Multiple sequence alignment - TraesCS3A01G274500

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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 TraesCS3A01G274500 chr3A 100.000 3284 0 0 1 3284 503752941 503756224 0.000000e+00 6065.0
1 TraesCS3A01G274500 chr3B 95.549 2561 93 13 1 2547 495151813 495154366 0.000000e+00 4078.0
2 TraesCS3A01G274500 chr3D 94.251 2522 90 24 1 2496 379537400 379539892 0.000000e+00 3803.0
3 TraesCS3A01G274500 chr3D 85.827 1016 83 15 1405 2419 150823978 150824933 0.000000e+00 1022.0
4 TraesCS3A01G274500 chr1D 88.488 1164 125 7 1049 2206 431828354 431829514 0.000000e+00 1399.0
5 TraesCS3A01G274500 chr1D 85.561 187 23 1 1212 1394 491900969 491900783 3.340000e-45 193.0
6 TraesCS3A01G274500 chr1B 88.402 1164 126 7 1049 2206 583209724 583210884 0.000000e+00 1393.0
7 TraesCS3A01G274500 chr1B 83.021 960 108 25 1108 2049 684277827 684276905 0.000000e+00 819.0
8 TraesCS3A01G274500 chr1A 87.973 1164 131 7 1049 2206 530259263 530260423 0.000000e+00 1365.0
9 TraesCS3A01G274500 chr1A 87.056 479 46 9 2816 3284 71547862 71547390 8.070000e-146 527.0
10 TraesCS3A01G274500 chr1A 81.739 115 8 6 2615 2716 71548255 71548141 2.100000e-12 84.2
11 TraesCS3A01G274500 chr4B 84.928 1181 154 11 1050 2206 667727559 667726379 0.000000e+00 1173.0
12 TraesCS3A01G274500 chr2D 88.361 653 59 11 2645 3284 567970122 567969474 0.000000e+00 769.0
13 TraesCS3A01G274500 chr4D 82.371 658 94 14 2645 3284 12023027 12022374 1.330000e-153 553.0
14 TraesCS3A01G274500 chr5B 78.552 373 49 17 2651 3020 486000675 486000331 1.980000e-52 217.0
15 TraesCS3A01G274500 chr7A 81.955 133 20 3 1889 2021 521341706 521341834 3.460000e-20 110.0


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 TraesCS3A01G274500 chr3A 503752941 503756224 3283 False 6065.0 6065 100.0000 1 3284 1 chr3A.!!$F1 3283
1 TraesCS3A01G274500 chr3B 495151813 495154366 2553 False 4078.0 4078 95.5490 1 2547 1 chr3B.!!$F1 2546
2 TraesCS3A01G274500 chr3D 379537400 379539892 2492 False 3803.0 3803 94.2510 1 2496 1 chr3D.!!$F2 2495
3 TraesCS3A01G274500 chr3D 150823978 150824933 955 False 1022.0 1022 85.8270 1405 2419 1 chr3D.!!$F1 1014
4 TraesCS3A01G274500 chr1D 431828354 431829514 1160 False 1399.0 1399 88.4880 1049 2206 1 chr1D.!!$F1 1157
5 TraesCS3A01G274500 chr1B 583209724 583210884 1160 False 1393.0 1393 88.4020 1049 2206 1 chr1B.!!$F1 1157
6 TraesCS3A01G274500 chr1B 684276905 684277827 922 True 819.0 819 83.0210 1108 2049 1 chr1B.!!$R1 941
7 TraesCS3A01G274500 chr1A 530259263 530260423 1160 False 1365.0 1365 87.9730 1049 2206 1 chr1A.!!$F1 1157
8 TraesCS3A01G274500 chr1A 71547390 71548255 865 True 305.6 527 84.3975 2615 3284 2 chr1A.!!$R1 669
