Multiple sequence alignment - TraesCS6B01G217800

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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 TraesCS6B01G217800 chr6B 100.000 3100 0 0 1 3100 299826879 299823780 0.000000e+00 5725.0
1 TraesCS6B01G217800 chr6B 90.607 2140 174 18 126 2242 299619083 299616948 0.000000e+00 2813.0
2 TraesCS6B01G217800 chr6B 92.275 466 34 1 2245 2708 299602798 299602333 0.000000e+00 660.0
3 TraesCS6B01G217800 chr6B 95.775 142 5 1 2747 2887 299602335 299602194 1.020000e-55 228.0
4 TraesCS6B01G217800 chr6B 100.000 100 0 0 3547 3646 299823333 299823234 6.220000e-43 185.0
5 TraesCS6B01G217800 chr6B 86.179 123 6 7 709 822 403890798 403890678 4.940000e-24 122.0
6 TraesCS6B01G217800 chr6D 91.819 2787 197 19 126 2887 162953844 162956624 0.000000e+00 3855.0
7 TraesCS6B01G217800 chr6A 90.828 2475 180 25 438 2887 222678559 222681011 0.000000e+00 3269.0
8 TraesCS6B01G217800 chr6A 95.865 1427 49 2 1470 2887 222135373 222136798 0.000000e+00 2300.0
9 TraesCS6B01G217800 chr6A 96.599 735 21 2 1 732 222127956 222128689 0.000000e+00 1216.0
10 TraesCS6B01G217800 chr6A 96.084 664 24 2 810 1473 222128690 222129351 0.000000e+00 1081.0
11 TraesCS6B01G217800 chr6A 90.798 326 25 3 126 447 222676002 222676326 7.230000e-117 431.0
12 TraesCS6B01G217800 chr6A 90.654 214 16 4 2888 3098 116945077 116944865 7.710000e-72 281.0
13 TraesCS6B01G217800 chr6A 95.349 86 2 2 734 818 158316547 158316631 6.350000e-28 135.0
14 TraesCS6B01G217800 chr7A 89.360 1109 97 13 1773 2872 438259935 438261031 0.000000e+00 1375.0
15 TraesCS6B01G217800 chr7A 90.660 621 51 5 1102 1722 438259321 438259934 0.000000e+00 819.0
16 TraesCS6B01G217800 chr7B 85.452 653 58 19 2225 2873 383514943 383515562 0.000000e+00 645.0
17 TraesCS6B01G217800 chr7B 86.842 76 10 0 3555 3630 103614362 103614287 6.490000e-13 86.1
18 TraesCS6B01G217800 chr7D 87.400 500 50 9 2374 2872 388035463 388035950 2.460000e-156 562.0
19 TraesCS6B01G217800 chr7D 90.654 214 16 4 2888 3098 68909300 68909088 7.710000e-72 281.0
20 TraesCS6B01G217800 chr7D 95.556 90 1 3 734 821 199127703 199127615 1.360000e-29 141.0
21 TraesCS6B01G217800 chr1B 92.488 213 15 1 2888 3100 40949815 40949604 1.650000e-78 303.0
22 TraesCS6B01G217800 chr2D 92.019 213 13 4 2888 3098 165539515 165539305 2.750000e-76 296.0
23 TraesCS6B01G217800 chr2D 91.121 214 16 3 2885 3095 547787106 547787319 1.660000e-73 287.0
24 TraesCS6B01G217800 chr2D 90.698 215 18 2 2885 3097 579763653 579763867 5.960000e-73 285.0
