Multiple sequence alignment - TraesCS5B01G411400

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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 TraesCS5B01G411400 chr5B 100.000 3642 0 0 1 3642 586622657 586619016 0.000000e+00 6726.0
1 TraesCS5B01G411400 chr5D 94.113 2769 116 21 903 3642 478610518 478607768 0.000000e+00 4167.0
2 TraesCS5B01G411400 chr5D 83.495 412 39 12 1 387 478611560 478611153 1.240000e-94 357.0
3 TraesCS5B01G411400 chr5A 90.409 2763 149 48 931 3642 597741481 597744178 0.000000e+00 3528.0
4 TraesCS5B01G411400 chr5A 86.410 390 19 10 1 388 597740471 597740828 2.640000e-106 396.0
5 TraesCS5B01G411400 chr5A 88.931 262 21 4 468 721 597740862 597741123 2.110000e-82 316.0
6 TraesCS5B01G411400 chr5A 89.231 195 14 2 736 930 597741177 597741364 1.690000e-58 237.0
7 TraesCS5B01G411400 chr7B 83.538 1628 189 35 1037 2648 672484810 672486374 0.000000e+00 1448.0
8 TraesCS5B01G411400 chr7A 83.733 1500 172 26 1022 2501 681794753 681796200 0.000000e+00 1352.0
9 TraesCS5B01G411400 chr7D 85.159 1004 105 20 1441 2416 591292855 591293842 0.000000e+00 989.0
10 TraesCS5B01G411400 chr7D 87.013 385 38 5 1022 1406 591290239 591290611 1.210000e-114 424.0
11 TraesCS5B01G411400 chr3D 81.886 933 138 24 999 1920 592592297 592593209 0.000000e+00 758.0
12 TraesCS5B01G411400 chr3B 79.757 988 168 24 1004 1980 794585174 794584208 0.000000e+00 688.0
13 TraesCS5B01G411400 chr3A 79.612 103 16 4 2342 2443 724006588 724006490 6.530000e-08 69.4


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 TraesCS5B01G411400 chr5B 586619016 586622657 3641 True 6726.00 6726 100.00000 1 3642 1 chr5B.!!$R1 3641
1 TraesCS5B01G411400 chr5D 478607768 478611560 3792 True 2262.00 4167 88.80400 1 3642 2 chr5D.!!$R1 3641
2 TraesCS5B01G411400 chr5A 597740471 597744178 3707 False 1119.25 3528 88.74525 1 3642 4 chr5A.!!$F1 3641
3 TraesCS5B01G411400 chr7B 672484810 672486374 1564 False 1448.00 1448 83.53800 1037 2648 1 chr7B.!!$F1 1611
4 TraesCS5B01G411400 chr7A 681794753 681796200 1447 False 1352.00 1352 83.73300 1022 2501 1 chr7A.!!$F1 1479
5 TraesCS5B01G411400 chr7D 591290239 591293842 3603 False 706.50 989 86.08600 1022 2416 2 chr7D.!!$F1 1394
6 TraesCS5B01G411400 chr3D 592592297 592593209 912 False 758.00 758 81.88600 999 1920 1 chr3D.!!$F1 921
7 TraesCS5B01G411400 chr3B 794584208 794585174 966 True 688.00 688 79.75700 1004 1980 1 chr3B.!!$R1 976

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
