Multiple sequence alignment - TraesCS5D01G200700

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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 TraesCS5D01G200700 chr5D 100.000 3334 0 0 1 3334 303423649 303426982 0.000000e+00 6157.0
1 TraesCS5D01G200700 chr5D 88.472 720 69 10 2627 3333 510034191 510034909 0.000000e+00 857.0
2 TraesCS5D01G200700 chr5D 100.000 34 0 0 2580 2613 457262267 457262300 2.780000e-06 63.9
3 TraesCS5D01G200700 chr5A 90.881 1623 85 20 1 1577 394558948 394557343 0.000000e+00 2119.0
4 TraesCS5D01G200700 chr5A 94.888 939 36 7 1573 2503 394557314 394556380 0.000000e+00 1458.0
5 TraesCS5D01G200700 chr5A 100.000 28 0 0 2586 2613 161092313 161092340 6.000000e-03 52.8
6 TraesCS5D01G200700 chr5A 100.000 28 0 0 2586 2613 525259461 525259434 6.000000e-03 52.8
7 TraesCS5D01G200700 chr5B 94.742 932 41 7 1573 2501 348197863 348198789 0.000000e+00 1443.0
8 TraesCS5D01G200700 chr5B 92.216 925 46 8 650 1574 348196933 348197831 0.000000e+00 1286.0
9 TraesCS5D01G200700 chr5B 94.554 661 18 6 1 651 348196141 348196793 0.000000e+00 1005.0
10 TraesCS5D01G200700 chr5B 89.552 67 4 3 2627 2692 608656008 608656072 7.670000e-12 82.4
11 TraesCS5D01G200700 chr7A 91.185 726 47 9 2625 3333 459463362 459464087 0.000000e+00 970.0
12 TraesCS5D01G200700 chr7D 90.634 726 49 8 2627 3333 579971631 579972356 0.000000e+00 946.0
13 TraesCS5D01G200700 chr3A 87.791 729 67 13 2627 3334 194700710 194699983 0.000000e+00 833.0
14 TraesCS5D01G200700 chr3A 84.615 65 6 3 2627 2691 535176108 535176048 9.990000e-06 62.1
15 TraesCS5D01G200700 chr2B 87.344 719 73 9 2629 3333 546007495 546006781 0.000000e+00 808.0
16 TraesCS5D01G200700 chr2B 100.000 28 0 0 2586 2613 522786937 522786910 6.000000e-03 52.8
17 TraesCS5D01G200700 chr3B 86.095 676 81 10 2670 3334 172739998 172740671 0.000000e+00 715.0
18 TraesCS5D01G200700 chr2D 83.241 722 103 14 2627 3333 277601034 277601752 0.000000e+00 647.0
19 TraesCS5D01G200700 chr2D 82.735 724 103 17 2628 3333 277528196 277528915 2.820000e-175 625.0
20 TraesCS5D01G200700 chr2D 91.549 71 3 3 2624 2692 134786960 134787029 9.850000e-16 95.3
21 TraesCS5D01G200700 chr6B 78.317 701 129 18 2628 3310 156403630 156402935 6.610000e-117 431.0
22 TraesCS5D01G200700 chr1D 88.235 68 4 4 2627 2692 460411131 460411196 9.920000e-11 78.7
23 TraesCS5D01G200700 chr7B 100.000 31 0 0 2583 2613 708439808 708439838 1.290000e-04 58.4
24 TraesCS5D01G200700 chr6D 96.970 33 0 1 2581 2613 45590718 45590687 2.000000e-03 54.7
25 TraesCS5D01G200700 chr2A 100.000 28 0 0 2586 2613 448557172 448557145 6.000000e-03 52.8
26 TraesCS5D01G200700 chr2A 100.000 28 0 0 2586 2613 587144111 587144084 6.000000e-03 52.8


