Multiple sequence alignment - TraesCS3A01G253700

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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 TraesCS3A01G253700 chr3A 100.000 4505 0 0 1 4505 474973067 474977571 0.000000e+00 8320.0
1 TraesCS3A01G253700 chr3D 96.583 2605 62 11 411 3007 355990140 355992725 0.000000e+00 4292.0
2 TraesCS3A01G253700 chr3D 88.693 964 54 12 3583 4505 355993338 355994287 0.000000e+00 1125.0
3 TraesCS3A01G253700 chr3D 93.144 423 21 3 3129 3544 355992839 355993260 8.280000e-172 614.0
4 TraesCS3A01G253700 chr3D 90.000 60 2 2 3011 3069 355992755 355992811 1.740000e-09 75.0
5 TraesCS3A01G253700 chr3B 95.088 1771 50 15 521 2269 457200116 457201871 0.000000e+00 2754.0
6 TraesCS3A01G253700 chr3B 91.527 1369 72 19 3161 4505 457202829 457204177 0.000000e+00 1845.0
7 TraesCS3A01G253700 chr3B 95.854 820 22 5 2296 3115 457201933 457202740 0.000000e+00 1315.0
8 TraesCS3A01G253700 chr3B 84.615 234 19 8 1 233 457199559 457199776 2.730000e-52 217.0
9 TraesCS3A01G253700 chr1A 86.861 137 16 2 415 551 47216275 47216141 7.810000e-33 152.0
10 TraesCS3A01G253700 chr6B 90.991 111 10 0 423 533 513685268 513685158 2.810000e-32 150.0
11 TraesCS3A01G253700 chr2A 88.983 118 13 0 423 540 459017196 459017313 3.630000e-31 147.0
12 TraesCS3A01G253700 chr7D 89.189 111 12 0 423 533 63396996 63397106 6.080000e-29 139.0
13 TraesCS3A01G253700 chr5D 89.189 111 12 0 423 533 30114881 30114771 6.080000e-29 139.0
14 TraesCS3A01G253700 chr5D 80.000 75 15 0 1653 1727 363177945 363178019 6.300000e-04 56.5
15 TraesCS3A01G253700 chr5D 80.000 75 15 0 1653 1727 363340189 363340263 6.300000e-04 56.5
16 TraesCS3A01G253700 chr5D 80.000 75 15 0 1653 1727 363976225 363976299 6.300000e-04 56.5
17 TraesCS3A01G253700 chr6D 87.931 116 14 0 415 530 263436459 263436574 2.190000e-28 137.0
18 TraesCS3A01G253700 chr6D 88.889 108 12 0 423 530 392032069 392031962 2.830000e-27 134.0
19 TraesCS3A01G253700 chr7A 87.826 115 12 2 423 536 29828506 29828393 2.830000e-27 134.0
20 TraesCS3A01G253700 chr5B 80.000 75 15 0 1653 1727 429727581 429727655 6.300000e-04 56.5
21 TraesCS3A01G253700 chr5B 80.000 75 15 0 1653 1727 429820607 429820681 6.300000e-04 56.5


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 TraesCS3A01G253700 chr3A 474973067 474977571 4504 False 8320.00 8320 100.000 1 4505 1 chr3A.!!$F1 4504
1 TraesCS3A01G253700 chr3D 355990140 355994287 4147 False 1526.50 4292 92.105 411 4505 4 chr3D.!!$F1 4094
2 TraesCS3A01G253700 chr3B 457199559 457204177 4618 False 1532.75 2754 91.771 1 4505 4 chr3B.!!$F1 4504

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
146 148 0.042581 TGGATGCCTAGTCACTGGGA 59.957 55.0 12.34 0.19 33.74 4.37 F
435 577 0.108041 GTGGAACGCCGGAAATCCTA 60.108 55.0 5.05 0.00 36.79 2.94 F
496 638 0.270699 TGGTGGGCAGGGGATACTAT 59.729 55.0 0.00 0.00 0.00 2.12 F
790 932 0.313987 CGAAACCAAAAGCTGACCCC 59.686 55.0 0.00 0.00 0.00 4.95 F
