Multiple sequence alignment - TraesCS6D01G262200

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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 TraesCS6D01G262200 chr6D 100.000 2591 0 0 1 2591 370369478 370366888 0.000000e+00 4785.0
1 TraesCS6D01G262200 chr6D 92.857 56 2 2 1989 2042 145788497 145788552 2.140000e-11 80.5
2 TraesCS6D01G262200 chr6B 89.161 1919 111 42 11 1857 555558331 555556438 0.000000e+00 2302.0
3 TraesCS6D01G262200 chr6B 93.250 563 32 5 2033 2591 555556264 555555704 0.000000e+00 824.0
4 TraesCS6D01G262200 chr6B 97.345 113 3 0 1859 1971 555556374 555556262 2.630000e-45 193.0
5 TraesCS6D01G262200 chr6B 95.833 48 2 0 1996 2043 431701397 431701444 7.690000e-11 78.7
6 TraesCS6D01G262200 chr6A 96.334 1173 21 8 687 1857 511425566 511424414 0.000000e+00 1908.0
7 TraesCS6D01G262200 chr6A 84.526 517 40 13 1 502 511426163 511425672 2.330000e-130 475.0
8 TraesCS6D01G262200 chr6A 85.393 356 28 6 2127 2482 511424173 511423842 5.310000e-92 348.0
9 TraesCS6D01G262200 chr6A 98.246 114 2 0 1859 1972 511424350 511424237 1.570000e-47 200.0
10 TraesCS6D01G262200 chr6A 93.182 44 2 1 2548 2591 511423409 511423367 2.150000e-06 63.9
11 TraesCS6D01G262200 chr1D 92.254 142 11 0 1383 1524 44620954 44620813 4.370000e-48 202.0
12 TraesCS6D01G262200 chr1D 100.000 43 0 0 1994 2036 337216849 337216891 2.140000e-11 80.5
13 TraesCS6D01G262200 chr1D 94.444 36 1 1 1967 2002 456271760 456271726 1.000000e-03 54.7
14 TraesCS6D01G262200 chr7D 76.190 399 70 20 3 379 222159823 222159428 1.220000e-43 187.0
15 TraesCS6D01G262200 chr7B 80.889 225 34 8 168 389 674790046 674790264 4.430000e-38 169.0
16 TraesCS6D01G262200 chr7B 88.889 72 7 1 1971 2041 293124637 293124566 1.280000e-13 87.9
17 TraesCS6D01G262200 chr7B 89.706 68 3 1 1973 2036 81689129 81689062 1.650000e-12 84.2
18 TraesCS6D01G262200 chr4B 74.815 405 63 22 3 379 658768164 658768557 2.080000e-31 147.0
19 TraesCS6D01G262200 chr4B 100.000 32 0 0 1963 1994 628123572 628123603 2.780000e-05 60.2
20 TraesCS6D01G262200 chr5B 74.684 395 66 17 3 371 436484900 436484514 7.470000e-31 145.0
21 TraesCS6D01G262200 chr4D 92.391 92 2 5 1382 1473 472678340 472678254 2.710000e-25 126.0
22 TraesCS6D01G262200 chr4D 98.485 66 1 0 1500 1565 472678178 472678243 1.630000e-22 117.0
23 TraesCS6D01G262200 chr5D 97.872 47 1 0 1994 2040 2137427 2137381 5.940000e-12 82.4
24 TraesCS6D01G262200 chr4A 84.524 84 8 3 1958 2037 165711690 165711772 7.690000e-11 78.7
25 TraesCS6D01G262200 chr3D 97.727 44 1 0 1994 2037 435704560 435704517 2.760000e-10 76.8
