Multiple sequence alignment - TraesCS4B01G112500

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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 TraesCS4B01G112500 chr4B 100.000 3227 0 0 1 3227 126509657 126506431 0.000000e+00 5960.0
1 TraesCS4B01G112500 chr4D 91.608 2848 146 29 191 3003 89436824 89434035 0.000000e+00 3849.0
2 TraesCS4B01G112500 chr4D 93.210 162 6 3 3067 3227 89434005 89433848 1.940000e-57 233.0
3 TraesCS4B01G112500 chr4A 91.685 2790 128 34 178 2914 501977213 501974475 0.000000e+00 3771.0
4 TraesCS4B01G112500 chr4A 83.721 129 4 6 3039 3165 501974330 501974217 4.400000e-19 106.0
5 TraesCS4B01G112500 chr4A 94.545 55 3 0 124 178 501977295 501977241 5.740000e-13 86.1
6 TraesCS4B01G112500 chr5B 81.310 1038 173 13 1189 2217 222127510 222126485 0.000000e+00 822.0
7 TraesCS4B01G112500 chr5D 81.232 1039 172 14 1189 2217 208536931 208535906 0.000000e+00 817.0
8 TraesCS4B01G112500 chr5A 81.232 1039 172 14 1189 2217 269320612 269319587 0.000000e+00 817.0
9 TraesCS4B01G112500 chr6B 94.444 36 1 1 3001 3035 157361069 157361104 2.000000e-03 54.7


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 TraesCS4B01G112500 chr4B 126506431 126509657 3226 True 5960.000000 5960 100.000000 1 3227 1 chr4B.!!$R1 3226
1 TraesCS4B01G112500 chr4D 89433848 89436824 2976 True 2041.000000 3849 92.409000 191 3227 2 chr4D.!!$R1 3036
2 TraesCS4B01G112500 chr4A 501974217 501977295 3078 True 1321.033333 3771 89.983667 124 3165 3 chr4A.!!$R1 3041
3 TraesCS4B01G112500 chr5B 222126485 222127510 1025 True 822.000000 822 81.310000 1189 2217 1 chr5B.!!$R1 1028
4 TraesCS4B01G112500 chr5D 208535906 208536931 1025 True 817.000000 817 81.232000 1189 2217 1 chr5D.!!$R1 1028
5 TraesCS4B01G112500 chr5A 269319587 269320612 1025 True 817.000000 817 81.232000 1189 2217 1 chr5A.!!$R1 1028

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
730 763 0.107831 GACCACAGGCCGCCATTATA 59.892 55.0 13.15 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 2590 0.851495 GATCAGAGCAAGCGACATCG 59.149 55.0 0.0 0.0 43.27 3.84 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
35 36 5.810525 GCATGAGCTAATAAAAAGAAGCGA 58.189 37.500 0.00 0.00 39.94 4.93
36 37 5.678919 GCATGAGCTAATAAAAAGAAGCGAC 59.321 40.000 0.00 0.00 39.94 5.19
37 38 6.675486 GCATGAGCTAATAAAAAGAAGCGACA 60.675 38.462 0.00 0.00 39.94 4.35
38 39 6.165659 TGAGCTAATAAAAAGAAGCGACAC 57.834 37.500 0.00 0.00 39.94 3.67
39 40 5.932303 TGAGCTAATAAAAAGAAGCGACACT 59.068 36.000 0.00 0.00 39.94 3.55
40 41 6.090898 TGAGCTAATAAAAAGAAGCGACACTC 59.909 38.462 0.00 0.00 39.94 3.51
41 42 5.351740 AGCTAATAAAAAGAAGCGACACTCC 59.648 40.000 0.00 0.00 39.94 3.85
42 43 4.663636 AATAAAAAGAAGCGACACTCCG 57.336 40.909 0.00 0.00 0.00 4.63
43 44 1.226746 AAAAAGAAGCGACACTCCGG 58.773 50.000 0.00 0.00 0.00 5.14
44 45 1.228657 AAAAGAAGCGACACTCCGGC 61.229 55.000 0.00 0.00 0.00 6.13
45 46 2.100879 AAAGAAGCGACACTCCGGCT 62.101 55.000 0.00 0.00 39.01 5.52
46 47 2.493907 AAGAAGCGACACTCCGGCTC 62.494 60.000 0.00 0.00 35.64 4.70
