Multiple sequence alignment - TraesCS5B01G190300

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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 TraesCS5B01G190300 chr5B 100.000 3928 0 0 1 3928 344307068 344310995 0 7254
1 TraesCS5B01G190300 chr5A 91.012 3349 157 60 11 3272 398277203 398280494 0 4385
2 TraesCS5B01G190300 chr5A 90.732 669 43 14 3258 3919 398280520 398281176 0 874
3 TraesCS5B01G190300 chr5D 88.447 3272 230 86 74 3272 301109565 301112761 0 3812
4 TraesCS5B01G190300 chr5D 92.982 684 32 10 3258 3928 301112787 301113467 0 983


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 TraesCS5B01G190300 chr5B 344307068 344310995 3927 False 7254.0 7254 100.0000 1 3928 1 chr5B.!!$F1 3927
1 TraesCS5B01G190300 chr5A 398277203 398281176 3973 False 2629.5 4385 90.8720 11 3919 2 chr5A.!!$F1 3908
2 TraesCS5B01G190300 chr5D 301109565 301113467 3902 False 2397.5 3812 90.7145 74 3928 2 chr5D.!!$F1 3854

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
462 533 0.605589 GGAGTCGAGGTTTGGGGTTG 60.606 60.000 0.0 0.0 0.00 3.77 F
1623 1756 0.254178 CCTGGTGGCAAGTAGCTGAT 59.746 55.000 0.0 0.0 44.79 2.90 F
1734 1867 1.001860 CATGGGGCAAAATTGAACGGT 59.998 47.619 0.0 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2366 0.035820 TACCCGGGTGCATTTGACTC 60.036 55.000 36.97 0.0 0.0 3.36 R
2783 2928 1.620822 TCTTCTTTGCCCTGCCTTTC 58.379 50.000 0.00 0.0 0.0 2.62 R
3236 3382 1.796459 GTACAGGCTTACACACCGTTG 59.204 52.381 0.00 0.0 0.0 4.10 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
31 32 6.435428 GCCTAACAAGAAATGACGAGAAAAA 58.565 36.000 0.00 0.00 0.00 1.94
70 71 9.912634 AATTTCATTTCACCAGTAGTAACAATG 57.087 29.630 0.00 0.00 0.00 2.82
173 176 3.483235 AAGCAACGCAACGCAAGGG 62.483 57.895 0.00 0.00 46.39 3.95
343 390 2.848691 CCTGGCTCAGAATCTTCATCC 58.151 52.381 4.00 0.00 32.44 3.51
374 421 3.461773 CACTCGTCCCGGCTCCAT 61.462 66.667 0.00 0.00 0.00 3.41
399 449 1.811266 CCGATCCAGGTCAAGCACG 60.811 63.158 0.00 0.00 0.00 5.34
415 465 1.606606 CACGCTCGCCTGAAAATTTC 58.393 50.000 0.00 0.00 0.00 2.17
416 466 1.197721 CACGCTCGCCTGAAAATTTCT 59.802 47.619 7.29 0.00 0.00 2.52
418 468 2.245096 CGCTCGCCTGAAAATTTCTTG 58.755 47.619 7.29 0.00 0.00 3.02
462 533 0.605589 GGAGTCGAGGTTTGGGGTTG 60.606 60.000 0.00 0.00 0.00 3.77
471 548 2.368548 AGGTTTGGGGTTGAAAAGATGC 59.631 45.455 0.00 0.00 0.00 3.91
482 559 3.270027 TGAAAAGATGCGTCAATCCGAT 58.730 40.909 8.99 0.00 0.00 4.18
