Multiple sequence alignment - TraesCS1B01G319000

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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 TraesCS1B01G319000 chr1B 100.000 4025 0 0 1 4025 543469756 543465732 0.000000e+00 7433.0
1 TraesCS1B01G319000 chr1B 87.941 2720 274 29 748 3444 611523270 611525958 0.000000e+00 3157.0
2 TraesCS1B01G319000 chr1B 92.308 65 4 1 242 305 543468655 543468591 1.540000e-14 91.6
3 TraesCS1B01G319000 chr1B 92.308 65 4 1 1102 1166 543469515 543469452 1.540000e-14 91.6
4 TraesCS1B01G319000 chr1D 95.389 3839 158 11 151 3977 403948954 403945123 0.000000e+00 6091.0
5 TraesCS1B01G319000 chr1D 88.382 2720 269 26 748 3444 446708254 446705559 0.000000e+00 3229.0
6 TraesCS1B01G319000 chr1D 93.069 101 7 0 1 101 403949077 403948977 9.010000e-32 148.0
7 TraesCS1B01G319000 chr1D 77.982 218 32 10 3442 3646 446705500 446705286 5.460000e-24 122.0
8 TraesCS1B01G319000 chr1D 93.846 65 3 1 242 305 403948001 403947937 3.310000e-16 97.1
9 TraesCS1B01G319000 chr1A 94.982 3268 132 20 732 3977 499623905 499620648 0.000000e+00 5097.0
10 TraesCS1B01G319000 chr1A 88.281 2722 267 35 748 3444 542440251 542437557 0.000000e+00 3212.0
11 TraesCS1B01G319000 chr1A 91.599 738 54 7 1 733 499624800 499624066 0.000000e+00 1013.0
12 TraesCS1B01G319000 chr1A 75.920 299 43 15 3442 3723 542437498 542437212 4.220000e-25 126.0
13 TraesCS1B01G319000 chr1A 95.385 65 2 1 242 305 499623532 499623468 7.120000e-18 102.0
14 TraesCS1B01G319000 chr3D 77.478 1483 300 27 1501 2966 442040142 442041607 0.000000e+00 857.0
15 TraesCS1B01G319000 chr3A 77.089 1484 310 25 1501 2966 582941864 582943335 0.000000e+00 830.0
16 TraesCS1B01G319000 chr3B 76.673 1479 319 20 1501 2966 579284923 579286388 0.000000e+00 797.0
17 TraesCS1B01G319000 chr3B 76.673 1479 319 20 1501 2966 579301580 579303045 0.000000e+00 797.0


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 TraesCS1B01G319000 chr1B 543465732 543469756 4024 True 2538.733333 7433 94.872000 1 4025 3 chr1B.!!$R1 4024
1 TraesCS1B01G319000 chr1B 611523270 611525958 2688 False 3157.000000 3157 87.941000 748 3444 1 chr1B.!!$F1 2696
2 TraesCS1B01G319000 chr1D 403945123 403949077 3954 True 2112.033333 6091 94.101333 1 3977 3 chr1D.!!$R1 3976
3 TraesCS1B01G319000 chr1D 446705286 446708254 2968 True 1675.500000 3229 83.182000 748 3646 2 chr1D.!!$R2 2898
4 TraesCS1B01G319000 chr1A 499620648 499624800 4152 True 2070.666667 5097 93.988667 1 3977 3 chr1A.!!$R1 3976
