Multiple sequence alignment - TraesCS4D01G339700

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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 TraesCS4D01G339700 chr4D 100.000 2847 0 0 384 3230 497205947 497208793 0.000000e+00 5258.0
1 TraesCS4D01G339700 chr4D 100.000 33 0 0 1 33 497205564 497205596 9.680000e-06 62.1
2 TraesCS4D01G339700 chr4B 92.379 2270 97 43 987 3230 638120962 638123181 0.000000e+00 3164.0
3 TraesCS4D01G339700 chr4B 88.250 400 17 8 444 833 638120184 638120563 4.910000e-123 451.0
4 TraesCS4D01G339700 chr4B 94.000 50 3 0 384 433 638119977 638120026 3.460000e-10 76.8
5 TraesCS4D01G339700 chr5A 89.296 1448 87 26 817 2222 677159430 677160851 0.000000e+00 1753.0
6 TraesCS4D01G339700 chr5A 94.286 1015 46 4 2226 3230 677160938 677161950 0.000000e+00 1543.0
7 TraesCS4D01G339700 chr5A 88.259 494 29 7 444 930 677140219 677140690 6.050000e-157 564.0
8 TraesCS4D01G339700 chr7A 75.475 579 130 11 2494 3066 7938702 7938130 4.110000e-69 272.0


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 TraesCS4D01G339700 chr4D 497205564 497208793 3229 False 2660.05 5258 100.000 1 3230 2 chr4D.!!$F1 3229
1 TraesCS4D01G339700 chr4B 638119977 638123181 3204 False 1230.60 3164 91.543 384 3230 3 chr4B.!!$F1 2846
2 TraesCS4D01G339700 chr5A 677159430 677161950 2520 False 1648.00 1753 91.791 817 3230 2 chr5A.!!$F2 2413
3 TraesCS4D01G339700 chr7A 7938130 7938702 572 True 272.00 272 75.475 2494 3066 1 chr7A.!!$R1 572

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
27 28 0.107508 CATCACCTAGCCACCACCAG 60.108 60.0 0.0 0.0 0.00 4.00 F
1302 1703 0.327924 CCAATGTCCACCAGGTAGCA 59.672 55.0 0.0 0.0 35.89 3.49 F
1644 2055 0.249155 CTGCCACACTTGCACTTTGG 60.249 55.0 0.0 0.0 34.46 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1741 0.373716 CTACGACGCAAGAAATGGGC 59.626 55.000 0.0 0.0 45.43 5.36 R
2106 2552 0.664466 GGAAGCAAAGCTCAAACGCC 60.664 55.000 0.0 0.0 38.25 5.68 R
2577 3121 2.736995 ATGTCCAACGTCACCGCG 60.737 61.111 0.0 0.0 37.70 6.46 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
19 20 1.884235 GTGGCATACATCACCTAGCC 58.116 55.000 0.00 0.00 42.32 3.93
21 22 1.140852 TGGCATACATCACCTAGCCAC 59.859 52.381 0.00 0.00 46.25 5.01
22 23 1.543429 GGCATACATCACCTAGCCACC 60.543 57.143 0.00 0.00 41.63 4.61
23 24 1.140852 GCATACATCACCTAGCCACCA 59.859 52.381 0.00 0.00 0.00 4.17
24 25 2.838736 CATACATCACCTAGCCACCAC 58.161 52.381 0.00 0.00 0.00 4.16
25 26 1.200519 TACATCACCTAGCCACCACC 58.799 55.000 0.00 0.00 0.00 4.61
