Multiple sequence alignment - TraesCS3B01G460200

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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 TraesCS3B01G460200 chr3B 100.000 3023 0 0 1 3023 703853485 703856507 0.000000e+00 5583
1 TraesCS3B01G460200 chr3A 91.754 2571 149 35 470 3017 667101695 667104225 0.000000e+00 3515
2 TraesCS3B01G460200 chr3A 85.280 428 36 13 1 417 667101034 667101445 1.680000e-112 416
3 TraesCS3B01G460200 chr3D 92.546 1811 76 20 1227 3023 532078730 532080495 0.000000e+00 2542
4 TraesCS3B01G460200 chr3D 87.246 345 25 8 1 328 532075645 532075987 2.850000e-100 375


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 TraesCS3B01G460200 chr3B 703853485 703856507 3022 False 5583.0 5583 100.000 1 3023 1 chr3B.!!$F1 3022
1 TraesCS3B01G460200 chr3A 667101034 667104225 3191 False 1965.5 3515 88.517 1 3017 2 chr3A.!!$F1 3016
2 TraesCS3B01G460200 chr3D 532075645 532080495 4850 False 1458.5 2542 89.896 1 3023 2 chr3D.!!$F1 3022

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
549 2179 0.249447 CGGTGCCGATGAATAGCTCA 60.249 55.0 4.35 0.00 42.83 4.26 F
1731 3676 0.243636 GGTACCTTTGTGCATGCCAC 59.756 55.0 16.68 13.73 44.90 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 3958 0.317770 ACATCCAAAACGCTTGCACG 60.318 50.0 0.0 0.0 39.5 5.34 R
2843 4805 0.749649 CTAGCAGAGTAGTGCCCAGG 59.250 60.0 0.0 0.0 45.2 4.45 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
46 47 6.500589 AGTTTGGCCTATGTACAGATGTAT 57.499 37.500 3.32 0.00 32.54 2.29
53 54 9.938280 TGGCCTATGTACAGATGTATTATTAAC 57.062 33.333 3.32 0.00 32.54 2.01
68 69 9.316730 TGTATTATTAACGGGACTGATTTACAC 57.683 33.333 0.00 0.00 0.00 2.90
94 95 4.548991 GCTGAATGCTCCATTAAGTCAG 57.451 45.455 4.66 0.00 35.37 3.51
95 96 3.314635 GCTGAATGCTCCATTAAGTCAGG 59.685 47.826 4.66 0.00 35.37 3.86
140 159 1.604604 GCAACCCAAGTGAAGTGCTA 58.395 50.000 0.00 0.00 0.00 3.49
141 160 1.266989 GCAACCCAAGTGAAGTGCTAC 59.733 52.381 0.00 0.00 0.00 3.58
142 161 2.571212 CAACCCAAGTGAAGTGCTACA 58.429 47.619 0.00 0.00 0.00 2.74
143 162 2.256117 ACCCAAGTGAAGTGCTACAC 57.744 50.000 0.00 0.00 37.30 2.90
152 171 3.558674 AGTGCTACACTTGATGGCC 57.441 52.632 0.00 0.00 42.59 5.36
161 180 4.090761 ACACTTGATGGCCCATGTATAG 57.909 45.455 0.00 0.00 0.00 1.31
240 262 3.826157 CACACAGCAGGGAGGAATTTTAA 59.174 43.478 0.00 0.00 0.00 1.52
248 270 5.122239 GCAGGGAGGAATTTTAAAATTGTGC 59.878 40.000 26.69 18.59 38.64 4.57
255 277 9.087424 GAGGAATTTTAAAATTGTGCATCCTAC 57.913 33.333 26.69 15.85 38.64 3.18
256 278 7.759433 AGGAATTTTAAAATTGTGCATCCTACG 59.241 33.333 26.69 0.00 38.64 3.51
257 279 7.757624 GGAATTTTAAAATTGTGCATCCTACGA 59.242 33.333 26.69 0.00 38.64 3.43
258 280 8.687824 AATTTTAAAATTGTGCATCCTACGAG 57.312 30.769 22.30 0.00 37.24 4.18
