Multiple sequence alignment - TraesCS6D01G184400

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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 TraesCS6D01G184400 chr6D 100.000 3604 0 0 1 3604 232378407 232374804 0.000000e+00 6656.0
1 TraesCS6D01G184400 chr6D 93.082 1590 96 7 754 2332 944485 942899 0.000000e+00 2314.0
2 TraesCS6D01G184400 chr6D 92.734 757 51 3 1 754 232391710 232390955 0.000000e+00 1090.0
3 TraesCS6D01G184400 chr6D 92.338 757 54 3 1 754 217245483 217246238 0.000000e+00 1074.0
4 TraesCS6D01G184400 chr6D 92.247 761 51 7 1 755 200683024 200683782 0.000000e+00 1072.0
5 TraesCS6D01G184400 chr6D 91.584 606 40 4 2331 2925 325417158 325416553 0.000000e+00 826.0
6 TraesCS6D01G184400 chr4D 91.622 2244 110 20 754 2921 84467643 84465402 0.000000e+00 3031.0
7 TraesCS6D01G184400 chr4D 93.428 1613 70 12 754 2332 486565699 486564089 0.000000e+00 2359.0
8 TraesCS6D01G184400 chr4D 92.206 757 56 2 1 754 240597061 240597817 0.000000e+00 1068.0
9 TraesCS6D01G184400 chr2D 90.504 2243 135 27 754 2925 644015428 644013193 0.000000e+00 2891.0
10 TraesCS6D01G184400 chr2D 92.203 1616 88 11 754 2332 596268248 596266634 0.000000e+00 2252.0
11 TraesCS6D01G184400 chr2D 95.340 1030 33 3 1318 2332 50129792 50128763 0.000000e+00 1622.0
12 TraesCS6D01G184400 chr2D 91.345 1190 58 13 1780 2925 56633347 56634535 0.000000e+00 1585.0
13 TraesCS6D01G184400 chr2D 92.328 756 55 2 1 753 304785625 304786380 0.000000e+00 1072.0
14 TraesCS6D01G184400 chr2B 89.236 2239 149 29 754 2923 412290957 412293172 0.000000e+00 2715.0
15 TraesCS6D01G184400 chr2B 90.769 1885 118 15 1099 2932 742783128 742785007 0.000000e+00 2466.0
16 TraesCS6D01G184400 chr2B 81.668 911 149 14 1192 2090 676027147 676028051 0.000000e+00 741.0
17 TraesCS6D01G184400 chr7D 94.040 1594 70 8 754 2332 207197852 207199435 0.000000e+00 2394.0
18 TraesCS6D01G184400 chr7D 93.000 1600 88 9 754 2332 126988527 126990123 0.000000e+00 2313.0
19 TraesCS6D01G184400 chr7D 91.946 596 38 4 2331 2916 14924614 14925209 0.000000e+00 826.0
20 TraesCS6D01G184400 chr5D 93.605 1595 79 10 754 2332 495796130 495794543 0.000000e+00 2359.0
21 TraesCS6D01G184400 chr5D 92.978 1595 82 15 754 2332 179972872 179971292 0.000000e+00 2298.0
22 TraesCS6D01G184400 chr1D 93.400 1606 73 12 754 2332 278102385 278100786 0.000000e+00 2348.0
23 TraesCS6D01G184400 chr1D 92.227 1621 82 9 754 2332 415505638 415504020 0.000000e+00 2255.0
24 TraesCS6D01G184400 chr1D 92.676 1024 70 5 754 1776 139135181 139134162 0.000000e+00 1471.0
25 TraesCS6D01G184400 chr1D 95.592 794 20 3 1554 2332 426391018 426390225 0.000000e+00 1258.0
