Multiple sequence alignment - TraesCS3B01G233100

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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 TraesCS3B01G233100 chr3B 100.000 3797 0 0 1 3797 360012537 360008741 0.000000e+00 7012.0
1 TraesCS3B01G233100 chr7B 97.592 2824 65 3 1 2822 483803985 483806807 0.000000e+00 4835.0
2 TraesCS3B01G233100 chr7B 97.094 2822 77 5 1 2819 304090370 304087551 0.000000e+00 4752.0
3 TraesCS3B01G233100 chr7B 87.059 85 8 2 3704 3785 727069210 727069294 4.040000e-15 93.5
4 TraesCS3B01G233100 chr4B 97.485 2823 68 3 1 2821 581206878 581209699 0.000000e+00 4817.0
5 TraesCS3B01G233100 chr4B 97.414 2823 70 3 1 2821 47024868 47022047 0.000000e+00 4806.0
6 TraesCS3B01G233100 chr6A 97.384 2829 71 3 1 2827 534646657 534643830 0.000000e+00 4811.0
7 TraesCS3B01G233100 chr5B 97.414 2823 70 3 1 2821 9841911 9839090 0.000000e+00 4806.0
8 TraesCS3B01G233100 chr2B 97.236 2822 74 4 1 2819 370338840 370341660 0.000000e+00 4776.0
9 TraesCS3B01G233100 chr2B 97.061 2824 78 5 1 2822 133001897 133004717 0.000000e+00 4750.0
10 TraesCS3B01G233100 chr2B 96.919 2824 81 5 1 2820 545417357 545420178 0.000000e+00 4728.0
11 TraesCS3B01G233100 chr3A 89.408 963 89 10 2846 3797 357519490 357520450 0.000000e+00 1201.0


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 TraesCS3B01G233100 chr3B 360008741 360012537 3796 True 7012 7012 100.000 1 3797 1 chr3B.!!$R1 3796
1 TraesCS3B01G233100 chr7B 483803985 483806807 2822 False 4835 4835 97.592 1 2822 1 chr7B.!!$F1 2821
2 TraesCS3B01G233100 chr7B 304087551 304090370 2819 True 4752 4752 97.094 1 2819 1 chr7B.!!$R1 2818
3 TraesCS3B01G233100 chr4B 581206878 581209699 2821 False 4817 4817 97.485 1 2821 1 chr4B.!!$F1 2820
4 TraesCS3B01G233100 chr4B 47022047 47024868 2821 True 4806 4806 97.414 1 2821 1 chr4B.!!$R1 2820
5 TraesCS3B01G233100 chr6A 534643830 534646657 2827 True 4811 4811 97.384 1 2827 1 chr6A.!!$R1 2826
6 TraesCS3B01G233100 chr5B 9839090 9841911 2821 True 4806 4806 97.414 1 2821 1 chr5B.!!$R1 2820
7 TraesCS3B01G233100 chr2B 370338840 370341660 2820 False 4776 4776 97.236 1 2819 1 chr2B.!!$F2 2818
8 TraesCS3B01G233100 chr2B 133001897 133004717 2820 False 4750 4750 97.061 1 2822 1 chr2B.!!$F1 2821
