Multiple sequence alignment - TraesCS1D01G414900

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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 TraesCS1D01G414900 chr1D 100.000 2540 0 0 1 2540 474506177 474508716 0.000000e+00 4691
1 TraesCS1D01G414900 chr1D 85.477 241 31 3 2209 2446 438211181 438210942 5.430000e-62 248
2 TraesCS1D01G414900 chr1A 89.260 2216 102 41 3 2149 569132185 569134333 0.000000e+00 2649
3 TraesCS1D01G414900 chr1A 88.761 347 36 2 2179 2525 569134451 569134794 3.020000e-114 422
4 TraesCS1D01G414900 chr1A 86.316 95 11 1 2431 2525 569137521 569137613 4.470000e-18 102
5 TraesCS1D01G414900 chr1B 89.840 1939 68 46 12 1897 659776684 659778546 0.000000e+00 2370
6 TraesCS1D01G414900 chr3A 87.665 227 23 4 2218 2440 222104085 222104310 2.510000e-65 259
7 TraesCS1D01G414900 chr2D 86.122 245 27 3 2207 2447 120561253 120561494 9.020000e-65 257
8 TraesCS1D01G414900 chr2B 84.524 252 31 6 2207 2452 801215340 801215589 2.520000e-60 243
9 TraesCS1D01G414900 chr6D 83.951 243 31 5 2209 2446 25458712 25458473 2.540000e-55 226
10 TraesCS1D01G414900 chr6D 83.468 248 31 9 2207 2447 210894622 210894378 3.290000e-54 222
11 TraesCS1D01G414900 chr4B 83.884 242 27 9 2209 2445 665819394 665819160 1.180000e-53 220
12 TraesCS1D01G414900 chr5B 83.471 242 31 6 2207 2446 663242396 663242162 1.530000e-52 217


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 TraesCS1D01G414900 chr1D 474506177 474508716 2539 False 4691.000000 4691 100.000000 1 2540 1 chr1D.!!$F1 2539
1 TraesCS1D01G414900 chr1A 569132185 569137613 5428 False 1057.666667 2649 88.112333 3 2525 3 chr1A.!!$F1 2522
2 TraesCS1D01G414900 chr1B 659776684 659778546 1862 False 2370.000000 2370 89.840000 12 1897 1 chr1B.!!$F1 1885

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
950 1022 0.036306 TTTTCTTCCCCTCTGCCGTC 59.964 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2018 0.108138 GCGATTCCTGCACCTGTACT 60.108 55.0 0.0 0.0 0.0 2.73 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
26 27 3.826754 CACCGCGCTCTCTGGCTA 61.827 66.667 5.56 0.00 0.00 3.93
27 28 3.068691 ACCGCGCTCTCTGGCTAA 61.069 61.111 5.56 0.00 0.00 3.09
43 44 0.326264 CTAAGTCAAGCCACCTGCCT 59.674 55.000 0.00 0.00 42.71 4.75
471 501 4.403113 TCGCGGCTTGGGTTGATATATATA 59.597 41.667 6.13 0.00 0.00 0.86
472 502 5.069914 TCGCGGCTTGGGTTGATATATATAT 59.930 40.000 6.13 4.86 0.00 0.86
