Multiple sequence alignment - TraesCS3D01G255300

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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 TraesCS3D01G255300 chr3D 100.000 3479 0 0 1 3479 356957796 356954318 0.000000e+00 6425.0
1 TraesCS3D01G255300 chr3A 92.833 3000 118 39 506 3474 476089464 476086531 0.000000e+00 4259.0
2 TraesCS3D01G255300 chr3A 94.118 51 3 0 468 518 476097134 476097084 1.040000e-10 78.7
3 TraesCS3D01G255300 chr3B 94.076 1401 35 10 897 2275 458171868 458170494 0.000000e+00 2084.0
4 TraesCS3D01G255300 chr3B 96.292 836 28 3 1 833 458173276 458172441 0.000000e+00 1369.0
5 TraesCS3D01G255300 chr3B 94.552 569 22 2 2327 2886 458170491 458169923 0.000000e+00 870.0
6 TraesCS3D01G255300 chr4D 86.100 259 32 3 96 353 506869949 506869694 3.420000e-70 276.0
7 TraesCS3D01G255300 chr4D 81.181 271 45 6 82 348 332376563 332376295 2.720000e-51 213.0
8 TraesCS3D01G255300 chr4B 83.846 260 38 3 96 354 664344439 664344695 9.650000e-61 244.0
9 TraesCS3D01G255300 chr5A 82.331 266 41 5 87 348 304124377 304124114 3.490000e-55 226.0
10 TraesCS3D01G255300 chr5A 82.329 249 40 4 103 348 25157936 25158183 2.720000e-51 213.0
11 TraesCS3D01G255300 chr2B 80.427 281 49 6 85 361 123205636 123205914 3.520000e-50 209.0
12 TraesCS3D01G255300 chr6D 81.111 270 41 8 85 348 99228733 99228468 1.270000e-49 207.0
13 TraesCS3D01G255300 chr1D 81.538 260 40 8 87 341 324489171 324489427 1.270000e-49 207.0
14 TraesCS3D01G255300 chr2D 82.051 117 19 1 3045 3161 39817702 39817588 7.950000e-17 99.0


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 TraesCS3D01G255300 chr3D 356954318 356957796 3478 True 6425 6425 100.000000 1 3479 1 chr3D.!!$R1 3478
1 TraesCS3D01G255300 chr3A 476086531 476089464 2933 True 4259 4259 92.833000 506 3474 1 chr3A.!!$R1 2968
2 TraesCS3D01G255300 chr3B 458169923 458173276 3353 True 1441 2084 94.973333 1 2886 3 chr3B.!!$R1 2885

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
48 49 0.315886 TCACTGAAAGGCGCGAGTAA 59.684 50.0 12.1 0.0 39.30 2.24 F
804 819 0.392327 GAGGAGCCAAGAGGAAGCAC 60.392 60.0 0.0 0.0 36.89 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1631 1.134280 CGCCTCAGGAAGATGAACCAT 60.134 52.381 0.0 0.0 0.0 3.55 R
2533 3100 0.529337 ATCGACGCATCTCTGGCTTG 60.529 55.000 0.0 0.0 0.0 4.01 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
48 49 0.315886 TCACTGAAAGGCGCGAGTAA 59.684 50.000 12.10 0.00 39.30 2.24
81 82 1.130955 CCTGCGAAAATGTGTTGTGC 58.869 50.000 0.00 0.00 0.00 4.57
82 83 1.535649 CCTGCGAAAATGTGTTGTGCA 60.536 47.619 0.00 0.00 0.00 4.57
124 125 6.671614 AGAGTATCATAGCTAGTATCACGC 57.328 41.667 0.00 0.00 37.82 5.34
165 166 6.721571 ACGTTGAGGTGACACATAATTTAG 57.278 37.500 8.08 0.00 0.00 1.85
188 189 5.134339 AGTGAGAGGAGAGAGGATTGAGTAT 59.866 44.000 0.00 0.00 0.00 2.12
243 244 6.455647 TGTAGTAGTATATGTCTTGCATGGC 58.544 40.000 0.00 0.00 38.47 4.40
