Multiple sequence alignment - TraesCS1A01G047100

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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 TraesCS1A01G047100 chr1A 100.000 6232 0 0 1 6232 28802191 28795960 0 11509
1 TraesCS1A01G047100 chr1A 96.062 6272 184 14 1 6232 57988903 57982655 0 10155
2 TraesCS1A01G047100 chr1A 98.295 4047 52 3 2202 6232 28826600 28822555 0 7075
3 TraesCS1A01G047100 chr1A 96.913 2138 46 3 1 2138 28828709 28826592 0 3565
4 TraesCS1A01G047100 chr3A 96.289 6251 195 13 1 6232 724441889 724448121 0 10224
5 TraesCS1A01G047100 chr3A 96.329 5312 172 8 940 6232 15651091 15645784 0 8708
6 TraesCS1A01G047100 chr3A 96.327 3567 108 12 2684 6232 745155749 745159310 0 5840
7 TraesCS1A01G047100 chr6A 95.796 6256 214 19 2 6232 582864632 582858401 0 10050
8 TraesCS1A01G047100 chr6A 96.621 5150 140 13 949 6075 80057537 80052399 0 8516
9 TraesCS1A01G047100 chr6A 96.644 2741 72 7 3509 6232 409182153 409179416 0 4534
10 TraesCS1A01G047100 chr7A 95.999 6098 202 13 2 6075 708406499 708400420 0 9871
11 TraesCS1A01G047100 chr7A 95.927 6114 193 23 1 6072 548012741 548018840 0 9860
12 TraesCS1A01G047100 chr7A 96.497 5139 156 9 958 6075 620443480 620438345 0 8471
13 TraesCS1A01G047100 chr4A 96.103 4824 150 11 958 5758 31823744 31818936 0 7832
14 TraesCS1A01G047100 chr3D 95.468 2648 91 15 3139 5758 553642697 553645343 0 4198
15 TraesCS1A01G047100 chr5D 93.766 2374 108 13 1 2343 551286072 551288436 0 3528
16 TraesCS1A01G047100 chr6D 92.977 2392 113 18 1 2343 365491493 365493878 0 3435
17 TraesCS1A01G047100 chr6D 94.376 1209 64 1 1 1205 30391854 30390646 0 1853
18 TraesCS1A01G047100 chr1D 91.928 2391 118 21 1 2343 482464239 482466602 0 3277
19 TraesCS1A01G047100 chr2A 93.575 2039 97 9 2 2011 770758899 770756866 0 3009
20 TraesCS1A01G047100 chr5A 95.443 1580 69 1 2 1578 46181019 46179440 0 2516
21 TraesCS1A01G047100 chr4D 93.529 1700 77 8 1 1669 407169878 407171575 0 2499
22 TraesCS1A01G047100 chr7D 94.274 1205 69 0 1 1205 108578359 108579563 0 1844


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 TraesCS1A01G047100 chr1A 28795960 28802191 6231 True 11509 11509 100.000 1 6232 1 chr1A.!!$R1 6231
1 TraesCS1A01G047100 chr1A 57982655 57988903 6248 True 10155 10155 96.062 1 6232 1 chr1A.!!$R2 6231
2 TraesCS1A01G047100 chr1A 28822555 28828709 6154 True 5320 7075 97.604 1 6232 2 chr1A.!!$R3 6231
3 TraesCS1A01G047100 chr3A 724441889 724448121 6232 False 10224 10224 96.289 1 6232 1 chr3A.!!$F1 6231
