Multiple sequence alignment - TraesCS3B01G114300

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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 TraesCS3B01G114300 chr3B 100.000 2216 0 0 1 2216 80198888 80201103 0.000000e+00 4093.0
1 TraesCS3B01G114300 chr3B 86.061 825 65 32 227 1044 59328723 59327942 0.000000e+00 841.0
2 TraesCS3B01G114300 chr3B 84.641 612 42 13 1060 1669 80657409 80657970 1.490000e-156 562.0
3 TraesCS3B01G114300 chr3B 84.264 394 32 17 657 1044 80656940 80657309 7.520000e-95 357.0
4 TraesCS3B01G114300 chr3B 84.278 388 33 9 1853 2216 59324442 59324059 9.730000e-94 353.0
5 TraesCS3B01G114300 chr3B 91.188 261 16 4 1958 2216 80658414 80658669 4.530000e-92 348.0
6 TraesCS3B01G114300 chr3B 86.154 325 30 7 1066 1388 59327854 59327543 9.800000e-89 337.0
7 TraesCS3B01G114300 chr3B 96.703 91 3 0 1526 1616 59327527 59327437 3.810000e-33 152.0
8 TraesCS3B01G114300 chr3D 91.454 1018 54 13 2 1005 50654794 50655792 0.000000e+00 1367.0
9 TraesCS3B01G114300 chr3D 91.181 669 25 7 1083 1744 50655828 50656469 0.000000e+00 878.0
10 TraesCS3B01G114300 chr3D 85.053 562 39 22 502 1044 36825119 36824584 4.190000e-147 531.0
11 TraesCS3B01G114300 chr3D 84.130 586 46 16 1060 1641 36824517 36823975 7.010000e-145 523.0
12 TraesCS3B01G114300 chr3D 89.272 261 22 5 1958 2216 36822934 36822678 2.740000e-84 322.0
13 TraesCS3B01G114300 chr3D 81.053 380 50 16 1843 2216 50657832 50658195 1.300000e-72 283.0
14 TraesCS3B01G114300 chr3D 77.852 447 64 21 103 532 134663354 134662926 6.110000e-61 244.0
15 TraesCS3B01G114300 chr3D 80.800 125 18 4 1622 1745 50657795 50657914 2.340000e-15 93.5
16 TraesCS3B01G114300 chr3D 97.143 35 1 0 1030 1064 50655792 50655826 2.380000e-05 60.2
17 TraesCS3B01G114300 chr3A 84.910 835 77 26 227 1044 47049018 47048216 0.000000e+00 798.0
18 TraesCS3B01G114300 chr3A 85.956 591 55 14 1060 1641 47048137 47047566 6.770000e-170 606.0
19 TraesCS3B01G114300 chr3A 81.193 436 46 10 1809 2216 47047114 47046687 3.550000e-83 318.0
20 TraesCS3B01G114300 chr1A 84.165 461 37 19 595 1044 552119700 552119265 4.400000e-112 414.0
21 TraesCS3B01G114300 chr1A 83.702 362 34 11 1066 1419 552119189 552118845 3.550000e-83 318.0
22 TraesCS3B01G114300 chr1D 84.951 412 28 14 1066 1455 460982401 460982002 9.600000e-104 387.0
23 TraesCS3B01G114300 chr1D 82.609 460 45 18 595 1044 460995944 460995510 7.470000e-100 374.0
24 TraesCS3B01G114300 chr1D 88.806 134 8 5 912 1044 460982610 460982483 8.190000e-35 158.0
25 TraesCS3B01G114300 chr1B 85.213 399 33 15 1066 1455 633260508 633260127 9.600000e-104 387.0
