Multiple sequence alignment - TraesCS5A01G551800

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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 TraesCS5A01G551800 chr5A 100.000 3577 0 0 1 3577 705300179 705296603 0.000000e+00 6606.0
1 TraesCS5A01G551800 chr5A 91.414 396 18 5 341 721 416180143 416180537 2.450000e-146 529.0
2 TraesCS5A01G551800 chr5A 79.915 707 107 17 45 722 37142544 37141844 1.490000e-133 486.0
3 TraesCS5A01G551800 chr5A 87.054 224 23 4 721 941 659378763 659378543 7.670000e-62 248.0
4 TraesCS5A01G551800 chr5A 86.607 224 24 4 721 941 708967207 708967427 3.570000e-60 243.0
5 TraesCS5A01G551800 chr4B 90.725 1283 93 12 2312 3574 665328559 665327283 0.000000e+00 1687.0
6 TraesCS5A01G551800 chr4B 86.162 1308 130 17 868 2162 665329827 665328558 0.000000e+00 1365.0
7 TraesCS5A01G551800 chr4B 93.002 443 29 2 43 485 579882278 579882718 0.000000e+00 645.0
8 TraesCS5A01G551800 chr4B 89.809 157 16 0 721 877 665331143 665330987 6.060000e-48 202.0
9 TraesCS5A01G551800 chr4B 82.803 157 22 2 958 1109 665324612 665324456 6.230000e-28 135.0
10 TraesCS5A01G551800 chr4B 100.000 32 0 0 10 41 579807240 579807271 3.860000e-05 60.2
11 TraesCS5A01G551800 chrUn 96.433 813 19 4 1932 2735 108700276 108701087 0.000000e+00 1332.0
12 TraesCS5A01G551800 chrUn 95.312 576 22 3 1365 1935 108697856 108698431 0.000000e+00 909.0
13 TraesCS5A01G551800 chrUn 91.216 148 13 0 2773 2920 108701499 108701646 6.060000e-48 202.0
14 TraesCS5A01G551800 chrUn 95.455 110 5 0 2752 2861 108701396 108701505 3.670000e-40 176.0
15 TraesCS5A01G551800 chrUn 89.873 79 6 2 2938 3015 108701618 108701695 2.270000e-17 100.0
16 TraesCS5A01G551800 chrUn 97.222 36 1 0 2733 2768 108701361 108701396 1.070000e-05 62.1
17 TraesCS5A01G551800 chr6B 93.974 697 23 4 43 721 558777704 558778399 0.000000e+00 1037.0
18 TraesCS5A01G551800 chr6B 93.400 697 27 4 43 721 558860445 558861140 0.000000e+00 1014.0
19 TraesCS5A01G551800 chr6B 93.257 697 28 4 43 721 558694846 558695541 0.000000e+00 1009.0
20 TraesCS5A01G551800 chr6B 91.908 692 25 6 46 721 215738712 215738036 0.000000e+00 939.0
21 TraesCS5A01G551800 chr6B 97.368 38 1 0 9 46 215740077 215740040 8.290000e-07 65.8
22 TraesCS5A01G551800 chr5B 93.381 695 25 3 43 721 339996664 339997353 0.000000e+00 1009.0
23 TraesCS5A01G551800 chr7B 91.534 626 38 4 1855 2480 742249102 742249712 0.000000e+00 848.0
24 TraesCS5A01G551800 chr7B 87.948 697 54 11 737 1424 742248429 742249104 0.000000e+00 795.0
25 TraesCS5A01G551800 chr3B 87.294 669 25 11 74 724 779056895 779056269 0.000000e+00 710.0
26 TraesCS5A01G551800 chr3B 85.169 472 47 12 723 1181 814228966 814228505 2.520000e-126 462.0
27 TraesCS5A01G551800 chr6A 91.688 397 16 2 341 721 453568089 453568484 5.260000e-148 534.0
28 TraesCS5A01G551800 chr6A 79.915 707 108 16 45 722 603077569 603078270 4.150000e-134 488.0
29 TraesCS5A01G551800 chr2A 79.915 707 108 16 45 722 142702131 142702832 4.150000e-134 488.0
30 TraesCS5A01G551800 chr2A 89.362 282 13 4 458 722 12091717 12091998 4.420000e-89 339.0
