Multiple sequence alignment - TraesCS1B01G314500

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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 TraesCS1B01G314500 chr1B 100.000 3386 0 0 1 3386 539459003 539462388 0.000000e+00 6253.0
1 TraesCS1B01G314500 chr1B 97.138 629 18 0 2757 3385 538169045 538169673 0.000000e+00 1062.0
2 TraesCS1B01G314500 chr1B 87.838 74 8 1 2629 2701 539477266 539477339 6.020000e-13 86.1
3 TraesCS1B01G314500 chr1A 90.906 2683 160 40 128 2754 497344697 497347351 0.000000e+00 3526.0
4 TraesCS1B01G314500 chr1D 91.430 2462 123 38 128 2525 401356773 401359210 0.000000e+00 3297.0
5 TraesCS1B01G314500 chr1D 94.468 1157 51 8 1377 2527 401435512 401436661 0.000000e+00 1770.0
6 TraesCS1B01G314500 chr1D 86.175 217 19 8 2512 2718 401359228 401359443 1.220000e-54 224.0
7 TraesCS1B01G314500 chr1D 86.175 217 19 8 2512 2718 401436683 401436898 1.220000e-54 224.0
8 TraesCS1B01G314500 chr5B 97.619 630 15 0 2756 3385 458617026 458617655 0.000000e+00 1081.0
9 TraesCS1B01G314500 chr2D 95.261 633 26 3 2753 3385 188839667 188840295 0.000000e+00 1000.0
10 TraesCS1B01G314500 chr5A 94.937 632 32 0 2754 3385 27780426 27779795 0.000000e+00 990.0
11 TraesCS1B01G314500 chr5A 93.641 629 40 0 2757 3385 47772142 47772770 0.000000e+00 941.0
12 TraesCS1B01G314500 chr5A 93.344 631 40 2 2756 3385 447650215 447649586 0.000000e+00 931.0
13 TraesCS1B01G314500 chr2B 93.323 629 41 1 2757 3385 209832074 209831447 0.000000e+00 928.0
14 TraesCS1B01G314500 chr7B 92.722 632 44 2 2754 3385 565968447 565967818 0.000000e+00 911.0
15 TraesCS1B01G314500 chr3B 92.722 632 43 3 2755 3385 671359634 671360263 0.000000e+00 909.0


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 TraesCS1B01G314500 chr1B 539459003 539462388 3385 False 6253.0 6253 100.0000 1 3386 1 chr1B.!!$F2 3385
1 TraesCS1B01G314500 chr1B 538169045 538169673 628 False 1062.0 1062 97.1380 2757 3385 1 chr1B.!!$F1 628
2 TraesCS1B01G314500 chr1A 497344697 497347351 2654 False 3526.0 3526 90.9060 128 2754 1 chr1A.!!$F1 2626
3 TraesCS1B01G314500 chr1D 401356773 401359443 2670 False 1760.5 3297 88.8025 128 2718 2 chr1D.!!$F1 2590
4 TraesCS1B01G314500 chr1D 401435512 401436898 1386 False 997.0 1770 90.3215 1377 2718 2 chr1D.!!$F2 1341
5 TraesCS1B01G314500 chr5B 458617026 458617655 629 False 1081.0 1081 97.6190 2756 3385 1 chr5B.!!$F1 629
6 TraesCS1B01G314500 chr2D 188839667 188840295 628 False 1000.0 1000 95.2610 2753 3385 1 chr2D.!!$F1 632
7 TraesCS1B01G314500 chr5A 27779795 27780426 631 True 990.0 990 94.9370 2754 3385 1 chr5A.!!$R1 631
8 TraesCS1B01G314500 chr5A 47772142 47772770 628 False 941.0 941 93.6410 2757 3385 1 chr5A.!!$F1 628
9 TraesCS1B01G314500 chr5A 447649586 447650215 629 True 931.0 931 93.3440 2756 3385 1 chr5A.!!$R2 629
10 TraesCS1B01G314500 chr2B 209831447 209832074 627 True 928.0 928 93.3230 2757 3385 1 chr2B.!!$R1 628