845 987 0.389817 CTCATTTCTCACGCCCGACA 60.390 55.0 0.00 0.00 0.00 4.35 F
995 1137 0.811915 GAAGCTAGTGTCCGAGAGCA 59.188 55.0 0.00 0.00 37.40 4.26 F
3145 3436 0.799917 CGACCGTGCTGATGTCTCTG 60.800 60.0 0.00 0.00 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1778 0.388907 CGTCCCCGATGTACGTGTTT 60.389 55.000 0.00 0.0 40.78 2.83 R
2279 2449 0.744874 CGATTCCCGGAGACAAGCTA 59.255 55.000 0.73 0.0 33.91 3.32 R
3004 3205 4.772100 GGACCAATCCATTTCCTCTTCAAA 59.228 41.667 0.00 0.0 45.47 2.69 R
3121 3412 0.108377 ACATCAGCACGGTCGCAATA 60.108 50.000 5.59 0.0 0.00 1.90 R
3127 3418 0.244994 ACAGAGACATCAGCACGGTC 59.755 55.000 0.00 0.0 0.00 4.79 R
3395 3686 1.071471 CTCCACTTGCGGTCCTTGT 59.929 57.895 0.00 0.0 0.00 3.16 R
4370 4763 1.465187 GCTTCCAACCGCAAACGATAC 60.465 52.381 0.00 0.0 43.93 2.24 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
29 30 1.866601 TGTCGAACAACATGTGAGCAG 59.133 47.619 0.00 0.00 0.00 4.24
63 65 1.885850 GCCCGACGTTGTCTGTTGT 60.886 57.895 1.30 0.00 0.00 3.32
75 77 4.422073 TGTCTGTTGTCTTTGGAGTCAT 57.578 40.909 0.00 0.00 0.00 3.06
77 79 3.499918 GTCTGTTGTCTTTGGAGTCATGG 59.500 47.826 0.00 0.00 0.00 3.66
104 106 0.968901 TACAACATCTCCTCGGCGGT 60.969 55.000 7.21 0.00 0.00 5.68
127 129 2.039084 ACGTCTTCCTTGAAGCCATCTT 59.961 45.455 0.00 0.00 39.29 2.40
132 134 3.008835 TCCTTGAAGCCATCTTGGATG 57.991 47.619 0.00 0.97 40.96 3.51
133 135 1.407979 CCTTGAAGCCATCTTGGATGC 59.592 52.381 0.00 0.00 40.96 3.91
134 136 1.407979 CTTGAAGCCATCTTGGATGCC 59.592 52.381 0.00 0.00 40.96 4.40
135 137 0.627451 TGAAGCCATCTTGGATGCCT 59.373 50.000 0.00 0.00 40.96 4.75
136 138 1.845791 TGAAGCCATCTTGGATGCCTA 59.154 47.619 0.00 0.00 40.96 3.93
137 139 2.158711 TGAAGCCATCTTGGATGCCTAG 60.159 50.000 0.00 0.00 40.96 3.02
138 140 1.516110 AGCCATCTTGGATGCCTAGT 58.484 50.000 0.00 0.00 40.96 2.57
139 141 1.419387 AGCCATCTTGGATGCCTAGTC 59.581 52.381 0.00 0.00 40.96 2.59
140 142 1.141657 GCCATCTTGGATGCCTAGTCA 59.858 52.381 0.00 0.00 40.96 3.41
141 143 2.843701 CCATCTTGGATGCCTAGTCAC 58.156 52.381 2.33 0.00 40.96 3.67
142 144 2.437281 CCATCTTGGATGCCTAGTCACT 59.563 50.000 2.33 0.00 40.96 3.41
143 145 3.464907 CATCTTGGATGCCTAGTCACTG 58.535 50.000 0.00 0.00 0.00 3.66
144 146 1.833630 TCTTGGATGCCTAGTCACTGG 59.166 52.381 0.00 0.00 0.00 4.00
145 147 0.911769 TTGGATGCCTAGTCACTGGG 59.088 55.000 1.91 1.91 35.09 4.45
146 148 0.042581 TGGATGCCTAGTCACTGGGA 59.957 55.000 12.34 0.19 33.74 4.37
147 149 0.755686 GGATGCCTAGTCACTGGGAG 59.244 60.000 12.34 0.00 33.74 4.30
148 150 0.755686 GATGCCTAGTCACTGGGAGG 59.244 60.000 12.34 0.00 33.74 4.30
188 190 1.071567 GCCGACGACTTCTTCCTTCG 61.072 60.000 0.00 0.00 38.73 3.79
192 194 0.959553 ACGACTTCTTCCTTCGCTCA 59.040 50.000 0.00 0.00 36.18 4.26
193 195 1.068194 ACGACTTCTTCCTTCGCTCAG 60.068 52.381 0.00 0.00 36.18 3.35
239 351 3.387091 CACACCGGACGGGATGGA 61.387 66.667 9.46 0.00 39.97 3.41
