Multiple sequence alignment - TraesCS1D01G098600

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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 TraesCS1D01G098600 chr1D 100.000 7259 0 0 1 7259 85642931 85650189 0.000000e+00 13405.0
1 TraesCS1D01G098600 chr1A 96.067 6001 140 32 743 6699 80189946 80195894 0.000000e+00 9686.0
2 TraesCS1D01G098600 chr1A 93.662 852 46 7 1 845 80188511 80189361 0.000000e+00 1267.0
3 TraesCS1D01G098600 chr1A 89.823 226 22 1 6636 6860 396280782 396281007 9.210000e-74 289.0
4 TraesCS1D01G098600 chr1B 94.137 5884 217 44 1 5826 138035865 138041678 0.000000e+00 8837.0
5 TraesCS1D01G098600 chr1B 95.598 886 34 4 5782 6666 138041690 138042571 0.000000e+00 1415.0
6 TraesCS1D01G098600 chr1B 94.177 395 23 0 6865 7259 138042765 138043159 2.900000e-168 603.0
7 TraesCS1D01G098600 chr1B 90.000 60 4 2 1540 1599 48112014 48111957 7.810000e-10 76.8
8 TraesCS1D01G098600 chr7B 88.776 392 44 0 6867 7258 13321243 13320852 1.420000e-131 481.0
9 TraesCS1D01G098600 chr7B 89.640 222 22 1 6639 6860 13321532 13321312 1.540000e-71 281.0
10 TraesCS1D01G098600 chr7B 90.000 60 4 2 1540 1599 720572147 720572204 7.810000e-10 76.8
11 TraesCS1D01G098600 chr6D 87.629 388 48 0 6871 7258 386638305 386638692 1.110000e-122 451.0
12 TraesCS1D01G098600 chr6D 88.739 222 22 3 6640 6860 386638013 386638232 1.200000e-67 268.0
13 TraesCS1D01G098600 chr6D 91.935 62 5 0 4132 4193 313014239 313014300 3.610000e-13 87.9
14 TraesCS1D01G098600 chr6A 87.629 388 48 0 6871 7258 52699918 52700305 1.110000e-122 451.0
15 TraesCS1D01G098600 chr6A 81.215 181 25 5 256 428 592460412 592460233 3.530000e-28 137.0
16 TraesCS1D01G098600 chr6A 86.765 68 3 4 1540 1601 109494806 109494873 3.630000e-08 71.3
17 TraesCS1D01G098600 chr5A 87.629 388 48 0 6871 7258 417294886 417295273 1.110000e-122 451.0
18 TraesCS1D01G098600 chr5A 88.940 217 23 1 6636 6851 417294588 417294804 4.320000e-67 267.0
19 TraesCS1D01G098600 chr2A 87.371 388 49 0 6871 7258 554048149 554047762 5.170000e-121 446.0
20 TraesCS1D01G098600 chr2D 86.990 392 50 1 6867 7258 370049303 370048913 2.400000e-119 440.0
21 TraesCS1D01G098600 chr2D 89.686 223 22 1 6639 6860 370049594 370049372 4.290000e-72 283.0
22 TraesCS1D01G098600 chr2D 100.000 46 0 0 1540 1585 20772871 20772826 1.300000e-12 86.1
23 TraesCS1D01G098600 chr3A 87.113 388 48 2 6871 7258 59463541 59463156 8.650000e-119 438.0
24 TraesCS1D01G098600 chr3A 86.260 393 52 2 6867 7258 82464084 82463693 6.730000e-115 425.0
25 TraesCS1D01G098600 chr3A 89.140 221 21 3 6641 6860 59463831 59463613 9.280000e-69 272.0
