Multiple sequence alignment - TraesCS4D01G097700

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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 TraesCS4D01G097700 chr4D 100.000 3710 0 0 1 3710 74354118 74357827 0.000000e+00 6852
1 TraesCS4D01G097700 chr4B 92.849 3412 174 36 61 3449 106822378 106825742 0.000000e+00 4885
2 TraesCS4D01G097700 chr4B 87.591 137 15 2 3523 3658 106825742 106825877 1.380000e-34 158
3 TraesCS4D01G097700 chr4A 93.826 1976 102 6 740 2710 513330267 513328307 0.000000e+00 2955
4 TraesCS4D01G097700 chr4A 92.215 745 43 8 4 744 513340607 513339874 0.000000e+00 1040
5 TraesCS4D01G097700 chr4A 83.588 524 29 24 2708 3226 513328000 513327529 4.400000e-119 438
6 TraesCS4D01G097700 chr4A 85.050 301 35 6 3412 3710 513327396 513327104 7.790000e-77 298


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 TraesCS4D01G097700 chr4D 74354118 74357827 3709 False 6852.000000 6852 100.000 1 3710 1 chr4D.!!$F1 3709
1 TraesCS4D01G097700 chr4B 106822378 106825877 3499 False 2521.500000 4885 90.220 61 3658 2 chr4B.!!$F1 3597
2 TraesCS4D01G097700 chr4A 513327104 513330267 3163 True 1230.333333 2955 87.488 740 3710 3 chr4A.!!$R2 2970
3 TraesCS4D01G097700 chr4A 513339874 513340607 733 True 1040.000000 1040 92.215 4 744 1 chr4A.!!$R1 740

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
778 787 0.322277 CAACCTGATGCTGTGAGGCT 60.322 55.0 0.00 0.00 33.99 4.58 F
918 928 0.895530 ATACGACAGTGGTCAGTGGG 59.104 55.0 10.15 4.66 44.54 4.61 F
1115 1125 0.951558 CCACTGCGGCTAAACAAAGT 59.048 50.0 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1816 0.107945 GGCTGCGAGAGAATCCTTGT 60.108 55.0 0.00 0.0 33.66 3.16 R
2424 2439 0.916086 ATGGTATCGGGCCAGACAAA 59.084 50.0 8.08 0.0 39.65 2.83 R
3071 3396 0.551396 TCCTGGATCAGTCTCGCCTA 59.449 55.0 0.00 0.0 0.00 3.93 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
29 30 1.601903 GTCCAGCAATTTGTCACACGA 59.398 47.619 0.00 0.00 0.00 4.35
56 57 2.374170 GGGGAACTAGGTCCAAAGTTGA 59.626 50.000 28.03 0.00 39.70 3.18
91 92 8.685838 TCAGTGCCTTTACTAAACAGTTATTT 57.314 30.769 0.00 0.00 0.00 1.40
132 133 7.040892 ACTGCATAGCATAAATGTACATCAAGG 60.041 37.037 9.23 3.36 38.13 3.61
274 276 9.430623 CTGTAAATAAAATAAAACCTGTTGGGG 57.569 33.333 0.00 0.00 40.03 4.96
341 345 4.537135 ATGAGTGAAAGGATACACGTGT 57.463 40.909 26.52 26.52 41.22 4.49
344 348 4.056050 GAGTGAAAGGATACACGTGTTGT 58.944 43.478 28.55 16.23 42.84 3.32
540 549 7.113658 TGTGCAAAATAAGGTTTACTTCCAA 57.886 32.000 0.00 0.00 40.64 3.53
602 611 5.507180 GGTTTATCTTTCTTTTTAGCGTCGC 59.493 40.000 9.80 9.80 0.00 5.19
612 621 1.279527 TTAGCGTCGCCGTTGACTTG 61.280 55.000 14.86 0.00 36.71 3.16
613 622 2.410638 TAGCGTCGCCGTTGACTTGT 62.411 55.000 14.86 0.00 36.71 3.16
617 626 1.153329 TCGCCGTTGACTTGTGGTT 60.153 52.632 0.00 0.00 0.00 3.67
621 630 1.858399 GCCGTTGACTTGTGGTTTTCG 60.858 52.381 0.00 0.00 0.00 3.46
676 685 7.767198 GGTAAATGAGTAAATGCTAGTGGTACA 59.233 37.037 0.00 0.00 0.00 2.90
736 745 2.159254 GGTTCAAACTTGCAAGCTGACA 60.159 45.455 26.27 15.17 0.00 3.58
778 787 0.322277 CAACCTGATGCTGTGAGGCT 60.322 55.000 0.00 0.00 33.99 4.58
826 836 2.430244 CTTCGTGTACGCCGCAGT 60.430 61.111 0.00 0.00 39.60 4.40
859 869 2.357009 GCCACTAATCTGACCATTGCTG 59.643 50.000 0.00 0.00 0.00 4.41
902 912 5.023533 TCTACCCATCTTCTTGCACATAC 57.976 43.478 0.00 0.00 0.00 2.39
