Multiple sequence alignment - TraesCS4D01G205300

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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 TraesCS4D01G205300 chr4D 100.000 2450 0 0 1 2450 352756519 352754070 0.000000e+00 4525.0
1 TraesCS4D01G205300 chr4D 91.703 458 28 4 994 1441 30195019 30195476 5.750000e-176 627.0
2 TraesCS4D01G205300 chr4B 90.780 2462 138 41 34 2450 436313242 436310825 0.000000e+00 3206.0
3 TraesCS4D01G205300 chr4A 92.417 1411 67 17 657 2045 112766831 112768223 0.000000e+00 1977.0
4 TraesCS4D01G205300 chr4A 92.222 450 26 3 1001 1441 572846014 572845565 1.600000e-176 628.0
5 TraesCS4D01G205300 chr4A 91.748 412 19 8 2046 2450 112768820 112769223 2.130000e-155 558.0
6 TraesCS4D01G205300 chr1B 91.429 455 27 5 999 1441 344375640 344375186 4.480000e-172 614.0
7 TraesCS4D01G205300 chr1B 90.989 455 30 6 997 1441 434429747 434429294 9.690000e-169 603.0
8 TraesCS4D01G205300 chr1A 91.170 453 29 6 999 1441 400955573 400956024 2.690000e-169 604.0
9 TraesCS4D01G205300 chr1A 88.742 453 28 14 999 1441 482767992 482768431 1.290000e-147 532.0
10 TraesCS4D01G205300 chr1D 90.949 453 30 6 999 1441 321710603 321710152 1.250000e-167 599.0
11 TraesCS4D01G205300 chr1D 90.110 455 33 6 999 1441 271837819 271837365 4.540000e-162 580.0
12 TraesCS4D01G205300 chr1D 88.143 447 31 10 1000 1441 382719801 382720230 1.680000e-141 512.0
13 TraesCS4D01G205300 chr1D 84.824 369 45 5 32 396 298008273 298008634 6.440000e-96 361.0
14 TraesCS4D01G205300 chr3D 93.478 46 0 1 1001 1043 462246628 462246583 5.650000e-07 65.8
15 TraesCS4D01G205300 chr3D 93.478 46 0 1 1001 1043 462455385 462455340 5.650000e-07 65.8
16 TraesCS4D01G205300 chr3B 93.478 46 0 1 1001 1043 613811866 613811821 5.650000e-07 65.8
17 TraesCS4D01G205300 chr3A 93.478 46 0 1 1001 1043 605241241 605241196 5.650000e-07 65.8


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 TraesCS4D01G205300 chr4D 352754070 352756519 2449 True 4525.0 4525 100.0000 1 2450 1 chr4D.!!$R1 2449
1 TraesCS4D01G205300 chr4B 436310825 436313242 2417 True 3206.0 3206 90.7800 34 2450 1 chr4B.!!$R1 2416
2 TraesCS4D01G205300 chr4A 112766831 112769223 2392 False 1267.5 1977 92.0825 657 2450 2 chr4A.!!$F1 1793

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
569 577 0.109319 CTGAACGGCCCAAATTTCGG 60.109 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1958 0.395724 TCGAGCATGAGCCAGAGGTA 60.396 55.0 0.0 0.0 43.56 3.08 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
