraesCS5D01G270100 chr5B 93.855 2262 105 7 822 3062 445196541 445194293 0.000000e+00 3376
4 TraesCS5D01G270100 chr5B 90.698 430 20 5 38 463 445200546 445200133 3.450000e-154 555
5 TraesCS5D01G270100 chr5B 86.905 168 12 5 752 914 445198553 445198391 2.430000e-41 180
6 TraesCS5D01G270100 chr5B 82.759 232 9 12 470 675 445199924 445199698 8.720000e-41 178
7 TraesCS5D01G270100 chr2D 89.136 359 36 2 2221 2576 626672958 626672600 7.790000e-121 444


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 TraesCS5D01G270100 chr5D 373774463 373777524 3061 True 5655.00 5655 100.00000 1 3062 1 chr5D.!!$R1 3061
1 TraesCS5D01G270100 chr5A 475633162 475636977 3815 True 2009.00 3441 88.65200 165 3062 2 chr5A.!!$R1 2897
2 TraesCS5D01G270100 chr5B 445194293 445200546 6253 True 1072.25 3376 88.55425 38 3062 4 chr5B.!!$R1 3024

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
28 29 0.321298 ATCCCTTTGTCCACGAACGG 60.321 55.0 0.0 0.0 0.00 4.44 F
1700 5853 0.179097 GAGGAGGTGCCGAAGCTTAG 60.179 60.0 0.0 0.0 43.43 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 5945 0.902984 TTGAAGTAGAGCGGGCAGGA 60.903 55.0 0.00 0.0 0.00 3.86 R
2959 7129 0.598419 GCTGGCCAAAGCAACTTGAC 60.598 55.0 7.01 0.0 43.01 3.18 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 3.799753 CGCGGACTGATCCCTTTG 58.200 61.111 0.00 0.00 42.83 2.77
18 19 1.079127 CGCGGACTGATCCCTTTGT 60.079 57.895 0.00 0.00 42.83 2.83
19 20 1.084370 CGCGGACTGATCCCTTTGTC 61.084 60.000 0.00 0.00 42.83 3.18
20 21 0.744771 GCGGACTGATCCCTTTGTCC 60.745 60.000 0.00 0.00 42.83 4.02
21 22 0.613260 CGGACTGATCCCTTTGTCCA 59.387 55.000 10.92 0.00 46.65 4.02
22 23 1.676014 CGGACTGATCCCTTTGTCCAC 60.676 57.143 10.92 0.00 46.65 4.02
23 24 1.676014 GGACTGATCCCTTTGTCCACG 60.676 57.143 6.18 0.00 45.87 4.94
24 25 1.275291 GACTGATCCCTTTGTCCACGA 59.725 52.381 0.00 0.00 0.00 4.35
25 26 1.697432 ACTGATCCCTTTGTCCACGAA 59.303 47.619 0.00 0.00 0.00 3.85
26 27 2.076863 CTGATCCCTTTGTCCACGAAC 58.923 52.381 0.00 0.00 0.00 3.95
27 28 1.076332 GATCCCTTTGTCCACGAACG 58.924 55.000 0.00 0.00 0.00 3.95
28 29 0.321298 ATCCCTTTGTCCACGAACGG 60.321 55.000 0.00 0.00 0.00 4.44
29 30 1.070105 CCCTTTGTCCACGAACGGA 59.930 57.895 0.00 0.00 0.00 4.69
35 36 3.780357 TCCACGAACGGACATGGA 58.220 55.556 0.00 0.00 38.94 3.41
36 37 2.051105 TCCACGAACGGACATGGAA 58.949 52.632 0.00 0.00 38.30 3.53
48 49 1.675310 CATGGAAGCTGCCGTTGGA 60.675 57.895 1.20 0.00 0.00 3.53
56 57 2.046023 TGCCGTTGGAGATGCCTG 60.046 61.111 0.00 0.00 37.63 4.85
