Multiple sequence alignment - TraesCS7A01G498100

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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 TraesCS7A01G498100 chr7A 100.000 2732 0 0 1 2732 688667066 688664335 0.000000e+00 5046.0
1 TraesCS7A01G498100 chr7A 81.912 868 91 25 991 1825 688652609 688651775 0.000000e+00 673.0
2 TraesCS7A01G498100 chr7A 87.614 549 53 6 1147 1680 688360435 688359887 8.310000e-175 623.0
3 TraesCS7A01G498100 chr7A 84.111 686 61 18 978 1638 688462870 688462208 1.070000e-173 619.0
4 TraesCS7A01G498100 chr7A 77.873 583 67 33 1148 1724 688460115 688459589 3.420000e-79 305.0
5 TraesCS7A01G498100 chr7A 89.831 59 6 0 1675 1733 688359856 688359798 2.920000e-10 76.8
6 TraesCS7A01G498100 chr7D 88.168 2113 134 35 710 2732 595669468 595667382 0.000000e+00 2410.0
7 TraesCS7A01G498100 chr7D 88.764 712 66 10 2 709 595670209 595669508 0.000000e+00 859.0
8 TraesCS7A01G498100 chr7D 84.971 692 69 17 973 1638 595587244 595586562 0.000000e+00 669.0
9 TraesCS7A01G498100 chr7D 86.301 511 58 5 1147 1645 595514267 595513757 1.850000e-151 545.0
10 TraesCS7A01G498100 chr7D 80.594 505 56 21 1149 1642 595581905 595581432 4.330000e-93 351.0
11 TraesCS7A01G498100 chr7D 81.046 153 22 7 2236 2385 96663811 96663959 6.180000e-22 115.0
12 TraesCS7A01G498100 chr7B 90.743 713 55 9 978 1680 673221701 673220990 0.000000e+00 941.0
13 TraesCS7A01G498100 chr7B 90.442 701 55 6 11 709 673222723 673222033 0.000000e+00 913.0
14 TraesCS7A01G498100 chr7B 83.094 905 72 29 1849 2732 673220712 673219868 0.000000e+00 749.0
15 TraesCS7A01G498100 chr7B 84.406 699 74 19 973 1645 672861073 672860384 0.000000e+00 654.0
16 TraesCS7A01G498100 chr7B 84.942 518 58 13 1147 1645 672779992 672779476 8.730000e-140 507.0
17 TraesCS7A01G498100 chr7B 90.146 274 13 6 710 978 673221993 673221729 7.240000e-91 344.0
18 TraesCS7A01G498100 chr7B 85.612 139 10 4 1675 1813 673220962 673220834 1.320000e-28 137.0
19 TraesCS7A01G498100 chr7B 83.146 89 9 2 1651 1733 672779449 672779361 2.920000e-10 76.8
20 TraesCS7A01G498100 chr2A 86.395 147 15 4 2241 2385 772996349 772996492 3.640000e-34 156.0
21 TraesCS7A01G498100 chr3A 83.465 127 19 2 2257 2383 731259248 731259372 1.720000e-22 117.0
22 TraesCS7A01G498100 chr3B 81.250 144 25 2 2245 2387 763164031 763163889 6.180000e-22 115.0
23 TraesCS7A01G498100 chr3B 81.379 145 23 3 2237 2381 800960386 800960246 6.180000e-22 115.0
24 TraesCS7A01G498100 chr3B 80.556 144 25 3 2245 2387 763135058 763134917 1.030000e-19 108.0
25 TraesCS7A01G498100 chr2D 81.208 149 22 6 2236 2380 577324929 577324783 6.180000e-22 115.0


