Multiple sequence alignment - TraesCS5B01G342800

Loading Multiple Alignment...

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 TraesCS5B01G342800 chr5B 100.000 2489 0 0 1 2489 527035575 527033087 0.000000e+00 4597.0
1 TraesCS5B01G342800 chr5B 90.698 172 15 1 3 173 648261647 648261476 6.930000e-56 228.0
2 TraesCS5B01G342800 chr5B 89.205 176 17 2 3 176 708880674 708880849 4.170000e-53 219.0
3 TraesCS5B01G342800 chr5D 91.173 2277 121 39 274 2489 434364860 434362603 0.000000e+00 3018.0
4 TraesCS5B01G342800 chr5D 92.117 685 45 6 1543 2224 434348378 434349056 0.000000e+00 957.0
5 TraesCS5B01G342800 chr5D 92.185 563 32 4 983 1545 434347700 434348250 0.000000e+00 785.0
6 TraesCS5B01G342800 chr5D 91.429 70 6 0 2418 2487 505397892 505397961 2.040000e-16 97.1
7 TraesCS5B01G342800 chr5D 79.279 111 14 3 361 470 434335960 434336062 4.440000e-08 69.4
8 TraesCS5B01G342800 chr5A 87.863 1549 95 31 44 1544 548222075 548220572 0.000000e+00 1733.0
9 TraesCS5B01G342800 chr5A 90.116 172 16 1 3 173 60443829 60444000 3.220000e-54 222.0
10 TraesCS5B01G342800 chr5A 90.116 172 16 1 3 173 563891715 563891886 3.220000e-54 222.0
11 TraesCS5B01G342800 chr5A 90.278 72 7 0 2418 2489 43489364 43489293 7.330000e-16 95.3
12 TraesCS5B01G342800 chr2A 90.344 756 65 5 1739 2489 776392274 776393026 0.000000e+00 985.0
13 TraesCS5B01G342800 chr2A 90.116 172 16 1 3 173 780720968 780720797 3.220000e-54 222.0
14 TraesCS5B01G342800 chr6A 90.230 174 16 1 1 173 596780825 596780652 2.490000e-55 226.0
15 TraesCS5B01G342800 chr6A 89.655 174 17 1 1 173 39064936 39065109 1.160000e-53 220.0
16 TraesCS5B01G342800 chrUn 90.116 172 16 1 3 173 75278589 75278418 3.220000e-54 222.0
17 TraesCS5B01G342800 chr3A 90.116 172 16 1 3 173 8568307 8568478 3.220000e-54 222.0
18 TraesCS5B01G342800 chr6D 91.429 70 6 0 2418 2487 455095314 455095383 2.040000e-16 97.1
19 TraesCS5B01G342800 chr6D 87.838 74 9 0 2416 2489 89701002 89700929 1.230000e-13 87.9
20 TraesCS5B01G342800 chr7D 91.045 67 6 0 2421 2487 102546464 102546398 9.480000e-15 91.6
21 TraesCS5B01G342800 chr7A 91.176 68 4 1 2419 2486 85603555 85603620 9.480000e-15 91.6
22 TraesCS5B01G342800 chr4A 90.000 70 7 0 2418 2487 659825564 659825495 9.480000e-15 91.6


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 TraesCS5B01G342800 chr5B 527033087 527035575 2488 True 4597 4597 100.000 1 2489 1 chr5B.!!$R1 2488
