Multiple sequence alignment - TraesCS5B01G221200

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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 TraesCS5B01G221200 chr5B 100.000 2942 0 0 1 2942 395710636 395707695 0.000000e+00 5433.0
1 TraesCS5B01G221200 chr5B 94.377 1067 51 5 869 1929 395683996 395682933 0.000000e+00 1629.0
2 TraesCS5B01G221200 chr5B 92.168 549 21 3 2412 2942 395682937 395682393 0.000000e+00 756.0
3 TraesCS5B01G221200 chr5B 85.849 318 33 6 38 351 395684796 395684487 7.860000e-86 327.0
4 TraesCS5B01G221200 chr5B 94.444 180 10 0 527 706 395684177 395683998 8.030000e-71 278.0
5 TraesCS5B01G221200 chr5B 94.400 125 7 0 411 535 395684336 395684212 2.990000e-45 193.0
6 TraesCS5B01G221200 chr5D 91.849 2061 111 11 908 2942 337218563 337216534 0.000000e+00 2822.0
7 TraesCS5B01G221200 chr5D 88.075 1065 107 7 871 1929 337185883 337184833 0.000000e+00 1245.0
8 TraesCS5B01G221200 chr5D 87.818 550 43 6 2412 2942 337184837 337184293 8.950000e-175 623.0
9 TraesCS5B01G221200 chr5D 94.444 180 10 0 527 706 337186066 337185887 8.030000e-71 278.0
10 TraesCS5B01G221200 chr5D 82.831 332 31 13 382 706 337218907 337218595 1.040000e-69 274.0
11 TraesCS5B01G221200 chr5D 79.353 402 68 12 2020 2411 14006685 14007081 4.830000e-68 268.0
12 TraesCS5B01G221200 chr5D 86.475 244 23 4 112 351 337186614 337186377 2.910000e-65 259.0
13 TraesCS5B01G221200 chr5D 85.882 255 15 5 38 289 337219250 337219014 4.870000e-63 252.0
14 TraesCS5B01G221200 chr5D 80.290 345 52 14 2056 2391 14025226 14025563 2.260000e-61 246.0
15 TraesCS5B01G221200 chr5D 92.632 95 3 3 3 93 337219435 337219341 1.840000e-27 134.0
16 TraesCS5B01G221200 chr5D 96.825 63 2 0 38 100 337186810 337186748 4.010000e-19 106.0
17 TraesCS5B01G221200 chr5A 92.613 1083 53 10 873 1928 438357645 438356563 0.000000e+00 1531.0
18 TraesCS5B01G221200 chr5A 92.536 1045 78 0 885 1929 438410742 438409698 0.000000e+00 1498.0
19 TraesCS5B01G221200 chr5A 92.714 549 18 3 2412 2942 438356566 438356022 0.000000e+00 773.0
20 TraesCS5B01G221200 chr5A 87.067 549 49 6 2412 2942 438409702 438409158 4.200000e-168 601.0
21 TraesCS5B01G221200 chr5A 87.464 351 28 8 7 351 438412373 438412033 9.890000e-105 390.0
22 TraesCS5B01G221200 chr5A 85.321 327 33 7 32 351 438358472 438358154 1.020000e-84 324.0
23 TraesCS5B01G221200 chr5A 95.000 180 6 1 527 706 438357834 438357658 2.230000e-71 279.0
24 TraesCS5B01G221200 chr5A 93.162 117 8 0 411 527 438358002 438357886 3.900000e-39 172.0
25 TraesCS5B01G221200 chr5A 90.698 86 8 0 621 706 438410848 438410763 6.660000e-22 115.0
26 TraesCS5B01G221200 chr4B 84.591 318 35 11 2074 2386 386024833 386024525 1.320000e-78 303.0
27 TraesCS5B01G221200 chr3B 95.930 172 5 2 704 873 112325302 112325131 8.030000e-71 278.0
28 TraesCS5B01G221200 chr3B 96.341 164 5 1 708 870 23408409 23408572 4.830000e-68 268.0