9 TraesCS3A01G274500 chr4B 667726379 667727559 1180 True 1173.0 1173 84.9280 1050 2206 1 chr4B.!!$R1 1156
10 TraesCS3A01G274500 chr2D 567969474 567970122 648 True 769.0 769 88.3610 2645 3284 1 chr2D.!!$R1 639
11 TraesCS3A01G274500 chr4D 12022374 12023027 653 True 553.0 553 82.3710 2645 3284 1 chr4D.!!$R1 639

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
172 173 0.10780 CCACCCTCTGATGCAGTCTG 60.108 60.0 0.0 0.0 32.61 3.51 F
563 566 0.89832 TCCTCTCTTTCTCCTTGCGG 59.102 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1148 1.135333 CTCAAGGAGAAGTACGAGGGC 59.865 57.143 0.0 0.0 0.00 5.19 R
2547 2642 0.035152 CCATAGTTGCAGGGCACAGA 60.035 55.000 0.0 0.0 38.71 3.41 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
127 128 1.578206 GCAAAACAGCCTCTCCGACC 61.578 60.000 0.00 0.00 0.00 4.79
172 173 0.107800 CCACCCTCTGATGCAGTCTG 60.108 60.000 0.00 0.00 32.61 3.51
178 179 0.971386 TCTGATGCAGTCTGTCAGCA 59.029 50.000 13.27 12.86 42.39 4.41
208 209 1.435408 GCCTCGCCTTCTCATTCTGC 61.435 60.000 0.00 0.00 0.00 4.26
289 290 3.849708 TCGTCTCAATACAACATCGTTCG 59.150 43.478 0.00 0.00 0.00 3.95
563 566 0.898320 TCCTCTCTTTCTCCTTGCGG 59.102 55.000 0.00 0.00 0.00 5.69
641 645 4.770010 ACCTGAAACAGTTCCAGTTTTTGA 59.230 37.500 0.00 0.00 39.15 2.69
646 650 6.811170 TGAAACAGTTCCAGTTTTTGAACATC 59.189 34.615 5.32 0.00 42.57 3.06
696 705 3.607422 TTGCACATTGTCAGAACGAAG 57.393 42.857 0.00 0.00 0.00 3.79
703 712 4.449068 ACATTGTCAGAACGAAGCAACTAG 59.551 41.667 0.00 0.00 0.00 2.57
751 771 9.725019 AATTCATCAGTTACTCACATCAACTAA 57.275 29.630 0.00 0.00 31.46 2.24
815 835 1.625818 AGCTCGACTTCCAACTGGATT 59.374 47.619 0.00 0.00 44.98 3.01
878 898 1.808531 GCTGCACCCTCACATTTGCA 61.809 55.000 0.00 0.00 42.60 4.08
890 910 2.034879 ATTTGCACAGGCCTCGTCG 61.035 57.895 0.00 0.00 40.13 5.12
936 956 4.439776 GCAAATGACGACCTGTAACAAAAC 59.560 41.667 0.00 0.00 0.00 2.43
941 963 4.391216 TGACGACCTGTAACAAAACGAAAA 59.609 37.500 0.00 0.00 0.00 2.29
944 966 5.087397 CGACCTGTAACAAAACGAAAACAA 58.913 37.500 0.00 0.00 0.00 2.83
949 971 7.095982 ACCTGTAACAAAACGAAAACAAAACAG 60.096 33.333 0.00 0.00 0.00 3.16
962 984 5.508200 AACAAAACAGCGATTTAAGACCA 57.492 34.783 0.00 0.00 0.00 4.02
963 985 5.508200 ACAAAACAGCGATTTAAGACCAA 57.492 34.783 0.00 0.00 0.00 3.67
985 1014 3.181476 ACGAAGGCAAAAACTCTGCAAAT 60.181 39.130 0.00 0.00 41.78 2.32
992 1021 4.332268 GCAAAAACTCTGCAAATTTGACCA 59.668 37.500 22.31 10.02 39.69 4.02
993 1022 5.727515 GCAAAAACTCTGCAAATTTGACCAC 60.728 40.000 22.31 4.54 39.69 4.16
1002 1031 3.120923 GCAAATTTGACCACGCAGAAATG 60.121 43.478 22.31 0.00 0.00 2.32
1006 1035 5.895636 ATTTGACCACGCAGAAATGATAA 57.104 34.783 0.00 0.00 0.00 1.75
1007 1036 5.895636 TTTGACCACGCAGAAATGATAAT 57.104 34.783 0.00 0.00 0.00 1.28
