Multiple sequence alignment - TraesCS6A01G306000

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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 TraesCS6A01G306000 chr6A 100.000 4558 0 0 1 4558 539647734 539652291 0.000000e+00 8418
1 TraesCS6A01G306000 chr6B 91.640 4378 215 63 11 4351 586654976 586659239 0.000000e+00 5917
2 TraesCS6A01G306000 chr6B 93.636 220 12 1 4341 4558 586661864 586662083 1.220000e-85 327
3 TraesCS6A01G306000 chr6D 94.996 3717 107 31 11 3702 392881607 392885269 0.000000e+00 5760
4 TraesCS6A01G306000 chr6D 93.459 688 24 9 3708 4395 392886585 392887251 0.000000e+00 1002


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 TraesCS6A01G306000 chr6A 539647734 539652291 4557 False 8418 8418 100.0000 1 4558 1 chr6A.!!$F1 4557
1 TraesCS6A01G306000 chr6B 586654976 586662083 7107 False 3122 5917 92.6380 11 4558 2 chr6B.!!$F1 4547
2 TraesCS6A01G306000 chr6D 392881607 392887251 5644 False 3381 5760 94.2275 11 4395 2 chr6D.!!$F1 4384

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
822 849 0.540365 AGATGGGGCCTGTTGTGTTG 60.540 55.0 0.84 0.0 0.0 3.33 F
1575 1612 0.322008 CAGAGGGGTTGGAGTCTTGC 60.322 60.0 0.00 0.0 0.0 4.01 F
3298 3353 0.253044 TGTCCCAGCTTCATAGTGCC 59.747 55.0 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2201 0.532862 ACACCAGAAGTTCAGTGCCG 60.533 55.0 20.15 4.04 33.46 5.69 R
3501 3563 1.072666 GATTCGGGCAAAAGCGCAAG 61.073 55.0 11.47 0.00 43.44 4.01 R
4530 8546 0.179000 ATGGCTGCCTAGAGAAACCG 59.821 55.0 21.03 0.00 0.00 4.44 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
167 178 2.514824 GAGGTGCGATTCCTGCCC 60.515 66.667 0.00 0.00 35.20 5.36
238 249 8.996024 ATTGTTTATAATACTGTTTGTTGCCC 57.004 30.769 0.00 0.00 0.00 5.36
267 278 9.886132 AATACGGTTGTATTATTTTCTCTCTGT 57.114 29.630 0.00 0.00 46.80 3.41
268 279 7.829378 ACGGTTGTATTATTTTCTCTCTGTC 57.171 36.000 0.00 0.00 0.00 3.51
269 280 6.530534 ACGGTTGTATTATTTTCTCTCTGTCG 59.469 38.462 0.00 0.00 0.00 4.35
270 281 6.019801 CGGTTGTATTATTTTCTCTCTGTCGG 60.020 42.308 0.00 0.00 0.00 4.79
290 303 4.210537 TCGGTTTTCACGATTCTGTTTCTC 59.789 41.667 0.00 0.00 35.12 2.87
344 357 1.065551 GATTGGCGGTCATTGGTTAGC 59.934 52.381 0.00 0.00 0.00 3.09
456 469 2.256445 TTTAATCCAGCGCGCTTTTC 57.744 45.000 34.58 0.37 0.00 2.29
521 534 7.661536 TGTAAGCTATGGATATCCCTATCAC 57.338 40.000 19.34 8.75 36.27 3.06
