Multiple sequence alignment - TraesCS2B01G545500

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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 TraesCS2B01G545500 chr2B 100.000 2636 0 0 1 2636 742453459 742456094 0.000000e+00 4868
1 TraesCS2B01G545500 chr2B 97.000 100 2 1 1 100 723031852 723031950 1.620000e-37 167
2 TraesCS2B01G545500 chr2B 88.235 102 10 2 2002 2101 521980523 521980422 1.280000e-23 121
3 TraesCS2B01G545500 chr2B 88.119 101 11 1 2002 2101 471305217 471305317 4.610000e-23 119
4 TraesCS2B01G545500 chr2D 91.541 1927 94 32 115 1995 608744841 608746744 0.000000e+00 2591
5 TraesCS2B01G545500 chr2D 92.457 464 18 6 2182 2636 608747971 608748426 0.000000e+00 647
6 TraesCS2B01G545500 chr2A 93.148 1080 47 10 769 1827 740346440 740347513 0.000000e+00 1559
7 TraesCS2B01G545500 chr2A 88.809 554 35 14 2095 2636 740347842 740348380 0.000000e+00 654
8 TraesCS2B01G545500 chr2A 85.366 656 26 25 94 724 740345829 740346439 1.340000e-172 616
9 TraesCS2B01G545500 chr2A 94.118 170 10 0 1826 1995 740347620 740347789 2.600000e-65 259
10 TraesCS2B01G545500 chr2A 89.888 89 5 2 1910 1995 740347768 740347855 7.710000e-21 111
11 TraesCS2B01G545500 chr3D 97.959 98 2 0 1 98 614964825 614964922 1.250000e-38 171
12 TraesCS2B01G545500 chr7A 97.917 96 2 0 2 97 681608182 681608087 1.620000e-37 167
13 TraesCS2B01G545500 chr7A 96.939 98 3 0 1 98 93486597 93486694 5.840000e-37 165
14 TraesCS2B01G545500 chr6D 97.895 95 2 0 1 95 462215759 462215665 5.840000e-37 165
15 TraesCS2B01G545500 chr5A 94.444 108 4 2 1 108 457781702 457781597 5.840000e-37 165
16 TraesCS2B01G545500 chr7D 96.907 97 3 0 1 97 426172101 426172197 2.100000e-36 163
17 TraesCS2B01G545500 chr7D 96.000 100 3 1 1 100 80466433 80466335 7.550000e-36 161
18 TraesCS2B01G545500 chr7D 82.609 115 16 4 2002 2114 255928590 255928702 6.000000e-17 99
19 TraesCS2B01G545500 chr1D 96.875 96 3 0 1 96 426025068 426024973 7.550000e-36 161
20 TraesCS2B01G545500 chr5B 89.109 101 10 1 2002 2101 11084514 11084614 9.910000e-25 124
21 TraesCS2B01G545500 chr1A 89.216 102 8 3 2002 2101 580668176 580668276 9.910000e-25 124
22 TraesCS2B01G545500 chr3B 87.000 100 11 2 2002 2099 706913994 706913895 7.710000e-21 111
23 TraesCS2B01G545500 chr3B 86.408 103 8 6 2002 2101 727276308 727276209 9.980000e-20 108
24 TraesCS2B01G545500 chr6B 86.139 101 11 3 2002 2101 149414831 149414733 3.590000e-19 106
25 TraesCS2B01G545500 chr6B 85.859 99 12 2 2002 2099 33568011 33567914 1.290000e-18 104


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 TraesCS2B01G545500 chr2B 742453459 742456094 2635 False 4868.0 4868 100.0000 1 2636 1 chr2B.!!$F3 2635
1 TraesCS2B01G545500 chr2D 608744841 608748426 3585 False 1619.0 2591 91.9990 115 2636 2 chr2D.!!$F1 2521
2 TraesCS2B01G545500 chr2A 740345829 740348380 2551 False 639.8 1559 90.2658 94 2636 5 chr2A.!!$F1 2542

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
