Multiple sequence alignment - TraesCS5B01G392300

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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 TraesCS5B01G392300 chr5B 100.000 3348 0 0 1 3348 571188773 571185426 0.000000e+00 6183.0
1 TraesCS5B01G392300 chr5D 90.874 2575 103 44 3 2512 464093055 464090548 0.000000e+00 3332.0
2 TraesCS5B01G392300 chr5D 95.346 838 33 6 2513 3348 464090502 464089669 0.000000e+00 1327.0
3 TraesCS5B01G392300 chr5A 90.259 2125 106 41 214 2308 584519563 584517510 0.000000e+00 2684.0
4 TraesCS5B01G392300 chr5A 94.132 835 31 4 2515 3348 584517149 584516332 0.000000e+00 1254.0
5 TraesCS5B01G392300 chr5A 87.059 85 4 6 2435 2512 584517282 584517198 4.600000e-14 89.8
6 TraesCS5B01G392300 chr7D 92.157 51 4 0 1933 1983 535563394 535563344 4.630000e-09 73.1
7 TraesCS5B01G392300 chr7A 92.157 51 4 0 1933 1983 618117453 618117503 4.630000e-09 73.1
8 TraesCS5B01G392300 chr7B 95.455 44 2 0 1933 1976 577301701 577301658 1.670000e-08 71.3
9 TraesCS5B01G392300 chr2A 89.286 56 6 0 1933 1988 406997432 406997487 1.670000e-08 71.3
10 TraesCS5B01G392300 chr2A 89.286 56 6 0 1933 1988 407125929 407125984 1.670000e-08 71.3


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 TraesCS5B01G392300 chr5B 571185426 571188773 3347 True 6183.0 6183 100.000000 1 3348 1 chr5B.!!$R1 3347
1 TraesCS5B01G392300 chr5D 464089669 464093055 3386 True 2329.5 3332 93.110000 3 3348 2 chr5D.!!$R1 3345
2 TraesCS5B01G392300 chr5A 584516332 584519563 3231 True 1342.6 2684 90.483333 214 3348 3 chr5A.!!$R1 3134

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
162 163 0.584396 TTCGTTCGTCATGGTGTTGC 59.416 50.0 0.0 0.0 0.0 4.17 F
196 213 0.605319 TGATCGGCTGTGGTGGTTTC 60.605 55.0 0.0 0.0 0.0 2.78 F
1841 1913 1.228657 GCCTTTCTCTTTCACGCCGT 61.229 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1962 1.134907 AGACACAAACGGACGAACACT 60.135 47.619 0.0 0.0 0.0 3.55 R
1904 1976 1.683385 CACACAGACAGAGGAGACACA 59.317 52.381 0.0 0.0 0.0 3.72 R
2727 3006 0.031994 CAAGGCTCGGGTTTTTGGTG 59.968 55.000 0.0 0.0 0.0 4.17 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
62 63 2.030457 CAGCCGTCGTTGACATTTATCC 59.970 50.000 0.00 0.00 32.09 2.59
74 75 6.813293 TGACATTTATCCTGAAGATGAGGA 57.187 37.500 0.00 0.00 43.92 3.71
76 77 6.156775 TGACATTTATCCTGAAGATGAGGACA 59.843 38.462 0.00 0.00 42.56 4.02
90 91 3.486383 TGAGGACACCAAATTGGACTTC 58.514 45.455 20.25 14.39 40.96 3.01
109 110 3.739077 GCAATGCGGGCTAACAATT 57.261 47.368 0.00 0.00 0.00 2.32
