Multiple sequence alignment - TraesCS2A01G223600

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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 TraesCS2A01G223600 chr2A 100.000 3077 0 0 1 3077 219148064 219151140 0.000000e+00 5683.0
1 TraesCS2A01G223600 chr2A 100.000 49 0 0 2644 2692 219150658 219150706 1.170000e-14 91.6
2 TraesCS2A01G223600 chr2A 100.000 49 0 0 2595 2643 219150707 219150755 1.170000e-14 91.6
3 TraesCS2A01G223600 chr2B 98.168 2566 39 2 1 2558 375543716 375546281 0.000000e+00 4471.0
4 TraesCS2A01G223600 chr2B 91.799 378 24 2 2700 3073 375546606 375546980 1.260000e-143 520.0
5 TraesCS2A01G223600 chr2D 97.882 2550 39 7 1 2538 199355340 199357886 0.000000e+00 4396.0
6 TraesCS2A01G223600 chr4A 89.106 358 32 7 2704 3059 314688635 314688283 3.640000e-119 438.0
7 TraesCS2A01G223600 chr4A 84.615 286 32 11 2793 3073 663369434 663369156 1.090000e-69 274.0
8 TraesCS2A01G223600 chr4B 87.569 362 37 8 2700 3059 295685524 295685879 2.210000e-111 412.0
9 TraesCS2A01G223600 chr3B 84.831 356 48 5 2700 3052 323463482 323463834 1.360000e-93 353.0
10 TraesCS2A01G223600 chr6B 86.145 332 35 8 2719 3048 339374079 339374401 6.310000e-92 348.0
11 TraesCS2A01G223600 chr3A 86.928 306 35 5 2700 3005 393098161 393098461 3.800000e-89 339.0
12 TraesCS2A01G223600 chr3A 81.180 356 55 12 2706 3056 362559020 362559368 3.020000e-70 276.0
13 TraesCS2A01G223600 chr3D 82.254 355 52 11 2711 3061 233656562 233656909 2.320000e-76 296.0


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 TraesCS2A01G223600 chr2A 219148064 219151140 3076 False 1955.4 5683 100.0000 1 3077 3 chr2A.!!$F1 3076
1 TraesCS2A01G223600 chr2B 375543716 375546980 3264 False 2495.5 4471 94.9835 1 3073 2 chr2B.!!$F1 3072
2 TraesCS2A01G223600 chr2D 199355340 199357886 2546 False 4396.0 4396 97.8820 1 2538 1 chr2D.!!$F1 2537

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
690 692 0.940126 CGCAGTGTATCCATTCCTGC 59.06 55.0 0.0 0.0 43.84 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 2684 0.174845 ACATTACGCTTGCTAGCCGA 59.825 50.0 17.08 3.51 44.86 5.54 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
345 347 4.201724 GCGAATCGTGATGCTCTTTACTTT 60.202 41.667 4.07 0.00 0.00 2.66
525 527 7.790823 AAAGTTGTTTGCATTTTATCAAGCT 57.209 28.000 0.00 0.00 0.00 3.74
