Multiple sequence alignment - TraesCS1D01G355700

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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 TraesCS1D01G355700 chr1D 100.000 2273 0 0 1 2273 440088327 440086055 0.000000e+00 4198
1 TraesCS1D01G355700 chr1D 96.250 80 3 0 668 747 486065940 486065861 5.090000e-27 132
2 TraesCS1D01G355700 chr1B 88.353 1099 72 20 1000 2062 597667952 597666874 0.000000e+00 1269
3 TraesCS1D01G355700 chr1B 88.396 767 62 11 4 744 597668981 597668216 0.000000e+00 898
4 TraesCS1D01G355700 chr1B 84.906 212 16 8 2078 2273 597666821 597666610 1.380000e-47 200
5 TraesCS1D01G355700 chr1B 97.333 75 2 0 668 742 676738918 676738844 6.590000e-26 128
6 TraesCS1D01G355700 chr1B 96.104 77 3 0 668 744 676774963 676774887 2.370000e-25 126
7 TraesCS1D01G355700 chr1B 94.872 78 3 1 671 748 676764512 676764436 1.100000e-23 121
8 TraesCS1D01G355700 chr1A 92.116 482 36 2 1 481 537817020 537817500 0.000000e+00 678
9 TraesCS1D01G355700 chr1A 86.207 609 51 18 884 1481 537817857 537818443 1.480000e-176 628
10 TraesCS1D01G355700 chr1A 88.476 269 21 6 481 741 537817543 537817809 1.310000e-82 316
11 TraesCS1D01G355700 chr1A 87.365 277 27 5 1517 1793 537818447 537818715 6.100000e-81 311
12 TraesCS1D01G355700 chr1A 96.203 79 3 0 668 746 583659484 583659406 1.830000e-26 130
13 TraesCS1D01G355700 chr1A 96.104 77 3 0 668 744 583586982 583586906 2.370000e-25 126
14 TraesCS1D01G355700 chr7B 85.476 420 52 7 1 413 679730697 679730280 1.610000e-116 429
15 TraesCS1D01G355700 chr7B 82.752 487 62 8 1 469 59676742 59676260 4.520000e-112 414
16 TraesCS1D01G355700 chr7B 82.119 453 71 9 1 449 63773981 63773535 1.650000e-101 379
17 TraesCS1D01G355700 chr5A 83.162 487 61 7 1 469 632143595 632143112 2.090000e-115 425
18 TraesCS1D01G355700 chr2D 83.087 473 70 10 1 469 189713835 189713369 2.700000e-114 422
19 TraesCS1D01G355700 chr2D 97.368 76 2 0 667 742 510217089 510217164 1.830000e-26 130
20 TraesCS1D01G355700 chr5D 82.887 485 61 10 3 469 561568815 561569295 1.260000e-112 416
21 TraesCS1D01G355700 chr7A 82.209 489 72 15 1 481 619289119 619289600 7.560000e-110 407
22 TraesCS1D01G355700 chr7A 84.049 326 37 11 1 312 418610886 418610562 1.320000e-77 300
23 TraesCS1D01G355700 chr6D 84.424 321 39 8 1 317 2665119 2665432 2.840000e-79 305
24 TraesCS1D01G355700 chr3D 84.308 325 37 7 6 317 80559252 80558929 2.840000e-79 305


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 TraesCS1D01G355700 chr1D 440086055 440088327 2272 True 4198.00 4198 100.000000 1 2273 1 chr1D.!!$R1 2272
1 TraesCS1D01G355700 chr1B 597666610 597668981 2371 True 789.00 1269 87.218333 4 2273 3 chr1B.!!$R4 2269
2 TraesCS1D01G355700 chr1A 537817020 537818715 1695 False 483.25 678 88.541000 1 1793 4 chr1A.!!$F1 1792

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
814 894 0.033503 CCCCACCCCACCAAGATAAC 60.034 60.0 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2329 0.179111 TTGGATGCTCGAACGCCTAG 60.179 55.0 0.0 0.0 0.0 3.02 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
121 122 5.719173 TGCCATTTTCTCCTTATTTTTCCG 58.281 37.500 0.00 0.00 0.00 4.30
204 205 2.095461 GGATTTTTGGAGGAGGCTGAC 58.905 52.381 0.00 0.00 0.00 3.51
323 324 8.185362 TGCTTAGCAAAACCAACATAGGGTTC 62.185 42.308 3.67 0.00 38.91 3.62
389 390 9.790344 CTTCTAATCCCATCTCTTGTAATGATT 57.210 33.333 0.00 0.00 0.00 2.57
