Multiple sequence alignment - TraesCS3D01G391400

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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 TraesCS3D01G391400 chr3D 100.000 3445 0 0 1 3445 506200286 506203730 0.000000e+00 6362
1 TraesCS3D01G391400 chr3D 90.741 216 14 5 2837 3047 506203045 506203259 2.020000e-72 283
2 TraesCS3D01G391400 chr3D 90.741 216 14 5 2760 2974 506203122 506203332 2.020000e-72 283
3 TraesCS3D01G391400 chr3D 90.210 143 9 4 2910 3047 506203045 506203187 7.590000e-42 182
4 TraesCS3D01G391400 chr3D 90.210 143 9 4 2760 2902 506203195 506203332 7.590000e-42 182
5 TraesCS3D01G391400 chr3B 96.163 2606 50 13 401 2974 668144271 668146858 0.000000e+00 4213
6 TraesCS3D01G391400 chr3B 94.137 614 30 5 2837 3445 668146643 668147255 0.000000e+00 929
7 TraesCS3D01G391400 chr3B 90.557 413 27 5 1 404 668142077 668142486 1.410000e-148 536
8 TraesCS3D01G391400 chr3B 90.909 143 9 3 2760 2902 668146720 668146858 4.540000e-44 189
9 TraesCS3D01G391400 chr3B 89.510 143 10 4 2910 3047 668146643 668146785 3.530000e-40 176


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 TraesCS3D01G391400 chr3D 506200286 506203730 3444 False 1458.4 6362 92.3804 1 3445 5 chr3D.!!$F1 3444
1 TraesCS3D01G391400 chr3B 668142077 668147255 5178 False 1208.6 4213 92.2552 1 3445 5 chr3B.!!$F1 3444

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
658 2468 0.036858 GCTCTCCTTTGCCGTCTTCT 60.037 55.0 0.0 0.0 0.0 2.85 F
664 2474 0.038159 CTTTGCCGTCTTCTCCGTCT 60.038 55.0 0.0 0.0 0.0 4.18 F
1872 3701 0.263172 TCCCTCCTCTCACTCCCATC 59.737 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3600 0.335019 TGGACGAGGAAGATGAGGGA 59.665 55.000 0.0 0.0 0.00 4.20 R
2432 4261 0.394192 TGTCAACTCACTGCCTCCTG 59.606 55.000 0.0 0.0 0.00 3.86 R
3118 4947 1.132657 TCCCACTTAGTTGGACCCTGA 60.133 52.381 0.6 0.0 39.24 3.86 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
30 31 4.758165 TGCATGCTATGTATGGTTGATCTG 59.242 41.667 20.33 0.00 0.00 2.90
31 32 4.758674 GCATGCTATGTATGGTTGATCTGT 59.241 41.667 11.37 0.00 0.00 3.41
32 33 5.334646 GCATGCTATGTATGGTTGATCTGTG 60.335 44.000 11.37 0.00 0.00 3.66
49 50 8.883954 TGATCTGTGCTATTTTCTATCTGAAG 57.116 34.615 0.00 0.00 35.89 3.02
88 89 2.675844 TGTTTGCTATGAATTCCGTCCG 59.324 45.455 2.27 0.00 0.00 4.79
152 153 0.178068 TAGCTTTGGATGACCGCCTC 59.822 55.000 0.00 0.00 39.42 4.70
176 177 0.465705 ATCTGTGTCGGCATACTGGG 59.534 55.000 0.00 0.00 0.00 4.45
184 185 1.461461 GGCATACTGGGCCCCTCTA 60.461 63.158 22.27 5.91 45.87 2.43
186 187 0.615850 GCATACTGGGCCCCTCTATC 59.384 60.000 22.27 0.12 0.00 2.08
193 194 2.140792 GGCCCCTCTATCCGCTGAA 61.141 63.158 0.00 0.00 0.00 3.02
196 197 0.470080 CCCCTCTATCCGCTGAAGGA 60.470 60.000 0.00 0.00 45.54 3.36