25 TraesCS6B01G217800 chr2D 85.039 127 8 7 705 822 594917897 594918021 6.400000e-23 119.0
26 TraesCS6B01G217800 chr3B 90.826 218 16 3 2884 3098 771329043 771329259 4.610000e-74 289.0
27 TraesCS6B01G217800 chr3B 95.402 87 2 2 734 818 557093204 557093118 1.770000e-28 137.0
28 TraesCS6B01G217800 chr3B 86.777 121 5 9 702 812 293739805 293739924 1.370000e-24 124.0
29 TraesCS6B01G217800 chr3B 92.063 63 5 0 3547 3609 228981262 228981324 5.010000e-14 89.8
30 TraesCS6B01G217800 chr1D 90.741 216 18 2 2885 3098 101104530 101104745 1.660000e-73 287.0
31 TraesCS6B01G217800 chr3A 91.121 214 13 5 2888 3097 743841064 743840853 5.960000e-73 285.0
32 TraesCS6B01G217800 chr4B 84.921 126 9 7 705 822 352292422 352292545 6.400000e-23 119.0
33 TraesCS6B01G217800 chrUn 87.500 88 11 0 3547 3634 63610297 63610384 6.440000e-18 102.0
34 TraesCS6B01G217800 chrUn 92.063 63 5 0 3547 3609 34571862 34571924 5.010000e-14 89.8


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 TraesCS6B01G217800 chr6B 299823234 299826879 3645 True 2955.0 5725 100.0000 1 3646 2 chr6B.!!$R4 3645
1 TraesCS6B01G217800 chr6B 299616948 299619083 2135 True 2813.0 2813 90.6070 126 2242 1 chr6B.!!$R1 2116
2 TraesCS6B01G217800 chr6B 299602194 299602798 604 True 444.0 660 94.0250 2245 2887 2 chr6B.!!$R3 642
3 TraesCS6B01G217800 chr6D 162953844 162956624 2780 False 3855.0 3855 91.8190 126 2887 1 chr6D.!!$F1 2761
4 TraesCS6B01G217800 chr6A 222135373 222136798 1425 False 2300.0 2300 95.8650 1470 2887 1 chr6A.!!$F2 1417
5 TraesCS6B01G217800 chr6A 222676002 222681011 5009 False 1850.0 3269 90.8130 126 2887 2 chr6A.!!$F4 2761
6 TraesCS6B01G217800 chr6A 222127956 222129351 1395 False 1148.5 1216 96.3415 1 1473 2 chr6A.!!$F3 1472
7 TraesCS6B01G217800 chr7A 438259321 438261031 1710 False 1097.0 1375 90.0100 1102 2872 2 chr7A.!!$F1 1770
8 TraesCS6B01G217800 chr7B 383514943 383515562 619 False 645.0 645 85.4520 2225 2873 1 chr7B.!!$F1 648

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
109 110 0.179145 CGTAAGGACCAGTACAGCGG 60.179 60.000 0.0 0.0 0.0 5.52 F
114 115 1.063867 AGGACCAGTACAGCGGACTAT 60.064 52.381 0.0 0.0 0.0 2.12 F
1468 3727 1.933853 CGACGAGGAATTGTCCCATTC 59.066 52.381 0.0 0.0 46.3 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 3961 0.529337 CCTGATTGCTGCTCGACGAT 60.529 55.000 0.0 0.0 0.00 3.73 R
1751 4010 1.151668 GCTCGTCTTGTCAGCATGTT 58.848 50.000 0.0 0.0 37.40 2.71 R
2917 5193 1.449778 GGCAGCGAACTAGGGTTCC 60.450 63.158 0.0 0.0 46.46 3.62 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
