Multiple sequence alignment - TraesCS2D01G162100

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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 TraesCS2D01G162100 chr2D 100.000 3809 0 0 1 3809 106634337 106638145 0.000000e+00 7035
1 TraesCS2D01G162100 chr3A 95.290 2845 128 6 1 2841 601391976 601394818 0.000000e+00 4506
2 TraesCS2D01G162100 chr3B 95.322 2843 123 7 1 2840 100978914 100976079 0.000000e+00 4505
3 TraesCS2D01G162100 chr3B 95.464 2822 123 5 1 2819 50027719 50030538 0.000000e+00 4497
4 TraesCS2D01G162100 chr3B 95.471 1965 85 4 880 2842 607488336 607486374 0.000000e+00 3133
5 TraesCS2D01G162100 chr3B 80.969 557 98 8 2864 3416 775734394 775734946 5.840000e-118 435
6 TraesCS2D01G162100 chr6A 95.072 2841 135 5 1 2839 455732589 455729752 0.000000e+00 4466
7 TraesCS2D01G162100 chr6A 80.224 536 97 9 2865 3395 591940384 591940915 9.920000e-106 394
8 TraesCS2D01G162100 chr7B 94.942 2847 131 11 1 2841 736043950 736041111 0.000000e+00 4447
9 TraesCS2D01G162100 chr7B 93.556 2250 134 8 597 2843 709922304 709924545 0.000000e+00 3341
10 TraesCS2D01G162100 chr5B 94.907 2847 135 10 1 2841 547533570 547536412 0.000000e+00 4446
11 TraesCS2D01G162100 chr1B 95.304 2257 100 6 588 2843 649663527 649661276 0.000000e+00 3576
12 TraesCS2D01G162100 chr2A 94.429 1113 53 6 297 1404 623747987 623749095 0.000000e+00 1703
13 TraesCS2D01G162100 chr2A 86.401 978 108 18 2842 3809 103105538 103106500 0.000000e+00 1046
14 TraesCS2D01G162100 chr2A 79.516 537 99 11 2865 3395 669746828 669747359 4.650000e-99 372
15 TraesCS2D01G162100 chr2B 85.445 955 117 14 2861 3796 156598579 156599530 0.000000e+00 974
16 TraesCS2D01G162100 chr2B 75.167 1349 300 33 5 1335 786947971 786949302 1.510000e-168 603
17 TraesCS2D01G162100 chr5D 81.753 559 97 5 2864 3419 62529978 62530534 2.680000e-126 462
18 TraesCS2D01G162100 chr7A 79.492 551 109 4 2871 3419 694104677 694104129 4.610000e-104 388
19 TraesCS2D01G162100 chrUn 80.000 530 97 9 2871 3395 136395254 136394729 2.150000e-102 383
20 TraesCS2D01G162100 chr6D 79.218 563 102 14 2864 3419 323008700 323008146 9.990000e-101 377


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 TraesCS2D01G162100 chr2D 106634337 106638145 3808 False 7035 7035 100.000 1 3809 1 chr2D.!!$F1 3808
1 TraesCS2D01G162100 chr3A 601391976 601394818 2842 False 4506 4506 95.290 1 2841 1 chr3A.!!$F1 2840
