Multiple sequence alignment - TraesCS5B01G312200

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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 TraesCS5B01G312200 chr5B 100.000 2945 0 0 1 2945 493696609 493693665 0.000000e+00 5439.0
1 TraesCS5B01G312200 chr5B 83.468 744 104 11 1083 1824 493174582 493173856 0.000000e+00 675.0
2 TraesCS5B01G312200 chr5D 89.502 2048 107 37 1 1994 411226943 411224950 0.000000e+00 2492.0
3 TraesCS5B01G312200 chr5D 88.171 913 47 22 2067 2945 411224756 411223871 0.000000e+00 1031.0
4 TraesCS5B01G312200 chr5D 81.250 928 127 31 1083 1995 410867021 410866126 0.000000e+00 706.0
5 TraesCS5B01G312200 chr5D 85.014 347 46 4 1167 1512 410444211 410444552 6.040000e-92 348.0
6 TraesCS5B01G312200 chr5D 84.857 350 47 5 1169 1512 411149305 411148956 6.040000e-92 348.0
7 TraesCS5B01G312200 chr5D 85.294 136 15 5 383 515 126263349 126263216 5.120000e-28 135.0
8 TraesCS5B01G312200 chr5A 89.908 1407 68 24 585 1946 523149308 523147931 0.000000e+00 1744.0
9 TraesCS5B01G312200 chr5A 91.591 987 40 14 1996 2945 523146663 523145683 0.000000e+00 1323.0
10 TraesCS5B01G312200 chr5A 83.715 743 104 9 1083 1824 522861743 522861017 0.000000e+00 686.0
11 TraesCS5B01G312200 chr5A 84.286 350 49 5 1169 1512 522956753 522956404 1.310000e-88 337.0
12 TraesCS5B01G312200 chr5A 82.564 390 56 8 1132 1512 522883399 522883013 1.690000e-87 333.0
13 TraesCS5B01G312200 chr5A 82.573 241 34 7 139 378 523149688 523149455 3.850000e-49 206.0
14 TraesCS5B01G312200 chr5A 100.000 30 0 0 1937 1966 523146694 523146665 4.100000e-04 56.5
15 TraesCS5B01G312200 chr2B 85.600 125 14 4 386 509 708245636 708245757 8.570000e-26 128.0
16 TraesCS5B01G312200 chr3D 81.333 150 22 5 371 515 368966365 368966513 1.850000e-22 117.0
17 TraesCS5B01G312200 chr2D 83.077 130 20 2 386 514 76902158 76902286 1.850000e-22 117.0
18 TraesCS5B01G312200 chr3B 81.081 148 22 6 371 514 177423476 177423331 2.400000e-21 113.0
19 TraesCS5B01G312200 chr6D 81.618 136 19 6 383 515 472539670 472539538 1.120000e-19 108.0
20 TraesCS5B01G312200 chr7A 87.912 91 8 3 417 505 546340 546429 1.440000e-18 104.0
21 TraesCS5B01G312200 chr7D 79.259 135 21 7 385 514 422617450 422617582 1.450000e-13 87.9


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 TraesCS5B01G312200 chr5B 493693665 493696609 2944 True 5439.000 5439 100.0000 1 2945 1 chr5B.!!$R2 2944
1 TraesCS5B01G312200 chr5B 493173856 493174582 726 True 675.000 675 83.4680 1083 1824 1 chr5B.!!$R1 741
2 TraesCS5B01G312200 chr5D 411223871 411226943 3072 True 1761.500 2492 88.8365 1 2945 2 chr5D.!!$R4 2944
3 TraesCS5B01G312200 chr5D 410866126 410867021 895 True 706.000 706 81.2500 1083 1995 1 chr5D.!!$R2 912
