Multiple sequence alignment - TraesCS4D01G287900

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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 TraesCS4D01G287900 chr4D 100.000 2363 0 0 1 2363 459312513 459310151 0.000000e+00 4364.0
1 TraesCS4D01G287900 chr4A 91.265 1099 72 13 563 1653 9456601 9457683 0.000000e+00 1476.0
2 TraesCS4D01G287900 chr4A 89.641 473 39 6 1790 2257 9457961 9458428 5.620000e-166 593.0
3 TraesCS4D01G287900 chr4A 88.333 120 13 1 2242 2360 9458443 9458562 2.450000e-30 143.0
4 TraesCS4D01G287900 chr4B 93.060 951 56 5 703 1645 574007631 574006683 0.000000e+00 1382.0
5 TraesCS4D01G287900 chr4B 88.483 547 51 6 1822 2363 573998277 573997738 0.000000e+00 651.0
6 TraesCS4D01G287900 chr4B 90.164 122 12 0 1701 1822 574006668 574006547 2.430000e-35 159.0
7 TraesCS4D01G287900 chr3B 94.182 275 16 0 273 547 463202685 463202959 1.010000e-113 420.0
8 TraesCS4D01G287900 chr3B 93.727 271 16 1 1 270 463202151 463202421 2.830000e-109 405.0
9 TraesCS4D01G287900 chr7A 90.551 254 21 3 295 547 698052806 698052555 1.350000e-87 333.0
10 TraesCS4D01G287900 chr7A 90.119 253 24 1 295 547 698079667 698079416 6.300000e-86 327.0
11 TraesCS4D01G287900 chr7A 88.538 253 28 1 295 547 697913270 697913019 2.950000e-79 305.0
12 TraesCS4D01G287900 chr7A 94.872 117 5 1 155 270 697934592 697934476 5.190000e-42 182.0
13 TraesCS4D01G287900 chr7A 91.597 119 9 1 153 270 698066935 698066817 1.880000e-36 163.0
14 TraesCS4D01G287900 chr7A 97.500 40 1 0 2 41 697934894 697934855 4.210000e-08 69.4
15 TraesCS4D01G287900 chr1B 94.595 37 0 1 585 619 529994556 529994520 3.280000e-04 56.5


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 TraesCS4D01G287900 chr4D 459310151 459312513 2362 True 4364.000000 4364 100.000000 1 2363 1 chr4D.!!$R1 2362
1 TraesCS4D01G287900 chr4A 9456601 9458562 1961 False 737.333333 1476 89.746333 563 2360 3 chr4A.!!$F1 1797
2 TraesCS4D01G287900 chr4B 574006547 574007631 1084 True 770.500000 1382 91.612000 703 1822 2 chr4B.!!$R2 1119
3 TraesCS4D01G287900 chr4B 573997738 573998277 539 True 651.000000 651 88.483000 1822 2363 1 chr4B.!!$R1 541
4 TraesCS4D01G287900 chr3B 463202151 463202959 808 False 412.500000 420 93.954500 1 547 2 chr3B.!!$F1 546

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
129 130 0.038526 ACTTCGTAAGGCGTGAGGTG 60.039 55.0 0.0 0.0 42.13 4.00 F
834 1099 0.537371 CCACTCCGCAAACCTTCCTT 60.537 55.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1333 0.17576 CTTCTCGGATCCAAAGGCGA 59.824 55.0 13.41 0.7 0.0 5.54 R
1758 2045 0.31179 CAACACTCATGCACACACCC 59.688 55.0 0.00 0.0 0.0 4.61 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
52 53 2.732094 GTTCGTGGACGGTGTCGG 60.732 66.667 0.00 0.00 41.39 4.79
117 118 2.040939 TGGTTGTCCCTGAACTTCGTA 58.959 47.619 0.00 0.00 0.00 3.43
128 129 0.677842 AACTTCGTAAGGCGTGAGGT 59.322 50.000 0.00 0.00 42.13 3.85
129 130 0.038526 ACTTCGTAAGGCGTGAGGTG 60.039 55.000 0.00 0.00 42.13 4.00
