Multiple sequence alignment - TraesCS3B01G538400

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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 TraesCS3B01G538400 chr3B 100.000 3161 0 0 1 3161 778343902 778340742 0.000000e+00 5838
1 TraesCS3B01G538400 chr3B 82.609 391 49 10 81 456 778371525 778371139 8.450000e-86 327
2 TraesCS3B01G538400 chr3D 95.305 1427 49 6 591 2017 582879453 582880861 0.000000e+00 2248
3 TraesCS3B01G538400 chr3D 95.420 1201 35 7 1971 3160 582880863 582882054 0.000000e+00 1895
4 TraesCS3B01G538400 chr3D 91.880 468 30 2 119 578 582878817 582879284 0.000000e+00 647
5 TraesCS3B01G538400 chr3D 85.845 219 27 3 346 564 582849410 582849624 2.450000e-56 230
6 TraesCS3B01G538400 chr6B 87.462 1659 141 27 1480 3105 16339450 16341074 0.000000e+00 1849
7 TraesCS3B01G538400 chr6B 84.773 1806 174 53 951 2709 15264333 15262582 0.000000e+00 1718
8 TraesCS3B01G538400 chr6B 84.994 1626 205 19 935 2537 16237248 16238857 0.000000e+00 1615
9 TraesCS3B01G538400 chr6B 85.726 1268 163 8 1130 2381 15715092 15713827 0.000000e+00 1323
10 TraesCS3B01G538400 chr6B 82.432 1480 215 28 938 2381 16320505 16321975 0.000000e+00 1251
11 TraesCS3B01G538400 chr6B 82.160 1463 227 28 922 2366 15234937 15233491 0.000000e+00 1225
12 TraesCS3B01G538400 chr6B 91.506 777 46 7 2336 3105 52979754 52978991 0.000000e+00 1051
13 TraesCS3B01G538400 chr6B 88.377 499 46 9 2614 3105 670590728 670590235 9.770000e-165 590
14 TraesCS3B01G538400 chr6B 84.496 387 42 8 2412 2789 15232891 15232514 1.790000e-97 366
15 TraesCS3B01G538400 chr6B 82.519 389 35 13 2412 2789 16269300 16269666 8.510000e-81 311
16 TraesCS3B01G538400 chr6D 84.269 1443 188 23 957 2381 33895008 33896429 0.000000e+00 1371
17 TraesCS3B01G538400 chr6D 80.895 827 139 14 1570 2381 8915622 8916444 4.450000e-178 634
18 TraesCS3B01G538400 chr6A 85.577 1144 152 6 1129 2261 9040185 9039044 0.000000e+00 1186
19 TraesCS3B01G538400 chr6A 83.196 1214 175 25 931 2133 30560630 30559435 0.000000e+00 1085
20 TraesCS3B01G538400 chr6A 79.275 1269 239 12 1133 2381 9355310 9356574 0.000000e+00 865
21 TraesCS3B01G538400 chr6A 87.349 498 53 7 2614 3105 9357206 9357699 2.130000e-156 562
22 TraesCS3B01G538400 chr2B 81.986 1249 205 17 931 2166 89494548 89495789 0.000000e+00 1042
23 TraesCS3B01G538400 chr5B 80.476 1429 218 34 990 2381 621238289 621236885 0.000000e+00 1037
24 TraesCS3B01G538400 chr5B 87.598 637 54 16 2412 3040 621236410 621235791 0.000000e+00 715
25 TraesCS3B01G538400 chr5B 83.846 390 41 12 2412 2789 556624598 556624219 5.020000e-93 351
26 TraesCS3B01G538400 chr5D 79.190 1432 225 35 985 2381 499865086 499863693 0.000000e+00 926
27 TraesCS3B01G538400 chr5D 88.201 695 61 13 2412 3100 499863106 499862427 0.000000e+00 809
28 TraesCS3B01G538400 chr5D 84.713 314 30 9 2412 2723 42077918 42078215 6.630000e-77 298
29 TraesCS3B01G538400 chrUn 78.577 1209 231 21 1193 2381 95438039 95439239 0.000000e+00 773
30 TraesCS3B01G538400 chrUn 89.773 352 29 6 2751 3100 95439808 95440154 8.050000e-121 444
31 TraesCS3B01G538400 chr5A 86.782 696 70 14 2412 3100 624203854 624203174 0.000000e+00 756
32 TraesCS3B01G538400 chr5A 84.409 635 87 10 1752 2381 624204954 624204327 5.790000e-172 614


