Multiple sequence alignment - TraesCS2D01G085000

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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 TraesCS2D01G085000 chr2D 100.000 2684 0 0 1 2684 36782452 36785135 0.000000e+00 4957.0
1 TraesCS2D01G085000 chr2D 79.412 306 41 15 1389 1686 36751455 36751746 2.110000e-46 196.0
2 TraesCS2D01G085000 chr2B 89.626 1976 144 26 750 2682 63249701 63251658 0.000000e+00 2457.0
3 TraesCS2D01G085000 chr2B 94.870 1384 58 5 1305 2684 63255479 63256853 0.000000e+00 2150.0
4 TraesCS2D01G085000 chr2B 87.469 1197 114 13 900 2076 63220895 63222075 0.000000e+00 1347.0
5 TraesCS2D01G085000 chr2B 96.403 556 18 1 2131 2684 63244323 63244878 0.000000e+00 915.0
6 TraesCS2D01G085000 chr2B 84.470 792 106 11 1 776 63219964 63220754 0.000000e+00 765.0
7 TraesCS2D01G085000 chr2B 89.176 619 38 11 745 1345 63254942 63255549 0.000000e+00 745.0
8 TraesCS2D01G085000 chr2B 80.811 740 122 12 29 760 63248212 63248939 1.800000e-156 562.0
9 TraesCS2D01G085000 chr2B 92.913 254 18 0 1057 1310 63260768 63261021 1.170000e-98 370.0
10 TraesCS2D01G085000 chr2B 79.925 533 78 12 191 719 63254208 63254715 5.460000e-97 364.0
11 TraesCS2D01G085000 chr2B 88.208 212 23 1 531 740 63247566 63247777 4.440000e-63 252.0
12 TraesCS2D01G085000 chr2B 90.000 80 8 0 654 733 63249395 63249474 1.310000e-18 104.0
13 TraesCS2D01G085000 chr2A 93.551 1132 56 7 900 2029 41208020 41209136 0.000000e+00 1670.0
14 TraesCS2D01G085000 chr2A 92.801 1139 56 10 898 2029 41217873 41218992 0.000000e+00 1626.0
15 TraesCS2D01G085000 chr2A 95.764 661 19 4 2024 2684 41220897 41221548 0.000000e+00 1057.0
16 TraesCS2D01G085000 chr2A 95.455 660 22 3 2025 2684 41211039 41211690 0.000000e+00 1046.0
17 TraesCS2D01G085000 chr2A 84.020 801 102 16 1 776 41207080 41207879 0.000000e+00 747.0
18 TraesCS2D01G085000 chr2A 90.585 393 28 4 898 1285 41227548 41227936 1.840000e-141 512.0
19 TraesCS2D01G085000 chr2A 85.185 378 47 6 1370 1742 41227934 41228307 1.950000e-101 379.0
20 TraesCS2D01G085000 chr2A 78.457 376 59 10 1382 1741 41170540 41170909 2.690000e-55 226.0
21 TraesCS2D01G085000 chr2A 77.850 307 44 18 1389 1686 41103734 41104025 4.600000e-38 169.0
22 TraesCS2D01G085000 chr2A 92.553 94 7 0 737 830 41214677 41214770 4.660000e-28 135.0
23 TraesCS2D01G085000 chr6D 88.391 491 55 2 1779 2267 89358078 89358568 8.280000e-165 590.0
24 TraesCS2D01G085000 chr4B 85.484 496 60 10 1779 2267 82319750 82319260 8.570000e-140 507.0
25 TraesCS2D01G085000 chr3B 84.725 491 70 4 1779 2267 788978096 788977609 1.120000e-133 486.0
