Multiple sequence alignment - TraesCS2A01G015400

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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 TraesCS2A01G015400 chr2A 100.000 3719 0 0 1 3719 6266922 6270640 0.000000e+00 6868
1 TraesCS2A01G015400 chr2A 94.936 1244 51 3 1803 3034 6127903 6129146 0.000000e+00 1938
2 TraesCS2A01G015400 chr2A 94.936 1244 51 3 1803 3034 6178942 6180185 0.000000e+00 1938
3 TraesCS2A01G015400 chr2A 94.534 1244 56 2 1803 3034 6075134 6076377 0.000000e+00 1910
4 TraesCS2A01G015400 chr2A 95.694 1045 32 3 1 1044 6074095 6075127 0.000000e+00 1668
5 TraesCS2A01G015400 chr2A 95.694 1045 32 4 1 1044 6126864 6127896 0.000000e+00 1668
6 TraesCS2A01G015400 chr2A 95.694 1045 32 4 1 1044 6177903 6178935 0.000000e+00 1668
7 TraesCS2A01G015400 chr2A 93.538 650 36 2 3073 3719 6180184 6180830 0.000000e+00 963
8 TraesCS2A01G015400 chr2A 93.385 650 37 2 3073 3719 6129145 6129791 0.000000e+00 957
9 TraesCS2A01G015400 chr2A 93.231 650 38 2 3073 3719 6076376 6077022 0.000000e+00 952
10 TraesCS2A01G015400 chr2A 95.402 261 8 1 2003 2259 5973574 5973834 2.670000e-111 412
11 TraesCS2A01G015400 chr5A 95.354 904 38 3 1 903 415195023 415194123 0.000000e+00 1434
12 TraesCS2A01G015400 chr5A 86.354 491 51 6 414 899 641776261 641776740 4.260000e-144 521
13 TraesCS2A01G015400 chr3D 93.916 904 48 4 1 902 126612129 126611231 0.000000e+00 1358
14 TraesCS2A01G015400 chr3D 91.910 445 34 2 414 857 489734218 489734661 4.080000e-174 621
15 TraesCS2A01G015400 chr3D 87.765 425 45 6 1 418 575922306 575921882 1.200000e-134 490
16 TraesCS2A01G015400 chr7A 88.009 934 87 8 995 1920 546060947 546060031 0.000000e+00 1081
17 TraesCS2A01G015400 chr7A 87.500 424 45 8 1 418 675068224 675067803 2.010000e-132 483
18 TraesCS2A01G015400 chr7A 80.351 285 49 4 2081 2364 546368519 546368797 3.760000e-50 209
19 TraesCS2A01G015400 chr7B 87.970 931 90 12 998 1920 468772135 468773051 0.000000e+00 1079
20 TraesCS2A01G015400 chr7B 85.496 131 18 1 1668 1798 467989786 467989657 6.480000e-28 135
21 TraesCS2A01G015400 chr7D 87.218 931 97 13 998 1917 451027981 451028900 0.000000e+00 1040
22 TraesCS2A01G015400 chr7D 84.448 643 96 4 2081 2721 451029029 451029669 6.780000e-177 630
23 TraesCS2A01G015400 chr2B 85.428 899 108 11 1024 1920 8750670 8749793 0.000000e+00 913
24 TraesCS2A01G015400 chr1B 80.093 859 148 16 993 1844 611675890 611676732 5.280000e-173 617
25 TraesCS2A01G015400 chr4D 88.730 488 49 3 414 897 464865386 464865871 3.200000e-165 592
26 TraesCS2A01G015400 chr3B 78.935 883 167 12 993 1870 32749420 32748552 1.930000e-162 582