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 TraesCS3B01G538400 chr3B 778340742 778343902 3160 True 5838.000000 5838 100.000000 1 3161 1 chr3B.!!$R1 3160
1 TraesCS3B01G538400 chr3D 582878817 582882054 3237 False 1596.666667 2248 94.201667 119 3160 3 chr3D.!!$F2 3041
2 TraesCS3B01G538400 chr6B 16339450 16341074 1624 False 1849.000000 1849 87.462000 1480 3105 1 chr6B.!!$F4 1625
3 TraesCS3B01G538400 chr6B 15262582 15264333 1751 True 1718.000000 1718 84.773000 951 2709 1 chr6B.!!$R1 1758
4 TraesCS3B01G538400 chr6B 16237248 16238857 1609 False 1615.000000 1615 84.994000 935 2537 1 chr6B.!!$F1 1602
5 TraesCS3B01G538400 chr6B 15713827 15715092 1265 True 1323.000000 1323 85.726000 1130 2381 1 chr6B.!!$R2 1251
6 TraesCS3B01G538400 chr6B 16320505 16321975 1470 False 1251.000000 1251 82.432000 938 2381 1 chr6B.!!$F3 1443
7 TraesCS3B01G538400 chr6B 52978991 52979754 763 True 1051.000000 1051 91.506000 2336 3105 1 chr6B.!!$R3 769
8 TraesCS3B01G538400 chr6B 15232514 15234937 2423 True 795.500000 1225 83.328000 922 2789 2 chr6B.!!$R5 1867
9 TraesCS3B01G538400 chr6D 33895008 33896429 1421 False 1371.000000 1371 84.269000 957 2381 1 chr6D.!!$F2 1424
10 TraesCS3B01G538400 chr6D 8915622 8916444 822 False 634.000000 634 80.895000 1570 2381 1 chr6D.!!$F1 811
11 TraesCS3B01G538400 chr6A 9039044 9040185 1141 True 1186.000000 1186 85.577000 1129 2261 1 chr6A.!!$R1 1132
12 TraesCS3B01G538400 chr6A 30559435 30560630 1195 True 1085.000000 1085 83.196000 931 2133 1 chr6A.!!$R2 1202
13 TraesCS3B01G538400 chr6A 9355310 9357699 2389 False 713.500000 865 83.312000 1133 3105 2 chr6A.!!$F1 1972
14 TraesCS3B01G538400 chr2B 89494548 89495789 1241 False 1042.000000 1042 81.986000 931 2166 1 chr2B.!!$F1 1235
15 TraesCS3B01G538400 chr5B 621235791 621238289 2498 True 876.000000 1037 84.037000 990 3040 2 chr5B.!!$R2 2050
16 TraesCS3B01G538400 chr5D 499862427 499865086 2659 True 867.500000 926 83.695500 985 3100 2 chr5D.!!$R1 2115
17 TraesCS3B01G538400 chrUn 95438039 95440154 2115 False 608.500000 773 84.175000 1193 3100 2 chrUn.!!$F1 1907
18 TraesCS3B01G538400 chr5A 624203174 624204954 1780 True 685.000000 756 85.595500 1752 3100 2 chr5A.!!$R1 1348

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
128 129 0.030092 TAGACATAGGCCTTGGCCCT 60.030 55.0 25.53 17.2 36.47 5.19 F
551 560 0.034767 TCCTCGTCCACGTACTCCAT 60.035 55.0 0.00 0.0 40.80 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1816 0.250038 TGAGCAGCGATGGCCTAATC 60.250 55.0 3.32 0.0 41.24 1.75 R
2377 2692 0.252881 AAGTGAGCCCTCCTCCATGA 60.253 55.0 0.00 0.0 39.98 3.07 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
24 25 6.914259 CCACTTCATTTCCTTCTTTCTTACC 58.086 40.000 0.00 0.00 0.00 2.85
25 26 6.490040 CCACTTCATTTCCTTCTTTCTTACCA 59.510 38.462 0.00 0.00 0.00 3.25
26 27 7.014230 CCACTTCATTTCCTTCTTTCTTACCAA 59.986 37.037 0.00 0.00 0.00 3.67
27 28 8.413229 CACTTCATTTCCTTCTTTCTTACCAAA 58.587 33.333 0.00 0.00 0.00 3.28
28 29 9.147732 ACTTCATTTCCTTCTTTCTTACCAAAT 57.852 29.630 0.00 0.00 0.00 2.32
34 35 9.462606 TTTCCTTCTTTCTTACCAAATATCTCC 57.537 33.333 0.00 0.00 0.00 3.71