234 235 1.278238 CGTCAGCGTTGAAGATACCC 58.722 55.000 9.47 0.00 35.16 3.69
235 236 1.135083 CGTCAGCGTTGAAGATACCCT 60.135 52.381 9.47 0.00 35.16 4.34
237 238 3.428452 CGTCAGCGTTGAAGATACCCTAA 60.428 47.826 9.47 0.00 35.16 2.69
238 239 3.864003 GTCAGCGTTGAAGATACCCTAAC 59.136 47.826 2.60 0.00 34.49 2.34
241 242 3.518303 AGCGTTGAAGATACCCTAACCTT 59.482 43.478 0.00 0.00 0.00 3.50
242 243 3.621715 GCGTTGAAGATACCCTAACCTTG 59.378 47.826 0.00 0.00 0.00 3.61
243 244 4.189231 CGTTGAAGATACCCTAACCTTGG 58.811 47.826 0.00 0.00 0.00 3.61
292 301 8.948853 TTTTTCACAATAGCTAAATTCAGTCG 57.051 30.769 0.00 0.00 0.00 4.18
354 363 0.729140 CCTTGCGTGCGGTTCATTTC 60.729 55.000 0.00 0.00 0.00 2.17
355 364 0.040514 CTTGCGTGCGGTTCATTTCA 60.041 50.000 0.00 0.00 0.00 2.69
374 384 5.509605 TTCACATTGACGTAACAATCGAG 57.490 39.130 0.00 0.00 38.25 4.04
379 389 3.909776 TGACGTAACAATCGAGTGACT 57.090 42.857 21.18 8.59 0.00 3.41
380 390 3.818387 TGACGTAACAATCGAGTGACTC 58.182 45.455 21.18 1.65 0.00 3.36
396 406 7.226523 TCGAGTGACTCAAATTCAAAAATCAGA 59.773 33.333 13.67 0.00 0.00 3.27
397 407 7.322222 CGAGTGACTCAAATTCAAAAATCAGAC 59.678 37.037 13.67 0.00 0.00 3.51
418 2216 4.694339 ACGACTTACATCTAGCCATTTCC 58.306 43.478 0.00 0.00 0.00 3.13
419 2217 4.161565 ACGACTTACATCTAGCCATTTCCA 59.838 41.667 0.00 0.00 0.00 3.53
420 2218 5.163301 ACGACTTACATCTAGCCATTTCCAT 60.163 40.000 0.00 0.00 0.00 3.41
629 2439 2.685380 CCCCGCCCTCTGTTCTCT 60.685 66.667 0.00 0.00 0.00 3.10
656 2466 1.374758 CGCTCTCCTTTGCCGTCTT 60.375 57.895 0.00 0.00 0.00 3.01
657 2467 1.355066 CGCTCTCCTTTGCCGTCTTC 61.355 60.000 0.00 0.00 0.00 2.87
658 2468 0.036858 GCTCTCCTTTGCCGTCTTCT 60.037 55.000 0.00 0.00 0.00 2.85
659 2469 2.003196 CTCTCCTTTGCCGTCTTCTC 57.997 55.000 0.00 0.00 0.00 2.87
660 2470 0.608640 TCTCCTTTGCCGTCTTCTCC 59.391 55.000 0.00 0.00 0.00 3.71
661 2471 0.737715 CTCCTTTGCCGTCTTCTCCG 60.738 60.000 0.00 0.00 0.00 4.63
662 2472 1.004918 CCTTTGCCGTCTTCTCCGT 60.005 57.895 0.00 0.00 0.00 4.69
663 2473 1.014564 CCTTTGCCGTCTTCTCCGTC 61.015 60.000 0.00 0.00 0.00 4.79
664 2474 0.038159 CTTTGCCGTCTTCTCCGTCT 60.038 55.000 0.00 0.00 0.00 4.18
718 2529 2.279469 GACGAATCGAACTGAGGCG 58.721 57.895 10.55 0.00 34.42 5.52
719 2530 1.743855 GACGAATCGAACTGAGGCGC 61.744 60.000 10.55 0.00 32.27 6.53
720 2531 2.849966 CGAATCGAACTGAGGCGCG 61.850 63.158 0.00 0.00 0.00 6.86
1100 2918 0.390340 CTGATCGCGGATATGGTGGG 60.390 60.000 6.13 0.00 0.00 4.61
1154 2972 0.933097 CGATTGATGAAGGCGTCCTG 59.067 55.000 0.00 0.00 32.13 3.86
1408 3226 0.905357 CACCTACCTCTCTTGGGTGG 59.095 60.000 0.00 0.00 42.39 4.61
1448 3266 2.162608 CCTCCGCTAGATACCTCATTCG 59.837 54.545 0.00 0.00 0.00 3.34
1458 3276 1.645710 ACCTCATTCGTCAGGAACCT 58.354 50.000 0.00 0.00 37.50 3.50
