Multiple sequence alignment - TraesCS1D01G296100

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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 TraesCS1D01G296100 chr1D 100.000 2333 0 0 862 3194 394279871 394277539 0.000000e+00 4309.0
1 TraesCS1D01G296100 chr1D 100.000 260 0 0 1 260 394280732 394280473 6.200000e-132 481.0
2 TraesCS1D01G296100 chr1A 92.991 2354 135 16 862 3194 491128557 491130901 0.000000e+00 3406.0
3 TraesCS1D01G296100 chr1A 91.736 121 6 2 133 253 491125676 491125792 7.090000e-37 165.0
4 TraesCS1D01G296100 chr1A 93.671 79 5 0 1 79 491124685 491124763 5.600000e-23 119.0
5 TraesCS1D01G296100 chr1A 88.136 59 6 1 2845 2902 491130440 491130498 5.720000e-08 69.4
6 TraesCS1D01G296100 chr1B 96.000 1825 69 3 876 2700 527646819 527648639 0.000000e+00 2963.0
7 TraesCS1D01G296100 chr1B 85.927 604 65 9 2583 3171 527648602 527649200 7.520000e-176 627.0
8 TraesCS1D01G296100 chr1B 92.683 82 3 1 172 253 527646044 527646122 7.240000e-22 115.0
9 TraesCS1D01G296100 chr1B 95.312 64 1 1 120 183 527645880 527645941 2.030000e-17 100.0
10 TraesCS1D01G296100 chrUn 93.333 45 3 0 120 164 153373932 153373976 2.060000e-07 67.6
11 TraesCS1D01G296100 chr7A 90.244 41 4 0 25 65 663549476 663549516 2.000000e-03 54.7


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 TraesCS1D01G296100 chr1D 394277539 394280732 3193 True 2395.00 4309 100.0000 1 3194 2 chr1D.!!$R1 3193
1 TraesCS1D01G296100 chr1A 491124685 491130901 6216 False 939.85 3406 91.6335 1 3194 4 chr1A.!!$F1 3193
2 TraesCS1D01G296100 chr1B 527645880 527649200 3320 False 951.25 2963 92.4805 120 3171 4 chr1B.!!$F1 3051

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
111 112 0.037303 CCGAGCATTGGCCTGGATAT 59.963 55.0 3.32 0.00 42.56 1.63 F
183 1080 0.610232 AGGCCTCAAATGGACAGCAC 60.610 55.0 0.00 0.00 37.66 4.40 F
2094 5269 0.392998 AACCTAGCAATGCAGGGTCG 60.393 55.0 21.50 2.07 35.45 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 4864 0.179051 GCCTCCTTGCTCTCATCCTG 60.179 60.0 0.0 0.0 0.00 3.86 R
2139 5314 0.752743 CGCCACCATCCACATCCAAT 60.753 55.0 0.0 0.0 0.00 3.16 R
3010 6307 0.179062 ATTGATCAGCAGAGCGTCCC 60.179 55.0 0.0 0.0 31.29 4.46 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
27 28 3.305267 CCGTGCTGGTTGAAATTCATCAA 60.305 43.478 0.00 0.00 36.99 2.57