4 TraesCS1A01G047100 chr3A 15645784 15651091 5307 True 8708 8708 96.329 940 6232 1 chr3A.!!$R1 5292
5 TraesCS1A01G047100 chr3A 745155749 745159310 3561 False 5840 5840 96.327 2684 6232 1 chr3A.!!$F2 3548
6 TraesCS1A01G047100 chr6A 582858401 582864632 6231 True 10050 10050 95.796 2 6232 1 chr6A.!!$R3 6230
7 TraesCS1A01G047100 chr6A 80052399 80057537 5138 True 8516 8516 96.621 949 6075 1 chr6A.!!$R1 5126
8 TraesCS1A01G047100 chr6A 409179416 409182153 2737 True 4534 4534 96.644 3509 6232 1 chr6A.!!$R2 2723
9 TraesCS1A01G047100 chr7A 708400420 708406499 6079 True 9871 9871 95.999 2 6075 1 chr7A.!!$R2 6073
10 TraesCS1A01G047100 chr7A 548012741 548018840 6099 False 9860 9860 95.927 1 6072 1 chr7A.!!$F1 6071
11 TraesCS1A01G047100 chr7A 620438345 620443480 5135 True 8471 8471 96.497 958 6075 1 chr7A.!!$R1 5117
12 TraesCS1A01G047100 chr4A 31818936 31823744 4808 True 7832 7832 96.103 958 5758 1 chr4A.!!$R1 4800
13 TraesCS1A01G047100 chr3D 553642697 553645343 2646 False 4198 4198 95.468 3139 5758 1 chr3D.!!$F1 2619
14 TraesCS1A01G047100 chr5D 551286072 551288436 2364 False 3528 3528 93.766 1 2343 1 chr5D.!!$F1 2342
15 TraesCS1A01G047100 chr6D 365491493 365493878 2385 False 3435 3435 92.977 1 2343 1 chr6D.!!$F1 2342
16 TraesCS1A01G047100 chr6D 30390646 30391854 1208 True 1853 1853 94.376 1 1205 1 chr6D.!!$R1 1204
17 TraesCS1A01G047100 chr1D 482464239 482466602 2363 False 3277 3277 91.928 1 2343 1 chr1D.!!$F1 2342
18 TraesCS1A01G047100 chr2A 770756866 770758899 2033 True 3009 3009 93.575 2 2011 1 chr2A.!!$R1 2009
19 TraesCS1A01G047100 chr5A 46179440 46181019 1579 True 2516 2516 95.443 2 1578 1 chr5A.!!$R1 1576
20 TraesCS1A01G047100 chr4D 407169878 407171575 1697 False 2499 2499 93.529 1 1669 1 chr4D.!!$F1 1668
21 TraesCS1A01G047100 chr7D 108578359 108579563 1204 False 1844 1844 94.274 1 1205 1 chr7D.!!$F1 1204

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
382 388 3.626996 TTGGCTCGGGGTGCATGAG 62.627 63.158 0.0 0.00 0.00 2.90 F
1076 1149 1.228245 AAGCATCCAAGCACCGTGT 60.228 52.632 0.0 0.00 36.85 4.49 F
2616 2772 0.109597 CGGCATGAAACTGTCCTTGC 60.110 55.000 0.0 10.46 34.94 4.01 F
2640 2796 0.032217 CCATTTATGTGGGCCCTGGT 60.032 55.000 25.7 11.04 35.55 4.00 F
2643 2799 0.257616 TTTATGTGGGCCCTGGTAGC 59.742 55.000 25.7 6.71 0.00 3.58 F
2644 2800 0.623324 TTATGTGGGCCCTGGTAGCT 60.623 55.000 25.7 3.05 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2349 1.680651 CCGTCTGAGGAGCCAGAGT 60.681 63.158 0.00 0.00 43.15 3.24 R
