Multiple sequence alignment - TraesCS7D01G390400

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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 TraesCS7D01G390400 chr7D 100.000 4098 0 0 1 4098 505617833 505613736 0.000000e+00 7568.0
1 TraesCS7D01G390400 chr7D 77.294 850 172 20 1331 2174 189430232 189431066 7.970000e-132 481.0
2 TraesCS7D01G390400 chr7B 90.946 3435 169 67 745 4098 533615220 533611847 0.000000e+00 4490.0
3 TraesCS7D01G390400 chr7B 87.313 670 34 11 1 644 533616038 533615394 0.000000e+00 719.0
4 TraesCS7D01G390400 chr7B 77.476 848 174 17 1331 2174 334322217 334323051 3.680000e-135 492.0
5 TraesCS7D01G390400 chr7A 90.753 1633 55 31 840 2415 573128752 573127159 0.000000e+00 2091.0
6 TraesCS7D01G390400 chr7A 94.013 952 43 8 2562 3501 573127111 573126162 0.000000e+00 1430.0
7 TraesCS7D01G390400 chr7A 77.921 856 174 15 1331 2183 194324647 194323804 1.690000e-143 520.0
8 TraesCS7D01G390400 chr7A 78.447 863 64 39 1 807 573129549 573128753 6.250000e-123 451.0
9 TraesCS7D01G390400 chr7A 92.241 232 13 1 3492 3718 573125327 573125096 1.420000e-84 324.0
10 TraesCS7D01G390400 chr6A 80.332 844 144 20 1331 2169 504624711 504623885 1.620000e-173 619.0
11 TraesCS7D01G390400 chr6D 79.976 844 147 20 1331 2169 363597028 363596202 1.630000e-168 603.0
12 TraesCS7D01G390400 chr6B 79.034 849 146 27 1331 2169 548384260 548383434 1.660000e-153 553.0
13 TraesCS7D01G390400 chr3A 92.537 67 4 1 1103 1169 23321092 23321157 1.210000e-15 95.3
14 TraesCS7D01G390400 chr5A 86.905 84 5 4 1103 1181 563100903 563100985 5.640000e-14 89.8
15 TraesCS7D01G390400 chr5A 86.905 84 5 4 1103 1181 563164782 563164864 5.640000e-14 89.8


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 TraesCS7D01G390400 chr7D 505613736 505617833 4097 True 7568.0 7568 100.0000 1 4098 1 chr7D.!!$R1 4097
1 TraesCS7D01G390400 chr7D 189430232 189431066 834 False 481.0 481 77.2940 1331 2174 1 chr7D.!!$F1 843
2 TraesCS7D01G390400 chr7B 533611847 533616038 4191 True 2604.5 4490 89.1295 1 4098 2 chr7B.!!$R1 4097
3 TraesCS7D01G390400 chr7B 334322217 334323051 834 False 492.0 492 77.4760 1331 2174 1 chr7B.!!$F1 843
4 TraesCS7D01G390400 chr7A 573125096 573129549 4453 True 1074.0 2091 88.8635 1 3718 4 chr7A.!!$R2 3717
5 TraesCS7D01G390400 chr7A 194323804 194324647 843 True 520.0 520 77.9210 1331 2183 1 chr7A.!!$R1 852
6 TraesCS7D01G390400 chr6A 504623885 504624711 826 True 619.0 619 80.3320 1331 2169 1 chr6A.!!$R1 838
7 TraesCS7D01G390400 chr6D 363596202 363597028 826 True 603.0 603 79.9760 1331 2169 1 chr6D.!!$R1 838
8 TraesCS7D01G390400 chr6B 548383434 548384260 826 True 553.0 553 79.0340 1331 2169 1 chr6B.!!$R1 838

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
932 1082 0.512518 AAAACTTTACCGCGCGTACC 59.487 50.000 29.95 0.0 0.00 3.34 F