26 TraesCS6D01G184400 chr1D 92.867 757 50 3 1 754 219719360 219718605 0.000000e+00 1096.0
27 TraesCS6D01G184400 chr1D 88.861 799 47 13 2166 2928 416629360 416628568 0.000000e+00 944.0
28 TraesCS6D01G184400 chr3D 92.978 1595 93 7 754 2332 382523004 382521413 0.000000e+00 2307.0
29 TraesCS6D01G184400 chr3D 91.070 1467 71 20 1504 2921 515977138 515975683 0.000000e+00 1929.0
30 TraesCS6D01G184400 chr3D 92.999 757 49 3 1 754 412255888 412255133 0.000000e+00 1101.0
31 TraesCS6D01G184400 chr3D 100.000 28 0 0 2922 2949 13414637 13414664 7.000000e-03 52.8
32 TraesCS6D01G184400 chr7B 92.351 1595 105 6 754 2332 549934324 549932731 0.000000e+00 2254.0
33 TraesCS6D01G184400 chr7B 71.936 563 112 32 2968 3515 517606695 517607226 4.890000e-24 122.0
34 TraesCS6D01G184400 chr4B 92.072 1602 102 10 754 2332 671183170 671184769 0.000000e+00 2231.0
35 TraesCS6D01G184400 chr4B 89.620 684 60 4 2921 3604 123871966 123871294 0.000000e+00 859.0
36 TraesCS6D01G184400 chr5A 92.055 1309 92 8 1035 2332 417293099 417291792 0.000000e+00 1831.0
37 TraesCS6D01G184400 chr5A 92.390 749 54 2 9 754 319320206 319319458 0.000000e+00 1064.0
38 TraesCS6D01G184400 chr4A 92.470 757 54 2 1 754 110753034 110752278 0.000000e+00 1079.0
39 TraesCS6D01G184400 chr1B 81.555 1106 178 17 1245 2332 410309084 410310181 0.000000e+00 889.0
40 TraesCS6D01G184400 chr1A 84.211 836 118 13 1505 2332 380530251 380531080 0.000000e+00 800.0
41 TraesCS6D01G184400 chrUn 90.221 542 45 3 3063 3604 117160087 117159554 0.000000e+00 701.0
42 TraesCS6D01G184400 chrUn 89.541 545 49 4 3060 3604 117179559 117180095 0.000000e+00 684.0
43 TraesCS6D01G184400 chrUn 92.647 136 9 1 3469 3604 117162233 117162099 1.020000e-45 195.0
44 TraesCS6D01G184400 chrUn 92.647 136 9 1 3469 3604 117177743 117177877 1.020000e-45 195.0
45 TraesCS6D01G184400 chrUn 92.647 136 9 1 3469 3604 379619351 379619485 1.020000e-45 195.0
46 TraesCS6D01G184400 chrUn 92.647 136 9 1 3469 3604 441974584 441974450 1.020000e-45 195.0
47 TraesCS6D01G184400 chrUn 88.235 119 13 1 2908 3026 117179440 117179557 1.350000e-29 141.0
48 TraesCS6D01G184400 chrUn 87.395 119 14 1 2908 3026 117160209 117160092 6.280000e-28 135.0
49 TraesCS6D01G184400 chr7A 83.382 686 89 17 2926 3604 497735922 497735255 2.380000e-171 612.0


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 TraesCS6D01G184400 chr6D 232374804 232378407 3603 True 6656.000000 6656 100.000000 1 3604 1 chr6D.!!$R2 3603
1 TraesCS6D01G184400 chr6D 942899 944485 1586 True 2314.000000 2314 93.082000 754 2332 1 chr6D.!!$R1 1578
