Multiple sequence alignment - TraesCS7B01G298400

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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 TraesCS7B01G298400 chr7B 100.000 3208 0 0 1 3208 535505031 535508238 0.000000e+00 5925.0
1 TraesCS7B01G298400 chr7B 89.504 1915 107 46 328 2198 535517414 535519278 0.000000e+00 2337.0
2 TraesCS7B01G298400 chr7B 89.650 1826 110 40 374 2178 535613707 535615474 0.000000e+00 2252.0
3 TraesCS7B01G298400 chr7B 88.689 778 66 9 2238 2995 159000768 159001543 0.000000e+00 929.0
4 TraesCS7B01G298400 chr7D 94.453 1875 79 13 329 2198 506881941 506883795 0.000000e+00 2863.0
5 TraesCS7B01G298400 chr7D 88.736 435 20 13 2753 3158 145919440 145919006 3.690000e-139 505.0
6 TraesCS7B01G298400 chr7D 88.993 427 20 8 2759 3158 21002197 21001771 1.330000e-138 503.0
7 TraesCS7B01G298400 chr7D 88.578 429 24 13 2755 3158 164761567 164761139 6.180000e-137 497.0
8 TraesCS7B01G298400 chr7A 88.618 2135 140 47 110 2198 574752926 574755003 0.000000e+00 2501.0
9 TraesCS7B01G298400 chr7A 90.927 1543 92 26 673 2189 574971097 574972617 0.000000e+00 2030.0
10 TraesCS7B01G298400 chr7A 80.319 188 23 8 424 605 574970768 574970947 2.600000e-26 130.0
11 TraesCS7B01G298400 chr1B 86.953 1165 130 16 1047 2194 539589592 539588433 0.000000e+00 1290.0
12 TraesCS7B01G298400 chr1B 88.617 940 82 12 2238 3158 287702284 287701351 0.000000e+00 1120.0
13 TraesCS7B01G298400 chr1D 87.611 1122 124 11 1085 2194 401921285 401920167 0.000000e+00 1288.0
14 TraesCS7B01G298400 chr1D 87.611 1122 124 11 1085 2194 402006503 402005385 0.000000e+00 1288.0
15 TraesCS7B01G298400 chr1D 87.522 1122 125 11 1085 2194 402108065 402106947 0.000000e+00 1282.0
16 TraesCS7B01G298400 chr2B 89.286 924 75 11 2258 3158 504788361 504787439 0.000000e+00 1136.0
17 TraesCS7B01G298400 chr2B 84.249 946 123 17 2231 3158 381609052 381609989 0.000000e+00 898.0
18 TraesCS7B01G298400 chr2B 100.000 38 0 0 3171 3208 453275032 453275069 1.600000e-08 71.3
19 TraesCS7B01G298400 chr6B 89.888 890 64 13 2280 3148 704606461 704605577 0.000000e+00 1122.0
20 TraesCS7B01G298400 chr6B 89.744 429 21 11 2753 3158 626809638 626809210 7.880000e-146 527.0
21 TraesCS7B01G298400 chr4B 85.445 955 100 23 2228 3158 594841183 594842122 0.000000e+00 957.0
22 TraesCS7B01G298400 chr4B 91.053 570 32 8 2608 3158 527620782 527620213 0.000000e+00 752.0
23 TraesCS7B01G298400 chr4B 95.238 42 0 2 3169 3208 409915478 409915437 7.430000e-07 65.8
24 TraesCS7B01G298400 chr5B 84.402 936 121 18 2240 3158 642913485 642912558 0.000000e+00 896.0
25 TraesCS7B01G298400 chr5B 84.222 938 127 15 2238 3158 249564568 249563635 0.000000e+00 893.0
26 TraesCS7B01G298400 chr5B 95.238 42 0 2 3169 3208 655801472 655801431 7.430000e-07 65.8
27 TraesCS7B01G298400 chr5A 83.763 930 122 18 2252 3158 475461649 475462572 0.000000e+00 854.0
28 TraesCS7B01G298400 chr2D 91.429 420 21 11 2753 3158 531682800 531682382 2.160000e-156 562.0
29 TraesCS7B01G298400 chr2D 90.210 429 19 4 2753 3158 425744203 425743775 3.640000e-149 538.0
