Multiple sequence alignment - TraesCS1D01G224200

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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 TraesCS1D01G224200 chr1D 100.000 2696 0 0 1 2696 312665373 312668068 0.000000e+00 4979.0
1 TraesCS1D01G224200 chr1B 95.241 1723 45 13 700 2420 423111137 423112824 0.000000e+00 2693.0
2 TraesCS1D01G224200 chr1B 87.080 387 32 9 122 495 423084327 423084708 3.210000e-114 422.0
3 TraesCS1D01G224200 chr1B 89.286 224 24 0 2473 2696 423113151 423113374 5.680000e-72 281.0
4 TraesCS1D01G224200 chr1B 100.000 29 0 0 672 700 423085230 423085258 1.000000e-03 54.7
5 TraesCS1D01G224200 chr1A 96.779 1366 41 2 700 2062 392481178 392482543 0.000000e+00 2276.0
6 TraesCS1D01G224200 chr1A 85.714 518 46 13 1 505 392479761 392480263 3.080000e-144 521.0
7 TraesCS1D01G224200 chr1A 91.413 361 27 2 2336 2696 392482895 392483251 2.410000e-135 492.0
8 TraesCS1D01G224200 chr1A 100.000 37 0 0 664 700 392481102 392481138 4.820000e-08 69.4
9 TraesCS1D01G224200 chr4B 88.372 215 20 3 1593 1803 23323227 23323440 1.240000e-63 254.0
10 TraesCS1D01G224200 chr4B 85.714 175 16 6 497 663 629770561 629770734 2.760000e-40 176.0
11 TraesCS1D01G224200 chr3D 89.677 155 12 2 513 663 458309711 458309865 7.620000e-46 195.0
12 TraesCS1D01G224200 chr3D 88.816 152 12 4 516 663 508202188 508202038 5.930000e-42 182.0
13 TraesCS1D01G224200 chr7D 87.500 176 10 8 494 663 45193472 45193641 2.740000e-45 193.0
14 TraesCS1D01G224200 chr3A 89.103 156 12 3 513 663 733479376 733479531 3.540000e-44 189.0
15 TraesCS1D01G224200 chr6D 87.425 167 16 3 502 663 388554259 388554093 1.270000e-43 187.0
16 TraesCS1D01G224200 chr5D 88.535 157 12 4 513 663 531900278 531900434 4.580000e-43 185.0
17 TraesCS1D01G224200 chr2B 88.462 156 13 3 512 663 20705391 20705237 1.650000e-42 183.0
18 TraesCS1D01G224200 chr2B 87.500 64 8 0 438 501 90200339 90200402 1.040000e-09 75.0
19 TraesCS1D01G224200 chr7B 85.057 174 19 5 496 663 37102789 37102961 1.280000e-38 171.0


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 TraesCS1D01G224200 chr1D 312665373 312668068 2695 False 4979.00 4979 100.0000 1 2696 1 chr1D.!!$F1 2695
1 TraesCS1D01G224200 chr1B 423111137 423113374 2237 False 1487.00 2693 92.2635 700 2696 2 chr1B.!!$F2 1996
2 TraesCS1D01G224200 chr1B 423084327 423085258 931 False 238.35 422 93.5400 122 700 2 chr1B.!!$F1 578
3 TraesCS1D01G224200 chr1A 392479761 392483251 3490 False 839.60 2276 93.4765 1 2696 4 chr1A.!!$F1 2695


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
410 424 0.034089 GGCAGGGTGGACATTTAGCT 60.034 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 3150 0.16747 TGACTCGCTAGAAACGGTCG 59.833 55.0 0.0 0.0 35.12 4.79 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