5 TraesCS1B01G319000 chr1A 542437212 542440251 3039 True 1669.000000 3212 82.100500 748 3723 2 chr1A.!!$R2 2975
6 TraesCS1B01G319000 chr3D 442040142 442041607 1465 False 857.000000 857 77.478000 1501 2966 1 chr3D.!!$F1 1465
7 TraesCS1B01G319000 chr3A 582941864 582943335 1471 False 830.000000 830 77.089000 1501 2966 1 chr3A.!!$F1 1465
8 TraesCS1B01G319000 chr3B 579284923 579286388 1465 False 797.000000 797 76.673000 1501 2966 1 chr3B.!!$F1 1465
9 TraesCS1B01G319000 chr3B 579301580 579303045 1465 False 797.000000 797 76.673000 1501 2966 1 chr3B.!!$F2 1465

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
108 109 0.322456 CAACCTCCCATTCGAAGGCA 60.322 55.0 3.84 0.0 33.21 4.75 F
1278 1451 0.032615 TGCCCATTGATGTTACCCCC 60.033 55.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1760 0.315251 TCAGGTCTGCACGTCTTCTG 59.685 55.0 0.00 0.0 0.0 3.02 R
3054 3244 1.340088 TGTTGGCCTGCATGTTGATT 58.660 45.0 3.32 0.0 0.0 2.57 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
41 42 8.485392 TCTCATTTTCATATCATGTACACCTCA 58.515 33.333 0.00 0.00 0.00 3.86
77 78 5.534207 AACAAGGAAATGCTGAATTGACA 57.466 34.783 0.00 0.00 0.00 3.58
90 91 5.560760 GCTGAATTGACAAATCGAACAGACA 60.561 40.000 0.00 0.00 32.74 3.41
101 102 2.076863 CGAACAGACAACCTCCCATTC 58.923 52.381 0.00 0.00 0.00 2.67
102 103 2.076863 GAACAGACAACCTCCCATTCG 58.923 52.381 0.00 0.00 0.00 3.34
105 106 2.289694 ACAGACAACCTCCCATTCGAAG 60.290 50.000 3.35 0.00 0.00 3.79
106 107 1.279271 AGACAACCTCCCATTCGAAGG 59.721 52.381 3.35 2.70 36.21 3.46
107 108 0.322546 ACAACCTCCCATTCGAAGGC 60.323 55.000 3.84 0.00 33.21 4.35
108 109 0.322456 CAACCTCCCATTCGAAGGCA 60.322 55.000 3.84 0.00 33.21 4.75
110 111 0.322546 ACCTCCCATTCGAAGGCAAC 60.323 55.000 3.84 0.00 33.21 4.17
204 207 0.724549 TACAAATGCGCCAGCTTACG 59.275 50.000 4.18 0.75 45.42 3.18
209 212 1.498865 ATGCGCCAGCTTACGTATGC 61.499 55.000 22.15 22.15 45.42 3.14
224 227 7.696453 GCTTACGTATGCTCAATTACAAATGTT 59.304 33.333 22.31 0.00 0.00 2.71
238 241 1.755179 AATGTTGCGGCTGCTAATCT 58.245 45.000 20.27 0.00 43.34 2.40
239 242 1.019673 ATGTTGCGGCTGCTAATCTG 58.980 50.000 20.27 0.00 43.34 2.90
254 257 3.947910 AATCTGCCAAATGAACCAGTG 57.052 42.857 0.00 0.00 0.00 3.66
266 269 2.282462 CCAGTGAAGCACCCCACC 60.282 66.667 0.00 0.00 34.49 4.61
325 328 3.621794 GCGCCAGCTTATGTATTTTCAG 58.378 45.455 0.00 0.00 41.01 3.02
333 336 7.917505 CCAGCTTATGTATTTTCAGTTTCCATC 59.082 37.037 0.00 0.00 0.00 3.51
349 352 2.423892 TCCATCTTGTCGTGACTCTAGC 59.576 50.000 1.23 0.00 0.00 3.42
397 400 2.353889 CTGGCAATCGATGGAAAGAGTG 59.646 50.000 3.24 0.00 35.80 3.51