62 63 3.056465 GGACCAGAGTCGACTGAAGAATT 60.056 47.826 25.58 0.00 44.54 2.17
68 69 4.524714 AGAGTCGACTGAAGAATTTGGAGA 59.475 41.667 25.58 0.00 0.00 3.71
90 91 7.065204 GGAGATGGAGAGAATAAAGACAACAAC 59.935 40.741 0.00 0.00 0.00 3.32
96 97 7.148623 GGAGAGAATAAAGACAACAACGTAAGG 60.149 40.741 0.00 0.00 46.39 2.69
109 110 0.179145 CGTAAGGACCAGTACAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
114 115 1.063867 AGGACCAGTACAGCGGACTAT 60.064 52.381 0.00 0.00 0.00 2.12
116 117 2.292845 GGACCAGTACAGCGGACTATAC 59.707 54.545 0.00 0.00 0.00 1.47
568 2818 7.978975 TGAACAAAAGAAGGTTAAAACAGATGG 59.021 33.333 0.00 0.00 0.00 3.51
742 2992 8.437575 TCTTCAACCATTTTATATACTCCCTCC 58.562 37.037 0.00 0.00 0.00 4.30
745 2995 6.356186 ACCATTTTATATACTCCCTCCGTC 57.644 41.667 0.00 0.00 0.00 4.79
746 2996 5.247792 ACCATTTTATATACTCCCTCCGTCC 59.752 44.000 0.00 0.00 0.00 4.79
748 2998 6.070194 CCATTTTATATACTCCCTCCGTCCAT 60.070 42.308 0.00 0.00 0.00 3.41
758 3009 6.320518 ACTCCCTCCGTCCATAATATAAGAA 58.679 40.000 0.00 0.00 0.00 2.52
764 3015 7.440255 CCTCCGTCCATAATATAAGAACGTTTT 59.560 37.037 0.46 0.00 0.00 2.43
765 3016 8.721019 TCCGTCCATAATATAAGAACGTTTTT 57.279 30.769 9.22 9.22 0.00 1.94
766 3017 8.605746 TCCGTCCATAATATAAGAACGTTTTTG 58.394 33.333 13.87 0.00 0.00 2.44
767 3018 8.605746 CCGTCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
799 3055 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
1021 3279 4.568152 ATGTACTTTGTTTGCACTGTCC 57.432 40.909 0.00 0.00 0.00 4.02
1048 3306 3.276091 TTGACGTGGCTGCAACGG 61.276 61.111 30.66 14.65 45.20 4.44
1049 3307 4.539083 TGACGTGGCTGCAACGGT 62.539 61.111 30.66 17.57 45.20 4.83
1119 3377 3.560902 ACGCGGTATGTGATCTGATAG 57.439 47.619 12.47 0.00 0.00 2.08
1379 3638 8.942338 TGCGTATACAATTATTTCTTGACTCT 57.058 30.769 3.32 0.00 0.00 3.24
1468 3727 1.933853 CGACGAGGAATTGTCCCATTC 59.066 52.381 0.00 0.00 46.30 2.67
1693 3952 4.276431 GGAGGAACTAGTATTCGTGAGGAG 59.724 50.000 0.00 0.00 41.55 3.69
1702 3961 6.222038 AGTATTCGTGAGGAGAAGCAAATA 57.778 37.500 0.00 0.00 0.00 1.40
1708 3967 3.487574 GTGAGGAGAAGCAAATATCGTCG 59.512 47.826 0.00 0.00 31.03 5.12
1751 4010 3.838271 CTCCTGGCCGCGCTCTTA 61.838 66.667 5.56 0.00 0.00 2.10
1761 4020 0.025513 CGCGCTCTTAACATGCTGAC 59.974 55.000 5.56 0.00 0.00 3.51
1771 4030 0.033920 ACATGCTGACAAGACGAGCA 59.966 50.000 0.00 0.00 46.32 4.26
1878 4137 3.070159 GCATCCTCATACCAGCTCAGTTA 59.930 47.826 0.00 0.00 0.00 2.24