2621 2777 0.032217 ACCAGGGCCCACATAAATGG 60.032 55.000 27.56 23.05 39.71 3.16 R
3810 3983 1.447945 TCGATGGCATTTTTGAGCGA 58.552 45.000 0.00 0.75 0.00 4.93 R
4052 4227 4.394729 TCCCAACAGCGTTCTTATTTTCT 58.605 39.130 0.00 0.00 0.00 2.52 R
4700 4900 0.673644 CTAAGGTGTGGCTGGAACCG 60.674 60.000 0.00 0.00 39.07 4.44 R
5429 5638 6.091713 ACGTTCACCAACAAAGTATAGCATAC 59.908 38.462 0.00 0.00 32.14 2.39 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
280 286 4.690748 GTCATTCACTAGTGCTAGCAAACA 59.309 41.667 21.29 6.49 36.66 2.83
382 388 3.626996 TTGGCTCGGGGTGCATGAG 62.627 63.158 0.00 0.00 0.00 2.90
874 900 6.239402 GCTTCCCCATTAGCATTTATCACATT 60.239 38.462 0.00 0.00 37.35 2.71
1076 1149 1.228245 AAGCATCCAAGCACCGTGT 60.228 52.632 0.00 0.00 36.85 4.49
1206 1279 3.598273 GGAGCAGGTGACTCCTCTA 57.402 57.895 11.17 0.00 45.14 2.43
1674 1803 3.906720 AGCCTCTTACGCTTAATCCAA 57.093 42.857 0.00 0.00 30.57 3.53
1902 2032 9.676861 ATCTTCATTTTCTGTCATTCATGTCTA 57.323 29.630 0.00 0.00 0.00 2.59
1992 2127 9.490379 AACTCTTTAATTTCGTGAGTAACAGAT 57.510 29.630 0.00 0.00 37.05 2.90
2211 2349 3.408157 TTATGTGGGACCAGGTAGCTA 57.592 47.619 0.00 0.00 0.00 3.32
2339 2495 4.286032 TGTAAAATCCTAGGTGTGCTCTGT 59.714 41.667 9.08 0.00 0.00 3.41
2589 2745 8.472007 TTTGGCCGAAATTTCTTATATATGGT 57.528 30.769 15.92 0.00 0.00 3.55
2590 2746 9.575868 TTTGGCCGAAATTTCTTATATATGGTA 57.424 29.630 15.92 0.00 0.00 3.25
2591 2747 8.556213 TGGCCGAAATTTCTTATATATGGTAC 57.444 34.615 15.92 5.77 0.00 3.34
2592 2748 8.380099 TGGCCGAAATTTCTTATATATGGTACT 58.620 33.333 15.92 0.00 0.00 2.73
2607 2763 1.467342 GGTACTTGACCGGCATGAAAC 59.533 52.381 0.00 7.26 38.87 2.78
2609 2765 1.238439 ACTTGACCGGCATGAAACTG 58.762 50.000 0.00 0.00 0.00 3.16
2611 2767 1.197721 CTTGACCGGCATGAAACTGTC 59.802 52.381 0.00 0.00 0.00 3.51
2613 2769 0.321653 GACCGGCATGAAACTGTCCT 60.322 55.000 0.00 0.00 0.00 3.85
2615 2771 0.523072 CCGGCATGAAACTGTCCTTG 59.477 55.000 0.00 0.00 0.00 3.61
2616 2772 0.109597 CGGCATGAAACTGTCCTTGC 60.110 55.000 0.00 10.46 34.94 4.01
2617 2773 0.961019 GGCATGAAACTGTCCTTGCA 59.039 50.000 16.69 0.00 36.54 4.08
2618 2774 1.336240 GGCATGAAACTGTCCTTGCAC 60.336 52.381 16.69 7.76 36.54 4.57
2619 2775 1.337703 GCATGAAACTGTCCTTGCACA 59.662 47.619 0.00 0.00 35.48 4.57
2621 2777 1.024271 TGAAACTGTCCTTGCACAGC 58.976 50.000 2.15 0.00 46.81 4.40
2623 2779 0.395586 AAACTGTCCTTGCACAGCCA 60.396 50.000 2.15 0.00 46.81 4.75
