Multiple sequence alignment - TraesCS1D01G380100

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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 TraesCS1D01G380100 chr1D 100.000 4022 0 0 1 4022 455788389 455784368 0.000000e+00 7428.0
1 TraesCS1D01G380100 chr1A 90.684 3145 168 43 920 4022 549423199 549420138 0.000000e+00 4069.0
2 TraesCS1D01G380100 chr1A 82.359 941 87 33 3 889 549424321 549423406 0.000000e+00 745.0
3 TraesCS1D01G380100 chr1B 90.277 2201 116 33 899 3032 626230004 626227835 0.000000e+00 2789.0
4 TraesCS1D01G380100 chr1B 89.448 815 48 18 3085 3869 626227816 626227010 0.000000e+00 994.0
5 TraesCS1D01G380100 chr1B 83.868 936 85 34 1 901 626230950 626230046 0.000000e+00 832.0
6 TraesCS1D01G380100 chr3A 90.699 1602 115 12 1464 3038 707169653 707168059 0.000000e+00 2102.0
7 TraesCS1D01G380100 chr3A 85.249 522 40 14 921 1422 707170152 707169648 1.670000e-138 503.0
8 TraesCS1D01G380100 chr3A 86.527 334 32 10 3436 3761 707135844 707135516 4.940000e-94 355.0
9 TraesCS1D01G380100 chr3A 85.405 370 20 12 3085 3434 707168046 707167691 1.780000e-93 353.0
10 TraesCS1D01G380100 chr3A 86.348 293 23 6 1825 2101 547413146 547413437 1.820000e-78 303.0
11 TraesCS1D01G380100 chr7B 93.617 1081 69 0 1952 3032 399794894 399793814 0.000000e+00 1615.0
12 TraesCS1D01G380100 chr7B 87.216 704 57 20 3085 3761 399793795 399793098 0.000000e+00 771.0
13 TraesCS1D01G380100 chr7B 89.706 272 18 4 921 1188 399795171 399794906 4.980000e-89 339.0
14 TraesCS1D01G380100 chr7B 92.982 57 4 0 921 977 399792494 399792550 2.580000e-12 84.2
15 TraesCS1D01G380100 chr3B 93.173 1084 70 3 1952 3032 237976521 237975439 0.000000e+00 1589.0
16 TraesCS1D01G380100 chr3B 86.648 704 60 21 3085 3761 237975420 237974724 0.000000e+00 749.0
17 TraesCS1D01G380100 chr3B 90.441 272 16 4 921 1188 237976798 237976533 2.300000e-92 350.0
18 TraesCS1D01G380100 chr3B 92.982 57 4 0 921 977 237974121 237974177 2.580000e-12 84.2
19 TraesCS1D01G380100 chr7D 87.273 220 23 2 2060 2279 626239853 626239639 3.100000e-61 246.0


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 TraesCS1D01G380100 chr1D 455784368 455788389 4021 True 7428.000000 7428 100.000000 1 4022 1 chr1D.!!$R1 4021
1 TraesCS1D01G380100 chr1A 549420138 549424321 4183 True 2407.000000 4069 86.521500 3 4022 2 chr1A.!!$R1 4019
2 TraesCS1D01G380100 chr1B 626227010 626230950 3940 True 1538.333333 2789 87.864333 1 3869 3 chr1B.!!$R1 3868