554 556 8.757982 ATATGCTTGTATCACCAGATTCTTTT 57.242 30.769 0.00 0.00 35.67 2.27
640 642 8.955388 TGAATATCGAATTTTGATTCACTTGGA 58.045 29.630 4.47 0.00 32.90 3.53
645 647 8.160521 TCGAATTTTGATTCACTTGGACTAAA 57.839 30.769 0.00 0.00 0.00 1.85
690 692 0.940126 CGCAGTGTATCCATTCCTGC 59.060 55.000 0.00 0.00 43.84 4.85
1575 1589 2.498167 GCCATTTGCGACCTCATCTAT 58.502 47.619 0.00 0.00 0.00 1.98
2086 2100 1.762460 TCCGGCTGATTCCTCCTCC 60.762 63.158 0.00 0.00 0.00 4.30
2091 2105 0.985490 GCTGATTCCTCCTCCCCACT 60.985 60.000 0.00 0.00 0.00 4.00
2567 2586 1.219124 GCCACTCGCTCTGATCCAA 59.781 57.895 0.00 0.00 0.00 3.53
2569 2588 0.809241 CCACTCGCTCTGATCCAAGC 60.809 60.000 6.40 6.40 35.13 4.01
2573 2592 2.188994 GCTCTGATCCAAGCGCCT 59.811 61.111 2.29 0.00 0.00 5.52
2574 2593 1.443407 GCTCTGATCCAAGCGCCTA 59.557 57.895 2.29 0.00 0.00 3.93
2576 2595 1.576356 CTCTGATCCAAGCGCCTAAC 58.424 55.000 2.29 0.00 0.00 2.34
2578 2597 1.555075 TCTGATCCAAGCGCCTAACTT 59.445 47.619 2.29 0.00 0.00 2.66
2582 2601 0.394938 TCCAAGCGCCTAACTTGTCA 59.605 50.000 2.29 0.00 42.41 3.58
2583 2602 0.798776 CCAAGCGCCTAACTTGTCAG 59.201 55.000 2.29 0.00 42.41 3.51
2586 2605 0.320771 AGCGCCTAACTTGTCAGTGG 60.321 55.000 2.29 0.00 31.60 4.00
2588 2607 1.676014 GCGCCTAACTTGTCAGTGGAT 60.676 52.381 0.00 0.00 31.60 3.41
2589 2608 2.002586 CGCCTAACTTGTCAGTGGATG 58.997 52.381 0.00 0.00 31.60 3.51
2591 2610 2.290323 GCCTAACTTGTCAGTGGATGGT 60.290 50.000 0.00 0.00 31.60 3.55
2592 2611 3.055385 GCCTAACTTGTCAGTGGATGGTA 60.055 47.826 0.00 0.00 31.60 3.25
2593 2612 4.384208 GCCTAACTTGTCAGTGGATGGTAT 60.384 45.833 0.00 0.00 31.60 2.73
2594 2613 5.118990 CCTAACTTGTCAGTGGATGGTATG 58.881 45.833 0.00 0.00 31.60 2.39
2597 2616 3.582647 ACTTGTCAGTGGATGGTATGTGA 59.417 43.478 0.00 0.00 0.00 3.58
2599 2618 4.141233 TGTCAGTGGATGGTATGTGATG 57.859 45.455 0.00 0.00 0.00 3.07
2600 2619 3.519107 TGTCAGTGGATGGTATGTGATGT 59.481 43.478 0.00 0.00 0.00 3.06
2601 2620 4.714308 TGTCAGTGGATGGTATGTGATGTA 59.286 41.667 0.00 0.00 0.00 2.29
2603 2622 4.962362 TCAGTGGATGGTATGTGATGTAGT 59.038 41.667 0.00 0.00 0.00 2.73
2604 2623 5.052481 CAGTGGATGGTATGTGATGTAGTG 58.948 45.833 0.00 0.00 0.00 2.74
2605 2624 4.716784 AGTGGATGGTATGTGATGTAGTGT 59.283 41.667 0.00 0.00 0.00 3.55
2606 2625 5.050490 GTGGATGGTATGTGATGTAGTGTC 58.950 45.833 0.00 0.00 0.00 3.67
