Multiple sequence alignment - TraesCS1D01G330600

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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 TraesCS1D01G330600 chr1D 100.000 2711 0 0 1 2711 421020425 421023135 0.000000e+00 5007
1 TraesCS1D01G330600 chr1B 86.160 1987 123 64 108 1972 570022338 570024294 0.000000e+00 2006
2 TraesCS1D01G330600 chr1B 87.736 424 22 10 2028 2429 570024396 570024811 4.090000e-128 468
3 TraesCS1D01G330600 chr1B 94.156 154 9 0 2552 2705 570025096 570025249 4.510000e-58 235
4 TraesCS1D01G330600 chr1A 88.068 1232 43 44 828 1975 517397885 517399096 0.000000e+00 1365
5 TraesCS1D01G330600 chr1A 83.148 629 38 29 2131 2711 517399168 517399776 1.860000e-141 512
6 TraesCS1D01G330600 chr1A 89.666 329 21 6 487 803 517396785 517397112 9.040000e-110 407
7 TraesCS1D01G330600 chr1A 92.135 89 7 0 400 488 517396666 517396754 2.830000e-25 126


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 TraesCS1D01G330600 chr1D 421020425 421023135 2710 False 5007.0 5007 100.000000 1 2711 1 chr1D.!!$F1 2710
1 TraesCS1D01G330600 chr1B 570022338 570025249 2911 False 903.0 2006 89.350667 108 2705 3 chr1B.!!$F1 2597
2 TraesCS1D01G330600 chr1A 517396666 517399776 3110 False 602.5 1365 88.254250 400 2711 4 chr1A.!!$F1 2311

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
19 20 0.108585 AGAGCACATCCGGTTGTGTT 59.891 50.0 34.65 31.74 46.93 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2967 1.442769 TTTGCAGGAATCGTGAGCTC 58.557 50.0 6.82 6.82 0.0 4.09 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
18 19 1.754745 AGAGCACATCCGGTTGTGT 59.245 52.632 34.65 25.18 46.93 3.72
19 20 0.108585 AGAGCACATCCGGTTGTGTT 59.891 50.000 34.65 31.74 46.93 3.32
20 21 0.238289 GAGCACATCCGGTTGTGTTG 59.762 55.000 34.65 18.54 46.93 3.33
21 22 0.179032 AGCACATCCGGTTGTGTTGA 60.179 50.000 34.65 2.57 46.93 3.18
22 23 0.881118 GCACATCCGGTTGTGTTGAT 59.119 50.000 34.65 4.94 46.93 2.57
23 24 2.080693 GCACATCCGGTTGTGTTGATA 58.919 47.619 34.65 1.06 46.93 2.15
24 25 2.095853 GCACATCCGGTTGTGTTGATAG 59.904 50.000 34.65 16.71 46.93 2.08
25 26 2.095853 CACATCCGGTTGTGTTGATAGC 59.904 50.000 29.65 0.00 41.65 2.97
26 27 1.670811 CATCCGGTTGTGTTGATAGCC 59.329 52.381 0.00 0.00 0.00 3.93
27 28 0.390603 TCCGGTTGTGTTGATAGCCG 60.391 55.000 0.00 0.00 39.89 5.52
28 29 0.672401 CCGGTTGTGTTGATAGCCGT 60.672 55.000 0.00 0.00 38.75 5.68
29 30 0.442310 CGGTTGTGTTGATAGCCGTG 59.558 55.000 0.00 0.00 36.17 4.94
30 31 0.168128 GGTTGTGTTGATAGCCGTGC 59.832 55.000 0.00 0.00 0.00 5.34
31 32 1.156736 GTTGTGTTGATAGCCGTGCT 58.843 50.000 3.87 3.87 43.41 4.40
32 33 1.128692 GTTGTGTTGATAGCCGTGCTC 59.871 52.381 1.46 0.00 40.44 4.26
33 34 0.608130 TGTGTTGATAGCCGTGCTCT 59.392 50.000 1.46 0.00 40.44 4.09
34 35 1.002366 GTGTTGATAGCCGTGCTCTG 58.998 55.000 1.46 0.00 40.44 3.35