332 360 0.038166 TTCCTTGGAAATCCGCAGCT 59.962 50.0 0.00 0.00 39.43 4.24 F
637 676 0.251608 AAAGGATTTGGACCCGGGTG 60.252 55.0 36.01 2.55 36.60 4.61 F
1990 4952 0.752658 TCTACCATGCATCCTCGTGG 59.247 55.0 0.00 0.00 46.15 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1976 0.622665 CCTTCATCACCTCCCTTGCT 59.377 55.0 0.0 0.0 0.0 3.91 R
2371 5360 0.108138 CGAACCTCTCGGGCTTGAAT 60.108 55.0 0.0 0.0 44.2 2.57 R
3174 6172 0.536460 TGGGTTTTCAGTTCCTCCGC 60.536 55.0 0.0 0.0 0.0 5.54 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
21 22 1.243342 CGCCAAACTTCTGGATGCCA 61.243 55.000 0.00 0.00 38.96 4.92
42 43 0.875059 CCCGTTTCTTCTTGTCCTGC 59.125 55.000 0.00 0.00 0.00 4.85
96 97 4.389992 TGCGACAGAATTGATCTCTTTCAC 59.610 41.667 0.00 0.00 35.73 3.18
116 117 0.755079 AGATGCGCTAGCTCCATGAA 59.245 50.000 18.72 0.00 45.42 2.57
126 127 5.468072 CGCTAGCTCCATGAATCACTAATTT 59.532 40.000 13.93 0.00 0.00 1.82
149 150 0.251922 ATTCCACACAGCAAGGCCAT 60.252 50.000 5.01 0.00 0.00 4.40
165 166 6.093909 GCAAGGCCATGCAATATAAAAAGTTT 59.906 34.615 27.36 0.00 45.70 2.66
166 167 7.677041 GCAAGGCCATGCAATATAAAAAGTTTC 60.677 37.037 27.36 0.00 45.70 2.78
170 171 7.548780 GGCCATGCAATATAAAAAGTTTCTTCA 59.451 33.333 0.00 0.00 0.00 3.02
175 176 9.486497 TGCAATATAAAAAGTTTCTTCATGCAA 57.514 25.926 10.55 0.00 34.96 4.08
183 184 9.476202 AAAAAGTTTCTTCATGCAATAAGTACC 57.524 29.630 10.25 0.00 0.00 3.34
184 185 7.759489 AAGTTTCTTCATGCAATAAGTACCA 57.241 32.000 10.25 0.00 0.00 3.25
215 240 2.165641 TCGTGCGTCTCTTTCATGGTAT 59.834 45.455 0.00 0.00 0.00 2.73
216 241 2.930040 CGTGCGTCTCTTTCATGGTATT 59.070 45.455 0.00 0.00 0.00 1.89
217 242 3.242091 CGTGCGTCTCTTTCATGGTATTG 60.242 47.826 0.00 0.00 0.00 1.90
218 243 3.063997 GTGCGTCTCTTTCATGGTATTGG 59.936 47.826 0.00 0.00 0.00 3.16
310 335 2.470990 TCTATCATGCATCGGCCCTAT 58.529 47.619 0.00 0.00 40.13 2.57
332 360 0.038166 TTCCTTGGAAATCCGCAGCT 59.962 50.000 0.00 0.00 39.43 4.24
377 408 6.286758 TGCATTTGGATTTTGCTCTTTTGTA 58.713 32.000 0.00 0.00 37.28 2.41
378 409 6.765036 TGCATTTGGATTTTGCTCTTTTGTAA 59.235 30.769 0.00 0.00 37.28 2.41
379 410 7.281774 TGCATTTGGATTTTGCTCTTTTGTAAA 59.718 29.630 0.00 0.00 37.28 2.01
380 411 8.291740 GCATTTGGATTTTGCTCTTTTGTAAAT 58.708 29.630 0.00 0.00 33.61 1.40
437 468 1.002134 CGCCCCTTTCACCTGACAT 60.002 57.895 0.00 0.00 0.00 3.06
438 469 1.308069 CGCCCCTTTCACCTGACATG 61.308 60.000 0.00 0.00 0.00 3.21
447 478 5.182001 CCTTTCACCTGACATGGTTTCTTAG 59.818 44.000 0.00 0.00 38.45 2.18
