Multiple sequence alignment - TraesCS1B01G159100

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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 TraesCS1B01G159100 chr1B 100.000 3782 0 0 1375 5156 269645238 269649019 0.000000e+00 6985.0
1 TraesCS1B01G159100 chr1B 100.000 1082 0 0 1 1082 269643864 269644945 0.000000e+00 1999.0
2 TraesCS1B01G159100 chr1B 96.341 82 2 1 3081 3161 571195859 571195778 3.240000e-27 134.0
3 TraesCS1B01G159100 chr1D 96.953 1838 35 10 3080 4911 195765306 195763484 0.000000e+00 3064.0
4 TraesCS1B01G159100 chr1D 98.486 1519 15 4 1375 2891 195767341 195765829 0.000000e+00 2671.0
5 TraesCS1B01G159100 chr1D 91.568 1103 57 20 1 1082 195768513 195767426 0.000000e+00 1489.0
6 TraesCS1B01G159100 chr1D 96.500 200 5 1 4959 5156 195763500 195763301 3.850000e-86 329.0
7 TraesCS1B01G159100 chr1D 95.690 116 5 0 2968 3083 195765450 195765335 2.450000e-43 187.0
8 TraesCS1B01G159100 chr1A 96.156 1847 48 8 3080 4911 243863952 243862114 0.000000e+00 2996.0
9 TraesCS1B01G159100 chr1A 97.444 1526 29 6 1375 2891 243865952 243864428 0.000000e+00 2593.0
10 TraesCS1B01G159100 chr1A 97.716 394 8 1 689 1082 243866430 243866038 0.000000e+00 676.0
11 TraesCS1B01G159100 chr1A 96.133 181 7 0 4976 5156 243862061 243861881 3.900000e-76 296.0
12 TraesCS1B01G159100 chr1A 95.690 116 5 0 2968 3083 243864096 243863981 2.450000e-43 187.0
13 TraesCS1B01G159100 chr5B 97.436 78 2 0 3080 3157 431062072 431061995 3.240000e-27 134.0
14 TraesCS1B01G159100 chr5B 87.838 74 9 0 1379 1452 219096775 219096702 2.560000e-13 87.9
15 TraesCS1B01G159100 chr4B 97.436 78 2 0 3080 3157 340640719 340640642 3.240000e-27 134.0
16 TraesCS1B01G159100 chr6B 96.250 80 3 0 3080 3159 439481338 439481417 1.160000e-26 132.0
17 TraesCS1B01G159100 chr6B 96.104 77 3 0 3080 3156 243245193 243245269 5.420000e-25 126.0
18 TraesCS1B01G159100 chr4A 95.238 84 3 1 3080 3162 472926062 472925979 1.160000e-26 132.0
19 TraesCS1B01G159100 chr4A 94.186 86 4 1 3080 3165 346062606 346062690 4.190000e-26 130.0
20 TraesCS1B01G159100 chr2B 89.189 74 8 0 1379 1452 18154919 18154992 5.500000e-15 93.5
21 TraesCS1B01G159100 chr3D 96.970 33 1 0 690 722 498865363 498865331 7.210000e-04 56.5


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 TraesCS1B01G159100 chr1B 269643864 269649019 5155 False 4492.0 6985 100.0000 1 5156 2 chr1B.!!$F1 5155
1 TraesCS1B01G159100 chr1D 195763301 195768513 5212 True 1548.0 3064 95.8394 1 5156 5 chr1D.!!$R1 5155
2 TraesCS1B01G159100 chr1A 243861881 243866430 4549 True 1349.6 2996 96.6278 689 5156 5 chr1A.!!$R1 4467

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
215 226 0.179094 TATGGCGCTAGGGTTTGTCG 60.179 55.000 7.64 0.0 0.0 4.35 F
390 404 1.152839 GAGGGAGGAGGACGAGGAG 60.153 68.421 0.00 0.0 0.0 3.69 F
393 407 1.306970 GGAGGAGGACGAGGAGGAA 59.693 63.158 0.00 0.0 0.0 3.36 F
478 492 1.605165 GAACAACCAATCGCCCCCA 60.605 57.895 0.00 0.0 0.0 4.96 F
585 608 1.757118 TGAAGATCTAACGGCTGAGGG 59.243 52.381 0.00 0.0 0.0 4.30 F
