Multiple sequence alignment - TraesCS4A01G057900

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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 TraesCS4A01G057900 chr4A 100.000 2444 0 0 1 2444 48529810 48527367 0.000000e+00 4514.0
1 TraesCS4A01G057900 chr4A 80.042 481 60 21 722 1190 48891352 48891808 8.430000e-85 324.0
2 TraesCS4A01G057900 chr4A 87.079 178 23 0 1974 2151 36573674 36573497 4.120000e-48 202.0
3 TraesCS4A01G057900 chr4A 95.122 82 3 1 2163 2243 36535361 36535280 7.090000e-26 128.0
4 TraesCS4A01G057900 chr4A 85.965 57 5 3 2166 2221 90434723 90434669 9.440000e-05 58.4
5 TraesCS4A01G057900 chr4D 94.259 1376 52 8 364 1727 414997620 414998980 0.000000e+00 2078.0
6 TraesCS4A01G057900 chr4D 89.474 399 24 4 1761 2159 414999191 414999571 2.820000e-134 488.0
7 TraesCS4A01G057900 chr4D 93.993 283 15 2 2163 2444 414999686 414999967 6.250000e-116 427.0
8 TraesCS4A01G057900 chr4D 88.615 325 14 13 24 337 414997313 414997625 8.250000e-100 374.0
9 TraesCS4A01G057900 chr4B 90.086 1392 75 30 66 1447 511161445 511162783 0.000000e+00 1748.0
10 TraesCS4A01G057900 chr4B 89.896 386 21 7 1774 2159 511163351 511163718 4.730000e-132 481.0
11 TraesCS4A01G057900 chr4B 95.374 281 10 1 1449 1726 511162878 511163158 6.200000e-121 444.0
12 TraesCS4A01G057900 chr4B 91.549 284 15 3 2163 2444 511163845 511164121 1.370000e-102 383.0
13 TraesCS4A01G057900 chr4B 85.093 161 22 2 1912 2071 535427929 535427770 1.940000e-36 163.0
14 TraesCS4A01G057900 chr4B 83.230 161 24 3 1912 2071 535298913 535298755 7.040000e-31 145.0
15 TraesCS4A01G057900 chr4B 88.618 123 7 4 707 826 510844630 510844512 2.530000e-30 143.0
16 TraesCS4A01G057900 chr4B 97.059 34 1 0 1 34 511161428 511161461 9.440000e-05 58.4
17 TraesCS4A01G057900 chr3D 92.593 54 2 2 2163 2215 332801415 332801467 2.610000e-10 76.8
18 TraesCS4A01G057900 chr6B 89.474 57 2 4 2165 2218 717880935 717880990 4.360000e-08 69.4
19 TraesCS4A01G057900 chr1A 100.000 32 0 0 2165 2196 32107487 32107518 2.620000e-05 60.2
20 TraesCS4A01G057900 chr1B 97.059 34 1 0 2163 2196 50896036 50896069 9.440000e-05 58.4
21 TraesCS4A01G057900 chr6D 94.595 37 1 1 2174 2209 406196956 406196920 3.390000e-04 56.5


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 TraesCS4A01G057900 chr4A 48527367 48529810 2443 True 4514.00 4514 100.00000 1 2444 1 chr4A.!!$R3 2443
1 TraesCS4A01G057900 chr4D 414997313 414999967 2654 False 841.75 2078 91.58525 24 2444 4 chr4D.!!$F1 2420
2 TraesCS4A01G057900 chr4B 511161428 511164121 2693 False 622.88 1748 92.79280 1 2444 5 chr4B.!!$F1 2443

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
516 549 0.036765 TGTCAGGTACATGGTTCGCC 60.037 55.0 7.81 0.0 31.43 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2240 0.977395 AGGGGAAGTTGGAGAGAACG 59.023 55.0 0.0 0.0 0.0 3.95 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
61 62 4.081198 ACCAAATCTGTTGGCTGACAAAAA 60.081 37.500 0.00 0.00 43.23 1.94
78 79 6.260050 TGACAAAAAGTACTAGGTTTGAGCAG 59.740 38.462 23.24 6.52 35.44 4.24
