Multiple sequence alignment - TraesCS7D01G239700

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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 TraesCS7D01G239700 chr7D 100.000 7556 0 0 1 7556 204245621 204253176 0.000000e+00 13954
1 TraesCS7D01G239700 chr7D 92.068 706 49 3 4 702 579772482 579771777 0.000000e+00 987
2 TraesCS7D01G239700 chr7D 92.286 700 46 6 4 702 610866578 610865886 0.000000e+00 987
3 TraesCS7D01G239700 chr7D 94.186 86 4 1 1569 1654 20238976 20239060 6.150000e-26 130
4 TraesCS7D01G239700 chr7A 96.564 5471 109 41 2140 7555 216345095 216350541 0.000000e+00 8988
5 TraesCS7D01G239700 chr7A 97.250 909 24 1 721 1629 216343488 216344395 0.000000e+00 1539
6 TraesCS7D01G239700 chr7A 94.737 513 24 3 1629 2139 216344557 216345068 0.000000e+00 795
7 TraesCS7D01G239700 chr7B 94.691 2166 103 10 3712 5869 168317816 168319977 0.000000e+00 3352
8 TraesCS7D01G239700 chr7B 92.738 1680 66 28 5899 7556 168320054 168321699 0.000000e+00 2375
9 TraesCS7D01G239700 chr7B 91.179 975 59 15 2743 3713 168316276 168317227 0.000000e+00 1299
10 TraesCS7D01G239700 chr7B 92.614 880 48 13 711 1580 168313918 168314790 0.000000e+00 1249
11 TraesCS7D01G239700 chr7B 94.784 556 25 2 2206 2758 168315686 168316240 0.000000e+00 863
12 TraesCS7D01G239700 chr7B 86.245 269 29 2 4097 4365 432763582 432763322 1.240000e-72 285
13 TraesCS7D01G239700 chr7B 85.317 252 21 4 1747 1996 168315022 168315259 5.860000e-61 246
14 TraesCS7D01G239700 chr7B 86.577 149 18 2 4970 5117 432763325 432763178 6.070000e-36 163
15 TraesCS7D01G239700 chr7B 92.391 92 5 2 1567 1656 165100269 165100178 6.150000e-26 130
16 TraesCS7D01G239700 chr7B 90.625 96 9 0 1643 1738 168314877 168314972 2.210000e-25 128
17 TraesCS7D01G239700 chr3D 92.725 701 43 6 4 702 431844760 431844066 0.000000e+00 1005
18 TraesCS7D01G239700 chr3D 94.186 86 4 1 1569 1654 565374332 565374416 6.150000e-26 130
19 TraesCS7D01G239700 chr5D 92.068 706 46 7 1 702 472718095 472718794 0.000000e+00 985
20 TraesCS7D01G239700 chr5D 91.678 709 50 4 1 702 403471159 403471865 0.000000e+00 974
21 TraesCS7D01G239700 chr6D 91.655 707 53 5 1 702 322611156 322611861 0.000000e+00 974
22 TraesCS7D01G239700 chr6D 88.710 124 14 0 1210 1333 372829659 372829536 1.310000e-32 152
23 TraesCS7D01G239700 chr2D 91.869 701 50 5 4 702 79851787 79851092 0.000000e+00 972
24 TraesCS7D01G239700 chr1D 91.631 705 53 5 1 702 477412286 477412987 0.000000e+00 970
25 TraesCS7D01G239700 chr1D 91.525 708 52 6 1 702 190536691 190537396 0.000000e+00 968
26 TraesCS7D01G239700 chr1A 85.766 274 29 4 4097 4369 541157698 541157434 1.610000e-71 281
27 TraesCS7D01G239700 chr1A 87.919 149 16 2 4970 5117 541157441 541157294 2.800000e-39 174
