Multiple sequence alignment - TraesCS6B01G062300

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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 TraesCS6B01G062300 chr6B 100.000 2879 0 0 1 2879 41523359 41520481 0 5317
1 TraesCS6B01G062300 chr6B 80.435 1104 198 16 785 1876 680086448 680087545 0 826
2 TraesCS6B01G062300 chr7A 89.318 2097 212 8 789 2879 98782607 98780517 0 2621
3 TraesCS6B01G062300 chr7A 78.470 1556 298 33 789 2326 26480501 26482037 0 983
4 TraesCS6B01G062300 chr3B 88.650 2097 229 9 790 2879 737453439 737451345 0 2545
5 TraesCS6B01G062300 chr3B 88.356 2087 232 10 800 2879 22641290 22643372 0 2497
6 TraesCS6B01G062300 chr3B 88.816 1994 214 9 893 2879 737488656 737486665 0 2438
7 TraesCS6B01G062300 chr7B 95.489 1574 69 2 1308 2879 686916541 686914968 0 2512
8 TraesCS6B01G062300 chr7B 93.696 698 43 1 96 793 125853924 125854620 0 1044
9 TraesCS6B01G062300 chr1B 87.738 2104 230 19 789 2879 139476613 139474525 0 2431
10 TraesCS6B01G062300 chr1B 79.162 1838 341 36 789 2598 624984058 624985881 0 1234
11 TraesCS6B01G062300 chr2D 82.272 1822 295 17 1073 2879 106125194 106127002 0 1550
12 TraesCS6B01G062300 chr2D 84.638 1380 196 15 1510 2879 447342427 447341054 0 1360
13 TraesCS6B01G062300 chr6D 79.943 2119 361 45 789 2879 5697382 5699464 0 1500
14 TraesCS6B01G062300 chr6D 94.009 701 41 1 93 793 63718937 63718238 0 1061
15 TraesCS6B01G062300 chr6D 93.857 700 40 2 94 793 418195573 418194877 0 1051
16 TraesCS6B01G062300 chr6D 93.939 693 37 3 94 786 367338155 367337468 0 1042
17 TraesCS6B01G062300 chr6D 93.795 693 42 1 94 786 139574896 139575587 0 1040
18 TraesCS6B01G062300 chr6D 93.786 692 42 1 95 786 471241148 471241838 0 1038
19 TraesCS6B01G062300 chr5B 78.555 2117 414 33 789 2879 9582151 9584253 0 1358
20 TraesCS6B01G062300 chr4D 94.143 700 39 2 94 793 10755999 10756696 0 1064
21 TraesCS6B01G062300 chr7D 93.571 700 41 3 94 793 458952278 458951583 0 1040
22 TraesCS6B01G062300 chr4B 93.220 708 43 3 90 793 585010491 585009785 0 1037
23 TraesCS6B01G062300 chr2B 79.318 1407 272 19 1075 2471 640697551 640696154 0 968
24 TraesCS6B01G062300 chr5A 80.752 1091 192 17 784 1864 638897319 638898401 0 835
25 TraesCS6B01G062300 chr5A 80.970 825 155 2 2056 2879 638898783 638899606 0 652
26 TraesCS6B01G062300 chr6A 84.375 832 123 7 797 1623 384332766 384333595 0 809


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 TraesCS6B01G062300 chr6B 41520481 41523359 2878 True 5317.0 5317 100.000 1 2879 1 chr6B.!!$R1 2878
1 TraesCS6B01G062300 chr6B 680086448 680087545 1097 False 826.0 826 80.435 785 1876 1 chr6B.!!$F1 1091