2 TraesCS2D01G162100 chr3B 100976079 100978914 2835 True 4505 4505 95.322 1 2840 1 chr3B.!!$R1 2839
3 TraesCS2D01G162100 chr3B 50027719 50030538 2819 False 4497 4497 95.464 1 2819 1 chr3B.!!$F1 2818
4 TraesCS2D01G162100 chr3B 607486374 607488336 1962 True 3133 3133 95.471 880 2842 1 chr3B.!!$R2 1962
5 TraesCS2D01G162100 chr3B 775734394 775734946 552 False 435 435 80.969 2864 3416 1 chr3B.!!$F2 552
6 TraesCS2D01G162100 chr6A 455729752 455732589 2837 True 4466 4466 95.072 1 2839 1 chr6A.!!$R1 2838
7 TraesCS2D01G162100 chr6A 591940384 591940915 531 False 394 394 80.224 2865 3395 1 chr6A.!!$F1 530
8 TraesCS2D01G162100 chr7B 736041111 736043950 2839 True 4447 4447 94.942 1 2841 1 chr7B.!!$R1 2840
9 TraesCS2D01G162100 chr7B 709922304 709924545 2241 False 3341 3341 93.556 597 2843 1 chr7B.!!$F1 2246
10 TraesCS2D01G162100 chr5B 547533570 547536412 2842 False 4446 4446 94.907 1 2841 1 chr5B.!!$F1 2840
11 TraesCS2D01G162100 chr1B 649661276 649663527 2251 True 3576 3576 95.304 588 2843 1 chr1B.!!$R1 2255
12 TraesCS2D01G162100 chr2A 623747987 623749095 1108 False 1703 1703 94.429 297 1404 1 chr2A.!!$F2 1107
13 TraesCS2D01G162100 chr2A 103105538 103106500 962 False 1046 1046 86.401 2842 3809 1 chr2A.!!$F1 967
14 TraesCS2D01G162100 chr2A 669746828 669747359 531 False 372 372 79.516 2865 3395 1 chr2A.!!$F3 530
15 TraesCS2D01G162100 chr2B 156598579 156599530 951 False 974 974 85.445 2861 3796 1 chr2B.!!$F1 935
16 TraesCS2D01G162100 chr2B 786947971 786949302 1331 False 603 603 75.167 5 1335 1 chr2B.!!$F2 1330
17 TraesCS2D01G162100 chr5D 62529978 62530534 556 False 462 462 81.753 2864 3419 1 chr5D.!!$F1 555
18 TraesCS2D01G162100 chr7A 694104129 694104677 548 True 388 388 79.492 2871 3419 1 chr7A.!!$R1 548
19 TraesCS2D01G162100 chrUn 136394729 136395254 525 True 383 383 80.000 2871 3395 1 chrUn.!!$R1 524
20 TraesCS2D01G162100 chr6D 323008146 323008700 554 True 377 377 79.218 2864 3419 1 chr6D.!!$R1 555

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
770 780 0.447406 TCATGAGCGCGGATGTTTTG 59.553 50.0 8.83 3.48 0.0 2.44 F
1795 1808 0.608856 TGCAAATGACACCAGCCGAT 60.609 50.0 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 1888 0.165079 AATTCCGTGCAGTAAACGCG 59.835 50.0 3.53 3.53 39.69 6.01 R
3400 3433 0.036010 AGTTTCTCGTGCCTCCCATG 60.036 55.0 0.00 0.00 0.00 3.66 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