101 102 4.081642 GGTAAATGAGGTCTGAGCTGTACA 60.082 45.833 14.96 6.65 0.00 2.90
122 123 5.609423 ACATCTGTACTACGTAGGGACTAG 58.391 45.833 25.63 19.15 44.14 2.57
123 124 4.065321 TCTGTACTACGTAGGGACTAGC 57.935 50.000 25.63 8.47 44.14 3.42
195 200 2.068837 ACCATGTTGAAATGCAAGCG 57.931 45.000 0.00 0.00 37.12 4.68
283 288 2.818921 ACTGCTCCTTCTCTGATGAGT 58.181 47.619 0.00 0.00 40.98 3.41
320 338 5.074804 GTCAACCCCATAACTAACAGGTTT 58.925 41.667 0.00 0.00 35.46 3.27
321 339 5.182570 GTCAACCCCATAACTAACAGGTTTC 59.817 44.000 0.00 0.00 35.46 2.78
322 340 4.311520 ACCCCATAACTAACAGGTTTCC 57.688 45.455 0.00 0.00 0.00 3.13
323 341 3.920841 ACCCCATAACTAACAGGTTTCCT 59.079 43.478 0.00 0.00 0.00 3.36
324 342 4.018688 ACCCCATAACTAACAGGTTTCCTC 60.019 45.833 0.00 0.00 0.00 3.71
325 343 4.227527 CCCCATAACTAACAGGTTTCCTCT 59.772 45.833 0.00 0.00 0.00 3.69
326 344 5.427481 CCCCATAACTAACAGGTTTCCTCTA 59.573 44.000 0.00 0.00 0.00 2.43
327 345 6.408206 CCCCATAACTAACAGGTTTCCTCTAG 60.408 46.154 0.00 0.00 0.00 2.43
328 346 6.408206 CCCATAACTAACAGGTTTCCTCTAGG 60.408 46.154 0.00 0.00 0.00 3.02
329 347 6.156429 CCATAACTAACAGGTTTCCTCTAGGT 59.844 42.308 0.00 0.00 36.34 3.08
330 348 7.311109 CCATAACTAACAGGTTTCCTCTAGGTT 60.311 40.741 0.00 0.00 36.34 3.50
351 369 5.247862 GTTTTCCCAAGCAAATGGATGATT 58.752 37.500 4.90 0.00 43.54 2.57
371 389 6.598525 TGATTAAACACGCAGTTCATTACAG 58.401 36.000 0.00 0.00 41.61 2.74
372 390 5.994887 TTAAACACGCAGTTCATTACAGT 57.005 34.783 0.00 0.00 41.61 3.55
373 391 7.385478 TGATTAAACACGCAGTTCATTACAGTA 59.615 33.333 0.00 0.00 41.61 2.74
374 392 4.985044 AACACGCAGTTCATTACAGTAC 57.015 40.909 0.00 0.00 41.61 2.73
555 788 3.902150 CTTTTCGAAAAGAAGAAGGGGC 58.098 45.455 36.28 0.00 46.39 5.80
556 789 2.649531 TTCGAAAAGAAGAAGGGGCA 57.350 45.000 0.00 0.00 34.26 5.36
557 790 2.879103 TCGAAAAGAAGAAGGGGCAT 57.121 45.000 0.00 0.00 0.00 4.40
558 791 2.436417 TCGAAAAGAAGAAGGGGCATG 58.564 47.619 0.00 0.00 0.00 4.06
577 810 6.886459 GGGCATGTACATTATCATAGATGGTT 59.114 38.462 5.37 0.00 0.00 3.67
592 825 2.277373 GTTCGCGTCGATCGAGCT 60.277 61.111 20.09 0.00 42.86 4.09
594 827 2.746803 TTCGCGTCGATCGAGCTGA 61.747 57.895 20.09 19.39 42.86 4.26
595 828 2.248274 TTCGCGTCGATCGAGCTGAA 62.248 55.000 20.09 22.91 42.86 3.02
596 829 2.282361 CGCGTCGATCGAGCTGAAG 61.282 63.158 20.09 7.73 42.86 3.02
598 831 1.197368 GCGTCGATCGAGCTGAAGTC 61.197 60.000 20.09 2.84 42.86 3.01
603 862 2.030274 TCGATCGAGCTGAAGTCAAACA 60.030 45.455 15.15 0.00 0.00 2.83
613 872 6.000219 AGCTGAAGTCAAACAGTACATCATT 59.000 36.000 0.00 0.00 36.62 2.57
