Multiple sequence alignment - TraesCS3A01G027300

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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 TraesCS3A01G027300 chr3A 100.000 2748 0 0 1 2748 14294769 14292022 0.000000e+00 5075.0
1 TraesCS3A01G027300 chr3A 91.405 1815 61 27 849 2619 14202577 14204340 0.000000e+00 2399.0
2 TraesCS3A01G027300 chr3A 90.840 131 11 1 2619 2748 14204498 14204628 1.010000e-39 174.0
3 TraesCS3A01G027300 chr3D 91.838 1752 66 25 913 2614 6192966 6194690 0.000000e+00 2372.0
4 TraesCS3A01G027300 chr3D 87.675 357 23 10 306 662 484725701 484726036 1.980000e-106 396.0
5 TraesCS3A01G027300 chr3B 91.878 591 44 2 988 1574 7333662 7334252 0.000000e+00 822.0
6 TraesCS3A01G027300 chr3B 84.458 637 54 20 1166 1772 7334963 7334342 1.100000e-163 586.0
7 TraesCS3A01G027300 chr3B 80.831 313 35 15 415 707 729937473 729937166 3.560000e-54 222.0
8 TraesCS3A01G027300 chr3B 84.021 194 22 8 317 510 729937725 729937541 7.820000e-41 178.0
9 TraesCS3A01G027300 chr3B 93.182 44 1 2 664 707 771625330 771625371 2.280000e-06 63.9
10 TraesCS3A01G027300 chrUn 91.667 396 17 9 830 1216 404662512 404662900 4.030000e-148 534.0
11 TraesCS3A01G027300 chrUn 91.473 129 10 1 2619 2747 4554451 4554578 2.810000e-40 176.0
12 TraesCS3A01G027300 chrUn 91.473 129 10 1 2619 2747 124164522 124164649 2.810000e-40 176.0
13 TraesCS3A01G027300 chrUn 91.473 129 10 1 2619 2747 131619103 131618976 2.810000e-40 176.0
14 TraesCS3A01G027300 chr7D 89.433 388 29 3 320 707 226126603 226126978 1.910000e-131 479.0
15 TraesCS3A01G027300 chr7D 83.660 459 44 14 1 458 136189801 136190229 1.190000e-108 403.0
16 TraesCS3A01G027300 chr7D 91.270 252 21 1 1 252 226118209 226118459 2.620000e-90 342.0
17 TraesCS3A01G027300 chr7D 92.571 175 12 1 510 684 136190226 136190399 1.630000e-62 250.0
18 TraesCS3A01G027300 chr7D 86.154 65 5 2 709 769 80276993 80277057 1.770000e-07 67.6
19 TraesCS3A01G027300 chr7D 96.875 32 0 1 676 707 478316864 478316834 5.000000e-03 52.8
20 TraesCS3A01G027300 chr6A 78.542 727 86 32 2 710 25475408 25474734 5.480000e-112 414.0
21 TraesCS3A01G027300 chr6A 80.000 490 75 14 2 487 25214623 25214153 9.420000e-90 340.0
22 TraesCS3A01G027300 chr6A 79.959 484 74 14 2 481 25138845 25138381 4.380000e-88 335.0
23 TraesCS3A01G027300 chr6A 80.930 430 61 12 2 428 25528351 25527940 1.230000e-83 320.0
24 TraesCS3A01G027300 chr6A 83.489 321 47 5 2 320 25317121 25316805 7.440000e-76 294.0
25 TraesCS3A01G027300 chr6A 81.944 288 26 12 447 710 25316769 25316484 1.280000e-53 220.0
26 TraesCS3A01G027300 chr6A 82.051 234 26 10 491 710 25410607 25410376 4.670000e-43 185.0
