Multiple sequence alignment - TraesCS3A01G205200

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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 TraesCS3A01G205200 chr3A 100.000 3813 0 0 1 3813 360823840 360827652 0.000000e+00 7042.0
1 TraesCS3A01G205200 chr3A 81.416 113 20 1 1151 1263 245400840 245400951 1.460000e-14 91.6
2 TraesCS3A01G205200 chr3D 95.916 2620 83 9 1215 3813 278450475 278447859 0.000000e+00 4224.0
3 TraesCS3A01G205200 chr3D 97.080 822 22 2 1 821 278451298 278450478 0.000000e+00 1384.0
4 TraesCS3A01G205200 chr3B 93.676 2688 116 28 1162 3813 372240297 372242966 0.000000e+00 3973.0
5 TraesCS3A01G205200 chr3B 96.717 731 17 3 1 725 372238891 372239620 0.000000e+00 1210.0
6 TraesCS3A01G205200 chr3B 93.667 300 11 3 707 1006 372239635 372239926 3.500000e-120 442.0
7 TraesCS3A01G205200 chr3B 85.833 120 14 2 1151 1269 167250751 167250868 1.440000e-24 124.0
8 TraesCS3A01G205200 chr3B 83.824 136 14 6 1169 1298 584108966 584109099 5.170000e-24 122.0
9 TraesCS3A01G205200 chr7B 85.926 135 14 3 1151 1282 2509184 2509052 5.140000e-29 139.0
10 TraesCS3A01G205200 chr5B 85.000 120 15 2 1151 1269 522945787 522945670 6.690000e-23 119.0
11 TraesCS3A01G205200 chr6B 82.143 140 18 5 1151 1285 189214925 189215062 3.110000e-21 113.0
12 TraesCS3A01G205200 chr6A 82.090 134 15 8 1151 1279 574234915 574235044 5.210000e-19 106.0
13 TraesCS3A01G205200 chr1A 81.343 134 19 6 1149 1279 580497284 580497154 1.870000e-18 104.0


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 TraesCS3A01G205200 chr3A 360823840 360827652 3812 False 7042 7042 100.000000 1 3813 1 chr3A.!!$F2 3812
1 TraesCS3A01G205200 chr3D 278447859 278451298 3439 True 2804 4224 96.498000 1 3813 2 chr3D.!!$R1 3812
2 TraesCS3A01G205200 chr3B 372238891 372242966 4075 False 1875 3973 94.686667 1 3813 3 chr3B.!!$F3 3812

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
550 557 0.170561 ACGAGCTGTACAAGGTAGCG 59.829 55.0 0.0 1.35 42.1 4.26 F
1046 1086 0.187361 CCAAGAAAACACCCCCTCCA 59.813 55.0 0.0 0.00 0.0 3.86 F
1809 2086 0.249911 ACTCCAAGGACAAGTGCGAC 60.250 55.0 0.0 0.00 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2314 0.390860 CCTCCATCTCCGCGAATTCT 59.609 55.000 8.23 0.0 0.00 2.40 R
2040 2317 1.742768 GTCCTCCATCTCCGCGAAT 59.257 57.895 8.23 0.0 0.00 3.34 R