3 TraesCS1D01G380100 chr3A 707167691 707170152 2461 True 986.000000 2102 87.117667 921 3434 3 chr3A.!!$R2 2513
4 TraesCS1D01G380100 chr7B 399793098 399795171 2073 True 908.333333 1615 90.179667 921 3761 3 chr7B.!!$R1 2840
5 TraesCS1D01G380100 chr3B 237974724 237976798 2074 True 896.000000 1589 90.087333 921 3761 3 chr3B.!!$R1 2840

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
382 418 0.108774 TTGTGTGTGCGGGGTATTCA 59.891 50.0 0.00 0.00 0.0 2.57 F
556 603 0.391597 GGAAACCGTGACCTGTCTGA 59.608 55.0 0.00 0.00 0.0 3.27 F
813 875 0.582005 GTTCAGACGCTGTCACCAAC 59.418 55.0 10.52 6.58 34.6 3.77 F
1189 1441 0.606604 GGTCGTCAAGGTAGGCTTCA 59.393 55.0 0.00 0.00 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1502 0.319555 CAGTCACCACGGTCGATGTT 60.320 55.000 0.0 0.0 0.00 2.71 R
2034 2367 1.728672 GGTGATCTCCGAGTCCGAC 59.271 63.158 0.0 0.0 38.22 4.79 R
2807 3144 4.459089 GTGTCCTCCGCTGCTCCC 62.459 72.222 0.0 0.0 0.00 4.30 R
3153 3512 1.078143 CTTGTACAGCCCCCTCTGC 60.078 63.158 0.0 0.0 37.59 4.26 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
54 55 4.019858 TCAAGATCTTCACAGAGACGGAT 58.980 43.478 4.57 0.00 30.36 4.18
66 67 2.232452 AGAGACGGATGAGAACAACCAG 59.768 50.000 0.00 0.00 38.62 4.00
121 122 5.701224 TCCTTTGACCTCCTTTGTACATTT 58.299 37.500 0.00 0.00 0.00 2.32
148 151 1.792367 GGCGATTTTCACTTTTGGTGC 59.208 47.619 0.00 0.00 44.98 5.01
270 295 3.071479 GTTTTGTCCTTCATCGCCTGTA 58.929 45.455 0.00 0.00 0.00 2.74
283 310 2.366266 TCGCCTGTACACACCTAAGTTT 59.634 45.455 0.00 0.00 0.00 2.66
290 317 7.820872 GCCTGTACACACCTAAGTTTAATTCTA 59.179 37.037 0.00 0.00 0.00 2.10
291 318 9.367444 CCTGTACACACCTAAGTTTAATTCTAG 57.633 37.037 0.00 0.00 0.00 2.43
292 319 9.924650 CTGTACACACCTAAGTTTAATTCTAGT 57.075 33.333 0.00 0.00 0.00 2.57
373 406 4.558470 GGATGAAATATTGTTGTGTGTGCG 59.442 41.667 0.00 0.00 0.00 5.34
377 410 0.179015 TATTGTTGTGTGTGCGGGGT 60.179 50.000 0.00 0.00 0.00 4.95
381 417 0.519961 GTTGTGTGTGCGGGGTATTC 59.480 55.000 0.00 0.00 0.00 1.75
382 418 0.108774 TTGTGTGTGCGGGGTATTCA 59.891 50.000 0.00 0.00 0.00 2.57
415 451 1.000283 AGTCAGCCGAAGAACTCTGTG 60.000 52.381 0.00 0.00 0.00 3.66
451 487 2.620863 CGGCGAACGCAATTAACAC 58.379 52.632 20.16 0.22 44.11 3.32
455 491 2.603652 GGCGAACGCAATTAACACTTGT 60.604 45.455 20.16 0.00 44.11 3.16
459 495 4.551990 CGAACGCAATTAACACTTGTGAGT 60.552 41.667 7.83 0.00 37.50 3.41
464 500 5.156355 GCAATTAACACTTGTGAGTCATGG 58.844 41.667 7.83 0.00 32.54 3.66
472 508 4.682860 CACTTGTGAGTCATGGCATTTTTC 59.317 41.667 0.00 0.00 32.54 2.29