9 TraesCS3B01G233100 chr2B 545417357 545420178 2821 False 4728 4728 96.919 1 2820 1 chr2B.!!$F3 2819
10 TraesCS3B01G233100 chr3A 357519490 357520450 960 False 1201 1201 89.408 2846 3797 1 chr3A.!!$F1 951

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
306 308 0.177604 CCCAAAGTGCTTTTGTGCCA 59.822 50.0 11.52 0.0 43.78 4.92 F
826 830 0.916086 ATCGGGGCAAATGGTGAGTA 59.084 50.0 0.00 0.0 0.00 2.59 F
1546 1550 1.118838 CACTCCTAGAAGAGGGCAGG 58.881 60.0 0.00 0.0 46.70 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1417 0.181350 GAGAATCCACTCCGGCCATT 59.819 55.000 2.24 0.00 33.14 3.16 R
1948 1952 1.202533 AGTATCTTCATGCCCGTTCGG 60.203 52.381 4.08 4.08 0.00 4.30 R
3457 3469 0.179034 GGAGATGGATCCAGCACCAC 60.179 60.000 33.43 20.15 41.51 4.16 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
211 213 8.177119 TCAATTTAGACCAATTAGTTTGTGCT 57.823 30.769 0.00 0.00 33.15 4.40
306 308 0.177604 CCCAAAGTGCTTTTGTGCCA 59.822 50.000 11.52 0.00 43.78 4.92
610 613 2.640332 GGACCCTCTCTCCCCATATTTC 59.360 54.545 0.00 0.00 0.00 2.17
646 650 1.219393 GGCCTGACTGCACTCCTAC 59.781 63.158 0.00 0.00 0.00 3.18
655 659 2.774234 ACTGCACTCCTACCTAATGCAT 59.226 45.455 0.00 0.00 44.73 3.96
826 830 0.916086 ATCGGGGCAAATGGTGAGTA 59.084 50.000 0.00 0.00 0.00 2.59
940 944 9.347240 CTCTCAATGACAAATATTTGGGTCTAT 57.653 33.333 27.43 13.47 42.34 1.98
999 1003 8.433421 TCCAATTCTTAATAGACCGAATTGTC 57.567 34.615 17.45 0.00 45.46 3.18
1247 1251 2.178984 ACCAAGGAGGAATGGGTTTTCA 59.821 45.455 0.00 0.00 41.17 2.69
1413 1417 2.483877 CTCTTTCACGTGGCAAAGCATA 59.516 45.455 19.64 7.00 30.84 3.14
1546 1550 1.118838 CACTCCTAGAAGAGGGCAGG 58.881 60.000 0.00 0.00 46.70 4.85
1868 1872 6.646240 GCAAAAGTGAAGATCTTTATTTGGCA 59.354 34.615 22.68 9.77 34.59 4.92
1894 1898 1.378762 CATGGAACCCTCCCGTGTT 59.621 57.895 0.00 0.00 41.64 3.32
1906 1910 3.493002 CCTCCCGTGTTGTGTTACACTTA 60.493 47.826 16.79 2.07 44.85 2.24
1948 1952 1.454479 CCCACCTGCCCATCATGTC 60.454 63.158 0.00 0.00 0.00 3.06
2026 2030 1.780309 TGTGGGAGAAACTGGGATTGT 59.220 47.619 0.00 0.00 0.00 2.71
2036 2040 1.338769 ACTGGGATTGTACGAAGCCAC 60.339 52.381 12.34 5.04 0.00 5.01
2148 2152 3.729526 CAGAATGTTCGCGAACTGATT 57.270 42.857 41.46 34.29 41.67 2.57
2238 2242 2.214376 ACCAAATTTCGATGGGAGCA 57.786 45.000 7.65 0.00 0.00 4.26