1 TraesCS5B01G342800 chr5D 434362603 434364860 2257 True 3018 3018 91.173 274 2489 1 chr5D.!!$R1 2215
2 TraesCS5B01G342800 chr5D 434347700 434349056 1356 False 871 957 92.151 983 2224 2 chr5D.!!$F3 1241
3 TraesCS5B01G342800 chr5A 548220572 548222075 1503 True 1733 1733 87.863 44 1544 1 chr5A.!!$R2 1500
4 TraesCS5B01G342800 chr2A 776392274 776393026 752 False 985 985 90.344 1739 2489 1 chr2A.!!$F1 750

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
958 1011 0.03601 ACACTCGCAATCCTCCCAAG 60.036 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2463 2676 2.10825 ACACCCTACCTTTGTGAGCATT 59.892 45.455 0.0 0.0 34.18 3.56 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
18 19 2.777536 ATCCCTGTGAGCACCTTCA 58.222 52.632 0.00 0.00 0.00 3.02
19 20 1.067295 ATCCCTGTGAGCACCTTCAA 58.933 50.000 0.00 0.00 0.00 2.69
20 21 0.843309 TCCCTGTGAGCACCTTCAAA 59.157 50.000 0.00 0.00 0.00 2.69
21 22 1.214175 TCCCTGTGAGCACCTTCAAAA 59.786 47.619 0.00 0.00 0.00 2.44
22 23 1.610522 CCCTGTGAGCACCTTCAAAAG 59.389 52.381 0.00 0.00 0.00 2.27
23 24 2.575532 CCTGTGAGCACCTTCAAAAGA 58.424 47.619 0.00 0.00 0.00 2.52
24 25 2.291741 CCTGTGAGCACCTTCAAAAGAC 59.708 50.000 0.00 0.00 0.00 3.01
25 26 3.209410 CTGTGAGCACCTTCAAAAGACT 58.791 45.455 0.00 0.00 0.00 3.24
26 27 2.945008 TGTGAGCACCTTCAAAAGACTG 59.055 45.455 0.00 0.00 0.00 3.51
27 28 3.206150 GTGAGCACCTTCAAAAGACTGA 58.794 45.455 0.00 0.00 0.00 3.41
28 29 3.249559 GTGAGCACCTTCAAAAGACTGAG 59.750 47.826 0.00 0.00 0.00 3.35
29 30 2.225255 GAGCACCTTCAAAAGACTGAGC 59.775 50.000 0.00 0.00 0.00 4.26
30 31 1.268079 GCACCTTCAAAAGACTGAGCC 59.732 52.381 0.00 0.00 0.00 4.70
31 32 1.532868 CACCTTCAAAAGACTGAGCCG 59.467 52.381 0.00 0.00 0.00 5.52
32 33 1.160137 CCTTCAAAAGACTGAGCCGG 58.840 55.000 0.00 0.00 0.00 6.13
33 34 0.519077 CTTCAAAAGACTGAGCCGGC 59.481 55.000 21.89 21.89 0.00 6.13
34 35 0.179032 TTCAAAAGACTGAGCCGGCA 60.179 50.000 31.54 7.98 0.00 5.69
35 36 0.036732 TCAAAAGACTGAGCCGGCAT 59.963 50.000 31.54 14.28 0.00 4.40
36 37 1.277842 TCAAAAGACTGAGCCGGCATA 59.722 47.619 31.54 16.21 0.00 3.14
37 38 2.092968 TCAAAAGACTGAGCCGGCATAT 60.093 45.455 31.54 8.11 0.00 1.78
38 39 2.246719 AAAGACTGAGCCGGCATATC 57.753 50.000 31.54 18.63 0.00 1.63
39 40 1.123077 AAGACTGAGCCGGCATATCA 58.877 50.000 31.54 22.44 0.00 2.15
40 41 1.346062 AGACTGAGCCGGCATATCAT 58.654 50.000 31.54 13.17 0.00 2.45