30 TraesCS7B01G298400 chr2D 89.145 433 20 13 2753 3158 276936139 276935707 6.140000e-142 514.0
31 TraesCS7B01G298400 chr2D 73.770 366 81 11 1708 2064 95685841 95686200 2.600000e-26 130.0
32 TraesCS7B01G298400 chr6D 88.889 432 22 13 2753 3158 446133518 446133087 2.860000e-140 508.0
33 TraesCS7B01G298400 chr6D 81.538 390 50 9 2787 3158 307784034 307783649 5.200000e-78 302.0
34 TraesCS7B01G298400 chr6D 100.000 37 0 0 3172 3208 309995926 309995890 5.740000e-08 69.4
35 TraesCS7B01G298400 chr6A 100.000 39 0 0 3170 3208 101994758 101994720 4.440000e-09 73.1
36 TraesCS7B01G298400 chr2A 100.000 39 0 0 3170 3208 765581674 765581712 4.440000e-09 73.1
37 TraesCS7B01G298400 chr2A 100.000 38 0 0 3171 3208 737383840 737383877 1.600000e-08 71.3
38 TraesCS7B01G298400 chr4D 100.000 37 0 0 3172 3208 334180049 334180085 5.740000e-08 69.4
39 TraesCS7B01G298400 chr3B 95.349 43 0 2 3166 3206 768027420 768027462 2.070000e-07 67.6


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 TraesCS7B01G298400 chr7B 535505031 535508238 3207 False 5925 5925 100.000 1 3208 1 chr7B.!!$F2 3207
1 TraesCS7B01G298400 chr7B 535517414 535519278 1864 False 2337 2337 89.504 328 2198 1 chr7B.!!$F3 1870
2 TraesCS7B01G298400 chr7B 535613707 535615474 1767 False 2252 2252 89.650 374 2178 1 chr7B.!!$F4 1804
3 TraesCS7B01G298400 chr7B 159000768 159001543 775 False 929 929 88.689 2238 2995 1 chr7B.!!$F1 757
4 TraesCS7B01G298400 chr7D 506881941 506883795 1854 False 2863 2863 94.453 329 2198 1 chr7D.!!$F1 1869
5 TraesCS7B01G298400 chr7A 574752926 574755003 2077 False 2501 2501 88.618 110 2198 1 chr7A.!!$F1 2088
6 TraesCS7B01G298400 chr7A 574970768 574972617 1849 False 1080 2030 85.623 424 2189 2 chr7A.!!$F2 1765
7 TraesCS7B01G298400 chr1B 539588433 539589592 1159 True 1290 1290 86.953 1047 2194 1 chr1B.!!$R2 1147
8 TraesCS7B01G298400 chr1B 287701351 287702284 933 True 1120 1120 88.617 2238 3158 1 chr1B.!!$R1 920
9 TraesCS7B01G298400 chr1D 401920167 401921285 1118 True 1288 1288 87.611 1085 2194 1 chr1D.!!$R1 1109
10 TraesCS7B01G298400 chr1D 402005385 402006503 1118 True 1288 1288 87.611 1085 2194 1 chr1D.!!$R2 1109
11 TraesCS7B01G298400 chr1D 402106947 402108065 1118 True 1282 1282 87.522 1085 2194 1 chr1D.!!$R3 1109
12 TraesCS7B01G298400 chr2B 504787439 504788361 922 True 1136 1136 89.286 2258 3158 1 chr2B.!!$R1 900
13 TraesCS7B01G298400 chr2B 381609052 381609989 937 False 898 898 84.249 2231 3158 1 chr2B.!!$F1 927
14 TraesCS7B01G298400 chr6B 704605577 704606461 884 True 1122 1122 89.888 2280 3148 1 chr6B.!!$R2 868
15 TraesCS7B01G298400 chr4B 594841183 594842122 939 False 957 957 85.445 2228 3158 1 chr4B.!!$F1 930
16 TraesCS7B01G298400 chr4B 527620213 527620782 569 True 752 752 91.053 2608 3158 1 chr4B.!!$R2 550
17 TraesCS7B01G298400 chr5B 642912558 642913485 927 True 896 896 84.402 2240 3158 1 chr5B.!!$R2 918
18 TraesCS7B01G298400 chr5B 249563635 249564568 933 True 893 893 84.222 2238 3158 1 chr5B.!!$R1 920
19 TraesCS7B01G298400 chr5A 475461649 475462572 923 False 854 854 83.763 2252 3158 1 chr5A.!!$F1 906

