Multiple sequence alignment - TraesCS4A01G107600

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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 TraesCS4A01G107600 chr4A 100.000 3904 0 0 1 3904 124406879 124402976 0.000000e+00 7210.0
1 TraesCS4A01G107600 chr4A 93.635 1964 60 20 996 2900 125027942 125029899 0.000000e+00 2874.0
2 TraesCS4A01G107600 chr4A 84.181 177 16 5 3613 3783 636064089 636064259 1.120000e-35 161.0
3 TraesCS4A01G107600 chr4D 93.588 1466 54 29 1788 3233 341923804 341925249 0.000000e+00 2150.0
4 TraesCS4A01G107600 chr4D 92.960 1463 53 24 129 1573 341921943 341923373 0.000000e+00 2085.0
5 TraesCS4A01G107600 chr4D 93.358 1355 64 13 1566 2900 341696464 341695116 0.000000e+00 1980.0
6 TraesCS4A01G107600 chr4D 94.839 620 25 3 996 1608 341697082 341696463 0.000000e+00 961.0
7 TraesCS4A01G107600 chr4D 90.615 309 25 2 3582 3890 341925904 341926208 1.310000e-109 407.0
8 TraesCS4A01G107600 chr4D 88.561 271 7 2 3345 3591 341925243 341925513 1.360000e-79 307.0
9 TraesCS4A01G107600 chr4B 90.579 1624 87 37 1788 3381 424061150 424062737 0.000000e+00 2091.0
10 TraesCS4A01G107600 chr4B 92.691 1464 48 24 132 1573 424059389 424060815 0.000000e+00 2056.0
11 TraesCS4A01G107600 chr4B 91.722 1353 59 16 1566 2900 423776532 423775215 0.000000e+00 1829.0
12 TraesCS4A01G107600 chr4B 95.016 622 22 2 996 1608 423777152 423776531 0.000000e+00 968.0
13 TraesCS4A01G107600 chr4B 94.118 85 0 4 1 84 424059308 424059388 1.470000e-24 124.0
14 TraesCS4A01G107600 chr4B 79.661 118 19 5 3410 3523 424063350 424063466 3.230000e-11 80.5
15 TraesCS4A01G107600 chr5D 94.231 884 49 2 2021 2903 483227761 483226879 0.000000e+00 1349.0
16 TraesCS4A01G107600 chr5D 95.876 485 19 1 991 1475 483228786 483228303 0.000000e+00 784.0
17 TraesCS4A01G107600 chr5D 96.025 478 18 1 994 1471 483372420 483371944 0.000000e+00 776.0
18 TraesCS4A01G107600 chr5A 94.111 883 52 0 2021 2903 603794302 603793420 0.000000e+00 1343.0
19 TraesCS4A01G107600 chr5A 96.033 479 18 1 994 1472 604312716 604312239 0.000000e+00 778.0
20 TraesCS4A01G107600 chr5B 94.098 881 50 2 2021 2900 593944221 593943342 0.000000e+00 1338.0
21 TraesCS4A01G107600 chr5B 93.891 884 52 2 2021 2903 593659272 593658390 0.000000e+00 1332.0
22 TraesCS4A01G107600 chr5B 96.653 478 15 1 994 1471 593945333 593944857 0.000000e+00 793.0
23 TraesCS4A01G107600 chr5B 89.032 155 17 0 3629 3783 16765119 16765273 3.980000e-45 193.0
24 TraesCS4A01G107600 chr6A 88.889 261 23 5 3623 3880 162806543 162806800 2.260000e-82 316.0
25 TraesCS4A01G107600 chr1B 86.316 285 22 7 3619 3887 440963493 440963776 1.060000e-75 294.0
26 TraesCS4A01G107600 chr7B 86.873 259 19 3 3650 3893 157203052 157202794 3.840000e-70 276.0
27 TraesCS4A01G107600 chr7B 86.517 89 8 4 3726 3813 107821396 107821311 1.150000e-15 95.3
28 TraesCS4A01G107600 chr1A 89.744 156 16 0 3628 3783 146813235 146813080 2.380000e-47 200.0
29 TraesCS4A01G107600 chr6B 93.966 116 6 1 3623 3738 548387958 548388072 1.440000e-39 174.0
