Multiple sequence alignment - TraesCS5A01G115700

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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 TraesCS5A01G115700 chr5A 100.000 2772 0 0 1 2772 234460592 234457821 0.000000e+00 5120
1 TraesCS5A01G115700 chr5A 81.355 1550 233 29 871 2401 524233555 524232043 0.000000e+00 1210
2 TraesCS5A01G115700 chr5A 90.575 870 77 5 1 867 234508544 234507677 0.000000e+00 1147
3 TraesCS5A01G115700 chr3A 90.596 1425 92 18 1022 2407 608111832 608110411 0.000000e+00 1851
4 TraesCS5A01G115700 chr3A 93.607 219 13 1 2555 2772 608110107 608109889 2.660000e-85 326
5 TraesCS5A01G115700 chr3A 92.517 147 11 0 2407 2553 608110299 608110153 7.780000e-51 211
6 TraesCS5A01G115700 chr3D 89.245 874 85 9 1 869 237529314 237530183 0.000000e+00 1085
7 TraesCS5A01G115700 chr3D 88.863 871 88 8 1 866 237531551 237532417 0.000000e+00 1062
8 TraesCS5A01G115700 chrUn 89.130 874 85 10 1 869 106708292 106709160 0.000000e+00 1079
9 TraesCS5A01G115700 chrUn 88.902 874 87 10 1 869 106713224 106714092 0.000000e+00 1068
10 TraesCS5A01G115700 chrUn 88.761 872 93 5 1 869 106445839 106446708 0.000000e+00 1062
11 TraesCS5A01G115700 chr5D 89.118 873 88 7 1 869 186598438 186599307 0.000000e+00 1079
12 TraesCS5A01G115700 chr5D 88.889 873 90 7 1 869 186597871 186598740 0.000000e+00 1068
13 TraesCS5A01G115700 chr5D 88.940 868 88 8 1 864 187392958 187393821 0.000000e+00 1064
14 TraesCS5A01G115700 chr2A 73.782 965 207 34 872 1805 57923724 57922775 3.420000e-89 339


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 TraesCS5A01G115700 chr5A 234457821 234460592 2771 True 5120.0 5120 100.0000 1 2772 1 chr5A.!!$R1 2771
1 TraesCS5A01G115700 chr5A 524232043 524233555 1512 True 1210.0 1210 81.3550 871 2401 1 chr5A.!!$R3 1530
2 TraesCS5A01G115700 chr5A 234507677 234508544 867 True 1147.0 1147 90.5750 1 867 1 chr5A.!!$R2 866
3 TraesCS5A01G115700 chr3A 608109889 608111832 1943 True 796.0 1851 92.2400 1022 2772 3 chr3A.!!$R1 1750
4 TraesCS5A01G115700 chr3D 237529314 237532417 3103 False 1073.5 1085 89.0540 1 869 2 chr3D.!!$F1 868
5 TraesCS5A01G115700 chrUn 106708292 106709160 868 False 1079.0 1079 89.1300 1 869 1 chrUn.!!$F2 868
6 TraesCS5A01G115700 chrUn 106713224 106714092 868 False 1068.0 1068 88.9020 1 869 1 chrUn.!!$F3 868
7 TraesCS5A01G115700 chrUn 106445839 106446708 869 False 1062.0 1062 88.7610 1 869 1 chrUn.!!$F1 868