245 357 2.666098 CGGACGGGATGGAAAGGGT 61.666 63.158 0.00 0.00 0.00 4.34
251 363 1.704641 GGGATGGAAAGGGTAATGGC 58.295 55.000 0.00 0.00 0.00 4.40
280 422 6.664428 TGGAAAGACAAGGGAAAATTTAGG 57.336 37.500 0.00 0.00 0.00 2.69
281 423 5.542251 TGGAAAGACAAGGGAAAATTTAGGG 59.458 40.000 0.00 0.00 0.00 3.53
304 446 9.950496 AGGGAAAGTTATATGCATACTATTGAG 57.050 33.333 8.99 0.00 0.00 3.02
305 447 9.944376 GGGAAAGTTATATGCATACTATTGAGA 57.056 33.333 8.99 0.00 0.00 3.27
381 523 1.812571 CACATAGTTTGGGCACACCTC 59.187 52.381 0.00 0.00 41.11 3.85
382 524 1.271926 ACATAGTTTGGGCACACCTCC 60.272 52.381 0.00 0.00 41.11 4.30
388 530 0.409092 TTGGGCACACCTCCAATCAT 59.591 50.000 0.00 0.00 38.04 2.45
393 535 3.513515 GGGCACACCTCCAATCATTTTTA 59.486 43.478 0.00 0.00 35.85 1.52
394 536 4.494484 GGCACACCTCCAATCATTTTTAC 58.506 43.478 0.00 0.00 0.00 2.01
395 537 4.220602 GGCACACCTCCAATCATTTTTACT 59.779 41.667 0.00 0.00 0.00 2.24
397 539 5.713025 CACACCTCCAATCATTTTTACTGG 58.287 41.667 0.00 0.00 0.00 4.00
414 556 2.490217 GGCAGCTTAGCGAGACGA 59.510 61.111 0.00 0.00 34.64 4.20
435 577 0.108041 GTGGAACGCCGGAAATCCTA 60.108 55.000 5.05 0.00 36.79 2.94
445 587 5.826208 ACGCCGGAAATCCTAAAATAAATCT 59.174 36.000 5.05 0.00 0.00 2.40
475 617 0.951040 CGAGCACCAGGACTTGAACC 60.951 60.000 0.00 0.00 0.00 3.62
476 618 0.951040 GAGCACCAGGACTTGAACCG 60.951 60.000 0.00 0.00 0.00 4.44
482 624 0.884704 CAGGACTTGAACCGTGGTGG 60.885 60.000 0.00 0.00 46.41 4.61
485 627 2.203280 CTTGAACCGTGGTGGGCA 60.203 61.111 0.00 0.00 44.64 5.36
494 636 2.001269 GTGGTGGGCAGGGGATACT 61.001 63.158 0.00 0.00 0.00 2.12
496 638 0.270699 TGGTGGGCAGGGGATACTAT 59.729 55.000 0.00 0.00 0.00 2.12
501 643 2.339769 GGGCAGGGGATACTATTGTCT 58.660 52.381 0.00 0.00 0.00 3.41
512 654 7.235812 GGGGATACTATTGTCTCTCTAACCATT 59.764 40.741 0.00 0.00 0.00 3.16
520 662 5.410924 TGTCTCTCTAACCATTCAATCACG 58.589 41.667 0.00 0.00 0.00 4.35
521 663 5.185056 TGTCTCTCTAACCATTCAATCACGA 59.815 40.000 0.00 0.00 0.00 4.35
751 893 4.594123 TGATACTGTCGAGGACAAACAA 57.406 40.909 0.00 0.00 42.26 2.83
790 932 0.313987 CGAAACCAAAAGCTGACCCC 59.686 55.000 0.00 0.00 0.00 4.95
845 987 0.389817 CTCATTTCTCACGCCCGACA 60.390 55.000 0.00 0.00 0.00 4.35
870 1012 2.639065 GCTCATACCATCGGGACAAAA 58.361 47.619 0.00 0.00 38.05 2.44
968 1110 1.068281 CATCATACTCGACTGGCAGCT 59.932 52.381 15.89 1.32 0.00 4.24
977 1119 1.950216 CGACTGGCAGCTATAGACAGA 59.050 52.381 15.89 0.00 33.57 3.41
978 1120 2.359214 CGACTGGCAGCTATAGACAGAA 59.641 50.000 15.89 0.00 33.57 3.02
990 1132 2.201921 AGACAGAAGCTAGTGTCCGA 57.798 50.000 19.79 0.00 43.54 4.55
994 1136 1.099689 AGAAGCTAGTGTCCGAGAGC 58.900 55.000 0.00 0.00 35.07 4.09
995 1137 0.811915 GAAGCTAGTGTCCGAGAGCA 59.188 55.000 0.00 0.00 37.40 4.26
1161 1303 2.558313 GTGGTCAAGAAGCAGCGC 59.442 61.111 0.00 0.00 35.67 5.92
1164 1306 2.738521 GTCAAGAAGCAGCGCGGA 60.739 61.111 13.03 0.00 0.00 5.54