47 48 2.992114 AAGCGACACTCCGGCTCT 60.992 61.111 0.00 0.00 35.64 4.09
48 49 2.875684 GAAGCGACACTCCGGCTCTC 62.876 65.000 0.00 0.00 35.64 3.20
49 50 3.444805 GCGACACTCCGGCTCTCT 61.445 66.667 0.00 0.00 0.00 3.10
50 51 2.995872 GCGACACTCCGGCTCTCTT 61.996 63.158 0.00 0.00 0.00 2.85
51 52 1.587054 CGACACTCCGGCTCTCTTT 59.413 57.895 0.00 0.00 0.00 2.52
52 53 0.456995 CGACACTCCGGCTCTCTTTC 60.457 60.000 0.00 0.00 0.00 2.62
53 54 0.892063 GACACTCCGGCTCTCTTTCT 59.108 55.000 0.00 0.00 0.00 2.52
54 55 0.605589 ACACTCCGGCTCTCTTTCTG 59.394 55.000 0.00 0.00 0.00 3.02
55 56 0.891373 CACTCCGGCTCTCTTTCTGA 59.109 55.000 0.00 0.00 0.00 3.27
56 57 1.480137 CACTCCGGCTCTCTTTCTGAT 59.520 52.381 0.00 0.00 0.00 2.90
57 58 1.754226 ACTCCGGCTCTCTTTCTGATC 59.246 52.381 0.00 0.00 0.00 2.92
58 59 1.753649 CTCCGGCTCTCTTTCTGATCA 59.246 52.381 0.00 0.00 0.00 2.92
59 60 2.167281 CTCCGGCTCTCTTTCTGATCAA 59.833 50.000 0.00 0.00 0.00 2.57
60 61 2.167281 TCCGGCTCTCTTTCTGATCAAG 59.833 50.000 0.00 0.00 0.00 3.02
61 62 2.167281 CCGGCTCTCTTTCTGATCAAGA 59.833 50.000 0.00 0.00 0.00 3.02
62 63 3.368843 CCGGCTCTCTTTCTGATCAAGAA 60.369 47.826 0.00 0.18 43.37 2.52
72 73 4.982241 TCTGATCAAGAAAGGAAGGTGT 57.018 40.909 0.00 0.00 29.54 4.16
73 74 4.645535 TCTGATCAAGAAAGGAAGGTGTG 58.354 43.478 0.00 0.00 29.54 3.82
74 75 4.347876 TCTGATCAAGAAAGGAAGGTGTGA 59.652 41.667 0.00 0.00 29.54 3.58
75 76 4.389374 TGATCAAGAAAGGAAGGTGTGAC 58.611 43.478 0.00 0.00 0.00 3.67
76 77 3.208747 TCAAGAAAGGAAGGTGTGACC 57.791 47.619 0.00 0.00 38.99 4.02
77 78 2.507886 TCAAGAAAGGAAGGTGTGACCA 59.492 45.455 0.00 0.00 41.95 4.02
78 79 3.053991 TCAAGAAAGGAAGGTGTGACCAA 60.054 43.478 0.00 0.00 41.95 3.67
79 80 2.932261 AGAAAGGAAGGTGTGACCAAC 58.068 47.619 0.00 0.00 41.95 3.77
80 81 1.954382 GAAAGGAAGGTGTGACCAACC 59.046 52.381 0.00 0.00 41.95 3.77
81 82 0.179029 AAGGAAGGTGTGACCAACCG 60.179 55.000 0.00 0.00 41.95 4.44
82 83 2.258726 GGAAGGTGTGACCAACCGC 61.259 63.158 0.00 0.00 41.95 5.68
83 84 2.590575 AAGGTGTGACCAACCGCG 60.591 61.111 0.00 0.00 41.95 6.46
86 87 4.012895 GTGTGACCAACCGCGCTG 62.013 66.667 5.56 0.00 0.00 5.18
90 91 3.737172 GACCAACCGCGCTGCAAT 61.737 61.111 5.56 0.00 0.00 3.56
91 92 3.267597 GACCAACCGCGCTGCAATT 62.268 57.895 5.56 0.00 0.00 2.32
92 93 2.806198 CCAACCGCGCTGCAATTG 60.806 61.111 5.56 0.00 0.00 2.32
93 94 3.472298 CAACCGCGCTGCAATTGC 61.472 61.111 23.69 23.69 42.50 3.56
112 113 4.477302 TGCATATGATGTGCAGATTTCG 57.523 40.909 12.96 0.00 46.76 3.46
113 114 3.231965 GCATATGATGTGCAGATTTCGC 58.768 45.455 9.37 0.00 42.08 4.70
114 115 3.818387 CATATGATGTGCAGATTTCGCC 58.182 45.455 0.00 0.00 0.00 5.54
115 116 0.659427 ATGATGTGCAGATTTCGCCG 59.341 50.000 0.00 0.00 0.00 6.46
116 117 0.390998 TGATGTGCAGATTTCGCCGA 60.391 50.000 0.00 0.00 0.00 5.54
117 118 0.726827 GATGTGCAGATTTCGCCGAA 59.273 50.000 0.00 0.00 0.00 4.30
118 119 1.331756 GATGTGCAGATTTCGCCGAAT 59.668 47.619 0.00 0.00 0.00 3.34
119 120 2.017138 TGTGCAGATTTCGCCGAATA 57.983 45.000 0.00 0.00 0.00 1.75
