Multiple sequence alignment - TraesCS3A01G218600

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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 TraesCS3A01G218600 chr3A 100.000 2826 0 0 1 2826 401413277 401410452 0.000000e+00 5219.0
1 TraesCS3A01G218600 chr3A 82.009 906 158 5 1 905 711694186 711693285 0.000000e+00 765.0
2 TraesCS3A01G218600 chr3A 90.909 66 3 2 2760 2825 575868126 575868188 5.020000e-13 86.1
3 TraesCS3A01G218600 chr3A 85.333 75 11 0 399 473 703382479 703382405 8.390000e-11 78.7
4 TraesCS3A01G218600 chr3D 93.797 1064 43 9 909 1969 322074792 322075835 0.000000e+00 1578.0
5 TraesCS3A01G218600 chr1D 91.015 857 72 4 1970 2826 329506454 329507305 0.000000e+00 1151.0
6 TraesCS3A01G218600 chr7D 90.995 844 70 5 1982 2825 478799662 478798825 0.000000e+00 1133.0
7 TraesCS3A01G218600 chr7D 90.662 846 72 6 1982 2825 611665640 611664800 0.000000e+00 1118.0
8 TraesCS3A01G218600 chr5D 91.707 820 63 4 1969 2788 464701900 464702714 0.000000e+00 1133.0
9 TraesCS3A01G218600 chr5D 90.651 845 74 4 1982 2826 423231173 423232012 0.000000e+00 1118.0
10 TraesCS3A01G218600 chr2B 90.559 858 76 3 1969 2826 593663151 593662299 0.000000e+00 1131.0
11 TraesCS3A01G218600 chr5B 90.548 857 76 2 1969 2825 617174753 617173902 0.000000e+00 1129.0
12 TraesCS3A01G218600 chr3B 90.974 842 65 6 1985 2825 708391930 708392761 0.000000e+00 1123.0
13 TraesCS3A01G218600 chr3B 90.292 855 75 8 1973 2825 264010459 264011307 0.000000e+00 1112.0
14 TraesCS3A01G218600 chr3B 95.741 634 18 6 901 1529 397557511 397558140 0.000000e+00 1013.0
15 TraesCS3A01G218600 chr3B 91.685 445 27 6 1521 1964 397559595 397560030 2.410000e-170 608.0
16 TraesCS3A01G218600 chr6B 89.492 571 60 0 318 888 256453109 256453679 0.000000e+00 723.0


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 TraesCS3A01G218600 chr3A 401410452 401413277 2825 True 5219.0 5219 100.000 1 2826 1 chr3A.!!$R1 2825
1 TraesCS3A01G218600 chr3A 711693285 711694186 901 True 765.0 765 82.009 1 905 1 chr3A.!!$R3 904
2 TraesCS3A01G218600 chr3D 322074792 322075835 1043 False 1578.0 1578 93.797 909 1969 1 chr3D.!!$F1 1060
3 TraesCS3A01G218600 chr1D 329506454 329507305 851 False 1151.0 1151 91.015 1970 2826 1 chr1D.!!$F1 856
4 TraesCS3A01G218600 chr7D 478798825 478799662 837 True 1133.0 1133 90.995 1982 2825 1 chr7D.!!$R1 843
5 TraesCS3A01G218600 chr7D 611664800 611665640 840 True 1118.0 1118 90.662 1982 2825 1 chr7D.!!$R2 843
6 TraesCS3A01G218600 chr5D 464701900 464702714 814 False 1133.0 1133 91.707 1969 2788 1 chr5D.!!$F2 819
7 TraesCS3A01G218600 chr5D 423231173 423232012 839 False 1118.0 1118 90.651 1982 2826 1 chr5D.!!$F1 844