26 TraesCS3B01G114300 chr7A 82.254 417 45 20 635 1044 37937691 37938085 1.270000e-87 333.0
27 TraesCS3B01G114300 chr4A 80.145 413 57 16 635 1044 642186952 642186562 3.600000e-73 285.0
28 TraesCS3B01G114300 chr4A 98.052 154 3 0 2063 2216 572845562 572845715 3.630000e-68 268.0
29 TraesCS3B01G114300 chr4A 79.616 417 43 21 1065 1455 686573223 686573623 6.070000e-66 261.0
30 TraesCS3B01G114300 chr4A 83.453 278 36 6 1080 1352 642186466 642186194 1.310000e-62 250.0
31 TraesCS3B01G114300 chr4A 81.724 290 30 10 1065 1352 642903292 642903024 1.030000e-53 220.0
32 TraesCS3B01G114300 chr4A 81.655 278 22 18 772 1044 686578920 686579173 1.040000e-48 204.0
33 TraesCS3B01G114300 chr5A 78.079 479 72 19 106 565 553372658 553372194 2.800000e-69 272.0
34 TraesCS3B01G114300 chr5A 79.188 394 50 21 190 565 619695654 619696033 6.110000e-61 244.0
35 TraesCS3B01G114300 chr5A 78.680 394 53 20 190 565 285636073 285636453 1.320000e-57 233.0
36 TraesCS3B01G114300 chrUn 96.835 158 5 0 2059 2216 69444044 69444201 4.690000e-67 265.0
37 TraesCS3B01G114300 chr6A 96.835 158 5 0 2059 2216 21078255 21078412 4.690000e-67 265.0
38 TraesCS3B01G114300 chr6A 96.835 158 5 0 2059 2216 21137345 21137502 4.690000e-67 265.0
39 TraesCS3B01G114300 chr6A 82.482 137 19 2 1608 1744 72998956 72998825 5.000000e-22 115.0
40 TraesCS3B01G114300 chr6A 81.752 137 20 2 1608 1744 73017995 73017864 2.330000e-20 110.0
41 TraesCS3B01G114300 chr5D 77.096 489 66 19 106 564 438354836 438354364 7.910000e-60 241.0
42 TraesCS3B01G114300 chr7D 82.374 278 42 6 1080 1352 38204263 38204538 3.680000e-58 235.0
43 TraesCS3B01G114300 chr7D 76.360 478 78 21 103 564 476752595 476753053 7.960000e-55 224.0
44 TraesCS3B01G114300 chr7D 77.590 415 43 24 635 1044 38203792 38204161 2.880000e-49 206.0
45 TraesCS3B01G114300 chr7D 79.424 243 38 9 730 972 38006199 38005969 6.330000e-36 161.0
46 TraesCS3B01G114300 chr6D 85.088 228 18 6 1528 1743 27758119 27757896 3.700000e-53 219.0
47 TraesCS3B01G114300 chr4D 84.672 137 16 2 1608 1744 6775771 6775902 4.960000e-27 132.0
48 TraesCS3B01G114300 chr2B 91.228 57 5 0 1631 1687 247942417 247942473 6.560000e-11 78.7


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 TraesCS3B01G114300 chr3B 80198888 80201103 2215 False 4093.000000 4093 100.000000 1 2216 1 chr3B.!!$F1 2215
1 TraesCS3B01G114300 chr3B 80656940 80658669 1729 False 422.333333 562 86.697667 657 2216 3 chr3B.!!$F2 1559
2 TraesCS3B01G114300 chr3B 59324059 59328723 4664 True 420.750000 841 88.299000 227 2216 4 chr3B.!!$R1 1989