80 81 2.656560 AGTACTAGGTTTGAGCAGCG 57.343 50.000 0.00 0.00 0.00 5.18
108 109 2.033141 TCAGTCTTGCCCTGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
109 110 3.060615 CAGTCTTGCCCTGCTGCC 61.061 66.667 0.00 0.00 0.00 4.85
110 111 3.255397 AGTCTTGCCCTGCTGCCT 61.255 61.111 0.00 0.00 0.00 4.75
111 112 3.060615 GTCTTGCCCTGCTGCCTG 61.061 66.667 0.00 0.00 0.00 4.85
233 235 3.443099 AAACTGAACAAGCCTTGAAGC 57.557 42.857 12.25 0.42 0.00 3.86
234 236 1.322442 ACTGAACAAGCCTTGAAGCC 58.678 50.000 12.25 0.00 0.00 4.35
235 237 1.321474 CTGAACAAGCCTTGAAGCCA 58.679 50.000 12.25 2.54 0.00 4.75
236 238 1.682854 CTGAACAAGCCTTGAAGCCAA 59.317 47.619 12.25 0.00 0.00 4.52
237 239 1.408702 TGAACAAGCCTTGAAGCCAAC 59.591 47.619 12.25 0.00 0.00 3.77
239 241 1.322442 ACAAGCCTTGAAGCCAACTC 58.678 50.000 12.25 0.00 0.00 3.01
240 242 1.321474 CAAGCCTTGAAGCCAACTCA 58.679 50.000 0.00 0.00 0.00 3.41
241 243 1.268899 CAAGCCTTGAAGCCAACTCAG 59.731 52.381 0.00 0.00 0.00 3.35
254 260 5.621193 AGCCAACTCAGTAACAATGTACTT 58.379 37.500 0.00 0.00 31.78 2.24
258 267 8.512138 GCCAACTCAGTAACAATGTACTTTATT 58.488 33.333 0.00 0.00 31.78 1.40
330 342 5.045505 TGGGTGTCATGTAAATGGTAAGCTA 60.046 40.000 0.00 0.00 0.00 3.32
331 343 5.296035 GGGTGTCATGTAAATGGTAAGCTAC 59.704 44.000 0.00 0.00 0.00 3.58
332 344 6.113411 GGTGTCATGTAAATGGTAAGCTACT 58.887 40.000 0.00 0.00 0.00 2.57
333 345 6.037172 GGTGTCATGTAAATGGTAAGCTACTG 59.963 42.308 0.00 0.00 0.00 2.74
334 346 6.816640 GTGTCATGTAAATGGTAAGCTACTGA 59.183 38.462 0.00 0.00 0.00 3.41
335 347 6.816640 TGTCATGTAAATGGTAAGCTACTGAC 59.183 38.462 0.00 0.00 0.00 3.51
336 348 7.042335 GTCATGTAAATGGTAAGCTACTGACT 58.958 38.462 0.00 0.00 0.00 3.41
337 349 7.549488 GTCATGTAAATGGTAAGCTACTGACTT 59.451 37.037 0.00 0.00 0.00 3.01
338 350 7.549134 TCATGTAAATGGTAAGCTACTGACTTG 59.451 37.037 0.00 0.00 0.00 3.16
339 351 6.999950 TGTAAATGGTAAGCTACTGACTTGA 58.000 36.000 0.00 0.00 0.00 3.02
340 352 7.446769 TGTAAATGGTAAGCTACTGACTTGAA 58.553 34.615 0.00 0.00 0.00 2.69
341 353 7.602644 TGTAAATGGTAAGCTACTGACTTGAAG 59.397 37.037 0.00 0.00 0.00 3.02
342 354 6.360370 AATGGTAAGCTACTGACTTGAAGA 57.640 37.500 0.00 0.00 0.00 2.87
343 355 6.552445 ATGGTAAGCTACTGACTTGAAGAT 57.448 37.500 0.00 0.00 0.00 2.40
361 373 5.832595 TGAAGATGAAACAGGTTCCATCAAA 59.167 36.000 12.85 0.00 35.12 2.69
381 393 0.764369 AGTGACTGGTTGCTGGGAGA 60.764 55.000 0.00 0.00 0.00 3.71
448 460 5.541101 TGACCAGGCTAACAAAGTACTCTAA 59.459 40.000 0.00 0.00 0.00 2.10
449 461 6.042322 TGACCAGGCTAACAAAGTACTCTAAA 59.958 38.462 0.00 0.00 0.00 1.85
450 462 6.465084 ACCAGGCTAACAAAGTACTCTAAAG 58.535 40.000 0.00 0.00 0.00 1.85
451 463 5.351740 CCAGGCTAACAAAGTACTCTAAAGC 59.648 44.000 0.00 2.35 0.00 3.51
452 464 5.351740 CAGGCTAACAAAGTACTCTAAAGCC 59.648 44.000 20.35 20.35 45.80 4.35
453 465 5.243207 GGCTAACAAAGTACTCTAAAGCCA 58.757 41.667 21.88 0.00 45.00 4.75
454 466 5.121925 GGCTAACAAAGTACTCTAAAGCCAC 59.878 44.000 21.88 5.22 45.00 5.01
