Multiple sequence alignment - TraesCS6D01G288900

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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 TraesCS6D01G288900 chr6D 100.000 3231 0 0 1 3231 399758391 399761621 0.000000e+00 5967
1 TraesCS6D01G288900 chr6A 91.456 2060 83 36 544 2560 545647616 545649625 0.000000e+00 2743
2 TraesCS6D01G288900 chr6A 88.936 470 33 7 41 508 545646792 545647244 2.180000e-156 562
3 TraesCS6D01G288900 chr6A 88.424 311 20 7 2923 3228 545649971 545650270 8.520000e-96 361
4 TraesCS6D01G288900 chr6A 84.848 330 24 2 2557 2886 545649661 545649964 3.130000e-80 309
5 TraesCS6D01G288900 chr6B 93.090 1505 68 20 115 1596 598450053 598451544 0.000000e+00 2170
6 TraesCS6D01G288900 chr6B 88.697 982 47 15 1594 2560 598451608 598452540 0.000000e+00 1140
7 TraesCS6D01G288900 chr6B 83.824 680 47 34 2558 3231 598452583 598453205 3.590000e-164 588
8 TraesCS6D01G288900 chr6B 94.828 116 4 2 1 114 598449906 598450021 2.560000e-41 180
9 TraesCS6D01G288900 chr7B 84.229 279 35 8 990 1268 113060445 113060714 2.470000e-66 263
10 TraesCS6D01G288900 chr7D 83.333 282 35 7 990 1268 150900634 150900906 1.920000e-62 250
11 TraesCS6D01G288900 chr7A 83.824 272 32 8 1000 1268 150559748 150560010 6.920000e-62 248


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 TraesCS6D01G288900 chr6D 399758391 399761621 3230 False 5967.00 5967 100.00000 1 3231 1 chr6D.!!$F1 3230
1 TraesCS6D01G288900 chr6A 545646792 545650270 3478 False 993.75 2743 88.41600 41 3228 4 chr6A.!!$F1 3187
2 TraesCS6D01G288900 chr6B 598449906 598453205 3299 False 1019.50 2170 90.10975 1 3231 4 chr6B.!!$F1 3230

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
713 1099 0.666374 GCACCCAAAAACGCAGTACT 59.334 50.0 0.0 0.0 45.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2734 0.105453 AGATCCACCGAGGGCTATGT 60.105 55.0 0.0 0.0 38.24 2.29 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
23 24 1.429930 TATAAGCCCATCCCTCGCAA 58.570 50.000 0.00 0.00 0.00 4.85
38 39 4.290622 CAACACCAGGGGGCAGCT 62.291 66.667 0.00 0.00 37.90 4.24
78 80 4.202253 TGACGAGCTAACAAGCCATCATAT 60.202 41.667 0.00 0.00 34.90 1.78
195 234 5.581874 GCATTCATGAATGGTTTAGTTTGGG 59.418 40.000 37.09 16.58 46.14 4.12
197 236 6.588719 TTCATGAATGGTTTAGTTTGGGAG 57.411 37.500 3.38 0.00 0.00 4.30
204 243 2.035449 GGTTTAGTTTGGGAGTGCAACC 59.965 50.000 0.00 0.00 37.80 3.77
224 263 0.896923 GCAAGGGGTTCATGCATGAA 59.103 50.000 33.08 33.08 43.94 2.57
252 291 1.029408 TCCGGTTGCACCATACATGC 61.029 55.000 0.00 0.00 43.68 4.06
321 361 3.141398 TCTTGCTGTTGTGATGGACTTC 58.859 45.455 0.00 0.00 0.00 3.01