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 TraesCS7A01G498100 chr7A 688664335 688667066 2731 True 5046.0 5046 100.0000 1 2732 1 chr7A.!!$R2 2731
1 TraesCS7A01G498100 chr7A 688651775 688652609 834 True 673.0 673 81.9120 991 1825 1 chr7A.!!$R1 834
2 TraesCS7A01G498100 chr7A 688459589 688462870 3281 True 462.0 619 80.9920 978 1724 2 chr7A.!!$R4 746
3 TraesCS7A01G498100 chr7A 688359798 688360435 637 True 349.9 623 88.7225 1147 1733 2 chr7A.!!$R3 586
4 TraesCS7A01G498100 chr7D 595667382 595670209 2827 True 1634.5 2410 88.4660 2 2732 2 chr7D.!!$R4 2730
5 TraesCS7A01G498100 chr7D 595586562 595587244 682 True 669.0 669 84.9710 973 1638 1 chr7D.!!$R3 665
6 TraesCS7A01G498100 chr7D 595513757 595514267 510 True 545.0 545 86.3010 1147 1645 1 chr7D.!!$R1 498
7 TraesCS7A01G498100 chr7B 672860384 672861073 689 True 654.0 654 84.4060 973 1645 1 chr7B.!!$R1 672
8 TraesCS7A01G498100 chr7B 673219868 673222723 2855 True 616.8 941 88.0074 11 2732 5 chr7B.!!$R3 2721
9 TraesCS7A01G498100 chr7B 672779361 672779992 631 True 291.9 507 84.0440 1147 1733 2 chr7B.!!$R2 586

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
577 581 0.172803 CTCCGACCGTACCTTCCTTG 59.827 60.0 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
2548 5332 0.108585 ACATCCACACCACACTGTCC 59.891 55.0 0.0 0.0 0.0 4.02 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
25 26 1.202806 CCGACATATGGCATTGACCCT 60.203 52.381 9.77 0.00 0.00 4.34
70 71 7.806690 TGTGCACATTTTAGAACTACAATCTC 58.193 34.615 17.42 0.00 0.00 2.75
214 218 9.959749 CCAACTAGTTTATGCAAAACTTAAGAA 57.040 29.630 22.95 10.68 40.58 2.52
228 232 7.761038 AAACTTAAGAAGGGAGGTAAATGTG 57.239 36.000 10.09 0.00 0.00 3.21
275 279 7.121315 GCTGTGAAGGATGGTCTTAAATTTACT 59.879 37.037 0.00 0.00 0.00 2.24
277 281 9.444600 TGTGAAGGATGGTCTTAAATTTACTAC 57.555 33.333 0.00 0.00 0.00 2.73
293 297 1.005569 ACTACTCCCTCCACATCGTGA 59.994 52.381 0.00 0.00 35.23 4.35
300 304 1.003118 CCTCCACATCGTGAAAAGGGA 59.997 52.381 0.00 0.00 35.23 4.20
301 305 2.350522 CTCCACATCGTGAAAAGGGAG 58.649 52.381 0.00 0.00 35.23 4.30
306 310 3.753272 CACATCGTGAAAAGGGAGTGAAT 59.247 43.478 0.00 0.00 35.23 2.57
311 315 7.176690 ACATCGTGAAAAGGGAGTGAATAATTT 59.823 33.333 0.00 0.00 0.00 1.82
313 317 6.940298 TCGTGAAAAGGGAGTGAATAATTTCT 59.060 34.615 0.00 0.00 32.78 2.52
315 319 7.094805 CGTGAAAAGGGAGTGAATAATTTCTCA 60.095 37.037 0.00 0.00 32.78 3.27
327 331 7.998212 GTGAATAATTTCTCACTTTTTGTTGCG 59.002 33.333 10.75 0.00 39.11 4.85
328 332 7.918033 TGAATAATTTCTCACTTTTTGTTGCGA 59.082 29.630 0.00 0.00 32.78 5.10
