Multiple sequence alignment - TraesCS3A01G113800

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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 TraesCS3A01G113800 chr3A 100.000 3337 0 0 1 3337 81094261 81097597 0.000000e+00 6163
1 TraesCS3A01G113800 chr3D 92.417 2321 131 28 1037 3337 69794470 69796765 0.000000e+00 3269
2 TraesCS3A01G113800 chr3D 85.928 1137 81 43 1 1092 69793366 69794468 0.000000e+00 1140
3 TraesCS3A01G113800 chr3B 94.036 2096 101 15 1251 3335 115553839 115555921 0.000000e+00 3157
4 TraesCS3A01G113800 chr3B 92.216 334 24 1 761 1092 115553124 115553457 3.900000e-129 472
5 TraesCS3A01G113800 chr3B 78.788 231 25 9 1037 1259 115553459 115553673 2.090000e-27 134
6 TraesCS3A01G113800 chr3B 84.211 133 10 7 3 128 115552312 115552440 5.850000e-23 119
7 TraesCS3A01G113800 chr7B 87.031 640 62 13 1090 1725 709579860 709579238 0.000000e+00 702


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 TraesCS3A01G113800 chr3A 81094261 81097597 3336 False 6163.0 6163 100.00000 1 3337 1 chr3A.!!$F1 3336
1 TraesCS3A01G113800 chr3D 69793366 69796765 3399 False 2204.5 3269 89.17250 1 3337 2 chr3D.!!$F1 3336
2 TraesCS3A01G113800 chr3B 115552312 115555921 3609 False 970.5 3157 87.31275 3 3335 4 chr3B.!!$F1 3332
3 TraesCS3A01G113800 chr7B 709579238 709579860 622 True 702.0 702 87.03100 1090 1725 1 chr7B.!!$R1 635

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
434 526 0.175073 AGGTAGTTGCGGATTCGTCC 59.825 55.0 0.0 0.0 38.89 4.79 F
1179 1367 0.110295 TGTTGGCATGTGTGGTAGCT 59.890 50.0 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1809 0.321996 AGGAAGCCGTCTCTCAAACC 59.678 55.000 0.00 0.0 0.00 3.27 R
2533 2941 1.133792 CAGTCAACTGTTCCCACCCTT 60.134 52.381 1.88 0.0 39.09 3.95 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
78 79 0.741326 CGTGTCTCCATCCATCGTCT 59.259 55.000 0.00 0.00 0.00 4.18
86 87 0.176449 CATCCATCGTCTGGCTCACA 59.824 55.000 2.40 0.00 45.52 3.58
87 88 0.904649 ATCCATCGTCTGGCTCACAA 59.095 50.000 2.40 0.00 45.52 3.33
88 89 0.904649 TCCATCGTCTGGCTCACAAT 59.095 50.000 2.40 0.00 45.52 2.71
331 423 7.147585 CCTCTCCCGATTGGATTATCTTGATAT 60.148 40.741 0.00 0.00 44.07 1.63
343 435 8.517878 GGATTATCTTGATATGGATTTGTGTGG 58.482 37.037 0.00 0.00 0.00 4.17
354 446 2.234300 TTTGTGTGGGAGTTCGTCTC 57.766 50.000 2.71 2.71 42.07 3.36
359 451 4.493747 GGGAGTTCGTCTCGCGGG 62.494 72.222 6.13 1.01 44.04 6.13
362 454 3.996744 GAGTTCGTCTCGCGGGTCG 62.997 68.421 19.53 19.53 41.72 4.79