117 118 8.366359 ACCCAAGAAGTTCTTATTGCAATTAT 57.634 30.769 18.75 0.00 33.78 1.28
164 166 6.385843 TGGAATGATACAACGATTGTTTTGG 58.614 36.000 8.33 0.00 42.22 3.28
272 274 2.975410 TGCTGCTCGATTGAAAACAG 57.025 45.000 0.00 3.83 0.00 3.16
275 277 3.066621 TGCTGCTCGATTGAAAACAGTTT 59.933 39.130 0.00 0.00 0.00 2.66
341 343 6.328934 TGGGAGGCTCATTACTGATAACATTA 59.671 38.462 17.69 0.00 0.00 1.90
524 532 2.885135 TGATGGCTTGTGTTGGATCT 57.115 45.000 0.00 0.00 0.00 2.75
631 641 6.903534 TCTCCCTATCTATTTCTCCTTTGTGT 59.096 38.462 0.00 0.00 0.00 3.72
654 664 8.741841 GTGTAGAAGGTCTTTCTAGTCTATTGT 58.258 37.037 4.74 0.00 46.38 2.71
680 690 2.297033 TGAAAAAGAAGCTGGTGGCATC 59.703 45.455 0.00 0.00 44.79 3.91
736 746 4.520492 AGTCTCACACCTTTTATTTGCTGG 59.480 41.667 0.00 0.00 0.00 4.85
770 780 0.447406 TCATGAGCGCGGATGTTTTG 59.553 50.000 8.83 3.48 0.00 2.44
847 857 5.761165 TTGGTAAGTTTGGCAAAGTCTAC 57.239 39.130 19.88 20.06 0.00 2.59
1106 1118 6.840780 AGCTATTCCTGTTTTTGCTATGTT 57.159 33.333 0.00 0.00 0.00 2.71
1221 1234 5.581874 GCATTGGTATTCTTGGTGGAAATTG 59.418 40.000 0.00 0.00 0.00 2.32
1294 1307 4.660789 AATTTGGCAATGCTAGCTAAGG 57.339 40.909 17.23 4.16 33.95 2.69
1422 1435 1.266718 TCGTTCACTTGGCAAAGCATC 59.733 47.619 0.00 0.00 36.84 3.91
1524 1537 4.105377 CCATGGATTCCTTCTAGTCCCAAT 59.895 45.833 5.56 0.00 0.00 3.16
1552 1565 0.742281 CATCACGCCCAGAGGTCAAG 60.742 60.000 0.00 0.00 34.57 3.02
1557 1570 1.073897 GCCCAGAGGTCAAGCAGTT 59.926 57.895 0.00 0.00 34.57 3.16
1742 1755 2.807967 TGTTCTCCATTCGAACAGCTTG 59.192 45.455 0.00 0.00 44.03 4.01
1744 1757 2.688507 TCTCCATTCGAACAGCTTGTC 58.311 47.619 0.00 0.00 0.00 3.18
1787 1800 1.806758 GGGCGCATGCAAATGACAC 60.807 57.895 19.57 0.00 45.35 3.67
1791 1804 1.074319 CGCATGCAAATGACACCAGC 61.074 55.000 19.57 0.00 0.00 4.85
1795 1808 0.608856 TGCAAATGACACCAGCCGAT 60.609 50.000 0.00 0.00 0.00 4.18
1805 1818 2.584608 CAGCCGATCGGGAGGTTT 59.415 61.111 33.98 0.00 38.47 3.27
1850 1864 5.945144 AATTATGGAAGCTGCAAATTCCT 57.055 34.783 23.24 14.56 44.46 3.36
1861 1875 4.982295 GCTGCAAATTCCTCGTAAAGTTTT 59.018 37.500 0.00 0.00 0.00 2.43
1873 1887 7.810759 TCCTCGTAAAGTTTTCAATATTTTGCC 59.189 33.333 0.00 0.00 32.61 4.52
1874 1888 7.062956 CCTCGTAAAGTTTTCAATATTTTGCCC 59.937 37.037 0.00 0.00 32.61 5.36
1896 1910 2.669434 GCGTTTACTGCACGGAATTCTA 59.331 45.455 5.23 0.00 38.13 2.10