500 536 6.095300 TCTGAAGCTTGTTTCATTTCTTGTGA 59.905 34.615 2.10 0.00 36.55 3.58
502 538 4.614946 AGCTTGTTTCATTTCTTGTGAGC 58.385 39.130 0.00 0.00 0.00 4.26
503 539 4.098349 AGCTTGTTTCATTTCTTGTGAGCA 59.902 37.500 0.00 0.00 0.00 4.26
528 572 7.065085 CAGTAATTCAGTAACAGATGGGTCTTG 59.935 40.741 0.00 0.00 30.42 3.02
548 595 2.604174 CCGCACTGGAAACCGTGAC 61.604 63.158 13.52 6.87 42.00 3.67
556 603 0.391597 GGAAACCGTGACCTGTCTGA 59.608 55.000 0.00 0.00 0.00 3.27
581 628 6.648310 ACAACACAGATTCACTGAGATGTAAG 59.352 38.462 0.00 0.00 45.31 2.34
627 684 2.531206 GAAACTCTTCGACCGAGATGG 58.469 52.381 15.66 0.00 46.41 3.51
643 700 3.569491 AGATGGGAATTCGCCAATTCAT 58.431 40.909 18.80 5.15 46.94 2.57
646 708 1.480205 GGAATTCGCCAATTCATGCG 58.520 50.000 17.01 7.10 46.94 4.73
649 711 5.569008 GGAATTCGCCAATTCATGCGTCA 62.569 47.826 17.01 3.24 46.94 4.35
709 771 2.037511 CCAAGCTGCCTCATTTCCAAAA 59.962 45.455 0.00 0.00 0.00 2.44
736 798 5.199982 TCTAGTTCTCTCCTCCTGATGTT 57.800 43.478 0.00 0.00 0.00 2.71
738 800 6.123651 TCTAGTTCTCTCCTCCTGATGTTAC 58.876 44.000 0.00 0.00 0.00 2.50
750 812 1.922447 TGATGTTACTGGCCCAGGAAT 59.078 47.619 12.59 0.00 36.63 3.01
773 835 4.218312 AGCAGAAAACTCCCATGTTCTTT 58.782 39.130 0.00 0.00 0.00 2.52
775 837 4.037923 GCAGAAAACTCCCATGTTCTTTCA 59.962 41.667 0.00 0.00 0.00 2.69
797 859 4.003648 AGACCATCGAAAACTCCATGTTC 58.996 43.478 0.00 0.00 38.03 3.18
813 875 0.582005 GTTCAGACGCTGTCACCAAC 59.418 55.000 10.52 6.58 34.60 3.77
819 881 0.932399 ACGCTGTCACCAACGTAAAC 59.068 50.000 0.00 0.00 41.28 2.01
822 884 2.796031 CGCTGTCACCAACGTAAACTAA 59.204 45.455 0.00 0.00 0.00 2.24
823 885 3.245754 CGCTGTCACCAACGTAAACTAAA 59.754 43.478 0.00 0.00 0.00 1.85
826 888 6.346758 CGCTGTCACCAACGTAAACTAAAATA 60.347 38.462 0.00 0.00 0.00 1.40
827 889 7.013529 GCTGTCACCAACGTAAACTAAAATAG 58.986 38.462 0.00 0.00 0.00 1.73
828 890 6.890558 TGTCACCAACGTAAACTAAAATAGC 58.109 36.000 0.00 0.00 0.00 2.97
863 925 4.961511 TCACCGCAGCGACACACC 62.962 66.667 18.75 0.00 0.00 4.16
889 1075 1.550524 CTGACTCCACGAGAAATCCCA 59.449 52.381 0.00 0.00 33.32 4.37
911 1097 3.402681 GCTGGAGGCTGGCAGGTA 61.403 66.667 17.64 0.00 38.06 3.08
912 1098 2.906458 CTGGAGGCTGGCAGGTAG 59.094 66.667 17.64 0.00 0.00 3.18
982 1225 3.262405 AGAACGTATTTAACCTGGCCTCA 59.738 43.478 3.32 0.00 0.00 3.86
1188 1440 0.896226 AGGTCGTCAAGGTAGGCTTC 59.104 55.000 0.00 0.00 0.00 3.86
1189 1441 0.606604 GGTCGTCAAGGTAGGCTTCA 59.393 55.000 0.00 0.00 0.00 3.02