27 TraesCS3A01G027300 chr6A 80.000 235 29 7 491 710 25527934 25527703 1.020000e-34 158.0
28 TraesCS3A01G027300 chr5D 83.492 315 41 7 54 368 386033266 386033569 1.610000e-72 283.0
29 TraesCS3A01G027300 chr5D 85.932 263 35 2 58 320 545639340 545639600 2.080000e-71 279.0
30 TraesCS3A01G027300 chr5D 77.316 313 63 6 1173 1481 109578060 109577752 7.820000e-41 178.0
31 TraesCS3A01G027300 chr6B 85.227 264 37 2 58 320 57002994 57002732 1.250000e-68 270.0
32 TraesCS3A01G027300 chr6B 96.970 33 0 1 675 707 713465800 713465831 1.000000e-03 54.7
33 TraesCS3A01G027300 chr5B 85.227 264 37 2 58 320 477519936 477519674 1.250000e-68 270.0
34 TraesCS3A01G027300 chr1A 82.595 316 30 10 416 711 23173200 23173510 3.510000e-64 255.0
35 TraesCS3A01G027300 chr1A 84.694 196 21 2 312 507 23173038 23173224 1.300000e-43 187.0
36 TraesCS3A01G027300 chr1A 86.154 65 5 2 709 769 159942426 159942490 1.770000e-07 67.6
37 TraesCS3A01G027300 chr5A 75.831 331 71 5 1171 1498 118253569 118253893 2.830000e-35 159.0
38 TraesCS3A01G027300 chr2D 90.323 62 5 1 709 769 618177085 618177024 2.270000e-11 80.5
39 TraesCS3A01G027300 chr2D 89.831 59 5 1 709 767 41266555 41266612 1.060000e-09 75.0
40 TraesCS3A01G027300 chr2D 87.500 64 4 3 708 768 19000038 19000100 1.370000e-08 71.3
41 TraesCS3A01G027300 chr2D 90.909 44 2 2 664 707 626271436 626271477 1.060000e-04 58.4
42 TraesCS3A01G027300 chr4D 90.164 61 4 2 709 768 326982663 326982722 8.160000e-11 78.7
43 TraesCS3A01G027300 chr4A 88.889 63 5 2 709 769 27327178 27327240 2.930000e-10 76.8
44 TraesCS3A01G027300 chr4A 88.889 63 5 2 709 769 401900716 401900654 2.930000e-10 76.8
45 TraesCS3A01G027300 chr7A 86.154 65 5 2 709 769 695004850 695004786 1.770000e-07 67.6


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 TraesCS3A01G027300 chr3A 14292022 14294769 2747 True 5075.0 5075 100.0000 1 2748 1 chr3A.!!$R1 2747
1 TraesCS3A01G027300 chr3A 14202577 14204628 2051 False 1286.5 2399 91.1225 849 2748 2 chr3A.!!$F1 1899
2 TraesCS3A01G027300 chr3D 6192966 6194690 1724 False 2372.0 2372 91.8380 913 2614 1 chr3D.!!$F1 1701
3 TraesCS3A01G027300 chr3B 7333662 7334252 590 False 822.0 822 91.8780 988 1574 1 chr3B.!!$F1 586
4 TraesCS3A01G027300 chr3B 7334342 7334963 621 True 586.0 586 84.4580 1166 1772 1 chr3B.!!$R1 606
5 TraesCS3A01G027300 chr7D 136189801 136190399 598 False 326.5 403 88.1155 1 684 2 chr7D.!!$F4 683
6 TraesCS3A01G027300 chr6A 25474734 25475408 674 True 414.0 414 78.5420 2 710 1 chr6A.!!$R4 708
7 TraesCS3A01G027300 chr6A 25316484 25317121 637 True 257.0 294 82.7165 2 710 2 chr6A.!!$R5 708
8 TraesCS3A01G027300 chr6A 25527703 25528351 648 True 239.0 320 80.4650 2 710 2 chr6A.!!$R6 708

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