610 653 2.577606 TCCATCCAATCCAACGTTGT 57.422 45.000 25.63 6.56 0.00 3.32
707 776 0.548510 GGATGCTCTTAGCTGGGGTT 59.451 55.000 0.00 0.00 42.97 4.11
708 777 1.064389 GGATGCTCTTAGCTGGGGTTT 60.064 52.381 0.00 0.00 42.97 3.27
709 778 2.621668 GGATGCTCTTAGCTGGGGTTTT 60.622 50.000 0.00 0.00 42.97 2.43
710 779 1.909700 TGCTCTTAGCTGGGGTTTTG 58.090 50.000 0.00 0.00 42.97 2.44
711 780 1.144913 TGCTCTTAGCTGGGGTTTTGT 59.855 47.619 0.00 0.00 42.97 2.83
712 781 2.239400 GCTCTTAGCTGGGGTTTTGTT 58.761 47.619 0.00 0.00 38.45 2.83
713 782 2.628178 GCTCTTAGCTGGGGTTTTGTTT 59.372 45.455 0.00 0.00 38.45 2.83
714 783 3.305403 GCTCTTAGCTGGGGTTTTGTTTC 60.305 47.826 0.00 0.00 38.45 2.78
715 784 4.145052 CTCTTAGCTGGGGTTTTGTTTCT 58.855 43.478 0.00 0.00 0.00 2.52
716 785 4.142038 TCTTAGCTGGGGTTTTGTTTCTC 58.858 43.478 0.00 0.00 0.00 2.87
717 786 2.452600 AGCTGGGGTTTTGTTTCTCA 57.547 45.000 0.00 0.00 0.00 3.27
718 787 2.310538 AGCTGGGGTTTTGTTTCTCAG 58.689 47.619 0.00 0.00 0.00 3.35
719 788 2.031870 GCTGGGGTTTTGTTTCTCAGT 58.968 47.619 0.00 0.00 0.00 3.41
720 789 2.223805 GCTGGGGTTTTGTTTCTCAGTG 60.224 50.000 0.00 0.00 0.00 3.66
721 790 1.754226 TGGGGTTTTGTTTCTCAGTGC 59.246 47.619 0.00 0.00 0.00 4.40
722 791 2.031870 GGGGTTTTGTTTCTCAGTGCT 58.968 47.619 0.00 0.00 0.00 4.40
723 792 3.219281 GGGGTTTTGTTTCTCAGTGCTA 58.781 45.455 0.00 0.00 0.00 3.49
724 793 3.004419 GGGGTTTTGTTTCTCAGTGCTAC 59.996 47.826 0.00 0.00 0.00 3.58
725 794 3.630312 GGGTTTTGTTTCTCAGTGCTACA 59.370 43.478 0.00 0.00 0.00 2.74
726 795 4.278419 GGGTTTTGTTTCTCAGTGCTACAT 59.722 41.667 0.00 0.00 0.00 2.29
727 796 5.452777 GGTTTTGTTTCTCAGTGCTACATC 58.547 41.667 0.00 0.00 0.00 3.06
728 797 4.990543 TTTGTTTCTCAGTGCTACATCG 57.009 40.909 0.00 0.00 0.00 3.84
729 798 3.934457 TGTTTCTCAGTGCTACATCGA 57.066 42.857 0.00 0.00 0.00 3.59
766 835 2.426522 TGTCATCTTCCTCCTTTTGCG 58.573 47.619 0.00 0.00 0.00 4.85
769 838 2.038426 TCATCTTCCTCCTTTTGCGTGA 59.962 45.455 0.00 0.00 0.00 4.35
833 902 2.501316 ACATTCTGATCACCGTCCATCA 59.499 45.455 0.00 0.00 0.00 3.07
834 903 2.967599 TTCTGATCACCGTCCATCAG 57.032 50.000 9.49 9.49 45.15 2.90
836 905 0.463204 CTGATCACCGTCCATCAGCT 59.537 55.000 0.00 0.00 39.64 4.24
841 910 0.752658 CACCGTCCATCAGCTATCCA 59.247 55.000 0.00 0.00 0.00 3.41
846 915 0.106708 TCCATCAGCTATCCAACGGC 59.893 55.000 0.00 0.00 0.00 5.68
