Multiple sequence alignment - TraesCS7D01G106000

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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 TraesCS7D01G106000 chr7D 100.000 4111 0 0 1 4111 64010871 64014981 0.000000e+00 7592
1 TraesCS7D01G106000 chr7D 84.475 219 14 5 3826 4044 64005871 64005673 9.010000e-47 198
2 TraesCS7D01G106000 chr7D 97.561 82 1 1 1008 1089 64011810 64011890 5.540000e-29 139
3 TraesCS7D01G106000 chr7D 97.561 82 1 1 940 1020 64011878 64011959 5.540000e-29 139
4 TraesCS7D01G106000 chr7B 93.346 3126 134 28 1008 4094 5059071 5062161 0.000000e+00 4553
5 TraesCS7D01G106000 chr7B 86.927 872 47 36 189 1020 5058308 5059152 0.000000e+00 917
6 TraesCS7D01G106000 chr7B 94.643 112 6 0 3904 4015 5052607 5052496 1.520000e-39 174
7 TraesCS7D01G106000 chr7B 77.151 337 40 15 3676 4010 5159965 5160266 1.180000e-35 161
8 TraesCS7D01G106000 chr7A 96.361 2116 75 2 1008 3122 67673426 67671312 0.000000e+00 3480
9 TraesCS7D01G106000 chr7A 89.631 1003 47 24 3121 4093 67671348 67670373 0.000000e+00 1223
10 TraesCS7D01G106000 chr7A 87.674 860 48 23 189 1020 67674174 67673345 0.000000e+00 948
11 TraesCS7D01G106000 chr7A 77.020 557 81 28 1054 1602 629879594 629879077 4.050000e-70 276
12 TraesCS7D01G106000 chr7A 87.831 189 18 2 2 189 67674407 67674223 2.490000e-52 217
13 TraesCS7D01G106000 chr2B 79.832 595 87 17 1107 1698 66034137 66033573 1.780000e-108 403
14 TraesCS7D01G106000 chr2B 79.669 605 88 19 1101 1698 708391507 708392083 1.780000e-108 403
15 TraesCS7D01G106000 chr2B 90.476 105 10 0 1607 1711 128531570 128531466 5.540000e-29 139
16 TraesCS7D01G106000 chr2B 89.524 105 11 0 1607 1711 775419168 775419272 2.580000e-27 134
17 TraesCS7D01G106000 chr2A 78.428 547 84 18 1125 1669 764661268 764660754 3.960000e-85 326
18 TraesCS7D01G106000 chr4A 81.053 285 45 7 1417 1698 714217647 714217925 6.920000e-53 219
19 TraesCS7D01G106000 chr6B 78.689 366 47 21 1341 1706 172276947 172277281 8.950000e-52 215
20 TraesCS7D01G106000 chr1B 89.524 105 11 0 1607 1711 189691025 189690921 2.580000e-27 134


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 TraesCS7D01G106000 chr7D 64010871 64014981 4110 False 2623.333333 7592 98.37400 1 4111 3 chr7D.!!$F1 4110
1 TraesCS7D01G106000 chr7B 5058308 5062161 3853 False 2735.000000 4553 90.13650 189 4094 2 chr7B.!!$F2 3905
2 TraesCS7D01G106000 chr7A 67670373 67674407 4034 True 1467.000000 3480 90.37425 2 4093 4 chr7A.!!$R2 4091
3 TraesCS7D01G106000 chr7A 629879077 629879594 517 True 276.000000 276 77.02000 1054 1602 1 chr7A.!!$R1 548
4 TraesCS7D01G106000 chr2B 66033573 66034137 564 True 403.000000 403 79.83200 1107 1698 1 chr2B.!!$R1 591
5 TraesCS7D01G106000 chr2B 708391507 708392083 576 False 403.000000 403 79.66900 1101 1698 1 chr2B.!!$F1 597
