Multiple sequence alignment - TraesCS5B01G077900

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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 TraesCS5B01G077900 chr5B 100.000 3645 0 0 1 3645 94047361 94051005 0.000000e+00 6732.0
1 TraesCS5B01G077900 chr5B 86.891 1724 190 20 999 2704 94087227 94088932 0.000000e+00 1899.0
2 TraesCS5B01G077900 chr5D 94.013 1971 65 22 765 2728 88464828 88466752 0.000000e+00 2937.0
3 TraesCS5B01G077900 chr5D 86.833 1724 179 19 999 2704 88469769 88471462 0.000000e+00 1882.0
4 TraesCS5B01G077900 chr5D 90.395 760 47 6 1 736 88464084 88464841 0.000000e+00 976.0
5 TraesCS5B01G077900 chr5D 83.765 850 45 37 2812 3625 88466916 88467708 0.000000e+00 719.0
6 TraesCS5B01G077900 chr5D 97.619 84 2 0 2727 2810 88466789 88466872 1.050000e-30 145.0
7 TraesCS5B01G077900 chr2D 87.013 1771 191 24 969 2719 610378211 610376460 0.000000e+00 1960.0
8 TraesCS5B01G077900 chr2D 85.722 1744 203 31 1000 2719 610404621 610402900 0.000000e+00 1799.0
9 TraesCS5B01G077900 chr5A 87.136 1718 187 19 999 2704 82299960 82301655 0.000000e+00 1917.0
10 TraesCS5B01G077900 chr5A 87.746 1575 123 29 1045 2584 567021747 567023286 0.000000e+00 1775.0
11 TraesCS5B01G077900 chr5A 84.114 598 68 17 1 594 548433774 548433200 1.480000e-153 553.0
12 TraesCS5B01G077900 chr5A 84.114 598 68 17 1 594 548481470 548480896 1.480000e-153 553.0
13 TraesCS5B01G077900 chr5A 88.814 447 47 2 1 444 548462524 548462078 2.470000e-151 545.0
14 TraesCS5B01G077900 chr5A 92.285 337 26 0 3308 3644 81803647 81803983 2.550000e-131 479.0
15 TraesCS5B01G077900 chr5A 80.000 355 35 20 2968 3300 81802307 81802647 2.830000e-56 230.0
16 TraesCS5B01G077900 chr5A 82.353 187 22 6 3390 3566 567023784 567023969 6.300000e-33 152.0
17 TraesCS5B01G077900 chr5A 100.000 43 0 0 2603 2645 567023284 567023326 3.020000e-11 80.5
18 TraesCS5B01G077900 chr2A 85.815 1706 205 28 969 2649 743266998 743265305 0.000000e+00 1775.0
19 TraesCS5B01G077900 chr2B 85.409 1309 149 28 969 2260 745769307 745768024 0.000000e+00 1321.0
20 TraesCS5B01G077900 chr2B 89.639 830 66 11 1816 2631 41473546 41472723 0.000000e+00 1038.0
21 TraesCS5B01G077900 chr2B 87.500 584 52 14 1073 1640 41474199 41473621 0.000000e+00 654.0
22 TraesCS5B01G077900 chr7A 87.368 1140 74 19 1048 2151 193686501 193685396 0.000000e+00 1243.0
23 TraesCS5B01G077900 chr7A 94.318 440 24 1 2139 2578 193685226 193684788 0.000000e+00 673.0
24 TraesCS5B01G077900 chr7A 82.353 187 19 7 3390 3566 193684283 193684101 2.270000e-32 150.0
25 TraesCS5B01G077900 chr1A 86.478 917 68 24 1035 1929 590767960 590767078 0.000000e+00 955.0
