Multiple sequence alignment - TraesCS1A01G371900

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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 TraesCS1A01G371900 chr1A 100.000 3578 0 0 1 3578 548673207 548676784 0.000000e+00 6608.0
1 TraesCS1A01G371900 chr1A 92.902 1127 71 5 1746 2868 548682956 548684077 0.000000e+00 1629.0
2 TraesCS1A01G371900 chr1A 90.803 685 44 7 2876 3555 548684139 548684809 0.000000e+00 898.0
3 TraesCS1A01G371900 chr1A 94.737 114 6 0 575 688 561971671 561971784 1.020000e-40 178.0
4 TraesCS1A01G371900 chr1A 94.690 113 6 0 575 687 533166610 533166498 3.670000e-40 176.0
5 TraesCS1A01G371900 chr1D 94.298 2087 74 11 808 2868 454565356 454563289 0.000000e+00 3153.0
6 TraesCS1A01G371900 chr1D 90.519 770 41 18 1 769 454567128 454566390 0.000000e+00 989.0
7 TraesCS1A01G371900 chr1D 80.848 731 80 28 2885 3578 454563210 454562503 1.470000e-143 520.0
8 TraesCS1A01G371900 chr1B 95.196 1790 72 10 1084 2868 624885304 624887084 0.000000e+00 2817.0
9 TraesCS1A01G371900 chr1B 93.976 581 25 4 1 580 624883521 624884092 0.000000e+00 870.0
10 TraesCS1A01G371900 chr1B 93.182 88 5 1 682 769 624884089 624884175 1.040000e-25 128.0
11 TraesCS1A01G371900 chr1B 100.000 35 0 0 277 311 624883764 624883798 8.290000e-07 65.8
12 TraesCS1A01G371900 chr3A 83.278 1507 240 12 1079 2579 482060543 482062043 0.000000e+00 1376.0
13 TraesCS1A01G371900 chr3A 95.413 109 5 0 578 686 506500695 506500587 1.320000e-39 174.0
14 TraesCS1A01G371900 chr3A 93.162 117 8 0 577 693 427104323 427104439 4.750000e-39 172.0
15 TraesCS1A01G371900 chr3B 82.844 1498 246 10 1084 2579 471475013 471476501 0.000000e+00 1332.0
16 TraesCS1A01G371900 chr3D 82.310 1498 254 10 1084 2579 361737303 361738791 0.000000e+00 1288.0
17 TraesCS1A01G371900 chrUn 93.277 119 8 0 568 686 150795941 150796059 3.670000e-40 176.0
18 TraesCS1A01G371900 chr7A 94.643 112 6 0 578 689 619039661 619039550 1.320000e-39 174.0
19 TraesCS1A01G371900 chr2A 94.545 110 6 0 575 684 79319150 79319259 1.710000e-38 171.0
20 TraesCS1A01G371900 chr4A 92.373 118 9 0 568 685 179550745 179550628 6.140000e-38 169.0
21 TraesCS1A01G371900 chr5B 93.694 111 7 0 575 685 29520042 29520152 2.210000e-37 167.0


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 TraesCS1A01G371900 chr1A 548673207 548676784 3577 False 6608.0 6608 100.0000 1 3578 1 chr1A.!!$F1 3577
1 TraesCS1A01G371900 chr1A 548682956 548684809 1853 False 1263.5 1629 91.8525 1746 3555 2 chr1A.!!$F3 1809