26 TraesCS6D01G262200 chr5A 84.416 77 11 1 1961 2037 510537483 510537558 9.940000e-10 75.0
27 TraesCS6D01G262200 chr2B 100.000 34 0 0 1961 1994 555843043 555843076 2.150000e-06 63.9
28 TraesCS6D01G262200 chr3B 96.970 33 1 0 1962 1994 636441526 636441558 3.600000e-04 56.5
29 TraesCS6D01G262200 chr3A 83.607 61 9 1 66 126 479494601 479494660 3.600000e-04 56.5
30 TraesCS6D01G262200 chr2D 92.308 39 2 1 1956 1994 600429662 600429625 1.000000e-03 54.7


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 TraesCS6D01G262200 chr6D 370366888 370369478 2590 True 4785.000000 4785 100.0000 1 2591 1 chr6D.!!$R1 2590
1 TraesCS6D01G262200 chr6B 555555704 555558331 2627 True 1106.333333 2302 93.2520 11 2591 3 chr6B.!!$R1 2580
2 TraesCS6D01G262200 chr6A 511423367 511426163 2796 True 598.980000 1908 91.5362 1 2591 5 chr6A.!!$R1 2590

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
322 344 0.036164 CGTGAGTGACCCCATCCAAA 59.964 55.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1735 0.108615 ACAGATCGAGCGGAACCTTG 60.109 55.0 8.05 0.0 0.0 3.61 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
37 38 3.616219 TGGTAATGACTACAACATGGGC 58.384 45.455 0.00 0.00 31.45 5.36
43 44 5.537300 ATGACTACAACATGGGCTACTAG 57.463 43.478 0.00 0.00 0.00 2.57
61 62 8.750298 GGCTACTAGCTGATTTATGGTATCTAA 58.250 37.037 7.99 0.00 41.99 2.10
68 69 8.538701 AGCTGATTTATGGTATCTAATCCTCAG 58.461 37.037 0.00 0.00 0.00 3.35
107 108 3.077359 GACCATCTTTGAGTCAGTTGGG 58.923 50.000 11.97 6.46 35.98 4.12
193 215 4.906437 GCAGTTGTTCGAGAAGCTAAAAAG 59.094 41.667 0.00 0.00 0.00 2.27
199 221 6.460781 TGTTCGAGAAGCTAAAAAGTATGGA 58.539 36.000 0.00 0.00 0.00 3.41
281 303 1.406614 GGATGACAGTGAAGGAGCTGG 60.407 57.143 0.00 0.00 37.07 4.85
322 344 0.036164 CGTGAGTGACCCCATCCAAA 59.964 55.000 0.00 0.00 0.00 3.28
326 348 2.017049 GAGTGACCCCATCCAAATTCG 58.983 52.381 0.00 0.00 0.00 3.34
339 361 4.186926 TCCAAATTCGAGCTCAGAATCTG 58.813 43.478 24.19 21.61 37.34 2.90
340 362 3.242673 CCAAATTCGAGCTCAGAATCTGC 60.243 47.826 24.19 0.00 37.34 4.26
347 369 1.284198 AGCTCAGAATCTGCCCATGTT 59.716 47.619 5.18 0.00 0.00 2.71
352 374 2.426024 CAGAATCTGCCCATGTTTGAGG 59.574 50.000 0.00 0.00 0.00 3.86
361 383 3.490348 CCCATGTTTGAGGAGTTTGTCT 58.510 45.455 0.00 0.00 0.00 3.41
424 446 6.964741 AATCTGATTGAGCATCTATAAGCG 57.035 37.500 1.31 0.00 30.01 4.68
438 465 7.173390 GCATCTATAAGCGGTTAAAGAGGATTT 59.827 37.037 11.60 0.00 0.00 2.17
508 538 7.882791 TGCCTTCTTACCATAATATATGTGGTG 59.117 37.037 23.61 13.55 45.38 4.17
523 553 4.566545 TGTGGTGTTAGCAGTTCATTTG 57.433 40.909 0.00 0.00 0.00 2.32
525 555 4.275689 TGTGGTGTTAGCAGTTCATTTGAG 59.724 41.667 0.00 0.00 0.00 3.02