35 36 0.894835 TGTTGATAGCCGTGCTCTGA 59.105 50.000 1.46 0.00 40.44 3.27
36 37 1.482182 TGTTGATAGCCGTGCTCTGAT 59.518 47.619 1.46 0.00 40.44 2.90
37 38 2.693074 TGTTGATAGCCGTGCTCTGATA 59.307 45.455 1.46 0.00 40.44 2.15
38 39 3.321968 TGTTGATAGCCGTGCTCTGATAT 59.678 43.478 1.46 0.00 40.44 1.63
39 40 4.202253 TGTTGATAGCCGTGCTCTGATATT 60.202 41.667 1.46 0.00 40.44 1.28
40 41 4.179926 TGATAGCCGTGCTCTGATATTC 57.820 45.455 1.46 0.00 40.44 1.75
41 42 2.706555 TAGCCGTGCTCTGATATTCG 57.293 50.000 1.46 0.00 40.44 3.34
42 43 0.747255 AGCCGTGCTCTGATATTCGT 59.253 50.000 0.00 0.00 30.62 3.85
43 44 1.132588 GCCGTGCTCTGATATTCGTC 58.867 55.000 0.00 0.00 0.00 4.20
44 45 1.269309 GCCGTGCTCTGATATTCGTCT 60.269 52.381 0.00 0.00 0.00 4.18
45 46 2.389059 CCGTGCTCTGATATTCGTCTG 58.611 52.381 0.00 0.00 0.00 3.51
46 47 1.783711 CGTGCTCTGATATTCGTCTGC 59.216 52.381 0.00 0.00 0.00 4.26
47 48 1.783711 GTGCTCTGATATTCGTCTGCG 59.216 52.381 0.00 0.00 39.92 5.18
48 49 0.781191 GCTCTGATATTCGTCTGCGC 59.219 55.000 0.00 0.00 38.14 6.09
49 50 1.048494 CTCTGATATTCGTCTGCGCG 58.952 55.000 0.00 0.00 38.14 6.86
50 51 0.380733 TCTGATATTCGTCTGCGCGT 59.619 50.000 8.43 0.00 38.14 6.01
51 52 0.772926 CTGATATTCGTCTGCGCGTC 59.227 55.000 8.43 0.00 38.14 5.19
52 53 0.928451 TGATATTCGTCTGCGCGTCG 60.928 55.000 8.43 7.67 38.14 5.12
77 78 2.259266 CGTAGGGAGAGAGGGTCTAC 57.741 60.000 0.00 0.00 34.71 2.59
78 79 1.540797 CGTAGGGAGAGAGGGTCTACG 60.541 61.905 0.00 0.00 44.23 3.51
79 80 0.473326 TAGGGAGAGAGGGTCTACGC 59.527 60.000 0.00 0.00 36.91 4.42
80 81 1.829096 GGGAGAGAGGGTCTACGCC 60.829 68.421 0.00 0.00 36.91 5.68
81 82 2.188161 GGAGAGAGGGTCTACGCCG 61.188 68.421 0.00 0.00 34.71 6.46
82 83 2.124236 AGAGAGGGTCTACGCCGG 60.124 66.667 0.00 0.00 31.71 6.13
83 84 2.439883 GAGAGGGTCTACGCCGGT 60.440 66.667 1.90 0.00 0.00 5.28
84 85 2.754658 AGAGGGTCTACGCCGGTG 60.755 66.667 14.93 14.93 0.00 4.94
85 86 4.509737 GAGGGTCTACGCCGGTGC 62.510 72.222 16.69 0.00 0.00 5.01
102 103 4.753662 CACCCCGAGTCCCCGAGA 62.754 72.222 0.00 0.00 0.00 4.04
103 104 3.752167 ACCCCGAGTCCCCGAGAT 61.752 66.667 0.00 0.00 0.00 2.75
104 105 2.389449 ACCCCGAGTCCCCGAGATA 61.389 63.158 0.00 0.00 0.00 1.98
105 106 1.902432 CCCCGAGTCCCCGAGATAC 60.902 68.421 0.00 0.00 0.00 2.24
106 107 2.259439 CCCGAGTCCCCGAGATACG 61.259 68.421 0.00 0.00 42.18 3.06
130 131 2.553247 GGGAGAAAGGACAAGACCCAAG 60.553 54.545 0.00 0.00 36.27 3.61
175 178 4.147449 CCGACGGGCAGCTGATGA 62.147 66.667 20.43 0.00 0.00 2.92
177 180 2.581354 GACGGGCAGCTGATGACT 59.419 61.111 20.43 0.00 36.99 3.41
188 195 1.329906 GCTGATGACTGATCCTTTGCG 59.670 52.381 0.00 0.00 0.00 4.85
193 200 1.648467 GACTGATCCTTTGCGTGGGC 61.648 60.000 0.00 0.00 40.52 5.36
284 292 4.156008 ACCCCAAAAGAAAGAATCGAATCG 59.844 41.667 0.00 0.00 0.00 3.34
339 357 4.070552 GCCGCCTTCCGTCTGTCT 62.071 66.667 0.00 0.00 34.38 3.41