413 414 4.719369 GTGCGACGCGTCCCTTCT 62.719 66.667 31.84 0.00 0.00 2.85
415 416 4.415332 GCGACGCGTCCCTTCTGA 62.415 66.667 31.84 0.00 0.00 3.27
423 424 2.162608 CGCGTCCCTTCTGAGGATATAG 59.837 54.545 0.00 0.00 46.74 1.31
588 652 6.530120 TGACAGAACTGCAAACCTTTAGATA 58.470 36.000 1.46 0.00 0.00 1.98
611 675 2.979130 GCCACTGATCTTAGGCGTC 58.021 57.895 7.03 0.00 37.41 5.19
616 680 0.924090 CTGATCTTAGGCGTCGCAAC 59.076 55.000 20.50 2.01 0.00 4.17
623 687 2.089887 TAGGCGTCGCAACAGACCAA 62.090 55.000 20.50 0.00 37.85 3.67
744 811 2.283143 ATCCCGGGCAGCAGCAATTA 62.283 55.000 18.49 0.00 44.61 1.40
745 812 2.774799 CCCGGGCAGCAGCAATTAC 61.775 63.158 8.08 0.00 44.61 1.89
747 814 0.463654 CCGGGCAGCAGCAATTACTA 60.464 55.000 2.65 0.00 44.61 1.82
749 816 1.742831 CGGGCAGCAGCAATTACTAAA 59.257 47.619 2.65 0.00 44.61 1.85
750 817 2.223340 CGGGCAGCAGCAATTACTAAAG 60.223 50.000 2.65 0.00 44.61 1.85
751 818 2.755103 GGGCAGCAGCAATTACTAAAGT 59.245 45.455 2.65 0.00 44.61 2.66
752 819 3.193479 GGGCAGCAGCAATTACTAAAGTT 59.807 43.478 2.65 0.00 44.61 2.66
754 821 5.230182 GGCAGCAGCAATTACTAAAGTTTT 58.770 37.500 2.65 0.00 44.61 2.43
756 823 6.866248 GGCAGCAGCAATTACTAAAGTTTTTA 59.134 34.615 2.65 0.00 44.61 1.52
799 879 4.291249 ACCTCACTATTCTTTTTAGCCCCA 59.709 41.667 0.00 0.00 0.00 4.96
801 881 4.595986 TCACTATTCTTTTTAGCCCCACC 58.404 43.478 0.00 0.00 0.00 4.61
802 882 3.699538 CACTATTCTTTTTAGCCCCACCC 59.300 47.826 0.00 0.00 0.00 4.61
804 884 0.861155 TTCTTTTTAGCCCCACCCCA 59.139 50.000 0.00 0.00 0.00 4.96
805 885 0.113580 TCTTTTTAGCCCCACCCCAC 59.886 55.000 0.00 0.00 0.00 4.61
806 886 0.902984 CTTTTTAGCCCCACCCCACC 60.903 60.000 0.00 0.00 0.00 4.61
807 887 1.665948 TTTTTAGCCCCACCCCACCA 61.666 55.000 0.00 0.00 0.00 4.17
808 888 1.665948 TTTTAGCCCCACCCCACCAA 61.666 55.000 0.00 0.00 0.00 3.67
809 889 2.087857 TTTAGCCCCACCCCACCAAG 62.088 60.000 0.00 0.00 0.00 3.61
811 891 2.798760 TAGCCCCACCCCACCAAGAT 62.799 60.000 0.00 0.00 0.00 2.40
812 892 2.313427 GCCCCACCCCACCAAGATA 61.313 63.158 0.00 0.00 0.00 1.98
814 894 0.033503 CCCCACCCCACCAAGATAAC 60.034 60.000 0.00 0.00 0.00 1.89
815 895 0.701731 CCCACCCCACCAAGATAACA 59.298 55.000 0.00 0.00 0.00 2.41
816 896 1.340991 CCCACCCCACCAAGATAACAG 60.341 57.143 0.00 0.00 0.00 3.16
818 898 2.618045 CCACCCCACCAAGATAACAGTC 60.618 54.545 0.00 0.00 0.00 3.51
819 899 2.305927 CACCCCACCAAGATAACAGTCT 59.694 50.000 0.00 0.00 0.00 3.24
820 900 2.572104 ACCCCACCAAGATAACAGTCTC 59.428 50.000 0.00 0.00 0.00 3.36
821 901 2.840651 CCCCACCAAGATAACAGTCTCT 59.159 50.000 0.00 0.00 0.00 3.10
822 902 3.369892 CCCCACCAAGATAACAGTCTCTG 60.370 52.174 0.00 0.00 37.52 3.35
823 903 3.265791 CCACCAAGATAACAGTCTCTGC 58.734 50.000 0.00 0.00 34.37 4.26
824 904 3.306989 CCACCAAGATAACAGTCTCTGCA 60.307 47.826 0.00 0.00 34.37 4.41
825 905 4.511527 CACCAAGATAACAGTCTCTGCAT 58.488 43.478 0.00 0.00 34.37 3.96
826 906 4.569966 CACCAAGATAACAGTCTCTGCATC 59.430 45.833 0.00 1.35 34.37 3.91
827 907 4.469227 ACCAAGATAACAGTCTCTGCATCT 59.531 41.667 0.00 7.96 37.83 2.90
828 908 5.046014 ACCAAGATAACAGTCTCTGCATCTT 60.046 40.000 15.28 15.28 42.24 2.40
829 909 5.879223 CCAAGATAACAGTCTCTGCATCTTT 59.121 40.000 17.03 7.20 40.92 2.52
830 910 6.036953 CCAAGATAACAGTCTCTGCATCTTTC 59.963 42.308 17.03 2.01 40.92 2.62
831 911 5.347342 AGATAACAGTCTCTGCATCTTTCG 58.653 41.667 0.00 0.00 34.84 3.46
