Multiple sequence alignment - TraesCS3B01G394600

Loading Multiple Alignment...

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 TraesCS3B01G394600 chr3B 100.000 3715 0 0 1 3715 621935424 621939138 0.000000e+00 6861.0
1 TraesCS3B01G394600 chr3A 90.509 3087 158 51 544 3576 610366709 610369714 0.000000e+00 3952.0
2 TraesCS3B01G394600 chr3A 89.655 464 24 6 69 509 610365853 610366315 1.500000e-158 569.0
3 TraesCS3B01G394600 chr3D 93.328 2323 129 18 560 2872 467748495 467750801 0.000000e+00 3408.0
4 TraesCS3B01G394600 chr3D 88.994 845 42 20 2885 3715 467750898 467751705 0.000000e+00 998.0
5 TraesCS3B01G394600 chr3D 91.858 479 25 6 100 569 467747721 467748194 0.000000e+00 656.0
6 TraesCS3B01G394600 chr7A 93.175 337 22 1 1688 2024 186401939 186401604 9.270000e-136 494.0
7 TraesCS3B01G394600 chr7A 97.115 104 3 0 1505 1608 186402035 186401932 3.810000e-40 176.0
8 TraesCS3B01G394600 chr1D 90.390 333 21 6 2239 2563 81485546 81485217 9.530000e-116 427.0
9 TraesCS3B01G394600 chr1D 90.955 199 17 1 1829 2027 81485751 81485554 2.200000e-67 267.0
10 TraesCS3B01G394600 chr6D 94.444 108 6 0 1214 1321 275477259 275477366 2.290000e-37 167.0
11 TraesCS3B01G394600 chr6D 92.537 67 3 2 1021 1086 275477191 275477256 1.100000e-15 95.3
12 TraesCS3B01G394600 chr6D 94.231 52 2 1 1929 1980 326171026 326170976 1.110000e-10 78.7
13 TraesCS3B01G394600 chr5B 84.906 159 22 2 2308 2465 331374730 331374887 3.840000e-35 159.0
14 TraesCS3B01G394600 chr2A 92.727 110 8 0 1212 1321 17999784 17999893 3.840000e-35 159.0
15 TraesCS3B01G394600 chr6A 90.000 110 9 1 1212 1321 306723333 306723440 1.390000e-29 141.0
16 TraesCS3B01G394600 chr6A 93.333 60 4 0 1027 1086 306723273 306723332 5.110000e-14 89.8
17 TraesCS3B01G394600 chr1B 81.618 136 23 2 2305 2439 662521084 662520950 1.090000e-20 111.0
18 TraesCS3B01G394600 chr1A 86.111 72 4 3 1020 1086 64568130 64568060 5.150000e-09 73.1


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 TraesCS3B01G394600 chr3B 621935424 621939138 3714 False 6861.000000 6861 100.000000 1 3715 1 chr3B.!!$F1 3714
1 TraesCS3B01G394600 chr3A 610365853 610369714 3861 False 2260.500000 3952 90.082000 69 3576 2 chr3A.!!$F1 3507
2 TraesCS3B01G394600 chr3D 467747721 467751705 3984 False 1687.333333 3408 91.393333 100 3715 3 chr3D.!!$F1 3615
3 TraesCS3B01G394600 chr1D 81485217 81485751 534 True 347.000000 427 90.672500 1829 2563 2 chr1D.!!$R1 734

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
822 1518 0.392595 CCGTTAGCTTCAACCTCCCC 60.393 60.0 0.00 0.00 0.00 4.81 F
1119 1822 0.034896 AGGTGTTTCGTGTAGGCCTG 59.965 55.0 17.99 0.00 0.00 4.85 F
1122 1825 0.320421 TGTTTCGTGTAGGCCTGAGC 60.320 55.0 17.99 6.16 38.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2772 0.025001 GTCATGGACAATTCGCGTCG 59.975 55.0 5.77 0.0 34.04 5.12 R
2068 2774 0.036388 AGGTCATGGACAATTCGCGT 60.036 50.0 5.77 0.0 33.68 6.01 R
2804 3529 0.387565 TCAACTTCTTTTTGGCGGGC 59.612 50.0 0.00 0.0 0.00 6.13 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
19 20 2.265589 CTTTTGTAACTGGGTCGGGT 57.734 50.000 0.00 0.00 0.00 5.28
