Multiple sequence alignment - TraesCS6A01G394800

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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 TraesCS6A01G394800 chr6A 100.000 4591 0 0 1 4591 608081790 608077200 0.000000e+00 8479
1 TraesCS6A01G394800 chr6D 93.476 3602 131 38 528 4074 461396983 461393431 0.000000e+00 5254
2 TraesCS6A01G394800 chr6D 93.662 852 28 11 3377 4217 461391679 461390843 0.000000e+00 1251
3 TraesCS6A01G394800 chr6D 91.509 530 25 8 11 526 461397541 461397018 0.000000e+00 712
4 TraesCS6A01G394800 chr6D 92.966 327 16 6 4265 4589 461393244 461392923 1.930000e-128 470
5 TraesCS6A01G394800 chr6D 85.674 356 23 13 4236 4589 461390855 461390526 2.630000e-92 350
6 TraesCS6A01G394800 chr6D 90.722 194 14 4 4089 4281 461393448 461393258 5.890000e-64 255
7 TraesCS6A01G394800 chr6B 92.511 2951 139 46 1668 4582 703155016 703152112 0.000000e+00 4150
8 TraesCS6A01G394800 chr6B 92.167 1149 61 12 530 1671 703156301 703155175 0.000000e+00 1596
9 TraesCS6A01G394800 chr6B 84.288 541 35 20 11 522 703156861 703156342 2.480000e-132 483
10 TraesCS6A01G394800 chr6B 86.111 144 15 4 2377 2520 707364581 707364719 2.860000e-32 150
11 TraesCS6A01G394800 chr6B 86.111 144 15 4 2377 2520 707384938 707385076 2.860000e-32 150
12 TraesCS6A01G394800 chr3B 81.088 386 43 19 562 941 22139806 22140167 9.720000e-72 281
13 TraesCS6A01G394800 chr5B 84.815 270 33 6 2252 2520 277236705 277236967 9.790000e-67 265
14 TraesCS6A01G394800 chr4D 82.741 197 29 5 2249 2443 400236119 400236312 2.200000e-38 171
15 TraesCS6A01G394800 chrUn 86.111 144 15 4 2377 2520 269561747 269561609 2.860000e-32 150


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 TraesCS6A01G394800 chr6A 608077200 608081790 4590 True 8479.000000 8479 100.000000 1 4591 1 chr6A.!!$R1 4590
1 TraesCS6A01G394800 chr6D 461390526 461397541 7015 True 1382.000000 5254 91.334833 11 4589 6 chr6D.!!$R1 4578
2 TraesCS6A01G394800 chr6B 703152112 703156861 4749 True 2076.333333 4150 89.655333 11 4582 3 chr6B.!!$R1 4571

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
514 552 0.179020 CGGCCTCCCAAGCATAATCA 60.179 55.000 0.00 0.00 0.00 2.57 F
1011 1090 0.171007 CCCAACGGATGAACATGTGC 59.829 55.000 0.00 0.00 0.00 4.57 F
1477 1559 0.179034 CCTCTTCATACCCTGGCAGC 60.179 60.000 9.56 0.00 0.00 5.25 F
1488 1570 1.080772 CTGGCAGCGACGACTGTTA 60.081 57.895 16.76 8.39 39.96 2.41 F
