Multiple sequence alignment - TraesCS5B01G162900

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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 TraesCS5B01G162900 chr5B 100.000 3910 0 0 1 3910 300375697 300379606 0.000000e+00 7221.0
1 TraesCS5B01G162900 chr5B 90.090 111 10 1 3224 3333 293534769 293534879 4.070000e-30 143.0
2 TraesCS5B01G162900 chr5B 85.915 71 9 1 460 529 430682382 430682452 1.510000e-09 75.0
3 TraesCS5B01G162900 chr5D 90.996 1877 100 28 2064 3902 266749451 266751296 0.000000e+00 2466.0
4 TraesCS5B01G162900 chr5D 93.252 741 22 15 759 1478 266747996 266748729 0.000000e+00 1066.0
5 TraesCS5B01G162900 chr5D 90.945 751 61 6 1 747 266741766 266742513 0.000000e+00 1003.0
6 TraesCS5B01G162900 chr5D 95.447 571 16 3 1476 2045 266748767 266749328 0.000000e+00 902.0
7 TraesCS5B01G162900 chr5A 87.958 1528 100 39 2442 3908 353861467 353859963 0.000000e+00 1725.0
8 TraesCS5B01G162900 chr5A 93.176 806 32 16 689 1478 353863324 353862526 0.000000e+00 1162.0
9 TraesCS5B01G162900 chr5A 94.965 576 17 5 1485 2051 353862482 353861910 0.000000e+00 893.0
10 TraesCS5B01G162900 chr5A 90.769 520 40 8 1 517 353864004 353863490 0.000000e+00 688.0
11 TraesCS5B01G162900 chr5A 89.355 310 20 8 2064 2362 353861772 353861465 1.030000e-100 377.0
12 TraesCS5B01G162900 chr5A 88.430 121 10 4 3217 3335 698226275 698226393 4.070000e-30 143.0
13 TraesCS5B01G162900 chr5A 88.235 119 12 2 3219 3335 71499345 71499463 1.460000e-29 141.0
14 TraesCS5B01G162900 chr2A 88.333 120 14 0 3214 3333 23884441 23884560 1.130000e-30 145.0
15 TraesCS5B01G162900 chr6A 89.565 115 8 4 3221 3333 38404625 38404513 4.070000e-30 143.0
16 TraesCS5B01G162900 chrUn 88.793 116 11 2 3219 3332 30689426 30689311 1.460000e-29 141.0
17 TraesCS5B01G162900 chr7A 88.793 116 9 4 3222 3335 732094364 732094477 5.270000e-29 139.0
18 TraesCS5B01G162900 chr7A 87.129 101 9 3 2360 2458 398927586 398927684 1.150000e-20 111.0
19 TraesCS5B01G162900 chr7A 85.897 78 9 2 460 536 369476290 369476366 9.000000e-12 82.4
20 TraesCS5B01G162900 chr7A 91.489 47 4 0 3737 3783 85900864 85900818 9.070000e-07 65.8
21 TraesCS5B01G162900 chr1A 86.992 123 13 3 3216 3335 309178222 309178344 6.810000e-28 135.0
22 TraesCS5B01G162900 chr6B 92.045 88 6 1 2360 2446 13827610 13827523 5.310000e-24 122.0
23 TraesCS5B01G162900 chr1D 92.857 84 6 0 2360 2443 263868008 263867925 5.310000e-24 122.0
24 TraesCS5B01G162900 chr1D 88.542 96 8 3 2359 2452 58573715 58573621 3.190000e-21 113.0
25 TraesCS5B01G162900 chr1D 84.146 82 10 3 460 539 122770096 122770176 4.190000e-10 76.8
