Multiple sequence alignment - TraesCS4D01G260200

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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 TraesCS4D01G260200 chr4D 100.000 5495 0 0 1 5495 429469146 429474640 0.000000e+00 10148.0
1 TraesCS4D01G260200 chr4A 92.170 4304 189 57 1 4243 37063297 37059081 0.000000e+00 5945.0
2 TraesCS4D01G260200 chr4A 87.247 792 51 27 4261 5008 37058669 37057884 0.000000e+00 857.0
3 TraesCS4D01G260200 chr4A 86.637 449 28 12 5055 5476 37055110 37054667 8.330000e-128 468.0
4 TraesCS4D01G260200 chr4A 96.429 84 3 0 2665 2748 37058977 37058894 7.420000e-29 139.0
5 TraesCS4D01G260200 chr4B 93.261 1380 51 12 851 2196 527281149 527282520 0.000000e+00 1995.0
6 TraesCS4D01G260200 chr4B 91.265 1202 54 23 4325 5495 527286983 527288164 0.000000e+00 1591.0
7 TraesCS4D01G260200 chr4B 96.187 918 30 3 2193 3109 527282632 527283545 0.000000e+00 1496.0
8 TraesCS4D01G260200 chr4B 97.233 795 18 4 3105 3896 527285762 527286555 0.000000e+00 1343.0
9 TraesCS4D01G260200 chr4B 92.697 671 31 7 1 663 527280181 527280841 0.000000e+00 952.0
10 TraesCS4D01G260200 chr4B 93.711 318 11 4 3947 4264 527286564 527286872 8.330000e-128 468.0
11 TraesCS4D01G260200 chr4B 100.000 58 0 0 808 865 527281079 527281136 2.090000e-19 108.0
12 TraesCS4D01G260200 chr3B 82.726 631 55 28 4098 4681 358640426 358639803 3.800000e-141 512.0
13 TraesCS4D01G260200 chr3B 81.962 632 59 28 4098 4681 259702882 259702258 8.280000e-133 484.0
14 TraesCS4D01G260200 chr3B 92.157 102 8 0 3107 3208 114098819 114098920 1.600000e-30 145.0
15 TraesCS4D01G260200 chr7B 93.519 108 6 1 3110 3217 162120910 162120804 5.700000e-35 159.0
16 TraesCS4D01G260200 chr3A 94.000 100 6 0 3110 3209 470095680 470095779 9.530000e-33 152.0
17 TraesCS4D01G260200 chr5B 93.814 97 6 0 3112 3208 166379086 166379182 4.440000e-31 147.0
18 TraesCS4D01G260200 chr5B 100.000 28 0 0 3916 3943 352309015 352309042 1.000000e-02 52.8
19 TraesCS4D01G260200 chr2D 92.157 102 8 0 3107 3208 74149727 74149828 1.600000e-30 145.0
20 TraesCS4D01G260200 chr2D 100.000 28 0 0 3916 3943 535728626 535728653 1.000000e-02 52.8
21 TraesCS4D01G260200 chr6A 89.286 112 11 1 3109 3219 503723194 503723305 7.420000e-29 139.0
22 TraesCS4D01G260200 chr1B 89.815 108 11 0 3105 3212 587275914 587275807 7.420000e-29 139.0
23 TraesCS4D01G260200 chr6D 100.000 31 0 0 3916 3946 126435262 126435292 2.140000e-04 58.4
24 TraesCS4D01G260200 chr5A 100.000 31 0 0 3916 3946 391518581 391518551 2.140000e-04 58.4
25 TraesCS4D01G260200 chr3D 100.000 31 0 0 3916 3946 479627429 479627399 2.140000e-04 58.4
26 TraesCS4D01G260200 chr6B 100.000 30 0 0 3916 3945 476122124 476122153 7.690000e-04 56.5
