Multiple sequence alignment - TraesCS7A01G336800

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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 TraesCS7A01G336800 chr7A 100.000 2639 0 0 1 2639 492819493 492816855 0.000000e+00 4874
1 TraesCS7A01G336800 chr7A 82.170 1576 274 6 1068 2639 40700428 40702000 0.000000e+00 1347
2 TraesCS7A01G336800 chr7A 80.165 242 20 18 2 242 492782689 492782475 3.520000e-34 156
3 TraesCS7A01G336800 chr7D 95.309 1471 69 0 1169 2639 245389560 245391030 0.000000e+00 2335
4 TraesCS7A01G336800 chr7D 89.388 801 73 4 1 798 441985582 441984791 0.000000e+00 998
5 TraesCS7A01G336800 chr7D 92.284 324 17 5 820 1136 245389256 245389578 1.110000e-123 453
6 TraesCS7A01G336800 chr7D 77.816 293 30 24 2 291 441983255 441982995 5.890000e-32 148
7 TraesCS7A01G336800 chr6A 88.740 1572 166 5 1068 2639 181588432 181586872 0.000000e+00 1912
8 TraesCS7A01G336800 chr6A 84.150 612 95 2 2029 2639 587756641 587757251 2.260000e-165 592
9 TraesCS7A01G336800 chr2D 90.781 1204 98 6 1439 2639 144375106 144373913 0.000000e+00 1596
10 TraesCS7A01G336800 chr2D 81.571 331 60 1 1068 1398 144375434 144375105 3.350000e-69 272
11 TraesCS7A01G336800 chr5A 95.742 963 41 0 1677 2639 564609730 564608768 0.000000e+00 1552
12 TraesCS7A01G336800 chr4B 88.889 1125 120 4 984 2107 469174915 469176035 0.000000e+00 1380
13 TraesCS7A01G336800 chr4B 94.355 248 14 0 2392 2639 469186570 469186817 5.330000e-102 381
14 TraesCS7A01G336800 chr5B 82.545 1564 259 8 820 2372 251506679 251508239 0.000000e+00 1363
15 TraesCS7A01G336800 chr7B 91.729 943 77 1 1698 2639 120359307 120360249 0.000000e+00 1308
16 TraesCS7A01G336800 chr7B 88.750 800 76 7 1 798 458615840 458615053 0.000000e+00 966
17 TraesCS7A01G336800 chr7B 78.070 342 35 28 2 336 458613510 458613202 2.090000e-41 180
18 TraesCS7A01G336800 chr6B 81.027 1207 223 5 1438 2639 436784479 436783274 0.000000e+00 955
19 TraesCS7A01G336800 chr6B 83.703 632 93 5 820 1443 436796044 436795415 2.930000e-164 588
20 TraesCS7A01G336800 chr3B 88.362 232 23 4 534 764 254160262 254160490 2.590000e-70 276


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 TraesCS7A01G336800 chr7A 492816855 492819493 2638 True 4874 4874 100.0000 1 2639 1 chr7A.!!$R2 2638
1 TraesCS7A01G336800 chr7A 40700428 40702000 1572 False 1347 1347 82.1700 1068 2639 1 chr7A.!!$F1 1571
2 TraesCS7A01G336800 chr7D 245389256 245391030 1774 False 1394 2335 93.7965 820 2639 2 chr7D.!!$F1 1819