6 TraesCS7D01G106000 chr2A 764660754 764661268 514 True 326.000000 326 78.42800 1125 1669 1 chr2A.!!$R1 544

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
139 141 0.473755 TCACACATTGACACCTGCCT 59.526 50.0 0.00 0.00 0.0 4.75 F
860 973 0.613777 GGAGGAGAAGAAAGCCGGAA 59.386 55.0 5.05 0.00 0.0 4.30 F
2217 2350 0.762082 TGGGATCAGGAGGCTAGCTG 60.762 60.0 15.72 4.91 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2216 1.131693 CGCAATTCTTGATGCAGAGCA 59.868 47.619 0.0 0.00 44.86 4.26 R
2384 2517 0.605319 GATCACTTCCGGTTGTGCCA 60.605 55.000 19.5 8.42 36.97 4.92 R
3879 4054 0.175073 GTACTTCTGTAGTGGCGGGG 59.825 60.000 0.0 0.00 37.73 5.73 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
37 38 8.849168 TCTACCGTATTATTTCCGTATTTCTGA 58.151 33.333 0.00 0.00 0.00 3.27
39 40 8.897872 ACCGTATTATTTCCGTATTTCTGAAT 57.102 30.769 0.00 0.00 0.00 2.57
41 42 9.594038 CCGTATTATTTCCGTATTTCTGAATTG 57.406 33.333 0.00 0.00 0.00 2.32
42 43 9.103048 CGTATTATTTCCGTATTTCTGAATTGC 57.897 33.333 0.00 0.00 0.00 3.56
46 47 6.817765 TTTCCGTATTTCTGAATTGCTTCT 57.182 33.333 0.00 0.00 32.29 2.85
48 49 5.487433 TCCGTATTTCTGAATTGCTTCTCA 58.513 37.500 0.00 0.00 32.29 3.27
49 50 5.937540 TCCGTATTTCTGAATTGCTTCTCAA 59.062 36.000 0.00 0.00 39.32 3.02
50 51 6.599244 TCCGTATTTCTGAATTGCTTCTCAAT 59.401 34.615 0.00 0.00 46.82 2.57
59 61 5.246656 TGAATTGCTTCTCAATGAAATGGGT 59.753 36.000 0.00 0.00 44.23 4.51
101 103 2.192263 GACCCCCATCTGAGAAACTCT 58.808 52.381 0.00 0.00 0.00 3.24
132 134 7.818446 CCATAATCCAATTTTCACACATTGACA 59.182 33.333 0.00 0.00 32.91 3.58
136 138 4.746115 CCAATTTTCACACATTGACACCTG 59.254 41.667 0.00 0.00 32.91 4.00
137 139 3.435105 TTTTCACACATTGACACCTGC 57.565 42.857 0.00 0.00 32.26 4.85
138 140 1.317613 TTCACACATTGACACCTGCC 58.682 50.000 0.00 0.00 32.26 4.85
139 141 0.473755 TCACACATTGACACCTGCCT 59.526 50.000 0.00 0.00 0.00 4.75
140 142 1.696884 TCACACATTGACACCTGCCTA 59.303 47.619 0.00 0.00 0.00 3.93
141 143 2.105649 TCACACATTGACACCTGCCTAA 59.894 45.455 0.00 0.00 0.00 2.69
142 144 3.084039 CACACATTGACACCTGCCTAAT 58.916 45.455 0.00 0.00 0.00 1.73
143 145 3.127548 CACACATTGACACCTGCCTAATC 59.872 47.826 0.00 0.00 0.00 1.75
144 146 2.352651 CACATTGACACCTGCCTAATCG 59.647 50.000 0.00 0.00 0.00 3.34
166 168 3.278574 GCTACCAAACATGCATAGGTCA 58.721 45.455 13.53 3.60 33.91 4.02
167 169 3.065371 GCTACCAAACATGCATAGGTCAC 59.935 47.826 13.53 6.10 33.91 3.67
168 170 2.446435 ACCAAACATGCATAGGTCACC 58.554 47.619 0.00 0.00 0.00 4.02
183 185 1.122632 TCACCGCCTCCAACCAACTA 61.123 55.000 0.00 0.00 0.00 2.24
245 301 1.484227 CGAGACGAGACGAGATCGCT 61.484 60.000 1.39 0.59 43.91 4.93
274 330 0.666577 CGAGGACGAGAAACCACCAC 60.667 60.000 0.00 0.00 42.66 4.16