2266 2270 8.749499 GTGCTATAACGACGAACTATGTTATTT 58.251 33.333 0.00 0.00 38.23 1.40
2275 2279 5.826208 ACGAACTATGTTATTTCCCAATCCC 59.174 40.000 0.00 0.00 0.00 3.85
2363 2370 4.091945 CGATGCTTCTTTCGATCAAGACAA 59.908 41.667 0.00 0.00 37.55 3.18
2408 2415 8.982723 AGCTGTACTTAGAGATGATAAAGGAAA 58.017 33.333 0.00 0.00 0.00 3.13
2486 2493 0.596082 GCCATGGCACTACGTTTTGT 59.404 50.000 32.08 0.00 41.49 2.83
2506 2513 9.296400 GTTTTGTCTTATTACTTGCACAAAAGA 57.704 29.630 7.78 0.00 41.78 2.52
2508 2515 7.561021 TGTCTTATTACTTGCACAAAAGACA 57.439 32.000 17.39 17.39 45.30 3.41
2545 2552 6.932400 ACTTGTTGTTAACTCCGACAATATGA 59.068 34.615 7.22 0.00 37.98 2.15
2577 2584 4.778579 ACATGATGAAGAATGGAGGACAG 58.221 43.478 0.00 0.00 0.00 3.51
2582 2589 3.242867 TGAAGAATGGAGGACAGACAGT 58.757 45.455 0.00 0.00 0.00 3.55
2842 2851 3.347958 CACAAACGGTATGTGCAACTT 57.652 42.857 4.86 0.00 41.42 2.66
2843 2852 3.296628 CACAAACGGTATGTGCAACTTC 58.703 45.455 4.86 0.00 41.42 3.01
2844 2853 2.946329 ACAAACGGTATGTGCAACTTCA 59.054 40.909 0.00 0.00 38.04 3.02
2896 2907 6.056884 ACCCTAAAATTGACACTTACGACAA 58.943 36.000 0.00 0.00 0.00 3.18
2901 2912 7.964545 AAAATTGACACTTACGACAAAGAAC 57.035 32.000 0.00 0.00 0.00 3.01
2904 2915 7.956420 ATTGACACTTACGACAAAGAACATA 57.044 32.000 0.00 0.00 0.00 2.29
2905 2916 6.758593 TGACACTTACGACAAAGAACATAC 57.241 37.500 0.00 0.00 0.00 2.39
2912 2923 9.701098 ACTTACGACAAAGAACATACTAAATCA 57.299 29.630 0.00 0.00 0.00 2.57
2933 2944 6.345096 TCAGGAATCTTTCAAATTTGACCC 57.655 37.500 20.35 13.49 36.83 4.46
2971 2982 5.242838 TCCTTCCACATTTTACCATTGACAC 59.757 40.000 0.00 0.00 0.00 3.67
3009 3021 3.992943 ACTGTTCATCCCGATTTGGTA 57.007 42.857 0.00 0.00 35.15 3.25
3010 3022 4.503714 ACTGTTCATCCCGATTTGGTAT 57.496 40.909 0.00 0.00 35.15 2.73
3023 3035 4.746115 CGATTTGGTATTGATTTGGCATGG 59.254 41.667 0.00 0.00 0.00 3.66
3029 3041 0.678395 TTGATTTGGCATGGCACGTT 59.322 45.000 23.26 9.51 0.00 3.99
3051 3063 7.148557 ACGTTGTCGGTTTTTCAAATTTCATTT 60.149 29.630 0.00 0.00 41.85 2.32
3087 3099 5.461032 TTTTTCACACACTTTGACCAGTT 57.539 34.783 0.00 0.00 0.00 3.16
3097 3109 4.157656 CACTTTGACCAGTTTTTGTGAGGA 59.842 41.667 0.00 0.00 0.00 3.71
3098 3110 4.956075 ACTTTGACCAGTTTTTGTGAGGAT 59.044 37.500 0.00 0.00 0.00 3.24
3102 3114 3.074412 ACCAGTTTTTGTGAGGATAGCG 58.926 45.455 0.00 0.00 0.00 4.26