911 963 0.031449 GTGACTCAGATAGCCCGAGC 59.969 60.0 0.0 0.0 40.32 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2104 0.09715 GTACCTTACCGACGGACGAC 59.903 60.0 23.38 5.68 45.77 4.34 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
78 81 9.827411 GTTTATTTTTGTTTTTGCTACAACCAA 57.173 25.926 0.00 0.00 35.39 3.67
81 84 7.497925 TTTTTGTTTTTGCTACAACCAAGTT 57.502 28.000 0.00 0.00 35.39 2.66
102 105 4.823276 TTTTTGCTGCAACCGGTG 57.177 50.000 15.72 3.35 0.00 4.94
155 158 1.794701 CTACAATGATGATGACGGGCG 59.205 52.381 0.00 0.00 0.00 6.13
159 162 2.513666 GATGATGACGGGCGGCAA 60.514 61.111 12.47 0.00 36.35 4.52
206 210 5.334569 GCGATAAACTTTTCTGCTACAACCA 60.335 40.000 0.00 0.00 0.00 3.67
264 268 1.476110 GGGCACACAACAAGGTACAGA 60.476 52.381 0.00 0.00 0.00 3.41
379 398 1.589727 GCTGCAACCACAAGTGCAC 60.590 57.895 9.40 9.40 31.85 4.57
444 463 4.420143 CCATCGATGGTGACCGAC 57.580 61.111 32.39 0.00 43.05 4.79
445 464 1.588932 CCATCGATGGTGACCGACG 60.589 63.158 32.39 12.61 43.05 5.12
446 465 1.431845 CATCGATGGTGACCGACGA 59.568 57.895 20.79 20.79 37.64 4.20
447 466 0.866061 CATCGATGGTGACCGACGAC 60.866 60.000 20.91 0.25 36.81 4.34
448 467 2.319011 ATCGATGGTGACCGACGACG 62.319 60.000 20.91 11.01 36.81 5.12
449 468 2.872557 GATGGTGACCGACGACGA 59.127 61.111 9.28 0.00 42.66 4.20
450 469 1.226323 GATGGTGACCGACGACGAG 60.226 63.158 9.28 1.47 42.66 4.18
582 611 0.229500 CGGCGCTGCTTTTGTTTTTC 59.771 50.000 7.64 0.00 0.00 2.29
606 649 3.428045 CCTCTGCGCTTTATTTGGAAAGG 60.428 47.826 9.73 0.00 36.99 3.11
609 652 4.082787 TCTGCGCTTTATTTGGAAAGGAAG 60.083 41.667 9.73 0.00 36.99 3.46
615 658 5.289434 GCTTTATTTGGAAAGGAAGCGATTG 59.711 40.000 0.00 0.00 36.99 2.67
622 665 0.183731 AAGGAAGCGATTGGGGATCC 59.816 55.000 1.92 1.92 0.00 3.36
624 667 1.598130 GAAGCGATTGGGGATCCGG 60.598 63.158 5.45 0.00 35.24 5.14
710 753 1.014564 GCGCAGAGTAGTCGCCTTTT 61.015 55.000 0.30 0.00 42.71 2.27
711 754 1.734707 GCGCAGAGTAGTCGCCTTTTA 60.735 52.381 0.30 0.00 42.71 1.52
712 755 2.186076 CGCAGAGTAGTCGCCTTTTAG 58.814 52.381 8.24 0.00 0.00 1.85
713 756 2.415625 CGCAGAGTAGTCGCCTTTTAGT 60.416 50.000 8.24 0.00 0.00 2.24
714 757 3.181503 CGCAGAGTAGTCGCCTTTTAGTA 60.182 47.826 8.24 0.00 0.00 1.82
715 758 4.104066 GCAGAGTAGTCGCCTTTTAGTAC 58.896 47.826 3.83 0.00 0.00 2.73
716 759 4.380233 GCAGAGTAGTCGCCTTTTAGTACA 60.380 45.833 0.00 0.00 0.00 2.90
717 760 5.706916 CAGAGTAGTCGCCTTTTAGTACAA 58.293 41.667 0.00 0.00 0.00 2.41
718 761 6.331061 CAGAGTAGTCGCCTTTTAGTACAAT 58.669 40.000 0.00 0.00 0.00 2.71
719 762 6.472808 CAGAGTAGTCGCCTTTTAGTACAATC 59.527 42.308 0.00 0.00 0.00 2.67
720 763 6.377712 AGAGTAGTCGCCTTTTAGTACAATCT 59.622 38.462 0.00 0.00 0.00 2.40