3526 3830 0.460109 TGACATCCGGTGCTTCATCG 60.460 55.000 0.00 0.0 37.76 3.84 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
209 210 1.394917 GTCGTCGAGGTAGCTTTACGA 59.605 52.381 21.46 21.46 37.05 3.43
221 222 8.699283 AGGTAGCTTTACGAAAACAAGTATAG 57.301 34.615 0.00 0.00 0.00 1.31
232 238 7.013529 CGAAAACAAGTATAGTAACCTGCAAC 58.986 38.462 0.00 0.00 0.00 4.17
251 257 4.672413 GCAACATGTCAAGAGAGTTTTTCG 59.328 41.667 0.00 0.00 0.00 3.46
285 291 0.880278 CACTGGTCGTCCAACAGGTG 60.880 60.000 2.32 3.80 43.81 4.00
413 419 3.950395 AGCAGAGCACTGAAAAAGAAAGT 59.050 39.130 15.88 0.00 46.03 2.66
418 424 5.014808 AGCACTGAAAAAGAAAGTTGCAT 57.985 34.783 0.00 0.00 0.00 3.96
550 557 0.170561 ACGAGCTGTACAAGGTAGCG 59.829 55.000 0.00 1.35 42.10 4.26
622 629 1.601759 GGCCAAAGTGCAGAGCTCA 60.602 57.895 17.77 0.00 0.00 4.26
833 873 7.653647 TGGTATGTTTGTAATCAAGTTTGGTC 58.346 34.615 0.00 0.00 34.88 4.02
845 885 1.344438 AGTTTGGTCATCGCAGTCAGA 59.656 47.619 0.00 0.00 0.00 3.27
925 965 2.285977 ACCGTGACCACTTCTCAAAAC 58.714 47.619 0.00 0.00 0.00 2.43
926 966 2.285083 CCGTGACCACTTCTCAAAACA 58.715 47.619 0.00 0.00 0.00 2.83
927 967 2.680841 CCGTGACCACTTCTCAAAACAA 59.319 45.455 0.00 0.00 0.00 2.83
928 968 3.127895 CCGTGACCACTTCTCAAAACAAA 59.872 43.478 0.00 0.00 0.00 2.83
929 969 4.380023 CCGTGACCACTTCTCAAAACAAAA 60.380 41.667 0.00 0.00 0.00 2.44
930 970 5.157781 CGTGACCACTTCTCAAAACAAAAA 58.842 37.500 0.00 0.00 0.00 1.94
931 971 5.060446 CGTGACCACTTCTCAAAACAAAAAC 59.940 40.000 0.00 0.00 0.00 2.43
932 972 5.923684 GTGACCACTTCTCAAAACAAAAACA 59.076 36.000 0.00 0.00 0.00 2.83
936 976 8.214721 ACCACTTCTCAAAACAAAAACAAAAA 57.785 26.923 0.00 0.00 0.00 1.94
951 991 3.427309 AAAAACCAACGGTGTGTGC 57.573 47.368 0.00 0.00 35.34 4.57
963 1003 0.234625 GTGTGTGCGTGTGTATGTGG 59.765 55.000 0.00 0.00 0.00 4.17
973 1013 3.122780 CGTGTGTATGTGGTGTGTATGTG 59.877 47.826 0.00 0.00 0.00 3.21
1006 1046 9.693739 TCTTTGAAGCTTTGGTTCCATTATATA 57.306 29.630 0.00 0.00 39.02 0.86
1017 1057 9.624037 TTGGTTCCATTATATATACTACACCCT 57.376 33.333 0.00 0.00 0.00 4.34
1018 1058 9.263446 TGGTTCCATTATATATACTACACCCTC 57.737 37.037 0.00 0.00 0.00 4.30
1019 1059 8.702819 GGTTCCATTATATATACTACACCCTCC 58.297 40.741 0.00 0.00 0.00 4.30
1020 1060 9.490083 GTTCCATTATATATACTACACCCTCCT 57.510 37.037 0.00 0.00 0.00 3.69