526 556 3.253188 TGGTGTTAGCAGTTCATTTGAGC 59.747 43.478 0.00 0.00 0.00 4.26
527 557 3.503748 GGTGTTAGCAGTTCATTTGAGCT 59.496 43.478 0.00 0.00 35.97 4.09
528 558 4.695455 GGTGTTAGCAGTTCATTTGAGCTA 59.305 41.667 0.00 0.00 33.74 3.32
529 559 5.390991 GGTGTTAGCAGTTCATTTGAGCTAC 60.391 44.000 0.00 0.00 37.51 3.58
530 560 5.409826 GTGTTAGCAGTTCATTTGAGCTACT 59.590 40.000 3.17 3.17 37.51 2.57
535 582 5.997746 AGCAGTTCATTTGAGCTACTAAACA 59.002 36.000 0.00 0.00 33.74 2.83
557 604 9.730705 AAACAACATATATGATGATACAGAGGG 57.269 33.333 24.88 0.27 34.99 4.30
558 605 8.670521 ACAACATATATGATGATACAGAGGGA 57.329 34.615 24.88 0.00 34.99 4.20
559 606 9.104713 ACAACATATATGATGATACAGAGGGAA 57.895 33.333 24.88 0.00 34.99 3.97
611 658 0.679640 TTGGGGCATTGCGGACTTAG 60.680 55.000 1.91 0.00 0.00 2.18
618 665 3.234386 GCATTGCGGACTTAGAACAAAC 58.766 45.455 0.00 0.00 0.00 2.93
620 667 2.228138 TGCGGACTTAGAACAAACGT 57.772 45.000 0.00 0.00 0.00 3.99
624 671 4.569966 TGCGGACTTAGAACAAACGTTTAA 59.430 37.500 14.20 3.06 0.00 1.52
626 673 5.562623 GCGGACTTAGAACAAACGTTTAATG 59.437 40.000 14.20 4.96 0.00 1.90
627 674 6.075280 CGGACTTAGAACAAACGTTTAATGG 58.925 40.000 14.20 3.78 0.00 3.16
628 675 6.073657 CGGACTTAGAACAAACGTTTAATGGA 60.074 38.462 14.20 0.00 0.00 3.41
629 676 7.360607 CGGACTTAGAACAAACGTTTAATGGAT 60.361 37.037 14.20 0.00 0.00 3.41
630 677 8.938906 GGACTTAGAACAAACGTTTAATGGATA 58.061 33.333 14.20 0.00 0.00 2.59
638 685 8.925161 ACAAACGTTTAATGGATAATTGGATG 57.075 30.769 14.20 0.00 0.00 3.51
647 694 6.906157 ATGGATAATTGGATGTGATTGGAC 57.094 37.500 0.00 0.00 0.00 4.02
649 696 6.064060 TGGATAATTGGATGTGATTGGACTC 58.936 40.000 0.00 0.00 0.00 3.36
652 699 0.918983 TGGATGTGATTGGACTCCCC 59.081 55.000 0.00 0.00 0.00 4.81
654 701 2.293519 TGGATGTGATTGGACTCCCCTA 60.294 50.000 0.00 0.00 35.38 3.53
662 724 1.776662 TGGACTCCCCTATCAGAACG 58.223 55.000 0.00 0.00 35.38 3.95
1031 1123 2.970639 GCAGGAGCACGTCTACCA 59.029 61.111 0.00 0.00 41.58 3.25
1642 1735 3.312828 CGTTCTGGATCTGATCGAATCC 58.687 50.000 15.86 15.86 30.13 3.01
1649 1742 4.061596 GGATCTGATCGAATCCAAGGTTC 58.938 47.826 17.21 0.00 33.55 3.62
1857 1951 4.186926 GAGCTACATTCTGATCTGCAACA 58.813 43.478 0.00 0.00 0.00 3.33
1972 2128 7.976734 AGATGTGTCTGTTTAGCTGATTAGTAC 59.023 37.037 0.00 0.00 32.13 2.73
1973 2129 7.228314 TGTGTCTGTTTAGCTGATTAGTACT 57.772 36.000 0.00 0.00 0.00 2.73
1974 2130 7.313646 TGTGTCTGTTTAGCTGATTAGTACTC 58.686 38.462 0.00 0.00 0.00 2.59
1975 2131 6.752815 GTGTCTGTTTAGCTGATTAGTACTCC 59.247 42.308 0.00 0.00 0.00 3.85
1976 2132 6.127423 TGTCTGTTTAGCTGATTAGTACTCCC 60.127 42.308 0.00 0.00 0.00 4.30