27 TraesCS4D01G260200 chr5D 100.000 28 0 0 3916 3943 541589793 541589820 1.000000e-02 52.8


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 TraesCS4D01G260200 chr4D 429469146 429474640 5494 False 10148.000000 10148 100.000000 1 5495 1 chr4D.!!$F1 5494
1 TraesCS4D01G260200 chr4A 37054667 37063297 8630 True 1852.250000 5945 90.620750 1 5476 4 chr4A.!!$R1 5475
2 TraesCS4D01G260200 chr4B 527280181 527288164 7983 False 1136.142857 1995 94.907714 1 5495 7 chr4B.!!$F1 5494
3 TraesCS4D01G260200 chr3B 358639803 358640426 623 True 512.000000 512 82.726000 4098 4681 1 chr3B.!!$R2 583
4 TraesCS4D01G260200 chr3B 259702258 259702882 624 True 484.000000 484 81.962000 4098 4681 1 chr3B.!!$R1 583

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
389 395 0.032813 ATCTCTGCATGGTTTGGGGG 60.033 55.000 0.00 0.00 0.00 5.40 F
915 1059 1.000607 GGAAAAGGAAAGTTGTCGCCC 60.001 52.381 0.00 0.00 0.00 6.13 F
2429 2723 0.466007 TGCCTGCAGAGTTTTGAGCA 60.466 50.000 17.39 10.74 35.43 4.26 F
4150 6671 0.721718 GGCAATCGTCTTTGGAGTCG 59.278 55.000 0.00 0.00 36.07 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1698 0.526211 CCTCACACACGATCTTCCGA 59.474 55.0 0.00 0.0 0.00 4.55 R
2879 3174 1.795768 TCAAGAACCATCGCACTCAC 58.204 50.0 0.00 0.0 0.00 3.51 R
4154 6676 0.591170 GCAAGTACCACATGCAACGT 59.409 50.0 0.00 0.0 41.89 3.99 R
5086 10851 0.327259 AGCAGCCAAGAGATGCAGAA 59.673 50.0 5.66 0.0 42.45 3.02 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
22 23 3.055530 AGGCAATGACTGATCGAGAAGTT 60.056 43.478 4.44 0.00 0.00 2.66
335 341 5.690997 AAAAGCCTACAACTTACAGAAGC 57.309 39.130 0.00 0.00 35.97 3.86
385 391 6.090358 GTGAATTTGAATCTCTGCATGGTTTG 59.910 38.462 0.00 0.00 0.00 2.93
387 393 2.449464 TGAATCTCTGCATGGTTTGGG 58.551 47.619 0.00 0.00 0.00 4.12
389 395 0.032813 ATCTCTGCATGGTTTGGGGG 60.033 55.000 0.00 0.00 0.00 5.40
426 432 8.799367 TGAATCTGATGAAATGTTGAATTCTGT 58.201 29.630 7.05 0.00 0.00 3.41
431 437 3.640498 TGAAATGTTGAATTCTGTGGGCA 59.360 39.130 7.05 0.00 0.00 5.36
442 448 1.811965 TCTGTGGGCAATTGAACGATG 59.188 47.619 10.34 0.00 0.00 3.84
691 732 6.864165 TCGCCAGAAAACATGTTTTTAATACC 59.136 34.615 31.42 19.84 42.26 2.73
731 772 8.538701 ACATTTTCCCATCATTTAAATGTGCTA 58.461 29.630 23.95 8.61 43.73 3.49
915 1059 1.000607 GGAAAAGGAAAGTTGTCGCCC 60.001 52.381 0.00 0.00 0.00 6.13
974 1118 1.099689 GAGTCCTCTCCTCGGTTCAG 58.900 60.000 0.00 0.00 34.87 3.02
1229 1383 6.625960 GCATTCTAACCAGATTTGTTTCCTCC 60.626 42.308 0.00 0.00 0.00 4.30
1248 1402 2.959484 CGCAGGAGCAGGGAAGGAA 61.959 63.158 0.00 0.00 42.27 3.36
1343 1497 2.586792 GCGGCAGGAGAAGGTCAT 59.413 61.111 0.00 0.00 0.00 3.06
1365 1534 2.670148 CCTCCTTAGGCTGGCCGTT 61.670 63.158 5.93 0.00 41.95 4.44
