Multiple sequence alignment - TraesCS6D01G240800

Loading Multiple Alignment...

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 TraesCS6D01G240800 chr6D 100.000 4793 0 0 1 4793 343293408 343298200 0.000000e+00 8852.0
1 TraesCS6D01G240800 chr6D 83.055 419 55 11 3989 4403 343303042 343302636 2.730000e-97 366.0
2 TraesCS6D01G240800 chr6A 91.894 3960 164 57 124 3999 483732592 483736478 0.000000e+00 5389.0
3 TraesCS6D01G240800 chr6B 91.316 2211 150 26 25 2214 518025195 518027384 0.000000e+00 2981.0
4 TraesCS6D01G240800 chr6B 86.844 1467 135 36 2564 3998 518027607 518029047 0.000000e+00 1587.0
5 TraesCS6D01G240800 chr6B 79.091 330 49 9 1893 2212 660277147 660277466 4.860000e-50 209.0
6 TraesCS6D01G240800 chr7D 98.489 794 11 1 4000 4793 594825024 594825816 0.000000e+00 1399.0
7 TraesCS6D01G240800 chr7D 98.363 794 12 1 4000 4793 594167895 594167103 0.000000e+00 1393.0
8 TraesCS6D01G240800 chr7D 92.857 168 11 1 4487 4653 131322338 131322171 4.790000e-60 243.0
9 TraesCS6D01G240800 chr3D 98.116 796 14 1 3998 4793 244829130 244829924 0.000000e+00 1386.0
10 TraesCS6D01G240800 chr3D 90.650 246 22 1 3996 4241 244833042 244832798 4.630000e-85 326.0
11 TraesCS6D01G240800 chr3D 85.542 83 6 5 2229 2307 177043281 177043201 1.110000e-11 82.4
12 TraesCS6D01G240800 chr3D 83.544 79 7 5 2232 2307 544774441 544774516 8.610000e-08 69.4
13 TraesCS6D01G240800 chr4D 98.496 665 8 2 4130 4793 314619173 314619836 0.000000e+00 1171.0
14 TraesCS6D01G240800 chr4D 83.990 406 52 8 4000 4402 314632668 314632273 1.260000e-100 377.0
15 TraesCS6D01G240800 chr4D 100.000 137 0 0 4000 4136 314609843 314609979 2.210000e-63 254.0
16 TraesCS6D01G240800 chr4D 89.888 89 8 1 2313 2401 20114939 20114852 3.920000e-21 113.0
17 TraesCS6D01G240800 chr4D 82.278 79 11 3 2237 2313 352753965 352753888 1.110000e-06 65.8
18 TraesCS6D01G240800 chr2B 84.615 312 46 2 25 335 370551602 370551292 4.660000e-80 309.0
19 TraesCS6D01G240800 chr2B 83.654 312 49 2 25 335 370491499 370491189 4.690000e-75 292.0
20 TraesCS6D01G240800 chr2B 91.765 85 7 0 2314 2398 247368538 247368622 8.430000e-23 119.0
21 TraesCS6D01G240800 chr5D 92.135 178 13 1 4488 4665 444784471 444784647 2.860000e-62 250.0
22 TraesCS6D01G240800 chr5D 95.652 138 6 0 4656 4793 444784855 444784992 6.240000e-54 222.0
23 TraesCS6D01G240800 chr5D 85.542 83 9 2 2236 2315 18186873 18186791 3.070000e-12 84.2
24 TraesCS6D01G240800 chr4A 92.638 163 12 0 4488 4650 12606895 12607057 8.020000e-58 235.0
25 TraesCS6D01G240800 chr4A 96.377 138 5 0 4656 4793 585435375 585435512 1.340000e-55 228.0
26 TraesCS6D01G240800 chr4A 95.652 138 6 0 4656 4793 12607255 12607392 6.240000e-54 222.0
