Multiple sequence alignment - TraesCS4B01G130300

Loading Multiple Alignment...

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 TraesCS4B01G130300 chr4B 100.000 4149 0 0 1 4149 171029698 171025550 0.000000e+00 7662.0
1 TraesCS4B01G130300 chr4B 87.788 737 81 6 3 732 119269394 119270128 0.000000e+00 854.0
2 TraesCS4B01G130300 chr4B 76.800 125 17 8 2585 2699 250806087 250805965 4.480000e-05 60.2
3 TraesCS4B01G130300 chr4B 76.000 125 18 8 2585 2699 250758337 250758215 2.000000e-03 54.7
4 TraesCS4B01G130300 chr4A 94.428 3446 126 24 740 4149 466925610 466929025 0.000000e+00 5240.0
5 TraesCS4B01G130300 chr4D 94.421 2599 76 24 740 3291 109912371 109909795 0.000000e+00 3932.0
6 TraesCS4B01G130300 chr4D 91.794 719 37 7 3367 4067 109909452 109908738 0.000000e+00 981.0
7 TraesCS4B01G130300 chr4D 87.821 739 77 9 2 732 396428180 396428913 0.000000e+00 854.0
8 TraesCS4B01G130300 chr4D 87.364 736 87 4 2 732 424107545 424108279 0.000000e+00 839.0
9 TraesCS4B01G130300 chr5D 83.396 1066 139 26 1159 2192 242356809 242357868 0.000000e+00 953.0
10 TraesCS4B01G130300 chr5D 87.653 737 83 6 2 732 250594041 250594775 0.000000e+00 850.0
11 TraesCS4B01G130300 chr5D 87.584 741 82 5 1 732 539986732 539985993 0.000000e+00 850.0
12 TraesCS4B01G130300 chr5A 86.754 838 102 5 1159 1991 310874921 310874088 0.000000e+00 924.0
13 TraesCS4B01G130300 chr5B 86.619 837 105 6 1159 1991 259538264 259539097 0.000000e+00 918.0
14 TraesCS4B01G130300 chr7D 88.467 737 76 7 2 732 179500765 179500032 0.000000e+00 881.0
15 TraesCS4B01G130300 chr2D 88.211 721 80 4 17 732 476985636 476984916 0.000000e+00 856.0
16 TraesCS4B01G130300 chr2D 87.415 739 83 8 2 732 159335281 159336017 0.000000e+00 841.0
17 TraesCS4B01G130300 chr1D 87.500 736 87 3 2 732 274945978 274945243 0.000000e+00 845.0
18 TraesCS4B01G130300 chr1D 79.610 1025 186 19 1183 2189 404970787 404969768 0.000000e+00 713.0
19 TraesCS4B01G130300 chr1A 82.713 833 138 6 1159 1988 500343352 500342523 0.000000e+00 736.0
20 TraesCS4B01G130300 chr1B 82.280 807 141 2 1183 1988 544726894 544726089 0.000000e+00 697.0
21 TraesCS4B01G130300 chr3A 87.547 530 64 2 1159 1687 579552998 579553526 2.740000e-171 612.0
22 TraesCS4B01G130300 chr3A 86.986 146 15 4 1684 1827 579553635 579553778 1.190000e-35 161.0
23 TraesCS4B01G130300 chr3A 79.562 137 28 0 2301 2437 579554290 579554426 9.490000e-17 99.0


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 TraesCS4B01G130300 chr4B 171025550 171029698 4148 True 7662.000000 7662 100.000000 1 4149 1 chr4B.!!$R1 4148
1 TraesCS4B01G130300 chr4B 119269394 119270128 734 False 854.000000 854 87.788000 3 732 1 chr4B.!!$F1 729
2 TraesCS4B01G130300 chr4A 466925610 466929025 3415 False 5240.000000 5240 94.428000 740 4149 1 chr4A.!!$F1 3409
3 TraesCS4B01G130300 chr4D 109908738 109912371 3633 True 2456.500000 3932 93.107500 740 4067 2 chr4D.!!$R1 3327
