Multiple sequence alignment - TraesCS3D01G417800

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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 TraesCS3D01G417800 chr3D 100.000 3081 0 0 1 3081 529769999 529773079 0.000000e+00 5690.0
1 TraesCS3D01G417800 chr3D 93.234 606 30 8 196 796 529756671 529757270 0.000000e+00 881.0
2 TraesCS3D01G417800 chr3B 92.768 2005 105 26 183 2159 700358579 700360571 0.000000e+00 2863.0
3 TraesCS3D01G417800 chr3B 83.063 555 40 21 2543 3081 700360963 700361479 3.620000e-124 455.0
4 TraesCS3D01G417800 chr3B 92.430 251 13 5 2202 2449 700360569 700360816 1.360000e-93 353.0
5 TraesCS3D01G417800 chr3A 91.849 687 40 7 525 1197 663574394 663575078 0.000000e+00 944.0
6 TraesCS3D01G417800 chr3A 80.970 1072 120 45 1397 2423 663575451 663576483 0.000000e+00 773.0
7 TraesCS3D01G417800 chr3A 89.970 329 20 7 140 457 663573412 663573738 2.210000e-111 412.0
8 TraesCS3D01G417800 chr3A 93.130 131 7 2 1 131 663572757 663572885 1.130000e-44 191.0
9 TraesCS3D01G417800 chr3A 84.783 184 23 5 2824 3005 573854649 573854829 2.440000e-41 180.0
10 TraesCS3D01G417800 chr5D 83.974 156 23 2 2849 3003 84429513 84429359 6.880000e-32 148.0
11 TraesCS3D01G417800 chr1D 80.423 189 31 6 2821 3005 33601754 33601568 4.140000e-29 139.0
12 TraesCS3D01G417800 chr2B 78.616 159 29 5 2821 2977 731040732 731040577 1.950000e-17 100.0
13 TraesCS3D01G417800 chr6B 97.059 34 1 0 3042 3075 224860212 224860179 1.190000e-04 58.4


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 TraesCS3D01G417800 chr3D 529769999 529773079 3080 False 5690.000000 5690 100.000000 1 3081 1 chr3D.!!$F2 3080
1 TraesCS3D01G417800 chr3D 529756671 529757270 599 False 881.000000 881 93.234000 196 796 1 chr3D.!!$F1 600
2 TraesCS3D01G417800 chr3B 700358579 700361479 2900 False 1223.666667 2863 89.420333 183 3081 3 chr3B.!!$F1 2898
3 TraesCS3D01G417800 chr3A 663572757 663576483 3726 False 580.000000 944 88.979750 1 2423 4 chr3A.!!$F2 2422

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
235 754 0.839946 GGAGAGCAGGGCAAGGATTA 59.160 55.0 0.00 0.0 0.0 1.75 F
707 1832 1.045911 AGGGGCTCTCGAGTTGGATC 61.046 60.0 13.13 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 2491 0.179234 TCAACGACCTCACCAAAGCA 59.821 50.0 0.00 0.0 0.00 3.91 R
2545 3957 0.324645 GGTGGGATGGCCACTCAAAT 60.325 55.0 8.16 0.0 38.17 2.32 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
24 25 6.810911 AGTTGTTTGTGGCATAACAATAACA 58.189 32.000 24.15 12.31 43.65 2.41
60 61 4.751600 TGAAGCATGCTTATATCAGGAACG 59.248 41.667 32.02 0.00 36.26 3.95
63 64 5.368145 AGCATGCTTATATCAGGAACGAAA 58.632 37.500 16.30 0.00 0.00 3.46
67 68 6.844696 TGCTTATATCAGGAACGAAACATC 57.155 37.500 0.00 0.00 0.00 3.06
131 132 2.198406 GTGCGATAAACCGATACAGCA 58.802 47.619 0.00 0.00 0.00 4.41
132 133 2.218759 GTGCGATAAACCGATACAGCAG 59.781 50.000 0.00 0.00 33.84 4.24
133 134 2.159156 TGCGATAAACCGATACAGCAGT 60.159 45.455 0.00 0.00 0.00 4.40
135 136 2.218759 CGATAAACCGATACAGCAGTGC 59.781 50.000 7.13 7.13 0.00 4.40
136 137 3.458189 GATAAACCGATACAGCAGTGCT 58.542 45.455 13.14 13.14 40.77 4.40
165 684 7.059156 ACATTTTCCTCTGATTTATCTCCCAG 58.941 38.462 0.00 0.00 0.00 4.45
169 688 8.567198 TTTCCTCTGATTTATCTCCCAGATTA 57.433 34.615 0.00 0.00 36.20 1.75
203 722 2.715737 TGCAAAACGCTTAATGGGAC 57.284 45.000 0.00 0.00 43.06 4.46
233 752 1.210204 TTGGAGAGCAGGGCAAGGAT 61.210 55.000 0.00 0.00 0.00 3.24