28 TraesCS7D01G239700 chr5B 85.978 271 26 6 4097 4365 562437780 562438040 5.770000e-71 279
29 TraesCS7D01G239700 chr5B 86.897 145 19 0 4970 5114 562438037 562438181 6.070000e-36 163
30 TraesCS7D01G239700 chr4A 85.130 269 32 2 4097 4365 640149391 640149131 1.250000e-67 268
31 TraesCS7D01G239700 chr4A 87.838 148 18 0 4970 5117 640149134 640148987 2.800000e-39 174
32 TraesCS7D01G239700 chr1B 84.387 269 34 2 4097 4365 8393198 8392938 2.710000e-64 257
33 TraesCS7D01G239700 chr1B 88.514 148 17 0 4970 5117 8392941 8392794 6.020000e-41 180
34 TraesCS7D01G239700 chr1B 82.550 149 19 3 4970 5117 493682586 493682444 2.860000e-24 124
35 TraesCS7D01G239700 chr6B 85.263 190 19 3 4176 4365 187226696 187226516 3.600000e-43 187
36 TraesCS7D01G239700 chr6B 86.667 105 12 2 4970 5073 187226519 187226416 1.720000e-21 115
37 TraesCS7D01G239700 chr6B 92.308 52 4 0 5066 5117 187205773 187205722 2.920000e-09 75
38 TraesCS7D01G239700 chr3B 92.308 91 6 1 1567 1657 723456001 723456090 2.210000e-25 128
39 TraesCS7D01G239700 chr3A 93.182 88 5 1 1567 1654 599863903 599863817 2.210000e-25 128
40 TraesCS7D01G239700 chr3A 93.103 87 4 2 1569 1654 434000979 434000894 7.960000e-25 126
41 TraesCS7D01G239700 chr4D 91.398 93 7 1 1565 1657 478669018 478668927 7.960000e-25 126
42 TraesCS7D01G239700 chr4B 85.841 113 11 4 1545 1655 252979202 252979311 1.720000e-21 115


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 TraesCS7D01G239700 chr7D 204245621 204253176 7555 False 13954.000000 13954 100.000000 1 7556 1 chr7D.!!$F2 7555
1 TraesCS7D01G239700 chr7D 579771777 579772482 705 True 987.000000 987 92.068000 4 702 1 chr7D.!!$R1 698
2 TraesCS7D01G239700 chr7D 610865886 610866578 692 True 987.000000 987 92.286000 4 702 1 chr7D.!!$R2 698
3 TraesCS7D01G239700 chr7A 216343488 216350541 7053 False 3774.000000 8988 96.183667 721 7555 3 chr7A.!!$F1 6834
4 TraesCS7D01G239700 chr7B 168313918 168321699 7781 False 1358.857143 3352 91.706857 711 7556 7 chr7B.!!$F1 6845
5 TraesCS7D01G239700 chr3D 431844066 431844760 694 True 1005.000000 1005 92.725000 4 702 1 chr3D.!!$R1 698
6 TraesCS7D01G239700 chr5D 472718095 472718794 699 False 985.000000 985 92.068000 1 702 1 chr5D.!!$F2 701
7 TraesCS7D01G239700 chr5D 403471159 403471865 706 False 974.000000 974 91.678000 1 702 1 chr5D.!!$F1 701
8 TraesCS7D01G239700 chr6D 322611156 322611861 705 False 974.000000 974 91.655000 1 702 1 chr6D.!!$F1 701
9 TraesCS7D01G239700 chr2D 79851092 79851787 695 True 972.000000 972 91.869000 4 702 1 chr2D.!!$R1 698
10 TraesCS7D01G239700 chr1D 477412286 477412987 701 False 970.000000 970 91.631000 1 702 1 chr1D.!!$F2 701
11 TraesCS7D01G239700 chr1D 190536691 190537396 705 False 968.000000 968 91.525000 1 702 1 chr1D.!!$F1 701