1517 3335 1.066908 CGATCCTGAGAAGAGGCAGAC 59.933 57.143 0.00 0.00 34.06 3.51
1572 3390 2.811317 GCTCAACGTGCCGAGGAG 60.811 66.667 10.78 8.22 35.25 3.69
1612 3430 2.328099 GCGGACAAGGAAGCACTGG 61.328 63.158 0.00 0.00 0.00 4.00
1627 3445 4.026744 AGCACTGGTTCTATTAGCAGAGA 58.973 43.478 9.52 0.00 44.37 3.10
1634 3452 4.286910 GTTCTATTAGCAGAGACAGCTCG 58.713 47.826 0.00 0.00 45.98 5.03
1713 3531 1.135859 CGAGCTTGGATGTTGCTGTTC 60.136 52.381 0.00 0.00 37.16 3.18
1744 3562 1.152271 ACAAGGGGAAGGAGAAGGAGA 59.848 52.381 0.00 0.00 0.00 3.71
1750 3568 1.478916 GGAAGGAGAAGGAGAACGAGG 59.521 57.143 0.00 0.00 0.00 4.63
1810 3628 2.357517 CCTCGTCCACAGGCACAC 60.358 66.667 0.00 0.00 0.00 3.82
1818 3636 1.821759 CACAGGCACACCCGAACAA 60.822 57.895 0.00 0.00 39.21 2.83
1829 3656 2.664851 CGAACAACCTCAGCGGCA 60.665 61.111 1.45 0.00 35.61 5.69
1832 3659 1.444119 GAACAACCTCAGCGGCAACA 61.444 55.000 1.45 0.00 35.61 3.33
1843 3670 1.946267 CGGCAACACAAGGTACACC 59.054 57.895 0.00 0.00 0.00 4.16
1844 3671 1.837538 CGGCAACACAAGGTACACCG 61.838 60.000 0.00 0.00 42.08 4.94
1872 3701 0.263172 TCCCTCCTCTCACTCCCATC 59.737 60.000 0.00 0.00 0.00 3.51
2167 3996 2.980233 GCTTGGCTTGCTGACCGT 60.980 61.111 0.00 0.00 0.00 4.83
2238 4067 1.418334 ATAGCACCAGAGGCCACTAG 58.582 55.000 5.01 0.00 0.00 2.57
2480 4309 5.048434 GTCAAACCTCTTTGCAAGAATAGCT 60.048 40.000 0.00 0.00 37.31 3.32
2532 4361 4.494515 GAACCGCCCTTGTTCCTT 57.505 55.556 0.00 0.00 36.87 3.36
2551 4380 5.253330 TCCTTACAGTTCCTAAGGCATTTG 58.747 41.667 0.00 0.00 40.11 2.32
2563 4392 2.183409 GCATTTGCCTCACCACGAT 58.817 52.632 0.00 0.00 34.31 3.73
2648 4477 3.399330 AGAGTGTGACCATACAAAACCG 58.601 45.455 0.03 0.00 31.36 4.44
2687 4516 3.375299 GCCTCGCAAGTGTTGATTCTAAT 59.625 43.478 0.00 0.00 39.48 1.73
2878 4707 6.165700 TCGGTCCTTGTAGTTTTAAGTTCT 57.834 37.500 0.00 0.00 0.00 3.01
2886 4715 9.490379 CCTTGTAGTTTTAAGTTCTGAGTACAT 57.510 33.333 0.00 0.00 0.00 2.29
2892 4721 9.046296 AGTTTTAAGTTCTGAGTACATTGACTG 57.954 33.333 0.00 0.00 0.00 3.51
2893 4722 7.962964 TTTAAGTTCTGAGTACATTGACTGG 57.037 36.000 0.00 0.00 0.00 4.00
2894 4723 5.808366 AAGTTCTGAGTACATTGACTGGA 57.192 39.130 0.00 0.00 0.00 3.86
2895 4724 6.365970 AAGTTCTGAGTACATTGACTGGAT 57.634 37.500 0.00 0.00 0.00 3.41
2896 4725 5.728471 AGTTCTGAGTACATTGACTGGATG 58.272 41.667 0.00 0.00 0.00 3.51
2897 4726 5.247110 AGTTCTGAGTACATTGACTGGATGT 59.753 40.000 0.00 0.00 40.59 3.06
2898 4727 5.745312 TCTGAGTACATTGACTGGATGTT 57.255 39.130 0.00 0.00 38.58 2.71
2899 4728 6.850752 TCTGAGTACATTGACTGGATGTTA 57.149 37.500 0.00 0.00 38.58 2.41
2900 4729 6.631016 TCTGAGTACATTGACTGGATGTTAC 58.369 40.000 0.00 0.00 38.58 2.50
2901 4730 6.210584 TCTGAGTACATTGACTGGATGTTACA 59.789 38.462 0.00 0.00 38.58 2.41
2902 4731 6.946340 TGAGTACATTGACTGGATGTTACAT 58.054 36.000 0.00 0.00 38.58 2.29