2214 2410 1.153628 CGATTCCGAGGCCGACTTT 60.154 57.895 0.00 0.0 38.22 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2457 0.399833 TGCAGCAATGGTGGTCTGTA 59.600 50.0 14.61 0.0 31.53 2.74 R
3793 4898 0.038618 GGCCCACCAAACAAACGATC 60.039 55.0 0.00 0.0 35.26 3.69 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
18 19 3.342627 CGTCCGCCGCTGAAAACA 61.343 61.111 0.00 0.00 0.00 2.83
24 25 1.869690 GCCGCTGAAAACAGAGTCC 59.130 57.895 0.00 0.00 0.00 3.85
69 70 1.880340 CCGCTGATTCGCTCACCTC 60.880 63.158 0.00 0.00 0.00 3.85
79 81 0.671251 CGCTCACCTCTCTACCCATC 59.329 60.000 0.00 0.00 0.00 3.51
345 357 2.573869 CGTCCTCGCTGACATGGT 59.426 61.111 0.00 0.00 34.88 3.55
444 456 1.476007 GGCTGTGAGCGGAGGGATAT 61.476 60.000 0.00 0.00 43.62 1.63
461 473 4.019681 GGGATATGACCGTTGGATGGATAA 60.020 45.833 0.00 0.00 0.00 1.75
519 561 6.147000 GCACTTTTTGTTTAGAGGAGAGAGAG 59.853 42.308 0.00 0.00 0.00 3.20
521 563 7.713073 CACTTTTTGTTTAGAGGAGAGAGAGTT 59.287 37.037 0.00 0.00 0.00 3.01
577 622 2.357517 CGGCAAGCACGAGAAGGT 60.358 61.111 0.00 0.00 0.00 3.50
583 628 1.461127 CAAGCACGAGAAGGTTGCTAC 59.539 52.381 0.00 0.00 37.61 3.58
585 633 1.071605 GCACGAGAAGGTTGCTACTG 58.928 55.000 0.00 0.00 0.00 2.74
587 635 0.969894 ACGAGAAGGTTGCTACTGCT 59.030 50.000 0.00 0.00 40.48 4.24
613 661 0.667184 CAACAAAATGTGGCTCCGGC 60.667 55.000 0.00 0.00 37.82 6.13
641 689 1.132453 GCATTAAACCGGGAGCTTCAC 59.868 52.381 6.32 0.00 0.00 3.18
649 697 2.238646 ACCGGGAGCTTCACATATCAAA 59.761 45.455 6.32 0.00 0.00 2.69
650 698 3.278574 CCGGGAGCTTCACATATCAAAA 58.721 45.455 0.00 0.00 0.00 2.44
652 700 3.689161 CGGGAGCTTCACATATCAAAACA 59.311 43.478 0.00 0.00 0.00 2.83
653 701 4.201851 CGGGAGCTTCACATATCAAAACAG 60.202 45.833 0.00 0.00 0.00 3.16
657 706 5.564550 AGCTTCACATATCAAAACAGGAGT 58.435 37.500 0.00 0.00 0.00 3.85
661 782 6.114187 TCACATATCAAAACAGGAGTGAGT 57.886 37.500 0.00 0.00 31.81 3.41
670 791 2.603021 ACAGGAGTGAGTGACAGTGAT 58.397 47.619 0.00 0.00 31.63 3.06
676 797 3.759086 GAGTGAGTGACAGTGATGGACTA 59.241 47.826 0.00 0.00 31.73 2.59
728 865 3.753434 CTCGACGCTGGCTGGAGT 61.753 66.667 0.00 0.00 0.00 3.85
731 868 2.031163 GACGCTGGCTGGAGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
738 875 2.028020 GCTGGCTGGAGTTGTAGTAGTT 60.028 50.000 0.00 0.00 0.00 2.24
739 876 3.851098 CTGGCTGGAGTTGTAGTAGTTC 58.149 50.000 0.00 0.00 0.00 3.01
740 877 3.507411 TGGCTGGAGTTGTAGTAGTTCT 58.493 45.455 0.00 0.00 0.00 3.01
743 880 4.440387 GGCTGGAGTTGTAGTAGTTCTAGC 60.440 50.000 0.27 0.27 40.37 3.42
793 933 1.257750 GGCCACCCAGAAACATTCCC 61.258 60.000 0.00 0.00 0.00 3.97
810 950 5.193325 ACATTCCCAAAATGAGGAGAGAGAT 59.807 40.000 4.86 0.00 32.57 2.75
932 1082 0.512518 AAAACTTTACCGCGCGTACC 59.487 50.000 29.95 0.00 0.00 3.34
954 1104 4.505039 CCCTCTGCAGTACTGTAAAAAGGT 60.505 45.833 23.44 0.00 0.00 3.50
955 1105 4.452455 CCTCTGCAGTACTGTAAAAAGGTG 59.548 45.833 23.44 6.29 0.00 4.00
1020 1173 3.775654 CGCTCCCACACTCCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