26 TraesCS1D01G098600 chr5B 91.441 222 17 2 6640 6860 369368013 369367793 3.290000e-78 303.0
27 TraesCS1D01G098600 chr4B 90.950 221 17 3 6640 6859 119851938 119851720 1.980000e-75 294.0
28 TraesCS1D01G098600 chr2B 89.593 221 22 1 6639 6858 626297947 626298167 5.550000e-71 279.0
29 TraesCS1D01G098600 chr7D 100.000 44 0 0 1540 1583 290544897 290544854 1.680000e-11 82.4
30 TraesCS1D01G098600 chr7A 100.000 44 0 0 1540 1583 328987844 328987801 1.680000e-11 82.4
31 TraesCS1D01G098600 chr6B 90.625 64 1 3 1540 1598 174971073 174971136 6.040000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G098600 chr1D 85642931 85650189 7258 False 13405.000000 13405 100.000000 1 7259 1 chr1D.!!$F1 7258
1 TraesCS1D01G098600 chr1A 80188511 80195894 7383 False 5476.500000 9686 94.864500 1 6699 2 chr1A.!!$F2 6698
2 TraesCS1D01G098600 chr1B 138035865 138043159 7294 False 3618.333333 8837 94.637333 1 7259 3 chr1B.!!$F1 7258
3 TraesCS1D01G098600 chr7B 13320852 13321532 680 True 381.000000 481 89.208000 6639 7258 2 chr7B.!!$R1 619
4 TraesCS1D01G098600 chr6D 386638013 386638692 679 False 359.500000 451 88.184000 6640 7258 2 chr6D.!!$F2 618
5 TraesCS1D01G098600 chr5A 417294588 417295273 685 False 359.000000 451 88.284500 6636 7258 2 chr5A.!!$F1 622
6 TraesCS1D01G098600 chr2D 370048913 370049594 681 True 361.500000 440 88.338000 6639 7258 2 chr2D.!!$R2 619
7 TraesCS1D01G098600 chr3A 59463156 59463831 675 True 355.000000 438 88.126500 6641 7258 2 chr3A.!!$R2 617

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
189 190 1.440145 GCGGGTGCTAGCCATCTTTC 61.440 60.000 13.29 0.0 34.89 2.62 F
1251 1963 0.879090 GGTTGGAATTTCGCGGTTCT 59.121 50.000 6.13 0.0 0.00 3.01 F
2008 2739 1.753073 AGTAGCAATGCCAGCCATTTC 59.247 47.619 0.00 0.0 42.15 2.17 F
3209 3949 0.393537 CATGCAAGACTGGACCTCCC 60.394 60.000 0.00 0.0 34.29 4.30 F
3212 3952 0.606673 GCAAGACTGGACCTCCCAAC 60.607 60.000 0.00 0.0 46.07 3.77 F
3213 3953 0.764890 CAAGACTGGACCTCCCAACA 59.235 55.000 0.00 0.0 46.07 3.33 F
3214 3954 0.765510 AAGACTGGACCTCCCAACAC 59.234 55.000 0.00 0.0 46.07 3.32 F
4821 5578 1.178276 ACCTGTTGTCCGCACAAAAA 58.822 45.000 0.00 0.0 44.32 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 2405 0.034186 CTGCCCTGATGCCCAGTAAA 60.034 55.000 3.06 0.0 41.33 2.01 R
2362 3093 6.364165 GCGCAAAATTGAATATATCTGCATGT 59.636 34.615 0.30 0.0 0.00 3.21 R
3943 4683 2.238353 GCGCTGAGCTGAAGTCAAA 58.762 52.632 1.78 0.0 44.04 2.69 R
4390 5147 0.823356 TGCCACCTCCAACTTTGCTC 60.823 55.000 0.00 0.0 0.00 4.26 R
4969 5726 1.131126 CAAGCATTAGACACAAGGGCG 59.869 52.381 0.00 0.0 0.00 6.13 R