27 TraesCS2A01G015400 chr3B 88.124 421 47 3 1 418 800997179 800997599 7.170000e-137 497
28 TraesCS2A01G015400 chr6D 89.311 421 39 3 1 418 306003218 306003635 1.180000e-144 523
29 TraesCS2A01G015400 chr2D 86.004 493 59 6 414 898 639615183 639614693 1.530000e-143 520
30 TraesCS2A01G015400 chr6B 87.028 424 48 7 1 418 148829192 148829614 4.350000e-129 472


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 TraesCS2A01G015400 chr2A 6266922 6270640 3718 False 6868 6868 100.000000 1 3719 1 chr2A.!!$F2 3718
1 TraesCS2A01G015400 chr2A 6177903 6180830 2927 False 1523 1938 94.722667 1 3719 3 chr2A.!!$F5 3718
2 TraesCS2A01G015400 chr2A 6126864 6129791 2927 False 1521 1938 94.671667 1 3719 3 chr2A.!!$F4 3718
3 TraesCS2A01G015400 chr2A 6074095 6077022 2927 False 1510 1910 94.486333 1 3719 3 chr2A.!!$F3 3718
4 TraesCS2A01G015400 chr5A 415194123 415195023 900 True 1434 1434 95.354000 1 903 1 chr5A.!!$R1 902
5 TraesCS2A01G015400 chr3D 126611231 126612129 898 True 1358 1358 93.916000 1 902 1 chr3D.!!$R1 901
6 TraesCS2A01G015400 chr7A 546060031 546060947 916 True 1081 1081 88.009000 995 1920 1 chr7A.!!$R1 925
7 TraesCS2A01G015400 chr7B 468772135 468773051 916 False 1079 1079 87.970000 998 1920 1 chr7B.!!$F1 922
8 TraesCS2A01G015400 chr7D 451027981 451029669 1688 False 835 1040 85.833000 998 2721 2 chr7D.!!$F1 1723
9 TraesCS2A01G015400 chr2B 8749793 8750670 877 True 913 913 85.428000 1024 1920 1 chr2B.!!$R1 896
10 TraesCS2A01G015400 chr1B 611675890 611676732 842 False 617 617 80.093000 993 1844 1 chr1B.!!$F1 851
11 TraesCS2A01G015400 chr3B 32748552 32749420 868 True 582 582 78.935000 993 1870 1 chr3B.!!$R1 877

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
557 559 1.367471 GAAAGTGGCTTGGCAACCC 59.633 57.895 4.55 4.55 31.88 4.11 F
1794 1811 1.064166 CACATGAGGAGGGGCAAGAAT 60.064 52.381 0.00 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2322 0.173708 ATCCGAAGCGTCTCCTTGAC 59.826 55.0 0.00 0.00 42.06 3.18 R
3120 3176 0.469144 TCTGGACTTTGGGCCCAAAC 60.469 55.0 40.46 31.43 40.51 2.93 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
142 143 6.833416 AGTCTTACTCTGTTGCATCTATCTCT 59.167 38.462 0.00 0.00 0.00 3.10
153 154 3.126858 GCATCTATCTCTAGTCTCGGCAG 59.873 52.174 0.00 0.00 0.00 4.85
185 186 9.807386 CTAATTGTTAACTACCAAGTTTCTTCG 57.193 33.333 7.22 0.00 43.60 3.79
440 442 6.342906 CACAACCTGCCATAAATGAATTGAT 58.657 36.000 0.00 0.00 0.00 2.57
557 559 1.367471 GAAAGTGGCTTGGCAACCC 59.633 57.895 4.55 4.55 31.88 4.11
