Multiple sequence alignment - TraesCS5D01G103500

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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 TraesCS5D01G103500 chr5D 100.000 3694 0 0 1 3694 117262892 117266585 0.000000e+00 6822.0
1 TraesCS5D01G103500 chr5D 92.727 55 2 2 2797 2850 117265648 117265701 1.100000e-10 78.7
2 TraesCS5D01G103500 chr5D 92.727 55 2 2 2757 2810 117265688 117265741 1.100000e-10 78.7
3 TraesCS5D01G103500 chr5B 96.412 1282 44 2 1487 2766 129721786 129720505 0.000000e+00 2111.0
4 TraesCS5D01G103500 chr5B 89.957 1394 99 21 103 1489 129723302 129721943 0.000000e+00 1760.0
5 TraesCS5D01G103500 chr5B 93.995 866 41 8 2837 3694 129720515 129719653 0.000000e+00 1301.0
6 TraesCS5D01G103500 chr5A 95.169 1242 30 8 277 1489 126267203 126268443 0.000000e+00 1934.0
7 TraesCS5D01G103500 chr5A 96.183 1048 35 2 1767 2810 126271822 126272868 0.000000e+00 1709.0
8 TraesCS5D01G103500 chr5A 89.592 932 40 18 2797 3694 126272816 126273724 0.000000e+00 1131.0
9 TraesCS5D01G103500 chr5A 97.518 282 6 1 1487 1768 126268524 126268804 7.170000e-132 481.0
10 TraesCS5D01G103500 chr5A 90.714 280 16 5 1 270 126265268 126265547 7.540000e-97 364.0
11 TraesCS5D01G103500 chr2D 86.765 136 17 1 1813 1947 114641066 114640931 2.300000e-32 150.0
12 TraesCS5D01G103500 chr4D 89.565 115 12 0 1833 1947 68488275 68488161 2.970000e-31 147.0
13 TraesCS5D01G103500 chr3D 91.509 106 9 0 1832 1937 590673559 590673664 2.970000e-31 147.0
14 TraesCS5D01G103500 chr7D 88.983 118 12 1 1813 1929 559103971 559104088 1.070000e-30 145.0
15 TraesCS5D01G103500 chr6B 91.429 70 4 2 458 526 640963822 640963890 1.090000e-15 95.3
16 TraesCS5D01G103500 chr6D 89.855 69 7 0 458 526 425887850 425887918 5.080000e-14 89.8
17 TraesCS5D01G103500 chr3A 92.308 52 4 0 478 529 523147694 523147643 1.420000e-09 75.0


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 TraesCS5D01G103500 chr5D 117262892 117266585 3693 False 2326.466667 6822 95.151333 1 3694 3 chr5D.!!$F1 3693
1 TraesCS5D01G103500 chr5B 129719653 129723302 3649 True 1724.000000 2111 93.454667 103 3694 3 chr5B.!!$R1 3591
2 TraesCS5D01G103500 chr5A 126265268 126273724 8456 False 1123.800000 1934 93.835200 1 3694 5 chr5A.!!$F1 3693

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
812 2501 0.669318 CACATGCCCTTTGCTTGCAG 60.669 55.0 0.0 0.0 46.26 4.41 F
1947 6823 1.466856 TGCAGCATCTGGGAAACATC 58.533 50.0 0.0 0.0 31.21 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 6960 1.006998 AGAGGCTCCAGATCACAGAGT 59.993 52.381 11.71 0.0 0.00 3.24 R