26 TraesCS5B01G162900 chr1D 84.932 73 11 0 3565 3637 482224772 482224700 1.510000e-09 75.0
27 TraesCS5B01G162900 chr7D 91.954 87 6 1 2359 2444 474349061 474349147 1.910000e-23 121.0
28 TraesCS5B01G162900 chr7D 90.217 92 7 2 2360 2449 19943780 19943871 6.860000e-23 119.0
29 TraesCS5B01G162900 chr7D 87.129 101 11 2 2360 2458 351587106 351587206 3.190000e-21 113.0
30 TraesCS5B01G162900 chr6D 90.110 91 5 3 2359 2448 113614071 113614158 8.880000e-22 115.0
31 TraesCS5B01G162900 chr6D 82.143 84 11 4 460 541 316155070 316155151 7.010000e-08 69.4
32 TraesCS5B01G162900 chr4B 85.333 75 8 3 460 532 657004728 657004655 1.510000e-09 75.0
33 TraesCS5B01G162900 chr4A 84.507 71 10 1 460 529 719098219 719098289 7.010000e-08 69.4
34 TraesCS5B01G162900 chr3D 90.385 52 4 1 3737 3788 111761289 111761239 2.520000e-07 67.6
35 TraesCS5B01G162900 chr2D 83.562 73 11 1 3565 3637 616935627 616935556 2.520000e-07 67.6
36 TraesCS5B01G162900 chr3A 82.051 78 13 1 460 536 200126741 200126818 9.070000e-07 65.8


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 TraesCS5B01G162900 chr5B 300375697 300379606 3909 False 7221 7221 100.000000 1 3910 1 chr5B.!!$F2 3909
1 TraesCS5B01G162900 chr5D 266747996 266751296 3300 False 1478 2466 93.231667 759 3902 3 chr5D.!!$F2 3143
2 TraesCS5B01G162900 chr5D 266741766 266742513 747 False 1003 1003 90.945000 1 747 1 chr5D.!!$F1 746
3 TraesCS5B01G162900 chr5A 353859963 353864004 4041 True 969 1725 91.244600 1 3908 5 chr5A.!!$R1 3907

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
936 982 0.103937 CGTGCTCCCTCCTGATCTTC 59.896 60.000 0.0 0.0 0.0 2.87 F
1105 1165 1.303615 GACCTCCTCGACTCCTCCA 59.696 63.158 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1859 0.179100 CCCATGCCTCTACACTGTCG 60.179 60.0 0.00 0.00 0.0 4.35 R
2969 3322 0.319405 AATTGCTTTCAGGGCAGTGC 59.681 50.0 6.55 6.55 40.9 4.40 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
43 44 4.406648 TCTGATCATATGTTTCCTGCGT 57.593 40.909 1.90 0.00 0.00 5.24
60 61 4.600576 TCAGCGCCACTTCGTGCA 62.601 61.111 2.29 0.00 41.82 4.57
119 120 1.532604 AAGGATCAGCGTCGTGGACA 61.533 55.000 0.00 0.00 32.09 4.02
149 150 4.083862 GCCCTCACCTCACGGTCC 62.084 72.222 0.00 0.00 43.24 4.46
150 151 3.760035 CCCTCACCTCACGGTCCG 61.760 72.222 10.48 10.48 43.24 4.79
185 186 1.152673 GGCCCATAGAGCCCCTTTG 60.153 63.158 0.00 0.00 45.16 2.77
206 208 0.843309 TTGGCTTCTGGTTCACTGGA 59.157 50.000 0.00 0.00 0.00 3.86
209 211 1.363744 GCTTCTGGTTCACTGGATCG 58.636 55.000 0.00 0.00 0.00 3.69
227 229 2.683968 TCGTTCCGGATGAGAAACTTG 58.316 47.619 4.15 0.00 0.00 3.16