489 566 1.067213 TGCGTCAATCCGATCTGTTCA 60.067 47.619 0.00 0.00 0.00 3.18
490 567 1.590238 GCGTCAATCCGATCTGTTCAG 59.410 52.381 0.00 0.00 0.00 3.02
491 568 2.881074 CGTCAATCCGATCTGTTCAGT 58.119 47.619 0.00 0.00 0.00 3.41
568 645 2.104331 CTGTCGGCGGCGATACTT 59.896 61.111 36.75 0.00 0.00 2.24
574 651 2.300787 GGCGGCGATACTTGCGTAG 61.301 63.158 12.98 0.00 0.00 3.51
649 729 4.813296 AGCAACGGTTACTTTCTTCTTG 57.187 40.909 0.00 0.00 0.00 3.02
707 805 1.106285 CCTTTGGGGAAGCAGCATAC 58.894 55.000 0.00 0.00 37.23 2.39
708 806 1.341383 CCTTTGGGGAAGCAGCATACT 60.341 52.381 0.00 0.00 37.23 2.12
709 807 2.019984 CTTTGGGGAAGCAGCATACTC 58.980 52.381 0.00 0.00 0.00 2.59
715 813 2.353208 GGGAAGCAGCATACTCGGATAG 60.353 54.545 0.00 0.00 0.00 2.08
779 892 6.943981 TCTGGCATCTAAATTAATTTCGACG 58.056 36.000 16.56 9.99 0.00 5.12
803 917 1.666872 CGGTTCACTGGGGACGTTC 60.667 63.158 0.00 0.00 0.00 3.95
827 941 7.269316 TCGTGAATGGTTTACATCATAAGCTA 58.731 34.615 0.00 0.00 39.40 3.32
831 945 7.442364 TGAATGGTTTACATCATAAGCTAGAGC 59.558 37.037 0.00 0.00 39.40 4.09
833 947 7.158021 ATGGTTTACATCATAAGCTAGAGCTC 58.842 38.462 5.27 5.27 43.41 4.09
863 977 5.055812 TGATTTTTGGGAATGTTTGTGAGC 58.944 37.500 0.00 0.00 0.00 4.26
865 979 3.731652 TTTGGGAATGTTTGTGAGCTG 57.268 42.857 0.00 0.00 0.00 4.24
887 1013 3.849911 CGTTGTGGCTCTCATCTCTTAA 58.150 45.455 0.00 0.00 0.00 1.85
889 1015 4.328440 CGTTGTGGCTCTCATCTCTTAAAG 59.672 45.833 0.00 0.00 0.00 1.85
890 1016 4.478206 TGTGGCTCTCATCTCTTAAAGG 57.522 45.455 0.00 0.00 0.00 3.11
910 1040 3.071479 GGGAGAACGTTTTGCTGATACA 58.929 45.455 10.10 0.00 0.00 2.29
911 1041 3.120304 GGGAGAACGTTTTGCTGATACAC 60.120 47.826 10.10 0.00 0.00 2.90
912 1042 3.746492 GGAGAACGTTTTGCTGATACACT 59.254 43.478 0.46 0.00 0.00 3.55
913 1043 4.927425 GGAGAACGTTTTGCTGATACACTA 59.073 41.667 0.46 0.00 0.00 2.74
914 1044 5.163982 GGAGAACGTTTTGCTGATACACTAC 60.164 44.000 0.46 0.00 0.00 2.73
915 1045 5.539048 AGAACGTTTTGCTGATACACTACT 58.461 37.500 0.46 0.00 0.00 2.57
916 1046 6.684686 AGAACGTTTTGCTGATACACTACTA 58.315 36.000 0.46 0.00 0.00 1.82
964 1097 4.025015 GCTAATGCTGATGGTCAACTTG 57.975 45.455 0.00 0.00 36.03 3.16
980 1113 0.958876 CTTGCTGATGTGCAGGCAGA 60.959 55.000 12.98 0.00 45.03 4.26
981 1114 1.239296 TTGCTGATGTGCAGGCAGAC 61.239 55.000 12.98 6.33 45.03 3.51
983 1116 0.959372 GCTGATGTGCAGGCAGACTT 60.959 55.000 12.98 0.00 45.03 3.01
1084 1217 3.446516 GGATGCAAAGAGAGCTCCAAAAT 59.553 43.478 10.93 0.00 32.85 1.82