26 27 0.840288 ACATCACCTAGCCACCACCA 60.840 55.000 0.00 0.00 0.00 4.17
27 28 0.107508 CATCACCTAGCCACCACCAG 60.108 60.000 0.00 0.00 0.00 4.00
28 29 1.274703 ATCACCTAGCCACCACCAGG 61.275 60.000 0.00 0.00 42.21 4.45
427 428 4.450976 TCTCAAAGCAAGAACTAGTGCAA 58.549 39.130 3.00 0.00 43.42 4.08
481 629 0.647410 CGTGGCGCTTGTAGAAGATG 59.353 55.000 7.64 0.00 0.00 2.90
521 669 2.028130 CCCTCTCGTACTTCTCTGCAT 58.972 52.381 0.00 0.00 0.00 3.96
532 680 2.662006 TCTCTGCATCGAGAACCAAG 57.338 50.000 3.30 0.00 37.12 3.61
544 692 5.543714 TCGAGAACCAAGCTATAACAACAA 58.456 37.500 0.00 0.00 0.00 2.83
558 706 1.063488 AACAACGTGGAAACAGCGC 59.937 52.632 0.00 0.00 44.46 5.92
561 709 1.522806 AACGTGGAAACAGCGCAGA 60.523 52.632 11.47 0.00 44.46 4.26
562 710 1.498865 AACGTGGAAACAGCGCAGAG 61.499 55.000 11.47 0.64 44.46 3.35
563 711 2.558313 GTGGAAACAGCGCAGAGC 59.442 61.111 11.47 0.00 44.46 4.09
576 726 1.202405 CGCAGAGCAAAAACAAGGGTT 60.202 47.619 0.00 0.00 39.43 4.11
578 728 2.866156 GCAGAGCAAAAACAAGGGTTTC 59.134 45.455 0.00 0.00 46.20 2.78
640 796 3.140814 GGAGGAATTGGTGGCGGC 61.141 66.667 0.00 0.00 0.00 6.53
658 814 1.657556 CGGAGGAGGAGATCTTCGC 59.342 63.158 0.00 0.00 34.88 4.70
718 874 3.255379 GAATCGGCGGCGACAGAC 61.255 66.667 37.06 22.10 0.00 3.51
719 875 3.982372 GAATCGGCGGCGACAGACA 62.982 63.158 37.06 14.09 0.00 3.41
720 876 3.989698 AATCGGCGGCGACAGACAG 62.990 63.158 37.06 2.54 0.00 3.51
726 882 4.394712 GGCGACAGACAGGGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
728 884 4.394712 CGACAGACAGGGGGTGCC 62.395 72.222 0.00 0.00 0.00 5.01
729 885 4.394712 GACAGACAGGGGGTGCCG 62.395 72.222 0.00 0.00 0.00 5.69
768 924 0.955919 CAGGGTTTCGAGGTTCCTGC 60.956 60.000 11.37 0.00 38.55 4.85
833 989 3.234630 CTCGTTTGGGCTGGACCGA 62.235 63.158 0.00 0.00 40.62 4.69
836 992 1.448922 CGTTTGGGCTGGACCGAAAA 61.449 55.000 0.00 0.00 46.33 2.29
837 993 0.747852 GTTTGGGCTGGACCGAAAAA 59.252 50.000 0.00 0.00 46.33 1.94
853 1009 2.387476 AAAAAGCTTGGCCCAGCAGC 62.387 55.000 28.99 16.99 42.84 5.25
870 1026 2.622962 GCAACGGGCCCAGTGTAAC 61.623 63.158 24.92 3.67 36.11 2.50
875 1031 1.153229 GGGCCCAGTGTAACGATCC 60.153 63.158 19.95 0.00 45.86 3.36
901 1057 0.815615 CTTATCGGAGGCCCAGTTGC 60.816 60.000 0.00 0.00 0.00 4.17
917 1073 0.598419 TTGCAGTGAGAGTGAGCGTG 60.598 55.000 0.00 0.00 0.00 5.34
918 1074 1.735920 GCAGTGAGAGTGAGCGTGG 60.736 63.158 0.00 0.00 0.00 4.94
932 1088 3.478780 GTGGAGCCACACCCACTA 58.521 61.111 14.53 0.00 46.94 2.74
933 1089 1.003718 GTGGAGCCACACCCACTAC 60.004 63.158 14.53 0.00 46.94 2.73