425 517 2.202570 CCCGTCGAGGTAGTTGCG 60.203 66.667 4.18 0.00 38.74 4.85
434 526 0.175073 AGGTAGTTGCGGATTCGTCC 59.825 55.000 0.00 0.00 38.89 4.79
575 699 9.478019 GTATGAATTCGTCTAGATTTGTTTGTG 57.522 33.333 2.72 0.00 0.00 3.33
576 700 7.490962 TGAATTCGTCTAGATTTGTTTGTGT 57.509 32.000 0.00 0.00 0.00 3.72
589 713 6.592798 TTTGTTTGTGTTCTACTAACGAGG 57.407 37.500 0.00 0.00 44.52 4.63
597 721 2.097825 TCTACTAACGAGGGTTGGAGC 58.902 52.381 0.00 0.00 37.97 4.70
617 742 6.112058 GGAGCATTAGAGTTCAGAGAACAAT 58.888 40.000 11.92 3.10 0.00 2.71
627 752 6.276847 AGTTCAGAGAACAATAATAGCTCGG 58.723 40.000 11.92 0.00 0.00 4.63
633 758 8.704234 CAGAGAACAATAATAGCTCGGAATTAC 58.296 37.037 0.00 0.00 0.00 1.89
636 761 8.993121 AGAACAATAATAGCTCGGAATTACATG 58.007 33.333 0.00 0.00 0.00 3.21
657 782 3.006967 TGCTCTCCTGAGTAAAGAACCAC 59.993 47.826 0.00 0.00 42.13 4.16
663 788 4.282703 TCCTGAGTAAAGAACCACTGTACC 59.717 45.833 0.00 0.00 39.47 3.34
681 806 0.460284 CCGCCGACTTCTGTATGCTT 60.460 55.000 0.00 0.00 0.00 3.91
782 907 2.445525 ACATTTGTCCCCACCAACTAGT 59.554 45.455 0.00 0.00 0.00 2.57
791 916 3.071602 CCCCACCAACTAGTCTGATATGG 59.928 52.174 7.36 7.36 0.00 2.74
797 922 4.442706 CAACTAGTCTGATATGGGCGTTT 58.557 43.478 0.00 0.00 0.00 3.60
803 928 6.360370 AGTCTGATATGGGCGTTTATACAT 57.640 37.500 0.00 0.00 0.00 2.29
888 1014 1.477700 GGATTTATGTGCCAAGCTGCA 59.522 47.619 1.02 0.00 39.37 4.41
891 1017 4.021719 GGATTTATGTGCCAAGCTGCATAT 60.022 41.667 11.98 11.98 44.30 1.78
909 1035 7.761249 GCTGCATATTGTTCTGTTTTATTCCTT 59.239 33.333 0.00 0.00 0.00 3.36
916 1042 7.452880 TGTTCTGTTTTATTCCTTGGATCAG 57.547 36.000 0.00 0.00 0.00 2.90
985 1113 4.943705 TGTTAAGCTTGCATCTTCCCTAAG 59.056 41.667 9.86 0.00 0.00 2.18
1036 1164 5.876357 ACTGCTTTTCCAACCTTGTATCTA 58.124 37.500 0.00 0.00 0.00 1.98
1045 1173 9.581289 TTTCCAACCTTGTATCTATCTTTTGAA 57.419 29.630 0.00 0.00 0.00 2.69
1092 1277 3.113260 AGATCCCTTACGTTATGCAGC 57.887 47.619 0.00 0.00 0.00 5.25
1099 1284 3.623060 CCTTACGTTATGCAGCAGAACAT 59.377 43.478 27.86 18.59 35.61 2.71
1106 1291 2.113860 TGCAGCAGAACATAACCCTC 57.886 50.000 0.00 0.00 0.00 4.30
1109 1294 2.012673 CAGCAGAACATAACCCTCAGC 58.987 52.381 0.00 0.00 0.00 4.26
1125 1310 4.463891 CCCTCAGCCTGTCATTGTAAAAAT 59.536 41.667 0.00 0.00 0.00 1.82
1127 1312 6.152661 CCCTCAGCCTGTCATTGTAAAAATAA 59.847 38.462 0.00 0.00 0.00 1.40
1128 1313 7.309744 CCCTCAGCCTGTCATTGTAAAAATAAA 60.310 37.037 0.00 0.00 0.00 1.40