340 358 2.182030 CCGCCTTCCGTCTGTCTC 59.818 66.667 0.00 0.00 34.38 3.36
341 359 2.636412 CCGCCTTCCGTCTGTCTCA 61.636 63.158 0.00 0.00 34.38 3.27
342 360 1.513158 CGCCTTCCGTCTGTCTCAT 59.487 57.895 0.00 0.00 0.00 2.90
344 362 1.086634 GCCTTCCGTCTGTCTCATGC 61.087 60.000 0.00 0.00 0.00 4.06
346 364 0.109086 CTTCCGTCTGTCTCATGCGT 60.109 55.000 0.00 0.00 0.00 5.24
347 365 0.317160 TTCCGTCTGTCTCATGCGTT 59.683 50.000 0.00 0.00 0.00 4.84
348 366 0.388520 TCCGTCTGTCTCATGCGTTG 60.389 55.000 0.00 0.00 0.00 4.10
349 367 1.417592 CGTCTGTCTCATGCGTTGC 59.582 57.895 0.00 0.00 0.00 4.17
350 368 1.417592 GTCTGTCTCATGCGTTGCG 59.582 57.895 0.00 0.00 0.00 4.85
370 388 2.520020 CCCATGCCCATGCGTCAT 60.520 61.111 2.75 0.00 41.78 3.06
380 398 4.840288 TGCGTCATACGGCGTCGG 62.840 66.667 19.21 10.55 42.82 4.79
413 437 1.370051 TCAGTTCGTGTCAGCGACG 60.370 57.895 0.00 0.00 40.85 5.12
488 512 4.846779 ATCTTATCTGAACCTCTCGCTC 57.153 45.455 0.00 0.00 0.00 5.03
577 650 2.358510 CCATCCAACCCAACCATGATCT 60.359 50.000 0.00 0.00 0.00 2.75
588 661 1.539388 ACCATGATCTCGATCGAGCTC 59.461 52.381 34.92 33.32 41.71 4.09
686 761 9.706529 ATTATTCCTCTTATTCCTTTGCTTTCT 57.293 29.630 0.00 0.00 0.00 2.52
694 769 3.328288 CTTTGCTTTCTCCCGCGGC 62.328 63.158 22.85 7.02 0.00 6.53
695 770 3.842925 TTTGCTTTCTCCCGCGGCT 62.843 57.895 22.85 0.00 0.00 5.52
807 886 2.367586 TATCCATCGCCGTCCCTCCT 62.368 60.000 0.00 0.00 0.00 3.69
808 887 3.470888 CCATCGCCGTCCCTCCTT 61.471 66.667 0.00 0.00 0.00 3.36
813 892 2.364448 GCCGTCCCTCCTTCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
814 893 1.990614 GCCGTCCCTCCTTCTCCTT 60.991 63.158 0.00 0.00 0.00 3.36
930 1802 2.199236 CGCTATTTACCACCTCGTTCC 58.801 52.381 0.00 0.00 0.00 3.62
931 1803 2.199236 GCTATTTACCACCTCGTTCCG 58.801 52.381 0.00 0.00 0.00 4.30
983 1855 1.294857 GCTAGTAGCTTTGAGCCAGC 58.705 55.000 15.16 0.00 43.77 4.85
990 1862 3.939837 CTTTGAGCCAGCCGAGCGA 62.940 63.158 0.00 0.00 34.64 4.93
1101 1979 1.347817 GCAAGACCACGCTCTTCTCG 61.348 60.000 0.00 0.00 0.00 4.04
1164 2042 4.516195 GCCTTCCGCCTCGAGACC 62.516 72.222 15.71 3.32 0.00 3.85
1737 2652 1.685421 GCTGGAGCTCTGTCCCTCT 60.685 63.158 14.64 0.00 35.49 3.69
1738 2653 1.675720 GCTGGAGCTCTGTCCCTCTC 61.676 65.000 14.64 0.00 35.49 3.20
1873 2823 0.239347 GAACATGGACACTGCACTGC 59.761 55.000 0.00 0.00 0.00 4.40
1883 2833 4.409570 GACACTGCACTGCTTGATTATTG 58.590 43.478 1.98 0.00 0.00 1.90
1897 2847 9.304731 TGCTTGATTATTGCATTAGTTTTGATC 57.695 29.630 0.00 0.00 0.00 2.92
2000 2974 1.069204 TGGATCCAATAGCGAGCTCAC 59.931 52.381 13.46 3.55 0.00 3.51
2003 2977 1.032794 TCCAATAGCGAGCTCACGAT 58.967 50.000 15.40 2.63 35.68 3.73
2023 3024 5.140177 CGATTCCTGCAAATTAAGCGATAC 58.860 41.667 2.63 0.00 32.89 2.24
2024 3025 4.530094 TTCCTGCAAATTAAGCGATACG 57.470 40.909 0.00 0.00 33.85 3.06
