Multiple sequence alignment - TraesCS2D01G429100

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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 TraesCS2D01G429100 chr2D 100.000 2831 0 0 1 2831 540950342 540953172 0.000000e+00 5228
1 TraesCS2D01G429100 chr2D 84.515 1001 153 2 820 1819 617052666 617053665 0.000000e+00 989
2 TraesCS2D01G429100 chr2D 83.569 992 162 1 829 1819 13421739 13422730 0.000000e+00 928
3 TraesCS2D01G429100 chr2D 87.500 376 43 3 2414 2788 540837632 540838004 5.600000e-117 431
4 TraesCS2D01G429100 chr2B 97.239 1775 45 3 125 1897 646592514 646594286 0.000000e+00 3003
5 TraesCS2D01G429100 chr2B 90.529 908 51 14 1948 2831 646594303 646595199 0.000000e+00 1168
6 TraesCS2D01G429100 chr2B 84.232 1002 154 4 820 1819 752786767 752787766 0.000000e+00 972
7 TraesCS2D01G429100 chr2B 82.834 1002 170 2 819 1819 24089826 24090826 0.000000e+00 896
8 TraesCS2D01G429100 chr2B 81.709 995 179 3 827 1819 792486600 792487593 0.000000e+00 826
9 TraesCS2D01G429100 chr2B 81.680 988 180 1 829 1815 17882904 17881917 0.000000e+00 821
10 TraesCS2D01G429100 chr2B 87.302 378 42 3 2414 2788 646454486 646454860 7.250000e-116 427
11 TraesCS2D01G429100 chr2A 91.098 865 32 20 1376 2237 684400980 684401802 0.000000e+00 1129
12 TraesCS2D01G429100 chr2A 94.461 668 31 3 719 1380 684395058 684395725 0.000000e+00 1024
13 TraesCS2D01G429100 chr2A 83.183 999 163 5 824 1819 747088674 747089670 0.000000e+00 909
14 TraesCS2D01G429100 chr2A 83.051 1003 165 5 819 1819 15395155 15396154 0.000000e+00 905
15 TraesCS2D01G429100 chr2A 94.766 535 23 3 2298 2831 684401897 684402427 0.000000e+00 828
16 TraesCS2D01G429100 chr2A 85.954 776 43 38 1680 2439 684417755 684418480 0.000000e+00 769
17 TraesCS2D01G429100 chr2A 94.602 389 15 3 2444 2831 684419406 684419789 5.220000e-167 597
18 TraesCS2D01G429100 chr2A 87.302 378 39 7 2414 2788 684270801 684271172 9.380000e-115 424
19 TraesCS2D01G429100 chr6D 100.000 103 0 0 1 103 131883122 131883224 1.040000e-44 191
20 TraesCS2D01G429100 chr6D 100.000 103 0 0 1 103 182451063 182450961 1.040000e-44 191
21 TraesCS2D01G429100 chr6D 100.000 103 0 0 1 103 400934146 400934044 1.040000e-44 191
22 TraesCS2D01G429100 chr4D 100.000 103 0 0 1 103 13455639 13455741 1.040000e-44 191
23 TraesCS2D01G429100 chr4D 100.000 103 0 0 1 103 87450837 87450939 1.040000e-44 191
24 TraesCS2D01G429100 chr4D 100.000 103 0 0 1 103 206617719 206617617 1.040000e-44 191
25 TraesCS2D01G429100 chr4D 100.000 103 0 0 1 103 276127811 276127709 1.040000e-44 191
26 TraesCS2D01G429100 chr4D 100.000 103 0 0 1 103 428082033 428081931 1.040000e-44 191
27 TraesCS2D01G429100 chr4B 100.000 103 0 0 1 103 486428964 486428862 1.040000e-44 191


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 TraesCS2D01G429100 chr2D 540950342 540953172 2830 False 5228.0 5228 100.000 1 2831 1 chr2D.!!$F3 2830