1129 1314 7.542130 CCTCAGCCTGTCATTGTAAAAATAAAC 59.458 37.037 0.00 0.00 0.00 2.01
1131 1316 8.081633 TCAGCCTGTCATTGTAAAAATAAACTG 58.918 33.333 0.00 0.00 0.00 3.16
1132 1317 7.867403 CAGCCTGTCATTGTAAAAATAAACTGT 59.133 33.333 0.00 0.00 0.00 3.55
1133 1318 8.421002 AGCCTGTCATTGTAAAAATAAACTGTT 58.579 29.630 0.00 0.00 0.00 3.16
1134 1319 9.040939 GCCTGTCATTGTAAAAATAAACTGTTT 57.959 29.630 10.98 10.98 0.00 2.83
1179 1367 0.110295 TGTTGGCATGTGTGGTAGCT 59.890 50.000 0.00 0.00 0.00 3.32
1185 1373 4.450976 TGGCATGTGTGGTAGCTTTATAG 58.549 43.478 0.00 0.00 0.00 1.31
1187 1375 4.881850 GGCATGTGTGGTAGCTTTATAGTT 59.118 41.667 0.00 0.00 0.00 2.24
1188 1376 5.220854 GGCATGTGTGGTAGCTTTATAGTTG 60.221 44.000 0.00 0.00 0.00 3.16
1411 1798 2.757868 ACTCAGAGATGAAGAGAACCCG 59.242 50.000 3.79 0.00 33.69 5.28
1422 1809 3.741476 GAACCCGCAGCTGGCAAG 61.741 66.667 17.12 4.57 45.17 4.01
1603 1991 2.095372 GCTTTGGTACTATGCAACGACC 59.905 50.000 0.00 0.00 0.00 4.79
1680 2068 2.364324 CCTCTGCTATTGCGGTAGGTTA 59.636 50.000 7.85 0.00 45.38 2.85
1810 2198 6.914757 CAGAAAGCAAAAGAGTTTTCCTGTAG 59.085 38.462 0.00 0.00 38.86 2.74
1854 2242 4.895668 AAACCATCATGCAACCTGATTT 57.104 36.364 0.00 0.00 31.00 2.17
1891 2279 5.814481 TGGTTCTGTCACCATATTGATTCA 58.186 37.500 0.00 0.00 42.27 2.57
1892 2280 5.647658 TGGTTCTGTCACCATATTGATTCAC 59.352 40.000 0.00 0.00 42.27 3.18
1893 2281 5.647658 GGTTCTGTCACCATATTGATTCACA 59.352 40.000 0.00 0.00 36.73 3.58
1894 2282 6.183360 GGTTCTGTCACCATATTGATTCACAG 60.183 42.308 0.00 0.00 36.73 3.66
1895 2283 6.298441 TCTGTCACCATATTGATTCACAGA 57.702 37.500 0.00 0.00 0.00 3.41
1896 2284 6.892485 TCTGTCACCATATTGATTCACAGAT 58.108 36.000 0.00 0.00 0.00 2.90
1897 2285 7.341030 TCTGTCACCATATTGATTCACAGATT 58.659 34.615 0.00 0.00 0.00 2.40
1898 2286 7.281549 TCTGTCACCATATTGATTCACAGATTG 59.718 37.037 0.00 0.00 0.00 2.67
1899 2287 7.111466 TGTCACCATATTGATTCACAGATTGA 58.889 34.615 0.00 0.00 0.00 2.57
2065 2466 1.559831 GTTTCAAACCAGTGTGCAGC 58.440 50.000 0.00 0.00 0.00 5.25
2074 2475 1.686052 CCAGTGTGCAGCCCTTTTAAA 59.314 47.619 0.00 0.00 0.00 1.52
2107 2508 6.935167 ACCTTGAAAAACTTGTTCTTCACAT 58.065 32.000 2.19 0.00 34.43 3.21
2234 2636 5.248870 AGTTCTGGTTACAGCAAGTTTTG 57.751 39.130 0.00 0.00 44.54 2.44
2236 2638 4.630894 TCTGGTTACAGCAAGTTTTGTG 57.369 40.909 1.01 0.00 44.54 3.33
2246 2648 4.186241 GCAAGTTTTGTGCTGAATGTTG 57.814 40.909 0.00 0.00 39.00 3.33
2285 2687 0.978146 AGGCGGCCATCTTCACTACT 60.978 55.000 23.09 0.00 0.00 2.57