30 TraesCS4A01G107600 chr3D 91.736 121 8 2 3620 3738 182983393 182983273 2.410000e-37 167.0
31 TraesCS4A01G107600 chr1D 91.736 121 8 2 3620 3738 300963506 300963626 2.410000e-37 167.0
32 TraesCS4A01G107600 chr2B 86.986 146 14 5 3595 3738 135777342 135777484 4.040000e-35 159.0
33 TraesCS4A01G107600 chr3A 80.117 171 15 10 3628 3779 33428124 33428294 4.120000e-20 110.0
34 TraesCS4A01G107600 chr7D 87.209 86 8 3 3725 3809 143976416 143976499 1.150000e-15 95.3


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 TraesCS4A01G107600 chr4A 124402976 124406879 3903 True 7210.000 7210 100.00000 1 3904 1 chr4A.!!$R1 3903
1 TraesCS4A01G107600 chr4A 125027942 125029899 1957 False 2874.000 2874 93.63500 996 2900 1 chr4A.!!$F1 1904
2 TraesCS4A01G107600 chr4D 341695116 341697082 1966 True 1470.500 1980 94.09850 996 2900 2 chr4D.!!$R1 1904
3 TraesCS4A01G107600 chr4D 341921943 341926208 4265 False 1237.250 2150 91.43100 129 3890 4 chr4D.!!$F1 3761
4 TraesCS4A01G107600 chr4B 423775215 423777152 1937 True 1398.500 1829 93.36900 996 2900 2 chr4B.!!$R1 1904
5 TraesCS4A01G107600 chr4B 424059308 424063466 4158 False 1087.875 2091 89.26225 1 3523 4 chr4B.!!$F1 3522
6 TraesCS4A01G107600 chr5D 483226879 483228786 1907 True 1066.500 1349 95.05350 991 2903 2 chr5D.!!$R2 1912
7 TraesCS4A01G107600 chr5A 603793420 603794302 882 True 1343.000 1343 94.11100 2021 2903 1 chr5A.!!$R1 882
8 TraesCS4A01G107600 chr5B 593658390 593659272 882 True 1332.000 1332 93.89100 2021 2903 1 chr5B.!!$R1 882
9 TraesCS4A01G107600 chr5B 593943342 593945333 1991 True 1065.500 1338 95.37550 994 2900 2 chr5B.!!$R2 1906

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
909 936 0.249657 CCTGCAGTCCGATAGCCTTC 60.250 60.0 13.81 0.0 0.0 3.46 F
911 938 0.461548 TGCAGTCCGATAGCCTTCTG 59.538 55.0 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 3531 0.040067 CAGCAAAACGACCAAGAGGC 60.04 55.000 0.0 0.0 39.06 4.70 R
3040 3794 2.869801 TGTAAAAGGCACAAGACAGACG 59.13 45.455 0.0 0.0 0.00 4.18 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
109 110 2.949451 TTTTTGACGCTTCTGGCAAA 57.051 40.000 0.00 0.00 41.91 3.68
110 111 2.490328 TTTTGACGCTTCTGGCAAAG 57.510 45.000 0.00 0.00 41.91 2.77
111 112 1.388547 TTTGACGCTTCTGGCAAAGT 58.611 45.000 9.90 0.00 41.91 2.66
112 113 2.248280 TTGACGCTTCTGGCAAAGTA 57.752 45.000 9.90 0.00 41.91 2.24
113 114 1.795768 TGACGCTTCTGGCAAAGTAG 58.204 50.000 9.90 7.75 41.91 2.57
114 115 1.070134 TGACGCTTCTGGCAAAGTAGT 59.930 47.619 9.90 9.94 41.91 2.73
115 116 1.727335 GACGCTTCTGGCAAAGTAGTC 59.273 52.381 15.74 15.74 41.91 2.59
116 117 0.716108 CGCTTCTGGCAAAGTAGTCG 59.284 55.000 9.90 3.50 41.91 4.18
117 118 1.668919 CGCTTCTGGCAAAGTAGTCGA 60.669 52.381 9.90 0.00 41.91 4.20
118 119 2.413837 GCTTCTGGCAAAGTAGTCGAA 58.586 47.619 9.90 0.00 41.35 3.71
119 120 2.806244 GCTTCTGGCAAAGTAGTCGAAA 59.194 45.455 9.90 0.00 41.35 3.46
120 121 3.437049 GCTTCTGGCAAAGTAGTCGAAAT 59.563 43.478 9.90 0.00 41.35 2.17
121 122 4.630069 GCTTCTGGCAAAGTAGTCGAAATA 59.370 41.667 9.90 0.00 41.35 1.40