2903 4732 7.394016 TGAGTACATTGACTGGATGTTACATT 58.606 34.615 0.00 0.00 38.58 2.71
2904 4733 7.334171 TGAGTACATTGACTGGATGTTACATTG 59.666 37.037 0.00 0.00 38.58 2.82
2905 4734 7.394016 AGTACATTGACTGGATGTTACATTGA 58.606 34.615 0.00 0.00 38.58 2.57
2906 4735 8.049117 AGTACATTGACTGGATGTTACATTGAT 58.951 33.333 0.00 0.00 38.58 2.57
2907 4736 7.707624 ACATTGACTGGATGTTACATTGATT 57.292 32.000 0.00 0.00 34.18 2.57
2908 4737 8.125978 ACATTGACTGGATGTTACATTGATTT 57.874 30.769 0.00 0.00 34.18 2.17
2909 4738 8.587608 ACATTGACTGGATGTTACATTGATTTT 58.412 29.630 0.00 0.00 34.18 1.82
2910 4739 9.079833 CATTGACTGGATGTTACATTGATTTTC 57.920 33.333 0.00 0.00 0.00 2.29
2911 4740 8.408043 TTGACTGGATGTTACATTGATTTTCT 57.592 30.769 0.00 0.00 0.00 2.52
2912 4741 8.408043 TGACTGGATGTTACATTGATTTTCTT 57.592 30.769 0.00 0.00 0.00 2.52
2913 4742 8.514594 TGACTGGATGTTACATTGATTTTCTTC 58.485 33.333 0.00 0.00 0.00 2.87
2914 4743 8.641498 ACTGGATGTTACATTGATTTTCTTCT 57.359 30.769 0.00 0.00 0.00 2.85
2915 4744 8.734386 ACTGGATGTTACATTGATTTTCTTCTC 58.266 33.333 0.00 0.00 0.00 2.87
2916 4745 8.634335 TGGATGTTACATTGATTTTCTTCTCA 57.366 30.769 0.00 0.00 0.00 3.27
2917 4746 9.076781 TGGATGTTACATTGATTTTCTTCTCAA 57.923 29.630 0.00 0.00 35.95 3.02
2931 4760 9.846248 ATTTTCTTCTCAATGTATTTTCTTCGG 57.154 29.630 0.00 0.00 0.00 4.30
2932 4761 7.979444 TTCTTCTCAATGTATTTTCTTCGGT 57.021 32.000 0.00 0.00 0.00 4.69
2933 4762 7.596749 TCTTCTCAATGTATTTTCTTCGGTC 57.403 36.000 0.00 0.00 0.00 4.79
2934 4763 6.594159 TCTTCTCAATGTATTTTCTTCGGTCC 59.406 38.462 0.00 0.00 0.00 4.46
2935 4764 6.049955 TCTCAATGTATTTTCTTCGGTCCT 57.950 37.500 0.00 0.00 0.00 3.85
2936 4765 6.472887 TCTCAATGTATTTTCTTCGGTCCTT 58.527 36.000 0.00 0.00 0.00 3.36
2937 4766 6.371548 TCTCAATGTATTTTCTTCGGTCCTTG 59.628 38.462 0.00 0.00 0.00 3.61
2938 4767 6.001460 TCAATGTATTTTCTTCGGTCCTTGT 58.999 36.000 0.00 0.00 0.00 3.16
2939 4768 7.162761 TCAATGTATTTTCTTCGGTCCTTGTA 58.837 34.615 0.00 0.00 0.00 2.41
2940 4769 7.333423 TCAATGTATTTTCTTCGGTCCTTGTAG 59.667 37.037 0.00 0.00 0.00 2.74
2941 4770 6.105397 TGTATTTTCTTCGGTCCTTGTAGT 57.895 37.500 0.00 0.00 0.00 2.73
2942 4771 6.527423 TGTATTTTCTTCGGTCCTTGTAGTT 58.473 36.000 0.00 0.00 0.00 2.24
2943 4772 6.993902 TGTATTTTCTTCGGTCCTTGTAGTTT 59.006 34.615 0.00 0.00 0.00 2.66
2944 4773 6.954487 ATTTTCTTCGGTCCTTGTAGTTTT 57.046 33.333 0.00 0.00 0.00 2.43
2945 4774 8.992073 GTATTTTCTTCGGTCCTTGTAGTTTTA 58.008 33.333 0.00 0.00 0.00 1.52
2946 4775 7.862512 TTTTCTTCGGTCCTTGTAGTTTTAA 57.137 32.000 0.00 0.00 0.00 1.52
2947 4776 7.486802 TTTCTTCGGTCCTTGTAGTTTTAAG 57.513 36.000 0.00 0.00 0.00 1.85
2948 4777 6.165700 TCTTCGGTCCTTGTAGTTTTAAGT 57.834 37.500 0.00 0.00 0.00 2.24
2949 4778 6.585416 TCTTCGGTCCTTGTAGTTTTAAGTT 58.415 36.000 0.00 0.00 0.00 2.66
