Multiple sequence alignment - TraesCS4D01G060300

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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 TraesCS4D01G060300 chr4D 100.000 2453 0 0 1 2453 36435005 36437457 0.000000e+00 4530.0
1 TraesCS4D01G060300 chr4D 96.774 62 2 0 623 684 36435571 36435632 1.200000e-18 104.0
2 TraesCS4D01G060300 chr4D 96.774 62 2 0 567 628 36435627 36435688 1.200000e-18 104.0
3 TraesCS4D01G060300 chr4B 86.762 1186 92 33 634 1780 53037328 53036169 0.000000e+00 1260.0
4 TraesCS4D01G060300 chr4B 85.714 1190 84 30 631 1780 52404741 52405884 0.000000e+00 1177.0
5 TraesCS4D01G060300 chr4B 90.881 636 37 13 3 628 53037902 53037278 0.000000e+00 833.0
6 TraesCS4D01G060300 chr4B 90.172 641 42 11 1 628 52934859 52935491 0.000000e+00 815.0
7 TraesCS4D01G060300 chr4B 88.207 619 41 17 660 1272 52407798 52408390 0.000000e+00 710.0
8 TraesCS4D01G060300 chr4B 90.068 443 37 2 1086 1528 53033335 53032900 3.540000e-158 568.0
9 TraesCS4D01G060300 chr4B 85.401 548 54 19 3 540 52404149 52404680 1.660000e-151 545.0
10 TraesCS4D01G060300 chr4B 88.930 271 18 6 623 882 52935430 52935699 8.460000e-85 324.0
11 TraesCS4D01G060300 chr4B 90.659 182 11 5 1572 1749 53032898 53032719 1.130000e-58 237.0
12 TraesCS4D01G060300 chr4B 83.810 105 10 5 1 103 50152511 50152610 2.600000e-15 93.5
13 TraesCS4D01G060300 chr4B 83.810 105 10 5 3 104 671101409 671101309 2.600000e-15 93.5
14 TraesCS4D01G060300 chr4A 92.045 264 16 2 1526 1784 565831689 565831426 1.390000e-97 366.0
15 TraesCS4D01G060300 chr4A 93.665 221 14 0 1261 1481 565832165 565831945 5.060000e-87 331.0
16 TraesCS4D01G060300 chr4A 84.164 341 28 12 716 1049 565833051 565832730 8.520000e-80 307.0
17 TraesCS4D01G060300 chr4A 85.978 271 26 10 1382 1644 565830100 565829834 1.860000e-71 279.0
18 TraesCS4D01G060300 chr4A 79.930 284 42 10 1932 2202 556386746 556387027 6.920000e-46 195.0
19 TraesCS4D01G060300 chr4A 91.473 129 10 1 1079 1207 565832733 565832606 2.510000e-40 176.0
20 TraesCS4D01G060300 chr2B 77.105 380 66 17 1867 2230 707379771 707380145 1.490000e-47 200.0
21 TraesCS4D01G060300 chr2B 78.453 181 21 17 2266 2436 668575456 668575284 4.320000e-18 102.0
22 TraesCS4D01G060300 chr2B 84.615 104 9 5 3 104 184366512 184366414 2.010000e-16 97.1
23 TraesCS4D01G060300 chr7A 77.597 308 47 20 1910 2207 526614735 526614440 1.510000e-37 167.0
24 TraesCS4D01G060300 chr7A 80.090 221 32 8 2023 2234 138008244 138008461 1.170000e-33 154.0
25 TraesCS4D01G060300 chr7A 83.333 78 9 4 2268 2343 696849164 696849089 4.380000e-08 69.4
26 TraesCS4D01G060300 chrUn 80.603 232 29 15 1925 2146 9985138 9985363 5.430000e-37 165.0
27 TraesCS4D01G060300 chr2D 83.246 191 16 12 2047 2230 622333810 622333629 7.020000e-36 161.0
28 TraesCS4D01G060300 chr2D 82.723 191 17 12 2047 2230 622332946 622332765 3.270000e-34 156.0
29 TraesCS4D01G060300 chr1A 82.564 195 22 9 2017 2205 318506775 318506587 7.020000e-36 161.0