1545 1691 5.901884 CACGGTAATAATGAATCAAAGACGC 59.098 40.000 0.00 0.00 0.00 5.19
1546 1692 5.815740 ACGGTAATAATGAATCAAAGACGCT 59.184 36.000 0.00 0.00 0.00 5.07
1547 1693 6.982141 ACGGTAATAATGAATCAAAGACGCTA 59.018 34.615 0.00 0.00 0.00 4.26
1613 1778 1.071228 ACAGCTGTGCAGACATCAAGA 59.929 47.619 20.97 0.00 0.00 3.02
2165 2330 1.376553 GAGCCAGCACTCCAAGTCC 60.377 63.158 0.00 0.00 0.00 3.85
2168 2333 2.046892 CAGCACTCCAAGTCCCCG 60.047 66.667 0.00 0.00 0.00 5.73
2279 2449 4.406648 TCCTCATCGTGCTATGAACATT 57.593 40.909 0.00 0.00 35.51 2.71
2996 3197 6.195600 ACTTCATCCTTGGGTAAGTACAAA 57.804 37.500 0.00 0.00 31.80 2.83
3001 3202 8.117813 TCATCCTTGGGTAAGTACAAATTTTC 57.882 34.615 0.00 0.00 31.80 2.29
3004 3205 8.541899 TCCTTGGGTAAGTACAAATTTTCTTT 57.458 30.769 0.00 0.00 31.80 2.52
3051 3282 4.045636 GCCAAAGCCCAATTAGTACATG 57.954 45.455 0.00 0.00 0.00 3.21
3053 3284 4.642885 GCCAAAGCCCAATTAGTACATGTA 59.357 41.667 0.08 0.08 0.00 2.29
3070 3301 1.202879 TGTAGGAAAACTGGGCCAGTG 60.203 52.381 38.18 16.00 44.62 3.66
3071 3302 1.145571 TAGGAAAACTGGGCCAGTGT 58.854 50.000 38.18 31.43 44.62 3.55
3072 3303 1.145571 AGGAAAACTGGGCCAGTGTA 58.854 50.000 38.18 0.00 44.62 2.90
3073 3304 1.073923 AGGAAAACTGGGCCAGTGTAG 59.926 52.381 38.18 14.35 44.62 2.74
3074 3305 0.881796 GAAAACTGGGCCAGTGTAGC 59.118 55.000 38.18 24.02 44.62 3.58
3115 3346 4.444306 GCTGGGCCAGAATTACATACAGTA 60.444 45.833 37.07 0.00 32.44 2.74
3121 3412 7.937394 GGGCCAGAATTACATACAGTAGTTTAT 59.063 37.037 4.39 0.00 33.36 1.40
3143 3434 2.161486 GCGACCGTGCTGATGTCTC 61.161 63.158 0.00 0.00 0.00 3.36
3145 3436 0.799917 CGACCGTGCTGATGTCTCTG 60.800 60.000 0.00 0.00 0.00 3.35
3153 3444 1.547820 GCTGATGTCTCTGTGTCTGGA 59.452 52.381 0.00 0.00 0.00 3.86
3154 3445 2.673610 GCTGATGTCTCTGTGTCTGGAC 60.674 54.545 0.00 0.00 0.00 4.02
3324 3615 2.125673 ATGAACGAGTTCGGCGGG 60.126 61.111 7.21 0.00 44.95 6.13
3394 3685 1.639298 GAACCTCACCATCAGCGTGC 61.639 60.000 0.00 0.00 0.00 5.34
3395 3686 2.046988 CCTCACCATCAGCGTGCA 60.047 61.111 0.00 0.00 0.00 4.57
3506 3797 3.008049 TCCAAGAACAAGAGGAAGTAGCC 59.992 47.826 0.00 0.00 0.00 3.93
3507 3798 3.008485 CCAAGAACAAGAGGAAGTAGCCT 59.992 47.826 0.00 0.00 42.17 4.58
3523 3826 2.336809 CTCGCCTCGCCTGTATCC 59.663 66.667 0.00 0.00 0.00 2.59
3544 3847 4.724074 CACATATCATGGTGGTTTGCTT 57.276 40.909 0.00 0.00 33.60 3.91
3545 3848 5.075858 CACATATCATGGTGGTTTGCTTT 57.924 39.130 0.00 0.00 33.60 3.51
3546 3849 4.865925 CACATATCATGGTGGTTTGCTTTG 59.134 41.667 0.00 0.00 33.60 2.77
3547 3850 2.460757 ATCATGGTGGTTTGCTTTGC 57.539 45.000 0.00 0.00 0.00 3.68
3548 3851 1.412079 TCATGGTGGTTTGCTTTGCT 58.588 45.000 0.00 0.00 0.00 3.91
3549 3852 1.068895 TCATGGTGGTTTGCTTTGCTG 59.931 47.619 0.00 0.00 0.00 4.41
3558 3861 2.995939 GTTTGCTTTGCTGGCTTAATCC 59.004 45.455 0.00 0.00 0.00 3.01
3559 3862 1.185315 TGCTTTGCTGGCTTAATCCC 58.815 50.000 0.00 0.00 0.00 3.85
