Multiple sequence alignment - TraesCS6D01G030800

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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 TraesCS6D01G030800 chr6D 100.000 3259 0 0 1 3259 12315102 12318360 0.000000e+00 6019.0
1 TraesCS6D01G030800 chr6D 100.000 1432 0 0 3703 5134 12318804 12320235 0.000000e+00 2645.0
2 TraesCS6D01G030800 chr6D 73.160 652 103 47 970 1579 11237935 11238556 8.840000e-38 169.0
3 TraesCS6D01G030800 chr6B 91.714 2305 117 33 991 3245 22584526 22586806 0.000000e+00 3131.0
4 TraesCS6D01G030800 chr6B 90.491 631 44 8 236 864 22583845 22584461 0.000000e+00 819.0
5 TraesCS6D01G030800 chr6B 93.608 485 18 3 4652 5134 22588438 22588911 0.000000e+00 712.0
6 TraesCS6D01G030800 chr6B 98.228 395 7 0 3703 4097 22587299 22587693 0.000000e+00 691.0
7 TraesCS6D01G030800 chr6B 77.401 1031 175 31 1002 1979 22715624 22716649 1.250000e-155 560.0
8 TraesCS6D01G030800 chr6B 97.951 244 4 1 4086 4328 22588059 22588302 6.150000e-114 422.0
9 TraesCS6D01G030800 chr6B 96.667 180 3 1 1 180 22583040 22583216 3.890000e-76 296.0
10 TraesCS6D01G030800 chr6B 96.154 130 2 1 4363 4489 22588303 22588432 5.210000e-50 209.0
11 TraesCS6D01G030800 chr6B 72.862 608 114 37 1002 1570 21124400 21124995 1.480000e-35 161.0
12 TraesCS6D01G030800 chr6B 84.810 79 12 0 1987 2065 22585451 22585529 4.260000e-11 80.5
13 TraesCS6D01G030800 chr6A 88.852 1794 116 29 236 1986 13671739 13673491 0.000000e+00 2128.0
14 TraesCS6D01G030800 chr6A 92.393 1446 81 22 3703 5134 13674793 13676223 0.000000e+00 2034.0
15 TraesCS6D01G030800 chr6A 95.426 1268 48 6 1987 3245 13673408 13674674 0.000000e+00 2012.0
16 TraesCS6D01G030800 chr6A 77.473 1021 183 27 1002 1979 13734090 13735106 7.460000e-158 568.0
17 TraesCS6D01G030800 chr6A 76.786 448 78 17 244 683 12952179 12951750 1.440000e-55 228.0
18 TraesCS6D01G030800 chr6A 76.805 457 69 25 244 683 12949896 12949460 6.690000e-54 222.0
19 TraesCS6D01G030800 chr6A 75.098 510 93 25 1025 1508 12459920 12460421 1.870000e-49 207.0
20 TraesCS6D01G030800 chr6A 97.030 101 3 0 138 238 13671014 13671114 2.460000e-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 TraesCS6D01G030800 chr6D 12315102 12320235 5133 False 4332.0000 6019 100.000000 1 5134 2 chr6D.!!$F2 5133
1 TraesCS6D01G030800 chr6B 22583040 22588911 5871 False 795.0625 3131 93.702875 1 5134 8 chr6B.!!$F3 5133
2 TraesCS6D01G030800 chr6B 22715624 22716649 1025 False 560.0000 560 77.401000 1002 1979 1 chr6B.!!$F2 977
3 TraesCS6D01G030800 chr6A 13671014 13676223 5209 False 1586.2500 2128 93.425250 138 5134 4 chr6A.!!$F3 4996
4 TraesCS6D01G030800 chr6A 13734090 13735106 1016 False 568.0000 568 77.473000 1002 1979 1 chr6A.!!$F2 977
5 TraesCS6D01G030800 chr6A 12949460 12952179 2719 True 225.0000 228 76.795500 244 683 2 chr6A.!!$R1 439