455 467 5.121925 GCTAACAAAGTACTCTAAAGCCACC 59.878 44.000 0.00 0.00 0.00 4.61
456 468 3.660865 ACAAAGTACTCTAAAGCCACCG 58.339 45.455 0.00 0.00 0.00 4.94
457 469 3.322828 ACAAAGTACTCTAAAGCCACCGA 59.677 43.478 0.00 0.00 0.00 4.69
458 470 3.589495 AAGTACTCTAAAGCCACCGAC 57.411 47.619 0.00 0.00 0.00 4.79
459 471 2.805194 AGTACTCTAAAGCCACCGACT 58.195 47.619 0.00 0.00 0.00 4.18
460 472 2.754002 AGTACTCTAAAGCCACCGACTC 59.246 50.000 0.00 0.00 0.00 3.36
461 473 1.926108 ACTCTAAAGCCACCGACTCT 58.074 50.000 0.00 0.00 0.00 3.24
462 474 1.546476 ACTCTAAAGCCACCGACTCTG 59.454 52.381 0.00 0.00 0.00 3.35
463 475 1.819288 CTCTAAAGCCACCGACTCTGA 59.181 52.381 0.00 0.00 0.00 3.27
491 524 5.106436 TGTGATGAAGATGTTGCATCAGTTC 60.106 40.000 13.95 12.59 46.24 3.01
516 549 0.036765 TGTCAGGTACATGGTTCGCC 60.037 55.000 7.81 0.00 31.43 5.54
647 681 2.795110 TTGCCACCAACAAGCTGCC 61.795 57.895 0.00 0.00 0.00 4.85
651 685 0.537143 CCACCAACAAGCTGCCACTA 60.537 55.000 0.00 0.00 0.00 2.74
705 739 3.364023 GTCCTAAGACAATGACGACAACG 59.636 47.826 0.00 0.00 42.99 4.10
817 854 3.350833 AGCAAATCTCCCACAATGTCTC 58.649 45.455 0.00 0.00 0.00 3.36
823 860 2.303022 TCTCCCACAATGTCTCCAGTTC 59.697 50.000 0.00 0.00 0.00 3.01
874 911 7.168972 GTGCAGTCTGTAAAACATAAAATGCAA 59.831 33.333 11.32 0.00 37.56 4.08
1221 1258 2.858745 CTCCTGGTCCTAGTAGCTCTC 58.141 57.143 0.00 0.00 0.00 3.20
1246 1283 1.032114 CGGCCTTTCTGAACCATCCC 61.032 60.000 0.00 0.00 0.00 3.85
1428 1465 5.684704 ACCAACATATACCTTGGTGATCAG 58.315 41.667 13.01 0.00 46.90 2.90
1454 1584 4.615588 AGCAAATCTGATAGGAGGTAGC 57.384 45.455 0.00 0.00 0.00 3.58
1500 1635 8.095169 ACTGCTACTAATTACTAAACAACAGCT 58.905 33.333 0.00 0.00 0.00 4.24
1517 1652 3.119101 ACAGCTTGTATAGAACAGTCCGG 60.119 47.826 0.00 0.00 39.87 5.14
1648 1783 0.110486 GTTTTGGTCCAGAGGGCAGA 59.890 55.000 0.00 0.00 0.00 4.26
1666 1801 3.118884 GCAGAATGAATCCAAGCCACAAT 60.119 43.478 0.00 0.00 39.69 2.71
1737 2053 2.430465 CAAGTACCTTGTGATGCAGCT 58.570 47.619 2.53 0.00 36.79 4.24
1738 2054 2.105006 AGTACCTTGTGATGCAGCTG 57.895 50.000 10.11 10.11 0.00 4.24
1739 2055 1.625315 AGTACCTTGTGATGCAGCTGA 59.375 47.619 20.43 2.70 0.00 4.26
1740 2056 2.038952 AGTACCTTGTGATGCAGCTGAA 59.961 45.455 20.43 7.68 0.00 3.02
1741 2057 2.211250 ACCTTGTGATGCAGCTGAAT 57.789 45.000 20.43 14.00 0.00 2.57
1742 2058 2.522185 ACCTTGTGATGCAGCTGAATT 58.478 42.857 20.43 0.00 0.00 2.17
1744 2060 3.441572 ACCTTGTGATGCAGCTGAATTAC 59.558 43.478 20.29 20.29 0.00 1.89
1745 2061 3.693085 CCTTGTGATGCAGCTGAATTACT 59.307 43.478 25.50 0.00 0.00 2.24
1746 2062 4.157289 CCTTGTGATGCAGCTGAATTACTT 59.843 41.667 25.50 0.00 0.00 2.24
1748 2064 6.127925 CCTTGTGATGCAGCTGAATTACTTTA 60.128 38.462 25.50 12.95 0.00 1.85
1749 2065 6.182039 TGTGATGCAGCTGAATTACTTTAC 57.818 37.500 25.50 11.74 0.00 2.01
1752 2068 7.552330 TGTGATGCAGCTGAATTACTTTACATA 59.448 33.333 25.50 6.85 0.00 2.29
1753 2069 8.562892 GTGATGCAGCTGAATTACTTTACATAT 58.437 33.333 19.92 0.00 0.00 1.78