1960 1974 2.347114 GGTGCCCAATTTGCCACC 59.653 61.111 16.59 16.59 0.00 4.61
2009 2023 8.251026 TCTATTCTTCACGTGTATTCACTCAAT 58.749 33.333 16.51 5.06 41.89 2.57
2112 2126 8.056407 TGGAGTATATCTTGTCTATTGATCGG 57.944 38.462 0.00 0.00 0.00 4.18
2131 2145 1.755380 GGACGCCACTACCTCTAATGT 59.245 52.381 0.00 0.00 0.00 2.71
2154 2168 7.100409 TGTCGACATTGGAGATTAAACATGTA 58.900 34.615 15.76 0.00 0.00 2.29
2175 2189 3.460825 AGTAGTGGTGGGATGTTGGTAT 58.539 45.455 0.00 0.00 0.00 2.73
2219 2233 7.716998 CCTTATAACACATAATGAGAGTTGCCT 59.283 37.037 0.00 0.00 0.00 4.75
2222 2236 3.011818 CACATAATGAGAGTTGCCTGCA 58.988 45.455 0.00 0.00 0.00 4.41
2224 2238 2.408271 TAATGAGAGTTGCCTGCAGG 57.592 50.000 29.34 29.34 38.53 4.85
2282 2298 2.905075 CAACTATCAACGAGCCATGGA 58.095 47.619 18.40 0.00 0.00 3.41
2385 2401 1.604915 GGAGGAAGGAGTTGGAGCC 59.395 63.158 0.00 0.00 0.00 4.70
2453 2469 8.220559 AGCTCAATGTAAGTTTATCCCATATGT 58.779 33.333 1.24 0.00 0.00 2.29
2493 2509 0.763652 AGGCAATGGCGATGAGAGAT 59.236 50.000 0.00 0.00 42.47 2.75
2500 2516 0.599728 GGCGATGAGAGATGGACTGC 60.600 60.000 0.00 0.00 0.00 4.40
2598 2614 0.830444 AGAGTACTTGGTGGGACGCA 60.830 55.000 0.00 0.00 43.02 5.24
2645 2661 4.777366 TGTGGACATCTCTACCTTGATTGA 59.223 41.667 0.00 0.00 0.00 2.57
2676 2692 6.577055 TCAACTTTAAGCATTGTTTTCGATCG 59.423 34.615 9.36 9.36 0.00 3.69
2754 2770 2.636412 TTGGACAGACGAGCCTCCG 61.636 63.158 0.00 0.00 0.00 4.63
2781 2797 1.135915 CTGGTGAGCAAGCTCGTAGAT 59.864 52.381 16.45 0.00 45.48 1.98
2792 2808 5.344665 GCAAGCTCGTAGATGATGTATCTTC 59.655 44.000 0.00 0.81 43.68 2.87
2796 2812 6.208402 AGCTCGTAGATGATGTATCTTCATGT 59.792 38.462 9.54 2.81 43.68 3.21
2797 2813 6.307558 GCTCGTAGATGATGTATCTTCATGTG 59.692 42.308 9.54 0.00 43.68 3.21
2828 2844 2.834638 AGCTAACCATGATGGCCTTT 57.165 45.000 12.25 0.87 42.67 3.11
2889 2905 2.030007 CCGTAGACCACCTAACAACGAA 60.030 50.000 0.00 0.00 0.00 3.85
2896 2912 4.964593 ACCACCTAACAACGAATACAAGT 58.035 39.130 0.00 0.00 0.00 3.16
2964 2981 3.945346 TGGAGCCGAGCAAACTTTATTA 58.055 40.909 0.00 0.00 0.00 0.98
2967 2984 5.526111 TGGAGCCGAGCAAACTTTATTATAC 59.474 40.000 0.00 0.00 0.00 1.47
2984 3001 8.890410 TTATTATACTAGATAGGCGGGAAGTT 57.110 34.615 0.00 0.00 0.00 2.66
2989 3006 0.458669 GATAGGCGGGAAGTTGTCGA 59.541 55.000 0.00 0.00 0.00 4.20
3004 3021 2.953453 TGTCGAGCTAAGGCCCTATAA 58.047 47.619 0.00 0.00 39.73 0.98