952 1108 1.067212 ACGCCTTATCTCGTCATCCAC 59.933 52.381 0.00 0.00 33.09 4.02
953 1109 1.603172 CGCCTTATCTCGTCATCCACC 60.603 57.143 0.00 0.00 0.00 4.61
954 1110 1.270358 GCCTTATCTCGTCATCCACCC 60.270 57.143 0.00 0.00 0.00 4.61
955 1111 2.039418 CCTTATCTCGTCATCCACCCA 58.961 52.381 0.00 0.00 0.00 4.51
956 1112 2.634940 CCTTATCTCGTCATCCACCCAT 59.365 50.000 0.00 0.00 0.00 4.00
957 1113 3.555795 CCTTATCTCGTCATCCACCCATG 60.556 52.174 0.00 0.00 0.00 3.66
959 1115 1.524621 CTCGTCATCCACCCATGGC 60.525 63.158 6.09 0.00 46.80 4.40
960 1116 2.256072 CTCGTCATCCACCCATGGCA 62.256 60.000 6.09 0.00 46.80 4.92
975 1131 3.279875 GCATAAAGCCCTCGCCCG 61.280 66.667 0.00 0.00 37.23 6.13
1301 1702 0.328258 ACCAATGTCCACCAGGTAGC 59.672 55.000 0.00 0.00 35.89 3.58
1302 1703 0.327924 CCAATGTCCACCAGGTAGCA 59.672 55.000 0.00 0.00 35.89 3.49
1307 1716 1.612442 TCCACCAGGTAGCACCCTC 60.612 63.158 0.00 0.00 39.75 4.30
1309 1718 2.285442 ACCAGGTAGCACCCTCCC 60.285 66.667 0.00 0.00 39.75 4.30
1328 1737 1.141254 CCCTGCTCTGCTCTGATGAAT 59.859 52.381 0.00 0.00 0.00 2.57
1332 1741 2.223758 TGCTCTGCTCTGATGAATCGAG 60.224 50.000 0.00 7.40 33.61 4.04
1361 1770 2.526120 GCGTCGTAGATTGGCCTGC 61.526 63.158 3.32 0.00 40.67 4.85
1362 1771 1.883084 CGTCGTAGATTGGCCTGCC 60.883 63.158 3.32 0.00 40.67 4.85
1370 1779 2.552231 GATTGGCCTGCCCGGTAGTT 62.552 60.000 3.32 0.00 35.87 2.24
1383 1792 4.069304 CCCGGTAGTTGTTTCTTGATTGA 58.931 43.478 0.00 0.00 0.00 2.57
1387 1796 6.086222 CGGTAGTTGTTTCTTGATTGATTGG 58.914 40.000 0.00 0.00 0.00 3.16
1390 1799 7.382218 GGTAGTTGTTTCTTGATTGATTGGTTG 59.618 37.037 0.00 0.00 0.00 3.77
1399 1808 5.559427 TGATTGATTGGTTGTTATCGGTG 57.441 39.130 0.00 0.00 0.00 4.94
1403 1812 0.878416 TTGGTTGTTATCGGTGCTGC 59.122 50.000 0.00 0.00 0.00 5.25
1627 2038 0.389166 GTGAGCCCTCTGTCGAACTG 60.389 60.000 0.00 0.00 0.00 3.16
1628 2039 1.446966 GAGCCCTCTGTCGAACTGC 60.447 63.158 0.00 0.00 0.00 4.40
1644 2055 0.249155 CTGCCACACTTGCACTTTGG 60.249 55.000 0.00 0.00 34.46 3.28
1645 2056 0.682532 TGCCACACTTGCACTTTGGA 60.683 50.000 6.95 0.00 32.85 3.53
1653 2088 2.036346 ACTTGCACTTTGGAAGATTGGC 59.964 45.455 13.61 0.00 46.92 4.52
1704 2139 6.486657 TCTTGCATTTCAGTTAAGCTGTAGTT 59.513 34.615 0.00 0.00 45.23 2.24
1706 2141 6.437928 TGCATTTCAGTTAAGCTGTAGTTTG 58.562 36.000 0.00 0.00 45.23 2.93
1710 2145 4.956085 TCAGTTAAGCTGTAGTTTGAGCA 58.044 39.130 0.00 0.00 45.23 4.26
1714 2149 7.659799 TCAGTTAAGCTGTAGTTTGAGCAATAA 59.340 33.333 0.00 0.00 45.23 1.40