616 875 7.095229 GCTGAAGTCAAACAGTACATCATTGTA 60.095 37.037 0.00 0.00 36.62 2.41
618 877 8.147704 TGAAGTCAAACAGTACATCATTGTAGA 58.852 33.333 0.00 0.00 38.98 2.59
661 927 2.555199 GCGATCCATTTGAGCTAGTGT 58.445 47.619 0.00 0.00 0.00 3.55
675 941 0.860533 TAGTGTTTGCGTTGGCGTAC 59.139 50.000 0.00 0.00 44.10 3.67
676 942 1.369568 GTGTTTGCGTTGGCGTACC 60.370 57.895 0.00 0.00 44.10 3.34
677 943 2.127534 GTTTGCGTTGGCGTACCG 60.128 61.111 0.00 0.00 44.10 4.02
678 944 2.588314 TTTGCGTTGGCGTACCGT 60.588 55.556 0.00 0.00 44.10 4.83
679 945 1.300465 TTTGCGTTGGCGTACCGTA 60.300 52.632 0.00 0.00 44.10 4.02
680 946 1.555741 TTTGCGTTGGCGTACCGTAC 61.556 55.000 0.00 0.00 44.10 3.67
700 987 1.531264 CGTAGCTGCTGTACCGTGTAG 60.531 57.143 13.43 0.00 0.00 2.74
708 996 3.256383 TGCTGTACCGTGTAGCTTTTCTA 59.744 43.478 0.00 0.00 38.25 2.10
769 2103 2.335712 CGTCCTTGAAGGGCCTTGC 61.336 63.158 26.47 15.54 36.37 4.01
777 2111 0.394192 GAAGGGCCTTGCAGCTTTTT 59.606 50.000 26.47 0.00 0.00 1.94
817 3019 3.744559 GTCGAAGGCCTTGCAACA 58.255 55.556 26.25 0.00 0.00 3.33
866 5015 1.228337 GTTACCAAACCAGGCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
870 5019 2.351276 CAAACCAGGCCCGTAGCT 59.649 61.111 0.00 0.00 43.05 3.32
888 5037 0.830648 CTCATAGGTCTGGCCCGAAA 59.169 55.000 0.00 0.00 38.26 3.46
937 5087 3.623281 TTGAATCGTTCACGCGCGC 62.623 57.895 32.58 23.91 39.87 6.86
1059 5212 3.324930 CTGCTGGGCCTCCACTCA 61.325 66.667 4.53 0.00 38.32 3.41
1574 5727 2.182825 CCACTACGACAACATCTACGC 58.817 52.381 0.00 0.00 0.00 4.42
1698 5851 2.665603 GAGGAGGTGCCGAAGCTT 59.334 61.111 0.00 0.00 43.43 3.74
1700 5853 0.179097 GAGGAGGTGCCGAAGCTTAG 60.179 60.000 0.00 0.00 43.43 2.18
1929 6082 1.315257 GGCTCACCATTGCCGTCAAT 61.315 55.000 0.00 0.00 43.31 2.57
1986 6139 4.745649 CCTACTTTAACTTCCTGAGGTCG 58.254 47.826 0.00 0.00 0.00 4.79
2058 6211 1.469308 GAGCTCGAGGAGAAGAACGAA 59.531 52.381 15.58 0.00 34.50 3.85
2072 6225 2.026822 AGAACGAATGAGCTCATGGGTT 60.027 45.455 30.59 30.59 36.56 4.11
2075 6228 2.086869 CGAATGAGCTCATGGGTTTGT 58.913 47.619 29.34 12.22 36.56 2.83
2080 6233 2.040145 TGAGCTCATGGGTTTGTGATCA 59.960 45.455 13.74 0.00 34.33 2.92
2091 6244 4.351192 GGTTTGTGATCATATTGGCGTTC 58.649 43.478 0.00 0.00 0.00 3.95
2247 6416 5.515797 AATTGCACATCAGGATTGATCTG 57.484 39.130 0.00 0.00 42.12 2.90
2268 6437 7.106439 TCTGTTAGCAAAAGAACATTTTGGA 57.894 32.000 13.27 0.98 39.19 3.53
2285 6454 9.758651 ACATTTTGGAAGGTGTTAAACTTTATC 57.241 29.630 0.00 0.00 0.00 1.75
2357 6526 2.930682 GGTCTAGAAACGGCATCTTGAC 59.069 50.000 15.28 15.28 43.99 3.18