475 478 9.450807 GAAAATGATATCCCAAAATGTAAGACG 57.549 33.333 0.00 0.00 0.00 4.18
560 594 8.635765 ATGTATAAAACACCTATAAGGGCATG 57.364 34.615 0.00 0.00 42.09 4.06
586 621 6.331845 CCAATTGTATGCTTCAAACATGCTA 58.668 36.000 4.43 0.00 32.12 3.49
589 624 4.331108 TGTATGCTTCAAACATGCTACCA 58.669 39.130 0.00 0.00 32.12 3.25
604 639 4.606210 TGCTACCACACTATCCAACTAGA 58.394 43.478 0.00 0.00 0.00 2.43
607 642 5.221087 GCTACCACACTATCCAACTAGACTC 60.221 48.000 0.00 0.00 0.00 3.36
608 646 4.673968 ACCACACTATCCAACTAGACTCA 58.326 43.478 0.00 0.00 0.00 3.41
626 664 4.036518 ACTCAGATACCAAATGGAGCTCT 58.963 43.478 14.64 2.33 38.94 4.09
628 666 5.663106 ACTCAGATACCAAATGGAGCTCTAA 59.337 40.000 14.64 2.61 38.94 2.10
629 667 5.918608 TCAGATACCAAATGGAGCTCTAAC 58.081 41.667 14.64 0.00 38.94 2.34
640 678 0.741915 AGCTCTAACAGTAGCCTCGC 59.258 55.000 0.00 0.00 39.64 5.03
642 680 0.592754 CTCTAACAGTAGCCTCGCGC 60.593 60.000 0.00 0.00 37.98 6.86
654 692 1.502190 CTCGCGCTGTGTCAGAGTA 59.498 57.895 5.56 0.00 33.92 2.59
693 731 3.015327 CTGCTCCATGGAAGAAAGAAGG 58.985 50.000 17.00 1.44 0.00 3.46
702 740 5.234466 TGGAAGAAAGAAGGAAAGGAGAG 57.766 43.478 0.00 0.00 0.00 3.20
717 755 3.449918 AGGAGAGGAGAAAGAGGGAAAG 58.550 50.000 0.00 0.00 0.00 2.62
738 776 1.954362 GAGGCCAGAGATGACGCTGT 61.954 60.000 5.01 0.00 41.21 4.40
754 792 0.250467 CTGTGTGTTCAGGTGGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
755 793 1.073199 GTGTGTTCAGGTGGGGAGG 59.927 63.158 0.00 0.00 0.00 4.30
814 852 2.431782 CCTCAATTTAGGGCATTGGGTG 59.568 50.000 0.00 0.00 31.04 4.61
815 853 3.364549 CTCAATTTAGGGCATTGGGTGA 58.635 45.455 0.00 0.00 33.17 4.02
816 854 3.364549 TCAATTTAGGGCATTGGGTGAG 58.635 45.455 0.00 0.00 33.17 3.51
817 855 3.011144 TCAATTTAGGGCATTGGGTGAGA 59.989 43.478 0.00 0.00 33.17 3.27
820 858 1.965414 TAGGGCATTGGGTGAGAGAA 58.035 50.000 0.00 0.00 0.00 2.87
856 898 5.124776 CCAATGCCTCGTTATTTTTCTACCA 59.875 40.000 0.00 0.00 0.00 3.25
866 908 6.639279 CGTTATTTTTCTACCAAACTGGGTTG 59.361 38.462 0.00 0.00 43.37 3.77
936 982 0.103937 CGTGCTCCCTCCTGATCTTC 59.896 60.000 0.00 0.00 0.00 2.87
939 985 2.238395 GTGCTCCCTCCTGATCTTCTTT 59.762 50.000 0.00 0.00 0.00 2.52
941 987 4.080863 GTGCTCCCTCCTGATCTTCTTTAA 60.081 45.833 0.00 0.00 0.00 1.52
942 988 4.163078 TGCTCCCTCCTGATCTTCTTTAAG 59.837 45.833 0.00 0.00 0.00 1.85
944 990 5.338789 GCTCCCTCCTGATCTTCTTTAAGTT 60.339 44.000 0.00 0.00 34.13 2.66
947 995 6.272324 TCCCTCCTGATCTTCTTTAAGTTGAA 59.728 38.462 0.00 0.00 34.13 2.69
975 1035 4.704833 CGCACCACCCCTGTCCTG 62.705 72.222 0.00 0.00 0.00 3.86
