Multiple sequence alignment - TraesCS3A01G326500

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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 TraesCS3A01G326500 chr3A 100.000 3173 0 0 1 3173 571795008 571798180 0.000000e+00 5860.0
1 TraesCS3A01G326500 chr3B 91.613 2623 175 22 98 2702 566182136 566184731 0.000000e+00 3583.0
2 TraesCS3A01G326500 chr3B 86.061 495 39 14 2701 3173 566184804 566185290 3.650000e-139 505.0
3 TraesCS3A01G326500 chr3D 90.724 2404 172 25 21 2397 433420415 433422794 0.000000e+00 3157.0
4 TraesCS3A01G326500 chr3D 86.278 532 64 5 2389 2916 433423582 433424108 1.280000e-158 569.0
5 TraesCS3A01G326500 chr3D 85.714 70 9 1 2949 3018 422753776 422753708 4.390000e-09 73.1
6 TraesCS3A01G326500 chr3D 86.111 72 4 1 2948 3013 474998260 474998189 4.390000e-09 73.1
7 TraesCS3A01G326500 chr6D 96.721 61 1 1 2910 2970 312136217 312136276 2.010000e-17 100.0
8 TraesCS3A01G326500 chr4B 94.643 56 2 1 2954 3009 191228443 191228389 5.640000e-13 86.1
9 TraesCS3A01G326500 chr4B 89.091 55 5 1 2908 2962 613151891 613151838 2.040000e-07 67.6
10 TraesCS3A01G326500 chr5A 89.394 66 5 2 2946 3009 2866297 2866232 7.290000e-12 82.4
11 TraesCS3A01G326500 chr5A 87.037 54 6 1 2901 2954 194450973 194451025 3.420000e-05 60.2
12 TraesCS3A01G326500 chr4A 92.982 57 2 2 2957 3011 624229904 624229848 7.290000e-12 82.4
13 TraesCS3A01G326500 chr6B 83.146 89 8 4 2948 3030 49622818 49622731 1.220000e-09 75.0
14 TraesCS3A01G326500 chr6B 82.022 89 9 5 2948 3030 49827765 49827678 5.680000e-08 69.4
15 TraesCS3A01G326500 chr1A 88.235 68 1 1 2951 3011 49277398 49277331 1.220000e-09 75.0
16 TraesCS3A01G326500 chr2B 87.302 63 8 0 2915 2977 625549822 625549884 4.390000e-09 73.1
17 TraesCS3A01G326500 chr7D 97.561 41 1 0 2913 2953 621646363 621646403 1.580000e-08 71.3
18 TraesCS3A01G326500 chr1B 97.561 41 1 0 2913 2953 222308871 222308831 1.580000e-08 71.3
19 TraesCS3A01G326500 chr5D 81.579 76 14 0 785 860 128550388 128550313 2.640000e-06 63.9
20 TraesCS3A01G326500 chr5D 85.714 63 5 1 2913 2971 501707298 501707360 2.640000e-06 63.9
21 TraesCS3A01G326500 chr5B 85.938 64 3 3 2913 2971 632809613 632809551 2.640000e-06 63.9


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 TraesCS3A01G326500 chr3A 571795008 571798180 3172 False 5860 5860 100.000 1 3173 1 chr3A.!!$F1 3172
1 TraesCS3A01G326500 chr3B 566182136 566185290 3154 False 2044 3583 88.837 98 3173 2 chr3B.!!$F1 3075
2 TraesCS3A01G326500 chr3D 433420415 433424108 3693 False 1863 3157 88.501 21 2916 2 chr3D.!!$F1 2895

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
545 554 0.038618 CATCAACGGACGTCAGGTGA 60.039 55.0 33.13 33.13 41.66 4.02 F
708 718 0.251354 TGGAGGAGAAGCATGCAGTC 59.749 55.0 21.98 16.45 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2091 0.940126 CCCTTTGCCTCATCGATTCG 59.060 55.00 0.0 0.0 0.0 3.34 R
2495 3332 3.191581 TGAAACACTGGAACGCAGAAAAA 59.808 39.13 0.0 0.0 0.0 1.94 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 2.736670 AAGCACTTGTCTTGGGTCTT 57.263 45.000 0.00 0.00 0.00 3.01
