Multiple sequence alignment - TraesCS3D01G493200

Loading Multiple Alignment...

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 TraesCS3D01G493200 chr3D 100.000 2312 0 0 1 2312 586578911 586576600 0.000000e+00 4270.0
1 TraesCS3D01G493200 chr3B 95.012 1223 50 8 264 1480 783141961 783143178 0.000000e+00 1910.0
2 TraesCS3D01G493200 chr3B 91.910 581 43 4 1735 2312 783145063 783145642 0.000000e+00 809.0
3 TraesCS3D01G493200 chr3B 96.689 302 10 0 38 339 783141660 783141961 9.530000e-139 503.0
4 TraesCS3D01G493200 chr3B 84.725 491 62 7 1330 1810 783145238 783145725 1.610000e-131 479.0
5 TraesCS3D01G493200 chr3B 91.571 261 18 3 1475 1735 783143349 783143605 7.860000e-95 357.0
6 TraesCS3D01G493200 chr3B 90.196 153 13 1 1908 2060 783143030 783143180 5.040000e-47 198.0
7 TraesCS3D01G493200 chr3B 95.745 47 2 0 1 47 783135074 783135120 2.460000e-10 76.8


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 TraesCS3D01G493200 chr3D 586576600 586578911 2311 True 4270.000000 4270 100.000000 1 2312 1 chr3D.!!$R1 2311
1 TraesCS3D01G493200 chr3B 783141660 783145725 4065 False 709.333333 1910 91.683833 38 2312 6 chr3B.!!$F2 2274

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
107 108 0.237498 GCGTTACAAACCTGAGCCAC 59.763 55.0 0.0 0.0 0.0 5.01 F
339 415 0.245539 TGCTTAGTCGGTTCTTCGGG 59.754 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1198 0.541998 TCCTCCAGCCTGAAGAACGA 60.542 55.0 0.00 0.0 0.00 3.85 R
2135 3854 0.106894 GGGTAATGCTAAGCCGAGCT 59.893 55.0 8.75 0.0 43.27 4.09 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
36 37 9.975218 AGTTTATGGAGTGTATCATAAAAAGGT 57.025 29.630 9.23 0.00 43.23 3.50
99 100 0.878416 TGATGCCTGCGTTACAAACC 59.122 50.000 0.00 0.00 0.00 3.27
100 101 1.165270 GATGCCTGCGTTACAAACCT 58.835 50.000 0.00 0.00 0.00 3.50
107 108 0.237498 GCGTTACAAACCTGAGCCAC 59.763 55.000 0.00 0.00 0.00 5.01
197 198 1.735386 AGAGCATGATGACACTGCAC 58.265 50.000 0.00 3.46 35.04 4.57
212 213 0.909133 TGCACTGGGAGGATGCTGTA 60.909 55.000 0.00 0.00 40.13 2.74
226 227 1.484653 TGCTGTACATATGGGCGAAGT 59.515 47.619 7.80 0.00 0.00 3.01
287 363 1.306654 ATCTTCGGTGGGGCCACTA 60.307 57.895 6.53 0.00 45.52 2.74
339 415 0.245539 TGCTTAGTCGGTTCTTCGGG 59.754 55.000 0.00 0.00 0.00 5.14
424 500 7.984617 ACAATGCTTAATTTTGTGTTACAACCT 59.015 29.630 0.00 0.00 37.90 3.50