3 TraesCS3B01G114300 chr3D 50654794 50658195 3401 False 536.340000 1367 88.326200 2 2216 5 chr3D.!!$F1 2214
4 TraesCS3B01G114300 chr3D 36822678 36825119 2441 True 458.666667 531 86.151667 502 2216 3 chr3D.!!$R2 1714
5 TraesCS3B01G114300 chr3A 47046687 47049018 2331 True 574.000000 798 84.019667 227 2216 3 chr3A.!!$R1 1989
6 TraesCS3B01G114300 chr1A 552118845 552119700 855 True 366.000000 414 83.933500 595 1419 2 chr1A.!!$R1 824
7 TraesCS3B01G114300 chr1D 460982002 460982610 608 True 272.500000 387 86.878500 912 1455 2 chr1D.!!$R2 543
8 TraesCS3B01G114300 chr4A 642186194 642186952 758 True 267.500000 285 81.799000 635 1352 2 chr4A.!!$R2 717
9 TraesCS3B01G114300 chr7D 38203792 38204538 746 False 220.500000 235 79.982000 635 1352 2 chr7D.!!$F2 717

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
890 967 0.041576 GCAAGCAAGCAAAGCAAAGC 60.042 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 5593 0.034476 TGGCAGATCAGATCGATGGC 59.966 55.0 15.67 15.67 33.17 4.4 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
49 50 4.657436 AACCATAAAACACGAAAAGGCA 57.343 36.364 0.00 0.00 0.00 4.75
52 53 3.367630 CCATAAAACACGAAAAGGCATGC 59.632 43.478 9.90 9.90 0.00 4.06
59 60 2.727798 CACGAAAAGGCATGCAGAAAAG 59.272 45.455 21.36 8.84 0.00 2.27
61 62 2.030007 CGAAAAGGCATGCAGAAAAGGA 60.030 45.455 21.36 0.00 0.00 3.36
62 63 3.552684 CGAAAAGGCATGCAGAAAAGGAA 60.553 43.478 21.36 0.00 0.00 3.36
106 107 4.974468 GCCAACGCGTGACATATG 57.026 55.556 14.98 5.84 0.00 1.78
142 143 3.169908 TGTGTACTTGGATGTGAGCCTA 58.830 45.455 0.00 0.00 0.00 3.93
162 163 4.031765 CCTAAATGTTCATGTCTCGTGACG 59.968 45.833 12.54 0.00 45.70 4.35
185 186 6.073873 ACGTTGGCAAATTTGAATATTGTGTG 60.074 34.615 22.31 3.09 0.00 3.82
302 307 7.658525 AAATCCAAGATATGCATGTTTACCA 57.341 32.000 10.16 0.00 0.00 3.25
305 310 4.279169 CCAAGATATGCATGTTTACCAGGG 59.721 45.833 10.16 0.00 0.00 4.45
454 461 6.796705 AAACCGTTAGTACTCAAAATGGAG 57.203 37.500 18.15 0.00 40.79 3.86
462 469 6.893020 AGTACTCAAAATGGAGGGAGTATT 57.107 37.500 0.00 0.00 42.75 1.89
464 471 8.024145 AGTACTCAAAATGGAGGGAGTATTAG 57.976 38.462 0.00 0.00 42.75 1.73
474 481 6.900194 TGGAGGGAGTATTAGAAAAGGAATG 58.100 40.000 0.00 0.00 0.00 2.67
516 524 9.594478 GTTAAATGAGGAAGAAAAAGGTTTCAA 57.406 29.630 2.35 0.00 44.82 2.69
580 589 3.744660 TCTCTTTCAGAAAAGGCCAGAC 58.255 45.455 5.01 0.00 41.88 3.51
761 821 0.179145 CCGCGTCCACGAGTATTCTT 60.179 55.000 4.92 0.00 43.02 2.52
886 963 1.008194 CGAGCAAGCAAGCAAAGCA 60.008 52.632 3.19 0.00 36.85 3.91