2047 3048 1.567537 GTGCAAAGCGTAACTGCGA 59.432 52.632 0.00 0.00 38.97 5.10
2073 3074 5.687730 CGCTGAATTACTAGTGACATCGAAT 59.312 40.000 5.39 0.00 0.00 3.34
2120 3122 9.994432 CTCTAATGTGATAAATCCAAACACTTC 57.006 33.333 0.00 0.00 33.41 3.01
2126 3128 9.906660 TGTGATAAATCCAAACACTTCATTAAC 57.093 29.630 0.00 0.00 33.41 2.01
2177 3181 3.699067 CAATTCATCCTGAAACGATGGC 58.301 45.455 0.00 0.00 40.12 4.40
2187 3191 3.417101 TGAAACGATGGCATAAACCAGT 58.583 40.909 0.00 0.00 44.71 4.00
2189 3193 1.094785 ACGATGGCATAAACCAGTGC 58.905 50.000 0.00 0.00 44.71 4.40
2194 3198 1.423845 GCATAAACCAGTGCCGACG 59.576 57.895 0.00 0.00 35.35 5.12
2195 3199 1.423845 CATAAACCAGTGCCGACGC 59.576 57.895 0.00 0.00 0.00 5.19
2353 3365 1.239347 GAAGAGAAGGCGGTGCTTTT 58.761 50.000 0.00 0.00 0.00 2.27
2372 3384 6.488006 TGCTTTTCAGACTGAGAAATTAAGCT 59.512 34.615 21.38 0.00 37.30 3.74
2373 3385 6.800892 GCTTTTCAGACTGAGAAATTAAGCTG 59.199 38.462 9.49 0.00 35.26 4.24
2378 3390 6.767902 TCAGACTGAGAAATTAAGCTGTGTTT 59.232 34.615 0.00 0.00 0.00 2.83
2379 3391 7.283127 TCAGACTGAGAAATTAAGCTGTGTTTT 59.717 33.333 0.00 0.00 0.00 2.43
2380 3392 7.377928 CAGACTGAGAAATTAAGCTGTGTTTTG 59.622 37.037 0.00 0.00 0.00 2.44
2417 3440 0.605319 GGTTTGGTCATGCGACTGGA 60.605 55.000 0.00 0.00 42.21 3.86
2430 3537 1.863267 GACTGGATCCAATCGCTCAG 58.137 55.000 17.00 3.75 0.00 3.35
2436 3543 0.387202 ATCCAATCGCTCAGGACTCG 59.613 55.000 0.00 0.00 33.57 4.18
2450 3557 2.168728 AGGACTCGTGGAATTAAGAGGC 59.831 50.000 0.00 0.00 38.00 4.70
2462 3579 5.986741 GGAATTAAGAGGCAGTAGAAGCTAC 59.013 44.000 0.00 0.00 0.00 3.58
2510 3639 6.214191 TCTGTGTAAATTGCAAGGTCAAAA 57.786 33.333 4.94 0.00 0.00 2.44
2527 3656 7.492524 AGGTCAAAATTTCAGAAAAGAAGACC 58.507 34.615 21.69 21.69 36.85 3.85
2532 3661 8.975439 CAAAATTTCAGAAAAGAAGACCATCAG 58.025 33.333 0.00 0.00 0.00 2.90
2544 3733 1.478105 GACCATCAGGAAACATTGGCC 59.522 52.381 0.00 0.00 38.69 5.36
2545 3734 0.457035 CCATCAGGAAACATTGGCCG 59.543 55.000 0.00 0.00 36.89 6.13
2546 3735 1.176527 CATCAGGAAACATTGGCCGT 58.823 50.000 0.00 0.00 0.00 5.68
2548 3737 2.107950 TCAGGAAACATTGGCCGTAG 57.892 50.000 0.00 0.00 0.00 3.51
2566 3763 3.044059 GCCGTGCACCATCTTCAGC 62.044 63.158 12.15 0.00 0.00 4.26
2620 3817 1.307097 GACCTACCTCGCTACGATGT 58.693 55.000 3.55 3.55 38.21 3.06
2665 3862 2.297033 TCAGCAAATTGGAAACTGGAGC 59.703 45.455 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.701663 CACAACCGGATGTGCTCT 57.298 55.556 28.88 0.00 43.67 4.09
5 6 2.356135 GCTATCAACACAACCGGATGT 58.644 47.619 12.22 12.22 0.00 3.06
6 7 1.670811 GGCTATCAACACAACCGGATG 59.329 52.381 9.46 10.13 0.00 3.51
7 8 1.742411 CGGCTATCAACACAACCGGAT 60.742 52.381 9.46 0.00 37.04 4.18
8 9 0.390603 CGGCTATCAACACAACCGGA 60.391 55.000 9.46 0.00 37.04 5.14
9 10 0.672401 ACGGCTATCAACACAACCGG 60.672 55.000 0.00 0.00 44.73 5.28