1329 1462 0.468226 AAGTGGACAGTTTCTCGCCA 59.532 50.000 0.00 0.00 0.00 5.69
1330 1463 0.468226 AGTGGACAGTTTCTCGCCAA 59.532 50.000 0.00 0.00 0.00 4.52
1365 1498 6.046593 TGACGACATAAACACAAAGAAGAGT 58.953 36.000 0.00 0.00 0.00 3.24
1382 1515 0.835543 AGTGAGTGCCCTTCTGAGCT 60.836 55.000 0.00 0.00 0.00 4.09
1461 1594 1.140052 TGCCCTCAAACGAGTCTCAAA 59.860 47.619 0.00 0.00 0.00 2.69
1474 1607 4.033817 CGAGTCTCAAATGCAGAGGAAATC 59.966 45.833 0.00 0.00 33.92 2.17
1476 1609 3.064545 GTCTCAAATGCAGAGGAAATCCG 59.935 47.826 0.00 0.00 42.08 4.18
1480 1613 4.096833 TCAAATGCAGAGGAAATCCGAATG 59.903 41.667 0.00 0.00 42.08 2.67
1491 1624 4.884164 GGAAATCCGAATGACTTCCTTCAT 59.116 41.667 0.00 0.00 37.87 2.57
1539 1672 7.390027 TCAAAACTTTTGATCCTTTGTTTCCA 58.610 30.769 12.12 0.00 0.00 3.53
1623 1756 0.254178 CCTGGTGGCAAGTAGCTGAT 59.746 55.000 0.00 0.00 44.79 2.90
1633 1766 3.791245 CAAGTAGCTGATGAGGAAGGAC 58.209 50.000 0.00 0.00 0.00 3.85
1734 1867 1.001860 CATGGGGCAAAATTGAACGGT 59.998 47.619 0.00 0.00 0.00 4.83
1766 1899 2.023695 AGGATGGCTGTGGGAATTCATT 60.024 45.455 7.93 0.00 0.00 2.57
1790 1923 2.631418 TCTTCTGGTAAAGAGTCGCG 57.369 50.000 0.00 0.00 35.91 5.87
1794 1927 2.884207 GGTAAAGAGTCGCGGCCG 60.884 66.667 24.05 24.05 0.00 6.13
1847 1980 2.354259 CCTCTCAAGCACCAATGAGAC 58.646 52.381 1.55 0.00 45.27 3.36
1896 2029 5.283294 CAACAGTCTCACAAAAATGATGCA 58.717 37.500 0.00 0.00 0.00 3.96
1953 2088 9.226606 CATAACCATCAAAACTACAACTAGGAA 57.773 33.333 0.00 0.00 0.00 3.36
1956 2091 6.183361 ACCATCAAAACTACAACTAGGAACCT 60.183 38.462 0.00 0.00 0.00 3.50
1957 2092 6.149474 CCATCAAAACTACAACTAGGAACCTG 59.851 42.308 3.36 0.00 0.00 4.00
1964 2099 2.174854 ACAACTAGGAACCTGCCTTTGT 59.825 45.455 3.36 4.91 39.50 2.83
1965 2100 3.393278 ACAACTAGGAACCTGCCTTTGTA 59.607 43.478 3.36 0.00 37.28 2.41
1979 2114 3.065371 GCCTTTGTATAGATTTGCACGCT 59.935 43.478 0.00 0.00 0.00 5.07
1982 2117 6.513393 GCCTTTGTATAGATTTGCACGCTATT 60.513 38.462 7.29 0.00 0.00 1.73
1984 2119 7.254761 CCTTTGTATAGATTTGCACGCTATTCA 60.255 37.037 7.29 6.30 0.00 2.57
1996 2131 6.908825 TGCACGCTATTCATACTTTCTTTTT 58.091 32.000 0.00 0.00 0.00 1.94
2040 2179 6.825721 ACAAGGAGTCTTTTATAGCTCCATTG 59.174 38.462 11.39 13.07 43.71 2.82
2059 2198 7.811282 TCCATTGTCTACATATTACACCCAAT 58.189 34.615 0.00 0.00 0.00 3.16
2060 2199 8.939932 TCCATTGTCTACATATTACACCCAATA 58.060 33.333 0.00 0.00 0.00 1.90
2078 2217 6.828785 ACCCAATACTACTTAGGCTGAAATTG 59.171 38.462 0.00 0.00 0.00 2.32