2815 7691 0.032130 CGCCCTTCGCTAGCTTATCA 59.968 55.000 13.93 0.0 34.21 2.15 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
48 51 2.158682 TGTACCAATCTTGCCACACACT 60.159 45.455 0.00 0.00 0.00 3.55
93 96 6.607004 TTCACCTTTTTCTTTGGGTTGTTA 57.393 33.333 0.00 0.00 0.00 2.41
95 98 6.635755 TCACCTTTTTCTTTGGGTTGTTAAG 58.364 36.000 0.00 0.00 0.00 1.85
173 176 3.639094 AGACAGAGTACTTTGCTCAGTGT 59.361 43.478 13.09 0.13 33.77 3.55
198 201 6.817184 TGTTCTAGCCAGGATATACAACTTC 58.183 40.000 0.00 0.00 0.00 3.01
249 260 3.308401 TGCATCACCCTAGAATAGCAGA 58.692 45.455 0.00 0.00 37.37 4.26
251 262 3.864160 GCATCACCCTAGAATAGCAGAGC 60.864 52.174 0.00 0.00 37.37 4.09
271 282 3.967987 AGCCTACTATGACCCGAGAATTT 59.032 43.478 0.00 0.00 0.00 1.82
444 2104 5.395325 TGCTACTAGTAATCGTGTACGTC 57.605 43.478 3.76 0.00 40.80 4.34
522 2182 9.519191 AATTGCATGTTGATATTAGGTAGCATA 57.481 29.630 0.00 0.00 0.00 3.14
597 2257 3.728076 TTAGCGATAAACATCGGAGCT 57.272 42.857 8.89 0.00 43.66 4.09
628 2288 3.270877 GTTGGATAGATGCGGTTGAACT 58.729 45.455 0.00 0.00 0.00 3.01
656 2316 1.621317 TGTGTTGGATCTCCGCAACTA 59.379 47.619 12.04 1.93 39.43 2.24
812 2501 0.669318 CACATGCCCTTTGCTTGCAG 60.669 55.000 0.00 0.00 46.26 4.41
938 2630 3.012518 CCCTTCTTGTATGAACCAGCTG 58.987 50.000 6.78 6.78 0.00 4.24
959 2651 1.571919 GTGCCATCACCACGTATCTC 58.428 55.000 0.00 0.00 37.24 2.75
1159 2851 3.515901 GGTCTTGAGTGAGTTATCCAGGT 59.484 47.826 0.00 0.00 0.00 4.00
1768 3621 3.638160 TGCTCCTTCAGTTTGAATTTGCT 59.362 39.130 0.00 0.00 35.59 3.91
1790 6662 4.635223 TGGAGATGCTATGCACTACATTC 58.365 43.478 0.00 0.00 43.04 2.67
1798 6670 4.034510 GCTATGCACTACATTCTTTCGCTT 59.965 41.667 0.00 0.00 40.38 4.68
1919 6795 3.243873 GGCAGATGTTCCAGTCGATGATA 60.244 47.826 0.00 0.00 0.00 2.15
1947 6823 1.466856 TGCAGCATCTGGGAAACATC 58.533 50.000 0.00 0.00 31.21 3.06
2081 6957 3.383505 CCGTCCTGTATTACTGGTCATCA 59.616 47.826 16.60 0.00 38.25 3.07
2084 6960 5.623596 CGTCCTGTATTACTGGTCATCAACA 60.624 44.000 16.60 0.00 38.25 3.33
2090 6966 4.955811 TTACTGGTCATCAACACTCTGT 57.044 40.909 0.00 0.00 0.00 3.41
2264 7140 0.108329 AGTGGGAAATGTACGCCTCG 60.108 55.000 0.00 0.00 0.00 4.63
2480 7356 0.476023 TGGCCAAGGGTAACAGGGTA 60.476 55.000 0.61 0.00 39.74 3.69
2525 7401 4.821589 GGCGAGGGAGCGGTCAAG 62.822 72.222 17.59 5.30 38.18 3.02
2741 7617 8.938883 AGGCTCAGAGGTTTATATTCATCTTAA 58.061 33.333 0.00 0.00 0.00 1.85
2779 7655 7.210174 AGCTTTGCTCATCGTAAGTTATGATA 58.790 34.615 15.66 0.16 30.62 2.15
2802 7678 2.358247 GCGAAGGGCGTCTTTCCA 60.358 61.111 6.27 0.00 43.41 3.53
2803 7679 1.745489 GCGAAGGGCGTCTTTCCAT 60.745 57.895 6.27 0.00 43.41 3.41