2352 2754 2.203584 AGTGATTTCTGAGGCAGGGAT 58.796 47.619 0.00 0.00 31.51 3.85
2357 2759 4.166725 TGATTTCTGAGGCAGGGATAACAT 59.833 41.667 0.00 0.00 31.51 2.71
2428 2830 6.932356 ACTTGTAATGTTGATGATAGCAGG 57.068 37.500 0.00 0.00 0.00 4.85
2492 2900 5.991606 TGTTTATCGAAGGGCTTCATCTATG 59.008 40.000 0.00 0.00 39.46 2.23
2533 2941 9.151471 CCGAGTCAGTTATTCAATCTTTCTAAA 57.849 33.333 0.00 0.00 0.00 1.85
2579 2987 4.520492 TCTTCTGAAAAGCTTCCAATCCAC 59.480 41.667 0.00 0.00 0.00 4.02
2684 3092 6.014584 ACTGTAGTCATTATCACCAACTCACA 60.015 38.462 0.00 0.00 0.00 3.58
2688 3096 6.475504 AGTCATTATCACCAACTCACAATGA 58.524 36.000 0.00 0.00 0.00 2.57
2873 3288 3.051392 TTCATCTCGAGAGCGCGCA 62.051 57.895 35.10 11.28 37.46 6.09
2874 3289 3.318555 CATCTCGAGAGCGCGCAC 61.319 66.667 35.10 28.25 37.46 5.34
2875 3290 3.513438 ATCTCGAGAGCGCGCACT 61.513 61.111 35.10 32.94 37.46 4.40
2876 3291 3.057547 ATCTCGAGAGCGCGCACTT 62.058 57.895 35.10 18.19 37.46 3.16
2877 3292 2.928313 ATCTCGAGAGCGCGCACTTC 62.928 60.000 35.10 24.26 37.46 3.01
2878 3293 3.953444 CTCGAGAGCGCGCACTTCA 62.953 63.158 35.10 20.34 37.46 3.02
2880 3295 3.847709 GAGAGCGCGCACTTCAGC 61.848 66.667 35.10 16.38 0.00 4.26
2881 3296 4.669842 AGAGCGCGCACTTCAGCA 62.670 61.111 35.10 0.00 0.00 4.41
2882 3297 3.716006 GAGCGCGCACTTCAGCAA 61.716 61.111 35.10 0.00 0.00 3.91
2883 3298 3.031964 GAGCGCGCACTTCAGCAAT 62.032 57.895 35.10 8.08 0.00 3.56
2884 3299 2.872925 GCGCGCACTTCAGCAATG 60.873 61.111 29.10 0.00 0.00 2.82
2885 3300 2.862436 CGCGCACTTCAGCAATGA 59.138 55.556 8.75 0.00 0.00 2.57
2886 3301 1.207339 CGCGCACTTCAGCAATGAA 59.793 52.632 8.75 0.00 0.00 2.57
2913 3328 2.417924 CCGTCTCTCCAGTTGATTCCAG 60.418 54.545 0.00 0.00 0.00 3.86
2984 3399 9.179909 TGAATTTTCTGGTTACAGTTTGAAGTA 57.820 29.630 0.00 0.00 45.14 2.24
3021 3436 5.860941 TTTTCCAAAACATCTGGCACTTA 57.139 34.783 0.00 0.00 33.63 2.24
3129 3545 1.209504 TCCCTAGCTAAAACATGCGCT 59.790 47.619 9.73 0.00 36.56 5.92
3145 3561 1.864711 GCGCTGCCTTATTCGTATCAA 59.135 47.619 0.00 0.00 0.00 2.57
3183 3599 5.970317 ACATGCAGACAAGAATGAATTCA 57.030 34.783 11.26 11.26 39.23 2.57
3217 3633 7.870826 TCAATGTCGAACAAGATACAACATTT 58.129 30.769 0.00 0.00 34.58 2.32
3236 3652 8.377681 CAACATTTGCATTTGAACATATCTGAC 58.622 33.333 3.62 0.00 0.00 3.51
3249 3665 9.944663 TGAACATATCTGACAAAGTGTTTAAAC 57.055 29.630 11.54 11.54 30.70 2.01
3311 3728 3.136808 GCTTATTTGAAAGCCACGGAG 57.863 47.619 0.00 0.00 44.98 4.63