34 35 7.014134 TGCTGGTTGAAATTCATCAAGTTTCTA 59.986 33.333 9.47 0.00 39.84 2.10
79 80 1.673767 ACTGAGGTGACCATTCCCAT 58.326 50.000 3.63 0.00 0.00 4.00
80 81 1.561542 ACTGAGGTGACCATTCCCATC 59.438 52.381 3.63 0.00 0.00 3.51
81 82 1.842562 CTGAGGTGACCATTCCCATCT 59.157 52.381 3.63 0.00 0.00 2.90
82 83 1.561076 TGAGGTGACCATTCCCATCTG 59.439 52.381 3.63 0.00 0.00 2.90
83 84 1.561542 GAGGTGACCATTCCCATCTGT 59.438 52.381 3.63 0.00 0.00 3.41
84 85 1.283029 AGGTGACCATTCCCATCTGTG 59.717 52.381 3.63 0.00 0.00 3.66
85 86 1.004745 GGTGACCATTCCCATCTGTGT 59.995 52.381 0.00 0.00 0.00 3.72
86 87 2.086869 GTGACCATTCCCATCTGTGTG 58.913 52.381 0.00 0.00 0.00 3.82
87 88 1.704628 TGACCATTCCCATCTGTGTGT 59.295 47.619 0.00 0.00 0.00 3.72
88 89 2.086869 GACCATTCCCATCTGTGTGTG 58.913 52.381 0.00 0.00 0.00 3.82
89 90 1.704628 ACCATTCCCATCTGTGTGTGA 59.295 47.619 0.00 0.00 0.00 3.58
90 91 2.108075 ACCATTCCCATCTGTGTGTGAA 59.892 45.455 0.00 0.00 0.00 3.18
91 92 3.245371 ACCATTCCCATCTGTGTGTGAAT 60.245 43.478 0.00 0.00 0.00 2.57
92 93 3.379372 CCATTCCCATCTGTGTGTGAATC 59.621 47.826 0.00 0.00 0.00 2.52
93 94 2.787473 TCCCATCTGTGTGTGAATCC 57.213 50.000 0.00 0.00 0.00 3.01
94 95 1.066215 TCCCATCTGTGTGTGAATCCG 60.066 52.381 0.00 0.00 0.00 4.18
95 96 1.066215 CCCATCTGTGTGTGAATCCGA 60.066 52.381 0.00 0.00 0.00 4.55
96 97 2.274437 CCATCTGTGTGTGAATCCGAG 58.726 52.381 0.00 0.00 0.00 4.63
97 98 1.662629 CATCTGTGTGTGAATCCGAGC 59.337 52.381 0.00 0.00 0.00 5.03
98 99 0.678950 TCTGTGTGTGAATCCGAGCA 59.321 50.000 0.00 0.00 0.00 4.26
99 100 1.276138 TCTGTGTGTGAATCCGAGCAT 59.724 47.619 0.00 0.00 0.00 3.79
100 101 2.079158 CTGTGTGTGAATCCGAGCATT 58.921 47.619 0.00 0.00 0.00 3.56
101 102 1.805943 TGTGTGTGAATCCGAGCATTG 59.194 47.619 0.00 0.00 0.00 2.82
102 103 1.131126 GTGTGTGAATCCGAGCATTGG 59.869 52.381 0.00 0.00 42.86 3.16
103 104 0.099436 GTGTGAATCCGAGCATTGGC 59.901 55.000 0.00 0.00 40.51 4.52
104 105 1.031571 TGTGAATCCGAGCATTGGCC 61.032 55.000 0.00 0.00 40.51 5.36
105 106 0.749454 GTGAATCCGAGCATTGGCCT 60.749 55.000 3.32 0.00 40.51 5.19
106 107 0.749091 TGAATCCGAGCATTGGCCTG 60.749 55.000 3.32 0.00 40.51 4.85
107 108 1.450531 GAATCCGAGCATTGGCCTGG 61.451 60.000 3.32 0.00 40.51 4.45
108 109 1.925285 AATCCGAGCATTGGCCTGGA 61.925 55.000 3.32 0.00 44.82 3.86