336 338 8.788238 ATCATATGCATGGTCCTAGTATATGA 57.212 34.615 23.44 23.44 45.03 2.15
356 358 6.814954 ATGATACTTCCCATTGTGACTAGT 57.185 37.500 0.00 0.00 0.00 2.57
376 378 5.228945 AGTCTAACTAAGGTGTGTTGCAT 57.771 39.130 0.00 0.00 0.00 3.96
393 395 1.658596 GCATGACGCGTAAAGATGTGA 59.341 47.619 13.97 0.00 0.00 3.58
804 819 0.392327 GAGGAGCCAAGAGGAAGCAC 60.392 60.000 0.00 0.00 36.89 4.40
1444 1968 6.194796 TCAAGCTTGATACCTTAATGTTGC 57.805 37.500 25.16 0.00 31.01 4.17
1674 2198 4.496336 GGCCTGCTCGCCTGGAAT 62.496 66.667 0.00 0.00 46.10 3.01
1860 2384 2.875485 CCGAGAGACCGCGAGAAA 59.125 61.111 8.23 0.00 37.82 2.52
1867 2391 0.179161 AGACCGCGAGAAAGACGATG 60.179 55.000 8.23 0.00 0.00 3.84
1900 2424 1.094785 CCGATTTCACCCGCATTTCT 58.905 50.000 0.00 0.00 0.00 2.52
1901 2425 1.064060 CCGATTTCACCCGCATTTCTC 59.936 52.381 0.00 0.00 0.00 2.87
1902 2426 2.009774 CGATTTCACCCGCATTTCTCT 58.990 47.619 0.00 0.00 0.00 3.10
1903 2427 2.223112 CGATTTCACCCGCATTTCTCTG 60.223 50.000 0.00 0.00 0.00 3.35
1904 2428 0.881118 TTTCACCCGCATTTCTCTGC 59.119 50.000 0.00 0.00 38.81 4.26
1905 2429 0.250684 TTCACCCGCATTTCTCTGCA 60.251 50.000 0.00 0.00 42.40 4.41
1906 2430 0.035152 TCACCCGCATTTCTCTGCAT 60.035 50.000 0.00 0.00 42.40 3.96
1907 2431 1.209261 TCACCCGCATTTCTCTGCATA 59.791 47.619 0.00 0.00 42.40 3.14
1908 2432 2.158769 TCACCCGCATTTCTCTGCATAT 60.159 45.455 0.00 0.00 42.40 1.78
1909 2433 2.620115 CACCCGCATTTCTCTGCATATT 59.380 45.455 0.00 0.00 42.40 1.28
1910 2434 3.067180 CACCCGCATTTCTCTGCATATTT 59.933 43.478 0.00 0.00 42.40 1.40
1911 2435 3.701040 ACCCGCATTTCTCTGCATATTTT 59.299 39.130 0.00 0.00 42.40 1.82
1912 2436 4.202050 ACCCGCATTTCTCTGCATATTTTC 60.202 41.667 0.00 0.00 42.40 2.29
1913 2437 4.202040 CCCGCATTTCTCTGCATATTTTCA 60.202 41.667 0.00 0.00 42.40 2.69
1914 2438 4.974275 CCGCATTTCTCTGCATATTTTCAG 59.026 41.667 0.00 0.00 42.40 3.02
1915 2439 4.974275 CGCATTTCTCTGCATATTTTCAGG 59.026 41.667 0.00 0.00 42.40 3.86
1916 2440 4.743644 GCATTTCTCTGCATATTTTCAGGC 59.256 41.667 0.00 0.00 41.87 4.85
1917 2441 5.680408 GCATTTCTCTGCATATTTTCAGGCA 60.680 40.000 0.00 0.00 41.87 4.75
1918 2442 4.970662 TTCTCTGCATATTTTCAGGCAC 57.029 40.909 0.00 0.00 32.06 5.01
1919 2443 3.954200 TCTCTGCATATTTTCAGGCACA 58.046 40.909 0.00 0.00 32.06 4.57
1920 2444 3.943381 TCTCTGCATATTTTCAGGCACAG 59.057 43.478 0.00 0.00 32.06 3.66
1921 2445 3.018856 TCTGCATATTTTCAGGCACAGG 58.981 45.455 0.00 0.00 32.06 4.00
2031 2582 4.500716 CCAAACATTGGCGACCTAAACTTT 60.501 41.667 0.00 0.00 45.17 2.66
2201 2764 4.058124 TCTCTCGTTGAAACATGAACTGG 58.942 43.478 0.00 0.00 0.00 4.00
2202 2765 3.804036 TCTCGTTGAAACATGAACTGGT 58.196 40.909 0.00 0.00 0.00 4.00
2203 2766 3.559655 TCTCGTTGAAACATGAACTGGTG 59.440 43.478 0.00 0.00 0.00 4.17
2204 2767 2.032799 TCGTTGAAACATGAACTGGTGC 59.967 45.455 0.00 0.00 0.00 5.01
2205 2768 2.033299 CGTTGAAACATGAACTGGTGCT 59.967 45.455 0.00 0.00 0.00 4.40