4 TraesCS5B01G312200 chr5A 523145683 523149688 4005 True 832.375 1744 91.0180 139 2945 4 chr5A.!!$R4 2806
5 TraesCS5B01G312200 chr5A 522861017 522861743 726 True 686.000 686 83.7150 1083 1824 1 chr5A.!!$R1 741

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
519 536 0.038599 TGACAGGAGTAGTACCCGCA 59.961 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 3351 0.034756 TGTGGTTCATGTGAGACCGG 59.965 55.0 0.0 0.0 0.0 5.28 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
59 61 3.525800 ATGCTTGTTTCCTAGGTTGGT 57.474 42.857 9.08 0.00 0.00 3.67
66 68 0.896940 TTCCTAGGTTGGTCGTCGCT 60.897 55.000 9.08 0.00 0.00 4.93
67 69 1.153823 CCTAGGTTGGTCGTCGCTG 60.154 63.158 0.00 0.00 0.00 5.18
68 70 1.153823 CTAGGTTGGTCGTCGCTGG 60.154 63.158 0.00 0.00 0.00 4.85
77 79 4.662961 CGTCGCTGGCTCCACACA 62.663 66.667 0.00 0.00 0.00 3.72
100 102 5.812642 CAGGGATGGATGCGAGTATTATAAC 59.187 44.000 0.00 0.00 0.00 1.89
189 204 0.108615 CTAGGCGGTCCAAGACACAG 60.109 60.000 0.00 0.00 33.68 3.66
209 224 4.020128 ACAGTTTTGTCCTCCAGTATCTCC 60.020 45.833 0.00 0.00 29.46 3.71
274 290 6.927381 GCTTTAGATGATTTGGCAAGCATAAT 59.073 34.615 14.89 10.63 39.18 1.28
303 319 7.075741 GCTAATTGCATCCGTAATACGAAAAT 58.924 34.615 15.03 2.20 42.40 1.82
312 328 7.655236 TCCGTAATACGAAAATCAAAAGTCA 57.345 32.000 15.03 0.00 46.05 3.41
323 339 7.221452 CGAAAATCAAAAGTCATTCATGGATCC 59.779 37.037 4.20 4.20 0.00 3.36
327 343 5.416639 TCAAAAGTCATTCATGGATCCAGTG 59.583 40.000 21.33 17.29 0.00 3.66
353 369 0.757512 TTGTGTGGTACCCGCTACAA 59.242 50.000 10.07 12.07 34.94 2.41
358 374 0.746063 TGGTACCCGCTACAATACCG 59.254 55.000 10.07 0.00 40.06 4.02
378 394 4.216902 ACCGGGAAAGCACATAAAAGTTAC 59.783 41.667 6.32 0.00 0.00 2.50
383 399 6.149633 GGAAAGCACATAAAAGTTACCACTG 58.850 40.000 0.00 0.00 31.60 3.66
384 400 5.705609 AAGCACATAAAAGTTACCACTGG 57.294 39.130 0.00 0.00 31.60 4.00
407 423 6.592607 TGGAAACTATGTTCAAGTACGAATCC 59.407 38.462 0.00 0.00 0.00 3.01
408 424 6.592607 GGAAACTATGTTCAAGTACGAATCCA 59.407 38.462 0.00 0.00 0.00 3.41
414 430 5.996219 TGTTCAAGTACGAATCCAACAATG 58.004 37.500 0.00 0.00 0.00 2.82
415 431 4.678509 TCAAGTACGAATCCAACAATGC 57.321 40.909 0.00 0.00 0.00 3.56
504 521 7.782049 ACGAAGGAGACTAATAAATCATGACA 58.218 34.615 0.00 0.00 42.68 3.58
506 523 7.383572 CGAAGGAGACTAATAAATCATGACAGG 59.616 40.741 0.00 0.00 42.68 4.00
507 524 7.921041 AGGAGACTAATAAATCATGACAGGA 57.079 36.000 0.00 0.00 40.61 3.86
519 536 0.038599 TGACAGGAGTAGTACCCGCA 59.961 55.000 0.00 0.00 0.00 5.69
520 537 0.739561 GACAGGAGTAGTACCCGCAG 59.260 60.000 0.00 0.00 0.00 5.18
528 545 1.378882 TAGTACCCGCAGCACTACCG 61.379 60.000 0.00 0.00 0.00 4.02
535 552 2.399356 GCAGCACTACCGGGAAAGC 61.399 63.158 6.32 3.68 0.00 3.51