30 TraesCS4D01G060300 chr3B 77.090 323 43 25 1926 2228 70601898 70602209 9.080000e-35 158.0
31 TraesCS4D01G060300 chr3B 83.810 105 10 5 3 105 26835680 26835779 2.600000e-15 93.5
32 TraesCS4D01G060300 chr5B 84.615 104 9 5 3 104 656802862 656802960 2.010000e-16 97.1
33 TraesCS4D01G060300 chr7B 82.727 110 13 4 3 110 742066071 742065966 2.600000e-15 93.5
34 TraesCS4D01G060300 chr6A 83.654 104 11 4 3 104 591194912 591195011 2.600000e-15 93.5
35 TraesCS4D01G060300 chr3D 87.692 65 6 2 2339 2402 538079104 538079041 9.410000e-10 75.0


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 TraesCS4D01G060300 chr4D 36435005 36437457 2452 False 1579.333333 4530 97.849333 1 2453 3 chr4D.!!$F1 2452
1 TraesCS4D01G060300 chr4B 52404149 52408390 4241 False 810.666667 1177 86.440667 3 1780 3 chr4B.!!$F2 1777
2 TraesCS4D01G060300 chr4B 53032719 53037902 5183 True 724.500000 1260 89.592500 3 1780 4 chr4B.!!$R2 1777
3 TraesCS4D01G060300 chr4B 52934859 52935699 840 False 569.500000 815 89.551000 1 882 2 chr4B.!!$F3 881
4 TraesCS4D01G060300 chr4A 565829834 565833051 3217 True 291.800000 366 89.465000 716 1784 5 chr4A.!!$R1 1068

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
501 516 0.036388 TTGCTTCCGGCCAACTCTAG 60.036 55.0 2.24 0.0 40.92 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2867 0.178068 TTTAGGGAGATGCCTGACGC 59.822 55.0 2.72 0.0 36.66 5.19 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
60 63 8.608844 ACTTCTTATGTTCTTTGTACTTCCTG 57.391 34.615 0.00 0.00 0.00 3.86
61 64 8.211629 ACTTCTTATGTTCTTTGTACTTCCTGT 58.788 33.333 0.00 0.00 0.00 4.00
67 70 5.941058 TGTTCTTTGTACTTCCTGTTGACAA 59.059 36.000 0.00 0.00 0.00 3.18
69 72 6.431198 TCTTTGTACTTCCTGTTGACAAAC 57.569 37.500 0.00 0.00 34.23 2.93
259 269 6.165577 GGTAATGTTGCATTTTCTTGTGGAT 58.834 36.000 0.00 0.00 0.00 3.41
271 281 7.979115 TTTTCTTGTGGATTGTTAAAACTCG 57.021 32.000 0.00 0.00 0.00 4.18
501 516 0.036388 TTGCTTCCGGCCAACTCTAG 60.036 55.000 2.24 0.00 40.92 2.43
507 522 0.537188 CCGGCCAACTCTAGTCACAT 59.463 55.000 2.24 0.00 0.00 3.21
530 572 6.510746 TCATCTCGAACGCAATAACATTAG 57.489 37.500 0.00 0.00 0.00 1.73
552 594 4.215613 AGAATAACCGACCAAGTCTTTTGC 59.784 41.667 0.00 0.00 0.00 3.68
575 618 7.725251 TGCCAAAACTTTTCAAATGATCTAGT 58.275 30.769 0.00 0.00 0.00 2.57
576 619 8.203485 TGCCAAAACTTTTCAAATGATCTAGTT 58.797 29.630 0.00 0.00 0.00 2.24
577 620 8.490355 GCCAAAACTTTTCAAATGATCTAGTTG 58.510 33.333 0.00 0.00 35.76 3.16
578 621 8.490355 CCAAAACTTTTCAAATGATCTAGTTGC 58.510 33.333 0.00 0.00 34.50 4.17
579 622 9.033481 CAAAACTTTTCAAATGATCTAGTTGCA 57.967 29.630 0.00 0.00 34.50 4.08
580 623 8.579682 AAACTTTTCAAATGATCTAGTTGCAC 57.420 30.769 0.00 0.00 34.50 4.57
581 624 6.373779 ACTTTTCAAATGATCTAGTTGCACG 58.626 36.000 0.00 0.00 34.50 5.34
582 625 5.940192 TTTCAAATGATCTAGTTGCACGT 57.060 34.783 0.00 0.00 34.50 4.49
583 626 7.172532 ACTTTTCAAATGATCTAGTTGCACGTA 59.827 33.333 0.00 0.00 34.50 3.57