1977 2133 6.097129 GTCTGTTTAGCTGATTAGTACTCCCT 59.903 42.308 0.00 0.00 0.00 4.20
1978 2134 6.321690 TCTGTTTAGCTGATTAGTACTCCCTC 59.678 42.308 0.00 0.00 0.00 4.30
1979 2135 5.363005 TGTTTAGCTGATTAGTACTCCCTCC 59.637 44.000 0.00 0.00 0.00 4.30
1980 2136 2.588620 AGCTGATTAGTACTCCCTCCG 58.411 52.381 0.00 0.00 0.00 4.63
1981 2137 2.091775 AGCTGATTAGTACTCCCTCCGT 60.092 50.000 0.00 0.00 0.00 4.69
1982 2138 2.293955 GCTGATTAGTACTCCCTCCGTC 59.706 54.545 0.00 0.00 0.00 4.79
1983 2139 2.885894 CTGATTAGTACTCCCTCCGTCC 59.114 54.545 0.00 0.00 0.00 4.79
1984 2140 2.237643 GATTAGTACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
1985 2141 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1986 2142 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1987 2143 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1988 2144 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1989 2145 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
1990 2146 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
1991 2147 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1992 2148 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1993 2149 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1994 2150 4.776308 ACTCCCTCCGTCCCATAATATAAC 59.224 45.833 0.00 0.00 0.00 1.89
1995 2151 5.019657 TCCCTCCGTCCCATAATATAACT 57.980 43.478 0.00 0.00 0.00 2.24
1996 2152 6.156554 TCCCTCCGTCCCATAATATAACTA 57.843 41.667 0.00 0.00 0.00 2.24
1997 2153 6.192773 TCCCTCCGTCCCATAATATAACTAG 58.807 44.000 0.00 0.00 0.00 2.57
1998 2154 5.956563 CCCTCCGTCCCATAATATAACTAGT 59.043 44.000 0.00 0.00 0.00 2.57
1999 2155 6.127423 CCCTCCGTCCCATAATATAACTAGTG 60.127 46.154 0.00 0.00 0.00 2.74
2000 2156 6.436532 CCTCCGTCCCATAATATAACTAGTGT 59.563 42.308 0.00 0.00 0.00 3.55
2001 2157 7.039223 CCTCCGTCCCATAATATAACTAGTGTT 60.039 40.741 0.00 0.00 39.98 3.32
2002 2158 8.938801 TCCGTCCCATAATATAACTAGTGTTA 57.061 34.615 0.00 0.00 42.11 2.41
2003 2159 9.365906 TCCGTCCCATAATATAACTAGTGTTAA 57.634 33.333 0.00 0.00 41.36 2.01
2004 2160 9.985730 CCGTCCCATAATATAACTAGTGTTAAA 57.014 33.333 0.00 0.00 41.36 1.52
2027 2183 7.647907 AAAACGCTCTTATATTATGGTACGG 57.352 36.000 0.00 0.00 0.00 4.02
2028 2184 6.579666 AACGCTCTTATATTATGGTACGGA 57.420 37.500 0.00 0.00 0.00 4.69
2029 2185 6.192234 ACGCTCTTATATTATGGTACGGAG 57.808 41.667 0.00 0.00 0.00 4.63
2030 2186 5.125097 ACGCTCTTATATTATGGTACGGAGG 59.875 44.000 0.00 0.00 0.00 4.30
2031 2187 5.450137 CGCTCTTATATTATGGTACGGAGGG 60.450 48.000 0.00 0.00 0.00 4.30
2032 2188 5.655532 GCTCTTATATTATGGTACGGAGGGA 59.344 44.000 0.00 0.00 0.00 4.20