4 TraesCS4B01G130300 chr4D 396428180 396428913 733 False 854.000000 854 87.821000 2 732 1 chr4D.!!$F1 730
5 TraesCS4B01G130300 chr4D 424107545 424108279 734 False 839.000000 839 87.364000 2 732 1 chr4D.!!$F2 730
6 TraesCS4B01G130300 chr5D 242356809 242357868 1059 False 953.000000 953 83.396000 1159 2192 1 chr5D.!!$F1 1033
7 TraesCS4B01G130300 chr5D 250594041 250594775 734 False 850.000000 850 87.653000 2 732 1 chr5D.!!$F2 730
8 TraesCS4B01G130300 chr5D 539985993 539986732 739 True 850.000000 850 87.584000 1 732 1 chr5D.!!$R1 731
9 TraesCS4B01G130300 chr5A 310874088 310874921 833 True 924.000000 924 86.754000 1159 1991 1 chr5A.!!$R1 832
10 TraesCS4B01G130300 chr5B 259538264 259539097 833 False 918.000000 918 86.619000 1159 1991 1 chr5B.!!$F1 832
11 TraesCS4B01G130300 chr7D 179500032 179500765 733 True 881.000000 881 88.467000 2 732 1 chr7D.!!$R1 730
12 TraesCS4B01G130300 chr2D 476984916 476985636 720 True 856.000000 856 88.211000 17 732 1 chr2D.!!$R1 715
13 TraesCS4B01G130300 chr2D 159335281 159336017 736 False 841.000000 841 87.415000 2 732 1 chr2D.!!$F1 730
14 TraesCS4B01G130300 chr1D 274945243 274945978 735 True 845.000000 845 87.500000 2 732 1 chr1D.!!$R1 730
15 TraesCS4B01G130300 chr1D 404969768 404970787 1019 True 713.000000 713 79.610000 1183 2189 1 chr1D.!!$R2 1006
16 TraesCS4B01G130300 chr1A 500342523 500343352 829 True 736.000000 736 82.713000 1159 1988 1 chr1A.!!$R1 829
17 TraesCS4B01G130300 chr1B 544726089 544726894 805 True 697.000000 697 82.280000 1183 1988 1 chr1B.!!$R1 805
18 TraesCS4B01G130300 chr3A 579552998 579554426 1428 False 290.666667 612 84.698333 1159 2437 3 chr3A.!!$F1 1278

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
749 765 0.107214 CATCCAACAGGGCGTACCAT 60.107 55.000 1.21 0.00 43.89 3.55 F
968 1006 0.395311 CTGGTTCTCCATGCATGCCT 60.395 55.000 21.69 1.31 43.43 4.75 F
971 1009 0.454600 GTTCTCCATGCATGCCTGTG 59.545 55.000 21.69 13.52 0.00 3.66 F
2279 2545 1.064758 AGTTTGTCAGGCACTCAACCA 60.065 47.619 0.00 0.00 34.60 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2271 0.036732 TTTCAGGCCATGAGCTTCGT 59.963 50.000 5.01 0.00 43.05 3.85 R
2453 2719 1.199327 CACTGCTTCCATGAGTTGCTG 59.801 52.381 0.00 0.11 0.00 4.41 R
2499 2765 2.230266 GTGCAATGGAACCCGTGTTATT 59.770 45.455 0.00 0.00 33.97 1.40 R
3347 3645 0.478072 ATGTGCAGGTGGGAGACAAA 59.522 50.000 0.00 0.00 0.00 2.83 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 5.991606 ACATTCTCAATCAGTTCGTTTCAGA 59.008 36.000 0.00 0.00 0.00 3.27
71 72 3.432378 AGTCACCTCCTTCGTGTTCTAT 58.568 45.455 0.00 0.00 32.86 1.98
84 85 5.212934 TCGTGTTCTATGATATCTTCGTGC 58.787 41.667 3.98 0.00 0.00 5.34
98 99 1.869574 CGTGCCACGATCTCTCACG 60.870 63.158 12.85 10.56 46.05 4.35
116 117 2.646175 GGCCTTTTCTTTCCCCGCC 61.646 63.158 0.00 0.00 0.00 6.13