404 407 2.894765 TCGATGGAAAGAGTGTGGTGTA 59.105 45.455 0.00 0.00 0.00 2.90
414 417 8.739972 GGAAAGAGTGTGGTGTAATTGATTTAT 58.260 33.333 0.00 0.00 0.00 1.40
423 426 9.651913 GTGGTGTAATTGATTTATTTTGGATGT 57.348 29.630 0.00 0.00 0.00 3.06
450 453 5.927281 ATTAATCAGCATGGCTTGAGTTT 57.073 34.783 4.32 0.83 36.40 2.66
458 461 2.869233 TGGCTTGAGTTTTGCTTGTC 57.131 45.000 0.00 0.00 0.00 3.18
471 474 7.141363 AGTTTTGCTTGTCTGTTGATATTGAC 58.859 34.615 0.00 0.00 0.00 3.18
533 536 1.753073 GCTCTTGCATTTGGTGGCTAT 59.247 47.619 0.00 0.00 39.41 2.97
548 551 4.262938 GGTGGCTATTCTACCCTTGATACC 60.263 50.000 0.00 0.00 40.16 2.73
554 557 7.379750 GCTATTCTACCCTTGATACCTGTTAG 58.620 42.308 0.00 0.00 0.00 2.34
563 566 9.893975 ACCCTTGATACCTGTTAGTATAGTAAT 57.106 33.333 3.37 0.00 33.05 1.89
671 676 4.013728 GGTACCAATGGTTCAATGCTACA 58.986 43.478 11.41 0.00 37.09 2.74
682 687 6.030228 GGTTCAATGCTACATCTTGTTTAGC 58.970 40.000 0.00 0.00 33.70 3.09
802 972 7.041848 GGTTTCTGATTTGGTTTGGAAAAGATG 60.042 37.037 0.00 0.00 0.00 2.90
1123 1296 5.182001 GTCAACATTAATCAGTCAAGCACCT 59.818 40.000 0.00 0.00 0.00 4.00
1198 1371 0.962855 GAGCCTTCCTGCCTTTGGAC 60.963 60.000 0.00 0.00 32.65 4.02
1278 1451 0.032615 TGCCCATTGATGTTACCCCC 60.033 55.000 0.00 0.00 0.00 5.40
1485 1661 1.731969 GCTGCTTGCTTTTCTGCCG 60.732 57.895 0.00 0.00 38.95 5.69
1656 1832 0.039618 GGGCCAATGTGGGAAAGAGA 59.960 55.000 4.39 0.00 38.19 3.10
1890 2069 3.069158 CAGGGGGTAACAGTAGGAATACG 59.931 52.174 0.00 0.00 39.74 3.06
2393 2572 2.230992 GTGCTTGTGGGCAACATAATGA 59.769 45.455 0.00 0.00 44.18 2.57
2763 2948 7.389884 AGCACATATGTATCACCTGATGAATTC 59.610 37.037 8.32 0.00 41.93 2.17
3035 3225 6.459024 CGCGGGTTATTTTGATTCATTTAGGA 60.459 38.462 0.00 0.00 0.00 2.94
3054 3244 3.133901 AGGACGCATGTATATTGTGGTGA 59.866 43.478 0.00 0.00 0.00 4.02
3072 3262 1.273048 TGAATCAACATGCAGGCCAAC 59.727 47.619 5.01 0.00 0.00 3.77
3162 3354 8.565896 TTACTCAAGTATGCATCAATTTCACT 57.434 30.769 0.19 0.00 0.00 3.41
3233 3436 5.655576 CATTGTTTTGCACGTTTGTATCAC 58.344 37.500 0.00 0.00 0.00 3.06
3304 3508 5.068460 ACAAACTGCTGTAATTACTTGGCAA 59.932 36.000 21.78 0.00 31.28 4.52
3314 3518 3.755965 TTACTTGGCAACGCATATGTG 57.244 42.857 14.72 14.72 42.51 3.21
3399 3613 3.007290 CCCATAGCTAAGCTGCATCTGTA 59.993 47.826 1.02 0.00 40.10 2.74
3483 3761 7.553044 AGCTAGATGTTAGTATGTTTTTCACCC 59.447 37.037 0.00 0.00 0.00 4.61
3487 3765 8.576442 AGATGTTAGTATGTTTTTCACCCTTTG 58.424 33.333 0.00 0.00 0.00 2.77
3494 3772 5.622346 TGTTTTTCACCCTTTGGCTTTAT 57.378 34.783 0.00 0.00 33.59 1.40
