Multiple sequence alignment - TraesCS4D01G093700

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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 TraesCS4D01G093700 chr4D 100.000 2639 0 0 1 2639 69214856 69212218 0.000000e+00 4874.0
1 TraesCS4D01G093700 chr4B 90.605 2150 144 34 1 2136 101939282 101937177 0.000000e+00 2798.0
2 TraesCS4D01G093700 chr4B 75.231 432 92 12 9 434 21482420 21482842 9.640000e-45 191.0
3 TraesCS4D01G093700 chr4A 89.582 1267 93 20 119 1373 520955884 520954645 0.000000e+00 1572.0
4 TraesCS4D01G093700 chr4A 95.585 453 15 1 1321 1768 520954661 520954209 0.000000e+00 721.0
5 TraesCS4D01G093700 chr4A 75.683 366 68 13 13 370 152758290 152758642 2.100000e-36 163.0
6 TraesCS4D01G093700 chr6D 97.239 507 11 3 2136 2639 86132920 86132414 0.000000e+00 856.0
7 TraesCS4D01G093700 chr1D 97.845 464 7 3 2177 2639 466939046 466939507 0.000000e+00 798.0
8 TraesCS4D01G093700 chr1D 96.507 229 7 1 2146 2373 466938819 466939047 6.900000e-101 377.0
9 TraesCS4D01G093700 chr2D 93.151 438 27 3 2137 2571 433238804 433238367 7.960000e-180 640.0
10 TraesCS4D01G093700 chr2D 95.385 65 3 0 2575 2639 433238237 433238173 1.290000e-18 104.0
11 TraesCS4D01G093700 chr6B 85.656 488 58 5 2146 2632 572666801 572667277 1.090000e-138 503.0
12 TraesCS4D01G093700 chr6B 85.992 257 30 6 2146 2399 572667927 572667674 1.200000e-68 270.0
13 TraesCS4D01G093700 chr3B 88.327 257 25 5 2145 2399 412249532 412249785 1.190000e-78 303.0
14 TraesCS4D01G093700 chr3B 81.203 399 39 8 2146 2542 412250621 412250257 3.320000e-74 289.0
15 TraesCS4D01G093700 chr3B 100.000 51 0 0 2584 2634 412250257 412250207 7.780000e-16 95.3
16 TraesCS4D01G093700 chr5B 86.154 260 28 5 2146 2404 663632028 663632280 9.310000e-70 274.0
17 TraesCS4D01G093700 chr5B 86.260 262 24 8 2140 2399 663633270 663633019 9.310000e-70 274.0
18 TraesCS4D01G093700 chr5B 86.620 142 17 2 2402 2542 663632412 663632552 3.520000e-34 156.0
19 TraesCS4D01G093700 chr5B 74.103 390 92 7 14 399 701055153 701054769 4.550000e-33 152.0
20 TraesCS4D01G093700 chr5B 98.214 56 1 0 2584 2639 663632552 663632607 6.010000e-17 99.0
21 TraesCS4D01G093700 chr7D 91.071 112 9 1 2527 2637 582056258 582056369 1.640000e-32 150.0
22 TraesCS4D01G093700 chr3D 78.090 178 34 3 208 383 84919351 84919177 9.990000e-20 108.0
23 TraesCS4D01G093700 chr3D 74.460 278 48 15 153 424 7577326 7577586 6.010000e-17 99.0
24 TraesCS4D01G093700 chr3D 73.646 277 54 13 113 383 519879016 519879279 3.620000e-14 89.8
25 TraesCS4D01G093700 chr6A 74.340 265 58 4 12 276 93934385 93934131 1.290000e-18 104.0