536 553 2.100631 CAGCACTACCGGGAAAGCG 61.101 63.158 6.32 0.00 0.00 4.68
544 561 0.808755 ACCGGGAAAGCGCATAAAAG 59.191 50.000 11.47 0.00 0.00 2.27
625 671 7.666623 TCACATCACAAGAACACACTAATCTA 58.333 34.615 0.00 0.00 0.00 1.98
665 711 2.297701 GCGAATGGGATACACCAACAT 58.702 47.619 0.00 0.00 45.13 2.71
745 791 5.910723 ACAAAACGCGGTTAAAAAGATACTG 59.089 36.000 11.16 2.61 0.00 2.74
754 800 6.332630 GGTTAAAAAGATACTGCATGCATGT 58.667 36.000 26.79 21.81 0.00 3.21
778 824 1.451028 GGCTGTGAGGTGATGGAGC 60.451 63.158 0.00 0.00 0.00 4.70
779 825 1.812922 GCTGTGAGGTGATGGAGCG 60.813 63.158 0.00 0.00 0.00 5.03
780 826 1.812922 CTGTGAGGTGATGGAGCGC 60.813 63.158 0.00 0.00 0.00 5.92
781 827 2.512515 GTGAGGTGATGGAGCGCC 60.513 66.667 2.29 0.00 38.73 6.53
782 828 3.785859 TGAGGTGATGGAGCGCCC 61.786 66.667 2.29 5.76 39.26 6.13
790 836 4.196778 TGGAGCGCCCAAACACCA 62.197 61.111 14.27 5.79 43.29 4.17
791 837 3.670377 GGAGCGCCCAAACACCAC 61.670 66.667 2.29 0.00 34.14 4.16
792 838 4.025401 GAGCGCCCAAACACCACG 62.025 66.667 2.29 0.00 0.00 4.94
795 841 3.591835 CGCCCAAACACCACGCTT 61.592 61.111 0.00 0.00 0.00 4.68
796 842 2.335011 GCCCAAACACCACGCTTC 59.665 61.111 0.00 0.00 0.00 3.86
797 843 2.637025 CCCAAACACCACGCTTCG 59.363 61.111 0.00 0.00 0.00 3.79
798 844 2.637025 CCAAACACCACGCTTCGG 59.363 61.111 0.00 0.00 0.00 4.30
799 845 1.890041 CCAAACACCACGCTTCGGA 60.890 57.895 0.00 0.00 0.00 4.55
800 846 1.569493 CAAACACCACGCTTCGGAG 59.431 57.895 0.00 0.00 0.00 4.63
812 858 2.190488 CTTCGGAGGGAAGCTGCCTT 62.190 60.000 11.64 1.38 45.21 4.35
820 866 3.041211 AGGGAAGCTGCCTTTTTCTTTT 58.959 40.909 11.64 0.00 32.70 2.27
853 899 3.787394 CCCCCACACGTCTACACT 58.213 61.111 0.00 0.00 0.00 3.55
865 911 2.152830 GTCTACACTGAGGAGTCACGT 58.847 52.381 0.00 0.00 0.00 4.49
1012 1058 5.105837 CCACTGGTTTACTGAGTACTCCTAC 60.106 48.000 20.11 10.11 0.00 3.18
1013 1059 5.015515 ACTGGTTTACTGAGTACTCCTACC 58.984 45.833 20.11 17.63 0.00 3.18
1052 1115 4.787280 CCCGGCTCCTCCTCCAGT 62.787 72.222 0.00 0.00 0.00 4.00
1060 1123 2.886391 GCTCCTCCTCCAGTCAACTAGT 60.886 54.545 0.00 0.00 0.00 2.57
1062 1125 2.378886 TCCTCCTCCAGTCAACTAGTCA 59.621 50.000 0.00 0.00 0.00 3.41
1078 1141 5.225642 ACTAGTCAAGCAAAAGTACGTACC 58.774 41.667 21.80 6.46 0.00 3.34
1264 1352 3.140141 CGGGGTAGTAACGGCCGA 61.140 66.667 35.90 7.50 0.00 5.54
1601 1695 2.110967 CCAGACAATGCCAGCTCGG 61.111 63.158 0.00 0.00 38.11 4.63
1826 1920 2.477825 CGCTATGGAACCACTGATGAG 58.522 52.381 0.00 0.00 0.00 2.90
1827 1921 2.159043 CGCTATGGAACCACTGATGAGT 60.159 50.000 0.00 0.00 0.00 3.41
1907 2008 0.513820 TTTACTCCGAAAAAGCGCCG 59.486 50.000 2.29 0.00 0.00 6.46
1984 3335 3.006940 GCATCAAAACCGGTCTCACATA 58.993 45.455 8.04 0.00 0.00 2.29