1754 2070 8.562052 TGATGCAGCTGAATTACTTTACATATG 58.438 33.333 20.43 0.00 0.00 1.78
1755 2071 7.864108 TGCAGCTGAATTACTTTACATATGT 57.136 32.000 20.43 13.93 0.00 2.29
1756 2072 8.279970 TGCAGCTGAATTACTTTACATATGTT 57.720 30.769 20.43 0.00 0.00 2.71
1757 2073 8.183536 TGCAGCTGAATTACTTTACATATGTTG 58.816 33.333 20.43 7.57 0.00 3.33
1758 2074 7.645340 GCAGCTGAATTACTTTACATATGTTGG 59.355 37.037 20.43 7.20 0.00 3.77
1786 2103 5.107875 GCAAATCACTTTACCTTTCAAAGCG 60.108 40.000 0.00 0.00 36.63 4.68
1865 2182 2.680913 AAGCGACGCCTCACATTGC 61.681 57.895 17.79 0.00 0.00 3.56
1868 2185 1.154205 GCGACGCCTCACATTGCTAT 61.154 55.000 9.14 0.00 0.00 2.97
1879 2196 5.008415 CCTCACATTGCTATGGTTCATTCTC 59.992 44.000 12.77 0.00 36.01 2.87
1883 2200 5.356190 ACATTGCTATGGTTCATTCTCTGTG 59.644 40.000 12.77 0.00 36.01 3.66
1886 2203 3.944015 GCTATGGTTCATTCTCTGTGCTT 59.056 43.478 0.00 0.00 0.00 3.91
1889 2206 5.796424 ATGGTTCATTCTCTGTGCTTTTT 57.204 34.783 0.00 0.00 0.00 1.94
1890 2207 4.935702 TGGTTCATTCTCTGTGCTTTTTG 58.064 39.130 0.00 0.00 0.00 2.44
1915 2232 0.179078 CTCCTGCCTGCTCACTCATC 60.179 60.000 0.00 0.00 0.00 2.92
1923 2240 2.475818 CTGCTCACTCATCTCATCTGC 58.524 52.381 0.00 0.00 0.00 4.26
1969 2286 3.320673 ACGTTGGAAGAGTTCATCCTC 57.679 47.619 5.15 0.00 34.96 3.71
1972 2289 3.056536 CGTTGGAAGAGTTCATCCTCTCA 60.057 47.826 5.15 0.00 40.93 3.27
1975 2292 5.350504 TGGAAGAGTTCATCCTCTCAATC 57.649 43.478 5.15 0.00 40.93 2.67
1987 2304 4.222336 TCCTCTCAATCCTCCTCTTCATC 58.778 47.826 0.00 0.00 0.00 2.92
2067 2384 0.680061 GGGAGTGAACTTGTCCTCGT 59.320 55.000 0.00 0.00 0.00 4.18
2082 2399 1.107114 CTCGTGAGGATACCTGCAGT 58.893 55.000 13.81 3.45 31.76 4.40
2084 2401 2.887783 CTCGTGAGGATACCTGCAGTAT 59.112 50.000 13.81 10.42 44.68 2.12
2085 2402 3.296854 TCGTGAGGATACCTGCAGTATT 58.703 45.455 13.81 0.00 41.94 1.89
2086 2403 3.318275 TCGTGAGGATACCTGCAGTATTC 59.682 47.826 13.81 9.36 41.94 1.75
2087 2404 3.553096 CGTGAGGATACCTGCAGTATTCC 60.553 52.174 13.81 14.48 41.94 3.01
2088 2405 3.388024 GTGAGGATACCTGCAGTATTCCA 59.612 47.826 21.38 11.97 41.94 3.53
2089 2406 4.040952 GTGAGGATACCTGCAGTATTCCAT 59.959 45.833 21.38 11.01 41.94 3.41
2090 2407 4.040829 TGAGGATACCTGCAGTATTCCATG 59.959 45.833 21.38 5.13 41.94 3.66
2091 2408 3.077359 GGATACCTGCAGTATTCCATGC 58.923 50.000 13.81 0.00 41.94 4.06
2093 2410 1.755179 ACCTGCAGTATTCCATGCAC 58.245 50.000 13.81 0.00 46.97 4.57
2094 2411 1.004628 ACCTGCAGTATTCCATGCACA 59.995 47.619 13.81 0.00 46.97 4.57
2095 2412 2.093890 CCTGCAGTATTCCATGCACAA 58.906 47.619 13.81 0.00 46.97 3.33
2096 2413 2.691526 CCTGCAGTATTCCATGCACAAT 59.308 45.455 13.81 0.00 46.97 2.71
2097 2414 3.490249 CCTGCAGTATTCCATGCACAATG 60.490 47.826 13.81 0.00 46.97 2.82
2098 2415 3.354467 TGCAGTATTCCATGCACAATGA 58.646 40.909 0.00 0.00 46.97 2.57
2099 2416 3.762823 TGCAGTATTCCATGCACAATGAA 59.237 39.130 0.00 0.00 46.97 2.57
2100 2417 4.220163 TGCAGTATTCCATGCACAATGAAA 59.780 37.500 0.00 0.00 46.97 2.69
2101 2418 5.170021 GCAGTATTCCATGCACAATGAAAA 58.830 37.500 0.00 0.00 42.11 2.29