329 333 8.641499 AATAATTTCTCACTTTTTGTTGCGAA 57.359 26.923 0.00 0.00 0.00 4.70
334 338 5.092781 TCTCACTTTTTGTTGCGAAAGAAC 58.907 37.500 3.14 0.00 36.58 3.01
343 347 3.011760 GCGAAAGAACGGCGAGTGG 62.012 63.158 16.62 0.00 0.00 4.00
382 386 4.020543 TGTGCTGAAATAACCCCCATAAC 58.979 43.478 0.00 0.00 0.00 1.89
405 409 3.823873 TGCGTTCATTTCAACCATTACCT 59.176 39.130 0.00 0.00 0.00 3.08
409 413 5.878116 CGTTCATTTCAACCATTACCTAGGA 59.122 40.000 17.98 0.00 0.00 2.94
433 437 7.336931 GGAGACTTAAAGCTAATTGGTCATCAA 59.663 37.037 0.00 0.00 40.01 2.57
435 439 7.665559 AGACTTAAAGCTAATTGGTCATCAACA 59.334 33.333 0.00 0.00 38.31 3.33
460 464 4.024893 CGCTGCACTATGGATTAAAATCGT 60.025 41.667 0.00 0.00 36.27 3.73
466 470 7.551262 TGCACTATGGATTAAAATCGTTGTAGT 59.449 33.333 0.00 1.21 36.27 2.73
488 492 3.571828 TCGATCATAGAAAGGAGAGCCAG 59.428 47.826 0.00 0.00 36.29 4.85
496 500 1.366319 AAGGAGAGCCAGAACCACAT 58.634 50.000 0.00 0.00 36.29 3.21
562 566 1.219393 GCAGGAAGTTCTCCCTCCG 59.781 63.158 2.25 0.00 46.81 4.63
567 571 1.228800 AAGTTCTCCCTCCGACCGT 60.229 57.895 0.00 0.00 0.00 4.83
577 581 0.172803 CTCCGACCGTACCTTCCTTG 59.827 60.000 0.00 0.00 0.00 3.61
618 623 5.390613 GTTTGGAAATTGACACGGTCTATG 58.609 41.667 5.77 0.00 33.15 2.23
632 637 6.029607 CACGGTCTATGACATGAAAATTTGG 58.970 40.000 0.00 0.00 33.68 3.28
652 657 1.133025 GGATGAAATTGGTGCACCTCG 59.867 52.381 34.75 0.00 36.82 4.63
685 690 1.964552 AGGGAGTGGTATCGAGTACG 58.035 55.000 0.00 0.00 41.26 3.67
699 704 5.987777 TCGAGTACGAGGATCTTTAGAAG 57.012 43.478 0.00 0.00 43.81 2.85
702 707 2.873133 ACGAGGATCTTTAGAAGCGG 57.127 50.000 0.00 0.00 0.00 5.52
718 762 2.258013 CGGAACACGCCATGGTTGT 61.258 57.895 14.67 14.11 34.82 3.32
741 785 5.991606 GTGCACACAATCTAGAGGCAATATA 59.008 40.000 13.17 0.00 0.00 0.86
742 786 6.652481 GTGCACACAATCTAGAGGCAATATAT 59.348 38.462 13.17 0.00 0.00 0.86
837 882 4.751028 GCCTATCCAAAGCCCTGATTGTAT 60.751 45.833 0.00 0.00 0.00 2.29
872 919 6.614657 AGCTATAAAAGTTGCATAGGGGATT 58.385 36.000 0.00 0.00 0.00 3.01
873 920 7.069344 AGCTATAAAAGTTGCATAGGGGATTT 58.931 34.615 0.00 0.00 0.00 2.17
874 921 7.231519 AGCTATAAAAGTTGCATAGGGGATTTC 59.768 37.037 0.00 0.00 0.00 2.17
875 922 4.718940 AAAAGTTGCATAGGGGATTTCG 57.281 40.909 0.00 0.00 0.00 3.46
921 976 7.251994 GTGTGGTATCTAGAAACAGAGTACAG 58.748 42.308 0.00 0.00 0.00 2.74
948 1003 6.239402 CCTCCAAACAAGAATTTCCTCATTGT 60.239 38.462 0.00 0.00 35.70 2.71
1040 1135 0.911525 CTCTCACCCCTCCACACCAT 60.912 60.000 0.00 0.00 0.00 3.55
1072 1168 1.600957 CAACAAGCACACACAGGAGAG 59.399 52.381 0.00 0.00 0.00 3.20
1082 1178 3.900601 ACACACAGGAGAGAAACAGAGAT 59.099 43.478 0.00 0.00 0.00 2.75