20 21 3.574284 TCAACAATGCCATTAGTGCAC 57.426 42.857 9.40 9.40 42.38 4.57
22 23 4.331108 TCAACAATGCCATTAGTGCACTA 58.669 39.130 22.67 22.67 42.38 2.74
29 30 2.945008 GCCATTAGTGCACTATTGAGCA 59.055 45.455 34.41 19.35 37.44 4.26
37 38 1.602851 GCACTATTGAGCATGCTCTGG 59.397 52.381 39.46 27.60 43.12 3.86
46 47 0.452987 GCATGCTCTGGCGATTTCAA 59.547 50.000 11.37 0.00 42.25 2.69
47 48 1.066605 GCATGCTCTGGCGATTTCAAT 59.933 47.619 11.37 0.00 42.25 2.57
53 54 3.549625 GCTCTGGCGATTTCAATGATTCC 60.550 47.826 0.00 0.00 0.00 3.01
57 58 2.035066 GGCGATTTCAATGATTCCAGGG 59.965 50.000 0.00 0.00 0.00 4.45
66 67 2.875102 TGATTCCAGGGATGAGGAGA 57.125 50.000 0.00 0.00 34.91 3.71
67 68 2.687297 TGATTCCAGGGATGAGGAGAG 58.313 52.381 0.00 0.00 34.91 3.20
68 69 1.977129 GATTCCAGGGATGAGGAGAGG 59.023 57.143 0.00 0.00 34.91 3.69
69 70 0.719015 TTCCAGGGATGAGGAGAGGT 59.281 55.000 0.00 0.00 34.91 3.85
70 71 0.719015 TCCAGGGATGAGGAGAGGTT 59.281 55.000 0.00 0.00 0.00 3.50
71 72 1.081174 TCCAGGGATGAGGAGAGGTTT 59.919 52.381 0.00 0.00 0.00 3.27
72 73 1.918957 CCAGGGATGAGGAGAGGTTTT 59.081 52.381 0.00 0.00 0.00 2.43
73 74 2.310052 CCAGGGATGAGGAGAGGTTTTT 59.690 50.000 0.00 0.00 0.00 1.94
90 91 2.861462 TTTTTGAGAGGTTTGCCACG 57.139 45.000 0.00 0.00 37.19 4.94
108 109 1.228769 GGTCCAGGGGTGGGTTTTC 60.229 63.158 0.00 0.00 0.00 2.29
109 110 1.602605 GTCCAGGGGTGGGTTTTCG 60.603 63.158 0.00 0.00 0.00 3.46
110 111 2.079911 TCCAGGGGTGGGTTTTCGT 61.080 57.895 0.00 0.00 0.00 3.85
133 134 0.038166 GTCTTGGTGCTGGGGATCAA 59.962 55.000 0.00 0.00 0.00 2.57
224 227 6.057321 AGCAATGATTTGGGTCAAATTGAT 57.943 33.333 0.00 0.21 43.05 2.57
233 236 2.424956 GGGTCAAATTGATCACTGAGGC 59.575 50.000 8.63 0.00 0.00 4.70
239 242 0.622136 TTGATCACTGAGGCTGGCAT 59.378 50.000 3.38 0.00 0.00 4.40
292 296 5.684704 TGGTAAAAATTTGGTGGCATTTGA 58.315 33.333 0.00 0.00 0.00 2.69
373 377 5.603170 AGTAATCCAAGCCAAATGAATGG 57.397 39.130 0.00 0.00 43.70 3.16
378 382 2.564062 CCAAGCCAAATGAATGGTCTGT 59.436 45.455 0.00 0.00 42.75 3.41
410 424 0.034089 GGCAGGGTGGACATTTAGCT 60.034 55.000 0.00 0.00 0.00 3.32
419 433 5.059833 GGTGGACATTTAGCTATCCAAGAG 58.940 45.833 14.07 0.00 42.79 2.85
428 442 7.568199 TTTAGCTATCCAAGAGTTATTTGGC 57.432 36.000 0.00 0.00 43.81 4.52
430 444 5.699143 AGCTATCCAAGAGTTATTTGGCAT 58.301 37.500 0.00 0.00 43.81 4.40
495 510 9.533831 AGAAATGGGTAGAACAGAAAATTGTAT 57.466 29.630 0.00 0.00 0.00 2.29
521 536 4.385358 ACGAAAATCCATATTTGCACCC 57.615 40.909 0.00 0.00 35.46 4.61
522 537 3.181491 ACGAAAATCCATATTTGCACCCG 60.181 43.478 0.00 0.00 35.46 5.28
524 539 1.039856 AATCCATATTTGCACCCGGC 58.960 50.000 0.00 0.00 45.13 6.13
525 540 0.185901 ATCCATATTTGCACCCGGCT 59.814 50.000 0.00 0.00 45.15 5.52
526 541 0.751277 TCCATATTTGCACCCGGCTG 60.751 55.000 0.00 0.00 45.15 4.85
