Multiple sequence alignment - TraesCS1B01G171600

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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 TraesCS1B01G171600 chr1B 100.000 5809 0 0 1 5809 305179202 305173394 0.000000e+00 10728.0
1 TraesCS1B01G171600 chr1B 89.516 124 13 0 2930 3053 173578367 173578490 2.170000e-34 158.0
2 TraesCS1B01G171600 chr1A 92.456 2691 97 25 816 3432 267141795 267144453 0.000000e+00 3747.0
3 TraesCS1B01G171600 chr1A 95.640 1445 45 5 3807 5251 267144874 267146300 0.000000e+00 2303.0
4 TraesCS1B01G171600 chr1A 97.683 561 8 1 5249 5809 267146375 267146930 0.000000e+00 959.0
5 TraesCS1B01G171600 chr1A 85.279 754 82 13 2 737 267140900 267141642 0.000000e+00 750.0
6 TraesCS1B01G171600 chr1A 96.512 344 10 1 3461 3804 267144452 267144793 8.450000e-158 568.0
7 TraesCS1B01G171600 chr1A 86.000 100 14 0 2928 3027 36130377 36130278 2.210000e-19 108.0
8 TraesCS1B01G171600 chr1D 96.471 2210 66 7 3602 5809 211684941 211687140 0.000000e+00 3639.0
9 TraesCS1B01G171600 chr1D 91.196 2056 89 36 65 2041 211681088 211683130 0.000000e+00 2710.0
10 TraesCS1B01G171600 chr1D 92.395 1591 67 20 2039 3613 211683198 211684750 0.000000e+00 2218.0
11 TraesCS1B01G171600 chr7B 79.945 723 113 21 2212 2918 51766837 51766131 2.420000e-138 503.0
12 TraesCS1B01G171600 chr7B 93.617 47 3 0 2275 2321 33072754 33072708 2.900000e-08 71.3
13 TraesCS1B01G171600 chr3A 79.096 708 97 27 2320 3016 44357509 44356842 1.920000e-119 440.0
14 TraesCS1B01G171600 chr3A 84.663 163 18 3 2111 2272 461843831 461843675 7.790000e-34 156.0
15 TraesCS1B01G171600 chr2B 86.831 243 18 5 2809 3051 66556653 66556425 5.770000e-65 259.0
16 TraesCS1B01G171600 chr2B 88.500 200 22 1 2822 3021 773006549 773006351 2.090000e-59 241.0
17 TraesCS1B01G171600 chr4B 86.782 174 17 1 2886 3053 94798089 94798262 7.680000e-44 189.0
18 TraesCS1B01G171600 chr4B 82.569 109 13 5 2216 2320 94792172 94792278 2.230000e-14 91.6
19 TraesCS1B01G171600 chr5D 87.342 158 15 5 2897 3052 307915887 307916041 5.980000e-40 176.0
20 TraesCS1B01G171600 chr3B 83.085 201 19 5 2840 3038 555095284 555095097 1.000000e-37 169.0
21 TraesCS1B01G171600 chr3B 84.706 170 19 3 2111 2279 440135455 440135618 4.660000e-36 163.0
22 TraesCS1B01G171600 chr3B 79.518 166 21 9 2094 2250 528660766 528660927 7.960000e-19 106.0
23 TraesCS1B01G171600 chr3D 85.890 163 15 3 2111 2272 341490821 341490976 3.600000e-37 167.0
24 TraesCS1B01G171600 chr2A 84.472 161 20 3 2111 2270 734097020 734097176 2.800000e-33 154.0
25 TraesCS1B01G171600 chr7A 89.167 120 12 1 2930 3049 446355413 446355531 1.300000e-31 148.0
