Multiple sequence alignment - TraesCS6D01G063100

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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 TraesCS6D01G063100 chr6D 100.000 3630 0 0 1 3630 29468121 29464492 0.000000e+00 6704.0
1 TraesCS6D01G063100 chr6D 97.810 959 15 1 2678 3630 11163412 11162454 0.000000e+00 1650.0
2 TraesCS6D01G063100 chr6D 97.796 953 21 0 2678 3630 147412669 147413621 0.000000e+00 1644.0
3 TraesCS6D01G063100 chr6D 97.796 953 21 0 2678 3630 158211759 158210807 0.000000e+00 1644.0
4 TraesCS6D01G063100 chr6D 97.778 45 1 0 744 788 10765737 10765781 1.080000e-10 78.7
5 TraesCS6D01G063100 chr2D 99.530 2552 12 0 1 2552 643049668 643052219 0.000000e+00 4647.0
6 TraesCS6D01G063100 chr2D 90.840 524 46 1 1 524 643173432 643173953 0.000000e+00 701.0
7 TraesCS6D01G063100 chr2D 90.081 494 40 2 1 494 643119795 643120279 1.840000e-177 632.0
8 TraesCS6D01G063100 chr2D 87.786 524 56 3 1 524 643142168 643142683 1.110000e-169 606.0
9 TraesCS6D01G063100 chr2D 99.265 136 1 0 2544 2679 643058660 643058795 2.800000e-61 246.0
10 TraesCS6D01G063100 chr1D 98.006 953 19 0 2678 3630 225440332 225439380 0.000000e+00 1655.0
11 TraesCS6D01G063100 chr1D 97.796 953 21 0 2678 3630 454655845 454654893 0.000000e+00 1644.0
12 TraesCS6D01G063100 chr1D 97.674 43 1 0 746 788 142656886 142656844 1.400000e-09 75.0
13 TraesCS6D01G063100 chr3D 98.006 953 18 1 2678 3630 481544410 481545361 0.000000e+00 1653.0
14 TraesCS6D01G063100 chr3D 97.706 959 16 1 2678 3630 288046781 288045823 0.000000e+00 1644.0
15 TraesCS6D01G063100 chr5D 97.803 956 18 1 2678 3630 32703041 32703996 0.000000e+00 1646.0
16 TraesCS6D01G063100 chr5D 97.619 42 1 0 747 788 528214360 528214319 5.030000e-09 73.1
17 TraesCS6D01G063100 chr5D 97.368 38 1 0 1835 1872 74419558 74419595 8.410000e-07 65.8
18 TraesCS6D01G063100 chr7D 97.706 959 16 1 2678 3630 256222482 256223440 0.000000e+00 1644.0
19 TraesCS6D01G063100 chr7D 97.619 42 1 0 747 788 462673295 462673254 5.030000e-09 73.1
20 TraesCS6D01G063100 chr2A 92.898 521 35 1 1 521 768037311 768037829 0.000000e+00 756.0
21 TraesCS6D01G063100 chr2A 94.737 38 2 0 2642 2679 239382057 239382094 3.910000e-05 60.2
22 TraesCS6D01G063100 chrUn 92.557 524 37 1 1 524 31642372 31642893 0.000000e+00 750.0
23 TraesCS6D01G063100 chr6B 97.674 43 1 0 746 788 20360128 20360170 1.400000e-09 75.0
24 TraesCS6D01G063100 chr1B 97.674 43 1 0 747 789 626147099 626147141 1.400000e-09 75.0
25 TraesCS6D01G063100 chr6A 97.619 42 1 0 747 788 498950132 498950173 5.030000e-09 73.1