6 TraesCS6D01G030800 chr6A 12459920 12460421 501 False 207.0000 207 75.098000 1025 1508 1 chr6A.!!$F1 483

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
924 3872 0.177604 CCTTCTTCTCCTGCGCATCT 59.822 55.000 12.24 0.0 0.00 2.90 F
1548 4613 0.183014 TAGCCCAGGTCTACTCCTCG 59.817 60.000 0.00 0.0 35.37 4.63 F
1950 5039 0.178903 TGGGGTACTCAGAGGTTGCT 60.179 55.000 1.53 0.0 0.00 3.91 F
1960 5049 0.773644 AGAGGTTGCTGGTGTGGATT 59.226 50.000 0.00 0.0 0.00 3.01 F
2406 5501 1.135915 TGCGAAGGTTTGCACACATTT 59.864 42.857 4.20 0.0 42.41 2.32 F
3204 6322 1.203050 AGGACCAAACTTCCCATGTGG 60.203 52.381 0.00 0.0 33.01 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 4862 0.035534 ATACTGCGATGCCAACACCA 60.036 50.000 0.00 0.0 0.00 4.17 R
3207 6325 3.241067 AGGTAGAACAAGCGCGAATAA 57.759 42.857 12.10 0.0 0.00 1.40 R
3717 6872 1.333619 TCACAGCCTTGTCTTTTTCGC 59.666 47.619 0.00 0.0 34.62 4.70 R
3901 7056 7.471721 TGCTTAAGTATGAAATGATCCAAACG 58.528 34.615 4.02 0.0 0.00 3.60 R
4108 7641 1.269723 CTCGAACAGTACCTGTGCAGA 59.730 52.381 3.41 0.0 44.62 4.26 R
5004 8551 0.027063 CCCAAAACACACGACACGAC 59.973 55.000 0.00 0.0 0.00 4.34 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
55 56 6.252599 AGTGATAGGCCATTAATCTGTTGA 57.747 37.500 5.01 0.00 0.00 3.18
56 57 6.845908 AGTGATAGGCCATTAATCTGTTGAT 58.154 36.000 5.01 0.00 33.70 2.57
57 58 6.713903 AGTGATAGGCCATTAATCTGTTGATG 59.286 38.462 5.01 0.00 32.68 3.07
113 114 5.045869 TCGGATGAAACCCAAGTAGAGAATT 60.046 40.000 0.00 0.00 0.00 2.17
119 120 7.940850 TGAAACCCAAGTAGAGAATTTTTGAG 58.059 34.615 0.00 0.00 0.00 3.02
216 217 5.163227 TGCTTTGCTCCTATCATCTTCATCT 60.163 40.000 0.00 0.00 0.00 2.90
315 3250 2.979120 TTGCGTGGCGGGGTTAAC 60.979 61.111 0.00 0.00 0.00 2.01
339 3274 2.622452 CCCATGCCTCTTCTGGTTCATT 60.622 50.000 0.00 0.00 0.00 2.57
345 3280 3.616560 GCCTCTTCTGGTTCATTGTCGTA 60.617 47.826 0.00 0.00 0.00 3.43
373 3308 1.728672 GACGAGTAGAAGGAGGCCG 59.271 63.158 0.00 0.00 0.00 6.13
683 3629 2.512515 GCGTCAGGTCCTCCATGC 60.513 66.667 0.00 0.00 35.89 4.06
684 3630 2.202797 CGTCAGGTCCTCCATGCG 60.203 66.667 0.00 0.00 35.89 4.73
685 3631 2.982130 GTCAGGTCCTCCATGCGT 59.018 61.111 0.00 0.00 35.89 5.24
686 3632 1.448540 GTCAGGTCCTCCATGCGTG 60.449 63.158 0.00 0.00 35.89 5.34
687 3633 1.609210 TCAGGTCCTCCATGCGTGA 60.609 57.895 7.72 0.00 35.89 4.35
688 3634 1.153489 CAGGTCCTCCATGCGTGAG 60.153 63.158 7.72 3.03 35.89 3.51
820 3767 4.290622 AACTGGGCTGGTGCTGGG 62.291 66.667 0.00 0.00 39.59 4.45
877 3825 4.800554 CCCACTGGCTTTTCTCGT 57.199 55.556 0.00 0.00 0.00 4.18
878 3826 2.247790 CCCACTGGCTTTTCTCGTG 58.752 57.895 0.00 0.00 0.00 4.35
879 3827 0.250295 CCCACTGGCTTTTCTCGTGA 60.250 55.000 0.00 0.00 0.00 4.35
