Multiple sequence alignment - TraesCS6A01G273000

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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 TraesCS6A01G273000 chr6A 100.000 3947 0 0 1 3947 499408713 499404767 0.000000e+00 7289.0
1 TraesCS6A01G273000 chr6D 87.922 4024 276 88 7 3947 357014742 357010846 0.000000e+00 4545.0
2 TraesCS6A01G273000 chr6D 92.417 211 15 1 2290 2500 450750166 450750375 2.310000e-77 300.0
3 TraesCS6A01G273000 chr6B 89.074 3533 194 74 346 3806 538377448 538374036 0.000000e+00 4209.0
4 TraesCS6A01G273000 chr6B 83.444 302 36 5 18 315 538377735 538377444 6.500000e-68 268.0
5 TraesCS6A01G273000 chr3B 84.922 451 35 17 855 1296 508758397 508757971 3.650000e-115 425.0
6 TraesCS6A01G273000 chr3B 96.875 32 1 0 1948 1979 10592010 10591979 2.000000e-03 54.7
7 TraesCS6A01G273000 chr7B 93.056 216 14 1 2290 2505 707684075 707683861 8.230000e-82 315.0
8 TraesCS6A01G273000 chr7B 83.784 74 10 2 1542 1614 541170922 541170850 7.080000e-08 69.4
9 TraesCS6A01G273000 chr7B 97.297 37 1 0 1943 1979 748599797 748599761 3.290000e-06 63.9
10 TraesCS6A01G273000 chr2A 92.857 210 14 1 2296 2505 231291588 231291796 1.780000e-78 303.0
11 TraesCS6A01G273000 chr2A 87.059 85 8 3 1753 1837 454692284 454692365 4.200000e-15 93.5
12 TraesCS6A01G273000 chr5B 92.056 214 16 1 2295 2508 504062622 504062410 2.310000e-77 300.0
13 TraesCS6A01G273000 chr5A 92.056 214 16 1 2295 2508 134749136 134748924 2.310000e-77 300.0
14 TraesCS6A01G273000 chr5A 92.056 214 16 1 2295 2508 505515343 505515131 2.310000e-77 300.0
15 TraesCS6A01G273000 chr4A 92.056 214 16 1 2295 2508 502593316 502593104 2.310000e-77 300.0
16 TraesCS6A01G273000 chr2D 87.059 85 8 3 1753 1837 343557405 343557486 4.200000e-15 93.5
17 TraesCS6A01G273000 chr2D 90.196 51 1 1 1933 1979 609903109 609903159 3.290000e-06 63.9
18 TraesCS6A01G273000 chr2B 85.882 85 9 3 1753 1837 408725946 408726027 1.950000e-13 87.9
19 TraesCS6A01G273000 chr2B 90.196 51 1 1 1933 1979 796475827 796475777 3.290000e-06 63.9
20 TraesCS6A01G273000 chr7A 83.784 74 10 2 1542 1614 584387791 584387863 7.080000e-08 69.4
21 TraesCS6A01G273000 chrUn 97.143 35 1 0 1945 1979 142663068 142663034 4.260000e-05 60.2


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 TraesCS6A01G273000 chr6A 499404767 499408713 3946 True 7289.0 7289 100.000 1 3947 1 chr6A.!!$R1 3946
1 TraesCS6A01G273000 chr6D 357010846 357014742 3896 True 4545.0 4545 87.922 7 3947 1 chr6D.!!$R1 3940
2 TraesCS6A01G273000 chr6B 538374036 538377735 3699 True 2238.5 4209 86.259 18 3806 2 chr6B.!!$R1 3788

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
669 690 0.257905 CCTTTACTTACCCAGCCCCC 59.742 60.0 0.0 0.0 0.00 5.4 F
1633 1704 0.107456 ATGCATTGCTACTCCGGGAG 59.893 55.0 22.4 22.4 35.52 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2524 0.504384 CTGACTGAAACTGTGCGTCG 59.496 55.0 0.0 0.0 0.0 5.12 R