8 TraesCS3A01G218600 chr2B 593662299 593663151 852 True 1131.0 1131 90.559 1969 2826 1 chr2B.!!$R1 857
9 TraesCS3A01G218600 chr5B 617173902 617174753 851 True 1129.0 1129 90.548 1969 2825 1 chr5B.!!$R1 856
10 TraesCS3A01G218600 chr3B 708391930 708392761 831 False 1123.0 1123 90.974 1985 2825 1 chr3B.!!$F2 840
11 TraesCS3A01G218600 chr3B 264010459 264011307 848 False 1112.0 1112 90.292 1973 2825 1 chr3B.!!$F1 852
12 TraesCS3A01G218600 chr3B 397557511 397560030 2519 False 810.5 1013 93.713 901 1964 2 chr3B.!!$F3 1063
13 TraesCS3A01G218600 chr6B 256453109 256453679 570 False 723.0 723 89.492 318 888 1 chr6B.!!$F1 570

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
189 190 0.035458 AGACCGGACTGCTTTTCCTG 59.965 55.0 9.46 0.00 0.00 3.86 F
690 691 0.169009 CCGCTTAAGCTGGTGAAAGC 59.831 55.0 24.33 13.97 43.88 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 3166 0.036732 TCTTCAGCGCCATTGGTCTT 59.963 50.0 2.29 0.0 0.00 3.01 R
2300 3780 0.321671 CGAGAACACAGGTCCACCAT 59.678 55.0 0.00 0.0 38.89 3.55 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
41 42 0.307760 CACACGAACAAGGAACAGGC 59.692 55.000 0.00 0.00 0.00 4.85
45 46 0.788391 CGAACAAGGAACAGGCGTAC 59.212 55.000 0.00 0.00 0.00 3.67
55 56 1.037493 ACAGGCGTACAGTCAGTGAA 58.963 50.000 0.00 0.00 0.00 3.18
58 59 0.601558 GGCGTACAGTCAGTGAAGGA 59.398 55.000 0.00 0.00 0.00 3.36
61 62 2.668457 GCGTACAGTCAGTGAAGGATTG 59.332 50.000 0.00 0.00 0.00 2.67
62 63 3.254060 CGTACAGTCAGTGAAGGATTGG 58.746 50.000 0.00 0.00 0.00 3.16
64 65 3.409026 ACAGTCAGTGAAGGATTGGAC 57.591 47.619 0.00 0.00 0.00 4.02
66 67 3.136443 ACAGTCAGTGAAGGATTGGACAA 59.864 43.478 0.00 0.00 0.00 3.18
92 93 2.158798 AGATGGATGCAGGATGTGACTG 60.159 50.000 0.00 0.00 39.31 3.51
111 112 1.003718 GGGACCTCACCTTCGTTGG 60.004 63.158 0.00 0.00 0.00 3.77
112 113 1.477685 GGGACCTCACCTTCGTTGGA 61.478 60.000 3.67 0.00 0.00 3.53
124 125 1.939974 TCGTTGGACATATGCAGCTC 58.060 50.000 1.58 0.00 0.00 4.09
142 143 0.107831 TCGTGCACCTAAACTTGGCT 59.892 50.000 12.15 0.00 0.00 4.75
145 146 2.351726 CGTGCACCTAAACTTGGCTATC 59.648 50.000 12.15 0.00 0.00 2.08
148 149 3.009033 TGCACCTAAACTTGGCTATCAGT 59.991 43.478 0.00 0.00 0.00 3.41
154 155 5.068198 CCTAAACTTGGCTATCAGTACGGTA 59.932 44.000 0.00 0.00 0.00 4.02
157 158 3.765511 ACTTGGCTATCAGTACGGTACAA 59.234 43.478 19.62 8.25 0.00 2.41
158 159 3.788333 TGGCTATCAGTACGGTACAAC 57.212 47.619 19.62 0.00 0.00 3.32
172 173 4.456911 ACGGTACAACGTGATCTAAGAAGA 59.543 41.667 0.00 0.00 46.64 2.87
174 175 5.100943 GGTACAACGTGATCTAAGAAGACC 58.899 45.833 0.00 0.00 33.57 3.85