3005 3022 3.302161 TGTCGAGCTAAGGCCCTATAAA 58.698 45.455 0.00 0.00 39.73 1.40
3007 3024 4.162698 TGTCGAGCTAAGGCCCTATAAAAA 59.837 41.667 0.00 0.00 39.73 1.94
3008 3025 5.163237 TGTCGAGCTAAGGCCCTATAAAAAT 60.163 40.000 0.00 0.00 39.73 1.82
3051 3068 1.593006 CGCCGATGAAGAAAAGCGTAT 59.407 47.619 0.00 0.00 38.81 3.06
3108 3136 5.114780 CAGACGAATGAAGACAAGATCCAT 58.885 41.667 0.00 0.00 0.00 3.41
3120 3148 1.371467 AGATCCATGTGAACCCACCA 58.629 50.000 0.00 0.00 42.53 4.17
3167 3195 0.179073 AGATCCGCCGGAGACAAATG 60.179 55.000 13.12 0.00 34.05 2.32
3196 3226 2.959707 CCCTCCGACTATGCTAGAAACT 59.040 50.000 0.00 0.00 0.00 2.66
3242 3272 7.288621 GTGGGGAGAATTTTATTCCATCTTCAT 59.711 37.037 0.00 0.00 32.50 2.57
3333 3366 1.078143 AGTTCTCCCATCGGCAAGC 60.078 57.895 0.00 0.00 0.00 4.01
3353 3386 2.677228 CGGGATCCACCTTGCCTT 59.323 61.111 15.23 0.00 38.98 4.35
3375 3408 3.118261 TCATGGCCCTAAGATCACAGAAC 60.118 47.826 0.00 0.00 0.00 3.01
3378 3411 2.237392 GGCCCTAAGATCACAGAACACT 59.763 50.000 0.00 0.00 0.00 3.55
3391 3424 1.005687 AGAACACTAGGTAGACCGGCT 59.994 52.381 0.00 1.78 42.08 5.52
3427 3460 2.354821 AGGCACGAGAAACTGTGAAAAC 59.645 45.455 0.00 0.00 38.36 2.43
3523 3557 9.167239 CACGTTTAATAATTTTCACGGTTAACA 57.833 29.630 8.10 0.00 31.93 2.41
3556 3590 2.977914 CAAGGATTGTCGACATGGAGT 58.022 47.619 20.80 2.27 42.34 3.85
3557 3591 2.932614 CAAGGATTGTCGACATGGAGTC 59.067 50.000 20.80 12.05 42.34 3.36
3574 3611 3.600388 GAGTCGAACCAGGATTGTTCAT 58.400 45.455 0.00 0.00 41.70 2.57
3578 3615 3.756434 TCGAACCAGGATTGTTCATTTCC 59.244 43.478 0.00 0.00 41.70 3.13
3585 3622 2.487762 GGATTGTTCATTTCCGCTGACA 59.512 45.455 0.00 0.00 0.00 3.58
3625 3664 0.388134 GCTCGTGCGTAGAAGTTGGA 60.388 55.000 0.00 0.00 0.00 3.53
3627 3666 0.956633 TCGTGCGTAGAAGTTGGACT 59.043 50.000 0.00 0.00 0.00 3.85
3658 3698 2.272146 CCACCCCGTCCATCCTTG 59.728 66.667 0.00 0.00 0.00 3.61
3740 3780 5.789535 ACTATCACCTGGGAGTAATTACCT 58.210 41.667 12.05 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 0.700564 AGCTGGGATCTGCCTTGAAA 59.299 50.000 0.00 0.00 38.41 2.69
164 166 5.244178 TCTCTGGAGAGTCAACTTTAGGAAC 59.756 44.000 3.61 0.00 42.60 3.62
272 274 9.803315 GGTTGGAGAAATAATATCAGGAAAAAC 57.197 33.333 0.00 0.00 0.00 2.43
275 277 7.647827 TGGGTTGGAGAAATAATATCAGGAAA 58.352 34.615 0.00 0.00 0.00 3.13
541 549 6.525121 TCTCAGTTTCTTGTGAATTGTACG 57.475 37.500 0.00 0.00 31.56 3.67