11 TraesCS1B01G314500 chr7B 565967818 565968447 629 True 911.0 911 92.7220 2754 3385 1 chr7B.!!$R1 631
12 TraesCS1B01G314500 chr3B 671359634 671360263 629 False 909.0 909 92.7220 2755 3385 1 chr3B.!!$F1 630

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
86 87 0.030235 GTTTGTTCTCAACCCGGTGC 59.970 55.0 0.00 0.0 32.93 5.01 F
87 88 0.106918 TTTGTTCTCAACCCGGTGCT 60.107 50.0 0.00 0.0 32.93 4.40 F
1201 1258 0.107081 AGAGAGGCAGCAGCATGATC 59.893 55.0 2.65 0.0 44.61 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 1995 1.369692 CACCAGCGTGACCACCTTA 59.630 57.895 0.0 0.0 43.14 2.69 R
1995 2052 1.737008 GACGAAGCGGTCCAGGAAC 60.737 63.158 0.0 0.0 0.00 3.62 R
2965 3088 1.458777 TCGTGGGGAGTCACTTGGT 60.459 57.895 0.0 0.0 35.63 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
25 26 7.357951 GCAAGGAGCTGACTGTAATAATATC 57.642 40.000 0.00 0.00 41.15 1.63
26 27 6.931281 GCAAGGAGCTGACTGTAATAATATCA 59.069 38.462 0.00 0.00 41.15 2.15
27 28 7.605691 GCAAGGAGCTGACTGTAATAATATCAT 59.394 37.037 0.00 0.00 41.15 2.45
28 29 9.149225 CAAGGAGCTGACTGTAATAATATCATC 57.851 37.037 0.00 0.00 0.00 2.92
29 30 8.663209 AGGAGCTGACTGTAATAATATCATCT 57.337 34.615 0.00 0.00 0.00 2.90
30 31 9.760926 AGGAGCTGACTGTAATAATATCATCTA 57.239 33.333 0.00 0.00 0.00 1.98
55 56 2.615774 CACCACATTGTGTGCTCGA 58.384 52.632 15.34 0.00 46.51 4.04
56 57 1.159285 CACCACATTGTGTGCTCGAT 58.841 50.000 15.34 0.00 46.51 3.59
57 58 1.129251 CACCACATTGTGTGCTCGATC 59.871 52.381 15.34 0.00 46.51 3.69
58 59 0.371301 CCACATTGTGTGCTCGATCG 59.629 55.000 15.34 9.36 46.51 3.69
59 60 1.070821 CACATTGTGTGCTCGATCGT 58.929 50.000 15.94 0.00 41.89 3.73
60 61 1.070821 ACATTGTGTGCTCGATCGTG 58.929 50.000 15.94 14.19 0.00 4.35
61 62 0.371301 CATTGTGTGCTCGATCGTGG 59.629 55.000 15.94 10.45 0.00 4.94
62 63 0.037326 ATTGTGTGCTCGATCGTGGT 60.037 50.000 15.94 0.00 0.00 4.16
63 64 0.249699 TTGTGTGCTCGATCGTGGTT 60.250 50.000 15.94 0.00 0.00 3.67
64 65 0.249699 TGTGTGCTCGATCGTGGTTT 60.250 50.000 15.94 0.00 0.00 3.27
65 66 0.865769 GTGTGCTCGATCGTGGTTTT 59.134 50.000 15.94 0.00 0.00 2.43
66 67 1.263217 GTGTGCTCGATCGTGGTTTTT 59.737 47.619 15.94 0.00 0.00 1.94
67 68 1.262950 TGTGCTCGATCGTGGTTTTTG 59.737 47.619 15.94 0.00 0.00 2.44
68 69 1.263217 GTGCTCGATCGTGGTTTTTGT 59.737 47.619 15.94 0.00 0.00 2.83
69 70 1.944024 TGCTCGATCGTGGTTTTTGTT 59.056 42.857 15.94 0.00 0.00 2.83
70 71 2.356382 TGCTCGATCGTGGTTTTTGTTT 59.644 40.909 15.94 0.00 0.00 2.83
71 72 2.719046 GCTCGATCGTGGTTTTTGTTTG 59.281 45.455 15.94 0.00 0.00 2.93
72 73 3.790789 GCTCGATCGTGGTTTTTGTTTGT 60.791 43.478 15.94 0.00 0.00 2.83
73 74 4.347813 CTCGATCGTGGTTTTTGTTTGTT 58.652 39.130 15.94 0.00 0.00 2.83
74 75 4.344448 TCGATCGTGGTTTTTGTTTGTTC 58.656 39.130 15.94 0.00 0.00 3.18
75 76 4.095185 TCGATCGTGGTTTTTGTTTGTTCT 59.905 37.500 15.94 0.00 0.00 3.01
76 77 4.436523 CGATCGTGGTTTTTGTTTGTTCTC 59.563 41.667 7.03 0.00 0.00 2.87