26 TraesCS1B01G171600 chr7A 85.246 122 16 2 2930 3051 20101235 20101354 2.200000e-24 124.0
27 TraesCS1B01G171600 chr7A 80.986 142 18 4 2146 2279 85206267 85206127 2.860000e-18 104.0


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 TraesCS1B01G171600 chr1B 305173394 305179202 5808 True 10728.000000 10728 100.000 1 5809 1 chr1B.!!$R1 5808
1 TraesCS1B01G171600 chr1A 267140900 267146930 6030 False 1665.400000 3747 93.514 2 5809 5 chr1A.!!$F1 5807
2 TraesCS1B01G171600 chr1D 211681088 211687140 6052 False 2855.666667 3639 93.354 65 5809 3 chr1D.!!$F1 5744
3 TraesCS1B01G171600 chr7B 51766131 51766837 706 True 503.000000 503 79.945 2212 2918 1 chr7B.!!$R2 706
4 TraesCS1B01G171600 chr3A 44356842 44357509 667 True 440.000000 440 79.096 2320 3016 1 chr3A.!!$R1 696

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
689 724 0.030638 CAAAGGCCCAACAACTCACG 59.969 55.0 0.00 0.0 0.00 4.35 F
807 895 0.107831 GCGTATTCCATGGTGCCCTA 59.892 55.0 12.58 0.0 0.00 3.53 F
1734 1877 0.383590 CAGACGACAGCCAGATCGAT 59.616 55.0 0.00 0.0 40.86 3.59 F
2477 2727 0.748450 CGCCATGCCAATTTGGATCT 59.252 50.0 19.76 0.0 40.96 2.75 F
4002 4563 0.964358 GCATGCTTTCCTCTGCTGGT 60.964 55.0 11.37 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2465 0.322456 TGCATCACTTGGTGCCCTAC 60.322 55.000 11.91 0.00 40.56 3.18 R
2258 2503 0.801251 GCTCATGTTTTGCTCGAGCT 59.199 50.000 35.27 13.88 44.47 4.09 R
2670 2920 1.684391 GGGGGCTGCCCGTAATTTT 60.684 57.895 30.32 0.00 46.66 1.82 R
4011 4572 0.250989 TAGGTTTTTCAGTGGCCCCG 60.251 55.000 0.00 0.00 0.00 5.73 R
5484 6129 1.076024 ACATGTGAATGAACTGCCCCT 59.924 47.619 0.00 0.00 0.00 4.79 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
29 30 6.925610 TGTAAATCATGGTTGTAGATGCTC 57.074 37.500 0.00 0.00 0.00 4.26
223 230 9.495754 GCAAACAAGATCTCAAATAATAGTGAC 57.504 33.333 0.00 0.00 0.00 3.67
305 312 4.779987 CATATGCTCACATACATGCACAC 58.220 43.478 0.00 0.00 41.50 3.82
306 313 2.181954 TGCTCACATACATGCACACA 57.818 45.000 0.00 0.00 0.00 3.72
307 314 1.805943 TGCTCACATACATGCACACAC 59.194 47.619 0.00 0.00 0.00 3.82
308 315 1.805943 GCTCACATACATGCACACACA 59.194 47.619 0.00 0.00 0.00 3.72
342 349 5.178623 CCTGTGAACGTATACACACACATTT 59.821 40.000 19.01 0.00 41.19 2.32
358 365 6.942576 ACACACATTTTATCCCTATAGATGCC 59.057 38.462 0.00 0.00 0.00 4.40
421 428 4.326548 GCACCATAGACGTTAAACTCACTC 59.673 45.833 0.00 0.00 0.00 3.51
464 471 8.408043 TGAAAGCTCTTATTGAAAGGAAATGA 57.592 30.769 0.00 0.00 0.00 2.57
485 492 1.508632 AACTCCGTTTGATCCGTGTG 58.491 50.000 0.00 0.00 0.00 3.82