1 TraesCS2D01G429100 chr2D 617052666 617053665 999 False 989.0 989 84.515 820 1819 1 chr2D.!!$F4 999
2 TraesCS2D01G429100 chr2D 13421739 13422730 991 False 928.0 928 83.569 829 1819 1 chr2D.!!$F1 990
3 TraesCS2D01G429100 chr2B 646592514 646595199 2685 False 2085.5 3003 93.884 125 2831 2 chr2B.!!$F5 2706
4 TraesCS2D01G429100 chr2B 752786767 752787766 999 False 972.0 972 84.232 820 1819 1 chr2B.!!$F3 999
5 TraesCS2D01G429100 chr2B 24089826 24090826 1000 False 896.0 896 82.834 819 1819 1 chr2B.!!$F1 1000
6 TraesCS2D01G429100 chr2B 792486600 792487593 993 False 826.0 826 81.709 827 1819 1 chr2B.!!$F4 992
7 TraesCS2D01G429100 chr2B 17881917 17882904 987 True 821.0 821 81.680 829 1815 1 chr2B.!!$R1 986
8 TraesCS2D01G429100 chr2A 684395058 684395725 667 False 1024.0 1024 94.461 719 1380 1 chr2A.!!$F3 661
9 TraesCS2D01G429100 chr2A 684400980 684402427 1447 False 978.5 1129 92.932 1376 2831 2 chr2A.!!$F5 1455
10 TraesCS2D01G429100 chr2A 747088674 747089670 996 False 909.0 909 83.183 824 1819 1 chr2A.!!$F4 995
11 TraesCS2D01G429100 chr2A 15395155 15396154 999 False 905.0 905 83.051 819 1819 1 chr2A.!!$F1 1000
12 TraesCS2D01G429100 chr2A 684417755 684419789 2034 False 683.0 769 90.278 1680 2831 2 chr2A.!!$F6 1151

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
49 50 0.321671 ACTTGCATACGTGGCAGACT 59.678 50.0 14.92 1.88 43.05 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1848 0.327259 GGGGAAAACGTAGAGGCCTT 59.673 55.0 6.77 0.0 0.0 4.35 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 7.625828 ACCACTAATAATGCCAAGAAACTAC 57.374 36.000 0.00 0.00 0.00 2.73
26 27 7.402862 ACCACTAATAATGCCAAGAAACTACT 58.597 34.615 0.00 0.00 0.00 2.57
27 28 8.545472 ACCACTAATAATGCCAAGAAACTACTA 58.455 33.333 0.00 0.00 0.00 1.82
28 29 8.827677 CCACTAATAATGCCAAGAAACTACTAC 58.172 37.037 0.00 0.00 0.00 2.73
29 30 8.827677 CACTAATAATGCCAAGAAACTACTACC 58.172 37.037 0.00 0.00 0.00 3.18
30 31 8.545472 ACTAATAATGCCAAGAAACTACTACCA 58.455 33.333 0.00 0.00 0.00 3.25
31 32 7.625828 AATAATGCCAAGAAACTACTACCAC 57.374 36.000 0.00 0.00 0.00 4.16
32 33 4.910458 ATGCCAAGAAACTACTACCACT 57.090 40.909 0.00 0.00 0.00 4.00
33 34 4.699925 TGCCAAGAAACTACTACCACTT 57.300 40.909 0.00 0.00 0.00 3.16
34 35 4.385825 TGCCAAGAAACTACTACCACTTG 58.614 43.478 0.00 0.00 35.84 3.16
35 36 3.188667 GCCAAGAAACTACTACCACTTGC 59.811 47.826 0.00 0.00 35.09 4.01
36 37 4.385825 CCAAGAAACTACTACCACTTGCA 58.614 43.478 0.00 0.00 35.09 4.08
37 38 5.003804 CCAAGAAACTACTACCACTTGCAT 58.996 41.667 0.00 0.00 35.09 3.96
38 39 6.170506 CCAAGAAACTACTACCACTTGCATA 58.829 40.000 0.00 0.00 35.09 3.14
39 40 6.092259 CCAAGAAACTACTACCACTTGCATAC 59.908 42.308 0.00 0.00 35.09 2.39
40 41 5.408356 AGAAACTACTACCACTTGCATACG 58.592 41.667 0.00 0.00 0.00 3.06
41 42 4.796038 AACTACTACCACTTGCATACGT 57.204 40.909 0.00 0.00 0.00 3.57