20 21 2.148768 CTTTTGTAACTGGGTCGGGTC 58.851 52.381 0.00 0.00 0.00 4.46
21 22 0.397564 TTTGTAACTGGGTCGGGTCC 59.602 55.000 0.00 0.00 0.00 4.46
22 23 1.818959 TTGTAACTGGGTCGGGTCCG 61.819 60.000 2.52 2.52 41.35 4.79
23 24 2.681064 TAACTGGGTCGGGTCCGG 60.681 66.667 9.68 0.00 40.25 5.14
27 28 4.700448 TGGGTCGGGTCCGGCTAA 62.700 66.667 13.85 0.00 44.25 3.09
28 29 3.393106 GGGTCGGGTCCGGCTAAA 61.393 66.667 13.85 0.00 44.25 1.85
29 30 2.125391 GGTCGGGTCCGGCTAAAC 60.125 66.667 13.85 2.06 44.25 2.01
30 31 2.507769 GTCGGGTCCGGCTAAACG 60.508 66.667 6.77 0.00 41.28 3.60
31 32 2.990967 TCGGGTCCGGCTAAACGT 60.991 61.111 9.68 0.00 40.25 3.99
32 33 2.812178 CGGGTCCGGCTAAACGTG 60.812 66.667 0.00 0.00 35.56 4.49
33 34 2.658422 GGGTCCGGCTAAACGTGA 59.342 61.111 0.00 0.00 0.00 4.35
34 35 1.739196 GGGTCCGGCTAAACGTGAC 60.739 63.158 0.00 0.00 35.08 3.67
35 36 1.739196 GGTCCGGCTAAACGTGACC 60.739 63.158 0.00 3.53 42.48 4.02
36 37 1.005867 GTCCGGCTAAACGTGACCA 60.006 57.895 0.00 0.00 32.01 4.02
37 38 1.005867 TCCGGCTAAACGTGACCAC 60.006 57.895 0.00 0.00 0.00 4.16
38 39 2.030958 CCGGCTAAACGTGACCACC 61.031 63.158 0.00 0.00 0.00 4.61
39 40 1.301087 CGGCTAAACGTGACCACCA 60.301 57.895 0.00 0.00 0.00 4.17
40 41 0.881159 CGGCTAAACGTGACCACCAA 60.881 55.000 0.00 0.00 0.00 3.67
41 42 1.310904 GGCTAAACGTGACCACCAAA 58.689 50.000 0.00 0.00 0.00 3.28
42 43 1.677052 GGCTAAACGTGACCACCAAAA 59.323 47.619 0.00 0.00 0.00 2.44
43 44 2.099427 GGCTAAACGTGACCACCAAAAA 59.901 45.455 0.00 0.00 0.00 1.94
44 45 3.368495 GCTAAACGTGACCACCAAAAAG 58.632 45.455 0.00 0.00 0.00 2.27
45 46 2.951457 AAACGTGACCACCAAAAAGG 57.049 45.000 0.00 0.00 45.67 3.11
56 57 2.977772 CCAAAAAGGTCAAAGGCACA 57.022 45.000 0.00 0.00 0.00 4.57
57 58 3.258971 CCAAAAAGGTCAAAGGCACAA 57.741 42.857 0.00 0.00 0.00 3.33
58 59 3.604582 CCAAAAAGGTCAAAGGCACAAA 58.395 40.909 0.00 0.00 0.00 2.83
59 60 4.006319 CCAAAAAGGTCAAAGGCACAAAA 58.994 39.130 0.00 0.00 0.00 2.44
60 61 4.639755 CCAAAAAGGTCAAAGGCACAAAAT 59.360 37.500 0.00 0.00 0.00 1.82
61 62 5.125257 CCAAAAAGGTCAAAGGCACAAAATT 59.875 36.000 0.00 0.00 0.00 1.82
62 63 6.350027 CCAAAAAGGTCAAAGGCACAAAATTT 60.350 34.615 0.00 0.00 0.00 1.82
63 64 7.148171 CCAAAAAGGTCAAAGGCACAAAATTTA 60.148 33.333 0.00 0.00 0.00 1.40
64 65 7.552458 AAAAGGTCAAAGGCACAAAATTTAG 57.448 32.000 0.00 0.00 0.00 1.85
65 66 4.631131 AGGTCAAAGGCACAAAATTTAGC 58.369 39.130 0.00 0.00 0.00 3.09
70 71 2.278026 GGCACAAAATTTAGCCTCCG 57.722 50.000 17.34 0.00 43.70 4.63
73 74 2.727916 GCACAAAATTTAGCCTCCGTCG 60.728 50.000 0.00 0.00 0.00 5.12
96 97 1.043116 CACTGCCTCCGGTCCATCTA 61.043 60.000 0.00 0.00 0.00 1.98
101 102 1.587054 CTCCGGTCCATCTATCCGC 59.413 63.158 0.00 0.00 42.48 5.54
118 124 0.457337 CGCGGTAGTTCAGTGGTACC 60.457 60.000 4.43 4.43 34.03 3.34
122 128 3.881937 GGTAGTTCAGTGGTACCGAAT 57.118 47.619 7.57 0.00 0.00 3.34
134 140 1.134788 GTACCGAATGCACAGTAGCCT 60.135 52.381 0.00 0.00 0.00 4.58
309 322 3.333189 CGCCACGCAGATCCATCG 61.333 66.667 0.00 0.00 0.00 3.84
530 556 4.567597 ACCACGTGTCCCTCCCCA 62.568 66.667 15.65 0.00 0.00 4.96