765 768 7.714813 TGATTAGTGCTATTGTTTGCAGCTATA 59.285 33.333 0.00 0.00 40.06 1.31
766 769 8.627208 ATTAGTGCTATTGTTTGCAGCTATAT 57.373 30.769 0.00 0.00 40.06 0.86
857 860 4.818546 AGCTTGATTAGTGCGCTCAATAAT 59.181 37.500 9.73 8.98 43.59 1.28
1061 1066 3.066208 TCCCCTGATCTGGCTATTTCT 57.934 47.619 13.02 0.00 0.00 2.52
1062 1067 3.397527 TCCCCTGATCTGGCTATTTCTT 58.602 45.455 13.02 0.00 0.00 2.52
1063 1068 3.137176 TCCCCTGATCTGGCTATTTCTTG 59.863 47.826 13.02 0.00 0.00 3.02
1064 1069 2.883386 CCCTGATCTGGCTATTTCTTGC 59.117 50.000 13.02 0.00 0.00 4.01
1065 1070 3.548770 CCTGATCTGGCTATTTCTTGCA 58.451 45.455 5.61 0.00 0.00 4.08
1066 1071 3.949754 CCTGATCTGGCTATTTCTTGCAA 59.050 43.478 5.61 0.00 0.00 4.08
1074 1079 2.851008 GCTATTTCTTGCAATCGCGTCC 60.851 50.000 5.77 0.00 42.97 4.79
1091 1096 2.350895 CGTGGCCTTGGTCATCCA 59.649 61.111 3.32 0.00 42.66 3.41
1096 1101 1.751927 GCCTTGGTCATCCAGCCAG 60.752 63.158 0.00 0.00 45.22 4.85
1101 1106 2.352422 GTCATCCAGCCAGTGCCA 59.648 61.111 0.00 0.00 38.69 4.92
1102 1107 1.303561 GTCATCCAGCCAGTGCCAA 60.304 57.895 0.00 0.00 38.69 4.52
1272 1289 2.522436 TTCGTGGTGTCGACCCCT 60.522 61.111 18.25 0.00 42.34 4.79
1321 1338 1.276421 AGGACAACGATGACTTCTGGG 59.724 52.381 0.00 0.00 0.00 4.45
1629 1646 3.106738 GGAGCTCATCCCCATGTTG 57.893 57.895 17.19 0.00 43.01 3.33
1631 1648 1.476471 GGAGCTCATCCCCATGTTGAG 60.476 57.143 17.19 7.47 43.01 3.02
1650 1667 1.627834 AGGGAGTTCTCCAAGCTCTTG 59.372 52.381 18.83 2.74 40.13 3.02
1773 1790 3.865446 TGCAGACAAGATCATTGACGAT 58.135 40.909 10.61 0.00 0.00 3.73
1794 1811 1.064166 CACATGAGGAGGGGCAAGAAT 60.064 52.381 0.00 0.00 0.00 2.40
1798 1815 1.230281 AGGAGGGGCAAGAATCCCA 60.230 57.895 0.00 0.00 45.73 4.37
1943 1963 6.073548 ACGGTAACAGCAGTACTATACGATAC 60.074 42.308 0.00 0.00 0.00 2.24
1999 2043 7.630470 TTACAAATTTTAATCTTGCCGTGTG 57.370 32.000 0.00 0.00 0.00 3.82
2224 2280 1.299976 GGGTTTGAGCGGATGGTCT 59.700 57.895 0.00 0.00 43.09 3.85
2232 2288 1.337071 GAGCGGATGGTCTACGAATCA 59.663 52.381 0.00 0.00 39.53 2.57
2266 2322 1.621814 TCCCCTTCCTTAAGTGTGTCG 59.378 52.381 0.97 0.00 0.00 4.35
2332 2388 1.616159 CGGGACCACCAAAGATTGTT 58.384 50.000 0.00 0.00 40.22 2.83
2334 2390 2.364002 CGGGACCACCAAAGATTGTTTT 59.636 45.455 0.00 0.00 40.22 2.43
2397 2453 2.671619 ACGTGGGCAATCAACCGG 60.672 61.111 0.00 0.00 0.00 5.28
2439 2495 0.321564 CTGACACTTTCCGGCCATCA 60.322 55.000 2.24 0.00 0.00 3.07
2460 2516 1.305930 GGTTCATGCTCAACGGGGAC 61.306 60.000 0.00 0.00 0.00 4.46
2574 2630 0.392998 CGGTGGAGTTTGCCATAGCT 60.393 55.000 0.00 0.00 40.68 3.32
2823 2879 1.469308 AGCTACTACTGTCACGAGTGC 59.531 52.381 0.00 0.00 0.00 4.40