26 27 9.135843 GTTTGGTCCAACTTATATTTTTGCTAC 57.864 33.333 2.98 0.00 0.00 3.58
27 28 8.410673 TTGGTCCAACTTATATTTTTGCTACA 57.589 30.769 0.00 0.00 0.00 2.74
28 29 8.050778 TGGTCCAACTTATATTTTTGCTACAG 57.949 34.615 0.00 0.00 0.00 2.74
29 30 7.668052 TGGTCCAACTTATATTTTTGCTACAGT 59.332 33.333 0.00 0.00 0.00 3.55
30 31 7.968405 GGTCCAACTTATATTTTTGCTACAGTG 59.032 37.037 0.00 0.00 0.00 3.66
31 32 7.484959 GTCCAACTTATATTTTTGCTACAGTGC 59.515 37.037 0.00 0.00 0.00 4.40
32 33 6.468956 CCAACTTATATTTTTGCTACAGTGCG 59.531 38.462 0.00 0.00 35.36 5.34
38 39 0.320421 TTTGCTACAGTGCGACTCCC 60.320 55.000 0.00 0.00 35.36 4.30
40 41 1.292223 GCTACAGTGCGACTCCCAA 59.708 57.895 0.00 0.00 0.00 4.12
55 56 5.345741 CGACTCCCAATTTGTTAATTTGCTG 59.654 40.000 0.00 0.00 31.63 4.41
57 58 4.965814 TCCCAATTTGTTAATTTGCTGCA 58.034 34.783 0.00 0.00 31.63 4.41
133 134 1.851658 GGTTTGCTGAAACAACGCAT 58.148 45.000 2.50 0.00 42.95 4.73
143 144 6.920758 TGCTGAAACAACGCATAATTTTACTT 59.079 30.769 0.00 0.00 0.00 2.24
144 145 7.436673 TGCTGAAACAACGCATAATTTTACTTT 59.563 29.630 0.00 0.00 0.00 2.66
176 178 3.560896 CCAATGACTTTTTGGTTTGCTGG 59.439 43.478 0.00 0.00 39.05 4.85
186 188 0.315251 GGTTTGCTGGAGCCAACTTC 59.685 55.000 13.51 0.00 43.61 3.01
202 204 5.600696 CCAACTTCAATTTTTGCTACCACT 58.399 37.500 0.00 0.00 0.00 4.00
240 245 3.313526 GCTACATCGTCCAATCTTGCATT 59.686 43.478 0.00 0.00 0.00 3.56
259 264 5.755375 TGCATTTTTGCTTCCATCGTTTTTA 59.245 32.000 0.00 0.00 35.49 1.52
260 265 6.073873 TGCATTTTTGCTTCCATCGTTTTTAG 60.074 34.615 0.00 0.00 35.49 1.85
262 267 7.518211 GCATTTTTGCTTCCATCGTTTTTAGTT 60.518 33.333 0.00 0.00 0.00 2.24
263 268 7.835634 TTTTTGCTTCCATCGTTTTTAGTTT 57.164 28.000 0.00 0.00 0.00 2.66
264 269 7.835634 TTTTGCTTCCATCGTTTTTAGTTTT 57.164 28.000 0.00 0.00 0.00 2.43
265 270 6.820470 TTGCTTCCATCGTTTTTAGTTTTG 57.180 33.333 0.00 0.00 0.00 2.44
266 271 4.742659 TGCTTCCATCGTTTTTAGTTTTGC 59.257 37.500 0.00 0.00 0.00 3.68
267 272 4.982295 GCTTCCATCGTTTTTAGTTTTGCT 59.018 37.500 0.00 0.00 0.00 3.91
268 273 6.146898 GCTTCCATCGTTTTTAGTTTTGCTA 58.853 36.000 0.00 0.00 0.00 3.49
282 287 4.213482 AGTTTTGCTAGAACCAACGCTAAG 59.787 41.667 0.00 0.00 0.00 2.18
288 293 3.349488 AGAACCAACGCTAAGTTTTGC 57.651 42.857 0.00 0.00 42.02 3.68
308 313 3.025287 CTACCATTGTTGTTGGTTGCC 57.975 47.619 0.01 0.00 45.19 4.52
310 315 1.138661 ACCATTGTTGTTGGTTGCCAG 59.861 47.619 0.00 0.00 45.19 4.85
313 318 1.965754 TTGTTGTTGGTTGCCAGCCC 61.966 55.000 0.00 0.00 33.72 5.19
315 320 1.832167 TTGTTGGTTGCCAGCCCTC 60.832 57.895 0.00 0.00 33.72 4.30