527 542 0.751277 CCATATTTGCACCCGGCTGA 60.751 55.000 0.00 0.00 45.15 4.26
528 543 0.381801 CATATTTGCACCCGGCTGAC 59.618 55.000 0.00 0.00 45.15 3.51
529 544 1.095228 ATATTTGCACCCGGCTGACG 61.095 55.000 0.00 0.00 45.15 4.35
601 747 3.120234 TGTGCAGTAGACAATTTGATGCG 60.120 43.478 2.79 0.00 35.00 4.73
602 748 3.073678 TGCAGTAGACAATTTGATGCGT 58.926 40.909 2.79 0.00 35.00 5.24
603 749 3.120234 TGCAGTAGACAATTTGATGCGTG 60.120 43.478 2.79 0.00 35.00 5.34
605 751 4.726021 GCAGTAGACAATTTGATGCGTGAG 60.726 45.833 2.79 0.00 0.00 3.51
606 752 3.935203 AGTAGACAATTTGATGCGTGAGG 59.065 43.478 2.79 0.00 0.00 3.86
608 754 2.744202 AGACAATTTGATGCGTGAGGTC 59.256 45.455 2.79 0.00 0.00 3.85
609 755 1.812571 ACAATTTGATGCGTGAGGTCC 59.187 47.619 2.79 0.00 0.00 4.46
610 756 1.086696 AATTTGATGCGTGAGGTCCG 58.913 50.000 0.00 0.00 0.00 4.79
617 763 2.579201 CGTGAGGTCCGCTCCAAT 59.421 61.111 0.00 0.00 0.00 3.16
619 765 0.673644 CGTGAGGTCCGCTCCAATTT 60.674 55.000 0.00 0.00 0.00 1.82
620 766 1.534729 GTGAGGTCCGCTCCAATTTT 58.465 50.000 0.00 0.00 0.00 1.82
621 767 1.886542 GTGAGGTCCGCTCCAATTTTT 59.113 47.619 0.00 0.00 0.00 1.94
622 768 3.078837 GTGAGGTCCGCTCCAATTTTTA 58.921 45.455 0.00 0.00 0.00 1.52
623 769 3.504520 GTGAGGTCCGCTCCAATTTTTAA 59.495 43.478 0.00 0.00 0.00 1.52
624 770 3.756434 TGAGGTCCGCTCCAATTTTTAAG 59.244 43.478 0.00 0.00 0.00 1.85
626 772 3.756963 AGGTCCGCTCCAATTTTTAAGTC 59.243 43.478 0.00 0.00 0.00 3.01
628 774 4.217767 GGTCCGCTCCAATTTTTAAGTCTT 59.782 41.667 0.00 0.00 0.00 3.01
629 775 5.278808 GGTCCGCTCCAATTTTTAAGTCTTT 60.279 40.000 0.00 0.00 0.00 2.52
630 776 6.213677 GTCCGCTCCAATTTTTAAGTCTTTT 58.786 36.000 0.00 0.00 0.00 2.27
631 777 6.143919 GTCCGCTCCAATTTTTAAGTCTTTTG 59.856 38.462 0.00 0.00 0.00 2.44
632 778 5.405269 CCGCTCCAATTTTTAAGTCTTTTGG 59.595 40.000 6.64 6.64 35.93 3.28
633 779 6.212955 CGCTCCAATTTTTAAGTCTTTTGGA 58.787 36.000 12.88 12.88 40.08 3.53
634 780 6.143919 CGCTCCAATTTTTAAGTCTTTTGGAC 59.856 38.462 10.41 7.86 44.80 4.02
635 781 6.983890 GCTCCAATTTTTAAGTCTTTTGGACA 59.016 34.615 10.41 0.00 46.72 4.02
636 782 7.657354 GCTCCAATTTTTAAGTCTTTTGGACAT 59.343 33.333 10.41 0.00 46.72 3.06
642 788 9.860898 ATTTTTAAGTCTTTTGGACATATGAGC 57.139 29.630 10.38 0.60 46.72 4.26
643 789 8.635765 TTTTAAGTCTTTTGGACATATGAGCT 57.364 30.769 10.38 0.00 46.72 4.09
644 790 7.849804 TTAAGTCTTTTGGACATATGAGCTC 57.150 36.000 10.38 6.82 46.72 4.09
646 792 5.669477 AGTCTTTTGGACATATGAGCTCTC 58.331 41.667 16.19 3.13 46.72 3.20
647 793 5.188555 AGTCTTTTGGACATATGAGCTCTCA 59.811 40.000 16.19 1.67 46.72 3.27
649 795 3.465742 TTGGACATATGAGCTCTCAGC 57.534 47.619 16.19 0.00 43.61 4.26
652 798 3.198417 TGGACATATGAGCTCTCAGCAAA 59.802 43.478 16.19 0.00 45.56 3.68
653 799 4.194640 GGACATATGAGCTCTCAGCAAAA 58.805 43.478 16.19 0.00 45.56 2.44