359 399 3.300590 GGTGAATAGCAACAAAATTCGCG 59.699 43.478 0.00 0.00 39.75 5.87
404 447 0.951558 AAGTTTAGTGCACGGCCAAG 59.048 50.000 12.01 0.00 0.00 3.61
435 478 3.602062 CACGTACGAATGCCAAACAATTC 59.398 43.478 24.41 0.00 0.00 2.17
439 482 2.297033 ACGAATGCCAAACAATTCAGCT 59.703 40.909 0.00 0.00 0.00 4.24
479 522 1.880340 GTCAAGATCAGCTCGGCGG 60.880 63.158 7.21 0.00 0.00 6.13
494 537 0.955905 GGCGGAACCAGCAACTTTTA 59.044 50.000 9.06 0.00 38.86 1.52
495 538 1.338655 GGCGGAACCAGCAACTTTTAA 59.661 47.619 9.06 0.00 38.86 1.52
527 591 9.108284 TGATCGAGTGCATAGAATTCAATTAAA 57.892 29.630 8.44 0.00 0.00 1.52
543 607 7.808279 TCAATTAAATCGGGGAGATAGGTAT 57.192 36.000 0.00 0.00 38.98 2.73
552 929 9.983024 AATCGGGGAGATAGGTATATATAGATG 57.017 37.037 0.00 0.00 38.98 2.90
628 1006 4.201576 CGAAAAGCGATCGTTTTATAGGC 58.798 43.478 26.72 14.27 44.57 3.93
705 1091 1.299850 GAGCGGTGCACCCAAAAAC 60.300 57.895 29.95 12.29 0.00 2.43
713 1099 0.666374 GCACCCAAAAACGCAGTACT 59.334 50.000 0.00 0.00 45.00 2.73
714 1100 1.334689 GCACCCAAAAACGCAGTACTC 60.335 52.381 0.00 0.00 45.00 2.59
1089 1484 4.326227 TACTGGTCCACCCCCGCT 62.326 66.667 0.00 0.00 34.29 5.52
1597 2058 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
1691 2152 1.390463 GTTGTTCCTCGCGATTCTCAC 59.610 52.381 10.36 3.10 0.00 3.51
1714 2178 1.068588 CTTCCTCAGTTCGTCCACACA 59.931 52.381 0.00 0.00 0.00 3.72
1729 2193 2.158957 CCACACACAACACTGTAGGTCT 60.159 50.000 0.00 0.00 33.22 3.85
1738 2202 5.012148 ACAACACTGTAGGTCTTCAGCTTAT 59.988 40.000 4.82 0.00 35.37 1.73
1739 2203 5.746990 ACACTGTAGGTCTTCAGCTTATT 57.253 39.130 4.82 0.00 35.37 1.40
1740 2204 6.852420 ACACTGTAGGTCTTCAGCTTATTA 57.148 37.500 4.82 0.00 35.37 0.98
1743 2207 7.178628 ACACTGTAGGTCTTCAGCTTATTAGAA 59.821 37.037 4.82 0.00 35.37 2.10
1750 2214 7.772757 AGGTCTTCAGCTTATTAGAAAAGATGG 59.227 37.037 1.75 0.00 40.04 3.51
1782 2246 6.039270 TCTGGGTAATCGCCATTAGAATTTTG 59.961 38.462 0.00 0.00 0.00 2.44
1877 2350 3.960571 ACCTGACAATTCTCAATCCCAG 58.039 45.455 0.00 0.00 0.00 4.45
1943 2424 0.107703 ATGCCATGTACCGTCCACAG 60.108 55.000 0.00 0.00 0.00 3.66
1985 2467 7.530426 AATAGGGGATGCAGAATGATAAAAC 57.470 36.000 0.00 0.00 39.69 2.43
2283 2775 0.674269 TGTATTTTCGGCGTCCACCC 60.674 55.000 6.85 0.00 0.00 4.61
2309 2801 5.751028 GCTTCAACAGATTAATCTAGCTCGT 59.249 40.000 21.93 12.60 34.85 4.18
2312 2804 6.631016 TCAACAGATTAATCTAGCTCGTGTT 58.369 36.000 17.53 13.04 34.85 3.32
2313 2805 7.097192 TCAACAGATTAATCTAGCTCGTGTTT 58.903 34.615 17.53 0.71 34.85 2.83
2318 2811 7.653713 CAGATTAATCTAGCTCGTGTTTATGGT 59.346 37.037 17.53 0.00 34.85 3.55