163 164 2.046285 GCCCATGCTACCAAACGCT 61.046 57.895 0.00 0.00 33.53 5.07
267 268 2.475466 CGCTGGCCATCACCATGTC 61.475 63.158 5.51 0.00 39.54 3.06
268 269 1.077212 GCTGGCCATCACCATGTCT 60.077 57.895 5.51 0.00 39.54 3.41
269 270 1.381928 GCTGGCCATCACCATGTCTG 61.382 60.000 5.51 0.00 39.54 3.51
303 566 1.654954 CTGCCATCTTGTGCTGCTCC 61.655 60.000 0.00 0.00 0.00 4.70
312 575 2.039462 TGCTGCTCCCCTCTGCTA 59.961 61.111 0.00 0.00 0.00 3.49
322 585 1.067821 CCCCTCTGCTAAAGCTAGTCG 59.932 57.143 3.26 0.00 42.66 4.18
324 587 2.950309 CCCTCTGCTAAAGCTAGTCGTA 59.050 50.000 3.26 0.00 42.66 3.43
325 588 3.570550 CCCTCTGCTAAAGCTAGTCGTAT 59.429 47.826 3.26 0.00 42.66 3.06
407 670 0.605589 GTACCCGGCCAGGATTATGC 60.606 60.000 13.45 0.00 45.00 3.14
420 683 2.618709 GGATTATGCTTTTCCCGGTCTG 59.381 50.000 0.00 0.00 0.00 3.51
468 731 2.483889 CCGAGATCAGAAAGGTTAGGGC 60.484 54.545 0.00 0.00 0.00 5.19
481 744 2.026262 GGTTAGGGCACAGATTTCAGGA 60.026 50.000 0.00 0.00 0.00 3.86
526 789 3.612479 GCGTCGACCTCTACAACCTTAAA 60.612 47.826 10.58 0.00 0.00 1.52
527 790 4.164294 CGTCGACCTCTACAACCTTAAAG 58.836 47.826 10.58 0.00 0.00 1.85
535 798 8.392372 ACCTCTACAACCTTAAAGTTCATTTC 57.608 34.615 0.00 0.00 32.01 2.17
547 810 8.964476 TTAAAGTTCATTTCAGACTTCACTCT 57.036 30.769 0.00 0.00 32.01 3.24
548 811 7.489574 AAAGTTCATTTCAGACTTCACTCTC 57.510 36.000 0.00 0.00 0.00 3.20
549 812 6.166984 AGTTCATTTCAGACTTCACTCTCA 57.833 37.500 0.00 0.00 0.00 3.27
550 813 6.586344 AGTTCATTTCAGACTTCACTCTCAA 58.414 36.000 0.00 0.00 0.00 3.02
551 814 6.481644 AGTTCATTTCAGACTTCACTCTCAAC 59.518 38.462 0.00 0.00 0.00 3.18
552 815 6.166984 TCATTTCAGACTTCACTCTCAACT 57.833 37.500 0.00 0.00 0.00 3.16
553 816 7.290110 TCATTTCAGACTTCACTCTCAACTA 57.710 36.000 0.00 0.00 0.00 2.24
554 817 7.901029 TCATTTCAGACTTCACTCTCAACTAT 58.099 34.615 0.00 0.00 0.00 2.12
555 818 7.816513 TCATTTCAGACTTCACTCTCAACTATG 59.183 37.037 0.00 0.00 0.00 2.23
556 819 6.901081 TTCAGACTTCACTCTCAACTATGA 57.099 37.500 0.00 0.00 0.00 2.15
580 843 9.358406 TGAGGTTCGGAGTATGATTAAGTTATA 57.642 33.333 0.00 0.00 0.00 0.98
581 844 9.843334 GAGGTTCGGAGTATGATTAAGTTATAG 57.157 37.037 0.00 0.00 0.00 1.31
583 846 7.544915 GGTTCGGAGTATGATTAAGTTATAGGC 59.455 40.741 0.00 0.00 0.00 3.93
586 849 6.531948 CGGAGTATGATTAAGTTATAGGCTGC 59.468 42.308 0.00 0.00 0.00 5.25
593 856 2.010145 AGTTATAGGCTGCGTGTGTG 57.990 50.000 4.91 0.00 0.00 3.82
602 865 1.136197 GCTGCGTGTGTGCGTTTATAA 60.136 47.619 0.00 0.00 37.81 0.98
603 866 2.757896 CTGCGTGTGTGCGTTTATAAG 58.242 47.619 0.00 0.00 37.81 1.73
609 872 4.259810 CGTGTGTGCGTTTATAAGGATGAG 60.260 45.833 0.00 0.00 0.00 2.90
618 881 5.294306 CGTTTATAAGGATGAGTGTGCATGT 59.706 40.000 0.00 0.00 0.00 3.21
623 886 1.339438 GGATGAGTGTGCATGTGTCCT 60.339 52.381 0.00 0.00 0.00 3.85
626 889 2.766313 TGAGTGTGCATGTGTCCTTAC 58.234 47.619 0.00 0.00 0.00 2.34
628 891 3.576550 TGAGTGTGCATGTGTCCTTACTA 59.423 43.478 0.00 0.00 0.00 1.82
