Multiple sequence alignment - TraesCS1D01G185100

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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 TraesCS1D01G185100 chr1D 100.000 5074 0 0 1 5074 255838407 255833334 0.000000e+00 9371.0
1 TraesCS1D01G185100 chr1B 94.892 3896 114 29 771 4621 357205718 357209573 0.000000e+00 6013.0
2 TraesCS1D01G185100 chr1B 91.533 685 34 13 23 696 357204629 357205300 0.000000e+00 922.0
3 TraesCS1D01G185100 chr1B 93.392 454 13 4 4621 5074 357209671 357210107 0.000000e+00 656.0
4 TraesCS1D01G185100 chr1A 93.027 3901 133 47 771 4620 328257727 328253915 0.000000e+00 5568.0
5 TraesCS1D01G185100 chr1A 94.305 439 9 4 4636 5074 328253586 328253164 0.000000e+00 658.0
6 TraesCS1D01G185100 chr1A 93.077 260 13 4 215 469 328258447 328258188 4.800000e-100 375.0
7 TraesCS1D01G185100 chr1A 89.450 218 18 3 1 218 328259252 328259040 2.330000e-68 270.0
8 TraesCS1D01G185100 chr1A 86.885 61 7 1 161 221 51695123 51695064 3.280000e-07 67.6
9 TraesCS1D01G185100 chr4D 86.957 115 14 1 340 454 94762213 94762326 1.480000e-25 128.0
10 TraesCS1D01G185100 chr7D 90.769 65 5 1 102 166 403560232 403560295 9.050000e-13 86.1
11 TraesCS1D01G185100 chr7B 88.732 71 7 1 342 411 59090805 59090875 9.050000e-13 86.1
12 TraesCS1D01G185100 chrUn 92.857 56 4 0 193 248 230602085 230602030 1.170000e-11 82.4


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 TraesCS1D01G185100 chr1D 255833334 255838407 5073 True 9371.000000 9371 100.000000 1 5074 1 chr1D.!!$R1 5073
1 TraesCS1D01G185100 chr1B 357204629 357210107 5478 False 2530.333333 6013 93.272333 23 5074 3 chr1B.!!$F1 5051
2 TraesCS1D01G185100 chr1A 328253164 328259252 6088 True 1717.750000 5568 92.464750 1 5074 4 chr1A.!!$R2 5073

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
551 1350 1.304713 CAAGGACCAAGCCAGCCAT 60.305 57.895 0.00 0.0 0.00 4.40 F
1849 3043 0.100325 TGTTTGCTGGTTTCACTGCG 59.900 50.000 0.00 0.0 38.04 5.18 F
3312 4588 0.390603 TCCATCCGGCGTGTTAACAG 60.391 55.000 8.98 4.7 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 3182 2.095617 GGGTGTTCAAATAACGGTTCCG 60.096 50.000 9.81 9.81 0.0 4.30 R
3679 4962 1.806542 AGTAGAGCAATGCAAACACGG 59.193 47.619 8.35 0.00 0.0 4.94 R
4894 6510 0.388649 GCGCCGTCAGAAGAAGAAGA 60.389 55.000 0.00 0.00 0.0 2.87 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
42 43 2.427905 GACACACACGCGTCGCTA 60.428 61.111 9.86 0.00 0.00 4.26
57 58 3.804325 CGTCGCTAATTGACAATGGATCT 59.196 43.478 0.34 0.00 36.11 2.75
156 157 1.592743 CCCACCACAACATGCATGG 59.407 57.895 29.41 16.32 39.57 3.66
166 167 6.155910 ACCACAACATGCATGGGATTATTTTA 59.844 34.615 29.41 0.00 37.86 1.52
167 168 7.147514 ACCACAACATGCATGGGATTATTTTAT 60.148 33.333 29.41 1.84 37.86 1.40
168 169 7.716123 CCACAACATGCATGGGATTATTTTATT 59.284 33.333 29.41 8.17 0.00 1.40
274 871 3.211865 GTCCACTCATCATGCATGTGAT 58.788 45.455 25.43 11.72 39.34 3.06