31 TraesCS5A01G551800 chr7D 95.833 96 3 1 858 952 8245923 8246018 1.720000e-33 154.0
32 TraesCS5A01G551800 chr7D 89.286 112 10 2 721 831 8245818 8245928 4.820000e-29 139.0
33 TraesCS5A01G551800 chr4D 82.192 73 13 0 1103 1175 506562034 506562106 2.980000e-06 63.9


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 TraesCS5A01G551800 chr5A 705296603 705300179 3576 True 6606.000000 6606 100.000000 1 3577 1 chr5A.!!$R3 3576
1 TraesCS5A01G551800 chr5A 37141844 37142544 700 True 486.000000 486 79.915000 45 722 1 chr5A.!!$R1 677
2 TraesCS5A01G551800 chr4B 665324456 665331143 6687 True 847.250000 1687 87.374750 721 3574 4 chr4B.!!$R1 2853
3 TraesCS5A01G551800 chrUn 108697856 108701695 3839 False 463.516667 1332 94.251833 1365 3015 6 chrUn.!!$F1 1650
4 TraesCS5A01G551800 chr6B 558777704 558778399 695 False 1037.000000 1037 93.974000 43 721 1 chr6B.!!$F2 678
5 TraesCS5A01G551800 chr6B 558860445 558861140 695 False 1014.000000 1014 93.400000 43 721 1 chr6B.!!$F3 678
6 TraesCS5A01G551800 chr6B 558694846 558695541 695 False 1009.000000 1009 93.257000 43 721 1 chr6B.!!$F1 678
7 TraesCS5A01G551800 chr6B 215738036 215740077 2041 True 502.400000 939 94.638000 9 721 2 chr6B.!!$R1 712
8 TraesCS5A01G551800 chr5B 339996664 339997353 689 False 1009.000000 1009 93.381000 43 721 1 chr5B.!!$F1 678
9 TraesCS5A01G551800 chr7B 742248429 742249712 1283 False 821.500000 848 89.741000 737 2480 2 chr7B.!!$F1 1743
10 TraesCS5A01G551800 chr3B 779056269 779056895 626 True 710.000000 710 87.294000 74 724 1 chr3B.!!$R1 650
11 TraesCS5A01G551800 chr6A 603077569 603078270 701 False 488.000000 488 79.915000 45 722 1 chr6A.!!$F2 677
12 TraesCS5A01G551800 chr2A 142702131 142702832 701 False 488.000000 488 79.915000 45 722 1 chr2A.!!$F2 677

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
955 3489 0.034896 TTCAAGCGAACCCTGAGTCC 59.965 55.0 0.00 0.0 0.00 3.85 F
1016 3555 0.106369 TCCATGGAGATACCGGACGT 60.106 55.0 11.44 0.0 42.61 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 4422 0.311477 GTATCTTCGGCGAGGTCTCC 59.689 60.0 18.75 2.38 0.00 3.71 R
2954 7727 0.598065 GCTTGTCCGGAGCAACAAAT 59.402 50.0 3.06 0.00 39.89 2.32 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
41 42 1.669760 GCGTGTCCCGGACAATGAA 60.670 57.895 22.12 0.00 44.49 2.57
87 1416 6.183360 GGTTGGATCAATGGATGAAGAAAGAG 60.183 42.308 0.00 0.00 42.54 2.85
298 1635 1.803334 TGCTCACGTGGAATGGTAAC 58.197 50.000 17.00 0.00 0.00 2.50
361 1698 7.276218 TGTTATACATTTTAAGACCTTCGACGG 59.724 37.037 6.37 6.37 0.00 4.79
727 2088 4.876107 ACGGGCATTCTACTAGTTGAATTG 59.124 41.667 24.20 20.01 33.89 2.32
730 2091 6.456988 CGGGCATTCTACTAGTTGAATTGAAC 60.457 42.308 24.20 15.70 33.89 3.18
798 2159 2.544903 CCTGGTTTTTGGGCTTAACACG 60.545 50.000 0.00 0.00 0.00 4.49
801 2162 3.117794 GGTTTTTGGGCTTAACACGAAC 58.882 45.455 0.00 0.00 0.00 3.95
840 2201 4.153117 GGCCTCTCGCAATTATAATGACTG 59.847 45.833 0.00 0.00 40.31 3.51
849 2210 5.277345 GCAATTATAATGACTGTGGTCCGAC 60.277 44.000 0.00 0.00 41.47 4.79