26 TraesCS4D01G093700 chr5A 73.896 249 63 2 12 259 633966079 633966326 6.010000e-17 99.0
27 TraesCS4D01G093700 chr5A 92.000 50 4 0 227 276 476838925 476838876 1.310000e-08 71.3
28 TraesCS4D01G093700 chr5A 93.333 45 3 0 219 263 534095261 534095305 1.700000e-07 67.6


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 TraesCS4D01G093700 chr4D 69212218 69214856 2638 True 4874.0 4874 100.0000 1 2639 1 chr4D.!!$R1 2638
1 TraesCS4D01G093700 chr4B 101937177 101939282 2105 True 2798.0 2798 90.6050 1 2136 1 chr4B.!!$R1 2135
2 TraesCS4D01G093700 chr4A 520954209 520955884 1675 True 1146.5 1572 92.5835 119 1768 2 chr4A.!!$R1 1649
3 TraesCS4D01G093700 chr6D 86132414 86132920 506 True 856.0 856 97.2390 2136 2639 1 chr6D.!!$R1 503
4 TraesCS4D01G093700 chr1D 466938819 466939507 688 False 587.5 798 97.1760 2146 2639 2 chr1D.!!$F1 493
5 TraesCS4D01G093700 chr2D 433238173 433238804 631 True 372.0 640 94.2680 2137 2639 2 chr2D.!!$R1 502

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
829 842 0.0293 AACTCAACGCATGCACACAC 59.971 50.0 19.57 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1860 1.11715 CCCATTTGCTCCCTTGATGG 58.883 55.0 0.0 0.0 37.57 3.51 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
23 24 3.869065 TGGTGACGTTTCTTCTTTGAGT 58.131 40.909 0.00 0.00 0.00 3.41
33 34 6.192863 CGTTTCTTCTTTGAGTTTGTCTTTCG 59.807 38.462 0.00 0.00 0.00 3.46
55 56 3.204526 GACTCCGATCTTCCTCGACTTA 58.795 50.000 0.00 0.00 41.12 2.24
64 65 5.369409 TCTTCCTCGACTTAGTCCATCTA 57.631 43.478 6.80 0.00 0.00 1.98
67 68 5.831702 TCCTCGACTTAGTCCATCTAAAC 57.168 43.478 6.80 0.00 38.05 2.01
76 77 7.192232 ACTTAGTCCATCTAAACGTAATCGAC 58.808 38.462 0.00 0.00 38.05 4.20
77 78 6.194463 TTAGTCCATCTAAACGTAATCGACG 58.806 40.000 0.00 0.00 43.77 5.12
98 99 3.372954 GGAGTTCCGACGTAGATTCATG 58.627 50.000 0.00 0.00 0.00 3.07
99 100 3.181489 GGAGTTCCGACGTAGATTCATGT 60.181 47.826 0.00 0.00 0.00 3.21
100 101 4.421948 GAGTTCCGACGTAGATTCATGTT 58.578 43.478 0.00 0.00 0.00 2.71
102 103 3.861276 TCCGACGTAGATTCATGTTGT 57.139 42.857 0.00 0.00 0.00 3.32
109 110 5.171476 ACGTAGATTCATGTTGTCTCCTTG 58.829 41.667 0.00 0.00 0.00 3.61
110 111 5.171476 CGTAGATTCATGTTGTCTCCTTGT 58.829 41.667 0.00 0.00 0.00 3.16
111 112 5.062683 CGTAGATTCATGTTGTCTCCTTGTG 59.937 44.000 0.00 0.00 0.00 3.33
112 113 4.330250 AGATTCATGTTGTCTCCTTGTGG 58.670 43.478 0.00 0.00 0.00 4.17
113 114 3.576078 TTCATGTTGTCTCCTTGTGGT 57.424 42.857 0.00 0.00 34.23 4.16
114 115 2.849942 TCATGTTGTCTCCTTGTGGTG 58.150 47.619 0.00 0.00 34.23 4.17
115 116 1.881973 CATGTTGTCTCCTTGTGGTGG 59.118 52.381 0.00 0.00 34.23 4.61