409 1012 8.038492 TCATGTTTCATACGATCAAATCACAA 57.962 30.769 0.00 0.00 0.00 3.33
434 1037 8.716674 ATGAAATATATTGCAACTGATTCCCT 57.283 30.769 10.26 0.00 0.00 4.20
445 1048 2.426522 CTGATTCCCTCAGCAAAACGA 58.573 47.619 0.00 0.00 44.73 3.85
551 1350 1.304713 CAAGGACCAAGCCAGCCAT 60.305 57.895 0.00 0.00 0.00 4.40
558 1357 1.322538 CCAAGCCAGCCATACCAACC 61.323 60.000 0.00 0.00 0.00 3.77
573 1372 2.301583 ACCAACCGCCTGCAAAAATAAT 59.698 40.909 0.00 0.00 0.00 1.28
631 1436 9.968870 ATCAACAATAAAACGGCTAAAAAGTAA 57.031 25.926 0.00 0.00 0.00 2.24
637 1442 9.806203 AATAAAACGGCTAAAAAGTAAACAACT 57.194 25.926 0.00 0.00 41.49 3.16
647 1452 4.893424 AAGTAAACAACTGACGCAACAT 57.107 36.364 0.00 0.00 38.88 2.71
692 1497 9.091784 AGCAAAGTTTTTCTTTTGAGATCTTTC 57.908 29.630 0.00 0.00 42.95 2.62
734 1920 1.603456 TTGTTTGAGATCAGGCGCAA 58.397 45.000 10.83 0.00 0.00 4.85
743 1929 3.349006 CAGGCGCAACGAAGTGCT 61.349 61.111 10.83 0.00 45.00 4.40
753 1939 3.758300 CAACGAAGTGCTTGTCAACTTT 58.242 40.909 0.00 0.00 45.00 2.66
755 1941 4.434713 ACGAAGTGCTTGTCAACTTTTT 57.565 36.364 0.00 0.00 42.51 1.94
756 1942 4.412207 ACGAAGTGCTTGTCAACTTTTTC 58.588 39.130 0.00 0.00 42.51 2.29
757 1943 4.156008 ACGAAGTGCTTGTCAACTTTTTCT 59.844 37.500 0.00 0.00 42.51 2.52
758 1944 5.095490 CGAAGTGCTTGTCAACTTTTTCTT 58.905 37.500 0.00 0.00 0.00 2.52
759 1945 5.572896 CGAAGTGCTTGTCAACTTTTTCTTT 59.427 36.000 0.00 0.00 0.00 2.52
760 1946 6.089417 CGAAGTGCTTGTCAACTTTTTCTTTT 59.911 34.615 0.00 0.00 0.00 2.27
761 1947 6.710692 AGTGCTTGTCAACTTTTTCTTTTG 57.289 33.333 0.00 0.00 0.00 2.44
762 1948 6.454795 AGTGCTTGTCAACTTTTTCTTTTGA 58.545 32.000 0.00 0.00 0.00 2.69
763 1949 6.587608 AGTGCTTGTCAACTTTTTCTTTTGAG 59.412 34.615 0.00 0.00 29.97 3.02
764 1950 5.868801 TGCTTGTCAACTTTTTCTTTTGAGG 59.131 36.000 0.00 0.00 29.97 3.86
765 1951 5.291858 GCTTGTCAACTTTTTCTTTTGAGGG 59.708 40.000 0.00 0.00 29.97 4.30
766 1952 5.337578 TGTCAACTTTTTCTTTTGAGGGG 57.662 39.130 0.00 0.00 29.97 4.79
767 1953 4.775253 TGTCAACTTTTTCTTTTGAGGGGT 59.225 37.500 0.00 0.00 29.97 4.95
768 1954 5.105513 TGTCAACTTTTTCTTTTGAGGGGTC 60.106 40.000 0.00 0.00 29.97 4.46
769 1955 4.404394 TCAACTTTTTCTTTTGAGGGGTCC 59.596 41.667 0.00 0.00 0.00 4.46
770 1956 4.265856 ACTTTTTCTTTTGAGGGGTCCT 57.734 40.909 0.00 0.00 36.03 3.85
816 2002 3.149899 GGCTCATGGGCTATCATCG 57.850 57.895 18.99 0.00 37.53 3.84
822 2008 4.321718 CTCATGGGCTATCATCGTCATTT 58.678 43.478 0.00 0.00 0.00 2.32
823 2009 5.482006 CTCATGGGCTATCATCGTCATTTA 58.518 41.667 0.00 0.00 0.00 1.40
824 2010 5.863965 TCATGGGCTATCATCGTCATTTAA 58.136 37.500 0.00 0.00 0.00 1.52
879 2065 3.637297 CCGTAGCGGGAGTCTTAAC 57.363 57.895 0.00 0.00 44.15 2.01
1271 2461 3.534056 CACCGCCCCTAGGTACCG 61.534 72.222 8.29 6.99 40.59 4.02
1302 2493 1.608590 CCTCTCTCGGATTCTCTCAGC 59.391 57.143 0.00 0.00 0.00 4.26
1306 2497 1.021202 CTCGGATTCTCTCAGCGAGT 58.979 55.000 0.00 0.00 40.75 4.18
1314 2505 0.679640 CTCTCAGCGAGTCCTCACCT 60.680 60.000 5.66 0.00 34.95 4.00
