Multiple sequence alignment - TraesCS5A01G354200

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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 TraesCS5A01G354200 chr5A 100.000 2903 0 0 1 2903 556824296 556821394 0.000000e+00 5361.0
1 TraesCS5A01G354200 chr5A 94.702 2095 107 3 115 2206 572042963 572040870 0.000000e+00 3251.0
2 TraesCS5A01G354200 chr5A 94.423 2080 112 2 128 2207 514263440 514261365 0.000000e+00 3195.0
3 TraesCS5A01G354200 chr5A 83.569 1059 159 9 1152 2208 480822806 480823851 0.000000e+00 977.0
4 TraesCS5A01G354200 chr1A 96.228 2121 68 6 99 2207 96354678 96356798 0.000000e+00 3463.0
5 TraesCS5A01G354200 chr1A 95.349 43 2 0 594 636 96356006 96356048 5.190000e-08 69.4
6 TraesCS5A01G354200 chrUn 94.904 2080 106 0 126 2205 281038937 281041016 0.000000e+00 3254.0
7 TraesCS5A01G354200 chrUn 80.500 1400 224 32 773 2158 170190948 170189584 0.000000e+00 1027.0
8 TraesCS5A01G354200 chrUn 81.250 96 14 3 2783 2876 26732879 26732972 1.120000e-09 75.0
9 TraesCS5A01G354200 chrUn 92.000 50 4 0 2825 2874 143847038 143847087 1.440000e-08 71.3
10 TraesCS5A01G354200 chrUn 89.796 49 5 0 2828 2876 26525443 26525395 2.420000e-06 63.9
11 TraesCS5A01G354200 chr7A 93.986 2095 108 5 122 2211 675052012 675049931 0.000000e+00 3155.0
12 TraesCS5A01G354200 chr7D 93.580 2056 117 4 154 2209 610424860 610422820 0.000000e+00 3051.0
13 TraesCS5A01G354200 chr5B 90.058 865 70 11 1346 2205 711861957 711861104 0.000000e+00 1107.0
14 TraesCS5A01G354200 chr6B 83.664 1059 159 8 1152 2209 171212112 171213157 0.000000e+00 985.0
15 TraesCS5A01G354200 chr6B 76.431 594 132 7 773 1364 626609863 626610450 6.040000e-82 315.0
16 TraesCS5A01G354200 chr6B 93.617 47 3 0 2828 2874 82958143 82958097 1.440000e-08 71.3
17 TraesCS5A01G354200 chr6B 93.333 45 3 0 2828 2872 83127839 83127795 1.870000e-07 67.6
18 TraesCS5A01G354200 chr2A 83.396 1060 155 9 1154 2207 729062297 729063341 0.000000e+00 963.0
19 TraesCS5A01G354200 chr2A 83.286 1059 157 8 1154 2206 642222822 642223866 0.000000e+00 957.0
20 TraesCS5A01G354200 chr7B 85.714 798 98 9 1411 2207 115224908 115225690 0.000000e+00 828.0
21 TraesCS5A01G354200 chr5D 89.508 305 15 4 2602 2903 440797428 440797718 1.270000e-98 370.0
22 TraesCS5A01G354200 chr5D 83.539 243 17 10 2208 2447 440795926 440796148 3.790000e-49 206.0
23 TraesCS5A01G354200 chr5D 97.403 77 2 0 298 374 553476196 553476272 6.530000e-27 132.0
24 TraesCS5A01G354200 chr5D 96.875 32 1 0 2515 2546 440797339 440797370 1.000000e-03 54.7
25 TraesCS5A01G354200 chr6A 93.617 47 3 0 2828 2874 34956875 34956829 1.440000e-08 71.3
26 TraesCS5A01G354200 chr6A 80.851 94 14 3 2783 2874 47701988 47702079 1.440000e-08 71.3
27 TraesCS5A01G354200 chr6A 80.851 94 14 3 2783 2874 47884701 47884792 1.440000e-08 71.3


