Multiple sequence alignment - TraesCS3D01G331900

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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 TraesCS3D01G331900 chr3D 100.000 3627 0 0 1 3627 444061289 444057663 0.000000e+00 6698.0
1 TraesCS3D01G331900 chr3D 96.774 62 2 0 2431 2492 444058799 444058738 1.780000e-18 104.0
2 TraesCS3D01G331900 chr3D 96.774 62 2 0 2491 2552 444058859 444058798 1.780000e-18 104.0
3 TraesCS3D01G331900 chr3A 90.502 3685 195 67 1 3627 585024339 585020752 0.000000e+00 4723.0
4 TraesCS3D01G331900 chr3A 100.000 62 0 0 2491 2552 585021970 585021909 8.230000e-22 115.0
5 TraesCS3D01G331900 chr3A 97.959 49 1 0 3307 3355 585021110 585021062 6.450000e-13 86.1
6 TraesCS3D01G331900 chr3B 90.126 2147 132 36 1516 3627 581965295 581963194 0.000000e+00 2717.0
7 TraesCS3D01G331900 chr3B 96.471 680 20 4 786 1464 581965979 581965303 0.000000e+00 1120.0
8 TraesCS3D01G331900 chr3B 91.980 611 24 7 4 603 581966950 581966354 0.000000e+00 833.0
9 TraesCS3D01G331900 chr3B 96.774 62 2 0 2431 2492 581964359 581964298 1.780000e-18 104.0
10 TraesCS3D01G331900 chr3B 95.161 62 3 0 2491 2552 581964419 581964358 8.290000e-17 99.0


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 TraesCS3D01G331900 chr3D 444057663 444061289 3626 True 2302.000000 6698 97.849333 1 3627 3 chr3D.!!$R1 3626
1 TraesCS3D01G331900 chr3A 585020752 585024339 3587 True 1641.366667 4723 96.153667 1 3627 3 chr3A.!!$R1 3626
2 TraesCS3D01G331900 chr3B 581963194 581966950 3756 True 974.600000 2717 94.102400 4 3627 5 chr3B.!!$R1 3623

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
701 840 1.704628 TGAAGTGAATGCCCTTGAGGA 59.295 47.619 0.0 0.0 38.24 3.71 F
1440 1655 0.687354 ACACGCATGGACTCTTCCTT 59.313 50.000 0.0 0.0 43.31 3.36 F
2413 2652 0.107703 CCGCAGTGGAAGAAGCCATA 60.108 55.000 0.0 0.0 42.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2193 0.037303 ACAGTTGAGTCCCCTGCATG 59.963 55.000 6.16 0.0 0.00 4.06 R
2417 2656 0.893447 GCCTTCAGTACAGGTACGGT 59.107 55.000 9.06 0.0 40.80 4.83 R
3440 3725 1.075482 CCCTCCACATGGTGTGCTT 59.925 57.895 4.60 0.0 46.51 3.91 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
697 836 2.821378 TGTCATGAAGTGAATGCCCTTG 59.179 45.455 0.00 0.00 38.90 3.61
701 840 1.704628 TGAAGTGAATGCCCTTGAGGA 59.295 47.619 0.00 0.00 38.24 3.71
722 869 9.474920 TGAGGATTTAAACATTTTAGTTGCTTG 57.525 29.630 0.00 0.00 0.00 4.01
743 894 6.479001 GCTTGATAAAATACTACTCGCCTGAA 59.521 38.462 0.00 0.00 0.00 3.02
749 900 5.455056 AATACTACTCGCCTGAACCATAG 57.545 43.478 0.00 0.00 0.00 2.23