286 342 4.974721 CACCACCAGCACACCCCC 62.975 72.222 0.00 0.00 0.00 5.40
345 401 2.990967 CCGCAGCACCCAACCAAT 60.991 61.111 0.00 0.00 0.00 3.16
360 420 2.843701 ACCAATCAATCCAGAGATCGC 58.156 47.619 0.00 0.00 0.00 4.58
365 425 1.299468 AATCCAGAGATCGCGCGAC 60.299 57.895 37.37 27.03 0.00 5.19
369 429 2.824489 AGAGATCGCGCGACCTCA 60.824 61.111 45.30 23.05 37.24 3.86
370 430 2.652496 GAGATCGCGCGACCTCAC 60.652 66.667 41.71 27.58 34.92 3.51
371 431 3.114647 GAGATCGCGCGACCTCACT 62.115 63.158 41.71 29.45 34.92 3.41
372 432 2.652496 GATCGCGCGACCTCACTC 60.652 66.667 37.37 23.63 0.00 3.51
634 734 4.631377 GGAAAAGGATAAAACAATGGCAGC 59.369 41.667 0.00 0.00 0.00 5.25
734 834 1.546998 GGGGAAGAAAAGGAAAGCGGA 60.547 52.381 0.00 0.00 0.00 5.54
768 874 3.068165 CGAGTATATCACTTCCCTGTGCA 59.932 47.826 0.00 0.00 37.72 4.57
770 876 2.315925 ATATCACTTCCCTGTGCACG 57.684 50.000 13.13 7.03 37.81 5.34
772 878 3.357079 CACTTCCCTGTGCACGCC 61.357 66.667 13.13 0.00 0.00 5.68
773 879 3.560251 ACTTCCCTGTGCACGCCT 61.560 61.111 13.13 0.00 0.00 5.52
775 881 4.329545 TTCCCTGTGCACGCCTCC 62.330 66.667 13.13 0.00 0.00 4.30
778 884 4.767255 CCTGTGCACGCCTCCCTC 62.767 72.222 13.13 0.00 0.00 4.30
793 903 4.862823 CTCCTCCGTCCCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
796 906 2.609610 CTCCGTCCCCTCCCCAAA 60.610 66.667 0.00 0.00 0.00 3.28
797 907 2.001269 CTCCGTCCCCTCCCCAAAT 61.001 63.158 0.00 0.00 0.00 2.32
799 909 2.595655 CGTCCCCTCCCCAAATCC 59.404 66.667 0.00 0.00 0.00 3.01
800 910 2.595655 GTCCCCTCCCCAAATCCG 59.404 66.667 0.00 0.00 0.00 4.18
801 911 2.126372 TCCCCTCCCCAAATCCGT 59.874 61.111 0.00 0.00 0.00 4.69
805 915 2.595655 CTCCCCAAATCCGTCCCC 59.404 66.667 0.00 0.00 0.00 4.81
806 916 2.001269 CTCCCCAAATCCGTCCCCT 61.001 63.158 0.00 0.00 0.00 4.79
859 972 1.265454 GGGAGGAGAAGAAAGCCGGA 61.265 60.000 5.05 0.00 0.00 5.14
860 973 0.613777 GGAGGAGAAGAAAGCCGGAA 59.386 55.000 5.05 0.00 0.00 4.30
873 986 2.202518 CGGAAGCTTTGCGGCATG 60.203 61.111 2.28 0.91 41.03 4.06
874 987 2.182537 GGAAGCTTTGCGGCATGG 59.817 61.111 2.28 0.54 34.17 3.66
875 988 2.507769 GAAGCTTTGCGGCATGGC 60.508 61.111 9.69 9.69 34.17 4.40
876 989 4.424566 AAGCTTTGCGGCATGGCG 62.425 61.111 34.70 34.70 35.06 5.69
879 992 4.183686 CTTTGCGGCATGGCGGAG 62.184 66.667 37.92 23.42 35.06 4.63
957 1070 3.574445 CCGCTGCTGCTGCTCATC 61.574 66.667 25.43 1.13 40.48 2.92
958 1071 3.574445 CGCTGCTGCTGCTCATCC 61.574 66.667 25.43 0.47 40.48 3.51
959 1072 2.124653 GCTGCTGCTGCTCATCCT 60.125 61.111 22.10 0.00 40.48 3.24
960 1073 2.181521 GCTGCTGCTGCTCATCCTC 61.182 63.158 22.10 0.00 40.48 3.71
961 1074 1.883544 CTGCTGCTGCTCATCCTCG 60.884 63.158 17.00 0.00 40.48 4.63
962 1075 2.588314 GCTGCTGCTCATCCTCGG 60.588 66.667 8.53 0.00 36.03 4.63