26 TraesCS5B01G077900 chr1A 92.962 611 38 4 1978 2584 590766866 590766257 0.000000e+00 885.0
27 TraesCS5B01G077900 chr1A 83.333 204 21 6 3390 3583 590765654 590765454 3.740000e-40 176.0
28 TraesCS5B01G077900 chr1D 86.989 538 60 7 64 592 468862927 468862391 6.740000e-167 597.0
29 TraesCS5B01G077900 chr3B 88.344 326 31 5 1 323 385480713 385481034 5.710000e-103 385.0
30 TraesCS5B01G077900 chr4D 81.971 416 65 5 189 594 264061035 264061450 9.690000e-91 344.0
31 TraesCS5B01G077900 chr7B 83.436 326 38 8 1 323 351930716 351931028 4.610000e-74 289.0


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 TraesCS5B01G077900 chr5B 94047361 94051005 3644 False 6732.000000 6732 100.0000 1 3645 1 chr5B.!!$F1 3644
1 TraesCS5B01G077900 chr5B 94087227 94088932 1705 False 1899.000000 1899 86.8910 999 2704 1 chr5B.!!$F2 1705
2 TraesCS5B01G077900 chr5D 88464084 88471462 7378 False 1331.800000 2937 90.5250 1 3625 5 chr5D.!!$F1 3624
3 TraesCS5B01G077900 chr2D 610376460 610378211 1751 True 1960.000000 1960 87.0130 969 2719 1 chr2D.!!$R1 1750
4 TraesCS5B01G077900 chr2D 610402900 610404621 1721 True 1799.000000 1799 85.7220 1000 2719 1 chr2D.!!$R2 1719
5 TraesCS5B01G077900 chr5A 82299960 82301655 1695 False 1917.000000 1917 87.1360 999 2704 1 chr5A.!!$F1 1705
6 TraesCS5B01G077900 chr5A 567021747 567023969 2222 False 669.166667 1775 90.0330 1045 3566 3 chr5A.!!$F3 2521
7 TraesCS5B01G077900 chr5A 548433200 548433774 574 True 553.000000 553 84.1140 1 594 1 chr5A.!!$R1 593
8 TraesCS5B01G077900 chr5A 548480896 548481470 574 True 553.000000 553 84.1140 1 594 1 chr5A.!!$R3 593
9 TraesCS5B01G077900 chr5A 81802307 81803983 1676 False 354.500000 479 86.1425 2968 3644 2 chr5A.!!$F2 676
10 TraesCS5B01G077900 chr2A 743265305 743266998 1693 True 1775.000000 1775 85.8150 969 2649 1 chr2A.!!$R1 1680
11 TraesCS5B01G077900 chr2B 745768024 745769307 1283 True 1321.000000 1321 85.4090 969 2260 1 chr2B.!!$R1 1291
12 TraesCS5B01G077900 chr2B 41472723 41474199 1476 True 846.000000 1038 88.5695 1073 2631 2 chr2B.!!$R2 1558
13 TraesCS5B01G077900 chr7A 193684101 193686501 2400 True 688.666667 1243 88.0130 1048 3566 3 chr7A.!!$R1 2518
14 TraesCS5B01G077900 chr1A 590765454 590767960 2506 True 672.000000 955 87.5910 1035 3583 3 chr1A.!!$R1 2548
15 TraesCS5B01G077900 chr1D 468862391 468862927 536 True 597.000000 597 86.9890 64 592 1 chr1D.!!$R1 528

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
629 647 0.248949 CGGAGGTTAACTCTAGCGGC 60.249 60.000 5.42 0.0 45.83 6.53 F
789 816 0.964358 AGACTAGTAACCGTGGCGCT 60.964 55.000 7.64 0.0 0.00 5.92 F