259 281 6.811253 TTTAAAATTGTGCATCCTACGAGT 57.189 33.333 0.00 0.00 0.00 4.18
260 282 6.811253 TTAAAATTGTGCATCCTACGAGTT 57.189 33.333 0.00 0.00 0.00 3.01
262 284 8.500753 TTAAAATTGTGCATCCTACGAGTTAT 57.499 30.769 0.00 0.00 0.00 1.89
306 340 4.386652 GCAATTAGCAGAAACACAACCATG 59.613 41.667 0.00 0.00 44.79 3.66
329 363 4.919754 GCACTTTGCTTCAGGAAGTAATTG 59.080 41.667 12.28 12.78 41.41 2.32
372 1737 1.826385 AAAGCTGGGCTGTATGTGTC 58.174 50.000 0.00 0.00 39.62 3.67
380 1745 3.006940 GGGCTGTATGTGTCGAATTTGA 58.993 45.455 0.00 0.00 0.00 2.69
384 1749 5.569059 GGCTGTATGTGTCGAATTTGAAAAG 59.431 40.000 0.00 0.00 0.00 2.27
434 2025 2.409651 GCGAGGAGAACGAGCGAT 59.590 61.111 0.00 0.00 0.00 4.58
435 2026 1.226717 GCGAGGAGAACGAGCGATT 60.227 57.895 0.00 0.00 0.00 3.34
436 2027 1.203600 GCGAGGAGAACGAGCGATTC 61.204 60.000 0.00 0.00 0.00 2.52
455 2084 4.407496 TTCGTGTTTTATTTCCGCGAAT 57.593 36.364 8.23 2.31 43.58 3.34
456 2085 5.527511 TTCGTGTTTTATTTCCGCGAATA 57.472 34.783 8.23 1.11 43.58 1.75
459 2088 7.410800 TCGTGTTTTATTTCCGCGAATATAT 57.589 32.000 8.23 0.00 38.07 0.86
460 2089 7.285069 TCGTGTTTTATTTCCGCGAATATATG 58.715 34.615 8.23 0.00 38.07 1.78
461 2090 6.518395 CGTGTTTTATTTCCGCGAATATATGG 59.482 38.462 8.23 0.00 34.22 2.74
462 2091 7.357303 GTGTTTTATTTCCGCGAATATATGGT 58.643 34.615 8.23 0.00 0.00 3.55
463 2092 7.322699 GTGTTTTATTTCCGCGAATATATGGTG 59.677 37.037 8.23 0.00 0.00 4.17
464 2093 7.226918 TGTTTTATTTCCGCGAATATATGGTGA 59.773 33.333 8.23 0.00 0.00 4.02
465 2094 7.731882 TTTATTTCCGCGAATATATGGTGAA 57.268 32.000 8.23 0.00 0.00 3.18
466 2095 7.731882 TTATTTCCGCGAATATATGGTGAAA 57.268 32.000 8.23 4.90 0.00 2.69
540 2170 3.803082 CTTGTGCCGGTGCCGATG 61.803 66.667 12.71 0.00 42.83 3.84
541 2171 4.321966 TTGTGCCGGTGCCGATGA 62.322 61.111 12.71 0.00 42.83 2.92
542 2172 3.834013 TTGTGCCGGTGCCGATGAA 62.834 57.895 12.71 0.00 42.83 2.57
543 2173 2.824041 GTGCCGGTGCCGATGAAT 60.824 61.111 12.71 0.00 42.83 2.57
545 2175 1.227527 TGCCGGTGCCGATGAATAG 60.228 57.895 12.71 0.00 42.83 1.73
546 2176 2.607892 GCCGGTGCCGATGAATAGC 61.608 63.158 12.71 1.14 42.83 2.97
547 2177 1.069765 CCGGTGCCGATGAATAGCT 59.930 57.895 12.71 0.00 42.83 3.32
549 2179 0.249447 CGGTGCCGATGAATAGCTCA 60.249 55.000 4.35 0.00 42.83 4.26
553 2183 2.874701 GTGCCGATGAATAGCTCATTGT 59.125 45.455 0.00 0.00 45.23 2.71
588 2229 2.913590 GCTAAAACGTAGAGGTCGTGAC 59.086 50.000 0.00 0.00 41.38 3.67
590 2231 2.412421 AAACGTAGAGGTCGTGACAC 57.588 50.000 2.00 0.00 41.38 3.67
594 2235 1.136029 CGTAGAGGTCGTGACACAGAC 60.136 57.143 17.00 17.00 36.70 3.51
595 2236 1.136029 GTAGAGGTCGTGACACAGACG 60.136 57.143 17.98 0.00 38.20 4.18
596 2237 1.729838 GAGGTCGTGACACAGACGC 60.730 63.158 17.98 13.28 38.20 5.19
597 2238 2.733593 GGTCGTGACACAGACGCC 60.734 66.667 17.98 7.48 38.20 5.68
609 2250 1.039068 CAGACGCCCTCATCTCATCT 58.961 55.000 0.00 0.00 0.00 2.90