45 46 0.179084 TTTGGAGGACGGCGATCATC 60.179 55.000 16.62 14.33 0.00 2.92
46 47 2.049985 GGAGGACGGCGATCATCG 60.050 66.667 16.62 1.50 43.89 3.84
47 48 2.552819 GGAGGACGGCGATCATCGA 61.553 63.158 16.62 0.00 43.74 3.59
63 64 3.056179 TCATCGACACCACTTGCATAAGA 60.056 43.478 0.00 0.00 37.36 2.10
66 67 2.668457 CGACACCACTTGCATAAGAGAC 59.332 50.000 0.00 0.00 37.36 3.36
68 69 4.380550 CGACACCACTTGCATAAGAGACTA 60.381 45.833 0.00 0.00 37.36 2.59
72 73 6.942576 ACACCACTTGCATAAGAGACTAAAAT 59.057 34.615 0.00 0.00 37.36 1.82
73 74 7.119846 ACACCACTTGCATAAGAGACTAAAATC 59.880 37.037 0.00 0.00 37.36 2.17
77 78 8.386606 CACTTGCATAAGAGACTAAAATCTGTC 58.613 37.037 0.00 0.00 37.36 3.51
87 88 8.402472 AGAGACTAAAATCTGTCTATTCACTCG 58.598 37.037 0.00 0.00 42.79 4.18
90 91 9.522804 GACTAAAATCTGTCTATTCACTCGATT 57.477 33.333 0.00 0.00 0.00 3.34
165 168 5.574188 AGACCTAGATGCACTTTGGAAAAT 58.426 37.500 6.74 0.00 0.00 1.82
174 178 8.316214 AGATGCACTTTGGAAAATAATGATTGT 58.684 29.630 0.00 0.00 0.00 2.71
196 200 6.894682 TGTATGTGAATATTTGTAGGGCTCA 58.105 36.000 0.00 0.00 0.00 4.26
246 250 2.225394 TGTTGAGGCCCTAGAGTTCTCT 60.225 50.000 0.00 7.50 0.00 3.10
276 280 3.134127 GGCGAAGGGTCATGGTGC 61.134 66.667 0.00 0.00 0.00 5.01
295 299 3.941657 GAGCTCGCCAGTGGTGGTC 62.942 68.421 22.42 16.73 46.96 4.02
364 369 1.618837 ACGAGCTACAACAGTGGTCAT 59.381 47.619 0.00 0.00 0.00 3.06
373 378 1.257750 ACAGTGGTCATGGCGAGCTA 61.258 55.000 0.00 0.00 42.88 3.32
374 379 0.105593 CAGTGGTCATGGCGAGCTAT 59.894 55.000 0.00 0.00 42.88 2.97
389 394 0.808453 GCTATAACCGCACGCCTCAA 60.808 55.000 0.00 0.00 0.00 3.02
409 414 1.157257 ATGCTGCAACGACGAACACA 61.157 50.000 6.36 0.00 0.00 3.72
452 460 3.823330 GAGTCGTCGGGATGCCGT 61.823 66.667 25.75 5.34 34.52 5.68
469 477 1.094073 CGTAGGGTGAGTCGGTCGAT 61.094 60.000 0.00 0.00 0.00 3.59
470 478 0.381089 GTAGGGTGAGTCGGTCGATG 59.619 60.000 0.00 0.00 0.00 3.84
475 483 1.443702 TGAGTCGGTCGATGTTGCG 60.444 57.895 0.00 0.00 0.00 4.85
477 485 0.731514 GAGTCGGTCGATGTTGCGAA 60.732 55.000 0.00 0.00 42.55 4.70
492 501 1.510383 CGAAAAATGCATGCGGGGA 59.490 52.632 14.09 0.00 0.00 4.81
507 516 2.681097 GCGGGGAAGACTTGCTAGAAAT 60.681 50.000 6.67 0.00 0.00 2.17
509 518 3.282885 GGGGAAGACTTGCTAGAAATGG 58.717 50.000 6.67 0.00 0.00 3.16
517 526 0.392461 TGCTAGAAATGGCGGGTGAC 60.392 55.000 0.00 0.00 0.00 3.67
532 541 0.989890 GTGACGACGGCTACATCAAC 59.010 55.000 0.65 0.00 0.00 3.18
540 549 0.108992 GGCTACATCAACGGACGTCA 60.109 55.000 18.91 0.00 0.00 4.35
545 554 0.038618 CATCAACGGACGTCAGGTGA 60.039 55.000 33.13 33.13 41.66 4.02
555 564 1.672356 GTCAGGTGATGCAACGGCT 60.672 57.895 0.00 0.00 41.91 5.52
562 571 3.951655 GATGCAACGGCTTGGTGCG 62.952 63.158 13.44 0.00 44.05 5.34
566 575 3.522731 AACGGCTTGGTGCGCAAA 61.523 55.556 14.00 2.12 44.05 3.68
570 579 1.883021 GGCTTGGTGCGCAAACTAT 59.117 52.632 14.00 0.00 44.05 2.12
577 586 2.556189 TGGTGCGCAAACTATGAACAAT 59.444 40.909 14.00 0.00 0.00 2.71