448 479 3.674997 TCACCTGACATGGTTTCTTAGC 58.325 45.455 0.00 0.00 38.45 3.09
449 480 2.749621 CACCTGACATGGTTTCTTAGCC 59.250 50.000 0.00 0.00 38.45 3.93
450 481 2.644798 ACCTGACATGGTTTCTTAGCCT 59.355 45.455 0.00 0.00 36.89 4.58
451 482 3.012518 CCTGACATGGTTTCTTAGCCTG 58.987 50.000 0.00 0.00 0.00 4.85
452 483 3.012518 CTGACATGGTTTCTTAGCCTGG 58.987 50.000 0.00 0.00 0.00 4.45
453 484 2.375174 TGACATGGTTTCTTAGCCTGGT 59.625 45.455 0.00 0.00 0.00 4.00
454 485 3.585289 TGACATGGTTTCTTAGCCTGGTA 59.415 43.478 0.00 0.00 0.00 3.25
455 486 3.939592 GACATGGTTTCTTAGCCTGGTAC 59.060 47.826 0.00 0.00 0.00 3.34
456 487 3.329520 ACATGGTTTCTTAGCCTGGTACA 59.670 43.478 0.00 0.00 0.00 2.90
457 488 3.412237 TGGTTTCTTAGCCTGGTACAC 57.588 47.619 0.00 0.00 0.00 2.90
458 489 2.976882 TGGTTTCTTAGCCTGGTACACT 59.023 45.455 0.00 0.00 0.00 3.55
459 490 3.393278 TGGTTTCTTAGCCTGGTACACTT 59.607 43.478 0.00 0.00 0.00 3.16
460 491 4.141344 TGGTTTCTTAGCCTGGTACACTTT 60.141 41.667 0.00 0.00 0.00 2.66
461 492 4.454847 GGTTTCTTAGCCTGGTACACTTTC 59.545 45.833 0.00 0.00 0.00 2.62
462 493 3.975168 TCTTAGCCTGGTACACTTTCC 57.025 47.619 0.00 0.00 0.00 3.13
463 494 2.570302 TCTTAGCCTGGTACACTTTCCC 59.430 50.000 0.00 0.00 0.00 3.97
464 495 2.032965 TAGCCTGGTACACTTTCCCA 57.967 50.000 0.00 0.00 0.00 4.37
465 496 0.693049 AGCCTGGTACACTTTCCCAG 59.307 55.000 0.00 0.00 44.39 4.45
466 497 0.960861 GCCTGGTACACTTTCCCAGC 60.961 60.000 0.00 0.00 43.61 4.85
492 523 1.067295 TGCCTCCCATGTTTCTCTGT 58.933 50.000 0.00 0.00 0.00 3.41
502 533 6.072175 TCCCATGTTTCTCTGTTTTTATTCCG 60.072 38.462 0.00 0.00 0.00 4.30
535 566 5.767269 TGTTGATTTTGTTGCGATGTATGT 58.233 33.333 0.00 0.00 0.00 2.29
568 601 6.512415 GCCAATACATGTCTAGCTGTGATTTC 60.512 42.308 0.00 0.00 0.00 2.17
579 612 7.217070 GTCTAGCTGTGATTTCTTTTTAATGCG 59.783 37.037 0.00 0.00 0.00 4.73
598 637 3.181466 TGCGGTATAGATGCTCACAACAT 60.181 43.478 0.00 0.00 0.00 2.71
603 642 7.312899 CGGTATAGATGCTCACAACATGTATA 58.687 38.462 0.00 0.00 36.00 1.47
606 645 9.476202 GTATAGATGCTCACAACATGTATACAA 57.524 33.333 18.60 0.00 46.37 2.41
616 655 3.352648 ACATGTATACAACTGGGCCAAC 58.647 45.455 10.14 0.72 0.00 3.77
617 656 3.010138 ACATGTATACAACTGGGCCAACT 59.990 43.478 10.14 0.00 0.00 3.16
624 663 2.110011 ACAACTGGGCCAACTAAAGGAT 59.890 45.455 8.04 0.00 0.00 3.24
628 667 2.497273 CTGGGCCAACTAAAGGATTTGG 59.503 50.000 8.04 0.00 42.80 3.28
635 674 1.283905 ACTAAAGGATTTGGACCCGGG 59.716 52.381 22.25 22.25 39.07 5.73