2088 2227 2.560105 AGGCTGAAATTGAAGGAACAGC 59.440 45.455 0.00 0.00 46.31 4.40
2107 2246 3.084786 AGCCTGTTGATTTAGTTCCAGC 58.915 45.455 0.00 0.00 0.00 4.85
2116 2255 7.498900 TGTTGATTTAGTTCCAGCCTGTATATG 59.501 37.037 0.00 0.00 0.00 1.78
2122 2262 5.712752 AGTTCCAGCCTGTATATGGTAGTA 58.287 41.667 0.00 0.00 35.51 1.82
2126 2266 7.626999 TCCAGCCTGTATATGGTAGTAAATT 57.373 36.000 0.00 0.00 35.51 1.82
2127 2267 8.730093 TCCAGCCTGTATATGGTAGTAAATTA 57.270 34.615 0.00 0.00 35.51 1.40
2128 2268 9.161572 TCCAGCCTGTATATGGTAGTAAATTAA 57.838 33.333 0.00 0.00 35.51 1.40
2142 2282 8.182227 GGTAGTAAATTAATGTCAGTCCTTTGC 58.818 37.037 0.00 0.00 0.00 3.68
2299 2440 3.555527 CATCATGTCCACTGATGTCCT 57.444 47.619 5.36 0.00 43.19 3.85
2669 2814 1.042229 AGTGGCTGAAAATGCTGCAA 58.958 45.000 6.36 0.00 34.81 4.08
2695 2840 2.158842 AGAACATATGCCTCCAGCTCAC 60.159 50.000 1.58 0.00 44.23 3.51
2963 3108 1.654105 GTGCAGTTCGACGAATAGGTG 59.346 52.381 14.27 10.10 0.00 4.00
2964 3109 1.278238 GCAGTTCGACGAATAGGTGG 58.722 55.000 14.27 1.75 0.00 4.61
2965 3110 1.403780 GCAGTTCGACGAATAGGTGGT 60.404 52.381 14.27 0.00 0.00 4.16
2985 3130 3.607741 GTGGTAGGTAAAGAAAGCTCCC 58.392 50.000 0.00 0.00 0.00 4.30
3068 3213 3.549794 GAAGCCTTGCTGGTGATATCTT 58.450 45.455 3.98 0.00 39.62 2.40
3071 3216 3.201708 AGCCTTGCTGGTGATATCTTTCT 59.798 43.478 3.98 0.00 37.57 2.52
3072 3217 3.563390 GCCTTGCTGGTGATATCTTTCTC 59.437 47.826 3.98 0.00 38.35 2.87
3073 3218 4.685575 GCCTTGCTGGTGATATCTTTCTCT 60.686 45.833 3.98 0.00 38.35 3.10
3074 3219 5.055812 CCTTGCTGGTGATATCTTTCTCTC 58.944 45.833 3.98 0.00 0.00 3.20
3236 3382 4.152580 GGAACTCCAAAATCAGTCGACTTC 59.847 45.833 17.26 6.13 35.64 3.01
3339 3524 3.067684 ACATGTAAACCTGGGCTGTAC 57.932 47.619 0.00 0.00 0.00 2.90
3417 3604 2.544267 GGTGTTGACTAACTGAGCACAC 59.456 50.000 0.00 0.00 37.68 3.82
3418 3605 3.194861 GTGTTGACTAACTGAGCACACA 58.805 45.455 0.00 0.00 37.68 3.72
3433 3620 2.031857 GCACACAATTTGGTGGCAATTG 60.032 45.455 15.32 0.00 44.15 2.32
3441 3628 2.747396 TGGTGGCAATTGCATCTTTC 57.253 45.000 30.32 13.32 44.36 2.62
3457 3644 5.456822 GCATCTTTCTGTTGTTCTTGTTGAC 59.543 40.000 0.00 0.00 0.00 3.18
3472 3662 7.397892 TCTTGTTGACAATTTGAAGTTACCA 57.602 32.000 2.79 0.00 35.02 3.25
3558 3748 9.617975 CTTTCTTTCTAGCTAACTCCAAAAATG 57.382 33.333 0.00 0.00 0.00 2.32
3565 3755 9.162764 TCTAGCTAACTCCAAAAATGAACATAC 57.837 33.333 0.00 0.00 0.00 2.39
3592 3782 6.878923 TGAAACAGATTGAGACGGATTGTATT 59.121 34.615 0.00 0.00 0.00 1.89