595 618 1.831652 CGGCTGAGGGAAGACAAGGT 61.832 60.000 0.00 0.0 0.0 3.50 F
1020 1044 3.249189 TCCTCCCCAAGCAAGCGT 61.249 61.111 0.00 0.0 0.0 5.07 F
2919 2957 0.853530 ACATGCTAATTCCCTCCCCC 59.146 55.000 0.00 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1044 0.751643 TCATGAGGTCCATCTCGCGA 60.752 55.000 9.26 9.26 36.61 5.87 R
1763 1787 7.993183 CAGACACCACCTTGATAAATACCTATT 59.007 37.037 0.00 0.00 0.00 1.73 R
2269 2294 9.862371 GACTCTAGAGTTGATATCAAGAACAAA 57.138 33.333 25.86 3.34 42.66 2.83 R
2712 2749 6.613153 ACAAGGACTAGAAAGCACTAGAAT 57.387 37.500 15.79 0.00 41.42 2.40 R
2727 2764 2.158623 TGCCTCAACATCAACAAGGACT 60.159 45.455 0.00 0.00 0.00 3.85 R
2728 2765 2.229792 TGCCTCAACATCAACAAGGAC 58.770 47.619 0.00 0.00 0.00 3.85 R
2924 2962 0.179004 TTGGCCCTCGCAAAAGAAGA 60.179 50.000 0.00 0.00 36.38 2.87 R
4372 4754 0.036294 GCGAGAAGCTAACCCCTTGT 60.036 55.000 0.00 0.00 44.04 3.16 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
30 32 4.904253 TGTAACCTCAAAGGAAAAACGG 57.096 40.909 0.00 0.00 37.67 4.44
54 62 0.996762 GAGAGGGAGGGAGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
57 65 2.612251 GGAGGGAGAGAGGGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
58 66 2.015726 GGAGGGAGAGAGGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
59 67 1.231928 GAGGGAGAGAGGGAGGGAC 59.768 68.421 0.00 0.00 0.00 4.46
62 70 2.691779 GGAGAGAGGGAGGGACGGA 61.692 68.421 0.00 0.00 0.00 4.69
71 82 1.539665 GAGGGACGGAGGGAGAGAT 59.460 63.158 0.00 0.00 0.00 2.75
104 115 1.841302 TTGGAGGCCATGAAGACGCT 61.841 55.000 5.01 0.00 31.53 5.07
134 145 4.600576 TGCGAGCTCGTGCACCAA 62.601 61.111 34.46 11.15 42.74 3.67
147 158 3.216292 ACCAACTGCAACCGCCAC 61.216 61.111 0.00 0.00 37.32 5.01
196 207 4.790962 CCACAGCATGAGCCGCCT 62.791 66.667 0.00 0.00 43.56 5.52
215 226 0.179094 TATGGCGCTAGGGTTTGTCG 60.179 55.000 7.64 0.00 0.00 4.35
219 230 2.047560 GCTAGGGTTTGTCGCGGT 60.048 61.111 6.13 0.00 0.00 5.68
235 246 4.047059 GTCGGGTCGCGAAGGACA 62.047 66.667 22.77 2.02 38.70 4.02
250 261 1.510480 GGACAGTGTTGAGTGCAGCC 61.510 60.000 0.00 0.00 0.00 4.85
295 306 2.683933 AAGGCCGACATCGAGGGT 60.684 61.111 0.69 0.00 43.02 4.34
347 361 2.691241 GCAGGGACATAAGAGGAGGAGA 60.691 54.545 0.00 0.00 0.00 3.71
348 362 3.647636 CAGGGACATAAGAGGAGGAGAA 58.352 50.000 0.00 0.00 0.00 2.87
359 373 1.258445 GGAGGAGAAAGGGAGTGCGA 61.258 60.000 0.00 0.00 0.00 5.10
362 376 1.585006 GAGAAAGGGAGTGCGACGA 59.415 57.895 0.00 0.00 0.00 4.20
378 392 2.829458 GACGGACGAGGGAGGGAG 60.829 72.222 0.00 0.00 0.00 4.30
379 393 4.444081 ACGGACGAGGGAGGGAGG 62.444 72.222 0.00 0.00 0.00 4.30
380 394 4.124943 CGGACGAGGGAGGGAGGA 62.125 72.222 0.00 0.00 0.00 3.71
381 395 2.123640 GGACGAGGGAGGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
382 396 2.123640 GACGAGGGAGGGAGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
383 397 2.617538 ACGAGGGAGGGAGGAGGA 60.618 66.667 0.00 0.00 0.00 3.71
384 398 2.123640 CGAGGGAGGGAGGAGGAC 60.124 72.222 0.00 0.00 0.00 3.85