919 991 7.203910 ACGTGACACATCTTCTTATCTTATCC 58.796 38.462 6.37 0.00 0.00 2.59
950 1022 0.036306 TTTTCTTCCCCTCTGCCGTC 59.964 55.000 0.00 0.00 0.00 4.79
1655 1747 4.929819 ATTGTAAAATTGTATCCGGCCC 57.070 40.909 0.00 0.00 0.00 5.80
1724 1818 4.642445 TTTAATCTCCACTACGATGCGA 57.358 40.909 0.00 0.00 0.00 5.10
1761 1865 8.754096 TGATGTTTCGTTTCAGAATTTTGATTG 58.246 29.630 0.00 0.00 0.00 2.67
1783 1887 6.702449 TGGATATGGTATGTAATTGGCTCT 57.298 37.500 0.00 0.00 0.00 4.09
1784 1888 6.711277 TGGATATGGTATGTAATTGGCTCTC 58.289 40.000 0.00 0.00 0.00 3.20
1788 1892 3.069586 TGGTATGTAATTGGCTCTCGAGG 59.930 47.826 13.56 4.50 0.00 4.63
1799 1903 2.289945 GGCTCTCGAGGGAATGCATTAT 60.290 50.000 18.81 1.05 0.00 1.28
1819 1923 2.635714 TGATATGCACTGGCTGTTCTG 58.364 47.619 0.00 0.00 41.91 3.02
1845 1949 1.676006 GGCCTGGTCGATGTAAAATGG 59.324 52.381 0.00 0.00 0.00 3.16
1889 1993 0.532573 ATGTGACTGACTACCTGCGG 59.467 55.000 0.00 0.00 0.00 5.69
1899 2003 1.153147 TACCTGCGGTGTTGCACAA 60.153 52.632 10.01 0.00 40.62 3.33
1906 2010 1.095228 CGGTGTTGCACAAGTCAGGT 61.095 55.000 1.61 0.00 35.86 4.00
1907 2011 1.102978 GGTGTTGCACAAGTCAGGTT 58.897 50.000 1.61 0.00 35.86 3.50
1908 2012 2.294074 GGTGTTGCACAAGTCAGGTTA 58.706 47.619 1.61 0.00 35.86 2.85
1909 2013 2.032924 GGTGTTGCACAAGTCAGGTTAC 59.967 50.000 1.61 0.00 35.86 2.50
1910 2014 2.680841 GTGTTGCACAAGTCAGGTTACA 59.319 45.455 0.00 0.00 34.08 2.41
1911 2015 2.942376 TGTTGCACAAGTCAGGTTACAG 59.058 45.455 0.00 0.00 0.00 2.74
1912 2016 2.943033 GTTGCACAAGTCAGGTTACAGT 59.057 45.455 0.00 0.00 0.00 3.55
1913 2017 2.560504 TGCACAAGTCAGGTTACAGTG 58.439 47.619 0.00 0.00 33.43 3.66
1914 2018 2.169561 TGCACAAGTCAGGTTACAGTGA 59.830 45.455 0.00 0.00 32.58 3.41
1915 2019 2.802816 GCACAAGTCAGGTTACAGTGAG 59.197 50.000 0.00 0.00 32.58 3.51
1916 2020 3.741388 GCACAAGTCAGGTTACAGTGAGT 60.741 47.826 0.00 0.00 32.58 3.41
1917 2021 4.500887 GCACAAGTCAGGTTACAGTGAGTA 60.501 45.833 0.00 0.00 32.58 2.59
1918 2022 4.982916 CACAAGTCAGGTTACAGTGAGTAC 59.017 45.833 0.00 0.00 32.58 2.73
1919 2023 4.647853 ACAAGTCAGGTTACAGTGAGTACA 59.352 41.667 0.00 0.00 30.91 2.90
1920 2024 5.221263 ACAAGTCAGGTTACAGTGAGTACAG 60.221 44.000 0.00 0.00 30.91 2.74
1921 2025 3.827302 AGTCAGGTTACAGTGAGTACAGG 59.173 47.826 0.00 0.00 30.91 4.00
1931 2035 2.234908 AGTGAGTACAGGTGCAGGAATC 59.765 50.000 0.00 0.00 0.00 2.52