637 900 5.874810 GCATGTGTCCTTACTATGTTTCTCA 59.125 40.000 0.00 0.00 0.00 3.27
834 1099 0.537371 CCACTCCGCAAACCTTCCTT 60.537 55.000 0.00 0.00 0.00 3.36
924 1191 0.581529 CACGCTCAACAAAAGCTCGA 59.418 50.000 0.00 0.00 37.62 4.04
1035 1304 1.045350 CCATCCTCTTCCTCCTCGCA 61.045 60.000 0.00 0.00 0.00 5.10
1039 1308 1.671901 CCTCTTCCTCCTCGCAGTCC 61.672 65.000 0.00 0.00 0.00 3.85
1041 1310 0.681564 TCTTCCTCCTCGCAGTCCTC 60.682 60.000 0.00 0.00 0.00 3.71
1165 1434 4.710695 TCGCGGTGCTGGTGTACG 62.711 66.667 6.13 0.00 0.00 3.67
1373 1642 2.737881 TAAACTGATCGGGCCGGGG 61.738 63.158 27.98 15.49 0.00 5.73
1389 1658 4.675029 GGGCGGTGCGTGTACACT 62.675 66.667 23.01 0.00 40.52 3.55
1400 1669 1.757574 GTGTACACTCGTGCACGTAA 58.242 50.000 35.74 19.13 46.56 3.18
1477 1747 6.710278 TGCATCTTGCCACTATATATAAGCA 58.290 36.000 7.38 7.38 44.23 3.91
1546 1816 2.034939 TCGGTCTACGTTGCAGAAGAAA 59.965 45.455 0.00 0.00 44.69 2.52
1594 1869 4.082081 TGTCAATTCAGGAATGTTGATGGC 60.082 41.667 0.00 0.00 0.00 4.40
1631 1906 3.262915 AGCCTTGAGTAGCTTGAGAATGT 59.737 43.478 0.00 0.00 35.22 2.71
1644 1931 5.626543 GCTTGAGAATGTGTGTGTATGTTTG 59.373 40.000 0.00 0.00 0.00 2.93
1645 1932 6.513230 GCTTGAGAATGTGTGTGTATGTTTGA 60.513 38.462 0.00 0.00 0.00 2.69
1646 1933 7.509141 TTGAGAATGTGTGTGTATGTTTGAT 57.491 32.000 0.00 0.00 0.00 2.57
1647 1934 7.132694 TGAGAATGTGTGTGTATGTTTGATC 57.867 36.000 0.00 0.00 0.00 2.92
1648 1935 6.128580 TGAGAATGTGTGTGTATGTTTGATCG 60.129 38.462 0.00 0.00 0.00 3.69
1649 1936 5.700832 AGAATGTGTGTGTATGTTTGATCGT 59.299 36.000 0.00 0.00 0.00 3.73
1650 1937 4.983215 TGTGTGTGTATGTTTGATCGTC 57.017 40.909 0.00 0.00 0.00 4.20
1651 1938 4.372656 TGTGTGTGTATGTTTGATCGTCA 58.627 39.130 0.00 0.00 0.00 4.35
1652 1939 4.994217 TGTGTGTGTATGTTTGATCGTCAT 59.006 37.500 0.00 0.00 0.00 3.06
1653 1940 5.107143 TGTGTGTGTATGTTTGATCGTCATG 60.107 40.000 7.15 0.00 0.00 3.07
1654 1941 4.391523 TGTGTGTATGTTTGATCGTCATGG 59.608 41.667 0.00 0.00 0.00 3.66
1655 1942 4.391830 GTGTGTATGTTTGATCGTCATGGT 59.608 41.667 0.00 0.00 0.00 3.55
1656 1943 4.391523 TGTGTATGTTTGATCGTCATGGTG 59.608 41.667 0.00 0.00 0.00 4.17
1657 1944 3.373748 TGTATGTTTGATCGTCATGGTGC 59.626 43.478 0.00 0.00 0.00 5.01
1658 1945 2.183478 TGTTTGATCGTCATGGTGCT 57.817 45.000 0.00 0.00 0.00 4.40
1659 1946 2.503331 TGTTTGATCGTCATGGTGCTT 58.497 42.857 0.00 0.00 0.00 3.91
1660 1947 2.884012 TGTTTGATCGTCATGGTGCTTT 59.116 40.909 0.00 0.00 0.00 3.51
1661 1948 4.068599 TGTTTGATCGTCATGGTGCTTTA 58.931 39.130 0.00 0.00 0.00 1.85
1662 1949 4.699735 TGTTTGATCGTCATGGTGCTTTAT 59.300 37.500 0.00 0.00 0.00 1.40
1663 1950 5.163764 TGTTTGATCGTCATGGTGCTTTATC 60.164 40.000 0.00 0.00 0.00 1.75
1664 1951 4.406648 TGATCGTCATGGTGCTTTATCT 57.593 40.909 0.00 0.00 0.00 1.98
1665 1952 5.529581 TGATCGTCATGGTGCTTTATCTA 57.470 39.130 0.00 0.00 0.00 1.98
1666 1953 6.101650 TGATCGTCATGGTGCTTTATCTAT 57.898 37.500 0.00 0.00 0.00 1.98
1667 1954 7.227049 TGATCGTCATGGTGCTTTATCTATA 57.773 36.000 0.00 0.00 0.00 1.31