3573 3886 4.742138 GCTTAATCCCAAGCTCTCTGGTAG 60.742 50.000 2.31 0.00 46.04 3.18
3623 3974 2.035193 ACGGATCATGTCAAGATCTCCG 59.965 50.000 15.23 15.23 41.24 4.63
3640 3991 6.551601 AGATCTCCGTCCAAGATTTGTAGTAT 59.448 38.462 0.00 0.00 33.64 2.12
3684 4035 9.725019 TTTCAGATAAGACATTGTGTTGATACT 57.275 29.630 9.29 1.51 0.00 2.12
3685 4036 9.725019 TTCAGATAAGACATTGTGTTGATACTT 57.275 29.630 9.29 0.46 0.00 2.24
3686 4037 9.154847 TCAGATAAGACATTGTGTTGATACTTG 57.845 33.333 9.29 0.94 0.00 3.16
3687 4038 9.154847 CAGATAAGACATTGTGTTGATACTTGA 57.845 33.333 9.29 0.00 0.00 3.02
3736 4087 3.557595 CAGTATTTTCTCCGATCAGTGGC 59.442 47.826 0.00 0.00 0.00 5.01
3775 4126 2.435059 GTCGCACCTCTTGGGCTC 60.435 66.667 0.00 0.00 38.07 4.70
3830 4181 1.852895 GTGACGTGACTGACAGACAAC 59.147 52.381 10.08 0.62 0.00 3.32
3834 4186 2.930040 ACGTGACTGACAGACAACTTTG 59.070 45.455 10.08 0.87 0.00 2.77
3880 4234 2.620112 CCTGCAGCCACCACGAAAG 61.620 63.158 8.66 0.00 0.00 2.62
3907 4261 1.614583 GGAACTGGCTTTCCTCCCTTC 60.615 57.143 10.25 0.00 41.80 3.46
3910 4264 2.438614 GGCTTTCCTCCCTTCGCC 60.439 66.667 0.00 0.00 0.00 5.54
3946 4300 2.611292 GCCAACCGATCTTGATCTCTTG 59.389 50.000 8.70 8.75 0.00 3.02
3957 4311 2.802256 TGATCTCTTGCTCAACGATCG 58.198 47.619 14.88 14.88 34.66 3.69
3981 4335 1.262640 GGACTAAACCTCGGGGAGCA 61.263 60.000 9.33 0.00 36.25 4.26
3982 4336 0.175989 GACTAAACCTCGGGGAGCAG 59.824 60.000 9.33 3.46 36.25 4.24
3983 4337 0.252103 ACTAAACCTCGGGGAGCAGA 60.252 55.000 9.33 0.00 36.25 4.26
3984 4338 0.175989 CTAAACCTCGGGGAGCAGAC 59.824 60.000 9.33 0.00 36.25 3.51
3985 4339 1.601419 TAAACCTCGGGGAGCAGACG 61.601 60.000 9.33 0.00 36.25 4.18
4120 4494 0.460987 CACAGGATCGTTCAGCCTCC 60.461 60.000 0.00 0.00 0.00 4.30
4122 4496 0.103937 CAGGATCGTTCAGCCTCCTC 59.896 60.000 0.00 0.00 35.95 3.71
4136 4517 3.260632 AGCCTCCTCTTTTCTGAAGTCTC 59.739 47.826 0.00 0.00 0.00 3.36
4195 4576 9.376075 CAATCCAGAATCTTATCTACGCATTAT 57.624 33.333 0.00 0.00 0.00 1.28
4234 4615 3.189287 CCCGTTTTCTGAAATCTGACCAG 59.811 47.826 3.31 0.00 0.00 4.00
4275 4657 1.968540 GCTCTGAAAGCGTGGCCTT 60.969 57.895 3.32 0.00 42.21 4.35
4307 4689 7.148820 GCTAAATTTGTTTGCGCAAAAGAGATA 60.149 33.333 35.09 21.39 41.03 1.98
4323 4716 3.387374 AGAGATACTCCATGAGTGGCAAG 59.613 47.826 7.00 0.00 43.30 4.01
4370 4763 5.121811 AGCCTGACATGCTAACAAGATAAG 58.878 41.667 3.10 0.00 37.28 1.73
4491 4884 1.939934 TGGAACTGCAAGAAACGTCAG 59.060 47.619 0.00 0.00 37.43 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 3.938963 TGACTCCAAAGACAACAGACAAC 59.061 43.478 0.00 0.00 0.00 3.32
54 56 3.904800 TGACTCCAAAGACAACAGACA 57.095 42.857 0.00 0.00 0.00 3.41
63 65 3.532896 GTCGCCATGACTCCAAAGA 57.467 52.632 0.00 0.00 44.58 2.52
75 77 0.885879 AGATGTTGTACGAGTCGCCA 59.114 50.000 13.59 6.94 0.00 5.69
77 79 1.132643 AGGAGATGTTGTACGAGTCGC 59.867 52.381 13.59 0.00 0.00 5.19
104 106 3.606886 GGCTTCAAGGAAGACGTCA 57.393 52.632 19.50 0.00 41.71 4.35