2950 4779 6.480981 TCTTCGGTCCTTGTAGTTTTAAGTTG 59.519 38.462 0.00 0.00 0.00 3.16
2951 4780 5.673514 TCGGTCCTTGTAGTTTTAAGTTGT 58.326 37.500 0.00 0.00 0.00 3.32
2952 4781 5.524646 TCGGTCCTTGTAGTTTTAAGTTGTG 59.475 40.000 0.00 0.00 0.00 3.33
2953 4782 5.524646 CGGTCCTTGTAGTTTTAAGTTGTGA 59.475 40.000 0.00 0.00 0.00 3.58
2954 4783 6.292703 CGGTCCTTGTAGTTTTAAGTTGTGAG 60.293 42.308 0.00 0.00 0.00 3.51
2955 4784 6.541278 GGTCCTTGTAGTTTTAAGTTGTGAGT 59.459 38.462 0.00 0.00 0.00 3.41
2956 4785 7.712205 GGTCCTTGTAGTTTTAAGTTGTGAGTA 59.288 37.037 0.00 0.00 0.00 2.59
2957 4786 8.546244 GTCCTTGTAGTTTTAAGTTGTGAGTAC 58.454 37.037 0.00 0.00 0.00 2.73
3115 4944 6.150976 TGCAGTGTTGTTATCCTTCCTAATTG 59.849 38.462 0.00 0.00 0.00 2.32
3118 4947 8.960591 CAGTGTTGTTATCCTTCCTAATTGATT 58.039 33.333 0.00 0.00 0.00 2.57
3127 4956 4.079787 CCTTCCTAATTGATTCAGGGTCCA 60.080 45.833 0.00 0.00 0.00 4.02
3138 4967 1.132657 TCAGGGTCCAACTAAGTGGGA 60.133 52.381 0.00 0.00 39.34 4.37
3142 4971 2.500504 GGGTCCAACTAAGTGGGAGTAG 59.499 54.545 0.00 0.00 36.15 2.57
3225 5054 1.906757 TGTGCTGAACTGCAAAAACG 58.093 45.000 7.84 0.00 45.12 3.60
3274 5103 6.509199 GCATTGTTGAAGATACTGATGTCTCG 60.509 42.308 0.00 0.00 0.00 4.04
3280 5109 2.158534 AGATACTGATGTCTCGGAGCCT 60.159 50.000 0.00 0.00 0.00 4.58
3337 5166 2.228103 AGAAATGTCACTGTGCATGCAG 59.772 45.455 23.41 13.42 41.92 4.41
3358 5187 1.456296 TGAGACCATCAGCACAATGC 58.544 50.000 0.00 0.00 45.46 3.56
3390 5219 8.068380 CGTAACGTCTTACTAGATCATTGATGA 58.932 37.037 3.32 0.00 34.71 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.758674 GCACAGATCAACCATACATAGCAT 59.241 41.667 0.00 0.00 0.00 3.79
30 31 9.713740 CATCAAACTTCAGATAGAAAATAGCAC 57.286 33.333 0.00 0.00 35.40 4.40
31 32 9.671279 TCATCAAACTTCAGATAGAAAATAGCA 57.329 29.630 0.00 0.00 35.40 3.49
49 50 5.108254 GCAAACACGACAGATTTCATCAAAC 60.108 40.000 0.00 0.00 0.00 2.93
122 123 0.239347 CCAAAGCTAGCCGCATATGC 59.761 55.000 18.08 18.08 42.61 3.14
170 171 1.155390 CGGATAGAGGGGCCCAGTA 59.845 63.158 27.72 16.07 0.00 2.74
176 177 1.369321 CTTCAGCGGATAGAGGGGC 59.631 63.158 0.00 0.00 0.00 5.80
222 223 4.524053 CCCAAGGTTAGGGTATCTTCAAC 58.476 47.826 0.00 0.00 41.61 3.18
234 235 2.654863 CCATTAGGCACCCAAGGTTAG 58.345 52.381 0.00 0.00 31.02 2.34
235 236 2.818751 CCATTAGGCACCCAAGGTTA 57.181 50.000 0.00 0.00 31.02 2.85
299 308 2.523015 CATCTCCAACGCTGAATTTGC 58.477 47.619 0.00 0.00 0.00 3.68
312 321 1.845791 TGCAGATTTAGGGCATCTCCA 59.154 47.619 0.00 0.00 36.21 3.86
354 363 4.384547 TCACTCGATTGTTACGTCAATGTG 59.615 41.667 7.17 9.06 38.03 3.21
355 364 4.384846 GTCACTCGATTGTTACGTCAATGT 59.615 41.667 7.17 0.00 38.03 2.71
374 384 7.112148 GTCGTCTGATTTTTGAATTTGAGTCAC 59.888 37.037 0.00 0.00 0.00 3.67
