Multiple sequence alignment - TraesCS2D01G195000

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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 TraesCS2D01G195000 chr2D 100.000 2930 0 0 1 2930 141190528 141193457 0.000000e+00 5411
1 TraesCS2D01G195000 chr2A 92.063 2016 69 46 975 2930 159937993 159936009 0.000000e+00 2752
2 TraesCS2D01G195000 chr2A 84.084 955 70 46 38 960 159938941 159938037 0.000000e+00 846
3 TraesCS2D01G195000 chr2B 92.639 1834 63 33 1120 2926 199123267 199121479 0.000000e+00 2573
4 TraesCS2D01G195000 chr2B 82.849 997 61 43 15 960 199124433 199123496 0.000000e+00 793
5 TraesCS2D01G195000 chr2B 94.340 106 6 0 975 1080 199123452 199123347 2.340000e-36 163


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 TraesCS2D01G195000 chr2D 141190528 141193457 2929 False 5411.000000 5411 100.000000 1 2930 1 chr2D.!!$F1 2929
1 TraesCS2D01G195000 chr2A 159936009 159938941 2932 True 1799.000000 2752 88.073500 38 2930 2 chr2A.!!$R1 2892
2 TraesCS2D01G195000 chr2B 199121479 199124433 2954 True 1176.333333 2573 89.942667 15 2926 3 chr2B.!!$R1 2911

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
313 327 0.030908 TCATACACACGACGCACACA 59.969 50.0 0.0 0.0 0.0 3.72 F
948 1035 0.040958 CGACTCAACCAAGCAGCAAC 60.041 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1331 0.469144 TCCCTCCTGCAAACCAAACC 60.469 55.0 0.0 0.0 0.0 3.27 R
2447 2650 0.373716 CCGACACAAATCTTAGCGGC 59.626 55.0 0.0 0.0 0.0 6.53 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
33 34 5.984147 TATATAAGCTCCCCGGCAGCAGA 62.984 52.174 21.92 11.66 39.56 4.26
35 36 4.496336 GCTCCCCGGCAGCAGATT 62.496 66.667 16.67 0.00 36.82 2.40
107 111 4.735132 GCACGACCGCACTAGCCA 62.735 66.667 0.00 0.00 37.52 4.75
108 112 2.809601 CACGACCGCACTAGCCAC 60.810 66.667 0.00 0.00 37.52 5.01
109 113 3.299977 ACGACCGCACTAGCCACA 61.300 61.111 0.00 0.00 37.52 4.17
110 114 2.809601 CGACCGCACTAGCCACAC 60.810 66.667 0.00 0.00 37.52 3.82
111 115 2.434359 GACCGCACTAGCCACACC 60.434 66.667 0.00 0.00 37.52 4.16
112 116 3.234630 GACCGCACTAGCCACACCA 62.235 63.158 0.00 0.00 37.52 4.17
185 192 1.005450 ACCAAATCACCGGCTAACCAT 59.995 47.619 0.00 0.00 34.57 3.55
193 200 3.211963 GGCTAACCATGGCGCCTG 61.212 66.667 29.70 21.88 39.42 4.85
204 211 3.499737 GCGCCTGATCAACCACCG 61.500 66.667 0.00 0.00 0.00 4.94