563 576 2.507102 CACCTCGCTGCTGTACCG 60.507 66.667 0.00 0.00 0.00 4.02
584 597 4.032558 CCGAATTGGTAGACGCTCTTAAAC 59.967 45.833 0.00 0.00 0.00 2.01
603 616 8.020819 TCTTAAACGAATTCAACAATGATCCAC 58.979 33.333 6.22 0.00 34.96 4.02
622 636 3.940852 CCACAAGCTGTGCATATCTGTTA 59.059 43.478 9.88 0.00 46.51 2.41
623 637 4.201851 CCACAAGCTGTGCATATCTGTTAC 60.202 45.833 9.88 0.00 46.51 2.50
624 638 4.633126 CACAAGCTGTGCATATCTGTTACT 59.367 41.667 0.00 0.00 41.89 2.24
625 639 4.872691 ACAAGCTGTGCATATCTGTTACTC 59.127 41.667 0.00 0.00 0.00 2.59
626 640 4.065321 AGCTGTGCATATCTGTTACTCC 57.935 45.455 0.00 0.00 0.00 3.85
627 641 3.708631 AGCTGTGCATATCTGTTACTCCT 59.291 43.478 0.00 0.00 0.00 3.69
628 642 4.163078 AGCTGTGCATATCTGTTACTCCTT 59.837 41.667 0.00 0.00 0.00 3.36
629 643 4.878397 GCTGTGCATATCTGTTACTCCTTT 59.122 41.667 0.00 0.00 0.00 3.11
630 644 5.355350 GCTGTGCATATCTGTTACTCCTTTT 59.645 40.000 0.00 0.00 0.00 2.27
631 645 6.457528 GCTGTGCATATCTGTTACTCCTTTTC 60.458 42.308 0.00 0.00 0.00 2.29
632 646 6.472016 TGTGCATATCTGTTACTCCTTTTCA 58.528 36.000 0.00 0.00 0.00 2.69
633 647 6.939730 TGTGCATATCTGTTACTCCTTTTCAA 59.060 34.615 0.00 0.00 0.00 2.69
634 648 7.446931 TGTGCATATCTGTTACTCCTTTTCAAA 59.553 33.333 0.00 0.00 0.00 2.69
635 649 8.296713 GTGCATATCTGTTACTCCTTTTCAAAA 58.703 33.333 0.00 0.00 0.00 2.44
636 650 8.855110 TGCATATCTGTTACTCCTTTTCAAAAA 58.145 29.630 0.00 0.00 0.00 1.94
691 717 2.451490 TGGTTCACCTGCAAGAAACAA 58.549 42.857 10.47 0.00 38.41 2.83
709 735 8.561738 AGAAACAAACAAATAGATATGACGGT 57.438 30.769 0.00 0.00 0.00 4.83
710 736 8.665685 AGAAACAAACAAATAGATATGACGGTC 58.334 33.333 0.00 0.00 0.00 4.79
760 786 8.030692 TCCAGCATGATTTTCTAGATTTGTTTG 58.969 33.333 0.00 0.00 39.69 2.93
761 787 7.816031 CCAGCATGATTTTCTAGATTTGTTTGT 59.184 33.333 0.00 0.00 39.69 2.83
822 849 0.540365 AGATGGGGCCTGTTGTGTTG 60.540 55.000 0.84 0.00 0.00 3.33
838 865 3.691609 TGTGTTGGGTTTTGCCAATTTTC 59.308 39.130 0.00 0.00 39.65 2.29
900 928 4.866508 TGTGTAAGACTGGAATCGTTCT 57.133 40.909 0.00 0.00 0.00 3.01
908 936 5.112686 AGACTGGAATCGTTCTGCTTATTC 58.887 41.667 0.00 0.00 0.00 1.75
928 956 2.104111 TCGCCTATGTATGTTGAAGGGG 59.896 50.000 0.00 0.00 40.59 4.79
929 957 2.158813 CGCCTATGTATGTTGAAGGGGT 60.159 50.000 0.00 0.00 35.99 4.95
1080 1109 0.995024 ATCCTTGCAGGTTGTAGCCT 59.005 50.000 0.00 0.00 39.99 4.58
1093 1122 8.683615 GCAGGTTGTAGCCTTTAGTTATTAATT 58.316 33.333 0.00 0.00 36.58 1.40