29 TraesCS5B01G221200 chr7B 96.364 165 5 1 708 871 11441304 11441140 1.340000e-68 270.0
30 TraesCS5B01G221200 chr7B 79.576 377 61 14 2020 2392 708570980 708570616 3.760000e-64 255.0
31 TraesCS5B01G221200 chr7B 80.000 360 57 13 2038 2392 708569526 708569177 4.870000e-63 252.0
32 TraesCS5B01G221200 chr7B 77.741 301 53 13 2091 2384 686164124 686163831 3.900000e-39 172.0
33 TraesCS5B01G221200 chr1B 96.914 162 4 1 708 868 647530685 647530524 1.340000e-68 270.0
34 TraesCS5B01G221200 chr1B 80.716 363 56 12 2038 2392 649690547 649690903 1.340000e-68 270.0
35 TraesCS5B01G221200 chr1B 79.255 376 63 12 2026 2392 649687419 649687788 6.300000e-62 248.0
36 TraesCS5B01G221200 chr4A 95.266 169 6 2 705 871 517406468 517406636 1.740000e-67 267.0
37 TraesCS5B01G221200 chr6B 95.238 168 7 1 705 871 450843591 450843758 6.250000e-67 265.0
38 TraesCS5B01G221200 chr6B 93.750 176 9 2 708 881 408626260 408626085 2.250000e-66 263.0
39 TraesCS5B01G221200 chr6B 90.306 196 13 6 677 869 131168902 131169094 4.870000e-63 252.0
40 TraesCS5B01G221200 chr6B 81.395 86 13 2 1927 2009 565615378 565615293 1.890000e-07 67.6
41 TraesCS5B01G221200 chr1D 95.758 165 6 1 705 868 463381902 463382066 6.250000e-67 265.0
42 TraesCS5B01G221200 chr6D 86.792 53 4 2 1927 1976 471797818 471797766 4.100000e-04 56.5


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 TraesCS5B01G221200 chr5B 395707695 395710636 2941 True 5433.0 5433 100.00000 1 2942 1 chr5B.!!$R1 2941
1 TraesCS5B01G221200 chr5B 395682393 395684796 2403 True 636.6 1629 92.24760 38 2942 5 chr5B.!!$R2 2904
2 TraesCS5B01G221200 chr5D 337216534 337219435 2901 True 870.5 2822 88.29850 3 2942 4 chr5D.!!$R2 2939
3 TraesCS5B01G221200 chr5D 337184293 337186810 2517 True 502.2 1245 90.72740 38 2942 5 chr5D.!!$R1 2904
4 TraesCS5B01G221200 chr5A 438409158 438412373 3215 True 651.0 1498 89.44125 7 2942 4 chr5A.!!$R2 2935
5 TraesCS5B01G221200 chr5A 438356022 438358472 2450 True 615.8 1531 91.76200 32 2942 5 chr5A.!!$R1 2910
6 TraesCS5B01G221200 chr7B 708569177 708570980 1803 True 253.5 255 79.78800 2020 2392 2 chr7B.!!$R3 372
7 TraesCS5B01G221200 chr1B 649687419 649690903 3484 False 259.0 270 79.98550 2026 2392 2 chr1B.!!$F1 366

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
398 769 0.030908 CTGTACGCGAGGGATTCTCC 59.969 60.0 15.93 0.0 39.3 3.71 F
1057 2410 0.031716 CCTCCTCCTCCACCTGATGA 60.032 60.0 0.00 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 2632 0.252012 CCTAGGGAGAGGCCGATGAT 60.252 60.0 0.0 0.0 37.63 2.45 R
2819 4201 0.113776 TGTCCGGTACCTCTCCAGTT 59.886 55.0 10.9 0.0 0.00 3.16 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
22 27 2.502142 TTGAGAGATGGCTTGTGCAT 57.498 45.000 0.00 0.00 41.91 3.96
100 251 4.785346 ATTGAGATGACCCAGCTTATGT 57.215 40.909 0.00 0.00 26.98 2.29
101 252 3.548745 TGAGATGACCCAGCTTATGTG 57.451 47.619 0.00 0.00 26.98 3.21
104 255 2.092753 AGATGACCCAGCTTATGTGTGG 60.093 50.000 0.00 0.00 0.00 4.17