3495 3773 5.606505 TGTTTTTCACCCTTTGGCTTTATC 58.393 37.500 0.00 0.00 33.59 1.75
3509 3787 5.132502 TGGCTTTATCTGTGGGTTCATATG 58.867 41.667 0.00 0.00 0.00 1.78
3517 3795 3.289836 TGTGGGTTCATATGCCATCTTG 58.710 45.455 4.14 0.00 0.00 3.02
3564 3846 5.238432 ACATCGTTTGAACATCTGCTTTACA 59.762 36.000 0.00 0.00 0.00 2.41
3569 3856 5.422666 TTGAACATCTGCTTTACACACTG 57.577 39.130 0.00 0.00 0.00 3.66
3624 3914 5.009710 TGCTACCTAGATTCTACCAATGTCG 59.990 44.000 0.00 0.00 0.00 4.35
3627 3917 4.341520 ACCTAGATTCTACCAATGTCGGAC 59.658 45.833 0.00 0.00 0.00 4.79
3660 3950 4.689345 GGAAGATGGTTAATAATCGGTCGG 59.311 45.833 0.00 0.00 0.00 4.79
3663 3953 5.295152 AGATGGTTAATAATCGGTCGGTTC 58.705 41.667 0.00 0.00 0.00 3.62
3730 4023 1.840630 CGTGTCAATGCCGCACTTGA 61.841 55.000 11.74 11.74 0.00 3.02
3743 4036 1.542108 GCACTTGACCTCTGTTCTGCT 60.542 52.381 0.00 0.00 0.00 4.24
3827 4123 1.137872 CCTGCTGCTAATCGGTCTTCT 59.862 52.381 0.00 0.00 0.00 2.85
3841 4137 2.614229 GGTCTTCTCTTCTCCTTGCCAC 60.614 54.545 0.00 0.00 0.00 5.01
3899 4196 2.047274 TGGCTGTTAGCTGCGACC 60.047 61.111 0.00 0.00 41.99 4.79
3903 4200 0.951040 GCTGTTAGCTGCGACCTGTT 60.951 55.000 0.00 0.00 38.45 3.16
3910 4207 0.037232 GCTGCGACCTGTTAAGACCT 60.037 55.000 0.00 0.00 0.00 3.85
3915 4212 1.337823 CGACCTGTTAAGACCTGGTGG 60.338 57.143 2.82 0.00 33.59 4.61
3935 4232 5.219633 GTGGTGTAAAAACATGTGGCTTAG 58.780 41.667 0.00 0.00 0.00 2.18
3936 4233 4.890581 TGGTGTAAAAACATGTGGCTTAGT 59.109 37.500 0.00 0.00 0.00 2.24
3937 4234 5.009210 TGGTGTAAAAACATGTGGCTTAGTC 59.991 40.000 0.00 0.00 0.00 2.59
3938 4235 5.240844 GGTGTAAAAACATGTGGCTTAGTCT 59.759 40.000 0.00 0.00 0.00 3.24
3939 4236 6.371389 GTGTAAAAACATGTGGCTTAGTCTC 58.629 40.000 0.00 0.00 0.00 3.36
3952 4249 0.108945 TAGTCTCGTCTCGTCTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
3984 4281 2.483583 TTTTTACCTGTGCGTTGCTG 57.516 45.000 0.00 0.00 0.00 4.41
3985 4282 1.384525 TTTTACCTGTGCGTTGCTGT 58.615 45.000 0.00 0.00 0.00 4.40
3986 4283 0.660488 TTTACCTGTGCGTTGCTGTG 59.340 50.000 0.00 0.00 0.00 3.66
3987 4284 0.462937 TTACCTGTGCGTTGCTGTGT 60.463 50.000 0.00 0.00 0.00 3.72
3988 4285 0.878523 TACCTGTGCGTTGCTGTGTC 60.879 55.000 0.00 0.00 0.00 3.67
3989 4286 1.889105 CCTGTGCGTTGCTGTGTCT 60.889 57.895 0.00 0.00 0.00 3.41
3990 4287 0.599991 CCTGTGCGTTGCTGTGTCTA 60.600 55.000 0.00 0.00 0.00 2.59
3991 4288 1.217001 CTGTGCGTTGCTGTGTCTAA 58.783 50.000 0.00 0.00 0.00 2.10
3992 4289 0.934496 TGTGCGTTGCTGTGTCTAAC 59.066 50.000 0.00 0.00 0.00 2.34
3993 4290 1.217882 GTGCGTTGCTGTGTCTAACT 58.782 50.000 0.00 0.00 0.00 2.24