1966 2237 1.335145 AAGCTGTGATTGCTGCCTTT 58.665 45.000 0.00 0.00 41.03 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2154 0.871722 TTTTCATCTGGACGTTGCCG 59.128 50.000 0.00 0.00 40.83 5.69 R
2886 3161 1.508632 TGAACTGTTGAGCTTACCGC 58.491 50.000 0.00 0.00 39.57 5.68 R
3314 3598 0.753479 TCCGCCCAAAAGCTCAACAA 60.753 50.000 0.00 0.00 0.00 2.83 R
3471 3756 3.998341 GGGTTTCAGCGATTACTGTTACA 59.002 43.478 0.00 0.00 38.84 2.41 R
3853 4146 2.105006 ATACACAACAGAGCCTGCAG 57.895 50.000 6.78 6.78 34.37 4.41 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
97 98 3.290710 CTTCAATCCCGGTTCCATGATT 58.709 45.455 0.00 0.00 0.00 2.57
154 155 0.685097 TCCCTCGTTTTCTGACTGGG 59.315 55.000 0.00 0.00 34.40 4.45
232 260 4.884164 GCCACTAACTCTGCAGGAATAATT 59.116 41.667 15.13 2.40 0.00 1.40
260 288 4.692228 TCTTGCAACTTTTCCACCATTTC 58.308 39.130 0.00 0.00 0.00 2.17
265 293 4.797275 GCAACTTTTCCACCATTTCTCCTG 60.797 45.833 0.00 0.00 0.00 3.86
266 294 4.184649 ACTTTTCCACCATTTCTCCTGT 57.815 40.909 0.00 0.00 0.00 4.00
269 297 3.874383 TTCCACCATTTCTCCTGTTGA 57.126 42.857 0.00 0.00 0.00 3.18
270 298 3.423539 TCCACCATTTCTCCTGTTGAG 57.576 47.619 0.00 0.00 42.90 3.02
272 300 1.815003 CACCATTTCTCCTGTTGAGGC 59.185 52.381 0.00 0.00 41.76 4.70
274 302 1.089920 CATTTCTCCTGTTGAGGCCG 58.910 55.000 0.00 0.00 41.76 6.13
308 336 0.771127 TGCAGGAAAACAGGGTAGCT 59.229 50.000 0.00 0.00 0.00 3.32
321 349 6.622427 ACAGGGTAGCTAGAAACAGTTATT 57.378 37.500 0.00 0.00 0.00 1.40
419 455 3.026694 GTGAGGCCCTCATTTAGCAATT 58.973 45.455 18.16 0.00 42.73 2.32
420 456 3.025978 TGAGGCCCTCATTTAGCAATTG 58.974 45.455 10.05 0.00 35.39 2.32
422 458 3.893813 GAGGCCCTCATTTAGCAATTGAT 59.106 43.478 10.34 5.28 0.00 2.57
457 493 5.710099 TCAGCCGTTCCTATCAAAGAAATTT 59.290 36.000 0.00 0.00 0.00 1.82
502 540 2.185608 GCTCTCTGAACGGCCTCC 59.814 66.667 0.00 0.00 0.00 4.30
504 542 1.984570 CTCTCTGAACGGCCTCCCA 60.985 63.158 0.00 0.00 0.00 4.37
505 543 1.535444 TCTCTGAACGGCCTCCCAA 60.535 57.895 0.00 0.00 0.00 4.12
514 552 0.179020 CGGCCTCCCAAGCATAATCA 60.179 55.000 0.00 0.00 0.00 2.57
526 564 3.152341 AGCATAATCAGCAGTTATGGCC 58.848 45.455 0.00 0.00 39.05 5.36
547 618 5.385198 GCCTTTGATTGGATTATGGGACTA 58.615 41.667 0.00 0.00 0.00 2.59
585 657 1.067142 TGCTAACGTGTGATGGGAGTC 60.067 52.381 0.00 0.00 0.00 3.36
612 684 7.171653 TCATATTGGGTTGTTCAATCAGTGTA 58.828 34.615 0.00 0.00 36.40 2.90
722 798 5.535029 TCTTATAATGTGGTAGTGGTCCCT 58.465 41.667 0.00 0.00 0.00 4.20
758 837 7.600065 TGCGTACTAATCTGTTAGTTTTCTCT 58.400 34.615 6.20 0.00 46.40 3.10
