Multiple sequence alignment - TraesCS1D01G293900

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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 TraesCS1D01G293900 chr1D 100.000 3272 0 0 1 3272 392946142 392942871 0.000000e+00 6043
1 TraesCS1D01G293900 chr1B 91.791 2083 76 29 605 2634 529707999 529710039 0.000000e+00 2811
2 TraesCS1D01G293900 chr1B 88.684 433 27 8 1 430 529707403 529707816 2.910000e-140 508
3 TraesCS1D01G293900 chr1B 91.176 136 4 3 481 608 529707820 529707955 9.330000e-41 178
4 TraesCS1D01G293900 chr1A 92.478 1356 49 23 1010 2334 492275302 492276635 0.000000e+00 1890
5 TraesCS1D01G293900 chr1A 88.396 767 63 18 2508 3268 492276744 492277490 0.000000e+00 900
6 TraesCS1D01G293900 chr1A 89.538 325 27 5 1 318 492274462 492274786 3.930000e-109 405
7 TraesCS1D01G293900 chr1A 85.714 224 19 7 454 675 492274924 492275136 1.180000e-54 224
8 TraesCS1D01G293900 chr1A 80.083 241 19 7 456 696 492275051 492275262 5.650000e-33 152
9 TraesCS1D01G293900 chr2D 82.022 178 18 12 2930 3098 183618226 183618398 4.400000e-29 139
10 TraesCS1D01G293900 chr3D 77.419 217 34 12 2797 3007 355626607 355626400 7.420000e-22 115
11 TraesCS1D01G293900 chr2B 77.901 181 25 12 2921 3090 239464780 239464956 7.470000e-17 99


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 TraesCS1D01G293900 chr1D 392942871 392946142 3271 True 6043.000000 6043 100.000000 1 3272 1 chr1D.!!$R1 3271
1 TraesCS1D01G293900 chr1B 529707403 529710039 2636 False 1165.666667 2811 90.550333 1 2634 3 chr1B.!!$F1 2633
2 TraesCS1D01G293900 chr1A 492274462 492277490 3028 False 714.200000 1890 87.241800 1 3268 5 chr1A.!!$F1 3267

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
466 474 0.031314 AGAGTGTGTGTGAGCTGTCG 59.969 55.0 0.0 0.0 0.0 4.35 F
1601 1804 0.532573 TCTCAGGTCAGCACGATTCC 59.467 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2117 0.933097 CATTTCGGTCTCAGCGGATG 59.067 55.000 0.00 0.00 39.89 3.51 R
2458 2693 1.830338 CAAAGCAACAACGAACGCG 59.170 52.632 3.53 3.53 44.79 6.01 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
137 143 1.212688 TGATGTCATCGGCCCTTCATT 59.787 47.619 8.29 0.00 0.00 2.57
166 172 1.150827 GTTACTGAAAACGTCGGGGG 58.849 55.000 0.00 0.00 36.88 5.40
343 351 6.044512 AGCTTAGCCGTTTAATTAATCACG 57.955 37.500 13.18 13.18 0.00 4.35
344 352 4.669283 GCTTAGCCGTTTAATTAATCACGC 59.331 41.667 14.26 10.44 0.00 5.34
346 354 4.531659 AGCCGTTTAATTAATCACGCTC 57.468 40.909 14.26 9.47 0.00 5.03
347 355 3.936453 AGCCGTTTAATTAATCACGCTCA 59.064 39.130 14.26 0.00 0.00 4.26
348 356 4.034048 AGCCGTTTAATTAATCACGCTCAG 59.966 41.667 14.26 5.09 0.00 3.35