8 TraesCS5A01G115700 chr5D 186597871 186599307 1436 False 1073.5 1079 89.0035 1 869 2 chr5D.!!$F2 868
9 TraesCS5A01G115700 chr5D 187392958 187393821 863 False 1064.0 1064 88.9400 1 864 1 chr5D.!!$F1 863
10 TraesCS5A01G115700 chr2A 57922775 57923724 949 True 339.0 339 73.7820 872 1805 1 chr2A.!!$R1 933

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
878 3686 0.179189 CCAGCGGCAAGTCGAAAATC 60.179 55.0 1.45 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 5741 0.036388 ATCACAACTTCCGGCGTCAT 60.036 50.0 6.01 0.0 0.0 3.06 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
76 1211 6.296662 CCCTCCTATTATTGGCTATCACACAT 60.297 42.308 0.00 0.00 0.00 3.21
80 1215 8.314021 TCCTATTATTGGCTATCACACATGTAG 58.686 37.037 0.00 0.00 0.00 2.74
101 1236 3.943479 TACGGCATGCCACACGGAC 62.943 63.158 34.93 6.89 35.37 4.79
296 3102 5.384063 TCAGAAACTTGTGTGAAAAGCAA 57.616 34.783 0.00 0.00 0.00 3.91
353 3160 4.706616 AGGTCCTCCTTAGGGTCAAATTA 58.293 43.478 0.00 0.00 42.12 1.40
388 3195 1.151668 CTCTTGCACAAGACGGAAGG 58.848 55.000 8.99 0.00 42.06 3.46
392 3199 2.380084 TGCACAAGACGGAAGGTATC 57.620 50.000 0.00 0.00 0.00 2.24
411 3218 5.010213 GGTATCTTCTAGATTCCAACGCTCT 59.990 44.000 7.28 0.00 40.60 4.09
527 3334 6.772716 AGTCCTTGAAAGCACTTCATTTTCTA 59.227 34.615 2.46 0.00 43.64 2.10
568 3375 3.254657 CCGCTCCAAAATTTTGTGTCCTA 59.745 43.478 25.25 6.65 36.45 2.94
643 3450 6.296662 CCCTCCTATTATTGGCTATCACACAT 60.297 42.308 0.00 0.00 0.00 3.21
652 3459 5.270893 TGGCTATCACACATGTACGTTAT 57.729 39.130 0.00 0.00 0.00 1.89
692 3499 9.088987 TCAAAAACAAGGAGAATAAGGCTTATT 57.911 29.630 27.85 27.85 38.49 1.40
707 3514 5.243426 GGCTTATTGTCGCCTTATTTTCA 57.757 39.130 0.00 0.00 42.98 2.69
733 3540 6.500049 TGAATTTACAACCAAATGGGATTCCT 59.500 34.615 4.17 0.00 41.15 3.36
759 3566 3.473625 TCATAGAGCATGTGCAGAATGG 58.526 45.455 7.83 0.00 45.16 3.16
859 3667 6.859017 TGGGTTCAGAAACTTGTCTAAAAAC 58.141 36.000 0.00 0.00 35.61 2.43
869 3677 1.606668 TGTCTAAAAACCAGCGGCAAG 59.393 47.619 1.45 0.00 0.00 4.01
878 3686 0.179189 CCAGCGGCAAGTCGAAAATC 60.179 55.000 1.45 0.00 0.00 2.17
881 3689 0.521735 GCGGCAAGTCGAAAATCCTT 59.478 50.000 0.00 0.00 0.00 3.36
888 3696 5.066505 GGCAAGTCGAAAATCCTTATGTGAT 59.933 40.000 0.00 0.00 0.00 3.06
903 3711 2.343426 TGATCGCGAGCTCACAGGT 61.343 57.895 26.10 0.00 30.21 4.00
908 3716 2.948720 GCGAGCTCACAGGTTCCCT 61.949 63.158 15.40 0.00 0.00 4.20