578 587 2.916716 GGTGCGCAAACTATGAACAATG 59.083 45.455 14.00 0.00 0.00 2.82
593 602 0.791983 CAATGTTCGCGAGCTGCAAG 60.792 55.000 23.51 5.88 46.97 4.01
616 625 4.021925 GTGGCAGGCGAGAGGGTT 62.022 66.667 0.00 0.00 0.00 4.11
621 631 1.433879 CAGGCGAGAGGGTTCTACG 59.566 63.158 0.00 0.00 32.53 3.51
653 663 2.264794 GAGGCCGTCAACACCGAT 59.735 61.111 0.00 0.00 0.00 4.18
659 669 0.942410 CCGTCAACACCGATGAACGT 60.942 55.000 0.00 0.00 40.78 3.99
701 711 1.376466 GCACCTTGGAGGAGAAGCA 59.624 57.895 0.07 0.00 37.67 3.91
707 717 0.694771 TTGGAGGAGAAGCATGCAGT 59.305 50.000 21.98 7.09 28.22 4.40
708 718 0.251354 TGGAGGAGAAGCATGCAGTC 59.749 55.000 21.98 16.45 0.00 3.51
709 719 0.251354 GGAGGAGAAGCATGCAGTCA 59.749 55.000 21.98 0.00 0.00 3.41
711 721 0.982704 AGGAGAAGCATGCAGTCAGT 59.017 50.000 21.98 1.62 0.00 3.41
734 744 1.728069 GCGACTAGCCGACATGAGA 59.272 57.895 1.37 0.00 40.81 3.27
735 745 0.317436 GCGACTAGCCGACATGAGAG 60.317 60.000 1.37 0.00 40.81 3.20
762 772 1.860676 TTCTGTACGTGTTGGTGAGC 58.139 50.000 0.00 0.00 0.00 4.26
764 774 1.137282 TCTGTACGTGTTGGTGAGCAA 59.863 47.619 0.00 0.00 0.00 3.91
779 789 3.555139 GTGAGCAAGAAGATGAATCGAGG 59.445 47.826 0.00 0.00 0.00 4.63
781 791 2.768527 AGCAAGAAGATGAATCGAGGGA 59.231 45.455 0.00 0.00 0.00 4.20
821 831 0.804989 CCCAGATCAAACGGCTTGTC 59.195 55.000 0.00 0.00 36.34 3.18
823 833 1.197721 CCAGATCAAACGGCTTGTCAC 59.802 52.381 0.00 0.00 36.34 3.67
879 889 2.698797 CCTATACTGCGAGAAAAGGGGA 59.301 50.000 0.00 0.00 0.00 4.81
953 970 3.735237 AAGCTTTCTCGTTCTCAGTCA 57.265 42.857 0.00 0.00 0.00 3.41
954 971 3.296322 AGCTTTCTCGTTCTCAGTCAG 57.704 47.619 0.00 0.00 0.00 3.51
965 982 2.003301 TCTCAGTCAGAGTGTCGATCG 58.997 52.381 9.36 9.36 44.98 3.69
975 992 0.797249 GTGTCGATCGTTCCCACTCG 60.797 60.000 15.94 0.00 0.00 4.18
1479 1496 0.462759 GCATCTTCCAGACCTTCCCG 60.463 60.000 0.00 0.00 0.00 5.14
1591 1608 2.658325 GTGTTCGATGAAATGTGCAAGC 59.342 45.455 0.00 0.00 0.00 4.01
1737 1754 2.351738 GCAAGTGTACAATGCAAGGGTC 60.352 50.000 23.11 0.00 39.81 4.46
2091 2108 0.042708 CGCGAATCGATGAGGCAAAG 60.043 55.000 6.91 0.00 41.67 2.77
2156 2173 0.542333 GGGTGGAAAGAGGTAGAGGC 59.458 60.000 0.00 0.00 0.00 4.70
2204 2221 7.383687 CACTCACAGGTATTGTTTTCCTACTA 58.616 38.462 0.00 0.00 38.16 1.82
2207 2224 8.842358 TCACAGGTATTGTTTTCCTACTAAAG 57.158 34.615 0.00 0.00 38.16 1.85
2233 2250 7.587757 GTGTTCTTAGAAACAATTACACAGCTG 59.412 37.037 13.48 13.48 40.62 4.24
2266 2297 6.983307 AGAATACTGATGTCTGAGTATGTTGC 59.017 38.462 0.00 0.00 35.89 4.17
2291 2331 8.667463 GCTTATTAAATTTGCCATTTCACATGT 58.333 29.630 0.00 0.00 0.00 3.21
2341 2381 8.597167 TGCATTATACAAGCTGTTCTATATCCT 58.403 33.333 0.00 0.00 0.00 3.24
2420 3256 0.322277 ACCATGAGGCTCTGCAACTG 60.322 55.000 16.72 3.84 39.06 3.16
2494 3331 3.969287 TGAACTGCATCTTAGAGCTGT 57.031 42.857 0.00 0.00 43.39 4.40
2517 3354 2.031258 TTCTGCGTTCCAGTGTTTCA 57.969 45.000 0.00 0.00 42.38 2.69
2630 3467 9.579768 GTCAGTTAGCATATCCATGTCTATAAG 57.420 37.037 0.00 0.00 34.40 1.73