546 622 9.527157 TTGTGACTGGATAAAAATCAGGATTAA 57.473 29.630 0.00 0.00 33.19 1.40
684 761 8.496872 AACCGTGACTATTTTTATTTCAAACG 57.503 30.769 0.00 0.00 0.00 3.60
692 769 8.964150 ACTATTTTTATTTCAAACGACAACAGC 58.036 29.630 0.00 0.00 0.00 4.40
834 911 1.064979 ACAAGACACCTCCAAAACCGT 60.065 47.619 0.00 0.00 0.00 4.83
836 913 2.806244 CAAGACACCTCCAAAACCGTAG 59.194 50.000 0.00 0.00 0.00 3.51
856 933 4.322057 AGCCTTCCATGAAAGTAACCAT 57.678 40.909 0.00 0.00 0.00 3.55
952 1032 7.903145 TGGTATATATAAATCGGTGCACTCTT 58.097 34.615 17.98 7.55 0.00 2.85
965 1046 1.897560 CACTCTTCCCCACAGTTTCC 58.102 55.000 0.00 0.00 0.00 3.13
966 1047 0.771755 ACTCTTCCCCACAGTTTCCC 59.228 55.000 0.00 0.00 0.00 3.97
986 1067 3.004171 CCATCACAAACGGGTCGAATAA 58.996 45.455 0.00 0.00 0.00 1.40
991 1072 3.061697 CACAAACGGGTCGAATAACTAGC 59.938 47.826 0.00 0.00 0.00 3.42
994 1075 5.163478 ACAAACGGGTCGAATAACTAGCTAT 60.163 40.000 0.00 0.00 0.00 2.97
1048 1129 0.522705 TGTCATCTTCGCGCTCGTAC 60.523 55.000 5.56 0.00 36.96 3.67
1121 1202 1.745087 GGTGATGCCAATGTCATCGTT 59.255 47.619 0.00 0.00 42.32 3.85
1125 1206 3.374988 TGATGCCAATGTCATCGTTCTTC 59.625 43.478 0.00 0.00 42.32 2.87
1299 1380 0.601057 GCCAAGCCATTTACGGTTGT 59.399 50.000 0.00 0.00 0.00 3.32
1301 1382 1.668628 CCAAGCCATTTACGGTTGTGC 60.669 52.381 0.00 0.00 0.00 4.57
1322 1404 6.491062 TGTGCCCCTAAATAATCTGATGAATG 59.509 38.462 0.00 0.00 0.00 2.67
1344 1426 2.356553 TGCACTACCGGCGTCAAC 60.357 61.111 6.01 0.00 0.00 3.18
1357 1439 2.503943 CGTCAACGCAACCTCATTAC 57.496 50.000 0.00 0.00 0.00 1.89
1383 1465 1.531739 TTCGGTTGCCAGGGAATTGC 61.532 55.000 0.00 0.00 0.00 3.56
1406 1488 5.431765 CAAGGGATGTAGTGATATATGCCC 58.568 45.833 0.00 0.00 31.17 5.36
1408 1490 5.353986 AGGGATGTAGTGATATATGCCCTT 58.646 41.667 0.00 0.00 40.34 3.95
1409 1491 5.426833 AGGGATGTAGTGATATATGCCCTTC 59.573 44.000 0.00 0.00 40.34 3.46
1410 1492 5.352284 GGATGTAGTGATATATGCCCTTCG 58.648 45.833 0.00 0.00 0.00 3.79
1411 1493 4.188247 TGTAGTGATATATGCCCTTCGC 57.812 45.455 0.00 0.00 38.31 4.70
1422 1504 2.978010 CCTTCGCTGGCCGTGTTT 60.978 61.111 0.00 0.00 38.35 2.83
1423 1505 2.252260 CTTCGCTGGCCGTGTTTG 59.748 61.111 0.00 0.00 38.35 2.93
1454 1536 6.749118 GTGGTGATTTTTCTACTGATCAATGC 59.251 38.462 0.00 0.00 31.01 3.56
1460 1542 2.463876 TCTACTGATCAATGCGCTTCG 58.536 47.619 9.73 0.00 0.00 3.79
1467 1549 2.124570 AATGCGCTTCGATGGCCT 60.125 55.556 9.73 0.00 0.00 5.19