721 764 6.932947 AGTAGTCGCCTTTTAGTACAATCTT 58.067 36.000 0.00 0.00 0.00 2.40
722 765 6.812160 AGTAGTCGCCTTTTAGTACAATCTTG 59.188 38.462 0.00 0.00 0.00 3.02
723 766 4.935808 AGTCGCCTTTTAGTACAATCTTGG 59.064 41.667 0.00 0.00 0.00 3.61
724 767 4.933400 GTCGCCTTTTAGTACAATCTTGGA 59.067 41.667 0.00 0.00 0.00 3.53
725 768 5.585047 GTCGCCTTTTAGTACAATCTTGGAT 59.415 40.000 0.00 0.00 0.00 3.41
726 769 6.759827 GTCGCCTTTTAGTACAATCTTGGATA 59.240 38.462 0.00 0.00 0.00 2.59
727 770 6.984474 TCGCCTTTTAGTACAATCTTGGATAG 59.016 38.462 0.00 0.00 0.00 2.08
728 771 6.984474 CGCCTTTTAGTACAATCTTGGATAGA 59.016 38.462 0.00 0.00 37.28 1.98
729 772 7.494625 CGCCTTTTAGTACAATCTTGGATAGAA 59.505 37.037 0.00 0.00 36.22 2.10
730 773 9.174166 GCCTTTTAGTACAATCTTGGATAGAAA 57.826 33.333 0.00 0.00 36.22 2.52
753 796 2.969443 AATTCTTTCAGCGGTGAACG 57.031 45.000 28.31 25.62 42.60 3.95
754 797 1.156736 ATTCTTTCAGCGGTGAACGG 58.843 50.000 28.31 22.26 42.60 4.44
755 798 0.105224 TTCTTTCAGCGGTGAACGGA 59.895 50.000 28.31 23.92 42.60 4.69
756 799 0.320374 TCTTTCAGCGGTGAACGGAT 59.680 50.000 28.31 0.00 42.60 4.18
757 800 0.443869 CTTTCAGCGGTGAACGGATG 59.556 55.000 28.31 12.84 42.60 3.51
758 801 0.034198 TTTCAGCGGTGAACGGATGA 59.966 50.000 28.31 11.11 42.60 2.92
759 802 0.034198 TTCAGCGGTGAACGGATGAA 59.966 50.000 25.16 15.06 45.03 2.57
760 803 0.034198 TCAGCGGTGAACGGATGAAA 59.966 50.000 16.20 0.00 44.51 2.69
761 804 0.871722 CAGCGGTGAACGGATGAAAA 59.128 50.000 9.50 0.00 44.51 2.29
762 805 1.265635 CAGCGGTGAACGGATGAAAAA 59.734 47.619 9.50 0.00 44.51 1.94
874 917 9.347934 CTTATAATTAATCACGGTTTTGCACAA 57.652 29.630 0.00 0.00 0.00 3.33
898 950 0.179161 CGTGGATCCGAGTGTGACTC 60.179 60.000 7.39 0.00 41.71 3.36
905 957 2.017782 TCCGAGTGTGACTCAGATAGC 58.982 52.381 4.69 0.00 45.30 2.97
910 962 1.066303 GTGTGACTCAGATAGCCCGAG 59.934 57.143 0.00 0.00 0.00 4.63
911 963 0.031449 GTGACTCAGATAGCCCGAGC 59.969 60.000 0.00 0.00 40.32 5.03
951 1008 5.163195 GGCTCAAACCAATATAAGGAGGAGA 60.163 44.000 13.32 0.00 0.00 3.71
958 1015 4.507512 CCAATATAAGGAGGAGAAAGCCCC 60.508 50.000 0.00 0.00 0.00 5.80
1091 1152 2.981350 GGCAAACGAAAGGCGGGA 60.981 61.111 0.00 0.00 46.49 5.14
1636 1717 4.890581 AGGCCAGTGACTCTTATGTAGTAG 59.109 45.833 5.01 0.00 0.00 2.57
1643 1743 8.767085 CAGTGACTCTTATGTAGTAGTACTAGC 58.233 40.741 10.38 6.62 30.12 3.42
1832 1948 5.926542 CAGCTCAGTTTTGTAGCTTACTGTA 59.073 40.000 0.00 0.00 43.97 2.74
1983 2104 8.537049 TTGCACATTATTTTCAGAGAAAATGG 57.463 30.769 21.59 15.05 32.64 3.16
1984 2105 7.669427 TGCACATTATTTTCAGAGAAAATGGT 58.331 30.769 21.59 15.51 32.64 3.55
1987 2108 8.023128 CACATTATTTTCAGAGAAAATGGTCGT 58.977 33.333 21.59 13.11 32.64 4.34