2102 2419 5.813672 GCAGTATTCCATGCACAATGAAAAT 59.186 36.000 0.00 0.00 42.11 1.82
2133 2450 3.389329 AGACCATCCTCGAAGTAATGCAT 59.611 43.478 0.00 0.00 0.00 3.96
2134 2451 3.470709 ACCATCCTCGAAGTAATGCATG 58.529 45.455 0.00 0.00 0.00 4.06
2148 2465 4.542662 AATGCATGCTCGCTTAAACTAG 57.457 40.909 20.33 0.00 0.00 2.57
2159 2476 3.952967 CGCTTAAACTAGTACTCCCTCCT 59.047 47.826 0.00 0.00 0.00 3.69
2160 2477 4.401837 CGCTTAAACTAGTACTCCCTCCTT 59.598 45.833 0.00 0.00 0.00 3.36
2161 2478 5.591877 CGCTTAAACTAGTACTCCCTCCTTA 59.408 44.000 0.00 0.00 0.00 2.69
2249 2690 5.121380 AGTATTGATGGTCATTTCAGGCT 57.879 39.130 0.00 0.00 0.00 4.58
2252 2693 6.713903 AGTATTGATGGTCATTTCAGGCTATG 59.286 38.462 0.00 0.00 0.00 2.23
2255 2696 4.102996 TGATGGTCATTTCAGGCTATGCTA 59.897 41.667 0.00 0.00 0.00 3.49
2309 2750 8.944138 TGACATCTTACATAAATAGATGGGGAA 58.056 33.333 13.88 0.00 46.01 3.97
2329 2770 0.552848 ATGACCCTAATGCCCCAGTG 59.447 55.000 0.00 0.00 0.00 3.66
2358 2805 3.641437 TGGCATGCTTCAACAAGTAAC 57.359 42.857 18.92 0.00 31.45 2.50
2359 2806 3.221771 TGGCATGCTTCAACAAGTAACT 58.778 40.909 18.92 0.00 31.45 2.24
2360 2807 3.636300 TGGCATGCTTCAACAAGTAACTT 59.364 39.130 18.92 0.00 31.45 2.66
2361 2808 4.824537 TGGCATGCTTCAACAAGTAACTTA 59.175 37.500 18.92 0.00 31.45 2.24
2362 2809 5.300539 TGGCATGCTTCAACAAGTAACTTAA 59.699 36.000 18.92 0.00 31.45 1.85
2363 2810 5.858581 GGCATGCTTCAACAAGTAACTTAAG 59.141 40.000 18.92 0.00 31.45 1.85
2364 2811 6.293955 GGCATGCTTCAACAAGTAACTTAAGA 60.294 38.462 18.92 0.00 31.45 2.10
2408 2855 5.359009 AGACTCCCAATGAAAATGCATACTG 59.641 40.000 0.00 0.00 0.00 2.74
2412 2859 6.135454 TCCCAATGAAAATGCATACTGGTAT 58.865 36.000 0.00 0.00 28.48 2.73
2419 2866 4.948341 AATGCATACTGGTATCGGTACA 57.052 40.909 8.35 0.00 37.54 2.90
2435 2883 6.117975 TCGGTACAGGAAACCTTTTTCTAT 57.882 37.500 0.00 0.00 40.98 1.98
2436 2884 7.243604 TCGGTACAGGAAACCTTTTTCTATA 57.756 36.000 0.00 0.00 40.98 1.31
2437 2885 7.854337 TCGGTACAGGAAACCTTTTTCTATAT 58.146 34.615 0.00 0.00 40.98 0.86
2438 2886 7.767198 TCGGTACAGGAAACCTTTTTCTATATG 59.233 37.037 0.00 0.00 40.98 1.78
2439 2887 7.767198 CGGTACAGGAAACCTTTTTCTATATGA 59.233 37.037 0.00 0.00 40.98 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.154918 GGTGAAAGTGATGCTCAAACCTAG 59.845 45.833 0.00 0.00 0.00 3.02
18 19 4.072131 GGTGAAAGTGATGCTCAAACCTA 58.928 43.478 0.00 0.00 0.00 3.08
19 20 2.887152 GGTGAAAGTGATGCTCAAACCT 59.113 45.455 0.00 0.00 0.00 3.50
20 21 2.622942 TGGTGAAAGTGATGCTCAAACC 59.377 45.455 0.00 0.00 0.00 3.27
21 22 3.988379 TGGTGAAAGTGATGCTCAAAC 57.012 42.857 0.00 0.00 0.00 2.93
22 23 4.998671 TTTGGTGAAAGTGATGCTCAAA 57.001 36.364 0.00 0.00 0.00 2.69
61 62 1.404315 GCGCTGCTCAAACCTAGTACT 60.404 52.381 0.00 0.00 0.00 2.73
78 79 0.528470 AGACTGAGACTACCTTGCGC 59.472 55.000 0.00 0.00 0.00 6.09
109 110 3.850098 AACCCGACAAGCCCAGCAG 62.850 63.158 0.00 0.00 0.00 4.24
110 111 3.884774 AACCCGACAAGCCCAGCA 61.885 61.111 0.00 0.00 0.00 4.41