1473 1555 1.871080 CGCTTCGATGGCCTAAGAAT 58.129 50.000 3.32 0.00 0.00 2.40
1480 1562 2.805099 CGATGGCCTAAGAATCTCTTGC 59.195 50.000 3.32 0.00 37.29 4.01
1491 1749 1.195115 ATCTCTTGCCGCCTTGTAGA 58.805 50.000 0.00 0.00 0.00 2.59
1494 1752 0.179111 TCTTGCCGCCTTGTAGATCG 60.179 55.000 0.00 0.00 0.00 3.69
1541 1799 0.179134 AGTATGTCGAGTTCGCTGCC 60.179 55.000 0.00 0.00 39.60 4.85
1549 1807 4.821589 GTTCGCTGCCGAGGGGAG 62.822 72.222 0.00 0.00 45.35 4.30
1582 1840 1.256812 GCTTAGCTTTGCCCTTTGGA 58.743 50.000 0.00 0.00 0.00 3.53
1584 1842 2.519013 CTTAGCTTTGCCCTTTGGAGT 58.481 47.619 0.00 0.00 0.00 3.85
1599 1857 2.972348 TGGAGTAGTTGGTGGTTCTCT 58.028 47.619 0.00 0.00 0.00 3.10
1624 1882 2.888414 TCATGGCGTAATCTCGGTGATA 59.112 45.455 0.00 0.00 34.45 2.15
1633 1891 3.883830 ATCTCGGTGATATGATGCCTC 57.116 47.619 0.00 0.00 32.79 4.70
1636 1894 2.824936 CTCGGTGATATGATGCCTCTCT 59.175 50.000 0.00 0.00 0.00 3.10
1641 1899 5.049818 CGGTGATATGATGCCTCTCTTTTTC 60.050 44.000 0.00 0.00 0.00 2.29
1642 1900 6.060788 GGTGATATGATGCCTCTCTTTTTCT 58.939 40.000 0.00 0.00 0.00 2.52
1643 1901 6.017275 GGTGATATGATGCCTCTCTTTTTCTG 60.017 42.308 0.00 0.00 0.00 3.02
1644 1902 5.530171 TGATATGATGCCTCTCTTTTTCTGC 59.470 40.000 0.00 0.00 0.00 4.26
1645 1903 3.430042 TGATGCCTCTCTTTTTCTGCT 57.570 42.857 0.00 0.00 0.00 4.24
1646 1904 3.759581 TGATGCCTCTCTTTTTCTGCTT 58.240 40.909 0.00 0.00 0.00 3.91
1647 1905 4.147321 TGATGCCTCTCTTTTTCTGCTTT 58.853 39.130 0.00 0.00 0.00 3.51
1648 1906 4.586001 TGATGCCTCTCTTTTTCTGCTTTT 59.414 37.500 0.00 0.00 0.00 2.27
1657 1915 8.856490 TCTCTTTTTCTGCTTTTGTGTATTTC 57.144 30.769 0.00 0.00 0.00 2.17
1668 1926 5.512753 TTTGTGTATTTCTGTGCATGTGT 57.487 34.783 0.00 0.00 0.00 3.72
1669 1927 4.747540 TGTGTATTTCTGTGCATGTGTC 57.252 40.909 0.00 0.00 0.00 3.67
1754 3471 4.439305 AATGAATGTCATGGTTCCGTTG 57.561 40.909 0.00 0.00 37.15 4.10
1762 3479 3.187842 GTCATGGTTCCGTTGTAAAGGAC 59.812 47.826 0.00 0.00 36.06 3.85
1764 3481 2.841215 TGGTTCCGTTGTAAAGGACTG 58.159 47.619 0.00 0.00 36.06 3.51
1769 3486 1.265905 CCGTTGTAAAGGACTGGTTGC 59.734 52.381 0.00 0.00 32.44 4.17
1773 3490 4.439563 CGTTGTAAAGGACTGGTTGCTTTT 60.440 41.667 0.00 0.00 42.91 2.27
1789 3506 3.880490 TGCTTTTACTGTTGTGATCGGTT 59.120 39.130 0.00 0.00 0.00 4.44
1790 3507 4.219033 GCTTTTACTGTTGTGATCGGTTG 58.781 43.478 0.00 0.00 0.00 3.77