3318 3433 0.034896 TGCTTTGAAGAGGGGACGAC 59.965 55.0 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
35 36 2.609610 GGTGTGTGGCCTAGGGGA 60.610 66.667 11.72 0.00 33.58 4.81
36 37 2.001269 GGTGTGTGGCCTAGGGGAT 61.001 63.158 11.72 0.00 33.58 3.85
50 51 0.830648 GGGGATGATGTGGAAGTCGA 59.169 55.000 0.00 0.00 0.00 4.20
59 60 2.202756 GGAAGTCGAAGCCGCGAT 60.203 61.111 8.23 0.00 42.82 4.58
60 61 1.065273 GGAAGTCGAAGCCGCGATA 59.935 57.895 8.23 0.00 42.82 2.92
80 82 1.803519 CTCCGAAGAGCGTCTGTGC 60.804 63.158 0.00 0.00 38.67 4.57
81 83 2.811317 CCGAAGAGCGTCTGTGCC 60.811 66.667 0.00 0.00 38.67 5.01
108 110 1.373748 TCGCTTCTGGTAACACGGC 60.374 57.895 0.00 0.00 46.17 5.68
113 115 0.887387 TTCTGGTAACACGGCTTGCC 60.887 55.000 0.75 0.75 46.17 4.52
115 117 4.097863 GGTAACACGGCTTGCCGC 62.098 66.667 30.58 15.56 36.58 6.53
131 133 2.177531 GCGTCGTTGGCTCGTCTA 59.822 61.111 0.00 0.00 0.00 2.59
147 149 0.750850 TCTAGTATGCAACCTCGGGC 59.249 55.000 0.00 0.00 0.00 6.13
167 169 1.408127 CCTGGTGTGTGTTGTTGAGGA 60.408 52.381 0.00 0.00 0.00 3.71
285 295 1.301677 CGAGAGCTGAACCAAAGCCC 61.302 60.000 0.00 0.00 41.82 5.19
289 299 2.597217 CTGAACCAAAGCCCGCCA 60.597 61.111 0.00 0.00 0.00 5.69
326 345 1.002900 CTTTGGCTGGTGTGTGTAACG 60.003 52.381 0.00 0.00 42.39 3.18
334 353 4.884901 GTGTGTAACGCGGTTGTG 57.115 55.556 12.47 0.00 42.39 3.33
348 367 1.292992 GTTGTGTCGGTTTTCGGTCT 58.707 50.000 0.00 0.00 39.77 3.85
361 380 4.625972 TTTCGGTCTGTTTTCCTTGTTC 57.374 40.909 0.00 0.00 0.00 3.18
445 466 3.859411 TGTTTTCGTATGCCCATTTCC 57.141 42.857 0.00 0.00 0.00 3.13
458 479 2.554032 CCCATTTCCGATCAATGGCTAC 59.446 50.000 14.91 0.00 46.63 3.58
479 500 1.663643 CGTTCACACATCATAACCGGG 59.336 52.381 6.32 0.00 0.00 5.73
480 501 2.706890 GTTCACACATCATAACCGGGT 58.293 47.619 6.32 0.00 0.00 5.28
481 502 2.676342 GTTCACACATCATAACCGGGTC 59.324 50.000 6.32 0.00 0.00 4.46
482 503 2.184533 TCACACATCATAACCGGGTCT 58.815 47.619 6.32 0.00 0.00 3.85
485 506 1.129058 ACATCATAACCGGGTCTCCC 58.871 55.000 6.32 0.00 41.09 4.30
486 507 1.344087 ACATCATAACCGGGTCTCCCT 60.344 52.381 6.32 0.00 42.67 4.20
487 508 2.090943 ACATCATAACCGGGTCTCCCTA 60.091 50.000 6.32 0.00 42.67 3.53
488 509 2.376695 TCATAACCGGGTCTCCCTAG 57.623 55.000 6.32 0.00 42.67 3.02
489 510 0.680061 CATAACCGGGTCTCCCTAGC 59.320 60.000 6.32 0.00 42.67 3.42
490 511 0.471401 ATAACCGGGTCTCCCTAGCC 60.471 60.000 6.32 0.00 42.67 3.93
624 645 3.138930 CTGCATGCATCTGCCAGCC 62.139 63.158 22.97 0.00 41.58 4.85
625 646 3.912907 GCATGCATCTGCCAGCCC 61.913 66.667 14.21 0.00 41.18 5.19
655 676 2.366435 CCGGCCCTCCCTCCTTTA 60.366 66.667 0.00 0.00 0.00 1.85
656 677 2.743179 CCGGCCCTCCCTCCTTTAC 61.743 68.421 0.00 0.00 0.00 2.01
669 690 0.257905 CCTTTACTTACCCAGCCCCC 59.742 60.000 0.00 0.00 0.00 5.40
722 743 1.051008 GGCCCAATCCAATCCAATCC 58.949 55.000 0.00 0.00 0.00 3.01