3994 4291 1.597663 GTGCGTTGCTGTGTCTAACTT 59.402 47.619 0.00 0.00 0.00 2.66
3995 4292 2.031683 GTGCGTTGCTGTGTCTAACTTT 59.968 45.455 0.00 0.00 0.00 2.66
3996 4293 3.246699 GTGCGTTGCTGTGTCTAACTTTA 59.753 43.478 0.00 0.00 0.00 1.85
3997 4294 3.872182 TGCGTTGCTGTGTCTAACTTTAA 59.128 39.130 0.00 0.00 0.00 1.52
3998 4295 4.513692 TGCGTTGCTGTGTCTAACTTTAAT 59.486 37.500 0.00 0.00 0.00 1.40
3999 4296 5.080068 GCGTTGCTGTGTCTAACTTTAATC 58.920 41.667 0.00 0.00 0.00 1.75
4000 4297 5.107065 GCGTTGCTGTGTCTAACTTTAATCT 60.107 40.000 0.00 0.00 0.00 2.40
4001 4298 6.299604 CGTTGCTGTGTCTAACTTTAATCTG 58.700 40.000 0.00 0.00 0.00 2.90
4002 4299 5.862924 TGCTGTGTCTAACTTTAATCTGC 57.137 39.130 0.00 0.00 0.00 4.26
4003 4300 5.304778 TGCTGTGTCTAACTTTAATCTGCA 58.695 37.500 0.00 0.00 0.00 4.41
4004 4301 5.409520 TGCTGTGTCTAACTTTAATCTGCAG 59.590 40.000 7.63 7.63 0.00 4.41
4005 4302 5.163814 GCTGTGTCTAACTTTAATCTGCAGG 60.164 44.000 15.13 0.00 0.00 4.85
4006 4303 4.695455 TGTGTCTAACTTTAATCTGCAGGC 59.305 41.667 15.13 0.00 0.00 4.85
4007 4304 4.938226 GTGTCTAACTTTAATCTGCAGGCT 59.062 41.667 15.13 3.64 0.00 4.58
4008 4305 4.937620 TGTCTAACTTTAATCTGCAGGCTG 59.062 41.667 15.13 10.94 0.00 4.85
4009 4306 3.941483 TCTAACTTTAATCTGCAGGCTGC 59.059 43.478 31.91 31.91 45.29 5.25
4019 4316 1.874562 GCAGGCTGCAGCTATATGC 59.125 57.895 35.82 31.65 44.26 3.14
4020 4317 1.584380 GCAGGCTGCAGCTATATGCC 61.584 60.000 35.82 20.06 45.91 4.40
4021 4318 0.959372 CAGGCTGCAGCTATATGCCC 60.959 60.000 35.82 17.96 45.91 5.36
4022 4319 1.073722 GGCTGCAGCTATATGCCCA 59.926 57.895 35.82 0.00 45.91 5.36
4023 4320 0.959372 GGCTGCAGCTATATGCCCAG 60.959 60.000 35.82 0.00 45.91 4.45
4024 4321 2.552802 CTGCAGCTATATGCCCAGC 58.447 57.895 0.00 0.00 45.91 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.144297 TGTTTCTTGCAGCTATTTGAGGT 58.856 39.130 0.00 0.00 35.84 3.85
41 42 5.789643 TTCCTTGTTTCTTGCAGCTATTT 57.210 34.783 0.00 0.00 0.00 1.40
77 78 2.105821 TGGGAGGTTGTCTGTTCGATTT 59.894 45.455 0.00 0.00 0.00 2.17
90 91 0.404040 TTGCCTTCGAATGGGAGGTT 59.596 50.000 7.59 0.00 0.00 3.50
121 122 5.239963 CCTAGGGCTGTCTTTTCGTTTAAAA 59.760 40.000 0.00 0.00 35.74 1.52
125 126 2.552373 CCCTAGGGCTGTCTTTTCGTTT 60.552 50.000 16.90 0.00 0.00 3.60
126 127 1.003233 CCCTAGGGCTGTCTTTTCGTT 59.997 52.381 16.90 0.00 0.00 3.85
169 172 6.692681 CGCATTTGTATTTGAACCTCTTATGG 59.307 38.462 0.00 0.00 0.00 2.74
204 207 5.229887 CCGCAACATTTGTAATTGAGCATAC 59.770 40.000 0.00 0.00 0.00 2.39