42 43 4.106029 ACTACTACCACTTGCATACGTG 57.894 45.455 0.00 0.00 0.00 4.49
45 46 3.979789 CCACTTGCATACGTGGCA 58.020 55.556 14.82 12.01 43.59 4.92
46 47 1.796151 CCACTTGCATACGTGGCAG 59.204 57.895 14.92 12.08 43.59 4.85
47 48 0.673333 CCACTTGCATACGTGGCAGA 60.673 55.000 14.92 7.46 43.59 4.26
48 49 0.443869 CACTTGCATACGTGGCAGAC 59.556 55.000 14.92 0.00 43.05 3.51
49 50 0.321671 ACTTGCATACGTGGCAGACT 59.678 50.000 14.92 1.88 43.05 3.24
50 51 1.270839 ACTTGCATACGTGGCAGACTT 60.271 47.619 14.92 1.38 43.05 3.01
51 52 2.028476 ACTTGCATACGTGGCAGACTTA 60.028 45.455 14.92 2.00 43.05 2.24
52 53 2.753055 TGCATACGTGGCAGACTTAA 57.247 45.000 12.01 0.00 36.11 1.85
53 54 2.616960 TGCATACGTGGCAGACTTAAG 58.383 47.619 12.01 0.00 36.11 1.85
54 55 2.232696 TGCATACGTGGCAGACTTAAGA 59.767 45.455 10.09 0.00 36.11 2.10
55 56 3.118775 TGCATACGTGGCAGACTTAAGAT 60.119 43.478 10.09 0.00 36.11 2.40
56 57 4.098807 TGCATACGTGGCAGACTTAAGATA 59.901 41.667 10.09 0.00 36.11 1.98
57 58 5.047847 GCATACGTGGCAGACTTAAGATAA 58.952 41.667 10.09 0.00 0.00 1.75
58 59 5.175856 GCATACGTGGCAGACTTAAGATAAG 59.824 44.000 10.09 0.00 0.00 1.73
59 60 6.504398 CATACGTGGCAGACTTAAGATAAGA 58.496 40.000 10.09 0.00 0.00 2.10
60 61 4.745649 ACGTGGCAGACTTAAGATAAGAC 58.254 43.478 10.09 0.00 0.00 3.01
61 62 4.463186 ACGTGGCAGACTTAAGATAAGACT 59.537 41.667 10.09 0.83 0.00 3.24
62 63 5.651139 ACGTGGCAGACTTAAGATAAGACTA 59.349 40.000 10.09 0.00 0.00 2.59
63 64 5.972382 CGTGGCAGACTTAAGATAAGACTAC 59.028 44.000 10.09 1.16 0.00 2.73
64 65 6.274579 GTGGCAGACTTAAGATAAGACTACC 58.725 44.000 10.09 10.18 0.00 3.18
65 66 6.097129 GTGGCAGACTTAAGATAAGACTACCT 59.903 42.308 10.09 0.00 30.30 3.08
66 67 6.668283 TGGCAGACTTAAGATAAGACTACCTT 59.332 38.462 10.09 0.00 38.87 3.50
67 68 7.837689 TGGCAGACTTAAGATAAGACTACCTTA 59.162 37.037 10.09 0.00 41.23 2.69
81 82 7.490657 AGACTACCTTATCAACCATTGTACA 57.509 36.000 0.00 0.00 0.00 2.90
82 83 8.090788 AGACTACCTTATCAACCATTGTACAT 57.909 34.615 0.00 0.00 0.00 2.29
83 84 7.987458 AGACTACCTTATCAACCATTGTACATG 59.013 37.037 0.00 0.00 0.00 3.21
84 85 5.835113 ACCTTATCAACCATTGTACATGC 57.165 39.130 0.00 0.00 0.00 4.06
85 86 4.644685 ACCTTATCAACCATTGTACATGCC 59.355 41.667 0.00 0.00 0.00 4.40
86 87 4.037923 CCTTATCAACCATTGTACATGCCC 59.962 45.833 0.00 0.00 0.00 5.36
87 88 2.897271 TCAACCATTGTACATGCCCT 57.103 45.000 0.00 0.00 0.00 5.19
88 89 3.168035 TCAACCATTGTACATGCCCTT 57.832 42.857 0.00 0.00 0.00 3.95
89 90 4.308526 TCAACCATTGTACATGCCCTTA 57.691 40.909 0.00 0.00 0.00 2.69
90 91 4.013728 TCAACCATTGTACATGCCCTTAC 58.986 43.478 0.00 0.00 0.00 2.34
91 92 3.012934 ACCATTGTACATGCCCTTACC 57.987 47.619 0.00 0.00 0.00 2.85
92 93 2.310349 ACCATTGTACATGCCCTTACCA 59.690 45.455 0.00 0.00 0.00 3.25
93 94 3.245443 ACCATTGTACATGCCCTTACCAA 60.245 43.478 0.00 0.00 0.00 3.67
94 95 3.130340 CCATTGTACATGCCCTTACCAAC 59.870 47.826 0.00 0.00 0.00 3.77