27 TraesCS6D01G240800 chr4A 87.500 96 10 2 2307 2402 697388895 697388802 5.070000e-20 110.0
28 TraesCS6D01G240800 chr2A 96.377 138 5 0 4656 4793 459832141 459832278 1.340000e-55 228.0
29 TraesCS6D01G240800 chr2A 90.854 164 15 0 4488 4651 585705275 585705438 2.250000e-53 220.0
30 TraesCS6D01G240800 chr2A 89.888 89 8 1 2311 2399 182008964 182009051 3.920000e-21 113.0
31 TraesCS6D01G240800 chr2A 85.882 85 8 3 2236 2317 591280076 591279993 2.380000e-13 87.9
32 TraesCS6D01G240800 chr7A 91.071 168 10 1 4488 4655 27099957 27100119 6.240000e-54 222.0
33 TraesCS6D01G240800 chr7A 84.337 83 10 2 2236 2315 623426260 623426342 1.430000e-10 78.7
34 TraesCS6D01G240800 chr1A 95.652 138 6 0 4656 4793 427503086 427502949 6.240000e-54 222.0
35 TraesCS6D01G240800 chr1A 89.888 89 5 2 2313 2398 331272194 331272281 1.410000e-20 111.0
36 TraesCS6D01G240800 chr4B 92.771 83 5 1 2319 2401 652001013 652000932 8.430000e-23 119.0
37 TraesCS6D01G240800 chr1B 92.593 81 6 0 2318 2398 85441628 85441708 3.030000e-22 117.0
38 TraesCS6D01G240800 chr1B 89.888 89 5 2 2313 2398 355408268 355408355 1.410000e-20 111.0
39 TraesCS6D01G240800 chr3B 87.013 77 6 2 2235 2308 778392818 778392743 3.070000e-12 84.2
40 TraesCS6D01G240800 chr3B 84.337 83 10 2 2236 2315 104369531 104369613 1.430000e-10 78.7


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 TraesCS6D01G240800 chr6D 343293408 343298200 4792 False 8852 8852 100.0000 1 4793 1 chr6D.!!$F1 4792
1 TraesCS6D01G240800 chr6A 483732592 483736478 3886 False 5389 5389 91.8940 124 3999 1 chr6A.!!$F1 3875
2 TraesCS6D01G240800 chr6B 518025195 518029047 3852 False 2284 2981 89.0800 25 3998 2 chr6B.!!$F2 3973
3 TraesCS6D01G240800 chr7D 594825024 594825816 792 False 1399 1399 98.4890 4000 4793 1 chr7D.!!$F1 793
4 TraesCS6D01G240800 chr7D 594167103 594167895 792 True 1393 1393 98.3630 4000 4793 1 chr7D.!!$R2 793
5 TraesCS6D01G240800 chr3D 244829130 244829924 794 False 1386 1386 98.1160 3998 4793 1 chr3D.!!$F1 795
6 TraesCS6D01G240800 chr4D 314619173 314619836 663 False 1171 1171 98.4960 4130 4793 1 chr4D.!!$F2 663
7 TraesCS6D01G240800 chr5D 444784471 444784992 521 False 236 250 93.8935 4488 4793 2 chr5D.!!$F1 305

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
43 44 0.035056 AAAGAACCAGGGCGATCCAG 60.035 55.000 0.00 0.0 38.24 3.86 F
836 888 0.323451 GATCCAACCTGTGTTCCCCC 60.323 60.000 0.00 0.0 30.42 5.40 F
969 1040 0.892063 GAAGGCCGTCTGTCTCTCTT 59.108 55.000 11.87 0.0 0.00 2.85 F
1920 1997 1.196808 TCCATCTTTGCTTTTCGTCGC 59.803 47.619 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1423 1.205179 TCGTTGGCACTATCGGCTTTA 59.795 47.619 0.00 0.00 0.00 1.85 R
2833 3001 0.911769 TAGAACAGGCATGTGAGGGG 59.088 55.000 4.03 0.00 40.39 4.79 R