385 399 2.123640 GAGGGAGGGAGGAGGACG 60.124 72.222 0.00 0.00 0.00 4.79
386 400 2.617538 AGGGAGGGAGGAGGACGA 60.618 66.667 0.00 0.00 0.00 4.20
387 401 2.123640 GGGAGGGAGGAGGACGAG 60.124 72.222 0.00 0.00 0.00 4.18
388 402 2.123640 GGAGGGAGGAGGACGAGG 60.124 72.222 0.00 0.00 0.00 4.63
389 403 2.691779 GGAGGGAGGAGGACGAGGA 61.692 68.421 0.00 0.00 0.00 3.71
390 404 1.152839 GAGGGAGGAGGACGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
391 405 2.123640 GGGAGGAGGACGAGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
392 406 2.691779 GGGAGGAGGACGAGGAGGA 61.692 68.421 0.00 0.00 0.00 3.71
393 407 1.306970 GGAGGAGGACGAGGAGGAA 59.693 63.158 0.00 0.00 0.00 3.36
406 420 3.316573 GAGGAAGGAGGGTGTGGCG 62.317 68.421 0.00 0.00 0.00 5.69
415 429 3.284449 GGTGTGGCGGTTGTGGAC 61.284 66.667 0.00 0.00 0.00 4.02
444 458 4.858680 TCGTGCGGTTGTGCCCAA 62.859 61.111 0.00 0.00 0.00 4.12
448 462 3.302344 GCGGTTGTGCCCAATGGT 61.302 61.111 0.00 0.00 32.11 3.55
457 471 2.202932 CCCAATGGTCTCTCCGCG 60.203 66.667 0.00 0.00 39.52 6.46
474 488 1.794222 CGAGGAACAACCAATCGCC 59.206 57.895 0.00 0.00 42.04 5.54
475 489 1.644786 CGAGGAACAACCAATCGCCC 61.645 60.000 0.00 0.00 42.04 6.13
478 492 1.605165 GAACAACCAATCGCCCCCA 60.605 57.895 0.00 0.00 0.00 4.96
532 555 2.708671 TGGCCCACAGGTCATACAT 58.291 52.632 0.00 0.00 45.08 2.29
580 603 6.902771 ACATATAGTGAAGATCTAACGGCT 57.097 37.500 0.00 0.00 0.00 5.52
581 604 6.682746 ACATATAGTGAAGATCTAACGGCTG 58.317 40.000 0.00 0.00 0.00 4.85
583 606 3.791973 AGTGAAGATCTAACGGCTGAG 57.208 47.619 0.00 0.00 0.00 3.35
585 608 1.757118 TGAAGATCTAACGGCTGAGGG 59.243 52.381 0.00 0.00 0.00 4.30
588 611 2.035632 AGATCTAACGGCTGAGGGAAG 58.964 52.381 0.00 0.00 0.00 3.46
595 618 1.831652 CGGCTGAGGGAAGACAAGGT 61.832 60.000 0.00 0.00 0.00 3.50
606 629 4.219944 GGGAAGACAAGGTGGGAAATTTAC 59.780 45.833 0.00 0.00 0.00 2.01
608 631 6.243148 GGAAGACAAGGTGGGAAATTTACTA 58.757 40.000 0.00 0.00 0.00 1.82
687 711 6.603201 CCAGCCTCTTTATTGGTTTAGATGAA 59.397 38.462 0.00 0.00 0.00 2.57
767 791 7.608376 AGAGAAGTATTTAGCTTTGTCCCTTTC 59.392 37.037 0.00 0.00 0.00 2.62
1020 1044 3.249189 TCCTCCCCAAGCAAGCGT 61.249 61.111 0.00 0.00 0.00 5.07
1078 1102 5.649831 TGGAAATTGTTTTTCTTTTGTGGGG 59.350 36.000 0.00 0.00 0.00 4.96
2269 2294 8.686334 GTGATTTGGTTCAACATTATCCACTAT 58.314 33.333 0.00 0.00 0.00 2.12
2712 2749 8.296713 CAGTTTGCCACTTTAGAGCTTTTATTA 58.703 33.333 0.00 0.00 30.92 0.98
2726 2763 9.898152 AGAGCTTTTATTATTCTAGTGCTTTCT 57.102 29.630 0.00 0.00 0.00 2.52
2886 2924 5.163237 TGTTCTTCCAGTTGCTAACCTAGTT 60.163 40.000 0.00 0.00 0.00 2.24
2891 2929 5.730550 TCCAGTTGCTAACCTAGTTACATG 58.269 41.667 0.00 0.00 0.00 3.21
2892 2930 5.247564 TCCAGTTGCTAACCTAGTTACATGT 59.752 40.000 2.69 2.69 0.00 3.21
2893 2931 5.938125 CCAGTTGCTAACCTAGTTACATGTT 59.062 40.000 2.30 0.00 0.00 2.71
2894 2932 6.430000 CCAGTTGCTAACCTAGTTACATGTTT 59.570 38.462 2.30 0.00 0.00 2.83
2895 2933 7.040686 CCAGTTGCTAACCTAGTTACATGTTTT 60.041 37.037 2.30 0.00 0.00 2.43