2607 2626 4.714308 TGGATGGTATGTGATGTAGTGTCA 59.286 41.667 0.00 0.00 0.00 3.58
2608 2627 5.366477 TGGATGGTATGTGATGTAGTGTCAT 59.634 40.000 0.00 0.00 0.00 3.06
2609 2628 5.698089 GGATGGTATGTGATGTAGTGTCATG 59.302 44.000 0.00 0.00 0.00 3.07
2611 2630 4.081198 TGGTATGTGATGTAGTGTCATGCA 60.081 41.667 0.00 0.00 0.00 3.96
2620 2639 3.020102 GTGTCATGCACATTTCGGC 57.980 52.632 13.27 0.00 46.91 5.54
2621 2640 0.523072 GTGTCATGCACATTTCGGCT 59.477 50.000 13.27 0.00 46.91 5.52
2624 2643 1.016627 TCATGCACATTTCGGCTAGC 58.983 50.000 6.04 6.04 0.00 3.42
2625 2644 0.734309 CATGCACATTTCGGCTAGCA 59.266 50.000 18.24 0.00 36.34 3.49
2626 2645 1.132834 CATGCACATTTCGGCTAGCAA 59.867 47.619 18.24 2.31 35.45 3.91
2627 2646 0.804364 TGCACATTTCGGCTAGCAAG 59.196 50.000 18.24 10.13 0.00 4.01
2638 2657 2.442189 GCTAGCAAGCGTAATGTGTG 57.558 50.000 10.63 0.00 39.39 3.82
2639 2658 1.732259 GCTAGCAAGCGTAATGTGTGT 59.268 47.619 10.63 0.00 39.39 3.72
2641 2660 3.000322 GCTAGCAAGCGTAATGTGTGTAG 60.000 47.826 10.63 0.00 39.39 2.74
2643 2662 1.526986 GCAAGCGTAATGTGTGTAGCG 60.527 52.381 0.00 0.00 0.00 4.26
2644 2663 1.724623 CAAGCGTAATGTGTGTAGCGT 59.275 47.619 0.00 0.00 0.00 5.07
2645 2664 1.346365 AGCGTAATGTGTGTAGCGTG 58.654 50.000 0.00 0.00 0.00 5.34
2646 2665 1.068125 AGCGTAATGTGTGTAGCGTGA 60.068 47.619 0.00 0.00 0.00 4.35
2647 2666 1.924524 GCGTAATGTGTGTAGCGTGAT 59.075 47.619 0.00 0.00 0.00 3.06
2648 2667 2.285026 GCGTAATGTGTGTAGCGTGATG 60.285 50.000 0.00 0.00 0.00 3.07
2649 2668 2.921121 CGTAATGTGTGTAGCGTGATGT 59.079 45.455 0.00 0.00 0.00 3.06
2650 2669 4.099824 CGTAATGTGTGTAGCGTGATGTA 58.900 43.478 0.00 0.00 0.00 2.29
2651 2670 4.204370 CGTAATGTGTGTAGCGTGATGTAG 59.796 45.833 0.00 0.00 0.00 2.74
2652 2671 3.868757 ATGTGTGTAGCGTGATGTAGT 57.131 42.857 0.00 0.00 0.00 2.73
2654 2673 2.295070 TGTGTGTAGCGTGATGTAGTGT 59.705 45.455 0.00 0.00 0.00 3.55
2655 2674 2.915463 GTGTGTAGCGTGATGTAGTGTC 59.085 50.000 0.00 0.00 0.00 3.67
2656 2675 2.554893 TGTGTAGCGTGATGTAGTGTCA 59.445 45.455 0.00 0.00 0.00 3.58
2657 2676 3.192633 TGTGTAGCGTGATGTAGTGTCAT 59.807 43.478 0.00 0.00 0.00 3.06
2658 2677 3.547868 GTGTAGCGTGATGTAGTGTCATG 59.452 47.826 0.00 0.00 36.04 3.07
2669 2688 3.020102 GTGTCATGCACATTTCGGC 57.980 52.632 13.27 0.00 46.91 5.54
2670 2689 0.523072 GTGTCATGCACATTTCGGCT 59.477 50.000 13.27 0.00 46.91 5.52