832 912 3.667497 AACAGTCTCTGCATCTTTCGA 57.333 42.857 0.00 0.00 34.37 3.71
833 913 3.883830 ACAGTCTCTGCATCTTTCGAT 57.116 42.857 0.00 0.00 34.37 3.59
834 914 3.779759 ACAGTCTCTGCATCTTTCGATC 58.220 45.455 0.00 0.00 34.37 3.69
835 915 3.194329 ACAGTCTCTGCATCTTTCGATCA 59.806 43.478 0.00 0.00 34.37 2.92
836 916 3.797796 CAGTCTCTGCATCTTTCGATCAG 59.202 47.826 0.00 0.00 0.00 2.90
837 917 2.539274 GTCTCTGCATCTTTCGATCAGC 59.461 50.000 0.00 0.00 31.04 4.26
838 918 2.429971 TCTCTGCATCTTTCGATCAGCT 59.570 45.455 0.00 0.00 31.04 4.24
839 919 2.540516 CTCTGCATCTTTCGATCAGCTG 59.459 50.000 7.63 7.63 31.04 4.24
840 920 1.003759 CTGCATCTTTCGATCAGCTGC 60.004 52.381 9.47 11.98 0.00 5.25
844 924 3.196463 CATCTTTCGATCAGCTGCTCTT 58.804 45.455 15.15 0.00 0.00 2.85
850 930 1.162698 GATCAGCTGCTCTTGTTGCA 58.837 50.000 9.47 0.00 38.81 4.08
853 933 0.318445 CAGCTGCTCTTGTTGCAACC 60.318 55.000 26.14 11.17 40.13 3.77
854 934 1.006922 GCTGCTCTTGTTGCAACCC 60.007 57.895 26.14 10.11 40.13 4.11
862 942 4.696455 CTCTTGTTGCAACCCAATTTCTT 58.304 39.130 26.14 0.00 35.55 2.52
865 945 5.584251 TCTTGTTGCAACCCAATTTCTTTTC 59.416 36.000 26.14 0.00 35.55 2.29
866 946 4.195416 TGTTGCAACCCAATTTCTTTTCC 58.805 39.130 26.14 0.00 35.55 3.13
867 947 3.483808 TGCAACCCAATTTCTTTTCCC 57.516 42.857 0.00 0.00 0.00 3.97
873 953 2.039746 CCCAATTTCTTTTCCCCCAACC 59.960 50.000 0.00 0.00 0.00 3.77
874 954 2.978978 CCAATTTCTTTTCCCCCAACCT 59.021 45.455 0.00 0.00 0.00 3.50
875 955 3.394274 CCAATTTCTTTTCCCCCAACCTT 59.606 43.478 0.00 0.00 0.00 3.50
878 958 2.675658 TCTTTTCCCCCAACCTTCAG 57.324 50.000 0.00 0.00 0.00 3.02
879 959 2.140224 TCTTTTCCCCCAACCTTCAGA 58.860 47.619 0.00 0.00 0.00 3.27
918 1025 2.025969 CAGCTGCAGAGTCACGGTG 61.026 63.158 20.43 0.56 0.00 4.94
945 1052 4.950479 CCTTCAGGCCAGCACTAG 57.050 61.111 5.01 0.00 0.00 2.57
946 1053 1.222936 CCTTCAGGCCAGCACTAGG 59.777 63.158 5.01 0.00 0.00 3.02
947 1054 1.267574 CCTTCAGGCCAGCACTAGGA 61.268 60.000 5.01 0.00 0.00 2.94
948 1055 0.177604 CTTCAGGCCAGCACTAGGAG 59.822 60.000 5.01 0.00 0.00 3.69
949 1056 0.252239 TTCAGGCCAGCACTAGGAGA 60.252 55.000 5.01 0.00 0.00 3.71
950 1057 0.685785 TCAGGCCAGCACTAGGAGAG 60.686 60.000 5.01 0.00 0.00 3.20
951 1058 1.382420 AGGCCAGCACTAGGAGAGG 60.382 63.158 5.01 0.00 0.00 3.69
952 1059 1.381872 GGCCAGCACTAGGAGAGGA 60.382 63.158 0.00 0.00 0.00 3.71
953 1060 1.398958 GGCCAGCACTAGGAGAGGAG 61.399 65.000 0.00 0.00 0.00 3.69
960 1067 2.687935 GCACTAGGAGAGGAGAGTGAAG 59.312 54.545 5.11 0.00 41.51 3.02
962 1069 1.946768 CTAGGAGAGGAGAGTGAAGCG 59.053 57.143 0.00 0.00 0.00 4.68
963 1070 0.329931 AGGAGAGGAGAGTGAAGCGA 59.670 55.000 0.00 0.00 0.00 4.93
965 1072 1.459450 GAGAGGAGAGTGAAGCGACT 58.541 55.000 0.00 0.00 0.00 4.18
966 1073 1.816224 GAGAGGAGAGTGAAGCGACTT 59.184 52.381 0.00 0.00 0.00 3.01
994 1101 2.687805 CGCGTCAACCCGAGAGAGA 61.688 63.158 0.00 0.00 0.00 3.10
1394 1540 3.634504 TCGCACTGTAATTCCCCTACTA 58.365 45.455 0.00 0.00 0.00 1.82
1398 1544 5.924825 CGCACTGTAATTCCCCTACTATTAC 59.075 44.000 0.00 0.00 36.02 1.89
1405 1551 2.326428 TCCCCTACTATTACTGCTGGC 58.674 52.381 0.00 0.00 0.00 4.85
1406 1552 1.000955 CCCCTACTATTACTGCTGGCG 59.999 57.143 0.00 0.00 0.00 5.69
1419 1565 0.594796 GCTGGCGTGGTTTCAAAGTG 60.595 55.000 0.00 0.00 0.00 3.16
1425 1572 3.548668 GGCGTGGTTTCAAAGTGTTTAAC 59.451 43.478 0.00 0.00 0.00 2.01