2896 2934 7.803189 CAGTTGCTAACCTAGTTACATGTTTTG 59.197 37.037 2.30 0.00 0.00 2.44
2897 2935 7.501225 AGTTGCTAACCTAGTTACATGTTTTGT 59.499 33.333 2.30 0.00 42.62 2.83
2898 2936 7.197071 TGCTAACCTAGTTACATGTTTTGTG 57.803 36.000 2.30 0.00 39.48 3.33
2901 2939 7.801783 GCTAACCTAGTTACATGTTTTGTGAAC 59.198 37.037 2.30 0.65 39.48 3.18
2902 2940 7.633193 AACCTAGTTACATGTTTTGTGAACA 57.367 32.000 2.30 0.00 39.48 3.18
2903 2941 7.817418 ACCTAGTTACATGTTTTGTGAACAT 57.183 32.000 2.30 0.00 41.18 2.71
2913 2951 5.537188 TGTTTTGTGAACATGCTAATTCCC 58.463 37.500 0.00 0.00 0.00 3.97
2914 2952 5.304101 TGTTTTGTGAACATGCTAATTCCCT 59.696 36.000 0.00 0.00 0.00 4.20
2915 2953 5.643379 TTTGTGAACATGCTAATTCCCTC 57.357 39.130 0.00 0.00 0.00 4.30
2916 2954 3.620488 TGTGAACATGCTAATTCCCTCC 58.380 45.455 0.00 0.00 0.00 4.30
2917 2955 2.952310 GTGAACATGCTAATTCCCTCCC 59.048 50.000 0.00 0.00 0.00 4.30
2918 2956 2.091885 TGAACATGCTAATTCCCTCCCC 60.092 50.000 0.00 0.00 0.00 4.81
2919 2957 0.853530 ACATGCTAATTCCCTCCCCC 59.146 55.000 0.00 0.00 0.00 5.40
2937 2975 2.859992 CCCCCTCTTCTTTTGCGAG 58.140 57.895 0.00 0.00 0.00 5.03
2938 2976 0.678048 CCCCCTCTTCTTTTGCGAGG 60.678 60.000 0.00 0.00 43.11 4.63
2940 2978 2.175236 CCTCTTCTTTTGCGAGGGC 58.825 57.895 0.00 0.00 40.47 5.19
2941 2979 1.308783 CCTCTTCTTTTGCGAGGGCC 61.309 60.000 0.00 0.00 40.47 5.80
2942 2980 0.606401 CTCTTCTTTTGCGAGGGCCA 60.606 55.000 6.18 0.00 38.85 5.36
2961 3229 3.369366 GCCAAAACCCCATTACAAGATGG 60.369 47.826 0.00 0.00 45.05 3.51
3000 3340 9.635520 GAATCTTATTTGCCATCCTCAATATTG 57.364 33.333 9.29 9.29 0.00 1.90
3039 3379 2.778299 TGTTTGTCCTGTGCCATAGTC 58.222 47.619 0.00 0.00 0.00 2.59
3430 3802 6.481434 TTTAAGGTATCCCTCAACTCTAGC 57.519 41.667 0.00 0.00 41.56 3.42
3500 3872 0.892358 ACTGTTGTCTGCTGGGCATG 60.892 55.000 0.00 0.00 38.13 4.06
3540 3912 1.008938 ACCCTCCTGCTTCTGTCCTAT 59.991 52.381 0.00 0.00 0.00 2.57
3807 4189 2.517650 TTTGACCGGGTTTTCAATGC 57.482 45.000 6.32 0.00 31.87 3.56
3867 4249 7.502561 GGCATATCTTTTAAAGTAGGGATGTGT 59.497 37.037 4.53 0.00 0.00 3.72
3942 4324 8.777865 TTCAATATGCATATTCTAGTAGCACC 57.222 34.615 25.71 0.00 38.12 5.01
3973 4355 2.228582 TGCTCAAATACACATGTGCACC 59.771 45.455 25.68 6.35 40.07 5.01
3979 4361 2.528041 TACACATGTGCACCGTTGTA 57.472 45.000 25.68 14.83 0.00 2.41
4304 4686 7.111247 TGTTTTCTTCAGTTGACCAATTGAT 57.889 32.000 7.12 0.00 37.00 2.57
4402 4784 1.360820 GCTTCTCGCTTAAGGTGTCC 58.639 55.000 4.29 0.00 35.14 4.02
4449 4831 9.346725 GTGATTTGCTTCTGTTTCCTTATTTAG 57.653 33.333 0.00 0.00 0.00 1.85
4547 4929 2.107204 AGTTGAAGTCCCATTGTCAGCT 59.893 45.455 0.00 0.00 0.00 4.24
4604 4986 2.819608 GCTGGGTGCAAATTTGACTAGA 59.180 45.455 22.31 1.35 42.31 2.43
4704 5091 1.576421 CTCGTTTGGAGGCACAAGC 59.424 57.895 0.00 0.00 39.22 4.01
4772 5160 2.386661 AAACTATCTGGTCCTGCACG 57.613 50.000 0.00 0.00 0.00 5.34
4797 5185 4.037923 AGAAACAACTTTGGGTGCATACAG 59.962 41.667 0.00 0.00 0.00 2.74
4919 5308 2.203806 TGGAACAGACCACGTGACA 58.796 52.632 19.30 0.00 34.77 3.58
4920 5309 0.104120 TGGAACAGACCACGTGACAG 59.896 55.000 19.30 10.09 34.77 3.51
