Multiple sequence alignment - TraesCS7A01G234800

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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 TraesCS7A01G234800 chr7A 100.000 5386 0 0 1 5386 206909726 206915111 0.000000e+00 9947.0
1 TraesCS7A01G234800 chr7B 94.155 4688 183 43 1 4622 161775505 161780167 0.000000e+00 7055.0
2 TraesCS7A01G234800 chr7D 94.940 3893 118 31 1 3848 197609691 197613549 0.000000e+00 6024.0
3 TraesCS7A01G234800 chr7D 91.436 759 23 17 3884 4620 197613782 197614520 0.000000e+00 1003.0
4 TraesCS7A01G234800 chr5A 79.484 3217 538 94 1093 4238 470193422 470196587 0.000000e+00 2172.0
5 TraesCS7A01G234800 chr5A 98.164 599 11 0 4788 5386 661219299 661219897 0.000000e+00 1046.0
6 TraesCS7A01G234800 chr5A 89.175 194 17 2 1049 1240 24400641 24400832 6.970000e-59 239.0
7 TraesCS7A01G234800 chr5B 79.211 3218 553 81 1093 4238 436256278 436259451 0.000000e+00 2130.0
8 TraesCS7A01G234800 chr5B 78.261 115 15 9 4680 4789 27480048 27480157 1.250000e-06 65.8
9 TraesCS7A01G234800 chr5D 79.971 2791 478 54 1093 3835 368330375 368333132 0.000000e+00 1982.0
10 TraesCS7A01G234800 chr5D 81.081 333 50 11 3910 4238 368333238 368333561 2.490000e-63 254.0
11 TraesCS7A01G234800 chr5D 84.906 106 15 1 4685 4789 397316911 397316806 7.380000e-19 106.0
12 TraesCS7A01G234800 chr2B 91.653 599 46 2 4788 5386 623397856 623397262 0.000000e+00 826.0
13 TraesCS7A01G234800 chr2B 76.488 336 60 13 3900 4231 3292131 3292451 1.200000e-36 165.0
14 TraesCS7A01G234800 chr2B 88.679 106 8 4 4686 4789 623398422 623398319 5.660000e-25 126.0
15 TraesCS7A01G234800 chr2B 100.000 28 0 0 4680 4707 765029985 765029958 1.000000e-02 52.8
16 TraesCS7A01G234800 chr3D 91.379 232 19 1 1049 1279 466417223 466416992 3.130000e-82 316.0
17 TraesCS7A01G234800 chr3D 71.587 1084 246 56 1082 2134 46580520 46581572 6.970000e-59 239.0
18 TraesCS7A01G234800 chr3D 76.190 315 63 9 3910 4218 46583415 46583723 7.220000e-34 156.0
19 TraesCS7A01G234800 chr4A 80.441 363 59 12 5012 5368 5068923 5069279 3.200000e-67 267.0
20 TraesCS7A01G234800 chr4A 80.000 80 8 6 4680 4756 18845646 18845572 1.000000e-02 52.8
21 TraesCS7A01G234800 chr3B 71.982 1085 240 58 1082 2134 72950373 72951425 1.490000e-65 261.0
22 TraesCS7A01G234800 chr3B 77.055 292 55 9 3933 4218 72953296 72953581 2.010000e-34 158.0
23 TraesCS7A01G234800 chr3A 71.901 1089 240 58 1082 2137 57947671 57946616 6.920000e-64 255.0
24 TraesCS7A01G234800 chr3A 76.161 323 64 11 3902 4218 57944795 57944480 2.010000e-34 158.0
25 TraesCS7A01G234800 chr6A 80.342 117 10 12 4680 4789 602589764 602589654 5.780000e-10 76.8
26 TraesCS7A01G234800 chr1B 100.000 29 0 0 4679 4707 154599884 154599912 3.000000e-03 54.7


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 TraesCS7A01G234800 chr7A 206909726 206915111 5385 False 9947.0 9947 100.0000 1 5386 1 chr7A.!!$F1 5385
1 TraesCS7A01G234800 chr7B 161775505 161780167 4662 False 7055.0 7055 94.1550 1 4622 1 chr7B.!!$F1 4621
