Multiple sequence alignment - TraesCS1B01G301400

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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 TraesCS1B01G301400 chr1B 100.000 4214 0 0 1 4214 522006438 522010651 0.000000e+00 7782.0
1 TraesCS1B01G301400 chr1A 91.885 2514 131 41 810 3267 487725284 487727780 0.000000e+00 3445.0
2 TraesCS1B01G301400 chr1A 84.868 760 55 32 1 734 487695196 487695921 0.000000e+00 712.0
3 TraesCS1B01G301400 chr1A 91.346 520 30 8 3296 3814 487728036 487728541 0.000000e+00 697.0
4 TraesCS1B01G301400 chr1A 94.277 332 15 3 3885 4213 487728534 487728864 4.860000e-139 505.0
5 TraesCS1B01G301400 chr1D 94.538 1483 55 13 2740 4214 388637344 388638808 0.000000e+00 2266.0
6 TraesCS1B01G301400 chr1D 93.123 1076 46 15 1544 2606 388636288 388637348 0.000000e+00 1552.0
7 TraesCS1B01G301400 chr1D 91.017 757 42 11 812 1554 388635524 388636268 0.000000e+00 998.0
8 TraesCS1B01G301400 chr1D 91.310 725 35 12 8 708 388629196 388629916 0.000000e+00 965.0
9 TraesCS1B01G301400 chr1D 94.737 38 0 2 765 800 388635503 388635540 1.640000e-04 58.4


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 TraesCS1B01G301400 chr1B 522006438 522010651 4213 False 7782.0 7782 100.000000 1 4214 1 chr1B.!!$F1 4213
1 TraesCS1B01G301400 chr1A 487725284 487728864 3580 False 1549.0 3445 92.502667 810 4213 3 chr1A.!!$F2 3403
2 TraesCS1B01G301400 chr1A 487695196 487695921 725 False 712.0 712 84.868000 1 734 1 chr1A.!!$F1 733
3 TraesCS1B01G301400 chr1D 388635503 388638808 3305 False 1218.6 2266 93.353750 765 4214 4 chr1D.!!$F2 3449
4 TraesCS1B01G301400 chr1D 388629196 388629916 720 False 965.0 965 91.310000 8 708 1 chr1D.!!$F1 700


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
539 540 0.179108 GGTTCGCGCCATAGAAGACT 60.179 55.0 0.0 0.0 0.00 3.24 F
857 885 0.521735 GGCCGTCCTGTCACAATTTC 59.478 55.0 0.0 0.0 0.00 2.17 F
2242 2325 0.673644 CTGAAGTGCGACCCCGATTT 60.674 55.0 0.0 0.0 38.22 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2306 0.673644 AAATCGGGGTCGCACTTCAG 60.674 55.0 0.0 0.00 36.13 3.02 R
2594 2697 0.869880 GCAAACGGTCCAGTGCAAAC 60.870 55.0 0.0 0.00 36.97 2.93 R
3508 3844 0.595095 CCTGACCAAGCTTTGCAGAC 59.405 55.0 17.2 1.29 0.00 3.51 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
29 30 2.969628 ATTCTTCGTCGCTGATCCTT 57.030 45.000 0.00 0.00 0.00 3.36
41 42 2.705127 GCTGATCCTTTCCCTGATCTCT 59.295 50.000 0.00 0.00 38.53 3.10
72 73 1.820481 GAGAGCGGCTCGAGGTACT 60.820 63.158 23.15 4.83 35.63 2.73
75 76 3.450115 GCGGCTCGAGGTACTGGT 61.450 66.667 15.58 0.00 41.55 4.00
77 78 2.893398 GGCTCGAGGTACTGGTGG 59.107 66.667 15.58 0.00 41.55 4.61
150 151 1.069668 GGTACCTGTGTTCCTCGTTGT 59.930 52.381 4.06 0.00 0.00 3.32
268 269 2.885861 GACGTGGTCGAGCTCCAT 59.114 61.111 16.64 2.00 40.62 3.41
276 277 3.790437 CGAGCTCCATGGCCCTGT 61.790 66.667 6.96 0.00 0.00 4.00
278 279 3.412624 GAGCTCCATGGCCCTGTCC 62.413 68.421 6.96 0.00 0.00 4.02