2 TraesCS6B01G062300 chr7A 98780517 98782607 2090 True 2621.0 2621 89.318 789 2879 1 chr7A.!!$R1 2090
3 TraesCS6B01G062300 chr7A 26480501 26482037 1536 False 983.0 983 78.470 789 2326 1 chr7A.!!$F1 1537
4 TraesCS6B01G062300 chr3B 737451345 737453439 2094 True 2545.0 2545 88.650 790 2879 1 chr3B.!!$R1 2089
5 TraesCS6B01G062300 chr3B 22641290 22643372 2082 False 2497.0 2497 88.356 800 2879 1 chr3B.!!$F1 2079
6 TraesCS6B01G062300 chr3B 737486665 737488656 1991 True 2438.0 2438 88.816 893 2879 1 chr3B.!!$R2 1986
7 TraesCS6B01G062300 chr7B 686914968 686916541 1573 True 2512.0 2512 95.489 1308 2879 1 chr7B.!!$R1 1571
8 TraesCS6B01G062300 chr7B 125853924 125854620 696 False 1044.0 1044 93.696 96 793 1 chr7B.!!$F1 697
9 TraesCS6B01G062300 chr1B 139474525 139476613 2088 True 2431.0 2431 87.738 789 2879 1 chr1B.!!$R1 2090
10 TraesCS6B01G062300 chr1B 624984058 624985881 1823 False 1234.0 1234 79.162 789 2598 1 chr1B.!!$F1 1809
11 TraesCS6B01G062300 chr2D 106125194 106127002 1808 False 1550.0 1550 82.272 1073 2879 1 chr2D.!!$F1 1806
12 TraesCS6B01G062300 chr2D 447341054 447342427 1373 True 1360.0 1360 84.638 1510 2879 1 chr2D.!!$R1 1369
13 TraesCS6B01G062300 chr6D 5697382 5699464 2082 False 1500.0 1500 79.943 789 2879 1 chr6D.!!$F1 2090
14 TraesCS6B01G062300 chr6D 63718238 63718937 699 True 1061.0 1061 94.009 93 793 1 chr6D.!!$R1 700
15 TraesCS6B01G062300 chr6D 418194877 418195573 696 True 1051.0 1051 93.857 94 793 1 chr6D.!!$R3 699
16 TraesCS6B01G062300 chr6D 367337468 367338155 687 True 1042.0 1042 93.939 94 786 1 chr6D.!!$R2 692
17 TraesCS6B01G062300 chr6D 139574896 139575587 691 False 1040.0 1040 93.795 94 786 1 chr6D.!!$F2 692
18 TraesCS6B01G062300 chr6D 471241148 471241838 690 False 1038.0 1038 93.786 95 786 1 chr6D.!!$F3 691
19 TraesCS6B01G062300 chr5B 9582151 9584253 2102 False 1358.0 1358 78.555 789 2879 1 chr5B.!!$F1 2090
20 TraesCS6B01G062300 chr4D 10755999 10756696 697 False 1064.0 1064 94.143 94 793 1 chr4D.!!$F1 699
21 TraesCS6B01G062300 chr7D 458951583 458952278 695 True 1040.0 1040 93.571 94 793 1 chr7D.!!$R1 699
22 TraesCS6B01G062300 chr4B 585009785 585010491 706 True 1037.0 1037 93.220 90 793 1 chr4B.!!$R1 703
23 TraesCS6B01G062300 chr2B 640696154 640697551 1397 True 968.0 968 79.318 1075 2471 1 chr2B.!!$R1 1396
24 TraesCS6B01G062300 chr5A 638897319 638899606 2287 False 743.5 835 80.861 784 2879 2 chr5A.!!$F1 2095
25 TraesCS6B01G062300 chr6A 384332766 384333595 829 False 809.0 809 84.375 797 1623 1 chr6A.!!$F1 826

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
51 52 0.031178 AGAAGCAGCCAAGCAAAACG 59.969 50.0 0.00 0.00 36.85 3.60 F