3679 3870 1.138069 TCCGCAGACTGAACTGAAACA 59.862 47.619 6.65 0.00 39.94 2.83
3721 3917 4.156182 GGGAAAAGAAATACAGTTTCGCG 58.844 43.478 0.00 0.00 34.56 5.87
3750 3946 3.245229 TGACTAATGTGGGAGTGGCAAAT 60.245 43.478 0.00 0.00 0.00 2.32
3864 4060 2.114616 GAGATGACATCCACCAGACCT 58.885 52.381 11.92 0.00 0.00 3.85
3903 4099 2.016604 GCCATCTGTAACGGCATTGGA 61.017 52.381 0.00 0.00 45.52 3.53
3904 4100 2.575532 CCATCTGTAACGGCATTGGAT 58.424 47.619 0.00 0.00 0.00 3.41
3908 4107 1.526887 CTGTAACGGCATTGGATAGCG 59.473 52.381 0.00 0.00 0.00 4.26
3919 4118 2.941453 TGGATAGCGAGTGAGAACAC 57.059 50.000 0.00 0.00 46.24 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.577763 ATTTCTTGTTAGGCGCGCGC 62.578 55.000 44.40 44.40 41.06 6.86
2 3 0.857311 CATTTCTTGTTAGGCGCGCG 60.857 55.000 28.44 28.44 0.00 6.86
3 4 0.446222 TCATTTCTTGTTAGGCGCGC 59.554 50.000 25.94 25.94 0.00 6.86
4 5 1.526986 CGTCATTTCTTGTTAGGCGCG 60.527 52.381 0.00 0.00 0.00 6.86
5 6 1.730064 TCGTCATTTCTTGTTAGGCGC 59.270 47.619 0.00 0.00 0.00 6.53
6 7 3.250744 TCTCGTCATTTCTTGTTAGGCG 58.749 45.455 0.00 0.00 0.00 5.52
7 8 5.607119 TTTCTCGTCATTTCTTGTTAGGC 57.393 39.130 0.00 0.00 0.00 3.93
8 9 9.118236 GAATTTTTCTCGTCATTTCTTGTTAGG 57.882 33.333 0.00 0.00 0.00 2.69
9 10 9.884465 AGAATTTTTCTCGTCATTTCTTGTTAG 57.116 29.630 0.00 0.00 34.07 2.34
173 176 2.588201 GGGGATGGGATCGGAGCTC 61.588 68.421 4.71 4.71 0.00 4.09
282 329 2.547642 CGAAGAGGAAGATGCTGATCCC 60.548 54.545 0.00 0.00 33.55 3.85
291 338 1.323271 TGAGCGGCGAAGAGGAAGAT 61.323 55.000 12.98 0.00 0.00 2.40
292 339 1.532604 TTGAGCGGCGAAGAGGAAGA 61.533 55.000 12.98 0.00 0.00 2.87
374 421 0.690192 TGACCTGGATCGGCAAGAAA 59.310 50.000 0.00 0.00 0.00 2.52
399 449 2.029918 ACCAAGAAATTTTCAGGCGAGC 60.030 45.455 16.19 0.00 32.37 5.03
415 465 1.679680 GATGGCATGACATGGACCAAG 59.320 52.381 21.56 0.00 33.30 3.61
416 466 1.005687 TGATGGCATGACATGGACCAA 59.994 47.619 21.56 0.72 33.30 3.67
418 468 1.991121 ATGATGGCATGACATGGACC 58.009 50.000 21.56 4.70 32.31 4.46
462 533 3.557595 AGATCGGATTGACGCATCTTTTC 59.442 43.478 0.00 0.00 31.53 2.29
471 548 2.600420 CACTGAACAGATCGGATTGACG 59.400 50.000 8.87 0.00 37.88 4.35
482 559 0.615331 GATCTGGCCCACTGAACAGA 59.385 55.000 0.00 0.00 43.33 3.41
489 566 2.362369 CGACTGGATCTGGCCCACT 61.362 63.158 0.00 0.00 0.00 4.00
490 567 2.187946 CGACTGGATCTGGCCCAC 59.812 66.667 0.00 0.00 0.00 4.61
491 568 3.785859 GCGACTGGATCTGGCCCA 61.786 66.667 0.00 0.00 0.00 5.36
574 651 7.335673 AGGGAAGTACGAGTAGTAGTAAAAGAC 59.664 40.741 0.00 0.00 37.98 3.01