1934 2038 0.108138 GTACAGGTGCAGGAATCGCT 60.108 55.000 0.00 0.00 0.00 4.93
1935 2039 0.108186 TACAGGTGCAGGAATCGCTG 60.108 55.000 0.00 0.00 0.00 5.18
1937 2041 1.078848 AGGTGCAGGAATCGCTGAC 60.079 57.895 0.00 0.33 0.00 3.51
1941 2045 1.929836 GTGCAGGAATCGCTGACTAAG 59.070 52.381 0.00 0.00 0.00 2.18
1946 2050 1.134560 GGAATCGCTGACTAAGTCCGT 59.865 52.381 0.00 0.00 0.00 4.69
1948 2052 0.179134 ATCGCTGACTAAGTCCGTGC 60.179 55.000 0.00 0.00 29.73 5.34
1993 2097 1.300971 CCCTGACTGACCAATGCACG 61.301 60.000 0.00 0.00 0.00 5.34
2030 2134 3.493176 GCAGGATTGCTGTTTTCCAAGTT 60.493 43.478 7.05 0.00 46.95 2.66
2044 2148 8.428063 TGTTTTCCAAGTTTATTGATCAACCAT 58.572 29.630 11.07 0.00 0.00 3.55
2089 2193 4.358851 ACACACAATGTTTGCATGTACAC 58.641 39.130 0.00 0.00 38.98 2.90
2098 2202 1.904287 TGCATGTACACAAAGGGGAC 58.096 50.000 0.00 0.00 0.00 4.46
2126 2230 2.932261 CCTACCCAGACTAAAATGGCC 58.068 52.381 0.00 0.00 35.10 5.36
2129 2233 1.272480 ACCCAGACTAAAATGGCCACC 60.272 52.381 8.16 0.00 35.10 4.61
2151 2315 5.780793 ACCCATATCTAAAGAAGTAGCGGAT 59.219 40.000 0.00 0.00 0.00 4.18
2169 2333 3.747388 CGGATTAGGGCATGTACAATGGT 60.747 47.826 0.00 0.00 0.00 3.55
2174 2338 7.120726 GGATTAGGGCATGTACAATGGTATTAC 59.879 40.741 0.00 0.00 0.00 1.89
2180 2344 6.430000 GGCATGTACAATGGTATTACCTTAGG 59.570 42.308 13.90 0.00 39.58 2.69
2182 2346 7.717875 GCATGTACAATGGTATTACCTTAGGAA 59.282 37.037 13.90 0.00 39.58 3.36
2185 2349 7.717875 TGTACAATGGTATTACCTTAGGAATGC 59.282 37.037 13.90 4.32 39.58 3.56
2200 2392 2.104281 GGAATGCCACGTAGAACCCTAT 59.896 50.000 0.00 0.00 0.00 2.57
2204 2396 4.127566 TGCCACGTAGAACCCTATAAAC 57.872 45.455 0.00 0.00 0.00 2.01
2213 2405 6.350780 CGTAGAACCCTATAAACAAGGAGTGT 60.351 42.308 0.00 0.00 44.64 3.55
2215 2407 4.467198 ACCCTATAAACAAGGAGTGTCG 57.533 45.455 0.00 0.00 40.60 4.35
2230 2422 2.864343 AGTGTCGCGTAGAATAAATGCC 59.136 45.455 5.77 0.00 0.00 4.40
2234 2426 1.455786 CGCGTAGAATAAATGCCGAGG 59.544 52.381 0.00 0.00 0.00 4.63
2237 2429 3.713288 CGTAGAATAAATGCCGAGGTGA 58.287 45.455 0.00 0.00 0.00 4.02
2327 2519 7.761409 TGTCTCACCATGTTTTTATGAATAGC 58.239 34.615 0.00 0.00 0.00 2.97
2360 2552 9.911788 TTGAAGATAAAGCTAAGAGAATCCATT 57.088 29.630 0.00 0.00 33.66 3.16
2370 2562 6.073331 GCTAAGAGAATCCATTGTAGACATGC 60.073 42.308 0.00 0.00 33.66 4.06
2402 2594 9.715123 TTTGTTATATCTGAATTACATGCAACG 57.285 29.630 0.00 0.00 0.00 4.10