289 290 1.913762 CCCTGTCCACGAGGGTCTT 60.914 63.158 0.00 0.00 44.85 3.01
503 504 0.839946 ACCACTTGAGCTTCACCACT 59.160 50.000 0.00 0.00 0.00 4.00
509 510 1.222113 GAGCTTCACCACTAGGGGC 59.778 63.158 12.22 0.00 42.91 5.80
539 540 0.179108 GGTTCGCGCCATAGAAGACT 60.179 55.000 0.00 0.00 0.00 3.24
586 587 2.556840 ATCGTCCCCGGTCGGTTCTA 62.557 60.000 8.67 0.00 33.95 2.10
593 594 2.960129 GGTCGGTTCTATGGCGCG 60.960 66.667 0.00 0.00 0.00 6.86
667 695 8.202137 TGGTAGACTATTTATAGACAAGCCAAC 58.798 37.037 3.85 0.00 34.50 3.77
695 723 1.542547 GGAGCTTTTGAACCGACCTCA 60.543 52.381 0.00 0.00 0.00 3.86
724 752 1.600107 GACGGCTGTGGGACCAATA 59.400 57.895 0.80 0.00 0.00 1.90
734 762 3.270877 GTGGGACCAATAGCTGTTACTG 58.729 50.000 0.00 0.00 0.00 2.74
735 763 2.910319 TGGGACCAATAGCTGTTACTGT 59.090 45.455 0.00 0.00 0.00 3.55
736 764 4.081309 GTGGGACCAATAGCTGTTACTGTA 60.081 45.833 0.00 0.00 0.00 2.74
737 765 4.719773 TGGGACCAATAGCTGTTACTGTAT 59.280 41.667 0.00 0.00 0.00 2.29
738 766 5.190925 TGGGACCAATAGCTGTTACTGTATT 59.809 40.000 0.00 0.00 0.00 1.89
739 767 6.120220 GGGACCAATAGCTGTTACTGTATTT 58.880 40.000 0.00 0.00 0.00 1.40
740 768 7.092802 TGGGACCAATAGCTGTTACTGTATTTA 60.093 37.037 0.00 0.00 0.00 1.40
741 769 7.937394 GGGACCAATAGCTGTTACTGTATTTAT 59.063 37.037 0.00 0.00 0.00 1.40
742 770 9.991906 GGACCAATAGCTGTTACTGTATTTATA 57.008 33.333 0.00 0.00 0.00 0.98
744 772 9.490379 ACCAATAGCTGTTACTGTATTTATAGC 57.510 33.333 0.00 0.00 0.00 2.97
745 773 9.489084 CCAATAGCTGTTACTGTATTTATAGCA 57.511 33.333 0.00 0.00 32.64 3.49
800 828 4.966168 TGGACTAATATTACTGGGCTGTCA 59.034 41.667 9.61 0.00 0.00 3.58
801 829 5.070446 TGGACTAATATTACTGGGCTGTCAG 59.930 44.000 0.00 0.00 40.40 3.51
802 830 5.511545 GGACTAATATTACTGGGCTGTCAGG 60.512 48.000 1.14 0.00 38.98 3.86
803 831 4.969359 ACTAATATTACTGGGCTGTCAGGT 59.031 41.667 1.14 0.00 38.98 4.00
804 832 4.862641 AATATTACTGGGCTGTCAGGTT 57.137 40.909 1.14 0.00 38.98 3.50
805 833 2.789409 ATTACTGGGCTGTCAGGTTC 57.211 50.000 1.14 0.00 38.98 3.62
806 834 1.429930 TTACTGGGCTGTCAGGTTCA 58.570 50.000 1.14 0.00 38.98 3.18
807 835 1.429930 TACTGGGCTGTCAGGTTCAA 58.570 50.000 1.14 0.00 38.98 2.69
808 836 0.550914 ACTGGGCTGTCAGGTTCAAA 59.449 50.000 1.14 0.00 38.98 2.69
809 837 1.064017 ACTGGGCTGTCAGGTTCAAAA 60.064 47.619 1.14 0.00 38.98 2.44
810 838 2.031120 CTGGGCTGTCAGGTTCAAAAA 58.969 47.619 1.14 0.00 0.00 1.94
832 860 1.901591 AATCACTGGGCTGTCTTGTG 58.098 50.000 0.00 0.00 0.00 3.33
854 882 2.351276 GGGCCGTCCTGTCACAAT 59.649 61.111 0.00 0.00 0.00 2.71
857 885 0.521735 GGCCGTCCTGTCACAATTTC 59.478 55.000 0.00 0.00 0.00 2.17
858 886 1.234821 GCCGTCCTGTCACAATTTCA 58.765 50.000 0.00 0.00 0.00 2.69
859 887 1.069227 GCCGTCCTGTCACAATTTCAC 60.069 52.381 0.00 0.00 0.00 3.18
861 889 1.194547 CGTCCTGTCACAATTTCACCG 59.805 52.381 0.00 0.00 0.00 4.94
862 890 2.218603 GTCCTGTCACAATTTCACCGT 58.781 47.619 0.00 0.00 0.00 4.83