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 TraesCS5D01G200700 chr5D 303423649 303426982 3333 False 6157.000000 6157 100.000000 1 3334 1 chr5D.!!$F1 3333
1 TraesCS5D01G200700 chr5D 510034191 510034909 718 False 857.000000 857 88.472000 2627 3333 1 chr5D.!!$F3 706
2 TraesCS5D01G200700 chr5A 394556380 394558948 2568 True 1788.500000 2119 92.884500 1 2503 2 chr5A.!!$R2 2502
3 TraesCS5D01G200700 chr5B 348196141 348198789 2648 False 1244.666667 1443 93.837333 1 2501 3 chr5B.!!$F2 2500
4 TraesCS5D01G200700 chr7A 459463362 459464087 725 False 970.000000 970 91.185000 2625 3333 1 chr7A.!!$F1 708
5 TraesCS5D01G200700 chr7D 579971631 579972356 725 False 946.000000 946 90.634000 2627 3333 1 chr7D.!!$F1 706
6 TraesCS5D01G200700 chr3A 194699983 194700710 727 True 833.000000 833 87.791000 2627 3334 1 chr3A.!!$R1 707
7 TraesCS5D01G200700 chr2B 546006781 546007495 714 True 808.000000 808 87.344000 2629 3333 1 chr2B.!!$R2 704
8 TraesCS5D01G200700 chr3B 172739998 172740671 673 False 715.000000 715 86.095000 2670 3334 1 chr3B.!!$F1 664
9 TraesCS5D01G200700 chr2D 277601034 277601752 718 False 647.000000 647 83.241000 2627 3333 1 chr2D.!!$F3 706
10 TraesCS5D01G200700 chr2D 277528196 277528915 719 False 625.000000 625 82.735000 2628 3333 1 chr2D.!!$F2 705
11 TraesCS5D01G200700 chr6B 156402935 156403630 695 True 431.000000 431 78.317000 2628 3310 1 chr6B.!!$R1 682

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
515 533 0.334676 CTCCCCTCTCTCTGTCAGGT 59.665 60.0 0.00 0.0 0.0 4.00 F
975 1162 1.285668 TGCGCGCGTTTGATGACTTA 61.286 50.0 32.35 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1827 0.682209 GGCACTGGCACATCCAAGAT 60.682 55.0 0.00 0.00 46.01 2.40 R
2530 2767 0.178981 AGCCATGCAGTGTTGGAGTT 60.179 50.0 15.88 1.18 34.81 3.01 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
261 262 3.785859 GAGGGCACATGGGCTCGA 61.786 66.667 21.47 0.00 39.95 4.04
439 455 4.938226 GTCTCTTATTTAAGTGTGGCTGCT 59.062 41.667 0.00 0.00 34.93 4.24
515 533 0.334676 CTCCCCTCTCTCTGTCAGGT 59.665 60.000 0.00 0.00 0.00 4.00
549 575 3.409636 TCCCATGTATCTCCCTTCCCTAT 59.590 47.826 0.00 0.00 0.00 2.57
554 580 4.936802 TGTATCTCCCTTCCCTATAGCTC 58.063 47.826 0.00 0.00 0.00 4.09
617 656 3.060003 CGAAGCTGAGAACTTCTTGTGTG 60.060 47.826 0.00 0.00 41.13 3.82
618 657 3.550437 AGCTGAGAACTTCTTGTGTGT 57.450 42.857 0.00 0.00 0.00 3.72
719 899 3.594312 GCGTAATTGATCGTGCAAGTAC 58.406 45.455 15.37 15.37 42.59 2.73
736 918 5.503520 GCAAGTACTAGTCACAACAAACCAC 60.504 44.000 0.00 0.00 0.00 4.16
745 927 1.313772 CAACAAACCACGGGTGATCA 58.686 50.000 0.00 0.00 35.34 2.92