880 3828 1.151668 CCACTGGCTTTTCTCGTGAG 58.848 55.000 0.00 0.00 0.00 3.51
881 3829 1.151668 CACTGGCTTTTCTCGTGAGG 58.848 55.000 0.00 0.00 0.00 3.86
882 3830 0.603975 ACTGGCTTTTCTCGTGAGGC 60.604 55.000 0.00 0.00 36.59 4.70
883 3831 1.301677 CTGGCTTTTCTCGTGAGGCC 61.302 60.000 16.02 16.02 39.93 5.19
884 3832 2.041115 GGCTTTTCTCGTGAGGCCC 61.041 63.158 0.00 0.00 34.19 5.80
885 3833 1.302511 GCTTTTCTCGTGAGGCCCA 60.303 57.895 0.00 0.00 0.00 5.36
886 3834 1.301677 GCTTTTCTCGTGAGGCCCAG 61.302 60.000 0.00 0.00 0.00 4.45
887 3835 1.301677 CTTTTCTCGTGAGGCCCAGC 61.302 60.000 0.00 0.00 0.00 4.85
924 3872 0.177604 CCTTCTTCTCCTGCGCATCT 59.822 55.000 12.24 0.00 0.00 2.90
957 3905 2.853705 TCCGTTTCAACCAAACCCTAG 58.146 47.619 0.00 0.00 41.40 3.02
970 3918 2.494918 CCTAGCCAACGAGTCCGG 59.505 66.667 0.00 0.00 40.78 5.14
1286 4333 1.594862 CGACGAGATTGATTTCTGGGC 59.405 52.381 0.00 0.00 0.00 5.36
1403 4450 1.356624 CCATTCCGCTGGATTTCGC 59.643 57.895 0.00 0.00 38.69 4.70
1405 4452 1.097547 CATTCCGCTGGATTTCGCCT 61.098 55.000 0.00 0.00 0.00 5.52
1416 4471 2.614057 GGATTTCGCCTGGTATGTCTTG 59.386 50.000 0.00 0.00 0.00 3.02
1534 4599 2.911221 GAACCACCCAGCCATAGCCC 62.911 65.000 0.00 0.00 41.25 5.19
1535 4600 3.419580 CCACCCAGCCATAGCCCA 61.420 66.667 0.00 0.00 41.25 5.36
1548 4613 0.183014 TAGCCCAGGTCTACTCCTCG 59.817 60.000 0.00 0.00 35.37 4.63
1554 4619 1.210967 CAGGTCTACTCCTCGGAGACT 59.789 57.143 19.35 6.53 44.53 3.24
1585 4650 1.668919 GCGATCTTGTCTCGACCACAA 60.669 52.381 5.33 5.33 38.38 3.33
1599 4664 1.729131 CACAAAACCATGCGACGGC 60.729 57.895 0.00 0.00 40.52 5.68
1602 4667 2.332654 AAAACCATGCGACGGCCTC 61.333 57.895 0.00 0.00 38.85 4.70
1604 4669 4.760047 ACCATGCGACGGCCTCAC 62.760 66.667 0.00 0.00 38.85 3.51
1610 4675 2.126307 CGACGGCCTCACTGACAG 60.126 66.667 0.00 0.00 0.00 3.51
1663 4749 3.678965 ATTGGTGGTTGTATGGGCATA 57.321 42.857 0.00 0.00 0.00 3.14
1725 4811 3.083997 GTGACCGAGGGGCCATCT 61.084 66.667 17.10 0.01 36.48 2.90
1727 4813 2.764128 GACCGAGGGGCCATCTCA 60.764 66.667 17.10 0.00 36.48 3.27
1737 4823 0.820891 GGCCATCTCATGCGGACATT 60.821 55.000 0.00 0.00 32.87 2.71
1738 4824 0.309922 GCCATCTCATGCGGACATTG 59.690 55.000 0.00 0.00 32.87 2.82
1767 4853 2.851102 AGCCGGATCATCAGGGGG 60.851 66.667 5.05 0.00 32.07 5.40
1786 4872 1.074775 GAGGATGGTGGTGTTGGCA 59.925 57.895 0.00 0.00 0.00 4.92
1876 4962 1.448985 GGTGCTGCCGAAGATTGTTA 58.551 50.000 0.00 0.00 0.00 2.41
1879 4965 1.933181 TGCTGCCGAAGATTGTTATCG 59.067 47.619 0.00 0.00 35.85 2.92
1881 4967 2.285834 GCTGCCGAAGATTGTTATCGTG 60.286 50.000 0.00 0.00 35.85 4.35
1915 5001 4.948847 TGATCTTACACATCCGATCAAGG 58.051 43.478 0.00 0.00 39.26 3.61
1919 5005 2.425143 ACACATCCGATCAAGGCAAT 57.575 45.000 0.00 0.00 0.00 3.56