1859 3577 5.407995 GGAGAGGCGAAATGATAAGAATCTG 59.592 44.000 0.00 0.00 32.93 2.90
1937 3655 5.861327 GCGTCAATGCAACCTCATTAGGC 62.861 52.174 0.00 0.00 39.75 3.93
1972 3690 4.578105 GCCAGAGAATTGAAAGGGATGTAG 59.422 45.833 0.00 0.00 0.00 2.74
1974 3692 5.587844 CCAGAGAATTGAAAGGGATGTAGTG 59.412 44.000 0.00 0.00 0.00 2.74
1983 3701 7.315066 TGAAAGGGATGTAGTGATATATGCA 57.685 36.000 0.00 0.00 0.00 3.96
1984 3702 7.921304 TGAAAGGGATGTAGTGATATATGCAT 58.079 34.615 3.79 3.79 0.00 3.96
1996 3714 2.592102 ATATGCATTTCGATGGCCCT 57.408 45.000 3.54 0.00 0.00 5.19
1997 3715 3.719268 ATATGCATTTCGATGGCCCTA 57.281 42.857 3.54 0.00 0.00 3.53
2001 3719 2.229792 GCATTTCGATGGCCCTATTCA 58.770 47.619 0.00 0.00 0.00 2.57
2006 3724 3.126001 TCGATGGCCCTATTCATGTTC 57.874 47.619 0.00 0.00 0.00 3.18
2007 3725 2.154462 CGATGGCCCTATTCATGTTCC 58.846 52.381 0.00 0.00 0.00 3.62
2025 3744 5.070001 TGTTCCTGGTGATTTTTCTACTGG 58.930 41.667 0.00 0.00 0.00 4.00
2060 3779 1.066858 TGGCCTAAGAAGCTCTTGTCG 60.067 52.381 3.32 0.00 37.29 4.35
2072 3791 2.726760 GCTCTTGTCGCCTTGTATATCG 59.273 50.000 0.00 0.00 0.00 2.92
2076 3795 1.328439 GTCGCCTTGTATATCGCTCG 58.672 55.000 0.00 0.00 0.00 5.03
2080 3799 2.478031 CGCCTTGTATATCGCTCGCTAT 60.478 50.000 0.00 0.00 0.00 2.97
2089 3808 0.951558 TCGCTCGCTATGCTGATGTA 59.048 50.000 0.00 0.00 0.00 2.29
2125 3844 1.078426 CCAGTTTGCTACCGAGGGG 60.078 63.158 0.00 0.00 40.11 4.79
2129 3848 1.229400 TTTGCTACCGAGGGGAGGT 60.229 57.895 0.00 0.00 45.28 3.85
2135 3854 2.754186 GCTACCGAGGGGAGGTACAATA 60.754 54.545 0.00 0.00 42.81 1.90
2151 3870 4.336889 ACAATAGCTCGGCTTAGCATTA 57.663 40.909 6.53 0.00 45.30 1.90
2159 3878 2.237643 TCGGCTTAGCATTACCCTTTGA 59.762 45.455 6.53 0.00 0.00 2.69
2189 3908 6.677781 TTTTTGTTCTCTGTGTCTTAGGTG 57.322 37.500 0.00 0.00 0.00 4.00
2205 3924 3.526931 AGGTGTAATCTCGGTGATGTG 57.473 47.619 0.00 0.00 35.21 3.21
2215 3934 1.278985 TCGGTGATGTGATGCCTTTCT 59.721 47.619 0.00 0.00 0.00 2.52
2239 3958 6.532365 TTTTCTGTTTTTGTGTGTGTTTCC 57.468 33.333 0.00 0.00 0.00 3.13
2252 3971 3.433957 GTGTGTTTCCGTGCATGTGTATA 59.566 43.478 4.96 0.00 0.00 1.47
2261 3980 5.522097 TCCGTGCATGTGTATATAGTTTGTG 59.478 40.000 4.96 0.00 0.00 3.33
2275 3994 1.067213 GTTTGTGGTGCTGGTTGTGTT 60.067 47.619 0.00 0.00 0.00 3.32