486 493 0.391597 ACTCCGTTTGATCCGTGTGT 59.608 50.000 0.00 0.00 0.00 3.72
487 494 1.614903 ACTCCGTTTGATCCGTGTGTA 59.385 47.619 0.00 0.00 0.00 2.90
488 495 2.036217 ACTCCGTTTGATCCGTGTGTAA 59.964 45.455 0.00 0.00 0.00 2.41
490 497 3.666274 TCCGTTTGATCCGTGTGTAAAT 58.334 40.909 0.00 0.00 0.00 1.40
506 528 4.023878 GTGTAAATGCTCAAAACGTGGGTA 60.024 41.667 0.00 0.00 0.00 3.69
521 543 1.076485 GGTACCAGGCCTACGAGGA 60.076 63.158 13.66 0.00 37.67 3.71
537 559 7.596494 CCTACGAGGAATATGAAATTACGGTA 58.404 38.462 0.00 0.00 37.67 4.02
551 573 8.788806 TGAAATTACGGTAGTTGATGTCAAATT 58.211 29.630 0.79 0.00 37.63 1.82
572 594 1.000843 TGACAGTCCAATCACACTCGG 59.999 52.381 0.00 0.00 0.00 4.63
576 598 0.037326 GTCCAATCACACTCGGCTGA 60.037 55.000 0.00 0.00 0.00 4.26
578 600 1.278985 TCCAATCACACTCGGCTGAAT 59.721 47.619 0.00 0.00 0.00 2.57
589 611 1.266718 TCGGCTGAATGTTTGCAAGAC 59.733 47.619 0.00 2.08 0.00 3.01
606 628 9.809096 TTTGCAAGACTTTACAAATAATTGACA 57.191 25.926 0.00 0.00 38.94 3.58
665 700 0.604578 AAACGCCGAGCACTAACCTA 59.395 50.000 0.00 0.00 0.00 3.08
689 724 0.030638 CAAAGGCCCAACAACTCACG 59.969 55.000 0.00 0.00 0.00 4.35
698 734 2.666508 CCAACAACTCACGTAAGGATCG 59.333 50.000 0.00 0.00 46.39 3.69
701 737 4.247267 ACAACTCACGTAAGGATCGAAA 57.753 40.909 0.00 0.00 46.39 3.46
710 746 3.865745 CGTAAGGATCGAAATGCTGTCTT 59.134 43.478 0.00 0.00 33.27 3.01
718 754 0.678048 AAATGCTGTCTTCGGCTCCC 60.678 55.000 0.90 0.00 45.38 4.30
740 776 0.600782 GAACAACAGTTCGGGCGGTA 60.601 55.000 0.00 0.00 33.10 4.02
753 805 2.100252 CGGGCGGTAGATCTTTTAGACA 59.900 50.000 0.00 0.00 0.00 3.41
772 824 1.404391 CAGACACGTAGCCGGATAGTT 59.596 52.381 5.05 0.00 38.78 2.24
773 825 1.674962 AGACACGTAGCCGGATAGTTC 59.325 52.381 5.05 0.00 38.78 3.01
774 826 1.402968 GACACGTAGCCGGATAGTTCA 59.597 52.381 5.05 0.00 38.78 3.18
775 827 2.029623 ACACGTAGCCGGATAGTTCAT 58.970 47.619 5.05 0.00 38.78 2.57
788 876 2.732412 AGTTCATCGATATGAGCCCG 57.268 50.000 0.00 0.00 42.56 6.13
805 893 2.542907 CGCGTATTCCATGGTGCCC 61.543 63.158 12.58 0.00 0.00 5.36
806 894 1.152963 GCGTATTCCATGGTGCCCT 60.153 57.895 12.58 0.00 0.00 5.19
807 895 0.107831 GCGTATTCCATGGTGCCCTA 59.892 55.000 12.58 0.00 0.00 3.53
809 897 1.270839 CGTATTCCATGGTGCCCTAGG 60.271 57.143 12.58 0.06 0.00 3.02
810 898 2.054799 GTATTCCATGGTGCCCTAGGA 58.945 52.381 11.48 0.00 0.00 2.94
811 899 1.143813 ATTCCATGGTGCCCTAGGAG 58.856 55.000 11.48 1.06 31.27 3.69
984 1124 2.195741 TCTGATTTCTGCTGCTGCTT 57.804 45.000 17.00 0.00 40.48 3.91
990 1130 1.235281 TTCTGCTGCTGCTTCTGCTG 61.235 55.000 17.00 4.89 40.48 4.41