26 TraesCS2D01G085000 chrUn 84.521 491 71 4 1779 2267 326890008 326889521 5.200000e-132 481.0
27 TraesCS2D01G085000 chrUn 87.121 396 48 2 2289 2684 28694921 28695313 1.900000e-121 446.0
28 TraesCS2D01G085000 chr1B 87.879 396 45 2 2289 2684 670290275 670290667 1.880000e-126 462.0
29 TraesCS2D01G085000 chr4A 87.626 396 45 3 2289 2684 467670082 467670473 8.760000e-125 457.0
30 TraesCS2D01G085000 chr1A 87.374 396 46 3 2289 2684 67734329 67734720 4.070000e-123 451.0
31 TraesCS2D01G085000 chr7D 95.745 47 2 0 1093 1139 294028689 294028735 2.870000e-10 76.8
32 TraesCS2D01G085000 chr6B 97.222 36 1 0 401 436 159283095 159283130 8.020000e-06 62.1


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 TraesCS2D01G085000 chr2D 36782452 36785135 2683 False 4957.000000 4957 100.000000 1 2684 1 chr2D.!!$F2 2683
1 TraesCS2D01G085000 chr2B 63219964 63222075 2111 False 1056.000000 1347 85.969500 1 2076 2 chr2B.!!$F1 2075
2 TraesCS2D01G085000 chr2B 63244323 63261021 16698 False 879.888889 2457 89.103556 29 2684 9 chr2B.!!$F2 2655
3 TraesCS2D01G085000 chr2A 41207080 41221548 14468 False 1046.833333 1670 92.357333 1 2684 6 chr2A.!!$F3 2683
4 TraesCS2D01G085000 chr2A 41227548 41228307 759 False 445.500000 512 87.885000 898 1742 2 chr2A.!!$F4 844

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
366 3185 0.037734 TCAGTGAGACCTCCGCTACA 59.962 55.0 0.00 0.0 0.00 2.74 F
951 5775 0.166161 CGTCGCATCGATCGTAGGAT 59.834 55.0 15.94 0.0 38.42 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 16648 0.329261 CCTTGATGGCCAACTCCTGA 59.671 55.000 10.96 0.0 0.0 3.86 R
2032 19007 1.003233 GGAGCGAAGAAAAAGGGGAGA 59.997 52.381 0.00 0.0 0.0 3.71 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
58 2877 0.984995 GTGAAGGACTAAGTGCCCCT 59.015 55.000 0.00 0.00 0.00 4.79
77 2896 2.158959 GGCGATCGTGAAGTCGTGG 61.159 63.158 17.81 0.00 39.87 4.94
100 2919 3.527641 CCTCCTCTACTCGGTGGC 58.472 66.667 0.00 0.00 0.00 5.01
102 2921 1.668101 CCTCCTCTACTCGGTGGCAC 61.668 65.000 9.70 9.70 0.00 5.01
153 2972 0.631753 ATCTCGGTGGAGGAGAAGGA 59.368 55.000 0.00 0.00 43.26 3.36
155 2974 1.203137 TCTCGGTGGAGGAGAAGGAAA 60.203 52.381 0.00 0.00 40.85 3.13
243 3062 3.148279 GACGGCCTCGGTCCTCAT 61.148 66.667 0.00 0.00 41.39 2.90
244 3063 2.683933 ACGGCCTCGGTCCTCATT 60.684 61.111 0.00 0.00 41.39 2.57
245 3064 1.380785 ACGGCCTCGGTCCTCATTA 60.381 57.895 0.00 0.00 41.39 1.90
285 3104 2.105128 GGTGACCATCGCGGAGAG 59.895 66.667 6.13 0.00 38.63 3.20
290 3109 2.343163 GACCATCGCGGAGAGGTCTG 62.343 65.000 23.29 5.03 40.68 3.51