2279 3998 1.953686 GTGGTGCTGGTTGTGTTGTAT 59.046 47.619 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.975218 ACCTTTTTATGATACACTCCATAAACT 57.025 29.630 0.00 0.00 41.88 2.66
12 13 9.747898 ACACCTTTTTATGATACACTCCATAAA 57.252 29.630 0.00 0.00 41.04 1.40
21 22 9.426837 GGCGTATATACACCTTTTTATGATACA 57.573 33.333 11.94 0.00 0.00 2.29
22 23 8.876790 GGGCGTATATACACCTTTTTATGATAC 58.123 37.037 17.40 0.00 0.00 2.24
23 24 8.595421 TGGGCGTATATACACCTTTTTATGATA 58.405 33.333 17.40 0.00 0.00 2.15
24 25 7.455058 TGGGCGTATATACACCTTTTTATGAT 58.545 34.615 17.40 0.00 0.00 2.45
25 26 6.828788 TGGGCGTATATACACCTTTTTATGA 58.171 36.000 17.40 0.00 0.00 2.15
26 27 7.361713 CCATGGGCGTATATACACCTTTTTATG 60.362 40.741 17.40 13.45 0.00 1.90
27 28 6.657541 CCATGGGCGTATATACACCTTTTTAT 59.342 38.462 17.40 4.42 0.00 1.40
28 29 5.998981 CCATGGGCGTATATACACCTTTTTA 59.001 40.000 17.40 2.53 0.00 1.52
29 30 4.825085 CCATGGGCGTATATACACCTTTTT 59.175 41.667 17.40 0.82 0.00 1.94
30 31 4.141344 ACCATGGGCGTATATACACCTTTT 60.141 41.667 18.09 2.90 0.00 2.27
31 32 3.393278 ACCATGGGCGTATATACACCTTT 59.607 43.478 18.09 5.01 0.00 3.11
32 33 2.976882 ACCATGGGCGTATATACACCTT 59.023 45.455 18.09 11.45 0.00 3.50
33 34 2.616524 ACCATGGGCGTATATACACCT 58.383 47.619 18.09 0.00 0.00 4.00
34 35 3.071479 CAACCATGGGCGTATATACACC 58.929 50.000 18.09 10.94 0.00 4.16
35 36 3.071479 CCAACCATGGGCGTATATACAC 58.929 50.000 18.09 3.02 43.51 2.90
36 37 3.410631 CCAACCATGGGCGTATATACA 57.589 47.619 18.09 0.00 43.51 2.29
168 169 6.983307 AGTGTCATCATGCTCTTCAGTTATAC 59.017 38.462 0.00 0.00 0.00 1.47
197 198 3.307269 CCATATGTACAGCATCCTCCCAG 60.307 52.174 0.33 0.00 38.94 4.45
212 213 0.464373 CTGCCACTTCGCCCATATGT 60.464 55.000 1.24 0.00 0.00 2.29
226 227 4.393155 ATGTTCCTCGCGCTGCCA 62.393 61.111 5.56 0.00 0.00 4.92
287 363 3.133003 AGCTATTCGTGGTAGACAATGCT 59.867 43.478 0.00 0.00 0.00 3.79
339 415 4.377431 CGGATATAGGAGAAAATGCAACGC 60.377 45.833 0.00 0.00 0.00 4.84
402 478 9.871238 TTTAAGGTTGTAACACAAAATTAAGCA 57.129 25.926 0.00 0.00 40.15 3.91
546 622 8.525290 AGCAGCTATAATCCTTTGTAACATTT 57.475 30.769 0.00 0.00 0.00 2.32
564 640 6.730175 TGTCGTTTGAAATAAAAAGCAGCTA 58.270 32.000 0.00 0.00 0.00 3.32
565 641 5.587289 TGTCGTTTGAAATAAAAAGCAGCT 58.413 33.333 0.00 0.00 0.00 4.24
623 700 7.666804 TGATATCAATGCTACATGTGCCTAATT 59.333 33.333 9.11 3.98 0.00 1.40
624 701 7.170277 TGATATCAATGCTACATGTGCCTAAT 58.830 34.615 9.11 4.70 0.00 1.73