77 78 4.768130 TCGTGGTTTTTGTTTGTTCTCA 57.232 36.364 0.00 0.00 0.00 3.27
78 79 5.122512 TCGTGGTTTTTGTTTGTTCTCAA 57.877 34.783 0.00 0.00 0.00 3.02
79 80 4.918583 TCGTGGTTTTTGTTTGTTCTCAAC 59.081 37.500 0.00 0.00 32.93 3.18
80 81 4.090786 CGTGGTTTTTGTTTGTTCTCAACC 59.909 41.667 0.00 0.00 32.93 3.77
81 82 4.390603 GTGGTTTTTGTTTGTTCTCAACCC 59.609 41.667 0.00 0.00 32.93 4.11
82 83 3.615056 GGTTTTTGTTTGTTCTCAACCCG 59.385 43.478 0.00 0.00 32.93 5.28
83 84 3.512033 TTTTGTTTGTTCTCAACCCGG 57.488 42.857 0.00 0.00 32.93 5.73
84 85 2.131776 TTGTTTGTTCTCAACCCGGT 57.868 45.000 0.00 0.00 32.93 5.28
85 86 1.384525 TGTTTGTTCTCAACCCGGTG 58.615 50.000 0.00 0.00 32.93 4.94
86 87 0.030235 GTTTGTTCTCAACCCGGTGC 59.970 55.000 0.00 0.00 32.93 5.01
87 88 0.106918 TTTGTTCTCAACCCGGTGCT 60.107 50.000 0.00 0.00 32.93 4.40
88 89 0.534203 TTGTTCTCAACCCGGTGCTC 60.534 55.000 0.00 0.00 0.00 4.26
89 90 1.371558 GTTCTCAACCCGGTGCTCT 59.628 57.895 0.00 0.00 0.00 4.09
90 91 0.951040 GTTCTCAACCCGGTGCTCTG 60.951 60.000 0.00 0.00 0.00 3.35
91 92 2.731691 TTCTCAACCCGGTGCTCTGC 62.732 60.000 0.00 0.00 0.00 4.26
92 93 4.329545 TCAACCCGGTGCTCTGCC 62.330 66.667 0.00 0.00 0.00 4.85
93 94 4.335647 CAACCCGGTGCTCTGCCT 62.336 66.667 0.00 0.00 0.00 4.75
94 95 4.021925 AACCCGGTGCTCTGCCTC 62.022 66.667 0.00 0.00 0.00 4.70
98 99 4.379243 CGGTGCTCTGCCTCGGTT 62.379 66.667 0.00 0.00 0.00 4.44
99 100 2.032681 GGTGCTCTGCCTCGGTTT 59.967 61.111 0.00 0.00 0.00 3.27
100 101 1.295423 GGTGCTCTGCCTCGGTTTA 59.705 57.895 0.00 0.00 0.00 2.01
101 102 0.107654 GGTGCTCTGCCTCGGTTTAT 60.108 55.000 0.00 0.00 0.00 1.40
102 103 1.138266 GGTGCTCTGCCTCGGTTTATA 59.862 52.381 0.00 0.00 0.00 0.98
103 104 2.224305 GGTGCTCTGCCTCGGTTTATAT 60.224 50.000 0.00 0.00 0.00 0.86
104 105 3.006537 GGTGCTCTGCCTCGGTTTATATA 59.993 47.826 0.00 0.00 0.00 0.86
105 106 4.322801 GGTGCTCTGCCTCGGTTTATATAT 60.323 45.833 0.00 0.00 0.00 0.86
106 107 4.865365 GTGCTCTGCCTCGGTTTATATATC 59.135 45.833 0.00 0.00 0.00 1.63
107 108 4.526650 TGCTCTGCCTCGGTTTATATATCA 59.473 41.667 0.00 0.00 0.00 2.15
108 109 5.187772 TGCTCTGCCTCGGTTTATATATCAT 59.812 40.000 0.00 0.00 0.00 2.45
109 110 6.109359 GCTCTGCCTCGGTTTATATATCATT 58.891 40.000 0.00 0.00 0.00 2.57
110 111 6.595716 GCTCTGCCTCGGTTTATATATCATTT 59.404 38.462 0.00 0.00 0.00 2.32
111 112 7.119846 GCTCTGCCTCGGTTTATATATCATTTT 59.880 37.037 0.00 0.00 0.00 1.82
112 113 8.918202 TCTGCCTCGGTTTATATATCATTTTT 57.082 30.769 0.00 0.00 0.00 1.94
185 186 1.969085 ACCAAGCGGTGTCGATACA 59.031 52.632 14.58 0.00 46.79 2.29
241 242 6.822667 AGTGATGCAAAATATGTGTGAGAA 57.177 33.333 0.00 0.00 0.00 2.87
246 247 6.012658 TGCAAAATATGTGTGAGAAAGTCC 57.987 37.500 0.00 0.00 0.00 3.85
249 250 7.392953 TGCAAAATATGTGTGAGAAAGTCCATA 59.607 33.333 0.00 0.00 0.00 2.74
255 256 9.988815 ATATGTGTGAGAAAGTCCATATTCTAC 57.011 33.333 0.00 0.00 36.08 2.59
297 298 4.569966 CACAGAGATGCAATTCTCCACTAC 59.430 45.833 12.68 0.00 42.63 2.73