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 TraesCS5A01G354200 chr5A 556821394 556824296 2902 True 5361.000000 5361 100.0000 1 2903 1 chr5A.!!$R2 2902
1 TraesCS5A01G354200 chr5A 572040870 572042963 2093 True 3251.000000 3251 94.7020 115 2206 1 chr5A.!!$R3 2091
2 TraesCS5A01G354200 chr5A 514261365 514263440 2075 True 3195.000000 3195 94.4230 128 2207 1 chr5A.!!$R1 2079
3 TraesCS5A01G354200 chr5A 480822806 480823851 1045 False 977.000000 977 83.5690 1152 2208 1 chr5A.!!$F1 1056
4 TraesCS5A01G354200 chr1A 96354678 96356798 2120 False 1766.200000 3463 95.7885 99 2207 2 chr1A.!!$F1 2108
5 TraesCS5A01G354200 chrUn 281038937 281041016 2079 False 3254.000000 3254 94.9040 126 2205 1 chrUn.!!$F3 2079
6 TraesCS5A01G354200 chrUn 170189584 170190948 1364 True 1027.000000 1027 80.5000 773 2158 1 chrUn.!!$R2 1385
7 TraesCS5A01G354200 chr7A 675049931 675052012 2081 True 3155.000000 3155 93.9860 122 2211 1 chr7A.!!$R1 2089
8 TraesCS5A01G354200 chr7D 610422820 610424860 2040 True 3051.000000 3051 93.5800 154 2209 1 chr7D.!!$R1 2055
9 TraesCS5A01G354200 chr5B 711861104 711861957 853 True 1107.000000 1107 90.0580 1346 2205 1 chr5B.!!$R1 859
10 TraesCS5A01G354200 chr6B 171212112 171213157 1045 False 985.000000 985 83.6640 1152 2209 1 chr6B.!!$F1 1057
11 TraesCS5A01G354200 chr6B 626609863 626610450 587 False 315.000000 315 76.4310 773 1364 1 chr6B.!!$F2 591
12 TraesCS5A01G354200 chr2A 729062297 729063341 1044 False 963.000000 963 83.3960 1154 2207 1 chr2A.!!$F2 1053
13 TraesCS5A01G354200 chr2A 642222822 642223866 1044 False 957.000000 957 83.2860 1154 2206 1 chr2A.!!$F1 1052
14 TraesCS5A01G354200 chr7B 115224908 115225690 782 False 828.000000 828 85.7140 1411 2207 1 chr7B.!!$F1 796
15 TraesCS5A01G354200 chr5D 440795926 440797718 1792 False 210.233333 370 89.9740 2208 2903 3 chr5D.!!$F2 695


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
36 37 0.322456 GGCATGCCTACAACCACTGA 60.322 55.0 29.98 0.0 0.0 3.41 F
473 489 0.893727 GTTGGGGGACAGCATCGTTT 60.894 55.0 0.00 0.0 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1070 1086 0.655733 CGGCGAAGAAACAACACTGT 59.344 50.0 0.0 0.0 37.39 3.55 R
2047 2096 0.388649 CACACCCGACTAGCACTCAC 60.389 60.0 0.0 0.0 0.00 3.51 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
33 34 4.743018 AGGCATGCCTACAACCAC 57.257 55.556 37.99 7.11 46.14 4.16
34 35 2.078452 AGGCATGCCTACAACCACT 58.922 52.632 37.99 10.83 46.14 4.00
35 36 0.322816 AGGCATGCCTACAACCACTG 60.323 55.000 37.99 0.00 46.14 3.66
36 37 0.322456 GGCATGCCTACAACCACTGA 60.322 55.000 29.98 0.00 0.00 3.41
37 38 1.533625 GCATGCCTACAACCACTGAA 58.466 50.000 6.36 0.00 0.00 3.02
38 39 1.470098 GCATGCCTACAACCACTGAAG 59.530 52.381 6.36 0.00 0.00 3.02
39 40 2.783135 CATGCCTACAACCACTGAAGT 58.217 47.619 0.00 0.00 0.00 3.01
40 41 2.543777 TGCCTACAACCACTGAAGTC 57.456 50.000 0.00 0.00 0.00 3.01