2624 2780 0.178981 AACTGTCCTTGCACAGCCAT 60.179 50.000 2.15 0.00 46.81 4.40
2627 2783 2.161855 CTGTCCTTGCACAGCCATTTA 58.838 47.619 0.00 0.00 37.58 1.40
2628 2784 2.756760 CTGTCCTTGCACAGCCATTTAT 59.243 45.455 0.00 0.00 37.58 1.40
2629 2785 2.492881 TGTCCTTGCACAGCCATTTATG 59.507 45.455 0.00 0.00 0.00 1.90
2630 2786 2.493278 GTCCTTGCACAGCCATTTATGT 59.507 45.455 0.00 0.00 0.00 2.29
2634 2790 0.179103 GCACAGCCATTTATGTGGGC 60.179 55.000 7.37 0.00 45.52 5.36
2637 2793 4.705482 GCCATTTATGTGGGCCCT 57.295 55.556 25.70 5.02 41.90 5.19
2638 2794 2.126951 GCCATTTATGTGGGCCCTG 58.873 57.895 25.70 10.95 41.90 4.45
2640 2796 0.032217 CCATTTATGTGGGCCCTGGT 60.032 55.000 25.70 11.04 35.55 4.00
2641 2797 1.216678 CCATTTATGTGGGCCCTGGTA 59.783 52.381 25.70 9.94 35.55 3.25
2642 2798 2.586425 CATTTATGTGGGCCCTGGTAG 58.414 52.381 25.70 1.25 0.00 3.18
2643 2799 0.257616 TTTATGTGGGCCCTGGTAGC 59.742 55.000 25.70 6.71 0.00 3.58
2644 2800 0.623324 TTATGTGGGCCCTGGTAGCT 60.623 55.000 25.70 3.05 0.00 3.32
2645 2801 1.344953 TATGTGGGCCCTGGTAGCTG 61.345 60.000 25.70 0.00 0.00 4.24
2646 2802 4.803908 GTGGGCCCTGGTAGCTGC 62.804 72.222 25.70 0.00 0.00 5.25
2648 2804 4.182433 GGGCCCTGGTAGCTGCTC 62.182 72.222 17.04 0.00 0.00 4.26
2649 2805 3.086600 GGCCCTGGTAGCTGCTCT 61.087 66.667 4.91 0.00 0.00 4.09
2650 2806 2.188994 GCCCTGGTAGCTGCTCTG 59.811 66.667 4.91 0.00 0.00 3.35
2652 2808 2.188994 CCTGGTAGCTGCTCTGGC 59.811 66.667 4.91 0.00 39.26 4.85
2653 2809 2.365586 CCTGGTAGCTGCTCTGGCT 61.366 63.158 4.91 0.00 43.02 4.75
2654 2810 1.143620 CTGGTAGCTGCTCTGGCTC 59.856 63.158 4.91 0.00 40.74 4.70
2656 2812 2.063378 GGTAGCTGCTCTGGCTCCT 61.063 63.158 4.91 0.00 40.74 3.69
2657 2813 1.441311 GTAGCTGCTCTGGCTCCTC 59.559 63.158 4.91 0.00 40.74 3.71
2658 2814 1.000866 TAGCTGCTCTGGCTCCTCA 59.999 57.895 4.91 0.00 40.74 3.86
2659 2815 1.042003 TAGCTGCTCTGGCTCCTCAG 61.042 60.000 4.91 0.00 40.74 3.35
2661 2817 1.688269 GCTGCTCTGGCTCCTCAGAT 61.688 60.000 0.00 0.00 42.19 2.90
2662 2818 1.702182 CTGCTCTGGCTCCTCAGATA 58.298 55.000 0.00 0.00 42.19 1.98
2664 2820 1.216427 TGCTCTGGCTCCTCAGATAGA 59.784 52.381 0.00 0.00 42.19 1.98
2665 2821 1.888512 GCTCTGGCTCCTCAGATAGAG 59.111 57.143 0.00 0.00 42.19 2.43
2673 2829 2.622942 CTCCTCAGATAGAGCAGGTGTC 59.377 54.545 0.00 0.00 43.31 3.67
2674 2830 2.243478 TCCTCAGATAGAGCAGGTGTCT 59.757 50.000 0.00 0.00 43.31 3.41
2675 2831 2.622942 CCTCAGATAGAGCAGGTGTCTC 59.377 54.545 0.00 0.00 43.31 3.36