692 769 4.142425 TGCATGCAACATAGTACAACATGG 60.142 41.667 20.30 0.00 35.21 3.66
723 800 7.170658 GCTTAGGTTCTGACATTGATATCTCAC 59.829 40.741 3.98 0.00 0.00 3.51
726 803 7.129457 TGCTTAGGTTCTGACATTGATATCT 57.871 36.000 3.98 0.00 0.00 1.98
827 904 2.871096 TCATGGAAGGCTACGGTTTT 57.129 45.000 0.00 0.00 0.00 2.43
834 911 4.919774 TGGTTACTTTCATGGAAGGCTA 57.080 40.909 18.18 3.32 0.00 3.93
836 913 5.047377 TCAAATGGTTACTTTCATGGAAGGC 60.047 40.000 18.18 7.55 0.00 4.35
856 933 0.181587 TTGCTTCCCGTCACCTCAAA 59.818 50.000 0.00 0.00 0.00 2.69
907 984 3.063452 CCATCGAGGTTAATTTGGTGTCG 59.937 47.826 0.00 0.00 0.00 4.35
952 1032 0.404040 GTGATGGGAAACTGTGGGGA 59.596 55.000 0.00 0.00 0.00 4.81
965 1046 1.448985 ATTCGACCCGTTTGTGATGG 58.551 50.000 0.00 0.00 0.00 3.51
966 1047 3.682858 AGTTATTCGACCCGTTTGTGATG 59.317 43.478 0.00 0.00 0.00 3.07
986 1067 4.604050 TCCTCTCCATGGTAGATAGCTAGT 59.396 45.833 12.58 0.00 0.00 2.57
991 1072 3.513515 GCCTTCCTCTCCATGGTAGATAG 59.486 52.174 12.58 0.74 0.00 2.08
994 1075 1.794714 GCCTTCCTCTCCATGGTAGA 58.205 55.000 12.58 12.10 0.00 2.59
1117 1198 0.541998 TCCTCCAGCCTGAAGAACGA 60.542 55.000 0.00 0.00 0.00 3.85
1121 1202 2.676232 CTGTCCTCCAGCCTGAAGA 58.324 57.895 0.00 0.00 33.59 2.87
1299 1380 6.012113 CCATTCATCAGATTATTTAGGGGCA 58.988 40.000 0.00 0.00 0.00 5.36
1301 1382 5.420104 GCCCATTCATCAGATTATTTAGGGG 59.580 44.000 0.00 0.00 32.10 4.79
1344 1426 2.098233 ACGGCGTAATGAGGTTGCG 61.098 57.895 12.58 0.00 46.78 4.85
1383 1465 5.190528 AGGGCATATATCACTACATCCCTTG 59.809 44.000 0.00 0.00 38.33 3.61
1406 1488 2.252260 CAAACACGGCCAGCGAAG 59.748 61.111 2.24 0.00 0.00 3.79
1408 1490 3.276091 CACAAACACGGCCAGCGA 61.276 61.111 2.24 0.00 0.00 4.93
1409 1491 3.119709 AACACAAACACGGCCAGCG 62.120 57.895 2.24 0.00 0.00 5.18
1410 1492 1.588667 CAACACAAACACGGCCAGC 60.589 57.895 2.24 0.00 0.00 4.85
1411 1493 1.065600 CCAACACAAACACGGCCAG 59.934 57.895 2.24 0.00 0.00 4.85
1422 1504 5.067153 CAGTAGAAAAATCACCACCAACACA 59.933 40.000 0.00 0.00 0.00 3.72
1423 1505 5.298276 TCAGTAGAAAAATCACCACCAACAC 59.702 40.000 0.00 0.00 0.00 3.32
1454 1536 1.795286 GATTCTTAGGCCATCGAAGCG 59.205 52.381 5.01 0.00 0.00 4.68
1460 1542 3.145286 GGCAAGAGATTCTTAGGCCATC 58.855 50.000 5.01 0.00 42.12 3.51
1467 1549 2.027192 ACAAGGCGGCAAGAGATTCTTA 60.027 45.455 13.08 0.00 33.78 2.10
1473 1555 1.137086 GATCTACAAGGCGGCAAGAGA 59.863 52.381 13.08 8.54 0.00 3.10