431 444 0.034767 AGCTGCATGTAGCCACACAT 60.035 50.0 29.19 9.51 44.76 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1566 0.546267 AGCCAGCTCCTTCTTCCTCA 60.546 55.0 0.0 0.0 0.0 3.86 R
1917 2132 0.616111 CACACCTCTAGCTCCACCCT 60.616 60.0 0.0 0.0 0.0 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
34 35 9.391006 ACAATATTTTCCTCGTAATTTAGCAGA 57.609 29.630 0.00 0.00 0.00 4.26
37 38 5.796350 TTTCCTCGTAATTTAGCAGAAGC 57.204 39.130 0.00 0.00 42.56 3.86
38 39 4.465632 TCCTCGTAATTTAGCAGAAGCA 57.534 40.909 0.00 0.00 45.49 3.91
39 40 4.433615 TCCTCGTAATTTAGCAGAAGCAG 58.566 43.478 0.00 0.00 45.49 4.24
40 41 3.001736 CCTCGTAATTTAGCAGAAGCAGC 59.998 47.826 0.00 0.00 45.49 5.25
41 42 2.936498 TCGTAATTTAGCAGAAGCAGCC 59.064 45.455 0.00 0.00 45.49 4.85
42 43 2.677836 CGTAATTTAGCAGAAGCAGCCA 59.322 45.455 0.00 0.00 45.49 4.75
43 44 3.126858 CGTAATTTAGCAGAAGCAGCCAA 59.873 43.478 0.00 0.00 45.49 4.52
44 45 3.863142 AATTTAGCAGAAGCAGCCAAG 57.137 42.857 0.00 0.00 45.49 3.61
45 46 0.883833 TTTAGCAGAAGCAGCCAAGC 59.116 50.000 0.00 0.00 45.49 4.01
46 47 0.250858 TTAGCAGAAGCAGCCAAGCA 60.251 50.000 0.00 0.00 45.49 3.91
47 48 0.250858 TAGCAGAAGCAGCCAAGCAA 60.251 50.000 0.00 0.00 45.49 3.91
48 49 1.111116 AGCAGAAGCAGCCAAGCAAA 61.111 50.000 0.00 0.00 45.49 3.68
49 50 0.249573 GCAGAAGCAGCCAAGCAAAA 60.250 50.000 0.00 0.00 41.58 2.44
50 51 1.494824 CAGAAGCAGCCAAGCAAAAC 58.505 50.000 0.00 0.00 36.85 2.43
51 52 0.031178 AGAAGCAGCCAAGCAAAACG 59.969 50.000 0.00 0.00 36.85 3.60
52 53 0.940991 GAAGCAGCCAAGCAAAACGG 60.941 55.000 0.00 0.00 36.85 4.44
53 54 1.391157 AAGCAGCCAAGCAAAACGGA 61.391 50.000 0.00 0.00 36.85 4.69
54 55 1.181098 AGCAGCCAAGCAAAACGGAT 61.181 50.000 0.00 0.00 36.85 4.18
55 56 0.525761 GCAGCCAAGCAAAACGGATA 59.474 50.000 0.00 0.00 0.00 2.59
56 57 1.468054 GCAGCCAAGCAAAACGGATAG 60.468 52.381 0.00 0.00 0.00 2.08
57 58 1.812571 CAGCCAAGCAAAACGGATAGT 59.187 47.619 0.00 0.00 0.00 2.12
58 59 2.084546 AGCCAAGCAAAACGGATAGTC 58.915 47.619 0.00 0.00 0.00 2.59
59 60 1.810151 GCCAAGCAAAACGGATAGTCA 59.190 47.619 0.00 0.00 0.00 3.41
60 61 2.414161 GCCAAGCAAAACGGATAGTCAC 60.414 50.000 0.00 0.00 0.00 3.67
61 62 2.159707 CCAAGCAAAACGGATAGTCACG 60.160 50.000 0.00 0.00 0.00 4.35
62 63 2.450609 AGCAAAACGGATAGTCACGT 57.549 45.000 0.00 0.00 46.48 4.49
63 64 2.334838 AGCAAAACGGATAGTCACGTC 58.665 47.619 0.00 0.00 43.31 4.34
64 65 2.029290 AGCAAAACGGATAGTCACGTCT 60.029 45.455 0.00 0.00 43.31 4.18
65 66 2.092211 GCAAAACGGATAGTCACGTCTG 59.908 50.000 0.00 0.00 43.31 3.51
66 67 3.571571 CAAAACGGATAGTCACGTCTGA 58.428 45.455 0.00 0.00 43.31 3.27
67 68 2.915738 AACGGATAGTCACGTCTGAC 57.084 50.000 0.00 0.00 46.50 3.51
78 79 5.659048 GTCACGTCTGACTTGAAGAAATT 57.341 39.130 17.19 0.00 43.26 1.82