1989 2110 5.629079 ATTTTCAGAGAAAATGGTCGTCC 57.371 39.130 14.81 0.00 0.00 4.79
1993 2114 0.989890 GAGAAAATGGTCGTCCGTCG 59.010 55.000 0.00 0.00 41.41 5.12
2000 2121 2.335712 GGTCGTCCGTCGGTAAGGT 61.336 63.158 11.88 0.00 40.32 3.50
2001 2122 1.024579 GGTCGTCCGTCGGTAAGGTA 61.025 60.000 11.88 0.00 40.32 3.08
2003 2124 1.060937 CGTCCGTCGGTAAGGTACG 59.939 63.158 11.88 8.85 36.42 3.67
2015 2136 5.357878 TCGGTAAGGTACGGCTATATATTGG 59.642 44.000 0.00 0.00 0.00 3.16
2019 2140 5.340439 AGGTACGGCTATATATTGGAAGC 57.660 43.478 0.00 0.00 0.00 3.86
2023 2144 4.968259 ACGGCTATATATTGGAAGCAACA 58.032 39.130 7.37 0.00 36.68 3.33
2026 2147 5.349817 CGGCTATATATTGGAAGCAACAGAG 59.650 44.000 7.37 0.00 36.68 3.35
2034 2155 6.655078 ATTGGAAGCAACAGAGTACAAAAT 57.345 33.333 0.00 0.00 0.00 1.82
2065 2186 2.916702 TCAGTCAGAAGCTCAGCAAA 57.083 45.000 0.00 0.00 0.00 3.68
2066 2187 3.413846 TCAGTCAGAAGCTCAGCAAAT 57.586 42.857 0.00 0.00 0.00 2.32
2110 2231 2.731968 GCTTGCACGTTATTGTCATGGG 60.732 50.000 0.00 0.00 0.00 4.00
2284 2426 5.211174 ACCTTGTTAGTGTCCTGTAGTTC 57.789 43.478 0.00 0.00 0.00 3.01
2294 2436 9.841295 TTAGTGTCCTGTAGTTCAGTAAATTTT 57.159 29.630 0.00 0.00 42.19 1.82
2313 2455 1.812235 TTCTGACAGCGTTGATGCAT 58.188 45.000 6.16 0.00 37.31 3.96
2314 2456 2.671130 TCTGACAGCGTTGATGCATA 57.329 45.000 6.16 0.00 37.31 3.14
2315 2457 2.270923 TCTGACAGCGTTGATGCATAC 58.729 47.619 6.16 0.00 37.31 2.39
2316 2458 0.998669 TGACAGCGTTGATGCATACG 59.001 50.000 15.97 15.97 40.55 3.06
2342 2484 6.062095 ACTTGTTTCAGTTATACTGCAACCT 58.938 36.000 15.99 1.27 46.75 3.50
2378 2520 2.885135 TTGAGGACATTGGCACATCT 57.115 45.000 0.00 0.00 39.30 2.90
2576 2721 1.383456 GCCTTGCGATGGTGCCATTA 61.383 55.000 5.08 0.00 36.70 1.90
2579 2724 1.034838 TTGCGATGGTGCCATTACCC 61.035 55.000 5.08 0.00 40.09 3.69
2585 2730 0.780637 TGGTGCCATTACCCTGGAAA 59.219 50.000 0.00 0.00 40.09 3.13
2586 2731 1.148027 TGGTGCCATTACCCTGGAAAA 59.852 47.619 0.00 0.00 40.09 2.29
2595 2740 1.149101 ACCCTGGAAAAGAGGCAAGA 58.851 50.000 0.00 0.00 0.00 3.02
2629 2932 3.511477 AGCTCTAGTTTTCAGGTCCAGA 58.489 45.455 0.00 0.00 0.00 3.86
2648 2952 7.250032 TCCAGATGGATAATAGATCACCAAG 57.750 40.000 0.00 0.00 39.78 3.61
2708 3012 7.122650 AGTTGAACATTCACTTCTTTTCCTTGA 59.877 33.333 0.00 0.00 36.83 3.02
2715 3019 7.444629 TTCACTTCTTTTCCTTGATGAGATG 57.555 36.000 0.00 0.00 0.00 2.90
2722 3026 6.441924 TCTTTTCCTTGATGAGATGTACCTCT 59.558 38.462 0.00 0.00 34.38 3.69
2723 3027 5.604758 TTCCTTGATGAGATGTACCTCTG 57.395 43.478 5.30 0.00 34.38 3.35
2742 3046 0.530870 GAATCTGGTAGGGCGCTGTC 60.531 60.000 14.51 6.40 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.435234 GCCGGCCGTTGTGTATGA 60.435 61.111 26.12 0.00 0.00 2.15