35 36 8.158025 TCCTTCTTTCTTACCAAATATCTCCA 57.842 34.615 0.00 0.00 0.00 3.86
36 37 8.781951 TCCTTCTTTCTTACCAAATATCTCCAT 58.218 33.333 0.00 0.00 0.00 3.41
37 38 9.413734 CCTTCTTTCTTACCAAATATCTCCATT 57.586 33.333 0.00 0.00 0.00 3.16
42 43 9.973661 TTTCTTACCAAATATCTCCATTTCTCA 57.026 29.630 0.00 0.00 0.00 3.27
44 45 9.784531 TCTTACCAAATATCTCCATTTCTCATC 57.215 33.333 0.00 0.00 0.00 2.92
45 46 9.790344 CTTACCAAATATCTCCATTTCTCATCT 57.210 33.333 0.00 0.00 0.00 2.90
46 47 9.784531 TTACCAAATATCTCCATTTCTCATCTC 57.215 33.333 0.00 0.00 0.00 2.75
47 48 7.230027 ACCAAATATCTCCATTTCTCATCTCC 58.770 38.462 0.00 0.00 0.00 3.71
48 49 6.658391 CCAAATATCTCCATTTCTCATCTCCC 59.342 42.308 0.00 0.00 0.00 4.30
49 50 7.229308 CAAATATCTCCATTTCTCATCTCCCA 58.771 38.462 0.00 0.00 0.00 4.37
50 51 4.978438 ATCTCCATTTCTCATCTCCCAG 57.022 45.455 0.00 0.00 0.00 4.45
51 52 2.437281 TCTCCATTTCTCATCTCCCAGC 59.563 50.000 0.00 0.00 0.00 4.85
52 53 2.172082 CTCCATTTCTCATCTCCCAGCA 59.828 50.000 0.00 0.00 0.00 4.41
53 54 2.092753 TCCATTTCTCATCTCCCAGCAC 60.093 50.000 0.00 0.00 0.00 4.40
54 55 2.356432 CCATTTCTCATCTCCCAGCACA 60.356 50.000 0.00 0.00 0.00 4.57
55 56 2.479566 TTTCTCATCTCCCAGCACAC 57.520 50.000 0.00 0.00 0.00 3.82
56 57 1.351076 TTCTCATCTCCCAGCACACA 58.649 50.000 0.00 0.00 0.00 3.72
57 58 1.351076 TCTCATCTCCCAGCACACAA 58.649 50.000 0.00 0.00 0.00 3.33
58 59 1.699083 TCTCATCTCCCAGCACACAAA 59.301 47.619 0.00 0.00 0.00 2.83
59 60 2.082231 CTCATCTCCCAGCACACAAAG 58.918 52.381 0.00 0.00 0.00 2.77
60 61 1.699083 TCATCTCCCAGCACACAAAGA 59.301 47.619 0.00 0.00 0.00 2.52
61 62 2.106338 TCATCTCCCAGCACACAAAGAA 59.894 45.455 0.00 0.00 0.00 2.52
62 63 1.967319 TCTCCCAGCACACAAAGAAC 58.033 50.000 0.00 0.00 0.00 3.01
63 64 1.211703 TCTCCCAGCACACAAAGAACA 59.788 47.619 0.00 0.00 0.00 3.18
64 65 2.158623 TCTCCCAGCACACAAAGAACAT 60.159 45.455 0.00 0.00 0.00 2.71
65 66 1.955778 TCCCAGCACACAAAGAACATG 59.044 47.619 0.00 0.00 0.00 3.21
66 67 1.000060 CCCAGCACACAAAGAACATGG 60.000 52.381 0.00 0.00 0.00 3.66
67 68 1.603678 CCAGCACACAAAGAACATGGC 60.604 52.381 0.00 0.00 0.00 4.40
68 69 0.311790 AGCACACAAAGAACATGGCG 59.688 50.000 0.00 0.00 0.00 5.69
69 70 0.310543 GCACACAAAGAACATGGCGA 59.689 50.000 0.00 0.00 0.00 5.54
70 71 1.925946 GCACACAAAGAACATGGCGAC 60.926 52.381 0.00 0.00 0.00 5.19
71 72 0.586319 ACACAAAGAACATGGCGACG 59.414 50.000 0.00 0.00 0.00 5.12
72 73 0.865111 CACAAAGAACATGGCGACGA 59.135 50.000 0.00 0.00 0.00 4.20
73 74 1.136252 CACAAAGAACATGGCGACGAG 60.136 52.381 0.00 0.00 0.00 4.18
100 101 3.058160 GCAGGCACCGCTTGACAT 61.058 61.111 1.88 0.00 37.87 3.06
101 102 2.872557 CAGGCACCGCTTGACATG 59.127 61.111 0.00 0.00 37.87 3.21
102 103 3.058160 AGGCACCGCTTGACATGC 61.058 61.111 3.27 3.27 34.40 4.06
103 104 3.364441 GGCACCGCTTGACATGCA 61.364 61.111 13.18 0.00 39.92 3.96
104 105 2.126734 GCACCGCTTGACATGCAC 60.127 61.111 13.18 0.00 38.00 4.57
105 106 2.562912 CACCGCTTGACATGCACC 59.437 61.111 13.18 0.00 0.00 5.01
106 107 1.968017 CACCGCTTGACATGCACCT 60.968 57.895 13.18 0.00 0.00 4.00
107 108 1.672356 ACCGCTTGACATGCACCTC 60.672 57.895 13.18 0.00 0.00 3.85
108 109 2.401766 CCGCTTGACATGCACCTCC 61.402 63.158 13.18 0.00 0.00 4.30