95 96 2.500392 TGTACATGCCCTTACCAACC 57.500 50.000 0.00 0.00 0.00 3.77
96 97 1.705745 TGTACATGCCCTTACCAACCA 59.294 47.619 0.00 0.00 0.00 3.67
97 98 2.290641 TGTACATGCCCTTACCAACCAG 60.291 50.000 0.00 0.00 0.00 4.00
98 99 0.611896 ACATGCCCTTACCAACCAGC 60.612 55.000 0.00 0.00 0.00 4.85
99 100 1.000359 ATGCCCTTACCAACCAGCC 60.000 57.895 0.00 0.00 0.00 4.85
100 101 2.362503 GCCCTTACCAACCAGCCC 60.363 66.667 0.00 0.00 0.00 5.19
101 102 2.919096 GCCCTTACCAACCAGCCCT 61.919 63.158 0.00 0.00 0.00 5.19
102 103 1.568118 GCCCTTACCAACCAGCCCTA 61.568 60.000 0.00 0.00 0.00 3.53
103 104 0.546598 CCCTTACCAACCAGCCCTAG 59.453 60.000 0.00 0.00 0.00 3.02
104 105 1.286248 CCTTACCAACCAGCCCTAGT 58.714 55.000 0.00 0.00 0.00 2.57
105 106 1.633945 CCTTACCAACCAGCCCTAGTT 59.366 52.381 0.00 0.00 0.00 2.24
106 107 2.618045 CCTTACCAACCAGCCCTAGTTG 60.618 54.545 0.47 0.47 42.41 3.16
107 108 1.737199 TACCAACCAGCCCTAGTTGT 58.263 50.000 6.00 0.00 41.42 3.32
108 109 1.737199 ACCAACCAGCCCTAGTTGTA 58.263 50.000 6.00 0.00 41.42 2.41
109 110 2.059490 ACCAACCAGCCCTAGTTGTAA 58.941 47.619 6.00 0.00 41.42 2.41
110 111 2.647802 ACCAACCAGCCCTAGTTGTAAT 59.352 45.455 6.00 0.00 41.42 1.89
111 112 3.075432 ACCAACCAGCCCTAGTTGTAATT 59.925 43.478 6.00 0.00 41.42 1.40
112 113 4.086457 CCAACCAGCCCTAGTTGTAATTT 58.914 43.478 6.00 0.00 41.42 1.82
113 114 4.526650 CCAACCAGCCCTAGTTGTAATTTT 59.473 41.667 6.00 0.00 41.42 1.82
114 115 5.011635 CCAACCAGCCCTAGTTGTAATTTTT 59.988 40.000 6.00 0.00 41.42 1.94
262 264 8.896320 ATGCGGAAACTTATATACACATACAA 57.104 30.769 0.00 0.00 0.00 2.41
420 422 5.628797 ACCATGGACTTTTTGTTTGGAAT 57.371 34.783 21.47 0.00 31.86 3.01
432 434 6.603940 TTTGTTTGGAATAGAAATCCCCTG 57.396 37.500 0.00 0.00 36.04 4.45
487 489 4.426313 CTGGCCCGTCCCCTTTCC 62.426 72.222 0.00 0.00 0.00 3.13
528 530 3.821421 ATCTCGGGCTTATTCGTCTTT 57.179 42.857 0.00 0.00 0.00 2.52
616 618 4.684703 CGTGAGAACAACGGATCTAAAGTT 59.315 41.667 0.00 0.00 0.00 2.66
650 652 7.041107 GGTGAATTTTCTAGGCATGCATAAAA 58.959 34.615 21.36 16.81 0.00 1.52
661 663 5.012239 GGCATGCATAAAATAGATCTGGGA 58.988 41.667 21.36 0.00 0.00 4.37
669 671 8.854117 GCATAAAATAGATCTGGGATGTTTTCT 58.146 33.333 5.18 0.00 0.00 2.52
1196 1203 2.027625 GACCTGGCCGAGAACAACG 61.028 63.158 0.00 0.00 0.00 4.10
1245 1253 2.767505 GGAGAACACGGTCATGACTTT 58.232 47.619 24.50 12.82 0.00 2.66
1473 1481 3.016736 CCGCAAGAATGTTCCCATACTT 58.983 45.455 0.00 0.00 43.02 2.24
1611 1619 2.749621 CGAGGCCAAAGTCAAGCTTAAT 59.250 45.455 5.01 0.00 36.17 1.40
1840 1848 0.984230 CTCCCTGTGAGGCCAGTAAA 59.016 55.000 5.01 0.00 37.45 2.01
1841 1849 1.351017 CTCCCTGTGAGGCCAGTAAAA 59.649 52.381 5.01 0.00 37.45 1.52
1867 1875 0.036483 TACGTTTTCCCCTTACCCGC 60.036 55.000 0.00 0.00 0.00 6.13
1868 1876 1.302671 CGTTTTCCCCTTACCCGCA 60.303 57.895 0.00 0.00 0.00 5.69
1873 1881 0.033894 TTCCCCTTACCCGCAAATCC 60.034 55.000 0.00 0.00 0.00 3.01