316 321 2.203480 GTTGGTTGCCAGCCCTCA 60.203 61.111 0.00 0.00 33.81 3.86
317 322 2.203480 TTGGTTGCCAGCCCTCAC 60.203 61.111 0.00 0.00 33.81 3.51
318 323 3.067084 TTGGTTGCCAGCCCTCACA 62.067 57.895 0.00 0.00 33.81 3.58
320 325 2.048603 GGTTGCCAGCCCTCACATC 61.049 63.158 0.00 0.00 0.00 3.06
322 327 2.894257 TTGCCAGCCCTCACATCGT 61.894 57.895 0.00 0.00 0.00 3.73
326 331 1.607801 CCAGCCCTCACATCGTCTCA 61.608 60.000 0.00 0.00 0.00 3.27
336 341 7.210174 CCCTCACATCGTCTCAATTAATTCTA 58.790 38.462 0.00 0.00 0.00 2.10
337 342 7.710907 CCCTCACATCGTCTCAATTAATTCTAA 59.289 37.037 0.00 0.00 0.00 2.10
339 344 8.648557 TCACATCGTCTCAATTAATTCTAAGG 57.351 34.615 0.00 0.00 0.00 2.69
359 364 4.188511 GGGAGGGGGAGGGGGTAG 62.189 77.778 0.00 0.00 0.00 3.18
360 365 4.902258 GGAGGGGGAGGGGGTAGC 62.902 77.778 0.00 0.00 0.00 3.58
361 366 4.103928 GAGGGGGAGGGGGTAGCA 62.104 72.222 0.00 0.00 0.00 3.49
362 367 4.433194 AGGGGGAGGGGGTAGCAC 62.433 72.222 0.00 0.00 0.00 4.40
421 426 3.368427 CGATAGACAGATGGGTGTTGTGT 60.368 47.826 0.00 0.00 39.76 3.72
465 471 4.636206 GCATGTCTCCCGAGTTTTCTTATT 59.364 41.667 0.00 0.00 0.00 1.40
478 484 8.921132 CGAGTTTTCTTATTAGATTTTTACGCG 58.079 33.333 3.53 3.53 0.00 6.01
495 502 1.941325 GCGAGACGATTGGGATTTCT 58.059 50.000 0.00 0.00 0.00 2.52
504 512 7.371159 AGACGATTGGGATTTCTTTTTCTTTC 58.629 34.615 0.00 0.00 0.00 2.62
514 522 8.898761 GGATTTCTTTTTCTTTCCTCTAGATCC 58.101 37.037 0.00 0.00 0.00 3.36
547 555 3.308595 TGTGATTTTATCCAACGCTAGCG 59.691 43.478 34.27 34.27 46.03 4.26
569 577 0.109319 CTGAACGGCCCAAATTTCGG 60.109 55.000 0.00 0.00 0.00 4.30
575 583 2.938086 GCCCAAATTTCGGCCGGTT 61.938 57.895 27.83 15.22 39.39 4.44
576 584 1.668867 CCCAAATTTCGGCCGGTTT 59.331 52.632 27.83 20.16 0.00 3.27
655 663 5.531122 AAAGGTTTTTAGTGGAAAGGCTC 57.469 39.130 0.00 0.00 0.00 4.70
734 743 3.801068 TTTGTCACCCCGCCCCTTG 62.801 63.158 0.00 0.00 0.00 3.61
777 793 0.749454 AATTGAGGCACGCCCATCTC 60.749 55.000 3.95 0.00 36.58 2.75
991 1007 0.951040 CCCGACACCTCAAGCTCAAC 60.951 60.000 0.00 0.00 0.00 3.18
1452 1468 1.729586 AGTTCACCAGCAACTAGGGA 58.270 50.000 0.00 0.00 32.08 4.20
1453 1469 1.625818 AGTTCACCAGCAACTAGGGAG 59.374 52.381 0.00 0.00 32.08 4.30
1454 1470 0.984230 TTCACCAGCAACTAGGGAGG 59.016 55.000 0.00 0.00 0.00 4.30
1455 1471 0.909610 TCACCAGCAACTAGGGAGGG 60.910 60.000 0.00 0.00 0.00 4.30
1456 1472 0.909610 CACCAGCAACTAGGGAGGGA 60.910 60.000 0.00 0.00 0.00 4.20
1457 1473 0.178873 ACCAGCAACTAGGGAGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
1491 1510 3.562779 TTCCGTCGCCGTGTTCTCC 62.563 63.158 0.00 0.00 0.00 3.71