1668 1955 7.666623 TGATCGTCATGGTGCTTTATCTATAA 58.333 34.615 0.00 0.00 0.00 0.98
1669 1956 8.147704 TGATCGTCATGGTGCTTTATCTATAAA 58.852 33.333 0.00 0.00 0.00 1.40
1670 1957 8.902540 ATCGTCATGGTGCTTTATCTATAAAA 57.097 30.769 0.00 0.00 32.39 1.52
1671 1958 8.138365 TCGTCATGGTGCTTTATCTATAAAAC 57.862 34.615 0.00 0.00 32.39 2.43
1672 1959 7.225931 TCGTCATGGTGCTTTATCTATAAAACC 59.774 37.037 8.46 8.46 35.32 3.27
1673 1960 7.352739 GTCATGGTGCTTTATCTATAAAACCG 58.647 38.462 9.92 1.33 36.56 4.44
1674 1961 6.485313 TCATGGTGCTTTATCTATAAAACCGG 59.515 38.462 0.00 0.00 36.56 5.28
1675 1962 5.127491 TGGTGCTTTATCTATAAAACCGGG 58.873 41.667 6.32 0.00 36.56 5.73
1676 1963 4.023450 GGTGCTTTATCTATAAAACCGGGC 60.023 45.833 6.32 0.00 32.39 6.13
1677 1964 3.810941 TGCTTTATCTATAAAACCGGGCG 59.189 43.478 6.32 0.00 32.39 6.13
1678 1965 4.060205 GCTTTATCTATAAAACCGGGCGA 58.940 43.478 6.32 0.00 32.39 5.54
1679 1966 4.512571 GCTTTATCTATAAAACCGGGCGAA 59.487 41.667 6.32 0.00 32.39 4.70
1680 1967 5.007921 GCTTTATCTATAAAACCGGGCGAAA 59.992 40.000 6.32 0.00 32.39 3.46
1681 1968 6.607735 TTTATCTATAAAACCGGGCGAAAG 57.392 37.500 6.32 0.00 29.93 2.62
1682 1969 5.007921 TTTATCTATAAAACCGGGCGAAAGC 59.992 40.000 6.32 0.00 41.85 3.51
1698 1985 4.489679 GAAAGCCTGTTTCGAGATGTTT 57.510 40.909 0.00 0.00 0.00 2.83
1699 1986 5.607119 GAAAGCCTGTTTCGAGATGTTTA 57.393 39.130 0.00 0.00 0.00 2.01
1734 2021 4.216257 GCACTCTTTTGTGTGTATCCATGT 59.784 41.667 0.00 0.00 43.52 3.21
1735 2022 5.692814 CACTCTTTTGTGTGTATCCATGTG 58.307 41.667 0.00 0.00 38.64 3.21
1736 2023 5.239306 CACTCTTTTGTGTGTATCCATGTGT 59.761 40.000 0.00 0.00 38.64 3.72
1737 2024 5.239306 ACTCTTTTGTGTGTATCCATGTGTG 59.761 40.000 0.00 0.00 0.00 3.82
1738 2025 5.129634 TCTTTTGTGTGTATCCATGTGTGT 58.870 37.500 0.00 0.00 0.00 3.72
1739 2026 4.827304 TTTGTGTGTATCCATGTGTGTG 57.173 40.909 0.00 0.00 0.00 3.82
1740 2027 2.150390 TGTGTGTATCCATGTGTGTGC 58.850 47.619 0.00 0.00 0.00 4.57
1741 2028 2.150390 GTGTGTATCCATGTGTGTGCA 58.850 47.619 0.00 0.00 0.00 4.57
1742 2029 2.749076 GTGTGTATCCATGTGTGTGCAT 59.251 45.455 0.00 0.00 0.00 3.96
1743 2030 2.748532 TGTGTATCCATGTGTGTGCATG 59.251 45.455 0.00 0.00 44.18 4.06
1744 2031 3.009026 GTGTATCCATGTGTGTGCATGA 58.991 45.455 0.00 0.00 46.65 3.07
1745 2032 3.064408 GTGTATCCATGTGTGTGCATGAG 59.936 47.826 0.00 0.00 46.65 2.90
1746 2033 2.502142 ATCCATGTGTGTGCATGAGT 57.498 45.000 0.00 0.00 46.65 3.41
1747 2034 1.525941 TCCATGTGTGTGCATGAGTG 58.474 50.000 0.00 0.00 46.65 3.51
1748 2035 1.202794 TCCATGTGTGTGCATGAGTGT 60.203 47.619 0.00 0.00 46.65 3.55
1749 2036 1.610038 CCATGTGTGTGCATGAGTGTT 59.390 47.619 0.00 0.00 46.65 3.32
1750 2037 2.034939 CCATGTGTGTGCATGAGTGTTT 59.965 45.455 0.00 0.00 46.65 2.83
1751 2038 3.491276 CCATGTGTGTGCATGAGTGTTTT 60.491 43.478 0.00 0.00 46.65 2.43
1752 2039 3.865011 TGTGTGTGCATGAGTGTTTTT 57.135 38.095 0.00 0.00 0.00 1.94