826 905 2.560981 TGCTCCTAACGTGATGACTCAA 59.439 45.455 0.00 0.00 31.85 3.02
877 956 0.746063 CCTTGACTTTGTTGCAGCCA 59.254 50.000 0.00 0.00 0.00 4.75
980 1059 0.251165 TAGGGGCAGTGCTTTTGACC 60.251 55.000 16.11 6.16 43.39 4.02
1011 1090 0.171007 CCCAACGGATGAACATGTGC 59.829 55.000 0.00 0.00 0.00 4.57
1170 1249 3.560481 TGGAACGTCGTGCAATTCTTTTA 59.440 39.130 5.55 0.00 0.00 1.52
1220 1299 8.306313 ACAGTATTGAGTTCCTCATGTGTATA 57.694 34.615 0.00 0.00 40.39 1.47
1355 1437 1.833630 TCCATAGTCTGGTTCAGCCTG 59.166 52.381 0.00 0.00 46.08 4.85
1363 1445 2.441750 TCTGGTTCAGCCTGTACCTTTT 59.558 45.455 19.60 0.00 38.46 2.27
1371 1453 3.742369 CAGCCTGTACCTTTTGCATTTTG 59.258 43.478 0.00 0.00 0.00 2.44
1391 1473 6.478512 TTTGTGCTTTCCCTCTTAATGTTT 57.521 33.333 0.00 0.00 0.00 2.83
1417 1499 2.693074 GTGTGTTCCAGGAAATGTTGGT 59.307 45.455 2.45 0.00 35.89 3.67
1477 1559 0.179034 CCTCTTCATACCCTGGCAGC 60.179 60.000 9.56 0.00 0.00 5.25
1483 1565 3.077519 ATACCCTGGCAGCGACGAC 62.078 63.158 9.56 0.00 0.00 4.34
1488 1570 1.080772 CTGGCAGCGACGACTGTTA 60.081 57.895 16.76 8.39 39.96 2.41
1510 1592 7.182026 TGTTATGAAATGGAGGAAGAAGTAGGA 59.818 37.037 0.00 0.00 0.00 2.94
1838 2083 9.833182 GTGATAAGAAATTCTTCCAAAAGTCTC 57.167 33.333 11.97 0.00 37.89 3.36
1916 2176 3.071479 GGCAACGTCCAGATGAAAACTA 58.929 45.455 0.00 0.00 0.00 2.24
1917 2177 3.120304 GGCAACGTCCAGATGAAAACTAC 60.120 47.826 0.00 0.00 0.00 2.73
1918 2178 3.746492 GCAACGTCCAGATGAAAACTACT 59.254 43.478 0.00 0.00 0.00 2.57
1926 2197 7.159372 GTCCAGATGAAAACTACTAGGTTCAA 58.841 38.462 7.97 0.00 33.93 2.69
1958 2229 5.908106 GTTTTGCATACAAAGCTGTGATTG 58.092 37.500 11.93 8.58 46.08 2.67
1966 2237 1.335145 AAGCTGTGATTGCTGCCTTT 58.665 45.000 0.00 0.00 41.03 3.11
2278 2549 6.036470 GGTTCCTTTTGATAGTAAATGCTGC 58.964 40.000 0.00 0.00 0.00 5.25
2288 2559 6.540551 TGATAGTAAATGCTGCGGAAACATTA 59.459 34.615 0.00 0.00 33.01 1.90
2303 2574 7.926018 GCGGAAACATTAAATTTATGAGGGATT 59.074 33.333 0.00 0.00 0.00 3.01
2363 2634 8.752766 TTAACTTTCTAAATAGAGTGTCCACG 57.247 34.615 0.00 0.00 36.20 4.94
2364 2635 6.342338 ACTTTCTAAATAGAGTGTCCACGT 57.658 37.500 0.00 0.00 36.20 4.49
2380 2651 5.241285 TGTCCACGTGTGTAGTTCAGTAATA 59.759 40.000 15.65 0.00 0.00 0.98
2471 2742 5.941948 ATTGTCAGGTTTGTACTTAGTGC 57.058 39.130 0.00 0.00 0.00 4.40
2472 2743 3.735591 TGTCAGGTTTGTACTTAGTGCC 58.264 45.455 0.00 0.00 0.00 5.01
2473 2744 3.134985 TGTCAGGTTTGTACTTAGTGCCA 59.865 43.478 0.00 0.00 0.00 4.92
2474 2745 4.202419 TGTCAGGTTTGTACTTAGTGCCAT 60.202 41.667 0.00 0.00 0.00 4.40