1923 5012 1.605710 CATCCGATCAAGGCAATGGAC 59.394 52.381 0.00 0.00 0.00 4.02
1946 5035 3.436761 GCTATAGTGGGGTACTCAGAGGT 60.437 52.174 1.53 0.00 40.89 3.85
1950 5039 0.178903 TGGGGTACTCAGAGGTTGCT 60.179 55.000 1.53 0.00 0.00 3.91
1955 5044 1.344763 GTACTCAGAGGTTGCTGGTGT 59.655 52.381 1.53 0.00 36.55 4.16
1960 5049 0.773644 AGAGGTTGCTGGTGTGGATT 59.226 50.000 0.00 0.00 0.00 3.01
1969 5058 3.563808 TGCTGGTGTGGATTTTATATCGC 59.436 43.478 0.00 0.00 0.00 4.58
1981 5070 2.620251 TATATCGCTGCCTTGCTGTT 57.380 45.000 0.00 0.00 0.00 3.16
1982 5071 1.303309 ATATCGCTGCCTTGCTGTTC 58.697 50.000 0.00 0.00 0.00 3.18
1987 5076 1.860484 GCTGCCTTGCTGTTCAGGTC 61.860 60.000 1.97 0.00 0.00 3.85
1988 5077 1.572085 CTGCCTTGCTGTTCAGGTCG 61.572 60.000 1.97 0.00 0.00 4.79
1989 5078 2.328099 GCCTTGCTGTTCAGGTCGG 61.328 63.158 1.97 0.00 0.00 4.79
2185 5274 6.554334 TCTTCACTGCAGGTAATTGTTTAC 57.446 37.500 19.93 0.00 37.55 2.01
2349 5440 9.567776 TGAACTGTATTTGTCCTGAAAAATAGA 57.432 29.630 3.30 2.18 30.84 1.98
2369 5464 4.327680 AGAGGACTATTTTGACCACTTGC 58.672 43.478 0.00 0.00 0.00 4.01
2406 5501 1.135915 TGCGAAGGTTTGCACACATTT 59.864 42.857 4.20 0.00 42.41 2.32
2556 5651 9.567848 GAAATTGGTCGATTTGCTTAAGATAAA 57.432 29.630 6.67 7.19 29.75 1.40
2652 5753 8.715191 TGCTTCTGTTTACACATTTTTCATTT 57.285 26.923 0.00 0.00 30.39 2.32
2903 6013 6.435277 AGACTTGTGTGGCTGATAATCAATTT 59.565 34.615 0.00 0.00 0.00 1.82
3100 6212 5.538053 AGTGTAGGTGTCATCTCTGATATGG 59.462 44.000 3.57 0.00 32.98 2.74
3204 6322 1.203050 AGGACCAAACTTCCCATGTGG 60.203 52.381 0.00 0.00 33.01 4.17
3207 6325 3.563479 GGACCAAACTTCCCATGTGGTAT 60.563 47.826 2.16 0.00 42.63 2.73
3747 6902 2.171448 ACAAGGCTGTGAGGATGATACC 59.829 50.000 0.00 0.00 33.30 2.73
3748 6903 2.171237 CAAGGCTGTGAGGATGATACCA 59.829 50.000 0.00 0.00 0.00 3.25
4108 7641 5.160607 TCGTCACTAATGGAGATTGGTTT 57.839 39.130 0.00 0.00 31.25 3.27
4289 7824 7.377766 TCTCTTATAACTTGGTTGATGCAAC 57.622 36.000 0.00 1.82 42.89 4.17
4335 7872 1.302511 CCCTGCGGTTAAGCTGTGT 60.303 57.895 2.76 0.00 38.13 3.72
4343 7880 2.924290 CGGTTAAGCTGTGTTAGAGAGC 59.076 50.000 2.76 0.00 41.44 4.09
4344 7881 3.614150 CGGTTAAGCTGTGTTAGAGAGCA 60.614 47.826 0.84 0.00 43.65 4.26
4345 7882 3.680458 GGTTAAGCTGTGTTAGAGAGCAC 59.320 47.826 0.84 0.00 43.65 4.40
4346 7883 4.561105 GTTAAGCTGTGTTAGAGAGCACT 58.439 43.478 0.84 0.00 43.65 4.40
4347 7884 2.739885 AGCTGTGTTAGAGAGCACTG 57.260 50.000 0.84 0.00 43.65 3.66
4348 7885 1.967066 AGCTGTGTTAGAGAGCACTGT 59.033 47.619 0.84 0.00 43.65 3.55
4349 7886 2.029470 AGCTGTGTTAGAGAGCACTGTC 60.029 50.000 0.84 0.00 43.65 3.51
4350 7887 2.288457 GCTGTGTTAGAGAGCACTGTCA 60.288 50.000 0.00 0.00 40.79 3.58
4351 7888 3.312828 CTGTGTTAGAGAGCACTGTCAC 58.687 50.000 0.00 0.00 36.63 3.67