109 110 1.713005 ATCCGAGCATTGGCCTGGAT 61.713 55.000 3.32 2.55 44.66 3.41
110 111 1.053835 TCCGAGCATTGGCCTGGATA 61.054 55.000 3.32 0.00 40.51 2.59
111 112 0.037303 CCGAGCATTGGCCTGGATAT 59.963 55.000 3.32 0.00 42.56 1.63
112 113 1.546323 CCGAGCATTGGCCTGGATATT 60.546 52.381 3.32 0.00 42.56 1.28
113 114 1.808945 CGAGCATTGGCCTGGATATTC 59.191 52.381 3.32 0.00 42.56 1.75
114 115 2.811504 CGAGCATTGGCCTGGATATTCA 60.812 50.000 3.32 0.00 42.56 2.57
115 116 3.428532 GAGCATTGGCCTGGATATTCAT 58.571 45.455 3.32 0.00 42.56 2.57
116 117 3.830755 GAGCATTGGCCTGGATATTCATT 59.169 43.478 3.32 0.00 42.56 2.57
117 118 3.576982 AGCATTGGCCTGGATATTCATTG 59.423 43.478 3.32 0.00 42.56 2.82
118 119 3.322828 GCATTGGCCTGGATATTCATTGT 59.677 43.478 3.32 0.00 0.00 2.71
183 1080 0.610232 AGGCCTCAAATGGACAGCAC 60.610 55.000 0.00 0.00 37.66 4.40
186 1083 1.615392 GCCTCAAATGGACAGCACTTT 59.385 47.619 0.00 0.00 0.00 2.66
193 1201 6.503524 TCAAATGGACAGCACTTTTTCTAAC 58.496 36.000 0.00 0.00 0.00 2.34
1254 4429 1.696832 GCTTTGAGATGGCCGACGAC 61.697 60.000 0.00 0.00 0.00 4.34
1407 4582 3.260205 TGGGAGAGGGAATTCAACTTCT 58.740 45.455 7.93 1.97 0.00 2.85
1659 4834 5.412640 CAGGAGATGATAGATCATGCTCAC 58.587 45.833 20.95 14.97 46.84 3.51
1689 4864 3.636381 CCGTCTAAGCCGAATTACTACC 58.364 50.000 0.00 0.00 0.00 3.18
2094 5269 0.392998 AACCTAGCAATGCAGGGTCG 60.393 55.000 21.50 2.07 35.45 4.79
2139 5314 0.389426 GAAGCGACGCCTTAGGTTCA 60.389 55.000 17.79 0.00 40.73 3.18
2185 5360 1.004918 CGGAACAAGAGAAGGCGGT 60.005 57.895 0.00 0.00 0.00 5.68
2215 5390 0.806492 CTAAGAAGGCCGAACCGAGC 60.806 60.000 0.00 0.00 46.52 5.03
2233 5408 1.280133 AGCATTGCAGAGGCTTCAGTA 59.720 47.619 11.91 0.00 44.24 2.74
2313 5489 5.798132 ACTCTATGCTGAGTGTGATCAAAA 58.202 37.500 0.00 0.00 44.64 2.44
2348 5524 6.403878 TCTGCTTGTTTAATAGGGTACTGTC 58.596 40.000 0.00 0.00 0.00 3.51
2510 5686 9.855021 AACTTTTAGTGTCATAAATAATGCACC 57.145 29.630 0.00 0.00 40.51 5.01
2545 5721 1.740025 GGTTGTAGATGGCTGAAGTGC 59.260 52.381 0.00 0.00 0.00 4.40
2552 5728 1.542915 GATGGCTGAAGTGCACATGTT 59.457 47.619 21.04 4.29 34.04 2.71
2564 5740 2.553602 TGCACATGTTAAACTGAGCTGG 59.446 45.455 0.00 0.00 31.37 4.85
2597 5773 3.438216 TGGAGTGAATGAATGCCAAGA 57.562 42.857 0.00 0.00 0.00 3.02