1431 1578 5.244178 TGGTTTCAAAGTGTTTAACCTGTGT 59.756 36.000 0.00 0.00 39.16 3.72
1446 1593 5.193663 ACCTGTGTCTGATTCTATCATCG 57.806 43.478 0.00 0.00 38.85 3.84
1451 1601 6.495706 TGTGTCTGATTCTATCATCGTACAC 58.504 40.000 0.00 0.00 38.85 2.90
1482 1632 1.174712 AAAACTCACCTGCGCTGCAT 61.175 50.000 9.73 0.00 38.13 3.96
1491 1641 3.285215 GCGCTGCATATGCCTGCT 61.285 61.111 28.08 0.00 42.75 4.24
1496 1646 0.818040 CTGCATATGCCTGCTCTGCA 60.818 55.000 24.54 3.41 42.75 4.41
1497 1647 1.099295 TGCATATGCCTGCTCTGCAC 61.099 55.000 24.54 0.00 42.38 4.57
1498 1648 1.099295 GCATATGCCTGCTCTGCACA 61.099 55.000 17.26 0.00 42.38 4.57
1499 1649 0.661552 CATATGCCTGCTCTGCACAC 59.338 55.000 0.00 0.00 42.38 3.82
1500 1650 0.253894 ATATGCCTGCTCTGCACACA 59.746 50.000 0.00 0.00 42.38 3.72
1501 1651 0.674581 TATGCCTGCTCTGCACACAC 60.675 55.000 0.00 0.00 42.38 3.82
1502 1652 2.281345 GCCTGCTCTGCACACACT 60.281 61.111 0.00 0.00 33.79 3.55
1503 1653 2.614446 GCCTGCTCTGCACACACTG 61.614 63.158 0.00 0.00 33.79 3.66
1512 1662 2.102252 TCTGCACACACTGTCACACATA 59.898 45.455 0.00 0.00 0.00 2.29
1523 1673 3.732212 TGTCACACATATAGCCTGATGC 58.268 45.455 0.00 0.00 41.71 3.91
1574 1724 2.949447 AGTTGACCAGGCAGTTTTCAT 58.051 42.857 0.00 0.00 0.00 2.57
1584 1734 5.127519 CCAGGCAGTTTTCATATCAAATGGA 59.872 40.000 0.00 0.00 0.00 3.41
1591 1741 7.709182 CAGTTTTCATATCAAATGGATGTGCAT 59.291 33.333 0.00 0.00 42.87 3.96
1644 1794 1.246649 TTCCAGCGACATTGTTGCAT 58.753 45.000 26.73 12.07 44.70 3.96
1686 1836 4.759183 GGAAAGTCTCATCTTCTTGTTGCT 59.241 41.667 0.00 0.00 0.00 3.91
1742 1892 2.052782 AATCCCCTACCGTTGCAATC 57.947 50.000 0.59 0.00 0.00 2.67
1756 1906 4.330894 CGTTGCAATCTGTGTGATGTAGAT 59.669 41.667 0.59 0.00 35.21 1.98
1784 1934 4.740741 GTTCTTCAGGAACTTGAAGAGC 57.259 45.455 21.80 21.02 45.58 4.09
1848 2000 3.808174 GCCTAGACTTGTTTTGTTCGAGT 59.192 43.478 0.00 0.00 32.87 4.18
1849 2001 4.986659 GCCTAGACTTGTTTTGTTCGAGTA 59.013 41.667 0.00 0.00 30.65 2.59
1863 2016 2.029623 TCGAGTACTTATGCAGGGTCC 58.970 52.381 0.00 0.00 0.00 4.46
1869 2022 2.200081 ACTTATGCAGGGTCCACAGAT 58.800 47.619 0.00 0.00 0.00 2.90
1881 2034 1.999295 TCCACAGATTGGGAATGGGAA 59.001 47.619 0.00 0.00 46.92 3.97
1904 2075 3.809832 CACAAGGAAAACATCGACAGAGT 59.190 43.478 0.00 0.00 0.00 3.24
1925 2096 2.888834 AACATGCCAAACTCCAACAC 57.111 45.000 0.00 0.00 0.00 3.32
1994 2165 5.726138 GCACACTTGCTCAATCGATTCTTAG 60.726 44.000 7.92 7.43 46.17 2.18
2011 2182 7.491372 CGATTCTTAGTAAACTAGCACAATGGA 59.509 37.037 0.00 0.00 0.00 3.41
2030 2202 1.204062 CGTGCATCGCAACGAAACT 59.796 52.632 0.00 0.00 41.47 2.66
2035 2207 1.136085 GCATCGCAACGAAACTGCTAA 60.136 47.619 6.77 0.00 39.99 3.09
2041 2213 2.307049 CAACGAAACTGCTAAAAGGCG 58.693 47.619 0.00 0.00 34.52 5.52
2042 2214 1.873698 ACGAAACTGCTAAAAGGCGA 58.126 45.000 0.00 0.00 34.52 5.54
2043 2215 1.798813 ACGAAACTGCTAAAAGGCGAG 59.201 47.619 0.00 0.00 34.52 5.03
2068 2240 2.743928 GCCACTGGCTTGTCTCGG 60.744 66.667 13.28 0.00 46.69 4.63
2075 2247 2.743928 GCTTGTCTCGGCCAGTGG 60.744 66.667 4.20 4.20 0.00 4.00
2107 2316 3.134458 GAGAACAAGAATATGAGGGCCG 58.866 50.000 0.00 0.00 0.00 6.13
2142 2351 1.226128 GCGTTCGAGCATCCAAAGC 60.226 57.895 0.00 0.00 37.05 3.51
2149 2358 0.379669 GAGCATCCAAAGCGACCATG 59.620 55.000 0.00 0.00 37.01 3.66
2152 2361 1.462616 CATCCAAAGCGACCATGGAA 58.537 50.000 21.47 0.00 45.75 3.53
2154 2363 1.533625 TCCAAAGCGACCATGGAAAG 58.466 50.000 21.47 10.09 40.19 2.62