635 2276 1.450025 CAGTTTTACCTCCCCGCTTC 58.550 55.000 0.00 0.00 0.00 3.86
673 2314 1.737008 GGCCGACGTCTTCAACCTC 60.737 63.158 14.70 0.00 0.00 3.85
750 2393 2.046217 GGCACCTCCTTCGGTTCC 60.046 66.667 0.00 0.00 34.29 3.62
775 2418 0.824182 ACCTCATCCCGATCTCCGTC 60.824 60.000 0.00 0.00 36.31 4.79
784 2427 0.590230 CGATCTCCGTCGAAGTCAGC 60.590 60.000 0.00 0.00 44.06 4.26
786 2429 0.453793 ATCTCCGTCGAAGTCAGCAG 59.546 55.000 0.00 0.00 0.00 4.24
792 2435 0.460987 GTCGAAGTCAGCAGGATGGG 60.461 60.000 0.00 0.00 35.86 4.00
793 2436 1.153289 CGAAGTCAGCAGGATGGGG 60.153 63.158 0.00 0.00 35.86 4.96
814 2457 3.478274 GAGGGAGGCAGCAGGGAG 61.478 72.222 0.00 0.00 0.00 4.30
828 2471 2.166829 CAGGGAGAGGTCGGATCTATG 58.833 57.143 0.00 0.00 0.00 2.23
832 2475 1.271102 GAGAGGTCGGATCTATGCACC 59.729 57.143 0.00 0.00 0.00 5.01
865 2508 4.437930 CGAACCAGCAAGATTCATCCTTTC 60.438 45.833 0.00 0.00 0.00 2.62
866 2509 3.359950 ACCAGCAAGATTCATCCTTTCC 58.640 45.455 0.00 0.00 0.00 3.13
889 2532 4.329545 GTTGGGTCAGGCTCGCCA 62.330 66.667 11.02 0.00 38.92 5.69
890 2533 4.329545 TTGGGTCAGGCTCGCCAC 62.330 66.667 11.02 0.12 38.92 5.01
905 2548 1.809567 GCCACTTTGGGACAGCCAAG 61.810 60.000 0.00 0.00 42.39 3.61
949 2731 0.393537 AAGCAGCATCTGTACCTGGC 60.394 55.000 0.00 0.00 33.43 4.85
964 2746 1.915614 CTGGCACTTGATGACCACGC 61.916 60.000 0.00 0.00 34.05 5.34
973 2755 0.460284 GATGACCACGCTGACGGATT 60.460 55.000 0.00 0.00 46.04 3.01
976 2758 0.669318 GACCACGCTGACGGATTCAA 60.669 55.000 0.00 0.00 46.04 2.69
1008 2790 0.251916 GGACATGGACAATGACCCGA 59.748 55.000 0.00 0.00 43.07 5.14
1012 2944 2.158559 CATGGACAATGACCCGACAAA 58.841 47.619 0.00 0.00 38.72 2.83
1135 3068 1.753930 CAGCCACATCATAGCCACAA 58.246 50.000 0.00 0.00 0.00 3.33
1160 3093 1.228793 CCGCCCATGAAATACCCCA 59.771 57.895 0.00 0.00 0.00 4.96
1161 3094 1.106944 CCGCCCATGAAATACCCCAC 61.107 60.000 0.00 0.00 0.00 4.61
1176 3109 1.375523 CCACGTACAAGAGGCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
1200 3133 1.637553 AGTGCCACCCTCATCTTTGAT 59.362 47.619 0.00 0.00 0.00 2.57
1221 3154 5.526479 TGATACGAAGACATCTACGCTTACT 59.474 40.000 0.00 0.00 0.00 2.24
1264 3208 6.317391 GCAAGGTCTAGAAAACTGCTATGATT 59.683 38.462 0.00 0.00 0.00 2.57
1287 3231 0.824109 CCATAGCCGTCAGGAACAGA 59.176 55.000 0.00 0.00 41.02 3.41
1425 3369 1.732259 CGACCCTTGTTCAATTCCTCG 59.268 52.381 0.00 0.00 0.00 4.63
1440 3384 1.355066 CCTCGCGTTTCTCTTGGAGC 61.355 60.000 5.77 0.00 0.00 4.70
1444 3388 1.301677 GCGTTTCTCTTGGAGCTGGG 61.302 60.000 0.00 0.00 0.00 4.45
1497 3441 4.142469 CCGTTTGATCCCAAGTTTATCACC 60.142 45.833 0.00 0.00 33.23 4.02
1505 3449 2.159517 CCAAGTTTATCACCTCGCTTGC 60.160 50.000 0.00 0.00 33.94 4.01
1549 3493 1.877443 TCTTTGTTTCCGCTTGTAGGC 59.123 47.619 0.00 0.00 0.00 3.93