111 112 3.365265 CAACCCGACAAGCCCAGC 61.365 66.667 0.00 0.00 0.00 4.85
112 113 0.821711 TTTCAACCCGACAAGCCCAG 60.822 55.000 0.00 0.00 0.00 4.45
113 114 0.821711 CTTTCAACCCGACAAGCCCA 60.822 55.000 0.00 0.00 0.00 5.36
114 115 0.822121 ACTTTCAACCCGACAAGCCC 60.822 55.000 0.00 0.00 0.00 5.19
122 123 2.504367 ACTCAATCCACTTTCAACCCG 58.496 47.619 0.00 0.00 0.00 5.28
233 235 9.825972 CAATAAAGTACATTGTTACTGAGTTGG 57.174 33.333 0.00 0.00 0.00 3.77
254 260 6.655003 CCTTCTGAGTTGGTAGCTTTCAATAA 59.345 38.462 0.00 0.00 0.00 1.40
258 267 3.391296 ACCTTCTGAGTTGGTAGCTTTCA 59.609 43.478 0.00 0.00 31.50 2.69
330 342 5.041191 ACCTGTTTCATCTTCAAGTCAGT 57.959 39.130 0.00 0.00 0.00 3.41
331 343 5.049129 GGAACCTGTTTCATCTTCAAGTCAG 60.049 44.000 0.00 0.00 35.70 3.51
332 344 4.821805 GGAACCTGTTTCATCTTCAAGTCA 59.178 41.667 0.00 0.00 35.70 3.41
333 345 4.821805 TGGAACCTGTTTCATCTTCAAGTC 59.178 41.667 0.00 0.00 35.70 3.01
334 346 4.792068 TGGAACCTGTTTCATCTTCAAGT 58.208 39.130 0.00 0.00 35.70 3.16
335 347 5.947443 GATGGAACCTGTTTCATCTTCAAG 58.053 41.667 19.56 0.00 46.89 3.02
336 348 5.964958 GATGGAACCTGTTTCATCTTCAA 57.035 39.130 19.56 0.00 46.89 2.69
342 354 5.598005 TCACTTTTGATGGAACCTGTTTCAT 59.402 36.000 3.45 3.45 41.29 2.57
343 355 4.952957 TCACTTTTGATGGAACCTGTTTCA 59.047 37.500 0.00 0.00 35.70 2.69
361 373 0.109342 CTCCCAGCAACCAGTCACTT 59.891 55.000 0.00 0.00 0.00 3.16
381 393 1.279496 TAGTGGCTGGCTTCTCACAT 58.721 50.000 2.00 0.00 33.01 3.21
448 460 1.066573 CATCTTCAGAGTCGGTGGCTT 60.067 52.381 0.00 0.00 0.00 4.35
449 461 0.534412 CATCTTCAGAGTCGGTGGCT 59.466 55.000 0.00 0.00 0.00 4.75
450 462 0.247736 ACATCTTCAGAGTCGGTGGC 59.752 55.000 0.00 0.00 0.00 5.01
451 463 1.546029 TCACATCTTCAGAGTCGGTGG 59.454 52.381 0.00 0.00 0.00 4.61
452 464 3.119352 TCATCACATCTTCAGAGTCGGTG 60.119 47.826 0.00 0.00 0.00 4.94
453 465 3.092301 TCATCACATCTTCAGAGTCGGT 58.908 45.455 0.00 0.00 0.00 4.69
454 466 3.790152 TCATCACATCTTCAGAGTCGG 57.210 47.619 0.00 0.00 0.00 4.79
455 467 4.991472 TCTTCATCACATCTTCAGAGTCG 58.009 43.478 0.00 0.00 0.00 4.18
456 468 6.339730 ACATCTTCATCACATCTTCAGAGTC 58.660 40.000 0.00 0.00 0.00 3.36
457 469 6.297080 ACATCTTCATCACATCTTCAGAGT 57.703 37.500 0.00 0.00 0.00 3.24
458 470 6.457122 GCAACATCTTCATCACATCTTCAGAG 60.457 42.308 0.00 0.00 0.00 3.35
459 471 5.353400 GCAACATCTTCATCACATCTTCAGA 59.647 40.000 0.00 0.00 0.00 3.27
460 472 5.123344 TGCAACATCTTCATCACATCTTCAG 59.877 40.000 0.00 0.00 0.00 3.02
461 473 5.005094 TGCAACATCTTCATCACATCTTCA 58.995 37.500 0.00 0.00 0.00 3.02
462 474 5.556355 TGCAACATCTTCATCACATCTTC 57.444 39.130 0.00 0.00 0.00 2.87
463 475 5.650703 TGATGCAACATCTTCATCACATCTT 59.349 36.000 8.87 0.00 40.91 2.40
491 524 2.467880 ACCATGTACCTGACACCCTAG 58.532 52.381 0.00 0.00 42.17 3.02
516 549 2.810274 CACCAGTTTCATGGAGTCAGTG 59.190 50.000 0.00 0.00 43.57 3.66
647 681 6.162079 CAGCCATGGTCTTGTAGATATAGTG 58.838 44.000 14.67 0.00 0.00 2.74
651 685 3.392285 TGCAGCCATGGTCTTGTAGATAT 59.608 43.478 14.67 0.00 0.00 1.63