298 299 4.469227 ACAGAGATGCAATTCTCCACTACT 59.531 41.667 12.68 0.00 42.63 2.57
299 300 5.049167 CAGAGATGCAATTCTCCACTACTC 58.951 45.833 12.68 0.00 42.63 2.59
300 301 4.100808 AGAGATGCAATTCTCCACTACTCC 59.899 45.833 12.68 0.00 42.63 3.85
301 302 4.036518 AGATGCAATTCTCCACTACTCCT 58.963 43.478 0.00 0.00 0.00 3.69
302 303 5.211973 AGATGCAATTCTCCACTACTCCTA 58.788 41.667 0.00 0.00 0.00 2.94
304 305 4.610333 TGCAATTCTCCACTACTCCTAGA 58.390 43.478 0.00 0.00 0.00 2.43
306 307 5.127845 TGCAATTCTCCACTACTCCTAGAAG 59.872 44.000 0.00 0.00 30.30 2.85
307 308 5.596845 CAATTCTCCACTACTCCTAGAAGC 58.403 45.833 0.00 0.00 30.30 3.86
308 309 3.300239 TCTCCACTACTCCTAGAAGCC 57.700 52.381 0.00 0.00 0.00 4.35
309 310 2.853707 TCTCCACTACTCCTAGAAGCCT 59.146 50.000 0.00 0.00 0.00 4.58
310 311 4.045736 TCTCCACTACTCCTAGAAGCCTA 58.954 47.826 0.00 0.00 0.00 3.93
413 414 4.145807 GACTCTGGCTAGCCTGTAGAATA 58.854 47.826 33.07 15.06 36.57 1.75
414 415 4.746466 ACTCTGGCTAGCCTGTAGAATAT 58.254 43.478 33.07 13.49 36.57 1.28
415 416 4.526262 ACTCTGGCTAGCCTGTAGAATATG 59.474 45.833 33.07 17.39 36.57 1.78
502 507 5.844396 GCACGTACAAAACACTCTAAATGTC 59.156 40.000 0.00 0.00 0.00 3.06
504 509 6.844279 CACGTACAAAACACTCTAAATGTCAC 59.156 38.462 0.00 0.00 0.00 3.67
509 514 8.677148 ACAAAACACTCTAAATGTCACATAGT 57.323 30.769 0.00 0.00 0.00 2.12
510 515 9.772973 ACAAAACACTCTAAATGTCACATAGTA 57.227 29.630 0.00 0.00 0.00 1.82
568 577 1.344438 TCAGAGCGATGTGTTCCAGTT 59.656 47.619 0.00 0.00 0.00 3.16
586 595 9.326339 GTTCCAGTTATCTTCACGTAAATTTTC 57.674 33.333 0.00 0.00 0.00 2.29
588 597 8.717821 TCCAGTTATCTTCACGTAAATTTTCAG 58.282 33.333 0.00 0.00 0.00 3.02
589 598 8.504005 CCAGTTATCTTCACGTAAATTTTCAGT 58.496 33.333 0.00 0.00 0.00 3.41
654 673 7.169158 CCTAATTGGCTACCTTTGATTTTCA 57.831 36.000 0.00 0.00 0.00 2.69
745 764 3.439129 TCAATGCAGCTCACAGAATCTTG 59.561 43.478 0.00 0.00 0.00 3.02
799 823 0.247736 AGCTAGCTTCCAGGTTGACG 59.752 55.000 12.68 0.00 0.00 4.35
833 883 7.124901 AGGCCACACTTGACTCCTATATATATG 59.875 40.741 5.01 0.00 0.00 1.78
834 884 7.268586 GCCACACTTGACTCCTATATATATGG 58.731 42.308 5.44 2.22 0.00 2.74
843 893 9.859152 TGACTCCTATATATATGGATCTGTCAG 57.141 37.037 18.35 0.00 31.85 3.51
846 896 9.365906 CTCCTATATATATGGATCTGTCAGCTT 57.634 37.037 7.62 0.00 0.00 3.74
847 897 9.360901 TCCTATATATATGGATCTGTCAGCTTC 57.639 37.037 7.62 0.00 0.00 3.86
848 898 8.584157 CCTATATATATGGATCTGTCAGCTTCC 58.416 40.741 7.62 12.44 0.00 3.46
850 900 6.949117 ATATATGGATCTGTCAGCTTCCTT 57.051 37.500 17.56 14.69 0.00 3.36
865 922 3.598299 CTTCCTTTTCTCTCCTGAGCTG 58.402 50.000 0.00 0.00 40.03 4.24
906 963 4.463891 ACCCTCATTGATTAGTTTTGGCTG 59.536 41.667 0.00 0.00 0.00 4.85
912 969 8.750515 TCATTGATTAGTTTTGGCTGATGATA 57.249 30.769 0.00 0.00 0.00 2.15
942 999 0.704664 TGTCAGGTAGAGGCTCCTCA 59.295 55.000 17.40 1.95 44.99 3.86