590 667 3.064931 GTGACTTTGGAAGGGAAGTACG 58.935 50.000 0.00 0.00 36.31 3.67
591 668 4.316645 GAGTGACTTTGGAAGGGAAGTAC 58.683 47.826 0.00 0.00 36.31 2.73
649 729 2.568623 ACTATTTCCATCCATCGCCC 57.431 50.000 0.00 0.00 0.00 6.13
707 805 8.740123 AATGATAGTAGTACCATCTATCCGAG 57.260 38.462 18.38 0.00 39.20 4.63
715 813 7.368833 ACGCTGTAAATGATAGTAGTACCATC 58.631 38.462 2.10 2.10 0.00 3.51
779 892 3.423154 CCCAGTGAACCGCTTCGC 61.423 66.667 0.00 0.00 37.19 4.70
786 899 1.666872 CGAACGTCCCCAGTGAACC 60.667 63.158 0.00 0.00 0.00 3.62
803 917 6.363577 AGCTTATGATGTAAACCATTCACG 57.636 37.500 0.00 0.00 32.56 4.35
827 941 4.888239 CCCAAAAATCATCTGATGAGCTCT 59.112 41.667 23.25 6.12 43.53 4.09
831 945 7.108841 ACATTCCCAAAAATCATCTGATGAG 57.891 36.000 23.25 10.80 43.53 2.90
833 947 7.604927 ACAAACATTCCCAAAAATCATCTGATG 59.395 33.333 11.42 11.42 34.49 3.07
837 951 7.065120 TCACAAACATTCCCAAAAATCATCT 57.935 32.000 0.00 0.00 0.00 2.90
838 952 6.128472 GCTCACAAACATTCCCAAAAATCATC 60.128 38.462 0.00 0.00 0.00 2.92
841 955 5.178067 CAGCTCACAAACATTCCCAAAAATC 59.822 40.000 0.00 0.00 0.00 2.17
843 957 4.440880 CAGCTCACAAACATTCCCAAAAA 58.559 39.130 0.00 0.00 0.00 1.94
863 977 0.390866 AGATGAGAGCCACAACGCAG 60.391 55.000 0.00 0.00 0.00 5.18
865 979 0.108424 AGAGATGAGAGCCACAACGC 60.108 55.000 0.00 0.00 0.00 4.84
887 1013 2.341846 TCAGCAAAACGTTCTCCCTT 57.658 45.000 0.00 0.00 0.00 3.95
889 1015 3.071479 TGTATCAGCAAAACGTTCTCCC 58.929 45.455 0.00 0.00 0.00 4.30
890 1016 3.746492 AGTGTATCAGCAAAACGTTCTCC 59.254 43.478 0.00 0.00 0.00 3.71
964 1097 0.959372 AAGTCTGCCTGCACATCAGC 60.959 55.000 0.00 0.00 41.50 4.26
980 1113 3.111853 TCAGTCTCGCATGTCAAAAGT 57.888 42.857 0.00 0.00 0.00 2.66
981 1114 3.181513 CCATCAGTCTCGCATGTCAAAAG 60.182 47.826 0.00 0.00 0.00 2.27
983 1116 2.349590 CCATCAGTCTCGCATGTCAAA 58.650 47.619 0.00 0.00 0.00 2.69
1038 1171 2.348605 GAAACAAGCAGCGGTTGGCA 62.349 55.000 19.32 0.00 44.10 4.92
1053 1186 3.679389 TCTCTTTGCATCCTCCTGAAAC 58.321 45.455 0.00 0.00 0.00 2.78
1084 1217 4.641645 CGGTGGACAGCAGGCCAA 62.642 66.667 4.67 0.00 35.63 4.52
1301 1434 1.972872 ACTGTCCACTTTCTTGGCAG 58.027 50.000 10.26 10.26 42.15 4.85
1329 1462 3.784701 ATGTCGTCAAGCGTAGAGATT 57.215 42.857 0.00 0.00 42.13 2.40
1330 1463 4.895224 TTATGTCGTCAAGCGTAGAGAT 57.105 40.909 0.00 0.00 42.13 2.75
1350 1483 3.378427 GGCACTCACTCTTCTTTGTGTTT 59.622 43.478 0.00 0.00 35.82 2.83
1356 1489 2.708325 AGAAGGGCACTCACTCTTCTTT 59.292 45.455 0.81 0.00 41.99 2.52
