Multiple sequence alignment - TraesCS3D01G480400

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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 TraesCS3D01G480400 chr3D 100.000 3287 0 0 1 3287 579128751 579132037 0.000000e+00 6071.0
1 TraesCS3D01G480400 chr3D 84.615 403 60 2 1899 2301 579159679 579160079 1.840000e-107 399.0
2 TraesCS3D01G480400 chr3D 77.647 510 66 32 746 1238 579114021 579114499 1.940000e-67 267.0
3 TraesCS3D01G480400 chr3D 91.781 146 12 0 2090 2235 579262694 579262839 1.550000e-48 204.0
4 TraesCS3D01G480400 chr3B 90.801 2348 137 38 319 2632 773245906 773248208 0.000000e+00 3066.0
5 TraesCS3D01G480400 chr3B 92.504 667 35 8 2631 3287 786279151 786278490 0.000000e+00 941.0
6 TraesCS3D01G480400 chr3B 95.692 325 13 1 1 325 773169226 773169549 3.760000e-144 521.0
7 TraesCS3D01G480400 chr3B 90.278 360 25 5 313 669 773169629 773169981 2.310000e-126 462.0
8 TraesCS3D01G480400 chr3B 84.163 442 42 12 1954 2394 773365736 773366150 1.420000e-108 403.0
9 TraesCS3D01G480400 chr3B 83.621 348 55 2 1899 2244 773263687 773264034 3.160000e-85 326.0
10 TraesCS3D01G480400 chr3B 81.150 313 56 2 1937 2249 773368441 773368750 7.040000e-62 248.0
11 TraesCS3D01G480400 chr3B 80.128 312 41 7 1869 2180 773319336 773319626 2.570000e-51 213.0
12 TraesCS3D01G480400 chr3B 93.798 129 8 0 2093 2221 773513931 773514059 9.310000e-46 195.0
13 TraesCS3D01G480400 chr3B 88.550 131 13 2 2091 2220 773377723 773377852 1.220000e-34 158.0
14 TraesCS3D01G480400 chr3B 85.981 107 13 2 2528 2632 769635518 769635624 2.680000e-21 113.0
15 TraesCS3D01G480400 chr3A 89.930 2006 111 32 612 2583 714457815 714459763 0.000000e+00 2501.0
16 TraesCS3D01G480400 chr2D 81.086 608 69 29 2629 3195 641182826 641182224 8.370000e-121 444.0
17 TraesCS3D01G480400 chr5D 83.761 117 17 2 2518 2632 23377741 23377857 3.470000e-20 110.0
18 TraesCS3D01G480400 chr5D 85.714 70 9 1 2629 2698 362583713 362583645 4.550000e-09 73.1
19 TraesCS3D01G480400 chr7D 85.047 107 14 2 2528 2632 379679048 379679154 1.250000e-19 108.0
20 TraesCS3D01G480400 chr7D 82.031 128 18 5 2510 2632 13508560 13508687 1.610000e-18 104.0
21 TraesCS3D01G480400 chr6D 85.047 107 14 2 2528 2632 322381607 322381713 1.250000e-19 108.0
22 TraesCS3D01G480400 chr4D 84.685 111 14 3 2525 2632 74783569 74783459 1.250000e-19 108.0
23 TraesCS3D01G480400 chr4D 83.193 119 18 2 2516 2632 438434673 438434555 1.250000e-19 108.0
24 TraesCS3D01G480400 chr4D 91.379 58 2 3 2635 2692 442846641 442846587 3.520000e-10 76.8