2623 5799 5.041287 CGAACTCTGTTGTCACTTTACTGA 58.959 41.667 0.00 0.00 0.00 3.41
2633 5809 4.154015 TGTCACTTTACTGAATGAATGCCG 59.846 41.667 0.00 0.00 0.00 5.69
2635 5811 5.000591 TCACTTTACTGAATGAATGCCGAA 58.999 37.500 0.00 0.00 0.00 4.30
2698 5950 3.650139 ACGAACTCTGTTGTCGCTTTAT 58.350 40.909 0.00 0.00 0.00 1.40
2705 5957 7.027778 ACTCTGTTGTCGCTTTATTCTTTTT 57.972 32.000 0.00 0.00 0.00 1.94
2746 5998 1.002134 TGCTACTGGGCAAAGAGGC 60.002 57.895 0.00 0.00 39.43 4.70
2769 6024 6.314784 GCATGTTAAGTCGCAATAAAGAAGT 58.685 36.000 0.00 0.00 0.00 3.01
2891 6187 9.860898 AGAAAAGCATTTCCTTTTGTGATATAC 57.139 29.630 10.64 0.00 44.96 1.47
2939 6236 7.502895 ACACTACTATCTATGTTCAGGATCGTT 59.497 37.037 0.00 0.00 0.00 3.85
2947 6244 4.295141 TGTTCAGGATCGTTTATTGGGT 57.705 40.909 0.00 0.00 0.00 4.51
2988 6285 6.516478 ACGATCGATATTTGTGTGATTCAG 57.484 37.500 24.34 0.00 0.00 3.02
3000 6297 3.068024 GTGTGATTCAGTGCCCTTTTTCA 59.932 43.478 0.00 0.00 0.00 2.69
3001 6298 3.896888 TGTGATTCAGTGCCCTTTTTCAT 59.103 39.130 0.00 0.00 0.00 2.57
3010 6307 2.562298 TGCCCTTTTTCATGCTGGTTAG 59.438 45.455 0.00 0.00 0.00 2.34
3014 6311 3.193479 CCTTTTTCATGCTGGTTAGGGAC 59.807 47.826 0.00 0.00 0.00 4.46
3021 6318 1.153549 CTGGTTAGGGACGCTCTGC 60.154 63.158 0.00 0.00 0.00 4.26
3022 6319 1.608717 CTGGTTAGGGACGCTCTGCT 61.609 60.000 0.00 0.00 0.00 4.24
3027 6324 0.395724 TAGGGACGCTCTGCTGATCA 60.396 55.000 0.00 0.00 0.00 2.92
3028 6325 1.219124 GGGACGCTCTGCTGATCAA 59.781 57.895 0.00 0.00 0.00 2.57
3033 6330 2.539274 GACGCTCTGCTGATCAATCTTC 59.461 50.000 0.00 0.00 0.00 2.87
3041 6338 2.897436 CTGATCAATCTTCGCTGTCCA 58.103 47.619 0.00 0.00 0.00 4.02
3042 6339 3.264947 CTGATCAATCTTCGCTGTCCAA 58.735 45.455 0.00 0.00 0.00 3.53
3043 6340 3.673902 TGATCAATCTTCGCTGTCCAAA 58.326 40.909 0.00 0.00 0.00 3.28
3045 6342 4.701651 TGATCAATCTTCGCTGTCCAAAAT 59.298 37.500 0.00 0.00 0.00 1.82
3046 6343 5.183713 TGATCAATCTTCGCTGTCCAAAATT 59.816 36.000 0.00 0.00 0.00 1.82
3063 6363 8.023706 GTCCAAAATTTTGCAACCAGTTTTAAA 58.976 29.630 22.90 0.00 36.86 1.52
3074 6374 6.526674 GCAACCAGTTTTAAATATTCAGGACG 59.473 38.462 0.00 0.00 0.00 4.79
3085 6385 2.226962 TTCAGGACGGTAGGCTTAGT 57.773 50.000 0.00 0.00 0.00 2.24
3091 6391 0.102481 ACGGTAGGCTTAGTCATGCG 59.898 55.000 0.00 0.00 0.00 4.73