2671 2690 1.737236 GTGTCATGCACATTTCGGCTA 59.263 47.619 13.27 0.00 46.91 3.93
2672 2691 2.009051 TGTCATGCACATTTCGGCTAG 58.991 47.619 0.00 0.00 0.00 3.42
2673 2692 1.016627 TCATGCACATTTCGGCTAGC 58.983 50.000 6.04 6.04 0.00 3.42
2674 2693 0.734309 CATGCACATTTCGGCTAGCA 59.266 50.000 18.24 0.00 36.34 3.49
2675 2694 1.132834 CATGCACATTTCGGCTAGCAA 59.867 47.619 18.24 2.31 35.45 3.91
2676 2695 0.804364 TGCACATTTCGGCTAGCAAG 59.196 50.000 18.24 10.13 0.00 4.01
2689 2708 2.927477 GCTAGCAAGCGTAATGTGTGTA 59.073 45.455 10.63 0.00 39.39 2.90
2690 2709 3.000322 GCTAGCAAGCGTAATGTGTGTAG 60.000 47.826 10.63 0.00 39.39 2.74
2691 2710 1.732259 AGCAAGCGTAATGTGTGTAGC 59.268 47.619 0.00 0.00 0.00 3.58
2709 2911 4.901849 TGTAGCACTGCTTTAGAGGGATAT 59.098 41.667 9.30 0.00 40.44 1.63
2740 2942 1.754226 GTCCAACACAAGAGGGCAAAA 59.246 47.619 0.00 0.00 0.00 2.44
2750 2952 4.141251 ACAAGAGGGCAAAAGAGGAACTAA 60.141 41.667 0.00 0.00 41.55 2.24
2783 2985 3.071602 TCCTTGAAGGAGTTGAGGTCTTG 59.928 47.826 10.46 0.00 40.06 3.02
2824 3030 0.178301 GGAAGGGGTCTCGAATCCAC 59.822 60.000 7.65 4.12 0.00 4.02
2829 3035 0.107654 GGGTCTCGAATCCACTTGGG 60.108 60.000 7.65 0.00 35.41 4.12
2845 3051 4.406972 CACTTGGGGATCTTCTCTCACATA 59.593 45.833 0.00 0.00 0.00 2.29
2863 3069 3.327172 ACATAGAGGCCTTGATCTCCATG 59.673 47.826 6.77 3.86 35.99 3.66
2878 3084 0.031111 CCATGGGAGAGGTAGGTGGA 60.031 60.000 2.85 0.00 0.00 4.02
2883 3089 0.255318 GGAGAGGTAGGTGGACGAGA 59.745 60.000 0.00 0.00 0.00 4.04
2896 3102 4.152580 GGTGGACGAGAAAAACTCAATCTC 59.847 45.833 0.00 0.00 45.14 2.75
2897 3103 4.750098 GTGGACGAGAAAAACTCAATCTCA 59.250 41.667 0.00 0.00 45.14 3.27
2936 3142 2.820105 GCTAACCCTAGCTAGGAGGAGG 60.820 59.091 36.80 23.08 46.12 4.30
2937 3143 1.621733 AACCCTAGCTAGGAGGAGGA 58.378 55.000 36.80 0.00 46.63 3.71
2938 3144 1.154430 ACCCTAGCTAGGAGGAGGAG 58.846 60.000 36.80 21.75 46.63 3.69
2944 3150 0.757561 GCTAGGAGGAGGAGTGGGTC 60.758 65.000 0.00 0.00 0.00 4.46
2948 3154 2.803215 AGGAGGAGGAGTGGGTCTATA 58.197 52.381 0.00 0.00 0.00 1.31
3020 3226 1.541310 CCCGGTTAGGCACTCACAGA 61.541 60.000 0.00 0.00 41.75 3.41
3032 3238 0.529833 CTCACAGATGCTGGACGTCT 59.470 55.000 16.46 0.00 45.98 4.18
3043 3249 1.671379 GGACGTCTGGGTTGAAGGC 60.671 63.158 16.46 0.00 0.00 4.35
3044 3250 1.671379 GACGTCTGGGTTGAAGGCC 60.671 63.158 8.70 0.00 0.00 5.19