963 1076 2.588314 CTGCTGCTCATCCTCGGC 60.588 66.667 0.00 0.00 35.26 5.54
964 1077 3.079478 TGCTGCTCATCCTCGGCT 61.079 61.111 0.00 0.00 35.69 5.52
965 1078 2.280052 GCTGCTCATCCTCGGCTC 60.280 66.667 0.00 0.00 0.00 4.70
966 1079 2.420890 CTGCTCATCCTCGGCTCC 59.579 66.667 0.00 0.00 0.00 4.70
967 1080 3.157252 TGCTCATCCTCGGCTCCC 61.157 66.667 0.00 0.00 0.00 4.30
968 1081 2.841988 GCTCATCCTCGGCTCCCT 60.842 66.667 0.00 0.00 0.00 4.20
969 1082 2.866726 GCTCATCCTCGGCTCCCTC 61.867 68.421 0.00 0.00 0.00 4.30
970 1083 2.123251 TCATCCTCGGCTCCCTCC 60.123 66.667 0.00 0.00 0.00 4.30
971 1084 2.444706 CATCCTCGGCTCCCTCCA 60.445 66.667 0.00 0.00 0.00 3.86
972 1085 2.444895 ATCCTCGGCTCCCTCCAC 60.445 66.667 0.00 0.00 0.00 4.02
975 1088 3.827898 CTCGGCTCCCTCCACGAC 61.828 72.222 0.00 0.00 0.00 4.34
2168 2301 1.372128 GAGGCTTGCCAAGTTTGCG 60.372 57.895 14.54 0.00 0.00 4.85
2217 2350 0.762082 TGGGATCAGGAGGCTAGCTG 60.762 60.000 15.72 4.91 0.00 4.24
2225 2358 4.154347 AGGCTAGCTGTGGCGCTC 62.154 66.667 15.72 1.21 44.37 5.03
2384 2517 4.349503 TCCAGCTGCGTGGCCAAT 62.350 61.111 7.24 0.00 37.53 3.16
2498 2631 8.551682 AAATGGATAATTATGAAAGCTGGGAA 57.448 30.769 1.78 0.00 0.00 3.97
2597 2730 2.538437 CCTGTGCTTGAGAAGATCTCG 58.462 52.381 0.00 0.00 46.25 4.04
2642 2775 1.358725 CGTGTCCGCGTCCATTTCAT 61.359 55.000 4.92 0.00 0.00 2.57
2729 2862 2.270850 GAGGCGGTGGGTTATGCA 59.729 61.111 0.00 0.00 0.00 3.96
2816 2949 5.120674 CGAGTCATTGCTGAGTTTGTATGAA 59.879 40.000 0.00 0.00 35.12 2.57
2885 3018 4.170062 CTGCCAGCGGTCGCATTG 62.170 66.667 17.71 7.77 44.88 2.82
3014 3147 2.667470 GAGGACTACTATCCAGCACCA 58.333 52.381 0.00 0.00 41.73 4.17
3173 3306 0.476338 TGGGTGCACCATTACAGTGT 59.524 50.000 35.78 0.00 46.80 3.55
3266 3421 5.237815 TGAGTGTAGTAACTGGAATTGCTG 58.762 41.667 2.24 2.24 0.00 4.41
3346 3501 8.103924 CGAATCTTTATTTGCATTCCTTTTTCG 58.896 33.333 0.00 0.00 0.00 3.46
3418 3573 6.072783 GGAGGCAAGATGATAAGTTAGCATTC 60.073 42.308 14.50 7.26 34.49 2.67
3621 3777 3.204526 CTCTCATTGTGAAGATGGCCTC 58.795 50.000 3.32 0.00 0.00 4.70
3668 3825 0.169009 GAATGGAGAAACTGGTGCGC 59.831 55.000 0.00 0.00 0.00 6.09
3673 3830 1.438651 GAGAAACTGGTGCGCACATA 58.561 50.000 38.60 26.21 0.00 2.29
3724 3884 2.996621 GCTGTGTCCTTGTGCTTACTAG 59.003 50.000 0.00 0.00 0.00 2.57
3751 3918 0.469705 TTTGCCTTGCATCCACAGGT 60.470 50.000 3.40 0.00 38.76 4.00
3756 3923 1.542915 CCTTGCATCCACAGGTTTGAG 59.457 52.381 0.00 0.00 0.00 3.02
3760 3927 1.135199 GCATCCACAGGTTTGAGCATG 60.135 52.381 0.00 0.00 0.00 4.06
3769 3936 4.202050 ACAGGTTTGAGCATGAGTTCAAAC 60.202 41.667 26.26 26.26 39.94 2.93
3792 3959 2.950433 CATGGCAAACAGGCTTACAAG 58.050 47.619 0.00 0.00 44.55 3.16
3812 3985 7.406031 ACAAGCTGCTATACTAAGTACTGAA 57.594 36.000 0.90 0.00 0.00 3.02