3 TraesCS7A01G336800 chr7D 441982995 441985582 2587 True 573 998 83.6020 1 798 2 chr7D.!!$R1 797
4 TraesCS7A01G336800 chr6A 181586872 181588432 1560 True 1912 1912 88.7400 1068 2639 1 chr6A.!!$R1 1571
5 TraesCS7A01G336800 chr6A 587756641 587757251 610 False 592 592 84.1500 2029 2639 1 chr6A.!!$F1 610
6 TraesCS7A01G336800 chr2D 144373913 144375434 1521 True 934 1596 86.1760 1068 2639 2 chr2D.!!$R1 1571
7 TraesCS7A01G336800 chr5A 564608768 564609730 962 True 1552 1552 95.7420 1677 2639 1 chr5A.!!$R1 962
8 TraesCS7A01G336800 chr4B 469174915 469176035 1120 False 1380 1380 88.8890 984 2107 1 chr4B.!!$F1 1123
9 TraesCS7A01G336800 chr5B 251506679 251508239 1560 False 1363 1363 82.5450 820 2372 1 chr5B.!!$F1 1552
10 TraesCS7A01G336800 chr7B 120359307 120360249 942 False 1308 1308 91.7290 1698 2639 1 chr7B.!!$F1 941
11 TraesCS7A01G336800 chr7B 458613202 458615840 2638 True 573 966 83.4100 1 798 2 chr7B.!!$R1 797
12 TraesCS7A01G336800 chr6B 436783274 436784479 1205 True 955 955 81.0270 1438 2639 1 chr6B.!!$R1 1201
13 TraesCS7A01G336800 chr6B 436795415 436796044 629 True 588 588 83.7030 820 1443 1 chr6B.!!$R2 623

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
374 375 0.468226 AGGGAAACGTTGCAGAGACA 59.532 50.0 8.91 0.0 0.0 3.41 F
1204 1421 0.036388 TGAAGATGGGGTCGCTGAAC 60.036 55.0 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1810 0.389817 CGATCAAGGCGTTCTCCACA 60.390 55.0 0.0 0.0 0.0 4.17 R
2435 3050 0.035152 AATCTGACAATGCGGCTCCA 60.035 50.0 0.0 0.0 0.0 3.86 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
33 34 8.498054 AGAAACTGATATCACTAAACACATGG 57.502 34.615 0.00 0.00 0.00 3.66
84 85 2.292828 AACAGTGGCTAGCAAACCAT 57.707 45.000 18.24 2.56 38.46 3.55
151 152 2.507484 TCAGCCATCCTTGAAACACTG 58.493 47.619 0.00 0.00 0.00 3.66
152 153 2.106338 TCAGCCATCCTTGAAACACTGA 59.894 45.455 0.00 0.00 0.00 3.41
153 154 2.486982 CAGCCATCCTTGAAACACTGAG 59.513 50.000 0.00 0.00 0.00 3.35
154 155 1.200948 GCCATCCTTGAAACACTGAGC 59.799 52.381 0.00 0.00 0.00 4.26
155 156 2.507484 CCATCCTTGAAACACTGAGCA 58.493 47.619 0.00 0.00 0.00 4.26
156 157 2.886523 CCATCCTTGAAACACTGAGCAA 59.113 45.455 0.00 0.00 0.00 3.91
157 158 3.304928 CCATCCTTGAAACACTGAGCAAC 60.305 47.826 0.00 0.00 0.00 4.17
158 159 1.939934 TCCTTGAAACACTGAGCAACG 59.060 47.619 0.00 0.00 0.00 4.10
162 163 2.080693 TGAAACACTGAGCAACGTTGT 58.919 42.857 27.78 15.49 0.00 3.32