109 110 1.376424 CGCTTGACATGCACCTCCT 60.376 57.895 13.18 0.00 0.00 3.69
110 111 0.108186 CGCTTGACATGCACCTCCTA 60.108 55.000 13.18 0.00 0.00 2.94
111 112 1.661341 GCTTGACATGCACCTCCTAG 58.339 55.000 8.37 0.00 0.00 3.02
112 113 1.208052 GCTTGACATGCACCTCCTAGA 59.792 52.381 8.37 0.00 0.00 2.43
113 114 2.898705 CTTGACATGCACCTCCTAGAC 58.101 52.381 0.00 0.00 0.00 2.59
114 115 1.937191 TGACATGCACCTCCTAGACA 58.063 50.000 0.00 0.00 0.00 3.41
115 116 2.470990 TGACATGCACCTCCTAGACAT 58.529 47.619 0.00 0.00 0.00 3.06
116 117 3.642141 TGACATGCACCTCCTAGACATA 58.358 45.455 0.00 0.00 0.00 2.29
117 118 3.638627 TGACATGCACCTCCTAGACATAG 59.361 47.826 0.00 0.00 0.00 2.23
127 128 0.398318 CTAGACATAGGCCTTGGCCC 59.602 60.000 25.53 10.99 0.00 5.80
128 129 0.030092 TAGACATAGGCCTTGGCCCT 60.030 55.000 25.53 17.20 36.47 5.19
196 198 2.716244 CAGATCTCCCCGACGACG 59.284 66.667 0.00 0.00 39.43 5.12
268 270 1.416401 TCACCGCAGAAGAACCTCTTT 59.584 47.619 0.00 0.00 36.73 2.52
270 272 1.270893 ACCGCAGAAGAACCTCTTTCC 60.271 52.381 0.00 0.00 36.73 3.13
292 294 2.204059 AGCTGCCCCTCCAGAAGT 60.204 61.111 0.00 0.00 34.77 3.01
342 351 1.381191 TGCTCCTCGCCACCATCTA 60.381 57.895 0.00 0.00 38.05 1.98
366 375 1.974957 TCGACCAAAAGGACATCCAGA 59.025 47.619 0.00 0.00 38.89 3.86
395 404 3.854784 GCTCAAACTGCAGGACAATGTTC 60.855 47.826 19.93 0.00 0.00 3.18
412 421 7.477494 ACAATGTTCAGTAACTAAAACCACAC 58.523 34.615 0.00 0.00 36.51 3.82
416 425 4.053295 TCAGTAACTAAAACCACACGAGC 58.947 43.478 0.00 0.00 0.00 5.03
422 431 6.569179 AACTAAAACCACACGAGCAAATAT 57.431 33.333 0.00 0.00 0.00 1.28
458 467 4.496507 GCTGGCTTTACCTTTTGATCGATC 60.497 45.833 18.72 18.72 40.22 3.69
468 477 2.315925 TTGATCGATCAAGTGAGCCC 57.684 50.000 31.83 1.71 41.51 5.19
551 560 0.034767 TCCTCGTCCACGTACTCCAT 60.035 55.000 0.00 0.00 40.80 3.41
570 579 1.652930 GATGACGAGCGAGCGACTC 60.653 63.158 4.36 0.00 34.83 3.36
578 587 3.209812 CGAGCGACTCCGGGATGA 61.210 66.667 0.00 0.00 36.06 2.92
579 588 2.413765 GAGCGACTCCGGGATGAC 59.586 66.667 0.00 0.00 36.06 3.06
582 591 2.716244 CGACTCCGGGATGACGAG 59.284 66.667 0.00 0.00 35.47 4.18
583 592 2.413765 GACTCCGGGATGACGAGC 59.586 66.667 0.00 0.00 35.47 5.03
584 593 3.471244 GACTCCGGGATGACGAGCG 62.471 68.421 0.00 0.00 35.47 5.03
587 596 4.933064 CCGGGATGACGAGCGAGC 62.933 72.222 0.00 0.00 35.47 5.03
595 760 1.315981 TGACGAGCGAGCTTCTCCAT 61.316 55.000 0.00 1.26 0.00 3.41
621 786 3.151022 CCTCTCGGTGCCCCTCTC 61.151 72.222 0.00 0.00 0.00 3.20
627 792 2.883828 CGGTGCCCCTCTCTGTTGT 61.884 63.158 0.00 0.00 0.00 3.32
667 832 2.504367 ACTAGCATCGCCAAAGTTGTT 58.496 42.857 0.00 0.00 0.00 2.83
671 836 1.001378 GCATCGCCAAAGTTGTTGACT 60.001 47.619 0.00 0.00 41.47 3.41
704 869 1.565156 GGACAGCGCGAACATCACAA 61.565 55.000 12.10 0.00 0.00 3.33
726 891 4.406173 CTGCACCGCGTCTCGAGT 62.406 66.667 13.13 0.00 41.67 4.18
740 905 5.096169 CGTCTCGAGTAAATGATGTCACTT 58.904 41.667 13.13 0.00 0.00 3.16
808 973 7.050377 TGTTTGATCTATGTTTGGGAGATCTC 58.950 38.462 14.75 14.75 43.96 2.75
1031 1215 1.958205 GAAGCTCCATCATCGCCCG 60.958 63.158 0.00 0.00 0.00 6.13
1099 1286 1.383456 CCTCCTCTCTGTCTCTGCCG 61.383 65.000 0.00 0.00 0.00 5.69