2156 2365 0.527565 CAAAGCGACCATGGAAAGGG 59.472 55.000 21.47 3.32 0.00 3.95
2157 2366 0.112412 AAAGCGACCATGGAAAGGGT 59.888 50.000 21.47 6.86 40.96 4.34
2176 2401 4.885325 AGGGTCGTTTGTGACATTTAAAGT 59.115 37.500 0.00 0.00 40.72 2.66
2178 2403 4.439776 GGTCGTTTGTGACATTTAAAGTGC 59.560 41.667 0.00 0.00 40.72 4.40
2183 2408 5.940192 TTGTGACATTTAAAGTGCGAGAT 57.060 34.783 0.00 0.00 0.00 2.75
2195 2420 5.437289 AAGTGCGAGATGACATTTCAAAA 57.563 34.783 6.76 0.00 34.61 2.44
2199 2424 7.592938 AGTGCGAGATGACATTTCAAAATTTA 58.407 30.769 6.76 0.00 34.61 1.40
2224 2449 1.758122 GGCAAGGTGGGGCATTAGG 60.758 63.158 0.00 0.00 0.00 2.69
2240 2465 4.081476 GCATTAGGGAGGAAACAAAGCAAT 60.081 41.667 0.00 0.00 0.00 3.56
2243 2468 3.782992 AGGGAGGAAACAAAGCAATGAT 58.217 40.909 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.534496 CCTTCCATAAGAAACCATTCAGAAAAT 58.466 33.333 0.00 0.00 38.06 1.82
121 122 3.704566 AGAACTCCTTTGAAAAACCCACC 59.295 43.478 0.00 0.00 0.00 4.61
178 179 3.054361 GCCTCCTCCAAAAATCCTGTAGA 60.054 47.826 0.00 0.00 0.00 2.59
204 205 7.764331 TGTAAACATCATCATCAACATCTTGG 58.236 34.615 0.00 0.00 0.00 3.61
239 240 5.104259 ACATTCTTCCTAATCTCCGCTTT 57.896 39.130 0.00 0.00 0.00 3.51
413 414 9.183368 GTGATGATGTACAGATCTATATCCTCA 57.817 37.037 15.28 0.91 31.98 3.86
415 416 9.539194 TTGTGATGATGTACAGATCTATATCCT 57.461 33.333 15.28 0.00 31.98 3.24
423 424 8.374327 TGATTGATTGTGATGATGTACAGATC 57.626 34.615 0.33 6.23 0.00 2.75
472 473 7.247728 CGCAATAAGTTATAGCCAAGAAACAA 58.752 34.615 0.00 0.00 0.00 2.83
514 561 8.686397 TGCGAATAAGTAGTACGTATTCAAAA 57.314 30.769 30.98 20.37 44.34 2.44
559 622 0.662619 TTTGCAGTTCTGTCAAGCCG 59.337 50.000 1.78 0.00 0.00 5.52
561 625 1.678101 AGGTTTGCAGTTCTGTCAAGC 59.322 47.619 1.78 7.98 0.00 4.01
588 652 1.065126 GCCTAAGATCAGTGGCCAACT 60.065 52.381 7.24 4.17 40.93 3.16
611 675 2.949106 CCAGCTTGGTCTGTTGCG 59.051 61.111 0.00 0.00 31.35 4.85
623 687 8.593945 TCCAGATTATTTATTTCAAACCAGCT 57.406 30.769 0.00 0.00 0.00 4.24
640 704 9.447279 TCTGGTATAGAAAGGAAATCCAGATTA 57.553 33.333 6.49 0.00 43.12 1.75
641 705 8.337118 TCTGGTATAGAAAGGAAATCCAGATT 57.663 34.615 6.49 0.00 43.12 2.40
653 717 4.569966 CACAGCAGCTTCTGGTATAGAAAG 59.430 45.833 17.84 0.00 44.47 2.62
660 724 0.035317 CACCACAGCAGCTTCTGGTA 59.965 55.000 17.84 0.00 40.40 3.25
771 838 9.623000 GGGCTAAAAAGAATAGTGAGGTAAATA 57.377 33.333 0.00 0.00 0.00 1.40
772 839 7.560262 GGGGCTAAAAAGAATAGTGAGGTAAAT 59.440 37.037 0.00 0.00 0.00 1.40
773 840 6.888088 GGGGCTAAAAAGAATAGTGAGGTAAA 59.112 38.462 0.00 0.00 0.00 2.01
774 841 6.012333 TGGGGCTAAAAAGAATAGTGAGGTAA 60.012 38.462 0.00 0.00 0.00 2.85
777 857 4.640647 GTGGGGCTAAAAAGAATAGTGAGG 59.359 45.833 0.00 0.00 0.00 3.86
783 863 2.655407 TGGGGTGGGGCTAAAAAGAATA 59.345 45.455 0.00 0.00 0.00 1.75
785 865 0.861155 TGGGGTGGGGCTAAAAAGAA 59.139 50.000 0.00 0.00 0.00 2.52
793 873 2.798760 TATCTTGGTGGGGTGGGGCT 62.799 60.000 0.00 0.00 0.00 5.19
795 875 0.033503 GTTATCTTGGTGGGGTGGGG 60.034 60.000 0.00 0.00 0.00 4.96
799 879 2.572104 GAGACTGTTATCTTGGTGGGGT 59.428 50.000 0.00 0.00 0.00 4.95
801 881 3.866651 CAGAGACTGTTATCTTGGTGGG 58.133 50.000 0.00 0.00 0.00 4.61
802 882 3.265791 GCAGAGACTGTTATCTTGGTGG 58.734 50.000 0.00 0.00 33.43 4.61
804 884 4.469227 AGATGCAGAGACTGTTATCTTGGT 59.531 41.667 0.00 0.00 35.61 3.67