905 915 2.609459 CCCATCTTCTTGCACATACGAC 59.391 50.000 0.00 0.00 0.00 4.34
906 916 3.261580 CCATCTTCTTGCACATACGACA 58.738 45.455 0.00 0.00 0.00 4.35
907 917 3.308053 CCATCTTCTTGCACATACGACAG 59.692 47.826 0.00 0.00 0.00 3.51
908 918 3.660501 TCTTCTTGCACATACGACAGT 57.339 42.857 0.00 0.00 0.00 3.55
909 919 3.317150 TCTTCTTGCACATACGACAGTG 58.683 45.455 0.00 0.00 38.74 3.66
910 920 2.078849 TCTTGCACATACGACAGTGG 57.921 50.000 0.00 0.00 36.29 4.00
911 921 1.343142 TCTTGCACATACGACAGTGGT 59.657 47.619 0.00 0.00 36.29 4.16
912 922 1.726791 CTTGCACATACGACAGTGGTC 59.273 52.381 0.00 0.00 40.77 4.02
918 928 0.895530 ATACGACAGTGGTCAGTGGG 59.104 55.000 10.15 4.66 44.54 4.61
972 982 2.270986 CCTGCAAACAGCTGACCCC 61.271 63.158 23.35 6.49 44.15 4.95
996 1006 6.406400 CCATAGGTTACAGAAGAGAAGAGGTG 60.406 46.154 0.00 0.00 0.00 4.00
1057 1067 1.290203 GTTATTGCTAGCGCTGCTGA 58.710 50.000 22.90 14.14 40.10 4.26
1115 1125 0.951558 CCACTGCGGCTAAACAAAGT 59.048 50.000 0.00 0.00 0.00 2.66
1156 1166 1.425066 ACCTTTCAAGCATGGTCTCCA 59.575 47.619 0.00 0.00 38.19 3.86
1216 1226 3.625897 CGTGCCTGTGGAGTGGGA 61.626 66.667 0.00 0.00 0.00 4.37
1350 1360 5.359194 TTGATACCTTGGAATCTCTGGAC 57.641 43.478 0.00 0.00 0.00 4.02
1382 1392 1.003839 GGTTCACCGATCTGCCACA 60.004 57.895 0.00 0.00 0.00 4.17
1419 1429 1.097547 CCTTGGGTGCTAGATTGCGG 61.098 60.000 0.00 0.00 35.36 5.69
1608 1618 1.562475 GGTGGTAGCCTCCCAACAATA 59.438 52.381 0.00 0.00 39.59 1.90
1621 1631 3.947834 CCCAACAATAATGGTCCACTCTC 59.052 47.826 0.00 0.00 36.14 3.20
1638 1648 3.181461 ACTCTCTGAAGGAACTGGTGTTG 60.181 47.826 0.00 0.00 40.86 3.33
1642 1652 2.874701 CTGAAGGAACTGGTGTTGTCTG 59.125 50.000 0.00 0.00 40.86 3.51
1659 1669 2.594592 GGCAACGGCTTCAGTGGT 60.595 61.111 0.00 0.00 40.87 4.16
1754 1764 1.280133 TCCTGATCTGTTCTTGGCTGG 59.720 52.381 0.00 0.00 0.00 4.85
1950 1965 2.372074 GGGAGGCATACCCCGACAA 61.372 63.158 0.00 0.00 41.38 3.18
1967 1982 2.417933 GACAAGTTGGCAGATGCAGTAG 59.582 50.000 3.05 0.00 44.36 2.57
1995 2010 3.693807 TCTCTTGAATCTGGCAAGCAAT 58.306 40.909 0.00 0.00 41.83 3.56
2383 2398 5.833131 GGGTCTATTCCTTCAAATATTGGCA 59.167 40.000 0.00 0.00 0.00 4.92
2424 2439 5.677319 TCCTTGATCTTTCCTACAACGAT 57.323 39.130 0.00 0.00 0.00 3.73
2482 2497 2.945008 CAAAGCTTGACAGAGTTGGTGA 59.055 45.455 0.00 0.00 0.00 4.02
2524 2539 2.216898 GATCCCTTCCAGCATTTCGAG 58.783 52.381 0.00 0.00 0.00 4.04
2525 2540 1.275666 TCCCTTCCAGCATTTCGAGA 58.724 50.000 0.00 0.00 0.00 4.04
2569 2584 5.189934 ACGGGAAATCCAGATCTTCTTAACT 59.810 40.000 6.60 0.00 37.91 2.24
2689 2704 2.907892 TCTATGGGGATGGGATCAGAC 58.092 52.381 0.00 0.00 0.00 3.51
2741 3065 1.063806 CTGACTACTTCGTGCTGCAC 58.936 55.000 22.38 22.38 0.00 4.57
2916 3241 5.619625 AAATAGTTGAACTGAAGCAGAGC 57.380 39.130 8.33 0.00 35.18 4.09
2976 3301 6.912203 TCAATTAAGAACACTCAACGAACA 57.088 33.333 0.00 0.00 0.00 3.18
2977 3302 7.310072 TCAATTAAGAACACTCAACGAACAA 57.690 32.000 0.00 0.00 0.00 2.83
2978 3303 7.184106 TCAATTAAGAACACTCAACGAACAAC 58.816 34.615 0.00 0.00 0.00 3.32
3001 3326 3.559238 ACAACGCATTGGACTTCAATC 57.441 42.857 0.00 0.00 43.70 2.67
3023 3348 4.738252 TCAAGAACAATCGATCGGTATTCG 59.262 41.667 16.41 4.84 40.90 3.34
3031 3356 0.594028 GATCGGTATTCGCGCAGTCA 60.594 55.000 8.75 0.00 39.05 3.41
3050 3375 7.170489 CGCAGTCATAGATACTGAACAATCAAT 59.830 37.037 7.39 0.00 45.89 2.57
3055 3380 9.899226 TCATAGATACTGAACAATCAATAGACG 57.101 33.333 0.00 0.00 34.49 4.18