1340 1538 0.482887 AAGGTGGAGAAAACCCTGGG 59.517 55.000 12.28 12.28 38.57 4.45
1497 1695 1.316706 CCGAGAACCTCCTTCGAGCT 61.317 60.000 0.00 0.00 34.49 4.09
1522 1730 2.811317 GTGGCTCTGTTCTCGGCG 60.811 66.667 0.00 0.00 0.00 6.46
1608 1816 2.472861 CGATATTGCCAAGCTCTACGTG 59.527 50.000 0.00 0.00 0.00 4.49
1690 1901 0.114954 AGGTCTTGGTGTACCCCGTA 59.885 55.000 0.00 0.00 36.34 4.02
2134 2410 2.373335 TGCTGCTTGTAAAGGGGAAA 57.627 45.000 0.00 0.00 46.35 3.13
2137 2413 2.094026 GCTGCTTGTAAAGGGGAAATGG 60.094 50.000 0.00 0.00 46.35 3.16
2189 2477 1.869754 CGGGCTATGATCTGGTTGTCG 60.870 57.143 0.00 0.00 0.00 4.35
2377 2692 5.808366 TGAAACTAAGTGTGAGATCAGGT 57.192 39.130 0.00 0.00 0.00 4.00
2510 3540 8.815565 TTTTATGCCAGTAATGTTATCCAGAA 57.184 30.769 0.00 0.00 0.00 3.02
2605 3654 1.317431 TTCATGCTCTGCACCATGGC 61.317 55.000 13.04 0.00 43.04 4.40
2606 3655 2.441532 ATGCTCTGCACCATGGCC 60.442 61.111 13.04 3.53 43.04 5.36
2607 3656 3.291031 ATGCTCTGCACCATGGCCA 62.291 57.895 13.04 8.56 43.04 5.36
2608 3657 2.441532 GCTCTGCACCATGGCCAT 60.442 61.111 14.09 14.09 0.00 4.40
2609 3658 1.152902 GCTCTGCACCATGGCCATA 60.153 57.895 20.30 0.50 0.00 2.74
2610 3659 1.170919 GCTCTGCACCATGGCCATAG 61.171 60.000 20.30 14.80 0.00 2.23
2611 3660 0.536687 CTCTGCACCATGGCCATAGG 60.537 60.000 20.30 22.95 0.00 2.57
2855 3916 6.291377 ACAGTTGGTATCATGTACATCCATC 58.709 40.000 13.21 12.39 0.00 3.51
2875 3936 4.743057 TCACTCTGAATACATGGTCTGG 57.257 45.455 0.00 0.00 0.00 3.86
2880 3941 7.290948 TCACTCTGAATACATGGTCTGGATATT 59.709 37.037 0.00 0.00 0.00 1.28
3017 4080 6.426937 TCTGTACTTGAATTAGTTTCTGCCAC 59.573 38.462 0.00 0.00 35.23 5.01
3123 4187 6.272318 TCACAACCATGTTTGATCTGAAAAC 58.728 36.000 10.27 0.00 37.82 2.43
3139 4204 6.591935 TCTGAAAACACAAGAACTCCAGTAT 58.408 36.000 0.00 0.00 0.00 2.12
3146 4215 8.514330 AACACAAGAACTCCAGTATTTTAACA 57.486 30.769 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.533569 TTTGGTAAGAAAGAAGGAAATGAAGT 57.466 30.769 0.00 0.00 0.00 3.01
8 9 9.462606 GGAGATATTTGGTAAGAAAGAAGGAAA 57.537 33.333 0.00 0.00 0.00 3.13
10 11 8.158025 TGGAGATATTTGGTAAGAAAGAAGGA 57.842 34.615 0.00 0.00 0.00 3.36
11 12 8.986929 ATGGAGATATTTGGTAAGAAAGAAGG 57.013 34.615 0.00 0.00 0.00 3.46
16 17 9.973661 TGAGAAATGGAGATATTTGGTAAGAAA 57.026 29.630 0.00 0.00 30.78 2.52
18 19 9.784531 GATGAGAAATGGAGATATTTGGTAAGA 57.215 33.333 0.00 0.00 30.78 2.10
19 20 9.790344 AGATGAGAAATGGAGATATTTGGTAAG 57.210 33.333 0.00 0.00 30.78 2.34
20 21 9.784531 GAGATGAGAAATGGAGATATTTGGTAA 57.215 33.333 0.00 0.00 30.78 2.85
21 22 8.378565 GGAGATGAGAAATGGAGATATTTGGTA 58.621 37.037 0.00 0.00 30.78 3.25
22 23 7.230027 GGAGATGAGAAATGGAGATATTTGGT 58.770 38.462 0.00 0.00 30.78 3.67
23 24 6.658391 GGGAGATGAGAAATGGAGATATTTGG 59.342 42.308 0.00 0.00 30.78 3.28
24 25 7.229308 TGGGAGATGAGAAATGGAGATATTTG 58.771 38.462 0.00 0.00 30.78 2.32
25 26 7.398289 TGGGAGATGAGAAATGGAGATATTT 57.602 36.000 0.00 0.00 33.19 1.40
26 27 6.522114 GCTGGGAGATGAGAAATGGAGATATT 60.522 42.308 0.00 0.00 0.00 1.28
27 28 5.045724 GCTGGGAGATGAGAAATGGAGATAT 60.046 44.000 0.00 0.00 0.00 1.63
28 29 4.285517 GCTGGGAGATGAGAAATGGAGATA 59.714 45.833 0.00 0.00 0.00 1.98
29 30 3.072768 GCTGGGAGATGAGAAATGGAGAT 59.927 47.826 0.00 0.00 0.00 2.75