130 131 3.393970 CGCCCCAGCTCTCTCCAA 61.394 66.667 0.00 0.00 36.60 3.53
169 170 1.974236 GCTATGTGGGCTAGTGATCCT 59.026 52.381 0.00 0.00 0.00 3.24
225 226 0.392193 CTTGGCGGCTCTCTCATTGT 60.392 55.000 11.43 0.00 0.00 2.71
275 276 0.177373 TCGCTCGAGTACAGAGGCTA 59.823 55.000 15.13 3.19 36.31 3.93
286 287 0.390340 CAGAGGCTAAGTTGCGAGCA 60.390 55.000 0.00 0.00 40.64 4.26
290 291 1.086696 GGCTAAGTTGCGAGCAATGA 58.913 50.000 13.89 2.00 40.64 2.57
300 301 3.534554 TGCGAGCAATGACTATGTTGAT 58.465 40.909 0.00 0.00 0.00 2.57
310 311 4.910195 TGACTATGTTGATTGCTGAGGTT 58.090 39.130 0.00 0.00 0.00 3.50
329 330 4.134563 GGTTATCTGGTTGCGATGGTTAT 58.865 43.478 0.00 0.00 0.00 1.89
332 333 4.900635 ATCTGGTTGCGATGGTTATTTC 57.099 40.909 0.00 0.00 0.00 2.17
342 343 4.438744 GCGATGGTTATTTCAGGACTTTGG 60.439 45.833 0.00 0.00 0.00 3.28
343 344 4.700213 CGATGGTTATTTCAGGACTTTGGT 59.300 41.667 0.00 0.00 0.00 3.67
348 349 5.278315 GGTTATTTCAGGACTTTGGTGTGTC 60.278 44.000 0.00 0.00 0.00 3.67
384 389 4.287552 ACTCCCTTATTGTCGGACAGTAT 58.712 43.478 13.21 7.27 0.00 2.12
409 414 1.858458 GCTATCAGTATTGCGCGTGAA 59.142 47.619 8.43 0.78 0.00 3.18
413 418 1.080366 AGTATTGCGCGTGAACCGA 60.080 52.632 8.43 0.00 39.56 4.69
479 484 1.154282 CGTGCTGCTGTGCAAGATG 60.154 57.895 0.00 0.00 45.12 2.90
507 512 1.406069 CGCTCTTCACTATGTGCCCTT 60.406 52.381 0.00 0.00 32.98 3.95
521 526 3.211045 GTGCCCTTTGAGTTACAGTTGA 58.789 45.455 0.00 0.00 0.00 3.18
529 534 6.984474 CCTTTGAGTTACAGTTGACAGACTTA 59.016 38.462 0.00 0.00 0.00 2.24
592 597 3.938963 TCTCCAAACTCAGTGTTGTTGAC 59.061 43.478 5.37 0.00 39.13 3.18
597 602 0.937304 CTCAGTGTTGTTGACCCACG 59.063 55.000 0.00 0.00 34.34 4.94
604 609 2.365941 TGTTGTTGACCCACGATGAGTA 59.634 45.455 0.00 0.00 0.00 2.59
605 610 2.993899 GTTGTTGACCCACGATGAGTAG 59.006 50.000 0.00 0.00 0.00 2.57
606 611 2.244695 TGTTGACCCACGATGAGTAGT 58.755 47.619 0.00 0.00 0.00 2.73
664 677 5.068215 TCCCCATTGTTTAAGAGGTTTCA 57.932 39.130 0.00 0.00 0.00 2.69
669 682 6.400568 CCATTGTTTAAGAGGTTTCATGCAT 58.599 36.000 0.00 0.00 0.00 3.96
672 685 7.945033 TTGTTTAAGAGGTTTCATGCATTTC 57.055 32.000 0.00 0.00 0.00 2.17
674 687 7.669427 TGTTTAAGAGGTTTCATGCATTTCAT 58.331 30.769 0.00 0.00 35.31 2.57
682 697 6.153170 AGGTTTCATGCATTTCATCACACATA 59.847 34.615 0.00 0.00 31.79 2.29
685 700 9.177304 GTTTCATGCATTTCATCACACATATAG 57.823 33.333 0.00 0.00 31.79 1.31
732 748 7.994911 TGTGAATAGAAGTTGCTCATTATCCAT 59.005 33.333 0.00 0.00 0.00 3.41
733 749 8.502387 GTGAATAGAAGTTGCTCATTATCCATC 58.498 37.037 0.00 0.00 0.00 3.51
734 750 7.663081 TGAATAGAAGTTGCTCATTATCCATCC 59.337 37.037 0.00 0.00 0.00 3.51
735 751 5.378230 AGAAGTTGCTCATTATCCATCCA 57.622 39.130 0.00 0.00 0.00 3.41
736 752 5.759059 AGAAGTTGCTCATTATCCATCCAA 58.241 37.500 0.00 0.00 0.00 3.53
737 753 5.591877 AGAAGTTGCTCATTATCCATCCAAC 59.408 40.000 0.00 0.00 33.29 3.77