1901 4160 6.872628 ATATAGTGATCACAATGGTTGCAG 57.127 37.500 27.02 0.00 0.00 4.41
1921 4180 5.936372 TGCAGAACTTCTCTCGTACTACTTA 59.064 40.000 0.00 0.00 29.07 2.24
1990 4259 5.353123 TGGTGGCATCTATTTTCGTAACTTC 59.647 40.000 0.00 0.00 0.00 3.01
2018 4287 6.541641 ACCATTCATCTTTCTTGCAGATCTAC 59.458 38.462 0.00 0.00 0.00 2.59
2050 4319 1.618074 GCTTCTCCCAGCCAAAATCCT 60.618 52.381 0.00 0.00 33.21 3.24
2368 4637 0.461693 GACCAGCACTCCAGAGATGC 60.462 60.000 0.70 7.73 36.45 3.91
2425 4694 1.802337 CTCGTCACCACCGACCTTCA 61.802 60.000 0.00 0.00 31.91 3.02
2435 4704 1.522355 CGACCTTCATGGCGCTGAT 60.522 57.895 7.64 0.00 40.22 2.90
2475 4744 4.700700 TGTCATCAACTATGATCTGCCAG 58.299 43.478 0.00 0.00 46.21 4.85
2519 4788 2.743636 ATGTTCGACGAAGTGGACAT 57.256 45.000 11.25 8.38 46.84 3.06
2652 4921 3.826236 CTGACCTCTTGTGAGCAATTG 57.174 47.619 0.00 0.00 38.93 2.32
2810 5086 5.236478 GGTATTATGTCATGGTGGTTCGAAG 59.764 44.000 0.00 0.00 0.00 3.79
2889 5165 9.511144 GTTGTTTACTATTGTTATATTGTGCCC 57.489 33.333 0.00 0.00 0.00 5.36
2890 5166 8.228035 TGTTTACTATTGTTATATTGTGCCCC 57.772 34.615 0.00 0.00 0.00 5.80
2891 5167 7.012515 TGTTTACTATTGTTATATTGTGCCCCG 59.987 37.037 0.00 0.00 0.00 5.73
2892 5168 5.043737 ACTATTGTTATATTGTGCCCCGT 57.956 39.130 0.00 0.00 0.00 5.28
2893 5169 4.819630 ACTATTGTTATATTGTGCCCCGTG 59.180 41.667 0.00 0.00 0.00 4.94
2894 5170 1.384525 TGTTATATTGTGCCCCGTGC 58.615 50.000 0.00 0.00 41.77 5.34
2895 5171 0.666374 GTTATATTGTGCCCCGTGCC 59.334 55.000 0.00 0.00 40.16 5.01
2896 5172 0.816018 TTATATTGTGCCCCGTGCCG 60.816 55.000 0.00 0.00 40.16 5.69
2935 5211 4.203618 GAACCCTAGTTCGCTGCC 57.796 61.111 0.00 0.00 42.85 4.85
2936 5212 1.810030 GAACCCTAGTTCGCTGCCG 60.810 63.158 0.00 0.00 42.85 5.69
2937 5213 3.952628 AACCCTAGTTCGCTGCCGC 62.953 63.158 0.00 0.00 0.00 6.53
2951 5227 4.840005 CCGCCGCTCCCCTTTCTC 62.840 72.222 0.00 0.00 0.00 2.87
2954 5230 4.840005 CCGCTCCCCTTTCTCGCC 62.840 72.222 0.00 0.00 0.00 5.54
2955 5231 3.775654 CGCTCCCCTTTCTCGCCT 61.776 66.667 0.00 0.00 0.00 5.52
2956 5232 2.188207 GCTCCCCTTTCTCGCCTC 59.812 66.667 0.00 0.00 0.00 4.70
2957 5233 2.904131 CTCCCCTTTCTCGCCTCC 59.096 66.667 0.00 0.00 0.00 4.30
2958 5234 1.687493 CTCCCCTTTCTCGCCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
2959 5235 1.681486 CTCCCCTTTCTCGCCTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
2960 5236 2.736826 CCCCTTTCTCGCCTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
2961 5237 2.736826 CCCTTTCTCGCCTCCTCCC 61.737 68.421 0.00 0.00 0.00 4.30