1985 3336 3.438781 GCATCAAAACCGGTCTCACATAA 59.561 43.478 8.04 0.00 0.00 1.90
1986 3337 4.083003 GCATCAAAACCGGTCTCACATAAA 60.083 41.667 8.04 0.00 0.00 1.40
1987 3338 5.390613 CATCAAAACCGGTCTCACATAAAC 58.609 41.667 8.04 0.00 0.00 2.01
1988 3339 3.816523 TCAAAACCGGTCTCACATAAACC 59.183 43.478 8.04 0.00 0.00 3.27
1989 3340 3.495434 AAACCGGTCTCACATAAACCA 57.505 42.857 8.04 0.00 32.35 3.67
1990 3341 2.467566 ACCGGTCTCACATAAACCAC 57.532 50.000 0.00 0.00 32.35 4.16
1991 3342 1.695242 ACCGGTCTCACATAAACCACA 59.305 47.619 0.00 0.00 32.35 4.17
1992 3343 2.304761 ACCGGTCTCACATAAACCACAT 59.695 45.455 0.00 0.00 32.35 3.21
1993 3344 3.516300 ACCGGTCTCACATAAACCACATA 59.484 43.478 0.00 0.00 32.35 2.29
1994 3345 4.163458 ACCGGTCTCACATAAACCACATAT 59.837 41.667 0.00 0.00 32.35 1.78
1995 3346 4.750098 CCGGTCTCACATAAACCACATATC 59.250 45.833 0.00 0.00 32.35 1.63
1996 3347 5.356426 CGGTCTCACATAAACCACATATCA 58.644 41.667 0.00 0.00 32.35 2.15
1997 3348 5.815222 CGGTCTCACATAAACCACATATCAA 59.185 40.000 0.00 0.00 32.35 2.57
1998 3349 6.018751 CGGTCTCACATAAACCACATATCAAG 60.019 42.308 0.00 0.00 32.35 3.02
1999 3350 7.047891 GGTCTCACATAAACCACATATCAAGA 58.952 38.462 0.00 0.00 33.11 3.02
2000 3351 7.011482 GGTCTCACATAAACCACATATCAAGAC 59.989 40.741 0.00 0.00 33.11 3.01
2001 3352 7.011482 GTCTCACATAAACCACATATCAAGACC 59.989 40.741 0.00 0.00 0.00 3.85
2002 3353 5.815222 TCACATAAACCACATATCAAGACCG 59.185 40.000 0.00 0.00 0.00 4.79
2003 3354 5.007626 CACATAAACCACATATCAAGACCGG 59.992 44.000 0.00 0.00 0.00 5.28
2004 3355 3.713826 AAACCACATATCAAGACCGGT 57.286 42.857 6.92 6.92 0.00 5.28
2005 3356 2.981859 ACCACATATCAAGACCGGTC 57.018 50.000 27.67 27.67 0.00 4.79
2006 3357 2.467880 ACCACATATCAAGACCGGTCT 58.532 47.619 31.69 31.69 42.75 3.85
2007 3358 2.431057 ACCACATATCAAGACCGGTCTC 59.569 50.000 36.29 11.85 39.39 3.36
2008 3359 2.430694 CCACATATCAAGACCGGTCTCA 59.569 50.000 36.29 25.62 39.39 3.27
2009 3360 3.448686 CACATATCAAGACCGGTCTCAC 58.551 50.000 36.29 10.58 39.39 3.51
2010 3361 3.096852 ACATATCAAGACCGGTCTCACA 58.903 45.455 36.29 22.76 39.39 3.58
2011 3362 3.706594 ACATATCAAGACCGGTCTCACAT 59.293 43.478 36.29 27.04 39.39 3.21
2012 3363 2.680312 ATCAAGACCGGTCTCACATG 57.320 50.000 36.29 28.73 39.39 3.21
2287 3805 1.918293 AAGATGTGGCCGAGACCCA 60.918 57.895 0.00 0.00 0.00 4.51
2408 3926 3.991051 CTGTCGCGTCAGTGGGGT 61.991 66.667 22.63 0.00 0.00 4.95
2458 3976 3.390521 CAGGCAGCTGGGACCGTA 61.391 66.667 17.12 0.00 0.00 4.02
2493 4011 2.363147 GTCACTCTCTCGCCCCCT 60.363 66.667 0.00 0.00 0.00 4.79
2494 4012 1.076923 GTCACTCTCTCGCCCCCTA 60.077 63.158 0.00 0.00 0.00 3.53
2496 4014 1.076632 CACTCTCTCGCCCCCTACT 60.077 63.158 0.00 0.00 0.00 2.57