2342 2835 1.741706 CTGCCACATCTGTGTTGGATC 59.258 52.381 9.33 0.00 44.21 3.36
2343 2836 0.729116 GCCACATCTGTGTTGGATCG 59.271 55.000 9.33 0.00 44.21 3.69
2344 2837 1.675714 GCCACATCTGTGTTGGATCGA 60.676 52.381 9.33 0.00 44.21 3.59
2345 2838 2.002586 CCACATCTGTGTTGGATCGAC 58.997 52.381 9.33 0.00 44.21 4.20
2346 2839 2.612721 CCACATCTGTGTTGGATCGACA 60.613 50.000 9.33 0.00 44.21 4.35
2347 2840 2.413112 CACATCTGTGTTGGATCGACAC 59.587 50.000 18.79 18.79 45.91 3.67
2348 2841 2.002586 CATCTGTGTTGGATCGACACC 58.997 52.381 21.29 3.06 45.33 4.16
2349 2842 0.320374 TCTGTGTTGGATCGACACCC 59.680 55.000 21.29 1.28 45.33 4.61
2350 2843 0.673644 CTGTGTTGGATCGACACCCC 60.674 60.000 21.29 4.91 45.33 4.95
2351 2844 1.740296 GTGTTGGATCGACACCCCG 60.740 63.158 16.14 0.00 41.47 5.73
2352 2845 1.909287 TGTTGGATCGACACCCCGA 60.909 57.895 7.82 0.00 43.16 5.14
2357 2850 4.565360 ATCGACACCCCGATACGA 57.435 55.556 0.00 0.00 46.16 3.43
2358 2851 2.328235 ATCGACACCCCGATACGAG 58.672 57.895 0.00 0.00 46.16 4.18
2359 2852 1.793134 ATCGACACCCCGATACGAGC 61.793 60.000 0.00 0.00 46.16 5.03
2360 2853 2.025727 GACACCCCGATACGAGCG 59.974 66.667 0.00 0.00 0.00 5.03
2400 2893 2.437895 TCGATCGGAGCGTGTCCT 60.438 61.111 16.41 0.00 44.35 3.85
2401 2894 2.278206 CGATCGGAGCGTGTCCTG 60.278 66.667 7.38 0.00 44.35 3.86
2402 2895 2.885861 GATCGGAGCGTGTCCTGT 59.114 61.111 4.67 0.00 44.35 4.00
2403 2896 1.517257 GATCGGAGCGTGTCCTGTG 60.517 63.158 4.67 0.00 44.35 3.66
2404 2897 2.214181 GATCGGAGCGTGTCCTGTGT 62.214 60.000 4.67 0.00 44.35 3.72
2405 2898 2.214181 ATCGGAGCGTGTCCTGTGTC 62.214 60.000 4.67 0.00 44.35 3.67
2406 2899 2.920645 CGGAGCGTGTCCTGTGTCT 61.921 63.158 4.67 0.00 44.35 3.41
2407 2900 1.367840 GGAGCGTGTCCTGTGTCTT 59.632 57.895 0.00 0.00 42.99 3.01
2450 2943 2.094442 GTCAGGGTCTGTTAGTGAGAGC 60.094 54.545 0.00 0.00 37.25 4.09
2459 2954 0.811915 TTAGTGAGAGCGAGACTGCC 59.188 55.000 0.00 0.00 34.65 4.85
2534 3029 5.449107 AGTTCAGAACACGACTAGCTAAA 57.551 39.130 15.85 0.00 0.00 1.85
2536 3031 6.456501 AGTTCAGAACACGACTAGCTAAAAT 58.543 36.000 15.85 0.00 0.00 1.82
2561 3104 4.103627 TCCATACAAGAGATGATGCCATGT 59.896 41.667 0.00 0.00 32.09 3.21
2566 3109 5.687780 ACAAGAGATGATGCCATGTTCATA 58.312 37.500 3.75 0.00 32.84 2.15
2573 3116 2.336945 TGCCATGTTCATAGCCTCTG 57.663 50.000 1.38 0.00 0.00 3.35
2575 3118 2.158856 TGCCATGTTCATAGCCTCTGAG 60.159 50.000 0.00 0.00 0.00 3.35
2584 3127 3.117360 TCATAGCCTCTGAGGAGTGATGA 60.117 47.826 27.53 21.90 37.67 2.92
2586 3129 1.189752 GCCTCTGAGGAGTGATGACA 58.810 55.000 27.53 0.00 37.67 3.58
2587 3130 1.134848 GCCTCTGAGGAGTGATGACAC 60.135 57.143 27.53 1.40 40.46 3.67