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
628 713 0.708370 CGAATGAACGTCGTGACCTG 59.292 55.000 0.00 0.0 33.80 4.00 F
1333 1602 3.139469 GTCCTCCTCGACCCGACC 61.139 72.222 0.00 0.0 0.00 4.79 F
2002 2271 0.549950 CCATGGTCAAGATGGGAGCT 59.450 55.000 2.57 0.0 37.33 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2141 0.318699 CGACGTGAAGAGCACCTTGA 60.319 55.000 0.0 0.0 44.85 3.02 R
2420 2713 0.395448 GGTAGGAGGCCTGACGTACT 60.395 60.000 12.0 0.0 34.61 2.73 R
2803 3104 1.068610 CCATGTGTTTTGCAGGGTACG 60.069 52.381 0.0 0.0 33.58 3.67 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
83 84 8.855279 TGTGAATTTAAAGTTTGTTCTTGTTCG 58.145 29.630 0.00 0.00 0.00 3.95
84 85 7.839358 GTGAATTTAAAGTTTGTTCTTGTTCGC 59.161 33.333 0.00 0.00 0.00 4.70
85 86 7.757624 TGAATTTAAAGTTTGTTCTTGTTCGCT 59.242 29.630 0.00 0.00 0.00 4.93
86 87 9.228636 GAATTTAAAGTTTGTTCTTGTTCGCTA 57.771 29.630 0.00 0.00 0.00 4.26
87 88 9.575783 AATTTAAAGTTTGTTCTTGTTCGCTAA 57.424 25.926 0.00 0.00 0.00 3.09
88 89 9.744468 ATTTAAAGTTTGTTCTTGTTCGCTAAT 57.256 25.926 0.00 0.00 0.00 1.73
89 90 9.575783 TTTAAAGTTTGTTCTTGTTCGCTAATT 57.424 25.926 0.00 0.00 0.00 1.40
90 91 7.679659 AAAGTTTGTTCTTGTTCGCTAATTC 57.320 32.000 0.00 0.00 0.00 2.17
91 92 6.371809 AGTTTGTTCTTGTTCGCTAATTCA 57.628 33.333 0.00 0.00 0.00 2.57
92 93 6.791303 AGTTTGTTCTTGTTCGCTAATTCAA 58.209 32.000 0.00 0.00 0.00 2.69
93 94 6.691388 AGTTTGTTCTTGTTCGCTAATTCAAC 59.309 34.615 0.00 0.00 0.00 3.18
94 95 5.743026 TGTTCTTGTTCGCTAATTCAACA 57.257 34.783 0.00 0.00 0.00 3.33
95 96 6.125327 TGTTCTTGTTCGCTAATTCAACAA 57.875 33.333 0.00 0.00 37.62 2.83
96 97 6.556212 TGTTCTTGTTCGCTAATTCAACAAA 58.444 32.000 0.00 0.00 39.04 2.83
97 98 7.199766 TGTTCTTGTTCGCTAATTCAACAAAT 58.800 30.769 0.00 0.00 39.04 2.32
98 99 7.167302 TGTTCTTGTTCGCTAATTCAACAAATG 59.833 33.333 0.00 0.00 39.04 2.32
99 100 6.734137 TCTTGTTCGCTAATTCAACAAATGT 58.266 32.000 0.00 0.00 39.04 2.71
100 101 7.199766 TCTTGTTCGCTAATTCAACAAATGTT 58.800 30.769 0.00 0.00 39.04 2.71
101 102 6.984740 TGTTCGCTAATTCAACAAATGTTC 57.015 33.333 0.00 0.00 35.83 3.18
102 103 5.623264 TGTTCGCTAATTCAACAAATGTTCG 59.377 36.000 0.00 0.00 35.83 3.95
103 104 5.351233 TCGCTAATTCAACAAATGTTCGT 57.649 34.783 0.00 0.00 35.83 3.85
104 105 5.143660 TCGCTAATTCAACAAATGTTCGTG 58.856 37.500 0.00 0.00 35.83 4.35
105 106 4.320690 CGCTAATTCAACAAATGTTCGTGG 59.679 41.667 0.00 0.00 35.83 4.94
106 107 5.457140 GCTAATTCAACAAATGTTCGTGGA 58.543 37.500 0.00 0.00 35.83 4.02
107 108 6.092748 GCTAATTCAACAAATGTTCGTGGAT 58.907 36.000 0.00 0.00 35.83 3.41
108 109 6.033831 GCTAATTCAACAAATGTTCGTGGATG 59.966 38.462 0.00 0.00 35.83 3.51
142 143 8.506168 ACTTTTGATTTTCTTGTAGTGTCTGA 57.494 30.769 0.00 0.00 0.00 3.27
145 146 8.506168 TTTGATTTTCTTGTAGTGTCTGAAGT 57.494 30.769 0.00 0.00 0.00 3.01
150 151 8.958119 TTTTCTTGTAGTGTCTGAAGTACAAT 57.042 30.769 14.70 0.00 42.31 2.71
234 240 1.725164 GAGTCAAACTCCGCGTTAAGG 59.275 52.381 4.92 0.00 39.28 2.69
265 271 1.803555 GTTTCTTCTGAGCTGCCTCAC 59.196 52.381 0.00 0.00 42.98 3.51