41 42 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
42 43 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
53 54 5.934043 CCGGCATATCATCTTGAGATTTACA 59.066 40.000 0.00 0.00 31.21 2.41
88 89 4.485834 TCGCCGTCGATGGGAACG 62.486 66.667 24.85 18.91 40.21 3.95
91 92 2.882876 CCGTCGATGGGAACGTCT 59.117 61.111 16.43 0.00 44.51 4.18
106 107 0.390472 CGTCTCCTCCCACTGAAAGC 60.390 60.000 0.00 0.00 37.60 3.51
108 109 1.280421 GTCTCCTCCCACTGAAAGCAT 59.720 52.381 0.00 0.00 37.60 3.79
113 114 2.619849 CCTCCCACTGAAAGCATGTCAT 60.620 50.000 0.00 0.00 37.60 3.06
122 123 3.378112 TGAAAGCATGTCATCGGAAATCC 59.622 43.478 0.00 0.00 0.00 3.01
133 134 8.292444 TGTCATCGGAAATCCTGAAATAAATT 57.708 30.769 0.00 0.00 0.00 1.82
151 152 8.792831 AATAAATTCAAGAATAATGCGAGCAG 57.207 30.769 3.58 0.00 0.00 4.24
162 163 2.659016 CGAGCAGCAGGACCTGAA 59.341 61.111 26.25 0.00 34.77 3.02
163 164 1.739562 CGAGCAGCAGGACCTGAAC 60.740 63.158 26.25 12.74 34.77 3.18
164 165 1.372683 GAGCAGCAGGACCTGAACA 59.627 57.895 26.25 0.00 34.77 3.18
165 166 0.952984 GAGCAGCAGGACCTGAACAC 60.953 60.000 26.25 10.57 34.77 3.32
166 167 1.072159 GCAGCAGGACCTGAACACT 59.928 57.895 26.25 9.59 34.77 3.55
167 168 1.233285 GCAGCAGGACCTGAACACTG 61.233 60.000 26.25 21.27 34.77 3.66
184 185 1.062505 ACTGGGGGTGGACATGTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
190 191 2.035632 GGTGGACATGTTTTTGGGTGA 58.964 47.619 0.00 0.00 0.00 4.02
202 203 0.394216 TTGGGTGAGATGGAATGGCG 60.394 55.000 0.00 0.00 0.00 5.69
203 204 1.271127 TGGGTGAGATGGAATGGCGA 61.271 55.000 0.00 0.00 0.00 5.54
227 228 2.053865 TAAGTGGCTACGGTCCGGG 61.054 63.158 17.28 9.14 0.00 5.73
264 265 1.169661 TGATTTGCGTCCGGTTTGCT 61.170 50.000 0.00 0.00 0.00 3.91
272 273 0.243636 GTCCGGTTTGCTGGGAAATG 59.756 55.000 0.00 0.00 41.53 2.32
342 343 2.493030 CGTCCGGACCGCTATGTT 59.507 61.111 28.52 0.00 0.00 2.71
343 344 1.727511 CCGTCCGGACCGCTATGTTA 61.728 60.000 28.52 0.00 37.50 2.41
348 364 1.931172 CCGGACCGCTATGTTAGTTTG 59.069 52.381 8.86 0.00 0.00 2.93
371 387 2.631062 AGGTCCGTGTTGAAGATGTACA 59.369 45.455 0.00 0.00 0.00 2.90
421 437 3.824443 GCACCTATTGTTGGTTGGTAGTT 59.176 43.478 0.00 0.00 35.28 2.24
422 438 4.320935 GCACCTATTGTTGGTTGGTAGTTG 60.321 45.833 0.00 0.00 35.28 3.16
423 439 4.825085 CACCTATTGTTGGTTGGTAGTTGT 59.175 41.667 0.00 0.00 35.28 3.32
424 440 5.998981 CACCTATTGTTGGTTGGTAGTTGTA 59.001 40.000 0.00 0.00 35.28 2.41