330 3149 2.047274 CGGAAAGCTCGCCAGGAA 60.047 61.111 5.74 0.00 0.00 3.36
345 3164 4.493747 GAACGGGAGGAGTCGCCG 62.494 72.222 0.00 0.00 43.43 6.46
350 3169 4.200283 GGAGGAGTCGCCGCTCAG 62.200 72.222 9.96 0.00 43.43 3.35
354 3173 2.202544 GAGTCGCCGCTCAGTGAG 60.203 66.667 16.21 16.21 35.67 3.51
360 3179 2.888863 CCGCTCAGTGAGACCTCC 59.111 66.667 24.55 4.50 0.00 4.30
364 3183 1.032657 GCTCAGTGAGACCTCCGCTA 61.033 60.000 24.55 0.00 0.00 4.26
366 3185 0.037734 TCAGTGAGACCTCCGCTACA 59.962 55.000 0.00 0.00 0.00 2.74
389 3210 4.387343 CAGGGGCAAGGGCATGGT 62.387 66.667 0.00 0.00 43.71 3.55
460 3288 1.147153 ATAGCAAAGCGGCTCCTCC 59.853 57.895 1.45 0.00 44.54 4.30
471 4411 4.244802 CTCCTCCGCGAGCGTCTC 62.245 72.222 8.23 0.00 37.81 3.36
501 4441 2.662070 GCAGGTTACCGTGCCCCTA 61.662 63.158 12.60 0.00 44.65 3.53
703 4662 5.223225 TCGCGTTTGCATGAATTATGTTA 57.777 34.783 5.77 0.00 42.97 2.41
760 4721 0.457166 TTGAATAGCCGGACGTGTCG 60.457 55.000 5.05 0.00 0.00 4.35
766 4727 3.708734 CCGGACGTGTCGGCAAAC 61.709 66.667 12.97 0.00 41.07 2.93
773 4734 3.365565 GGACGTGTCGGCAAACAAATATT 60.366 43.478 0.00 0.00 36.10 1.28
774 4735 4.142859 GGACGTGTCGGCAAACAAATATTA 60.143 41.667 0.00 0.00 36.10 0.98
775 4736 5.448089 GGACGTGTCGGCAAACAAATATTAT 60.448 40.000 0.00 0.00 36.10 1.28
777 4738 7.074507 ACGTGTCGGCAAACAAATATTATTA 57.925 32.000 0.00 0.00 0.00 0.98
778 4739 7.699566 ACGTGTCGGCAAACAAATATTATTAT 58.300 30.769 0.00 0.00 0.00 1.28
779 4740 7.642194 ACGTGTCGGCAAACAAATATTATTATG 59.358 33.333 0.00 0.00 0.00 1.90
780 4741 7.642194 CGTGTCGGCAAACAAATATTATTATGT 59.358 33.333 0.00 0.00 0.00 2.29
781 4742 9.296400 GTGTCGGCAAACAAATATTATTATGTT 57.704 29.630 0.00 0.00 37.59 2.71
782 4743 9.295214 TGTCGGCAAACAAATATTATTATGTTG 57.705 29.630 4.44 8.45 36.23 3.33
783 4744 8.751335 GTCGGCAAACAAATATTATTATGTTGG 58.249 33.333 4.44 3.20 36.23 3.77
794 4755 5.838531 TTATTATGTTGGTTTTAGGGCCG 57.161 39.130 0.00 0.00 0.00 6.13
795 4756 2.883122 TATGTTGGTTTTAGGGCCGT 57.117 45.000 2.24 2.24 0.00 5.68
796 4757 1.253100 ATGTTGGTTTTAGGGCCGTG 58.747 50.000 8.57 0.00 0.00 4.94
797 4758 1.287815 GTTGGTTTTAGGGCCGTGC 59.712 57.895 8.57 0.00 0.00 5.34
807 4768 4.162690 GGCCGTGCCTGAGTAGGG 62.163 72.222 7.58 0.00 46.69 3.53
808 4769 4.162690 GCCGTGCCTGAGTAGGGG 62.163 72.222 0.00 0.00 44.75 4.79
809 4770 4.162690 CCGTGCCTGAGTAGGGGC 62.163 72.222 0.00 0.00 44.75 5.80
829 4790 1.079681 GCGACCCACGATGTACCAA 60.080 57.895 0.00 0.00 45.77 3.67
834 4810 1.451387 CCACGATGTACCAAGGCCC 60.451 63.158 0.00 0.00 0.00 5.80