266 272 1.051008 TTCTTCTGAGCTGCCTCACA 58.949 50.000 0.00 0.00 42.98 3.58
279 289 1.684248 GCCTCACAATGCTCCATCCTT 60.684 52.381 0.00 0.00 0.00 3.36
291 301 2.421424 CTCCATCCTTTCAAGGCTTTCG 59.579 50.000 0.00 0.00 46.06 3.46
315 351 3.994931 ACCTTATGGTCCTGTGGTTAC 57.005 47.619 0.00 0.00 44.78 2.50
316 352 3.253220 ACCTTATGGTCCTGTGGTTACA 58.747 45.455 0.00 0.00 44.78 2.41
317 353 3.653836 ACCTTATGGTCCTGTGGTTACAA 59.346 43.478 0.00 0.00 44.78 2.41
318 354 4.105057 ACCTTATGGTCCTGTGGTTACAAA 59.895 41.667 0.00 0.00 44.78 2.83
319 355 4.700213 CCTTATGGTCCTGTGGTTACAAAG 59.300 45.833 0.00 0.00 36.14 2.77
320 356 5.514136 CCTTATGGTCCTGTGGTTACAAAGA 60.514 44.000 0.00 0.00 33.50 2.52
321 357 4.657814 ATGGTCCTGTGGTTACAAAGAT 57.342 40.909 0.00 0.00 33.50 2.40
322 358 4.015872 TGGTCCTGTGGTTACAAAGATC 57.984 45.455 0.00 0.00 33.50 2.75
323 359 3.244770 TGGTCCTGTGGTTACAAAGATCC 60.245 47.826 0.00 0.00 33.50 3.36
324 360 3.244770 GGTCCTGTGGTTACAAAGATCCA 60.245 47.826 0.00 0.00 33.50 3.41
348 387 2.756691 TAGCCCGCCAGCGACTTA 60.757 61.111 14.67 0.00 42.83 2.24
349 388 3.072486 TAGCCCGCCAGCGACTTAC 62.072 63.158 14.67 0.00 42.83 2.34
352 391 1.810030 CCCGCCAGCGACTTACTTC 60.810 63.158 14.67 0.00 42.83 3.01
357 397 1.135944 GCCAGCGACTTACTTCTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
375 415 5.650266 TCTTTGCTGGTTCTACAAAAGTCAA 59.350 36.000 0.00 0.00 33.24 3.18
376 416 5.906113 TTGCTGGTTCTACAAAAGTCAAA 57.094 34.783 0.00 0.00 0.00 2.69
398 438 1.560505 GCCAAACTGATCCCCATGTT 58.439 50.000 0.00 0.00 0.00 2.71
404 444 6.891908 GCCAAACTGATCCCCATGTTATATAT 59.108 38.462 0.00 0.00 0.00 0.86
406 446 7.890127 CCAAACTGATCCCCATGTTATATATGT 59.110 37.037 0.00 0.00 0.00 2.29
522 596 2.664402 ACTTGATTCAGCAACCACCT 57.336 45.000 0.00 0.00 0.00 4.00
553 634 0.827368 AAAAAGTGCCGGAAGCCAAA 59.173 45.000 5.05 0.00 42.71 3.28
595 680 3.339547 GGCAAAAGACAGCCCACTA 57.660 52.632 0.00 0.00 45.18 2.74
627 712 3.102515 CGAATGAACGTCGTGACCT 57.897 52.632 0.00 0.00 33.80 3.85
628 713 0.708370 CGAATGAACGTCGTGACCTG 59.292 55.000 0.00 0.00 33.80 4.00
702 900 6.086502 CGGAAGTTAAGCTCGTATCTTAATCG 59.913 42.308 0.00 0.00 38.03 3.34
890 1125 7.172190 CCATGTTCTATACCAGCTAAATCACAG 59.828 40.741 0.00 0.00 0.00 3.66
1042 1296 6.147328 CGATCACACTCTCGATATTGGTAGTA 59.853 42.308 0.00 0.00 37.05 1.82
1043 1297 6.615264 TCACACTCTCGATATTGGTAGTAC 57.385 41.667 0.00 0.00 0.00 2.73
1083 1349 8.135382 TGATAACTTAGTTAAGAGCTTGAGGT 57.865 34.615 8.99 0.00 37.08 3.85
1333 1602 3.139469 GTCCTCCTCGACCCGACC 61.139 72.222 0.00 0.00 0.00 4.79
1872 2141 1.812686 TACAAGAACGTCCTGGCGCT 61.813 55.000 7.64 0.00 34.88 5.92
2002 2271 0.549950 CCATGGTCAAGATGGGAGCT 59.450 55.000 2.57 0.00 37.33 4.09
2126 2405 1.394618 TTAGTTTTTGCACTGGCGGT 58.605 45.000 0.00 0.00 45.35 5.68
2194 2483 8.600449 TTTGTTTGTTGTTTCAACTCTTCAAT 57.400 26.923 12.66 0.00 0.00 2.57
2196 2485 9.698309 TTGTTTGTTGTTTCAACTCTTCAATAA 57.302 25.926 12.66 0.00 0.00 1.40
2197 2486 9.868277 TGTTTGTTGTTTCAACTCTTCAATAAT 57.132 25.926 12.66 0.00 0.00 1.28