1557 1726 1.635663 CGTGTGTGAGGGCGATTTCC 61.636 60.000 0.00 0.00 0.00 3.13
1571 1740 2.609491 CGATTTCCACACGGAGAAGTCA 60.609 50.000 0.00 0.00 44.10 3.41
1613 1782 1.591703 GAGCATCTCCGGTGTGACA 59.408 57.895 0.00 0.00 0.00 3.58
1754 1924 3.259123 ACATTGTCCATTTCCTTTGAGCC 59.741 43.478 0.00 0.00 0.00 4.70
1765 1935 2.036217 TCCTTTGAGCCGACGTCTTAAA 59.964 45.455 14.70 3.72 0.00 1.52
1767 1937 3.435671 CCTTTGAGCCGACGTCTTAAATT 59.564 43.478 14.70 0.00 0.00 1.82
1771 1941 4.418392 TGAGCCGACGTCTTAAATTAGTC 58.582 43.478 14.70 0.00 0.00 2.59
1813 1983 3.934457 AAGCCATTTCCAGTTTTACCG 57.066 42.857 0.00 0.00 0.00 4.02
1858 2028 8.777578 ATTACCATTACGCCTATCATATCCTA 57.222 34.615 0.00 0.00 0.00 2.94
1859 2029 8.598202 TTACCATTACGCCTATCATATCCTAA 57.402 34.615 0.00 0.00 0.00 2.69
1861 2031 5.977725 CCATTACGCCTATCATATCCTAACG 59.022 44.000 0.00 0.00 0.00 3.18
1889 2059 5.385198 ACAAGGTATCAAACACATCAAGGT 58.615 37.500 0.00 0.00 0.00 3.50
1892 2062 7.336931 ACAAGGTATCAAACACATCAAGGTATC 59.663 37.037 0.00 0.00 0.00 2.24
2019 2189 4.248859 TCAGCAGAGAAAGCATGAACTAC 58.751 43.478 0.00 0.00 0.00 2.73
2065 2235 7.559533 TGTACATATTGGGTTCTGCATATTTGT 59.440 33.333 0.00 0.00 0.00 2.83
2429 2723 0.466007 TGCCTGCAGAGTTTTGAGCA 60.466 50.000 17.39 10.74 35.43 4.26
2431 2725 1.601412 GCCTGCAGAGTTTTGAGCAAC 60.601 52.381 17.39 0.00 36.44 4.17
2494 2789 2.095692 TCCGCAAATCATGATCACAACG 59.904 45.455 9.06 8.80 0.00 4.10
2500 2795 6.634035 CGCAAATCATGATCACAACGAATAAT 59.366 34.615 9.06 0.00 0.00 1.28
2800 3095 1.656652 CAGAGGTGATTTACAGCCCG 58.343 55.000 0.00 0.00 46.73 6.13
2853 3148 4.591924 TCATCTGATCAGGCTATCATGTGT 59.408 41.667 22.42 0.00 35.40 3.72
2920 3215 5.871524 TGAACTCTCTAAATGATGACACTGC 59.128 40.000 0.00 0.00 0.00 4.40
3059 3354 4.072131 TGGGTCTTATGTCAGTTTTGAGC 58.928 43.478 0.00 0.00 32.98 4.26
3122 5638 4.682778 TGGTATTCATTACTCCTTCCGG 57.317 45.455 0.00 0.00 0.00 5.14
3639 6156 3.743521 TCATCAACCTTGTCTCCAGTTG 58.256 45.455 0.00 0.00 40.72 3.16
3725 6244 8.637986 ACCATTTTGTGTCAGTTATATGTTTGT 58.362 29.630 0.00 0.00 0.00 2.83
3961 6481 4.090761 ACCATGGTCTAAGCACATATGG 57.909 45.455 13.00 0.00 38.00 2.74
4025 6545 1.819753 TGCTTATCCATAGCAGGGGT 58.180 50.000 0.00 0.00 43.30 4.95
4150 6671 0.721718 GGCAATCGTCTTTGGAGTCG 59.278 55.000 0.00 0.00 36.07 4.18
4151 6672 1.671850 GGCAATCGTCTTTGGAGTCGA 60.672 52.381 0.00 0.00 44.93 4.20
4154 6676 3.057019 CAATCGTCTTTGGAGTCGACAA 58.943 45.455 19.50 0.00 43.98 3.18
4208 6730 0.593128 CTGGTGTGCCAACTTACAGC 59.407 55.000 0.00 0.00 45.51 4.40
4264 7185 4.211920 GACTGAAGCACTAGGATCTAGGT 58.788 47.826 6.86 0.00 0.00 3.08
4298 7219 7.035612 CCAAATGGAATTACTGTAGGAAAAGC 58.964 38.462 0.00 0.00 33.67 3.51
4314 7235 5.774690 AGGAAAAGCATGTGTTGGAGAAATA 59.225 36.000 0.00 0.00 0.00 1.40