2 TraesCS1A01G371900 chr1D 454562503 454567128 4625 True 1554.0 3153 88.5550 1 3578 3 chr1D.!!$R1 3577
3 TraesCS1A01G371900 chr1B 624883521 624887084 3563 False 970.2 2817 95.5885 1 2868 4 chr1B.!!$F1 2867
4 TraesCS1A01G371900 chr3A 482060543 482062043 1500 False 1376.0 1376 83.2780 1079 2579 1 chr3A.!!$F2 1500
5 TraesCS1A01G371900 chr3B 471475013 471476501 1488 False 1332.0 1332 82.8440 1084 2579 1 chr3B.!!$F1 1495
6 TraesCS1A01G371900 chr3D 361737303 361738791 1488 False 1288.0 1288 82.3100 1084 2579 1 chr3D.!!$F1 1495

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
898 1990 0.035458 CCGCTTTCCAGTCTCCACTT 59.965 55.0 0.0 0.0 0.00 3.16 F
1861 3402 0.098200 CGACTTCGACGGCTGTATGA 59.902 55.0 0.0 0.0 43.02 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 3428 0.114168 TGGCAAGGTAAATGGGCAGT 59.886 50.0 0.0 0.0 0.00 4.40 R
3008 4626 0.112995 TGAAAAGATGGGTGCTGCCT 59.887 50.0 0.0 0.0 37.43 4.75 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
58 59 1.949525 CGGATAATGTTGCTGGAAGGG 59.050 52.381 0.00 0.00 0.00 3.95
139 140 7.020827 TGAAGAGATGAAAATAACCTGACCT 57.979 36.000 0.00 0.00 0.00 3.85
229 230 3.364764 GCTGCAGAAACTAGAAAGCACAG 60.365 47.826 20.43 0.00 0.00 3.66
253 254 4.622701 GACCATTGTCCTTTGAGCATAC 57.377 45.455 0.00 0.00 35.34 2.39
349 350 1.225855 CGCACACCAGAGCTTGTAAA 58.774 50.000 0.00 0.00 0.00 2.01
406 407 7.298122 CGTGAAGCATTTATTTGTTCTAGTGT 58.702 34.615 0.00 0.00 0.00 3.55
443 444 4.908601 TTGTTCCAAGCAGATCTCCTTA 57.091 40.909 0.00 0.00 0.00 2.69
444 445 4.207891 TGTTCCAAGCAGATCTCCTTAC 57.792 45.455 0.00 0.00 0.00 2.34
445 446 3.055094 TGTTCCAAGCAGATCTCCTTACC 60.055 47.826 0.00 0.00 0.00 2.85
451 452 5.355596 CAAGCAGATCTCCTTACCTAACAG 58.644 45.833 0.00 0.00 0.00 3.16
533 536 9.653287 CTCTGTAATGAAACTTAGGTTATGTGA 57.347 33.333 0.00 0.00 34.90 3.58
543 546 9.520515 AAACTTAGGTTATGTGAATCTGTTGAT 57.479 29.630 0.00 0.00 34.90 2.57
547 550 5.889853 AGGTTATGTGAATCTGTTGATGCAT 59.110 36.000 0.00 0.00 40.15 3.96
548 551 7.056006 AGGTTATGTGAATCTGTTGATGCATA 58.944 34.615 0.00 0.00 40.15 3.14
549 552 7.228108 AGGTTATGTGAATCTGTTGATGCATAG 59.772 37.037 0.00 0.00 40.15 2.23
550 553 7.012704 GGTTATGTGAATCTGTTGATGCATAGT 59.987 37.037 0.00 0.00 40.15 2.12
586 589 6.210287 ACTTTCTAGAAATGTACTCCCTCG 57.790 41.667 18.02 4.98 0.00 4.63
590 593 3.889520 AGAAATGTACTCCCTCGGTTC 57.110 47.619 0.00 0.00 0.00 3.62