1428 2620 1.839994 AGGTATGGAGTGTGGTGATGG 59.160 52.381 0.00 0.00 0.00 3.51
1439 2631 3.252458 GTGTGGTGATGGTTTGGTACTTC 59.748 47.826 0.00 0.00 0.00 3.01
1448 2640 7.824779 GTGATGGTTTGGTACTTCTCTTCTTAT 59.175 37.037 0.00 0.00 0.00 1.73
1623 2816 5.073311 TGTGCACTCTACATAAGGTTCTC 57.927 43.478 19.41 0.00 0.00 2.87
1629 2822 4.336993 ACTCTACATAAGGTTCTCGCTCTG 59.663 45.833 0.00 0.00 0.00 3.35
1763 2957 3.519510 AGAAGGATGACAGGGAATCGAAA 59.480 43.478 0.00 0.00 0.00 3.46
1764 2958 3.550437 AGGATGACAGGGAATCGAAAG 57.450 47.619 0.00 0.00 0.00 2.62
1765 2959 2.840651 AGGATGACAGGGAATCGAAAGT 59.159 45.455 0.00 0.00 0.00 2.66
1767 2961 4.469945 AGGATGACAGGGAATCGAAAGTAA 59.530 41.667 0.00 0.00 0.00 2.24
1768 2962 5.045869 AGGATGACAGGGAATCGAAAGTAAA 60.046 40.000 0.00 0.00 0.00 2.01
1769 2963 5.294552 GGATGACAGGGAATCGAAAGTAAAG 59.705 44.000 0.00 0.00 0.00 1.85
1770 2964 4.000988 TGACAGGGAATCGAAAGTAAAGC 58.999 43.478 0.00 0.00 0.00 3.51
1771 2965 3.344515 ACAGGGAATCGAAAGTAAAGCC 58.655 45.455 0.00 0.00 0.00 4.35
1772 2966 3.009143 ACAGGGAATCGAAAGTAAAGCCT 59.991 43.478 0.00 0.00 0.00 4.58
1773 2967 4.224370 ACAGGGAATCGAAAGTAAAGCCTA 59.776 41.667 0.00 0.00 0.00 3.93
1774 2968 5.183228 CAGGGAATCGAAAGTAAAGCCTAA 58.817 41.667 0.00 0.00 0.00 2.69
1775 2969 5.646360 CAGGGAATCGAAAGTAAAGCCTAAA 59.354 40.000 0.00 0.00 0.00 1.85
1776 2970 5.646793 AGGGAATCGAAAGTAAAGCCTAAAC 59.353 40.000 0.00 0.00 0.00 2.01
1777 2971 5.646793 GGGAATCGAAAGTAAAGCCTAAACT 59.353 40.000 0.00 0.00 0.00 2.66
1849 3043 0.100325 TGTTTGCTGGTTTCACTGCG 59.900 50.000 0.00 0.00 38.04 5.18
1856 3056 2.031157 GCTGGTTTCACTGCGTGTATTT 60.031 45.455 8.22 0.00 34.79 1.40
1893 3093 5.565045 GCCAATACTAGAACCAGAGATACGG 60.565 48.000 0.00 0.00 0.00 4.02
1914 3114 3.617263 GGGAAAGTACTGTGCATCTAACG 59.383 47.826 6.91 0.00 0.00 3.18
1925 3125 5.423886 TGTGCATCTAACGGATACATTTCA 58.576 37.500 0.00 0.00 31.23 2.69
2261 3470 2.872245 CAAACTCCGTGTCATCTTGTGT 59.128 45.455 0.00 0.00 0.00 3.72
2520 3729 7.655732 GCAATACCATGTTTAATTATGTTCCCC 59.344 37.037 0.00 0.00 0.00 4.81
2696 3934 5.278604 CAAGAATGGATGCATGTACATGTG 58.721 41.667 31.10 16.66 40.80 3.21
2787 4025 5.799827 TTTGGTTGCAAAGGCTTACTAAT 57.200 34.783 0.00 0.00 41.91 1.73
2788 4026 4.782019 TGGTTGCAAAGGCTTACTAATG 57.218 40.909 0.00 0.00 41.91 1.90
2950 4188 4.298332 CCTTACAGTTGCAACATGGTTTC 58.702 43.478 30.11 1.60 0.00 2.78
2957 4195 5.803461 CAGTTGCAACATGGTTTCATCTATG 59.197 40.000 30.11 11.27 33.53 2.23
2987 4225 5.687166 TTAACTGGACTTGGACGGATTAT 57.313 39.130 0.00 0.00 0.00 1.28
2999 4237 7.497909 ACTTGGACGGATTATTAAGTATGTTGG 59.502 37.037 0.00 0.00 0.00 3.77
3046 4289 4.201628 CGCAACTTCAGCAATACTCAGTAC 60.202 45.833 0.00 0.00 0.00 2.73
3093 4343 5.410355 AGCATTGCAAGTGGTTTCAATAT 57.590 34.783 11.91 0.00 0.00 1.28
3118 4368 4.772886 AGTTATATCGTCCTTTTGGGCT 57.227 40.909 0.00 0.00 43.43 5.19
3119 4369 4.451900 AGTTATATCGTCCTTTTGGGCTG 58.548 43.478 0.00 0.00 43.43 4.85