2889 2945 6.658188 ACTACTTATTACTCAGATGCCTCC 57.342 41.667 0.00 0.00 0.00 4.30
2895 2951 2.777832 ACTCAGATGCCTCCTGTTTC 57.222 50.000 0.00 0.00 33.57 2.78
2910 2966 3.580458 CCTGTTTCTCCTCTTTCTCTCCA 59.420 47.826 0.00 0.00 0.00 3.86
2922 2978 1.221840 CTCTCCATCCACCCGGTTG 59.778 63.158 0.00 0.00 0.00 3.77
2930 2986 2.203098 CACCCGGTTGTTGGACGT 60.203 61.111 0.00 0.00 0.00 4.34
2980 3036 0.745845 CGGCCTTCTCAACCATGGAG 60.746 60.000 21.47 10.83 0.00 3.86
3027 3083 5.586243 AGAACATGATCTTTGTAATGGTCCG 59.414 40.000 0.00 0.00 37.44 4.79
3034 3090 6.537301 TGATCTTTGTAATGGTCCGTATGAAC 59.463 38.462 0.00 0.00 0.00 3.18
3035 3091 5.795972 TCTTTGTAATGGTCCGTATGAACA 58.204 37.500 0.00 0.00 46.93 3.18
3040 3096 2.572191 TGGTCCGTATGAACATCGTC 57.428 50.000 0.00 0.00 35.14 4.20
3041 3097 1.819903 TGGTCCGTATGAACATCGTCA 59.180 47.619 0.00 0.00 35.14 4.35
3042 3098 2.231721 TGGTCCGTATGAACATCGTCAA 59.768 45.455 0.00 0.00 35.14 3.18
3043 3099 3.118920 TGGTCCGTATGAACATCGTCAAT 60.119 43.478 0.00 0.00 35.14 2.57
3044 3100 3.245284 GGTCCGTATGAACATCGTCAATG 59.755 47.826 0.00 0.00 41.48 2.82
3045 3101 4.109766 GTCCGTATGAACATCGTCAATGA 58.890 43.478 0.00 0.00 38.83 2.57
3046 3102 4.565166 GTCCGTATGAACATCGTCAATGAA 59.435 41.667 0.00 0.00 38.83 2.57
3047 3103 5.234329 GTCCGTATGAACATCGTCAATGAAT 59.766 40.000 0.00 0.00 38.83 2.57
3048 3104 6.419710 GTCCGTATGAACATCGTCAATGAATA 59.580 38.462 0.00 0.00 38.83 1.75
3049 3105 6.981559 TCCGTATGAACATCGTCAATGAATAA 59.018 34.615 0.00 0.00 38.83 1.40
3050 3106 7.492994 TCCGTATGAACATCGTCAATGAATAAA 59.507 33.333 0.00 0.00 38.83 1.40
3051 3107 7.793888 CCGTATGAACATCGTCAATGAATAAAG 59.206 37.037 0.00 0.00 38.83 1.85
3052 3108 8.328146 CGTATGAACATCGTCAATGAATAAAGT 58.672 33.333 0.00 0.00 38.83 2.66
3053 3109 9.425893 GTATGAACATCGTCAATGAATAAAGTG 57.574 33.333 0.00 0.00 38.83 3.16
3054 3110 6.314018 TGAACATCGTCAATGAATAAAGTGC 58.686 36.000 0.00 0.00 38.83 4.40
3055 3111 5.878332 ACATCGTCAATGAATAAAGTGCA 57.122 34.783 0.00 0.00 38.83 4.57
3056 3112 5.872635 ACATCGTCAATGAATAAAGTGCAG 58.127 37.500 0.00 0.00 38.83 4.41
3057 3113 4.340894 TCGTCAATGAATAAAGTGCAGC 57.659 40.909 0.00 0.00 0.00 5.25
3058 3114 3.093574 CGTCAATGAATAAAGTGCAGCG 58.906 45.455 0.00 0.00 0.00 5.18
3059 3115 3.181521 CGTCAATGAATAAAGTGCAGCGA 60.182 43.478 0.00 0.00 0.00 4.93
3060 3116 4.494690 CGTCAATGAATAAAGTGCAGCGAT 60.495 41.667 0.00 0.00 0.00 4.58
3061 3117 4.731961 GTCAATGAATAAAGTGCAGCGATG 59.268 41.667 0.00 0.00 0.00 3.84
3062 3118 4.395854 TCAATGAATAAAGTGCAGCGATGT 59.604 37.500 1.22 0.00 0.00 3.06