2033 2189 6.183360 GCTCTTATATTATGGTACGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
2034 2190 6.797707 TCTTATATTATGGTACGGAGGGAGT 58.202 40.000 0.00 0.00 0.00 3.85
2035 2191 7.932134 TCTTATATTATGGTACGGAGGGAGTA 58.068 38.462 0.00 0.00 0.00 2.59
2058 2214 8.531982 AGTAGAAATCTATCTATGGCGCAATTA 58.468 33.333 10.83 0.00 34.59 1.40
2106 2262 7.620880 AGAACTTGTAATATGCTAGTGTGGAA 58.379 34.615 0.00 0.00 0.00 3.53
2117 2273 5.499313 TGCTAGTGTGGAATTCATGATTCA 58.501 37.500 7.93 0.00 44.91 2.57
2215 2371 6.757897 TCTTGTTATGACATGGATTGTTCC 57.242 37.500 0.00 0.00 39.18 3.62
2250 2406 6.041979 GGCCCAATATAACTTGATTTGGATGT 59.958 38.462 0.00 0.00 39.33 3.06
2348 2505 8.099364 TGAGTTCTTGCAAGTAAGAATTAAGG 57.901 34.615 25.19 0.00 45.40 2.69
2414 2572 4.732672 AAAACCCGAGGCTACTTACTAG 57.267 45.455 0.00 0.00 0.00 2.57
2451 2609 2.722629 CGATCTTTGTGCTGCTGTTTTG 59.277 45.455 0.00 0.00 0.00 2.44
2478 2636 3.005155 GCTGTGTTTCTTTGCTCCTGAAT 59.995 43.478 0.00 0.00 0.00 2.57
2504 3046 0.746063 TTTGTTGCTTGGTCTGCCTG 59.254 50.000 0.00 0.00 35.27 4.85
2522 3064 3.713968 GCAAATTTGTTGCGTGCTG 57.286 47.368 19.03 0.00 35.58 4.41
2579 3121 5.052481 AGCTTTCTTTGCTTGATTTTGACC 58.948 37.500 0.00 0.00 37.52 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 8.317679 ACTGAGGATTAGATACCATAAATCAGC 58.682 37.037 0.00 0.00 34.14 4.26
61 62 4.919936 ACGAAGGTCGCCTACTGAGGAT 62.920 54.545 0.00 0.00 45.12 3.24
68 69 0.524862 TCTTGACGAAGGTCGCCTAC 59.475 55.000 0.00 0.00 46.49 3.18
107 108 4.836175 TGGGAAAAGTGGGTTATTTTCTCC 59.164 41.667 7.58 8.53 42.63 3.71
193 215 6.014755 TCACATGAGATCTCTGGATTCCATAC 60.015 42.308 22.95 0.00 30.82 2.39
199 221 4.101274 CACCTCACATGAGATCTCTGGATT 59.899 45.833 22.95 1.15 44.74 3.01
256 278 3.370315 GCTCCTTCACTGTCATCCTTCAT 60.370 47.826 0.00 0.00 0.00 2.57
259 281 2.027377 CAGCTCCTTCACTGTCATCCTT 60.027 50.000 0.00 0.00 0.00 3.36
281 303 4.084328 CGTTCTCAAATTCCATATCTCCGC 60.084 45.833 0.00 0.00 0.00 5.54
322 344 1.202627 GGGCAGATTCTGAGCTCGAAT 60.203 52.381 24.22 24.22 32.44 3.34
326 348 1.134159 ACATGGGCAGATTCTGAGCTC 60.134 52.381 17.87 6.82 32.44 4.09
339 361 1.963515 ACAAACTCCTCAAACATGGGC 59.036 47.619 0.00 0.00 0.00 5.36
340 362 3.490348 AGACAAACTCCTCAAACATGGG 58.510 45.455 0.00 0.00 0.00 4.00
347 369 6.003326 TGATGCATTTAGACAAACTCCTCAA 58.997 36.000 0.00 0.00 0.00 3.02
352 374 6.902341 TCTGTTGATGCATTTAGACAAACTC 58.098 36.000 0.00 0.00 0.00 3.01
361 383 8.305317 TCAATGTCAAATCTGTTGATGCATTTA 58.695 29.630 0.00 0.00 32.44 1.40
420 442 7.368059 CAAACTTAAATCCTCTTTAACCGCTT 58.632 34.615 0.00 0.00 0.00 4.68