913 3721 3.567397 GAGCTCACAGGTTCCCTCTATA 58.433 50.000 9.40 0.00 0.00 1.31
928 3736 7.328404 TCCCTCTATATGTGCCATTTATTCA 57.672 36.000 0.00 0.00 0.00 2.57
932 3740 8.321353 CCTCTATATGTGCCATTTATTCACCTA 58.679 37.037 0.00 0.00 0.00 3.08
934 3742 6.824305 ATATGTGCCATTTATTCACCTAGC 57.176 37.500 0.00 0.00 0.00 3.42
940 3748 5.011635 TGCCATTTATTCACCTAGCGATCTA 59.988 40.000 0.00 0.00 0.00 1.98
941 3749 5.932303 GCCATTTATTCACCTAGCGATCTAA 59.068 40.000 0.00 0.00 0.00 2.10
960 3768 3.931907 AAGCTGCAATGGGTATAGTGA 57.068 42.857 1.02 0.00 0.00 3.41
962 3770 3.748083 AGCTGCAATGGGTATAGTGATG 58.252 45.455 1.02 0.00 0.00 3.07
968 3776 5.074377 TGCAATGGGTATAGTGATGGGTATT 59.926 40.000 0.00 0.00 0.00 1.89
969 3777 5.648092 GCAATGGGTATAGTGATGGGTATTC 59.352 44.000 0.00 0.00 0.00 1.75
970 3778 6.180472 CAATGGGTATAGTGATGGGTATTCC 58.820 44.000 0.00 0.00 0.00 3.01
986 3794 8.018537 TGGGTATTCCTCCACATATATTATCG 57.981 38.462 0.00 0.00 36.20 2.92
998 3806 7.041780 CCACATATATTATCGCTCCAAATAGGC 60.042 40.741 0.00 0.00 37.29 3.93
999 3807 6.992715 ACATATATTATCGCTCCAAATAGGCC 59.007 38.462 0.00 0.00 37.29 5.19
1025 3833 1.079612 ACTACGCAGTTAACCCCGC 60.080 57.895 13.46 8.38 37.78 6.13
1343 4164 2.579860 AGGATCTTCACCTGGATTGCTT 59.420 45.455 0.00 0.00 36.30 3.91
1347 4168 0.482446 TTCACCTGGATTGCTTGGGT 59.518 50.000 0.00 0.00 0.00 4.51
1384 4205 6.149308 CAGGCATTCATTTCTACAAGTGTGTA 59.851 38.462 0.00 0.00 39.30 2.90
1418 4239 4.777366 TGAGTACAATCCATTCTCCAGTCA 59.223 41.667 0.00 0.00 0.00 3.41
1458 4279 1.878102 GCCAATCGGATCGGCTAACAT 60.878 52.381 12.70 0.00 42.78 2.71
1470 4291 6.308282 GGATCGGCTAACATATCGAGTTTTAG 59.692 42.308 0.00 0.00 35.07 1.85
1474 4295 6.914215 CGGCTAACATATCGAGTTTTAGTGTA 59.086 38.462 0.00 0.00 0.00 2.90
1482 4303 5.505165 TCGAGTTTTAGTGTACGATTTGC 57.495 39.130 0.00 0.00 0.00 3.68
1489 4310 7.642586 AGTTTTAGTGTACGATTTGCTTTGTTC 59.357 33.333 0.00 0.00 0.00 3.18
1504 4351 4.500375 GCTTTGTTCTTGCAGTCTGGAATT 60.500 41.667 7.29 0.00 0.00 2.17
1529 4376 3.474798 ACTACATGAGGACCAAGGAGA 57.525 47.619 0.00 0.00 29.34 3.71
1563 4410 5.420104 CAGAGTTAAGCTTTCATTTGGGGAT 59.580 40.000 3.20 0.00 0.00 3.85
1565 4412 5.332743 AGTTAAGCTTTCATTTGGGGATGA 58.667 37.500 3.20 0.00 34.37 2.92
1566 4413 5.779771 AGTTAAGCTTTCATTTGGGGATGAA 59.220 36.000 3.20 0.00 42.58 2.57
1576 4423 3.593442 TTGGGGATGAAACAACAGACT 57.407 42.857 0.00 0.00 0.00 3.24
1577 4424 4.715534 TTGGGGATGAAACAACAGACTA 57.284 40.909 0.00 0.00 0.00 2.59