2677 2833 3.688126 CTCAGATAGAGCAGGTGTCTCCT 60.688 52.174 0.00 0.00 40.55 3.69
2678 2834 2.622942 CAGATAGAGCAGGTGTCTCCTC 59.377 54.545 0.00 0.00 46.24 3.71
2679 2835 2.513738 AGATAGAGCAGGTGTCTCCTCT 59.486 50.000 0.00 0.00 46.24 3.69
2680 2836 2.136298 TAGAGCAGGTGTCTCCTCTG 57.864 55.000 0.00 0.00 46.24 3.35
2683 2839 2.575993 CAGGTGTCTCCTCTGCCG 59.424 66.667 0.00 0.00 46.24 5.69
2684 2840 3.386237 AGGTGTCTCCTCTGCCGC 61.386 66.667 0.00 0.00 44.42 6.53
2685 2841 4.803426 GGTGTCTCCTCTGCCGCG 62.803 72.222 0.00 0.00 0.00 6.46
3155 3314 7.545615 GTCATTCATGTCAGTACTGTCATTACA 59.454 37.037 26.45 20.59 37.27 2.41
3441 3600 3.982372 TTCGTCTGCCGCGGATGTC 62.982 63.158 33.48 16.52 36.19 3.06
3582 3755 9.869757 ACAAGGCAAATAAGGTATTAAAATGTC 57.130 29.630 0.00 0.00 0.00 3.06
3612 3785 4.068599 TGTTTGGTTGCACTTGATCGATA 58.931 39.130 0.00 0.00 0.00 2.92
3650 3823 1.533625 TAAGTGGCTGTGGCAATGAC 58.466 50.000 0.00 0.00 40.46 3.06
3807 3980 9.945904 CTACTCAGTTTTTCCCTTAGAAGTTAT 57.054 33.333 0.00 0.00 35.40 1.89
3810 3983 9.945904 CTCAGTTTTTCCCTTAGAAGTTATAGT 57.054 33.333 0.00 0.00 35.40 2.12
4039 4214 4.262463 CCACTTGTGAGGAGTAAGTAAGCA 60.262 45.833 1.89 0.00 33.63 3.91
4700 4900 6.093633 AGTTTGACCAACTTAAGTGAGTGTTC 59.906 38.462 9.34 2.73 43.89 3.18
5368 5577 2.750166 GCTTCTTTGAGGCTTTAGGGAC 59.250 50.000 0.00 0.00 31.81 4.46
5429 5638 7.975616 TGGTTTTAACTATGCTAAGTACTACCG 59.024 37.037 0.00 0.00 0.00 4.02
5511 5720 5.243730 AGTGGTGCTTGCTTTTGTATGTATT 59.756 36.000 0.00 0.00 0.00 1.89
6037 6250 3.863142 AAGATTGAGTTGCATTGAGCC 57.137 42.857 0.00 0.00 44.83 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 286 0.757512 AGAGATGCTCATGCGGACAT 59.242 50.000 0.00 0.00 43.34 3.06
382 388 2.972625 TGTGTTTCGTCTGGATCCATC 58.027 47.619 16.63 10.76 0.00 3.51
660 666 5.507985 GCCATGATTTAGGAGTAATGCAACC 60.508 44.000 0.00 0.00 0.00 3.77
750 756 1.600164 CCGTGCATTGTTCACACCAAG 60.600 52.381 0.00 0.00 34.27 3.61
1078 1151 0.524862 GGTTTCTCCATGTGCAGCTG 59.475 55.000 10.11 10.11 35.97 4.24
1541 1647 3.056465 GGCAAATAATTTCGGGTGGTTGA 60.056 43.478 0.00 0.00 0.00 3.18
1691 1821 6.215121 CAATTGGTGTAGAGCAAATTGAACA 58.785 36.000 8.69 0.00 42.66 3.18
1820 1950 5.594725 TGGTGTTGTTATCCTTTACTTGCAA 59.405 36.000 0.00 0.00 0.00 4.08
1980 2115 2.275318 GCCTCTGCATCTGTTACTCAC 58.725 52.381 0.00 0.00 37.47 3.51
1992 2127 1.746615 GCATTCTTCCGCCTCTGCA 60.747 57.895 0.00 0.00 37.32 4.41
2184 2322 5.263872 ACCTGGTCCCACATAAATAACAA 57.736 39.130 0.00 0.00 0.00 2.83