26 TraesCS6D01G063100 chr2B 90.909 55 3 2 747 801 101515944 101515996 5.030000e-09 73.1
27 TraesCS6D01G063100 chr5A 97.368 38 1 0 1835 1872 69546086 69546123 8.410000e-07 65.8
28 TraesCS6D01G063100 chr3A 100.000 35 0 0 2639 2673 715353487 715353521 8.410000e-07 65.8


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 TraesCS6D01G063100 chr6D 29464492 29468121 3629 True 6704 6704 100.000 1 3630 1 chr6D.!!$R2 3629
1 TraesCS6D01G063100 chr6D 11162454 11163412 958 True 1650 1650 97.810 2678 3630 1 chr6D.!!$R1 952
2 TraesCS6D01G063100 chr6D 147412669 147413621 952 False 1644 1644 97.796 2678 3630 1 chr6D.!!$F2 952
3 TraesCS6D01G063100 chr6D 158210807 158211759 952 True 1644 1644 97.796 2678 3630 1 chr6D.!!$R3 952
4 TraesCS6D01G063100 chr2D 643049668 643052219 2551 False 4647 4647 99.530 1 2552 1 chr2D.!!$F1 2551
5 TraesCS6D01G063100 chr2D 643173432 643173953 521 False 701 701 90.840 1 524 1 chr2D.!!$F5 523
6 TraesCS6D01G063100 chr2D 643142168 643142683 515 False 606 606 87.786 1 524 1 chr2D.!!$F4 523
7 TraesCS6D01G063100 chr1D 225439380 225440332 952 True 1655 1655 98.006 2678 3630 1 chr1D.!!$R2 952
8 TraesCS6D01G063100 chr1D 454654893 454655845 952 True 1644 1644 97.796 2678 3630 1 chr1D.!!$R3 952
9 TraesCS6D01G063100 chr3D 481544410 481545361 951 False 1653 1653 98.006 2678 3630 1 chr3D.!!$F1 952
10 TraesCS6D01G063100 chr3D 288045823 288046781 958 True 1644 1644 97.706 2678 3630 1 chr3D.!!$R1 952
11 TraesCS6D01G063100 chr5D 32703041 32703996 955 False 1646 1646 97.803 2678 3630 1 chr5D.!!$F1 952
12 TraesCS6D01G063100 chr7D 256222482 256223440 958 False 1644 1644 97.706 2678 3630 1 chr7D.!!$F1 952
13 TraesCS6D01G063100 chr2A 768037311 768037829 518 False 756 756 92.898 1 521 1 chr2A.!!$F2 520
14 TraesCS6D01G063100 chrUn 31642372 31642893 521 False 750 750 92.557 1 524 1 chrUn.!!$F1 523

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
272 273 0.323302 TAAGACCGCTGCCATTCACA 59.677 50.000 0.00 0.0 0.0 3.58 F
406 407 1.292223 GCCGGAGTGTCAACAGCTA 59.708 57.895 5.05 0.0 0.0 3.32 F
2385 2386 0.108804 GGGAGCAAGATCGACGTGAA 60.109 55.000 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 1963 4.092968 TCCTGATCGACGATCGTGTATATG 59.907 45.833 28.12 11.24 41.51 1.78 R
2391 2392 1.680522 CGGTAGCAGCTCCATGTCCT 61.681 60.000 0.00 0.00 0.00 3.85 R
3554 3571 1.065551 GTCCTTGCGAGCTTGTGTTTT 59.934 47.619 2.14 0.00 0.00 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
272 273 0.323302 TAAGACCGCTGCCATTCACA 59.677 50.000 0.00 0.00 0.00 3.58
406 407 1.292223 GCCGGAGTGTCAACAGCTA 59.708 57.895 5.05 0.00 0.00 3.32