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
708 724 0.246635 TGTCTCTAGGGCACTTTCGC 59.753 55.000 0.00 0.0 0.00 4.70 F
1396 1414 0.387565 CAAACGGTTTCTTGTGGGGG 59.612 55.000 2.51 0.0 0.00 5.40 F
1888 2115 0.829182 CAGCAAGGGCCAAGGAGTTT 60.829 55.000 6.18 0.0 42.56 2.66 F
2715 3168 2.305009 AGGATTGCTCTTATTGCAGCC 58.695 47.619 0.00 0.0 41.71 4.85 F
3709 4216 2.095110 CCACGTCGTAGTAACATGGTGA 60.095 50.000 0.00 0.0 0.00 4.02 F
3935 5033 1.768870 AGAACTGTAGGTGGCTTGTGT 59.231 47.619 0.00 0.0 0.00 3.72 F
5642 6749 1.829222 CATGGCAATGAAAGAGGGCTT 59.171 47.619 0.00 0.0 35.67 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2234 0.178992 CAACCCCCACTCAAAGCTCA 60.179 55.000 0.0 0.00 0.00 4.26 R
2715 3168 0.661552 CAATTCCAGCAGCTGATCCG 59.338 55.000 24.9 7.03 32.44 4.18 R
3328 3834 2.373169 AGAACCAGGTGCAAGATGAGAA 59.627 45.455 0.0 0.00 0.00 2.87 R
3779 4876 3.153369 TGTAGCCAAAAATGCTGGAGA 57.847 42.857 0.0 0.00 39.91 3.71 R
5642 6749 1.070786 GTCGGGAAAGCAGGTCACA 59.929 57.895 0.0 0.00 0.00 3.58 R
5897 7023 7.213178 ACACCAGGGTCAATAGATTTATCTT 57.787 36.000 0.0 0.00 38.32 2.40 R
6705 7871 0.752054 CCTGGCAAGCTCCAAAACAA 59.248 50.000 0.0 0.00 35.36 2.83 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
115 116 8.354711 GTATCATCATACCTAGTCCAATCTCA 57.645 38.462 0.00 0.00 30.07 3.27
118 119 8.267620 TCATCATACCTAGTCCAATCTCATTT 57.732 34.615 0.00 0.00 0.00 2.32
166 167 5.464057 CGTAATGCATCATCCCGTAACTAAA 59.536 40.000 0.00 0.00 0.00 1.85
191 192 1.696063 AGTCACATTGCTTGCAAGGT 58.304 45.000 27.10 18.02 0.00 3.50
197 198 6.015519 AGTCACATTGCTTGCAAGGTTTATAA 60.016 34.615 27.10 4.46 0.00 0.98
218 219 2.808202 ATGATGTGCATTACCGAGAGGC 60.808 50.000 0.00 0.00 46.13 4.70
311 313 2.092592 TCGGAGACACCTGTAGAGCATA 60.093 50.000 0.00 0.00 36.31 3.14
435 440 7.002879 AGTCATGAAGAAGGCAATAGCAATAT 58.997 34.615 0.00 0.00 44.61 1.28
496 509 2.620251 TGATGTGATCCCGTTCATCC 57.380 50.000 0.00 0.00 36.75 3.51
577 592 4.750833 AGTAGAGGCATACTAGGGACAT 57.249 45.455 0.00 0.00 34.21 3.06
582 598 2.370189 AGGCATACTAGGGACATTCTGC 59.630 50.000 0.00 0.00 0.00 4.26
587 603 5.453339 GCATACTAGGGACATTCTGCTTGTA 60.453 44.000 0.00 0.00 0.00 2.41
702 718 7.553044 ACAACTTTATTATTGTCTCTAGGGCAC 59.447 37.037 0.00 0.00 33.80 5.01
703 719 7.439108 ACTTTATTATTGTCTCTAGGGCACT 57.561 36.000 0.00 0.00 0.00 4.40
704 720 7.862675 ACTTTATTATTGTCTCTAGGGCACTT 58.137 34.615 0.00 0.00 0.00 3.16
705 721 8.329502 ACTTTATTATTGTCTCTAGGGCACTTT 58.670 33.333 0.00 0.00 0.00 2.66
706 722 8.732746 TTTATTATTGTCTCTAGGGCACTTTC 57.267 34.615 0.00 0.00 0.00 2.62
707 723 2.743636 TTGTCTCTAGGGCACTTTCG 57.256 50.000 0.00 0.00 0.00 3.46