167 168 3.664107 ACACTGAGCAACGTTGTATCAT 58.336 40.909 27.28 18.66 0.00 2.45
199 200 2.351418 CACAACAGAAAGCACGAGTGAA 59.649 45.455 7.50 0.00 0.00 3.18
202 203 1.202371 ACAGAAAGCACGAGTGAACGA 60.202 47.619 7.50 0.00 37.03 3.85
212 213 0.867746 GAGTGAACGACATGCAGCAA 59.132 50.000 0.00 0.00 0.00 3.91
269 270 5.451798 GCTATAGATGCAGCTATCTCTTCCC 60.452 48.000 26.79 6.27 38.35 3.97
272 273 0.687757 TGCAGCTATCTCTTCCCGGT 60.688 55.000 0.00 0.00 0.00 5.28
280 281 0.754472 TCTCTTCCCGGTGTCGTTTT 59.246 50.000 0.00 0.00 33.95 2.43
309 310 2.356313 CCAGACTGTTCACGCGCT 60.356 61.111 5.73 0.00 0.00 5.92
374 375 0.468226 AGGGAAACGTTGCAGAGACA 59.532 50.000 8.91 0.00 0.00 3.41
376 377 1.583054 GGAAACGTTGCAGAGACAGT 58.417 50.000 8.91 0.00 0.00 3.55
403 404 1.203758 CAGGTGTACGTGCATCCAGTA 59.796 52.381 13.65 0.00 0.00 2.74
425 426 2.690778 GCGTGGATTGGAGTGGCAC 61.691 63.158 10.29 10.29 0.00 5.01
430 431 1.430632 GATTGGAGTGGCACGCATG 59.569 57.895 22.65 0.00 44.14 4.06
444 445 2.029470 CACGCATGGAGCCCTTTTTAAA 60.029 45.455 0.00 0.00 41.38 1.52
445 446 2.630580 ACGCATGGAGCCCTTTTTAAAA 59.369 40.909 0.00 0.00 41.38 1.52
454 455 9.806448 ATGGAGCCCTTTTTAAAATTTTAACAT 57.194 25.926 20.35 14.31 32.77 2.71
478 479 2.328099 CGGCTTGTCCACTTGGCTC 61.328 63.158 0.00 0.00 34.44 4.70
481 482 0.674895 GCTTGTCCACTTGGCTCGAT 60.675 55.000 0.00 0.00 34.44 3.59
486 487 3.257561 CACTTGGCTCGATCGCGG 61.258 66.667 11.09 6.90 38.28 6.46
557 559 6.183360 TGCAGAAAGTCACTTTGAACGTTAAT 60.183 34.615 7.75 0.00 33.49 1.40
589 591 3.809832 CGGTAACAATCTCACCATCCATC 59.190 47.826 0.00 0.00 32.32 3.51
596 598 1.065199 TCTCACCATCCATCAGTTGCC 60.065 52.381 0.00 0.00 0.00 4.52
614 616 5.243060 AGTTGCCTTAAGATTTGGGTTGTAC 59.757 40.000 3.36 0.00 0.00 2.90
623 625 7.448748 AAGATTTGGGTTGTACACATCTAAC 57.551 36.000 0.00 0.00 35.08 2.34
624 626 6.779860 AGATTTGGGTTGTACACATCTAACT 58.220 36.000 0.00 0.00 34.56 2.24
630 633 6.002082 GGGTTGTACACATCTAACTTTTCCT 58.998 40.000 0.00 0.00 0.00 3.36
632 635 6.148976 GGTTGTACACATCTAACTTTTCCTCC 59.851 42.308 0.00 0.00 0.00 4.30
708 711 4.671831 TGTCCTTGATATGGCAGGAAAAA 58.328 39.130 0.00 0.00 0.00 1.94
717 720 2.942804 TGGCAGGAAAAACAGTGATGA 58.057 42.857 0.00 0.00 0.00 2.92
720 723 3.256631 GGCAGGAAAAACAGTGATGACAT 59.743 43.478 0.00 0.00 0.00 3.06
731 734 3.063588 CAGTGATGACATCATGTGACAGC 59.936 47.826 20.67 5.93 42.04 4.40
732 735 2.353889 GTGATGACATCATGTGACAGCC 59.646 50.000 20.67 1.63 42.04 4.85