1026 1066 5.803237 ATATACTACACCCTCCTTTTCCG 57.197 43.478 0.00 0.00 0.00 4.30
1027 1067 0.323957 ACTACACCCTCCTTTTCCGC 59.676 55.000 0.00 0.00 0.00 5.54
1028 1068 0.392595 CTACACCCTCCTTTTCCGCC 60.393 60.000 0.00 0.00 0.00 6.13
1029 1069 1.128809 TACACCCTCCTTTTCCGCCA 61.129 55.000 0.00 0.00 0.00 5.69
1030 1070 1.228429 CACCCTCCTTTTCCGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
1031 1071 1.074951 ACCCTCCTTTTCCGCCAAG 59.925 57.895 0.00 0.00 0.00 3.61
1032 1072 1.378762 CCCTCCTTTTCCGCCAAGA 59.621 57.895 0.00 0.00 0.00 3.02
1033 1073 0.251165 CCCTCCTTTTCCGCCAAGAA 60.251 55.000 0.00 0.00 0.00 2.52
1034 1074 1.616159 CCTCCTTTTCCGCCAAGAAA 58.384 50.000 0.00 0.00 33.98 2.52
1035 1075 1.960689 CCTCCTTTTCCGCCAAGAAAA 59.039 47.619 4.47 4.47 42.07 2.29
1036 1076 2.288213 CCTCCTTTTCCGCCAAGAAAAC 60.288 50.000 0.00 0.00 40.04 2.43
1037 1077 2.360801 CTCCTTTTCCGCCAAGAAAACA 59.639 45.455 0.00 0.00 40.04 2.83
1038 1078 2.100087 TCCTTTTCCGCCAAGAAAACAC 59.900 45.455 0.00 0.00 40.04 3.32
1039 1079 2.469826 CTTTTCCGCCAAGAAAACACC 58.530 47.619 0.00 0.00 40.04 4.16
1040 1080 0.747852 TTTCCGCCAAGAAAACACCC 59.252 50.000 0.00 0.00 32.90 4.61
1041 1081 1.110518 TTCCGCCAAGAAAACACCCC 61.111 55.000 0.00 0.00 0.00 4.95
1042 1082 2.570284 CCGCCAAGAAAACACCCCC 61.570 63.158 0.00 0.00 0.00 5.40
1043 1083 1.530655 CGCCAAGAAAACACCCCCT 60.531 57.895 0.00 0.00 0.00 4.79
1044 1084 1.524008 CGCCAAGAAAACACCCCCTC 61.524 60.000 0.00 0.00 0.00 4.30
1045 1085 1.185618 GCCAAGAAAACACCCCCTCC 61.186 60.000 0.00 0.00 0.00 4.30
1046 1086 0.187361 CCAAGAAAACACCCCCTCCA 59.813 55.000 0.00 0.00 0.00 3.86
1047 1087 1.203174 CCAAGAAAACACCCCCTCCAT 60.203 52.381 0.00 0.00 0.00 3.41
1048 1088 2.042433 CCAAGAAAACACCCCCTCCATA 59.958 50.000 0.00 0.00 0.00 2.74
1049 1089 3.501385 CCAAGAAAACACCCCCTCCATAA 60.501 47.826 0.00 0.00 0.00 1.90
1050 1090 3.739401 AGAAAACACCCCCTCCATAAG 57.261 47.619 0.00 0.00 0.00 1.73
1051 1091 3.265489 AGAAAACACCCCCTCCATAAGA 58.735 45.455 0.00 0.00 0.00 2.10
1052 1092 3.858638 AGAAAACACCCCCTCCATAAGAT 59.141 43.478 0.00 0.00 0.00 2.40
1053 1093 3.669939 AAACACCCCCTCCATAAGATG 57.330 47.619 0.00 0.00 0.00 2.90
1054 1094 2.286935 ACACCCCCTCCATAAGATGT 57.713 50.000 0.00 0.00 0.00 3.06
1055 1095 2.573463 ACACCCCCTCCATAAGATGTT 58.427 47.619 0.00 0.00 0.00 2.71