3839 4014 5.300752 AGATGAACTTGTAACACCTGACAG 58.699 41.667 0.00 0.00 0.00 3.51
3851 4026 4.446371 ACACCTGACAGAAGAAAGTTCAG 58.554 43.478 3.32 0.00 0.00 3.02
3878 4053 5.332883 CGCCATTAAGAATTCAGTCTGATCG 60.333 44.000 8.44 4.03 0.00 3.69
3879 4054 5.559799 GCCATTAAGAATTCAGTCTGATCGC 60.560 44.000 8.44 0.00 0.00 4.58
3880 4055 5.049818 CCATTAAGAATTCAGTCTGATCGCC 60.050 44.000 8.44 0.00 0.00 5.54
3882 4057 1.139853 AGAATTCAGTCTGATCGCCCC 59.860 52.381 8.44 0.00 0.00 5.80
3883 4058 0.179073 AATTCAGTCTGATCGCCCCG 60.179 55.000 2.68 0.00 0.00 5.73
3884 4059 2.650813 ATTCAGTCTGATCGCCCCGC 62.651 60.000 2.68 0.00 0.00 6.13
3885 4060 4.899239 CAGTCTGATCGCCCCGCC 62.899 72.222 0.00 0.00 0.00 6.13
3889 4064 3.536917 CTGATCGCCCCGCCACTA 61.537 66.667 0.00 0.00 0.00 2.74
3890 4065 3.792053 CTGATCGCCCCGCCACTAC 62.792 68.421 0.00 0.00 0.00 2.73
3891 4066 3.845259 GATCGCCCCGCCACTACA 61.845 66.667 0.00 0.00 0.00 2.74
3892 4067 3.792053 GATCGCCCCGCCACTACAG 62.792 68.421 0.00 0.00 0.00 2.74
3894 4069 4.077184 CGCCCCGCCACTACAGAA 62.077 66.667 0.00 0.00 0.00 3.02
3895 4070 2.125106 GCCCCGCCACTACAGAAG 60.125 66.667 0.00 0.00 0.00 2.85
3902 4077 2.159366 CCGCCACTACAGAAGTACAGAG 60.159 54.545 0.00 0.00 35.76 3.35
3952 4127 2.494471 TGCAGGCATCAAAGATCAAAGG 59.506 45.455 0.00 0.00 0.00 3.11
3995 4171 0.468648 CAGCCCATCATCAGAGCAGA 59.531 55.000 0.00 0.00 0.00 4.26
3999 4175 2.288948 GCCCATCATCAGAGCAGACTAG 60.289 54.545 0.00 0.00 0.00 2.57
4070 4246 2.941210 GGAGTGGTTCCGCAAATCA 58.059 52.632 5.19 0.00 35.91 2.57
4071 4247 1.463674 GGAGTGGTTCCGCAAATCAT 58.536 50.000 5.19 0.00 35.91 2.45
4094 4270 1.625315 CATGACAAGGAGGACAGGACA 59.375 52.381 0.00 0.00 0.00 4.02
4095 4271 1.342074 TGACAAGGAGGACAGGACAG 58.658 55.000 0.00 0.00 0.00 3.51
4096 4272 0.610687 GACAAGGAGGACAGGACAGG 59.389 60.000 0.00 0.00 0.00 4.00
4097 4273 0.191064 ACAAGGAGGACAGGACAGGA 59.809 55.000 0.00 0.00 0.00 3.86
4098 4274 0.610687 CAAGGAGGACAGGACAGGAC 59.389 60.000 0.00 0.00 0.00 3.85
4099 4275 0.900647 AAGGAGGACAGGACAGGACG 60.901 60.000 0.00 0.00 0.00 4.79
4100 4276 2.352032 GGAGGACAGGACAGGACGG 61.352 68.421 0.00 0.00 0.00 4.79
4101 4277 1.304217 GAGGACAGGACAGGACGGA 60.304 63.158 0.00 0.00 0.00 4.69
4102 4278 1.304547 AGGACAGGACAGGACGGAG 60.305 63.158 0.00 0.00 0.00 4.63
4103 4279 1.304217 GGACAGGACAGGACGGAGA 60.304 63.158 0.00 0.00 0.00 3.71
4104 4280 1.316706 GGACAGGACAGGACGGAGAG 61.317 65.000 0.00 0.00 0.00 3.20
4105 4281 1.304547 ACAGGACAGGACGGAGAGG 60.305 63.158 0.00 0.00 0.00 3.69
4106 4282 2.363147 AGGACAGGACGGAGAGGC 60.363 66.667 0.00 0.00 0.00 4.70
4107 4283 3.827898 GGACAGGACGGAGAGGCG 61.828 72.222 0.00 0.00 0.00 5.52
4108 4284 3.063084 GACAGGACGGAGAGGCGT 61.063 66.667 0.00 0.00 0.00 5.68