1601 3546 2.776526 AGGTGGTGGCCAGTGGAA 60.777 61.111 15.20 0.00 32.34 3.53
1686 3631 3.083997 GTCGGGCTCCACCTCCAT 61.084 66.667 0.00 0.00 39.10 3.41
1687 3632 2.285368 TCGGGCTCCACCTCCATT 60.285 61.111 0.00 0.00 39.10 3.16
1688 3633 2.190578 CGGGCTCCACCTCCATTC 59.809 66.667 0.00 0.00 39.10 2.67
1689 3634 2.597903 GGGCTCCACCTCCATTCC 59.402 66.667 0.00 0.00 39.10 3.01
1690 3635 2.190578 GGCTCCACCTCCATTCCG 59.809 66.667 0.00 0.00 34.51 4.30
1691 3636 2.514824 GCTCCACCTCCATTCCGC 60.515 66.667 0.00 0.00 0.00 5.54
1707 3652 2.029288 CGCTGACACGGTTGATGCT 61.029 57.895 0.00 0.00 0.00 3.79
1710 3655 1.073964 CTGACACGGTTGATGCTGAG 58.926 55.000 0.00 0.00 0.00 3.35
1731 3676 0.243636 GGTACCTTTGTGCATGCCAC 59.756 55.000 16.68 13.73 44.90 5.01
1767 3712 0.890996 AGCCGCCAAAGAGGAAAGTG 60.891 55.000 0.00 0.00 41.22 3.16
1772 3717 1.251251 CCAAAGAGGAAAGTGGGCAG 58.749 55.000 0.00 0.00 41.22 4.85
1789 3734 1.901591 CAGGGAGCAGCTTTTTCTCA 58.098 50.000 0.00 0.00 0.00 3.27
1810 3755 1.160137 GCAACCACACTGGAGACATC 58.840 55.000 0.00 0.00 40.96 3.06
1865 3810 1.185618 AAGTACTGCCTCGTGGAGCA 61.186 55.000 7.92 0.00 37.46 4.26
1888 3833 2.680352 GACCTGAGGGAGCGGACA 60.680 66.667 2.38 0.00 36.25 4.02
1889 3834 2.997897 ACCTGAGGGAGCGGACAC 60.998 66.667 2.38 0.00 36.25 3.67
1936 3881 4.158209 CCACATTCATTGTCAAGTATGGCA 59.842 41.667 0.00 0.00 40.01 4.92
2098 4055 2.883386 CCCCTTCTATTTGATGAGCTGC 59.117 50.000 0.00 0.00 0.00 5.25
2099 4056 2.883386 CCCTTCTATTTGATGAGCTGCC 59.117 50.000 0.00 0.00 0.00 4.85
2219 4179 6.985645 TGATAATTTGCTCCCAAACAATATGC 59.014 34.615 0.00 0.00 43.20 3.14
2226 4186 1.682854 CCCAAACAATATGCGCCTCAT 59.317 47.619 4.18 0.00 39.17 2.90
2234 4194 8.503196 CAAACAATATGCGCCTCATAATACTTA 58.497 33.333 4.18 0.00 40.73 2.24
2239 4199 6.727824 ATGCGCCTCATAATACTTATGTTC 57.272 37.500 4.18 0.00 42.77 3.18
2243 4203 6.368791 GCGCCTCATAATACTTATGTTCATGA 59.631 38.462 0.00 0.00 42.77 3.07
2295 4255 2.476686 GCGTTCGTAAAAATGCTACCCC 60.477 50.000 0.00 0.00 38.00 4.95
2308 4268 1.631898 GCTACCCCCTTGTCTGGTTTA 59.368 52.381 0.00 0.00 33.55 2.01
2429 4389 7.067372 TCCATTTGAGGATTGCTTGTATAGTTG 59.933 37.037 0.00 0.00 31.23 3.16
2636 4596 5.127519 TGCTAATGTATTCCTTGCAAGCATT 59.872 36.000 23.64 23.64 31.43 3.56
2712 4672 7.043986 GCAAATCAGTATGTACTACACGAGAAG 60.044 40.741 0.00 0.00 37.40 2.85
2810 4772 9.123709 GTTTTGATATCTCTCTTAGTGATAGCG 57.876 37.037 3.98 0.00 38.93 4.26
2832 4794 1.774856 CCCGGATTCCTTTACCTGGAT 59.225 52.381 0.73 0.00 33.09 3.41
2837 4799 3.181439 GGATTCCTTTACCTGGATCTGGG 60.181 52.174 0.00 6.60 33.09 4.45
2843 4805 3.866582 CCTGGATCTGGGCCCGAC 61.867 72.222 19.37 8.05 0.00 4.79
2872 4834 6.432107 GCACTACTCTGCTAGTTATGTCTAC 58.568 44.000 0.00 0.00 39.80 2.59
2890 4852 2.418368 ACGATATGCTTTGCCAAGGA 57.582 45.000 0.00 0.00 34.38 3.36