752 903 4.471548 ACTACTCGCCTGAACCATAGTAT 58.528 43.478 0.00 0.00 0.00 2.12
754 905 6.066690 ACTACTCGCCTGAACCATAGTATTA 58.933 40.000 0.00 0.00 0.00 0.98
755 906 5.864418 ACTCGCCTGAACCATAGTATTAA 57.136 39.130 0.00 0.00 0.00 1.40
756 907 6.420913 ACTCGCCTGAACCATAGTATTAAT 57.579 37.500 0.00 0.00 0.00 1.40
757 908 6.827727 ACTCGCCTGAACCATAGTATTAATT 58.172 36.000 0.00 0.00 0.00 1.40
758 909 6.706270 ACTCGCCTGAACCATAGTATTAATTG 59.294 38.462 0.00 0.00 0.00 2.32
824 1038 9.959721 TTTTACTAGAAATGTTGCCTTAGATCT 57.040 29.630 0.00 0.00 0.00 2.75
878 1092 7.879677 TGCACCTATTTCTATCATATGGTCTTG 59.120 37.037 2.13 0.00 0.00 3.02
919 1133 4.495565 TCTAGGGTGTGGTCCTTAAGAAA 58.504 43.478 3.36 0.00 35.92 2.52
925 1139 4.700692 GGTGTGGTCCTTAAGAAATCCTTC 59.299 45.833 3.36 0.76 36.34 3.46
1207 1422 2.467838 CTGAGGTGATGCGTGTCTATG 58.532 52.381 0.00 0.00 0.00 2.23
1304 1519 2.198827 TCGGCTGATGATTTGGTTGT 57.801 45.000 0.00 0.00 0.00 3.32
1318 1533 7.776107 TGATTTGGTTGTTATTGACACTGAAA 58.224 30.769 0.00 0.00 38.18 2.69
1391 1606 8.198807 ACTGGAAATTCAGAGAATGGAAATTT 57.801 30.769 1.40 0.00 38.11 1.82
1440 1655 0.687354 ACACGCATGGACTCTTCCTT 59.313 50.000 0.00 0.00 43.31 3.36
1459 1674 9.373450 TCTTCCTTATCTGTCTTATCTTGCTAT 57.627 33.333 0.00 0.00 0.00 2.97
1463 1678 9.729023 CCTTATCTGTCTTATCTTGCTATATCG 57.271 37.037 0.00 0.00 0.00 2.92
1466 1681 7.745620 TCTGTCTTATCTTGCTATATCGTCA 57.254 36.000 0.00 0.00 0.00 4.35
1468 1683 7.661847 TCTGTCTTATCTTGCTATATCGTCAGA 59.338 37.037 0.00 0.00 0.00 3.27
1469 1684 7.811653 TGTCTTATCTTGCTATATCGTCAGAG 58.188 38.462 0.00 0.00 0.00 3.35
1471 1686 7.748683 GTCTTATCTTGCTATATCGTCAGAGTG 59.251 40.741 0.00 0.00 0.00 3.51
1473 1688 5.836821 TCTTGCTATATCGTCAGAGTGTT 57.163 39.130 0.00 0.00 0.00 3.32
1474 1689 6.208988 TCTTGCTATATCGTCAGAGTGTTT 57.791 37.500 0.00 0.00 0.00 2.83
1475 1690 6.036470 TCTTGCTATATCGTCAGAGTGTTTG 58.964 40.000 0.00 0.00 0.00 2.93
1477 1692 5.720202 TGCTATATCGTCAGAGTGTTTGTT 58.280 37.500 0.00 0.00 0.00 2.83
1482 1697 5.560966 ATCGTCAGAGTGTTTGTTTTGTT 57.439 34.783 0.00 0.00 0.00 2.83
1489 1704 8.798153 GTCAGAGTGTTTGTTTTGTTATCTTTG 58.202 33.333 0.00 0.00 0.00 2.77
1491 1706 9.781834 CAGAGTGTTTGTTTTGTTATCTTTGTA 57.218 29.630 0.00 0.00 0.00 2.41
1520 1746 2.751166 TTGTCAGTAAGCCAGCTCTC 57.249 50.000 0.00 0.00 0.00 3.20
1524 1750 1.483827 TCAGTAAGCCAGCTCTCCATG 59.516 52.381 0.00 0.00 0.00 3.66
1538 1764 5.587844 AGCTCTCCATGTAAAAATGTGCTAG 59.412 40.000 0.00 0.00 0.00 3.42
1541 1767 7.362056 GCTCTCCATGTAAAAATGTGCTAGAAA 60.362 37.037 0.00 0.00 0.00 2.52