2 TraesCS7A01G234800 chr7D 197609691 197614520 4829 False 3513.5 6024 93.1880 1 4620 2 chr7D.!!$F1 4619
3 TraesCS7A01G234800 chr5A 470193422 470196587 3165 False 2172.0 2172 79.4840 1093 4238 1 chr5A.!!$F2 3145
4 TraesCS7A01G234800 chr5A 661219299 661219897 598 False 1046.0 1046 98.1640 4788 5386 1 chr5A.!!$F3 598
5 TraesCS7A01G234800 chr5B 436256278 436259451 3173 False 2130.0 2130 79.2110 1093 4238 1 chr5B.!!$F2 3145
6 TraesCS7A01G234800 chr5D 368330375 368333561 3186 False 1118.0 1982 80.5260 1093 4238 2 chr5D.!!$F1 3145
7 TraesCS7A01G234800 chr2B 623397262 623398422 1160 True 476.0 826 90.1660 4686 5386 2 chr2B.!!$R2 700
8 TraesCS7A01G234800 chr3B 72950373 72953581 3208 False 209.5 261 74.5185 1082 4218 2 chr3B.!!$F1 3136
9 TraesCS7A01G234800 chr3A 57944480 57947671 3191 True 206.5 255 74.0310 1082 4218 2 chr3A.!!$R1 3136

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
474 514 0.098728 ACTTGCACAACAACGACAGC 59.901 50.000 0.0 0.0 33.68 4.40 F
2403 2492 0.108138 ACTGCACCAATCTCTACCGC 60.108 55.000 0.0 0.0 0.00 5.68 F
2976 3146 1.444553 GGAGAACCTCGTCACGCTG 60.445 63.158 0.0 0.0 0.00 5.18 F
3839 4317 0.246910 TACATCGCGCCAGGTAACAA 59.753 50.000 0.0 0.0 41.41 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2976 3146 5.688176 GGAGAAGCTGTTGTACGAGATATTC 59.312 44.000 0.00 0.0 0.00 1.75 R
3378 3616 0.321653 ACCACATCTTCTTCACGGCC 60.322 55.000 0.00 0.0 0.00 6.13 R
3891 4375 0.861837 GCTCCCACAAGAATATCGCG 59.138 55.000 0.00 0.0 0.00 5.87 R
4661 5183 1.135333 GGGAGCGTTCCTCTGTTCTAG 59.865 57.143 18.44 0.0 43.49 2.43 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
28 29 5.940470 ACAGCCTCTGAATTAGTTTAACTGG 59.060 40.000 8.00 0.00 35.18 4.00
149 157 4.637276 TGCTGCTGCTACTGTAAGTTTTA 58.363 39.130 17.00 0.00 42.57 1.52
189 197 1.627329 TGCAGTGCAGGAGAAGAAGAT 59.373 47.619 15.37 0.00 33.32 2.40
221 229 4.918810 AAGGTTGGTTTCTTTGCTAGTG 57.081 40.909 0.00 0.00 0.00 2.74
222 230 4.164843 AGGTTGGTTTCTTTGCTAGTGA 57.835 40.909 0.00 0.00 0.00 3.41
223 231 4.137543 AGGTTGGTTTCTTTGCTAGTGAG 58.862 43.478 0.00 0.00 0.00 3.51
224 232 3.883489 GGTTGGTTTCTTTGCTAGTGAGT 59.117 43.478 0.00 0.00 0.00 3.41
225 233 5.061179 GGTTGGTTTCTTTGCTAGTGAGTA 58.939 41.667 0.00 0.00 0.00 2.59
226 234 5.179555 GGTTGGTTTCTTTGCTAGTGAGTAG 59.820 44.000 0.00 0.00 0.00 2.57
227 235 5.546621 TGGTTTCTTTGCTAGTGAGTAGT 57.453 39.130 0.00 0.00 0.00 2.73
229 237 6.688578 TGGTTTCTTTGCTAGTGAGTAGTAG 58.311 40.000 0.00 0.00 33.73 2.57
250 258 1.279496 CAGGTCATCAGTCCCAAGGA 58.721 55.000 0.00 0.00 0.00 3.36
283 291 1.570803 AGAGCTCAGAGCATGTTCCT 58.429 50.000 24.64 8.15 45.56 3.36
389 397 3.118261 CCATGCTTAGCTTAACCTCTGGA 60.118 47.826 5.60 0.00 0.00 3.86
424 463 4.787551 TCCAGCAGGTACAAAAGAAGAAA 58.212 39.130 0.00 0.00 35.89 2.52
427 466 5.979517 CCAGCAGGTACAAAAGAAGAAAAAG 59.020 40.000 0.00 0.00 0.00 2.27
437 477 7.441836 ACAAAAGAAGAAAAAGTTTCACAGGT 58.558 30.769 3.74 0.00 0.00 4.00
474 514 0.098728 ACTTGCACAACAACGACAGC 59.901 50.000 0.00 0.00 33.68 4.40
498 538 9.700831 AGCTTAATTAAAGTTGGATGGATTACT 57.299 29.630 0.00 0.00 37.53 2.24