726 747 0.311790 CAATCCAATCCAATCCCGCG 59.688 55.000 0.00 0.00 0.00 6.46
795 827 2.636768 GAAAAATTCCAGGGAGCACG 57.363 50.000 0.00 0.00 0.00 5.34
825 857 2.760385 GGGAGGGAGACAGGGACG 60.760 72.222 0.00 0.00 0.00 4.79
877 924 1.869690 GCCTCGTTGCTTGTCTTCC 59.130 57.895 0.00 0.00 0.00 3.46
893 940 4.142227 TGTCTTCCAAGATCCGTAGTTAGC 60.142 45.833 0.00 0.00 37.39 3.09
902 949 1.413767 CCGTAGTTAGCTGCACTGCG 61.414 60.000 22.98 22.98 46.32 5.18
949 996 3.989104 CGACTTAATCGCCATCCCT 57.011 52.632 0.00 0.00 45.52 4.20
950 997 2.240493 CGACTTAATCGCCATCCCTT 57.760 50.000 0.00 0.00 45.52 3.95
951 998 2.135933 CGACTTAATCGCCATCCCTTC 58.864 52.381 0.00 0.00 45.52 3.46
952 999 2.224066 CGACTTAATCGCCATCCCTTCT 60.224 50.000 0.00 0.00 45.52 2.85
953 1000 3.741388 CGACTTAATCGCCATCCCTTCTT 60.741 47.826 0.00 0.00 45.52 2.52
954 1001 3.545703 ACTTAATCGCCATCCCTTCTTG 58.454 45.455 0.00 0.00 0.00 3.02
955 1002 3.054361 ACTTAATCGCCATCCCTTCTTGT 60.054 43.478 0.00 0.00 0.00 3.16
959 1006 0.527565 CGCCATCCCTTCTTGTTTGG 59.472 55.000 0.00 0.00 0.00 3.28
968 1015 3.194542 CCCTTCTTGTTTGGTGTTGTTGA 59.805 43.478 0.00 0.00 0.00 3.18
969 1016 4.322349 CCCTTCTTGTTTGGTGTTGTTGAA 60.322 41.667 0.00 0.00 0.00 2.69
1297 1365 0.813610 TGTGGACGCAAAGGTGAGTG 60.814 55.000 0.00 0.00 37.97 3.51
1298 1366 0.531974 GTGGACGCAAAGGTGAGTGA 60.532 55.000 0.00 0.00 37.97 3.41
1299 1367 0.249868 TGGACGCAAAGGTGAGTGAG 60.250 55.000 0.00 0.00 37.97 3.51
1300 1368 0.249911 GGACGCAAAGGTGAGTGAGT 60.250 55.000 0.00 0.00 37.97 3.41
1380 1451 1.131883 GCTCTGCTTATTGGTGTGCTG 59.868 52.381 0.00 0.00 0.00 4.41
1494 1565 1.222113 GAAAGGGAGGCCGGAGAAG 59.778 63.158 5.05 0.00 0.00 2.85
1566 1637 1.063649 CGACTACATCCACGTCCGG 59.936 63.158 0.00 0.00 0.00 5.14
1617 1688 2.960129 CTCGCCGAACGGGTATGC 60.960 66.667 15.01 0.00 43.89 3.14
1622 1693 1.355210 CCGAACGGGTATGCATTGC 59.645 57.895 3.54 0.46 0.00 3.56
1629 1700 1.512926 GGGTATGCATTGCTACTCCG 58.487 55.000 3.54 0.00 0.00 4.63
1632 1703 1.070134 GTATGCATTGCTACTCCGGGA 59.930 52.381 3.54 0.00 0.00 5.14
1633 1704 0.107456 ATGCATTGCTACTCCGGGAG 59.893 55.000 22.40 22.40 35.52 4.30
1652 1723 2.100749 GAGGCCGGGGAAATAACAATTG 59.899 50.000 2.18 3.24 0.00 2.32
1664 1735 9.520204 GGGAAATAACAATTGATCTTGTGTATG 57.480 33.333 13.59 0.00 39.25 2.39
1690 1769 1.064505 ACAATTTGATCCTGATGCGCG 59.935 47.619 0.00 0.00 0.00 6.86
1845 1926 3.170585 GTCGAGGTACGCACGCAC 61.171 66.667 0.00 0.00 42.26 5.34
1846 1927 4.746951 TCGAGGTACGCACGCACG 62.747 66.667 0.00 0.00 42.26 5.34
1849 1930 4.735132 AGGTACGCACGCACGCAT 62.735 61.111 0.00 0.00 36.19 4.73
1852 1933 2.735100 TACGCACGCACGCATCAA 60.735 55.556 0.00 0.00 36.19 2.57
1855 1936 4.024143 GCACGCACGCATCAACCA 62.024 61.111 0.00 0.00 0.00 3.67
1856 1937 2.869646 CACGCACGCATCAACCAT 59.130 55.556 0.00 0.00 0.00 3.55
1891 1977 2.999355 AGCTTGAATCTGTTTCTCTCGC 59.001 45.455 0.70 0.00 35.23 5.03