954 955 1.488527 CGATAAACTAGCAGCCGTCC 58.511 55.000 0.00 0.00 0.00 4.79
1962 1963 4.230745 TCCTTATTTCCAGCCAGGTTAC 57.769 45.455 0.00 0.00 39.02 2.50
2385 2386 0.108804 GGGAGCAAGATCGACGTGAA 60.109 55.000 0.00 0.00 0.00 3.18
2391 2392 1.541310 AAGATCGACGTGAAGGGGCA 61.541 55.000 0.00 0.00 0.00 5.36
2502 2503 0.167470 CTTCTGCATGGCTTCACGTG 59.833 55.000 9.94 9.94 0.00 4.49
2526 2527 2.047274 CCCTGACGGCACAACGAT 60.047 61.111 0.00 0.00 37.61 3.73
2533 2534 2.324330 CGGCACAACGATGGAGCAA 61.324 57.895 12.84 0.00 34.53 3.91
2552 2553 4.411540 AGCAACTCAACATGGAGGAGATAT 59.588 41.667 14.89 1.85 39.27 1.63
2553 2554 5.604231 AGCAACTCAACATGGAGGAGATATA 59.396 40.000 14.89 0.00 39.27 0.86
2554 2555 6.271857 AGCAACTCAACATGGAGGAGATATAT 59.728 38.462 14.89 0.00 39.27 0.86
2555 2556 6.370994 GCAACTCAACATGGAGGAGATATATG 59.629 42.308 14.89 8.17 39.27 1.78
2556 2557 6.617782 ACTCAACATGGAGGAGATATATGG 57.382 41.667 14.89 0.00 39.27 2.74
2557 2558 5.486775 ACTCAACATGGAGGAGATATATGGG 59.513 44.000 14.89 0.00 39.27 4.00
2558 2559 4.225942 TCAACATGGAGGAGATATATGGGC 59.774 45.833 0.00 0.00 0.00 5.36
2559 2560 4.085854 ACATGGAGGAGATATATGGGCT 57.914 45.455 0.00 0.00 0.00 5.19
2560 2561 4.036518 ACATGGAGGAGATATATGGGCTC 58.963 47.826 0.00 0.00 0.00 4.70
2561 2562 3.852858 TGGAGGAGATATATGGGCTCA 57.147 47.619 0.00 0.00 0.00 4.26
2562 2563 3.445008 TGGAGGAGATATATGGGCTCAC 58.555 50.000 0.00 0.00 0.00 3.51
2563 2564 2.769095 GGAGGAGATATATGGGCTCACC 59.231 54.545 0.00 0.00 40.81 4.02
2575 2576 4.081030 CTCACCACTGCGCGCAAG 62.081 66.667 35.50 28.02 43.44 4.01
2576 2577 4.908687 TCACCACTGCGCGCAAGT 62.909 61.111 35.50 28.89 41.68 3.16
2577 2578 3.952675 CACCACTGCGCGCAAGTT 61.953 61.111 35.50 19.27 41.68 2.66
2578 2579 3.649986 ACCACTGCGCGCAAGTTC 61.650 61.111 35.50 3.27 41.68 3.01
2579 2580 4.389576 CCACTGCGCGCAAGTTCC 62.390 66.667 35.50 2.41 41.68 3.62
2580 2581 4.389576 CACTGCGCGCAAGTTCCC 62.390 66.667 35.50 1.54 41.68 3.97
2584 2585 3.416382 GCGCGCAAGTTCCCGTTA 61.416 61.111 29.10 0.00 41.68 3.18
2585 2586 2.776072 CGCGCAAGTTCCCGTTAG 59.224 61.111 8.75 0.00 41.68 2.34
2586 2587 1.735198 CGCGCAAGTTCCCGTTAGA 60.735 57.895 8.75 0.00 41.68 2.10
2587 2588 1.683790 CGCGCAAGTTCCCGTTAGAG 61.684 60.000 8.75 0.00 41.68 2.43
2588 2589 1.359459 GCGCAAGTTCCCGTTAGAGG 61.359 60.000 0.30 0.00 41.68 3.69
2589 2590 1.359459 CGCAAGTTCCCGTTAGAGGC 61.359 60.000 0.00 0.00 0.00 4.70
2590 2591 0.321298 GCAAGTTCCCGTTAGAGGCA 60.321 55.000 0.00 0.00 0.00 4.75
2591 2592 1.726853 CAAGTTCCCGTTAGAGGCAG 58.273 55.000 0.00 0.00 0.00 4.85