2207 2770 4.083324 CGTTGAAACATGAACTGGTGCTAT 60.083 41.667 0.00 0.00 0.00 2.97
2232 2795 2.389962 ATGGTGAACATTTGGCATGC 57.610 45.000 9.90 9.90 35.97 4.06
2247 2810 1.202177 GCATGCGTGTTTAGTCCATGG 60.202 52.381 4.97 4.97 35.15 3.66
2278 2845 9.630098 AAATATTGTGTAATCAACTTGCTTCAG 57.370 29.630 0.00 0.00 0.00 3.02
2282 2849 5.140177 GTGTAATCAACTTGCTTCAGTTCG 58.860 41.667 0.00 0.00 34.60 3.95
2533 3100 1.674962 GATCAGTGGAGCTTGCATTCC 59.325 52.381 5.67 5.67 0.00 3.01
2720 3287 9.191995 GGGAAATGTGTAAAGAAATTGTTGTAG 57.808 33.333 0.00 0.00 0.00 2.74
2740 3314 3.083349 ATGAGCAGGCGGCCTACA 61.083 61.111 23.37 20.94 46.50 2.74
2743 3317 1.334384 TGAGCAGGCGGCCTACAATA 61.334 55.000 23.37 3.56 46.50 1.90
2751 3325 2.159000 GGCGGCCTACAATACAAGTACT 60.159 50.000 12.87 0.00 0.00 2.73
2805 3379 1.662044 CCAACAGCCAAGAACTGCC 59.338 57.895 0.00 0.00 38.79 4.85
2825 3399 1.532437 CAGATGCTGTTGTTCTTGCGA 59.468 47.619 0.00 0.00 0.00 5.10
2826 3400 2.031769 CAGATGCTGTTGTTCTTGCGAA 60.032 45.455 0.00 0.00 0.00 4.70
2827 3401 2.618241 AGATGCTGTTGTTCTTGCGAAA 59.382 40.909 0.00 0.00 0.00 3.46
2892 3466 9.996554 ACAAAAACAAGGGGAAATAAGAAATAG 57.003 29.630 0.00 0.00 0.00 1.73
2893 3467 9.435688 CAAAAACAAGGGGAAATAAGAAATAGG 57.564 33.333 0.00 0.00 0.00 2.57
2894 3468 6.791867 AACAAGGGGAAATAAGAAATAGGC 57.208 37.500 0.00 0.00 0.00 3.93
2897 3471 5.686535 AGGGGAAATAAGAAATAGGCCAT 57.313 39.130 5.01 0.00 0.00 4.40
2934 3508 6.589830 TCAATAATCTCGTAGCAAGAAAGC 57.410 37.500 0.00 0.00 0.00 3.51
2935 3509 6.106003 TCAATAATCTCGTAGCAAGAAAGCA 58.894 36.000 0.00 0.00 36.85 3.91
2936 3510 6.593770 TCAATAATCTCGTAGCAAGAAAGCAA 59.406 34.615 0.00 0.00 36.85 3.91
2993 3571 3.303132 GCAAAATGTATACGCTCCCTTCG 60.303 47.826 0.00 0.00 0.00 3.79
2994 3572 2.814280 AATGTATACGCTCCCTTCGG 57.186 50.000 0.00 0.00 0.00 4.30
3064 3647 2.886523 TGAGCATCTCCAACAACCTTTG 59.113 45.455 0.00 0.00 34.92 2.77
3065 3648 1.615392 AGCATCTCCAACAACCTTTGC 59.385 47.619 0.00 0.00 0.00 3.68
3084 3667 5.673337 TTGCATATTGGATCGCTAAAGAC 57.327 39.130 0.00 0.00 0.00 3.01
3085 3668 4.065088 TGCATATTGGATCGCTAAAGACC 58.935 43.478 0.00 0.00 0.00 3.85
3128 3711 6.774656 AGAGAAGGTTTAGCAATCCAATATGG 59.225 38.462 0.00 0.00 39.43 2.74
3129 3712 6.435164 AGAAGGTTTAGCAATCCAATATGGT 58.565 36.000 0.00 0.00 39.03 3.55
3130 3713 6.897413 AGAAGGTTTAGCAATCCAATATGGTT 59.103 34.615 0.00 0.00 39.03 3.67
3131 3714 7.400052 AGAAGGTTTAGCAATCCAATATGGTTT 59.600 33.333 0.00 0.00 39.03 3.27
3132 3715 7.494922 AGGTTTAGCAATCCAATATGGTTTT 57.505 32.000 0.00 0.00 39.03 2.43
3133 3716 7.917003 AGGTTTAGCAATCCAATATGGTTTTT 58.083 30.769 0.00 0.00 39.03 1.94
3216 3799 6.748333 AACATGTGGAGATAGTTTGTCATG 57.252 37.500 0.00 0.00 37.83 3.07
3224 3807 3.873361 AGATAGTTTGTCATGGACGCATG 59.127 43.478 0.00 0.00 34.95 4.06
3225 3808 1.167851 AGTTTGTCATGGACGCATGG 58.832 50.000 0.00 0.00 34.95 3.66
3262 3845 8.634335 ATGCACATTTATACATATACTGGCAA 57.366 30.769 0.00 0.00 0.00 4.52