112 113 2.159310 GCAATGCGGGCTAACAATTACA 60.159 45.455 0.00 0.00 0.00 2.41
117 118 2.745281 GCGGGCTAACAATTACACAAGA 59.255 45.455 0.00 0.00 0.00 3.02
118 119 3.189702 GCGGGCTAACAATTACACAAGAA 59.810 43.478 0.00 0.00 0.00 2.52
119 120 4.320641 GCGGGCTAACAATTACACAAGAAA 60.321 41.667 0.00 0.00 0.00 2.52
120 121 5.764131 CGGGCTAACAATTACACAAGAAAA 58.236 37.500 0.00 0.00 0.00 2.29
121 122 6.386654 CGGGCTAACAATTACACAAGAAAAT 58.613 36.000 0.00 0.00 0.00 1.82
122 123 6.866248 CGGGCTAACAATTACACAAGAAAATT 59.134 34.615 0.00 0.00 0.00 1.82
146 147 5.779806 AAATTGTACAGGAGACGAATTCG 57.220 39.130 25.64 25.64 46.33 3.34
162 163 0.584396 TTCGTTCGTCATGGTGTTGC 59.416 50.000 0.00 0.00 0.00 4.17
168 169 0.943673 CGTCATGGTGTTGCTGTTGA 59.056 50.000 0.00 0.00 0.00 3.18
182 199 4.786507 TGCTGTTGAGAATTGTTTGATCG 58.213 39.130 0.00 0.00 0.00 3.69
186 203 4.161333 GTTGAGAATTGTTTGATCGGCTG 58.839 43.478 0.00 0.00 0.00 4.85
187 204 3.411446 TGAGAATTGTTTGATCGGCTGT 58.589 40.909 0.00 0.00 0.00 4.40
196 213 0.605319 TGATCGGCTGTGGTGGTTTC 60.605 55.000 0.00 0.00 0.00 2.78
199 216 2.260869 CGGCTGTGGTGGTTTCTGG 61.261 63.158 0.00 0.00 0.00 3.86
206 223 2.240160 TGTGGTGGTTTCTGGTACAAGT 59.760 45.455 0.00 0.00 38.70 3.16
237 254 3.509967 GGAACACGAATTCCCTTCCAAAT 59.490 43.478 14.44 0.00 42.16 2.32
391 411 2.753043 GGCGAGGTACACGGAGGA 60.753 66.667 12.21 0.00 43.91 3.71
410 430 1.748500 GCCCTTCTTCCTCAGCAGC 60.749 63.158 0.00 0.00 0.00 5.25
709 729 1.897225 CTCCTGCAGGTCACCTCCAG 61.897 65.000 31.58 7.97 39.05 3.86
739 759 2.411904 GCCGATAATTGCTCAGAGAGG 58.588 52.381 0.00 0.00 0.00 3.69
797 817 3.797546 GCTTGTGCTCTGAGCGGC 61.798 66.667 23.35 19.28 46.26 6.53
944 964 2.998316 GCAGGAGCAGAGGAATACTT 57.002 50.000 0.00 0.00 41.58 2.24
945 965 3.274095 GCAGGAGCAGAGGAATACTTT 57.726 47.619 0.00 0.00 41.58 2.66
946 966 3.615155 GCAGGAGCAGAGGAATACTTTT 58.385 45.455 0.00 0.00 41.58 2.27
947 967 4.013050 GCAGGAGCAGAGGAATACTTTTT 58.987 43.478 0.00 0.00 41.58 1.94
948 968 4.142513 GCAGGAGCAGAGGAATACTTTTTG 60.143 45.833 0.00 0.00 41.58 2.44
949 969 5.006386 CAGGAGCAGAGGAATACTTTTTGT 58.994 41.667 0.00 0.00 0.00 2.83
950 970 5.474876 CAGGAGCAGAGGAATACTTTTTGTT 59.525 40.000 0.00 0.00 0.00 2.83
951 971 6.015940 CAGGAGCAGAGGAATACTTTTTGTTT 60.016 38.462 0.00 0.00 0.00 2.83
952 972 6.551227 AGGAGCAGAGGAATACTTTTTGTTTT 59.449 34.615 0.00 0.00 0.00 2.43
953 973 7.069950 AGGAGCAGAGGAATACTTTTTGTTTTT 59.930 33.333 0.00 0.00 0.00 1.94
954 974 7.169813 GGAGCAGAGGAATACTTTTTGTTTTTG 59.830 37.037 0.00 0.00 0.00 2.44