106 257 1.000896 ACCCAGCTTATGTGTGGCC 60.001 57.895 0.00 0.00 0.00 5.36
149 424 3.127895 TGTGCTTCTGTTTGTTACACACC 59.872 43.478 0.00 0.00 32.12 4.16
158 433 6.095580 TCTGTTTGTTACACACCTGCAAAATA 59.904 34.615 0.00 0.00 31.99 1.40
209 484 1.202114 GCTCGGCATGAATTGGTTCAA 59.798 47.619 0.00 0.00 46.67 2.69
289 572 3.882326 CCCGGCCTCTGCATGGAT 61.882 66.667 0.00 0.00 40.13 3.41
290 573 2.194056 CCGGCCTCTGCATGGATT 59.806 61.111 0.00 0.00 40.13 3.01
302 585 4.712829 TCTGCATGGATTGATTGTGGATTT 59.287 37.500 0.00 0.00 0.00 2.17
347 634 8.821894 CAGGTTAGTTCAATCTAGCTTTATCAC 58.178 37.037 0.00 0.00 0.00 3.06
351 638 6.109359 AGTTCAATCTAGCTTTATCACGCTT 58.891 36.000 0.00 0.00 37.68 4.68
353 640 4.271049 TCAATCTAGCTTTATCACGCTTGC 59.729 41.667 0.00 0.00 37.68 4.01
356 643 2.691409 AGCTTTATCACGCTTGCCTA 57.309 45.000 0.00 0.00 31.17 3.93
360 647 3.869246 GCTTTATCACGCTTGCCTAACTA 59.131 43.478 0.00 0.00 0.00 2.24
361 648 4.025647 GCTTTATCACGCTTGCCTAACTAG 60.026 45.833 0.00 0.00 0.00 2.57
363 650 0.606096 TCACGCTTGCCTAACTAGCA 59.394 50.000 0.00 0.00 46.08 3.49
364 651 0.721718 CACGCTTGCCTAACTAGCAC 59.278 55.000 0.00 0.00 46.08 4.40
367 654 2.232941 ACGCTTGCCTAACTAGCACTTA 59.767 45.455 0.00 0.00 46.08 2.24
368 655 3.259064 CGCTTGCCTAACTAGCACTTAA 58.741 45.455 0.00 0.00 46.08 1.85
369 656 3.062234 CGCTTGCCTAACTAGCACTTAAC 59.938 47.826 0.00 0.00 46.08 2.01
370 657 4.000988 GCTTGCCTAACTAGCACTTAACA 58.999 43.478 0.00 0.00 45.23 2.41
372 659 4.884668 TGCCTAACTAGCACTTAACAGT 57.115 40.909 0.00 0.00 34.69 3.55
375 745 6.395629 TGCCTAACTAGCACTTAACAGTAAG 58.604 40.000 0.00 0.00 42.23 2.34
392 762 0.892358 AAGACACTGTACGCGAGGGA 60.892 55.000 15.93 0.00 0.00 4.20
393 763 0.680280 AGACACTGTACGCGAGGGAT 60.680 55.000 15.93 0.00 0.00 3.85
398 769 0.030908 CTGTACGCGAGGGATTCTCC 59.969 60.000 15.93 0.00 39.30 3.71
424 803 3.508845 AGGCACCACAACAGTATTTCT 57.491 42.857 0.00 0.00 0.00 2.52
510 889 1.087771 GGCCATTACAACCTCGTCCG 61.088 60.000 0.00 0.00 0.00 4.79
555 987 2.817834 GCCCGCTTATCGTGCACA 60.818 61.111 18.64 4.45 41.27 4.57
666 1985 2.317040 TCCATCTATCCTCGTTCCCAC 58.683 52.381 0.00 0.00 0.00 4.61
706 2025 2.749076 TGCTTCAACATCCTTTCCGATG 59.251 45.455 0.00 0.00 44.38 3.84
713 2032 3.113260 CATCCTTTCCGATGTACTCCC 57.887 52.381 0.00 0.00 35.83 4.30
716 2035 1.413077 CCTTTCCGATGTACTCCCTCC 59.587 57.143 0.00 0.00 0.00 4.30
717 2036 1.067212 CTTTCCGATGTACTCCCTCCG 59.933 57.143 0.00 0.00 0.00 4.63
718 2037 0.033796 TTCCGATGTACTCCCTCCGT 60.034 55.000 0.00 0.00 0.00 4.69
719 2038 0.033796 TCCGATGTACTCCCTCCGTT 60.034 55.000 0.00 0.00 0.00 4.44
722 2041 1.749634 CGATGTACTCCCTCCGTTTCT 59.250 52.381 0.00 0.00 0.00 2.52
723 2042 2.947652 CGATGTACTCCCTCCGTTTCTA 59.052 50.000 0.00 0.00 0.00 2.10
724 2043 3.379372 CGATGTACTCCCTCCGTTTCTAA 59.621 47.826 0.00 0.00 0.00 2.10
725 2044 4.142315 CGATGTACTCCCTCCGTTTCTAAA 60.142 45.833 0.00 0.00 0.00 1.85