534 560 3.480133 CGTGTCCCTCCCCATCCC 61.480 72.222 0.00 0.00 0.00 3.85
535 561 2.042930 GTGTCCCTCCCCATCCCT 59.957 66.667 0.00 0.00 0.00 4.20
644 1340 4.100084 CTGCATGGGCCGGTCAGA 62.100 66.667 9.07 0.00 40.13 3.27
739 1435 2.684881 CGGGCATCAATAAAGAAGCTGT 59.315 45.455 0.00 0.00 33.10 4.40
815 1511 3.115892 CGCCGCCGTTAGCTTCAA 61.116 61.111 0.00 0.00 40.39 2.69
822 1518 0.392595 CCGTTAGCTTCAACCTCCCC 60.393 60.000 0.00 0.00 0.00 4.81
903 1599 2.783122 ATCAGGTGGAGACGGACGGT 62.783 60.000 0.00 0.00 0.00 4.83
1061 1757 3.493350 GCTTAGCTTCTACTGCTGCCATA 60.493 47.826 0.00 0.00 41.32 2.74
1063 1759 2.114616 AGCTTCTACTGCTGCCATACT 58.885 47.619 0.00 0.00 39.56 2.12
1094 1797 3.036084 CGCGAAGGCAGTGTCGTT 61.036 61.111 0.00 0.00 39.46 3.85
1119 1822 0.034896 AGGTGTTTCGTGTAGGCCTG 59.965 55.000 17.99 0.00 0.00 4.85
1122 1825 0.320421 TGTTTCGTGTAGGCCTGAGC 60.320 55.000 17.99 6.16 38.76 4.26
1167 1870 1.141185 GGGTTGAGGGAATCTAGGGG 58.859 60.000 0.00 0.00 0.00 4.79
1169 1872 1.345112 GGTTGAGGGAATCTAGGGGGA 60.345 57.143 0.00 0.00 0.00 4.81
1338 2043 1.302033 CAGGTTGGAGCTGAAGCGT 60.302 57.895 0.00 0.00 45.98 5.07
1469 2174 4.853507 CGAGAACACGGAGCGTTA 57.146 55.556 0.00 0.00 38.32 3.18
1473 2178 1.005867 GAACACGGAGCGTTACCCA 60.006 57.895 0.00 0.00 38.32 4.51
1491 2196 0.977395 CAAGGTTCGGGTTCTCCTCT 59.023 55.000 0.00 0.00 0.00 3.69
1494 2199 1.076677 AGGTTCGGGTTCTCCTCTGTA 59.923 52.381 0.00 0.00 0.00 2.74
1500 2205 0.824759 GGTTCTCCTCTGTATGCGGT 59.175 55.000 0.00 0.00 0.00 5.68
1546 2251 2.440247 CCATCAGGCCGGGTTTCC 60.440 66.667 2.18 0.00 0.00 3.13
1618 2323 1.589076 CTCACACGTACGTCGAACTC 58.411 55.000 19.94 0.00 42.86 3.01
1620 2325 1.193203 TCACACGTACGTCGAACTCTC 59.807 52.381 19.94 0.00 42.86 3.20
1623 2328 1.196354 CACGTACGTCGAACTCTCCTT 59.804 52.381 19.94 0.00 42.86 3.36
1624 2329 1.876156 ACGTACGTCGAACTCTCCTTT 59.124 47.619 16.72 0.00 42.86 3.11
1641 2346 3.248363 TCCTTTCATATGAGCGCAATTCG 59.752 43.478 11.47 0.00 42.12 3.34
1659 2364 2.351455 TCGTGTTGTTTCTGCACAAGA 58.649 42.857 0.00 0.00 37.33 3.02
2044 2749 2.351157 GGTATGTATACCCTCGCGTCAC 60.351 54.545 5.77 0.00 45.62 3.67
2045 2750 0.672342 ATGTATACCCTCGCGTCACC 59.328 55.000 5.77 0.00 0.00 4.02
2046 2751 1.009222 GTATACCCTCGCGTCACCG 60.009 63.158 5.77 0.00 37.07 4.94
2066 2772 1.154150 GCATGGCACGCTCTGTTTC 60.154 57.895 0.00 0.00 0.00 2.78
2067 2773 1.133253 CATGGCACGCTCTGTTTCG 59.867 57.895 0.00 0.00 0.00 3.46
2068 2774 1.005037 ATGGCACGCTCTGTTTCGA 60.005 52.632 0.00 0.00 0.00 3.71
2069 2775 1.291877 ATGGCACGCTCTGTTTCGAC 61.292 55.000 0.00 0.00 0.00 4.20
2075 2781 1.674611 CGCTCTGTTTCGACGCGAAT 61.675 55.000 15.93 0.00 45.28 3.34
2083 2789 0.718904 TTCGACGCGAATTGTCCATG 59.281 50.000 15.93 0.00 41.05 3.66
2089 2795 2.276201 CGCGAATTGTCCATGACCTTA 58.724 47.619 0.00 0.00 0.00 2.69
2090 2796 2.030457 CGCGAATTGTCCATGACCTTAC 59.970 50.000 0.00 0.00 0.00 2.34
2091 2797 2.030457 GCGAATTGTCCATGACCTTACG 59.970 50.000 0.00 0.00 0.00 3.18
2092 2798 3.259064 CGAATTGTCCATGACCTTACGT 58.741 45.455 0.00 0.00 0.00 3.57