2213 2409 1.885163 AACGATTCCGAGGCCGACTT 61.885 55.000 0.00 0.00 39.50 3.01
2214 2410 1.153628 CGATTCCGAGGCCGACTTT 60.154 57.895 0.00 0.00 38.22 2.66
2249 2445 2.293122 CCGTTTCCTGCACAGAATTTGA 59.707 45.455 0.00 0.00 0.00 2.69
2253 2449 5.569059 CGTTTCCTGCACAGAATTTGATTAC 59.431 40.000 0.00 0.00 0.00 1.89
2255 2451 5.885230 TCCTGCACAGAATTTGATTACTG 57.115 39.130 0.00 0.00 36.58 2.74
2257 2453 5.412594 TCCTGCACAGAATTTGATTACTGTC 59.587 40.000 0.00 0.00 40.84 3.51
2258 2454 5.413833 CCTGCACAGAATTTGATTACTGTCT 59.586 40.000 0.00 0.00 40.84 3.41
2259 2455 6.402983 CCTGCACAGAATTTGATTACTGTCTC 60.403 42.308 0.00 0.00 40.84 3.36
2260 2456 5.997129 TGCACAGAATTTGATTACTGTCTCA 59.003 36.000 0.00 0.00 40.84 3.27
2261 2457 6.656270 TGCACAGAATTTGATTACTGTCTCAT 59.344 34.615 0.00 0.00 40.84 2.90
2293 2509 4.152759 CCATTGCTGCATCGTTTGAATTTT 59.847 37.500 1.84 0.00 0.00 1.82
2313 2531 2.161855 TGGCATGTTGATGTGACCTTC 58.838 47.619 0.00 0.00 31.50 3.46
2360 2578 6.423776 AACCTTCATGTGTCATTTTCCATT 57.576 33.333 0.00 0.00 0.00 3.16
2364 2582 5.389859 TCATGTGTCATTTTCCATTGACC 57.610 39.130 0.00 0.00 41.22 4.02
2388 2606 6.883756 CCAAAAGTGCCCATTTGGTTATAAAT 59.116 34.615 7.64 0.00 46.73 1.40
2391 2609 8.560355 AAAGTGCCCATTTGGTTATAAATTTC 57.440 30.769 0.00 0.00 36.04 2.17
2395 2613 8.261522 GTGCCCATTTGGTTATAAATTTCCTTA 58.738 33.333 0.00 0.00 36.04 2.69
2433 2653 3.433031 CGTGCAATCCCACCCTAATCTAA 60.433 47.826 0.00 0.00 32.10 2.10
2438 2658 5.221925 GCAATCCCACCCTAATCTAAGATCA 60.222 44.000 0.00 0.00 0.00 2.92
2447 2667 5.013495 CCCTAATCTAAGATCATTGGAGCCA 59.987 44.000 0.00 0.00 0.00 4.75
2449 2669 5.643421 AATCTAAGATCATTGGAGCCAGT 57.357 39.130 0.00 0.00 0.00 4.00
2461 2681 5.549742 TTGGAGCCAGTCATTTCATTTTT 57.450 34.783 0.00 0.00 0.00 1.94
2462 2682 6.662865 TTGGAGCCAGTCATTTCATTTTTA 57.337 33.333 0.00 0.00 0.00 1.52
2492 2712 9.950680 CTTGTTTTCATTTTCAGTAGCTCTAAA 57.049 29.630 0.00 0.00 0.00 1.85
2548 2771 1.546923 CTGGTGATGCAATGGCTGAAA 59.453 47.619 0.00 0.00 41.91 2.69
2590 2813 7.321153 TGCAGTCCTAGTTGTATTACTTCTTC 58.679 38.462 0.00 0.00 0.00 2.87
2639 2866 7.698628 TCTGAAAGACTGACTCATATTACTCG 58.301 38.462 0.00 0.00 38.67 4.18
2644 2871 6.004574 AGACTGACTCATATTACTCGCCATA 58.995 40.000 0.00 0.00 0.00 2.74
2676 2903 0.178961 GGGGGTTTGAGAAGCTGGTT 60.179 55.000 0.00 0.00 33.81 3.67
2904 3131 4.430765 GGCGTGACGTGGTCCGAT 62.431 66.667 6.91 0.00 40.70 4.18
3118 3351 5.181811 TGAACCTAACAAACAGCTCATGATG 59.818 40.000 0.00 0.00 35.42 3.07
3132 3365 2.568509 TCATGATGTGGAGCTTGTGAGA 59.431 45.455 0.00 0.00 0.00 3.27
3143 3376 5.010820 TGGAGCTTGTGAGATGATAGAGATG 59.989 44.000 0.00 0.00 0.00 2.90
3158 3391 0.543749 AGATGGGGAGGAAAGCGAAG 59.456 55.000 0.00 0.00 0.00 3.79
3289 3523 4.934075 TCTCATTGTTGAATTGCTCTCG 57.066 40.909 0.00 0.00 0.00 4.04
3312 3547 6.040729 TCGGTCATATTCATTGCATTCCATTT 59.959 34.615 0.00 0.00 0.00 2.32