209 212 3.609373 CAGCCGCAACATTTGTAATTGAG 59.391 43.478 0.00 0.00 0.00 3.02
224 227 2.514592 GGCAGATTAGCAGCCGCA 60.515 61.111 0.00 0.00 39.53 5.69
238 241 1.340889 GCTTCACTGGTTCATTTGGCA 59.659 47.619 0.00 0.00 0.00 4.92
239 242 1.340889 TGCTTCACTGGTTCATTTGGC 59.659 47.619 0.00 0.00 0.00 4.52
254 257 2.983592 CCAACGGTGGGGTGCTTC 60.984 66.667 13.17 0.00 41.77 3.86
266 269 1.545614 CGGAGTCACAACGACCAACG 61.546 60.000 0.00 0.00 46.69 4.10
315 318 6.485313 ACGACAAGATGGAAACTGAAAATACA 59.515 34.615 0.00 0.00 0.00 2.29
316 319 6.797033 CACGACAAGATGGAAACTGAAAATAC 59.203 38.462 0.00 0.00 0.00 1.89
320 323 4.272504 GTCACGACAAGATGGAAACTGAAA 59.727 41.667 0.00 0.00 0.00 2.69
325 328 3.654414 AGAGTCACGACAAGATGGAAAC 58.346 45.455 0.00 0.00 0.00 2.78
333 336 2.088423 AGGAGCTAGAGTCACGACAAG 58.912 52.381 0.00 0.00 0.00 3.16
397 400 9.651913 ACATCCAAAATAAATCAATTACACCAC 57.348 29.630 0.00 0.00 0.00 4.16
414 417 9.752961 CATGCTGATTAATATTGACATCCAAAA 57.247 29.630 0.00 0.00 38.43 2.44
423 426 6.774170 ACTCAAGCCATGCTGATTAATATTGA 59.226 34.615 0.00 0.00 39.62 2.57
435 438 1.335145 AGCAAAACTCAAGCCATGCT 58.665 45.000 0.00 0.00 42.56 3.79
450 453 6.486320 TGAAGTCAATATCAACAGACAAGCAA 59.514 34.615 0.00 0.00 33.56 3.91
533 536 9.584008 CTATACTAACAGGTATCAAGGGTAGAA 57.416 37.037 0.00 0.00 34.65 2.10
573 576 6.320164 AGCACACCAAGATAACACTAACAAAA 59.680 34.615 0.00 0.00 0.00 2.44
577 582 6.164176 ACTAGCACACCAAGATAACACTAAC 58.836 40.000 0.00 0.00 0.00 2.34
586 591 6.116126 GGAAGAATTACTAGCACACCAAGAT 58.884 40.000 0.00 0.00 0.00 2.40
596 601 9.007901 AGCATTGATAATGGAAGAATTACTAGC 57.992 33.333 3.97 0.00 39.31 3.42
647 652 3.505386 AGCATTGAACCATTGGTACCAA 58.495 40.909 28.95 28.95 40.47 3.67
671 676 5.489792 TCCTTCTGAGTGCTAAACAAGAT 57.510 39.130 0.00 0.00 0.00 2.40
682 687 4.942483 AGATGAAGCATTTCCTTCTGAGTG 59.058 41.667 3.89 0.00 41.36 3.51
802 972 6.012658 TCACCTGCATTTGTTACTCATTTC 57.987 37.500 0.00 0.00 0.00 2.17
817 987 3.084039 CCAAGCTAAAATCTCACCTGCA 58.916 45.455 0.00 0.00 0.00 4.41
853 1023 1.739466 CTGCATGCGATTACAACCAGT 59.261 47.619 14.09 0.00 0.00 4.00
1198 1371 1.507141 GCACTGAAGGTGGTGAACGG 61.507 60.000 0.00 0.00 45.44 4.44
1485 1661 6.190346 TCCCTAGGAGTACTATCTGAAGTC 57.810 45.833 11.48 0.00 0.00 3.01
1584 1760 0.315251 TCAGGTCTGCACGTCTTCTG 59.685 55.000 0.00 0.00 0.00 3.02
1587 1763 1.871080 CTTTCAGGTCTGCACGTCTT 58.129 50.000 0.00 0.00 0.00 3.01
1656 1832 0.616111 CACCAGGAGCAGTCCCTACT 60.616 60.000 0.00 0.00 45.26 2.57
1890 2069 0.689080 TCTGGTCATGCCTCTCCTCC 60.689 60.000 7.54 0.00 38.35 4.30