805 885 5.021033 AGATGCAGAGACTGTTATCTTGG 57.979 43.478 0.00 0.00 35.61 3.61
806 886 6.237781 CGAAAGATGCAGAGACTGTTATCTTG 60.238 42.308 21.27 13.14 41.58 3.02
807 887 5.809562 CGAAAGATGCAGAGACTGTTATCTT 59.190 40.000 18.07 18.07 42.79 2.40
808 888 5.126222 TCGAAAGATGCAGAGACTGTTATCT 59.874 40.000 0.00 0.00 38.30 1.98
809 889 5.344066 TCGAAAGATGCAGAGACTGTTATC 58.656 41.667 0.00 0.00 31.63 1.75
811 891 4.783764 TCGAAAGATGCAGAGACTGTTA 57.216 40.909 0.00 0.00 31.63 2.41
812 892 3.667497 TCGAAAGATGCAGAGACTGTT 57.333 42.857 0.00 0.00 31.63 3.16
826 906 2.344950 ACAAGAGCAGCTGATCGAAAG 58.655 47.619 25.12 17.78 35.26 2.62
827 907 2.462456 ACAAGAGCAGCTGATCGAAA 57.538 45.000 25.12 0.00 35.26 3.46
828 908 2.071540 CAACAAGAGCAGCTGATCGAA 58.928 47.619 25.12 0.00 35.26 3.71
829 909 1.718396 CAACAAGAGCAGCTGATCGA 58.282 50.000 25.12 0.00 35.26 3.59
830 910 0.096628 GCAACAAGAGCAGCTGATCG 59.903 55.000 25.12 15.03 35.26 3.69
831 911 1.162698 TGCAACAAGAGCAGCTGATC 58.837 50.000 24.27 24.27 37.02 2.92
832 912 1.268899 GTTGCAACAAGAGCAGCTGAT 59.731 47.619 24.52 12.64 43.75 2.90
833 913 0.664761 GTTGCAACAAGAGCAGCTGA 59.335 50.000 24.52 0.00 43.75 4.26
834 914 0.318445 GGTTGCAACAAGAGCAGCTG 60.318 55.000 29.55 10.11 43.75 4.24
835 915 1.458639 GGGTTGCAACAAGAGCAGCT 61.459 55.000 29.55 0.00 43.75 4.24
836 916 1.006922 GGGTTGCAACAAGAGCAGC 60.007 57.895 29.55 10.44 43.75 5.25
837 917 0.746063 TTGGGTTGCAACAAGAGCAG 59.254 50.000 29.55 0.00 43.75 4.24
838 918 1.412079 ATTGGGTTGCAACAAGAGCA 58.588 45.000 29.55 8.52 40.85 4.26
839 919 2.531522 AATTGGGTTGCAACAAGAGC 57.468 45.000 29.55 12.59 0.00 4.09
840 920 4.326504 AGAAATTGGGTTGCAACAAGAG 57.673 40.909 29.55 0.00 0.00 2.85
844 924 4.195416 GGAAAAGAAATTGGGTTGCAACA 58.805 39.130 29.55 11.21 0.00 3.33
850 930 3.067645 TGGGGGAAAAGAAATTGGGTT 57.932 42.857 0.00 0.00 0.00 4.11
853 933 2.978978 AGGTTGGGGGAAAAGAAATTGG 59.021 45.455 0.00 0.00 0.00 3.16
854 934 4.102367 TGAAGGTTGGGGGAAAAGAAATTG 59.898 41.667 0.00 0.00 0.00 2.32
862 942 0.777446 CCTCTGAAGGTTGGGGGAAA 59.223 55.000 0.00 0.00 37.94 3.13
865 945 1.140134 TTCCCTCTGAAGGTTGGGGG 61.140 60.000 0.00 0.00 41.59 5.40
866 946 0.329596 CTTCCCTCTGAAGGTTGGGG 59.670 60.000 0.00 0.00 45.66 4.96
867 947 3.965888 CTTCCCTCTGAAGGTTGGG 57.034 57.895 0.00 0.00 45.66 4.12
874 954 2.964209 ACAGTCTGTCTTCCCTCTGAA 58.036 47.619 0.00 0.00 0.00 3.02
875 955 2.630098 CAACAGTCTGTCTTCCCTCTGA 59.370 50.000 5.82 0.00 0.00 3.27
878 958 1.694696 ACCAACAGTCTGTCTTCCCTC 59.305 52.381 5.82 0.00 0.00 4.30
879 959 1.807814 ACCAACAGTCTGTCTTCCCT 58.192 50.000 5.82 0.00 0.00 4.20
887 991 0.590195 GCAGCTGAACCAACAGTCTG 59.410 55.000 20.43 0.00 40.87 3.51
936 1043 1.064017 ACTCTCCTCTCCTAGTGCTGG 60.064 57.143 0.00 0.00 0.00 4.85
937 1044 2.023673 CACTCTCCTCTCCTAGTGCTG 58.976 57.143 0.00 0.00 33.59 4.41
939 1046 2.428544 TCACTCTCCTCTCCTAGTGC 57.571 55.000 0.00 0.00 39.33 4.40
944 1051 0.329931 TCGCTTCACTCTCCTCTCCT 59.670 55.000 0.00 0.00 0.00 3.69
945 1052 0.454196 GTCGCTTCACTCTCCTCTCC 59.546 60.000 0.00 0.00 0.00 3.71
946 1053 1.459450 AGTCGCTTCACTCTCCTCTC 58.541 55.000 0.00 0.00 0.00 3.20
947 1054 1.543802 CAAGTCGCTTCACTCTCCTCT 59.456 52.381 0.00 0.00 0.00 3.69
948 1055 1.989430 CAAGTCGCTTCACTCTCCTC 58.011 55.000 0.00 0.00 0.00 3.71
949 1056 0.037790 GCAAGTCGCTTCACTCTCCT 60.038 55.000 0.00 0.00 37.77 3.69