955 975 7.781056 AGCAGAGGAATACTTTTTGTTTTTGA 58.219 30.769 0.00 0.00 0.00 2.69
956 976 7.922811 AGCAGAGGAATACTTTTTGTTTTTGAG 59.077 33.333 0.00 0.00 0.00 3.02
957 977 7.169813 GCAGAGGAATACTTTTTGTTTTTGAGG 59.830 37.037 0.00 0.00 0.00 3.86
958 978 7.653311 CAGAGGAATACTTTTTGTTTTTGAGGG 59.347 37.037 0.00 0.00 0.00 4.30
959 979 7.563556 AGAGGAATACTTTTTGTTTTTGAGGGA 59.436 33.333 0.00 0.00 0.00 4.20
960 980 8.084985 AGGAATACTTTTTGTTTTTGAGGGAA 57.915 30.769 0.00 0.00 0.00 3.97
961 981 8.544622 AGGAATACTTTTTGTTTTTGAGGGAAA 58.455 29.630 0.00 0.00 0.00 3.13
962 982 8.609176 GGAATACTTTTTGTTTTTGAGGGAAAC 58.391 33.333 0.00 0.00 37.48 2.78
963 983 9.378551 GAATACTTTTTGTTTTTGAGGGAAACT 57.621 29.630 0.00 0.00 37.75 2.66
1094 1114 4.437587 ATCCCACCTGCTGCTGCC 62.438 66.667 13.47 0.00 38.71 4.85
1729 1801 3.277211 TTCTTCGACTCCACCGCGG 62.277 63.158 26.86 26.86 0.00 6.46
1730 1802 3.744719 CTTCGACTCCACCGCGGA 61.745 66.667 35.90 8.90 43.61 5.54
1841 1913 1.228657 GCCTTTCTCTTTCACGCCGT 61.229 55.000 0.00 0.00 0.00 5.68
1874 1946 1.573829 GAGATCGCGTGGTTTTGCCA 61.574 55.000 5.77 0.00 46.95 4.92
1904 1976 1.854126 CGTAACAGTGTTCGTCCGTTT 59.146 47.619 12.82 0.00 0.00 3.60
1920 1996 2.398498 CGTTTGTGTCTCCTCTGTCTG 58.602 52.381 0.00 0.00 0.00 3.51
1921 1997 2.223829 CGTTTGTGTCTCCTCTGTCTGT 60.224 50.000 0.00 0.00 0.00 3.41
1922 1998 3.126831 GTTTGTGTCTCCTCTGTCTGTG 58.873 50.000 0.00 0.00 0.00 3.66
1923 1999 2.073252 TGTGTCTCCTCTGTCTGTGT 57.927 50.000 0.00 0.00 0.00 3.72
2187 2282 1.777878 TCTACCAAGAACCCTTTGCCA 59.222 47.619 0.00 0.00 0.00 4.92
2223 2318 1.437573 GCGGCGTCGTTTTGTACAC 60.438 57.895 12.58 0.00 38.89 2.90
2229 2328 3.162068 GCGTCGTTTTGTACACAAACAA 58.838 40.909 22.17 10.32 44.56 2.83
2259 2358 2.496679 TAGCCTAGCCCCAGAATTCT 57.503 50.000 0.88 0.88 0.00 2.40
2298 2398 1.948508 GCATGGAGTGCGTTGAACA 59.051 52.632 0.00 0.00 45.23 3.18
2307 2407 4.391830 GGAGTGCGTTGAACATTCATTAGA 59.608 41.667 0.00 0.00 37.00 2.10
2308 2408 5.446473 GGAGTGCGTTGAACATTCATTAGAG 60.446 44.000 0.00 0.00 37.00 2.43
2381 2482 7.329226 CACATCTCAAATTACCCAAACACAATC 59.671 37.037 0.00 0.00 0.00 2.67
2392 2494 4.021192 CCCAAACACAATCAGCACCTTATT 60.021 41.667 0.00 0.00 0.00 1.40
2393 2495 5.184864 CCCAAACACAATCAGCACCTTATTA 59.815 40.000 0.00 0.00 0.00 0.98
2395 2497 7.322664 CCAAACACAATCAGCACCTTATTATT 58.677 34.615 0.00 0.00 0.00 1.40
2396 2498 7.489113 CCAAACACAATCAGCACCTTATTATTC 59.511 37.037 0.00 0.00 0.00 1.75
2397 2499 6.363577 ACACAATCAGCACCTTATTATTCG 57.636 37.500 0.00 0.00 0.00 3.34