2592 2593 1.002087 CAAGTTCCCGTTAGAGGCAGT 59.998 52.381 0.00 0.00 0.00 4.40
2593 2594 0.608640 AGTTCCCGTTAGAGGCAGTG 59.391 55.000 0.00 0.00 0.00 3.66
2594 2595 0.391263 GTTCCCGTTAGAGGCAGTGG 60.391 60.000 0.00 0.00 0.00 4.00
2595 2596 0.834687 TTCCCGTTAGAGGCAGTGGT 60.835 55.000 0.00 0.00 0.00 4.16
2596 2597 1.079127 CCCGTTAGAGGCAGTGGTG 60.079 63.158 0.00 0.00 0.00 4.17
2597 2598 1.079127 CCGTTAGAGGCAGTGGTGG 60.079 63.158 0.00 0.00 0.00 4.61
2598 2599 1.541310 CCGTTAGAGGCAGTGGTGGA 61.541 60.000 0.00 0.00 0.00 4.02
2599 2600 0.108615 CGTTAGAGGCAGTGGTGGAG 60.109 60.000 0.00 0.00 0.00 3.86
2600 2601 0.391793 GTTAGAGGCAGTGGTGGAGC 60.392 60.000 0.00 0.00 0.00 4.70
2604 2605 3.077907 GGCAGTGGTGGAGCCTAA 58.922 61.111 0.00 0.00 44.92 2.69
2605 2606 1.078143 GGCAGTGGTGGAGCCTAAG 60.078 63.158 0.00 0.00 44.92 2.18
2606 2607 1.746991 GCAGTGGTGGAGCCTAAGC 60.747 63.158 0.00 0.00 38.35 3.09
2618 2619 1.079503 GCCTAAGCTCCAAGAACACG 58.920 55.000 0.00 0.00 35.50 4.49
2619 2620 1.608283 GCCTAAGCTCCAAGAACACGT 60.608 52.381 0.00 0.00 35.50 4.49
2620 2621 2.338500 CCTAAGCTCCAAGAACACGTC 58.662 52.381 0.00 0.00 0.00 4.34
2621 2622 2.028930 CCTAAGCTCCAAGAACACGTCT 60.029 50.000 0.00 0.00 38.69 4.18
2623 2624 2.156343 AGCTCCAAGAACACGTCTTC 57.844 50.000 0.00 0.00 45.25 2.87
2624 2625 1.689273 AGCTCCAAGAACACGTCTTCT 59.311 47.619 0.00 0.00 45.25 2.85
2625 2626 2.062519 GCTCCAAGAACACGTCTTCTC 58.937 52.381 6.54 0.00 45.25 2.87
2626 2627 2.320367 CTCCAAGAACACGTCTTCTCG 58.680 52.381 6.54 0.00 45.25 4.04
2627 2628 1.679680 TCCAAGAACACGTCTTCTCGT 59.320 47.619 6.54 0.00 45.25 4.18
2628 2629 2.880268 TCCAAGAACACGTCTTCTCGTA 59.120 45.455 6.54 0.00 45.25 3.43
2629 2630 3.058432 TCCAAGAACACGTCTTCTCGTAG 60.058 47.826 6.54 0.00 45.25 3.51
2630 2631 2.615489 AGAACACGTCTTCTCGTAGC 57.385 50.000 0.00 0.00 42.27 3.58
2631 2632 1.136029 AGAACACGTCTTCTCGTAGCG 60.136 52.381 0.00 0.00 42.27 4.26
2632 2633 0.728466 AACACGTCTTCTCGTAGCGC 60.728 55.000 0.00 0.00 42.27 5.92
2633 2634 1.868251 CACGTCTTCTCGTAGCGCC 60.868 63.158 2.29 0.00 42.27 6.53
2634 2635 2.648102 CGTCTTCTCGTAGCGCCG 60.648 66.667 2.29 0.45 0.00 6.46
2635 2636 2.950194 GTCTTCTCGTAGCGCCGC 60.950 66.667 2.29 0.00 0.00 6.53
2636 2637 4.189188 TCTTCTCGTAGCGCCGCC 62.189 66.667 4.98 0.00 0.00 6.13
2651 2652 2.180518 GCCGCCGCAAAAATGCTA 59.819 55.556 0.00 0.00 34.03 3.49
2652 2653 1.873572 GCCGCCGCAAAAATGCTAG 60.874 57.895 0.00 0.00 34.03 3.42
2653 2654 1.800032 CCGCCGCAAAAATGCTAGA 59.200 52.632 0.00 0.00 0.00 2.43
2654 2655 0.523335 CCGCCGCAAAAATGCTAGAC 60.523 55.000 0.00 0.00 0.00 2.59