950 1057 1.016653 GGCAAGTCGCTTCACTCTCC 61.017 60.000 0.00 0.00 41.91 3.71
951 1058 1.016653 GGGCAAGTCGCTTCACTCTC 61.017 60.000 0.00 0.00 41.91 3.20
952 1059 1.004440 GGGCAAGTCGCTTCACTCT 60.004 57.895 0.00 0.00 41.91 3.24
953 1060 0.674895 ATGGGCAAGTCGCTTCACTC 60.675 55.000 0.00 0.00 41.91 3.51
962 1069 3.554692 CGCGACGATGGGCAAGTC 61.555 66.667 0.00 0.00 0.00 3.01
963 1070 4.373116 ACGCGACGATGGGCAAGT 62.373 61.111 15.93 0.00 0.00 3.16
965 1072 3.867700 TTGACGCGACGATGGGCAA 62.868 57.895 15.93 0.00 0.00 4.52
966 1073 4.365505 TTGACGCGACGATGGGCA 62.366 61.111 15.93 0.00 0.00 5.36
969 1076 3.186047 GGGTTGACGCGACGATGG 61.186 66.667 15.93 0.00 0.00 3.51
994 1101 3.474570 GCCGCCCCTCATCTCTGT 61.475 66.667 0.00 0.00 0.00 3.41
1369 1515 3.492337 AGGGGAATTACAGTGCGAAAAA 58.508 40.909 0.00 0.00 0.00 1.94
1370 1516 3.149005 AGGGGAATTACAGTGCGAAAA 57.851 42.857 0.00 0.00 0.00 2.29
1371 1517 2.871096 AGGGGAATTACAGTGCGAAA 57.129 45.000 0.00 0.00 0.00 3.46
1374 1520 2.981859 AGTAGGGGAATTACAGTGCG 57.018 50.000 0.00 0.00 0.00 5.34
1376 1522 6.929606 GCAGTAATAGTAGGGGAATTACAGTG 59.070 42.308 7.08 0.00 38.15 3.66
1378 1524 7.155328 CAGCAGTAATAGTAGGGGAATTACAG 58.845 42.308 7.08 1.31 38.15 2.74
1380 1526 6.465084 CCAGCAGTAATAGTAGGGGAATTAC 58.535 44.000 0.00 0.00 36.68 1.89
1381 1527 5.012768 GCCAGCAGTAATAGTAGGGGAATTA 59.987 44.000 0.00 0.00 0.00 1.40
1386 1532 1.000955 CGCCAGCAGTAATAGTAGGGG 59.999 57.143 0.00 0.00 0.00 4.79
1394 1540 1.165270 GAAACCACGCCAGCAGTAAT 58.835 50.000 0.00 0.00 0.00 1.89
1398 1544 0.318107 CTTTGAAACCACGCCAGCAG 60.318 55.000 0.00 0.00 0.00 4.24
1405 1551 4.796312 CAGGTTAAACACTTTGAAACCACG 59.204 41.667 5.44 0.00 41.67 4.94
1406 1552 5.575218 CACAGGTTAAACACTTTGAAACCAC 59.425 40.000 5.44 0.00 41.67 4.16
1419 1565 8.723942 ATGATAGAATCAGACACAGGTTAAAC 57.276 34.615 0.00 0.00 43.53 2.01
1425 1572 5.193663 ACGATGATAGAATCAGACACAGG 57.806 43.478 0.00 0.00 43.53 4.00
1431 1578 8.678593 ACTAAGTGTACGATGATAGAATCAGA 57.321 34.615 0.00 0.00 43.53 3.27
1446 1593 7.254353 GGTGAGTTTTCAGTGAACTAAGTGTAC 60.254 40.741 4.68 3.55 37.46 2.90
1451 1601 5.277538 GCAGGTGAGTTTTCAGTGAACTAAG 60.278 44.000 4.68 0.00 37.46 2.18
1482 1632 0.674581 GTGTGTGCAGAGCAGGCATA 60.675 55.000 0.00 0.00 44.11 3.14
1491 1641 0.248843 TGTGTGACAGTGTGTGCAGA 59.751 50.000 0.00 0.00 0.00 4.26
1496 1646 3.515502 AGGCTATATGTGTGACAGTGTGT 59.484 43.478 0.00 0.00 0.00 3.72
1497 1647 3.867493 CAGGCTATATGTGTGACAGTGTG 59.133 47.826 0.00 0.00 0.00 3.82
1498 1648 3.769300 TCAGGCTATATGTGTGACAGTGT 59.231 43.478 0.00 0.00 0.00 3.55
1499 1649 4.391405 TCAGGCTATATGTGTGACAGTG 57.609 45.455 0.00 0.00 0.00 3.66
1500 1650 4.741837 GCATCAGGCTATATGTGTGACAGT 60.742 45.833 9.87 0.00 40.25 3.55
1501 1651 3.744942 GCATCAGGCTATATGTGTGACAG 59.255 47.826 9.87 0.00 40.25 3.51
1502 1652 3.732212 GCATCAGGCTATATGTGTGACA 58.268 45.455 9.87 0.00 40.25 3.58
1503 1653 2.733552 CGCATCAGGCTATATGTGTGAC 59.266 50.000 12.18 0.00 41.67 3.67
1512 1662 1.347050 AGCATCTTCGCATCAGGCTAT 59.653 47.619 0.00 0.00 41.67 2.97
1523 1673 4.400845 CAATCACAGTTTCAGCATCTTCG 58.599 43.478 0.00 0.00 0.00 3.79
1584 1734 6.702449 TTCCTGGACCTATAATATGCACAT 57.298 37.500 0.00 0.00 0.00 3.21
1591 1741 4.528596 GCTCTGCTTCCTGGACCTATAATA 59.471 45.833 0.00 0.00 0.00 0.98
1600 1750 1.209019 GAAGATGCTCTGCTTCCTGGA 59.791 52.381 0.00 0.00 35.60 3.86