3047 3253 2.528127 TCTGGGTTGAAGGCCGGA 60.528 61.111 5.05 0.00 0.00 5.14
3048 3254 2.359975 CTGGGTTGAAGGCCGGAC 60.360 66.667 5.05 0.00 0.00 4.79
3065 3271 2.030562 CGTCTGGGGCTTCACGTT 59.969 61.111 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
545 547 5.359009 CAGATGCCACATACCAAAAGAATCT 59.641 40.000 0.00 0.00 0.00 2.40
554 556 4.984194 GCCAGATGCCACATACCA 57.016 55.556 0.00 0.00 0.00 3.25
614 616 8.955388 TCCAAGTGAATCAAAATTCGATATTCA 58.045 29.630 0.00 0.00 43.61 2.57
769 774 2.756760 TGCCTGCTTCCATTTCTCAATC 59.243 45.455 0.00 0.00 0.00 2.67
1122 1136 0.454600 GGACAGAGTCGATGCGGTTA 59.545 55.000 0.00 0.00 32.65 2.85
1575 1589 1.292223 CTCGGCGACAAAGAGGGAA 59.708 57.895 4.99 0.00 0.00 3.97
2086 2100 2.435586 CGGCTCAGCTCAAGTGGG 60.436 66.667 0.00 0.00 0.00 4.61
2268 2287 1.151810 ATATGGGTGGAGGCGGGAT 60.152 57.895 0.00 0.00 0.00 3.85
2304 2323 3.328931 ACTGCATATGGGATTACTCTGGG 59.671 47.826 4.56 0.00 0.00 4.45
2384 2403 5.947566 GCCCTTTGGGTGTCTTTTATAAGTA 59.052 40.000 4.42 0.00 46.51 2.24
2458 2477 8.659925 TCTAGTTTTTACATGTCGGTTTGTAA 57.340 30.769 0.00 0.00 36.73 2.41
2459 2478 8.659925 TTCTAGTTTTTACATGTCGGTTTGTA 57.340 30.769 0.00 0.00 0.00 2.41
2558 2577 1.195115 AGTTAGGCGCTTGGATCAGA 58.805 50.000 7.64 0.00 0.00 3.27
2559 2578 1.667724 CAAGTTAGGCGCTTGGATCAG 59.332 52.381 7.64 0.00 39.53 2.90
2560 2579 1.003118 ACAAGTTAGGCGCTTGGATCA 59.997 47.619 7.64 0.00 45.38 2.92
2563 2582 0.394938 TGACAAGTTAGGCGCTTGGA 59.605 50.000 7.64 0.00 45.38 3.53
2565 2584 1.195448 CACTGACAAGTTAGGCGCTTG 59.805 52.381 7.64 6.01 46.23 4.01
2567 2586 0.320771 CCACTGACAAGTTAGGCGCT 60.321 55.000 7.64 0.00 32.98 5.92
2569 2588 2.002586 CATCCACTGACAAGTTAGGCG 58.997 52.381 0.00 0.00 32.98 5.52
2570 2589 2.290323 ACCATCCACTGACAAGTTAGGC 60.290 50.000 0.00 0.00 32.98 3.93
2571 2590 3.703001 ACCATCCACTGACAAGTTAGG 57.297 47.619 0.00 0.00 32.98 2.69
2572 2591 5.582269 CACATACCATCCACTGACAAGTTAG 59.418 44.000 0.00 0.00 32.98 2.34
2573 2592 5.247337 TCACATACCATCCACTGACAAGTTA 59.753 40.000 0.00 0.00 32.98 2.24
2574 2593 4.041567 TCACATACCATCCACTGACAAGTT 59.958 41.667 0.00 0.00 32.98 2.66
2576 2595 4.206477 TCACATACCATCCACTGACAAG 57.794 45.455 0.00 0.00 0.00 3.16
2578 2597 3.519107 ACATCACATACCATCCACTGACA 59.481 43.478 0.00 0.00 0.00 3.58