235 754 0.839946 GGAGAGCAGGGCAAGGATTA 59.160 55.000 0.00 0.00 0.00 1.75
240 759 4.723309 AGAGCAGGGCAAGGATTATAAAG 58.277 43.478 0.00 0.00 0.00 1.85
249 768 6.407979 GGGCAAGGATTATAAAGGCAAAATCA 60.408 38.462 0.00 0.00 31.38 2.57
274 799 1.280142 CCGTAGCGACCGAGATCAG 59.720 63.158 0.00 0.00 0.00 2.90
504 1036 1.379977 CTCCAGAGGTACGCCCTGA 60.380 63.158 0.00 0.00 46.51 3.86
670 1794 6.267496 TGTTGTCTGATCTCTAATTCGTGA 57.733 37.500 0.00 0.00 0.00 4.35
695 1820 2.456073 TAGGTGTTAGAGAGGGGCTC 57.544 55.000 0.00 0.00 44.29 4.70
707 1832 1.045911 AGGGGCTCTCGAGTTGGATC 61.046 60.000 13.13 0.00 0.00 3.36
740 1865 2.943653 CGATTATTTCGGGGCCGC 59.056 61.111 10.38 10.38 44.28 6.53
754 1879 1.448893 GCCGCCGTCATGGAAGTAA 60.449 57.895 0.00 0.00 42.00 2.24
837 1963 5.303971 GGATGGTCTGATCTGTTGGATTAG 58.696 45.833 0.00 0.00 38.80 1.73
841 1967 6.194967 TGGTCTGATCTGTTGGATTAGTCTA 58.805 40.000 0.00 0.00 38.64 2.59
889 2015 3.222603 AGGGAGTTTGCACCAGTAAAAG 58.777 45.455 0.00 0.00 31.07 2.27
925 2052 4.450976 ACAAATTTGTGCCTTTTTCCTCC 58.549 39.130 22.71 0.00 40.49 4.30
956 2086 1.501604 TCTAACCCTGTTTGCCCCTTT 59.498 47.619 0.00 0.00 0.00 3.11
957 2087 1.893137 CTAACCCTGTTTGCCCCTTTC 59.107 52.381 0.00 0.00 0.00 2.62
1146 2290 1.228657 GCTCCAAGCTTTTCGTCGGT 61.229 55.000 0.00 0.00 38.45 4.69
1170 2314 5.420739 TGGTGAGTTTTCTTGCCTTACTTTT 59.579 36.000 0.00 0.00 0.00 2.27
1233 2448 9.232473 AGGTTTCAGTTTTATTTATCAGGTCTC 57.768 33.333 0.00 0.00 0.00 3.36
1276 2491 1.168714 GCTGAAGGAGGCGTTTCAAT 58.831 50.000 3.67 0.00 33.30 2.57
1317 2532 8.660373 GTTGAAGGTCAGTGTATATCTTTCAAG 58.340 37.037 0.00 0.00 0.00 3.02
1355 2570 8.984891 TGCCAAAAGTCATTTTATCTGTTATG 57.015 30.769 0.00 0.00 36.47 1.90
1369 2584 2.659757 CTGTTATGTACACACGGTGTCG 59.340 50.000 11.54 9.68 43.92 4.35
1381 2687 1.652563 GGTGTCGGCTGTTTGTTCC 59.347 57.895 0.00 0.00 0.00 3.62
1384 2690 1.890510 GTCGGCTGTTTGTTCCGGT 60.891 57.895 0.00 0.00 43.10 5.28
1388 2694 1.530323 GGCTGTTTGTTCCGGTATGT 58.470 50.000 0.00 0.00 0.00 2.29
1389 2695 1.199097 GGCTGTTTGTTCCGGTATGTG 59.801 52.381 0.00 0.00 0.00 3.21
1403 2723 5.875910 TCCGGTATGTGGTAGTTATTGTTTG 59.124 40.000 0.00 0.00 0.00 2.93
1416 2736 9.495754 GTAGTTATTGTTTGAAGATCTGAATGC 57.504 33.333 0.00 0.00 0.00 3.56
1499 2820 9.248291 ACCTTGTACGGTGTATTAATTATTACG 57.752 33.333 11.13 0.00 35.52 3.18
1531 2852 4.973168 TCCTTGTCTTTCATGTTACAGCT 58.027 39.130 0.00 0.00 0.00 4.24
1647 2968 0.586802 GACGGCAAGGTGAGTCAAAC 59.413 55.000 0.00 0.00 34.09 2.93
1655 2977 4.058817 CAAGGTGAGTCAAACCAGAGTAC 58.941 47.826 0.00 0.00 40.40 2.73
1679 3001 4.035558 CAGACATGTGTGCTGTTGTACTTT 59.964 41.667 10.38 0.00 0.00 2.66
1869 3217 5.537674 GGATCTAATGTCCATCCAATGCTTT 59.462 40.000 0.00 0.00 36.78 3.51
2004 3352 2.272146 CTATGGTGGCGGTGGCTT 59.728 61.111 0.00 0.00 39.81 4.35
2192 3541 4.693283 TGCGATAGTTGAACTCAATAGGG 58.307 43.478 0.00 0.00 38.24 3.53
2227 3576 8.279800 GTGGTTCTATGTTATTTTTGGTTTTGC 58.720 33.333 0.00 0.00 0.00 3.68
2296 3647 3.307339 GCTTGGATGAGTCTCAAGGAAGT 60.307 47.826 6.64 0.00 38.52 3.01
2316 3667 4.175516 AGTTTCATGCATTTTGCCGTATG 58.824 39.130 0.00 0.00 44.23 2.39
2321 3672 0.639756 GCATTTTGCCGTATGTTGCG 59.360 50.000 0.00 0.00 37.42 4.85
2344 3705 5.807520 CGCTGTGTACTTGTAGAGAATGATT 59.192 40.000 0.00 0.00 0.00 2.57
2452 3818 2.066262 CGAGTGGCGTATTTTCTGTGT 58.934 47.619 0.00 0.00 34.64 3.72