736 1598 6.764308 TTCAGCTTCCAAATTAAGAGATGG 57.236 37.500 0.00 0.00 0.00 3.51
869 1731 6.379988 CCAACTAATTAGGTACCAAAGCCAAT 59.620 38.462 15.94 0.75 0.00 3.16
1073 1935 1.660560 CCGTCGTTATCCCCGTCTGT 61.661 60.000 0.00 0.00 0.00 3.41
1736 2598 0.512952 GACCATATCGCGCATGGAAC 59.487 55.000 33.00 24.35 44.95 3.62
1932 2797 7.148018 GCAGATTTCTCACCCTATTTTTCATGA 60.148 37.037 0.00 0.00 0.00 3.07
1958 2823 4.610605 TGGGTGAAATCGTAGTTGAAGA 57.389 40.909 0.00 0.00 0.00 2.87
2006 2871 4.870021 AATTTGCTACTCCCTCCATTCT 57.130 40.909 0.00 0.00 0.00 2.40
2096 2961 9.950680 TTTCAGATTCGGCATATTAGAAATTTC 57.049 29.630 10.33 10.33 0.00 2.17
2148 3013 2.094675 GTGTTTGGTAGGCTGCATCAT 58.905 47.619 4.64 0.00 0.00 2.45
2150 3015 2.290832 TGTTTGGTAGGCTGCATCATCA 60.291 45.455 4.64 0.00 0.00 3.07
2152 3017 2.265589 TGGTAGGCTGCATCATCATG 57.734 50.000 4.64 0.00 0.00 3.07
2177 3042 0.034337 GGCCGAGTGTGTGTAGGAAA 59.966 55.000 0.00 0.00 0.00 3.13
2178 3043 1.541670 GGCCGAGTGTGTGTAGGAAAA 60.542 52.381 0.00 0.00 0.00 2.29
2180 3045 2.032290 GCCGAGTGTGTGTAGGAAAAAC 60.032 50.000 0.00 0.00 0.00 2.43
2182 3047 3.001939 CCGAGTGTGTGTAGGAAAAACAC 59.998 47.826 0.00 0.00 45.96 3.32
2197 3062 4.608073 AAAACACATTTGGGAAAAACGC 57.392 36.364 0.00 0.00 0.00 4.84
2208 3073 3.175929 GGGAAAAACGCATTTGATACCG 58.824 45.455 0.00 0.00 0.00 4.02
2217 3082 3.241963 CGCATTTGATACCGTACACACAG 60.242 47.826 0.00 0.00 0.00 3.66
2218 3083 3.063452 GCATTTGATACCGTACACACAGG 59.937 47.826 0.00 0.00 0.00 4.00
2229 3094 0.478072 ACACACAGGGATTTGGCTCA 59.522 50.000 0.00 0.00 0.00 4.26
2232 3097 1.076024 ACACAGGGATTTGGCTCACAT 59.924 47.619 0.00 0.00 0.00 3.21
2233 3098 1.475280 CACAGGGATTTGGCTCACATG 59.525 52.381 0.00 0.00 0.00 3.21
2234 3099 1.076024 ACAGGGATTTGGCTCACATGT 59.924 47.619 0.00 0.00 0.00 3.21
2240 3105 2.535012 TTTGGCTCACATGTACACGA 57.465 45.000 0.00 0.00 0.00 4.35
2243 3108 1.069358 TGGCTCACATGTACACGAACA 59.931 47.619 0.00 0.00 0.00 3.18
2259 3124 3.244976 CGAACATTAAAGCAGCCCAAAG 58.755 45.455 0.00 0.00 0.00 2.77
2275 3140 2.094182 CCAAAGTCTGGCTCGCTAGTAA 60.094 50.000 2.19 0.00 38.76 2.24
2280 3145 1.338337 TCTGGCTCGCTAGTAATGCTC 59.662 52.381 2.19 0.00 0.00 4.26
2281 3146 1.067669 CTGGCTCGCTAGTAATGCTCA 59.932 52.381 0.00 0.00 0.00 4.26
2282 3147 1.480545 TGGCTCGCTAGTAATGCTCAA 59.519 47.619 0.00 0.00 0.00 3.02
2283 3148 2.093711 TGGCTCGCTAGTAATGCTCAAA 60.094 45.455 0.00 0.00 0.00 2.69
2284 3149 3.134458 GGCTCGCTAGTAATGCTCAAAT 58.866 45.455 0.00 0.00 0.00 2.32
2285 3150 3.185391 GGCTCGCTAGTAATGCTCAAATC 59.815 47.826 0.00 0.00 0.00 2.17
2287 3152 4.290969 CTCGCTAGTAATGCTCAAATCGA 58.709 43.478 0.00 0.00 0.00 3.59
2294 3159 3.471495 AATGCTCAAATCGACCGTTTC 57.529 42.857 0.00 0.00 0.00 2.78
2299 3164 2.256174 TCAAATCGACCGTTTCTAGCG 58.744 47.619 0.00 0.00 0.00 4.26