2892 4854 3.290710 ACGATATGCTTTGCCAAGGAAT 58.709 40.909 0.00 0.00 33.45 3.01
2920 4882 2.294449 TCTCTGAGGCTGTGTGTACT 57.706 50.000 4.59 0.00 0.00 2.73
2921 4883 1.889170 TCTCTGAGGCTGTGTGTACTG 59.111 52.381 4.59 0.00 0.00 2.74
2922 4884 1.615883 CTCTGAGGCTGTGTGTACTGT 59.384 52.381 0.00 0.00 0.00 3.55
2923 4885 1.341209 TCTGAGGCTGTGTGTACTGTG 59.659 52.381 0.00 0.00 0.00 3.66
2924 4886 1.069204 CTGAGGCTGTGTGTACTGTGT 59.931 52.381 0.00 0.00 0.00 3.72
2925 4887 2.296190 CTGAGGCTGTGTGTACTGTGTA 59.704 50.000 0.00 0.00 0.00 2.90
2926 4888 2.035449 TGAGGCTGTGTGTACTGTGTAC 59.965 50.000 0.00 1.33 0.00 2.90
2929 4891 3.071023 AGGCTGTGTGTACTGTGTACATT 59.929 43.478 12.74 0.00 0.00 2.71
2938 4900 8.552865 GTGTGTACTGTGTACATTGAAATGTTA 58.447 33.333 13.53 2.07 46.95 2.41
2966 4928 7.029563 CGCCTTTAAAATGCAAGATCTTTACT 58.970 34.615 4.86 0.00 0.00 2.24
2994 4956 4.442706 AGCGTTGAAATATAGTCTGTGGG 58.557 43.478 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.582431 CCCGTTAATAATACATCTGTACATAGG 57.418 37.037 0.00 0.00 32.72 2.57
46 47 7.388437 ACTGTGTAAATCAGTCCCGTTAATAA 58.612 34.615 0.00 0.00 41.52 1.40
53 54 3.119101 AGCTACTGTGTAAATCAGTCCCG 60.119 47.826 1.82 0.00 43.76 5.14
117 123 0.178990 ACTTCACTTGGGTTGCCCTC 60.179 55.000 5.73 0.00 45.70 4.30
140 159 3.748668 GCTATACATGGGCCATCAAGTGT 60.749 47.826 18.16 15.56 0.00 3.55
141 160 2.816087 GCTATACATGGGCCATCAAGTG 59.184 50.000 18.16 9.54 0.00 3.16
142 161 2.224867 GGCTATACATGGGCCATCAAGT 60.225 50.000 18.16 14.55 44.69 3.16
143 162 2.440409 GGCTATACATGGGCCATCAAG 58.560 52.381 18.16 12.27 44.69 3.02
144 163 2.584835 GGCTATACATGGGCCATCAA 57.415 50.000 18.16 8.02 44.69 2.57
149 168 0.178992 TTGCAGGCTATACATGGGCC 60.179 55.000 0.00 0.00 45.57 5.80
150 169 1.691196 TTTGCAGGCTATACATGGGC 58.309 50.000 0.00 0.00 0.00 5.36
151 170 4.460382 CCTAATTTGCAGGCTATACATGGG 59.540 45.833 0.00 0.00 0.00 4.00
152 171 4.460382 CCCTAATTTGCAGGCTATACATGG 59.540 45.833 0.00 0.00 0.00 3.66
161 180 3.704061 TCATTTACCCCTAATTTGCAGGC 59.296 43.478 0.00 0.00 0.00 4.85
220 242 5.467035 TTTTAAAATTCCTCCCTGCTGTG 57.533 39.130 0.00 0.00 0.00 3.66
240 262 9.944376 ATATATAACTCGTAGGATGCACAATTT 57.056 29.630 0.00 0.00 0.00 1.82
306 340 4.773323 ATTACTTCCTGAAGCAAAGTGC 57.227 40.909 6.81 0.00 45.46 4.40
329 363 5.290386 TCTCTTTCTTCTTTCGTCCTGTTC 58.710 41.667 0.00 0.00 0.00 3.18
372 1737 8.638565 CAATTTACTGCTACCTTTTCAAATTCG 58.361 33.333 0.00 0.00 0.00 3.34
380 1745 9.953565 TCAGTATACAATTTACTGCTACCTTTT 57.046 29.630 5.50 0.00 44.00 2.27
384 1749 7.985752 ACCTTCAGTATACAATTTACTGCTACC 59.014 37.037 5.50 0.00 44.00 3.18
400 1765 2.358267 CTCGCGGACTAACCTTCAGTAT 59.642 50.000 6.13 0.00 36.31 2.12
434 2025 3.874400 TTCGCGGAAATAAAACACGAA 57.126 38.095 6.13 0.00 35.89 3.85