762 945 6.024049 GGTGATCAGAATGTGTTTCGATTTC 58.976 40.000 0.00 0.00 39.46 2.17
766 949 4.695455 TCAGAATGTGTTTCGATTTCTCCC 59.305 41.667 0.00 0.00 39.46 4.30
767 950 4.697352 CAGAATGTGTTTCGATTTCTCCCT 59.303 41.667 0.00 0.00 39.46 4.20
768 951 4.697352 AGAATGTGTTTCGATTTCTCCCTG 59.303 41.667 0.00 0.00 39.46 4.45
780 963 2.523168 TCCCTGTCGCTGTCACCA 60.523 61.111 0.00 0.00 0.00 4.17
837 1020 8.922058 TTGAAAATATCTAGACGGAACAGTAC 57.078 34.615 0.00 0.00 0.00 2.73
866 1049 2.820787 AGGGATCATAACCTCGTCGATC 59.179 50.000 0.00 0.00 28.88 3.69
867 1050 2.414293 GGGATCATAACCTCGTCGATCG 60.414 54.545 9.36 9.36 41.41 3.69
868 1051 2.483106 GGATCATAACCTCGTCGATCGA 59.517 50.000 15.15 15.15 46.83 3.59
882 1065 1.916651 CGATCGATCGGCTCAATCATC 59.083 52.381 34.54 7.16 45.93 2.92
909 1096 2.661866 GTGCCGCTATACCTGCCG 60.662 66.667 0.00 0.00 0.00 5.69
975 1162 1.285668 TGCGCGCGTTTGATGACTTA 61.286 50.000 32.35 0.00 0.00 2.24
1016 1203 3.917760 GATGGCGTCTCGGGGAGG 61.918 72.222 0.00 0.00 0.00 4.30
1017 1204 4.458829 ATGGCGTCTCGGGGAGGA 62.459 66.667 0.94 0.00 32.10 3.71
1242 1429 1.973281 CATGGCCTCTTGCACCGTT 60.973 57.895 3.32 0.00 43.89 4.44
1245 1432 2.281484 GCCTCTTGCACCGTTGGA 60.281 61.111 0.00 0.00 40.77 3.53
1554 1751 7.954788 TGGTCCAAATTTTAACATTAAGCAC 57.045 32.000 0.00 0.00 0.00 4.40
1590 1820 2.421751 TCTAGAGAGAGACCCCAACG 57.578 55.000 0.00 0.00 0.00 4.10
1597 1827 3.236896 AGAGAGACCCCAACGTTTTCTA 58.763 45.455 0.00 0.00 0.00 2.10
1651 1886 9.699703 ACCGCAACTAATTAATTTTGTTTGTAT 57.300 25.926 5.91 0.00 32.07 2.29
1685 1920 3.003763 GGTGGAGAGGAAGCCGGT 61.004 66.667 1.90 0.00 0.00 5.28
1762 1997 4.065281 CGGGAGGACCACCACGAC 62.065 72.222 10.41 0.00 40.22 4.34
1858 2093 2.091112 CCGTCGTGAAGCTGCTCAG 61.091 63.158 1.00 0.00 0.00 3.35
1970 2205 2.116125 GCACTCCCCACTGCCTTT 59.884 61.111 0.00 0.00 0.00 3.11
2015 2250 2.649034 GTGTCCGACCTGCTCGAA 59.351 61.111 0.00 0.00 46.14 3.71
2409 2645 3.408634 TCTTTTAGGTTTTCTGGAGCCG 58.591 45.455 0.00 0.00 0.00 5.52
2470 2707 6.280855 TGATCTAGTGCTAAGTGTGCTAAA 57.719 37.500 0.00 0.00 0.00 1.85
2483 2720 6.115448 AGTGTGCTAAAGACCTAAGAATGT 57.885 37.500 0.00 0.00 0.00 2.71
2489 2726 6.599244 TGCTAAAGACCTAAGAATGTTCATGG 59.401 38.462 0.00 0.00 0.00 3.66
2519 2756 8.433421 TTTAATCATAACCTTTTAGCCTCTCG 57.567 34.615 0.00 0.00 0.00 4.04
2520 2757 3.793559 TCATAACCTTTTAGCCTCTCGC 58.206 45.455 0.00 0.00 37.98 5.03
2521 2758 2.685850 TAACCTTTTAGCCTCTCGCC 57.314 50.000 0.00 0.00 38.78 5.54
2522 2759 0.984995 AACCTTTTAGCCTCTCGCCT 59.015 50.000 0.00 0.00 38.78 5.52
2523 2760 0.537653 ACCTTTTAGCCTCTCGCCTC 59.462 55.000 0.00 0.00 38.78 4.70
2524 2761 0.827368 CCTTTTAGCCTCTCGCCTCT 59.173 55.000 0.00 0.00 38.78 3.69