3056 3381 9.133627 CATAGATACTGAACAATCAATAGACGG 57.866 37.037 0.00 0.00 34.49 4.79
3057 3382 7.113658 AGATACTGAACAATCAATAGACGGT 57.886 36.000 0.00 0.00 34.49 4.83
3058 3383 8.234136 AGATACTGAACAATCAATAGACGGTA 57.766 34.615 0.00 0.00 34.49 4.02
3059 3384 8.692710 AGATACTGAACAATCAATAGACGGTAA 58.307 33.333 0.00 0.00 34.49 2.85
3061 3386 7.596749 ACTGAACAATCAATAGACGGTAAAG 57.403 36.000 0.00 0.00 34.49 1.85
3062 3387 7.159372 ACTGAACAATCAATAGACGGTAAAGT 58.841 34.615 0.00 0.00 34.49 2.66
3063 3388 8.308931 ACTGAACAATCAATAGACGGTAAAGTA 58.691 33.333 0.00 0.00 34.49 2.24
3065 3390 9.309516 TGAACAATCAATAGACGGTAAAGTATC 57.690 33.333 0.00 0.00 30.99 2.24
3066 3391 9.309516 GAACAATCAATAGACGGTAAAGTATCA 57.690 33.333 0.00 0.00 0.00 2.15
3067 3392 9.832445 AACAATCAATAGACGGTAAAGTATCAT 57.168 29.630 0.00 0.00 0.00 2.45
3068 3393 9.261180 ACAATCAATAGACGGTAAAGTATCATG 57.739 33.333 0.00 0.00 0.00 3.07
3069 3394 9.476202 CAATCAATAGACGGTAAAGTATCATGA 57.524 33.333 0.00 0.00 0.00 3.07
3075 3400 6.456501 AGACGGTAAAGTATCATGATTAGGC 58.543 40.000 14.65 2.60 0.00 3.93
3076 3401 5.227908 ACGGTAAAGTATCATGATTAGGCG 58.772 41.667 14.65 0.00 0.00 5.52
3096 3421 2.817258 CGAGACTGATCCAGGAGATACC 59.183 54.545 0.00 0.00 34.42 2.73
3151 3476 0.861837 CTTGCAACCTGACACTCGAC 59.138 55.000 0.00 0.00 0.00 4.20
3226 3554 3.349927 TGAAGCAATCAGAGGAATGGTG 58.650 45.455 0.00 0.00 35.00 4.17
3227 3555 3.245016 TGAAGCAATCAGAGGAATGGTGT 60.245 43.478 0.00 0.00 35.00 4.16
3311 3640 0.543749 GCACCTACCTCATCCTGCTT 59.456 55.000 0.00 0.00 0.00 3.91
3434 3792 1.545841 GGTGGAAAGAAAGGCCGAAT 58.454 50.000 0.00 0.00 0.00 3.34
3462 3820 4.803426 CACGCGGCTCCTGGACTC 62.803 72.222 12.47 0.00 0.00 3.36
3465 3823 4.154347 GCGGCTCCTGGACTCCTG 62.154 72.222 0.00 0.00 0.00 3.86
3466 3824 3.465403 CGGCTCCTGGACTCCTGG 61.465 72.222 13.77 13.77 42.93 4.45
3467 3825 2.284995 GGCTCCTGGACTCCTGGT 60.285 66.667 18.16 0.00 42.31 4.00
3468 3826 1.920835 GGCTCCTGGACTCCTGGTT 60.921 63.158 18.16 0.00 42.31 3.67
3469 3827 1.599576 GCTCCTGGACTCCTGGTTC 59.400 63.158 18.16 9.30 42.31 3.62
3470 3828 1.904990 GCTCCTGGACTCCTGGTTCC 61.905 65.000 18.16 9.41 42.31 3.62
3471 3829 0.252467 CTCCTGGACTCCTGGTTCCT 60.252 60.000 18.16 0.00 42.31 3.36
3472 3830 0.252284 TCCTGGACTCCTGGTTCCTC 60.252 60.000 18.16 0.00 42.31 3.71
3473 3831 0.545309 CCTGGACTCCTGGTTCCTCA 60.545 60.000 12.05 0.00 37.76 3.86
3474 3832 0.901124 CTGGACTCCTGGTTCCTCAG 59.099 60.000 15.25 4.98 34.70 3.35
3475 3833 0.487325 TGGACTCCTGGTTCCTCAGA 59.513 55.000 15.25 0.00 36.93 3.27
3476 3834 1.190643 GGACTCCTGGTTCCTCAGAG 58.809 60.000 9.15 0.00 36.93 3.35
3477 3835 0.534873 GACTCCTGGTTCCTCAGAGC 59.465 60.000 0.00 0.00 36.93 4.09
3478 3836 0.178921 ACTCCTGGTTCCTCAGAGCA 60.179 55.000 0.00 0.00 36.93 4.26
3479 3837 0.248843 CTCCTGGTTCCTCAGAGCAC 59.751 60.000 0.00 0.00 36.93 4.40
3480 3838 0.471780 TCCTGGTTCCTCAGAGCACA 60.472 55.000 0.00 0.00 36.93 4.57
3481 3839 0.321122 CCTGGTTCCTCAGAGCACAC 60.321 60.000 0.00 0.00 36.93 3.82
3482 3840 0.668706 CTGGTTCCTCAGAGCACACG 60.669 60.000 0.00 0.00 36.93 4.49
3483 3841 1.112916 TGGTTCCTCAGAGCACACGA 61.113 55.000 0.00 0.00 0.00 4.35
3484 3842 0.389166 GGTTCCTCAGAGCACACGAG 60.389 60.000 0.00 0.00 0.00 4.18
3485 3843 0.389166 GTTCCTCAGAGCACACGAGG 60.389 60.000 11.78 11.78 46.49 4.63