1216 1245 5.294356 TGGCCATGTTATTCGTATGAGTAC 58.706 41.667 0.00 0.00 0.00 2.73
1249 1278 6.323739 TCTTCTGTTTATTCCCTGCTGTTTTT 59.676 34.615 0.00 0.00 0.00 1.94
1302 1331 5.335897 GCCAAACTTCTAATGTTCATCTGCA 60.336 40.000 0.00 0.00 0.00 4.41
1322 1351 6.014070 TCTGCATTTGTAGTCTGGTAAGGTTA 60.014 38.462 0.00 0.00 0.00 2.85
1328 1357 8.983702 TTTGTAGTCTGGTAAGGTTATTTTGT 57.016 30.769 0.00 0.00 0.00 2.83
1575 1612 0.322008 CAGAGGGGTTGGAGTCTTGC 60.322 60.000 0.00 0.00 0.00 4.01
1576 1613 1.002011 GAGGGGTTGGAGTCTTGCC 60.002 63.158 0.00 0.00 0.00 4.52
1762 1799 1.408822 GGGGTCCTGGCTATTGAACAG 60.409 57.143 0.00 0.00 0.00 3.16
1924 1961 2.288666 TCAATCAATTGTCTAGCCCGC 58.711 47.619 5.13 0.00 38.84 6.13
2009 2046 3.901222 TGATGGTGGTCTGTACAGAGAAA 59.099 43.478 25.81 11.48 38.27 2.52
2164 2201 3.224884 GACAAGGAGTCACTAGCTGTC 57.775 52.381 0.00 0.00 46.77 3.51
2227 2264 9.645059 TCACATATTGTTCTTAGCTATAGCATC 57.355 33.333 26.07 9.90 45.16 3.91
2331 2368 1.991121 ATAGCTGGTGGCATGGATTG 58.009 50.000 0.00 0.00 44.79 2.67
2340 2377 2.038295 GTGGCATGGATTGTTTTGGGAA 59.962 45.455 0.00 0.00 0.00 3.97
2906 2943 0.458669 CATGGGGTGCTGATTTCTGC 59.541 55.000 2.80 2.80 40.61 4.26
2910 2947 3.266964 GTGCTGATTTCTGCGCCA 58.733 55.556 4.18 0.00 42.84 5.69
3014 3051 3.686691 GCCTGATTGGTAATCTCTGCCTT 60.687 47.826 3.53 0.00 38.72 4.35
3015 3052 4.133078 CCTGATTGGTAATCTCTGCCTTC 58.867 47.826 3.53 0.00 38.72 3.46
3016 3053 4.141528 CCTGATTGGTAATCTCTGCCTTCT 60.142 45.833 3.53 0.00 38.72 2.85
3058 3095 5.874810 TCTGGACATTTCAGATTTTACTCCG 59.125 40.000 0.00 0.00 36.46 4.63
3106 3143 6.594159 ACATCCTTCCTTGTATTCGTTAACAG 59.406 38.462 6.39 0.00 0.00 3.16
3107 3144 6.105397 TCCTTCCTTGTATTCGTTAACAGT 57.895 37.500 6.39 0.00 0.00 3.55
3108 3145 6.527423 TCCTTCCTTGTATTCGTTAACAGTT 58.473 36.000 6.39 0.00 0.00 3.16
3109 3146 7.669427 TCCTTCCTTGTATTCGTTAACAGTTA 58.331 34.615 6.39 0.00 0.00 2.24
3110 3147 7.599998 TCCTTCCTTGTATTCGTTAACAGTTAC 59.400 37.037 6.39 4.46 0.00 2.50
3111 3148 7.385752 CCTTCCTTGTATTCGTTAACAGTTACA 59.614 37.037 6.39 6.87 0.00 2.41
3112 3149 7.642071 TCCTTGTATTCGTTAACAGTTACAC 57.358 36.000 6.39 0.00 0.00 2.90
3113 3150 7.436118 TCCTTGTATTCGTTAACAGTTACACT 58.564 34.615 6.39 0.00 0.00 3.55
3298 3353 0.253044 TGTCCCAGCTTCATAGTGCC 59.747 55.000 0.00 0.00 0.00 5.01
3322 3377 4.118410 CTGTGCAAAATGCCTGTTAACAA 58.882 39.130 10.03 0.00 44.23 2.83