2322 3187 0.601046 CAGGCTGAGTCGAGTGCAAA 60.601 55.000 9.42 0.00 0.00 3.68
2327 3192 1.376037 GAGTCGAGTGCAAAGGGGG 60.376 63.158 0.00 0.00 0.00 5.40
2328 3193 3.056328 GTCGAGTGCAAAGGGGGC 61.056 66.667 0.00 0.00 0.00 5.80
2329 3194 3.565214 TCGAGTGCAAAGGGGGCA 61.565 61.111 0.00 0.00 39.32 5.36
2363 3366 4.035102 GCAGGGAGAAAGGGGCGT 62.035 66.667 0.00 0.00 0.00 5.68
2429 3432 3.757248 CTAGCATCACCGCACCCCC 62.757 68.421 0.00 0.00 0.00 5.40
2461 3464 7.772332 AAAATATTTACTCGCTCACCTGTAG 57.228 36.000 0.01 0.00 0.00 2.74
2476 3753 2.353803 CCTGTAGCGCTAGAACAAACCT 60.354 50.000 19.48 0.00 0.00 3.50
2560 3837 4.518249 CTTCAATCTTTGGTAGGAGGACC 58.482 47.826 0.00 0.00 40.21 4.46
2574 3851 3.404773 GACCTGGTCCTCCCCTTG 58.595 66.667 16.14 0.00 0.00 3.61
2660 3937 4.301072 AAGCAGCATACAAACCTCCTTA 57.699 40.909 0.00 0.00 0.00 2.69
2682 3959 8.139350 CCTTATGATGTTAGGTCGTTATGTACA 58.861 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.567164 GCTCAATAGTGCACTAATGGCAT 59.433 43.478 31.80 15.29 44.11 4.40
20 21 0.866427 CGCCAGAGCATGCTCAATAG 59.134 55.000 40.91 28.24 44.99 1.73
22 23 0.179026 ATCGCCAGAGCATGCTCAAT 60.179 50.000 40.91 24.38 44.99 2.57
29 30 2.646930 TCATTGAAATCGCCAGAGCAT 58.353 42.857 0.00 0.00 39.83 3.79
37 38 2.951642 TCCCTGGAATCATTGAAATCGC 59.048 45.455 0.00 0.00 0.00 4.58
46 47 3.249752 CTCTCCTCATCCCTGGAATCAT 58.750 50.000 0.00 0.00 31.23 2.45
47 48 2.687297 CTCTCCTCATCCCTGGAATCA 58.313 52.381 0.00 0.00 31.23 2.57
53 54 3.728385 AAAAACCTCTCCTCATCCCTG 57.272 47.619 0.00 0.00 0.00 4.45
71 72 1.407258 CCGTGGCAAACCTCTCAAAAA 59.593 47.619 0.00 0.00 36.63 1.94
72 73 1.028905 CCGTGGCAAACCTCTCAAAA 58.971 50.000 0.00 0.00 36.63 2.44
73 74 0.106918 ACCGTGGCAAACCTCTCAAA 60.107 50.000 0.00 0.00 36.63 2.69
74 75 0.534203 GACCGTGGCAAACCTCTCAA 60.534 55.000 0.00 0.00 36.63 3.02
75 76 1.070786 GACCGTGGCAAACCTCTCA 59.929 57.895 0.00 0.00 36.63 3.27
76 77 1.671379 GGACCGTGGCAAACCTCTC 60.671 63.158 0.00 0.00 36.63 3.20
77 78 2.397413 CTGGACCGTGGCAAACCTCT 62.397 60.000 0.00 0.00 36.63 3.69
78 79 1.966451 CTGGACCGTGGCAAACCTC 60.966 63.158 0.00 0.00 36.63 3.85
79 80 2.113139 CTGGACCGTGGCAAACCT 59.887 61.111 0.00 0.00 36.63 3.50
90 91 1.228769 GAAAACCCACCCCTGGACC 60.229 63.158 0.00 0.00 40.55 4.46
108 109 1.230635 CCCAGCACCAAGACTTGACG 61.231 60.000 16.99 7.97 0.00 4.35
109 110 0.890996 CCCCAGCACCAAGACTTGAC 60.891 60.000 16.99 5.82 0.00 3.18
110 111 1.059584 TCCCCAGCACCAAGACTTGA 61.060 55.000 16.99 0.00 0.00 3.02
133 134 6.022315 TCTTTCTCTCTCCCTCATCTTCTTT 58.978 40.000 0.00 0.00 0.00 2.52
213 216 3.128242 CAGCCTCAGTGATCAATTTGACC 59.872 47.826 0.15 0.00 0.00 4.02
224 227 1.571955 TCTAATGCCAGCCTCAGTGA 58.428 50.000 0.00 0.00 0.00 3.41
233 236 4.556898 GCAATGAAGCTCATCTAATGCCAG 60.557 45.833 0.00 0.00 35.76 4.85