1500 1522 1.470112 GCCGTGTTCTCCTCTAGCTTC 60.470 57.143 0.00 0.00 0.00 3.86
1535 1557 2.597305 GTCGTGTCCATGTGTATCGTTC 59.403 50.000 0.00 0.00 0.00 3.95
1598 1620 3.129287 GTGATGGACGGCTTTGATTTCAT 59.871 43.478 0.00 0.00 0.00 2.57
1606 1628 5.418676 ACGGCTTTGATTTCATTTAATGGG 58.581 37.500 5.02 0.00 0.00 4.00
1616 1641 7.454380 TGATTTCATTTAATGGGAGAGGTTGTT 59.546 33.333 5.02 0.00 0.00 2.83
1764 1798 1.741770 GATGCGTTTGGCCTCTCGT 60.742 57.895 3.32 0.00 42.61 4.18
1768 1802 1.006102 CGTTTGGCCTCTCGTCACT 60.006 57.895 3.32 0.00 0.00 3.41
1831 1865 6.149973 CAGTAAGCAATCATCCTCTGTTTTCA 59.850 38.462 0.00 0.00 0.00 2.69
1849 1883 2.354729 CCCCATTCCCGTGCTTGA 59.645 61.111 0.00 0.00 0.00 3.02
1855 1889 3.194542 CCCATTCCCGTGCTTGAATAAAA 59.805 43.478 0.00 0.00 30.31 1.52
1856 1890 4.141959 CCCATTCCCGTGCTTGAATAAAAT 60.142 41.667 0.00 0.00 30.31 1.82
1857 1891 4.805192 CCATTCCCGTGCTTGAATAAAATG 59.195 41.667 0.00 0.00 30.31 2.32
1858 1892 3.502191 TCCCGTGCTTGAATAAAATGC 57.498 42.857 0.00 0.00 0.00 3.56
1860 1894 3.509575 TCCCGTGCTTGAATAAAATGCTT 59.490 39.130 0.00 0.00 0.00 3.91
1862 1896 3.613737 CCGTGCTTGAATAAAATGCTTGG 59.386 43.478 0.00 0.00 0.00 3.61
1863 1897 4.236935 CGTGCTTGAATAAAATGCTTGGT 58.763 39.130 0.00 0.00 0.00 3.67
1864 1898 5.398169 CGTGCTTGAATAAAATGCTTGGTA 58.602 37.500 0.00 0.00 0.00 3.25
1865 1899 5.286082 CGTGCTTGAATAAAATGCTTGGTAC 59.714 40.000 0.00 0.00 0.00 3.34
1866 1900 6.389906 GTGCTTGAATAAAATGCTTGGTACT 58.610 36.000 0.00 0.00 0.00 2.73
1867 1901 6.528072 GTGCTTGAATAAAATGCTTGGTACTC 59.472 38.462 0.00 0.00 0.00 2.59
1919 1957 7.438160 GTGATTATGGTGACGATTATTGTCTGA 59.562 37.037 13.14 0.00 37.26 3.27
1920 1958 8.150296 TGATTATGGTGACGATTATTGTCTGAT 58.850 33.333 13.14 5.75 37.26 2.90
1929 1967 4.926238 CGATTATTGTCTGATACCTCTGGC 59.074 45.833 0.00 0.00 0.00 4.85
1958 1996 0.532862 AGAGTGTTGTTCGCCTGTGG 60.533 55.000 0.00 0.00 0.00 4.17
2085 2723 4.020662 GCCTGCTACTGATAGGAGCTTTAT 60.021 45.833 13.71 0.00 43.68 1.40
2136 2774 1.555075 ACACCACGGATGCTTCATACT 59.445 47.619 1.64 0.00 0.00 2.12
2137 2775 2.764010 ACACCACGGATGCTTCATACTA 59.236 45.455 1.64 0.00 0.00 1.82
2138 2776 3.123804 CACCACGGATGCTTCATACTAC 58.876 50.000 1.64 0.00 0.00 2.73
2243 2882 3.052455 TGCCGACTGATTATGTGTGTT 57.948 42.857 0.00 0.00 0.00 3.32
2264 2903 7.222417 TGTGTTGATGAAAACTAATTGTTGCTG 59.778 33.333 0.00 0.00 39.13 4.41
2270 2909 6.686630 TGAAAACTAATTGTTGCTGTATGGG 58.313 36.000 0.00 0.00 39.13 4.00
2288 2927 2.224892 TGGGCAGTACAATTTGTAGCCA 60.225 45.455 27.64 17.44 42.58 4.75