637 676 0.251608 AAAGGATTTGGACCCGGGTG 60.252 55.000 36.01 2.55 36.60 4.61
674 713 9.802039 ACCACTGAAATCTAACCATTTAAGTTA 57.198 29.630 0.00 0.00 35.87 2.24
721 760 6.496565 TGTGATTTGGGAGGACATTTTTGTAT 59.503 34.615 0.00 0.00 0.00 2.29
722 761 7.016072 TGTGATTTGGGAGGACATTTTTGTATT 59.984 33.333 0.00 0.00 0.00 1.89
723 762 7.331687 GTGATTTGGGAGGACATTTTTGTATTG 59.668 37.037 0.00 0.00 0.00 1.90
724 763 5.736951 TTGGGAGGACATTTTTGTATTGG 57.263 39.130 0.00 0.00 0.00 3.16
726 765 3.769300 GGGAGGACATTTTTGTATTGGCT 59.231 43.478 0.00 0.00 0.00 4.75
754 832 4.537135 AGTAGAAATCGGCAAGTCTTCA 57.463 40.909 0.00 0.00 0.00 3.02
767 845 6.090493 CGGCAAGTCTTCAGATATGATATGTG 59.910 42.308 3.38 3.38 0.00 3.21
768 846 6.128336 GGCAAGTCTTCAGATATGATATGTGC 60.128 42.308 4.82 0.00 0.00 4.57
769 847 6.649973 GCAAGTCTTCAGATATGATATGTGCT 59.350 38.462 4.82 0.00 0.00 4.40
776 854 5.478332 TCAGATATGATATGTGCTTCCGACT 59.522 40.000 4.82 0.00 0.00 4.18
784 862 8.902540 TGATATGTGCTTCCGACTTATTTAAT 57.097 30.769 0.00 0.00 0.00 1.40
829 907 3.071602 AGCACAGGAACACACTAAGACAT 59.928 43.478 0.00 0.00 0.00 3.06
835 913 3.997021 GGAACACACTAAGACATGGTGAG 59.003 47.826 0.89 0.00 35.28 3.51
836 914 3.045601 ACACACTAAGACATGGTGAGC 57.954 47.619 0.89 0.00 35.28 4.26
888 1122 5.992217 GCCTCCGACTTATTTATGTCTCATT 59.008 40.000 0.00 0.00 0.00 2.57
889 1123 7.152645 GCCTCCGACTTATTTATGTCTCATTA 58.847 38.462 0.00 0.00 0.00 1.90
890 1124 7.819900 GCCTCCGACTTATTTATGTCTCATTAT 59.180 37.037 0.00 0.00 0.00 1.28
936 1605 6.402983 GGACTCTCGATTTGTTTACGACTAGA 60.403 42.308 0.00 0.00 32.72 2.43
1083 1753 2.607187 GTCCTTGTCGTCACCATAGTG 58.393 52.381 0.00 0.00 46.00 2.74
1284 1967 3.691744 GACGCTGGTGCTCTCCTCG 62.692 68.421 0.00 0.00 36.97 4.63
1376 2059 3.129502 CGTCCTCACCTACGGCGA 61.130 66.667 16.62 0.00 35.51 5.54
1695 4619 3.460103 GTTCAACCTGACCGACTTGTTA 58.540 45.455 0.00 0.00 0.00 2.41
1987 4949 2.353505 CCATCTCTACCATGCATCCTCG 60.354 54.545 0.00 0.00 0.00 4.63
1989 4951 1.683385 TCTCTACCATGCATCCTCGTG 59.317 52.381 0.00 0.00 0.00 4.35
1990 4952 0.752658 TCTACCATGCATCCTCGTGG 59.247 55.000 0.00 0.00 46.15 4.94
1992 4954 1.695114 TACCATGCATCCTCGTGGGG 61.695 60.000 0.00 0.00 45.25 4.96
1994 4956 2.366837 ATGCATCCTCGTGGGGGA 60.367 61.111 3.23 0.00 37.26 4.81
2014 5002 3.153919 GAGGGGTATGAAGTGTTGCAAA 58.846 45.455 0.00 0.00 0.00 3.68
2041 5029 2.237143 TCATCAGGACATTTTCTCCGCT 59.763 45.455 0.00 0.00 32.45 5.52
2277 5266 1.859998 GCTGTGCACGGAACAGAAAAC 60.860 52.381 29.83 4.08 46.55 2.43