960 1017 0.647410 CAGTCGACATGCACGATTCC 59.353 55.000 19.50 6.43 41.62 3.01
1058 1115 4.856801 CGGCTTCATCCACCCCGG 62.857 72.222 0.00 0.00 35.54 5.73
1199 1256 0.392595 CAAGAGAGGCAGCAGCATGA 60.393 55.000 2.65 0.00 44.61 3.07
1200 1257 0.547075 AAGAGAGGCAGCAGCATGAT 59.453 50.000 2.65 0.00 44.61 2.45
1201 1258 0.107081 AGAGAGGCAGCAGCATGATC 59.893 55.000 2.65 0.00 44.61 2.92
1278 1335 3.200593 CTGCTCATGGAGTGCGCC 61.201 66.667 4.18 0.00 37.76 6.53
1344 1401 2.894387 GAGCTGTCGCAGATGGCC 60.894 66.667 10.46 0.00 40.67 5.36
1947 2004 1.142097 GCTCGAGCCTAAGGTGGTC 59.858 63.158 27.22 0.00 34.31 4.02
1974 2031 4.814041 GAGCAGGAGAGGGGGCCT 62.814 72.222 0.84 0.00 36.03 5.19
2178 2235 3.467226 GGGCGGGAGATGTTCGGA 61.467 66.667 0.00 0.00 0.00 4.55
2189 2246 2.032681 GTTCGGAAGCTGGCAGGT 59.967 61.111 14.51 14.51 0.00 4.00
2393 2450 1.601903 TGCACGAGCTTAACCAAGTTG 59.398 47.619 6.36 0.00 42.74 3.16
2395 2452 3.640389 GCACGAGCTTAACCAAGTTGGT 61.640 50.000 22.30 22.30 45.63 3.67
2396 2453 5.675880 GCACGAGCTTAACCAAGTTGGTG 62.676 52.174 28.04 16.49 46.91 4.17
2430 2493 3.815401 CACCATATGCCAGGTTTAGCTAC 59.185 47.826 0.00 0.00 35.52 3.58
2457 2523 1.380403 CGAGACGGGCTCTCACAGAT 61.380 60.000 9.58 0.00 45.43 2.90
2477 2543 6.208204 ACAGATTTAGCTCCATTTGGCATATC 59.792 38.462 0.00 0.00 34.44 1.63
2555 2655 7.492352 TTCAGTTCCTTGCTACTTTTTCTAC 57.508 36.000 0.00 0.00 0.00 2.59
2564 2664 7.809806 CCTTGCTACTTTTTCTACCAAAATCTG 59.190 37.037 0.00 0.00 0.00 2.90
2575 2697 3.290710 ACCAAAATCTGCACTGACACTT 58.709 40.909 0.00 0.00 0.00 3.16
2663 2785 2.969950 AGTCACCTAAACCTGCACACTA 59.030 45.455 0.00 0.00 0.00 2.74
2688 2810 8.621532 AACACTGCTCAGTTCAAAATTATCTA 57.378 30.769 0.00 0.00 40.20 1.98
2712 2835 3.737559 AGGGCACAAATTATCTGTGGA 57.262 42.857 10.06 0.00 43.61 4.02
2718 2841 4.941263 GCACAAATTATCTGTGGAGTACCA 59.059 41.667 10.06 0.00 43.61 3.25
2747 2870 5.014123 TGGTTCTATTTGGAGGAGTTGATGT 59.986 40.000 0.00 0.00 0.00 3.06
2965 3088 2.320681 ACCCCTTCACTGCTACTACA 57.679 50.000 0.00 0.00 0.00 2.74
3078 3201 5.191323 AGAGACCAAAGATCATCCATCAAGT 59.809 40.000 0.00 0.00 33.29 3.16
3128 3252 2.376228 TTTGCCTTTGCCCGCCTTTC 62.376 55.000 0.00 0.00 36.33 2.62
3147 3271 5.221621 CCTTTCTTTGTTTGCCCCTTATTGA 60.222 40.000 0.00 0.00 0.00 2.57
3235 3359 2.807967 CAAATCACAGAGTTCCTTCGCA 59.192 45.455 0.00 0.00 0.00 5.10
3385 3509 3.551863 CGATGCTGAGAGATAGGTTGTCC 60.552 52.174 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.931281 TGATATTATTACAGTCAGCTCCTTGC 59.069 38.462 0.00 0.00 43.29 4.01
2 3 9.149225 GATGATATTATTACAGTCAGCTCCTTG 57.851 37.037 0.00 0.00 0.00 3.61
3 4 9.099071 AGATGATATTATTACAGTCAGCTCCTT 57.901 33.333 0.00 0.00 30.52 3.36
4 5 8.663209 AGATGATATTATTACAGTCAGCTCCT 57.337 34.615 0.00 0.00 30.52 3.69
41 42 1.070821 CACGATCGAGCACACAATGT 58.929 50.000 24.34 0.00 0.00 2.71
42 43 0.371301 CCACGATCGAGCACACAATG 59.629 55.000 24.34 5.83 0.00 2.82