1056 1096 2.509964 ACACCCCCTCCATAAGATGTTC 59.490 50.000 0.00 0.00 0.00 3.18
1057 1097 2.780010 CACCCCCTCCATAAGATGTTCT 59.220 50.000 0.00 0.00 0.00 3.01
1058 1098 3.973973 CACCCCCTCCATAAGATGTTCTA 59.026 47.826 0.00 0.00 0.00 2.10
1059 1099 4.412199 CACCCCCTCCATAAGATGTTCTAA 59.588 45.833 0.00 0.00 0.00 2.10
1060 1100 5.043762 ACCCCCTCCATAAGATGTTCTAAA 58.956 41.667 0.00 0.00 0.00 1.85
1061 1101 5.494706 ACCCCCTCCATAAGATGTTCTAAAA 59.505 40.000 0.00 0.00 0.00 1.52
1062 1102 6.011096 ACCCCCTCCATAAGATGTTCTAAAAA 60.011 38.462 0.00 0.00 0.00 1.94
1116 1344 2.747446 AGTGTGTTTGTTCACTCGCTTT 59.253 40.909 0.00 0.00 40.28 3.51
1135 1363 5.306394 GCTTTAGTCTTTGTGTACTCCCTT 58.694 41.667 0.00 0.00 0.00 3.95
1140 1368 3.739810 GTCTTTGTGTACTCCCTTCGTTC 59.260 47.826 0.00 0.00 0.00 3.95
1141 1369 3.640029 TCTTTGTGTACTCCCTTCGTTCT 59.360 43.478 0.00 0.00 0.00 3.01
1145 1373 5.534207 TGTGTACTCCCTTCGTTCTTAAA 57.466 39.130 0.00 0.00 0.00 1.52
1146 1374 6.105397 TGTGTACTCCCTTCGTTCTTAAAT 57.895 37.500 0.00 0.00 0.00 1.40
1147 1375 7.230849 TGTGTACTCCCTTCGTTCTTAAATA 57.769 36.000 0.00 0.00 0.00 1.40
1148 1376 7.092716 TGTGTACTCCCTTCGTTCTTAAATAC 58.907 38.462 0.00 0.00 0.00 1.89
1149 1377 7.039504 TGTGTACTCCCTTCGTTCTTAAATACT 60.040 37.037 0.00 0.00 0.00 2.12
1241 1501 5.699839 AGTTTCATTCATTTTGCTCCGTAC 58.300 37.500 0.00 0.00 0.00 3.67
1254 1514 6.375945 TTGCTCCGTACGTAGTTCATATTA 57.624 37.500 15.21 0.00 37.78 0.98
1337 1602 2.531771 TGTAACAGTGATCGGAGGGAA 58.468 47.619 0.00 0.00 0.00 3.97
1338 1603 3.104512 TGTAACAGTGATCGGAGGGAAT 58.895 45.455 0.00 0.00 0.00 3.01
1540 1811 2.915659 ACGTCTTCAGCCCGTCCA 60.916 61.111 0.00 0.00 0.00 4.02
1656 1927 3.827898 GACGGGAGGCTCTCGGTG 61.828 72.222 37.08 13.75 46.41 4.94
1717 1988 1.886585 GACTGCGAGCTCAAGGAGA 59.113 57.895 15.40 0.00 0.00 3.71
1737 2008 3.672293 GGGGACGTCGTACTGTCA 58.328 61.111 9.92 0.00 36.83 3.58
1785 2056 4.695231 CTCGTGTTCGTCGGCCGT 62.695 66.667 27.15 0.00 37.94 5.68
1788 2059 2.256461 GTGTTCGTCGGCCGTAGT 59.744 61.111 27.15 0.00 37.94 2.73
1795 2072 1.647545 CGTCGGCCGTAGTAACTCCA 61.648 60.000 27.15 0.00 0.00 3.86
1804 2081 3.257624 CCGTAGTAACTCCAAGGACAAGT 59.742 47.826 0.00 0.00 0.00 3.16
1805 2082 4.235360 CGTAGTAACTCCAAGGACAAGTG 58.765 47.826 0.00 0.00 0.00 3.16
1806 2083 3.127425 AGTAACTCCAAGGACAAGTGC 57.873 47.619 0.00 0.00 0.00 4.40