2611 3154 2.481104 CCTCCGTGTTTTGTTGTTGCAT 60.481 45.455 0.00 0.00 0.00 3.96
2612 3155 2.788786 CTCCGTGTTTTGTTGTTGCATC 59.211 45.455 0.00 0.00 0.00 3.91
2772 3315 2.806288 CGCTGCGCATTAGTTTAGTT 57.194 45.000 12.24 0.00 0.00 2.24
2774 3317 4.253352 CGCTGCGCATTAGTTTAGTTTA 57.747 40.909 12.24 0.00 0.00 2.01
2775 3318 4.643953 CGCTGCGCATTAGTTTAGTTTAA 58.356 39.130 12.24 0.00 0.00 1.52
2776 3319 4.723862 CGCTGCGCATTAGTTTAGTTTAAG 59.276 41.667 12.24 0.00 0.00 1.85
2777 3320 4.495828 GCTGCGCATTAGTTTAGTTTAAGC 59.504 41.667 12.24 0.00 0.00 3.09
2778 3321 5.673818 GCTGCGCATTAGTTTAGTTTAAGCT 60.674 40.000 12.24 0.00 33.65 3.74
2779 3322 5.864986 TGCGCATTAGTTTAGTTTAAGCTC 58.135 37.500 5.66 0.00 31.49 4.09
2799 3342 4.393371 GCTCCTGCGAAGAGAGTTTAAAAT 59.607 41.667 9.76 0.00 32.86 1.82
2818 3361 0.674269 TTTTGACGCCCACGATACCC 60.674 55.000 0.00 0.00 43.93 3.69
2886 3429 0.392193 GTCACATGCTCTCTGTGGGG 60.392 60.000 3.83 0.00 43.33 4.96
2887 3430 1.748122 CACATGCTCTCTGTGGGGC 60.748 63.158 0.00 0.00 40.23 5.80
2889 3432 3.005539 ATGCTCTCTGTGGGGCGT 61.006 61.111 0.00 0.00 0.00 5.68
2890 3433 3.320879 ATGCTCTCTGTGGGGCGTG 62.321 63.158 0.00 0.00 0.00 5.34
2891 3434 4.767255 GCTCTCTGTGGGGCGTGG 62.767 72.222 0.00 0.00 0.00 4.94
2892 3435 4.087892 CTCTCTGTGGGGCGTGGG 62.088 72.222 0.00 0.00 0.00 4.61
2901 3444 4.626081 GGGCGTGGGCTGCGATAT 62.626 66.667 5.54 0.00 39.81 1.63
2902 3445 3.349006 GGCGTGGGCTGCGATATG 61.349 66.667 5.54 0.00 39.81 1.78
2903 3446 4.017877 GCGTGGGCTGCGATATGC 62.018 66.667 5.54 0.00 46.70 3.14
2904 3447 2.280389 CGTGGGCTGCGATATGCT 60.280 61.111 0.00 0.00 46.63 3.79
2905 3448 2.601398 CGTGGGCTGCGATATGCTG 61.601 63.158 0.00 0.00 46.63 4.41
2910 3453 4.044721 CTGCGATATGCTGCTGCT 57.955 55.556 17.00 5.09 46.63 4.24
2911 3454 1.569984 CTGCGATATGCTGCTGCTG 59.430 57.895 17.00 0.77 46.63 4.41
2912 3455 2.251667 GCGATATGCTGCTGCTGC 59.748 61.111 22.51 22.51 41.73 5.25
2913 3456 2.252346 GCGATATGCTGCTGCTGCT 61.252 57.895 27.67 17.30 41.73 4.24
2914 3457 1.569984 CGATATGCTGCTGCTGCTG 59.430 57.895 27.67 16.73 40.48 4.41
2915 3458 0.878961 CGATATGCTGCTGCTGCTGA 60.879 55.000 27.67 17.63 40.01 4.26
2916 3459 1.524848 GATATGCTGCTGCTGCTGAT 58.475 50.000 27.67 20.84 40.01 2.90
2917 3460 1.197949 GATATGCTGCTGCTGCTGATG 59.802 52.381 27.67 9.61 40.01 3.07
2918 3461 0.179468 TATGCTGCTGCTGCTGATGA 59.821 50.000 27.67 11.28 40.01 2.92
2919 3462 0.466372 ATGCTGCTGCTGCTGATGAT 60.466 50.000 27.67 12.92 40.01 2.45
2920 3463 1.356979 GCTGCTGCTGCTGATGATG 59.643 57.895 23.39 4.47 40.01 3.07
2921 3464 1.095807 GCTGCTGCTGCTGATGATGA 61.096 55.000 23.39 0.00 40.01 2.92