3318 3735 2.288666 TGAAAGCCACGGAGCATATTC 58.711 47.619 1.62 4.10 34.23 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.484356 CGGATAATGACCCGTTCGTC 58.516 55.000 0.00 0.00 40.78 4.20
78 79 2.739609 CGCTATGTGAGATTGTGAGCCA 60.740 50.000 0.00 0.00 0.00 4.75
128 132 4.397832 TGGAAACCGGTAGGGCGC 62.398 66.667 8.00 0.00 43.47 6.53
131 135 0.108963 TTGTGTGGAAACCGGTAGGG 59.891 55.000 8.00 0.00 43.47 3.53
132 136 1.970092 TTTGTGTGGAAACCGGTAGG 58.030 50.000 8.00 0.00 45.13 3.18
133 137 4.320870 AGTATTTGTGTGGAAACCGGTAG 58.679 43.478 8.00 0.00 0.00 3.18
261 343 3.929948 GAAGCCGATTCGCGCCAG 61.930 66.667 0.00 0.00 39.11 4.85
262 344 3.950794 AAGAAGCCGATTCGCGCCA 62.951 57.895 0.00 0.00 43.16 5.69
263 345 3.156740 GAAGAAGCCGATTCGCGCC 62.157 63.158 0.00 0.00 43.16 6.53
264 346 2.083599 GAGAAGAAGCCGATTCGCGC 62.084 60.000 0.00 0.00 43.16 6.86
265 347 0.526524 AGAGAAGAAGCCGATTCGCG 60.527 55.000 0.00 0.00 43.16 5.87
267 349 2.222908 GCAAAGAGAAGAAGCCGATTCG 60.223 50.000 0.00 0.00 43.16 3.34
268 350 2.222908 CGCAAAGAGAAGAAGCCGATTC 60.223 50.000 0.00 0.00 38.28 2.52
269 351 1.734465 CGCAAAGAGAAGAAGCCGATT 59.266 47.619 0.00 0.00 0.00 3.34
331 423 1.142060 ACGAACTCCCACACAAATCCA 59.858 47.619 0.00 0.00 0.00 3.41
359 451 0.519077 CAGCAAAAGGAAGAGGCGAC 59.481 55.000 0.00 0.00 0.00 5.19
362 454 1.211190 CGCAGCAAAAGGAAGAGGC 59.789 57.895 0.00 0.00 0.00 4.70
364 456 0.239347 CCACGCAGCAAAAGGAAGAG 59.761 55.000 0.00 0.00 0.00 2.85
399 491 3.145551 CTCGACGGGGATTCGGGT 61.146 66.667 0.00 0.00 37.09 5.28
402 494 1.099879 ACTACCTCGACGGGGATTCG 61.100 60.000 23.53 7.75 36.97 3.34
425 517 2.167861 GCAGCAGACGGACGAATCC 61.168 63.158 0.00 0.00 42.28 3.01
434 526 1.801913 GTCTACCACGCAGCAGACG 60.802 63.158 0.00 0.00 0.00 4.18
575 699 3.675502 GCTCCAACCCTCGTTAGTAGAAC 60.676 52.174 0.00 0.00 0.00 3.01
576 700 2.494870 GCTCCAACCCTCGTTAGTAGAA 59.505 50.000 0.00 0.00 0.00 2.10
589 713 4.081420 TCTCTGAACTCTAATGCTCCAACC 60.081 45.833 0.00 0.00 0.00 3.77
617 742 6.346477 AGAGCATGTAATTCCGAGCTATTA 57.654 37.500 0.00 0.00 31.61 0.98
627 752 7.268586 TCTTTACTCAGGAGAGCATGTAATTC 58.731 38.462 2.79 0.00 46.09 2.17
633 758 4.187694 GGTTCTTTACTCAGGAGAGCATG 58.812 47.826 2.79 0.00 46.09 4.06
636 761 3.259625 AGTGGTTCTTTACTCAGGAGAGC 59.740 47.826 2.79 0.00 46.09 4.09
657 782 0.806868 TACAGAAGTCGGCGGTACAG 59.193 55.000 7.21 0.00 0.00 2.74
663 788 2.203800 TAAGCATACAGAAGTCGGCG 57.796 50.000 0.00 0.00 33.59 6.46
681 806 5.012458 TGCCATGTCCAAAATTCCAAACATA 59.988 36.000 0.00 0.00 0.00 2.29