2294 2933 5.689819 CAGTACAATTTGTAGCCACAAGTC 58.310 41.667 9.49 0.00 45.17 3.01
2299 2938 2.823924 TTGTAGCCACAAGTCGCTTA 57.176 45.000 0.00 0.00 39.75 3.09
2391 3030 7.812690 TTATCATCTTGGATGAAATGTCTGG 57.187 36.000 13.15 0.00 0.00 3.86
2392 3031 5.183530 TCATCTTGGATGAAATGTCTGGT 57.816 39.130 7.64 0.00 0.00 4.00
2393 3032 4.945543 TCATCTTGGATGAAATGTCTGGTG 59.054 41.667 7.64 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.135843 GTAGCAAAAATATAAGTTGGACCAAAC 57.864 33.333 8.94 3.63 0.00 2.93
1 2 8.861086 TGTAGCAAAAATATAAGTTGGACCAAA 58.139 29.630 8.94 0.00 0.00 3.28
2 3 8.410673 TGTAGCAAAAATATAAGTTGGACCAA 57.589 30.769 1.69 1.69 0.00 3.67
3 4 7.668052 ACTGTAGCAAAAATATAAGTTGGACCA 59.332 33.333 0.00 0.00 0.00 4.02
4 5 7.968405 CACTGTAGCAAAAATATAAGTTGGACC 59.032 37.037 0.00 0.00 0.00 4.46
5 6 7.484959 GCACTGTAGCAAAAATATAAGTTGGAC 59.515 37.037 0.00 0.00 0.00 4.02
6 7 7.535139 GCACTGTAGCAAAAATATAAGTTGGA 58.465 34.615 0.00 0.00 0.00 3.53
7 8 6.468956 CGCACTGTAGCAAAAATATAAGTTGG 59.531 38.462 0.00 0.00 0.00 3.77
8 9 7.216317 GTCGCACTGTAGCAAAAATATAAGTTG 59.784 37.037 0.00 0.00 0.00 3.16
9 10 7.119262 AGTCGCACTGTAGCAAAAATATAAGTT 59.881 33.333 0.00 0.00 0.00 2.66
10 11 6.594159 AGTCGCACTGTAGCAAAAATATAAGT 59.406 34.615 0.00 0.00 0.00 2.24
11 12 7.005062 AGTCGCACTGTAGCAAAAATATAAG 57.995 36.000 0.00 0.00 0.00 1.73
12 13 6.036735 GGAGTCGCACTGTAGCAAAAATATAA 59.963 38.462 0.00 0.00 0.00 0.98
13 14 5.522460 GGAGTCGCACTGTAGCAAAAATATA 59.478 40.000 0.00 0.00 0.00 0.86
14 15 4.332819 GGAGTCGCACTGTAGCAAAAATAT 59.667 41.667 0.00 0.00 0.00 1.28
15 16 3.682858 GGAGTCGCACTGTAGCAAAAATA 59.317 43.478 0.00 0.00 0.00 1.40
16 17 2.484264 GGAGTCGCACTGTAGCAAAAAT 59.516 45.455 0.00 0.00 0.00 1.82
17 18 1.871039 GGAGTCGCACTGTAGCAAAAA 59.129 47.619 0.00 0.00 0.00 1.94
18 19 1.508632 GGAGTCGCACTGTAGCAAAA 58.491 50.000 0.00 0.00 0.00 2.44
19 20 0.320421 GGGAGTCGCACTGTAGCAAA 60.320 55.000 1.64 0.00 0.00 3.68
20 21 1.292223 GGGAGTCGCACTGTAGCAA 59.708 57.895 1.64 0.00 0.00 3.91
21 22 1.468506 TTGGGAGTCGCACTGTAGCA 61.469 55.000 9.78 0.00 0.00 3.49
22 23 0.108138 ATTGGGAGTCGCACTGTAGC 60.108 55.000 9.78 0.00 0.00 3.58
23 24 2.386661 AATTGGGAGTCGCACTGTAG 57.613 50.000 9.78 0.00 0.00 2.74
24 25 2.224426 ACAAATTGGGAGTCGCACTGTA 60.224 45.455 9.78 0.00 0.00 2.74
25 26 1.238439 CAAATTGGGAGTCGCACTGT 58.762 50.000 9.78 0.00 0.00 3.55
26 27 1.238439 ACAAATTGGGAGTCGCACTG 58.762 50.000 9.78 9.96 0.00 3.66
27 28 1.981256 AACAAATTGGGAGTCGCACT 58.019 45.000 9.78 1.27 0.00 4.40