2211 2349 1.680651 CCGTCTGAGGAGCCAGAGT 60.681 63.158 0.00 0.00 43.15 3.24
2567 2723 8.788325 AGTACCATATATAAGAAATTTCGGCC 57.212 34.615 12.42 0.00 0.00 6.13
2587 2743 1.467342 GTTTCATGCCGGTCAAGTACC 59.533 52.381 1.90 0.00 45.77 3.34
2589 2745 2.224426 ACAGTTTCATGCCGGTCAAGTA 60.224 45.455 1.90 0.00 0.00 2.24
2590 2746 1.238439 CAGTTTCATGCCGGTCAAGT 58.762 50.000 1.90 0.00 0.00 3.16
2591 2747 1.197721 GACAGTTTCATGCCGGTCAAG 59.802 52.381 1.90 0.00 0.00 3.02
2592 2748 1.234821 GACAGTTTCATGCCGGTCAA 58.765 50.000 1.90 0.00 0.00 3.18
2594 2750 0.321653 AGGACAGTTTCATGCCGGTC 60.322 55.000 1.90 0.00 0.00 4.79
2595 2751 0.110486 AAGGACAGTTTCATGCCGGT 59.890 50.000 1.90 0.00 0.00 5.28
2596 2752 0.523072 CAAGGACAGTTTCATGCCGG 59.477 55.000 0.00 0.00 0.00 6.13
2598 2754 0.961019 TGCAAGGACAGTTTCATGCC 59.039 50.000 4.46 0.00 37.65 4.40
2600 2756 2.606308 GCTGTGCAAGGACAGTTTCATG 60.606 50.000 20.35 0.00 44.53 3.07
2601 2757 1.610522 GCTGTGCAAGGACAGTTTCAT 59.389 47.619 20.35 0.00 44.53 2.57
2602 2758 1.024271 GCTGTGCAAGGACAGTTTCA 58.976 50.000 20.35 0.00 44.53 2.69
2603 2759 0.312102 GGCTGTGCAAGGACAGTTTC 59.688 55.000 20.35 9.07 44.53 2.78
2604 2760 0.395586 TGGCTGTGCAAGGACAGTTT 60.396 50.000 20.35 0.00 44.53 2.66
2607 2763 0.963962 AAATGGCTGTGCAAGGACAG 59.036 50.000 16.17 16.17 45.34 3.51
2609 2765 2.493278 ACATAAATGGCTGTGCAAGGAC 59.507 45.455 0.00 0.00 0.00 3.85
2611 2767 2.417651 CCACATAAATGGCTGTGCAAGG 60.418 50.000 0.00 0.00 41.10 3.61
2613 2769 1.549620 CCCACATAAATGGCTGTGCAA 59.450 47.619 0.00 0.00 41.10 4.08
2615 2771 0.179103 GCCCACATAAATGGCTGTGC 60.179 55.000 0.00 0.00 41.10 4.57
2616 2772 0.461135 GGCCCACATAAATGGCTGTG 59.539 55.000 0.00 0.00 44.71 3.66
2617 2773 0.687427 GGGCCCACATAAATGGCTGT 60.687 55.000 19.95 0.00 44.71 4.40
2618 2774 0.397535 AGGGCCCACATAAATGGCTG 60.398 55.000 27.56 0.00 44.71 4.85
2619 2775 0.397535 CAGGGCCCACATAAATGGCT 60.398 55.000 27.56 0.00 44.71 4.75
2620 2776 1.402107 CCAGGGCCCACATAAATGGC 61.402 60.000 27.56 0.00 44.59 4.40
2621 2777 0.032217 ACCAGGGCCCACATAAATGG 60.032 55.000 27.56 23.05 39.71 3.16
2623 2779 1.133482 GCTACCAGGGCCCACATAAAT 60.133 52.381 27.56 0.00 0.00 1.40
2624 2780 0.257616 GCTACCAGGGCCCACATAAA 59.742 55.000 27.56 2.66 0.00 1.40
2627 2783 2.286425 AGCTACCAGGGCCCACAT 60.286 61.111 27.56 11.08 0.00 3.21
2628 2784 3.329889 CAGCTACCAGGGCCCACA 61.330 66.667 27.56 4.30 0.00 4.17
2629 2785 4.803908 GCAGCTACCAGGGCCCAC 62.804 72.222 27.56 5.64 0.00 4.61