379 389 8.616942 TGTAAGTCGTCTGATTTTTGAATTTGA 58.383 29.630 0.00 0.00 0.00 2.69
380 390 8.781067 TGTAAGTCGTCTGATTTTTGAATTTG 57.219 30.769 0.00 0.00 0.00 2.32
396 406 4.161565 TGGAAATGGCTAGATGTAAGTCGT 59.838 41.667 0.00 0.00 0.00 4.34
397 407 4.693283 TGGAAATGGCTAGATGTAAGTCG 58.307 43.478 0.00 0.00 0.00 4.18
615 2425 1.550976 AGGTTAAGAGAACAGAGGGCG 59.449 52.381 0.00 0.00 0.00 6.13
629 2439 2.874457 GCAAAGGAGAGCGGAAGGTTAA 60.874 50.000 0.00 0.00 45.11 2.01
656 2466 1.975407 GTGGGGACGAAGACGGAGA 60.975 63.158 0.00 0.00 44.46 3.71
657 2467 1.935327 GAGTGGGGACGAAGACGGAG 61.935 65.000 0.00 0.00 44.46 4.63
658 2468 1.975407 GAGTGGGGACGAAGACGGA 60.975 63.158 0.00 0.00 44.46 4.69
659 2469 2.572284 GAGTGGGGACGAAGACGG 59.428 66.667 0.00 0.00 44.46 4.79
660 2470 2.572284 GGAGTGGGGACGAAGACG 59.428 66.667 0.00 0.00 45.75 4.18
661 2471 2.657066 GGGGAGTGGGGACGAAGAC 61.657 68.421 0.00 0.00 0.00 3.01
662 2472 2.284405 GGGGAGTGGGGACGAAGA 60.284 66.667 0.00 0.00 0.00 2.87
663 2473 2.606519 TGGGGAGTGGGGACGAAG 60.607 66.667 0.00 0.00 0.00 3.79
664 2474 2.926242 GTGGGGAGTGGGGACGAA 60.926 66.667 0.00 0.00 0.00 3.85
977 2795 1.134175 CTCTCCTTCTTGAGTCGCCTC 59.866 57.143 0.00 0.00 38.27 4.70
1057 2875 2.257371 CTTCTTGGCGTCGACGGA 59.743 61.111 36.13 22.99 40.23 4.69
1154 2972 3.209410 GGTTCACATCCCATCAGATGAC 58.791 50.000 12.41 0.00 45.43 3.06
1408 3226 2.741747 GTAGGCCACCCTATCCGC 59.258 66.667 5.01 0.00 45.22 5.54
1448 3266 2.675317 CGGAGTGATTCAGGTTCCTGAC 60.675 54.545 19.57 10.89 42.04 3.51
1458 3276 0.909610 AAGCCTCCCGGAGTGATTCA 60.910 55.000 13.62 0.00 0.00 2.57
1484 3302 2.653702 GATCGGATGAGGCGAGGG 59.346 66.667 0.00 0.00 0.00 4.30
1612 3430 4.286910 CGAGCTGTCTCTGCTAATAGAAC 58.713 47.826 0.00 0.00 38.70 3.01
1652 3470 1.378514 GCCTCCCCGAATTGCTTGA 60.379 57.895 0.00 0.00 0.00 3.02
1731 3549 1.478916 CCCTCGTTCTCCTTCTCCTTC 59.521 57.143 0.00 0.00 0.00 3.46
1781 3599 0.747852 GGACGAGGAAGATGAGGGAC 59.252 60.000 0.00 0.00 0.00 4.46
1782 3600 0.335019 TGGACGAGGAAGATGAGGGA 59.665 55.000 0.00 0.00 0.00 4.20
1810 3628 2.742372 CCGCTGAGGTTGTTCGGG 60.742 66.667 0.00 0.00 36.73 5.14
1818 3636 1.893808 CTTGTGTTGCCGCTGAGGT 60.894 57.895 0.00 0.00 43.70 3.85
1829 3656 2.248835 GCGCGGTGTACCTTGTGTT 61.249 57.895 8.83 0.00 0.00 3.32
1872 3701 2.567497 GGATTGGATGGCCATGGCG 61.567 63.158 29.90 0.00 45.46 5.69
1883 3712 2.264455 CCAAATTTGGGGTGGATTGGA 58.736 47.619 26.87 0.00 44.70 3.53
1910 3739 3.565764 TCCTCATTTCAATCAGGCGAT 57.434 42.857 0.00 0.00 0.00 4.58
2273 4102 8.057246 ACCAAAATGGAAGACCCTATATGTAT 57.943 34.615 2.85 0.00 40.96 2.29
2339 4168 5.551233 TCAATTACCAAGAGACCAGAACAG 58.449 41.667 0.00 0.00 0.00 3.16
2432 4261 0.394192 TGTCAACTCACTGCCTCCTG 59.606 55.000 0.00 0.00 0.00 3.86