239 242 4.449131 CTCCTGCAATGAAGCTCATCTAA 58.551 43.478 0.00 0.00 35.76 2.10
302 306 6.987386 TCTGGTTTTGAAACTTTTGTGAAGA 58.013 32.000 6.57 0.00 38.89 2.87
361 365 2.932187 GCCAACAGACCATTCATTTGGC 60.932 50.000 7.35 7.35 46.54 4.52
373 377 2.224018 TGCCAATTTTGAGCCAACAGAC 60.224 45.455 0.00 0.00 0.00 3.51
378 382 0.686224 CCCTGCCAATTTTGAGCCAA 59.314 50.000 0.00 0.00 0.00 4.52
495 510 8.952278 GGGTGCAAATATGGATTTTCGTATATA 58.048 33.333 0.00 0.00 32.73 0.86
498 513 5.278266 CGGGTGCAAATATGGATTTTCGTAT 60.278 40.000 0.00 0.00 32.73 3.06
501 516 3.371168 CGGGTGCAAATATGGATTTTCG 58.629 45.455 0.00 0.00 32.73 3.46
505 520 1.039856 GCCGGGTGCAAATATGGATT 58.960 50.000 2.18 0.00 40.77 3.01
508 523 0.751277 TCAGCCGGGTGCAAATATGG 60.751 55.000 28.72 1.75 44.83 2.74
509 524 0.381801 GTCAGCCGGGTGCAAATATG 59.618 55.000 28.72 2.56 44.83 1.78
510 525 1.095228 CGTCAGCCGGGTGCAAATAT 61.095 55.000 28.72 0.00 44.83 1.28
512 527 3.055719 CGTCAGCCGGGTGCAAAT 61.056 61.111 28.72 0.00 44.83 2.32
513 528 3.758973 TTCGTCAGCCGGGTGCAAA 62.759 57.895 28.72 18.08 44.83 3.68
514 529 3.758973 TTTCGTCAGCCGGGTGCAA 62.759 57.895 28.72 17.16 44.83 4.08
516 531 2.548295 TTTTTCGTCAGCCGGGTGC 61.548 57.895 28.72 21.12 41.71 5.01
517 532 3.739167 TTTTTCGTCAGCCGGGTG 58.261 55.556 27.73 27.73 37.11 4.61
580 726 3.120199 ACGCATCAAATTGTCTACTGCAC 60.120 43.478 0.00 0.00 0.00 4.57
585 731 3.684788 ACCTCACGCATCAAATTGTCTAC 59.315 43.478 0.00 0.00 0.00 2.59
586 732 3.932710 GACCTCACGCATCAAATTGTCTA 59.067 43.478 0.00 0.00 0.00 2.59
590 736 1.202065 CGGACCTCACGCATCAAATTG 60.202 52.381 0.00 0.00 0.00 2.32
591 737 1.086696 CGGACCTCACGCATCAAATT 58.913 50.000 0.00 0.00 0.00 1.82
592 738 2.767536 CGGACCTCACGCATCAAAT 58.232 52.632 0.00 0.00 0.00 2.32
601 747 1.534729 AAAATTGGAGCGGACCTCAC 58.465 50.000 0.00 0.00 42.62 3.51
602 748 2.286365 AAAAATTGGAGCGGACCTCA 57.714 45.000 0.00 0.00 42.62 3.86
603 749 3.756963 ACTTAAAAATTGGAGCGGACCTC 59.243 43.478 0.00 0.00 39.98 3.85
605 751 3.756963 AGACTTAAAAATTGGAGCGGACC 59.243 43.478 0.00 0.00 0.00 4.46
606 752 5.372547 AAGACTTAAAAATTGGAGCGGAC 57.627 39.130 0.00 0.00 0.00 4.79
608 754 5.405269 CCAAAAGACTTAAAAATTGGAGCGG 59.595 40.000 9.19 0.00 39.69 5.52
609 755 6.143919 GTCCAAAAGACTTAAAAATTGGAGCG 59.856 38.462 15.52 0.00 44.92 5.03
610 756 6.983890 TGTCCAAAAGACTTAAAAATTGGAGC 59.016 34.615 15.52 11.88 44.92 4.70
616 762 9.860898 GCTCATATGTCCAAAAGACTTAAAAAT 57.139 29.630 1.90 0.00 46.46 1.82
617 763 9.077885 AGCTCATATGTCCAAAAGACTTAAAAA 57.922 29.630 1.90 0.00 46.46 1.94
619 765 8.103305 AGAGCTCATATGTCCAAAAGACTTAAA 58.897 33.333 17.77 0.00 46.46 1.52
620 766 7.624549 AGAGCTCATATGTCCAAAAGACTTAA 58.375 34.615 17.77 0.00 46.46 1.85
621 767 7.093333 TGAGAGCTCATATGTCCAAAAGACTTA 60.093 37.037 17.77 0.00 39.42 2.24