2093 2799 3.062099 CGAATTGTCCATGACCTTACGTG 59.938 47.826 0.00 0.00 0.00 4.49
2095 2801 1.344065 TGTCCATGACCTTACGTGGT 58.656 50.000 0.00 0.00 44.54 4.16
2096 2802 1.695242 TGTCCATGACCTTACGTGGTT 59.305 47.619 0.00 0.00 44.54 3.67
2097 2803 2.105134 TGTCCATGACCTTACGTGGTTT 59.895 45.455 0.00 0.00 44.54 3.27
2098 2804 3.324268 TGTCCATGACCTTACGTGGTTTA 59.676 43.478 0.00 0.00 44.54 2.01
2099 2805 3.681417 GTCCATGACCTTACGTGGTTTAC 59.319 47.826 0.00 0.00 44.54 2.01
2621 3336 2.126031 GGGAGCTCCGACAACGTC 60.126 66.667 26.36 6.14 37.88 4.34
2642 3357 1.985447 GCGTCGTGGTCGTGGATCTA 61.985 60.000 0.00 0.00 38.33 1.98
2744 3459 6.793492 AATTTCTTTCTCTCCTCGTTTCTG 57.207 37.500 0.00 0.00 0.00 3.02
2769 3484 1.376543 ATCTTTGCTGCCTCGATGTG 58.623 50.000 0.00 0.00 0.00 3.21
2841 3566 2.625737 TGAACAGATAAGCTCAGCTGC 58.374 47.619 9.47 0.00 39.62 5.25
2856 3581 0.453950 GCTGCTTCAACTGCATCGTG 60.454 55.000 0.00 0.00 39.86 4.35
2857 3582 0.453950 CTGCTTCAACTGCATCGTGC 60.454 55.000 0.00 3.44 45.29 5.34
2858 3583 0.886043 TGCTTCAACTGCATCGTGCT 60.886 50.000 10.54 0.00 45.31 4.40
2861 3586 2.068519 CTTCAACTGCATCGTGCTACA 58.931 47.619 10.54 0.00 45.31 2.74
2879 3604 6.303496 GTGCTACATACACGAAGATATTCGAG 59.697 42.308 27.65 21.89 46.52 4.04
2900 3709 6.525628 TCGAGATGTTGTTAACAAGTCGATAC 59.474 38.462 25.77 15.11 46.10 2.24
2902 3711 4.634349 TGTTGTTAACAAGTCGATACGC 57.366 40.909 21.12 7.02 38.72 4.42
2916 3725 8.420945 CAAGTCGATACGCAGATCTTTATTTAG 58.579 37.037 0.00 0.00 0.00 1.85
2946 3755 6.783162 AGCTATTCATATCCATCGTACGTAC 58.217 40.000 15.90 15.90 0.00 3.67
2948 3757 6.468319 GCTATTCATATCCATCGTACGTACAC 59.532 42.308 24.50 2.17 0.00 2.90
2949 3758 4.394099 TCATATCCATCGTACGTACACG 57.606 45.455 24.50 15.12 46.33 4.49
2958 3770 2.034591 TCGTACGTACACGAGATAAGCG 60.035 50.000 24.50 6.97 45.45 4.68
3038 3853 2.201732 CTCGTTGATATTCGTGGGTGG 58.798 52.381 0.00 0.00 0.00 4.61
3039 3854 1.134640 TCGTTGATATTCGTGGGTGGG 60.135 52.381 0.00 0.00 0.00 4.61
3040 3855 1.406341 CGTTGATATTCGTGGGTGGGT 60.406 52.381 0.00 0.00 0.00 4.51
3042 3857 1.574263 TGATATTCGTGGGTGGGTGA 58.426 50.000 0.00 0.00 0.00 4.02
3043 3858 2.123589 TGATATTCGTGGGTGGGTGAT 58.876 47.619 0.00 0.00 0.00 3.06
3044 3859 2.104111 TGATATTCGTGGGTGGGTGATC 59.896 50.000 0.00 0.00 0.00 2.92
3053 3870 1.226888 GTGGGTGATCGCCTCGTAC 60.227 63.158 24.15 14.17 0.00 3.67
3059 3876 2.817423 GATCGCCTCGTACCGTCGT 61.817 63.158 0.00 0.00 0.00 4.34
3104 3921 4.739228 CGAAGAACAGATGCTGATCTAGTG 59.261 45.833 7.50 0.00 41.57 2.74
3105 3922 5.659463 GAAGAACAGATGCTGATCTAGTGT 58.341 41.667 7.50 0.00 41.57 3.55
3106 3923 5.261209 AGAACAGATGCTGATCTAGTGTC 57.739 43.478 5.55 0.00 40.83 3.67
3107 3924 4.955450 AGAACAGATGCTGATCTAGTGTCT 59.045 41.667 5.55 0.00 40.83 3.41
3108 3925 6.125719 AGAACAGATGCTGATCTAGTGTCTA 58.874 40.000 5.55 0.00 40.83 2.59
3155 3981 3.500680 GCTGTACTGAACCCGAATGAAAA 59.499 43.478 3.61 0.00 0.00 2.29
3156 3982 4.612939 GCTGTACTGAACCCGAATGAAAAC 60.613 45.833 3.61 0.00 0.00 2.43
3157 3983 3.495377 TGTACTGAACCCGAATGAAAACG 59.505 43.478 0.00 0.00 0.00 3.60