2804 7680 1.706287 GCGAAGGGCGTCTTTCCATC 61.706 60.000 6.27 0.00 43.41 3.51
2805 7681 0.391130 CGAAGGGCGTCTTTCCATCA 60.391 55.000 6.27 0.00 35.50 3.07
2806 7682 1.743772 CGAAGGGCGTCTTTCCATCAT 60.744 52.381 6.27 0.00 35.50 2.45
2807 7683 1.672881 GAAGGGCGTCTTTCCATCATG 59.327 52.381 0.00 0.00 35.50 3.07
2808 7684 0.911769 AGGGCGTCTTTCCATCATGA 59.088 50.000 0.00 0.00 0.00 3.07
2809 7685 1.281867 AGGGCGTCTTTCCATCATGAA 59.718 47.619 0.00 0.00 0.00 2.57
2810 7686 2.091541 GGGCGTCTTTCCATCATGAAA 58.908 47.619 0.00 0.00 33.42 2.69
2822 7698 9.674824 CTTTCCATCATGAAAGTTATGATAAGC 57.325 33.333 0.00 0.00 43.95 3.09
2823 7699 8.985315 TTCCATCATGAAAGTTATGATAAGCT 57.015 30.769 0.00 0.00 41.91 3.74
2825 7701 9.716531 TCCATCATGAAAGTTATGATAAGCTAG 57.283 33.333 0.00 0.00 41.91 3.42
2826 7702 8.449397 CCATCATGAAAGTTATGATAAGCTAGC 58.551 37.037 6.62 6.62 41.91 3.42
2827 7703 7.643528 TCATGAAAGTTATGATAAGCTAGCG 57.356 36.000 9.55 0.00 30.03 4.26
2828 7704 7.433680 TCATGAAAGTTATGATAAGCTAGCGA 58.566 34.615 9.55 1.39 30.03 4.93
2829 7705 7.926018 TCATGAAAGTTATGATAAGCTAGCGAA 59.074 33.333 9.55 1.26 30.03 4.70
2830 7706 7.700322 TGAAAGTTATGATAAGCTAGCGAAG 57.300 36.000 9.55 0.00 0.00 3.79
2831 7707 6.701841 TGAAAGTTATGATAAGCTAGCGAAGG 59.298 38.462 9.55 0.00 0.00 3.46
2832 7708 5.140747 AGTTATGATAAGCTAGCGAAGGG 57.859 43.478 9.55 0.00 0.00 3.95
2833 7709 2.464157 ATGATAAGCTAGCGAAGGGC 57.536 50.000 9.55 0.00 44.05 5.19
2869 7745 2.942710 ACGGAGTACAGTTCATGAACG 58.057 47.619 28.18 24.23 42.85 3.95
2875 7751 5.924825 GGAGTACAGTTCATGAACGTTACTT 59.075 40.000 33.11 24.36 45.50 2.24
2876 7752 6.423001 GGAGTACAGTTCATGAACGTTACTTT 59.577 38.462 33.11 22.82 45.50 2.66
2877 7753 7.042254 GGAGTACAGTTCATGAACGTTACTTTT 60.042 37.037 33.11 22.36 45.50 2.27
2878 7754 7.848491 AGTACAGTTCATGAACGTTACTTTTC 58.152 34.615 30.29 16.89 45.50 2.29
2879 7755 6.671614 ACAGTTCATGAACGTTACTTTTCA 57.328 33.333 28.18 0.00 45.50 2.69
2880 7756 6.483687 ACAGTTCATGAACGTTACTTTTCAC 58.516 36.000 28.18 5.20 45.50 3.18
2881 7757 5.907391 CAGTTCATGAACGTTACTTTTCACC 59.093 40.000 28.18 4.16 45.50 4.02
2882 7758 5.587043 AGTTCATGAACGTTACTTTTCACCA 59.413 36.000 28.18 0.00 45.50 4.17
2883 7759 6.262273 AGTTCATGAACGTTACTTTTCACCAT 59.738 34.615 28.18 6.49 45.50 3.55
2884 7760 5.996219 TCATGAACGTTACTTTTCACCATG 58.004 37.500 0.00 7.59 34.61 3.66
2885 7761 5.529430 TCATGAACGTTACTTTTCACCATGT 59.471 36.000 15.88 0.00 34.61 3.21
2886 7762 6.706716 TCATGAACGTTACTTTTCACCATGTA 59.293 34.615 15.88 5.43 34.61 2.29
2887 7763 6.922247 TGAACGTTACTTTTCACCATGTAA 57.078 33.333 0.00 0.00 0.00 2.41