1365 1498 0.898320 GTAGCTCAGAAGGGCACTCA 59.102 55.000 0.00 0.00 0.00 3.41
1461 1594 3.118112 AGTCATTCGGATTTCCTCTGCAT 60.118 43.478 0.00 0.00 0.00 3.96
1491 1624 6.672218 TGAAGTCCATAACCTCTTTATCCTCA 59.328 38.462 0.00 0.00 0.00 3.86
1539 1672 3.389002 AGCATGCCTTCTTTGGTTTCTTT 59.611 39.130 15.66 0.00 0.00 2.52
1590 1723 1.298014 CCAGGGCTGACACTTCCTC 59.702 63.158 0.00 0.00 0.00 3.71
1623 1756 1.975327 CGAAGCCAGTCCTTCCTCA 59.025 57.895 0.00 0.00 38.35 3.86
1734 1867 3.256383 CACAGCCATCCTTGTTTTCATGA 59.744 43.478 0.00 0.00 0.00 3.07
1766 1899 5.448768 CGCGACTCTTTACCAGAAGAAGATA 60.449 44.000 0.00 0.00 35.38 1.98
1794 1927 1.790755 TCATAGTGTCGTGTGGTTGC 58.209 50.000 0.00 0.00 0.00 4.17
1799 1932 2.336667 TGCACATCATAGTGTCGTGTG 58.663 47.619 0.00 0.00 41.52 3.82
1847 1980 2.196749 CTCCACCGTCAGATGAATTCG 58.803 52.381 0.04 0.00 0.00 3.34
1896 2029 6.267471 AGACAAATGAAAACACATACCCATGT 59.733 34.615 0.00 0.00 46.58 3.21
1953 2088 4.399303 GTGCAAATCTATACAAAGGCAGGT 59.601 41.667 0.00 0.00 0.00 4.00
1956 2091 3.181501 GCGTGCAAATCTATACAAAGGCA 60.182 43.478 0.00 0.00 0.00 4.75
1957 2092 3.065371 AGCGTGCAAATCTATACAAAGGC 59.935 43.478 0.00 0.00 0.00 4.35
1964 2099 9.489084 AAAGTATGAATAGCGTGCAAATCTATA 57.511 29.630 0.00 0.00 0.00 1.31
1965 2100 7.969536 AAGTATGAATAGCGTGCAAATCTAT 57.030 32.000 0.00 0.00 0.00 1.98
2022 2161 8.894768 ATGTAGACAATGGAGCTATAAAAGAC 57.105 34.615 0.00 0.00 0.00 3.01
2059 2198 7.490657 TCCTTCAATTTCAGCCTAAGTAGTA 57.509 36.000 0.00 0.00 0.00 1.82
2060 2199 6.374417 TCCTTCAATTTCAGCCTAAGTAGT 57.626 37.500 0.00 0.00 0.00 2.73
2064 2203 5.620879 GCTGTTCCTTCAATTTCAGCCTAAG 60.621 44.000 0.00 0.00 41.26 2.18
2078 2217 4.762251 ACTAAATCAACAGGCTGTTCCTTC 59.238 41.667 29.07 0.00 44.75 3.46
2088 2227 3.441572 CAGGCTGGAACTAAATCAACAGG 59.558 47.826 6.61 0.00 0.00 4.00
2094 2233 6.534634 ACCATATACAGGCTGGAACTAAATC 58.465 40.000 20.34 0.00 34.08 2.17
2101 2240 7.626999 ATTTACTACCATATACAGGCTGGAA 57.373 36.000 20.34 6.88 34.08 3.53
2116 2255 8.182227 GCAAAGGACTGACATTAATTTACTACC 58.818 37.037 0.00 0.00 0.00 3.18
2122 2262 4.485163 GCGCAAAGGACTGACATTAATTT 58.515 39.130 0.30 0.00 0.00 1.82
2126 2266 1.075542 CGCGCAAAGGACTGACATTA 58.924 50.000 8.75 0.00 0.00 1.90
2127 2267 0.884704 ACGCGCAAAGGACTGACATT 60.885 50.000 5.73 0.00 0.00 2.71
2128 2268 0.884704 AACGCGCAAAGGACTGACAT 60.885 50.000 5.73 0.00 0.00 3.06
2142 2282 4.323070 TGCAATTTTGATTATGACAACGCG 59.677 37.500 3.53 3.53 0.00 6.01