2408 2600 6.247727 TCTGAATTACATGCAACGCTTAAA 57.752 33.333 0.00 0.00 0.00 1.52
2413 2605 9.071221 TGAATTACATGCAACGCTTAAAATAAG 57.929 29.630 0.00 0.00 0.00 1.73
2417 2609 7.372451 ACATGCAACGCTTAAAATAAGACTA 57.628 32.000 0.00 0.00 0.00 2.59
2421 2613 7.684670 TGCAACGCTTAAAATAAGACTATCTG 58.315 34.615 1.42 0.00 0.00 2.90
2461 2653 2.157738 CTTAGCAAGGCTGTGAGCTTT 58.842 47.619 8.88 0.00 41.48 3.51
2476 2668 4.676924 GTGAGCTTTGAAATTGAAGTTCCG 59.323 41.667 2.74 0.00 33.72 4.30
2480 2672 5.474876 AGCTTTGAAATTGAAGTTCCGAGAT 59.525 36.000 2.74 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.822192 CGGCGTCCGTGGAGATGA 61.822 66.667 9.69 0.00 42.73 2.92
194 204 2.431683 TGCACCAAGAGGCACCTC 59.568 61.111 8.74 8.74 43.03 3.85
399 416 1.674322 CATTCCACCGGTCACCACC 60.674 63.158 2.59 0.00 39.69 4.61
471 501 0.175302 CTCGAGCTCACTCCAAGCAT 59.825 55.000 15.40 0.00 42.35 3.79
472 502 1.588597 CTCGAGCTCACTCCAAGCA 59.411 57.895 15.40 0.00 42.35 3.91
553 583 3.064324 GCCGGCAAGGAACAGCAT 61.064 61.111 24.80 0.00 45.00 3.79
556 586 2.409870 GGATGCCGGCAAGGAACAG 61.410 63.158 36.33 0.00 45.00 3.16
610 653 1.349688 AGGAATACGGTGAGTGGCAAA 59.650 47.619 0.00 0.00 0.00 3.68
707 776 4.627058 TCGATGTAGCACTGAGAAACAAA 58.373 39.130 0.00 0.00 0.00 2.83
708 777 4.251543 TCGATGTAGCACTGAGAAACAA 57.748 40.909 0.00 0.00 0.00 2.83
709 778 3.934457 TCGATGTAGCACTGAGAAACA 57.066 42.857 0.00 0.00 0.00 2.83
710 779 3.553511 CCATCGATGTAGCACTGAGAAAC 59.446 47.826 23.27 0.00 0.00 2.78
711 780 3.447229 TCCATCGATGTAGCACTGAGAAA 59.553 43.478 23.27 0.00 0.00 2.52
712 781 3.023832 TCCATCGATGTAGCACTGAGAA 58.976 45.455 23.27 0.00 0.00 2.87
713 782 2.654863 TCCATCGATGTAGCACTGAGA 58.345 47.619 23.27 7.77 0.00 3.27
714 783 3.315418 CATCCATCGATGTAGCACTGAG 58.685 50.000 23.27 5.50 40.97 3.35
715 784 2.036346 CCATCCATCGATGTAGCACTGA 59.964 50.000 23.27 12.00 43.87 3.41
716 785 2.036346 TCCATCCATCGATGTAGCACTG 59.964 50.000 23.27 6.92 43.87 3.66
717 786 2.319844 TCCATCCATCGATGTAGCACT 58.680 47.619 23.27 0.00 43.87 4.40
718 787 2.820059 TCCATCCATCGATGTAGCAC 57.180 50.000 23.27 0.00 43.87 4.40
719 788 2.027837 CCATCCATCCATCGATGTAGCA 60.028 50.000 23.27 5.45 43.87 3.49
720 789 2.234661 TCCATCCATCCATCGATGTAGC 59.765 50.000 23.27 0.00 43.87 3.58
721 790 4.439968 CATCCATCCATCCATCGATGTAG 58.560 47.826 23.27 12.36 43.87 2.74