2888 7764 6.717413 TGAACGTTACTTTTCACCATGTAAC 58.283 36.000 0.00 0.00 40.45 2.50
2889 7765 6.539464 TGAACGTTACTTTTCACCATGTAACT 59.461 34.615 0.00 0.00 41.20 2.24
2890 7766 6.535274 ACGTTACTTTTCACCATGTAACTC 57.465 37.500 11.38 0.00 41.20 3.01
2997 7916 8.567948 TCAACAAAGAAACAAGATGAGAATACC 58.432 33.333 0.00 0.00 0.00 2.73
2998 7917 8.352201 CAACAAAGAAACAAGATGAGAATACCA 58.648 33.333 0.00 0.00 0.00 3.25
2999 7918 7.875971 ACAAAGAAACAAGATGAGAATACCAC 58.124 34.615 0.00 0.00 0.00 4.16
3017 7937 3.523564 ACCACCCAGTATGACAAGCTTAT 59.476 43.478 0.00 0.00 39.69 1.73
3121 8043 8.287503 AGTACAAACTGGTAACGATCAAATTTC 58.712 33.333 0.00 0.00 42.51 2.17
3133 8056 7.684062 ACGATCAAATTTCAAGAACACAAAG 57.316 32.000 0.00 0.00 0.00 2.77
3152 8075 5.365314 ACAAAGACCCCAAGCTCAAAAATTA 59.635 36.000 0.00 0.00 0.00 1.40
3153 8076 5.468540 AAGACCCCAAGCTCAAAAATTAC 57.531 39.130 0.00 0.00 0.00 1.89
3338 8264 0.524862 CAGCCAAGCATCACCACTTC 59.475 55.000 0.00 0.00 0.00 3.01
3339 8265 0.111061 AGCCAAGCATCACCACTTCA 59.889 50.000 0.00 0.00 0.00 3.02
3521 8449 3.264193 TCATTCCAGCAGGTACAACATCT 59.736 43.478 0.00 0.00 35.89 2.90
3524 8452 5.435686 TTCCAGCAGGTACAACATCTTAT 57.564 39.130 0.00 0.00 35.89 1.73
3556 8484 7.335924 TGTGAGTATACAACCCAAAAGATAAGC 59.664 37.037 5.50 0.00 0.00 3.09
3577 8505 6.369059 AGCATCAAAATGGTAGAGAAATCG 57.631 37.500 0.00 0.00 41.71 3.34
3633 8561 1.296715 GCCGCTTTCCTCCTTCTCA 59.703 57.895 0.00 0.00 0.00 3.27
3636 8564 0.737715 CGCTTTCCTCCTTCTCACGG 60.738 60.000 0.00 0.00 0.00 4.94
3653 8581 4.004982 TCACGGCCAAGGAACTAATAAAC 58.995 43.478 2.24 0.00 38.49 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.812571 GTGTGGCAAGATTGGTACAGG 59.187 52.381 0.00 0.00 42.39 4.00
93 96 4.284746 AGAAGTCGGGAAAGTTCATCTCTT 59.715 41.667 0.00 0.00 32.10 2.85
95 98 3.929610 CAGAAGTCGGGAAAGTTCATCTC 59.070 47.826 0.00 0.00 32.10 2.75
136 139 4.464597 ACTCTGTCTAGTTGGAACATCTCC 59.535 45.833 0.00 0.00 45.64 3.71
173 176 6.808321 AGTTGTATATCCTGGCTAGAACAA 57.192 37.500 0.00 8.09 0.00 2.83
249 260 2.750141 TTCTCGGGTCATAGTAGGCT 57.250 50.000 0.00 0.00 0.00 4.58
251 262 5.531122 TGAAATTCTCGGGTCATAGTAGG 57.469 43.478 0.00 0.00 0.00 3.18
271 282 1.271871 ACCGCAATTCCAAGGTGATGA 60.272 47.619 0.00 0.00 35.36 2.92
522 2182 9.137459 AGCATACCTAATATCAGCGATAGTTAT 57.863 33.333 4.40 0.00 39.35 1.89
526 2186 8.787852 TGATAGCATACCTAATATCAGCGATAG 58.212 37.037 0.00 0.00 32.38 2.08
557 2217 4.373156 AAACATGTTTAGCACTCTCCCT 57.627 40.909 22.10 0.00 0.00 4.20
583 2243 5.694910 CGGTTTATGTAGCTCCGATGTTTAT 59.305 40.000 1.71 0.00 43.22 1.40