572 615 3.544698 TTCACTCTCACCTCCTAACCT 57.455 47.619 0.00 0.00 0.00 3.50
580 623 4.715297 TCTCACCTCCTAACCTGGATTAAC 59.285 45.833 0.00 0.00 35.30 2.01
581 624 4.431378 TCACCTCCTAACCTGGATTAACA 58.569 43.478 0.00 0.00 35.30 2.41
583 626 5.491078 TCACCTCCTAACCTGGATTAACAAT 59.509 40.000 0.00 0.00 35.30 2.71
584 627 5.590259 CACCTCCTAACCTGGATTAACAATG 59.410 44.000 0.00 0.00 35.30 2.82
587 636 6.889722 CCTCCTAACCTGGATTAACAATGAAA 59.110 38.462 0.00 0.00 35.30 2.69
588 637 7.396055 CCTCCTAACCTGGATTAACAATGAAAA 59.604 37.037 0.00 0.00 35.30 2.29
608 657 8.565896 TGAAAATAATCAGTGCATCAACTAGT 57.434 30.769 0.00 0.00 0.00 2.57
611 660 9.672673 AAAATAATCAGTGCATCAACTAGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
613 662 9.751542 AATAATCAGTGCATCAACTAGTAGTAC 57.248 33.333 2.50 0.00 0.00 2.73
614 663 7.411486 AATCAGTGCATCAACTAGTAGTACT 57.589 36.000 8.14 8.14 0.00 2.73
615 664 8.521170 AATCAGTGCATCAACTAGTAGTACTA 57.479 34.615 9.66 9.66 0.00 1.82
616 665 7.317842 TCAGTGCATCAACTAGTAGTACTAC 57.682 40.000 23.03 23.03 36.35 2.73
617 666 6.318144 TCAGTGCATCAACTAGTAGTACTACC 59.682 42.308 25.97 11.01 36.75 3.18
618 667 6.319152 CAGTGCATCAACTAGTAGTACTACCT 59.681 42.308 25.97 16.73 36.75 3.08
645 697 1.034292 GCATCAAGAGCCACCTTCCC 61.034 60.000 0.00 0.00 0.00 3.97
674 726 4.519540 TCTCCTTGCTTAAACAAATGCC 57.480 40.909 0.00 0.00 0.00 4.40
736 788 1.633561 CACGCTCATCCAGTGTACTG 58.366 55.000 5.05 5.05 44.55 2.74
934 987 0.790993 TCCCTCCCACTCTACAACCT 59.209 55.000 0.00 0.00 0.00 3.50
937 990 0.818296 CTCCCACTCTACAACCTCGG 59.182 60.000 0.00 0.00 0.00 4.63
953 1010 4.066139 GGCCCTCCCAATGCCACT 62.066 66.667 0.00 0.00 44.70 4.00
954 1011 2.689691 GGCCCTCCCAATGCCACTA 61.690 63.158 0.00 0.00 44.70 2.74
956 1013 1.153168 CCCTCCCAATGCCACTACG 60.153 63.158 0.00 0.00 0.00 3.51
959 1016 1.541233 CCTCCCAATGCCACTACGATC 60.541 57.143 0.00 0.00 0.00 3.69
973 1031 0.968901 ACGATCGTAGGAGGTGCCAA 60.969 55.000 21.32 0.00 40.02 4.52
996 1054 3.075005 GCCTCACTCCACGGCCTA 61.075 66.667 0.00 0.00 37.86 3.93
1008 1066 0.617820 ACGGCCTACCAATGTCTCCT 60.618 55.000 0.00 0.00 34.57 3.69
1780 1860 1.068083 ATCTACACCGCCATGCTCG 59.932 57.895 0.00 0.00 0.00 5.03
1848 1928 5.083821 AGCCTCTATCTCTACCAGAATTCC 58.916 45.833 0.65 0.00 33.62 3.01
2403 2492 0.108138 ACTGCACCAATCTCTACCGC 60.108 55.000 0.00 0.00 0.00 5.68
2976 3146 1.444553 GGAGAACCTCGTCACGCTG 60.445 63.158 0.00 0.00 0.00 5.18
3839 4317 0.246910 TACATCGCGCCAGGTAACAA 59.753 50.000 0.00 0.00 41.41 2.83
3863 4341 8.764287 CAACAAAATTCTTCAAAATCTGTACCC 58.236 33.333 0.00 0.00 0.00 3.69
3872 4350 6.928348 TCAAAATCTGTACCCTCTCTAACA 57.072 37.500 0.00 0.00 0.00 2.41
3879 4363 6.936279 TCTGTACCCTCTCTAACAGAAATTG 58.064 40.000 1.73 0.00 43.90 2.32
3896 4387 5.812642 AGAAATTGTTCTTACTGATCGCGAT 59.187 36.000 23.97 23.97 41.55 4.58
4148 4642 1.742880 GATGCTGCAGGTCTTCGCA 60.743 57.895 17.12 6.41 36.52 5.10
4398 4893 1.749638 AGCTGAGCTGCTTGATGCC 60.750 57.895 5.97 0.00 40.93 4.40