2582 2601 4.716784 ACACTACATCACATACCATCCACT 59.283 41.667 0.00 0.00 0.00 4.00
2583 2602 5.023533 ACACTACATCACATACCATCCAC 57.976 43.478 0.00 0.00 0.00 4.02
2586 2605 5.178252 GCATGACACTACATCACATACCATC 59.822 44.000 0.00 0.00 0.00 3.51
2588 2607 4.081198 TGCATGACACTACATCACATACCA 60.081 41.667 0.00 0.00 0.00 3.25
2589 2608 4.271049 GTGCATGACACTACATCACATACC 59.729 45.833 11.51 0.00 46.41 2.73
2603 2622 2.009051 CTAGCCGAAATGTGCATGACA 58.991 47.619 0.00 0.00 39.53 3.58
2604 2623 1.268234 GCTAGCCGAAATGTGCATGAC 60.268 52.381 2.29 0.00 0.00 3.06
2605 2624 1.016627 GCTAGCCGAAATGTGCATGA 58.983 50.000 2.29 0.00 0.00 3.07
2606 2625 0.734309 TGCTAGCCGAAATGTGCATG 59.266 50.000 13.29 0.00 0.00 4.06
2607 2626 1.402968 CTTGCTAGCCGAAATGTGCAT 59.597 47.619 13.29 0.00 0.00 3.96
2608 2627 0.804364 CTTGCTAGCCGAAATGTGCA 59.196 50.000 13.29 0.00 0.00 4.57
2609 2628 0.524180 GCTTGCTAGCCGAAATGTGC 60.524 55.000 13.29 1.26 41.74 4.57
2611 2630 0.673644 ACGCTTGCTAGCCGAAATGT 60.674 50.000 17.08 2.56 44.86 2.71
2614 2633 1.663643 CATTACGCTTGCTAGCCGAAA 59.336 47.619 17.08 6.73 44.86 3.46
2615 2634 1.286501 CATTACGCTTGCTAGCCGAA 58.713 50.000 17.08 8.95 44.86 4.30
2617 2636 0.301687 CACATTACGCTTGCTAGCCG 59.698 55.000 13.29 11.33 44.86 5.52
2619 2638 1.732259 ACACACATTACGCTTGCTAGC 59.268 47.619 8.10 8.10 44.21 3.42
2620 2639 3.000322 GCTACACACATTACGCTTGCTAG 60.000 47.826 0.00 0.00 0.00 3.42
2621 2640 2.927477 GCTACACACATTACGCTTGCTA 59.073 45.455 0.00 0.00 0.00 3.49
2624 2643 1.724623 ACGCTACACACATTACGCTTG 59.275 47.619 0.00 0.00 0.00 4.01
2625 2644 1.724623 CACGCTACACACATTACGCTT 59.275 47.619 0.00 0.00 0.00 4.68
2626 2645 1.068125 TCACGCTACACACATTACGCT 60.068 47.619 0.00 0.00 0.00 5.07
2627 2646 1.342555 TCACGCTACACACATTACGC 58.657 50.000 0.00 0.00 0.00 4.42
2628 2647 2.921121 ACATCACGCTACACACATTACG 59.079 45.455 0.00 0.00 0.00 3.18
2629 2648 5.004440 CACTACATCACGCTACACACATTAC 59.996 44.000 0.00 0.00 0.00 1.89
2630 2649 5.099575 CACTACATCACGCTACACACATTA 58.900 41.667 0.00 0.00 0.00 1.90
2632 2651 3.056821 ACACTACATCACGCTACACACAT 60.057 43.478 0.00 0.00 0.00 3.21
2633 2652 2.295070 ACACTACATCACGCTACACACA 59.705 45.455 0.00 0.00 0.00 3.72
2634 2653 2.915463 GACACTACATCACGCTACACAC 59.085 50.000 0.00 0.00 0.00 3.82
2636 2655 3.211803 TGACACTACATCACGCTACAC 57.788 47.619 0.00 0.00 0.00 2.90