120 121 1.933181 TGTGCAGATTTCGCCGAATAG 59.067 47.619 0.00 0.00 0.00 1.73
121 122 1.261619 GTGCAGATTTCGCCGAATAGG 59.738 52.381 0.00 0.00 44.97 2.57
122 123 1.138069 TGCAGATTTCGCCGAATAGGA 59.862 47.619 0.00 0.00 45.00 2.94
126 127 2.135933 GATTTCGCCGAATAGGACCTG 58.864 52.381 3.53 0.00 45.00 4.00
138 139 0.692419 AGGACCTGGATGTGGCTAGG 60.692 60.000 0.00 0.00 41.83 3.02
145 146 1.922447 TGGATGTGGCTAGGTTCCAAT 59.078 47.619 0.00 0.00 33.66 3.16
215 244 1.234615 CGGTGCCGACATTTTGGAGT 61.235 55.000 4.35 0.00 42.83 3.85
299 329 8.778141 GTCGATCTTCAAGACGTATAACATAA 57.222 34.615 8.58 0.00 0.00 1.90
329 359 7.347748 TCATGTTTGATCCAATTTCCCCATAAT 59.652 33.333 0.00 0.00 0.00 1.28
383 413 1.071699 TCTAAACGAGCTTTGTGCCCT 59.928 47.619 0.00 0.00 44.23 5.19
387 417 0.250901 ACGAGCTTTGTGCCCTCATT 60.251 50.000 0.00 0.00 44.23 2.57
398 428 1.209504 TGCCCTCATTAAGGTTCCTCG 59.790 52.381 0.00 0.00 44.56 4.63
412 442 2.024176 TCCTCGAAAACATAGCAGGC 57.976 50.000 0.00 0.00 0.00 4.85
414 444 1.017387 CTCGAAAACATAGCAGGCCC 58.983 55.000 0.00 0.00 0.00 5.80
436 466 0.761187 ATGAGCATCGTATGTGGCCT 59.239 50.000 3.32 0.00 38.61 5.19
450 480 6.038825 CGTATGTGGCCTTTTGATGGTATAAA 59.961 38.462 3.32 0.00 0.00 1.40
467 497 6.150976 TGGTATAAACTTCCAAGATTGCACTG 59.849 38.462 0.00 0.00 0.00 3.66
479 509 7.014134 TCCAAGATTGCACTGTTTCTTGAATAA 59.986 33.333 17.42 4.72 44.97 1.40
534 565 3.929094 TCCTTGCAAAATCATTGAAGCC 58.071 40.909 0.00 0.00 0.00 4.35
621 653 7.073342 ACTTGTCCGCAATTACTAATCTTTC 57.927 36.000 0.00 0.00 33.65 2.62
652 684 8.122472 ACCATCTACAAAAAGGGTCAAATAAG 57.878 34.615 0.00 0.00 0.00 1.73
670 702 8.478877 TCAAATAAGGCTAAACAAAAACCAGAA 58.521 29.630 0.00 0.00 0.00 3.02
680 712 7.751768 AAACAAAAACCAGAAACATTCCAAA 57.248 28.000 0.00 0.00 0.00 3.28
689 721 5.702209 CCAGAAACATTCCAAATCCAAAAGG 59.298 40.000 0.00 0.00 0.00 3.11
694 726 9.671279 GAAACATTCCAAATCCAAAAGGATATT 57.329 29.630 0.00 0.00 0.00 1.28
727 760 2.713531 AAAGACCACAGGCCGCCATT 62.714 55.000 13.15 0.00 0.00 3.16
728 761 1.847798 AAGACCACAGGCCGCCATTA 61.848 55.000 13.15 0.00 0.00 1.90
729 762 1.152963 GACCACAGGCCGCCATTAT 60.153 57.895 13.15 0.00 0.00 1.28
730 763 0.107831 GACCACAGGCCGCCATTATA 59.892 55.000 13.15 0.00 0.00 0.98
731 764 0.548989 ACCACAGGCCGCCATTATAA 59.451 50.000 13.15 0.00 0.00 0.98
732 765 1.064314 ACCACAGGCCGCCATTATAAA 60.064 47.619 13.15 0.00 0.00 1.40
733 766 1.336755 CCACAGGCCGCCATTATAAAC 59.663 52.381 13.15 0.00 0.00 2.01
764 797 4.216411 TCAACAGGTGTAAGGGATTAGC 57.784 45.455 0.00 0.00 0.00 3.09
765 798 3.844211 TCAACAGGTGTAAGGGATTAGCT 59.156 43.478 0.00 0.00 0.00 3.32
853 889 2.672714 ACATATATACGCGCACACCTG 58.327 47.619 5.73 0.00 0.00 4.00
876 912 1.691196 CCATCAACAACACCACACCT 58.309 50.000 0.00 0.00 0.00 4.00
890 926 1.188219 ACACCTCACCTCATCGCAGT 61.188 55.000 0.00 0.00 0.00 4.40
897 933 2.028203 TCACCTCATCGCAGTTTCATCA 60.028 45.455 0.00 0.00 0.00 3.07
1220 1279 4.889856 CATCGCGTGGATCCGGCA 62.890 66.667 22.81 12.90 31.28 5.69
1560 1619 4.821589 GGCGTCGCCTCCTTCCTG 62.822 72.222 28.98 0.00 46.69 3.86