184 185 2.897969 TCTAAGAAGACCGGACTGCTTT 59.102 45.455 28.60 14.88 37.08 3.51
189 190 0.035458 AGACCGGACTGCTTTTCCTG 59.965 55.000 9.46 0.00 0.00 3.86
195 196 2.282462 CTGCTTTTCCTGGCCGGT 60.282 61.111 11.58 0.00 0.00 5.28
218 219 3.617368 CCTCGGGGAGGTACACTG 58.383 66.667 0.00 0.00 44.25 3.66
222 223 2.642254 CGGGGAGGTACACTGCGAA 61.642 63.158 0.00 0.00 38.63 4.70
241 242 0.529378 AATCCACGTACCACCGACTC 59.471 55.000 0.00 0.00 0.00 3.36
243 244 0.324614 TCCACGTACCACCGACTCTA 59.675 55.000 0.00 0.00 0.00 2.43
244 245 1.065199 TCCACGTACCACCGACTCTAT 60.065 52.381 0.00 0.00 0.00 1.98
248 249 1.526041 CGTACCACCGACTCTATCTCG 59.474 57.143 0.00 0.00 0.00 4.04
257 258 1.338655 GACTCTATCTCGGAACCCAGC 59.661 57.143 0.00 0.00 0.00 4.85
280 281 1.123077 TCTCCTACGCCTCATGCATT 58.877 50.000 0.00 0.00 41.33 3.56
293 294 3.760151 CTCATGCATTTGGAAGAGTTGGA 59.240 43.478 0.00 0.00 0.00 3.53
298 299 4.072131 GCATTTGGAAGAGTTGGACACTA 58.928 43.478 0.00 0.00 35.01 2.74
352 353 2.030457 GCAACATCGTATTTGGACCTCG 59.970 50.000 0.00 0.00 0.00 4.63
353 354 3.517602 CAACATCGTATTTGGACCTCGA 58.482 45.455 0.00 0.00 35.14 4.04
357 358 3.226346 TCGTATTTGGACCTCGAACAG 57.774 47.619 0.00 0.00 0.00 3.16
394 395 3.797184 GCCTACAAGATAGTCCTTCAGCG 60.797 52.174 0.00 0.00 0.00 5.18
462 463 0.454600 CAGTGTGTATACGCGAGGGT 59.545 55.000 15.93 0.00 42.10 4.34
463 464 1.135199 CAGTGTGTATACGCGAGGGTT 60.135 52.381 15.93 0.00 42.10 4.11
537 538 2.620115 CGGACAACGGCCTACTAGATTA 59.380 50.000 0.00 0.00 39.42 1.75
565 566 4.660938 GCCAGGAAGGGTTGCGGT 62.661 66.667 0.00 0.00 38.09 5.68
616 617 0.405198 TGATTGTGGTGACATGGGCT 59.595 50.000 0.00 0.00 46.14 5.19
638 639 5.476091 TTTGTGGAAACAAAGGAACACTT 57.524 34.783 0.04 0.00 46.06 3.16
654 655 4.450082 ACACTTGGGTTTTCAACAGAAC 57.550 40.909 0.00 0.00 0.00 3.01
677 678 1.550130 CCAACAGAGGACCCCGCTTA 61.550 60.000 0.00 0.00 29.38 3.09
686 687 2.180159 GACCCCGCTTAAGCTGGTGA 62.180 60.000 31.47 0.00 42.89 4.02
688 689 0.608035 CCCCGCTTAAGCTGGTGAAA 60.608 55.000 29.29 0.00 42.89 2.69
690 691 0.169009 CCGCTTAAGCTGGTGAAAGC 59.831 55.000 24.33 13.97 43.88 3.51
698 699 2.246719 GCTGGTGAAAGCGATCCTAT 57.753 50.000 0.00 0.00 36.92 2.57
717 718 1.361204 TGGGAGATGCAAGAGTGGAA 58.639 50.000 0.00 0.00 0.00 3.53
721 722 3.614092 GGAGATGCAAGAGTGGAATTCA 58.386 45.455 7.93 0.00 0.00 2.57
725 726 1.202915 TGCAAGAGTGGAATTCAGCCA 60.203 47.619 7.93 0.00 0.00 4.75
727 728 2.089980 CAAGAGTGGAATTCAGCCAGG 58.910 52.381 7.93 0.00 35.77 4.45
749 750 1.961277 GGCGGTGGTGAGTTGTCAG 60.961 63.158 0.00 0.00 31.53 3.51
754 755 2.154462 GGTGGTGAGTTGTCAGGATTG 58.846 52.381 0.00 0.00 31.53 2.67