726 2045 5.451520 CGATGTACTCCCTCCGTTTCTAAAT 60.452 44.000 0.00 0.00 0.00 1.40
727 2046 6.238842 CGATGTACTCCCTCCGTTTCTAAATA 60.239 42.308 0.00 0.00 0.00 1.40
728 2047 7.523380 CGATGTACTCCCTCCGTTTCTAAATAT 60.523 40.741 0.00 0.00 0.00 1.28
729 2048 8.716674 ATGTACTCCCTCCGTTTCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
730 2049 8.537728 TGTACTCCCTCCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
731 2050 8.636213 TGTACTCCCTCCGTTTCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
732 2051 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
733 2052 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
734 2053 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
736 2055 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
767 2086 5.977489 TCCATTATGGACTACATACGGAG 57.023 43.478 10.29 0.00 42.67 4.63
768 2087 4.219944 TCCATTATGGACTACATACGGAGC 59.780 45.833 10.29 0.00 42.67 4.70
769 2088 4.021456 CCATTATGGACTACATACGGAGCA 60.021 45.833 5.05 0.00 41.61 4.26
770 2089 5.510690 CCATTATGGACTACATACGGAGCAA 60.511 44.000 5.05 0.00 41.61 3.91
773 2092 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
774 2093 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
776 2095 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
777 2096 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
778 2097 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
779 2098 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
780 2099 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
781 2100 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
782 2101 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
783 2102 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
784 2103 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
785 2104 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
786 2105 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
829 2148 6.519679 ACATCCGTATGTAGTTTGTAGTGA 57.480 37.500 0.00 0.00 44.66 3.41
830 2149 6.927416 ACATCCGTATGTAGTTTGTAGTGAA 58.073 36.000 0.00 0.00 44.66 3.18
831 2150 7.380536 ACATCCGTATGTAGTTTGTAGTGAAA 58.619 34.615 0.00 0.00 44.66 2.69
832 2151 8.038944 ACATCCGTATGTAGTTTGTAGTGAAAT 58.961 33.333 0.00 0.00 44.66 2.17
834 2153 7.833786 TCCGTATGTAGTTTGTAGTGAAATCT 58.166 34.615 0.00 0.00 0.00 2.40
836 2155 7.974501 CCGTATGTAGTTTGTAGTGAAATCTCT 59.025 37.037 0.00 0.00 0.00 3.10
837 2156 9.999009 CGTATGTAGTTTGTAGTGAAATCTCTA 57.001 33.333 0.00 0.00 0.00 2.43
860 2179 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
861 2180 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
863 2182 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
864 2183 5.021458 AGACTTACATTTAGGAACGGAGGA 58.979 41.667 0.00 0.00 0.00 3.71
865 2184 5.127356 AGACTTACATTTAGGAACGGAGGAG 59.873 44.000 0.00 0.00 0.00 3.69