598 601 1.479730 ACTCCCTCGGTTCGGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
602 605 2.354403 CCCTCGGTTCGGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
603 606 2.928116 CCTCGGTTCGGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
604 607 3.368116 CCTCGGTTCGGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
605 608 3.841643 TCGGTTCGGAATTACTTGTCTC 58.158 45.455 0.00 0.00 0.00 3.36
606 609 2.597305 CGGTTCGGAATTACTTGTCTCG 59.403 50.000 0.00 0.00 0.00 4.04
607 610 2.928116 GGTTCGGAATTACTTGTCTCGG 59.072 50.000 0.00 0.00 0.00 4.63
608 611 3.367703 GGTTCGGAATTACTTGTCTCGGA 60.368 47.826 0.00 0.00 0.00 4.55
613 616 4.923871 CGGAATTACTTGTCTCGGATATGG 59.076 45.833 0.00 0.00 0.00 2.74
620 623 6.672266 ACTTGTCTCGGATATGGATGTATT 57.328 37.500 0.00 0.00 0.00 1.89
625 628 8.417273 TGTCTCGGATATGGATGTATTTAGAA 57.583 34.615 0.00 0.00 0.00 2.10
626 629 8.304596 TGTCTCGGATATGGATGTATTTAGAAC 58.695 37.037 0.00 0.00 0.00 3.01
653 656 7.426929 AAATACGTCTAGATGCATCCATTTC 57.573 36.000 23.06 9.30 0.00 2.17
656 659 3.186001 CGTCTAGATGCATCCATTTCTGC 59.814 47.826 23.06 5.10 38.87 4.26
668 671 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
669 672 4.092821 TCCATTTCTGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 38.31 3.34
687 690 3.031660 GGAACGGAGCGAGTACTTG 57.968 57.895 5.68 5.68 0.00 3.16
701 704 5.061808 GCGAGTACTTGTGTGGTATGTTTAG 59.938 44.000 11.83 0.00 0.00 1.85
704 707 3.071479 ACTTGTGTGGTATGTTTAGCCG 58.929 45.455 0.00 0.00 0.00 5.52
728 731 5.454613 GGTTGATTTCAAAACCTGGGATGTT 60.455 40.000 0.00 0.00 42.20 2.71
778 1162 6.038271 TGTTTCTGCATCTGATCATGAGAATG 59.962 38.462 0.09 3.57 0.00 2.67
805 1189 3.755378 GCTTTGTCTGAATGACCATCAGT 59.245 43.478 3.72 0.00 44.75 3.41
859 1948 0.911769 AGATGTCGGCCAAATCAGGA 59.088 50.000 2.24 0.00 0.00 3.86
869 1958 1.065491 CCAAATCAGGACCGTCCATCA 60.065 52.381 19.95 3.07 39.61 3.07
870 1959 2.283298 CAAATCAGGACCGTCCATCAG 58.717 52.381 19.95 6.66 39.61 2.90
871 1960 1.866015 AATCAGGACCGTCCATCAGA 58.134 50.000 19.95 11.54 39.61 3.27
872 1961 1.115467 ATCAGGACCGTCCATCAGAC 58.885 55.000 19.95 0.00 39.61 3.51
891 1983 2.994578 GACTTTCTACCGCTTTCCAGTC 59.005 50.000 0.00 0.00 0.00 3.51
897 1989 1.122019 ACCGCTTTCCAGTCTCCACT 61.122 55.000 0.00 0.00 0.00 4.00
898 1990 0.035458 CCGCTTTCCAGTCTCCACTT 59.965 55.000 0.00 0.00 0.00 3.16
899 1991 1.543429 CCGCTTTCCAGTCTCCACTTT 60.543 52.381 0.00 0.00 0.00 2.66