4110 4286 4.803426 CAGGACGGAGAGGCGTGC 62.803 72.222 0.00 0.00 36.90 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.736023 GAAGCAATTCAGAAATACGGAAATAAT 57.264 29.630 0.00 0.00 36.43 1.28
37 38 5.246656 TCACCCATTTCATTGAGAAGCAATT 59.753 36.000 0.00 0.00 44.68 2.32
39 40 4.151121 TCACCCATTTCATTGAGAAGCAA 58.849 39.130 0.00 0.00 41.53 3.91
41 42 4.460382 TCTTCACCCATTTCATTGAGAAGC 59.540 41.667 0.00 0.00 37.57 3.86
42 43 6.770746 ATCTTCACCCATTTCATTGAGAAG 57.229 37.500 0.00 0.00 37.57 2.85
43 44 6.950041 AGAATCTTCACCCATTTCATTGAGAA 59.050 34.615 0.00 0.00 0.00 2.87
46 47 5.653769 GGAGAATCTTCACCCATTTCATTGA 59.346 40.000 0.00 0.00 32.58 2.57
59 61 2.191400 CAGGTCAGGGGAGAATCTTCA 58.809 52.381 0.00 0.00 33.73 3.02
74 76 3.083997 AGATGGGGGTCGCAGGTC 61.084 66.667 0.00 0.00 0.00 3.85
101 103 6.268617 TGTGTGAAAATTGGATTATGGTTGGA 59.731 34.615 0.00 0.00 0.00 3.53
137 139 2.290641 GCATGTTTGGTAGCCGATTAGG 59.709 50.000 0.00 0.00 44.97 2.69
138 140 2.942376 TGCATGTTTGGTAGCCGATTAG 59.058 45.455 0.00 0.00 0.00 1.73
139 141 2.992593 TGCATGTTTGGTAGCCGATTA 58.007 42.857 0.00 0.00 0.00 1.75
140 142 1.832883 TGCATGTTTGGTAGCCGATT 58.167 45.000 0.00 0.00 0.00 3.34
141 143 2.057137 ATGCATGTTTGGTAGCCGAT 57.943 45.000 0.00 0.00 0.00 4.18
142 144 2.560504 CTATGCATGTTTGGTAGCCGA 58.439 47.619 10.16 0.00 0.00 5.54
143 145 1.603802 CCTATGCATGTTTGGTAGCCG 59.396 52.381 10.16 0.00 0.00 5.52
144 146 2.618709 GACCTATGCATGTTTGGTAGCC 59.381 50.000 10.16 0.00 0.00 3.93
157 159 2.109181 GGAGGCGGTGACCTATGC 59.891 66.667 0.00 0.00 41.32 3.14
166 168 1.677552 CTAGTTGGTTGGAGGCGGT 59.322 57.895 0.00 0.00 0.00 5.68
167 169 1.745489 GCTAGTTGGTTGGAGGCGG 60.745 63.158 0.00 0.00 0.00 6.13
168 170 1.745489 GGCTAGTTGGTTGGAGGCG 60.745 63.158 0.00 0.00 0.00 5.52
274 330 0.967380 GAATGAAGGGGGTGTGCTGG 60.967 60.000 0.00 0.00 0.00 4.85
286 342 5.163478 GGGGGAGTTGAATGAATGAATGAAG 60.163 44.000 0.00 0.00 0.00 3.02
336 392 3.370840 TCTCTGGATTGATTGGTTGGG 57.629 47.619 0.00 0.00 0.00 4.12
345 401 1.299392 CGCGCGATCTCTGGATTGA 60.299 57.895 28.94 0.00 35.83 2.57
360 420 2.126307 CAGGTGAGTGAGGTCGCG 60.126 66.667 0.00 0.00 0.00 5.87
634 734 5.047943 CCCTTCGTATATTGTACTCCTCCTG 60.048 48.000 0.00 0.00 0.00 3.86
734 834 0.179026 TATACTCGACAGCTCCGCCT 60.179 55.000 0.45 0.00 0.00 5.52
772 878 3.742248 GAGGGGACGGAGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
773 879 3.752167 GAGGGGACGGAGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
775 881 4.862823 GGGAGGGGACGGAGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
778 884 4.733725 TTGGGGAGGGGACGGAGG 62.734 72.222 0.00 0.00 0.00 4.30
780 886 1.999002 GATTTGGGGAGGGGACGGA 60.999 63.158 0.00 0.00 0.00 4.69