3270 3853 8.812147 TTATACATATACTGGCAAAACTCTCG 57.188 34.615 0.00 0.00 0.00 4.04
3285 3874 2.810274 ACTCTCGTACACGTACACACAT 59.190 45.455 8.02 0.00 40.80 3.21
3287 3876 1.647213 CTCGTACACGTACACACATGC 59.353 52.381 8.02 0.00 40.80 4.06
3322 3911 2.537578 CGTACACACGCACACACG 59.462 61.111 0.00 0.00 42.05 4.49
3323 3912 2.244382 GTACACACGCACACACGC 59.756 61.111 0.00 0.00 36.19 5.34
3332 3921 2.254951 CACACACGCGTACCCGTA 59.745 61.111 13.44 0.00 39.83 4.02
3333 3922 2.082366 CACACACGCGTACCCGTAC 61.082 63.158 13.44 0.00 39.83 3.67
3334 3923 2.254951 CACACGCGTACCCGTACA 59.745 61.111 13.44 0.00 39.83 2.90
3335 3924 1.153978 CACACGCGTACCCGTACAT 60.154 57.895 13.44 0.00 39.83 2.29
3336 3925 1.153978 ACACGCGTACCCGTACATG 60.154 57.895 13.44 0.00 39.83 3.21
3337 3926 1.153978 CACGCGTACCCGTACATGT 60.154 57.895 13.44 2.69 39.83 3.21
3338 3927 0.098552 CACGCGTACCCGTACATGTA 59.901 55.000 13.44 0.08 39.83 2.29
3339 3928 0.098728 ACGCGTACCCGTACATGTAC 59.901 55.000 23.53 23.53 40.08 2.90
3340 3929 0.098552 CGCGTACCCGTACATGTACA 59.901 55.000 30.17 12.38 37.73 2.90
3341 3930 1.548986 GCGTACCCGTACATGTACAC 58.451 55.000 30.17 20.82 37.73 2.90
3342 3931 1.135431 GCGTACCCGTACATGTACACA 60.135 52.381 30.17 12.73 37.73 3.72
3343 3932 2.518949 CGTACCCGTACATGTACACAC 58.481 52.381 30.17 20.52 37.73 3.82
3344 3933 2.731968 CGTACCCGTACATGTACACACC 60.732 54.545 30.17 15.24 37.73 4.16
3366 3955 2.427232 AGTACGCGTACAACACACAT 57.573 45.000 41.10 21.81 38.48 3.21
3367 3956 2.055838 AGTACGCGTACAACACACATG 58.944 47.619 41.10 0.00 38.48 3.21
3375 3964 2.276472 ACAACACACATGCACACAAC 57.724 45.000 0.00 0.00 0.00 3.32
3376 3965 1.543358 ACAACACACATGCACACAACA 59.457 42.857 0.00 0.00 0.00 3.33
3377 3966 1.919263 CAACACACATGCACACAACAC 59.081 47.619 0.00 0.00 0.00 3.32
3378 3967 1.172175 ACACACATGCACACAACACA 58.828 45.000 0.00 0.00 0.00 3.72
3379 3968 1.135431 ACACACATGCACACAACACAC 60.135 47.619 0.00 0.00 0.00 3.82
3380 3969 1.132834 CACACATGCACACAACACACT 59.867 47.619 0.00 0.00 0.00 3.55
3381 3970 2.354199 CACACATGCACACAACACACTA 59.646 45.455 0.00 0.00 0.00 2.74
3382 3971 2.613595 ACACATGCACACAACACACTAG 59.386 45.455 0.00 0.00 0.00 2.57
3383 3972 2.613595 CACATGCACACAACACACTAGT 59.386 45.455 0.00 0.00 0.00 2.57
3384 3973 3.807071 CACATGCACACAACACACTAGTA 59.193 43.478 0.00 0.00 0.00 1.82
3385 3974 3.807622 ACATGCACACAACACACTAGTAC 59.192 43.478 0.00 0.00 0.00 2.73
3386 3975 3.528597 TGCACACAACACACTAGTACA 57.471 42.857 0.00 0.00 0.00 2.90
3387 3976 3.191669 TGCACACAACACACTAGTACAC 58.808 45.455 0.00 0.00 0.00 2.90
3388 3977 3.191669 GCACACAACACACTAGTACACA 58.808 45.455 0.00 0.00 0.00 3.72
3389 3978 3.000925 GCACACAACACACTAGTACACAC 59.999 47.826 0.00 0.00 0.00 3.82
3390 3979 4.177783 CACACAACACACTAGTACACACA 58.822 43.478 0.00 0.00 0.00 3.72
3391 3980 4.032445 CACACAACACACTAGTACACACAC 59.968 45.833 0.00 0.00 0.00 3.82