3063 3119 4.970662 ATGAATAAAGTGCAGCGATGTT 57.029 36.364 1.22 0.00 0.00 2.71
3064 3120 4.764679 TGAATAAAGTGCAGCGATGTTT 57.235 36.364 1.22 0.00 0.00 2.83
3065 3121 5.119931 TGAATAAAGTGCAGCGATGTTTT 57.880 34.783 1.22 4.00 0.00 2.43
3066 3122 4.916831 TGAATAAAGTGCAGCGATGTTTTG 59.083 37.500 1.22 0.00 0.00 2.44
3067 3123 1.490621 AAAGTGCAGCGATGTTTTGC 58.509 45.000 1.22 0.00 38.30 3.68
3068 3124 0.670162 AAGTGCAGCGATGTTTTGCT 59.330 45.000 1.22 0.00 43.77 3.91
3069 3125 1.522668 AGTGCAGCGATGTTTTGCTA 58.477 45.000 1.22 0.00 40.84 3.49
3070 3126 1.879380 AGTGCAGCGATGTTTTGCTAA 59.121 42.857 1.22 0.00 40.84 3.09
3071 3127 2.293122 AGTGCAGCGATGTTTTGCTAAA 59.707 40.909 1.22 0.00 40.84 1.85
3072 3128 3.049206 GTGCAGCGATGTTTTGCTAAAA 58.951 40.909 1.22 0.00 40.84 1.52
3073 3129 3.489047 GTGCAGCGATGTTTTGCTAAAAA 59.511 39.130 1.22 0.00 40.84 1.94
3097 3153 8.836268 AAAACTAGTACCAACGATTGTATCAA 57.164 30.769 0.00 0.00 0.00 2.57
3104 3160 3.433957 CCAACGATTGTATCAACGGTCAA 59.566 43.478 0.00 0.00 0.00 3.18
3141 3197 0.251742 TTGGGCCCAAAGTCCAGATG 60.252 55.000 35.47 0.00 32.44 2.90
3149 3205 2.486982 CCAAAGTCCAGATGCTCTTGTG 59.513 50.000 0.00 0.00 0.00 3.33
3164 3220 4.462280 GTGGTACGCGGGAAGGGG 62.462 72.222 12.47 0.00 37.07 4.79
3173 3229 0.540133 GCGGGAAGGGGTTTTGGTTA 60.540 55.000 0.00 0.00 0.00 2.85
3195 3251 0.402121 GAGGGTGGTGCTTCCTTTCT 59.598 55.000 0.00 0.00 37.07 2.52
3201 3257 0.538287 GGTGCTTCCTTTCTGTGCCT 60.538 55.000 0.00 0.00 0.00 4.75
3202 3258 0.595095 GTGCTTCCTTTCTGTGCCTG 59.405 55.000 0.00 0.00 0.00 4.85
3204 3260 1.322442 GCTTCCTTTCTGTGCCTGTT 58.678 50.000 0.00 0.00 0.00 3.16
3293 3349 1.279271 GAAGGAAACCAGAGCTAGGCA 59.721 52.381 4.63 0.00 0.00 4.75
3319 3375 6.149633 GTCCTTTGTAAAGCATTGTACCTTG 58.850 40.000 0.00 0.00 34.69 3.61
3320 3376 5.830991 TCCTTTGTAAAGCATTGTACCTTGT 59.169 36.000 0.00 0.00 34.69 3.16
3394 3450 1.393539 CGTTCGCAGAAACTACATGGG 59.606 52.381 0.00 0.00 45.90 4.00
3455 3511 0.958822 AAAAGGCAGCCTACCAAACG 59.041 50.000 16.56 0.00 31.13 3.60
3469 3525 2.147958 CCAAACGCTAACCTACTGCAA 58.852 47.619 0.00 0.00 0.00 4.08
3470 3526 2.095919 CCAAACGCTAACCTACTGCAAC 60.096 50.000 0.00 0.00 0.00 4.17
3471 3527 2.536761 AACGCTAACCTACTGCAACA 57.463 45.000 0.00 0.00 0.00 3.33
3481 3537 3.133721 ACCTACTGCAACATTTTGGCAAA 59.866 39.130 8.93 8.93 32.81 3.68
3523 3579 0.036294 GTTGCCACCCTACTCTCACC 60.036 60.000 0.00 0.00 0.00 4.02
3529 3585 3.757461 GCCACCCTACTCTCACCCATATA 60.757 52.174 0.00 0.00 0.00 0.86
3540 3596 8.359875 ACTCTCACCCATATACATCATTCTAG 57.640 38.462 0.00 0.00 0.00 2.43