425 441 6.148811 CACCTATTGTTGGTTGGTAGTTGTAG 59.851 42.308 0.00 0.00 35.28 2.74
426 442 5.123344 CCTATTGTTGGTTGGTAGTTGTAGC 59.877 44.000 0.00 0.00 0.00 3.58
427 443 2.853705 TGTTGGTTGGTAGTTGTAGCC 58.146 47.619 0.00 0.00 0.00 3.93
428 444 2.440253 TGTTGGTTGGTAGTTGTAGCCT 59.560 45.455 0.00 0.00 0.00 4.58
474 490 7.821359 TGTTGATTTGAAAAACAGTCATTTCCA 59.179 29.630 8.55 0.00 35.23 3.53
531 551 0.978907 AAAAGGAGCCCATTTGCAGG 59.021 50.000 0.00 0.00 0.00 4.85
535 573 1.304381 GAGCCCATTTGCAGGTCCA 60.304 57.895 0.00 0.00 0.00 4.02
629 677 3.250762 TGACAGCTTACAACTTGCATCAC 59.749 43.478 0.00 0.00 0.00 3.06
645 693 2.030562 ACCCACGACAAAGCTCCG 59.969 61.111 0.00 0.00 0.00 4.63
647 695 2.027625 CCCACGACAAAGCTCCGTC 61.028 63.158 5.58 5.58 33.96 4.79
663 711 2.674296 GTCGATAACGGTTGGAGCC 58.326 57.895 3.07 0.00 40.21 4.70
780 829 5.684704 TGTGGAATAGGAAATGATGACCTC 58.315 41.667 0.00 0.00 35.52 3.85
803 852 3.254060 CCAGACTACAAGGTTGACATCG 58.746 50.000 0.00 0.00 0.00 3.84
848 897 2.811317 CGTTCTCTGTGGAGCGCC 60.811 66.667 2.29 0.00 39.31 6.53
849 898 2.811317 GTTCTCTGTGGAGCGCCG 60.811 66.667 2.29 0.00 39.31 6.46
850 899 3.303135 TTCTCTGTGGAGCGCCGT 61.303 61.111 2.29 0.00 39.31 5.68
851 900 1.974875 TTCTCTGTGGAGCGCCGTA 60.975 57.895 2.29 0.00 39.31 4.02
868 917 3.734735 GCCGTACGTCTATCCTTTTCATC 59.265 47.826 15.21 0.00 0.00 2.92
901 950 3.118775 TGGCTGGCTGGCTTATATATACG 60.119 47.826 18.27 0.00 42.34 3.06
908 957 2.769663 TGGCTTATATATACGCCCCCTG 59.230 50.000 28.28 1.26 44.48 4.45
958 1011 0.036010 ACACTCGCAATCCTCCCAAG 60.036 55.000 0.00 0.00 0.00 3.61
965 1018 1.401905 GCAATCCTCCCAAGCTTTACG 59.598 52.381 0.00 0.00 0.00 3.18
980 1033 6.532365 AGCTTTACGAACTTCTTCTTCTTG 57.468 37.500 0.00 0.00 0.00 3.02
1341 1406 4.603946 GGGTACATCTCCGCCGCC 62.604 72.222 0.00 0.00 0.00 6.13
1425 1490 2.357881 ATGATCGCCGCGCATGAT 60.358 55.556 8.75 7.00 0.00 2.45
1503 1568 6.348213 CCGGTATGTAAATGTAATGGCTTAGC 60.348 42.308 0.00 0.00 0.00 3.09
1506 1571 9.280174 GGTATGTAAATGTAATGGCTTAGCTAA 57.720 33.333 5.94 5.94 0.00 3.09
1516 1584 3.531538 TGGCTTAGCTAAACGAATCTGG 58.468 45.455 7.74 0.00 0.00 3.86
1578 1777 3.119459 ACGTACAAGCTAGTCAGTCATGG 60.119 47.826 0.00 0.00 0.00 3.66
1622 1821 3.273434 GCCAAGCTAATCTGTCATGTGA 58.727 45.455 0.00 0.00 0.00 3.58
1700 1902 3.846588 TCTCCTGTAGCCTCTGGATTTTT 59.153 43.478 5.18 0.00 35.49 1.94