1500 1570 1.076923 GTCCCTCGTCCAGAGCCTA 60.077 63.158 0.00 0.0 45.54 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1924 0.171455 CTTCTTCTCCACGTCTCGGG 59.829 60.0 0.00 0.00 0.00 5.14 R
1941 2056 0.603707 ACACATCGTGGTGCTGAAGG 60.604 55.0 8.71 0.00 42.55 3.46 R
2810 3501 0.592247 GCGCTTTCATGGGTAATGCG 60.592 55.0 16.63 16.63 46.88 4.73 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
37 38 3.929610 AGCTCTAGAACTAAAGCAAAGCG 59.070 43.478 9.37 0.00 37.22 4.68
84 85 0.366871 CTTCACGGAAGCAACGATCG 59.633 55.000 14.88 14.88 32.78 3.69
116 117 3.719871 TCCCAGACTCATTAGCAAGGTA 58.280 45.455 0.00 0.00 0.00 3.08
145 146 4.715534 TCCCTTACCATCACAACTTCAA 57.284 40.909 0.00 0.00 0.00 2.69
148 149 3.758554 CCTTACCATCACAACTTCAAGGG 59.241 47.826 0.00 0.00 0.00 3.95
177 178 1.003580 TCCTCATGCTGGTTCAAGGTC 59.996 52.381 4.83 0.00 0.00 3.85
257 260 5.356470 GGTAGATAGAGCCCGTTACGAATAT 59.644 44.000 6.24 0.00 0.00 1.28
262 265 3.383825 AGAGCCCGTTACGAATATCACTT 59.616 43.478 6.24 0.00 0.00 3.16
394 398 2.631696 GATGAAATGCGGCGTCCACG 62.632 60.000 9.37 0.00 43.27 4.94
432 436 1.079750 GAGGCGGTCTCTTCCACAC 60.080 63.158 1.53 0.00 39.38 3.82
488 492 6.482308 AGTCGTTGCTCTTATAAAGTTTGTGT 59.518 34.615 0.00 0.00 0.00 3.72
497 501 8.827177 TCTTATAAAGTTTGTGTCCAGTACTG 57.173 34.615 16.34 16.34 0.00 2.74
520 538 2.239400 ACGATCAGGATCAGGCGATTA 58.761 47.619 9.72 0.00 37.69 1.75
523 541 3.427368 CGATCAGGATCAGGCGATTAGAG 60.427 52.174 9.72 0.00 37.69 2.43
531 549 3.826524 TCAGGCGATTAGAGAGTCTCAT 58.173 45.455 22.05 7.77 32.06 2.90
567 585 1.202486 ACCGTTGCCACCAGATATACG 60.202 52.381 0.00 0.00 0.00 3.06
575 593 0.966179 ACCAGATATACGATGCCGCA 59.034 50.000 0.00 0.00 39.95 5.69
577 595 2.224185 ACCAGATATACGATGCCGCAAA 60.224 45.455 0.00 0.00 39.95 3.68
629 647 0.248949 CGGAGGTTAACTCTAGCGGC 60.249 60.000 5.42 0.00 45.83 6.53
726 753 6.944862 AGAAGAAAAGTGATTCTACAGCCAAT 59.055 34.615 0.00 0.00 38.69 3.16
728 755 6.240894 AGAAAAGTGATTCTACAGCCAATCA 58.759 36.000 0.00 0.00 37.88 2.57
729 756 6.373774 AGAAAAGTGATTCTACAGCCAATCAG 59.626 38.462 0.00 0.00 39.22 2.90
730 757 5.426689 AAGTGATTCTACAGCCAATCAGA 57.573 39.130 0.00 0.00 39.22 3.27
731 758 4.764172 AGTGATTCTACAGCCAATCAGAC 58.236 43.478 0.00 0.00 39.22 3.51
732 759 4.469227 AGTGATTCTACAGCCAATCAGACT 59.531 41.667 0.00 0.00 39.22 3.24
733 760 5.658634 AGTGATTCTACAGCCAATCAGACTA 59.341 40.000 0.00 0.00 39.22 2.59
734 761 5.982516 GTGATTCTACAGCCAATCAGACTAG 59.017 44.000 0.00 0.00 39.22 2.57
735 762 5.658634 TGATTCTACAGCCAATCAGACTAGT 59.341 40.000 0.00 0.00 34.71 2.57
736 763 6.155221 TGATTCTACAGCCAATCAGACTAGTT 59.845 38.462 0.00 0.00 34.71 2.24