1715 2150 8.289618 CAGTTAAGCTGTAGTTTGAGCAATAAA 58.710 33.333 0.00 0.00 40.27 1.40
1716 2151 8.846211 AGTTAAGCTGTAGTTTGAGCAATAAAA 58.154 29.630 0.00 0.00 37.70 1.52
1717 2152 8.902735 GTTAAGCTGTAGTTTGAGCAATAAAAC 58.097 33.333 0.00 0.00 37.70 2.43
1718 2153 6.013842 AGCTGTAGTTTGAGCAATAAAACC 57.986 37.500 0.00 0.00 37.04 3.27
1719 2154 5.534654 AGCTGTAGTTTGAGCAATAAAACCA 59.465 36.000 0.00 0.00 37.04 3.67
1720 2155 6.040391 AGCTGTAGTTTGAGCAATAAAACCAA 59.960 34.615 0.00 0.00 37.04 3.67
1721 2156 6.143919 GCTGTAGTTTGAGCAATAAAACCAAC 59.856 38.462 0.00 0.00 37.04 3.77
1722 2157 7.341445 TGTAGTTTGAGCAATAAAACCAACT 57.659 32.000 0.00 0.00 37.04 3.16
1723 2158 7.777095 TGTAGTTTGAGCAATAAAACCAACTT 58.223 30.769 0.00 0.00 37.04 2.66
1724 2159 7.704472 TGTAGTTTGAGCAATAAAACCAACTTG 59.296 33.333 0.00 0.00 37.04 3.16
1725 2160 6.639563 AGTTTGAGCAATAAAACCAACTTGT 58.360 32.000 0.00 0.00 37.04 3.16
1732 2167 6.640907 AGCAATAAAACCAACTTGTTCGATTC 59.359 34.615 0.00 0.00 0.00 2.52
1734 2169 7.116233 GCAATAAAACCAACTTGTTCGATTCAT 59.884 33.333 0.00 0.00 0.00 2.57
1736 2171 5.766150 AAACCAACTTGTTCGATTCATGA 57.234 34.783 0.00 0.00 0.00 3.07
1742 2177 3.931468 ACTTGTTCGATTCATGAGCTCAG 59.069 43.478 22.96 13.90 0.00 3.35
1904 2339 2.267961 GGCGTGTTCCCGGAGATT 59.732 61.111 0.73 0.00 0.00 2.40
1910 2345 2.047830 GTGTTCCCGGAGATTCCCTAT 58.952 52.381 0.73 0.00 31.13 2.57
2030 2465 0.888619 TCGCCGAGAACATCAAGTCT 59.111 50.000 0.00 0.00 0.00 3.24
2033 2468 2.736719 CGCCGAGAACATCAAGTCTGAT 60.737 50.000 0.00 0.00 43.40 2.90
2106 2552 2.600867 GGAAGAAAGTGAAGATCGAGCG 59.399 50.000 0.00 0.00 0.00 5.03
2107 2553 2.285827 AGAAAGTGAAGATCGAGCGG 57.714 50.000 0.00 0.00 0.00 5.52
2108 2554 0.647925 GAAAGTGAAGATCGAGCGGC 59.352 55.000 0.00 0.00 0.00 6.53
2110 2556 2.202623 GTGAAGATCGAGCGGCGT 60.203 61.111 9.37 0.00 41.80 5.68
2111 2557 1.805945 GTGAAGATCGAGCGGCGTT 60.806 57.895 9.37 0.48 41.80 4.84
2112 2558 1.080093 TGAAGATCGAGCGGCGTTT 60.080 52.632 9.37 0.00 41.80 3.60
2113 2559 1.345176 GAAGATCGAGCGGCGTTTG 59.655 57.895 9.37 6.72 41.80 2.93
2114 2560 1.076533 GAAGATCGAGCGGCGTTTGA 61.077 55.000 16.13 16.13 41.80 2.69
2115 2561 1.078759 AAGATCGAGCGGCGTTTGAG 61.079 55.000 18.49 4.37 41.80 3.02
2116 2562 3.144120 GATCGAGCGGCGTTTGAGC 62.144 63.158 18.49 15.99 41.80 4.26
2117 2563 3.649277 ATCGAGCGGCGTTTGAGCT 62.649 57.895 18.49 0.56 44.80 4.09
2188 2641 6.294473 AGATATTTGATGATCCTTTCGCTGT 58.706 36.000 0.00 0.00 0.00 4.40
2196 2649 5.592104 TGATCCTTTCGCTGTCTGTTATA 57.408 39.130 0.00 0.00 0.00 0.98