887 964 0.595567 CGAGCAAGCAAGCAAAGCAA 60.596 50.000 3.19 0.00 36.85 3.91
888 965 1.574134 GAGCAAGCAAGCAAAGCAAA 58.426 45.000 3.19 0.00 36.85 3.68
889 966 1.525619 GAGCAAGCAAGCAAAGCAAAG 59.474 47.619 3.19 0.00 36.85 2.77
890 967 0.041576 GCAAGCAAGCAAAGCAAAGC 60.042 50.000 0.00 0.00 0.00 3.51
932 1017 0.510359 CAAAGACACAGAGCGAGTGC 59.490 55.000 6.20 1.01 40.59 4.40
978 1071 2.031360 GCTGCAGCTGGAATCATCC 58.969 57.895 31.33 0.00 46.76 3.51
979 1072 1.453762 GCTGCAGCTGGAATCATCCC 61.454 60.000 31.33 0.00 45.95 3.85
980 1073 0.822532 CTGCAGCTGGAATCATCCCC 60.823 60.000 17.12 0.00 45.95 4.81
981 1074 1.895707 GCAGCTGGAATCATCCCCG 60.896 63.158 17.12 0.00 45.95 5.73
982 1075 1.528824 CAGCTGGAATCATCCCCGT 59.471 57.895 5.57 0.00 45.95 5.28
1029 1137 0.326522 TGCTGGCCTTCTCCATCCTA 60.327 55.000 3.32 0.00 35.22 2.94
1033 1141 0.839946 GGCCTTCTCCATCCTAAGCA 59.160 55.000 0.00 0.00 0.00 3.91
1077 1289 1.225704 GGCTACAGCAGGGCAAGAT 59.774 57.895 3.24 0.00 44.36 2.40
1078 1290 0.469917 GGCTACAGCAGGGCAAGATA 59.530 55.000 3.24 0.00 44.36 1.98
1350 1591 0.107831 AACTGAAGCCGCCTGTTGTA 59.892 50.000 0.00 0.00 0.00 2.41
1351 1592 0.602905 ACTGAAGCCGCCTGTTGTAC 60.603 55.000 0.00 0.00 0.00 2.90
1352 1593 0.320771 CTGAAGCCGCCTGTTGTACT 60.321 55.000 0.00 0.00 0.00 2.73
1353 1594 0.107831 TGAAGCCGCCTGTTGTACTT 59.892 50.000 0.00 0.00 0.00 2.24
1354 1595 0.517316 GAAGCCGCCTGTTGTACTTG 59.483 55.000 0.00 0.00 0.00 3.16
1355 1596 0.179029 AAGCCGCCTGTTGTACTTGT 60.179 50.000 0.00 0.00 0.00 3.16
1417 1665 7.542130 GTGATTACTTGGATAAGCTTTGGTTTG 59.458 37.037 3.20 0.00 37.43 2.93
1420 1668 6.575162 ACTTGGATAAGCTTTGGTTTGTAG 57.425 37.500 3.20 0.00 37.43 2.74
1421 1669 5.048013 ACTTGGATAAGCTTTGGTTTGTAGC 60.048 40.000 3.20 0.00 37.43 3.58
1595 1855 1.614241 ATAGACTCACCACCCCACGC 61.614 60.000 0.00 0.00 0.00 5.34
1689 1953 1.139989 CAGAGAAACGCGAGCTTCAA 58.860 50.000 15.93 0.00 38.61 2.69
1718 1982 6.585695 AGTAGATCGAACCAAGACAAAGTA 57.414 37.500 0.00 0.00 0.00 2.24
1727 1991 3.064820 ACCAAGACAAAGTAGCACAAACG 59.935 43.478 0.00 0.00 0.00 3.60
1734 1998 2.851263 AGTAGCACAAACGGGATCAA 57.149 45.000 0.00 0.00 0.00 2.57
1744 2008 2.568623 ACGGGATCAAAGCAAGAACT 57.431 45.000 0.00 0.00 0.00 3.01
1746 2010 1.394917 CGGGATCAAAGCAAGAACTCG 59.605 52.381 0.00 0.00 0.00 4.18
1747 2011 1.131315 GGGATCAAAGCAAGAACTCGC 59.869 52.381 0.00 0.00 0.00 5.03
1748 2012 2.079925 GGATCAAAGCAAGAACTCGCT 58.920 47.619 0.00 0.00 41.20 4.93
1749 2013 2.159599 GGATCAAAGCAAGAACTCGCTG 60.160 50.000 0.00 0.00 38.82 5.18