2655 2656 0.447801 CGCCGCAAAAATGCTAGACT 59.552 50.000 0.00 0.00 0.00 3.24
2656 2657 1.529826 CGCCGCAAAAATGCTAGACTC 60.530 52.381 0.00 0.00 0.00 3.36
2657 2658 1.468520 GCCGCAAAAATGCTAGACTCA 59.531 47.619 0.00 0.00 0.00 3.41
2658 2659 2.729156 GCCGCAAAAATGCTAGACTCAC 60.729 50.000 0.00 0.00 0.00 3.51
2659 2660 2.474526 CCGCAAAAATGCTAGACTCACG 60.475 50.000 0.00 0.00 0.00 4.35
2660 2661 2.509870 GCAAAAATGCTAGACTCACGC 58.490 47.619 0.00 0.00 0.00 5.34
2661 2662 2.095768 GCAAAAATGCTAGACTCACGCA 60.096 45.455 0.00 0.00 38.14 5.24
2662 2663 3.426695 GCAAAAATGCTAGACTCACGCAT 60.427 43.478 0.00 0.00 45.50 4.73
2663 2664 4.337763 CAAAAATGCTAGACTCACGCATC 58.662 43.478 0.00 0.00 43.02 3.91
2664 2665 2.967599 AATGCTAGACTCACGCATCA 57.032 45.000 0.00 0.00 43.02 3.07
2665 2666 3.465742 AATGCTAGACTCACGCATCAT 57.534 42.857 0.00 0.00 43.02 2.45
2666 2667 2.967599 TGCTAGACTCACGCATCATT 57.032 45.000 0.00 0.00 0.00 2.57
2667 2668 4.590850 ATGCTAGACTCACGCATCATTA 57.409 40.909 0.00 0.00 40.05 1.90
2668 2669 3.706698 TGCTAGACTCACGCATCATTAC 58.293 45.455 0.00 0.00 0.00 1.89
2669 2670 2.721603 GCTAGACTCACGCATCATTACG 59.278 50.000 0.00 0.00 0.00 3.18
2670 2671 2.209838 AGACTCACGCATCATTACGG 57.790 50.000 0.00 0.00 0.00 4.02
2671 2672 1.749063 AGACTCACGCATCATTACGGA 59.251 47.619 0.00 0.00 0.00 4.69
2672 2673 2.120232 GACTCACGCATCATTACGGAG 58.880 52.381 0.00 0.00 34.71 4.63
2673 2674 1.202417 ACTCACGCATCATTACGGAGG 60.202 52.381 0.00 0.00 33.62 4.30
2674 2675 0.821517 TCACGCATCATTACGGAGGT 59.178 50.000 0.00 0.00 0.00 3.85
2675 2676 1.206132 TCACGCATCATTACGGAGGTT 59.794 47.619 0.00 0.00 0.00 3.50
2676 2677 1.593006 CACGCATCATTACGGAGGTTC 59.407 52.381 0.00 0.00 0.00 3.62
2685 2686 5.902681 TCATTACGGAGGTTCTAGTCATTG 58.097 41.667 0.00 0.00 0.00 2.82
2717 2718 6.040166 ACGACTTCTAGTCCAAGTCAGTTTTA 59.960 38.462 18.00 0.00 46.99 1.52
2729 2731 4.969133 AGTCAGTTTTATACCCCTACCCT 58.031 43.478 0.00 0.00 0.00 4.34
2802 2804 9.844790 CATCAATAAGCAACAGTTTTATTCAGA 57.155 29.630 1.43 0.00 0.00 3.27
2906 2923 2.434884 CCGCACTCATCGCCAAGT 60.435 61.111 0.00 0.00 0.00 3.16
2918 2935 2.594303 CCAAGTCTGCCAACGCCA 60.594 61.111 0.00 0.00 0.00 5.69
3051 3068 2.223829 CCATAGTTCTTGATCTCGCCGT 60.224 50.000 0.00 0.00 0.00 5.68
3201 3218 1.053424 GTCCAGTGGTTCTACACCCA 58.947 55.000 9.54 0.00 46.68 4.51
3457 3474 1.009078 TCAATATCGTCGTCGTCGGT 58.991 50.000 11.74 7.45 38.33 4.69
3554 3571 3.561217 TTGCTACAACTCGCGGCGA 62.561 57.895 24.84 24.84 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 0.826256 TAGGCGCAGTATCGGGACAT 60.826 55.000 10.83 0.00 0.00 3.06