4921 5310 0.387929 GGAACAGACCACGTGACAGA 59.612 55.000 19.30 0.00 0.00 3.41
4922 5311 1.000955 GGAACAGACCACGTGACAGAT 59.999 52.381 19.30 2.42 0.00 2.90
4923 5312 2.061773 GAACAGACCACGTGACAGATG 58.938 52.381 19.30 10.54 0.00 2.90
4924 5313 1.040646 ACAGACCACGTGACAGATGT 58.959 50.000 19.30 11.18 0.00 3.06
4925 5314 1.000163 ACAGACCACGTGACAGATGTC 60.000 52.381 19.30 14.34 44.97 3.06
4941 5330 8.240883 GACAGATGTCGTAAACAATCTAAACT 57.759 34.615 0.00 0.00 42.37 2.66
4942 5331 9.350357 GACAGATGTCGTAAACAATCTAAACTA 57.650 33.333 0.00 0.00 42.37 2.24
4943 5332 9.136952 ACAGATGTCGTAAACAATCTAAACTAC 57.863 33.333 0.00 0.00 42.37 2.73
4944 5333 9.355215 CAGATGTCGTAAACAATCTAAACTACT 57.645 33.333 0.00 0.00 42.37 2.57
4945 5334 9.570488 AGATGTCGTAAACAATCTAAACTACTC 57.430 33.333 0.00 0.00 42.37 2.59
4946 5335 9.350357 GATGTCGTAAACAATCTAAACTACTCA 57.650 33.333 0.00 0.00 42.37 3.41
4947 5336 9.701098 ATGTCGTAAACAATCTAAACTACTCAA 57.299 29.630 0.00 0.00 42.37 3.02
4948 5337 9.531942 TGTCGTAAACAATCTAAACTACTCAAA 57.468 29.630 0.00 0.00 34.03 2.69
5003 5392 4.275443 CGAGTGTTCCCTACTACATAGTCC 59.725 50.000 0.00 0.00 37.73 3.85
5046 5485 5.339008 TCCTTGAATCGTAACTAGCACAT 57.661 39.130 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.419710 CCGTTTTTCCTTTGAGGTTACAATTC 59.580 38.462 0.00 0.00 36.53 2.17
30 32 0.478507 CTCTCCCTCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
54 62 1.356398 GATATCTCTCCCTCCGTCCCT 59.644 57.143 0.00 0.00 0.00 4.20
57 65 2.164338 GGTGATATCTCTCCCTCCGTC 58.836 57.143 3.98 0.00 0.00 4.79
58 66 1.783979 AGGTGATATCTCTCCCTCCGT 59.216 52.381 3.98 0.00 35.96 4.69
59 67 2.166829 CAGGTGATATCTCTCCCTCCG 58.833 57.143 3.98 0.00 35.96 4.63
62 70 1.626686 CGCAGGTGATATCTCTCCCT 58.373 55.000 3.98 1.58 35.96 4.20
71 82 0.108186 CTCCAAGTGCGCAGGTGATA 60.108 55.000 12.22 2.81 0.00 2.15
196 207 0.179094 CGACAAACCCTAGCGCCATA 60.179 55.000 2.29 0.00 0.00 2.74
202 213 2.047560 ACCGCGACAAACCCTAGC 60.048 61.111 8.23 0.00 0.00 3.42
219 230 3.744719 CTGTCCTTCGCGACCCGA 61.745 66.667 9.15 0.69 45.77 5.14
235 246 1.595382 GACGGCTGCACTCAACACT 60.595 57.895 0.50 0.00 0.00 3.55
295 306 2.680352 GCCTCCGGTCTCACCAGA 60.680 66.667 0.00 0.00 38.47 3.86
324 335 1.403814 CTCCTCTTATGTCCCTGCGA 58.596 55.000 0.00 0.00 0.00 5.10
337 348 1.899438 GCACTCCCTTTCTCCTCCTCT 60.899 57.143 0.00 0.00 0.00 3.69
347 361 2.049433 CGTCGTCGCACTCCCTTT 60.049 61.111 0.00 0.00 0.00 3.11
348 362 4.052229 CCGTCGTCGCACTCCCTT 62.052 66.667 0.00 0.00 35.54 3.95
362 376 4.444081 CCTCCCTCCCTCGTCCGT 62.444 72.222 0.00 0.00 0.00 4.69
371 385 2.123640 CCTCGTCCTCCTCCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
378 392 0.753848 CTCCTTCCTCCTCGTCCTCC 60.754 65.000 0.00 0.00 0.00 4.30
379 393 0.753848 CCTCCTTCCTCCTCGTCCTC 60.754 65.000 0.00 0.00 0.00 3.71
380 394 1.308326 CCTCCTTCCTCCTCGTCCT 59.692 63.158 0.00 0.00 0.00 3.85
381 395 1.758906 CCCTCCTTCCTCCTCGTCC 60.759 68.421 0.00 0.00 0.00 4.79