124 125 0.327259 CAGCCATGGATGGATCCGAT 59.673 55.0 22.65 1.61 44.64 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2193 0.031616 AGGCCGAGATCTCCTCCTTT 60.032 55.0 19.47 4.8 38.71 3.11 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
70 71 6.503616 GACTTCAGTCAACTCTAATATGCG 57.496 41.667 1.86 0.00 44.18 4.73
71 72 5.352284 ACTTCAGTCAACTCTAATATGCGG 58.648 41.667 0.00 0.00 0.00 5.69
72 73 5.127194 ACTTCAGTCAACTCTAATATGCGGA 59.873 40.000 0.00 0.00 0.00 5.54
73 74 5.188327 TCAGTCAACTCTAATATGCGGAG 57.812 43.478 0.00 0.00 0.00 4.63
74 75 4.645136 TCAGTCAACTCTAATATGCGGAGT 59.355 41.667 0.00 0.00 41.37 3.85
75 76 5.826208 TCAGTCAACTCTAATATGCGGAGTA 59.174 40.000 6.10 0.00 39.09 2.59
76 77 6.320418 TCAGTCAACTCTAATATGCGGAGTAA 59.680 38.462 6.10 0.00 39.09 2.24
77 78 6.978659 CAGTCAACTCTAATATGCGGAGTAAA 59.021 38.462 6.10 0.00 39.09 2.01
78 79 7.653713 CAGTCAACTCTAATATGCGGAGTAAAT 59.346 37.037 6.10 0.00 39.09 1.40
79 80 8.857098 AGTCAACTCTAATATGCGGAGTAAATA 58.143 33.333 6.10 0.00 39.09 1.40
80 81 9.472361 GTCAACTCTAATATGCGGAGTAAATAA 57.528 33.333 6.10 0.00 39.09 1.40
85 86 9.793245 CTCTAATATGCGGAGTAAATAAAAACG 57.207 33.333 0.00 0.00 0.00 3.60
86 87 8.767085 TCTAATATGCGGAGTAAATAAAAACGG 58.233 33.333 0.00 0.00 0.00 4.44
87 88 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
88 89 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
89 90 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
90 91 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
91 92 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
92 93 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
93 94 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
94 95 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
95 96 6.536582 GGAGTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
96 97 7.008021 AGTAAATAAAAACGGAGGGAGTACA 57.992 36.000 0.00 0.00 0.00 2.90
97 98 7.627311 AGTAAATAAAAACGGAGGGAGTACAT 58.373 34.615 0.00 0.00 0.00 2.29
98 99 8.761689 AGTAAATAAAAACGGAGGGAGTACATA 58.238 33.333 0.00 0.00 0.00 2.29
99 100 9.551734 GTAAATAAAAACGGAGGGAGTACATAT 57.448 33.333 0.00 0.00 0.00 1.78
100 101 8.446599 AAATAAAAACGGAGGGAGTACATATG 57.553 34.615 0.00 0.00 0.00 1.78
101 102 3.470645 AAACGGAGGGAGTACATATGC 57.529 47.619 1.58 0.00 0.00 3.14
102 103 2.383442 ACGGAGGGAGTACATATGCT 57.617 50.000 1.58 0.00 0.00 3.79
123 124 1.756665 CAGCCATGGATGGATCCGA 59.243 57.895 22.65 0.00 44.64 4.55
124 125 0.327259 CAGCCATGGATGGATCCGAT 59.673 55.000 22.65 1.61 44.64 4.18
238 247 2.187424 CTCTGGCTCTGGCTCAGC 59.813 66.667 0.00 0.00 36.99 4.26
431 444 1.860950 CGCTGATGCACCATGTACTAC 59.139 52.381 0.00 0.00 39.64 2.73
478 491 4.039609 TGACTCATGAGACAAGAAGAAGCA 59.960 41.667 29.27 0.20 30.73 3.91
580 594 0.462581 CTATGTGCACGCCTCATGGT 60.463 55.000 13.13 0.00 35.27 3.55
637 651 1.284491 TGCATGTACATCCATGTGGGT 59.716 47.619 5.07 0.00 43.33 4.51
638 652 1.949525 GCATGTACATCCATGTGGGTC 59.050 52.381 5.07 0.00 43.33 4.46
679 708 2.426425 GCAGTCGTCGTCGTCGTT 60.426 61.111 11.41 0.00 38.33 3.85