2236 2525 8.454570 AAAAATACTACCTCCGTTTCTTTTGA 57.545 30.769 0.00 0.00 0.00 2.69
2408 2701 6.037172 GTCTGCGTGTGGACAAAATAGATAAT 59.963 38.462 0.00 0.00 33.19 1.28
2416 2709 6.040842 GTGGACAAAATAGATAATGCCCACAT 59.959 38.462 0.00 0.00 39.85 3.21
2420 2713 3.812611 ATAGATAATGCCCACATGCCA 57.187 42.857 0.00 0.00 36.36 4.92
2496 2790 2.990967 CCCGCAGTTGCCATGGTT 60.991 61.111 14.67 0.00 37.91 3.67
2512 2806 2.638325 TGGTTTGGACCCTCTTCCATA 58.362 47.619 0.00 0.00 45.42 2.74
2531 2825 7.701539 TCCATATTCATTTAACTGCAGTTGT 57.298 32.000 36.50 21.64 38.90 3.32
2628 2924 3.264706 TGCCACCTATTAACACTAGGCAA 59.735 43.478 9.53 0.00 46.76 4.52
2671 2968 1.616865 ACAAGCACGCTAGGACAGTTA 59.383 47.619 0.00 0.00 0.00 2.24
2704 3004 4.284490 AGGAAGAGTTGTCATCTGCTTACA 59.716 41.667 0.00 0.00 0.00 2.41
2742 3042 3.509740 TGCCATGTATCATGCAAAAACG 58.490 40.909 0.00 0.00 0.00 3.60
2744 3044 2.531103 CCATGTATCATGCAAAAACGCG 59.469 45.455 3.53 3.53 33.35 6.01
2751 3051 1.914634 ATGCAAAAACGCGTGACAAA 58.085 40.000 14.98 0.00 33.35 2.83
2756 3057 0.938713 AAAACGCGTGACAAATCGGA 59.061 45.000 14.98 0.00 0.00 4.55
2975 3299 1.005037 CAGCCCTTGTGCGTGAGTA 60.005 57.895 0.00 0.00 36.02 2.59
2991 3315 3.866910 GTGAGTAAAAACTGACGTGTGGA 59.133 43.478 0.00 0.00 0.00 4.02
3169 3496 5.051891 GCAAGATGCAATAGTGTTTCTGT 57.948 39.130 0.00 0.00 44.26 3.41
3170 3497 5.464168 GCAAGATGCAATAGTGTTTCTGTT 58.536 37.500 0.00 0.00 44.26 3.16
3171 3498 5.922544 GCAAGATGCAATAGTGTTTCTGTTT 59.077 36.000 0.00 0.00 44.26 2.83
3172 3499 6.421801 GCAAGATGCAATAGTGTTTCTGTTTT 59.578 34.615 0.00 0.00 44.26 2.43
3173 3500 7.042523 GCAAGATGCAATAGTGTTTCTGTTTTT 60.043 33.333 0.00 0.00 44.26 1.94
3198 3525 9.679661 TTTTAGTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
3199 3526 9.679661 TTTAGTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
3200 3527 9.679661 TTAGTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
3201 3528 8.218338 AGTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
3202 3529 7.831193 AGTCTGCATATAAGATTTGGTCAAAGT 59.169 33.333 2.55 0.00 33.32 2.66
3203 3530 8.462016 GTCTGCATATAAGATTTGGTCAAAGTT 58.538 33.333 2.55 1.84 33.32 2.66
3204 3531 9.679661 TCTGCATATAAGATTTGGTCAAAGTTA 57.320 29.630 2.55 3.72 33.32 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 8.855279 CGAACAAGAACAAACTTTAAATTCACA 58.145 29.630 2.32 0.00 0.00 3.58
58 59 7.839358 GCGAACAAGAACAAACTTTAAATTCAC 59.161 33.333 0.00 0.00 0.00 3.18
59 60 7.757624 AGCGAACAAGAACAAACTTTAAATTCA 59.242 29.630 0.00 0.00 0.00 2.57
60 61 8.115491 AGCGAACAAGAACAAACTTTAAATTC 57.885 30.769 0.00 0.00 0.00 2.17
61 62 9.575783 TTAGCGAACAAGAACAAACTTTAAATT 57.424 25.926 0.00 0.00 0.00 1.82
62 63 9.744468 ATTAGCGAACAAGAACAAACTTTAAAT 57.256 25.926 0.00 0.00 0.00 1.40
63 64 9.575783 AATTAGCGAACAAGAACAAACTTTAAA 57.424 25.926 0.00 0.00 0.00 1.52
64 65 9.228636 GAATTAGCGAACAAGAACAAACTTTAA 57.771 29.630 0.00 0.00 0.00 1.52
65 66 8.399425 TGAATTAGCGAACAAGAACAAACTTTA 58.601 29.630 0.00 0.00 0.00 1.85
66 67 7.254852 TGAATTAGCGAACAAGAACAAACTTT 58.745 30.769 0.00 0.00 0.00 2.66