984 1013 3.432326 GCATTATCTCATATCCCCCGTCC 60.432 52.174 0.00 0.00 0.00 4.79
1026 1055 1.451747 GGCGACCGAGGTCTACTCT 60.452 63.158 18.85 0.00 44.33 3.24
1112 1141 0.906756 CTCCTGCAGGTCCTTCTCCA 60.907 60.000 31.58 8.74 36.34 3.86
1185 1214 4.787280 CGCCACCCCCTCCTCTCT 62.787 72.222 0.00 0.00 0.00 3.10
1321 1351 5.105752 GCGAAAGGATATAGTCTGCTATGG 58.894 45.833 0.00 0.00 38.31 2.74
1324 1362 7.577046 GCGAAAGGATATAGTCTGCTATGGTAA 60.577 40.741 0.00 0.00 38.31 2.85
1352 1390 2.086094 CGTGGTGGTTGGGGTTTATAC 58.914 52.381 0.00 0.00 0.00 1.47
1402 1441 2.815478 CTGCGGTTCTAGAACTGGATC 58.185 52.381 34.69 23.14 44.95 3.36
1440 1487 1.464997 GTGTCGAGCAAGGTTCATTCC 59.535 52.381 0.00 0.00 0.00 3.01
1471 1518 8.985315 TGATTTCTTAGGCATGATTAACAGAT 57.015 30.769 0.00 0.00 0.00 2.90
1512 1559 9.595823 TCTTAATTAAGAAGCATGGTACTGTAC 57.404 33.333 22.73 9.46 39.22 2.90
1513 1560 9.378551 CTTAATTAAGAAGCATGGTACTGTACA 57.621 33.333 18.69 6.45 35.33 2.90
1517 1564 5.326200 AGAAGCATGGTACTGTACACTAC 57.674 43.478 18.79 6.29 0.00 2.73
1518 1565 4.770531 AGAAGCATGGTACTGTACACTACA 59.229 41.667 18.79 8.41 37.13 2.74
1559 1639 8.495949 TGTTGTTTTCGATATCAAGTCTTCTTC 58.504 33.333 3.12 0.00 0.00 2.87
1658 1741 3.400505 TTAGTCTGTGCATACGAGTCG 57.599 47.619 11.85 11.85 0.00 4.18
1674 1757 2.579787 CGTCGAGCCTTACTGCCG 60.580 66.667 0.00 0.00 0.00 5.69
1760 1843 2.056223 GGCAAGCATGTGGCCATCT 61.056 57.895 9.72 0.72 46.92 2.90
1769 1852 1.388133 GTGGCCATCTTTTCCCCCT 59.612 57.895 9.72 0.00 0.00 4.79
1786 1869 5.393866 TCCCCCTTTTTCCTATGATATTGC 58.606 41.667 0.00 0.00 0.00 3.56
1793 1876 9.736023 CCTTTTTCCTATGATATTGCTGTTAAC 57.264 33.333 0.00 0.00 0.00 2.01
1813 1896 8.258007 TGTTAACTTCTCACTTTCTCAAGAAGA 58.742 33.333 15.68 0.02 44.81 2.87
1889 1972 5.491982 AGGGTGAATCATGTAACTGTCTTC 58.508 41.667 0.00 0.00 0.00 2.87
1904 1987 1.068055 GTCTTCGAGCGTCCTGGTTTA 60.068 52.381 0.00 0.00 0.00 2.01
1907 1990 0.675083 TCGAGCGTCCTGGTTTACAA 59.325 50.000 0.00 0.00 0.00 2.41
1908 1991 0.788391 CGAGCGTCCTGGTTTACAAC 59.212 55.000 0.00 0.00 0.00 3.32
1909 1992 1.604693 CGAGCGTCCTGGTTTACAACT 60.605 52.381 0.00 0.00 0.00 3.16
1910 1993 2.490991 GAGCGTCCTGGTTTACAACTT 58.509 47.619 0.00 0.00 0.00 2.66
1911 1994 3.656559 GAGCGTCCTGGTTTACAACTTA 58.343 45.455 0.00 0.00 0.00 2.24
1912 1995 3.396560 AGCGTCCTGGTTTACAACTTAC 58.603 45.455 0.00 0.00 0.00 2.34
1913 1996 3.132925 GCGTCCTGGTTTACAACTTACA 58.867 45.455 0.00 0.00 0.00 2.41
1914 1997 3.560896 GCGTCCTGGTTTACAACTTACAA 59.439 43.478 0.00 0.00 0.00 2.41
1934 2017 9.567848 CTTACAAGAGTTTTTGCAGAAAACTAA 57.432 29.630 25.80 18.99 46.81 2.24
1983 2066 2.031870 GCTGGTTTGGAAGGTTTGTCT 58.968 47.619 0.00 0.00 0.00 3.41
1987 2070 3.835395 TGGTTTGGAAGGTTTGTCTTGTT 59.165 39.130 0.00 0.00 0.00 2.83
1997 2080 5.894807 AGGTTTGTCTTGTTGAACATTCAG 58.105 37.500 0.00 0.00 38.61 3.02
2036 2119 4.551671 AGCCCTGTATCTAACTGATCTGT 58.448 43.478 0.00 0.00 36.65 3.41