1692 4551 3.092301 GGGTTAATCAAGCAGGCTCTTT 58.908 45.455 0.00 0.00 33.68 2.52
1716 4575 4.430423 CGCGCTCCGTGTTCTTGC 62.430 66.667 5.56 0.00 32.40 4.01
1759 4619 6.126409 ACTCTTTGTGGGTGTCTTATTTTCA 58.874 36.000 0.00 0.00 0.00 2.69
1775 4635 0.597568 TTCATGGCGTTGCTGAAAGG 59.402 50.000 0.00 0.00 0.00 3.11
1843 4703 8.884323 TGCCAGACTAGAAATAATGATTAGGAT 58.116 33.333 0.00 0.00 0.00 3.24
1845 4705 9.664332 CCAGACTAGAAATAATGATTAGGATGG 57.336 37.037 0.00 0.00 0.00 3.51
1879 4739 1.956297 TTGTAACCCAGTCGTTGGTG 58.044 50.000 7.71 3.04 46.25 4.17
1889 4749 3.368843 CCAGTCGTTGGTGATCAGAATCT 60.369 47.826 0.00 0.00 42.41 2.40
1911 4771 3.007074 TGGTAGTGCGTCCTTTGTATTGA 59.993 43.478 0.00 0.00 0.00 2.57
1932 4792 6.126863 TGAAGTGGTTGGTAATGAGAATCT 57.873 37.500 0.00 0.00 34.92 2.40
1939 4799 5.189180 GTTGGTAATGAGAATCTGGAAGCT 58.811 41.667 0.00 0.00 34.92 3.74
1963 4823 2.514803 ACTTTGTATCCCAGTGGTTGC 58.485 47.619 8.74 0.00 0.00 4.17
1972 4832 2.642311 TCCCAGTGGTTGCTAATGAGAA 59.358 45.455 8.74 0.00 0.00 2.87
1985 4846 6.472016 TGCTAATGAGAATTGACTGTGGTTA 58.528 36.000 0.00 0.00 0.00 2.85
1990 4851 5.875224 TGAGAATTGACTGTGGTTATTCCA 58.125 37.500 0.00 0.00 45.01 3.53
2015 4876 9.261180 CATAAGACCGTTGTTAAGATATGTGAT 57.739 33.333 0.00 0.00 0.00 3.06
2016 4877 7.772332 AAGACCGTTGTTAAGATATGTGATC 57.228 36.000 0.00 0.00 0.00 2.92
2019 4880 6.873997 ACCGTTGTTAAGATATGTGATCTGA 58.126 36.000 0.00 0.00 0.00 3.27
2021 4882 7.277981 ACCGTTGTTAAGATATGTGATCTGAAC 59.722 37.037 7.57 7.57 39.09 3.18
2022 4883 7.277760 CCGTTGTTAAGATATGTGATCTGAACA 59.722 37.037 11.79 11.79 43.93 3.18
2043 4904 8.149647 TGAACAATCAGCAATCAATTAAGGTTT 58.850 29.630 0.00 0.00 0.00 3.27
2189 5051 4.320456 CCGGCAGGTGCTGTCAGT 62.320 66.667 9.88 0.00 45.66 3.41
2231 5093 1.696097 AATGCTAGCACCTACCCCGG 61.696 60.000 22.07 0.00 0.00 5.73
2301 5163 0.035152 CAACAGCCCTCATACCAGCA 60.035 55.000 0.00 0.00 0.00 4.41
2395 5257 2.851102 CCAGCGGGGGAGATCCAT 60.851 66.667 0.47 0.00 37.91 3.41
2427 5401 3.772572 TCCCCAGTCGATCTGTAATTTCA 59.227 43.478 12.10 0.00 42.19 2.69
2435 5409 3.303329 CGATCTGTAATTTCATGGTGCCG 60.303 47.826 0.00 0.00 0.00 5.69
2441 5415 0.678395 ATTTCATGGTGCCGCACAAA 59.322 45.000 24.43 15.88 35.86 2.83
2493 5467 4.345859 AGTTATTCGAACCACCAGTCAA 57.654 40.909 0.00 0.00 0.00 3.18
2499 5473 4.561735 TCGAACCACCAGTCAAAATTTC 57.438 40.909 0.00 0.00 0.00 2.17
2502 5476 2.661718 ACCACCAGTCAAAATTTCGGT 58.338 42.857 0.00 0.00 0.00 4.69