3374 3429 5.393866 ACATGGTTTACATTTCCTTGGACT 58.606 37.500 0.00 0.00 37.84 3.85
3378 3433 4.280929 GGTTTACATTTCCTTGGACTGCTT 59.719 41.667 0.00 0.00 0.00 3.91
3402 3464 6.841119 TGTTGACATATTCAAGAACCAATCG 58.159 36.000 1.96 0.00 45.23 3.34
3456 3518 5.599715 GCTGCTTCATCGTTACGTAATATG 58.400 41.667 19.74 19.74 0.00 1.78
3481 3543 0.322322 TCGACACCATAACCACCCAC 59.678 55.000 0.00 0.00 0.00 4.61
3492 3554 5.946972 CCATAACCACCCACATGTAACTTTA 59.053 40.000 0.00 0.00 0.00 1.85
3501 3563 5.121768 CCCACATGTAACTTTACACTACTGC 59.878 44.000 0.00 0.00 45.47 4.40
3599 3664 7.372714 TCAACCATTTCAGATGAAACATCAAG 58.627 34.615 10.04 6.29 45.55 3.02
3600 3665 6.276832 ACCATTTCAGATGAAACATCAAGG 57.723 37.500 10.04 8.13 45.55 3.61
3706 5087 0.962356 CCCTGGTGACACTTGATGCC 60.962 60.000 5.39 0.00 35.60 4.40
3729 5110 4.463879 CGCTGCTGGGTGGAGGAG 62.464 72.222 0.00 0.00 34.46 3.69
3892 5273 1.025113 ATCCGAGAGACGACAAGCGA 61.025 55.000 0.00 0.00 45.77 4.93
3893 5274 1.209383 CCGAGAGACGACAAGCGAA 59.791 57.895 0.00 0.00 45.77 4.70
3894 5275 1.066114 CCGAGAGACGACAAGCGAAC 61.066 60.000 0.00 0.00 45.77 3.95
3895 5276 1.389204 CGAGAGACGACAAGCGAACG 61.389 60.000 0.00 0.00 45.77 3.95
3914 5295 1.602237 CGGGGGCTAATCAGTGTGT 59.398 57.895 0.00 0.00 0.00 3.72
3915 5296 0.744414 CGGGGGCTAATCAGTGTGTG 60.744 60.000 0.00 0.00 0.00 3.82
3916 5297 0.328258 GGGGGCTAATCAGTGTGTGT 59.672 55.000 0.00 0.00 0.00 3.72
3917 5298 1.453155 GGGGCTAATCAGTGTGTGTG 58.547 55.000 0.00 0.00 0.00 3.82
3918 5299 1.453155 GGGCTAATCAGTGTGTGTGG 58.547 55.000 0.00 0.00 0.00 4.17
3919 5300 1.453155 GGCTAATCAGTGTGTGTGGG 58.547 55.000 0.00 0.00 0.00 4.61
4000 5381 1.568612 CGAGTTGTTGCGTGCATCCT 61.569 55.000 0.00 0.00 0.00 3.24
4001 5382 0.110056 GAGTTGTTGCGTGCATCCTG 60.110 55.000 0.00 0.00 0.00 3.86
4102 5483 2.722071 TGAATGTTTTCGTTCGGTTGC 58.278 42.857 0.00 0.00 45.73 4.17
4159 5540 1.200020 GATTCTTGTCGGGTTGCTTGG 59.800 52.381 0.00 0.00 0.00 3.61
4255 5636 4.458397 TGGCTGATGGATCTGAGAATTTC 58.542 43.478 0.00 0.00 0.00 2.17
4274 5655 7.841222 AGAATTTCCTTTATCAATTGGCTAGGT 59.159 33.333 5.42 0.00 0.00 3.08
4281 5662 9.793259 CCTTTATCAATTGGCTAGGTTATCTAA 57.207 33.333 5.42 0.00 0.00 2.10
4283 5664 9.793259 TTTATCAATTGGCTAGGTTATCTAAGG 57.207 33.333 5.42 0.00 0.00 2.69
4284 5665 5.621193 TCAATTGGCTAGGTTATCTAAGGC 58.379 41.667 5.42 0.00 0.00 4.35