738 754 4.858850 AGTTGCTCATTATCCATCCAACA 58.141 39.130 0.00 0.00 34.98 3.33
749 765 0.107214 CATCCAACAGGGCGTACCAT 60.107 55.000 1.21 0.00 43.89 3.55
766 782 1.100510 CATGAACTCACAGCCATGGG 58.899 55.000 15.13 0.00 34.39 4.00
776 792 4.865905 TCACAGCCATGGGTATAAAACAT 58.134 39.130 17.80 0.00 0.00 2.71
777 793 5.268387 TCACAGCCATGGGTATAAAACATT 58.732 37.500 17.80 0.00 0.00 2.71
790 806 7.656542 GGGTATAAAACATTTTGACCGGAAAAA 59.343 33.333 9.46 15.17 37.89 1.94
791 807 9.210329 GGTATAAAACATTTTGACCGGAAAAAT 57.790 29.630 19.95 19.95 37.64 1.82
796 812 3.378911 TTTTGACCGGAAAAATGAGCC 57.621 42.857 9.46 0.00 0.00 4.70
870 906 1.512926 CTCCACACCTTCCAAACTCG 58.487 55.000 0.00 0.00 0.00 4.18
877 913 2.488153 CACCTTCCAAACTCGAAATCCC 59.512 50.000 0.00 0.00 0.00 3.85
926 964 4.495514 CCAACCAAACAAAGCGAAAAATGG 60.496 41.667 0.00 0.00 0.00 3.16
950 988 0.767375 TGCTGGTCTCTCTTTTGGCT 59.233 50.000 0.00 0.00 0.00 4.75
967 1005 2.012902 GCTGGTTCTCCATGCATGCC 62.013 60.000 21.69 16.24 43.43 4.40
968 1006 0.395311 CTGGTTCTCCATGCATGCCT 60.395 55.000 21.69 1.31 43.43 4.75
969 1007 0.681887 TGGTTCTCCATGCATGCCTG 60.682 55.000 21.69 15.92 39.03 4.85
970 1008 0.682209 GGTTCTCCATGCATGCCTGT 60.682 55.000 21.69 2.04 0.00 4.00
971 1009 0.454600 GTTCTCCATGCATGCCTGTG 59.545 55.000 21.69 13.52 0.00 3.66
972 1010 1.317431 TTCTCCATGCATGCCTGTGC 61.317 55.000 21.69 0.00 45.25 4.57
973 1011 2.756691 TCCATGCATGCCTGTGCC 60.757 61.111 21.69 0.00 44.43 5.01
974 1012 2.758327 CCATGCATGCCTGTGCCT 60.758 61.111 21.69 0.00 44.43 4.75
975 1013 2.494445 CATGCATGCCTGTGCCTG 59.506 61.111 14.93 0.00 44.43 4.85
976 1014 2.036731 ATGCATGCCTGTGCCTGT 59.963 55.556 16.68 0.00 44.43 4.00
977 1015 2.348104 ATGCATGCCTGTGCCTGTG 61.348 57.895 16.68 0.00 44.43 3.66
978 1016 4.430765 GCATGCCTGTGCCTGTGC 62.431 66.667 6.36 0.00 39.18 4.57
1278 1316 3.612247 GACCCACCTCTGCACGCAT 62.612 63.158 0.00 0.00 0.00 4.73
2028 2271 2.971307 TGCGTCATATGCTTCTTGTGA 58.029 42.857 0.00 0.00 0.00 3.58
2279 2545 1.064758 AGTTTGTCAGGCACTCAACCA 60.065 47.619 0.00 0.00 34.60 3.67
2287 2553 3.776257 CAGGCACTCAACCATGATGGTG 61.776 54.545 19.32 12.28 45.82 4.17
2453 2719 6.143438 CACAAAGCTGTCAGACAATGAAATTC 59.857 38.462 4.41 0.00 40.43 2.17
2499 2765 2.369394 TCACTCTTCAGCGAGCTATCA 58.631 47.619 0.00 0.00 34.35 2.15
2521 2787 0.753479 AACACGGGTTCCATTGCACA 60.753 50.000 0.00 0.00 29.00 4.57
2525 2791 0.602562 CGGGTTCCATTGCACAACAT 59.397 50.000 0.00 0.00 0.00 2.71
2703 2969 3.452627 AGGATAACAGTGGGTAAGCTGAG 59.547 47.826 0.00 0.00 36.62 3.35
3265 3563 7.341256 AGCTCAAAATCATGGACAGATTTGTAT 59.659 33.333 0.00 0.00 42.98 2.29
3293 3591 7.575505 TCTACTTACTAGTTGCTGAGGAGTAT 58.424 38.462 0.00 0.00 35.78 2.12
3296 3594 6.663953 ACTTACTAGTTGCTGAGGAGTATCAA 59.336 38.462 0.00 0.00 36.25 2.57
3347 3645 5.592795 TGAATTTGGGGAAGAAAGATGGAT 58.407 37.500 0.00 0.00 0.00 3.41