1008 1037 4.880886 TGACCACGCAGAAATGATAATG 57.119 40.909 0.00 0.00 0.00 1.90
1009 1038 4.260985 TGACCACGCAGAAATGATAATGT 58.739 39.130 0.00 0.00 0.00 2.71
1010 1039 4.332543 TGACCACGCAGAAATGATAATGTC 59.667 41.667 0.00 0.00 0.00 3.06
2206 2298 3.074412 GTGAACTTGTCGGGATTCATGT 58.926 45.455 0.00 0.00 33.85 3.21
2212 2304 2.187958 TGTCGGGATTCATGTCTTCCT 58.812 47.619 9.93 0.00 0.00 3.36
2235 2327 1.066605 TCTGCGAGCTACGGATTAACC 59.933 52.381 7.50 0.00 42.12 2.85
2338 2432 2.356992 GGGGGATCGGAGATGAGAC 58.643 63.158 0.00 0.00 45.12 3.36
2473 2568 3.635836 ACCGTTTTATTTGGAAAACCCGA 59.364 39.130 6.26 0.00 43.41 5.14
2496 2591 1.787155 CCGTGCGCATTACTGTATCTC 59.213 52.381 15.91 0.00 0.00 2.75
2502 2597 4.099120 GCGCATTACTGTATCTCCTATCG 58.901 47.826 0.30 0.00 0.00 2.92
2518 2613 0.669077 ATCGCACGAGACAGTATCCC 59.331 55.000 0.00 0.00 0.00 3.85
2547 2642 2.369394 GTTCCGATTTCATGCCTTCCT 58.631 47.619 0.00 0.00 0.00 3.36
2548 2643 2.332063 TCCGATTTCATGCCTTCCTC 57.668 50.000 0.00 0.00 0.00 3.71
2549 2644 1.839994 TCCGATTTCATGCCTTCCTCT 59.160 47.619 0.00 0.00 0.00 3.69
2550 2645 1.945394 CCGATTTCATGCCTTCCTCTG 59.055 52.381 0.00 0.00 0.00 3.35
2551 2646 2.636830 CGATTTCATGCCTTCCTCTGT 58.363 47.619 0.00 0.00 0.00 3.41
2552 2647 2.353889 CGATTTCATGCCTTCCTCTGTG 59.646 50.000 0.00 0.00 0.00 3.66
2553 2648 1.538047 TTTCATGCCTTCCTCTGTGC 58.462 50.000 0.00 0.00 0.00 4.57
2554 2649 0.322816 TTCATGCCTTCCTCTGTGCC 60.323 55.000 0.00 0.00 0.00 5.01
2555 2650 1.751927 CATGCCTTCCTCTGTGCCC 60.752 63.158 0.00 0.00 0.00 5.36
2556 2651 1.927527 ATGCCTTCCTCTGTGCCCT 60.928 57.895 0.00 0.00 0.00 5.19
2557 2652 2.045536 GCCTTCCTCTGTGCCCTG 60.046 66.667 0.00 0.00 0.00 4.45
2558 2653 2.045536 CCTTCCTCTGTGCCCTGC 60.046 66.667 0.00 0.00 0.00 4.85
2559 2654 2.752358 CTTCCTCTGTGCCCTGCA 59.248 61.111 0.00 0.00 35.60 4.41
2560 2655 1.073722 CTTCCTCTGTGCCCTGCAA 59.926 57.895 0.00 0.00 41.47 4.08
2561 2656 1.228245 TTCCTCTGTGCCCTGCAAC 60.228 57.895 0.00 0.00 41.47 4.17
2562 2657 1.708993 TTCCTCTGTGCCCTGCAACT 61.709 55.000 0.00 0.00 41.47 3.16
2563 2658 0.835971 TCCTCTGTGCCCTGCAACTA 60.836 55.000 0.00 0.00 41.47 2.24
2564 2659 0.254178 CCTCTGTGCCCTGCAACTAT 59.746 55.000 0.00 0.00 41.47 2.12
2565 2660 1.376543 CTCTGTGCCCTGCAACTATG 58.623 55.000 0.00 0.00 41.47 2.23
2566 2661 0.035152 TCTGTGCCCTGCAACTATGG 60.035 55.000 0.00 0.00 41.47 2.74
2567 2662 0.035152 CTGTGCCCTGCAACTATGGA 60.035 55.000 0.00 0.00 41.47 3.41
2568 2663 0.322456 TGTGCCCTGCAACTATGGAC 60.322 55.000 0.00 0.00 41.47 4.02
2569 2664 0.322456 GTGCCCTGCAACTATGGACA 60.322 55.000 0.00 0.00 41.47 4.02
2570 2665 0.625316 TGCCCTGCAACTATGGACAT 59.375 50.000 0.00 0.00 34.76 3.06