122 123 5.121768 GCTTCTGGCAAAGTAGTCGAAATAA 59.878 40.000 9.90 0.00 41.35 1.40
123 124 6.673316 GCTTCTGGCAAAGTAGTCGAAATAAG 60.673 42.308 9.90 0.00 41.35 1.73
124 125 6.032956 TCTGGCAAAGTAGTCGAAATAAGA 57.967 37.500 0.00 0.00 0.00 2.10
125 126 6.460781 TCTGGCAAAGTAGTCGAAATAAGAA 58.539 36.000 0.00 0.00 0.00 2.52
126 127 6.590292 TCTGGCAAAGTAGTCGAAATAAGAAG 59.410 38.462 0.00 0.00 0.00 2.85
127 128 5.642063 TGGCAAAGTAGTCGAAATAAGAAGG 59.358 40.000 0.00 0.00 0.00 3.46
181 182 2.759973 CGGCCTCCTGCTCCAGTA 60.760 66.667 0.00 0.00 40.92 2.74
183 184 1.751563 GGCCTCCTGCTCCAGTATC 59.248 63.158 0.00 0.00 40.92 2.24
245 246 3.127533 GCGGCCTGCGAAATGTCT 61.128 61.111 0.00 0.00 0.00 3.41
274 275 8.429237 AACCCATTCATCAACCTGTAAAATAA 57.571 30.769 0.00 0.00 0.00 1.40
495 504 1.107945 CCTCTCCTTCCTTCGAGGTC 58.892 60.000 0.00 0.00 38.54 3.85
499 508 1.474879 CTCCTTCCTTCGAGGTCAGTC 59.525 57.143 0.00 0.00 36.53 3.51
536 553 2.359214 AGTGCGCTTAGATCTTCATCGA 59.641 45.455 9.73 0.00 33.75 3.59
588 609 1.149401 GGTAGCCTCCAATCCAGCC 59.851 63.158 0.00 0.00 0.00 4.85
641 662 4.019867 GCATCGTTTGTTTGTATAGCGTC 58.980 43.478 0.00 0.00 0.00 5.19
777 798 5.563876 ATCTGTCGGTAGATGGACTAGTA 57.436 43.478 0.00 0.00 36.12 1.82
797 818 9.344772 ACTAGTATCTCAATTTCGTAGACTGAT 57.655 33.333 0.00 0.00 34.32 2.90
800 821 9.522804 AGTATCTCAATTTCGTAGACTGATTTC 57.477 33.333 0.00 0.00 34.32 2.17
801 822 6.871044 TCTCAATTTCGTAGACTGATTTCG 57.129 37.500 0.00 0.00 34.32 3.46
802 823 6.387465 TCTCAATTTCGTAGACTGATTTCGT 58.613 36.000 0.00 0.00 34.32 3.85
803 824 7.532571 TCTCAATTTCGTAGACTGATTTCGTA 58.467 34.615 0.00 0.00 34.32 3.43
831 852 6.428385 AACTAGTGATTGCAAACTATCTGC 57.572 37.500 1.71 0.00 40.35 4.26
880 902 1.064505 TCGTCTTCGTGTCGTGTTTCT 59.935 47.619 0.00 0.00 38.33 2.52
881 903 2.287644 TCGTCTTCGTGTCGTGTTTCTA 59.712 45.455 0.00 0.00 38.33 2.10
909 936 0.249657 CCTGCAGTCCGATAGCCTTC 60.250 60.000 13.81 0.00 0.00 3.46
910 937 0.749649 CTGCAGTCCGATAGCCTTCT 59.250 55.000 5.25 0.00 0.00 2.85
911 938 0.461548 TGCAGTCCGATAGCCTTCTG 59.538 55.000 0.00 0.00 0.00 3.02
912 939 0.878086 GCAGTCCGATAGCCTTCTGC 60.878 60.000 0.00 0.00 40.66 4.26
956 988 1.070134 CCAGTTCTTCGTTCTGGTCCA 59.930 52.381 0.00 0.00 42.42 4.02
968 1000 5.237779 TCGTTCTGGTCCATTTTTGTCTAAC 59.762 40.000 0.00 0.00 0.00 2.34
1086 1120 1.135094 CCACTGGCCACCTGATCTAT 58.865 55.000 0.00 0.00 0.00 1.98
1561 1749 9.288576 CTTATTTGAGGTTGCTATATGATCCAA 57.711 33.333 0.00 0.00 0.00 3.53
1562 1750 7.756395 ATTTGAGGTTGCTATATGATCCAAG 57.244 36.000 0.00 0.00 0.00 3.61
1563 1751 5.894298 TGAGGTTGCTATATGATCCAAGT 57.106 39.130 0.00 0.00 0.00 3.16
1564 1752 6.252599 TGAGGTTGCTATATGATCCAAGTT 57.747 37.500 0.00 0.00 0.00 2.66
1565 1753 6.291377 TGAGGTTGCTATATGATCCAAGTTC 58.709 40.000 0.00 0.00 0.00 3.01
1567 1755 6.904626 AGGTTGCTATATGATCCAAGTTCTT 58.095 36.000 0.00 0.00 0.00 2.52
1568 1756 6.769822 AGGTTGCTATATGATCCAAGTTCTTG 59.230 38.462 5.66 5.66 0.00 3.02
1569 1757 6.767902 GGTTGCTATATGATCCAAGTTCTTGA 59.232 38.462 13.29 1.67 0.00 3.02