1750 2014 1.953559 TCAAAGCAAGAACTCGCTGT 58.046 45.000 0.00 0.00 38.82 4.40
1751 2015 1.599071 TCAAAGCAAGAACTCGCTGTG 59.401 47.619 0.00 0.00 43.61 3.66
1752 2016 1.331756 CAAAGCAAGAACTCGCTGTGT 59.668 47.619 0.00 0.00 38.45 3.72
1753 2017 1.668419 AAGCAAGAACTCGCTGTGTT 58.332 45.000 0.00 0.00 38.82 3.32
1754 2018 1.668419 AGCAAGAACTCGCTGTGTTT 58.332 45.000 0.00 0.00 37.02 2.83
1755 2019 2.833794 AGCAAGAACTCGCTGTGTTTA 58.166 42.857 0.00 0.00 37.02 2.01
1770 5281 6.476706 CGCTGTGTTTATGTCTGAAGATATCA 59.523 38.462 5.32 0.00 36.38 2.15
1778 5289 8.948631 TTATGTCTGAAGATATCAACACTTCC 57.051 34.615 5.32 0.00 39.14 3.46
1779 5290 5.410924 TGTCTGAAGATATCAACACTTCCG 58.589 41.667 5.32 0.00 39.14 4.30
1784 5295 3.786635 AGATATCAACACTTCCGTCAGC 58.213 45.455 5.32 0.00 0.00 4.26
1803 5314 2.158608 AGCTAACTGAAACCTGGTGCTT 60.159 45.455 0.00 0.00 0.00 3.91
1804 5315 2.030805 GCTAACTGAAACCTGGTGCTTG 60.031 50.000 0.00 0.00 0.00 4.01
1805 5316 2.143876 AACTGAAACCTGGTGCTTGT 57.856 45.000 0.00 0.00 0.00 3.16
1818 5364 2.158449 GGTGCTTGTCAGAAACATCTCG 59.842 50.000 0.00 0.00 37.82 4.04
1828 5374 3.438087 CAGAAACATCTCGGCAAGTTCAT 59.562 43.478 0.00 0.00 0.00 2.57
1831 5377 5.525378 AGAAACATCTCGGCAAGTTCATATC 59.475 40.000 0.00 0.00 0.00 1.63
1832 5378 4.679373 ACATCTCGGCAAGTTCATATCT 57.321 40.909 0.00 0.00 0.00 1.98
1833 5379 4.626042 ACATCTCGGCAAGTTCATATCTC 58.374 43.478 0.00 0.00 0.00 2.75
1836 5382 0.861837 CGGCAAGTTCATATCTCCGC 59.138 55.000 0.00 0.00 0.00 5.54
1841 5387 1.693627 AGTTCATATCTCCGCCGTCT 58.306 50.000 0.00 0.00 0.00 4.18
1846 5392 2.427540 ATATCTCCGCCGTCTGCAGC 62.428 60.000 9.47 3.23 41.33 5.25
1857 5405 2.983136 CCGTCTGCAGCGATTTATAGAG 59.017 50.000 25.33 7.41 0.00 2.43
1860 5408 4.147306 CGTCTGCAGCGATTTATAGAGAAC 59.853 45.833 21.01 3.92 0.00 3.01
1864 5412 2.472696 GCGATTTATAGAGAACGCGC 57.527 50.000 5.73 0.00 37.06 6.86
1880 5428 1.208870 CGCGCTTGCACAACCAATA 59.791 52.632 5.56 0.00 39.07 1.90
1881 5429 1.065031 CGCGCTTGCACAACCAATAC 61.065 55.000 5.56 0.00 39.07 1.89
1886 5434 2.660490 CTTGCACAACCAATACAACCG 58.340 47.619 0.00 0.00 0.00 4.44
1890 5438 2.159627 GCACAACCAATACAACCGAGAG 59.840 50.000 0.00 0.00 0.00 3.20
1915 5464 5.939764 AGTAGCACAAACAGGATCATAGA 57.060 39.130 0.00 0.00 0.00 1.98
1922 5471 6.623767 GCACAAACAGGATCATAGAAAGAACC 60.624 42.308 0.00 0.00 0.00 3.62
1982 5554 3.494626 CAGCACAAGTTACAAGACGACAT 59.505 43.478 0.00 0.00 0.00 3.06
2004 5576 2.557056 AGCACGAACAGCTAACTACAGA 59.443 45.455 0.00 0.00 41.32 3.41