3392 3981 4.081862 ACACAACACACTAGTACACACACT 60.082 41.667 0.00 0.00 0.00 3.55
3393 3982 4.503007 CACAACACACTAGTACACACACTC 59.497 45.833 0.00 0.00 0.00 3.51
3398 3987 3.242969 ACACTAGTACACACACTCACACG 60.243 47.826 0.00 0.00 0.00 4.49
3403 3992 0.461870 ACACACACTCACACGTGCAT 60.462 50.000 17.22 0.00 38.45 3.96
3420 4009 1.201769 GCATAACACACGCGTACACAG 60.202 52.381 13.44 0.50 0.00 3.66
3421 4010 2.055838 CATAACACACGCGTACACAGT 58.944 47.619 13.44 1.32 0.00 3.55
3422 4011 3.236005 CATAACACACGCGTACACAGTA 58.764 45.455 13.44 0.00 0.00 2.74
3423 4012 1.480205 AACACACGCGTACACAGTAC 58.520 50.000 13.44 0.00 0.00 2.73
3424 4013 0.381445 ACACACGCGTACACAGTACA 59.619 50.000 13.44 0.00 0.00 2.90
3425 4014 1.001048 ACACACGCGTACACAGTACAT 60.001 47.619 13.44 0.00 0.00 2.29
3426 4015 1.385409 CACACGCGTACACAGTACATG 59.615 52.381 13.44 0.00 0.00 3.21
3453 4046 0.802994 ACACGTACACACCACACACG 60.803 55.000 0.00 0.00 38.52 4.49
3465 4058 1.125384 CCACACACGCGTATACAACAC 59.875 52.381 13.44 0.00 0.00 3.32
3469 4062 2.218987 CACACGCGTATACAACACACAA 59.781 45.455 13.44 0.00 0.00 3.33
3474 4067 6.128499 ACACGCGTATACAACACACAAATAAT 60.128 34.615 13.44 0.00 0.00 1.28
3475 4068 7.063191 ACACGCGTATACAACACACAAATAATA 59.937 33.333 13.44 0.00 0.00 0.98
3476 4069 7.368768 CACGCGTATACAACACACAAATAATAC 59.631 37.037 13.44 0.00 0.00 1.89
3477 4070 7.063191 ACGCGTATACAACACACAAATAATACA 59.937 33.333 11.67 0.00 0.00 2.29
3478 4071 7.368768 CGCGTATACAACACACAAATAATACAC 59.631 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.624015 TGCCTACACTGTGTAGTACAAAC 58.376 43.478 33.86 20.89 46.68 2.93
16 17 4.564406 CCTTTCAGTGAATCTGCCTACACT 60.564 45.833 6.36 0.00 43.32 3.55
70 71 3.306225 CCAGCCTTAATGCACAACACATT 60.306 43.478 5.50 0.00 40.68 2.71
81 82 5.882557 ACTCTTATTGTGACCAGCCTTAATG 59.117 40.000 0.00 0.00 0.00 1.90
82 83 6.067217 ACTCTTATTGTGACCAGCCTTAAT 57.933 37.500 0.00 0.00 0.00 1.40
118 119 1.066215 TGTCTAGTTGGCATGCGTGAT 60.066 47.619 12.44 0.19 0.00 3.06
122 123 3.544048 CGTAAATGTCTAGTTGGCATGCG 60.544 47.826 12.44 0.00 40.61 4.73
123 124 3.374058 ACGTAAATGTCTAGTTGGCATGC 59.626 43.478 9.90 9.90 40.61 4.06
124 125 5.121611 TCAACGTAAATGTCTAGTTGGCATG 59.878 40.000 6.76 0.00 40.61 4.06
165 166 3.631250 ACTCAATCCTCTCTCCTCTCAC 58.369 50.000 0.00 0.00 0.00 3.51
336 338 7.620094 AGTTAGACTAGTCACAATGGGAAGTAT 59.380 37.037 24.44 1.44 0.00 2.12
356 358 4.994852 GTCATGCAACACACCTTAGTTAGA 59.005 41.667 0.00 0.00 0.00 2.10
376 378 1.658596 GCATCACATCTTTACGCGTCA 59.341 47.619 18.63 0.00 0.00 4.35
393 395 1.375908 ACCTTCATGTGTCGCGCAT 60.376 52.632 8.75 0.00 34.71 4.73
405 407 2.833533 GCAGCGCAACACACCTTCA 61.834 57.895 11.47 0.00 0.00 3.02
426 428 3.308438 ACATAACTTCACGTAAGCGGT 57.692 42.857 0.00 0.00 43.45 5.68
589 594 5.738118 TTCGACAAACTATTTTTGGACGT 57.262 34.783 13.70 0.00 36.04 4.34
804 819 4.796231 CGTCTCCTTCCCGCCGTG 62.796 72.222 0.00 0.00 0.00 4.94