1785 2072 3.125658 TGTGCATGAGTGTTGATCATTCG 59.874 43.478 0.00 0.00 35.20 3.34
1891 2401 5.571784 AGTACATGCAATCAAGTGAATGG 57.428 39.130 3.66 0.00 38.69 3.16
1903 2413 4.039973 TCAAGTGAATGGACGGTTAGAGTT 59.960 41.667 0.00 0.00 0.00 3.01
1904 2414 3.926616 AGTGAATGGACGGTTAGAGTTG 58.073 45.455 0.00 0.00 0.00 3.16
1930 2441 9.581099 GGTTGTTGATAAAATAACCATCGAATT 57.419 29.630 10.70 0.00 40.31 2.17
2014 2527 5.949952 AGGGACACATGGTAAAACTTTATCC 59.050 40.000 0.00 0.00 0.00 2.59
2023 2536 9.807921 CATGGTAAAACTTTATCCCCTATGTAT 57.192 33.333 0.00 0.00 0.00 2.29
2066 2579 6.674278 GCATTGGTTTTGTTTGTGGTTTAGTG 60.674 38.462 0.00 0.00 0.00 2.74
2107 2620 7.790823 TTATGATGGTGTGTATGTGATTGAG 57.209 36.000 0.00 0.00 0.00 3.02
2108 2621 3.940852 TGATGGTGTGTATGTGATTGAGC 59.059 43.478 0.00 0.00 0.00 4.26
2109 2622 3.415457 TGGTGTGTATGTGATTGAGCA 57.585 42.857 0.00 0.00 0.00 4.26
2110 2623 3.954200 TGGTGTGTATGTGATTGAGCAT 58.046 40.909 0.00 0.00 0.00 3.79
2161 2674 1.696884 TGGATGGCGGCATAGTTCATA 59.303 47.619 25.86 3.54 0.00 2.15
2174 2687 6.464465 GGCATAGTTCATAGATAACACCCACT 60.464 42.308 0.00 0.00 0.00 4.00
2182 2695 0.108329 ATAACACCCACTTCCTCGCG 60.108 55.000 0.00 0.00 0.00 5.87
2220 2733 6.238621 CCAGTGTGCTATGACTTTGTTGTTTA 60.239 38.462 0.00 0.00 0.00 2.01
2262 2805 1.695813 GCATGCATGCGTTTGTGTTA 58.304 45.000 33.99 0.00 44.67 2.41
2275 2818 4.975502 CGTTTGTGTTAATTGTGTGCATCT 59.024 37.500 0.00 0.00 0.00 2.90
2282 2825 3.855689 AATTGTGTGCATCTTAGCCAC 57.144 42.857 0.00 0.00 36.71 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.240134 AAGCCGCTCATGACACCGT 62.240 57.895 0.00 0.00 0.00 4.83
117 118 2.426023 GACCACACCTCACGCCTT 59.574 61.111 0.00 0.00 0.00 4.35
128 129 4.308458 CCCACTTCGCCGACCACA 62.308 66.667 0.00 0.00 0.00 4.17
148 149 0.095245 CGACAGCGTTTGGTAGCATG 59.905 55.000 0.00 0.00 35.48 4.06
150 151 3.945436 CGACAGCGTTTGGTAGCA 58.055 55.556 0.00 0.00 35.48 3.49
163 164 2.342279 GGCACCAGCAGTACGACA 59.658 61.111 0.00 0.00 44.61 4.35
258 259 1.535444 ACGACCCCAGACATGGTGA 60.535 57.895 0.00 0.00 46.10 4.02
303 566 1.751924 ACGACTAGCTTTAGCAGAGGG 59.248 52.381 4.33 1.23 45.16 4.30
312 575 4.649674 TCCCATCTCAATACGACTAGCTTT 59.350 41.667 0.00 0.00 0.00 3.51
322 585 8.624776 CATTTTTCCTAGTTCCCATCTCAATAC 58.375 37.037 0.00 0.00 0.00 1.89
324 587 6.608808 CCATTTTTCCTAGTTCCCATCTCAAT 59.391 38.462 0.00 0.00 0.00 2.57
325 588 5.951747 CCATTTTTCCTAGTTCCCATCTCAA 59.048 40.000 0.00 0.00 0.00 3.02
385 648 0.761702 TAATCCTGGCCGGGTACTCC 60.762 60.000 30.31 0.00 0.00 3.85
407 670 0.313987 GTTTGGCAGACCGGGAAAAG 59.686 55.000 6.32 0.00 39.70 2.27
420 683 4.448210 TCCGAACCTTAGATATGTTTGGC 58.552 43.478 0.00 0.00 41.42 4.52
450 713 2.912956 TGTGCCCTAACCTTTCTGATCT 59.087 45.455 0.00 0.00 0.00 2.75
454 717 2.859165 TCTGTGCCCTAACCTTTCTG 57.141 50.000 0.00 0.00 0.00 3.02
468 731 4.768968 ACCTCCAAATTCCTGAAATCTGTG 59.231 41.667 0.00 0.00 0.00 3.66
481 744 3.833559 ATGAACCCTCACCTCCAAATT 57.166 42.857 0.00 0.00 33.30 1.82