1105 1165 1.303615 GACCTCCTCGACTCCTCCA 59.696 63.158 0.00 0.00 0.00 3.86
1165 1225 3.866582 CATCCACCTCCTCGGGGC 61.867 72.222 0.00 0.00 33.53 5.80
1243 1303 3.429372 AACCCCTTTGCGTGCCTCA 62.429 57.895 0.00 0.00 0.00 3.86
1378 1438 3.332493 GAGAACGTCCGCCGCTACA 62.332 63.158 0.00 0.00 41.42 2.74
1467 1529 2.379907 TCTTTCCTTCATCCCTGCCTTT 59.620 45.455 0.00 0.00 0.00 3.11
1678 1780 2.516227 TTGGTGAGTGTTGGGTTTCA 57.484 45.000 0.00 0.00 0.00 2.69
1793 1899 5.123979 GCATGGGTCCTTTGTTTTCTAGTAG 59.876 44.000 0.00 0.00 0.00 2.57
1796 1902 7.377696 TGGGTCCTTTGTTTTCTAGTAGTAA 57.622 36.000 0.00 0.00 0.00 2.24
1797 1903 7.981142 TGGGTCCTTTGTTTTCTAGTAGTAAT 58.019 34.615 0.00 0.00 0.00 1.89
1798 1904 9.103582 TGGGTCCTTTGTTTTCTAGTAGTAATA 57.896 33.333 0.00 0.00 0.00 0.98
1799 1905 9.948964 GGGTCCTTTGTTTTCTAGTAGTAATAA 57.051 33.333 0.00 0.00 0.00 1.40
1932 2045 4.275689 TGATGATTCTGACGTGTTTGCTTT 59.724 37.500 0.00 0.00 0.00 3.51
1934 2047 3.625313 TGATTCTGACGTGTTTGCTTTGA 59.375 39.130 0.00 0.00 0.00 2.69
1952 2066 8.075593 TGCTTTGATAATTTTTCAGCAACTTC 57.924 30.769 0.00 0.00 0.00 3.01
2051 2174 8.825667 ACAAAACACATAAGTTGTTCAACTTT 57.174 26.923 27.84 16.67 42.48 2.66
2053 2176 8.920665 CAAAACACATAAGTTGTTCAACTTTGA 58.079 29.630 27.84 16.23 42.48 2.69
2337 2682 1.761784 AGCAACCTGGTTTTTGATGCA 59.238 42.857 18.19 0.00 34.89 3.96
2383 2728 8.087136 CCTACTCCCTCCGTAAAGAAATATAAC 58.913 40.741 0.00 0.00 0.00 1.89
2410 2755 9.376075 AGTGTTTAGATCATTCAAGTAGTGATG 57.624 33.333 0.00 0.00 35.70 3.07
2743 3092 4.018870 TGGGTTGAGTTATGCAGGTGAATA 60.019 41.667 0.00 0.00 0.00 1.75
2825 3178 5.220912 GCTATGTTTTGCAGTCATGATGCTA 60.221 40.000 22.27 15.99 44.17 3.49
2911 3264 1.067495 ACAGCCAAGACGAAGCTAGTC 60.067 52.381 12.75 12.75 38.81 2.59
2924 3277 0.530870 GCTAGTCGCCATTGGAGGTC 60.531 60.000 6.95 0.85 0.00 3.85
2956 3309 0.378257 CAGGTACATTGCCATGTCGC 59.622 55.000 6.70 2.12 43.06 5.19
2969 3322 1.945354 ATGTCGCAGTACGGTGGAGG 61.945 60.000 6.72 0.00 43.89 4.30
3003 3356 7.394016 TGAAAGCAATTCTACACCTAAGATCA 58.606 34.615 0.00 0.00 38.92 2.92
3178 3533 2.524569 AAAATCCAGTTTTGGCACCG 57.475 45.000 0.00 0.00 44.63 4.94
3201 3556 5.286082 CGACGCTGATTAAAGAATTTTTGGG 59.714 40.000 0.00 0.00 40.09 4.12
3232 3587 8.441312 TTTCGGAGTTCTTAATACAGTTTTGT 57.559 30.769 0.00 0.00 41.39 2.83
3289 3644 6.927936 CACATCTAAGTCCTATGTCCTTGATG 59.072 42.308 0.00 0.00 34.10 3.07
3295 3650 4.080129 AGTCCTATGTCCTTGATGTTGCAT 60.080 41.667 0.00 0.00 0.00 3.96
3308 3663 2.937519 TGTTGCATGGAGGTTTGTGTA 58.062 42.857 0.00 0.00 0.00 2.90