116 117 0.916086 TGTTGTCTCCTTGTGGTGGT 59.084 50.000 0.00 0.00 34.23 4.16
117 118 1.308998 GTTGTCTCCTTGTGGTGGTG 58.691 55.000 0.00 0.00 34.23 4.17
123 124 1.697432 CTCCTTGTGGTGGTGAGGTTA 59.303 52.381 0.00 0.00 34.23 2.85
133 134 2.370849 GTGGTGAGGTTAGGGTTTCTCA 59.629 50.000 0.00 0.00 34.34 3.27
136 137 3.263425 GGTGAGGTTAGGGTTTCTCATCA 59.737 47.826 0.00 0.00 37.34 3.07
139 140 2.904434 AGGTTAGGGTTTCTCATCACGT 59.096 45.455 0.00 0.00 0.00 4.49
148 149 0.243636 TCTCATCACGTGTGTGCGAT 59.756 50.000 16.51 0.00 46.01 4.58
150 151 0.038709 TCATCACGTGTGTGCGATGA 60.039 50.000 16.51 12.92 46.01 2.92
154 155 0.367887 CACGTGTGTGCGATGATGAG 59.632 55.000 7.58 0.00 39.67 2.90
164 165 3.127548 GTGCGATGATGAGATTTGGTGTT 59.872 43.478 0.00 0.00 0.00 3.32
169 170 6.481134 CGATGATGAGATTTGGTGTTAGTTG 58.519 40.000 0.00 0.00 0.00 3.16
170 171 5.627499 TGATGAGATTTGGTGTTAGTTGC 57.373 39.130 0.00 0.00 0.00 4.17
173 174 5.689383 TGAGATTTGGTGTTAGTTGCTTC 57.311 39.130 0.00 0.00 0.00 3.86
178 179 6.491403 AGATTTGGTGTTAGTTGCTTCTGATT 59.509 34.615 0.00 0.00 0.00 2.57
183 184 7.816640 TGGTGTTAGTTGCTTCTGATTTATTC 58.183 34.615 0.00 0.00 0.00 1.75
189 191 4.989279 TGCTTCTGATTTATTCAAGGGC 57.011 40.909 0.00 0.00 32.78 5.19
191 193 4.641989 TGCTTCTGATTTATTCAAGGGCTC 59.358 41.667 0.00 0.00 32.78 4.70
216 218 1.648174 GACGACTACGGCTCTAGGC 59.352 63.158 0.00 0.00 45.04 3.93
225 227 2.269241 GCTCTAGGCCGCTGGTTT 59.731 61.111 0.00 0.00 34.27 3.27
248 250 2.186826 GGGCACGTGCACAAAGACT 61.187 57.895 38.60 0.00 45.57 3.24
250 252 0.100503 GGCACGTGCACAAAGACTTT 59.899 50.000 38.60 0.00 44.36 2.66
251 253 1.469079 GGCACGTGCACAAAGACTTTT 60.469 47.619 38.60 0.00 44.36 2.27
253 255 2.101125 CACGTGCACAAAGACTTTTCG 58.899 47.619 18.64 0.02 0.00 3.46
262 264 5.619981 GCACAAAGACTTTTCGGCTATCATT 60.620 40.000 0.00 0.00 0.00 2.57
280 282 1.865865 TTGACAAGGTCAAGCGACTC 58.134 50.000 7.66 0.00 45.88 3.36
281 283 1.040646 TGACAAGGTCAAGCGACTCT 58.959 50.000 0.00 0.00 39.78 3.24
282 284 1.269778 TGACAAGGTCAAGCGACTCTG 60.270 52.381 0.00 0.00 39.78 3.35
284 286 1.004440 AAGGTCAAGCGACTCTGGC 60.004 57.895 0.00 0.00 42.21 4.85
285 287 1.758440 AAGGTCAAGCGACTCTGGCA 61.758 55.000 0.00 0.00 42.21 4.92
286 288 1.739562 GGTCAAGCGACTCTGGCAG 60.740 63.158 8.58 8.58 42.21 4.85
332 334 1.263776 GACGACTCATTCTGACAGCG 58.736 55.000 0.00 0.00 0.00 5.18
335 337 1.132453 CGACTCATTCTGACAGCGGTA 59.868 52.381 0.00 0.00 0.00 4.02
338 340 3.353557 ACTCATTCTGACAGCGGTAGTA 58.646 45.455 0.00 0.00 0.00 1.82
339 341 3.378742 ACTCATTCTGACAGCGGTAGTAG 59.621 47.826 0.00 0.00 0.00 2.57