3313 3548 6.364165 CGGTCATATTCATTGCATTCCATTTC 59.636 38.462 0.00 0.00 0.00 2.17
3314 3549 7.439381 GGTCATATTCATTGCATTCCATTTCT 58.561 34.615 0.00 0.00 0.00 2.52
3324 3559 6.594788 TGCATTCCATTTCTCTTAAAGCTT 57.405 33.333 0.00 0.00 0.00 3.74
3350 3585 7.763985 TCAAGTTGATAATAGCTTCGTTCATCA 59.236 33.333 0.08 0.00 0.00 3.07
3389 3625 6.494893 TTGTAGATTACATTGTTGCACCTC 57.505 37.500 0.00 0.00 38.68 3.85
3391 3627 3.674997 AGATTACATTGTTGCACCTCGT 58.325 40.909 0.00 0.00 0.00 4.18
3407 3643 3.181454 ACCTCGTGACTTCCTTTGTTGAT 60.181 43.478 0.00 0.00 0.00 2.57
3470 3706 6.826893 AATTTTTGTTGGATCGACAAGTTG 57.173 33.333 0.00 0.00 38.72 3.16
3471 3707 3.980646 TTTGTTGGATCGACAAGTTGG 57.019 42.857 7.96 0.00 38.72 3.77
3512 4592 2.817538 ATAAATCGGCCGTTTTGTCG 57.182 45.000 33.81 6.43 0.00 4.35
3514 4594 1.512156 AAATCGGCCGTTTTGTCGCT 61.512 50.000 28.53 7.93 0.00 4.93
3520 4600 0.096454 GCCGTTTTGTCGCTGGATAC 59.904 55.000 0.00 0.00 0.00 2.24
3547 4627 0.889186 ATTCGTGTTGCAGGGGTGTC 60.889 55.000 0.00 0.00 0.00 3.67
3552 4632 0.820871 TGTTGCAGGGGTGTCAAAAC 59.179 50.000 0.00 0.00 0.00 2.43
3598 4686 0.667993 TTTCTTGCGCCAAACTCCTG 59.332 50.000 4.18 0.00 0.00 3.86
3656 4756 1.979155 GCAAAGGAAGGCAGGGGAC 60.979 63.158 0.00 0.00 0.00 4.46
3668 4768 2.584608 GGGGACCGTGGTGAGATG 59.415 66.667 0.00 0.00 40.86 2.90
3797 4902 1.205657 GCATTGGCATTTGCTGATCG 58.794 50.000 13.81 0.00 41.70 3.69
3798 4903 1.470285 GCATTGGCATTTGCTGATCGT 60.470 47.619 13.81 0.00 41.70 3.73
3819 4933 1.211709 GTTTGGTGGGCCGAATTCG 59.788 57.895 20.92 20.92 40.12 3.34
3820 4934 1.073373 TTTGGTGGGCCGAATTCGA 59.927 52.632 28.76 6.12 43.02 3.71
3827 4941 1.647084 GGCCGAATTCGAATTCCCG 59.353 57.895 34.00 26.73 41.30 5.14
3833 4947 3.123804 CGAATTCGAATTCCCGATCTGT 58.876 45.455 34.00 8.15 41.30 3.41
3834 4948 3.182572 CGAATTCGAATTCCCGATCTGTC 59.817 47.826 34.00 14.83 41.30 3.51
3835 4949 3.182572 GAATTCGAATTCCCGATCTGTCG 59.817 47.826 31.77 0.00 40.08 4.35
3836 4950 5.027394 GAATTCGAATTCCCGATCTGTCGA 61.027 45.833 31.77 0.00 42.93 4.20
3837 4951 6.791922 GAATTCGAATTCCCGATCTGTCGAG 61.792 48.000 31.77 0.00 42.93 4.04
3838 4952 8.861834 GAATTCGAATTCCCGATCTGTCGAGA 62.862 46.154 31.77 0.00 42.93 4.04
3850 4964 6.150738 GATCTGTCGAGATGTGAATAATGC 57.849 41.667 0.00 0.00 39.19 3.56
3851 4965 4.044426 TCTGTCGAGATGTGAATAATGCG 58.956 43.478 0.00 0.00 0.00 4.73
3852 4966 2.539688 TGTCGAGATGTGAATAATGCGC 59.460 45.455 0.00 0.00 0.00 6.09
3853 4967 2.539688 GTCGAGATGTGAATAATGCGCA 59.460 45.455 14.96 14.96 0.00 6.09
3854 4968 2.539688 TCGAGATGTGAATAATGCGCAC 59.460 45.455 14.90 0.00 0.00 5.34
3855 4969 2.541346 CGAGATGTGAATAATGCGCACT 59.459 45.455 14.90 3.33 33.83 4.40
3856 4970 3.603173 CGAGATGTGAATAATGCGCACTG 60.603 47.826 14.90 0.00 33.83 3.66
3857 4971 3.273434 AGATGTGAATAATGCGCACTGT 58.727 40.909 14.90 0.00 33.83 3.55
3858 4972 2.898181 TGTGAATAATGCGCACTGTG 57.102 45.000 14.90 2.76 33.83 3.66