4408 4903 1.911293 GCTTGATGCCGTTGCGAGAA 61.911 55.000 0.00 0.00 41.78 2.87
4429 4928 1.817099 CAGCAGCCTTAGCGGGAAG 60.817 63.158 0.00 0.00 46.67 3.46
4455 4954 7.762159 GGAAACTTTGTGTAGAAATTTTGGACA 59.238 33.333 0.00 0.00 0.00 4.02
4459 4959 8.908903 ACTTTGTGTAGAAATTTTGGACACATA 58.091 29.630 23.31 19.54 46.98 2.29
4460 4960 9.912634 CTTTGTGTAGAAATTTTGGACACATAT 57.087 29.630 23.31 0.00 46.98 1.78
4461 4961 9.906660 TTTGTGTAGAAATTTTGGACACATATC 57.093 29.630 23.31 6.66 46.98 1.63
4589 5111 2.768253 TAACAGACATGGGTGAGCAG 57.232 50.000 0.00 0.00 0.00 4.24
4603 5125 1.613925 TGAGCAGTTGAGTTACGCTCT 59.386 47.619 10.66 0.00 44.41 4.09
4646 5168 7.698836 AAACAGGAAGAATCAAAAATTGACG 57.301 32.000 0.00 0.00 43.48 4.35
4647 5169 6.391227 ACAGGAAGAATCAAAAATTGACGT 57.609 33.333 0.00 0.00 43.48 4.34
4648 5170 6.208644 ACAGGAAGAATCAAAAATTGACGTG 58.791 36.000 0.00 0.00 43.48 4.49
4649 5171 6.183360 ACAGGAAGAATCAAAAATTGACGTGT 60.183 34.615 0.00 0.00 43.48 4.49
4650 5172 7.012894 ACAGGAAGAATCAAAAATTGACGTGTA 59.987 33.333 0.00 0.00 43.48 2.90
4651 5173 8.023128 CAGGAAGAATCAAAAATTGACGTGTAT 58.977 33.333 0.00 0.00 43.48 2.29
4652 5174 8.023128 AGGAAGAATCAAAAATTGACGTGTATG 58.977 33.333 0.00 0.00 43.48 2.39
4653 5175 7.201350 GGAAGAATCAAAAATTGACGTGTATGC 60.201 37.037 0.00 0.00 43.48 3.14
4654 5176 6.676950 AGAATCAAAAATTGACGTGTATGCA 58.323 32.000 0.00 0.00 43.48 3.96
4655 5177 7.315142 AGAATCAAAAATTGACGTGTATGCAT 58.685 30.769 3.79 3.79 43.48 3.96
4656 5178 8.458052 AGAATCAAAAATTGACGTGTATGCATA 58.542 29.630 1.16 1.16 43.48 3.14
4657 5179 8.619146 AATCAAAAATTGACGTGTATGCATAG 57.381 30.769 6.67 0.00 43.48 2.23
4658 5180 6.550843 TCAAAAATTGACGTGTATGCATAGG 58.449 36.000 6.67 2.27 34.08 2.57
4659 5181 6.372937 TCAAAAATTGACGTGTATGCATAGGA 59.627 34.615 6.67 0.00 34.08 2.94
4660 5182 5.991328 AAATTGACGTGTATGCATAGGAG 57.009 39.130 6.67 3.78 0.00 3.69
4661 5183 2.509052 TGACGTGTATGCATAGGAGC 57.491 50.000 6.67 0.00 0.00 4.70
4662 5184 2.031870 TGACGTGTATGCATAGGAGCT 58.968 47.619 6.67 0.00 34.99 4.09
4663 5185 3.219281 TGACGTGTATGCATAGGAGCTA 58.781 45.455 6.67 0.00 34.99 3.32
4664 5186 3.253432 TGACGTGTATGCATAGGAGCTAG 59.747 47.826 6.67 0.00 34.99 3.42
4665 5187 3.487372 ACGTGTATGCATAGGAGCTAGA 58.513 45.455 6.67 0.00 34.99 2.43
4666 5188 3.889538 ACGTGTATGCATAGGAGCTAGAA 59.110 43.478 6.67 0.00 34.99 2.10
4667 5189 4.230657 CGTGTATGCATAGGAGCTAGAAC 58.769 47.826 6.67 0.00 34.99 3.01
4668 5190 4.261614 CGTGTATGCATAGGAGCTAGAACA 60.262 45.833 6.67 0.00 34.99 3.18
4669 5191 5.226396 GTGTATGCATAGGAGCTAGAACAG 58.774 45.833 6.67 0.00 34.99 3.16
4670 5192 5.010112 GTGTATGCATAGGAGCTAGAACAGA 59.990 44.000 6.67 0.00 34.99 3.41
4671 5193 4.870123 ATGCATAGGAGCTAGAACAGAG 57.130 45.455 0.00 0.00 34.99 3.35
4672 5194 2.961741 TGCATAGGAGCTAGAACAGAGG 59.038 50.000 0.00 0.00 34.99 3.69
4673 5195 3.226777 GCATAGGAGCTAGAACAGAGGA 58.773 50.000 0.00 0.00 0.00 3.71
4674 5196 3.639094 GCATAGGAGCTAGAACAGAGGAA 59.361 47.826 0.00 0.00 0.00 3.36
4675 5197 4.500716 GCATAGGAGCTAGAACAGAGGAAC 60.501 50.000 0.00 0.00 0.00 3.62