704 739 6.014925 TGTGGTGACATGTTACATGTACTACT 60.015 38.462 29.37 15.06 46.14 2.57
705 740 7.177041 TGTGGTGACATGTTACATGTACTACTA 59.823 37.037 29.37 23.64 46.14 1.82
724 762 2.086510 GTACGTACGTACTCGGCCA 58.913 57.895 38.40 14.31 45.30 5.36
725 763 0.657840 GTACGTACGTACTCGGCCAT 59.342 55.000 38.40 11.44 45.30 4.40
726 764 0.657312 TACGTACGTACTCGGCCATG 59.343 55.000 23.60 7.67 41.85 3.66
727 765 1.298863 CGTACGTACTCGGCCATGG 60.299 63.158 22.55 7.63 41.85 3.66
753 791 1.061131 CACGCACGGCAATAAAGAGAG 59.939 52.381 0.00 0.00 0.00 3.20
784 822 1.338200 GGAGCTCGCAGAAAGAAAGGA 60.338 52.381 7.83 0.00 34.09 3.36
962 1013 1.090052 CCGCCCGCTTCTTCTTTAGG 61.090 60.000 0.00 0.00 0.00 2.69
995 1046 1.182667 TAGCTAGCTTGCTCGGTTGA 58.817 50.000 25.94 4.90 42.97 3.18
1371 1422 2.672651 CACCACGGGCTCATGCAA 60.673 61.111 0.00 0.00 41.91 4.08
1383 1434 0.809636 TCATGCAATACTCGCCGGTG 60.810 55.000 9.28 9.28 0.00 4.94
1403 1454 2.717044 CGACCATGGACTACGCCCA 61.717 63.158 21.47 0.00 38.19 5.36
1405 1456 1.895020 GACCATGGACTACGCCCACA 61.895 60.000 21.47 0.00 36.36 4.17
1417 1468 1.383803 GCCCACATCTCCTCCTCCT 60.384 63.158 0.00 0.00 0.00 3.69
1425 1476 0.914902 TCTCCTCCTCCTCCTCGTCA 60.915 60.000 0.00 0.00 0.00 4.35
1474 1525 2.270850 GCGGGGTGGTGATAAGCA 59.729 61.111 0.00 0.00 0.00 3.91
1533 1584 0.545309 AGGCCTTCTACCTGCACTCA 60.545 55.000 0.00 0.00 35.72 3.41
1653 1709 5.656480 GCCTAGCTCTAGTAATTAGCCATC 58.344 45.833 0.00 0.00 36.92 3.51
1677 1741 3.307480 CCTCTAGGCTCTAGCTAGACTCC 60.307 56.522 19.72 20.85 41.70 3.85
1745 1809 3.507411 TCTCTGTACCACCTAGCTGTTT 58.493 45.455 0.00 0.00 0.00 2.83
1746 1810 3.510360 TCTCTGTACCACCTAGCTGTTTC 59.490 47.826 0.00 0.00 0.00 2.78
1747 1811 3.236047 TCTGTACCACCTAGCTGTTTCA 58.764 45.455 0.00 0.00 0.00 2.69
1748 1812 3.006537 TCTGTACCACCTAGCTGTTTCAC 59.993 47.826 0.00 0.00 0.00 3.18
1749 1813 2.701423 TGTACCACCTAGCTGTTTCACA 59.299 45.455 0.00 0.00 0.00 3.58
1838 2014 7.765695 TGCTTTCTCTCTACATTTCCATTTT 57.234 32.000 0.00 0.00 0.00 1.82
1839 2015 7.820648 TGCTTTCTCTCTACATTTCCATTTTC 58.179 34.615 0.00 0.00 0.00 2.29
1841 2017 7.629437 GCTTTCTCTCTACATTTCCATTTTCCC 60.629 40.741 0.00 0.00 0.00 3.97
1858 2034 9.312904 CCATTTTCCCACTAATATTACATCCAT 57.687 33.333 0.00 0.00 0.00 3.41
1937 2119 2.200373 AAACCTGCGGTCAAAGCTAT 57.800 45.000 0.69 0.00 33.12 2.97
1995 2177 6.650807 TGCTAAACATAGAAACTGAGGTCAAG 59.349 38.462 0.00 0.00 0.00 3.02
1998 2180 4.899502 ACATAGAAACTGAGGTCAAGGTG 58.100 43.478 0.00 0.00 0.00 4.00
1999 2181 2.262423 AGAAACTGAGGTCAAGGTGC 57.738 50.000 0.00 0.00 0.00 5.01
2002 2184 0.846693 AACTGAGGTCAAGGTGCCTT 59.153 50.000 0.00 0.00 34.81 4.35
2003 2185 0.846693 ACTGAGGTCAAGGTGCCTTT 59.153 50.000 0.00 0.00 34.81 3.11
2026 2208 3.784701 TTCGAAAAGGAGGAGATCTCG 57.215 47.619 16.46 2.87 43.34 4.04
2029 2211 0.833949 AAAAGGAGGAGATCTCGGCC 59.166 55.000 19.53 19.53 43.34 6.13
2031 2213 0.469144 AAGGAGGAGATCTCGGCCTC 60.469 60.000 26.18 21.87 45.88 4.70