1130 1232 1.661498 CTCCTCTGCTCTGCTACGCA 61.661 60.000 0.00 0.00 36.92 5.24
1739 4406 3.715854 GCTTGCAATGAAGCCTGAG 57.284 52.632 0.00 0.00 42.23 3.35
1842 4583 1.486211 ACATGAAGTCCTACCCGGAG 58.514 55.000 0.73 0.00 44.20 4.63
1949 4712 1.078918 CGCAAGGATGAGGACTGCA 60.079 57.895 0.00 0.00 0.00 4.41
1952 4715 0.747283 CAAGGATGAGGACTGCAGCC 60.747 60.000 15.27 16.08 41.98 4.85
2024 4799 4.703093 ACAACAAGGAGGAAAAAGACGAAA 59.297 37.500 0.00 0.00 0.00 3.46
2062 4837 2.933287 ACGGTGGCCCCTTGATGA 60.933 61.111 0.00 0.00 0.00 2.92
2064 4839 2.276740 GGTGGCCCCTTGATGAGG 59.723 66.667 0.00 0.00 45.86 3.86
2069 4844 4.113815 CCCCTTGATGAGGCGGCA 62.114 66.667 13.08 0.00 44.85 5.69
2070 4845 2.825836 CCCTTGATGAGGCGGCAC 60.826 66.667 13.08 5.35 44.85 5.01
2071 4846 2.270205 CCTTGATGAGGCGGCACT 59.730 61.111 13.08 0.00 39.09 4.40
2072 4847 1.817099 CCTTGATGAGGCGGCACTC 60.817 63.158 13.08 6.91 39.09 3.51
2094 4876 0.179094 GGCAATGGTCGGATCGTGTA 60.179 55.000 0.00 0.00 0.00 2.90
2222 5004 3.004326 GCATCGTGCCATGCCCAAA 62.004 57.895 1.76 0.00 43.03 3.28
2326 5108 3.140814 GCCGGGCATTCCTTCACC 61.141 66.667 15.62 0.00 0.00 4.02
2334 5116 0.953471 CATTCCTTCACCGCGGTTGA 60.953 55.000 32.11 25.55 0.00 3.18
2339 5121 1.086696 CTTCACCGCGGTTGAATCAT 58.913 50.000 32.11 0.00 0.00 2.45
2358 5140 9.310716 TGAATCATCTCGATATATCAATTGAGC 57.689 33.333 14.54 0.34 37.32 4.26
2359 5141 9.310716 GAATCATCTCGATATATCAATTGAGCA 57.689 33.333 14.54 4.67 37.32 4.26
2366 5148 9.888878 CTCGATATATCAATTGAGCAAAATGTT 57.111 29.630 14.54 0.00 32.06 2.71
2375 5157 8.296000 TCAATTGAGCAAAATGTTCTTTATCGA 58.704 29.630 3.38 0.00 0.00 3.59
2430 5212 2.585247 GTATCGTGGGTGCTCGCC 60.585 66.667 0.00 0.00 0.00 5.54
2431 5213 4.201679 TATCGTGGGTGCTCGCCG 62.202 66.667 0.00 4.25 0.00 6.46
2484 5268 1.971167 GCAAGGGCAACGACCATCA 60.971 57.895 0.00 0.00 40.72 3.07
2506 5290 0.606401 CGAGGAGGTTTGTGGTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
2519 5303 3.461458 TGTGGTGCATTAGATATTCCCCA 59.539 43.478 0.00 0.00 0.00 4.96
2530 5314 4.104086 AGATATTCCCCATCGGCATCTAA 58.896 43.478 0.00 0.00 0.00 2.10
2548 5332 2.457366 AACTTCAAGGTAGTGGCTCG 57.543 50.000 0.00 0.00 0.00 5.03
2574 5358 3.644265 AGTGTGGTGTGGATGTTACAGTA 59.356 43.478 0.00 0.00 0.00 2.74
2680 5464 2.290916 TGAGAAGATCTCGCCGATGTAC 59.709 50.000 0.00 0.00 46.25 2.90
2689 5482 1.030457 CGCCGATGTACTAGGTCCTT 58.970 55.000 0.00 0.00 0.00 3.36
2700 5493 4.611564 ACTAGGTCCTTGAGTGGAGTAT 57.388 45.455 7.38 0.00 36.69 2.12
2725 5518 4.421033 TGCTACTATCGAATGATCCGTC 57.579 45.455 0.00 0.00 35.99 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.165907 AATGCCATATGTCGGTGCCG 61.166 55.000 3.94 3.94 41.35 5.69