2937 3480 4.622260 TGATGATGAACAACACAGGAGA 57.378 40.909 0.00 0.00 0.00 3.71
2993 3540 6.220930 TGTTAGTTACTCCTACTTGTTGCTG 58.779 40.000 0.00 0.00 0.00 4.41
3003 3550 4.759693 CCTACTTGTTGCTGACCACAATTA 59.240 41.667 0.00 0.00 0.00 1.40
3005 3552 4.207165 ACTTGTTGCTGACCACAATTAGT 58.793 39.130 0.00 0.00 0.00 2.24
3071 3618 1.887344 AATGTGGCCGGCACCAAATC 61.887 55.000 30.85 9.47 42.70 2.17
3088 3635 2.896677 ATCGATCCACCCAGCCTCCA 62.897 60.000 0.00 0.00 0.00 3.86
3136 3683 2.000429 CAGCTTTTGGCCACTAATGC 58.000 50.000 3.88 12.56 43.05 3.56
3158 3705 0.808125 GCATCAACCGTATGTGGCAA 59.192 50.000 0.00 0.00 0.00 4.52
3159 3706 1.202177 GCATCAACCGTATGTGGCAAG 60.202 52.381 0.00 0.00 0.00 4.01
3160 3707 1.094785 ATCAACCGTATGTGGCAAGC 58.905 50.000 0.00 0.00 0.00 4.01
3162 3709 0.881118 CAACCGTATGTGGCAAGCTT 59.119 50.000 0.00 0.00 0.00 3.74
3164 3711 0.960364 ACCGTATGTGGCAAGCTTGG 60.960 55.000 27.10 10.16 0.00 3.61
3213 3768 3.396685 AAAGGCCAATTATGCAGGGTA 57.603 42.857 5.01 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.359214 CGTCATCATTCTTCCTCTCCGA 59.641 50.000 0.00 0.00 0.00 4.55
78 80 6.554982 ACTGATCTGCCCTTGTATCACTATTA 59.445 38.462 0.00 0.00 0.00 0.98
109 111 8.405531 GGCTCAATATGCATACTCAACTAAAAA 58.594 33.333 8.99 0.00 0.00 1.94
161 195 0.904649 TCATGAATGCCACGGAGAGT 59.095 50.000 0.00 0.00 0.00 3.24
204 243 1.140161 CATGCATGAACCCCTTGCG 59.860 57.895 22.59 0.00 45.72 4.85
213 252 3.507233 GGAAGTCCACTTTCATGCATGAA 59.493 43.478 33.08 33.08 39.30 2.57
220 259 2.504367 CAACCGGAAGTCCACTTTCAT 58.496 47.619 9.46 0.00 36.11 2.57
224 263 0.818040 GTGCAACCGGAAGTCCACTT 60.818 55.000 9.46 0.00 39.23 3.16
252 291 2.309528 TAGTGGGAGCGCAAACTATG 57.690 50.000 11.47 0.00 0.00 2.23
321 361 5.551760 ATTCACCTGCACGAGAATTTTAG 57.448 39.130 3.27 0.00 0.00 1.85
404 447 2.588106 GCATTCGTACGTGCAATTTGTC 59.412 45.455 21.76 0.38 40.94 3.18
435 478 1.874019 CTACGCACGCACCTAGCTG 60.874 63.158 0.00 0.00 42.61 4.24
439 482 4.137872 GGCCTACGCACGCACCTA 62.138 66.667 0.00 0.00 36.38 3.08
494 537 4.445453 TCTATGCACTCGATCAAGCAATT 58.555 39.130 0.00 0.00 40.76 2.32
495 538 4.063998 TCTATGCACTCGATCAAGCAAT 57.936 40.909 0.00 0.00 40.76 3.56
527 591 9.352839 TCATCTATATATACCTATCTCCCCGAT 57.647 37.037 0.00 0.00 36.11 4.18
552 929 7.149031 CGGTCGAATCAACCAGTTTTTAATTTC 60.149 37.037 0.00 0.00 36.53 2.17
556 933 4.815308 TCGGTCGAATCAACCAGTTTTTAA 59.185 37.500 0.00 0.00 36.53 1.52
557 934 4.378774 TCGGTCGAATCAACCAGTTTTTA 58.621 39.130 0.00 0.00 36.53 1.52
569 946 2.576406 GATGACGAGATCGGTCGAATC 58.424 52.381 10.96 9.25 42.85 2.52
614 992 0.163146 GCCGCGCCTATAAAACGATC 59.837 55.000 0.00 0.00 0.00 3.69