1793 1995 7.623268 GTCATGTGACAATTGGTTTTCTTAC 57.377 36.000 10.83 0.00 44.18 2.34
1798 2000 8.472683 TGTGACAATTGGTTTTCTTACAAAAG 57.527 30.769 10.83 0.00 0.00 2.27
1830 2032 8.659527 AGAATTATTCCCCACAAAAAGAAACAT 58.340 29.630 0.78 0.00 0.00 2.71
1873 2075 9.642327 GGTTTAAAAGGTTTTCACAGTTCTTAA 57.358 29.630 0.00 0.00 0.00 1.85
2053 2256 8.073467 ACTTCCTTCAAACAAAAATAAGTGGA 57.927 30.769 0.00 0.00 0.00 4.02
2337 2550 6.983474 ATACATGAATTGTTGATCGTCACA 57.017 33.333 0.00 0.00 39.87 3.58
2341 2554 4.854399 TGAATTGTTGATCGTCACAAACC 58.146 39.130 8.51 5.27 0.00 3.27
2390 2603 2.147387 GGTATCCCCGCCCATCAGT 61.147 63.158 0.00 0.00 0.00 3.41
2413 2626 8.447833 CAGTGTTCAAGTCTTAAACTTAACACA 58.552 33.333 26.35 17.74 46.69 3.72
2438 2651 3.119316 AGCGACTTCGTCAATCTCAAGAT 60.119 43.478 0.00 0.00 42.22 2.40
2463 2676 0.320771 GCCGGCTCAGTCTCTCAAAA 60.321 55.000 22.15 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.067295 TTGAAGGTGCTCACAGGGAT 58.933 50.000 2.21 0.00 0.00 3.85
1 2 0.843309 TTTGAAGGTGCTCACAGGGA 59.157 50.000 2.21 0.00 0.00 4.20
2 3 1.610522 CTTTTGAAGGTGCTCACAGGG 59.389 52.381 2.21 0.00 0.00 4.45
3 4 2.291741 GTCTTTTGAAGGTGCTCACAGG 59.708 50.000 2.21 0.00 0.00 4.00
4 5 3.003068 CAGTCTTTTGAAGGTGCTCACAG 59.997 47.826 2.21 0.00 0.00 3.66
5 6 2.945008 CAGTCTTTTGAAGGTGCTCACA 59.055 45.455 2.21 0.00 0.00 3.58
6 7 3.206150 TCAGTCTTTTGAAGGTGCTCAC 58.794 45.455 0.00 0.00 0.00 3.51
7 8 3.470709 CTCAGTCTTTTGAAGGTGCTCA 58.529 45.455 0.00 0.00 0.00 4.26
8 9 2.225255 GCTCAGTCTTTTGAAGGTGCTC 59.775 50.000 0.00 0.00 0.00 4.26
9 10 2.225467 GCTCAGTCTTTTGAAGGTGCT 58.775 47.619 0.00 0.00 0.00 4.40
10 11 1.268079 GGCTCAGTCTTTTGAAGGTGC 59.732 52.381 0.00 0.00 0.00 5.01
11 12 1.532868 CGGCTCAGTCTTTTGAAGGTG 59.467 52.381 0.00 0.00 0.00 4.00
12 13 1.543429 CCGGCTCAGTCTTTTGAAGGT 60.543 52.381 0.00 0.00 0.00 3.50
13 14 1.160137 CCGGCTCAGTCTTTTGAAGG 58.840 55.000 0.00 0.00 0.00 3.46
14 15 0.519077 GCCGGCTCAGTCTTTTGAAG 59.481 55.000 22.15 0.00 0.00 3.02
15 16 0.179032 TGCCGGCTCAGTCTTTTGAA 60.179 50.000 29.70 0.00 0.00 2.69
16 17 0.036732 ATGCCGGCTCAGTCTTTTGA 59.963 50.000 29.70 1.81 0.00 2.69
17 18 1.737838 TATGCCGGCTCAGTCTTTTG 58.262 50.000 29.70 0.00 0.00 2.44
18 19 2.092968 TGATATGCCGGCTCAGTCTTTT 60.093 45.455 29.70 1.60 0.00 2.27
19 20 1.486310 TGATATGCCGGCTCAGTCTTT 59.514 47.619 29.70 3.35 0.00 2.52