782 907 7.712204 TCTATGTATAAACGCCCATATCAGA 57.288 36.000 0.00 0.00 0.00 3.27
852 977 0.251354 ATCCTGCAAGTGCGTCAGAT 59.749 50.000 0.00 0.00 45.83 2.90
891 1017 7.723616 TCTGATCCAAGGAATAAAACAGAACAA 59.276 33.333 0.00 0.00 0.00 2.83
909 1035 2.634453 TCAGCTCAACAAGTCTGATCCA 59.366 45.455 0.00 0.00 34.97 3.41
944 1070 3.441496 ACACCAAGTTGTTGCAGATTG 57.559 42.857 0.00 0.00 31.64 2.67
954 1080 3.435105 TGCAAGCTTAACACCAAGTTG 57.565 42.857 0.00 0.00 41.50 3.16
955 1081 3.891366 AGATGCAAGCTTAACACCAAGTT 59.109 39.130 0.00 0.00 44.27 2.66
956 1082 3.490348 AGATGCAAGCTTAACACCAAGT 58.510 40.909 0.00 0.00 0.00 3.16
985 1113 5.220710 TCTCCCATTTAATCTAGAGCTGC 57.779 43.478 0.00 0.00 0.00 5.25
1045 1173 6.422701 GCGGCAAAGGAAAACTTAAGTTTAAT 59.577 34.615 28.97 17.45 46.47 1.40
1092 1277 2.026822 ACAGGCTGAGGGTTATGTTCTG 60.027 50.000 23.66 0.00 0.00 3.02
1099 1284 1.985159 ACAATGACAGGCTGAGGGTTA 59.015 47.619 23.66 0.00 0.00 2.85
1106 1291 7.867403 ACAGTTTATTTTTACAATGACAGGCTG 59.133 33.333 14.16 14.16 0.00 4.85
1135 1320 9.613428 CATGATGTAATAGGAGTTACTGGAAAA 57.387 33.333 0.00 0.00 35.94 2.29
1136 1321 8.768397 ACATGATGTAATAGGAGTTACTGGAAA 58.232 33.333 0.00 0.00 35.94 3.13
1137 1322 8.319057 ACATGATGTAATAGGAGTTACTGGAA 57.681 34.615 0.00 0.00 35.94 3.53
1169 1357 8.314143 TGTTTACAACTATAAAGCTACCACAC 57.686 34.615 0.00 0.00 0.00 3.82
1185 1373 7.920682 AGGTTGAAACTTGATGATGTTTACAAC 59.079 33.333 18.48 18.48 39.64 3.32
1187 1375 7.581213 AGGTTGAAACTTGATGATGTTTACA 57.419 32.000 0.00 0.00 36.64 2.41
1242 1455 7.283127 TGATCAAGCTAAAGCCCTAATAAACAG 59.717 37.037 0.00 0.00 43.38 3.16
1411 1798 1.174712 TCTCAAACCTTGCCAGCTGC 61.175 55.000 8.66 4.57 41.77 5.25
1422 1809 0.321996 AGGAAGCCGTCTCTCAAACC 59.678 55.000 0.00 0.00 0.00 3.27
1603 1991 4.566004 TGTAGTACTTGCAGCAGTAAAGG 58.434 43.478 0.00 0.00 30.86 3.11
1680 2068 4.384647 GCTCAGGATTTACTGTGGAAGGAT 60.385 45.833 0.00 0.00 39.48 3.24
1810 2198 8.642020 GTTTACATGCATGAAGAAATGACTTTC 58.358 33.333 32.75 11.35 40.95 2.62
1854 2242 2.815503 CAGAACCATCAACACATCTGCA 59.184 45.455 0.00 0.00 0.00 4.41
1895 2283 9.912634 CACACCTTGACTACAAAAATAATCAAT 57.087 29.630 0.00 0.00 35.49 2.57
1896 2284 8.908903 ACACACCTTGACTACAAAAATAATCAA 58.091 29.630 0.00 0.00 35.49 2.57
1897 2285 8.458573 ACACACCTTGACTACAAAAATAATCA 57.541 30.769 0.00 0.00 35.49 2.57
1898 2286 9.744468 AAACACACCTTGACTACAAAAATAATC 57.256 29.630 0.00 0.00 35.49 1.75
2107 2508 3.928727 AACATTAGGAACGACACTCGA 57.071 42.857 0.00 0.00 43.74 4.04