1570 1758 7.446625 GGTTGCTATATGATCCAAGTTCTTGAT 59.553 37.037 13.29 5.86 0.00 2.57
1571 1759 8.844244 GTTGCTATATGATCCAAGTTCTTGATT 58.156 33.333 13.29 1.40 0.00 2.57
1572 1760 8.985315 TGCTATATGATCCAAGTTCTTGATTT 57.015 30.769 13.29 0.00 0.00 2.17
1573 1761 9.412460 TGCTATATGATCCAAGTTCTTGATTTT 57.588 29.630 13.29 0.00 0.00 1.82
1584 1772 9.965824 CCAAGTTCTTGATTTTAACTAACATGT 57.034 29.630 13.29 0.00 33.24 3.21
1606 1794 7.872163 TGTAAACATGTTCTGAATCAATTGC 57.128 32.000 12.39 0.00 0.00 3.56
1607 1795 7.660112 TGTAAACATGTTCTGAATCAATTGCT 58.340 30.769 12.39 0.00 0.00 3.91
1608 1796 8.791675 TGTAAACATGTTCTGAATCAATTGCTA 58.208 29.630 12.39 0.00 0.00 3.49
1637 1825 9.465985 CATATTGCTGCACACATATTTTGATTA 57.534 29.630 0.00 0.00 0.00 1.75
1758 2215 8.927411 TGGATGTGACTTTTCATCATCTAGATA 58.073 33.333 4.54 0.00 41.26 1.98
1876 2615 8.256611 TCTAATGTTTAATTCTCACTCTGTGC 57.743 34.615 0.00 0.00 32.98 4.57
1882 2621 2.533266 TTCTCACTCTGTGCTTGGTC 57.467 50.000 0.00 0.00 32.98 4.02
1883 2622 1.413118 TCTCACTCTGTGCTTGGTCA 58.587 50.000 0.00 0.00 32.98 4.02
1925 2664 7.751732 TGTTCTGCTTGTTTATGCTAGTTATG 58.248 34.615 0.00 0.00 0.00 1.90
1983 2722 9.529325 TTCGTAATATCTTACAGTTCCATCTTG 57.471 33.333 2.37 0.00 37.65 3.02
2780 3531 0.036306 AGACCTTTGCCACTTACCCG 59.964 55.000 0.00 0.00 0.00 5.28
3040 3794 0.180406 ATATCGTGCCCTTGGTGGTC 59.820 55.000 0.00 0.00 0.00 4.02
3057 3811 1.583054 GTCGTCTGTCTTGTGCCTTT 58.417 50.000 0.00 0.00 0.00 3.11
3065 3819 5.701290 GTCTGTCTTGTGCCTTTTACATACT 59.299 40.000 0.00 0.00 0.00 2.12
3066 3820 5.700832 TCTGTCTTGTGCCTTTTACATACTG 59.299 40.000 0.00 0.00 0.00 2.74
3155 3910 5.801947 GCTTGTTGCATTTTATCTGTGTAGG 59.198 40.000 0.00 0.00 42.31 3.18
3196 3951 7.846644 TTTTTGAAAGACACAAATGCATCTT 57.153 28.000 0.00 0.00 37.15 2.40
3242 3997 4.307443 AGGTGTTCTTTTAGTTGCAAGC 57.693 40.909 0.00 0.00 0.00 4.01
3244 3999 4.402474 AGGTGTTCTTTTAGTTGCAAGCTT 59.598 37.500 0.00 0.00 0.00 3.74
3248 4003 6.750039 GTGTTCTTTTAGTTGCAAGCTTAACA 59.250 34.615 13.26 6.13 0.00 2.41
3259 4014 6.603940 TGCAAGCTTAACAATTTATTCCCT 57.396 33.333 0.00 0.00 0.00 4.20
3260 4015 6.397272 TGCAAGCTTAACAATTTATTCCCTG 58.603 36.000 0.00 0.00 0.00 4.45
3261 4016 6.014669 TGCAAGCTTAACAATTTATTCCCTGT 60.015 34.615 0.00 0.00 0.00 4.00
3280 4035 3.609853 TGTCTACTGATGGTTCATTGGC 58.390 45.455 0.00 0.00 0.00 4.52
3281 4036 2.945668 GTCTACTGATGGTTCATTGGCC 59.054 50.000 0.00 0.00 0.00 5.36
3283 4038 2.610438 ACTGATGGTTCATTGGCCTT 57.390 45.000 3.32 0.00 0.00 4.35
3288 4043 2.397044 TGGTTCATTGGCCTTTCCTT 57.603 45.000 3.32 0.00 35.26 3.36
3289 4044 1.969923 TGGTTCATTGGCCTTTCCTTG 59.030 47.619 3.32 0.00 35.26 3.61
3302 4057 4.203226 CCTTTCCTTGCCTCTATTTCCTC 58.797 47.826 0.00 0.00 0.00 3.71
3321 4087 1.894466 TCGACAACGAAGATACCCCAA 59.106 47.619 0.00 0.00 45.74 4.12
3326 4092 4.918588 ACAACGAAGATACCCCAAATTCT 58.081 39.130 0.00 0.00 0.00 2.40
3331 4097 6.718294 ACGAAGATACCCCAAATTCTAAACT 58.282 36.000 0.00 0.00 0.00 2.66