708 724 0.246635 TGTCTCTAGGGCACTTTCGC 59.753 55.000 0.00 0.00 0.00 4.70
720 736 3.376540 GCACTTTCGCCAAAAATGTACA 58.623 40.909 0.00 0.00 0.00 2.90
721 737 3.987220 GCACTTTCGCCAAAAATGTACAT 59.013 39.130 1.41 1.41 0.00 2.29
722 738 4.447389 GCACTTTCGCCAAAAATGTACATT 59.553 37.500 15.47 15.47 0.00 2.71
723 739 5.050431 GCACTTTCGCCAAAAATGTACATTT 60.050 36.000 24.88 24.88 42.35 2.32
724 740 6.354080 CACTTTCGCCAAAAATGTACATTTG 58.646 36.000 29.54 20.89 40.57 2.32
725 741 6.019156 CACTTTCGCCAAAAATGTACATTTGT 60.019 34.615 29.54 23.41 40.57 2.83
726 742 6.536941 ACTTTCGCCAAAAATGTACATTTGTT 59.463 30.769 29.54 21.95 40.57 2.83
727 743 5.896922 TCGCCAAAAATGTACATTTGTTG 57.103 34.783 29.54 28.33 40.57 3.33
728 744 4.747108 TCGCCAAAAATGTACATTTGTTGG 59.253 37.500 35.61 35.61 42.94 3.77
729 745 4.509600 CGCCAAAAATGTACATTTGTTGGT 59.490 37.500 36.90 24.02 42.60 3.67
730 746 5.692204 CGCCAAAAATGTACATTTGTTGGTA 59.308 36.000 36.90 9.61 42.60 3.25
786 802 7.428826 CCATGTATTTTGGAAATAGAGCCTTC 58.571 38.462 0.00 0.00 36.26 3.46
925 941 1.893808 CAAATCCCCCAGATCCGCG 60.894 63.158 0.00 0.00 32.47 6.46
1023 1039 4.056125 CACAGCGACCTCGAGCCA 62.056 66.667 6.99 0.00 43.02 4.75
1347 1363 3.117046 GGTAAGTAAGAGATCTGCGTGC 58.883 50.000 0.00 0.00 0.00 5.34
1396 1414 0.387565 CAAACGGTTTCTTGTGGGGG 59.612 55.000 2.51 0.00 0.00 5.40
1718 1903 8.470805 GTGGAAGAAACTTATAGTCTCATCTGA 58.529 37.037 0.00 0.00 0.00 3.27
1721 1906 7.049799 AGAAACTTATAGTCTCATCTGAGGC 57.950 40.000 3.59 3.59 46.62 4.70
1801 2027 4.100653 TGCTACAGAGAATTGCTGATAGCT 59.899 41.667 22.34 0.00 42.97 3.32
1869 2096 1.477558 CCTTGTGATGCTATGGGGGTC 60.478 57.143 0.00 0.00 0.00 4.46
1888 2115 0.829182 CAGCAAGGGCCAAGGAGTTT 60.829 55.000 6.18 0.00 42.56 2.66
1915 2142 5.817296 TGTGCAGTATGTTAACCTGATGATC 59.183 40.000 12.79 0.00 39.31 2.92
2007 2234 3.023119 TGTTCTGATTGTGTGCTTTGGT 58.977 40.909 0.00 0.00 0.00 3.67
2048 2442 7.364939 GGTTGTGGTACATTGGGAGTAGTATTA 60.365 40.741 0.00 0.00 44.52 0.98
2068 2462 9.314321 AGTATTATTGTGTTATTTCAGGTCTCG 57.686 33.333 0.00 0.00 0.00 4.04
2129 2523 7.584108 TCTATGTTCTTGCACTGTAATTGTTG 58.416 34.615 0.00 0.00 0.00 3.33
2130 2524 5.826601 TGTTCTTGCACTGTAATTGTTGA 57.173 34.783 0.00 0.00 0.00 3.18
2131 2525 5.820131 TGTTCTTGCACTGTAATTGTTGAG 58.180 37.500 0.00 0.00 0.00 3.02
2133 2527 5.673337 TCTTGCACTGTAATTGTTGAGTC 57.327 39.130 0.00 0.00 0.00 3.36
2134 2528 5.122519 TCTTGCACTGTAATTGTTGAGTCA 58.877 37.500 0.00 0.00 0.00 3.41
2135 2529 5.764686 TCTTGCACTGTAATTGTTGAGTCAT 59.235 36.000 0.00 0.00 0.00 3.06
2136 2530 5.361135 TGCACTGTAATTGTTGAGTCATG 57.639 39.130 0.00 0.00 0.00 3.07
2137 2531 4.821260 TGCACTGTAATTGTTGAGTCATGT 59.179 37.500 0.00 0.00 0.00 3.21