2183 2266 7.094377 GCTGTAAATAATGGACTCTTTGTTCCA 60.094 37.037 0.00 0.00 36.61 3.53
2223 2306 1.909376 TCTCGTGCTCGCTGAAATAC 58.091 50.000 2.69 0.00 36.96 1.89
2237 2320 2.007608 GAAATACTGAAGTGCGACCCC 58.992 52.381 0.00 0.00 0.00 4.95
2242 2325 0.673644 CTGAAGTGCGACCCCGATTT 60.674 55.000 0.00 0.00 38.22 2.17
2249 2332 4.263435 AGTGCGACCCCGATTTATTTTAA 58.737 39.130 0.00 0.00 38.22 1.52
2291 2374 9.379791 AGTAGTAACTTAAATATCACAAGTGCC 57.620 33.333 0.00 0.00 32.96 5.01
2384 2475 6.850752 TGGTGTCATCTACAACTTCTATCA 57.149 37.500 0.00 0.00 46.70 2.15
2386 2477 7.676004 TGGTGTCATCTACAACTTCTATCAAA 58.324 34.615 0.00 0.00 46.70 2.69
2533 2635 2.694616 AATGCCACCAAGGGTTAGTT 57.305 45.000 0.00 0.00 38.09 2.24
2594 2697 0.469917 AACCAGATCTATGGGGCACG 59.530 55.000 6.01 0.00 45.25 5.34
2612 2715 0.591236 CGTTTGCACTGGACCGTTTG 60.591 55.000 0.00 0.00 0.00 2.93
2625 2728 0.249405 CCGTTTGCCAACACAAGCAT 60.249 50.000 1.21 0.00 39.11 3.79
2683 2786 6.135290 TGCCTGATGTTATCTTGTTTATGC 57.865 37.500 0.00 0.00 0.00 3.14
2730 2834 1.468520 CCGTATGTTCCTGCCAACTTG 59.531 52.381 0.00 0.00 0.00 3.16
2732 2836 2.095768 CGTATGTTCCTGCCAACTTGTG 60.096 50.000 0.00 0.00 0.00 3.33
2737 2841 2.884639 GTTCCTGCCAACTTGTGTATGT 59.115 45.455 0.00 0.00 0.00 2.29
2757 2861 4.556233 TGTTGTTGATCCTAGTCTGTTCG 58.444 43.478 0.00 0.00 0.00 3.95
2759 2863 4.436242 TGTTGATCCTAGTCTGTTCGTC 57.564 45.455 0.00 0.00 0.00 4.20
2920 3029 6.368791 TGCTTGTCGATAACAATCCATATAGC 59.631 38.462 0.00 0.00 46.53 2.97
2935 3044 4.142359 CCATATAGCTTCCTACTACAGCCG 60.142 50.000 0.00 0.00 33.73 5.52
2938 3047 2.731572 AGCTTCCTACTACAGCCGTTA 58.268 47.619 0.00 0.00 33.73 3.18
3023 3132 6.855914 GCACTGTTGATAAAATCGTTCTTTGA 59.144 34.615 0.00 0.00 0.00 2.69
3135 3244 5.095145 TCTCTCTCCAAAATGATGTGAGG 57.905 43.478 0.00 0.00 0.00 3.86
3206 3315 2.102578 GATCCCACAAATTGACCAGGG 58.897 52.381 0.00 5.68 37.65 4.45
3278 3387 3.632855 GCTCAAAAGCTAGCTGTTGTT 57.367 42.857 35.69 18.38 45.55 2.83
3279 3388 3.559504 GCTCAAAAGCTAGCTGTTGTTC 58.440 45.455 35.69 26.70 45.55 3.18
3280 3389 3.610349 GCTCAAAAGCTAGCTGTTGTTCC 60.610 47.826 35.69 24.42 45.55 3.62
3286 3395 1.677217 GCTAGCTGTTGTTCCTCTGGG 60.677 57.143 7.70 0.00 0.00 4.45
3357 3693 5.570205 TTGTTCAACATGGAGTAACCCTA 57.430 39.130 0.00 0.00 38.00 3.53
3379 3715 3.190874 CCCGCAGAGAAGAAAGATGTAC 58.809 50.000 0.00 0.00 0.00 2.90
3381 3717 3.862267 CCGCAGAGAAGAAAGATGTACTG 59.138 47.826 0.00 0.00 0.00 2.74
3384 3720 6.093404 CGCAGAGAAGAAAGATGTACTGTAA 58.907 40.000 0.00 0.00 0.00 2.41
3385 3721 6.754209 CGCAGAGAAGAAAGATGTACTGTAAT 59.246 38.462 0.00 0.00 0.00 1.89
3386 3722 7.915923 CGCAGAGAAGAAAGATGTACTGTAATA 59.084 37.037 0.00 0.00 0.00 0.98
3387 3723 9.757227 GCAGAGAAGAAAGATGTACTGTAATAT 57.243 33.333 0.00 0.00 0.00 1.28
3403 3739 5.336945 TGTAATATCCTAGCTCTGGCAGAT 58.663 41.667 19.11 6.77 41.70 2.90
3405 3741 5.839517 AATATCCTAGCTCTGGCAGATTT 57.160 39.130 19.11 11.61 41.70 2.17