774 775 4.857130 TGGTGAGAGAGTAGGCTTAGTA 57.143 45.455 0.00 0.00 0.00 1.82
797 798 9.796180 AGTATTATTAAGTGTGGGTTGTGTTTA 57.204 29.630 0.00 0.00 0.00 2.01
840 841 7.912056 TGTATGCATCTATTCTTAAGCATCC 57.088 36.000 0.19 0.00 41.32 3.51
854 855 7.857456 TCTTAAGCATCCCTTGTAAATCACTA 58.143 34.615 0.00 0.00 34.95 2.74
899 900 2.755929 GCCTTTGGCGTACTCTGAG 58.244 57.895 2.45 2.45 39.62 3.35
900 901 0.246635 GCCTTTGGCGTACTCTGAGA 59.753 55.000 12.44 0.00 39.62 3.27
901 902 1.337823 GCCTTTGGCGTACTCTGAGAA 60.338 52.381 12.44 0.00 39.62 2.87
902 903 2.870435 GCCTTTGGCGTACTCTGAGAAA 60.870 50.000 12.44 0.00 39.62 2.52
903 904 3.399330 CCTTTGGCGTACTCTGAGAAAA 58.601 45.455 12.44 1.92 0.00 2.29
904 905 3.813166 CCTTTGGCGTACTCTGAGAAAAA 59.187 43.478 12.44 2.24 0.00 1.94
905 906 4.083802 CCTTTGGCGTACTCTGAGAAAAAG 60.084 45.833 12.44 10.38 0.00 2.27
906 907 3.746045 TGGCGTACTCTGAGAAAAAGT 57.254 42.857 12.44 0.00 0.00 2.66
907 908 4.859304 TGGCGTACTCTGAGAAAAAGTA 57.141 40.909 12.44 0.00 0.00 2.24
1000 1002 1.534336 TAAGACGCGGGCTACAACCA 61.534 55.000 12.47 0.00 0.00 3.67
1026 1028 1.351017 AGCCCATCAAGAAACTTCGGA 59.649 47.619 0.00 0.00 0.00 4.55
1086 1088 1.191096 CAATTGCTAAACGGCGCATC 58.809 50.000 10.83 0.00 35.85 3.91
1162 1164 0.600557 AGATCGACCGAGATGCATCC 59.399 55.000 23.06 13.29 0.00 3.51
1177 1179 1.215244 CATCCGTCGTCGAGCTACTA 58.785 55.000 2.98 0.00 39.71 1.82
1482 1492 1.687146 CCCTACTCTGCCCTGCTGA 60.687 63.158 0.00 0.00 35.38 4.26
1483 1493 1.267574 CCCTACTCTGCCCTGCTGAA 61.268 60.000 0.00 0.00 36.19 3.02
1547 3020 3.545481 CGTGTGCTGCCGATCGAC 61.545 66.667 18.66 5.29 0.00 4.20
1606 3079 3.270027 CCTGTTCCGTTTGATGCTCATA 58.730 45.455 0.00 0.00 0.00 2.15
1607 3080 3.063997 CCTGTTCCGTTTGATGCTCATAC 59.936 47.826 0.00 0.00 0.00 2.39
1608 3081 3.006940 TGTTCCGTTTGATGCTCATACC 58.993 45.455 0.00 0.00 0.00 2.73
1693 3166 3.188460 GCGTGATTGTGCTAAAGAAGGAA 59.812 43.478 0.00 0.00 0.00 3.36
1698 3171 5.473504 TGATTGTGCTAAAGAAGGAAAGACC 59.526 40.000 0.00 0.00 39.35 3.85
1743 3216 4.069232 CAGCTCGAACGGCCCTCA 62.069 66.667 0.00 0.00 0.00 3.86
1766 3239 1.748403 GTGGCTGCGATGGAGGATA 59.252 57.895 0.00 0.00 0.00 2.59
1805 3281 4.287067 ACACTGCTGGGAGAAGAATAAAGA 59.713 41.667 0.00 0.00 0.00 2.52
1806 3282 5.221925 ACACTGCTGGGAGAAGAATAAAGAA 60.222 40.000 0.00 0.00 0.00 2.52
1807 3283 5.353678 CACTGCTGGGAGAAGAATAAAGAAG 59.646 44.000 0.00 0.00 0.00 2.85
1831 3307 7.391620 AGGACGGACTTAAGAAATGAAATGTA 58.608 34.615 10.09 0.00 0.00 2.29
1832 3308 7.549488 AGGACGGACTTAAGAAATGAAATGTAG 59.451 37.037 10.09 0.00 0.00 2.74
1923 3400 1.330306 AAAACGACCGACGACGTATG 58.670 50.000 17.00 0.00 45.77 2.39