877 2238 3.874392 GCAATTGCATGTAGGTTTCCT 57.126 42.857 25.36 0.00 41.59 3.36
878 2239 3.514645 GCAATTGCATGTAGGTTTCCTG 58.485 45.455 25.36 0.00 41.59 3.86
879 2240 3.514645 CAATTGCATGTAGGTTTCCTGC 58.485 45.455 0.00 0.00 36.77 4.85
941 3475 1.003866 GCGCCGCCTTTATAGTTCAAG 60.004 52.381 0.00 0.00 0.00 3.02
953 3487 3.307379 GTTCAAGCGAACCCTGAGT 57.693 52.632 0.00 0.00 44.92 3.41
954 3488 1.149148 GTTCAAGCGAACCCTGAGTC 58.851 55.000 0.00 0.00 44.92 3.36
955 3489 0.034896 TTCAAGCGAACCCTGAGTCC 59.965 55.000 0.00 0.00 0.00 3.85
956 3490 1.376037 CAAGCGAACCCTGAGTCCC 60.376 63.158 0.00 0.00 0.00 4.46
957 3491 1.536662 AAGCGAACCCTGAGTCCCT 60.537 57.895 0.00 0.00 0.00 4.20
958 3492 1.831652 AAGCGAACCCTGAGTCCCTG 61.832 60.000 0.00 0.00 0.00 4.45
959 3493 2.283529 GCGAACCCTGAGTCCCTGA 61.284 63.158 0.00 0.00 0.00 3.86
961 3495 1.889530 CGAACCCTGAGTCCCTGACC 61.890 65.000 0.00 0.00 32.18 4.02
975 3509 3.772572 TCCCTGACCAATCTATCGAACAA 59.227 43.478 0.00 0.00 0.00 2.83
977 3511 3.551890 CCTGACCAATCTATCGAACAACG 59.448 47.826 0.00 0.00 44.09 4.10
983 3517 2.898181 TCTATCGAACAACGCGTACA 57.102 45.000 14.46 0.00 42.26 2.90
1016 3555 0.106369 TCCATGGAGATACCGGACGT 60.106 55.000 11.44 0.00 42.61 4.34
1037 3576 4.117661 GCTCGCCGACGTTCTCCT 62.118 66.667 0.00 0.00 41.18 3.69
1038 3577 2.758089 GCTCGCCGACGTTCTCCTA 61.758 63.158 0.00 0.00 41.18 2.94
1050 3589 1.529152 TTCTCCTACGCGTGCTCCAA 61.529 55.000 24.59 6.33 0.00 3.53
1350 3889 2.885644 CCGGTGACTTGGCGATCG 60.886 66.667 11.69 11.69 0.00 3.69
1447 3986 1.079750 GCCGTGTCTCTCCACTTCC 60.080 63.158 0.00 0.00 33.07 3.46
1553 4092 2.899339 GCTCTTCATGGCCGGAGC 60.899 66.667 5.05 15.02 43.07 4.70
1615 4157 2.165030 GACGACGGAGAGGATTGGTTTA 59.835 50.000 0.00 0.00 0.00 2.01
1651 4193 3.303132 GGATGAAACACGTCCGCATTATC 60.303 47.826 0.00 0.00 43.60 1.75
1667 4209 4.635982 CATTATCATTCGAGCGAGCATTC 58.364 43.478 0.00 0.00 0.00 2.67
1683 4225 0.904865 ATTCTGAGGTGAGGGACGCA 60.905 55.000 0.00 0.00 34.39 5.24
1778 4320 4.451435 GGAGAGGACTTTTGTACGGAAAAG 59.549 45.833 13.93 13.93 44.95 2.27
1817 4359 1.718757 GCAGACATGTGGCCGGATTC 61.719 60.000 5.05 0.00 0.00 2.52
1821 4363 1.889105 CATGTGGCCGGATTCCTCG 60.889 63.158 5.05 0.00 0.00 4.63
1829 4371 1.541233 GCCGGATTCCTCGTCAATCAT 60.541 52.381 5.05 0.00 32.65 2.45
1835 4377 4.640201 GGATTCCTCGTCAATCATTTTGGA 59.360 41.667 0.00 0.00 32.65 3.53
1845 4387 5.410355 CAATCATTTTGGATTGGTCACCT 57.590 39.130 0.00 0.00 46.58 4.00
1868 4410 2.100631 CGGATTGGTCACCTCGTGC 61.101 63.158 0.00 0.00 32.98 5.34
1880 4422 1.196808 ACCTCGTGCGCAAAGTAATTG 59.803 47.619 14.00 2.21 42.21 2.32
1903 4445 0.968901 ACCTCGCCGAAGATACACCA 60.969 55.000 0.00 0.00 0.00 4.17
1966 6356 5.817816 GGTTTCATCATGAGGTACTACTTGG 59.182 44.000 7.33 0.00 41.55 3.61
2016 6411 9.959721 GGTGATTAATATGGCTTTAGAAGGATA 57.040 33.333 0.00 0.00 0.00 2.59
2249 6648 2.821366 GCATCTCGTGGGGCACTG 60.821 66.667 0.00 0.00 31.34 3.66
2556 6955 1.301716 GGCAGTCGAGAAGTTGGCA 60.302 57.895 0.00 0.00 36.27 4.92