2377 6546 9.399797 TCTTGACTAAATTATGCATGAGACATT 57.600 29.630 10.16 0.00 0.00 2.71
2382 6551 8.133627 ACTAAATTATGCATGAGACATTTGAGC 58.866 33.333 10.16 0.00 0.00 4.26
2384 6553 5.494632 TTATGCATGAGACATTTGAGCAG 57.505 39.130 10.16 0.00 33.69 4.24
2415 6584 3.130633 TCAGACGGAAGACAACACAATG 58.869 45.455 0.00 0.00 0.00 2.82
2427 6596 5.833406 ACAACACAATGTCAGTTGATGAA 57.167 34.783 19.18 0.00 43.93 2.57
2496 6665 5.376625 ACCAATTCTGCAACCGATACATAT 58.623 37.500 0.00 0.00 0.00 1.78
2609 6779 4.265904 TGGATATACGCGGTTGATTCAT 57.734 40.909 12.47 0.00 0.00 2.57
2621 6791 6.128956 CGCGGTTGATTCATTTTGTGTTAATT 60.129 34.615 0.00 0.00 0.00 1.40
2654 6824 6.650807 TCTTGGTGACTGTTCTGAACATATTC 59.349 38.462 22.28 17.96 41.26 1.75
2694 6864 7.383572 AGTCGTCATAACATAATCTGATTCTGC 59.616 37.037 13.72 0.00 0.00 4.26
2732 6902 6.016276 ACACCCAAATTCTAAAACTGCTAGTG 60.016 38.462 0.00 0.00 0.00 2.74
2757 6927 6.712095 GTGATATTTCTCATGTAGGCATCCAA 59.288 38.462 0.00 0.00 31.99 3.53
2800 6970 9.520204 CATTTCCCTTTACATAAATAGCTTGTG 57.480 33.333 0.00 0.00 32.63 3.33
2959 7129 1.217882 AGTCGTTCCAAGCAGTTTCG 58.782 50.000 0.00 0.00 0.00 3.46
3005 7175 1.214175 TCCACAGCCACCTTCAGAAAA 59.786 47.619 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.079127 ACAAAGGGATCAGTCCGCG 60.079 57.895 0.00 0.00 46.09 6.46
1 2 0.744771 GGACAAAGGGATCAGTCCGC 60.745 60.000 0.00 0.00 46.09 5.54
2 3 3.460648 GGACAAAGGGATCAGTCCG 57.539 57.895 0.00 0.00 46.09 4.79
4 5 1.275291 TCGTGGACAAAGGGATCAGTC 59.725 52.381 0.00 0.00 0.00 3.51
5 6 1.348064 TCGTGGACAAAGGGATCAGT 58.652 50.000 0.00 0.00 0.00 3.41
6 7 2.076863 GTTCGTGGACAAAGGGATCAG 58.923 52.381 0.00 0.00 0.00 2.90
7 8 1.606994 CGTTCGTGGACAAAGGGATCA 60.607 52.381 0.00 0.00 0.00 2.92
8 9 1.076332 CGTTCGTGGACAAAGGGATC 58.924 55.000 0.00 0.00 0.00 3.36
9 10 0.321298 CCGTTCGTGGACAAAGGGAT 60.321 55.000 0.00 0.00 33.29 3.85
10 11 1.070105 CCGTTCGTGGACAAAGGGA 59.930 57.895 0.00 0.00 33.29 4.20
11 12 1.070105 TCCGTTCGTGGACAAAGGG 59.930 57.895 0.00 0.00 31.53 3.95
12 13 4.762825 TCCGTTCGTGGACAAAGG 57.237 55.556 0.00 0.00 31.53 3.11
19 20 1.635663 GCTTCCATGTCCGTTCGTGG 61.636 60.000 8.46 8.46 43.59 4.94
20 21 0.670546 AGCTTCCATGTCCGTTCGTG 60.671 55.000 0.00 0.00 0.00 4.35
21 22 0.670546 CAGCTTCCATGTCCGTTCGT 60.671 55.000 0.00 0.00 0.00 3.85
22 23 1.970917 GCAGCTTCCATGTCCGTTCG 61.971 60.000 0.00 0.00 0.00 3.95
23 24 1.648467 GGCAGCTTCCATGTCCGTTC 61.648 60.000 0.00 0.00 0.00 3.95
24 25 1.675641 GGCAGCTTCCATGTCCGTT 60.676 57.895 0.00 0.00 0.00 4.44