406 407 3.073062 ACCAACTGCTGATACTCCACTTT 59.927 43.478 0.00 0.00 0.00 2.66
954 955 1.238439 ACTTGCAAGGTTGATGACGG 58.762 50.000 29.18 1.85 0.00 4.79
1962 1963 4.092968 TCCTGATCGACGATCGTGTATATG 59.907 45.833 28.12 11.24 41.51 1.78
2385 2386 3.415087 GCTCCATGTCCTGCCCCT 61.415 66.667 0.00 0.00 0.00 4.79
2391 2392 1.680522 CGGTAGCAGCTCCATGTCCT 61.681 60.000 0.00 0.00 0.00 3.85
2526 2527 1.271543 CCTCCATGTTGAGTTGCTCCA 60.272 52.381 0.00 0.00 0.00 3.86
2533 2534 5.486775 CCCATATATCTCCTCCATGTTGAGT 59.513 44.000 0.00 0.00 0.00 3.41
2558 2559 4.081030 CTTGCGCGCAGTGGTGAG 62.081 66.667 34.25 23.15 39.19 3.51
2559 2560 4.908687 ACTTGCGCGCAGTGGTGA 62.909 61.111 34.25 17.56 39.19 4.02
2560 2561 3.862063 GAACTTGCGCGCAGTGGTG 62.862 63.158 34.25 22.71 39.19 4.17
2561 2562 3.649986 GAACTTGCGCGCAGTGGT 61.650 61.111 34.25 28.13 39.19 4.16
2562 2563 4.389576 GGAACTTGCGCGCAGTGG 62.390 66.667 34.25 27.28 39.19 4.00
2563 2564 4.389576 GGGAACTTGCGCGCAGTG 62.390 66.667 34.25 29.84 43.41 3.66
2567 2568 3.362851 CTAACGGGAACTTGCGCGC 62.363 63.158 27.26 27.26 46.51 6.86
2569 2570 1.359459 CCTCTAACGGGAACTTGCGC 61.359 60.000 0.00 0.00 0.00 6.09
2570 2571 1.359459 GCCTCTAACGGGAACTTGCG 61.359 60.000 0.00 0.00 0.00 4.85
2571 2572 0.321298 TGCCTCTAACGGGAACTTGC 60.321 55.000 0.00 0.00 0.00 4.01
2572 2573 1.002087 ACTGCCTCTAACGGGAACTTG 59.998 52.381 0.00 0.00 0.00 3.16
2573 2574 1.002087 CACTGCCTCTAACGGGAACTT 59.998 52.381 0.00 0.00 0.00 2.66
2574 2575 0.608640 CACTGCCTCTAACGGGAACT 59.391 55.000 0.00 0.00 0.00 3.01
2575 2576 0.391263 CCACTGCCTCTAACGGGAAC 60.391 60.000 0.00 0.00 0.00 3.62
2576 2577 0.834687 ACCACTGCCTCTAACGGGAA 60.835 55.000 0.00 0.00 0.00 3.97
2577 2578 1.229082 ACCACTGCCTCTAACGGGA 60.229 57.895 0.00 0.00 0.00 5.14
2578 2579 1.079127 CACCACTGCCTCTAACGGG 60.079 63.158 0.00 0.00 0.00 5.28
2579 2580 1.079127 CCACCACTGCCTCTAACGG 60.079 63.158 0.00 0.00 0.00 4.44
2580 2581 0.108615 CTCCACCACTGCCTCTAACG 60.109 60.000 0.00 0.00 0.00 3.18
2581 2582 0.391793 GCTCCACCACTGCCTCTAAC 60.392 60.000 0.00 0.00 0.00 2.34
2582 2583 1.553690 GGCTCCACCACTGCCTCTAA 61.554 60.000 0.00 0.00 43.05 2.10
2583 2584 1.990060 GGCTCCACCACTGCCTCTA 60.990 63.158 0.00 0.00 43.05 2.43
2584 2585 3.325753 GGCTCCACCACTGCCTCT 61.326 66.667 0.00 0.00 43.05 3.69
2587 2588 1.078143 CTTAGGCTCCACCACTGCC 60.078 63.158 0.00 0.00 46.42 4.85
2588 2589 1.746991 GCTTAGGCTCCACCACTGC 60.747 63.158 0.00 0.00 43.14 4.40
2589 2590 4.625800 GCTTAGGCTCCACCACTG 57.374 61.111 0.00 0.00 43.14 3.66