2754 3665 4.040829 TCATTTATCCGGACAGCTGATCAT 59.959 41.667 23.35 7.14 0.00 2.45
2800 3711 5.189928 AGGATGCACTCTATAGTAGATCGG 58.810 45.833 0.00 0.00 33.48 4.18
2803 3714 3.502595 TGCACTCTATAGTAGATCGGCAC 59.497 47.826 0.00 0.00 33.23 5.01
2920 3841 6.320518 TCGGAGGTATTAAATCATACTCCCT 58.679 40.000 0.00 0.00 30.63 4.20
2921 3842 6.436532 TCGGAGGTATTAAATCATACTCCCTC 59.563 42.308 0.00 0.00 30.63 4.30
2922 3843 6.351117 CGGAGGTATTAAATCATACTCCCTCC 60.351 46.154 10.24 10.24 34.91 4.30
2923 3844 6.351117 GGAGGTATTAAATCATACTCCCTCCG 60.351 46.154 0.00 0.00 31.46 4.63
2924 3845 6.082707 AGGTATTAAATCATACTCCCTCCGT 58.917 40.000 0.00 0.00 31.24 4.69
2925 3846 6.210984 AGGTATTAAATCATACTCCCTCCGTC 59.789 42.308 0.00 0.00 31.24 4.79
2926 3847 4.950205 TTAAATCATACTCCCTCCGTCC 57.050 45.455 0.00 0.00 0.00 4.79
2927 3848 1.718280 AATCATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
2928 3849 0.561184 ATCATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
2929 3850 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
2930 3851 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2931 3852 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2932 3853 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2933 3854 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2934 3855 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2935 3856 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2936 3857 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2937 3858 3.452878 TCCCTCCGTCCCAAAATAAGTA 58.547 45.455 0.00 0.00 0.00 2.24
2938 3859 4.042174 TCCCTCCGTCCCAAAATAAGTAT 58.958 43.478 0.00 0.00 0.00 2.12
2939 3860 4.102054 TCCCTCCGTCCCAAAATAAGTATC 59.898 45.833 0.00 0.00 0.00 2.24
2940 3861 4.056050 CCTCCGTCCCAAAATAAGTATCG 58.944 47.826 0.00 0.00 0.00 2.92
2941 3862 3.460103 TCCGTCCCAAAATAAGTATCGC 58.540 45.455 0.00 0.00 0.00 4.58
2942 3863 3.133362 TCCGTCCCAAAATAAGTATCGCT 59.867 43.478 0.00 0.00 0.00 4.93
2943 3864 3.247648 CCGTCCCAAAATAAGTATCGCTG 59.752 47.826 0.00 0.00 0.00 5.18
2944 3865 3.247648 CGTCCCAAAATAAGTATCGCTGG 59.752 47.826 0.00 0.00 0.00 4.85
2945 3866 4.196971 GTCCCAAAATAAGTATCGCTGGT 58.803 43.478 0.00 0.00 0.00 4.00
2946 3867 4.638865 GTCCCAAAATAAGTATCGCTGGTT 59.361 41.667 0.00 0.00 0.00 3.67
2947 3868 5.124936 GTCCCAAAATAAGTATCGCTGGTTT 59.875 40.000 0.00 0.00 0.00 3.27
2948 3869 6.316890 GTCCCAAAATAAGTATCGCTGGTTTA 59.683 38.462 0.00 0.00 0.00 2.01
2949 3870 6.540914 TCCCAAAATAAGTATCGCTGGTTTAG 59.459 38.462 0.00 0.00 0.00 1.85
2950 3871 6.317893 CCCAAAATAAGTATCGCTGGTTTAGT 59.682 38.462 0.00 0.00 0.00 2.24
2951 3872 7.496591 CCCAAAATAAGTATCGCTGGTTTAGTA 59.503 37.037 0.00 0.00 0.00 1.82
2952 3873 8.333186 CCAAAATAAGTATCGCTGGTTTAGTAC 58.667 37.037 0.00 0.00 0.00 2.73
2953 3874 9.095065 CAAAATAAGTATCGCTGGTTTAGTACT 57.905 33.333 0.00 0.00 0.00 2.73
2954 3875 8.868635 AAATAAGTATCGCTGGTTTAGTACTC 57.131 34.615 0.00 0.00 0.00 2.59