4374 7914 7.222611 TCACTTTTGTCTCTTTATTTTGCTTGC 59.777 33.333 0.00 0.00 0.00 4.01
4454 7997 1.267121 ATCCCGATGCGCTATACCTT 58.733 50.000 9.73 0.00 0.00 3.50
4534 8077 2.231478 GCTGCCGCTTGTAGGAGATATA 59.769 50.000 0.00 0.00 0.00 0.86
4613 8157 0.953727 GCTGATGGTGCAAGTTGTGA 59.046 50.000 4.48 0.00 0.00 3.58
4616 8160 1.948834 TGATGGTGCAAGTTGTGAGTG 59.051 47.619 4.48 0.00 0.00 3.51
4624 8168 2.796032 GCAAGTTGTGAGTGGTTTGAGC 60.796 50.000 4.48 0.00 0.00 4.26
4791 8336 7.120285 GCAATCTCACCACATGCAGTATAATAT 59.880 37.037 0.00 0.00 37.00 1.28
4820 8365 6.884295 TGTATTACTTCCTTCAAATGGTCCTG 59.116 38.462 0.00 0.00 0.00 3.86
4825 8370 1.542915 CCTTCAAATGGTCCTGCACTG 59.457 52.381 0.00 0.00 0.00 3.66
4898 8443 5.861787 GGTATTTGCTTGTTTATCGCAACTT 59.138 36.000 0.00 0.00 42.65 2.66
4902 8447 3.815962 TGCTTGTTTATCGCAACTTACCA 59.184 39.130 0.00 0.00 0.00 3.25
5077 8624 6.148811 CCTCTTTTTCACATAGGCTTTTCGTA 59.851 38.462 0.00 0.00 0.00 3.43
5078 8625 7.308348 CCTCTTTTTCACATAGGCTTTTCGTAA 60.308 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.456277 GTCTTCCTCCATACACCCTTCAT 59.544 47.826 0.00 0.00 0.00 2.57
56 57 2.838202 GTCTTCCTCCATACACCCTTCA 59.162 50.000 0.00 0.00 0.00 3.02
57 58 2.159085 CGTCTTCCTCCATACACCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
113 114 1.603802 CAAAGCAGAGTCGCCTCAAAA 59.396 47.619 0.00 0.00 40.40 2.44
119 120 0.246635 TAGGTCAAAGCAGAGTCGCC 59.753 55.000 3.79 0.00 0.00 5.54
216 217 8.548025 TGGATGATAAACTGGATCTTAAAGTGA 58.452 33.333 0.00 0.00 0.00 3.41
315 3250 1.077212 CCAGAAGAGGCATGGGTGG 60.077 63.158 0.00 0.00 0.00 4.61
339 3274 3.176661 TCGCCGACGATTACGACA 58.823 55.556 0.00 0.00 45.12 4.35
489 3426 2.627699 GGCATTTTCTTCCACCTCAACA 59.372 45.455 0.00 0.00 0.00 3.33
683 3629 0.109086 AGTCAAGCATCGACCTCACG 60.109 55.000 0.00 0.00 33.70 4.35
684 3630 1.354040 CAGTCAAGCATCGACCTCAC 58.646 55.000 0.00 0.00 33.70 3.51
685 3631 0.390340 GCAGTCAAGCATCGACCTCA 60.390 55.000 0.00 0.00 33.70 3.86
686 3632 0.108424 AGCAGTCAAGCATCGACCTC 60.108 55.000 0.00 0.00 36.85 3.85
687 3633 0.322975 AAGCAGTCAAGCATCGACCT 59.677 50.000 0.00 0.00 36.85 3.85
688 3634 0.445436 CAAGCAGTCAAGCATCGACC 59.555 55.000 0.00 0.00 36.85 4.79
753 3700 9.226606 CAACATGTCTCCCTGTACTTTTTAATA 57.773 33.333 0.00 0.00 0.00 0.98
755 3702 6.488683 CCAACATGTCTCCCTGTACTTTTTAA 59.511 38.462 0.00 0.00 0.00 1.52
757 3704 4.827284 CCAACATGTCTCCCTGTACTTTTT 59.173 41.667 0.00 0.00 0.00 1.94
758 3705 4.398319 CCAACATGTCTCCCTGTACTTTT 58.602 43.478 0.00 0.00 0.00 2.27
860 3808 0.250295 TCACGAGAAAAGCCAGTGGG 60.250 55.000 12.15 0.00 33.98 4.61
868 3816 1.301677 GCTGGGCCTCACGAGAAAAG 61.302 60.000 4.53 0.00 0.00 2.27
869 3817 1.302511 GCTGGGCCTCACGAGAAAA 60.303 57.895 4.53 0.00 0.00 2.29
881 3829 1.984288 AAGGAATAGACGGGCTGGGC 61.984 60.000 0.00 0.00 0.00 5.36