3158 3984 2.567985 ACTGAACCCGAATGAAAACGT 58.432 42.857 0.00 0.00 0.00 3.99
3159 3985 2.289547 ACTGAACCCGAATGAAAACGTG 59.710 45.455 0.00 0.00 0.00 4.49
3164 3990 1.211709 CGAATGAAAACGTGCCCCC 59.788 57.895 0.00 0.00 0.00 5.40
3205 4031 3.053991 TCTTCAGTGGGACAACAAAAGGA 60.054 43.478 0.00 0.00 44.16 3.36
3329 4164 0.396811 AAAAGTCTCCACTGACCCCG 59.603 55.000 0.00 0.00 37.66 5.73
3481 4320 0.103608 TGGAAAAGGGGAGGGAGGAA 60.104 55.000 0.00 0.00 0.00 3.36
3490 4329 2.543637 AGGGAGGAAGGAGGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
3491 4330 1.954994 AGGGAGGAAGGAGGGGGAT 60.955 63.158 0.00 0.00 0.00 3.85
3492 4331 1.006227 GGGAGGAAGGAGGGGGATT 59.994 63.158 0.00 0.00 0.00 3.01
3576 4418 0.458669 GATCCCTTCGCGTAACTCCA 59.541 55.000 5.77 0.00 0.00 3.86
3578 4420 1.804326 CCCTTCGCGTAACTCCACG 60.804 63.158 5.77 0.00 44.71 4.94
3579 4421 1.804326 CCTTCGCGTAACTCCACGG 60.804 63.158 5.77 0.00 42.18 4.94
3580 4422 1.210931 CTTCGCGTAACTCCACGGA 59.789 57.895 5.77 0.00 42.18 4.69
3659 4509 1.764454 GGGAGGGAGGAGAGAAGGC 60.764 68.421 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.202794 GGACCCGACCCAGTTACAAAA 60.203 52.381 0.00 0.00 0.00 2.44
3 4 1.818959 CGGACCCGACCCAGTTACAA 61.819 60.000 1.54 0.00 42.83 2.41
4 5 2.277591 CGGACCCGACCCAGTTACA 61.278 63.158 1.54 0.00 42.83 2.41
5 6 2.575461 CGGACCCGACCCAGTTAC 59.425 66.667 1.54 0.00 42.83 2.50
6 7 2.681064 CCGGACCCGACCCAGTTA 60.681 66.667 10.42 0.00 42.83 2.24
10 11 4.700448 TTAGCCGGACCCGACCCA 62.700 66.667 5.05 0.00 42.83 4.51
11 12 3.393106 TTTAGCCGGACCCGACCC 61.393 66.667 5.05 0.00 42.83 4.46
12 13 2.125391 GTTTAGCCGGACCCGACC 60.125 66.667 5.05 0.63 42.83 4.79
13 14 2.507769 CGTTTAGCCGGACCCGAC 60.508 66.667 5.05 0.00 42.83 4.79
14 15 2.990967 ACGTTTAGCCGGACCCGA 60.991 61.111 5.05 0.00 42.83 5.14
15 16 2.812178 CACGTTTAGCCGGACCCG 60.812 66.667 5.05 0.66 39.44 5.28
16 17 1.739196 GTCACGTTTAGCCGGACCC 60.739 63.158 5.05 0.00 0.00 4.46
17 18 1.739196 GGTCACGTTTAGCCGGACC 60.739 63.158 5.05 3.53 39.34 4.46
18 19 1.005867 TGGTCACGTTTAGCCGGAC 60.006 57.895 5.05 0.00 0.00 4.79
19 20 1.005867 GTGGTCACGTTTAGCCGGA 60.006 57.895 5.05 0.00 0.00 5.14
20 21 2.030958 GGTGGTCACGTTTAGCCGG 61.031 63.158 0.00 0.00 0.00 6.13
21 22 0.881159 TTGGTGGTCACGTTTAGCCG 60.881 55.000 0.00 0.00 0.00 5.52
22 23 1.310904 TTTGGTGGTCACGTTTAGCC 58.689 50.000 0.00 0.00 0.00 3.93
23 24 3.368495 CTTTTTGGTGGTCACGTTTAGC 58.632 45.455 0.00 0.00 0.00 3.09
24 25 3.959943 CCTTTTTGGTGGTCACGTTTAG 58.040 45.455 0.00 0.00 0.00 1.85
26 27 2.951457 CCTTTTTGGTGGTCACGTTT 57.049 45.000 0.00 0.00 0.00 3.60
37 38 2.977772 TGTGCCTTTGACCTTTTTGG 57.022 45.000 0.00 0.00 42.93 3.28
38 39 5.816449 ATTTTGTGCCTTTGACCTTTTTG 57.184 34.783 0.00 0.00 0.00 2.44
39 40 6.832520 AAATTTTGTGCCTTTGACCTTTTT 57.167 29.167 0.00 0.00 0.00 1.94
40 41 6.038161 GCTAAATTTTGTGCCTTTGACCTTTT 59.962 34.615 0.00 0.00 0.00 2.27
41 42 5.527214 GCTAAATTTTGTGCCTTTGACCTTT 59.473 36.000 0.00 0.00 0.00 3.11
42 43 5.056480 GCTAAATTTTGTGCCTTTGACCTT 58.944 37.500 0.00 0.00 0.00 3.50