3284 3459 1.999648 AGCCTGCCAAACAAATCAGA 58.000 45.000 0.00 0.00 0.00 3.27 R
3833 4019 2.228925 TCAGCTATGTTTGCAGCAACA 58.771 42.857 7.54 9.93 40.36 3.33 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
32 33 6.159988 TCGCAAAAAGAAAAAGAAAGAACCA 58.840 32.000 0.00 0.00 0.00 3.67
34 35 6.455513 CGCAAAAAGAAAAAGAAAGAACCAGG 60.456 38.462 0.00 0.00 0.00 4.45
40 41 2.115343 AAGAAAGAACCAGGGCGATC 57.885 50.000 0.00 0.00 0.00 3.69
43 44 0.035056 AAAGAACCAGGGCGATCCAG 60.035 55.000 0.00 0.00 38.24 3.86
48 49 1.760086 CCAGGGCGATCCAGAGACT 60.760 63.158 0.00 0.00 38.24 3.24
69 70 4.446371 CTCACGAGGAGCAAATTTATCCT 58.554 43.478 19.26 19.26 46.22 3.24
70 71 4.191544 TCACGAGGAGCAAATTTATCCTG 58.808 43.478 22.59 17.42 43.57 3.86
71 72 3.313526 CACGAGGAGCAAATTTATCCTGG 59.686 47.826 22.59 22.26 43.57 4.45
72 73 3.054361 ACGAGGAGCAAATTTATCCTGGT 60.054 43.478 22.89 22.89 44.41 4.00
77 79 4.035208 GGAGCAAATTTATCCTGGTGTACG 59.965 45.833 12.35 0.00 0.00 3.67
80 82 4.493545 GCAAATTTATCCTGGTGTACGTCG 60.494 45.833 0.00 0.00 0.00 5.12
83 85 2.330440 TATCCTGGTGTACGTCGCTA 57.670 50.000 0.00 0.00 0.00 4.26
86 88 1.588824 CCTGGTGTACGTCGCTACCA 61.589 60.000 13.18 13.18 40.67 3.25
87 89 0.455633 CTGGTGTACGTCGCTACCAC 60.456 60.000 10.66 4.28 38.23 4.16
89 91 1.580942 GTGTACGTCGCTACCACCA 59.419 57.895 0.00 0.00 0.00 4.17
90 92 0.455633 GTGTACGTCGCTACCACCAG 60.456 60.000 0.00 0.00 0.00 4.00
99 101 1.153369 CTACCACCAGCGGACATGG 60.153 63.158 0.00 1.39 43.87 3.66
112 114 2.745152 CGGACATGGGATCCAAACTACC 60.745 54.545 15.23 8.38 36.95 3.18
132 134 2.282555 CCGCTTGATACACAGATCAACG 59.717 50.000 0.00 11.03 40.18 4.10
213 215 5.163311 TGGCAGATTTATTTCTCCAGATCGA 60.163 40.000 0.00 0.00 0.00 3.59
240 242 1.978580 ACCCTTCTCCAAATCGACACT 59.021 47.619 0.00 0.00 0.00 3.55
256 258 2.171448 GACACTGACATGGCCTAATCCT 59.829 50.000 3.32 0.00 0.00 3.24
294 296 4.280677 CCTAAAGAAGATGAGCGAGATCCT 59.719 45.833 0.00 0.00 0.00 3.24
395 397 3.921677 ACACTCCTTATTTCGCTTTCGA 58.078 40.909 0.00 0.00 43.89 3.71
414 416 2.669670 CGAATCTCTCGCACACTGAGTT 60.670 50.000 0.00 0.00 41.49 3.01
415 417 2.360553 ATCTCTCGCACACTGAGTTG 57.639 50.000 0.00 0.00 34.99 3.16
491 493 3.266510 TGCCAGCGAACATCTAGATTT 57.733 42.857 1.33 1.33 0.00 2.17
497 499 5.985530 CCAGCGAACATCTAGATTTGACATA 59.014 40.000 1.33 0.00 0.00 2.29
540 543 2.351544 GCCGCCGTGTAAAATTTACCAA 60.352 45.455 12.72 0.00 0.00 3.67
549 560 9.733219 CCGTGTAAAATTTACCAAGTTCTAAAA 57.267 29.630 12.72 0.00 0.00 1.52
613 628 8.176814 TGTCGTGCTACAGTAAATAATTGTAC 57.823 34.615 0.00 0.00 0.00 2.90
614 629 8.030692 TGTCGTGCTACAGTAAATAATTGTACT 58.969 33.333 0.00 0.00 0.00 2.73
683 699 9.586435 CTTTTCTTTTTAGGACAACAAGAACAT 57.414 29.630 0.00 0.00 34.08 2.71