4285 5666 3.746045 TTGGCTAGGTTATCTAAGGCG 57.254 47.619 0.00 0.00 0.00 5.52
4335 5716 0.612229 ATCTGGCAGACACTCAGTGG 59.388 55.000 21.37 0.00 37.94 4.00
4354 8370 1.136500 GGGACGTCATCTAGAACACCC 59.864 57.143 18.91 0.83 0.00 4.61
4386 8402 4.376225 AACGGGAATGTTAGGAAGGAAA 57.624 40.909 0.00 0.00 0.00 3.13
4393 8409 2.706890 TGTTAGGAAGGAAATCACGCC 58.293 47.619 0.00 0.00 0.00 5.68
4432 8448 5.295292 CGCAGATTTCATGTCTTGGATAAGT 59.705 40.000 0.00 0.00 35.38 2.24
4455 8471 6.207810 AGTTCTAGAGTATGTACTATGGCAGC 59.792 42.308 0.00 0.00 36.50 5.25
4459 8475 4.038522 AGAGTATGTACTATGGCAGCAGTG 59.961 45.833 13.24 0.00 36.50 3.66
4530 8546 8.286191 AGAATGGTGTAATCTGATTCTTTTCC 57.714 34.615 6.10 4.96 30.82 3.13
4549 8565 0.179000 CGGTTTCTCTAGGCAGCCAT 59.821 55.000 15.80 0.95 0.00 4.40
4550 8566 1.407437 CGGTTTCTCTAGGCAGCCATT 60.407 52.381 15.80 0.00 0.00 3.16
4552 8568 2.424956 GGTTTCTCTAGGCAGCCATTTG 59.575 50.000 15.80 0.89 0.00 2.32
4554 8570 3.439857 TTCTCTAGGCAGCCATTTGTT 57.560 42.857 15.80 0.00 0.00 2.83
4555 8571 2.715046 TCTCTAGGCAGCCATTTGTTG 58.285 47.619 15.80 0.00 0.00 3.33
4557 8573 2.821969 CTCTAGGCAGCCATTTGTTGTT 59.178 45.455 15.80 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 192 4.748679 CAAAGCAGAGCACGCCGC 62.749 66.667 0.00 0.00 42.91 6.53
188 199 2.399356 GCCGGGTACAAAGCAGAGC 61.399 63.158 2.18 0.00 0.00 4.09
238 249 9.931210 GAGAGAAAATAATACAACCGTATTTGG 57.069 33.333 3.40 0.00 44.27 3.28
255 266 4.211374 CGTGAAAACCGACAGAGAGAAAAT 59.789 41.667 0.00 0.00 0.00 1.82
257 268 3.120792 CGTGAAAACCGACAGAGAGAAA 58.879 45.455 0.00 0.00 0.00 2.52
259 270 1.951602 TCGTGAAAACCGACAGAGAGA 59.048 47.619 0.00 0.00 0.00 3.10
263 274 3.057019 CAGAATCGTGAAAACCGACAGA 58.943 45.455 0.00 0.00 37.12 3.41
264 275 2.800544 ACAGAATCGTGAAAACCGACAG 59.199 45.455 0.00 0.00 37.12 3.51
265 276 2.828877 ACAGAATCGTGAAAACCGACA 58.171 42.857 0.00 0.00 37.12 4.35
267 278 4.124238 AGAAACAGAATCGTGAAAACCGA 58.876 39.130 0.00 0.00 38.89 4.69
268 279 4.211374 AGAGAAACAGAATCGTGAAAACCG 59.789 41.667 0.00 0.00 0.00 4.44
269 280 5.334182 GGAGAGAAACAGAATCGTGAAAACC 60.334 44.000 0.00 0.00 0.00 3.27
270 281 5.467063 AGGAGAGAAACAGAATCGTGAAAAC 59.533 40.000 0.00 0.00 0.00 2.43
290 303 0.251916 TCACCGGCCATTACAAGGAG 59.748 55.000 0.00 0.00 0.00 3.69
521 534 4.847757 CGAGCATATGCAAAATTATCGGTG 59.152 41.667 28.62 0.94 45.16 4.94
563 576 4.860907 TCGTTTAAGAGCGTCTACCAATTC 59.139 41.667 0.00 0.00 0.00 2.17