7 8 6.006449 AGAATAAGGGTCAATGCCATATGTC 58.994 40.000 1.24 0.00 0.00 3.06
8 9 5.957132 AGAATAAGGGTCAATGCCATATGT 58.043 37.500 1.24 0.00 0.00 2.29
25 26 5.064707 GCACAAGAACGGCTTCATAGAATAA 59.935 40.000 0.00 0.00 33.60 1.40
70 71 2.990066 AGGATTCTGCTTTAGGGACG 57.010 50.000 0.00 0.00 0.00 4.79
214 218 4.141251 AGTGTGTTTCACATTTACCTCCCT 60.141 41.667 5.88 0.00 46.32 4.20
216 220 4.819630 TGAGTGTGTTTCACATTTACCTCC 59.180 41.667 5.88 0.00 46.32 4.30
228 232 6.088824 CAGCAAGGATTATTGAGTGTGTTTC 58.911 40.000 0.00 0.00 31.55 2.78
275 279 2.225382 TTCACGATGTGGAGGGAGTA 57.775 50.000 0.00 0.00 33.87 2.59
277 281 2.350522 CTTTTCACGATGTGGAGGGAG 58.649 52.381 0.00 0.00 33.87 4.30
301 305 7.998212 CGCAACAAAAAGTGAGAAATTATTCAC 59.002 33.333 12.13 12.13 43.08 3.18
306 310 7.971168 TCTTTCGCAACAAAAAGTGAGAAATTA 59.029 29.630 3.61 0.00 34.73 1.40
311 315 4.955925 TCTTTCGCAACAAAAAGTGAGA 57.044 36.364 0.00 0.00 34.73 3.27
313 317 3.849145 CGTTCTTTCGCAACAAAAAGTGA 59.151 39.130 0.00 0.00 34.73 3.41
315 319 3.175929 CCGTTCTTTCGCAACAAAAAGT 58.824 40.909 0.00 0.00 34.73 2.66
319 323 0.590230 CGCCGTTCTTTCGCAACAAA 60.590 50.000 0.00 0.00 0.00 2.83
320 324 1.010574 CGCCGTTCTTTCGCAACAA 60.011 52.632 0.00 0.00 0.00 2.83
321 325 1.827315 CTCGCCGTTCTTTCGCAACA 61.827 55.000 0.00 0.00 0.00 3.33
322 326 1.154654 CTCGCCGTTCTTTCGCAAC 60.155 57.895 0.00 0.00 0.00 4.17
323 327 1.593209 ACTCGCCGTTCTTTCGCAA 60.593 52.632 0.00 0.00 0.00 4.85
324 328 2.028484 ACTCGCCGTTCTTTCGCA 59.972 55.556 0.00 0.00 0.00 5.10
325 329 2.470286 CACTCGCCGTTCTTTCGC 59.530 61.111 0.00 0.00 0.00 4.70
326 330 2.380410 CCCACTCGCCGTTCTTTCG 61.380 63.158 0.00 0.00 0.00 3.46
327 331 2.677979 GCCCACTCGCCGTTCTTTC 61.678 63.158 0.00 0.00 0.00 2.62
328 332 2.668550 GCCCACTCGCCGTTCTTT 60.669 61.111 0.00 0.00 0.00 2.52
329 333 4.699522 GGCCCACTCGCCGTTCTT 62.700 66.667 0.00 0.00 39.64 2.52
382 386 4.082787 AGGTAATGGTTGAAATGAACGCAG 60.083 41.667 0.00 0.00 0.00 5.18
405 409 7.490657 TGACCAATTAGCTTTAAGTCTCCTA 57.509 36.000 0.00 0.00 0.00 2.94
409 413 7.665559 TGTTGATGACCAATTAGCTTTAAGTCT 59.334 33.333 0.00 0.00 37.08 3.24
433 437 2.627515 AATCCATAGTGCAGCGATGT 57.372 45.000 1.22 0.00 0.00 3.06
435 439 5.106948 CGATTTTAATCCATAGTGCAGCGAT 60.107 40.000 0.00 0.00 31.68 4.58
460 464 6.238786 GCTCTCCTTTCTATGATCGACTACAA 60.239 42.308 0.00 0.00 0.00 2.41
466 470 3.566351 TGGCTCTCCTTTCTATGATCGA 58.434 45.455 0.00 0.00 0.00 3.59
562 566 0.683412 ACACCAAGGAAGGTACGGTC 59.317 55.000 0.00 0.00 40.77 4.79
567 571 7.945664 ACATGTTATTTTACACCAAGGAAGGTA 59.054 33.333 0.00 0.00 40.77 3.08