3120 4370 4.163458 AGTTATATCGTCCTTTTGGGCTGA 59.837 41.667 0.00 0.00 43.43 4.26
3121 4371 2.396590 TATCGTCCTTTTGGGCTGAC 57.603 50.000 0.00 0.00 43.43 3.51
3122 4372 0.693049 ATCGTCCTTTTGGGCTGACT 59.307 50.000 0.00 0.00 43.43 3.41
3123 4373 1.344065 TCGTCCTTTTGGGCTGACTA 58.656 50.000 0.00 0.00 43.43 2.59
3124 4374 1.906574 TCGTCCTTTTGGGCTGACTAT 59.093 47.619 0.00 0.00 43.43 2.12
3125 4375 2.304761 TCGTCCTTTTGGGCTGACTATT 59.695 45.455 0.00 0.00 43.43 1.73
3126 4376 3.516300 TCGTCCTTTTGGGCTGACTATTA 59.484 43.478 0.00 0.00 43.43 0.98
3127 4377 3.871594 CGTCCTTTTGGGCTGACTATTAG 59.128 47.826 0.00 0.00 43.43 1.73
3128 4378 4.382685 CGTCCTTTTGGGCTGACTATTAGA 60.383 45.833 0.00 0.00 43.43 2.10
3129 4379 5.497474 GTCCTTTTGGGCTGACTATTAGAA 58.503 41.667 0.00 0.00 42.03 2.10
3130 4380 5.586643 GTCCTTTTGGGCTGACTATTAGAAG 59.413 44.000 0.00 0.00 42.03 2.85
3131 4381 5.250774 TCCTTTTGGGCTGACTATTAGAAGT 59.749 40.000 0.00 0.00 40.87 3.01
3132 4382 5.946377 CCTTTTGGGCTGACTATTAGAAGTT 59.054 40.000 0.00 0.00 35.46 2.66
3133 4383 6.127897 CCTTTTGGGCTGACTATTAGAAGTTG 60.128 42.308 0.00 0.00 35.46 3.16
3134 4384 5.755409 TTGGGCTGACTATTAGAAGTTGA 57.245 39.130 0.00 0.00 0.00 3.18
3135 4385 5.086104 TGGGCTGACTATTAGAAGTTGAC 57.914 43.478 0.00 0.00 0.00 3.18
3136 4386 4.777896 TGGGCTGACTATTAGAAGTTGACT 59.222 41.667 0.00 0.00 0.00 3.41
3137 4387 5.105310 TGGGCTGACTATTAGAAGTTGACTC 60.105 44.000 0.00 0.00 0.00 3.36
3138 4388 5.105310 GGGCTGACTATTAGAAGTTGACTCA 60.105 44.000 0.00 0.00 0.00 3.41
3139 4389 6.407525 GGGCTGACTATTAGAAGTTGACTCAT 60.408 42.308 0.00 0.00 0.00 2.90
3140 4390 7.044798 GGCTGACTATTAGAAGTTGACTCATT 58.955 38.462 0.00 0.00 0.00 2.57
3141 4391 8.198109 GGCTGACTATTAGAAGTTGACTCATTA 58.802 37.037 0.00 0.00 0.00 1.90
3142 4392 9.757227 GCTGACTATTAGAAGTTGACTCATTAT 57.243 33.333 0.00 0.00 0.00 1.28
3184 4460 8.739039 TCATTATTTGGTGGTTTCAATACTCAG 58.261 33.333 0.00 0.00 0.00 3.35
3312 4588 0.390603 TCCATCCGGCGTGTTAACAG 60.391 55.000 8.98 4.70 0.00 3.16
3340 4616 3.395639 TGTTATCACACTTGGTTCGTCC 58.604 45.455 0.00 0.00 0.00 4.79
3400 4676 8.821686 ACATTGTCTTCCATAATGTATTGGAA 57.178 30.769 4.48 4.48 43.13 3.53
3461 4737 1.139734 CACCTGACGAGATCACCCG 59.860 63.158 0.00 0.00 32.37 5.28
3501 4783 1.378531 TTACATGCATCGGGTCTTGC 58.621 50.000 0.00 0.00 39.33 4.01
3591 4873 2.833631 ACGGAAGGTACCACTTCAAG 57.166 50.000 15.94 10.19 46.73 3.02
3679 4962 8.553459 AGATATAATAAGCTACAACCATGTGC 57.447 34.615 0.00 0.00 40.84 4.57
3695 4978 1.007502 TGCCGTGTTTGCATTGCTC 60.008 52.632 10.49 1.58 32.85 4.26
3785 5068 4.694339 AGGTAAAGCGACTTCATGATACC 58.306 43.478 9.05 9.05 33.39 2.73
3997 5280 3.785859 GATCCGCAGTCAGGGCCA 61.786 66.667 6.18 0.00 0.00 5.36
4064 5347 3.694072 TGGAAGGTGACAAGACAAAACAG 59.306 43.478 0.00 0.00 0.00 3.16
4201 5484 9.274206 TGCATTGTACTAATTGTTGTTGTAGTA 57.726 29.630 0.00 0.00 0.00 1.82
4244 5527 1.901833 AGGGGTGGATTTTGCATTGTC 59.098 47.619 0.00 0.00 0.00 3.18