56 59 7.680442 ACTTGGTTGTAGCAAAAACAAAAAT 57.320 28.000 0.00 0.00 38.50 1.82
101 104 3.181445 ACTGGATGTAGCTTTTGTGGTCA 60.181 43.478 0.00 0.00 0.00 4.02
102 105 3.412386 ACTGGATGTAGCTTTTGTGGTC 58.588 45.455 0.00 0.00 0.00 4.02
149 152 2.510691 CTTATCGTTGCCGCCCGT 60.511 61.111 0.00 0.00 0.00 5.28
252 256 1.272769 GAGGTCGCTCTGTACCTTGTT 59.727 52.381 0.00 0.00 46.22 2.83
253 257 0.889306 GAGGTCGCTCTGTACCTTGT 59.111 55.000 0.00 0.00 46.22 3.16
264 268 0.036952 CACCTGTCATTGAGGTCGCT 60.037 55.000 0.00 0.00 42.25 4.93
333 337 4.415150 ATGGCCACAGCTCCGGTG 62.415 66.667 8.16 0.00 39.73 4.94
334 338 4.101448 GATGGCCACAGCTCCGGT 62.101 66.667 8.16 0.00 39.73 5.28
335 339 3.790437 AGATGGCCACAGCTCCGG 61.790 66.667 8.16 0.00 39.62 5.14
340 344 4.512914 GGGGGAGATGGCCACAGC 62.513 72.222 8.16 0.00 38.76 4.40
341 345 4.181010 CGGGGGAGATGGCCACAG 62.181 72.222 8.16 0.00 31.00 3.66
379 398 1.074319 GCTCCATGCATGCAACAACG 61.074 55.000 26.68 13.12 42.31 4.10
419 438 4.996434 CCATCGATGGCCGCCCTC 62.996 72.222 30.53 5.71 41.75 4.30
428 447 0.866061 GTCGTCGGTCACCATCGATG 60.866 60.000 18.76 18.76 41.96 3.84
429 448 1.432251 GTCGTCGGTCACCATCGAT 59.568 57.895 12.48 0.00 37.73 3.59
430 449 2.872557 GTCGTCGGTCACCATCGA 59.127 61.111 6.29 6.29 0.00 3.59
431 450 2.576053 CGTCGTCGGTCACCATCG 60.576 66.667 0.00 0.00 0.00 3.84
432 451 1.226323 CTCGTCGTCGGTCACCATC 60.226 63.158 1.55 0.00 37.69 3.51
433 452 2.697761 CCTCGTCGTCGGTCACCAT 61.698 63.158 1.55 0.00 37.69 3.55
434 453 3.359523 CCTCGTCGTCGGTCACCA 61.360 66.667 1.55 0.00 37.69 4.17
435 454 4.112341 CCCTCGTCGTCGGTCACC 62.112 72.222 1.55 0.00 37.69 4.02
436 455 4.773117 GCCCTCGTCGTCGGTCAC 62.773 72.222 1.55 0.00 37.69 3.67
582 611 2.632377 TCCAAATAAAGCGCAGAGGAG 58.368 47.619 11.47 0.00 0.00 3.69
606 649 1.598130 CCGGATCCCCAATCGCTTC 60.598 63.158 6.06 0.00 34.99 3.86
615 658 0.397564 TATTTAACCGCCGGATCCCC 59.602 55.000 11.71 0.00 0.00 4.81
622 665 9.537848 GTTTGATTAGATTATATTTAACCGCCG 57.462 33.333 0.00 0.00 0.00 6.46
624 667 9.537848 CCGTTTGATTAGATTATATTTAACCGC 57.462 33.333 0.00 0.00 0.00 5.68
662 705 1.153862 GCGCAATCAATTTGGCCGA 60.154 52.632 0.30 0.00 35.75 5.54
668 711 1.445926 GCACCGGCGCAATCAATTT 60.446 52.632 10.19 0.00 0.00 1.82
698 741 6.035758 CCAAGATTGTACTAAAAGGCGACTAC 59.964 42.308 0.00 0.00 42.68 2.73
731 774 4.041723 CGTTCACCGCTGAAAGAATTTTT 58.958 39.130 0.66 0.00 39.27 1.94
732 775 3.550030 CCGTTCACCGCTGAAAGAATTTT 60.550 43.478 7.82 0.00 37.92 1.82
733 776 2.031157 CCGTTCACCGCTGAAAGAATTT 60.031 45.455 7.82 0.00 37.92 1.82
734 777 1.535462 CCGTTCACCGCTGAAAGAATT 59.465 47.619 7.82 0.00 37.92 2.17