3129 3141 4.762825 GTGACTACGCACACCCAA 57.237 55.556 0.00 0.00 38.63 4.12
3131 3143 0.949105 GTGACTACGCACACCCAAGG 60.949 60.000 0.00 0.00 38.63 3.61
3134 3146 1.189524 ACTACGCACACCCAAGGCTA 61.190 55.000 0.00 0.00 0.00 3.93
3135 3147 0.460284 CTACGCACACCCAAGGCTAG 60.460 60.000 0.00 0.00 0.00 3.42
3141 3153 2.928396 ACCCAAGGCTAGCCACGT 60.928 61.111 34.70 20.64 38.92 4.49
3146 3158 3.358076 AAGGCTAGCCACGTCGAGC 62.358 63.158 34.70 5.08 38.92 5.03
3153 3165 2.126307 CCACGTCGAGCTGGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
3161 3173 3.941657 GAGCTGGTCTGGTCGCACC 62.942 68.421 0.00 0.00 39.22 5.01
3169 3181 3.879844 TGGTCGCACCAGGTAGTT 58.120 55.556 0.00 0.00 44.79 2.24
3173 3185 0.032952 GTCGCACCAGGTAGTTGTCA 59.967 55.000 0.00 0.00 0.00 3.58
3180 3192 1.610624 CCAGGTAGTTGTCACGCCAAT 60.611 52.381 0.00 0.00 0.00 3.16
3182 3194 2.095768 CAGGTAGTTGTCACGCCAATTG 60.096 50.000 0.00 0.00 0.00 2.32
3189 3201 2.106074 TCACGCCAATTGCTAGCCG 61.106 57.895 13.29 9.77 38.05 5.52
3190 3202 2.046314 ACGCCAATTGCTAGCCGT 60.046 55.556 13.29 10.47 38.05 5.68
3195 3207 2.045708 CAATTGCTAGCCGTGCCCA 61.046 57.895 13.29 0.00 0.00 5.36
3223 3235 3.321648 TGGTGGACAGAGCGCCAT 61.322 61.111 2.29 0.00 36.41 4.40
3243 3255 3.721087 TGACCCCATCTTTCCTTTCTC 57.279 47.619 0.00 0.00 0.00 2.87
3288 3300 2.689034 CTGTCCTCCCACTCCCCC 60.689 72.222 0.00 0.00 0.00 5.40
3291 3303 1.996187 GTCCTCCCACTCCCCCTTC 60.996 68.421 0.00 0.00 0.00 3.46
3295 3307 0.621082 CTCCCACTCCCCCTTCTTTC 59.379 60.000 0.00 0.00 0.00 2.62
3296 3308 0.104144 TCCCACTCCCCCTTCTTTCA 60.104 55.000 0.00 0.00 0.00 2.69
3303 3315 3.657727 ACTCCCCCTTCTTTCATTTCTCA 59.342 43.478 0.00 0.00 0.00 3.27
3306 3318 4.292041 TCCCCCTTCTTTCATTTCTCATCA 59.708 41.667 0.00 0.00 0.00 3.07
3321 3333 0.448990 CATCAACGGTGCAGTCATGG 59.551 55.000 0.00 0.00 0.00 3.66
3323 3335 3.049674 AACGGTGCAGTCATGGCG 61.050 61.111 0.00 0.00 0.00 5.69
3337 3349 1.521457 TGGCGATCAAGGCGACATC 60.521 57.895 0.00 0.00 42.70 3.06
3353 3365 3.371097 ATCGCGTTGGACGGAGCAT 62.371 57.895 5.77 0.00 42.82 3.79
3354 3366 3.853330 CGCGTTGGACGGAGCATG 61.853 66.667 0.00 0.00 42.82 4.06
3411 3423 3.033909 TGTCCATCTCCTCCATGTACTG 58.966 50.000 0.00 0.00 0.00 2.74
3425 3437 4.305769 CATGTACTGATTAGCTCTGCCTC 58.694 47.826 0.00 0.00 0.00 4.70