2480 4309 0.976641 AAGAGTGAGAACCGATGCCA 59.023 50.000 0.00 0.00 0.00 4.92
2807 4636 8.716646 TCAATGTAACATTCAATCGATGTACT 57.283 30.769 0.00 0.00 0.00 2.73
2878 4707 6.353404 TGTAACATCCAGTCAATGTACTCA 57.647 37.500 0.00 0.00 36.35 3.41
2886 4715 8.408043 AGAAAATCAATGTAACATCCAGTCAA 57.592 30.769 0.00 0.00 0.00 3.18
2887 4716 8.408043 AAGAAAATCAATGTAACATCCAGTCA 57.592 30.769 0.00 0.00 0.00 3.41
2888 4717 8.734386 AGAAGAAAATCAATGTAACATCCAGTC 58.266 33.333 0.00 0.00 0.00 3.51
2889 4718 8.641498 AGAAGAAAATCAATGTAACATCCAGT 57.359 30.769 0.00 0.00 0.00 4.00
2890 4719 8.733458 TGAGAAGAAAATCAATGTAACATCCAG 58.267 33.333 0.00 0.00 0.00 3.86
2891 4720 8.634335 TGAGAAGAAAATCAATGTAACATCCA 57.366 30.769 0.00 0.00 0.00 3.41
2905 4734 9.846248 CCGAAGAAAATACATTGAGAAGAAAAT 57.154 29.630 0.00 0.00 0.00 1.82
2906 4735 8.846211 ACCGAAGAAAATACATTGAGAAGAAAA 58.154 29.630 0.00 0.00 0.00 2.29
2907 4736 8.391075 ACCGAAGAAAATACATTGAGAAGAAA 57.609 30.769 0.00 0.00 0.00 2.52
2908 4737 7.119262 GGACCGAAGAAAATACATTGAGAAGAA 59.881 37.037 0.00 0.00 0.00 2.52
2909 4738 6.594159 GGACCGAAGAAAATACATTGAGAAGA 59.406 38.462 0.00 0.00 0.00 2.87
2910 4739 6.595716 AGGACCGAAGAAAATACATTGAGAAG 59.404 38.462 0.00 0.00 0.00 2.85
2911 4740 6.472887 AGGACCGAAGAAAATACATTGAGAA 58.527 36.000 0.00 0.00 0.00 2.87
2912 4741 6.049955 AGGACCGAAGAAAATACATTGAGA 57.950 37.500 0.00 0.00 0.00 3.27
2913 4742 6.149474 ACAAGGACCGAAGAAAATACATTGAG 59.851 38.462 0.00 0.00 0.00 3.02
2914 4743 6.001460 ACAAGGACCGAAGAAAATACATTGA 58.999 36.000 0.00 0.00 0.00 2.57
2915 4744 6.254281 ACAAGGACCGAAGAAAATACATTG 57.746 37.500 0.00 0.00 0.00 2.82
2916 4745 7.166167 ACTACAAGGACCGAAGAAAATACATT 58.834 34.615 0.00 0.00 0.00 2.71
2917 4746 6.708285 ACTACAAGGACCGAAGAAAATACAT 58.292 36.000 0.00 0.00 0.00 2.29
2918 4747 6.105397 ACTACAAGGACCGAAGAAAATACA 57.895 37.500 0.00 0.00 0.00 2.29
2919 4748 7.430992 AAACTACAAGGACCGAAGAAAATAC 57.569 36.000 0.00 0.00 0.00 1.89
2920 4749 9.558396 TTAAAACTACAAGGACCGAAGAAAATA 57.442 29.630 0.00 0.00 0.00 1.40
2921 4750 6.954487 AAAACTACAAGGACCGAAGAAAAT 57.046 33.333 0.00 0.00 0.00 1.82
2922 4751 7.553760 ACTTAAAACTACAAGGACCGAAGAAAA 59.446 33.333 0.00 0.00 0.00 2.29
2923 4752 7.049754 ACTTAAAACTACAAGGACCGAAGAAA 58.950 34.615 0.00 0.00 0.00 2.52
2924 4753 6.585416 ACTTAAAACTACAAGGACCGAAGAA 58.415 36.000 0.00 0.00 0.00 2.52
2925 4754 6.165700 ACTTAAAACTACAAGGACCGAAGA 57.834 37.500 0.00 0.00 0.00 2.87
2926 4755 6.259387 ACAACTTAAAACTACAAGGACCGAAG 59.741 38.462 0.00 0.00 0.00 3.79
2927 4756 6.037391 CACAACTTAAAACTACAAGGACCGAA 59.963 38.462 0.00 0.00 0.00 4.30
2928 4757 5.524646 CACAACTTAAAACTACAAGGACCGA 59.475 40.000 0.00 0.00 0.00 4.69
2929 4758 5.524646 TCACAACTTAAAACTACAAGGACCG 59.475 40.000 0.00 0.00 0.00 4.79