4347 5646 3.055240 AGAACTCTCAGAGCCATCCAAAG 60.055 47.826 0.00 0.00 32.04 2.77
4452 5751 5.346822 GGCTCGATTAACTTTCGTGTTTAGA 59.653 40.000 0.00 0.00 37.82 2.10
4488 5787 1.076332 GCGTACGTTTGCCTCTTCAT 58.924 50.000 17.90 0.00 0.00 2.57
4523 5822 3.805971 GCGTACTTTTCACACTACTTGGT 59.194 43.478 0.00 0.00 0.00 3.67
4524 5823 4.984161 GCGTACTTTTCACACTACTTGGTA 59.016 41.667 0.00 0.00 0.00 3.25
4525 5824 5.107722 GCGTACTTTTCACACTACTTGGTAC 60.108 44.000 0.00 0.00 0.00 3.34
4650 6266 5.418524 ACAAAATTATACATGCCACTGCTGA 59.581 36.000 0.00 0.00 38.71 4.26
4754 6370 6.923012 TCACAAATGTTTGAATGATAGGTGG 58.077 36.000 12.09 0.00 40.55 4.61
4784 6400 1.078426 GGGAATGCACAGTACCGCT 60.078 57.895 0.00 0.00 0.00 5.52
4892 6508 2.180674 GGAGCACGTCCCCATTTTC 58.819 57.895 0.00 0.00 39.88 2.29
4893 6509 0.322546 GGAGCACGTCCCCATTTTCT 60.323 55.000 0.00 0.00 39.88 2.52
4894 6510 1.534729 GAGCACGTCCCCATTTTCTT 58.465 50.000 0.00 0.00 0.00 2.52
4895 6511 1.468914 GAGCACGTCCCCATTTTCTTC 59.531 52.381 0.00 0.00 0.00 2.87
4982 6600 7.475137 AGTACTGCTTCTCTTATGAAACTCT 57.525 36.000 0.00 0.00 0.00 3.24
4983 6601 7.543756 AGTACTGCTTCTCTTATGAAACTCTC 58.456 38.462 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 4.675976 AATAATCCCATGCATGTTGTGG 57.324 40.909 24.58 17.99 0.00 4.17
254 851 3.570912 ATCACATGCATGATGAGTGGA 57.429 42.857 32.75 16.43 37.93 4.02
409 1012 8.716674 AGGGAATCAGTTGCAATATATTTCAT 57.283 30.769 0.59 0.00 0.00 2.57
434 1037 3.394674 TGATACCACTCGTTTTGCTGA 57.605 42.857 0.00 0.00 0.00 4.26
442 1045 8.809468 ATGTGATACTATATGATACCACTCGT 57.191 34.615 0.00 0.00 0.00 4.18
521 1320 4.379918 GCTTGGTCCTTGTCTTTAGATTGC 60.380 45.833 0.00 0.00 0.00 3.56
551 1350 1.333177 ATTTTTGCAGGCGGTTGGTA 58.667 45.000 0.00 0.00 0.00 3.25
558 1357 3.986572 TGTGTCAATTATTTTTGCAGGCG 59.013 39.130 0.00 0.00 0.00 5.52
573 1372 3.077359 TGATGTGTGTGTGTTGTGTCAA 58.923 40.909 0.00 0.00 0.00 3.18
712 1898 2.360483 TGCGCCTGATCTCAAACAAAAA 59.640 40.909 4.18 0.00 0.00 1.94
713 1899 1.952990 TGCGCCTGATCTCAAACAAAA 59.047 42.857 4.18 0.00 0.00 2.44
717 1903 0.179215 CGTTGCGCCTGATCTCAAAC 60.179 55.000 4.18 0.00 0.00 2.93
734 1920 4.156008 AGAAAAAGTTGACAAGCACTTCGT 59.844 37.500 0.00 0.00 0.00 3.85
743 1929 5.247337 ACCCCTCAAAAGAAAAAGTTGACAA 59.753 36.000 0.00 0.00 0.00 3.18
762 1948 0.178929 ACTCGAAGTTGAGGACCCCT 60.179 55.000 0.71 0.00 40.39 4.79
763 1949 0.246910 GACTCGAAGTTGAGGACCCC 59.753 60.000 0.71 0.00 40.39 4.95
764 1950 0.246910 GGACTCGAAGTTGAGGACCC 59.753 60.000 0.71 0.00 40.39 4.46
765 1951 0.966920 TGGACTCGAAGTTGAGGACC 59.033 55.000 0.71 4.37 40.39 4.46
766 1952 2.814280 TTGGACTCGAAGTTGAGGAC 57.186 50.000 0.71 0.00 40.39 3.85
767 1953 4.065088 CAATTTGGACTCGAAGTTGAGGA 58.935 43.478 3.76 0.00 40.39 3.71
768 1954 3.189287 CCAATTTGGACTCGAAGTTGAGG 59.811 47.826 10.03 0.00 40.96 3.86
769 1955 3.365364 GCCAATTTGGACTCGAAGTTGAG 60.365 47.826 19.76 0.00 40.96 3.02