1555 1781 4.153475 GTGCTAGAAATGTTGGACGCTTAA 59.847 41.667 0.00 0.00 0.00 1.85
1561 1787 7.637709 AGAAATGTTGGACGCTTAATTTTTC 57.362 32.000 0.00 0.00 0.00 2.29
1563 1789 7.872483 AGAAATGTTGGACGCTTAATTTTTCAT 59.128 29.630 0.00 0.00 0.00 2.57
1568 1794 9.944663 TGTTGGACGCTTAATTTTTCATATATC 57.055 29.630 0.00 0.00 0.00 1.63
1569 1795 9.944663 GTTGGACGCTTAATTTTTCATATATCA 57.055 29.630 0.00 0.00 0.00 2.15
1627 1856 9.362151 CCATTTAGGATTTTGGGTAGCTAAATA 57.638 33.333 4.20 0.00 41.22 1.40
1644 1873 8.202745 AGCTAAATATTATTCCGCTCTTATGC 57.797 34.615 6.59 0.00 0.00 3.14
1688 1917 5.215252 TGTTAGGAGGTATCATAGCTTGC 57.785 43.478 0.00 0.00 36.51 4.01
1690 1919 2.983296 AGGAGGTATCATAGCTTGCCT 58.017 47.619 0.00 0.00 36.51 4.75
1695 1924 4.860022 AGGTATCATAGCTTGCCTTTGTT 58.140 39.130 0.00 0.00 31.36 2.83
1697 1926 5.716703 AGGTATCATAGCTTGCCTTTGTTTT 59.283 36.000 0.00 0.00 31.36 2.43
1720 1949 9.482627 TTTTGGTAAATTGATTGTGTTGATACC 57.517 29.630 0.00 0.00 0.00 2.73
1722 1951 7.825681 TGGTAAATTGATTGTGTTGATACCAG 58.174 34.615 0.00 0.00 36.32 4.00
1723 1952 7.450014 TGGTAAATTGATTGTGTTGATACCAGT 59.550 33.333 0.00 0.00 36.32 4.00
1725 1954 9.128107 GTAAATTGATTGTGTTGATACCAGTTG 57.872 33.333 0.00 0.00 0.00 3.16
1726 1955 6.899393 ATTGATTGTGTTGATACCAGTTGT 57.101 33.333 0.00 0.00 0.00 3.32
1727 1956 5.687770 TGATTGTGTTGATACCAGTTGTG 57.312 39.130 0.00 0.00 0.00 3.33
1728 1957 5.372373 TGATTGTGTTGATACCAGTTGTGA 58.628 37.500 0.00 0.00 0.00 3.58
1729 1958 5.825151 TGATTGTGTTGATACCAGTTGTGAA 59.175 36.000 0.00 0.00 0.00 3.18
1767 1996 7.878477 TTTGTTTGAATTGATCTGAGAATGC 57.122 32.000 0.00 0.00 0.00 3.56
1771 2000 6.432607 TTGAATTGATCTGAGAATGCTGTC 57.567 37.500 0.00 0.00 0.00 3.51
1772 2001 4.880120 TGAATTGATCTGAGAATGCTGTCC 59.120 41.667 0.00 0.00 0.00 4.02
1773 2002 3.986996 TTGATCTGAGAATGCTGTCCA 57.013 42.857 0.00 0.00 0.00 4.02
1786 2020 2.892852 TGCTGTCCATTCTTTTCCCTTG 59.107 45.455 0.00 0.00 0.00 3.61
1793 2027 6.183360 TGTCCATTCTTTTCCCTTGTTTCTTC 60.183 38.462 0.00 0.00 0.00 2.87
1794 2028 5.009610 TCCATTCTTTTCCCTTGTTTCTTCG 59.990 40.000 0.00 0.00 0.00 3.79
1798 2032 6.796705 TCTTTTCCCTTGTTTCTTCGTATC 57.203 37.500 0.00 0.00 0.00 2.24
1801 2035 6.796705 TTTCCCTTGTTTCTTCGTATCTTC 57.203 37.500 0.00 0.00 0.00 2.87
1805 2039 6.014499 TCCCTTGTTTCTTCGTATCTTCTTCT 60.014 38.462 0.00 0.00 0.00 2.85
1825 2059 9.691362 TTCTTCTTTCATTATTAAACCAACTGC 57.309 29.630 0.00 0.00 0.00 4.40
1828 2062 8.402798 TCTTTCATTATTAAACCAACTGCTGA 57.597 30.769 0.00 0.00 0.00 4.26