2009 5584 3.430931 GAACAGCTAACTACAGAGCGAG 58.569 50.000 0.00 0.00 43.72 5.03
2010 5585 1.133407 ACAGCTAACTACAGAGCGAGC 59.867 52.381 0.00 0.00 43.72 5.03
2011 5593 0.378962 AGCTAACTACAGAGCGAGCG 59.621 55.000 0.00 0.00 43.72 5.03
2013 5595 0.592754 CTAACTACAGAGCGAGCGCC 60.593 60.000 11.66 3.34 43.17 6.53
2024 5606 4.983628 GAGCGCCATCGATCTGAT 57.016 55.556 2.29 0.00 46.50 2.90
2025 5607 2.735634 GAGCGCCATCGATCTGATC 58.264 57.895 2.29 7.60 46.50 2.92
2026 5608 0.243365 GAGCGCCATCGATCTGATCT 59.757 55.000 15.16 0.00 46.50 2.75
2027 5609 0.038435 AGCGCCATCGATCTGATCTG 60.038 55.000 15.16 7.81 34.13 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.343307 TCTTTGCTCTTTGCCTTCTTTTT 57.657 34.783 0.00 0.00 42.00 1.94
6 7 5.343307 TTCTTTGCTCTTTGCCTTCTTTT 57.657 34.783 0.00 0.00 42.00 2.27
16 17 6.475402 CGTGTTTTATGGTTTCTTTGCTCTTT 59.525 34.615 0.00 0.00 0.00 2.52
33 34 3.316588 TCTGCATGCCTTTTCGTGTTTTA 59.683 39.130 16.68 0.00 0.00 1.52
90 91 1.463056 ACAACATATGTCACGCGTTGG 59.537 47.619 10.22 0.00 37.96 3.77
106 107 9.811995 TCCAAGTACACATATATGACTTACAAC 57.188 33.333 19.63 7.20 0.00 3.32
142 143 3.390135 ACGTCACGAGACATGAACATTT 58.610 40.909 2.91 0.00 45.23 2.32
162 163 7.188468 ACACACAATATTCAAATTTGCCAAC 57.812 32.000 13.54 0.00 0.00 3.77
210 211 4.522405 TGTAATTTGATGCAATATCCCCCG 59.478 41.667 0.00 0.00 0.00 5.73
211 212 5.047092 CCTGTAATTTGATGCAATATCCCCC 60.047 44.000 0.00 0.00 0.00 5.40
377 384 3.916172 CGATGCAACTTGGTGATCAAAAG 59.084 43.478 14.83 14.83 34.56 2.27
383 390 0.680921 CCCCGATGCAACTTGGTGAT 60.681 55.000 0.00 0.00 0.00 3.06
388 395 3.651803 TTTTTACCCCGATGCAACTTG 57.348 42.857 0.00 0.00 0.00 3.16
413 420 6.741109 ACGGTTTAAATGACACCTAAAAAGG 58.259 36.000 0.00 0.00 0.00 3.11
419 426 7.895759 AGTACTAACGGTTTAAATGACACCTA 58.104 34.615 0.00 0.00 0.00 3.08
464 471 9.196552 CACCAACTCTAAAATTCATTCCTTTTC 57.803 33.333 0.00 0.00 0.00 2.29
474 481 9.626045 CCTCATTTAACACCAACTCTAAAATTC 57.374 33.333 0.00 0.00 0.00 2.17
568 577 3.626217 CCCGTAATAAGTCTGGCCTTTTC 59.374 47.826 3.32 0.00 0.00 2.29
761 821 3.150335 CTAGCGCTGGAGGAGCCA 61.150 66.667 22.90 0.00 46.01 4.75
777 837 2.190578 GCATGGCGGGTTCTAGCT 59.809 61.111 0.00 0.00 0.00 3.32
785 845 2.505635 GAAGTTTTGGGCATGGCGGG 62.506 60.000 13.76 0.00 0.00 6.13
886 963 5.182380 CCAATCAATCAATTGGCTTTGCTTT 59.818 36.000 5.42 3.27 46.73 3.51
887 964 4.698304 CCAATCAATCAATTGGCTTTGCTT 59.302 37.500 5.42 3.35 46.73 3.91
888 965 4.258543 CCAATCAATCAATTGGCTTTGCT 58.741 39.130 5.42 0.00 46.73 3.91
889 966 4.609691 CCAATCAATCAATTGGCTTTGC 57.390 40.909 5.42 0.00 46.73 3.68