2203 2656 3.920446 TCGCTGTCTGTTATAACTTGCA 58.080 40.909 16.33 10.61 0.00 4.08
2265 2805 2.128771 TGCTTTGGTCAGGCTATTCC 57.871 50.000 0.00 0.00 0.00 3.01
2268 2808 2.685388 GCTTTGGTCAGGCTATTCCTTC 59.315 50.000 0.00 0.00 44.75 3.46
2323 2863 8.519492 TTATTCTACAGCATTTTTCAAACTGC 57.481 30.769 6.52 6.52 42.70 4.40
2398 2942 5.977635 TGATGGCTATAGCATACCACATAC 58.022 41.667 25.53 12.18 44.36 2.39
2460 3004 0.174617 CGAGCTCTTCCTCTGGGAAC 59.825 60.000 12.85 0.00 45.72 3.62
2466 3010 0.951040 CTTCCTCTGGGAACGTGCAC 60.951 60.000 6.82 6.82 45.72 4.57
2568 3112 1.228675 CAGCTTCTTGGCCTTGGGT 60.229 57.895 3.32 0.00 0.00 4.51
2883 3430 1.070786 AATGTTGTCCTCCACGCGT 59.929 52.632 5.58 5.58 0.00 6.01
2992 3539 1.880819 CTGGCTGGGCATGTTGAACC 61.881 60.000 0.00 0.00 0.00 3.62
3109 3656 0.675633 ACAAGCAATGGCAGTTCACC 59.324 50.000 0.00 0.00 44.61 4.02
3111 3658 0.537143 AAGCAATGGCAGTTCACCGA 60.537 50.000 0.00 0.00 44.61 4.69
3112 3659 0.957395 AGCAATGGCAGTTCACCGAG 60.957 55.000 0.00 0.00 44.61 4.63
3137 3687 5.946298 TCAGATTCAGAAACACATTCATGC 58.054 37.500 0.00 0.00 40.72 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.140852 TGGCTAGGTGATGTATGCCAC 59.859 52.381 0.00 0.00 44.35 5.01
1 2 1.140852 GTGGCTAGGTGATGTATGCCA 59.859 52.381 0.00 0.00 46.59 4.92
2 3 1.543429 GGTGGCTAGGTGATGTATGCC 60.543 57.143 0.00 0.00 40.62 4.40
3 4 1.140852 TGGTGGCTAGGTGATGTATGC 59.859 52.381 0.00 0.00 0.00 3.14
4 5 2.485479 GGTGGTGGCTAGGTGATGTATG 60.485 54.545 0.00 0.00 0.00 2.39
5 6 1.768870 GGTGGTGGCTAGGTGATGTAT 59.231 52.381 0.00 0.00 0.00 2.29
6 7 1.200519 GGTGGTGGCTAGGTGATGTA 58.799 55.000 0.00 0.00 0.00 2.29
7 8 0.840288 TGGTGGTGGCTAGGTGATGT 60.840 55.000 0.00 0.00 0.00 3.06
8 9 0.107508 CTGGTGGTGGCTAGGTGATG 60.108 60.000 0.00 0.00 0.00 3.07
9 10 1.274703 CCTGGTGGTGGCTAGGTGAT 61.275 60.000 0.00 0.00 33.12 3.06
10 11 1.918293 CCTGGTGGTGGCTAGGTGA 60.918 63.158 0.00 0.00 33.12 4.02
11 12 2.224159 ACCTGGTGGTGGCTAGGTG 61.224 63.158 0.00 0.00 46.53 4.00
12 13 2.207189 ACCTGGTGGTGGCTAGGT 59.793 61.111 0.00 0.00 46.51 3.08
395 396 2.957402 TGCTTTGAGAAGGATGTGGT 57.043 45.000 0.00 0.00 33.34 4.16
396 397 3.415212 TCTTGCTTTGAGAAGGATGTGG 58.585 45.455 0.00 0.00 32.96 4.17
427 428 6.228258 TGCGATTCTTGGTTTACTCTAGTTT 58.772 36.000 0.00 0.00 0.00 2.66
433 434 3.751698 AGGTTGCGATTCTTGGTTTACTC 59.248 43.478 0.00 0.00 0.00 2.59
435 436 4.226761 CAAGGTTGCGATTCTTGGTTTAC 58.773 43.478 10.48 0.00 35.53 2.01
436 437 3.886505 ACAAGGTTGCGATTCTTGGTTTA 59.113 39.130 18.34 0.00 41.35 2.01