1906 1914 0.874390 GCATCTGTTCCGTTGCTGAA 59.126 50.000 0.00 0.00 32.41 3.02
1908 1916 2.416747 CATCTGTTCCGTTGCTGAAGA 58.583 47.619 0.00 0.00 0.00 2.87
1942 1950 1.927174 CCCGACGCTATTTGTTCTCAG 59.073 52.381 0.00 0.00 0.00 3.35
1968 1976 1.346395 TCTGTTGCTCACGGTTATGGT 59.654 47.619 0.00 0.00 32.85 3.55
1989 1997 5.763204 TGGTTGTGATTTAGTTTCTGAGACC 59.237 40.000 0.00 0.00 0.00 3.85
2010 2018 8.974060 AGACCTACTCAGTTTCAAAATTGTTA 57.026 30.769 0.00 0.00 0.00 2.41
2011 2019 8.837389 AGACCTACTCAGTTTCAAAATTGTTAC 58.163 33.333 0.00 0.00 0.00 2.50
2013 2021 7.778382 ACCTACTCAGTTTCAAAATTGTTACCT 59.222 33.333 0.00 0.00 0.00 3.08
2014 2022 8.076178 CCTACTCAGTTTCAAAATTGTTACCTG 58.924 37.037 0.00 0.00 0.00 4.00
2015 2023 6.273071 ACTCAGTTTCAAAATTGTTACCTGC 58.727 36.000 0.00 0.00 0.00 4.85
2016 2024 6.127479 ACTCAGTTTCAAAATTGTTACCTGCA 60.127 34.615 0.00 0.00 0.00 4.41
2107 2116 9.210426 CTATGTATTCTGTTTCATTTGCGTAAC 57.790 33.333 0.00 0.00 0.00 2.50
2203 2213 7.359181 GGCAATTTAGCACACTACAATCAAAAC 60.359 37.037 0.00 0.00 35.83 2.43
2215 2225 8.239314 CACTACAATCAAAACTGCTCACATATT 58.761 33.333 0.00 0.00 0.00 1.28
2279 2359 5.598417 TGATAAGATCAGGGAGTTCATCGAA 59.402 40.000 0.00 0.00 33.59 3.71
2349 2429 3.345414 GAGGTACGACGATCTATGGGAT 58.655 50.000 0.00 0.00 37.37 3.85
2386 2466 2.220586 TCCGGCTGTGGGATCAACA 61.221 57.895 0.00 0.00 0.00 3.33
2387 2467 1.746615 CCGGCTGTGGGATCAACAG 60.747 63.158 18.72 18.72 34.83 3.16
2421 2501 2.831685 ATCAACAGCTCACACGGTAA 57.168 45.000 0.00 0.00 0.00 2.85
2426 2506 1.548719 ACAGCTCACACGGTAATGCTA 59.451 47.619 0.00 0.00 0.00 3.49
2487 3488 6.990349 ACTTAGTGTTAAAGTTCAAGCTGCTA 59.010 34.615 0.90 0.00 33.39 3.49
2508 3509 5.292345 GCTAGAAATTTCTCGGGAGAACTTC 59.708 44.000 23.70 14.58 46.13 3.01
2509 3510 4.580868 AGAAATTTCTCGGGAGAACTTCC 58.419 43.478 15.11 8.43 46.13 3.46
2586 3587 7.454380 TGTCCAAATGTTTTAGGGATCTTCAAT 59.546 33.333 0.00 0.00 0.00 2.57
2668 3670 5.334414 GGATGCAACAATTAGGCTATTCTCG 60.334 44.000 0.00 0.00 0.00 4.04
2747 3749 6.538742 GTGAACAATAAGCCTATCTAGTGCAA 59.461 38.462 0.00 0.00 0.00 4.08
2818 3820 5.591099 CAACTTGCCAACTCTATTGTTTGT 58.409 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.402862 AGTAGTTTCTTGGCATTATTAGTGGT 58.597 34.615 0.00 0.00 0.00 4.16
2 3 7.865706 AGTAGTTTCTTGGCATTATTAGTGG 57.134 36.000 0.00 0.00 0.00 4.00
5 6 8.827677 GTGGTAGTAGTTTCTTGGCATTATTAG 58.172 37.037 0.00 0.00 0.00 1.73
7 8 7.402862 AGTGGTAGTAGTTTCTTGGCATTATT 58.597 34.615 0.00 0.00 0.00 1.40
8 9 6.958767 AGTGGTAGTAGTTTCTTGGCATTAT 58.041 36.000 0.00 0.00 0.00 1.28
9 10 6.368779 AGTGGTAGTAGTTTCTTGGCATTA 57.631 37.500 0.00 0.00 0.00 1.90
10 11 5.242795 AGTGGTAGTAGTTTCTTGGCATT 57.757 39.130 0.00 0.00 0.00 3.56
11 12 4.910458 AGTGGTAGTAGTTTCTTGGCAT 57.090 40.909 0.00 0.00 0.00 4.40
12 13 4.385825 CAAGTGGTAGTAGTTTCTTGGCA 58.614 43.478 0.00 0.00 31.79 4.92