526 789 6.166984 TGAGAGTGAAGTCTGAAATGAACT 57.833 37.500 0.00 0.00 0.00 3.01
527 790 6.481644 AGTTGAGAGTGAAGTCTGAAATGAAC 59.518 38.462 0.00 0.00 0.00 3.18
547 810 5.198207 TCATACTCCGAACCTCATAGTTGA 58.802 41.667 0.00 0.00 0.00 3.18
548 811 5.515797 TCATACTCCGAACCTCATAGTTG 57.484 43.478 0.00 0.00 0.00 3.16
549 812 6.732896 AATCATACTCCGAACCTCATAGTT 57.267 37.500 0.00 0.00 0.00 2.24
550 813 7.506261 ACTTAATCATACTCCGAACCTCATAGT 59.494 37.037 0.00 0.00 0.00 2.12
551 814 7.887381 ACTTAATCATACTCCGAACCTCATAG 58.113 38.462 0.00 0.00 0.00 2.23
552 815 7.834881 ACTTAATCATACTCCGAACCTCATA 57.165 36.000 0.00 0.00 0.00 2.15
553 816 6.732896 ACTTAATCATACTCCGAACCTCAT 57.267 37.500 0.00 0.00 0.00 2.90
554 817 6.540438 AACTTAATCATACTCCGAACCTCA 57.460 37.500 0.00 0.00 0.00 3.86
555 818 9.843334 CTATAACTTAATCATACTCCGAACCTC 57.157 37.037 0.00 0.00 0.00 3.85
556 819 8.804204 CCTATAACTTAATCATACTCCGAACCT 58.196 37.037 0.00 0.00 0.00 3.50
557 820 7.544915 GCCTATAACTTAATCATACTCCGAACC 59.455 40.741 0.00 0.00 0.00 3.62
558 821 8.305317 AGCCTATAACTTAATCATACTCCGAAC 58.695 37.037 0.00 0.00 0.00 3.95
559 822 8.304596 CAGCCTATAACTTAATCATACTCCGAA 58.695 37.037 0.00 0.00 0.00 4.30
560 823 7.577046 GCAGCCTATAACTTAATCATACTCCGA 60.577 40.741 0.00 0.00 0.00 4.55
561 824 6.531948 GCAGCCTATAACTTAATCATACTCCG 59.468 42.308 0.00 0.00 0.00 4.63
568 831 4.808895 CACACGCAGCCTATAACTTAATCA 59.191 41.667 0.00 0.00 0.00 2.57
581 844 2.182614 ATAAACGCACACACGCAGCC 62.183 55.000 0.00 0.00 36.19 4.85
583 846 2.473868 CCTTATAAACGCACACACGCAG 60.474 50.000 0.00 0.00 36.19 5.18
586 849 3.615056 TCATCCTTATAAACGCACACACG 59.385 43.478 0.00 0.00 39.50 4.49
593 856 3.621268 TGCACACTCATCCTTATAAACGC 59.379 43.478 0.00 0.00 0.00 4.84
602 865 1.339438 GGACACATGCACACTCATCCT 60.339 52.381 0.00 0.00 0.00 3.24
603 866 1.089920 GGACACATGCACACTCATCC 58.910 55.000 0.00 0.00 0.00 3.51
609 872 4.253685 ACATAGTAAGGACACATGCACAC 58.746 43.478 0.00 0.00 0.00 3.82
676 939 8.035984 TGTCGTGTAAATACTGGTGATCAAATA 58.964 33.333 0.00 0.00 0.00 1.40
707 970 5.535333 CCTTTGTTCATCAAAAGATGCAGT 58.465 37.500 0.00 0.00 44.08 4.40
708 971 4.387862 GCCTTTGTTCATCAAAAGATGCAG 59.612 41.667 0.00 0.00 44.08 4.41
749 1013 4.171005 TCCGTCAGATTTAAACAGCGTAG 58.829 43.478 0.00 0.00 0.00 3.51
1064 1333 0.175760 CTTCTCGGATCCAAAGGCGA 59.824 55.000 13.41 0.70 0.00 5.54
1068 1337 1.432270 GCGGCTTCTCGGATCCAAAG 61.432 60.000 13.41 12.65 0.00 2.77
1224 1493 2.046023 CTGATGCCGGCCTTGTCA 60.046 61.111 26.77 20.46 0.00 3.58
1232 1501 0.250038 CATCTGGTACCTGATGCCGG 60.250 60.000 35.06 20.18 42.41 6.13
1373 1642 3.110178 GAGTGTACACGCACCGCC 61.110 66.667 22.84 3.98 40.04 6.13
1388 1657 1.334992 CGTCCTGTTACGTGCACGAG 61.335 60.000 42.94 28.82 43.02 4.18
1389 1658 1.370778 CGTCCTGTTACGTGCACGA 60.371 57.895 42.94 24.54 43.02 4.35
1400 1669 3.864983 ATGACCACCCCCGTCCTGT 62.865 63.158 0.00 0.00 0.00 4.00
1473 1743 8.063200 TGATGTAGTTGTACAGTAGTATGCTT 57.937 34.615 0.00 0.00 42.53 3.91