584 627 7.609760 TTTCAAATGATCTAGTTGCACGTAT 57.390 32.000 0.00 0.00 34.50 3.06
585 628 6.588348 TCAAATGATCTAGTTGCACGTATG 57.412 37.500 0.00 0.00 34.50 2.39
586 629 6.106003 TCAAATGATCTAGTTGCACGTATGT 58.894 36.000 0.00 0.00 34.50 2.29
587 630 7.262048 TCAAATGATCTAGTTGCACGTATGTA 58.738 34.615 0.00 0.00 34.50 2.29
588 631 7.926018 TCAAATGATCTAGTTGCACGTATGTAT 59.074 33.333 0.00 0.00 34.50 2.29
589 632 7.643528 AATGATCTAGTTGCACGTATGTATG 57.356 36.000 0.00 0.00 0.00 2.39
590 633 6.385649 TGATCTAGTTGCACGTATGTATGA 57.614 37.500 0.00 0.00 0.00 2.15
591 634 6.981722 TGATCTAGTTGCACGTATGTATGAT 58.018 36.000 0.00 0.00 0.00 2.45
592 635 8.106247 TGATCTAGTTGCACGTATGTATGATA 57.894 34.615 0.00 0.00 0.00 2.15
593 636 8.021396 TGATCTAGTTGCACGTATGTATGATAC 58.979 37.037 0.00 0.00 0.00 2.24
602 645 4.795268 CGTATGTATGATACGCCTCAAGT 58.205 43.478 0.00 0.00 40.42 3.16
603 646 5.220381 CGTATGTATGATACGCCTCAAGTT 58.780 41.667 0.00 0.00 40.42 2.66
604 647 5.342525 CGTATGTATGATACGCCTCAAGTTC 59.657 44.000 0.00 0.00 40.42 3.01
605 648 4.729227 TGTATGATACGCCTCAAGTTCA 57.271 40.909 0.00 0.00 0.00 3.18
606 649 5.276461 TGTATGATACGCCTCAAGTTCAT 57.724 39.130 0.00 0.00 0.00 2.57
607 650 5.289595 TGTATGATACGCCTCAAGTTCATC 58.710 41.667 0.00 0.00 0.00 2.92
608 651 4.679373 ATGATACGCCTCAAGTTCATCT 57.321 40.909 0.00 0.00 0.00 2.90
609 652 4.471904 TGATACGCCTCAAGTTCATCTT 57.528 40.909 0.00 0.00 36.75 2.40
624 667 8.545229 AAGTTCATCTTGACTTTCAGTAGATG 57.455 34.615 9.97 9.97 40.50 2.90
625 668 7.901029 AGTTCATCTTGACTTTCAGTAGATGA 58.099 34.615 13.16 13.16 43.49 2.92
626 669 8.034215 AGTTCATCTTGACTTTCAGTAGATGAG 58.966 37.037 15.29 0.00 44.70 2.90
627 670 6.336566 TCATCTTGACTTTCAGTAGATGAGC 58.663 40.000 13.16 0.00 41.83 4.26
628 671 5.991933 TCTTGACTTTCAGTAGATGAGCT 57.008 39.130 0.00 0.00 39.68 4.09
629 672 7.340487 TCATCTTGACTTTCAGTAGATGAGCTA 59.660 37.037 13.16 0.00 41.83 3.32
632 675 6.842437 TGACTTTCAGTAGATGAGCTAGTT 57.158 37.500 0.00 0.00 39.68 2.24
720 763 1.335964 ACTCATCAACACGACGTCCAG 60.336 52.381 10.58 5.10 0.00 3.86
974 1051 0.036388 CTCCCAGGCGCTAAGAAACA 60.036 55.000 7.64 0.00 0.00 2.83
1193 1272 2.358247 CGGGTTCCACTTCCACCG 60.358 66.667 0.00 0.00 35.01 4.94
1497 1999 5.041940 CCGGTGTATTCACTAGCTAGAAAC 58.958 45.833 27.45 15.69 43.41 2.78
1498 2000 5.393787 CCGGTGTATTCACTAGCTAGAAACA 60.394 44.000 27.45 17.76 43.41 2.83
1542 2306 1.128200 TATAGTTGGCGGCCTGATGT 58.872 50.000 21.46 6.50 0.00 3.06
1588 2356 0.599991 TGCTGCGTGTCAAGTAGTGG 60.600 55.000 5.83 0.00 0.00 4.00
1601 2369 5.875359 GTCAAGTAGTGGGAAACTATGAAGG 59.125 44.000 0.00 0.00 43.30 3.46
1619 2387 3.021177 AGGTTTTGTTCTTTTCCCGGA 57.979 42.857 0.73 0.00 0.00 5.14
1677 2446 2.768698 TCTTGACCGTCGCCATTAAAA 58.231 42.857 0.00 0.00 0.00 1.52
1763 2540 1.146263 AGGCGATGGATCCGGTTTC 59.854 57.895 7.39 0.00 0.00 2.78
1782 2575 1.071071 TCCTCCATTCAACGACGGTTT 59.929 47.619 0.00 0.00 32.98 3.27
1817 2837 0.452184 GCCTTCTTTTCCTTAGCGCC 59.548 55.000 2.29 0.00 0.00 6.53