597 2257 4.986034 CGCATCTATCCAACGGTTTATGTA 59.014 41.667 0.00 0.00 0.00 2.29
628 2288 2.237143 GGAGATCCAACACATCTCACCA 59.763 50.000 10.95 0.00 45.71 4.17
938 2630 1.762222 GATACGTGGTGATGGCACGC 61.762 60.000 0.00 0.00 46.09 5.34
959 2651 6.675026 TGAAGCACAGATTTCTTCAAATGAG 58.325 36.000 1.88 0.00 42.00 2.90
1070 2762 4.518970 TCTCCCATTTCCAAAGAAGAAACG 59.481 41.667 0.00 0.00 36.13 3.60
1159 2851 6.575244 TCTTGGGCTTATAATTTGAGAGGA 57.425 37.500 0.00 0.00 0.00 3.71
1357 3050 0.755686 CTATGGTCAGAGGTGGAGGC 59.244 60.000 0.00 0.00 0.00 4.70
1578 3431 2.785868 CCAGAATACAGTGGCCTGC 58.214 57.895 3.32 0.00 42.81 4.85
1697 3550 3.367703 GCAGCTTGAAACAGTGGCATATT 60.368 43.478 0.00 0.00 0.00 1.28
1706 3559 2.298163 AGAATTGGGCAGCTTGAAACAG 59.702 45.455 0.00 0.00 0.00 3.16
1707 3560 2.318908 AGAATTGGGCAGCTTGAAACA 58.681 42.857 0.00 0.00 0.00 2.83
1768 3621 4.346127 AGAATGTAGTGCATAGCATCTCCA 59.654 41.667 0.00 0.00 41.91 3.86
1790 6662 6.670077 AGCTCTAAAAATCCTAAGCGAAAG 57.330 37.500 0.00 0.00 34.99 2.62
1798 6670 9.975218 ATTACCTGAAAAGCTCTAAAAATCCTA 57.025 29.630 0.00 0.00 0.00 2.94
1843 6719 6.446318 GTTTTATCCTGCATTCTGAAACACA 58.554 36.000 0.00 0.00 0.00 3.72
1844 6720 5.863935 GGTTTTATCCTGCATTCTGAAACAC 59.136 40.000 13.52 0.00 0.00 3.32
1931 6807 3.952323 CTGAATGATGTTTCCCAGATGCT 59.048 43.478 0.00 0.00 0.00 3.79
1947 6823 3.630769 CCAACATCCTCCACATCTGAATG 59.369 47.826 0.00 0.00 38.93 2.67
1961 6837 1.369625 CGTACTTGGAGCCAACATCC 58.630 55.000 0.00 0.00 37.35 3.51
2081 6957 1.277557 GGCTCCAGATCACAGAGTGTT 59.722 52.381 0.00 0.00 34.79 3.32
2084 6960 1.006998 AGAGGCTCCAGATCACAGAGT 59.993 52.381 11.71 0.00 0.00 3.24
2090 6966 3.220629 CCTGAGAGGCTCCAGATCA 57.779 57.895 25.29 16.12 0.00 2.92
2264 7140 1.597663 CGATTGTTATTCGGTGCTCCC 59.402 52.381 0.00 0.00 33.05 4.30
2525 7401 1.127343 AGAGCTTGATCCTAGTGCCC 58.873 55.000 0.00 0.00 0.00 5.36
2741 7617 2.152016 GCAAAGCTTCTAAAGACGGGT 58.848 47.619 0.00 0.00 0.00 5.28
2779 7655 1.889530 AAGACGCCCTTCGCTAGCTT 61.890 55.000 13.93 0.00 43.23 3.74
2797 7673 9.412460 AGCTTATCATAACTTTCATGATGGAAA 57.588 29.630 0.00 0.00 41.92 3.13
2798 7674 8.985315 AGCTTATCATAACTTTCATGATGGAA 57.015 30.769 0.00 0.00 41.92 3.53
2799 7675 9.716531 CTAGCTTATCATAACTTTCATGATGGA 57.283 33.333 0.00 0.00 41.92 3.41
2800 7676 8.449397 GCTAGCTTATCATAACTTTCATGATGG 58.551 37.037 7.70 0.00 41.92 3.51
2801 7677 8.167345 CGCTAGCTTATCATAACTTTCATGATG 58.833 37.037 13.93 0.00 41.92 3.07
2802 7678 8.090831 TCGCTAGCTTATCATAACTTTCATGAT 58.909 33.333 13.93 3.55 43.72 2.45
2803 7679 7.433680 TCGCTAGCTTATCATAACTTTCATGA 58.566 34.615 13.93 0.00 36.86 3.07