2955 3876 4.915158 AGTATCGCTGGTTTAGTACTCC 57.085 45.455 0.00 0.00 0.00 3.85
2956 3877 3.635836 AGTATCGCTGGTTTAGTACTCCC 59.364 47.826 0.00 0.00 0.00 4.30
2959 3880 1.136500 CGCTGGTTTAGTACTCCCTCC 59.864 57.143 0.00 0.00 0.00 4.30
2962 3883 2.426381 CTGGTTTAGTACTCCCTCCGTC 59.574 54.545 0.00 0.00 0.00 4.79
2977 3898 2.671396 CTCCGTCCCAAAATAAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
2989 3910 7.308109 CCAAAATAAGTGTCGCTGGTTTAGTAA 60.308 37.037 0.00 0.00 0.00 2.24
2990 3911 7.916914 AAATAAGTGTCGCTGGTTTAGTAAT 57.083 32.000 0.00 0.00 0.00 1.89
2991 3912 7.916914 AATAAGTGTCGCTGGTTTAGTAATT 57.083 32.000 0.00 0.00 0.00 1.40
2992 3913 7.916914 ATAAGTGTCGCTGGTTTAGTAATTT 57.083 32.000 0.00 0.00 0.00 1.82
2994 3915 5.997385 AGTGTCGCTGGTTTAGTAATTTTG 58.003 37.500 0.00 0.00 0.00 2.44
2995 3916 5.048991 AGTGTCGCTGGTTTAGTAATTTTGG 60.049 40.000 0.00 0.00 0.00 3.28
2996 3917 4.216687 TGTCGCTGGTTTAGTAATTTTGGG 59.783 41.667 0.00 0.00 0.00 4.12
2997 3918 4.456566 GTCGCTGGTTTAGTAATTTTGGGA 59.543 41.667 0.00 0.00 0.00 4.37
3033 3992 8.548880 ACATAACTAATAGGAAGTTAGAGGCA 57.451 34.615 2.58 0.00 41.42 4.75
3039 3998 1.625818 AGGAAGTTAGAGGCACACCAG 59.374 52.381 0.00 0.00 39.06 4.00
3040 3999 1.339151 GGAAGTTAGAGGCACACCAGG 60.339 57.143 0.00 0.00 39.06 4.45
3094 4053 9.733556 TTTTCTTTCATAACTGGTAGCATAAGA 57.266 29.630 0.00 0.00 0.00 2.10
3095 4054 8.948631 TTCTTTCATAACTGGTAGCATAAGAG 57.051 34.615 0.00 0.00 0.00 2.85
3097 4056 8.758829 TCTTTCATAACTGGTAGCATAAGAGAA 58.241 33.333 0.00 0.00 0.00 2.87
3103 4062 6.299805 ACTGGTAGCATAAGAGAATGTTGA 57.700 37.500 0.00 0.00 0.00 3.18
3128 4089 3.667497 AATGTCGAGACTGCAGAGAAA 57.333 42.857 23.35 9.46 0.00 2.52
3136 4097 2.298729 AGACTGCAGAGAAACTCCTGAC 59.701 50.000 23.35 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.736670 AAGACCCAAGACAAGTGCTT 57.263 45.000 0.00 0.00 0.00 3.91
1 2 2.736670 AAAGACCCAAGACAAGTGCT 57.263 45.000 0.00 0.00 0.00 4.40
2 3 3.801114 AAAAAGACCCAAGACAAGTGC 57.199 42.857 0.00 0.00 0.00 4.40
19 20 3.147629 TCGCCGTCCTCCAAAATAAAAA 58.852 40.909 0.00 0.00 0.00 1.94
24 25 0.251916 TGATCGCCGTCCTCCAAAAT 59.748 50.000 0.00 0.00 0.00 1.82
30 31 1.370657 GTCGATGATCGCCGTCCTC 60.371 63.158 10.45 0.00 40.21 3.71
34 35 2.104331 GGTGTCGATGATCGCCGT 59.896 61.111 10.45 0.00 40.21 5.68
36 37 0.460284 AAGTGGTGTCGATGATCGCC 60.460 55.000 10.45 6.50 40.21 5.54
45 46 2.668457 GTCTCTTATGCAAGTGGTGTCG 59.332 50.000 0.00 0.00 33.20 4.35
46 47 3.931578 AGTCTCTTATGCAAGTGGTGTC 58.068 45.455 0.00 0.00 33.20 3.67
47 48 5.483685 TTAGTCTCTTATGCAAGTGGTGT 57.516 39.130 0.00 0.00 33.20 4.16
63 64 8.282455 TCGAGTGAATAGACAGATTTTAGTCT 57.718 34.615 0.00 0.00 46.19 3.24
73 74 9.899226 TGATACATTAATCGAGTGAATAGACAG 57.101 33.333 0.00 0.00 0.00 3.51
93 94 9.913310 TGACATTAAATTGTAGGGATTGATACA 57.087 29.630 0.00 0.00 0.00 2.29
113 114 9.558396 AATGTTTGTTTTGGTATTGATGACATT 57.442 25.926 0.00 0.00 0.00 2.71
174 178 7.573710 ACTTGAGCCCTACAAATATTCACATA 58.426 34.615 0.00 0.00 0.00 2.29