796 848 3.139077 GCTGTACCTGCACTACAAAACT 58.861 45.455 3.49 0.00 0.00 2.66
797 849 3.058914 GCTGTACCTGCACTACAAAACTG 60.059 47.826 3.49 0.00 0.00 3.16
836 888 0.323451 GATCCAACCTGTGTTCCCCC 60.323 60.000 0.00 0.00 30.42 5.40
969 1040 0.892063 GAAGGCCGTCTGTCTCTCTT 59.108 55.000 11.87 0.00 0.00 2.85
1247 1318 3.290710 GGCAAGAGAATATTTGGCAGGA 58.709 45.455 6.56 0.00 45.84 3.86
1323 1394 6.603237 AAGGCTGTTTTTATTTGCTTTGTC 57.397 33.333 0.00 0.00 0.00 3.18
1328 1399 6.267500 TGTTTTTATTTGCTTTGTCGCTTC 57.733 33.333 0.00 0.00 0.00 3.86
1350 1421 7.693951 GCTTCAGCATAATACTAGTGTTTTGTG 59.306 37.037 18.89 15.83 41.59 3.33
1352 1423 8.615878 TCAGCATAATACTAGTGTTTTGTGTT 57.384 30.769 18.89 8.93 32.23 3.32
1363 1434 5.997385 AGTGTTTTGTGTTAAAGCCGATAG 58.003 37.500 0.00 0.00 0.00 2.08
1367 1438 2.352388 TGTGTTAAAGCCGATAGTGCC 58.648 47.619 0.00 0.00 33.53 5.01
1490 1567 4.949856 TCTCTAATCCATGAAAACCTTGGC 59.050 41.667 0.00 0.00 39.30 4.52
1574 1651 1.247567 ACCTCGGTTCCTTGCAAATG 58.752 50.000 0.00 0.00 0.00 2.32
1618 1695 9.526713 GGTTCTACTAGTAAGGTTTATACTTGC 57.473 37.037 3.76 0.00 35.34 4.01
1686 1763 6.884832 TCGAGGAAGAGAAGGCAATATTAAA 58.115 36.000 0.00 0.00 0.00 1.52
1699 1776 8.525290 AGGCAATATTAAAACTGAGCTATGTT 57.475 30.769 0.00 0.00 0.00 2.71
1742 1819 2.005451 GCCAGAATACAGCACAGAGTG 58.995 52.381 0.00 0.00 36.51 3.51
1841 1918 3.572255 TCAACTGGGGTAAAACTTGCATC 59.428 43.478 0.00 0.00 0.00 3.91
1855 1932 8.773033 AAAACTTGCATCCTCATTTATATCCT 57.227 30.769 0.00 0.00 0.00 3.24
1876 1953 7.859325 TCCTGTGTAATGCTAATTTTACTCC 57.141 36.000 0.00 0.00 31.16 3.85
1914 1991 4.696455 CAAGGTGTTCCATCTTTGCTTTT 58.304 39.130 0.00 0.00 31.84 2.27
1920 1997 1.196808 TCCATCTTTGCTTTTCGTCGC 59.803 47.619 0.00 0.00 0.00 5.19
2168 2246 5.158141 TGGCCTCAGATCAGGTTTCTATAT 58.842 41.667 3.32 0.00 35.72 0.86
2203 2281 4.457603 TCGTTTATGCAATGCAGGTAAAGT 59.542 37.500 14.98 0.00 43.65 2.66
2242 2321 7.539034 AAATTTGCACTATTTGTTACTCCCT 57.461 32.000 5.43 0.00 0.00 4.20
2243 2322 6.759497 ATTTGCACTATTTGTTACTCCCTC 57.241 37.500 0.00 0.00 0.00 4.30
2244 2323 5.499004 TTGCACTATTTGTTACTCCCTCT 57.501 39.130 0.00 0.00 0.00 3.69
2245 2324 4.832248 TGCACTATTTGTTACTCCCTCTG 58.168 43.478 0.00 0.00 0.00 3.35
2246 2325 4.286032 TGCACTATTTGTTACTCCCTCTGT 59.714 41.667 0.00 0.00 0.00 3.41
2247 2326 5.482526 TGCACTATTTGTTACTCCCTCTGTA 59.517 40.000 0.00 0.00 0.00 2.74
2248 2327 5.811100 GCACTATTTGTTACTCCCTCTGTAC 59.189 44.000 0.00 0.00 0.00 2.90
2249 2328 6.338937 CACTATTTGTTACTCCCTCTGTACC 58.661 44.000 0.00 0.00 0.00 3.34
2250 2329 6.021030 ACTATTTGTTACTCCCTCTGTACCA 58.979 40.000 0.00 0.00 0.00 3.25
2251 2330 5.836024 ATTTGTTACTCCCTCTGTACCAA 57.164 39.130 0.00 0.00 0.00 3.67