41 42 1.071699 TGCCTACAACCACTGAAGTCC 59.928 52.381 0.00 0.00 0.00 3.85
42 43 1.071699 GCCTACAACCACTGAAGTCCA 59.928 52.381 0.00 0.00 0.00 4.02
43 44 2.486548 GCCTACAACCACTGAAGTCCAA 60.487 50.000 0.00 0.00 0.00 3.53
44 45 3.139077 CCTACAACCACTGAAGTCCAAC 58.861 50.000 0.00 0.00 0.00 3.77
45 46 2.052782 ACAACCACTGAAGTCCAACC 57.947 50.000 0.00 0.00 0.00 3.77
46 47 1.564348 ACAACCACTGAAGTCCAACCT 59.436 47.619 0.00 0.00 0.00 3.50
47 48 2.775384 ACAACCACTGAAGTCCAACCTA 59.225 45.455 0.00 0.00 0.00 3.08
48 49 3.201266 ACAACCACTGAAGTCCAACCTAA 59.799 43.478 0.00 0.00 0.00 2.69
49 50 4.204012 CAACCACTGAAGTCCAACCTAAA 58.796 43.478 0.00 0.00 0.00 1.85
50 51 4.513406 ACCACTGAAGTCCAACCTAAAA 57.487 40.909 0.00 0.00 0.00 1.52
51 52 4.862371 ACCACTGAAGTCCAACCTAAAAA 58.138 39.130 0.00 0.00 0.00 1.94
78 79 3.761481 GCAATCAGCAGTGTCACAC 57.239 52.632 0.00 0.00 44.79 3.82
79 80 0.946528 GCAATCAGCAGTGTCACACA 59.053 50.000 11.40 0.00 44.79 3.72
80 81 1.538512 GCAATCAGCAGTGTCACACAT 59.461 47.619 11.40 0.00 44.79 3.21
81 82 2.667448 GCAATCAGCAGTGTCACACATG 60.667 50.000 11.40 6.10 44.79 3.21
82 83 2.809696 CAATCAGCAGTGTCACACATGA 59.190 45.455 11.40 11.49 36.74 3.07
83 84 2.845363 TCAGCAGTGTCACACATGAT 57.155 45.000 11.40 1.38 37.14 2.45
84 85 2.691927 TCAGCAGTGTCACACATGATC 58.308 47.619 11.40 0.00 37.14 2.92
85 86 2.037511 TCAGCAGTGTCACACATGATCA 59.962 45.455 11.40 0.00 37.14 2.92
86 87 3.007635 CAGCAGTGTCACACATGATCAT 58.992 45.455 11.40 1.18 37.14 2.45
87 88 4.081531 TCAGCAGTGTCACACATGATCATA 60.082 41.667 11.40 0.00 37.14 2.15
88 89 4.814771 CAGCAGTGTCACACATGATCATAT 59.185 41.667 11.40 0.00 37.14 1.78
89 90 4.814771 AGCAGTGTCACACATGATCATATG 59.185 41.667 12.46 12.46 37.14 1.78
90 91 4.024302 GCAGTGTCACACATGATCATATGG 60.024 45.833 17.92 7.39 37.14 2.74
91 92 5.121105 CAGTGTCACACATGATCATATGGT 58.879 41.667 17.92 9.18 37.14 3.55
92 93 5.007332 CAGTGTCACACATGATCATATGGTG 59.993 44.000 17.92 18.15 37.14 4.17
93 94 5.104817 AGTGTCACACATGATCATATGGTGA 60.105 40.000 24.00 23.14 37.82 4.02
94 95 5.761726 GTGTCACACATGATCATATGGTGAT 59.238 40.000 25.98 12.92 41.09 3.06
95 96 6.293244 GTGTCACACATGATCATATGGTGATG 60.293 42.308 25.98 13.21 39.76 3.07
96 97 9.575777 GTGTCACACATGATCATATGGTGATGC 62.576 44.444 25.98 20.37 39.76 3.91
209 210 1.687493 CCTCCTCGGCTTCCTCCTT 60.687 63.158 0.00 0.00 0.00 3.36
473 489 0.893727 GTTGGGGGACAGCATCGTTT 60.894 55.000 0.00 0.00 0.00 3.60
486 502 1.942657 CATCGTTTGCGGATGGAGAAT 59.057 47.619 0.00 0.00 38.89 2.40
498 514 3.267860 GAGAATGCGCCTGCTCCG 61.268 66.667 9.42 0.00 43.34 4.63
811 827 4.154347 CCTCTCCGGCTGTGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
884 900 2.289694 ACCTCGTCAAGTCTTCCATTGG 60.290 50.000 0.00 0.00 0.00 3.16
973 989 1.219124 CTGGCTGCCACTCGTACAT 59.781 57.895 19.30 0.00 0.00 2.29