79 80 5.671074 GTCACGTCTGACTTGAAGAAATTC 58.329 41.667 17.19 1.63 43.26 2.17
80 81 5.463724 GTCACGTCTGACTTGAAGAAATTCT 59.536 40.000 17.19 0.00 43.26 2.40
81 82 6.641314 GTCACGTCTGACTTGAAGAAATTCTA 59.359 38.462 17.19 0.00 43.26 2.10
82 83 6.641314 TCACGTCTGACTTGAAGAAATTCTAC 59.359 38.462 13.79 0.00 0.00 2.59
83 84 5.629849 ACGTCTGACTTGAAGAAATTCTACG 59.370 40.000 6.21 1.88 35.58 3.51
84 85 5.061064 CGTCTGACTTGAAGAAATTCTACGG 59.939 44.000 6.21 0.00 30.86 4.02
85 86 5.348997 GTCTGACTTGAAGAAATTCTACGGG 59.651 44.000 0.00 0.00 0.00 5.28
86 87 4.000988 TGACTTGAAGAAATTCTACGGGC 58.999 43.478 0.00 0.00 0.00 6.13
87 88 4.254492 GACTTGAAGAAATTCTACGGGCT 58.746 43.478 0.00 0.00 0.00 5.19
88 89 5.046878 TGACTTGAAGAAATTCTACGGGCTA 60.047 40.000 0.00 0.00 0.00 3.93
89 90 5.801380 ACTTGAAGAAATTCTACGGGCTAA 58.199 37.500 0.00 0.00 0.00 3.09
90 91 6.415573 ACTTGAAGAAATTCTACGGGCTAAT 58.584 36.000 0.00 0.00 0.00 1.73
91 92 6.884836 ACTTGAAGAAATTCTACGGGCTAATT 59.115 34.615 0.00 0.00 0.00 1.40
110 111 6.866770 GCTAATTCTTACCGAAAAAGGCTTTT 59.133 34.615 19.14 19.14 37.46 2.27
157 158 1.490621 GCACAACAAGCATCCAACAC 58.509 50.000 0.00 0.00 0.00 3.32
171 172 1.468395 CCAACACGGTCCAACACAAAC 60.468 52.381 0.00 0.00 0.00 2.93
176 177 1.091537 CGGTCCAACACAAACACACT 58.908 50.000 0.00 0.00 0.00 3.55
187 200 3.081061 ACAAACACACTCACACACACAT 58.919 40.909 0.00 0.00 0.00 3.21
214 227 2.158871 TCCACAGGGACACAAAGTACAC 60.159 50.000 0.00 0.00 38.64 2.90
253 266 0.528249 GCACAACACAACAAGCCCTG 60.528 55.000 0.00 0.00 0.00 4.45
299 312 2.336809 CCCGGCGATCTAGTCAGC 59.663 66.667 9.30 0.00 0.00 4.26
402 415 4.733725 TCCTGGGGGCGGCTAAGT 62.734 66.667 9.56 0.00 0.00 2.24
419 432 2.282391 TGGCCGACAAAGCTGCAT 60.282 55.556 1.02 0.00 0.00 3.96
431 444 0.034767 AGCTGCATGTAGCCACACAT 60.035 50.000 29.19 9.51 44.76 3.21
462 475 3.733960 TCAGTCGCACGTCGGAGG 61.734 66.667 0.00 0.00 39.05 4.30
513 526 1.896660 GTTCCAAAGCGTCCAGGCA 60.897 57.895 0.00 0.00 34.64 4.75
525 538 1.152567 CCAGGCAAGAACCCCAACA 60.153 57.895 0.00 0.00 0.00 3.33
570 583 1.183549 GAGTAGGGGAAGCGTTGAGA 58.816 55.000 0.00 0.00 0.00 3.27
689 703 3.878778 AGATGTGGTTAGCATCCTCAAC 58.121 45.455 0.00 0.00 42.58 3.18
849 864 3.072468 CGCCGGAGTCCACCCTTA 61.072 66.667 5.05 0.00 0.00 2.69
883 899 2.483329 ATCACCTGGCCCTCTCCTGT 62.483 60.000 0.00 0.00 0.00 4.00
885 901 3.086600 CCTGGCCCTCTCCTGTCC 61.087 72.222 0.00 0.00 0.00 4.02
907 923 1.686587 TCGACATGCGTAGGGATCAAT 59.313 47.619 8.91 0.00 41.80 2.57
1010 1031 3.494749 CCAGATGAGAAGATGAAGGGAGC 60.495 52.174 0.00 0.00 0.00 4.70
1040 1061 2.125106 GGCTGGTCCGTCATCCAC 60.125 66.667 0.00 0.00 0.00 4.02
1069 1090 2.375014 TCCGGACCATACTGCTGATA 57.625 50.000 0.00 0.00 0.00 2.15