2579 2850 7.798596 ATTCCATCATTCATGACTTACTGTC 57.201 36.000 0.00 0.00 45.54 3.51
2722 2996 5.482908 AGCAGATAATTAGCCAGGTAATCG 58.517 41.667 2.79 0.00 0.00 3.34
2745 3019 6.800408 TCGACAGTAGTAATCTTTCTTTCGTG 59.200 38.462 0.00 0.00 33.36 4.35
2746 3020 6.800408 CGACAGTAGTAATCTTTCTTTCGTGA 59.200 38.462 0.00 0.00 30.51 4.35
2747 3021 7.325338 CGACAGTAGTAATCTTTCTTTCGTGAA 59.675 37.037 0.00 0.00 30.51 3.18
2748 3022 9.141400 GACAGTAGTAATCTTTCTTTCGTGAAT 57.859 33.333 0.00 0.00 0.00 2.57
2749 3023 9.141400 ACAGTAGTAATCTTTCTTTCGTGAATC 57.859 33.333 0.00 0.00 0.00 2.52
2750 3024 9.140286 CAGTAGTAATCTTTCTTTCGTGAATCA 57.860 33.333 0.00 0.00 0.00 2.57
2751 3025 9.877178 AGTAGTAATCTTTCTTTCGTGAATCAT 57.123 29.630 0.00 0.00 0.00 2.45
2764 3038 5.674525 TCGTGAATCATGATCCTTAGCTTT 58.325 37.500 9.06 0.00 0.00 3.51
2792 3066 8.464770 TCTTTGTTTTCACACTTTCATCTTTG 57.535 30.769 0.00 0.00 30.32 2.77
2886 3161 7.208225 TGATGAGTATCTGGAGAAAGTATCG 57.792 40.000 0.00 0.00 34.92 2.92
3084 3363 2.349100 ATATCACAGCTGGCAGGGGC 62.349 60.000 19.93 2.33 40.13 5.80
3162 3441 4.690748 GTGAAGATTTTCGTCATGACCTCA 59.309 41.667 20.03 7.21 37.24 3.86
3276 3556 4.399934 TGGGTTGGTTTTGACACTTAACTC 59.600 41.667 0.00 0.00 0.00 3.01
3286 3566 3.384789 TGACACTTAACTCTGCACTCTGT 59.615 43.478 0.00 0.00 0.00 3.41
3314 3598 3.644966 TTTCTCTGGTTTCAGTGGTGT 57.355 42.857 0.00 0.00 41.59 4.16
3471 3756 2.185350 CACCGCGATCTCTGCCTT 59.815 61.111 8.23 0.00 0.00 4.35
3472 3757 2.169789 CACCGCGATCTCTGCCTTG 61.170 63.158 8.23 0.00 0.00 3.61
3499 3784 2.393271 AATCGCTGAAACCCTCTCTG 57.607 50.000 0.00 0.00 0.00 3.35
3507 3792 3.107601 TGAAACCCTCTCTGTCCTATGG 58.892 50.000 0.00 0.00 0.00 2.74
3508 3793 2.950990 AACCCTCTCTGTCCTATGGT 57.049 50.000 0.00 0.00 0.00 3.55
3510 3795 3.207044 ACCCTCTCTGTCCTATGGTTT 57.793 47.619 0.00 0.00 0.00 3.27
3511 3796 3.532102 ACCCTCTCTGTCCTATGGTTTT 58.468 45.455 0.00 0.00 0.00 2.43
3512 3797 3.264450 ACCCTCTCTGTCCTATGGTTTTG 59.736 47.826 0.00 0.00 0.00 2.44
3749 4038 0.393673 CTCGCTCTGACAGGAGGAGA 60.394 60.000 1.81 0.71 35.06 3.71
3750 4039 0.393673 TCGCTCTGACAGGAGGAGAG 60.394 60.000 1.81 0.00 36.99 3.20
3751 4040 0.393673 CGCTCTGACAGGAGGAGAGA 60.394 60.000 1.81 0.00 36.14 3.10
3753 4042 2.175202 GCTCTGACAGGAGGAGAGAAA 58.825 52.381 1.81 0.00 36.14 2.52
3853 4146 3.492011 CCGTATATAGTTTTGGGTCGCAC 59.508 47.826 0.00 0.00 0.00 5.34
3867 4160 2.952245 GCACTGCAGGCTCTGTTG 59.048 61.111 19.93 6.26 33.43 3.33