735 778 1.156736 CCGTTCACCGCTGAAAGAAT 58.843 50.000 7.82 0.00 37.92 2.40
736 779 0.105224 TCCGTTCACCGCTGAAAGAA 59.895 50.000 7.82 0.00 37.92 2.52
737 780 0.320374 ATCCGTTCACCGCTGAAAGA 59.680 50.000 7.82 3.08 37.92 2.52
738 781 0.443869 CATCCGTTCACCGCTGAAAG 59.556 55.000 0.00 0.00 38.17 2.62
739 782 0.034198 TCATCCGTTCACCGCTGAAA 59.966 50.000 0.00 0.00 38.17 2.69
740 783 0.034198 TTCATCCGTTCACCGCTGAA 59.966 50.000 0.00 0.00 35.60 3.02
741 784 0.034198 TTTCATCCGTTCACCGCTGA 59.966 50.000 0.00 0.00 34.38 4.26
742 785 0.871722 TTTTCATCCGTTCACCGCTG 59.128 50.000 0.00 0.00 34.38 5.18
743 786 1.600023 TTTTTCATCCGTTCACCGCT 58.400 45.000 0.00 0.00 34.38 5.52
844 887 9.016623 GCAAAACCGTGATTAATTATAAGGAAC 57.983 33.333 6.43 0.00 0.00 3.62
845 888 8.740906 TGCAAAACCGTGATTAATTATAAGGAA 58.259 29.630 6.43 0.00 0.00 3.36
846 889 8.185505 GTGCAAAACCGTGATTAATTATAAGGA 58.814 33.333 0.00 0.00 0.00 3.36
847 890 7.971168 TGTGCAAAACCGTGATTAATTATAAGG 59.029 33.333 0.00 0.00 0.00 2.69
848 891 8.903570 TGTGCAAAACCGTGATTAATTATAAG 57.096 30.769 0.00 0.00 0.00 1.73
849 892 9.692749 TTTGTGCAAAACCGTGATTAATTATAA 57.307 25.926 0.00 0.00 0.00 0.98
850 893 9.347934 CTTTGTGCAAAACCGTGATTAATTATA 57.652 29.630 0.00 0.00 0.00 0.98
851 894 7.148656 GCTTTGTGCAAAACCGTGATTAATTAT 60.149 33.333 0.00 0.00 42.31 1.28
852 895 6.144724 GCTTTGTGCAAAACCGTGATTAATTA 59.855 34.615 0.00 0.00 42.31 1.40
853 896 5.050431 GCTTTGTGCAAAACCGTGATTAATT 60.050 36.000 0.00 0.00 42.31 1.40
854 897 4.447389 GCTTTGTGCAAAACCGTGATTAAT 59.553 37.500 0.00 0.00 42.31 1.40
874 917 3.760035 ACTCGGATCCACGCGCTT 61.760 61.111 13.41 0.00 0.00 4.68
879 922 0.179161 GAGTCACACTCGGATCCACG 60.179 60.000 13.41 4.01 35.28 4.94
880 923 3.723554 GAGTCACACTCGGATCCAC 57.276 57.895 13.41 0.00 35.28 4.02
898 950 2.912542 TCGGGCTCGGGCTATCTG 60.913 66.667 7.48 0.00 38.73 2.90
926 978 4.726825 TCCTCCTTATATTGGTTTGAGCCT 59.273 41.667 0.00 0.00 0.00 4.58
958 1015 2.099098 CGATTTTCGATTTTGGGGAGGG 59.901 50.000 0.00 0.00 43.74 4.30
1091 1152 0.613777 ACTCCTCGCCGGAAAAAGAT 59.386 50.000 5.05 0.00 42.53 2.40
1636 1717 5.163733 GCTAGATCCCTCGTAATGCTAGTAC 60.164 48.000 0.00 0.00 0.00 2.73
1643 1743 4.156922 CACCTAGCTAGATCCCTCGTAATG 59.843 50.000 22.70 2.95 0.00 1.90
1648 1748 2.279935 ACACCTAGCTAGATCCCTCG 57.720 55.000 22.70 5.87 0.00 4.63
1832 1948 7.129504 AGGGTTGATAAATCAGAGGTAATTCCT 59.870 37.037 0.00 0.00 40.00 3.36
1981 2102 2.334946 CCTTACCGACGGACGACCA 61.335 63.158 23.38 0.00 45.77 4.02
1982 2103 1.024579 TACCTTACCGACGGACGACC 61.025 60.000 23.38 0.00 45.77 4.79
1983 2104 0.097150 GTACCTTACCGACGGACGAC 59.903 60.000 23.38 5.68 45.77 4.34
1984 2105 1.358725 CGTACCTTACCGACGGACGA 61.359 60.000 23.38 1.92 45.77 4.20