196 200 1.545651 GCCAGTTCAAGGCCACTACTT 60.546 52.381 5.01 0.00 46.50 2.24
223 227 3.185455 AGAACTCTAGGGCCTCAACATT 58.815 45.455 10.74 0.00 0.00 2.71
286 290 2.991076 GCTCGTAGCGACCACCACT 61.991 63.158 0.00 0.00 0.00 4.00
335 340 0.039798 TTGTAGCTCGTCGTGGTCAC 60.040 55.000 1.81 1.76 0.00 3.67
373 378 0.732571 CATTTGAGGCGTGCGGTTAT 59.267 50.000 0.00 0.00 0.00 1.89
374 379 1.917782 GCATTTGAGGCGTGCGGTTA 61.918 55.000 0.00 0.00 0.00 2.85
383 388 0.730494 GTCGTTGCAGCATTTGAGGC 60.730 55.000 0.00 0.00 0.00 4.70
389 394 0.041312 GTGTTCGTCGTTGCAGCATT 60.041 50.000 0.00 0.00 0.00 3.56
409 414 1.070275 GTCCCGGTTCCAACTCGTT 59.930 57.895 0.00 0.00 0.00 3.85
452 460 0.034767 ACATCGACCGACTCACCCTA 60.035 55.000 0.00 0.00 0.00 3.53
457 465 1.443702 CGCAACATCGACCGACTCA 60.444 57.895 0.00 0.00 0.00 3.41
469 477 0.782981 CGCATGCATTTTTCGCAACA 59.217 45.000 19.57 0.00 43.84 3.33
470 478 0.093365 CCGCATGCATTTTTCGCAAC 59.907 50.000 19.57 0.00 43.84 4.17
475 483 1.204467 TCTTCCCCGCATGCATTTTTC 59.796 47.619 19.57 0.00 0.00 2.29
477 485 0.532115 GTCTTCCCCGCATGCATTTT 59.468 50.000 19.57 0.00 0.00 1.82
492 501 2.359900 CCGCCATTTCTAGCAAGTCTT 58.640 47.619 0.00 0.00 0.00 3.01
517 526 1.138036 TCCGTTGATGTAGCCGTCG 59.862 57.895 0.00 0.00 0.00 5.12
519 528 1.153901 CGTCCGTTGATGTAGCCGT 60.154 57.895 0.00 0.00 0.00 5.68
532 541 1.374125 TTGCATCACCTGACGTCCG 60.374 57.895 14.12 6.54 0.00 4.79
540 549 1.973281 CCAAGCCGTTGCATCACCT 60.973 57.895 0.00 0.00 41.13 4.00
545 554 4.041917 CGCACCAAGCCGTTGCAT 62.042 61.111 0.00 0.00 41.38 3.96
555 564 1.950216 TGTTCATAGTTTGCGCACCAA 59.050 42.857 11.12 0.00 0.00 3.67
562 571 3.297979 CGCGAACATTGTTCATAGTTTGC 59.702 43.478 24.96 17.59 44.17 3.68
566 575 2.348666 GCTCGCGAACATTGTTCATAGT 59.651 45.455 24.96 0.00 0.00 2.12
570 579 0.512518 CAGCTCGCGAACATTGTTCA 59.487 50.000 24.96 8.67 0.00 3.18
577 586 3.716006 GCTTGCAGCTCGCGAACA 61.716 61.111 11.33 3.24 46.97 3.18
640 650 0.942410 ACGTTCATCGGTGTTGACGG 60.942 55.000 19.85 7.78 44.69 4.79
665 675 3.390521 ATCCCTTGCGAGGCACGA 61.391 61.111 15.36 7.19 45.77 4.35
676 686 0.846427 TCCTCCAAGGTGCATCCCTT 60.846 55.000 2.79 2.79 45.85 3.95
687 697 1.339824 ACTGCATGCTTCTCCTCCAAG 60.340 52.381 20.33 6.02 0.00 3.61
701 711 2.359107 CGCCACCACTGACTGCAT 60.359 61.111 0.00 0.00 0.00 3.96
707 717 2.970639 GCTAGTCGCCACCACTGA 59.029 61.111 0.00 0.00 0.00 3.41
745 755 1.526887 CTTGCTCACCAACACGTACAG 59.473 52.381 0.00 0.00 0.00 2.74
746 756 1.137282 TCTTGCTCACCAACACGTACA 59.863 47.619 0.00 0.00 0.00 2.90
747 757 1.860676 TCTTGCTCACCAACACGTAC 58.139 50.000 0.00 0.00 0.00 3.67
748 758 2.101750 TCTTCTTGCTCACCAACACGTA 59.898 45.455 0.00 0.00 0.00 3.57
762 772 4.662468 TCTCCCTCGATTCATCTTCTTG 57.338 45.455 0.00 0.00 0.00 3.02
764 774 4.283212 GGATTCTCCCTCGATTCATCTTCT 59.717 45.833 0.00 0.00 0.00 2.85
779 789 1.008767 CGTAGCCGTCGGATTCTCC 60.009 63.158 17.49 0.00 0.00 3.71
788 798 1.140375 CTGGGTTACCGTAGCCGTC 59.860 63.158 5.44 0.00 40.75 4.79