2357 5346 1.684049 AGGGACGAGAAGAGCTGGG 60.684 63.158 0.00 0.00 0.00 4.45
2419 5408 0.112995 AGGTGGACTACGGTGGTACA 59.887 55.000 5.33 5.33 0.00 2.90
2485 5474 3.334691 CGGTATGATGTTTGGTGTGTCT 58.665 45.455 0.00 0.00 0.00 3.41
2527 5516 3.065510 CGAGCCTTCTCTATCACTTCGAA 59.934 47.826 0.00 0.00 37.19 3.71
2621 5610 4.755629 GGAAGACTAACCTCTTGTTGGAAC 59.244 45.833 0.00 0.00 37.62 3.62
2739 5728 7.577979 TGTTACATTGGACTTTGTCGAAATAC 58.422 34.615 0.00 0.00 34.32 1.89
2863 5853 2.462889 AGCGCATCAAAAGTTTGTGTG 58.537 42.857 11.47 8.80 39.18 3.82
3003 5999 2.262637 AGTGGACTTCCGGTTAATCCA 58.737 47.619 13.22 13.22 39.43 3.41
3022 6018 3.129113 TCCATTTGATCTCAACCATTGCG 59.871 43.478 0.00 0.00 35.28 4.85
3059 6055 5.171476 CAGATGGAACTGTTTAGTCGTCAT 58.829 41.667 0.00 0.00 35.69 3.06
3174 6172 5.639931 TCAAATCACATGCCATGTTGAATTG 59.360 36.000 20.28 20.28 42.70 2.32
3191 6189 1.314730 TTGCGGAGGAACTGAAAACC 58.685 50.000 0.00 0.00 41.55 3.27
3249 6247 5.818136 TGAGATTTGTCCGATGGAAATTC 57.182 39.130 0.00 0.00 31.38 2.17
3253 6251 4.301072 TTTGTCCGATGGAAATTCTCCT 57.699 40.909 7.78 0.00 45.64 3.69
3273 6271 4.635765 TCCTTTACATGCAGCATAGACAAC 59.364 41.667 7.82 0.00 0.00 3.32
3530 6531 6.015095 TCTCAGTGCTAGAAGAAAACAGATCA 60.015 38.462 0.00 0.00 0.00 2.92
3632 6636 4.495422 ACTACACGTGGAGATTAAAGCAG 58.505 43.478 34.16 4.69 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.876079 GCAGGACAAGAAGAAACGGGAT 60.876 50.000 0.00 0.00 0.00 3.85
42 43 3.950395 GGAAATGAAACAGGAGAGATGGG 59.050 47.826 0.00 0.00 0.00 4.00
96 97 0.033090 TCATGGAGCTAGCGCATCTG 59.967 55.000 20.45 13.12 39.10 2.90
116 117 6.350445 GCTGTGTGGAATTGGAAATTAGTGAT 60.350 38.462 0.00 0.00 0.00 3.06
126 127 1.619654 CCTTGCTGTGTGGAATTGGA 58.380 50.000 0.00 0.00 0.00 3.53
149 150 9.486497 TTGCATGAAGAAACTTTTTATATTGCA 57.514 25.926 0.00 0.00 0.00 4.08
165 166 5.703592 ACGTTTGGTACTTATTGCATGAAGA 59.296 36.000 13.49 0.00 0.00 2.87
166 167 5.938322 ACGTTTGGTACTTATTGCATGAAG 58.062 37.500 0.00 6.57 0.00 3.02
170 171 7.694784 CGAATTAACGTTTGGTACTTATTGCAT 59.305 33.333 5.91 0.00 0.00 3.96
175 176 6.536688 GCACGAATTAACGTTTGGTACTTAT 58.463 36.000 5.91 0.00 44.76 1.73
177 178 4.608890 CGCACGAATTAACGTTTGGTACTT 60.609 41.667 5.91 0.00 44.76 2.24
178 179 3.120923 CGCACGAATTAACGTTTGGTACT 60.121 43.478 5.91 0.00 44.76 2.73
182 183 2.096614 AGACGCACGAATTAACGTTTGG 60.097 45.455 5.91 0.00 44.76 3.28
183 184 3.121126 AGAGACGCACGAATTAACGTTTG 60.121 43.478 5.91 0.00 44.76 2.93