2169 2348 4.759693 TGTTGTATAACCTTGCCTCTTGTG 59.240 41.667 0.00 0.00 35.92 3.33
2393 2572 2.688958 GAGCTGTACGGTAGATCACCTT 59.311 50.000 3.10 5.90 46.19 3.50
2596 2775 2.359900 CTCCCCAGCATACTCACAAAC 58.640 52.381 0.00 0.00 0.00 2.93
2949 3134 2.669569 CCAGCTCCAACCACACCG 60.670 66.667 0.00 0.00 0.00 4.94
3035 3225 5.122519 TGATTCACCACAATATACATGCGT 58.877 37.500 0.00 0.00 0.00 5.24
3054 3244 1.340088 TGTTGGCCTGCATGTTGATT 58.660 45.000 3.32 0.00 0.00 2.57
3072 3262 3.323115 TGGCAGAGAAGATACCTAGCATG 59.677 47.826 0.00 0.00 0.00 4.06
3154 3346 3.731867 GCGATTCGGCATCAAGTGAAATT 60.732 43.478 8.34 0.00 0.00 1.82
3162 3354 5.120674 CAGAAATATAGCGATTCGGCATCAA 59.879 40.000 8.34 0.00 34.64 2.57
3233 3436 5.906073 AGGAAGATAAAATGCCAAATTCGG 58.094 37.500 0.00 0.00 0.00 4.30
3304 3508 5.173664 CCTATCATCATCACACATATGCGT 58.826 41.667 1.58 0.00 0.00 5.24
3314 3518 1.196354 GCGCTTGCCTATCATCATCAC 59.804 52.381 0.00 0.00 0.00 3.06
3477 3755 3.826157 CACAGATAAAGCCAAAGGGTGAA 59.174 43.478 0.00 0.00 36.17 3.18
3483 3761 3.826157 TGAACCCACAGATAAAGCCAAAG 59.174 43.478 0.00 0.00 0.00 2.77
3487 3765 4.022849 GCATATGAACCCACAGATAAAGCC 60.023 45.833 6.97 0.00 0.00 4.35
3494 3772 2.779430 AGATGGCATATGAACCCACAGA 59.221 45.455 6.97 0.00 0.00 3.41
3495 3773 3.219176 AGATGGCATATGAACCCACAG 57.781 47.619 6.97 0.00 0.00 3.66
3509 3787 6.024552 TCTTATCCAAACAAACAAGATGGC 57.975 37.500 0.00 0.00 0.00 4.40
3540 3822 4.836125 AAAGCAGATGTTCAAACGATGT 57.164 36.364 0.00 0.00 0.00 3.06
3545 3827 5.682862 CAGTGTGTAAAGCAGATGTTCAAAC 59.317 40.000 0.00 0.00 0.00 2.93
3551 3833 3.131709 AGCAGTGTGTAAAGCAGATGT 57.868 42.857 0.00 0.00 0.00 3.06
3564 3846 2.579873 AGATGAGCAAACAAGCAGTGT 58.420 42.857 0.00 0.00 44.64 3.55
3569 3856 2.030540 TCTGCAAGATGAGCAAACAAGC 60.031 45.455 0.00 0.00 38.67 4.01
3627 3917 1.277580 ACCATCTTCCCAGGAGCCAG 61.278 60.000 0.00 0.00 0.00 4.85
3663 3953 3.050619 AGTTTACTGTCTTCGCAGTTCG 58.949 45.455 4.01 0.00 46.45 3.95
3730 4023 0.617413 CCATCCAGCAGAACAGAGGT 59.383 55.000 0.00 0.00 0.00 3.85
3743 4036 3.776158 GCACAAAGCCACCATCCA 58.224 55.556 0.00 0.00 37.23 3.41
3765 4061 6.318648 GCATCCACCAAGTATCTGAACAAATA 59.681 38.462 0.00 0.00 0.00 1.40
3820 4116 1.625818 TGGCAAGGAGAAGAGAAGACC 59.374 52.381 0.00 0.00 0.00 3.85
3827 4123 1.415672 AACGGGTGGCAAGGAGAAGA 61.416 55.000 0.00 0.00 0.00 2.87
3841 4137 0.460311 CTAGCCTACACAGGAACGGG 59.540 60.000 0.00 0.00 45.91 5.28
3910 4207 2.101582 GCCACATGTTTTTACACCACCA 59.898 45.455 0.00 0.00 0.00 4.17
3915 4212 6.313744 AGACTAAGCCACATGTTTTTACAC 57.686 37.500 0.00 0.00 0.00 2.90