1070 1086 1.395045 CGGCTGGAGGCTATCAGTGA 61.395 60.000 15.70 0.00 41.46 3.41
1090 1106 0.934496 CAGTGTTGTTTCTTCGCCGA 59.066 50.000 0.00 0.00 0.00 5.54
1143 1159 0.902531 GGACTTTGAGGATCGGTGGA 59.097 55.000 0.00 0.00 38.61 4.02
1148 1164 0.252057 TTGAGGATCGGTGGAGGACA 60.252 55.000 0.00 0.00 38.61 4.02
1291 1314 1.038280 GGTACTGGCTACTATGGCGT 58.962 55.000 0.00 0.00 35.06 5.68
1351 1374 4.519730 TGCACAAGATGATGATTCAACACA 59.480 37.500 0.00 0.00 34.96 3.72
1556 1603 2.124570 CATGCCTCAAGGTCCGGG 60.125 66.667 0.00 0.00 37.57 5.73
1605 1652 3.199880 AGTAGTTTCAGTTGCACAGCT 57.800 42.857 0.00 0.00 0.00 4.24
1715 1762 4.734398 AGAACAAAAGTTGCAACATCCA 57.266 36.364 30.11 0.00 0.00 3.41
1915 1964 8.806146 AGGTTAATGTGTGATAGCATTTTTCTT 58.194 29.630 0.00 0.00 36.75 2.52
2109 2159 3.620427 TGATTAACCGTGCCATGTACT 57.380 42.857 0.00 0.00 0.00 2.73
2121 2171 2.890945 GCCATGTACTGTTTTTGGGTCT 59.109 45.455 0.00 0.00 0.00 3.85
2226 2276 6.882610 AAAAAGCAGTGTCATACATCTTCA 57.117 33.333 0.00 0.00 0.00 3.02
2262 2315 0.964700 TTTGGAATCGTGCCATGCAA 59.035 45.000 0.00 0.00 41.47 4.08
2264 2317 1.314534 TGGAATCGTGCCATGCAAGG 61.315 55.000 2.86 2.86 41.47 3.61
2266 2319 0.527565 GAATCGTGCCATGCAAGGTT 59.472 50.000 10.15 0.16 43.24 3.50
2267 2320 0.968405 AATCGTGCCATGCAAGGTTT 59.032 45.000 10.15 0.00 38.07 3.27
2274 2327 2.754552 TGCCATGCAAGGTTTAGCTAAG 59.245 45.455 10.15 0.00 34.76 2.18
2389 2442 1.665679 GACTTGCATGTCACCGTATGG 59.334 52.381 23.72 0.00 42.84 2.74
2396 2449 2.022764 TGTCACCGTATGGAAGCATG 57.977 50.000 8.33 0.00 39.21 4.06
2398 2451 2.290008 TGTCACCGTATGGAAGCATGTT 60.290 45.455 8.33 0.00 39.21 2.71
2405 2458 5.417580 ACCGTATGGAAGCATGTTTGTATTT 59.582 36.000 8.33 0.00 39.21 1.40
2406 2459 5.971202 CCGTATGGAAGCATGTTTGTATTTC 59.029 40.000 0.00 0.00 37.49 2.17
2447 2500 3.359950 GCCAATTTCCTGGATCAGAGTT 58.640 45.455 0.00 0.00 38.96 3.01
2450 2503 5.595952 GCCAATTTCCTGGATCAGAGTTAAT 59.404 40.000 0.00 0.00 38.96 1.40
2452 2505 7.486647 CCAATTTCCTGGATCAGAGTTAATTG 58.513 38.462 14.76 14.76 38.96 2.32
2453 2506 7.340232 CCAATTTCCTGGATCAGAGTTAATTGA 59.660 37.037 20.00 0.00 38.96 2.57
2455 2508 8.688747 ATTTCCTGGATCAGAGTTAATTGATC 57.311 34.615 14.40 14.40 45.66 2.92
2509 2587 7.527568 TTCCGTAAAAGGGATGTTTTTATGT 57.472 32.000 8.18 0.00 36.19 2.29
2510 2588 7.527568 TCCGTAAAAGGGATGTTTTTATGTT 57.472 32.000 8.18 0.00 36.19 2.71
2511 2589 7.953752 TCCGTAAAAGGGATGTTTTTATGTTT 58.046 30.769 8.18 0.00 36.19 2.83
2512 2590 8.422566 TCCGTAAAAGGGATGTTTTTATGTTTT 58.577 29.630 8.18 0.00 36.19 2.43
2513 2591 8.705134 CCGTAAAAGGGATGTTTTTATGTTTTC 58.295 33.333 8.18 0.00 36.19 2.29
2557 3750 3.008049 ACGTATTCCAAAGTCTTGCTCCT 59.992 43.478 0.00 0.00 0.00 3.69
2560 3753 4.861102 ATTCCAAAGTCTTGCTCCTTTG 57.139 40.909 5.39 5.39 44.48 2.77