4323 7244 8.677300 GCATGTGTTGGAGAAATAAGAGAATAA 58.323 33.333 0.00 0.00 0.00 1.40
4339 7338 6.940739 AGAGAATAACATTAGTGCACAGACT 58.059 36.000 21.04 0.00 0.00 3.24
4347 7346 5.707298 ACATTAGTGCACAGACTATTTTGCT 59.293 36.000 21.04 0.00 35.91 3.91
4351 7350 4.394300 AGTGCACAGACTATTTTGCTCATC 59.606 41.667 21.04 0.00 35.91 2.92
4352 7351 3.371898 TGCACAGACTATTTTGCTCATCG 59.628 43.478 0.00 0.00 35.91 3.84
4361 7360 3.872511 TTTTGCTCATCGCCATTCATT 57.127 38.095 0.00 0.00 38.05 2.57
4362 7361 4.979943 TTTTGCTCATCGCCATTCATTA 57.020 36.364 0.00 0.00 38.05 1.90
4422 7421 9.515226 TGACCACTTTTATCTTTTGCTATTACT 57.485 29.630 0.00 0.00 0.00 2.24
4513 7512 1.371183 CAGGAGTGCAGGACCGAAA 59.629 57.895 0.00 0.00 0.00 3.46
4514 7513 0.036010 CAGGAGTGCAGGACCGAAAT 60.036 55.000 0.00 0.00 0.00 2.17
4535 7534 4.608170 TCCAATAAAGCCTTTCCTCCAT 57.392 40.909 0.00 0.00 0.00 3.41
4561 7563 7.820386 TCGTGTACCTATTTTATGAAGCTCAAA 59.180 33.333 0.00 0.00 0.00 2.69
4608 7610 4.082274 CAAGCGTTGCATCTGTATTTCA 57.918 40.909 0.00 0.00 0.00 2.69
4610 7612 5.809464 CAAGCGTTGCATCTGTATTTCATA 58.191 37.500 0.00 0.00 0.00 2.15
4611 7613 6.432936 CAAGCGTTGCATCTGTATTTCATAT 58.567 36.000 0.00 0.00 0.00 1.78
4614 7616 5.611919 CGTTGCATCTGTATTTCATATCGG 58.388 41.667 0.00 0.00 0.00 4.18
4615 7617 5.389830 CGTTGCATCTGTATTTCATATCGGG 60.390 44.000 0.00 0.00 0.00 5.14
4632 7647 1.389784 CGGGCATTGTTTTCGCATTTC 59.610 47.619 0.00 0.00 0.00 2.17
4644 7663 2.503331 TCGCATTTCATATCGGGCATT 58.497 42.857 0.00 0.00 0.00 3.56
4645 7664 2.483877 TCGCATTTCATATCGGGCATTC 59.516 45.455 0.00 0.00 0.00 2.67
4646 7665 2.725759 CGCATTTCATATCGGGCATTCG 60.726 50.000 0.00 0.00 0.00 3.34
4647 7666 2.855180 CATTTCATATCGGGCATTCGC 58.145 47.619 0.00 0.00 37.44 4.70
4648 7667 2.254546 TTTCATATCGGGCATTCGCT 57.745 45.000 0.00 0.00 38.60 4.93
4649 7668 1.795768 TTCATATCGGGCATTCGCTC 58.204 50.000 0.00 0.00 38.60 5.03
4650 7669 0.678950 TCATATCGGGCATTCGCTCA 59.321 50.000 0.00 0.00 39.27 4.26
4651 7670 1.073964 CATATCGGGCATTCGCTCAG 58.926 55.000 0.00 0.00 39.27 3.35
4703 7725 4.993028 AGTTTTGTTAGCCTACCATCCAA 58.007 39.130 0.00 0.00 0.00 3.53
4707 7729 2.771943 TGTTAGCCTACCATCCAAGGAG 59.228 50.000 0.00 0.00 34.58 3.69
4711 7733 1.428869 CCTACCATCCAAGGAGAGGG 58.571 60.000 13.10 8.46 43.44 4.30
4721 7743 3.272285 TCCAAGGAGAGGGAGAAGACATA 59.728 47.826 0.00 0.00 0.00 2.29
4739 7761 7.906199 AGACATAGCTAACTATTCCAGTTCT 57.094 36.000 0.00 0.00 44.48 3.01
4746 7768 5.459434 GCTAACTATTCCAGTTCTTCGTAGC 59.541 44.000 0.00 0.00 44.48 3.58
4747 7769 5.401531 AACTATTCCAGTTCTTCGTAGCA 57.598 39.130 0.00 0.00 44.48 3.49
4748 7770 5.599999 ACTATTCCAGTTCTTCGTAGCAT 57.400 39.130 0.00 0.00 31.59 3.79