2265 2344 8.365647 CCCTCTGTACCAAAATATAAGACGTAT 58.634 37.037 0.00 0.00 0.00 3.06
2266 2345 9.193133 CCTCTGTACCAAAATATAAGACGTATG 57.807 37.037 0.00 0.00 0.00 2.39
2267 2346 9.745880 CTCTGTACCAAAATATAAGACGTATGT 57.254 33.333 0.00 0.00 0.00 2.29
2327 2410 4.466255 ACATAGGTACTCCCTCCGTATT 57.534 45.455 0.00 0.00 44.81 1.89
2378 2461 8.963130 CAAATTGAACTGCAAAAACGTCTTATA 58.037 29.630 0.00 0.00 40.48 0.98
2379 2462 9.691362 AAATTGAACTGCAAAAACGTCTTATAT 57.309 25.926 0.00 0.00 40.48 0.86
2380 2463 9.691362 AATTGAACTGCAAAAACGTCTTATATT 57.309 25.926 0.00 0.00 40.48 1.28
2387 2470 9.567848 CTGCAAAAACGTCTTATATTTTGGTAT 57.432 29.630 17.78 0.00 41.02 2.73
2479 2568 6.546772 TGTTTTCCCTTTTATCGTACTGGTTT 59.453 34.615 0.00 0.00 0.00 3.27
2498 2617 9.719355 ACTGGTTTATTTGTGAAAACTCTTTTT 57.281 25.926 0.00 0.00 37.65 1.94
2597 2741 6.072728 TCGAGGTTTAACTTTGACCATCAATG 60.073 38.462 0.00 3.60 36.11 2.82
2604 2758 3.007940 ACTTTGACCATCAATGAGACCGA 59.992 43.478 10.43 0.00 36.11 4.69
3213 3387 6.325545 TGGTACTGTAGACTATACCCATTTGG 59.674 42.308 7.88 0.00 36.95 3.28
3284 3459 3.955650 ACTAACTGTATCCGTGTGCTT 57.044 42.857 0.00 0.00 0.00 3.91
3367 3542 1.069636 CAACAAAAGCTGAGCGAGGTC 60.070 52.381 0.00 0.00 0.00 3.85
3833 4019 6.213195 CCCCTTCTGAGCTGAAATATAGAGAT 59.787 42.308 0.00 0.00 0.00 2.75
3913 4099 6.299604 GTCTGATCGTTCAAAATGTGTACAG 58.700 40.000 0.00 0.00 0.00 2.74
3919 4105 4.319477 CGTTCAAAATGTGTACAGACAGGG 60.319 45.833 0.00 0.00 35.82 4.45
3937 4123 2.431057 AGGGATCTGAAATCTACGCGTT 59.569 45.455 20.78 0.00 0.00 4.84
3965 4151 1.732259 CTTGTGTAGCCGCTAACTTGG 59.268 52.381 0.46 0.00 0.00 3.61
3984 4171 6.178324 ACTTGGTAGTTAAGGGTGCTAATTC 58.822 40.000 0.00 0.00 0.00 2.17
3991 4178 6.120220 AGTTAAGGGTGCTAATTCCATGTAC 58.880 40.000 0.00 0.00 0.00 2.90
4366 4553 5.334879 GGATGCACCGCCTAGTAAATAAATG 60.335 44.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.432359 GTTCTTTCTTTTTCTTTTTGCGAGAAA 58.568 29.630 0.00 0.00 40.36 2.52
5 6 7.062956 GGTTCTTTCTTTTTCTTTTTGCGAGAA 59.937 33.333 0.00 0.00 0.00 2.87
6 7 6.530181 GGTTCTTTCTTTTTCTTTTTGCGAGA 59.470 34.615 0.00 0.00 0.00 4.04
8 9 6.159988 TGGTTCTTTCTTTTTCTTTTTGCGA 58.840 32.000 0.00 0.00 0.00 5.10
9 10 6.401955 TGGTTCTTTCTTTTTCTTTTTGCG 57.598 33.333 0.00 0.00 0.00 4.85
10 11 6.183360 CCCTGGTTCTTTCTTTTTCTTTTTGC 60.183 38.462 0.00 0.00 0.00 3.68
11 12 6.183360 GCCCTGGTTCTTTCTTTTTCTTTTTG 60.183 38.462 0.00 0.00 0.00 2.44
12 13 5.880332 GCCCTGGTTCTTTCTTTTTCTTTTT 59.120 36.000 0.00 0.00 0.00 1.94
13 14 5.428253 GCCCTGGTTCTTTCTTTTTCTTTT 58.572 37.500 0.00 0.00 0.00 2.27
14 15 4.441495 CGCCCTGGTTCTTTCTTTTTCTTT 60.441 41.667 0.00 0.00 0.00 2.52
15 16 3.068165 CGCCCTGGTTCTTTCTTTTTCTT 59.932 43.478 0.00 0.00 0.00 2.52