3560 3616 8.664669 TTCTAGCAACATCCCAGATATATACA 57.335 34.615 0.00 0.00 0.00 2.29
3561 3617 8.844865 TCTAGCAACATCCCAGATATATACAT 57.155 34.615 0.00 0.00 0.00 2.29
3581 3637 2.376109 TCATCTTGGACTACGAGGACC 58.624 52.381 0.00 0.00 0.00 4.46
3584 3640 0.450983 CTTGGACTACGAGGACCGAC 59.549 60.000 0.00 0.00 41.76 4.79
3621 3677 5.262009 AGTATCCAAGTTTTAAAGGAGGCC 58.738 41.667 0.00 0.00 32.91 5.19
3622 3678 3.603965 TCCAAGTTTTAAAGGAGGCCA 57.396 42.857 5.01 0.00 0.00 5.36
3639 3695 3.791545 AGGCCATTTCCACTTAGGGATAA 59.208 43.478 5.01 0.00 36.67 1.75
3650 3706 5.163152 CCACTTAGGGATAATGCTTCTTCCT 60.163 44.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 6.694447 ACAATTAGTAAAACTGCCGAGACTA 58.306 36.000 0.00 0.00 0.00 2.59
185 186 3.281727 TGAAATGGACTGGTATGCTCC 57.718 47.619 0.00 0.00 0.00 4.70
367 369 6.033966 CCTAAAAACCGATGCATAAAACCTC 58.966 40.000 0.00 0.00 0.00 3.85
440 442 3.182590 AAGCAAGAGGAGCGCACCA 62.183 57.895 26.04 0.00 37.01 4.17
1061 1066 3.418913 CCACGGACGCGATTGCAA 61.419 61.111 15.93 0.00 42.97 4.08
1065 1070 4.388499 AAGGCCACGGACGCGATT 62.388 61.111 15.93 0.00 0.00 3.34
1074 1079 1.746615 CTGGATGACCAAGGCCACG 60.747 63.158 5.01 0.00 46.32 4.94
1113 1130 2.767496 CCTGGAGCTGGAGGGAGG 60.767 72.222 0.00 0.00 0.00 4.30
1120 1137 4.479993 CTTCGGGCCTGGAGCTGG 62.480 72.222 12.87 0.00 43.05 4.85
1237 1254 3.564218 GATCCGGAGCCAGCCCAT 61.564 66.667 9.02 0.00 0.00 4.00
1251 1268 0.458025 GGGTCGACACCACGAAGATC 60.458 60.000 18.91 0.00 45.94 2.75
1309 1326 1.153349 GGCGGTCCCAGAAGTCATC 60.153 63.158 0.00 0.00 0.00 2.92
1321 1338 4.554036 GATGGAGGCAGGGCGGTC 62.554 72.222 0.00 0.00 0.00 4.79
1472 1489 3.152400 GCTCCCCATACCCGTCGT 61.152 66.667 0.00 0.00 0.00 4.34
1523 1540 3.744719 CCTCGCCGAGGTTCACGA 61.745 66.667 24.93 0.00 44.25 4.35
1540 1557 1.195448 CACGGTGTGCTTGAAGATGAC 59.805 52.381 0.00 0.00 0.00 3.06
1615 1632 1.216064 TCCCTCAACATGGGGATGAG 58.784 55.000 3.49 7.91 41.85 2.90
1674 1691 0.328258 TCCAGCTAAGCCAAGGGAAC 59.672 55.000 0.00 0.00 0.00 3.62
1755 1772 5.077134 TGTGATCGTCAATGATCTTGTCT 57.923 39.130 12.23 0.00 44.12 3.41
1773 1790 0.547471 TCTTGCCCCTCCTCATGTGA 60.547 55.000 0.00 0.00 0.00 3.58
1943 1963 1.785041 CTTGGGGCAAGTGTGTGTCG 61.785 60.000 0.00 0.00 36.79 4.35
2224 2280 3.118629 AGCTTGGCAAGATCTGATTCGTA 60.119 43.478 30.45 0.00 0.00 3.43
2232 2288 0.918310 AGGGGAGCTTGGCAAGATCT 60.918 55.000 35.68 22.66 43.26 2.75
2266 2322 0.173708 ATCCGAAGCGTCTCCTTGAC 59.826 55.000 0.00 0.00 42.06 3.18
2332 2388 2.614481 GCACCGAGTATCCACCAAGAAA 60.614 50.000 0.00 0.00 0.00 2.52