3408 3744 3.878778 TCCTAGCTCTGGCAGATTTTTC 58.121 45.455 19.11 5.32 41.70 2.29
3422 3758 7.867403 TGGCAGATTTTTCTTTCTGTAATGAAC 59.133 33.333 2.30 0.00 41.16 3.18
3496 3832 3.929094 TCCTGATGGTTTTACGTGTACC 58.071 45.455 0.00 3.30 34.23 3.34
3508 3844 1.897802 ACGTGTACCAGGGAGTAAAGG 59.102 52.381 0.00 0.00 0.00 3.11
3519 3855 2.553247 GGGAGTAAAGGTCTGCAAAGCT 60.553 50.000 0.00 0.00 0.00 3.74
3531 3867 0.032540 GCAAAGCTTGGTCAGGGTTG 59.967 55.000 0.00 0.00 0.00 3.77
3613 3949 5.507985 GCTTGTTGAAGTTACAATGCCTCTT 60.508 40.000 0.00 0.00 35.18 2.85
3766 4102 2.258286 GCACCGCGCCAAAGAAAT 59.742 55.556 0.00 0.00 32.94 2.17
3767 4103 1.801512 GCACCGCGCCAAAGAAATC 60.802 57.895 0.00 0.00 32.94 2.17
3768 4104 1.511887 CACCGCGCCAAAGAAATCG 60.512 57.895 0.00 0.00 0.00 3.34
3855 4191 9.699410 TTGATTAATTAGGTGAAATGAGGATGT 57.301 29.630 0.00 0.00 0.00 3.06
3957 4294 2.238521 TCCAAACAATCTTCCAGTGCC 58.761 47.619 0.00 0.00 0.00 5.01
3966 4303 5.188434 CAATCTTCCAGTGCCAAAGATAGA 58.812 41.667 11.67 0.00 38.47 1.98
3984 4321 0.107459 GAGCCCAGGACTGCCTAAAG 60.107 60.000 0.00 0.00 44.80 1.85
4138 4480 0.322816 CCTAGCAAAGCAGGCCAAGA 60.323 55.000 5.01 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.041238 ACCACCGAGAGATCAGGGAA 59.959 55.000 0.00 0.00 0.00 3.97
41 42 2.927580 GCTCTCCAACGACCACCGA 61.928 63.158 0.00 0.00 41.76 4.69
150 151 4.563630 CGTCGTCGGGTTCATCAA 57.436 55.556 0.00 0.00 0.00 2.57
276 277 3.379445 GGCGAAGACCCTCGTGGA 61.379 66.667 4.76 0.00 40.99 4.02
278 279 4.052229 ACGGCGAAGACCCTCGTG 62.052 66.667 16.62 0.00 40.99 4.35
397 398 4.988716 TCGACTGGGCCGTGGAGT 62.989 66.667 5.76 0.00 0.00 3.85
443 444 2.183046 GAGACGGAGGAGCAGTGC 59.817 66.667 7.13 7.13 0.00 4.40
530 531 1.332997 CCGCGGTTCGTAGTCTTCTAT 59.667 52.381 19.50 0.00 36.19 1.98
603 604 2.610859 AATCCCAGTCCCACCGCT 60.611 61.111 0.00 0.00 0.00 5.52
613 614 2.350458 CCGCAAACCCCAATCCCAG 61.350 63.158 0.00 0.00 0.00 4.45
651 673 2.356330 CGGGGGTTGGCTTGTCTATAAA 60.356 50.000 0.00 0.00 0.00 1.40
708 736 1.819632 GCTATTGGTCCCACAGCCG 60.820 63.158 7.56 0.00 0.00 5.52
751 779 8.621286 ACTTGTGTCTAAAATTGTCTCGAAAAT 58.379 29.630 0.00 0.00 0.00 1.82
752 780 7.908082 CACTTGTGTCTAAAATTGTCTCGAAAA 59.092 33.333 0.00 0.00 0.00 2.29
753 781 7.406553 CACTTGTGTCTAAAATTGTCTCGAAA 58.593 34.615 0.00 0.00 0.00 3.46
754 782 6.018262 CCACTTGTGTCTAAAATTGTCTCGAA 60.018 38.462 0.00 0.00 0.00 3.71
755 783 5.465390 CCACTTGTGTCTAAAATTGTCTCGA 59.535 40.000 0.00 0.00 0.00 4.04
756 784 5.465390 TCCACTTGTGTCTAAAATTGTCTCG 59.535 40.000 0.00 0.00 0.00 4.04
757 785 6.483640 AGTCCACTTGTGTCTAAAATTGTCTC 59.516 38.462 0.00 0.00 0.00 3.36
758 786 6.357367 AGTCCACTTGTGTCTAAAATTGTCT 58.643 36.000 0.00 0.00 0.00 3.41
759 787 6.619801 AGTCCACTTGTGTCTAAAATTGTC 57.380 37.500 0.00 0.00 0.00 3.18
760 788 8.691661 ATTAGTCCACTTGTGTCTAAAATTGT 57.308 30.769 14.37 0.00 0.00 2.71
767 795 8.692710 CCAGTAATATTAGTCCACTTGTGTCTA 58.307 37.037 0.00 0.63 0.00 2.59