16 17 2.623416 CGCCCTGGTTCTTTCTTTTTCT 59.377 45.455 0.00 0.00 0.00 2.52
17 18 2.621526 TCGCCCTGGTTCTTTCTTTTTC 59.378 45.455 0.00 0.00 0.00 2.29
18 19 2.661718 TCGCCCTGGTTCTTTCTTTTT 58.338 42.857 0.00 0.00 0.00 1.94
19 20 2.358322 TCGCCCTGGTTCTTTCTTTT 57.642 45.000 0.00 0.00 0.00 2.27
20 21 2.437413 GATCGCCCTGGTTCTTTCTTT 58.563 47.619 0.00 0.00 0.00 2.52
21 22 1.340114 GGATCGCCCTGGTTCTTTCTT 60.340 52.381 0.00 0.00 0.00 2.52
22 23 0.253327 GGATCGCCCTGGTTCTTTCT 59.747 55.000 0.00 0.00 0.00 2.52
23 24 0.035439 TGGATCGCCCTGGTTCTTTC 60.035 55.000 0.00 0.00 35.38 2.62
32 33 1.040339 GTGAGTCTCTGGATCGCCCT 61.040 60.000 0.65 0.00 35.38 5.19
34 35 1.064946 CGTGAGTCTCTGGATCGCC 59.935 63.158 0.65 0.00 0.00 5.54
40 41 0.962855 TGCTCCTCGTGAGTCTCTGG 60.963 60.000 0.65 0.00 43.48 3.86
43 44 2.663826 ATTTGCTCCTCGTGAGTCTC 57.336 50.000 6.59 0.00 43.48 3.36
48 49 4.191544 CAGGATAAATTTGCTCCTCGTGA 58.808 43.478 16.99 0.00 37.30 4.35
62 63 1.820519 AGCGACGTACACCAGGATAAA 59.179 47.619 0.00 0.00 0.00 1.40
65 66 0.737219 GTAGCGACGTACACCAGGAT 59.263 55.000 0.00 0.00 0.00 3.24
66 67 1.308069 GGTAGCGACGTACACCAGGA 61.308 60.000 0.00 0.00 0.00 3.86
67 68 1.138247 GGTAGCGACGTACACCAGG 59.862 63.158 9.01 0.00 0.00 4.45
69 70 1.580942 GTGGTAGCGACGTACACCA 59.419 57.895 11.65 11.65 38.72 4.17
70 71 1.153958 GGTGGTAGCGACGTACACC 60.154 63.158 13.56 13.56 0.00 4.16
71 72 0.455633 CTGGTGGTAGCGACGTACAC 60.456 60.000 0.00 1.01 0.00 2.90
72 73 1.878070 CTGGTGGTAGCGACGTACA 59.122 57.895 0.00 0.00 0.00 2.90
80 82 1.815421 CATGTCCGCTGGTGGTAGC 60.815 63.158 0.00 0.00 40.29 3.58
83 85 4.033776 CCCATGTCCGCTGGTGGT 62.034 66.667 0.00 0.00 31.44 4.16
86 88 2.746375 GGATCCCATGTCCGCTGGT 61.746 63.158 0.00 0.00 31.44 4.00
87 89 2.111878 GGATCCCATGTCCGCTGG 59.888 66.667 0.00 0.00 0.00 4.85
89 91 0.394352 GTTTGGATCCCATGTCCGCT 60.394 55.000 9.90 0.00 38.64 5.52
90 92 0.394352 AGTTTGGATCCCATGTCCGC 60.394 55.000 9.90 0.00 38.64 5.54
94 96 1.408266 GCGGTAGTTTGGATCCCATGT 60.408 52.381 9.90 0.00 31.53 3.21
99 101 2.396590 TCAAGCGGTAGTTTGGATCC 57.603 50.000 4.20 4.20 38.80 3.36
112 114 2.282555 CCGTTGATCTGTGTATCAAGCG 59.717 50.000 0.00 6.93 44.39 4.68
158 160 2.530497 CGTGTCGGTGTTGGTGGTG 61.530 63.158 0.00 0.00 0.00 4.17
160 162 2.970324 CCGTGTCGGTGTTGGTGG 60.970 66.667 0.00 0.00 42.73 4.61
161 163 2.970324 CCCGTGTCGGTGTTGGTG 60.970 66.667 7.40 0.00 46.80 4.17
213 215 0.754472 TTTGGAGAAGGGTTCGTCGT 59.246 50.000 0.00 0.00 34.02 4.34
240 242 2.054799 GGGTAGGATTAGGCCATGTCA 58.945 52.381 5.01 0.00 0.00 3.58
256 258 5.052693 TCTTTAGGCGTGTAGATAGGGTA 57.947 43.478 0.00 0.00 0.00 3.69
321 323 3.878667 CGGATCCCTGCCTTCCCC 61.879 72.222 6.06 0.00 0.00 4.81
325 327 3.483869 GGAGCGGATCCCTGCCTT 61.484 66.667 6.06 0.00 45.76 4.35