2576 6975 1.231221 ATGGTTGTGCGTTCGCTTAA 58.769 45.000 17.63 9.95 0.00 1.85
2640 7039 3.118775 TCCAGTACGAGGTGAATGGATTG 60.119 47.826 7.19 0.00 32.04 2.67
2737 7412 7.553334 GGTACATCCACTGATTTGAGTTACTA 58.447 38.462 0.00 0.00 35.97 1.82
2786 7477 7.015195 AGGTAGGTTTGAATGCAAAAATAGTGT 59.985 33.333 0.00 0.00 44.91 3.55
2820 7593 4.111198 GTTGAACACAATGCATCAACACA 58.889 39.130 18.96 6.16 42.31 3.72
2840 7613 6.237901 ACACAGTGCTTAATTGGTTCATCTA 58.762 36.000 0.00 0.00 0.00 1.98
2871 7644 8.470040 AAGATGTGATGTAAATGCAATTCAAC 57.530 30.769 0.00 0.00 33.67 3.18
2913 7686 1.885388 TTGGTCTGTGTCGGCGTTG 60.885 57.895 6.85 0.00 0.00 4.10
2932 7705 2.862541 TGTTGCTCCAACTAATGCACT 58.137 42.857 9.23 0.00 43.85 4.40
2941 7714 1.372501 ACTAATGCACTCCCCTTGGT 58.627 50.000 0.00 0.00 0.00 3.67
2954 7727 1.338674 CCCTTGGTTCGCTGTGTCATA 60.339 52.381 0.00 0.00 0.00 2.15
2965 7738 3.728864 CGCTGTGTCATATTTGTTGCTCC 60.729 47.826 0.00 0.00 0.00 4.70
2974 7747 1.452145 TTTGTTGCTCCGGACAAGCC 61.452 55.000 16.54 9.06 39.05 4.35
3019 7792 3.066369 GACACAGTCGCATCGAATCTA 57.934 47.619 0.00 0.00 37.72 1.98
3020 7793 3.039405 GACACAGTCGCATCGAATCTAG 58.961 50.000 0.00 0.00 37.72 2.43
3041 7814 2.414161 GCCACAAAGTTCAATACCGAGC 60.414 50.000 0.00 0.00 0.00 5.03
3058 7831 9.561069 AATACCGAGCACATTAATTTAGAGATT 57.439 29.630 0.00 0.00 0.00 2.40
3063 7836 6.498304 AGCACATTAATTTAGAGATTTGGCG 58.502 36.000 0.00 0.00 0.00 5.69
3068 7841 9.003658 ACATTAATTTAGAGATTTGGCGGATAG 57.996 33.333 0.00 0.00 0.00 2.08
3114 7887 0.679960 GGGTGATAGTGGGTGGTTGC 60.680 60.000 0.00 0.00 0.00 4.17
3130 7903 2.188994 GCTGGAGGCTGCTGGTAG 59.811 66.667 14.31 0.98 38.06 3.18
3144 7917 2.025155 CTGGTAGCGGAGTGTACATCT 58.975 52.381 0.00 0.00 0.00 2.90
3150 7923 5.240183 GGTAGCGGAGTGTACATCTTGTATA 59.760 44.000 0.00 0.00 35.05 1.47
3153 7926 4.534168 CGGAGTGTACATCTTGTATACCG 58.466 47.826 0.00 3.22 43.27 4.02
3163 7936 1.924524 CTTGTATACCGAGTGCCAACG 59.075 52.381 0.00 0.00 0.00 4.10
3168 7941 0.598158 TACCGAGTGCCAACGTTGTC 60.598 55.000 25.63 15.19 0.00 3.18
3169 7942 2.544359 CGAGTGCCAACGTTGTCG 59.456 61.111 25.63 22.53 43.34 4.35
3173 7946 0.874607 AGTGCCAACGTTGTCGAGAC 60.875 55.000 25.63 14.03 40.62 3.36
3179 7952 1.187271 CAACGTTGTCGAGACTTGACG 59.813 52.381 20.21 18.10 39.22 4.35
3191 7964 0.759346 ACTTGACGGTGAGGAAGCTT 59.241 50.000 0.00 0.00 0.00 3.74
3192 7965 1.270358 ACTTGACGGTGAGGAAGCTTC 60.270 52.381 18.54 18.54 0.00 3.86
3224 7997 0.250295 TGGAACAGCTTGACCTTCCG 60.250 55.000 0.00 0.00 35.81 4.30
3228 8001 1.004560 CAGCTTGACCTTCCGCTCA 60.005 57.895 0.00 0.00 0.00 4.26
3231 8004 1.092345 GCTTGACCTTCCGCTCATCC 61.092 60.000 0.00 0.00 0.00 3.51
3252 8025 0.108520 CCTTTAGGCGCGTAGAACCA 60.109 55.000 8.43 0.00 0.00 3.67
3261 8034 2.143122 CGCGTAGAACCATATGGCAAT 58.857 47.619 22.18 8.34 39.32 3.56
3262 8035 2.157668 CGCGTAGAACCATATGGCAATC 59.842 50.000 22.18 16.61 39.32 2.67
3263 8036 2.484264 GCGTAGAACCATATGGCAATCC 59.516 50.000 22.18 6.47 39.32 3.01
3300 8073 7.399245 TGTGGTAGTTCTTTTATATTTGCCC 57.601 36.000 0.00 0.00 0.00 5.36