1566 1625 3.011517 GCCTCCTTCCTGGCCTCA 61.012 66.667 3.32 0.00 43.11 3.86
2328 2403 3.263261 TCTGTCTCGCAGTCAGTAGTAG 58.737 50.000 9.06 0.00 45.23 2.57
2329 2404 1.738350 TGTCTCGCAGTCAGTAGTAGC 59.262 52.381 0.00 0.00 0.00 3.58
2348 2423 9.983804 GTAGTAGCAAGTTTAAAATGTGTATCC 57.016 33.333 0.00 0.00 0.00 2.59
2460 2536 7.636359 GTGTATCATCAGATTTTTGTTAGTCGC 59.364 37.037 0.00 0.00 35.67 5.19
2465 2541 4.933400 TCAGATTTTTGTTAGTCGCCTACC 59.067 41.667 0.00 0.00 0.00 3.18
2513 2589 0.319383 ACTTGCGTCTGTGAGCTCTG 60.319 55.000 16.19 5.48 0.00 3.35
2514 2590 1.624865 CTTGCGTCTGTGAGCTCTGC 61.625 60.000 16.19 8.54 0.00 4.26
2516 2592 2.563427 CGTCTGTGAGCTCTGCGA 59.437 61.111 16.19 5.33 0.00 5.10
2517 2593 1.138459 CGTCTGTGAGCTCTGCGAT 59.862 57.895 16.19 0.00 0.00 4.58
2679 2765 6.588719 TTGAACATTAGCTTAAGGCATTGT 57.411 33.333 4.29 0.43 44.79 2.71
2680 2766 7.695480 TTGAACATTAGCTTAAGGCATTGTA 57.305 32.000 4.29 0.00 44.79 2.41
2681 2767 7.083875 TGAACATTAGCTTAAGGCATTGTAC 57.916 36.000 4.29 0.00 44.79 2.90
2682 2768 6.884295 TGAACATTAGCTTAAGGCATTGTACT 59.116 34.615 4.29 0.00 44.79 2.73
2683 2769 6.927294 ACATTAGCTTAAGGCATTGTACTC 57.073 37.500 4.29 0.00 44.79 2.59
2684 2770 6.653989 ACATTAGCTTAAGGCATTGTACTCT 58.346 36.000 4.29 0.00 44.79 3.24
2703 2789 3.822735 CTCTTTTGTCCAGAGAAATGCCA 59.177 43.478 0.00 0.00 40.39 4.92
2706 2792 2.655090 TGTCCAGAGAAATGCCACAA 57.345 45.000 0.00 0.00 0.00 3.33
2722 2808 3.008485 GCCACAATTAAAAATGTCCCCCA 59.992 43.478 0.00 0.00 0.00 4.96
2723 2809 4.574892 CCACAATTAAAAATGTCCCCCAC 58.425 43.478 0.00 0.00 0.00 4.61
2774 2860 8.744652 ACTATTTCCCAGTTCTCTATATGATCG 58.255 37.037 0.00 0.00 0.00 3.69
2788 2874 9.743057 CTCTATATGATCGAGATTATTTCCCAC 57.257 37.037 0.00 0.00 0.00 4.61
2834 2920 6.013725 TGTCTGCTTATCAGGAGTAAAAAGGA 60.014 38.462 0.00 0.00 43.06 3.36
2835 2921 6.879458 GTCTGCTTATCAGGAGTAAAAAGGAA 59.121 38.462 0.00 0.00 43.06 3.36
2844 2930 5.649831 CAGGAGTAAAAAGGAAATCTCAGGG 59.350 44.000 0.00 0.00 0.00 4.45
2937 3030 5.231147 GCAGAACACAAACGCTTCAAATAAA 59.769 36.000 0.00 0.00 0.00 1.40
2951 3044 8.397906 CGCTTCAAATAAATCTGAATACCAAGA 58.602 33.333 0.00 0.00 31.40 3.02
3014 3137 2.305858 ACAAAGTACTCCCTCCGTCT 57.694 50.000 0.00 0.00 0.00 4.18
3018 3141 2.060050 AGTACTCCCTCCGTCTCATG 57.940 55.000 0.00 0.00 0.00 3.07
3021 3148 1.407936 ACTCCCTCCGTCTCATGATG 58.592 55.000 0.00 0.00 0.00 3.07
3033 3160 6.878923 TCCGTCTCATGATGTAAGACATTTTT 59.121 34.615 12.82 0.00 39.27 1.94
3034 3161 8.038351 TCCGTCTCATGATGTAAGACATTTTTA 58.962 33.333 12.82 0.00 39.27 1.52
3083 3237 8.988064 ATATAGCAACAGATCACGGTTAATAG 57.012 34.615 0.00 0.00 33.56 1.73
3086 3240 5.581085 AGCAACAGATCACGGTTAATAGAAC 59.419 40.000 0.00 0.00 33.56 3.01
3093 3247 5.717078 TCACGGTTAATAGAACAGTCTGT 57.283 39.130 0.00 0.00 35.12 3.41
3094 3248 5.466819 TCACGGTTAATAGAACAGTCTGTG 58.533 41.667 6.18 0.00 35.12 3.66
3120 3274 7.296660 CAGAGTAAGAAATTGCAGAACAGAAG 58.703 38.462 0.00 0.00 0.00 2.85
3152 3307 5.126061 ACTGAATCCAAATACCAAGTGCATC 59.874 40.000 0.00 0.00 0.00 3.91