2032 2214 1.152830 GGAGGAGATCTCGGCCTCT 59.847 63.158 22.02 12.10 45.87 3.69
2033 2215 1.178534 GGAGGAGATCTCGGCCTCTG 61.179 65.000 22.02 0.00 45.87 3.35
2034 2216 1.805428 GAGGAGATCTCGGCCTCTGC 61.805 65.000 17.75 1.52 43.79 4.26
2035 2217 2.130426 GGAGATCTCGGCCTCTGCA 61.130 63.158 16.46 0.00 40.13 4.41
2037 2219 0.038343 GAGATCTCGGCCTCTGCATC 60.038 60.000 7.04 0.00 40.13 3.91
2038 2220 0.758310 AGATCTCGGCCTCTGCATCA 60.758 55.000 0.00 0.00 40.13 3.07
2039 2221 0.319727 GATCTCGGCCTCTGCATCAG 60.320 60.000 0.00 0.00 40.13 2.90
2053 2235 1.066136 CATCAGAGCGATGCATACGG 58.934 55.000 16.56 4.54 44.95 4.02
2054 2236 0.676184 ATCAGAGCGATGCATACGGT 59.324 50.000 18.50 18.50 43.87 4.83
2057 2239 4.420143 AGCGATGCATACGGTCAC 57.580 55.556 14.55 2.95 36.82 3.67
2094 2276 9.965824 AAACAAATAAGTTCAATACAGGTCTTG 57.034 29.630 0.00 0.00 0.00 3.02
2095 2277 8.918202 ACAAATAAGTTCAATACAGGTCTTGA 57.082 30.769 0.00 0.00 0.00 3.02
2096 2278 9.349713 ACAAATAAGTTCAATACAGGTCTTGAA 57.650 29.630 8.39 8.39 38.64 2.69
2097 2279 9.831737 CAAATAAGTTCAATACAGGTCTTGAAG 57.168 33.333 11.71 0.00 40.86 3.02
2098 2280 9.574516 AAATAAGTTCAATACAGGTCTTGAAGT 57.425 29.630 11.71 12.01 43.44 3.01
2112 2294 5.221461 GGTCTTGAAGTCTGAGGTCAAAGTA 60.221 44.000 0.00 0.00 31.21 2.24
2113 2295 6.281405 GTCTTGAAGTCTGAGGTCAAAGTAA 58.719 40.000 0.00 0.00 31.21 2.24
2121 2303 7.884257 AGTCTGAGGTCAAAGTAACTACTAAC 58.116 38.462 0.00 0.00 34.99 2.34
2141 2323 3.551846 ACGGCCTTTTGAAAGAAGAAGA 58.448 40.909 0.00 0.00 38.28 2.87
2177 3439 7.254932 CCTCTAAGAGAAGTCAACAAACTTTGG 60.255 40.741 6.47 0.00 39.55 3.28
2179 3441 4.855340 AGAGAAGTCAACAAACTTTGGGA 58.145 39.130 6.47 0.98 39.55 4.37
2380 3656 4.085055 CGTCAATTGGTTATTCGATCTCCG 60.085 45.833 5.42 0.00 40.25 4.63
2384 3660 2.307768 TGGTTATTCGATCTCCGCTCT 58.692 47.619 0.00 0.00 38.37 4.09
2387 3668 2.423926 TATTCGATCTCCGCTCTTGC 57.576 50.000 0.00 0.00 38.37 4.01
2422 3703 3.201708 AGAGGGCAGCAAACATAGATCTT 59.798 43.478 0.00 0.00 0.00 2.40
2427 3708 3.790123 GCAGCAAACATAGATCTTTCCGC 60.790 47.826 0.00 0.00 0.00 5.54
2469 3759 3.059188 GTGGAATATATTTCGTGGGTGCG 60.059 47.826 0.00 0.00 0.00 5.34
2470 3760 2.095919 GGAATATATTTCGTGGGTGCGC 60.096 50.000 0.00 0.00 0.00 6.09
2551 3841 4.260743 CGCATGTTGTTATGAATCGGATGT 60.261 41.667 0.00 0.00 0.00 3.06
2602 3892 7.960738 CGTCAAACGTAGTATTCATTTGGAATT 59.039 33.333 0.00 0.00 45.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.460419 CCGCATATTAGAGTTGACTGAAGTC 59.540 44.000 3.41 3.41 44.97 3.01
48 49 5.127194 TCCGCATATTAGAGTTGACTGAAGT 59.873 40.000 0.00 0.00 0.00 3.01
49 50 5.592054 TCCGCATATTAGAGTTGACTGAAG 58.408 41.667 0.00 0.00 0.00 3.02
50 51 5.127194 ACTCCGCATATTAGAGTTGACTGAA 59.873 40.000 0.00 0.00 37.60 3.02
51 52 4.645136 ACTCCGCATATTAGAGTTGACTGA 59.355 41.667 0.00 0.00 37.60 3.41
52 53 4.938080 ACTCCGCATATTAGAGTTGACTG 58.062 43.478 0.00 0.00 37.60 3.51
53 54 6.710597 TTACTCCGCATATTAGAGTTGACT 57.289 37.500 4.78 0.00 41.09 3.41
54 55 7.948278 ATTTACTCCGCATATTAGAGTTGAC 57.052 36.000 4.78 0.00 41.09 3.18