1930 2016 3.138304 TCACGTTGCATGCTTCTTACTT 58.862 40.909 20.33 0.46 0.00 2.24
1935 2021 3.940209 TGCATGCTTCTTACTTTTGGG 57.060 42.857 20.33 0.00 0.00 4.12
2183 2273 1.812922 GGCTGGACATGCTCGTCAG 60.813 63.158 8.11 0.00 37.66 3.51
2293 2383 1.676678 ATGCCTCGACGTATGTGCCT 61.677 55.000 0.00 0.00 0.00 4.75
2309 2399 2.491022 CCTGGAGATCGACCGTCCC 61.491 68.421 6.99 0.00 0.00 4.46
2377 2476 3.568538 CTGTATTTTGCTGCAGGTGAAC 58.431 45.455 17.12 0.00 0.00 3.18
2425 2524 2.622942 TCAGCATTTGTTCAGTGGGTTC 59.377 45.455 0.00 0.00 0.00 3.62
2540 2639 8.723942 AAAAACATAGATACAGAGTTAGCCAG 57.276 34.615 0.00 0.00 0.00 4.85
2555 2655 5.893824 AGTTAGCCAGGGAAAAATAAGATGG 59.106 40.000 0.00 0.00 0.00 3.51
2679 2788 8.901748 CAAACAGTTTATTTCATTTGTACTCGG 58.098 33.333 0.00 0.00 0.00 4.63
2692 2801 7.820386 TCATTTGTACTCGGCTAAAAATGAGTA 59.180 33.333 11.59 0.78 41.60 2.59
2744 2854 2.635714 TGAGCACAGGAAGCATATGTG 58.364 47.619 4.29 6.91 45.59 3.21
2767 2877 6.497437 TGATGAACACATTGAAACTTGAGTG 58.503 36.000 0.00 0.00 0.00 3.51
2798 2908 4.151121 TGCTGAACATTTTCCTGAATCCA 58.849 39.130 0.00 0.00 0.00 3.41
2857 2970 6.012658 TGAAGTGTCCATTTGTGCTATTTC 57.987 37.500 0.00 0.00 0.00 2.17
2860 2973 6.992063 AGTGTCCATTTGTGCTATTTCTAG 57.008 37.500 0.00 0.00 0.00 2.43
2949 3062 6.183360 ACAACCTCAAAATGGAATTGTAAGCA 60.183 34.615 0.00 0.00 36.10 3.91
3051 3164 3.937079 TGCAGTATTCTGTCAGCAATGAG 59.063 43.478 1.02 0.00 43.05 2.90
3079 3192 2.473530 CACATTTGTGCGTGAAGTGT 57.526 45.000 0.00 0.00 39.39 3.55
3114 3227 4.808895 TGCTAGTGTACCAAATCATAAGCG 59.191 41.667 0.00 0.00 31.52 4.68
3119 3232 4.814234 GTGTACCAAATCATAAGCGATCCA 59.186 41.667 0.00 0.00 0.00 3.41
3135 3249 4.503910 CGATCCACAATTCTTCACTACCA 58.496 43.478 0.00 0.00 0.00 3.25
3149 3263 3.644265 TCACTACCAAGCTACACAAAGGA 59.356 43.478 0.00 0.00 0.00 3.36
3174 3288 9.525409 GATTCAGATTACAGCAAAAGCATTTAT 57.475 29.630 0.00 0.00 37.28 1.40
3195 3309 7.884816 TTATAATATGTTCTCGCTACCTTGC 57.115 36.000 0.00 0.00 0.00 4.01
3318 3433 0.179161 CCGCTGTCTCCTACTTGTCG 60.179 60.000 0.00 0.00 0.00 4.35
3319 3434 0.522180 CGCTGTCTCCTACTTGTCGT 59.478 55.000 0.00 0.00 0.00 4.34
3320 3435 1.466024 CGCTGTCTCCTACTTGTCGTC 60.466 57.143 0.00 0.00 0.00 4.20
3331 3446 0.109226 CTTGTCGTCGTCCCCTCTTC 60.109 60.000 0.00 0.00 0.00 2.87
3408 3523 6.109320 ACTCGAAGTAGAAGATAACTCGTG 57.891 41.667 0.00 0.00 0.00 4.35
3420 3535 1.070821 AACTCGTGTGCACATCATCG 58.929 50.000 24.69 21.06 0.00 3.84
3591 3724 3.696548 ACTATGCTCTCATTGTGACTCGA 59.303 43.478 0.00 0.00 37.30 4.04
3745 3882 1.511254 GCCTTTTTAACCGAGCGCG 60.511 57.895 0.00 0.00 37.24 6.86
3785 3924 5.698545 ACAGCAGAAATTACTCTCTGAACAC 59.301 40.000 8.71 0.00 41.38 3.32
3790 3929 5.703130 AGAAATTACTCTCTGAACACAAGGC 59.297 40.000 0.00 0.00 0.00 4.35
3806 3945 3.983044 AAGGCGGACTTGTAGAGAAAT 57.017 42.857 0.00 0.00 38.21 2.17