654 664 4.700213 GCCACCAGCTTCTTTTTCATACTA 59.300 41.667 0.00 0.00 38.99 1.82
663 673 0.036732 TCGATGCCACCAGCTTCTTT 59.963 50.000 0.00 0.00 42.17 2.52
680 690 2.420022 CCTGCACACTTTAATTCCCTCG 59.580 50.000 0.00 0.00 0.00 4.63
770 780 2.086869 TGCTGTAAGGAAGCTGCATTC 58.913 47.619 0.00 2.94 41.42 2.67
871 882 6.444633 CAAACTTCAGATCTTGAAACTGCAT 58.555 36.000 0.00 0.00 44.84 3.96
1001 1012 7.839907 CCATCCTTGGATTCTTTGTTTAATCA 58.160 34.615 0.00 0.00 46.92 2.57
1031 1043 9.626045 CTTTACCTCCAACTGATAATTGTTTTC 57.374 33.333 0.00 0.00 0.00 2.29
1221 1234 3.564225 CACCTTCACTCTTTGGGTAACAC 59.436 47.826 0.00 0.00 39.74 3.32
1294 1307 7.824779 AGGTGAAGTAATAAGTCTCCAACATTC 59.175 37.037 0.00 0.00 0.00 2.67
1422 1435 8.925161 TTTTAAACACTTCAAGACCTTTCATG 57.075 30.769 0.00 0.00 0.00 3.07
1524 1537 2.965147 TCTGGGCGTGATGATCATTCTA 59.035 45.455 10.14 0.00 0.00 2.10
1552 1565 1.337823 ACTCACCACCGATACAACTGC 60.338 52.381 0.00 0.00 0.00 4.40
1557 1570 1.919240 AGTCACTCACCACCGATACA 58.081 50.000 0.00 0.00 0.00 2.29
1742 1755 9.019764 CAAATTTATGTAACCATTGGATTCGAC 57.980 33.333 10.37 0.48 32.29 4.20
1744 1757 7.437862 CCCAAATTTATGTAACCATTGGATTCG 59.562 37.037 10.37 0.00 29.11 3.34
1787 1800 2.536997 AAAACCTCCCGATCGGCTGG 62.537 60.000 29.86 29.86 34.09 4.85
1791 1804 0.177141 TAGCAAAACCTCCCGATCGG 59.823 55.000 27.65 27.65 0.00 4.18
1795 1808 0.611714 GGAGTAGCAAAACCTCCCGA 59.388 55.000 0.00 0.00 39.10 5.14
1850 1864 6.583050 CGGGCAAAATATTGAAAACTTTACGA 59.417 34.615 0.00 0.00 38.94 3.43
1861 1875 3.440872 AGTAAACGCGGGCAAAATATTGA 59.559 39.130 12.47 0.00 38.94 2.57
1874 1888 0.165079 AATTCCGTGCAGTAAACGCG 59.835 50.000 3.53 3.53 39.69 6.01
1896 1910 3.650948 AGCGAGTATACCTTTTAGGGGT 58.349 45.455 0.00 0.00 40.58 4.95
1960 1974 3.243670 TGGCGAATATCTTCAGAGCTCTG 60.244 47.826 33.73 33.73 45.08 3.35
2009 2023 1.754803 CAAGTCGGCTCCACATACCTA 59.245 52.381 0.00 0.00 0.00 3.08
2111 2125 1.755380 ACATTAGAGGTAGTGGCGTCC 59.245 52.381 0.00 0.00 0.00 4.79
2112 2126 2.541178 CGACATTAGAGGTAGTGGCGTC 60.541 54.545 0.00 0.00 41.33 5.19
2131 2145 7.327975 ACTACATGTTTAATCTCCAATGTCGA 58.672 34.615 2.30 0.00 0.00 4.20
2154 2168 1.742308 ACCAACATCCCACCACTACT 58.258 50.000 0.00 0.00 0.00 2.57
2175 2189 3.680786 CGGCGTGTCCACCAGAGA 61.681 66.667 0.00 0.00 34.01 3.10
2219 2233 1.207488 AGGCCATCTTACCACCTGCA 61.207 55.000 5.01 0.00 0.00 4.41