713 1099 2.197605 TGAACGGACGCTGTCAGGA 61.198 57.895 1.14 0.00 33.68 3.86
714 1100 2.022129 GTGAACGGACGCTGTCAGG 61.022 63.158 1.14 0.00 33.68 3.86
750 1136 1.566077 GGTGACCGGTTCGTTTTCG 59.434 57.895 9.42 0.00 45.64 3.46
915 1304 1.301293 GCTGGTCCTGGCTTAGCTT 59.699 57.895 3.59 0.00 0.00 3.74
916 1305 2.993853 GCTGGTCCTGGCTTAGCT 59.006 61.111 3.59 0.00 0.00 3.32
1691 2152 0.596577 TGGACGAACTGAGGAAGACG 59.403 55.000 0.00 0.00 36.15 4.18
1714 2178 2.700897 AGCTGAAGACCTACAGTGTTGT 59.299 45.455 0.00 0.00 41.39 3.32
1740 2204 9.942526 ATTACCCAGATAAAATCCATCTTTTCT 57.057 29.630 0.00 0.00 30.18 2.52
1743 2207 7.040409 GCGATTACCCAGATAAAATCCATCTTT 60.040 37.037 0.00 0.00 30.18 2.52
1750 2214 6.575162 AATGGCGATTACCCAGATAAAATC 57.425 37.500 0.00 0.00 35.48 2.17
1808 2272 4.282873 GCTAAATGCTAACGATTTCTGCC 58.717 43.478 0.00 0.00 38.95 4.85
1832 2298 5.885465 ACTCCAAACTGATTCTCTCCATTT 58.115 37.500 0.00 0.00 0.00 2.32
1877 2350 6.089820 CCACATCTTGTTTTATGCATGTCAAC 59.910 38.462 10.16 9.70 0.00 3.18
1912 2392 2.104967 ACATGGCATCAATCAGTTGGG 58.895 47.619 0.00 0.00 35.99 4.12
2242 2734 0.105453 AGATCCACCGAGGGCTATGT 60.105 55.000 0.00 0.00 38.24 2.29
2283 2775 5.053145 AGCTAGATTAATCTGTTGAAGCCG 58.947 41.667 25.22 5.94 35.25 5.52
2287 2779 6.631016 ACACGAGCTAGATTAATCTGTTGAA 58.369 36.000 25.22 6.48 37.76 2.69
2290 2782 9.035607 CATAAACACGAGCTAGATTAATCTGTT 57.964 33.333 25.22 16.78 37.76 3.16
2309 2801 2.034878 TGTGGCAGCAAACCATAAACA 58.965 42.857 0.00 0.00 39.95 2.83
2312 2804 2.492881 CAGATGTGGCAGCAAACCATAA 59.507 45.455 0.00 0.00 39.95 1.90
2313 2805 2.093890 CAGATGTGGCAGCAAACCATA 58.906 47.619 0.00 0.00 39.95 2.74
2342 2835 2.025727 GCTCGTATCGGGGTGTCG 59.974 66.667 0.00 0.00 0.00 4.35
2343 2836 2.025727 CGCTCGTATCGGGGTGTC 59.974 66.667 0.00 0.00 0.00 3.67
2344 2837 3.524606 CCGCTCGTATCGGGGTGT 61.525 66.667 5.17 0.00 42.99 4.16
2400 2893 5.197451 ACCCTGAAAATGTACAAAGACACA 58.803 37.500 0.00 0.00 30.52 3.72
2401 2894 5.767816 ACCCTGAAAATGTACAAAGACAC 57.232 39.130 0.00 0.00 30.52 3.67
2402 2895 6.605594 AGAAACCCTGAAAATGTACAAAGACA 59.394 34.615 0.00 0.00 0.00 3.41
2403 2896 7.039313 AGAAACCCTGAAAATGTACAAAGAC 57.961 36.000 0.00 0.00 0.00 3.01
2404 2897 6.017440 CGAGAAACCCTGAAAATGTACAAAGA 60.017 38.462 0.00 0.00 0.00 2.52
2405 2898 6.142817 CGAGAAACCCTGAAAATGTACAAAG 58.857 40.000 0.00 0.00 0.00 2.77
2406 2899 5.591067 ACGAGAAACCCTGAAAATGTACAAA 59.409 36.000 0.00 0.00 0.00 2.83
2407 2900 5.127491 ACGAGAAACCCTGAAAATGTACAA 58.873 37.500 0.00 0.00 0.00 2.41
2450 2943 4.820284 AAGAAAGAAAAAGGCAGTCTCG 57.180 40.909 0.00 0.00 0.00 4.04