2525 2762 2.032620 CCTTTTAGCCTCTCGCCTCTA 58.967 52.381 0.00 0.00 38.78 2.43
2526 2763 2.630580 CCTTTTAGCCTCTCGCCTCTAT 59.369 50.000 0.00 0.00 38.78 1.98
2527 2764 3.827302 CCTTTTAGCCTCTCGCCTCTATA 59.173 47.826 0.00 0.00 38.78 1.31
2528 2765 4.464597 CCTTTTAGCCTCTCGCCTCTATAT 59.535 45.833 0.00 0.00 38.78 0.86
2529 2766 5.652891 CCTTTTAGCCTCTCGCCTCTATATA 59.347 44.000 0.00 0.00 38.78 0.86
2530 2767 6.153000 CCTTTTAGCCTCTCGCCTCTATATAA 59.847 42.308 0.00 0.00 38.78 0.98
2531 2768 7.309867 CCTTTTAGCCTCTCGCCTCTATATAAA 60.310 40.741 0.00 0.00 38.78 1.40
2532 2769 6.512342 TTAGCCTCTCGCCTCTATATAAAC 57.488 41.667 0.00 0.00 38.78 2.01
2533 2770 4.668636 AGCCTCTCGCCTCTATATAAACT 58.331 43.478 0.00 0.00 38.78 2.66
2534 2771 4.703093 AGCCTCTCGCCTCTATATAAACTC 59.297 45.833 0.00 0.00 38.78 3.01
2535 2772 4.142337 GCCTCTCGCCTCTATATAAACTCC 60.142 50.000 0.00 0.00 0.00 3.85
2536 2773 5.010933 CCTCTCGCCTCTATATAAACTCCA 58.989 45.833 0.00 0.00 0.00 3.86
2537 2774 5.477291 CCTCTCGCCTCTATATAAACTCCAA 59.523 44.000 0.00 0.00 0.00 3.53
2538 2775 6.328641 TCTCGCCTCTATATAAACTCCAAC 57.671 41.667 0.00 0.00 0.00 3.77
2539 2776 5.831525 TCTCGCCTCTATATAAACTCCAACA 59.168 40.000 0.00 0.00 0.00 3.33
2540 2777 5.839621 TCGCCTCTATATAAACTCCAACAC 58.160 41.667 0.00 0.00 0.00 3.32
2541 2778 5.597182 TCGCCTCTATATAAACTCCAACACT 59.403 40.000 0.00 0.00 0.00 3.55
2542 2779 5.692204 CGCCTCTATATAAACTCCAACACTG 59.308 44.000 0.00 0.00 0.00 3.66
2543 2780 5.467063 GCCTCTATATAAACTCCAACACTGC 59.533 44.000 0.00 0.00 0.00 4.40
2544 2781 6.582636 CCTCTATATAAACTCCAACACTGCA 58.417 40.000 0.00 0.00 0.00 4.41
2545 2782 7.220030 CCTCTATATAAACTCCAACACTGCAT 58.780 38.462 0.00 0.00 0.00 3.96
2546 2783 7.172190 CCTCTATATAAACTCCAACACTGCATG 59.828 40.741 0.00 0.00 0.00 4.06
2547 2784 6.992123 TCTATATAAACTCCAACACTGCATGG 59.008 38.462 0.00 0.00 38.09 3.66
2548 2785 0.675633 AAACTCCAACACTGCATGGC 59.324 50.000 0.00 0.00 36.62 4.40
2549 2786 0.178981 AACTCCAACACTGCATGGCT 60.179 50.000 0.00 0.00 36.62 4.75
2550 2787 0.692476 ACTCCAACACTGCATGGCTA 59.308 50.000 0.00 0.00 36.62 3.93
2551 2788 1.073763 ACTCCAACACTGCATGGCTAA 59.926 47.619 0.00 0.00 36.62 3.09
2552 2789 1.741706 CTCCAACACTGCATGGCTAAG 59.258 52.381 0.00 0.00 36.62 2.18
2553 2790 1.073763 TCCAACACTGCATGGCTAAGT 59.926 47.619 0.00 0.00 36.62 2.24
2554 2791 1.888512 CCAACACTGCATGGCTAAGTT 59.111 47.619 0.00 0.00 0.00 2.66
2555 2792 3.081061 CCAACACTGCATGGCTAAGTTA 58.919 45.455 0.00 0.00 0.00 2.24
2556 2793 3.696051 CCAACACTGCATGGCTAAGTTAT 59.304 43.478 0.00 0.00 0.00 1.89
2557 2794 4.201950 CCAACACTGCATGGCTAAGTTATC 60.202 45.833 0.00 0.00 0.00 1.75