2599 2600 1.079503 CGTGTTCTTGGAGCTTAGGC 58.920 55.000 0.00 0.00 39.06 3.93
2600 2601 2.028930 AGACGTGTTCTTGGAGCTTAGG 60.029 50.000 0.00 0.00 0.00 2.69
2601 2602 3.305398 AGACGTGTTCTTGGAGCTTAG 57.695 47.619 0.00 0.00 0.00 2.18
2602 2603 3.321111 AGAAGACGTGTTCTTGGAGCTTA 59.679 43.478 21.27 0.00 45.24 3.09
2603 2604 2.103263 AGAAGACGTGTTCTTGGAGCTT 59.897 45.455 21.27 0.16 45.24 3.74
2604 2605 1.689273 AGAAGACGTGTTCTTGGAGCT 59.311 47.619 21.27 0.00 45.24 4.09
2605 2606 2.062519 GAGAAGACGTGTTCTTGGAGC 58.937 52.381 26.57 11.63 45.24 4.70
2606 2607 2.287668 ACGAGAAGACGTGTTCTTGGAG 60.288 50.000 33.84 23.91 45.24 3.86
2607 2608 1.679680 ACGAGAAGACGTGTTCTTGGA 59.320 47.619 33.84 0.00 45.24 3.53
2608 2609 2.135664 ACGAGAAGACGTGTTCTTGG 57.864 50.000 33.84 26.49 45.24 3.61
2609 2610 2.657372 GCTACGAGAAGACGTGTTCTTG 59.343 50.000 31.07 31.07 45.24 3.02
2611 2612 1.136029 CGCTACGAGAAGACGTGTTCT 60.136 52.381 26.24 26.24 46.02 3.01
2612 2613 1.248721 CGCTACGAGAAGACGTGTTC 58.751 55.000 17.14 17.14 46.02 3.18
2613 2614 0.728466 GCGCTACGAGAAGACGTGTT 60.728 55.000 0.00 0.00 46.02 3.32
2614 2615 1.154263 GCGCTACGAGAAGACGTGT 60.154 57.895 0.00 0.00 46.02 4.49
2615 2616 1.868251 GGCGCTACGAGAAGACGTG 60.868 63.158 7.64 0.00 46.02 4.49
2617 2618 2.648102 CGGCGCTACGAGAAGACG 60.648 66.667 7.64 0.00 39.31 4.18
2618 2619 2.950194 GCGGCGCTACGAGAAGAC 60.950 66.667 26.86 0.00 35.47 3.01
2619 2620 4.189188 GGCGGCGCTACGAGAAGA 62.189 66.667 32.30 0.00 35.47 2.87
2633 2634 3.675482 TAGCATTTTTGCGGCGGCG 62.675 57.895 28.70 28.70 44.10 6.46
2634 2635 1.873572 CTAGCATTTTTGCGGCGGC 60.874 57.895 9.78 9.68 40.27 6.53
2635 2636 0.523335 GTCTAGCATTTTTGCGGCGG 60.523 55.000 9.78 0.00 40.27 6.13
2636 2637 0.447801 AGTCTAGCATTTTTGCGGCG 59.552 50.000 0.51 0.51 40.27 6.46
2637 2638 1.468520 TGAGTCTAGCATTTTTGCGGC 59.531 47.619 0.00 0.00 40.27 6.53
2638 2639 2.474526 CGTGAGTCTAGCATTTTTGCGG 60.475 50.000 0.00 0.00 40.27 5.69
2639 2640 2.762472 CGTGAGTCTAGCATTTTTGCG 58.238 47.619 0.00 0.00 40.27 4.85
2640 2641 2.095768 TGCGTGAGTCTAGCATTTTTGC 60.096 45.455 8.63 0.00 35.81 3.68
2641 2642 3.811722 TGCGTGAGTCTAGCATTTTTG 57.188 42.857 8.63 0.00 35.81 2.44
2647 2648 2.967599 AATGATGCGTGAGTCTAGCA 57.032 45.000 13.77 13.77 45.46 3.49
2648 2649 2.721603 CGTAATGATGCGTGAGTCTAGC 59.278 50.000 3.90 3.90 0.00 3.42
2649 2650 3.003378 TCCGTAATGATGCGTGAGTCTAG 59.997 47.826 0.00 0.00 32.28 2.43
2650 2651 2.946990 TCCGTAATGATGCGTGAGTCTA 59.053 45.455 0.00 0.00 32.28 2.59
2651 2652 1.749063 TCCGTAATGATGCGTGAGTCT 59.251 47.619 0.00 0.00 32.28 3.24