1070 1091 1.961394 TCCGGACCATACTGCTGATAC 59.039 52.381 0.00 0.00 0.00 2.24
1095 1116 2.835895 GAGGAGGAGGAGGCGGAC 60.836 72.222 0.00 0.00 0.00 4.79
1131 1152 5.960811 GGATGATGAGGAGTGGGATAATCTA 59.039 44.000 0.00 0.00 0.00 1.98
1224 1246 3.784178 TCTGTCAGGAGAAGTGGAAGAT 58.216 45.455 0.00 0.00 0.00 2.40
1316 1338 5.352569 CGTTGCTAAATTCTCTGAGGAATGT 59.647 40.000 4.59 2.03 36.24 2.71
1327 1349 0.602638 GAGGAATGTGTGGTCGTGCA 60.603 55.000 0.00 0.00 0.00 4.57
1341 1363 1.218875 CGTGCACGCAAGGAGTTACA 61.219 55.000 28.16 0.00 46.39 2.41
1447 1469 2.438021 CAATTTAGGAGGGATCCGGTCA 59.562 50.000 5.45 0.00 34.28 4.02
1527 1549 5.908831 TCCACTATGGGCTAGAATTAAAGGA 59.091 40.000 0.00 0.00 38.32 3.36
1529 1551 5.998363 CACTATGGGCTAGAATTAAAGGACC 59.002 44.000 0.00 0.00 0.00 4.46
1830 1855 1.567357 TCCATCGGAGTGTGATTGGA 58.433 50.000 0.00 0.00 0.00 3.53
1833 1858 0.179000 ATCGGAGTGTGATTGGAGGC 59.821 55.000 0.00 0.00 0.00 4.70
1987 2202 6.081356 AGGAGTAGGAAATAGAGGGAGATTG 58.919 44.000 0.00 0.00 0.00 2.67
2209 2428 1.965414 TGGAGGGAGGTAATGCTTCA 58.035 50.000 0.00 0.00 0.00 3.02
2214 2433 3.118531 AGGGAGGTAATGCTTCAGATGT 58.881 45.455 0.00 0.00 0.00 3.06
2498 2717 1.757118 GATGAGAAGGATCCGTGGTCA 59.243 52.381 4.38 8.30 0.00 4.02
2558 2777 1.620822 ATGAGTGGTGGTTTGGCTTC 58.379 50.000 0.00 0.00 0.00 3.86
2584 2803 1.409064 GGCATGAGTCGTATGAGGTGA 59.591 52.381 0.00 0.00 0.00 4.02
2606 2825 9.525826 GGTGAAGATTTTGGATAAGGATGATAT 57.474 33.333 0.00 0.00 0.00 1.63
2718 2937 5.707298 GCATATTATGTGGGACAAGCTACAT 59.293 40.000 5.60 3.23 44.16 2.29
2781 3000 3.058293 GTGATTTCAATGAGGCGTTGTGA 60.058 43.478 0.00 0.00 32.76 3.58
2812 3031 3.680475 GCATTTGTCATCTACACCCCGTA 60.680 47.826 0.00 0.00 38.00 4.02
2862 3081 2.665165 ACTCTAGAGATCTGTGGGCTG 58.335 52.381 26.57 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.391006 TCTGCTAAATTACGAGGAAAATATTGT 57.609 29.630 0.00 0.00 0.00 2.71
11 12 8.560374 GCTTCTGCTAAATTACGAGGAAAATAT 58.440 33.333 0.00 0.00 36.03 1.28
12 13 7.551262 TGCTTCTGCTAAATTACGAGGAAAATA 59.449 33.333 0.00 0.00 40.48 1.40
13 14 6.374333 TGCTTCTGCTAAATTACGAGGAAAAT 59.626 34.615 0.00 0.00 40.48 1.82
14 15 5.703592 TGCTTCTGCTAAATTACGAGGAAAA 59.296 36.000 0.00 0.00 40.48 2.29
15 16 5.242434 TGCTTCTGCTAAATTACGAGGAAA 58.758 37.500 0.00 0.00 40.48 3.13
16 17 4.827692 TGCTTCTGCTAAATTACGAGGAA 58.172 39.130 0.00 0.00 40.48 3.36
17 18 4.433615 CTGCTTCTGCTAAATTACGAGGA 58.566 43.478 0.00 0.00 40.48 3.71
18 19 3.001736 GCTGCTTCTGCTAAATTACGAGG 59.998 47.826 0.00 0.00 40.48 4.63
19 20 3.001736 GGCTGCTTCTGCTAAATTACGAG 59.998 47.826 0.00 0.00 40.48 4.18