421 443 6.072119 CCAAACTTAAATCCTCTTTAACCGCT 60.072 38.462 0.00 0.00 0.00 5.52
422 444 6.090783 CCAAACTTAAATCCTCTTTAACCGC 58.909 40.000 0.00 0.00 0.00 5.68
423 445 6.072119 AGCCAAACTTAAATCCTCTTTAACCG 60.072 38.462 0.00 0.00 0.00 4.44
424 446 7.228314 AGCCAAACTTAAATCCTCTTTAACC 57.772 36.000 0.00 0.00 0.00 2.85
483 513 7.883311 ACACCACATATATTATGGTAAGAAGGC 59.117 37.037 15.22 0.00 45.11 4.35
505 535 3.503748 AGCTCAAATGAACTGCTAACACC 59.496 43.478 0.00 0.00 31.71 4.16
508 538 7.596749 TTAGTAGCTCAAATGAACTGCTAAC 57.403 36.000 15.73 7.14 39.09 2.34
595 642 0.733150 GTTCTAAGTCCGCAATGCCC 59.267 55.000 0.00 0.00 0.00 5.36
596 643 1.448985 TGTTCTAAGTCCGCAATGCC 58.551 50.000 0.00 0.00 0.00 4.40
598 645 3.059188 ACGTTTGTTCTAAGTCCGCAATG 60.059 43.478 0.00 0.00 0.00 2.82
611 658 8.973835 TCCAATTATCCATTAAACGTTTGTTC 57.026 30.769 23.46 0.00 37.31 3.18
618 665 9.184062 CAATCACATCCAATTATCCATTAAACG 57.816 33.333 0.00 0.00 0.00 3.60
620 667 9.431690 TCCAATCACATCCAATTATCCATTAAA 57.568 29.630 0.00 0.00 0.00 1.52
624 671 6.617538 AGTCCAATCACATCCAATTATCCAT 58.382 36.000 0.00 0.00 0.00 3.41
626 673 5.474876 GGAGTCCAATCACATCCAATTATCC 59.525 44.000 3.60 0.00 0.00 2.59
627 674 5.474876 GGGAGTCCAATCACATCCAATTATC 59.525 44.000 12.30 0.00 0.00 1.75
628 675 5.388654 GGGAGTCCAATCACATCCAATTAT 58.611 41.667 12.30 0.00 0.00 1.28
629 676 4.386312 GGGGAGTCCAATCACATCCAATTA 60.386 45.833 12.30 0.00 35.00 1.40
630 677 3.628257 GGGGAGTCCAATCACATCCAATT 60.628 47.826 12.30 0.00 35.00 2.32
631 678 2.091665 GGGGAGTCCAATCACATCCAAT 60.092 50.000 12.30 0.00 35.00 3.16
632 679 1.284785 GGGGAGTCCAATCACATCCAA 59.715 52.381 12.30 0.00 35.00 3.53
633 680 0.918983 GGGGAGTCCAATCACATCCA 59.081 55.000 12.30 0.00 35.00 3.41
634 681 1.216990 AGGGGAGTCCAATCACATCC 58.783 55.000 12.30 0.00 38.24 3.51
638 685 3.309296 TCTGATAGGGGAGTCCAATCAC 58.691 50.000 12.30 0.00 34.93 3.06
647 694 0.030908 GACGCGTTCTGATAGGGGAG 59.969 60.000 15.53 0.00 0.00 4.30
649 696 2.116383 AGACGCGTTCTGATAGGGG 58.884 57.895 15.53 0.00 31.12 4.79
668 730 3.106407 GACTCACACTCCGTGCGC 61.106 66.667 0.00 0.00 45.92 6.09
677 739 1.859080 GAACACAAGACGGACTCACAC 59.141 52.381 0.00 0.00 0.00 3.82
678 740 1.478916 TGAACACAAGACGGACTCACA 59.521 47.619 0.00 0.00 0.00 3.58
681 743 3.093717 TCTTGAACACAAGACGGACTC 57.906 47.619 8.32 0.00 43.06 3.36
795 857 3.372554 GAGGAAGGCGGACCCGAAG 62.373 68.421 13.24 0.00 42.83 3.79
857 920 0.537653 GAAAGGGGAAGACGGAGGAG 59.462 60.000 0.00 0.00 0.00 3.69
901 989 1.582610 TTGCGGCGAGGGTTTGATTC 61.583 55.000 12.98 0.00 0.00 2.52
1620 1713 2.871182 TTCGATCAGATCCAGAACGG 57.129 50.000 13.05 0.00 32.96 4.44