3382 3947 5.860182 CCTGCACATTTTTGTCATCTTGTAG 59.140 40.000 0.00 0.00 0.00 2.74
3407 3980 3.439857 ACATAAGATGTTGGTGGTGCT 57.560 42.857 0.00 0.00 41.63 4.40
3487 4060 3.388913 AGGGAGAAGAAACATAGAGGGG 58.611 50.000 0.00 0.00 0.00 4.79
3511 4088 7.041107 GGAGACTAGATGAAGATATGATTGGC 58.959 42.308 0.00 0.00 0.00 4.52
3609 4186 9.050601 CAGGTCTGAACTAAATAGATGATTTCC 57.949 37.037 0.00 0.00 38.70 3.13
3631 4208 5.880332 TCCTTTGCTTATGTAACACCAGATC 59.120 40.000 0.00 0.00 0.00 2.75
3647 4224 7.170965 ACACCAGATCAATACAAGAAGTTGAT 58.829 34.615 0.00 0.00 43.23 2.57
3698 4281 0.946221 CACTGCGTCTGGTGTTCCTC 60.946 60.000 0.00 0.00 34.23 3.71
3699 4282 1.367471 CTGCGTCTGGTGTTCCTCA 59.633 57.895 0.00 0.00 34.23 3.86
3720 4307 6.367422 CCTCAGTTTGTCATTACAGAGAACTC 59.633 42.308 8.64 0.00 33.79 3.01
3758 4345 6.765036 AGCATCACGAAACAAGATCTAATGAT 59.235 34.615 0.00 0.00 35.26 2.45
3759 4346 6.849811 GCATCACGAAACAAGATCTAATGATG 59.150 38.462 15.93 15.93 42.34 3.07
3762 4349 6.539826 TCACGAAACAAGATCTAATGATGCAT 59.460 34.615 0.00 0.00 32.19 3.96
3775 4362 5.375417 AATGATGCATCGACACTGAAAAA 57.625 34.783 21.34 0.00 0.00 1.94
3792 4379 1.757682 AAACCTGGTCGCAACTTCAA 58.242 45.000 0.00 0.00 0.00 2.69
3793 4380 1.757682 AACCTGGTCGCAACTTCAAA 58.242 45.000 0.00 0.00 0.00 2.69
3794 4381 1.021968 ACCTGGTCGCAACTTCAAAC 58.978 50.000 0.00 0.00 0.00 2.93
3795 4382 1.308998 CCTGGTCGCAACTTCAAACT 58.691 50.000 0.00 0.00 0.00 2.66
3796 4383 1.676006 CCTGGTCGCAACTTCAAACTT 59.324 47.619 0.00 0.00 0.00 2.66
3797 4384 2.099098 CCTGGTCGCAACTTCAAACTTT 59.901 45.455 0.00 0.00 0.00 2.66
3805 4395 4.261155 CGCAACTTCAAACTTTCTCCATCA 60.261 41.667 0.00 0.00 0.00 3.07
3839 4429 5.894298 ACAATCCAGGATGTGATAAGCTA 57.106 39.130 1.44 0.00 0.00 3.32
3840 4430 6.252599 ACAATCCAGGATGTGATAAGCTAA 57.747 37.500 1.44 0.00 0.00 3.09
3841 4431 6.845908 ACAATCCAGGATGTGATAAGCTAAT 58.154 36.000 1.44 0.00 0.00 1.73
3842 4432 7.977818 ACAATCCAGGATGTGATAAGCTAATA 58.022 34.615 1.44 0.00 0.00 0.98
3882 4472 5.043248 ACCTGCACGAATGAAAAGAAAAAG 58.957 37.500 0.00 0.00 0.00 2.27
3887 4477 6.067039 GCACGAATGAAAAGAAAAAGATTGC 58.933 36.000 0.00 0.00 0.00 3.56
3899 4489 6.279882 AGAAAAAGATTGCGTCAATGGAAAA 58.720 32.000 9.33 0.00 33.90 2.29
3906 4496 2.228582 TGCGTCAATGGAAAATGAGGTG 59.771 45.455 0.00 0.00 34.73 4.00
3909 4499 2.094026 GTCAATGGAAAATGAGGTGGCC 60.094 50.000 0.00 0.00 0.00 5.36
3943 4533 7.321717 ACTATTTGCTATGGGATACATCAGT 57.678 36.000 0.00 0.00 41.03 3.41
3945 4535 5.628797 TTTGCTATGGGATACATCAGTGA 57.371 39.130 0.00 0.00 41.03 3.41
4049 4640 9.640963 GAATATCAGTGTAGTGTAGTTGAAGTT 57.359 33.333 0.00 0.00 0.00 2.66
4070 4661 7.989416 AGTTTAGTTAATTCACCGGAAATCA 57.011 32.000 9.46 0.00 36.43 2.57
4072 4663 8.674607 AGTTTAGTTAATTCACCGGAAATCATC 58.325 33.333 9.46 2.12 36.43 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.697432 TGGGGTCTGAAACGAACTGAT 59.303 47.619 0.00 0.00 0.00 2.90