3340 4106 6.158598 CCCCAAATTCTAAACTGTCACATTG 58.841 40.000 0.00 0.00 0.00 2.82
3342 4108 6.215121 CCAAATTCTAAACTGTCACATTGCA 58.785 36.000 0.00 0.00 0.00 4.08
3343 4109 6.144402 CCAAATTCTAAACTGTCACATTGCAC 59.856 38.462 0.00 0.00 0.00 4.57
3344 4110 6.639632 AATTCTAAACTGTCACATTGCACT 57.360 33.333 0.00 0.00 0.00 4.40
3346 4112 5.673337 TCTAAACTGTCACATTGCACTTC 57.327 39.130 0.00 0.00 0.00 3.01
3347 4113 5.368145 TCTAAACTGTCACATTGCACTTCT 58.632 37.500 0.00 0.00 0.00 2.85
3348 4114 4.989279 AAACTGTCACATTGCACTTCTT 57.011 36.364 0.00 0.00 0.00 2.52
3349 4115 4.989279 AACTGTCACATTGCACTTCTTT 57.011 36.364 0.00 0.00 0.00 2.52
3385 4151 7.399245 ACTTTCTAGTGTAGCAAAACCAAAA 57.601 32.000 0.00 0.00 31.99 2.44
3543 4917 1.751351 TCCAAGAGCACCGACTGATAG 59.249 52.381 0.00 0.00 0.00 2.08
3662 5436 8.579006 CCAATAGCATGTGTATATTTGGATGTT 58.421 33.333 0.00 0.00 0.00 2.71
3702 5476 6.552008 ACAATGGTCTAAAAAGATTCCCTCA 58.448 36.000 0.00 0.00 0.00 3.86
3705 5479 9.359653 CAATGGTCTAAAAAGATTCCCTCATAT 57.640 33.333 0.00 0.00 0.00 1.78
3709 5483 9.274206 GGTCTAAAAAGATTCCCTCATATACAC 57.726 37.037 0.00 0.00 0.00 2.90
3724 5498 9.084164 CCTCATATACACATATAGTTTTACGGC 57.916 37.037 0.00 0.00 0.00 5.68
3841 5615 8.633075 AAAAATGGCAGAAATGTCATATTACG 57.367 30.769 0.00 0.00 32.30 3.18
3842 5616 5.947228 ATGGCAGAAATGTCATATTACGG 57.053 39.130 0.00 0.00 31.63 4.02
3864 5638 3.252974 ACATCACCTAAGTAGCAGCAC 57.747 47.619 0.00 0.00 0.00 4.40
3894 5668 7.739022 TCAACAAAATCATCAACAATATCGC 57.261 32.000 0.00 0.00 0.00 4.58
3895 5669 7.537715 TCAACAAAATCATCAACAATATCGCT 58.462 30.769 0.00 0.00 0.00 4.93
3896 5670 8.028354 TCAACAAAATCATCAACAATATCGCTT 58.972 29.630 0.00 0.00 0.00 4.68
3897 5671 8.649841 CAACAAAATCATCAACAATATCGCTTT 58.350 29.630 0.00 0.00 0.00 3.51
3898 5672 8.761575 ACAAAATCATCAACAATATCGCTTTT 57.238 26.923 0.00 0.00 0.00 2.27
3899 5673 8.863049 ACAAAATCATCAACAATATCGCTTTTC 58.137 29.630 0.00 0.00 0.00 2.29
3900 5674 7.992180 AAATCATCAACAATATCGCTTTTCC 57.008 32.000 0.00 0.00 0.00 3.13
3901 5675 5.499139 TCATCAACAATATCGCTTTTCCC 57.501 39.130 0.00 0.00 0.00 3.97
3902 5676 4.338118 TCATCAACAATATCGCTTTTCCCC 59.662 41.667 0.00 0.00 0.00 4.81
3903 5677 3.963129 TCAACAATATCGCTTTTCCCCT 58.037 40.909 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.080286 TCGACTACTTTGCCAGAAGC 57.920 50.000 0.00 0.00 44.14 3.86
99 100 6.590292 TCTTATTTCGACTACTTTGCCAGAAG 59.410 38.462 0.00 0.00 0.00 2.85
100 101 6.460781 TCTTATTTCGACTACTTTGCCAGAA 58.539 36.000 0.00 0.00 0.00 3.02
101 102 6.032956 TCTTATTTCGACTACTTTGCCAGA 57.967 37.500 0.00 0.00 0.00 3.86
102 103 6.183360 CCTTCTTATTTCGACTACTTTGCCAG 60.183 42.308 0.00 0.00 0.00 4.85
103 104 5.642063 CCTTCTTATTTCGACTACTTTGCCA 59.358 40.000 0.00 0.00 0.00 4.92
104 105 5.064834 CCCTTCTTATTTCGACTACTTTGCC 59.935 44.000 0.00 0.00 0.00 4.52
105 106 5.873164 TCCCTTCTTATTTCGACTACTTTGC 59.127 40.000 0.00 0.00 0.00 3.68
106 107 7.064728 CCTTCCCTTCTTATTTCGACTACTTTG 59.935 40.741 0.00 0.00 0.00 2.77