3094 6394 2.629051 GGTAGGCTTAGTCATGCGTTT 58.371 47.619 0.00 0.00 0.00 3.60
3104 6404 7.587757 GGCTTAGTCATGCGTTTATTTGATAAG 59.412 37.037 0.00 0.00 0.00 1.73
3106 6406 6.435430 AGTCATGCGTTTATTTGATAAGCA 57.565 33.333 0.00 0.00 32.69 3.91
3115 6415 7.268722 CGTTTATTTGATAAGCATTTGCATCG 58.731 34.615 5.20 0.00 45.16 3.84
3116 6416 7.044117 CGTTTATTTGATAAGCATTTGCATCGT 60.044 33.333 5.20 0.00 45.16 3.73
3127 6427 4.438608 GCATTTGCATCGTCAGGTTCATTA 60.439 41.667 0.00 0.00 41.59 1.90
3147 6447 7.252708 TCATTAATCTGTTGTGCAATGTCATC 58.747 34.615 0.00 0.00 0.00 2.92
3174 6474 0.394192 TGGAGCAAGACTGGACACTG 59.606 55.000 0.00 0.00 0.00 3.66
3178 6478 0.607489 GCAAGACTGGACACTGGCAT 60.607 55.000 0.00 0.00 33.71 4.40
3189 6489 3.316308 GGACACTGGCATTGGAATGATAC 59.684 47.826 9.77 0.00 38.70 2.24
3190 6490 3.947196 GACACTGGCATTGGAATGATACA 59.053 43.478 9.77 0.00 38.70 2.29
3191 6491 3.696051 ACACTGGCATTGGAATGATACAC 59.304 43.478 9.77 0.00 38.70 2.90
3192 6492 3.695556 CACTGGCATTGGAATGATACACA 59.304 43.478 3.47 0.00 38.70 3.72
3193 6493 4.340097 CACTGGCATTGGAATGATACACAT 59.660 41.667 3.47 0.00 41.45 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.228582 TGATGAATTTCAACCAGCACGG 59.771 45.455 2.68 0.00 42.50 4.94
10 11 9.565213 GATAGAAACTTGATGAATTTCAACCAG 57.435 33.333 2.68 4.85 35.26 4.00
27 28 9.959721 TTTAGTGCTCTTTAATGGATAGAAACT 57.040 29.630 0.00 0.00 0.00 2.66
79 80 0.678950 TGCTCGGATTCACACACAGA 59.321 50.000 0.00 0.00 0.00 3.41
80 81 1.730501 ATGCTCGGATTCACACACAG 58.269 50.000 0.00 0.00 0.00 3.66
81 82 1.805943 CAATGCTCGGATTCACACACA 59.194 47.619 0.00 0.00 0.00 3.72
82 83 1.131126 CCAATGCTCGGATTCACACAC 59.869 52.381 0.00 0.00 0.00 3.82
83 84 1.452110 CCAATGCTCGGATTCACACA 58.548 50.000 0.00 0.00 0.00 3.72
84 85 0.099436 GCCAATGCTCGGATTCACAC 59.901 55.000 0.00 0.00 33.53 3.82
85 86 1.031571 GGCCAATGCTCGGATTCACA 61.032 55.000 0.00 0.00 37.74 3.58
86 87 0.749454 AGGCCAATGCTCGGATTCAC 60.749 55.000 5.01 0.00 37.74 3.18
87 88 0.749091 CAGGCCAATGCTCGGATTCA 60.749 55.000 5.01 0.00 37.74 2.57
88 89 1.450531 CCAGGCCAATGCTCGGATTC 61.451 60.000 5.01 0.00 37.74 2.52
89 90 1.454479 CCAGGCCAATGCTCGGATT 60.454 57.895 5.01 0.00 37.74 3.01
90 91 1.713005 ATCCAGGCCAATGCTCGGAT 61.713 55.000 5.01 1.24 41.02 4.18