2 TraesCS6D01G184400 chr6D 232390955 232391710 755 True 1090.000000 1090 92.734000 1 754 1 chr6D.!!$R3 753
3 TraesCS6D01G184400 chr6D 217245483 217246238 755 False 1074.000000 1074 92.338000 1 754 1 chr6D.!!$F2 753
4 TraesCS6D01G184400 chr6D 200683024 200683782 758 False 1072.000000 1072 92.247000 1 755 1 chr6D.!!$F1 754
5 TraesCS6D01G184400 chr6D 325416553 325417158 605 True 826.000000 826 91.584000 2331 2925 1 chr6D.!!$R4 594
6 TraesCS6D01G184400 chr4D 84465402 84467643 2241 True 3031.000000 3031 91.622000 754 2921 1 chr4D.!!$R1 2167
7 TraesCS6D01G184400 chr4D 486564089 486565699 1610 True 2359.000000 2359 93.428000 754 2332 1 chr4D.!!$R2 1578
8 TraesCS6D01G184400 chr4D 240597061 240597817 756 False 1068.000000 1068 92.206000 1 754 1 chr4D.!!$F1 753
9 TraesCS6D01G184400 chr2D 644013193 644015428 2235 True 2891.000000 2891 90.504000 754 2925 1 chr2D.!!$R3 2171
10 TraesCS6D01G184400 chr2D 596266634 596268248 1614 True 2252.000000 2252 92.203000 754 2332 1 chr2D.!!$R2 1578
11 TraesCS6D01G184400 chr2D 50128763 50129792 1029 True 1622.000000 1622 95.340000 1318 2332 1 chr2D.!!$R1 1014
12 TraesCS6D01G184400 chr2D 56633347 56634535 1188 False 1585.000000 1585 91.345000 1780 2925 1 chr2D.!!$F1 1145
13 TraesCS6D01G184400 chr2D 304785625 304786380 755 False 1072.000000 1072 92.328000 1 753 1 chr2D.!!$F2 752
14 TraesCS6D01G184400 chr2B 412290957 412293172 2215 False 2715.000000 2715 89.236000 754 2923 1 chr2B.!!$F1 2169
15 TraesCS6D01G184400 chr2B 742783128 742785007 1879 False 2466.000000 2466 90.769000 1099 2932 1 chr2B.!!$F3 1833
16 TraesCS6D01G184400 chr2B 676027147 676028051 904 False 741.000000 741 81.668000 1192 2090 1 chr2B.!!$F2 898
17 TraesCS6D01G184400 chr7D 207197852 207199435 1583 False 2394.000000 2394 94.040000 754 2332 1 chr7D.!!$F3 1578
18 TraesCS6D01G184400 chr7D 126988527 126990123 1596 False 2313.000000 2313 93.000000 754 2332 1 chr7D.!!$F2 1578
19 TraesCS6D01G184400 chr7D 14924614 14925209 595 False 826.000000 826 91.946000 2331 2916 1 chr7D.!!$F1 585
20 TraesCS6D01G184400 chr5D 495794543 495796130 1587 True 2359.000000 2359 93.605000 754 2332 1 chr5D.!!$R2 1578
21 TraesCS6D01G184400 chr5D 179971292 179972872 1580 True 2298.000000 2298 92.978000 754 2332 1 chr5D.!!$R1 1578
22 TraesCS6D01G184400 chr1D 278100786 278102385 1599 True 2348.000000 2348 93.400000 754 2332 1 chr1D.!!$R3 1578
23 TraesCS6D01G184400 chr1D 415504020 415505638 1618 True 2255.000000 2255 92.227000 754 2332 1 chr1D.!!$R4 1578
24 TraesCS6D01G184400 chr1D 139134162 139135181 1019 True 1471.000000 1471 92.676000 754 1776 1 chr1D.!!$R1 1022