4795 7817 2.481952 GACTGTTGCCAGAGACATTGAC 59.518 50.000 0.00 0.00 41.50 3.18
4853 7877 1.216678 TCATTTTCCACCACCACCACT 59.783 47.619 0.00 0.00 0.00 4.00
5008 8041 1.303309 AACACAGCACAGCTCTTGAC 58.697 50.000 4.60 0.00 36.40 3.18
5009 8042 0.467384 ACACAGCACAGCTCTTGACT 59.533 50.000 4.60 0.00 36.40 3.41
5010 8043 1.134280 ACACAGCACAGCTCTTGACTT 60.134 47.619 4.60 0.00 36.40 3.01
5011 8044 1.263484 CACAGCACAGCTCTTGACTTG 59.737 52.381 0.00 0.00 36.40 3.16
5012 8045 1.139654 ACAGCACAGCTCTTGACTTGA 59.860 47.619 0.00 0.00 36.40 3.02
5013 8046 1.799403 CAGCACAGCTCTTGACTTGAG 59.201 52.381 0.00 0.00 36.40 3.02
5016 8049 2.222911 GCACAGCTCTTGACTTGAGAAC 59.777 50.000 0.00 0.00 33.68 3.01
5017 8050 2.805099 CACAGCTCTTGACTTGAGAACC 59.195 50.000 0.00 0.00 33.68 3.62
5018 8051 2.703007 ACAGCTCTTGACTTGAGAACCT 59.297 45.455 0.00 0.00 33.68 3.50
5034 10799 3.051727 AGAACCTATGGCCCTCTACTCTT 60.052 47.826 0.00 0.00 0.00 2.85
5037 10802 3.051727 ACCTATGGCCCTCTACTCTTCTT 60.052 47.826 0.00 0.00 0.00 2.52
5038 10803 3.576550 CCTATGGCCCTCTACTCTTCTTC 59.423 52.174 0.00 0.00 0.00 2.87
5039 10804 1.475403 TGGCCCTCTACTCTTCTTCG 58.525 55.000 0.00 0.00 0.00 3.79
5040 10805 0.103390 GGCCCTCTACTCTTCTTCGC 59.897 60.000 0.00 0.00 0.00 4.70
5041 10806 0.103390 GCCCTCTACTCTTCTTCGCC 59.897 60.000 0.00 0.00 0.00 5.54
5042 10807 1.770294 CCCTCTACTCTTCTTCGCCT 58.230 55.000 0.00 0.00 0.00 5.52
5044 10809 1.679153 CCTCTACTCTTCTTCGCCTCC 59.321 57.143 0.00 0.00 0.00 4.30
5045 10810 2.370349 CTCTACTCTTCTTCGCCTCCA 58.630 52.381 0.00 0.00 0.00 3.86
5046 10811 2.955660 CTCTACTCTTCTTCGCCTCCAT 59.044 50.000 0.00 0.00 0.00 3.41
5047 10812 2.952978 TCTACTCTTCTTCGCCTCCATC 59.047 50.000 0.00 0.00 0.00 3.51
5048 10813 1.859302 ACTCTTCTTCGCCTCCATCT 58.141 50.000 0.00 0.00 0.00 2.90
5049 10814 2.183679 ACTCTTCTTCGCCTCCATCTT 58.816 47.619 0.00 0.00 0.00 2.40
5050 10815 2.569404 ACTCTTCTTCGCCTCCATCTTT 59.431 45.455 0.00 0.00 0.00 2.52
5051 10816 3.194062 CTCTTCTTCGCCTCCATCTTTC 58.806 50.000 0.00 0.00 0.00 2.62
5052 10817 2.834549 TCTTCTTCGCCTCCATCTTTCT 59.165 45.455 0.00 0.00 0.00 2.52
5053 10818 3.261897 TCTTCTTCGCCTCCATCTTTCTT 59.738 43.478 0.00 0.00 0.00 2.52
5086 10851 2.923121 TGCTGTTTTCTCTGCTTGTCT 58.077 42.857 0.00 0.00 34.27 3.41
5331 11122 4.440880 CTTGAGGAGGAGTTGATGTGATC 58.559 47.826 0.00 0.00 0.00 2.92
5332 11123 3.444029 TGAGGAGGAGTTGATGTGATCA 58.556 45.455 0.00 0.00 37.55 2.92
5333 11124 4.035814 TGAGGAGGAGTTGATGTGATCAT 58.964 43.478 0.00 0.00 39.39 2.45
5406 11202 0.811281 GCTGCTTAAATGGCCGTCTT 59.189 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 6.194235 TCTCACATAATTTACAGCCCCAATT 58.806 36.000 0.00 0.00 0.00 2.32