2334 2390 0.535335 GCACCGAGTATCCACCAAGA 59.465 55.000 0.00 0.00 0.00 3.02
2397 2453 1.450312 CTTCCATGCCTCACCGTCC 60.450 63.158 0.00 0.00 0.00 4.79
2403 2459 1.229951 AGGGTCCTTCCATGCCTCA 60.230 57.895 0.00 0.00 38.11 3.86
2439 2495 0.609131 CCCCGTTGAGCATGAACCTT 60.609 55.000 0.00 0.00 0.00 3.50
2574 2630 2.089887 TAAACCCGTGCACGAGCTGA 62.090 55.000 39.10 18.69 43.02 4.26
2735 2791 0.780002 GTTTTGCTTCATGCGCACAG 59.220 50.000 14.90 10.79 46.63 3.66
2794 2850 5.966503 CGTGACAGTAGTAGCTTTCAGATAC 59.033 44.000 0.00 0.00 37.36 2.24
2823 2879 0.905357 AGAAGGAAGGTCATGTCCCG 59.095 55.000 5.28 0.00 34.13 5.14
2862 2918 7.721402 AGGCATCTGAGTAATAAGTAGTTGAG 58.279 38.462 0.00 0.00 0.00 3.02
2889 2945 4.881019 TGGAGAGAAAGAGGAGAAACAG 57.119 45.455 0.00 0.00 0.00 3.16
2895 2951 2.433970 GGTGGATGGAGAGAAAGAGGAG 59.566 54.545 0.00 0.00 0.00 3.69
2910 2966 1.074248 GTCCAACAACCGGGTGGAT 59.926 57.895 26.30 9.68 39.21 3.41
2922 2978 0.883370 GAGACCCCACAACGTCCAAC 60.883 60.000 0.00 0.00 0.00 3.77
2971 3027 4.096003 CCGCCGTCCTCCATGGTT 62.096 66.667 12.58 0.00 37.07 3.67
2980 3036 1.808390 GTACACATCACCGCCGTCC 60.808 63.158 0.00 0.00 0.00 4.79
3027 3083 9.425893 CACTTTATTCATTGACGATGTTCATAC 57.574 33.333 2.54 0.00 37.06 2.39
3034 3090 4.731961 GCTGCACTTTATTCATTGACGATG 59.268 41.667 0.00 0.00 37.08 3.84
3035 3091 4.494690 CGCTGCACTTTATTCATTGACGAT 60.495 41.667 0.00 0.00 0.00 3.73
3036 3092 3.181521 CGCTGCACTTTATTCATTGACGA 60.182 43.478 0.00 0.00 0.00 4.20
3037 3093 3.093574 CGCTGCACTTTATTCATTGACG 58.906 45.455 0.00 0.00 0.00 4.35
3038 3094 4.340894 TCGCTGCACTTTATTCATTGAC 57.659 40.909 0.00 0.00 0.00 3.18
3039 3095 4.395854 ACATCGCTGCACTTTATTCATTGA 59.604 37.500 0.00 0.00 0.00 2.57
3040 3096 4.665212 ACATCGCTGCACTTTATTCATTG 58.335 39.130 0.00 0.00 0.00 2.82
3041 3097 4.970662 ACATCGCTGCACTTTATTCATT 57.029 36.364 0.00 0.00 0.00 2.57
3042 3098 4.970662 AACATCGCTGCACTTTATTCAT 57.029 36.364 0.00 0.00 0.00 2.57
3043 3099 4.764679 AAACATCGCTGCACTTTATTCA 57.235 36.364 0.00 0.00 0.00 2.57
3044 3100 4.201523 GCAAAACATCGCTGCACTTTATTC 60.202 41.667 0.00 0.00 36.09 1.75
3045 3101 3.674753 GCAAAACATCGCTGCACTTTATT 59.325 39.130 0.00 0.00 36.09 1.40
3046 3102 3.057315 AGCAAAACATCGCTGCACTTTAT 60.057 39.130 0.00 0.00 38.58 1.40
3047 3103 2.293122 AGCAAAACATCGCTGCACTTTA 59.707 40.909 0.00 0.00 38.58 1.85
3048 3104 1.067516 AGCAAAACATCGCTGCACTTT 59.932 42.857 0.00 0.00 38.58 2.66
3049 3105 0.670162 AGCAAAACATCGCTGCACTT 59.330 45.000 0.00 0.00 38.58 3.16
3050 3106 1.522668 TAGCAAAACATCGCTGCACT 58.477 45.000 0.00 0.00 39.30 4.40