1927 3404 1.069296 ACGACCGACGACGTATGAAAA 60.069 47.619 15.66 0.00 45.77 2.29
1932 3409 3.176708 CCGACGACGTATGAAAACAGAT 58.823 45.455 0.00 0.00 37.88 2.90
1964 3441 7.661968 TCCTAATCATTAGAGATTTGACTCCG 58.338 38.462 5.94 0.00 38.97 4.63
1976 3453 0.917821 TGACTCCGGGGTCTCTCCTA 60.918 60.000 33.64 11.11 37.16 2.94
2008 3485 2.125106 GCTGGAACCCTAGCCGTG 60.125 66.667 0.00 0.00 33.89 4.94
2067 3546 3.148279 CTCTCCGCCGGCTACCTT 61.148 66.667 26.68 0.00 0.00 3.50
2072 3551 4.077184 CGCCGGCTACCTTGGTCA 62.077 66.667 26.68 0.00 0.00 4.02
2127 3606 4.406069 CGTGGATCGTTTTTACTCTCGTA 58.594 43.478 0.00 0.00 34.52 3.43
2128 3607 5.032863 CGTGGATCGTTTTTACTCTCGTAT 58.967 41.667 0.00 0.00 34.52 3.06
2129 3608 6.194463 CGTGGATCGTTTTTACTCTCGTATA 58.806 40.000 0.00 0.00 34.52 1.47
2162 3641 6.148976 GGTTTTTAGGCTGTTTATCGTCTTCT 59.851 38.462 0.00 0.00 0.00 2.85
2166 3645 5.153950 AGGCTGTTTATCGTCTTCTCTTT 57.846 39.130 0.00 0.00 0.00 2.52
2190 3669 1.779025 GCAATGATGACGGCGCTGAT 61.779 55.000 25.98 6.69 0.00 2.90
2250 3729 2.716424 TCCTATGGTTGGGGATGGATTC 59.284 50.000 0.00 0.00 0.00 2.52
2273 3753 3.319122 GGAAACCAGTCTGTTCAAGCAAT 59.681 43.478 0.00 0.00 0.00 3.56
2315 3795 0.401738 CCTCATGGTGGACCTGTGTT 59.598 55.000 0.00 0.00 36.82 3.32
2350 3830 3.342627 CGACGGCGTTTGCTCCAA 61.343 61.111 16.19 0.00 42.25 3.53
2355 3835 2.539338 GGCGTTTGCTCCAACGTCA 61.539 57.895 13.69 0.00 42.25 4.35
2448 3928 2.110213 TGTGCTGGGTTCGTGGTC 59.890 61.111 0.00 0.00 0.00 4.02
2461 3941 2.927856 TGGTCCGTGGATGGCAGT 60.928 61.111 0.00 0.00 0.00 4.40
2464 3944 0.743345 GGTCCGTGGATGGCAGTTAC 60.743 60.000 0.00 0.00 0.00 2.50
2470 3950 1.883926 GTGGATGGCAGTTACGGTTTT 59.116 47.619 0.00 0.00 0.00 2.43
2489 3969 1.542492 TCTCCTTCGGCGTCTTAGTT 58.458 50.000 6.85 0.00 0.00 2.24
2551 4031 1.002624 GTTGCCCCGGTCTGATTCA 60.003 57.895 0.00 0.00 0.00 2.57
2571 4051 1.255882 TTCAACGGCAATGGCTTCAT 58.744 45.000 5.02 0.00 40.87 2.57
2689 4170 4.624364 CTGCTGTGGTGGTGCCGA 62.624 66.667 0.00 0.00 41.21 5.54
2711 4192 1.661480 CAGGTGACGGACGTTGGTA 59.339 57.895 0.00 0.00 0.00 3.25
2764 4245 5.995282 TCAGTTTTGTCATGTCGGTTCTTAT 59.005 36.000 0.00 0.00 0.00 1.73
2765 4246 7.156000 TCAGTTTTGTCATGTCGGTTCTTATA 58.844 34.615 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.140252 ACTGTACGCCTGTTCCTTGTT 59.860 47.619 0.00 0.00 0.00 2.83
31 32 1.000955 CTGACTGTACGCCTGTTCCTT 59.999 52.381 0.00 0.00 0.00 3.36
41 42 3.056821 TCCAATCCTTCACTGACTGTACG 60.057 47.826 0.00 0.00 0.00 3.67
45 46 3.407424 TGTCCAATCCTTCACTGACTG 57.593 47.619 0.00 0.00 0.00 3.51
55 56 3.528905 TCCATCTTCCATTGTCCAATCCT 59.471 43.478 0.00 0.00 0.00 3.24