760 765 5.592282 TCTCTCTCTTCTCTCACGCATAAAT 59.408 40.000 0.00 0.00 0.00 1.40
766 771 2.499693 TCTCTCACGCATAAATCCACCA 59.500 45.455 0.00 0.00 0.00 4.17
803 808 9.823647 CATAGGCTATATTAAATTGATCGAGGT 57.176 33.333 6.72 0.00 0.00 3.85
804 809 9.823647 ATAGGCTATATTAAATTGATCGAGGTG 57.176 33.333 4.92 0.00 0.00 4.00
805 810 7.907389 AGGCTATATTAAATTGATCGAGGTGA 58.093 34.615 0.00 0.00 0.00 4.02
806 811 7.819900 AGGCTATATTAAATTGATCGAGGTGAC 59.180 37.037 0.00 0.00 0.00 3.67
807 812 7.201444 GGCTATATTAAATTGATCGAGGTGACG 60.201 40.741 0.00 0.00 0.00 4.35
808 813 7.201444 GCTATATTAAATTGATCGAGGTGACGG 60.201 40.741 0.00 0.00 0.00 4.79
809 814 1.369625 AAATTGATCGAGGTGACGGC 58.630 50.000 0.00 0.00 0.00 5.68
810 815 0.806102 AATTGATCGAGGTGACGGCG 60.806 55.000 4.80 4.80 34.94 6.46
811 816 2.629050 ATTGATCGAGGTGACGGCGG 62.629 60.000 13.24 0.00 34.50 6.13
846 852 2.854777 CGACGTCATTCAGATCAAGTCC 59.145 50.000 17.16 0.00 0.00 3.85
892 898 0.951558 CCGTGCTGCACCTTACTTTT 59.048 50.000 25.61 0.00 0.00 2.27
982 995 1.507141 CTGCCCACTCGTTGGTGAAC 61.507 60.000 5.31 0.00 45.25 3.18
995 1008 1.965930 GTGAACTGCGATGCACCCA 60.966 57.895 0.00 0.00 33.79 4.51
1011 1024 1.072678 CCATGAGATGGCGCTGGAT 59.927 57.895 7.64 0.00 44.70 3.41
1114 1127 4.262164 CCTTTCCAGGATCAAGTTTTGTGG 60.262 45.833 0.00 0.00 44.19 4.17
1119 1132 1.963515 GGATCAAGTTTTGTGGTGGCT 59.036 47.619 0.00 0.00 0.00 4.75
1152 1165 0.958876 CTGCTGCTGATCTGCACCAA 60.959 55.000 21.87 10.22 43.38 3.67
1179 1192 1.209019 CTGGAAGCTGCTACACCTGAT 59.791 52.381 0.90 0.00 0.00 2.90
1193 1410 3.181447 ACACCTGATATGCCTGAAGATGG 60.181 47.826 0.00 0.00 0.00 3.51
1204 1421 0.036388 TGAAGATGGGGTCGCTGAAC 60.036 55.000 0.00 0.00 0.00 3.18
1232 1449 0.122435 ACCCCCATCTTTGTCCCCTA 59.878 55.000 0.00 0.00 0.00 3.53
1551 1810 1.217511 CTGCGACCTGATGTCAGCT 59.782 57.895 4.48 0.00 44.71 4.24
1732 2279 2.319136 ACGTCTGTTTGTACCTGCAA 57.681 45.000 0.00 0.00 0.00 4.08
1736 2283 2.548480 GTCTGTTTGTACCTGCAACCTC 59.452 50.000 0.00 0.00 0.00 3.85
1777 2324 3.567397 TGGCAAGGCTGGTTTTTAGTAA 58.433 40.909 0.00 0.00 0.00 2.24
1863 2410 6.047870 CAGACTAAGATGTTATTGCTGCTCT 58.952 40.000 0.00 0.00 0.00 4.09
1899 2446 0.467290 TCCTCCCAGTTGTTGTTGCC 60.467 55.000 0.00 0.00 0.00 4.52
1945 2495 2.158740 TGGTTTCCAAATGACAGACCGA 60.159 45.455 0.00 0.00 0.00 4.69
1951 2501 2.819608 CCAAATGACAGACCGAAACCAT 59.180 45.455 0.00 0.00 0.00 3.55