30 31 0.417841 ATAGTGGACAGAGGTGGGGT 59.582 55.000 0.00 0.00 0.00 4.95
84 85 1.949847 AAGGCCGTGAGAGATCGTGG 61.950 60.000 0.00 0.00 0.00 4.94
98 99 2.646175 GGCGGGGAAAGAAAAGGCC 61.646 63.158 0.00 0.00 0.00 5.19
116 117 0.906756 TGGAGTTGGAGAGAGCTGGG 60.907 60.000 0.00 0.00 0.00 4.45
130 131 1.786937 CATCAGAGTAGGCCTGGAGT 58.213 55.000 17.99 0.00 32.73 3.85
169 170 2.929960 GACAACGAGTGTCGATCAGAA 58.070 47.619 2.82 0.00 46.99 3.02
225 226 5.118990 CAGTCTGTTTCTTTGTCTTCCAGA 58.881 41.667 0.00 0.00 0.00 3.86
275 276 3.338249 ACATAGTCATTGCTCGCAACTT 58.662 40.909 6.46 0.00 38.88 2.66
286 287 5.503927 ACCTCAGCAATCAACATAGTCATT 58.496 37.500 0.00 0.00 0.00 2.57
290 291 6.765036 CAGATAACCTCAGCAATCAACATAGT 59.235 38.462 0.00 0.00 0.00 2.12
300 301 2.436417 GCAACCAGATAACCTCAGCAA 58.564 47.619 0.00 0.00 0.00 3.91
310 311 5.432645 TGAAATAACCATCGCAACCAGATA 58.567 37.500 0.00 0.00 0.00 1.98
329 330 3.644966 AGACACACCAAAGTCCTGAAA 57.355 42.857 0.00 0.00 35.38 2.69
332 333 3.753294 AGTAGACACACCAAAGTCCTG 57.247 47.619 0.00 0.00 35.38 3.86
342 343 5.006552 GGAGTCGATGTAGTAGTAGACACAC 59.993 48.000 0.00 0.00 0.00 3.82
343 344 5.114780 GGAGTCGATGTAGTAGTAGACACA 58.885 45.833 0.00 0.00 0.00 3.72
348 349 7.444792 ACAATAAGGGAGTCGATGTAGTAGTAG 59.555 40.741 0.00 0.00 0.00 2.57
376 381 7.316640 CAATACTGATAGCACCTATACTGTCC 58.683 42.308 0.00 0.00 0.00 4.02
384 389 2.607038 CGCGCAATACTGATAGCACCTA 60.607 50.000 8.75 0.00 0.00 3.08
451 456 1.601759 AGCAGCACGCACAAAGGAT 60.602 52.632 0.00 0.00 46.13 3.24
479 484 4.975502 CACATAGTGAAGAGCGAGAATCTC 59.024 45.833 0.00 0.00 35.23 2.75
507 512 8.201464 TGAATAAGTCTGTCAACTGTAACTCAA 58.799 33.333 0.00 0.00 0.00 3.02
521 526 4.910195 TGTGCCTTCATGAATAAGTCTGT 58.090 39.130 8.96 0.00 0.00 3.41
529 534 4.008330 CTCAAGTCTGTGCCTTCATGAAT 58.992 43.478 8.96 0.00 0.00 2.57
597 602 4.406003 ACATCTAACACCCCACTACTCATC 59.594 45.833 0.00 0.00 0.00 2.92
604 609 5.278061 ACTATACACATCTAACACCCCACT 58.722 41.667 0.00 0.00 0.00 4.00
605 610 5.363005 AGACTATACACATCTAACACCCCAC 59.637 44.000 0.00 0.00 0.00 4.61
606 611 5.525484 AGACTATACACATCTAACACCCCA 58.475 41.667 0.00 0.00 0.00 4.96
637 650 9.588096 GAAACCTCTTAAACAATGGGGATATAT 57.412 33.333 0.00 0.00 0.00 0.86
652 665 7.039853 TGTGATGAAATGCATGAAACCTCTTAA 60.040 33.333 0.00 0.00 37.34 1.85
664 677 8.631480 ACATCTATATGTGTGATGAAATGCAT 57.369 30.769 8.86 0.00 44.79 3.96
672 685 9.881649 AAGGCTAATACATCTATATGTGTGATG 57.118 33.333 4.09 0.00 45.99 3.07
674 687 9.710900 CAAAGGCTAATACATCTATATGTGTGA 57.289 33.333 4.09 0.00 45.99 3.58
705 720 7.280876 TGGATAATGAGCAACTTCTATTCACAC 59.719 37.037 0.00 0.00 0.00 3.82
706 721 7.337938 TGGATAATGAGCAACTTCTATTCACA 58.662 34.615 0.00 0.00 0.00 3.58
732 748 1.195442 TCATGGTACGCCCTGTTGGA 61.195 55.000 0.00 0.00 35.39 3.53
733 749 0.322098 TTCATGGTACGCCCTGTTGG 60.322 55.000 0.00 0.00 32.98 3.77