5063 5823 4.387559 GCCCAATTTGGTGAAACGAATAAC 59.612 41.667 14.26 0.0 38.12 1.89 R
5064 5824 4.561105 GCCCAATTTGGTGAAACGAATAA 58.439 39.130 14.26 0.0 38.12 1.40 R
6794 7613 0.036388 GCTTTCGTCCATCTCCACCA 60.036 55.000 0.00 0.0 0.00 4.17 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
55 56 4.144703 GTCCTTCGGCCCCGTCTC 62.145 72.222 6.61 0.00 40.74 3.36
126 127 4.350368 TTCTAGGAAGTGTTGCATGTCA 57.650 40.909 0.00 0.00 0.00 3.58
166 167 2.813474 GTGGCGCGTGCTATGACA 60.813 61.111 21.89 6.84 42.25 3.58
189 190 1.440145 GCGGGTGCTAGCCATCTTTC 61.440 60.000 13.29 0.00 34.89 2.62
272 273 4.047059 GTGACTTCCCGTCCGCGA 62.047 66.667 8.23 0.00 42.13 5.87
360 362 2.797278 GCCATGGTCGTCGGGATCT 61.797 63.158 14.67 0.00 0.00 2.75
413 415 1.551019 GGGTCTCCTTGTAAGGCCGT 61.551 60.000 5.77 0.00 46.06 5.68
577 583 7.681939 ACTAAAGGCAAATATGAACTTTCGA 57.318 32.000 0.00 0.00 36.92 3.71
581 587 4.458989 AGGCAAATATGAACTTTCGAAGCA 59.541 37.500 0.00 0.00 0.00 3.91
607 613 3.890147 AGGTCGGCTGGTCTAAAGTATAG 59.110 47.826 0.00 0.00 0.00 1.31
618 624 6.203530 TGGTCTAAAGTATAGTCGTACCATCG 59.796 42.308 0.00 0.00 29.85 3.84
629 635 5.531634 AGTCGTACCATCGTCAAAACTAAA 58.468 37.500 0.00 0.00 0.00 1.85
726 735 4.633126 CCGATTCTACATATTCTGGGCATG 59.367 45.833 0.00 0.00 0.00 4.06
858 1559 7.441890 TTCAAAAAGTAATCATCACGGCTAA 57.558 32.000 0.00 0.00 0.00 3.09
859 1560 6.837992 TCAAAAAGTAATCATCACGGCTAAC 58.162 36.000 0.00 0.00 0.00 2.34
860 1561 5.813080 AAAAGTAATCATCACGGCTAACC 57.187 39.130 0.00 0.00 0.00 2.85
942 1644 3.041940 GCGTCAGACCACCAACCG 61.042 66.667 0.00 0.00 0.00 4.44
1251 1963 0.879090 GGTTGGAATTTCGCGGTTCT 59.121 50.000 6.13 0.00 0.00 3.01
1322 2034 2.486191 GGCTATGAGATTGGGTGAGGTG 60.486 54.545 0.00 0.00 0.00 4.00
1323 2035 2.486191 GCTATGAGATTGGGTGAGGTGG 60.486 54.545 0.00 0.00 0.00 4.61
1442 2154 2.821366 GTCGCCCATGACCTGCAG 60.821 66.667 6.78 6.78 32.61 4.41
1593 2307 5.880054 TGCAGTTCAATTTAGTTAGAGGC 57.120 39.130 0.00 0.00 0.00 4.70
1685 2405 6.097915 TCCTTAGTTGATTCGACTCTGTTT 57.902 37.500 9.90 0.00 29.93 2.83
1767 2498 4.157289 GTGGCATCACTGATCTGTTTGAAT 59.843 41.667 13.54 0.79 40.58 2.57
1874 2605 6.136541 AGTTTTTACAAGAAGGTGAAGCAG 57.863 37.500 0.00 0.00 0.00 4.24
1911 2642 3.849911 TGGATACAGAAGCTCTTGTTCG 58.150 45.455 8.19 0.00 46.17 3.95
2008 2739 1.753073 AGTAGCAATGCCAGCCATTTC 59.247 47.619 0.00 0.00 42.15 2.17
2027 2758 4.780275 TTCGGATTTCACATTGCATCAA 57.220 36.364 0.00 0.00 0.00 2.57
2028 2759 4.780275 TCGGATTTCACATTGCATCAAA 57.220 36.364 0.00 0.00 0.00 2.69