184 185 3.054878 AGAGACGCACGAATTAACGTTT 58.945 40.909 5.91 0.00 44.76 3.60
215 240 0.737019 GCGACGGAAATCGGTACCAA 60.737 55.000 13.54 0.00 42.49 3.67
216 241 1.153784 GCGACGGAAATCGGTACCA 60.154 57.895 13.54 0.00 42.49 3.25
217 242 3.697095 GCGACGGAAATCGGTACC 58.303 61.111 0.16 0.16 42.49 3.34
293 318 2.191400 AGTATAGGGCCGATGCATGAT 58.809 47.619 16.27 0.00 40.13 2.45
310 335 2.939640 GCTGCGGATTTCCAAGGAAGTA 60.940 50.000 0.00 0.00 35.38 2.24
332 360 3.990959 TGTGAATACTACATGGGTGCA 57.009 42.857 0.00 0.00 0.00 4.57
396 427 9.797556 GGCGGAACTAGATAAATTTACAAATTT 57.202 29.630 15.01 15.01 46.85 1.82
397 428 8.410912 GGGCGGAACTAGATAAATTTACAAATT 58.589 33.333 0.00 0.00 40.15 1.82
398 429 7.013942 GGGGCGGAACTAGATAAATTTACAAAT 59.986 37.037 0.00 0.00 0.00 2.32
399 430 6.319405 GGGGCGGAACTAGATAAATTTACAAA 59.681 38.462 0.00 0.00 0.00 2.83
400 431 5.824097 GGGGCGGAACTAGATAAATTTACAA 59.176 40.000 0.00 0.00 0.00 2.41
401 432 5.131475 AGGGGCGGAACTAGATAAATTTACA 59.869 40.000 0.00 0.00 0.00 2.41
414 445 2.154074 AGGTGAAAGGGGCGGAACT 61.154 57.895 0.00 0.00 0.00 3.01
437 468 2.976882 AGTGTACCAGGCTAAGAAACCA 59.023 45.455 0.00 0.00 0.00 3.67
438 469 3.697619 AGTGTACCAGGCTAAGAAACC 57.302 47.619 0.00 0.00 0.00 3.27
447 478 3.249687 CTGGGAAAGTGTACCAGGC 57.750 57.895 3.15 0.00 46.24 4.85
450 481 0.400213 CAGGCTGGGAAAGTGTACCA 59.600 55.000 6.61 0.00 0.00 3.25
451 482 0.960861 GCAGGCTGGGAAAGTGTACC 60.961 60.000 17.64 0.00 0.00 3.34
452 483 0.960861 GGCAGGCTGGGAAAGTGTAC 60.961 60.000 17.64 0.00 0.00 2.90
453 484 1.133809 AGGCAGGCTGGGAAAGTGTA 61.134 55.000 17.64 0.00 0.00 2.90
454 485 2.011617 AAGGCAGGCTGGGAAAGTGT 62.012 55.000 17.64 0.00 0.00 3.55
455 486 1.228675 AAGGCAGGCTGGGAAAGTG 60.229 57.895 17.64 0.00 0.00 3.16
456 487 1.228675 CAAGGCAGGCTGGGAAAGT 60.229 57.895 17.64 0.00 0.00 2.66
457 488 2.643232 GCAAGGCAGGCTGGGAAAG 61.643 63.158 17.64 0.00 0.00 2.62
458 489 2.601367 GCAAGGCAGGCTGGGAAA 60.601 61.111 17.64 0.00 0.00 3.13
459 490 4.684134 GGCAAGGCAGGCTGGGAA 62.684 66.667 17.64 0.00 0.00 3.97
465 496 4.453892 ATGGGAGGCAAGGCAGGC 62.454 66.667 0.00 0.00 0.00 4.85
466 497 2.441532 CATGGGAGGCAAGGCAGG 60.442 66.667 0.00 0.00 0.00 4.85
481 512 6.016276 AGTGCGGAATAAAAACAGAGAAACAT 60.016 34.615 0.00 0.00 0.00 2.71
492 523 4.013728 ACATAGCCAGTGCGGAATAAAAA 58.986 39.130 0.00 0.00 44.33 1.94
502 533 4.178545 ACAAAATCAACATAGCCAGTGC 57.821 40.909 0.00 0.00 37.95 4.40