2631 2787 4.182433 GAGCAGCTACCAGGGCCC 62.182 72.222 16.46 16.46 0.00 5.80
2634 2790 2.906458 CCAGAGCAGCTACCAGGG 59.094 66.667 0.00 0.00 0.00 4.45
2637 2793 2.362369 GGAGCCAGAGCAGCTACCA 61.362 63.158 0.00 0.00 41.75 3.25
2638 2794 2.026945 GAGGAGCCAGAGCAGCTACC 62.027 65.000 0.00 0.00 42.62 3.18
2640 2796 1.000866 TGAGGAGCCAGAGCAGCTA 59.999 57.895 0.00 0.00 41.75 3.32
2641 2797 2.284478 TGAGGAGCCAGAGCAGCT 60.284 61.111 0.00 0.00 45.23 4.24
2642 2798 1.688269 ATCTGAGGAGCCAGAGCAGC 61.688 60.000 0.00 0.00 45.27 5.25
2643 2799 1.614903 CTATCTGAGGAGCCAGAGCAG 59.385 57.143 0.00 0.00 45.27 4.24
2644 2800 1.216427 TCTATCTGAGGAGCCAGAGCA 59.784 52.381 0.00 0.00 45.27 4.26
2645 2801 1.888512 CTCTATCTGAGGAGCCAGAGC 59.111 57.143 0.00 0.00 45.27 4.09
2646 2802 1.888512 GCTCTATCTGAGGAGCCAGAG 59.111 57.143 18.54 8.57 46.32 3.35
2647 2803 1.993956 GCTCTATCTGAGGAGCCAGA 58.006 55.000 18.54 0.00 46.32 3.86
2653 2809 2.243478 AGACACCTGCTCTATCTGAGGA 59.757 50.000 0.00 0.00 42.87 3.71
2654 2810 2.622942 GAGACACCTGCTCTATCTGAGG 59.377 54.545 0.00 0.00 42.87 3.86
2656 2812 2.660572 GGAGACACCTGCTCTATCTGA 58.339 52.381 0.00 0.00 35.41 3.27
3155 3314 8.641498 ACATGTGAAAAGATTCTTAGTCCATT 57.359 30.769 0.00 0.00 36.48 3.16
3216 3375 9.988815 TTATATTGCAAACTAAAACCACAACAT 57.011 25.926 1.71 0.00 0.00 2.71
3350 3509 3.306156 GGAGCTACCTGTTCCGGATTATC 60.306 52.174 4.15 0.00 36.35 1.75
3549 3722 5.242795 ACCTTATTTGCCTTGTACTGACT 57.757 39.130 0.00 0.00 0.00 3.41
3582 3755 2.548057 AGTGCAACCAAACATGTACTCG 59.452 45.455 0.00 0.00 37.90 4.18
3807 3980 2.351418 CGATGGCATTTTTGAGCGACTA 59.649 45.455 0.00 0.00 0.00 2.59
3810 3983 1.447945 TCGATGGCATTTTTGAGCGA 58.552 45.000 0.00 0.75 0.00 4.93
4052 4227 4.394729 TCCCAACAGCGTTCTTATTTTCT 58.605 39.130 0.00 0.00 0.00 2.52
4700 4900 0.673644 CTAAGGTGTGGCTGGAACCG 60.674 60.000 0.00 0.00 39.07 4.44
5429 5638 6.091713 ACGTTCACCAACAAAGTATAGCATAC 59.908 38.462 0.00 0.00 32.14 2.39
5511 5720 7.120923 AGTTCTACCTTAGTTCAACACTTCA 57.879 36.000 0.00 0.00 36.88 3.02
5927 6140 1.953686 CAATAACCAACCATAGCCGGG 59.046 52.381 2.18 0.00 0.00 5.73
6025 6238 3.733077 GCATAACTCAGGCTCAATGCAAC 60.733 47.826 0.00 0.00 45.15 4.17
6030 6243 3.641434 AGTGCATAACTCAGGCTCAAT 57.359 42.857 0.00 0.00 31.64 2.57
6031 6244 3.118629 CCTAGTGCATAACTCAGGCTCAA 60.119 47.826 0.00 0.00 40.56 3.02


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

AutoCloner maintained by Alex Coulton.