25 TraesCS6D01G184400 chr1D 426390225 426391018 793 True 1258.000000 1258 95.592000 1554 2332 1 chr1D.!!$R6 778
26 TraesCS6D01G184400 chr1D 219718605 219719360 755 True 1096.000000 1096 92.867000 1 754 1 chr1D.!!$R2 753
27 TraesCS6D01G184400 chr1D 416628568 416629360 792 True 944.000000 944 88.861000 2166 2928 1 chr1D.!!$R5 762
28 TraesCS6D01G184400 chr3D 382521413 382523004 1591 True 2307.000000 2307 92.978000 754 2332 1 chr3D.!!$R1 1578
29 TraesCS6D01G184400 chr3D 515975683 515977138 1455 True 1929.000000 1929 91.070000 1504 2921 1 chr3D.!!$R3 1417
30 TraesCS6D01G184400 chr3D 412255133 412255888 755 True 1101.000000 1101 92.999000 1 754 1 chr3D.!!$R2 753
31 TraesCS6D01G184400 chr7B 549932731 549934324 1593 True 2254.000000 2254 92.351000 754 2332 1 chr7B.!!$R1 1578
32 TraesCS6D01G184400 chr4B 671183170 671184769 1599 False 2231.000000 2231 92.072000 754 2332 1 chr4B.!!$F1 1578
33 TraesCS6D01G184400 chr4B 123871294 123871966 672 True 859.000000 859 89.620000 2921 3604 1 chr4B.!!$R1 683
34 TraesCS6D01G184400 chr5A 417291792 417293099 1307 True 1831.000000 1831 92.055000 1035 2332 1 chr5A.!!$R2 1297
35 TraesCS6D01G184400 chr5A 319319458 319320206 748 True 1064.000000 1064 92.390000 9 754 1 chr5A.!!$R1 745
36 TraesCS6D01G184400 chr4A 110752278 110753034 756 True 1079.000000 1079 92.470000 1 754 1 chr4A.!!$R1 753
37 TraesCS6D01G184400 chr1B 410309084 410310181 1097 False 889.000000 889 81.555000 1245 2332 1 chr1B.!!$F1 1087
38 TraesCS6D01G184400 chr1A 380530251 380531080 829 False 800.000000 800 84.211000 1505 2332 1 chr1A.!!$F1 827
39 TraesCS6D01G184400 chrUn 117159554 117162233 2679 True 343.666667 701 90.087667 2908 3604 3 chrUn.!!$R2 696
40 TraesCS6D01G184400 chrUn 117177743 117180095 2352 False 340.000000 684 90.141000 2908 3604 3 chrUn.!!$F2 696
41 TraesCS6D01G184400 chr7A 497735255 497735922 667 True 612.000000 612 83.382000 2926 3604 1 chr7A.!!$R1 678

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
527 534 0.179137 TCGTCATGGCTCACGTCATC 60.179 55.0 0.00 0.0 31.91 2.92 F
752 760 0.321564 CCGTTCCCAGAATGCTGACA 60.322 55.0 0.74 0.0 45.17 3.58 F
1316 1414 0.392863 TGTGATTCAGGCATGGGTCG 60.393 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1640 1.202639 TCGACACTGGTGTTGATGCTT 60.203 47.619 16.99 0.0 46.09 3.91 R
1889 2022 2.589540 CCCCTGTATGCCGCAGAA 59.410 61.111 0.00 0.0 36.12 3.02 R
2961 3160 0.327924 ACCGCCATTGTCAGGAATCA 59.672 50.000 0.00 0.0 0.00 2.57 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
93 94 4.080243 TGAACAGTACAAGGGGAAGAACAA 60.080 41.667 0.00 0.00 0.00 2.83