695 729 3.864003 TGTTATTGTTGTCGTTGTCGTCA 59.136 39.130 0.00 0.00 38.33 4.35
705 739 7.855904 CACTTGTTTCCTACTGTTATTGTTGTC 59.144 37.037 0.00 0.00 0.00 3.18
810 847 8.095452 ACTTATTATCCTGAACTGGAGACATT 57.905 34.615 6.58 0.00 41.51 2.71
817 854 9.751542 CAGTACTTACTTATTATCCTGAACTGG 57.248 37.037 0.00 0.00 33.46 4.00
1394 1431 8.397906 CAAGGTATATGTTGGTGTGTAATCTTG 58.602 37.037 0.00 0.00 0.00 3.02
1428 1465 3.814283 CCTCCTATCAGATTTGCTTCTGC 59.186 47.826 6.92 0.00 42.37 4.26
1447 1484 7.094377 TGGTTCTTATTTCAATGTTGCTACCTC 60.094 37.037 0.00 0.00 0.00 3.85
1454 1584 6.925165 AGCAGTTGGTTCTTATTTCAATGTTG 59.075 34.615 0.00 0.00 0.00 3.33
1500 1635 7.002276 TGATAGATCCGGACTGTTCTATACAA 58.998 38.462 20.32 10.17 36.02 2.41
1554 1689 6.095440 GCAAGGATACCAATAATTGACTGTGT 59.905 38.462 0.00 0.00 37.17 3.72
1557 1692 6.319658 ACTGCAAGGATACCAATAATTGACTG 59.680 38.462 0.00 0.00 39.30 3.51
1648 1783 8.732531 CAAATTAAATTGTGGCTTGGATTCATT 58.267 29.630 0.00 0.00 0.00 2.57
1666 1801 5.305644 AGCAACATACACCCACCAAATTAAA 59.694 36.000 0.00 0.00 0.00 1.52
1744 2060 9.289303 GTGATTTGCTAACCAACATATGTAAAG 57.711 33.333 9.21 3.54 31.97 1.85
1745 2061 9.019656 AGTGATTTGCTAACCAACATATGTAAA 57.980 29.630 9.21 3.80 31.97 2.01
1746 2062 8.574251 AGTGATTTGCTAACCAACATATGTAA 57.426 30.769 9.21 0.00 31.97 2.41
1748 2064 7.466746 AAGTGATTTGCTAACCAACATATGT 57.533 32.000 1.41 1.41 31.97 2.29
1749 2065 9.289303 GTAAAGTGATTTGCTAACCAACATATG 57.711 33.333 0.00 0.00 31.97 1.78
1752 2068 6.493458 AGGTAAAGTGATTTGCTAACCAACAT 59.507 34.615 0.00 0.00 31.97 2.71
1753 2069 5.830991 AGGTAAAGTGATTTGCTAACCAACA 59.169 36.000 0.00 0.00 31.97 3.33
1754 2070 6.327279 AGGTAAAGTGATTTGCTAACCAAC 57.673 37.500 0.00 0.00 31.97 3.77
1755 2071 6.969993 AAGGTAAAGTGATTTGCTAACCAA 57.030 33.333 0.00 0.00 0.00 3.67
1756 2072 6.547880 TGAAAGGTAAAGTGATTTGCTAACCA 59.452 34.615 0.00 0.00 0.00 3.67
1757 2073 6.977213 TGAAAGGTAAAGTGATTTGCTAACC 58.023 36.000 0.00 0.00 0.00 2.85
1758 2074 8.865590 TTTGAAAGGTAAAGTGATTTGCTAAC 57.134 30.769 0.00 0.00 0.00 2.34
1768 2085 4.561735 TTCCGCTTTGAAAGGTAAAGTG 57.438 40.909 7.09 0.00 42.38 3.16
1865 2182 6.506500 AAAAGCACAGAGAATGAACCATAG 57.493 37.500 0.00 0.00 0.00 2.23
1868 2185 4.737352 GCAAAAAGCACAGAGAATGAACCA 60.737 41.667 0.00 0.00 44.79 3.67
1883 2200 1.606480 GGCAGGAGGAAAGCAAAAAGC 60.606 52.381 0.00 0.00 46.19 3.51
1886 2203 1.331214 CAGGCAGGAGGAAAGCAAAA 58.669 50.000 0.00 0.00 0.00 2.44
1889 2206 2.034687 GCAGGCAGGAGGAAAGCA 59.965 61.111 0.00 0.00 0.00 3.91
1890 2207 1.748500 GAGCAGGCAGGAGGAAAGC 60.749 63.158 0.00 0.00 0.00 3.51
1915 2232 2.094286 AGTTGGAGAGAACGCAGATGAG 60.094 50.000 0.00 0.00 0.00 2.90
1923 2240 0.977395 AGGGGAAGTTGGAGAGAACG 59.023 55.000 0.00 0.00 0.00 3.95
1969 2286 3.888323 TCGAGATGAAGAGGAGGATTGAG 59.112 47.826 0.00 0.00 0.00 3.02
1972 2289 3.909732 ACTCGAGATGAAGAGGAGGATT 58.090 45.455 21.68 0.00 38.72 3.01
1975 2292 3.194542 ACAAACTCGAGATGAAGAGGAGG 59.805 47.826 21.68 0.00 38.72 4.30