737 764 6.360370 TTCTACAGCCAATCAGACTAGTTT 57.640 37.500 0.00 0.00 0.00 2.66
738 765 6.360370 TCTACAGCCAATCAGACTAGTTTT 57.640 37.500 0.00 0.00 0.00 2.43
739 766 6.769512 TCTACAGCCAATCAGACTAGTTTTT 58.230 36.000 0.00 0.00 0.00 1.94
782 809 8.848182 AGAACTATCCAATAAGACTAGTAACCG 58.152 37.037 0.00 0.00 0.00 4.44
789 816 0.964358 AGACTAGTAACCGTGGCGCT 60.964 55.000 7.64 0.00 0.00 5.92
811 838 5.616488 TTTACCGAGCCATGAAAGTAAAC 57.384 39.130 0.00 0.00 0.00 2.01
842 869 1.506309 TTGTCCACGCATGTGCAGAC 61.506 55.000 17.87 17.87 45.04 3.51
882 909 2.645604 GGATCCTTCCCAATCCCCA 58.354 57.895 3.84 0.00 36.26 4.96
883 910 1.161603 GGATCCTTCCCAATCCCCAT 58.838 55.000 3.84 0.00 36.26 4.00
886 913 2.295269 TCCTTCCCAATCCCCATACA 57.705 50.000 0.00 0.00 0.00 2.29
887 914 2.800656 TCCTTCCCAATCCCCATACAT 58.199 47.619 0.00 0.00 0.00 2.29
888 915 3.961239 TCCTTCCCAATCCCCATACATA 58.039 45.455 0.00 0.00 0.00 2.29
889 916 3.655777 TCCTTCCCAATCCCCATACATAC 59.344 47.826 0.00 0.00 0.00 2.39
890 917 3.559171 CCTTCCCAATCCCCATACATACG 60.559 52.174 0.00 0.00 0.00 3.06
891 918 2.696775 TCCCAATCCCCATACATACGT 58.303 47.619 0.00 0.00 0.00 3.57
892 919 3.859370 TCCCAATCCCCATACATACGTA 58.141 45.455 0.00 0.00 0.00 3.57
894 921 3.581755 CCAATCCCCATACATACGTACG 58.418 50.000 15.01 15.01 0.00 3.67
895 922 3.256383 CCAATCCCCATACATACGTACGA 59.744 47.826 24.41 6.04 0.00 3.43
896 923 4.262121 CCAATCCCCATACATACGTACGAA 60.262 45.833 24.41 1.85 0.00 3.85
897 924 3.988379 TCCCCATACATACGTACGAAC 57.012 47.619 24.41 0.00 0.00 3.95
898 925 3.554934 TCCCCATACATACGTACGAACT 58.445 45.455 24.41 1.48 0.00 3.01
899 926 3.953612 TCCCCATACATACGTACGAACTT 59.046 43.478 24.41 1.05 0.00 2.66
900 927 5.129634 TCCCCATACATACGTACGAACTTA 58.870 41.667 24.41 3.75 0.00 2.24
901 928 5.008613 TCCCCATACATACGTACGAACTTAC 59.991 44.000 24.41 0.00 0.00 2.34
907 934 3.090598 CGTACGAACTTACGTGCCA 57.909 52.632 10.44 0.00 46.02 4.92
947 974 4.222145 CCACTTCAGGGCTACTACTACAAA 59.778 45.833 0.00 0.00 0.00 2.83
948 975 5.104900 CCACTTCAGGGCTACTACTACAAAT 60.105 44.000 0.00 0.00 0.00 2.32
949 976 6.043411 CACTTCAGGGCTACTACTACAAATC 58.957 44.000 0.00 0.00 0.00 2.17
1004 1038 2.677971 CACTACTACGTGCCATGGC 58.322 57.895 30.54 30.54 42.35 4.40
1496 1566 4.180946 CGCGTCCCTCGTCCAGAG 62.181 72.222 0.00 0.00 46.44 3.35
1500 1570 1.076923 GTCCCTCGTCCAGAGCCTA 60.077 63.158 0.00 0.00 45.54 3.93
1811 1921 4.083600 GCGAACGCACAATGCCGA 62.084 61.111 14.26 0.00 41.12 5.54
1814 1924 1.869132 GAACGCACAATGCCGATGC 60.869 57.895 1.06 0.00 41.12 3.91
1924 2039 2.263077 GCATCGTCTTGGTGAGTACTG 58.737 52.381 0.00 0.00 0.00 2.74