1837 2071 7.994425 TTAAACCAACTGCTGATCTGAATTA 57.006 32.000 3.42 0.00 0.00 1.40
1844 2078 7.487189 CCAACTGCTGATCTGAATTATGAAAAC 59.513 37.037 3.42 0.00 0.00 2.43
1859 2093 8.594881 ATTATGAAAACGAGTATGACCTCATC 57.405 34.615 0.00 0.00 37.76 2.92
1861 2095 4.157105 TGAAAACGAGTATGACCTCATCGA 59.843 41.667 4.27 0.00 37.76 3.59
1863 2097 1.604755 ACGAGTATGACCTCATCGAGC 59.395 52.381 4.27 0.00 37.76 5.03
1872 2106 4.281941 ATGACCTCATCGAGCTATTGCTTA 59.718 41.667 2.44 0.00 40.26 3.09
1873 2107 5.046735 ATGACCTCATCGAGCTATTGCTTAT 60.047 40.000 2.44 0.00 40.26 1.73
1874 2108 6.848364 ATGACCTCATCGAGCTATTGCTTATC 60.848 42.308 2.44 0.00 40.26 1.75
1875 2109 8.932790 ATGACCTCATCGAGCTATTGCTTATCT 61.933 40.741 2.44 0.00 40.26 1.98
1921 2155 7.334421 TGTGAAATGTTCTATTCTCTACTTGGC 59.666 37.037 0.00 0.00 0.00 4.52
1924 2158 6.798427 ATGTTCTATTCTCTACTTGGCTGA 57.202 37.500 0.00 0.00 0.00 4.26
1925 2159 5.967088 TGTTCTATTCTCTACTTGGCTGAC 58.033 41.667 0.00 0.00 0.00 3.51
1926 2160 5.105310 TGTTCTATTCTCTACTTGGCTGACC 60.105 44.000 0.00 0.00 0.00 4.02
1943 2177 7.517320 TGGCTGACCATATAGTGATTTGTAAT 58.483 34.615 0.00 0.00 42.67 1.89
1944 2178 8.655901 TGGCTGACCATATAGTGATTTGTAATA 58.344 33.333 0.00 0.00 42.67 0.98
1945 2179 9.502091 GGCTGACCATATAGTGATTTGTAATAA 57.498 33.333 0.00 0.00 35.26 1.40
1987 2223 2.945668 GACTCAACTGTTGGTTTCTGCT 59.054 45.455 19.55 0.00 35.74 4.24
2031 2267 3.255642 CGGGGAATTGTGACAAAGTTGAT 59.744 43.478 0.62 0.00 0.00 2.57
2251 2490 6.153510 GCAAAAGAGATAAGAAACCTTCCCAT 59.846 38.462 0.00 0.00 0.00 4.00
2280 2519 0.613853 AATGGTGGCAGCAGCAGAAT 60.614 50.000 24.68 3.83 44.61 2.40
2413 2652 0.107703 CCGCAGTGGAAGAAGCCATA 60.108 55.000 0.00 0.00 42.00 2.74
2416 2655 1.065126 GCAGTGGAAGAAGCCATACCT 60.065 52.381 0.00 0.00 40.68 3.08
2417 2656 2.170607 GCAGTGGAAGAAGCCATACCTA 59.829 50.000 0.00 0.00 40.68 3.08
2665 2905 2.006772 CGCTATTCACAGGCGTTCC 58.993 57.895 0.00 0.00 43.28 3.62
2699 2939 1.188863 AGGCTTTCATGTTGGATGGC 58.811 50.000 0.00 0.00 0.00 4.40
2738 2979 2.571212 TGTTTGGACATCAGTGGACAC 58.429 47.619 0.00 0.00 0.00 3.67
2770 3011 5.643379 AATTCTTTGGTTGACGTATGCAT 57.357 34.783 3.79 3.79 0.00 3.96
2796 3038 9.793259 TGACCTTGAGATTATTAACTGTCTTTT 57.207 29.630 0.00 0.00 0.00 2.27
2989 3232 4.434545 ACTGATTCCTTCATGGATCAGG 57.565 45.455 12.62 10.07 44.94 3.86
2995 3238 4.712051 TCCTTCATGGATCAGGTAATGG 57.288 45.455 0.00 0.00 40.56 3.16
3028 3271 3.366052 AACACATGGAGGGATGTAACC 57.634 47.619 0.00 0.00 34.69 2.85
3107 3360 7.810658 ACACAACATTTCAGTAATCTTAGCTG 58.189 34.615 0.00 0.00 0.00 4.24