107 108 7.104290 CCTTCCCTTCTTATTTCGACTACTTT 58.896 38.462 0.00 0.00 0.00 2.66
108 109 6.351966 CCCTTCCCTTCTTATTTCGACTACTT 60.352 42.308 0.00 0.00 0.00 2.24
109 110 5.128991 CCCTTCCCTTCTTATTTCGACTACT 59.871 44.000 0.00 0.00 0.00 2.57
110 111 5.105023 ACCCTTCCCTTCTTATTTCGACTAC 60.105 44.000 0.00 0.00 0.00 2.73
111 112 5.028131 ACCCTTCCCTTCTTATTTCGACTA 58.972 41.667 0.00 0.00 0.00 2.59
112 113 3.844804 ACCCTTCCCTTCTTATTTCGACT 59.155 43.478 0.00 0.00 0.00 4.18
113 114 4.217836 ACCCTTCCCTTCTTATTTCGAC 57.782 45.455 0.00 0.00 0.00 4.20
114 115 6.377245 TTTACCCTTCCCTTCTTATTTCGA 57.623 37.500 0.00 0.00 0.00 3.71
115 116 6.431852 TGTTTTACCCTTCCCTTCTTATTTCG 59.568 38.462 0.00 0.00 0.00 3.46
116 117 7.770366 TGTTTTACCCTTCCCTTCTTATTTC 57.230 36.000 0.00 0.00 0.00 2.17
117 118 8.736097 AATGTTTTACCCTTCCCTTCTTATTT 57.264 30.769 0.00 0.00 0.00 1.40
118 119 8.736097 AAATGTTTTACCCTTCCCTTCTTATT 57.264 30.769 0.00 0.00 0.00 1.40
119 120 8.736097 AAAATGTTTTACCCTTCCCTTCTTAT 57.264 30.769 0.00 0.00 0.00 1.73
120 121 8.555896 AAAAATGTTTTACCCTTCCCTTCTTA 57.444 30.769 0.00 0.00 0.00 2.10
121 122 7.446106 AAAAATGTTTTACCCTTCCCTTCTT 57.554 32.000 0.00 0.00 0.00 2.52
183 184 2.978010 GTGCACGTTCCCTGTGGG 60.978 66.667 0.00 0.00 46.11 4.61
245 246 7.841282 TTACAGGTTGATGAATGGGTTTTTA 57.159 32.000 0.00 0.00 0.00 1.52
274 275 6.260377 TCGATTTTGATCGTACGAACTGTAT 58.740 36.000 23.56 12.95 43.85 2.29
495 504 1.739049 GAGATGGCTCGGGAGACTG 59.261 63.158 2.78 0.00 37.35 3.51
499 508 1.760086 ACTGGAGATGGCTCGGGAG 60.760 63.158 0.00 0.00 42.25 4.30
558 575 0.176680 AGGCTACCAAGATGAGCGTG 59.823 55.000 0.00 0.00 37.07 5.34
588 609 1.792006 AAGTGCCTAAAACTCGACCG 58.208 50.000 0.00 0.00 0.00 4.79
661 682 1.816835 AGATCGAGGCAACAGTACGAA 59.183 47.619 0.00 0.00 41.41 3.85
749 770 2.101415 CCATCTACCGACAGATTCAGCA 59.899 50.000 0.00 0.00 32.83 4.41
751 772 3.634448 AGTCCATCTACCGACAGATTCAG 59.366 47.826 0.00 0.00 32.83 3.02
777 798 7.036220 ACGAAATCAGTCTACGAAATTGAGAT 58.964 34.615 0.00 0.00 0.00 2.75
797 818 9.642327 TTTGCAATCACTAGTTATACTACGAAA 57.358 29.630 0.00 0.00 0.00 3.46
798 819 9.079833 GTTTGCAATCACTAGTTATACTACGAA 57.920 33.333 0.00 0.00 0.00 3.85
799 820 8.464404 AGTTTGCAATCACTAGTTATACTACGA 58.536 33.333 10.05 0.00 0.00 3.43
800 821 8.630278 AGTTTGCAATCACTAGTTATACTACG 57.370 34.615 10.05 0.00 0.00 3.51
831 852 6.151985 ACAAACTGATCGGGCTAGATCTATAG 59.848 42.308 18.79 12.85 45.35 1.31
880 902 1.819697 CGGACTGCAGGCCTAGATCTA 60.820 57.143 35.47 1.69 0.00 1.98
881 903 1.112315 CGGACTGCAGGCCTAGATCT 61.112 60.000 35.47 1.54 0.00 2.75
909 936 6.108687 TGAACTGGAACACTAATATGAGCAG 58.891 40.000 0.00 0.00 0.00 4.24
910 937 6.048732 TGAACTGGAACACTAATATGAGCA 57.951 37.500 0.00 0.00 0.00 4.26
911 938 6.512415 GCATGAACTGGAACACTAATATGAGC 60.512 42.308 0.00 0.00 0.00 4.26
912 939 6.017605 GGCATGAACTGGAACACTAATATGAG 60.018 42.308 0.00 0.00 0.00 2.90
913 940 5.822519 GGCATGAACTGGAACACTAATATGA 59.177 40.000 0.00 0.00 0.00 2.15
968 1000 5.345202 GCTCTGCACAATCAATCAGAAAAAG 59.655 40.000 0.00 0.00 35.44 2.27