3426 3438 3.636679 TGTACTGATTAGCTCTGCCTCT 58.363 45.455 0.00 0.00 0.00 3.69
3427 3439 3.382865 TGTACTGATTAGCTCTGCCTCTG 59.617 47.826 0.00 0.00 0.00 3.35
3439 3451 3.466836 TCTGCCTCTGTTGTGTTACTTG 58.533 45.455 0.00 0.00 0.00 3.16
3457 3469 4.973396 ACTTGTAATGCATGTCAATGTCG 58.027 39.130 14.33 7.83 36.08 4.35
3463 3475 0.454957 GCATGTCAATGTCGTGGTGC 60.455 55.000 2.26 0.00 36.08 5.01
3470 3482 0.392998 AATGTCGTGGTGCTGGATCC 60.393 55.000 4.20 4.20 0.00 3.36
3471 3483 1.552799 ATGTCGTGGTGCTGGATCCA 61.553 55.000 15.27 15.27 0.00 3.41
3504 3521 1.236628 GATCTGCTCCATGTCCATGC 58.763 55.000 1.64 0.00 37.49 4.06
3519 3536 4.404394 TGTCCATGCCGTTATCTTCTTCTA 59.596 41.667 0.00 0.00 0.00 2.10
3568 3585 9.143155 TGTACTAATTGCTGAAGATATGGTCTA 57.857 33.333 0.00 0.00 35.67 2.59
3603 3620 2.416972 GCGTGACTTCGAAGATAGGGTT 60.417 50.000 31.08 7.05 35.04 4.11
3611 3628 7.012661 ACTTCGAAGATAGGGTTTTAAGGAA 57.987 36.000 31.08 0.00 35.04 3.36
3624 3641 5.209977 GTTTTAAGGAATGTTGACACGACC 58.790 41.667 0.00 0.00 0.00 4.79
3629 3646 3.315191 AGGAATGTTGACACGACCAAAAG 59.685 43.478 0.00 0.00 0.00 2.27
3630 3647 3.550030 GGAATGTTGACACGACCAAAAGG 60.550 47.826 0.00 0.00 0.00 3.11
3663 3680 2.563179 TCAGGACTGAAGCACTAACCTC 59.437 50.000 0.00 0.00 36.53 3.85
3734 3753 5.365619 TGGTTAGAGTGGTCAGAAAAGTTC 58.634 41.667 0.00 0.00 0.00 3.01
3748 3767 6.489700 TCAGAAAAGTTCAGTTATTGGCATGA 59.510 34.615 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 203 8.098286 ACTTTATACACCACATAGCACAAACTA 58.902 33.333 0.00 0.00 0.00 2.24
447 449 6.823689 GCCTAGTCTCAACATGATTTCCTTTA 59.176 38.462 0.00 0.00 0.00 1.85
545 548 4.949856 TGGTTTGAAGCTCTCTGTTTCTTT 59.050 37.500 0.00 0.00 36.91 2.52
610 613 4.007659 AGGCCTTCCGTACATAACAAAAG 58.992 43.478 0.00 0.00 37.47 2.27
655 659 8.722622 ATTCCGGAAATACTTCTATTCTCCTA 57.277 34.615 23.08 0.00 0.00 2.94
940 944 4.649267 TGTCCATACCCACATTTGAAGA 57.351 40.909 0.00 0.00 0.00 2.87
999 1003 4.523943 TCCTTCCAACCACTGATTTTCATG 59.476 41.667 0.00 0.00 0.00 3.07
1065 1069 4.910458 AGTTGGGATAGCTTGTACAACT 57.090 40.909 16.10 16.10 42.40 3.16
1247 1251 6.350445 GGCCAGATTGAAACAATGTATGTCTT 60.350 38.462 0.00 0.00 42.99 3.01
1413 1417 0.181350 GAGAATCCACTCCGGCCATT 59.819 55.000 2.24 0.00 33.14 3.16
1868 1872 3.053826 GGGAGGGTTCCATGTAAGGTAT 58.946 50.000 0.00 0.00 45.98 2.73