2027 2577 4.679639 GCACTACCGTTCATGAGACCATAA 60.680 45.833 0.00 0.00 0.00 1.90
2076 2626 4.324874 CCTTCAGGAGTCCAAGATGGATTT 60.325 45.833 22.24 0.00 43.04 2.17
2272 2858 4.664267 AGCCCAGCTCCCACCTCA 62.664 66.667 0.00 0.00 30.62 3.86
2331 2943 1.543429 CCTCAAGGACGCCTTCTTTGT 60.543 52.381 7.99 0.00 42.67 2.83
2407 3022 6.071616 GGTACTTCAATCAAATTTACCAGGCA 60.072 38.462 0.00 0.00 0.00 4.75
2435 3050 8.561738 AGATAAGAACCGTACAAATGTTGATT 57.438 30.769 0.00 0.00 0.00 2.57
2557 3172 0.445436 CCACATTGAGCAAGCTCGAC 59.555 55.000 13.91 0.00 45.48 4.20
2559 3174 1.532437 CACATTGAGCAAGCTCGACAA 59.468 47.619 13.91 5.72 45.48 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.667076 TTGATCCATGTGTTTAGTGATATCAG 57.333 34.615 5.42 0.00 0.00 2.90
19 20 4.764823 GGGTTTGATCCATGTGTTTAGTGA 59.235 41.667 0.00 0.00 0.00 3.41
24 25 2.256306 GGGGGTTTGATCCATGTGTTT 58.744 47.619 0.00 0.00 0.00 2.83
32 33 2.034999 TGCGTGGGGGTTTGATCC 59.965 61.111 0.00 0.00 0.00 3.36
33 34 2.686816 CGTGCGTGGGGGTTTGATC 61.687 63.158 0.00 0.00 0.00 2.92
57 58 2.878406 TGCTAGCCACTGTTTTGAGAAC 59.122 45.455 13.29 0.00 0.00 3.01
62 63 2.100584 TGGTTTGCTAGCCACTGTTTTG 59.899 45.455 13.29 0.00 0.00 2.44
84 85 6.382859 AGGATGGATGTAAGTGTATGTGTACA 59.617 38.462 0.00 0.00 38.46 2.90
131 132 2.106338 TCAGTGTTTCAAGGATGGCTGA 59.894 45.455 0.00 0.00 0.00 4.26
151 152 4.424626 TCTCTCATGATACAACGTTGCTC 58.575 43.478 27.61 22.82 0.00 4.26
152 153 4.456280 TCTCTCATGATACAACGTTGCT 57.544 40.909 27.61 15.57 0.00 3.91
153 154 4.493220 GCTTCTCTCATGATACAACGTTGC 60.493 45.833 27.61 12.48 0.00 4.17
154 155 4.627035 TGCTTCTCTCATGATACAACGTTG 59.373 41.667 26.20 26.20 0.00 4.10
155 156 4.627467 GTGCTTCTCTCATGATACAACGTT 59.373 41.667 0.00 0.00 0.00 3.99
156 157 4.177026 GTGCTTCTCTCATGATACAACGT 58.823 43.478 0.00 0.00 0.00 3.99
157 158 4.032217 GTGTGCTTCTCTCATGATACAACG 59.968 45.833 0.00 0.00 0.00 4.10
158 159 4.931601 TGTGTGCTTCTCTCATGATACAAC 59.068 41.667 0.00 0.00 0.00 3.32
162 163 5.047092 TCTGTTGTGTGCTTCTCTCATGATA 60.047 40.000 0.00 0.00 0.00 2.15
167 168 3.541996 TTCTGTTGTGTGCTTCTCTCA 57.458 42.857 0.00 0.00 0.00 3.27
199 200 0.537143 TTTCCCTTGCTGCATGTCGT 60.537 50.000 1.84 0.00 0.00 4.34
202 203 0.828762 TGCTTTCCCTTGCTGCATGT 60.829 50.000 1.84 0.00 0.00 3.21
212 213 3.188880 TCCATTTTGGATGCTTTCCCT 57.811 42.857 4.13 0.00 42.67 4.20
239 240 1.827344 AGCTGCATCTATAGCCGCATA 59.173 47.619 14.06 0.00 43.45 3.14