2500 4018 0.924823 TCTCTCGCCCCCTACTACTT 59.075 55.000 0.00 0.00 0.00 2.24
2502 4020 0.465097 TCTCGCCCCCTACTACTTCG 60.465 60.000 0.00 0.00 0.00 3.79
2528 4052 1.630369 ACAGCAAGGCAGGTCAAGATA 59.370 47.619 0.00 0.00 0.00 1.98
2623 4147 3.118738 GGGAAAAGACATTCCTAGAGCGA 60.119 47.826 6.08 0.00 46.66 4.93
2628 4152 2.428890 AGACATTCCTAGAGCGAAGGTG 59.571 50.000 2.84 0.00 39.88 4.00
2637 4161 3.443045 GCGAAGGTGGTGCCATGG 61.443 66.667 7.63 7.63 40.61 3.66
2732 4257 3.632145 TGCTCGTGTAGATTAGATGCAGA 59.368 43.478 0.00 0.00 0.00 4.26
2748 4275 3.330720 GAGGGGGTGGTCCAGGTG 61.331 72.222 0.00 0.00 37.22 4.00
2834 4374 7.465960 AGCTATCTCCTATCTGTATCACTCAA 58.534 38.462 0.00 0.00 0.00 3.02
2880 4420 2.045634 GGAGCAGCTGCATGGTCA 60.046 61.111 38.24 0.00 46.97 4.02
2921 4461 2.122989 TCCCCTCCTACGCATCCC 60.123 66.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 23 6.440328 ACAAGCATAGGGTGTAATTTCCAATT 59.560 34.615 0.00 0.00 0.00 2.32
22 24 5.957774 ACAAGCATAGGGTGTAATTTCCAAT 59.042 36.000 0.00 0.00 0.00 3.16
23 25 5.329399 ACAAGCATAGGGTGTAATTTCCAA 58.671 37.500 0.00 0.00 0.00 3.53
24 26 4.929479 ACAAGCATAGGGTGTAATTTCCA 58.071 39.130 0.00 0.00 0.00 3.53
36 38 3.947834 CCAACCTAGGAAACAAGCATAGG 59.052 47.826 17.98 0.00 43.49 2.57
37 39 4.589908 ACCAACCTAGGAAACAAGCATAG 58.410 43.478 17.98 0.00 0.00 2.23
59 61 4.357947 GTGTGGAGCCAGCGACGA 62.358 66.667 0.00 0.00 0.00 4.20
66 68 2.605607 CCATCCCTGTGTGGAGCCA 61.606 63.158 0.00 0.00 37.96 4.75
67 69 1.639635 ATCCATCCCTGTGTGGAGCC 61.640 60.000 0.37 0.00 46.87 4.70
68 70 0.465097 CATCCATCCCTGTGTGGAGC 60.465 60.000 0.37 0.00 46.87 4.70
77 79 5.721960 AGTTATAATACTCGCATCCATCCCT 59.278 40.000 0.00 0.00 0.00 4.20
122 124 3.116079 ACCAACACGAGTAAACGGAAT 57.884 42.857 0.00 0.00 37.61 3.01
127 129 5.166398 ACTAGCATACCAACACGAGTAAAC 58.834 41.667 0.00 0.00 0.00 2.01
131 133 5.593679 ATTACTAGCATACCAACACGAGT 57.406 39.130 0.00 0.00 0.00 4.18
189 204 3.194968 TCGGAGATACTGGAGGACAAAAC 59.805 47.826 0.00 0.00 0.00 2.43
209 224 3.183754 TGCGTGTAGGTACAATCATTCG 58.816 45.455 0.00 0.00 38.04 3.34
274 290 0.840617 TACGGATGCAATTAGCCCCA 59.159 50.000 0.00 0.00 44.83 4.96
303 319 5.416639 CACTGGATCCATGAATGACTTTTGA 59.583 40.000 16.63 0.00 0.00 2.69
312 328 3.744940 AACCACACTGGATCCATGAAT 57.255 42.857 16.63 0.00 40.96 2.57
318 334 2.693074 ACACAAAAACCACACTGGATCC 59.307 45.455 4.20 4.20 40.96 3.36
323 339 3.428316 GGTACCACACAAAAACCACACTG 60.428 47.826 7.15 0.00 0.00 3.66
353 369 4.595986 ACTTTTATGTGCTTTCCCGGTAT 58.404 39.130 0.00 0.00 0.00 2.73
358 374 5.243060 AGTGGTAACTTTTATGTGCTTTCCC 59.757 40.000 0.00 0.00 30.14 3.97
378 394 5.120208 CGTACTTGAACATAGTTTCCAGTGG 59.880 44.000 1.40 1.40 33.61 4.00