2571 2666 1.027357 GCCCTGCAACTATGGACATG 58.973 55.000 0.00 0.00 0.00 3.21
2572 2667 1.408683 GCCCTGCAACTATGGACATGA 60.409 52.381 0.00 0.00 0.00 3.07
2573 2668 2.945440 GCCCTGCAACTATGGACATGAA 60.945 50.000 0.00 0.00 0.00 2.57
2574 2669 3.355378 CCCTGCAACTATGGACATGAAA 58.645 45.455 0.00 0.00 0.00 2.69
2575 2670 3.956199 CCCTGCAACTATGGACATGAAAT 59.044 43.478 0.00 0.00 0.00 2.17
2576 2671 4.403432 CCCTGCAACTATGGACATGAAATT 59.597 41.667 0.00 0.00 0.00 1.82
2577 2672 5.450965 CCCTGCAACTATGGACATGAAATTC 60.451 44.000 0.00 0.00 0.00 2.17
2578 2673 5.450965 CCTGCAACTATGGACATGAAATTCC 60.451 44.000 0.00 0.00 0.00 3.01
2579 2674 4.402155 TGCAACTATGGACATGAAATTCCC 59.598 41.667 0.00 0.00 0.00 3.97
2580 2675 4.646492 GCAACTATGGACATGAAATTCCCT 59.354 41.667 0.00 0.00 0.00 4.20
2581 2676 5.127682 GCAACTATGGACATGAAATTCCCTT 59.872 40.000 0.00 0.00 0.00 3.95
2582 2677 6.321181 GCAACTATGGACATGAAATTCCCTTA 59.679 38.462 0.00 0.00 0.00 2.69
2583 2678 7.147915 GCAACTATGGACATGAAATTCCCTTAA 60.148 37.037 0.00 0.00 0.00 1.85
2584 2679 8.748412 CAACTATGGACATGAAATTCCCTTAAA 58.252 33.333 0.00 0.00 0.00 1.52
2585 2680 8.893563 ACTATGGACATGAAATTCCCTTAAAA 57.106 30.769 0.00 0.00 0.00 1.52
2586 2681 9.320295 ACTATGGACATGAAATTCCCTTAAAAA 57.680 29.630 0.00 0.00 0.00 1.94
2611 2706 9.520515 AAACTATGGACATGAAGTACAATTTCT 57.479 29.630 0.00 0.00 46.24 2.52
2612 2707 8.498054 ACTATGGACATGAAGTACAATTTCTG 57.502 34.615 0.00 0.00 46.24 3.02
2613 2708 8.321353 ACTATGGACATGAAGTACAATTTCTGA 58.679 33.333 0.00 0.00 46.24 3.27
2635 2730 5.360714 TGAAGGAAAATGCTTGGTATCATCC 59.639 40.000 0.00 0.00 0.00 3.51
2637 2732 3.882888 GGAAAATGCTTGGTATCATCCGA 59.117 43.478 0.00 0.00 0.00 4.55
2639 2734 2.154854 ATGCTTGGTATCATCCGACG 57.845 50.000 0.00 0.00 0.00 5.12
2641 2736 1.222115 GCTTGGTATCATCCGACGGC 61.222 60.000 9.66 0.00 0.00 5.68
2642 2737 0.600255 CTTGGTATCATCCGACGGCC 60.600 60.000 9.66 3.81 0.00 6.13
2653 2758 2.586792 GACGGCCTCCTCTGCAAT 59.413 61.111 0.00 0.00 0.00 3.56
2711 2821 7.786178 TTCTTATTATACGCATGAGCTTTGT 57.214 32.000 0.00 0.00 39.10 2.83
2730 2840 3.814625 TGTAACATGGCTCTTGTTGTGA 58.185 40.909 13.23 0.00 37.81 3.58
2734 2847 2.233271 CATGGCTCTTGTTGTGAAGGT 58.767 47.619 0.00 0.00 0.00 3.50
2744 2857 0.662619 TTGTGAAGGTTGCTTCTGCG 59.337 50.000 0.00 0.00 43.34 5.18
2745 2858 1.165907 TGTGAAGGTTGCTTCTGCGG 61.166 55.000 0.00 0.00 43.34 5.69
2779 2894 3.157881 TGCAAAACCCAATCCGATTGTA 58.842 40.909 17.86 0.00 38.59 2.41
2803 3138 1.362717 CGTGCCTACATAGGACCCG 59.637 63.158 9.25 3.48 46.63 5.28
2809 3144 2.421877 CTACATAGGACCCGCAGCCG 62.422 65.000 0.00 0.00 0.00 5.52
2837 3172 7.236432 TCTCCCATTCTTATCTTCTTATCCCAG 59.764 40.741 0.00 0.00 0.00 4.45