1820 2840 2.556622 CCTTCTTTTCCTTAGCGCCAAA 59.443 45.455 2.29 0.00 0.00 3.28
1828 2848 1.880027 CCTTAGCGCCAAAGTTTGTCT 59.120 47.619 14.36 10.26 0.00 3.41
1829 2849 2.293399 CCTTAGCGCCAAAGTTTGTCTT 59.707 45.455 14.36 0.53 38.10 3.01
1830 2850 3.243401 CCTTAGCGCCAAAGTTTGTCTTT 60.243 43.478 14.36 0.86 45.96 2.52
1849 2869 4.320928 TTTTTGGGTGCGCTCGCG 62.321 61.111 19.54 6.98 45.51 5.87
1859 2879 4.862092 CGCTCGCGTCAGGCATCT 62.862 66.667 5.77 0.00 43.84 2.90
1861 2881 2.279120 CTCGCGTCAGGCATCTCC 60.279 66.667 5.77 0.00 43.84 3.71
1863 2883 3.842923 CGCGTCAGGCATCTCCCT 61.843 66.667 0.00 0.00 43.84 4.20
1865 2885 1.823295 GCGTCAGGCATCTCCCTAA 59.177 57.895 0.00 0.00 42.87 2.69
1866 2886 0.178068 GCGTCAGGCATCTCCCTAAA 59.822 55.000 0.00 0.00 42.87 1.85
1893 2913 3.636231 CCAGTGAACGGGAGGCCA 61.636 66.667 5.01 0.00 32.68 5.36
1897 2917 2.847234 TGAACGGGAGGCCACTGT 60.847 61.111 5.01 5.69 0.00 3.55
1898 2918 2.047179 GAACGGGAGGCCACTGTC 60.047 66.667 5.01 0.00 0.00 3.51
1900 2920 2.113243 GAACGGGAGGCCACTGTCTT 62.113 60.000 5.01 0.00 0.00 3.01
1901 2921 2.046892 CGGGAGGCCACTGTCTTG 60.047 66.667 5.01 0.00 0.00 3.02
1902 2922 2.883828 CGGGAGGCCACTGTCTTGT 61.884 63.158 5.01 0.00 0.00 3.16
1905 2925 1.692411 GGAGGCCACTGTCTTGTTTT 58.308 50.000 5.01 0.00 0.00 2.43
2029 3049 9.777297 ATTTGAATTACTGTTAACCAAGCATTT 57.223 25.926 2.48 0.00 0.00 2.32
2030 3050 8.586570 TTGAATTACTGTTAACCAAGCATTTG 57.413 30.769 2.48 0.00 0.00 2.32
2031 3051 7.946207 TGAATTACTGTTAACCAAGCATTTGA 58.054 30.769 2.48 0.00 36.36 2.69
2045 4327 6.899243 CCAAGCATTTGAAAAACGTTTAAGTG 59.101 34.615 15.03 12.64 36.36 3.16
2047 4329 6.988329 AGCATTTGAAAAACGTTTAAGTGTG 58.012 32.000 15.03 10.27 0.00 3.82
2148 4756 9.823647 TGTTAATAAAGCATTTGAAGAAAACCA 57.176 25.926 0.00 0.00 39.63 3.67
2150 4758 7.967890 AATAAAGCATTTGAAGAAAACCAGG 57.032 32.000 0.00 0.00 39.63 4.45
2151 4759 5.357742 AAAGCATTTGAAGAAAACCAGGT 57.642 34.783 0.00 0.00 36.60 4.00
2152 4760 6.478512 AAAGCATTTGAAGAAAACCAGGTA 57.521 33.333 0.00 0.00 36.60 3.08
2153 4761 6.670695 AAGCATTTGAAGAAAACCAGGTAT 57.329 33.333 0.00 0.00 0.00 2.73
2154 4762 6.670695 AGCATTTGAAGAAAACCAGGTATT 57.329 33.333 0.00 0.00 0.00 1.89
2155 4763 7.066307 AGCATTTGAAGAAAACCAGGTATTT 57.934 32.000 0.00 0.00 0.00 1.40
2156 4764 6.930722 AGCATTTGAAGAAAACCAGGTATTTG 59.069 34.615 0.00 0.00 0.00 2.32
2213 4821 8.994429 AAATGTGTGTAGAAAAATGTTTGTCA 57.006 26.923 0.00 0.00 0.00 3.58
2214 4822 9.598517 AAATGTGTGTAGAAAAATGTTTGTCAT 57.401 25.926 0.00 0.00 38.57 3.06
2215 4823 7.984002 TGTGTGTAGAAAAATGTTTGTCATG 57.016 32.000 0.00 0.00 36.81 3.07
2217 4825 8.678199 TGTGTGTAGAAAAATGTTTGTCATGTA 58.322 29.630 0.00 0.00 36.81 2.29
2218 4826 9.677567 GTGTGTAGAAAAATGTTTGTCATGTAT 57.322 29.630 0.00 0.00 36.81 2.29
2262 4870 7.982761 AAATTCAATGTGTATGCAAAATGGT 57.017 28.000 0.00 0.00 0.00 3.55
2263 4871 7.982761 AATTCAATGTGTATGCAAAATGGTT 57.017 28.000 0.00 0.00 0.00 3.67