3205 3361 6.294176 GCATGTGTTCTTCTTTCCTTGTACAT 60.294 38.462 0.00 0.00 0.00 2.29
3206 3362 7.094805 GCATGTGTTCTTCTTTCCTTGTACATA 60.095 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.678919 GTCGCTTCTTTTTATTAGCTCATGC 59.321 40.000 0.00 0.00 40.05 4.06
13 14 6.684555 GTGTCGCTTCTTTTTATTAGCTCATG 59.315 38.462 0.00 0.00 0.00 3.07
14 15 6.595716 AGTGTCGCTTCTTTTTATTAGCTCAT 59.404 34.615 0.00 0.00 0.00 2.90
15 16 5.932303 AGTGTCGCTTCTTTTTATTAGCTCA 59.068 36.000 0.00 0.00 0.00 4.26
16 17 6.410243 AGTGTCGCTTCTTTTTATTAGCTC 57.590 37.500 0.00 0.00 0.00 4.09
17 18 5.351740 GGAGTGTCGCTTCTTTTTATTAGCT 59.648 40.000 0.00 0.00 0.00 3.32
18 19 5.561070 GGAGTGTCGCTTCTTTTTATTAGC 58.439 41.667 0.00 0.00 0.00 3.09
19 20 5.220416 CCGGAGTGTCGCTTCTTTTTATTAG 60.220 44.000 0.00 0.00 0.00 1.73
20 21 4.628333 CCGGAGTGTCGCTTCTTTTTATTA 59.372 41.667 0.00 0.00 0.00 0.98
21 22 3.435671 CCGGAGTGTCGCTTCTTTTTATT 59.564 43.478 0.00 0.00 0.00 1.40
22 23 3.000727 CCGGAGTGTCGCTTCTTTTTAT 58.999 45.455 0.00 0.00 0.00 1.40
23 24 2.409975 CCGGAGTGTCGCTTCTTTTTA 58.590 47.619 0.00 0.00 0.00 1.52
24 25 1.226746 CCGGAGTGTCGCTTCTTTTT 58.773 50.000 0.00 0.00 0.00 1.94
25 26 1.228657 GCCGGAGTGTCGCTTCTTTT 61.229 55.000 5.05 0.00 0.00 2.27
26 27 1.668151 GCCGGAGTGTCGCTTCTTT 60.668 57.895 5.05 0.00 0.00 2.52
27 28 2.048127 GCCGGAGTGTCGCTTCTT 60.048 61.111 5.05 0.00 0.00 2.52
28 29 2.992114 AGCCGGAGTGTCGCTTCT 60.992 61.111 5.05 0.00 0.00 2.85
29 30 2.507324 GAGCCGGAGTGTCGCTTC 60.507 66.667 5.05 0.00 0.00 3.86
30 31 2.992114 AGAGCCGGAGTGTCGCTT 60.992 61.111 5.05 0.00 0.00 4.68
31 32 3.444805 GAGAGCCGGAGTGTCGCT 61.445 66.667 5.05 0.00 0.00 4.93
32 33 2.493907 AAAGAGAGCCGGAGTGTCGC 62.494 60.000 5.05 0.00 0.00 5.19
33 34 0.456995 GAAAGAGAGCCGGAGTGTCG 60.457 60.000 5.05 0.00 0.00 4.35
34 35 0.892063 AGAAAGAGAGCCGGAGTGTC 59.108 55.000 5.05 0.00 0.00 3.67
35 36 0.605589 CAGAAAGAGAGCCGGAGTGT 59.394 55.000 5.05 0.00 0.00 3.55
36 37 0.891373 TCAGAAAGAGAGCCGGAGTG 59.109 55.000 5.05 0.00 0.00 3.51
37 38 1.754226 GATCAGAAAGAGAGCCGGAGT 59.246 52.381 5.05 0.00 0.00 3.85
38 39 1.753649 TGATCAGAAAGAGAGCCGGAG 59.246 52.381 5.05 0.00 0.00 4.63
39 40 1.852633 TGATCAGAAAGAGAGCCGGA 58.147 50.000 5.05 0.00 0.00 5.14
40 41 2.167281 TCTTGATCAGAAAGAGAGCCGG 59.833 50.000 0.00 0.00 0.00 6.13
41 42 3.516981 TCTTGATCAGAAAGAGAGCCG 57.483 47.619 0.00 0.00 0.00 5.52
50 51 5.065914 CACACCTTCCTTTCTTGATCAGAA 58.934 41.667 0.00 0.00 39.99 3.02
51 52 4.347876 TCACACCTTCCTTTCTTGATCAGA 59.652 41.667 0.00 0.00 0.00 3.27
52 53 4.453819 GTCACACCTTCCTTTCTTGATCAG 59.546 45.833 0.00 0.00 0.00 2.90
53 54 4.389374 GTCACACCTTCCTTTCTTGATCA 58.611 43.478 0.00 0.00 0.00 2.92
54 55 3.753797 GGTCACACCTTCCTTTCTTGATC 59.246 47.826 0.00 0.00 34.73 2.92
55 56 3.138283 TGGTCACACCTTCCTTTCTTGAT 59.862 43.478 0.00 0.00 39.58 2.57
56 57 2.507886 TGGTCACACCTTCCTTTCTTGA 59.492 45.455 0.00 0.00 39.58 3.02
57 58 2.930950 TGGTCACACCTTCCTTTCTTG 58.069 47.619 0.00 0.00 39.58 3.02