1480 1562 0.872021 GTGAGCGATCTACAAGGCGG 60.872 60.000 0.90 0.00 0.00 6.13
1491 1749 3.571828 ACTACATCAGCATAGTGAGCGAT 59.428 43.478 0.00 0.00 37.01 4.58
1541 1799 2.124570 CCATTGCACCTCCCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
1549 1807 1.718757 CTAAGCCGAGCCATTGCACC 61.719 60.000 0.00 0.00 41.13 5.01
1551 1809 2.114670 GCTAAGCCGAGCCATTGCA 61.115 57.895 0.00 0.00 41.13 4.08
1582 1840 3.039011 ACACAGAGAACCACCAACTACT 58.961 45.455 0.00 0.00 0.00 2.57
1584 1842 3.035363 TGACACAGAGAACCACCAACTA 58.965 45.455 0.00 0.00 0.00 2.24
1599 1857 1.470805 CCGAGATTACGCCATGACACA 60.471 52.381 0.00 0.00 0.00 3.72
1624 1882 3.965694 AGCAGAAAAAGAGAGGCATCAT 58.034 40.909 0.00 0.00 0.00 2.45
1633 1891 8.749499 CAGAAATACACAAAAGCAGAAAAAGAG 58.251 33.333 0.00 0.00 0.00 2.85
1636 1894 7.201513 GCACAGAAATACACAAAAGCAGAAAAA 60.202 33.333 0.00 0.00 0.00 1.94
1641 1899 4.609947 TGCACAGAAATACACAAAAGCAG 58.390 39.130 0.00 0.00 0.00 4.24
1642 1900 4.645762 TGCACAGAAATACACAAAAGCA 57.354 36.364 0.00 0.00 0.00 3.91
1643 1901 4.984161 ACATGCACAGAAATACACAAAAGC 59.016 37.500 0.00 0.00 0.00 3.51
1644 1902 5.978919 ACACATGCACAGAAATACACAAAAG 59.021 36.000 0.00 0.00 0.00 2.27
1645 1903 5.900425 ACACATGCACAGAAATACACAAAA 58.100 33.333 0.00 0.00 0.00 2.44
1646 1904 5.512753 ACACATGCACAGAAATACACAAA 57.487 34.783 0.00 0.00 0.00 2.83
1647 1905 4.319405 CGACACATGCACAGAAATACACAA 60.319 41.667 0.00 0.00 0.00 3.33
1648 1906 3.186205 CGACACATGCACAGAAATACACA 59.814 43.478 0.00 0.00 0.00 3.72
1657 1915 3.511699 ACTACATACGACACATGCACAG 58.488 45.455 0.00 0.00 0.00 3.66
1668 1926 3.427909 CCGGCACTACAAACTACATACGA 60.428 47.826 0.00 0.00 0.00 3.43
1669 1927 2.855963 CCGGCACTACAAACTACATACG 59.144 50.000 0.00 0.00 0.00 3.06
1735 1993 2.857483 ACAACGGAACCATGACATTCA 58.143 42.857 0.00 0.00 0.00 2.57
1736 1994 5.365403 TTTACAACGGAACCATGACATTC 57.635 39.130 0.00 0.00 0.00 2.67
1754 3471 5.298527 ACAGTAAAAGCAACCAGTCCTTTAC 59.701 40.000 0.00 0.00 0.00 2.01
1762 3479 4.630894 TCACAACAGTAAAAGCAACCAG 57.369 40.909 0.00 0.00 0.00 4.00
1764 3481 4.219033 CGATCACAACAGTAAAAGCAACC 58.781 43.478 0.00 0.00 0.00 3.77
1769 3486 4.513692 TCCAACCGATCACAACAGTAAAAG 59.486 41.667 0.00 0.00 0.00 2.27
1773 3490 2.894765 TCTCCAACCGATCACAACAGTA 59.105 45.455 0.00 0.00 0.00 2.74