2264 4872 7.982761 ATTCAATGTGTATGCAAAATGGTTT 57.017 28.000 0.00 0.00 0.00 3.27
2265 4873 9.499479 AATTCAATGTGTATGCAAAATGGTTTA 57.501 25.926 0.00 0.00 0.00 2.01
2266 4874 9.669887 ATTCAATGTGTATGCAAAATGGTTTAT 57.330 25.926 0.00 0.00 0.00 1.40
2267 4875 8.700722 TCAATGTGTATGCAAAATGGTTTATC 57.299 30.769 0.00 0.00 0.00 1.75
2268 4876 8.309656 TCAATGTGTATGCAAAATGGTTTATCA 58.690 29.630 0.00 0.00 0.00 2.15
2269 4877 9.100554 CAATGTGTATGCAAAATGGTTTATCAT 57.899 29.630 0.00 0.00 0.00 2.45
2270 4878 8.651391 ATGTGTATGCAAAATGGTTTATCATG 57.349 30.769 0.00 0.00 0.00 3.07
2271 4879 7.609960 TGTGTATGCAAAATGGTTTATCATGT 58.390 30.769 0.00 0.00 0.00 3.21
2272 4880 8.743714 TGTGTATGCAAAATGGTTTATCATGTA 58.256 29.630 0.00 0.00 0.00 2.29
2273 4881 9.748708 GTGTATGCAAAATGGTTTATCATGTAT 57.251 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 63 7.445900 TTCGATCTATACATCGTTTGTCAAC 57.554 36.000 9.75 0.00 44.99 3.18
61 64 7.758076 ACTTTCGATCTATACATCGTTTGTCAA 59.242 33.333 9.75 0.00 44.99 3.18
104 109 2.300152 GTTCAGACACACAGGGAGATGA 59.700 50.000 0.00 0.00 0.00 2.92
106 111 2.614259 AGTTCAGACACACAGGGAGAT 58.386 47.619 0.00 0.00 0.00 2.75
108 113 2.028930 GGTAGTTCAGACACACAGGGAG 60.029 54.545 0.00 0.00 0.00 4.30
111 116 3.685139 ATGGTAGTTCAGACACACAGG 57.315 47.619 0.00 0.00 0.00 4.00
113 118 4.681074 TCAATGGTAGTTCAGACACACA 57.319 40.909 0.00 0.00 0.00 3.72
114 119 5.277828 GGTTTCAATGGTAGTTCAGACACAC 60.278 44.000 0.00 0.00 0.00 3.82
115 120 4.819630 GGTTTCAATGGTAGTTCAGACACA 59.180 41.667 0.00 0.00 0.00 3.72
116 121 5.063880 AGGTTTCAATGGTAGTTCAGACAC 58.936 41.667 0.00 0.00 0.00 3.67
120 125 4.010349 GGGAGGTTTCAATGGTAGTTCAG 58.990 47.826 0.00 0.00 0.00 3.02
195 202 1.154035 GCAACAAGATTTCGGCCGG 60.154 57.895 27.83 9.81 0.00 6.13
399 409 8.961294 TGATGTGGAATTGAAGATTTGTTTTT 57.039 26.923 0.00 0.00 0.00 1.94
403 413 6.925165 GTGTTGATGTGGAATTGAAGATTTGT 59.075 34.615 0.00 0.00 0.00 2.83
405 415 6.151691 CGTGTTGATGTGGAATTGAAGATTT 58.848 36.000 0.00 0.00 0.00 2.17
419 429 4.634703 TGCCCCGCGTGTTGATGT 62.635 61.111 4.92 0.00 0.00 3.06
444 454 5.301551 TGTGGTTGCACTCACTGATTTTTAT 59.698 36.000 16.49 0.00 35.15 1.40
501 516 1.629013 TGCGTTCGAGATGATGTGAC 58.371 50.000 0.00 0.00 0.00 3.67
507 522 6.270064 TCTAATGTTATTGCGTTCGAGATGA 58.730 36.000 0.00 0.00 0.00 2.92
530 572 4.473199 GCAAAAGACTTGGTCGGTTATTC 58.527 43.478 0.00 0.00 37.67 1.75
552 594 8.490355 GCAACTAGATCATTTGAAAAGTTTTGG 58.510 33.333 5.36 0.00 0.00 3.28
575 618 3.054166 GGCGTATCATACATACGTGCAA 58.946 45.455 13.94 0.00 46.30 4.08
576 619 2.295070 AGGCGTATCATACATACGTGCA 59.705 45.455 13.94 0.00 46.30 4.57
577 620 2.915463 GAGGCGTATCATACATACGTGC 59.085 50.000 13.94 0.94 46.30 5.34
578 621 4.155310 TGAGGCGTATCATACATACGTG 57.845 45.455 13.94 0.00 46.30 4.49
579 622 4.277672 ACTTGAGGCGTATCATACATACGT 59.722 41.667 13.94 0.00 46.30 3.57
581 624 6.213677 TGAACTTGAGGCGTATCATACATAC 58.786 40.000 0.00 0.00 0.00 2.39