10 11 0.442310 CACGGCTATCAACACAACCG 59.558 55.000 0.00 0.00 45.86 4.44
11 12 0.168128 GCACGGCTATCAACACAACC 59.832 55.000 0.00 0.00 0.00 3.77
12 13 1.128692 GAGCACGGCTATCAACACAAC 59.871 52.381 0.00 0.00 39.88 3.32
13 14 1.001974 AGAGCACGGCTATCAACACAA 59.998 47.619 0.00 0.00 39.88 3.33
14 15 0.608130 AGAGCACGGCTATCAACACA 59.392 50.000 0.00 0.00 39.88 3.72
15 16 1.002366 CAGAGCACGGCTATCAACAC 58.998 55.000 0.00 0.00 39.88 3.32
16 17 0.894835 TCAGAGCACGGCTATCAACA 59.105 50.000 0.00 0.00 39.88 3.33
17 18 2.231215 ATCAGAGCACGGCTATCAAC 57.769 50.000 0.00 0.00 39.88 3.18
18 19 4.560128 GAATATCAGAGCACGGCTATCAA 58.440 43.478 0.00 0.00 39.88 2.57
19 20 3.366374 CGAATATCAGAGCACGGCTATCA 60.366 47.826 0.00 0.00 39.88 2.15
20 21 3.175152 CGAATATCAGAGCACGGCTATC 58.825 50.000 0.00 0.00 39.88 2.08
21 22 2.558795 ACGAATATCAGAGCACGGCTAT 59.441 45.455 0.00 0.00 39.88 2.97
22 23 1.954382 ACGAATATCAGAGCACGGCTA 59.046 47.619 0.00 0.00 39.88 3.93
23 24 0.747255 ACGAATATCAGAGCACGGCT 59.253 50.000 0.00 0.00 43.88 5.52
24 25 1.132588 GACGAATATCAGAGCACGGC 58.867 55.000 0.00 0.00 0.00 5.68
25 26 2.389059 CAGACGAATATCAGAGCACGG 58.611 52.381 0.00 0.00 0.00 4.94
26 27 1.783711 GCAGACGAATATCAGAGCACG 59.216 52.381 0.00 0.00 0.00 5.34
27 28 1.783711 CGCAGACGAATATCAGAGCAC 59.216 52.381 0.00 0.00 43.93 4.40
28 29 1.865655 GCGCAGACGAATATCAGAGCA 60.866 52.381 0.30 0.00 43.93 4.26
29 30 0.781191 GCGCAGACGAATATCAGAGC 59.219 55.000 0.30 0.00 43.93 4.09
30 31 1.048494 CGCGCAGACGAATATCAGAG 58.952 55.000 8.75 0.00 43.93 3.35
31 32 0.380733 ACGCGCAGACGAATATCAGA 59.619 50.000 5.73 0.00 43.93 3.27
32 33 0.772926 GACGCGCAGACGAATATCAG 59.227 55.000 5.73 0.00 43.93 2.90
33 34 0.928451 CGACGCGCAGACGAATATCA 60.928 55.000 5.73 0.00 43.93 2.15
34 35 1.761357 CGACGCGCAGACGAATATC 59.239 57.895 5.73 0.00 43.93 1.63
35 36 3.903646 CGACGCGCAGACGAATAT 58.096 55.556 5.73 0.00 43.93 1.28
47 48 4.849329 CCCTACGGTGAGCGACGC 62.849 72.222 13.03 13.03 0.00 5.19
48 49 3.109612 CTCCCTACGGTGAGCGACG 62.110 68.421 12.27 0.33 0.00 5.12
49 50 1.716826 CTCTCCCTACGGTGAGCGAC 61.717 65.000 12.27 0.00 41.57 5.19
50 51 1.451567 CTCTCCCTACGGTGAGCGA 60.452 63.158 12.27 0.00 41.57 4.93
51 52 1.440938 CTCTCTCCCTACGGTGAGCG 61.441 65.000 1.13 1.13 45.60 5.03
52 53 1.104577 CCTCTCTCCCTACGGTGAGC 61.105 65.000 5.29 0.00 45.60 4.26
53 54 0.466555 CCCTCTCTCCCTACGGTGAG 60.467 65.000 4.08 4.08 46.81 3.51
54 55 1.212934 ACCCTCTCTCCCTACGGTGA 61.213 60.000 0.00 0.00 0.00 4.02
55 56 0.752376 GACCCTCTCTCCCTACGGTG 60.752 65.000 0.00 0.00 0.00 4.94
56 57 0.920271 AGACCCTCTCTCCCTACGGT 60.920 60.000 0.00 0.00 0.00 4.83
57 58 1.138568 TAGACCCTCTCTCCCTACGG 58.861 60.000 0.00 0.00 0.00 4.02
58 59 1.540797 CGTAGACCCTCTCTCCCTACG 60.541 61.905 0.00 0.00 43.96 3.51
59 60 1.815021 GCGTAGACCCTCTCTCCCTAC 60.815 61.905 0.00 0.00 0.00 3.18