3169 3447 1.200252 ACTGTCTCCATCGACACGAAG 59.800 52.381 0.00 0.00 39.99 3.79
3230 3508 1.278238 CCTACGATCGTTGCTTCCAC 58.722 55.000 27.88 0.00 0.00 4.02
3370 3654 2.093306 TGTTTCAGTATGCCGACCTG 57.907 50.000 0.00 0.00 34.76 4.00
3462 3754 4.402851 CACCATGTGGAGGGTGTG 57.597 61.111 5.96 0.00 46.95 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
411 426 2.027192 ACACAGACACAGACACCAAACT 60.027 45.455 0.00 0.00 0.00 2.66
539 556 7.136822 ACTGGCATATTTTCACATAGGAGTA 57.863 36.000 0.00 0.00 0.00 2.59
540 557 6.006275 ACTGGCATATTTTCACATAGGAGT 57.994 37.500 0.00 0.00 0.00 3.85
541 558 6.949352 AACTGGCATATTTTCACATAGGAG 57.051 37.500 0.00 0.00 0.00 3.69
542 559 8.052748 AGTAAACTGGCATATTTTCACATAGGA 58.947 33.333 2.63 0.00 0.00 2.94
543 560 8.225603 AGTAAACTGGCATATTTTCACATAGG 57.774 34.615 2.63 0.00 0.00 2.57
544 561 9.113838 AGAGTAAACTGGCATATTTTCACATAG 57.886 33.333 2.63 0.00 0.00 2.23
613 630 8.880878 TCGAAAGAATCATAATTCCATCGTTA 57.119 30.769 11.36 0.00 43.66 3.18
673 812 5.057843 AGGGCATTCACTTCATGACATAT 57.942 39.130 0.00 0.00 36.92 1.78
677 816 3.084039 TCAAGGGCATTCACTTCATGAC 58.916 45.455 0.00 0.00 36.92 3.06
683 822 3.463048 AATCCTCAAGGGCATTCACTT 57.537 42.857 0.00 0.00 35.41 3.16
697 836 9.691362 TCAAGCAACTAAAATGTTTAAATCCTC 57.309 29.630 0.00 0.00 0.00 3.71
722 869 6.278363 TGGTTCAGGCGAGTAGTATTTTATC 58.722 40.000 0.00 0.00 0.00 1.75
743 894 8.677148 AAATCAGCGACAATTAATACTATGGT 57.323 30.769 0.00 0.00 0.00 3.55
749 900 7.406553 TGCACTAAATCAGCGACAATTAATAC 58.593 34.615 0.00 0.00 0.00 1.89
752 903 5.871465 TGCACTAAATCAGCGACAATTAA 57.129 34.783 0.00 0.00 0.00 1.40
754 905 4.023279 TGTTGCACTAAATCAGCGACAATT 60.023 37.500 4.37 0.00 46.48 2.32
755 906 3.501828 TGTTGCACTAAATCAGCGACAAT 59.498 39.130 4.37 0.00 46.48 2.71
756 907 2.875317 TGTTGCACTAAATCAGCGACAA 59.125 40.909 4.37 0.00 46.48 3.18
758 909 3.536158 TTGTTGCACTAAATCAGCGAC 57.464 42.857 0.00 0.00 41.84 5.19
802 1016 9.553064 CATTAGATCTAAGGCAACATTTCTAGT 57.447 33.333 19.51 0.00 41.41 2.57
887 1101 6.334774 AGGACCACACCCTAGATTACTAGATA 59.665 42.308 0.00 0.00 46.34 1.98
989 1204 1.524621 CCGCCCATCCACAAGCTAG 60.525 63.158 0.00 0.00 0.00 3.42
1207 1422 6.985059 TCTGTCTCTTCATCATCATTGTCATC 59.015 38.462 0.00 0.00 0.00 2.92
1304 1519 6.128309 CGATGTGACCATTTCAGTGTCAATAA 60.128 38.462 0.00 0.00 40.41 1.40
1318 1533 0.615331 AAGGCTGACGATGTGACCAT 59.385 50.000 0.00 0.00 0.00 3.55
1391 1606 8.243426 GCAATCAAATACTTACATTGGTTGAGA 58.757 33.333 13.26 0.00 44.18 3.27
1440 1655 9.449719 TGACGATATAGCAAGATAAGACAGATA 57.550 33.333 0.00 0.00 0.00 1.98