340 342 3.353557 TCATTCTGACAGCGGTAGTAGT 58.646 45.455 0.00 0.00 0.00 2.73
341 343 3.377485 TCATTCTGACAGCGGTAGTAGTC 59.623 47.826 0.00 0.00 0.00 2.59
342 344 1.366679 TCTGACAGCGGTAGTAGTCG 58.633 55.000 0.00 0.00 33.83 4.18
343 345 1.085091 CTGACAGCGGTAGTAGTCGT 58.915 55.000 0.00 0.00 33.83 4.34
344 346 1.467734 CTGACAGCGGTAGTAGTCGTT 59.532 52.381 0.00 0.00 33.83 3.85
345 347 1.881973 TGACAGCGGTAGTAGTCGTTT 59.118 47.619 0.00 0.00 33.83 3.60
346 348 2.248487 GACAGCGGTAGTAGTCGTTTG 58.752 52.381 0.00 0.00 0.00 2.93
347 349 1.068055 ACAGCGGTAGTAGTCGTTTGG 60.068 52.381 0.00 0.00 0.00 3.28
353 355 1.205655 GTAGTAGTCGTTTGGGGTCCC 59.794 57.143 0.00 0.00 0.00 4.46
402 409 8.588290 ATGTTTTATGTGCTTTATACTTGGGA 57.412 30.769 0.00 0.00 0.00 4.37
413 422 9.555727 TGCTTTATACTTGGGATGAACTTATAC 57.444 33.333 0.00 0.00 0.00 1.47
487 499 3.629855 TCCTCTCAGAGCTCATAACTTCG 59.370 47.826 17.77 0.00 0.00 3.79
488 500 3.629855 CCTCTCAGAGCTCATAACTTCGA 59.370 47.826 17.77 0.00 0.00 3.71
489 501 4.261155 CCTCTCAGAGCTCATAACTTCGAG 60.261 50.000 17.77 9.14 0.00 4.04
490 502 3.629855 TCTCAGAGCTCATAACTTCGAGG 59.370 47.826 17.77 0.00 0.00 4.63
491 503 3.357203 TCAGAGCTCATAACTTCGAGGT 58.643 45.455 17.77 0.00 42.42 3.85
492 504 3.764434 TCAGAGCTCATAACTTCGAGGTT 59.236 43.478 17.55 17.55 39.95 3.50
493 505 4.109050 CAGAGCTCATAACTTCGAGGTTC 58.891 47.826 16.93 2.06 39.95 3.62
494 506 3.109619 GAGCTCATAACTTCGAGGTTCG 58.890 50.000 16.93 9.56 39.95 3.95
532 544 4.082625 TGTGCCATCAACATCAGAAATCAC 60.083 41.667 0.00 0.00 0.00 3.06
551 564 7.856145 AATCACACACTTATCTTCTCCATTC 57.144 36.000 0.00 0.00 0.00 2.67
828 841 0.737804 AAACTCAACGCATGCACACA 59.262 45.000 19.57 0.00 0.00 3.72
829 842 0.029300 AACTCAACGCATGCACACAC 59.971 50.000 19.57 0.00 0.00 3.82
830 843 0.815213 ACTCAACGCATGCACACACT 60.815 50.000 19.57 0.00 0.00 3.55
923 936 3.802675 GCCACCCACGACCTCTATAAATC 60.803 52.174 0.00 0.00 0.00 2.17
994 1011 5.771666 AGAGAGAGGATTTCATTGCAAAACA 59.228 36.000 1.71 0.00 0.00 2.83
1065 1082 0.393077 CGTTCAAGTGGGAGGTCTGT 59.607 55.000 0.00 0.00 0.00 3.41
1176 1193 3.866582 CCTCCCTCCATGGCGTCC 61.867 72.222 6.96 0.00 0.00 4.79
1357 1410 2.202756 CGAAGGAGTACGGCAGCC 60.203 66.667 0.00 0.00 0.00 4.85
1716 1774 9.618890 TTGTTGAAGAAATATAGGAGGAAGATG 57.381 33.333 0.00 0.00 0.00 2.90
1790 1849 3.378112 TGTCTGGAGACTGTTTGCTTTTG 59.622 43.478 8.24 0.00 44.99 2.44
1819 1878 2.148446 TCCATCAAGGGAGCAAATGG 57.852 50.000 0.00 0.00 38.58 3.16
1824 1883 2.213310 TCAAGGGAGCAAATGGGGATA 58.787 47.619 0.00 0.00 0.00 2.59
1846 1905 7.012704 GGATAAACAGTTGCTCACATGATGTAT 59.987 37.037 0.00 0.00 0.00 2.29