395 397 2.611473 CCAACTCAGTGTGCGAGAGATT 60.611 50.000 0.00 0.00 34.47 2.40
497 499 7.132213 CGGCGTGATAAATTTATCTGTTTCAT 58.868 34.615 29.37 2.40 40.11 2.57
518 521 1.526646 GTAAATTTTACACGGCGGCG 58.473 50.000 31.06 31.06 0.00 6.46
575 586 5.935206 TGTAGCACGACAATTTTCCTGATAA 59.065 36.000 0.00 0.00 0.00 1.75
582 593 9.769093 ATTATTTACTGTAGCACGACAATTTTC 57.231 29.630 0.00 0.00 0.00 2.29
587 599 7.661127 ACAATTATTTACTGTAGCACGACAA 57.339 32.000 0.00 0.00 0.00 3.18
613 628 2.464865 GTCGGATCCTGATCAAACGAG 58.535 52.381 10.75 0.00 39.54 4.18
614 629 1.202256 CGTCGGATCCTGATCAAACGA 60.202 52.381 20.02 12.60 43.61 3.85
683 699 2.040545 TCCGGGGAAACATCAGCTTTTA 59.959 45.455 0.00 0.00 0.00 1.52
785 822 5.163834 ACGTGTTTGGTACAGTTTTGTAGTG 60.164 40.000 0.00 0.00 42.39 2.74
796 848 0.598158 GAGCCGACGTGTTTGGTACA 60.598 55.000 0.00 0.00 0.00 2.90
797 849 1.287041 GGAGCCGACGTGTTTGGTAC 61.287 60.000 0.00 0.00 0.00 3.34
836 888 2.049475 CTTCGTAGCTCGGACGGGAG 62.049 65.000 7.61 3.27 40.70 4.30
936 989 1.320507 GCCTTCCTCTCCGGTAGTAG 58.679 60.000 0.00 0.00 0.00 2.57
938 991 1.381463 GGCCTTCCTCTCCGGTAGT 60.381 63.158 0.00 0.00 0.00 2.73
969 1040 1.198094 TGCACGGAGATCCCTGGAAA 61.198 55.000 0.00 0.00 0.00 3.13
1247 1318 8.506168 ACATCACAAATTTATTCATCGGTACT 57.494 30.769 0.00 0.00 0.00 2.73
1323 1394 6.589830 AAACACTAGTATTATGCTGAAGCG 57.410 37.500 0.00 0.00 45.83 4.68
1350 1421 2.222953 CGTTGGCACTATCGGCTTTAAC 60.223 50.000 0.00 0.00 0.00 2.01
1352 1423 1.205179 TCGTTGGCACTATCGGCTTTA 59.795 47.619 0.00 0.00 0.00 1.85
1363 1434 2.030946 GTGAGATGCTATTCGTTGGCAC 59.969 50.000 1.80 0.00 45.37 5.01
1367 1438 3.244814 GCTCTGTGAGATGCTATTCGTTG 59.755 47.826 0.00 0.00 0.00 4.10
1431 1505 2.776526 ACAGGTCCTTGGCCACCA 60.777 61.111 3.88 0.00 34.80 4.17
1437 1511 1.338020 GAAAGCAACACAGGTCCTTGG 59.662 52.381 0.00 0.00 0.00 3.61
1490 1567 6.237942 GGATGATATCAACGCATTCTTATCCG 60.238 42.308 9.99 0.00 0.00 4.18
1599 1676 6.255020 CACGTGGCAAGTATAAACCTTACTAG 59.745 42.308 7.95 0.00 29.86 2.57
1602 1679 4.436451 GCACGTGGCAAGTATAAACCTTAC 60.436 45.833 18.88 0.00 43.97 2.34
1603 1680 3.685756 GCACGTGGCAAGTATAAACCTTA 59.314 43.478 18.88 0.00 43.97 2.69
1604 1681 2.486592 GCACGTGGCAAGTATAAACCTT 59.513 45.455 18.88 0.00 43.97 3.50
1618 1695 1.444724 CATTGGCATGTGCACGTGG 60.445 57.895 33.97 19.24 44.36 4.94
1686 1763 6.823182 TGCATATACACAAACATAGCTCAGTT 59.177 34.615 0.00 0.00 0.00 3.16
1699 1776 5.066375 GCAACTTGGATCTGCATATACACAA 59.934 40.000 0.00 0.00 36.09 3.33
1742 1819 3.316308 GTGTTGTCCATCCATATTCAGGC 59.684 47.826 0.00 0.00 0.00 4.85
1834 1911 6.713903 ACACAGGATATAAATGAGGATGCAAG 59.286 38.462 0.00 0.00 0.00 4.01