1809 2086 0.249911 ACTCCAAGGACAAGTGCGAC 60.250 55.000 0.00 0.00 0.00 5.19
1882 2159 4.443266 GCTTCGTGCTCGGGCTCT 62.443 66.667 9.62 0.00 39.59 4.09
2040 2317 2.358247 GCCTTCCCGCACGAAGAA 60.358 61.111 10.58 0.00 41.57 2.52
2123 2400 4.891727 CTTCGCCATCGACCCCGG 62.892 72.222 0.00 0.00 45.43 5.73
2226 2503 2.599597 GCCATGAGGATGTGCCCT 59.400 61.111 0.00 0.00 39.77 5.19
2385 2662 4.175337 GCTGCAGCCCGGTGGATA 62.175 66.667 28.76 0.00 34.31 2.59
2453 2730 1.870055 GACTACGTGGAAGTGGCCGA 61.870 60.000 5.70 0.00 0.00 5.54
2541 2818 2.822701 GATTTCGGGTGGGGCGAC 60.823 66.667 0.00 0.00 0.00 5.19
2597 2874 2.024414 GGAGGTGGTCATGTTTATGCC 58.976 52.381 0.00 0.00 34.21 4.40
2692 2969 9.331282 ACATGGTAGATTTGATCTAAAACTAGC 57.669 33.333 18.78 18.78 45.10 3.42
2693 2970 8.778358 CATGGTAGATTTGATCTAAAACTAGCC 58.222 37.037 20.64 16.40 44.66 3.93
2694 2971 8.090788 TGGTAGATTTGATCTAAAACTAGCCT 57.909 34.615 20.64 6.08 44.66 4.58
2695 2972 9.209048 TGGTAGATTTGATCTAAAACTAGCCTA 57.791 33.333 20.64 10.44 44.66 3.93
2696 2973 9.478768 GGTAGATTTGATCTAAAACTAGCCTAC 57.521 37.037 16.84 0.00 41.98 3.18
2719 3009 2.091541 TGGCCATTTTAGCTTCCTTCG 58.908 47.619 0.00 0.00 0.00 3.79
2729 3019 2.076863 AGCTTCCTTCGTAATGTGTGC 58.923 47.619 0.00 0.00 0.00 4.57
2756 3046 3.031013 TGGGATCTCAATCTCAGCGTTA 58.969 45.455 0.00 0.00 37.47 3.18
2906 3210 1.017387 GCTAACATGTGCCTGCTACC 58.983 55.000 0.00 0.00 0.00 3.18
3283 3587 0.178975 TTTGGGTTCCGCTCATGGTT 60.179 50.000 0.00 0.00 0.00 3.67
3526 3830 3.118542 CAAAGTTGCTTGCTCAAAGTCC 58.881 45.455 0.00 0.00 38.25 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 210 7.811117 TGTTGCAGGTTACTATACTTGTTTT 57.189 32.000 0.00 0.00 0.00 2.43
221 222 4.065088 TCTCTTGACATGTTGCAGGTTAC 58.935 43.478 0.00 0.00 0.00 2.50
232 238 5.914085 AGACGAAAAACTCTCTTGACATG 57.086 39.130 0.00 0.00 0.00 3.21
251 257 0.321653 CAGTGCACCCTGGGTTAGAC 60.322 60.000 17.76 12.78 31.02 2.59
285 291 5.039333 GCATTGATAGCACCTTGTGAAATC 58.961 41.667 0.00 1.15 35.23 2.17
418 424 3.745975 CAGATTAAGACGAGGTGCAACAA 59.254 43.478 3.64 0.00 39.98 2.83
550 557 3.577313 GCGAGGCCCAGCGATTTC 61.577 66.667 13.66 0.00 0.00 2.17
622 629 6.314896 GCTGAAGAAACAATATCTAGTGCTGT 59.685 38.462 0.00 0.00 0.00 4.40
772 812 0.544120 TTCCCCCTTTGCATGGGTTC 60.544 55.000 19.92 0.00 43.09 3.62