91 92 1.053835 TATCCAGGCCAATGCTCGGA 61.054 55.000 5.01 0.00 40.46 4.55
92 93 0.037303 ATATCCAGGCCAATGCTCGG 59.963 55.000 5.01 0.00 37.74 4.63
93 94 1.808945 GAATATCCAGGCCAATGCTCG 59.191 52.381 5.01 0.00 37.74 5.03
94 95 2.867624 TGAATATCCAGGCCAATGCTC 58.132 47.619 5.01 0.00 37.74 4.26
95 96 3.537795 ATGAATATCCAGGCCAATGCT 57.462 42.857 5.01 0.00 37.74 3.79
96 97 3.322828 ACAATGAATATCCAGGCCAATGC 59.677 43.478 5.01 0.00 0.00 3.56
97 98 5.771666 AGTACAATGAATATCCAGGCCAATG 59.228 40.000 5.01 0.00 0.00 2.82
98 99 5.957132 AGTACAATGAATATCCAGGCCAAT 58.043 37.500 5.01 0.00 0.00 3.16
99 100 5.387113 AGTACAATGAATATCCAGGCCAA 57.613 39.130 5.01 0.00 0.00 4.52
100 101 6.044287 ACATAGTACAATGAATATCCAGGCCA 59.956 38.462 5.01 0.00 0.00 5.36
101 102 6.476378 ACATAGTACAATGAATATCCAGGCC 58.524 40.000 0.00 0.00 0.00 5.19
102 103 6.595716 GGACATAGTACAATGAATATCCAGGC 59.404 42.308 0.00 0.00 0.00 4.85
103 104 7.604164 GTGGACATAGTACAATGAATATCCAGG 59.396 40.741 0.00 0.00 32.18 4.45
104 105 7.604164 GGTGGACATAGTACAATGAATATCCAG 59.396 40.741 0.00 0.00 32.18 3.86
105 106 7.450074 GGTGGACATAGTACAATGAATATCCA 58.550 38.462 0.00 0.00 30.17 3.41
106 107 6.879458 GGGTGGACATAGTACAATGAATATCC 59.121 42.308 0.00 0.00 0.00 2.59
107 108 7.450074 TGGGTGGACATAGTACAATGAATATC 58.550 38.462 0.00 0.00 0.00 1.63
108 109 7.387265 TGGGTGGACATAGTACAATGAATAT 57.613 36.000 0.00 0.00 0.00 1.28
109 110 6.816616 TGGGTGGACATAGTACAATGAATA 57.183 37.500 0.00 0.00 0.00 1.75
110 111 5.708736 TGGGTGGACATAGTACAATGAAT 57.291 39.130 0.00 0.00 0.00 2.57
111 112 5.428457 AGATGGGTGGACATAGTACAATGAA 59.572 40.000 0.00 0.00 0.00 2.57
112 113 4.968719 AGATGGGTGGACATAGTACAATGA 59.031 41.667 0.00 0.00 0.00 2.57
113 114 5.070981 AGAGATGGGTGGACATAGTACAATG 59.929 44.000 0.00 0.00 0.00 2.82
114 115 5.070981 CAGAGATGGGTGGACATAGTACAAT 59.929 44.000 0.00 0.00 0.00 2.71
115 116 4.405680 CAGAGATGGGTGGACATAGTACAA 59.594 45.833 0.00 0.00 0.00 2.41
116 117 3.960755 CAGAGATGGGTGGACATAGTACA 59.039 47.826 0.00 0.00 0.00 2.90
117 118 3.961408 ACAGAGATGGGTGGACATAGTAC 59.039 47.826 0.00 0.00 0.00 2.73
118 119 3.960755 CACAGAGATGGGTGGACATAGTA 59.039 47.826 0.00 0.00 0.00 1.82
183 1080 5.611374 TGGACCTCACTCAGTTAGAAAAAG 58.389 41.667 0.00 0.00 0.00 2.27
186 1083 4.899457 TCTTGGACCTCACTCAGTTAGAAA 59.101 41.667 0.00 0.00 0.00 2.52