25 TraesCS3D01G480400 chrUn 82.927 123 16 5 2516 2634 248003662 248003783 4.490000e-19 106.0
26 TraesCS3D01G480400 chr5B 89.062 64 7 0 2635 2698 599553912 599553849 2.720000e-11 80.5
27 TraesCS3D01G480400 chr6B 87.500 64 8 0 2635 2698 414239587 414239650 1.260000e-09 75.0
28 TraesCS3D01G480400 chr1D 84.615 78 8 4 2631 2706 372548740 372548815 1.260000e-09 75.0
29 TraesCS3D01G480400 chr1B 87.500 64 8 0 2635 2698 590415315 590415378 1.260000e-09 75.0
30 TraesCS3D01G480400 chr4A 84.507 71 11 0 2630 2700 711666813 711666743 1.640000e-08 71.3
31 TraesCS3D01G480400 chr2A 86.567 67 6 3 2641 2705 763338035 763337970 1.640000e-08 71.3


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 TraesCS3D01G480400 chr3D 579128751 579132037 3286 False 6071.0 6071 100.0000 1 3287 1 chr3D.!!$F2 3286
1 TraesCS3D01G480400 chr3B 773245906 773248208 2302 False 3066.0 3066 90.8010 319 2632 1 chr3B.!!$F2 2313
2 TraesCS3D01G480400 chr3B 786278490 786279151 661 True 941.0 941 92.5040 2631 3287 1 chr3B.!!$R1 656
3 TraesCS3D01G480400 chr3B 773169226 773169981 755 False 491.5 521 92.9850 1 669 2 chr3B.!!$F7 668
4 TraesCS3D01G480400 chr3B 773365736 773368750 3014 False 325.5 403 82.6565 1937 2394 2 chr3B.!!$F8 457
5 TraesCS3D01G480400 chr3A 714457815 714459763 1948 False 2501.0 2501 89.9300 612 2583 1 chr3A.!!$F1 1971
6 TraesCS3D01G480400 chr2D 641182224 641182826 602 True 444.0 444 81.0860 2629 3195 1 chr2D.!!$R1 566

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
722 831 0.321475 GCTCTGCTATGATCCAGCCC 60.321 60.0 12.46 0.0 38.29 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 4569 0.179468 GACGCCTATTACTGCCCCAA 59.821 55.0 0.0 0.0 0.0 4.12 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
20 21 0.810031 CGATTCGGGGATGTGGTCAC 60.810 60.000 0.00 0.00 0.00 3.67
34 35 1.004918 GTCACCACCGTTCCAGAGG 60.005 63.158 0.00 0.00 0.00 3.69
62 63 1.333619 CCAACACTTCTTTCCCGTGTG 59.666 52.381 0.00 0.00 40.68 3.82
63 64 1.021968 AACACTTCTTTCCCGTGTGC 58.978 50.000 0.00 0.00 40.68 4.57
64 65 0.818040 ACACTTCTTTCCCGTGTGCC 60.818 55.000 0.00 0.00 40.11 5.01
176 177 2.290260 TGTCGATCTGTGGGATGCTTTT 60.290 45.455 0.00 0.00 34.33 2.27
211 212 4.564769 GTCTCCAGATCACACGATTTCTTC 59.435 45.833 0.00 0.00 29.66 2.87
252 253 0.457851 AGCGACATCTGTGACTAGGC 59.542 55.000 0.00 0.00 0.00 3.93
281 282 1.967343 ATCACCCTCCCCTCCCTCTC 61.967 65.000 0.00 0.00 0.00 3.20
307 308 3.000819 TGCCGACGAGTTCCCCAT 61.001 61.111 0.00 0.00 0.00 4.00