171 172 1.489649 CCAAGATGAGATGGCTGAGGT 59.510 52.381 0.00 0.00 0.00 3.85
260 264 2.435938 GAAGGGATGCCGCAACGA 60.436 61.111 0.00 0.00 0.00 3.85
364 369 2.997897 GGCTCCGTGGTGACCTCT 60.998 66.667 2.11 0.00 0.00 3.69
371 376 0.673985 CGTGGTGACCTCTGTCTTGA 59.326 55.000 2.11 0.00 42.28 3.02
527 534 0.179137 TCGTCATGGCTCACGTCATC 60.179 55.000 0.00 0.00 31.91 2.92
528 535 0.458370 CGTCATGGCTCACGTCATCA 60.458 55.000 0.00 0.00 31.91 3.07
616 623 2.100197 CCGAGGAGGTCTTGTGTCATA 58.900 52.381 0.00 0.00 34.51 2.15
747 755 2.440247 CCCCCGTTCCCAGAATGC 60.440 66.667 0.00 0.00 31.97 3.56
749 757 1.750399 CCCCGTTCCCAGAATGCTG 60.750 63.158 0.00 0.00 41.93 4.41
750 758 1.299648 CCCGTTCCCAGAATGCTGA 59.700 57.895 0.74 0.00 45.17 4.26
751 759 1.026718 CCCGTTCCCAGAATGCTGAC 61.027 60.000 0.74 0.00 45.17 3.51
752 760 0.321564 CCGTTCCCAGAATGCTGACA 60.322 55.000 0.74 0.00 45.17 3.58
947 961 1.574263 AAACTAGCCTCACCCCTCTC 58.426 55.000 0.00 0.00 0.00 3.20
1066 1146 3.508840 GTTTGCGGCGGATCTGGG 61.509 66.667 9.78 0.00 0.00 4.45
1316 1414 0.392863 TGTGATTCAGGCATGGGTCG 60.393 55.000 0.00 0.00 0.00 4.79
1522 1640 1.375908 CAGGCGGCTGCTACAAGAA 60.376 57.895 27.04 0.00 42.25 2.52
1776 1895 6.653020 TCAAGGTGAGCATTGACAATATACT 58.347 36.000 0.00 0.00 40.00 2.12
1778 1897 6.932356 AGGTGAGCATTGACAATATACTTG 57.068 37.500 0.00 0.00 0.00 3.16
1889 2022 1.834263 GCCAGAGTTCCTAGGTCACAT 59.166 52.381 9.08 0.00 0.00 3.21
1944 2077 0.170561 CCAGAATGTGCTTGCTGCTC 59.829 55.000 0.00 1.48 43.37 4.26
2502 2693 1.228184 AAGCAGCAGCAGCAGAAGT 60.228 52.632 12.92 0.00 45.49 3.01
2522 2713 3.831911 AGTAGCAGAAGCAGAAGAAGAGT 59.168 43.478 0.00 0.00 45.49 3.24
2636 2833 9.520515 AGTTAGGATGAACTGTCATTTGTTTAT 57.479 29.630 0.00 0.00 44.83 1.40
2642 2839 6.908825 TGAACTGTCATTTGTTTATGTAGCC 58.091 36.000 0.00 0.00 0.00 3.93
2645 2842 4.580868 TGTCATTTGTTTATGTAGCCGGA 58.419 39.130 5.05 0.00 0.00 5.14
2786 2983 0.032815 CGCCGGGTCAAAAATGGTTT 59.967 50.000 2.18 0.00 0.00 3.27
2788 2985 2.566913 GCCGGGTCAAAAATGGTTTTT 58.433 42.857 2.18 0.00 43.20 1.94
2812 3010 1.609239 CAACTAGGGGCATGCAGGA 59.391 57.895 21.36 0.00 0.00 3.86
2813 3011 0.184451 CAACTAGGGGCATGCAGGAT 59.816 55.000 21.36 4.56 0.00 3.24
2961 3160 3.382832 CTCAACCCGTCCTCCGCT 61.383 66.667 0.00 0.00 34.38 5.52
3028 3259 2.203337 TGCCAAAGCACTTCGGCT 60.203 55.556 13.24 0.00 46.52 5.52
3029 3260 2.260869 TGCCAAAGCACTTCGGCTC 61.261 57.895 13.24 0.00 46.52 4.70
3030 3261 2.863153 CCAAAGCACTTCGGCTCG 59.137 61.111 0.00 0.00 45.07 5.03
3031 3262 2.174349 CAAAGCACTTCGGCTCGC 59.826 61.111 0.00 0.00 45.07 5.03
3032 3263 2.031163 AAAGCACTTCGGCTCGCT 59.969 55.556 0.00 0.00 45.07 4.93