3315 3670 4.705023 GCATGGAGGTTTGTGTAGGTATTT 59.295 41.667 0.00 0.00 0.00 1.40
3317 3672 6.295067 GCATGGAGGTTTGTGTAGGTATTTTT 60.295 38.462 0.00 0.00 0.00 1.94
3358 3733 3.508840 CCAATGAGGGCCGTTCGC 61.509 66.667 0.00 0.00 0.00 4.70
3359 3734 2.436646 CAATGAGGGCCGTTCGCT 60.437 61.111 0.00 0.00 41.07 4.93
3360 3735 2.040544 CAATGAGGGCCGTTCGCTT 61.041 57.895 0.00 0.00 38.18 4.68
3361 3736 1.745489 AATGAGGGCCGTTCGCTTC 60.745 57.895 0.00 0.00 38.18 3.86
3362 3737 3.682292 ATGAGGGCCGTTCGCTTCC 62.682 63.158 0.00 0.00 38.18 3.46
3363 3738 4.083862 GAGGGCCGTTCGCTTCCT 62.084 66.667 0.00 0.00 38.18 3.36
3364 3739 3.607370 GAGGGCCGTTCGCTTCCTT 62.607 63.158 0.00 0.00 38.18 3.36
3365 3740 3.431725 GGGCCGTTCGCTTCCTTG 61.432 66.667 0.00 0.00 37.74 3.61
3366 3741 4.103103 GGCCGTTCGCTTCCTTGC 62.103 66.667 0.00 0.00 37.74 4.01
3367 3742 4.103103 GCCGTTCGCTTCCTTGCC 62.103 66.667 0.00 0.00 0.00 4.52
3368 3743 2.358737 CCGTTCGCTTCCTTGCCT 60.359 61.111 0.00 0.00 0.00 4.75
3369 3744 2.391389 CCGTTCGCTTCCTTGCCTC 61.391 63.158 0.00 0.00 0.00 4.70
3370 3745 2.391389 CGTTCGCTTCCTTGCCTCC 61.391 63.158 0.00 0.00 0.00 4.30
3432 3807 2.561419 TCCACGTTCCCTTGTCTTAGAG 59.439 50.000 0.00 0.00 0.00 2.43
3451 3826 5.289083 AGAGATAATGCTCCCTTGTCTTC 57.711 43.478 0.00 0.00 35.49 2.87
3461 3836 5.119694 GCTCCCTTGTCTTCGAAATAATCT 58.880 41.667 0.00 0.00 0.00 2.40
3556 3955 9.359653 AGCTTAAATCTTGCCAATATTATGTCT 57.640 29.630 0.00 0.00 0.00 3.41
3654 4053 6.182507 TCCAATATGATGGGTGTAAGGTAC 57.817 41.667 0.00 0.00 41.05 3.34
3670 4070 7.543172 GTGTAAGGTACATGTTTGACTCGATTA 59.457 37.037 2.30 0.00 41.34 1.75
3680 4080 9.825972 CATGTTTGACTCGATTATTGTTTAACT 57.174 29.630 0.00 0.00 0.00 2.24
3682 4082 9.268268 TGTTTGACTCGATTATTGTTTAACTCT 57.732 29.630 0.00 0.00 0.00 3.24
3713 4113 2.032634 GGCTCATTCCAACGCACGA 61.033 57.895 0.00 0.00 0.00 4.35
3718 4118 1.671328 TCATTCCAACGCACGAACAAA 59.329 42.857 0.00 0.00 0.00 2.83
3719 4119 2.097629 TCATTCCAACGCACGAACAAAA 59.902 40.909 0.00 0.00 0.00 2.44
3720 4120 2.631418 TTCCAACGCACGAACAAAAA 57.369 40.000 0.00 0.00 0.00 1.94
3791 4223 2.347500 TCCCTATGAATGCATGCCCTA 58.653 47.619 16.68 0.00 35.94 3.53
3795 4227 2.283145 ATGAATGCATGCCCTACCTC 57.717 50.000 16.68 3.22 32.31 3.85
3796 4228 0.179048 TGAATGCATGCCCTACCTCG 60.179 55.000 16.68 0.00 0.00 4.63
3839 4273 5.545588 TGAGCTGGCATATAATCTTGAGAC 58.454 41.667 0.00 0.00 0.00 3.36
3865 4299 3.698539 TGAAGTTGCCACAAACATCTTCA 59.301 39.130 11.32 11.32 45.07 3.02
3866 4300 4.341806 TGAAGTTGCCACAAACATCTTCAT 59.658 37.500 11.32 0.00 43.64 2.57