43 44 0.037326 ACCACGATCGAGCACACAAT 60.037 50.000 24.34 0.00 0.00 2.71
44 45 0.249699 AACCACGATCGAGCACACAA 60.250 50.000 24.34 0.00 0.00 3.33
45 46 0.249699 AAACCACGATCGAGCACACA 60.250 50.000 24.34 0.00 0.00 3.72
46 47 0.865769 AAAACCACGATCGAGCACAC 59.134 50.000 24.34 0.00 0.00 3.82
47 48 1.262950 CAAAAACCACGATCGAGCACA 59.737 47.619 24.34 0.00 0.00 4.57
48 49 1.263217 ACAAAAACCACGATCGAGCAC 59.737 47.619 24.34 0.00 0.00 4.40
49 50 1.588674 ACAAAAACCACGATCGAGCA 58.411 45.000 24.34 0.00 0.00 4.26
50 51 2.681152 AACAAAAACCACGATCGAGC 57.319 45.000 24.34 0.00 0.00 5.03
51 52 3.947626 ACAAACAAAAACCACGATCGAG 58.052 40.909 24.34 14.64 0.00 4.04
52 53 4.095185 AGAACAAACAAAAACCACGATCGA 59.905 37.500 24.34 0.00 0.00 3.59
53 54 4.347813 AGAACAAACAAAAACCACGATCG 58.652 39.130 14.88 14.88 0.00 3.69
54 55 5.336744 TGAGAACAAACAAAAACCACGATC 58.663 37.500 0.00 0.00 0.00 3.69
55 56 5.317733 TGAGAACAAACAAAAACCACGAT 57.682 34.783 0.00 0.00 0.00 3.73
56 57 4.768130 TGAGAACAAACAAAAACCACGA 57.232 36.364 0.00 0.00 0.00 4.35
57 58 4.090786 GGTTGAGAACAAACAAAAACCACG 59.909 41.667 0.00 0.00 42.61 4.94
58 59 4.390603 GGGTTGAGAACAAACAAAAACCAC 59.609 41.667 0.00 0.00 44.61 4.16
59 60 4.570930 GGGTTGAGAACAAACAAAAACCA 58.429 39.130 0.00 0.00 44.61 3.67
60 61 3.615056 CGGGTTGAGAACAAACAAAAACC 59.385 43.478 0.00 0.00 44.61 3.27
61 62 3.615056 CCGGGTTGAGAACAAACAAAAAC 59.385 43.478 0.00 0.00 44.61 2.43
62 63 3.258622 ACCGGGTTGAGAACAAACAAAAA 59.741 39.130 6.32 0.00 44.61 1.94
63 64 2.826725 ACCGGGTTGAGAACAAACAAAA 59.173 40.909 6.32 0.00 44.61 2.44
64 65 2.164624 CACCGGGTTGAGAACAAACAAA 59.835 45.455 6.32 0.00 44.61 2.83
65 66 1.746220 CACCGGGTTGAGAACAAACAA 59.254 47.619 6.32 0.00 44.61 2.83
66 67 1.384525 CACCGGGTTGAGAACAAACA 58.615 50.000 6.32 0.00 44.61 2.83
67 68 0.030235 GCACCGGGTTGAGAACAAAC 59.970 55.000 6.32 0.00 42.37 2.93
68 69 0.106918 AGCACCGGGTTGAGAACAAA 60.107 50.000 6.32 0.00 37.77 2.83
69 70 0.534203 GAGCACCGGGTTGAGAACAA 60.534 55.000 6.32 0.00 0.00 2.83
70 71 1.070786 GAGCACCGGGTTGAGAACA 59.929 57.895 6.32 0.00 0.00 3.18
71 72 0.951040 CAGAGCACCGGGTTGAGAAC 60.951 60.000 6.32 0.00 0.00 3.01
72 73 1.371183 CAGAGCACCGGGTTGAGAA 59.629 57.895 6.32 0.00 0.00 2.87
73 74 3.059982 CAGAGCACCGGGTTGAGA 58.940 61.111 6.32 0.00 0.00 3.27
74 75 2.743928 GCAGAGCACCGGGTTGAG 60.744 66.667 6.32 0.00 0.00 3.02
75 76 4.329545 GGCAGAGCACCGGGTTGA 62.330 66.667 6.32 0.00 0.00 3.18
76 77 4.335647 AGGCAGAGCACCGGGTTG 62.336 66.667 6.32 0.00 0.00 3.77
77 78 4.021925 GAGGCAGAGCACCGGGTT 62.022 66.667 6.32 0.00 0.00 4.11
81 82 2.501223 TAAACCGAGGCAGAGCACCG 62.501 60.000 0.00 0.00 0.00 4.94
82 83 0.107654 ATAAACCGAGGCAGAGCACC 60.108 55.000 0.00 0.00 0.00 5.01
83 84 2.596904 TATAAACCGAGGCAGAGCAC 57.403 50.000 0.00 0.00 0.00 4.40
84 85 4.526650 TGATATATAAACCGAGGCAGAGCA 59.473 41.667 0.00 0.00 0.00 4.26
85 86 5.073311 TGATATATAAACCGAGGCAGAGC 57.927 43.478 0.00 0.00 0.00 4.09