30 31 2.437281 GCTGGGAGATGAGAAATGGAGA 59.563 50.000 0.00 0.00 0.00 3.71
31 32 2.172082 TGCTGGGAGATGAGAAATGGAG 59.828 50.000 0.00 0.00 0.00 3.86
32 33 2.092753 GTGCTGGGAGATGAGAAATGGA 60.093 50.000 0.00 0.00 0.00 3.41
33 34 2.295885 GTGCTGGGAGATGAGAAATGG 58.704 52.381 0.00 0.00 0.00 3.16
34 35 2.681848 GTGTGCTGGGAGATGAGAAATG 59.318 50.000 0.00 0.00 0.00 2.32
35 36 2.306805 TGTGTGCTGGGAGATGAGAAAT 59.693 45.455 0.00 0.00 0.00 2.17
36 37 1.699083 TGTGTGCTGGGAGATGAGAAA 59.301 47.619 0.00 0.00 0.00 2.52
37 38 1.351076 TGTGTGCTGGGAGATGAGAA 58.649 50.000 0.00 0.00 0.00 2.87
38 39 1.351076 TTGTGTGCTGGGAGATGAGA 58.649 50.000 0.00 0.00 0.00 3.27
39 40 2.082231 CTTTGTGTGCTGGGAGATGAG 58.918 52.381 0.00 0.00 0.00 2.90
40 41 1.699083 TCTTTGTGTGCTGGGAGATGA 59.301 47.619 0.00 0.00 0.00 2.92
41 42 2.189594 TCTTTGTGTGCTGGGAGATG 57.810 50.000 0.00 0.00 0.00 2.90
42 43 2.158623 TGTTCTTTGTGTGCTGGGAGAT 60.159 45.455 0.00 0.00 0.00 2.75
43 44 1.211703 TGTTCTTTGTGTGCTGGGAGA 59.788 47.619 0.00 0.00 0.00 3.71
44 45 1.679139 TGTTCTTTGTGTGCTGGGAG 58.321 50.000 0.00 0.00 0.00 4.30
45 46 1.955778 CATGTTCTTTGTGTGCTGGGA 59.044 47.619 0.00 0.00 0.00 4.37
46 47 1.000060 CCATGTTCTTTGTGTGCTGGG 60.000 52.381 0.00 0.00 0.00 4.45
47 48 1.603678 GCCATGTTCTTTGTGTGCTGG 60.604 52.381 0.00 0.00 0.00 4.85
48 49 1.774639 GCCATGTTCTTTGTGTGCTG 58.225 50.000 0.00 0.00 0.00 4.41
49 50 0.311790 CGCCATGTTCTTTGTGTGCT 59.688 50.000 0.00 0.00 0.00 4.40
50 51 0.310543 TCGCCATGTTCTTTGTGTGC 59.689 50.000 0.00 0.00 0.00 4.57
51 52 1.660052 CGTCGCCATGTTCTTTGTGTG 60.660 52.381 0.00 0.00 0.00 3.82
52 53 0.586319 CGTCGCCATGTTCTTTGTGT 59.414 50.000 0.00 0.00 0.00 3.72
53 54 0.865111 TCGTCGCCATGTTCTTTGTG 59.135 50.000 0.00 0.00 0.00 3.33
54 55 1.148310 CTCGTCGCCATGTTCTTTGT 58.852 50.000 0.00 0.00 0.00 2.83
55 56 0.179215 GCTCGTCGCCATGTTCTTTG 60.179 55.000 0.00 0.00 0.00 2.77
56 57 1.626654 CGCTCGTCGCCATGTTCTTT 61.627 55.000 0.00 0.00 34.21 2.52
57 58 2.094659 CGCTCGTCGCCATGTTCTT 61.095 57.895 0.00 0.00 34.21 2.52
58 59 2.507102 CGCTCGTCGCCATGTTCT 60.507 61.111 0.00 0.00 34.21 3.01
83 84 3.058160 ATGTCAAGCGGTGCCTGC 61.058 61.111 0.00 0.00 0.00 4.85
84 85 2.872557 CATGTCAAGCGGTGCCTG 59.127 61.111 0.00 0.00 0.00 4.85
85 86 3.058160 GCATGTCAAGCGGTGCCT 61.058 61.111 0.00 0.00 0.00 4.75
86 87 3.364441 TGCATGTCAAGCGGTGCC 61.364 61.111 0.00 0.00 36.79 5.01
87 88 2.126734 GTGCATGTCAAGCGGTGC 60.127 61.111 0.00 0.00 38.05 5.01
88 89 1.915614 GAGGTGCATGTCAAGCGGTG 61.916 60.000 0.00 0.00 33.85 4.94
89 90 1.672356 GAGGTGCATGTCAAGCGGT 60.672 57.895 0.00 0.00 33.85 5.68
90 91 2.401766 GGAGGTGCATGTCAAGCGG 61.402 63.158 0.00 0.00 33.85 5.52
91 92 0.108186 TAGGAGGTGCATGTCAAGCG 60.108 55.000 0.00 0.00 33.85 4.68
92 93 1.208052 TCTAGGAGGTGCATGTCAAGC 59.792 52.381 0.00 0.00 0.00 4.01
93 94 2.234661 TGTCTAGGAGGTGCATGTCAAG 59.765 50.000 0.00 0.00 0.00 3.02
94 95 2.256306 TGTCTAGGAGGTGCATGTCAA 58.744 47.619 0.00 0.00 0.00 3.18
95 96 1.937191 TGTCTAGGAGGTGCATGTCA 58.063 50.000 0.00 0.00 0.00 3.58
96 97 3.006323 CCTATGTCTAGGAGGTGCATGTC 59.994 52.174 0.00 0.00 46.66 3.06
97 98 2.968574 CCTATGTCTAGGAGGTGCATGT 59.031 50.000 0.00 0.00 46.66 3.21