2258 2660 1.823470 GATGGCCGCCTGCACATAA 60.823 57.895 11.61 0.00 43.89 1.90
2285 2687 1.138266 GAGAGGGTAATAGTTGCCGCA 59.862 52.381 0.00 0.00 36.12 5.69
2352 2754 3.668141 ACCAATCATCCAGCCATGTTA 57.332 42.857 0.00 0.00 0.00 2.41
2357 2759 2.307496 AACAACCAATCATCCAGCCA 57.693 45.000 0.00 0.00 0.00 4.75
2492 2900 2.490165 TCGGGAGAGACGACAATCC 58.510 57.895 0.00 0.00 35.12 3.01
2533 2941 1.133792 CAGTCAACTGTTCCCACCCTT 60.134 52.381 1.88 0.00 39.09 3.95
2579 2987 7.946655 TTTATGTAATTCGATCTGTAGCCTG 57.053 36.000 0.00 0.00 0.00 4.85
2684 3092 4.408270 AGGTGTATCAGTGCATCTCTCATT 59.592 41.667 0.00 0.00 22.60 2.57
2688 3096 2.433604 CCAGGTGTATCAGTGCATCTCT 59.566 50.000 0.00 0.00 27.97 3.10
2873 3288 2.489329 CGGAATGGTTCATTGCTGAAGT 59.511 45.455 9.70 0.00 41.96 3.01
2874 3289 2.489329 ACGGAATGGTTCATTGCTGAAG 59.511 45.455 9.70 0.00 41.96 3.02
2875 3290 2.487762 GACGGAATGGTTCATTGCTGAA 59.512 45.455 9.70 0.00 39.46 3.02
2876 3291 2.083774 GACGGAATGGTTCATTGCTGA 58.916 47.619 9.70 0.00 39.46 4.26
2877 3292 2.086869 AGACGGAATGGTTCATTGCTG 58.913 47.619 9.70 6.54 39.46 4.41
2878 3293 2.026822 AGAGACGGAATGGTTCATTGCT 60.027 45.455 9.70 0.00 39.46 3.91
2880 3295 2.939103 GGAGAGACGGAATGGTTCATTG 59.061 50.000 0.00 0.00 33.90 2.82
2881 3296 2.571653 TGGAGAGACGGAATGGTTCATT 59.428 45.455 0.00 0.00 36.72 2.57
2882 3297 2.169352 CTGGAGAGACGGAATGGTTCAT 59.831 50.000 0.00 0.00 0.00 2.57
2883 3298 1.550524 CTGGAGAGACGGAATGGTTCA 59.449 52.381 0.00 0.00 0.00 3.18
2884 3299 1.550976 ACTGGAGAGACGGAATGGTTC 59.449 52.381 0.00 0.00 0.00 3.62
2885 3300 1.645710 ACTGGAGAGACGGAATGGTT 58.354 50.000 0.00 0.00 0.00 3.67
2886 3301 1.276421 CAACTGGAGAGACGGAATGGT 59.724 52.381 0.00 0.00 0.00 3.55
2984 3399 2.156917 GGAAAAAGAAATCCCGGTCGT 58.843 47.619 0.00 0.00 0.00 4.34
3044 3459 4.077822 CTGAGCTCATCCCTCAAACTTTT 58.922 43.478 18.63 0.00 38.73 2.27
3129 3545 2.101750 TCCGCTTGATACGAATAAGGCA 59.898 45.455 0.00 0.00 0.00 4.75
3145 3561 1.541147 CATGTTTCAACCATGTCCGCT 59.459 47.619 0.00 0.00 0.00 5.52
3162 3578 5.705902 TGTGAATTCATTCTTGTCTGCATG 58.294 37.500 12.12 0.00 37.67 4.06
3183 3599 3.566261 CGACATTGAGGCGCTTGT 58.434 55.556 7.64 3.71 45.03 3.16
3217 3633 7.085746 CACTTTGTCAGATATGTTCAAATGCA 58.914 34.615 11.40 0.00 0.00 3.96
3308 3725 6.740411 TTTTTGGCATTTTGAATATGCTCC 57.260 33.333 17.66 5.51 45.91 4.70


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

AutoCloner maintained by Alex Coulton.