58 59 3.288092 GTTGGTCACACCTTCCTTTCTT 58.712 45.455 0.00 0.00 39.58 2.52
59 60 2.422945 GGTTGGTCACACCTTCCTTTCT 60.423 50.000 0.00 0.00 39.58 2.52
60 61 1.954382 GGTTGGTCACACCTTCCTTTC 59.046 52.381 0.00 0.00 39.58 2.62
61 62 1.749286 CGGTTGGTCACACCTTCCTTT 60.749 52.381 0.00 0.00 39.58 3.11
62 63 0.179029 CGGTTGGTCACACCTTCCTT 60.179 55.000 0.00 0.00 39.58 3.36
63 64 1.450211 CGGTTGGTCACACCTTCCT 59.550 57.895 0.00 0.00 39.58 3.36
64 65 2.258726 GCGGTTGGTCACACCTTCC 61.259 63.158 0.00 0.00 39.58 3.46
65 66 2.604174 CGCGGTTGGTCACACCTTC 61.604 63.158 0.00 0.00 39.58 3.46
66 67 2.590575 CGCGGTTGGTCACACCTT 60.591 61.111 0.00 0.00 39.58 3.50
69 70 4.012895 CAGCGCGGTTGGTCACAC 62.013 66.667 8.73 0.00 0.00 3.82
73 74 3.267597 AATTGCAGCGCGGTTGGTC 62.268 57.895 8.73 0.00 0.00 4.02
74 75 3.294493 AATTGCAGCGCGGTTGGT 61.294 55.556 8.73 0.00 0.00 3.67
75 76 2.806198 CAATTGCAGCGCGGTTGG 60.806 61.111 8.73 0.00 0.00 3.77
76 77 3.472298 GCAATTGCAGCGCGGTTG 61.472 61.111 25.36 5.12 41.59 3.77
92 93 3.231965 GCGAAATCTGCACATCATATGC 58.768 45.455 0.00 0.00 43.68 3.14
93 94 3.666111 CGGCGAAATCTGCACATCATATG 60.666 47.826 0.00 0.00 0.00 1.78
94 95 2.481568 CGGCGAAATCTGCACATCATAT 59.518 45.455 0.00 0.00 0.00 1.78
95 96 1.866601 CGGCGAAATCTGCACATCATA 59.133 47.619 0.00 0.00 0.00 2.15
96 97 0.659427 CGGCGAAATCTGCACATCAT 59.341 50.000 0.00 0.00 0.00 2.45
97 98 0.390998 TCGGCGAAATCTGCACATCA 60.391 50.000 7.35 0.00 0.00 3.07
98 99 0.726827 TTCGGCGAAATCTGCACATC 59.273 50.000 21.53 0.00 0.00 3.06
99 100 1.382522 ATTCGGCGAAATCTGCACAT 58.617 45.000 27.40 3.32 0.00 3.21
100 101 1.933181 CTATTCGGCGAAATCTGCACA 59.067 47.619 27.40 0.00 0.00 4.57
101 102 1.261619 CCTATTCGGCGAAATCTGCAC 59.738 52.381 27.40 0.00 0.00 4.57
102 103 1.138069 TCCTATTCGGCGAAATCTGCA 59.862 47.619 27.40 1.20 0.00 4.41
103 104 1.527311 GTCCTATTCGGCGAAATCTGC 59.473 52.381 27.40 13.02 0.00 4.26
104 105 2.135933 GGTCCTATTCGGCGAAATCTG 58.864 52.381 27.40 14.89 0.00 2.90
105 106 2.040178 AGGTCCTATTCGGCGAAATCT 58.960 47.619 27.40 12.77 0.00 2.40
106 107 2.135933 CAGGTCCTATTCGGCGAAATC 58.864 52.381 27.40 10.43 0.00 2.17
107 108 1.202651 CCAGGTCCTATTCGGCGAAAT 60.203 52.381 27.40 16.66 0.00 2.17
108 109 0.177141 CCAGGTCCTATTCGGCGAAA 59.823 55.000 27.40 14.42 0.00 3.46
109 110 0.685131 TCCAGGTCCTATTCGGCGAA 60.685 55.000 25.88 25.88 0.00 4.70
110 111 0.469331 ATCCAGGTCCTATTCGGCGA 60.469 55.000 4.99 4.99 0.00 5.54
111 112 0.319900 CATCCAGGTCCTATTCGGCG 60.320 60.000 0.00 0.00 0.00 6.46
112 113 0.759346 ACATCCAGGTCCTATTCGGC 59.241 55.000 0.00 0.00 0.00 5.54
113 114 1.070758 CCACATCCAGGTCCTATTCGG 59.929 57.143 0.00 0.00 0.00 4.30
114 115 1.541233 GCCACATCCAGGTCCTATTCG 60.541 57.143 0.00 0.00 0.00 3.34
115 116 1.771255 AGCCACATCCAGGTCCTATTC 59.229 52.381 0.00 0.00 0.00 1.75
116 117 1.898863 AGCCACATCCAGGTCCTATT 58.101 50.000 0.00 0.00 0.00 1.73
117 118 2.614259 CTAGCCACATCCAGGTCCTAT 58.386 52.381 0.00 0.00 0.00 2.57
118 119 1.413082 CCTAGCCACATCCAGGTCCTA 60.413 57.143 0.00 0.00 0.00 2.94