3813 3952 4.215399 CGGACTTGTAGAGAAATGGCAAAA 59.785 41.667 0.00 0.00 0.00 2.44
3864 4003 4.773323 ATTCCTCACAACTAAAAGCTGC 57.227 40.909 0.00 0.00 0.00 5.25
3865 4004 3.492102 TCCTCACAACTAAAAGCTGCT 57.508 42.857 0.00 0.00 0.00 4.24
3866 4005 4.617253 TCCTCACAACTAAAAGCTGCTA 57.383 40.909 0.90 0.00 0.00 3.49
3867 4006 4.569943 TCCTCACAACTAAAAGCTGCTAG 58.430 43.478 0.90 0.00 0.00 3.42
3917 4056 6.647229 CATATCAGTATGGGCATACACAGAT 58.353 40.000 0.00 2.98 44.58 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.741770 GCCACACACCCGATGAGTC 60.742 63.158 0.00 0.00 28.36 3.36
21 22 0.109342 CATCATCCCCTAGGCCACAC 59.891 60.000 5.01 0.00 0.00 3.82
22 23 0.327480 ACATCATCCCCTAGGCCACA 60.327 55.000 5.01 0.00 0.00 4.17
35 36 1.740380 CGGCTTCGACTTCCACATCAT 60.740 52.381 0.00 0.00 35.61 2.45
36 37 0.389817 CGGCTTCGACTTCCACATCA 60.390 55.000 0.00 0.00 35.61 3.07
50 51 2.685387 CTTCGGAGCTATCGCGGCTT 62.685 60.000 6.13 0.00 40.40 4.35
67 68 1.213013 CTACGGCACAGACGCTCTT 59.787 57.895 0.00 0.00 37.73 2.85
80 82 1.153823 CAGAAGCGACACCCTACGG 60.154 63.158 0.00 0.00 0.00 4.02
81 83 1.153823 CCAGAAGCGACACCCTACG 60.154 63.158 0.00 0.00 0.00 3.51
93 95 0.517316 GCAAGCCGTGTTACCAGAAG 59.483 55.000 0.00 0.00 0.00 2.85
113 115 3.656243 TAGACGAGCCAACGACGCG 62.656 63.158 3.53 3.53 37.03 6.01
115 117 0.723414 TACTAGACGAGCCAACGACG 59.277 55.000 0.00 0.00 37.03 5.12
131 133 1.995626 AGGCCCGAGGTTGCATACT 60.996 57.895 0.00 0.00 0.00 2.12
147 149 1.024271 CCTCAACAACACACACCAGG 58.976 55.000 0.00 0.00 0.00 4.45
167 169 3.007635 GGTTGCCGTTCTAGCTTACAAT 58.992 45.455 0.00 0.00 0.00 2.71
193 203 1.142314 TCGCCACCCTACAATACGC 59.858 57.895 0.00 0.00 0.00 4.42
253 263 4.812476 TCTCGGGGCGATGTTGCG 62.812 66.667 0.00 0.00 34.61 4.85
285 295 2.398498 CTCTATGGTCTCGAAATGGCG 58.602 52.381 0.00 0.00 0.00 5.69
289 299 4.446371 CCAAAGCTCTATGGTCTCGAAAT 58.554 43.478 5.26 0.00 31.84 2.17
326 345 1.368374 CGAAAACCGACACAACCGC 60.368 57.895 0.00 0.00 41.76 5.68
334 353 2.286595 GGAAAACAGACCGAAAACCGAC 60.287 50.000 0.00 0.00 41.76 4.79
348 367 5.713792 TTGACAGTTGAACAAGGAAAACA 57.286 34.783 0.00 0.00 0.00 2.83
425 446 2.162608 CGGAAATGGGCATACGAAAACA 59.837 45.455 0.00 0.00 0.00 2.83
426 447 2.420722 TCGGAAATGGGCATACGAAAAC 59.579 45.455 0.00 0.00 0.00 2.43
427 448 2.712709 TCGGAAATGGGCATACGAAAA 58.287 42.857 0.00 0.00 0.00 2.29
445 466 1.593006 GTGAACGGTAGCCATTGATCG 59.407 52.381 0.00 0.00 0.00 3.69
458 479 1.663643 CCGGTTATGATGTGTGAACGG 59.336 52.381 0.00 0.00 0.00 4.44
479 500 1.381872 TGAGGCTGGCTAGGGAGAC 60.382 63.158 2.77 0.00 0.00 3.36
480 501 1.381872 GTGAGGCTGGCTAGGGAGA 60.382 63.158 2.77 0.00 0.00 3.71
481 502 2.439104 GGTGAGGCTGGCTAGGGAG 61.439 68.421 2.77 0.00 0.00 4.30
482 503 2.365635 GGTGAGGCTGGCTAGGGA 60.366 66.667 2.77 0.00 0.00 4.20
490 511 3.633094 CTGTCGACCGGTGAGGCTG 62.633 68.421 14.63 7.88 46.52 4.85