2558 2795 4.494091 ACACTGCATGGCTAAGTTATCT 57.506 40.909 0.00 0.00 0.00 1.98
2559 2796 5.614324 ACACTGCATGGCTAAGTTATCTA 57.386 39.130 0.00 0.00 0.00 1.98
2560 2797 6.179906 ACACTGCATGGCTAAGTTATCTAT 57.820 37.500 0.00 0.00 0.00 1.98
2561 2798 7.303182 ACACTGCATGGCTAAGTTATCTATA 57.697 36.000 0.00 0.00 0.00 1.31
2562 2799 7.911651 ACACTGCATGGCTAAGTTATCTATAT 58.088 34.615 0.00 0.00 0.00 0.86
2563 2800 9.035890 ACACTGCATGGCTAAGTTATCTATATA 57.964 33.333 0.00 0.00 0.00 0.86
2591 2828 8.533569 TGTGTAGACCATTTGTGAGATATAGA 57.466 34.615 0.00 0.00 0.00 1.98
2592 2829 8.633561 TGTGTAGACCATTTGTGAGATATAGAG 58.366 37.037 0.00 0.00 0.00 2.43
2593 2830 7.596995 GTGTAGACCATTTGTGAGATATAGAGC 59.403 40.741 0.00 0.00 0.00 4.09
2594 2831 6.737720 AGACCATTTGTGAGATATAGAGCA 57.262 37.500 0.00 0.00 0.00 4.26
2595 2832 7.313740 AGACCATTTGTGAGATATAGAGCAT 57.686 36.000 0.00 0.00 0.00 3.79
2596 2833 8.427902 AGACCATTTGTGAGATATAGAGCATA 57.572 34.615 0.00 0.00 0.00 3.14
2597 2834 8.874156 AGACCATTTGTGAGATATAGAGCATAA 58.126 33.333 0.00 0.00 0.00 1.90
2598 2835 9.664332 GACCATTTGTGAGATATAGAGCATAAT 57.336 33.333 0.00 0.00 0.00 1.28
2603 2840 9.851686 TTTGTGAGATATAGAGCATAATTGGTT 57.148 29.630 0.00 0.00 32.62 3.67
2604 2841 9.851686 TTGTGAGATATAGAGCATAATTGGTTT 57.148 29.630 0.00 0.00 32.62 3.27
2605 2842 9.276590 TGTGAGATATAGAGCATAATTGGTTTG 57.723 33.333 0.00 0.00 32.62 2.93
2606 2843 8.233190 GTGAGATATAGAGCATAATTGGTTTGC 58.767 37.037 0.00 0.00 32.62 3.68
2608 2845 9.658799 GAGATATAGAGCATAATTGGTTTGCTA 57.341 33.333 6.90 0.00 46.21 3.49
2609 2846 9.442047 AGATATAGAGCATAATTGGTTTGCTAC 57.558 33.333 6.90 3.20 46.21 3.58
2610 2847 6.884280 ATAGAGCATAATTGGTTTGCTACC 57.116 37.500 6.90 2.04 46.21 3.18
2723 2969 3.172108 AATGCGAACATACGGCACACG 62.172 52.381 0.00 0.00 41.90 4.49
2833 3092 4.441415 CACTCGGCTATCTCAATTAACGTC 59.559 45.833 0.00 0.00 0.00 4.34
2845 3104 5.946298 TCAATTAACGTCGATGTGACTAGT 58.054 37.500 11.82 0.00 45.87 2.57
2884 3147 4.639078 TCTTCATCCCATTGAACACTCA 57.361 40.909 0.00 0.00 32.39 3.41
2899 3164 4.214980 ACACTCACATTTCTTTGCTTCG 57.785 40.909 0.00 0.00 0.00 3.79
2946 3211 2.495084 GTGGTGTCAAAACCTCTCCTC 58.505 52.381 0.00 0.00 41.16 3.71
2957 3222 4.377760 TCTCCTCTCCGGCCCGTT 62.378 66.667 0.85 0.00 0.00 4.44
3019 3284 2.112297 TTGGTGTCGAAGGTGGCC 59.888 61.111 0.00 0.00 0.00 5.36
3092 3357 2.028748 GGCACTGCAAAAGGATGTGATT 60.029 45.455 2.82 0.00 0.00 2.57
3192 3457 3.009723 CGTCCAAATCCTGTACTGCATT 58.990 45.455 0.00 0.00 0.00 3.56
3203 3468 0.256752 TACTGCATTGCCAGCCAGAT 59.743 50.000 6.12 0.00 36.29 2.90
3206 3471 1.337071 CTGCATTGCCAGCCAGATAAG 59.663 52.381 6.12 0.00 0.00 1.73
3250 3516 1.490490 AGCTCCTCCAAACACACTTCA 59.510 47.619 0.00 0.00 0.00 3.02