734 750 0.802494 GTTCATGGTACGCCCTGTTG 59.198 55.000 0.00 0.00 32.98 3.33
735 751 0.690762 AGTTCATGGTACGCCCTGTT 59.309 50.000 0.00 0.00 32.98 3.16
736 752 0.249398 GAGTTCATGGTACGCCCTGT 59.751 55.000 0.00 0.00 32.98 4.00
737 753 0.249120 TGAGTTCATGGTACGCCCTG 59.751 55.000 0.00 0.00 0.00 4.45
738 754 0.249398 GTGAGTTCATGGTACGCCCT 59.751 55.000 0.00 0.00 0.00 5.19
749 765 1.357137 TACCCATGGCTGTGAGTTCA 58.643 50.000 6.09 0.00 0.00 3.18
755 771 5.596836 AATGTTTTATACCCATGGCTGTG 57.403 39.130 6.09 0.00 0.00 3.66
776 792 2.695666 TGGCTCATTTTTCCGGTCAAAA 59.304 40.909 14.15 14.15 0.00 2.44
777 793 2.295909 CTGGCTCATTTTTCCGGTCAAA 59.704 45.455 0.00 1.91 0.00 2.69
790 806 0.694771 TTGCTTCCTCACTGGCTCAT 59.305 50.000 0.00 0.00 35.26 2.90
791 807 0.035881 CTTGCTTCCTCACTGGCTCA 59.964 55.000 0.00 0.00 35.26 4.26
796 812 0.240411 GCTTGCTTGCTTCCTCACTG 59.760 55.000 0.00 0.00 0.00 3.66
870 906 5.765182 TGTGACAGAGAAAAAGAGGGATTTC 59.235 40.000 0.00 0.00 36.11 2.17
877 913 4.578105 AGCCTTTGTGACAGAGAAAAAGAG 59.422 41.667 4.51 0.00 31.01 2.85
926 964 1.818642 AAAGAGAGACCAGCATGCAC 58.181 50.000 21.98 8.21 31.97 4.57
967 1005 2.203252 ACACAGGCACAGGCACAG 60.203 61.111 0.00 0.00 43.71 3.66
968 1006 2.203195 GACACAGGCACAGGCACA 60.203 61.111 0.00 0.00 43.71 4.57
969 1007 1.963338 GAGACACAGGCACAGGCAC 60.963 63.158 0.00 0.00 43.71 5.01
970 1008 2.427320 GAGACACAGGCACAGGCA 59.573 61.111 0.00 0.00 43.71 4.75
971 1009 2.359230 GGAGACACAGGCACAGGC 60.359 66.667 0.00 0.00 40.13 4.85
972 1010 2.047844 CGGAGACACAGGCACAGG 60.048 66.667 0.00 0.00 0.00 4.00
973 1011 1.373497 GACGGAGACACAGGCACAG 60.373 63.158 0.00 0.00 0.00 3.66
974 1012 2.734591 GACGGAGACACAGGCACA 59.265 61.111 0.00 0.00 0.00 4.57
975 1013 2.430921 CGACGGAGACACAGGCAC 60.431 66.667 0.00 0.00 0.00 5.01
976 1014 3.680786 CCGACGGAGACACAGGCA 61.681 66.667 8.64 0.00 0.00 4.75
977 1015 3.371063 TCCGACGGAGACACAGGC 61.371 66.667 13.88 0.00 0.00 4.85
1071 1109 3.506743 TCCACCTTTGGGGCTGCA 61.507 61.111 0.50 0.00 44.11 4.41
1368 1406 3.034635 GGAGAGGTGGTACATGATCTGT 58.965 50.000 0.00 0.00 44.52 3.41
1662 1700 3.156288 TCCTTGAAGAAGACGGAGAGA 57.844 47.619 0.00 0.00 0.00 3.10
1836 2075 1.434696 GGCGGTGAAGATGGCATTG 59.565 57.895 0.00 0.00 0.00 2.82
1839 2078 4.015406 ACGGCGGTGAAGATGGCA 62.015 61.111 13.24 0.00 0.00 4.92
2028 2271 0.036732 TTTCAGGCCATGAGCTTCGT 59.963 50.000 5.01 0.00 43.05 3.85
2279 2545 1.985473 AAGCACACACACACCATCAT 58.015 45.000 0.00 0.00 0.00 2.45
2287 2553 4.378459 GCTATAACCTGAAAGCACACACAC 60.378 45.833 0.00 0.00 35.05 3.82
2288 2554 3.751175 GCTATAACCTGAAAGCACACACA 59.249 43.478 0.00 0.00 35.05 3.72
2453 2719 1.199327 CACTGCTTCCATGAGTTGCTG 59.801 52.381 0.00 0.11 0.00 4.41
2499 2765 2.230266 GTGCAATGGAACCCGTGTTATT 59.770 45.455 0.00 0.00 33.97 1.40