513 534 4.016444 TCTGCCTTAATTTGTAAGCCTGG 58.984 43.478 0.00 0.00 0.00 4.45
517 538 5.343249 CCACATCTGCCTTAATTTGTAAGC 58.657 41.667 0.00 0.00 0.00 3.09
648 669 1.212195 GGGGCTGGGTAAGTAAAGGAG 59.788 57.143 0.00 0.00 0.00 3.69
649 670 1.292085 GGGGCTGGGTAAGTAAAGGA 58.708 55.000 0.00 0.00 0.00 3.36
650 671 0.257905 GGGGGCTGGGTAAGTAAAGG 59.742 60.000 0.00 0.00 0.00 3.11
651 672 0.107361 CGGGGGCTGGGTAAGTAAAG 60.107 60.000 0.00 0.00 0.00 1.85
652 673 1.992844 CGGGGGCTGGGTAAGTAAA 59.007 57.895 0.00 0.00 0.00 2.01
653 674 2.672181 GCGGGGGCTGGGTAAGTAA 61.672 63.158 0.00 0.00 0.00 2.24
654 675 3.085296 GCGGGGGCTGGGTAAGTA 61.085 66.667 0.00 0.00 0.00 2.24
669 690 0.752658 TGATCATGTGAGGTAGGGCG 59.247 55.000 0.00 0.00 0.00 6.13
722 743 1.589779 GTAATCGTACTTTTCCCGCGG 59.410 52.381 21.04 21.04 0.00 6.46
795 827 3.798511 CTCCCCCGGCCCTCTTTC 61.799 72.222 0.00 0.00 0.00 2.62
810 842 3.827898 CGCGTCCCTGTCTCCCTC 61.828 72.222 0.00 0.00 0.00 4.30
877 924 2.860735 GTGCAGCTAACTACGGATCTTG 59.139 50.000 0.00 0.00 0.00 3.02
902 949 3.006217 AGCTTTGGTTGATTCTTCTTGGC 59.994 43.478 0.00 0.00 0.00 4.52
949 996 4.282195 AGGTTCAACAACACCAAACAAGAA 59.718 37.500 0.00 0.00 35.25 2.52
950 997 3.829601 AGGTTCAACAACACCAAACAAGA 59.170 39.130 0.00 0.00 35.25 3.02
951 998 4.173256 GAGGTTCAACAACACCAAACAAG 58.827 43.478 0.00 0.00 35.25 3.16
952 999 3.366476 CGAGGTTCAACAACACCAAACAA 60.366 43.478 0.00 0.00 35.25 2.83
953 1000 2.162608 CGAGGTTCAACAACACCAAACA 59.837 45.455 0.00 0.00 35.25 2.83
954 1001 2.420722 TCGAGGTTCAACAACACCAAAC 59.579 45.455 0.00 0.00 35.25 2.93
955 1002 2.712709 TCGAGGTTCAACAACACCAAA 58.287 42.857 0.00 0.00 35.25 3.28
959 1006 2.400399 TCGATCGAGGTTCAACAACAC 58.600 47.619 15.15 0.00 33.70 3.32
968 1015 0.249073 CGCCAAGATCGATCGAGGTT 60.249 55.000 28.25 15.53 0.00 3.50
969 1016 1.360551 CGCCAAGATCGATCGAGGT 59.639 57.895 28.25 7.53 0.00 3.85
1095 1163 1.448540 CTGCTGCAGGTACCCGAAG 60.449 63.158 21.71 2.89 0.00 3.79
1182 1250 3.345808 TTGCTGGTCGCTTGCGTC 61.346 61.111 14.70 9.19 40.11 5.19
1183 1251 3.649986 GTTGCTGGTCGCTTGCGT 61.650 61.111 14.70 0.00 40.11 5.24
1184 1252 4.724697 CGTTGCTGGTCGCTTGCG 62.725 66.667 8.87 8.87 40.11 4.85
1185 1253 4.389576 CCGTTGCTGGTCGCTTGC 62.390 66.667 0.00 0.00 40.11 4.01
1186 1254 4.389576 GCCGTTGCTGGTCGCTTG 62.390 66.667 0.00 0.00 40.11 4.01
1255 1323 0.164002 GCGTCAGGTTTTCTCTTCGC 59.836 55.000 0.00 0.00 36.06 4.70
1297 1365 2.661979 GCACAAAAACATCGTCCGACTC 60.662 50.000 0.00 0.00 0.00 3.36
1298 1366 1.263217 GCACAAAAACATCGTCCGACT 59.737 47.619 0.00 0.00 0.00 4.18
1299 1367 1.003331 TGCACAAAAACATCGTCCGAC 60.003 47.619 0.00 0.00 0.00 4.79
1300 1368 1.300481 TGCACAAAAACATCGTCCGA 58.700 45.000 0.00 0.00 0.00 4.55
1359 1427 1.167851 GCACACCAATAAGCAGAGCA 58.832 50.000 0.00 0.00 0.00 4.26
1617 1688 1.227674 GCCTCCCGGAGTAGCAATG 60.228 63.158 13.62 0.00 0.00 2.82