205 212 2.819595 CGCCTGATCAACCACCGG 60.820 66.667 0.00 0.00 0.00 5.28
206 213 2.351276 GCCTGATCAACCACCGGT 59.649 61.111 0.00 0.00 37.65 5.28
208 215 1.374947 CCTGATCAACCACCGGTGT 59.625 57.895 31.80 17.78 35.34 4.16
313 327 0.030908 TCATACACACGACGCACACA 59.969 50.000 0.00 0.00 0.00 3.72
315 329 1.459209 CATACACACGACGCACACAAT 59.541 47.619 0.00 0.00 0.00 2.71
316 330 0.855995 TACACACGACGCACACAATG 59.144 50.000 0.00 0.00 0.00 2.82
322 336 1.730064 ACGACGCACACAATGAATACC 59.270 47.619 0.00 0.00 0.00 2.73
323 337 1.062002 CGACGCACACAATGAATACCC 59.938 52.381 0.00 0.00 0.00 3.69
379 407 0.872021 CGATGCTTAGCGAGGGACAC 60.872 60.000 0.00 0.00 0.00 3.67
380 408 0.530870 GATGCTTAGCGAGGGACACC 60.531 60.000 0.00 0.00 0.00 4.16
414 443 3.359523 CAGGGACGACGACGGTGA 61.360 66.667 12.58 0.00 44.46 4.02
415 444 2.360852 AGGGACGACGACGGTGAT 60.361 61.111 12.58 0.00 44.46 3.06
416 445 2.202570 GGGACGACGACGGTGATG 60.203 66.667 12.58 0.00 44.46 3.07
417 446 2.564975 GGACGACGACGGTGATGT 59.435 61.111 12.58 0.00 44.46 3.06
418 447 1.800315 GGACGACGACGGTGATGTG 60.800 63.158 12.58 0.00 44.46 3.21
419 448 2.430244 ACGACGACGGTGATGTGC 60.430 61.111 12.58 0.00 44.46 4.57
420 449 2.430075 CGACGACGGTGATGTGCA 60.430 61.111 0.00 0.00 35.72 4.57
421 450 1.805539 CGACGACGGTGATGTGCAT 60.806 57.895 0.00 0.00 35.72 3.96
422 451 1.742900 CGACGACGGTGATGTGCATC 61.743 60.000 0.00 5.30 35.79 3.91
705 757 6.366630 CGATCTTTTGTTCTCTTTGTTCTCC 58.633 40.000 0.00 0.00 0.00 3.71
706 758 5.734855 TCTTTTGTTCTCTTTGTTCTCCG 57.265 39.130 0.00 0.00 0.00 4.63
707 759 4.574828 TCTTTTGTTCTCTTTGTTCTCCGG 59.425 41.667 0.00 0.00 0.00 5.14
708 760 3.553828 TTGTTCTCTTTGTTCTCCGGT 57.446 42.857 0.00 0.00 0.00 5.28
709 761 2.833794 TGTTCTCTTTGTTCTCCGGTG 58.166 47.619 0.00 0.00 0.00 4.94
710 762 2.143925 GTTCTCTTTGTTCTCCGGTGG 58.856 52.381 0.00 0.00 0.00 4.61
711 763 0.685097 TCTCTTTGTTCTCCGGTGGG 59.315 55.000 0.00 0.00 0.00 4.61
712 764 0.396811 CTCTTTGTTCTCCGGTGGGT 59.603 55.000 0.00 0.00 33.83 4.51
713 765 0.395312 TCTTTGTTCTCCGGTGGGTC 59.605 55.000 0.00 0.00 33.83 4.46
714 766 0.949105 CTTTGTTCTCCGGTGGGTCG 60.949 60.000 0.00 0.00 33.83 4.79
829 915 2.285668 CCCTCCCCTGCCTTGAGA 60.286 66.667 0.00 0.00 0.00 3.27
888 974 2.264813 CGTCCCCGGTATATATTTGCG 58.735 52.381 0.00 0.00 0.00 4.85