246 247 5.221028 CGGGAAGAGATAGCTGCATCTATAG 60.221 48.000 9.98 0.00 35.37 1.31
248 249 3.446873 CGGGAAGAGATAGCTGCATCTAT 59.553 47.826 9.79 9.79 35.37 1.98
249 250 2.822561 CGGGAAGAGATAGCTGCATCTA 59.177 50.000 12.42 0.00 35.37 1.98
269 270 0.306533 CTGGACCAAAAACGACACCG 59.693 55.000 0.00 0.00 42.50 4.94
272 273 2.011222 GTGTCTGGACCAAAAACGACA 58.989 47.619 8.94 8.94 0.00 4.35
280 281 0.758734 CAGTCTGGTGTCTGGACCAA 59.241 55.000 0.00 0.00 45.60 3.67
309 310 1.152030 AGCCTTGAGGGTGTGAGGA 60.152 57.895 0.04 0.00 45.50 3.71
320 321 3.057548 CATGCACGGCAGCCTTGA 61.058 61.111 21.99 7.26 43.65 3.02
341 342 3.557264 CGTTTCCCTTGCTAAACCTCTCT 60.557 47.826 0.00 0.00 33.05 3.10
342 343 2.742589 CGTTTCCCTTGCTAAACCTCTC 59.257 50.000 0.00 0.00 33.05 3.20
403 404 1.176527 CCACTCCAATCCACGCAAAT 58.823 50.000 0.00 0.00 0.00 2.32
425 426 3.311486 TTTTAAAAAGGGCTCCATGCG 57.689 42.857 0.00 0.00 44.05 4.73
430 431 9.278978 TCATGTTAAAATTTTAAAAAGGGCTCC 57.721 29.630 21.81 9.26 34.71 4.70
444 445 4.522789 ACAAGCCGTCCTCATGTTAAAATT 59.477 37.500 0.00 0.00 0.00 1.82
445 446 4.079253 ACAAGCCGTCCTCATGTTAAAAT 58.921 39.130 0.00 0.00 0.00 1.82
461 462 2.328099 CGAGCCAAGTGGACAAGCC 61.328 63.158 0.18 0.00 37.39 4.35
478 479 3.699955 TTGTCTCCAGCCGCGATCG 62.700 63.158 11.69 11.69 0.00 3.69
481 482 1.667830 CTTTTGTCTCCAGCCGCGA 60.668 57.895 8.23 0.00 0.00 5.87
486 487 4.354587 CTGAAACAACTTTTGTCTCCAGC 58.645 43.478 0.00 0.00 44.59 4.85
489 490 4.370364 TGCTGAAACAACTTTTGTCTCC 57.630 40.909 0.00 0.00 44.59 3.71
566 568 2.093181 TGGATGGTGAGATTGTTACCGG 60.093 50.000 0.00 0.00 37.29 5.28
596 598 7.687941 AGATGTGTACAACCCAAATCTTAAG 57.312 36.000 0.00 0.00 33.96 1.85
614 616 6.642540 GCAAAAAGGAGGAAAAGTTAGATGTG 59.357 38.462 0.00 0.00 0.00 3.21
655 658 5.944007 GGGCCAATAGTTGTATTAGGTATGG 59.056 44.000 4.39 0.00 0.00 2.74
708 711 4.251268 CTGTCACATGATGTCATCACTGT 58.749 43.478 17.74 17.81 43.01 3.55
717 720 1.746615 GCGGGCTGTCACATGATGT 60.747 57.895 0.00 0.00 0.00 3.06
720 723 2.230994 GAGAGCGGGCTGTCACATGA 62.231 60.000 12.40 0.00 36.49 3.07
731 734 1.308998 GAGAGAAGAGAGAGAGCGGG 58.691 60.000 0.00 0.00 0.00 6.13
732 735 1.670811 GTGAGAGAAGAGAGAGAGCGG 59.329 57.143 0.00 0.00 0.00 5.52
760 765 6.194235 AGCCTATGTGAAATAAAATGGTGGA 58.806 36.000 0.00 0.00 0.00 4.02
818 823 1.416813 CTGAATGACGTCGCAGGAGC 61.417 60.000 19.27 3.99 37.42 4.70
846 852 2.141517 CAGTCAACAGCAACAGAGGAG 58.858 52.381 0.00 0.00 0.00 3.69