1644 1794 7.410174 ACTTTCCCATTAGGATCACACAAATA 58.590 34.615 0.00 0.00 46.94 1.40
1668 1818 5.180868 ACATGAAGCAACAAGAAGATGAGAC 59.819 40.000 0.00 0.00 0.00 3.36
1686 1836 5.607477 AGTAAGTCGGAACAAGAACATGAA 58.393 37.500 0.00 0.00 0.00 2.57
1742 1892 9.809096 AAGAACTAACATATCTACATCACACAG 57.191 33.333 0.00 0.00 0.00 3.66
1784 1934 9.499479 AGTGATGCTTAATCATTTAGACCTATG 57.501 33.333 0.00 0.00 46.90 2.23
1848 2000 2.827755 TCTGTGGACCCTGCATAAGTA 58.172 47.619 0.00 0.00 0.00 2.24
1849 2001 1.656587 TCTGTGGACCCTGCATAAGT 58.343 50.000 0.00 0.00 0.00 2.24
1863 2016 2.493278 GTGTTCCCATTCCCAATCTGTG 59.507 50.000 0.00 0.00 0.00 3.66
1869 2022 1.501170 TCCTTGTGTTCCCATTCCCAA 59.499 47.619 0.00 0.00 0.00 4.12
1881 2034 3.804036 TCTGTCGATGTTTTCCTTGTGT 58.196 40.909 0.00 0.00 0.00 3.72
1888 2041 5.790495 GCATGTTTACTCTGTCGATGTTTTC 59.210 40.000 0.00 0.00 0.00 2.29
1895 2048 3.394674 TTGGCATGTTTACTCTGTCGA 57.605 42.857 0.00 0.00 0.00 4.20
1896 2049 3.498397 AGTTTGGCATGTTTACTCTGTCG 59.502 43.478 0.00 0.00 0.00 4.35
1904 2075 3.701542 TGTGTTGGAGTTTGGCATGTTTA 59.298 39.130 0.00 0.00 0.00 2.01
1925 2096 8.456471 TGAAATCTGAAATGAAATCACTAGCTG 58.544 33.333 0.00 0.00 0.00 4.24
1982 2153 8.997621 TTGTGCTAGTTTACTAAGAATCGATT 57.002 30.769 11.20 11.20 0.00 3.34
1994 2165 4.322101 CACGTCCATTGTGCTAGTTTAC 57.678 45.455 0.00 0.00 0.00 2.01
2011 2182 1.083015 GTTTCGTTGCGATGCACGT 60.083 52.632 9.76 0.00 44.60 4.49
2030 2202 1.563924 TACCTCCTCGCCTTTTAGCA 58.436 50.000 0.00 0.00 0.00 3.49
2035 2207 1.271840 TGGCATACCTCCTCGCCTTT 61.272 55.000 0.00 0.00 45.13 3.11
2059 2231 2.743928 GCCACTGGCCGAGACAAG 60.744 66.667 9.13 0.00 44.06 3.16
2081 2290 6.153510 GGCCCTCATATTCTTGTTCTCTTTTT 59.846 38.462 0.00 0.00 0.00 1.94
2114 2323 1.586564 CTCGAACGCCTAGCCTTCG 60.587 63.158 12.48 12.48 44.04 3.79
2118 2327 1.951631 GATGCTCGAACGCCTAGCC 60.952 63.158 4.49 0.00 35.33 3.93
2120 2329 0.179111 TTGGATGCTCGAACGCCTAG 60.179 55.000 0.00 0.00 0.00 3.02
2121 2330 0.248012 TTTGGATGCTCGAACGCCTA 59.752 50.000 0.00 0.00 0.00 3.93
2149 2358 1.670791 TGTCACAAACGACCCTTTCC 58.329 50.000 0.00 0.00 34.88 3.13
2152 2361 5.358725 ACTTTAAATGTCACAAACGACCCTT 59.641 36.000 0.00 0.00 34.88 3.95
2154 2363 4.973663 CACTTTAAATGTCACAAACGACCC 59.026 41.667 0.00 0.00 34.88 4.46
2156 2365 4.144051 CGCACTTTAAATGTCACAAACGAC 59.856 41.667 0.00 0.00 36.40 4.34
2157 2366 4.034163 TCGCACTTTAAATGTCACAAACGA 59.966 37.500 0.00 0.00 0.00 3.85
2158 2367 4.275662 TCGCACTTTAAATGTCACAAACG 58.724 39.130 0.00 0.00 0.00 3.60
2159 2368 5.507077 TCTCGCACTTTAAATGTCACAAAC 58.493 37.500 0.00 0.00 0.00 2.93
2160 2369 5.743026 TCTCGCACTTTAAATGTCACAAA 57.257 34.783 0.00 0.00 0.00 2.83
2176 2401 8.809159 TTTAAATTTTGAAATGTCATCTCGCA 57.191 26.923 0.00 0.00 32.48 5.10
2183 2408 8.950210 TGCCAAGTTTTAAATTTTGAAATGTCA 58.050 25.926 11.64 0.00 0.00 3.58
2195 2420 3.072330 CCCCACCTTGCCAAGTTTTAAAT 59.928 43.478 3.37 0.00 0.00 1.40
2199 2424 1.695114 GCCCCACCTTGCCAAGTTTT 61.695 55.000 3.37 0.00 0.00 2.43
2205 2430 1.000233 CTAATGCCCCACCTTGCCA 60.000 57.895 0.00 0.00 0.00 4.92
2224 2449 4.488879 GTCATCATTGCTTTGTTTCCTCC 58.511 43.478 0.00 0.00 0.00 4.30
2240 2465 0.942252 CTATCCGACCGTCGTCATCA 59.058 55.000 19.13 0.00 39.11 3.07
2243 2468 0.812811 CTCCTATCCGACCGTCGTCA 60.813 60.000 19.13 6.25 39.11 4.35


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

AutoCloner maintained by Alex Coulton.