20 21 1.123077 TGATATGCCGGCTCAGTCTT 58.877 50.000 29.70 5.10 0.00 3.01
21 22 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
22 23 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
23 24 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
24 25 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
25 26 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
26 27 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
27 28 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
28 29 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
29 30 5.934043 TGTAAATCTCAAGATGATATGCCGG 59.066 40.000 0.00 0.00 34.49 6.13
30 31 7.425577 TTGTAAATCTCAAGATGATATGCCG 57.574 36.000 0.00 0.00 34.49 5.69
31 32 8.844244 ACTTTGTAAATCTCAAGATGATATGCC 58.156 33.333 0.00 0.00 34.49 4.40
32 33 9.875675 GACTTTGTAAATCTCAAGATGATATGC 57.124 33.333 0.00 0.00 34.49 3.14
35 36 9.383519 GGTGACTTTGTAAATCTCAAGATGATA 57.616 33.333 0.00 0.00 34.49 2.15
36 37 7.065085 CGGTGACTTTGTAAATCTCAAGATGAT 59.935 37.037 0.00 0.00 34.49 2.45
37 38 6.368791 CGGTGACTTTGTAAATCTCAAGATGA 59.631 38.462 0.00 0.00 34.49 2.92
38 39 6.147821 ACGGTGACTTTGTAAATCTCAAGATG 59.852 38.462 0.00 0.00 34.49 2.90
39 40 6.231211 ACGGTGACTTTGTAAATCTCAAGAT 58.769 36.000 0.00 0.00 36.07 2.40
40 41 5.607477 ACGGTGACTTTGTAAATCTCAAGA 58.393 37.500 0.00 0.00 0.00 3.02
41 42 5.924475 ACGGTGACTTTGTAAATCTCAAG 57.076 39.130 0.00 0.00 0.00 3.02
42 43 5.929992 CCTACGGTGACTTTGTAAATCTCAA 59.070 40.000 0.00 0.00 0.00 3.02
53 54 2.047560 GGCGCCTACGGTGACTTT 60.048 61.111 22.15 0.00 38.38 2.66
74 75 1.226603 GAGACGTTCCCATCGACGG 60.227 63.158 0.00 0.00 43.16 4.79
88 89 0.687354 TGCTTTCAGTGGGAGGAGAC 59.313 55.000 0.00 0.00 0.00 3.36
91 92 1.003580 GACATGCTTTCAGTGGGAGGA 59.996 52.381 0.00 0.00 0.00 3.71
106 107 5.762825 ATTTCAGGATTTCCGATGACATG 57.237 39.130 0.00 0.00 42.08 3.21
108 109 7.880160 ATTTATTTCAGGATTTCCGATGACA 57.120 32.000 0.00 0.00 42.08 3.58
113 114 8.574251 TCTTGAATTTATTTCAGGATTTCCGA 57.426 30.769 0.00 0.00 43.30 4.55
133 134 2.631267 TGCTGCTCGCATTATTCTTGA 58.369 42.857 0.00 0.00 45.47 3.02
151 152 1.302832 CCCAGTGTTCAGGTCCTGC 60.303 63.158 14.64 1.61 0.00 4.85
158 159 1.073199 GTCCACCCCCAGTGTTCAG 59.927 63.158 0.00 0.00 45.74 3.02
160 161 0.609131 CATGTCCACCCCCAGTGTTC 60.609 60.000 0.00 0.00 45.74 3.18
161 162 1.360393 ACATGTCCACCCCCAGTGTT 61.360 55.000 0.00 0.00 45.74 3.32