438 439 2.293399 GACAAGGTTGCGATTCTTGGTT 59.707 45.455 18.34 4.71 41.35 3.67
440 441 1.200020 GGACAAGGTTGCGATTCTTGG 59.800 52.381 18.34 6.49 41.35 3.61
442 443 2.427506 GAGGACAAGGTTGCGATTCTT 58.572 47.619 0.00 0.00 0.00 2.52
481 629 4.509737 GCGCGGAGGTACTGGGAC 62.510 72.222 8.83 0.00 41.55 4.46
521 669 5.142061 TGTTGTTATAGCTTGGTTCTCGA 57.858 39.130 0.00 0.00 0.00 4.04
532 680 5.098218 TGTTTCCACGTTGTTGTTATAGC 57.902 39.130 0.00 0.00 0.00 2.97
544 692 1.956170 CTCTGCGCTGTTTCCACGT 60.956 57.895 9.73 0.00 0.00 4.49
558 706 4.114794 CTGAAACCCTTGTTTTTGCTCTG 58.885 43.478 0.00 0.00 44.57 3.35
561 709 2.501316 AGCTGAAACCCTTGTTTTTGCT 59.499 40.909 10.72 10.72 44.57 3.91
562 710 2.866156 GAGCTGAAACCCTTGTTTTTGC 59.134 45.455 0.00 0.00 44.57 3.68
563 711 3.115554 CGAGCTGAAACCCTTGTTTTTG 58.884 45.455 0.00 0.00 44.57 2.44
565 713 1.067060 GCGAGCTGAAACCCTTGTTTT 59.933 47.619 0.00 0.00 44.57 2.43
569 717 2.335712 GGGCGAGCTGAAACCCTTG 61.336 63.158 0.00 0.00 39.42 3.61
570 718 2.034221 GGGCGAGCTGAAACCCTT 59.966 61.111 0.00 0.00 39.42 3.95
571 719 4.394712 CGGGCGAGCTGAAACCCT 62.395 66.667 0.00 0.00 40.45 4.34
636 792 3.984749 GATCTCCTCCTCCGCCGC 61.985 72.222 0.00 0.00 0.00 6.53
637 793 1.801309 GAAGATCTCCTCCTCCGCCG 61.801 65.000 0.00 0.00 0.00 6.46
640 796 1.657556 GCGAAGATCTCCTCCTCCG 59.342 63.158 0.00 0.00 0.00 4.63
798 954 2.108344 GAGTCGATCGGCTCCGTCTC 62.108 65.000 34.11 13.18 40.68 3.36
811 967 2.204461 TCCAGCCCAAACGAGTCGA 61.204 57.895 21.50 0.00 0.00 4.20
813 969 1.671379 GGTCCAGCCCAAACGAGTC 60.671 63.158 0.00 0.00 0.00 3.36
836 992 3.308705 GCTGCTGGGCCAAGCTTT 61.309 61.111 32.14 0.00 43.90 3.51
837 993 4.608774 TGCTGCTGGGCCAAGCTT 62.609 61.111 32.14 0.00 43.90 3.74
838 994 4.608774 TTGCTGCTGGGCCAAGCT 62.609 61.111 32.14 0.00 43.90 3.74
839 995 4.368543 GTTGCTGCTGGGCCAAGC 62.369 66.667 26.51 26.51 43.82 4.01
840 996 4.047059 CGTTGCTGCTGGGCCAAG 62.047 66.667 8.04 1.30 0.00 3.61
850 1006 3.545124 TACACTGGGCCCGTTGCTG 62.545 63.158 19.37 9.78 40.92 4.41
853 1009 2.322081 CGTTACACTGGGCCCGTTG 61.322 63.158 19.37 19.05 0.00 4.10
870 1026 1.070134 TCCGATAAGGCAAAGGGATCG 59.930 52.381 0.00 0.00 40.77 3.69
901 1057 0.109365 CTCCACGCTCACTCTCACTG 60.109 60.000 0.00 0.00 0.00 3.66
917 1073 2.264794 CGTAGTGGGTGTGGCTCC 59.735 66.667 0.00 0.00 0.00 4.70
918 1074 2.434359 GCGTAGTGGGTGTGGCTC 60.434 66.667 0.00 0.00 0.00 4.70
930 1086 2.552743 TGGATGACGAGATAAGGCGTAG 59.447 50.000 0.00 0.00 41.34 3.51
932 1088 1.067212 GTGGATGACGAGATAAGGCGT 59.933 52.381 0.00 0.00 44.33 5.68