1191 1443 2.271800 GTCGTCAAGGTAGGCTTCATG 58.728 52.381 0.00 0.00 0.00 3.07
1192 1444 1.899814 TCGTCAAGGTAGGCTTCATGT 59.100 47.619 0.00 0.00 0.00 3.21
1197 1449 3.776969 TCAAGGTAGGCTTCATGTGAGAT 59.223 43.478 0.00 0.00 0.00 2.75
1201 1469 2.306341 AGGCTTCATGTGAGATCGTG 57.694 50.000 0.00 0.00 0.00 4.35
1206 1474 1.884464 CATGTGAGATCGTGCCGGG 60.884 63.158 2.18 0.00 0.00 5.73
1225 1502 2.552155 GGGTCTTGGTGTTGTGCTGATA 60.552 50.000 0.00 0.00 0.00 2.15
1263 1540 3.231501 GTGCAGAACGTGTCGTCC 58.768 61.111 0.00 0.00 39.99 4.79
1355 1638 2.031870 GGAGAGAGAGAAGGAGAAGGC 58.968 57.143 0.00 0.00 0.00 4.35
1440 1723 3.060615 GCCAAGCAGCTGGTGGAG 61.061 66.667 27.66 17.93 38.86 3.86
1932 2241 2.647158 GGAGGTGACGAGGTGGACC 61.647 68.421 0.00 0.00 0.00 4.46
2442 2775 3.823330 GTCCAGGACGACGCGGAT 61.823 66.667 12.47 0.00 0.00 4.18
2874 3214 2.456119 GCGAGCCGTGATGGTGAAG 61.456 63.158 0.00 0.00 41.21 3.02
2906 3258 1.604693 GGCGACGTCAAGAAGGAAGAA 60.605 52.381 17.16 0.00 0.00 2.52
2907 3259 1.456165 GCGACGTCAAGAAGGAAGAAC 59.544 52.381 17.16 0.00 0.00 3.01
2913 3265 0.512952 CAAGAAGGAAGAACACGCCG 59.487 55.000 0.00 0.00 0.00 6.46
3066 3422 1.580942 GTGCAGCTCAAATGGCGAA 59.419 52.632 0.00 0.00 34.52 4.70
3120 3479 2.086869 GCATGTGTGCCTGTGTATCTT 58.913 47.619 0.00 0.00 45.76 2.40
3134 3493 7.360361 CCTGTGTATCTTTTCTTACAACAACC 58.640 38.462 0.00 0.00 30.59 3.77
3153 3512 3.736720 ACCATGTGTATATGCAGAGCAG 58.263 45.455 0.00 0.00 43.65 4.24
3259 3626 1.045407 ACAAACTGTGGCGTAGGAGA 58.955 50.000 0.00 0.00 0.00 3.71
3371 3754 2.063378 GCAGCTCAGCCTCCCTACT 61.063 63.158 0.00 0.00 0.00 2.57
3389 3772 3.409026 ACTTCCTCACTCGCTTCAAAT 57.591 42.857 0.00 0.00 0.00 2.32
3434 3817 8.795786 TGATTTGTAAGTTCATGTTAACTTGC 57.204 30.769 18.17 17.22 46.49 4.01
3456 3839 1.228063 GAGCCGATGCCCATGTGAT 60.228 57.895 0.00 0.00 38.69 3.06
3688 4084 8.958043 CAATGTTCTTTGTTAAGTAAAGACAGC 58.042 33.333 12.16 8.07 42.15 4.40
3733 4130 2.329539 GATGATGGGCAGCGGAAGGA 62.330 60.000 0.00 0.00 0.00 3.36
3761 4158 4.974275 ACCTCGTAATTCATGTTATCGACG 59.026 41.667 0.00 0.00 0.00 5.12
3847 4244 8.390354 TCGAAACATCATTATCTGAATGTTGTC 58.610 33.333 12.13 5.47 38.75 3.18
3895 4292 9.877178 CTTAGGAGTAACAGATAACATGAGTTT 57.123 33.333 0.00 0.00 39.15 2.66
3907 4304 5.458041 AACATGAGTTTAAAGTGCATGCT 57.542 34.783 20.33 14.55 39.82 3.79
3928 4325 9.557061 CATGCTACATATATCCATTAGCAGAAT 57.443 33.333 15.12 3.07 46.14 2.40
3952 4349 7.973048 TTACTCAAGGGATCTAAAGAGCTTA 57.027 36.000 0.00 0.00 0.00 3.09