855 4831 3.488721 CCACGACCTACTCCAATTCTACG 60.489 52.174 0.00 0.00 0.00 3.51
861 5643 3.632604 CCTACTCCAATTCTACGCAGAGA 59.367 47.826 0.00 0.00 30.73 3.10
873 5655 2.437413 ACGCAGAGACAGAGTCATACA 58.563 47.619 0.00 0.00 34.60 2.29
876 5658 4.035792 ACGCAGAGACAGAGTCATACATAC 59.964 45.833 0.00 0.00 34.60 2.39
878 5660 5.449177 CGCAGAGACAGAGTCATACATACAA 60.449 44.000 0.00 0.00 34.60 2.41
879 5661 5.976534 GCAGAGACAGAGTCATACATACAAG 59.023 44.000 0.00 0.00 34.60 3.16
881 5663 7.629437 GCAGAGACAGAGTCATACATACAAGAA 60.629 40.741 0.00 0.00 34.60 2.52
896 5697 0.621082 AAGAAACCTAGAGGCAGGGC 59.379 55.000 0.00 0.00 40.29 5.19
897 5698 1.153349 GAAACCTAGAGGCAGGGCG 60.153 63.158 0.00 0.00 40.29 6.13
898 5699 3.330992 AAACCTAGAGGCAGGGCGC 62.331 63.158 0.00 0.00 40.29 6.53
917 5741 3.908382 GCGCGCATTATAAATCTTCCAAG 59.092 43.478 29.10 0.00 0.00 3.61
924 5748 2.826674 TAAATCTTCCAAGCCCAGGG 57.173 50.000 0.00 0.00 0.00 4.45
948 5772 0.507358 TCTCGTCGCATCGATCGTAG 59.493 55.000 15.94 9.95 38.42 3.51
949 5773 0.451299 CTCGTCGCATCGATCGTAGG 60.451 60.000 15.94 7.01 38.42 3.18
950 5774 0.877213 TCGTCGCATCGATCGTAGGA 60.877 55.000 15.94 5.95 38.42 2.94
951 5775 0.166161 CGTCGCATCGATCGTAGGAT 59.834 55.000 15.94 0.00 38.42 3.24
952 5776 1.399855 CGTCGCATCGATCGTAGGATT 60.400 52.381 15.94 0.00 38.42 3.01
953 5777 2.662700 GTCGCATCGATCGTAGGATTT 58.337 47.619 15.94 0.00 38.42 2.17
993 5821 3.363378 GCGTTTCCATCATCAATCTAGCG 60.363 47.826 0.00 0.00 0.00 4.26
995 5823 4.380531 GTTTCCATCATCAATCTAGCGGA 58.619 43.478 0.00 0.00 0.00 5.54
1013 5841 0.171455 GAAGAGATGCCGTCGTGTCT 59.829 55.000 0.00 0.00 33.74 3.41
1208 6036 0.691078 GGCCACACCTGGAGGATCTA 60.691 60.000 0.00 0.00 40.55 1.98
1257 6085 4.189188 GCCGGCTTCGTCTCGCTA 62.189 66.667 22.15 0.00 0.00 4.26
1265 6093 2.287909 GCTTCGTCTCGCTATTCCTCAT 60.288 50.000 0.00 0.00 0.00 2.90
1267 6095 2.298610 TCGTCTCGCTATTCCTCATGT 58.701 47.619 0.00 0.00 0.00 3.21
1508 16563 1.000396 GCAAGATGTGGGGCTTCCT 60.000 57.895 0.00 0.00 36.20 3.36
1593 16648 1.227853 GTGCAAGGTCACCGTCCTT 60.228 57.895 0.00 0.00 44.93 3.36
1742 16805 7.799447 TGTTCGGAGAAAATTGTTATACGTTTG 59.201 33.333 0.00 0.00 45.90 2.93
1848 16913 4.558226 TCTTGATCCATACAAGCACACT 57.442 40.909 0.00 0.00 42.76 3.55
1855 16920 3.580895 TCCATACAAGCACACTCTAACCA 59.419 43.478 0.00 0.00 0.00 3.67
1885 16950 9.950680 CATAAATAACCGAATAACAAAGAGCAT 57.049 29.630 0.00 0.00 0.00 3.79
1937 17002 3.768215 TCTGAAGCTCTGTGTCATCATCT 59.232 43.478 0.00 0.00 0.00 2.90
1938 17003 4.952335 TCTGAAGCTCTGTGTCATCATCTA 59.048 41.667 0.00 0.00 0.00 1.98