3486 3844 1.536073 TTCCTCAGAGCACACGAGGG 61.536 60.000 16.10 0.00 45.40 4.30
3487 3845 2.279069 CCTCAGAGCACACGAGGGT 61.279 63.158 10.57 0.00 42.27 4.34
3488 3846 1.668294 CTCAGAGCACACGAGGGTT 59.332 57.895 0.00 0.00 0.00 4.11
3489 3847 0.668706 CTCAGAGCACACGAGGGTTG 60.669 60.000 0.00 0.00 0.00 3.77
3490 3848 1.112916 TCAGAGCACACGAGGGTTGA 61.113 55.000 0.00 0.00 0.00 3.18
3491 3849 0.249868 CAGAGCACACGAGGGTTGAA 60.250 55.000 0.00 0.00 0.00 2.69
3492 3850 0.468226 AGAGCACACGAGGGTTGAAA 59.532 50.000 0.00 0.00 0.00 2.69
3493 3851 1.072331 AGAGCACACGAGGGTTGAAAT 59.928 47.619 0.00 0.00 0.00 2.17
3494 3852 1.880027 GAGCACACGAGGGTTGAAATT 59.120 47.619 0.00 0.00 0.00 1.82
3495 3853 2.293399 GAGCACACGAGGGTTGAAATTT 59.707 45.455 0.00 0.00 0.00 1.82
3496 3854 2.693074 AGCACACGAGGGTTGAAATTTT 59.307 40.909 0.00 0.00 0.00 1.82
3497 3855 2.794350 GCACACGAGGGTTGAAATTTTG 59.206 45.455 0.00 0.00 0.00 2.44
3498 3856 3.380142 CACACGAGGGTTGAAATTTTGG 58.620 45.455 0.00 0.00 0.00 3.28
3499 3857 3.028130 ACACGAGGGTTGAAATTTTGGT 58.972 40.909 0.00 0.00 0.00 3.67
3500 3858 3.449377 ACACGAGGGTTGAAATTTTGGTT 59.551 39.130 0.00 0.00 0.00 3.67
3501 3859 4.048504 CACGAGGGTTGAAATTTTGGTTC 58.951 43.478 0.00 0.00 0.00 3.62
3502 3860 3.958147 ACGAGGGTTGAAATTTTGGTTCT 59.042 39.130 0.00 0.00 0.00 3.01
3503 3861 4.202111 ACGAGGGTTGAAATTTTGGTTCTG 60.202 41.667 0.00 0.00 0.00 3.02
3504 3862 4.202111 CGAGGGTTGAAATTTTGGTTCTGT 60.202 41.667 0.00 0.00 0.00 3.41
3505 3863 5.670485 GAGGGTTGAAATTTTGGTTCTGTT 58.330 37.500 0.00 0.00 0.00 3.16
3506 3864 5.670485 AGGGTTGAAATTTTGGTTCTGTTC 58.330 37.500 0.00 0.00 0.00 3.18
3507 3865 4.506288 GGGTTGAAATTTTGGTTCTGTTCG 59.494 41.667 0.00 0.00 0.00 3.95
3508 3866 5.344884 GGTTGAAATTTTGGTTCTGTTCGA 58.655 37.500 0.00 0.00 0.00 3.71
3509 3867 5.458779 GGTTGAAATTTTGGTTCTGTTCGAG 59.541 40.000 0.00 0.00 0.00 4.04
3510 3868 4.606961 TGAAATTTTGGTTCTGTTCGAGC 58.393 39.130 0.00 0.00 0.00 5.03
3511 3869 4.338118 TGAAATTTTGGTTCTGTTCGAGCT 59.662 37.500 0.00 0.00 0.00 4.09
3512 3870 4.918810 AATTTTGGTTCTGTTCGAGCTT 57.081 36.364 0.00 0.00 0.00 3.74
3513 3871 4.918810 ATTTTGGTTCTGTTCGAGCTTT 57.081 36.364 0.00 0.00 0.00 3.51
3514 3872 3.963383 TTTGGTTCTGTTCGAGCTTTC 57.037 42.857 0.00 0.00 0.00 2.62
3515 3873 1.878953 TGGTTCTGTTCGAGCTTTCC 58.121 50.000 0.00 0.00 0.00 3.13
3516 3874 1.157585 GGTTCTGTTCGAGCTTTCCC 58.842 55.000 0.00 0.00 0.00 3.97
3517 3875 1.542547 GGTTCTGTTCGAGCTTTCCCA 60.543 52.381 0.00 0.00 0.00 4.37
3518 3876 2.427506 GTTCTGTTCGAGCTTTCCCAT 58.572 47.619 0.00 0.00 0.00 4.00
3519 3877 2.386661 TCTGTTCGAGCTTTCCCATC 57.613 50.000 0.00 0.00 0.00 3.51
3520 3878 1.902508 TCTGTTCGAGCTTTCCCATCT 59.097 47.619 0.00 0.00 0.00 2.90
3521 3879 2.303022 TCTGTTCGAGCTTTCCCATCTT 59.697 45.455 0.00 0.00 0.00 2.40
3528 3952 1.508088 CTTTCCCATCTTGTGCGGC 59.492 57.895 0.00 0.00 0.00 6.53
3571 3995 1.492764 GGGATGACGGAAACCCTAGA 58.507 55.000 0.00 0.00 39.28 2.43
3649 4075 1.887707 CCCCGCGCATTCCTTCTAC 60.888 63.158 8.75 0.00 0.00 2.59
3664 4090 2.682494 TACCCTCCTCCACACGCC 60.682 66.667 0.00 0.00 0.00 5.68
3681 4107 1.753463 CCGACTCGGCTAACTCCCT 60.753 63.158 4.10 0.00 41.17 4.20
3688 4114 1.078143 GGCTAACTCCCTGCCAGTG 60.078 63.158 0.00 0.00 45.46 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.084287 ACAAATTGCTGGACTCATGACAT 58.916 39.130 0.00 0.00 0.00 3.06