1014 1154 2.046892 CTCGCACCTTCCACCCTG 60.047 66.667 0.00 0.00 0.00 4.45
1064 1204 3.893753 TCTTCCCATCAAGAACCCAAA 57.106 42.857 0.00 0.00 29.01 3.28
1080 1220 2.028748 CCCAAATCCAAACCTCAGCTTG 60.029 50.000 0.00 0.00 0.00 4.01
1113 1255 4.411013 CAAGAGATTCCCCAAGAGGTTTT 58.589 43.478 0.00 0.00 0.00 2.43
1217 1360 2.155279 CTCCTAATCTGATCTCGCGGA 58.845 52.381 6.13 2.40 0.00 5.54
1241 1384 5.235186 ACATTGTCTATTCGATTGTAGCAGC 59.765 40.000 0.00 0.00 0.00 5.25
1314 1457 2.659610 GAGGCCTTCGAGCACACT 59.340 61.111 6.77 0.00 0.00 3.55
1551 1694 3.580916 GAGACCGTGCTCGACTCT 58.419 61.111 19.68 14.43 39.71 3.24
1704 1847 0.466124 AGCAAGATAAGGAGACCGGC 59.534 55.000 0.00 0.00 0.00 6.13
1707 1850 0.686769 AAGATAAGGAGACCGGCGGT 60.687 55.000 34.81 34.81 39.44 5.68
1731 1874 1.520342 GGCAGACGACAGCCAGATC 60.520 63.158 15.78 0.00 45.97 2.75
1734 1877 0.383590 CAGACGACAGCCAGATCGAT 59.616 55.000 0.00 0.00 40.86 3.59
1782 1925 3.254657 TCAAGGTAACAGAAAAATGCCCG 59.745 43.478 0.00 0.00 41.41 6.13
1952 2115 8.915057 ATCTAATATGCTGCTACAAAATGTCT 57.085 30.769 0.00 0.00 0.00 3.41
1953 2116 8.737168 TCTAATATGCTGCTACAAAATGTCTT 57.263 30.769 0.00 0.00 0.00 3.01
1986 2149 6.605594 TGTTCAAAATAATAAGGGCCAGTAGG 59.394 38.462 6.18 0.00 38.23 3.18
2018 2181 8.533657 ACATAATGACCAAATGAACAATCACAT 58.466 29.630 0.00 0.00 38.69 3.21
2214 2459 2.688507 TGCTCGAGTTTTCTCCATGAC 58.311 47.619 15.13 0.00 43.49 3.06
2220 2465 4.921515 TCGAGTTTTCTCCATGACGTAAAG 59.078 41.667 0.00 0.00 43.49 1.85
2258 2503 2.768698 CAAATTTGCATCACTTGGGCA 58.231 42.857 5.01 0.00 35.41 5.36
2477 2727 0.748450 CGCCATGCCAATTTGGATCT 59.252 50.000 19.76 0.00 40.96 2.75
2496 2746 3.043713 CCGCTGCGCAGAGTTTCA 61.044 61.111 40.21 0.00 0.00 2.69
2555 2805 3.382111 CTCCTGGAGCTCGTGGTT 58.618 61.111 11.42 0.00 0.00 3.67
2559 2809 1.367471 CTGGAGCTCGTGGTTGTCA 59.633 57.895 7.83 0.00 0.00 3.58
2580 2830 2.219458 TCCATCGTAGGTCTTCTAGCG 58.781 52.381 0.00 0.00 0.00 4.26
2581 2831 1.335142 CCATCGTAGGTCTTCTAGCGC 60.335 57.143 0.00 0.00 0.00 5.92
2941 3221 8.150945 AGCACTAGTACCCTATTTTACATCATG 58.849 37.037 0.00 0.00 0.00 3.07
3016 3296 9.176181 TGTAAATTTTACTCGAAGCACAATTTC 57.824 29.630 17.70 0.00 0.00 2.17
3029 3309 6.932901 AGCACAATTTCGTGATGTATTTTG 57.067 33.333 0.30 0.00 39.34 2.44
3129 3409 3.516512 ATGGGTGTTGGTGGGCCA 61.517 61.111 0.00 0.00 44.38 5.36
3163 3443 3.616721 AGGCAGACGTGTCCGCTT 61.617 61.111 8.02 0.00 37.70 4.68
3245 3525 4.415881 TTATGGGTATGCGAACAGTCAT 57.584 40.909 0.00 0.00 0.00 3.06
3247 3527 1.552792 TGGGTATGCGAACAGTCATGA 59.447 47.619 0.00 0.00 0.00 3.07
3304 3584 3.660111 GACCCACTTGCACACCGC 61.660 66.667 0.00 0.00 42.89 5.68