722 791 3.198417 CCATCCATCCATCCATCGATGTA 59.802 47.826 23.27 9.09 43.87 2.29
723 792 2.026542 CCATCCATCCATCCATCGATGT 60.027 50.000 23.27 3.55 43.87 3.06
724 793 2.237893 TCCATCCATCCATCCATCGATG 59.762 50.000 18.76 18.76 44.80 3.84
725 794 2.554563 TCCATCCATCCATCCATCGAT 58.445 47.619 0.00 0.00 0.00 3.59
726 795 2.028561 TCCATCCATCCATCCATCGA 57.971 50.000 0.00 0.00 0.00 3.59
727 796 2.026542 ACATCCATCCATCCATCCATCG 60.027 50.000 0.00 0.00 0.00 3.84
728 797 3.009805 TGACATCCATCCATCCATCCATC 59.990 47.826 0.00 0.00 0.00 3.51
729 798 2.990998 TGACATCCATCCATCCATCCAT 59.009 45.455 0.00 0.00 0.00 3.41
766 835 5.475273 TCATGCAGAAAGAATCGATTCAC 57.525 39.130 33.42 24.19 39.23 3.18
769 838 5.591472 TCCATTCATGCAGAAAGAATCGATT 59.409 36.000 11.20 11.20 40.22 3.34
812 881 2.501316 TGATGGACGGTGATCAGAATGT 59.499 45.455 0.00 0.00 37.40 2.71
833 902 0.618458 TTTCTGGCCGTTGGATAGCT 59.382 50.000 0.00 0.00 0.00 3.32
834 903 1.334869 CATTTCTGGCCGTTGGATAGC 59.665 52.381 0.00 0.00 0.00 2.97
836 905 2.364632 CACATTTCTGGCCGTTGGATA 58.635 47.619 0.00 0.00 0.00 2.59
841 910 1.959085 CTGCACATTTCTGGCCGTT 59.041 52.632 0.00 0.00 0.00 4.44
846 915 0.167470 CGACAGCTGCACATTTCTGG 59.833 55.000 15.27 0.00 0.00 3.86
919 991 2.285064 GAAGAAAAGAGGCGCGCGAG 62.285 60.000 37.18 8.39 0.00 5.03
1077 1162 1.071314 TGGGGAAGAATGGGTGTGGT 61.071 55.000 0.00 0.00 0.00 4.16
1636 1728 2.290464 CGGGCCGGATACAATTTTACA 58.710 47.619 20.56 0.00 0.00 2.41
1637 1729 2.291365 ACGGGCCGGATACAATTTTAC 58.709 47.619 31.78 0.00 0.00 2.01
1638 1730 2.683867 CAACGGGCCGGATACAATTTTA 59.316 45.455 31.78 0.00 0.00 1.52
1639 1731 1.474879 CAACGGGCCGGATACAATTTT 59.525 47.619 31.78 8.99 0.00 1.82
1640 1732 1.099689 CAACGGGCCGGATACAATTT 58.900 50.000 31.78 9.80 0.00 1.82
1641 1733 1.381165 GCAACGGGCCGGATACAATT 61.381 55.000 31.78 10.64 36.11 2.32
1642 1734 1.822186 GCAACGGGCCGGATACAAT 60.822 57.895 31.78 3.51 36.11 2.71
1643 1735 2.437002 GCAACGGGCCGGATACAA 60.437 61.111 31.78 0.00 36.11 2.41
1706 1799 2.481449 GGTTCGCATCGTAGTGGAGATT 60.481 50.000 0.00 0.00 0.00 2.40
1724 1818 6.039270 TGAAACGAAACATCAGAATTCAGGTT 59.961 34.615 8.44 0.00 0.00 3.50
1761 1865 5.812642 CGAGAGCCAATTACATACCATATCC 59.187 44.000 0.00 0.00 0.00 2.59
1778 1882 0.179034 AATGCATTCCCTCGAGAGCC 60.179 55.000 15.71 0.00 0.00 4.70
1779 1883 2.533266 TAATGCATTCCCTCGAGAGC 57.467 50.000 16.86 10.10 0.00 4.09