349 357 4.785341 GCCGTTTAATTAATCACGCTCAGG 60.785 45.833 14.26 4.81 0.00 3.86
351 359 4.598062 GTTTAATTAATCACGCTCAGGCC 58.402 43.478 0.00 0.00 34.44 5.19
430 438 6.332735 CAGATTACTGTCCTCCGATTATCA 57.667 41.667 0.00 0.00 39.11 2.15
433 441 8.690884 CAGATTACTGTCCTCCGATTATCATAT 58.309 37.037 0.00 0.00 39.11 1.78
434 442 9.922477 AGATTACTGTCCTCCGATTATCATATA 57.078 33.333 0.00 0.00 0.00 0.86
435 443 9.953697 GATTACTGTCCTCCGATTATCATATAC 57.046 37.037 0.00 0.00 0.00 1.47
436 444 6.777213 ACTGTCCTCCGATTATCATATACC 57.223 41.667 0.00 0.00 0.00 2.73
439 447 4.643784 GTCCTCCGATTATCATATACCGGT 59.356 45.833 13.98 13.98 38.25 5.28
440 448 5.126707 GTCCTCCGATTATCATATACCGGTT 59.873 44.000 15.04 3.05 38.25 4.44
441 449 5.126545 TCCTCCGATTATCATATACCGGTTG 59.873 44.000 15.04 5.13 38.25 3.77
442 450 5.333299 TCCGATTATCATATACCGGTTGG 57.667 43.478 15.04 0.00 42.84 3.77
452 460 2.347490 CCGGTTGGTCCCAGAGTG 59.653 66.667 0.00 0.00 0.00 3.51
454 462 1.301716 CGGTTGGTCCCAGAGTGTG 60.302 63.158 0.00 0.00 0.00 3.82
459 467 0.689412 TGGTCCCAGAGTGTGTGTGA 60.689 55.000 0.00 0.00 0.00 3.58
461 469 0.601311 GTCCCAGAGTGTGTGTGAGC 60.601 60.000 0.00 0.00 0.00 4.26
463 471 0.602106 CCCAGAGTGTGTGTGAGCTG 60.602 60.000 0.00 0.00 0.00 4.24
464 472 0.105593 CCAGAGTGTGTGTGAGCTGT 59.894 55.000 0.00 0.00 0.00 4.40
465 473 1.495878 CAGAGTGTGTGTGAGCTGTC 58.504 55.000 0.00 0.00 0.00 3.51
466 474 0.031314 AGAGTGTGTGTGAGCTGTCG 59.969 55.000 0.00 0.00 0.00 4.35
467 475 0.941463 GAGTGTGTGTGAGCTGTCGG 60.941 60.000 0.00 0.00 0.00 4.79
475 485 2.924290 GTGTGAGCTGTCGGATTAACTC 59.076 50.000 0.00 0.00 0.00 3.01
490 500 7.039923 TCGGATTAACTCTAGATGGTTATGGTC 60.040 40.741 5.65 5.32 0.00 4.02
547 560 9.050601 AGATGCTCATAAGTAGCTGTAAATTTC 57.949 33.333 0.00 0.00 40.73 2.17
662 824 7.464358 ACAACACGCATAAAGAAGATCATAAC 58.536 34.615 0.00 0.00 0.00 1.89
709 872 9.931210 AGTAAAGCATTAGAAACGCATTATTAC 57.069 29.630 0.00 0.00 0.00 1.89
710 873 9.931210 GTAAAGCATTAGAAACGCATTATTACT 57.069 29.630 0.00 0.00 0.00 2.24
711 874 8.841444 AAAGCATTAGAAACGCATTATTACTG 57.159 30.769 0.00 0.00 0.00 2.74
712 875 6.959361 AGCATTAGAAACGCATTATTACTGG 58.041 36.000 0.00 0.00 0.00 4.00
713 876 6.542370 AGCATTAGAAACGCATTATTACTGGT 59.458 34.615 0.00 0.00 0.00 4.00
714 877 6.632834 GCATTAGAAACGCATTATTACTGGTG 59.367 38.462 0.00 0.00 0.00 4.17
715 878 7.678690 GCATTAGAAACGCATTATTACTGGTGT 60.679 37.037 0.00 0.00 0.00 4.16
716 879 8.822855 CATTAGAAACGCATTATTACTGGTGTA 58.177 33.333 0.00 0.00 0.00 2.90
717 880 6.903883 AGAAACGCATTATTACTGGTGTAG 57.096 37.500 0.00 0.00 0.00 2.74