108 110 2.751806 CCAAGATGGCTTCAAGGAAGAC 59.248 50.000 10.01 7.50 46.98 3.01
115 117 1.477553 GGCATCCAAGATGGCTTCAA 58.522 50.000 20.30 0.00 40.85 2.69
127 129 0.042581 TCCCAGTGACTAGGCATCCA 59.957 55.000 0.00 0.00 0.00 3.41
133 135 2.427245 CGGCCTCCCAGTGACTAGG 61.427 68.421 0.00 0.00 0.00 3.02
134 136 2.427245 CCGGCCTCCCAGTGACTAG 61.427 68.421 0.00 0.00 0.00 2.57
135 137 2.363795 CCGGCCTCCCAGTGACTA 60.364 66.667 0.00 0.00 0.00 2.59
136 138 3.846405 TTCCGGCCTCCCAGTGACT 62.846 63.158 0.00 0.00 0.00 3.41
137 139 3.319198 TTCCGGCCTCCCAGTGAC 61.319 66.667 0.00 0.00 0.00 3.67
138 140 3.319198 GTTCCGGCCTCCCAGTGA 61.319 66.667 0.00 0.00 0.00 3.41
139 141 3.612247 CTGTTCCGGCCTCCCAGTG 62.612 68.421 0.00 0.00 0.00 3.66
140 142 3.322466 CTGTTCCGGCCTCCCAGT 61.322 66.667 0.00 0.00 0.00 4.00
141 143 3.003173 TCTGTTCCGGCCTCCCAG 61.003 66.667 0.00 1.49 0.00 4.45
142 144 3.319198 GTCTGTTCCGGCCTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
143 145 3.003763 AGTCTGTTCCGGCCTCCC 61.004 66.667 0.00 0.00 0.00 4.30
144 146 2.579738 GAGTCTGTTCCGGCCTCC 59.420 66.667 0.00 0.00 0.00 4.30
145 147 2.182030 CGAGTCTGTTCCGGCCTC 59.818 66.667 0.00 0.00 0.00 4.70
146 148 3.382832 CCGAGTCTGTTCCGGCCT 61.383 66.667 0.00 0.00 36.62 5.19
147 149 4.452733 CCCGAGTCTGTTCCGGCC 62.453 72.222 0.00 0.00 41.74 6.13
148 150 3.236003 AACCCGAGTCTGTTCCGGC 62.236 63.158 0.00 0.00 41.74 6.13
192 194 3.823330 GATCCGTCCGTCGTGGCT 61.823 66.667 0.00 0.00 37.80 4.75
224 226 1.449601 CTTTCCATCCCGTCCGGTG 60.450 63.158 0.00 0.00 0.00 4.94
228 230 0.913924 TTACCCTTTCCATCCCGTCC 59.086 55.000 0.00 0.00 0.00 4.79
236 348 2.189676 TCTACGCCATTACCCTTTCCA 58.810 47.619 0.00 0.00 0.00 3.53
239 351 2.775384 TCCATCTACGCCATTACCCTTT 59.225 45.455 0.00 0.00 0.00 3.11
245 357 4.746535 TGTCTTTCCATCTACGCCATTA 57.253 40.909 0.00 0.00 0.00 1.90
251 363 3.887621 TCCCTTGTCTTTCCATCTACG 57.112 47.619 0.00 0.00 0.00 3.51
291 433 7.070447 ACTCTCTCCAATTCTCAATAGTATGCA 59.930 37.037 0.00 0.00 0.00 3.96
360 502 0.887933 GGTGTGCCCAAACTATGTGG 59.112 55.000 0.00 0.00 35.77 4.17
381 523 3.196254 AGCTGCCCAGTAAAAATGATTGG 59.804 43.478 0.00 0.00 0.00 3.16
382 524 4.460948 AGCTGCCCAGTAAAAATGATTG 57.539 40.909 0.00 0.00 0.00 2.67
388 530 1.810151 CGCTAAGCTGCCCAGTAAAAA 59.190 47.619 0.00 0.00 0.00 1.94
393 535 1.984570 TCTCGCTAAGCTGCCCAGT 60.985 57.895 0.00 0.00 0.00 4.00
394 536 1.520342 GTCTCGCTAAGCTGCCCAG 60.520 63.158 0.00 0.00 0.00 4.45
395 537 2.579201 GTCTCGCTAAGCTGCCCA 59.421 61.111 0.00 0.00 0.00 5.36
397 539 1.142778 CTTCGTCTCGCTAAGCTGCC 61.143 60.000 0.00 0.00 0.00 4.85
414 556 0.958876 GGATTTCCGGCGTTCCACTT 60.959 55.000 6.01 0.00 0.00 3.16
421 563 5.826208 AGATTTATTTTAGGATTTCCGGCGT 59.174 36.000 6.01 0.00 42.08 5.68
435 577 9.066892 TGCTCGCATTATTCCTAGATTTATTTT 57.933 29.630 0.00 0.00 0.00 1.82
445 587 2.224281 CCTGGTGCTCGCATTATTCCTA 60.224 50.000 0.00 0.00 0.00 2.94