13 14 3.188667 GCAAGTGGTAGTAGTTTCTTGGC 59.811 47.826 0.00 0.00 34.69 4.52
14 15 4.385825 TGCAAGTGGTAGTAGTTTCTTGG 58.614 43.478 0.00 0.00 34.69 3.61
15 16 6.183360 CGTATGCAAGTGGTAGTAGTTTCTTG 60.183 42.308 0.00 0.00 36.42 3.02
16 17 5.867716 CGTATGCAAGTGGTAGTAGTTTCTT 59.132 40.000 0.00 0.00 0.00 2.52
17 18 5.047519 ACGTATGCAAGTGGTAGTAGTTTCT 60.048 40.000 0.00 0.00 0.00 2.52
18 19 5.061808 CACGTATGCAAGTGGTAGTAGTTTC 59.938 44.000 11.13 0.00 34.93 2.78
19 20 4.927425 CACGTATGCAAGTGGTAGTAGTTT 59.073 41.667 11.13 0.00 34.93 2.66
20 21 4.491676 CACGTATGCAAGTGGTAGTAGTT 58.508 43.478 11.13 0.00 34.93 2.24
21 22 4.106029 CACGTATGCAAGTGGTAGTAGT 57.894 45.455 11.13 0.00 34.93 2.73
29 30 0.443869 GTCTGCCACGTATGCAAGTG 59.556 55.000 12.35 11.80 38.46 3.16
30 31 0.321671 AGTCTGCCACGTATGCAAGT 59.678 50.000 12.35 5.18 38.46 3.16
31 32 1.442769 AAGTCTGCCACGTATGCAAG 58.557 50.000 12.35 7.55 38.46 4.01
32 33 2.753055 TAAGTCTGCCACGTATGCAA 57.247 45.000 12.35 2.76 38.46 4.08
33 34 2.232696 TCTTAAGTCTGCCACGTATGCA 59.767 45.455 11.01 11.01 37.17 3.96
34 35 2.888594 TCTTAAGTCTGCCACGTATGC 58.111 47.619 1.63 2.46 0.00 3.14
35 36 6.418226 GTCTTATCTTAAGTCTGCCACGTATG 59.582 42.308 1.63 0.00 0.00 2.39
36 37 6.321690 AGTCTTATCTTAAGTCTGCCACGTAT 59.678 38.462 1.63 0.00 0.00 3.06
37 38 5.651139 AGTCTTATCTTAAGTCTGCCACGTA 59.349 40.000 1.63 0.00 0.00 3.57
38 39 4.463186 AGTCTTATCTTAAGTCTGCCACGT 59.537 41.667 1.63 0.00 0.00 4.49
39 40 5.000012 AGTCTTATCTTAAGTCTGCCACG 58.000 43.478 1.63 0.00 0.00 4.94
40 41 6.097129 AGGTAGTCTTATCTTAAGTCTGCCAC 59.903 42.308 21.09 7.43 39.33 5.01
41 42 6.195700 AGGTAGTCTTATCTTAAGTCTGCCA 58.804 40.000 21.09 0.00 39.33 4.92
42 43 6.718522 AGGTAGTCTTATCTTAAGTCTGCC 57.281 41.667 15.47 15.47 38.02 4.85
55 56 9.038072 TGTACAATGGTTGATAAGGTAGTCTTA 57.962 33.333 0.00 0.00 41.66 2.10
56 57 7.913789 TGTACAATGGTTGATAAGGTAGTCTT 58.086 34.615 0.00 0.00 39.40 3.01
57 58 7.490657 TGTACAATGGTTGATAAGGTAGTCT 57.509 36.000 0.00 0.00 0.00 3.24
58 59 7.254795 GCATGTACAATGGTTGATAAGGTAGTC 60.255 40.741 0.00 0.00 0.00 2.59
59 60 6.542370 GCATGTACAATGGTTGATAAGGTAGT 59.458 38.462 0.00 0.00 0.00 2.73
60 61 6.017109 GGCATGTACAATGGTTGATAAGGTAG 60.017 42.308 0.00 0.00 0.00 3.18
61 62 5.825679 GGCATGTACAATGGTTGATAAGGTA 59.174 40.000 0.00 0.00 0.00 3.08
62 63 4.644685 GGCATGTACAATGGTTGATAAGGT 59.355 41.667 0.00 0.00 0.00 3.50
63 64 4.037923 GGGCATGTACAATGGTTGATAAGG 59.962 45.833 0.00 0.00 0.00 2.69
64 65 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
65 66 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
66 67 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
67 68 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
68 69 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
69 70 3.130340 GGTAAGGGCATGTACAATGGTTG 59.870 47.826 0.00 0.00 0.00 3.77