2962 5238 1.687493 CCTTTCTCGCCTCCTCCCT 60.687 63.158 0.00 0.00 0.00 4.20
2963 5239 1.681486 CCTTTCTCGCCTCCTCCCTC 61.681 65.000 0.00 0.00 0.00 4.30
2964 5240 1.681486 CTTTCTCGCCTCCTCCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
2965 5241 2.169590 TTTCTCGCCTCCTCCCTCCT 62.170 60.000 0.00 0.00 0.00 3.69
2966 5242 2.520741 CTCGCCTCCTCCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
2967 5243 4.507916 TCGCCTCCTCCCTCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
3049 5325 2.837291 CTCTCGGGAGGCTCCTGG 60.837 72.222 35.92 27.00 43.23 4.45
3050 5326 4.465446 TCTCGGGAGGCTCCTGGG 62.465 72.222 35.92 34.47 45.07 4.45
3563 5839 4.153330 GGCTACCCCTCCTCCCGA 62.153 72.222 0.00 0.00 0.00 5.14
3564 5840 2.201771 GCTACCCCTCCTCCCGAT 59.798 66.667 0.00 0.00 0.00 4.18
3565 5841 1.909287 GCTACCCCTCCTCCCGATC 60.909 68.421 0.00 0.00 0.00 3.69
3566 5842 1.854874 CTACCCCTCCTCCCGATCT 59.145 63.158 0.00 0.00 0.00 2.75
3567 5843 0.540830 CTACCCCTCCTCCCGATCTG 60.541 65.000 0.00 0.00 0.00 2.90
3568 5844 0.997307 TACCCCTCCTCCCGATCTGA 60.997 60.000 0.00 0.00 0.00 3.27
3569 5845 1.157276 CCCCTCCTCCCGATCTGAT 59.843 63.158 0.00 0.00 0.00 2.90
3570 5846 1.190833 CCCCTCCTCCCGATCTGATG 61.191 65.000 0.00 0.00 0.00 3.07
3571 5847 1.190833 CCCTCCTCCCGATCTGATGG 61.191 65.000 0.00 0.00 0.00 3.51
3572 5848 0.470833 CCTCCTCCCGATCTGATGGT 60.471 60.000 0.00 0.00 0.00 3.55
3573 5849 0.678395 CTCCTCCCGATCTGATGGTG 59.322 60.000 0.00 0.00 0.00 4.17
3574 5850 1.070445 CCTCCCGATCTGATGGTGC 59.930 63.158 0.00 0.00 0.00 5.01
3575 5851 1.070445 CTCCCGATCTGATGGTGCC 59.930 63.158 0.00 0.00 0.00 5.01
3576 5852 2.280389 CCCGATCTGATGGTGCCG 60.280 66.667 0.00 0.00 0.00 5.69
3577 5853 2.501128 CCGATCTGATGGTGCCGT 59.499 61.111 0.00 0.00 0.00 5.68
3578 5854 1.884464 CCGATCTGATGGTGCCGTG 60.884 63.158 0.00 0.00 0.00 4.94
3579 5855 1.884464 CGATCTGATGGTGCCGTGG 60.884 63.158 0.00 0.00 0.00 4.94
3580 5856 1.221840 GATCTGATGGTGCCGTGGT 59.778 57.895 0.00 0.00 0.00 4.16
3581 5857 1.078214 ATCTGATGGTGCCGTGGTG 60.078 57.895 0.00 0.00 0.00 4.17
3582 5858 2.541547 ATCTGATGGTGCCGTGGTGG 62.542 60.000 0.00 0.00 42.50 4.61
3643 5919 2.887568 CGCGTGACCTGATGGCTC 60.888 66.667 0.00 0.00 36.63 4.70
3644 5920 2.512515 GCGTGACCTGATGGCTCC 60.513 66.667 0.00 0.00 36.63 4.70
3645 5921 2.981302 CGTGACCTGATGGCTCCA 59.019 61.111 0.00 0.00 36.63 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 6.874278 TGTCTTTATTCTCTCCATCTCCAA 57.126 37.500 0.00 0.00 0.00 3.53