3983 4380 5.690865 AGTGAACTGGAACAACCTATCAAA 58.309 37.500 0.00 0.00 38.70 2.69
3984 4381 6.306987 AGTGAACTGGAACAACCTATCAAAT 58.693 36.000 0.00 0.00 38.70 2.32
3985 4382 6.207417 AGTGAACTGGAACAACCTATCAAATG 59.793 38.462 0.00 0.00 38.70 2.32
4019 4416 4.448060 GCCAACAACTAGTGTAGAACAGAC 59.552 45.833 0.00 0.00 40.60 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.762418 TCTCTTTCCTGCCAACGGAA 59.238 50.000 0.00 0.00 38.71 4.30
54 55 1.338105 CCTCGCATCTGGTTGTTCTCA 60.338 52.381 0.00 0.00 0.00 3.27
66 67 2.279784 CTTCTCGGCCCTCGCATC 60.280 66.667 0.00 0.00 39.05 3.91
168 171 4.081309 TCAGATGATCAGATTGCACTGTGA 60.081 41.667 12.86 6.36 38.79 3.58
240 246 2.522193 GGACAAAACCGGGGCCAA 60.522 61.111 6.32 0.00 0.00 4.52
290 317 8.588290 TGCATAAGTTGGTTCCAAAATATACT 57.412 30.769 5.81 0.00 0.00 2.12
291 318 9.816354 AATGCATAAGTTGGTTCCAAAATATAC 57.184 29.630 0.00 4.21 0.00 1.47
293 320 8.761689 AGAATGCATAAGTTGGTTCCAAAATAT 58.238 29.630 0.00 5.46 0.00 1.28
300 327 6.823689 TCTTCTAGAATGCATAAGTTGGTTCC 59.176 38.462 5.44 0.00 0.00 3.62
373 406 2.620585 GCTGAGCAAGATTGAATACCCC 59.379 50.000 0.00 0.00 0.00 4.95
377 410 4.835678 TGACTGCTGAGCAAGATTGAATA 58.164 39.130 9.07 0.00 38.41 1.75
381 417 1.130749 GCTGACTGCTGAGCAAGATTG 59.869 52.381 9.07 0.00 38.41 2.67
382 418 1.451067 GCTGACTGCTGAGCAAGATT 58.549 50.000 9.07 0.00 38.41 2.40
402 438 2.509052 TGTGTCCACAGAGTTCTTCG 57.491 50.000 0.00 0.00 36.21 3.79
415 451 2.414161 GCCGCAGAATTTAACTGTGTCC 60.414 50.000 0.00 0.00 42.17 4.02
451 487 5.130292 AGAAAAATGCCATGACTCACAAG 57.870 39.130 0.00 0.00 0.00 3.16
455 491 5.535783 TCAGAAAGAAAAATGCCATGACTCA 59.464 36.000 0.00 0.00 0.00 3.41
459 495 5.011329 AGCTTCAGAAAGAAAAATGCCATGA 59.989 36.000 0.00 0.00 35.40 3.07
464 500 6.594284 AACAAGCTTCAGAAAGAAAAATGC 57.406 33.333 0.00 0.00 35.40 3.56
472 508 7.490402 ACAAGAAATGAAACAAGCTTCAGAAAG 59.510 33.333 0.00 0.00 38.66 2.62
500 536 5.045578 ACCCATCTGTTACTGAATTACTGCT 60.046 40.000 0.00 0.00 0.00 4.24
502 538 6.644347 AGACCCATCTGTTACTGAATTACTG 58.356 40.000 0.00 0.00 32.29 2.74
503 539 6.875972 AGACCCATCTGTTACTGAATTACT 57.124 37.500 0.00 0.00 32.29 2.24
528 572 2.280592 ACGGTTTCCAGTGCGGAC 60.281 61.111 0.00 0.00 46.36 4.79
548 595 3.496130 GTGAATCTGTGTTGTCAGACAGG 59.504 47.826 2.82 0.00 45.40 4.00
556 603 4.965814 ACATCTCAGTGAATCTGTGTTGT 58.034 39.130 0.00 7.39 43.97 3.32
574 621 8.810652 TTTTTCAGTTTGGTATTGCTTACATC 57.189 30.769 0.00 0.00 31.99 3.06