577 581 6.670233 TCCAAACGACATGTTATTTTACACC 58.330 36.000 0.00 0.00 40.84 4.16
618 623 7.391275 ACCAATTTCATCCCAAATTTTCATGTC 59.609 33.333 0.00 0.00 34.37 3.06
632 637 1.133025 CGAGGTGCACCAATTTCATCC 59.867 52.381 36.39 6.60 38.89 3.51
652 657 4.280929 ACCACTCCCTTTGTTTAGAATTGC 59.719 41.667 0.00 0.00 0.00 3.56
685 690 3.866327 GTGTTCCGCTTCTAAAGATCCTC 59.134 47.826 0.00 0.00 0.00 3.71
702 707 1.371635 GCACAACCATGGCGTGTTC 60.372 57.895 27.08 16.61 33.13 3.18
718 762 2.857186 TTGCCTCTAGATTGTGTGCA 57.143 45.000 0.00 0.00 0.00 4.57
741 785 4.552674 AGGCGTTATTTAAATTGGGGGAT 58.447 39.130 5.91 0.00 0.00 3.85
742 786 3.983821 AGGCGTTATTTAAATTGGGGGA 58.016 40.909 5.91 0.00 0.00 4.81
816 861 8.641498 ATTTATACAATCAGGGCTTTGGATAG 57.359 34.615 0.00 0.00 31.87 2.08
818 863 7.919385 AATTTATACAATCAGGGCTTTGGAT 57.081 32.000 0.00 0.00 31.42 3.41
921 976 4.827284 TGAGGAAATTCTTGTTTGGAGGTC 59.173 41.667 0.00 0.00 0.00 3.85
948 1003 6.380560 TGTGATGCCAAGGAATATCAAATGAA 59.619 34.615 0.00 0.00 31.98 2.57
1040 1135 3.211045 GTGCTTGTTGTTGTCTTAGGGA 58.789 45.455 0.00 0.00 0.00 4.20
1072 1168 4.248859 TGCTGCTCTGTTATCTCTGTTTC 58.751 43.478 0.00 0.00 0.00 2.78
1082 1178 3.999001 CTGATGAGTTTGCTGCTCTGTTA 59.001 43.478 0.00 0.00 34.30 2.41
1586 1717 4.826556 CTCGTCCATCTTCTTCTCCTTTT 58.173 43.478 0.00 0.00 0.00 2.27
1588 1719 2.167487 GCTCGTCCATCTTCTTCTCCTT 59.833 50.000 0.00 0.00 0.00 3.36
1739 4406 6.166279 TGAGTTAGTTGTCATCTCATTGTCC 58.834 40.000 0.00 0.00 31.51 4.02
1845 4586 4.514577 CTCCGCCCACCACGCTAG 62.515 72.222 0.00 0.00 0.00 3.42
1991 4766 4.025401 CTTGTTGTCGGCGCCACC 62.025 66.667 28.98 16.61 0.00 4.61
1992 4767 4.025401 CCTTGTTGTCGGCGCCAC 62.025 66.667 28.98 22.84 0.00 5.01
1993 4768 4.243008 TCCTTGTTGTCGGCGCCA 62.243 61.111 28.98 11.20 0.00 5.69
1994 4769 3.423154 CTCCTTGTTGTCGGCGCC 61.423 66.667 19.07 19.07 0.00 6.53
1995 4770 3.423154 CCTCCTTGTTGTCGGCGC 61.423 66.667 0.00 0.00 0.00 6.53
1996 4771 0.882927 TTTCCTCCTTGTTGTCGGCG 60.883 55.000 0.00 0.00 0.00 6.46
1997 4772 1.314730 TTTTCCTCCTTGTTGTCGGC 58.685 50.000 0.00 0.00 0.00 5.54
1998 4773 3.003378 GTCTTTTTCCTCCTTGTTGTCGG 59.997 47.826 0.00 0.00 0.00 4.79
1999 4774 3.303132 CGTCTTTTTCCTCCTTGTTGTCG 60.303 47.826 0.00 0.00 0.00 4.35
2000 4775 3.875134 TCGTCTTTTTCCTCCTTGTTGTC 59.125 43.478 0.00 0.00 0.00 3.18
2001 4776 3.881220 TCGTCTTTTTCCTCCTTGTTGT 58.119 40.909 0.00 0.00 0.00 3.32
2002 4777 4.893424 TTCGTCTTTTTCCTCCTTGTTG 57.107 40.909 0.00 0.00 0.00 3.33
2003 4778 4.948004 AGTTTCGTCTTTTTCCTCCTTGTT 59.052 37.500 0.00 0.00 0.00 2.83