535 566 7.227314 CAGCTAGACATGTATTGGCAAAGAATA 59.773 37.037 16.86 0.00 34.87 1.75
555 588 6.470235 CCGCATTAAAAAGAAATCACAGCTAG 59.530 38.462 0.00 0.00 0.00 3.42
568 601 7.072030 GTGAGCATCTATACCGCATTAAAAAG 58.928 38.462 0.00 0.00 34.92 2.27
577 610 2.821546 TGTTGTGAGCATCTATACCGC 58.178 47.619 0.00 0.00 34.92 5.68
579 612 8.088365 TGTATACATGTTGTGAGCATCTATACC 58.912 37.037 2.30 0.00 33.59 2.73
598 637 4.912317 TTAGTTGGCCCAGTTGTATACA 57.088 40.909 0.08 0.08 0.00 2.29
603 642 1.497286 TCCTTTAGTTGGCCCAGTTGT 59.503 47.619 0.00 0.00 0.00 3.32
606 645 3.165071 CAAATCCTTTAGTTGGCCCAGT 58.835 45.455 0.00 0.00 29.47 4.00
616 655 1.283905 ACCCGGGTCCAAATCCTTTAG 59.716 52.381 24.16 0.00 0.00 1.85
617 656 1.004979 CACCCGGGTCCAAATCCTTTA 59.995 52.381 27.51 0.00 0.00 1.85
624 663 0.540830 CAAATCCACCCGGGTCCAAA 60.541 55.000 27.51 9.94 38.11 3.28
628 667 2.563297 GAACAAATCCACCCGGGTC 58.437 57.895 27.51 5.05 38.11 4.46
674 713 6.369890 CACAGCAAGACATATGAACTAAGTGT 59.630 38.462 10.38 9.00 0.00 3.55
680 719 6.127814 CCAAATCACAGCAAGACATATGAACT 60.128 38.462 10.38 5.58 0.00 3.01
686 725 4.264253 CTCCCAAATCACAGCAAGACATA 58.736 43.478 0.00 0.00 0.00 2.29
733 772 4.220821 TCTGAAGACTTGCCGATTTCTACT 59.779 41.667 0.00 0.00 0.00 2.57
742 820 6.090493 CACATATCATATCTGAAGACTTGCCG 59.910 42.308 0.00 0.00 34.37 5.69
754 832 5.991933 AGTCGGAAGCACATATCATATCT 57.008 39.130 0.00 0.00 0.00 1.98
767 845 9.567848 TCATTTTGAATTAAATAAGTCGGAAGC 57.432 29.630 0.00 0.00 33.37 3.86
784 862 7.548427 TGCTCATCAAACTTGTTTCATTTTGAA 59.452 29.630 0.00 0.00 40.40 2.69
799 877 2.618241 TGTGTTCCTGTGCTCATCAAAC 59.382 45.455 0.00 0.00 0.00 2.93
829 907 3.500448 TTGTTTCATAGTGGCTCACCA 57.500 42.857 2.18 0.00 46.51 4.17
835 913 5.527951 TCATTGTGTTTGTTTCATAGTGGC 58.472 37.500 0.00 0.00 0.00 5.01
836 914 9.292846 CATATCATTGTGTTTGTTTCATAGTGG 57.707 33.333 0.00 0.00 0.00 4.00
838 916 9.844790 CACATATCATTGTGTTTGTTTCATAGT 57.155 29.630 0.00 0.00 41.65 2.12
844 922 6.100404 AGGCACATATCATTGTGTTTGTTT 57.900 33.333 6.46 0.00 46.93 2.83
845 923 5.336690 GGAGGCACATATCATTGTGTTTGTT 60.337 40.000 6.46 0.00 46.93 2.83
846 924 4.158394 GGAGGCACATATCATTGTGTTTGT 59.842 41.667 6.46 0.00 46.93 2.83
847 925 4.675510 GGAGGCACATATCATTGTGTTTG 58.324 43.478 6.46 0.00 46.93 2.93
888 1122 1.804151 GGAGTGCAAGCGACACAAATA 59.196 47.619 9.04 0.00 40.59 1.40
889 1123 0.593128 GGAGTGCAAGCGACACAAAT 59.407 50.000 9.04 0.00 40.59 2.32
890 1124 0.746204 TGGAGTGCAAGCGACACAAA 60.746 50.000 9.04 0.00 40.59 2.83