3312 3578 4.708726 AACAGATTTGGCAGAGTATTGC 57.291 40.909 0.00 0.00 43.34 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.418264 TGAATGGAACCGGTCAGTCAA 59.582 47.619 20.20 4.22 35.48 3.18
363 372 1.675720 GGAGGGAGAGCAGAGCAGAC 61.676 65.000 0.00 0.00 0.00 3.51
439 455 1.203112 ACTGAGAGGGAGAGAGTGCAA 60.203 52.381 0.00 0.00 0.00 4.08
617 656 5.404667 GTGTACTGCTTAGTTCTTACCACAC 59.595 44.000 0.00 0.00 0.00 3.82
618 657 5.303589 AGTGTACTGCTTAGTTCTTACCACA 59.696 40.000 0.00 0.00 0.00 4.17
719 899 1.871039 CCCGTGGTTTGTTGTGACTAG 59.129 52.381 0.00 0.00 0.00 2.57
736 918 2.094258 CGAAACACATTCTGATCACCCG 59.906 50.000 0.00 0.00 35.79 5.28
745 927 4.697352 CAGGGAGAAATCGAAACACATTCT 59.303 41.667 0.00 0.00 35.79 2.40
762 945 2.262915 GGTGACAGCGACAGGGAG 59.737 66.667 0.00 0.00 0.00 4.30
780 963 8.825774 TCCCATCAACACATAATATATGCTACT 58.174 33.333 0.00 0.00 0.00 2.57
812 995 7.699391 CGTACTGTTCCGTCTAGATATTTTCAA 59.301 37.037 0.00 0.00 0.00 2.69
836 1019 2.102588 GGTTATGATCCCTACAGTGCGT 59.897 50.000 0.00 0.00 0.00 5.24
837 1020 2.365617 AGGTTATGATCCCTACAGTGCG 59.634 50.000 0.00 0.00 0.00 5.34
846 1029 2.414293 CGATCGACGAGGTTATGATCCC 60.414 54.545 10.26 0.00 45.77 3.85
866 1049 3.249091 CCTAAGATGATTGAGCCGATCG 58.751 50.000 8.51 8.51 0.00 3.69
867 1050 2.999355 GCCTAAGATGATTGAGCCGATC 59.001 50.000 0.00 0.00 0.00 3.69
868 1051 2.369860 TGCCTAAGATGATTGAGCCGAT 59.630 45.455 0.00 0.00 0.00 4.18
869 1052 1.762370 TGCCTAAGATGATTGAGCCGA 59.238 47.619 0.00 0.00 0.00 5.54
909 1096 2.811792 TGCATGCACGCACAATTTC 58.188 47.368 18.46 0.00 36.86 2.17
1016 1203 2.420890 CATGCGCTCCTCCTCCTC 59.579 66.667 9.73 0.00 0.00 3.71
1017 1204 3.859414 GCATGCGCTCCTCCTCCT 61.859 66.667 9.73 0.00 34.30 3.69
1371 1558 3.264897 CATTTCCTCTCCGCGGCG 61.265 66.667 23.51 16.47 0.00 6.46
1554 1751 4.686972 TCTAGAGATTCGTGCATTTCTGG 58.313 43.478 0.00 0.00 0.00 3.86
1586 1816 5.088739 GCACATCCAAGATAGAAAACGTTG 58.911 41.667 0.00 0.00 0.00 4.10
1588 1818 3.689649 GGCACATCCAAGATAGAAAACGT 59.310 43.478 0.00 0.00 34.01 3.99
1589 1819 3.689161 TGGCACATCCAAGATAGAAAACG 59.311 43.478 0.00 0.00 43.21 3.60
1590 1820 4.702131 ACTGGCACATCCAAGATAGAAAAC 59.298 41.667 0.00 0.00 46.01 2.43
1597 1827 0.682209 GGCACTGGCACATCCAAGAT 60.682 55.000 0.00 0.00 46.01 2.40
1651 1886 4.900684 TCCACCTGAACATAATCGAACAA 58.099 39.130 0.00 0.00 0.00 2.83
1685 1920 3.243816 TGCTGGCTCTGCTGGTCA 61.244 61.111 5.84 0.00 0.00 4.02
1892 2127 1.003839 GGTGATTGTCAGGTGCCGA 60.004 57.895 0.00 0.00 0.00 5.54
2015 2250 3.893763 CGGCTCGTCTCGATGGCT 61.894 66.667 0.00 0.00 34.61 4.75
2214 2449 1.171308 CTGCCACCTTTGAGACCATG 58.829 55.000 0.00 0.00 0.00 3.66