25 26 2.045926 GGCAGCTTCCATGTCCGT 60.046 61.111 0.00 0.00 0.00 4.69
26 27 3.197790 CGGCAGCTTCCATGTCCG 61.198 66.667 2.54 0.00 33.40 4.79
27 28 1.675641 AACGGCAGCTTCCATGTCC 60.676 57.895 2.54 0.00 0.00 4.02
28 29 1.503542 CAACGGCAGCTTCCATGTC 59.496 57.895 2.54 0.00 0.00 3.06
29 30 1.973281 CCAACGGCAGCTTCCATGT 60.973 57.895 2.54 0.00 0.00 3.21
30 31 1.651240 CTCCAACGGCAGCTTCCATG 61.651 60.000 2.54 0.57 0.00 3.66
31 32 1.377725 CTCCAACGGCAGCTTCCAT 60.378 57.895 2.54 0.00 0.00 3.41
32 33 1.841302 ATCTCCAACGGCAGCTTCCA 61.841 55.000 2.54 0.00 0.00 3.53
33 34 1.078143 ATCTCCAACGGCAGCTTCC 60.078 57.895 0.00 0.00 0.00 3.46
34 35 1.986575 GCATCTCCAACGGCAGCTTC 61.987 60.000 0.00 0.00 0.00 3.86
35 36 2.042831 GCATCTCCAACGGCAGCTT 61.043 57.895 0.00 0.00 0.00 3.74
36 37 2.437359 GCATCTCCAACGGCAGCT 60.437 61.111 0.00 0.00 0.00 4.24
56 57 2.726760 CTCAAGTATAATCGGCAGCGTC 59.273 50.000 0.00 0.00 0.00 5.19
101 102 4.102210 TGCTAGTCCCTACGTAGTACAGAT 59.898 45.833 20.73 6.37 45.11 2.90
117 118 4.655762 TGATCACTACCATGTGCTAGTC 57.344 45.455 0.00 0.00 37.81 2.59
122 123 5.121811 AGAAGAATGATCACTACCATGTGC 58.878 41.667 0.00 0.00 37.81 4.57
123 124 8.899427 AATAGAAGAATGATCACTACCATGTG 57.101 34.615 0.00 0.00 39.15 3.21
161 166 5.411361 TCAACATGGTTCTAATCTTTGTCGG 59.589 40.000 0.00 0.00 0.00 4.79
195 200 3.233425 GCACACATTGCCGCAAAC 58.767 55.556 10.42 0.00 46.63 2.93
283 288 2.367567 GGGTTGACCTACTCACAGTGAA 59.632 50.000 4.41 0.00 35.85 3.18
320 338 2.344592 TGCTTGGGAAAACCTAGAGGA 58.655 47.619 1.60 0.00 43.79 3.71
321 339 2.879103 TGCTTGGGAAAACCTAGAGG 57.121 50.000 0.00 0.00 43.79 3.69
322 340 4.082026 CCATTTGCTTGGGAAAACCTAGAG 60.082 45.833 0.00 0.00 43.79 2.43
323 341 3.831911 CCATTTGCTTGGGAAAACCTAGA 59.168 43.478 0.00 0.00 43.79 2.43
324 342 3.831911 TCCATTTGCTTGGGAAAACCTAG 59.168 43.478 1.84 0.00 43.89 3.02
325 343 3.850752 TCCATTTGCTTGGGAAAACCTA 58.149 40.909 1.84 0.00 41.11 3.08
326 344 2.688477 TCCATTTGCTTGGGAAAACCT 58.312 42.857 1.84 0.00 41.11 3.50
327 345 3.007831 TCATCCATTTGCTTGGGAAAACC 59.992 43.478 0.00 0.00 37.37 3.27
328 346 4.270245 TCATCCATTTGCTTGGGAAAAC 57.730 40.909 0.00 0.00 37.37 2.43
329 347 5.502089 AATCATCCATTTGCTTGGGAAAA 57.498 34.783 0.00 0.00 37.37 2.29
330 348 6.617782 TTAATCATCCATTTGCTTGGGAAA 57.382 33.333 0.00 0.00 37.37 3.13
351 369 5.117440 CGTACTGTAATGAACTGCGTGTTTA 59.883 40.000 0.00 0.00 39.30 2.01
371 389 4.143179 GCTTGTGGACAGTGAAATACGTAC 60.143 45.833 0.00 0.00 0.00 3.67
372 390 3.991773 GCTTGTGGACAGTGAAATACGTA 59.008 43.478 0.00 0.00 0.00 3.57