3033 3264 1.014044 CAAAGCACTTCGGCTCGCTA 61.014 55.000 0.00 0.00 45.07 4.26
3034 3265 0.108138 AAAGCACTTCGGCTCGCTAT 60.108 50.000 0.00 0.00 45.07 2.97
3035 3266 0.528684 AAGCACTTCGGCTCGCTATC 60.529 55.000 0.00 0.00 45.07 2.08
3036 3267 2.296480 GCACTTCGGCTCGCTATCG 61.296 63.158 0.00 0.00 0.00 2.92
3037 3268 1.355563 CACTTCGGCTCGCTATCGA 59.644 57.895 0.00 0.00 43.28 3.59
3055 3286 4.522971 GCTTTAGGAGCGTGAGGG 57.477 61.111 0.00 0.00 42.46 4.30
3056 3287 1.898154 GCTTTAGGAGCGTGAGGGA 59.102 57.895 0.00 0.00 42.46 4.20
3057 3288 0.179097 GCTTTAGGAGCGTGAGGGAG 60.179 60.000 0.00 0.00 42.46 4.30
3058 3289 1.187087 CTTTAGGAGCGTGAGGGAGT 58.813 55.000 0.00 0.00 0.00 3.85
3061 3292 0.917533 TAGGAGCGTGAGGGAGTAGT 59.082 55.000 0.00 0.00 0.00 2.73
3066 3297 3.150767 GAGCGTGAGGGAGTAGTGATAT 58.849 50.000 0.00 0.00 0.00 1.63
3105 3336 2.043852 ACGCCGAGGAGATGGAGT 60.044 61.111 0.00 0.00 33.12 3.85
3132 3364 3.391382 GGAGGCTAGCCGGTGTGT 61.391 66.667 27.83 9.60 41.95 3.72
3143 3375 0.902531 CCGGTGTGTAGATGGACCTT 59.097 55.000 0.00 0.00 0.00 3.50
3150 3382 2.232941 GTGTAGATGGACCTTTCGGACA 59.767 50.000 0.00 0.00 0.00 4.02
3170 3402 5.118203 GGACAATGTGTAAGACGTTAGTGAC 59.882 44.000 0.00 0.00 32.16 3.67
3235 3470 1.271379 CTATACCGACGGCCATAGCAA 59.729 52.381 15.39 0.00 42.56 3.91
3275 3510 0.834612 AGGGCCCGACGATAAAATGA 59.165 50.000 18.44 0.00 0.00 2.57
3283 3518 5.374080 CCCGACGATAAAATGATGATTTCG 58.626 41.667 0.00 0.00 30.02 3.46
3341 3579 2.030007 TGTTTAACTACTGTCCGGTCGG 60.030 50.000 5.93 5.93 0.00 4.79
3369 3607 7.539710 GGAAACTATTTATTTTGGTTGTCCGAC 59.460 37.037 0.00 0.00 36.30 4.79
3401 3639 2.032178 GTGAATTATGCCTGACTTCCGC 59.968 50.000 0.00 0.00 0.00 5.54
3434 3672 1.599071 CGGGCGTTGATCTACGTAGTA 59.401 52.381 26.20 9.50 45.11 1.82
3457 3695 5.177326 AGGTTAAATTCCGTACGTTGCATA 58.823 37.500 15.21 0.00 0.00 3.14
3523 3761 1.661463 AGGAGGAGTGCTGGATTTGA 58.339 50.000 0.00 0.00 0.00 2.69
3530 3768 1.278985 AGTGCTGGATTTGATGACCGA 59.721 47.619 0.00 0.00 0.00 4.69
3533 3771 2.013563 GCTGGATTTGATGACCGAGCA 61.014 52.381 0.00 0.00 32.48 4.26
3572 3810 4.998033 TGGTACAATTATCGAGCAAACACA 59.002 37.500 0.00 0.00 31.92 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.526575 CCACCACACCACATTGGAGC 61.527 60.000 0.00 0.00 40.96 4.70
36 37 0.899717 GGCAATCCACCACACCACAT 60.900 55.000 0.00 0.00 0.00 3.21
171 172 0.320374 CACAGTAGGAGGCAACGGAA 59.680 55.000 0.00 0.00 46.39 4.30
254 258 2.403259 CCCTTTCAAATTGGTCGTTGC 58.597 47.619 0.00 0.00 0.00 4.17
260 264 1.970640 GCTGTCCCCTTTCAAATTGGT 59.029 47.619 0.00 0.00 0.00 3.67