897 983 1.372501 ATATATTTGCGGCCTCCCCT 58.627 50.000 0.00 0.00 0.00 4.79
948 1035 0.040958 CGACTCAACCAAGCAGCAAC 60.041 55.000 0.00 0.00 0.00 4.17
960 1049 2.431601 AGCAACGAGACGCAGAGC 60.432 61.111 0.00 0.00 0.00 4.09
961 1050 2.734723 GCAACGAGACGCAGAGCA 60.735 61.111 0.00 0.00 0.00 4.26
964 1053 2.024319 AACGAGACGCAGAGCAAGC 61.024 57.895 0.00 0.00 0.00 4.01
965 1054 2.431430 CGAGACGCAGAGCAAGCA 60.431 61.111 0.00 0.00 0.00 3.91
967 1056 2.738695 GAGACGCAGAGCAAGCAGC 61.739 63.158 0.00 0.00 46.19 5.25
1038 1156 1.597854 TGACAACTTGCCCTGCTCG 60.598 57.895 0.00 0.00 0.00 5.03
1044 1162 1.004560 CTTGCCCTGCTCGACTTCA 60.005 57.895 0.00 0.00 0.00 3.02
1086 1204 1.078497 CTGGTAAGCATGTGCCCGA 60.078 57.895 0.57 0.00 43.38 5.14
1089 1226 0.179045 GGTAAGCATGTGCCCGATCT 60.179 55.000 0.57 0.00 43.38 2.75
1102 1239 1.543429 CCCGATCTTCCCTATTGTGCC 60.543 57.143 0.00 0.00 0.00 5.01
1103 1240 1.543429 CCGATCTTCCCTATTGTGCCC 60.543 57.143 0.00 0.00 0.00 5.36
1104 1241 1.873903 CGATCTTCCCTATTGTGCCCG 60.874 57.143 0.00 0.00 0.00 6.13
1107 1244 1.416401 TCTTCCCTATTGTGCCCGATC 59.584 52.381 0.00 0.00 0.00 3.69
1108 1245 1.417890 CTTCCCTATTGTGCCCGATCT 59.582 52.381 0.00 0.00 0.00 2.75
1110 1247 1.416401 TCCCTATTGTGCCCGATCTTC 59.584 52.381 0.00 0.00 0.00 2.87
1112 1249 1.140852 CCTATTGTGCCCGATCTTCCA 59.859 52.381 0.00 0.00 0.00 3.53
1113 1250 2.487934 CTATTGTGCCCGATCTTCCAG 58.512 52.381 0.00 0.00 0.00 3.86
1116 1253 1.078143 GTGCCCGATCTTCCAGCTT 60.078 57.895 0.00 0.00 0.00 3.74
1117 1254 1.078214 TGCCCGATCTTCCAGCTTG 60.078 57.895 0.00 0.00 0.00 4.01
1118 1255 2.476320 GCCCGATCTTCCAGCTTGC 61.476 63.158 0.00 0.00 0.00 4.01
1143 1324 2.349886 GAGGAATGCGTGTCTCATGTTC 59.650 50.000 0.00 0.00 0.00 3.18
1144 1325 1.398390 GGAATGCGTGTCTCATGTTCC 59.602 52.381 0.00 0.00 0.00 3.62
1145 1326 1.398390 GAATGCGTGTCTCATGTTCCC 59.602 52.381 0.00 0.00 0.00 3.97
1147 1328 0.320683 TGCGTGTCTCATGTTCCCTG 60.321 55.000 0.00 0.00 0.00 4.45
1150 1331 1.800586 CGTGTCTCATGTTCCCTGTTG 59.199 52.381 0.00 0.00 0.00 3.33
1152 1333 1.774254 TGTCTCATGTTCCCTGTTGGT 59.226 47.619 0.00 0.00 34.77 3.67
1246 1436 4.382541 TGGAGAGGCAGGAGCGGA 62.383 66.667 0.00 0.00 43.41 5.54
1320 1510 2.338620 CACGAGCTGGTGGACGAA 59.661 61.111 20.15 0.00 34.27 3.85
1916 2106 4.717629 CGACAGCGACGGCAGGAA 62.718 66.667 0.00 0.00 43.41 3.36