3859 4973 1.135717 TGTGAATAATGCGCACTGTGC 60.136 47.619 22.38 22.38 40.69 4.57
3882 4996 6.353318 CAATTTTGCTGTATTATCATCGCG 57.647 37.500 0.00 0.00 0.00 5.87
3900 5014 0.739813 CGTCAGGTTTTAGGAGCCCG 60.740 60.000 0.00 0.00 0.00 6.13
3911 5025 0.831307 AGGAGCCCGTTCCTGATTAC 59.169 55.000 0.00 0.00 45.84 1.89
3924 5038 6.293244 CGTTCCTGATTACTTTCCGTTTCTTT 60.293 38.462 0.00 0.00 0.00 2.52
3928 5042 8.098286 TCCTGATTACTTTCCGTTTCTTTCATA 58.902 33.333 0.00 0.00 0.00 2.15
3929 5043 8.391106 CCTGATTACTTTCCGTTTCTTTCATAG 58.609 37.037 0.00 0.00 0.00 2.23
3930 5044 8.263940 TGATTACTTTCCGTTTCTTTCATAGG 57.736 34.615 0.00 0.00 0.00 2.57
3939 5054 5.048713 CCGTTTCTTTCATAGGTTTTCTGCT 60.049 40.000 0.00 0.00 0.00 4.24
3947 5062 1.230324 AGGTTTTCTGCTGCGTCTTC 58.770 50.000 0.00 0.00 0.00 2.87
3955 5070 0.603065 TGCTGCGTCTTCTTGCTCTA 59.397 50.000 0.00 0.00 0.00 2.43
3958 5073 2.675348 GCTGCGTCTTCTTGCTCTATTT 59.325 45.455 0.00 0.00 0.00 1.40
4003 5118 8.115490 CAATAAATTGTTCTGAACTCCTTCCT 57.885 34.615 20.18 3.05 33.22 3.36
4018 5133 9.674068 GAACTCCTTCCTCTAGAATAAAATTGT 57.326 33.333 0.00 0.00 32.82 2.71
4033 5148 4.590850 AAATTGTTGAGCCTTCTTCACC 57.409 40.909 0.00 0.00 0.00 4.02
4075 5190 3.484229 GCTTACTGCAGCTTATGACAACG 60.484 47.826 15.27 0.00 42.31 4.10
4093 5208 0.525311 CGAGTGAGAAGCTGAGAGCA 59.475 55.000 0.00 0.00 45.56 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.471119 TCCAAGCGTAATCGGACTCT 58.529 50.000 0.00 0.00 37.56 3.24
24 25 1.323534 CTTCCGTTCCAAGCGTAATCG 59.676 52.381 0.00 0.00 40.37 3.34
69 70 1.141881 AGTTGCGCGATGGGTAGAG 59.858 57.895 12.10 0.00 0.00 2.43
156 159 3.238497 CACCACGTCCCAGGTCCA 61.238 66.667 0.00 0.00 35.52 4.02
273 285 3.127533 GACGTGGATGGCTGCACC 61.128 66.667 0.50 2.33 40.35 5.01
275 287 4.758251 CGGACGTGGATGGCTGCA 62.758 66.667 0.50 0.00 0.00 4.41
345 357 0.850100 AGGTGTCACCATGGGAAACA 59.150 50.000 24.02 13.88 41.95 2.83
417 429 2.740055 GCTCACAGCCTGACACCG 60.740 66.667 0.00 0.00 34.48 4.94
444 456 1.134220 GCCTTATCCATCCAACGGTCA 60.134 52.381 0.00 0.00 0.00 4.02
519 561 2.805671 GCACAAAGCCCCAATTAACAAC 59.194 45.455 0.00 0.00 37.23 3.32
521 563 2.829741 GCACAAAGCCCCAATTAACA 57.170 45.000 0.00 0.00 37.23 2.41
583 628 4.082787 CCACATTTTGTTGGGTACTAGCAG 60.083 45.833 0.00 0.00 29.18 4.24
585 633 3.366985 GCCACATTTTGTTGGGTACTAGC 60.367 47.826 0.00 0.00 0.00 3.42
587 635 4.076394 GAGCCACATTTTGTTGGGTACTA 58.924 43.478 0.00 0.00 32.39 1.82
613 661 2.169769 TCCCGGTTTAATGCTAGGACAG 59.830 50.000 0.00 0.00 0.00 3.51
628 676 1.496060 TGATATGTGAAGCTCCCGGT 58.504 50.000 0.00 0.00 0.00 5.28
641 689 5.934043 TGTCACTCACTCCTGTTTTGATATG 59.066 40.000 0.00 0.00 0.00 1.78
649 697 2.388735 TCACTGTCACTCACTCCTGTT 58.611 47.619 0.00 0.00 0.00 3.16
650 698 2.073252 TCACTGTCACTCACTCCTGT 57.927 50.000 0.00 0.00 0.00 4.00
652 700 1.898472 CCATCACTGTCACTCACTCCT 59.102 52.381 0.00 0.00 0.00 3.69
653 701 1.895798 TCCATCACTGTCACTCACTCC 59.104 52.381 0.00 0.00 0.00 3.85