28 29 3.907894 TTAACAAATTGGGAGTCGCAC 57.092 42.857 9.78 0.00 0.00 5.34
29 30 5.226396 CAAATTAACAAATTGGGAGTCGCA 58.774 37.500 5.66 5.66 0.00 5.10
30 31 4.091365 GCAAATTAACAAATTGGGAGTCGC 59.909 41.667 0.00 0.00 0.00 5.19
31 32 5.345741 CAGCAAATTAACAAATTGGGAGTCG 59.654 40.000 0.00 0.00 0.00 4.18
32 33 5.120674 GCAGCAAATTAACAAATTGGGAGTC 59.879 40.000 0.00 0.00 0.00 3.36
38 39 4.213694 TGGCTGCAGCAAATTAACAAATTG 59.786 37.500 37.63 0.00 44.36 2.32
40 41 4.005487 TGGCTGCAGCAAATTAACAAAT 57.995 36.364 37.63 0.00 44.36 2.32
113 114 0.524392 TGCGTTGTTTCAGCAAACCG 60.524 50.000 0.00 0.00 41.25 4.44
176 178 4.686091 GGTAGCAAAAATTGAAGTTGGCTC 59.314 41.667 7.83 2.34 0.00 4.70
186 188 4.320608 ACACCAGTGGTAGCAAAAATTG 57.679 40.909 16.22 0.59 32.11 2.32
220 222 5.895636 AAAATGCAAGATTGGACGATGTA 57.104 34.783 0.00 0.00 0.00 2.29
240 245 7.675170 GCAAAACTAAAAACGATGGAAGCAAAA 60.675 33.333 0.00 0.00 0.00 2.44
259 264 2.572290 AGCGTTGGTTCTAGCAAAACT 58.428 42.857 0.00 0.00 37.34 2.66
260 265 4.024302 ACTTAGCGTTGGTTCTAGCAAAAC 60.024 41.667 0.00 0.00 37.34 2.43
262 267 3.735591 ACTTAGCGTTGGTTCTAGCAAA 58.264 40.909 0.00 0.00 37.34 3.68
263 268 3.396260 ACTTAGCGTTGGTTCTAGCAA 57.604 42.857 0.00 0.00 32.60 3.91
264 269 3.396260 AACTTAGCGTTGGTTCTAGCA 57.604 42.857 0.00 0.00 33.72 3.49
265 270 4.464112 CAAAACTTAGCGTTGGTTCTAGC 58.536 43.478 0.00 0.00 35.61 3.42
266 271 4.213482 AGCAAAACTTAGCGTTGGTTCTAG 59.787 41.667 0.00 0.00 35.61 2.43
267 272 4.131596 AGCAAAACTTAGCGTTGGTTCTA 58.868 39.130 0.00 0.00 35.61 2.10
268 273 2.949644 AGCAAAACTTAGCGTTGGTTCT 59.050 40.909 0.00 0.00 35.61 3.01
307 312 1.142748 GAGACGATGTGAGGGCTGG 59.857 63.158 0.00 0.00 0.00 4.85
308 313 0.247460 TTGAGACGATGTGAGGGCTG 59.753 55.000 0.00 0.00 0.00 4.85
310 315 2.029838 AATTGAGACGATGTGAGGGC 57.970 50.000 0.00 0.00 0.00 5.19
313 318 8.759641 CCTTAGAATTAATTGAGACGATGTGAG 58.240 37.037 5.17 0.00 0.00 3.51
315 320 7.041780 CCCCTTAGAATTAATTGAGACGATGTG 60.042 40.741 5.17 0.00 0.00 3.21
316 321 6.992715 CCCCTTAGAATTAATTGAGACGATGT 59.007 38.462 5.17 0.00 0.00 3.06
317 322 6.428159 CCCCCTTAGAATTAATTGAGACGATG 59.572 42.308 5.17 0.00 0.00 3.84
318 323 6.534634 CCCCCTTAGAATTAATTGAGACGAT 58.465 40.000 5.17 0.00 0.00 3.73
345 350 4.433194 GTGCTACCCCCTCCCCCT 62.433 72.222 0.00 0.00 0.00 4.79
376 381 2.709475 GACCATCGCCGTTGATGC 59.291 61.111 8.24 0.00 43.52 3.91
378 383 1.518572 GTCGACCATCGCCGTTGAT 60.519 57.895 3.51 0.00 40.21 2.57
381 386 2.025418 GTTGTCGACCATCGCCGTT 61.025 57.895 14.12 0.00 40.21 4.44
398 403 2.832129 ACAACACCCATCTGTCTATCGT 59.168 45.455 0.00 0.00 0.00 3.73