67 68 6.791303 TGAATTAGCGAACAAGAACAAACTT 58.209 32.000 0.00 0.00 0.00 2.66
68 69 6.371809 TGAATTAGCGAACAAGAACAAACT 57.628 33.333 0.00 0.00 0.00 2.66
69 70 6.470877 TGTTGAATTAGCGAACAAGAACAAAC 59.529 34.615 0.00 0.00 0.00 2.93
70 71 6.556212 TGTTGAATTAGCGAACAAGAACAAA 58.444 32.000 0.00 0.00 0.00 2.83
71 72 6.125327 TGTTGAATTAGCGAACAAGAACAA 57.875 33.333 0.00 0.00 0.00 2.83
72 73 5.743026 TGTTGAATTAGCGAACAAGAACA 57.257 34.783 0.00 0.00 0.00 3.18
73 74 7.167468 ACATTTGTTGAATTAGCGAACAAGAAC 59.833 33.333 0.00 0.00 39.90 3.01
74 75 7.199766 ACATTTGTTGAATTAGCGAACAAGAA 58.800 30.769 0.00 0.00 39.90 2.52
75 76 6.734137 ACATTTGTTGAATTAGCGAACAAGA 58.266 32.000 0.00 0.00 39.90 3.02
76 77 6.991485 ACATTTGTTGAATTAGCGAACAAG 57.009 33.333 0.00 0.00 39.90 3.16
77 78 6.141527 CGAACATTTGTTGAATTAGCGAACAA 59.858 34.615 0.00 0.00 38.56 2.83
78 79 5.623264 CGAACATTTGTTGAATTAGCGAACA 59.377 36.000 0.00 0.00 38.56 3.18
79 80 5.623673 ACGAACATTTGTTGAATTAGCGAAC 59.376 36.000 0.00 0.00 38.56 3.95
80 81 5.623264 CACGAACATTTGTTGAATTAGCGAA 59.377 36.000 0.00 0.00 38.56 4.70
81 82 5.143660 CACGAACATTTGTTGAATTAGCGA 58.856 37.500 0.00 0.00 38.56 4.93
82 83 4.320690 CCACGAACATTTGTTGAATTAGCG 59.679 41.667 0.00 0.00 38.56 4.26
83 84 5.457140 TCCACGAACATTTGTTGAATTAGC 58.543 37.500 0.00 0.00 38.56 3.09
84 85 7.271223 GTCATCCACGAACATTTGTTGAATTAG 59.729 37.037 0.00 0.00 38.56 1.73
85 86 7.040755 AGTCATCCACGAACATTTGTTGAATTA 60.041 33.333 0.00 0.00 38.56 1.40
86 87 5.920273 GTCATCCACGAACATTTGTTGAATT 59.080 36.000 0.00 0.00 38.56 2.17
87 88 5.241506 AGTCATCCACGAACATTTGTTGAAT 59.758 36.000 0.00 0.00 38.56 2.57
88 89 4.578516 AGTCATCCACGAACATTTGTTGAA 59.421 37.500 0.00 0.00 38.56 2.69
89 90 4.133820 AGTCATCCACGAACATTTGTTGA 58.866 39.130 0.00 0.00 38.56 3.18
90 91 4.488126 AGTCATCCACGAACATTTGTTG 57.512 40.909 0.00 0.00 38.56 3.33
91 92 4.695455 CCTAGTCATCCACGAACATTTGTT 59.305 41.667 0.00 0.00 41.64 2.83
92 93 4.253685 CCTAGTCATCCACGAACATTTGT 58.746 43.478 0.00 0.00 0.00 2.83
93 94 3.063997 GCCTAGTCATCCACGAACATTTG 59.936 47.826 0.00 0.00 0.00 2.32
94 95 3.270877 GCCTAGTCATCCACGAACATTT 58.729 45.455 0.00 0.00 0.00 2.32
95 96 2.236146 TGCCTAGTCATCCACGAACATT 59.764 45.455 0.00 0.00 0.00 2.71
96 97 1.831106 TGCCTAGTCATCCACGAACAT 59.169 47.619 0.00 0.00 0.00 2.71
97 98 1.262417 TGCCTAGTCATCCACGAACA 58.738 50.000 0.00 0.00 0.00 3.18
98 99 2.000447 GTTGCCTAGTCATCCACGAAC 59.000 52.381 0.00 0.00 0.00 3.95
99 100 1.899814 AGTTGCCTAGTCATCCACGAA 59.100 47.619 0.00 0.00 0.00 3.85
100 101 1.557099 AGTTGCCTAGTCATCCACGA 58.443 50.000 0.00 0.00 0.00 4.35
101 102 2.386661 AAGTTGCCTAGTCATCCACG 57.613 50.000 0.00 0.00 0.00 4.94
102 103 4.072131 TCAAAAGTTGCCTAGTCATCCAC 58.928 43.478 0.00 0.00 0.00 4.02
103 104 4.365514 TCAAAAGTTGCCTAGTCATCCA 57.634 40.909 0.00 0.00 0.00 3.41
104 105 5.904362 AATCAAAAGTTGCCTAGTCATCC 57.096 39.130 0.00 0.00 0.00 3.51
105 106 7.597386 AGAAAATCAAAAGTTGCCTAGTCATC 58.403 34.615 0.00 0.00 0.00 2.92
106 107 7.530426 AGAAAATCAAAAGTTGCCTAGTCAT 57.470 32.000 0.00 0.00 0.00 3.06