1799 1903 2.635714 CAGAACAGCCAGTGCATATCA 58.364 47.619 0.00 0.00 41.13 2.15
1806 1910 1.162698 CATGTCCAGAACAGCCAGTG 58.837 55.000 0.00 0.00 42.37 3.66
1819 1923 1.524621 CATCGACCAGGCCATGTCC 60.525 63.158 16.41 0.00 0.00 4.02
1845 1949 2.100605 ATCGAACTCCAAGTGGCTTC 57.899 50.000 0.00 0.00 34.44 3.86
1899 2003 3.827302 CCTGTACTCACTGTAACCTGACT 59.173 47.826 0.00 0.00 32.25 3.41
1906 2010 2.299013 CCTGCACCTGTACTCACTGTAA 59.701 50.000 0.00 0.00 32.25 2.41
1907 2011 1.893137 CCTGCACCTGTACTCACTGTA 59.107 52.381 0.00 0.00 0.00 2.74
1908 2012 0.681733 CCTGCACCTGTACTCACTGT 59.318 55.000 0.00 0.00 0.00 3.55
1909 2013 0.969149 TCCTGCACCTGTACTCACTG 59.031 55.000 0.00 0.00 0.00 3.66
1910 2014 1.717032 TTCCTGCACCTGTACTCACT 58.283 50.000 0.00 0.00 0.00 3.41
1911 2015 2.622436 GATTCCTGCACCTGTACTCAC 58.378 52.381 0.00 0.00 0.00 3.51
1912 2016 1.204704 CGATTCCTGCACCTGTACTCA 59.795 52.381 0.00 0.00 0.00 3.41
1913 2017 1.927895 CGATTCCTGCACCTGTACTC 58.072 55.000 0.00 0.00 0.00 2.59
1914 2018 0.108138 GCGATTCCTGCACCTGTACT 60.108 55.000 0.00 0.00 0.00 2.73
1915 2019 0.108138 AGCGATTCCTGCACCTGTAC 60.108 55.000 0.00 0.00 33.85 2.90
1916 2020 0.108186 CAGCGATTCCTGCACCTGTA 60.108 55.000 0.00 0.00 33.85 2.74
1917 2021 1.376424 CAGCGATTCCTGCACCTGT 60.376 57.895 0.00 0.00 33.85 4.00
1918 2022 1.078918 TCAGCGATTCCTGCACCTG 60.079 57.895 0.00 0.00 32.87 4.00
1919 2023 1.078848 GTCAGCGATTCCTGCACCT 60.079 57.895 0.00 0.00 32.87 4.00
1920 2024 0.175760 TAGTCAGCGATTCCTGCACC 59.824 55.000 0.00 0.00 32.87 5.01
1921 2025 1.929836 CTTAGTCAGCGATTCCTGCAC 59.070 52.381 0.00 0.00 32.87 4.57
1931 2035 2.152699 CGCACGGACTTAGTCAGCG 61.153 63.158 23.26 23.26 40.79 5.18
1934 2038 1.211969 GAGCGCACGGACTTAGTCA 59.788 57.895 11.47 0.00 33.68 3.41
1935 2039 0.388134 TTGAGCGCACGGACTTAGTC 60.388 55.000 11.47 3.36 0.00 2.59
1937 2041 1.352156 GGTTGAGCGCACGGACTTAG 61.352 60.000 11.47 0.00 0.00 2.18
1946 2050 0.604243 ATTGTTACCGGTTGAGCGCA 60.604 50.000 15.04 0.00 0.00 6.09
1948 2052 0.179200 GCATTGTTACCGGTTGAGCG 60.179 55.000 15.04 0.00 0.00 5.03
1993 2097 4.329545 TGCCTGGGCTGTCGTTCC 62.330 66.667 13.05 0.00 42.51 3.62
2089 2193 1.230212 GGCCCTATGGTCCCCTTTG 59.770 63.158 0.00 0.00 0.00 2.77
2105 2209 2.298610 GCCATTTTAGTCTGGGTAGGC 58.701 52.381 0.00 0.00 32.90 3.93
2107 2211 3.279434 GTGGCCATTTTAGTCTGGGTAG 58.721 50.000 9.72 0.00 32.90 3.18