435 2026 5.721876 ATATTCGCGGAAATAAAACACGA 57.278 34.783 6.13 0.00 0.00 4.35
436 2027 6.518395 CCATATATTCGCGGAAATAAAACACG 59.482 38.462 6.13 0.00 0.00 4.49
437 2028 7.322699 CACCATATATTCGCGGAAATAAAACAC 59.677 37.037 6.13 0.00 0.00 3.32
438 2029 7.226918 TCACCATATATTCGCGGAAATAAAACA 59.773 33.333 6.13 0.00 0.00 2.83
445 2074 5.504994 GCTTTTCACCATATATTCGCGGAAA 60.505 40.000 6.13 0.63 0.00 3.13
455 2084 5.889289 GGTTACTTGGGCTTTTCACCATATA 59.111 40.000 0.00 0.00 36.48 0.86
456 2085 4.709886 GGTTACTTGGGCTTTTCACCATAT 59.290 41.667 0.00 0.00 36.48 1.78
459 2088 2.312390 GGTTACTTGGGCTTTTCACCA 58.688 47.619 0.00 0.00 34.29 4.17
460 2089 2.035449 GTGGTTACTTGGGCTTTTCACC 59.965 50.000 0.00 0.00 0.00 4.02
461 2090 2.691011 TGTGGTTACTTGGGCTTTTCAC 59.309 45.455 0.00 0.00 0.00 3.18
462 2091 2.955660 CTGTGGTTACTTGGGCTTTTCA 59.044 45.455 0.00 0.00 0.00 2.69
463 2092 2.956333 ACTGTGGTTACTTGGGCTTTTC 59.044 45.455 0.00 0.00 0.00 2.29
464 2093 2.693074 CACTGTGGTTACTTGGGCTTTT 59.307 45.455 0.00 0.00 0.00 2.27
465 2094 2.306847 CACTGTGGTTACTTGGGCTTT 58.693 47.619 0.00 0.00 0.00 3.51
466 2095 1.478654 CCACTGTGGTTACTTGGGCTT 60.479 52.381 18.76 0.00 31.35 4.35
516 2146 2.906897 ACCGGCACAAGCTGTTGG 60.907 61.111 0.00 0.00 45.95 3.77
517 2147 2.332514 CACCGGCACAAGCTGTTG 59.667 61.111 0.00 0.00 45.95 3.33
523 2153 3.803082 CATCGGCACCGGCACAAG 61.803 66.667 9.58 0.00 43.71 3.16
536 2166 7.222417 GGATGATCTACAATGAGCTATTCATCG 59.778 40.741 0.00 0.00 45.82 3.84
539 2169 6.209391 TCGGATGATCTACAATGAGCTATTCA 59.791 38.462 0.00 0.00 40.85 2.57
540 2170 6.529829 GTCGGATGATCTACAATGAGCTATTC 59.470 42.308 0.00 0.00 0.00 1.75
541 2171 6.393990 GTCGGATGATCTACAATGAGCTATT 58.606 40.000 0.00 0.00 0.00 1.73
542 2172 5.392487 CGTCGGATGATCTACAATGAGCTAT 60.392 44.000 0.00 0.00 0.00 2.97
543 2173 4.083271 CGTCGGATGATCTACAATGAGCTA 60.083 45.833 0.00 0.00 0.00 3.32
545 2175 2.983136 CGTCGGATGATCTACAATGAGC 59.017 50.000 0.00 0.00 0.00 4.26
546 2176 3.569548 CCGTCGGATGATCTACAATGAG 58.430 50.000 4.91 0.00 0.00 2.90
547 2177 2.288213 GCCGTCGGATGATCTACAATGA 60.288 50.000 17.49 0.00 0.00 2.57
549 2179 1.964223 AGCCGTCGGATGATCTACAAT 59.036 47.619 17.49 0.00 0.00 2.71
550 2180 1.399714 AGCCGTCGGATGATCTACAA 58.600 50.000 17.49 0.00 0.00 2.41
553 2183 3.549423 CGTTTTAGCCGTCGGATGATCTA 60.549 47.826 17.49 3.27 0.00 1.98
588 2229 0.463204 ATGAGATGAGGGCGTCTGTG 59.537 55.000 8.82 0.00 40.42 3.66
590 2231 1.039068 AGATGAGATGAGGGCGTCTG 58.961 55.000 8.82 0.00 40.42 3.51
594 2235 1.134280 ACCAAAGATGAGATGAGGGCG 60.134 52.381 0.00 0.00 0.00 6.13
595 2236 2.295885 CACCAAAGATGAGATGAGGGC 58.704 52.381 0.00 0.00 0.00 5.19
596 2237 2.295885 GCACCAAAGATGAGATGAGGG 58.704 52.381 0.00 0.00 0.00 4.30
597 2238 2.943690 CTGCACCAAAGATGAGATGAGG 59.056 50.000 0.00 0.00 0.00 3.86