2362 3093 4.877251 GCTTGGTGTCCGTATTTTATACCA 59.123 41.667 0.00 0.00 35.14 3.25
2427 3158 6.126768 CCCTAATGTTATCTGACTTCCTTGGA 60.127 42.308 0.00 0.00 0.00 3.53
2428 3159 7.420680 CCCTAATGTTATCTGACTTCCTTGGAT 60.421 40.741 0.00 0.00 0.00 3.41
2429 3160 8.651389 CCTAATGTTATCTGACTTCCTTGGATA 58.349 37.037 0.00 0.00 0.00 2.59
2432 3163 9.927081 AATGTTATCTGACTTCCTTGGATAATT 57.073 29.630 0.00 0.00 33.43 1.40
2511 3248 5.444122 GTTTTGTGTCTAACAGCTGTCATC 58.556 41.667 21.95 11.54 40.74 2.92
2542 3279 5.464389 AGTTTCTGCATGTTTGAATTTCTGC 59.536 36.000 0.00 0.00 0.00 4.26
3206 3946 2.575279 AGAATCATGCAAGACTGGACCT 59.425 45.455 0.00 0.00 0.00 3.85
3208 3948 0.615331 TCATGCAAGACTGGACCTCC 59.385 55.000 0.00 0.00 0.00 4.30
3209 3949 0.393537 CATGCAAGACTGGACCTCCC 60.394 60.000 0.00 0.00 34.29 4.30
3210 3950 0.842030 ATGCAAGACTGGACCTCCCA 60.842 55.000 0.00 0.00 44.25 4.37
3211 3951 1.059584 TGCAAGACTGGACCTCCCAA 61.060 55.000 0.00 0.00 46.07 4.12
3212 3952 0.606673 GCAAGACTGGACCTCCCAAC 60.607 60.000 0.00 0.00 46.07 3.77
3213 3953 0.764890 CAAGACTGGACCTCCCAACA 59.235 55.000 0.00 0.00 46.07 3.33
3214 3954 0.765510 AAGACTGGACCTCCCAACAC 59.234 55.000 0.00 0.00 46.07 3.32
3218 3958 2.505819 GACTGGACCTCCCAACACATAT 59.494 50.000 0.00 0.00 46.07 1.78
3219 3959 3.709653 GACTGGACCTCCCAACACATATA 59.290 47.826 0.00 0.00 46.07 0.86
3409 4149 3.199946 TCCTTCAACCTCATGTATGGACC 59.800 47.826 8.63 0.00 0.00 4.46
3817 4557 5.858581 GTGCAAATTTGGTCATCTTGTACTC 59.141 40.000 19.47 0.00 32.13 2.59
3819 4559 6.939730 TGCAAATTTGGTCATCTTGTACTCTA 59.060 34.615 19.47 0.00 0.00 2.43
3830 4570 9.719279 GTCATCTTGTACTCTACAGTGTAATAC 57.281 37.037 4.21 7.97 40.24 1.89
4013 4753 6.662865 TTCTTTTGCCATTGAGGTCATTTA 57.337 33.333 0.00 0.00 40.61 1.40
4055 4795 5.123186 TGTTTTTCATTCCCGTGCAGTATAG 59.877 40.000 0.00 0.00 0.00 1.31
4207 4947 7.596494 TCTTCGTCGAAAGAGGTTAAAATCTA 58.404 34.615 9.30 0.00 45.61 1.98
4390 5147 1.364721 TTGATGAACATGTACGCCGG 58.635 50.000 0.00 0.00 0.00 6.13
4435 5192 4.221703 AGTCGTGAGATGGATTTTGAGAGT 59.778 41.667 0.00 0.00 45.19 3.24
4689 5446 1.282157 GTACTGATGCAACCCCCTTCT 59.718 52.381 0.00 0.00 0.00 2.85
4819 5576 2.039818 TTACCTGTTGTCCGCACAAA 57.960 45.000 0.00 0.00 44.32 2.83
4821 5578 1.178276 ACCTGTTGTCCGCACAAAAA 58.822 45.000 0.00 0.00 44.32 1.94
4958 5715 8.027189 GCAGTAATTTATTCGGAAGGAAAACTT 58.973 33.333 0.00 0.00 43.65 2.66
4969 5726 7.590279 TCGGAAGGAAAACTTTATTCAATGAC 58.410 34.615 0.00 0.00 40.21 3.06
5062 5822 6.837048 ACAGGGGTTTAAACAATTCTGTACTT 59.163 34.615 19.57 3.57 33.45 2.24