4676 5198 2.096248 AGGAGCTAGAACAGAGGAACG 58.904 52.381 0.00 0.00 0.00 3.95
4677 5199 1.470112 GGAGCTAGAACAGAGGAACGC 60.470 57.143 0.00 0.00 0.00 4.84
4678 5200 1.474879 GAGCTAGAACAGAGGAACGCT 59.525 52.381 0.00 0.00 40.82 5.07
4679 5201 1.474879 AGCTAGAACAGAGGAACGCTC 59.525 52.381 0.00 0.00 35.27 5.03
4680 5202 1.470112 GCTAGAACAGAGGAACGCTCC 60.470 57.143 0.00 0.00 35.27 4.70
4681 5203 1.135333 CTAGAACAGAGGAACGCTCCC 59.865 57.143 0.00 0.00 43.64 4.30
4682 5204 1.446272 GAACAGAGGAACGCTCCCG 60.446 63.158 0.00 0.00 43.64 5.14
4726 5248 1.814169 GAGAAAACCCTAGCCGCCG 60.814 63.158 0.00 0.00 0.00 6.46
5233 6222 2.347490 GATGGTGGCGTCTGTGGT 59.653 61.111 0.00 0.00 0.00 4.16
5240 6229 0.884259 TGGCGTCTGTGGTGTCATTG 60.884 55.000 0.00 0.00 0.00 2.82
5308 6297 0.841594 GGGTTAGTGGTGGGGTGGTA 60.842 60.000 0.00 0.00 0.00 3.25
5359 6348 1.620822 GGAGTCTTTGGTGGTGCATT 58.379 50.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.471904 TCCACATGGACAGAGAATACAC 57.528 45.455 0.00 0.00 39.78 2.90
149 157 3.619487 GCAGCTTCTTTCTCCAGATCTGT 60.619 47.826 21.11 0.00 31.41 3.41
203 211 5.758784 ACTACTCACTAGCAAAGAAACCAAC 59.241 40.000 0.00 0.00 0.00 3.77
221 229 3.292460 ACTGATGACCTGGCTACTACTC 58.708 50.000 0.00 0.00 0.00 2.59
222 230 3.292460 GACTGATGACCTGGCTACTACT 58.708 50.000 0.00 0.00 0.00 2.57
223 231 2.362717 GGACTGATGACCTGGCTACTAC 59.637 54.545 0.00 0.00 0.00 2.73
224 232 2.667470 GGACTGATGACCTGGCTACTA 58.333 52.381 0.00 0.00 0.00 1.82
225 233 1.490574 GGACTGATGACCTGGCTACT 58.509 55.000 0.00 0.00 0.00 2.57
226 234 0.466124 GGGACTGATGACCTGGCTAC 59.534 60.000 0.00 0.00 0.00 3.58
227 235 0.042581 TGGGACTGATGACCTGGCTA 59.957 55.000 0.00 0.00 0.00 3.93
229 237 0.393537 CTTGGGACTGATGACCTGGC 60.394 60.000 0.00 0.00 0.00 4.85
250 258 5.273208 TCTGAGCTCTTGGTAATCTAACCT 58.727 41.667 16.19 0.00 40.44 3.50
352 360 3.689347 AGCATGGCAGTACATTTTCTGA 58.311 40.909 0.00 0.00 34.02 3.27
389 397 0.478072 TGCTGGAACTGGGTTGATGT 59.522 50.000 0.00 0.00 0.00 3.06
424 463 5.123936 GTGTTCTAGGACCTGTGAAACTTT 58.876 41.667 3.53 0.00 38.04 2.66
427 466 3.400255 GGTGTTCTAGGACCTGTGAAAC 58.600 50.000 3.53 9.16 37.35 2.78
437 477 1.001020 TACGGCCGGTGTTCTAGGA 60.001 57.895 31.76 0.00 0.00 2.94
498 538 4.385825 ACGGTGCTTTTGTAATTCTCTCA 58.614 39.130 0.00 0.00 0.00 3.27
572 615 9.585099 GCACTGATTATTTTCATTGTTAATCCA 57.415 29.630 0.00 0.00 32.54 3.41
580 623 8.697846 AGTTGATGCACTGATTATTTTCATTG 57.302 30.769 0.00 0.00 31.47 2.82
583 626 8.565896 ACTAGTTGATGCACTGATTATTTTCA 57.434 30.769 0.00 0.00 0.00 2.69
587 636 9.751542 GTACTACTAGTTGATGCACTGATTATT 57.248 33.333 11.43 0.00 0.00 1.40
588 637 9.137459 AGTACTACTAGTTGATGCACTGATTAT 57.863 33.333 11.43 0.00 0.00 1.28
608 657 7.728532 TCTTGATGCCATCATTAGGTAGTACTA 59.271 37.037 8.45 0.00 39.39 1.82
610 659 6.759272 TCTTGATGCCATCATTAGGTAGTAC 58.241 40.000 8.45 0.00 39.39 2.73
611 660 6.519043 GCTCTTGATGCCATCATTAGGTAGTA 60.519 42.308 8.45 0.00 39.39 1.82
613 662 4.694509 GCTCTTGATGCCATCATTAGGTAG 59.305 45.833 8.45 1.85 39.39 3.18