2138 2532 5.149273 GCACTGTAATTGTTGAGTCATGTG 58.851 41.667 0.00 0.00 0.00 3.21
2299 2752 5.648330 AGGTTCTTTTGTAGTCTTTCCCT 57.352 39.130 0.00 0.00 0.00 4.20
2304 2757 6.937436 TCTTTTGTAGTCTTTCCCTTTCAC 57.063 37.500 0.00 0.00 0.00 3.18
2715 3168 2.305009 AGGATTGCTCTTATTGCAGCC 58.695 47.619 0.00 0.00 41.71 4.85
2752 3256 5.998363 GGAATTGCTTCAGGTATACCTAAGG 59.002 44.000 24.15 12.09 46.65 2.69
2853 3357 7.385205 CAGAAGTTAAAGAAGAAAGGACGATGA 59.615 37.037 0.00 0.00 0.00 2.92
3235 3740 4.948341 TCTGCCGCTGGTATTTTATCTA 57.052 40.909 0.00 0.00 0.00 1.98
3327 3833 9.638176 CTCTACTGTAGTAGGAAAATTAGGGTA 57.362 37.037 16.66 0.00 46.01 3.69
3709 4216 2.095110 CCACGTCGTAGTAACATGGTGA 60.095 50.000 0.00 0.00 0.00 4.02
3724 4821 9.744468 GTAACATGGTGAATAATATTTCCAACC 57.256 33.333 12.26 7.58 0.00 3.77
3745 4842 3.508793 CCTGCCAATCTTTTGTCTGACAT 59.491 43.478 11.86 0.00 0.00 3.06
3935 5033 1.768870 AGAACTGTAGGTGGCTTGTGT 59.231 47.619 0.00 0.00 0.00 3.72
4172 5271 7.421530 TTTCAGTTGTCTAAGTATGCAACTC 57.578 36.000 5.90 0.00 46.48 3.01
4711 5810 8.685838 TTGATATGGCCAAAAGTAATACTACC 57.314 34.615 10.96 0.00 0.00 3.18
4783 5882 6.850752 TCAGTTCCATTGACATCTGTACTA 57.149 37.500 0.00 0.00 0.00 1.82
5495 6595 6.611236 TCTGATCTGGATGTATGTAACCTCAA 59.389 38.462 0.00 0.00 0.00 3.02
5642 6749 1.829222 CATGGCAATGAAAGAGGGCTT 59.171 47.619 0.00 0.00 35.67 4.35
5865 6972 5.505181 AGGTGGACTATTTCTGTGACAAT 57.495 39.130 0.00 0.00 0.00 2.71
5882 7008 9.761504 CTGTGACAATGATAATTCATCTAGAGT 57.238 33.333 0.00 0.00 41.83 3.24
6054 7216 4.238761 TCCTCTCACTGTCTAACAAACG 57.761 45.455 0.00 0.00 0.00 3.60
6093 7255 5.254115 ACTGACCTTATTTTCCTACCAAGC 58.746 41.667 0.00 0.00 0.00 4.01
6217 7379 2.877168 AGTGCACAAAGCTTCTTCTGAG 59.123 45.455 21.04 0.00 45.94 3.35
6238 7400 2.490509 GCAAACTAGTATTTGGCCCGTT 59.509 45.455 0.00 0.00 39.52 4.44
6263 7425 4.209703 GCCATCCGTTAAATTGCATTGATG 59.790 41.667 0.00 0.00 0.00 3.07
6283 7445 6.519382 TGATGGACATTAGACAGATAGCAAG 58.481 40.000 0.00 0.00 0.00 4.01
6387 7552 6.206634 TGTTACATTGATTGAAACTGAGTCCC 59.793 38.462 0.00 0.00 0.00 4.46
6453 7618 1.406069 CCTGCCATACGAAAGCACTCT 60.406 52.381 0.00 0.00 32.06 3.24
6704 7870 6.884280 AAAGAGTCCTTCACCAAATGTAAG 57.116 37.500 0.00 0.00 0.00 2.34
6705 7871 5.568620 AGAGTCCTTCACCAAATGTAAGT 57.431 39.130 0.00 0.00 0.00 2.24
6739 7905 4.209307 TGCCAGGATACACATTTCGTAA 57.791 40.909 0.00 0.00 41.41 3.18
6911 8080 5.706916 ACTTCGTGTCGTATCTTATGTTGT 58.293 37.500 0.00 0.00 0.00 3.32
7140 8309 4.021192 CCAGAAACCATATGGCAAGTTTGT 60.021 41.667 22.18 10.16 39.32 2.83
7184 8353 8.782339 AATCCATTTTTCCTGCTTAAAATCAG 57.218 30.769 0.00 0.00 33.04 2.90
7481 8656 2.031674 GCAGCACAAGCCTTGGGTTT 62.032 55.000 8.76 0.00 43.56 3.27