2511 5485 7.090173 CCAGTCAAAATTTCGGTTGTAATCAT 58.910 34.615 0.00 0.00 0.00 2.45
2546 5520 7.191551 CGCATGAATTAATCAAGTTCAGTCAT 58.808 34.615 0.00 0.00 42.54 3.06
2553 5527 9.965902 AATTAATCAAGTTCAGTCATACTCCTT 57.034 29.630 0.00 0.00 0.00 3.36
2560 5578 7.784470 AGTTCAGTCATACTCCTTTCTAGTT 57.216 36.000 0.00 0.00 0.00 2.24
2610 5629 1.133699 CATGAGGGGCCACACATGTAT 60.134 52.381 30.82 3.79 36.42 2.29
2615 5634 3.838317 GAGGGGCCACACATGTATAGATA 59.162 47.826 8.31 0.00 0.00 1.98
2677 5696 9.862371 CTATCATATTCTAGCCTACATTCGTTT 57.138 33.333 0.00 0.00 0.00 3.60
2684 5703 3.532542 AGCCTACATTCGTTTAAGCTCC 58.467 45.455 0.00 0.00 0.00 4.70
2685 5704 2.284417 GCCTACATTCGTTTAAGCTCCG 59.716 50.000 0.00 0.00 0.00 4.63
2689 5708 2.735134 ACATTCGTTTAAGCTCCGTCAC 59.265 45.455 0.00 0.00 0.00 3.67
2704 5723 4.915704 TCCGTCACAATCAAAGTTTTCAC 58.084 39.130 0.00 0.00 0.00 3.18
2722 5741 7.888021 AGTTTTCACATTGGTAGGAATCATGTA 59.112 33.333 0.00 0.00 0.00 2.29
2751 5770 2.988684 GTTGTGATGGGGCCGCAA 60.989 61.111 27.86 8.56 0.00 4.85
2767 5786 1.751927 CAACCTCTGGGGATGCAGC 60.752 63.158 0.00 0.00 38.76 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.718757 GCATTCCTGGCATCGGTCAC 61.719 60.000 0.00 0.00 0.00 3.67
76 1211 0.391927 GTGGCATGCCGTAACCTACA 60.392 55.000 30.87 7.94 39.42 2.74
80 1215 2.874751 GTGTGGCATGCCGTAACC 59.125 61.111 30.87 16.17 39.42 2.85
101 1236 7.040409 ACTGTAAGCCTTATTCTCCTTGTTTTG 60.040 37.037 0.00 0.00 37.60 2.44
196 1331 2.158726 AGTCCGCCTGGTAAGAAAAACA 60.159 45.455 0.00 0.00 36.30 2.83
201 2439 2.835764 ACATTAGTCCGCCTGGTAAGAA 59.164 45.455 0.00 0.00 36.30 2.52
262 3068 5.047802 CACAAGTTTCTGAACCCATTAGCAT 60.048 40.000 0.00 0.00 36.39 3.79
296 3102 6.377327 AAGTCAAAGAACATCATTTGTCGT 57.623 33.333 0.00 0.00 37.68 4.34
348 3155 3.508952 TCCTGGAGGACCCTCTAATTT 57.491 47.619 15.03 0.00 42.38 1.82
372 3179 2.301870 AGATACCTTCCGTCTTGTGCAA 59.698 45.455 0.00 0.00 0.00 4.08
388 3195 6.079424 AGAGCGTTGGAATCTAGAAGATAC 57.921 41.667 0.00 0.00 32.89 2.24
392 3199 4.932200 ACAAAGAGCGTTGGAATCTAGAAG 59.068 41.667 0.00 0.00 32.50 2.85
411 3218 6.700960 CCACAAGTAATCAAAATGCTCACAAA 59.299 34.615 0.00 0.00 0.00 2.83
427 3234 1.868469 CGTTTCGGACCCACAAGTAA 58.132 50.000 0.00 0.00 0.00 2.24
458 3265 7.280428 TGTTCACTAAAACGGTCATAAGTTTGA 59.720 33.333 0.00 0.00 40.07 2.69
463 3270 5.389098 CGGTGTTCACTAAAACGGTCATAAG 60.389 44.000 2.98 0.00 31.58 1.73