2534 3029 7.024345 TGGCATCATCTCTTGTATGGATATT 57.976 36.000 0.00 0.00 0.00 1.28
2536 3031 6.013119 ACATGGCATCATCTCTTGTATGGATA 60.013 38.462 0.00 0.00 0.00 2.59
2561 3104 3.388552 TCACTCCTCAGAGGCTATGAA 57.611 47.619 13.50 0.00 45.11 2.57
2566 3109 1.272928 TGTCATCACTCCTCAGAGGCT 60.273 52.381 12.26 0.00 45.11 4.58
2586 3129 2.718563 ACAACAAAACACGGAGGAAGT 58.281 42.857 0.00 0.00 0.00 3.01
2587 3130 3.434637 CAACAACAAAACACGGAGGAAG 58.565 45.455 0.00 0.00 0.00 3.46
2590 3133 1.135257 TGCAACAACAAAACACGGAGG 60.135 47.619 0.00 0.00 0.00 4.30
2594 3137 3.694734 AGAGATGCAACAACAAAACACG 58.305 40.909 0.00 0.00 0.00 4.49
2598 3141 3.456280 GCCAAGAGATGCAACAACAAAA 58.544 40.909 0.00 0.00 0.00 2.44
2611 3154 2.214181 GAGAACTCGGCGCCAAGAGA 62.214 60.000 30.61 18.01 37.87 3.10
2612 3155 1.807573 GAGAACTCGGCGCCAAGAG 60.808 63.158 28.98 26.42 40.16 2.85
2759 3302 6.258899 GCAGGAGCTTAAACTAAACTAATGC 58.741 40.000 0.00 0.00 37.91 3.56
2770 3313 2.926838 CTCTCTTCGCAGGAGCTTAAAC 59.073 50.000 0.00 0.00 39.10 2.01
2771 3314 2.563179 ACTCTCTTCGCAGGAGCTTAAA 59.437 45.455 0.00 0.00 39.10 1.52
2772 3315 2.171840 ACTCTCTTCGCAGGAGCTTAA 58.828 47.619 0.00 0.00 39.10 1.85
2774 3317 0.972883 AACTCTCTTCGCAGGAGCTT 59.027 50.000 0.00 0.00 39.10 3.74
2775 3318 0.972883 AAACTCTCTTCGCAGGAGCT 59.027 50.000 0.00 0.00 39.10 4.09
2776 3319 2.656560 TAAACTCTCTTCGCAGGAGC 57.343 50.000 1.66 0.00 37.42 4.70
2777 3320 6.487689 AATTTTAAACTCTCTTCGCAGGAG 57.512 37.500 0.00 0.48 0.00 3.69
2778 3321 6.877611 AAATTTTAAACTCTCTTCGCAGGA 57.122 33.333 0.00 0.00 0.00 3.86
2779 3322 7.113544 GTCAAAATTTTAAACTCTCTTCGCAGG 59.886 37.037 2.44 0.00 0.00 4.85
2799 3342 0.674269 GGGTATCGTGGGCGTCAAAA 60.674 55.000 0.00 0.00 39.49 2.44
2818 3361 2.032550 CCAAACAGACACACAGAGCTTG 59.967 50.000 0.00 0.00 0.00 4.01
2857 3400 2.625823 GCATGTGACCAACCACCGG 61.626 63.158 0.00 0.00 36.26 5.28
2886 3429 4.017877 GCATATCGCAGCCCACGC 62.018 66.667 0.00 0.00 41.79 5.34
2887 3430 2.280389 AGCATATCGCAGCCCACG 60.280 61.111 0.00 0.00 46.13 4.94
2889 3432 2.592574 GCAGCATATCGCAGCCCA 60.593 61.111 0.00 0.00 46.80 5.36
2893 3436 1.569984 CAGCAGCAGCATATCGCAG 59.430 57.895 3.17 0.00 46.13 5.18
2894 3437 2.540228 GCAGCAGCAGCATATCGCA 61.540 57.895 4.63 0.00 46.13 5.10
2895 3438 2.251667 GCAGCAGCAGCATATCGC 59.748 61.111 4.63 0.00 45.49 4.58
2896 3439 0.878961 TCAGCAGCAGCAGCATATCG 60.879 55.000 12.92 0.00 45.49 2.92
2897 3440 1.197949 CATCAGCAGCAGCAGCATATC 59.802 52.381 12.92 0.00 45.49 1.63
2898 3441 1.202770 TCATCAGCAGCAGCAGCATAT 60.203 47.619 12.92 1.87 45.49 1.78
2899 3442 0.179468 TCATCAGCAGCAGCAGCATA 59.821 50.000 12.92 0.00 45.49 3.14