657 706 4.013050 CTCTAGTCCATCACTGTCACTCA 58.987 47.826 0.00 0.00 36.43 3.41
661 782 3.458044 ACCTCTAGTCCATCACTGTCA 57.542 47.619 0.00 0.00 36.43 3.58
670 791 8.429641 GGTTCATCAATATTAACCTCTAGTCCA 58.570 37.037 9.67 0.00 36.71 4.02
728 865 5.723672 ACAAGCTGCTAGAACTACTACAA 57.276 39.130 0.90 0.00 0.00 2.41
731 868 6.591750 AGAAACAAGCTGCTAGAACTACTA 57.408 37.500 0.90 0.00 0.00 1.82
738 875 5.215252 ACAGTAAGAAACAAGCTGCTAGA 57.785 39.130 0.90 0.00 0.00 2.43
739 876 5.062809 GCTACAGTAAGAAACAAGCTGCTAG 59.937 44.000 0.90 0.00 31.51 3.42
740 877 4.929808 GCTACAGTAAGAAACAAGCTGCTA 59.070 41.667 0.90 0.00 31.51 3.49
743 880 4.065088 TGGCTACAGTAAGAAACAAGCTG 58.935 43.478 0.00 0.00 33.50 4.24
793 933 6.818233 TCATCTCATCTCTCTCCTCATTTTG 58.182 40.000 0.00 0.00 0.00 2.44
810 950 0.470080 GGGTCCGGGATCTCATCTCA 60.470 60.000 7.34 0.00 0.00 3.27
932 1082 4.452455 CACCTTTTTACAGTACTGCAGAGG 59.548 45.833 23.35 21.53 0.00 3.69
939 1089 9.749340 ATTAATTAGCCACCTTTTTACAGTACT 57.251 29.630 0.00 0.00 0.00 2.73
1020 1173 0.466922 GGATGGGGAGCAATGAGTGG 60.467 60.000 0.00 0.00 0.00 4.00
1107 1285 1.515020 CTTGAGGTCGGAGCAGAGG 59.485 63.158 10.15 0.00 0.00 3.69
1371 1558 3.481903 ATCTGCACGAACAGCGCG 61.482 61.111 0.00 0.00 46.04 6.86
1818 2014 4.408821 GCCATCCACTCCCGCACA 62.409 66.667 0.00 0.00 0.00 4.57
2213 2409 3.469739 GAAACGGTCACCTACTTGGAAA 58.530 45.455 0.00 0.00 39.71 3.13
2214 2410 2.224354 GGAAACGGTCACCTACTTGGAA 60.224 50.000 0.00 0.00 39.71 3.53
2257 2453 2.941064 CAGCAATGGTGGTCTGTATGAG 59.059 50.000 4.25 0.00 31.53 2.90
2258 2454 2.940971 GCAGCAATGGTGGTCTGTATGA 60.941 50.000 14.61 0.00 31.53 2.15
2259 2455 1.402968 GCAGCAATGGTGGTCTGTATG 59.597 52.381 14.61 0.00 31.53 2.39
2260 2456 1.004628 TGCAGCAATGGTGGTCTGTAT 59.995 47.619 14.61 0.00 31.53 2.29
2261 2457 0.399833 TGCAGCAATGGTGGTCTGTA 59.600 50.000 14.61 0.00 31.53 2.74
2265 2481 1.308069 ACGATGCAGCAATGGTGGTC 61.308 55.000 14.61 0.00 31.53 4.02
2293 2509 2.161855 GAAGGTCACATCAACATGCCA 58.838 47.619 0.00 0.00 32.57 4.92
2313 2531 6.423182 TCCTAATTGGGTAATTCCAGTTCAG 58.577 40.000 7.83 0.00 37.76 3.02
2360 2578 2.906691 CAAATGGGCACTTTTGGTCA 57.093 45.000 17.35 0.00 37.81 4.02
2364 2582 7.920160 ATTTATAACCAAATGGGCACTTTTG 57.080 32.000 18.01 18.01 42.05 2.44
2388 2606 7.775397 CGAATACGGAACCTTTATAAGGAAA 57.225 36.000 12.21 0.00 42.60 3.13
2395 2613 3.864243 TGCACGAATACGGAACCTTTAT 58.136 40.909 0.00 0.00 44.46 1.40
2433 2653 3.947612 AATGACTGGCTCCAATGATCT 57.052 42.857 0.00 0.00 0.00 2.75
2438 2658 5.750352 AAAATGAAATGACTGGCTCCAAT 57.250 34.783 0.00 0.00 0.00 3.16
2461 2681 9.066892 AGCTACTGAAAATGAAAACAAGACATA 57.933 29.630 0.00 0.00 0.00 2.29
2462 2682 7.945134 AGCTACTGAAAATGAAAACAAGACAT 58.055 30.769 0.00 0.00 0.00 3.06
2481 2701 7.048512 ACTGAACTGTTGTTTTTAGAGCTACT 58.951 34.615 0.00 0.00 36.39 2.57
2484 2704 6.555315 CAACTGAACTGTTGTTTTTAGAGCT 58.445 36.000 13.65 0.00 41.50 4.09