475 617 3.087253 TATCCCCTGCCCACCACG 61.087 66.667 0.00 0.00 0.00 4.94
476 618 0.693092 TAGTATCCCCTGCCCACCAC 60.693 60.000 0.00 0.00 0.00 4.16
482 624 3.243724 AGAGACAATAGTATCCCCTGCC 58.756 50.000 0.00 0.00 36.65 4.85
485 627 6.125860 TGGTTAGAGAGACAATAGTATCCCCT 60.126 42.308 0.00 0.00 36.65 4.79
494 636 7.706607 CGTGATTGAATGGTTAGAGAGACAATA 59.293 37.037 0.00 0.00 0.00 1.90
496 638 5.869344 CGTGATTGAATGGTTAGAGAGACAA 59.131 40.000 0.00 0.00 0.00 3.18
501 643 5.661056 ACTCGTGATTGAATGGTTAGAGA 57.339 39.130 0.00 0.00 0.00 3.10
512 654 3.130633 CTGTGAACCAACTCGTGATTGA 58.869 45.455 0.00 0.00 0.00 2.57
608 750 7.704578 TGCCAGGTGTCTATAATAGAGTATC 57.295 40.000 0.00 0.00 35.04 2.24
722 864 0.668535 TCGACAGTATCATGGCCTCG 59.331 55.000 3.32 0.86 0.00 4.63
790 932 0.790207 CATCGGAGTGAACGTTGGTG 59.210 55.000 5.00 0.00 0.00 4.17
845 987 1.774254 TCCCGATGGTATGAGCCAATT 59.226 47.619 0.00 0.00 42.48 2.32
947 1089 1.202463 GCTGCCAGTCGAGTATGATGT 60.202 52.381 0.00 0.00 0.00 3.06
957 1099 1.950216 TCTGTCTATAGCTGCCAGTCG 59.050 52.381 0.00 0.00 0.00 4.18
968 1110 5.032327 TCGGACACTAGCTTCTGTCTATA 57.968 43.478 18.14 6.29 37.53 1.31
977 1119 0.528470 GTGCTCTCGGACACTAGCTT 59.472 55.000 0.00 0.00 35.95 3.74
978 1120 0.609406 TGTGCTCTCGGACACTAGCT 60.609 55.000 0.00 0.00 36.50 3.32
990 1132 4.334118 TGCGCCATGGTGTGCTCT 62.334 61.111 25.68 0.00 42.20 4.09
1035 1177 0.824109 CTATCACGGCTTCCAGGTCA 59.176 55.000 0.00 0.00 0.00 4.02
1518 1660 7.010183 CGTCTTTGATTCATTATTACCGTGAGT 59.990 37.037 0.00 0.00 0.00 3.41
1545 1691 4.142397 CGCACGTACGAATGATCTAGTAG 58.858 47.826 24.41 0.00 34.06 2.57
1546 1692 3.605461 GCGCACGTACGAATGATCTAGTA 60.605 47.826 24.41 0.00 34.06 1.82
1547 1693 2.853662 GCGCACGTACGAATGATCTAGT 60.854 50.000 24.41 0.00 34.06 2.57
1613 1778 0.388907 CGTCCCCGATGTACGTGTTT 60.389 55.000 0.00 0.00 40.78 2.83
2279 2449 0.744874 CGATTCCCGGAGACAAGCTA 59.255 55.000 0.73 0.00 33.91 3.32
3001 3202 6.762333 ACCAATCCATTTCCTCTTCAAAAAG 58.238 36.000 0.00 0.00 0.00 2.27
3004 3205 4.772100 GGACCAATCCATTTCCTCTTCAAA 59.228 41.667 0.00 0.00 45.47 2.69
3007 3208 2.945668 CGGACCAATCCATTTCCTCTTC 59.054 50.000 0.00 0.00 46.67 2.87
3008 3209 2.357154 CCGGACCAATCCATTTCCTCTT 60.357 50.000 0.00 0.00 46.67 2.85
3009 3210 1.212935 CCGGACCAATCCATTTCCTCT 59.787 52.381 0.00 0.00 46.67 3.69
3045 3276 3.014623 GGCCCAGTTTTCCTACATGTAC 58.985 50.000 0.08 0.00 0.00 2.90
3046 3277 2.645297 TGGCCCAGTTTTCCTACATGTA 59.355 45.455 5.25 5.25 0.00 2.29
3047 3278 1.427368 TGGCCCAGTTTTCCTACATGT 59.573 47.619 2.69 2.69 0.00 3.21
3051 3282 1.202891 ACACTGGCCCAGTTTTCCTAC 60.203 52.381 15.33 0.00 42.59 3.18
3053 3284 1.073923 CTACACTGGCCCAGTTTTCCT 59.926 52.381 15.33 0.00 42.59 3.36
3070 3301 1.933853 CGCTAACCCATGTTCAGCTAC 59.066 52.381 0.00 0.00 35.87 3.58
3071 3302 1.134521 CCGCTAACCCATGTTCAGCTA 60.135 52.381 0.00 0.00 35.87 3.32
3072 3303 0.392998 CCGCTAACCCATGTTCAGCT 60.393 55.000 0.00 0.00 35.87 4.24