882 3830 0.106894 GAAGGAATAGACGGGCTGGG 59.893 60.000 0.00 0.00 0.00 4.45
883 3831 0.106894 GGAAGGAATAGACGGGCTGG 59.893 60.000 0.00 0.00 0.00 4.85
884 3832 1.123928 AGGAAGGAATAGACGGGCTG 58.876 55.000 0.00 0.00 0.00 4.85
885 3833 1.763545 GAAGGAAGGAATAGACGGGCT 59.236 52.381 0.00 0.00 0.00 5.19
886 3834 1.202663 GGAAGGAAGGAATAGACGGGC 60.203 57.143 0.00 0.00 0.00 6.13
887 3835 2.399580 AGGAAGGAAGGAATAGACGGG 58.600 52.381 0.00 0.00 0.00 5.28
888 3836 3.707102 AGAAGGAAGGAAGGAATAGACGG 59.293 47.826 0.00 0.00 0.00 4.79
889 3837 5.128008 AGAAGAAGGAAGGAAGGAATAGACG 59.872 44.000 0.00 0.00 0.00 4.18
890 3838 6.407639 GGAGAAGAAGGAAGGAAGGAATAGAC 60.408 46.154 0.00 0.00 0.00 2.59
891 3839 5.663556 GGAGAAGAAGGAAGGAAGGAATAGA 59.336 44.000 0.00 0.00 0.00 1.98
892 3840 5.665360 AGGAGAAGAAGGAAGGAAGGAATAG 59.335 44.000 0.00 0.00 0.00 1.73
893 3841 5.426833 CAGGAGAAGAAGGAAGGAAGGAATA 59.573 44.000 0.00 0.00 0.00 1.75
894 3842 4.227073 CAGGAGAAGAAGGAAGGAAGGAAT 59.773 45.833 0.00 0.00 0.00 3.01
924 3872 0.774908 AAACGGAAATGGGGAGTGGA 59.225 50.000 0.00 0.00 0.00 4.02
995 3952 1.096416 GTTCTCGTCCTCCATCTCGT 58.904 55.000 0.00 0.00 0.00 4.18
1259 4285 3.554692 CAATCTCGTCGCCGTGGC 61.555 66.667 0.00 0.00 35.01 5.01
1260 4286 0.806102 AATCAATCTCGTCGCCGTGG 60.806 55.000 0.00 0.00 35.01 4.94
1261 4287 0.999406 AAATCAATCTCGTCGCCGTG 59.001 50.000 0.00 0.00 35.01 4.94
1262 4288 1.135083 AGAAATCAATCTCGTCGCCGT 60.135 47.619 0.00 0.00 35.01 5.68
1263 4289 1.256376 CAGAAATCAATCTCGTCGCCG 59.744 52.381 0.00 0.00 0.00 6.46
1264 4290 1.594862 CCAGAAATCAATCTCGTCGCC 59.405 52.381 0.00 0.00 0.00 5.54
1265 4291 1.594862 CCCAGAAATCAATCTCGTCGC 59.405 52.381 0.00 0.00 0.00 5.19
1266 4292 1.594862 GCCCAGAAATCAATCTCGTCG 59.405 52.381 0.00 0.00 0.00 5.12
1267 4293 2.869192 GAGCCCAGAAATCAATCTCGTC 59.131 50.000 0.00 0.00 0.00 4.20
1275 4322 0.107993 CGAGCAGAGCCCAGAAATCA 60.108 55.000 0.00 0.00 0.00 2.57
1403 4450 1.210478 CTCCACCCAAGACATACCAGG 59.790 57.143 0.00 0.00 0.00 4.45
1405 4452 0.618458 GCTCCACCCAAGACATACCA 59.382 55.000 0.00 0.00 0.00 3.25
1454 4516 3.224324 AGTCTCCGTGCACGTGGT 61.224 61.111 34.81 16.31 37.74 4.16
1513 4575 0.323360 GCTATGGCTGGGTGGTTCAA 60.323 55.000 0.00 0.00 35.22 2.69
1514 4576 1.302949 GCTATGGCTGGGTGGTTCA 59.697 57.895 0.00 0.00 35.22 3.18
1534 4599 1.210967 AGTCTCCGAGGAGTAGACCTG 59.789 57.143 17.75 0.00 40.42 4.00
1535 4600 1.210967 CAGTCTCCGAGGAGTAGACCT 59.789 57.143 17.75 5.84 40.42 3.85
1548 4613 2.273449 CCCCACATGCCAGTCTCC 59.727 66.667 0.00 0.00 0.00 3.71
1554 4619 2.982643 AAGATCGCCCCACATGCCA 61.983 57.895 0.00 0.00 0.00 4.92
1585 4650 2.746277 GAGGCCGTCGCATGGTTT 60.746 61.111 0.00 0.00 36.38 3.27
1599 4664 1.059913 AGGGGAAACTGTCAGTGAGG 58.940 55.000 6.18 0.00 0.00 3.86