2455 3821 3.211045 AGTGGCGTATTTTCTGTGTTGT 58.789 40.909 0.00 0.00 0.00 3.32
2456 3822 4.382291 AGTGGCGTATTTTCTGTGTTGTA 58.618 39.130 0.00 0.00 0.00 2.41
2457 3823 5.001232 AGTGGCGTATTTTCTGTGTTGTAT 58.999 37.500 0.00 0.00 0.00 2.29
2458 3824 5.086058 GTGGCGTATTTTCTGTGTTGTATG 58.914 41.667 0.00 0.00 0.00 2.39
2459 3825 4.095610 GGCGTATTTTCTGTGTTGTATGC 58.904 43.478 0.00 0.00 0.00 3.14
2460 3826 4.142687 GGCGTATTTTCTGTGTTGTATGCT 60.143 41.667 0.00 0.00 0.00 3.79
2462 3828 4.788100 CGTATTTTCTGTGTTGTATGCTGC 59.212 41.667 0.00 0.00 0.00 5.25
2463 3829 3.641437 TTTTCTGTGTTGTATGCTGCC 57.359 42.857 0.00 0.00 0.00 4.85
2465 3831 2.268762 TCTGTGTTGTATGCTGCCAA 57.731 45.000 0.00 0.00 0.00 4.52
2467 3833 3.156293 TCTGTGTTGTATGCTGCCAAAT 58.844 40.909 0.00 0.00 0.00 2.32
2470 3836 5.418524 TCTGTGTTGTATGCTGCCAAATAAT 59.581 36.000 0.00 0.00 0.00 1.28
2474 3840 6.475402 GTGTTGTATGCTGCCAAATAATAACC 59.525 38.462 0.00 0.00 0.00 2.85
2476 3842 6.142818 TGTATGCTGCCAAATAATAACCAC 57.857 37.500 0.00 0.00 0.00 4.16
2478 3844 5.674052 ATGCTGCCAAATAATAACCACAA 57.326 34.783 0.00 0.00 0.00 3.33
2479 3845 5.070770 TGCTGCCAAATAATAACCACAAG 57.929 39.130 0.00 0.00 0.00 3.16
2487 3899 7.201821 GCCAAATAATAACCACAAGCAGATAGT 60.202 37.037 0.00 0.00 0.00 2.12
2489 3901 9.113838 CAAATAATAACCACAAGCAGATAGTCT 57.886 33.333 0.00 0.00 0.00 3.24
2490 3902 9.686683 AAATAATAACCACAAGCAGATAGTCTT 57.313 29.630 0.00 0.00 0.00 3.01
2499 3911 5.163499 ACAAGCAGATAGTCTTACCAGCTAC 60.163 44.000 0.00 0.00 0.00 3.58
2513 3925 5.450818 ACCAGCTACCAATGGAGAATTAA 57.549 39.130 6.16 0.00 39.02 1.40
2514 3926 6.018433 ACCAGCTACCAATGGAGAATTAAT 57.982 37.500 6.16 0.00 39.02 1.40
2515 3927 5.829924 ACCAGCTACCAATGGAGAATTAATG 59.170 40.000 6.16 0.00 39.02 1.90
2516 3928 6.064060 CCAGCTACCAATGGAGAATTAATGA 58.936 40.000 6.16 0.00 39.02 2.57
2520 3932 7.500559 AGCTACCAATGGAGAATTAATGAAGAC 59.499 37.037 6.16 0.00 0.00 3.01
2521 3933 7.500559 GCTACCAATGGAGAATTAATGAAGACT 59.499 37.037 6.16 0.00 0.00 3.24
2522 3934 7.872113 ACCAATGGAGAATTAATGAAGACTC 57.128 36.000 6.16 0.00 0.00 3.36
2526 3938 9.605275 CAATGGAGAATTAATGAAGACTCACTA 57.395 33.333 0.00 0.00 33.30 2.74
2536 3948 9.841880 TTAATGAAGACTCACTATATATGCGTC 57.158 33.333 0.00 6.97 33.30 5.19
2537 3949 5.928153 TGAAGACTCACTATATATGCGTCG 58.072 41.667 0.00 0.00 36.99 5.12
2538 3950 5.699458 TGAAGACTCACTATATATGCGTCGA 59.301 40.000 0.00 0.00 36.99 4.20
2539 3951 6.204108 TGAAGACTCACTATATATGCGTCGAA 59.796 38.462 0.00 0.00 36.99 3.71
2541 3953 6.777101 AGACTCACTATATATGCGTCGAATC 58.223 40.000 0.00 0.00 36.99 2.52
2542 3954 6.596106 AGACTCACTATATATGCGTCGAATCT 59.404 38.462 0.00 0.00 36.99 2.40
2543 3955 7.764901 AGACTCACTATATATGCGTCGAATCTA 59.235 37.037 0.00 0.00 36.99 1.98
2544 3956 8.439993 ACTCACTATATATGCGTCGAATCTAT 57.560 34.615 0.00 0.00 0.00 1.98
2545 3957 9.543783 ACTCACTATATATGCGTCGAATCTATA 57.456 33.333 0.00 0.00 0.00 1.31
2553 3965 6.696825 ATGCGTCGAATCTATATTTGAGTG 57.303 37.500 0.00 0.00 36.39 3.51
2554 3966 4.982295 TGCGTCGAATCTATATTTGAGTGG 59.018 41.667 0.00 0.00 36.39 4.00
2602 4019 7.276658 TGTCCATTTTTAAGTCTGTGACACTA 58.723 34.615 7.20 0.00 34.60 2.74
2605 4022 9.179909 TCCATTTTTAAGTCTGTGACACTAAAA 57.820 29.630 7.20 6.41 33.99 1.52
2681 4098 8.971321 CAACAGAGATTTTCAATAGGTTTGTTG 58.029 33.333 0.00 0.00 35.97 3.33