60 61 0.473326 GCGTAGACCCTCTCTCCCTA 59.527 60.000 0.00 0.00 0.00 3.53
61 62 1.227946 GCGTAGACCCTCTCTCCCT 59.772 63.158 0.00 0.00 0.00 4.20
62 63 1.829096 GGCGTAGACCCTCTCTCCC 60.829 68.421 0.00 0.00 0.00 4.30
63 64 2.188161 CGGCGTAGACCCTCTCTCC 61.188 68.421 0.00 0.00 0.00 3.71
64 65 2.188161 CCGGCGTAGACCCTCTCTC 61.188 68.421 6.01 0.00 0.00 3.20
65 66 2.124236 CCGGCGTAGACCCTCTCT 60.124 66.667 6.01 0.00 0.00 3.10
66 67 2.439883 ACCGGCGTAGACCCTCTC 60.440 66.667 6.01 0.00 0.00 3.20
67 68 2.754658 CACCGGCGTAGACCCTCT 60.755 66.667 6.01 0.00 0.00 3.69
68 69 4.509737 GCACCGGCGTAGACCCTC 62.510 72.222 6.01 0.00 0.00 4.30
85 86 2.635787 TATCTCGGGGACTCGGGGTG 62.636 65.000 0.00 0.00 0.00 4.61
86 87 2.389449 TATCTCGGGGACTCGGGGT 61.389 63.158 0.00 0.00 0.00 4.95
87 88 1.902432 GTATCTCGGGGACTCGGGG 60.902 68.421 0.00 0.00 0.00 5.73
88 89 2.259439 CGTATCTCGGGGACTCGGG 61.259 68.421 0.00 0.00 35.71 5.14
89 90 3.341848 CGTATCTCGGGGACTCGG 58.658 66.667 0.00 0.00 35.71 4.63
98 99 1.609555 CCTTTCTCCCTCCGTATCTCG 59.390 57.143 0.00 0.00 39.52 4.04
99 100 2.624364 GTCCTTTCTCCCTCCGTATCTC 59.376 54.545 0.00 0.00 0.00 2.75
100 101 2.024273 TGTCCTTTCTCCCTCCGTATCT 60.024 50.000 0.00 0.00 0.00 1.98
101 102 2.385803 TGTCCTTTCTCCCTCCGTATC 58.614 52.381 0.00 0.00 0.00 2.24
102 103 2.544844 TGTCCTTTCTCCCTCCGTAT 57.455 50.000 0.00 0.00 0.00 3.06
103 104 2.176889 CTTGTCCTTTCTCCCTCCGTA 58.823 52.381 0.00 0.00 0.00 4.02
104 105 0.977395 CTTGTCCTTTCTCCCTCCGT 59.023 55.000 0.00 0.00 0.00 4.69
105 106 1.066787 GTCTTGTCCTTTCTCCCTCCG 60.067 57.143 0.00 0.00 0.00 4.63
106 107 1.279558 GGTCTTGTCCTTTCTCCCTCC 59.720 57.143 0.00 0.00 0.00 4.30
110 111 2.553247 CCTTGGGTCTTGTCCTTTCTCC 60.553 54.545 0.00 0.00 0.00 3.71
164 167 0.469070 AGGATCAGTCATCAGCTGCC 59.531 55.000 9.47 0.43 34.21 4.85
165 168 2.328819 AAGGATCAGTCATCAGCTGC 57.671 50.000 9.47 0.00 34.21 5.25
166 169 2.355132 GCAAAGGATCAGTCATCAGCTG 59.645 50.000 7.63 7.63 32.33 4.24
168 171 1.329906 CGCAAAGGATCAGTCATCAGC 59.670 52.381 0.00 0.00 32.33 4.26
169 172 2.350804 CACGCAAAGGATCAGTCATCAG 59.649 50.000 0.00 0.00 32.33 2.90
170 173 2.349590 CACGCAAAGGATCAGTCATCA 58.650 47.619 0.00 0.00 32.33 3.07
172 175 1.679944 CCCACGCAAAGGATCAGTCAT 60.680 52.381 0.00 0.00 0.00 3.06
173 176 0.321564 CCCACGCAAAGGATCAGTCA 60.322 55.000 0.00 0.00 0.00 3.41
175 178 1.675641 GCCCACGCAAAGGATCAGT 60.676 57.895 0.00 0.00 34.03 3.41
177 180 2.361104 GGCCCACGCAAAGGATCA 60.361 61.111 0.00 0.00 36.38 2.92
207 214 3.100862 GATTCTTCTGCACGCCCGC 62.101 63.158 0.00 0.00 0.00 6.13
209 216 1.131315 GAAAGATTCTTCTGCACGCCC 59.869 52.381 0.00 0.00 30.72 6.13
210 217 1.131315 GGAAAGATTCTTCTGCACGCC 59.869 52.381 0.00 0.00 30.72 5.68
211 218 2.079925 AGGAAAGATTCTTCTGCACGC 58.920 47.619 0.00 0.00 30.72 5.34