1930 2045 3.368013 CGTCTTGGTGAGTACTGGCATTA 60.368 47.826 0.00 0.00 0.00 1.90
1931 2046 4.184629 GTCTTGGTGAGTACTGGCATTAG 58.815 47.826 0.00 0.00 0.00 1.73
1932 2047 2.691409 TGGTGAGTACTGGCATTAGC 57.309 50.000 0.00 0.00 41.10 3.09
1933 2048 1.905894 TGGTGAGTACTGGCATTAGCA 59.094 47.619 0.00 0.00 44.61 3.49
1934 2049 2.505407 TGGTGAGTACTGGCATTAGCAT 59.495 45.455 0.00 0.00 44.61 3.79
1935 2050 2.874701 GGTGAGTACTGGCATTAGCATG 59.125 50.000 0.00 0.00 44.61 4.06
1936 2051 3.535561 GTGAGTACTGGCATTAGCATGT 58.464 45.455 0.00 0.00 44.61 3.21
1938 2053 4.508124 GTGAGTACTGGCATTAGCATGTAC 59.492 45.833 0.00 11.50 44.17 2.90
1975 2262 0.595588 TGTGTGCCATTTTCGCGATT 59.404 45.000 10.88 0.00 0.00 3.34
2170 2673 1.816863 GCCGACTGGTTGAGGAGTCA 61.817 60.000 0.00 0.00 38.87 3.41
2204 2707 0.682852 ACCTTACCTGCAGTGCGTTA 59.317 50.000 13.81 0.00 0.00 3.18
2357 2860 3.553828 GGGACGTCAAAATCTGGGATA 57.446 47.619 18.91 0.00 0.00 2.59
2523 3027 0.961019 TGCTTTGAGTGGGATGTTGC 59.039 50.000 0.00 0.00 0.00 4.17
2645 3168 1.417517 TGCTCTCTGCTTCCACTTGAA 59.582 47.619 0.00 0.00 43.37 2.69
2739 3430 9.349713 AGTGATTTCTTTAGAACATTACAACCA 57.650 29.630 0.00 0.00 33.13 3.67
2810 3501 7.694388 TCGATATGACAAGTAATGCAGTAAC 57.306 36.000 0.00 0.00 0.00 2.50
2811 3502 6.416750 TCGATATGACAAGTAATGCAGTAACG 59.583 38.462 0.00 0.00 0.00 3.18
2812 3503 4.600012 ATGACAAGTAATGCAGTAACGC 57.400 40.909 0.00 0.00 0.00 4.84
2927 3711 6.311690 GTCATACAGAACTTGAGTTTCTAGCC 59.688 42.308 0.00 0.00 38.56 3.93
2941 3725 4.685169 TTCTAGCCGCAGAAAAATCTTG 57.315 40.909 0.00 0.00 31.63 3.02
2951 3735 3.192212 CAGAAAAATCTTGGGAGAGGCAC 59.808 47.826 0.00 0.00 34.85 5.01
2956 3740 0.842030 TCTTGGGAGAGGCACCACAT 60.842 55.000 0.00 0.00 36.27 3.21
3021 3805 2.749076 CGTTGGATGATGATTGTGTGGT 59.251 45.455 0.00 0.00 0.00 4.16
3052 3839 3.121868 TTCCTCCCCTCCCACACCA 62.122 63.158 0.00 0.00 0.00 4.17
3065 3852 3.959975 CACCACCAAACGTGCCGG 61.960 66.667 0.00 0.00 41.53 6.13
3168 3989 1.457643 TCTAGCCCCTCCCGTGATG 60.458 63.158 0.00 0.00 0.00 3.07
3170 3991 2.946988 CTAGCCCCTCCCGTGATGGA 62.947 65.000 0.00 0.00 42.00 3.41
3286 4109 0.534873 GCGAGCTCCTTCCTTCTCTT 59.465 55.000 8.47 0.00 0.00 2.85
3290 4113 1.187087 GCTCCTTCCTTCTCTTCGGA 58.813 55.000 0.00 0.00 0.00 4.55
3309 5124 2.827755 GAGAGGTCCTCCCTTCTTCTT 58.172 52.381 15.72 0.00 46.51 2.52
3462 5278 6.653273 TGATTCAGAGATTAACGCTCTTTG 57.347 37.500 6.90 0.00 40.60 2.77
3505 5321 6.978343 TGCAAACACATCAAGTATACCTAC 57.022 37.500 0.00 0.00 0.00 3.18
3614 5439 5.841957 ACTTCATTGCCAATACAGGAATC 57.158 39.130 0.00 0.00 0.00 2.52