768 796 7.364762 CCCAGTAATATTAGTCCACTTGTGTCT 60.365 40.741 0.00 1.48 0.00 3.41
769 797 6.761714 CCCAGTAATATTAGTCCACTTGTGTC 59.238 42.308 0.00 0.00 0.00 3.67
810 838 3.068590 CACAAGACAGCCCAGTGATTTTT 59.931 43.478 0.00 0.00 32.14 1.94
811 839 2.624838 CACAAGACAGCCCAGTGATTTT 59.375 45.455 0.00 0.00 32.14 1.82
812 840 2.158623 TCACAAGACAGCCCAGTGATTT 60.159 45.455 0.00 0.00 34.59 2.17
813 841 1.421268 TCACAAGACAGCCCAGTGATT 59.579 47.619 0.00 0.00 34.59 2.57
814 842 1.059098 TCACAAGACAGCCCAGTGAT 58.941 50.000 0.00 0.00 34.59 3.06
815 843 0.836606 TTCACAAGACAGCCCAGTGA 59.163 50.000 0.00 0.00 37.43 3.41
816 844 0.947244 GTTCACAAGACAGCCCAGTG 59.053 55.000 0.00 0.00 0.00 3.66
817 845 0.839946 AGTTCACAAGACAGCCCAGT 59.160 50.000 0.00 0.00 0.00 4.00
818 846 1.233019 CAGTTCACAAGACAGCCCAG 58.767 55.000 0.00 0.00 0.00 4.45
832 860 2.047179 GACAGGACGGCCCAGTTC 60.047 66.667 1.76 0.00 34.49 3.01
854 882 1.005394 GCGAGGAGGAACGGTGAAA 60.005 57.895 0.00 0.00 0.00 2.69
857 885 4.452733 GGGCGAGGAGGAACGGTG 62.453 72.222 0.00 0.00 0.00 4.94
859 887 4.452733 GTGGGCGAGGAGGAACGG 62.453 72.222 0.00 0.00 0.00 4.44
861 889 3.379445 TCGTGGGCGAGGAGGAAC 61.379 66.667 0.00 0.00 42.81 3.62
952 981 2.204463 TGAGATAATGCTGGGGTGGAA 58.796 47.619 0.00 0.00 0.00 3.53
1040 1069 4.172512 CCTGCTCCCGATGCTGCT 62.173 66.667 0.00 0.00 0.00 4.24
1080 1109 4.722535 AGGAGGAGCCCGAGCCAA 62.723 66.667 0.00 0.00 41.25 4.52
1201 1230 4.021925 GGGGAGCTGCACGAAGGT 62.022 66.667 7.79 0.00 0.00 3.50
1352 1390 2.412089 GCTGCAGTTAACCACTAACTCG 59.588 50.000 16.64 0.00 46.01 4.18
1385 1424 1.405821 AGCGATCCAGTTCTAGAACCG 59.594 52.381 28.05 23.69 42.06 4.44
1402 1441 5.868687 GACACTCCTGTCTGCAGATAGCG 62.869 56.522 29.46 23.83 45.28 4.26
1440 1487 7.664082 AATCATGCCTAAGAAATCATACTCG 57.336 36.000 0.00 0.00 0.00 4.18
1497 1544 5.477607 TTGTAGTGTACAGTACCATGCTT 57.522 39.130 29.45 0.00 40.24 3.91
1500 1547 7.667043 AACATTTGTAGTGTACAGTACCATG 57.333 36.000 29.45 28.93 40.24 3.66
1533 1580 7.962964 AGAAGACTTGATATCGAAAACAACA 57.037 32.000 0.00 0.00 0.00 3.33
1542 1589 4.921547 TCACCGAAGAAGACTTGATATCG 58.078 43.478 0.00 0.00 36.39 2.92
1559 1639 1.001406 AGTCAGAAAGGAAGCTCACCG 59.999 52.381 0.00 0.00 0.00 4.94
1658 1741 2.886124 GCGGCAGTAAGGCTCGAC 60.886 66.667 0.00 0.00 41.46 4.20
1704 1787 2.230508 ACTCCATGTCAAAGCAATGCAG 59.769 45.455 8.35 0.00 0.00 4.41
1760 1843 7.147567 GCAATATCATAGGAAAAAGGGGGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
1786 1869 8.425577 TTCTTGAGAAAGTGAGAAGTTAACAG 57.574 34.615 8.61 0.00 0.00 3.16
1889 1972 0.788391 GTTGTAAACCAGGACGCTCG 59.212 55.000 0.00 0.00 42.21 5.03
1904 1987 6.509418 TCTGCAAAAACTCTTGTAAGTTGT 57.491 33.333 0.00 0.00 39.40 3.32
1907 1990 7.602753 AGTTTTCTGCAAAAACTCTTGTAAGT 58.397 30.769 22.81 8.06 44.50 2.24
1908 1991 9.567848 TTAGTTTTCTGCAAAAACTCTTGTAAG 57.432 29.630 27.66 0.00 44.50 2.34
1910 1993 9.515020 CATTAGTTTTCTGCAAAAACTCTTGTA 57.485 29.630 27.66 16.14 44.50 2.41