346 438 1.296392 CTTCCTGACCGTCATGGCA 59.704 57.895 0.62 0.00 43.94 4.92
384 476 2.121385 TCCAGGAGGAGCAGCAGT 59.879 61.111 0.00 0.00 39.61 4.40
683 792 2.747855 GAGCCTTGGCCACGAAGG 60.748 66.667 16.54 16.54 42.68 3.46
712 821 2.954989 TGACGATTCTCTGCTCTGCTAT 59.045 45.455 0.00 0.00 0.00 2.97
714 823 2.954989 ACGATTCTCTGCTCTGCTATGA 59.045 45.455 0.00 0.00 0.00 2.15
715 824 3.573538 ACGATTCTCTGCTCTGCTATGAT 59.426 43.478 0.00 0.00 0.00 2.45
716 825 4.168014 CGATTCTCTGCTCTGCTATGATC 58.832 47.826 0.00 0.00 0.00 2.92
717 826 4.497300 GATTCTCTGCTCTGCTATGATCC 58.503 47.826 0.00 0.00 0.00 3.36
718 827 2.954792 TCTCTGCTCTGCTATGATCCA 58.045 47.619 0.00 0.00 0.00 3.41
719 828 2.892215 TCTCTGCTCTGCTATGATCCAG 59.108 50.000 0.00 0.00 0.00 3.86
720 829 1.343789 TCTGCTCTGCTATGATCCAGC 59.656 52.381 9.00 9.00 39.56 4.85
721 830 0.395686 TGCTCTGCTATGATCCAGCC 59.604 55.000 12.46 0.38 38.29 4.85
722 831 0.321475 GCTCTGCTATGATCCAGCCC 60.321 60.000 12.46 0.00 38.29 5.19
723 832 0.324285 CTCTGCTATGATCCAGCCCC 59.676 60.000 12.46 0.00 38.29 5.80
724 833 1.004080 CTGCTATGATCCAGCCCCG 60.004 63.158 12.46 0.40 38.29 5.73
725 834 2.348998 GCTATGATCCAGCCCCGG 59.651 66.667 0.00 0.00 32.68 5.73
726 835 2.348998 CTATGATCCAGCCCCGGC 59.651 66.667 0.00 0.00 42.33 6.13
861 977 1.403249 CCGGTGGTCGTCGTCTTAAAT 60.403 52.381 0.00 0.00 37.11 1.40
910 1026 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
913 1029 4.179599 CCCTCCCCTCCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
914 1030 3.039526 CCTCCCCTCCCCTCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
915 1031 2.285180 CTCCCCTCCCCTCCTCTG 59.715 72.222 0.00 0.00 0.00 3.35
933 1049 4.132336 CTCTGCTCTGCAATTATAGCCAA 58.868 43.478 0.00 0.00 38.41 4.52
940 1058 1.889170 GCAATTATAGCCAAGCCTCCC 59.111 52.381 0.00 0.00 0.00 4.30
941 1059 2.752829 GCAATTATAGCCAAGCCTCCCA 60.753 50.000 0.00 0.00 0.00 4.37
942 1060 3.565307 CAATTATAGCCAAGCCTCCCAA 58.435 45.455 0.00 0.00 0.00 4.12
1090 1230 1.076632 GCCTCCTCCTCCTTCTCGA 60.077 63.158 0.00 0.00 0.00 4.04
1092 1232 0.753848 CCTCCTCCTCCTTCTCGACC 60.754 65.000 0.00 0.00 0.00 4.79
1128 1268 1.751162 CTTCTCGGCGTCCTCCTCT 60.751 63.158 6.85 0.00 0.00 3.69
1816 1962 3.569210 CACACACCCTCCTGGCCA 61.569 66.667 4.71 4.71 37.83 5.36
2285 2431 1.541310 CCCTGCGTGTTCCTGAGGTA 61.541 60.000 0.00 0.00 0.00 3.08
2321 2467 1.086634 CGGCTTGCCTAGAAGAGTGC 61.087 60.000 10.12 0.00 0.00 4.40
2325 2471 2.938756 GCTTGCCTAGAAGAGTGCACAT 60.939 50.000 21.04 3.86 32.94 3.21