887 893 0.396811 ACAGGAGTAGGCGCAAAAGT 59.603 50.000 10.83 0.00 0.00 2.66
892 898 0.320421 GTTGAACAGGAGTAGGCGCA 60.320 55.000 10.83 0.00 0.00 6.09
974 980 1.514678 GGTGCATCGCAGTTCACCAA 61.515 55.000 9.48 0.00 46.09 3.67
982 995 0.534427 ATCTCATGGGTGCATCGCAG 60.534 55.000 10.68 5.09 40.08 5.18
995 1008 0.536687 CCAATCCAGCGCCATCTCAT 60.537 55.000 2.29 0.00 0.00 2.90
1119 1132 3.303189 GCAGGCTGCTCTGGAGTA 58.697 61.111 31.37 0.00 40.96 2.59
1152 1165 2.104170 GTAGCAGCTTCCAGGACTAGT 58.896 52.381 0.00 0.00 0.00 2.57
1179 1192 0.758734 CGACCCCATCTTCAGGCATA 59.241 55.000 0.00 0.00 0.00 3.14
1193 1410 2.384203 GTAGCATGTTCAGCGACCC 58.616 57.895 0.00 0.00 37.01 4.46
1204 1421 0.552848 AAGATGGGGGTGGTAGCATG 59.447 55.000 0.00 0.00 0.00 4.06
1232 1449 2.753029 GGAGAAGTGCTGGCCTGT 59.247 61.111 11.69 0.00 0.00 4.00
1551 1810 0.389817 CGATCAAGGCGTTCTCCACA 60.390 55.000 0.00 0.00 0.00 4.17
1732 2279 2.430465 CAACATGTAGCTGCAAGAGGT 58.570 47.619 14.08 5.15 34.07 3.85
1736 2283 0.518636 ACGCAACATGTAGCTGCAAG 59.481 50.000 18.44 7.10 39.28 4.01
1754 2301 2.102420 ACTAAAAACCAGCCTTGCCAAC 59.898 45.455 0.00 0.00 0.00 3.77
1777 2324 3.560068 GCAGCAAATAGGCGTACAAGTAT 59.440 43.478 0.00 0.00 39.27 2.12
1863 2410 4.224274 AACGGCGACACGGGTCAA 62.224 61.111 19.62 0.00 44.54 3.18
1899 2446 1.227999 ACAACGATGTTCACGGCAGG 61.228 55.000 0.00 0.00 35.91 4.85
1945 2495 3.517901 TCAGGATCGTGAGGTTATGGTTT 59.482 43.478 13.94 0.00 0.00 3.27
1951 2501 2.496070 CCAGTTCAGGATCGTGAGGTTA 59.504 50.000 16.92 1.12 0.00 2.85
2027 2577 2.188817 GATGTGACAAGGGGTAGAGGT 58.811 52.381 0.00 0.00 0.00 3.85
2076 2626 1.610038 CTGCAGTGAAAGCATCAACCA 59.390 47.619 5.25 0.00 41.82 3.67
2272 2858 4.511527 CATAGACAGTGGTCAGCTTGAAT 58.488 43.478 0.00 0.00 46.80 2.57
2331 2943 3.564644 TGGTTTTTCGGCGATAAGTTCAA 59.435 39.130 11.76 0.00 0.00 2.69
2384 2999 7.450014 TCTTGCCTGGTAAATTTGATTGAAGTA 59.550 33.333 0.00 0.00 0.00 2.24
2407 3022 7.876068 TCAACATTTGTACGGTTCTTATCTCTT 59.124 33.333 0.00 0.00 0.00 2.85
2435 3050 0.035152 AATCTGACAATGCGGCTCCA 60.035 50.000 0.00 0.00 0.00 3.86
2515 3130 0.471617 CCCTCTGCCCATTACTCCAG 59.528 60.000 0.00 0.00 0.00 3.86
2557 3172 6.073440 CCCAATCTTCATTGCAAAAGAAGTTG 60.073 38.462 29.03 27.78 46.97 3.16
2559 3174 5.305128 TCCCAATCTTCATTGCAAAAGAAGT 59.695 36.000 29.03 19.90 46.97 3.01


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

AutoCloner maintained by Alex Coulton.