212 219 3.126000 GGAAGGAAAGATTCTTCTGCACG 59.874 47.826 0.00 0.00 39.30 5.34
214 221 3.074390 TGGGAAGGAAAGATTCTTCTGCA 59.926 43.478 0.00 0.00 39.30 4.41
217 224 4.339748 GCTTGGGAAGGAAAGATTCTTCT 58.660 43.478 0.00 0.00 39.30 2.85
218 225 3.445450 GGCTTGGGAAGGAAAGATTCTTC 59.555 47.826 0.00 0.00 38.79 2.87
265 273 6.409185 CGATTCCGATTCGATTCTTTCTTTTG 59.591 38.462 7.83 0.00 38.88 2.44
340 358 4.118995 ATGGGCACGCAACGCATG 62.119 61.111 2.34 0.00 39.03 4.06
341 359 4.118995 CATGGGCACGCAACGCAT 62.119 61.111 0.00 0.00 40.91 4.73
380 398 3.546417 CGAACTGACTGTACTATCGAGGC 60.546 52.174 0.00 0.00 0.00 4.70
381 399 3.622163 ACGAACTGACTGTACTATCGAGG 59.378 47.826 10.17 0.00 33.42 4.63
387 405 3.058432 GCTGACACGAACTGACTGTACTA 60.058 47.826 0.00 0.00 0.00 1.82
391 415 0.595053 CGCTGACACGAACTGACTGT 60.595 55.000 0.00 0.00 34.06 3.55
413 437 0.745468 CTGGGCTACGAGTAGGGTTC 59.255 60.000 11.69 0.00 33.87 3.62
488 512 2.066999 GGGTGCTGGGAGTAGGAGG 61.067 68.421 0.00 0.00 0.00 4.30
609 682 6.415206 TGGAAGATAACGTAATTAGGAGGG 57.585 41.667 11.96 0.00 0.00 4.30
694 769 0.036294 GGAAAGGGACCGGACTGAAG 60.036 60.000 9.46 0.00 0.00 3.02
695 770 1.486145 GGGAAAGGGACCGGACTGAA 61.486 60.000 9.46 0.00 0.00 3.02
727 802 2.380084 TCGTTATCGAAGCTTTGGCT 57.620 45.000 13.87 4.60 43.34 4.75
807 886 0.321671 CGCCACAAGGAGAAGGAGAA 59.678 55.000 0.00 0.00 36.74 2.87
808 887 1.975327 CGCCACAAGGAGAAGGAGA 59.025 57.895 0.00 0.00 36.74 3.71
813 892 4.697756 CGGGCGCCACAAGGAGAA 62.698 66.667 30.85 0.00 36.74 2.87
938 1810 2.287849 TGCTCTCGTCTGTCAGTTTCAG 60.288 50.000 0.00 0.00 0.00 3.02
939 1811 1.681264 TGCTCTCGTCTGTCAGTTTCA 59.319 47.619 0.00 0.00 0.00 2.69
942 1814 1.539388 CTCTGCTCTCGTCTGTCAGTT 59.461 52.381 0.00 0.00 0.00 3.16
945 1817 1.447945 CTCTCTGCTCTCGTCTGTCA 58.552 55.000 0.00 0.00 0.00 3.58
968 1840 1.079127 TCGGCTGGCTCAAAGCTAC 60.079 57.895 0.00 0.00 41.99 3.58
969 1841 1.219124 CTCGGCTGGCTCAAAGCTA 59.781 57.895 0.00 0.00 41.99 3.32
970 1842 2.046507 CTCGGCTGGCTCAAAGCT 60.047 61.111 0.00 0.00 41.99 3.74
971 1843 3.808656 GCTCGGCTGGCTCAAAGC 61.809 66.667 0.00 0.00 41.46 3.51
974 1846 4.441695 CTCGCTCGGCTGGCTCAA 62.442 66.667 0.00 0.00 0.00 3.02
980 1852 3.898509 CTCTCCCTCGCTCGGCTG 61.899 72.222 0.00 0.00 0.00 4.85
981 1853 4.116585 TCTCTCCCTCGCTCGGCT 62.117 66.667 0.00 0.00 0.00 5.52
982 1854 3.591835 CTCTCTCCCTCGCTCGGC 61.592 72.222 0.00 0.00 0.00 5.54
983 1855 1.228124 ATCTCTCTCCCTCGCTCGG 60.228 63.158 0.00 0.00 0.00 4.63
990 1862 0.267356 CCCCCTTCATCTCTCTCCCT 59.733 60.000 0.00 0.00 0.00 4.20
1396 2283 4.699522 GAACTCCTTGGCGGCGGT 62.700 66.667 9.78 0.00 0.00 5.68
1749 2664 3.755628 GACGACCCTGCCTGCGTA 61.756 66.667 0.00 0.00 37.07 4.42
1796 2720 2.975536 CAACAATGCCAGCCAGGG 59.024 61.111 0.00 0.00 38.09 4.45
1839 2775 5.182001 GTCCATGTTCACTCAAAGCTACAAT 59.818 40.000 0.00 0.00 0.00 2.71