402 407 2.969262 TCACACAACACCCATCTGTCTA 59.031 45.455 0.00 0.00 0.00 2.59
407 412 1.810031 CGTGTCACACAACACCCATCT 60.810 52.381 9.06 0.00 45.41 2.90
421 426 2.037367 CCCTCCTCCTCCGTGTCA 59.963 66.667 0.00 0.00 0.00 3.58
442 447 2.100605 AGAAAACTCGGGAGACATGC 57.899 50.000 2.08 0.00 33.60 4.06
465 471 4.501559 CCAATCGTCTCGCGTAAAAATCTA 59.498 41.667 5.77 0.00 42.13 1.98
478 484 6.502136 AGAAAAAGAAATCCCAATCGTCTC 57.498 37.500 0.00 0.00 0.00 3.36
494 501 5.517054 CGTCGGATCTAGAGGAAAGAAAAAG 59.483 44.000 0.00 0.00 0.00 2.27
495 502 5.408356 CGTCGGATCTAGAGGAAAGAAAAA 58.592 41.667 0.00 0.00 0.00 1.94
504 512 2.569059 TGTAACCGTCGGATCTAGAGG 58.431 52.381 20.51 0.00 0.00 3.69
514 522 5.292345 TGGATAAAATCACATGTAACCGTCG 59.708 40.000 0.00 0.00 0.00 5.12
547 555 0.033366 AAATTTGGGCCGTTCAGCAC 59.967 50.000 0.00 0.00 36.41 4.40
575 583 4.794648 AATGCTAGGCGCCGGCAA 62.795 61.111 38.38 26.96 42.47 4.52
582 590 4.051922 AGAATTAAGACGAATGCTAGGCG 58.948 43.478 0.00 0.00 0.00 5.52
584 592 5.977725 TCGAAGAATTAAGACGAATGCTAGG 59.022 40.000 0.00 0.00 0.00 3.02
637 645 2.228103 CCCGAGCCTTTCCACTAAAAAC 59.772 50.000 0.00 0.00 0.00 2.43
655 663 1.202268 TGTTTTTGTAAACGCACCCCG 60.202 47.619 0.00 0.00 45.29 5.73
734 743 1.227674 CAGGCTCGTATGGCTTCCC 60.228 63.158 0.00 0.00 41.04 3.97
777 793 1.448540 GAGTGCACGGTGGAGATGG 60.449 63.158 12.01 0.00 0.00 3.51
1152 1168 2.158645 GCTCTTCTTGTTCTTCTTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
1452 1468 2.866454 ACCCTAGAGATACACCTTCCCT 59.134 50.000 0.00 0.00 0.00 4.20
1453 1469 3.331718 ACCCTAGAGATACACCTTCCC 57.668 52.381 0.00 0.00 0.00 3.97
1454 1470 3.642377 GGAACCCTAGAGATACACCTTCC 59.358 52.174 0.00 0.00 0.00 3.46
1455 1471 3.318557 CGGAACCCTAGAGATACACCTTC 59.681 52.174 0.00 0.00 0.00 3.46
1456 1472 3.297736 CGGAACCCTAGAGATACACCTT 58.702 50.000 0.00 0.00 0.00 3.50
1457 1473 2.244252 ACGGAACCCTAGAGATACACCT 59.756 50.000 0.00 0.00 0.00 4.00
1491 1510 1.337260 ACGGCAACACAGAAGCTAGAG 60.337 52.381 0.00 0.00 0.00 2.43
1500 1522 3.403057 CGACCGACGGCAACACAG 61.403 66.667 15.39 0.00 38.46 3.66
1535 1557 1.897615 AGGCGCGCTACCTACCTAG 60.898 63.158 32.29 0.00 35.10 3.02
1598 1620 5.300792 GTCACAAACAACCTCTCCCATTAAA 59.699 40.000 0.00 0.00 0.00 1.52
1606 1628 4.442706 TGAGAAGTCACAAACAACCTCTC 58.557 43.478 0.00 0.00 0.00 3.20
1616 1641 4.020751 AGCTAGCAGATTGAGAAGTCACAA 60.021 41.667 18.83 0.00 30.10 3.33
1718 1746 1.061411 CGCAACATCATCGGCAGTG 59.939 57.895 0.00 0.00 0.00 3.66