68 69 6.231211 ACGTTGTTGTCTTTATTCTCTCCAT 58.769 36.000 0.00 0.00 0.00 3.41
90 91 0.179145 CCGCTGTACTGGTCCTTACG 60.179 60.000 1.65 0.00 0.00 3.18
96 97 2.032204 CGTATAGTCCGCTGTACTGGTC 60.032 54.545 1.65 0.00 37.23 4.02
109 110 6.462073 TGCTGTTTTGTTTCTCGTATAGTC 57.538 37.500 0.00 0.00 0.00 2.59
114 115 2.033236 CGCTGCTGTTTTGTTTCTCGTA 60.033 45.455 0.00 0.00 0.00 3.43
116 117 1.003972 TCGCTGCTGTTTTGTTTCTCG 60.004 47.619 0.00 0.00 0.00 4.04
412 418 0.456995 GCACGCTCTCTACAGTCCAC 60.457 60.000 0.00 0.00 0.00 4.02
477 2727 9.613428 CAGTAATGTAAGATGGTTTCCTTATGA 57.387 33.333 0.00 0.00 0.00 2.15
568 2818 8.237267 CACATCTCCCTAGTTGTTTTTGTATTC 58.763 37.037 0.00 0.00 34.16 1.75
701 2951 8.691661 ATGGTTGAAGACAGTAAAACATAGTT 57.308 30.769 0.00 0.00 0.00 2.24
742 2992 9.417284 GTCAAAAACGTTCTTATATTATGGACG 57.583 33.333 0.00 0.00 39.79 4.79
773 3024 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
775 3026 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
777 3028 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
778 3029 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
779 3030 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
784 3040 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
785 3041 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
795 3051 3.421394 TCAATACTCCCTCTGTCCCAT 57.579 47.619 0.00 0.00 0.00 4.00
796 3052 2.940514 TCAATACTCCCTCTGTCCCA 57.059 50.000 0.00 0.00 0.00 4.37
797 3053 5.888982 TTAATCAATACTCCCTCTGTCCC 57.111 43.478 0.00 0.00 0.00 4.46
798 3054 8.214364 AGAAATTAATCAATACTCCCTCTGTCC 58.786 37.037 0.00 0.00 0.00 4.02
799 3055 9.050601 CAGAAATTAATCAATACTCCCTCTGTC 57.949 37.037 0.00 0.00 0.00 3.51
958 3216 6.478512 AACCCAAAACTTCAATAAAGCAGA 57.521 33.333 0.00 0.00 38.67 4.26
1021 3279 1.507141 GCCACGTCAACACCTTCAGG 61.507 60.000 0.00 0.00 42.17 3.86
1048 3306 3.442977 TCAAACCGAGCTCCTTCTAGTAC 59.557 47.826 8.47 0.00 0.00 2.73
1049 3307 3.693807 TCAAACCGAGCTCCTTCTAGTA 58.306 45.455 8.47 0.00 0.00 1.82
1089 3347 2.789339 CACATACCGCGTAGTCATCTTG 59.211 50.000 4.92 0.00 0.00 3.02
1119 3377 6.900299 CGAGAAACAAACAGACAGAAGTAAAC 59.100 38.462 0.00 0.00 0.00 2.01
1190 3449 6.099701 AGTTAGCCTATACCATGTCATGTTGA 59.900 38.462 11.84 0.00 0.00 3.18
1252 3511 3.125829 CCCATCTCAACGAAACTGTCATG 59.874 47.826 0.00 0.00 0.00 3.07
1407 3666 3.253188 CGCCAGACCTTCAAGAAAAATCA 59.747 43.478 0.00 0.00 0.00 2.57
1468 3727 2.787473 TAACATCCAGACCCTTGCAG 57.213 50.000 0.00 0.00 0.00 4.41