3935 4232 0.097325 AATGCGAGACGAGACGAGAC 59.903 55.000 0.00 0.00 0.00 3.36
3936 4233 0.374063 GAATGCGAGACGAGACGAGA 59.626 55.000 0.00 0.00 0.00 4.04
3937 4234 0.921662 CGAATGCGAGACGAGACGAG 60.922 60.000 0.00 0.00 40.82 4.18
3938 4235 1.060465 CGAATGCGAGACGAGACGA 59.940 57.895 0.00 0.00 40.82 4.20
3939 4236 1.934956 CCGAATGCGAGACGAGACG 60.935 63.158 0.00 0.00 40.82 4.18
3969 4266 0.878523 GACACAGCAACGCACAGGTA 60.879 55.000 0.00 0.00 0.00 3.08
3970 4267 2.124736 ACACAGCAACGCACAGGT 60.125 55.556 0.00 0.00 0.00 4.00
3972 4269 1.070577 GTTAGACACAGCAACGCACAG 60.071 52.381 0.00 0.00 0.00 3.66
3973 4270 0.934496 GTTAGACACAGCAACGCACA 59.066 50.000 0.00 0.00 0.00 4.57
3974 4271 1.217882 AGTTAGACACAGCAACGCAC 58.782 50.000 0.00 0.00 0.00 5.34
3975 4272 1.948104 AAGTTAGACACAGCAACGCA 58.052 45.000 0.00 0.00 0.00 5.24
3976 4273 4.461992 TTAAAGTTAGACACAGCAACGC 57.538 40.909 0.00 0.00 0.00 4.84
3977 4274 6.299604 CAGATTAAAGTTAGACACAGCAACG 58.700 40.000 0.00 0.00 0.00 4.10
3978 4275 6.080406 GCAGATTAAAGTTAGACACAGCAAC 58.920 40.000 0.00 0.00 0.00 4.17
3979 4276 5.762711 TGCAGATTAAAGTTAGACACAGCAA 59.237 36.000 0.00 0.00 0.00 3.91
3980 4277 5.304778 TGCAGATTAAAGTTAGACACAGCA 58.695 37.500 0.00 0.00 0.00 4.41
3981 4278 5.163814 CCTGCAGATTAAAGTTAGACACAGC 60.164 44.000 17.39 0.00 0.00 4.40
3982 4279 5.163814 GCCTGCAGATTAAAGTTAGACACAG 60.164 44.000 17.39 0.00 0.00 3.66
3983 4280 4.695455 GCCTGCAGATTAAAGTTAGACACA 59.305 41.667 17.39 0.00 0.00 3.72
3984 4281 4.938226 AGCCTGCAGATTAAAGTTAGACAC 59.062 41.667 17.39 0.00 0.00 3.67
3985 4282 4.937620 CAGCCTGCAGATTAAAGTTAGACA 59.062 41.667 17.39 0.00 0.00 3.41
3986 4283 4.201861 GCAGCCTGCAGATTAAAGTTAGAC 60.202 45.833 17.39 0.00 44.26 2.59
3987 4284 3.941483 GCAGCCTGCAGATTAAAGTTAGA 59.059 43.478 17.39 0.00 44.26 2.10
3988 4285 4.284378 GCAGCCTGCAGATTAAAGTTAG 57.716 45.455 17.39 0.00 44.26 2.34
4001 4298 1.584380 GGCATATAGCTGCAGCCTGC 61.584 60.000 34.39 31.70 44.12 4.85
4002 4299 0.959372 GGGCATATAGCTGCAGCCTG 60.959 60.000 34.39 25.15 44.12 4.85
4003 4300 1.377994 GGGCATATAGCTGCAGCCT 59.622 57.895 34.39 23.95 44.12 4.58
4004 4301 0.959372 CTGGGCATATAGCTGCAGCC 60.959 60.000 34.39 18.51 44.12 4.85
4005 4302 1.584380 GCTGGGCATATAGCTGCAGC 61.584 60.000 31.53 31.53 44.12 5.25
4006 4303 2.552802 GCTGGGCATATAGCTGCAG 58.447 57.895 10.11 10.11 44.12 4.41
4007 4304 4.806936 GCTGGGCATATAGCTGCA 57.193 55.556 1.02 0.00 44.12 4.41


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

AutoCloner maintained by Alex Coulton.