718 881 6.403878 AGAAACGCATTATTACTGGTGTAGT 58.596 36.000 0.00 0.00 43.56 2.73
719 882 7.549839 AGAAACGCATTATTACTGGTGTAGTA 58.450 34.615 0.00 0.00 40.89 1.82
720 883 7.705325 AGAAACGCATTATTACTGGTGTAGTAG 59.295 37.037 0.00 0.00 42.57 2.57
721 884 5.287226 ACGCATTATTACTGGTGTAGTAGC 58.713 41.667 0.00 0.00 42.57 3.58
722 885 5.068723 ACGCATTATTACTGGTGTAGTAGCT 59.931 40.000 0.00 0.00 42.57 3.32
884 1056 3.142838 CCCAGGCTCAAATGGCGG 61.143 66.667 0.00 0.00 35.10 6.13
886 1058 3.830192 CAGGCTCAAATGGCGGCC 61.830 66.667 13.32 13.32 44.38 6.13
894 1066 2.305607 AAATGGCGGCCCTCCTACA 61.306 57.895 17.97 0.00 0.00 2.74
907 1079 2.500504 CCTCCTACACCTACAAGAACCC 59.499 54.545 0.00 0.00 0.00 4.11
913 1085 1.279271 CACCTACAAGAACCCTCCCAG 59.721 57.143 0.00 0.00 0.00 4.45
919 1091 2.038659 CAAGAACCCTCCCAGCAAAAA 58.961 47.619 0.00 0.00 0.00 1.94
944 1117 4.711949 CGCCAGCCAACCTCTGCT 62.712 66.667 0.00 0.00 38.67 4.24
955 1128 2.356673 CTCTGCTGCACTCGCACA 60.357 61.111 0.00 0.00 45.36 4.57
970 1149 3.542676 ACACCACCGCCGAGTGAA 61.543 61.111 8.51 0.00 40.34 3.18
976 1155 0.878523 CACCGCCGAGTGAACTTTGA 60.879 55.000 0.20 0.00 40.34 2.69
987 1166 6.036517 CCGAGTGAACTTTGATCTTTCATAGG 59.963 42.308 0.00 0.72 35.82 2.57
1597 1800 0.813821 CATCTCTCAGGTCAGCACGA 59.186 55.000 0.00 0.00 0.00 4.35
1598 1801 1.408340 CATCTCTCAGGTCAGCACGAT 59.592 52.381 0.00 0.00 0.00 3.73
1599 1802 1.550327 TCTCTCAGGTCAGCACGATT 58.450 50.000 0.00 0.00 0.00 3.34
1600 1803 1.474478 TCTCTCAGGTCAGCACGATTC 59.526 52.381 0.00 0.00 0.00 2.52
1601 1804 0.532573 TCTCAGGTCAGCACGATTCC 59.467 55.000 0.00 0.00 0.00 3.01
1619 1822 6.094603 ACGATTCCTTCCTTCAATCATCAAAG 59.905 38.462 0.00 0.00 0.00 2.77
1683 1886 2.472861 GGTGTCGCATCGTATCTGATTG 59.527 50.000 0.00 0.00 0.00 2.67
1684 1887 3.116300 GTGTCGCATCGTATCTGATTGT 58.884 45.455 0.00 0.00 0.00 2.71
1698 1906 1.003355 ATTGTCTGCTGGTGGTCCG 60.003 57.895 0.00 0.00 36.30 4.79
1700 1908 2.357517 GTCTGCTGGTGGTCCGTG 60.358 66.667 0.00 0.00 36.30 4.94
1763 1977 2.764128 ATCGGGATGTCGCTGGGT 60.764 61.111 0.00 0.00 0.00 4.51
1898 2117 2.835027 AGTTTCTTTCTCCACGTGTCC 58.165 47.619 15.65 0.00 0.00 4.02
1902 2121 1.275291 TCTTTCTCCACGTGTCCATCC 59.725 52.381 15.65 0.00 0.00 3.51
2022 2244 1.515304 GCTCTTCTCGCTGACGACC 60.515 63.158 0.00 0.00 45.12 4.79
2345 2575 0.394565 AGGCAATCGATCAGTAGCCC 59.605 55.000 16.91 4.10 42.97 5.19
2350 2580 3.242870 GCAATCGATCAGTAGCCCTTTTG 60.243 47.826 0.00 0.00 0.00 2.44
2382 2612 3.142174 AGCTCAAAGTTTGGAGTACAGC 58.858 45.455 15.47 14.58 33.66 4.40