5063 5823 7.145323 CAGGGGTTTAAACAATTCTGTACTTG 58.855 38.462 19.57 0.00 33.45 3.16
5064 5824 6.837048 AGGGGTTTAAACAATTCTGTACTTGT 59.163 34.615 19.57 0.00 37.19 3.16
5117 5877 4.392940 AGTGTTCTTCATGTTCTGGGAAG 58.607 43.478 0.00 0.00 39.44 3.46
5272 6032 7.148018 ACAGGCAGGACATCATTGTTTTAATAG 60.148 37.037 0.00 0.00 35.79 1.73
5327 6087 5.934402 TTACACTCTCAAGTTCCCTATCC 57.066 43.478 0.00 0.00 31.71 2.59
5365 6126 7.119116 CAGTTGCACTATGTTAGGTATGAAACA 59.881 37.037 0.00 0.00 39.73 2.83
5381 6142 6.712241 ATGAAACATGAAGTGAGTAAGTCG 57.288 37.500 0.00 0.00 0.00 4.18
5425 6186 3.955524 TGAACTAAACTTGGGGTTGGA 57.044 42.857 0.00 0.00 38.29 3.53
5454 6215 3.595190 ACTCTAAAGCAGGTTTTGGGT 57.405 42.857 6.26 6.26 30.61 4.51
5532 6293 5.220931 GCTGCATGAATAGGGAACTTTACTG 60.221 44.000 0.00 0.00 43.67 2.74
5601 6362 7.332430 CACAATCATCTAACAACCATTTGCATT 59.668 33.333 0.00 0.00 36.00 3.56
6066 6883 2.084546 GGGAACTACGAGCTTTGCATT 58.915 47.619 0.00 0.00 0.00 3.56
6246 7063 2.461695 CAGGAAGAGGAGGAGCAAGTA 58.538 52.381 0.00 0.00 0.00 2.24
6307 7124 0.829990 TGTCTCAACACTGGTGCAGA 59.170 50.000 0.17 0.00 35.18 4.26
6327 7144 3.690745 GCATGTGCTTCCTGCCTT 58.309 55.556 0.00 0.00 42.00 4.35
6339 7156 2.901249 TCCTGCCTTCGTTATTGTAGC 58.099 47.619 0.00 0.00 0.00 3.58
6418 7235 5.671493 AGTGGGTTAAATCCGAGTGATTAG 58.329 41.667 0.00 0.00 42.97 1.73
6441 7258 1.402613 GTTTGTAAGTGTGGCGTGGTT 59.597 47.619 0.00 0.00 0.00 3.67
6470 7287 5.658634 AGGCTAACTGTGTATCATTCTCAGA 59.341 40.000 0.81 0.00 32.82 3.27
6496 7313 1.593196 TTGAACGGTGAAAGCCTCAG 58.407 50.000 0.00 0.00 33.60 3.35
6560 7377 4.084537 AGTGCGTGTATTTTCTGTTTCTCG 60.085 41.667 0.00 0.00 0.00 4.04
6582 7399 3.119849 GCACCGATTTGTAACTGCAGAAT 60.120 43.478 23.35 9.17 0.00 2.40
6637 7455 2.684881 ACCTGATGAATTTGCCGATGTC 59.315 45.455 0.00 0.00 0.00 3.06
6664 7482 2.096248 TGTTGAAACGGAGGCAAAAGT 58.904 42.857 0.00 0.00 0.00 2.66
6666 7484 3.695060 TGTTGAAACGGAGGCAAAAGTTA 59.305 39.130 0.00 0.00 0.00 2.24
6667 7485 4.158025 TGTTGAAACGGAGGCAAAAGTTAA 59.842 37.500 0.00 0.00 0.00 2.01
6668 7486 4.985538 TGAAACGGAGGCAAAAGTTAAA 57.014 36.364 0.00 0.00 0.00 1.52
6680 7498 5.639082 GGCAAAAGTTAAACCTCATCCATTG 59.361 40.000 0.00 0.00 0.00 2.82
6681 7499 5.639082 GCAAAAGTTAAACCTCATCCATTGG 59.361 40.000 0.00 0.00 0.00 3.16
6751 7570 3.541711 GATTACTCGCGCGCAATAAAAT 58.458 40.909 32.61 21.53 0.00 1.82
6851 7670 4.261801 GCACTCTTATGCTTAAGAACCCA 58.738 43.478 19.30 0.00 42.46 4.51
6860 7679 3.008157 TGCTTAAGAACCCATACGTTCCA 59.992 43.478 6.67 0.00 42.63 3.53
6861 7680 4.004982 GCTTAAGAACCCATACGTTCCAA 58.995 43.478 6.67 0.00 42.63 3.53