1906 1910 7.441458 GGGCGAAACTTTCATATGTCTATTAGT 59.559 37.037 1.90 0.00 0.00 2.24
1948 1952 1.202533 AGTATCTTCATGCCCGTTCGG 60.203 52.381 4.08 4.08 0.00 4.30
2238 2242 2.907910 AGTTCGTCGTTATAGCACGT 57.092 45.000 9.84 0.00 41.16 4.49
2266 2270 2.173299 TTGCCTTGGGGGATTGGGA 61.173 57.895 0.00 0.00 37.23 4.37
2275 2279 6.340522 CCTCTATTTTATTTGTTGCCTTGGG 58.659 40.000 0.00 0.00 0.00 4.12
2363 2370 2.581354 CCGCTGTGCCTCTAAGCT 59.419 61.111 0.00 0.00 34.72 3.74
2408 2415 7.457535 TCTTCCAATTCCCTCCAACAATAAATT 59.542 33.333 0.00 0.00 0.00 1.82
2486 2493 6.995686 TCCTGTCTTTTGTGCAAGTAATAAGA 59.004 34.615 0.00 0.00 0.00 2.10
2506 2513 3.118519 ACAACAAGTCGGTTACTTCCTGT 60.119 43.478 0.00 0.00 45.64 4.00
2508 2515 3.832615 ACAACAAGTCGGTTACTTCCT 57.167 42.857 0.00 0.00 45.64 3.36
2545 2552 7.884877 TCCATTCTTCATCATGTCAACTACTTT 59.115 33.333 0.00 0.00 0.00 2.66
2822 2831 3.242903 TGAAGTTGCACATACCGTTTGTG 60.243 43.478 15.47 15.47 45.74 3.33
2823 2832 2.946329 TGAAGTTGCACATACCGTTTGT 59.054 40.909 0.00 0.00 0.00 2.83
2824 2833 3.617540 TGAAGTTGCACATACCGTTTG 57.382 42.857 0.00 0.00 0.00 2.93
2825 2834 7.801716 ATATATGAAGTTGCACATACCGTTT 57.198 32.000 0.00 0.00 32.90 3.60
2828 2837 8.957028 CAAAAATATATGAAGTTGCACATACCG 58.043 33.333 0.00 0.00 32.90 4.02
2867 2876 9.118300 TCGTAAGTGTCAATTTTAGGGTAAAAA 57.882 29.630 0.00 0.00 38.78 1.94
2872 2881 5.613329 TGTCGTAAGTGTCAATTTTAGGGT 58.387 37.500 0.00 0.00 39.48 4.34
2875 2886 9.155053 GTTCTTTGTCGTAAGTGTCAATTTTAG 57.845 33.333 0.00 0.00 39.48 1.85
2885 2896 9.953825 GATTTAGTATGTTCTTTGTCGTAAGTG 57.046 33.333 0.00 0.00 39.48 3.16
2886 2897 9.701098 TGATTTAGTATGTTCTTTGTCGTAAGT 57.299 29.630 0.00 0.00 39.48 2.24
2891 2902 7.827819 TCCTGATTTAGTATGTTCTTTGTCG 57.172 36.000 0.00 0.00 0.00 4.35
2912 2923 5.406163 AGGGGTCAAATTTGAAAGATTCCT 58.594 37.500 22.07 17.17 39.21 3.36
2933 2944 9.942850 AAATGTGGAAGGAATGTTTAAATTAGG 57.057 29.630 0.00 0.00 0.00 2.69
2961 2972 3.169908 GGGGGTAATTTGTGTCAATGGT 58.830 45.455 0.00 0.00 0.00 3.55
2971 2982 7.445945 TGAACAGTAAAAATGGGGGTAATTTG 58.554 34.615 0.00 0.00 0.00 2.32
3009 3021 0.896923 ACGTGCCATGCCAAATCAAT 59.103 45.000 0.00 0.00 0.00 2.57
3010 3022 0.678395 AACGTGCCATGCCAAATCAA 59.322 45.000 0.00 0.00 0.00 2.57