1629 1700 1.152819 GTTATTTCCCCGGCCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
1632 1703 2.107366 CAATTGTTATTTCCCCGGCCT 58.893 47.619 0.00 0.00 0.00 5.19
1633 1704 2.104170 TCAATTGTTATTTCCCCGGCC 58.896 47.619 5.13 0.00 0.00 6.13
1638 1709 9.520204 CATACACAAGATCAATTGTTATTTCCC 57.480 33.333 5.13 0.00 41.41 3.97
1644 1715 9.171877 TGCATACATACACAAGATCAATTGTTA 57.828 29.630 5.13 0.00 41.41 2.41
1664 1735 4.980434 GCATCAGGATCAAATTGTGCATAC 59.020 41.667 0.00 0.00 0.00 2.39
1690 1769 2.821366 CCGCCTCACCTGCATCAC 60.821 66.667 0.00 0.00 0.00 3.06
1845 1926 1.299541 GGTCTGGTATGGTTGATGCG 58.700 55.000 0.00 0.00 0.00 4.73
1846 1927 2.418368 TGGTCTGGTATGGTTGATGC 57.582 50.000 0.00 0.00 0.00 3.91
1847 1928 3.443681 GGTTTGGTCTGGTATGGTTGATG 59.556 47.826 0.00 0.00 0.00 3.07
1848 1929 3.075283 TGGTTTGGTCTGGTATGGTTGAT 59.925 43.478 0.00 0.00 0.00 2.57
1849 1930 2.443632 TGGTTTGGTCTGGTATGGTTGA 59.556 45.455 0.00 0.00 0.00 3.18
1852 1933 1.271926 GCTGGTTTGGTCTGGTATGGT 60.272 52.381 0.00 0.00 0.00 3.55
1855 1936 2.375174 TCAAGCTGGTTTGGTCTGGTAT 59.625 45.455 0.00 0.00 0.00 2.73
1856 1937 1.771854 TCAAGCTGGTTTGGTCTGGTA 59.228 47.619 0.00 0.00 0.00 3.25
2255 2345 4.789075 AATCGACGGACGCGGTGG 62.789 66.667 12.47 0.00 42.26 4.61
2256 2346 3.245315 GAATCGACGGACGCGGTG 61.245 66.667 12.47 1.26 42.26 4.94
2257 2347 3.060020 ATGAATCGACGGACGCGGT 62.060 57.895 12.47 0.00 42.26 5.68
2271 2361 1.921243 CACATACGTCGAGGCATGAA 58.079 50.000 21.83 0.00 0.00 2.57
2293 2383 1.753078 CAGGGACGGTCGATCTCCA 60.753 63.158 13.83 0.00 0.00 3.86
2309 2399 1.935873 CCAGAACCGTACATCATGCAG 59.064 52.381 0.00 0.00 0.00 4.41
2425 2524 0.504384 CTGACTGAAACTGTGCGTCG 59.496 55.000 0.00 0.00 0.00 5.12
2517 2616 6.183361 CCCTGGCTAACTCTGTATCTATGTTT 60.183 42.308 0.00 0.00 0.00 2.83
2540 2639 7.462571 ACTGTAACACCATCTTATTTTTCCC 57.537 36.000 0.00 0.00 0.00 3.97
2555 2655 4.575885 TGGCCTCATCTTAACTGTAACAC 58.424 43.478 3.32 0.00 0.00 3.32
2582 2682 3.568430 TCAGTATAGCAGGTACGTGATGG 59.432 47.826 19.35 2.99 0.00 3.51
2663 2772 8.519526 TCATTTTTAGCCGAGTACAAATGAAAT 58.480 29.630 12.28 0.00 37.57 2.17
2679 2788 9.691362 TCTTCCAAATTTGTACTCATTTTTAGC 57.309 29.630 16.73 0.00 0.00 3.09
2692 2801 5.217978 ACACATGCATCTTCCAAATTTGT 57.782 34.783 16.73 0.00 0.00 2.83
2744 2854 6.728200 TCACTCAAGTTTCAATGTGTTCATC 58.272 36.000 0.00 0.00 32.56 2.92
2767 2877 3.764885 AAATGTTCAGCATAACCGCTC 57.235 42.857 0.00 0.00 41.38 5.03
2798 2908 7.318141 TGCATTACGTACTAAAAGTAGAAGCT 58.682 34.615 0.00 0.00 30.12 3.74
2857 2970 4.633565 GGGAACATGTTCTTCTGAAGCTAG 59.366 45.833 31.81 3.65 39.45 3.42
2860 2973 3.190118 CAGGGAACATGTTCTTCTGAAGC 59.810 47.826 33.56 20.15 40.04 3.86
2949 3062 6.838401 ACTCCAGGAATGAGAATTAATCCT 57.162 37.500 0.00 0.00 41.12 3.24
3070 3183 6.831769 AGCAATACAAGAATAACACTTCACG 58.168 36.000 0.00 0.00 0.00 4.35