119 120 0.692419 CCTAGCCACATCCAGGTCCT 60.692 60.000 0.00 0.00 0.00 3.85
120 121 0.983378 ACCTAGCCACATCCAGGTCC 60.983 60.000 0.00 0.00 36.69 4.46
121 122 0.912486 AACCTAGCCACATCCAGGTC 59.088 55.000 0.00 0.00 40.54 3.85
122 123 0.912486 GAACCTAGCCACATCCAGGT 59.088 55.000 0.00 0.00 43.28 4.00
126 127 2.689983 CAATTGGAACCTAGCCACATCC 59.310 50.000 0.00 0.00 34.56 3.51
145 146 1.676916 GCACTCTAGCAGCACCATCAA 60.677 52.381 0.00 0.00 0.00 2.57
178 179 5.163703 GGCACCGAACAACACATAATTGATA 60.164 40.000 0.00 0.00 0.00 2.15
180 181 3.057876 GGCACCGAACAACACATAATTGA 60.058 43.478 0.00 0.00 0.00 2.57
181 182 3.241701 GGCACCGAACAACACATAATTG 58.758 45.455 0.00 0.00 0.00 2.32
183 184 1.466950 CGGCACCGAACAACACATAAT 59.533 47.619 2.01 0.00 42.83 1.28
215 244 5.961272 TCATGCTTGTAGTTAGATTCGTCA 58.039 37.500 0.00 0.00 0.00 4.35
297 327 8.093927 GGGAAATTGGATCAAACATGAAACTTA 58.906 33.333 0.00 0.00 0.00 2.24
299 329 6.466812 GGGAAATTGGATCAAACATGAAACT 58.533 36.000 0.00 0.00 0.00 2.66
362 392 2.084546 GGGCACAAAGCTCGTTTAGAT 58.915 47.619 0.00 0.00 44.79 1.98
383 413 6.315393 GCTATGTTTTCGAGGAACCTTAATGA 59.685 38.462 10.17 0.00 0.00 2.57
387 417 5.155278 TGCTATGTTTTCGAGGAACCTTA 57.845 39.130 10.17 3.66 0.00 2.69
398 428 2.729028 TAGGGGCCTGCTATGTTTTC 57.271 50.000 0.84 0.00 0.00 2.29
412 442 2.354103 CCACATACGATGCTCATAGGGG 60.354 54.545 0.00 0.00 0.00 4.79
414 444 2.341257 GCCACATACGATGCTCATAGG 58.659 52.381 0.00 0.00 0.00 2.57
450 480 4.210331 AGAAACAGTGCAATCTTGGAAGT 58.790 39.130 0.00 0.00 0.00 3.01
479 509 9.211485 CTTGATTTTAGGCAGAAATTTGTCAAT 57.789 29.630 0.00 0.00 0.00 2.57
534 565 4.963276 TTGAAAGATTCGGCCAATACTG 57.037 40.909 2.24 0.00 0.00 2.74
580 611 2.256117 AGTTCCTTTCAAGTGGACGG 57.744 50.000 0.00 0.00 31.24 4.79
621 653 3.689649 CCCTTTTTGTAGATGGTCCTTCG 59.310 47.826 0.00 0.00 0.00 3.79
652 684 6.018262 GGAATGTTTCTGGTTTTTGTTTAGCC 60.018 38.462 0.00 0.00 0.00 3.93
731 764 9.063615 CCTTACACCTGTTGAATTAGTTTAGTT 57.936 33.333 0.00 0.00 0.00 2.24
732 765 7.664318 CCCTTACACCTGTTGAATTAGTTTAGT 59.336 37.037 0.00 0.00 0.00 2.24
733 766 7.881232 TCCCTTACACCTGTTGAATTAGTTTAG 59.119 37.037 0.00 0.00 0.00 1.85
753 786 2.132686 GGGTTCCCAGCTAATCCCTTA 58.867 52.381 2.59 0.00 32.89 2.69
853 889 0.031994 GTGGTGTTGTTGATGGGTGC 59.968 55.000 0.00 0.00 0.00 5.01
876 912 2.028203 TGATGAAACTGCGATGAGGTGA 60.028 45.455 0.00 0.00 0.00 4.02
890 926 7.118390 ACGTTTTGTTTTGGATTTGTGATGAAA 59.882 29.630 0.00 0.00 0.00 2.69
897 933 5.106442 GGAGACGTTTTGTTTTGGATTTGT 58.894 37.500 0.00 0.00 0.00 2.83
935 971 1.152312 GGAGAAGGGGGCTATCGGA 60.152 63.158 0.00 0.00 0.00 4.55
973 1029 2.110213 TGAGACCGTTGTGGGTGC 59.890 61.111 0.00 0.00 44.64 5.01
975 1031 2.826702 GGTGAGACCGTTGTGGGT 59.173 61.111 0.00 0.00 44.64 4.51
1204 1263 4.592192 CTGCCGGATCCACGCGAT 62.592 66.667 15.93 0.00 0.00 4.58
1220 1279 3.453679 GGAACGCCTCGAGGAGCT 61.454 66.667 35.69 23.88 38.67 4.09
2106 2168 2.117156 GTCCTTCATGGCGCTGCAT 61.117 57.895 7.64 0.00 35.26 3.96
2328 2403 8.082242 ACAGAAGGATACACATTTTAAACTTGC 58.918 33.333 0.00 0.00 41.41 4.01