2804 7680 7.643528 TCGCTAGCTTATCATAACTTTCATG 57.356 36.000 13.93 0.00 0.00 3.07
2805 7681 7.386299 CCTTCGCTAGCTTATCATAACTTTCAT 59.614 37.037 13.93 0.00 0.00 2.57
2806 7682 6.701841 CCTTCGCTAGCTTATCATAACTTTCA 59.298 38.462 13.93 0.00 0.00 2.69
2807 7683 6.146347 CCCTTCGCTAGCTTATCATAACTTTC 59.854 42.308 13.93 0.00 0.00 2.62
2808 7684 5.992217 CCCTTCGCTAGCTTATCATAACTTT 59.008 40.000 13.93 0.00 0.00 2.66
2809 7685 5.542779 CCCTTCGCTAGCTTATCATAACTT 58.457 41.667 13.93 0.00 0.00 2.66
2810 7686 4.561734 GCCCTTCGCTAGCTTATCATAACT 60.562 45.833 13.93 0.00 0.00 2.24
2811 7687 3.680458 GCCCTTCGCTAGCTTATCATAAC 59.320 47.826 13.93 0.00 0.00 1.89
2812 7688 3.614150 CGCCCTTCGCTAGCTTATCATAA 60.614 47.826 13.93 0.00 34.21 1.90
2813 7689 2.094700 CGCCCTTCGCTAGCTTATCATA 60.095 50.000 13.93 0.00 34.21 2.15
2814 7690 1.337260 CGCCCTTCGCTAGCTTATCAT 60.337 52.381 13.93 0.00 34.21 2.45
2815 7691 0.032130 CGCCCTTCGCTAGCTTATCA 59.968 55.000 13.93 0.00 34.21 2.15
2816 7692 0.032267 ACGCCCTTCGCTAGCTTATC 59.968 55.000 13.93 0.00 43.23 1.75
2817 7693 0.032267 GACGCCCTTCGCTAGCTTAT 59.968 55.000 13.93 0.00 43.23 1.73
2818 7694 1.035932 AGACGCCCTTCGCTAGCTTA 61.036 55.000 13.93 0.00 43.23 3.09
2819 7695 1.889530 AAGACGCCCTTCGCTAGCTT 61.890 55.000 13.93 0.00 43.23 3.74
2820 7696 1.889530 AAAGACGCCCTTCGCTAGCT 61.890 55.000 13.93 0.00 43.23 3.32
2821 7697 1.422179 GAAAGACGCCCTTCGCTAGC 61.422 60.000 4.06 4.06 43.23 3.42
2822 7698 0.806492 GGAAAGACGCCCTTCGCTAG 60.806 60.000 0.00 0.00 43.23 3.42
2823 7699 1.217244 GGAAAGACGCCCTTCGCTA 59.783 57.895 0.00 0.00 43.23 4.26
2824 7700 2.047179 GGAAAGACGCCCTTCGCT 60.047 61.111 0.00 0.00 43.23 4.93
2825 7701 1.706287 GATGGAAAGACGCCCTTCGC 61.706 60.000 0.00 0.00 43.23 4.70
2826 7702 0.391130 TGATGGAAAGACGCCCTTCG 60.391 55.000 0.00 0.00 45.38 3.79
2827 7703 1.672881 CATGATGGAAAGACGCCCTTC 59.327 52.381 0.00 0.00 33.02 3.46
2828 7704 1.281867 TCATGATGGAAAGACGCCCTT 59.718 47.619 0.00 0.00 36.47 3.95
2829 7705 0.911769 TCATGATGGAAAGACGCCCT 59.088 50.000 0.00 0.00 0.00 5.19
2830 7706 1.401905 GTTCATGATGGAAAGACGCCC 59.598 52.381 0.00 0.00 0.00 6.13
2831 7707 1.062587 CGTTCATGATGGAAAGACGCC 59.937 52.381 0.00 0.00 0.00 5.68
2832 7708 1.062587 CCGTTCATGATGGAAAGACGC 59.937 52.381 8.48 0.00 36.44 5.19
2833 7709 2.604914 CTCCGTTCATGATGGAAAGACG 59.395 50.000 15.74 11.52 42.88 4.18
2834 7710 3.600388 ACTCCGTTCATGATGGAAAGAC 58.400 45.455 15.74 0.79 42.88 3.01
2869 7745 7.492352 ACAGAGTTACATGGTGAAAAGTAAC 57.508 36.000 0.00 0.00 43.95 2.50