7502 8677 1.301165 CTGCATCGCCGATGGATGA 60.301 57.895 26.71 0.00 43.07 2.92
7503 8678 0.672711 CTGCATCGCCGATGGATGAT 60.673 55.000 26.71 0.00 43.07 2.45
7504 8679 0.952010 TGCATCGCCGATGGATGATG 60.952 55.000 26.71 3.18 43.07 3.07
7505 8680 1.642037 GCATCGCCGATGGATGATGG 61.642 60.000 26.71 0.85 43.07 3.51
7506 8681 1.376424 ATCGCCGATGGATGATGGC 60.376 57.895 0.00 0.00 44.09 4.40
7508 8683 2.433446 GCCGATGGATGATGGCCT 59.567 61.111 3.32 0.00 41.70 5.19
7509 8684 1.970114 GCCGATGGATGATGGCCTG 60.970 63.158 3.32 0.00 41.70 4.85
7510 8685 1.970114 CCGATGGATGATGGCCTGC 60.970 63.158 3.32 0.00 0.00 4.85
7545 8720 3.064324 GAACAAGCGCCAGGCCAT 61.064 61.111 5.01 0.00 45.17 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.577164 AGTTTGACCGATAAAGATCTTCGTG 59.423 40.000 8.78 5.50 0.00 4.35
107 108 2.094675 ACTTGCCGGAAATGAGATTGG 58.905 47.619 5.05 0.00 0.00 3.16
115 116 4.254492 GAGTAAAGAGACTTGCCGGAAAT 58.746 43.478 5.05 0.00 0.00 2.17
118 119 1.201647 CGAGTAAAGAGACTTGCCGGA 59.798 52.381 5.05 0.00 0.00 5.14
166 167 5.393787 CCTTGCAAGCAATGTGACTAATGAT 60.394 40.000 21.43 0.00 35.20 2.45
191 192 7.387673 CCTCTCGGTAATGCACATCATTATAAA 59.612 37.037 0.00 0.00 46.08 1.40
197 198 2.808202 GCCTCTCGGTAATGCACATCAT 60.808 50.000 0.00 0.00 36.87 2.45
245 246 5.848406 AGATCGAGATTAGGATTTGTCACC 58.152 41.667 0.00 0.00 0.00 4.02
311 313 7.825270 TCACAACGTAACTGGGTGATTATAAAT 59.175 33.333 0.00 0.00 33.88 1.40
405 409 7.658982 TGCTATTGCCTTCTTCATGACTTATAG 59.341 37.037 0.00 0.00 38.71 1.31
535 548 8.086522 TCTACTTGACTAGCTCGTTAAACAAAT 58.913 33.333 0.00 0.00 0.00 2.32
540 553 5.392811 GCCTCTACTTGACTAGCTCGTTAAA 60.393 44.000 0.00 0.00 0.00 1.52
577 592 8.829612 CATGTGTGAATACATATACAAGCAGAA 58.170 33.333 0.00 0.00 39.17 3.02
702 718 6.523676 ACAAATGTACATTTTTGGCGAAAG 57.476 33.333 27.33 16.49 38.84 2.62
703 719 6.238211 CCAACAAATGTACATTTTTGGCGAAA 60.238 34.615 33.15 0.00 39.30 3.46
704 720 5.235186 CCAACAAATGTACATTTTTGGCGAA 59.765 36.000 33.15 3.84 39.30 4.70
705 721 4.747108 CCAACAAATGTACATTTTTGGCGA 59.253 37.500 33.15 4.25 39.30 5.54
706 722 4.509600 ACCAACAAATGTACATTTTTGGCG 59.490 37.500 37.16 27.40 43.29 5.69
707 723 7.484035 TTACCAACAAATGTACATTTTTGGC 57.516 32.000 37.16 5.20 43.29 4.52
745 761 7.985634 AATACATGGCGTGTTTTATTTCATC 57.014 32.000 18.82 0.00 42.29 2.92
786 802 1.252904 TTCCAGGTTACCCCTCGTCG 61.253 60.000 0.00 0.00 43.86 5.12
903 919 1.212935 CGGATCTGGGGGATTTGTCTT 59.787 52.381 0.00 0.00 34.33 3.01
946 962 2.454055 GCAATCGCATCAAAACTAGGC 58.546 47.619 0.00 0.00 38.36 3.93
1347 1363 8.687824 AACTGATAAATAACGCATTTTTCCTG 57.312 30.769 1.40 3.12 37.93 3.86
1376 1394 0.387565 CCCCACAAGAAACCGTTTGG 59.612 55.000 0.00 0.00 42.84 3.28