2348 2423 4.767409 CCTTTCCCCTTTCCTTTACAGAAG 59.233 45.833 0.00 0.00 0.00 2.85
2460 2536 3.864686 GCGCGCACATGTGGTAGG 61.865 66.667 29.10 11.31 0.00 3.18
2514 2590 0.851495 GATCAGAGCAAGCGACATCG 59.149 55.000 0.00 0.00 43.27 3.84
2516 2592 2.687700 AAGATCAGAGCAAGCGACAT 57.312 45.000 0.00 0.00 0.00 3.06
2517 2593 2.755103 TCTAAGATCAGAGCAAGCGACA 59.245 45.455 0.00 0.00 0.00 4.35
2571 2657 5.246203 ACACAGAAGCTAATCACTCCAGTAA 59.754 40.000 0.00 0.00 0.00 2.24
2679 2765 5.003804 GGCATTTCTCTGGACAAAAGAGTA 58.996 41.667 0.73 0.00 41.64 2.59
2680 2766 3.823304 GGCATTTCTCTGGACAAAAGAGT 59.177 43.478 0.73 0.00 41.64 3.24
2681 2767 3.822735 TGGCATTTCTCTGGACAAAAGAG 59.177 43.478 0.00 0.00 42.18 2.85
2682 2768 3.569701 GTGGCATTTCTCTGGACAAAAGA 59.430 43.478 0.00 0.00 0.00 2.52
2683 2769 3.318839 TGTGGCATTTCTCTGGACAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
2684 2770 3.295093 TGTGGCATTTCTCTGGACAAAA 58.705 40.909 0.00 0.00 0.00 2.44
2703 2789 4.235372 TGGTGGGGGACATTTTTAATTGT 58.765 39.130 0.00 0.00 0.00 2.71
2706 2792 5.913946 TTTTGGTGGGGGACATTTTTAAT 57.086 34.783 0.00 0.00 0.00 1.40
2788 2874 8.824781 CAGACAAACAATCCACATATAGAGAAG 58.175 37.037 0.00 0.00 0.00 2.85
2834 2920 5.023452 GGTGGGAATTTTACCCTGAGATTT 58.977 41.667 0.00 0.00 46.82 2.17
2835 2921 4.045334 TGGTGGGAATTTTACCCTGAGATT 59.955 41.667 0.00 0.00 46.82 2.40
2882 2975 9.185680 TGTCACTCTGCAGACTACTTTATTATA 57.814 33.333 13.74 0.00 35.81 0.98
2937 3030 4.141528 CCTCTTGCCTCTTGGTATTCAGAT 60.142 45.833 0.00 0.00 35.27 2.90
2951 3044 3.285484 CATTGCTATTGTCCTCTTGCCT 58.715 45.455 0.00 0.00 0.00 4.75
2982 3105 5.808030 GGAGTACTTTGTAGCTCTTGATCAC 59.192 44.000 0.00 0.00 0.00 3.06
3033 3160 3.775866 TCCCTCCGTCCATAATGTTTGTA 59.224 43.478 0.00 0.00 0.00 2.41
3034 3161 2.574369 TCCCTCCGTCCATAATGTTTGT 59.426 45.455 0.00 0.00 0.00 2.83
3040 3167 5.834204 GCTATATACTCCCTCCGTCCATAAT 59.166 44.000 0.00 0.00 0.00 1.28
3041 3168 5.198965 GCTATATACTCCCTCCGTCCATAA 58.801 45.833 0.00 0.00 0.00 1.90
3042 3169 4.228895 TGCTATATACTCCCTCCGTCCATA 59.771 45.833 0.00 0.00 0.00 2.74
3043 3170 3.011369 TGCTATATACTCCCTCCGTCCAT 59.989 47.826 0.00 0.00 0.00 3.41
3044 3171 2.377531 TGCTATATACTCCCTCCGTCCA 59.622 50.000 0.00 0.00 0.00 4.02
3083 3237 4.244425 TCTTACTCTGCACAGACTGTTC 57.756 45.455 5.04 1.00 33.22 3.18
3086 3240 5.616424 GCAATTTCTTACTCTGCACAGACTG 60.616 44.000 0.00 0.00 33.22 3.51
3093 3247 4.821260 TGTTCTGCAATTTCTTACTCTGCA 59.179 37.500 0.00 0.00 40.54 4.41
3094 3248 5.180117 TCTGTTCTGCAATTTCTTACTCTGC 59.820 40.000 0.00 0.00 0.00 4.26
3120 3274 4.261197 GGTATTTGGATTCAGTCGGATTGC 60.261 45.833 0.00 0.00 0.00 3.56
3125 3280 4.094887 CACTTGGTATTTGGATTCAGTCGG 59.905 45.833 0.00 0.00 0.00 4.79
3152 3307 6.541278 TCAGTCAAGAGATCATAAGCCATTTG 59.459 38.462 0.00 0.00 0.00 2.32
3205 3361 4.792521 GAGACCTGACAGAAGAAGCTTA 57.207 45.455 3.32 0.00 0.00 3.09
3206 3362 3.676291 GAGACCTGACAGAAGAAGCTT 57.324 47.619 3.32 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.