382 396 1.000612 ACCCTCCTTCCTCCTCGTC 59.999 63.158 0.00 0.00 0.00 4.20
383 397 1.305381 CACCCTCCTTCCTCCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
384 398 1.305381 ACACCCTCCTTCCTCCTCG 60.305 63.158 0.00 0.00 0.00 4.63
385 399 1.268283 CCACACCCTCCTTCCTCCTC 61.268 65.000 0.00 0.00 0.00 3.71
386 400 1.229658 CCACACCCTCCTTCCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
387 401 2.972819 GCCACACCCTCCTTCCTCC 61.973 68.421 0.00 0.00 0.00 4.30
388 402 2.671682 GCCACACCCTCCTTCCTC 59.328 66.667 0.00 0.00 0.00 3.71
389 403 3.322466 CGCCACACCCTCCTTCCT 61.322 66.667 0.00 0.00 0.00 3.36
390 404 4.410400 CCGCCACACCCTCCTTCC 62.410 72.222 0.00 0.00 0.00 3.46
391 405 3.192103 AACCGCCACACCCTCCTTC 62.192 63.158 0.00 0.00 0.00 3.46
392 406 3.175710 AACCGCCACACCCTCCTT 61.176 61.111 0.00 0.00 0.00 3.36
393 407 3.953775 CAACCGCCACACCCTCCT 61.954 66.667 0.00 0.00 0.00 3.69
406 420 1.683441 CCTACCCCAGTCCACAACC 59.317 63.158 0.00 0.00 0.00 3.77
415 429 2.267961 GCACGAACCCTACCCCAG 59.732 66.667 0.00 0.00 0.00 4.45
457 471 1.313091 GGGGCGATTGGTTGTTCCTC 61.313 60.000 0.00 0.00 37.07 3.71
474 488 3.579302 TCTTGGCTGGGTGTGGGG 61.579 66.667 0.00 0.00 0.00 4.96
475 489 2.282462 GTCTTGGCTGGGTGTGGG 60.282 66.667 0.00 0.00 0.00 4.61
478 492 1.149174 CTGTGTCTTGGCTGGGTGT 59.851 57.895 0.00 0.00 0.00 4.16
562 585 3.632604 CCTCAGCCGTTAGATCTTCACTA 59.367 47.826 0.00 0.00 0.00 2.74
580 603 0.104672 TCCCACCTTGTCTTCCCTCA 60.105 55.000 0.00 0.00 0.00 3.86
581 604 1.064825 TTCCCACCTTGTCTTCCCTC 58.935 55.000 0.00 0.00 0.00 4.30
583 606 2.604912 ATTTCCCACCTTGTCTTCCC 57.395 50.000 0.00 0.00 0.00 3.97
585 608 6.150641 GGTAGTAAATTTCCCACCTTGTCTTC 59.849 42.308 0.00 0.00 0.00 2.87
588 611 5.318630 TGGTAGTAAATTTCCCACCTTGTC 58.681 41.667 13.26 0.00 0.00 3.18
595 618 5.416326 CCGTTTGATGGTAGTAAATTTCCCA 59.584 40.000 0.00 0.00 0.00 4.37
606 629 0.251916 TCCTGGCCGTTTGATGGTAG 59.748 55.000 0.00 0.00 0.00 3.18
608 631 0.039618 ATTCCTGGCCGTTTGATGGT 59.960 50.000 0.00 0.00 0.00 3.55
643 666 4.838152 CGACCCGCTCCCATGGTG 62.838 72.222 11.73 4.22 30.97 4.17
767 791 2.045536 GCACAGCAGAGGGGAAGG 60.046 66.667 0.00 0.00 0.00 3.46
809 833 1.079543 GCTGCCGCAGAGAGAGAAA 60.080 57.895 24.80 0.00 32.44 2.52
1020 1044 0.751643 TCATGAGGTCCATCTCGCGA 60.752 55.000 9.26 9.26 36.61 5.87
1763 1787 7.993183 CAGACACCACCTTGATAAATACCTATT 59.007 37.037 0.00 0.00 0.00 1.73
2269 2294 9.862371 GACTCTAGAGTTGATATCAAGAACAAA 57.138 33.333 25.86 3.34 42.66 2.83
2712 2749 6.613153 ACAAGGACTAGAAAGCACTAGAAT 57.387 37.500 15.79 0.00 41.42 2.40
2720 2757 5.470098 TCAACATCAACAAGGACTAGAAAGC 59.530 40.000 0.00 0.00 0.00 3.51
2724 2761 4.563580 GCCTCAACATCAACAAGGACTAGA 60.564 45.833 0.00 0.00 0.00 2.43
2725 2762 3.686726 GCCTCAACATCAACAAGGACTAG 59.313 47.826 0.00 0.00 0.00 2.57
2726 2763 3.072330 TGCCTCAACATCAACAAGGACTA 59.928 43.478 0.00 0.00 0.00 2.59
2727 2764 2.158623 TGCCTCAACATCAACAAGGACT 60.159 45.455 0.00 0.00 0.00 3.85
2728 2765 2.229792 TGCCTCAACATCAACAAGGAC 58.770 47.619 0.00 0.00 0.00 3.85