3489 3770 3.055602 GTGAGAATTACCCGGTTACTGGT 60.056 47.826 9.62 5.96 37.92 4.00
3613 4096 9.345517 CATTTTTCTCCATGTGTATGTAACTTG 57.654 33.333 0.00 0.00 32.21 3.16
3649 4132 2.079925 CCTAGACAGGTGAAGCTTTGC 58.920 52.381 0.00 0.00 37.15 3.68
3688 4171 9.778741 TCTGGTTATTATCACAAGGTTGATATC 57.221 33.333 0.00 0.00 38.10 1.63
3804 4287 5.407691 AGATGCATGCATGTTCTCTAATACG 59.592 40.000 36.73 0.00 36.70 3.06
3805 4288 4.441792 TGCATGCATGTTCTCTAATACGT 58.558 39.130 26.79 0.00 0.00 3.57
3855 4416 4.104738 CCATCAGGGTAATGGGACTAATGT 59.895 45.833 0.00 0.00 40.07 2.71
3905 4466 6.316390 GGTTGTATATCTGTTCCTGACCTTTG 59.684 42.308 0.00 0.00 0.00 2.77
3942 4503 2.223377 GCTGTTGTAGGAAGGTGAAACG 59.777 50.000 0.00 0.00 38.12 3.60
3976 4537 4.336993 ACGTGAAAAACAAGCCATCAACTA 59.663 37.500 0.00 0.00 0.00 2.24
4002 4563 0.964358 GCATGCTTTCCTCTGCTGGT 60.964 55.000 11.37 0.00 0.00 4.00
4011 4572 1.210478 TCCTCTGCTGGTTTATCTGGC 59.790 52.381 0.00 0.00 0.00 4.85
4104 4665 2.376165 GCTCCCACCTCCCCCTAAC 61.376 68.421 0.00 0.00 0.00 2.34
4221 4782 9.801873 GATATTTCTGCTATAGAGGTGAGAATC 57.198 37.037 3.21 0.00 36.61 2.52
4255 4817 6.456501 ACTTTCACTACAATCTCTACGCTTT 58.543 36.000 0.00 0.00 0.00 3.51
4413 4975 2.831526 ACTGGGACAAACAAAAAGCACT 59.168 40.909 0.00 0.00 38.70 4.40
4463 5025 1.400846 GAATGCCATCTGCTGTGTCAG 59.599 52.381 0.00 0.00 42.00 3.51
4468 5030 1.274447 CCATCTGCTGTGTCAGAGACA 59.726 52.381 0.14 0.00 45.22 3.41
4469 5031 2.289257 CCATCTGCTGTGTCAGAGACAA 60.289 50.000 1.44 0.00 44.49 3.18
4470 5032 3.396560 CATCTGCTGTGTCAGAGACAAA 58.603 45.455 1.44 0.00 44.49 2.83
4602 5169 2.677875 CCTTTGGGGAGGTGCTGC 60.678 66.667 0.00 0.00 37.23 5.25
4623 5190 4.349048 TGCTATCTATCAAGGCATCAACCT 59.651 41.667 0.00 0.00 43.91 3.50
4654 5221 0.174617 GGGAGCTCCGAAAGTCTGAG 59.825 60.000 26.36 0.00 36.71 3.35
4771 5338 8.571336 CACTTGTATTTCTGTCCTGAAAGATTT 58.429 33.333 5.73 0.00 39.01 2.17
4849 5416 6.089820 CGTTTGAAAACTAGAGCACGGTTATA 59.910 38.462 0.00 0.00 36.77 0.98
4949 5516 5.299279 ACAGTCGTGAAACCAAGAATGATTT 59.701 36.000 13.62 0.00 39.33 2.17
5063 5630 2.779282 CATACATGGACGCCAAGCA 58.221 52.632 0.00 0.00 36.95 3.91
5065 5632 0.748005 ATACATGGACGCCAAGCACC 60.748 55.000 0.00 0.00 36.95 5.01
5066 5633 2.118233 TACATGGACGCCAAGCACCA 62.118 55.000 0.00 5.26 36.95 4.17
5068 5635 1.304381 ATGGACGCCAAGCACCATT 60.304 52.632 8.75 0.00 40.39 3.16
5069 5636 1.597797 ATGGACGCCAAGCACCATTG 61.598 55.000 8.75 0.00 40.39 2.82
5073 5640 0.031994 ACGCCAAGCACCATTGTTTC 59.968 50.000 0.00 0.00 0.00 2.78