799 809 2.224670 ACAAGCCGTTTGATCTGGGTTA 60.225 45.455 1.53 0.00 41.25 2.85
823 833 4.547367 GGATCCAGAACGGGGCCG 62.547 72.222 6.95 0.00 46.03 6.13
864 874 3.578688 CAAATTTCCCCTTTTCTCGCAG 58.421 45.455 0.00 0.00 0.00 5.18
865 875 2.288763 GCAAATTTCCCCTTTTCTCGCA 60.289 45.455 0.00 0.00 0.00 5.10
879 889 1.077005 TCAGCCCCTGGTAGCAAATTT 59.923 47.619 8.46 0.00 31.51 1.82
953 970 0.526662 GTGGGAACGATCGACACTCT 59.473 55.000 24.34 0.00 33.71 3.24
954 971 0.526662 AGTGGGAACGATCGACACTC 59.473 55.000 24.34 16.06 39.03 3.51
965 982 3.683365 TTAGGGTTTACGAGTGGGAAC 57.317 47.619 0.00 0.00 0.00 3.62
975 992 1.456296 CGGCTGGGTTTAGGGTTTAC 58.544 55.000 0.00 0.00 0.00 2.01
1608 1625 1.240641 CGGCAGTAAATGTGGTGGCA 61.241 55.000 0.00 0.00 35.28 4.92
2074 2091 0.940126 CCCTTTGCCTCATCGATTCG 59.060 55.000 0.00 0.00 0.00 3.34
2091 2108 4.103785 TCCTTCATCTTCTCAATGATCCCC 59.896 45.833 0.00 0.00 33.36 4.81
2176 2193 4.023193 GGAAAACAATACCTGTGAGTGGTG 60.023 45.833 0.00 0.00 38.67 4.17
2207 2224 7.587757 CAGCTGTGTAATTGTTTCTAAGAACAC 59.412 37.037 5.25 0.00 39.11 3.32
2233 2250 7.065563 ACTCAGACATCAGTATTCTCAAATTGC 59.934 37.037 0.00 0.00 0.00 3.56
2420 3256 5.816919 TGAAGTGAAACGGAAAAACATCTC 58.183 37.500 0.00 0.00 45.86 2.75
2495 3332 3.191581 TGAAACACTGGAACGCAGAAAAA 59.808 39.130 0.00 0.00 0.00 1.94
2655 3492 9.899661 AATACAAGGTTCTTGCTAATATACACA 57.100 29.630 7.48 0.00 0.00 3.72
2722 3633 1.318576 CGGATAAATGAAGCACCCCC 58.681 55.000 0.00 0.00 0.00 5.40
2800 3711 5.985530 AGTTCCAATTTCTTAAAAGCAGTGC 59.014 36.000 7.13 7.13 0.00 4.40
2803 3714 8.424274 AAACAGTTCCAATTTCTTAAAAGCAG 57.576 30.769 0.00 0.00 0.00 4.24
2920 3841 3.133362 AGCGATACTTATTTTGGGACGGA 59.867 43.478 0.00 0.00 0.00 4.69
2921 3842 3.247648 CAGCGATACTTATTTTGGGACGG 59.752 47.826 0.00 0.00 0.00 4.79
2922 3843 3.247648 CCAGCGATACTTATTTTGGGACG 59.752 47.826 0.00 0.00 0.00 4.79
2923 3844 4.196971 ACCAGCGATACTTATTTTGGGAC 58.803 43.478 0.00 0.00 0.00 4.46
2924 3845 4.497291 ACCAGCGATACTTATTTTGGGA 57.503 40.909 0.00 0.00 0.00 4.37
2925 3846 5.576447 AAACCAGCGATACTTATTTTGGG 57.424 39.130 0.00 0.00 0.00 4.12
2926 3847 7.316544 ACTAAACCAGCGATACTTATTTTGG 57.683 36.000 0.00 0.00 0.00 3.28
2927 3848 9.095065 AGTACTAAACCAGCGATACTTATTTTG 57.905 33.333 0.00 0.00 0.00 2.44
2928 3849 9.310716 GAGTACTAAACCAGCGATACTTATTTT 57.689 33.333 0.00 0.00 0.00 1.82
2929 3850 7.924947 GGAGTACTAAACCAGCGATACTTATTT 59.075 37.037 0.00 0.00 0.00 1.40
2930 3851 7.432059 GGAGTACTAAACCAGCGATACTTATT 58.568 38.462 0.00 0.00 0.00 1.40
2931 3852 6.015603 GGGAGTACTAAACCAGCGATACTTAT 60.016 42.308 0.00 0.00 0.00 1.73
2932 3853 5.300286 GGGAGTACTAAACCAGCGATACTTA 59.700 44.000 0.00 0.00 0.00 2.24
2933 3854 4.099113 GGGAGTACTAAACCAGCGATACTT 59.901 45.833 0.00 0.00 0.00 2.24
2934 3855 3.635836 GGGAGTACTAAACCAGCGATACT 59.364 47.826 0.00 0.00 0.00 2.12
2935 3856 3.635836 AGGGAGTACTAAACCAGCGATAC 59.364 47.826 11.89 0.00 0.00 2.24
2936 3857 3.887716 GAGGGAGTACTAAACCAGCGATA 59.112 47.826 11.89 0.00 0.00 2.92