577 590 8.020819 GTGGATCATTGTTGAATTCGTTTAAGA 58.979 33.333 0.04 0.00 34.96 2.10
578 591 7.807433 TGTGGATCATTGTTGAATTCGTTTAAG 59.193 33.333 0.04 0.00 34.96 1.85
584 597 4.560035 GCTTGTGGATCATTGTTGAATTCG 59.440 41.667 0.04 0.00 34.96 3.34
603 616 4.272018 GGAGTAACAGATATGCACAGCTTG 59.728 45.833 0.00 0.00 0.00 4.01
637 651 9.290988 TGGTGTCACAAGTACATAAACATATTT 57.709 29.630 5.12 0.00 0.00 1.40
638 652 8.856153 TGGTGTCACAAGTACATAAACATATT 57.144 30.769 5.12 0.00 0.00 1.28
639 653 9.461312 AATGGTGTCACAAGTACATAAACATAT 57.539 29.630 5.12 0.00 0.00 1.78
640 654 8.856153 AATGGTGTCACAAGTACATAAACATA 57.144 30.769 5.12 0.00 0.00 2.29
641 655 7.759489 AATGGTGTCACAAGTACATAAACAT 57.241 32.000 5.12 0.00 0.00 2.71
642 656 7.500892 AGAAATGGTGTCACAAGTACATAAACA 59.499 33.333 5.12 0.00 0.00 2.83
643 657 7.871853 AGAAATGGTGTCACAAGTACATAAAC 58.128 34.615 5.12 0.00 0.00 2.01
644 658 8.458573 AAGAAATGGTGTCACAAGTACATAAA 57.541 30.769 5.12 0.00 0.00 1.40
645 659 9.733556 ATAAGAAATGGTGTCACAAGTACATAA 57.266 29.630 5.12 0.00 0.00 1.90
691 717 6.420008 GCTAACGACCGTCATATCTATTTGTT 59.580 38.462 0.00 0.00 0.00 2.83
709 735 8.514330 AAAATAAATTACATCTGGGCTAACGA 57.486 30.769 0.00 0.00 0.00 3.85
710 736 7.860872 GGAAAATAAATTACATCTGGGCTAACG 59.139 37.037 0.00 0.00 0.00 3.18
760 786 3.444388 ACGATACCAACAGAGAGAAGGAC 59.556 47.826 0.00 0.00 0.00 3.85
761 787 3.444034 CACGATACCAACAGAGAGAAGGA 59.556 47.826 0.00 0.00 0.00 3.36
822 849 2.412870 CTCCGAAAATTGGCAAAACCC 58.587 47.619 3.01 0.00 37.83 4.11
838 865 2.969628 AGTAAAGCATCAGTCCTCCG 57.030 50.000 0.00 0.00 0.00 4.63
900 928 5.606505 TCAACATACATAGGCGAATAAGCA 58.393 37.500 0.00 0.00 39.27 3.91
908 936 2.158813 ACCCCTTCAACATACATAGGCG 60.159 50.000 0.00 0.00 0.00 5.52
928 956 8.564574 TCATAACCCGCAAATATCTAAAATGAC 58.435 33.333 0.00 0.00 0.00 3.06
929 957 8.684386 TCATAACCCGCAAATATCTAAAATGA 57.316 30.769 0.00 0.00 0.00 2.57
980 1008 0.904649 CAGTCCACCATACCAGCAGA 59.095 55.000 0.00 0.00 0.00 4.26
981 1009 0.904649 TCAGTCCACCATACCAGCAG 59.095 55.000 0.00 0.00 0.00 4.24
982 1010 0.904649 CTCAGTCCACCATACCAGCA 59.095 55.000 0.00 0.00 0.00 4.41
983 1011 0.905357 ACTCAGTCCACCATACCAGC 59.095 55.000 0.00 0.00 0.00 4.85
984 1012 4.023980 TCTAACTCAGTCCACCATACCAG 58.976 47.826 0.00 0.00 0.00 4.00
1139 1168 7.175641 ACCCATTGAGTAAAAGACAATCTCAAG 59.824 37.037 10.71 2.28 44.47 3.02