3073 3304 1.376609 CCCGCTAACCCATGTTCAGC 61.377 60.000 0.00 0.00 35.87 4.26
3074 3305 1.376609 GCCCGCTAACCCATGTTCAG 61.377 60.000 0.00 0.00 35.87 3.02
3115 3346 2.607635 CAGCACGGTCGCAATATAAACT 59.392 45.455 5.59 0.00 0.00 2.66
3121 3412 0.108377 ACATCAGCACGGTCGCAATA 60.108 50.000 5.59 0.00 0.00 1.90
3123 3414 2.027073 GACATCAGCACGGTCGCAA 61.027 57.895 5.59 0.00 0.00 4.85
3124 3415 2.432456 GACATCAGCACGGTCGCA 60.432 61.111 5.59 0.00 0.00 5.10
3127 3418 0.244994 ACAGAGACATCAGCACGGTC 59.755 55.000 0.00 0.00 0.00 4.79
3143 3434 2.258591 CCGTCCGTCCAGACACAG 59.741 66.667 0.00 0.00 36.52 3.66
3145 3436 2.257676 GACCGTCCGTCCAGACAC 59.742 66.667 0.00 0.00 36.52 3.67
3324 3615 1.941734 CGAGGAGAAGATGCGCGTC 60.942 63.158 22.11 22.11 37.75 5.19
3332 3623 2.348888 GGCGGGTTCGAGGAGAAGA 61.349 63.158 0.00 0.00 39.95 2.87
3394 3685 1.227823 TCCACTTGCGGTCCTTGTG 60.228 57.895 0.00 0.00 0.00 3.33
3395 3686 1.071471 CTCCACTTGCGGTCCTTGT 59.929 57.895 0.00 0.00 0.00 3.16
3506 3797 2.336809 GGATACAGGCGAGGCGAG 59.663 66.667 0.00 0.00 0.00 5.03
3507 3798 2.441348 TGGATACAGGCGAGGCGA 60.441 61.111 0.00 0.00 46.17 5.54
3523 3826 4.724074 AAGCAAACCACCATGATATGTG 57.276 40.909 0.00 0.00 0.00 3.21
3544 3847 1.185315 GCTTGGGATTAAGCCAGCAA 58.815 50.000 15.20 8.77 45.62 3.91
3545 3848 2.886382 GCTTGGGATTAAGCCAGCA 58.114 52.632 15.20 1.26 45.62 4.41
3558 3861 3.196469 TGAATGACTACCAGAGAGCTTGG 59.804 47.826 1.15 1.15 0.00 3.61
3559 3862 4.462508 TGAATGACTACCAGAGAGCTTG 57.537 45.455 0.00 0.00 0.00 4.01
3573 3886 5.095490 GTCCCGTCAATTCAAATGAATGAC 58.905 41.667 9.28 15.15 43.41 3.06
3736 4087 0.512518 TGCAATCAGAGCGAACAACG 59.487 50.000 0.00 0.00 45.66 4.10
3805 4156 2.016704 GTCAGTCACGTCACCGCAG 61.017 63.158 0.00 0.00 37.70 5.18
3834 4186 3.529807 ACCTACGGGTCAGTAGCATGAC 61.530 54.545 0.00 7.89 43.38 3.06
3843 4197 0.175073 GCTACCAACCTACGGGTCAG 59.825 60.000 0.00 0.00 46.67 3.51
3855 4209 2.034066 GTGGCTGCAGGCTACCAA 59.966 61.111 36.39 16.97 45.00 3.67
3946 4300 2.271800 AGTCCATTTCGATCGTTGAGC 58.728 47.619 15.94 7.73 0.00 4.26
3957 4311 2.237893 TCCCCGAGGTTTAGTCCATTTC 59.762 50.000 0.00 0.00 0.00 2.17
4120 4494 7.727331 AGATTGTTGAGACTTCAGAAAAGAG 57.273 36.000 0.00 0.00 34.15 2.85
4136 4517 5.651172 TGTCCGCGATAAATAGATTGTTG 57.349 39.130 8.23 0.00 0.00 3.33
4195 4576 8.035984 AGAAAACGGGTTGTTGAAGAATAAAAA 58.964 29.630 0.00 0.00 40.84 1.94
4203 4584 4.364415 TTCAGAAAACGGGTTGTTGAAG 57.636 40.909 2.23 0.00 40.84 3.02
4234 4615 5.502544 GCCTCGCTGTTCACAATAAATAGAC 60.503 44.000 0.00 0.00 0.00 2.59
4275 4657 3.303001 GCGCAAACAAATTTAGCAAGCAA 60.303 39.130 0.30 0.00 33.36 3.91
4323 4716 2.500509 TGGACGGCACACAATTTTTC 57.499 45.000 0.00 0.00 0.00 2.29
4370 4763 1.465187 GCTTCCAACCGCAAACGATAC 60.465 52.381 0.00 0.00 43.93 2.24
4456 4849 5.412594 TGCAGTTCCAGTTCAGAATCATTAC 59.587 40.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.