1693 3952 2.348032 GCTGCTCGACGATATTTGCTTC 60.348 50.000 0.00 0.00 0.00 3.86
1702 3961 0.529337 CCTGATTGCTGCTCGACGAT 60.529 55.000 0.00 0.00 0.00 3.73
1708 3967 3.242543 CGACAATAACCTGATTGCTGCTC 60.243 47.826 0.00 0.00 39.94 4.26
1751 4010 1.151668 GCTCGTCTTGTCAGCATGTT 58.848 50.000 0.00 0.00 37.40 2.71
1761 4020 1.528586 CTGGACAAAGTGCTCGTCTTG 59.471 52.381 0.00 0.00 0.00 3.02
1771 4030 7.170965 ACATTCTGATGTTATCTGGACAAAGT 58.829 34.615 0.00 0.00 43.92 2.66
1798 4057 2.897436 TCATCAGCTTCATCCAAGACG 58.103 47.619 0.00 0.00 33.29 4.18
1878 4137 6.594744 TCTGCAACCATTGTGATCACTATAT 58.405 36.000 25.55 13.68 0.00 0.86
1960 4229 5.527582 ACGAAAATAGATGCCACCATAGAAC 59.472 40.000 0.00 0.00 0.00 3.01
1990 4259 4.698780 TCTGCAAGAAAGATGAATGGTCAG 59.301 41.667 0.00 0.00 42.31 3.51
2018 4287 4.753233 CTGGGAGAAGCTGGATAATATCG 58.247 47.826 0.00 0.00 0.00 2.92
2050 4319 3.259064 GCGGTAGAGAATACAGCAAACA 58.741 45.455 5.47 0.00 38.26 2.83
2368 4637 2.025767 CTGGAGATCCTGGACGGCAG 62.026 65.000 0.00 0.00 36.82 4.85
2425 4694 2.349969 CTGCAATGCATCAGCGCCAT 62.350 55.000 8.91 0.00 46.23 4.40
2475 4744 3.124636 CGAAGGTATTGTACTGGTTGTGC 59.875 47.826 0.00 0.00 0.00 4.57
2652 4921 3.605634 TGTGCACCATATCCAACTACAC 58.394 45.455 15.69 0.00 0.00 2.90
2810 5086 2.728690 TGCACCACATTCAATTCAGC 57.271 45.000 0.00 0.00 0.00 4.26
2851 5127 9.077885 ACAATAGTAAACAACAGATGAACCAAT 57.922 29.630 0.00 0.00 0.00 3.16
2914 5190 2.510918 GCGAACTAGGGTTCCGCC 60.511 66.667 0.00 0.00 46.46 6.13
2915 5191 1.810030 CAGCGAACTAGGGTTCCGC 60.810 63.158 0.00 0.00 46.46 5.54
2916 5192 1.810030 GCAGCGAACTAGGGTTCCG 60.810 63.158 0.00 0.00 46.46 4.30
2917 5193 1.449778 GGCAGCGAACTAGGGTTCC 60.450 63.158 0.00 0.00 46.46 3.62
2918 5194 1.810030 CGGCAGCGAACTAGGGTTC 60.810 63.158 0.00 0.00 45.91 3.62
2919 5195 2.264794 CGGCAGCGAACTAGGGTT 59.735 61.111 0.00 0.00 38.52 4.11
2920 5196 4.452733 GCGGCAGCGAACTAGGGT 62.453 66.667 0.00 0.00 0.00 4.34
2934 5210 4.840005 GAGAAAGGGGAGCGGCGG 62.840 72.222 9.78 0.00 0.00 6.13
2937 5213 4.840005 GGCGAGAAAGGGGAGCGG 62.840 72.222 0.00 0.00 0.00 5.52
2938 5214 3.724914 GAGGCGAGAAAGGGGAGCG 62.725 68.421 0.00 0.00 0.00 5.03
2939 5215 2.188207 GAGGCGAGAAAGGGGAGC 59.812 66.667 0.00 0.00 0.00 4.70
2940 5216 1.681486 GAGGAGGCGAGAAAGGGGAG 61.681 65.000 0.00 0.00 0.00 4.30
2941 5217 1.686110 GAGGAGGCGAGAAAGGGGA 60.686 63.158 0.00 0.00 0.00 4.81
2942 5218 2.736826 GGAGGAGGCGAGAAAGGGG 61.737 68.421 0.00 0.00 0.00 4.79
2943 5219 2.736826 GGGAGGAGGCGAGAAAGGG 61.737 68.421 0.00 0.00 0.00 3.95