2108 2302 4.758674 TCCCGAACGAACGATCTATCTATT 59.241 41.667 0.14 0.00 35.09 1.73
2109 2303 5.934043 TCCCGAACGAACGATCTATCTATTA 59.066 40.000 0.14 0.00 35.09 0.98
2110 2304 6.596888 TCCCGAACGAACGATCTATCTATTAT 59.403 38.462 0.14 0.00 35.09 1.28
2238 2436 5.507974 TCTAGTCTGTACATGTTAATCGCG 58.492 41.667 2.30 0.00 0.00 5.87
2245 2443 4.632251 TGTACATGTTAATCGCGTTTCCAT 59.368 37.500 2.30 7.52 0.00 3.41
2308 2511 4.837860 AGTATTTTCCATGGACTTTTGCCA 59.162 37.500 15.91 0.00 40.24 4.92
2309 2512 4.703379 ATTTTCCATGGACTTTTGCCAA 57.297 36.364 15.91 0.00 39.21 4.52
2313 2516 5.815233 TTCCATGGACTTTTGCCAAATTA 57.185 34.783 15.91 0.00 39.21 1.40
2318 2521 2.353307 GGACTTTTGCCAAATTACCCCG 60.353 50.000 0.00 0.00 0.00 5.73
2319 2522 2.297880 GACTTTTGCCAAATTACCCCGT 59.702 45.455 0.00 0.00 0.00 5.28
2320 2523 2.036604 ACTTTTGCCAAATTACCCCGTG 59.963 45.455 0.00 0.00 0.00 4.94
2321 2524 0.318762 TTTGCCAAATTACCCCGTGC 59.681 50.000 0.00 0.00 0.00 5.34
2322 2525 0.827925 TTGCCAAATTACCCCGTGCA 60.828 50.000 0.00 0.00 0.00 4.57
2323 2526 0.613292 TGCCAAATTACCCCGTGCAT 60.613 50.000 0.00 0.00 0.00 3.96
2324 2527 1.341089 TGCCAAATTACCCCGTGCATA 60.341 47.619 0.00 0.00 0.00 3.14
2433 2636 0.684153 CCCCCACATTCCACCATCAC 60.684 60.000 0.00 0.00 0.00 3.06
2447 2650 1.473965 CCATCACCAGGAACTCATCGG 60.474 57.143 0.00 0.00 34.60 4.18
2542 2745 1.814793 CACACACGGAGAGAGAGAGA 58.185 55.000 0.00 0.00 0.00 3.10
2543 2746 1.737236 CACACACGGAGAGAGAGAGAG 59.263 57.143 0.00 0.00 0.00 3.20
2544 2747 1.339631 ACACACGGAGAGAGAGAGAGG 60.340 57.143 0.00 0.00 0.00 3.69
2545 2748 1.065782 CACACGGAGAGAGAGAGAGGA 60.066 57.143 0.00 0.00 0.00 3.71
2546 2749 1.065709 ACACGGAGAGAGAGAGAGGAC 60.066 57.143 0.00 0.00 0.00 3.85
2564 2768 3.095738 GGACGAAACAAACAACGACAAG 58.904 45.455 0.00 0.00 0.00 3.16
2580 2784 3.120060 CGACAAGAATGAAAGGAAGGCTG 60.120 47.826 0.00 0.00 0.00 4.85
2602 2806 1.871039 CTTTTCACACCCAACGATCGT 59.129 47.619 16.60 16.60 0.00 3.73
2710 2919 1.363807 GTGAAAGTGCAGGTTGGGC 59.636 57.895 0.00 0.00 0.00 5.36
2831 3051 6.575201 CCGAAATGAGAGAAAGAAAAGAAACG 59.425 38.462 0.00 0.00 0.00 3.60
2844 3064 7.078011 AGAAAAGAAACGAAATATCTGAGCC 57.922 36.000 0.00 0.00 0.00 4.70
2883 3103 2.182030 CCGACAGCTCGAGGAACC 59.818 66.667 15.58 0.00 43.06 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.591072 GCCGGGGAGCTTATATATAATTGTATA 58.409 37.037 2.18 4.60 0.00 1.47