193 1201 4.342862 TTTTCTCTTGGACCTCACTCAG 57.657 45.455 0.00 0.00 0.00 3.35
1194 4369 2.432628 GTGCTCTTCCCACGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
1203 4378 1.881973 TCAAACATGGCAGTGCTCTTC 59.118 47.619 16.11 0.00 0.00 2.87
1254 4429 1.966451 GCAAGAAGTGACCACCGGG 60.966 63.158 6.32 0.00 41.29 5.73
1407 4582 2.037121 TGCGACTTTCTTCTCCACATCA 59.963 45.455 0.00 0.00 0.00 3.07
1440 4615 2.304761 GGGAATGTTAGGACTGGACACA 59.695 50.000 0.00 0.00 0.00 3.72
1545 4720 4.894784 TCCAAGAAGATAATATCCCGTGC 58.105 43.478 0.00 0.00 0.00 5.34
1548 4723 5.403246 CGTCTCCAAGAAGATAATATCCCG 58.597 45.833 0.00 0.00 0.00 5.14
1689 4864 0.179051 GCCTCCTTGCTCTCATCCTG 60.179 60.000 0.00 0.00 0.00 3.86
2094 5269 1.552792 CTCCTCCTCAGGGTTCTTGAC 59.447 57.143 0.00 0.00 40.80 3.18
2139 5314 0.752743 CGCCACCATCCACATCCAAT 60.753 55.000 0.00 0.00 0.00 3.16
2185 5360 4.000988 CGGCCTTCTTAGCTTTAGTTCAA 58.999 43.478 0.00 0.00 0.00 2.69
2215 5390 3.488721 GCAATACTGAAGCCTCTGCAATG 60.489 47.826 0.00 0.00 41.13 2.82
2233 5408 3.058501 CGAACCGTAAAAACTGGAGCAAT 60.059 43.478 0.00 0.00 0.00 3.56
2313 5489 4.429854 AAACAAGCAGAAGAGGAAGACT 57.570 40.909 0.00 0.00 0.00 3.24
2348 5524 7.913821 GGAGGAACTAAACAAACAAACAACTAG 59.086 37.037 0.00 0.00 41.55 2.57
2510 5686 1.269102 ACAACCGAGACTCAAGTGACG 60.269 52.381 2.82 0.00 0.00 4.35
2545 5721 6.500684 AATACCAGCTCAGTTTAACATGTG 57.499 37.500 0.00 0.00 0.00 3.21
2552 5728 6.614694 TGGACTAAATACCAGCTCAGTTTA 57.385 37.500 0.00 0.00 0.00 2.01
2564 5740 8.506168 TTCATTCACTCCATTGGACTAAATAC 57.494 34.615 0.00 0.00 0.00 1.89
2597 5773 2.981859 AGTGACAACAGAGTTCGGTT 57.018 45.000 0.00 0.00 34.69 4.44
2633 5809 6.490566 AACCAACAACATAGTCCGTTATTC 57.509 37.500 0.00 0.00 0.00 1.75
2635 5811 7.118680 CAGTAAACCAACAACATAGTCCGTTAT 59.881 37.037 0.00 0.00 0.00 1.89
2645 5897 6.690530 CATTCATCCAGTAAACCAACAACAT 58.309 36.000 0.00 0.00 0.00 2.71
2652 5904 3.355378 CTGGCATTCATCCAGTAAACCA 58.645 45.455 1.07 0.00 44.62 3.67
2746 5998 9.988350 AATACTTCTTTATTGCGACTTAACATG 57.012 29.630 0.00 0.00 0.00 3.21
2799 6059 5.883115 CAGAGATAGTAGTGTTGAGTCAGGA 59.117 44.000 0.00 0.00 0.00 3.86
2800 6060 5.650266 ACAGAGATAGTAGTGTTGAGTCAGG 59.350 44.000 0.00 0.00 0.00 3.86
2883 6179 9.571810 GAGTCATGAGATGAGATTGTATATCAC 57.428 37.037 0.00 0.00 40.53 3.06