2584 3777 3.058457 GCACGAAGCGTTCAACTTC 57.942 52.632 0.00 0.00 38.32 3.01
2593 3786 2.510615 CGTTCAACTTCGCAGAATCC 57.489 50.000 0.00 0.00 45.90 3.01
2594 3787 1.798223 CGTTCAACTTCGCAGAATCCA 59.202 47.619 0.00 0.00 45.90 3.41
2595 3788 2.223144 CGTTCAACTTCGCAGAATCCAA 59.777 45.455 0.00 0.00 45.90 3.53
2596 3789 3.303725 CGTTCAACTTCGCAGAATCCAAA 60.304 43.478 0.00 0.00 45.90 3.28
2597 3790 4.606961 GTTCAACTTCGCAGAATCCAAAA 58.393 39.130 0.00 0.00 45.90 2.44
2598 3791 4.909696 TCAACTTCGCAGAATCCAAAAA 57.090 36.364 0.00 0.00 45.90 1.94
2647 3840 1.406065 CCATGGACGATCTGGAGGCT 61.406 60.000 5.56 0.00 31.38 4.58
2658 3851 3.534941 GGAGGCTTCCGTATCCGT 58.465 61.111 0.00 0.00 32.79 4.69
2659 3852 2.724520 GGAGGCTTCCGTATCCGTA 58.275 57.895 0.00 0.00 32.79 4.02
2660 3853 1.254954 GGAGGCTTCCGTATCCGTAT 58.745 55.000 0.00 0.00 32.79 3.06
2661 3854 1.201880 GGAGGCTTCCGTATCCGTATC 59.798 57.143 0.00 0.00 32.79 2.24
2670 3863 2.415857 CCGTATCCGTATCCGAGAAGAG 59.584 54.545 0.00 0.00 35.63 2.85
2677 3870 0.472898 TATCCGAGAAGAGGAGGCGA 59.527 55.000 0.00 0.00 41.66 5.54
2715 3911 1.287191 CGTCGGCGATCATGGATCT 59.713 57.895 14.79 0.00 41.33 2.75
2716 3912 0.319040 CGTCGGCGATCATGGATCTT 60.319 55.000 14.79 0.00 41.33 2.40
2747 3943 2.951745 GCGTCGACCTCATCAGCG 60.952 66.667 10.58 0.00 0.00 5.18
2767 3963 0.807667 CGCTCCCTGACGAAATCCTG 60.808 60.000 0.00 0.00 0.00 3.86
2780 3976 0.554305 AATCCTGGGCAGCATCATCA 59.446 50.000 0.00 0.00 0.00 3.07
2781 3977 0.110678 ATCCTGGGCAGCATCATCAG 59.889 55.000 0.00 0.00 0.00 2.90
2782 3978 0.984432 TCCTGGGCAGCATCATCAGA 60.984 55.000 0.00 0.00 0.00 3.27
2783 3979 0.110678 CCTGGGCAGCATCATCAGAT 59.889 55.000 0.00 0.00 33.87 2.90
2784 3980 1.524848 CTGGGCAGCATCATCAGATC 58.475 55.000 0.00 0.00 30.20 2.75
2785 3981 0.841289 TGGGCAGCATCATCAGATCA 59.159 50.000 0.00 0.00 30.20 2.92
2786 3982 1.423921 TGGGCAGCATCATCAGATCAT 59.576 47.619 0.00 0.00 30.20 2.45
2787 3983 2.085320 GGGCAGCATCATCAGATCATC 58.915 52.381 0.00 0.00 30.20 2.92
2809 4005 1.562475 CCCTTATCCCCGTCAAGGAAA 59.438 52.381 1.17 0.00 45.00 3.13
2838 4034 1.076192 AACCGTTCTCTCCTCCCGA 59.924 57.895 0.00 0.00 0.00 5.14
2894 4090 1.507174 CCGTCGACAAGGACCTCTC 59.493 63.158 17.16 0.00 33.30 3.20
2897 4093 0.528470 GTCGACAAGGACCTCTCCAG 59.472 60.000 11.55 0.00 39.39 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.037121 GTGGTTGTAGGCATGCCTTTTT 59.963 45.455 42.49 22.57 45.70 1.94
13 14 1.618343 GTGGTTGTAGGCATGCCTTTT 59.382 47.619 42.49 22.96 45.70 2.27
14 15 1.203050 AGTGGTTGTAGGCATGCCTTT 60.203 47.619 42.49 23.74 45.70 3.11
15 16 0.405585 AGTGGTTGTAGGCATGCCTT 59.594 50.000 42.49 26.18 45.70 4.35
17 18 0.322456 TCAGTGGTTGTAGGCATGCC 60.322 55.000 30.12 30.12 0.00 4.40
18 19 1.470098 CTTCAGTGGTTGTAGGCATGC 59.530 52.381 9.90 9.90 0.00 4.06
19 20 2.744202 GACTTCAGTGGTTGTAGGCATG 59.256 50.000 0.00 0.00 32.74 4.06