1970 17035 0.668535 GAAGACCCCTGCAACACAAC 59.331 55.000 0.00 0.00 0.00 3.32
1976 17041 1.271871 CCCCTGCAACACAACCATCTA 60.272 52.381 0.00 0.00 0.00 1.98
1977 17042 2.513753 CCCTGCAACACAACCATCTAA 58.486 47.619 0.00 0.00 0.00 2.10
1986 17051 5.862924 ACACAACCATCTAAAATCAGACG 57.137 39.130 0.00 0.00 0.00 4.18
2023 17088 6.887626 AACTTCAACCACGGTATAATTGTT 57.112 33.333 0.00 0.00 0.00 2.83
2032 19007 2.096819 CGGTATAATTGTTGCCACGCTT 59.903 45.455 0.00 0.00 0.00 4.68
2130 19113 2.868583 CCATCTGTGGCTTTGAGTATCG 59.131 50.000 0.00 0.00 39.01 2.92
2174 19157 3.316868 GGAAGAGAACTAGGATCCAGTCG 59.683 52.174 15.82 1.18 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 2877 1.443702 CACGACTTCACGATCGCCA 60.444 57.895 16.60 0.00 42.12 5.69
77 2896 3.228017 GAGTAGAGGAGGCGCCCC 61.228 72.222 26.15 23.87 37.37 5.80
82 2901 3.527641 CCACCGAGTAGAGGAGGC 58.472 66.667 0.00 0.00 32.96 4.70
204 3023 1.729276 ACGTCGGACTTCGTCAACA 59.271 52.632 6.57 0.00 40.32 3.33
276 3095 2.041115 CACTCAGACCTCTCCGCGA 61.041 63.158 8.23 0.00 0.00 5.87
285 3104 1.373497 CACTGTCGCCACTCAGACC 60.373 63.158 0.00 0.00 36.61 3.85
341 3160 3.691744 GAGGTCTCACTGAGCGGCG 62.692 68.421 0.51 0.51 46.86 6.46
345 3164 1.032657 TAGCGGAGGTCTCACTGAGC 61.033 60.000 0.62 0.00 43.05 4.26
350 3169 0.108756 GGTTGTAGCGGAGGTCTCAC 60.109 60.000 0.14 0.00 40.68 3.51
364 3183 4.974721 CTTGCCCCTGCCGGTTGT 62.975 66.667 1.90 0.00 36.33 3.32
437 3265 0.744414 GAGCCGCTTTGCTATGTCCA 60.744 55.000 0.00 0.00 42.95 4.02
438 3266 1.440145 GGAGCCGCTTTGCTATGTCC 61.440 60.000 0.00 0.00 42.95 4.02
442 3270 1.147153 GGAGGAGCCGCTTTGCTAT 59.853 57.895 0.00 0.00 42.95 2.97
484 4424 1.219935 GTAGGGGCACGGTAACCTG 59.780 63.158 7.47 0.00 34.59 4.00
493 4433 4.484872 GGAAGGGCGTAGGGGCAC 62.485 72.222 0.00 0.00 44.56 5.01
511 4451 1.371558 GAGTGGTCCTTTCAGCGGT 59.628 57.895 0.00 0.00 0.00 5.68
544 4493 2.436646 CGGTGGCACCTCCATCAC 60.437 66.667 32.28 5.66 46.69 3.06
576 4532 2.267961 GAGGGTGGCCTTGTACGG 59.732 66.667 3.32 0.00 0.00 4.02
591 4547 2.032178 GCTAAATTAACCTGCAGCGGAG 59.968 50.000 8.66 0.00 0.00 4.63
598 4554 6.796426 CCTAAAAGAGGCTAAATTAACCTGC 58.204 40.000 0.00 0.00 38.96 4.85
640 4599 6.836577 TCACATAAATCACGCGATATTTCA 57.163 33.333 15.93 7.61 0.00 2.69
641 4600 8.713765 ATTTCACATAAATCACGCGATATTTC 57.286 30.769 15.93 0.00 0.00 2.17
679 4638 4.037021 ACATAATTCATGCAAACGCGATG 58.963 39.130 15.93 13.05 38.29 3.84
683 4642 7.684062 ATTCTAACATAATTCATGCAAACGC 57.316 32.000 0.00 0.00 38.29 4.84