59 60 9.793245 CGTTTTTATTTACTCCGCATATTAGAG 57.207 33.333 0.00 0.00 0.00 2.43
60 61 8.767085 CCGTTTTTATTTACTCCGCATATTAGA 58.233 33.333 0.00 0.00 0.00 2.10
61 62 8.767085 TCCGTTTTTATTTACTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
62 63 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
63 64 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
64 65 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
65 66 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
66 67 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
67 68 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
68 69 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
69 70 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
70 71 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
71 72 7.099120 TGTACTCCCTCCGTTTTTATTTACTC 58.901 38.462 0.00 0.00 0.00 2.59
72 73 7.008021 TGTACTCCCTCCGTTTTTATTTACT 57.992 36.000 0.00 0.00 0.00 2.24
73 74 7.854557 ATGTACTCCCTCCGTTTTTATTTAC 57.145 36.000 0.00 0.00 0.00 2.01
74 75 9.550406 CATATGTACTCCCTCCGTTTTTATTTA 57.450 33.333 0.00 0.00 0.00 1.40
75 76 7.012989 GCATATGTACTCCCTCCGTTTTTATTT 59.987 37.037 4.29 0.00 0.00 1.40
76 77 6.485648 GCATATGTACTCCCTCCGTTTTTATT 59.514 38.462 4.29 0.00 0.00 1.40
77 78 5.995897 GCATATGTACTCCCTCCGTTTTTAT 59.004 40.000 4.29 0.00 0.00 1.40
78 79 5.129815 AGCATATGTACTCCCTCCGTTTTTA 59.870 40.000 4.29 0.00 0.00 1.52
79 80 4.080526 AGCATATGTACTCCCTCCGTTTTT 60.081 41.667 4.29 0.00 0.00 1.94
80 81 3.454812 AGCATATGTACTCCCTCCGTTTT 59.545 43.478 4.29 0.00 0.00 2.43
81 82 3.039011 AGCATATGTACTCCCTCCGTTT 58.961 45.455 4.29 0.00 0.00 3.60
82 83 2.365617 CAGCATATGTACTCCCTCCGTT 59.634 50.000 4.29 0.00 0.00 4.44
83 84 1.964223 CAGCATATGTACTCCCTCCGT 59.036 52.381 4.29 0.00 0.00 4.69
84 85 1.273606 CCAGCATATGTACTCCCTCCG 59.726 57.143 4.29 0.00 0.00 4.63
85 86 1.002544 GCCAGCATATGTACTCCCTCC 59.997 57.143 4.29 0.00 0.00 4.30
86 87 1.694150 TGCCAGCATATGTACTCCCTC 59.306 52.381 4.29 0.00 0.00 4.30
87 88 1.696336 CTGCCAGCATATGTACTCCCT 59.304 52.381 4.29 0.00 0.00 4.20
88 89 1.879796 GCTGCCAGCATATGTACTCCC 60.880 57.143 12.82 0.00 41.89 4.30
89 90 1.517242 GCTGCCAGCATATGTACTCC 58.483 55.000 12.82 0.00 41.89 3.85
90 91 1.202687 TGGCTGCCAGCATATGTACTC 60.203 52.381 19.30 0.00 44.75 2.59
91 92 0.839277 TGGCTGCCAGCATATGTACT 59.161 50.000 19.30 0.00 44.75 2.73
92 93 1.538512 CATGGCTGCCAGCATATGTAC 59.461 52.381 27.20 0.00 44.75 2.90
93 94 1.546099 CCATGGCTGCCAGCATATGTA 60.546 52.381 27.20 0.00 44.75 2.29
94 95 0.826256 CCATGGCTGCCAGCATATGT 60.826 55.000 27.20 5.08 44.75 2.29
95 96 0.538746 TCCATGGCTGCCAGCATATG 60.539 55.000 27.20 20.03 44.75 1.78
96 97 0.408309 ATCCATGGCTGCCAGCATAT 59.592 50.000 27.20 14.11 44.75 1.78
97 98 0.538746 CATCCATGGCTGCCAGCATA 60.539 55.000 27.20 12.41 44.75 3.14
98 99 1.832608 CATCCATGGCTGCCAGCAT 60.833 57.895 27.20 14.84 44.75 3.79
99 100 2.441348 CATCCATGGCTGCCAGCA 60.441 61.111 27.20 13.15 44.75 4.41