2 3 7.071950 TGCCGGGGAGCTTATATATAATTGTAT 59.928 37.037 2.18 0.12 0.00 2.29
3 4 6.384595 TGCCGGGGAGCTTATATATAATTGTA 59.615 38.462 2.18 0.00 0.00 2.41
4 5 5.190925 TGCCGGGGAGCTTATATATAATTGT 59.809 40.000 2.18 0.00 0.00 2.71
5 6 5.680619 TGCCGGGGAGCTTATATATAATTG 58.319 41.667 2.18 0.00 0.00 2.32
6 7 5.687706 GCTGCCGGGGAGCTTATATATAATT 60.688 44.000 30.51 0.00 33.37 1.40
7 8 4.202367 GCTGCCGGGGAGCTTATATATAAT 60.202 45.833 30.51 0.00 33.37 1.28
8 9 3.134081 GCTGCCGGGGAGCTTATATATAA 59.866 47.826 30.51 5.10 33.37 0.98
9 10 2.698797 GCTGCCGGGGAGCTTATATATA 59.301 50.000 30.51 0.00 33.37 0.86
10 11 1.486726 GCTGCCGGGGAGCTTATATAT 59.513 52.381 30.51 0.00 33.37 0.86
11 12 0.902531 GCTGCCGGGGAGCTTATATA 59.097 55.000 30.51 0.00 33.37 0.86
12 13 1.127567 TGCTGCCGGGGAGCTTATAT 61.128 55.000 35.38 0.00 37.35 0.86
13 14 1.758440 CTGCTGCCGGGGAGCTTATA 61.758 60.000 35.38 18.30 37.35 0.98
21 22 0.604780 CTGATAATCTGCTGCCGGGG 60.605 60.000 2.18 0.00 0.00 5.73
33 34 2.350498 CCGCGTTCGTTTTCCTGATAAT 59.650 45.455 4.92 0.00 0.00 1.28
34 35 1.727880 CCGCGTTCGTTTTCCTGATAA 59.272 47.619 4.92 0.00 0.00 1.75
35 36 1.352114 CCGCGTTCGTTTTCCTGATA 58.648 50.000 4.92 0.00 0.00 2.15
107 111 2.277404 GGGTGTGGGTGTTGGTGT 59.723 61.111 0.00 0.00 0.00 4.16
108 112 2.904866 CGGGTGTGGGTGTTGGTG 60.905 66.667 0.00 0.00 0.00 4.17
109 113 4.887190 GCGGGTGTGGGTGTTGGT 62.887 66.667 0.00 0.00 0.00 3.67
111 115 4.920112 TCGCGGGTGTGGGTGTTG 62.920 66.667 6.13 0.00 0.00 3.33
112 116 4.619227 CTCGCGGGTGTGGGTGTT 62.619 66.667 6.13 0.00 0.00 3.32
185 192 2.359850 GTGGTTGATCAGGCGCCA 60.360 61.111 31.54 9.64 0.00 5.69
193 200 0.953960 GGTGACACCGGTGGTTGATC 60.954 60.000 36.47 24.55 31.02 2.92
204 211 2.034221 GGGAAGGCTGGTGACACC 59.966 66.667 18.28 18.28 39.22 4.16
205 212 2.034221 GGGGAAGGCTGGTGACAC 59.966 66.667 0.00 0.00 35.60 3.67
206 213 3.256960 GGGGGAAGGCTGGTGACA 61.257 66.667 0.00 0.00 39.59 3.58
208 215 2.935481 CAGGGGGAAGGCTGGTGA 60.935 66.667 0.00 0.00 0.00 4.02
313 327 2.507407 ACTTGTGCGGGGTATTCATT 57.493 45.000 0.00 0.00 0.00 2.57
315 329 1.624312 TGTACTTGTGCGGGGTATTCA 59.376 47.619 0.00 0.00 0.00 2.57
316 330 2.277084 CTGTACTTGTGCGGGGTATTC 58.723 52.381 0.00 0.00 0.00 1.75
397 426 2.697761 ATCACCGTCGTCGTCCCTG 61.698 63.158 0.71 0.00 35.01 4.45