1610 4675 1.609841 CGACAAGGGTACAGGGGAAAC 60.610 57.143 0.00 0.00 0.00 2.78
1663 4749 2.930040 CGAACTCGAGTATGCCATTGTT 59.070 45.455 20.39 0.00 43.02 2.83
1687 4773 2.045524 AGCTAGTGTCTGGCTATGCAT 58.954 47.619 3.79 3.79 46.12 3.96
1722 4808 2.433604 AGAGTCAATGTCCGCATGAGAT 59.566 45.455 0.00 0.00 35.15 2.75
1725 4811 3.384467 TGATAGAGTCAATGTCCGCATGA 59.616 43.478 0.00 0.00 35.15 3.07
1727 4813 4.406648 TTGATAGAGTCAATGTCCGCAT 57.593 40.909 0.00 0.00 41.79 4.73
1737 4823 1.847328 TCCGGCTGTTGATAGAGTCA 58.153 50.000 0.00 0.00 34.25 3.41
1738 4824 2.362397 TGATCCGGCTGTTGATAGAGTC 59.638 50.000 0.00 0.00 0.00 3.36
1767 4853 1.678970 GCCAACACCACCATCCTCC 60.679 63.158 0.00 0.00 0.00 4.30
1776 4862 0.035534 ATACTGCGATGCCAACACCA 60.036 50.000 0.00 0.00 0.00 4.17
1786 4872 4.681942 GCTCAGATACGAAAATACTGCGAT 59.318 41.667 0.00 0.00 0.00 4.58
1865 4951 3.989705 TGTGCACGATAACAATCTTCG 57.010 42.857 13.13 0.00 38.76 3.79
1876 4962 4.449131 AGATCAATGATCTTGTGCACGAT 58.551 39.130 19.24 9.69 45.86 3.73
1907 4993 1.091771 AGCGTCCATTGCCTTGATCG 61.092 55.000 0.00 0.00 0.00 3.69
1915 5001 1.512926 CCCACTATAGCGTCCATTGC 58.487 55.000 0.00 0.00 0.00 3.56
1919 5005 1.216175 AGTACCCCACTATAGCGTCCA 59.784 52.381 0.00 0.00 34.98 4.02
1923 5012 2.814919 CTCTGAGTACCCCACTATAGCG 59.185 54.545 0.00 0.00 37.72 4.26
1946 5035 4.036262 GCGATATAAAATCCACACCAGCAA 59.964 41.667 0.00 0.00 0.00 3.91
1950 5039 3.563808 GCAGCGATATAAAATCCACACCA 59.436 43.478 0.00 0.00 0.00 4.17
1955 5044 3.253188 GCAAGGCAGCGATATAAAATCCA 59.747 43.478 0.00 0.00 0.00 3.41
1960 5049 2.917933 ACAGCAAGGCAGCGATATAAA 58.082 42.857 0.00 0.00 40.15 1.40
1969 5058 1.572085 CGACCTGAACAGCAAGGCAG 61.572 60.000 0.00 0.00 0.00 4.85
1981 5070 0.684479 CCTGTCCTGATCCGACCTGA 60.684 60.000 7.39 0.00 0.00 3.86
1982 5071 1.680522 CCCTGTCCTGATCCGACCTG 61.681 65.000 7.39 2.02 0.00 4.00
1987 5076 0.687757 TCCTTCCCTGTCCTGATCCG 60.688 60.000 0.00 0.00 0.00 4.18
1988 5077 1.488393 CTTCCTTCCCTGTCCTGATCC 59.512 57.143 0.00 0.00 0.00 3.36
1989 5078 1.134250 GCTTCCTTCCCTGTCCTGATC 60.134 57.143 0.00 0.00 0.00 2.92
2185 5274 9.202273 GATTCAGCTACTTCTGTGATATAAAGG 57.798 37.037 0.00 0.00 35.63 3.11
2349 5440 4.373156 AGCAAGTGGTCAAAATAGTCCT 57.627 40.909 0.00 0.00 0.00 3.85
2365 5460 5.271625 GCACAACTGATATGATCAAGCAAG 58.728 41.667 0.00 0.00 39.11 4.01
2369 5464 5.277202 CCTTCGCACAACTGATATGATCAAG 60.277 44.000 0.00 0.00 39.11 3.02
2406 5501 6.719370 AGGTTCCTTGCAATGAGTTTGTATAA 59.281 34.615 0.00 0.00 37.65 0.98
2515 5610 8.961634 TCGACCAATTTCCACAATGATTTTATA 58.038 29.630 0.00 0.00 0.00 0.98
2556 5651 3.788227 TGAAGGTGCCTTTGACTACAT 57.212 42.857 4.83 0.00 36.26 2.29
2587 5682 4.506654 AGCATCGTATACTTAAAAGGTGCG 59.493 41.667 0.56 0.00 34.33 5.34