550 3357 7.040062 CCACTATGTAGGACACAAAATTTTGGA 60.040 37.037 29.37 9.11 41.55 3.53
643 3450 3.863407 TGGCATGCCATAACGTACA 57.137 47.368 35.59 9.66 41.89 2.90
652 3459 1.046204 TTTTGACATGTGGCATGCCA 58.954 45.000 35.59 35.59 45.02 4.92
664 3471 5.833131 AGCCTTATTCTCCTTGTTTTTGACA 59.167 36.000 0.00 0.00 36.19 3.58
666 3473 6.976934 AAGCCTTATTCTCCTTGTTTTTGA 57.023 33.333 0.00 0.00 0.00 2.69
692 3499 7.821652 TGTAAATTCATGAAAATAAGGCGACA 58.178 30.769 13.09 4.37 0.00 4.35
707 3514 7.182568 AGGAATCCCATTTGGTTGTAAATTCAT 59.817 33.333 0.00 0.00 34.77 2.57
733 3540 1.688197 TGCACATGCTCTATGATCCGA 59.312 47.619 5.31 0.00 42.66 4.55
759 3566 2.349155 CGCTTGGTAAGGACAAACGTTC 60.349 50.000 0.00 0.00 33.99 3.95
859 3667 0.179189 GATTTTCGACTTGCCGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
869 3677 4.606232 CGCGATCACATAAGGATTTTCGAC 60.606 45.833 0.00 0.00 0.00 4.20
878 3686 1.269257 TGAGCTCGCGATCACATAAGG 60.269 52.381 10.36 0.00 29.10 2.69
888 3696 2.258591 GAACCTGTGAGCTCGCGA 59.741 61.111 21.66 9.26 0.00 5.87
928 3736 1.403814 TGCAGCTTAGATCGCTAGGT 58.596 50.000 0.00 0.00 35.63 3.08
932 3740 1.590932 CCATTGCAGCTTAGATCGCT 58.409 50.000 0.00 0.00 38.49 4.93
934 3742 1.959042 ACCCATTGCAGCTTAGATCG 58.041 50.000 0.00 0.00 0.00 3.69
940 3748 3.931907 TCACTATACCCATTGCAGCTT 57.068 42.857 0.00 0.00 0.00 3.74
941 3749 3.497405 CCATCACTATACCCATTGCAGCT 60.497 47.826 0.00 0.00 0.00 4.24
960 3768 8.651389 CGATAATATATGTGGAGGAATACCCAT 58.349 37.037 0.00 0.00 37.41 4.00
962 3770 6.929606 GCGATAATATATGTGGAGGAATACCC 59.070 42.308 0.00 0.00 36.73 3.69
968 3776 5.269189 TGGAGCGATAATATATGTGGAGGA 58.731 41.667 0.00 0.00 0.00 3.71
969 3777 5.598416 TGGAGCGATAATATATGTGGAGG 57.402 43.478 0.00 0.00 0.00 4.30
970 3778 9.254133 CTATTTGGAGCGATAATATATGTGGAG 57.746 37.037 0.00 0.00 0.00 3.86
985 3793 1.799258 GCCATGGCCTATTTGGAGCG 61.799 60.000 27.24 0.00 38.35 5.03
986 3794 2.044452 GCCATGGCCTATTTGGAGC 58.956 57.895 27.24 0.00 38.35 4.70
998 3806 2.514592 CTGCGTAGTGGGCCATGG 60.515 66.667 10.70 7.63 0.00 3.66
999 3807 0.107897 TAACTGCGTAGTGGGCCATG 60.108 55.000 10.70 1.05 37.19 3.66
1012 3820 2.033602 ACTGGCGGGGTTAACTGC 59.966 61.111 5.42 7.44 42.02 4.40
1016 3824 1.373435 CACTGACTGGCGGGGTTAA 59.627 57.895 0.00 0.00 0.00 2.01
1025 3833 4.704833 CGCCACCCCACTGACTGG 62.705 72.222 0.00 0.00 40.26 4.00
1101 3909 5.221880 GTGCTGTCATAAATGAGCAAAACA 58.778 37.500 8.06 0.00 38.94 2.83