1396 1414 6.919721 AGAGATCTCGGCAGAATACTATTTC 58.080 40.000 16.97 0.00 30.24 2.17
1718 1903 2.086869 CATGAACAATCACCTTCGCCT 58.913 47.619 0.00 0.00 38.69 5.52
1721 1906 4.747540 TTCACATGAACAATCACCTTCG 57.252 40.909 0.00 0.00 38.69 3.79
1750 1935 3.897239 TCCATGTGAAGACAACCAAACT 58.103 40.909 0.00 0.00 35.11 2.66
1801 2027 3.791320 AGAAGAGACCATAACTGGACCA 58.209 45.455 0.00 0.00 46.37 4.02
1820 2046 6.150641 ACACTAACACGAATGCTCTAACTAGA 59.849 38.462 0.00 0.00 0.00 2.43
1869 2096 0.829182 AAACTCCTTGGCCCTTGCTG 60.829 55.000 0.00 0.00 37.74 4.41
1888 2115 7.334858 TCATCAGGTTAACATACTGCACATAA 58.665 34.615 8.10 0.00 32.42 1.90
1915 2142 1.545582 ACCTCATCAAACCGGCAAATG 59.454 47.619 0.00 0.27 0.00 2.32
2007 2234 0.178992 CAACCCCCACTCAAAGCTCA 60.179 55.000 0.00 0.00 0.00 4.26
2048 2442 5.160607 TCCGAGACCTGAAATAACACAAT 57.839 39.130 0.00 0.00 0.00 2.71
2068 2462 4.462483 CAGAGATGGCCTTAGTCTCTATCC 59.538 50.000 21.68 3.53 45.06 2.59
2129 2523 0.610174 TCTCACCCTGCACATGACTC 59.390 55.000 0.00 0.00 0.00 3.36
2130 2524 1.209019 GATCTCACCCTGCACATGACT 59.791 52.381 0.00 0.00 0.00 3.41
2131 2525 1.661341 GATCTCACCCTGCACATGAC 58.339 55.000 0.00 0.00 0.00 3.06
2133 2527 0.253894 TGGATCTCACCCTGCACATG 59.746 55.000 0.00 0.00 0.00 3.21
2134 2528 0.994247 TTGGATCTCACCCTGCACAT 59.006 50.000 0.00 0.00 0.00 3.21
2135 2529 0.770499 TTTGGATCTCACCCTGCACA 59.230 50.000 0.00 0.00 0.00 4.57
2136 2530 2.019984 GATTTGGATCTCACCCTGCAC 58.980 52.381 0.00 0.00 0.00 4.57
2137 2531 1.064463 GGATTTGGATCTCACCCTGCA 60.064 52.381 0.00 0.00 32.66 4.41
2138 2532 1.213926 AGGATTTGGATCTCACCCTGC 59.786 52.381 0.00 0.00 32.66 4.85
2299 2752 5.233988 CAGGTGTTTTTCAAACAGGTGAAA 58.766 37.500 2.26 0.00 43.92 2.69
2304 2757 2.168313 AGGCAGGTGTTTTTCAAACAGG 59.832 45.455 2.26 0.00 0.00 4.00
2715 3168 0.661552 CAATTCCAGCAGCTGATCCG 59.338 55.000 24.90 7.03 32.44 4.18
2804 3308 4.744867 GCCTAGCATCTTAGCAGGATTTCA 60.745 45.833 0.00 0.00 35.91 2.69
2853 3357 7.669722 TGGTCCTTCTTGCTTGTCTAATTATTT 59.330 33.333 0.00 0.00 0.00 1.40
2984 3489 5.310857 GTGTCAGGGGAGGAATATAGGAAAT 59.689 44.000 0.00 0.00 0.00 2.17
3147 3652 5.398603 ACAAAACATTGGACACAGTTGAA 57.601 34.783 0.00 0.00 0.00 2.69
3235 3740 9.184523 TCTGTAATACCAAATTTGATCGGAATT 57.815 29.630 19.86 10.88 0.00 2.17
3327 3833 3.009916 AGAACCAGGTGCAAGATGAGAAT 59.990 43.478 0.00 0.00 0.00 2.40
3328 3834 2.373169 AGAACCAGGTGCAAGATGAGAA 59.627 45.455 0.00 0.00 0.00 2.87
3518 4024 6.569179 TGACTTACTATTTGGAAAACAGGC 57.431 37.500 0.00 0.00 0.00 4.85
3652 4158 8.466798 CCACATGTTATCATCATATTGCATGAT 58.533 33.333 0.00 3.86 41.62 2.45
3653 4159 7.094118 CCCACATGTTATCATCATATTGCATGA 60.094 37.037 0.00 0.00 36.80 3.07