6862 7681 4.456566 GCTTAAGAACCCATACGTTCCAAA 59.543 41.667 6.67 0.00 42.63 3.28
6878 7759 1.817941 AAACTGTCGGCGCAAGTGT 60.818 52.632 10.83 6.83 41.68 3.55
6899 7780 1.150536 GCCCACCACTCTTCAACCA 59.849 57.895 0.00 0.00 0.00 3.67
6917 7798 1.303317 ATGTCGAACAAGGGCCACC 60.303 57.895 6.18 0.00 0.00 4.61
7002 7883 5.878669 TGTAGCGACACTTGTAGAAGAGATA 59.121 40.000 6.63 0.00 32.98 1.98
7080 7961 0.588252 CGCTTTGCCAATCTATCCGG 59.412 55.000 0.00 0.00 0.00 5.14
7228 8109 2.443390 GCCGAGTACTGCCCCCTA 60.443 66.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.134521 GGACAATATCCTCACCACGCA 60.135 52.381 0.00 0.00 45.22 5.24
126 127 3.655211 CCACCCCAAGAGCCAGCT 61.655 66.667 0.00 0.00 0.00 4.24
189 190 0.392998 AGCGTATGTGCCCCTGAAAG 60.393 55.000 0.00 0.00 34.65 2.62
272 273 5.013599 CCTTGAATCTAGGGCTAGCCTATTT 59.986 44.000 32.18 18.27 36.10 1.40
286 287 3.556999 CTCCTCCTCGACCTTGAATCTA 58.443 50.000 0.00 0.00 0.00 1.98
326 327 2.391389 GGCTTTCAAGACGAGCCGG 61.391 63.158 0.00 0.00 45.64 6.13
339 341 1.910580 ATCCCGACGACCATGGCTTT 61.911 55.000 13.04 0.00 0.00 3.51
517 523 6.803642 AGTAATAACGTGTGAATAGAGGACC 58.196 40.000 0.00 0.00 0.00 4.46
577 583 1.377725 CCAGCCGACCTTGATGCTT 60.378 57.895 0.00 0.00 30.08 3.91
581 587 1.568504 TTAGACCAGCCGACCTTGAT 58.431 50.000 0.00 0.00 0.00 2.57
607 613 5.827568 TTTAGTTTTGACGATGGTACGAC 57.172 39.130 0.00 0.00 37.03 4.34
858 1559 3.735591 AGCAGTGTGTTTATTGTACGGT 58.264 40.909 0.00 0.00 0.00 4.83
859 1560 4.742438 AAGCAGTGTGTTTATTGTACGG 57.258 40.909 0.00 0.00 0.00 4.02
860 1561 4.378616 GCAAAGCAGTGTGTTTATTGTACG 59.621 41.667 0.00 0.00 0.00 3.67
942 1644 0.036294 GGGACTGTAGCTGGTTGTCC 60.036 60.000 16.55 16.55 44.51 4.02
1206 1918 1.698506 AGCCTAGCCTAGCACTACAG 58.301 55.000 0.00 0.00 0.00 2.74
1231 1943 0.109458 GAACCGCGAAATTCCAACCC 60.109 55.000 8.23 0.00 0.00 4.11
1251 1963 0.177141 CTACCGCCATTCCCGAAGAA 59.823 55.000 0.00 0.00 39.32 2.52
1322 2034 2.359478 CTAACACCCGGCACCACC 60.359 66.667 0.00 0.00 0.00 4.61
1323 2035 1.375523 CTCTAACACCCGGCACCAC 60.376 63.158 0.00 0.00 0.00 4.16
1355 2067 1.264557 ACGGTAATCTCATCTCGCTCG 59.735 52.381 0.00 0.00 0.00 5.03
1442 2154 0.608035 TCTCAACCCAAATCACCGGC 60.608 55.000 0.00 0.00 0.00 6.13
1565 2277 9.515020 CTCTAACTAAATTGAACTGCAAAAACA 57.485 29.630 0.00 0.00 40.48 2.83
1685 2405 0.034186 CTGCCCTGATGCCCAGTAAA 60.034 55.000 3.06 0.00 41.33 2.01
1767 2498 4.808364 CCTTTTCGTTTCCAATTCTGCAAA 59.192 37.500 0.00 0.00 0.00 3.68
1874 2605 6.877322 TCTGTATCCAAGTAAGTAAACCAAGC 59.123 38.462 0.00 0.00 0.00 4.01