58 59 3.640029 GCATCCATCTTCCATTGTCCAAT 59.360 43.478 0.00 0.00 0.00 3.16
61 62 2.621998 CTGCATCCATCTTCCATTGTCC 59.378 50.000 0.00 0.00 0.00 4.02
62 63 2.621998 CCTGCATCCATCTTCCATTGTC 59.378 50.000 0.00 0.00 0.00 3.18
64 65 2.940158 TCCTGCATCCATCTTCCATTG 58.060 47.619 0.00 0.00 0.00 2.82
66 67 2.445905 ACATCCTGCATCCATCTTCCAT 59.554 45.455 0.00 0.00 0.00 3.41
92 93 1.003718 CAACGAAGGTGAGGTCCCC 60.004 63.158 0.00 0.00 0.00 4.81
103 104 2.283298 AGCTGCATATGTCCAACGAAG 58.717 47.619 4.29 0.00 0.00 3.79
106 107 0.578683 CGAGCTGCATATGTCCAACG 59.421 55.000 4.29 2.44 0.00 4.10
124 125 1.803334 TAGCCAAGTTTAGGTGCACG 58.197 50.000 11.45 0.00 0.00 5.34
130 131 4.142004 ACCGTACTGATAGCCAAGTTTAGG 60.142 45.833 0.00 0.00 0.00 2.69
133 134 3.975168 ACCGTACTGATAGCCAAGTTT 57.025 42.857 0.00 0.00 0.00 2.66
142 143 4.877823 AGATCACGTTGTACCGTACTGATA 59.122 41.667 10.03 0.00 39.45 2.15
145 146 3.482722 AGATCACGTTGTACCGTACTG 57.517 47.619 10.03 0.42 39.45 2.74
148 149 5.643348 TCTTCTTAGATCACGTTGTACCGTA 59.357 40.000 0.00 0.00 39.45 4.02
154 155 3.367087 CCGGTCTTCTTAGATCACGTTGT 60.367 47.826 0.00 0.00 30.42 3.32
157 158 2.422832 GTCCGGTCTTCTTAGATCACGT 59.577 50.000 0.00 0.00 30.42 4.49
158 159 2.683867 AGTCCGGTCTTCTTAGATCACG 59.316 50.000 0.00 0.00 30.42 4.35
160 161 2.427453 GCAGTCCGGTCTTCTTAGATCA 59.573 50.000 0.00 0.00 30.42 2.92
165 166 3.556423 GGAAAAGCAGTCCGGTCTTCTTA 60.556 47.826 13.19 0.00 0.00 2.10
166 167 2.495084 GAAAAGCAGTCCGGTCTTCTT 58.505 47.619 7.70 7.70 0.00 2.52
169 170 0.765510 AGGAAAAGCAGTCCGGTCTT 59.234 50.000 0.00 0.00 40.36 3.01
172 173 1.073199 CCAGGAAAAGCAGTCCGGT 59.927 57.895 0.00 0.00 40.36 5.28
174 175 2.335712 GGCCAGGAAAAGCAGTCCG 61.336 63.158 0.00 0.00 40.36 4.79
184 185 3.961414 GGGTCAACCGGCCAGGAA 61.961 66.667 18.74 3.10 45.00 3.36
208 209 2.000447 GTGGATTTCGCAGTGTACCTC 59.000 52.381 0.00 0.00 0.00 3.85
211 212 1.425412 ACGTGGATTTCGCAGTGTAC 58.575 50.000 0.00 0.00 0.00 2.90
218 219 1.689352 CGGTGGTACGTGGATTTCGC 61.689 60.000 0.00 0.00 0.00 4.70
222 223 0.529378 GAGTCGGTGGTACGTGGATT 59.471 55.000 0.00 0.00 34.94 3.01
241 242 1.364171 CCGCTGGGTTCCGAGATAG 59.636 63.158 5.09 0.00 0.00 2.08
243 244 3.470888 CCCGCTGGGTTCCGAGAT 61.471 66.667 5.09 0.00 38.25 2.75
254 255 4.208686 GGCGTAGGAGACCCGCTG 62.209 72.222 10.13 0.00 46.71 5.18
257 258 1.828660 ATGAGGCGTAGGAGACCCG 60.829 63.158 0.00 0.00 37.58 5.28
271 272 3.760151 TCCAACTCTTCCAAATGCATGAG 59.240 43.478 0.00 3.77 0.00 2.90
280 281 6.099269 ACTTAAGTAGTGTCCAACTCTTCCAA 59.901 38.462 6.26 0.00 40.56 3.53
298 299 7.951591 ACCATGCAAAAATCTTACACTTAAGT 58.048 30.769 1.12 1.12 36.75 2.24