582 625 6.399639 TGAACTTGAGGCGTATCATACATA 57.600 37.500 0.00 0.00 0.00 2.29
583 626 5.276461 TGAACTTGAGGCGTATCATACAT 57.724 39.130 0.00 0.00 0.00 2.29
584 627 4.729227 TGAACTTGAGGCGTATCATACA 57.271 40.909 0.00 0.00 0.00 2.29
585 628 5.533482 AGATGAACTTGAGGCGTATCATAC 58.467 41.667 0.00 0.00 0.00 2.39
586 629 5.791336 AGATGAACTTGAGGCGTATCATA 57.209 39.130 0.00 0.00 0.00 2.15
587 630 4.679373 AGATGAACTTGAGGCGTATCAT 57.321 40.909 0.00 0.00 0.00 2.45
588 631 4.471904 AAGATGAACTTGAGGCGTATCA 57.528 40.909 0.00 0.00 37.45 2.15
608 651 8.267361 GCAACTAGCTCATCTACTGAAAGTCAA 61.267 40.741 0.00 0.00 44.26 3.18
609 652 6.847040 GCAACTAGCTCATCTACTGAAAGTCA 60.847 42.308 0.00 0.00 44.26 3.41
610 653 5.518487 GCAACTAGCTCATCTACTGAAAGTC 59.482 44.000 0.00 0.00 44.26 3.01
611 654 5.415221 GCAACTAGCTCATCTACTGAAAGT 58.585 41.667 0.00 0.00 46.39 2.66
612 655 5.290643 GTGCAACTAGCTCATCTACTGAAAG 59.709 44.000 0.00 0.00 45.94 2.62
613 656 5.171476 GTGCAACTAGCTCATCTACTGAAA 58.829 41.667 0.00 0.00 45.94 2.69
614 657 4.675408 CGTGCAACTAGCTCATCTACTGAA 60.675 45.833 0.00 0.00 45.94 3.02
615 658 3.181496 CGTGCAACTAGCTCATCTACTGA 60.181 47.826 0.00 0.00 45.94 3.41
616 659 3.111838 CGTGCAACTAGCTCATCTACTG 58.888 50.000 0.00 0.00 45.94 2.74
617 660 2.755655 ACGTGCAACTAGCTCATCTACT 59.244 45.455 0.00 0.00 45.94 2.57
618 661 3.152261 ACGTGCAACTAGCTCATCTAC 57.848 47.619 0.00 0.00 45.94 2.59
619 662 4.338400 ACATACGTGCAACTAGCTCATCTA 59.662 41.667 0.00 0.00 45.94 1.98
620 663 3.131223 ACATACGTGCAACTAGCTCATCT 59.869 43.478 0.00 0.00 45.94 2.90
621 664 3.448686 ACATACGTGCAACTAGCTCATC 58.551 45.455 0.00 0.00 45.94 2.92
622 665 3.526931 ACATACGTGCAACTAGCTCAT 57.473 42.857 0.00 0.00 45.94 2.90
623 666 4.097286 TCATACATACGTGCAACTAGCTCA 59.903 41.667 0.00 0.00 45.94 4.26
624 667 4.607955 TCATACATACGTGCAACTAGCTC 58.392 43.478 0.00 0.00 45.94 4.09
625 668 4.649088 TCATACATACGTGCAACTAGCT 57.351 40.909 0.00 0.00 45.94 3.32
626 669 5.059343 CGTATCATACATACGTGCAACTAGC 59.941 44.000 0.00 0.00 41.51 3.42
627 670 5.059343 GCGTATCATACATACGTGCAACTAG 59.941 44.000 13.94 0.00 46.30 2.57
628 671 4.913345 GCGTATCATACATACGTGCAACTA 59.087 41.667 13.94 0.00 46.30 2.24
629 672 3.734231 GCGTATCATACATACGTGCAACT 59.266 43.478 13.94 0.00 46.30 3.16
632 675 2.295070 AGGCGTATCATACATACGTGCA 59.705 45.455 13.94 0.00 46.30 4.57
695 738 2.229062 ACGTCGTGTTGATGAGTCTCAT 59.771 45.455 15.40 15.40 40.34 2.90
698 741 1.068472 GGACGTCGTGTTGATGAGTCT 60.068 52.381 9.92 0.00 37.05 3.24
699 742 1.335597 TGGACGTCGTGTTGATGAGTC 60.336 52.381 9.92 0.00 37.05 3.36
720 763 0.524392 CTCTGTCTGGCACGTCGATC 60.524 60.000 0.00 0.00 0.00 3.69
797 858 3.462678 GGGAGGTCTGACCCGCTC 61.463 72.222 22.81 13.83 39.75 5.03
802 863 2.997897 AGCACGGGAGGTCTGACC 60.998 66.667 19.20 19.20 38.99 4.02
832 893 4.430765 GACGCGTCGTGGGTGGAT 62.431 66.667 25.19 0.00 44.90 3.41
852 918 1.006571 TCGTTCTGGGCGAAGTGAC 60.007 57.895 0.00 0.00 35.28 3.67