383 399 6.592607 TGGATTCGTACTTGAACATAGTTTCC 59.407 38.462 0.00 0.00 0.00 3.13
384 400 7.591006 TGGATTCGTACTTGAACATAGTTTC 57.409 36.000 0.00 0.00 0.00 2.78
464 481 8.669243 AGTCTCCTTCGTAATTTGAATCAAATC 58.331 33.333 20.01 9.05 42.32 2.17
467 484 9.667107 ATTAGTCTCCTTCGTAATTTGAATCAA 57.333 29.630 0.00 0.00 0.00 2.57
477 494 9.745880 GTCATGATTTATTAGTCTCCTTCGTAA 57.254 33.333 0.00 0.00 0.00 3.18
504 521 1.000019 TGCTGCGGGTACTACTCCT 60.000 57.895 0.00 0.00 0.00 3.69
506 523 1.386533 TAGTGCTGCGGGTACTACTC 58.613 55.000 0.00 0.00 41.08 2.59
507 524 3.583054 TAGTGCTGCGGGTACTACT 57.417 52.632 0.00 0.00 41.08 2.57
519 536 2.264794 CGCTTTCCCGGTAGTGCT 59.735 61.111 0.00 0.00 0.00 4.40
520 537 3.497031 GCGCTTTCCCGGTAGTGC 61.497 66.667 15.32 15.32 40.25 4.40
528 545 3.191791 TGTAACCTTTTATGCGCTTTCCC 59.808 43.478 9.73 0.00 0.00 3.97
535 552 6.559810 TGGATCAATTGTAACCTTTTATGCG 58.440 36.000 5.13 0.00 0.00 4.73
536 553 8.655970 GTTTGGATCAATTGTAACCTTTTATGC 58.344 33.333 5.13 0.00 0.00 3.14
544 561 4.929211 GCCTTGTTTGGATCAATTGTAACC 59.071 41.667 5.13 8.12 0.00 2.85
625 671 2.205074 CGGCGTTCTCATCTTAGCATT 58.795 47.619 0.00 0.00 0.00 3.56
665 711 3.057174 CGGCCAACTTGCTAATTTTGGTA 60.057 43.478 2.24 0.00 40.65 3.25
745 791 2.131709 AGCCCATGGACATGCATGC 61.132 57.895 26.53 18.01 37.49 4.06
754 800 0.915872 ATCACCTCACAGCCCATGGA 60.916 55.000 15.22 0.00 0.00 3.41
778 824 3.536498 GAAGCGTGGTGTTTGGGCG 62.536 63.158 0.00 0.00 0.00 6.13
779 825 2.335011 GAAGCGTGGTGTTTGGGC 59.665 61.111 0.00 0.00 0.00 5.36
780 826 2.637025 CGAAGCGTGGTGTTTGGG 59.363 61.111 0.00 0.00 0.00 4.12
781 827 1.841663 CTCCGAAGCGTGGTGTTTGG 61.842 60.000 0.00 0.00 0.00 3.28
782 828 1.569493 CTCCGAAGCGTGGTGTTTG 59.431 57.895 0.00 0.00 0.00 2.93
783 829 1.597027 CCTCCGAAGCGTGGTGTTT 60.597 57.895 0.00 0.00 0.00 2.83
784 830 2.030562 CCTCCGAAGCGTGGTGTT 59.969 61.111 0.00 0.00 0.00 3.32
785 831 4.003788 CCCTCCGAAGCGTGGTGT 62.004 66.667 0.00 0.00 0.00 4.16
786 832 3.234630 TTCCCTCCGAAGCGTGGTG 62.235 63.158 0.00 0.00 0.00 4.17
787 833 2.920912 TTCCCTCCGAAGCGTGGT 60.921 61.111 0.00 0.00 0.00 4.16
788 834 2.125512 CTTCCCTCCGAAGCGTGG 60.126 66.667 0.00 0.00 41.61 4.94
794 840 1.779061 AAAGGCAGCTTCCCTCCGAA 61.779 55.000 0.00 0.00 0.00 4.30
795 841 1.779061 AAAAGGCAGCTTCCCTCCGA 61.779 55.000 0.00 0.00 0.00 4.55
796 842 0.895559 AAAAAGGCAGCTTCCCTCCG 60.896 55.000 0.00 0.00 0.00 4.63
797 843 0.891373 GAAAAAGGCAGCTTCCCTCC 59.109 55.000 0.00 0.00 0.00 4.30
798 844 1.916506 AGAAAAAGGCAGCTTCCCTC 58.083 50.000 0.00 0.00 0.00 4.30
799 845 2.388526 AAGAAAAAGGCAGCTTCCCT 57.611 45.000 0.00 0.00 0.00 4.20
800 846 3.070159 AGAAAAGAAAAAGGCAGCTTCCC 59.930 43.478 0.00 0.00 0.00 3.97