307 308 4.346418 ACCACCAACCATGCAAAAATCTTA 59.654 37.500 0.00 0.00 0.00 2.10
313 314 0.179062 GCACCACCAACCATGCAAAA 60.179 50.000 0.00 0.00 38.00 2.44
352 353 2.559440 CCATGCTTAGCTCTCCTGTTC 58.441 52.381 5.60 0.00 0.00 3.18
353 354 1.407989 GCCATGCTTAGCTCTCCTGTT 60.408 52.381 5.60 0.00 0.00 3.16
357 358 1.051812 TAGGCCATGCTTAGCTCTCC 58.948 55.000 5.01 1.71 0.00 3.71
394 395 1.284982 CCTGCAGACACGTGTAGCAC 61.285 60.000 32.22 17.93 35.26 4.40
451 452 1.515954 CCAGACAACCCTCGCGTAT 59.484 57.895 5.77 0.00 0.00 3.06
462 463 1.552337 GGAGACTCTCATGCCAGACAA 59.448 52.381 8.35 0.00 31.08 3.18
463 464 1.189752 GGAGACTCTCATGCCAGACA 58.810 55.000 8.35 0.00 31.08 3.41
521 522 2.364647 GCCACTAATCTAGTAGGCCGTT 59.635 50.000 0.00 0.00 42.23 4.44
523 524 2.029828 CAGCCACTAATCTAGTAGGCCG 60.030 54.545 16.76 8.67 45.66 6.13
565 566 2.934886 AACCACGTTTGTTAGCCCTA 57.065 45.000 0.00 0.00 0.00 3.53
654 655 2.266055 GGGTCCTCTGTTGGCTCG 59.734 66.667 0.00 0.00 0.00 5.03
677 678 0.326264 AGGATCGCTTTCACCAGCTT 59.674 50.000 0.00 0.00 37.68 3.74
686 687 2.289945 GCATCTCCCATAGGATCGCTTT 60.290 50.000 0.00 0.00 42.93 3.51
688 689 0.901124 GCATCTCCCATAGGATCGCT 59.099 55.000 0.00 0.00 42.93 4.93
690 691 2.564504 TCTTGCATCTCCCATAGGATCG 59.435 50.000 0.00 0.00 42.93 3.69
694 695 2.224475 CCACTCTTGCATCTCCCATAGG 60.224 54.545 0.00 0.00 0.00 2.57
698 699 1.361204 TTCCACTCTTGCATCTCCCA 58.639 50.000 0.00 0.00 0.00 4.37
727 728 4.309950 AACTCACCACCGCCGACC 62.310 66.667 0.00 0.00 0.00 4.79
741 742 3.242867 TCTCTCACCAATCCTGACAACT 58.757 45.455 0.00 0.00 0.00 3.16
749 750 2.393646 AGCCTACTCTCTCACCAATCC 58.606 52.381 0.00 0.00 0.00 3.01
754 755 8.411991 AATAATACTAAGCCTACTCTCTCACC 57.588 38.462 0.00 0.00 0.00 4.02
774 775 7.726738 ACCTAAACACAACCCACACTTAATAAT 59.273 33.333 0.00 0.00 0.00 1.28
781 782 2.025699 ACACCTAAACACAACCCACACT 60.026 45.455 0.00 0.00 0.00 3.55
797 798 0.620556 ATCCATTCTCGGCAACACCT 59.379 50.000 0.00 0.00 35.61 4.00
834 835 4.823989 GCATAGTGATTTACAAGGGATGCT 59.176 41.667 0.00 0.00 35.44 3.79
840 841 7.271511 AGAAGAGAGCATAGTGATTTACAAGG 58.728 38.462 0.00 0.00 0.00 3.61
937 938 8.379331 ACCTACAGCTTATTCTTCTCTTCTTTT 58.621 33.333 0.00 0.00 0.00 2.27
1000 1002 0.966875 TTTCTTGATGGGCTGCGCAT 60.967 50.000 29.05 29.05 39.69 4.73
1026 1028 2.049802 GCGCTTTGTGCATGCAGT 60.050 55.556 23.41 0.00 43.06 4.40
1051 1053 0.960364 ATTGGCTTACGTGGTGGCAG 60.960 55.000 0.00 0.00 37.55 4.85
1077 1079 2.203070 GATTGGGAGATGCGCCGT 60.203 61.111 4.18 0.00 0.00 5.68
1086 1088 2.037620 CTGCCGAGGGAGATTGGGAG 62.038 65.000 4.52 0.00 36.03 4.30
1162 1164 1.005340 AGGTTAGTAGCTCGACGACG 58.995 55.000 0.00 0.00 41.26 5.12