43 44 4.503123 GGCTAAATTTTGTGCCTTTGACCT 60.503 41.667 17.02 0.00 41.92 3.85
44 45 3.745975 GGCTAAATTTTGTGCCTTTGACC 59.254 43.478 17.02 0.00 41.92 4.02
45 46 4.990543 GGCTAAATTTTGTGCCTTTGAC 57.009 40.909 17.02 0.00 41.92 3.18
51 52 1.544246 ACGGAGGCTAAATTTTGTGCC 59.456 47.619 16.74 16.74 45.21 5.01
52 53 2.727916 CGACGGAGGCTAAATTTTGTGC 60.728 50.000 0.00 0.00 0.00 4.57
53 54 2.727916 GCGACGGAGGCTAAATTTTGTG 60.728 50.000 0.00 0.00 0.00 3.33
54 55 1.467342 GCGACGGAGGCTAAATTTTGT 59.533 47.619 0.00 0.00 0.00 2.83
55 56 1.737793 AGCGACGGAGGCTAAATTTTG 59.262 47.619 0.00 0.00 39.39 2.44
56 57 2.007608 GAGCGACGGAGGCTAAATTTT 58.992 47.619 0.00 0.00 41.72 1.82
57 58 1.653151 GAGCGACGGAGGCTAAATTT 58.347 50.000 0.00 0.00 41.72 1.82
58 59 0.179081 GGAGCGACGGAGGCTAAATT 60.179 55.000 0.00 0.00 41.72 1.82
59 60 1.327690 TGGAGCGACGGAGGCTAAAT 61.328 55.000 0.00 0.00 41.72 1.40
60 61 1.980232 TGGAGCGACGGAGGCTAAA 60.980 57.895 0.00 0.00 41.72 1.85
61 62 2.361992 TGGAGCGACGGAGGCTAA 60.362 61.111 0.00 0.00 41.72 3.09
62 63 3.138798 GTGGAGCGACGGAGGCTA 61.139 66.667 0.00 0.00 41.72 3.93
64 65 4.803426 CAGTGGAGCGACGGAGGC 62.803 72.222 0.00 0.00 0.00 4.70
65 66 4.803426 GCAGTGGAGCGACGGAGG 62.803 72.222 0.00 0.00 0.00 4.30
66 67 4.803426 GGCAGTGGAGCGACGGAG 62.803 72.222 0.00 0.00 34.64 4.63
70 71 4.803426 CGGAGGCAGTGGAGCGAC 62.803 72.222 0.00 0.00 34.64 5.19
84 85 2.265904 CGCGGATAGATGGACCGGA 61.266 63.158 9.46 0.00 45.66 5.14
96 97 1.255667 ACCACTGAACTACCGCGGAT 61.256 55.000 35.90 18.92 0.00 4.18
101 102 3.708195 CGGTACCACTGAACTACCG 57.292 57.895 13.54 1.38 45.04 4.02
118 124 0.179137 TCGAGGCTACTGTGCATTCG 60.179 55.000 15.14 15.14 40.41 3.34
121 127 0.608130 TTGTCGAGGCTACTGTGCAT 59.392 50.000 0.00 0.00 34.04 3.96
122 128 0.319555 GTTGTCGAGGCTACTGTGCA 60.320 55.000 0.00 0.00 34.04 4.57
134 140 0.391793 TGTTGTGTGGCAGTTGTCGA 60.392 50.000 0.00 0.00 0.00 4.20
397 423 4.124126 GGGGTGAGGGAGGGGGAT 62.124 72.222 0.00 0.00 0.00 3.85
424 450 4.766088 GAGCCTTTTGCCGCGCTG 62.766 66.667 5.56 0.00 42.71 5.18
512 538 4.016706 GGGGAGGGACACGTGGTG 62.017 72.222 21.57 0.00 39.75 4.17
613 1308 4.101448 GCAGCGAGGGGTCATGGT 62.101 66.667 0.00 0.00 0.00 3.55
644 1340 0.388294 GTTATTCTACTCCGGCCGCT 59.612 55.000 22.85 6.53 0.00 5.52
779 1475 4.823419 CGCCGGTGTTATCGCCCA 62.823 66.667 6.91 0.00 40.82 5.36
822 1518 3.814268 CGCAATCTTGGCCCCACG 61.814 66.667 0.00 0.00 0.00 4.94
831 1527 1.617755 CGACACGTGCTCGCAATCTT 61.618 55.000 17.22 0.00 41.18 2.40
903 1599 2.190841 TGAGTCCGTGACGTGCTCA 61.191 57.895 19.45 19.45 37.67 4.26
973 1669 1.144276 GCGGTAGAAGAAGGGGAGC 59.856 63.158 0.00 0.00 0.00 4.70
1061 1757 4.796231 CGCGCGTTCCCAGCTAGT 62.796 66.667 24.19 0.00 0.00 2.57
1085 1781 0.852777 CACCTCGACAAACGACACTG 59.147 55.000 0.00 0.00 46.45 3.66
1094 1797 2.544277 CCTACACGAAACACCTCGACAA 60.544 50.000 0.00 0.00 41.44 3.18
1152 1855 0.267960 GGTCCCCCTAGATTCCCTCA 59.732 60.000 0.00 0.00 0.00 3.86
1154 1857 1.236282 CGGTCCCCCTAGATTCCCT 59.764 63.158 0.00 0.00 0.00 4.20