770 1956 2.552315 GCCAATTTGGACTCGAAGTTGA 59.448 45.455 19.76 0.00 40.96 3.18
771 1957 2.351738 GGCCAATTTGGACTCGAAGTTG 60.352 50.000 19.76 3.04 44.12 3.16
772 1958 1.886542 GGCCAATTTGGACTCGAAGTT 59.113 47.619 19.76 0.00 44.12 2.66
773 1959 1.534729 GGCCAATTTGGACTCGAAGT 58.465 50.000 19.76 0.00 44.12 3.01
899 2085 1.131638 TCAGGCTATTGTGGGCTAGG 58.868 55.000 0.00 0.00 37.82 3.02
901 2087 3.578716 GACTATCAGGCTATTGTGGGCTA 59.421 47.826 0.00 0.00 37.82 3.93
977 2163 4.803908 GCGGGGGCCTCAAAGGAG 62.804 72.222 4.16 0.00 37.67 3.69
1096 2283 2.517402 CGTCGAGGAGGAGGAGGG 60.517 72.222 0.00 0.00 0.00 4.30
1244 2434 3.792736 GGGCGGTGGATGGCTGTA 61.793 66.667 0.00 0.00 0.00 2.74
1271 2461 1.826487 GAGAGAGGGCGAGGGAGAC 60.826 68.421 0.00 0.00 0.00 3.36
1302 2493 1.961793 CCTAGAGAGGTGAGGACTCG 58.038 60.000 0.00 0.00 39.90 4.18
1314 2505 5.163385 TGTTCAAAGAAACCGAACCTAGAGA 60.163 40.000 0.00 0.00 38.59 3.10
1439 2631 9.500785 GGGGAGAAGATTGATTAATAAGAAGAG 57.499 37.037 0.00 0.00 0.00 2.85
1448 2640 8.806146 CAAAAGAAAGGGGAGAAGATTGATTAA 58.194 33.333 0.00 0.00 0.00 1.40
1623 2816 4.393062 ACCAACAAATAGAATGACAGAGCG 59.607 41.667 0.00 0.00 0.00 5.03
1750 2943 3.009143 AGGCTTTACTTTCGATTCCCTGT 59.991 43.478 0.00 0.00 0.00 4.00
1770 2964 5.123936 GTGGAATGGCCTAGTTAGTTTAGG 58.876 45.833 3.32 0.00 40.57 2.69
1771 2965 5.123936 GGTGGAATGGCCTAGTTAGTTTAG 58.876 45.833 3.32 0.00 37.63 1.85
1772 2966 4.536888 TGGTGGAATGGCCTAGTTAGTTTA 59.463 41.667 3.32 0.00 37.63 2.01
1773 2967 3.332485 TGGTGGAATGGCCTAGTTAGTTT 59.668 43.478 3.32 0.00 37.63 2.66
1774 2968 2.916934 TGGTGGAATGGCCTAGTTAGTT 59.083 45.455 3.32 0.00 37.63 2.24
1775 2969 2.557869 TGGTGGAATGGCCTAGTTAGT 58.442 47.619 3.32 0.00 37.63 2.24
1776 2970 3.644966 TTGGTGGAATGGCCTAGTTAG 57.355 47.619 3.32 0.00 37.63 2.34
1777 2971 4.390129 TTTTGGTGGAATGGCCTAGTTA 57.610 40.909 3.32 0.00 37.63 2.24
1786 2980 3.891366 ACCTCTCTGTTTTTGGTGGAATG 59.109 43.478 0.00 0.00 0.00 2.67
1849 3043 3.118555 GGCCCCCAATGGTAAAAATACAC 60.119 47.826 0.00 0.00 0.00 2.90
1893 3093 3.617263 CCGTTAGATGCACAGTACTTTCC 59.383 47.826 0.00 0.00 0.00 3.13
1982 3182 2.095617 GGGTGTTCAAATAACGGTTCCG 60.096 50.000 9.81 9.81 0.00 4.30
2370 3579 9.775854 CTTTACTACATCTTCCTGATCATGAAT 57.224 33.333 13.01 2.58 32.05 2.57
2562 3780 7.631717 AAGGAACCTAAACAAGATCTTATGC 57.368 36.000 7.86 0.00 0.00 3.14
2696 3934 5.126061 TTGGAGAGCCATTAGCATTTCTTTC 59.874 40.000 0.00 0.00 45.46 2.62
2747 3985 7.201723 GCAACCAAATCAGTACATCATCATGTA 60.202 37.037 0.00 0.00 41.81 2.29
2787 4025 2.722094 ACAGTTTGGTCAAAGAGCACA 58.278 42.857 0.00 0.00 39.84 4.57
2788 4026 3.378427 AGAACAGTTTGGTCAAAGAGCAC 59.622 43.478 0.00 0.00 39.84 4.40
2938 4176 7.227314 TGAGATACATAGATGAAACCATGTTGC 59.773 37.037 0.00 0.00 33.78 4.17
2957 4195 5.749109 CGTCCAAGTCCAGTTAATGAGATAC 59.251 44.000 0.00 0.00 0.00 2.24
2976 4214 6.126710 ACCCAACATACTTAATAATCCGTCCA 60.127 38.462 0.00 0.00 0.00 4.02