622 768 6.059787 AGAGCTCATATGTCCAAAAGACTT 57.940 37.500 17.77 0.00 46.46 3.01
623 769 5.188555 TGAGAGCTCATATGTCCAAAAGACT 59.811 40.000 17.77 0.00 39.42 3.24
624 770 5.423015 TGAGAGCTCATATGTCCAAAAGAC 58.577 41.667 17.77 0.00 39.26 3.01
626 772 4.272991 GCTGAGAGCTCATATGTCCAAAAG 59.727 45.833 17.77 0.00 39.13 2.27
628 774 3.198417 TGCTGAGAGCTCATATGTCCAAA 59.802 43.478 17.77 0.00 42.97 3.28
629 775 2.767960 TGCTGAGAGCTCATATGTCCAA 59.232 45.455 17.77 0.00 42.97 3.53
630 776 2.391678 TGCTGAGAGCTCATATGTCCA 58.608 47.619 17.77 0.50 42.97 4.02
631 777 3.465742 TTGCTGAGAGCTCATATGTCC 57.534 47.619 17.77 0.00 42.97 4.02
632 778 5.808042 TTTTTGCTGAGAGCTCATATGTC 57.192 39.130 17.77 4.63 42.97 3.06
736 1598 6.428159 TGGTTTTCTTTGATCTGTTCTAGCTC 59.572 38.462 0.00 0.00 0.00 4.09
935 1797 1.543896 CCTTGGAGGGGAAGGGGAA 60.544 63.158 0.00 0.00 37.00 3.97
1081 1943 0.878523 CCGCTGTGTTCTTTGGACGA 60.879 55.000 0.00 0.00 0.00 4.20
1736 2598 1.483827 TGAGATAGCCAGCACTTCCAG 59.516 52.381 0.00 0.00 0.00 3.86
1932 2797 6.642707 TCAACTACGATTTCACCCAATTTT 57.357 33.333 0.00 0.00 0.00 1.82
2006 2871 5.655532 GGGCGTAATCATATCTACTCCCTAA 59.344 44.000 6.84 0.00 39.17 2.69
2148 3013 1.296392 CACTCGGCCTGTTCCATGA 59.704 57.895 0.00 0.00 0.00 3.07
2150 3015 1.003355 CACACTCGGCCTGTTCCAT 60.003 57.895 0.00 0.00 0.00 3.41
2152 3017 1.961277 CACACACTCGGCCTGTTCC 60.961 63.158 0.00 0.00 0.00 3.62
2161 3026 4.191662 GTGTTTTTCCTACACACACTCG 57.808 45.455 0.00 0.00 44.08 4.18
2177 3042 3.600388 TGCGTTTTTCCCAAATGTGTTT 58.400 36.364 0.00 0.00 0.00 2.83
2178 3043 3.252974 TGCGTTTTTCCCAAATGTGTT 57.747 38.095 0.00 0.00 0.00 3.32
2180 3045 4.272018 TCAAATGCGTTTTTCCCAAATGTG 59.728 37.500 0.00 0.00 0.00 3.21
2182 3047 5.610235 ATCAAATGCGTTTTTCCCAAATG 57.390 34.783 0.00 0.00 0.00 2.32
2183 3048 5.641636 GGTATCAAATGCGTTTTTCCCAAAT 59.358 36.000 0.00 0.00 0.00 2.32
2184 3049 4.991687 GGTATCAAATGCGTTTTTCCCAAA 59.008 37.500 0.00 0.00 0.00 3.28
2185 3050 4.561105 GGTATCAAATGCGTTTTTCCCAA 58.439 39.130 0.00 0.00 0.00 4.12
2186 3051 3.366476 CGGTATCAAATGCGTTTTTCCCA 60.366 43.478 0.00 0.00 0.00 4.37
2187 3052 3.175929 CGGTATCAAATGCGTTTTTCCC 58.824 45.455 0.00 0.00 0.00 3.97
2188 3053 3.828786 ACGGTATCAAATGCGTTTTTCC 58.171 40.909 0.00 1.63 0.00 3.13
2197 3062 3.621268 CCCTGTGTGTACGGTATCAAATG 59.379 47.826 0.00 0.00 0.00 2.32
2208 3073 2.084546 GAGCCAAATCCCTGTGTGTAC 58.915 52.381 0.00 0.00 0.00 2.90
2217 3082 2.423538 GTGTACATGTGAGCCAAATCCC 59.576 50.000 9.11 0.00 0.00 3.85
2218 3083 2.095853 CGTGTACATGTGAGCCAAATCC 59.904 50.000 9.11 0.00 0.00 3.01
2229 3094 5.616866 GCTGCTTTAATGTTCGTGTACATGT 60.617 40.000 14.63 2.69 38.69 3.21
2232 3097 3.187637 GGCTGCTTTAATGTTCGTGTACA 59.812 43.478 0.00 0.00 0.00 2.90