1 2 3.489355 ACAAATTGCTGGACTCATGACA 58.511 40.909 0.00 0.00 0.00 3.58
2 3 3.503363 TGACAAATTGCTGGACTCATGAC 59.497 43.478 0.00 0.00 0.00 3.06
29 30 1.651770 TGGACCTAGTTCCCCAGAGAT 59.348 52.381 3.53 0.00 34.33 2.75
56 57 6.115448 AGTAAAGGCACTGAAGATTACTGT 57.885 37.500 0.00 0.00 40.86 3.55
91 92 7.715265 GCTATGCAGTGATAGCTTAAAACTA 57.285 36.000 19.17 0.00 45.08 2.24
132 133 9.646427 TTGGCTTACATTGGTAAATTTGAATAC 57.354 29.630 0.00 0.00 38.92 1.89
172 174 8.138074 ACTAAAGGAAAGAAAATGAGCTGTTTC 58.862 33.333 0.00 0.00 34.57 2.78
341 345 6.053005 GTCCACCATTAGGATTATTCGACAA 58.947 40.000 0.00 0.00 37.52 3.18
344 348 4.798263 GCGTCCACCATTAGGATTATTCGA 60.798 45.833 0.00 0.00 37.52 3.71
505 512 7.385267 ACCTTATTTTGCACAATTATTCAGCA 58.615 30.769 2.94 0.00 0.00 4.41
576 585 7.073265 CGACGCTAAAAAGAAAGATAAACCAA 58.927 34.615 0.00 0.00 0.00 3.67
602 611 1.399089 ACGAAAACCACAAGTCAACGG 59.601 47.619 0.00 0.00 0.00 4.44
612 621 6.036844 GGAATGGTCTATTCTACGAAAACCAC 59.963 42.308 8.63 2.18 43.81 4.16
613 622 6.110707 GGAATGGTCTATTCTACGAAAACCA 58.889 40.000 8.63 9.68 43.81 3.67
676 685 4.262164 GCAAGTGGTCTGATTTGTGGAATT 60.262 41.667 0.00 0.00 0.00 2.17
736 745 5.163488 TGGTATCAATCGTCATCGTTACCTT 60.163 40.000 0.00 0.00 38.33 3.50
800 809 0.033781 CGTACACGAAGGGGGTCAAA 59.966 55.000 0.00 0.00 43.02 2.69
859 869 4.940654 AGAAGAAGCAATGGTAGAGAAAGC 59.059 41.667 0.00 0.00 0.00 3.51
902 912 1.006102 GACCCACTGACCACTGTCG 60.006 63.158 0.00 0.00 44.86 4.35
905 915 0.108615 GATCGACCCACTGACCACTG 60.109 60.000 0.00 0.00 0.00 3.66
906 916 0.541998 TGATCGACCCACTGACCACT 60.542 55.000 0.00 0.00 0.00 4.00
907 917 0.320374 TTGATCGACCCACTGACCAC 59.680 55.000 0.00 0.00 0.00 4.16
908 918 0.608130 CTTGATCGACCCACTGACCA 59.392 55.000 0.00 0.00 0.00 4.02
909 919 0.741221 GCTTGATCGACCCACTGACC 60.741 60.000 0.00 0.00 0.00 4.02
910 920 0.741221 GGCTTGATCGACCCACTGAC 60.741 60.000 0.00 0.00 0.00 3.51
911 921 1.596934 GGCTTGATCGACCCACTGA 59.403 57.895 0.00 0.00 0.00 3.41
912 922 1.450312 GGGCTTGATCGACCCACTG 60.450 63.158 11.59 0.00 43.64 3.66
918 928 0.881118 TTGCAAAGGGCTTGATCGAC 59.119 50.000 0.00 0.00 45.15 4.20
972 982 6.378564 TCACCTCTTCTCTTCTGTAACCTATG 59.621 42.308 0.00 0.00 0.00 2.23
996 1006 0.908198 ACCTGCTCTTCTCCATGGTC 59.092 55.000 12.58 0.00 0.00 4.02
1057 1067 4.512571 GGACAAATCAAACAGCAAGCAAAT 59.487 37.500 0.00 0.00 0.00 2.32
1098 1108 0.310854 GCACTTTGTTTAGCCGCAGT 59.689 50.000 0.00 0.00 0.00 4.40
1115 1125 0.401356 TCTCATGGTGCTTTCCTGCA 59.599 50.000 0.00 0.00 41.05 4.41
1266 1276 1.520342 GCGAGACATGGAGAGGTGC 60.520 63.158 0.00 0.00 0.00 5.01
1382 1392 2.744243 GGGCATGAGGAGAGCTGCT 61.744 63.158 0.00 0.00 35.03 4.24
1608 1618 2.907892 TCCTTCAGAGAGTGGACCATT 58.092 47.619 0.00 0.00 0.00 3.16
1621 1631 2.874701 CAGACAACACCAGTTCCTTCAG 59.125 50.000 0.00 0.00 35.28 3.02
1638 1648 1.598130 ACTGAAGCCGTTGCCAGAC 60.598 57.895 0.00 0.00 38.69 3.51
1642 1652 1.734388 AAACCACTGAAGCCGTTGCC 61.734 55.000 0.00 0.00 38.69 4.52
1659 1669 7.629157 TCATGGTGATTTCACTAGGTATCAAA 58.371 34.615 10.32 0.00 45.73 2.69
1689 1699 9.739276 TTATTGTAACTCAAATCCAACATCTCT 57.261 29.630 0.00 0.00 39.62 3.10
1735 1745 1.004044 ACCAGCCAAGAACAGATCAGG 59.996 52.381 0.00 0.00 0.00 3.86
1754 1764 2.747446 AGATCAACGGTATGCAAACCAC 59.253 45.455 0.00 0.00 39.71 4.16
1806 1816 0.107945 GGCTGCGAGAGAATCCTTGT 60.108 55.000 0.00 0.00 33.66 3.16