20 21 2.936498 GGCTGCTTCTGCTAAATTACGA 59.064 45.455 0.00 0.00 40.48 3.43
21 22 2.677836 TGGCTGCTTCTGCTAAATTACG 59.322 45.455 0.00 0.00 40.48 3.18
22 23 4.666237 CTTGGCTGCTTCTGCTAAATTAC 58.334 43.478 0.00 0.00 40.48 1.89
23 24 3.129287 GCTTGGCTGCTTCTGCTAAATTA 59.871 43.478 0.00 0.00 40.48 1.40
24 25 2.094338 GCTTGGCTGCTTCTGCTAAATT 60.094 45.455 0.00 0.00 40.48 1.82
25 26 1.475682 GCTTGGCTGCTTCTGCTAAAT 59.524 47.619 0.00 0.00 40.48 1.40
26 27 0.883833 GCTTGGCTGCTTCTGCTAAA 59.116 50.000 0.00 0.00 40.48 1.85
27 28 0.250858 TGCTTGGCTGCTTCTGCTAA 60.251 50.000 0.00 0.00 40.48 3.09
28 29 0.250858 TTGCTTGGCTGCTTCTGCTA 60.251 50.000 0.00 0.00 40.48 3.49
29 30 1.111116 TTTGCTTGGCTGCTTCTGCT 61.111 50.000 0.00 0.00 40.48 4.24
30 31 0.249573 TTTTGCTTGGCTGCTTCTGC 60.250 50.000 0.00 0.19 40.20 4.26
31 32 1.494824 GTTTTGCTTGGCTGCTTCTG 58.505 50.000 0.00 0.00 0.00 3.02
32 33 0.031178 CGTTTTGCTTGGCTGCTTCT 59.969 50.000 0.00 0.00 0.00 2.85
33 34 0.940991 CCGTTTTGCTTGGCTGCTTC 60.941 55.000 0.00 0.00 0.00 3.86
34 35 1.067916 CCGTTTTGCTTGGCTGCTT 59.932 52.632 0.00 0.00 0.00 3.91
35 36 1.181098 ATCCGTTTTGCTTGGCTGCT 61.181 50.000 0.00 0.00 0.00 4.24
36 37 0.525761 TATCCGTTTTGCTTGGCTGC 59.474 50.000 0.00 0.00 0.00 5.25
37 38 1.812571 ACTATCCGTTTTGCTTGGCTG 59.187 47.619 0.00 0.00 0.00 4.85
38 39 2.084546 GACTATCCGTTTTGCTTGGCT 58.915 47.619 0.00 0.00 0.00 4.75
39 40 1.810151 TGACTATCCGTTTTGCTTGGC 59.190 47.619 0.00 0.00 0.00 4.52
40 41 2.159707 CGTGACTATCCGTTTTGCTTGG 60.160 50.000 0.00 0.00 0.00 3.61
41 42 2.478894 ACGTGACTATCCGTTTTGCTTG 59.521 45.455 0.00 0.00 32.50 4.01
42 43 2.735134 GACGTGACTATCCGTTTTGCTT 59.265 45.455 0.00 0.00 37.44 3.91
43 44 2.029290 AGACGTGACTATCCGTTTTGCT 60.029 45.455 0.00 0.00 37.44 3.91
44 45 2.092211 CAGACGTGACTATCCGTTTTGC 59.908 50.000 0.00 0.00 37.44 3.68
45 46 3.571571 TCAGACGTGACTATCCGTTTTG 58.428 45.455 0.00 0.00 37.44 2.44
46 47 3.928727 TCAGACGTGACTATCCGTTTT 57.071 42.857 0.00 0.00 37.44 2.43
56 57 5.463724 AGAATTTCTTCAAGTCAGACGTGAC 59.536 40.000 17.69 2.33 42.41 3.67
57 58 5.601662 AGAATTTCTTCAAGTCAGACGTGA 58.398 37.500 14.50 14.50 34.91 4.35
58 59 5.914085 AGAATTTCTTCAAGTCAGACGTG 57.086 39.130 10.04 10.04 31.46 4.49
59 60 5.629849 CGTAGAATTTCTTCAAGTCAGACGT 59.370 40.000 3.86 0.00 36.81 4.34
60 61 5.061064 CCGTAGAATTTCTTCAAGTCAGACG 59.939 44.000 3.86 5.10 39.18 4.18
61 62 5.348997 CCCGTAGAATTTCTTCAAGTCAGAC 59.651 44.000 3.86 0.00 31.46 3.51
62 63 5.479306 CCCGTAGAATTTCTTCAAGTCAGA 58.521 41.667 3.86 0.00 31.46 3.27
63 64 4.093556 GCCCGTAGAATTTCTTCAAGTCAG 59.906 45.833 3.86 0.00 31.46 3.51
64 65 4.000988 GCCCGTAGAATTTCTTCAAGTCA 58.999 43.478 3.86 0.00 31.46 3.41