2432 2668 8.319881 AGCACTAGATCATGCATCTAAATGTAT 58.680 33.333 16.16 0.00 42.58 2.29
2470 2707 9.533831 AAATTAACCATGAACATTCTTAGGTCT 57.466 29.630 0.00 0.00 0.00 3.85
2513 2750 5.010933 TGGAGTTTATATAGAGGCGAGAGG 58.989 45.833 0.00 0.00 0.00 3.69
2514 2751 6.016192 TGTTGGAGTTTATATAGAGGCGAGAG 60.016 42.308 0.00 0.00 0.00 3.20
2515 2752 5.831525 TGTTGGAGTTTATATAGAGGCGAGA 59.168 40.000 0.00 0.00 0.00 4.04
2516 2753 5.921408 GTGTTGGAGTTTATATAGAGGCGAG 59.079 44.000 0.00 0.00 0.00 5.03
2517 2754 5.597182 AGTGTTGGAGTTTATATAGAGGCGA 59.403 40.000 0.00 0.00 0.00 5.54
2518 2755 5.692204 CAGTGTTGGAGTTTATATAGAGGCG 59.308 44.000 0.00 0.00 0.00 5.52
2519 2756 5.467063 GCAGTGTTGGAGTTTATATAGAGGC 59.533 44.000 0.00 0.00 0.00 4.70
2520 2757 6.582636 TGCAGTGTTGGAGTTTATATAGAGG 58.417 40.000 0.00 0.00 0.00 3.69
2521 2758 7.172190 CCATGCAGTGTTGGAGTTTATATAGAG 59.828 40.741 8.16 0.00 34.81 2.43
2522 2759 6.992123 CCATGCAGTGTTGGAGTTTATATAGA 59.008 38.462 8.16 0.00 34.81 1.98
2523 2760 6.293626 GCCATGCAGTGTTGGAGTTTATATAG 60.294 42.308 15.88 0.00 34.81 1.31
2524 2761 5.530915 GCCATGCAGTGTTGGAGTTTATATA 59.469 40.000 15.88 0.00 34.81 0.86
2525 2762 4.339247 GCCATGCAGTGTTGGAGTTTATAT 59.661 41.667 15.88 0.00 34.81 0.86
2526 2763 3.694072 GCCATGCAGTGTTGGAGTTTATA 59.306 43.478 15.88 0.00 34.81 0.98
2527 2764 2.493278 GCCATGCAGTGTTGGAGTTTAT 59.507 45.455 15.88 0.00 34.81 1.40
2528 2765 1.885887 GCCATGCAGTGTTGGAGTTTA 59.114 47.619 15.88 0.00 34.81 2.01
2529 2766 0.675633 GCCATGCAGTGTTGGAGTTT 59.324 50.000 15.88 0.00 34.81 2.66
2530 2767 0.178981 AGCCATGCAGTGTTGGAGTT 60.179 50.000 15.88 1.18 34.81 3.01
2531 2768 0.692476 TAGCCATGCAGTGTTGGAGT 59.308 50.000 15.88 6.61 34.81 3.85
2532 2769 1.741706 CTTAGCCATGCAGTGTTGGAG 59.258 52.381 15.88 3.65 34.81 3.86
2533 2770 1.073763 ACTTAGCCATGCAGTGTTGGA 59.926 47.619 15.88 0.00 34.81 3.53
2534 2771 1.538047 ACTTAGCCATGCAGTGTTGG 58.462 50.000 9.24 9.24 36.03 3.77
2535 2772 4.637534 AGATAACTTAGCCATGCAGTGTTG 59.362 41.667 0.00 0.00 0.00 3.33
2536 2773 4.848357 AGATAACTTAGCCATGCAGTGTT 58.152 39.130 0.00 0.00 0.00 3.32
2537 2774 4.494091 AGATAACTTAGCCATGCAGTGT 57.506 40.909 0.00 0.00 0.00 3.55
2565 2802 9.147732 TCTATATCTCACAAATGGTCTACACAT 57.852 33.333 0.00 0.00 0.00 3.21
2566 2803 8.533569 TCTATATCTCACAAATGGTCTACACA 57.466 34.615 0.00 0.00 0.00 3.72
2567 2804 7.596995 GCTCTATATCTCACAAATGGTCTACAC 59.403 40.741 0.00 0.00 0.00 2.90
2568 2805 7.287696 TGCTCTATATCTCACAAATGGTCTACA 59.712 37.037 0.00 0.00 0.00 2.74
2569 2806 7.661968 TGCTCTATATCTCACAAATGGTCTAC 58.338 38.462 0.00 0.00 0.00 2.59
2570 2807 7.839680 TGCTCTATATCTCACAAATGGTCTA 57.160 36.000 0.00 0.00 0.00 2.59