162 163 1.360393 AACATGTCCACCCCCAGTGT 61.360 55.000 0.00 0.00 45.74 3.55
163 164 0.178964 AAACATGTCCACCCCCAGTG 60.179 55.000 0.00 0.00 46.83 3.66
164 165 0.560688 AAAACATGTCCACCCCCAGT 59.439 50.000 0.00 0.00 0.00 4.00
165 166 1.344114 CAAAAACATGTCCACCCCCAG 59.656 52.381 0.00 0.00 0.00 4.45
166 167 1.418334 CAAAAACATGTCCACCCCCA 58.582 50.000 0.00 0.00 0.00 4.96
167 168 0.684535 CCAAAAACATGTCCACCCCC 59.315 55.000 0.00 0.00 0.00 5.40
178 179 3.577848 CCATTCCATCTCACCCAAAAACA 59.422 43.478 0.00 0.00 0.00 2.83
184 185 1.224315 CGCCATTCCATCTCACCCA 59.776 57.895 0.00 0.00 0.00 4.51
190 191 0.036388 ACACGTTCGCCATTCCATCT 60.036 50.000 0.00 0.00 0.00 2.90
202 203 1.336240 ACCGTAGCCACTTACACGTTC 60.336 52.381 0.00 0.00 32.66 3.95
203 204 0.675633 ACCGTAGCCACTTACACGTT 59.324 50.000 0.00 0.00 32.66 3.99
227 228 2.332654 AATGGGGCTTTGTCGACGC 61.333 57.895 11.62 8.25 0.00 5.19
229 230 1.463674 ATCAATGGGGCTTTGTCGAC 58.536 50.000 9.11 9.11 0.00 4.20
233 234 1.338011 CGCAAATCAATGGGGCTTTGT 60.338 47.619 0.00 0.00 32.51 2.83
243 244 1.668628 GCAAACCGGACGCAAATCAAT 60.669 47.619 9.46 0.00 0.00 2.57
264 265 0.323629 GTCCAGACGTCCATTTCCCA 59.676 55.000 13.01 0.00 0.00 4.37
292 293 4.383173 TCCAACGCGATACTCTATCAGTA 58.617 43.478 15.93 0.00 42.09 2.74
301 302 1.732941 TTGCAATCCAACGCGATACT 58.267 45.000 15.93 0.00 0.00 2.12
342 343 3.823281 TCAACACGGACCTTCAAACTA 57.177 42.857 0.00 0.00 0.00 2.24
343 344 2.702592 TCAACACGGACCTTCAAACT 57.297 45.000 0.00 0.00 0.00 2.66
348 364 2.767505 ACATCTTCAACACGGACCTTC 58.232 47.619 0.00 0.00 0.00 3.46
371 387 9.428097 GTCTTTTTCCTGCAAATCAATCTTTAT 57.572 29.630 0.00 0.00 0.00 1.40
394 410 0.690762 ACCAACAATAGGTGCCGTCT 59.309 50.000 0.00 0.00 38.13 4.18
421 437 3.185880 AGTTTCTCCTACCAGGCTACA 57.814 47.619 0.00 0.00 34.61 2.74
422 438 4.710865 AGTTAGTTTCTCCTACCAGGCTAC 59.289 45.833 0.00 0.00 34.61 3.58
423 439 4.944177 AGTTAGTTTCTCCTACCAGGCTA 58.056 43.478 0.00 0.00 34.61 3.93
424 440 3.792515 AGTTAGTTTCTCCTACCAGGCT 58.207 45.455 0.00 0.00 34.61 4.58
425 441 5.873146 ATAGTTAGTTTCTCCTACCAGGC 57.127 43.478 0.00 0.00 34.61 4.85
426 442 7.184067 ACAATAGTTAGTTTCTCCTACCAGG 57.816 40.000 0.00 0.00 36.46 4.45
427 443 8.311836 TCAACAATAGTTAGTTTCTCCTACCAG 58.688 37.037 0.00 0.00 35.85 4.00
428 444 8.197592 TCAACAATAGTTAGTTTCTCCTACCA 57.802 34.615 0.00 0.00 35.85 3.25
531 551 7.031372 GGAAAAATAAAACGGGACTTATGGAC 58.969 38.462 0.00 0.00 0.00 4.02