933 1089 1.603172 GGTGGATGACGAGATAAGGCG 60.603 57.143 0.00 0.00 0.00 5.52
958 1114 3.279875 CGGGCGAGGGCTTTATGC 61.280 66.667 0.00 0.00 39.81 3.14
959 1115 3.279875 GCGGGCGAGGGCTTTATG 61.280 66.667 0.00 0.00 39.81 1.90
960 1116 3.462199 GAGCGGGCGAGGGCTTTAT 62.462 63.158 0.00 0.00 40.16 1.40
1301 1702 4.106925 GCAGAGCAGGGGAGGGTG 62.107 72.222 0.00 0.00 0.00 4.61
1302 1703 4.345286 AGCAGAGCAGGGGAGGGT 62.345 66.667 0.00 0.00 0.00 4.34
1307 1716 1.146485 CATCAGAGCAGAGCAGGGG 59.854 63.158 0.00 0.00 0.00 4.79
1309 1718 2.485903 GATTCATCAGAGCAGAGCAGG 58.514 52.381 0.00 0.00 0.00 4.85
1328 1737 1.003839 ACGCAAGAAATGGGCTCGA 60.004 52.632 0.00 0.00 45.43 4.04
1332 1741 0.373716 CTACGACGCAAGAAATGGGC 59.626 55.000 0.00 0.00 45.43 5.36
1361 1770 4.069304 TCAATCAAGAAACAACTACCGGG 58.931 43.478 6.32 0.00 0.00 5.73
1362 1771 5.880054 ATCAATCAAGAAACAACTACCGG 57.120 39.130 0.00 0.00 0.00 5.28
1370 1779 7.807433 CGATAACAACCAATCAATCAAGAAACA 59.193 33.333 0.00 0.00 0.00 2.83
1383 1792 1.472480 GCAGCACCGATAACAACCAAT 59.528 47.619 0.00 0.00 0.00 3.16
1387 1796 1.933853 CCTAGCAGCACCGATAACAAC 59.066 52.381 0.00 0.00 0.00 3.32
1390 1799 1.571919 CACCTAGCAGCACCGATAAC 58.428 55.000 0.00 0.00 0.00 1.89
1627 2038 0.459489 TTCCAAAGTGCAAGTGTGGC 59.541 50.000 2.05 0.00 0.00 5.01
1628 2039 2.023673 TCTTCCAAAGTGCAAGTGTGG 58.976 47.619 0.58 0.58 0.00 4.17
1644 2055 8.355169 TGCTAGAAATTTCATATGCCAATCTTC 58.645 33.333 19.99 6.21 0.00 2.87
1645 2056 8.241497 TGCTAGAAATTTCATATGCCAATCTT 57.759 30.769 19.99 0.00 0.00 2.40
1704 2139 5.746245 CGAACAAGTTGGTTTTATTGCTCAA 59.254 36.000 7.96 0.00 0.00 3.02
1706 2141 5.516090 TCGAACAAGTTGGTTTTATTGCTC 58.484 37.500 7.96 0.00 0.00 4.26
1710 2145 8.356657 TCATGAATCGAACAAGTTGGTTTTATT 58.643 29.630 7.96 2.21 0.00 1.40
1714 2149 5.762045 CTCATGAATCGAACAAGTTGGTTT 58.238 37.500 7.96 0.00 0.00 3.27
1715 2150 4.320494 GCTCATGAATCGAACAAGTTGGTT 60.320 41.667 7.96 0.00 0.00 3.67
1716 2151 3.189287 GCTCATGAATCGAACAAGTTGGT 59.811 43.478 7.96 0.00 0.00 3.67
1717 2152 3.438087 AGCTCATGAATCGAACAAGTTGG 59.562 43.478 7.96 0.00 0.00 3.77
1718 2153 4.152938 TGAGCTCATGAATCGAACAAGTTG 59.847 41.667 13.74 0.00 0.00 3.16
1719 2154 4.318332 TGAGCTCATGAATCGAACAAGTT 58.682 39.130 13.74 0.00 0.00 2.66
1720 2155 3.930336 TGAGCTCATGAATCGAACAAGT 58.070 40.909 13.74 0.00 0.00 3.16
1721 2156 3.931468 ACTGAGCTCATGAATCGAACAAG 59.069 43.478 18.63 2.91 0.00 3.16
1722 2157 3.930336 ACTGAGCTCATGAATCGAACAA 58.070 40.909 18.63 0.00 0.00 2.83