2372 2518 5.434408 GGTCTGTAAAATTTACCCGAGGAT 58.566 41.667 12.72 0.00 0.00 3.24
2396 2542 4.119136 GGTGTTGTTCAGATTGTTTTGGG 58.881 43.478 0.00 0.00 0.00 4.12
2397 2543 4.382577 GGTGTTGTTCAGATTGTTTTGGGT 60.383 41.667 0.00 0.00 0.00 4.51
2398 2544 5.175127 GTGTTGTTCAGATTGTTTTGGGTT 58.825 37.500 0.00 0.00 0.00 4.11
2399 2545 5.641636 GTGTTGTTCAGATTGTTTTGGGTTT 59.358 36.000 0.00 0.00 0.00 3.27
2405 2555 5.423886 TCAGATTGTTTTGGGTTTGGTTTC 58.576 37.500 0.00 0.00 0.00 2.78
2467 2656 4.321675 GGTTGTTGGGTGTAAAATAGCTGG 60.322 45.833 0.00 0.00 0.00 4.85
2558 4247 9.533831 AATATGTTTTTATCCCTCAAGTTCACT 57.466 29.630 0.00 0.00 0.00 3.41
2572 4509 8.713271 CCTCAAGTTCACTAAAAATAGACACTC 58.287 37.037 0.00 0.00 0.00 3.51
2589 4527 7.001099 AGACACTCGGTTCCTAAGAATTTTA 57.999 36.000 0.00 0.00 33.67 1.52
2611 4549 5.379706 AGGAAGATATTTGGTCCCTCAAG 57.620 43.478 0.00 0.00 0.00 3.02
2615 4553 5.622346 AGATATTTGGTCCCTCAAGTCTC 57.378 43.478 0.00 0.00 0.00 3.36
2621 4559 2.158667 TGGTCCCTCAAGTCTCAAAACC 60.159 50.000 0.00 0.00 0.00 3.27
2622 4560 2.143925 GTCCCTCAAGTCTCAAAACCG 58.856 52.381 0.00 0.00 0.00 4.44
2624 4562 1.071699 CCCTCAAGTCTCAAAACCGGA 59.928 52.381 9.46 0.00 0.00 5.14
2625 4563 2.290323 CCCTCAAGTCTCAAAACCGGAT 60.290 50.000 9.46 0.00 0.00 4.18
2626 4564 3.055385 CCCTCAAGTCTCAAAACCGGATA 60.055 47.826 9.46 0.00 0.00 2.59
2627 4565 4.564821 CCCTCAAGTCTCAAAACCGGATAA 60.565 45.833 9.46 0.00 0.00 1.75
2628 4566 5.001232 CCTCAAGTCTCAAAACCGGATAAA 58.999 41.667 9.46 0.00 0.00 1.40
2629 4567 5.648092 CCTCAAGTCTCAAAACCGGATAAAT 59.352 40.000 9.46 0.00 0.00 1.40
2630 4568 6.151144 CCTCAAGTCTCAAAACCGGATAAATT 59.849 38.462 9.46 0.00 0.00 1.82
2631 4569 7.309194 CCTCAAGTCTCAAAACCGGATAAATTT 60.309 37.037 9.46 0.00 0.00 1.82
2632 4570 7.947282 TCAAGTCTCAAAACCGGATAAATTTT 58.053 30.769 9.46 0.14 0.00 1.82
2633 4571 7.865385 TCAAGTCTCAAAACCGGATAAATTTTG 59.135 33.333 9.46 14.56 42.21 2.44
2656 4594 1.065273 AGTAATAGGCGTCGGTGCG 59.935 57.895 0.00 0.00 35.06 5.34
2709 4647 0.179092 ACGCGATTTGCCCCTACTAC 60.179 55.000 15.93 0.00 42.08 2.73
2710 4648 0.104304 CGCGATTTGCCCCTACTACT 59.896 55.000 0.00 0.00 42.08 2.57
2711 4649 1.338973 CGCGATTTGCCCCTACTACTA 59.661 52.381 0.00 0.00 42.08 1.82
2712 4650 2.607282 CGCGATTTGCCCCTACTACTAG 60.607 54.545 0.00 0.00 42.08 2.57
2814 4757 4.214383 CTCAACGATGCAGCGGCG 62.214 66.667 29.52 18.62 45.35 6.46
2834 4777 2.280524 CGGCTTCGTCCCACACAA 60.281 61.111 0.00 0.00 0.00 3.33
2879 4845 4.749310 CTGCTTGCCGTCCTCGCT 62.749 66.667 0.00 0.00 35.54 4.93