1911 1994 8.250332 TCATTAGTTTTCTGCAAAAACTCTTGT 58.750 29.630 27.66 16.79 44.50 3.16
1912 1995 8.633075 TCATTAGTTTTCTGCAAAAACTCTTG 57.367 30.769 27.66 24.92 44.50 3.02
1913 1996 9.822185 ATTCATTAGTTTTCTGCAAAAACTCTT 57.178 25.926 27.66 19.24 44.50 2.85
1914 1997 9.822185 AATTCATTAGTTTTCTGCAAAAACTCT 57.178 25.926 27.66 19.37 44.50 3.24
1934 2017 7.933577 TGAAGAGTATAAGATCGGCAAATTCAT 59.066 33.333 0.00 0.00 0.00 2.57
1983 2066 5.048504 GGAGAGCAATCTGAATGTTCAACAA 60.049 40.000 11.37 0.00 36.64 2.83
1987 2070 4.290711 TGGAGAGCAATCTGAATGTTCA 57.709 40.909 11.37 0.00 35.57 3.18
2036 2119 0.992970 TGCATATCCTGGGGGAAGCA 60.993 55.000 0.00 0.00 45.78 3.91
2223 2306 0.673644 AAATCGGGGTCGCACTTCAG 60.674 55.000 0.00 0.00 36.13 3.02
2237 2320 6.405278 AAGGCCTCCCATTAAAATAAATCG 57.595 37.500 5.23 0.00 0.00 3.34
2242 2325 4.357325 TGCAAAGGCCTCCCATTAAAATA 58.643 39.130 5.23 0.00 40.13 1.40
2249 2332 4.447734 CTTGCAAAGGCCTCCCAT 57.552 55.556 5.23 0.00 41.27 4.00
2291 2374 5.119588 CCGTGTTATTGTGTACCTTGTACAG 59.880 44.000 7.30 0.00 0.00 2.74
2306 2397 2.208132 TGGAATGCCACCGTGTTATT 57.792 45.000 0.00 0.00 39.92 1.40
2341 2432 7.474190 ACACCAAATCAAAAGAAATGCAAAAG 58.526 30.769 0.00 0.00 0.00 2.27
2386 2477 9.153721 CCAATTTGCACAACATGATAATAAAGT 57.846 29.630 0.00 0.00 0.00 2.66
2396 2495 3.389925 ACCTCCAATTTGCACAACATG 57.610 42.857 0.00 0.00 0.00 3.21
2533 2635 5.888982 AGAAGAAAACTCTACCAACCAGA 57.111 39.130 0.00 0.00 0.00 3.86
2567 2669 5.068636 CCCCATAGATCTGGTTTCAATCTG 58.931 45.833 5.18 0.00 34.23 2.90
2594 2697 0.869880 GCAAACGGTCCAGTGCAAAC 60.870 55.000 0.00 0.00 36.97 2.93
2607 2710 1.522258 GAATGCTTGTGTTGGCAAACG 59.478 47.619 0.00 0.00 41.90 3.60
2612 2715 1.001181 ACCATGAATGCTTGTGTTGGC 59.999 47.619 0.00 0.00 0.00 4.52
2651 2754 6.808321 AGATAACATCAGGCAAAGGTAGTA 57.192 37.500 0.00 0.00 0.00 1.82
2652 2755 5.700402 AGATAACATCAGGCAAAGGTAGT 57.300 39.130 0.00 0.00 0.00 2.73
2653 2756 5.882557 ACAAGATAACATCAGGCAAAGGTAG 59.117 40.000 0.00 0.00 0.00 3.18
2699 2803 5.989777 GCAGGAACATACGGTACAATAATCT 59.010 40.000 0.00 0.00 0.00 2.40
2701 2805 5.061179 GGCAGGAACATACGGTACAATAAT 58.939 41.667 0.00 0.00 0.00 1.28
2730 2834 6.398918 ACAGACTAGGATCAACAACATACAC 58.601 40.000 0.00 0.00 0.00 2.90
2732 2836 6.253727 CGAACAGACTAGGATCAACAACATAC 59.746 42.308 0.00 0.00 0.00 2.39
2737 2841 4.321750 GGACGAACAGACTAGGATCAACAA 60.322 45.833 0.00 0.00 0.00 2.83
2757 2861 5.123027 CAGAAAGCTTGATAAACAGGAGGAC 59.877 44.000 0.00 0.00 0.00 3.85
2759 2863 4.142513 GCAGAAAGCTTGATAAACAGGAGG 60.143 45.833 0.00 0.00 41.15 4.30
2920 3029 4.809426 CCATTTAACGGCTGTAGTAGGAAG 59.191 45.833 0.00 0.00 0.00 3.46
2935 3044 2.927028 AGGCACGGTATCCCATTTAAC 58.073 47.619 0.00 0.00 0.00 2.01
2938 3047 2.927028 GTAAGGCACGGTATCCCATTT 58.073 47.619 0.00 0.00 0.00 2.32
3206 3315 5.400485 CAGAGTTGCTGCAAAACTTACATTC 59.600 40.000 17.80 0.31 37.98 2.67