1167 1870 4.493747 CTCGCTCGAACCCGGTCC 62.494 72.222 0.00 0.00 36.24 4.46
1175 1880 0.179197 CAAGTAGTCGCTCGCTCGAA 60.179 55.000 0.63 0.00 40.43 3.71
1324 2029 2.629002 GGAAACGCTTCAGCTCCAA 58.371 52.632 0.35 0.00 39.32 3.53
1473 2178 0.977395 CAGAGGAGAACCCGAACCTT 59.023 55.000 0.00 0.00 40.87 3.50
1491 2196 2.098871 CGACGACGACCGCATACA 59.901 61.111 0.00 0.00 43.32 2.29
1500 2205 2.810012 CTCCATCTCGCGACGACGA 61.810 63.158 12.29 0.20 42.66 4.20
1618 2323 4.610007 CGAATTGCGCTCATATGAAAGGAG 60.610 45.833 9.73 0.00 0.00 3.69
1620 2325 3.002656 ACGAATTGCGCTCATATGAAAGG 59.997 43.478 9.73 0.23 46.04 3.11
1623 2328 2.935849 ACACGAATTGCGCTCATATGAA 59.064 40.909 9.73 0.00 46.04 2.57
1624 2329 2.549926 ACACGAATTGCGCTCATATGA 58.450 42.857 9.73 5.07 46.04 2.15
1641 2346 4.355543 TTCTCTTGTGCAGAAACAACAC 57.644 40.909 0.00 0.00 35.16 3.32
1659 2364 2.025605 ACCATGTCATCAGCACCATTCT 60.026 45.455 0.00 0.00 0.00 2.40
1772 2477 0.544357 TCCATCACCTCCTTCCACGT 60.544 55.000 0.00 0.00 0.00 4.49
1773 2478 0.176680 CTCCATCACCTCCTTCCACG 59.823 60.000 0.00 0.00 0.00 4.94
1996 2701 2.029844 GACGGAGAGTGCAACAGGC 61.030 63.158 0.00 0.00 41.43 4.85
2027 2732 2.109431 GGTGACGCGAGGGTATACA 58.891 57.895 15.93 0.00 0.00 2.29
2047 2752 2.839324 GAAACAGAGCGTGCCATGCG 62.839 60.000 2.72 0.00 34.72 4.73
2048 2753 1.154150 GAAACAGAGCGTGCCATGC 60.154 57.895 0.00 0.00 0.00 4.06
2049 2754 1.133253 CGAAACAGAGCGTGCCATG 59.867 57.895 0.00 0.00 0.00 3.66
2050 2755 1.005037 TCGAAACAGAGCGTGCCAT 60.005 52.632 0.00 0.00 0.00 4.40
2051 2756 1.954146 GTCGAAACAGAGCGTGCCA 60.954 57.895 0.00 0.00 0.00 4.92
2052 2757 2.853914 GTCGAAACAGAGCGTGCC 59.146 61.111 0.00 0.00 0.00 5.01
2055 2761 3.097728 CGCGTCGAAACAGAGCGT 61.098 61.111 0.00 0.00 44.96 5.07
2057 2763 3.534160 TTCGCGTCGAAACAGAGC 58.466 55.556 5.77 0.00 43.00 4.09
2066 2772 0.025001 GTCATGGACAATTCGCGTCG 59.975 55.000 5.77 0.00 34.04 5.12
2067 2773 0.373716 GGTCATGGACAATTCGCGTC 59.626 55.000 5.77 0.00 33.68 5.19
2068 2774 0.036388 AGGTCATGGACAATTCGCGT 60.036 50.000 5.77 0.00 33.68 6.01
2069 2775 1.086696 AAGGTCATGGACAATTCGCG 58.913 50.000 0.00 0.00 33.68 5.87
2075 2781 1.695242 ACCACGTAAGGTCATGGACAA 59.305 47.619 0.00 0.00 37.28 3.18
2083 2789 4.635223 AGGAAAGTAAACCACGTAAGGTC 58.365 43.478 0.00 0.00 42.25 3.85
2089 2795 2.490991 GCTGAGGAAAGTAAACCACGT 58.509 47.619 0.00 0.00 0.00 4.49
2090 2796 1.804748 GGCTGAGGAAAGTAAACCACG 59.195 52.381 0.00 0.00 0.00 4.94
2091 2797 2.814336 CAGGCTGAGGAAAGTAAACCAC 59.186 50.000 9.42 0.00 0.00 4.16
2092 2798 2.708861 TCAGGCTGAGGAAAGTAAACCA 59.291 45.455 14.43 0.00 0.00 3.67
2093 2799 3.075148 GTCAGGCTGAGGAAAGTAAACC 58.925 50.000 19.38 0.00 0.00 3.27
2095 2801 2.289444 CGGTCAGGCTGAGGAAAGTAAA 60.289 50.000 19.38 0.00 0.00 2.01
2096 2802 1.275291 CGGTCAGGCTGAGGAAAGTAA 59.725 52.381 19.38 0.00 0.00 2.24
2097 2803 0.895530 CGGTCAGGCTGAGGAAAGTA 59.104 55.000 19.38 0.00 0.00 2.24
2098 2804 1.674057 CGGTCAGGCTGAGGAAAGT 59.326 57.895 19.38 0.00 0.00 2.66
2099 2805 1.078848 CCGGTCAGGCTGAGGAAAG 60.079 63.158 19.38 7.48 0.00 2.62