2682 4099 8.463930 ACAGAGATTTTCAATAGGTTTGTTGA 57.536 30.769 0.00 0.00 33.29 3.18
2683 4100 8.912988 ACAGAGATTTTCAATAGGTTTGTTGAA 58.087 29.630 0.00 0.00 41.02 2.69
2688 4105 8.831715 ATTTTCAATAGGTTTGTTGAATCCAC 57.168 30.769 1.89 0.00 41.89 4.02
2691 4108 5.048083 TCAATAGGTTTGTTGAATCCACAGC 60.048 40.000 0.00 0.00 32.36 4.40
2724 4141 6.093404 TCAACGAGTTAGAATCACATCTCAC 58.907 40.000 0.00 0.00 0.00 3.51
2725 4142 4.663166 ACGAGTTAGAATCACATCTCACG 58.337 43.478 0.00 0.00 30.58 4.35
2726 4143 3.483922 CGAGTTAGAATCACATCTCACGC 59.516 47.826 0.00 0.00 30.58 5.34
2727 4144 4.424626 GAGTTAGAATCACATCTCACGCA 58.575 43.478 0.00 0.00 30.58 5.24
2728 4145 5.016051 AGTTAGAATCACATCTCACGCAT 57.984 39.130 0.00 0.00 30.58 4.73
2729 4146 5.423015 AGTTAGAATCACATCTCACGCATT 58.577 37.500 0.00 0.00 30.58 3.56
2730 4147 6.573434 AGTTAGAATCACATCTCACGCATTA 58.427 36.000 0.00 0.00 30.58 1.90
2731 4148 7.212976 AGTTAGAATCACATCTCACGCATTAT 58.787 34.615 0.00 0.00 30.58 1.28
2732 4149 5.919272 AGAATCACATCTCACGCATTATG 57.081 39.130 0.00 0.00 0.00 1.90
2733 4150 5.363101 AGAATCACATCTCACGCATTATGT 58.637 37.500 0.00 0.00 32.91 2.29
2734 4151 5.235831 AGAATCACATCTCACGCATTATGTG 59.764 40.000 4.01 4.01 46.75 3.21
2745 4162 1.035139 CATTATGTGCCCCTTGCTCC 58.965 55.000 0.00 0.00 42.00 4.70
2746 4163 0.630673 ATTATGTGCCCCTTGCTCCA 59.369 50.000 0.00 0.00 42.00 3.86
2747 4164 0.630673 TTATGTGCCCCTTGCTCCAT 59.369 50.000 0.00 0.00 42.00 3.41
2748 4165 0.183492 TATGTGCCCCTTGCTCCATC 59.817 55.000 0.00 0.00 42.00 3.51
2749 4166 2.440980 GTGCCCCTTGCTCCATCC 60.441 66.667 0.00 0.00 42.00 3.51
2750 4167 2.940467 TGCCCCTTGCTCCATCCA 60.940 61.111 0.00 0.00 42.00 3.41
2751 4168 2.360191 GCCCCTTGCTCCATCCAA 59.640 61.111 0.00 0.00 36.87 3.53
2760 4177 0.743097 GCTCCATCCAACTCCATTGC 59.257 55.000 0.00 0.00 36.93 3.56
2771 4188 3.830192 CCATTGCGCCCCTTGAGC 61.830 66.667 4.18 0.00 40.63 4.26
2777 4194 2.203126 CGCCCCTTGAGCTCCATC 60.203 66.667 12.15 0.00 0.00 3.51
2781 4198 0.332632 CCCCTTGAGCTCCATCCAAA 59.667 55.000 12.15 0.00 0.00 3.28
2805 4225 4.142966 GGTACAAGCGTAAATCACAGGTTC 60.143 45.833 0.00 0.00 0.00 3.62
2807 4227 4.072131 ACAAGCGTAAATCACAGGTTCAT 58.928 39.130 0.00 0.00 0.00 2.57
2851 4271 9.247126 CAATTTGATGATTGTCAAGTTGTAACA 57.753 29.630 13.40 0.00 44.26 2.41
2852 4272 9.985730 AATTTGATGATTGTCAAGTTGTAACAT 57.014 25.926 2.11 3.66 39.13 2.71
2853 4273 9.985730 ATTTGATGATTGTCAAGTTGTAACATT 57.014 25.926 2.11 0.00 39.13 2.71
2892 4324 2.813754 GACTGGCATGTAGAGCAACAAA 59.186 45.455 6.18 0.00 32.02 2.83
2894 4326 3.828451 ACTGGCATGTAGAGCAACAAAAT 59.172 39.130 6.18 0.00 32.02 1.82
2908 4340 6.470557 GCAACAAAATGCACAACTTATGAT 57.529 33.333 0.00 0.00 45.70 2.45
2909 4341 6.527957 GCAACAAAATGCACAACTTATGATC 58.472 36.000 0.00 0.00 45.70 2.92
2927 4359 0.976641 TCTTCATGGTTGACGAGCCT 59.023 50.000 0.00 0.00 0.00 4.58
2933 4365 1.296715 GGTTGACGAGCCTGATGGT 59.703 57.895 0.00 0.00 35.27 3.55
2934 4366 1.021390 GGTTGACGAGCCTGATGGTG 61.021 60.000 0.00 0.00 35.27 4.17
2954 4386 2.135139 GACATTGTCTTCACTCGTGCA 58.865 47.619 9.59 0.00 0.00 4.57
2957 4389 3.565482 ACATTGTCTTCACTCGTGCAATT 59.435 39.130 0.00 0.00 0.00 2.32
2983 4415 5.991328 TCACAAAACTTCATGACTGAGTC 57.009 39.130 5.47 5.47 31.68 3.36
2989 4422 7.284034 ACAAAACTTCATGACTGAGTCAAAGAT 59.716 33.333 25.61 15.71 45.96 2.40
3011 4444 1.924524 GTGTACCACCGATGATTCACG 59.075 52.381 0.00 0.00 0.00 4.35