1947 1962 2.430465 CTACTGCATCTGCCAACTTGT 58.570 47.619 0.00 0.00 41.18 3.16
1950 1965 0.987294 ACCTACTGCATCTGCCAACT 59.013 50.000 0.00 0.00 41.18 3.16
1967 1982 2.489722 GCCAGATTCAAGAGAACCAACC 59.510 50.000 0.00 0.00 36.39 3.77
1995 2010 1.436195 GCACTGCACCGTTCAACTGA 61.436 55.000 0.00 0.00 0.00 3.41
2017 2032 1.442769 TCAAGTTTGCCGATCTCAGC 58.557 50.000 0.00 0.00 0.00 4.26
2383 2398 3.854994 AGGATCTCCAGGTCCTTCAAAAT 59.145 43.478 2.15 0.00 42.09 1.82
2424 2439 0.916086 ATGGTATCGGGCCAGACAAA 59.084 50.000 8.08 0.00 39.65 2.83
2482 2497 8.320617 GGATCCAGAGAGCTGATTATAAGAAAT 58.679 37.037 6.95 0.00 45.17 2.17
2524 2539 1.936547 GGAATCGACTGCCACAGATTC 59.063 52.381 0.78 8.12 44.76 2.52
2525 2540 1.278985 TGGAATCGACTGCCACAGATT 59.721 47.619 0.78 0.00 36.19 2.40
2689 2704 1.072505 AACCTGTAAGCCACCCGTG 59.927 57.895 0.00 0.00 0.00 4.94
2741 3065 1.069596 GTTGGGTTTGGCTTGCAGG 59.930 57.895 0.00 0.00 0.00 4.85
2789 3113 8.058847 AGCATTGGTATCTTTAATCCTAACCAA 58.941 33.333 6.50 6.50 46.29 3.67
2841 3165 9.628500 ATTATGGGGAGAAAAAGATAACTGTAC 57.372 33.333 0.00 0.00 0.00 2.90
2916 3241 6.016527 CCATGTTCCATAGGACAATCTGAATG 60.017 42.308 0.00 0.00 0.00 2.67
2976 3301 1.305201 AGTCCAATGCGTTGTTCGTT 58.695 45.000 17.19 0.00 42.13 3.85
2977 3302 1.263217 GAAGTCCAATGCGTTGTTCGT 59.737 47.619 17.19 7.95 42.13 3.85
2978 3303 1.262950 TGAAGTCCAATGCGTTGTTCG 59.737 47.619 17.19 2.68 43.12 3.95
2979 3304 3.347958 TTGAAGTCCAATGCGTTGTTC 57.652 42.857 17.19 14.04 33.36 3.18
3001 3326 4.606232 GCGAATACCGATCGATTGTTCTTG 60.606 45.833 18.66 6.68 42.76 3.02
3023 3348 3.706698 TGTTCAGTATCTATGACTGCGC 58.293 45.455 0.00 0.00 43.37 6.09
3031 3356 8.861086 ACCGTCTATTGATTGTTCAGTATCTAT 58.139 33.333 0.00 0.00 32.27 1.98
3050 3375 7.574404 CGCCTAATCATGATACTTTACCGTCTA 60.574 40.741 9.04 0.00 0.00 2.59
3052 3377 5.345202 CGCCTAATCATGATACTTTACCGTC 59.655 44.000 9.04 0.00 0.00 4.79
3053 3378 5.010314 TCGCCTAATCATGATACTTTACCGT 59.990 40.000 9.04 0.00 0.00 4.83
3054 3379 5.466819 TCGCCTAATCATGATACTTTACCG 58.533 41.667 9.04 6.20 0.00 4.02
3055 3380 6.586844 GTCTCGCCTAATCATGATACTTTACC 59.413 42.308 9.04 0.00 0.00 2.85
3056 3381 7.327275 CAGTCTCGCCTAATCATGATACTTTAC 59.673 40.741 9.04 1.06 0.00 2.01
3057 3382 7.230712 TCAGTCTCGCCTAATCATGATACTTTA 59.769 37.037 9.04 0.00 0.00 1.85
3058 3383 6.040955 TCAGTCTCGCCTAATCATGATACTTT 59.959 38.462 9.04 0.00 0.00 2.66
3059 3384 5.536538 TCAGTCTCGCCTAATCATGATACTT 59.463 40.000 9.04 0.00 0.00 2.24
3061 3386 5.378292 TCAGTCTCGCCTAATCATGATAC 57.622 43.478 9.04 0.58 0.00 2.24
3062 3387 5.126222 GGATCAGTCTCGCCTAATCATGATA 59.874 44.000 9.04 0.00 0.00 2.15
3063 3388 4.081752 GGATCAGTCTCGCCTAATCATGAT 60.082 45.833 1.18 1.18 0.00 2.45
3065 3390 3.006217 TGGATCAGTCTCGCCTAATCATG 59.994 47.826 0.00 0.00 0.00 3.07
3066 3391 3.234353 TGGATCAGTCTCGCCTAATCAT 58.766 45.455 0.00 0.00 0.00 2.45
3067 3392 2.625314 CTGGATCAGTCTCGCCTAATCA 59.375 50.000 0.00 0.00 0.00 2.57
3068 3393 2.029470 CCTGGATCAGTCTCGCCTAATC 60.029 54.545 0.00 0.00 0.00 1.75
3069 3394 1.967066 CCTGGATCAGTCTCGCCTAAT 59.033 52.381 0.00 0.00 0.00 1.73
3070 3395 1.063942 TCCTGGATCAGTCTCGCCTAA 60.064 52.381 0.00 0.00 0.00 2.69
3071 3396 0.551396 TCCTGGATCAGTCTCGCCTA 59.449 55.000 0.00 0.00 0.00 3.93
3072 3397 0.754957 CTCCTGGATCAGTCTCGCCT 60.755 60.000 0.00 0.00 0.00 5.52
3073 3398 0.753479 TCTCCTGGATCAGTCTCGCC 60.753 60.000 0.00 0.00 0.00 5.54