2398 2500 6.112734 ACACAATCAGCACCTTATTATTCGA 58.887 36.000 0.00 0.00 0.00 3.71
2399 2501 6.767902 ACACAATCAGCACCTTATTATTCGAT 59.232 34.615 0.00 0.00 0.00 3.59
2400 2502 7.041780 ACACAATCAGCACCTTATTATTCGATC 60.042 37.037 0.00 0.00 0.00 3.69
2407 2513 6.870965 AGCACCTTATTATTCGATCTTAGCAG 59.129 38.462 0.00 0.00 0.00 4.24
2418 2524 3.986572 CGATCTTAGCAGAATACAGCCAG 59.013 47.826 0.00 0.00 30.76 4.85
2420 2526 4.662468 TCTTAGCAGAATACAGCCAGAG 57.338 45.455 0.00 0.00 0.00 3.35
2425 2531 2.675348 GCAGAATACAGCCAGAGTGAAC 59.325 50.000 0.00 0.00 0.00 3.18
2426 2532 3.618507 GCAGAATACAGCCAGAGTGAACT 60.619 47.826 0.00 0.00 0.00 3.01
2427 2533 4.573900 CAGAATACAGCCAGAGTGAACTT 58.426 43.478 0.00 0.00 0.00 2.66
2428 2534 5.724328 CAGAATACAGCCAGAGTGAACTTA 58.276 41.667 0.00 0.00 0.00 2.24
2482 2713 0.036010 CCGGAAGACAGCCTCACAAT 60.036 55.000 0.00 0.00 0.00 2.71
2488 2719 1.421268 AGACAGCCTCACAATCCACAA 59.579 47.619 0.00 0.00 0.00 3.33
2501 2732 0.104487 TCCACAACGCCTTTCACGTA 59.896 50.000 0.00 0.00 44.30 3.57
2503 2734 0.110823 CACAACGCCTTTCACGTAGC 60.111 55.000 0.00 0.00 44.30 3.58
2508 2739 0.666274 CGCCTTTCACGTAGCTCACA 60.666 55.000 0.00 0.00 0.00 3.58
2512 2743 2.668457 CCTTTCACGTAGCTCACACATC 59.332 50.000 0.00 0.00 0.00 3.06
2513 2744 3.579709 CTTTCACGTAGCTCACACATCT 58.420 45.455 0.00 0.00 0.00 2.90
2516 2747 4.092771 TCACGTAGCTCACACATCTAAC 57.907 45.455 0.00 0.00 0.00 2.34
2517 2748 3.504520 TCACGTAGCTCACACATCTAACA 59.495 43.478 0.00 0.00 0.00 2.41
2658 2936 2.671888 GGCCTACTACTCTTTTTCGCAC 59.328 50.000 0.00 0.00 0.00 5.34
2731 3010 2.306805 ACTCATGGAGCAATCTTCACCA 59.693 45.455 0.00 0.00 28.73 4.17
2787 3066 4.567159 CACTTCTTAGAAGGCGTACCATTC 59.433 45.833 23.72 1.89 39.06 2.67
2827 3106 1.965414 TGCTTGGGGATCCTTCACTA 58.035 50.000 12.58 0.00 0.00 2.74
2847 3126 0.740868 TCTTGGATGAAGAAGCGCCG 60.741 55.000 2.29 0.00 37.78 6.46
3006 3285 0.533491 CATCAAACCATGGGTGCTGG 59.467 55.000 18.09 0.30 35.34 4.85
3192 3471 3.822996 ACGATTGAAGTAGTCACGTGAG 58.177 45.455 20.73 4.93 37.51 3.51
3221 3500 3.306019 CCACCCAAGGCAATCTACAAAAC 60.306 47.826 0.00 0.00 0.00 2.43
3232 3511 6.128929 GGCAATCTACAAAACGGAAATTCAAC 60.129 38.462 0.00 0.00 0.00 3.18
3235 3514 8.479280 CAATCTACAAAACGGAAATTCAACTTG 58.521 33.333 0.00 0.00 0.00 3.16
3240 3519 6.041069 ACAAAACGGAAATTCAACTTGGGATA 59.959 34.615 0.00 0.00 0.00 2.59
3336 3615 6.470278 CATCATTCCAAGTAGCTCCATCATA 58.530 40.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.164843 TCAACCATTGGTATTCTAGCCC 57.835 45.455 9.20 0.00 33.12 5.19