913 990 1.724654 CGTCGTGCAAATTACAGTGCC 60.725 52.381 0.00 0.00 40.14 5.01
920 997 1.412987 CGCGACGTCGTGCAAATTA 59.587 52.632 34.88 0.00 43.06 1.40
1089 1168 2.559840 CTCACGTACAGGTCGCGT 59.440 61.111 5.77 0.00 39.59 6.01
1296 1790 4.473520 CTCCCGATGGCCACGCTT 62.474 66.667 8.16 0.00 0.00 4.68
1481 1975 3.179830 CGCGTGTTTCTAGCTAGTGAAT 58.820 45.455 20.10 0.00 0.00 2.57
1482 1976 2.030540 ACGCGTGTTTCTAGCTAGTGAA 60.031 45.455 20.10 13.20 0.00 3.18
1497 1999 1.007734 ACACTGTCACCTACGCGTG 60.008 57.895 24.59 8.81 37.83 5.34
1498 2000 1.007734 CACACTGTCACCTACGCGT 60.008 57.895 19.17 19.17 0.00 6.01
1542 2306 1.132453 CGTAGCACTCAGAATCGGACA 59.868 52.381 0.00 0.00 0.00 4.02
1588 2356 8.942338 AAAAGAACAAAACCTTCATAGTTTCC 57.058 30.769 0.00 0.00 36.44 3.13
1601 2369 4.109766 CAAGTCCGGGAAAAGAACAAAAC 58.890 43.478 0.00 0.00 0.00 2.43
1707 2476 4.796231 GTCGCCGAGCATGTCCGT 62.796 66.667 0.00 0.00 0.00 4.69
1753 2530 2.683362 GTTGAATGGAGGAAACCGGATC 59.317 50.000 9.46 5.87 0.00 3.36
1763 2540 1.196808 CAAACCGTCGTTGAATGGAGG 59.803 52.381 0.00 0.00 30.72 4.30
1782 2575 4.462394 GCTAATCAGCCGCCATCA 57.538 55.556 0.00 0.00 42.37 3.07
1843 2863 2.959071 GAGATGCCTGACGCGAGC 60.959 66.667 15.93 10.83 42.08 5.03
1845 2865 2.904178 TAGGGAGATGCCTGACGCGA 62.904 60.000 15.93 0.00 42.08 5.87
1846 2866 2.016393 TTAGGGAGATGCCTGACGCG 62.016 60.000 3.53 3.53 42.08 6.01
1847 2867 0.178068 TTTAGGGAGATGCCTGACGC 59.822 55.000 2.72 0.00 36.66 5.19
1848 2868 2.487934 CATTTAGGGAGATGCCTGACG 58.512 52.381 2.72 0.00 36.66 4.35
1849 2869 2.856222 CCATTTAGGGAGATGCCTGAC 58.144 52.381 2.72 0.00 36.66 3.51
1871 2891 3.612247 CTCCCGTTCACTGGGCTGG 62.612 68.421 0.00 0.00 46.92 4.85
1872 2892 2.046892 CTCCCGTTCACTGGGCTG 60.047 66.667 0.00 0.00 46.92 4.85
1873 2893 3.322466 CCTCCCGTTCACTGGGCT 61.322 66.667 0.00 0.00 46.92 5.19
1877 2897 2.358737 GTGGCCTCCCGTTCACTG 60.359 66.667 3.32 0.00 0.00 3.66
1879 2899 2.358737 CAGTGGCCTCCCGTTCAC 60.359 66.667 3.32 0.00 0.00 3.18
1881 2901 2.047179 GACAGTGGCCTCCCGTTC 60.047 66.667 3.32 0.00 0.00 3.95
1883 2903 2.526873 AAGACAGTGGCCTCCCGT 60.527 61.111 3.32 0.00 0.00 5.28
1884 2904 2.046892 CAAGACAGTGGCCTCCCG 60.047 66.667 3.32 0.00 0.00 5.14
1885 2905 0.178990 AAACAAGACAGTGGCCTCCC 60.179 55.000 3.32 0.00 0.00 4.30
2003 3023 9.777297 AAATGCTTGGTTAACAGTAATTCAAAT 57.223 25.926 8.10 0.00 0.00 2.32
2004 3024 9.039870 CAAATGCTTGGTTAACAGTAATTCAAA 57.960 29.630 8.10 0.00 0.00 2.69
2005 3025 8.417106 TCAAATGCTTGGTTAACAGTAATTCAA 58.583 29.630 8.10 0.00 33.01 2.69
2006 3026 7.946207 TCAAATGCTTGGTTAACAGTAATTCA 58.054 30.769 8.10 2.13 33.01 2.57
2007 3027 8.810652 TTCAAATGCTTGGTTAACAGTAATTC 57.189 30.769 8.10 0.00 33.01 2.17
2008 3028 9.606631 TTTTCAAATGCTTGGTTAACAGTAATT 57.393 25.926 8.10 0.22 33.01 1.40
2009 3029 9.606631 TTTTTCAAATGCTTGGTTAACAGTAAT 57.393 25.926 8.10 0.00 33.01 1.89
2010 3030 8.874816 GTTTTTCAAATGCTTGGTTAACAGTAA 58.125 29.630 8.10 0.00 33.01 2.24