2432 2662 3.529533 GCTAGCACACACTGATTCAGAT 58.470 45.455 20.33 5.13 35.18 2.90
2458 2693 0.667993 CAGAGGAGCGGAGTCTCATC 59.332 60.000 1.47 0.00 40.03 2.92
2475 2710 0.306533 ATCGCGTTCGTTGTTGCTTT 59.693 45.000 5.77 0.00 36.96 3.51
2478 2713 1.830338 CGTTCGTTGTTGCTTTGCG 59.170 52.632 0.00 0.00 0.00 4.85
2586 2832 7.658261 TCGAATATAATCCAGTTGTCTGTAGG 58.342 38.462 0.00 0.00 39.82 3.18
2591 2837 2.047061 TCCAGTTGTCTGTAGGTGCTT 58.953 47.619 0.00 0.00 39.82 3.91
2614 2862 3.388024 TCAGCATAGGTGGAATGGAGTAC 59.612 47.826 0.00 0.00 0.00 2.73
2615 2863 2.365617 AGCATAGGTGGAATGGAGTACG 59.634 50.000 0.00 0.00 0.00 3.67
2616 2864 2.102588 GCATAGGTGGAATGGAGTACGT 59.897 50.000 0.00 0.00 0.00 3.57
2617 2865 3.717707 CATAGGTGGAATGGAGTACGTG 58.282 50.000 0.00 0.00 0.00 4.49
2792 3042 8.151596 TGTGTATGAGAAATGTTAACCTGTGTA 58.848 33.333 2.48 0.00 0.00 2.90
2859 3110 7.470289 AAAACATGTACGCAGCATTTAAAAA 57.530 28.000 0.00 0.00 0.00 1.94
2962 3213 8.217778 TGAAAAATGTTCACGAGTTTCAAAAAC 58.782 29.630 0.00 0.00 33.37 2.43
2970 3221 4.791163 CACGAGTTTCAAAAACGTGTTCAT 59.209 37.500 16.99 0.00 41.42 2.57
2978 3229 7.588143 TTCAAAAACGTGTTCATGACATTTT 57.412 28.000 0.00 0.20 41.10 1.82
2981 3232 9.140286 TCAAAAACGTGTTCATGACATTTTAAA 57.860 25.926 0.00 0.00 41.10 1.52
3066 3318 2.742053 GCTCCAGCGTGTATCTGAAAAA 59.258 45.455 0.00 0.00 33.54 1.94
3077 3329 7.377397 GCGTGTATCTGAAAAATGTTTAACACA 59.623 33.333 0.00 0.00 40.71 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 51 6.742264 TCATTTTCATTTGTCGATTCGTGATG 59.258 34.615 5.89 6.66 0.00 3.07
47 52 6.841119 TCATTTTCATTTGTCGATTCGTGAT 58.159 32.000 5.89 0.00 0.00 3.06
137 143 3.245754 CGTTTTCAGTAACGTGTAGCCAA 59.754 43.478 0.00 0.00 44.28 4.52
166 172 2.665603 GGAGTGAGGACACCCTGC 59.334 66.667 0.00 0.00 46.99 4.85
343 351 2.595463 TGCACACAAGGCCTGAGC 60.595 61.111 5.69 5.91 38.76 4.26
344 352 0.035317 TAGTGCACACAAGGCCTGAG 59.965 55.000 21.04 4.64 0.00 3.35
346 354 2.009774 GTATAGTGCACACAAGGCCTG 58.990 52.381 21.04 2.82 0.00 4.85
347 355 1.628340 TGTATAGTGCACACAAGGCCT 59.372 47.619 21.04 0.00 0.00 5.19
348 356 2.107950 TGTATAGTGCACACAAGGCC 57.892 50.000 21.04 0.00 0.00 5.19
349 357 2.159517 GCTTGTATAGTGCACACAAGGC 60.160 50.000 32.64 25.12 45.92 4.35
385 393 0.100325 TCACAAACAAAGTGCGCCAG 59.900 50.000 4.18 0.00 36.93 4.85
435 443 2.347490 CACTCTGGGACCAACCGG 59.653 66.667 0.00 0.00 40.11 5.28
436 444 1.301716 CACACTCTGGGACCAACCG 60.302 63.158 0.00 0.00 40.11 4.44
439 447 0.180171 CACACACACTCTGGGACCAA 59.820 55.000 0.00 0.00 0.00 3.67
440 448 0.689412 TCACACACACTCTGGGACCA 60.689 55.000 0.00 0.00 0.00 4.02