838 853 2.114411 GGGTGAACGAAGGGGCAA 59.886 61.111 0.00 0.00 0.00 4.52
839 854 3.961414 GGGGTGAACGAAGGGGCA 61.961 66.667 0.00 0.00 0.00 5.36
840 855 3.623703 GAGGGGTGAACGAAGGGGC 62.624 68.421 0.00 0.00 0.00 5.80
1107 1631 1.134280 CGCCTCAGGAAGATGAACCAT 60.134 52.381 0.00 0.00 0.00 3.55
1466 1990 7.921787 TCGTCAAGAAACTTAAGCATGTAAAA 58.078 30.769 1.29 0.00 0.00 1.52
1467 1991 7.485418 TCGTCAAGAAACTTAAGCATGTAAA 57.515 32.000 1.29 0.00 0.00 2.01
1674 2198 2.745100 AGCGAGTAGACGACGGCA 60.745 61.111 2.19 0.00 35.54 5.69
1818 2342 2.044946 GGCTCCTTGAACCGCCAT 60.045 61.111 0.00 0.00 42.06 4.40
1860 2384 4.674623 CGGCAAGTACTTACTTCATCGTCT 60.675 45.833 8.04 0.00 44.19 4.18
1867 2391 5.163884 GGTGAAATCGGCAAGTACTTACTTC 60.164 44.000 8.04 3.49 44.19 3.01
1900 2424 3.018856 CCTGTGCCTGAAAATATGCAGA 58.981 45.455 0.00 0.00 33.80 4.26
1901 2425 2.756760 ACCTGTGCCTGAAAATATGCAG 59.243 45.455 0.00 0.00 33.80 4.41
1902 2426 2.754552 GACCTGTGCCTGAAAATATGCA 59.245 45.455 0.00 0.00 0.00 3.96
1903 2427 2.099756 GGACCTGTGCCTGAAAATATGC 59.900 50.000 0.00 0.00 0.00 3.14
1904 2428 3.624777 AGGACCTGTGCCTGAAAATATG 58.375 45.455 0.00 0.00 33.59 1.78
1913 2437 2.205462 AGACCAGGACCTGTGCCT 59.795 61.111 20.24 10.65 35.75 4.75
1914 2438 2.348998 CAGACCAGGACCTGTGCC 59.651 66.667 20.24 8.58 0.00 5.01
1915 2439 1.557269 ATCCAGACCAGGACCTGTGC 61.557 60.000 20.24 11.26 41.30 4.57
1916 2440 1.866015 TATCCAGACCAGGACCTGTG 58.134 55.000 20.24 13.60 41.30 3.66
1917 2441 2.225650 ACTTATCCAGACCAGGACCTGT 60.226 50.000 20.24 8.41 41.30 4.00
1918 2442 2.472029 ACTTATCCAGACCAGGACCTG 58.528 52.381 15.15 15.15 41.30 4.00
1919 2443 2.950990 ACTTATCCAGACCAGGACCT 57.049 50.000 0.00 0.00 41.30 3.85
1920 2444 3.912248 TCTACTTATCCAGACCAGGACC 58.088 50.000 0.00 0.00 41.30 4.46
1921 2445 4.202172 GCTTCTACTTATCCAGACCAGGAC 60.202 50.000 0.00 0.00 41.30 3.85
2201 2764 7.915397 CCAAATGTTCACCATAACTAATAGCAC 59.085 37.037 0.00 0.00 31.97 4.40
2202 2765 7.416213 GCCAAATGTTCACCATAACTAATAGCA 60.416 37.037 0.00 0.00 31.97 3.49
2203 2766 6.918022 GCCAAATGTTCACCATAACTAATAGC 59.082 38.462 0.00 0.00 31.97 2.97
2204 2767 7.995289 TGCCAAATGTTCACCATAACTAATAG 58.005 34.615 0.00 0.00 31.97 1.73
2205 2768 7.946381 TGCCAAATGTTCACCATAACTAATA 57.054 32.000 0.00 0.00 31.97 0.98
2207 2770 6.629128 CATGCCAAATGTTCACCATAACTAA 58.371 36.000 0.00 0.00 31.97 2.24
2232 2795 5.621197 TTTTCATCCATGGACTAAACACG 57.379 39.130 18.99 0.00 0.00 4.49
2303 2870 3.184379 CACGCGAAACAATTTCAGAGAGA 59.816 43.478 15.93 0.00 39.63 3.10
2308 2875 4.144108 CGTTTACACGCGAAACAATTTCAG 60.144 41.667 15.93 0.00 40.18 3.02
2533 3100 0.529337 ATCGACGCATCTCTGGCTTG 60.529 55.000 0.00 0.00 0.00 4.01
2740 3314 5.178809 GCGGAGAACAAACAGTACTTGTATT 59.821 40.000 0.00 0.00 39.73 1.89
2743 3317 2.870411 GCGGAGAACAAACAGTACTTGT 59.130 45.455 0.00 0.00 43.45 3.16
2751 3325 2.224185 TGAGCTAAGCGGAGAACAAACA 60.224 45.455 0.00 0.00 0.00 2.83