2891 6187 7.119407 AGTGTTTTGAGTCATGAGATGAGATTG 59.881 37.037 0.00 0.00 40.53 2.67
2896 6192 6.997655 AGTAGTGTTTTGAGTCATGAGATGA 58.002 36.000 0.00 0.00 36.84 2.92
2939 6236 3.268072 TCCATGACCACATCACCCAATAA 59.732 43.478 0.00 0.00 41.24 1.40
2947 6244 4.479786 TCGTAAATCCATGACCACATCA 57.520 40.909 0.00 0.00 43.13 3.07
2988 6285 0.681175 ACCAGCATGAAAAAGGGCAC 59.319 50.000 0.00 0.00 39.69 5.01
3000 6297 0.978146 AGAGCGTCCCTAACCAGCAT 60.978 55.000 0.00 0.00 0.00 3.79
3001 6298 1.609501 AGAGCGTCCCTAACCAGCA 60.610 57.895 0.00 0.00 0.00 4.41
3010 6307 0.179062 ATTGATCAGCAGAGCGTCCC 60.179 55.000 0.00 0.00 31.29 4.46
3014 6311 1.521840 CGAAGATTGATCAGCAGAGCG 59.478 52.381 0.00 0.00 31.29 5.03
3021 6318 2.897436 TGGACAGCGAAGATTGATCAG 58.103 47.619 0.00 0.00 0.00 2.90
3022 6319 3.333029 TTGGACAGCGAAGATTGATCA 57.667 42.857 0.00 0.00 0.00 2.92
3027 6324 4.448732 GCAAAATTTTGGACAGCGAAGATT 59.551 37.500 27.60 0.00 38.57 2.40
3028 6325 3.989817 GCAAAATTTTGGACAGCGAAGAT 59.010 39.130 27.60 0.00 38.57 2.40
3033 6330 2.032979 GGTTGCAAAATTTTGGACAGCG 60.033 45.455 27.60 5.57 38.25 5.18
3045 6342 9.050601 CCTGAATATTTAAAACTGGTTGCAAAA 57.949 29.630 0.00 0.00 0.00 2.44
3046 6343 8.424918 TCCTGAATATTTAAAACTGGTTGCAAA 58.575 29.630 0.00 0.00 0.00 3.68
3063 6363 4.481072 ACTAAGCCTACCGTCCTGAATAT 58.519 43.478 0.00 0.00 0.00 1.28
3067 6367 1.005097 TGACTAAGCCTACCGTCCTGA 59.995 52.381 0.00 0.00 0.00 3.86
3074 6374 2.311124 AACGCATGACTAAGCCTACC 57.689 50.000 0.00 0.00 0.00 3.18
3085 6385 7.254050 GCAAATGCTTATCAAATAAACGCATGA 60.254 33.333 0.00 0.00 36.98 3.07
3091 6391 8.118893 ACGATGCAAATGCTTATCAAATAAAC 57.881 30.769 6.97 0.00 42.66 2.01
3094 6394 7.025485 TGACGATGCAAATGCTTATCAAATA 57.975 32.000 6.97 0.00 42.66 1.40
3104 6404 1.199789 TGAACCTGACGATGCAAATGC 59.800 47.619 0.00 0.00 42.50 3.56
3106 6406 5.895636 TTAATGAACCTGACGATGCAAAT 57.104 34.783 0.00 0.00 0.00 2.32
3115 6415 5.048782 TGCACAACAGATTAATGAACCTGAC 60.049 40.000 8.45 0.00 0.00 3.51
3116 6416 5.069318 TGCACAACAGATTAATGAACCTGA 58.931 37.500 8.45 0.00 0.00 3.86
3127 6427 5.008331 AGAGATGACATTGCACAACAGATT 58.992 37.500 0.00 0.00 0.00 2.40
3147 6447 2.551459 CCAGTCTTGCTCCAAAACAGAG 59.449 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.