2875 7751 6.588204 AGTGTTACAGAGTTACATGGTGAAA 58.412 36.000 0.00 0.00 28.20 2.69
2876 7752 6.169557 AGTGTTACAGAGTTACATGGTGAA 57.830 37.500 0.00 0.00 28.20 3.18
2877 7753 5.801531 AGTGTTACAGAGTTACATGGTGA 57.198 39.130 0.00 0.00 28.20 4.02
2878 7754 5.758296 ACAAGTGTTACAGAGTTACATGGTG 59.242 40.000 0.00 0.00 28.20 4.17
2879 7755 5.925509 ACAAGTGTTACAGAGTTACATGGT 58.074 37.500 0.00 0.00 28.20 3.55
2880 7756 6.861065 AACAAGTGTTACAGAGTTACATGG 57.139 37.500 0.00 0.00 36.32 3.66
2881 7757 7.957484 GCATAACAAGTGTTACAGAGTTACATG 59.043 37.037 6.05 0.00 42.55 3.21
2882 7758 7.119262 GGCATAACAAGTGTTACAGAGTTACAT 59.881 37.037 6.05 0.00 42.55 2.29
2883 7759 6.425721 GGCATAACAAGTGTTACAGAGTTACA 59.574 38.462 6.05 0.00 42.55 2.41
2884 7760 6.400727 CGGCATAACAAGTGTTACAGAGTTAC 60.401 42.308 6.05 0.00 42.55 2.50
2885 7761 5.636121 CGGCATAACAAGTGTTACAGAGTTA 59.364 40.000 6.05 6.65 42.55 2.24
2886 7762 4.451096 CGGCATAACAAGTGTTACAGAGTT 59.549 41.667 6.05 0.00 42.55 3.01
2887 7763 3.994392 CGGCATAACAAGTGTTACAGAGT 59.006 43.478 6.05 0.00 42.55 3.24
2888 7764 3.370978 CCGGCATAACAAGTGTTACAGAG 59.629 47.826 6.05 0.28 42.55 3.35
2889 7765 3.244284 ACCGGCATAACAAGTGTTACAGA 60.244 43.478 0.00 0.00 42.55 3.41
2890 7766 3.071479 ACCGGCATAACAAGTGTTACAG 58.929 45.455 0.00 4.08 42.55 2.74
2997 7916 6.524734 TGATATAAGCTTGTCATACTGGGTG 58.475 40.000 9.86 0.00 0.00 4.61
2998 7917 6.747414 TGATATAAGCTTGTCATACTGGGT 57.253 37.500 9.86 0.00 0.00 4.51
2999 7918 7.220030 ACTTGATATAAGCTTGTCATACTGGG 58.780 38.462 9.86 1.52 0.00 4.45
3121 8043 2.223805 GCTTGGGGTCTTTGTGTTCTTG 60.224 50.000 0.00 0.00 0.00 3.02
3133 8056 4.864704 TGTAATTTTTGAGCTTGGGGTC 57.135 40.909 0.00 0.00 40.08 4.46
3152 8075 5.105310 GGTCACATGTATCACTAGGTCTTGT 60.105 44.000 0.00 0.00 0.00 3.16
3153 8076 5.127845 AGGTCACATGTATCACTAGGTCTTG 59.872 44.000 0.00 0.00 0.00 3.02
3338 8264 7.066163 TGCCAGTTATGATTGACAACTTATCTG 59.934 37.037 0.00 3.45 30.20 2.90
3339 8265 7.112122 TGCCAGTTATGATTGACAACTTATCT 58.888 34.615 0.00 0.00 30.20 1.98
3505 8431 6.500684 AACAATAAGATGTTGTACCTGCTG 57.499 37.500 0.00 0.00 41.78 4.41
3536 8464 8.815565 TTGATGCTTATCTTTTGGGTTGTATA 57.184 30.769 0.00 0.00 0.00 1.47
3537 8465 7.716799 TTGATGCTTATCTTTTGGGTTGTAT 57.283 32.000 0.00 0.00 0.00 2.29
3545 8473 9.512435 CTCTACCATTTTGATGCTTATCTTTTG 57.488 33.333 0.00 0.00 0.00 2.44
3556 8484 6.540189 AGGACGATTTCTCTACCATTTTGATG 59.460 38.462 0.00 0.00 0.00 3.07
3577 8505 3.326880 TCTGGTAAAAAGGTGAGGAGGAC 59.673 47.826 0.00 0.00 0.00 3.85
3633 8561 4.023726 TGTTTATTAGTTCCTTGGCCGT 57.976 40.909 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.