3026 4459 0.466543 TCACGTGCAAGTTGTAGGGT 59.533 50.000 11.67 5.39 0.00 4.34
3059 4493 3.512329 TCCTCATGAAACAAAGCATGCAT 59.488 39.130 21.98 4.57 41.18 3.96
3076 4510 2.559440 GCATGTTTTGCCAAAAGGTCA 58.441 42.857 2.15 0.00 46.15 4.02
3077 4511 2.941720 GCATGTTTTGCCAAAAGGTCAA 59.058 40.909 2.15 0.00 46.15 3.18
3078 4512 3.002553 GCATGTTTTGCCAAAAGGTCAAG 59.997 43.478 2.15 0.00 46.15 3.02
3079 4513 3.971245 TGTTTTGCCAAAAGGTCAAGT 57.029 38.095 2.15 0.00 0.00 3.16
3080 4514 3.855858 TGTTTTGCCAAAAGGTCAAGTC 58.144 40.909 2.15 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 8.344098 ACATAAAAATGTTGCACAATCCTTTTG 58.656 29.630 0.00 0.00 0.00 2.44
90 91 5.409214 GCACATAAAAATGTTGCACAATCCT 59.591 36.000 0.00 0.00 32.67 3.24
99 100 6.524933 TCGGTTTATCGCACATAAAAATGTTG 59.475 34.615 0.49 0.00 31.37 3.33
107 108 4.446385 GCTGTATCGGTTTATCGCACATAA 59.554 41.667 0.00 0.00 0.00 1.90
131 132 2.295349 CAGAGGAAAATGTTGCAGCACT 59.705 45.455 5.00 0.00 0.00 4.40
132 133 2.294233 TCAGAGGAAAATGTTGCAGCAC 59.706 45.455 5.00 0.00 0.00 4.40
133 134 2.585330 TCAGAGGAAAATGTTGCAGCA 58.415 42.857 5.46 5.46 0.00 4.41
135 136 7.769220 AGATAAATCAGAGGAAAATGTTGCAG 58.231 34.615 0.00 0.00 0.00 4.41
136 137 7.148018 GGAGATAAATCAGAGGAAAATGTTGCA 60.148 37.037 0.00 0.00 0.00 4.08
137 138 7.199078 GGAGATAAATCAGAGGAAAATGTTGC 58.801 38.462 0.00 0.00 0.00 4.17
138 139 7.340232 TGGGAGATAAATCAGAGGAAAATGTTG 59.660 37.037 0.00 0.00 0.00 3.33
147 666 7.365473 GGGATAATCTGGGAGATAAATCAGAGG 60.365 44.444 0.00 0.00 39.26 3.69
165 684 2.481952 GCATTCACTCGCTGGGATAATC 59.518 50.000 0.00 0.00 0.00 1.75
169 688 0.035152 TTGCATTCACTCGCTGGGAT 60.035 50.000 0.00 0.00 0.00 3.85
203 722 4.553323 CCTGCTCTCCAAGAAAACATTTG 58.447 43.478 0.00 0.00 0.00 2.32
249 768 4.530857 GGTCGCTACGGGCATGCT 62.531 66.667 18.92 0.00 41.91 3.79
274 799 0.952984 GATAGGAATGAGCCAGCCGC 60.953 60.000 0.00 0.00 37.98 6.53
415 946 1.306633 GGGCTGGGGTTTAAGAGGG 59.693 63.158 0.00 0.00 0.00 4.30
499 1031 2.692741 GGGGGAAGAGGGTCAGGG 60.693 72.222 0.00 0.00 0.00 4.45
504 1036 1.413227 CGAGATAAGGGGGAAGAGGGT 60.413 57.143 0.00 0.00 0.00 4.34
670 1794 3.451890 CCCTCTCTAACACCTAAACCCT 58.548 50.000 0.00 0.00 0.00 4.34
707 1832 3.515071 AATCGAACAAAACCGAACGAG 57.485 42.857 0.00 0.00 38.36 4.18
740 1865 2.356135 CAACCCTTACTTCCATGACGG 58.644 52.381 0.00 0.00 0.00 4.79
749 1874 2.140717 CGAAACTCGCAACCCTTACTT 58.859 47.619 0.00 0.00 31.14 2.24
754 1879 1.004918 CTCCGAAACTCGCAACCCT 60.005 57.895 0.00 0.00 38.82 4.34
837 1963 9.111613 ACACGATATACTCCTGCTATAATAGAC 57.888 37.037 0.00 0.00 0.00 2.59
841 1967 9.026121 AGAAACACGATATACTCCTGCTATAAT 57.974 33.333 0.00 0.00 0.00 1.28
925 2052 2.289444 ACAGGGTTAGACACATCAACCG 60.289 50.000 0.00 0.00 42.21 4.44
956 2086 4.634004 ACCGACAAAATAAATCATCAGCGA 59.366 37.500 0.00 0.00 0.00 4.93
957 2087 4.730042 CACCGACAAAATAAATCATCAGCG 59.270 41.667 0.00 0.00 0.00 5.18
1146 2290 4.164843 AGTAAGGCAAGAAAACTCACCA 57.835 40.909 0.00 0.00 0.00 4.17
1170 2314 7.038587 ACAAGGTAATGGACATACAGTACAAGA 60.039 37.037 4.26 0.00 46.24 3.02
1211 2355 6.315393 GGCGAGACCTGATAAATAAAACTGAA 59.685 38.462 0.00 0.00 34.51 3.02
1276 2491 0.179234 TCAACGACCTCACCAAAGCA 59.821 50.000 0.00 0.00 0.00 3.91
1317 2532 5.700373 TGACTTTTGGCAAATTTGATAAGGC 59.300 36.000 22.31 17.96 32.20 4.35
1330 2545 8.584157 ACATAACAGATAAAATGACTTTTGGCA 58.416 29.630 0.00 0.00 44.56 4.92