2850 3185 2.859165 ATCCCAGACGAAAAGAGCAA 57.141 45.000 0.00 0.00 0.00 3.91
2864 3199 7.494298 ACGAAAAGAGCAAAACCACATATTTTT 59.506 29.630 0.00 0.00 0.00 1.94
2867 3202 6.670695 AGAGCAAAACCACATATTTTTCCT 57.329 33.333 0.00 0.00 0.00 3.36
2892 3227 1.076923 TCGTCTCCTACCTCCAGGC 60.077 63.158 0.00 0.00 39.32 4.85
2934 3269 0.527113 CCAAGCACGCATCCAAATCA 59.473 50.000 0.00 0.00 0.00 2.57
2936 3271 2.190161 CAAGCACGCATCCAAATCATG 58.810 47.619 0.00 0.00 0.00 3.07
2966 3301 3.027412 GTGAGAAGAGAGAGCACCCATA 58.973 50.000 0.00 0.00 0.00 2.74
2969 3304 0.749649 AAGAGAGAGCACCCATAGCG 59.250 55.000 0.00 0.00 37.01 4.26
3013 3348 2.285743 GAGCTTGGGGAGAGGGGT 60.286 66.667 0.00 0.00 0.00 4.95
3021 3356 1.301293 GGGAGAGGGGTGAAGCTTG 59.699 63.158 2.10 0.00 0.00 4.01
3022 3357 1.492993 GGGAGAGGGGTGAAGCTTGT 61.493 60.000 2.10 0.00 0.00 3.16
3031 3366 3.320826 GGGGTGAAGCTTGTGTTGTTTAT 59.679 43.478 2.10 0.00 0.00 1.40
3090 3426 0.974525 GGACCTTACCCAGCTACCGT 60.975 60.000 0.00 0.00 0.00 4.83
3093 3429 1.594833 CTTACCCAGCTACCGTGCA 59.405 57.895 0.00 0.00 34.99 4.57
3094 3430 0.036765 CTTACCCAGCTACCGTGCAA 60.037 55.000 0.00 0.00 34.99 4.08
3141 3478 0.596600 TGGTGTTGCGAGACGAGTTC 60.597 55.000 0.00 0.00 0.00 3.01
3180 3517 2.037053 CAAATGGTGGTGGCGAACA 58.963 52.632 0.00 0.00 0.00 3.18
3182 3519 1.000731 CAAATGGTGGTGGCGAACAAT 59.999 47.619 0.00 0.00 0.00 2.71
3237 3580 2.567615 GGCTTCTTGTTGTAGAGGGAGA 59.432 50.000 0.00 0.00 0.00 3.71
3252 3601 2.241176 AGGGAGAACACAACACAAAGGA 59.759 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.375013 GGGTAAAACCGAGCTCGCA 60.375 57.895 30.49 9.36 39.83 5.10
127 128 0.530650 AGTATGAGGCCGTCAATGCG 60.531 55.000 8.66 0.00 39.19 4.73
172 173 2.467826 GCTGATCGGGCTTGCTGAC 61.468 63.158 3.14 0.00 0.00 3.51
178 179 4.537433 GCGAGGCTGATCGGGCTT 62.537 66.667 29.45 14.81 42.94 4.35
254 255 7.436933 TGTATTGAGACGATCTCTTTGCATAT 58.563 34.615 13.65 0.00 43.73 1.78
289 290 4.067972 TGGTGTTCTTCACTTCAGGTAC 57.932 45.455 0.00 0.00 45.50 3.34
563 566 0.460987 AGCCGCTGCAGATGAAGTAC 60.461 55.000 20.43 0.00 41.13 2.73
641 645 2.611473 CCTGCTCTGTTCTGACGATGTT 60.611 50.000 0.00 0.00 0.00 2.71
646 650 1.269723 TGTACCTGCTCTGTTCTGACG 59.730 52.381 0.00 0.00 0.00 4.35
696 705 9.102757 TGATCTTGATTTTATCAGTCTAGTTGC 57.897 33.333 0.00 0.00 40.94 4.17
703 712 9.727627 GAATTGGTGATCTTGATTTTATCAGTC 57.272 33.333 0.00 0.00 40.94 3.51
731 750 5.242171 TCGGTTAGTTGATGTGAGTAACTGA 59.758 40.000 8.53 8.53 42.06 3.41
836 856 0.990374 ACAGCCAGCCTGAAGAGATT 59.010 50.000 0.00 0.00 44.64 2.40
860 880 0.038892 GTGCAAATGTGAGGGTGCAG 60.039 55.000 0.00 0.00 46.94 4.41
890 910 5.514279 CCTGATAAAGCAATCGATTTGGTC 58.486 41.667 8.21 2.35 45.06 4.02