812 858 5.289917 GGTTTGCAGCGTTAAGAAAAGAAAA 59.710 36.000 0.00 0.00 0.00 2.29
820 866 0.891904 GGGGGTTTGCAGCGTTAAGA 60.892 55.000 0.00 0.00 0.00 2.10
840 886 1.880675 ACTCCTCAGTGTAGACGTGTG 59.119 52.381 0.00 0.00 0.00 3.82
865 911 4.403137 CCCGGTCGACGCGTGTAA 62.403 66.667 20.70 0.00 42.52 2.41
1036 1091 3.151022 GACTGGAGGAGGAGCCGG 61.151 72.222 0.00 0.00 43.43 6.13
1037 1092 1.984570 TTGACTGGAGGAGGAGCCG 60.985 63.158 0.00 0.00 43.43 5.52
1038 1093 0.907230 AGTTGACTGGAGGAGGAGCC 60.907 60.000 0.00 0.00 0.00 4.70
1039 1094 1.754226 CTAGTTGACTGGAGGAGGAGC 59.246 57.143 0.00 0.00 0.00 4.70
1041 1096 2.378886 TGACTAGTTGACTGGAGGAGGA 59.621 50.000 0.00 0.00 0.00 3.71
1052 1115 5.353938 ACGTACTTTTGCTTGACTAGTTGA 58.646 37.500 0.00 0.00 0.00 3.18
1252 1340 0.971959 ACACCCATCGGCCGTTACTA 60.972 55.000 27.15 5.24 0.00 1.82
1255 1343 2.266372 CACACCCATCGGCCGTTA 59.734 61.111 27.15 7.11 0.00 3.18
1582 1676 1.376424 CGAGCTGGCATTGTCTGGT 60.376 57.895 0.00 0.00 0.00 4.00
1792 1886 1.539560 ATAGCGCCGCATCATCTCCT 61.540 55.000 13.36 0.00 0.00 3.69
1826 1920 1.136500 GGAGTCCCTCGGTGTTATCAC 59.864 57.143 0.00 0.00 43.19 3.06
1827 1921 1.481871 GGAGTCCCTCGGTGTTATCA 58.518 55.000 0.00 0.00 0.00 2.15
1829 1923 1.041447 CCGGAGTCCCTCGGTGTTAT 61.041 60.000 2.80 0.00 41.23 1.89
1830 1924 1.679977 CCGGAGTCCCTCGGTGTTA 60.680 63.158 2.80 0.00 41.23 2.41
1836 1930 0.669625 GTTTTGACCGGAGTCCCTCG 60.670 60.000 9.46 0.00 42.81 4.63
1837 1931 0.685660 AGTTTTGACCGGAGTCCCTC 59.314 55.000 9.46 0.00 42.81 4.30
1838 1932 2.019807 TAGTTTTGACCGGAGTCCCT 57.980 50.000 9.46 0.00 42.81 4.20
1892 1993 4.794241 CGCGGCGCTTTTTCGGAG 62.794 66.667 30.54 6.78 0.00 4.63
1907 2008 4.041917 TCCACCGTCCACGTACGC 62.042 66.667 16.72 0.00 41.51 4.42
1916 2017 0.314302 CCGATGATAGGTCCACCGTC 59.686 60.000 0.00 0.00 42.08 4.79
1984 3335 3.263425 AGACCGGTCTTGATATGTGGTTT 59.737 43.478 31.69 4.17 36.31 3.27
1985 3336 2.838202 AGACCGGTCTTGATATGTGGTT 59.162 45.455 31.69 4.66 36.31 3.67
1986 3337 2.431057 GAGACCGGTCTTGATATGTGGT 59.569 50.000 36.55 11.54 40.61 4.16
1987 3338 2.430694 TGAGACCGGTCTTGATATGTGG 59.569 50.000 36.55 0.00 40.61 4.17
1988 3339 3.119137 TGTGAGACCGGTCTTGATATGTG 60.119 47.826 36.55 0.00 40.61 3.21
1989 3340 3.096852 TGTGAGACCGGTCTTGATATGT 58.903 45.455 36.55 13.72 40.61 2.29
1990 3341 3.801114 TGTGAGACCGGTCTTGATATG 57.199 47.619 36.55 0.00 40.61 1.78
1991 3342 3.960755 TCATGTGAGACCGGTCTTGATAT 59.039 43.478 36.55 24.94 40.61 1.63
1992 3343 3.361786 TCATGTGAGACCGGTCTTGATA 58.638 45.455 36.55 23.94 40.61 2.15
1993 3344 2.179427 TCATGTGAGACCGGTCTTGAT 58.821 47.619 36.55 24.29 40.61 2.57
1994 3345 1.627864 TCATGTGAGACCGGTCTTGA 58.372 50.000 36.55 30.57 40.61 3.02