2225 2366 0.035820 TACCCGGGTGCATTTGACTC 60.036 55.000 36.97 0.00 0.00 3.36
2229 2370 1.616374 ACTTTTACCCGGGTGCATTTG 59.384 47.619 36.97 21.40 0.00 2.32
2274 2415 2.118313 TCAGTGGACATGATGCCAAG 57.882 50.000 9.57 6.68 35.63 3.61
2783 2928 1.620822 TCTTCTTTGCCCTGCCTTTC 58.379 50.000 0.00 0.00 0.00 2.62
2818 2963 1.871126 GCAGAAGCCACCTTCCTTGC 61.871 60.000 0.17 1.82 46.97 4.01
2882 3027 3.673599 GTCCAGCCAAGGAGCAAC 58.326 61.111 0.00 0.00 38.64 4.17
2963 3108 3.607741 GGAGCTTTCTTTACCTACCACC 58.392 50.000 0.00 0.00 0.00 4.61
2964 3109 3.607741 GGGAGCTTTCTTTACCTACCAC 58.392 50.000 0.00 0.00 0.00 4.16
2965 3110 2.235402 CGGGAGCTTTCTTTACCTACCA 59.765 50.000 0.00 0.00 0.00 3.25
2985 3130 4.038042 TCCTACTCCACAAAGCAGATATCG 59.962 45.833 0.00 0.00 0.00 2.92
3068 3213 3.744719 CGTGGACCGCGGAGAGAA 61.745 66.667 35.90 9.56 33.47 2.87
3236 3382 1.796459 GTACAGGCTTACACACCGTTG 59.204 52.381 0.00 0.00 0.00 4.10
3339 3524 5.622770 AACAAAGAACCAAGTTATAGGCG 57.377 39.130 0.00 0.00 0.00 5.52
3417 3604 3.340034 AGATGCAATTGCCACCAAATTG 58.660 40.909 26.94 4.84 41.18 2.32
3418 3605 3.706600 AGATGCAATTGCCACCAAATT 57.293 38.095 26.94 2.89 41.18 1.82
3433 3620 5.456822 GTCAACAAGAACAACAGAAAGATGC 59.543 40.000 0.00 0.00 0.00 3.91
3441 3628 7.329226 ACTTCAAATTGTCAACAAGAACAACAG 59.671 33.333 1.69 0.00 39.47 3.16
3457 3644 9.696917 AAAATAGCTCTTGGTAACTTCAAATTG 57.303 29.630 0.00 0.00 37.61 2.32
3472 3662 9.520515 TTGGTTTCTGAGATTAAAATAGCTCTT 57.479 29.630 0.00 0.00 0.00 2.85
3558 3748 6.526222 GTCTCAATCTGTTTCACGTATGTTC 58.474 40.000 0.00 0.00 0.00 3.18
3565 3755 2.672714 TCCGTCTCAATCTGTTTCACG 58.327 47.619 0.00 0.00 0.00 4.35
3592 3782 7.733773 TCTAGATATTCTGTTGGAGGTTTCA 57.266 36.000 0.00 0.00 0.00 2.69
3679 3870 4.569719 CCCCCTCACTGTTGTAATACTT 57.430 45.455 0.00 0.00 0.00 2.24
3704 3900 2.415512 GGAGCGCGAAACTGTATTTCTT 59.584 45.455 12.10 0.00 0.00 2.52
3750 3946 2.226330 AGCGTTACTGTGCAATTTCCA 58.774 42.857 0.00 0.00 0.00 3.53
3825 4021 0.471617 CTGGATTCGGGAGCCATCTT 59.528 55.000 0.00 0.00 0.00 2.40
3864 4060 2.677524 GCTGTTGCTGGGCATGGA 60.678 61.111 0.00 0.00 38.76 3.41
3900 4096 2.167662 TGTGTTCTCACTCGCTATCCA 58.832 47.619 0.00 0.00 44.14 3.41
3903 4099 3.944055 ACTTGTGTTCTCACTCGCTAT 57.056 42.857 0.00 0.00 44.14 2.97
3904 4100 3.639538 GAACTTGTGTTCTCACTCGCTA 58.360 45.455 2.11 0.00 46.56 4.26


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

AutoCloner maintained by Alex Coulton.