364 369 1.367471 CCAGCAGGACGTCAAGACA 59.633 57.895 18.91 0.00 36.89 3.41
371 376 2.100879 GACCAAGACCAGCAGGACGT 62.101 60.000 0.35 0.00 38.69 4.34
527 534 0.371645 GCAAATCTCGCGAGGTTCTG 59.628 55.000 32.99 28.86 28.76 3.02
528 535 0.741221 GGCAAATCTCGCGAGGTTCT 60.741 55.000 32.99 20.28 28.76 3.01
747 755 2.513204 CGATGCAGGCCCTGTCAG 60.513 66.667 13.35 0.00 33.43 3.51
749 757 4.783621 TGCGATGCAGGCCCTGTC 62.784 66.667 13.35 5.41 33.32 3.51
781 789 1.000486 AGCGAACTAGGCTCTGGGA 60.000 57.895 0.00 0.00 35.37 4.37
887 897 0.472471 GGTTTCCATCTCCCGCCATA 59.528 55.000 0.00 0.00 0.00 2.74
930 941 0.260523 GAGAGAGGGGTGAGGCTAGT 59.739 60.000 0.00 0.00 0.00 2.57
947 961 0.249238 GCTATGGGTGAGCGAGTGAG 60.249 60.000 0.00 0.00 0.00 3.51
1066 1146 2.649129 GCCAACAACATGGGGAGCC 61.649 63.158 0.00 0.00 41.01 4.70
1316 1414 2.175878 ACTCTCTGGTGCATGAACAC 57.824 50.000 6.08 0.15 39.94 3.32
1522 1640 1.202639 TCGACACTGGTGTTGATGCTT 60.203 47.619 16.99 0.00 46.09 3.91
1776 1895 7.036996 TCAACTTGAACAATACAAGCATCAA 57.963 32.000 0.00 0.00 45.66 2.57
1778 1897 5.570589 GCTCAACTTGAACAATACAAGCATC 59.429 40.000 0.00 0.00 45.66 3.91
1889 2022 2.589540 CCCCTGTATGCCGCAGAA 59.410 61.111 0.00 0.00 36.12 3.02
1944 2077 6.609237 TGTGAACTTCAGATCAAAGTCAAG 57.391 37.500 12.34 0.52 35.96 3.02
2502 2693 5.712446 TCTTACTCTTCTTCTGCTTCTGCTA 59.288 40.000 0.00 0.00 40.48 3.49
2522 2713 3.639094 GCTGCTACCAGATCTTCCTCTTA 59.361 47.826 0.00 0.00 41.77 2.10
2642 2839 3.308053 CACAATCTGAACATGTAGCTCCG 59.692 47.826 0.00 0.00 0.00 4.63
2645 2842 4.453478 CACACACAATCTGAACATGTAGCT 59.547 41.667 0.00 0.00 0.00 3.32
2786 2983 2.300956 TGCCCCTAGTTGCATGAAAA 57.699 45.000 0.00 0.00 31.31 2.29
2812 3010 7.886629 AAATCAGATGCACATAGTTTGGTAT 57.113 32.000 0.00 0.00 0.00 2.73
2813 3011 7.701539 AAAATCAGATGCACATAGTTTGGTA 57.298 32.000 0.00 0.00 0.00 3.25
2844 3043 2.046314 CGGTTTGAGGGGACGCAT 60.046 61.111 0.00 0.00 40.84 4.73
2848 3047 2.046217 GAGCCGGTTTGAGGGGAC 60.046 66.667 1.90 0.00 0.00 4.46
2891 3090 3.168035 TGGTTACATTGCCAATCCAGT 57.832 42.857 0.00 0.00 0.00 4.00
2916 3115 1.414181 GCTGTAGATGCTCTAAGGGCA 59.586 52.381 0.00 0.00 44.05 5.36
2961 3160 0.327924 ACCGCCATTGTCAGGAATCA 59.672 50.000 0.00 0.00 0.00 2.57
3039 3270 1.187087 ACTCCCTCACGCTCCTAAAG 58.813 55.000 0.00 0.00 0.00 1.85
3040 3271 2.291411 ACTACTCCCTCACGCTCCTAAA 60.291 50.000 0.00 0.00 0.00 1.85
3041 3272 1.284198 ACTACTCCCTCACGCTCCTAA 59.716 52.381 0.00 0.00 0.00 2.69
3042 3273 0.917533 ACTACTCCCTCACGCTCCTA 59.082 55.000 0.00 0.00 0.00 2.94
3043 3274 0.681564 CACTACTCCCTCACGCTCCT 60.682 60.000 0.00 0.00 0.00 3.69