902 1994 2.487265 GCTTTCCAGTCTCCACTTTCCA 60.487 50.000 0.00 0.00 0.00 3.53
906 1998 1.142870 CCAGTCTCCACTTTCCACCAA 59.857 52.381 0.00 0.00 0.00 3.67
909 2001 0.476771 TCTCCACTTTCCACCAACCC 59.523 55.000 0.00 0.00 0.00 4.11
910 2002 0.539669 CTCCACTTTCCACCAACCCC 60.540 60.000 0.00 0.00 0.00 4.95
911 2003 1.901464 CCACTTTCCACCAACCCCG 60.901 63.158 0.00 0.00 0.00 5.73
912 2004 1.152839 CACTTTCCACCAACCCCGT 60.153 57.895 0.00 0.00 0.00 5.28
932 2024 3.597255 GTGCTACAGTCTAAAACCCTCC 58.403 50.000 0.00 0.00 0.00 4.30
939 2031 1.281287 GTCTAAAACCCTCCTCCACCC 59.719 57.143 0.00 0.00 0.00 4.61
1245 2783 2.669240 GCCTGGTACGAGCCCTTT 59.331 61.111 0.00 0.00 0.00 3.11
1596 3137 4.408821 TGCGGCATCTCCCACACC 62.409 66.667 0.00 0.00 0.00 4.16
1861 3402 0.098200 CGACTTCGACGGCTGTATGA 59.902 55.000 0.00 0.00 43.02 2.15
1920 3461 0.881118 TTGCCAATTCGCTCAACTCC 59.119 50.000 0.00 0.00 0.00 3.85
2013 3554 0.036388 TCATCGTTCCAGGAGGCAAC 60.036 55.000 0.00 0.00 33.74 4.17
2058 3599 2.247437 GGGATTCGAGATGTGCCGC 61.247 63.158 0.00 0.00 0.00 6.53
2079 3620 1.200020 GTTCTTGGCCTTGTTGATCGG 59.800 52.381 3.32 0.00 0.00 4.18
2139 3680 1.135315 CCGCTGTACCGCTACTACAAA 60.135 52.381 7.70 0.00 0.00 2.83
2142 3683 3.121544 GCTGTACCGCTACTACAAATCC 58.878 50.000 1.52 0.00 0.00 3.01
2307 3848 2.746277 AACGCAATGTCCCTCGCC 60.746 61.111 0.00 0.00 0.00 5.54
2579 4120 2.553247 GGCTCAAGGGTAAGCTTTGAGT 60.553 50.000 20.70 0.00 45.93 3.41
2583 4124 5.734720 CTCAAGGGTAAGCTTTGAGTATGA 58.265 41.667 14.39 8.10 41.66 2.15
2584 4125 6.313519 TCAAGGGTAAGCTTTGAGTATGAT 57.686 37.500 3.20 0.00 0.00 2.45
2585 4126 6.115446 TCAAGGGTAAGCTTTGAGTATGATG 58.885 40.000 3.20 0.00 0.00 3.07
2596 4137 2.251818 GAGTATGATGCCCTCCTGCTA 58.748 52.381 0.00 0.00 0.00 3.49
2700 4248 4.019174 AGCATTCGAACCCTTGATTTGAT 58.981 39.130 0.00 0.00 0.00 2.57
2736 4284 0.889306 AGACTCTTGTAGGCGTGTCC 59.111 55.000 0.00 0.00 38.81 4.02
2758 4307 1.219131 GGGGAATGGTTAGGGGGTGT 61.219 60.000 0.00 0.00 0.00 4.16
2805 4354 8.875803 GTGTTGTGTTCTATGGATAATAAACGA 58.124 33.333 0.00 0.00 0.00 3.85
2868 4417 2.553602 CTGTTTGCTCCATGTTGCACTA 59.446 45.455 9.02 0.00 39.05 2.74
2870 4419 2.554032 GTTTGCTCCATGTTGCACTAGT 59.446 45.455 9.02 0.00 39.05 2.57
2871 4420 3.694043 TTGCTCCATGTTGCACTAGTA 57.306 42.857 9.02 0.00 39.05 1.82
2873 4422 5.351948 TTGCTCCATGTTGCACTAGTATA 57.648 39.130 9.02 0.00 39.05 1.47
2874 4423 5.551305 TGCTCCATGTTGCACTAGTATAT 57.449 39.130 0.00 0.00 33.94 0.86