387 393 3.881220 TCAGATTCACCGATAAAACCCC 58.119 45.455 0.00 0.00 0.00 4.95
389 395 6.677781 TTCATCAGATTCACCGATAAAACC 57.322 37.500 0.00 0.00 0.00 3.27
390 396 8.184192 ACATTTCATCAGATTCACCGATAAAAC 58.816 33.333 0.00 0.00 0.00 2.43
391 397 8.279970 ACATTTCATCAGATTCACCGATAAAA 57.720 30.769 0.00 0.00 0.00 1.52
401 407 9.073368 CACAGAATTCAACATTTCATCAGATTC 57.927 33.333 8.44 0.00 0.00 2.52
426 432 2.016318 CTAGCATCGTTCAATTGCCCA 58.984 47.619 0.00 0.00 37.07 5.36
431 437 2.991250 AGTGCCTAGCATCGTTCAATT 58.009 42.857 0.00 0.00 41.91 2.32
461 467 2.009681 AAGGAACCCAACCCATGTTC 57.990 50.000 0.00 0.00 38.08 3.18
667 707 6.866248 AGGTATTAAAAACATGTTTTCTGGCG 59.134 34.615 31.10 0.00 41.45 5.69
672 712 9.522804 TGTGTCAGGTATTAAAAACATGTTTTC 57.477 29.630 31.10 19.99 41.45 2.29
691 732 4.232221 GGAAAATGTCAGCATTGTGTCAG 58.768 43.478 0.00 0.00 43.89 3.51
769 819 9.555727 TTAACTAAAAATCGAATCCCCATAGAG 57.444 33.333 0.00 0.00 0.00 2.43
770 820 9.333724 GTTAACTAAAAATCGAATCCCCATAGA 57.666 33.333 0.00 0.00 0.00 1.98
791 841 8.250332 TGCCCAGATTTAGATTTGAATGTTAAC 58.750 33.333 0.00 0.00 0.00 2.01
887 1031 6.756542 CGACAACTTTCCTTTTCCTTTTCATT 59.243 34.615 0.00 0.00 0.00 2.57
888 1032 6.273071 CGACAACTTTCCTTTTCCTTTTCAT 58.727 36.000 0.00 0.00 0.00 2.57
889 1033 5.646606 CGACAACTTTCCTTTTCCTTTTCA 58.353 37.500 0.00 0.00 0.00 2.69
974 1118 3.508840 CTGCGAACGATTGGGGGC 61.509 66.667 0.00 0.00 0.00 5.80
1074 1219 3.319198 GCGTGGGAAGTGGAGGGA 61.319 66.667 0.00 0.00 0.00 4.20
1229 1383 4.479993 CCTTCCCTGCTCCTGCGG 62.480 72.222 0.00 0.00 44.81 5.69
1343 1497 1.384082 GCCAGCCTAAGGAGGGGTA 60.384 63.158 0.00 0.00 43.97 3.69
1365 1534 4.377661 GCGTTAAGCGTGCGCCAA 62.378 61.111 13.21 5.12 44.67 4.52
1386 1555 2.369860 ACAGCACAGAGTGAGGATTTCA 59.630 45.455 0.58 0.00 35.23 2.69
1529 1698 0.526211 CCTCACACACGATCTTCCGA 59.474 55.000 0.00 0.00 0.00 4.55
1557 1726 2.802787 AAGACTGACTTCTCCGTGTG 57.197 50.000 0.00 0.00 32.91 3.82
1571 1740 2.756283 CGAGGCCCGAGGAAGACT 60.756 66.667 0.00 0.00 41.76 3.24
1613 1782 7.721399 GGAGTGATCACATAATACCCATTTTCT 59.279 37.037 27.02 0.21 0.00 2.52
1708 1877 6.201234 GTGAACTGTGAAGAAACTAGAGTTCC 59.799 42.308 0.00 0.00 37.91 3.62
1709 1879 6.757010 TGTGAACTGTGAAGAAACTAGAGTTC 59.243 38.462 0.00 0.00 38.75 3.01
1754 1924 6.549952 AGTGTAGGACTAATTTAAGACGTCG 58.450 40.000 10.46 0.00 30.86 5.12
1765 1935 6.042781 TGTTCAAGTGGAAGTGTAGGACTAAT 59.957 38.462 0.00 0.00 35.82 1.73
1767 1937 4.897076 TGTTCAAGTGGAAGTGTAGGACTA 59.103 41.667 0.00 0.00 35.82 2.59
1771 1941 5.828299 TTTTGTTCAAGTGGAAGTGTAGG 57.172 39.130 0.00 0.00 35.82 3.18
1813 1983 8.475639 TGGTAATCAGATTCTAAACCTGACTAC 58.524 37.037 12.27 0.00 38.30 2.73
1858 2028 5.239744 TGTGTTTGATACCTTGTATTGCGTT 59.760 36.000 0.00 0.00 0.00 4.84