793 903 1.153429 GGACGAGGGGACGGATTTG 60.153 63.158 0.00 0.00 37.61 2.32
794 904 1.305887 AGGACGAGGGGACGGATTT 60.306 57.895 0.00 0.00 37.61 2.17
796 906 2.123812 GAGGACGAGGGGACGGAT 60.124 66.667 0.00 0.00 37.61 4.18
797 907 4.437587 GGAGGACGAGGGGACGGA 62.438 72.222 0.00 0.00 37.61 4.69
859 972 4.424566 CGCCATGCCGCAAAGCTT 62.425 61.111 14.08 0.00 0.00 3.74
949 1062 2.420890 GGAGCCGAGGATGAGCAG 59.579 66.667 0.00 0.00 0.00 4.24
950 1063 3.157252 GGGAGCCGAGGATGAGCA 61.157 66.667 0.00 0.00 0.00 4.26
951 1064 2.841988 AGGGAGCCGAGGATGAGC 60.842 66.667 0.00 0.00 0.00 4.26
954 1067 2.444706 TGGAGGGAGCCGAGGATG 60.445 66.667 0.00 0.00 0.00 3.51
955 1068 2.444895 GTGGAGGGAGCCGAGGAT 60.445 66.667 0.00 0.00 0.00 3.24
958 1071 3.827898 GTCGTGGAGGGAGCCGAG 61.828 72.222 0.00 0.00 0.00 4.63
1994 2127 1.987855 CCCCAGCGTCAGGACCTTA 60.988 63.158 0.00 0.00 0.00 2.69
2083 2216 1.131693 CGCAATTCTTGATGCAGAGCA 59.868 47.619 0.00 0.00 44.86 4.26
2225 2358 1.815421 CTCCTTCAATGTCGGCCGG 60.815 63.158 27.83 8.93 0.00 6.13
2231 2364 3.070018 CACACTGACCTCCTTCAATGTC 58.930 50.000 0.00 0.00 33.78 3.06
2384 2517 0.605319 GATCACTTCCGGTTGTGCCA 60.605 55.000 19.50 8.42 36.97 4.92
2597 2730 1.694696 AGATCGCCCTCCACCTTAATC 59.305 52.381 0.00 0.00 0.00 1.75
2651 2784 1.068541 CCAAGGTCGCTTAAGCCAAAC 60.069 52.381 21.53 15.96 37.91 2.93
2685 2818 2.238521 GTCCAGTTTCATCTTGGCCAA 58.761 47.619 19.25 19.25 0.00 4.52
2816 2949 3.391382 GGCGGCCAGTAGTCCAGT 61.391 66.667 15.62 0.00 0.00 4.00
2883 3016 0.321564 CCGATGGAGTGCTGGAACAA 60.322 55.000 0.00 0.00 38.70 2.83
2885 3018 0.741221 GTCCGATGGAGTGCTGGAAC 60.741 60.000 0.00 0.00 29.39 3.62
3014 3147 4.400567 TCTGTGATCATCATGTCGTTCTCT 59.599 41.667 0.00 0.00 0.00 3.10
3266 3421 8.855110 TCTTCTACTCTTATCATCAATGGACTC 58.145 37.037 0.00 0.00 0.00 3.36
3346 3501 8.927721 GTCTCTCTCTTATTACACCAGAAAAAC 58.072 37.037 0.00 0.00 0.00 2.43
3418 3573 2.790433 TCCCTTGACAAAATTCCCTCG 58.210 47.619 0.00 0.00 0.00 4.63
3668 3825 1.482182 TCCCAGTGCTGCTACTATGTG 59.518 52.381 0.00 0.00 0.00 3.21
3673 3830 1.059913 AACTTCCCAGTGCTGCTACT 58.940 50.000 0.00 0.00 31.60 2.57
3724 3884 1.200948 GATGCAAGGCAAAGGAGACAC 59.799 52.381 0.00 0.00 43.62 3.67
3751 3918 3.380954 TGCAGTTTGAACTCATGCTCAAA 59.619 39.130 11.24 11.24 38.81 2.69
3756 3923 2.602878 CCATGCAGTTTGAACTCATGC 58.397 47.619 19.54 12.10 39.92 4.06
3760 3927 2.796593 GTTTGCCATGCAGTTTGAACTC 59.203 45.455 0.00 0.00 40.61 3.01
3769 3936 0.889994 TAAGCCTGTTTGCCATGCAG 59.110 50.000 0.00 0.00 40.61 4.41
3785 3952 8.622157 TCAGTACTTAGTATAGCAGCTTGTAAG 58.378 37.037 0.00 5.80 0.00 2.34
3789 3956 8.759641 CATTTCAGTACTTAGTATAGCAGCTTG 58.240 37.037 0.00 0.00 0.00 4.01
3790 3957 8.696374 TCATTTCAGTACTTAGTATAGCAGCTT 58.304 33.333 0.00 0.00 0.00 3.74