65 66 4.254492 AGCCCGTAGAATTTCTTCAAGTC 58.746 43.478 3.86 0.00 33.56 3.01
66 67 4.287766 AGCCCGTAGAATTTCTTCAAGT 57.712 40.909 3.86 0.00 33.56 3.16
67 68 6.927294 ATTAGCCCGTAGAATTTCTTCAAG 57.073 37.500 3.86 0.00 33.56 3.02
68 69 7.110155 AGAATTAGCCCGTAGAATTTCTTCAA 58.890 34.615 3.86 0.00 33.56 2.69
69 70 6.650120 AGAATTAGCCCGTAGAATTTCTTCA 58.350 36.000 3.86 0.00 33.56 3.02
70 71 7.555306 AAGAATTAGCCCGTAGAATTTCTTC 57.445 36.000 3.86 0.00 0.00 2.87
71 72 7.498239 GGTAAGAATTAGCCCGTAGAATTTCTT 59.502 37.037 3.86 0.00 42.92 2.52
72 73 6.990939 GGTAAGAATTAGCCCGTAGAATTTCT 59.009 38.462 4.03 4.03 42.92 2.52
73 74 6.073927 CGGTAAGAATTAGCCCGTAGAATTTC 60.074 42.308 0.00 0.00 45.75 2.17
74 75 5.756833 CGGTAAGAATTAGCCCGTAGAATTT 59.243 40.000 0.00 0.00 45.75 1.82
75 76 5.069516 TCGGTAAGAATTAGCCCGTAGAATT 59.930 40.000 0.00 0.00 45.75 2.17
76 77 4.586001 TCGGTAAGAATTAGCCCGTAGAAT 59.414 41.667 0.00 0.00 45.75 2.40
77 78 3.953612 TCGGTAAGAATTAGCCCGTAGAA 59.046 43.478 0.00 0.00 45.75 2.10
78 79 3.554934 TCGGTAAGAATTAGCCCGTAGA 58.445 45.455 0.00 0.00 45.75 2.59
79 80 3.996150 TCGGTAAGAATTAGCCCGTAG 57.004 47.619 0.00 0.00 45.75 3.51
80 81 4.734398 TTTCGGTAAGAATTAGCCCGTA 57.266 40.909 0.00 0.00 45.75 4.02
81 82 3.615224 TTTCGGTAAGAATTAGCCCGT 57.385 42.857 0.00 0.00 45.75 5.28
82 83 4.201881 CCTTTTTCGGTAAGAATTAGCCCG 60.202 45.833 0.00 0.00 45.75 6.13
83 84 4.439700 GCCTTTTTCGGTAAGAATTAGCCC 60.440 45.833 0.00 0.00 45.75 5.19
84 85 4.398358 AGCCTTTTTCGGTAAGAATTAGCC 59.602 41.667 0.00 0.00 45.75 3.93
85 86 5.562506 AGCCTTTTTCGGTAAGAATTAGC 57.437 39.130 0.00 0.00 45.10 3.09
86 87 7.148804 GCAAAAGCCTTTTTCGGTAAGAATTAG 60.149 37.037 0.00 0.00 38.86 1.73
87 88 6.643360 GCAAAAGCCTTTTTCGGTAAGAATTA 59.357 34.615 0.00 0.00 38.86 1.40
88 89 5.465390 GCAAAAGCCTTTTTCGGTAAGAATT 59.535 36.000 0.00 0.00 38.86 2.17
89 90 4.988540 GCAAAAGCCTTTTTCGGTAAGAAT 59.011 37.500 0.00 0.00 38.86 2.40
90 91 4.364860 GCAAAAGCCTTTTTCGGTAAGAA 58.635 39.130 0.00 0.00 34.34 2.52
91 92 3.243602 GGCAAAAGCCTTTTTCGGTAAGA 60.244 43.478 0.00 0.00 34.34 2.10
110 111 5.890424 GCTTTATAATATAAAGCGGGGCA 57.110 39.130 30.20 0.66 46.31 5.36
157 158 1.063469 GAGTGTGTTTGTGTTGGACCG 59.937 52.381 0.00 0.00 0.00 4.79
171 172 1.952193 TCCATGTGTGTGTGAGTGTG 58.048 50.000 0.00 0.00 0.00 3.82
176 177 1.488393 TGGACTTCCATGTGTGTGTGA 59.512 47.619 0.00 0.00 42.01 3.58
201 214 3.200483 ACCCTTTCGTGTACTTTGTGTC 58.800 45.455 0.00 0.00 0.00 3.67
205 218 4.783242 CATTGACCCTTTCGTGTACTTTG 58.217 43.478 0.00 0.00 0.00 2.77
214 227 1.089920 CCTCAGCATTGACCCTTTCG 58.910 55.000 0.00 0.00 0.00 3.46
253 266 0.526739 GGCGTGTGTGTTTTGGGTTC 60.527 55.000 0.00 0.00 0.00 3.62