2882 4848 4.379243 CTTGCCGTCCTCGCTGGT 62.379 66.667 0.00 0.00 37.07 4.00
3057 5030 6.144724 CGTGTTCCAACAAAGAAACTCAAAAA 59.855 34.615 0.00 0.00 41.21 1.94
3059 5032 6.425417 TGTTCCAACAAAGAAACTCAAAAACC 59.575 34.615 0.00 0.00 35.67 3.27
3061 5034 6.764379 TCCAACAAAGAAACTCAAAAACCTT 58.236 32.000 0.00 0.00 0.00 3.50
3062 5035 7.897864 TCCAACAAAGAAACTCAAAAACCTTA 58.102 30.769 0.00 0.00 0.00 2.69
3064 5037 9.161629 CCAACAAAGAAACTCAAAAACCTTATT 57.838 29.630 0.00 0.00 0.00 1.40
3065 5038 9.971744 CAACAAAGAAACTCAAAAACCTTATTG 57.028 29.630 0.00 0.00 0.00 1.90
3115 5093 2.306847 ACATCGGTTCCAGCAAAAAGT 58.693 42.857 0.00 0.00 0.00 2.66
3142 5120 5.708230 ACAGAAACAAAAACACCAGTACTCA 59.292 36.000 0.00 0.00 0.00 3.41
3266 5441 2.953821 CCGAACGCAACAAGCCAT 59.046 55.556 0.00 0.00 41.38 4.40
3282 5457 4.356442 ATGGCCGCGGCACAAAAC 62.356 61.111 46.88 30.52 41.84 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.343941 TTTATTCCTCTGGAACGGTGG 57.656 47.619 0.71 0.00 45.07 4.61
34 35 6.072119 ACGGGAAAGAAGTGTTGGATTTATTC 60.072 38.462 0.00 0.00 0.00 1.75
63 64 4.619227 ACGGAACCACCTGCACGG 62.619 66.667 1.16 1.16 36.31 4.94
64 65 3.041940 GACGGAACCACCTGCACG 61.042 66.667 0.00 0.00 36.31 5.34
121 122 0.748005 CCTGGGATACAAAGCACGGG 60.748 60.000 0.00 0.00 33.78 5.28
123 124 0.035439 ACCCTGGGATACAAAGCACG 60.035 55.000 22.23 0.00 39.74 5.34
176 177 3.311110 GGAGACCCACACGGAGCA 61.311 66.667 0.00 0.00 34.64 4.26
184 185 0.108615 CGTGTGATCTGGAGACCCAC 60.109 60.000 0.00 0.00 37.58 4.61
346 438 0.687354 CCAGCACCCTTGTGTAGACT 59.313 55.000 0.00 0.00 44.65 3.24
413 505 1.215382 CATCGAAGGCCACACTCGA 59.785 57.895 17.79 17.79 37.24 4.04
608 717 1.217916 TCCTTGGAACCAGACAACCA 58.782 50.000 0.00 0.00 0.00 3.67
683 792 2.858260 GCAGAGAATCGTCAGCTAGCTC 60.858 54.545 16.15 3.47 42.67 4.09
789 898 4.421033 AGAAAAGTTTAAAGGCTAGCGC 57.579 40.909 9.00 0.00 0.00 5.92
818 927 4.320935 GCTGCCGTTTCTTTCCAATCTTAA 60.321 41.667 0.00 0.00 0.00 1.85
819 928 3.190535 GCTGCCGTTTCTTTCCAATCTTA 59.809 43.478 0.00 0.00 0.00 2.10
820 929 2.029918 GCTGCCGTTTCTTTCCAATCTT 60.030 45.455 0.00 0.00 0.00 2.40
821 930 1.541588 GCTGCCGTTTCTTTCCAATCT 59.458 47.619 0.00 0.00 0.00 2.40
822 931 1.402852 GGCTGCCGTTTCTTTCCAATC 60.403 52.381 1.35 0.00 0.00 2.67
823 932 0.603065 GGCTGCCGTTTCTTTCCAAT 59.397 50.000 1.35 0.00 0.00 3.16
897 1013 3.039526 AGAGGAGGGGAGGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
902 1018 1.761667 CAGAGCAGAGGAGGGGAGG 60.762 68.421 0.00 0.00 0.00 4.30