3301 8074 6.378848 TGTGGTAGTTCTTTTATATTTGCCCC 59.621 38.462 0.00 0.00 0.00 5.80
3302 8075 6.605995 GTGGTAGTTCTTTTATATTTGCCCCT 59.394 38.462 0.00 0.00 0.00 4.79
3308 8081 8.279361 AGTTCTTTTATATTTGCCCCTAGCTTA 58.721 33.333 0.00 0.00 44.23 3.09
3311 8084 7.669722 TCTTTTATATTTGCCCCTAGCTTATGG 59.330 37.037 0.00 0.00 44.23 2.74
3315 8088 1.131638 TGCCCCTAGCTTATGGTGAG 58.868 55.000 0.00 0.00 44.23 3.51
3332 8105 2.490115 GTGAGACTACTGAGGTGTCTGG 59.510 54.545 12.87 0.00 40.63 3.86
3335 8108 0.969894 ACTACTGAGGTGTCTGGCAC 59.030 55.000 3.25 3.25 46.97 5.01
3347 8120 1.808945 GTCTGGCACAACTGAGGATTG 59.191 52.381 0.00 0.00 38.70 2.67
3348 8121 1.699083 TCTGGCACAACTGAGGATTGA 59.301 47.619 0.00 0.00 38.70 2.57
3349 8122 2.082231 CTGGCACAACTGAGGATTGAG 58.918 52.381 0.00 0.00 38.70 3.02
3350 8123 1.271543 TGGCACAACTGAGGATTGAGG 60.272 52.381 0.00 0.00 31.92 3.86
3351 8124 1.003580 GGCACAACTGAGGATTGAGGA 59.996 52.381 0.00 0.00 0.00 3.71
3355 8128 4.252073 CACAACTGAGGATTGAGGAAGAG 58.748 47.826 0.00 0.00 0.00 2.85
3356 8129 3.269178 CAACTGAGGATTGAGGAAGAGC 58.731 50.000 0.00 0.00 0.00 4.09
3357 8130 2.831565 ACTGAGGATTGAGGAAGAGCT 58.168 47.619 0.00 0.00 0.00 4.09
3358 8131 2.500910 ACTGAGGATTGAGGAAGAGCTG 59.499 50.000 0.00 0.00 0.00 4.24
3359 8132 2.765135 CTGAGGATTGAGGAAGAGCTGA 59.235 50.000 0.00 0.00 0.00 4.26
3360 8133 3.382278 TGAGGATTGAGGAAGAGCTGAT 58.618 45.455 0.00 0.00 0.00 2.90
3361 8134 3.779183 TGAGGATTGAGGAAGAGCTGATT 59.221 43.478 0.00 0.00 0.00 2.57
3362 8135 4.226846 TGAGGATTGAGGAAGAGCTGATTT 59.773 41.667 0.00 0.00 0.00 2.17
3395 8168 5.422970 TCATGGGAGAAAAGCAAAGCATAAT 59.577 36.000 0.00 0.00 0.00 1.28
3449 8222 8.790718 TCTTAGTAACATAATAGATGACCCGTC 58.209 37.037 0.00 0.00 0.00 4.79
3450 8223 6.971726 AGTAACATAATAGATGACCCGTCA 57.028 37.500 0.00 0.00 44.59 4.35
3453 8226 3.635373 ACATAATAGATGACCCGTCACGT 59.365 43.478 0.00 0.00 43.11 4.49
3467 8240 1.082431 CACGTCGATGGCGCAAAAA 60.082 52.632 10.83 0.00 37.46 1.94
3492 8265 8.218338 AGCCATTTAGAAGTGATTATGAAGTG 57.782 34.615 0.00 0.00 0.00 3.16
3494 8267 7.201767 GCCATTTAGAAGTGATTATGAAGTGCT 60.202 37.037 0.00 0.00 0.00 4.40
3496 8269 9.499585 CATTTAGAAGTGATTATGAAGTGCTTG 57.500 33.333 0.00 0.00 0.00 4.01
3555 8341 5.796350 AAAGAATGAACCGTTCTATTCCG 57.204 39.130 20.81 0.00 38.58 4.30
3558 8344 2.267188 TGAACCGTTCTATTCCGTCG 57.733 50.000 12.43 0.00 0.00 5.12
3574 8360 5.443185 TCCGTCGTTTTCTATATGTAGGG 57.557 43.478 0.00 0.00 0.00 3.53
3575 8361 5.132502 TCCGTCGTTTTCTATATGTAGGGA 58.867 41.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.218759 CACGGACGTATAGCATTGCTTC 59.781 50.000 17.71 7.60 40.44 3.86
1 2 2.201732 CACGGACGTATAGCATTGCTT 58.798 47.619 17.71 7.45 40.44 3.91
2 3 1.538204 CCACGGACGTATAGCATTGCT 60.538 52.381 16.63 16.63 43.41 3.91
4 5 1.497991 CCCACGGACGTATAGCATTG 58.502 55.000 0.00 0.00 0.00 2.82
5 6 0.249741 GCCCACGGACGTATAGCATT 60.250 55.000 0.00 0.00 0.00 3.56
6 7 1.366366 GCCCACGGACGTATAGCAT 59.634 57.895 0.00 0.00 0.00 3.79