2883 4486 4.855715 TGCACTAGTATATGGAGTCTGC 57.144 45.455 0.00 0.00 0.00 4.26
2910 4522 3.815401 ACTGAAACCTGAAGTTGGATTCG 59.185 43.478 0.00 0.00 39.19 3.34
2920 4532 4.102524 TGAAGTTGGATTCGGGTGCTATAT 59.897 41.667 0.00 0.00 31.52 0.86
2929 4542 4.937201 TCGGGTGCTATATATGCCTATG 57.063 45.455 0.00 0.00 0.00 2.23
2948 4561 0.170339 GCCCGCATTCCAGTTTACAC 59.830 55.000 0.00 0.00 0.00 2.90
2962 4576 5.258456 AGTTTACACTGAGTCTTGTCGAA 57.742 39.130 1.69 0.00 0.00 3.71
2971 4585 5.642063 ACTGAGTCTTGTCGAAACTTTTCAA 59.358 36.000 2.77 0.00 37.01 2.69
3019 4637 0.252057 TAGACAGTAGGCAGCACCCA 60.252 55.000 0.00 0.00 40.58 4.51
3021 4639 0.462759 GACAGTAGGCAGCACCCATC 60.463 60.000 0.00 0.00 40.58 3.51
3022 4640 0.911525 ACAGTAGGCAGCACCCATCT 60.912 55.000 0.00 0.00 40.58 2.90
3034 4652 5.394443 GCAGCACCCATCTTTTCATTCATAA 60.394 40.000 0.00 0.00 0.00 1.90
3078 4696 3.037549 CCTCATAGCTTCAGGTTCCTCT 58.962 50.000 0.00 0.00 0.00 3.69
3116 4737 7.865889 GCATTGATCATATTCTGCAGATTTTGA 59.134 33.333 24.36 24.36 0.00 2.69
3128 4749 5.224888 TGCAGATTTTGAAAGAACATGAGC 58.775 37.500 0.00 0.00 0.00 4.26
3131 4752 5.862323 CAGATTTTGAAAGAACATGAGCTGG 59.138 40.000 0.00 0.00 0.00 4.85
3132 4753 5.771666 AGATTTTGAAAGAACATGAGCTGGA 59.228 36.000 0.00 0.00 0.00 3.86
3191 4812 8.819643 ATTACTAGATAAAAACATCGAGGCTC 57.180 34.615 3.87 3.87 33.41 4.70
3264 4885 7.383102 ACTCACTTTGCACCTTATTTATCAG 57.617 36.000 0.00 0.00 0.00 2.90
3272 4893 7.009179 TGCACCTTATTTATCAGAGATAGGG 57.991 40.000 0.00 0.00 0.00 3.53
3306 4952 6.553852 TGAACTACCTACCTCTGAAAACTCTT 59.446 38.462 0.00 0.00 0.00 2.85
3313 4959 7.508296 ACCTACCTCTGAAAACTCTTAACTACA 59.492 37.037 0.00 0.00 0.00 2.74
3318 4964 9.057089 CCTCTGAAAACTCTTAACTACAACATT 57.943 33.333 0.00 0.00 0.00 2.71
3442 5094 2.422479 CCTGCACTGATCCATGAACAAG 59.578 50.000 0.00 0.00 0.00 3.16
3465 5117 1.731720 GCCTAGACCAGCTTGTTCAG 58.268 55.000 0.00 0.00 0.00 3.02
3466 5118 1.276421 GCCTAGACCAGCTTGTTCAGA 59.724 52.381 0.00 0.00 0.00 3.27
3467 5119 2.933056 GCCTAGACCAGCTTGTTCAGAC 60.933 54.545 0.00 0.00 0.00 3.51
3468 5120 2.564947 CCTAGACCAGCTTGTTCAGACT 59.435 50.000 0.00 0.00 0.00 3.24
3469 5121 3.007398 CCTAGACCAGCTTGTTCAGACTT 59.993 47.826 0.00 0.00 0.00 3.01
3470 5122 3.118905 AGACCAGCTTGTTCAGACTTC 57.881 47.619 0.00 0.00 0.00 3.01
3471 5123 2.435805 AGACCAGCTTGTTCAGACTTCA 59.564 45.455 0.00 0.00 0.00 3.02