904 1020 2.364842 GCAGAGCAGAGGAGGGGA 60.365 66.667 0.00 0.00 0.00 4.81
905 1021 1.633915 ATTGCAGAGCAGAGGAGGGG 61.634 60.000 0.00 0.00 40.61 4.79
906 1022 0.255318 AATTGCAGAGCAGAGGAGGG 59.745 55.000 0.00 0.00 40.61 4.30
907 1023 2.996249 TAATTGCAGAGCAGAGGAGG 57.004 50.000 0.00 0.00 40.61 4.30
908 1024 3.995705 GCTATAATTGCAGAGCAGAGGAG 59.004 47.826 0.00 0.00 40.61 3.69
909 1025 3.244353 GGCTATAATTGCAGAGCAGAGGA 60.244 47.826 8.31 0.00 40.61 3.71
910 1026 3.072944 GGCTATAATTGCAGAGCAGAGG 58.927 50.000 8.31 0.00 40.61 3.69
911 1027 3.736720 TGGCTATAATTGCAGAGCAGAG 58.263 45.455 8.31 0.00 40.61 3.35
912 1028 3.843893 TGGCTATAATTGCAGAGCAGA 57.156 42.857 8.31 0.00 40.61 4.26
913 1029 3.304525 GCTTGGCTATAATTGCAGAGCAG 60.305 47.826 10.06 1.49 40.61 4.24
914 1030 2.620115 GCTTGGCTATAATTGCAGAGCA 59.380 45.455 10.06 0.00 38.68 4.26
915 1031 2.030451 GGCTTGGCTATAATTGCAGAGC 60.030 50.000 0.00 0.00 38.36 4.09
940 1058 4.636435 AGACGTTGGGCGGGGTTG 62.636 66.667 0.00 0.00 46.52 3.77
941 1059 4.324991 GAGACGTTGGGCGGGGTT 62.325 66.667 0.00 0.00 46.52 4.11
1068 1208 2.364448 AAGGAGGAGGAGGCGGAC 60.364 66.667 0.00 0.00 0.00 4.79
1428 1574 2.126424 AACGCGTTCTCGGAGCTC 60.126 61.111 20.79 4.71 37.56 4.09
1692 1838 2.019951 GTTGATGGCGTCGTCGTGT 61.020 57.895 4.52 0.00 39.49 4.49
1797 1943 4.269523 GCCAGGAGGGTGTGTGCA 62.270 66.667 0.00 0.00 39.65 4.57
1800 1946 2.532715 ATGGCCAGGAGGGTGTGT 60.533 61.111 13.05 0.00 39.65 3.72
2285 2431 0.591170 CCGGACAAATCACACGCTTT 59.409 50.000 0.00 0.00 0.00 3.51
2372 2518 4.382470 CCAAAACAATCTGAACAACACCCA 60.382 41.667 0.00 0.00 0.00 4.51
2425 2613 4.436242 ACCTATGACTAGTTGTGTGTCG 57.564 45.455 0.00 0.00 33.81 4.35
2558 4247 8.125978 TCTTAGGAACCGAGTGTCTATTTTTA 57.874 34.615 0.00 0.00 0.00 1.52
2589 4527 4.790790 ACTTGAGGGACCAAATATCTTCCT 59.209 41.667 0.00 0.00 0.00 3.36
2595 4533 5.779241 TTGAGACTTGAGGGACCAAATAT 57.221 39.130 0.00 0.00 0.00 1.28
2596 4534 5.576563 TTTGAGACTTGAGGGACCAAATA 57.423 39.130 0.00 0.00 0.00 1.40
2611 4549 5.867174 CCCAAAATTTATCCGGTTTTGAGAC 59.133 40.000 22.16 0.00 42.47 3.36
2615 4553 3.687212 GCCCCAAAATTTATCCGGTTTTG 59.313 43.478 16.39 16.39 40.63 2.44
2621 4559 4.993029 TTACTGCCCCAAAATTTATCCG 57.007 40.909 0.00 0.00 0.00 4.18
2622 4560 6.518369 GCCTATTACTGCCCCAAAATTTATCC 60.518 42.308 0.00 0.00 0.00 2.59
2624 4562 5.010617 CGCCTATTACTGCCCCAAAATTTAT 59.989 40.000 0.00 0.00 0.00 1.40
2625 4563 4.339814 CGCCTATTACTGCCCCAAAATTTA 59.660 41.667 0.00 0.00 0.00 1.40