2652 2653 2.120232 CTCCGTAATGATGCGTGAGTC 58.880 52.381 0.00 0.00 32.03 3.36
2653 2654 1.202417 CCTCCGTAATGATGCGTGAGT 60.202 52.381 0.00 0.00 33.50 3.41
2654 2655 1.202417 ACCTCCGTAATGATGCGTGAG 60.202 52.381 0.00 0.00 34.37 3.51
2655 2656 0.821517 ACCTCCGTAATGATGCGTGA 59.178 50.000 0.00 0.00 32.28 4.35
2656 2657 1.593006 GAACCTCCGTAATGATGCGTG 59.407 52.381 0.00 0.00 32.28 5.34
2657 2658 1.480954 AGAACCTCCGTAATGATGCGT 59.519 47.619 0.00 0.00 32.28 5.24
2658 2659 2.225068 AGAACCTCCGTAATGATGCG 57.775 50.000 0.00 0.00 0.00 4.73
2659 2660 4.202121 TGACTAGAACCTCCGTAATGATGC 60.202 45.833 0.00 0.00 0.00 3.91
2660 2661 5.515797 TGACTAGAACCTCCGTAATGATG 57.484 43.478 0.00 0.00 0.00 3.07
2661 2662 6.098409 ACAATGACTAGAACCTCCGTAATGAT 59.902 38.462 0.00 0.00 0.00 2.45
2662 2663 5.421056 ACAATGACTAGAACCTCCGTAATGA 59.579 40.000 0.00 0.00 0.00 2.57
2663 2664 5.520288 CACAATGACTAGAACCTCCGTAATG 59.480 44.000 0.00 0.00 0.00 1.90
2664 2665 5.395324 CCACAATGACTAGAACCTCCGTAAT 60.395 44.000 0.00 0.00 0.00 1.89
2665 2666 4.081862 CCACAATGACTAGAACCTCCGTAA 60.082 45.833 0.00 0.00 0.00 3.18
2666 2667 3.446161 CCACAATGACTAGAACCTCCGTA 59.554 47.826 0.00 0.00 0.00 4.02
2667 2668 2.233922 CCACAATGACTAGAACCTCCGT 59.766 50.000 0.00 0.00 0.00 4.69
2668 2669 2.233922 ACCACAATGACTAGAACCTCCG 59.766 50.000 0.00 0.00 0.00 4.63
2669 2670 3.983044 ACCACAATGACTAGAACCTCC 57.017 47.619 0.00 0.00 0.00 4.30
2670 2671 6.039047 TCGTATACCACAATGACTAGAACCTC 59.961 42.308 0.00 0.00 0.00 3.85
2671 2672 5.889853 TCGTATACCACAATGACTAGAACCT 59.110 40.000 0.00 0.00 0.00 3.50
2672 2673 5.975939 GTCGTATACCACAATGACTAGAACC 59.024 44.000 0.00 0.00 0.00 3.62
2673 2674 6.793349 AGTCGTATACCACAATGACTAGAAC 58.207 40.000 3.38 0.00 39.59 3.01
2674 2675 7.338703 AGAAGTCGTATACCACAATGACTAGAA 59.661 37.037 3.38 0.00 40.29 2.10
2675 2676 6.827251 AGAAGTCGTATACCACAATGACTAGA 59.173 38.462 3.38 0.00 40.29 2.43
2676 2677 7.028926 AGAAGTCGTATACCACAATGACTAG 57.971 40.000 3.38 0.00 40.29 2.57
2685 2686 5.356470 ACTTGGACTAGAAGTCGTATACCAC 59.644 44.000 0.00 0.00 45.96 4.16
2717 2718 1.862242 ACCGACTTAGGGTAGGGGTAT 59.138 52.381 0.00 0.00 43.65 2.73
2918 2935 3.816524 CGAGAGAGAAGCGGCCGT 61.817 66.667 28.70 7.71 0.00 5.68
3051 3068 5.719563 TGTCTCCAATGATAGTAGTTGTGGA 59.280 40.000 0.00 0.00 32.87 4.02
3201 3218 2.179427 TGAAGATCTCGGTGGTGATGT 58.821 47.619 0.00 0.00 0.00 3.06
3457 3474 3.384668 CTTGTCAAAGTCTTCGCTGAGA 58.615 45.455 0.00 0.00 0.00 3.27
3554 3571 1.065551 GTCCTTGCGAGCTTGTGTTTT 59.934 47.619 2.14 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.