1149 3958 2.930562 AGTGGGAGGAGGTGTGCC 60.931 66.667 0.00 0.00 0.00 5.01
1210 4031 2.771943 TGGCCCTAGTCTGGATTAGTTG 59.228 50.000 0.00 0.00 0.00 3.16
1267 4088 1.375908 TTGCTCGAAGCCGCTTGAT 60.376 52.632 11.20 0.00 41.51 2.57
1343 4164 3.588511 TGCATTCTGCCCCACCCA 61.589 61.111 0.00 0.00 44.23 4.51
1347 4168 2.808761 AATGCCTGCATTCTGCCCCA 62.809 55.000 11.43 0.00 44.23 4.96
1368 4189 8.567948 CATCCTTGTTTACACACTTGTAGAAAT 58.432 33.333 0.00 0.00 39.44 2.17
1384 4205 5.630121 TGGATTGTACTCACATCCTTGTTT 58.370 37.500 12.35 0.00 35.28 2.83
1418 4239 4.159693 TGGCACACGACTACTTAGATGAAT 59.840 41.667 0.00 0.00 0.00 2.57
1458 4279 7.031372 AGCAAATCGTACACTAAAACTCGATA 58.969 34.615 0.00 0.00 37.11 2.92
1470 4291 4.146443 GCAAGAACAAAGCAAATCGTACAC 59.854 41.667 0.00 0.00 0.00 2.90
1474 4295 3.181487 ACTGCAAGAACAAAGCAAATCGT 60.181 39.130 0.00 0.00 37.89 3.73
1482 4303 4.843220 ATTCCAGACTGCAAGAACAAAG 57.157 40.909 0.00 0.00 37.43 2.77
1489 4310 3.374220 TTGCAAATTCCAGACTGCAAG 57.626 42.857 8.51 0.00 46.76 4.01
1504 4351 3.411446 CTTGGTCCTCATGTAGTTGCAA 58.589 45.455 0.00 0.00 0.00 4.08
1563 4410 4.021807 TGCCGTATCTAGTCTGTTGTTTCA 60.022 41.667 0.00 0.00 0.00 2.69
1565 4412 4.495422 CTGCCGTATCTAGTCTGTTGTTT 58.505 43.478 0.00 0.00 0.00 2.83
1566 4413 3.676324 GCTGCCGTATCTAGTCTGTTGTT 60.676 47.826 0.00 0.00 0.00 2.83
1613 4460 0.250424 TCGACCACACGGACTCTGTA 60.250 55.000 0.00 0.00 35.59 2.74
1716 4575 1.331756 GTATGGCAGCATCCAAGAACG 59.668 52.381 0.93 0.00 39.96 3.95
1759 4619 0.250901 ACTCCTTTCAGCAACGCCAT 60.251 50.000 0.00 0.00 0.00 4.40
1843 4703 3.080300 ACAAAAGACACACTTCACCCA 57.920 42.857 0.00 0.00 37.93 4.51
1845 4705 4.201980 GGGTTACAAAAGACACACTTCACC 60.202 45.833 0.00 0.00 37.93 4.02
1879 4739 3.376540 GACGCACTACCAGATTCTGATC 58.623 50.000 15.36 0.00 32.44 2.92
1889 4749 3.007074 TCAATACAAAGGACGCACTACCA 59.993 43.478 0.00 0.00 0.00 3.25
1911 4771 5.014123 TCCAGATTCTCATTACCAACCACTT 59.986 40.000 0.00 0.00 0.00 3.16
1932 4792 4.042311 TGGGATACAAAGTACAAGCTTCCA 59.958 41.667 0.00 0.00 39.74 3.53
1939 4799 4.986054 ACCACTGGGATACAAAGTACAA 57.014 40.909 0.00 0.00 38.05 2.41
1963 4823 8.616076 GGAATAACCACAGTCAATTCTCATTAG 58.384 37.037 0.00 0.00 38.79 1.73
1985 4846 9.273016 CATATCTTAACAACGGTCTTATGGAAT 57.727 33.333 0.00 0.00 0.00 3.01
1990 4851 9.477484 GATCACATATCTTAACAACGGTCTTAT 57.523 33.333 0.00 0.00 0.00 1.73
2019 4880 9.643693 CTAAACCTTAATTGATTGCTGATTGTT 57.356 29.630 0.00 0.00 0.00 2.83