981 1651 4.825634 TCCATCGATCGTAGGTGTAAAGAT 59.174 41.667 21.71 1.02 0.00 2.40
1105 1775 4.459089 GCCGGCAGAGTCTGGTCC 62.459 72.222 24.80 13.64 34.92 4.46
1284 1967 3.011517 TCCCTTGCTGCCTCCTCC 61.012 66.667 0.00 0.00 0.00 4.30
1293 1976 0.622665 CCTTCATCACCTCCCTTGCT 59.377 55.000 0.00 0.00 0.00 3.91
1987 4949 0.623617 ACTTCATACCCCTCCCCCAC 60.624 60.000 0.00 0.00 0.00 4.61
1989 4951 0.623617 ACACTTCATACCCCTCCCCC 60.624 60.000 0.00 0.00 0.00 5.40
1990 4952 1.064685 CAACACTTCATACCCCTCCCC 60.065 57.143 0.00 0.00 0.00 4.81
1992 4954 1.004277 TGCAACACTTCATACCCCTCC 59.996 52.381 0.00 0.00 0.00 4.30
1994 4956 2.969821 TTGCAACACTTCATACCCCT 57.030 45.000 0.00 0.00 0.00 4.79
1997 4980 6.478344 TGACAAAATTTGCAACACTTCATACC 59.522 34.615 5.52 0.00 0.00 2.73
2041 5029 2.761195 CGCCGTCGTCTCTGATCCA 61.761 63.158 0.00 0.00 0.00 3.41
2277 5266 0.930310 CACGTCGTAGCCCATGATTG 59.070 55.000 0.00 0.00 0.00 2.67
2357 5346 4.267013 GAATTCGCTCGCGTCGGC 62.267 66.667 19.37 14.93 40.74 5.54
2371 5360 0.108138 CGAACCTCTCGGGCTTGAAT 60.108 55.000 0.00 0.00 44.20 2.57
2527 5516 2.851102 CCATCGGGGAGCCTCCAT 60.851 66.667 13.90 0.00 38.64 3.41
2621 5610 5.767816 AACTAAGGCACAAAAACAGTAGG 57.232 39.130 0.00 0.00 0.00 3.18
2752 5741 9.897744 ACACTCAATGAGTTAACACAAATTATG 57.102 29.630 13.99 8.57 41.37 1.90
2863 5853 9.764363 TTGTATCTCAAATGAGTCCATATACAC 57.236 33.333 15.73 0.00 42.60 2.90
3003 5999 3.758023 TGACGCAATGGTTGAGATCAAAT 59.242 39.130 0.00 0.00 37.63 2.32
3022 6018 3.420893 TCCATCTGGTTGATTGGTTGAC 58.579 45.455 0.00 0.00 36.34 3.18
3059 6055 8.375506 AGTTTTGAATAGTTGAGTCATAGGACA 58.624 33.333 10.58 0.00 46.80 4.02
3096 6092 1.549203 TCCTGCAAATCAAAGAGGCC 58.451 50.000 0.00 0.00 0.00 5.19
3174 6172 0.536460 TGGGTTTTCAGTTCCTCCGC 60.536 55.000 0.00 0.00 0.00 5.54
3249 6247 4.445453 TGTCTATGCTGCATGTAAAGGAG 58.555 43.478 24.59 12.10 0.00 3.69
3253 6251 4.395854 CCTGTTGTCTATGCTGCATGTAAA 59.604 41.667 24.59 10.82 0.00 2.01
3273 6271 9.877178 AGATTGTAACTATAGAAACTTGTCCTG 57.123 33.333 6.78 0.00 0.00 3.86
3362 6361 8.992349 TGAGATATCTATCCAGGTTTCTTTGAA 58.008 33.333 4.89 0.00 33.17 2.69
3407 6406 2.824689 TTTGATTATCAGGCCAGCCA 57.175 45.000 12.03 0.00 38.92 4.75
3530 6531 3.504906 CCAATCATTCACTCTGTTGCACT 59.495 43.478 0.00 0.00 0.00 4.40
3614 6618 2.416547 CCACTGCTTTAATCTCCACGTG 59.583 50.000 9.08 9.08 0.00 4.49


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

AutoCloner maintained by Alex Coulton.