100 101 3.224324 CCATCCATGGCTGCCAGC 61.224 66.667 27.20 8.55 41.75 4.85
143 144 1.467713 GCACTGTACCTGCTCGTACTC 60.468 57.143 12.95 0.67 39.51 2.59
185 193 2.973316 CTTAACCGTTGCGCCCACC 61.973 63.158 4.18 0.00 0.00 4.61
238 247 0.514691 GGTACCGTATACTCCTCGCG 59.485 60.000 0.00 0.00 0.00 5.87
339 352 4.767255 GTGTCCGCCTGGCTCTGG 62.767 72.222 17.92 10.97 34.14 3.86
340 353 4.767255 GGTGTCCGCCTGGCTCTG 62.767 72.222 17.92 5.25 34.14 3.35
452 465 5.990120 TCTTCTTGTCTCATGAGTCATGA 57.010 39.130 29.39 29.39 46.84 3.07
453 466 5.063691 GCTTCTTCTTGTCTCATGAGTCATG 59.936 44.000 24.60 24.60 42.60 3.07
454 467 5.177326 GCTTCTTCTTGTCTCATGAGTCAT 58.823 41.667 20.86 0.00 0.00 3.06
455 468 4.039609 TGCTTCTTCTTGTCTCATGAGTCA 59.960 41.667 21.92 19.46 0.00 3.41
456 469 4.564041 TGCTTCTTCTTGTCTCATGAGTC 58.436 43.478 21.92 17.02 0.00 3.36
457 470 4.613925 TGCTTCTTCTTGTCTCATGAGT 57.386 40.909 21.92 0.00 0.00 3.41
478 491 0.112995 ACATGGAGCATGGTGGTGTT 59.887 50.000 0.00 0.00 45.16 3.32
550 564 2.671070 CGTGCACATAGGCGCATAGATA 60.671 50.000 18.64 0.00 44.30 1.98
580 594 1.134098 GGATCCATCTTTTCGCCTGGA 60.134 52.381 6.95 0.00 41.76 3.86
637 651 0.535780 GCTTGCCATCCATCCATCGA 60.536 55.000 0.00 0.00 0.00 3.59
638 652 1.521450 GGCTTGCCATCCATCCATCG 61.521 60.000 6.79 0.00 0.00 3.84
679 708 5.222079 AGTACATGTAACATGTCACCACA 57.778 39.130 7.25 1.83 36.78 4.17
724 762 3.126879 CCGTGCGTGCATGTCCAT 61.127 61.111 12.65 0.00 0.00 3.41
727 765 1.976478 TATTGCCGTGCGTGCATGTC 61.976 55.000 12.65 0.61 38.76 3.06
753 791 2.335712 CGAGCTCCCAACCTTTGCC 61.336 63.158 8.47 0.00 0.00 4.52
784 822 2.230750 CGTAGGACGAGGGTCTTTTCTT 59.769 50.000 0.00 0.00 46.05 2.52
828 875 4.079253 GGACAGAAAGGGTGCATTAAAGA 58.921 43.478 0.00 0.00 0.00 2.52
995 1046 3.197614 ACGACGACGGCATGAGAT 58.802 55.556 12.58 0.00 44.46 2.75
1078 1129 2.668212 CGTGGTGTTGGCGTCCAT 60.668 61.111 0.00 0.00 31.53 3.41
1245 1296 2.725312 CCGCCTCTCCTGCAGCTTA 61.725 63.158 8.66 0.00 0.00 3.09
1371 1422 2.768492 GGTCGACACCGGCGAGTAT 61.768 63.158 18.91 0.00 42.18 2.12
1383 1434 1.226888 GGCGTAGTCCATGGTCGAC 60.227 63.158 12.58 11.81 0.00 4.20
1403 1454 0.184933 CGAGGAGGAGGAGGAGATGT 59.815 60.000 0.00 0.00 0.00 3.06
1405 1456 0.476771 GACGAGGAGGAGGAGGAGAT 59.523 60.000 0.00 0.00 0.00 2.75
1417 1468 4.753662 CGGGGAGGGTGACGAGGA 62.754 72.222 0.00 0.00 0.00 3.71
1474 1525 1.156322 TCCCTCTCCACCTCCTCCTT 61.156 60.000 0.00 0.00 0.00 3.36
1533 1584 4.115199 GGGGCGGCTCTTGGTGAT 62.115 66.667 9.56 0.00 0.00 3.06
1653 1709 3.072476 AGTCTAGCTAGAGCCTAGAGGTG 59.928 52.174 23.87 0.00 43.38 4.00
1745 1809 4.262592 CCGGTCATGGATCATCTAATGTGA 60.263 45.833 0.00 0.00 0.00 3.58
1746 1810 3.999001 CCGGTCATGGATCATCTAATGTG 59.001 47.826 0.00 0.00 0.00 3.21
1747 1811 3.903714 TCCGGTCATGGATCATCTAATGT 59.096 43.478 0.00 0.00 31.53 2.71
1748 1812 4.248859 GTCCGGTCATGGATCATCTAATG 58.751 47.826 0.00 0.00 40.91 1.90
1749 1813 3.261897 GGTCCGGTCATGGATCATCTAAT 59.738 47.826 0.00 0.00 40.91 1.73