2805 3379 1.959747 CGCAAGAACAACAGCATCTG 58.040 50.000 0.00 0.00 43.02 2.90
2825 3399 7.275888 TCTTGTAATTGTTGAGATGTGCTTT 57.724 32.000 0.00 0.00 0.00 3.51
2826 3400 6.882610 TCTTGTAATTGTTGAGATGTGCTT 57.117 33.333 0.00 0.00 0.00 3.91
2827 3401 6.262944 TGTTCTTGTAATTGTTGAGATGTGCT 59.737 34.615 0.00 0.00 0.00 4.40
2892 3466 6.930667 ATTGATAAAAGAATTGCAATGGCC 57.069 33.333 13.82 5.69 40.13 5.36
2922 3496 6.381801 ACACATGTATTTGCTTTCTTGCTAC 58.618 36.000 0.00 0.00 0.00 3.58
3020 3598 1.878953 ACTTTGTCGGGCTAAGTGTG 58.121 50.000 8.58 0.00 40.60 3.82
3064 3647 4.670227 GGTCTTTAGCGATCCAATATGC 57.330 45.455 0.00 0.00 0.00 3.14
3084 3667 6.875948 TCTCTCTTCTCTTTCTATCATCGG 57.124 41.667 0.00 0.00 0.00 4.18
3085 3668 7.013274 ACCTTCTCTCTTCTCTTTCTATCATCG 59.987 40.741 0.00 0.00 0.00 3.84
3131 3714 7.826744 ACAAAGGATACCAAAGCAAAAGAAAAA 59.173 29.630 0.00 0.00 37.17 1.94
3132 3715 7.334858 ACAAAGGATACCAAAGCAAAAGAAAA 58.665 30.769 0.00 0.00 37.17 2.29
3133 3716 6.883744 ACAAAGGATACCAAAGCAAAAGAAA 58.116 32.000 0.00 0.00 37.17 2.52
3134 3717 6.478512 ACAAAGGATACCAAAGCAAAAGAA 57.521 33.333 0.00 0.00 37.17 2.52
3135 3718 7.775053 ATACAAAGGATACCAAAGCAAAAGA 57.225 32.000 0.00 0.00 37.17 2.52
3177 3760 5.809562 CCACATGTTATTGTGTGTTTTGTGT 59.190 36.000 0.00 0.00 44.42 3.72
3193 3776 5.649395 CCATGACAAACTATCTCCACATGTT 59.351 40.000 0.00 0.00 34.17 2.71
3198 3781 3.865745 CGTCCATGACAAACTATCTCCAC 59.134 47.826 0.00 0.00 32.09 4.02
3201 3784 3.521560 TGCGTCCATGACAAACTATCTC 58.478 45.455 0.00 0.00 32.09 2.75
3202 3785 3.610040 TGCGTCCATGACAAACTATCT 57.390 42.857 0.00 0.00 32.09 1.98
3216 3799 2.464459 GCTAGTGTGCCATGCGTCC 61.464 63.158 0.00 0.00 0.00 4.79
3224 3807 1.667236 TGTGCATATGCTAGTGTGCC 58.333 50.000 27.13 6.72 42.66 5.01
3225 3808 3.976793 AATGTGCATATGCTAGTGTGC 57.023 42.857 27.13 9.84 42.66 4.57
3238 3821 8.457238 TTTGCCAGTATATGTATAAATGTGCA 57.543 30.769 0.00 0.00 0.00 4.57
3258 3841 1.494824 ACGTGTACGAGAGTTTTGCC 58.505 50.000 11.79 0.00 46.40 4.52
3262 3845 3.065233 TGTGTGTACGTGTACGAGAGTTT 59.935 43.478 11.79 0.00 46.40 2.66
3270 3853 1.411394 ACGCATGTGTGTACGTGTAC 58.589 50.000 11.96 3.21 44.06 2.90
3306 3895 2.244382 GCGTGTGTGCGTGTGTAC 59.756 61.111 0.00 0.00 0.00 2.90
3321 3910 0.098552 TGTACATGTACGGGTACGCG 59.901 55.000 28.27 28.27 46.04 6.01
3322 3911 1.135431 TGTGTACATGTACGGGTACGC 60.135 52.381 26.59 23.10 46.12 4.42
3323 3912 2.518949 GTGTGTACATGTACGGGTACG 58.481 52.381 26.59 0.00 42.09 3.67
3324 3913 2.417243 GGGTGTGTACATGTACGGGTAC 60.417 54.545 26.59 20.10 40.15 3.34
3325 3914 1.824230 GGGTGTGTACATGTACGGGTA 59.176 52.381 26.59 10.13 38.85 3.69
3326 3915 0.609662 GGGTGTGTACATGTACGGGT 59.390 55.000 26.59 0.00 38.85 5.28
3327 3916 0.899720 AGGGTGTGTACATGTACGGG 59.100 55.000 26.59 0.00 38.85 5.28
3328 3917 2.756760 ACTAGGGTGTGTACATGTACGG 59.243 50.000 26.59 13.17 38.85 4.02