609 2250 2.312390 GGGAGGTAAAACTGCACCAAA 58.688 47.619 0.00 0.00 37.28 3.28
635 2276 0.947244 GCCGCCACAATATCTGGAAG 59.053 55.000 3.94 0.00 0.00 3.46
666 2307 3.575630 CTCGAAACGATGAAGAGGTTGA 58.424 45.455 0.00 0.00 34.61 3.18
673 2314 2.263077 CCTGACCTCGAAACGATGAAG 58.737 52.381 0.00 0.00 34.61 3.02
775 2418 1.153289 CCCCATCCTGCTGACTTCG 60.153 63.158 0.00 0.00 0.00 3.79
801 2444 2.686835 ACCTCTCCCTGCTGCCTC 60.687 66.667 0.00 0.00 0.00 4.70
810 2453 0.892063 GCATAGATCCGACCTCTCCC 59.108 60.000 0.00 0.00 0.00 4.30
814 2457 0.039074 CGGTGCATAGATCCGACCTC 60.039 60.000 6.86 0.00 46.05 3.85
832 2475 3.716006 CTGGTTCGTGCAGGTGCG 61.716 66.667 6.26 0.00 45.83 5.34
845 2488 3.011032 AGGAAAGGATGAATCTTGCTGGT 59.989 43.478 0.00 0.00 0.00 4.00
866 2509 4.410400 GCCTGACCCAACCCGGAG 62.410 72.222 0.73 0.00 36.56 4.63
917 2699 1.301244 CTGCTTCGTGGTCTGCTGT 60.301 57.895 0.00 0.00 0.00 4.40
949 2731 0.792640 GTCAGCGTGGTCATCAAGTG 59.207 55.000 0.00 0.00 0.00 3.16
964 2746 2.698803 TGTGGATGTTGAATCCGTCAG 58.301 47.619 0.19 0.00 41.03 3.51
1147 3080 4.509616 TCTTGTACGTGGGGTATTTCATG 58.490 43.478 0.00 0.00 32.74 3.07
1148 3081 4.383770 CCTCTTGTACGTGGGGTATTTCAT 60.384 45.833 0.00 0.00 32.74 2.57
1149 3082 3.055675 CCTCTTGTACGTGGGGTATTTCA 60.056 47.826 0.00 0.00 32.74 2.69
1160 3093 2.654877 CGTGGGCCTCTTGTACGT 59.345 61.111 4.53 0.00 0.00 3.57
1161 3094 2.125673 CCGTGGGCCTCTTGTACG 60.126 66.667 4.53 4.79 34.78 3.67
1180 3113 1.067295 TCAAAGATGAGGGTGGCACT 58.933 50.000 18.45 0.00 0.00 4.40
1191 3124 6.129326 GCGTAGATGTCTTCGTATCAAAGATG 60.129 42.308 10.08 0.00 38.70 2.90
1200 3133 5.051441 CGTAGTAAGCGTAGATGTCTTCGTA 60.051 44.000 10.08 0.00 38.70 3.43
1221 3154 5.642919 ACCTTGCGGTAAAATATTTGACGTA 59.357 36.000 9.21 7.59 43.29 3.57
1287 3231 6.582672 CGCTGTATGATTCGAACACATATAGT 59.417 38.462 28.89 13.16 37.73 2.12
1299 3243 3.659735 GTTGTTGTCGCTGTATGATTCG 58.340 45.455 0.00 0.00 0.00 3.34
1425 3369 1.301677 CCCAGCTCCAAGAGAAACGC 61.302 60.000 0.00 0.00 0.00 4.84
1440 3384 1.745489 GCCACCGAACTTAGCCCAG 60.745 63.158 0.00 0.00 0.00 4.45
1444 3388 1.019805 GGACTGCCACCGAACTTAGC 61.020 60.000 0.00 0.00 0.00 3.09
1581 3526 2.348998 CACTGGCCACCACCTCTC 59.651 66.667 0.00 0.00 0.00 3.20
1587 3532 4.641645 CGCTTCCACTGGCCACCA 62.642 66.667 0.00 0.00 0.00 4.17
1601 3546 2.437716 CCCAATTACCACGGCGCT 60.438 61.111 6.90 0.00 0.00 5.92
1689 3634 2.029288 AGCATCAACCGTGTCAGCG 61.029 57.895 0.00 0.00 0.00 5.18
1690 3635 0.950555 TCAGCATCAACCGTGTCAGC 60.951 55.000 0.00 0.00 0.00 4.26
1691 3636 1.073964 CTCAGCATCAACCGTGTCAG 58.926 55.000 0.00 0.00 0.00 3.51
1700 3645 1.668826 AAGGTACCCCTCAGCATCAA 58.331 50.000 8.74 0.00 41.56 2.57
1707 3652 1.072266 ATGCACAAAGGTACCCCTCA 58.928 50.000 8.74 0.00 41.56 3.86
1710 3655 1.604147 GGCATGCACAAAGGTACCCC 61.604 60.000 21.36 0.00 0.00 4.95