3051 3107 2.330231 TTAGCAAAACATCGCTGCAC 57.670 45.000 0.00 0.00 39.30 4.57
3052 3108 3.361794 TTTTAGCAAAACATCGCTGCA 57.638 38.095 0.00 0.00 39.30 4.41
3071 3127 8.836268 TGATACAATCGTTGGTACTAGTTTTT 57.164 30.769 0.00 0.00 34.12 1.94
3072 3128 8.715088 GTTGATACAATCGTTGGTACTAGTTTT 58.285 33.333 0.00 0.00 34.12 2.43
3073 3129 7.062605 CGTTGATACAATCGTTGGTACTAGTTT 59.937 37.037 0.00 0.00 34.12 2.66
3097 3153 3.425713 CGCATGCTGCTTGACCGT 61.426 61.111 17.13 0.00 42.25 4.83
3120 3176 0.469144 TCTGGACTTTGGGCCCAAAC 60.469 55.000 40.46 31.43 40.51 2.93
3141 3197 2.775032 TTCCCGCGTACCACAAGAGC 62.775 60.000 4.92 0.00 0.00 4.09
3149 3205 2.753009 AAAACCCCTTCCCGCGTACC 62.753 60.000 4.92 0.00 0.00 3.34
3164 3220 2.621526 CACCACCCTCACTAACCAAAAC 59.378 50.000 0.00 0.00 0.00 2.43
3173 3229 1.062488 AAGGAAGCACCACCCTCACT 61.062 55.000 2.96 0.00 42.04 3.41
3195 3251 2.371841 AGAAGGTGTATGAACAGGCACA 59.628 45.455 11.34 0.00 35.91 4.57
3280 3336 2.352032 GGACGTGCCTAGCTCTGGT 61.352 63.158 0.00 0.00 0.00 4.00
3293 3349 4.214758 GGTACAATGCTTTACAAAGGACGT 59.785 41.667 4.01 0.00 39.20 4.34
3319 3375 3.424433 CGAAACCAAAGCGACATCCTTAC 60.424 47.826 0.00 0.00 0.00 2.34
3320 3376 2.739913 CGAAACCAAAGCGACATCCTTA 59.260 45.455 0.00 0.00 0.00 2.69
3378 3434 2.095768 CACAACCCATGTAGTTTCTGCG 60.096 50.000 0.00 0.00 41.46 5.18
3394 3450 8.293867 TGTAAAAATACATGCTACCTTCACAAC 58.706 33.333 0.00 0.00 0.00 3.32
3436 3492 0.958822 CGTTTGGTAGGCTGCCTTTT 59.041 50.000 28.55 5.15 34.61 2.27
3455 3511 4.485163 CCAAAATGTTGCAGTAGGTTAGC 58.515 43.478 0.00 0.00 33.01 3.09
3523 3579 7.281774 GGGATGTTGCTAGAATGATGTATATGG 59.718 40.741 0.00 0.00 0.00 2.74
3529 3585 4.164796 TCTGGGATGTTGCTAGAATGATGT 59.835 41.667 0.00 0.00 0.00 3.06
3540 3596 8.209584 AGATGATGTATATATCTGGGATGTTGC 58.790 37.037 10.42 0.00 30.41 4.17
3560 3616 2.959707 GGTCCTCGTAGTCCAAGATGAT 59.040 50.000 0.00 0.00 0.00 2.45
3561 3617 2.376109 GGTCCTCGTAGTCCAAGATGA 58.624 52.381 0.00 0.00 0.00 2.92
3581 3637 7.137490 TGGATACTTACGTAATATGGAGTCG 57.863 40.000 8.76 0.00 37.61 4.18
3584 3640 9.760077 AAACTTGGATACTTACGTAATATGGAG 57.240 33.333 8.76 0.00 37.61 3.86
3621 3677 6.774656 AGAAGCATTATCCCTAAGTGGAAATG 59.225 38.462 0.00 0.00 38.10 2.32
3622 3678 6.915786 AGAAGCATTATCCCTAAGTGGAAAT 58.084 36.000 0.00 0.00 38.10 2.17
3639 3695 4.922206 TGTTGGTATCAAGGAAGAAGCAT 58.078 39.130 0.00 0.00 32.92 3.79
3650 3706 9.699410 AGGATTCAAAGATAATGTTGGTATCAA 57.301 29.630 0.00 0.00 31.49 2.57


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

AutoCloner maintained by Alex Coulton.