3235 3344 6.825721 AGCTTTCACCTACTAATCCAATTCAG 59.174 38.462 0.00 0.00 0.00 3.02
3269 3378 1.763770 CCCCAGAGGAACAACAGCT 59.236 57.895 0.00 0.00 38.24 4.24
3286 3395 8.579863 ACGAATATAACTGTACAAGTATACCCC 58.420 37.037 0.00 0.00 38.56 4.95
3357 3693 1.625818 ACATCTTTCTTCTCTGCGGGT 59.374 47.619 0.00 0.00 0.00 5.28
3379 3715 4.769488 TCTGCCAGAGCTAGGATATTACAG 59.231 45.833 8.81 5.41 40.80 2.74
3381 3717 5.930837 ATCTGCCAGAGCTAGGATATTAC 57.069 43.478 8.81 0.00 40.80 1.89
3384 3720 5.839517 AAAATCTGCCAGAGCTAGGATAT 57.160 39.130 8.81 0.00 40.80 1.63
3385 3721 5.367937 AGAAAAATCTGCCAGAGCTAGGATA 59.632 40.000 8.81 0.00 40.80 2.59
3386 3722 4.165758 AGAAAAATCTGCCAGAGCTAGGAT 59.834 41.667 8.81 0.00 40.80 3.24
3387 3723 3.521126 AGAAAAATCTGCCAGAGCTAGGA 59.479 43.478 8.81 0.00 40.80 2.94
3388 3724 3.883669 AGAAAAATCTGCCAGAGCTAGG 58.116 45.455 0.00 0.27 40.80 3.02
3389 3725 5.647225 AGAAAGAAAAATCTGCCAGAGCTAG 59.353 40.000 0.00 0.00 40.80 3.42
3476 3812 3.666274 TGGTACACGTAAAACCATCAGG 58.334 45.455 10.79 0.00 38.36 3.86
3496 3832 2.859165 TTGCAGACCTTTACTCCCTG 57.141 50.000 0.00 0.00 0.00 4.45
3508 3844 0.595095 CCTGACCAAGCTTTGCAGAC 59.405 55.000 17.20 1.29 0.00 3.51
3519 3855 2.708861 ACTGATGTACAACCCTGACCAA 59.291 45.455 0.00 0.00 0.00 3.67
3553 3889 7.912250 CAGCAACCAAAAAGAGCTATATACAAG 59.088 37.037 0.00 0.00 33.59 3.16
3561 3897 2.548057 CGTCAGCAACCAAAAAGAGCTA 59.452 45.455 0.00 0.00 33.59 3.32
3562 3898 1.334869 CGTCAGCAACCAAAAAGAGCT 59.665 47.619 0.00 0.00 35.63 4.09
3563 3899 1.333619 TCGTCAGCAACCAAAAAGAGC 59.666 47.619 0.00 0.00 0.00 4.09
3564 3900 3.691049 TTCGTCAGCAACCAAAAAGAG 57.309 42.857 0.00 0.00 0.00 2.85
3565 3901 3.442273 ACTTTCGTCAGCAACCAAAAAGA 59.558 39.130 0.00 0.00 0.00 2.52
3594 3930 6.093495 CGGAATAAGAGGCATTGTAACTTCAA 59.907 38.462 0.00 0.00 0.00 2.69
3613 3949 9.525409 GAAGTTACTCTATGTAAAAGCGGAATA 57.475 33.333 0.00 0.00 42.12 1.75
3649 3985 5.668471 ACAGACATATGATGTGAGTTCTGG 58.332 41.667 10.38 0.00 45.03 3.86
3664 4000 5.542635 ACACAGGAGAAGGTTTACAGACATA 59.457 40.000 0.00 0.00 0.00 2.29
3757 4093 2.223572 GCCATGCTACCGATTTCTTTGG 60.224 50.000 0.00 0.00 34.63 3.28
3765 4101 2.838736 CTTAGTTGCCATGCTACCGAT 58.161 47.619 0.00 0.00 35.09 4.18
3766 4102 1.742411 GCTTAGTTGCCATGCTACCGA 60.742 52.381 0.00 0.00 35.09 4.69
3767 4103 0.657840 GCTTAGTTGCCATGCTACCG 59.342 55.000 0.00 0.00 35.09 4.02
3850 4186 6.012745 AGCTCCAAAAATATATCCCACATCC 58.987 40.000 0.00 0.00 0.00 3.51
3854 4190 5.985530 GCAAAGCTCCAAAAATATATCCCAC 59.014 40.000 0.00 0.00 0.00 4.61
3855 4191 5.898972 AGCAAAGCTCCAAAAATATATCCCA 59.101 36.000 0.00 0.00 30.62 4.37
3957 4294 2.744494 GCAGTCCTGGGCTCTATCTTTG 60.744 54.545 0.00 0.00 0.00 2.77
3966 4303 1.994463 CTTTAGGCAGTCCTGGGCT 59.006 57.895 0.00 0.00 44.08 5.19
4026 4363 9.174166 TCTGATGGAGCTTTTTAAAATACTACC 57.826 33.333 0.55 6.80 0.00 3.18



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

AutoCloner maintained by Alex Coulton.