107 108 6.959639 AGAAAATCAAAAGTTGCCTAGTCA 57.040 33.333 0.00 0.00 0.00 3.41
108 109 7.203218 ACAAGAAAATCAAAAGTTGCCTAGTC 58.797 34.615 0.00 0.00 0.00 2.59
226 230 9.539139 GAAGAAACTTAAGATAAACCTTAACGC 57.461 33.333 10.09 0.00 34.68 4.84
234 240 7.960195 GCAGCTCAGAAGAAACTTAAGATAAAC 59.040 37.037 10.09 0.00 0.00 2.01
255 261 1.378250 GGAGCATTGTGAGGCAGCT 60.378 57.895 0.00 0.00 38.43 4.24
265 271 5.893501 AAGCCTTGAAAGGATGGAGCATTG 61.894 45.833 13.40 0.00 45.74 2.82
266 272 3.820486 AAGCCTTGAAAGGATGGAGCATT 60.820 43.478 13.40 0.00 45.74 3.56
279 289 5.182380 CCATAAGGTTAACGAAAGCCTTGAA 59.818 40.000 16.03 2.65 41.02 2.69
291 301 8.175219 TTGTAACCACAGGACCATAAGGTTAAC 61.175 40.741 15.24 0.00 41.75 2.01
310 346 3.412386 ACAGCAGTGGATCTTTGTAACC 58.588 45.455 0.00 0.00 0.00 2.85
312 348 4.253685 GCTACAGCAGTGGATCTTTGTAA 58.746 43.478 0.00 0.00 41.59 2.41
313 349 3.369471 GGCTACAGCAGTGGATCTTTGTA 60.369 47.826 3.24 0.00 44.36 2.41
314 350 2.616510 GGCTACAGCAGTGGATCTTTGT 60.617 50.000 3.24 0.00 44.36 2.83
315 351 2.012673 GGCTACAGCAGTGGATCTTTG 58.987 52.381 3.24 0.00 44.36 2.77
316 352 1.065126 GGGCTACAGCAGTGGATCTTT 60.065 52.381 3.24 0.00 44.36 2.52
317 353 0.543749 GGGCTACAGCAGTGGATCTT 59.456 55.000 3.24 0.00 44.36 2.40
318 354 1.680522 CGGGCTACAGCAGTGGATCT 61.681 60.000 3.24 0.00 44.36 2.75
319 355 1.227380 CGGGCTACAGCAGTGGATC 60.227 63.158 3.24 0.00 44.36 3.36
320 356 2.903357 CGGGCTACAGCAGTGGAT 59.097 61.111 3.24 0.00 44.36 3.41
321 357 4.082523 GCGGGCTACAGCAGTGGA 62.083 66.667 3.24 0.00 44.36 4.02
323 359 4.393155 TGGCGGGCTACAGCAGTG 62.393 66.667 2.38 0.00 44.36 3.66
324 360 4.087892 CTGGCGGGCTACAGCAGT 62.088 66.667 2.38 0.00 44.36 4.40
345 381 6.861065 TTGTAGAACCAGCAAAGAAGTAAG 57.139 37.500 0.00 0.00 0.00 2.34
348 387 5.652452 ACTTTTGTAGAACCAGCAAAGAAGT 59.348 36.000 0.00 0.00 34.25 3.01
349 388 6.136541 ACTTTTGTAGAACCAGCAAAGAAG 57.863 37.500 0.00 0.00 34.25 2.85
352 391 5.499139 TGACTTTTGTAGAACCAGCAAAG 57.501 39.130 0.00 0.00 34.25 2.77
357 397 5.281727 GCCTTTTGACTTTTGTAGAACCAG 58.718 41.667 0.00 0.00 0.00 4.00
375 415 0.486879 TGGGGATCAGTTTGGCCTTT 59.513 50.000 3.32 0.00 0.00 3.11
376 416 0.712380 ATGGGGATCAGTTTGGCCTT 59.288 50.000 3.32 0.00 0.00 4.35
398 438 9.899661 AACAAAACTCCAGCAACTACATATATA 57.100 29.630 0.00 0.00 0.00 0.86
404 444 6.761099 TTAAACAAAACTCCAGCAACTACA 57.239 33.333 0.00 0.00 0.00 2.74
406 446 8.057536 TCTTTTAAACAAAACTCCAGCAACTA 57.942 30.769 0.00 0.00 0.00 2.24
595 680 4.671508 CGTTCATTCGTAAACATGCATGGT 60.672 41.667 29.41 22.35 0.00 3.55
660 745 3.924114 TCCGTGATAATTGTGATGGGT 57.076 42.857 0.27 0.00 0.00 4.51
702 900 4.448537 TTGTTGGCACCAGTATAATTGC 57.551 40.909 0.00 0.00 0.00 3.56
890 1125 3.259207 GTCGATAATTGACCAGCATGC 57.741 47.619 10.51 10.51 31.97 4.06
912 1147 8.296713 TCATCAGATGATTAATCGACGACATTA 58.703 33.333 9.21 0.00 40.54 1.90
1042 1296 6.607004 AGTTATCAGCCTTTGTGTACTAGT 57.393 37.500 0.00 0.00 0.00 2.57
1043 1297 8.251721 ACTAAGTTATCAGCCTTTGTGTACTAG 58.748 37.037 0.00 0.00 0.00 2.57
1597 1866 0.738975 CGATGAGCTGGTCGAGGTTA 59.261 55.000 10.91 0.00 40.11 2.85