2637 2656 3.769536 CATGACACTACATCACGCTACA 58.230 45.455 0.00 0.00 0.00 2.74
2638 2657 2.535984 GCATGACACTACATCACGCTAC 59.464 50.000 0.00 0.00 0.00 3.58
2639 2658 2.165437 TGCATGACACTACATCACGCTA 59.835 45.455 0.00 0.00 0.00 4.26
2641 2660 1.061131 GTGCATGACACTACATCACGC 59.939 52.381 11.51 0.00 46.41 5.34
2652 2671 2.009051 CTAGCCGAAATGTGCATGACA 58.991 47.619 0.00 0.00 39.53 3.58
2654 2673 1.016627 GCTAGCCGAAATGTGCATGA 58.983 50.000 2.29 0.00 0.00 3.07
2655 2674 0.734309 TGCTAGCCGAAATGTGCATG 59.266 50.000 13.29 0.00 0.00 4.06
2656 2675 1.402968 CTTGCTAGCCGAAATGTGCAT 59.597 47.619 13.29 0.00 0.00 3.96
2657 2676 0.804364 CTTGCTAGCCGAAATGTGCA 59.196 50.000 13.29 0.00 0.00 4.57
2658 2677 0.524180 GCTTGCTAGCCGAAATGTGC 60.524 55.000 13.29 1.26 41.74 4.57
2659 2678 0.247814 CGCTTGCTAGCCGAAATGTG 60.248 55.000 13.29 0.00 44.86 3.21
2660 2679 0.673644 ACGCTTGCTAGCCGAAATGT 60.674 50.000 17.08 2.56 44.86 2.71
2661 2680 1.286501 TACGCTTGCTAGCCGAAATG 58.713 50.000 17.08 1.92 44.86 2.32
2663 2682 1.663643 CATTACGCTTGCTAGCCGAAA 59.336 47.619 17.08 6.73 44.86 3.46
2664 2683 1.286501 CATTACGCTTGCTAGCCGAA 58.713 50.000 17.08 8.95 44.86 4.30
2665 2684 0.174845 ACATTACGCTTGCTAGCCGA 59.825 50.000 17.08 3.51 44.86 5.54
2666 2685 0.301687 CACATTACGCTTGCTAGCCG 59.698 55.000 13.29 11.33 44.86 5.52
2667 2686 1.062587 CACACATTACGCTTGCTAGCC 59.937 52.381 13.29 0.00 44.86 3.93
2668 2687 1.732259 ACACACATTACGCTTGCTAGC 59.268 47.619 8.10 8.10 44.21 3.42
2669 2688 3.000322 GCTACACACATTACGCTTGCTAG 60.000 47.826 0.00 0.00 0.00 3.42
2670 2689 2.927477 GCTACACACATTACGCTTGCTA 59.073 45.455 0.00 0.00 0.00 3.49
2671 2690 1.732259 GCTACACACATTACGCTTGCT 59.268 47.619 0.00 0.00 0.00 3.91
2672 2691 1.463056 TGCTACACACATTACGCTTGC 59.537 47.619 0.00 0.00 0.00 4.01
2684 2703 2.028112 CCCTCTAAAGCAGTGCTACACA 60.028 50.000 20.09 2.23 38.25 3.72
2685 2704 2.233922 TCCCTCTAAAGCAGTGCTACAC 59.766 50.000 20.09 0.00 38.25 2.90
2689 2708 5.012561 CCTTATATCCCTCTAAAGCAGTGCT 59.987 44.000 13.14 13.14 42.56 4.40
2690 2709 5.241662 CCTTATATCCCTCTAAAGCAGTGC 58.758 45.833 7.13 7.13 0.00 4.40
2691 2710 5.308237 ACCCTTATATCCCTCTAAAGCAGTG 59.692 44.000 0.00 0.00 0.00 3.66
2693 2712 5.046231 GGACCCTTATATCCCTCTAAAGCAG 60.046 48.000 0.00 0.00 0.00 4.24
2695 2714 4.844655 TGGACCCTTATATCCCTCTAAAGC 59.155 45.833 0.00 0.00 33.69 3.51