3644 5781 5.635417 TTTGGATAACGATGACAATGCAA 57.365 34.783 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 9.434420 AGATGAGATAGCAGATTATTTAGCAAC 57.566 33.333 0.00 0.00 0.00 4.17
79 80 2.597305 CTGGGAAAGTTTCGTACGATCG 59.403 50.000 20.27 14.88 0.00 3.69
84 85 3.986277 TGAGTCTGGGAAAGTTTCGTAC 58.014 45.455 9.46 5.15 0.00 3.67
116 117 3.299503 GTGATGGTAAGGGAATGCCATT 58.700 45.455 0.00 0.00 44.57 3.16
145 146 1.115467 CATGAGGACTACTTCGCCCT 58.885 55.000 0.00 0.00 0.00 5.19
148 149 1.565305 CAGCATGAGGACTACTTCGC 58.435 55.000 0.00 0.00 39.69 4.70
177 178 7.658179 ATCAGATAATACATTTGCGGTACAG 57.342 36.000 0.00 0.00 0.00 2.74
257 260 3.987868 GTCGATTGTGCAGAACTAAGTGA 59.012 43.478 0.00 0.00 0.00 3.41
262 265 4.926860 CAATGTCGATTGTGCAGAACTA 57.073 40.909 0.00 0.00 35.19 2.24
294 297 4.222588 TGGCTGCAGCTAATTGGTTTTTAT 59.777 37.500 35.82 0.00 41.70 1.40
371 375 0.317269 GACGCCGCATTTCATCATGG 60.317 55.000 0.00 0.00 0.00 3.66
394 398 5.354513 GCCTCAGGGTTTAGTTAAGATCAAC 59.645 44.000 0.00 0.00 34.45 3.18
450 454 2.436417 CAACGACTCCCAATCAACCAT 58.564 47.619 0.00 0.00 0.00 3.55
488 492 7.390790 TGATCCTGATCGTACCAGTACTGGA 62.391 48.000 41.87 25.12 45.70 3.86
497 501 0.039074 CGCCTGATCCTGATCGTACC 60.039 60.000 2.91 0.00 40.63 3.34
498 502 0.952280 TCGCCTGATCCTGATCGTAC 59.048 55.000 2.91 0.00 40.63 3.67
499 503 1.911057 ATCGCCTGATCCTGATCGTA 58.089 50.000 2.91 0.00 40.63 3.43
501 505 2.489722 TCTAATCGCCTGATCCTGATCG 59.510 50.000 2.91 0.00 40.63 3.69
502 506 3.761218 TCTCTAATCGCCTGATCCTGATC 59.239 47.826 0.06 0.06 38.29 2.92
503 507 3.763360 CTCTCTAATCGCCTGATCCTGAT 59.237 47.826 0.00 0.00 32.24 2.90
504 508 3.153130 CTCTCTAATCGCCTGATCCTGA 58.847 50.000 0.00 0.00 32.24 3.86
505 509 2.890311 ACTCTCTAATCGCCTGATCCTG 59.110 50.000 0.00 0.00 32.24 3.86
507 511 3.153919 AGACTCTCTAATCGCCTGATCC 58.846 50.000 0.00 0.00 32.24 3.36
520 538 4.837860 AGTTTGTGAAGGATGAGACTCTCT 59.162 41.667 7.58 0.00 0.00 3.10
523 541 4.867608 GCTAGTTTGTGAAGGATGAGACTC 59.132 45.833 0.00 0.00 0.00 3.36
531 549 1.414919 ACGGTGCTAGTTTGTGAAGGA 59.585 47.619 0.00 0.00 0.00 3.36
567 585 0.445436 CTGACTGTCTTTGCGGCATC 59.555 55.000 2.28 0.00 0.00 3.91
612 630 0.822164 TGGCCGCTAGAGTTAACCTC 59.178 55.000 0.88 0.00 40.80 3.85
629 647 4.392940 GGGTACTCATCTGATTGGATTGG 58.607 47.826 0.00 0.00 0.00 3.16
660 687 3.120511 GCAAAACGTCTTGGACTCATCTC 60.121 47.826 3.40 0.00 0.00 2.75
756 783 8.848182 CGGTTACTAGTCTTATTGGATAGTTCT 58.152 37.037 0.00 0.00 0.00 3.01
757 784 8.628280 ACGGTTACTAGTCTTATTGGATAGTTC 58.372 37.037 0.00 0.00 0.00 3.01