535 573 9.701098 GAAAAGGAAAAATAAAACGGGACTTAT 57.299 29.630 0.00 0.00 0.00 1.73
629 677 2.027625 GACGGAGCTTTGTCGTGGG 61.028 63.158 9.41 0.00 37.25 4.61
645 693 2.674296 GGCTCCAACCGTTATCGAC 58.326 57.895 0.00 0.00 39.71 4.20
663 711 0.301687 CTTGCTTGCTGTATACGCCG 59.698 55.000 14.28 8.55 0.00 6.46
780 829 1.697432 TGTCAACCTTGTAGTCTGGGG 59.303 52.381 0.00 0.00 0.00 4.96
803 852 3.008049 ACCAAATACGATGGGCTCCTATC 59.992 47.826 2.52 2.52 42.48 2.08
848 897 4.976731 CCAGATGAAAAGGATAGACGTACG 59.023 45.833 15.01 15.01 0.00 3.67
849 898 4.745620 GCCAGATGAAAAGGATAGACGTAC 59.254 45.833 0.00 0.00 0.00 3.67
850 899 4.404394 TGCCAGATGAAAAGGATAGACGTA 59.596 41.667 0.00 0.00 0.00 3.57
851 900 3.197766 TGCCAGATGAAAAGGATAGACGT 59.802 43.478 0.00 0.00 0.00 4.34
868 917 1.375013 GCCAGCCATTGTTTGCCAG 60.375 57.895 0.00 0.00 0.00 4.85
918 967 0.937304 TGTTTGCTTGTGAGAGCGAC 59.063 50.000 0.00 0.00 45.64 5.19
958 1011 5.140872 GCAAGAAGAAGAAGTTCGTAAAGC 58.859 41.667 0.00 0.00 37.79 3.51
965 1018 6.026873 GCTATACGCAAGAAGAAGAAGTTC 57.973 41.667 0.00 0.00 43.62 3.01
1508 1573 2.683968 TGGAACGAGAAACCAGATTCG 58.316 47.619 0.00 0.00 38.88 3.34
1516 1584 4.989168 AGTACATCACTTGGAACGAGAAAC 59.011 41.667 0.00 0.00 31.59 2.78
1603 1802 7.628235 CAGTATTCACATGACAGATTAGCTTG 58.372 38.462 0.00 0.00 0.00 4.01
1700 1902 2.771943 ACACAACCTGAAACAGAGAGGA 59.228 45.455 0.00 0.00 32.44 3.71
1793 1995 8.757877 TGTGGGGAATAATTCTATTTCCTTTTG 58.242 33.333 2.88 0.00 41.48 2.44
1798 2000 9.599866 CTTTTTGTGGGGAATAATTCTATTTCC 57.400 33.333 0.00 0.00 41.14 3.13
1830 2032 7.589958 TTTAAACCTGCCAGACAAGAAATTA 57.410 32.000 0.00 0.00 0.00 1.40
1935 2137 3.974871 TTTTAAAGACGTGGGCACTTC 57.025 42.857 0.00 0.00 0.00 3.01
2095 2300 9.797473 CTTCTTTCTTGTTGTGTTTTTCTTTTC 57.203 29.630 0.00 0.00 0.00 2.29
2313 2526 7.376435 TGTGACGATCAACAATTCATGTATT 57.624 32.000 0.00 0.00 42.99 1.89
2320 2533 4.854399 TGGTTTGTGACGATCAACAATTC 58.146 39.130 6.48 4.34 0.00 2.17
2341 2554 7.331026 TCTCCTAACTATCAAACCACAGATTG 58.669 38.462 0.00 0.00 0.00 2.67
2353 2566 6.550108 GGATACCACTGTTCTCCTAACTATCA 59.450 42.308 0.00 0.00 0.00 2.15
2438 2651 2.230994 GAGACTGAGCCGGCACATCA 62.231 60.000 31.54 22.44 0.00 3.07
2463 2676 2.108250 ACACCCTACCTTTGTGAGCATT 59.892 45.455 0.00 0.00 34.18 3.56


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

AutoCloner maintained by Alex Coulton.