866 2185 4.776308 ACTTACATTTAGGAACGGAGGAGT 59.224 41.667 0.00 0.00 0.00 3.85
867 2186 5.954150 ACTTACATTTAGGAACGGAGGAGTA 59.046 40.000 0.00 0.00 0.00 2.59
868 2187 4.732672 ACATTTAGGAACGGAGGAGTAC 57.267 45.455 0.00 0.00 0.00 2.73
869 2188 4.091549 ACATTTAGGAACGGAGGAGTACA 58.908 43.478 0.00 0.00 0.00 2.90
870 2189 4.715297 ACATTTAGGAACGGAGGAGTACAT 59.285 41.667 0.00 0.00 0.00 2.29
871 2190 4.996788 TTTAGGAACGGAGGAGTACATC 57.003 45.455 0.00 0.00 0.00 3.06
872 2191 2.830651 AGGAACGGAGGAGTACATCT 57.169 50.000 0.00 0.00 0.00 2.90
873 2192 2.657143 AGGAACGGAGGAGTACATCTC 58.343 52.381 0.00 1.17 42.07 2.75
874 2193 2.242708 AGGAACGGAGGAGTACATCTCT 59.757 50.000 12.95 0.00 42.40 3.10
875 2194 2.359531 GGAACGGAGGAGTACATCTCTG 59.640 54.545 17.45 17.45 42.40 3.35
921 2252 4.647615 CCGGAGATGCTACCGCCG 62.648 72.222 0.00 8.25 46.59 6.46
957 2289 2.548295 GCTCCGAGGTCCGAGCTAG 61.548 68.421 11.64 0.00 41.76 3.42
1004 2336 3.700538 TGCCTTTCCAGTAAAGCATGAT 58.299 40.909 0.00 0.00 42.85 2.45
1057 2410 0.031716 CCTCCTCCTCCACCTGATGA 60.032 60.000 0.00 0.00 0.00 2.92
1830 3186 2.981909 TTCTCGAGCCACGACGGT 60.982 61.111 7.81 0.00 46.45 4.83
1885 3241 1.398390 CGAACTGCTCCCAAATACTGC 59.602 52.381 0.00 0.00 0.00 4.40
1887 3243 2.584835 ACTGCTCCCAAATACTGCAA 57.415 45.000 0.00 0.00 33.07 4.08
1900 3256 4.713735 TGCAAATCGAGGCCGGCA 62.714 61.111 30.85 7.96 36.24 5.69
1920 3276 3.458163 GTGAGGATGGGCGGTCGA 61.458 66.667 0.00 0.00 0.00 4.20
1988 3344 1.528076 TGTGTGTGCATGGTGGACC 60.528 57.895 0.00 0.00 37.97 4.46
2051 3407 4.339809 CGAGTGTGTGCGTGCGTG 62.340 66.667 0.00 0.00 0.00 5.34
2052 3408 4.649954 GAGTGTGTGCGTGCGTGC 62.650 66.667 0.00 0.00 0.00 5.34
2219 3577 4.662961 CCGGCGTGTCAGAGCACA 62.663 66.667 6.01 0.00 39.19 4.57
2269 3629 2.224426 ACTTGTTGCCCGATCAAGTACA 60.224 45.455 7.81 0.00 46.19 2.90
2394 3757 4.287781 TCGCCGTCGAGTGCCAAA 62.288 61.111 0.00 0.00 40.21 3.28
2538 3901 2.364002 TCACACTGATGAACCTGTCGAA 59.636 45.455 0.00 0.00 0.00 3.71
2583 3947 2.751436 TTCCATCTGCGGCTTGCC 60.751 61.111 0.00 0.75 45.60 4.52
2699 4063 0.109153 TGTCAGGCAATGCACTGTCT 59.891 50.000 18.38 0.00 36.17 3.41
2726 4090 2.579201 CCAAGCGTCATCGGGACT 59.421 61.111 6.58 0.00 44.68 3.85
2740 4104 1.966451 GGACTGGGCTTGTCAACCG 60.966 63.158 11.19 0.00 36.26 4.44
2766 4148 1.912971 GGGGAGATACCGGCAAACT 59.087 57.895 0.00 0.00 40.11 2.66
2819 4201 2.626266 TGACCTCTCGAACAACAGCTTA 59.374 45.455 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.471684 GCACAAGCCATCTCTCAAAGG 59.528 52.381 0.00 0.00 33.58 3.11
22 27 1.203063 AGAGTAGCGGGGCATCTATCA 60.203 52.381 0.00 0.00 0.00 2.15
100 251 4.892934 AGAAATTTTACTCACTTGGCCACA 59.107 37.500 3.88 0.00 0.00 4.17
101 252 5.221244 ACAGAAATTTTACTCACTTGGCCAC 60.221 40.000 3.88 0.00 0.00 5.01
104 255 6.756542 ACAAACAGAAATTTTACTCACTTGGC 59.243 34.615 0.00 0.00 0.00 4.52
106 257 7.489113 AGCACAAACAGAAATTTTACTCACTTG 59.511 33.333 0.00 0.00 0.00 3.16