1358 2573 2.177580 AAACAGCCGACACCGTGTG 61.178 57.895 9.42 0.00 39.75 3.82
1369 2584 1.199097 CACATACCGGAACAAACAGCC 59.801 52.381 9.46 0.00 0.00 4.85
1381 2687 6.971527 TCAAACAATAACTACCACATACCG 57.028 37.500 0.00 0.00 0.00 4.02
1388 2694 9.739276 ATTCAGATCTTCAAACAATAACTACCA 57.261 29.630 0.00 0.00 0.00 3.25
1389 2695 9.994432 CATTCAGATCTTCAAACAATAACTACC 57.006 33.333 0.00 0.00 0.00 3.18
1403 2723 8.871862 CATGTATAGCTAAGCATTCAGATCTTC 58.128 37.037 0.00 0.00 0.00 2.87
1416 2736 8.623903 TCAAGCAAATTTCCATGTATAGCTAAG 58.376 33.333 0.00 0.00 0.00 2.18
1499 2820 6.096001 ACATGAAAGACAAGGATTATGAAGCC 59.904 38.462 0.00 0.00 37.16 4.35
1531 2852 7.997643 CAGTCTCTCTGTCAGTGATAACACGA 61.998 46.154 5.11 0.00 43.46 4.35
1594 2915 1.448540 ACTCTTTGCATCCTCGCCG 60.449 57.895 0.00 0.00 0.00 6.46
1647 2968 2.932622 GCACACATGTCTGGTACTCTGG 60.933 54.545 3.15 0.00 0.00 3.86
1655 2977 1.311859 ACAACAGCACACATGTCTGG 58.688 50.000 15.27 0.00 35.51 3.86
1679 3001 9.474313 AAATGGCAGAAGTTTAACTCCATATTA 57.526 29.630 13.94 0.00 33.00 0.98
1882 3230 3.308705 ACACGGACGTTCCTCCCC 61.309 66.667 0.00 0.00 33.30 4.81
1987 3335 1.378514 AAAGCCACCGCCACCATAG 60.379 57.895 0.00 0.00 34.57 2.23
2050 3398 2.202878 CGGTCACCACCATAGCCG 60.203 66.667 0.00 0.00 44.02 5.52
2192 3541 3.550437 ACATAGAACCACATCTCTGCC 57.450 47.619 0.00 0.00 29.25 4.85
2241 3591 7.031372 CAGCATACACAAATTAACTCTTGCAT 58.969 34.615 0.00 0.00 0.00 3.96
2316 3667 2.400399 TCTACAAGTACACAGCGCAAC 58.600 47.619 11.47 0.00 0.00 4.17
2321 3672 6.456181 GCAATCATTCTCTACAAGTACACAGC 60.456 42.308 0.00 0.00 0.00 4.40
2344 3705 8.432110 AATTTATGATCACACTAACATACGCA 57.568 30.769 0.00 0.00 0.00 5.24
2433 3799 3.250040 ACAACACAGAAAATACGCCACTC 59.750 43.478 0.00 0.00 0.00 3.51
2449 3815 6.475402 GGTTATTATTTGGCAGCATACAACAC 59.525 38.462 0.00 0.00 0.00 3.32
2452 3818 6.153510 TGTGGTTATTATTTGGCAGCATACAA 59.846 34.615 0.00 0.00 0.00 2.41
2455 3821 6.682611 GCTTGTGGTTATTATTTGGCAGCATA 60.683 38.462 0.00 0.00 0.00 3.14
2456 3822 5.663456 CTTGTGGTTATTATTTGGCAGCAT 58.337 37.500 0.00 0.00 0.00 3.79
2457 3823 4.620332 GCTTGTGGTTATTATTTGGCAGCA 60.620 41.667 0.00 0.00 0.00 4.41
2458 3824 3.865164 GCTTGTGGTTATTATTTGGCAGC 59.135 43.478 0.00 0.00 0.00 5.25
2459 3825 5.070770 TGCTTGTGGTTATTATTTGGCAG 57.929 39.130 0.00 0.00 0.00 4.85
2460 3826 4.769488 TCTGCTTGTGGTTATTATTTGGCA 59.231 37.500 0.00 0.00 0.00 4.92
2462 3828 8.225603 ACTATCTGCTTGTGGTTATTATTTGG 57.774 34.615 0.00 0.00 0.00 3.28
2463 3829 9.113838 AGACTATCTGCTTGTGGTTATTATTTG 57.886 33.333 0.00 0.00 0.00 2.32
2467 3833 8.202137 GGTAAGACTATCTGCTTGTGGTTATTA 58.798 37.037 0.00 0.00 0.00 0.98
2470 3836 5.482526 TGGTAAGACTATCTGCTTGTGGTTA 59.517 40.000 0.00 0.00 0.00 2.85
2474 3840 3.868077 GCTGGTAAGACTATCTGCTTGTG 59.132 47.826 0.00 0.00 32.00 3.33
2476 3842 4.399004 AGCTGGTAAGACTATCTGCTTG 57.601 45.455 0.00 0.00 39.64 4.01
2478 3844 3.892588 GGTAGCTGGTAAGACTATCTGCT 59.107 47.826 0.00 2.90 43.57 4.24
2479 3845 3.637229 TGGTAGCTGGTAAGACTATCTGC 59.363 47.826 0.00 0.00 34.24 4.26
2487 3899 3.719871 TCTCCATTGGTAGCTGGTAAGA 58.280 45.455 1.86 0.00 34.03 2.10
2489 3901 5.450818 AATTCTCCATTGGTAGCTGGTAA 57.549 39.130 1.86 0.00 34.03 2.85
2490 3902 6.569127 TTAATTCTCCATTGGTAGCTGGTA 57.431 37.500 1.86 0.00 34.03 3.25
2499 3911 7.555554 AGTGAGTCTTCATTAATTCTCCATTGG 59.444 37.037 0.00 0.00 35.39 3.16