373 391 2.806244 GCTTGTGGACAGTGAAATACGT 59.194 45.455 0.00 0.00 0.00 3.57
374 392 2.159841 CGCTTGTGGACAGTGAAATACG 60.160 50.000 0.00 0.00 0.00 3.06
552 785 6.418101 ACCATCTATGATAATGTACATGCCC 58.582 40.000 9.63 2.09 0.00 5.36
553 786 7.201556 CGAACCATCTATGATAATGTACATGCC 60.202 40.741 9.63 2.45 0.00 4.40
554 787 7.674937 GCGAACCATCTATGATAATGTACATGC 60.675 40.741 9.63 3.00 0.00 4.06
555 788 7.463251 CGCGAACCATCTATGATAATGTACATG 60.463 40.741 9.63 0.00 0.00 3.21
556 789 6.531594 CGCGAACCATCTATGATAATGTACAT 59.468 38.462 0.00 1.41 0.00 2.29
557 790 5.861787 CGCGAACCATCTATGATAATGTACA 59.138 40.000 0.00 0.00 0.00 2.90
558 791 5.862323 ACGCGAACCATCTATGATAATGTAC 59.138 40.000 15.93 0.00 0.00 2.90
577 810 2.633198 CTTCAGCTCGATCGACGCGA 62.633 60.000 24.02 21.33 42.26 5.87
592 825 8.147704 TCTACAATGATGTACTGTTTGACTTCA 58.852 33.333 0.00 0.00 41.05 3.02
594 827 8.902540 TTCTACAATGATGTACTGTTTGACTT 57.097 30.769 0.00 0.00 41.05 3.01
595 828 8.902540 TTTCTACAATGATGTACTGTTTGACT 57.097 30.769 0.00 0.00 41.05 3.41
596 829 9.944663 TTTTTCTACAATGATGTACTGTTTGAC 57.055 29.630 0.00 0.00 41.05 3.18
675 941 0.248377 GGTACAGCAGCTACGTACGG 60.248 60.000 21.06 3.45 37.06 4.02
676 942 0.588233 CGGTACAGCAGCTACGTACG 60.588 60.000 15.01 15.01 37.06 3.67
677 943 0.449388 ACGGTACAGCAGCTACGTAC 59.551 55.000 12.64 12.64 35.77 3.67
678 944 0.448990 CACGGTACAGCAGCTACGTA 59.551 55.000 11.68 0.00 32.85 3.57
679 945 1.211969 CACGGTACAGCAGCTACGT 59.788 57.895 0.00 0.84 34.61 3.57
680 946 0.448990 TACACGGTACAGCAGCTACG 59.551 55.000 0.00 0.13 0.00 3.51
681 947 1.798079 GCTACACGGTACAGCAGCTAC 60.798 57.143 0.00 0.00 35.35 3.58
737 1166 2.103042 GGACGTGCATCCTCACTGC 61.103 63.158 0.63 0.00 40.10 4.40
777 2111 7.520937 CGACCCCTTAATTCGAAAAGAAAAGAA 60.521 37.037 10.51 0.00 42.91 2.52
778 2112 6.072893 CGACCCCTTAATTCGAAAAGAAAAGA 60.073 38.462 10.51 0.00 42.91 2.52
779 2113 6.072893 TCGACCCCTTAATTCGAAAAGAAAAG 60.073 38.462 10.51 6.34 42.91 2.27
780 2114 5.764192 TCGACCCCTTAATTCGAAAAGAAAA 59.236 36.000 10.51 0.00 42.91 2.29
781 2115 5.307204 TCGACCCCTTAATTCGAAAAGAAA 58.693 37.500 10.51 0.00 42.91 2.52
782 2116 4.897140 TCGACCCCTTAATTCGAAAAGAA 58.103 39.130 10.51 1.24 43.93 2.52
783 2117 4.540359 TCGACCCCTTAATTCGAAAAGA 57.460 40.909 10.51 0.00 38.77 2.52
793 2127 0.326927 CAAGGCCTTCGACCCCTTAA 59.673 55.000 17.29 0.00 36.86 1.85
817 3019 3.494398 GGGCTGTAATCATGTGGACGTAT 60.494 47.826 0.00 0.00 0.00 3.06
866 5015 0.827925 CGGGCCAGACCTATGAGCTA 60.828 60.000 4.39 0.00 39.10 3.32