3329 3918 4.494690 CGTACTAGGGTGTGTACATGTACG 60.495 50.000 26.59 14.48 43.24 3.67
3330 3919 4.731773 GCGTACTAGGGTGTGTACATGTAC 60.732 50.000 25.99 25.99 39.00 2.90
3331 3920 3.378112 GCGTACTAGGGTGTGTACATGTA 59.622 47.826 0.08 0.08 39.00 2.29
3332 3921 2.165030 GCGTACTAGGGTGTGTACATGT 59.835 50.000 2.69 2.69 39.00 3.21
3333 3922 2.793585 CGCGTACTAGGGTGTGTACATG 60.794 54.545 0.00 0.00 39.00 3.21
3334 3923 1.402968 CGCGTACTAGGGTGTGTACAT 59.597 52.381 0.00 0.00 39.00 2.29
3335 3924 0.804364 CGCGTACTAGGGTGTGTACA 59.196 55.000 0.00 0.00 39.00 2.90
3336 3925 0.804989 ACGCGTACTAGGGTGTGTAC 59.195 55.000 11.67 0.00 35.90 2.90
3337 3926 2.006888 GTACGCGTACTAGGGTGTGTA 58.993 52.381 35.66 3.62 37.83 2.90
3338 3927 0.804989 GTACGCGTACTAGGGTGTGT 59.195 55.000 35.66 2.03 37.83 3.72
3339 3928 0.804364 TGTACGCGTACTAGGGTGTG 59.196 55.000 39.69 0.00 37.83 3.82
3340 3929 1.200020 GTTGTACGCGTACTAGGGTGT 59.800 52.381 39.69 7.35 37.83 4.16
3341 3930 1.199789 TGTTGTACGCGTACTAGGGTG 59.800 52.381 39.69 0.00 37.83 4.61
3342 3931 1.200020 GTGTTGTACGCGTACTAGGGT 59.800 52.381 39.69 8.87 40.47 4.34
3343 3932 1.199789 TGTGTTGTACGCGTACTAGGG 59.800 52.381 39.69 0.00 37.00 3.53
3344 3933 2.245096 GTGTGTTGTACGCGTACTAGG 58.755 52.381 39.69 0.59 37.00 3.02
3366 3955 3.191669 GTGTACTAGTGTGTTGTGTGCA 58.808 45.455 5.39 0.00 0.00 4.57
3367 3956 3.000925 GTGTGTACTAGTGTGTTGTGTGC 59.999 47.826 5.39 0.00 0.00 4.57
3375 3964 4.042398 GTGTGAGTGTGTGTACTAGTGTG 58.958 47.826 5.39 0.00 0.00 3.82
3376 3965 3.242969 CGTGTGAGTGTGTGTACTAGTGT 60.243 47.826 5.39 0.00 0.00 3.55
3377 3966 3.242969 ACGTGTGAGTGTGTGTACTAGTG 60.243 47.826 5.39 0.00 0.00 2.74
3378 3967 2.947652 ACGTGTGAGTGTGTGTACTAGT 59.052 45.455 0.00 0.00 0.00 2.57
3379 3968 3.297472 CACGTGTGAGTGTGTGTACTAG 58.703 50.000 7.58 0.00 37.35 2.57
3380 3969 2.542205 GCACGTGTGAGTGTGTGTACTA 60.542 50.000 18.38 0.00 43.61 1.82
3381 3970 1.801395 GCACGTGTGAGTGTGTGTACT 60.801 52.381 18.38 0.00 43.61 2.73
3382 3971 0.575390 GCACGTGTGAGTGTGTGTAC 59.425 55.000 18.38 0.00 43.61 2.90
3383 3972 0.173708 TGCACGTGTGAGTGTGTGTA 59.826 50.000 18.38 0.00 43.61 2.90
3384 3973 0.461870 ATGCACGTGTGAGTGTGTGT 60.462 50.000 18.38 0.00 43.61 3.72
3385 3974 1.496934 TATGCACGTGTGAGTGTGTG 58.503 50.000 18.38 0.00 43.61 3.82
3386 3975 1.864711 GTTATGCACGTGTGAGTGTGT 59.135 47.619 18.38 0.00 43.61 3.72
3387 3976 1.864082 TGTTATGCACGTGTGAGTGTG 59.136 47.619 18.38 0.00 43.61 3.82
3388 3977 1.864711 GTGTTATGCACGTGTGAGTGT 59.135 47.619 18.38 0.00 43.61 3.55
3389 3978 2.577300 GTGTTATGCACGTGTGAGTG 57.423 50.000 18.38 0.00 44.47 3.51
3403 3992 2.032675 TGTACTGTGTACGCGTGTGTTA 59.967 45.455 24.59 0.00 0.00 2.41
3433 4026 1.361793 GTGTGTGGTGTGTACGTGTT 58.638 50.000 0.00 0.00 0.00 3.32
3453 4046 8.524466 GTGTATTATTTGTGTGTTGTATACGC 57.476 34.615 0.00 0.00 37.77 4.42


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

AutoCloner maintained by Alex Coulton.