284 297 1.284408 GAGGCTGACTAGATCGCCG 59.716 63.158 0.00 0.00 45.83 6.46
289 302 1.786937 CCACCTGAGGCTGACTAGAT 58.213 55.000 0.00 0.00 0.00 1.98
402 415 2.282391 ATGCAGCTTTGTCGGCCA 60.282 55.556 2.24 0.00 0.00 5.36
408 421 0.883833 GTGGCTACATGCAGCTTTGT 59.116 50.000 17.34 6.76 45.15 2.83
419 432 5.771469 CAATCTTCAAAATGTGTGGCTACA 58.229 37.500 0.00 0.00 34.63 2.74
431 444 3.519908 CGACTGACGCAATCTTCAAAA 57.480 42.857 0.00 0.00 34.51 2.44
462 475 2.164422 GCTTGTTATTCAGAAGGTGCCC 59.836 50.000 0.00 0.00 0.00 5.36
513 526 1.272760 TGGTTGTGTGTTGGGGTTCTT 60.273 47.619 0.00 0.00 0.00 2.52
525 538 3.118038 ACCGCCATATTAGATGGTTGTGT 60.118 43.478 7.74 0.00 41.17 3.72
570 583 4.473520 CCCGACCTGCTTGCCGAT 62.474 66.667 0.00 0.00 0.00 4.18
849 864 1.541379 GTGATTGGCGGTAGGGTTTT 58.459 50.000 0.00 0.00 0.00 2.43
883 899 0.753848 TCCCTACGCATGTCGATGGA 60.754 55.000 14.88 13.02 41.67 3.41
885 901 1.000274 TGATCCCTACGCATGTCGATG 60.000 52.381 14.88 7.65 41.67 3.84
907 923 0.684535 TCCATCGTGTCAGGCTTTGA 59.315 50.000 0.00 0.00 0.00 2.69
1069 1090 2.641746 CCTCCTCCTCCCTCCCAGT 61.642 68.421 0.00 0.00 0.00 4.00
1070 1091 2.285180 CCTCCTCCTCCCTCCCAG 59.715 72.222 0.00 0.00 0.00 4.45
1095 1116 2.446848 ATCATCCTCCTGGCGGTGG 61.447 63.158 2.05 9.30 43.84 4.61
1131 1152 4.680537 AGGGCCGAGTCGTGACCT 62.681 66.667 19.29 19.29 32.34 3.85
1224 1246 3.945285 GCCATCGAACCTCCTTAATCAAA 59.055 43.478 0.00 0.00 0.00 2.69
1316 1338 3.268603 CTTGCGTGCACGACCACA 61.269 61.111 41.19 26.24 43.02 4.17
1327 1349 6.112734 TGATATTGAATGTAACTCCTTGCGT 58.887 36.000 0.00 0.00 0.00 5.24
1341 1363 7.763613 AGAGATTAGGCCCTTTGATATTGAAT 58.236 34.615 0.00 0.00 0.00 2.57
1447 1469 4.487714 ACCCATCGTACTCAACAATGAT 57.512 40.909 0.00 0.00 34.37 2.45
1544 1566 0.546267 AGCCAGCTCCTTCTTCCTCA 60.546 55.000 0.00 0.00 0.00 3.86
1917 2132 0.616111 CACACCTCTAGCTCCACCCT 60.616 60.000 0.00 0.00 0.00 4.34
1987 2202 3.122850 CCCTCCGAATGCATTGCC 58.877 61.111 18.59 1.94 0.00 4.52
2126 2345 1.296715 GCTGTCCCCGAACACTCAT 59.703 57.895 0.00 0.00 0.00 2.90
2209 2428 0.983378 GGCCTACCTCCACCACATCT 60.983 60.000 0.00 0.00 0.00 2.90
2214 2433 1.692749 GATGGGCCTACCTCCACCA 60.693 63.158 4.53 0.00 41.11 4.17
2498 2717 3.611025 TGAATCCCTTCAAACCAAGGT 57.389 42.857 0.00 0.00 41.48 3.50
2558 2777 1.854743 CATACGACTCATGCCAGAACG 59.145 52.381 0.00 0.00 0.00 3.95
2632 2851 0.606401 CATTGAGTTGCACCCTCCGT 60.606 55.000 9.48 0.00 0.00 4.69
2718 2937 6.106673 GGCATTACTTGTAGTCTTTAGCTGA 58.893 40.000 0.00 0.00 0.00 4.26
2781 3000 7.066284 GGTGTAGATGACAAATGCTCATAGTTT 59.934 37.037 0.00 0.00 40.66 2.66
2847 3066 1.270414 CCACCAGCCCACAGATCTCT 61.270 60.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.