441 449 0.034059 CTCACACACACTCTGGGACC 59.966 60.000 0.00 0.00 0.00 4.46
442 450 0.601311 GCTCACACACACTCTGGGAC 60.601 60.000 0.00 0.00 0.00 4.46
443 451 0.760567 AGCTCACACACACTCTGGGA 60.761 55.000 0.00 0.00 0.00 4.37
444 452 0.602106 CAGCTCACACACACTCTGGG 60.602 60.000 0.00 0.00 0.00 4.45
445 453 0.105593 ACAGCTCACACACACTCTGG 59.894 55.000 0.00 0.00 0.00 3.86
446 454 1.495878 GACAGCTCACACACACTCTG 58.504 55.000 0.00 0.00 0.00 3.35
447 455 0.031314 CGACAGCTCACACACACTCT 59.969 55.000 0.00 0.00 0.00 3.24
448 456 0.941463 CCGACAGCTCACACACACTC 60.941 60.000 0.00 0.00 0.00 3.51
449 457 1.068083 CCGACAGCTCACACACACT 59.932 57.895 0.00 0.00 0.00 3.55
450 458 0.319900 ATCCGACAGCTCACACACAC 60.320 55.000 0.00 0.00 0.00 3.82
452 460 2.363788 TAATCCGACAGCTCACACAC 57.636 50.000 0.00 0.00 0.00 3.82
454 462 2.924290 GAGTTAATCCGACAGCTCACAC 59.076 50.000 0.00 0.00 0.00 3.82
459 467 4.279671 CCATCTAGAGTTAATCCGACAGCT 59.720 45.833 0.00 0.00 0.00 4.24
461 469 5.776173 ACCATCTAGAGTTAATCCGACAG 57.224 43.478 0.00 0.00 0.00 3.51
463 471 7.091443 CCATAACCATCTAGAGTTAATCCGAC 58.909 42.308 8.24 0.00 32.52 4.79
464 472 6.781014 ACCATAACCATCTAGAGTTAATCCGA 59.219 38.462 8.24 0.00 32.52 4.55
465 473 6.994221 ACCATAACCATCTAGAGTTAATCCG 58.006 40.000 8.24 1.38 32.52 4.18
466 474 7.963532 TGACCATAACCATCTAGAGTTAATCC 58.036 38.462 8.24 1.68 32.52 3.01
467 475 8.643324 ACTGACCATAACCATCTAGAGTTAATC 58.357 37.037 8.24 7.49 32.52 1.75
475 485 5.065218 GCAACAACTGACCATAACCATCTAG 59.935 44.000 0.00 0.00 0.00 2.43
490 500 0.457851 TTTTGACGGGGCAACAACTG 59.542 50.000 0.00 0.00 39.74 3.16
557 570 6.920758 CACATGCTCTAGGTTCATCTTACTAC 59.079 42.308 0.00 0.00 0.00 2.73
558 571 6.833933 TCACATGCTCTAGGTTCATCTTACTA 59.166 38.462 0.00 0.00 0.00 1.82
679 841 6.788684 TGCGTTTCTAATGCTTTACTTACA 57.211 33.333 5.35 0.00 43.78 2.41
680 842 9.931210 ATAATGCGTTTCTAATGCTTTACTTAC 57.069 29.630 11.67 0.00 42.26 2.34
684 847 9.931210 AGTAATAATGCGTTTCTAATGCTTTAC 57.069 29.630 11.67 10.20 42.26 2.01
698 861 5.068723 AGCTACTACACCAGTAATAATGCGT 59.931 40.000 0.00 0.00 39.28 5.24
708 871 8.763984 AATATAACTACAGCTACTACACCAGT 57.236 34.615 0.00 0.00 41.62 4.00
709 872 8.016229 CGAATATAACTACAGCTACTACACCAG 58.984 40.741 0.00 0.00 0.00 4.00
710 873 7.040892 CCGAATATAACTACAGCTACTACACCA 60.041 40.741 0.00 0.00 0.00 4.17
711 874 7.303998 CCGAATATAACTACAGCTACTACACC 58.696 42.308 0.00 0.00 0.00 4.16
712 875 6.800892 GCCGAATATAACTACAGCTACTACAC 59.199 42.308 0.00 0.00 0.00 2.90
713 876 6.072286 GGCCGAATATAACTACAGCTACTACA 60.072 42.308 0.00 0.00 0.00 2.74