5155 5722 3.102052 AGCAAAGCCACAAAACTCATG 57.898 42.857 0.00 0.00 0.00 3.07
5484 6129 7.437862 GCAAACAAAATTGTGATCCTAACTTCA 59.562 33.333 1.62 0.00 41.31 3.02
5584 6229 0.984230 CTTCCTAGACAAGGGTGCCA 59.016 55.000 0.00 0.00 46.55 4.92
5645 6290 1.067706 CCGTTTGCAATGGATTCTGCA 60.068 47.619 11.80 0.00 46.50 4.41
5786 6431 1.501741 CGCGGCAAAGCAGTACATT 59.498 52.632 0.00 0.00 36.85 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.810427 CATCTACAACCATGATTTACAAATTGC 58.190 33.333 0.00 0.00 0.00 3.56
45 46 2.897969 AGTGGGACGTTACATGAGTCTT 59.102 45.455 0.00 0.00 35.42 3.01
120 121 5.011635 ACATTTTAGGTGGCAGGTTAAAAGG 59.988 40.000 15.25 15.25 34.67 3.11
305 312 2.022764 TCACAGGTTGAGTGTGTGTG 57.977 50.000 3.33 0.00 44.75 3.82
306 313 2.356135 GTTCACAGGTTGAGTGTGTGT 58.644 47.619 3.33 0.00 44.75 3.72
307 314 1.327460 CGTTCACAGGTTGAGTGTGTG 59.673 52.381 3.33 0.00 44.75 3.82
308 315 1.066430 ACGTTCACAGGTTGAGTGTGT 60.066 47.619 3.33 0.00 44.75 3.72
342 349 6.441924 CCTCTCAAAGGCATCTATAGGGATAA 59.558 42.308 0.00 0.00 38.67 1.75
358 365 5.486526 AGTTGTTAGATCTGCCTCTCAAAG 58.513 41.667 5.18 0.00 0.00 2.77
393 400 5.242434 AGTTTAACGTCTATGGTGCATTCA 58.758 37.500 0.00 0.00 0.00 2.57
421 428 6.319152 AGCTTTCATTTTCATGGATGAGAGAG 59.681 38.462 19.60 13.77 36.91 3.20
485 492 3.636282 ACCCACGTTTTGAGCATTTAC 57.364 42.857 0.00 0.00 0.00 2.01
486 493 3.502979 GGTACCCACGTTTTGAGCATTTA 59.497 43.478 0.00 0.00 0.00 1.40
487 494 2.295070 GGTACCCACGTTTTGAGCATTT 59.705 45.455 0.00 0.00 0.00 2.32
488 495 1.883926 GGTACCCACGTTTTGAGCATT 59.116 47.619 0.00 0.00 0.00 3.56
490 497 0.180642 TGGTACCCACGTTTTGAGCA 59.819 50.000 10.07 0.00 0.00 4.26
506 528 1.971357 CATATTCCTCGTAGGCCTGGT 59.029 52.381 17.99 0.00 34.61 4.00
516 538 7.650504 TCAACTACCGTAATTTCATATTCCTCG 59.349 37.037 0.00 0.00 0.00 4.63
521 543 9.607988 TGACATCAACTACCGTAATTTCATATT 57.392 29.630 0.00 0.00 0.00 1.28
551 573 2.547855 CCGAGTGTGATTGGACTGTCAA 60.548 50.000 10.38 0.00 0.00 3.18
572 594 5.280945 TGTAAAGTCTTGCAAACATTCAGC 58.719 37.500 0.00 0.00 0.00 4.26
578 600 9.809096 TCAATTATTTGTAAAGTCTTGCAAACA 57.191 25.926 14.15 0.00 45.85 2.83
619 641 5.473066 ACACAAGCCTTATTGCAATTTCT 57.527 34.783 18.75 6.90 33.28 2.52
622 644 3.747529 GCAACACAAGCCTTATTGCAATT 59.252 39.130 18.75 1.81 44.01 2.32
630 661 2.803451 CGTTTTGCAACACAAGCCTTA 58.197 42.857 15.56 0.00 40.06 2.69
665 700 1.490069 AGTTGTTGGGCCTTTGCAATT 59.510 42.857 4.53 0.00 40.13 2.32
689 724 4.026475 CGAAGACAGCATTTCGATCCTTAC 60.026 45.833 0.70 0.00 46.67 2.34
698 734 0.729690 GGAGCCGAAGACAGCATTTC 59.270 55.000 0.00 0.00 0.00 2.17