2551 2817 3.181489 GCATCAGCCTGGAGAAATTTGAG 60.181 47.826 0.00 0.00 33.58 3.02
2660 2926 3.953712 TGTCGAAGAACTGGAATGCTA 57.046 42.857 0.00 0.00 39.69 3.49
2703 2969 5.438761 ACCTAGTCTGTTGATTTTGTTGC 57.561 39.130 0.00 0.00 0.00 4.17
2768 3034 6.917533 ACCTGCAAGATTTGTGAGATAAAAG 58.082 36.000 0.00 0.00 34.07 2.27
2985 3255 8.946085 CAACTGAGTAAACTGGCTATCAATTTA 58.054 33.333 0.00 0.00 0.00 1.40
3265 3563 8.053963 ACTCCTCAGCAACTAGTAAGTAGATTA 58.946 37.037 0.00 0.00 33.75 1.75
3347 3645 0.478072 ATGTGCAGGTGGGAGACAAA 59.522 50.000 0.00 0.00 0.00 2.83
3382 3947 5.163754 GCACCACCAACATCTTATGTAAGTC 60.164 44.000 0.16 0.00 44.07 3.01
3407 3980 1.403814 CGATGACCTCTAGGGCTTGA 58.596 55.000 2.95 0.00 45.91 3.02
3487 4060 7.041107 GGCCAATCATATCTTCATCTAGTCTC 58.959 42.308 0.00 0.00 0.00 3.36
3511 4088 5.520376 AGTCTTGAAATTGTTGGTGAAGG 57.480 39.130 0.00 0.00 0.00 3.46
3551 4128 5.127682 ACAAGTAAATCAAATCATCTGGCCC 59.872 40.000 0.00 0.00 0.00 5.80
3609 4186 6.741992 TGATCTGGTGTTACATAAGCAAAG 57.258 37.500 0.00 0.00 0.00 2.77
3621 4198 6.998074 TCAACTTCTTGTATTGATCTGGTGTT 59.002 34.615 0.00 0.00 0.00 3.32
3698 4281 6.479990 TGTGAGTTCTCTGTAATGACAAACTG 59.520 38.462 3.85 0.00 35.33 3.16
3699 4282 6.480320 GTGTGAGTTCTCTGTAATGACAAACT 59.520 38.462 0.00 0.00 37.03 2.66
3758 4345 2.290367 CAGGTTTTTCAGTGTCGATGCA 59.710 45.455 0.00 0.00 0.00 3.96
3759 4346 2.350772 CCAGGTTTTTCAGTGTCGATGC 60.351 50.000 0.00 0.00 0.00 3.91
3762 4349 2.557317 GACCAGGTTTTTCAGTGTCGA 58.443 47.619 0.00 0.00 0.00 4.20
3775 4362 1.021968 GTTTGAAGTTGCGACCAGGT 58.978 50.000 0.00 0.00 0.00 4.00
3792 4379 5.995282 TCATTTACGTGTGATGGAGAAAGTT 59.005 36.000 0.00 0.00 0.00 2.66
3793 4380 5.547465 TCATTTACGTGTGATGGAGAAAGT 58.453 37.500 0.00 0.00 0.00 2.66
3794 4381 6.073276 TGTTCATTTACGTGTGATGGAGAAAG 60.073 38.462 0.00 0.00 0.00 2.62
3795 4382 5.760743 TGTTCATTTACGTGTGATGGAGAAA 59.239 36.000 0.00 0.00 0.00 2.52
3796 4383 5.301555 TGTTCATTTACGTGTGATGGAGAA 58.698 37.500 0.00 0.00 0.00 2.87
3797 4384 4.888917 TGTTCATTTACGTGTGATGGAGA 58.111 39.130 0.00 0.00 0.00 3.71
3805 4395 4.647611 TCCTGGATTGTTCATTTACGTGT 58.352 39.130 0.00 0.00 0.00 4.49
3882 4472 4.107622 CCTCATTTTCCATTGACGCAATC 58.892 43.478 2.65 0.00 31.05 2.67
3887 4477 2.415893 GCCACCTCATTTTCCATTGACG 60.416 50.000 0.00 0.00 0.00 4.35
3899 4489 2.442236 CCAATAAGTGGCCACCTCAT 57.558 50.000 32.29 19.23 41.72 2.90
3909 4499 6.998074 TCCCATAGCAAATAGTCCAATAAGTG 59.002 38.462 0.00 0.00 0.00 3.16
4020 4611 8.306313 TCAACTACACTACACTGATATTCCAT 57.694 34.615 0.00 0.00 0.00 3.41
4049 4640 7.562454 GGATGATTTCCGGTGAATTAACTAA 57.438 36.000 0.00 0.00 33.93 2.24
4070 4661 7.841222 TGTACTCATAGTATGGCATCATAGGAT 59.159 37.037 1.65 0.00 36.62 3.24
4072 4663 7.410120 TGTACTCATAGTATGGCATCATAGG 57.590 40.000 1.65 0.00 36.62 2.57


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

AutoCloner maintained by Alex Coulton.