3994 4288 4.393371 GGAGGCAGTGTTAAAGAATCTGTC 59.607 45.833 0.00 0.00 0.00 3.51
4051 4345 6.738114 TGTTTGAGATGTCTTTGATTTGGTC 58.262 36.000 0.00 0.00 0.00 4.02
4054 4348 3.347216 AGATGTCTTTGATTTGGTCCGG 58.653 45.455 0.00 0.00 0.00 5.14
4110 4409 5.122396 GTGAGAAATGTTGCTCGGTTAGAAT 59.878 40.000 0.00 0.00 33.89 2.40
4172 4471 0.108472 GTACTAACCCGAGTGGCACC 60.108 60.000 15.27 4.98 37.83 5.01
4173 4472 0.251922 TACTAACCCGAGTGGCACCT 60.252 55.000 15.27 1.14 37.83 4.00
4185 4484 1.219935 GGCACCTAGTAACCACGGG 59.780 63.158 0.00 0.00 0.00 5.28
4188 4487 1.492764 CACCTAGTAACCACGGGGAT 58.507 55.000 12.96 0.00 38.05 3.85
4414 4746 9.710900 AATCAAAGATGTAAATTTTCCTTCCAC 57.289 29.630 0.00 0.00 0.00 4.02
4553 7281 7.482743 CACGGTTTCAATGTCAGAATAAATGAG 59.517 37.037 0.00 0.00 0.00 2.90
4589 7317 8.682710 TCATATTTTTGGGAAATACTTTCTCCG 58.317 33.333 0.00 0.00 39.44 4.63
4590 7318 6.911250 ATTTTTGGGAAATACTTTCTCCGT 57.089 33.333 0.00 0.00 39.44 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.638239 GGCAAATCATTTGTACAGAGAAAATAA 57.362 29.630 11.80 0.00 42.56 1.40
4 5 8.250332 GGGCAAATCATTTGTACAGAGAAAATA 58.750 33.333 11.80 0.00 42.56 1.40
5 6 7.099120 GGGCAAATCATTTGTACAGAGAAAAT 58.901 34.615 11.80 0.00 42.56 1.82
6 7 6.454795 GGGCAAATCATTTGTACAGAGAAAA 58.545 36.000 11.80 0.00 42.56 2.29
7 8 5.047377 GGGGCAAATCATTTGTACAGAGAAA 60.047 40.000 11.80 0.00 42.56 2.52
8 9 4.462483 GGGGCAAATCATTTGTACAGAGAA 59.538 41.667 11.80 0.00 42.56 2.87
9 10 4.016444 GGGGCAAATCATTTGTACAGAGA 58.984 43.478 11.80 0.00 42.56 3.10
17 18 3.940319 TGTTCATGGGGCAAATCATTTG 58.060 40.909 5.68 5.68 43.44 2.32
97 98 0.597568 CCTGAAAAGCGGCATCAACA 59.402 50.000 1.45 0.00 0.00 3.33
208 236 1.352083 TTCCTGCAGAGTTAGTGGCT 58.648 50.000 17.39 0.00 0.00 4.75
232 260 7.531857 TGGTGGAAAAGTTGCAAGATTATTA 57.468 32.000 0.00 0.00 30.97 0.98
260 288 3.965539 CTGCCGGCCTCAACAGGAG 62.966 68.421 26.77 7.17 43.65 3.69
274 302 3.198489 GCAGAGTTAGCGGCTGCC 61.198 66.667 15.55 9.11 46.94 4.85
287 315 1.271379 GCTACCCTGTTTTCCTGCAGA 60.271 52.381 17.39 0.00 34.87 4.26
367 403 7.064966 TGCTGTCCGCTCAAAATATGATATATG 59.935 37.037 0.00 0.00 37.44 1.78
419 455 1.138883 GCTGACGTGCTCGGTATCA 59.861 57.895 13.32 6.47 41.85 2.15
420 456 1.589196 GGCTGACGTGCTCGGTATC 60.589 63.158 13.32 1.83 41.85 2.24
422 458 4.111016 CGGCTGACGTGCTCGGTA 62.111 66.667 13.32 0.00 41.85 4.02
470 506 0.969894 AGAGCGAACTAACTGCAGGT 59.030 50.000 19.93 15.51 0.00 4.00
502 540 4.558095 GCCATAACTGCTGATTATGCTTGG 60.558 45.833 14.60 8.39 38.28 3.61