719 4678 3.181448 ACACTTACAAAACCTCCGTCCAT 60.181 43.478 0.00 0.00 0.00 3.41
724 4683 4.886247 TTCAACACTTACAAAACCTCCG 57.114 40.909 0.00 0.00 0.00 4.63
773 4734 4.641094 CACGGCCCTAAAACCAACATAATA 59.359 41.667 0.00 0.00 0.00 0.98
774 4735 3.445805 CACGGCCCTAAAACCAACATAAT 59.554 43.478 0.00 0.00 0.00 1.28
775 4736 2.820787 CACGGCCCTAAAACCAACATAA 59.179 45.455 0.00 0.00 0.00 1.90
777 4738 1.253100 CACGGCCCTAAAACCAACAT 58.747 50.000 0.00 0.00 0.00 2.71
778 4739 1.457009 GCACGGCCCTAAAACCAACA 61.457 55.000 0.00 0.00 0.00 3.33
779 4740 1.287815 GCACGGCCCTAAAACCAAC 59.712 57.895 0.00 0.00 0.00 3.77
780 4741 1.904378 GGCACGGCCCTAAAACCAA 60.904 57.895 0.00 0.00 44.06 3.67
781 4742 2.282603 GGCACGGCCCTAAAACCA 60.283 61.111 0.00 0.00 44.06 3.67
791 4752 4.162690 CCCCTACTCAGGCACGGC 62.163 72.222 0.00 0.00 41.08 5.68
798 4759 4.208686 GTCGCGGCCCCTACTCAG 62.209 72.222 6.13 0.00 0.00 3.35
808 4769 4.501714 TACATCGTGGGTCGCGGC 62.502 66.667 6.13 3.04 37.97 6.53
809 4770 2.581409 GTACATCGTGGGTCGCGG 60.581 66.667 6.13 0.00 37.97 6.46
810 4771 2.581409 GGTACATCGTGGGTCGCG 60.581 66.667 0.00 0.00 39.67 5.87
818 4779 1.298667 GTGGGCCTTGGTACATCGT 59.701 57.895 4.53 0.00 39.30 3.73
829 4790 2.363925 GGAGTAGGTCGTGGGCCT 60.364 66.667 4.53 0.00 40.00 5.19
834 4810 3.692576 CGTAGAATTGGAGTAGGTCGTG 58.307 50.000 0.00 0.00 0.00 4.35
855 4831 5.506686 TGTATGTATGACTCTGTCTCTGC 57.493 43.478 0.00 0.00 33.15 4.26
861 5643 7.246171 AGGTTTCTTGTATGTATGACTCTGT 57.754 36.000 0.00 0.00 0.00 3.41
873 5655 3.456277 CCCTGCCTCTAGGTTTCTTGTAT 59.544 47.826 0.00 0.00 36.02 2.29
876 5658 1.680249 GCCCTGCCTCTAGGTTTCTTG 60.680 57.143 0.00 0.00 36.02 3.02
878 5660 1.617947 CGCCCTGCCTCTAGGTTTCT 61.618 60.000 0.00 0.00 36.02 2.52
879 5661 1.153349 CGCCCTGCCTCTAGGTTTC 60.153 63.158 0.00 0.00 36.02 2.78
881 5663 3.787001 GCGCCCTGCCTCTAGGTT 61.787 66.667 0.00 0.00 37.76 3.50
896 5697 3.908382 GCTTGGAAGATTTATAATGCGCG 59.092 43.478 0.00 0.00 0.00 6.86
897 5698 4.229876 GGCTTGGAAGATTTATAATGCGC 58.770 43.478 0.00 0.00 0.00 6.09
898 5699 4.278170 TGGGCTTGGAAGATTTATAATGCG 59.722 41.667 0.00 0.00 0.00 4.73
899 5700 5.279156 CCTGGGCTTGGAAGATTTATAATGC 60.279 44.000 0.00 0.00 0.00 3.56
900 5701 5.244626 CCCTGGGCTTGGAAGATTTATAATG 59.755 44.000 0.00 0.00 0.00 1.90
901 5702 5.136048 TCCCTGGGCTTGGAAGATTTATAAT 59.864 40.000 8.22 0.00 0.00 1.28
902 5703 4.480537 TCCCTGGGCTTGGAAGATTTATAA 59.519 41.667 8.22 0.00 0.00 0.98
917 5741 2.363147 ACGAGACTCTCCCTGGGC 60.363 66.667 8.22 0.00 0.00 5.36
924 5748 0.584396 ATCGATGCGACGAGACTCTC 59.416 55.000 0.00 0.00 45.22 3.20