7 8 2.809706 GCCCACGGACGTATAGCA 59.190 61.111 0.00 0.00 0.00 3.49
41 42 0.840722 CCTCCACTACACCCCACCTT 60.841 60.000 0.00 0.00 0.00 3.50
87 1416 4.343814 TGTTCTTCCTCCAAATGTTTTCCC 59.656 41.667 0.00 0.00 0.00 3.97
240 1574 9.748708 CAGACAAATCTCTCCAATTTTGTAAAA 57.251 29.630 0.00 0.00 41.10 1.52
298 1635 7.689400 GTCGTACAAATTGGGTTTACTAATTCG 59.311 37.037 0.00 0.00 0.00 3.34
559 1902 4.321745 GCAACGTAGCAATTTGACAATGAG 59.678 41.667 0.00 0.00 0.00 2.90
751 2112 6.600822 CCCAGCTTCATCTCTTTTCTGAAATA 59.399 38.462 3.31 0.00 0.00 1.40
753 2114 4.763793 CCCAGCTTCATCTCTTTTCTGAAA 59.236 41.667 0.00 0.00 0.00 2.69
766 2127 0.178924 AAAACCAGGCCCAGCTTCAT 60.179 50.000 0.00 0.00 0.00 2.57
771 2132 2.743060 CCAAAAACCAGGCCCAGC 59.257 61.111 0.00 0.00 0.00 4.85
798 2159 3.561503 GCCCAACATCAAAACTACGTTC 58.438 45.455 0.00 0.00 0.00 3.95
801 2162 2.159382 AGGCCCAACATCAAAACTACG 58.841 47.619 0.00 0.00 0.00 3.51
840 2201 1.155424 TGCAAACTTCGTCGGACCAC 61.155 55.000 1.91 0.00 0.00 4.16
874 2235 4.202182 ACTGTTTTCGTACTACTTGCAGGA 60.202 41.667 1.40 0.00 0.00 3.86
877 2238 5.220700 CCAAACTGTTTTCGTACTACTTGCA 60.221 40.000 2.41 0.00 0.00 4.08
878 2239 5.006941 TCCAAACTGTTTTCGTACTACTTGC 59.993 40.000 2.41 0.00 0.00 4.01
879 2240 6.416514 GTCCAAACTGTTTTCGTACTACTTG 58.583 40.000 2.41 0.00 0.00 3.16
941 3475 2.266055 CAGGGACTCAGGGTTCGC 59.734 66.667 0.00 0.00 34.60 4.70
977 3511 1.691061 CGATCGATCGCATGTACGC 59.309 57.895 32.34 0.00 43.84 4.42
987 3521 4.261405 GGTATCTCCATGGATCGATCGATC 60.261 50.000 38.31 38.31 41.78 3.69
995 3529 1.202582 CGTCCGGTATCTCCATGGATC 59.797 57.143 16.63 6.38 35.57 3.36
999 3538 0.032130 CCACGTCCGGTATCTCCATG 59.968 60.000 0.00 0.00 35.57 3.66
1006 3545 2.890371 GAGCACCACGTCCGGTAT 59.110 61.111 0.00 0.00 37.07 2.73
1032 3571 1.974875 TTGGAGCACGCGTAGGAGA 60.975 57.895 13.44 0.00 0.00 3.71
1259 3798 2.431771 CGATGACCGCGTTCCACA 60.432 61.111 4.92 0.00 0.00 4.17
1447 3986 1.550976 GTCAGGGAGTAGGAACACCTG 59.449 57.143 11.03 11.03 46.41 4.00
1553 4092 0.099968 CCACAAATCGCCATCTGCAG 59.900 55.000 7.63 7.63 41.33 4.41
1615 4157 5.416952 GTGTTTCATCCTCTTGTGAATCCAT 59.583 40.000 0.00 0.00 34.60 3.41
1651 4193 1.521840 CTCAGAATGCTCGCTCGAATG 59.478 52.381 0.00 0.00 34.76 2.67
1667 4209 0.742281 CATTGCGTCCCTCACCTCAG 60.742 60.000 0.00 0.00 0.00 3.35
1683 4225 0.761702 GCCATTCCATCAGGCCCATT 60.762 55.000 0.00 0.00 42.58 3.16
1709 4251 0.533491 GACCTGCACCACGTATACCA 59.467 55.000 0.00 0.00 0.00 3.25
1793 4335 3.434319 GCCACATGTCTGCCACCG 61.434 66.667 0.00 0.00 0.00 4.94
1829 4371 1.337118 GGCAGGTGACCAATCCAAAA 58.663 50.000 3.63 0.00 0.00 2.44
1835 4377 1.852157 ATCCGTGGCAGGTGACCAAT 61.852 55.000 3.63 0.00 39.39 3.16
1868 4410 2.348666 CGAGGTCTCCAATTACTTTGCG 59.651 50.000 0.00 0.00 33.73 4.85
1880 4422 0.311477 GTATCTTCGGCGAGGTCTCC 59.689 60.000 18.75 2.38 0.00 3.71
1903 4445 9.101655 GATGTAAAGAAATTGCTGCCAATAAAT 57.898 29.630 0.00 0.00 40.69 1.40
1966 6356 6.808212 CCAGATTGTAACAAACATGATTGGAC 59.192 38.462 18.61 15.48 38.10 4.02