3654 4160 7.033185 CCCACATGTTATCATCATATTGCATG 58.967 38.462 0.00 0.00 38.57 4.06
3655 4161 6.153851 CCCCACATGTTATCATCATATTGCAT 59.846 38.462 0.00 0.00 31.15 3.96
3709 4216 7.919385 AGATTGGCAGGTTGGAAATATTATT 57.081 32.000 0.00 0.00 0.00 1.40
3724 4821 9.123955 TCAGAATGTCAGACAAAAGATTGGCAG 62.124 40.741 7.50 0.00 41.95 4.85
3745 4842 6.665992 AAGTACATAGTCAACTGGTCAGAA 57.334 37.500 4.84 0.00 0.00 3.02
3779 4876 3.153369 TGTAGCCAAAAATGCTGGAGA 57.847 42.857 0.00 0.00 39.91 3.71
3935 5033 7.817962 GTGCTACAACTATTGTTTTCTCTCCTA 59.182 37.037 0.00 0.00 42.22 2.94
4172 5271 8.430801 AAGCTCTGCAGAATATAACTTTAGTG 57.569 34.615 18.85 1.60 0.00 2.74
4711 5810 6.543831 CCATTCCCACCTGAATTAAGTAGAAG 59.456 42.308 0.00 0.00 32.71 2.85
4783 5882 8.738645 AATCTTTTGTCAGTTCAAAGAGTAGT 57.261 30.769 4.29 0.00 38.32 2.73
5009 6108 2.253758 CGCATAACCATGGCGAGGG 61.254 63.158 13.04 0.00 35.23 4.30
5642 6749 1.070786 GTCGGGAAAGCAGGTCACA 59.929 57.895 0.00 0.00 0.00 3.58
5894 7020 9.627123 CACCAGGGTCAATAGATTTATCTTTAA 57.373 33.333 0.00 0.00 38.32 1.52
5895 7021 8.778059 ACACCAGGGTCAATAGATTTATCTTTA 58.222 33.333 0.00 0.00 38.32 1.85
5896 7022 7.643123 ACACCAGGGTCAATAGATTTATCTTT 58.357 34.615 0.00 0.00 38.32 2.52
5897 7023 7.213178 ACACCAGGGTCAATAGATTTATCTT 57.787 36.000 0.00 0.00 38.32 2.40
6054 7216 4.757149 AGGTCAGTTGTGCTTTTAGATGTC 59.243 41.667 0.00 0.00 0.00 3.06
6217 7379 2.089201 ACGGGCCAAATACTAGTTTGC 58.911 47.619 4.39 0.00 37.67 3.68
6238 7400 1.550327 TGCAATTTAACGGATGGCCA 58.450 45.000 8.56 8.56 0.00 5.36
6245 7407 4.742417 TGTCCATCAATGCAATTTAACGG 58.258 39.130 0.00 0.00 31.22 4.44
6263 7425 7.493367 AGTTACTTGCTATCTGTCTAATGTCC 58.507 38.462 0.00 0.00 0.00 4.02
6283 7445 9.419297 TGTAAGATATGACTGTCAACAAGTTAC 57.581 33.333 15.31 16.77 0.00 2.50
6387 7552 1.614824 AGTCCTCTCCCCCTTGCAG 60.615 63.158 0.00 0.00 0.00 4.41
6453 7618 4.502282 GCATTGTTCAAACATTCGTGTCAA 59.498 37.500 0.00 0.00 38.95 3.18
6704 7870 1.538849 CCTGGCAAGCTCCAAAACAAC 60.539 52.381 0.00 0.00 35.36 3.32
6705 7871 0.752054 CCTGGCAAGCTCCAAAACAA 59.248 50.000 0.00 0.00 35.36 2.83
6739 7905 8.820831 CCATCACCTCTTATAATCTGTAATCCT 58.179 37.037 0.00 0.00 0.00 3.24
6980 8149 1.277557 ACTCACTGCAGTTCAGATCCC 59.722 52.381 23.69 0.00 45.72 3.85
7057 8226 7.653311 GGTTTCAAGCTAACATTGAATCAACTT 59.347 33.333 0.00 0.00 43.96 2.66
7105 8274 1.467920 GTTTCTGGGAGAGGGCATTG 58.532 55.000 0.00 0.00 0.00 2.82
7140 8309 7.914427 TGGATTAAGATCTGAGGTAGCTAAA 57.086 36.000 0.00 0.00 32.66 1.85
7184 8353 3.064900 AGGGAACACAGAGAATTCAGC 57.935 47.619 8.44 0.00 0.00 4.26
7481 8656 4.240103 CCATCGGCGATGCAGGGA 62.240 66.667 37.35 3.49 38.59 4.20


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

AutoCloner maintained by Alex Coulton.