3074 3399 1.327303 ATCTCCTGGATCAGTCTCGC 58.673 55.000 0.00 0.00 0.00 5.03
3075 3400 2.817258 GGTATCTCCTGGATCAGTCTCG 59.183 54.545 0.00 0.00 35.98 4.04
3076 3401 4.112634 AGGTATCTCCTGGATCAGTCTC 57.887 50.000 0.00 0.00 46.19 3.36
3096 3421 4.479619 GCAAATAGAGCACCAACTTTCAG 58.520 43.478 0.00 0.00 0.00 3.02
3101 3426 2.472695 TCGCAAATAGAGCACCAACT 57.527 45.000 0.00 0.00 0.00 3.16
3151 3476 0.240945 AAAAACAATCGGCCTCTGCG 59.759 50.000 0.00 0.00 38.85 5.18
3267 3595 0.323629 TTCTTAGCCTTCCGTGGGTG 59.676 55.000 0.00 0.00 38.41 4.61
3268 3596 1.003233 CTTTCTTAGCCTTCCGTGGGT 59.997 52.381 0.00 0.00 41.20 4.51
3269 3597 1.278127 TCTTTCTTAGCCTTCCGTGGG 59.722 52.381 0.00 0.00 0.00 4.61
3365 3723 4.180946 CCTCCACCGCTCTCGTCG 62.181 72.222 0.00 0.00 0.00 5.12
3424 3782 1.153353 CACGTACACATTCGGCCTTT 58.847 50.000 0.00 0.00 0.00 3.11
3448 3806 4.154347 CAGGAGTCCAGGAGCCGC 62.154 72.222 12.86 0.00 0.00 6.53
3449 3807 3.465403 CCAGGAGTCCAGGAGCCG 61.465 72.222 15.54 0.00 31.24 5.52
3450 3808 1.904990 GAACCAGGAGTCCAGGAGCC 61.905 65.000 26.47 10.95 34.08 4.70
3451 3809 1.599576 GAACCAGGAGTCCAGGAGC 59.400 63.158 26.47 13.53 34.08 4.70
3452 3810 0.252467 AGGAACCAGGAGTCCAGGAG 60.252 60.000 26.47 6.90 34.08 3.69
3453 3811 0.252284 GAGGAACCAGGAGTCCAGGA 60.252 60.000 26.47 0.00 34.08 3.86
3454 3812 0.545309 TGAGGAACCAGGAGTCCAGG 60.545 60.000 18.76 18.76 36.18 4.45
3455 3813 0.901124 CTGAGGAACCAGGAGTCCAG 59.099 60.000 12.86 2.60 0.00 3.86
3456 3814 0.487325 TCTGAGGAACCAGGAGTCCA 59.513 55.000 12.86 0.00 34.99 4.02
3457 3815 1.190643 CTCTGAGGAACCAGGAGTCC 58.809 60.000 0.00 0.00 34.99 3.85
3458 3816 0.534873 GCTCTGAGGAACCAGGAGTC 59.465 60.000 6.83 0.00 34.99 3.36
3459 3817 0.178921 TGCTCTGAGGAACCAGGAGT 60.179 55.000 6.83 0.00 34.99 3.85
3460 3818 0.248843 GTGCTCTGAGGAACCAGGAG 59.751 60.000 6.83 0.00 34.99 3.69
3461 3819 0.471780 TGTGCTCTGAGGAACCAGGA 60.472 55.000 6.83 0.00 34.99 3.86
3462 3820 0.321122 GTGTGCTCTGAGGAACCAGG 60.321 60.000 6.83 0.00 34.99 4.45
3463 3821 0.668706 CGTGTGCTCTGAGGAACCAG 60.669 60.000 6.83 0.00 35.55 4.00
3464 3822 1.112916 TCGTGTGCTCTGAGGAACCA 61.113 55.000 6.83 0.00 0.00 3.67
3465 3823 0.389166 CTCGTGTGCTCTGAGGAACC 60.389 60.000 6.83 0.00 0.00 3.62
3466 3824 3.114558 CTCGTGTGCTCTGAGGAAC 57.885 57.895 6.83 4.45 0.00 3.62
3470 3828 0.668706 CAACCCTCGTGTGCTCTGAG 60.669 60.000 0.00 0.00 0.00 3.35
3471 3829 1.112916 TCAACCCTCGTGTGCTCTGA 61.113 55.000 0.00 0.00 0.00 3.27
3472 3830 0.249868 TTCAACCCTCGTGTGCTCTG 60.250 55.000 0.00 0.00 0.00 3.35
3473 3831 0.468226 TTTCAACCCTCGTGTGCTCT 59.532 50.000 0.00 0.00 0.00 4.09
3474 3832 1.523758 ATTTCAACCCTCGTGTGCTC 58.476 50.000 0.00 0.00 0.00 4.26
3475 3833 1.981256 AATTTCAACCCTCGTGTGCT 58.019 45.000 0.00 0.00 0.00 4.40
3476 3834 2.793278 AAATTTCAACCCTCGTGTGC 57.207 45.000 0.00 0.00 0.00 4.57
3477 3835 3.181480 ACCAAAATTTCAACCCTCGTGTG 60.181 43.478 0.00 0.00 0.00 3.82
3478 3836 3.028130 ACCAAAATTTCAACCCTCGTGT 58.972 40.909 0.00 0.00 0.00 4.49
3479 3837 3.726291 ACCAAAATTTCAACCCTCGTG 57.274 42.857 0.00 0.00 0.00 4.35
3480 3838 3.958147 AGAACCAAAATTTCAACCCTCGT 59.042 39.130 0.00 0.00 0.00 4.18
3481 3839 4.202111 ACAGAACCAAAATTTCAACCCTCG 60.202 41.667 0.00 0.00 0.00 4.63
3482 3840 5.276461 ACAGAACCAAAATTTCAACCCTC 57.724 39.130 0.00 0.00 0.00 4.30