3871 4305 4.009675 TGCCACAAACATCTTCATAGTCC 58.990 43.478 0.00 0.00 0.00 3.85
3873 4307 4.641989 GCCACAAACATCTTCATAGTCCAT 59.358 41.667 0.00 0.00 0.00 3.41
3874 4308 5.822519 GCCACAAACATCTTCATAGTCCATA 59.177 40.000 0.00 0.00 0.00 2.74
3885 4319 7.002276 TCTTCATAGTCCATAGAACGTATCCA 58.998 38.462 0.00 0.00 0.00 3.41
3892 4326 6.070995 AGTCCATAGAACGTATCCAACTGAAA 60.071 38.462 0.00 0.00 0.00 2.69
3908 4342 2.476619 CTGAAAGCACATCGTCGAAAGT 59.523 45.455 0.00 0.00 0.00 2.66
3909 4343 2.475111 TGAAAGCACATCGTCGAAAGTC 59.525 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.622132 TGGATCCTTCCCCCATGCA 60.622 57.895 14.23 0.00 41.83 3.96
60 61 1.387926 CCCTGGATCCTTCCCCCAT 60.388 63.158 14.23 0.00 41.83 4.00
75 76 1.076677 TCGTAGTTCCTTCTCCACCCT 59.923 52.381 0.00 0.00 0.00 4.34
79 80 2.872732 AGTGTCGTAGTTCCTTCTCCA 58.127 47.619 0.00 0.00 0.00 3.86
149 150 2.829914 CCACATGGCCCATGGTCG 60.830 66.667 26.79 14.60 45.16 4.79
150 151 2.442643 CCCACATGGCCCATGGTC 60.443 66.667 26.79 0.00 45.16 4.02
182 183 3.096092 AGTGAACCAGAAGCCAAACAAA 58.904 40.909 0.00 0.00 0.00 2.83
183 184 2.426738 CAGTGAACCAGAAGCCAAACAA 59.573 45.455 0.00 0.00 0.00 2.83
185 186 1.338020 CCAGTGAACCAGAAGCCAAAC 59.662 52.381 0.00 0.00 0.00 2.93
209 211 4.817517 TCTACAAGTTTCTCATCCGGAAC 58.182 43.478 9.01 0.00 0.00 3.62
257 259 7.907214 ACTTCTAGAAAAATAGCGTGTTGAT 57.093 32.000 6.63 0.00 0.00 2.57
308 311 9.762381 TTGGACTAACCTATTAATCCAATGTTT 57.238 29.630 6.00 0.00 46.65 2.83
560 594 3.924144 TGTTTGAAGCATACAATTGGCC 58.076 40.909 10.83 0.00 0.00 5.36
567 602 4.155826 GTGGTAGCATGTTTGAAGCATACA 59.844 41.667 0.00 0.00 30.86 2.29
586 621 4.673968 TGAGTCTAGTTGGATAGTGTGGT 58.326 43.478 0.00 0.00 0.00 4.16
589 624 6.773685 GGTATCTGAGTCTAGTTGGATAGTGT 59.226 42.308 0.00 0.00 0.00 3.55
604 639 4.036518 AGAGCTCCATTTGGTATCTGAGT 58.963 43.478 10.93 0.00 36.34 3.41
607 642 5.674525 TGTTAGAGCTCCATTTGGTATCTG 58.325 41.667 10.93 0.00 36.34 2.90
608 646 5.426833 ACTGTTAGAGCTCCATTTGGTATCT 59.573 40.000 10.93 2.15 36.34 1.98
642 680 0.039165 TGCACGCTACTCTGACACAG 60.039 55.000 0.00 0.00 0.00 3.66
648 686 0.100325 CTCCTCTGCACGCTACTCTG 59.900 60.000 0.00 0.00 0.00 3.35
679 717 5.280934 CCTCTCCTTTCCTTCTTTCTTCCAT 60.281 44.000 0.00 0.00 0.00 3.41
693 731 3.445987 TCCCTCTTTCTCCTCTCCTTTC 58.554 50.000 0.00 0.00 0.00 2.62
702 740 1.562008 CCTCCCTTTCCCTCTTTCTCC 59.438 57.143 0.00 0.00 0.00 3.71
717 755 2.818132 CGTCATCTCTGGCCTCCC 59.182 66.667 3.32 0.00 0.00 4.30
738 776 0.104882 TACCTCCCCACCTGAACACA 60.105 55.000 0.00 0.00 0.00 3.72
754 792 5.163652 GCCTCACCTGTGTCATATTTTTACC 60.164 44.000 0.00 0.00 0.00 2.85