614 663 4.645535 GCTCTTGATGCCATCATTAGGTA 58.354 43.478 8.45 0.00 39.39 3.08
615 664 3.484407 GCTCTTGATGCCATCATTAGGT 58.516 45.455 8.45 0.00 39.39 3.08
645 697 5.248640 TGTTTAAGCAAGGAGAAGATGGAG 58.751 41.667 0.00 0.00 0.00 3.86
674 726 2.025981 TGTGGATCAGGAAGGAACATGG 60.026 50.000 0.00 0.00 0.00 3.66
716 768 0.532573 AGTACACTGGATGAGCGTGG 59.467 55.000 0.00 0.00 33.13 4.94
717 769 1.633561 CAGTACACTGGATGAGCGTG 58.366 55.000 1.21 0.00 40.20 5.34
718 770 0.108615 GCAGTACACTGGATGAGCGT 60.109 55.000 11.18 0.00 43.94 5.07
736 788 2.799412 CTGAGTGAGTGTTTGTCTGAGC 59.201 50.000 0.00 0.00 0.00 4.26
765 817 6.764308 TGAGCTAGAGATTTGATTTTTGGG 57.236 37.500 0.00 0.00 0.00 4.12
937 990 1.453928 GTAGTGGCATTGGGAGGGC 60.454 63.158 0.00 0.00 0.00 5.19
952 1009 0.592148 GGCACCTCCTACGATCGTAG 59.408 60.000 37.08 37.08 45.50 3.51
953 1010 0.107066 TGGCACCTCCTACGATCGTA 60.107 55.000 25.37 25.37 35.26 3.43
954 1011 0.968901 TTGGCACCTCCTACGATCGT 60.969 55.000 25.94 25.94 35.26 3.73
956 1013 0.530870 GCTTGGCACCTCCTACGATC 60.531 60.000 0.00 0.00 35.26 3.69
959 1016 2.125106 GGCTTGGCACCTCCTACG 60.125 66.667 0.00 0.00 35.26 3.51
982 1040 0.907704 ATTGGTAGGCCGTGGAGTGA 60.908 55.000 0.00 0.00 37.67 3.41
983 1041 0.744414 CATTGGTAGGCCGTGGAGTG 60.744 60.000 0.00 0.00 37.67 3.51
984 1042 1.198759 ACATTGGTAGGCCGTGGAGT 61.199 55.000 0.00 0.00 37.67 3.85
986 1044 0.907704 AGACATTGGTAGGCCGTGGA 60.908 55.000 0.00 0.00 37.67 4.02
989 1047 0.617820 AGGAGACATTGGTAGGCCGT 60.618 55.000 0.00 0.00 37.67 5.68
990 1048 0.105039 GAGGAGACATTGGTAGGCCG 59.895 60.000 0.00 0.00 37.67 6.13
991 1049 0.470341 GGAGGAGACATTGGTAGGCC 59.530 60.000 0.00 0.00 0.00 5.19
992 1050 1.414550 GAGGAGGAGACATTGGTAGGC 59.585 57.143 0.00 0.00 0.00 3.93
993 1051 2.043227 GGAGGAGGAGACATTGGTAGG 58.957 57.143 0.00 0.00 0.00 3.18
994 1052 2.962421 GAGGAGGAGGAGACATTGGTAG 59.038 54.545 0.00 0.00 0.00 3.18
995 1053 2.359355 GGAGGAGGAGGAGACATTGGTA 60.359 54.545 0.00 0.00 0.00 3.25
996 1054 1.623834 GGAGGAGGAGGAGACATTGGT 60.624 57.143 0.00 0.00 0.00 3.67
1087 1161 2.126618 CTGCTCGTTCACGGCGTA 60.127 61.111 14.22 0.00 40.29 4.42
1239 1313 1.144565 CCGACTTGATGAGCAGCGAG 61.145 60.000 1.61 1.61 34.50 5.03
2976 3146 5.688176 GGAGAAGCTGTTGTACGAGATATTC 59.312 44.000 0.00 0.00 0.00 1.75
3330 3565 3.755628 TACACCACGCCCGAGCTC 61.756 66.667 2.73 2.73 36.60 4.09
3378 3616 0.321653 ACCACATCTTCTTCACGGCC 60.322 55.000 0.00 0.00 0.00 6.13
3510 3763 2.426381 GTTCGGGAGGTAGGTGTAGAAG 59.574 54.545 0.00 0.00 0.00 2.85
3669 3937 1.271325 ACGTTCATGGCCTTGATGTCA 60.271 47.619 21.05 4.48 0.00 3.58
3839 4317 8.250143 AGGGTACAGATTTTGAAGAATTTTGT 57.750 30.769 0.00 0.00 0.00 2.83
3872 4350 5.168569 TCGCGATCAGTAAGAACAATTTCT 58.831 37.500 3.71 0.00 44.53 2.52
3878 4362 6.073327 AGAATATCGCGATCAGTAAGAACA 57.927 37.500 27.45 3.80 0.00 3.18
3879 4363 6.418226 ACAAGAATATCGCGATCAGTAAGAAC 59.582 38.462 27.45 7.92 0.00 3.01
3885 4369 3.384668 CCACAAGAATATCGCGATCAGT 58.615 45.455 27.45 12.01 0.00 3.41