1177 1179 1.202582 CGACGAAGAGGATGACAGGTT 59.797 52.381 0.00 0.00 0.00 3.50
1423 1433 4.834892 CGTGTACGTACCGGCGGG 62.835 72.222 31.78 15.34 35.98 6.13
1482 1492 4.442706 AGTAATTGATCTCGGCGTTGATT 58.557 39.130 6.85 3.22 0.00 2.57
1483 1493 4.060038 AGTAATTGATCTCGGCGTTGAT 57.940 40.909 6.85 12.17 0.00 2.57
1547 3020 6.093082 AGGGGAAACAAAGATTAAATACGTCG 59.907 38.462 0.00 0.00 0.00 5.12
1631 3104 4.202284 ACACATGGCAGAAGCAAGAAAATT 60.202 37.500 0.00 0.00 44.61 1.82
1693 3166 0.036732 TCTTCAGCGCCATTGGTCTT 59.963 50.000 2.29 0.00 0.00 3.01
1698 3171 1.651240 CCCACTCTTCAGCGCCATTG 61.651 60.000 2.29 0.00 0.00 2.82
1743 3216 2.438975 CCATCGCAGCCACCATGT 60.439 61.111 0.00 0.00 0.00 3.21
1766 3239 1.985662 TGTTGCCTACCGGATCCGT 60.986 57.895 31.22 21.20 37.81 4.69
1788 3261 5.112686 CGTCCTTCTTTATTCTTCTCCCAG 58.887 45.833 0.00 0.00 0.00 4.45
1794 3267 8.033626 TCTTAAGTCCGTCCTTCTTTATTCTTC 58.966 37.037 1.63 0.00 0.00 2.87
1805 3281 6.715264 ACATTTCATTTCTTAAGTCCGTCCTT 59.285 34.615 1.63 0.00 0.00 3.36
1806 3282 6.238648 ACATTTCATTTCTTAAGTCCGTCCT 58.761 36.000 1.63 0.00 0.00 3.85
1807 3283 6.496338 ACATTTCATTTCTTAAGTCCGTCC 57.504 37.500 1.63 0.00 0.00 4.79
1831 3307 5.520748 AAAACAACAGGGACCATATCTCT 57.479 39.130 0.00 0.00 39.54 3.10
1943 3420 5.455326 CCCCGGAGTCAAATCTCTAATGATT 60.455 44.000 0.73 0.00 38.19 2.57
1964 3441 0.757561 GAGCAGGTAGGAGAGACCCC 60.758 65.000 0.00 0.00 37.73 4.95
2051 3530 3.458163 CAAGGTAGCCGGCGGAGA 61.458 66.667 33.44 13.92 0.00 3.71
2062 3541 0.611200 CACCACCGATGACCAAGGTA 59.389 55.000 0.00 0.00 36.34 3.08
2067 3546 2.290287 CCCTCACCACCGATGACCA 61.290 63.158 0.00 0.00 0.00 4.02
2129 3608 9.833917 GATAAACAGCCTAAAAACCTAGACTAT 57.166 33.333 0.00 0.00 0.00 2.12
2162 3641 1.811965 CGTCATCATTGCCACCAAAGA 59.188 47.619 0.00 0.00 33.72 2.52
2166 3645 2.045708 GCCGTCATCATTGCCACCA 61.046 57.895 0.00 0.00 0.00 4.17
2250 3729 1.264288 GCTTGAACAGACTGGTTTCCG 59.736 52.381 7.51 0.00 0.00 4.30
2300 3780 0.321671 CGAGAACACAGGTCCACCAT 59.678 55.000 0.00 0.00 38.89 3.55
2372 3852 0.760567 TGCATCCGCTCCTGGACTAT 60.761 55.000 0.00 0.00 41.85 2.12
2448 3928 1.813753 CCGTAACTGCCATCCACGG 60.814 63.158 0.00 0.00 45.25 4.94
2489 3969 2.858476 ATCTGGCACCCCACCACA 60.858 61.111 0.00 0.00 35.79 4.17
2551 4031 1.255882 TGAAGCCATTGCCGTTGAAT 58.744 45.000 0.00 0.00 38.69 2.57
2689 4170 2.803817 AACGTCCGTCACCTGCCTT 61.804 57.895 0.00 0.00 0.00 4.35
2723 4204 9.066892 ACAAAACTGAAAAGATAGCAGAACATA 57.933 29.630 0.00 0.00 33.94 2.29
2765 4246 9.337396 TCATAAAGAACAAAGTACAAGTCACAT 57.663 29.630 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.