1642 1735 0.108615 ACAGATCGAGCGGAACCTTG 60.109 55.000 8.05 0.00 0.00 3.61
1649 1742 3.260483 GCAGCACAGATCGAGCGG 61.260 66.667 0.00 0.00 36.17 5.52
1857 1951 2.885135 TCACAGAAAGCCCATGACAT 57.115 45.000 0.00 0.00 0.00 3.06
1972 2128 5.024118 AGTTATATTATGGGACGGAGGGAG 58.976 45.833 0.00 0.00 0.00 4.30
1973 2129 5.019657 AGTTATATTATGGGACGGAGGGA 57.980 43.478 0.00 0.00 0.00 4.20
1974 2130 5.956563 ACTAGTTATATTATGGGACGGAGGG 59.043 44.000 0.00 0.00 0.00 4.30
1975 2131 6.436532 ACACTAGTTATATTATGGGACGGAGG 59.563 42.308 0.00 0.00 0.00 4.30
1976 2132 7.463961 ACACTAGTTATATTATGGGACGGAG 57.536 40.000 0.00 0.00 0.00 4.63
1977 2133 7.844493 AACACTAGTTATATTATGGGACGGA 57.156 36.000 0.00 0.00 35.85 4.69
1978 2134 9.985730 TTTAACACTAGTTATATTATGGGACGG 57.014 33.333 0.00 0.00 39.78 4.79
2001 2157 9.195411 CCGTACCATAATATAAGAGCGTTTTTA 57.805 33.333 0.00 0.00 0.00 1.52
2002 2158 7.927629 TCCGTACCATAATATAAGAGCGTTTTT 59.072 33.333 0.00 0.00 0.00 1.94
2003 2159 7.436118 TCCGTACCATAATATAAGAGCGTTTT 58.564 34.615 0.00 0.00 0.00 2.43
2004 2160 6.985117 TCCGTACCATAATATAAGAGCGTTT 58.015 36.000 0.00 0.00 0.00 3.60
2005 2161 6.349944 CCTCCGTACCATAATATAAGAGCGTT 60.350 42.308 0.00 0.00 0.00 4.84
2006 2162 5.125097 CCTCCGTACCATAATATAAGAGCGT 59.875 44.000 0.00 0.00 0.00 5.07
2007 2163 5.450137 CCCTCCGTACCATAATATAAGAGCG 60.450 48.000 0.00 0.00 0.00 5.03
2008 2164 5.655532 TCCCTCCGTACCATAATATAAGAGC 59.344 44.000 0.00 0.00 0.00 4.09
2009 2165 6.890814 ACTCCCTCCGTACCATAATATAAGAG 59.109 42.308 0.00 0.00 0.00 2.85
2010 2166 6.797707 ACTCCCTCCGTACCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
2011 2167 8.051535 TCTACTCCCTCCGTACCATAATATAAG 58.948 40.741 0.00 0.00 0.00 1.73
2012 2168 7.932134 TCTACTCCCTCCGTACCATAATATAA 58.068 38.462 0.00 0.00 0.00 0.98
2013 2169 7.515004 TCTACTCCCTCCGTACCATAATATA 57.485 40.000 0.00 0.00 0.00 0.86
2014 2170 6.398655 TCTACTCCCTCCGTACCATAATAT 57.601 41.667 0.00 0.00 0.00 1.28
2015 2171 5.848286 TCTACTCCCTCCGTACCATAATA 57.152 43.478 0.00 0.00 0.00 0.98
2016 2172 4.736611 TCTACTCCCTCCGTACCATAAT 57.263 45.455 0.00 0.00 0.00 1.28
2017 2173 4.524802 TTCTACTCCCTCCGTACCATAA 57.475 45.455 0.00 0.00 0.00 1.90
2018 2174 4.524802 TTTCTACTCCCTCCGTACCATA 57.475 45.455 0.00 0.00 0.00 2.74
2019 2175 3.393426 TTTCTACTCCCTCCGTACCAT 57.607 47.619 0.00 0.00 0.00 3.55
2020 2176 2.905415 TTTCTACTCCCTCCGTACCA 57.095 50.000 0.00 0.00 0.00 3.25
2021 2177 3.564264 AGATTTCTACTCCCTCCGTACC 58.436 50.000 0.00 0.00 0.00 3.34
2022 2178 6.240145 AGATAGATTTCTACTCCCTCCGTAC 58.760 44.000 0.00 0.00 0.00 3.67