755 793 5.163652 GGCCTCACCTGTGTCATATTTTTAC 60.164 44.000 0.00 0.00 34.51 2.01
842 880 6.926826 CCAACCCAGTTTGGTAGAAAAATAAC 59.073 38.462 0.00 0.00 41.18 1.89
856 898 4.082125 CAATCTTAGAGCCAACCCAGTTT 58.918 43.478 0.00 0.00 0.00 2.66
919 961 2.260639 AAGAAGATCAGGAGGGAGCA 57.739 50.000 0.00 0.00 0.00 4.26
924 966 7.986085 TTTCAACTTAAAGAAGATCAGGAGG 57.014 36.000 0.00 0.00 36.45 4.30
936 982 6.745450 TGCGTGTTTCTCTTTTCAACTTAAAG 59.255 34.615 0.00 0.00 34.63 1.85
939 985 5.448089 GGTGCGTGTTTCTCTTTTCAACTTA 60.448 40.000 0.00 0.00 0.00 2.24
941 987 3.181500 GGTGCGTGTTTCTCTTTTCAACT 60.181 43.478 0.00 0.00 0.00 3.16
942 988 3.105937 GGTGCGTGTTTCTCTTTTCAAC 58.894 45.455 0.00 0.00 0.00 3.18
944 990 2.096819 GTGGTGCGTGTTTCTCTTTTCA 59.903 45.455 0.00 0.00 0.00 2.69
947 995 1.021968 GGTGGTGCGTGTTTCTCTTT 58.978 50.000 0.00 0.00 0.00 2.52
975 1035 1.954651 GCTGGGCCGTACGATTAGC 60.955 63.158 18.76 16.08 0.00 3.09
1071 1131 2.124403 TCGAGGTAGCCGGAGTCC 60.124 66.667 5.05 0.00 0.00 3.85
1306 1366 2.042843 CCAGGAGTAGGAGGCGGT 60.043 66.667 0.00 0.00 0.00 5.68
1307 1367 3.541713 GCCAGGAGTAGGAGGCGG 61.542 72.222 0.00 0.00 37.41 6.13
1467 1529 4.472286 GCAGCTGCTTTAATAACGAAACA 58.528 39.130 31.33 0.00 38.21 2.83
1678 1780 1.860326 GTTTGCGCAGAAACAGCATTT 59.140 42.857 17.81 0.00 40.83 2.32
1756 1859 0.179100 CCCATGCCTCTACACTGTCG 60.179 60.000 0.00 0.00 0.00 4.35
1844 1950 8.101309 TCAAGATATCCTTTCTATCCCACAAA 57.899 34.615 0.00 0.00 31.42 2.83
1932 2045 9.906660 ATTTACGAAGTTGCTGAAAAATTATCA 57.093 25.926 0.00 0.00 37.78 2.15
1934 2047 8.647226 GCATTTACGAAGTTGCTGAAAAATTAT 58.353 29.630 0.00 0.00 37.78 1.28
2337 2682 7.008332 AGTAGGCCTTAAGGTTTGTGTTTTAT 58.992 34.615 22.55 0.00 37.57 1.40
2383 2728 8.763049 TCACTACTTGAATGATCTAAACACTG 57.237 34.615 0.00 0.00 0.00 3.66
2534 2883 9.020731 AGGTATGGTATTCAAAACGAAAAGAAT 57.979 29.630 0.00 0.00 37.12 2.40
2743 3092 2.424684 AGGAGAGAGGTGAAAGGGTT 57.575 50.000 0.00 0.00 0.00 4.11
2751 3100 2.300437 ACGAAAAGGAAGGAGAGAGGTG 59.700 50.000 0.00 0.00 0.00 4.00
2825 3178 3.070018 CAACTTCCGAAGAGAAGCATGT 58.930 45.455 15.23 0.00 45.95 3.21
2956 3309 1.079819 CAGTGCCTCCACCGTACTG 60.080 63.158 0.00 0.00 43.09 2.74
2969 3322 0.319405 AATTGCTTTCAGGGCAGTGC 59.681 50.000 6.55 6.55 40.90 4.40
3003 3356 2.163815 GGCGTATATAGTCGGAGCACAT 59.836 50.000 0.00 0.00 0.00 3.21
3178 3533 6.386654 TCCCAAAAATTCTTTAATCAGCGTC 58.613 36.000 0.00 0.00 0.00 5.19
3201 3556 7.764901 ACTGTATTAAGAACTCCGAAATTCCTC 59.235 37.037 0.00 0.00 0.00 3.71