403 432 1.742900 GATGCACATCACCGTCGTCG 61.743 60.000 5.76 0.00 37.74 5.12
406 435 0.811219 ATGGATGCACATCACCGTCG 60.811 55.000 12.43 0.00 39.54 5.12
408 437 2.784547 CATGGATGCACATCACCGT 58.215 52.632 12.43 0.00 39.54 4.83
543 579 0.959867 TTGCTTGCTGCCTGCGAATA 60.960 50.000 0.00 0.00 46.63 1.75
586 626 0.751643 TCGATCTCAGACGGATGGCA 60.752 55.000 0.00 0.00 0.00 4.92
671 714 3.771577 ACAAAAGATCGCTATAGGGGG 57.228 47.619 16.09 0.00 0.00 5.40
705 757 1.093496 GGAATAAAGGCGACCCACCG 61.093 60.000 0.00 0.00 0.00 4.94
706 758 0.750546 GGGAATAAAGGCGACCCACC 60.751 60.000 0.00 0.00 40.20 4.61
707 759 1.093496 CGGGAATAAAGGCGACCCAC 61.093 60.000 0.00 0.00 40.45 4.61
708 760 1.222387 CGGGAATAAAGGCGACCCA 59.778 57.895 0.00 0.00 40.45 4.51
709 761 2.184830 GCGGGAATAAAGGCGACCC 61.185 63.158 0.00 0.00 37.42 4.46
710 762 2.184830 GGCGGGAATAAAGGCGACC 61.185 63.158 0.00 0.00 0.00 4.79
711 763 0.818040 ATGGCGGGAATAAAGGCGAC 60.818 55.000 0.00 0.00 0.00 5.19
712 764 0.106918 AATGGCGGGAATAAAGGCGA 60.107 50.000 0.00 0.00 0.00 5.54
713 765 1.600023 TAATGGCGGGAATAAAGGCG 58.400 50.000 0.00 0.00 0.00 5.52
714 766 3.383505 AGTTTAATGGCGGGAATAAAGGC 59.616 43.478 0.00 0.00 0.00 4.35
756 810 1.319614 TTGGGCCGAATTTGCTAGCC 61.320 55.000 13.29 3.47 43.09 3.93
757 811 0.746659 ATTGGGCCGAATTTGCTAGC 59.253 50.000 7.24 8.10 0.00 3.42
758 812 1.338020 GGATTGGGCCGAATTTGCTAG 59.662 52.381 14.77 0.00 0.00 3.42
759 813 1.064017 AGGATTGGGCCGAATTTGCTA 60.064 47.619 14.77 0.00 0.00 3.49
823 909 3.533547 CTGGCAGGATCTTTCTCTCAAG 58.466 50.000 6.61 0.00 0.00 3.02
829 915 0.255318 CAGCCTGGCAGGATCTTTCT 59.745 55.000 37.07 19.73 37.67 2.52
874 960 2.277084 GGAGGCCGCAAATATATACCG 58.723 52.381 9.31 0.00 0.00 4.02
886 972 3.712907 TGTGTAAGGGGAGGCCGC 61.713 66.667 0.00 0.00 36.67 6.53
888 974 0.404426 AAAGTGTGTAAGGGGAGGCC 59.596 55.000 0.00 0.00 0.00 5.19
897 983 5.011329 AGGATGTCGTAAGGAAAGTGTGTAA 59.989 40.000 0.00 0.00 38.47 2.41
948 1035 2.431430 TGCTTGCTCTGCGTCTCG 60.431 61.111 0.00 0.00 0.00 4.04
960 1049 2.663879 CGAAGCTACTTGTTGCTGCTTG 60.664 50.000 10.10 0.00 42.95 4.01
961 1050 1.532868 CGAAGCTACTTGTTGCTGCTT 59.467 47.619 10.10 0.00 45.15 3.91
964 1053 1.461127 GGTCGAAGCTACTTGTTGCTG 59.539 52.381 10.10 0.40 39.71 4.41
965 1054 1.344763 AGGTCGAAGCTACTTGTTGCT 59.655 47.619 4.03 4.03 41.82 3.91