2249 6648 4.856801 ATCATCGCCCACACCGGC 62.857 66.667 0.00 0.00 46.13 6.13
2260 6659 2.941064 AGGTCAGCATTGTGAATCATCG 59.059 45.455 0.00 0.00 0.00 3.84
2556 6955 1.231221 TAAGCGAACGCACAACCATT 58.769 45.000 20.66 7.29 44.88 3.16
2576 6975 4.402474 TCACACTTCATCGTGTCCAGATAT 59.598 41.667 0.00 0.00 45.74 1.63
2640 7039 1.338655 TCGTACTTTGGGCCAAAAAGC 59.661 47.619 30.00 20.51 38.03 3.51
2737 7412 7.843252 ACCTACCTACCTAAGCTTATTGTAACT 59.157 37.037 6.64 3.09 0.00 2.24
2813 7586 4.642437 TGAACCAATTAAGCACTGTGTTGA 59.358 37.500 9.86 0.00 0.00 3.18
2814 7587 4.930963 TGAACCAATTAAGCACTGTGTTG 58.069 39.130 9.86 5.48 0.00 3.33
2820 7593 7.611467 TCACAATAGATGAACCAATTAAGCACT 59.389 33.333 0.00 0.00 0.00 4.40
2840 7613 7.160547 TGCATTTACATCACATCTTCACAAT 57.839 32.000 0.00 0.00 0.00 2.71
2871 7644 6.110707 ACCAACTTTTACGTATCCATGGTAG 58.889 40.000 12.58 4.39 36.91 3.18
2913 7686 2.162408 GGAGTGCATTAGTTGGAGCAAC 59.838 50.000 0.00 0.00 43.83 4.17
2932 7705 2.391724 GACACAGCGAACCAAGGGGA 62.392 60.000 0.00 0.00 38.05 4.81
2941 7714 3.501828 AGCAACAAATATGACACAGCGAA 59.498 39.130 0.00 0.00 0.00 4.70
2954 7727 0.598065 GCTTGTCCGGAGCAACAAAT 59.402 50.000 3.06 0.00 39.89 2.32
2974 7747 4.621034 AGTTTGCAATTAAAATCTTCGCGG 59.379 37.500 6.13 0.00 0.00 6.46
2977 7750 6.577055 TGTCGAGTTTGCAATTAAAATCTTCG 59.423 34.615 0.00 0.43 33.75 3.79
3016 7789 4.020928 TCGGTATTGAACTTTGTGGCTAGA 60.021 41.667 0.00 0.00 0.00 2.43
3017 7790 4.250464 TCGGTATTGAACTTTGTGGCTAG 58.750 43.478 0.00 0.00 0.00 3.42
3019 7792 3.074412 CTCGGTATTGAACTTTGTGGCT 58.926 45.455 0.00 0.00 0.00 4.75
3020 7793 2.414161 GCTCGGTATTGAACTTTGTGGC 60.414 50.000 0.00 0.00 0.00 5.01
3041 7814 7.026631 TCCGCCAAATCTCTAAATTAATGTG 57.973 36.000 0.00 0.00 0.00 3.21
3114 7887 2.188994 GCTACCAGCAGCCTCCAG 59.811 66.667 0.00 0.00 41.89 3.86
3130 7903 4.296690 GGTATACAAGATGTACACTCCGC 58.703 47.826 5.01 0.00 35.42 5.54
3136 7909 4.202080 GGCACTCGGTATACAAGATGTACA 60.202 45.833 5.01 0.00 35.42 2.90
3144 7917 1.273048 ACGTTGGCACTCGGTATACAA 59.727 47.619 14.10 0.00 0.00 2.41
3150 7923 1.885850 GACAACGTTGGCACTCGGT 60.886 57.895 29.05 6.36 35.83 4.69
3153 7926 0.596600 TCTCGACAACGTTGGCACTC 60.597 55.000 32.13 18.79 35.35 3.51
3163 7936 1.129326 CACCGTCAAGTCTCGACAAC 58.871 55.000 0.00 0.00 32.72 3.32
3168 7941 0.596577 TTCCTCACCGTCAAGTCTCG 59.403 55.000 0.00 0.00 0.00 4.04
3169 7942 1.670380 GCTTCCTCACCGTCAAGTCTC 60.670 57.143 0.00 0.00 0.00 3.36
3173 7946 1.433534 GAAGCTTCCTCACCGTCAAG 58.566 55.000 15.97 0.00 0.00 3.02
3191 7964 0.458543 GTTCCAGCATCTTCTCGCGA 60.459 55.000 9.26 9.26 0.00 5.87
3192 7965 0.737367 TGTTCCAGCATCTTCTCGCG 60.737 55.000 0.00 0.00 0.00 5.87
3248 8021 4.270317 AGGAAAGGATTGCCATATGGTT 57.730 40.909 22.79 7.39 37.57 3.67
3252 8025 8.771286 ACATTAAAAAGGAAAGGATTGCCATAT 58.229 29.630 0.00 0.00 36.29 1.78
3261 8034 8.002459 AGAACTACCACATTAAAAAGGAAAGGA 58.998 33.333 0.00 0.00 0.00 3.36
3262 8035 8.178313 AGAACTACCACATTAAAAAGGAAAGG 57.822 34.615 0.00 0.00 0.00 3.11
3291 8064 4.353788 TCACCATAAGCTAGGGGCAAATAT 59.646 41.667 4.97 0.00 44.79 1.28