643 700 0.865111 CACCAAGATTTCGTGACGCA 59.135 50.000 0.00 0.00 0.00 5.24
646 708 2.875933 TGGTTCACCAAGATTTCGTGAC 59.124 45.455 0.00 0.00 44.35 3.67
669 731 3.420893 TGGGACAAACTAGCAATCCTTG 58.579 45.455 0.00 0.00 31.92 3.61
709 771 3.960102 CAGGAGGAGAGAACTAGATTGCT 59.040 47.826 0.00 0.00 0.00 3.91
736 798 1.131638 CTGCTATTCCTGGGCCAGTA 58.868 55.000 30.68 19.13 0.00 2.74
738 800 0.548031 TTCTGCTATTCCTGGGCCAG 59.452 55.000 27.04 27.04 0.00 4.85
750 812 4.640771 AGAACATGGGAGTTTTCTGCTA 57.359 40.909 0.00 0.00 38.36 3.49
773 835 3.007940 ACATGGAGTTTTCGATGGTCTGA 59.992 43.478 0.00 0.00 42.04 3.27
775 837 3.703001 ACATGGAGTTTTCGATGGTCT 57.297 42.857 0.00 0.00 42.04 3.85
857 919 0.603569 GGAGTCAGACGATGGTGTGT 59.396 55.000 4.93 0.00 38.50 3.72
863 925 1.087501 TCTCGTGGAGTCAGACGATG 58.912 55.000 14.80 10.31 43.26 3.84
864 926 1.822506 TTCTCGTGGAGTCAGACGAT 58.177 50.000 14.80 0.00 43.26 3.73
901 1087 0.322008 AGTTCTTGCTACCTGCCAGC 60.322 55.000 0.00 0.00 42.00 4.85
903 1089 1.545428 CCAAGTTCTTGCTACCTGCCA 60.545 52.381 7.00 0.00 42.00 4.92
904 1090 1.168714 CCAAGTTCTTGCTACCTGCC 58.831 55.000 7.00 0.00 42.00 4.85
905 1091 2.079925 CTCCAAGTTCTTGCTACCTGC 58.920 52.381 7.00 0.00 43.25 4.85
907 1093 3.744660 CAACTCCAAGTTCTTGCTACCT 58.255 45.455 7.00 0.00 36.03 3.08
908 1094 2.226674 GCAACTCCAAGTTCTTGCTACC 59.773 50.000 7.00 0.00 36.03 3.18
909 1095 2.226674 GGCAACTCCAAGTTCTTGCTAC 59.773 50.000 7.00 0.00 36.03 3.58
910 1096 2.158682 TGGCAACTCCAAGTTCTTGCTA 60.159 45.455 7.00 0.00 43.21 3.49
911 1097 1.322442 GGCAACTCCAAGTTCTTGCT 58.678 50.000 7.00 0.00 36.03 3.91
912 1098 1.032014 TGGCAACTCCAAGTTCTTGC 58.968 50.000 7.00 0.00 43.21 4.01
982 1225 0.818296 ATAGTTTGCTCGGAGCGACT 59.182 50.000 29.31 29.31 46.26 4.18
1050 1302 3.103911 GACACCGACTCGTTGCCG 61.104 66.667 0.00 0.00 0.00 5.69
1051 1303 3.103911 CGACACCGACTCGTTGCC 61.104 66.667 0.00 0.00 38.22 4.52
1201 1469 2.203294 ACAACACCAAGACCCGGC 60.203 61.111 0.00 0.00 0.00 6.13
1206 1474 3.563808 TGTTATCAGCACAACACCAAGAC 59.436 43.478 0.00 0.00 29.93 3.01
1225 1502 0.319555 CAGTCACCACGGTCGATGTT 60.320 55.000 0.00 0.00 0.00 2.71
1262 1539 2.401766 GCCACCTGCTTGACATCGG 61.402 63.158 0.00 0.00 36.87 4.18
1263 1540 2.743752 CGCCACCTGCTTGACATCG 61.744 63.158 0.00 0.00 38.05 3.84
1341 1618 1.190643 CCTTCGCCTTCTCCTTCTCT 58.809 55.000 0.00 0.00 0.00 3.10
1355 1638 3.554692 GATCCACACGCGCCTTCG 61.555 66.667 5.73 0.00 39.07 3.79