823 863 1.872952 TGACTGCGATGACCAAACTTG 59.127 47.619 0.00 0.00 0.00 3.16
833 873 5.277202 CCATTTCTAACATCTGACTGCGATG 60.277 44.000 0.00 0.00 42.97 3.84
891 931 3.251571 GTCACGGTTGGTCAGATAGTTC 58.748 50.000 0.00 0.00 0.00 3.01
936 976 2.437002 ACGCACACACCGTTGGTT 60.437 55.556 0.00 0.00 34.96 3.67
938 978 3.199190 ACACGCACACACCGTTGG 61.199 61.111 0.00 0.00 36.69 3.77
950 990 1.785768 TACACACCACATACACACGC 58.214 50.000 0.00 0.00 0.00 5.34
951 991 3.122780 CACATACACACCACATACACACG 59.877 47.826 0.00 0.00 0.00 4.49
963 1003 7.693951 GCTTCAAAGACATATTCACATACACAC 59.306 37.037 0.00 0.00 0.00 3.82
973 1013 6.808704 GGAACCAAAGCTTCAAAGACATATTC 59.191 38.462 0.00 0.00 0.00 1.75
1006 1046 2.169978 GCGGAAAAGGAGGGTGTAGTAT 59.830 50.000 0.00 0.00 0.00 2.12
1007 1047 1.551883 GCGGAAAAGGAGGGTGTAGTA 59.448 52.381 0.00 0.00 0.00 1.82
1008 1048 0.323957 GCGGAAAAGGAGGGTGTAGT 59.676 55.000 0.00 0.00 0.00 2.73
1009 1049 0.392595 GGCGGAAAAGGAGGGTGTAG 60.393 60.000 0.00 0.00 0.00 2.74
1010 1050 1.128809 TGGCGGAAAAGGAGGGTGTA 61.129 55.000 0.00 0.00 0.00 2.90
1011 1051 2.002018 TTGGCGGAAAAGGAGGGTGT 62.002 55.000 0.00 0.00 0.00 4.16
1012 1052 1.228429 TTGGCGGAAAAGGAGGGTG 60.228 57.895 0.00 0.00 0.00 4.61
1013 1053 1.074951 CTTGGCGGAAAAGGAGGGT 59.925 57.895 0.00 0.00 0.00 4.34
1014 1054 0.251165 TTCTTGGCGGAAAAGGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
1015 1055 1.616159 TTTCTTGGCGGAAAAGGAGG 58.384 50.000 3.54 0.00 33.04 4.30
1016 1056 2.360801 TGTTTTCTTGGCGGAAAAGGAG 59.639 45.455 15.15 0.00 43.12 3.69
1017 1057 2.100087 GTGTTTTCTTGGCGGAAAAGGA 59.900 45.455 15.15 6.01 43.12 3.36
1018 1058 2.469826 GTGTTTTCTTGGCGGAAAAGG 58.530 47.619 15.15 0.00 43.12 3.11
1019 1059 2.469826 GGTGTTTTCTTGGCGGAAAAG 58.530 47.619 15.15 0.00 43.12 2.27
1020 1060 1.137282 GGGTGTTTTCTTGGCGGAAAA 59.863 47.619 12.09 12.09 41.17 2.29
1021 1061 0.747852 GGGTGTTTTCTTGGCGGAAA 59.252 50.000 2.13 2.13 33.98 3.13
1022 1062 1.110518 GGGGTGTTTTCTTGGCGGAA 61.111 55.000 0.00 0.00 0.00 4.30
1023 1063 1.529713 GGGGTGTTTTCTTGGCGGA 60.530 57.895 0.00 0.00 0.00 5.54
1024 1064 2.570284 GGGGGTGTTTTCTTGGCGG 61.570 63.158 0.00 0.00 0.00 6.13
1025 1065 1.524008 GAGGGGGTGTTTTCTTGGCG 61.524 60.000 0.00 0.00 0.00 5.69
1026 1066 1.185618 GGAGGGGGTGTTTTCTTGGC 61.186 60.000 0.00 0.00 0.00 4.52