70 71 3.245443 TGGTAAGGGCATGTACAATGGTT 60.245 43.478 0.00 0.00 0.00 3.67
71 72 2.310349 TGGTAAGGGCATGTACAATGGT 59.690 45.455 0.00 0.00 0.00 3.55
72 73 3.011566 TGGTAAGGGCATGTACAATGG 57.988 47.619 0.00 0.00 0.00 3.16
73 74 3.130340 GGTTGGTAAGGGCATGTACAATG 59.870 47.826 0.00 0.12 0.00 2.82
74 75 3.245443 TGGTTGGTAAGGGCATGTACAAT 60.245 43.478 0.00 0.00 0.00 2.71
75 76 2.108425 TGGTTGGTAAGGGCATGTACAA 59.892 45.455 0.00 0.00 0.00 2.41
76 77 1.705745 TGGTTGGTAAGGGCATGTACA 59.294 47.619 0.00 0.00 0.00 2.90
77 78 2.365582 CTGGTTGGTAAGGGCATGTAC 58.634 52.381 0.00 0.00 0.00 2.90
78 79 1.340600 GCTGGTTGGTAAGGGCATGTA 60.341 52.381 0.00 0.00 0.00 2.29
79 80 0.611896 GCTGGTTGGTAAGGGCATGT 60.612 55.000 0.00 0.00 0.00 3.21
80 81 1.322538 GGCTGGTTGGTAAGGGCATG 61.323 60.000 0.00 0.00 0.00 4.06
81 82 1.000359 GGCTGGTTGGTAAGGGCAT 60.000 57.895 0.00 0.00 0.00 4.40
82 83 2.438795 GGCTGGTTGGTAAGGGCA 59.561 61.111 0.00 0.00 0.00 5.36
83 84 1.568118 TAGGGCTGGTTGGTAAGGGC 61.568 60.000 0.00 0.00 0.00 5.19
84 85 0.546598 CTAGGGCTGGTTGGTAAGGG 59.453 60.000 0.00 0.00 0.00 3.95
85 86 1.286248 ACTAGGGCTGGTTGGTAAGG 58.714 55.000 0.00 0.00 0.00 2.69
86 87 2.711542 CAACTAGGGCTGGTTGGTAAG 58.288 52.381 0.00 0.00 44.84 2.34
87 88 2.871096 CAACTAGGGCTGGTTGGTAA 57.129 50.000 0.00 0.00 44.84 2.85
112 113 8.877195 AGGTCCATAGAACACTAGAAGTAAAAA 58.123 33.333 0.00 0.00 29.15 1.94
113 114 8.431910 AGGTCCATAGAACACTAGAAGTAAAA 57.568 34.615 0.00 0.00 29.15 1.52
114 115 9.186837 CTAGGTCCATAGAACACTAGAAGTAAA 57.813 37.037 0.00 0.00 31.86 2.01
115 116 8.334734 ACTAGGTCCATAGAACACTAGAAGTAA 58.665 37.037 0.00 0.00 33.83 2.24
116 117 7.870027 ACTAGGTCCATAGAACACTAGAAGTA 58.130 38.462 0.00 0.00 33.83 2.24
117 118 6.733509 ACTAGGTCCATAGAACACTAGAAGT 58.266 40.000 0.00 0.00 33.83 3.01
118 119 7.122948 ACAACTAGGTCCATAGAACACTAGAAG 59.877 40.741 0.00 0.00 33.83 2.85
119 120 6.952358 ACAACTAGGTCCATAGAACACTAGAA 59.048 38.462 0.00 0.00 33.83 2.10
120 121 6.491383 ACAACTAGGTCCATAGAACACTAGA 58.509 40.000 0.00 0.00 33.83 2.43
121 122 6.777213 ACAACTAGGTCCATAGAACACTAG 57.223 41.667 0.00 0.00 35.31 2.57
122 123 8.834004 ATTACAACTAGGTCCATAGAACACTA 57.166 34.615 0.00 0.00 29.15 2.74
123 124 7.735326 ATTACAACTAGGTCCATAGAACACT 57.265 36.000 0.00 0.00 29.15 3.55
262 264 6.238211 GCTTGCAAGTCTCGTATTTCATATGT 60.238 38.462 26.55 0.00 0.00 2.29
357 359 8.836413 TCTGTTCTGACAAGGTTACAAAAATAG 58.164 33.333 0.00 0.00 34.85 1.73
360 362 7.455641 TTCTGTTCTGACAAGGTTACAAAAA 57.544 32.000 0.00 0.00 34.85 1.94
420 422 6.155565 TCGAAACATAAGTCAGGGGATTTCTA 59.844 38.462 0.00 0.00 0.00 2.10
432 434 6.467723 ACAGTGAATGTCGAAACATAAGTC 57.532 37.500 0.00 0.00 45.48 3.01
528 530 0.611896 TCACTGACGAGCATGGGAGA 60.612 55.000 0.00 0.00 0.00 3.71
597 599 4.755123 CCACAACTTTAGATCCGTTGTTCT 59.245 41.667 14.12 0.00 46.33 3.01
616 618 3.593442 AGAAAATTCACCAGGACCACA 57.407 42.857 0.00 0.00 0.00 4.17