98 99 2.289320 GCCTATGTCTAGGAGGTGCATG 60.289 54.545 2.84 0.00 46.66 4.06
99 100 1.974236 GCCTATGTCTAGGAGGTGCAT 59.026 52.381 2.84 0.00 46.66 3.96
100 101 1.414158 GCCTATGTCTAGGAGGTGCA 58.586 55.000 2.84 0.00 46.66 4.57
101 102 0.682292 GGCCTATGTCTAGGAGGTGC 59.318 60.000 0.00 0.00 46.66 5.01
102 103 2.366916 CAAGGCCTATGTCTAGGAGGTG 59.633 54.545 5.16 0.00 46.66 4.00
103 104 2.683768 CAAGGCCTATGTCTAGGAGGT 58.316 52.381 5.16 0.00 46.66 3.85
104 105 1.974236 CCAAGGCCTATGTCTAGGAGG 59.026 57.143 5.16 0.00 46.66 4.30
105 106 1.346068 GCCAAGGCCTATGTCTAGGAG 59.654 57.143 5.16 0.00 46.66 3.69
106 107 1.424638 GCCAAGGCCTATGTCTAGGA 58.575 55.000 5.16 0.00 46.66 2.94
225 227 3.138930 ATCCGCCTCGTGGACATCG 62.139 63.158 7.92 0.84 45.43 3.84
235 237 2.592861 GGTGATGCCATCCGCCTC 60.593 66.667 1.49 0.00 36.24 4.70
240 242 1.442526 CTTCTGCGGTGATGCCATCC 61.443 60.000 1.49 0.00 36.97 3.51
241 243 0.462581 TCTTCTGCGGTGATGCCATC 60.463 55.000 0.00 0.00 36.97 3.51
247 249 1.270907 AGAGGTTCTTCTGCGGTGAT 58.729 50.000 0.00 0.00 0.00 3.06
250 252 1.270893 GGAAAGAGGTTCTTCTGCGGT 60.271 52.381 0.00 0.00 35.27 5.68
268 270 3.011517 GAGGGGCAGCTGAAGGGA 61.012 66.667 20.43 0.00 0.00 4.20
270 272 3.333219 TGGAGGGGCAGCTGAAGG 61.333 66.667 20.43 0.00 0.00 3.46
292 294 1.004758 AGCCAAGGGGATCCTGCTA 59.995 57.895 12.58 0.00 44.07 3.49
342 351 2.550208 GGATGTCCTTTTGGTCGACTGT 60.550 50.000 16.46 0.00 41.38 3.55
366 375 3.127533 GCAGTTTGAGCGGCCGAT 61.128 61.111 33.48 27.37 0.00 4.18
395 404 3.805422 TGCTCGTGTGGTTTTAGTTACTG 59.195 43.478 0.00 0.00 0.00 2.74
412 421 4.029972 CAGACGATCGATCATATTTGCTCG 59.970 45.833 24.34 10.84 41.59 5.03
416 425 4.091075 CCAGCAGACGATCGATCATATTTG 59.909 45.833 24.34 14.72 0.00 2.32
422 431 1.066422 GCCAGCAGACGATCGATCA 59.934 57.895 24.34 0.00 0.00 2.92
428 437 0.905357 AGGTAAAGCCAGCAGACGAT 59.095 50.000 0.00 0.00 40.61 3.73
458 467 2.037136 CGGCTTCTGGGCTCACTTG 61.037 63.158 0.00 0.00 38.46 3.16
491 500 4.678269 CGGACGACACGCACGACT 62.678 66.667 0.00 0.00 32.72 4.18
498 507 4.778415 CTCCTGCCGGACGACACG 62.778 72.222 5.05 0.00 34.92 4.49
518 527 2.032681 AGGACTTGAACGGGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
520 529 2.156051 GACGAGGACTTGAACGGGCT 62.156 60.000 0.00 0.00 0.00 5.19
551 560 2.100410 GTCGCTCGCTCGTCATCA 59.900 61.111 0.00 0.00 0.00 3.07
570 579 4.933064 GCTCGCTCGTCATCCCGG 62.933 72.222 0.00 0.00 0.00 5.73
578 587 1.315981 TGATGGAGAAGCTCGCTCGT 61.316 55.000 9.62 2.77 33.19 4.18
579 588 0.031857 ATGATGGAGAAGCTCGCTCG 59.968 55.000 9.62 0.00 33.19 5.03
582 591 3.434984 GGAAATATGATGGAGAAGCTCGC 59.565 47.826 0.00 0.00 0.00 5.03
583 592 3.999663 GGGAAATATGATGGAGAAGCTCG 59.000 47.826 0.00 0.00 0.00 5.03
584 593 5.012975 AGAGGGAAATATGATGGAGAAGCTC 59.987 44.000 0.00 0.00 0.00 4.09
587 596 5.477510 CGAGAGGGAAATATGATGGAGAAG 58.522 45.833 0.00 0.00 0.00 2.85
621 786 1.352156 GCCGCCGACTAGAACAACAG 61.352 60.000 0.00 0.00 0.00 3.16
627 792 4.143333 GCAGGCCGCCGACTAGAA 62.143 66.667 3.05 0.00 32.94 2.10
646 811 3.328382 ACAACTTTGGCGATGCTAGTA 57.672 42.857 0.00 0.00 0.00 1.82
704 869 3.997064 GAGACGCGGTGCAGCATCT 62.997 63.158 17.33 14.65 42.77 2.90