967 1056 3.390135 TGAAGGTCGAAGCTACTTGTTG 58.610 45.455 0.00 0.00 0.00 3.33
969 1058 2.610727 GCTGAAGGTCGAAGCTACTTGT 60.611 50.000 0.00 0.00 34.05 3.16
970 1059 1.996191 GCTGAAGGTCGAAGCTACTTG 59.004 52.381 0.00 0.00 34.05 3.16
971 1060 1.896465 AGCTGAAGGTCGAAGCTACTT 59.104 47.619 6.77 0.00 45.26 2.24
972 1061 1.551452 AGCTGAAGGTCGAAGCTACT 58.449 50.000 6.77 0.00 45.26 2.57
973 1062 2.094442 AGAAGCTGAAGGTCGAAGCTAC 60.094 50.000 8.89 0.00 46.36 3.58
1008 1126 2.033448 TTGTCACGCACCCCCATC 59.967 61.111 0.00 0.00 0.00 3.51
1038 1156 2.495270 TGTGAGCTCTCTCCATGAAGTC 59.505 50.000 16.19 0.00 38.58 3.01
1044 1162 1.274728 GTGTGTGTGAGCTCTCTCCAT 59.725 52.381 16.19 0.00 38.58 3.41
1083 1201 1.543429 GGGCACAATAGGGAAGATCGG 60.543 57.143 0.00 0.00 0.00 4.18
1086 1204 1.507140 TCGGGCACAATAGGGAAGAT 58.493 50.000 0.00 0.00 0.00 2.40
1089 1226 1.507140 AGATCGGGCACAATAGGGAA 58.493 50.000 0.00 0.00 0.00 3.97
1102 1239 1.424493 GACGCAAGCTGGAAGATCGG 61.424 60.000 0.00 0.00 45.62 4.18
1103 1240 1.746727 CGACGCAAGCTGGAAGATCG 61.747 60.000 0.00 0.00 45.62 3.69
1104 1241 0.458543 TCGACGCAAGCTGGAAGATC 60.459 55.000 0.00 0.00 45.62 2.75
1107 1244 2.097038 CCTCGACGCAAGCTGGAAG 61.097 63.158 0.00 0.00 45.62 3.46
1108 1245 2.048222 CCTCGACGCAAGCTGGAA 60.048 61.111 0.00 0.00 45.62 3.53
1110 1247 1.448540 ATTCCTCGACGCAAGCTGG 60.449 57.895 0.00 0.00 45.62 4.85
1112 1249 2.103042 GCATTCCTCGACGCAAGCT 61.103 57.895 0.00 0.00 45.62 3.74
1113 1250 2.401195 GCATTCCTCGACGCAAGC 59.599 61.111 0.00 0.00 45.62 4.01
1116 1253 2.809174 CACGCATTCCTCGACGCA 60.809 61.111 0.00 0.00 0.00 5.24
1117 1254 2.789203 GACACGCATTCCTCGACGC 61.789 63.158 0.00 0.00 0.00 5.19
1118 1255 1.134530 GAGACACGCATTCCTCGACG 61.135 60.000 0.00 0.00 0.00 5.12
1143 1324 0.539051 TGCAAACCAAACCAACAGGG 59.461 50.000 0.00 0.00 44.81 4.45
1144 1325 1.473080 CCTGCAAACCAAACCAACAGG 60.473 52.381 0.00 0.00 37.47 4.00
1145 1326 1.480137 TCCTGCAAACCAAACCAACAG 59.520 47.619 0.00 0.00 0.00 3.16
1147 1328 1.202521 CCTCCTGCAAACCAAACCAAC 60.203 52.381 0.00 0.00 0.00 3.77
1150 1331 0.469144 TCCCTCCTGCAAACCAAACC 60.469 55.000 0.00 0.00 0.00 3.27
1152 1333 1.146774 TCATCCCTCCTGCAAACCAAA 59.853 47.619 0.00 0.00 0.00 3.28
1394 1584 4.814294 CGGTCGGCCTTTCCTCGG 62.814 72.222 3.66 0.00 0.00 4.63