936 956 6.344702 GGTCTTAAATCGCTGTTTTGTTTTCG 60.345 38.462 0.00 0.00 0.00 3.46
941 963 5.278604 GTTGGTCTTAAATCGCTGTTTTGT 58.721 37.500 0.00 0.00 0.00 2.83
944 966 3.810941 TCGTTGGTCTTAAATCGCTGTTT 59.189 39.130 0.00 0.00 0.00 2.83
949 971 2.475685 GCCTTCGTTGGTCTTAAATCGC 60.476 50.000 0.00 0.00 0.00 4.58
962 984 1.748493 TGCAGAGTTTTTGCCTTCGTT 59.252 42.857 0.00 0.00 40.81 3.85
963 985 1.388547 TGCAGAGTTTTTGCCTTCGT 58.611 45.000 0.00 0.00 40.81 3.85
985 1014 5.182950 ACATTATCATTTCTGCGTGGTCAAA 59.817 36.000 0.00 0.00 0.00 2.69
992 1021 5.585844 TGACATGACATTATCATTTCTGCGT 59.414 36.000 0.00 0.00 46.54 5.24
993 1022 6.018507 TCTGACATGACATTATCATTTCTGCG 60.019 38.462 0.00 0.00 46.54 5.18
1002 1031 7.486647 AGCCAATTTTCTGACATGACATTATC 58.513 34.615 0.00 0.00 0.00 1.75
1006 1035 5.475719 CAAGCCAATTTTCTGACATGACAT 58.524 37.500 0.00 0.00 0.00 3.06
1007 1036 4.262121 CCAAGCCAATTTTCTGACATGACA 60.262 41.667 0.00 0.00 0.00 3.58
1008 1037 4.240096 CCAAGCCAATTTTCTGACATGAC 58.760 43.478 0.00 0.00 0.00 3.06
1009 1038 3.306225 GCCAAGCCAATTTTCTGACATGA 60.306 43.478 0.00 0.00 0.00 3.07
1010 1039 2.997986 GCCAAGCCAATTTTCTGACATG 59.002 45.455 0.00 0.00 0.00 3.21
1119 1148 1.135333 CTCAAGGAGAAGTACGAGGGC 59.865 57.143 0.00 0.00 0.00 5.19
2206 2298 1.746220 GTAGCTCGCAGAAGAGGAAGA 59.254 52.381 0.00 0.00 38.63 2.87
2212 2304 1.103803 AATCCGTAGCTCGCAGAAGA 58.896 50.000 0.00 0.00 38.35 2.87
2235 2327 1.442520 CATTGCCAGTTCCGTTGCG 60.443 57.895 0.00 0.00 0.00 4.85
2278 2370 1.017387 GACACCAAGGCGAATCATCC 58.983 55.000 0.00 0.00 0.00 3.51
2338 2432 0.317479 CTCCCGCCTCTTATTACCCG 59.683 60.000 0.00 0.00 0.00 5.28
2432 2527 3.679980 CGGTTCCACACTAGAATGTTCTG 59.320 47.826 5.55 0.00 38.19 3.02
2473 2568 1.798283 TACAGTAATGCGCACGGTTT 58.202 45.000 14.90 5.54 0.00 3.27
2496 2591 2.095668 GGATACTGTCTCGTGCGATAGG 60.096 54.545 0.00 0.00 0.00 2.57
2502 2597 4.711980 CGGGATACTGTCTCGTGC 57.288 61.111 0.00 0.00 45.83 5.34
2518 2613 0.441145 GAAATCGGAACCAACGGTCG 59.559 55.000 0.00 0.00 33.12 4.79
2547 2642 0.035152 CCATAGTTGCAGGGCACAGA 60.035 55.000 0.00 0.00 38.71 3.41
2548 2643 0.035152 TCCATAGTTGCAGGGCACAG 60.035 55.000 0.00 0.00 38.71 3.66
2549 2644 0.322456 GTCCATAGTTGCAGGGCACA 60.322 55.000 0.00 0.00 38.71 4.57
2550 2645 0.322456 TGTCCATAGTTGCAGGGCAC 60.322 55.000 0.00 0.00 38.71 5.01
2551 2646 0.625316 ATGTCCATAGTTGCAGGGCA 59.375 50.000 0.00 0.00 41.91 5.36
2552 2647 1.027357 CATGTCCATAGTTGCAGGGC 58.973 55.000 0.00 0.00 0.00 5.19
2553 2648 2.715749 TCATGTCCATAGTTGCAGGG 57.284 50.000 0.00 0.00 0.00 4.45
2554 2649 5.450965 GGAATTTCATGTCCATAGTTGCAGG 60.451 44.000 0.00 0.00 33.79 4.85
2555 2650 5.450965 GGGAATTTCATGTCCATAGTTGCAG 60.451 44.000 2.79 0.00 35.44 4.41