1160 1189 9.500785 CAAACTAAATCCAAATTTAACACCCAT 57.499 29.630 0.00 0.00 37.00 4.00
1196 1225 7.426410 ACTGAGTACTCATACGAATAACATGG 58.574 38.462 25.35 11.08 39.13 3.66
1216 1245 7.011857 GCAGGGAATAAACAGAAGATTACTGAG 59.988 40.741 0.00 0.00 38.55 3.35
1249 1278 6.645306 TGGTCCATCGTGAATACAGAATAAA 58.355 36.000 0.00 0.00 0.00 1.40
1265 1294 3.683365 AGTTTGGCAAAATGGTCCATC 57.317 42.857 15.29 0.00 0.00 3.51
1302 1331 9.582648 ACAAAATAACCTTACCAGACTACAAAT 57.417 29.630 0.00 0.00 0.00 2.32
1328 1357 7.490725 CGCATTGAATATATGTTTCCAAACCAA 59.509 33.333 0.00 0.00 38.11 3.67
1502 1539 3.510388 TGTCAGCAGGAATTCTACTCG 57.490 47.619 5.23 0.00 0.00 4.18
1762 1799 1.434696 CGCCACAGCAATTCCATCC 59.565 57.895 0.00 0.00 39.83 3.51
1924 1961 2.865670 GCCATAATCAGACCGAGAGCAG 60.866 54.545 0.00 0.00 0.00 4.24
2009 2046 1.984288 GCAATCCCTAACCTCCGCCT 61.984 60.000 0.00 0.00 0.00 5.52
2164 2201 0.532862 ACACCAGAAGTTCAGTGCCG 60.533 55.000 20.15 4.04 33.46 5.69
2331 2368 5.222631 CAGAACTAAGCACATTCCCAAAAC 58.777 41.667 0.00 0.00 0.00 2.43
2340 2377 2.027377 AGCTCAGCAGAACTAAGCACAT 60.027 45.455 0.00 0.00 35.42 3.21
2662 2699 2.294233 CCCAAGAGTTGTCCATGTGTTG 59.706 50.000 0.00 0.00 0.00 3.33
2910 2947 3.932483 GTTCGACGGGTGGGTGGT 61.932 66.667 0.00 0.00 0.00 4.16
3106 3143 3.470645 ACAGAGACCCAACAGTGTAAC 57.529 47.619 0.00 0.00 0.00 2.50
3107 3144 4.497291 AAACAGAGACCCAACAGTGTAA 57.503 40.909 0.00 0.00 0.00 2.41
3108 3145 4.448210 GAAAACAGAGACCCAACAGTGTA 58.552 43.478 0.00 0.00 0.00 2.90
3109 3146 3.279434 GAAAACAGAGACCCAACAGTGT 58.721 45.455 0.00 0.00 0.00 3.55
3110 3147 2.618709 GGAAAACAGAGACCCAACAGTG 59.381 50.000 0.00 0.00 0.00 3.66
3111 3148 2.745152 CGGAAAACAGAGACCCAACAGT 60.745 50.000 0.00 0.00 0.00 3.55
3112 3149 1.873591 CGGAAAACAGAGACCCAACAG 59.126 52.381 0.00 0.00 0.00 3.16
3113 3150 1.210967 ACGGAAAACAGAGACCCAACA 59.789 47.619 0.00 0.00 0.00 3.33
3374 3429 5.534278 TGGTTCTTGAATATGTCAACAAGCA 59.466 36.000 12.08 12.08 44.89 3.91
3378 3433 6.429692 ACGATTGGTTCTTGAATATGTCAACA 59.570 34.615 0.00 0.00 41.47 3.33
3402 3464 8.220434 GGTTGAATGTTTTGCAAATGTATGTAC 58.780 33.333 13.65 6.83 0.00 2.90
3456 3518 2.095919 GTGGTTATGGTGTCGACAAAGC 60.096 50.000 21.95 19.74 0.00 3.51
3481 3543 6.307155 GCAAGCAGTAGTGTAAAGTTACATG 58.693 40.000 7.14 3.32 44.59 3.21
3501 3563 1.072666 GATTCGGGCAAAAGCGCAAG 61.073 55.000 11.47 0.00 43.44 4.01