3293 8066 2.513738 TCACCATAAGCTAGGGGCAAAT 59.486 45.455 4.97 0.00 44.79 2.32
3300 8073 5.133941 TCAGTAGTCTCACCATAAGCTAGG 58.866 45.833 0.00 0.00 0.00 3.02
3301 8074 5.240623 CCTCAGTAGTCTCACCATAAGCTAG 59.759 48.000 0.00 0.00 0.00 3.42
3302 8075 5.133941 CCTCAGTAGTCTCACCATAAGCTA 58.866 45.833 0.00 0.00 0.00 3.32
3308 8081 3.093057 GACACCTCAGTAGTCTCACCAT 58.907 50.000 0.00 0.00 0.00 3.55
3311 8084 2.490115 CCAGACACCTCAGTAGTCTCAC 59.510 54.545 0.00 0.00 40.42 3.51
3315 8088 1.067495 GTGCCAGACACCTCAGTAGTC 60.067 57.143 0.00 0.00 44.02 2.59
3332 8105 2.479566 TCCTCAATCCTCAGTTGTGC 57.520 50.000 0.00 0.00 0.00 4.57
3335 8108 3.055240 AGCTCTTCCTCAATCCTCAGTTG 60.055 47.826 0.00 0.00 0.00 3.16
3339 8112 2.825223 TCAGCTCTTCCTCAATCCTCA 58.175 47.619 0.00 0.00 0.00 3.86
3347 8120 2.774809 ACCCCTAAATCAGCTCTTCCTC 59.225 50.000 0.00 0.00 0.00 3.71
3348 8121 2.852130 ACCCCTAAATCAGCTCTTCCT 58.148 47.619 0.00 0.00 0.00 3.36
3349 8122 4.772886 TTACCCCTAAATCAGCTCTTCC 57.227 45.455 0.00 0.00 0.00 3.46
3350 8123 5.930135 TGATTACCCCTAAATCAGCTCTTC 58.070 41.667 0.00 0.00 38.19 2.87
3351 8124 5.975988 TGATTACCCCTAAATCAGCTCTT 57.024 39.130 0.00 0.00 38.19 2.85
3355 8128 4.082125 CCCATGATTACCCCTAAATCAGC 58.918 47.826 0.00 0.00 44.27 4.26
3356 8129 5.310594 TCTCCCATGATTACCCCTAAATCAG 59.689 44.000 0.00 0.00 44.27 2.90
3357 8130 5.231552 TCTCCCATGATTACCCCTAAATCA 58.768 41.667 0.00 1.37 44.92 2.57
3358 8131 5.843019 TCTCCCATGATTACCCCTAAATC 57.157 43.478 0.00 0.00 34.55 2.17
3359 8132 6.606241 TTTCTCCCATGATTACCCCTAAAT 57.394 37.500 0.00 0.00 0.00 1.40
3360 8133 6.410222 TTTTCTCCCATGATTACCCCTAAA 57.590 37.500 0.00 0.00 0.00 1.85
3361 8134 5.633854 GCTTTTCTCCCATGATTACCCCTAA 60.634 44.000 0.00 0.00 0.00 2.69
3362 8135 4.141251 GCTTTTCTCCCATGATTACCCCTA 60.141 45.833 0.00 0.00 0.00 3.53
3404 8177 8.974060 ACTAAGAGTGAAGTAAACCATTTTCA 57.026 30.769 0.00 0.00 0.00 2.69
3436 8209 0.661552 CGACGTGACGGGTCATCTAT 59.338 55.000 10.66 0.00 42.18 1.98
3439 8212 0.866061 CATCGACGTGACGGGTCATC 60.866 60.000 10.66 0.00 42.18 2.92
3442 8215 2.202570 CCATCGACGTGACGGGTC 60.203 66.667 10.66 0.00 0.00 4.46
3449 8222 1.059657 CTTTTTGCGCCATCGACGTG 61.060 55.000 4.18 0.00 38.10 4.49
3450 8223 1.206578 CTTTTTGCGCCATCGACGT 59.793 52.632 4.18 0.00 38.10 4.34
3453 8226 2.566010 GGCTTTTTGCGCCATCGA 59.434 55.556 4.18 0.00 46.77 3.59
3461 8234 8.598075 CATAATCACTTCTAAATGGCTTTTTGC 58.402 33.333 3.54 0.00 41.94 3.68
3467 8240 7.201767 GCACTTCATAATCACTTCTAAATGGCT 60.202 37.037 0.00 0.00 0.00 4.75
3474 8247 7.386059 TCACAAGCACTTCATAATCACTTCTA 58.614 34.615 0.00 0.00 0.00 2.10
3476 8249 6.486253 TCACAAGCACTTCATAATCACTTC 57.514 37.500 0.00 0.00 0.00 3.01
3492 8265 1.188863 AATTGGCTCCCATCACAAGC 58.811 50.000 0.00 0.00 31.53 4.01
3494 8267 1.818060 CGAAATTGGCTCCCATCACAA 59.182 47.619 0.00 0.00 31.53 3.33
3496 8269 0.740737 CCGAAATTGGCTCCCATCAC 59.259 55.000 0.00 0.00 31.53 3.06


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

AutoCloner maintained by Alex Coulton.