701 737 1.965754 GAGGGAGCCGAAGACAGCAT 61.966 60.000 0.00 0.00 0.00 3.79
710 746 2.154798 CTGTTGTTCGAGGGAGCCGA 62.155 60.000 0.00 0.00 0.00 5.54
733 769 3.383825 TCTGTCTAAAAGATCTACCGCCC 59.616 47.826 0.00 0.00 0.00 6.13
740 776 5.393243 GGCTACGTGTCTGTCTAAAAGATCT 60.393 44.000 0.00 0.00 0.00 2.75
753 805 1.674962 GAACTATCCGGCTACGTGTCT 59.325 52.381 0.00 0.00 38.78 3.41
772 824 1.212751 CGCGGGCTCATATCGATGA 59.787 57.895 8.54 0.00 39.88 2.92
773 825 0.170339 TACGCGGGCTCATATCGATG 59.830 55.000 12.47 0.00 0.00 3.84
774 826 1.103803 ATACGCGGGCTCATATCGAT 58.896 50.000 12.47 2.16 0.00 3.59
775 827 0.885879 AATACGCGGGCTCATATCGA 59.114 50.000 12.47 0.00 0.00 3.59
929 1060 1.626356 TTTGCCCCTCTGATCGGGAG 61.626 60.000 12.86 7.85 44.90 4.30
984 1124 3.456365 GCGAGGAGGAGCAGCAGA 61.456 66.667 0.00 0.00 0.00 4.26
990 1130 2.185608 GAAGGTGCGAGGAGGAGC 59.814 66.667 0.00 0.00 39.07 4.70
1014 1154 0.739561 AGGAGAAGACGTGGTATCGC 59.260 55.000 0.00 0.00 0.00 4.58
1113 1255 2.682856 GGGCTTGATCTGACGCAAAATA 59.317 45.455 0.00 0.00 0.00 1.40
1217 1360 5.235186 GCTGCTACAATCGAATAGACAATGT 59.765 40.000 0.00 0.00 0.00 2.71
1241 1384 2.652496 GCTCGCCGCTCTACTTCG 60.652 66.667 0.00 0.00 35.14 3.79
1551 1694 1.800315 GAGCACGAAGTAGCGCGAA 60.800 57.895 12.10 0.00 41.61 4.70
1704 1847 3.062466 TCGTCTGCCTCCTCACCG 61.062 66.667 0.00 0.00 0.00 4.94
1707 1850 2.640302 GCTGTCGTCTGCCTCCTCA 61.640 63.158 0.21 0.00 33.40 3.86
1782 1925 3.277715 AGCAATAGCAAAGAGAGAAGCC 58.722 45.455 0.00 0.00 45.49 4.35
1833 1976 6.924111 ACTAATTTGGCAGTGAAAATGTAGG 58.076 36.000 0.00 0.00 32.28 3.18
1986 2149 9.906660 TTGTTCATTTGGTCATTATGTAACTTC 57.093 29.630 0.00 0.00 0.00 3.01
2214 2459 2.073816 CACTTGGTGCCCTACTTTACG 58.926 52.381 0.00 0.00 0.00 3.18
2220 2465 0.322456 TGCATCACTTGGTGCCCTAC 60.322 55.000 11.91 0.00 40.56 3.18
2258 2503 0.801251 GCTCATGTTTTGCTCGAGCT 59.199 50.000 35.27 13.88 44.47 4.09
2326 2571 4.671590 TGGTCGGGTGGAGAGCGA 62.672 66.667 0.00 0.00 38.81 4.93
2555 2805 3.632333 AGAAGACCTACGATGGATGACA 58.368 45.455 5.55 0.00 0.00 3.58
2559 2809 2.814919 CGCTAGAAGACCTACGATGGAT 59.185 50.000 0.00 0.00 0.00 3.41
2638 2888 3.118454 CGCGATGCCGACCAAAGT 61.118 61.111 0.00 0.00 38.22 2.66
2670 2920 1.684391 GGGGGCTGCCCGTAATTTT 60.684 57.895 30.32 0.00 46.66 1.82
2941 3221 3.430236 CCAAAAACCTCCAACTCCAACAC 60.430 47.826 0.00 0.00 0.00 3.32
3129 3409 1.727062 CCTGCATCCCTAGTCAGGAT 58.273 55.000 1.09 0.96 46.80 3.24
3174 3454 2.722094 AGGATTAGTGCAATTTCGGCA 58.278 42.857 0.00 0.00 39.32 5.69
3211 3491 7.663905 TCGCATACCCATAATTAAAACTAGCAT 59.336 33.333 0.00 0.00 0.00 3.79