1957 2912 1.528586 CGCATGGATCCGAATCTTCAC 59.471 52.381 7.39 0.00 32.12 3.18
1993 2967 1.442769 TTTGCAGGAATCGTGAGCTC 58.557 50.000 6.82 6.82 0.00 4.09
1994 2968 2.119801 ATTTGCAGGAATCGTGAGCT 57.880 45.000 7.17 0.00 0.00 4.09
2000 2974 3.673746 TCGCTTAATTTGCAGGAATCG 57.326 42.857 0.00 0.00 0.00 3.34
2003 2977 3.936453 ACGTATCGCTTAATTTGCAGGAA 59.064 39.130 0.00 0.00 0.00 3.36
2023 3024 0.110823 GTTACGCTTTGCACCAGACG 60.111 55.000 0.00 0.00 0.00 4.18
2024 3025 1.069906 CAGTTACGCTTTGCACCAGAC 60.070 52.381 0.00 0.00 0.00 3.51
2047 3048 3.868757 TGTCACTAGTAATTCAGCGCT 57.131 42.857 2.64 2.64 0.00 5.92
2073 3074 3.517901 AGTGGTCCTGGTAAATTCGATGA 59.482 43.478 0.00 0.00 0.00 2.92
2088 3089 6.591935 TGGATTTATCACATTAGAGTGGTCC 58.408 40.000 0.00 0.00 39.93 4.46
2089 3090 8.398665 GTTTGGATTTATCACATTAGAGTGGTC 58.601 37.037 0.00 0.00 39.93 4.02
2177 3181 1.423845 GCGTCGGCACTGGTTTATG 59.576 57.895 0.00 0.00 39.62 1.90
2190 3194 3.853330 CAATGCAGTCGGGCGTCG 61.853 66.667 0.00 0.00 40.90 5.12
2191 3195 2.740714 GACAATGCAGTCGGGCGTC 61.741 63.158 0.00 0.00 36.28 5.19
2192 3196 2.731691 AAGACAATGCAGTCGGGCGT 62.732 55.000 0.00 0.00 43.24 5.68
2193 3197 2.034879 AAGACAATGCAGTCGGGCG 61.035 57.895 0.00 0.00 43.24 6.13
2194 3198 1.237285 ACAAGACAATGCAGTCGGGC 61.237 55.000 0.00 0.00 43.24 6.13
2195 3199 2.093306 TACAAGACAATGCAGTCGGG 57.907 50.000 0.00 0.00 43.24 5.14
2313 3325 1.078072 TGCCACACCACGTTGTTCT 60.078 52.632 0.00 0.00 0.00 3.01
2353 3365 5.858381 ACACAGCTTAATTTCTCAGTCTGA 58.142 37.500 1.78 1.78 0.00 3.27
2378 3390 5.231702 ACCCGAATCTTTTGTAGGTACAA 57.768 39.130 0.00 0.00 43.80 2.41
2379 3391 4.895668 ACCCGAATCTTTTGTAGGTACA 57.104 40.909 0.00 0.00 0.00 2.90
2380 3392 5.106436 CCAAACCCGAATCTTTTGTAGGTAC 60.106 44.000 0.00 0.00 0.00 3.34
2417 3440 0.387202 CGAGTCCTGAGCGATTGGAT 59.613 55.000 0.00 0.00 32.03 3.41
2426 3533 4.440802 CCTCTTAATTCCACGAGTCCTGAG 60.441 50.000 0.00 0.00 0.00 3.35
2430 3537 2.093658 TGCCTCTTAATTCCACGAGTCC 60.094 50.000 0.00 0.00 0.00 3.85
2436 3543 4.572795 GCTTCTACTGCCTCTTAATTCCAC 59.427 45.833 0.00 0.00 0.00 4.02
2510 3639 6.546484 TCCTGATGGTCTTCTTTTCTGAAAT 58.454 36.000 3.31 0.00 34.23 2.17
2527 3656 1.176527 ACGGCCAATGTTTCCTGATG 58.823 50.000 2.24 0.00 0.00 3.07
2545 3734 0.391130 TGAAGATGGTGCACGGCTAC 60.391 55.000 11.45 0.00 0.00 3.58
2546 3735 0.108186 CTGAAGATGGTGCACGGCTA 60.108 55.000 11.45 0.00 0.00 3.93
2548 3737 3.044059 GCTGAAGATGGTGCACGGC 62.044 63.158 11.45 2.25 0.00 5.68
2566 3763 2.762535 ATTATACGGGGCAATCGAGG 57.237 50.000 0.00 0.00 0.00 4.63
2620 3817 6.767456 ACCCTGAATTTTGAAAATGCATACA 58.233 32.000 11.51 0.00 0.00 2.29
2665 3862 0.751277 TCACTGCCACACAAACTGGG 60.751 55.000 0.00 0.00 0.00 4.45
2673 3870 1.571460 CTTCGCTTCACTGCCACAC 59.429 57.895 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.