1872 1931 3.243907 CCGGGCAACAAAATAAAAGGACA 60.244 43.478 0.00 0.00 39.74 4.02
1891 1950 8.697507 AAGGACAGTGAATCTTAGAATTTGTT 57.302 30.769 0.00 0.00 0.00 2.83
1892 1951 8.697507 AGGACAGTGAATCTTAGAATTTGTTT 57.302 30.769 0.00 0.00 0.00 2.83
1960 2019 4.278170 AGAAAAATGCAATTCTCACGGACA 59.722 37.500 6.88 0.00 33.67 4.02
1976 2035 2.289694 CGGACAAAGAATCACTCACCCT 60.290 50.000 0.00 0.00 0.00 4.34
1990 2049 1.529948 ACCCTTCTCGTCGTGGACA 60.530 57.895 0.00 0.00 32.09 4.02
1999 2058 1.068895 TCGTCGTGGACAAAAAGCCTA 59.931 47.619 0.00 0.00 32.09 3.93
2002 2061 3.058501 CGTCGTGGACAAAAAGCCTATTT 60.059 43.478 0.00 0.00 32.09 1.40
2004 2063 5.286438 GTCGTGGACAAAAAGCCTATTTTT 58.714 37.500 0.00 0.00 30.31 1.94
2024 2083 4.349663 TTTATCCGATTTCGCACAAAGG 57.650 40.909 0.00 0.00 38.18 3.11
2025 2084 2.107950 ATCCGATTTCGCACAAAGGA 57.892 45.000 0.00 0.00 38.18 3.36
2032 2092 3.624326 TTTCGCACAAAGGATGTCTTG 57.376 42.857 0.00 0.00 41.46 3.02
2042 2102 7.467811 GCACAAAGGATGTCTTGGTTATGATAG 60.468 40.741 0.00 0.00 41.46 2.08
2052 2112 4.866508 TGGTTATGATAGCTACGGAAGG 57.133 45.455 0.00 0.00 0.00 3.46
2053 2113 4.476297 TGGTTATGATAGCTACGGAAGGA 58.524 43.478 0.00 0.00 0.00 3.36
2061 2121 6.411376 TGATAGCTACGGAAGGAAATGAAAA 58.589 36.000 0.00 0.00 0.00 2.29
2064 2124 4.695928 AGCTACGGAAGGAAATGAAAAGAC 59.304 41.667 0.00 0.00 0.00 3.01
2065 2125 4.454504 GCTACGGAAGGAAATGAAAAGACA 59.545 41.667 0.00 0.00 0.00 3.41
2098 2158 3.023119 AGCATCTCTAGCCGATATCCTG 58.977 50.000 0.00 0.00 0.00 3.86
2121 2181 1.123928 CCTGGCCGATCTCCTAAACT 58.876 55.000 0.00 0.00 0.00 2.66
2136 2196 7.468496 TCTCCTAAACTGGTTAGAGTTAGAGT 58.532 38.462 13.93 0.00 41.70 3.24
2137 2197 8.609483 TCTCCTAAACTGGTTAGAGTTAGAGTA 58.391 37.037 13.93 0.69 41.70 2.59
2138 2198 9.240734 CTCCTAAACTGGTTAGAGTTAGAGTAA 57.759 37.037 13.93 0.00 41.70 2.24
2139 2199 9.765295 TCCTAAACTGGTTAGAGTTAGAGTAAT 57.235 33.333 13.93 0.00 41.70 1.89
2211 2467 7.163441 TCGCTTTAGTCCCTGTACTTAAAAAT 58.837 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.373216 TCCGAAAGACAAACTCAAAGAAGAAA 59.627 34.615 0.00 0.00 0.00 2.52
33 34 0.664224 GTCGAGGAAGATCGGAGTCC 59.336 60.000 0.00 0.00 42.93 3.85
41 42 4.798882 AGATGGACTAAGTCGAGGAAGAT 58.201 43.478 0.00 0.00 32.65 2.40
44 45 5.163683 CGTTTAGATGGACTAAGTCGAGGAA 60.164 44.000 0.00 0.00 41.33 3.36
46 47 4.096081 ACGTTTAGATGGACTAAGTCGAGG 59.904 45.833 16.03 2.51 41.33 4.63
55 56 4.595116 CGTCGATTACGTTTAGATGGACT 58.405 43.478 0.00 0.00 46.72 3.85
77 78 3.181489 ACATGAATCTACGTCGGAACTCC 60.181 47.826 0.00 0.00 0.00 3.85
81 82 4.082408 AGACAACATGAATCTACGTCGGAA 60.082 41.667 0.00 0.00 0.00 4.30