504 542 3.571401 GGCCATAACTGCTGATTATGCTT 59.429 43.478 0.00 0.00 38.28 3.91
505 543 3.152341 GGCCATAACTGCTGATTATGCT 58.848 45.455 0.00 0.00 38.28 3.79
514 552 2.762327 CCAATCAAAGGCCATAACTGCT 59.238 45.455 5.01 0.00 0.00 4.24
526 564 7.725397 TGGAATAGTCCCATAATCCAATCAAAG 59.275 37.037 6.78 0.00 44.23 2.77
585 657 6.976349 CACTGATTGAACAACCCAATATGATG 59.024 38.462 0.00 0.00 34.67 3.07
612 684 1.995376 AGGCCCTTTTGATTTGTCGT 58.005 45.000 0.00 0.00 0.00 4.34
722 798 2.447408 TAGTACGCAATCCTCCTCCA 57.553 50.000 0.00 0.00 0.00 3.86
758 837 4.874396 ACTAGTCACGATTACGACAGATCA 59.126 41.667 0.00 0.00 42.66 2.92
800 879 3.377485 GTCATCACGTTAGGAGCACTCTA 59.623 47.826 0.00 0.00 0.00 2.43
877 956 5.338614 GTGATATACGGCTAATTTTGCGT 57.661 39.130 0.00 0.00 0.00 5.24
980 1059 0.447801 CCGTTGGGCTCAAATTCTCG 59.552 55.000 0.00 0.00 34.28 4.04
1011 1090 6.088824 CCAGTGGAAATTTTGATCTTTCTCG 58.911 40.000 1.68 0.00 33.02 4.04
1205 1284 8.739972 AGAACCAAAAATATACACATGAGGAAC 58.260 33.333 0.00 0.00 0.00 3.62
1346 1427 1.953686 TGCAAAAGGTACAGGCTGAAC 59.046 47.619 23.66 10.50 0.00 3.18
1391 1473 5.413309 ACATTTCCTGGAACACACAAAAA 57.587 34.783 9.04 0.00 0.00 1.94
1417 1499 4.119363 GCCTCATGCTCCTGCCCA 62.119 66.667 0.00 0.00 38.71 5.36
1477 1559 3.551890 CCTCCATTTCATAACAGTCGTCG 59.448 47.826 0.00 0.00 0.00 5.12
1483 1565 7.497249 CCTACTTCTTCCTCCATTTCATAACAG 59.503 40.741 0.00 0.00 0.00 3.16
1488 1570 6.642733 TTCCTACTTCTTCCTCCATTTCAT 57.357 37.500 0.00 0.00 0.00 2.57
1639 1721 3.189287 CAGTGAGCAAACATGGGACTTAC 59.811 47.826 0.00 0.00 0.00 2.34
1811 2056 9.354673 AGACTTTTGGAAGAATTTCTTATCACA 57.645 29.630 11.55 6.46 36.73 3.58
1894 2154 0.871722 TTTTCATCTGGACGTTGCCG 59.128 50.000 0.00 0.00 40.83 5.69
1916 2176 9.515226 TGCAAAACTCTATAAATTGAACCTAGT 57.485 29.630 0.00 0.00 0.00 2.57
1926 2197 9.793252 CAGCTTTGTATGCAAAACTCTATAAAT 57.207 29.630 8.95 0.00 43.17 1.40
1958 2229 5.221126 CCCATGAAACTATAAGAAAGGCAGC 60.221 44.000 0.00 0.00 0.00 5.25
2048 2319 8.023128 TCGGAAAAGAAAAGAATGCTGATTAAG 58.977 33.333 0.00 0.00 0.00 1.85
2146 2417 3.634397 TTTTAGGGACATGCTGGAGAG 57.366 47.619 0.00 0.00 0.00 3.20
2278 2549 9.248291 CAATCCCTCATAAATTTAATGTTTCCG 57.752 33.333 1.21 0.00 0.00 4.30
2288 2559 9.799106 CTAGTACATCCAATCCCTCATAAATTT 57.201 33.333 0.00 0.00 0.00 1.82
2471 2742 3.649981 AGTATTCAGGTGAGGATGGATGG 59.350 47.826 0.00 0.00 0.00 3.51
2472 2743 4.970860 AGTATTCAGGTGAGGATGGATG 57.029 45.455 0.00 0.00 0.00 3.51