1459 1674 6.671614 AACAAAACAAACACTCTGACGATA 57.328 33.333 0.00 0.00 0.00 2.92
1460 1675 5.560966 AACAAAACAAACACTCTGACGAT 57.439 34.783 0.00 0.00 0.00 3.73
1461 1676 6.537301 AGATAACAAAACAAACACTCTGACGA 59.463 34.615 0.00 0.00 0.00 4.20
1462 1677 6.715464 AGATAACAAAACAAACACTCTGACG 58.285 36.000 0.00 0.00 0.00 4.35
1463 1678 8.798153 CAAAGATAACAAAACAAACACTCTGAC 58.202 33.333 0.00 0.00 0.00 3.51
1464 1679 8.519526 ACAAAGATAACAAAACAAACACTCTGA 58.480 29.630 0.00 0.00 0.00 3.27
1465 1680 8.687824 ACAAAGATAACAAAACAAACACTCTG 57.312 30.769 0.00 0.00 0.00 3.35
1466 1681 9.783256 GTACAAAGATAACAAAACAAACACTCT 57.217 29.630 0.00 0.00 0.00 3.24
1468 1683 8.524487 TGGTACAAAGATAACAAAACAAACACT 58.476 29.630 0.00 0.00 31.92 3.55
1469 1684 8.690680 TGGTACAAAGATAACAAAACAAACAC 57.309 30.769 0.00 0.00 31.92 3.32
1489 1704 7.822658 TGGCTTACTGACAAATATTTTGGTAC 58.177 34.615 0.00 0.00 0.00 3.34
1491 1706 6.572314 GCTGGCTTACTGACAAATATTTTGGT 60.572 38.462 0.00 0.00 30.26 3.67
1498 1713 4.383118 GGAGAGCTGGCTTACTGACAAATA 60.383 45.833 0.00 0.00 30.26 1.40
1499 1714 3.604582 GAGAGCTGGCTTACTGACAAAT 58.395 45.455 0.00 0.00 30.26 2.32
1500 1715 2.289694 GGAGAGCTGGCTTACTGACAAA 60.290 50.000 0.00 0.00 30.26 2.83
1504 1719 1.483827 CATGGAGAGCTGGCTTACTGA 59.516 52.381 0.00 0.00 0.00 3.41
1507 1722 3.543680 TTACATGGAGAGCTGGCTTAC 57.456 47.619 0.00 0.00 0.00 2.34
1510 1725 3.439857 TTTTTACATGGAGAGCTGGCT 57.560 42.857 0.00 0.00 0.00 4.75
1520 1746 8.649841 CAACATTTCTAGCACATTTTTACATGG 58.350 33.333 0.00 0.00 0.00 3.66
1524 1750 7.060633 CGTCCAACATTTCTAGCACATTTTTAC 59.939 37.037 0.00 0.00 0.00 2.01
1538 1764 7.401484 TGAAAAATTAAGCGTCCAACATTTC 57.599 32.000 0.00 0.00 0.00 2.17
1598 1824 4.161377 GCTACCCAAAATCCTAAATGGCAA 59.839 41.667 0.00 0.00 35.26 4.52
1601 1827 7.654022 TTTAGCTACCCAAAATCCTAAATGG 57.346 36.000 0.00 0.00 37.10 3.16
1644 1873 2.737252 GGTAGAAAAAGGAGCAGTGACG 59.263 50.000 0.00 0.00 0.00 4.35
1645 1874 3.748568 CAGGTAGAAAAAGGAGCAGTGAC 59.251 47.826 0.00 0.00 0.00 3.67
1647 1876 3.744660 ACAGGTAGAAAAAGGAGCAGTG 58.255 45.455 0.00 0.00 0.00 3.66
1648 1877 4.439253 AACAGGTAGAAAAAGGAGCAGT 57.561 40.909 0.00 0.00 0.00 4.40
1688 1917 8.207521 ACACAATCAATTTACCAAAACAAAGG 57.792 30.769 0.00 0.00 0.00 3.11
1690 1919 9.219603 TCAACACAATCAATTTACCAAAACAAA 57.780 25.926 0.00 0.00 0.00 2.83
1695 1924 8.642432 TGGTATCAACACAATCAATTTACCAAA 58.358 29.630 0.00 0.00 35.03 3.28
1697 1926 7.450014 ACTGGTATCAACACAATCAATTTACCA 59.550 33.333 0.00 0.00 36.20 3.25
1727 1956 9.994432 ATTCAAACAAATATCGAAGATGACTTC 57.006 29.630 0.00 0.00 45.12 3.01