90 91 4.202503 ACCACAAGGAGACAACATGAATCT 60.203 41.667 0.00 0.00 38.69 2.40
96 97 1.494721 ACCACCACAAGGAGACAACAT 59.505 47.619 0.00 0.00 38.69 2.71
98 99 1.134220 TCACCACCACAAGGAGACAAC 60.134 52.381 0.00 0.00 38.69 3.32
99 100 1.140852 CTCACCACCACAAGGAGACAA 59.859 52.381 0.00 0.00 38.69 3.18
100 101 0.758734 CTCACCACCACAAGGAGACA 59.241 55.000 0.00 0.00 38.69 3.41
102 103 0.399949 ACCTCACCACCACAAGGAGA 60.400 55.000 0.00 0.00 38.69 3.71
109 110 0.769247 AACCCTAACCTCACCACCAC 59.231 55.000 0.00 0.00 0.00 4.16
110 111 1.422402 GAAACCCTAACCTCACCACCA 59.578 52.381 0.00 0.00 0.00 4.17
111 112 1.703513 AGAAACCCTAACCTCACCACC 59.296 52.381 0.00 0.00 0.00 4.61
112 113 2.370849 TGAGAAACCCTAACCTCACCAC 59.629 50.000 0.00 0.00 31.45 4.16
113 114 2.696775 TGAGAAACCCTAACCTCACCA 58.303 47.619 0.00 0.00 31.45 4.17
114 115 3.263425 TGATGAGAAACCCTAACCTCACC 59.737 47.826 0.00 0.00 38.32 4.02
115 116 4.254492 GTGATGAGAAACCCTAACCTCAC 58.746 47.826 0.00 0.00 38.32 3.51
116 117 3.056107 CGTGATGAGAAACCCTAACCTCA 60.056 47.826 0.00 0.00 39.60 3.86
117 118 3.056035 ACGTGATGAGAAACCCTAACCTC 60.056 47.826 0.00 0.00 0.00 3.85
123 124 1.416401 ACACACGTGATGAGAAACCCT 59.584 47.619 25.01 0.00 0.00 4.34
133 134 1.001624 CATCATCGCACACACGTGAT 58.998 50.000 25.01 6.94 46.80 3.06
136 137 0.243636 TCTCATCATCGCACACACGT 59.756 50.000 0.00 0.00 0.00 4.49
139 140 2.679336 CCAAATCTCATCATCGCACACA 59.321 45.455 0.00 0.00 0.00 3.72
148 149 5.316167 AGCAACTAACACCAAATCTCATCA 58.684 37.500 0.00 0.00 0.00 3.07
150 151 6.006449 AGAAGCAACTAACACCAAATCTCAT 58.994 36.000 0.00 0.00 0.00 2.90
154 155 5.689383 TCAGAAGCAACTAACACCAAATC 57.311 39.130 0.00 0.00 0.00 2.17
164 165 6.095440 GCCCTTGAATAAATCAGAAGCAACTA 59.905 38.462 0.00 0.00 39.77 2.24
169 170 4.641989 TGAGCCCTTGAATAAATCAGAAGC 59.358 41.667 0.00 0.00 39.77 3.86
170 171 6.558909 GTTGAGCCCTTGAATAAATCAGAAG 58.441 40.000 0.00 0.00 39.77 2.85
173 174 4.201950 CCGTTGAGCCCTTGAATAAATCAG 60.202 45.833 0.00 0.00 39.77 2.90
178 179 1.459450 GCCGTTGAGCCCTTGAATAA 58.541 50.000 0.00 0.00 0.00 1.40
183 184 3.423154 GTCGCCGTTGAGCCCTTG 61.423 66.667 0.00 0.00 0.00 3.61
189 191 1.862147 CGTAGTCGTCGCCGTTGAG 60.862 63.158 0.00 0.00 35.01 3.02
191 193 2.872925 CCGTAGTCGTCGCCGTTG 60.873 66.667 0.00 0.00 35.01 4.10
212 214 0.034863 CCCTAAAAACCAGCGGCCTA 60.035 55.000 0.00 0.00 0.00 3.93
216 218 1.605165 TGCCCCTAAAAACCAGCGG 60.605 57.895 0.00 0.00 0.00 5.52
225 227 0.752009 TTTGTGCACGTGCCCCTAAA 60.752 50.000 35.72 25.52 41.18 1.85
248 250 4.331968 ACCTTGTCAATGATAGCCGAAAA 58.668 39.130 0.00 0.00 0.00 2.29