1027 1067 0.187361 TGGAGGGGGTGTTTTCTTGG 59.813 55.000 0.00 0.00 0.00 3.61
1028 1068 2.309136 ATGGAGGGGGTGTTTTCTTG 57.691 50.000 0.00 0.00 0.00 3.02
1029 1069 3.660669 TCTTATGGAGGGGGTGTTTTCTT 59.339 43.478 0.00 0.00 0.00 2.52
1030 1070 3.265489 TCTTATGGAGGGGGTGTTTTCT 58.735 45.455 0.00 0.00 0.00 2.52
1031 1071 3.732048 TCTTATGGAGGGGGTGTTTTC 57.268 47.619 0.00 0.00 0.00 2.29
1032 1072 3.336694 ACATCTTATGGAGGGGGTGTTTT 59.663 43.478 0.00 0.00 33.60 2.43
1033 1073 2.926329 ACATCTTATGGAGGGGGTGTTT 59.074 45.455 0.00 0.00 33.60 2.83
1034 1074 2.573463 ACATCTTATGGAGGGGGTGTT 58.427 47.619 0.00 0.00 33.60 3.32
1035 1075 2.286935 ACATCTTATGGAGGGGGTGT 57.713 50.000 0.00 0.00 33.60 4.16
1036 1076 2.780010 AGAACATCTTATGGAGGGGGTG 59.220 50.000 0.00 0.00 33.60 4.61
1037 1077 3.151542 AGAACATCTTATGGAGGGGGT 57.848 47.619 0.00 0.00 33.60 4.95
1038 1078 5.646692 TTTAGAACATCTTATGGAGGGGG 57.353 43.478 0.00 0.00 33.60 5.40
1063 1103 9.452065 GCGTGTATATACATCTGATTCGATTAT 57.548 33.333 18.27 0.00 38.63 1.28
1064 1104 8.455682 TGCGTGTATATACATCTGATTCGATTA 58.544 33.333 18.27 4.06 38.63 1.75
1065 1105 7.312899 TGCGTGTATATACATCTGATTCGATT 58.687 34.615 18.27 0.00 38.63 3.34
1066 1106 6.852664 TGCGTGTATATACATCTGATTCGAT 58.147 36.000 18.27 0.00 38.63 3.59
1067 1107 6.249035 TGCGTGTATATACATCTGATTCGA 57.751 37.500 18.27 4.10 38.63 3.71
1068 1108 6.927933 TTGCGTGTATATACATCTGATTCG 57.072 37.500 18.27 15.10 38.63 3.34
1071 1111 9.929180 ACTAAATTGCGTGTATATACATCTGAT 57.071 29.630 18.27 8.44 38.63 2.90
1072 1112 9.191995 CACTAAATTGCGTGTATATACATCTGA 57.808 33.333 18.27 6.63 38.63 3.27
1073 1113 8.978539 ACACTAAATTGCGTGTATATACATCTG 58.021 33.333 18.27 12.27 42.14 2.90
1074 1114 8.978539 CACACTAAATTGCGTGTATATACATCT 58.021 33.333 18.27 0.29 42.05 2.90
1075 1115 8.761497 ACACACTAAATTGCGTGTATATACATC 58.239 33.333 18.27 13.35 42.05 3.06
1076 1116 8.657074 ACACACTAAATTGCGTGTATATACAT 57.343 30.769 18.27 3.74 42.05 2.29
1077 1117 8.481974 AACACACTAAATTGCGTGTATATACA 57.518 30.769 11.62 11.62 42.05 2.29
1085 1313 4.795795 TGAACAAACACACTAAATTGCGTG 59.204 37.500 5.98 5.98 37.18 5.34
1088 1316 5.171337 CGAGTGAACAAACACACTAAATTGC 59.829 40.000 0.00 0.00 45.54 3.56
1096 1324 2.825086 AAGCGAGTGAACAAACACAC 57.175 45.000 0.00 0.00 42.45 3.82
1116 1344 4.147321 ACGAAGGGAGTACACAAAGACTA 58.853 43.478 0.00 0.00 0.00 2.59