1995 3346 2.069273 GTTCATGTGAGACCGGTCTTG 58.931 52.381 36.55 28.92 40.61 3.02
1996 3347 1.002087 GGTTCATGTGAGACCGGTCTT 59.998 52.381 36.55 19.46 40.61 3.01
1997 3348 0.608640 GGTTCATGTGAGACCGGTCT 59.391 55.000 36.89 36.89 43.78 3.85
1998 3349 0.320374 TGGTTCATGTGAGACCGGTC 59.680 55.000 27.67 27.67 0.00 4.79
1999 3350 0.034896 GTGGTTCATGTGAGACCGGT 59.965 55.000 6.92 6.92 0.00 5.28
2000 3351 0.034756 TGTGGTTCATGTGAGACCGG 59.965 55.000 0.00 0.00 0.00 5.28
2001 3352 2.099141 ATGTGGTTCATGTGAGACCG 57.901 50.000 0.00 0.00 35.19 4.79
2002 3353 4.184629 GAGTATGTGGTTCATGTGAGACC 58.815 47.826 0.00 0.00 37.91 3.85
2003 3354 4.081420 AGGAGTATGTGGTTCATGTGAGAC 60.081 45.833 0.00 0.00 37.91 3.36
2004 3355 4.081476 CAGGAGTATGTGGTTCATGTGAGA 60.081 45.833 0.00 0.00 37.91 3.27
2005 3356 4.186926 CAGGAGTATGTGGTTCATGTGAG 58.813 47.826 0.00 0.00 37.91 3.51
2006 3357 3.055167 CCAGGAGTATGTGGTTCATGTGA 60.055 47.826 0.00 0.00 37.91 3.58
2007 3358 3.055167 TCCAGGAGTATGTGGTTCATGTG 60.055 47.826 0.00 0.00 37.91 3.21
2008 3359 3.055094 GTCCAGGAGTATGTGGTTCATGT 60.055 47.826 0.00 0.00 37.91 3.21
2009 3360 3.055167 TGTCCAGGAGTATGTGGTTCATG 60.055 47.826 0.00 0.00 37.91 3.07
2010 3361 3.181329 TGTCCAGGAGTATGTGGTTCAT 58.819 45.455 0.00 0.00 40.25 2.57
2011 3362 2.615391 TGTCCAGGAGTATGTGGTTCA 58.385 47.619 0.00 0.00 35.14 3.18
2012 3363 3.914426 ATGTCCAGGAGTATGTGGTTC 57.086 47.619 0.00 0.00 35.14 3.62
2287 3805 2.063015 TTTCACCGGCTGACATGGGT 62.063 55.000 0.00 0.00 0.00 4.51
2408 3926 3.228017 TCACGGACAGCGACCCAA 61.228 61.111 0.00 0.00 0.00 4.12
2493 4011 2.433436 TGCTGTGCTCTCGAAGTAGTA 58.567 47.619 0.00 0.00 0.00 1.82
2494 4012 1.248486 TGCTGTGCTCTCGAAGTAGT 58.752 50.000 0.00 0.00 0.00 2.73
2496 4014 1.067565 CCTTGCTGTGCTCTCGAAGTA 60.068 52.381 0.00 0.00 0.00 2.24
2500 4018 2.047844 GCCTTGCTGTGCTCTCGA 60.048 61.111 0.00 0.00 0.00 4.04
2502 4020 2.039405 CCTGCCTTGCTGTGCTCTC 61.039 63.158 0.00 0.00 0.00 3.20
2610 4134 1.482593 ACCACCTTCGCTCTAGGAATG 59.517 52.381 0.00 0.00 36.58 2.67
2623 4147 2.036256 GCTCCATGGCACCACCTT 59.964 61.111 6.96 0.00 40.22 3.50
2637 4161 0.534652 CTATTCTGGGCAGGCAGCTC 60.535 60.000 0.81 0.00 46.89 4.09
2677 4202 2.672996 GCTGCCCGTTGTGGTGAT 60.673 61.111 0.00 0.00 35.15 3.06
2748 4275 3.152341 CATCCTGTGGATTGATTAGCCC 58.848 50.000 0.00 0.00 39.79 5.19
2749 4276 3.567164 CACATCCTGTGGATTGATTAGCC 59.433 47.826 0.00 0.00 44.27 3.93
2834 4374 4.052518 GGTCAGCTGCCCCACCAT 62.053 66.667 15.56 0.00 0.00 3.55
2880 4420 2.202743 AGCGCGACGTGCATGTAT 60.203 55.556 32.41 11.11 46.97 2.29
2921 4461 2.208619 TTGCACCCTGTTGGCCATG 61.209 57.895 6.09 0.68 37.83 3.66


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

AutoCloner maintained by Alex Coulton.