1723 2158 3.599730 ACTGAGCTCATGAATCGAACA 57.400 42.857 18.63 0.00 0.00 3.18
1724 2159 4.389992 TGAAACTGAGCTCATGAATCGAAC 59.610 41.667 18.63 3.24 0.00 3.95
1725 2160 4.389992 GTGAAACTGAGCTCATGAATCGAA 59.610 41.667 18.63 0.00 0.00 3.71
1732 2167 3.057736 CCAAAGGTGAAACTGAGCTCATG 60.058 47.826 18.63 13.72 36.74 3.07
1734 2169 2.092429 ACCAAAGGTGAAACTGAGCTCA 60.092 45.455 17.19 17.19 36.74 4.26
1736 2171 2.736670 ACCAAAGGTGAAACTGAGCT 57.263 45.000 0.00 0.00 36.74 4.09
1910 2345 3.551496 CTTCTTGCCGCCCACCTCA 62.551 63.158 0.00 0.00 0.00 3.86
2030 2465 5.815233 ACCTCTTCTTCTTGAACTGATCA 57.185 39.130 0.00 0.00 35.85 2.92
2033 2468 5.614324 TCAACCTCTTCTTCTTGAACTGA 57.386 39.130 0.00 0.00 0.00 3.41
2106 2552 0.664466 GGAAGCAAAGCTCAAACGCC 60.664 55.000 0.00 0.00 38.25 5.68
2107 2553 0.664466 GGGAAGCAAAGCTCAAACGC 60.664 55.000 0.00 0.00 38.25 4.84
2108 2554 0.667993 TGGGAAGCAAAGCTCAAACG 59.332 50.000 0.00 0.00 38.25 3.60
2110 2556 2.071778 AGTGGGAAGCAAAGCTCAAA 57.928 45.000 0.00 0.00 38.25 2.69
2111 2557 2.071778 AAGTGGGAAGCAAAGCTCAA 57.928 45.000 0.00 0.00 38.25 3.02
2112 2558 1.682854 CAAAGTGGGAAGCAAAGCTCA 59.317 47.619 0.00 0.00 38.25 4.26
2113 2559 1.683385 ACAAAGTGGGAAGCAAAGCTC 59.317 47.619 0.00 0.00 38.25 4.09
2114 2560 1.683385 GACAAAGTGGGAAGCAAAGCT 59.317 47.619 0.00 0.00 42.56 3.74
2115 2561 1.408702 TGACAAAGTGGGAAGCAAAGC 59.591 47.619 0.00 0.00 0.00 3.51
2116 2562 3.799281 TTGACAAAGTGGGAAGCAAAG 57.201 42.857 0.00 0.00 0.00 2.77
2117 2563 4.081198 ACAATTGACAAAGTGGGAAGCAAA 60.081 37.500 13.59 0.00 35.69 3.68
2183 2636 4.250570 CTGCAAGTTATAACAGACAGCG 57.749 45.455 17.65 6.74 31.67 5.18
2203 2656 3.326588 TGGCAGTAGGTACAACATGAACT 59.673 43.478 0.00 0.00 0.00 3.01
2265 2805 3.675228 GCAATGCAATGAACTCCCAGAAG 60.675 47.826 5.79 0.00 0.00 2.85
2268 2808 1.546923 TGCAATGCAATGAACTCCCAG 59.453 47.619 5.01 0.00 34.76 4.45
2323 2863 6.544197 TCTGAGTCTTAGTATAGTCAAGCAGG 59.456 42.308 0.00 0.00 0.00 4.85
2398 2942 7.004555 TGCCCAAATGTACCTACTGATATAG 57.995 40.000 0.00 0.00 0.00 1.31
2577 3121 2.736995 ATGTCCAACGTCACCGCG 60.737 61.111 0.00 0.00 37.70 6.46
2883 3430 3.845259 GGCGGCATCCAGGACGTA 61.845 66.667 3.07 0.00 42.62 3.57
3109 3656 5.852738 ATGTGTTTCTGAATCTGAACTCG 57.147 39.130 1.96 0.00 0.00 4.18
3111 3658 7.591165 CATGAATGTGTTTCTGAATCTGAACT 58.409 34.615 1.96 0.00 35.23 3.01
3112 3659 6.307318 GCATGAATGTGTTTCTGAATCTGAAC 59.693 38.462 0.00 0.14 35.23 3.18


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

AutoCloner maintained by Alex Coulton.