1812 3530 1.313772 CAAACACACGGATGGAACCA 58.686 50.000 0.00 0.00 0.00 3.67
1813 3531 0.596082 CCAAACACACGGATGGAACC 59.404 55.000 0.00 0.00 34.82 3.62
1859 3577 3.922171 ATGGAAGAGGTGAGTGGAATC 57.078 47.619 0.00 0.00 0.00 2.52
1972 3690 4.201950 GGGCCATCGAAATGCATATATCAC 60.202 45.833 4.39 0.00 0.00 3.06
1974 3692 4.202441 AGGGCCATCGAAATGCATATATC 58.798 43.478 6.18 0.00 0.00 1.63
1983 3701 4.104383 ACATGAATAGGGCCATCGAAAT 57.896 40.909 6.18 0.00 0.00 2.17
1984 3702 3.576078 ACATGAATAGGGCCATCGAAA 57.424 42.857 6.18 0.00 0.00 3.46
1996 3714 8.956426 GTAGAAAAATCACCAGGAACATGAATA 58.044 33.333 0.00 0.00 0.00 1.75
1997 3715 6.923199 AGAAAAATCACCAGGAACATGAAT 57.077 33.333 0.00 0.00 0.00 2.57
2001 3719 5.711976 CCAGTAGAAAAATCACCAGGAACAT 59.288 40.000 0.00 0.00 0.00 2.71
2006 3724 4.651778 TGACCAGTAGAAAAATCACCAGG 58.348 43.478 0.00 0.00 0.00 4.45
2007 3725 6.615088 CATTGACCAGTAGAAAAATCACCAG 58.385 40.000 0.00 0.00 0.00 4.00
2025 3744 1.297893 GCCATCGAAGCGCATTGAC 60.298 57.895 11.47 0.00 0.00 3.18
2060 3779 2.631418 TAGCGAGCGATATACAAGGC 57.369 50.000 0.00 0.00 0.00 4.35
2089 3808 4.924625 ACTGGACATACTCCTATATCGCT 58.075 43.478 0.00 0.00 40.26 4.93
2125 3844 2.892784 AAGCCGAGCTATTGTACCTC 57.107 50.000 0.00 0.00 38.25 3.85
2129 3848 4.336889 AATGCTAAGCCGAGCTATTGTA 57.663 40.909 8.75 0.00 43.27 2.41
2135 3854 0.106894 GGGTAATGCTAAGCCGAGCT 59.893 55.000 8.75 0.00 43.27 4.09
2167 3886 5.741011 ACACCTAAGACACAGAGAACAAAA 58.259 37.500 0.00 0.00 0.00 2.44
2168 3887 5.353394 ACACCTAAGACACAGAGAACAAA 57.647 39.130 0.00 0.00 0.00 2.83
2170 3889 6.493802 AGATTACACCTAAGACACAGAGAACA 59.506 38.462 0.00 0.00 0.00 3.18
2185 3904 3.096852 TCACATCACCGAGATTACACCT 58.903 45.455 0.00 0.00 33.72 4.00
2187 3906 3.246226 GCATCACATCACCGAGATTACAC 59.754 47.826 0.00 0.00 33.72 2.90
2188 3907 3.457234 GCATCACATCACCGAGATTACA 58.543 45.455 0.00 0.00 33.72 2.41
2189 3908 2.802816 GGCATCACATCACCGAGATTAC 59.197 50.000 0.00 0.00 33.72 1.89
2205 3924 7.148423 ACACAAAAACAGAAAAAGAAAGGCATC 60.148 33.333 0.00 0.00 0.00 3.91
2215 3934 6.292381 CGGAAACACACACAAAAACAGAAAAA 60.292 34.615 0.00 0.00 0.00 1.94
2239 3958 5.293324 ACCACAAACTATATACACATGCACG 59.707 40.000 0.00 0.00 0.00 5.34
2252 3971 2.622942 CACAACCAGCACCACAAACTAT 59.377 45.455 0.00 0.00 0.00 2.12
2261 3980 1.539827 GGATACAACACAACCAGCACC 59.460 52.381 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.