2222 2236 1.710809 ACAAAGGCCATCTTACCACCT 59.289 47.619 5.01 0.00 34.78 4.00
2224 2238 1.737793 CGACAAAGGCCATCTTACCAC 59.262 52.381 5.01 0.00 34.78 4.16
2282 2298 6.013379 TCCTCTTCTGTCACAACTATCTTCT 58.987 40.000 0.00 0.00 0.00 2.85
2371 2387 1.376037 CCGTGGCTCCAACTCCTTC 60.376 63.158 0.00 0.00 0.00 3.46
2385 2401 4.751600 TCATCTCTAATAATTGCTGCCGTG 59.248 41.667 0.00 0.00 0.00 4.94
2453 2469 2.495669 TCTGATGTCATTGTGTCCGCTA 59.504 45.455 0.00 0.00 0.00 4.26
2598 2614 1.951130 CGTGAATATCGCTGCCGCT 60.951 57.895 0.00 0.00 0.00 5.52
2645 2661 6.715347 AACAATGCTTAAAGTTGACCTTCT 57.285 33.333 0.00 0.00 31.27 2.85
2676 2692 3.704908 ATGCGCCGCTTGATTTGCC 62.705 57.895 11.67 0.00 0.00 4.52
2754 2770 0.807496 GCTTGCTCACCAGACAATCC 59.193 55.000 0.00 0.00 0.00 3.01
2797 2813 9.683069 CCATCATGGTTAGCTTTATTGATTAAC 57.317 33.333 0.00 0.00 31.35 2.01
2814 2830 3.756082 TTTAGGAAAGGCCATCATGGT 57.244 42.857 5.01 0.00 40.46 3.55
2847 2863 6.238648 ACGGATCTATCTTTCTGGTGTTTTT 58.761 36.000 0.00 0.00 0.00 1.94
2848 2864 5.805728 ACGGATCTATCTTTCTGGTGTTTT 58.194 37.500 0.00 0.00 0.00 2.43
2849 2865 5.422214 ACGGATCTATCTTTCTGGTGTTT 57.578 39.130 0.00 0.00 0.00 2.83
2850 2866 5.892119 TCTACGGATCTATCTTTCTGGTGTT 59.108 40.000 0.00 0.00 0.00 3.32
2851 2867 5.299782 GTCTACGGATCTATCTTTCTGGTGT 59.700 44.000 0.00 0.00 0.00 4.16
2852 2868 5.278561 GGTCTACGGATCTATCTTTCTGGTG 60.279 48.000 0.00 0.00 0.00 4.17
2853 2869 4.828387 GGTCTACGGATCTATCTTTCTGGT 59.172 45.833 0.00 0.00 0.00 4.00
2854 2870 4.827835 TGGTCTACGGATCTATCTTTCTGG 59.172 45.833 0.00 0.00 0.00 3.86
2855 2871 5.278561 GGTGGTCTACGGATCTATCTTTCTG 60.279 48.000 0.00 0.00 0.00 3.02
2856 2872 4.828387 GGTGGTCTACGGATCTATCTTTCT 59.172 45.833 0.00 0.00 0.00 2.52
2857 2873 4.828387 AGGTGGTCTACGGATCTATCTTTC 59.172 45.833 0.00 0.00 0.00 2.62
2858 2874 4.805744 AGGTGGTCTACGGATCTATCTTT 58.194 43.478 0.00 0.00 0.00 2.52
2859 2875 4.456662 AGGTGGTCTACGGATCTATCTT 57.543 45.455 0.00 0.00 0.00 2.40
2889 2905 1.409427 GGCTCGCTCCAGTACTTGTAT 59.591 52.381 0.00 0.00 0.00 2.29
2896 2912 2.415608 CCTTCGGCTCGCTCCAGTA 61.416 63.158 0.00 0.00 0.00 2.74
2964 2981 4.481072 ACAACTTCCCGCCTATCTAGTAT 58.519 43.478 0.00 0.00 0.00 2.12
2967 2984 2.287668 CGACAACTTCCCGCCTATCTAG 60.288 54.545 0.00 0.00 0.00 2.43
2975 2992 0.389426 TTAGCTCGACAACTTCCCGC 60.389 55.000 0.00 0.00 0.00 6.13
2989 3006 6.004574 GTGCTATTTTTATAGGGCCTTAGCT 58.995 40.000 24.15 7.53 39.73 3.32