2999 4237 6.213677 GGGATTTCCGCAAATCTTAATTACC 58.786 40.000 11.45 0.00 45.18 2.85
3046 4289 8.592105 TTGGAACTTGATAAATGAAAAAGCAG 57.408 30.769 0.00 0.00 0.00 4.24
3093 4343 6.099269 AGCCCAAAAGGACGATATAACTTCTA 59.901 38.462 0.00 0.00 38.24 2.10
3123 4373 9.236006 ACAGCAAATAATGAGTCAACTTCTAAT 57.764 29.630 0.00 0.00 0.00 1.73
3124 4374 8.621532 ACAGCAAATAATGAGTCAACTTCTAA 57.378 30.769 0.00 0.00 0.00 2.10
3125 4375 9.719355 TTACAGCAAATAATGAGTCAACTTCTA 57.281 29.630 0.00 0.00 0.00 2.10
3126 4376 8.507249 GTTACAGCAAATAATGAGTCAACTTCT 58.493 33.333 0.00 0.00 0.00 2.85
3127 4377 8.289618 TGTTACAGCAAATAATGAGTCAACTTC 58.710 33.333 0.00 0.00 0.00 3.01
3128 4378 8.165239 TGTTACAGCAAATAATGAGTCAACTT 57.835 30.769 0.00 0.00 0.00 2.66
3129 4379 7.744087 TGTTACAGCAAATAATGAGTCAACT 57.256 32.000 0.00 0.00 0.00 3.16
3130 4380 7.059488 CGTTGTTACAGCAAATAATGAGTCAAC 59.941 37.037 0.00 0.00 0.00 3.18
3131 4381 7.041712 TCGTTGTTACAGCAAATAATGAGTCAA 60.042 33.333 0.00 0.00 0.00 3.18
3132 4382 6.425417 TCGTTGTTACAGCAAATAATGAGTCA 59.575 34.615 0.00 0.00 0.00 3.41
3133 4383 6.827641 TCGTTGTTACAGCAAATAATGAGTC 58.172 36.000 0.00 0.00 0.00 3.36
3134 4384 6.795098 TCGTTGTTACAGCAAATAATGAGT 57.205 33.333 0.00 0.00 0.00 3.41
3135 4385 7.463544 TGATCGTTGTTACAGCAAATAATGAG 58.536 34.615 0.00 0.00 31.63 2.90
3136 4386 7.371126 TGATCGTTGTTACAGCAAATAATGA 57.629 32.000 0.00 0.00 32.34 2.57
3137 4387 8.619146 AATGATCGTTGTTACAGCAAATAATG 57.381 30.769 0.00 0.00 0.00 1.90
3141 4391 9.075519 CAAATAATGATCGTTGTTACAGCAAAT 57.924 29.630 10.54 0.00 0.00 2.32
3142 4392 7.540400 CCAAATAATGATCGTTGTTACAGCAAA 59.460 33.333 10.54 0.00 0.00 3.68
3143 4393 7.026562 CCAAATAATGATCGTTGTTACAGCAA 58.973 34.615 10.54 0.00 0.00 3.91
3184 4460 2.035576 ACTCCGAACAGGGCGATATAAC 59.964 50.000 0.00 0.00 41.52 1.89
3312 4588 6.560253 AACCAAGTGTGATAACATCTGTTC 57.440 37.500 0.00 0.00 39.31 3.18
3340 4616 7.067494 CAGTTCTTATTCCATCTTACCCCAAAG 59.933 40.741 0.00 0.00 0.00 2.77
3400 4676 8.846211 ACAGTAATAAAGCTGTACACAACAATT 58.154 29.630 0.00 0.00 43.30 2.32
3437 4713 3.368427 GGTGATCTCGTCAGGTGAAATGA 60.368 47.826 0.00 0.00 37.56 2.57
3451 4727 3.751175 TGAATTGTTTGACGGGTGATCTC 59.249 43.478 0.00 0.00 0.00 2.75
3501 4783 1.879380 TCGGGAAAGTGACTGCAAATG 59.121 47.619 0.00 0.00 0.00 2.32
3591 4873 5.733676 ACCATGACAAATAAAATTGGAGGC 58.266 37.500 0.00 0.00 34.56 4.70
3679 4962 1.806542 AGTAGAGCAATGCAAACACGG 59.193 47.619 8.35 0.00 0.00 4.94
3695 4978 9.490663 CTTTCATGTTATTAAGCGGAAAAGTAG 57.509 33.333 0.00 0.00 0.00 2.57
3731 5014 5.046591 ACAAACTCTACATGTTAGCCTAGCA 60.047 40.000 2.30 0.00 0.00 3.49
3785 5068 5.942872 ACTCGTTTAAATGGCTCATGAAAG 58.057 37.500 7.56 0.00 0.00 2.62
3893 5176 2.597510 GTGCCTGGCTTTTCCGGT 60.598 61.111 21.03 0.00 39.73 5.28
4015 5298 0.391793 GCTGCTAGGACCTTCACCAC 60.392 60.000 0.00 0.00 0.00 4.16
4064 5347 6.718522 ACTCCTTCCTACTGCTAATCTAAC 57.281 41.667 0.00 0.00 0.00 2.34