2011 3031 7.221067 CGTTTTTCAAATGCTTGGTTAACAGTA 59.779 33.333 8.10 0.00 33.01 2.74
2012 3032 6.035542 CGTTTTTCAAATGCTTGGTTAACAGT 59.964 34.615 8.10 0.00 33.01 3.55
2013 3033 6.035542 ACGTTTTTCAAATGCTTGGTTAACAG 59.964 34.615 8.10 0.00 33.01 3.16
2014 3034 5.869888 ACGTTTTTCAAATGCTTGGTTAACA 59.130 32.000 8.10 0.00 33.01 2.41
2015 3035 6.339194 ACGTTTTTCAAATGCTTGGTTAAC 57.661 33.333 0.00 0.00 33.01 2.01
2016 3036 6.969828 AACGTTTTTCAAATGCTTGGTTAA 57.030 29.167 0.00 0.00 33.01 2.01
2017 3037 6.969828 AAACGTTTTTCAAATGCTTGGTTA 57.030 29.167 7.96 0.00 33.01 2.85
2018 3038 5.871465 AAACGTTTTTCAAATGCTTGGTT 57.129 30.435 7.96 0.00 33.01 3.67
2019 3039 6.592220 ACTTAAACGTTTTTCAAATGCTTGGT 59.408 30.769 20.19 0.00 33.01 3.67
2020 3040 6.899243 CACTTAAACGTTTTTCAAATGCTTGG 59.101 34.615 20.19 0.00 33.01 3.61
2021 3041 7.422179 CACACTTAAACGTTTTTCAAATGCTTG 59.578 33.333 20.19 0.00 0.00 4.01
2022 3042 7.117092 ACACACTTAAACGTTTTTCAAATGCTT 59.883 29.630 20.19 0.00 0.00 3.91
2023 3043 6.588373 ACACACTTAAACGTTTTTCAAATGCT 59.412 30.769 20.19 0.00 0.00 3.79
2024 3044 6.757162 ACACACTTAAACGTTTTTCAAATGC 58.243 32.000 20.19 0.00 0.00 3.56
2122 4730 9.823647 TGGTTTTCTTCAAATGCTTTATTAACA 57.176 25.926 0.00 0.00 0.00 2.41
2124 4732 9.487790 CCTGGTTTTCTTCAAATGCTTTATTAA 57.512 29.630 0.00 0.00 0.00 1.40
2125 4733 8.646900 ACCTGGTTTTCTTCAAATGCTTTATTA 58.353 29.630 0.00 0.00 0.00 0.98
2126 4734 7.508687 ACCTGGTTTTCTTCAAATGCTTTATT 58.491 30.769 0.00 0.00 0.00 1.40
2127 4735 7.066307 ACCTGGTTTTCTTCAAATGCTTTAT 57.934 32.000 0.00 0.00 0.00 1.40
2128 4736 6.478512 ACCTGGTTTTCTTCAAATGCTTTA 57.521 33.333 0.00 0.00 0.00 1.85
2129 4737 5.357742 ACCTGGTTTTCTTCAAATGCTTT 57.642 34.783 0.00 0.00 0.00 3.51
2130 4738 6.670695 ATACCTGGTTTTCTTCAAATGCTT 57.329 33.333 3.84 0.00 0.00 3.91
2131 4739 6.670695 AATACCTGGTTTTCTTCAAATGCT 57.329 33.333 3.84 0.00 0.00 3.79
2132 4740 6.928492 TCAAATACCTGGTTTTCTTCAAATGC 59.072 34.615 3.84 0.00 0.00 3.56
2133 4741 8.885494 TTCAAATACCTGGTTTTCTTCAAATG 57.115 30.769 3.84 0.00 0.00 2.32
2189 4797 9.033481 CATGACAAACATTTTTCTACACACATT 57.967 29.630 0.00 0.00 37.07 2.71
2191 4799 7.542890 ACATGACAAACATTTTTCTACACACA 58.457 30.769 0.00 0.00 37.07 3.72
2237 4845 8.393671 ACCATTTTGCATACACATTGAATTTT 57.606 26.923 0.00 0.00 0.00 1.82
2238 4846 7.982761 ACCATTTTGCATACACATTGAATTT 57.017 28.000 0.00 0.00 0.00 1.82
2239 4847 7.982761 AACCATTTTGCATACACATTGAATT 57.017 28.000 0.00 0.00 0.00 2.17
2241 4849 9.149225 GATAAACCATTTTGCATACACATTGAA 57.851 29.630 0.00 0.00 0.00 2.69
2243 4851 8.476657 TGATAAACCATTTTGCATACACATTG 57.523 30.769 0.00 0.00 0.00 2.82
2245 4853 8.259411 ACATGATAAACCATTTTGCATACACAT 58.741 29.630 0.00 0.00 0.00 3.21
2246 4854 7.609960 ACATGATAAACCATTTTGCATACACA 58.390 30.769 0.00 0.00 0.00 3.72
2247 4855 9.748708 ATACATGATAAACCATTTTGCATACAC 57.251 29.630 0.00 0.00 0.00 2.90
2369 7455 9.816354 AACAATTTTTAAACACATAGTCAGCTT 57.184 25.926 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.