2571 2808 6.737720 TGCTCTATATCTCACAAATGGTCT 57.262 37.500 0.00 0.00 0.00 3.85
2572 2809 9.664332 ATTATGCTCTATATCTCACAAATGGTC 57.336 33.333 0.00 0.00 0.00 4.02
2577 2814 9.851686 AACCAATTATGCTCTATATCTCACAAA 57.148 29.630 0.00 0.00 0.00 2.83
2578 2815 9.851686 AAACCAATTATGCTCTATATCTCACAA 57.148 29.630 0.00 0.00 0.00 3.33
2579 2816 9.276590 CAAACCAATTATGCTCTATATCTCACA 57.723 33.333 0.00 0.00 0.00 3.58
2580 2817 8.233190 GCAAACCAATTATGCTCTATATCTCAC 58.767 37.037 0.00 0.00 37.12 3.51
2581 2818 8.159447 AGCAAACCAATTATGCTCTATATCTCA 58.841 33.333 0.00 0.00 46.98 3.27
2582 2819 8.558973 AGCAAACCAATTATGCTCTATATCTC 57.441 34.615 0.00 0.00 46.98 2.75
2583 2820 9.442047 GTAGCAAACCAATTATGCTCTATATCT 57.558 33.333 2.36 0.00 46.98 1.98
2584 2821 8.669243 GGTAGCAAACCAATTATGCTCTATATC 58.331 37.037 2.36 0.00 46.98 1.63
2585 2822 8.567285 GGTAGCAAACCAATTATGCTCTATAT 57.433 34.615 2.36 0.00 46.98 0.86
2586 2823 7.979444 GGTAGCAAACCAATTATGCTCTATA 57.021 36.000 2.36 0.00 46.98 1.31
2587 2824 6.884280 GGTAGCAAACCAATTATGCTCTAT 57.116 37.500 2.36 0.00 46.98 1.98
2693 2939 0.673333 TGTTCGCATTCGAGCCACAT 60.673 50.000 0.00 0.00 46.34 3.21
2723 2969 1.604438 GGTTGGTGTTGGGAATTTCGC 60.604 52.381 6.52 6.52 0.00 4.70
2833 3092 2.445316 CAGCTCGAACTAGTCACATCG 58.555 52.381 8.13 8.13 36.67 3.84
2862 3123 4.761739 GTGAGTGTTCAATGGGATGAAGAA 59.238 41.667 0.00 0.00 39.84 2.52
2866 3129 3.786368 TGTGAGTGTTCAATGGGATGA 57.214 42.857 0.00 0.00 34.49 2.92
2869 3132 4.728772 AGAAATGTGAGTGTTCAATGGGA 58.271 39.130 0.00 0.00 34.49 4.37
2872 3135 5.981315 AGCAAAGAAATGTGAGTGTTCAATG 59.019 36.000 0.00 0.00 34.49 2.82
2899 3164 1.016653 GCGGTCCTCTGAGCTTTGTC 61.017 60.000 0.00 0.00 36.84 3.18
2907 3172 1.657751 CGATCACTGCGGTCCTCTGA 61.658 60.000 0.00 0.00 0.00 3.27
2946 3211 1.746470 AGAATTTTAACGGGCCGGAG 58.254 50.000 31.78 2.48 0.00 4.63
2955 3220 6.146184 GGCTTTGAGCAAGGAAGAATTTTAAC 59.854 38.462 2.04 0.00 44.75 2.01
2957 3222 5.304101 TGGCTTTGAGCAAGGAAGAATTTTA 59.696 36.000 2.04 0.00 44.75 1.52
3019 3284 5.661056 TGGGACACTCTACAGATTAACAG 57.339 43.478 0.00 0.00 0.00 3.16
3092 3357 1.658114 CAGGACGAGGACAACGTGA 59.342 57.895 0.00 0.00 43.97 4.35
3192 3457 0.984961 AGCTCCTTATCTGGCTGGCA 60.985 55.000 3.18 3.18 33.50 4.92
3203 3468 5.734720 CACCTCTGAAATGTAAGCTCCTTA 58.265 41.667 0.00 0.00 0.00 2.69
3206 3471 2.680339 GCACCTCTGAAATGTAAGCTCC 59.320 50.000 0.00 0.00 0.00 4.70
3250 3516 4.021925 GCCCAAGTCGCCTCTGGT 62.022 66.667 0.00 0.00 0.00 4.00
3277 3543 6.464222 CCAAATCTGTTTATCGGAGCCTATA 58.536 40.000 0.00 0.00 34.66 1.31


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

AutoCloner maintained by Alex Coulton.