20 21 2.290323 GGACTTCAGTGGTTGTAGGCAT 60.290 50.000 0.00 0.00 34.07 4.40
21 22 1.071699 GGACTTCAGTGGTTGTAGGCA 59.928 52.381 0.00 0.00 34.07 4.75
22 23 1.071699 TGGACTTCAGTGGTTGTAGGC 59.928 52.381 0.00 0.00 31.74 3.93
23 24 3.139077 GTTGGACTTCAGTGGTTGTAGG 58.861 50.000 0.00 0.00 0.00 3.18
24 25 3.139077 GGTTGGACTTCAGTGGTTGTAG 58.861 50.000 0.00 0.00 0.00 2.74
25 26 2.775384 AGGTTGGACTTCAGTGGTTGTA 59.225 45.455 0.00 0.00 0.00 2.41
26 27 1.564348 AGGTTGGACTTCAGTGGTTGT 59.436 47.619 0.00 0.00 0.00 3.32
27 28 2.348411 AGGTTGGACTTCAGTGGTTG 57.652 50.000 0.00 0.00 0.00 3.77
28 29 4.513406 TTTAGGTTGGACTTCAGTGGTT 57.487 40.909 0.00 0.00 0.00 3.67
29 30 4.513406 TTTTAGGTTGGACTTCAGTGGT 57.487 40.909 0.00 0.00 0.00 4.16
60 61 0.946528 TGTGTGACACTGCTGATTGC 59.053 50.000 17.47 0.00 35.11 3.56
61 62 2.809696 TCATGTGTGACACTGCTGATTG 59.190 45.455 17.47 3.80 35.11 2.67
62 63 3.130280 TCATGTGTGACACTGCTGATT 57.870 42.857 17.47 0.00 35.11 2.57
63 64 2.845363 TCATGTGTGACACTGCTGAT 57.155 45.000 17.47 0.00 35.11 2.90
64 65 2.037511 TGATCATGTGTGACACTGCTGA 59.962 45.455 17.47 15.94 37.14 4.26
65 66 2.419667 TGATCATGTGTGACACTGCTG 58.580 47.619 17.47 11.43 37.14 4.41
66 67 2.845363 TGATCATGTGTGACACTGCT 57.155 45.000 17.47 4.45 37.14 4.24
67 68 4.024302 CCATATGATCATGTGTGACACTGC 60.024 45.833 25.29 2.56 37.14 4.40
68 69 5.007332 CACCATATGATCATGTGTGACACTG 59.993 44.000 25.29 12.20 37.14 3.66
69 70 5.104817 TCACCATATGATCATGTGTGACACT 60.105 40.000 25.29 0.00 37.14 3.55
70 71 5.118286 TCACCATATGATCATGTGTGACAC 58.882 41.667 25.29 9.14 37.14 3.67
71 72 5.356291 TCACCATATGATCATGTGTGACA 57.644 39.130 25.29 10.10 37.14 3.58
72 73 5.334646 GCATCACCATATGATCATGTGTGAC 60.335 44.000 25.87 16.77 45.52 3.67
73 74 4.758165 GCATCACCATATGATCATGTGTGA 59.242 41.667 25.29 25.51 45.52 3.58
74 75 4.517453 TGCATCACCATATGATCATGTGTG 59.483 41.667 25.29 22.30 45.52 3.82
75 76 4.721132 TGCATCACCATATGATCATGTGT 58.279 39.130 25.29 14.02 45.52 3.72
76 77 5.414454 TCATGCATCACCATATGATCATGTG 59.586 40.000 21.91 21.91 45.52 3.21
77 78 5.566469 TCATGCATCACCATATGATCATGT 58.434 37.500 18.72 8.98 45.52 3.21
78 79 6.699575 ATCATGCATCACCATATGATCATG 57.300 37.500 18.72 3.77 45.52 3.07
79 80 7.665974 GGATATCATGCATCACCATATGATCAT 59.334 37.037 13.81 13.81 45.52 2.45
80 81 6.996282 GGATATCATGCATCACCATATGATCA 59.004 38.462 3.65 0.00 45.52 2.92
81 82 7.225011 AGGATATCATGCATCACCATATGATC 58.775 38.462 3.65 0.00 45.52 2.92
83 84 6.570654 AGGATATCATGCATCACCATATGA 57.429 37.500 3.65 0.00 43.13 2.15
84 85 7.331193 CGATAGGATATCATGCATCACCATATG 59.669 40.741 4.83 0.00 0.00 1.78
85 86 7.384477 CGATAGGATATCATGCATCACCATAT 58.616 38.462 4.83 0.00 0.00 1.78
86 87 6.752168 CGATAGGATATCATGCATCACCATA 58.248 40.000 4.83 0.00 0.00 2.74
87 88 5.608449 CGATAGGATATCATGCATCACCAT 58.392 41.667 4.83 0.00 0.00 3.55