2556 2651 4.402155 GGGAATTTCATGTCCATAGTTGCA 59.598 41.667 2.79 0.00 35.44 4.08
2557 2652 4.646492 AGGGAATTTCATGTCCATAGTTGC 59.354 41.667 2.79 0.00 35.44 4.17
2558 2653 6.780457 AAGGGAATTTCATGTCCATAGTTG 57.220 37.500 2.79 0.00 35.44 3.16
2559 2654 8.893563 TTTAAGGGAATTTCATGTCCATAGTT 57.106 30.769 2.79 0.00 35.44 2.24
2560 2655 8.893563 TTTTAAGGGAATTTCATGTCCATAGT 57.106 30.769 2.79 0.00 35.44 2.12
2585 2680 9.520515 AGAAATTGTACTTCATGTCCATAGTTT 57.479 29.630 0.00 0.00 0.00 2.66
2586 2681 8.950210 CAGAAATTGTACTTCATGTCCATAGTT 58.050 33.333 0.00 0.00 0.00 2.24
2587 2682 8.321353 TCAGAAATTGTACTTCATGTCCATAGT 58.679 33.333 0.00 0.00 0.00 2.12
2588 2683 8.722480 TCAGAAATTGTACTTCATGTCCATAG 57.278 34.615 0.00 0.00 0.00 2.23
2589 2684 9.166173 CTTCAGAAATTGTACTTCATGTCCATA 57.834 33.333 0.00 0.00 0.00 2.74
2590 2685 7.121759 CCTTCAGAAATTGTACTTCATGTCCAT 59.878 37.037 0.00 0.00 0.00 3.41
2591 2686 6.430925 CCTTCAGAAATTGTACTTCATGTCCA 59.569 38.462 0.00 0.00 0.00 4.02
2592 2687 6.655003 TCCTTCAGAAATTGTACTTCATGTCC 59.345 38.462 0.00 0.00 0.00 4.02
2593 2688 7.672983 TCCTTCAGAAATTGTACTTCATGTC 57.327 36.000 0.00 0.00 0.00 3.06
2594 2689 8.463930 TTTCCTTCAGAAATTGTACTTCATGT 57.536 30.769 0.00 0.00 39.60 3.21
2595 2690 9.918630 ATTTTCCTTCAGAAATTGTACTTCATG 57.081 29.630 0.00 0.00 43.93 3.07
2596 2691 9.918630 CATTTTCCTTCAGAAATTGTACTTCAT 57.081 29.630 0.00 0.00 43.93 2.57
2597 2692 7.867403 GCATTTTCCTTCAGAAATTGTACTTCA 59.133 33.333 10.16 0.00 43.93 3.02
2598 2693 8.084684 AGCATTTTCCTTCAGAAATTGTACTTC 58.915 33.333 10.16 0.00 43.93 3.01
2599 2694 7.955918 AGCATTTTCCTTCAGAAATTGTACTT 58.044 30.769 10.16 0.00 43.93 2.24
2600 2695 7.530426 AGCATTTTCCTTCAGAAATTGTACT 57.470 32.000 10.16 0.91 43.93 2.73
2601 2696 7.116805 CCAAGCATTTTCCTTCAGAAATTGTAC 59.883 37.037 10.16 0.00 43.93 2.90
2602 2697 7.153985 CCAAGCATTTTCCTTCAGAAATTGTA 58.846 34.615 10.16 0.00 43.93 2.41
2603 2698 5.993441 CCAAGCATTTTCCTTCAGAAATTGT 59.007 36.000 10.16 0.00 43.93 2.71
2604 2699 5.993441 ACCAAGCATTTTCCTTCAGAAATTG 59.007 36.000 5.94 5.94 43.93 2.32
2605 2700 6.178607 ACCAAGCATTTTCCTTCAGAAATT 57.821 33.333 0.00 0.00 43.93 1.82
2606 2701 5.813513 ACCAAGCATTTTCCTTCAGAAAT 57.186 34.783 0.00 0.00 43.93 2.17
2607 2702 6.493115 TGATACCAAGCATTTTCCTTCAGAAA 59.507 34.615 0.00 0.00 42.82 2.52
2608 2703 6.009589 TGATACCAAGCATTTTCCTTCAGAA 58.990 36.000 0.00 0.00 0.00 3.02
2609 2704 5.569355 TGATACCAAGCATTTTCCTTCAGA 58.431 37.500 0.00 0.00 0.00 3.27
2610 2705 5.902613 TGATACCAAGCATTTTCCTTCAG 57.097 39.130 0.00 0.00 0.00 3.02
2611 2706 5.360714 GGATGATACCAAGCATTTTCCTTCA 59.639 40.000 0.00 0.00 30.10 3.02
2612 2707 5.506317 CGGATGATACCAAGCATTTTCCTTC 60.506 44.000 0.00 0.00 30.10 3.46