149 424 8.130469 TGCAGTTATACATGTCATATTTTGCAG 58.870 33.333 0.00 0.00 32.33 4.41
158 433 8.091385 CACATATGTGCAGTTATACATGTCAT 57.909 34.615 22.27 0.00 39.39 3.06
289 572 5.718724 TGTGTGCATAAATCCACAATCAA 57.281 34.783 3.32 0.00 42.90 2.57
290 573 5.468592 GTTGTGTGCATAAATCCACAATCA 58.531 37.500 17.86 0.00 46.06 2.57
302 585 3.761218 CCTGGTTATTGGTTGTGTGCATA 59.239 43.478 0.00 0.00 0.00 3.14
312 595 6.790319 AGATTGAACTAACCTGGTTATTGGT 58.210 36.000 19.02 11.27 38.35 3.67
313 596 7.012421 GCTAGATTGAACTAACCTGGTTATTGG 59.988 40.741 19.02 10.66 0.00 3.16
347 634 1.726853 AAGTGCTAGTTAGGCAAGCG 58.273 50.000 0.00 0.00 41.54 4.68
351 638 4.884668 ACTGTTAAGTGCTAGTTAGGCA 57.115 40.909 0.00 0.00 34.48 4.75
353 640 7.541437 GTGTCTTACTGTTAAGTGCTAGTTAGG 59.459 40.741 0.00 0.00 37.19 2.69
356 643 7.052142 AGTGTCTTACTGTTAAGTGCTAGTT 57.948 36.000 0.00 0.00 38.49 2.24
370 657 1.467734 CCTCGCGTACAGTGTCTTACT 59.532 52.381 5.77 0.00 41.36 2.24
372 659 0.806868 CCCTCGCGTACAGTGTCTTA 59.193 55.000 5.77 0.00 0.00 2.10
375 745 0.172803 AATCCCTCGCGTACAGTGTC 59.827 55.000 5.77 0.00 0.00 3.67
392 762 1.000396 GGTGCCTTGCCAGGAGAAT 60.000 57.895 8.31 0.00 44.19 2.40
393 763 2.436109 GGTGCCTTGCCAGGAGAA 59.564 61.111 8.31 0.00 44.19 2.87
398 769 2.079020 CTGTTGTGGTGCCTTGCCAG 62.079 60.000 0.00 0.00 36.57 4.85
424 803 1.112113 GCTGGGGTTATCTGTCTCGA 58.888 55.000 0.00 0.00 0.00 4.04
666 1985 2.289002 GCAGGTCGCAGAAAATATGGAG 59.711 50.000 0.00 0.00 39.69 3.86
706 2025 8.637099 ACTTATATTTAGAAACGGAGGGAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
707 2026 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
709 2028 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
711 2030 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
747 2066 5.134202 TGCTCCGTATGTAGTCCATAATG 57.866 43.478 0.00 0.00 37.77 1.90
748 2067 5.801531 TTGCTCCGTATGTAGTCCATAAT 57.198 39.130 0.00 0.00 37.77 1.28
749 2068 5.601583 TTTGCTCCGTATGTAGTCCATAA 57.398 39.130 0.00 0.00 37.77 1.90
750 2069 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
751 2070 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
752 2071 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
754 2073 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
755 2074 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
756 2075 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
757 2076 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
758 2077 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
760 2079 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
761 2080 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
763 2082 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
765 2084 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
803 2122 9.341078 TCACTACAAACTACATACGGATGTATA 57.659 33.333 20.64 9.08 45.42 1.47