1838 2014 7.158697 CACGAATGGATGTAATATTAGTGGGA 58.841 38.462 0.00 0.00 35.31 4.37
1839 2015 6.128282 GCACGAATGGATGTAATATTAGTGGG 60.128 42.308 0.00 0.00 37.67 4.61
1841 2017 7.420184 TGCACGAATGGATGTAATATTAGTG 57.580 36.000 0.00 0.00 39.12 2.74
1858 2034 7.648142 AGAAATGAAATTAAGACTTGCACGAA 58.352 30.769 0.00 0.00 33.67 3.85
1937 2119 5.694006 CGTGGAAATGAAACAAGGCAATAAA 59.306 36.000 0.00 0.00 0.00 1.40
2003 2185 4.929808 CGAGATCTCCTCCTTTTCGAAAAA 59.070 41.667 22.67 9.49 38.71 1.94
2006 2188 2.427453 CCGAGATCTCCTCCTTTTCGAA 59.573 50.000 17.13 0.00 38.71 3.71
2008 2190 1.537135 GCCGAGATCTCCTCCTTTTCG 60.537 57.143 17.13 2.80 38.71 3.46
2010 2192 0.833949 GGCCGAGATCTCCTCCTTTT 59.166 55.000 17.13 0.00 38.71 2.27
2011 2193 0.031616 AGGCCGAGATCTCCTCCTTT 60.032 55.000 19.47 4.80 38.71 3.11
2012 2194 0.469144 GAGGCCGAGATCTCCTCCTT 60.469 60.000 23.66 12.68 40.29 3.36
2013 2195 1.152830 GAGGCCGAGATCTCCTCCT 59.847 63.158 23.27 23.27 40.29 3.69
2015 2197 1.805428 GCAGAGGCCGAGATCTCCTC 61.805 65.000 17.13 17.32 45.11 3.71
2016 2198 1.832167 GCAGAGGCCGAGATCTCCT 60.832 63.158 17.13 9.17 0.00 3.69
2017 2199 1.470996 ATGCAGAGGCCGAGATCTCC 61.471 60.000 17.13 3.90 40.13 3.71
2018 2200 0.038343 GATGCAGAGGCCGAGATCTC 60.038 60.000 13.05 13.05 40.13 2.75
2020 2202 0.319727 CTGATGCAGAGGCCGAGATC 60.320 60.000 0.00 0.00 40.13 2.75
2021 2203 0.758310 TCTGATGCAGAGGCCGAGAT 60.758 55.000 0.00 0.00 35.39 2.75
2035 2217 0.676184 ACCGTATGCATCGCTCTGAT 59.324 50.000 0.19 0.00 38.01 2.90
2037 2219 0.249031 TGACCGTATGCATCGCTCTG 60.249 55.000 0.19 0.00 0.00 3.35
2038 2220 0.249073 GTGACCGTATGCATCGCTCT 60.249 55.000 0.19 0.00 0.00 4.09
2039 2221 1.540607 CGTGACCGTATGCATCGCTC 61.541 60.000 0.19 4.80 0.00 5.03
2041 2223 2.920869 CGTGACCGTATGCATCGC 59.079 61.111 0.19 0.00 0.00 4.58
2068 2250 9.965824 CAAGACCTGTATTGAACTTATTTGTTT 57.034 29.630 0.00 0.00 33.96 2.83
2069 2251 9.349713 TCAAGACCTGTATTGAACTTATTTGTT 57.650 29.630 4.96 0.00 37.79 2.83
2070 2252 8.918202 TCAAGACCTGTATTGAACTTATTTGT 57.082 30.769 4.96 0.00 37.79 2.83
2071 2253 9.831737 CTTCAAGACCTGTATTGAACTTATTTG 57.168 33.333 14.22 2.30 43.30 2.32
2072 2254 9.574516 ACTTCAAGACCTGTATTGAACTTATTT 57.425 29.630 14.22 0.00 43.30 1.40
2073 2255 9.220767 GACTTCAAGACCTGTATTGAACTTATT 57.779 33.333 14.22 0.28 43.30 1.40
2074 2256 8.598041 AGACTTCAAGACCTGTATTGAACTTAT 58.402 33.333 14.22 2.13 43.30 1.73
2075 2257 7.872993 CAGACTTCAAGACCTGTATTGAACTTA 59.127 37.037 14.22 0.00 43.30 2.24
2076 2258 6.708054 CAGACTTCAAGACCTGTATTGAACTT 59.292 38.462 14.22 6.31 43.30 2.66
2077 2259 6.042093 TCAGACTTCAAGACCTGTATTGAACT 59.958 38.462 14.22 9.40 43.30 3.01
2078 2260 6.223852 TCAGACTTCAAGACCTGTATTGAAC 58.776 40.000 14.22 7.62 43.30 3.18
2079 2261 6.419484 TCAGACTTCAAGACCTGTATTGAA 57.581 37.500 16.52 16.52 45.15 2.69
2080 2262 5.047021 CCTCAGACTTCAAGACCTGTATTGA 60.047 44.000 3.38 3.38 38.81 2.57
2081 2263 5.174395 CCTCAGACTTCAAGACCTGTATTG 58.826 45.833 10.05 0.00 33.43 1.90