86 87 8.553459 AAAATGATATATAAACCGAGGCAGAG 57.447 34.615 0.00 0.00 0.00 3.35
87 88 8.918202 AAAAATGATATATAAACCGAGGCAGA 57.082 30.769 0.00 0.00 0.00 4.26
114 115 9.877178 ACAATATATAAACCATTTCGCCAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
115 116 9.877178 AACAATATATAAACCATTTCGCCAAAA 57.123 25.926 0.00 0.00 0.00 2.44
117 118 9.953697 GTAACAATATATAAACCATTTCGCCAA 57.046 29.630 0.00 0.00 0.00 4.52
118 119 9.344772 AGTAACAATATATAAACCATTTCGCCA 57.655 29.630 0.00 0.00 0.00 5.69
185 186 3.225104 ACTGTCATTTCTGTGTGCCAAT 58.775 40.909 0.00 0.00 0.00 3.16
241 242 8.274322 TGGTGATTTGATGTAGAATATGGACTT 58.726 33.333 0.00 0.00 0.00 3.01
249 250 6.040166 GCCATCTTGGTGATTTGATGTAGAAT 59.960 38.462 0.00 0.00 40.46 2.40
255 256 3.193903 TGTGCCATCTTGGTGATTTGATG 59.806 43.478 0.00 0.00 40.46 3.07
297 298 2.038164 TGCATGCATAGGCTTCTAGGAG 59.962 50.000 18.46 0.00 41.91 3.69
298 299 2.038164 CTGCATGCATAGGCTTCTAGGA 59.962 50.000 22.97 0.00 41.91 2.94
299 300 2.424557 CTGCATGCATAGGCTTCTAGG 58.575 52.381 22.97 0.21 41.91 3.02
300 301 1.805345 GCTGCATGCATAGGCTTCTAG 59.195 52.381 22.97 6.35 42.31 2.43
301 302 1.888215 GCTGCATGCATAGGCTTCTA 58.112 50.000 22.97 0.00 42.31 2.10
302 303 2.716814 GCTGCATGCATAGGCTTCT 58.283 52.632 22.97 0.00 42.31 2.85
323 324 4.281688 ACCAAATCTCAGTTCAACAATGGG 59.718 41.667 0.00 0.00 0.00 4.00
413 414 1.265905 GAAAACCGAAACCGACTGCAT 59.734 47.619 0.00 0.00 0.00 3.96
414 415 0.658897 GAAAACCGAAACCGACTGCA 59.341 50.000 0.00 0.00 0.00 4.41
415 416 0.040692 GGAAAACCGAAACCGACTGC 60.041 55.000 0.00 0.00 0.00 4.40
525 534 7.814642 TGACGTGTAGTTTTTGTTAGGAAAAA 58.185 30.769 0.00 0.00 33.42 1.94
534 543 2.538449 CGCTCTGACGTGTAGTTTTTGT 59.462 45.455 0.00 0.00 0.00 2.83
568 577 8.373048 ACACACTGAAAATTTACGTGAAGATA 57.627 30.769 16.54 0.00 0.00 1.98
588 597 1.372499 TAAGCCGACGCAGACACAC 60.372 57.895 0.00 0.00 37.52 3.82
589 598 1.372499 GTAAGCCGACGCAGACACA 60.372 57.895 0.00 0.00 37.52 3.72
654 673 8.887717 CAAATATAGCTAGTGCAAGTTTCTCTT 58.112 33.333 0.00 0.00 42.74 2.85
665 684 8.830580 TGAAGAACATTCAAATATAGCTAGTGC 58.169 33.333 0.00 0.00 40.05 4.40
716 735 2.089980 GTGAGCTGCATTGAGATTGGT 58.910 47.619 1.02 0.00 0.00 3.67
745 764 0.739813 ATCTACGAAACCGCAGCCAC 60.740 55.000 0.00 0.00 0.00 5.01
799 823 3.195825 AGTCAAGTGTGGCCTGATACTAC 59.804 47.826 3.32 0.00 0.00 2.73
833 883 3.938334 GAGAAAAGGAAGCTGACAGATCC 59.062 47.826 16.18 16.18 0.00 3.36
834 884 4.831107 AGAGAAAAGGAAGCTGACAGATC 58.169 43.478 6.65 3.37 0.00 2.75
839 889 3.007398 TCAGGAGAGAAAAGGAAGCTGAC 59.993 47.826 0.00 0.00 0.00 3.51
843 893 2.027285 AGCTCAGGAGAGAAAAGGAAGC 60.027 50.000 0.00 0.00 44.98 3.86
846 896 2.830923 CTCAGCTCAGGAGAGAAAAGGA 59.169 50.000 0.00 0.00 44.98 3.36
847 897 2.677613 GCTCAGCTCAGGAGAGAAAAGG 60.678 54.545 3.81 0.00 44.98 3.11
848 898 2.234414 AGCTCAGCTCAGGAGAGAAAAG 59.766 50.000 0.00 0.00 44.98 2.27