2004 4779 4.335594 CAGTTTCGTCTTTTTCCTCCTTGT 59.664 41.667 0.00 0.00 0.00 3.16
2005 4780 4.261197 CCAGTTTCGTCTTTTTCCTCCTTG 60.261 45.833 0.00 0.00 0.00 3.61
2057 4832 2.265739 GTGAGTGCCGCCTCATCA 59.734 61.111 12.78 0.00 43.03 3.07
2059 4834 4.457496 CCGTGAGTGCCGCCTCAT 62.457 66.667 12.78 0.00 43.03 2.90
2064 4839 4.465512 CATTGCCGTGAGTGCCGC 62.466 66.667 0.00 0.00 0.00 6.53
2069 4844 1.899437 ATCCGACCATTGCCGTGAGT 61.899 55.000 0.00 0.00 0.00 3.41
2070 4845 1.153369 ATCCGACCATTGCCGTGAG 60.153 57.895 0.00 0.00 0.00 3.51
2071 4846 1.153449 GATCCGACCATTGCCGTGA 60.153 57.895 0.00 0.00 0.00 4.35
2072 4847 2.525248 CGATCCGACCATTGCCGTG 61.525 63.158 0.00 0.00 0.00 4.94
2073 4848 2.202878 CGATCCGACCATTGCCGT 60.203 61.111 0.00 0.00 0.00 5.68
2074 4849 2.202878 ACGATCCGACCATTGCCG 60.203 61.111 0.00 0.00 0.00 5.69
2075 4850 0.179094 TACACGATCCGACCATTGCC 60.179 55.000 0.00 0.00 0.00 4.52
2076 4851 1.593006 CTTACACGATCCGACCATTGC 59.407 52.381 0.00 0.00 0.00 3.56
2259 5041 2.680841 CACGTCCAACACCTCAGAAAAA 59.319 45.455 0.00 0.00 0.00 1.94
2264 5046 1.330521 CAAACACGTCCAACACCTCAG 59.669 52.381 0.00 0.00 0.00 3.35
2326 5108 1.491670 ATCGAGATGATTCAACCGCG 58.508 50.000 0.00 0.00 31.57 6.46
2334 5116 9.662947 TTGCTCAATTGATATATCGAGATGATT 57.337 29.630 8.96 1.19 38.57 2.57
2339 5121 9.276590 ACATTTTGCTCAATTGATATATCGAGA 57.723 29.630 8.96 5.89 0.00 4.04
2432 5214 3.595758 ATTTATGCCGCCAGCCGC 61.596 61.111 0.00 0.00 42.71 6.53
2433 5215 2.332514 CATTTATGCCGCCAGCCG 59.667 61.111 0.00 0.00 42.71 5.52
2434 5216 1.181098 ATCCATTTATGCCGCCAGCC 61.181 55.000 0.00 0.00 42.71 4.85
2475 5259 1.595993 CCTCCTCGTGTGATGGTCGT 61.596 60.000 0.00 0.00 0.00 4.34
2484 5268 0.179056 CACCACAAACCTCCTCGTGT 60.179 55.000 0.00 0.00 0.00 4.49
2506 5290 4.104086 AGATGCCGATGGGGAATATCTAA 58.896 43.478 0.00 0.00 32.35 2.10
2519 5303 3.914426 ACCTTGAAGTTAGATGCCGAT 57.086 42.857 0.00 0.00 0.00 4.18
2530 5314 0.608640 CCGAGCCACTACCTTGAAGT 59.391 55.000 0.00 0.00 0.00 3.01
2548 5332 0.108585 ACATCCACACCACACTGTCC 59.891 55.000 0.00 0.00 0.00 4.02
2574 5358 1.079405 CCACACCGGCGTTAGTCAT 60.079 57.895 6.01 0.00 0.00 3.06
2598 5382 3.205815 GGCATGGAATTGGCCACTA 57.794 52.632 3.88 0.00 46.92 2.74
2673 5457 3.066900 CCACTCAAGGACCTAGTACATCG 59.933 52.174 0.00 0.00 0.00 3.84
2680 5464 3.639094 CCATACTCCACTCAAGGACCTAG 59.361 52.174 0.00 0.00 33.19 3.02
2689 5482 3.916035 AGTAGCATCCATACTCCACTCA 58.084 45.455 0.00 0.00 0.00 3.41
2700 5493 4.142381 CGGATCATTCGATAGTAGCATCCA 60.142 45.833 0.00 0.00 37.40 3.41


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

AutoCloner maintained by Alex Coulton.