1 2 6.076981 CAATCAACCATTGGTATTCTAGCC 57.923 41.667 9.20 0.00 38.67 3.93
16 17 5.840243 TGATGATGATGAACCAATCAACC 57.160 39.130 0.00 0.00 42.54 3.77
27 28 3.612479 CGACGGCTGTATGATGATGATGA 60.612 47.826 0.00 0.00 0.00 2.92
28 29 2.665052 CGACGGCTGTATGATGATGATG 59.335 50.000 0.00 0.00 0.00 3.07
29 30 2.297315 ACGACGGCTGTATGATGATGAT 59.703 45.455 0.00 0.00 0.00 2.45
62 63 4.157289 CCAATTTGGTGTCCTCATCTTCAG 59.843 45.833 7.31 0.00 31.35 3.02
74 75 1.686355 TGCGAAGTCCAATTTGGTGT 58.314 45.000 14.98 1.22 39.03 4.16
76 77 2.610232 GCATTGCGAAGTCCAATTTGGT 60.610 45.455 14.98 0.00 39.03 3.67
120 121 8.388103 CGAATTCGTCTCCTGTACAATTTTAAT 58.612 33.333 19.67 0.00 34.11 1.40
121 122 7.735500 CGAATTCGTCTCCTGTACAATTTTAA 58.264 34.615 19.67 0.00 34.11 1.52
122 123 7.285783 CGAATTCGTCTCCTGTACAATTTTA 57.714 36.000 19.67 0.00 34.11 1.52
146 147 0.944386 ACAGCAACACCATGACGAAC 59.056 50.000 0.00 0.00 0.00 3.95
157 158 5.321959 TCAAACAATTCTCAACAGCAACA 57.678 34.783 0.00 0.00 0.00 3.33
162 163 4.083110 AGCCGATCAAACAATTCTCAACAG 60.083 41.667 0.00 0.00 0.00 3.16
168 169 2.489329 CCACAGCCGATCAAACAATTCT 59.511 45.455 0.00 0.00 0.00 2.40
182 199 0.109723 TACCAGAAACCACCACAGCC 59.890 55.000 0.00 0.00 0.00 4.85
186 203 2.927028 ACTTGTACCAGAAACCACCAC 58.073 47.619 0.08 0.00 0.00 4.16
187 204 3.655615 AACTTGTACCAGAAACCACCA 57.344 42.857 0.08 0.00 0.00 4.17
196 213 5.124776 TGTTCCTTTGTGAAACTTGTACCAG 59.875 40.000 0.00 0.00 38.04 4.00
199 216 5.025826 CGTGTTCCTTTGTGAAACTTGTAC 58.974 41.667 0.00 0.00 38.04 2.90
206 223 4.202070 GGGAATTCGTGTTCCTTTGTGAAA 60.202 41.667 16.98 0.00 45.62 2.69
237 254 7.701924 GCAGAATTTTCGATCCATTTTGTCATA 59.298 33.333 0.00 0.00 0.00 2.15
259 279 2.382882 CTCCTCAGTCCATGTAGCAGA 58.617 52.381 0.00 0.00 0.00 4.26
391 411 1.989620 CTGCTGAGGAAGAAGGGCT 59.010 57.895 0.00 0.00 0.00 5.19
709 729 1.334869 CAATTATCGGCCTGCAGTTCC 59.665 52.381 13.81 12.28 0.00 3.62
722 742 7.665690 TGTAGAATCCTCTCTGAGCAATTATC 58.334 38.462 0.00 0.00 32.70 1.75
940 960 9.027202 ACTAGTTTCCCTCAAAAACAAAAAGTA 57.973 29.630 0.00 0.00 38.73 2.24
941 961 7.903145 ACTAGTTTCCCTCAAAAACAAAAAGT 58.097 30.769 0.00 0.00 38.73 2.66
943 963 9.027202 ACTACTAGTTTCCCTCAAAAACAAAAA 57.973 29.630 0.00 0.00 38.73 1.94
944 964 8.463607 CACTACTAGTTTCCCTCAAAAACAAAA 58.536 33.333 0.00 0.00 38.73 2.44
945 965 7.067737 CCACTACTAGTTTCCCTCAAAAACAAA 59.932 37.037 0.00 0.00 38.73 2.83
946 966 6.544564 CCACTACTAGTTTCCCTCAAAAACAA 59.455 38.462 0.00 0.00 38.73 2.83