1086 1120 2.877097 TGTCAATGCCTCCAAGCTTA 57.123 45.000 0.00 0.00 0.00 3.09
1473 1507 4.797275 GCCTTTCAGGGATGAAGTGTTTTG 60.797 45.833 0.00 0.00 35.37 2.44
1479 1513 1.075601 TGGCCTTTCAGGGATGAAGT 58.924 50.000 3.32 0.00 35.37 3.01
1505 1548 6.036083 CCACACAAGTAGCAACATCTATACAC 59.964 42.308 0.00 0.00 0.00 2.90
1581 1769 8.308931 AGCAATTGATTCAGAACATGTTTACAT 58.691 29.630 13.36 3.05 36.96 2.29
1582 1770 7.660112 AGCAATTGATTCAGAACATGTTTACA 58.340 30.769 13.36 4.68 0.00 2.41
1583 1771 9.793252 ATAGCAATTGATTCAGAACATGTTTAC 57.207 29.630 13.36 0.37 0.00 2.01
1585 1773 9.362539 GAATAGCAATTGATTCAGAACATGTTT 57.637 29.630 13.36 0.00 33.16 2.83
1586 1774 8.525316 TGAATAGCAATTGATTCAGAACATGTT 58.475 29.630 11.78 11.78 37.19 2.71
1587 1775 8.058667 TGAATAGCAATTGATTCAGAACATGT 57.941 30.769 10.34 0.00 37.19 3.21
1592 1780 9.687210 GCAATATGAATAGCAATTGATTCAGAA 57.313 29.630 20.72 14.56 43.40 3.02
1593 1781 9.074576 AGCAATATGAATAGCAATTGATTCAGA 57.925 29.630 20.72 18.17 43.40 3.27
1594 1782 9.129209 CAGCAATATGAATAGCAATTGATTCAG 57.871 33.333 20.72 12.28 43.40 3.02
1595 1783 7.597369 GCAGCAATATGAATAGCAATTGATTCA 59.403 33.333 19.27 19.27 44.07 2.57
1596 1784 7.597369 TGCAGCAATATGAATAGCAATTGATTC 59.403 33.333 10.34 10.89 32.00 2.52
1597 1785 7.384115 GTGCAGCAATATGAATAGCAATTGATT 59.616 33.333 10.34 0.29 32.00 2.57
1598 1786 6.866770 GTGCAGCAATATGAATAGCAATTGAT 59.133 34.615 10.34 5.28 32.00 2.57
1599 1787 6.183360 TGTGCAGCAATATGAATAGCAATTGA 60.183 34.615 10.34 0.00 32.00 2.57
1600 1788 5.980715 TGTGCAGCAATATGAATAGCAATTG 59.019 36.000 0.00 0.00 32.75 2.32
1601 1789 5.981315 GTGTGCAGCAATATGAATAGCAATT 59.019 36.000 0.00 0.00 31.78 2.32
1602 1790 5.068067 TGTGTGCAGCAATATGAATAGCAAT 59.932 36.000 0.00 0.00 31.78 3.56
1603 1791 4.398673 TGTGTGCAGCAATATGAATAGCAA 59.601 37.500 0.00 0.00 31.78 3.91
1604 1792 3.946558 TGTGTGCAGCAATATGAATAGCA 59.053 39.130 0.00 0.00 0.00 3.49
1605 1793 4.556942 TGTGTGCAGCAATATGAATAGC 57.443 40.909 0.00 0.00 0.00 2.97
1606 1794 9.687210 AAAATATGTGTGCAGCAATATGAATAG 57.313 29.630 0.00 0.00 0.00 1.73
1607 1795 9.465985 CAAAATATGTGTGCAGCAATATGAATA 57.534 29.630 0.00 0.00 0.00 1.75
1608 1796 8.198778 TCAAAATATGTGTGCAGCAATATGAAT 58.801 29.630 0.00 0.00 0.00 2.57
1806 2436 0.897621 GGAAAAACTGCAGGGATGGG 59.102 55.000 19.93 0.00 0.00 4.00
1876 2615 2.105006 ACTAGCACAGCATGACCAAG 57.895 50.000 0.00 0.00 39.69 3.61
1882 2621 4.155462 AGAACAATCAACTAGCACAGCATG 59.845 41.667 0.00 0.00 46.00 4.06
1883 2622 4.155462 CAGAACAATCAACTAGCACAGCAT 59.845 41.667 0.00 0.00 0.00 3.79
1941 2680 5.814764 TTACGAACAGGTAACAGCAAAAA 57.185 34.783 0.00 0.00 41.41 1.94
1953 2692 7.262772 TGGAACTGTAAGATATTACGAACAGG 58.737 38.462 5.81 0.00 38.87 4.00
1961 2700 7.933577 CAGCCAAGATGGAACTGTAAGATATTA 59.066 37.037 0.00 0.00 40.96 0.98
1983 2722 7.982354 AGTAGAACAGTTAAATGATACTCAGCC 59.018 37.037 10.35 0.00 0.00 4.85
2017 2768 0.537188 AGTGGTGGCGTCCATCTAAG 59.463 55.000 9.95 0.00 39.81 2.18
2072 2823 3.028130 CAGGTAGGAAGAGACCTCCTTC 58.972 54.545 0.00 0.00 44.54 3.46