2937 3858 2.694109 GAGGGAGTACTAAACCAGCGAT 59.306 50.000 11.89 0.00 0.00 4.58
2938 3859 2.097825 GAGGGAGTACTAAACCAGCGA 58.902 52.381 11.89 0.00 0.00 4.93
2939 3860 1.136500 GGAGGGAGTACTAAACCAGCG 59.864 57.143 11.89 0.00 0.00 5.18
2940 3861 1.136500 CGGAGGGAGTACTAAACCAGC 59.864 57.143 11.89 4.93 0.00 4.85
2941 3862 2.426381 GACGGAGGGAGTACTAAACCAG 59.574 54.545 11.89 6.48 0.00 4.00
2942 3863 2.450476 GACGGAGGGAGTACTAAACCA 58.550 52.381 11.89 0.00 0.00 3.67
2943 3864 1.753649 GGACGGAGGGAGTACTAAACC 59.246 57.143 0.00 0.00 0.00 3.27
2944 3865 1.753649 GGGACGGAGGGAGTACTAAAC 59.246 57.143 0.00 0.00 0.00 2.01
2945 3866 1.358787 TGGGACGGAGGGAGTACTAAA 59.641 52.381 0.00 0.00 0.00 1.85
2946 3867 1.002069 TGGGACGGAGGGAGTACTAA 58.998 55.000 0.00 0.00 0.00 2.24
2947 3868 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
2948 3869 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
2949 3870 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2950 3871 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2951 3872 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2952 3873 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2953 3874 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2954 3875 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2955 3876 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2956 3877 2.671396 CGACACTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
2959 3880 2.073816 AGCGACACTTATTTTGGGACG 58.926 47.619 0.00 0.00 0.00 4.79
2962 3883 2.159382 ACCAGCGACACTTATTTTGGG 58.841 47.619 0.00 0.00 0.00 4.12
2977 3898 4.380128 CCGTCCCAAAATTACTAAACCAGC 60.380 45.833 0.00 0.00 0.00 4.85
2989 3910 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2990 3911 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2991 3912 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2992 3913 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2994 3915 1.685517 GTTATGTACTCCCTCCGTCCC 59.314 57.143 0.00 0.00 0.00 4.46
2995 3916 2.664015 AGTTATGTACTCCCTCCGTCC 58.336 52.381 0.00 0.00 28.23 4.79
2996 3917 6.150809 CCTATTAGTTATGTACTCCCTCCGTC 59.849 46.154 0.00 0.00 38.33 4.79
2997 3918 6.008960 CCTATTAGTTATGTACTCCCTCCGT 58.991 44.000 0.00 0.00 38.33 4.69
3027 3986 2.527624 TCTGCCTGGTGTGCCTCT 60.528 61.111 0.00 0.00 35.27 3.69
3033 3992 1.899814 TCTAAATCGTCTGCCTGGTGT 59.100 47.619 0.00 0.00 0.00 4.16
3039 3998 7.277981 TGAAACTCTAAATCTAAATCGTCTGCC 59.722 37.037 0.00 0.00 0.00 4.85
3040 3999 8.186178 TGAAACTCTAAATCTAAATCGTCTGC 57.814 34.615 0.00 0.00 0.00 4.26
3079 4038 6.595716 GTCAACATTCTCTTATGCTACCAGTT 59.404 38.462 0.00 0.00 0.00 3.16
3103 4062 2.297315 TCTGCAGTCTCGACATTTCTGT 59.703 45.455 14.67 0.00 38.67 3.41
3128 4089 5.255687 TGTGCATTCAATATTGTCAGGAGT 58.744 37.500 14.97 0.00 0.00 3.85
3136 4097 6.270064 TGCTCAAGATGTGCATTCAATATTG 58.730 36.000 9.29 9.29 41.27 1.90


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

AutoCloner maintained by Alex Coulton.