804 2123 8.229253 TCACTACAAACTACATACGGATGTAT 57.771 34.615 20.64 8.38 45.42 2.29
805 2124 7.628769 TCACTACAAACTACATACGGATGTA 57.371 36.000 19.32 19.32 44.77 2.29
808 2127 8.475639 AGATTTCACTACAAACTACATACGGAT 58.524 33.333 0.00 0.00 0.00 4.18
809 2128 7.833786 AGATTTCACTACAAACTACATACGGA 58.166 34.615 0.00 0.00 0.00 4.69
810 2129 7.974501 AGAGATTTCACTACAAACTACATACGG 59.025 37.037 0.00 0.00 0.00 4.02
811 2130 8.912787 AGAGATTTCACTACAAACTACATACG 57.087 34.615 0.00 0.00 0.00 3.06
834 2153 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
836 2155 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
837 2156 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
838 2157 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
839 2158 6.013984 TCCTCCGTTCCTAAATGTAAGTCTTT 60.014 38.462 0.00 0.00 0.00 2.52
840 2159 5.482878 TCCTCCGTTCCTAAATGTAAGTCTT 59.517 40.000 0.00 0.00 0.00 3.01
841 2160 5.021458 TCCTCCGTTCCTAAATGTAAGTCT 58.979 41.667 0.00 0.00 0.00 3.24
844 2163 5.340439 ACTCCTCCGTTCCTAAATGTAAG 57.660 43.478 0.00 0.00 0.00 2.34
845 2164 5.716228 TGTACTCCTCCGTTCCTAAATGTAA 59.284 40.000 0.00 0.00 0.00 2.41
846 2165 5.263599 TGTACTCCTCCGTTCCTAAATGTA 58.736 41.667 0.00 0.00 0.00 2.29
848 2167 4.730949 TGTACTCCTCCGTTCCTAAATG 57.269 45.455 0.00 0.00 0.00 2.32
849 2168 5.209659 AGATGTACTCCTCCGTTCCTAAAT 58.790 41.667 0.00 0.00 0.00 1.40
850 2169 4.607239 AGATGTACTCCTCCGTTCCTAAA 58.393 43.478 0.00 0.00 0.00 1.85
851 2170 4.079901 AGAGATGTACTCCTCCGTTCCTAA 60.080 45.833 10.19 0.00 45.96 2.69
852 2171 3.458857 AGAGATGTACTCCTCCGTTCCTA 59.541 47.826 10.19 0.00 45.96 2.94
853 2172 2.242708 AGAGATGTACTCCTCCGTTCCT 59.757 50.000 10.19 0.00 45.96 3.36
855 2174 2.359531 CCAGAGATGTACTCCTCCGTTC 59.640 54.545 10.19 0.00 45.96 3.95
856 2175 2.291670 ACCAGAGATGTACTCCTCCGTT 60.292 50.000 10.19 0.00 45.96 4.44
857 2176 1.285373 ACCAGAGATGTACTCCTCCGT 59.715 52.381 10.19 5.86 45.96 4.69
858 2177 2.060050 ACCAGAGATGTACTCCTCCG 57.940 55.000 10.19 2.67 45.96 4.63
859 2178 4.173290 ACTACCAGAGATGTACTCCTCC 57.827 50.000 10.19 0.00 45.96 4.30
860 2179 5.682659 TGTACTACCAGAGATGTACTCCTC 58.317 45.833 6.89 6.89 45.96 3.71
861 2180 5.712084 TGTACTACCAGAGATGTACTCCT 57.288 43.478 0.00 0.00 45.96 3.69
863 2182 5.990386 TCGATGTACTACCAGAGATGTACTC 59.010 44.000 0.00 0.00 45.22 2.59
864 2183 5.926663 TCGATGTACTACCAGAGATGTACT 58.073 41.667 0.00 0.00 36.98 2.73
865 2184 5.334260 GCTCGATGTACTACCAGAGATGTAC 60.334 48.000 0.00 0.00 36.69 2.90
866 2185 4.755629 GCTCGATGTACTACCAGAGATGTA 59.244 45.833 0.00 0.00 0.00 2.29
867 2186 3.566322 GCTCGATGTACTACCAGAGATGT 59.434 47.826 0.00 0.00 0.00 3.06
868 2187 3.057876 GGCTCGATGTACTACCAGAGATG 60.058 52.174 0.00 0.00 0.00 2.90
869 2188 3.150767 GGCTCGATGTACTACCAGAGAT 58.849 50.000 0.00 0.00 0.00 2.75
870 2189 2.172930 AGGCTCGATGTACTACCAGAGA 59.827 50.000 0.00 0.00 0.00 3.10