2652 5753 8.677148 ATTGCCGATAGAAAATCTTTAGCTAA 57.323 30.769 0.86 0.86 39.76 3.09
2923 6033 5.448632 GGTGAGTAAAACAAGGACACAAGTG 60.449 44.000 0.00 0.00 0.00 3.16
3114 6226 6.203723 GTCAAGATAACAGAATAGGATGCACC 59.796 42.308 0.00 0.00 39.35 5.01
3204 6322 4.743644 AGGTAGAACAAGCGCGAATAATAC 59.256 41.667 12.10 2.99 0.00 1.89
3207 6325 3.241067 AGGTAGAACAAGCGCGAATAA 57.759 42.857 12.10 0.00 0.00 1.40
3717 6872 1.333619 TCACAGCCTTGTCTTTTTCGC 59.666 47.619 0.00 0.00 34.62 4.70
3901 7056 7.471721 TGCTTAAGTATGAAATGATCCAAACG 58.528 34.615 4.02 0.00 0.00 3.60
4108 7641 1.269723 CTCGAACAGTACCTGTGCAGA 59.730 52.381 3.41 0.00 44.62 4.26
4289 7824 4.053983 CCCACATTATGAGTCACATCTCG 58.946 47.826 0.00 0.00 40.07 4.04
4328 7865 1.967066 ACAGTGCTCTCTAACACAGCT 59.033 47.619 0.00 0.00 39.30 4.24
4335 7872 5.023533 ACAAAAGTGACAGTGCTCTCTAA 57.976 39.130 0.00 0.00 0.00 2.10
4343 7880 9.013490 CAAAATAAAGAGACAAAAGTGACAGTG 57.987 33.333 0.00 0.00 0.00 3.66
4344 7881 7.702348 GCAAAATAAAGAGACAAAAGTGACAGT 59.298 33.333 0.00 0.00 0.00 3.55
4345 7882 7.917505 AGCAAAATAAAGAGACAAAAGTGACAG 59.082 33.333 0.00 0.00 0.00 3.51
4346 7883 7.771183 AGCAAAATAAAGAGACAAAAGTGACA 58.229 30.769 0.00 0.00 0.00 3.58
4347 7884 8.534778 CAAGCAAAATAAAGAGACAAAAGTGAC 58.465 33.333 0.00 0.00 0.00 3.67
4348 7885 7.222611 GCAAGCAAAATAAAGAGACAAAAGTGA 59.777 33.333 0.00 0.00 0.00 3.41
4349 7886 7.223387 AGCAAGCAAAATAAAGAGACAAAAGTG 59.777 33.333 0.00 0.00 0.00 3.16
4350 7887 7.267857 AGCAAGCAAAATAAAGAGACAAAAGT 58.732 30.769 0.00 0.00 0.00 2.66
4351 7888 7.436080 TGAGCAAGCAAAATAAAGAGACAAAAG 59.564 33.333 0.00 0.00 0.00 2.27
4374 7914 4.514441 AGCAGAACAATTGACTGAGTTGAG 59.486 41.667 27.50 10.61 34.07 3.02
4454 7997 8.356657 CACACAAAAAGGAAGAATACATAACCA 58.643 33.333 0.00 0.00 0.00 3.67
4534 8077 7.587037 TTCAGATTCAACAAGAAATGAGGTT 57.413 32.000 0.00 0.00 40.22 3.50
4575 8119 1.955683 GCCCTAGGGAAAAAGTGGAGC 60.956 57.143 33.21 7.26 37.50 4.70
4641 8186 0.921166 AATTTACACCCCTACCCCCG 59.079 55.000 0.00 0.00 0.00 5.73
4648 8193 9.408648 CTATTGACTCATTTAATTTACACCCCT 57.591 33.333 0.00 0.00 0.00 4.79
4791 8336 8.877864 ACCATTTGAAGGAAGTAATACATTCA 57.122 30.769 0.00 0.00 35.56 2.57
4820 8365 4.106925 CTCTCCCAGCCCCAGTGC 62.107 72.222 0.00 0.00 0.00 4.40
4898 8443 2.653890 CTTCGACGAAAACGAGTGGTA 58.346 47.619 12.03 0.00 40.72 3.25
4902 8447 1.268896 TGAGCTTCGACGAAAACGAGT 60.269 47.619 12.03 0.00 40.72 4.18
5004 8551 0.027063 CCCAAAACACACGACACGAC 59.973 55.000 0.00 0.00 0.00 4.34
5077 8624 1.463674 GCAGATCCACGGGACAATTT 58.536 50.000 0.00 0.00 32.98 1.82
5078 8625 0.394352 GGCAGATCCACGGGACAATT 60.394 55.000 0.00 0.00 32.98 2.32


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

AutoCloner maintained by Alex Coulton.