1477 1747 8.007405 TGCATGATGTAGTTGTACAGTAGTAT 57.993 34.615 0.00 0.00 42.53 2.12
1594 1869 6.099341 ACTCAAGGCTTACACAAAAACTTTG 58.901 36.000 0.00 0.00 0.00 2.77
1627 1902 5.468409 TGACGATCAAACATACACACACATT 59.532 36.000 0.00 0.00 0.00 2.71
1631 1906 4.391523 CCATGACGATCAAACATACACACA 59.608 41.667 0.00 0.00 0.00 3.72
1644 1931 8.534333 TTTATAGATAAAGCACCATGACGATC 57.466 34.615 0.00 0.00 0.00 3.69
1645 1932 8.774586 GTTTTATAGATAAAGCACCATGACGAT 58.225 33.333 0.00 0.00 34.75 3.73
1646 1933 7.225931 GGTTTTATAGATAAAGCACCATGACGA 59.774 37.037 9.99 0.00 35.06 4.20
1647 1934 7.352739 GGTTTTATAGATAAAGCACCATGACG 58.647 38.462 9.99 0.00 35.06 4.35
1648 1935 7.352739 CGGTTTTATAGATAAAGCACCATGAC 58.647 38.462 12.91 1.14 34.82 3.06
1649 1936 6.485313 CCGGTTTTATAGATAAAGCACCATGA 59.515 38.462 12.91 0.00 34.82 3.07
1650 1937 6.293955 CCCGGTTTTATAGATAAAGCACCATG 60.294 42.308 0.00 0.00 34.82 3.66
1651 1938 5.768164 CCCGGTTTTATAGATAAAGCACCAT 59.232 40.000 0.00 0.00 34.82 3.55
1652 1939 5.127491 CCCGGTTTTATAGATAAAGCACCA 58.873 41.667 0.00 0.00 34.82 4.17
1653 1940 4.023450 GCCCGGTTTTATAGATAAAGCACC 60.023 45.833 0.00 7.95 35.84 5.01
1654 1941 4.319261 CGCCCGGTTTTATAGATAAAGCAC 60.319 45.833 0.00 1.39 35.84 4.40
1655 1942 3.810941 CGCCCGGTTTTATAGATAAAGCA 59.189 43.478 0.00 0.00 35.84 3.91
1656 1943 4.060205 TCGCCCGGTTTTATAGATAAAGC 58.940 43.478 0.00 1.43 34.13 3.51
1657 1944 6.607735 TTTCGCCCGGTTTTATAGATAAAG 57.392 37.500 0.00 0.00 34.13 1.85
1658 1945 5.007921 GCTTTCGCCCGGTTTTATAGATAAA 59.992 40.000 0.00 0.00 0.00 1.40
1659 1946 4.512571 GCTTTCGCCCGGTTTTATAGATAA 59.487 41.667 0.00 0.00 0.00 1.75
1660 1947 4.060205 GCTTTCGCCCGGTTTTATAGATA 58.940 43.478 0.00 0.00 0.00 1.98
1661 1948 2.876550 GCTTTCGCCCGGTTTTATAGAT 59.123 45.455 0.00 0.00 0.00 1.98
1662 1949 2.282407 GCTTTCGCCCGGTTTTATAGA 58.718 47.619 0.00 0.00 0.00 1.98
1663 1950 2.750301 GCTTTCGCCCGGTTTTATAG 57.250 50.000 0.00 0.00 0.00 1.31
1677 1964 4.489679 AAACATCTCGAAACAGGCTTTC 57.510 40.909 0.00 0.00 0.00 2.62
1678 1965 6.206634 TGATTAAACATCTCGAAACAGGCTTT 59.793 34.615 0.00 0.00 0.00 3.51
1679 1966 5.705441 TGATTAAACATCTCGAAACAGGCTT 59.295 36.000 0.00 0.00 0.00 4.35
1680 1967 5.245531 TGATTAAACATCTCGAAACAGGCT 58.754 37.500 0.00 0.00 0.00 4.58
1681 1968 5.545658 TGATTAAACATCTCGAAACAGGC 57.454 39.130 0.00 0.00 0.00 4.85
1682 1969 6.316140 TGGATGATTAAACATCTCGAAACAGG 59.684 38.462 20.96 0.00 44.02 4.00
1683 1970 7.278646 TCTGGATGATTAAACATCTCGAAACAG 59.721 37.037 20.96 17.74 44.02 3.16
1684 1971 7.102993 TCTGGATGATTAAACATCTCGAAACA 58.897 34.615 20.96 11.05 44.02 2.83
1685 1972 7.539712 TCTGGATGATTAAACATCTCGAAAC 57.460 36.000 20.96 7.70 44.02 2.78
1686 1973 7.201644 GCTTCTGGATGATTAAACATCTCGAAA 60.202 37.037 20.96 11.76 44.02 3.46
1687 1974 6.258727 GCTTCTGGATGATTAAACATCTCGAA 59.741 38.462 20.96 19.78 44.02 3.71
1688 1975 5.755375 GCTTCTGGATGATTAAACATCTCGA 59.245 40.000 20.96 15.45 44.02 4.04