2473 2744 6.146760 ACTAAGTATTCAGGTGAGGATGGAT 58.853 40.000 0.00 0.00 0.00 3.41
2474 2745 5.529289 ACTAAGTATTCAGGTGAGGATGGA 58.471 41.667 0.00 0.00 0.00 3.41
2579 2850 5.050490 GTGGCTTATGTACTACATGGTCTG 58.950 45.833 11.39 0.10 39.53 3.51
2722 2996 8.516811 TTCACGAAAGAAAGATTACTACTGTC 57.483 34.615 0.00 0.00 0.00 3.51
2747 3021 9.638176 ACAAAGAATAAAGCTAAGGATCATGAT 57.362 29.630 8.25 8.25 0.00 2.45
2748 3022 9.466497 AACAAAGAATAAAGCTAAGGATCATGA 57.534 29.630 0.00 0.00 0.00 3.07
2807 3082 4.461431 CCCGGTTACTTTTAAGCTGGAAAT 59.539 41.667 0.00 0.00 40.64 2.17
2886 3161 1.508632 TGAACTGTTGAGCTTACCGC 58.491 50.000 0.00 0.00 39.57 5.68
3084 3363 8.827677 GTTAGAATGGGCATTAGTAAAGTACAG 58.172 37.037 0.00 0.00 0.00 2.74
3162 3441 4.037565 TCGATGTAGCACGTATCCTTGAAT 59.962 41.667 0.00 0.00 0.00 2.57
3314 3598 0.753479 TCCGCCCAAAAGCTCAACAA 60.753 50.000 0.00 0.00 0.00 2.83
3471 3756 3.998341 GGGTTTCAGCGATTACTGTTACA 59.002 43.478 0.00 0.00 38.84 2.41
3472 3757 4.251268 AGGGTTTCAGCGATTACTGTTAC 58.749 43.478 0.00 0.00 38.84 2.50
3512 3797 2.946762 GGAGCGTCTGTTGGCAAC 59.053 61.111 23.12 23.12 0.00 4.17
3641 3927 3.005155 GGAGAAACAAGAGTGCTTTGCAT 59.995 43.478 0.00 0.00 41.91 3.96
3749 4038 5.784578 ACCATAACGCCTTTTTCTTTTCT 57.215 34.783 0.00 0.00 0.00 2.52
3750 4039 5.751509 ACAACCATAACGCCTTTTTCTTTTC 59.248 36.000 0.00 0.00 0.00 2.29
3751 4040 5.666462 ACAACCATAACGCCTTTTTCTTTT 58.334 33.333 0.00 0.00 0.00 2.27
3753 4042 4.583073 AGACAACCATAACGCCTTTTTCTT 59.417 37.500 0.00 0.00 0.00 2.52
3796 4089 7.633334 GCATGTTCATTATTCCTTCCATTCCAA 60.633 37.037 0.00 0.00 0.00 3.53
3853 4146 2.105006 ATACACAACAGAGCCTGCAG 57.895 50.000 6.78 6.78 34.37 4.41
3867 4160 8.376942 CCGGCAAAATTTTGTATGTAAATACAC 58.623 33.333 27.13 9.50 38.50 2.90
3903 4197 9.754382 ATTCCAAATGAATGATTAACTGTATGC 57.246 29.630 0.00 0.00 42.18 3.14
3994 4288 7.453034 TCTAAAAAGAACATCGCAAATACTCG 58.547 34.615 0.00 0.00 0.00 4.18
4051 4345 1.153745 CGAGCAACTCTCTTCCCGG 60.154 63.158 0.00 0.00 39.70 5.73
4054 4348 2.231721 ACTAACCGAGCAACTCTCTTCC 59.768 50.000 0.00 0.00 39.70 3.46
4082 4378 2.096069 CCGAGCAACATTTCTCACACAG 60.096 50.000 0.00 0.00 0.00 3.66
4172 4471 2.623889 CTCTGATCCCCGTGGTTACTAG 59.376 54.545 0.00 0.00 0.00 2.57
4173 4472 2.242965 TCTCTGATCCCCGTGGTTACTA 59.757 50.000 0.00 0.00 0.00 1.82
4185 4484 2.045524 TCAATGGGCTCTCTCTGATCC 58.954 52.381 0.00 0.00 0.00 3.36
4188 4487 2.755686 TGATCAATGGGCTCTCTCTGA 58.244 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.