3792 3959 8.353684 TCTCATTTCAGTACTTAGTATAGCAGC 58.646 37.037 0.00 0.00 0.00 5.25
3800 3967 9.429359 CAAGTTCATCTCATTTCAGTACTTAGT 57.571 33.333 0.00 0.00 0.00 2.24
3803 3976 9.778741 TTACAAGTTCATCTCATTTCAGTACTT 57.221 29.630 0.00 0.00 0.00 2.24
3812 3985 6.428159 GTCAGGTGTTACAAGTTCATCTCATT 59.572 38.462 0.00 0.00 0.00 2.57
3839 4014 0.889186 TGGCGGGCTGAACTTTCTTC 60.889 55.000 0.00 0.00 0.00 2.87
3851 4026 2.024414 ACTGAATTCTTAATGGCGGGC 58.976 47.619 7.05 0.00 0.00 6.13
3878 4053 1.610554 TACTTCTGTAGTGGCGGGGC 61.611 60.000 0.00 0.00 37.73 5.80
3879 4054 0.175073 GTACTTCTGTAGTGGCGGGG 59.825 60.000 0.00 0.00 37.73 5.73
3880 4055 0.892755 TGTACTTCTGTAGTGGCGGG 59.107 55.000 0.00 0.00 37.73 6.13
3882 4057 2.488545 ACTCTGTACTTCTGTAGTGGCG 59.511 50.000 0.00 0.00 37.73 5.69
3883 4058 3.839293 CACTCTGTACTTCTGTAGTGGC 58.161 50.000 0.00 0.00 37.73 5.01
3884 4059 3.508012 AGCACTCTGTACTTCTGTAGTGG 59.492 47.826 0.00 0.00 37.73 4.00
3885 4060 4.216472 TCAGCACTCTGTACTTCTGTAGTG 59.784 45.833 0.00 0.00 41.10 2.74
3886 4061 4.399219 TCAGCACTCTGTACTTCTGTAGT 58.601 43.478 0.00 0.00 41.10 2.73
3887 4062 5.378292 TTCAGCACTCTGTACTTCTGTAG 57.622 43.478 0.00 0.00 41.10 2.74
3888 4063 5.784578 TTTCAGCACTCTGTACTTCTGTA 57.215 39.130 0.00 0.00 41.10 2.74
3889 4064 4.672587 TTTCAGCACTCTGTACTTCTGT 57.327 40.909 0.00 0.00 41.10 3.41
3890 4065 7.386299 AGTTAATTTCAGCACTCTGTACTTCTG 59.614 37.037 0.00 0.00 41.10 3.02
3891 4066 7.445945 AGTTAATTTCAGCACTCTGTACTTCT 58.554 34.615 0.00 0.00 41.10 2.85
3892 4067 7.659652 AGTTAATTTCAGCACTCTGTACTTC 57.340 36.000 0.00 0.00 41.10 3.01
3893 4068 8.451908 AAAGTTAATTTCAGCACTCTGTACTT 57.548 30.769 0.00 0.00 41.10 2.24
3894 4069 8.089115 GAAAGTTAATTTCAGCACTCTGTACT 57.911 34.615 0.00 0.00 45.63 2.73
3952 4127 1.163554 CTTGGACCTTGCAGAAGCTC 58.836 55.000 0.00 0.00 42.74 4.09
4014 4190 4.748857 GCCTTTGGGTTAACAAGTACTCCT 60.749 45.833 8.10 0.00 34.45 3.69
4015 4191 3.504906 GCCTTTGGGTTAACAAGTACTCC 59.495 47.826 8.10 0.00 34.45 3.85
4016 4192 3.504906 GGCCTTTGGGTTAACAAGTACTC 59.495 47.826 8.10 0.00 34.45 2.59
4017 4193 3.493334 GGCCTTTGGGTTAACAAGTACT 58.507 45.455 8.10 0.00 34.45 2.73
4018 4194 2.559668 GGGCCTTTGGGTTAACAAGTAC 59.440 50.000 8.10 0.00 34.45 2.73
4019 4195 2.491271 GGGGCCTTTGGGTTAACAAGTA 60.491 50.000 8.10 0.00 34.45 2.24
4020 4196 1.712056 GGGCCTTTGGGTTAACAAGT 58.288 50.000 8.10 0.00 34.45 3.16
4021 4197 0.973632 GGGGCCTTTGGGTTAACAAG 59.026 55.000 8.10 2.70 34.45 3.16
4022 4198 0.828343 CGGGGCCTTTGGGTTAACAA 60.828 55.000 8.10 0.00 34.45 2.83
4070 4246 2.437281 CCTGTCCTCCTTGTCATGCTAT 59.563 50.000 0.00 0.00 0.00 2.97
4071 4247 1.833630 CCTGTCCTCCTTGTCATGCTA 59.166 52.381 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.