1424 1707 3.060615 GCTCCACCAGCTGCTTGG 61.061 66.667 21.32 21.32 45.83 3.61
1432 1715 2.360852 CTTGGGCTGCTCCACCAG 60.361 66.667 9.02 2.80 36.38 4.00
1433 1716 3.970410 CCTTGGGCTGCTCCACCA 61.970 66.667 9.02 0.52 36.38 4.17
1461 1747 3.787001 CTCTCCTTGTCCGGCCCC 61.787 72.222 0.00 0.00 0.00 5.80
1566 1852 2.657237 CGCGGTCCTTTGAGGAGT 59.343 61.111 0.00 0.00 46.90 3.85
1671 1959 3.573772 CTTGACGCGGTCCAGCTCA 62.574 63.158 12.47 0.00 34.40 4.26
1750 2038 3.866582 GTCCTCCTCGGCCATGGG 61.867 72.222 15.13 0.70 0.00 4.00
1783 2080 3.382832 CGAACCAGGGCTCCTCGT 61.383 66.667 0.00 0.00 0.00 4.18
1902 2211 1.755008 CACCTCCTCCTCCGTCTCC 60.755 68.421 0.00 0.00 0.00 3.71
1950 2283 3.028366 CTCGCTCGACACGCTCTGA 62.028 63.158 0.00 0.00 0.00 3.27
2034 2367 1.728672 GGTGATCTCCGAGTCCGAC 59.271 63.158 0.00 0.00 38.22 4.79
2807 3144 4.459089 GTGTCCTCCGCTGCTCCC 62.459 72.222 0.00 0.00 0.00 4.30
2857 3194 1.811266 CCTTCACCATCACGGCTCG 60.811 63.158 0.00 0.00 39.03 5.03
3066 3422 1.348064 TTCTTGTCCCCATCGTCTGT 58.652 50.000 0.00 0.00 0.00 3.41
3120 3479 8.240682 GCATATACACATGGTTGTTGTAAGAAA 58.759 33.333 0.00 0.00 32.34 2.52
3134 3493 3.135994 TGCTGCTCTGCATATACACATG 58.864 45.455 0.00 0.00 38.13 3.21
3153 3512 1.078143 CTTGTACAGCCCCCTCTGC 60.078 63.158 0.00 0.00 37.59 4.26
3371 3754 4.008074 AGAATTTGAAGCGAGTGAGGAA 57.992 40.909 0.00 0.00 0.00 3.36
3389 3772 8.561212 CAAATCATTGCAATTTTTCAGGAAGAA 58.439 29.630 9.83 0.00 0.00 2.52
3434 3817 2.109799 ATGGGCATCGGCTCTTCG 59.890 61.111 0.00 0.00 42.67 3.79
3449 3832 3.999001 CGATTCAGTCCCCATATCACATG 59.001 47.826 0.00 0.00 0.00 3.21
3456 3839 3.380393 TCCTTTCGATTCAGTCCCCATA 58.620 45.455 0.00 0.00 0.00 2.74
3733 4130 6.516194 CGATAACATGAATTACGAGGTACCCT 60.516 42.308 8.74 0.00 36.03 4.34
3761 4158 2.409870 CCAGGATTGGCGCCTTGAC 61.410 63.158 29.70 15.52 37.73 3.18
3869 4266 9.877178 AAACTCATGTTATCTGTTACTCCTAAG 57.123 33.333 0.00 0.00 34.96 2.18
3882 4279 7.253422 AGCATGCACTTTAAACTCATGTTATC 58.747 34.615 21.98 5.13 37.44 1.75
3891 4288 9.003658 GGATATATGTAGCATGCACTTTAAACT 57.996 33.333 21.98 0.00 29.56 2.66
3928 4325 6.875972 AAGCTCTTTAGATCCCTTGAGTAA 57.124 37.500 0.00 0.00 0.00 2.24
3931 4328 6.229733 CCATAAGCTCTTTAGATCCCTTGAG 58.770 44.000 0.00 0.00 0.00 3.02
3983 4380 2.756760 GTTGTTGGCATCAGGTCATCAT 59.243 45.455 0.00 0.00 31.34 2.45
3984 4381 2.161855 GTTGTTGGCATCAGGTCATCA 58.838 47.619 0.00 0.00 0.00 3.07
3985 4382 2.440409 AGTTGTTGGCATCAGGTCATC 58.560 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.