1212 1472 7.147976 GGAGCAAAATGAATGAAACTACACTT 58.852 34.615 0.00 0.00 0.00 3.16
1220 1480 4.214545 ACGTACGGAGCAAAATGAATGAAA 59.785 37.500 21.06 0.00 0.00 2.69
1360 1625 1.384409 CGTACGTTCTTTGTGCCTACG 59.616 52.381 7.22 0.00 38.14 3.51
1400 1671 1.450312 GCCCTCGTCACCCTCATTG 60.450 63.158 0.00 0.00 0.00 2.82
1455 1726 3.566853 TAGTACTCGTCGGCGGCG 61.567 66.667 29.88 29.88 38.89 6.46
1717 1988 1.372087 GACAGTACGACGTCCCCGAT 61.372 60.000 10.58 0.00 37.88 4.18
1785 2056 3.305813 CGCACTTGTCCTTGGAGTTACTA 60.306 47.826 0.00 0.00 0.00 1.82
1788 2059 1.689813 TCGCACTTGTCCTTGGAGTTA 59.310 47.619 0.00 0.00 0.00 2.24
1795 2072 1.660575 CGTCGTCGCACTTGTCCTT 60.661 57.895 0.00 0.00 0.00 3.36
1882 2159 3.286404 CCAGGCAATGGTTCATGGA 57.714 52.632 0.00 0.00 44.91 3.41
2037 2314 0.390860 CCTCCATCTCCGCGAATTCT 59.609 55.000 8.23 0.00 0.00 2.40
2040 2317 1.742768 GTCCTCCATCTCCGCGAAT 59.257 57.895 8.23 0.00 0.00 3.34
2046 2323 1.817209 GGACACGTCCTCCATCTCC 59.183 63.158 9.04 0.00 46.16 3.71
2373 2650 2.064581 GTCCTGTATCCACCGGGCT 61.065 63.158 6.32 0.00 31.39 5.19
2692 2969 4.142160 GGAAGCTAAAATGGCCAAAGTAGG 60.142 45.833 10.96 0.00 0.00 3.18
2693 2970 4.706962 AGGAAGCTAAAATGGCCAAAGTAG 59.293 41.667 10.96 12.43 0.00 2.57
2694 2971 4.672899 AGGAAGCTAAAATGGCCAAAGTA 58.327 39.130 10.96 0.35 0.00 2.24
2695 2972 3.510459 AGGAAGCTAAAATGGCCAAAGT 58.490 40.909 10.96 0.00 0.00 2.66
2696 2973 4.498241 GAAGGAAGCTAAAATGGCCAAAG 58.502 43.478 10.96 6.46 0.00 2.77
2697 2974 3.056891 CGAAGGAAGCTAAAATGGCCAAA 60.057 43.478 10.96 0.00 0.00 3.28
2719 3009 1.750206 TCCCATGCATGCACACATTAC 59.250 47.619 25.37 0.00 32.87 1.89
2729 3019 3.751518 TGAGATTGAGATCCCATGCATG 58.248 45.455 20.19 20.19 32.44 4.06
2756 3046 3.482156 AATATTCTGCTCATCAGCCGT 57.518 42.857 0.00 0.00 46.26 5.68
2770 3060 8.196771 TGGTCATGAAAGTTGCCAATAATATTC 58.803 33.333 0.00 0.00 0.00 1.75
2906 3210 5.165676 CACATGGAGGAAAATTCACACATG 58.834 41.667 15.42 15.42 0.00 3.21
3072 3376 3.070159 GTCTTAGCATCCATAGGTCTGCA 59.930 47.826 13.07 0.00 35.85 4.41
3169 3473 2.599645 CTTCACCCCCATCTCCAGCG 62.600 65.000 0.00 0.00 0.00 5.18
3526 3830 0.460109 TGACATCCGGTGCTTCATCG 60.460 55.000 0.00 0.00 37.76 3.84


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

AutoCloner maintained by Alex Coulton.