714 877 6.072286 TGGCCGAATATAACTACAGCTACTAC 60.072 42.308 0.00 0.00 0.00 2.73
715 878 6.005823 TGGCCGAATATAACTACAGCTACTA 58.994 40.000 0.00 0.00 0.00 1.82
716 879 4.831155 TGGCCGAATATAACTACAGCTACT 59.169 41.667 0.00 0.00 0.00 2.57
717 880 5.130292 TGGCCGAATATAACTACAGCTAC 57.870 43.478 0.00 0.00 0.00 3.58
718 881 5.794726 TTGGCCGAATATAACTACAGCTA 57.205 39.130 0.00 0.00 0.00 3.32
719 882 4.682778 TTGGCCGAATATAACTACAGCT 57.317 40.909 0.00 0.00 0.00 4.24
720 883 5.334879 CCATTTGGCCGAATATAACTACAGC 60.335 44.000 18.23 0.00 0.00 4.40
721 884 5.995282 TCCATTTGGCCGAATATAACTACAG 59.005 40.000 18.23 2.64 34.44 2.74
722 885 5.931294 TCCATTTGGCCGAATATAACTACA 58.069 37.500 18.23 0.00 34.44 2.74
771 934 1.219646 TCGGTTTGGACGTTTGCTAC 58.780 50.000 0.00 0.00 0.00 3.58
827 990 1.140452 CCCAGATGTGCTCACTATGCT 59.860 52.381 1.47 0.00 0.00 3.79
865 1037 2.703798 CGCCATTTGAGCCTGGGTG 61.704 63.158 1.59 0.00 32.90 4.61
866 1038 2.361610 CGCCATTTGAGCCTGGGT 60.362 61.111 0.00 0.00 32.90 4.51
884 1056 1.861982 TCTTGTAGGTGTAGGAGGGC 58.138 55.000 0.00 0.00 0.00 5.19
886 1058 2.500504 GGGTTCTTGTAGGTGTAGGAGG 59.499 54.545 0.00 0.00 0.00 4.30
894 1066 1.657804 CTGGGAGGGTTCTTGTAGGT 58.342 55.000 0.00 0.00 0.00 3.08
933 1106 2.031516 CGAGTGCAGCAGAGGTTGG 61.032 63.158 0.00 0.00 0.00 3.77
955 1128 2.319890 AAAGTTCACTCGGCGGTGGT 62.320 55.000 22.21 10.87 37.75 4.16
967 1146 5.874810 CGGACCTATGAAAGATCAAAGTTCA 59.125 40.000 0.00 0.00 39.49 3.18
968 1147 5.220681 GCGGACCTATGAAAGATCAAAGTTC 60.221 44.000 0.00 0.00 39.49 3.01
970 1149 4.192317 GCGGACCTATGAAAGATCAAAGT 58.808 43.478 0.00 0.00 39.49 2.66
976 1155 2.288273 GCTACGCGGACCTATGAAAGAT 60.288 50.000 12.47 0.00 0.00 2.40
987 1166 4.944372 CCCATCGGCTACGCGGAC 62.944 72.222 12.47 0.00 40.43 4.79
1597 1800 7.837689 TGATCTTTGATGATTGAAGGAAGGAAT 59.162 33.333 0.00 0.00 0.00 3.01
1598 1801 7.177184 TGATCTTTGATGATTGAAGGAAGGAA 58.823 34.615 0.00 0.00 0.00 3.36
1599 1802 6.724351 TGATCTTTGATGATTGAAGGAAGGA 58.276 36.000 0.00 0.00 0.00 3.36
1600 1803 7.400599 TTGATCTTTGATGATTGAAGGAAGG 57.599 36.000 0.00 0.00 0.00 3.46
1601 1804 8.301720 TGTTTGATCTTTGATGATTGAAGGAAG 58.698 33.333 0.00 0.00 0.00 3.46
1619 1822 9.604626 CTCTGTTTTGTTTCTATCTGTTTGATC 57.395 33.333 0.00 0.00 36.65 2.92
1683 1886 2.357517 CACGGACCACCAGCAGAC 60.358 66.667 0.00 0.00 35.59 3.51
1684 1887 3.625897 CCACGGACCACCAGCAGA 61.626 66.667 0.00 0.00 35.59 4.26
1698 1906 3.730761 CAGCACCTTCGCAGCCAC 61.731 66.667 0.00 0.00 0.00 5.01
1700 1908 4.704833 TCCAGCACCTTCGCAGCC 62.705 66.667 0.00 0.00 0.00 4.85
1702 1910 3.123620 GCTCCAGCACCTTCGCAG 61.124 66.667 0.00 0.00 41.59 5.18