2082 2264 4.841246 ACCTCAGACTTCAAGACCTGTATT 59.159 41.667 10.05 0.00 0.00 1.89
2083 2265 4.421131 ACCTCAGACTTCAAGACCTGTAT 58.579 43.478 10.05 0.00 0.00 2.29
2084 2266 3.827302 GACCTCAGACTTCAAGACCTGTA 59.173 47.826 10.05 0.49 0.00 2.74
2085 2267 2.630580 GACCTCAGACTTCAAGACCTGT 59.369 50.000 10.05 0.00 0.00 4.00
2086 2268 2.630098 TGACCTCAGACTTCAAGACCTG 59.370 50.000 0.00 0.00 0.00 4.00
2087 2269 2.964209 TGACCTCAGACTTCAAGACCT 58.036 47.619 0.00 0.00 0.00 3.85
2088 2270 3.753294 TTGACCTCAGACTTCAAGACC 57.247 47.619 0.00 0.00 0.00 3.85
2089 2271 4.698575 ACTTTGACCTCAGACTTCAAGAC 58.301 43.478 0.00 0.00 31.11 3.01
2090 2272 6.098409 AGTTACTTTGACCTCAGACTTCAAGA 59.902 38.462 0.00 0.00 31.11 3.02
2091 2273 6.284459 AGTTACTTTGACCTCAGACTTCAAG 58.716 40.000 0.00 0.00 31.11 3.02
2092 2274 6.235231 AGTTACTTTGACCTCAGACTTCAA 57.765 37.500 0.00 0.00 0.00 2.69
2093 2275 5.871396 AGTTACTTTGACCTCAGACTTCA 57.129 39.130 0.00 0.00 0.00 3.02
2094 2276 6.983984 AGTAGTTACTTTGACCTCAGACTTC 58.016 40.000 0.00 0.00 31.13 3.01
2095 2277 6.980416 AGTAGTTACTTTGACCTCAGACTT 57.020 37.500 0.00 0.00 31.13 3.01
2096 2278 7.308469 CGTTAGTAGTTACTTTGACCTCAGACT 60.308 40.741 0.00 0.00 37.73 3.24
2097 2279 6.800892 CGTTAGTAGTTACTTTGACCTCAGAC 59.199 42.308 0.00 0.00 37.73 3.51
2098 2280 6.072286 CCGTTAGTAGTTACTTTGACCTCAGA 60.072 42.308 0.00 0.00 37.73 3.27
2112 2294 5.370679 TCTTTCAAAAGGCCGTTAGTAGTT 58.629 37.500 3.72 0.00 36.67 2.24
2113 2295 4.964593 TCTTTCAAAAGGCCGTTAGTAGT 58.035 39.130 3.72 0.00 36.67 2.73
2121 2303 4.568152 TTCTTCTTCTTTCAAAAGGCCG 57.432 40.909 0.00 0.00 36.67 6.13
2149 2331 6.517605 AGTTTGTTGACTTCTCTTAGAGGAC 58.482 40.000 9.58 0.00 0.00 3.85
2161 3423 4.926832 CGTTTTCCCAAAGTTTGTTGACTT 59.073 37.500 14.36 0.00 41.44 3.01
2177 3439 2.137523 TGCCTTTCTCGTACGTTTTCC 58.862 47.619 16.05 0.17 0.00 3.13
2179 3441 3.395639 TGATGCCTTTCTCGTACGTTTT 58.604 40.909 16.05 0.00 0.00 2.43
2398 3679 1.210478 TCTATGTTTGCTGCCCTCTCC 59.790 52.381 0.00 0.00 0.00 3.71
2427 3708 2.428925 GGCCCCCACATGCAAGATG 61.429 63.158 0.00 0.00 0.00 2.90
2469 3759 7.013464 TGACTGCTAGTACTAAATCTTCTAGGC 59.987 40.741 3.76 0.65 31.72 3.93
2470 3760 8.347035 GTGACTGCTAGTACTAAATCTTCTAGG 58.653 40.741 3.76 0.00 31.72 3.02
2514 3804 1.203994 ACATGCGTGTAGGTAGACCAC 59.796 52.381 10.57 0.00 36.63 4.16
2523 3813 5.190342 CGATTCATAACAACATGCGTGTAG 58.810 41.667 12.96 0.00 37.67 2.74
2525 3815 3.181511 CCGATTCATAACAACATGCGTGT 60.182 43.478 5.51 5.51 41.28 4.49
2526 3816 3.063316 TCCGATTCATAACAACATGCGTG 59.937 43.478 3.82 3.82 0.00 5.34
2551 3841 1.687840 CCCTATCCGACCCACCACA 60.688 63.158 0.00 0.00 0.00 4.17
2602 3892 7.201609 GCTCCAACAATCGTCAAACATCTATTA 60.202 37.037 0.00 0.00 0.00 0.98
2603 3893 6.403636 GCTCCAACAATCGTCAAACATCTATT 60.404 38.462 0.00 0.00 0.00 1.73
2604 3894 5.065218 GCTCCAACAATCGTCAAACATCTAT 59.935 40.000 0.00 0.00 0.00 1.98
2605 3895 4.391830 GCTCCAACAATCGTCAAACATCTA 59.608 41.667 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.