1729 1958 9.778993 CAATTCAAACAAATATCGAAGATGACT 57.221 29.630 0.00 0.00 45.12 3.41
1757 1986 4.564782 AAGAATGGACAGCATTCTCAGA 57.435 40.909 0.05 0.00 45.48 3.27
1759 1988 4.460382 GGAAAAGAATGGACAGCATTCTCA 59.540 41.667 0.05 0.00 45.48 3.27
1767 1996 5.302823 AGAAACAAGGGAAAAGAATGGACAG 59.697 40.000 0.00 0.00 0.00 3.51
1771 2000 5.221244 ACGAAGAAACAAGGGAAAAGAATGG 60.221 40.000 0.00 0.00 0.00 3.16
1772 2001 5.831997 ACGAAGAAACAAGGGAAAAGAATG 58.168 37.500 0.00 0.00 0.00 2.67
1773 2002 7.665974 AGATACGAAGAAACAAGGGAAAAGAAT 59.334 33.333 0.00 0.00 0.00 2.40
1776 2010 6.803154 AGATACGAAGAAACAAGGGAAAAG 57.197 37.500 0.00 0.00 0.00 2.27
1778 2012 6.531021 AGAAGATACGAAGAAACAAGGGAAA 58.469 36.000 0.00 0.00 0.00 3.13
1780 2014 5.740290 AGAAGATACGAAGAAACAAGGGA 57.260 39.130 0.00 0.00 0.00 4.20
1782 2016 7.659652 AAGAAGAAGATACGAAGAAACAAGG 57.340 36.000 0.00 0.00 0.00 3.61
1801 2035 9.132521 CAGCAGTTGGTTTAATAATGAAAGAAG 57.867 33.333 0.00 0.00 0.00 2.85
1805 2039 9.023962 AGATCAGCAGTTGGTTTAATAATGAAA 57.976 29.630 0.00 0.00 0.00 2.69
1815 2049 6.660521 TCATAATTCAGATCAGCAGTTGGTTT 59.339 34.615 0.00 0.00 0.00 3.27
1816 2050 6.182627 TCATAATTCAGATCAGCAGTTGGTT 58.817 36.000 0.00 0.00 0.00 3.67
1817 2051 5.748402 TCATAATTCAGATCAGCAGTTGGT 58.252 37.500 0.00 0.00 0.00 3.67
1819 2053 7.217636 CGTTTTCATAATTCAGATCAGCAGTTG 59.782 37.037 0.00 0.00 0.00 3.16
1820 2054 7.119699 TCGTTTTCATAATTCAGATCAGCAGTT 59.880 33.333 0.00 0.00 0.00 3.16
1828 2062 9.046296 GGTCATACTCGTTTTCATAATTCAGAT 57.954 33.333 0.00 0.00 0.00 2.90
1837 2071 5.043903 CGATGAGGTCATACTCGTTTTCAT 58.956 41.667 0.00 0.00 40.39 2.57
1844 2078 1.876799 AGCTCGATGAGGTCATACTCG 59.123 52.381 0.00 0.00 35.30 4.18
1882 2116 8.947055 AGAACATTTCACAAGCAAAATTACTT 57.053 26.923 0.00 0.00 0.00 2.24
1886 2120 9.768662 AGAATAGAACATTTCACAAGCAAAATT 57.231 25.926 0.00 0.00 0.00 1.82
1887 2121 9.415544 GAGAATAGAACATTTCACAAGCAAAAT 57.584 29.630 0.00 0.00 0.00 1.82
1888 2122 8.632679 AGAGAATAGAACATTTCACAAGCAAAA 58.367 29.630 0.00 0.00 0.00 2.44
1889 2123 8.169977 AGAGAATAGAACATTTCACAAGCAAA 57.830 30.769 0.00 0.00 0.00 3.68
1890 2124 7.750229 AGAGAATAGAACATTTCACAAGCAA 57.250 32.000 0.00 0.00 0.00 3.91
1891 2125 8.097038 AGTAGAGAATAGAACATTTCACAAGCA 58.903 33.333 0.00 0.00 0.00 3.91
1892 2126 8.485976 AGTAGAGAATAGAACATTTCACAAGC 57.514 34.615 0.00 0.00 0.00 4.01
1894 2128 9.219603 CCAAGTAGAGAATAGAACATTTCACAA 57.780 33.333 0.00 0.00 0.00 3.33
1898 2132 7.766278 TCAGCCAAGTAGAGAATAGAACATTTC 59.234 37.037 0.00 0.00 0.00 2.17