3023 3035 1.897641 TTGAAAAACCGACAACGTGC 58.102 45.000 0.00 0.00 37.88 5.34
3072 3084 4.804108 TCACAAAAACTGGTCAAAGTGTG 58.196 39.130 0.00 0.00 0.00 3.82
3073 3085 4.082245 CCTCACAAAAACTGGTCAAAGTGT 60.082 41.667 0.00 0.00 0.00 3.55
3074 3086 4.157656 TCCTCACAAAAACTGGTCAAAGTG 59.842 41.667 0.00 0.00 0.00 3.16
3076 3088 4.981806 TCCTCACAAAAACTGGTCAAAG 57.018 40.909 0.00 0.00 0.00 2.77
3079 3091 4.072131 GCTATCCTCACAAAAACTGGTCA 58.928 43.478 0.00 0.00 0.00 4.02
3084 3096 3.751698 GGTTCGCTATCCTCACAAAAACT 59.248 43.478 0.00 0.00 0.00 2.66
3087 3099 2.343101 CGGTTCGCTATCCTCACAAAA 58.657 47.619 0.00 0.00 0.00 2.44
3097 3109 4.524318 CACCCGCCGGTTCGCTAT 62.524 66.667 1.90 0.00 42.04 2.97
3102 3114 2.125793 GTAGTCACCCGCCGGTTC 60.126 66.667 1.90 0.00 42.04 3.62
3118 3130 2.347490 CTAGCCTTGGGTGTGCGT 59.653 61.111 1.12 0.00 0.00 5.24
3122 3134 2.757077 GTGGCTAGCCTTGGGTGT 59.243 61.111 33.07 0.00 36.94 4.16
3129 3141 3.827898 GCTCGACGTGGCTAGCCT 61.828 66.667 33.07 14.87 36.94 4.58
3131 3143 2.580867 CAGCTCGACGTGGCTAGC 60.581 66.667 6.04 6.04 37.00 3.42
3134 3146 4.057428 GACCAGCTCGACGTGGCT 62.057 66.667 8.02 11.04 37.34 4.75
3135 3147 4.057428 AGACCAGCTCGACGTGGC 62.057 66.667 8.02 5.35 37.34 5.01
3141 3153 3.749064 GCGACCAGACCAGCTCGA 61.749 66.667 0.00 0.00 0.00 4.04
3153 3165 0.669625 GACAACTACCTGGTGCGACC 60.670 60.000 10.23 0.00 36.69 4.79
3161 3173 1.808411 ATTGGCGTGACAACTACCTG 58.192 50.000 0.00 0.00 32.39 4.00
3180 3192 4.715523 GGTGGGCACGGCTAGCAA 62.716 66.667 18.24 0.00 0.00 3.91
3189 3201 4.626081 ACACGAGCTGGTGGGCAC 62.626 66.667 29.18 0.00 42.23 5.01
3190 3202 4.624364 CACACGAGCTGGTGGGCA 62.624 66.667 29.18 0.00 42.23 5.36
3195 3207 2.842462 TCCACCACACGAGCTGGT 60.842 61.111 0.00 0.00 43.22 4.00
3210 3222 2.512515 GGTCATGGCGCTCTGTCC 60.513 66.667 7.64 8.74 0.00 4.02
3213 3225 3.411114 ATGGGGTCATGGCGCTCTG 62.411 63.158 14.52 5.28 31.34 3.35
3223 3235 2.027192 CGAGAAAGGAAAGATGGGGTCA 60.027 50.000 0.00 0.00 0.00 4.02
3288 3300 6.082338 CACCGTTGATGAGAAATGAAAGAAG 58.918 40.000 0.00 0.00 0.00 2.85
3291 3303 4.161333 GCACCGTTGATGAGAAATGAAAG 58.839 43.478 0.00 0.00 0.00 2.62
3295 3307 2.485426 ACTGCACCGTTGATGAGAAATG 59.515 45.455 0.00 0.00 0.00 2.32
3296 3308 2.744202 GACTGCACCGTTGATGAGAAAT 59.256 45.455 0.00 0.00 0.00 2.17