947 967 6.059484 CCACTACTAGTTTCCCTCAAAAACA 58.941 40.000 0.00 0.00 38.73 2.83
948 968 6.060136 ACCACTACTAGTTTCCCTCAAAAAC 58.940 40.000 0.00 0.00 36.97 2.43
949 969 6.256643 ACCACTACTAGTTTCCCTCAAAAA 57.743 37.500 0.00 0.00 0.00 1.94
950 970 5.899631 ACCACTACTAGTTTCCCTCAAAA 57.100 39.130 0.00 0.00 0.00 2.44
951 971 5.367352 TCAACCACTACTAGTTTCCCTCAAA 59.633 40.000 0.00 0.00 0.00 2.69
952 972 4.903049 TCAACCACTACTAGTTTCCCTCAA 59.097 41.667 0.00 0.00 0.00 3.02
953 973 4.282703 GTCAACCACTACTAGTTTCCCTCA 59.717 45.833 0.00 0.00 0.00 3.86
954 974 4.527427 AGTCAACCACTACTAGTTTCCCTC 59.473 45.833 0.00 0.00 31.37 4.30
955 975 4.490706 AGTCAACCACTACTAGTTTCCCT 58.509 43.478 0.00 0.00 31.37 4.20
956 976 4.886496 AGTCAACCACTACTAGTTTCCC 57.114 45.455 0.00 0.00 31.37 3.97
957 977 5.608449 ACAAGTCAACCACTACTAGTTTCC 58.392 41.667 0.00 0.00 32.30 3.13
958 978 8.652810 TTTACAAGTCAACCACTACTAGTTTC 57.347 34.615 0.00 0.00 32.30 2.78
959 979 9.623000 AATTTACAAGTCAACCACTACTAGTTT 57.377 29.630 0.00 0.00 32.30 2.66
960 980 9.269453 GAATTTACAAGTCAACCACTACTAGTT 57.731 33.333 0.00 0.00 32.30 2.24
961 981 8.426489 TGAATTTACAAGTCAACCACTACTAGT 58.574 33.333 0.00 0.00 32.30 2.57
962 982 8.709646 GTGAATTTACAAGTCAACCACTACTAG 58.290 37.037 0.00 0.00 37.23 2.57
963 983 7.383029 CGTGAATTTACAAGTCAACCACTACTA 59.617 37.037 0.95 0.00 37.23 1.82
964 984 6.202188 CGTGAATTTACAAGTCAACCACTACT 59.798 38.462 0.95 0.00 37.23 2.57
1282 1303 2.750637 CTGGCTCTTGCTGGGCAG 60.751 66.667 4.67 0.00 46.47 4.85
1890 1962 1.134907 AGACACAAACGGACGAACACT 60.135 47.619 0.00 0.00 0.00 3.55
1904 1976 1.683385 CACACAGACAGAGGAGACACA 59.317 52.381 0.00 0.00 0.00 3.72
1922 1998 4.760047 ATCGCCGTCCACCTGCAC 62.760 66.667 0.00 0.00 0.00 4.57
1923 1999 4.451150 GATCGCCGTCCACCTGCA 62.451 66.667 0.00 0.00 0.00 4.41
2207 2302 2.103388 GTTTGTGTACAAAACGACGCC 58.897 47.619 11.38 0.00 46.08 5.68
2259 2358 5.277601 GCGTTTGCAGAGTAATCTTAACA 57.722 39.130 0.00 0.00 42.15 2.41
2290 2390 7.351414 TCTTCACTCTAATGAATGTTCAACG 57.649 36.000 0.00 0.00 41.13 4.10
2307 2407 8.899427 ATGTCGATCAAAATGATATCTTCACT 57.101 30.769 3.98 0.00 37.20 3.41
2308 2408 8.768019 TGATGTCGATCAAAATGATATCTTCAC 58.232 33.333 3.98 0.00 37.20 3.18
2327 2427 2.278596 CTACGCCCGGTGATGTCG 60.279 66.667 4.58 0.00 0.00 4.35
2359 2459 6.516527 GCTGATTGTGTTTGGGTAATTTGAGA 60.517 38.462 0.00 0.00 0.00 3.27
2381 2482 6.646653 TGCTAAGATCGAATAATAAGGTGCTG 59.353 38.462 0.00 0.00 0.00 4.41
2392 2494 6.015434 TGGCTGTATTCTGCTAAGATCGAATA 60.015 38.462 0.00 0.00 38.34 1.75