1728 1997 1.973515 AGCCAGTGTTGATGTCAGAGA 59.026 47.619 0.00 0.00 0.00 3.10
1872 2141 0.318699 CGACGTGAAGAGCACCTTGA 60.319 55.000 0.00 0.00 44.85 3.02
2002 2271 3.129287 GGTAACCGGTCTTCACTTCGATA 59.871 47.826 8.04 0.00 0.00 2.92
2211 2500 8.454570 TCAAAAGAAACGGAGGTAGTATTTTT 57.545 30.769 0.00 0.00 0.00 1.94
2212 2501 8.347771 GTTCAAAAGAAACGGAGGTAGTATTTT 58.652 33.333 0.00 0.00 0.00 1.82
2213 2502 7.307573 CGTTCAAAAGAAACGGAGGTAGTATTT 60.308 37.037 0.70 0.00 44.27 1.40
2214 2503 6.146673 CGTTCAAAAGAAACGGAGGTAGTATT 59.853 38.462 0.70 0.00 44.27 1.89
2215 2504 5.636543 CGTTCAAAAGAAACGGAGGTAGTAT 59.363 40.000 0.70 0.00 44.27 2.12
2216 2505 4.984161 CGTTCAAAAGAAACGGAGGTAGTA 59.016 41.667 0.70 0.00 44.27 1.82
2217 2506 3.805971 CGTTCAAAAGAAACGGAGGTAGT 59.194 43.478 0.70 0.00 44.27 2.73
2218 2507 4.385244 CGTTCAAAAGAAACGGAGGTAG 57.615 45.455 0.70 0.00 44.27 3.18
2226 2515 4.088071 GCTTTATCGGCGTTCAAAAGAAAC 59.912 41.667 20.93 7.65 30.44 2.78
2227 2516 4.223659 GCTTTATCGGCGTTCAAAAGAAA 58.776 39.130 20.93 6.84 30.44 2.52
2228 2517 3.365565 GGCTTTATCGGCGTTCAAAAGAA 60.366 43.478 20.93 0.00 30.44 2.52
2229 2518 2.160813 GGCTTTATCGGCGTTCAAAAGA 59.839 45.455 20.93 0.00 30.44 2.52
2236 2525 1.003112 TGTGGGCTTTATCGGCGTT 60.003 52.632 6.85 0.00 0.00 4.84
2368 2661 1.269958 CAGACATGTGAGAGGGACCA 58.730 55.000 1.15 0.00 0.00 4.02
2395 2688 5.221501 GGCATGTGGGCATTATCTATTTTGT 60.222 40.000 0.00 0.00 42.77 2.83
2420 2713 0.395448 GGTAGGAGGCCTGACGTACT 60.395 60.000 12.00 0.00 34.61 2.73
2512 2806 6.015180 ACCATGACAACTGCAGTTAAATGAAT 60.015 34.615 30.75 21.98 36.32 2.57
2531 2825 1.241165 CTGCAGTTGAGCAACCATGA 58.759 50.000 5.25 0.00 45.13 3.07
2628 2924 2.089980 GCACATGGCAACTCTCTCAAT 58.910 47.619 0.00 0.00 43.97 2.57
2671 2968 5.690865 TGACAACTCTTCCTTTTACATGGT 58.309 37.500 0.00 0.00 0.00 3.55
2704 3004 1.746615 CAACTGCCCTAGCGTGCAT 60.747 57.895 0.00 0.00 44.31 3.96
2742 3042 4.328983 TCTCTTTTATCCGATTTGTCACGC 59.671 41.667 0.00 0.00 0.00 5.34
2744 3044 6.969828 ACTCTCTTTTATCCGATTTGTCAC 57.030 37.500 0.00 0.00 0.00 3.67
2751 3051 4.487714 TGGCAACTCTCTTTTATCCGAT 57.512 40.909 0.00 0.00 37.61 4.18
2803 3104 1.068610 CCATGTGTTTTGCAGGGTACG 60.069 52.381 0.00 0.00 33.58 3.67
2956 3280 1.468506 TACTCACGCACAAGGGCTGA 61.469 55.000 0.00 0.00 0.00 4.26
2975 3299 2.012937 TCGTCCACACGTCAGTTTTT 57.987 45.000 0.00 0.00 46.76 1.94
3172 3499 9.679661 TGACCAAATCTTATATGCAGACTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
3173 3500 9.679661 TTGACCAAATCTTATATGCAGACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
3174 3501 9.679661 TTTGACCAAATCTTATATGCAGACTAA 57.320 29.630 0.00 0.00 0.00 2.24
3175 3502 9.330063 CTTTGACCAAATCTTATATGCAGACTA 57.670 33.333 0.00 0.00 0.00 2.59
3176 3503 7.831193 ACTTTGACCAAATCTTATATGCAGACT 59.169 33.333 0.00 0.00 0.00 3.24
3177 3504 7.989826 ACTTTGACCAAATCTTATATGCAGAC 58.010 34.615 0.00 0.00 0.00 3.51
3178 3505 8.579850 AACTTTGACCAAATCTTATATGCAGA 57.420 30.769 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.