3004 3021 5.348164 GTTGTTGTTCTGGTGTGCTATTTT 58.652 37.500 0.00 0.00 0.00 1.82
3005 3022 4.202111 GGTTGTTGTTCTGGTGTGCTATTT 60.202 41.667 0.00 0.00 0.00 1.40
3007 3024 2.884639 GGTTGTTGTTCTGGTGTGCTAT 59.115 45.455 0.00 0.00 0.00 2.97
3008 3025 2.294074 GGTTGTTGTTCTGGTGTGCTA 58.706 47.619 0.00 0.00 0.00 3.49
3051 3068 6.787458 TGTCTATAGGCTGGATCCTTTTGATA 59.213 38.462 14.23 4.90 37.66 2.15
3108 3136 2.494073 GTTTGTCTTTGGTGGGTTCACA 59.506 45.455 0.00 0.00 45.32 3.58
3120 3148 0.810823 TTCGGTCGGCGTTTGTCTTT 60.811 50.000 6.85 0.00 0.00 2.52
3167 3195 1.043673 ATAGTCGGAGGGCTGTGGAC 61.044 60.000 0.00 0.00 0.00 4.02
3196 3226 2.547640 CTAGTCCTCGTCCCGGTGGA 62.548 65.000 0.00 0.00 38.75 4.02
3208 3238 2.972153 AATTCTCCCCACCTAGTCCT 57.028 50.000 0.00 0.00 0.00 3.85
3242 3272 2.679837 AGGCGAAACGATAACGACTCTA 59.320 45.455 0.00 0.00 41.74 2.43
3333 3366 2.438434 GCAAGGTGGATCCCGGTG 60.438 66.667 9.90 3.39 36.75 4.94
3353 3386 2.763039 TCTGTGATCTTAGGGCCATGA 58.237 47.619 6.18 0.17 0.00 3.07
3375 3408 1.437986 GCAGCCGGTCTACCTAGTG 59.562 63.158 1.90 0.00 0.00 2.74
3400 3433 0.036010 AGTTTCTCGTGCCTCCCATG 60.036 55.000 0.00 0.00 0.00 3.66
3401 3434 0.036010 CAGTTTCTCGTGCCTCCCAT 60.036 55.000 0.00 0.00 0.00 4.00
3402 3435 1.371183 CAGTTTCTCGTGCCTCCCA 59.629 57.895 0.00 0.00 0.00 4.37
3523 3557 6.435904 TCGACAATCCTTGTTTGGGAAAATAT 59.564 34.615 0.00 0.00 45.52 1.28
3554 3588 3.703001 ATGAACAATCCTGGTTCGACT 57.297 42.857 0.00 0.00 45.86 4.18
3555 3589 4.379499 GGAAATGAACAATCCTGGTTCGAC 60.379 45.833 0.00 0.00 45.86 4.20
3556 3590 3.756434 GGAAATGAACAATCCTGGTTCGA 59.244 43.478 0.00 0.00 45.86 3.71
3557 3591 3.426159 CGGAAATGAACAATCCTGGTTCG 60.426 47.826 0.00 0.00 45.86 3.95
3558 3592 3.673323 GCGGAAATGAACAATCCTGGTTC 60.673 47.826 0.00 0.00 43.78 3.62
3559 3593 2.231235 GCGGAAATGAACAATCCTGGTT 59.769 45.455 0.00 0.00 0.00 3.67
3560 3594 1.818674 GCGGAAATGAACAATCCTGGT 59.181 47.619 0.00 0.00 0.00 4.00
3578 3615 2.753966 CCGGCCATTTCTGTCAGCG 61.754 63.158 2.24 0.00 0.00 5.18
3714 3754 8.685311 AGGTAATTACTCCCAGGTGATAGTATA 58.315 37.037 15.05 0.00 0.00 1.47
3717 3757 5.789535 AGGTAATTACTCCCAGGTGATAGT 58.210 41.667 15.05 0.00 0.00 2.12
3740 3780 3.686227 ATAAAGGACATGGGGCATGAA 57.314 42.857 0.00 0.00 43.81 2.57


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

AutoCloner maintained by Alex Coulton.