1989 2110 0.947244 ATAGCCGTACCTTACCGACG 59.053 55.000 0.00 0.00 36.36 5.12
1993 2114 6.780457 TCCAATATATAGCCGTACCTTACC 57.220 41.667 0.00 0.00 0.00 2.85
2000 2121 6.014925 TCTGTTGCTTCCAATATATAGCCGTA 60.015 38.462 3.35 0.00 32.75 4.02
2001 2122 4.968259 TGTTGCTTCCAATATATAGCCGT 58.032 39.130 3.35 0.00 32.75 5.68
2003 2124 6.234177 ACTCTGTTGCTTCCAATATATAGCC 58.766 40.000 3.35 0.00 32.75 3.93
2015 2136 7.064016 CCTCTCTATTTTGTACTCTGTTGCTTC 59.936 40.741 0.00 0.00 0.00 3.86
2019 2140 6.533367 GCTCCTCTCTATTTTGTACTCTGTTG 59.467 42.308 0.00 0.00 0.00 3.33
2023 2144 6.665680 TGAAGCTCCTCTCTATTTTGTACTCT 59.334 38.462 0.00 0.00 0.00 3.24
2026 2147 6.635755 ACTGAAGCTCCTCTCTATTTTGTAC 58.364 40.000 0.00 0.00 0.00 2.90
2034 2155 4.269183 CTTCTGACTGAAGCTCCTCTCTA 58.731 47.826 8.90 0.00 44.62 2.43
2072 2193 3.269178 CAAGCAGAACTCTTCCATCTCC 58.731 50.000 0.00 0.00 0.00 3.71
2079 2200 1.221414 ACGTGCAAGCAGAACTCTTC 58.779 50.000 0.00 0.00 0.00 2.87
2110 2231 9.683069 CCTATTATAACAAGAAAATGACCATGC 57.317 33.333 0.00 0.00 0.00 4.06
2141 2262 3.199946 TGAAAACAGGAGGACACAACTCT 59.800 43.478 0.00 0.00 35.34 3.24
2258 2400 4.602340 ACAGGACACTAACAAGGTACAG 57.398 45.455 0.00 0.00 0.00 2.74
2284 2426 6.198687 TCAACGCTGTCAGAAAAATTTACTG 58.801 36.000 3.32 15.00 0.00 2.74
2294 2436 1.812235 ATGCATCAACGCTGTCAGAA 58.188 45.000 3.32 0.00 0.00 3.02
2342 2484 5.048504 GTCCTCAAAAGAGACAAATGCATCA 60.049 40.000 0.00 0.00 0.00 3.07
2576 2721 1.074566 CTCTTGCCTCTTTTCCAGGGT 59.925 52.381 0.00 0.00 0.00 4.34
2579 2724 4.023365 CAGAAACTCTTGCCTCTTTTCCAG 60.023 45.833 0.00 0.00 0.00 3.86
2585 2730 3.117888 TGGAACAGAAACTCTTGCCTCTT 60.118 43.478 0.00 0.00 0.00 2.85
2586 2731 2.439507 TGGAACAGAAACTCTTGCCTCT 59.560 45.455 0.00 0.00 0.00 3.69
2595 2740 4.965200 ACTAGAGCTTGGAACAGAAACT 57.035 40.909 0.00 0.00 42.39 2.66
2629 2932 8.469309 CCAAAACTTGGTGATCTATTATCCAT 57.531 34.615 0.00 0.00 45.93 3.41
2647 2951 1.402787 CTGCACCCAGTTCCAAAACT 58.597 50.000 0.00 0.00 46.80 2.66
2648 2952 3.965780 CTGCACCCAGTTCCAAAAC 57.034 52.632 0.00 0.00 34.31 2.43
2680 2984 7.484140 AGGAAAAGAAGTGAATGTTCAACTTC 58.516 34.615 19.20 19.20 40.95 3.01
2689 2993 7.444629 TCTCATCAAGGAAAAGAAGTGAATG 57.555 36.000 0.00 0.00 0.00 2.67
2698 3002 6.538021 CAGAGGTACATCTCATCAAGGAAAAG 59.462 42.308 7.16 0.00 36.30 2.27
2708 3012 5.215069 ACCAGATTCAGAGGTACATCTCAT 58.785 41.667 7.16 2.73 36.30 2.90
2715 3019 2.365941 GCCCTACCAGATTCAGAGGTAC 59.634 54.545 0.00 0.00 36.87 3.34
2722 3026 1.264749 ACAGCGCCCTACCAGATTCA 61.265 55.000 2.29 0.00 0.00 2.57
2723 3027 0.530870 GACAGCGCCCTACCAGATTC 60.531 60.000 2.29 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.