1395 1585 4.814294 CCGGTCGGCCTTTCCTCG 62.814 72.222 3.66 0.00 0.00 4.63
1916 2106 4.098044 TGTTCTCTTCTCACTCGAACAACT 59.902 41.667 0.00 0.00 40.43 3.16
2108 2302 9.504708 GAATCCTACTAGTAGTACAAGCTGATA 57.495 37.037 24.84 0.00 0.00 2.15
2109 2303 7.999545 TGAATCCTACTAGTAGTACAAGCTGAT 59.000 37.037 24.84 15.62 0.00 2.90
2110 2304 7.344134 TGAATCCTACTAGTAGTACAAGCTGA 58.656 38.462 24.84 14.26 0.00 4.26
2281 2484 6.526674 GCAAAAGTCCATGGAAAATACTTACG 59.473 38.462 18.20 10.92 30.51 3.18
2285 2488 4.837860 TGGCAAAAGTCCATGGAAAATACT 59.162 37.500 18.20 6.62 0.00 2.12
2308 2511 4.783055 TGTATGTATGCACGGGGTAATTT 58.217 39.130 0.00 0.00 0.00 1.82
2309 2512 4.425180 TGTATGTATGCACGGGGTAATT 57.575 40.909 0.00 0.00 0.00 1.40
2313 2516 1.071699 GGATGTATGTATGCACGGGGT 59.928 52.381 0.00 0.00 0.00 4.95
2318 2521 3.664107 ACGGATGGATGTATGTATGCAC 58.336 45.455 0.00 0.00 31.02 4.57
2319 2522 5.476091 TTACGGATGGATGTATGTATGCA 57.524 39.130 0.00 0.00 32.84 3.96
2320 2523 5.523916 GGATTACGGATGGATGTATGTATGC 59.476 44.000 0.00 0.00 0.00 3.14
2321 2524 5.748630 CGGATTACGGATGGATGTATGTATG 59.251 44.000 0.00 0.00 39.42 2.39
2322 2525 5.902681 CGGATTACGGATGGATGTATGTAT 58.097 41.667 0.00 0.00 39.42 2.29
2323 2526 5.319140 CGGATTACGGATGGATGTATGTA 57.681 43.478 0.00 0.00 39.42 2.29
2324 2527 4.188247 CGGATTACGGATGGATGTATGT 57.812 45.455 0.00 0.00 39.42 2.29
2433 2636 2.202932 CGGCCGATGAGTTCCTGG 60.203 66.667 24.07 0.00 0.00 4.45
2447 2650 0.373716 CCGACACAAATCTTAGCGGC 59.626 55.000 0.00 0.00 0.00 6.53
2542 2745 2.348660 TGTCGTTGTTTGTTTCGTCCT 58.651 42.857 0.00 0.00 0.00 3.85
2543 2746 2.810028 TGTCGTTGTTTGTTTCGTCC 57.190 45.000 0.00 0.00 0.00 4.79
2544 2747 3.993547 TCTTGTCGTTGTTTGTTTCGTC 58.006 40.909 0.00 0.00 0.00 4.20
2545 2748 4.407496 TTCTTGTCGTTGTTTGTTTCGT 57.593 36.364 0.00 0.00 0.00 3.85
2546 2749 5.025190 TCATTCTTGTCGTTGTTTGTTTCG 58.975 37.500 0.00 0.00 0.00 3.46
2564 2768 1.844687 AGGCAGCCTTCCTTTCATTC 58.155 50.000 8.70 0.00 0.00 2.67
2580 2784 0.958822 ATCGTTGGGTGTGAAAAGGC 59.041 50.000 0.00 0.00 0.00 4.35
2602 2806 0.731514 CGCTTCTCCGCACGTTTCTA 60.732 55.000 0.00 0.00 0.00 2.10
2831 3051 1.262683 GCACTGCGGCTCAGATATTTC 59.737 52.381 12.12 0.00 45.72 2.17
2883 3103 2.032030 ACGTTTTTCAGAGGTTGCATCG 60.032 45.455 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.