3488 5140 0.884704 TCAGAGTGGGCAAAAGTCGC 60.885 55.000 0.00 0.00 0.00 5.19
3567 5219 4.077300 TGATGAGGTATTGAGGTCATGC 57.923 45.455 0.00 0.00 29.66 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.583054 AGGTCGCACTCTTGTTGAAC 58.417 50.000 0.00 0.00 0.00 3.18
105 106 7.914537 ATTTTCATCTCTTCAACGTTTTCAC 57.085 32.000 0.00 0.00 0.00 3.18
139 140 2.875317 TGTGCATCTCAGCGTTGTTTAA 59.125 40.909 0.00 0.00 37.31 1.52
253 254 7.502120 AAATGAATCTGGAATTCAGGATACG 57.498 36.000 7.93 0.00 43.53 3.06
349 350 3.955771 AAACGTCGTACAACTGCAATT 57.044 38.095 0.00 0.00 0.00 2.32
451 452 8.045176 AGCCATGTAAAATAGAGAAACTCAAC 57.955 34.615 0.00 0.00 32.06 3.18
505 508 9.436957 ACATAACCTAAGTTTCATTACAGAGTG 57.563 33.333 0.00 0.00 37.42 3.51
586 589 2.928116 CCGAGACAAGTAATTCCGAACC 59.072 50.000 0.00 0.00 0.00 3.62
590 593 4.923871 CCATATCCGAGACAAGTAATTCCG 59.076 45.833 0.00 0.00 0.00 4.30
598 601 8.523658 TCTAAATACATCCATATCCGAGACAAG 58.476 37.037 0.00 0.00 0.00 3.16
602 605 8.651589 AGTTCTAAATACATCCATATCCGAGA 57.348 34.615 0.00 0.00 0.00 4.04
625 628 7.050970 TGGATGCATCTAGACGTATTTTAGT 57.949 36.000 25.28 0.00 0.00 2.24
626 629 8.539770 AATGGATGCATCTAGACGTATTTTAG 57.460 34.615 25.28 0.00 0.00 1.85
629 632 7.172190 CAGAAATGGATGCATCTAGACGTATTT 59.828 37.037 25.28 15.24 0.00 1.40
630 633 6.648310 CAGAAATGGATGCATCTAGACGTATT 59.352 38.462 25.28 7.52 0.00 1.89
631 634 6.162079 CAGAAATGGATGCATCTAGACGTAT 58.838 40.000 25.28 1.05 0.00 3.06
634 637 3.186001 GCAGAAATGGATGCATCTAGACG 59.814 47.826 25.28 9.46 42.11 4.18
635 638 3.186001 CGCAGAAATGGATGCATCTAGAC 59.814 47.826 25.28 14.42 42.68 2.59
637 640 3.186001 GTCGCAGAAATGGATGCATCTAG 59.814 47.826 25.28 9.06 42.68 2.43
643 646 1.470098 ACTTGTCGCAGAAATGGATGC 59.530 47.619 0.00 0.00 39.69 3.91
653 656 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
656 659 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
668 671 0.797249 CAAGTACTCGCTCCGTTCCG 60.797 60.000 0.00 0.00 0.00 4.30
669 672 0.243095 ACAAGTACTCGCTCCGTTCC 59.757 55.000 0.00 0.00 0.00 3.62
678 681 5.061808 GCTAAACATACCACACAAGTACTCG 59.938 44.000 0.00 0.00 0.00 4.18
684 687 2.418628 CCGGCTAAACATACCACACAAG 59.581 50.000 0.00 0.00 0.00 3.16
685 688 2.224572 ACCGGCTAAACATACCACACAA 60.225 45.455 0.00 0.00 0.00 3.33
687 690 2.103537 ACCGGCTAAACATACCACAC 57.896 50.000 0.00 0.00 0.00 3.82
701 704 2.403259 CAGGTTTTGAAATCAACCGGC 58.597 47.619 0.00 0.00 46.25 6.13