3886 4370 2.733552 CCCACAAGAATATCGCGATCAG 59.266 50.000 27.45 11.54 0.00 2.90
3890 4374 1.538204 GCTCCCACAAGAATATCGCGA 60.538 52.381 13.09 13.09 0.00 5.87
3891 4375 0.861837 GCTCCCACAAGAATATCGCG 59.138 55.000 0.00 0.00 0.00 5.87
3892 4376 1.869767 CTGCTCCCACAAGAATATCGC 59.130 52.381 0.00 0.00 0.00 4.58
3896 4387 3.130516 CGTACTCTGCTCCCACAAGAATA 59.869 47.826 0.00 0.00 0.00 1.75
4398 4893 1.154525 CTGCTGCTTTCTCGCAACG 60.155 57.895 0.00 0.00 39.80 4.10
4408 4903 2.437359 CCGCTAAGGCTGCTGCTT 60.437 61.111 15.64 4.74 39.59 3.91
4429 4928 7.762159 TGTCCAAAATTTCTACACAAAGTTTCC 59.238 33.333 0.00 0.00 32.65 3.13
4430 4929 8.592155 GTGTCCAAAATTTCTACACAAAGTTTC 58.408 33.333 18.45 0.00 40.08 2.78
4432 4931 7.607250 TGTGTCCAAAATTTCTACACAAAGTT 58.393 30.769 21.52 0.00 45.30 2.66
4433 4932 7.164230 TGTGTCCAAAATTTCTACACAAAGT 57.836 32.000 21.52 0.00 45.30 2.66
4439 4938 8.243426 GCTTGATATGTGTCCAAAATTTCTACA 58.757 33.333 0.00 0.00 0.00 2.74
4440 4939 8.243426 TGCTTGATATGTGTCCAAAATTTCTAC 58.757 33.333 0.00 0.00 0.00 2.59
4441 4940 8.347004 TGCTTGATATGTGTCCAAAATTTCTA 57.653 30.769 0.00 0.00 0.00 2.10
4442 4941 7.230849 TGCTTGATATGTGTCCAAAATTTCT 57.769 32.000 0.00 0.00 0.00 2.52
4443 4942 7.814107 TCTTGCTTGATATGTGTCCAAAATTTC 59.186 33.333 0.00 0.00 0.00 2.17
4444 4943 7.669427 TCTTGCTTGATATGTGTCCAAAATTT 58.331 30.769 0.00 0.00 0.00 1.82
4459 4959 8.680903 CCTACAAATTTACTGATCTTGCTTGAT 58.319 33.333 0.00 0.00 0.00 2.57
4460 4960 7.665559 ACCTACAAATTTACTGATCTTGCTTGA 59.334 33.333 0.00 0.00 0.00 3.02
4461 4961 7.820648 ACCTACAAATTTACTGATCTTGCTTG 58.179 34.615 0.00 0.00 0.00 4.01
4622 5144 7.222611 CACGTCAATTTTTGATTCTTCCTGTTT 59.777 33.333 0.00 0.00 42.47 2.83
4623 5145 6.697019 CACGTCAATTTTTGATTCTTCCTGTT 59.303 34.615 0.00 0.00 42.47 3.16
4624 5146 6.183360 ACACGTCAATTTTTGATTCTTCCTGT 60.183 34.615 0.00 0.00 42.47 4.00
4625 5147 6.208644 ACACGTCAATTTTTGATTCTTCCTG 58.791 36.000 0.00 0.00 42.47 3.86
4626 5148 6.391227 ACACGTCAATTTTTGATTCTTCCT 57.609 33.333 0.00 0.00 42.47 3.36
4627 5149 7.201350 GCATACACGTCAATTTTTGATTCTTCC 60.201 37.037 0.00 0.00 42.47 3.46
4628 5150 7.325821 TGCATACACGTCAATTTTTGATTCTTC 59.674 33.333 0.00 0.00 42.47 2.87
4629 5151 7.144661 TGCATACACGTCAATTTTTGATTCTT 58.855 30.769 0.00 0.00 42.47 2.52
4630 5152 6.676950 TGCATACACGTCAATTTTTGATTCT 58.323 32.000 0.00 0.00 42.47 2.40
4631 5153 6.926280 TGCATACACGTCAATTTTTGATTC 57.074 33.333 0.00 0.00 42.47 2.52
4632 5154 7.701924 CCTATGCATACACGTCAATTTTTGATT 59.298 33.333 1.16 0.00 42.47 2.57
4633 5155 7.066887 TCCTATGCATACACGTCAATTTTTGAT 59.933 33.333 1.16 0.00 42.47 2.57
4634 5156 6.372937 TCCTATGCATACACGTCAATTTTTGA 59.627 34.615 1.16 0.00 37.33 2.69
4635 5157 6.550843 TCCTATGCATACACGTCAATTTTTG 58.449 36.000 1.16 0.00 0.00 2.44
4636 5158 6.677920 GCTCCTATGCATACACGTCAATTTTT 60.678 38.462 1.16 0.00 0.00 1.94
4637 5159 5.220854 GCTCCTATGCATACACGTCAATTTT 60.221 40.000 1.16 0.00 0.00 1.82
4638 5160 4.273480 GCTCCTATGCATACACGTCAATTT 59.727 41.667 1.16 0.00 0.00 1.82
4639 5161 3.809832 GCTCCTATGCATACACGTCAATT 59.190 43.478 1.16 0.00 0.00 2.32