2548 2771 1.985159 TGCAAGGAGAACATGGTAGGT 59.015 47.619 0.00 0.00 0.00 3.08
2590 2813 9.006839 AGATATACCATGCATTGACAAATGTAG 57.993 33.333 4.52 0.00 44.34 2.74
2630 2857 6.230472 TGTCTGCAAATATGGCGAGTAATAT 58.770 36.000 0.00 0.00 0.00 1.28
2632 2859 4.450976 TGTCTGCAAATATGGCGAGTAAT 58.549 39.130 0.00 0.00 0.00 1.89
2639 2866 2.224113 CCCCATTGTCTGCAAATATGGC 60.224 50.000 9.97 0.00 38.21 4.40
2644 2871 2.028561 AACCCCCATTGTCTGCAAAT 57.971 45.000 0.00 0.00 38.21 2.32
2676 2903 1.647346 CGGTGATCGAATTCCGGAAA 58.353 50.000 23.08 4.58 42.43 3.13
2904 3131 1.065491 TCGTAGTACCAGGGCGTCTTA 60.065 52.381 0.00 0.00 0.00 2.10
2964 3191 3.507162 TTGCCAATGGTTCTCTTCTCA 57.493 42.857 0.00 0.00 0.00 3.27
3118 3351 4.340666 TCTCTATCATCTCACAAGCTCCAC 59.659 45.833 0.00 0.00 0.00 4.02
3132 3365 3.586618 GCTTTCCTCCCCATCTCTATCAT 59.413 47.826 0.00 0.00 0.00 2.45
3143 3376 2.438614 GGCTTCGCTTTCCTCCCC 60.439 66.667 0.00 0.00 0.00 4.81
3168 3401 2.108514 ACAATCTGCCATGCCGTCG 61.109 57.895 0.00 0.00 0.00 5.12
3253 3486 5.118990 ACAATGAGATTTACACGGATGAGG 58.881 41.667 0.00 0.00 0.00 3.86
3289 3523 7.439381 AGAAATGGAATGCAATGAATATGACC 58.561 34.615 0.00 0.00 0.00 4.02
3313 3548 9.928236 GCTATTATCAACTTGAAGCTTTAAGAG 57.072 33.333 31.10 22.91 0.00 2.85
3314 3549 9.672673 AGCTATTATCAACTTGAAGCTTTAAGA 57.327 29.630 31.10 14.27 34.28 2.10
3324 3559 7.763985 TGATGAACGAAGCTATTATCAACTTGA 59.236 33.333 0.00 0.00 0.00 3.02
3368 3603 4.630069 ACGAGGTGCAACAATGTAATCTAC 59.370 41.667 3.64 0.00 39.98 2.59
3376 3612 1.229428 AGTCACGAGGTGCAACAATG 58.771 50.000 3.64 0.00 39.98 2.82
3391 3627 9.066892 GGCATATATAATCAACAAAGGAAGTCA 57.933 33.333 0.00 0.00 0.00 3.41
3407 3643 8.931775 CAGTTTATACTGTTGCGGCATATATAA 58.068 33.333 2.28 7.44 45.46 0.98
3512 4592 4.156008 ACACGAATTTTTCCAGTATCCAGC 59.844 41.667 0.00 0.00 0.00 4.85
3514 4594 5.563867 GCAACACGAATTTTTCCAGTATCCA 60.564 40.000 0.00 0.00 0.00 3.41
3520 4600 3.052036 CCTGCAACACGAATTTTTCCAG 58.948 45.455 0.00 0.00 0.00 3.86
3566 4646 3.432782 CGCAAGAAATTTCAGAGCCATC 58.567 45.455 19.99 0.33 43.02 3.51
3598 4686 0.961019 TGGCATTGCTTGGTGACTTC 59.039 50.000 8.82 0.00 0.00 3.01
3656 4756 0.105593 CCCATCTCATCTCACCACGG 59.894 60.000 0.00 0.00 0.00 4.94
3661 4761 0.531532 CCGTGCCCATCTCATCTCAC 60.532 60.000 0.00 0.00 0.00 3.51
3664 4764 2.068821 AGCCGTGCCCATCTCATCT 61.069 57.895 0.00 0.00 0.00 2.90
3665 4765 1.890979 CAGCCGTGCCCATCTCATC 60.891 63.158 0.00 0.00 0.00 2.92
3666 4766 2.191375 CAGCCGTGCCCATCTCAT 59.809 61.111 0.00 0.00 0.00 2.90
3667 4767 4.783621 GCAGCCGTGCCCATCTCA 62.784 66.667 0.00 0.00 44.72 3.27
3762 4867 5.243507 TGCCAATGCAAAGAGAAAGAATGTA 59.756 36.000 0.00 0.00 46.66 2.29
3791 4896 1.335872 GCCCACCAAACAAACGATCAG 60.336 52.381 0.00 0.00 0.00 2.90
3792 4897 0.671251 GCCCACCAAACAAACGATCA 59.329 50.000 0.00 0.00 0.00 2.92
3793 4898 0.038618 GGCCCACCAAACAAACGATC 60.039 55.000 0.00 0.00 35.26 3.69