1841 1918 9.725019 TTAGCATTACACAGGATATAAATGAGG 57.275 33.333 0.00 0.00 0.00 3.86
1855 1932 7.523219 CAACGGAGTAAAATTAGCATTACACA 58.477 34.615 1.69 0.00 45.00 3.72
1920 1997 1.880027 GGGTTCACTAGTTGCACTTGG 59.120 52.381 0.00 0.00 0.00 3.61
1953 2030 5.351465 TCGAGTGACAGAAAATAATGAAGGC 59.649 40.000 0.00 0.00 0.00 4.35
2168 2246 7.433719 GCATTGCATAAACGACACCATTAATAA 59.566 33.333 3.15 0.00 0.00 1.40
2175 2253 1.882623 TGCATTGCATAAACGACACCA 59.117 42.857 7.38 0.00 31.71 4.17
2231 2310 5.633655 TTTTGGTACAGAGGGAGTAACAA 57.366 39.130 0.09 0.09 44.77 2.83
2232 2311 5.836024 ATTTTGGTACAGAGGGAGTAACA 57.164 39.130 0.00 0.00 42.39 2.41
2233 2312 9.543783 CTTATATTTTGGTACAGAGGGAGTAAC 57.456 37.037 0.00 0.00 42.39 2.50
2234 2313 9.496710 TCTTATATTTTGGTACAGAGGGAGTAA 57.503 33.333 0.00 0.00 42.39 2.24
2235 2314 8.921205 GTCTTATATTTTGGTACAGAGGGAGTA 58.079 37.037 0.00 0.00 42.39 2.59
2236 2315 7.417570 CGTCTTATATTTTGGTACAGAGGGAGT 60.418 40.741 0.00 0.00 42.39 3.85
2237 2316 6.924060 CGTCTTATATTTTGGTACAGAGGGAG 59.076 42.308 0.00 0.00 42.39 4.30
2238 2317 6.381994 ACGTCTTATATTTTGGTACAGAGGGA 59.618 38.462 0.00 0.00 42.39 4.20
2239 2318 6.579865 ACGTCTTATATTTTGGTACAGAGGG 58.420 40.000 0.00 0.00 42.39 4.30
2240 2319 9.193133 CATACGTCTTATATTTTGGTACAGAGG 57.807 37.037 0.00 0.00 42.39 3.69
2241 2320 9.745880 ACATACGTCTTATATTTTGGTACAGAG 57.254 33.333 0.00 0.00 42.39 3.35
2265 2344 4.948608 TTGCAGTTCAAAAGACGTTACA 57.051 36.364 0.00 0.00 0.00 2.41
2413 2496 3.088789 AGGGTCAGACAGTTCTCGTAT 57.911 47.619 2.17 0.00 0.00 3.06
2597 2741 8.915036 ACAGAACCCATATATATTATCGGTCTC 58.085 37.037 0.00 0.00 0.00 3.36
2616 2770 5.428253 TCCATTGCAGATAAGTACAGAACC 58.572 41.667 0.00 0.00 0.00 3.62
2833 3001 0.911769 TAGAACAGGCATGTGAGGGG 59.088 55.000 4.03 0.00 40.39 4.79
3284 3459 1.999648 AGCCTGCCAAACAAATCAGA 58.000 45.000 0.00 0.00 0.00 3.27
3380 3555 5.010012 CCAAGAAGCAACAGGAACAAATAGT 59.990 40.000 0.00 0.00 0.00 2.12
3635 3810 8.271458 TGATGGTTTCAATTTATAGACTAGGCA 58.729 33.333 0.00 0.00 0.00 4.75
3833 4019 2.228925 TCAGCTATGTTTGCAGCAACA 58.771 42.857 7.54 9.93 40.36 3.33
3913 4099 3.385577 GCGTAGATTTCAGATCCCTGTC 58.614 50.000 0.00 0.00 41.16 3.51
3919 4105 6.570690 AAGTTAACGCGTAGATTTCAGATC 57.429 37.500 14.46 0.00 0.00 2.75
3937 4123 2.564062 AGCGGCTACACAAGGTAAGTTA 59.436 45.455 0.00 0.00 0.00 2.24
3965 4151 6.120220 ACATGGAATTAGCACCCTTAACTAC 58.880 40.000 0.00 0.00 0.00 2.73
4299 4486 3.121030 GTGTGGTGGCTAGCGCAG 61.121 66.667 16.16 6.31 44.51 5.18
4379 4566 2.430751 CTGTGCGTGCTACAGCGA 60.431 61.111 10.09 0.00 45.83 4.93
4497 4684 6.982160 ATCTACCACACGGTTACCATATAA 57.018 37.500 1.13 0.00 46.31 0.98


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

AutoCloner maintained by Alex Coulton.