3303 3315 1.308069 GCCATGACTGCACCGTTGAT 61.308 55.000 0.00 0.00 0.00 2.57
3306 3318 2.803155 ATCGCCATGACTGCACCGTT 62.803 55.000 0.00 0.00 0.00 4.44
3321 3333 2.923854 CGATGTCGCCTTGATCGC 59.076 61.111 0.00 0.00 33.26 4.58
3335 3347 3.371097 ATGCTCCGTCCAACGCGAT 62.371 57.895 15.93 0.00 40.91 4.58
3337 3349 3.853330 CATGCTCCGTCCAACGCG 61.853 66.667 3.53 3.53 40.91 6.01
3339 3351 3.027170 GCACATGCTCCGTCCAACG 62.027 63.158 0.00 0.00 38.62 4.10
3341 3353 2.359850 GGCACATGCTCCGTCCAA 60.360 61.111 3.48 0.00 41.70 3.53
3367 3379 2.280628 GACATGGAGGAAAGCTTACCG 58.719 52.381 0.00 0.00 0.00 4.02
3383 3395 2.053244 GGAGGAGATGGACATGGACAT 58.947 52.381 0.00 0.23 0.00 3.06
3411 3423 2.935201 CACAACAGAGGCAGAGCTAATC 59.065 50.000 0.00 0.00 0.00 1.75
3425 3437 6.437928 ACATGCATTACAAGTAACACAACAG 58.562 36.000 0.00 0.00 0.00 3.16
3426 3438 6.038714 TGACATGCATTACAAGTAACACAACA 59.961 34.615 0.00 0.00 28.28 3.33
3427 3439 6.434596 TGACATGCATTACAAGTAACACAAC 58.565 36.000 0.00 0.00 28.28 3.32
3439 3451 3.126858 ACCACGACATTGACATGCATTAC 59.873 43.478 0.00 0.00 33.05 1.89
3457 3469 0.179034 GGAGATGGATCCAGCACCAC 60.179 60.000 33.43 20.15 41.51 4.16
3490 3507 0.463654 TAACGGCATGGACATGGAGC 60.464 55.000 13.63 0.00 39.16 4.70
3499 3516 6.226787 AGAATAGAAGAAGATAACGGCATGG 58.773 40.000 0.00 0.00 0.00 3.66
3504 3521 7.812191 CAGATGGAGAATAGAAGAAGATAACGG 59.188 40.741 0.00 0.00 0.00 4.44
3519 3536 7.285566 ACACAAATATGTAGCAGATGGAGAAT 58.714 34.615 0.00 0.00 37.82 2.40
3584 3601 6.313164 CCTTAAAACCCTATCTTCGAAGTCAC 59.687 42.308 23.85 0.00 0.00 3.67
3603 3620 4.452825 TGGTCGTGTCAACATTCCTTAAA 58.547 39.130 0.00 0.00 0.00 1.52
3611 3628 1.336755 GCCTTTTGGTCGTGTCAACAT 59.663 47.619 0.00 0.00 42.99 2.71
3624 3641 3.323243 CTGAAGAAAGCCATGCCTTTTG 58.677 45.455 2.80 0.00 35.31 2.44
3629 3646 0.813821 GTCCTGAAGAAAGCCATGCC 59.186 55.000 0.00 0.00 0.00 4.40
3630 3647 1.471684 CAGTCCTGAAGAAAGCCATGC 59.528 52.381 0.00 0.00 0.00 4.06
3663 3680 4.750098 ACATAACTGGACTTTCTTGACACG 59.250 41.667 0.00 0.00 0.00 4.49
3710 3727 5.367945 ACTTTTCTGACCACTCTAACCAA 57.632 39.130 0.00 0.00 0.00 3.67
3734 3753 6.072286 ACTCTTCAAAGTCATGCCAATAACTG 60.072 38.462 0.00 0.00 0.00 3.16
3748 3767 7.865706 AGACACATAAACAACTCTTCAAAGT 57.134 32.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.