3794 4899 1.801309 CGGCCCACCAAACAAACGAT 61.801 55.000 0.00 0.00 34.57 3.73
3795 4900 2.482333 CGGCCCACCAAACAAACGA 61.482 57.895 0.00 0.00 34.57 3.85
3796 4901 2.005960 TTCGGCCCACCAAACAAACG 62.006 55.000 0.00 0.00 34.57 3.60
3797 4902 0.391228 ATTCGGCCCACCAAACAAAC 59.609 50.000 0.00 0.00 34.57 2.93
3798 4903 1.069358 GAATTCGGCCCACCAAACAAA 59.931 47.619 0.00 0.00 34.57 2.83
3827 4941 5.164109 CGCATTATTCACATCTCGACAGATC 60.164 44.000 0.00 0.00 37.25 2.75
3833 4947 2.539688 GTGCGCATTATTCACATCTCGA 59.460 45.455 15.91 0.00 0.00 4.04
3834 4948 2.541346 AGTGCGCATTATTCACATCTCG 59.459 45.455 15.91 0.00 33.44 4.04
3835 4949 3.310774 ACAGTGCGCATTATTCACATCTC 59.689 43.478 15.91 0.00 33.44 2.75
3836 4950 3.064408 CACAGTGCGCATTATTCACATCT 59.936 43.478 15.91 0.00 33.44 2.90
3837 4951 3.357021 CACAGTGCGCATTATTCACATC 58.643 45.455 15.91 0.00 33.44 3.06
3838 4952 2.478370 GCACAGTGCGCATTATTCACAT 60.478 45.455 15.91 0.00 31.71 3.21
3839 4953 1.135717 GCACAGTGCGCATTATTCACA 60.136 47.619 15.91 0.00 31.71 3.58
3840 4954 1.538276 GCACAGTGCGCATTATTCAC 58.462 50.000 15.91 0.00 31.71 3.18
3841 4955 3.994729 GCACAGTGCGCATTATTCA 57.005 47.368 15.91 0.00 31.71 2.57
3859 4973 5.909054 ACGCGATGATAATACAGCAAAATTG 59.091 36.000 15.93 0.00 0.00 2.32
3860 4974 6.060028 ACGCGATGATAATACAGCAAAATT 57.940 33.333 15.93 0.00 0.00 1.82
3882 4996 0.323957 ACGGGCTCCTAAAACCTGAC 59.676 55.000 0.00 0.00 33.80 3.51
3900 5014 6.555812 AAGAAACGGAAAGTAATCAGGAAC 57.444 37.500 0.00 0.00 0.00 3.62
3911 5025 7.591426 CAGAAAACCTATGAAAGAAACGGAAAG 59.409 37.037 0.00 0.00 0.00 2.62
3924 5038 2.028112 AGACGCAGCAGAAAACCTATGA 60.028 45.455 0.00 0.00 0.00 2.15
3928 5042 1.202698 AGAAGACGCAGCAGAAAACCT 60.203 47.619 0.00 0.00 0.00 3.50
3929 5043 1.230324 AGAAGACGCAGCAGAAAACC 58.770 50.000 0.00 0.00 0.00 3.27
3930 5044 2.644078 CAAGAAGACGCAGCAGAAAAC 58.356 47.619 0.00 0.00 0.00 2.43
3958 5073 3.691575 TGTCAACTGGGTGAACTGAAAA 58.308 40.909 0.00 0.00 0.00 2.29
3995 5110 9.672673 TCAACAATTTTATTCTAGAGGAAGGAG 57.327 33.333 0.00 0.00 37.36 3.69
3999 5114 8.109634 AGGCTCAACAATTTTATTCTAGAGGAA 58.890 33.333 0.00 0.00 38.41 3.36
4001 5116 7.872113 AGGCTCAACAATTTTATTCTAGAGG 57.128 36.000 0.00 0.00 0.00 3.69
4002 5117 9.171877 AGAAGGCTCAACAATTTTATTCTAGAG 57.828 33.333 0.00 0.00 0.00 2.43
4003 5118 9.520515 AAGAAGGCTCAACAATTTTATTCTAGA 57.479 29.630 0.00 0.00 0.00 2.43
4018 5133 4.041567 TCAAGTATGGTGAAGAAGGCTCAA 59.958 41.667 0.00 0.00 0.00 3.02
4033 5148 2.031807 GCACAGCAGCTCATCAAGTATG 59.968 50.000 0.00 0.00 36.88 2.39
4064 5179 4.325741 CAGCTTCTCACTCGTTGTCATAAG 59.674 45.833 0.00 0.00 0.00 1.73
4066 5181 3.506067 TCAGCTTCTCACTCGTTGTCATA 59.494 43.478 0.00 0.00 0.00 2.15
4075 5190 2.739885 TTGCTCTCAGCTTCTCACTC 57.260 50.000 0.00 0.00 42.97 3.51


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

AutoCloner maintained by Alex Coulton.