1943 2177 6.210784 GTCCCCTGCATGTAGAGTATATGTTA 59.789 42.308 12.93 0.00 30.90 2.41
1944 2178 5.012148 GTCCCCTGCATGTAGAGTATATGTT 59.988 44.000 12.93 0.00 30.90 2.71
1945 2179 4.528596 GTCCCCTGCATGTAGAGTATATGT 59.471 45.833 12.93 0.00 30.90 2.29
1946 2180 4.774726 AGTCCCCTGCATGTAGAGTATATG 59.225 45.833 12.93 0.00 0.00 1.78
1947 2181 5.017093 AGTCCCCTGCATGTAGAGTATAT 57.983 43.478 12.93 0.00 0.00 0.86
1948 2182 4.141018 TGAGTCCCCTGCATGTAGAGTATA 60.141 45.833 12.93 0.00 0.00 1.47
1954 2190 1.556911 AGTTGAGTCCCCTGCATGTAG 59.443 52.381 3.45 3.45 0.00 2.74
1957 2193 0.037303 ACAGTTGAGTCCCCTGCATG 59.963 55.000 6.16 0.00 0.00 4.06
1987 2223 2.192664 TTGCACGGCTTCCTTTCATA 57.807 45.000 0.00 0.00 0.00 2.15
2031 2267 0.541764 GTCAGGGGCCCATGAAACAA 60.542 55.000 39.17 16.16 0.00 2.83
2251 2490 1.745115 GCCACCATTGCTACTGCGA 60.745 57.895 0.00 0.00 43.34 5.10
2322 2561 1.963515 TGTCAGTTCTGCTGCTAGTGA 59.036 47.619 0.00 2.58 44.66 3.41
2325 2564 2.739885 AGTGTCAGTTCTGCTGCTAG 57.260 50.000 0.00 0.00 44.66 3.42
2328 2567 2.064762 CACTAGTGTCAGTTCTGCTGC 58.935 52.381 15.06 0.00 44.66 5.25
2413 2652 3.350833 CTTCAGTACAGGTACGGTAGGT 58.649 50.000 9.06 0.00 40.10 3.08
2416 2655 2.094675 GCCTTCAGTACAGGTACGGTA 58.905 52.381 9.06 0.46 40.80 4.02
2417 2656 0.893447 GCCTTCAGTACAGGTACGGT 59.107 55.000 9.06 0.00 40.80 4.83
2636 2875 1.407258 GTGAATAGCGCAGGAGTCTCT 59.593 52.381 11.47 0.00 0.00 3.10
2663 2903 1.210478 GCCTTGCTGATAACCAGAGGA 59.790 52.381 0.00 0.00 45.78 3.71
2665 2905 2.706339 AGCCTTGCTGATAACCAGAG 57.294 50.000 0.00 0.00 45.78 3.35
2699 2939 7.860373 TCCAAACAAAAGTTCATAGATCAAACG 59.140 33.333 0.00 0.00 0.00 3.60
2738 2979 6.474364 GTCAACCAAAGAATTTTCAAAACCG 58.526 36.000 0.00 0.00 35.03 4.44
2770 3011 9.793259 AAAAGACAGTTAATAATCTCAAGGTCA 57.207 29.630 0.00 0.00 0.00 4.02
2989 3232 7.429636 TGTGTTACTTTACTTCAGCCATTAC 57.570 36.000 0.00 0.00 0.00 1.89
2995 3238 5.122396 CCTCCATGTGTTACTTTACTTCAGC 59.878 44.000 0.00 0.00 0.00 4.26
3028 3271 7.067372 ACATCCACAGATACATTGTTACCATTG 59.933 37.037 0.00 0.00 0.00 2.82
3107 3360 1.080434 AAGAGCAGACGAGAACCGC 60.080 57.895 0.00 0.00 43.32 5.68
3212 3490 2.279582 AGTGGAAGCAACGATCGTAG 57.720 50.000 23.04 0.00 0.00 3.51
3355 3636 2.063979 CCCCAGGTCGGCATACTGA 61.064 63.158 0.00 0.00 34.21 3.41
3370 3654 1.378646 GGCTTGTTCAGGCTACCCC 60.379 63.158 6.84 0.00 45.03 4.95
3440 3725 1.075482 CCCTCCACATGGTGTGCTT 59.925 57.895 4.60 0.00 46.51 3.91
3462 3754 1.448540 CACCGTGATGCTCAGTCCC 60.449 63.158 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.