2626 4564 3.132111 CGCCTATTACTGCCCCAAAATTT 59.868 43.478 0.00 0.00 0.00 1.82
2627 4565 2.693074 CGCCTATTACTGCCCCAAAATT 59.307 45.455 0.00 0.00 0.00 1.82
2628 4566 2.306847 CGCCTATTACTGCCCCAAAAT 58.693 47.619 0.00 0.00 0.00 1.82
2629 4567 1.004979 ACGCCTATTACTGCCCCAAAA 59.995 47.619 0.00 0.00 0.00 2.44
2630 4568 0.621609 ACGCCTATTACTGCCCCAAA 59.378 50.000 0.00 0.00 0.00 3.28
2631 4569 0.179468 GACGCCTATTACTGCCCCAA 59.821 55.000 0.00 0.00 0.00 4.12
2632 4570 1.827394 GACGCCTATTACTGCCCCA 59.173 57.895 0.00 0.00 0.00 4.96
2633 4571 1.300697 CGACGCCTATTACTGCCCC 60.301 63.158 0.00 0.00 0.00 5.80
2692 4630 2.626743 TCTAGTAGTAGGGGCAAATCGC 59.373 50.000 4.74 0.00 41.28 4.58
2709 4647 9.270640 CTTGGTGAGGATTAGATTTGATTCTAG 57.729 37.037 0.00 0.00 30.20 2.43
2710 4648 8.772250 ACTTGGTGAGGATTAGATTTGATTCTA 58.228 33.333 0.00 0.00 0.00 2.10
2711 4649 7.637511 ACTTGGTGAGGATTAGATTTGATTCT 58.362 34.615 0.00 0.00 0.00 2.40
2712 4650 7.554118 TGACTTGGTGAGGATTAGATTTGATTC 59.446 37.037 0.00 0.00 0.00 2.52
2822 4765 1.514678 GCTGCAATTGTGTGGGACGA 61.515 55.000 7.40 0.00 0.00 4.20
2827 4770 1.372004 CGGTGCTGCAATTGTGTGG 60.372 57.895 2.77 0.00 0.00 4.17
2879 4845 4.738998 CAATCCCTGCGGCCACCA 62.739 66.667 2.24 0.00 0.00 4.17
2882 4848 2.130821 TACAACAATCCCTGCGGCCA 62.131 55.000 2.24 0.00 0.00 5.36
2919 4885 1.230324 GTCAACAACAGGAGCTGGAC 58.770 55.000 0.00 0.00 35.51 4.02
2920 4886 0.249868 CGTCAACAACAGGAGCTGGA 60.250 55.000 0.00 0.00 35.51 3.86
3057 5030 5.112129 ACCGGCTAATTCTTCAATAAGGT 57.888 39.130 0.00 0.00 33.22 3.50
3059 5032 5.588648 TGGAACCGGCTAATTCTTCAATAAG 59.411 40.000 0.00 0.00 0.00 1.73
3061 5034 5.105567 TGGAACCGGCTAATTCTTCAATA 57.894 39.130 0.00 0.00 0.00 1.90
3062 5035 3.947834 CTGGAACCGGCTAATTCTTCAAT 59.052 43.478 0.00 0.00 0.00 2.57
3064 5037 2.939640 GCTGGAACCGGCTAATTCTTCA 60.940 50.000 16.37 0.00 44.39 3.02
3065 5038 1.671328 GCTGGAACCGGCTAATTCTTC 59.329 52.381 16.37 0.00 44.39 2.87
3092 5070 4.522789 ACTTTTTGCTGGAACCGATGTTAT 59.477 37.500 0.00 0.00 33.97 1.89
3115 5093 5.461032 ACTGGTGTTTTTGTTTCTGTGAA 57.539 34.783 0.00 0.00 0.00 3.18
3142 5120 6.062095 ACTGACTAGTGTTTTTGCTACCATT 58.938 36.000 0.00 0.00 35.34 3.16
3252 5231 2.339712 GCCATGGCTTGTTGCGTT 59.660 55.556 29.98 0.00 44.05 4.84
3253 5232 3.683937 GGCCATGGCTTGTTGCGT 61.684 61.111 34.70 0.00 44.05 5.24
3254 5233 4.781959 CGGCCATGGCTTGTTGCG 62.782 66.667 34.70 24.26 44.05 4.85


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

AutoCloner maintained by Alex Coulton.