3599 3664 1.421410 CGATTAGTGCTCCGTGTGCC 61.421 60.000 0.00 0.00 0.00 5.01
3600 3665 1.421410 CCGATTAGTGCTCCGTGTGC 61.421 60.000 0.00 0.00 0.00 4.57
3714 5095 3.406200 CCCTCCTCCACCCAGCAG 61.406 72.222 0.00 0.00 0.00 4.24
3715 5096 3.931631 CTCCCTCCTCCACCCAGCA 62.932 68.421 0.00 0.00 0.00 4.41
3716 5097 3.086600 CTCCCTCCTCCACCCAGC 61.087 72.222 0.00 0.00 0.00 4.85
3717 5098 3.086600 GCTCCCTCCTCCACCCAG 61.087 72.222 0.00 0.00 0.00 4.45
3718 5099 3.615811 AGCTCCCTCCTCCACCCA 61.616 66.667 0.00 0.00 0.00 4.51
3719 5100 2.766229 GAGCTCCCTCCTCCACCC 60.766 72.222 0.87 0.00 31.68 4.61
3892 5273 2.189521 CTGATTAGCCCCCGCGTT 59.810 61.111 4.92 0.00 41.18 4.84
3893 5274 3.081409 ACTGATTAGCCCCCGCGT 61.081 61.111 4.92 0.00 41.18 6.01
3894 5275 2.588877 CACTGATTAGCCCCCGCG 60.589 66.667 0.00 0.00 41.18 6.46
3895 5276 1.819632 CACACTGATTAGCCCCCGC 60.820 63.158 0.00 0.00 0.00 6.13
4000 5381 2.582226 CGAGCCTAATCGCGCACA 60.582 61.111 8.75 0.00 35.66 4.57
4001 5382 1.693083 AAACGAGCCTAATCGCGCAC 61.693 55.000 8.75 0.00 46.60 5.34
4004 5385 1.925052 GGAAACGAGCCTAATCGCG 59.075 57.895 0.00 0.00 46.60 5.87
4118 5499 1.470098 CCATCAGGGCTGAACGAAAAG 59.530 52.381 0.00 0.00 43.58 2.27
4228 5609 2.105993 CTCAGATCCATCAGCCAATCCA 59.894 50.000 0.00 0.00 0.00 3.41
4255 5636 9.793259 TTAGATAACCTAGCCAATTGATAAAGG 57.207 33.333 7.12 10.29 0.00 3.11
4274 5655 0.693092 AGGGTGCCCGCCTTAGATAA 60.693 55.000 0.98 0.00 41.95 1.75
4283 5664 4.162690 CTACAGGAGGGTGCCCGC 62.163 72.222 2.15 2.15 41.95 6.13
4284 5665 1.961180 CTTCTACAGGAGGGTGCCCG 61.961 65.000 0.98 0.00 41.95 6.13
4285 5666 0.617820 TCTTCTACAGGAGGGTGCCC 60.618 60.000 0.00 0.00 0.00 5.36
4311 5692 4.569966 CACTGAGTGTCTGCCAGATATTTC 59.430 45.833 4.01 0.00 0.00 2.17
4335 5716 1.822990 TGGGTGTTCTAGATGACGTCC 59.177 52.381 14.12 0.00 0.00 4.79
4354 8370 3.873910 ACATTCCCGTTTGGATAGAGTG 58.126 45.455 0.00 0.00 44.66 3.51
4386 8402 2.042831 GCAAAGGCTCTGGCGTGAT 61.043 57.895 0.00 0.00 39.81 3.06
4432 8448 6.068670 TGCTGCCATAGTACATACTCTAGAA 58.931 40.000 0.00 0.00 37.73 2.10
4455 8471 1.337260 ACTCGGAGCTAGCAAACACTG 60.337 52.381 18.83 7.78 0.00 3.66
4459 8475 2.806244 TGAAAACTCGGAGCTAGCAAAC 59.194 45.455 18.83 7.74 0.00 2.93
4466 8482 1.228657 GCCGTTGAAAACTCGGAGCT 61.229 55.000 4.58 0.00 46.99 4.09
4530 8546 0.179000 ATGGCTGCCTAGAGAAACCG 59.821 55.000 21.03 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.