709 874 2.523184 TTACTCGAGACGCGGTGCAG 62.523 60.000 21.68 1.59 41.33 4.41
781 946 7.718753 AGATCTCCCAAACATAGATCAAACATC 59.281 37.037 12.61 0.00 38.18 3.06
808 973 0.093535 CGTGATGTGCTGCAGTTACG 59.906 55.000 16.64 10.12 0.00 3.18
866 1031 9.192642 GGGAGAGAAGAGATTACTACTACTTTT 57.807 37.037 0.00 0.00 0.00 2.27
867 1032 7.781219 GGGGAGAGAAGAGATTACTACTACTTT 59.219 40.741 0.00 0.00 0.00 2.66
907 1072 4.142160 ACGGCTGCTTTTCTTTTCTCTTTT 60.142 37.500 0.00 0.00 0.00 2.27
909 1074 2.952310 ACGGCTGCTTTTCTTTTCTCTT 59.048 40.909 0.00 0.00 0.00 2.85
910 1075 2.550180 GACGGCTGCTTTTCTTTTCTCT 59.450 45.455 0.00 0.00 0.00 3.10
913 1078 1.674908 CGACGGCTGCTTTTCTTTTC 58.325 50.000 0.00 0.00 0.00 2.29
915 1080 1.282875 GCGACGGCTGCTTTTCTTT 59.717 52.632 0.00 0.00 35.83 2.52
916 1081 2.946762 GCGACGGCTGCTTTTCTT 59.053 55.556 0.00 0.00 35.83 2.52
917 1082 3.414700 CGCGACGGCTGCTTTTCT 61.415 61.111 0.00 0.00 36.88 2.52
1024 1208 1.076632 AAGAGAGGAGACGGGCGAT 60.077 57.895 0.00 0.00 0.00 4.58
1031 1215 2.427095 GCTGGAGAAGAAGAGAGGAGAC 59.573 54.545 0.00 0.00 0.00 3.36
1099 1286 2.967615 GGAGATTGCGGGCGCTAC 60.968 66.667 7.64 0.00 42.51 3.58
1192 1388 4.475135 GTGGGAGAGCTTCGGGGC 62.475 72.222 0.00 0.00 0.00 5.80
1497 1695 2.560542 GAGAACAGAGCCACTCTTGAGA 59.439 50.000 4.49 0.00 38.99 3.27
1608 1816 0.250038 TGAGCAGCGATGGCCTAATC 60.250 55.000 3.32 0.00 41.24 1.75
1690 1901 3.369261 GCATGTCTGAACATCTGAGACCT 60.369 47.826 0.00 0.00 44.41 3.85
1692 1903 2.602211 CGCATGTCTGAACATCTGAGAC 59.398 50.000 0.00 0.00 44.41 3.36
2134 2410 3.316308 GTGAATCTGAAATTAGCCGCCAT 59.684 43.478 0.00 0.00 0.00 4.40
2137 2413 4.035558 TCATGTGAATCTGAAATTAGCCGC 59.964 41.667 0.00 0.00 0.00 6.53
2189 2477 4.184629 CACCTAAGAGTCATACAACAGCC 58.815 47.826 0.00 0.00 0.00 4.85
2377 2692 0.252881 AAGTGAGCCCTCCTCCATGA 60.253 55.000 0.00 0.00 39.98 3.07
2506 3536 3.572584 GCAAGTGCTTCTCCATTTTCTG 58.427 45.455 0.00 0.00 38.21 3.02
2605 3654 4.410099 ACACATGATTTATGGGCCTATGG 58.590 43.478 12.67 0.00 44.37 2.74
2606 3655 6.409524 AAACACATGATTTATGGGCCTATG 57.590 37.500 12.67 0.00 44.37 2.23
2607 3656 8.725606 AATAAACACATGATTTATGGGCCTAT 57.274 30.769 6.88 6.88 44.37 2.57
2608 3657 8.546083 AAATAAACACATGATTTATGGGCCTA 57.454 30.769 4.53 0.00 44.37 3.93
2609 3658 7.436320 AAATAAACACATGATTTATGGGCCT 57.564 32.000 4.53 0.00 44.37 5.19
2610 3659 7.012232 CCAAAATAAACACATGATTTATGGGCC 59.988 37.037 15.67 0.00 44.37 5.80
2611 3660 7.768120 TCCAAAATAAACACATGATTTATGGGC 59.232 33.333 15.67 0.00 44.37 5.36
2612 3661 9.835389 ATCCAAAATAAACACATGATTTATGGG 57.165 29.630 15.67 16.01 46.03 4.00
2733 3788 7.616150 AGAGGTAGCTCAGTTATAGAAGACAAA 59.384 37.037 23.18 0.00 0.00 2.83
2855 3916 4.743057 TCCAGACCATGTATTCAGAGTG 57.257 45.455 0.00 0.00 0.00 3.51
2875 3936 2.224066 ACCTGCAGTCGCTACCAATATC 60.224 50.000 13.81 0.00 39.64 1.63
2880 3941 1.185618 AGAACCTGCAGTCGCTACCA 61.186 55.000 13.81 0.00 39.64 3.25
3017 4080 4.808414 TCTCTAGATGAACACACCCAAG 57.192 45.455 0.00 0.00 0.00 3.61
3048 4112 6.662414 TTACTATTCGCCAATGAACTTCAG 57.338 37.500 0.00 0.00 0.00 3.02
3123 4187 8.237267 GGATGTTAAAATACTGGAGTTCTTGTG 58.763 37.037 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.