2233 3098 3.425758 GGGCTGCTTTAATGTTCGTGTAC 60.426 47.826 0.00 0.00 0.00 2.90
2234 3099 2.745281 GGGCTGCTTTAATGTTCGTGTA 59.255 45.455 0.00 0.00 0.00 2.90
2240 3105 3.897505 AGACTTTGGGCTGCTTTAATGTT 59.102 39.130 0.00 0.00 0.00 2.71
2243 3108 2.827921 CCAGACTTTGGGCTGCTTTAAT 59.172 45.455 0.00 0.00 43.75 1.40
2259 3124 1.067821 AGCATTACTAGCGAGCCAGAC 59.932 52.381 0.00 0.00 37.01 3.51
2265 3130 4.147306 GTCGATTTGAGCATTACTAGCGAG 59.853 45.833 0.00 0.00 37.01 5.03
2275 3140 2.699954 AGAAACGGTCGATTTGAGCAT 58.300 42.857 4.10 0.00 45.52 3.79
2280 3145 2.256174 TCGCTAGAAACGGTCGATTTG 58.744 47.619 0.00 0.00 0.00 2.32
2281 3146 2.094854 ACTCGCTAGAAACGGTCGATTT 60.095 45.455 0.00 0.00 0.00 2.17
2282 3147 1.471684 ACTCGCTAGAAACGGTCGATT 59.528 47.619 0.00 0.00 0.00 3.34
2283 3148 1.063764 GACTCGCTAGAAACGGTCGAT 59.936 52.381 0.00 0.00 0.00 3.59
2284 3149 0.445436 GACTCGCTAGAAACGGTCGA 59.555 55.000 0.00 0.00 0.00 4.20
2285 3150 0.167470 TGACTCGCTAGAAACGGTCG 59.833 55.000 0.00 0.00 35.12 4.79
2287 3152 0.526662 CCTGACTCGCTAGAAACGGT 59.473 55.000 0.00 0.00 0.00 4.83
2294 3159 0.380378 GACTCAGCCTGACTCGCTAG 59.620 60.000 0.00 0.00 33.91 3.42
2299 3164 0.170116 CACTCGACTCAGCCTGACTC 59.830 60.000 0.00 0.00 0.00 3.36
2322 3187 4.109675 GCATACACCGTGCCCCCT 62.110 66.667 0.00 0.00 36.61 4.79
2328 3193 3.115892 AACGCCGCATACACCGTG 61.116 61.111 0.00 0.00 33.78 4.94
2329 3194 3.115892 CAACGCCGCATACACCGT 61.116 61.111 0.00 0.00 35.14 4.83
2330 3195 4.514569 GCAACGCCGCATACACCG 62.515 66.667 0.00 0.00 0.00 4.94
2331 3196 3.381169 CTGCAACGCCGCATACACC 62.381 63.158 0.00 0.00 42.06 4.16
2332 3197 2.098298 CTGCAACGCCGCATACAC 59.902 61.111 0.00 0.00 42.06 2.90
2333 3198 3.124270 CCTGCAACGCCGCATACA 61.124 61.111 0.00 0.00 42.06 2.29
2334 3199 3.876198 CCCTGCAACGCCGCATAC 61.876 66.667 0.00 0.00 42.06 2.39
2363 3366 5.907662 AGATTTTGGTCTCCCATCATCTCTA 59.092 40.000 0.00 0.00 41.49 2.43
2429 3432 8.850452 GTGAGCGAGTAAATATTTTTCTTTTGG 58.150 33.333 5.91 0.14 0.00 3.28
2430 3433 8.850452 GGTGAGCGAGTAAATATTTTTCTTTTG 58.150 33.333 5.91 2.56 0.00 2.44
2441 3444 4.303086 GCTACAGGTGAGCGAGTAAATA 57.697 45.455 0.00 0.00 0.00 1.40
2507 3784 2.430465 TGCTTCTGCAGATTTGAGTCC 58.570 47.619 19.04 0.75 45.31 3.85
2560 3837 0.842467 AAGACCAAGGGGAGGACCAG 60.842 60.000 0.00 0.00 42.91 4.00
2565 3842 1.003696 GAGTCAAAGACCAAGGGGAGG 59.996 57.143 0.00 0.00 38.05 4.30
2574 3851 3.949113 AGGACGAGATAGAGTCAAAGACC 59.051 47.826 0.00 0.00 39.01 3.85
2621 3898 0.996583 TTACCCCCTTTGAAGCCGAT 59.003 50.000 0.00 0.00 0.00 4.18
2624 3901 0.251608 TGCTTACCCCCTTTGAAGCC 60.252 55.000 3.24 0.00 42.93 4.35
2660 3937 7.108841 ACTGTACATAACGACCTAACATCAT 57.891 36.000 0.00 0.00 0.00 2.45



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

AutoCloner maintained by Alex Coulton.