2023 2179 6.451292 AGATAGATTTCTACTCCCTCCGTA 57.549 41.667 0.00 0.00 0.00 4.02
2024 2180 5.327737 AGATAGATTTCTACTCCCTCCGT 57.672 43.478 0.00 0.00 0.00 4.69
2025 2181 6.320164 CCATAGATAGATTTCTACTCCCTCCG 59.680 46.154 0.00 0.00 31.25 4.63
2026 2182 6.097696 GCCATAGATAGATTTCTACTCCCTCC 59.902 46.154 0.00 0.00 31.25 4.30
2027 2183 6.183360 CGCCATAGATAGATTTCTACTCCCTC 60.183 46.154 0.00 0.00 31.25 4.30
2028 2184 5.654650 CGCCATAGATAGATTTCTACTCCCT 59.345 44.000 0.00 0.00 31.25 4.20
2029 2185 5.680151 GCGCCATAGATAGATTTCTACTCCC 60.680 48.000 0.00 0.00 31.25 4.30
2030 2186 5.105716 TGCGCCATAGATAGATTTCTACTCC 60.106 44.000 4.18 0.00 31.25 3.85
2031 2187 5.955488 TGCGCCATAGATAGATTTCTACTC 58.045 41.667 4.18 0.00 31.25 2.59
2032 2188 5.984695 TGCGCCATAGATAGATTTCTACT 57.015 39.130 4.18 0.00 31.25 2.57
2033 2189 7.602517 AATTGCGCCATAGATAGATTTCTAC 57.397 36.000 4.18 0.00 31.25 2.59
2034 2190 9.317936 CATAATTGCGCCATAGATAGATTTCTA 57.682 33.333 4.18 0.00 32.94 2.10
2035 2191 7.201679 GCATAATTGCGCCATAGATAGATTTCT 60.202 37.037 4.18 0.00 39.49 2.52
2058 2214 5.896073 AGCCTAGTCAAAGGTATAAGCAT 57.104 39.130 0.00 0.00 39.02 3.79
2077 2233 7.169982 CACACTAGCATATTACAAGTTCTAGCC 59.830 40.741 0.00 0.00 0.00 3.93
2117 2273 4.164796 TGCTGTTAGGGACATGATTCAGAT 59.835 41.667 0.00 0.00 37.69 2.90
2215 2371 5.440610 AGTTATATTGGGCCAAGAACAGAG 58.559 41.667 28.70 0.00 0.00 3.35
2250 2406 5.482006 CAGACATGAAATCTGTCCACAGTA 58.518 41.667 0.00 0.00 43.24 2.74
2317 2474 2.856222 ACTTGCAAGAACTCAAGGAGG 58.144 47.619 32.50 2.55 42.82 4.30
2348 2505 4.386954 GCATTTAAAAGAACTCCAAGCTGC 59.613 41.667 0.00 0.00 0.00 5.25
2396 2553 4.084011 CTACTAGTAAGTAGCCTCGGGT 57.916 50.000 3.76 0.00 46.53 5.28
2405 2562 7.064371 CGTTCTCACAGAAGCTACTAGTAAGTA 59.936 40.741 3.76 0.00 34.42 2.24
2406 2563 6.128227 CGTTCTCACAGAAGCTACTAGTAAGT 60.128 42.308 3.76 0.00 34.42 2.24
2407 2564 6.092396 TCGTTCTCACAGAAGCTACTAGTAAG 59.908 42.308 3.76 0.00 34.42 2.34
2408 2565 5.936372 TCGTTCTCACAGAAGCTACTAGTAA 59.064 40.000 3.76 0.00 34.42 2.24
2410 2567 4.325119 TCGTTCTCACAGAAGCTACTAGT 58.675 43.478 0.00 0.00 34.42 2.57
2414 2572 4.364415 AGATCGTTCTCACAGAAGCTAC 57.636 45.455 0.00 0.00 34.42 3.58
2451 2609 4.022849 AGGAGCAAAGAAACACAGCATAAC 60.023 41.667 0.00 0.00 0.00 1.89
2478 2636 5.229423 GCAGACCAAGCAACAAATCATTTA 58.771 37.500 0.00 0.00 0.00 1.40
2504 3046 0.929615 ACAGCACGCAACAAATTTGC 59.070 45.000 18.12 4.24 41.71 3.68
2520 3062 8.032952 TGTCATGTGCTAGAAGATTTAAACAG 57.967 34.615 0.00 0.00 0.00 3.16
2522 3064 8.887717 AGATGTCATGTGCTAGAAGATTTAAAC 58.112 33.333 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.