2039 4900 7.650504 GTCGGGGCAAAAATAAATATCTAAACC 59.349 37.037 0.00 0.00 0.00 3.27
2043 4904 6.366340 TGGTCGGGGCAAAAATAAATATCTA 58.634 36.000 0.00 0.00 0.00 1.98
2173 5035 3.046087 CACTGACAGCACCTGCCG 61.046 66.667 1.25 0.00 43.38 5.69
2180 5042 1.302752 GGTCATGCCACTGACAGCA 60.303 57.895 1.25 0.00 45.95 4.41
2210 5072 1.680338 GGGGTAGGTGCTAGCATTTG 58.320 55.000 22.51 0.00 36.32 2.32
2215 5077 2.762875 ACCGGGGTAGGTGCTAGC 60.763 66.667 8.10 8.10 44.07 3.42
2301 5163 2.031163 GGGCAAGCGAGACACAGT 59.969 61.111 0.00 0.00 0.00 3.55
2360 5222 1.078988 GAATGGTTACGCCGTGGGA 60.079 57.895 0.00 0.00 41.21 4.37
2395 5257 5.715279 CAGATCGACTGGGGAATAATACCTA 59.285 44.000 7.01 0.00 42.39 3.08
2427 5401 0.392336 AAACATTTGTGCGGCACCAT 59.608 45.000 28.57 18.09 32.73 3.55
2435 5409 6.625740 AGGATACAGCATACAAACATTTGTGC 60.626 38.462 18.13 14.00 45.70 4.57
2441 5415 6.000219 GGATCAGGATACAGCATACAAACAT 59.000 40.000 0.00 0.00 41.41 2.71
2449 5423 1.051008 TGCGGATCAGGATACAGCAT 58.949 50.000 6.84 0.00 41.41 3.79
2451 5425 1.270518 ACATGCGGATCAGGATACAGC 60.271 52.381 0.00 0.00 41.41 4.40
2452 5426 2.827800 ACATGCGGATCAGGATACAG 57.172 50.000 0.00 0.00 41.41 2.74
2493 5467 6.515272 AGAGCATGATTACAACCGAAATTT 57.485 33.333 0.00 0.00 0.00 1.82
2499 5473 3.063997 GGTGAAGAGCATGATTACAACCG 59.936 47.826 0.00 0.00 0.00 4.44
2502 5476 2.677836 GCGGTGAAGAGCATGATTACAA 59.322 45.455 0.00 0.00 0.00 2.41
2546 5520 7.470702 GCTGAGCATGATAACTAGAAAGGAGTA 60.471 40.741 0.00 0.00 0.00 2.59
2553 5527 4.953667 CTGGCTGAGCATGATAACTAGAA 58.046 43.478 6.82 0.00 0.00 2.10
2641 5660 6.323482 GGCTAGAATATGATAGATGGAGAGCA 59.677 42.308 0.00 0.00 0.00 4.26
2644 5663 8.560903 TGTAGGCTAGAATATGATAGATGGAGA 58.439 37.037 0.00 0.00 0.00 3.71
2677 5696 4.002906 ACTTTGATTGTGACGGAGCTTA 57.997 40.909 0.00 0.00 0.00 3.09
2684 5703 6.291743 CCAATGTGAAAACTTTGATTGTGACG 60.292 38.462 6.17 0.00 0.00 4.35
2685 5704 6.534793 ACCAATGTGAAAACTTTGATTGTGAC 59.465 34.615 6.17 0.00 0.00 3.67
2689 5708 7.432869 TCCTACCAATGTGAAAACTTTGATTG 58.567 34.615 6.17 0.00 0.00 2.67
2704 5723 5.106948 GCGTCATACATGATTCCTACCAATG 60.107 44.000 0.00 0.00 39.30 2.82
2722 5741 0.036388 ATCACAACTTCCGGCGTCAT 60.036 50.000 6.01 0.00 0.00 3.06
2751 5770 2.285969 AGCTGCATCCCCAGAGGT 60.286 61.111 1.02 0.00 34.77 3.85


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

AutoCloner maintained by Alex Coulton.