1763 1977 3.068691 CTCGGGAAGTCGGAGGCA 61.069 66.667 0.00 0.00 38.64 4.75
1863 2082 0.944311 AAACTACGGTGTGCTCTGCG 60.944 55.000 0.00 0.00 0.00 5.18
1898 2117 0.933097 CATTTCGGTCTCAGCGGATG 59.067 55.000 0.00 0.00 39.89 3.51
1902 2121 1.448540 AGGCATTTCGGTCTCAGCG 60.449 57.895 0.00 0.00 40.97 5.18
2001 2223 0.955919 TCGTCAGCGAGAAGAGCAGA 60.956 55.000 0.00 0.00 42.81 4.26
2278 2500 2.569404 AGTTCAGAAGGTGATCTCCCAC 59.431 50.000 10.22 5.16 34.17 4.61
2345 2575 2.087646 GAGCTCCAGCCTAACCAAAAG 58.912 52.381 0.87 0.00 43.38 2.27
2350 2580 1.003696 ACTTTGAGCTCCAGCCTAACC 59.996 52.381 12.15 0.00 43.38 2.85
2382 2612 3.290710 CCTTGTATTCCATGGTCCCTTG 58.709 50.000 12.58 0.00 34.43 3.61
2432 2662 1.881903 CTCCGCTCCTCTGTTCAGCA 61.882 60.000 0.00 0.00 32.27 4.41
2458 2693 1.830338 CAAAGCAACAACGAACGCG 59.170 52.632 3.53 3.53 44.79 6.01
2475 2710 2.607668 CTAACGACCGCTCATCCGCA 62.608 60.000 0.00 0.00 0.00 5.69
2478 2713 1.944676 CGCTAACGACCGCTCATCC 60.945 63.158 0.00 0.00 43.93 3.51
2591 2837 2.846206 ACTCCATTCCACCTATGCTGAA 59.154 45.455 0.00 0.00 0.00 3.02
2881 3132 9.113876 CGAAACTTTTTCTAATTACATGGACAC 57.886 33.333 0.00 0.00 0.00 3.67
2925 3176 8.018520 TCGTGAACATTTTTCAAAATATAGCGT 58.981 29.630 0.00 0.00 36.52 5.07
2926 3177 8.375717 TCGTGAACATTTTTCAAAATATAGCG 57.624 30.769 0.00 1.25 36.52 4.26
2927 3178 9.341899 ACTCGTGAACATTTTTCAAAATATAGC 57.658 29.630 0.00 0.00 36.52 2.97
2931 3182 9.574458 TGAAACTCGTGAACATTTTTCAAAATA 57.426 25.926 0.00 0.00 36.52 1.40
2932 3183 8.472683 TGAAACTCGTGAACATTTTTCAAAAT 57.527 26.923 0.00 0.00 39.07 1.82
2933 3184 7.875316 TGAAACTCGTGAACATTTTTCAAAA 57.125 28.000 0.00 0.00 31.71 2.44
2934 3185 7.875316 TTGAAACTCGTGAACATTTTTCAAA 57.125 28.000 5.13 0.00 39.03 2.69
2935 3186 7.875316 TTTGAAACTCGTGAACATTTTTCAA 57.125 28.000 3.76 3.76 39.79 2.69
2936 3187 7.875316 TTTTGAAACTCGTGAACATTTTTCA 57.125 28.000 0.00 0.00 32.54 2.69
2937 3188 7.418521 CGTTTTTGAAACTCGTGAACATTTTTC 59.581 33.333 2.53 0.00 0.00 2.29
2938 3189 7.095982 ACGTTTTTGAAACTCGTGAACATTTTT 60.096 29.630 5.93 0.00 33.55 1.94
2939 3190 6.363896 ACGTTTTTGAAACTCGTGAACATTTT 59.636 30.769 5.93 0.00 33.55 1.82
3041 3293 2.093500 TCAGATACACGCTGGAGCATTT 60.093 45.455 0.00 0.00 42.21 2.32
3046 3298 4.393062 ACATTTTTCAGATACACGCTGGAG 59.607 41.667 0.00 0.00 34.20 3.86
3051 3303 7.377397 TGTGTTAAACATTTTTCAGATACACGC 59.623 33.333 0.00 0.00 36.01 5.34
3170 3423 9.645059 TTTCAAATGTTTGTTTTGATGTCTACA 57.355 25.926 5.48 0.00 41.36 2.74


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

AutoCloner maintained by Alex Coulton.