1859 2029 4.757657 TGTGTTTGATACCTTGTATTGCGT 59.242 37.500 0.00 0.00 0.00 5.24
1861 2031 6.851609 TGATGTGTTTGATACCTTGTATTGC 58.148 36.000 0.00 0.00 0.00 3.56
1889 2059 7.506114 ACTAGAGTTCAGGTTGTGTTTTGATA 58.494 34.615 0.00 0.00 0.00 2.15
1892 2062 6.128007 ACAACTAGAGTTCAGGTTGTGTTTTG 60.128 38.462 16.25 0.00 46.61 2.44
2019 2189 8.360325 TGTACATAGCGGTTAATTTCACTATG 57.640 34.615 0.00 0.00 41.61 2.23
2065 2235 5.238650 GCTTCACTTCTAGGCAACAAAACTA 59.761 40.000 0.00 0.00 41.41 2.24
2429 2723 3.445096 GGTAATGAGATTGCAGCTTGGTT 59.555 43.478 0.00 0.00 0.00 3.67
2431 2725 3.285484 AGGTAATGAGATTGCAGCTTGG 58.715 45.455 0.00 0.00 0.00 3.61
2800 3095 7.861630 ACTATTGATATGCATACGTTTGGTTC 58.138 34.615 8.99 0.57 0.00 3.62
2879 3174 1.795768 TCAAGAACCATCGCACTCAC 58.204 50.000 0.00 0.00 0.00 3.51
2920 3215 4.210331 AGTTATCCTTTAATGGGCTGCAG 58.790 43.478 10.11 10.11 0.00 4.41
2980 3275 6.071447 AGCAACCATCAATAACTGCATTTGTA 60.071 34.615 0.00 0.00 32.21 2.41
3059 3354 1.064621 GCGTGGCAGCATGTATTGG 59.935 57.895 0.00 0.00 39.31 3.16
3122 5638 5.796350 AAACTGCGACACTTATTATGGAC 57.204 39.130 0.00 0.00 0.00 4.02
3172 5688 7.647715 CGATCCAAAATAAGTGTCACAGTTTTT 59.352 33.333 2.42 0.00 0.00 1.94
3573 6090 5.698741 AGGTGTATTTCAGATGGTCATCA 57.301 39.130 12.75 0.00 40.22 3.07
3720 6238 2.483876 TCTAGTGACAGCAGCACAAAC 58.516 47.619 0.00 0.00 38.70 2.93
3725 6244 1.342074 AGGTTCTAGTGACAGCAGCA 58.658 50.000 0.00 0.00 0.00 4.41
3961 6481 2.035066 ACTGAGTTTTGCATGTTCAGCC 59.965 45.455 14.31 0.00 39.01 4.85
4150 6671 1.871039 AGTACCACATGCAACGTTGTC 59.129 47.619 27.78 20.05 0.00 3.18
4151 6672 1.961793 AGTACCACATGCAACGTTGT 58.038 45.000 27.78 7.51 0.00 3.32
4154 6676 0.591170 GCAAGTACCACATGCAACGT 59.409 50.000 0.00 0.00 41.89 3.99
4298 7219 9.994432 GTTATTCTCTTATTTCTCCAACACATG 57.006 33.333 0.00 0.00 0.00 3.21
4314 7235 7.390027 AGTCTGTGCACTAATGTTATTCTCTT 58.610 34.615 19.41 0.00 0.00 2.85
4323 7244 5.707298 AGCAAAATAGTCTGTGCACTAATGT 59.293 36.000 19.41 0.95 39.50 2.71
4351 7350 9.069078 CAGCATAATTAAGAATAATGAATGGCG 57.931 33.333 0.00 0.00 32.06 5.69
4352 7351 9.918630 ACAGCATAATTAAGAATAATGAATGGC 57.081 29.630 0.00 0.00 32.06 4.40
4361 7360 8.849168 CCACCATCAACAGCATAATTAAGAATA 58.151 33.333 0.00 0.00 0.00 1.75
4362 7361 7.685155 GCCACCATCAACAGCATAATTAAGAAT 60.685 37.037 0.00 0.00 0.00 2.40
4422 7421 3.056536 CAGCAGCAGAAAGAGTGTACCTA 60.057 47.826 0.00 0.00 0.00 3.08
4513 7512 4.608170 TGGAGGAAAGGCTTTATTGGAT 57.392 40.909 13.37 0.00 0.00 3.41
4514 7513 4.536765 GATGGAGGAAAGGCTTTATTGGA 58.463 43.478 13.37 0.00 0.00 3.53
4535 7534 6.869695 TGAGCTTCATAAAATAGGTACACGA 58.130 36.000 0.00 0.00 0.00 4.35