2733 2770 2.562298 GGGAAATGCCTCAACATCAACA 59.438 45.455 0.00 0.00 36.66 3.33
2891 2929 5.783111 AGGGAATTAGCATGTTCACAAAAC 58.217 37.500 0.00 0.00 30.16 2.43
2892 2930 5.047377 GGAGGGAATTAGCATGTTCACAAAA 60.047 40.000 0.00 0.00 30.16 2.44
2893 2931 4.462483 GGAGGGAATTAGCATGTTCACAAA 59.538 41.667 0.00 0.00 30.16 2.83
2894 2932 4.016444 GGAGGGAATTAGCATGTTCACAA 58.984 43.478 0.00 0.00 30.16 3.33
2895 2933 3.620488 GGAGGGAATTAGCATGTTCACA 58.380 45.455 0.00 0.00 30.16 3.58
2896 2934 2.952310 GGGAGGGAATTAGCATGTTCAC 59.048 50.000 0.00 0.00 0.00 3.18
2897 2935 2.091885 GGGGAGGGAATTAGCATGTTCA 60.092 50.000 0.00 0.00 0.00 3.18
2898 2936 2.587522 GGGGAGGGAATTAGCATGTTC 58.412 52.381 0.00 0.00 0.00 3.18
2901 2939 3.753787 GGGGGAGGGAATTAGCATG 57.246 57.895 0.00 0.00 0.00 4.06
2919 2957 0.678048 CCTCGCAAAAGAAGAGGGGG 60.678 60.000 2.97 0.00 45.77 5.40
2920 2958 2.859992 CCTCGCAAAAGAAGAGGGG 58.140 57.895 2.97 0.00 45.77 4.79
2923 2961 0.606401 TGGCCCTCGCAAAAGAAGAG 60.606 55.000 0.00 0.00 36.38 2.85
2924 2962 0.179004 TTGGCCCTCGCAAAAGAAGA 60.179 50.000 0.00 0.00 36.38 2.87
2925 2963 0.673437 TTTGGCCCTCGCAAAAGAAG 59.327 50.000 0.00 0.00 32.75 2.85
2926 2964 1.115467 TTTTGGCCCTCGCAAAAGAA 58.885 45.000 0.00 0.00 39.12 2.52
2927 2965 0.387565 GTTTTGGCCCTCGCAAAAGA 59.612 50.000 0.00 0.00 39.12 2.52
2928 2966 0.599991 GGTTTTGGCCCTCGCAAAAG 60.600 55.000 0.00 0.00 39.12 2.27
2930 2968 2.503382 GGGTTTTGGCCCTCGCAAA 61.503 57.895 0.00 0.00 45.22 3.68
2931 2969 2.915137 GGGTTTTGGCCCTCGCAA 60.915 61.111 0.00 0.00 45.22 4.85
2938 2976 2.252714 TCTTGTAATGGGGTTTTGGCC 58.747 47.619 0.00 0.00 0.00 5.36
2939 2977 3.369366 CCATCTTGTAATGGGGTTTTGGC 60.369 47.826 0.00 0.00 42.19 4.52
2940 2978 3.369366 GCCATCTTGTAATGGGGTTTTGG 60.369 47.826 5.15 0.00 45.40 3.28
2941 2979 3.515104 AGCCATCTTGTAATGGGGTTTTG 59.485 43.478 5.15 0.00 45.40 2.44
2942 2980 3.769300 GAGCCATCTTGTAATGGGGTTTT 59.231 43.478 5.15 0.00 45.40 2.43
2961 3229 5.859521 AATAAGATTCGAGCATCATGAGC 57.140 39.130 0.09 5.31 33.17 4.26
3000 3340 9.442033 GACAAACAAATAACTAAAGGTGTGTAC 57.558 33.333 0.00 0.00 27.50 2.90
3215 3587 1.843206 TGCCAAGTGCCTACATGGATA 59.157 47.619 5.93 0.00 46.12 2.59
3345 3717 4.083324 TCTCAACATTCTTCGCATCAAACC 60.083 41.667 0.00 0.00 0.00 3.27
3391 3763 6.670695 ACCTTAAATTCCACAAGAGCAAAT 57.329 33.333 0.00 0.00 0.00 2.32
3500 3872 2.192187 CCTACCCCGTCTAGGCGAC 61.192 68.421 20.35 0.00 39.21 5.19
3540 3912 2.232452 GCAGAAGAGCACCTAACTCTCA 59.768 50.000 0.00 0.00 43.71 3.27
3688 4068 0.249447 GCAGCTTTGTTTCACCACCC 60.249 55.000 0.00 0.00 0.00 4.61
3867 4249 5.830799 ATGCTGTCAGTATCCCATATTGA 57.169 39.130 0.93 0.00 0.00 2.57
3886 4268 8.763049 ATAAAAAGGCAAGAGTAAGAAAATGC 57.237 30.769 0.00 0.00 0.00 3.56
3939 4321 3.799281 TTTGAGCAACCAAAAGAGGTG 57.201 42.857 0.00 0.00 42.25 4.00
3942 4324 5.830912 TGTGTATTTGAGCAACCAAAAGAG 58.169 37.500 0.00 0.00 39.20 2.85
3979 4361 9.574516 AAGCAACTAAATAATAGATCGGGAAAT 57.425 29.630 0.00 0.00 0.00 2.17