704 707 4.040339 ACATCCCAGGTTTTGAAATCAACC 59.960 41.667 0.00 0.00 42.61 3.77
805 1189 4.225717 TCTGTTCCATCAGATCACATCCAA 59.774 41.667 0.00 0.00 39.20 3.53
869 1958 2.633481 ACTGGAAAGCGGTAGAAAGTCT 59.367 45.455 0.00 0.00 0.00 3.24
870 1959 2.994578 GACTGGAAAGCGGTAGAAAGTC 59.005 50.000 0.00 0.00 0.00 3.01
871 1960 2.633481 AGACTGGAAAGCGGTAGAAAGT 59.367 45.455 0.00 0.00 0.00 2.66
872 1961 3.254892 GAGACTGGAAAGCGGTAGAAAG 58.745 50.000 0.00 0.00 0.00 2.62
891 1983 0.539669 GGGGTTGGTGGAAAGTGGAG 60.540 60.000 0.00 0.00 0.00 3.86
897 1989 1.706995 TAGCACGGGGTTGGTGGAAA 61.707 55.000 0.00 0.00 35.94 3.13
898 1990 2.148052 TAGCACGGGGTTGGTGGAA 61.148 57.895 0.00 0.00 35.94 3.53
899 1991 2.527123 TAGCACGGGGTTGGTGGA 60.527 61.111 0.00 0.00 35.94 4.02
902 1994 2.108278 GACTGTAGCACGGGGTTGGT 62.108 60.000 0.00 0.00 0.00 3.67
906 1998 1.636148 TTTAGACTGTAGCACGGGGT 58.364 50.000 0.00 0.00 0.00 4.95
909 2001 2.028385 AGGGTTTTAGACTGTAGCACGG 60.028 50.000 0.00 0.00 0.00 4.94
910 2002 3.251571 GAGGGTTTTAGACTGTAGCACG 58.748 50.000 0.00 0.00 0.00 5.34
911 2003 3.261137 AGGAGGGTTTTAGACTGTAGCAC 59.739 47.826 0.00 0.00 0.00 4.40
912 2004 3.514309 GAGGAGGGTTTTAGACTGTAGCA 59.486 47.826 0.00 0.00 0.00 3.49
932 2024 2.529136 TGGACTGTGGGGGTGGAG 60.529 66.667 0.00 0.00 0.00 3.86
939 2031 1.002134 GTGGGATGTGGACTGTGGG 60.002 63.158 0.00 0.00 0.00 4.61
1029 2135 1.443828 GAAGGAGAGGGATGGCGAC 59.556 63.158 0.00 0.00 0.00 5.19
1032 2138 1.414866 GGAGGAAGGAGAGGGATGGC 61.415 65.000 0.00 0.00 0.00 4.40
1035 2141 1.503347 GAGAGGAGGAAGGAGAGGGAT 59.497 57.143 0.00 0.00 0.00 3.85
1176 2714 4.593864 GCCTCCTCGCGGATGTCC 62.594 72.222 6.13 0.00 39.01 4.02
1861 3402 0.980231 GTCACCTCCCTGATGAGCCT 60.980 60.000 0.00 0.00 0.00 4.58
1887 3428 0.114168 TGGCAAGGTAAATGGGCAGT 59.886 50.000 0.00 0.00 0.00 4.40
2013 3554 8.394971 TGTAGAATGCATATATGTTTCCAAGG 57.605 34.615 14.14 0.00 0.00 3.61
2058 3599 1.135972 CGATCAACAAGGCCAAGAACG 60.136 52.381 5.01 1.81 0.00 3.95
2070 3611 2.741985 CGTGGCAGCCGATCAACA 60.742 61.111 7.03 0.00 0.00 3.33
2079 3620 3.730761 CAGACAAGCCGTGGCAGC 61.731 66.667 14.29 0.00 44.88 5.25
2139 3680 3.310860 GAACTGCGTCCACCCGGAT 62.311 63.158 0.73 0.00 45.33 4.18
2142 3683 4.308458 TGGAACTGCGTCCACCCG 62.308 66.667 0.00 0.00 42.97 5.28
2579 4120 1.973515 CAGTAGCAGGAGGGCATCATA 59.026 52.381 0.08 0.00 35.83 2.15
2583 4124 1.692042 AGCAGTAGCAGGAGGGCAT 60.692 57.895 0.00 0.00 45.49 4.40