910 987 1.066914 CTCGCTCTGTGTCTTTGCTC 58.933 55.000 0.00 0.00 0.00 4.26
932 1017 1.135315 CGATGCTTTCTTGCACCCG 59.865 57.895 0.00 0.00 46.33 5.28
968 1053 3.655358 GGGACGGGGATGATTCCA 58.345 61.111 0.00 0.00 44.60 3.53
1064 1276 1.964552 CTTCCTATCTTGCCCTGCTG 58.035 55.000 0.00 0.00 0.00 4.41
1077 1289 2.038975 AGACCGCCCTGCTTCCTA 59.961 61.111 0.00 0.00 0.00 2.94
1078 1290 3.710722 CAGACCGCCCTGCTTCCT 61.711 66.667 0.00 0.00 0.00 3.36
1255 1484 1.024579 AAGAATTAGCCCCACACGCG 61.025 55.000 3.53 3.53 0.00 6.01
1256 1485 1.132453 GAAAGAATTAGCCCCACACGC 59.868 52.381 0.00 0.00 0.00 5.34
1257 1486 1.743394 GGAAAGAATTAGCCCCACACG 59.257 52.381 0.00 0.00 0.00 4.49
1258 1487 3.017442 GAGGAAAGAATTAGCCCCACAC 58.983 50.000 0.00 0.00 0.00 3.82
1265 1494 4.804139 TGATCGAACGAGGAAAGAATTAGC 59.196 41.667 2.94 0.00 0.00 3.09
1350 1591 6.037786 TCTAGCTTTGTATGCTGTACAAGT 57.962 37.500 12.70 7.10 41.32 3.16
1351 1592 6.968131 TTCTAGCTTTGTATGCTGTACAAG 57.032 37.500 12.70 9.65 41.32 3.16
1352 1593 7.158697 TCTTTCTAGCTTTGTATGCTGTACAA 58.841 34.615 10.06 10.06 41.32 2.41
1353 1594 6.697395 TCTTTCTAGCTTTGTATGCTGTACA 58.303 36.000 0.00 0.00 41.32 2.90
1354 1595 7.596749 TTCTTTCTAGCTTTGTATGCTGTAC 57.403 36.000 0.00 0.00 41.32 2.90
1355 1596 7.119262 GGTTTCTTTCTAGCTTTGTATGCTGTA 59.881 37.037 0.00 0.00 41.32 2.74
1417 1665 0.640768 GTCATGACGTCAAGCGCTAC 59.359 55.000 24.13 5.01 46.11 3.58
1571 1831 2.304761 TGGGGTGGTGAGTCTATTTCAC 59.695 50.000 0.00 0.00 43.25 3.18
1595 1855 2.260844 TGAACTCTGAACTTGCAGGG 57.739 50.000 0.00 0.00 42.18 4.45
1718 1982 0.598065 GCTTTGATCCCGTTTGTGCT 59.402 50.000 0.00 0.00 0.00 4.40
1727 1991 1.131315 GCGAGTTCTTGCTTTGATCCC 59.869 52.381 4.93 0.00 0.00 3.85
1734 1998 1.668419 AACACAGCGAGTTCTTGCTT 58.332 45.000 11.39 2.37 40.03 3.91
1744 2008 4.251543 TCTTCAGACATAAACACAGCGA 57.748 40.909 0.00 0.00 0.00 4.93
1746 2010 7.776933 TGATATCTTCAGACATAAACACAGC 57.223 36.000 3.98 0.00 0.00 4.40
1747 2011 9.154847 TGTTGATATCTTCAGACATAAACACAG 57.845 33.333 3.98 0.00 35.27 3.66
1748 2012 8.935844 GTGTTGATATCTTCAGACATAAACACA 58.064 33.333 18.16 0.00 36.66 3.72
1749 2013 9.155975 AGTGTTGATATCTTCAGACATAAACAC 57.844 33.333 16.32 16.32 36.80 3.32
1750 2014 9.725019 AAGTGTTGATATCTTCAGACATAAACA 57.275 29.630 3.98 0.00 35.27 2.83
1752 2016 9.383519 GGAAGTGTTGATATCTTCAGACATAAA 57.616 33.333 3.98 0.00 39.19 1.40
1753 2017 7.706607 CGGAAGTGTTGATATCTTCAGACATAA 59.293 37.037 3.98 0.00 39.19 1.90
1754 2018 7.147897 ACGGAAGTGTTGATATCTTCAGACATA 60.148 37.037 3.98 0.00 46.97 2.29