1731 3676 1.597302 CTGCCGGCCAGAGATGATG 60.597 63.158 26.77 0.00 44.64 3.07
1759 3704 2.911926 GCTCCCTGCCCACTTTCCT 61.912 63.158 0.00 0.00 35.15 3.36
1767 3712 1.881903 GAAAAAGCTGCTCCCTGCCC 61.882 60.000 1.00 0.00 42.00 5.36
1782 3727 2.426738 CCAGTGTGGTTGCTTGAGAAAA 59.573 45.455 0.00 0.00 31.35 2.29
1789 3734 0.546122 TGTCTCCAGTGTGGTTGCTT 59.454 50.000 0.00 0.00 39.03 3.91
1794 3739 0.891373 CGAGATGTCTCCAGTGTGGT 59.109 55.000 4.54 0.00 39.79 4.16
1810 3755 4.383774 TGTAAACGAGTTTTGCATCGAG 57.616 40.909 13.96 0.00 41.40 4.04
1875 3820 2.362503 ATCGTGTCCGCTCCCTCA 60.363 61.111 0.00 0.00 0.00 3.86
1888 3833 2.923655 CACGAAGCACATACTTCATCGT 59.076 45.455 5.25 0.00 45.22 3.73
1889 3834 2.923655 ACACGAAGCACATACTTCATCG 59.076 45.455 5.25 0.00 45.22 3.84
1936 3881 1.901948 TCGTGAGCTCACCGTCCTT 60.902 57.895 35.07 0.00 43.66 3.36
1969 3914 1.086634 GCCTTGTAGAAGCGAGCAGG 61.087 60.000 0.00 0.00 0.00 4.85
2001 3958 0.317770 ACATCCAAAACGCTTGCACG 60.318 50.000 0.00 0.00 39.50 5.34
2083 4040 3.127548 ACAAACGGCAGCTCATCAAATAG 59.872 43.478 0.00 0.00 0.00 1.73
2098 4055 6.978343 TCATCATTAAGAACCTACAAACGG 57.022 37.500 0.00 0.00 0.00 4.44
2138 4095 4.978099 AGAGCCACCATCGAATTTGATAT 58.022 39.130 7.90 0.00 0.00 1.63
2234 4194 8.362639 GGCTAAATTCCATAACATCATGAACAT 58.637 33.333 0.00 0.00 0.00 2.71
2239 4199 6.605849 CGAGGCTAAATTCCATAACATCATG 58.394 40.000 0.00 0.00 0.00 3.07
2243 4203 4.460263 TGCGAGGCTAAATTCCATAACAT 58.540 39.130 0.00 0.00 0.00 2.71
2295 4255 9.449719 ACAAAAGTATATCTAAACCAGACAAGG 57.550 33.333 0.00 0.00 35.62 3.61
2336 4296 7.758495 ACCAACAGTGAAACAAAGTTAGTAAG 58.242 34.615 0.00 0.00 41.43 2.34
2429 4389 6.036470 GCTCATATGCTTTTGGTAAGGAAAC 58.964 40.000 0.00 0.00 0.00 2.78
2636 4596 8.830580 GTTGCTCTAAAGTAGATCATGCAATAA 58.169 33.333 10.83 0.00 41.29 1.40
2650 4610 7.908453 AGATACCTTTGTAGTTGCTCTAAAGT 58.092 34.615 0.00 0.00 0.00 2.66
2712 4672 1.202615 GGCCCGGTACCACTAGAAATC 60.203 57.143 13.54 0.00 0.00 2.17
2783 4745 9.973450 GCTATCACTAAGAGAGATATCAAAACA 57.027 33.333 5.32 0.00 37.80 2.83
2810 4772 1.134189 CCAGGTAAAGGAATCCGGGAC 60.134 57.143 0.00 0.00 38.52 4.46
2843 4805 0.749649 CTAGCAGAGTAGTGCCCAGG 59.250 60.000 0.00 0.00 45.20 4.45
2872 4834 3.316029 TGATTCCTTGGCAAAGCATATCG 59.684 43.478 0.00 0.00 31.51 2.92
2890 4852 4.008330 CAGCCTCAGAGAATTGTGTGATT 58.992 43.478 2.73 0.00 0.00 2.57
2892 4854 2.369860 ACAGCCTCAGAGAATTGTGTGA 59.630 45.455 0.00 2.33 0.00 3.58
2926 4888 3.508744 AAGGCGCCTAACATTTCAATG 57.491 42.857 33.07 0.00 42.10 2.82
2929 4891 5.455056 TTTTAAAGGCGCCTAACATTTCA 57.545 34.783 33.07 8.66 0.00 2.69
2938 4900 1.892474 TCTTGCATTTTAAAGGCGCCT 59.108 42.857 27.08 27.08 0.00 5.52
2966 4928 5.753438 CAGACTATATTTCAACGCTAGCCAA 59.247 40.000 9.66 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.