758 785 8.411683 CACGGTTACTAGTCTTATTGGATAGTT 58.588 37.037 0.00 0.00 0.00 2.24
759 786 7.014038 CCACGGTTACTAGTCTTATTGGATAGT 59.986 40.741 0.00 0.00 0.00 2.12
760 787 7.368833 CCACGGTTACTAGTCTTATTGGATAG 58.631 42.308 0.00 0.00 0.00 2.08
761 788 6.239120 GCCACGGTTACTAGTCTTATTGGATA 60.239 42.308 14.09 0.00 0.00 2.59
762 789 5.452917 GCCACGGTTACTAGTCTTATTGGAT 60.453 44.000 14.09 0.00 0.00 3.41
763 790 4.142093 GCCACGGTTACTAGTCTTATTGGA 60.142 45.833 14.09 0.00 0.00 3.53
764 791 4.117685 GCCACGGTTACTAGTCTTATTGG 58.882 47.826 0.00 3.49 0.00 3.16
765 792 3.795101 CGCCACGGTTACTAGTCTTATTG 59.205 47.826 0.00 0.00 0.00 1.90
766 793 3.736126 GCGCCACGGTTACTAGTCTTATT 60.736 47.826 0.00 0.00 0.00 1.40
767 794 2.223665 GCGCCACGGTTACTAGTCTTAT 60.224 50.000 0.00 0.00 0.00 1.73
768 795 1.133025 GCGCCACGGTTACTAGTCTTA 59.867 52.381 0.00 0.00 0.00 2.10
769 796 0.108945 GCGCCACGGTTACTAGTCTT 60.109 55.000 0.00 0.00 0.00 3.01
780 807 3.186047 CTCGGTAAAGCGCCACGG 61.186 66.667 2.29 4.64 0.00 4.94
782 809 3.497031 GGCTCGGTAAAGCGCCAC 61.497 66.667 2.29 0.00 43.45 5.01
789 816 4.456566 GGTTTACTTTCATGGCTCGGTAAA 59.543 41.667 0.00 0.00 0.00 2.01
842 869 2.203070 CCTGCGGGAAGGGAATCG 60.203 66.667 5.28 0.00 33.28 3.34
894 921 4.224317 GAGGATCACTGGCACGTAAGTTC 61.224 52.174 0.00 0.00 42.61 3.01
895 922 2.353803 GAGGATCACTGGCACGTAAGTT 60.354 50.000 0.00 0.00 42.61 2.66
896 923 1.204941 GAGGATCACTGGCACGTAAGT 59.795 52.381 0.00 0.00 45.83 2.24
897 924 1.471676 GGAGGATCACTGGCACGTAAG 60.472 57.143 0.00 0.00 40.26 2.34
898 925 0.535335 GGAGGATCACTGGCACGTAA 59.465 55.000 0.00 0.00 36.25 3.18
899 926 0.613572 TGGAGGATCACTGGCACGTA 60.614 55.000 0.00 0.00 36.25 3.57
900 927 1.913262 TGGAGGATCACTGGCACGT 60.913 57.895 0.00 0.00 36.25 4.49
901 928 1.448540 GTGGAGGATCACTGGCACG 60.449 63.158 0.00 0.00 36.25 5.34
902 929 0.326264 AAGTGGAGGATCACTGGCAC 59.674 55.000 0.00 0.00 46.17 5.01
903 930 0.325933 CAAGTGGAGGATCACTGGCA 59.674 55.000 0.00 0.00 46.17 4.92
904 931 0.615331 TCAAGTGGAGGATCACTGGC 59.385 55.000 0.00 0.00 46.17 4.85
905 932 1.065854 GGTCAAGTGGAGGATCACTGG 60.066 57.143 0.00 0.00 46.17 4.00
906 933 1.625315 TGGTCAAGTGGAGGATCACTG 59.375 52.381 0.00 0.00 46.17 3.66
947 974 3.954904 ACAGCGAGTGTTATGGTAGAGAT 59.045 43.478 0.00 0.00 34.94 2.75
948 975 3.128764 CACAGCGAGTGTTATGGTAGAGA 59.871 47.826 4.42 0.00 43.40 3.10
949 976 3.439293 CACAGCGAGTGTTATGGTAGAG 58.561 50.000 4.42 0.00 43.40 2.43
975 1002 2.014857 CGTAGTAGTGCTAGGCAGTCA 58.985 52.381 2.98 0.00 41.66 3.41
1155 1203 1.071987 CTTGAGCAGGTGCAGGTGA 59.928 57.895 4.48 0.00 45.16 4.02
1496 1566 3.701604 CTGGCGTCGTGGAGTAGGC 62.702 68.421 0.00 0.00 0.00 3.93