1899 2630 6.582636 TCATGGAATATACGAACAAGAGCTT 58.417 36.000 0.00 0.00 0.00 3.74
1911 2642 7.871853 ACGGCAAGTTTTATCATGGAATATAC 58.128 34.615 0.00 0.00 0.00 1.47
2008 2739 3.861113 CCTTTGATGCAATGTGAAATCCG 59.139 43.478 0.00 0.00 0.00 4.18
2027 2758 0.956633 TGACAAGTCGCGTAGTCCTT 59.043 50.000 5.77 0.00 0.00 3.36
2028 2759 0.956633 TTGACAAGTCGCGTAGTCCT 59.043 50.000 5.77 0.00 0.00 3.85
2362 3093 6.364165 GCGCAAAATTGAATATATCTGCATGT 59.636 34.615 0.30 0.00 0.00 3.21
3240 3980 8.721478 GCTGAGACTTCAAACTTGTGATATTTA 58.279 33.333 0.00 0.00 31.69 1.40
3241 3981 7.229306 TGCTGAGACTTCAAACTTGTGATATTT 59.771 33.333 0.00 0.00 31.69 1.40
3259 3999 2.393271 ACATAAGTGGCTGCTGAGAC 57.607 50.000 0.00 0.00 0.00 3.36
3409 4149 7.871973 TGAAATTTCATTAACATGTGTTGGGAG 59.128 33.333 16.91 0.00 34.41 4.30
3830 4570 9.363763 CAGTCCAGAATATATTGTATAGTGCAG 57.636 37.037 1.78 0.00 0.00 4.41
3859 4599 3.874383 TGATGAGAACCAACAGGGAAA 57.126 42.857 0.00 0.00 41.15 3.13
3943 4683 2.238353 GCGCTGAGCTGAAGTCAAA 58.762 52.632 1.78 0.00 44.04 2.69
4030 4770 2.034558 ACTGCACGGGAATGAAAAACAG 59.965 45.455 0.00 0.00 0.00 3.16
4207 4947 3.244491 ACAATGAAAGCAGAGCAGAGAGT 60.244 43.478 0.00 0.00 0.00 3.24
4390 5147 0.823356 TGCCACCTCCAACTTTGCTC 60.823 55.000 0.00 0.00 0.00 4.26
4435 5192 3.429684 GGGCCAAAACAAAGTCGAGAAAA 60.430 43.478 4.39 0.00 0.00 2.29
4656 5413 5.195185 TGCATCAGTACATCCATGAACAAT 58.805 37.500 0.00 0.00 0.00 2.71
4689 5446 4.038642 GCATGACAAAGTAAAGTGGGGAAA 59.961 41.667 0.00 0.00 0.00 3.13
4819 5576 7.530426 ACTTTGAAGAGAATGGTGCTATTTT 57.470 32.000 0.00 0.00 0.00 1.82
4821 5578 6.716628 TCAACTTTGAAGAGAATGGTGCTATT 59.283 34.615 0.00 0.00 33.55 1.73
4958 5715 3.417101 ACACAAGGGCGTCATTGAATAA 58.583 40.909 22.50 0.00 37.99 1.40
4969 5726 1.131126 CAAGCATTAGACACAAGGGCG 59.869 52.381 0.00 0.00 0.00 6.13
5062 5822 5.533482 CCCAATTTGGTGAAACGAATAACA 58.467 37.500 14.26 0.00 38.12 2.41
5063 5823 4.387559 GCCCAATTTGGTGAAACGAATAAC 59.612 41.667 14.26 0.00 38.12 1.89
5064 5824 4.561105 GCCCAATTTGGTGAAACGAATAA 58.439 39.130 14.26 0.00 38.12 1.40
5283 6043 1.099879 AAGGTACTCCGTCCGATCCG 61.100 60.000 0.00 0.00 38.49 4.18
5365 6126 2.732597 GCGAGCGACTTACTCACTTCAT 60.733 50.000 0.00 0.00 33.58 2.57
5381 6142 3.053455 GTTCATGGATACTACTGCGAGC 58.947 50.000 0.00 0.00 37.61 5.03
5425 6186 2.505819 CCTGCTTTAGAGTACCATGGGT 59.494 50.000 18.09 4.30 40.16 4.51
5429 6190 5.010282 CCAAAACCTGCTTTAGAGTACCAT 58.990 41.667 0.00 0.00 0.00 3.55
5607 6368 6.258727 CACTGTGAACTGCGATTCCTAATAAT 59.741 38.462 0.32 0.00 0.00 1.28
5609 6370 5.109210 CACTGTGAACTGCGATTCCTAATA 58.891 41.667 0.32 0.00 0.00 0.98