2900 3443 0.466372 ATCATCAGCAGCAGCAGCAT 60.466 50.000 12.92 0.00 45.49 3.79
2901 3444 1.077716 ATCATCAGCAGCAGCAGCA 60.078 52.632 12.92 0.00 45.49 4.41
2902 3445 1.095807 TCATCATCAGCAGCAGCAGC 61.096 55.000 3.17 0.46 45.49 5.25
2903 3446 1.265365 CATCATCATCAGCAGCAGCAG 59.735 52.381 3.17 0.00 45.49 4.24
2904 3447 1.134220 TCATCATCATCAGCAGCAGCA 60.134 47.619 3.17 0.00 45.49 4.41
2905 3448 1.594331 TCATCATCATCAGCAGCAGC 58.406 50.000 0.00 0.00 42.56 5.25
2906 3449 2.943033 TGTTCATCATCATCAGCAGCAG 59.057 45.455 0.00 0.00 0.00 4.24
2907 3450 2.993937 TGTTCATCATCATCAGCAGCA 58.006 42.857 0.00 0.00 0.00 4.41
2908 3451 3.128068 TGTTGTTCATCATCATCAGCAGC 59.872 43.478 0.00 0.00 0.00 5.25
2909 3452 4.155280 TGTGTTGTTCATCATCATCAGCAG 59.845 41.667 0.00 0.00 0.00 4.24
2910 3453 4.073549 TGTGTTGTTCATCATCATCAGCA 58.926 39.130 0.00 0.00 0.00 4.41
2911 3454 4.438336 CCTGTGTTGTTCATCATCATCAGC 60.438 45.833 0.00 0.00 31.55 4.26
2912 3455 4.939439 TCCTGTGTTGTTCATCATCATCAG 59.061 41.667 0.00 0.00 32.04 2.90
2913 3456 4.909001 TCCTGTGTTGTTCATCATCATCA 58.091 39.130 0.00 0.00 0.00 3.07
2914 3457 5.181009 TCTCCTGTGTTGTTCATCATCATC 58.819 41.667 0.00 0.00 0.00 2.92
2915 3458 5.169992 TCTCCTGTGTTGTTCATCATCAT 57.830 39.130 0.00 0.00 0.00 2.45
2916 3459 4.622260 TCTCCTGTGTTGTTCATCATCA 57.378 40.909 0.00 0.00 0.00 3.07
2917 3460 5.064452 GTCATCTCCTGTGTTGTTCATCATC 59.936 44.000 0.00 0.00 0.00 2.92
2918 3461 4.940046 GTCATCTCCTGTGTTGTTCATCAT 59.060 41.667 0.00 0.00 0.00 2.45
2919 3462 4.202346 TGTCATCTCCTGTGTTGTTCATCA 60.202 41.667 0.00 0.00 0.00 3.07
2920 3463 4.318332 TGTCATCTCCTGTGTTGTTCATC 58.682 43.478 0.00 0.00 0.00 2.92
2921 3464 4.356405 TGTCATCTCCTGTGTTGTTCAT 57.644 40.909 0.00 0.00 0.00 2.57
2937 3480 6.486657 CCATTAATCTACGGTGGAAATGTCAT 59.513 38.462 14.10 0.00 31.59 3.06
2993 3540 8.730680 AGTATTCAATTGTCACTAATTGTGGTC 58.269 33.333 5.13 4.03 46.20 4.02
3003 3550 3.441572 GCTGCCAGTATTCAATTGTCACT 59.558 43.478 5.13 4.62 0.00 3.41
3005 3552 3.419943 TGCTGCCAGTATTCAATTGTCA 58.580 40.909 5.13 0.00 0.00 3.58
3071 3618 1.987807 ATTGGAGGCTGGGTGGATCG 61.988 60.000 0.00 0.00 0.00 3.69
3088 3635 2.231380 AGGAACTCACCCCGCCATT 61.231 57.895 0.00 0.00 0.00 3.16
3132 3679 1.063912 CATACGGTTGATGCGTGCATT 59.936 47.619 8.98 0.00 36.70 3.56
3136 3683 0.373370 CCACATACGGTTGATGCGTG 59.627 55.000 0.00 0.00 0.00 5.34
3173 3720 2.676471 ATGGACAAAGCGGCCACC 60.676 61.111 2.24 0.00 33.93 4.61
3174 3721 1.523154 TTGATGGACAAAGCGGCCAC 61.523 55.000 2.24 0.00 35.39 5.01


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

AutoCloner maintained by Alex Coulton.