4640 5162 3.070159 AGCTCCTATGCATACACGTCAAT 59.930 43.478 1.16 0.00 34.99 2.57
4641 5163 2.430694 AGCTCCTATGCATACACGTCAA 59.569 45.455 1.16 0.00 34.99 3.18
4642 5164 2.031870 AGCTCCTATGCATACACGTCA 58.968 47.619 1.16 0.00 34.99 4.35
4643 5165 2.802787 AGCTCCTATGCATACACGTC 57.197 50.000 1.16 0.00 34.99 4.34
4644 5166 3.487372 TCTAGCTCCTATGCATACACGT 58.513 45.455 1.16 0.00 34.99 4.49
4645 5167 4.230657 GTTCTAGCTCCTATGCATACACG 58.769 47.826 1.16 0.00 34.99 4.49
4646 5168 5.010112 TCTGTTCTAGCTCCTATGCATACAC 59.990 44.000 1.16 0.00 34.99 2.90
4647 5169 5.140454 TCTGTTCTAGCTCCTATGCATACA 58.860 41.667 1.16 0.00 34.99 2.29
4648 5170 5.336372 CCTCTGTTCTAGCTCCTATGCATAC 60.336 48.000 1.16 0.00 34.99 2.39
4649 5171 4.769488 CCTCTGTTCTAGCTCCTATGCATA 59.231 45.833 6.20 6.20 34.99 3.14
4650 5172 3.577848 CCTCTGTTCTAGCTCCTATGCAT 59.422 47.826 3.79 3.79 34.99 3.96
4651 5173 2.961741 CCTCTGTTCTAGCTCCTATGCA 59.038 50.000 0.00 0.00 34.99 3.96
4652 5174 3.226777 TCCTCTGTTCTAGCTCCTATGC 58.773 50.000 0.00 0.00 0.00 3.14
4653 5175 4.261405 CGTTCCTCTGTTCTAGCTCCTATG 60.261 50.000 0.00 0.00 0.00 2.23
4654 5176 3.886505 CGTTCCTCTGTTCTAGCTCCTAT 59.113 47.826 0.00 0.00 0.00 2.57
4655 5177 3.280295 CGTTCCTCTGTTCTAGCTCCTA 58.720 50.000 0.00 0.00 0.00 2.94
4656 5178 2.096248 CGTTCCTCTGTTCTAGCTCCT 58.904 52.381 0.00 0.00 0.00 3.69
4657 5179 1.470112 GCGTTCCTCTGTTCTAGCTCC 60.470 57.143 0.00 0.00 0.00 4.70
4658 5180 1.474879 AGCGTTCCTCTGTTCTAGCTC 59.525 52.381 0.00 0.00 0.00 4.09
4659 5181 1.474879 GAGCGTTCCTCTGTTCTAGCT 59.525 52.381 0.00 0.00 37.60 3.32
4660 5182 1.470112 GGAGCGTTCCTCTGTTCTAGC 60.470 57.143 11.59 0.00 40.58 3.42
4661 5183 1.135333 GGGAGCGTTCCTCTGTTCTAG 59.865 57.143 18.44 0.00 43.49 2.43
4662 5184 1.183549 GGGAGCGTTCCTCTGTTCTA 58.816 55.000 18.44 0.00 43.49 2.10
4663 5185 1.878656 CGGGAGCGTTCCTCTGTTCT 61.879 60.000 18.44 0.00 43.49 3.01
4664 5186 1.446272 CGGGAGCGTTCCTCTGTTC 60.446 63.158 18.44 0.00 43.49 3.18
4665 5187 2.207924 ACGGGAGCGTTCCTCTGTT 61.208 57.895 18.44 0.00 43.49 3.16
4666 5188 2.600769 ACGGGAGCGTTCCTCTGT 60.601 61.111 18.44 11.34 43.49 3.41
4667 5189 2.125912 CACGGGAGCGTTCCTCTG 60.126 66.667 18.44 10.71 43.49 3.35
4668 5190 4.070552 GCACGGGAGCGTTCCTCT 62.071 66.667 18.44 0.22 43.49 3.69
4697 5219 4.404098 TTTTCTCTCCCGGGCCGC 62.404 66.667 23.20 0.00 0.00 6.53
4778 5300 2.380410 CGAAGGTCGCTTTGTCCGG 61.380 63.158 0.00 0.00 31.14 5.14
4981 5967 1.833630 TGTAGATCACTGGCCAAGAGG 59.166 52.381 7.01 0.00 38.23 3.69
4982 5968 3.118482 ACATGTAGATCACTGGCCAAGAG 60.118 47.826 7.01 0.00 0.00 2.85
4983 5969 2.840038 ACATGTAGATCACTGGCCAAGA 59.160 45.455 7.01 8.66 0.00 3.02
5115 6104 4.716794 ACCACACCCAAAAAGTATCGTTA 58.283 39.130 0.00 0.00 0.00 3.18
5233 6222 2.189594 CTCCCAACAGAGCAATGACA 57.810 50.000 0.00 0.00 0.00 3.58
5308 6297 2.909577 GCTGCCTGCTCCTGATCT 59.090 61.111 0.00 0.00 38.95 2.75
5359 6348 2.710377 CGAGTGACCAATCCCAAATGA 58.290 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.