850 900 1.935799 AGCTCAGCTCAGGAGAGAAA 58.064 50.000 0.00 0.00 44.98 2.52
906 963 6.294473 ACCTGACATGAGGTGATTTATCATC 58.706 40.000 5.32 0.00 45.20 2.92
912 969 4.163078 CCTCTACCTGACATGAGGTGATTT 59.837 45.833 14.83 0.00 46.43 2.17
930 987 0.618981 TGTCGACTGAGGAGCCTCTA 59.381 55.000 17.92 3.79 43.12 2.43
942 999 0.532573 AGGAATCGTGCATGTCGACT 59.467 50.000 17.92 6.68 40.07 4.18
960 1017 2.015736 ACTGCATCAAGCCTAACGAG 57.984 50.000 0.00 0.00 44.83 4.18
1086 1143 3.158537 TTGCTCGACCAACGCAGGA 62.159 57.895 0.10 0.00 42.26 3.86
1089 1146 3.345808 GCTTGCTCGACCAACGCA 61.346 61.111 8.90 1.97 42.26 5.24
1116 1173 4.361971 TCCACCTCCTCGGCGACT 62.362 66.667 4.99 0.00 35.61 4.18
1119 1176 3.358076 GAACTCCACCTCCTCGGCG 62.358 68.421 0.00 0.00 35.61 6.46
1172 1229 1.461268 TGCCTCTCTTGACCCACCA 60.461 57.895 0.00 0.00 0.00 4.17
1938 1995 1.369692 CACCAGCGTGACCACCTTA 59.630 57.895 0.00 0.00 43.14 2.69
1995 2052 1.737008 GACGAAGCGGTCCAGGAAC 60.737 63.158 0.00 0.00 0.00 3.62
2121 2178 2.746277 GCCAGCACGTTCCCGATT 60.746 61.111 0.00 0.00 37.88 3.34
2163 2220 2.174319 GCTTCCGAACATCTCCCGC 61.174 63.158 0.00 0.00 0.00 6.13
2178 2235 3.255397 AGCTCCACCTGCCAGCTT 61.255 61.111 0.00 0.00 40.77 3.74
2189 2246 1.741401 CCATTTCGTGCGAGCTCCA 60.741 57.895 8.47 4.37 0.00 3.86
2373 2430 1.601903 CAACTTGGTTAAGCTCGTGCA 59.398 47.619 12.58 0.00 42.74 4.57
2409 2472 3.494398 CGTAGCTAAACCTGGCATATGGT 60.494 47.826 4.56 0.00 38.35 3.55
2412 2475 3.386726 TGACGTAGCTAAACCTGGCATAT 59.613 43.478 0.00 0.00 0.00 1.78
2413 2476 2.761767 TGACGTAGCTAAACCTGGCATA 59.238 45.455 0.00 0.00 0.00 3.14
2457 2523 4.275689 CACGATATGCCAAATGGAGCTAAA 59.724 41.667 2.98 0.00 37.39 1.85
2477 2543 6.851222 ATATTTTTCATCTCTACTGCCACG 57.149 37.500 0.00 0.00 0.00 4.94
2510 2610 6.279123 TGAAAATTAGCATGCAGAAACAACA 58.721 32.000 21.98 8.06 0.00 3.33
2555 2655 3.567164 AGAAGTGTCAGTGCAGATTTTGG 59.433 43.478 0.00 0.00 0.00 3.28
2564 2664 3.032017 TGAGCTTAGAAGTGTCAGTGC 57.968 47.619 0.00 0.00 0.00 4.40
2627 2749 5.083533 AGGTGACTGAGATTTTGCTAGAG 57.916 43.478 0.00 0.00 41.13 2.43
2663 2785 7.516198 AGATAATTTTGAACTGAGCAGTGTT 57.484 32.000 3.57 0.00 41.58 3.32
2688 2810 6.194235 TCCACAGATAATTTGTGCCCTTTAT 58.806 36.000 3.63 0.00 43.50 1.40
2694 2817 4.335594 GGTACTCCACAGATAATTTGTGCC 59.664 45.833 3.63 0.00 43.50 5.01
2718 2841 6.394345 ACTCCTCCAAATAGAACCAAAGAT 57.606 37.500 0.00 0.00 0.00 2.40
2733 2856 2.325661 TCCTCACATCAACTCCTCCA 57.674 50.000 0.00 0.00 0.00 3.86
2817 2940 5.299782 CCCGGTTTTCCATAAATTAATCGGA 59.700 40.000 7.90 0.00 40.70 4.55
2965 3088 1.458777 TCGTGGGGAGTCACTTGGT 60.459 57.895 0.00 0.00 35.63 3.67
3078 3201 4.009675 CAAAAGCAAGGTGTCTATGGCTA 58.990 43.478 0.00 0.00 0.00 3.93
3128 3252 3.005367 ACGTCAATAAGGGGCAAACAAAG 59.995 43.478 0.00 0.00 0.00 2.77
3235 3359 6.178607 ACTCCAAATCCAAATGCTCTTTTT 57.821 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.