871 2190 2.577700 AGGCTCGATGTACTACCAGAG 58.422 52.381 0.00 0.00 0.00 3.35
872 2191 2.730934 AGGCTCGATGTACTACCAGA 57.269 50.000 0.00 0.00 0.00 3.86
873 2192 5.489249 TCTATAGGCTCGATGTACTACCAG 58.511 45.833 0.00 0.00 0.00 4.00
874 2193 5.012871 ACTCTATAGGCTCGATGTACTACCA 59.987 44.000 0.00 0.00 0.00 3.25
875 2194 5.490159 ACTCTATAGGCTCGATGTACTACC 58.510 45.833 0.00 0.00 0.00 3.18
921 2252 3.068448 GGAGCTAGCTAAGGGTTCTACAC 59.932 52.174 19.38 0.00 0.00 2.90
957 2289 1.071385 CCAGTGATGGACTATGGGAGC 59.929 57.143 0.00 0.00 31.73 4.70
1034 2369 0.326048 CAGGTGGAGGAGGAGGACAT 60.326 60.000 0.00 0.00 0.00 3.06
1036 2371 0.031616 ATCAGGTGGAGGAGGAGGAC 60.032 60.000 0.00 0.00 0.00 3.85
1091 2444 3.842923 CGATCGTCCCAGCCTGCT 61.843 66.667 7.03 0.00 0.00 4.24
1165 2521 0.946221 AAGGTGAGCGAGCGTTTCAG 60.946 55.000 0.00 0.00 0.00 3.02
1276 2632 0.252012 CCTAGGGAGAGGCCGATGAT 60.252 60.000 0.00 0.00 37.63 2.45
1830 3186 0.770557 AGGGCTCCAGGTTGGTGTTA 60.771 55.000 0.00 0.00 39.03 2.41
1885 3241 3.864686 CGTGCCGGCCTCGATTTG 61.865 66.667 28.67 6.18 39.00 2.32
1906 3262 3.461773 CAGTCGACCGCCCATCCT 61.462 66.667 13.01 0.00 0.00 3.24
1969 3325 1.654220 GTCCACCATGCACACACAC 59.346 57.895 0.00 0.00 0.00 3.82
1988 3344 2.035626 ACAGGCCAAACCCGATGG 59.964 61.111 5.01 0.00 40.58 3.51
1990 3346 2.035626 CCACAGGCCAAACCCGAT 59.964 61.111 5.01 0.00 40.58 4.18
2029 3385 2.279252 ACGCACACACTCGGTCAC 60.279 61.111 0.00 0.00 0.00 3.67
2050 3406 1.732941 CTAACTAACCCATGCACGCA 58.267 50.000 0.00 0.00 0.00 5.24
2051 3407 0.377203 GCTAACTAACCCATGCACGC 59.623 55.000 0.00 0.00 0.00 5.34
2052 3408 0.650512 CGCTAACTAACCCATGCACG 59.349 55.000 0.00 0.00 0.00 5.34
2053 3409 1.933853 CTCGCTAACTAACCCATGCAC 59.066 52.381 0.00 0.00 0.00 4.57
2054 3410 1.134521 CCTCGCTAACTAACCCATGCA 60.135 52.381 0.00 0.00 0.00 3.96
2055 3411 1.583054 CCTCGCTAACTAACCCATGC 58.417 55.000 0.00 0.00 0.00 4.06
2056 3412 1.485066 ACCCTCGCTAACTAACCCATG 59.515 52.381 0.00 0.00 0.00 3.66
2057 3413 1.875488 ACCCTCGCTAACTAACCCAT 58.125 50.000 0.00 0.00 0.00 4.00
2124 3481 4.451150 TCTCATCGCGCACCCACC 62.451 66.667 8.75 0.00 0.00 4.61
2269 3629 3.070018 CTGTTCTTTTCACCTCGAGCAT 58.930 45.455 6.99 0.00 0.00 3.79
2538 3901 1.227853 GTCCCGTTCAGCTGGTTGT 60.228 57.895 15.13 0.00 0.00 3.32
2583 3947 4.186433 AGAGCCGCTCGAGCTTCG 62.186 66.667 32.88 21.07 41.75 3.79
2665 4029 4.862092 ACAGATCCAGCTCGCGCG 62.862 66.667 26.76 26.76 42.32 6.86
2666 4030 2.959071 GACAGATCCAGCTCGCGC 60.959 66.667 0.00 0.00 0.00 6.86
2667 4031 1.588403 CTGACAGATCCAGCTCGCG 60.588 63.158 0.00 0.00 0.00 5.87
2716 4080 1.899437 GACAAGCCCAGTCCCGATGA 61.899 60.000 0.00 0.00 0.00 2.92
2726 4090 3.884774 AGCCGGTTGACAAGCCCA 61.885 61.111 11.61 0.00 0.00 5.36
2740 4104 2.508751 GGTATCTCCCCGGACAGCC 61.509 68.421 0.73 0.00 0.00 4.85
2819 4201 0.113776 TGTCCGGTACCTCTCCAGTT 59.886 55.000 10.90 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.