2115 2219 4.814224 AGATATGGGTGGCCATTTTAGT 57.186 40.909 9.72 0.00 0.00 2.24
2126 2230 5.010719 TCCGCTACTTCTTTAGATATGGGTG 59.989 44.000 0.00 0.00 0.00 4.61
2129 2233 7.976734 CCTAATCCGCTACTTCTTTAGATATGG 59.023 40.741 0.00 0.00 0.00 2.74
2151 2315 6.102027 AGGTAATACCATTGTACATGCCCTAA 59.898 38.462 12.54 0.00 41.95 2.69
2169 2333 5.834742 TCTACGTGGCATTCCTAAGGTAATA 59.165 40.000 0.00 0.00 0.00 0.98
2174 2338 3.195661 GTTCTACGTGGCATTCCTAAGG 58.804 50.000 0.00 0.00 0.00 2.69
2180 2344 2.973694 TAGGGTTCTACGTGGCATTC 57.026 50.000 0.00 0.00 0.00 2.67
2182 2346 4.162698 TGTTTATAGGGTTCTACGTGGCAT 59.837 41.667 0.00 0.00 0.00 4.40
2185 2349 5.105228 TCCTTGTTTATAGGGTTCTACGTGG 60.105 44.000 0.00 0.00 33.41 4.94
2200 2392 2.553602 TCTACGCGACACTCCTTGTTTA 59.446 45.455 15.93 0.00 39.17 2.01
2204 2396 2.279582 ATTCTACGCGACACTCCTTG 57.720 50.000 15.93 0.00 0.00 3.61
2213 2405 2.390938 CTCGGCATTTATTCTACGCGA 58.609 47.619 15.93 0.00 0.00 5.87
2215 2407 2.221055 CACCTCGGCATTTATTCTACGC 59.779 50.000 0.00 0.00 0.00 4.42
2230 2422 9.243637 CTTATATTTTCTCTCTTCTTCACCTCG 57.756 37.037 0.00 0.00 0.00 4.63
2335 2527 9.334947 CAATGGATTCTCTTAGCTTTATCTTCA 57.665 33.333 0.00 0.00 0.00 3.02
2336 2528 9.336171 ACAATGGATTCTCTTAGCTTTATCTTC 57.664 33.333 0.00 0.00 0.00 2.87
2339 2531 9.988815 TCTACAATGGATTCTCTTAGCTTTATC 57.011 33.333 0.00 0.00 0.00 1.75
2344 2536 6.798427 TGTCTACAATGGATTCTCTTAGCT 57.202 37.500 0.00 0.00 0.00 3.32
2384 2576 4.970662 AAGCGTTGCATGTAATTCAGAT 57.029 36.364 0.00 0.00 0.00 2.90
2387 2579 8.972262 TTATTTTAAGCGTTGCATGTAATTCA 57.028 26.923 0.00 0.00 0.00 2.57
2388 2580 9.284594 TCTTATTTTAAGCGTTGCATGTAATTC 57.715 29.630 0.00 0.00 0.00 2.17
2413 2605 8.122952 GCATGTACAATGGTTAAACAGATAGTC 58.877 37.037 0.00 0.00 0.00 2.59
2417 2609 5.127031 GGGCATGTACAATGGTTAAACAGAT 59.873 40.000 0.00 0.00 0.00 2.90
2421 2613 5.400066 AAGGGCATGTACAATGGTTAAAC 57.600 39.130 0.00 0.00 0.00 2.01
2424 2616 4.204012 GCTAAGGGCATGTACAATGGTTA 58.796 43.478 0.00 0.00 41.35 2.85
2455 2647 5.049405 TCTCGGAACTTCAATTTCAAAGCTC 60.049 40.000 0.00 0.00 0.00 4.09
2461 2653 6.623549 GCATGAATCTCGGAACTTCAATTTCA 60.624 38.462 0.00 0.00 33.03 2.69
2462 2654 5.741040 GCATGAATCTCGGAACTTCAATTTC 59.259 40.000 0.00 0.00 33.03 2.17
2476 2668 9.793252 AGTATATTGTTTTTGTGCATGAATCTC 57.207 29.630 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.