3304 3584 2.190578 CTCGCCAAGGCCCTAAGG 59.809 66.667 5.34 0.00 37.98 2.69
3312 3592 5.420409 GTCTTAATATATCCCTCGCCAAGG 58.580 45.833 0.00 0.00 45.77 3.61
3317 3597 5.401531 TGTGGTCTTAATATATCCCTCGC 57.598 43.478 0.00 0.00 0.00 5.03
3318 3598 7.170393 TCATGTGGTCTTAATATATCCCTCG 57.830 40.000 0.00 0.00 0.00 4.63
3489 3770 2.703007 ACACCATTTTTGGCCAGCTAAA 59.297 40.909 5.11 8.84 0.00 1.85
3635 4118 3.051081 ACTCTAGCAAAGCTTCACCTG 57.949 47.619 0.00 0.00 40.44 4.00
3636 4119 3.778954 AACTCTAGCAAAGCTTCACCT 57.221 42.857 0.00 0.00 40.44 4.00
3876 4437 7.514127 AGGTCAGGAACAGATATACAACCATAT 59.486 37.037 0.00 0.00 0.00 1.78
3905 4466 0.465097 CAGCAGGGACACCATCATCC 60.465 60.000 0.00 0.00 40.13 3.51
3942 4503 7.272731 GGCTTGTTTTTCACGTTTATCCTAATC 59.727 37.037 0.00 0.00 0.00 1.75
3976 4537 1.353694 AGAGGAAAGCATGCCACTTCT 59.646 47.619 15.66 13.74 0.00 2.85
4011 4572 0.250989 TAGGTTTTTCAGTGGCCCCG 60.251 55.000 0.00 0.00 0.00 5.73
4234 4795 6.347402 GCAAAAAGCGTAGAGATTGTAGTGAA 60.347 38.462 0.00 0.00 0.00 3.18
4386 4948 1.384525 TTGTTTGTCCCAGTTCGGTG 58.615 50.000 0.00 0.00 0.00 4.94
4463 5025 5.351465 TCAGTCACACAGTTTTCTTTGTCTC 59.649 40.000 0.00 0.00 38.58 3.36
4468 5030 7.433680 ACTTTTTCAGTCACACAGTTTTCTTT 58.566 30.769 0.00 0.00 0.00 2.52
4469 5031 6.981722 ACTTTTTCAGTCACACAGTTTTCTT 58.018 32.000 0.00 0.00 0.00 2.52
4470 5032 6.575162 ACTTTTTCAGTCACACAGTTTTCT 57.425 33.333 0.00 0.00 0.00 2.52
4471 5033 7.270579 GTGTACTTTTTCAGTCACACAGTTTTC 59.729 37.037 0.00 0.00 38.53 2.29
4472 5034 7.081976 GTGTACTTTTTCAGTCACACAGTTTT 58.918 34.615 0.00 0.00 38.53 2.43
4602 5169 4.694509 GCAGGTTGATGCCTTGATAGATAG 59.305 45.833 0.00 0.00 40.43 2.08
4623 5190 0.182061 GAGCTCCCTGAATCCATGCA 59.818 55.000 0.87 0.00 0.00 3.96
4654 5221 6.884836 ACCCACACTTCTATTCAGGAAAATAC 59.115 38.462 0.00 0.00 0.00 1.89
4771 5338 5.120208 GCTTTTCGCATAAACAGTACTCTCA 59.880 40.000 0.00 0.00 38.92 3.27
4796 5363 7.188834 TCTTCGCAAATGATAGCATAAAACAG 58.811 34.615 0.00 0.00 33.44 3.16
4831 5398 7.822822 AGAACAAATATAACCGTGCTCTAGTTT 59.177 33.333 0.00 0.00 0.00 2.66
4849 5416 2.676839 CAGATCAGCGCAGAGAACAAAT 59.323 45.455 11.47 0.00 0.00 2.32
5155 5722 4.742438 TTGAAGCTGTGATACCGTTTTC 57.258 40.909 0.00 0.00 0.00 2.29
5484 6129 1.076024 ACATGTGAATGAACTGCCCCT 59.924 47.619 0.00 0.00 0.00 4.79
5584 6229 6.720112 ACAATCAAATGCATAAGCCTATGT 57.280 33.333 0.00 0.00 41.13 2.29
5645 6290 1.133668 AGCTTGTTGAACCAGCTCCTT 60.134 47.619 17.07 0.00 0.00 3.36
5786 6431 1.970640 TGCTCCTTGTAGTGCTTCTCA 59.029 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.