1629 1738 0.831307 TCTCCTCGACGATCTCCTGA 59.169 55.000 0.00 0.00 0.00 3.86
1802 1911 2.514592 CTCGGGCATCGGCATTGT 60.515 61.111 0.00 0.00 43.71 2.71
1811 1921 1.949847 CTTCTCCACGTCTCGGGCAT 61.950 60.000 0.00 0.00 0.00 4.40
1814 1924 0.171455 CTTCTTCTCCACGTCTCGGG 59.829 60.000 0.00 0.00 0.00 5.14
1869 1983 4.161565 GTGTCAGTGTAATACCCAGGATCA 59.838 45.833 0.00 0.00 0.00 2.92
1940 2055 1.672356 ACATCGTGGTGCTGAAGGC 60.672 57.895 0.00 0.00 42.22 4.35
1941 2056 0.603707 ACACATCGTGGTGCTGAAGG 60.604 55.000 8.71 0.00 42.55 3.46
1943 2058 1.506309 GCACACATCGTGGTGCTGAA 61.506 55.000 9.32 0.00 46.45 3.02
1975 2262 3.023832 TGTCACAGTCTCACTCTCACAA 58.976 45.455 0.00 0.00 0.00 3.33
2047 2367 1.741770 GGTCAGTGCCGATGTGTCC 60.742 63.158 0.00 0.00 0.00 4.02
2170 2673 3.518303 GGTAAGGTAGGTTGGTGATGTCT 59.482 47.826 0.00 0.00 0.00 3.41
2204 2707 1.754226 GAGCCGAAGAGTCTCCTTGAT 59.246 52.381 0.00 0.00 0.00 2.57
2271 2774 2.063015 ATGAAAGCCACCCACCGTGA 62.063 55.000 0.00 0.00 46.20 4.35
2357 2860 3.382111 CCTGAACTCCTCTGGCGT 58.618 61.111 0.00 0.00 36.46 5.68
2645 3168 5.574970 ATTTCTTCAGAAACCTGTCTCCT 57.425 39.130 4.08 0.00 45.55 3.69
2648 3171 7.967908 TCTTCTATTTCTTCAGAAACCTGTCT 58.032 34.615 4.08 0.00 45.55 3.41
2810 3501 0.592247 GCGCTTTCATGGGTAATGCG 60.592 55.000 16.63 16.63 46.88 4.73
2811 3502 0.740737 AGCGCTTTCATGGGTAATGC 59.259 50.000 2.64 0.00 36.11 3.56
2812 3503 2.031682 GCTAGCGCTTTCATGGGTAATG 60.032 50.000 18.68 0.00 37.66 1.90
2845 3629 4.986034 GGCTACCGCTTTTGTAAAATTTGT 59.014 37.500 0.00 0.00 36.09 2.83
2927 3711 2.421424 CCTCTCCCAAGATTTTTCTGCG 59.579 50.000 0.00 0.00 0.00 5.18
2941 3725 0.912486 ACTAATGTGGTGCCTCTCCC 59.088 55.000 0.00 0.00 0.00 4.30
2976 3760 3.921677 TCACAAATCGACTGACCCTAAC 58.078 45.455 3.45 0.00 0.00 2.34
2982 3766 1.792949 ACGCTTCACAAATCGACTGAC 59.207 47.619 3.45 0.00 0.00 3.51
3021 3805 1.978580 GGGAGGAAGAAGGTTCAGACA 59.021 52.381 0.00 0.00 0.00 3.41
3148 3969 3.541713 CACGGGAGGGGCTAGAGC 61.542 72.222 0.00 0.00 41.14 4.09
3228 4051 1.212935 CATCTTAGGGTTCAGGGGTGG 59.787 57.143 0.00 0.00 0.00 4.61
3230 4053 1.082194 TCCATCTTAGGGTTCAGGGGT 59.918 52.381 0.00 0.00 0.00 4.95
3309 5124 3.205519 TGAATGGAGGAAGGAGAAGGA 57.794 47.619 0.00 0.00 0.00 3.36
3371 5186 8.902540 TCAGAAGATTTTTCAGTTTAGCTACA 57.097 30.769 0.00 0.00 0.00 2.74
3462 5278 3.119708 GCATCCAGAAATCACCAGTCAAC 60.120 47.826 0.00 0.00 0.00 3.18
3505 5321 7.672983 ATTGGTTGTGTACATTCTAGTCTTG 57.327 36.000 0.00 0.00 0.00 3.02
3614 5439 7.786178 TGTCATCGTTATCCAAATAGAAAGG 57.214 36.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.