3289 3644 2.228822 CCTACACAAACCTCCATGCAAC 59.771 50.000 0.00 0.00 0.00 4.17
3346 3721 3.607370 AAGGAAGCGAACGGCCCTC 62.607 63.158 0.00 0.00 45.17 4.30
3347 3722 3.637273 AAGGAAGCGAACGGCCCT 61.637 61.111 0.00 0.00 45.17 5.19
3350 3725 4.103103 GGCAAGGAAGCGAACGGC 62.103 66.667 0.00 0.00 44.05 5.68
3352 3727 2.391389 GGAGGCAAGGAAGCGAACG 61.391 63.158 0.00 0.00 34.64 3.95
3353 3728 2.391389 CGGAGGCAAGGAAGCGAAC 61.391 63.158 0.00 0.00 34.64 3.95
3355 3730 4.082523 CCGGAGGCAAGGAAGCGA 62.083 66.667 0.00 0.00 46.14 4.93
3367 3742 1.848652 TGTAGAGAGGAAACCCGGAG 58.151 55.000 0.73 0.00 0.00 4.63
3368 3743 2.385803 GATGTAGAGAGGAAACCCGGA 58.614 52.381 0.73 0.00 0.00 5.14
3369 3744 1.413077 GGATGTAGAGAGGAAACCCGG 59.587 57.143 0.00 0.00 0.00 5.73
3370 3745 1.413077 GGGATGTAGAGAGGAAACCCG 59.587 57.143 0.00 0.00 0.00 5.28
3417 3792 6.183361 GGAGCATTATCTCTAAGACAAGGGAA 60.183 42.308 0.00 0.00 33.70 3.97
3432 3807 4.060038 TCGAAGACAAGGGAGCATTATC 57.940 45.455 0.00 0.00 0.00 1.75
3498 3873 2.592102 ATGCAGGACATGTGGTTTCT 57.408 45.000 1.15 0.00 37.70 2.52
3654 4053 9.825972 AGTTAAACAATAATCGAGTCAAACATG 57.174 29.630 0.00 0.00 0.00 3.21
3682 4082 8.729756 CGTTGGAATGAGCCATATATATTTCAA 58.270 33.333 0.00 0.00 37.86 2.69
3696 4096 0.452784 GTTCGTGCGTTGGAATGAGC 60.453 55.000 0.00 0.00 0.00 4.26
3721 4121 7.219344 GCGTTTGTGTCTACTGTGTTAATTTTT 59.781 33.333 0.00 0.00 0.00 1.94
3722 4122 6.689669 GCGTTTGTGTCTACTGTGTTAATTTT 59.310 34.615 0.00 0.00 0.00 1.82
3723 4123 6.037830 AGCGTTTGTGTCTACTGTGTTAATTT 59.962 34.615 0.00 0.00 0.00 1.82
3724 4124 5.526111 AGCGTTTGTGTCTACTGTGTTAATT 59.474 36.000 0.00 0.00 0.00 1.40
3725 4125 5.054477 AGCGTTTGTGTCTACTGTGTTAAT 58.946 37.500 0.00 0.00 0.00 1.40
3781 4213 1.960040 CTCACGAGGTAGGGCATGCA 61.960 60.000 21.36 0.00 0.00 3.96
3791 4223 3.374402 CGGAGGTGCTCACGAGGT 61.374 66.667 0.00 0.00 31.08 3.85
3795 4227 2.041115 TCTCTCGGAGGTGCTCACG 61.041 63.158 4.96 0.00 31.08 4.35
3796 4228 0.963355 AGTCTCTCGGAGGTGCTCAC 60.963 60.000 4.96 0.00 31.08 3.51
3839 4273 3.713858 TGTTTGTGGCAACTTCATCAG 57.286 42.857 0.00 0.00 37.61 2.90
3865 4299 6.776116 TCAGTTGGATACGTTCTATGGACTAT 59.224 38.462 0.00 0.00 42.51 2.12
3866 4300 6.124340 TCAGTTGGATACGTTCTATGGACTA 58.876 40.000 0.00 0.00 42.51 2.59
3871 4305 5.580691 TGCTTTCAGTTGGATACGTTCTATG 59.419 40.000 0.00 0.00 42.51 2.23
3873 4307 4.927425 GTGCTTTCAGTTGGATACGTTCTA 59.073 41.667 0.00 0.00 42.51 2.10
3874 4308 3.746492 GTGCTTTCAGTTGGATACGTTCT 59.254 43.478 0.00 0.00 42.51 3.01
3885 4319 2.148916 TCGACGATGTGCTTTCAGTT 57.851 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.