250 252 3.055458 TGACCTTGTCAATGATAGCCGAA 60.055 43.478 0.00 0.00 39.78 4.30
251 253 2.499693 TGACCTTGTCAATGATAGCCGA 59.500 45.455 0.00 0.00 39.78 5.54
262 264 1.040646 AGAGTCGCTTGACCTTGTCA 58.959 50.000 0.00 0.00 43.97 3.58
292 294 4.659874 GTGTCGTTGTTGCCGCCG 62.660 66.667 0.00 0.00 0.00 6.46
293 295 4.659874 CGTGTCGTTGTTGCCGCC 62.660 66.667 0.00 0.00 0.00 6.13
295 297 2.244382 GACGTGTCGTTGTTGCCG 59.756 61.111 0.00 0.00 41.37 5.69
296 298 2.244382 CGACGTGTCGTTGTTGCC 59.756 61.111 13.93 0.00 46.99 4.52
321 323 2.355132 CGACTACTACCGCTGTCAGAAT 59.645 50.000 3.32 0.00 0.00 2.40
332 334 1.205655 GGACCCCAAACGACTACTACC 59.794 57.143 0.00 0.00 0.00 3.18
335 337 1.538687 CGGGACCCCAAACGACTACT 61.539 60.000 4.46 0.00 35.37 2.57
338 340 2.524887 TCGGGACCCCAAACGACT 60.525 61.111 4.46 0.00 35.37 4.18
339 341 2.047560 CTCGGGACCCCAAACGAC 60.048 66.667 4.46 0.00 35.37 4.34
340 342 2.203669 TCTCGGGACCCCAAACGA 60.204 61.111 4.46 0.00 35.37 3.85
341 343 2.047560 GTCTCGGGACCCCAAACG 60.048 66.667 3.28 0.00 36.53 3.60
383 390 7.573710 AGTTCATCCCAAGTATAAAGCACATA 58.426 34.615 0.00 0.00 0.00 2.29
399 406 7.451877 TCCAGATCTACTGTATAAGTTCATCCC 59.548 40.741 0.00 0.00 44.40 3.85
443 452 6.539103 AGGACTTGTGTAAAAGAGAAGACAAC 59.461 38.462 0.00 0.00 0.00 3.32
444 453 6.650120 AGGACTTGTGTAAAAGAGAAGACAA 58.350 36.000 0.00 0.00 0.00 3.18
445 454 6.098409 AGAGGACTTGTGTAAAAGAGAAGACA 59.902 38.462 0.00 0.00 0.00 3.41
456 468 3.501349 AGCTCTGAGAGGACTTGTGTAA 58.499 45.455 12.01 0.00 0.00 2.41
457 469 3.085533 GAGCTCTGAGAGGACTTGTGTA 58.914 50.000 12.01 0.00 0.00 2.90
463 475 4.249638 AGTTATGAGCTCTGAGAGGACT 57.750 45.455 16.19 0.00 0.00 3.85
487 499 1.808411 TGAACAGGCATTCGAACCTC 58.192 50.000 0.00 0.00 32.56 3.85
488 500 2.270352 TTGAACAGGCATTCGAACCT 57.730 45.000 0.00 0.00 36.45 3.50
489 501 3.244976 CAATTGAACAGGCATTCGAACC 58.755 45.455 0.00 0.00 0.00 3.62
490 502 3.670055 CACAATTGAACAGGCATTCGAAC 59.330 43.478 13.59 0.00 0.00 3.95
491 503 3.856638 GCACAATTGAACAGGCATTCGAA 60.857 43.478 13.59 0.00 0.00 3.71
492 504 2.351641 GCACAATTGAACAGGCATTCGA 60.352 45.455 13.59 0.00 0.00 3.71
493 505 1.987770 GCACAATTGAACAGGCATTCG 59.012 47.619 13.59 0.00 0.00 3.34
494 506 2.288948 TGGCACAATTGAACAGGCATTC 60.289 45.455 13.59 0.00 31.92 2.67
532 544 5.102953 TGGGAATGGAGAAGATAAGTGTG 57.897 43.478 0.00 0.00 0.00 3.82
579 592 3.430862 TTGGCGGCTTCATCGTGC 61.431 61.111 11.43 0.00 0.00 5.34
641 654 4.463879 CCGGTGCAGAGCCCAGAG 62.464 72.222 0.00 0.00 0.00 3.35
923 936 2.549611 CTTCCTCGTCACGCTCCTGG 62.550 65.000 0.00 0.00 0.00 4.45
994 1011 4.992951 GTCTTCAATTGCTGCCATCTTTTT 59.007 37.500 0.00 0.00 0.00 1.94