4201 5484 3.333680 TGTTGAGAAAAGGGAAGGCCTAT 59.666 43.478 5.16 0.00 0.00 2.57
4244 5527 1.101331 GGAAAGAGAAGGCCTGCATG 58.899 55.000 15.05 0.00 0.00 4.06
4296 5595 7.553334 AGGCAGAAACGTATACTGATAGAAAA 58.447 34.615 16.77 0.00 34.07 2.29
4297 5596 7.108841 AGGCAGAAACGTATACTGATAGAAA 57.891 36.000 16.77 0.00 34.07 2.52
4298 5597 6.710597 AGGCAGAAACGTATACTGATAGAA 57.289 37.500 16.77 0.00 34.07 2.10
4299 5598 6.461092 CCAAGGCAGAAACGTATACTGATAGA 60.461 42.308 16.77 0.00 34.07 1.98
4300 5599 5.692204 CCAAGGCAGAAACGTATACTGATAG 59.308 44.000 16.77 6.37 34.07 2.08
4301 5600 5.361571 TCCAAGGCAGAAACGTATACTGATA 59.638 40.000 16.77 0.00 34.07 2.15
4302 5601 4.161565 TCCAAGGCAGAAACGTATACTGAT 59.838 41.667 16.77 5.34 34.07 2.90
4303 5602 3.512329 TCCAAGGCAGAAACGTATACTGA 59.488 43.478 16.77 0.00 34.07 3.41
4304 5603 3.857052 TCCAAGGCAGAAACGTATACTG 58.143 45.455 0.56 10.72 35.14 2.74
4305 5604 3.767673 TCTCCAAGGCAGAAACGTATACT 59.232 43.478 0.56 0.00 0.00 2.12
4306 5605 4.119442 TCTCCAAGGCAGAAACGTATAC 57.881 45.455 0.00 0.00 0.00 1.47
4307 5606 4.222145 AGTTCTCCAAGGCAGAAACGTATA 59.778 41.667 0.00 0.00 31.60 1.47
4308 5607 3.008049 AGTTCTCCAAGGCAGAAACGTAT 59.992 43.478 0.00 0.00 31.60 3.06
4309 5608 2.367567 AGTTCTCCAAGGCAGAAACGTA 59.632 45.455 0.00 0.00 31.60 3.57
4310 5609 1.141053 AGTTCTCCAAGGCAGAAACGT 59.859 47.619 0.00 0.00 31.60 3.99
4311 5610 1.801178 GAGTTCTCCAAGGCAGAAACG 59.199 52.381 0.00 0.00 31.60 3.60
4312 5611 3.070748 GAGAGTTCTCCAAGGCAGAAAC 58.929 50.000 0.00 0.00 37.02 2.78
4313 5612 2.705658 TGAGAGTTCTCCAAGGCAGAAA 59.294 45.455 6.68 0.00 42.20 2.52
4347 5646 4.939439 ACAGATTACATTTTCCGGTGTACC 59.061 41.667 0.00 0.00 31.05 3.34
4426 5725 0.997196 ACGAAAGTTAATCGAGCCGC 59.003 50.000 4.04 0.00 46.40 6.53
4452 5751 3.011949 ACGCAAACGCATCTTCAAAAT 57.988 38.095 0.00 0.00 45.53 1.82
4472 5771 4.181578 GAGCTAATGAAGAGGCAAACGTA 58.818 43.478 0.00 0.00 0.00 3.57
4523 5822 3.780804 TTTGGGCAGCAAGAAGTAGTA 57.219 42.857 0.00 0.00 0.00 1.82
4524 5823 2.656947 TTTGGGCAGCAAGAAGTAGT 57.343 45.000 0.00 0.00 0.00 2.73
4525 5824 4.525912 ATTTTTGGGCAGCAAGAAGTAG 57.474 40.909 0.00 0.00 0.00 2.57
4754 6370 1.228675 CATTCCCCTGCTATGGCCC 60.229 63.158 0.00 0.00 37.74 5.80
4778 6394 2.158430 TGGTGGGTCATAGATAGCGGTA 60.158 50.000 0.00 0.00 0.00 4.02
4784 6400 7.128109 TCAATAGGTTTTGGTGGGTCATAGATA 59.872 37.037 0.00 0.00 0.00 1.98
4892 6508 1.989165 CGCCGTCAGAAGAAGAAGAAG 59.011 52.381 0.00 0.00 0.00 2.85
4893 6509 1.935300 GCGCCGTCAGAAGAAGAAGAA 60.935 52.381 0.00 0.00 0.00 2.52
4894 6510 0.388649 GCGCCGTCAGAAGAAGAAGA 60.389 55.000 0.00 0.00 0.00 2.87
4895 6511 0.389166 AGCGCCGTCAGAAGAAGAAG 60.389 55.000 2.29 0.00 0.00 2.85
4982 6600 3.867493 CACTTAGCTTTCGCATCATCTGA 59.133 43.478 0.00 0.00 39.10 3.27
4983 6601 3.545624 GCACTTAGCTTTCGCATCATCTG 60.546 47.826 0.00 0.00 41.15 2.90


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

AutoCloner maintained by Alex Coulton.