870 5019 0.539986 GTTTCGGGCCAGACCTATGA 59.460 55.000 4.56 0.00 39.10 2.15
900 5049 0.470080 AGGGATTAGCAGGCGAGCTA 60.470 55.000 10.05 10.05 44.50 3.32
1698 5851 1.418334 GCTCTTCCATCTCCAGCCTA 58.582 55.000 0.00 0.00 0.00 3.93
1700 5853 1.148048 GGCTCTTCCATCTCCAGCC 59.852 63.158 0.00 0.00 42.87 4.85
1761 5914 3.620785 GCCATCTCCTCCGGCGAT 61.621 66.667 9.30 0.00 35.79 4.58
1792 5945 0.902984 TTGAAGTAGAGCGGGCAGGA 60.903 55.000 0.00 0.00 0.00 3.86
1854 6007 1.134995 CACATGCTCGGCAAGTAGAGA 60.135 52.381 6.46 0.00 43.62 3.10
1929 6082 5.411361 GTCAAACTGCATGTCATACCAGTAA 59.589 40.000 15.03 5.59 37.55 2.24
2058 6211 2.885135 TCACAAACCCATGAGCTCAT 57.115 45.000 23.75 23.75 36.96 2.90
2106 6259 5.958380 AGCCATATACTGCTAATACTGCCTA 59.042 40.000 0.00 0.00 35.69 3.93
2107 6260 4.780021 AGCCATATACTGCTAATACTGCCT 59.220 41.667 0.00 0.00 35.69 4.75
2108 6261 5.091261 AGCCATATACTGCTAATACTGCC 57.909 43.478 0.00 0.00 35.69 4.85
2247 6416 6.761242 ACCTTCCAAAATGTTCTTTTGCTAAC 59.239 34.615 5.18 0.00 37.89 2.34
2268 6437 7.232737 CCCTTTCTGGATAAAGTTTAACACCTT 59.767 37.037 0.00 0.00 38.35 3.50
2285 6454 2.056223 CCCATGCTGCCCTTTCTGG 61.056 63.158 0.00 0.00 0.00 3.86
2357 6526 8.132995 TGCTCAAATGTCTCATGCATAATTTAG 58.867 33.333 0.00 0.00 0.00 1.85
2377 6546 2.237893 TCTGATTCATCTGCCTGCTCAA 59.762 45.455 0.00 0.00 0.00 3.02
2382 6551 1.137675 TCCGTCTGATTCATCTGCCTG 59.862 52.381 0.00 0.00 0.00 4.85
2384 6553 2.159043 TCTTCCGTCTGATTCATCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
2415 6584 6.870965 ACTGTCAGAATAGTTCATCAACTGAC 59.129 38.462 6.91 1.27 46.91 3.51
2427 6596 5.105554 CCAGAGCTAACACTGTCAGAATAGT 60.106 44.000 6.91 0.00 33.10 2.12
2555 6725 7.404671 AAAGTACATTTCACTTCAACACCTT 57.595 32.000 0.00 0.00 35.19 3.50
2589 6759 5.607119 AAATGAATCAACCGCGTATATCC 57.393 39.130 4.92 0.00 0.00 2.59
2609 6779 9.883142 ACCAAGAAGAATCAAATTAACACAAAA 57.117 25.926 0.00 0.00 0.00 2.44
2621 6791 5.528690 CAGAACAGTCACCAAGAAGAATCAA 59.471 40.000 0.00 0.00 0.00 2.57
2686 6856 5.576384 GTGTTTTGTTTTCACTGCAGAATCA 59.424 36.000 23.35 7.00 0.00 2.57
2694 6864 6.371271 AGAATTTGGGTGTTTTGTTTTCACTG 59.629 34.615 0.00 0.00 33.30 3.66
2732 6902 6.233434 TGGATGCCTACATGAGAAATATCAC 58.767 40.000 0.00 0.00 36.35 3.06
2814 6984 2.498167 ACAGAAGCCACAACATCAGTC 58.502 47.619 0.00 0.00 0.00 3.51
2959 7129 0.598419 GCTGGCCAAAGCAACTTGAC 60.598 55.000 7.01 0.00 43.01 3.18
3005 7175 2.584391 GGTGGTCGAGGAAGGCAGT 61.584 63.158 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.