1182 1199 1.068127 GAGTGGTGGTAATACGGCGAT 59.932 52.381 16.62 1.24 0.00 4.58
1338 1391 1.805945 GCTGCCGTACTCCTTCGTG 60.806 63.158 0.00 0.00 0.00 4.35
1339 1392 2.572284 GCTGCCGTACTCCTTCGT 59.428 61.111 0.00 0.00 0.00 3.85
1445 1498 4.717629 TGAAGCTGGACGCGGACG 62.718 66.667 12.47 0.00 45.59 4.79
1716 1774 4.032217 CGTCATCTCATCACACAAAGCTAC 59.968 45.833 0.00 0.00 0.00 3.58
1719 1777 2.995939 TCGTCATCTCATCACACAAAGC 59.004 45.455 0.00 0.00 0.00 3.51
1790 1849 3.290710 TCCCTTGATGGAGCAAATAAGC 58.709 45.455 0.00 0.00 38.35 3.09
1801 1860 1.117150 CCCATTTGCTCCCTTGATGG 58.883 55.000 0.00 0.00 37.57 3.51
1805 1864 2.754012 TATCCCCATTTGCTCCCTTG 57.246 50.000 0.00 0.00 0.00 3.61
1819 1878 4.009675 TCATGTGAGCAACTGTTTATCCC 58.990 43.478 0.00 0.00 0.00 3.85
1824 1883 5.706833 TGATACATCATGTGAGCAACTGTTT 59.293 36.000 0.00 0.00 0.00 2.83
1846 1905 4.372656 CTTTTATTTTGTTGCCCGGTTGA 58.627 39.130 0.00 0.00 0.00 3.18
1930 1989 7.591057 CGTGAGAATTGCATTTTTCTTAACAGA 59.409 33.333 11.68 0.00 32.46 3.41
1945 2004 3.896648 TTCTTTGTCCGTGAGAATTGC 57.103 42.857 0.00 0.00 0.00 3.56
1951 2010 3.430218 GTGAGTGATTCTTTGTCCGTGAG 59.570 47.826 0.00 0.00 0.00 3.51
1960 2019 3.325135 ACGAGAAGGGTGAGTGATTCTTT 59.675 43.478 0.00 0.00 32.31 2.52
1976 2035 1.595794 GCTTTTTGTCCACGACGAGAA 59.404 47.619 0.00 0.00 34.95 2.87
2002 2061 4.456222 TCCTTTGTGCGAAATCGGATAAAA 59.544 37.500 16.87 11.98 45.91 1.52
2004 2063 3.601435 TCCTTTGTGCGAAATCGGATAA 58.399 40.909 4.84 3.68 42.66 1.75
2011 2070 3.057315 CCAAGACATCCTTTGTGCGAAAT 60.057 43.478 0.00 0.00 39.18 2.17
2024 2083 5.864474 CCGTAGCTATCATAACCAAGACATC 59.136 44.000 0.00 0.00 0.00 3.06
2025 2084 5.538813 TCCGTAGCTATCATAACCAAGACAT 59.461 40.000 0.00 0.00 0.00 3.06
2032 2092 5.464030 TTCCTTCCGTAGCTATCATAACC 57.536 43.478 0.00 0.00 0.00 2.85
2042 2102 4.454504 TGTCTTTTCATTTCCTTCCGTAGC 59.545 41.667 0.00 0.00 0.00 3.58
2052 2112 8.099364 TCTTATGGACAGTGTCTTTTCATTTC 57.901 34.615 22.18 3.56 32.47 2.17
2053 2113 7.308830 GCTCTTATGGACAGTGTCTTTTCATTT 60.309 37.037 22.18 1.62 32.47 2.32
2061 2121 4.029520 AGATGCTCTTATGGACAGTGTCT 58.970 43.478 22.18 6.74 32.47 3.41
2064 2124 4.669206 AGAGATGCTCTTATGGACAGTG 57.331 45.455 0.00 0.00 37.60 3.66
2065 2125 4.280677 GCTAGAGATGCTCTTATGGACAGT 59.719 45.833 1.88 0.00 41.50 3.55
2089 2149 1.302033 GCCAGGTGCCAGGATATCG 60.302 63.158 3.68 0.00 0.00 2.92
2155 2215 4.464951 AGACAAGTACGATGACCACCAATA 59.535 41.667 8.45 0.00 0.00 1.90
2211 2467 8.284945 AGTACATAGTGACCGTATTGACTAAA 57.715 34.615 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.