2584 4125 2.284921 AGCAGTAGCAGGAGGGCA 60.285 61.111 0.00 0.00 45.49 5.36
2585 4126 2.188994 CAGCAGTAGCAGGAGGGC 59.811 66.667 0.00 0.00 45.49 5.19
2596 4137 3.325753 GGAGGGGTCAGCAGCAGT 61.326 66.667 0.00 0.00 0.00 4.40
2736 4284 2.203153 CCCTAACCATTCCCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
2758 4307 5.046878 ACACGGTACAAGAGATAATCAACCA 60.047 40.000 0.00 0.00 0.00 3.67
2805 4354 3.865011 TGAACAGCAACACAACACAAT 57.135 38.095 0.00 0.00 0.00 2.71
2883 4486 3.741344 CCAACTTCAGGTTTCAGTAGTCG 59.259 47.826 0.00 0.00 35.74 4.18
2910 4522 3.496870 GGGCATAGGCATATATAGCACCC 60.497 52.174 0.15 0.00 43.71 4.61
2929 4542 0.170339 GTGTAAACTGGAATGCGGGC 59.830 55.000 0.00 0.00 0.00 6.13
2948 4561 5.718649 TGAAAAGTTTCGACAAGACTCAG 57.281 39.130 0.00 0.00 40.01 3.35
3006 4624 1.745653 GAAAAGATGGGTGCTGCCTAC 59.254 52.381 0.00 0.00 37.43 3.18
3008 4626 0.112995 TGAAAAGATGGGTGCTGCCT 59.887 50.000 0.00 0.00 37.43 4.75
3034 4652 6.438425 AGGACCAATGCTTGTAATGAAAAGAT 59.562 34.615 0.00 0.00 0.00 2.40
3078 4696 3.419943 TGATCAATGCTGCTGGTACAAA 58.580 40.909 0.00 0.00 38.70 2.83
3116 4737 2.957402 TGGTCCAGCTCATGTTCTTT 57.043 45.000 0.00 0.00 0.00 2.52
3128 4749 4.789012 AAATGTTGTAGCAATGGTCCAG 57.211 40.909 0.00 0.00 0.00 3.86
3131 4752 7.312154 TCATGTAAAATGTTGTAGCAATGGTC 58.688 34.615 0.00 0.00 0.00 4.02
3132 4753 7.225784 TCATGTAAAATGTTGTAGCAATGGT 57.774 32.000 0.00 0.00 0.00 3.55
3165 4786 9.909644 GAGCCTCGATGTTTTTATCTAGTAATA 57.090 33.333 0.00 0.00 0.00 0.98
3166 4787 8.643324 AGAGCCTCGATGTTTTTATCTAGTAAT 58.357 33.333 0.00 0.00 0.00 1.89
3191 4812 9.265901 CAATGTCCAAGATAGTACCAAGAATAG 57.734 37.037 0.00 0.00 0.00 1.73
3272 4893 1.829849 GTAGGTAGTTCAGACCACCCC 59.170 57.143 0.00 0.00 38.19 4.95
3318 4964 8.677300 GCATGAGTTCAGGTTTTCATAAGATAA 58.323 33.333 0.00 0.00 0.00 1.75
3442 5094 3.787001 AAGCTGGTCTAGGCGCCC 61.787 66.667 26.15 7.48 0.00 6.13
3465 5117 2.550180 GACTTTTGCCCACTCTGAAGTC 59.450 50.000 0.00 0.00 37.09 3.01
3466 5118 2.576615 GACTTTTGCCCACTCTGAAGT 58.423 47.619 0.00 0.00 35.60 3.01
3467 5119 1.532868 CGACTTTTGCCCACTCTGAAG 59.467 52.381 0.00 0.00 0.00 3.02
3468 5120 1.593196 CGACTTTTGCCCACTCTGAA 58.407 50.000 0.00 0.00 0.00 3.02
3469 5121 0.884704 GCGACTTTTGCCCACTCTGA 60.885 55.000 0.00 0.00 0.00 3.27
3470 5122 1.576421 GCGACTTTTGCCCACTCTG 59.424 57.895 0.00 0.00 0.00 3.35
3471 5123 4.065110 GCGACTTTTGCCCACTCT 57.935 55.556 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.