88 89 5.014808 CGATAGGATATCATGCATCACCA 57.985 43.478 4.83 0.00 0.00 4.17
209 210 3.092511 GGGCTGCTGGGGAGATGA 61.093 66.667 0.00 0.00 0.00 2.92
370 386 2.683933 GGGAAGGCGAGGTGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
473 489 2.896854 GCGCATTCTCCATCCGCA 60.897 61.111 0.30 0.00 43.67 5.69
602 618 1.353394 ACCCAGGCACCTTATAGGGC 61.353 60.000 9.27 0.00 40.58 5.19
663 679 0.467290 AAGCTTGTTTGGCCGGAAGA 60.467 50.000 5.05 0.00 0.00 2.87
811 827 0.460987 CTACAAGGCGCCTCCTGAAG 60.461 60.000 32.93 18.55 46.94 3.02
884 900 1.980772 AGCAGCCCCAATTCAGCAC 60.981 57.895 0.00 0.00 0.00 4.40
1070 1086 0.655733 CGGCGAAGAAACAACACTGT 59.344 50.000 0.00 0.00 37.39 3.55
1090 1106 1.842562 CTCAGGAGACCCATTGATGGT 59.157 52.381 9.07 0.00 46.65 3.55
1143 1159 1.208293 GCCGAGGAAGAGAAATGTCCT 59.792 52.381 0.00 0.00 44.67 3.85
1148 1164 1.153349 GGCGCCGAGGAAGAGAAAT 60.153 57.895 12.58 0.00 0.00 2.17
1291 1314 3.795688 AGGAAGAACATCTGCAGGAAA 57.204 42.857 15.13 0.00 0.00 3.13
1351 1374 1.128188 ACCGTTCCTTGCTCCTCCTT 61.128 55.000 0.00 0.00 0.00 3.36
1684 1731 8.611757 GTTGCAACTTTTGTTCTTTTTATCCAT 58.388 29.630 22.36 0.00 41.35 3.41
1715 1762 2.665008 TTCAGCACGCTTGGCAGTCT 62.665 55.000 0.00 0.00 0.00 3.24
1915 1964 0.970640 TGCACTCACGCCTAACCTTA 59.029 50.000 0.00 0.00 0.00 2.69
2047 2096 0.388649 CACACCCGACTAGCACTCAC 60.389 60.000 0.00 0.00 0.00 3.51
2217 2267 7.285629 ACTTGTACTAGCTAGCATGAAGATGTA 59.714 37.037 20.91 5.02 31.50 2.29
2226 2276 5.677319 TCCAAACTTGTACTAGCTAGCAT 57.323 39.130 20.91 4.85 0.00 3.79
2262 2315 6.769512 TGACTCAACATTCTTAGCTAAACCT 58.230 36.000 7.74 0.00 0.00 3.50
2264 2317 9.899226 AAAATGACTCAACATTCTTAGCTAAAC 57.101 29.630 7.74 0.00 39.19 2.01
2309 2362 9.766277 GACTCAACATTGATCTAGAAAAATGAC 57.234 33.333 25.89 12.60 36.46 3.06
2345 2398 9.334693 GTCACTTAAAATGACTCAACATTGATC 57.665 33.333 10.82 0.00 42.68 2.92
2383 2436 6.785191 AGAAATACAAACATGCTTCCATACG 58.215 36.000 0.00 0.00 0.00 3.06
2384 2437 8.986477 AAAGAAATACAAACATGCTTCCATAC 57.014 30.769 0.00 0.00 0.00 2.39
2410 2463 8.627377 AGGAAATTGGCCCATCTTCTATATTAT 58.373 33.333 0.00 0.00 0.00 1.28
2413 2466 6.251471 CAGGAAATTGGCCCATCTTCTATAT 58.749 40.000 0.00 0.00 0.00 0.86
2416 2469 3.373001 CCAGGAAATTGGCCCATCTTCTA 60.373 47.826 0.00 0.00 0.00 2.10
2417 2470 2.625087 CCAGGAAATTGGCCCATCTTCT 60.625 50.000 0.00 0.00 0.00 2.85
2418 2471 1.758862 CCAGGAAATTGGCCCATCTTC 59.241 52.381 0.00 1.96 0.00 2.87
2424 2477 1.063717 TCTGATCCAGGAAATTGGCCC 60.064 52.381 0.00 0.00 38.16 5.80
2483 2561 9.245481 ACATAAAAACATCCCTTTTACGGAATA 57.755 29.630 0.00 0.00 32.56 1.75
2484 2562 8.129496 ACATAAAAACATCCCTTTTACGGAAT 57.871 30.769 0.00 0.00 32.56 3.01
2486 2564 7.527568 AACATAAAAACATCCCTTTTACGGA 57.472 32.000 0.00 0.00 32.56 4.69