2393 2495 5.221521 TGGCTGTATTCTGCTAAGATCGAAT 60.222 40.000 0.00 0.00 38.34 3.34
2395 2497 3.636764 TGGCTGTATTCTGCTAAGATCGA 59.363 43.478 0.00 0.00 38.34 3.59
2396 2498 3.982475 TGGCTGTATTCTGCTAAGATCG 58.018 45.455 1.48 0.00 38.34 3.69
2397 2499 5.207110 TCTGGCTGTATTCTGCTAAGATC 57.793 43.478 1.48 0.00 38.34 2.75
2398 2500 4.653341 ACTCTGGCTGTATTCTGCTAAGAT 59.347 41.667 1.48 0.00 38.34 2.40
2399 2501 4.026744 ACTCTGGCTGTATTCTGCTAAGA 58.973 43.478 1.48 4.68 38.34 2.10
2400 2502 4.118410 CACTCTGGCTGTATTCTGCTAAG 58.882 47.826 1.48 1.00 38.34 2.18
2407 2513 5.525378 CCATAAGTTCACTCTGGCTGTATTC 59.475 44.000 0.00 0.00 0.00 1.75
2418 2524 5.232463 TGTCGGTTAACCATAAGTTCACTC 58.768 41.667 24.14 0.00 40.05 3.51
2420 2526 4.992951 ACTGTCGGTTAACCATAAGTTCAC 59.007 41.667 24.14 7.52 40.05 3.18
2425 2531 8.091385 ACTTTTTACTGTCGGTTAACCATAAG 57.909 34.615 24.14 18.04 35.14 1.73
2426 2532 9.723601 ATACTTTTTACTGTCGGTTAACCATAA 57.276 29.630 24.14 10.83 35.14 1.90
2427 2533 9.369904 GATACTTTTTACTGTCGGTTAACCATA 57.630 33.333 24.14 8.95 35.14 2.74
2428 2534 8.098912 AGATACTTTTTACTGTCGGTTAACCAT 58.901 33.333 24.14 4.85 35.14 3.55
2482 2713 0.104487 TACGTGAAAGGCGTTGTGGA 59.896 50.000 0.00 0.00 42.85 4.02
2488 2719 0.666577 GTGAGCTACGTGAAAGGCGT 60.667 55.000 0.00 0.00 45.11 5.68
2501 2732 6.882610 TTTGAATTGTTAGATGTGTGAGCT 57.117 33.333 0.00 0.00 0.00 4.09
2529 2807 8.846943 TCTTTTGTACTATCAGAATCTGCAAA 57.153 30.769 5.18 6.40 0.00 3.68
2658 2936 5.243060 TGTGATGTGTTAGGATATCTACCCG 59.757 44.000 2.05 0.00 0.00 5.28
2727 3006 0.031994 CAAGGCTCGGGTTTTTGGTG 59.968 55.000 0.00 0.00 0.00 4.17
2731 3010 2.501261 GTCTACAAGGCTCGGGTTTTT 58.499 47.619 0.00 0.00 0.00 1.94
2827 3106 1.673168 GGCGCTTCTTCATCCAAGAT 58.327 50.000 7.64 0.00 41.02 2.40
2946 3225 3.233980 AGAGTGCTGGCGGACACA 61.234 61.111 18.56 0.00 39.30 3.72
2982 3261 2.204748 CCCATGGTTTGATGCTGGG 58.795 57.895 11.73 0.00 40.59 4.45
3006 3285 1.079819 TACAGCCGCTCAGTTGCTC 60.080 57.895 0.00 0.00 31.77 4.26
3018 3297 1.226717 CGAGAAGCGTCCTACAGCC 60.227 63.158 0.00 0.00 34.64 4.85
3192 3471 2.516225 GCCTTGGGTGGCCGATAC 60.516 66.667 0.00 0.00 46.82 2.24
3221 3500 7.228507 TGTGATATATCCCAAGTTGAATTTCCG 59.771 37.037 10.25 0.00 0.00 4.30
3232 3511 8.548721 GTTCGTAGTTTTGTGATATATCCCAAG 58.451 37.037 10.25 0.00 0.00 3.61
3235 3514 8.428186 TTGTTCGTAGTTTTGTGATATATCCC 57.572 34.615 10.25 0.00 0.00 3.85
3272 3551 6.183360 GGTGTTTGCATTTTCCTTTTTAAGCA 60.183 34.615 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.