3044 3275 0.680280 TCACTACTCCCTCACGCTCC 60.680 60.000 0.00 0.00 0.00 4.70
3045 3276 1.394618 ATCACTACTCCCTCACGCTC 58.605 55.000 0.00 0.00 0.00 5.03
3046 3277 2.730934 TATCACTACTCCCTCACGCT 57.269 50.000 0.00 0.00 0.00 5.07
3047 3278 2.095668 CGATATCACTACTCCCTCACGC 60.096 54.545 3.12 0.00 0.00 5.34
3048 3279 3.400255 TCGATATCACTACTCCCTCACG 58.600 50.000 3.12 0.00 0.00 4.35
3049 3280 5.704888 CATTCGATATCACTACTCCCTCAC 58.295 45.833 3.12 0.00 0.00 3.51
3050 3281 4.218635 GCATTCGATATCACTACTCCCTCA 59.781 45.833 3.12 0.00 0.00 3.86
3051 3282 4.673061 CGCATTCGATATCACTACTCCCTC 60.673 50.000 3.12 0.00 38.10 4.30
3052 3283 3.191581 CGCATTCGATATCACTACTCCCT 59.808 47.826 3.12 0.00 38.10 4.20
3053 3284 3.190744 TCGCATTCGATATCACTACTCCC 59.809 47.826 3.12 0.00 40.21 4.30
3054 3285 4.421033 TCGCATTCGATATCACTACTCC 57.579 45.455 3.12 0.00 40.21 3.85
3055 3286 4.854291 CCTTCGCATTCGATATCACTACTC 59.146 45.833 3.12 0.00 45.04 2.59
3056 3287 4.799678 CCTTCGCATTCGATATCACTACT 58.200 43.478 3.12 0.00 45.04 2.57
3057 3288 3.365220 GCCTTCGCATTCGATATCACTAC 59.635 47.826 3.12 0.00 45.04 2.73
3058 3289 3.575630 GCCTTCGCATTCGATATCACTA 58.424 45.455 3.12 0.00 45.04 2.74
3061 3292 1.000717 TCGCCTTCGCATTCGATATCA 60.001 47.619 3.12 0.00 45.04 2.15
3066 3297 2.202743 CCTCGCCTTCGCATTCGA 60.203 61.111 0.00 0.00 43.89 3.71
3105 3336 2.683572 TAGCCTCCGGAGCAAGCA 60.684 61.111 26.87 11.69 0.00 3.91
3143 3375 3.374220 ACGTCTTACACATTGTCCGAA 57.626 42.857 0.00 0.00 0.00 4.30
3170 3402 0.580578 CATCGCCAGAGCTTGATTCG 59.419 55.000 0.00 0.00 36.60 3.34
3254 3489 1.333619 CATTTTATCGTCGGGCCCTTG 59.666 52.381 22.43 9.51 0.00 3.61
3268 3503 3.314080 GGGCGGACGAAATCATCATTTTA 59.686 43.478 0.00 0.00 31.94 1.52
3275 3510 1.379527 GAAAGGGCGGACGAAATCAT 58.620 50.000 0.00 0.00 0.00 2.45
3283 3518 0.465287 TTATACGGGAAAGGGCGGAC 59.535 55.000 0.00 0.00 0.00 4.79
3341 3579 7.327518 CGGACAACCAAAATAAATAGTTTCCAC 59.672 37.037 0.00 0.00 35.59 4.02
3369 3607 5.579904 CAGGCATAATTCACAGATAGGATCG 59.420 44.000 0.00 0.00 0.00 3.69
3401 3639 2.644992 GCCCGAGCAACAAACCTG 59.355 61.111 0.00 0.00 39.53 4.00
3433 3671 4.564041 TGCAACGTACGGAATTTAACCTA 58.436 39.130 21.06 0.00 0.00 3.08
3434 3672 3.401182 TGCAACGTACGGAATTTAACCT 58.599 40.909 21.06 0.00 0.00 3.50
3435 3673 3.809918 TGCAACGTACGGAATTTAACC 57.190 42.857 21.06 0.00 0.00 2.85
3457 3695 6.126863 TCACAAATTCTGTCCCTCATAACT 57.873 37.500 0.00 0.00 35.47 2.24
3505 3743 2.092753 TCATCAAATCCAGCACTCCTCC 60.093 50.000 0.00 0.00 0.00 4.30
3554 3792 5.685068 TGTTTGTGTGTTTGCTCGATAATTG 59.315 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.