2613 2708 4.339247 CGGATGATACCAAGCATTTTCCTT 59.661 41.667 0.00 0.00 30.10 3.36
2635 2730 3.376935 ATTGCAGAGGAGGCCGTCG 62.377 63.158 0.00 0.00 32.77 5.12
2637 2732 2.586792 GATTGCAGAGGAGGCCGT 59.413 61.111 0.00 0.00 0.00 5.68
2639 2734 1.522580 GACGATTGCAGAGGAGGCC 60.523 63.158 0.00 0.00 0.00 5.19
2641 2736 0.820226 TCTGACGATTGCAGAGGAGG 59.180 55.000 0.00 0.00 37.46 4.30
2642 2737 2.886862 ATCTGACGATTGCAGAGGAG 57.113 50.000 11.24 0.00 44.75 3.69
2653 2758 6.453265 CGCACGATTAAAAGTTAATCTGACGA 60.453 38.462 15.26 0.00 33.12 4.20
2687 2797 7.786178 ACAAAGCTCATGCGTATAATAAGAA 57.214 32.000 0.00 0.00 45.42 2.52
2711 2821 3.820467 CCTTCACAACAAGAGCCATGTTA 59.180 43.478 0.00 0.00 38.90 2.41
2730 2840 2.203337 TGCCGCAGAAGCAACCTT 60.203 55.556 0.00 0.00 42.27 3.50
2734 2847 3.952508 TCCCTGCCGCAGAAGCAA 61.953 61.111 22.35 0.00 40.35 3.91
2744 2857 4.947147 TGCAACACGGTCCCTGCC 62.947 66.667 0.00 0.00 33.78 4.85
2745 2858 2.010582 TTTTGCAACACGGTCCCTGC 62.011 55.000 0.00 0.00 35.32 4.85
2803 3138 2.883267 AAGAATGGGAGAGCGGCTGC 62.883 60.000 10.33 10.33 43.24 5.25
2809 3144 7.102993 GGATAAGAAGATAAGAATGGGAGAGC 58.897 42.308 0.00 0.00 0.00 4.09
2837 3172 3.414549 TGTGGTTTTGCTCTTTTCGTC 57.585 42.857 0.00 0.00 0.00 4.20
2850 3185 7.373617 AGGTTCAAGGAAAAATATGTGGTTT 57.626 32.000 0.00 0.00 0.00 3.27
2864 3199 2.444421 GTAGGAGACGAGGTTCAAGGA 58.556 52.381 0.00 0.00 0.00 3.36
2867 3202 2.444421 GAGGTAGGAGACGAGGTTCAA 58.556 52.381 0.00 0.00 0.00 2.69
2936 3271 2.094494 TCTCTCTTCTCACGAATGGCAC 60.094 50.000 0.00 0.00 0.00 5.01
2966 3301 3.396260 TTACAACAGCTAGGTTTCGCT 57.604 42.857 0.00 0.00 36.83 4.93
2969 3304 5.763698 AGGAGTTTTACAACAGCTAGGTTTC 59.236 40.000 0.00 0.00 35.05 2.78
3013 3348 3.605922 CGCGATAAACAACACAAGCTTCA 60.606 43.478 0.00 0.00 0.00 3.02
3021 3356 0.096454 GAGGGCGCGATAAACAACAC 59.904 55.000 12.10 0.00 0.00 3.32
3022 3357 1.355796 CGAGGGCGCGATAAACAACA 61.356 55.000 12.10 0.00 0.00 3.33
3072 3408 0.175073 CACGGTAGCTGGGTAAGGTC 59.825 60.000 0.00 0.00 37.85 3.85
3073 3409 1.896122 GCACGGTAGCTGGGTAAGGT 61.896 60.000 0.00 0.00 40.55 3.50
3075 3411 0.036765 TTGCACGGTAGCTGGGTAAG 60.037 55.000 0.00 0.00 34.99 2.34
3076 3412 0.320946 GTTGCACGGTAGCTGGGTAA 60.321 55.000 0.00 0.00 34.99 2.85
3117 3453 1.372499 GTCTCGCAACACCACGCTA 60.372 57.895 0.00 0.00 0.00 4.26
3127 3464 2.257371 CGGGAACTCGTCTCGCAA 59.743 61.111 0.00 0.00 44.92 4.85
3141 3478 4.607024 CAAAGTCGTTGTTGCGGG 57.393 55.556 0.00 0.00 32.08 6.13
3180 3517 6.625532 AAAATCCCCTTGCAATTAGTGATT 57.374 33.333 0.00 2.09 0.00 2.57
3216 3559 2.567615 TCTCCCTCTACAACAAGAAGCC 59.432 50.000 0.00 0.00 0.00 4.35
3237 3580 1.846007 TGCCTCCTTTGTGTTGTGTT 58.154 45.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.