3483 3841 5.670485 GAACAGAACCAAAATTTCAACCCT 58.330 37.500 0.00 0.00 0.00 4.34
3484 3842 4.506288 CGAACAGAACCAAAATTTCAACCC 59.494 41.667 0.00 0.00 0.00 4.11
3485 3843 5.344884 TCGAACAGAACCAAAATTTCAACC 58.655 37.500 0.00 0.00 0.00 3.77
3486 3844 5.051708 GCTCGAACAGAACCAAAATTTCAAC 60.052 40.000 0.00 0.00 0.00 3.18
3487 3845 5.040635 GCTCGAACAGAACCAAAATTTCAA 58.959 37.500 0.00 0.00 0.00 2.69
3488 3846 4.338118 AGCTCGAACAGAACCAAAATTTCA 59.662 37.500 0.00 0.00 0.00 2.69
3489 3847 4.860072 AGCTCGAACAGAACCAAAATTTC 58.140 39.130 0.00 0.00 0.00 2.17
3490 3848 4.918810 AGCTCGAACAGAACCAAAATTT 57.081 36.364 0.00 0.00 0.00 1.82
3491 3849 4.918810 AAGCTCGAACAGAACCAAAATT 57.081 36.364 0.00 0.00 0.00 1.82
3492 3850 4.261614 GGAAAGCTCGAACAGAACCAAAAT 60.262 41.667 0.00 0.00 0.00 1.82
3493 3851 3.066203 GGAAAGCTCGAACAGAACCAAAA 59.934 43.478 0.00 0.00 0.00 2.44
3494 3852 2.616842 GGAAAGCTCGAACAGAACCAAA 59.383 45.455 0.00 0.00 0.00 3.28
3495 3853 2.218603 GGAAAGCTCGAACAGAACCAA 58.781 47.619 0.00 0.00 0.00 3.67
3496 3854 1.542547 GGGAAAGCTCGAACAGAACCA 60.543 52.381 0.00 0.00 0.00 3.67
3497 3855 1.157585 GGGAAAGCTCGAACAGAACC 58.842 55.000 0.00 0.00 0.00 3.62
3498 3856 1.878953 TGGGAAAGCTCGAACAGAAC 58.121 50.000 0.00 0.00 0.00 3.01
3499 3857 2.303022 AGATGGGAAAGCTCGAACAGAA 59.697 45.455 0.00 0.00 0.00 3.02
3500 3858 1.902508 AGATGGGAAAGCTCGAACAGA 59.097 47.619 0.00 0.00 0.00 3.41
3501 3859 2.393271 AGATGGGAAAGCTCGAACAG 57.607 50.000 0.00 0.00 0.00 3.16
3502 3860 2.224523 ACAAGATGGGAAAGCTCGAACA 60.225 45.455 0.00 0.00 0.00 3.18
3503 3861 2.160417 CACAAGATGGGAAAGCTCGAAC 59.840 50.000 0.00 0.00 0.00 3.95
3504 3862 2.426522 CACAAGATGGGAAAGCTCGAA 58.573 47.619 0.00 0.00 0.00 3.71
3505 3863 1.945819 GCACAAGATGGGAAAGCTCGA 60.946 52.381 0.00 0.00 0.00 4.04
3506 3864 0.449388 GCACAAGATGGGAAAGCTCG 59.551 55.000 0.00 0.00 0.00 5.03
3507 3865 0.449388 CGCACAAGATGGGAAAGCTC 59.551 55.000 0.00 0.00 43.98 4.09
3508 3866 0.962356 CCGCACAAGATGGGAAAGCT 60.962 55.000 0.00 0.00 43.98 3.74
3509 3867 1.508088 CCGCACAAGATGGGAAAGC 59.492 57.895 0.00 0.00 43.98 3.51
3510 3868 1.508088 GCCGCACAAGATGGGAAAG 59.492 57.895 0.00 0.00 43.98 2.62
3511 3869 2.331893 CGCCGCACAAGATGGGAAA 61.332 57.895 0.00 0.00 43.98 3.13
3512 3870 2.745884 CGCCGCACAAGATGGGAA 60.746 61.111 0.00 0.00 43.98 3.97
3513 3871 3.545124 AACGCCGCACAAGATGGGA 62.545 57.895 0.00 0.00 43.98 4.37
3514 3872 3.055719 AACGCCGCACAAGATGGG 61.056 61.111 0.00 0.00 40.94 4.00
3515 3873 2.176546 CAACGCCGCACAAGATGG 59.823 61.111 0.00 0.00 0.00 3.51
3516 3874 2.176546 CCAACGCCGCACAAGATG 59.823 61.111 0.00 0.00 0.00 2.90
3517 3875 3.055719 CCCAACGCCGCACAAGAT 61.056 61.111 0.00 0.00 0.00 2.40
3540 3964 1.808891 CGTCATCCCCAATTCCGGTAC 60.809 57.143 0.00 0.00 0.00 3.34
3612 4036 3.820843 GGATGGGTTGGGGCGGAT 61.821 66.667 0.00 0.00 0.00 4.18
3635 4061 0.533085 GGAGGGTAGAAGGAATGCGC 60.533 60.000 0.00 0.00 0.00 6.09
3640 4066 1.435563 TGTGGAGGAGGGTAGAAGGAA 59.564 52.381 0.00 0.00 0.00 3.36
3664 4090 1.433879 CAGGGAGTTAGCCGAGTCG 59.566 63.158 5.29 5.29 0.00 4.18
3671 4097 1.746991 GCACTGGCAGGGAGTTAGC 60.747 63.158 23.56 7.77 40.72 3.09
3673 4099 2.602676 GGGCACTGGCAGGGAGTTA 61.603 63.158 23.56 0.00 43.71 2.24
3692 4118 2.438434 CATCCCCACGGGCAAGAC 60.438 66.667 0.00 0.00 43.94 3.01


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

AutoCloner maintained by Alex Coulton.