2930 4759 6.541278 ACTCACAACTTAAAACTACAAGGACC 59.459 38.462 0.00 0.00 0.00 4.46
2931 4760 7.549615 ACTCACAACTTAAAACTACAAGGAC 57.450 36.000 0.00 0.00 0.00 3.85
2932 4761 8.480501 AGTACTCACAACTTAAAACTACAAGGA 58.519 33.333 0.00 0.00 0.00 3.36
2933 4762 8.658499 AGTACTCACAACTTAAAACTACAAGG 57.342 34.615 0.00 0.00 0.00 3.61
2934 4763 9.916397 CAAGTACTCACAACTTAAAACTACAAG 57.084 33.333 0.00 0.00 35.44 3.16
2935 4764 9.656040 TCAAGTACTCACAACTTAAAACTACAA 57.344 29.630 0.00 0.00 35.44 2.41
2936 4765 9.826574 ATCAAGTACTCACAACTTAAAACTACA 57.173 29.630 0.00 0.00 35.44 2.74
2939 4768 9.391006 TCAATCAAGTACTCACAACTTAAAACT 57.609 29.630 0.00 0.00 35.44 2.66
2940 4769 9.997482 TTCAATCAAGTACTCACAACTTAAAAC 57.003 29.630 0.00 0.00 35.44 2.43
2943 4772 9.337396 ACATTCAATCAAGTACTCACAACTTAA 57.663 29.630 0.00 0.00 35.44 1.85
2944 4773 8.902540 ACATTCAATCAAGTACTCACAACTTA 57.097 30.769 0.00 0.00 35.44 2.24
2945 4774 7.807977 ACATTCAATCAAGTACTCACAACTT 57.192 32.000 0.00 0.00 37.67 2.66
2946 4775 7.807977 AACATTCAATCAAGTACTCACAACT 57.192 32.000 0.00 0.00 0.00 3.16
2947 4776 8.556194 TGTAACATTCAATCAAGTACTCACAAC 58.444 33.333 0.00 0.00 0.00 3.32
2948 4777 8.669946 TGTAACATTCAATCAAGTACTCACAA 57.330 30.769 0.00 0.00 0.00 3.33
2949 4778 8.846943 ATGTAACATTCAATCAAGTACTCACA 57.153 30.769 0.00 0.00 0.00 3.58
2950 4779 9.546909 CAATGTAACATTCAATCAAGTACTCAC 57.453 33.333 0.00 0.00 0.00 3.51
2951 4780 9.500785 TCAATGTAACATTCAATCAAGTACTCA 57.499 29.630 0.00 0.00 0.00 3.41
3032 4861 8.450578 TCATGAACTTTTGTAACATTCAGTCT 57.549 30.769 0.00 0.00 33.09 3.24
3035 4864 7.651808 ACCTCATGAACTTTTGTAACATTCAG 58.348 34.615 0.00 0.00 33.09 3.02
3069 4898 4.022676 GCAAACCGACAAGGATAAAAAGGA 60.023 41.667 0.00 0.00 45.00 3.36
3115 4944 3.610911 CCACTTAGTTGGACCCTGAATC 58.389 50.000 0.00 0.00 39.24 2.52
3118 4947 1.132657 TCCCACTTAGTTGGACCCTGA 60.133 52.381 0.60 0.00 39.24 3.86
3127 4956 6.653989 CATTCCAATCTACTCCCACTTAGTT 58.346 40.000 0.00 0.00 0.00 2.24
3138 4967 6.721318 TGGTAAAAGAGCATTCCAATCTACT 58.279 36.000 0.00 0.00 0.00 2.57
3142 4971 6.212888 ACATGGTAAAAGAGCATTCCAATC 57.787 37.500 0.00 0.00 43.93 2.67
3274 5103 9.869757 AATTACAATTATTTGTACAAAGGCTCC 57.130 29.630 24.22 0.00 45.60 4.70
3309 5138 3.559171 GCACAGTGACATTTCTTCCCCTA 60.559 47.826 4.15 0.00 0.00 3.53
3320 5149 1.743394 CATCTGCATGCACAGTGACAT 59.257 47.619 18.46 4.70 38.84 3.06
3337 5166 2.033049 GCATTGTGCTGATGGTCTCATC 59.967 50.000 0.00 0.00 40.96 2.92
3355 5184 1.425412 AAGACGTTACGAAAGCGCAT 58.575 45.000 13.03 0.00 42.48 4.73
3358 5187 4.641954 TCTAGTAAGACGTTACGAAAGCG 58.358 43.478 13.03 0.00 43.04 4.68
3367 5196 6.913132 CGTCATCAATGATCTAGTAAGACGTT 59.087 38.462 16.63 0.00 39.90 3.99


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

AutoCloner maintained by Alex Coulton.