1689 1976 5.525012 TGCTTCTGGATGATTAAACATCTCG 59.475 40.000 20.96 13.87 44.02 4.04
1690 1977 6.541641 AGTGCTTCTGGATGATTAAACATCTC 59.458 38.462 20.96 13.55 44.02 2.75
1691 1978 6.421485 AGTGCTTCTGGATGATTAAACATCT 58.579 36.000 20.96 0.44 44.02 2.90
1692 1979 6.541641 AGAGTGCTTCTGGATGATTAAACATC 59.458 38.462 15.40 15.40 43.88 3.06
1693 1980 6.421485 AGAGTGCTTCTGGATGATTAAACAT 58.579 36.000 0.00 0.00 33.93 2.71
1694 1981 5.809001 AGAGTGCTTCTGGATGATTAAACA 58.191 37.500 0.00 0.00 33.93 2.83
1695 1982 6.749923 AAGAGTGCTTCTGGATGATTAAAC 57.250 37.500 0.00 0.00 35.91 2.01
1696 1983 7.231317 ACAAAAGAGTGCTTCTGGATGATTAAA 59.769 33.333 0.00 0.00 35.91 1.52
1697 1984 6.716628 ACAAAAGAGTGCTTCTGGATGATTAA 59.283 34.615 0.00 0.00 35.91 1.40
1698 1985 6.149973 CACAAAAGAGTGCTTCTGGATGATTA 59.850 38.462 0.00 0.00 35.91 1.75
1699 1986 5.048224 CACAAAAGAGTGCTTCTGGATGATT 60.048 40.000 0.00 0.00 35.91 2.57
1751 2038 2.292016 CTCATGCACACACCCGTAAAAA 59.708 45.455 0.00 0.00 0.00 1.94
1752 2039 1.876799 CTCATGCACACACCCGTAAAA 59.123 47.619 0.00 0.00 0.00 1.52
1753 2040 1.202710 ACTCATGCACACACCCGTAAA 60.203 47.619 0.00 0.00 0.00 2.01
1754 2041 0.394938 ACTCATGCACACACCCGTAA 59.605 50.000 0.00 0.00 0.00 3.18
1755 2042 0.320334 CACTCATGCACACACCCGTA 60.320 55.000 0.00 0.00 0.00 4.02
1756 2043 1.597854 CACTCATGCACACACCCGT 60.598 57.895 0.00 0.00 0.00 5.28
1757 2044 1.165907 AACACTCATGCACACACCCG 61.166 55.000 0.00 0.00 0.00 5.28
1758 2045 0.311790 CAACACTCATGCACACACCC 59.688 55.000 0.00 0.00 0.00 4.61
1759 2046 1.308047 TCAACACTCATGCACACACC 58.692 50.000 0.00 0.00 0.00 4.16
1760 2047 2.549329 TGATCAACACTCATGCACACAC 59.451 45.455 0.00 0.00 0.00 3.82
1785 2072 2.127118 GCGCTCATGCACACACAC 60.127 61.111 0.00 0.00 39.64 3.82
1856 2363 3.745975 TGCATGTACTAGTTGAACACTGC 59.254 43.478 0.00 11.49 35.97 4.40
1891 2401 3.460103 TCAACAACCAACTCTAACCGTC 58.540 45.455 0.00 0.00 0.00 4.79
1904 2414 9.581099 AATTCGATGGTTATTTTATCAACAACC 57.419 29.630 0.00 0.00 39.28 3.77
2014 2527 6.989659 ACAACGGTAGATAACATACATAGGG 58.010 40.000 0.00 0.00 0.00 3.53
2023 2536 5.525745 CCAATGCATACAACGGTAGATAACA 59.474 40.000 0.00 0.00 31.88 2.41
2032 2545 3.648009 ACAAAACCAATGCATACAACGG 58.352 40.909 0.00 0.00 0.00 4.44
2107 2620 1.303561 TCCTTGACCACCTGCATGC 60.304 57.895 11.82 11.82 0.00 4.06
2108 2621 1.310933 GCTCCTTGACCACCTGCATG 61.311 60.000 0.00 0.00 0.00 4.06
2109 2622 1.001641 GCTCCTTGACCACCTGCAT 60.002 57.895 0.00 0.00 0.00 3.96
2110 2623 2.431683 GCTCCTTGACCACCTGCA 59.568 61.111 0.00 0.00 0.00 4.41
2161 2674 1.207329 GCGAGGAAGTGGGTGTTATCT 59.793 52.381 0.00 0.00 0.00 1.98
2182 2695 1.196808 CACACTGGAACCATGCGTAAC 59.803 52.381 0.00 0.00 0.00 2.50
2262 2805 3.424703 AGTGGCTAAGATGCACACAATT 58.575 40.909 0.00 0.00 36.94 2.32
2275 2818 8.699130 CCATACATCATATCTATGAGTGGCTAA 58.301 37.037 6.12 0.00 45.01 3.09


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

AutoCloner maintained by Alex Coulton.