4561 7563 3.280295 CTCCTTCTGAAGCAGCATGAAT 58.720 45.455 11.93 0.00 39.69 2.57
4604 7606 4.667262 CGAAAACAATGCCCGATATGAAA 58.333 39.130 0.00 0.00 0.00 2.69
4606 7608 2.032799 GCGAAAACAATGCCCGATATGA 59.967 45.455 0.00 0.00 0.00 2.15
4607 7609 2.223456 TGCGAAAACAATGCCCGATATG 60.223 45.455 0.00 0.00 0.00 1.78
4608 7610 2.020720 TGCGAAAACAATGCCCGATAT 58.979 42.857 0.00 0.00 0.00 1.63
4610 7612 0.817013 ATGCGAAAACAATGCCCGAT 59.183 45.000 0.00 0.00 0.00 4.18
4611 7613 0.600557 AATGCGAAAACAATGCCCGA 59.399 45.000 0.00 0.00 0.00 5.14
4614 7616 5.331756 CGATATGAAATGCGAAAACAATGCC 60.332 40.000 0.00 0.00 0.00 4.40
4615 7617 5.331756 CCGATATGAAATGCGAAAACAATGC 60.332 40.000 0.00 0.00 0.00 3.56
4632 7647 1.073964 CTGAGCGAATGCCCGATATG 58.926 55.000 0.00 0.00 44.31 1.78
4647 7666 0.746063 ATTCTCCGAGCTCAGCTGAG 59.254 55.000 34.82 34.82 39.88 3.35
4648 7667 1.189752 AATTCTCCGAGCTCAGCTGA 58.810 50.000 17.19 17.19 39.88 4.26
4649 7668 2.159184 TGTAATTCTCCGAGCTCAGCTG 60.159 50.000 2.14 7.63 39.88 4.24
4650 7669 2.100584 CTGTAATTCTCCGAGCTCAGCT 59.899 50.000 15.40 0.00 43.88 4.24
4651 7670 2.099921 TCTGTAATTCTCCGAGCTCAGC 59.900 50.000 15.40 0.00 0.00 4.26
4703 7725 2.517980 AGCTATGTCTTCTCCCTCTCCT 59.482 50.000 0.00 0.00 0.00 3.69
4707 7729 7.309560 GGAATAGTTAGCTATGTCTTCTCCCTC 60.310 44.444 0.00 0.00 37.92 4.30
4711 7733 7.947282 ACTGGAATAGTTAGCTATGTCTTCTC 58.053 38.462 0.00 0.00 37.92 2.87
4782 7804 1.073964 CAGCACGTCAATGTCTCTGG 58.926 55.000 0.00 0.00 0.00 3.86
4853 7877 2.343758 GAGCAGCCGTCTTGGTGA 59.656 61.111 0.00 0.00 41.21 4.02
5008 8041 2.122768 AGAGGGCCATAGGTTCTCAAG 58.877 52.381 6.18 0.00 0.00 3.02
5009 8042 2.270434 AGAGGGCCATAGGTTCTCAA 57.730 50.000 6.18 0.00 0.00 3.02
5010 8043 2.247635 AGTAGAGGGCCATAGGTTCTCA 59.752 50.000 6.18 0.00 0.00 3.27
5011 8044 2.894765 GAGTAGAGGGCCATAGGTTCTC 59.105 54.545 6.18 0.00 0.00 2.87
5012 8045 2.520549 AGAGTAGAGGGCCATAGGTTCT 59.479 50.000 6.18 0.29 0.00 3.01
5013 8046 2.965562 AGAGTAGAGGGCCATAGGTTC 58.034 52.381 6.18 0.00 0.00 3.62
5016 8049 3.252554 AGAAGAGTAGAGGGCCATAGG 57.747 52.381 6.18 0.00 0.00 2.57
5017 8050 3.254657 CGAAGAAGAGTAGAGGGCCATAG 59.745 52.174 6.18 0.00 0.00 2.23
5018 8051 3.223435 CGAAGAAGAGTAGAGGGCCATA 58.777 50.000 6.18 0.00 0.00 2.74
5034 10799 3.703001 AAAGAAAGATGGAGGCGAAGA 57.297 42.857 0.00 0.00 0.00 2.87
5053 10818 3.540314 AAACAGCATCACAGCCAAAAA 57.460 38.095 0.00 0.00 34.23 1.94
5060 10825 2.812591 AGCAGAGAAAACAGCATCACAG 59.187 45.455 0.00 0.00 0.00 3.66
5062 10827 3.004106 ACAAGCAGAGAAAACAGCATCAC 59.996 43.478 0.00 0.00 0.00 3.06
5086 10851 0.327259 AGCAGCCAAGAGATGCAGAA 59.673 50.000 5.66 0.00 42.45 3.02


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

AutoCloner maintained by Alex Coulton.