1755 2019 6.045318 CGGAAGTGTTGATATCTTCAGACAT 58.955 40.000 3.98 0.00 39.19 3.06
1784 5295 3.214328 ACAAGCACCAGGTTTCAGTTAG 58.786 45.455 0.00 0.00 32.07 2.34
1795 5306 3.144506 AGATGTTTCTGACAAGCACCAG 58.855 45.455 0.00 0.00 42.62 4.00
1796 5307 3.141398 GAGATGTTTCTGACAAGCACCA 58.859 45.455 0.00 0.00 42.62 4.17
1803 5314 2.224281 ACTTGCCGAGATGTTTCTGACA 60.224 45.455 0.00 0.00 43.71 3.58
1804 5315 2.417719 ACTTGCCGAGATGTTTCTGAC 58.582 47.619 0.00 0.00 30.30 3.51
1805 5316 2.839486 ACTTGCCGAGATGTTTCTGA 57.161 45.000 0.00 0.00 30.30 3.27
1818 5364 1.230324 GGCGGAGATATGAACTTGCC 58.770 55.000 0.00 0.00 34.16 4.52
1836 5382 2.983136 CTCTATAAATCGCTGCAGACGG 59.017 50.000 20.43 5.65 0.00 4.79
1841 5387 2.794910 GCGTTCTCTATAAATCGCTGCA 59.205 45.455 0.00 0.00 40.39 4.41
1846 5392 1.201566 GCGCGCGTTCTCTATAAATCG 60.202 52.381 32.35 0.00 0.00 3.34
1864 5412 2.050691 GTTGTATTGGTTGTGCAAGCG 58.949 47.619 9.16 0.00 41.36 4.68
1876 5424 5.062308 GTGCTACTTTCTCTCGGTTGTATTG 59.938 44.000 0.00 0.00 0.00 1.90
1880 5428 2.364324 TGTGCTACTTTCTCTCGGTTGT 59.636 45.455 0.00 0.00 0.00 3.32
1881 5429 3.026630 TGTGCTACTTTCTCTCGGTTG 57.973 47.619 0.00 0.00 0.00 3.77
1886 5434 4.632153 TCCTGTTTGTGCTACTTTCTCTC 58.368 43.478 0.00 0.00 0.00 3.20
1890 5438 5.886960 ATGATCCTGTTTGTGCTACTTTC 57.113 39.130 0.00 0.00 0.00 2.62
1915 5464 2.812011 ACAGCGCTTATTTCGGTTCTTT 59.188 40.909 7.50 0.00 35.32 2.52
1922 5471 6.934210 AGAAATAGTAACAGCGCTTATTTCG 58.066 36.000 28.56 14.59 37.46 3.46
1982 5554 3.754850 TCTGTAGTTAGCTGTTCGTGCTA 59.245 43.478 0.00 0.00 41.46 3.49
2004 5576 3.600694 AGATCGATGGCGCTCGCT 61.601 61.111 13.63 4.65 37.70 4.93
2009 5584 1.624865 GCAGATCAGATCGATGGCGC 61.625 60.000 0.54 0.00 33.17 6.53
2010 5585 1.013005 GGCAGATCAGATCGATGGCG 61.013 60.000 0.54 0.00 33.17 5.69
2011 5593 0.034476 TGGCAGATCAGATCGATGGC 59.966 55.000 15.67 15.67 33.17 4.40
2013 5595 3.725490 TCTTTGGCAGATCAGATCGATG 58.275 45.455 0.54 0.28 33.17 3.84
2021 5603 3.071457 TCTGTGTCTTCTTTGGCAGATCA 59.929 43.478 0.00 0.00 0.00 2.92
2022 5604 3.434984 GTCTGTGTCTTCTTTGGCAGATC 59.565 47.826 0.00 0.00 35.77 2.75
2023 5605 3.406764 GTCTGTGTCTTCTTTGGCAGAT 58.593 45.455 0.00 0.00 35.77 2.90
2024 5606 2.803133 CGTCTGTGTCTTCTTTGGCAGA 60.803 50.000 0.00 0.00 0.00 4.26
2025 5607 1.528586 CGTCTGTGTCTTCTTTGGCAG 59.471 52.381 0.00 0.00 0.00 4.85
2026 5608 1.138069 TCGTCTGTGTCTTCTTTGGCA 59.862 47.619 0.00 0.00 0.00 4.92
2027 5609 1.527311 GTCGTCTGTGTCTTCTTTGGC 59.473 52.381 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.