2780 3531 0.040067 CAGCAAAACGACCAAGAGGC 60.040 55.000 0.00 0.00 39.06 4.70
3040 3794 2.869801 TGTAAAAGGCACAAGACAGACG 59.130 45.455 0.00 0.00 0.00 4.18
3065 3819 3.259876 ACCGAAGCTTACATTAGGACACA 59.740 43.478 0.00 0.00 0.00 3.72
3066 3820 3.617263 CACCGAAGCTTACATTAGGACAC 59.383 47.826 0.00 0.00 0.00 3.67
3155 3910 8.519492 TTTCAAAAATGCACTAGATAAAGCAC 57.481 30.769 0.00 0.00 40.14 4.40
3234 3989 6.873605 AGGGAATAAATTGTTAAGCTTGCAAC 59.126 34.615 9.86 7.21 0.00 4.17
3237 3992 6.398095 ACAGGGAATAAATTGTTAAGCTTGC 58.602 36.000 9.86 2.36 0.00 4.01
3242 3997 9.667107 TCAGTAGACAGGGAATAAATTGTTAAG 57.333 33.333 0.00 0.00 0.00 1.85
3244 3999 9.613428 CATCAGTAGACAGGGAATAAATTGTTA 57.387 33.333 0.00 0.00 0.00 2.41
3248 4003 7.213178 ACCATCAGTAGACAGGGAATAAATT 57.787 36.000 0.00 0.00 0.00 1.82
3259 4014 3.609853 GCCAATGAACCATCAGTAGACA 58.390 45.455 0.00 0.00 39.39 3.41
3260 4015 2.945668 GGCCAATGAACCATCAGTAGAC 59.054 50.000 0.00 0.00 39.39 2.59
3261 4016 2.846206 AGGCCAATGAACCATCAGTAGA 59.154 45.455 5.01 0.00 39.39 2.59
3280 4035 4.203226 GAGGAAATAGAGGCAAGGAAAGG 58.797 47.826 0.00 0.00 0.00 3.11
3281 4036 3.873952 CGAGGAAATAGAGGCAAGGAAAG 59.126 47.826 0.00 0.00 0.00 2.62
3283 4038 3.104512 TCGAGGAAATAGAGGCAAGGAA 58.895 45.455 0.00 0.00 0.00 3.36
3288 4043 2.416836 CGTTGTCGAGGAAATAGAGGCA 60.417 50.000 0.00 0.00 39.71 4.75
3289 4044 2.159282 TCGTTGTCGAGGAAATAGAGGC 60.159 50.000 0.00 0.00 41.35 4.70
3302 4057 2.373540 TTGGGGTATCTTCGTTGTCG 57.626 50.000 0.00 0.00 38.55 4.35
3317 4083 5.634859 GCAATGTGACAGTTTAGAATTTGGG 59.365 40.000 0.00 0.00 0.00 4.12
3321 4087 6.639632 AGTGCAATGTGACAGTTTAGAATT 57.360 33.333 0.00 0.00 0.00 2.17
3326 4092 6.449635 AAAGAAGTGCAATGTGACAGTTTA 57.550 33.333 0.00 0.00 29.71 2.01
3331 4097 5.581126 AGAAAAAGAAGTGCAATGTGACA 57.419 34.783 0.00 0.00 0.00 3.58
3365 4131 8.001881 TGAAATTTTGGTTTTGCTACACTAGA 57.998 30.769 0.00 0.00 0.00 2.43
3407 4173 3.114809 TGCTGCACGTCATTTCTTTTTG 58.885 40.909 0.00 0.00 0.00 2.44
3408 4174 3.435105 TGCTGCACGTCATTTCTTTTT 57.565 38.095 0.00 0.00 0.00 1.94
3543 4917 2.156343 AGTGACAAAGAGCGGAGTTC 57.844 50.000 0.00 0.00 38.31 3.01
3625 5399 5.163269 ACACATGCTATTGGAGATGCTCTTA 60.163 40.000 0.00 0.00 0.00 2.10
3626 5400 4.135306 CACATGCTATTGGAGATGCTCTT 58.865 43.478 0.00 0.00 0.00 2.85
3627 5401 3.136077 ACACATGCTATTGGAGATGCTCT 59.864 43.478 0.00 0.00 0.00 4.09
3697 5471 9.582431 CCGTAAAACTATATGTGTATATGAGGG 57.418 37.037 0.00 0.00 31.97 4.30
3705 5479 7.982919 ACATTCTGCCGTAAAACTATATGTGTA 59.017 33.333 0.00 0.00 0.00 2.90
3709 5483 7.715265 AGACATTCTGCCGTAAAACTATATG 57.285 36.000 0.00 0.00 0.00 1.78
3712 5486 9.998106 AATATAGACATTCTGCCGTAAAACTAT 57.002 29.630 0.00 0.00 0.00 2.12
3713 5487 9.472361 GAATATAGACATTCTGCCGTAAAACTA 57.528 33.333 0.00 0.00 33.05 2.24
3820 5594 5.376625 ACCGTAATATGACATTTCTGCCAT 58.623 37.500 0.00 0.00 29.99 4.40
3842 5616 4.113354 GTGCTGCTACTTAGGTGATGTAC 58.887 47.826 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.