2513 3925 6.371825 TCGACGCATATATAGTGAGTCTTCAT 59.628 38.462 16.83 0.00 42.05 2.57
2514 3926 5.699458 TCGACGCATATATAGTGAGTCTTCA 59.301 40.000 16.83 4.68 42.05 3.02
2515 3927 6.166911 TCGACGCATATATAGTGAGTCTTC 57.833 41.667 16.83 0.49 42.05 2.87
2516 3928 6.555812 TTCGACGCATATATAGTGAGTCTT 57.444 37.500 16.83 0.00 42.05 3.01
2527 3939 9.503427 CACTCAAATATAGATTCGACGCATATA 57.497 33.333 0.00 0.00 0.00 0.86
2528 3940 7.489435 CCACTCAAATATAGATTCGACGCATAT 59.511 37.037 0.00 0.00 0.00 1.78
2529 3941 6.806739 CCACTCAAATATAGATTCGACGCATA 59.193 38.462 0.00 0.00 0.00 3.14
2531 3943 4.982295 CCACTCAAATATAGATTCGACGCA 59.018 41.667 0.00 0.00 0.00 5.24
2532 3944 4.143305 GCCACTCAAATATAGATTCGACGC 60.143 45.833 0.00 0.00 0.00 5.19
2533 3945 4.386049 GGCCACTCAAATATAGATTCGACG 59.614 45.833 0.00 0.00 0.00 5.12
2534 3946 5.297547 TGGCCACTCAAATATAGATTCGAC 58.702 41.667 0.00 0.00 0.00 4.20
2535 3947 5.545063 TGGCCACTCAAATATAGATTCGA 57.455 39.130 0.00 0.00 0.00 3.71
2536 3948 5.352569 GGATGGCCACTCAAATATAGATTCG 59.647 44.000 8.16 0.00 0.00 3.34
2537 3949 5.649831 GGGATGGCCACTCAAATATAGATTC 59.350 44.000 8.16 0.00 35.15 2.52
2538 3950 5.074929 TGGGATGGCCACTCAAATATAGATT 59.925 40.000 8.16 0.00 35.15 2.40
2539 3951 4.603171 TGGGATGGCCACTCAAATATAGAT 59.397 41.667 8.16 0.00 35.15 1.98
2541 3953 4.074970 GTGGGATGGCCACTCAAATATAG 58.925 47.826 8.16 0.00 35.53 1.31
2542 3954 3.181434 GGTGGGATGGCCACTCAAATATA 60.181 47.826 8.16 0.00 38.17 0.86
2543 3955 2.424812 GGTGGGATGGCCACTCAAATAT 60.425 50.000 8.16 0.00 38.17 1.28
2544 3956 1.064017 GGTGGGATGGCCACTCAAATA 60.064 52.381 8.16 0.00 38.17 1.40
2545 3957 0.324645 GGTGGGATGGCCACTCAAAT 60.325 55.000 8.16 0.00 38.17 2.32
2546 3958 1.076549 GGTGGGATGGCCACTCAAA 59.923 57.895 8.16 0.00 38.17 2.69
2547 3959 1.434513 AAGGTGGGATGGCCACTCAA 61.435 55.000 8.16 0.00 38.17 3.02
2548 3960 1.852157 AAGGTGGGATGGCCACTCA 60.852 57.895 8.16 5.54 38.17 3.41
2549 3961 1.379044 CAAGGTGGGATGGCCACTC 60.379 63.158 8.16 7.14 38.17 3.51
2551 3963 1.678970 GACAAGGTGGGATGGCCAC 60.679 63.158 8.16 1.35 37.44 5.01
2552 3964 2.763215 GACAAGGTGGGATGGCCA 59.237 61.111 8.56 8.56 35.15 5.36
2553 3965 2.043953 GGACAAGGTGGGATGGCC 60.044 66.667 0.00 0.00 37.62 5.36
2554 3966 2.043953 GGGACAAGGTGGGATGGC 60.044 66.667 0.00 0.00 0.00 4.40
2665 4082 7.353414 TGTGGATTCAACAAACCTATTGAAA 57.647 32.000 3.73 0.00 45.34 2.69
2681 4098 6.024049 CGTTGAATTTAGAAGCTGTGGATTC 58.976 40.000 0.00 0.00 38.05 2.52
2682 4099 5.705441 TCGTTGAATTTAGAAGCTGTGGATT 59.295 36.000 0.00 0.00 0.00 3.01
2683 4100 5.245531 TCGTTGAATTTAGAAGCTGTGGAT 58.754 37.500 0.00 0.00 0.00 3.41
2688 4105 7.582435 TCTAACTCGTTGAATTTAGAAGCTG 57.418 36.000 0.00 0.00 29.57 4.24
2691 4108 9.959775 GTGATTCTAACTCGTTGAATTTAGAAG 57.040 33.333 8.23 0.00 41.51 2.85
2734 4151 2.054453 GTTGGATGGAGCAAGGGGC 61.054 63.158 0.00 0.00 45.30 5.80
2735 4152 0.394899 GAGTTGGATGGAGCAAGGGG 60.395 60.000 0.00 0.00 0.00 4.79
2736 4153 0.394899 GGAGTTGGATGGAGCAAGGG 60.395 60.000 0.00 0.00 0.00 3.95
2737 4154 0.329261 TGGAGTTGGATGGAGCAAGG 59.671 55.000 0.00 0.00 0.00 3.61
2738 4155 2.426024 CAATGGAGTTGGATGGAGCAAG 59.574 50.000 0.00 0.00 34.06 4.01
2739 4156 2.449464 CAATGGAGTTGGATGGAGCAA 58.551 47.619 0.00 0.00 34.06 3.91
2740 4157 1.956636 GCAATGGAGTTGGATGGAGCA 60.957 52.381 0.00 0.00 38.29 4.26
2741 4158 0.743097 GCAATGGAGTTGGATGGAGC 59.257 55.000 0.00 0.00 38.29 4.70