2621 3336 3.626680 ATCCACGACCACGACGCTG 62.627 63.158 0.00 0.00 42.66 5.18
2642 3357 3.441011 GAATCACGATCCCCGGCGT 62.441 63.158 6.01 0.00 43.93 5.68
2729 3444 7.411486 AGATAAATTCAGAAACGAGGAGAGA 57.589 36.000 0.00 0.00 0.00 3.10
2730 3445 8.386606 CAAAGATAAATTCAGAAACGAGGAGAG 58.613 37.037 0.00 0.00 0.00 3.20
2731 3446 7.148407 GCAAAGATAAATTCAGAAACGAGGAGA 60.148 37.037 0.00 0.00 0.00 3.71
2732 3447 6.963805 GCAAAGATAAATTCAGAAACGAGGAG 59.036 38.462 0.00 0.00 0.00 3.69
2733 3448 6.655003 AGCAAAGATAAATTCAGAAACGAGGA 59.345 34.615 0.00 0.00 0.00 3.71
2744 3459 4.882671 TCGAGGCAGCAAAGATAAATTC 57.117 40.909 0.00 0.00 0.00 2.17
2804 3529 0.387565 TCAACTTCTTTTTGGCGGGC 59.612 50.000 0.00 0.00 0.00 6.13
2879 3604 5.164031 TGCGTATCGACTTGTTAACAACATC 60.164 40.000 17.01 15.29 41.79 3.06
2900 3709 5.106908 GCTTAGGGCTAAATAAAGATCTGCG 60.107 44.000 0.00 0.00 38.06 5.18
2916 3725 5.053145 CGATGGATATGAATAGCTTAGGGC 58.947 45.833 0.00 0.00 42.19 5.19
2926 3735 5.179929 TCGTGTACGTACGATGGATATGAAT 59.820 40.000 24.41 0.00 46.94 2.57
2946 3755 2.405357 CCTAATTCGCGCTTATCTCGTG 59.595 50.000 5.56 0.00 38.63 4.35
2948 3757 2.405357 CACCTAATTCGCGCTTATCTCG 59.595 50.000 5.56 0.00 0.00 4.04
2949 3758 2.731976 CCACCTAATTCGCGCTTATCTC 59.268 50.000 5.56 0.00 0.00 2.75
2955 3767 0.597637 CGATCCACCTAATTCGCGCT 60.598 55.000 5.56 0.00 0.00 5.92
2958 3770 1.859080 GTCACGATCCACCTAATTCGC 59.141 52.381 0.00 0.00 35.08 4.70
3009 3824 4.082408 ACGAATATCAACGAGTTGTCAGGA 60.082 41.667 14.64 0.00 41.16 3.86
3053 3870 2.119147 CTGCTCCGATCCTACGACGG 62.119 65.000 0.00 0.00 46.71 4.79
3059 3876 3.366396 ACTTTTCTCTGCTCCGATCCTA 58.634 45.455 0.00 0.00 0.00 2.94
3104 3921 2.791560 CACGCACAGTGCATAGATAGAC 59.208 50.000 25.19 0.00 45.36 2.59
3105 3922 3.084070 CACGCACAGTGCATAGATAGA 57.916 47.619 25.19 0.00 45.36 1.98
3130 3956 3.512329 TCATTCGGGTTCAGTACAGCTTA 59.488 43.478 0.00 0.00 0.00 3.09
3164 3990 6.205784 TGAAGAAAAATCGTGCAGTAAAAGG 58.794 36.000 0.00 0.00 0.00 3.11
3165 3991 6.912591 ACTGAAGAAAAATCGTGCAGTAAAAG 59.087 34.615 0.00 0.00 33.78 2.27
3166 3992 6.690957 CACTGAAGAAAAATCGTGCAGTAAAA 59.309 34.615 0.00 0.00 33.78 1.52
3172 3998 2.293122 CCCACTGAAGAAAAATCGTGCA 59.707 45.455 0.00 0.00 0.00 4.57
3205 4031 1.399714 TCATCCCGTTCTATCAGCGT 58.600 50.000 0.00 0.00 0.00 5.07
3249 4078 4.057428 GACGACAGCGACAGGCCT 62.057 66.667 0.00 0.00 45.17 5.19
3291 4126 0.966920 TCTCTTTCTCCCCACGACAC 59.033 55.000 0.00 0.00 0.00 3.67
3481 4320 0.909623 CACGTTACAATCCCCCTCCT 59.090 55.000 0.00 0.00 0.00 3.69
3589 4433 4.344865 AACCACGCCAAGGCCGAT 62.345 61.111 5.34 0.00 37.98 4.18
3636 4486 3.742248 CTCTCCTCCCTCCCCGACC 62.742 73.684 0.00 0.00 0.00 4.79
3637 4487 2.123640 CTCTCCTCCCTCCCCGAC 60.124 72.222 0.00 0.00 0.00 4.79
3638 4488 1.934341 TTCTCTCCTCCCTCCCCGA 60.934 63.158 0.00 0.00 0.00 5.14
3639 4489 1.456705 CTTCTCTCCTCCCTCCCCG 60.457 68.421 0.00 0.00 0.00 5.73
3651 4501 1.274712 CACTTCCAGGAGCCTTCTCT 58.725 55.000 0.00 0.00 39.31 3.10
3659 4509 4.785453 GCCCGCCACTTCCAGGAG 62.785 72.222 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.