2696 2715 6.559157 ACTTGGACCCTTATATCCCTCTAAAG 59.441 42.308 0.00 0.00 33.69 1.85
2697 2716 6.458784 ACTTGGACCCTTATATCCCTCTAAA 58.541 40.000 0.00 0.00 33.69 1.85
2698 2717 6.051946 ACTTGGACCCTTATATCCCTCTAA 57.948 41.667 0.00 0.00 33.69 2.10
2709 2911 2.128535 TGTGTTGGACTTGGACCCTTA 58.871 47.619 0.00 0.00 0.00 2.69
2740 2942 5.674035 AGGATTGGGATGAATTAGTTCCTCT 59.326 40.000 3.86 0.00 33.26 3.69
2811 3013 0.107654 CCCCAAGTGGATTCGAGACC 60.108 60.000 0.00 3.48 37.39 3.85
2812 3014 0.902531 TCCCCAAGTGGATTCGAGAC 59.097 55.000 0.00 0.00 37.39 3.36
2813 3015 1.762957 GATCCCCAAGTGGATTCGAGA 59.237 52.381 0.00 0.00 45.25 4.04
2814 3016 1.765314 AGATCCCCAAGTGGATTCGAG 59.235 52.381 0.00 0.00 45.25 4.04
2815 3017 1.879575 AGATCCCCAAGTGGATTCGA 58.120 50.000 0.00 0.00 45.25 3.71
2816 3018 2.171448 AGAAGATCCCCAAGTGGATTCG 59.829 50.000 0.00 0.00 45.25 3.34
2824 3030 4.898265 TCTATGTGAGAGAAGATCCCCAAG 59.102 45.833 0.00 0.00 0.00 3.61
2845 3051 1.138568 CCATGGAGATCAAGGCCTCT 58.861 55.000 5.23 0.00 0.00 3.69
2863 3069 0.752376 CTCGTCCACCTACCTCTCCC 60.752 65.000 0.00 0.00 0.00 4.30
2878 3084 7.496529 TCATTTGAGATTGAGTTTTTCTCGT 57.503 32.000 0.00 0.00 45.46 4.18
2896 3102 7.973944 GGGTTAGCAAAGGTTATAACTCATTTG 59.026 37.037 22.88 22.88 33.81 2.32
2897 3103 7.893833 AGGGTTAGCAAAGGTTATAACTCATTT 59.106 33.333 15.05 10.72 32.20 2.32
2936 3142 8.021973 CGTGAAACACTATATATAGACCCACTC 58.978 40.741 23.70 12.85 35.74 3.51
2937 3143 7.722728 TCGTGAAACACTATATATAGACCCACT 59.277 37.037 23.70 5.45 35.74 4.00
2938 3144 7.879070 TCGTGAAACACTATATATAGACCCAC 58.121 38.462 23.70 19.05 35.74 4.61
2948 3154 8.788806 CCTCTCTTATCTCGTGAAACACTATAT 58.211 37.037 0.00 0.00 35.74 0.86
2967 3173 1.031112 ATCCCCTCTTCCCCTCTCTT 58.969 55.000 0.00 0.00 0.00 2.85
3020 3226 1.003355 CAACCCAGACGTCCAGCAT 60.003 57.895 13.01 0.00 0.00 3.79
3032 3238 4.323477 CGTCCGGCCTTCAACCCA 62.323 66.667 0.00 0.00 0.00 4.51
3043 3249 4.452733 GAAGCCCCAGACGTCCGG 62.453 72.222 13.01 11.99 0.00 5.14
3044 3250 3.691342 TGAAGCCCCAGACGTCCG 61.691 66.667 13.01 0.70 0.00 4.79
3047 3253 2.803817 AACGTGAAGCCCCAGACGT 61.804 57.895 0.00 0.00 46.46 4.34
3048 3254 2.030562 AACGTGAAGCCCCAGACG 59.969 61.111 0.00 0.00 37.82 4.18


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

AutoCloner maintained by Alex Coulton.