2487 2565 8.596271 AAAACATAAAAACATCCCTTTTACGG 57.404 30.769 0.00 0.00 32.56 4.02
2488 2566 9.471084 AGAAAACATAAAAACATCCCTTTTACG 57.529 29.630 0.00 0.00 32.56 3.18
2506 2584 7.588488 CGGTTTATAACACGTGAAAGAAAACAT 59.412 33.333 25.01 4.04 0.00 2.71
2508 2586 6.357766 CCGGTTTATAACACGTGAAAGAAAAC 59.642 38.462 25.01 21.51 0.00 2.43
2509 2587 6.038050 ACCGGTTTATAACACGTGAAAGAAAA 59.962 34.615 25.01 12.36 0.00 2.29
2510 2588 5.526846 ACCGGTTTATAACACGTGAAAGAAA 59.473 36.000 25.01 15.46 0.00 2.52
2511 2589 5.055812 ACCGGTTTATAACACGTGAAAGAA 58.944 37.500 25.01 10.11 0.00 2.52
2512 2590 4.630111 ACCGGTTTATAACACGTGAAAGA 58.370 39.130 25.01 3.64 0.00 2.52
2513 2591 4.996062 ACCGGTTTATAACACGTGAAAG 57.004 40.909 25.01 3.35 0.00 2.62
2546 3722 0.394565 ACGAGCAAAGGAGCAAGACT 59.605 50.000 0.00 0.00 36.85 3.24
2547 3723 0.514691 CACGAGCAAAGGAGCAAGAC 59.485 55.000 0.00 0.00 36.85 3.01
2548 3724 1.230635 GCACGAGCAAAGGAGCAAGA 61.231 55.000 0.00 0.00 41.58 3.02
2574 3767 1.798223 TGGATTCTGCGAAGTTGAACG 59.202 47.619 0.00 0.00 0.00 3.95
2595 3788 6.091577 CGTAAAAAGGGTTCTGCAAAGTTTTT 59.908 34.615 0.00 0.00 32.16 1.94
2596 3789 5.579119 CGTAAAAAGGGTTCTGCAAAGTTTT 59.421 36.000 0.00 0.00 0.00 2.43
2597 3790 5.106442 CGTAAAAAGGGTTCTGCAAAGTTT 58.894 37.500 0.00 0.00 0.00 2.66
2598 3791 4.440940 CCGTAAAAAGGGTTCTGCAAAGTT 60.441 41.667 0.00 0.00 0.00 2.66
2599 3792 3.067601 CCGTAAAAAGGGTTCTGCAAAGT 59.932 43.478 0.00 0.00 0.00 2.66
2600 3793 3.638484 CCGTAAAAAGGGTTCTGCAAAG 58.362 45.455 0.00 0.00 0.00 2.77
2657 3850 0.594110 CGCCTCCTCTTCTCGGATAC 59.406 60.000 0.00 0.00 0.00 2.24
2658 3851 0.472898 TCGCCTCCTCTTCTCGGATA 59.527 55.000 0.00 0.00 0.00 2.59
2659 3852 0.821711 CTCGCCTCCTCTTCTCGGAT 60.822 60.000 0.00 0.00 0.00 4.18
2660 3853 1.452289 CTCGCCTCCTCTTCTCGGA 60.452 63.158 0.00 0.00 0.00 4.55
2661 3854 1.452289 TCTCGCCTCCTCTTCTCGG 60.452 63.158 0.00 0.00 0.00 4.63
2677 3870 3.537874 GTATGCCCCGGCTCGTCT 61.538 66.667 7.35 0.00 42.51 4.18
2747 3943 2.174319 GGATTTCGTCAGGGAGCGC 61.174 63.158 0.00 0.00 0.00 5.92
2767 3963 2.085320 GATGATCTGATGATGCTGCCC 58.915 52.381 0.00 0.00 32.19 5.36
2780 3976 2.112691 ACGGGGATAAGGGAGATGATCT 59.887 50.000 0.00 0.00 0.00 2.75
2781 3977 2.498078 GACGGGGATAAGGGAGATGATC 59.502 54.545 0.00 0.00 0.00 2.92
2782 3978 2.158158 TGACGGGGATAAGGGAGATGAT 60.158 50.000 0.00 0.00 0.00 2.45
2783 3979 1.219469 TGACGGGGATAAGGGAGATGA 59.781 52.381 0.00 0.00 0.00 2.92
2784 3980 1.717032 TGACGGGGATAAGGGAGATG 58.283 55.000 0.00 0.00 0.00 2.90
2785 3981 2.330216 CTTGACGGGGATAAGGGAGAT 58.670 52.381 0.00 0.00 0.00 2.75
2786 3982 1.691482 CCTTGACGGGGATAAGGGAGA 60.691 57.143 0.00 0.00 37.82 3.71
2787 3983 0.759346 CCTTGACGGGGATAAGGGAG 59.241 60.000 0.00 0.00 37.82 4.30



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

AutoCloner maintained by Alex Coulton.