5620 6381 6.423905 TCTTAATAACTGACACTGTGAACTGC 59.576 38.462 15.86 0.00 0.00 4.40
5769 6530 6.650390 ACAGCCATTAAAATTTTGGTCACATC 59.350 34.615 13.76 0.00 32.90 3.06
6066 6883 5.419542 CAGATTTCATCCCTTACGTCTTCA 58.580 41.667 0.00 0.00 0.00 3.02
6327 7144 6.611381 ACAACTACGTAAGCTACAATAACGA 58.389 36.000 0.00 0.00 45.62 3.85
6418 7235 1.263217 CACGCCACACTTACAAACTCC 59.737 52.381 0.00 0.00 0.00 3.85
6441 7258 2.301583 TGATACACAGTTAGCCTGCACA 59.698 45.455 0.00 0.00 45.68 4.57
6470 7287 2.479560 GCTTTCACCGTTCAAACAAGCT 60.480 45.455 7.33 0.00 33.03 3.74
6496 7313 7.064253 AGCGTTCAAGTAAATACTTCACATACC 59.936 37.037 2.88 0.00 44.19 2.73
6560 7377 1.804151 TCTGCAGTTACAAATCGGTGC 59.196 47.619 14.67 0.00 0.00 5.01
6582 7399 0.975556 TCCACAAGGGAGCGCATAGA 60.976 55.000 11.47 0.00 42.15 1.98
6643 7461 2.494073 ACTTTTGCCTCCGTTTCAACAA 59.506 40.909 0.00 0.00 0.00 2.83
6644 7462 2.096248 ACTTTTGCCTCCGTTTCAACA 58.904 42.857 0.00 0.00 0.00 3.33
6645 7463 2.863401 ACTTTTGCCTCCGTTTCAAC 57.137 45.000 0.00 0.00 0.00 3.18
6664 7482 8.101309 TCTCTTATCCAATGGATGAGGTTTAA 57.899 34.615 27.12 11.51 43.36 1.52
6666 7484 6.388100 TCTCTCTTATCCAATGGATGAGGTTT 59.612 38.462 27.12 4.56 43.36 3.27
6667 7485 5.907662 TCTCTCTTATCCAATGGATGAGGTT 59.092 40.000 27.12 5.25 43.36 3.50
6668 7486 5.471424 TCTCTCTTATCCAATGGATGAGGT 58.529 41.667 27.12 5.95 43.36 3.85
6751 7570 2.235402 CCGGAGCAAAGAAACTAGGGTA 59.765 50.000 0.00 0.00 0.00 3.69
6794 7613 0.036388 GCTTTCGTCCATCTCCACCA 60.036 55.000 0.00 0.00 0.00 4.17
6851 7670 1.435577 GCCGACAGTTTGGAACGTAT 58.564 50.000 0.00 0.00 36.23 3.06
6860 7679 1.373590 AACACTTGCGCCGACAGTTT 61.374 50.000 4.18 0.00 0.00 2.66
6861 7680 1.373590 AAACACTTGCGCCGACAGTT 61.374 50.000 4.18 0.19 0.00 3.16
6862 7681 1.817941 AAACACTTGCGCCGACAGT 60.818 52.632 4.18 0.00 0.00 3.55
6878 7759 1.398692 GTTGAAGAGTGGTGGGCAAA 58.601 50.000 0.00 0.00 0.00 3.68
6899 7780 1.303317 GGTGGCCCTTGTTCGACAT 60.303 57.895 0.00 0.00 0.00 3.06
6917 7798 2.125912 CGGGCTCGACACTTCTGG 60.126 66.667 0.00 0.00 39.00 3.86
6943 7824 4.657969 TGGTCTTTGGTCATTGGGAAATTT 59.342 37.500 0.00 0.00 0.00 1.82
7080 7961 3.243201 CCTTCAAGATAGAATTTGGGCGC 60.243 47.826 0.00 0.00 0.00 6.53
7083 7964 3.638627 GGCCCTTCAAGATAGAATTTGGG 59.361 47.826 0.00 0.00 34.98 4.12
7147 8028 4.285775 TCGCCCATGTATAGGATGATTTGA 59.714 41.667 0.00 0.00 0.00 2.69
7225 8106 4.693283 TCATTTGGAAGCATACGAGTAGG 58.307 43.478 0.00 0.00 0.00 3.18
7228 8109 5.647658 TGAAATCATTTGGAAGCATACGAGT 59.352 36.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.