3078 3191 8.712285 TGGTACACTAGCAATACAAGAATAAC 57.288 34.615 0.00 0.00 32.53 1.89
3079 3192 9.727859 TTTGGTACACTAGCAATACAAGAATAA 57.272 29.630 0.00 0.00 44.53 1.40
3114 3227 5.163713 GCTTGGTAGTGAAGAATTGTGGATC 60.164 44.000 0.00 0.00 0.00 3.36
3119 3232 5.701290 GTGTAGCTTGGTAGTGAAGAATTGT 59.299 40.000 0.00 0.00 0.00 2.71
3135 3249 7.168219 TGTAATCTGAATCCTTTGTGTAGCTT 58.832 34.615 0.00 0.00 0.00 3.74
3174 3288 5.068591 TGAGCAAGGTAGCGAGAACATATTA 59.931 40.000 0.00 0.00 40.15 0.98
3222 3336 3.737266 GTGCATGTTGTTGTTCTGGATTG 59.263 43.478 0.00 0.00 0.00 2.67
3318 3433 0.034896 TGCTTTGAAGAGGGGACGAC 59.965 55.000 0.00 0.00 0.00 4.34
3319 3434 0.034896 GTGCTTTGAAGAGGGGACGA 59.965 55.000 0.00 0.00 0.00 4.20
3320 3435 0.250295 TGTGCTTTGAAGAGGGGACG 60.250 55.000 0.00 0.00 0.00 4.79
3331 3446 2.016318 TGGTGAACAGTCTGTGCTTTG 58.984 47.619 12.38 0.00 0.00 2.77
3408 3523 1.925415 TTGCCAGCGATGATGTGCAC 61.925 55.000 10.75 10.75 28.68 4.57
3420 3535 4.156556 TGTTCATCAGAAGTTATTGCCAGC 59.843 41.667 0.00 0.00 33.63 4.85
3673 3807 5.598005 TGTTGGTGATGATTCTGTTTTCCTT 59.402 36.000 0.00 0.00 0.00 3.36
3692 3826 4.126437 TCACACTCACACTGTAATGTTGG 58.874 43.478 0.00 0.00 0.00 3.77
3745 3882 3.084039 TGCTGTTCCTCACATCAAATCC 58.916 45.455 0.00 0.00 33.76 3.01
3752 3889 5.564550 AGTAATTTCTGCTGTTCCTCACAT 58.435 37.500 0.00 0.00 33.76 3.21
3790 3929 2.972625 TGCCATTTCTCTACAAGTCCG 58.027 47.619 0.00 0.00 0.00 4.79
3813 3952 6.774170 TGCCAGTAGATATTCAAGCAAATGAT 59.226 34.615 0.00 0.00 0.00 2.45
3843 3982 4.401925 AGCAGCTTTTAGTTGTGAGGAAT 58.598 39.130 0.00 0.00 0.00 3.01
3850 3989 7.829211 TGGATAATTCTAGCAGCTTTTAGTTGT 59.171 33.333 0.00 0.00 0.00 3.32
3851 3990 8.125448 GTGGATAATTCTAGCAGCTTTTAGTTG 58.875 37.037 0.00 0.00 0.00 3.16
3856 3995 6.405176 GCAAGTGGATAATTCTAGCAGCTTTT 60.405 38.462 0.00 0.00 0.00 2.27
3857 3996 5.067023 GCAAGTGGATAATTCTAGCAGCTTT 59.933 40.000 0.00 0.00 0.00 3.51
3858 3997 4.578105 GCAAGTGGATAATTCTAGCAGCTT 59.422 41.667 0.00 0.00 0.00 3.74
3861 4000 5.180868 GGATGCAAGTGGATAATTCTAGCAG 59.819 44.000 0.00 0.00 32.59 4.24
3862 4001 5.065914 GGATGCAAGTGGATAATTCTAGCA 58.934 41.667 0.00 0.00 0.00 3.49
3863 4002 5.049129 GTGGATGCAAGTGGATAATTCTAGC 60.049 44.000 0.00 0.00 0.00 3.42
3864 4003 5.471456 GGTGGATGCAAGTGGATAATTCTAG 59.529 44.000 0.00 0.00 0.00 2.43
3865 4004 5.104151 TGGTGGATGCAAGTGGATAATTCTA 60.104 40.000 0.00 0.00 0.00 2.10
3866 4005 4.210331 GGTGGATGCAAGTGGATAATTCT 58.790 43.478 0.00 0.00 0.00 2.40
3867 4006 3.953612 TGGTGGATGCAAGTGGATAATTC 59.046 43.478 0.00 0.00 0.00 2.17
3897 4036 3.494924 GCATCTGTGTATGCCCATACTGA 60.495 47.826 16.73 12.79 45.31 3.41
3898 4037 2.810274 GCATCTGTGTATGCCCATACTG 59.190 50.000 16.73 9.16 45.31 2.74
3900 4039 5.283909 ATGTGCATCTGTGTATGCCCATAC 61.284 45.833 10.69 10.69 45.34 2.39


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

AutoCloner maintained by Alex Coulton.