948 5772 1.500396 GACGGTGGCGAACAAATCC 59.500 57.895 0.00 0.00 0.00 3.01
949 5773 1.131826 CGACGGTGGCGAACAAATC 59.868 57.895 0.00 0.00 0.00 2.17
950 5774 1.301087 TCGACGGTGGCGAACAAAT 60.301 52.632 0.00 0.00 34.45 2.32
951 5775 2.106534 TCGACGGTGGCGAACAAA 59.893 55.556 0.00 0.00 34.45 2.83
952 5776 2.659244 GTCGACGGTGGCGAACAA 60.659 61.111 0.00 0.00 39.73 2.83
953 5777 3.598715 AGTCGACGGTGGCGAACA 61.599 61.111 10.46 0.00 39.73 3.18
993 5821 0.802607 GACACGACGGCATCTCTTCC 60.803 60.000 0.00 0.00 0.00 3.46
995 5823 0.109086 CAGACACGACGGCATCTCTT 60.109 55.000 0.00 0.00 0.00 2.85
1038 5866 1.479709 AGGACTCCTCAGGTTCATCG 58.520 55.000 0.00 0.00 0.00 3.84
1208 6036 0.460311 CTTCCCGTCGAGGTAGCAAT 59.540 55.000 4.18 0.00 38.74 3.56
1257 6085 1.224592 GGGGTCGCACATGAGGAAT 59.775 57.895 0.00 0.00 0.00 3.01
1377 16432 1.660355 GTGGACGACACTCTCAGCA 59.340 57.895 7.56 0.00 46.72 4.41
1386 16441 2.042259 ATACTCCGCGTGGACGACA 61.042 57.895 15.21 0.00 40.17 4.35
1508 16563 0.674581 CTCCTTGCTGATGAACCGCA 60.675 55.000 0.00 0.00 36.98 5.69
1593 16648 0.329261 CCTTGATGGCCAACTCCTGA 59.671 55.000 10.96 0.00 0.00 3.86
1742 16805 6.958193 CACATGAAACGAGAAGAAGAAATAGC 59.042 38.462 0.00 0.00 0.00 2.97
1848 16913 7.867305 TTCGGTTATTTATGCATTGGTTAGA 57.133 32.000 3.54 0.00 0.00 2.10
1885 16950 5.809562 TCGTGTTTTACTCGTTGTTTTAGGA 59.190 36.000 0.00 0.00 36.59 2.94
1937 17002 3.118519 GGGGTCTTCTCGCAAGGTTTATA 60.119 47.826 0.00 0.00 38.47 0.98
1938 17003 2.355818 GGGGTCTTCTCGCAAGGTTTAT 60.356 50.000 0.00 0.00 38.47 1.40
1970 17035 5.235186 CCTGCTTACGTCTGATTTTAGATGG 59.765 44.000 0.00 0.00 37.89 3.51
1976 17041 8.448615 GTTTATTACCTGCTTACGTCTGATTTT 58.551 33.333 0.00 0.00 0.00 1.82
1977 17042 7.822822 AGTTTATTACCTGCTTACGTCTGATTT 59.177 33.333 0.00 0.00 0.00 2.17
1986 17051 7.303261 GTGGTTGAAGTTTATTACCTGCTTAC 58.697 38.462 0.00 0.00 0.00 2.34
2023 17088 2.351924 AAAAGGGGAGAAGCGTGGCA 62.352 55.000 0.00 0.00 0.00 4.92
2032 19007 1.003233 GGAGCGAAGAAAAAGGGGAGA 59.997 52.381 0.00 0.00 0.00 3.71
2110 19085 3.785486 TCGATACTCAAAGCCACAGATG 58.215 45.455 0.00 0.00 0.00 2.90
2111 19086 4.141846 ACATCGATACTCAAAGCCACAGAT 60.142 41.667 0.00 0.00 0.00 2.90
2112 19087 3.195610 ACATCGATACTCAAAGCCACAGA 59.804 43.478 0.00 0.00 0.00 3.41
2113 19088 3.525537 ACATCGATACTCAAAGCCACAG 58.474 45.455 0.00 0.00 0.00 3.66
2130 19113 1.212935 ACTGGAAGGGGCACATACATC 59.787 52.381 0.00 0.00 39.30 3.06


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

AutoCloner maintained by Alex Coulton.