2944 5220 1.681486 GAGGGAGGAGGCGAGAAAGG 61.681 65.000 0.00 0.00 0.00 3.11
2945 5221 1.681486 GGAGGGAGGAGGCGAGAAAG 61.681 65.000 0.00 0.00 0.00 2.62
2946 5222 1.686110 GGAGGGAGGAGGCGAGAAA 60.686 63.158 0.00 0.00 0.00 2.52
2947 5223 2.042843 GGAGGGAGGAGGCGAGAA 60.043 66.667 0.00 0.00 0.00 2.87
2948 5224 3.024356 AGGAGGGAGGAGGCGAGA 61.024 66.667 0.00 0.00 0.00 4.04
2949 5225 2.520741 GAGGAGGGAGGAGGCGAG 60.521 72.222 0.00 0.00 0.00 5.03
2950 5226 4.507916 CGAGGAGGGAGGAGGCGA 62.508 72.222 0.00 0.00 0.00 5.54
3032 5308 2.837291 CCAGGAGCCTCCCGAGAG 60.837 72.222 7.26 0.00 37.19 3.20
3033 5309 4.465446 CCCAGGAGCCTCCCGAGA 62.465 72.222 7.26 0.00 37.19 4.04
3546 5822 3.469978 ATCGGGAGGAGGGGTAGCC 62.470 68.421 1.07 1.07 0.00 3.93
3547 5823 1.909287 GATCGGGAGGAGGGGTAGC 60.909 68.421 0.00 0.00 0.00 3.58
3548 5824 0.540830 CAGATCGGGAGGAGGGGTAG 60.541 65.000 0.00 0.00 0.00 3.18
3549 5825 0.997307 TCAGATCGGGAGGAGGGGTA 60.997 60.000 0.00 0.00 0.00 3.69
3550 5826 1.669927 ATCAGATCGGGAGGAGGGGT 61.670 60.000 0.00 0.00 0.00 4.95
3551 5827 1.157276 ATCAGATCGGGAGGAGGGG 59.843 63.158 0.00 0.00 0.00 4.79
3552 5828 1.190833 CCATCAGATCGGGAGGAGGG 61.191 65.000 4.05 0.00 0.00 4.30
3553 5829 0.470833 ACCATCAGATCGGGAGGAGG 60.471 60.000 10.43 7.70 0.00 4.30
3554 5830 0.678395 CACCATCAGATCGGGAGGAG 59.322 60.000 10.43 0.94 0.00 3.69
3555 5831 1.402896 GCACCATCAGATCGGGAGGA 61.403 60.000 10.43 0.00 0.00 3.71
3556 5832 1.070445 GCACCATCAGATCGGGAGG 59.930 63.158 0.00 0.00 0.00 4.30
3557 5833 1.070445 GGCACCATCAGATCGGGAG 59.930 63.158 0.00 0.00 0.00 4.30
3558 5834 2.796193 CGGCACCATCAGATCGGGA 61.796 63.158 0.00 0.00 0.00 5.14
3559 5835 2.280389 CGGCACCATCAGATCGGG 60.280 66.667 0.00 0.00 0.00 5.14
3560 5836 1.884464 CACGGCACCATCAGATCGG 60.884 63.158 0.00 0.00 0.00 4.18
3561 5837 1.884464 CCACGGCACCATCAGATCG 60.884 63.158 0.00 0.00 0.00 3.69
3562 5838 1.091771 CACCACGGCACCATCAGATC 61.092 60.000 0.00 0.00 0.00 2.75
3563 5839 1.078214 CACCACGGCACCATCAGAT 60.078 57.895 0.00 0.00 0.00 2.90
3564 5840 2.347114 CACCACGGCACCATCAGA 59.653 61.111 0.00 0.00 0.00 3.27
3565 5841 2.747460 CCACCACGGCACCATCAG 60.747 66.667 0.00 0.00 0.00 2.90
3626 5902 2.887568 GAGCCATCAGGTCACGCG 60.888 66.667 3.53 3.53 42.81 6.01
3627 5903 2.512515 GGAGCCATCAGGTCACGC 60.513 66.667 0.00 0.00 45.21 5.34
3628 5904 2.981302 TGGAGCCATCAGGTCACG 59.019 61.111 0.00 0.00 45.21 4.35


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

AutoCloner maintained by Alex Coulton.