1719 1747 1.079197 TCGCAACATCATCGGCAGT 60.079 52.632 0.00 0.00 0.00 4.40
1831 1865 2.035626 CAAGCACGGGAATGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
1849 1883 8.686334 CATACAAGGAGTACCAAGCATTTTATT 58.314 33.333 0.00 0.00 38.94 1.40
1855 1889 3.545703 GCATACAAGGAGTACCAAGCAT 58.454 45.455 0.00 0.00 38.94 3.79
1856 1890 2.676750 CGCATACAAGGAGTACCAAGCA 60.677 50.000 0.00 0.00 38.94 3.91
1857 1891 1.933853 CGCATACAAGGAGTACCAAGC 59.066 52.381 0.00 0.00 38.94 4.01
1858 1892 3.520290 TCGCATACAAGGAGTACCAAG 57.480 47.619 0.00 0.00 38.94 3.61
1860 1894 3.028130 TCATCGCATACAAGGAGTACCA 58.972 45.455 0.00 0.00 38.94 3.25
1862 1896 5.050091 CCAATTCATCGCATACAAGGAGTAC 60.050 44.000 0.00 0.00 35.05 2.73
1863 1897 5.056480 CCAATTCATCGCATACAAGGAGTA 58.944 41.667 0.00 0.00 37.06 2.59
1864 1898 3.879295 CCAATTCATCGCATACAAGGAGT 59.121 43.478 0.00 0.00 0.00 3.85
1865 1899 3.879295 ACCAATTCATCGCATACAAGGAG 59.121 43.478 0.00 0.00 0.00 3.69
1866 1900 3.627123 CACCAATTCATCGCATACAAGGA 59.373 43.478 0.00 0.00 0.00 3.36
1867 1901 3.793129 GCACCAATTCATCGCATACAAGG 60.793 47.826 0.00 0.00 0.00 3.61
1919 1957 0.678395 CGAGCATGAGCCAGAGGTAT 59.322 55.000 0.00 0.00 43.56 2.73
1920 1958 0.395724 TCGAGCATGAGCCAGAGGTA 60.396 55.000 0.00 0.00 43.56 3.08
1929 1967 2.360553 ACAACACTCTCGAGCATGAG 57.639 50.000 19.04 9.76 37.33 2.90
1958 1996 1.202405 CCACACCCAAACAACTTCAGC 60.202 52.381 0.00 0.00 0.00 4.26
2085 2723 8.547481 TGTAACTGTCCAGAGGAATCATATTA 57.453 34.615 0.40 0.00 31.38 0.98
2098 2736 3.684788 GGTGTTGCTATGTAACTGTCCAG 59.315 47.826 0.00 0.00 0.00 3.86
2136 2774 7.333423 CCGTGATAAAGTTCTCAAAAGATGGTA 59.667 37.037 0.00 0.00 0.00 3.25
2137 2775 6.149474 CCGTGATAAAGTTCTCAAAAGATGGT 59.851 38.462 0.00 0.00 0.00 3.55
2138 2776 6.403636 CCCGTGATAAAGTTCTCAAAAGATGG 60.404 42.308 0.00 0.00 0.00 3.51
2243 2882 8.028354 CCATACAGCAACAATTAGTTTTCATCA 58.972 33.333 0.00 0.00 38.74 3.07
2264 2903 4.036380 GGCTACAAATTGTACTGCCCATAC 59.964 45.833 19.71 1.68 37.89 2.39
2270 2909 4.023193 ACTTGTGGCTACAAATTGTACTGC 60.023 41.667 16.89 5.38 45.53 4.40
2288 2927 2.884639 ACTTTTGGCATAAGCGACTTGT 59.115 40.909 16.21 0.00 43.41 3.16
2294 2933 3.063997 CCAGTCTACTTTTGGCATAAGCG 59.936 47.826 16.21 8.87 43.41 4.68
2299 2938 2.558359 GCAACCAGTCTACTTTTGGCAT 59.442 45.455 0.00 0.00 35.35 4.40
2360 2999 5.114764 TCATCCAAGATGATAAAGTGCCA 57.885 39.130 3.17 0.00 0.00 4.92
2391 3030 9.736023 AACTAGAGATGAAAACAAATTGTTCAC 57.264 29.630 12.11 9.53 40.14 3.18


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

AutoCloner maintained by Alex Coulton.