4372 4754 0.036294 GCGAGAAGCTAACCCCTTGT 60.036 55.000 0.00 0.00 44.04 3.16
4449 4831 7.832685 AGTACTGGAATTTGGGAGGTAAAATAC 59.167 37.037 0.00 0.00 0.00 1.89
4604 4986 1.065551 GTTCAAAAGCCAACGTGAGCT 59.934 47.619 6.76 6.76 42.40 4.09
4704 5091 8.507249 GTGATATTTTTCCATAATTCCCGAGAG 58.493 37.037 0.00 0.00 0.00 3.20
4772 5160 1.134848 TGCACCCAAAGTTGTTTCTGC 60.135 47.619 0.00 0.00 0.00 4.26
4797 5185 7.575365 CCCATTTGAGAATTTAAAAGTTGTGC 58.425 34.615 0.00 0.00 0.00 4.57
4911 5300 3.047093 TGTTTACGACATCTGTCACGTG 58.953 45.455 9.94 9.94 44.99 4.49
4913 5302 4.621460 AGATTGTTTACGACATCTGTCACG 59.379 41.667 10.69 1.05 44.99 4.35
4914 5303 7.576750 TTAGATTGTTTACGACATCTGTCAC 57.423 36.000 10.69 2.10 44.99 3.67
4915 5304 7.870954 AGTTTAGATTGTTTACGACATCTGTCA 59.129 33.333 10.69 0.00 44.99 3.58
4916 5305 8.240883 AGTTTAGATTGTTTACGACATCTGTC 57.759 34.615 0.07 0.07 38.26 3.51
4917 5306 9.136952 GTAGTTTAGATTGTTTACGACATCTGT 57.863 33.333 0.00 0.00 38.26 3.41
4918 5307 9.355215 AGTAGTTTAGATTGTTTACGACATCTG 57.645 33.333 0.00 0.00 38.26 2.90
4919 5308 9.570488 GAGTAGTTTAGATTGTTTACGACATCT 57.430 33.333 0.00 0.00 38.26 2.90
4920 5309 9.350357 TGAGTAGTTTAGATTGTTTACGACATC 57.650 33.333 0.00 0.00 38.26 3.06
4921 5310 9.701098 TTGAGTAGTTTAGATTGTTTACGACAT 57.299 29.630 0.00 0.00 38.26 3.06
4922 5311 9.531942 TTTGAGTAGTTTAGATTGTTTACGACA 57.468 29.630 0.00 0.00 36.19 4.35
4956 5345 5.594926 CTGCAGTCTTTTCCATCAGTTTTT 58.405 37.500 5.25 0.00 0.00 1.94
4957 5346 4.500375 GCTGCAGTCTTTTCCATCAGTTTT 60.500 41.667 16.64 0.00 0.00 2.43
4958 5347 3.005155 GCTGCAGTCTTTTCCATCAGTTT 59.995 43.478 16.64 0.00 0.00 2.66
4959 5348 2.555757 GCTGCAGTCTTTTCCATCAGTT 59.444 45.455 16.64 0.00 0.00 3.16
4960 5349 2.157738 GCTGCAGTCTTTTCCATCAGT 58.842 47.619 16.64 0.00 0.00 3.41
4961 5350 1.129998 CGCTGCAGTCTTTTCCATCAG 59.870 52.381 16.64 0.00 0.00 2.90
4962 5351 1.159285 CGCTGCAGTCTTTTCCATCA 58.841 50.000 16.64 0.00 0.00 3.07
4963 5352 1.396301 CTCGCTGCAGTCTTTTCCATC 59.604 52.381 16.64 0.00 0.00 3.51
4964 5353 1.271054 ACTCGCTGCAGTCTTTTCCAT 60.271 47.619 16.64 0.00 0.00 3.41
4965 5354 0.106708 ACTCGCTGCAGTCTTTTCCA 59.893 50.000 16.64 0.00 0.00 3.53
4966 5355 0.514691 CACTCGCTGCAGTCTTTTCC 59.485 55.000 16.64 0.00 0.00 3.13
4967 5356 1.221414 ACACTCGCTGCAGTCTTTTC 58.779 50.000 16.64 0.00 0.00 2.29
4968 5357 1.599542 GAACACTCGCTGCAGTCTTTT 59.400 47.619 16.64 1.40 0.00 2.27
4969 5358 1.221414 GAACACTCGCTGCAGTCTTT 58.779 50.000 16.64 0.29 0.00 2.52
4970 5359 0.601311 GGAACACTCGCTGCAGTCTT 60.601 55.000 16.64 0.00 0.00 3.01
4971 5360 1.005630 GGAACACTCGCTGCAGTCT 60.006 57.895 16.64 0.00 0.00 3.24
4972 5361 2.029844 GGGAACACTCGCTGCAGTC 61.030 63.158 16.64 6.83 0.00 3.51
4973 5362 1.185618 TAGGGAACACTCGCTGCAGT 61.186 55.000 16.64 0.00 44.15 4.40
4974 5363 0.737715 GTAGGGAACACTCGCTGCAG 60.738 60.000 10.11 10.11 44.15 4.41
5003 5392 1.002017 AATTGGCACCATGGGGGAG 59.998 57.895 17.80 3.66 41.15 4.30


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

AutoCloner maintained by Alex Coulton.