620 622 3.686016 TGCCTAGAAAATTCACCAGGAC 58.314 45.455 0.00 5.17 0.00 3.85
650 652 5.128919 GTGCAGAAAACATCCCAGATCTAT 58.871 41.667 0.00 0.00 0.00 1.98
661 663 8.659925 TGTGATTTATTTTGTGCAGAAAACAT 57.340 26.923 22.45 14.83 0.00 2.71
669 671 9.926158 ACTTATGAATGTGATTTATTTTGTGCA 57.074 25.926 0.00 0.00 0.00 4.57
1021 1028 2.356535 GCAGAAGATGAGGTGGGTGATT 60.357 50.000 0.00 0.00 0.00 2.57
1245 1253 2.359169 GGACTCGTCAGGGCCATGA 61.359 63.158 17.85 17.85 0.00 3.07
1419 1427 2.759973 CCCGCCTCCAGTAGCTGA 60.760 66.667 0.00 0.00 32.44 4.26
1473 1481 2.688446 ACGCTCGATGTTCTTGGAGATA 59.312 45.455 0.00 0.00 0.00 1.98
1826 1834 3.339547 GCCTTTTACTGGCCTCACA 57.660 52.632 3.32 0.00 44.32 3.58
1840 1848 0.327259 GGGGAAAACGTAGAGGCCTT 59.673 55.000 6.77 0.00 0.00 4.35
1841 1849 0.546988 AGGGGAAAACGTAGAGGCCT 60.547 55.000 3.86 3.86 0.00 5.19
1867 1875 6.718454 AGATGCCCTCTTATTATGTGGATTTG 59.282 38.462 0.54 0.00 0.00 2.32
1868 1876 6.718454 CAGATGCCCTCTTATTATGTGGATTT 59.282 38.462 0.54 0.00 29.16 2.17
1873 1881 5.471456 GGAACAGATGCCCTCTTATTATGTG 59.529 44.000 0.00 0.00 29.16 3.21
1906 1914 1.278985 TCGGGCAATCATGAACACTCT 59.721 47.619 0.00 0.00 0.00 3.24
1908 1916 1.453155 GTCGGGCAATCATGAACACT 58.547 50.000 0.00 0.00 0.00 3.55
1942 1950 0.389166 CCGTGAGCAACAGAGAGGTC 60.389 60.000 0.00 0.00 0.00 3.85
1968 1976 7.963532 AGTAGGTCTCAGAAACTAAATCACAA 58.036 34.615 0.00 0.00 0.00 3.33
1989 1997 7.591426 GCAGGTAACAATTTTGAAACTGAGTAG 59.409 37.037 15.00 0.00 35.75 2.57
2005 2013 1.250154 GGCCAGCATGCAGGTAACAA 61.250 55.000 27.67 0.00 33.52 2.83
2013 2021 3.746436 ATCAGGGGCCAGCATGCA 61.746 61.111 21.98 0.00 31.97 3.96
2014 2022 3.224324 CATCAGGGGCCAGCATGC 61.224 66.667 10.51 10.51 31.97 4.06
2015 2023 2.125326 CACATCAGGGGCCAGCATG 61.125 63.158 4.39 6.06 0.00 4.06
2016 2024 2.277737 CACATCAGGGGCCAGCAT 59.722 61.111 4.39 0.00 0.00 3.79
2076 2085 9.793252 GCAAATGAAACAGAATACATAGTTCAT 57.207 29.630 0.00 0.00 0.00 2.57
2089 2098 3.132160 TCCGTTACGCAAATGAAACAGA 58.868 40.909 0.00 0.00 0.00 3.41
2203 2213 7.255569 CCATAATGGCATTAATATGTGAGCAG 58.744 38.462 22.65 2.29 34.12 4.24
2326 2406 1.463831 CCATAGATCGTCGTACCTCGG 59.536 57.143 0.00 0.00 40.32 4.63
2386 2466 4.454678 TGTTGATTCTGCTCTTTGTGTCT 58.545 39.130 0.00 0.00 0.00 3.41
2387 2467 4.781071 CTGTTGATTCTGCTCTTTGTGTC 58.219 43.478 0.00 0.00 0.00 3.67
2421 2501 4.450976 TGATTAACCGAAGTGCATAGCAT 58.549 39.130 0.00 0.00 41.91 3.79
2426 2506 7.807977 AAATATCTGATTAACCGAAGTGCAT 57.192 32.000 0.00 0.00 0.00 3.96
2469 3470 8.803201 AAATTTCTAGCAGCTTGAACTTTAAC 57.197 30.769 23.79 0.00 31.17 2.01
2586 3587 2.548280 CCACCAATGCAAAATGTGAGCA 60.548 45.455 9.70 0.00 43.14 4.26
2639 3641 1.102154 CTAATTGTTGCATCCGCCCA 58.898 50.000 0.00 0.00 37.32 5.36
2777 3779 3.502211 AGTTGCTCCACTGAAAATTACGG 59.498 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.