2742 4159 1.019673 CGCAATGGAGTTGGATGGAG 58.980 55.000 0.00 0.00 38.29 3.86
2743 4160 1.031571 GCGCAATGGAGTTGGATGGA 61.032 55.000 0.30 0.00 38.29 3.41
2744 4161 1.434696 GCGCAATGGAGTTGGATGG 59.565 57.895 0.30 0.00 38.29 3.51
2745 4162 1.434696 GGCGCAATGGAGTTGGATG 59.565 57.895 10.83 0.00 38.29 3.51
2746 4163 1.754234 GGGCGCAATGGAGTTGGAT 60.754 57.895 10.83 0.00 38.29 3.41
2747 4164 2.361104 GGGCGCAATGGAGTTGGA 60.361 61.111 10.83 0.00 38.29 3.53
2748 4165 3.451894 GGGGCGCAATGGAGTTGG 61.452 66.667 10.83 0.00 38.29 3.77
2749 4166 1.978617 AAGGGGCGCAATGGAGTTG 60.979 57.895 10.83 0.00 40.90 3.16
2750 4167 1.978617 CAAGGGGCGCAATGGAGTT 60.979 57.895 10.83 0.00 0.00 3.01
2751 4168 2.361610 CAAGGGGCGCAATGGAGT 60.362 61.111 10.83 0.00 0.00 3.85
2760 4177 2.203126 GATGGAGCTCAAGGGGCG 60.203 66.667 17.19 0.00 34.52 6.13
2771 4188 2.009774 CGCTTGTACCTTTGGATGGAG 58.990 52.381 0.00 0.00 0.00 3.86
2777 4194 4.214545 TGTGATTTACGCTTGTACCTTTGG 59.785 41.667 0.00 0.00 0.00 3.28
2781 4198 3.007614 ACCTGTGATTTACGCTTGTACCT 59.992 43.478 0.00 0.00 0.00 3.08
2805 4225 2.472232 TATAGGACGCGCTGCCGATG 62.472 60.000 5.73 0.00 36.29 3.84
2807 4227 2.903350 TATAGGACGCGCTGCCGA 60.903 61.111 5.73 1.66 36.29 5.54
2848 4268 6.857964 GTCAATTCGTTGATTCACTCAATGTT 59.142 34.615 6.97 0.00 46.62 2.71
2849 4269 6.205464 AGTCAATTCGTTGATTCACTCAATGT 59.795 34.615 6.97 0.00 46.62 2.71
2851 4271 6.348786 CCAGTCAATTCGTTGATTCACTCAAT 60.349 38.462 0.00 0.00 45.36 2.57
2852 4272 5.049474 CCAGTCAATTCGTTGATTCACTCAA 60.049 40.000 0.00 0.00 41.61 3.02
2853 4273 4.452114 CCAGTCAATTCGTTGATTCACTCA 59.548 41.667 0.00 0.00 33.02 3.41
2865 4297 2.286294 GCTCTACATGCCAGTCAATTCG 59.714 50.000 0.00 0.00 0.00 3.34
2866 4298 3.273434 TGCTCTACATGCCAGTCAATTC 58.727 45.455 0.00 0.00 0.00 2.17
2872 4304 2.566833 TTGTTGCTCTACATGCCAGT 57.433 45.000 0.00 0.00 0.00 4.00
2876 4308 3.365820 GTGCATTTTGTTGCTCTACATGC 59.634 43.478 0.00 0.00 43.18 4.06
2892 4324 6.379133 ACCATGAAGATCATAAGTTGTGCATT 59.621 34.615 0.00 0.00 34.28 3.56
2894 4326 5.255687 ACCATGAAGATCATAAGTTGTGCA 58.744 37.500 0.00 0.00 34.28 4.57
2898 4330 6.313658 TCGTCAACCATGAAGATCATAAGTTG 59.686 38.462 19.39 19.39 43.90 3.16
2901 4333 5.050499 GCTCGTCAACCATGAAGATCATAAG 60.050 44.000 0.00 0.00 42.05 1.73
2908 4340 0.976641 AGGCTCGTCAACCATGAAGA 59.023 50.000 0.00 0.00 40.97 2.87
2909 4341 1.081892 CAGGCTCGTCAACCATGAAG 58.918 55.000 0.00 0.00 37.30 3.02
2927 4359 4.318332 GAGTGAAGACAATGTCACCATCA 58.682 43.478 16.38 10.86 44.30 3.07
2933 4365 2.135139 GCACGAGTGAAGACAATGTCA 58.865 47.619 16.38 0.00 34.60 3.58
2934 4366 2.135139 TGCACGAGTGAAGACAATGTC 58.865 47.619 5.02 5.02 0.00 3.06
2954 4386 6.422701 CAGTCATGAAGTTTTGTGATGCAATT 59.577 34.615 0.00 0.00 36.89 2.32
2957 4389 4.579753 TCAGTCATGAAGTTTTGTGATGCA 59.420 37.500 0.00 0.00 30.61 3.96
3006 4439 1.134340 ACCCTACAACTTGCACGTGAA 60.134 47.619 22.23 5.66 0.00 3.18
3008 4441 0.586319 CACCCTACAACTTGCACGTG 59.414 55.000 12.28 12.28 0.00 4.49
3011 4444 1.961793 TCACACCCTACAACTTGCAC 58.038 50.000 0.00 0.00 0.00 4.57
3038 4472 3.306917 TGCATGCTTTGTTTCATGAGG 57.693 42.857 20.33 0.00 41.82 3.86
3042 4476 5.753744 CAAAACATGCATGCTTTGTTTCAT 58.246 33.333 32.87 23.47 38.42 2.57
3059 4493 3.855858 GACTTGACCTTTTGGCAAAACA 58.144 40.909 20.81 14.64 45.59 2.83


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

AutoCloner maintained by Alex Coulton.