2067 2384 3.653164 TGGAATACTGCAGGTATCCTCA 58.347 45.455 25.06 10.86 39.94 3.86
2084 2401 9.531942 GACAATATATTTTCATTGTGCATGGAA 57.468 29.630 6.35 0.00 43.58 3.53
2085 2402 8.693625 TGACAATATATTTTCATTGTGCATGGA 58.306 29.630 9.72 0.00 43.58 3.41
2086 2403 8.874744 TGACAATATATTTTCATTGTGCATGG 57.125 30.769 9.72 0.00 43.58 3.66
2087 2404 9.738832 TCTGACAATATATTTTCATTGTGCATG 57.261 29.630 13.35 2.11 43.58 4.06
2088 2405 9.740239 GTCTGACAATATATTTTCATTGTGCAT 57.260 29.630 13.35 0.00 43.58 3.96
2089 2406 8.190122 GGTCTGACAATATATTTTCATTGTGCA 58.810 33.333 13.35 4.60 43.58 4.57
2090 2407 8.190122 TGGTCTGACAATATATTTTCATTGTGC 58.810 33.333 13.35 4.52 43.58 4.57
2093 2410 9.903682 GGATGGTCTGACAATATATTTTCATTG 57.096 33.333 13.35 5.06 37.99 2.82
2094 2411 9.872684 AGGATGGTCTGACAATATATTTTCATT 57.127 29.630 13.35 0.00 0.00 2.57
2095 2412 9.512588 GAGGATGGTCTGACAATATATTTTCAT 57.487 33.333 13.35 0.63 0.00 2.57
2096 2413 7.657354 CGAGGATGGTCTGACAATATATTTTCA 59.343 37.037 12.55 12.55 0.00 2.69
2097 2414 7.872993 TCGAGGATGGTCTGACAATATATTTTC 59.127 37.037 10.38 4.89 0.00 2.29
2098 2415 7.735917 TCGAGGATGGTCTGACAATATATTTT 58.264 34.615 10.38 0.00 0.00 1.82
2099 2416 7.303182 TCGAGGATGGTCTGACAATATATTT 57.697 36.000 10.38 0.00 0.00 1.40
2100 2417 6.918067 TCGAGGATGGTCTGACAATATATT 57.082 37.500 10.38 0.00 0.00 1.28
2101 2418 6.495181 ACTTCGAGGATGGTCTGACAATATAT 59.505 38.462 10.38 0.00 0.00 0.86
2102 2419 5.833667 ACTTCGAGGATGGTCTGACAATATA 59.166 40.000 10.38 0.00 0.00 0.86
2133 2450 3.129988 GGGAGTACTAGTTTAAGCGAGCA 59.870 47.826 0.00 0.00 0.00 4.26
2134 2451 3.380954 AGGGAGTACTAGTTTAAGCGAGC 59.619 47.826 0.00 0.00 0.00 5.03
2223 2664 6.939163 GCCTGAAATGACCATCAATACTATCT 59.061 38.462 0.00 0.00 0.00 1.98
2231 2672 3.633525 GCATAGCCTGAAATGACCATCAA 59.366 43.478 0.00 0.00 0.00 2.57
2249 2690 5.012664 TGGTCCAGTCAAGAACTTTAGCATA 59.987 40.000 0.00 0.00 35.45 3.14
2252 2693 3.740115 TGGTCCAGTCAAGAACTTTAGC 58.260 45.455 0.00 0.00 35.45 3.09
2255 2696 4.536765 ACATTGGTCCAGTCAAGAACTTT 58.463 39.130 0.00 0.00 35.45 2.66
2309 2750 1.063717 CACTGGGGCATTAGGGTCATT 60.064 52.381 0.00 0.00 0.00 2.57
2329 2770 4.202040 TGTTGAAGCATGCCAATATAGTGC 60.202 41.667 15.66 0.00 36.11 4.40
2358 2805 5.054477 TGGTTTCTCGTTGTTCCTCTTAAG 58.946 41.667 0.00 0.00 0.00 1.85
2359 2806 5.026038 TGGTTTCTCGTTGTTCCTCTTAA 57.974 39.130 0.00 0.00 0.00 1.85
2360 2807 4.628074 CTGGTTTCTCGTTGTTCCTCTTA 58.372 43.478 0.00 0.00 0.00 2.10
2361 2808 3.467803 CTGGTTTCTCGTTGTTCCTCTT 58.532 45.455 0.00 0.00 0.00 2.85
2362 2809 2.807108 GCTGGTTTCTCGTTGTTCCTCT 60.807 50.000 0.00 0.00 0.00 3.69
2363 2810 1.531578 GCTGGTTTCTCGTTGTTCCTC 59.468 52.381 0.00 0.00 0.00 3.71
2364 2811 1.134220 TGCTGGTTTCTCGTTGTTCCT 60.134 47.619 0.00 0.00 0.00 3.36
2408 2855 3.900966 AAGGTTTCCTGTACCGATACC 57.099 47.619 10.06 10.06 40.69 2.73
2412 2859 4.426736 AGAAAAAGGTTTCCTGTACCGA 57.573 40.909 0.00 0.00 43.65 4.69


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

AutoCloner maintained by Alex Coulton.